@article {pmid40271218,
year = {2025},
author = {Tomsia, M and Grzywacz, A and Szpila, K and Walczak, K and Mahlerová, K and Vaněk, D and Matuszewski, S},
title = {Human costal cartilage, tooth cavities, and femur nutrient canals-new niches for insects used in forensic entomology.},
journal = {Forensic sciences research},
volume = {10},
number = {2},
pages = {owae028},
doi = {10.1093/fsr/owae028},
pmid = {40271218},
issn = {2471-1411},
abstract = {UNLABELLED: The study aimed to analyze the entomological material collected during 13 autopsies performed on the unidentified cadavers revealed at different stages of decay in the Upper Silesia Region (Poland) over 2016-2022. During the preparation of human tissues for genetic identification, we revealed larvae, puparia, and adult insects in previously undescribed locations: costal cartilage, femur nutrient canals (foramen nutrients), and tooth cavities. The taxonomical assessment was done using morphological examination or DNA barcoding, where necessary. Based on our observations, we conclude that the apical constriction, foramen, and cavities may serve as migration paths inside teeth, and the femur nutrient canals to the bone marrow. The study also revealed that the beetle Necrobia ruficollis (Fabricius, 1775) and the moth family Pyralidae Latreille, 1802 (Phycitinae) moths can form pupal chambers inside the costal cartilage, indicating that these insects can complete their life cycle inside this cache. We believe that the newly reported locations of carrion insects in human remains may be relevant to forensic entomology, as they provide new opportunities to collect insect evidence.<br><br>KEY POINTS: Costal cartilage may serve as an occasional cache for adults and immatures of carrion insects.Tooth cavities and apical foramen may serve as entryways for necrophilous insect larvae.Insect larvae use nutrient canals as migratory pathways to the bone marrow.},
}
@article {pmid40270798,
year = {2025},
author = {Kireta, D and van Dijk, KJ and Crotty, S and Malik, A and Bell, K and Hogendoorn, K and Lowe, AJ},
title = {A Novel Approach for Pollen Identification and Quantification Using Hybrid Capture-Based DNA Metabarcoding.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71311},
doi = {10.1002/ece3.71311},
pmid = {40270798},
issn = {2045-7758},
abstract = {Pollen identification (ID) and quantification is important in many fields, including pollination ecology and agricultural sciences, and efforts to explore optimal molecular methods for identifying low concentrations of DNA from plant mixtures are increasing, but quantifying mixture proportions remains challenging. Traditional pollen ID using microscopy is time-consuming, requires expertise and has limited accuracy and throughput. Molecular barcoding approaches being explored offer improved accuracy and throughput. The common approach, amplicon sequencing, employs PCR amplification to isolate DNA barcodes, but introduces significant bias, impairing downstream quantification. We apply a novel molecular hybrid capture approach to artificial pollen mixtures to improve upon current taxon ID and quantification methods. The method randomly fragments DNA and uses RNA baits to capture DNA barcodes, which allows for PCR duplicate removal, reducing downstream quantification bias. Four reference databases were used to explore identification and quantification. A restricted matK database containing only mixture species yielded sequence proportions highly correlated with input pollen proportions, demonstrating the potential usefulness of hybrid capture for metabarcoding and quantifying pollen mixtures. Identification power was further tested using two reference libraries constructed from publicly available sequences: the matK plastid barcode and RefSeq complete chloroplast references. Single barcode-based taxon ID did not consistently resolve to species or genus level. The RefSeq chloroplast database performed better qualitatively but had limited taxon coverage (relative to species used here) and introduced ID issues. At the family level, both databases yielded comparable qualitative results, but the RefSeq database performed better quantitatively. Whilst the method developed here has tremendous potential, the choice and expansion of reference databases remains one of the most important factors allowing qualitative and quantitative accuracy using the full set of genomic regions screened by this hybrid capture method.},
}
@article {pmid40270465,
year = {2025},
author = {Borer, G and Monteiro, C and Lima, FP and Martins, FMS},
title = {Performance of DNA Metabarcoding vs. Morphological Methods for Assessing Intertidal Turf and Foliose Algae Diversity.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14115},
doi = {10.1111/1755-0998.14115},
pmid = {40270465},
issn = {1755-0998},
support = {BIOINTERACT/https://doi.org/10.54499/2022.02887//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; CEECInd/10.54499/CEECIND/03185/2018/CP1546/CP164//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; OceanLog/10.54499/PTDC/BIA-BMA/4848/2021//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; ANERIS/101094924//Horizon 2020 Framework Programme/ ; FutureMares/869300//Horizon 2020 Framework Programme/ ; NORTE-01-0246-FEDER-000063//European Commission/ ; },
abstract = {Large biogeographical shifts in marine communities are taking place in response to climate change and biological invasions yet we still lack a full understanding of their diversity and distribution. An important example of this is turf and foliose algae that are key coastal primary producers in several regions and are expanding into new environments. Traditionally, monitoring turf and foliose algae communities involves species identification based on morphological traits, which is challenging due to their reduced dimensions and highly variable morphology. Molecular methods promise to revolutionise this field, but their effectiveness in detecting turf and foliose algae has yet to be tested. Here, we evaluate the performance of DNA metabarcoding (COI and rbcL markers) and morphological identification (in situ and photoquadrat) to describe intertidal turf and foliose algae communities along the Portuguese coast. Both molecular markers detected more taxa than the morphological methods and showed greater discrimination of turf and foliose algae communities between regions, matching our knowledge of the geographical and climatic patterns for the region. In sum, our multi-marker metabarcoding approach was more efficient than morphology-based methods in characterising turf and foliose algae communities along the Portuguese coast, differentiating morphologically similar species, and detecting unicellular organisms. However, certain taxa that were identified by in situ and photoquadrat approaches were not detected through metabarcoding, partly due to lack of reference barcodes or taxonomic resolution. Metabarcoding emerges as a valuable tool for monitoring these communities, particularly in long-term programmes requiring accuracy, speed, and reproducibility.},
}
@article {pmid40270210,
year = {2025},
author = {Pedersen, FB and Hauge, AW and Hansen, JF and Andersen, LS and Blomsterberg, S and Bruunsgaard, H},
title = {Cost-Effective and Highly Scalable Typing of HLA Classes I and II Genes of up to 96 Individuals Using Nanopore Sequencing.},
journal = {HLA},
volume = {105},
number = {4},
pages = {e70164},
doi = {10.1111/tan.70164},
pmid = {40270210},
issn = {2059-2310},
support = {FF 2022/01//Bloddonorernes Forskningsfond/ ; },
mesh = {Humans ; *Histocompatibility Testing/methods/economics ; *Nanopore Sequencing/economics/methods ; Cost-Benefit Analysis ; Alleles ; *Histocompatibility Antigens Class II/genetics ; Multiplex Polymerase Chain Reaction/economics ; },
abstract = {HLA typing of large donor registries and biobanks as well as acute single patient/donor samples remains expensive, slow and logistically challenging, despite recent developments in the field. We have tested and validated a cost-effective, accurate and highly scalable method for typing specific genes in the HLA region. This enables HLA typing from 1 to 96 individuals simultaneously, using a targeted PCR and Native Barcoding kit from Oxford Nanopore Technologies. A primer set for seven HLA genes (HLA-A, -B, -C, -DRB1, -DQA1, -DQB1 and -DPB1) was developed to work in a multiplex PCR reaction. The resulting amplicons provide a possible four-field resolution of the HLA Class I genes and G-group resolution of the HLA Class II genes. The entire process, from DNA to HLA typing result, takes a total of 5.5-10.5 h depending on the number of samples processed simultaneously. Data analysis was conducted using NGSEngine-Turbo from GenDx (Utrecht, The Netherlands), with analysis time ranging from 1 to 5 min per sample. Samples from 96 Danish registered stem cell donors were typed using this method. One allele out of 1128 analysed alleles was inaccurately called homozygous, leading to an accuracy of 99.91%. The rapid turnaround, low cost and high accuracy make this new method highly relevant for HLA typing of large biobanks and donor registries, as well as for acute single samples. HLA typing can be obtained within 1 day, with a cost per sample of approximately €7 when 96 samples are sequenced simultaneously.},
}
@article {pmid40269967,
year = {2025},
author = {Isiye, E and Valcarcel Olmeda, A and Curran, T and O'Neill, D and de Waal, T and Barry, G and O'Hanlon, A and O'Shaughnessy, J and Keohane McCarthy, N and Vellinga, A and Jenkinson, A and Johnson, A and Barrett, D and Costello, S and Zintl, A and O'Meara, D},
title = {Molecular characterisation of common Culicoides biting midges (Diptera: Ceratopogonidae) in Ireland.},
journal = {Parasites &amp; vectors},
volume = {18},
number = {1},
pages = {149},
pmid = {40269967},
issn = {1756-3305},
mesh = {Animals ; *Ceratopogonidae/genetics/classification/virology ; Ireland ; *Insect Vectors/genetics/classification/virology ; DNA Barcoding, Taxonomic ; Phylogeny ; Electron Transport Complex IV/genetics ; Genetic Variation ; Bluetongue virus ; Bluetongue/transmission ; Female ; },
abstract = {BACKGROUND: Biting midges of the genus Culicoides (Diptera: Ceratopogonidae) act as vectors for several arboviruses, including bluetongue virus (BTV) and Schmallenberg virus (SBV), which affect livestock health and productivity. In Ireland, limited genetic data are available regarding the diversity of Culicoides species. This study represents the first attempt to characterise Culicoides in this region using molecular techniques.<br><br>METHODS: Adult Culicoides samples were captured using Onderstepoort Veterinary Institute (OVI) traps across six locations in Ireland. Subsequent molecular analyses involved polymerase chain reaction (PCR) and sequencing of the cytochrome oxidase subunit 1 (CO1) and the internal transcriber spacer (ITS) barcoding regions to obtain species identities. In addition, using both markers, we inferred the population genetic structure and potential colonisation pathways of Culicoides obsoletus sensu stricto (s. str.), the major vector species in Ireland.<br><br>RESULTS: DNA barcoding facilitated identification of 177 specimens. Eight common Culicoides species were identified through DNA barcoding of CO1 and ITS gene regions. The presence of putative vectors of bluetongue virus (BTV) and Schmallenberg virus (SBV) were also confirmed, including species in the subgenus Avaritia (C. obsoletus s. str., C. scoticus, C. chiopterus, and C. dewulfi) and subgenus Culicoides s. str. (C. pulicaris and C. punctatus). Phylogenetic analysis confirmed the relationship between these vector species and facilitated the placement of Culicoides spp. that could not be identified to species level through DNA barcoding. Haplotype network analysis of C. obsoletus showed that some haplotypes of these species are shared between Continental Europe, the UK, and Ireland, suggesting a possible incursion pathway for this vector.<br><br>CONCLUSIONS: DNA barcoding employing a combination of two barcodes, CO1 and ITS, proved effective in identifying Culicoides, especially species within the obsoletus complex, which are difficult to morphologically distinguish. Our findings also suggest that investigation of the population genetic structure of Culicoides spp. could be used to model the potential introduction routes of midge-borne pathogens into the country.},
}
@article {pmid40266812,
year = {2025},
author = {Wu, Y and Liu, Y and Huang, Z and Yin, H and Xu, X},
title = {New Species of the Purse-Web Spider Genus Atypus Latreille, 1804 from Southern China (Araneae, Atypidae), with the General Natural History of Atypus Spiders.},
journal = {Insects},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/insects16030301},
pmid = {40266812},
issn = {2075-4450},
support = {32070429/31772423/31471963/31372160//National Natural Sciences Foundation of China/ ; 2023JJ30399//Hunan Provincial Natural Science Foundation of China/ ; CX20230525//Hunan Provincial Innovation Foundation for Postgraduate/ ; },
abstract = {Three species of the purse-web spider genus Atypus Latreille, 1804, collected from Hunan and Sichuan Provinces of China, are diagnosed and described as new to science: A. yaozu sp. nov. (♂♀), A. siyiensis sp. nov. (♂♀) and A. yanjingensis sp. nov. (♂♀). Detailed descriptions, photographs and DNA barcodes of the three new species and a distribution map of Atypus species in China are provided. Additionally, we enrich the general natural history of the genus Atypus through a decade of observation.},
}
@article {pmid40265169,
year = {2025},
author = {Renou, L and Sun, W and Friedrich, C and Galant, K and Conrad, C and Consalus, A and Plantier, E and Schallmoser, K and Krisch, L and Barroca, V and Devanand, S and Dechamps, N and Reinisch, A and Martinovic, J and Magnani, A and Faivre, L and Lewandowski, D and Calvo, J and Perie, L and Kosmider, O and Pflumio, F},
title = {Orchestration of human multi-lineage hematopoietic cell development by humanized in vivo bone marrow models.},
journal = {HemaSphere},
volume = {9},
number = {4},
pages = {e70120},
pmid = {40265169},
issn = {2572-9241},
abstract = {Hematopoiesis develops in the bone marrow (BM) where multiple interactions regulate the differentiation and preservation of hematopoietic stem and progenitor cells (HSPCs). Immune-deficient murine models have enabled the analysis of molecular and cellular regulation of human HSPCs, but the physiology of these models is questioned as human hematopoietic cells develop in xenogenic microenvironments. In this study, we thoroughly characterized a humanized (h) in vivo BM model, developed from fetal (F/) and post-natal (P-N/) mesenchymal stromal cell (MSC) differentiation (called hOssicles [hOss]), in which human hematopoietic cells are generated following the transplantation of CD34[+] cells. Serial isolation and transplant experiments of hMSCs and HSPCs from hOss revealed the dynamic nature of these hBM niches. hOss modified human hematopoietic development by modulating myeloid/lymphoid cell production and HSPC levels, with no major transcriptional changes in HSPCs at the single-cell level. Clonal tracking using genetic barcodes highlighted hematopoietic cell cross-talks between the endogenous murine BM and hOss and differences in clonal myeloid/multipotent cell production between F/hOss and P-N/hOss, uncovering ontogeny-related impact of the BM on human hematopoietic cell production.},
}
@article {pmid40263935,
year = {2025},
author = {Becker, J and Domenger, C and Choksi, P and Krämer, C and Baumgartl, C and Maiakovska, O and Kim, JJ and Weinmann, J and Huber, G and Schmidt, F and Thirion, C and Müller, OJ and Willenbring, H and Grimm, D},
title = {Identification of a robust promoter in mouse and human hepatocytes by in vivo biopanning of a barcoded AAV library.},
journal = {Molecular therapy : the journal of the American Society of Gene Therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymthe.2025.04.027},
pmid = {40263935},
issn = {1525-0024},
abstract = {Recombinant adeno-associated viruses (AAV) are leading vectors for in vivo human gene therapy. An integral vector element are promoters, which control transgene expression in either a ubiquitous or cell-type-selective manner. Identifying optimal capsid-promoter combinations is challenging, especially when considering on- versus off-target expression. Here, we report a pipeline for in vivo promoter biopanning in AAV building on our AAV capsid barcoding technology and illustrate its potential by screening 53 promoters in 16 murine tissues using an AAV9 vector. Surprisingly, the 2.2 kb human glial fibrillary acidic protein (GFAP) promoter was the top hit in the liver, where it outperformed robust benchmarks such as the human alpha-1-antitrypsin promoter or the clinically used liver-specific promoter 1 (LP1). Analysis of hepatic cell populations revealed preferred GFAP promoter activity in hepatocytes. Notably, the GFAP promoter also surpassed the LP1 and cytomegalovirus (CMV) promoters in human hepatocytes engrafted in an immune-deficient mouse. These findings establish the GFAP promoter as an exciting alternative for research and clinical applications requiring efficient and specific transgene expression in hepatocytes. Our pipeline expands the arsenal of technologies for high-throughput in vivo screening of viral vector components and is compatible with capsid barcoding, facilitating the combinatorial interrogation of complex AAV libraries.},
}
@article {pmid40263541,
year = {2025},
author = {Boutelle, AM and Mabene, AR and Yao, D and Xu, H and Wang, M and Tang, YJ and Lopez, SS and Sinha, S and Demeter, J and Cheng, R and Benard, BA and McCrea, EM and Valente, LJ and Drainas, AP and Fischer, M and Majeti, R and Petrov, DA and Jackson, PK and Yang, F and Winslow, MM and Bassik, MC and Attardi, LD},
title = {Integrative multiomic approaches reveal ZMAT3 and p21 as conserved hubs in the p53 tumor suppression network.},
journal = {Cell death and differentiation},
volume = {},
number = {},
pages = {},
pmid = {40263541},
issn = {1476-5403},
support = {R35CA197591//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; T32CA009302//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R01CA234349//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R01CA234349//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; 28IP-0037//Tobacco-Related Disease Research Program (TRDRP)/ ; T31DT1713//Tobacco-Related Disease Research Program (TRDRP)/ ; },
abstract = {TP53, the most frequently mutated gene in human cancer, encodes a transcriptional activator that induces myriad downstream target genes. Despite the importance of p53 in tumor suppression, the specific p53 target genes important for tumor suppression remain unclear. Recent studies have identified the p53-inducible gene Zmat3 as a critical effector of tumor suppression, but many questions remain regarding its p53-dependence, activity across contexts, and mechanism of tumor suppression alone and in cooperation with other p53-inducible genes. To address these questions, we used Tuba-seq[Ultra] somatic genome editing and tumor barcoding in a mouse lung adenocarcinoma model, combinatorial in vivo CRISPR/Cas9 screens, meta-analyses of gene expression and Cancer Dependency Map data, and integrative RNA-sequencing and shotgun proteomic analyses. We established Zmat3 as a core component of p53-mediated tumor suppression and identified Cdkn1a as the most potent cooperating p53-induced gene in tumor suppression. We discovered that ZMAT3/CDKN1A serve as near-universal effectors of p53-mediated tumor suppression that regulate cell division, migration, and extracellular matrix organization. Accordingly, combined Zmat3-Cdkn1a inactivation dramatically enhanced cell proliferation and migration compared to controls, akin to p53 inactivation. Together, our findings place ZMAT3 and CDKN1A as hubs of a p53-induced gene program that opposes tumorigenesis across various cellular and genetic contexts.},
}
@article {pmid40263346,
year = {2025},
author = {Yamamoto, PK and Takasuka, K and Mori, M and Masuda, T and Kono, N},
title = {Non-invasive molecular species identification using spider silk proteomics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13844},
pmid = {40263346},
issn = {2045-2322},
support = {23K21203//Japan Society for the Promotion of Science/ ; },
abstract = {Accurate species identification is essential in biology, ecology, medicine, and agriculture, yet traditional methods relying on morphological characteristics often fail due to phenotypic plasticity and cryptic species. These limitations are particularly pronounced in small organisms with minimal distinguishing features. DNA barcoding has become a popular alternative; however, it requires invasive tissue sampling, making it unsuitable for delicate or rare organisms like insects and spiders. To address this challenge, we propose a non-invasive molecular method using proteomic analysis focused on species-specific protein sequences in spider silk, offering a viable solution for species identification without harming specimens. We developed a universal silk-dissolving method, followed by sequence similarity analysis to classify species into those identifiable at the species level and those distinguishable only to a group of closely related species. A bioinformatics pipeline was established to analyze peptide sequences, achieving 96% accuracy across 15 spider species, even in the presence of contaminants. This technique complements DNA barcoding and can be extended to other organisms producing biological materials. It holds promise in pest management, medical diagnostics, and improving public health by enabling accurate species identification without invasive procedures.},
}
@article {pmid40262372,
year = {2025},
author = {Finney, J and Kuraoka, M and Song, S and Watanabe, A and Liang, X and Liao, D and Moody, MA and Walter, EB and Harrison, SC and Kelsoe, G},
title = {Fluorescence-barcoded cell lines stably expressing membrane-anchored influenza neuraminidases.},
journal = {Vaccine},
volume = {56},
number = {},
pages = {127157},
doi = {10.1016/j.vaccine.2025.127157},
pmid = {40262372},
issn = {1873-2518},
abstract = {The discovery of broadly protective antibodies to the influenza virus neuraminidase (NA) has raised interest in NA as a vaccine target. However, recombinant, solubilized tetrameric NA ectodomains are often challenging to express and isolate, hindering the study of anti-NA humoral responses. To address this obstacle, we established a panel of 22 non-adherent cell lines stably expressing native, historical N1, N2, N3, N9, and NB NAs anchored on the cell surface. The cell lines are barcoded with fluorescent proteins, enabling high-throughput, 16-plex analyses of antibody binding with commonly available flow cytometers. The cell lines were at least as efficient as a Luminex multiplex binding assay at identifying NA antibodies from a library of unselected clonal IgGs derived from human memory B cells. The cell lines were also useful for measuring the magnitude and breadth of the serum antibody response elicited by experimental infection of rhesus macaques with influenza virus. The membrane-anchored NAs are catalytically active and are compatible with established sialidase activity assays. NA-expressing K530 cell lines therefore represent a useful tool for studying NA immunity and evaluating influenza vaccine efficacy.},
}
@article {pmid40262024,
year = {2025},
author = {Tong, Y and Wang, H and Li, H and Jia, Y and Zhou, Z},
title = {Molecular Diet Analysis of Leaf-Grazing Katydids Based on DNA Barcoding.},
journal = {Archives of insect biochemistry and physiology},
volume = {118},
number = {4},
pages = {e70062},
doi = {10.1002/arch.70062},
pmid = {40262024},
issn = {1520-6327},
support = {//This study was supported by Engineering Research Center of Ecological Safety and Conservation in Beijing-Tianjin-Hebei (Xiong'an New Area) of MOE, China (2024-11)./ ; },
abstract = {The diversity of herbivorous insects is associated with host plant diversity. The determination of dietary profile is a central topic in insect ecology. DNA barcoding, that is, taxon identification using a standardized DNA region, have been important to the recent advances in food web understandings. In this study, three commonly plant barcoding loci (i.e., rbcL, matK, and trnH-psbA) were chosen for screening of ingested plant DNA in 207 specimens of 18 leaf-grazing katydid species representing 4 subfamilies in China. The obtained sequences were queried against the Barcode of Life Database (BOLD) and GenBank for taxa identification. The results of identification were as follow: 3 Conocephalinae species consumed 10 plant families, with preference for Poaceae; 1 Mecopodinae species consumed 18 plant families, with preference for Fabaceae and Vitaceae; 11 Phaneropterinae species consumed 43 plant families, with preference for Juglandaceae; 3 species Pseudophyllinae species consumed 9 plant families, with preference for Balsaminaceae. Among these, only 81 out of 207 samples were identified at the species level when compares with NCBI and BOLD database. Our study added a significant amount of dietary information for leaf-grazing katydids in China. It is crucial to fully understand coevolution of katydids and plant, katydids diet resource requirements, and best practices for habitat conservation.},
}
@article {pmid40261157,
year = {2025},
author = {Kumar, A and Mishra, DK and Kanojiya, S},
title = {Identification of Botanicals Based on Their Mass Spectrum Fingerprints Using Ultra-Performance Liquid Chromatography-Mass Spectrometry.},
journal = {Journal of mass spectrometry : JMS},
volume = {60},
number = {5},
pages = {e5131},
doi = {10.1002/jms.5131},
pmid = {40261157},
issn = {1096-9888},
support = {YSS/2015/001048//Science &amp; Engineering Research Board (SERB) DST Government of India/ ; },
mesh = {Chromatography, High Pressure Liquid/methods ; *Mass Spectrometry/methods ; *Plants, Medicinal/chemistry/classification ; *Plant Extracts/chemistry/analysis ; Liquid Chromatography-Mass Spectrometry ; },
abstract = {In the current scenario, herbal raw materials are identified via morphotaxonomy, microscopic pharmacognosy, or DNA barcoding. However, these methods do not reveal their chemical integrity, while plant raw materials play a crucial role in the quality of plant-based medicine. To overcome this limitation, we used a mass spectrometry-based method to identify 30 botanicals. This assay followed a standard operating procedure (SOP) from sample preparation to the reference library's mass spectrum fingerprint (MSFP) search. The MS1 score showed a similarity index between the input data and the reference mass spectrum. A more than 50% MS1 score was the critical threshold for accurately identifying botanicals based on their chemical integrity. Interestingly, the analysis of 30 different plant species yielded no false results. The results were 100% accurate and selective for tested botanical samples. However, we found that the standard deviation of analytical assays and biological replicates was ± 3.5 and ± 6.3 (MS1 score) for all analyzed samples, respectively. Intraspecies variability showed MS1 scores > 50% ± 10, whereas interspecies variability was observed with MS1 scores < 50% ± 10. The MS1 score was observed, dependent on the plant species, ranging from 53.00% (± 2.65) to 89.76% (± 4.08). In addition, the method was tested to see how seasonal and geographical changes affected search results. The MS1 score changed by less than 15%. We simultaneously created a chemical barcode (unique molecular weight sequence) for each plant species to validate search results and ensure the reliable identification of botanicals.},
}
@article {pmid40260151,
year = {2025},
author = {Shapkin, V and Caboň, M and Kolařík, M and Adamčíková, K and Baldrian, P and Michalková, T and Větrovský, T and Adamčík, S},
title = {Protein Coding Low-Copy rpb2 and ef1-α Regions Are Viable Fungal Metabarcoding DNA Markers Which Can Supplement ITS for Better Accuracy.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71352},
pmid = {40260151},
issn = {2045-7758},
abstract = {The nuclear ribosomal DNA Internal Transcribed Spacer (ITS) region is used as a universal fungal barcode marker, but often lacks a significant DNA barcoding gap between sister taxa. Here we tested the reliability of protein coding low-copy genes as alternative barcode markers. Mock communities of three unrelated agaric genera (Dermoloma, Hodophilus, and Russula) representing lineages of closely related species were sequenced by the Illumina platform targeting the ITS1, ITS2, the second largest subunit of RNA polymerase II gene (rpb2) and the transcription elongation factor 1-alpha gene (ef1-α) regions. Species representation and their relative abundances were similar across all tested barcode regions, despite a lower copy number in protein coding markers. ITS1 and ITS2 required more sophisticated sequence filtering because they produced a high number of chimeric sequences requiring reference-based chimera removal and had a higher number of sequence variants per species. Although clustering of filtered ITS sequences resulted in an average higher number of correctly clustered units at optimal similarity thresholds, these thresholds varied substantially among genera. Best-fitted thresholds of low-copy markers were more consistent across genera but frequently lacked species resolution due to low intraspecific variability. At some thresholds, we observed multiple species lumped together, and at the same time, species split into multiple partial clusters, which should be taken into consideration when assessing the best clustering thresholds and taxonomic identity of clusters. To achieve the best taxonomic resolution and improve species detection, we recommend combining different markers and applying additional reference-based sorting of clusters. The current availability of rpb2 and ef1-α reference sequences in public databases is far from being complete for all fungal groups, but a combined marker approach can be used for group-specific studies that can build reference data for their own purposes.},
}
@article {pmid40260148,
year = {2025},
author = {Wong, A and Eizirik, E and Koepfli, KP and de Ferran, V and Shihepo, T and Lay, AR and Zumbroich, J and Rooney, N and Marker, L and Schmidt-Küntzel, A},
title = {Identifying Cryptic Mammals With Non-Invasive Methods: An Effective Molecular Species Identification Tool to Survey Southern African Terrestrial Carnivores.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71223},
pmid = {40260148},
issn = {2045-7758},
abstract = {Carnivores play a vital role in ecosystem health and are thus an important focus for conservation management. Non-invasive methods have gained traction for carnivore monitoring as carnivores are often elusive and wide-ranging, making visual counts particularly difficult. Faecal mini-barcoding combines field collection of scats with genetic analysis for species identification. Here, we assessed the applicability of a mini-barcode based on the mitochondrial ATP6 gene in southern Africa. We predicted amplification success based on in silico evaluation of reference sequences from 34 of the 42 terrestrial carnivore species existing in southern Africa, including the Congo clawless otter (Aonyx congicus) for which we contributed a mitochondrial assembly. We further tested amplification success on available reference samples of 23 species. We expanded the existing ATP6 mini-barcode reference database by contributing additional sequences for 22 species, including the Cape genet (Genetta tigrina) and the side-striped jackal (Lupulella adusta) for which no complete mini-barcode sequences were available on GenBank, and compiled a representative reference dataset of 61 unique sequences as a tool for species identification. As a proof of principle, we applied the ATP6 mini-barcode to a small scat-based carnivore survey conducted in Namibia 13 years prior, which showed a 95% identification success and detected six species among 157 samples collected. With southern Africa's mammalian carnivores facing escalating threats, this robust mini-barcode offers a vital tool for accurate species identification from non-invasive samples, enabling crucial monitoring and conservation efforts.},
}
@article {pmid40259706,
year = {2025},
author = {Woodford, DJ and Magoro, M and Kadye, WT and Scheepers, M and Sithole, Y and Mutizwa, TI and Ntokoane, T and Chakona, A},
title = {Freshwater fishes of the Waterberg aquatic ecoregion, South Africa: Diversity, taxonomic conflicts and conservation concerns.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70007},
pmid = {40259706},
issn = {1095-8649},
support = {FBIP-211006643719//National Research Foundation/ ; IBIP-BS13100251309//National Research Foundation/ ; FBIC200227507229//National Research Foundation/ ; },
abstract = {Southern Africa is a region denoted by both high levels of fish diversity, some of it cryptic and unrecognised by current taxonomy, and severely threatened freshwater ecosystems. The Waterberg, a key aquatic ecoregion of the greater Limpopo River basin in South Africa, represents an area with high terrestrial conservation value but is lacking in aquatic biodiversity information. This study characterised this unique aquatic ecoregion's fish diversity, their biogeographic patterns and threats to this biodiversity. A total of 29 fish species (11 families, 19 genera) were identified, with many distinct upland fish communities occurring within the high-altitude headwaters of the ecoregion, whereas lowland fish communities tended to be more homogeneous. Mitochondrial CO1 barcoding revealed genetically distinct lineages in four presumed-widespread southern African species: the shortfin barb, Enteromius brevipinnis (Jubb, 1966); hyphen barb, Enteromius bifrenatus (Fowler, 1935); straightfin barb, Enteromius paludinosus (Peters, 1852) and snake catfish, Clarias theodorae Weber, 1897, that were restricted to the Waterberg aquatic ecoregion. The level of genetic divergence suggests that these four Waterberg-restricted lineages are likely new candidate species. These findings indicate the Waterberg to be a biogeographic island within the greater Zambezian ichthyofaunal region of southern Africa, which should be prioritised for aquatic ecosystem conservation. Current terrestrial conservation structures in the region, encapsulated within the Waterberg Biosphere Reserve, appear to protect this distinct ichthyofauna from human land-use-derived impacts. Nonetheless, the presence of the invasive predatory largemouth bass (Micropterus nigricans) inside the biosphere represents a credible conservation threat. Engagement with biosphere stakeholders will be critical for managing this threat to the Waterberg's unique ichthyofauna going forward.},
}
@article {pmid40258808,
year = {2025},
author = {van der Toorn, W and Bohn, P and Liu-Wei, W and Olguin-Nava, M and Gribling-Burrer, AS and Smyth, RP and von Kleist, M},
title = {Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3742},
pmid = {40258808},
issn = {2041-1723},
support = {390685689//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 01KI2016//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 955974//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; VH-NG-1347//Helmholtz Association/ ; ANR 20-SFRI-0012//Universit&#xe9; de Strasbourg (University of Strasbourg)/ ; },
mesh = {*SARS-CoV-2/genetics ; RNA, Viral/genetics ; Humans ; *Sequence Analysis, RNA/methods ; *Nanopore Sequencing/methods ; COVID-19/virology ; *Nanopores ; Software ; Algorithms ; Machine Learning ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Nanopore direct RNA sequencing (dRNA-seq) enables unique insights into RNA biology. However, applications are currently limited by the lack of accurate and cost-effective sample multiplexing. Here we introduce WarpDemuX, an ultra-fast and highly accurate adapter-barcoding and demultiplexing approach for dRNA-seq with SQK-RNA002 and SQK-RNA004 chemistries. WarpDemuX enhances speed and accuracy by fast processing of the raw nanopore signal, use of a light-weight machine-learning algorithm and design of optimized barcode sets. We demonstrate its utility by performing rapid phenotypic profiling of different SARS-CoV-2 viruses through multiplexed sequencing of longitudinal samples on a single flowcell, identifying systematic differences in transcript abundance and poly(A) tail lengths during infection. Additionally, integrating WarpDemuX into sequencing control software enables real-time enrichment of target molecules through barcode-specific adaptive sampling, which we demonstrate by enriching low abundance viral RNA. In summary, WarpDemuX represents a broadly applicable, high-performance, economical multiplexing solution for dRNA-seq, facilitating advanced (epi-) transcriptomic research.},
}
@article {pmid40258437,
year = {2025},
author = {Kioulos, I and Grigoriadou, AM and Papadakis, A and Vontas, J and Mavridis, K},
title = {Molecular genotyping of pyrethroid resistant mutations and their haplotypes in bed bug populations from Greece.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107624},
doi = {10.1016/j.actatropica.2025.107624},
pmid = {40258437},
issn = {1873-6254},
abstract = {The resurgence of bed bugs poses significant risks to public health and tourism-driven economies in Southern Europe, including Greece. Control efforts largely rely on pyrethroids; however, the widespread selection of knockdown resistance (kdr) mutations has compromised their effectiveness. Molecular monitoring is therefore essential for accurate species identification and resistance surveillance to support evidence-based pest management strategies. In this study, we analyzed bed bug populations collected from Athens, Thessaloniki, and Heraklion between 2021 and 2024. Species identification was performed via DNA barcoding of the cytochrome oxidase I (COI) gene, while kdr mutations in the voltage-gated sodium channel (VGSC) gene-specifically V419L, L925I, and I936F-were assessed to determine their frequencies and haplotype distributions. All specimens were identified as Cimex lectularius. The L925I mutation reached fixation (100%) in Thessaloniki and Heraklion, while V419L was detected at frequencies of 30.00% and 50.00%, respectively; I936F was not detected in these populations. In Athens, L925I was highly prevalent (98.40%), while V419L (5.27%) and I936F (0.60%) were detected at lower frequencies. Haplotype analysis revealed Haplotype B (L925I only) as the most common in Athens (91.20%) and Thessaloniki (60.0%), while Haplotype C (L925I + V419L) predominated in Heraklion (76.92%). Additional haplotypes were identified in Athens, including Haplotype B[b] (L925I + I936F), marking its first detection in Europe. These findings highlight the widespread presence of kdr mutations and underscore the urgent need for integrated pest management (IPM) strategies, incorporating resistance monitoring, alternative insecticides, and non-chemical control methods to mitigate the growing challenge of pyrethroid resistance in bed bugs.},
}
@article {pmid40257565,
year = {2025},
author = {Marsolier, J and Moutaux, E and Grosselin, K and Griffiths, A and Vallot, C},
title = {Single-cell Epigenomic Profiling with High-throughput Droplet scChIP-seq.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2919},
number = {},
pages = {213-239},
pmid = {40257565},
issn = {1940-6029},
mesh = {*Single-Cell Analysis/methods ; *Epigenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Histones/genetics ; Microfluidics/methods ; *Epigenesis, Genetic ; },
abstract = {Our high-throughput scChIP-seq approach combines droplet microfluidics with single-cell DNA barcoding to study the heterogeneity of epigenomes (H3K27me3, H3K4me3, H3K27Ac, H3K4me1) in a cellular population of several thousand cells with a coverage of up to 10,000 unique loci per cell.},
}
@article {pmid40253081,
year = {2025},
author = {Llera-Oyola, J and Pérez-Moraga, R and Parras, M and Rosón, B},
title = {How to view the female reproductive tract through single-cell looking glasses.},
journal = {American journal of obstetrics and gynecology},
volume = {232},
number = {4S},
pages = {S21-S43},
doi = {10.1016/j.ajog.2024.08.040},
pmid = {40253081},
issn = {1097-6868},
mesh = {Female ; Humans ; *Single-Cell Analysis/methods ; *Genitalia, Female/cytology ; Sequence Analysis, RNA ; Pregnancy ; },
abstract = {Single-cell technologies have emerged as an unprecedented tool for biologists and clinicians, allowing them to assess organs and tissues at the level of individual cells. In the field of women's reproductive biology, single-cell studies have provided insights into the cellular and molecular processes that regulate reproductive and obstetrical functions in health and disease. The knowledge that these studies generate is helping clinicians to improve the understanding and diagnosis of infertility related issues or pregnancy complications and to find new avenues for their treatment. However, navigating the expansive landscape of this type of transcriptomic data analysis represents a pivotal challenge in current research. Single cell RNA sequencing involves isolating cells into droplets, reverse transcribing RNA to generate complementary DNA, with each droplet content uniquely labeled by a barcode. Upon sequencing the complementary DNAs, the barcodes enable the reassignment of sequencing reads to individual droplets, facilitating the reconstruction of the cellular landscape of the sample obtained from a tissue or organ and beyond. Researchers, equipped with the metaphorical 'single-cell glasses,' must adequately choose from a plethora of strategies to dissect and interpret cellular information. Sophisticated algorithms and the decision-making process are often underestimated, resulting in artefactual or cumbersome interpreted results. Computational biologists apply and innovate computational tools designed to process, model, and interpret expansive datasets. The ramifications of their work extend far beyond the realm of data processing; they give shape to the outcome of analyses, playing a pivotal role in drawing meaningful conclusions from the wealth of information garnered. In this review, we describe the wide variety of approaches and analytical steps available with enough detail to gain a concise picture of what a complete examination of a single-cell dataset would be. We commence with a discussion on key points in experimental design, highlighting crucial questions one should consider. Following this, we delve into the various preprocessing and quality control steps essential for any single-cell dataset. The subsequent section offers a detailed guide on constructing a single-cell atlas, exploring nuances such as differential characteristics in visualization and clustering techniques, as well as strategies for assigning identity to cell populations through gene marker annotations. Moving beyond the creation of an atlas, we explore methods for investigating pathological conditions. This involves conducting cell population comparison tests between conditions and analyzing specific cell-to-cell communications and cellular differentiation trajectories in both health and disease scenarios. This work aims to furnish a newcomer researcher and/or clinician with essential guidelines to embark on a single-cell adventure without succumbing to common pitfalls. By bridging the gap between theory and practice, it facilitates the translation of single-cell technologies into clinically relevant applications. Throughout the manuscript, practical examples of its usage in women's reproductive health studies are provided. Various sections delve into specific clinical scenarios, demonstrating how these guidelines can be instrumental in unraveling the molecular landscapes of diseases and physiological processes related to women's reproduction.},
}
@article {pmid40248651,
year = {2025},
author = {Liu, WW and Yin, CZ and Zhang, ZX and Wang, XS and Meng, Z and Zhang, XG and Wang, S},
title = {Four new species of Beltraniella (Amphisphaeriales, Beltraniaceae) revealed by morphology and phylogenetic analyses from China.},
journal = {MycoKeys},
volume = {116},
number = {},
pages = {125-144},
pmid = {40248651},
issn = {1314-4049},
abstract = {Beltraniella is a widely-distributed genus on Earth, although its abundance is relatively limited in relation to other dematiaceous hyphomycetes. In the present study, diseased leaves of Myristicafragrans and decaying leaves were collected from Hainan and Sichuan Province. Fungal DNA was amplified and sequenced using two barcodes, the internal transcribed spacer (ITS) and large subunit of ribosomal RNA (LSU), and phylogenetic analyses were conducted through maximum likelihood (ML) and Bayesian inference (BI) algorithms. Four new species of Beltraniella, B.dujiangyanensis, B.jianfengensis, B.myristicae, and B.xinglongensis are identified through phylogenetic analyses and morphological comparison during a survey of fungal diversity in Hainan and Sichuan Provinces, China. Detailed descriptions of the morphological characteristics of these four new species are provided and illustrated with figures.},
}
@article {pmid40248647,
year = {2024},
author = {Wibisana, JN and Plessy, C and Dierckxsens, N and Masunaga, A and Miao, J and Luscombe, NM},
title = {The complete mitogenome of an unidentified Oikopleura species.},
journal = {F1000Research},
volume = {13},
number = {},
pages = {1357},
pmid = {40248647},
issn = {2046-1402},
mesh = {*Genome, Mitochondrial ; Animals ; *Urochordata/genetics/classification ; Japan ; Sequence Analysis, DNA ; },
abstract = {Appendicularians are planktonic tunicates abundant all over the world. Currently, only two complete annotated mitochondrial genome assemblies are available for appendicularians, both for cryptic species of Oikopleura dioica. This underrepresentation of available appendicularian mitochondrial genomes limits environmental DNA sequencing (eDNA) studies that rely on mitochondrial markers as a taxonomic barcode. We report the complete mitochondrial genome assembly and annotation of an unknown appendicularian species isolated from the Amami Oshima island, Kagoshima prefecture, Japan, that has significant sequence difference with other currently available assemblies and will serve as a useful resource for ecological studies and further mitochondrial studies of appendicularians.},
}
@article {pmid40248491,
year = {2025},
author = {Fulci, V},
title = {Fast analysis of Spatial Transcriptomics (FaST): an ultra lightweight and fast pipeline for the analysis of high resolution spatial transcriptomics.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {2},
pages = {lqaf044},
pmid = {40248491},
issn = {2631-9268},
mesh = {*Software ; *Gene Expression Profiling/methods ; *Transcriptome ; Humans ; Sequence Analysis, RNA/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Recently, several protocols repurposing the Illumina flow cells or DNA nanoballs as an RNA capture device for spatial transcriptomics have been reported. These protocols yield high volumes of sequencing data which are usually analyzed through the use of high-performance computing clusters. I report Fast analysis of Spatial Transcriptomic (FaST), a novel pipeline for the analysis of subcellular resolution spatial transcriptomics datasets based on barcoding. FaST is compatible with OpenST, seq-scope, Stereo-seq, and potentially other protocols. It allows full reconstruction of the spatially resolved transcriptome, including cell segmentation, of datasets consisting of >500 M million reads in as little as 1 h on a standard multi core workstation with 32 Gb of RAM. The FaST pipeline returns RNA segmented Spatial Transcriptomics datasets suitable for subsequent analysis through commonly used packages (e.g scanpy or seurat). Notably, the pipeline I present relies on the spateo-release package for RNA segmentation and does not require hematoxylin/eosin or any other imaging procedure to guide cell segmentation. Nevertheless, integration with other software for imaging-guided cell segmentation is still possible. FaST is publicly available on github (https://github.com/flcvlr/FaST).},
}
@article {pmid40248452,
year = {2025},
author = {Hrivniak, &#x13d; and Sroka, P and Godunko, RJ and Martynov, AV and Palatov, DM and Bojková, J},
title = {Discovering diversity of Central Asian and Himalayan Epeorus (Caucasiron) mayflies (Ephemeroptera, Heptageniidae) using DNA barcoding and morphology.},
journal = {ZooKeys},
volume = {1234},
number = {},
pages = {89-125},
pmid = {40248452},
issn = {1313-2989},
abstract = {The mayflies of the genus Epeorus Eaton, 1881 subgenus Caucasiron Kluge, 1997 are distributed from the eastern Mediterranean to the mountains of south-west China. In contrast to the Caucasus, the Mediterranean and Irano-Anatolian regions, where E. (Caucasiron) represents one of the most extensively studied mayfly taxa, the species diversity in the more eastern mountains of Asia has been studied only sporadically. In this study, the species diversity of E. (Caucasiron) from the mountains of Central Asia (Pamir, Tian Shan) and the western part of the Himalayas was analysed using DNA barcoding and the morphology of larvae and adults. The distance- and phylogenetic tree-based molecular species delimitation analyses revealed five E. (Caucasiron) species occurring in the study area. Three of them did not correspond morphologically to any known species of the genus Epeorus. These species were described herein as E. (C.) himalayensis Hrivniak &amp; Sroka, sp. nov., E. (C.) lanceolatus Hrivniak &amp; Sroka, sp. nov. and E. (C.) lineatus Hrivniak &amp; Sroka, sp. nov. All new species were compared with other representatives of the subgenus and other related species of the genus Epeorus, and appropriate morphological diagnostic characters were provided. Morphological revision, main diagnostic characters, and information on the distribution of E. (C.) guttatus Braasch &amp; Soldán, 1979 and two other potentially related Epeorus species from the area, E.psi Eaton, 1885 and E.suspicatus (Braasch, 2006), are also given.},
}
@article {pmid40247933,
year = {2025},
author = {Moulin, N},
title = {MANGF: a reference library of DNA barcodes for Mantodea from French Guiana (Insecta, Dictyoptera).},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e149486},
pmid = {40247933},
issn = {1314-2828},
abstract = {BACKGROUND: Mantodea plays a special role in the food chain as a group charismatic generalist predators. They regulate invertebrate populations while themselves being prey for many larger animals such as reptiles and birds. The present study focuses on Fench Guiana where about 78 species are known within eight families. This diversity represents a challenge for specimen identification.<br><br>NEW INFORMATION: The MANGF project aims at developing a DNA metabarcoding approach to facilitate and enhance the monitoring of mantises as indicators in ecological studies. As a first step towards that goal, we assembled a library of DNA barcodes using the standard genetic marker for animals, i.e. a portion of the COI mitochondrial gene. In the present contribution, we release a library including 425 records representing 68 species in eight different families. Species were identified by expert taxonomists and each record is linked to a voucher specimen to enable future morphological examination. We also highlight and briefly discuss cases of low interspecific divergences, as well as cases of high intraspecific divergences that might represent cases of overlooked or cryptic diversity.},
}
@article {pmid40246065,
year = {2025},
author = {Oskolas, H and Nogueira, FCN and Domont, GB and Yu, KH and Semenov, YR and Sorger, P and Steinfelder, E and Corps, L and Schulz, L and Wieslander, E and Fenyö, D and Kárpáti, S and Holló, P and Kemény, LV and Döme, B and Megyesfalvi, Z and Pawłowski, K and Nishimura, T and Kwon, H and Encarnación-Guevara, S and Szasz, AM and Veréb, Z and Gyulai, R and Németh, IB and Appelqvist, R and Rezeli, M and Baldetorp, B and Horvatovich, P and Malmström, J and Pla, I and Sanchez, A and Knudsen, B and Kiss, A and Malm, J and Marko-Varga, G and Gil, J},
title = {Comprehensive biobanking strategy with clinical impact at the European Cancer Moonshot Lund Center.},
journal = {Journal of proteomics},
volume = {},
number = {},
pages = {105442},
doi = {10.1016/j.jprot.2025.105442},
pmid = {40246065},
issn = {1876-7737},
abstract = {This white paper presents a comprehensive biobanking framework developed at the European Cancer Moonshot Lund Center that merges rigorous sample handling, advanced automation, and multi-omic analyses to accelerate precision oncology. Tumor and blood-based workflows, supported by automated fractionation systems and standardized protocols, ensure the collection of high-quality biospecimens suitable for proteomic, genomic, and metabolic studies. A robust informatics infrastructure, integrating LIMS, barcoding, and REDCap, supports end-to-end traceability and realtime data synchronization, thereby enriching each sample with critical clinical metadata. Proteogenomic integration lies at the core of this initiative, uncovering tumor- and blood-based molecular profiles that inform cancer heterogeneity, metastasis, and therapeutic resistance. Machine learning and AI-driven models further enhance these datasets by stratifying patient populations, predicting therapeutic responses, and expediting the discovery of actionable targets and companion biomarkers. This synergy between technology, automation, and high-dimensional data analytics enables individualized treatment strategies in melanoma, lung, and other cancer types. Aligned with international programs such as the Cancer Moonshot and the ICPC, the Lund Center's approach fosters open collaboration and data sharing on a global scale. This scalable, patient-centric biobanking paradigm provides an adaptable model for institutions aiming to unify clinical, molecular, and computational resources for transformative cancer research.},
}
@article {pmid40245615,
year = {2025},
author = {Wu, Q and Nakano, T and Ishida, S and Komai, T and Fujiwara, Y and Yoshida, T and Kawato, M and Oka, SI and Fujikura, K and Miya, M and Minamoto, T},
title = {Development of universal PCR primers for the environmental DNA metabarcoding of cephalopod (Mollusca) diversity.},
journal = {Marine environmental research},
volume = {208},
number = {},
pages = {107094},
doi = {10.1016/j.marenvres.2025.107094},
pmid = {40245615},
issn = {1879-0291},
abstract = {Cephalopods play crucial roles in marine ecosystems, acting as both predators and prey for apex predators, thereby contributing to the distribution of energy and nutrients across the food web. Traditional net capture methods are often ineffective for studying cephalopods owing to their wide distribution in marine environments, necessitating the development of simple and efficient surveying techniques to assess cephalopod diversity. Therefore, in this study, we aimed to establish universal polymerase chain reaction primers specifically targeting mitochondrial 16S rRNA genes for environmental DNA metabarcoding in cephalopods. Two primer sets, Cep16S_D and Cep16S_O, were designed for squids and octopuses, respectively. Taxonomic specificity, resolution, and coverage of these primers were evaluated via in silico and in vitro analyses. Additionally, efficiency of these primer sets was assessed using tissue samples and mock communities. Finally, their applicability and performance were tested at various depths. The developed primers exhibited a relatively large amplification size with mixed bases that enhanced their amplification efficiency and sensitivity for cephalopod detection. We successfully identified cephalopod species with different body sizes, from small species, such as Heteroteuthis dagamensis, to large species, such as Architeuthis dux, at varying water depths. Overall, the primer sets established in this study serve as powerful tools to study cephalopod diversity and exhibit great potential for barcoding and genetic diversity investigations.},
}
@article {pmid40242636,
year = {2025},
author = {Munkhtulga, D and Baasanmunkh, S and Nyamgerel, N and Park, JH and Tsegmed, Z and Tojibaev, KS and Choi, HJ},
title = {Morphological and phylogenetic analysis approach to three new species and a new section of Astragalus (Fabaceae) from Mongolia.},
journal = {PhytoKeys},
volume = {255},
number = {},
pages = {51-73},
pmid = {40242636},
issn = {1314-2011},
abstract = {Astragalus L. is the largest genus worldwide, comprising more than 3,100 species belonging to 250 sections. In Mongolia, approximately 130 species, including 15 endemic and 25 subendemic species have been previously recognized from 42 sections and 6 subgenera. In this study, we investigated several species within section Laguropsis in Mongolia based on extensive morphological analyses and molecular evidence. Based on these results, we describe three new species and a new section. Two of the newly described species, A.oyunicus and A.teshigicus, belong to the section Laguropsis, whereas the remaining species, A.uvsicus, is the type species of the new section Uvsicus. Furthermore, our findings revealed that (i) A.tamiricus, previously considered endemic to Mongolia, is an additional synonym of A.laguroides, and (ii) A.gobi-altaicus, previously a synonym of A.laguroides, is an independent species. Finally, we provide taxonomic nomenclature, morphological observations, distribution maps and wild photo illustrations of each species.},
}
@article {pmid40238250,
year = {2025},
author = {Zhao, J and Yang, W and Cai, H and Cao, G and Li, Z},
title = {Current Progress and Future Trends of Genomics-Based Techniques for Food Adulteration Identification.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/foods14071116},
pmid = {40238250},
issn = {2304-8158},
support = {Grant No. ZDYF2024GXJS316//Key Research and Development Projects in Hainan Province/ ; },
abstract = {Addressing the pervasive issue of food adulteration and fraud driven by economic interests has long presented a complex challenge. Such adulteration not only compromises the safety of the food supply chain and destabilizes the market economy but also poses significant risks to public health. Food adulteration encompasses practices such as substitution, process manipulation, mislabeling, the introduction of undeclared ingredients, and the adulteration of genetically modified foods. Given the diverse range of deceptive methods employed, genomics-based identification techniques have increasingly been utilized for detecting food adulteration. Compared to traditional detection methods, technologies such as polymerase chain reaction (PCR), next-generation sequencing (NGS), high-resolution melt (HRM) analysis, DNA barcoding, and the CRISPR-Cas system have demonstrated efficacy in accurately and sensitively detecting even trace amounts of adulterants. This paper provides an overview of genomics-based approaches for identifying food adulteration, summarizes the latest applications in certification procedures, discusses current limitations, and explores potential future trends, thereby offering new insights to enhance the control of food quality and contributing to the development of more robust regulatory frameworks and food safety policies.},
}
@article {pmid40237570,
year = {2025},
author = {Bignotto, TS and de Souza, HB and da Silva Bronzim, RC and Maniglia, TC and Baumgartner, D},
title = {Integrative morphometric and molecular analyses reveal possible genetic contamination of silver catfish populations of the genus Rhamdia in Neotropical River basins.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70057},
pmid = {40237570},
issn = {1095-8649},
abstract = {Rhamdia quelen, Rhamdia branneri and Rhamdia voulezi are morphologically similar species that, until recently, were considered synonymous. Although R. quelen has wide distribution in the Neotropical region, R. branneri and R. voulezi are sympatric and endemic species of the Iguaçu River basin. We used an integrative approach, including morphometric and molecular data (barcodes DNA, COI gene), to assist in the identification and delimitation of these species. We also intended to investigate genetic contamination of the Paraná III and lower Iguaçu River basins, as silver catfish production has increased in southern Brazil, and accidental or occasional escapes to nature may pose risks to the genetic integrity of native populations. COI sequences and morphometric data were efficient in the characterization and differentiation of Rhamdia species and may be helpful tools in correctly identifying R. quelen, R. branneri and R. voulezi. Both morphometric and molecular analyses indicated the segregation of specimens into three groups. Although this separation coincided with the taxonomy and the collection site in the morphometric analyses, the taxonomic identification of most samples did not coincide with the molecular identification. This fact may be due to (i) incorrect morphological identification and/or (ii) escapes of pure species and/or interspecific hybrids from fish farms. The detection of COI haplotypes of R. quelen in the lower Iguaçu River, as well as COI haplotypes of R. branneri and R. voulezi in the Paraná III basin, combined with the morphometric and morphological characteristics of the specimens, reinforces the occurrence of hybrid specimens in these river basins. These results reveal the importance of characterizing species and interspecific hybrids of Rhamdia and the urgency to regulate aquaculture activities.},
}
@article {pmid40236044,
year = {2025},
author = {Blois, S and Goetz, BM and Mojumder, A and Sullivan, CS},
title = {Shedding dynamics of a DNA virus population during acute and long-term persistent infection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.31.646279},
pmid = {40236044},
issn = {2692-8205},
abstract = {UNLABELLED: Although much is known of the molecular mechanisms of virus infection within cells, substantially less is understood about within-host infection. Such knowledge is key to understanding how viruses take up residence and transmit infectious virus, in some cases throughout the life of the host. Here, using murine polyomavirus (muPyV) as a tractable model, we monitor parallel infections of thousands of differentially barcoded viruses within a single host. In individual mice, we show that numerous viruses (>2600) establish infection and are maintained for long periods post-infection. Strikingly, a low level of many different barcodes is shed in urine at all times post-infection, with a minimum of at least 80 different barcodes present in every sample throughout months of infection. During the early acute phase, bulk shed virus genomes derive from numerous different barcodes. This is followed by long term persistent infection detectable in diverse organs. Consistent with limited productive exchange of virus genomes between organs, each displays a unique pattern of relative barcode abundance. During the persistent phase, constant low-level shedding of typically hundreds of barcodes is maintained but is overlapped with rare, punctuated shedding of high amounts of one or a few individual barcodes. In contrast to the early acute phase, these few infrequent highly shed barcodes comprise the majority of bulk shed genomes observed during late times of persistent infection, contributing to a stark decrease in bulk barcode diversity that is shed over time. These temporally shifting patterns, which are conserved across hosts, suggest that polyomaviruses balance continuous transmission potential with reservoir-driven high-level reactivation. This offers a mechanistic basis for polyomavirus ubiquity and long-term persistence, which are typical of many DNA viruses.<br><br>AUTHOR SUMMARY / IMPORTANCE: Polyomavirus infections, mostly benign but potentially fatal for immunocompromised individuals, undergo acute and long-term persistent infections. Typically, polyomavirus-associated diseases arise due to virus infection occurring in the context of a persistently infected individual. However, little is understood regarding the mechanisms of how polyomaviruses establish, maintain, and reactivate from persistent infection. We developed a non-invasive virus shedding assay combining barcoded murine polyomavirus, massively parallel sequencing technology, and novel computational approaches to track long-term infections in mice. We expect these methods to be of use not only to the study of DNA viruses but also for understanding persitent infection of diverse microbes. The study revealed organ-specific virus reservoirs and two distinct shedding patterns: constant low-level shedding of numerous barcodes and episodic high-level shedding of few barcodes. Over time, the diversity of shed barcodes decreased substantially. These findings suggest a persistent low-level infection in multiple reservoirs, with occasional bursts of replication in a small subset of infected cells. This combination of broad reservoirs and varied shedding mechanisms may contribute to polyomavirus success in transmission and maintaining long-term infections.},
}
@article {pmid40236020,
year = {2025},
author = {Tasca, JA and Doherty, JF and Shields, EJ and Mudiyanselage, SD and Reich, LN and Sarma, K and Garcia, BA and Bonasio, R},
title = {Pooled scanning of protein variants identifies novel RNA-binding mutants.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.04.02.646914},
pmid = {40236020},
issn = {2692-8205},
abstract = {Binding to RNA has been observed for an ever-increasing number of proteins, which often have other functions. The contributions of RNA binding to protein function are best discerned by studying separation-of-function mutants that hamper interaction with RNA without affecting other aspects of protein function. To design these mutants, we need precise knowledge of the residues that contribute to the affinity of the protein for its RNA ligands. Here, we present RBR-scan: a technology to simultaneously measure RNA-binding affinity of a large number of protein variants. We fused individual variants with unique peptide barcodes optimized for detection by mass spectrometry (MS), purified protein pools from single bacterial culture, and assayed proteins in parallel for RNA binding. Mutations in the MS2 coat protein known to impair RNA-binding were correctly identified, as well as a previously unreported mutant, which we validated with orthogonal biochemical methods. We used RBR-scan to discover novel RNA-binding mutants in the cancer-associated splicing regulator SRSF2. Together, our results demonstrate that RBR-scan is a powerful and scalable platform for linking RNA-binding affinity to protein sequence, offering a novel strategy to decode the functional consequences of protein-RNA interactions.},
}
@article {pmid40235722,
year = {2025},
author = {Chai, Y and Tian, T and Wang, L and Wei, J and Xu, Y and Liu, P and Xiang, C and Yue, M},
title = {Using Plant DNA Barcodes and Functional Traits to Assess Community Assembly of Quercus Forests at Different Scales in the Semiarid Loess Plateau of China.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71103},
pmid = {40235722},
issn = {2045-7758},
abstract = {Trait and evolutionary differences among coexisting species are increasingly used to comprehend the processes shaping communities. However, they do not consistently yield congruent insights due to methodological limitations and scale dependence. Utilizing two plastid DNA genes (rbcL and matK) and one nuclear DNA gene (internal transcribed spacer, ITS), we first constructed the phylogenies of 147 woody species from 98 line transects in the forest areas of the Loess Plateau and subsequently measured three functional traits. Five plots (2500 m[2]) were constructed within Quercus forests to analyze the functional and phylogenetic structures at three spatial scales (100, 400, 2500 m[2]) and two vertical structural layers (tree colonization and shrub layer). In contrast to the phylogenetic convergence observed at the genus level, using plant DNA barcodes, we found that the entire forest communities and the tree layer exhibited phylogenetic randomness across all three spatial scales; even the shrub layer showed phylogenetic overdispersion with increasing scale. Specific leaf area (SLA) exhibited functional convergence in both the shrub and tree layers. In contrast, seed mass (SM) and plant height (PH) displayed distinct functional structures. In the tree layer, these traits showed phylogenetic overdispersion, while in the shrub layer, they demonstrated functional convergence. This contrast highlights the different ecological roles and processes at play in the two layers. Specifically, the scale dependency of assembly patterns in the shrub layer was more pronounced than in the tree layer for both functional and phylogenetic structures. Our findings underscore the significance of employing DNA barcodes to assess the phylogenetic structure of communities with closely related coexisting species and emphasize niche-based functional assembly and multi-process phylogenetic assembly among vertical structural layers in the Quercus community. Decoupling functional and phylogenetic disparities between species could facilitate the understanding of complex species differences influencing community assembly.},
}
@article {pmid40234750,
year = {2025},
author = {Shen, X and Li, Y and Liu, Y and Jiang, D},
title = {Creating an effective DNA identification system for discriminating cherries (Prunus subgenus Cerasus).},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {475},
pmid = {40234750},
issn = {1471-2229},
support = {2021C02071-4-2//Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding/ ; },
abstract = {BACKGROUND: Cherries, a subgenus of Cerasus within Rosaceae, as fruit trees with high economic value and elegant garden plants, have broad prospects for development and utilization. However, traditional morphology and molecular data have struggled to accurately identify cherry species due to their extensive overlap in the distribution, frequent hybridization, both open and closed flowers, hysteranthy and limited species coverage, hindering the advancement of the cherry industry. In this study, 61 well-documented cherry species were collected and whole chloroplast genome data was used to develop an effective DNA identification system for precise species identification.<br><br>RESULTS: 36 new cherry chloroplast genomes were added to the public database, resulting in the most comprehensive phylogenetic relationship of cherry species to date. While whole chloroplast genome data achieved an 85.26% species identification success rate, it did not fully resolve all species identification. Relying solely on whole chloroplast genome data is resource-intensive. Therefore, we explored using highly variable regions, species-specific SNPs, and structural variations for accurate species identification. This study revealed that 14 newly developed DNA barcodes could identify 71.88% of cherry samples, while 106 SNPs and Indels allowed for precise identification of 59 out of 61 cherry species.<br><br>CONCLUSIONS: This study not only clarified the phylogenetic relationships of major cherry species but also developed a precise identification system, providing a robust tool for accurate species identification and laying a solid foundation for breeding and the broader promotion of cherry species.<br><br>CLINICAL TRIAL NUMBER: Not applicable.},
}
@article {pmid40231940,
year = {2025},
author = {Grbin, D and Zrnčić, S and Oraić, D and Alfier, M and Cindrić, M and Jović, L and Sučec, I and Zupičić, IG},
title = {Seafood Labeling in Croatia: Molecular Evidence and Regulatory Insights.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/foods14060917},
pmid = {40231940},
issn = {2304-8158},
support = {Project MetaPatvor NPOO.C3.2.R3-I1.04.0122//European Union NextGenerationEU/ ; },
abstract = {Fisheries and aquaculture play a crucial role in global food security, yet species mislabeling remains a persistent challenge, undermining consumer trust and market transparency. Proper food labeling is essential for protecting public health due to the presence of unknown toxic or allergenic substances and preventing illegally sourced products from entering the market. Despite extensive research across Europe, seafood mislabeling in Croatia has remained unexplored. This study aims to provide the first comprehensive assessment of seafood labeling accuracy in Croatia, where fisheries are integral to the coastal economies and tourism. Using DNA barcoding of the COI gene, 109 seafood samples were collected over two years from various sources, including restaurants, markets, and fishing vessels, and analyzed for potential mislabeling. Results revealed a mislabeling rate of 3% among fish samples and 20% among cephalopods, with notable substitutions, such as the yellowfin tuna mislabeled as bigeye tuna and Bluefin tuna and the European squid mislabeled as Patagonian squid. Additionally, 38.5% of samples were partially labeled, while 32% lacked clear country-of-origin information, complicating traceability. While the findings align with the mislabeling rates in other European countries, this study underscores the ongoing challenges in seafood labeling compliance. Establishing standardized monitoring protocols will be essential for improving comparability and effectively addressing seafood fraud.},
}
@article {pmid40228207,
year = {2025},
author = {Leibovich, N and Goyal, S},
title = {Limitations and optimizations of cellular lineages tracking.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1012880},
doi = {10.1371/journal.pcbi.1012880},
pmid = {40228207},
issn = {1553-7358},
mesh = {*Cell Lineage/genetics ; Computational Biology/methods ; *DNA Barcoding, Taxonomic/methods ; *Cell Tracking/methods ; Humans ; Animals ; },
abstract = {Tracking cellular lineages using genetic barcodes provides insights across biology and has become an important tool. However, barcoding strategies remain ad hoc. We show that elevating barcode insertion probability and thus increasing the average number of barcodes within the cells, adds to the number of traceable lineages but may decrease the accuracy of lineages inference due to reading errors. We establish the trade-off between accuracy in tracing lineages and the total number of traceable lineages, and find optimal experimental parameters under limited resources concerning the populations size of tracked cells and barcode pool complexity.},
}
@article {pmid40226864,
year = {2025},
author = {Huang, Y and Zhang, Z and Yang, T and Zhang, Y and Cheng, X and Kang, Y and Guang, Y and Zou, Y and Zhang, X and Luo, Z and Chen, J and Cheng, W},
title = {Gemini Molecular Assembly Colocalization (GOAL): Accurate and Efficient Fusion Genotyping for Chronic Myeloid Leukemia Intelligent Diagnosis.},
journal = {Small methods},
volume = {},
number = {},
pages = {e2500194},
doi = {10.1002/smtd.202500194},
pmid = {40226864},
issn = {2366-9608},
support = {82372334//National Natural Science Foundation of China/ ; 82302621//National Natural Science Foundation of China/ ; U24A20751//National Natural Science Foundation of China/ ; KJZD-K202200404//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; KJQN202300435//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; CSTB2023NSCQ-LZX0022//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; W0183//Future Medical Youth Innovation Team Development Support Program Project of Chongqing Medical University/ ; CYYY-DSTDXM-202305//The First Affiliated Hospital of Chongqing Medical University Graduate Tutor Team Building Project Grants/ ; CYYY-YJSJXCX-202303//The First Affiliated Hospital of Chongqing Medical University Graduate Teaching Innovation Team Project Grants/ ; },
abstract = {RNA small fragment aberrances are associated with diseases by mediating a range of pathogenesis and pathological processes. DNA assembly-based barcoding and amplification technologies are currently being actively explored for RNA in situ analysis. However, these modular integrated DNA assembly processes are inevitably accompanied with false positive signals caused by unexpected misassembly. Completely avoiding this phenomenon through simple and universal methods is challenging. Here, a novel dual-input to dual-output in situ analysis paradigm is proposed, aiming to improve target specificity through co-recognition (dual-input) and to eliminate false positive misassembly through fluorescent signal co-localization (dual-output). Based on this paradigm, Gemini molecular assembly co-localization (GOAL) in situ imaging system is launched to accurately distinguish the fusion gene subtypes associated with chronic myeloid leukemia (CML), and to precisely report the proportion of minimum residual cancer cells in clinical samples by intelligent co-localization counting and sorting. GOAL achieves highly sensitive and accurate genotyping recognition of 0.01% CML tumor cells and realizes fully automatic rapid diagnosis with a customized Intelligent Cell Image Sorter (iCis). iCis-assisted GOAL represents an innovative and versatile molecular toolkit for accurate, rapid, user-friendly, and professional-independent profiling of cancer cells with RNA small fragment aberrances, providing efficient clinical decision support for disease diagnosis.},
}
@article {pmid40221509,
year = {2025},
author = {Siriwan, W and Charoenlappanit, S and Phaonakrop, N and Thaisakun, S and Roytrakul, S},
title = {Identification of peptidome-based biomarkers of cassava mosaic disease resistance in different cassava varieties.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12653},
pmid = {40221509},
issn = {2045-2322},
support = {FF(KU)18.65//Kasetsart University Research and Development (KURDI)/ ; },
mesh = {*Manihot/virology/metabolism/genetics ; *Disease Resistance ; Biomarkers/metabolism/analysis ; *Plant Diseases/virology/genetics ; *Peptides/metabolism/analysis ; Tandem Mass Spectrometry ; Chromatography, Liquid ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Plant Proteins/metabolism ; Proteomics/methods ; },
abstract = {Cassava, a major economic crop in Thailand, yielded over 3 million USD in exports in 2023. However, its production has been declining since 2021 due to cassava mosaic disease (CMD) outbreaks, which affect cassava plantations. CMD infections have recently increased due to the scarcity of healthy stems and CMD-resistant varieties, the latter being key to controlling its spread. Developing novel methods is critical for accelerating the cultivation of high-yield, CMD-resistant varieties. In this study, signature peptide patterns were determined using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and liquid chromatography-tandem MS (LC-MS/MS) to screen for CMD-resistant varieties. Peptide mass fingerprint (PMF) analyses revealed distinct peptide barcodes across 11 varieties, clearly delineating CMD-resistant and CMD-tolerant phenotypes. LC-MS/MS and orthogonal partial least squares-discriminant analysis (OPLS-DA) further demonstrated clear distinctions between the peptide profiles of different phenotypes. Heatmap and PMF analyses consistently revealed unique peptide patterns across the varieties. Volcano plot analysis identified seven upregulated peptides-TATTVAGS, PAAGGGGG, PNELLSYSE, SSIEEGGS, GGGVGGPL, NNGGGFSV, and GPGPAPAA-in CMD-resistant plants. These peptides were associated with proteins containing CONSTANS-like zinc finger, C2H2-type, GST N-terminal, Tubby-like F-box, nuclear-localized AT-hook motif, auxin response factor, and C2 domains. Altogether, this study identified peptidome-based biomarkers for screening CMD-resistant varieties; however, further validation using larger samples is necessary.},
}
@article {pmid40221395,
year = {2025},
author = {Huayamares, SG and Lian, L and Rab, R and Hou, Y and Radmand, A and Kim, H and Zenhausern, R and Achyut, BR and Gilbert Ross, M and Lokugamage, MP and Loughrey, D and Peck, HE and Echeverri, ES and Da Silva Sanchez, AJ and Shajii, A and Li, A and Tiegreen, KE and Santangelo, PJ and Sorscher, EJ and Dahlman, JE},
title = {Nanoparticle delivery of a prodrug-activating bacterial enzyme leads to anti-tumor responses.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3490},
pmid = {40221395},
issn = {2041-1723},
support = {R01DE026941//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
mesh = {Animals ; *Prodrugs/administration &amp; dosage/metabolism/pharmacology ; *Purine-Nucleoside Phosphorylase/genetics/metabolism ; *Nanoparticles/chemistry/administration &amp; dosage ; Mice ; Humans ; Cell Line, Tumor ; Escherichia coli/enzymology/genetics ; *Antineoplastic Agents/pharmacology/administration &amp; dosage ; Vidarabine/analogs &amp; derivatives/metabolism/pharmacology/administration &amp; dosage ; Female ; Vidarabine Phosphate/analogs &amp; derivatives/pharmacology/metabolism ; Xenograft Model Antitumor Assays ; RNA, Messenger/metabolism/genetics ; *Head and Neck Neoplasms/drug therapy ; Drug Delivery Systems ; *Escherichia coli Proteins/genetics/metabolism ; },
abstract = {Most cancer patients diagnosed with late-stage head and neck squamous cell carcinoma are treated with chemoradiotherapy, which can lead to toxicity. One potential alternative is tumor-limited conversion of a prodrug into its cytotoxic form. We reason this could be achieved by transient and tumor-specific expression of purine nucleoside phosphorylase (PNP), an Escherichia coli enzyme that converts fludarabine into 2-fluoroadenine, a potent cytotoxic drug. To efficiently express bacterial PNP in tumors, we evaluate 44 chemically distinct lipid nanoparticles (LNPs) using species-agnostic DNA barcoding in tumor-bearing mice. Our lead LNP, designated LNP intratumoral (LNP[IT]), delivers mRNA that leads to PNP expression in vivo. Additionally, in tumor cells transfected with LNP[IT], we observe upregulated pathways related to RNA and protein metabolism, providing insight into the tumor cell response to LNPs in vivo. When mice are treated with LNP[IT]-PNP, then subsequently given fludarabine phosphate, we observe anti-tumor responses. These data are consistent with an approach in which LNP-mRNA expression of a bacterial enzyme activates a prodrug in solid tumors.},
}
@article {pmid40220447,
year = {2025},
author = {Duft, RG and Griffin, JL and Stead, DA},
title = {MEATiCode: A comprehensive proteomic LC-MS/MS method for simultaneous species identification in meat authentication.},
journal = {Food chemistry},
volume = {483},
number = {},
pages = {144231},
doi = {10.1016/j.foodchem.2025.144231},
pmid = {40220447},
issn = {1873-7072},
abstract = {Food fraud in the meat industry threatens consumer trust, market stability, and public health. Traditional methods like DNA barcoding are limited, especially for processed foods where DNA is often degraded. This paper introduces the workflow MEATiCode, a comprehensive proteomic liquid chromatography tandem mass spectrometry (LC-MS/MS) method for the simultaneous identification of species in meat authentication. Application of a novel database search approach - MEATiCode - enabled the differentiation of meat species (as demonstrated for beef, pork, chicken and lamb) in raw and cooked food products following a simple sample preparation procedure and LC-MS/MS analysis of extracted meat peptides. The efficacy of the MEATiCode method was demonstrated through its application to a range of meat products, achieving high sensitivity (0.5 % Limit of Detection (LoD)) and reliability in the detection of adulteration, even in highly processed or cooked meats.},
}
@article {pmid40218301,
year = {2025},
author = {Yang, S and Zhao, Z and Xu, Z and Liu, Y and Jiang, M and Fu, L and Zhang, J and Jing, Z and Pang, X and Shao, W and Zhang, C and Li, Y and Du, X and Wu, J},
title = {Identification of Hybrid Sturgeon (Acipenser baerii × Acipenser schrenckii) from Their Parents Using Germplasm.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/ani15070907},
pmid = {40218301},
issn = {2076-2615},
support = {2021YFYZ0015//the Sichuan Science and Technology Program/ ; SCCXTD-2024-15//Project of Sichuan Innovation Team of National Modern Agricultural Industry Technology System/ ; kczx2023-2025-19//2023 Aquaculture Breeding Research Project, Integration and application demonstration of key technologies for sturgeon breeding/ ; },
abstract = {The hybrid sturgeon Acipenser baerii × A. schrenckii is the most widely cultured commercial sturgeon in China. However, its morphological similarity to the parental species frequently leads to misuse of germplasm in the breeding process, resulting in a decline in the quality of the sturgeon production. In this study, we have developed a protocol by using mitochondrial DNA barcoding and microsatellite locus analysis for the accurate identification of sturgeon species. Genetic distance and phylogenetic analysis based on the mitochondrial COI segment showed that A. baerii exhibited the closest genetic relationship with orthogonal individuals A. baerii (♀) × A. schrenckii (♂). Conversely, A. schrenckii displayed the highest genetic similarity with reciprocal individuals A. schrenckii (♀) × A. baerii (♂). Additionally, genetic structure analysis and factor correlation analysis (FCA) were conducted using six microsatellite loci among 100 samples, including eight species and two hybrid sturgeon. The results showed that all samples, encompassing both hybrid sturgeon (A. baerii × A. schrenckii) and their parental species, were accurately grouped into ten clusters, thereby validating the precision of this species assignment method.},
}
@article {pmid40212379,
year = {2025},
author = {Qiu, Y and Fan, D and Wang, J and Zhou, X and Teng, X and Rao, C},
title = {High throughput construction of species characterized bacterial biobank for functional bacteria screening: demonstration with GABA-producing bacteria.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1545877},
pmid = {40212379},
issn = {1664-302X},
abstract = {Bacteria and their metabolites exhibit remarkable diversity, offering substantial potential for industrial biotechnology. However, the low throughput for constructing and screening bacterial biobanks limits the exploration and utilization of this diversity. In this study, we developed a cost-effective, high-throughput platform for bacterial biobank construction and functional screening. We employed a double-ended barcoding strategy, enabling thousands of bacterial isolates to be pooled for simultaneous Nanopore sequencing of full-length 16S rDNA for species identification. This approach demonstrated 99% accuracy compared to Sanger sequencing while reducing per-sample costs to under 10%. Using this platform, we established a bacterial biobank comprising 15,337 bacterial isolates derived from fermented foods and infant feces collected across China. To identify functional bacteria within the biobank, we designed a versatile fluorescence-based biosensor system employing dual plasmids to decouple metabolite sensing from signal reporting. This modular biosensor framework can be readily adapted for detecting diverse metabolites. As a proof-of-concept, we screened 1,740 isolates and identified 46 with high γ-aminobutyric acid (GABA)-producing capacity, demonstrating potential for probiotic development. Together, our integrated bacterial identification and functional screening platform provides an efficient pipeline for the discovery of functional bacteria, advancing industrial biotechnology through synthetic biology.},
}
@article {pmid40208941,
year = {2025},
author = {Zhao, X and Zhao, Y and Li, Z and Liu, H and Fu, W and Chen, F and Sun, Y and Song, D and Fan, C and Zhao, Y},
title = {Proximity-activated DNA scanning encoded sequencing for massive access to membrane proteins nanoscale organization.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {15},
pages = {e2425000122},
doi = {10.1073/pnas.2425000122},
pmid = {40208941},
issn = {1091-6490},
support = {22125404//MOST | National Natural Science Foundation of China (NSFC)/ ; 22004096//MOST | National Natural Science Foundation of China (NSFC)/ ; 22474107//MOST | National Natural Science Foundation of China (NSFC)/ ; 2023YFB3210103//MOST | National Key Research and Development Program of China (NKPs)/ ; 2023JC-JQ-23//Natural Science Foundation of Shaanxi Province (Shaanxi Natural Science Foundation)/ ; 2023-CX-TD-62//Innovation Capability Support Program of Shaanxi/ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Membrane Proteins/genetics/metabolism ; *Sequence Analysis, DNA/methods ; Breast Neoplasms/genetics/metabolism ; Epithelial Cell Adhesion Molecule/metabolism/genetics ; Receptor, ErbB-2/metabolism/genetics ; DNA Probes/genetics ; Cell Line, Tumor ; Female ; DNA, Single-Stranded/genetics ; },
abstract = {Cellular structure maintenance and function regulation critically depend on the composition and spatial distribution of numerous membrane proteins. However, current methods face limitations in spatial coverage and data scalability, hindering the comprehensive analysis of protein interactions in complex cellular nanoenvironment. Herein, we introduce proximity-activated DNA scanning encoded sequencing (PADSE-seq), an innovative technique that utilizes flexible DNA probes with adjustable lengths. These dynamic probes are anchored at a single end, enabling free swings within a nanoscale range to perform global scanning, recording, and accumulating of information on diverse proximal proteins in random directions along unrestricted paths. PADSE-seq leverages the autonomous cyclic cleavage of single-stranded DNA to sequentially activate encoded probes distributed throughout the local area. This process triggers strand displacement amplification and bidirectional extension reactions, linking proteins barcodes with molecular barcodes in tandem and further generating millions to billions of amplicons embedded with the combinatorial identifiers for next-generation sequencing analysis. As a proof of concept, we validated PADSE-seq for mapping the distribution of over a dozen kinds of proteins, including HER1, EpCAM, and PDL1, in proximity to HER2 in breast cancer cell lines, demonstrating its ability to decode multiplexed protein proximities at the nanoscale. Notably, we observed that the spatial distribution of proximal proteins around low-abundance target proteins exhibited greater diversity across regions with variable proximity ranges. This method offers a massive access for high-resolution and comprehensive mapping of cellular molecular interactions, paving the way for deeper insights into complex biological processes and advancing the field of precision medicine.},
}
@article {pmid40208109,
year = {2025},
author = {Stevenson, ZC and Laufer, E and Estevez, AO and Robinson, K and Phillips, PC},
title = {Precise Lineage Tracking Using Molecular Barcodes Demonstrates Fitness Trade-offs for Ivermectin Resistance in Nematodes.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf081},
pmid = {40208109},
issn = {2160-1836},
abstract = {A fundamental tenet of evolutionary genetics is that the direction and strength of selection on individual loci varies with the environment. Barcoded evolutionary lineage tracking is a powerful approach for high-throughput measurement of selection within experimental evolution that to date has largely been restricted to studies within microbial systems, largely because the random integration of barcodes within animals is limited by physical and molecular protection of the germline. Here, we use the recently developed TARDIS barcoding system in Caenorhabditis elegans (Stevenson et al., 2023) to implement the first randomly inserted genomic-barcode fitness experiment within an animal model and use this system to precisely measure the influence of the concentration of the anthelmintic compound ivermectin on the strength of selection on an ivermectin resistance cassette. The combination of the trio of knockouts in neuronally expressed GluCl channels, avr-14, avr-15, and glc-1, has been previously demonstrated to provide resistance to ivermectin at high concentrations. Varying the concentration of ivermectin in liquid culture allows the strength of selection on these genes to be precisely controlled within populations of millions of individuals, with the frequency of each barcode then being measured at multiple time points via sequencing at deep coverage and used to estimate the fitness of the individual lineages in the population. The mutations display a high cost to resistance at low concentrations, rapidly losing out to wildtype genotypes, but the balance tips in their favor when the ivermectin concentration exceeds 2nM. This trade-off in resistance is likely generated by a hindered rate of development in resistant individuals. Our results demonstrate that C. elegans can be used to generate high precision estimates of fitness using a high-throughput barcoding approach to yield novel insights into evolutionarily and economically important traits.},
}
@article {pmid40204808,
year = {2025},
author = {Xu, S and Ouyang, Y and Qin, Y and Chen, D and Duan, Z and Song, D and Harries, D and Xia, F and Willner, I and Huang, F},
title = {Spatiotemporal dynamic and catalytically mediated reconfiguration of compartmentalized cyanuric acid/polyadenine DNA microdroplet condensates.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3352},
pmid = {40204808},
issn = {2041-1723},
support = {21874121//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*DNA/chemistry ; Catalysis ; *Triazines/chemistry ; *Poly A/chemistry ; *Artificial Cells/chemistry/metabolism ; },
abstract = {Native cells possess membrane-bound subcompartments, organelles, such as mitochondria and lysosomes, that intercommunicate and regulate cellular functions. Extensive efforts are directed to develop synthetic cells, or protocells, that replicate these structures and functions. Among these approaches, phase-separated coacervate microdroplets composed of polymers, polysaccharides, proteins, or nucleic acids are gaining interest as cell-mimicking systems. Particularly, compartmentalization of the synthetic protocell assemblies and the integration of functional constituents in the containments allowing signaling, programmed transfer of chemical agents, and spatiotemporal controlled catalytic transformations across the protocell subdomains, are challenging goals in developing artificial cells. Here, we report the assembly of compartmentalized, phase-separated cyanuric acid/polyadenine coacervate microdroplets. Hierarchical, co-centric compartmentalization is achieved through the dynamic and competitive spatiotemporal occupation of pre-engineered barcode domains within the polyadenine microdroplet framework by invading DNA strands. By encoding structural and functional information within these DNA-invaded compartments, the light-triggered, switchable reconfiguration of compartments, switchable catalytic reconfiguration of containments, and reversible aggregation/deaggregation of the compartmentalized microdroplets are demonstrated.},
}
@article {pmid40204203,
year = {2025},
author = {Zhou, X and Faust, K},
title = {A high-throughput and time-efficient Nanopore full-length 16S rRNA gene sequencing protocol for synthetic microbial communities.},
journal = {Methods (San Diego, Calif.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymeth.2025.04.003},
pmid = {40204203},
issn = {1095-9130},
abstract = {Next-generation sequencing (NGS) has transitioned from primarily research-focused applications to a mature technology. However, resolving microbial community composition on the species level based on the 16S rRNA gene is impeded by several critical bottlenecks that limit the efficiency and scalability of analyses. Specifically, standard MiSeq sequencing suffers from read-length limitation; library preparation requires multiple labour-intensive steps from DNA isolation to amplification and barcoding; and prolonged turnaround times delay results. These challenges underscore the need for improved methods, which our study aims to address. Recent advancements in Oxford Nanopore long-read sequencing technology (ONT), including a smaller and cheaper benchtop instrument and support for diverse sample types, have enabled faster sequencing in-house with reduced costs. To address the need for standardized, reproducible workflows, we present an optimized and state-of-the-art protocol for full-length 16S rRNA gene sequencing using the ONT MinION sequencing device. Furthermore, we quantified the reproducibility and accuracy of our protocol and compared it with the previous MiSeq results. The results showed that the accuracy of our sequencing pipeline for synthetic communities is significantly higher than for MiSeq pipeline. In summary, our protocol elucidates the composition of synthetic microbial communities in an easy, fast and accurate manner while ensuring reproducible results.},
}
@article {pmid40202150,
year = {2025},
author = {Tnah, LH and Ahmad-Farhan, NR and Nur-Nabilah, A and Soo, P and Hazwani-Humaira', Z and Ng, K and Lee, C and Ng, C and Lee, S},
title = {Genetic insights: integrating DNA barcoding with taxonomy in the study of Baccaurea (Phyllanthaceae).},
journal = {Genome},
volume = {68},
number = {},
pages = {1-7},
doi = {10.1139/gen-2024-0105},
pmid = {40202150},
issn = {1480-3321},
mesh = {*DNA Barcoding, Taxonomic/methods ; Phylogeny ; DNA, Plant/genetics ; },
abstract = {Traditional taxonomic revisions based on macromorphological and leaf anatomical traits may have limitations in accurately distinguishing certain species within the genus. To improve taxonomic clarity, this study applied DNA barcoding to enhance the understanding of the taxonomy and phylogeny of Baccaurea Lour., a plant genus widely utilized for food, medicine, and building materials. DNA barcode regions, including rbcL, ITS2, and trnH-psbA, were used to analyze 64 samples representing 19 Baccaurea species. Using similarity Basic Local Alignment Search Tool and phylogenetic tree inference, we determined the discriminatory efficiencies of rbcL, ITS2, trnH-psbA, and their combinations rbcL + ITS2 and rbcL + ITS2 + trnH-psbA as 21.1%, 89.5%, 87.5%, 89.5%, and 89.5%, respectively. The Neighbor-Joining tree revealed well-defined, monophyletic species clusters that largely align with phylogenetic positions based on macromorphological features. Notably, our results indicate that Baccaurea parviflora and the synonymized Baccaurea scortechinii are distinct species, recommending the re-establishment of B. scortechinii as a separate species. DNA barcoding is useful in delineating species boundaries, facilitating routine specimen identification, and flagging atypical samples for detailed examination.},
}
@article {pmid40202117,
year = {2025},
author = {Shapiro, JR and Simard, N and Bolotin, S and Watts, TH},
title = {Fluorescent Cell Barcoding of Peripheral Blood Mononuclear Cells for High-Throughput Assessment of Vaccine-Induced T Cell Responses in Low-Volume Research Samples.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {},
number = {},
pages = {},
doi = {10.1002/cyto.a.24933},
pmid = {40202117},
issn = {1552-4930},
support = {//Donation from Juan and Stefania Speck/ ; //Canadian Immunization Research Network/ ; /CAPMC/CIHR/Canada ; },
abstract = {T cell responses are rarely measured in large-scale human vaccine studies due to the sample volumes required, as well as the logistical, technical, and financial challenges associated with available assays. Fluorescent cell barcoding has been proposed in other contexts to allow for more high-throughput flow cytometry-based assays. Here, we aimed to expand on existing barcoding approaches to develop a reagent and sample-sparing assay for in-depth assessment of T cell responses to vaccine antigens. By using various concentrations of two fixable viability dyes in a matrix format, up to 25 samples that were pooled and acquired together could be successfully deconvoluted based on their unique fluorescent signature. This fluorescent cell barcoding approach was then combined with extracellular and intracellular staining to identify functional (i.e., producing at least one cytokine) and polyfunctional (i.e., producing multiple cytokines) T cells in response to vaccine antigen stimulation. As a proof-of-concept, we plated just 200,000 peripheral blood mononuclear cells (PBMC) per condition, and by staining and acquiring only two pooled samples, we were able to detect rare antigen-specific T cell responses in eight donors to four stimulants each. The frequencies of antigen-induced cytokine-positive cells detected in barcoded samples with 200,000 input PBMC were strongly correlated with those detected in non-barcoded samples from the same donors with 1 million input PBMC, demonstrating the validity of this approach. In conclusion, by reducing the number of PBMC needed by five-fold, and the volume of staining reagents needed by 25-fold, this assay has widespread potential applications to human vaccine studies.},
}
@article {pmid40201216,
year = {2025},
author = {Huang, MC and Kawai, T},
title = {A new species of supergiant Bathynomus A. Milne-Edwards, 1879 (Isopoda: Cirolanidae) from the Paracel Islands, South China Sea.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e144238},
pmid = {40201216},
issn = {1314-2828},
abstract = {BACKGROUND: Bathynomusparacelensis sp. nov., a medium-sized supergiant Bathynomus, is described from specimens obtained at Zhengbin fishing port in Keelung, Taiwan and had been caught in the water near Paracel Islands, South China Sea. Due to its similar shape to B.jamesi, this species has often been mistaken for juveniles or immatures of B.jamesi by fishermen working in this area. Species of Bathynomus can be distinguished morphologically and genetically. The differences from B.jamesi are in the shorter body, clypeus shape, uropod endopod and gene sequence. The difference from B.vaderi is in the body shape, clypeus shape, hook number of maxilliped endite and spines number of maxilulla. Based on the morphological and genetic data results, the specimen is a hitherto undescribed species. The samples were collected as a bycatch species in the deep-sea bottom trawl fishery. The distribution area and depth of this new species and population size are still unclear.<br><br>NEW INFORMATION: B.paracelensis sp. nov. is the third supergiant Bathynomus discovered in the South China Sea after B.jamesi and B.vaderi. Its remarkable feature is its short body length and sub-parallel shape. In addition, it is different from B.jamesi and B.vaderi in features such as clypeus shape, number of maxillula keratinised spine and pleotelson spine almost straight. Phylogenetic and barcoding gap analyses confirm that B.paracelensis sp. nov. is not the same species as B.jamsei. Many morphological differences also indicate that it should be a different species from B.vaderi. B.paracelensis sp. nov. may be an intermediate species between giant and supergiant, possessing characteristics of both categories, which can increase researchers' understanding of Bathynomus biodiversity.},
}
@article {pmid40201215,
year = {2025},
author = {Fetnassi, N and Er-Rguibi, O and Aglagane, A and Ghamizi, M and Õunap, E},
title = {Updates to the checklist of nocturnal Macroheterocera (Lepidoptera) of the Central High Atlas of Morocco: One new species added for Morocco.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e137839},
pmid = {40201215},
issn = {1314-2828},
abstract = {BACKGROUND: This paper provides updates to the checklist of Macroheteroceran moths (Lepidoptera) of the central High Atlas of Morocco, following the initial inventory conducted by Charles Rungs nearly five decades ago. Sampling was carried out using sugar bait traps deployed across various habitat types in the region (natural, semi-natural and agricultural lands). Identification of the collected specimens involved a comprehensive approach, including examination of external morphology, dissections of genitalia and DNA barcoding.<br><br>NEW INFORMATION: In this study, we recorded a total of 123 species belonging to the families Noctuidae, Erebidae, Geometridae, Eutelidae and Drepanidae. Euxoacos (Noctuidae) was recorded as a new species for Morocco. The presence of Apameamaroccana (Noctuidae) and Chersotisrungsi (Noctuidae), both endemic to Morocco, was verified in the study area. Four of the 123 species were only identified at the genus level. Our inventory also sheds light on species that were previously not known to occur within our study area, reporting twelve species from the High Atlas Mountains for the first time. We also suggest omitting Eupitheciafarinosa (Geometridae) from the Moroccan Lepidoptera list. This study significantly contributes to uncovering an overlooked aspect of Lepidopteran biodiversity in Morocco, which is crucial for future conservation efforts.},
}
@article {pmid40201154,
year = {2025},
author = {Li, Y and Lu, JJ and An, YB and Jiang, L and Wu, HJ and Wang, K and Phurbu, D and Luobu, J and Ma, C and Yang, RH and Dong, CH and Yao, YJ},
title = {An attempt of DNA barcodes based geographical origin authentication of the Chinese caterpillar fungus, Ophiocordycepssinensis.},
journal = {IMA fungus},
volume = {16},
number = {},
pages = {e144783},
pmid = {40201154},
issn = {2210-6340},
abstract = {Ophiocordycepssinensis is one of the best-known traditional Chinese medicines with distribution confined to the Tibetan Plateau and its surrounding regions. Harvesting the fungus contributes greatly to the livelihood of local communities. The quality and price varies amongst different production regions, usually resulting in an intentional mix-up of its production locality during trading processes, which leads to a demand of developing a reliable way that can trace the geographical origin of this fungus. In the present study, a DNA barcoding-based method applying two universal DNA barcodes for identifying fungal and insect, respectively i.e. the nuclear ribosomal internal transcribed spacer (ITS) and the mitochondrial cytochrome oxidase I (COI), was evaluated and used for geographical origin authentication of O.sinensis. A total of 24 ITS and 78 COI haplotypes were recognised from 215 individuals collected from 75 different geographic localities (county level). Ninety-nine haplotypes were defined using the combination of ITS and COI, discriminating the 75 investigated production counties into 99 distinct regions. A "core" production region was recognised which covers areas of Nagqu and Qamdo in Xizang, Yushu and Guoluo in Qinghai, Gannan (Maqu and Xiahe) in Gansu and certain regions in Nyingch (Bomi and Zayü) and Lhasa (Damxung) in Xizang and Garzê (Sêrxü) in Sichuan Province. Haplotype analyses using the combined barcodes of ITS and COI showed an excellent performance in the geographical origin authentication of O.sinensis and the definition of "core" and "non-core" production region.},
}
@article {pmid40200683,
year = {2025},
author = {Wang, Y and Ma, J and Cai, W and Song, M and Wang, Z and Xu, Z and Shen, Y and Zheng, S and Zhang, S and Tang, Z and Wang, Y},
title = {Fast Encapsulation of Microbes into Dissolvable Hydrogel Beads Enables High-Throughput Microbial Single-Cell RNA Sequencing of Clinical Microbiome Samples.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e2500481},
doi = {10.1002/adma.202500481},
pmid = {40200683},
issn = {1521-4095},
support = {32200073//National Natural Science Foundation of China/ ; 32250710678//National Natural Science Foundation of China/ ; 52203282//National Natural Science Foundation of China/ ; LY23B040002//Natural Science Foundation of Zhejiang Province/ ; 2021R01012//Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang/ ; 2024C03005//"Pioneer" R&amp;D programs of Zhejiang Province/ ; 2024SSYS0022//Key R&amp;D Program of Zhejiang/ ; },
abstract = {Microbial single-cell RNA-seq (mscRNA-seq) can achieve resolution at the cellular level, enhancing the understanding of microbial communities. However, current high-throughput mscRNA-seq methods are limited by multiple centrifugation steps, which can lead to microbial loss and bias. smGel-seq is reported, a high-throughput single-microbe RNA sequencing method for clinical microbiome samples that employs hydrogel beads to encapsulate individual microbes to reduce microbial loss and input requirements. In this method, a novel microchannel array device is implemented for encapsulating single microbe in dissolvable hydrogel beads (smDHBs), along with an optimized automated microfluidic platform to co-encapsulate barcoded beads and smDHBs, enabling high-throughput barcoding of individual microbes. smGel-seq significantly increases the microbial recovery rate in a gut microbiome sample from 8.8% to 91.8%. Furthermore, this method successfully processes clinical microbiome samples with microbial inputs 20 times lower than those required by previous methods. Notably, smGel-seq enables the first mscRNA-seq in a clinical sputum microbiome sample, revealing a specific microbial subpopulation that may play a key role in environmental adaptability, antibiotic resistance, and pathogenicity. These results highlight the compatibility of smGel-seq with clinical microbiome samples and demonstrate its potential for widespread application in diverse clinical and research settings.},
}
@article {pmid40200529,
year = {2025},
author = {Barro, SG and Ouattara, TA and Staccini, P},
title = {Assignment of Unique Specimen IDs and Barcodes to Pathology Image Samples in Medical Laboratories in Burkina Faso.},
journal = {Studies in health technology and informatics},
volume = {323},
number = {},
pages = {458-462},
doi = {10.3233/SHTI250132},
pmid = {40200529},
issn = {1879-8365},
mesh = {Burkina Faso ; Humans ; *Specimen Handling/methods ; *Laboratories, Clinical/organization &amp; administration ; *Patient Identification Systems/methods ; *Clinical Laboratory Information Systems/organization &amp; administration ; },
abstract = {The accurate and efficient assignment of unique identifiers to biomedical specimens, along with the generation of barcodes for pathology samples, are crucial elements in ensuring the quality and reliability of medical diagnostics. In Burkina Faso, the adoption of an automated system for these tasks marks a significant advancement in laboratory management. This article explores the impact of this automation on reducing human errors, improving sample traceability, and optimizing operational processes. Indeed, the integration of AJAX queries for the dynamic management of specimen numbers allows for real-time updates and reduces the risks of duplication or incorrect assignment. Furthermore, the use of specialized libraries for the automatic generation of barcodes ensures a unique and secure identification of each sample, thereby facilitating its tracking throughout the analysis process. This modernization of sample management practices not only improves the efficiency of laboratories but also optimizes processing times, thus enhancing the quality of care and diagnostics provided to patients.},
}
@article {pmid40198433,
year = {2025},
author = {Watanabe, K and Imanishi, S and Kayukawa, T and Tateishi, K},
title = {Establishment of 27 cell lines derived from various insects.},
journal = {In vitro cellular &amp; developmental biology. Animal},
volume = {},
number = {},
pages = {},
pmid = {40198433},
issn = {1543-706X},
support = {20K06083//Japan Society for the Promotion of Science/ ; 23K05264//Japan Society for the Promotion of Science/ ; },
abstract = {Insect cell lines are valuable for basic and applied biological research. In this study, we established 27 cell lines from various insect species, including Hemiptera: Nilaparvata lugens, Coleoptera: Sitophilus oryzae, Hymenoptera: Allantus luctifer and Trichogramma ssp., Diptera: Culicoides oxystoma, Lepidoptera: Spodoptera litura, Mythimna separata, Bombyx mori, Agrius convolvuli, Plodia interpunctella, and Cryptophlebia horii. This is the first report of cell lines derived from A. luctifer, C. oxystoma, A. convolvuli, and C. horii. Additionally, cell lines from S. litura and M. separata were established from different tissues including the hemocytes, fat bodies, embryos, and Malpighian tubules. Eighteen cell lines were successfully adapted to commercial culture media, with the population doubling time ranging from 1 to 8 d. The identities of the cell lines were confirmed using DNA barcoding. These established cell lines could be valuable for various research applications.},
}
@article {pmid40197720,
year = {2025},
author = {Snoeck, HW},
title = {Direct megakaryopoiesis.},
journal = {Current opinion in hematology},
volume = {},
number = {},
pages = {},
pmid = {40197720},
issn = {1531-7048},
abstract = {PURPOSE OF REVIEW: Megakaryocytes are large, polyploid cells that produce platelets and originate from hematopoietic stem cells (HSCs) in the bone marrow. While in the classical paradigm, megakaryocytes are generated in a stepwise fashion through increasingly committed progenitor stages, studies using in-vivo barcoding, transplantation, and in-vitro culture have suggested that, in addition, a more direct pathway existed. The relevance of this direct pathway and its functional and phenotypic characteristics were unclear, however.<br><br>RECENT FINDINGS: Recent publications using fate-mapping and single-cell transplantation now unequivocally demonstrate the existence of a direct megakaryocyte differentiation pathway, provide molecular characterization, and indicate distinct roles and regulation of both pathways. The direct pathway originates from a separate subset of 'top' HSCs, is enhanced by hematopoietic stress, inflammation and aging, bypasses multipotential progenitors, may be more active in myeloproliferative neoplasms, and generates phenotypically distinct megakaryocyte progenitors and more reactive platelets.<br><br>SUMMARY: Novel insights into the direct megakaryocyte differentiation pathway provide a deeper understanding of HSC biology, hematological recovery after myeloablation, and aging of the hematopoietic system, and suggest that this pathway may contribute to the increase in thrombotic incidents with age and in myeloproliferative neoplasms.},
}
@article {pmid40197053,
year = {2025},
author = {Langsiri, N and Meyer, W and Irinyi, L and Worasilchai, N and Pombubpa, N and Wongsurawat, T and Jenjaroenpun, P and Luangsa-Ard, JJ and Chindamporn, A},
title = {Optimizing fungal DNA extraction and purification for Oxford Nanopore untargeted shotgun metagenomic sequencing from simulated hemoculture specimens.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0116624},
doi = {10.1128/msystems.01166-24},
pmid = {40197053},
issn = {2379-5077},
abstract = {UNLABELLED: Long-read metagenomics provides a promising alternative approach to fungal identification, circumventing methodological biases, associated with DNA amplification, which is a prerequisite for DNA barcoding/metabarcoding based on the primary fungal DNA barcode (Internal Transcribed Spacer (ITS) region). However, DNA extraction for long-read sequencing-based fungal identification poses a significant challenge, as obtaining long and intact fungal DNA is imperative. Comparing different lysis methods showed that chemical lysis with CTAB/SDS generated DNA from pure fungal cultures with high yields (ranging from 11.20 ± 0.17 µg to 22.99 ± 2.22 µg depending on the species) while preserving integrity. Evaluating the efficacy of human DNA depletion protocols demonstrated an 88.73% reduction in human reads and a 99.53% increase in fungal reads compared to the untreated yeast-spiked human blood control. Evaluation of the developed DNA extraction protocol on simulated clinical hemocultures revealed that the obtained DNA sequences exceed 10 kb in length, enabling a highly efficient sequencing run with over 80% active pores. The quality of the DNA, as indicated by the 260/280 and 260/230 ratios obtained from NanoDrop spectrophotometer readings, exceeded 1.8 and 2.0, respectively. This demonstrated the great potential of the herein optimized protocol to extract high-quality fungal DNA from clinical specimens enabling long-read metagenomics sequencing.<br><br>IMPORTANCE: A novel streamlined DNA extraction protocol was developed to efficiently isolate high molecular weight fungal DNA from hemoculture samples, which is crucial for long-read sequencing applications. By eliminating the need for labor-intensive and shear-force-inducing steps, such as liquid nitrogen grinding or bead beating, the protocol is more user-friendly and better suited for clinical laboratory settings. The automation of cleanup and extraction steps further shortens the overall turnaround time to under 6 hours. Although not specifically designed for ultra-long DNA extraction, this protocol effectively supports fungal identification through Oxford Nanopore Technology (ONT) sequencing. It yields high molecular weight DNA, resulting in longer sequence fragments that improve the number of fungal reads over human reads. Future improvements, including adaptive sampling technology, could further simplify the process by reducing the need for human DNA depletion, paving the way for more automated, bioinformatics-driven workflows.},
}
@article {pmid40196009,
year = {2025},
author = {Smolka, M and Comstock, W and Navarro, M and Maybee, D and Rho, Y and Wagner, M and Wang, Y},
title = {Proteomic Sensors for Quantitative, Multiplexed and Spatial Monitoring of Kinase Signaling.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-6220494/v1},
pmid = {40196009},
issn = {2693-5015},
abstract = {Understanding kinase action requires precise quantitative measurements of their activity in vivo . In addition, the ability to capture spatial information of kinase activity is crucial to deconvolute complex signaling networks, interrogate multifaceted kinase actions, and assess drug effects or genetic perturbations. Here we developed a proteomic kinase activity sensor platform (ProKAS) for the analysis of kinase signaling using mass spectrometry. ProKAS is based on a tandem array of peptide sensors with amino acid barcodes that allow multiplexed analysis for spatial, kinetic, and screening applications. We engineered a ProKAS module to simultaneously monitor the activities of the DNA damage response kinases ATR, ATM, and CHK1 in response to genotoxic drugs, while also uncovering differences between these signaling responses in the nucleus, cytosol, and replication factories. Furthermore, we developed an in silico approach for the rational design of specific substrate peptides expandable to other kinases. Overall, ProKAS is a novel versatile system for systematically and spatially probing kinase action in cells.},
}
@article {pmid40191542,
year = {2025},
author = {Liu, B},
title = {Contribution to the knowledge of the genus Calcyopa Stüning, 2000 (Lepidoptera, Geometridae, Ennominae, Boarmiini), with description of a new species.},
journal = {ZooKeys},
volume = {1233},
number = {},
pages = {125-138},
pmid = {40191542},
issn = {1313-2989},
abstract = {The genus Calcyopa Stüning, 2000, is briefly reviewed. A new species, Calcyopahainana Liu, sp. nov., is described from Hainan Province, China. Within the genus Calcyopa, two species groups are identified, characterized by shared traits yet distinguished by a set of consistent features. The difoveata-group, comprises C.difoveata, C.fansipana and C.hainana sp. nov., and the rosearia-group, includes C.rosearia, C.prasina and C.subprasina. The relationship of both species groups is discussed, and an identification key of all known Calcyopa species is presented. Illustrations are provided for adult males and females of the difoveata-group, along with their genitalia, except for C.fansipana, which is known only from males. DNA barcodes are provided for the type species and the newly described species.},
}
@article {pmid40190802,
year = {2025},
author = {McCulloch, GA and Pohe, SR and Wilkinson, SP and Drinan, TJ and Waters, JM},
title = {Targeted eDNA Metabarcoding Reveals New Populations of a Range-Limited Stonefly.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71244},
pmid = {40190802},
issn = {2045-7758},
abstract = {Understanding the geographic distributions of rare species can be crucial for conservation management. New environmental DNA (eDNA) technologies offer the potential to efficiently document the distributions of endangered species, but to date, such screening has focused largely on vertebrate taxa. Here we use freshwater eDNA to assess the geographic distribution of the Maungatua stonefly, Zelandoperla maungatuaensis, a flightless insect previously known from only a handful of streams draining a 4-km section of the Maungatua mountain range in southern New Zealand. We analyzed freshwater eDNA from 12 stream localities across the Maungatua range. Screening with commercial eDNA COI primers failed to detect the focal species Z. maungatuaensis. However, newly designed species-specific primers detected this taxon from four adjacent east-flowing streams known to contain Z. maungatuaensis, and two streams from which it had not previously been detected. Subsequent manual surveys confirmed the presence of two newly discovered Z. maungatuaensis populations, with COI barcoding revealing that they together represent a previously unknown, genetically divergent subclade. Our results illustrate the potential of eDNA metabarcoding to help delineate the geographic ranges of rare taxa, and highlight the importance of primer specificity when screening for rare taxa. These findings also have considerable implications for commercial companies offering biodiversity and stream health eDNA services targeting invertebrates.},
}
@article {pmid40188161,
year = {2025},
author = {Ramesh, KB and Mahendra, C and Gouda, MNR and Salim, R and Subramanian, S},
title = {Genetic structure and haplotype analysis of predominant genetic group of Bemisia tabaci Asia II 1 from Asia and India.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {11672},
pmid = {40188161},
issn = {2045-2322},
mesh = {Animals ; *Hemiptera/genetics/classification ; *Haplotypes ; India ; Genetic Variation ; Phylogeny ; Asia ; },
abstract = {Whitefly, Bemisia tabaci is a globally recognized invasive cryptic pest species complex and a primary vector for 90% of begomoviruses. Understanding the species composition and diversity within the B. tabaci cryptic species complex is essential for developing effective pest management strategies. The Asia II 1 genetic group of B. tabaci is notably widespread in India and across Asia, demonstrating significant genetic diversity. Our study investigates the haplotype diversity of Asia II 1 using the mtCOI barcoding gene, analyzing 676 sequences from various Asian countries and 190 sequences from India. We identified 241 distinct haplotypes in Asia II 1 across Asia, with the highest haplotype diversity in China (Hd: 1.000) and the lowest in Vietnam (Hd: 0.667). Nucleotide diversity peaked in Pakistan (pi: 0.0145) and was lowest in Vietnam (pi: 0.0010). In India, we identified 77 haplotypes with a diversity of 0.926 and nucleotide diversity of 0.0076. When grouped by hostplant families, 79 haplotypes were recorded, with the highest diversity in Cucurbitaceae and the lowest in Solanaceae. Our findings suggest that hostplants and geographical location significantly influence genetic group development, offering novel insights into Asia II 1's genetic structure and evolution. This marks the first comprehensive study of Asia II 1 genetic diversity in Asia and India.},
}
@article {pmid40187791,
year = {2025},
author = {He, Z and Wang, H and Chen, Y and Chen, N},
title = {Comparative genomic and phylogenetic analysis of mitochondrial genomes of the Pseudo-nitzschia HAB species.},
journal = {Harmful algae},
volume = {144},
number = {},
pages = {102829},
doi = {10.1016/j.hal.2025.102829},
pmid = {40187791},
issn = {1878-1470},
mesh = {*Genome, Mitochondrial ; *Phylogeny ; *Diatoms/genetics/classification ; DNA, Mitochondrial/genetics ; Harmful Algal Bloom ; Genomics ; },
abstract = {The genus Pseudo-nitzschia within Bacillariophyta (diatoms) is best known for its rich collection of toxigenic harmful algal bloom (HAB) species capable of producing the neurotoxin domoic acid (DA), which causes amnesic shellfish poisoning (ASP) in humans. Molecular markers such as 18S rDNA, ITS1, and ITS2 have been applied to facilitate Pseudo-nitzschia species identification because morphology-based methods often could not adequately distinguish different species due to their morphological similarities and plasticity. In this study, we constructed mitochondrial genomes (mtDNAs) for 11 Pseudo-nitzschia species and assessed their utility as "super-barcodes" for species identification and evolutionary analysis. These mtDNAs exhibited conserved genome structures despite variability in repeat regions. A potential tatA-tatC gene fusion event was observed in a single Pseudo-nitzschia species P. brasiliana. We also observed intron variability in cox1 genes. Phylogenetic analyses of mtDNAs, chloroplast genomes (cpDNAs), and nuclear ribosomal DNA (nrDNA) arrays revealed consistent results, supporting the closely related but distinct clustering of the genera Fragilariopsis and Pseudo-nitzschia. We further designed a high-resolution molecular marker tatA for species identification based on the comparative analysis of these mtDNAs, which could be used to track Pseudo-nitzschia diversity. These findings offer new genome resources and new insights into the genetic evolution and classification of Pseudo-nitzschia, underscoring the need for continued research in this field.},
}
@article {pmid40187273,
year = {2025},
author = {Prasetyo, DB and Yean, S and Boyer, S},
title = {Reevaluating the presence of Rhipicephalus australis (Acari: Ixodidae) in Southeast Asia: A phylogenetic approach based on Cambodian tick samples.},
journal = {Ticks and tick-borne diseases},
volume = {16},
number = {3},
pages = {102478},
doi = {10.1016/j.ttbdis.2025.102478},
pmid = {40187273},
issn = {1877-9603},
abstract = {Morphological variability between Rhipicephalus australis and R. microplus has led to taxonomic ambiguity, leading to species misidentification. Rhipicephalus australis is reported to have a distribution range in Pacific Ocean region extending to several Southeast Asian countries, including Cambodia, although its presence in continental Southeast Asia has not been supported by molecular data. With growing evidence of conflicting morphological characters, this study aimed to evaluate the presence of R. australis in Cambodia using both morphological and molecular identification. Tick specimens were collected from cattle across 21 provinces of Cambodia, and a subset of 95 R. microplus complex (37 morphologically identified as R. australis, 39 R. microplus, and 19 nymphs) was selected for molecular analysis. DNA barcoding of the cox1 gene was performed, and a maximum likelihood phylogenetic tree revealed that all specimens clustered within R. microplus clade A. These findings, along with previous observations from other regions, suggest that, in the absence of molecular data, there is no definitive evidence to support the presence of R. australis in continental Southeast Asia, particularly in Cambodia.},
}
@article {pmid40186944,
year = {2025},
author = {Solbach, MD and Siemensma, F and Holzmann, M},
title = {A remarkable new monothalamid (Rhizaria, Foraminifera) from the shoreline of Livingston Island, Antarctica.},
journal = {European journal of protistology},
volume = {99},
number = {},
pages = {126148},
doi = {10.1016/j.ejop.2025.126148},
pmid = {40186944},
issn = {1618-0429},
abstract = {In this study, we describe a novel monothalamous Foraminifera, discovered in shoreline sediment samples from the Southern Ocean. The individuals, approximately 75 μm in diameter, are relatively small for Foraminifera, mostly spherical, with an organic-walled test. Notably, these Foraminifera exhibit a unique behavior in culture: they surround themselves in planktonic diatoms, enabling them to float in the water column. This floating behavior is unusual for Foraminifera, which are often larger and possess a thick test made of calcite or agglutinated particles. We hypothesize that the small size of the organism, its lightweight organic test, and the habit of surrounding itself with centric diatoms may enable the floating behavior observed in culture and potentially aid dispersal in nature. Phylogenetic analysis of the 18S rDNA barcoding fragment places this undescribed organism as an independent lineage among monothalamid Foraminifera. We erect the novel genus Pensilisphaera with its type species Pensilisphaera antarcticaensis.},
}
@article {pmid40185067,
year = {2025},
author = {Papapetrou, EP},
title = {The clones have STRACK: Tracing responses to leukemic mutations.},
journal = {Cell stem cell},
volume = {32},
number = {4},
pages = {499-501},
doi = {10.1016/j.stem.2025.03.001},
pmid = {40185067},
issn = {1875-9777},
mesh = {Animals ; *Mutation/genetics ; *Leukemia/genetics/pathology ; Clone Cells/pathology ; Mice ; *Hematopoietic Stem Cells/metabolism/pathology ; Humans ; },
abstract = {Rodriguez-Fraticelli and colleagues combine genetic barcoding with ex vivo expansion and sister-cell analysis of murine hematopoietic stem cells (HSCs) carrying inducible leukemia driver mutations. This approach allows them to capture the intrinsic heterogeneity of clonal cell behaviors and study how these impact cell fates upon acquisition of leukemia driver mutations.},
}
@article {pmid40183470,
year = {2025},
author = {Haley, RM and Padilla, MS and El-Mayta, RD and Joseph, RA and Weber, JA and Figueroa-Espada, CG and Mukalel, AJ and Ricciardi, AS and Palanki, R and Geisler, HC and Jester, MT and Davidson, BL and Mitchell, MJ},
title = {Lipid Nanoparticles for In Vivo Lung Delivery of CRISPR-Cas9 Ribonucleoproteins Allow Gene Editing of Clinical Targets.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.4c16617},
pmid = {40183470},
issn = {1936-086X},
abstract = {In the past 10 years, CRISPR-Cas9 has revolutionized the gene-editing field due to its modularity, simplicity, and efficacy. It has been applied for the creation of in vivo models, to further understand human biology, and toward the curing of genetic diseases. However, there remain significant delivery barriers for CRISPR-Cas9 application in the clinic, especially for in vivo and extrahepatic applications. In this work, high-throughput molecular barcoding techniques were used alongside traditional screening methodologies to simultaneously evaluate LNP formulations encapsulating ribonucleoproteins (RNPs) for in vitro gene-editing efficiency and in vivo biodistribution. This resulted in the identification of a lung-tropic LNP formulation, which shows efficient gene editing in endothelial and epithelial cells within the lung, targeting both model reporter and clinically relevant genomic targets. Further, this LNP shows no off-target indel formation in the liver, making it a highly specific extrahepatic delivery system for lung-editing applications.},
}
@article {pmid40182483,
year = {2025},
author = {Kipkoech, A and Li, K and Milne, RI and Oyebanji, OO and Wambulwa, MC and Fu, XG and Wakhungu, DA and Wu, ZY and Liu, J},
title = {An integrative approach clarifies species delimitation and biogeographic history of Debregeasia (Urticaceae).},
journal = {Plant diversity},
volume = {47},
number = {2},
pages = {229-243},
doi = {10.1016/j.pld.2024.11.004},
pmid = {40182483},
issn = {2468-2659},
abstract = {Integrative data from plastid and nuclear loci are increasingly utilized to resolve species boundaries and phylogenetic relationships within major angiosperm clades. Debregeasia (Urticaceae), an economically important genus, presents challenges in species delimitation due to its overlapping morphological traits and unstable taxonomic assignments. Here, we analyzed 14 morphological traits and generated 12 data matrices from the plastomes and nrDNA using genome skimming from the nine recognized morphospecies to clarify species boundaries and assess barcode performance in Debregeasia. We also used a universal set of 353 nuclear genes to explore reticulate evolution and biogeographic history of Debregeasia. Plastomes of Debregeasia exhibited the typical quadripartite structure with conserved gene content and marginal independent variations in the SC/IR boundary at inter- and intra-specific levels. Three Debregeasia species were non-monophyletic and could not be discerned by any barcode; however, ultra-barcodes identified the remaining six (67%), outperforming standard barcodes (56%). Our phylogenetic analyses placed Debregeasia wallichiana outside the genus and suggested six monophyletic clades in Debregeasia, although the placement between Debregeasia hekouensis and Debregeasia libera varied. There was extensive trait overlap in key morphologically diagnostic characters, with reticulation analysis showing potentially pervasive hybridization, likely influenced by speciation patterns and overlaps between species ranges. We inferred that Debregeasia crown diversification began at ca. 12.82 Ma (95% HPD: 11.54-14.63 Ma) in the mid-Miocene within Australia, followed by vicariance and later long-distance dispersal, mainly out of southern China. Our findings highlight the utility of genomic data with integrative lines of evidence to refine species delimitation and explore evolutionary relationships in complex plant lineages.},
}
@article {pmid40181733,
year = {2025},
author = {Congrains, C and Bremer, F and Dupuis, JR and Barr, NB and Garzón-Orduña, IJ and Rubinoff, D and Doorenweerd, C and Jose, MS and Morris, K and Kauwe, A and Geib, S},
title = {CCS-Consensuser: A Haplotype-Aware Consensus Generator for PacBio Amplicon Sequences.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14113},
doi = {10.1111/1755-0998.14113},
pmid = {40181733},
issn = {1755-0998},
support = {8130-0565-CA//U.S. Department of Agriculture-Animal and Plant Health Inspection Service/ ; 8130-0984-IA//U.S. Department of Agriculture-Animal and Plant Health Inspection Service/ ; },
abstract = {DNA sequencing technology has undergone substantial improvements in recent years, to the extent that Third Generation Sequencing platforms are capable of massively generating long-reads. Amplicon sequencing has been among the most popular techniques due to its wide application in diverse fields of biological sciences. However, there is a lack of software specifically designed to analyse intra-individual genetic variation using amplicon long-read data. Here, we present CCS-consensuser, an end-to-end pipeline that generates consensus sequences from amplicon sequencing using high-fidelity reads produced by PacBio circular consensus sequencing (CCS). We evaluated the concordance of the results produced using CCS + CCS-consensuser and other sequencing platforms (Illumina and Sanger), as well as accuracy using a simulated dataset. This assessment showed that CCS amplicon data coupled with CCS-consensuser can produce high-quality sequences (PHRED > 30). The pipeline resulted in high proportions of identical sequence bins for real data, achieving up to 94.94% concordance with COI Sanger sequences and 92.61% with nuclear loci Illumina sequences (considering heterozygous loci), and 95.55% with a fully phased nuclear simulated dataset. Furthermore, our pipeline can be used to detect heteroplasmy in mtDNA, cross-contamination, resolve the phase of nuclear genes in diploid organisms, and conceivably for multi-copy gene systems such as rDNA. These results not only support its potential for application in studies using haploid data such as DNA barcoding, but also demonstrate its unique capacity to explore within individual haplotype variation. Therefore, our strategy shows promise for a broad range of applications in biology and medicine that have been challenging to assess using traditional techniques.},
}
@article {pmid40180452,
year = {2025},
author = {Schares, HAM and Hayes, MJ and Balsamo, JA and Thirman, HL and Bachmann, BO and Irish, JM},
title = {Multiplexed cytometry for single cell chemical biology.},
journal = {Methods in cell biology},
volume = {195},
number = {},
pages = {143-172},
doi = {10.1016/bs.mcb.2023.03.007},
pmid = {40180452},
issn = {0091-679X},
mesh = {Humans ; *Flow Cytometry/methods ; *Single-Cell Analysis/methods ; Animals ; Mice ; Small Molecule Libraries ; Histones/metabolism ; DNA Damage ; },
abstract = {Flow cytometry has great potential for screening in translational research areas due to its deep quantification of cellular features, ability to collect millions of cells in minutes, and consistently expanding suite of validated antibodies that detect cell identity and functions. However, cytometry remains under-utilized in discovery chemical biology due to the differences in expertise between chemistry groups developing chemical libraries and cell biologists developing single cell assays. This chapter is designed to bridge this gap by providing a detailed protocol aimed at both chemistry and biology audiences with the goal of helping train novice researchers. Assay users select from three elements: a small molecule input, a target cell type, and a module of cytometry readouts. For each, we explore basic and advanced examples of inputs, including screening fractionated microbial extracts and pure compounds, and target cells, including primary human blood cells, mouse cells, and cancer cell lines. One such module of cytometry readouts focuses on cell function and measures DNA damage response (γH2AX), growth (phosphorylated S6), DNA content, apoptosis (cleaved Caspase3), cell cycle M phase (phosphorylated Histone H3), and viability (membrane permeabilization). The protocol can also be adapted to measure different functional readouts, such as cell identity or differentiation and contrasting cell injury mechanisms. The protocol is designed to be used in 96-well plate format with fluorescent cell barcoding and the debarcodeR algorithm. Ultimately, the goal is to encourage the next generation of chemical biologists to use functional cell-based cytometry assays in discovery and translational research.},
}
@article {pmid40179197,
year = {2025},
author = {de Haan, S and He, J and Corbat, AA and Belicova, L and Ratz, M and Vinsland, E and Frisén, J and Kelley, MW and Andersson, ER},
title = {Ectoderm barcoding reveals neural and cochlear compartmentalization.},
journal = {Science (New York, N.Y.)},
volume = {388},
number = {6742},
pages = {60-68},
doi = {10.1126/science.adq9248},
pmid = {40179197},
issn = {1095-9203},
mesh = {Animals ; Mice ; *Ectoderm/embryology/cytology ; Cell Lineage ; *Cochlea/embryology/cytology ; *Neural Crest/embryology/cytology ; *DNA Barcoding, Taxonomic/methods ; Single-Cell Analysis ; Cell Differentiation ; Neurogenesis ; *Nervous System/embryology ; },
abstract = {Placodes and the neural crest are defining features of vertebrates. In this study, we investigate their lineages in mice using in utero approaches. We demonstrated that nanoinjection at embryonic day 7.5 targeted the ectoderm, including the future nervous system, placodes, and neural crest, allowing highly efficient manipulation of the future nervous system and inner ear. By using heritable DNA barcodes and high-throughput next-generation single-cell lineage tracing, we elucidated convergent differentiation pathways and identified distinct nervous system-, neural crest-, and otic placode-derived lineages. Clonal analyses identified early neural and cochlear compartmentalization, linking differentiated cell types to their progenitors or cellular siblings. This provides foundational insights for neuroscience and developmental biology.},
}
@article {pmid40179100,
year = {2025},
author = {Long, Z and Yu, J and Bing, T},
title = {Theoretical Basis for the Highly Efficient Aptamer Selection Using Unique Molecular Identifiers.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c00118},
pmid = {40179100},
issn = {1520-6882},
abstract = {Rapid selection methods are crucial for promoting the discovery and application of aptamers across various fields. We previously reported a highly efficient aptamer selection strategy by using unique molecular identifiers (UMIs), enabling the efficient isolation of aptamers from a single cell by only one round. The strategy integrates an ultrasensitive DNA barcoding technology with high-throughput sequencing to accurately quantify aptamer candidates, thereby mitigating issues such as PCR bias and sequence overenrichment that are inherent in traditional multiround selection. Here, we conduct a systematically theoretical analysis of this strategy in the elucidation of the theoretical basis, advantages, and applicability. The feasibility and advantages of isolating aptamers from low-enriched DNA libraries was investigated at a theoretical level, showing that this strategy is effective in reducing nonspecific binding and thus increasing the success of selecting high-affinity aptamers. Our theoretical analysis supports the broad applicability of the strategy for the single-round aptamer selection, paving the way for its widespread adoption in high-efficiency aptamer discovery and aptamer-based cell atlas.},
}
@article {pmid40177347,
year = {2025},
author = {Gong, L and Zhong, Y},
title = {Re-description of Sinopodacurva Zhong, Jäger, Chen &amp; Liu, 2019 (Araneae, Sparassidae), with a first description of the female.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e152100},
doi = {10.3897/BDJ.13.e152100},
pmid = {40177347},
issn = {1314-2828},
abstract = {BACKGROUND: Sinopoda Jäger, 1999 is a relatively large spider genus that currently comprises 141 species distributed worldwide. However, the genus remains inadequately studied because nearly half of the species are known from a single sex or juvenile specimens. Sinopodacurva Zhong, Jäger, Chen &amp; Liu, 2019 was described, based on two male specimens from Damingshan National Nature Reserve, Guangxi Zhuang Autonomous Region, China and no additional specimens have been recorded since.<br><br>NEW INFORMATION: Recently, new materials of huntsman spiders have been collected from Mt. Wuyishan, including specimens of both sexes. Several males were identified as S.curva, based on morphological comparison with the holotype. Based on morphological characters and DNA barcodes, we confidently matched the females and males as S.curva. Herein, S.curva is re-described, based on these new materials and the female is described and illustrated for the first time.},
}
@article {pmid40174196,
year = {2025},
author = {Kohlmann, B and Solís, &#xc1;},
title = {A review of the species groups of the Western Hemisphere Onthophagus Latreille (Coleoptera: Scarabaeidae: Scarabaeinae) using COI barcoding and gene trees.},
journal = {Zootaxa},
volume = {5604},
number = {4},
pages = {401-447},
doi = {10.11646/zootaxa.5604.4.1},
pmid = {40174196},
issn = {1175-5334},
abstract = {Species groups of Western Hemispheric Onthophagus Latreille (Coleoptera: Scarabaeidae: Scarabaeinae: Onthophagini) are suggested using COI barcoding and gene trees and supported by congruence with external morphology, behavior, ecology, and biogeographic evidence. New species groups, complexes, and taxonomic statuses are offered, and other preexisting proposals are confirmed. No barcoding gap w as found between the intragroup and intergroup genetic distance blocks, but the average intragroup (8.38%) and intergroup (13.88%) Kimura-two-parameter distances are statistically different. The following seven preexisting species groups were supported by the congruence between the mtDNA barcode analysis and other independent evidence: O. chevrolati, O. clypeatus, O. dicranius, O. gazellinus, O. hircus, O. landolti, and O. mexicanus. Eight new species groups are suggested: O. crinitus, O. curvicornis, O. eulophus, O. hecate, O. hoepfneri, O. marginatus, O. nasutus, and O. velutinus. Possible behavioral/ecological adaptations of morphological characters are also discussed. New biogeographic and evolutionary hypotheses are also advanced. An identification key for species groups is presented.},
}
@article {pmid40174133,
year = {2025},
author = {Mori, E and Viviano, A and Baratti, M and Serafini, E and Gabbrielli, B and Picchi, MS and Giannetti, D and Mascalchi, C and Ancillotto, L},
title = {A light in the dark: DNA barcoding provides new data about the taxonomy of the Italian Luciola (Coleoptera, Lampyridae) fireflies.},
journal = {Zootaxa},
volume = {5609},
number = {4},
pages = {525-536},
doi = {10.11646/zootaxa.5609.4.4},
pmid = {40174133},
issn = {1175-5334},
abstract = {Environmental pollution and agricultural intensification are threatening insects worldwide, and reliable taxonomy is pivotal to protect these taxa, particularly endemic species. Despite their wide distribution, lampyrid beetles (Lampyridae)-well-known as fireflies-are poorly studied in terms of taxonomy, particularly in Europe. Accordingly, as for almost all insects, the description of most species is only based on a few morphological featuresSince genetic analyses can provide valuable support in taxonomic studies, in this work, we investigated the species identity of an Italian endemic firefly, Luciola pedemontana (Curtis, 1843), with respect to other congeneric species, namely Luciola italica (Linnaeus, 1767) and Luciola lusitanica (Charpentier, 1825) by applying Barcoding technique. Particularly, L. pedemontana has been for long considered as a synonym of L. lusitanica or as a subspecies of L. italica. Italy hosts the highest diversity of firefly species in Europe, but the Luciola inter-specific phylogenetic relationships and species delimitations are still poorly known. With the aim to assist morphological analyses in the taxonomic characterization of species of the genus Luciola in Italy, we sequenced the cytochrome oxidase subunit I gene (COI) fragment of 40 individuals from 18 sites in Central Italy. Our analysis confirmed L. pedemontana as a well-supported monophyletic clade and as the sister taxon of L. italica. Furthermore, a low intraspecific genetic variation was found between L. lusitanica and L. pedemontana and between Luciola unmunsana + Luciola papariensis. Genetic data obtained for the Luciola species can help to improve conservation measures for L. pedemontana, strongly required to protect this Italian endemic taxon, which is currently threatened by light pollution and environmental alterations.},
}
@article {pmid40174117,
year = {2025},
author = {Girdley, J and Garre, M and Rubio, RM and Ortiz, AS},
title = {Eucosma callei sp. nov.-a new species of Olethreutinae from South-eastern Iberian Peninsula (Lepidoptera, Tortricidae).},
journal = {Zootaxa},
volume = {5583},
number = {1},
pages = {186-194},
doi = {10.11646/zootaxa.5583.1.11},
pmid = {40174117},
issn = {1175-5334},
abstract = {Eucosma callei sp. nov. is described and illustrated from the Iberian Peninsula. It differs from its Iberian congener, Eucosma gonzalezalvarezi Agenjo, 1970, in external appearance and genitalia. The 5' barcode fragments of the mitochondrial gene COI (the DNA barcode) are presented and confirms the description of this new species.},
}
@article {pmid40174108,
year = {2025},
author = {Cava, S and Rijllo, G and Zucco, G and Scalercio, S},
title = {Revisiting the genus Diplodoma Zeller, 1852 in Europe: DNA barcoding reveals the presence of an undescribed species from forested habitats of southern Italy (Lepidoptera: Psychidae).},
journal = {Zootaxa},
volume = {5583},
number = {2},
pages = {371-382},
doi = {10.11646/zootaxa.5583.2.8},
pmid = {40174108},
issn = {1175-5334},
abstract = {Diplodoma Zeller, 1852 is a Eurasian genus belonging to the family Psychidae Boisduval, 1829 of which three species are known in Europe: Diplodoma adspersella Heinmann, 1870, D. laichartingella (Goeze, 1783), and D. taurica Zagulajev, 1986. Some authors have argued that Diplodoma adspersella may be a subspecies or even a form of D. laichartingella. The revision of literature and the study of DNA barcoding fragments confirmed the inconsistency of D. adspersella as a valid species, and therefore we propose the new synonymy of Diplodoma adspersella with D. laichartingella (syn. nov.). During recent surveys in southern Italy, three specimens of Diplodoma were collected. DNA barcoding and morphological analyses showed that COI sequences and male genitalia significantly differ from any previously studied specimen. As a result, we described Diplodoma giulioregenii sp. nov., leaving unaltered the number of species belonging to this genus known from Europe.},
}
@article {pmid40174101,
year = {2025},
author = {Thiel, R and Knebelsberger, T and Chernova, N and Eidus, I},
title = {Two new species of eelpout genus Lycenchelys (Perciformes: Zoarcidae) from the Kuril-Kamchatka Trench, based on morphological and molecular evidence.},
journal = {Zootaxa},
volume = {5583},
number = {3},
pages = {491-508},
doi = {10.11646/zootaxa.5583.3.4},
pmid = {40174101},
issn = {1175-5334},
abstract = {Two new species of eelpout genus Lycenchelys Gill, 1884 are described based on eight specimens caught at a depth between 3517 and 3580 m at the western slope of the upper margin of the Kuril-Kamchatka Trench, relatively close to the Bussol Strait and Simushir Island in the center of the Kuril Islands chain. Lycenchelys delanglei sp. nov. differs from its congeners by the following combination of characters: vertebrae 28-29 + 91-93 = 120-121; interorbital and occipital pores absent; postorbital pores 4; suborbital pores 10-12; preoperculomandibular pores 4 + 5; gill rakers 11-16; dorsal-fin rays 114-117, 2-3 free pterygiophores at the beginning of dorsal fin; anal-fin rays 96-98; pelvic-fin rays 2; pectoral-fin rays 16-17, ray tips of the pectoral fin exserted, especially the middle and lower ones; lateral line absent; pyloric caeca not developed. Lycenchelys renatae sp. nov. differs from its congeners by the following combination of characters: vertebrae 26-27 + 99-103 = 125-130; interorbital pores 0-1; occipital pores absent; postorbital pores 1-4; suborbital pores 6-9; preoperculomandibular pores 3-4 + 5; gill rakers 13-15; dorsal-fin rays 115-122, 1-3 free pterygiophores at the beginning of dorsal fin; anal-fin rays 102-106; pelvic-fin rays two; pectoral-fin rays 16-17, ray tips of the pectoral fin exserted, the middle and lower ones more so than the upper ones; lateral line mediolateral, poorly developed; pyloric caeca not developed. For each of the two described new species four mitochondrial COI sequences were analysed and share the same haplotype within species. The obtained DNA barcodes allowed discrimination of L. delanglei sp. nov. and L. renatae sp. nov. from each other and exhibit a genetic distance of 2,61%. The closest match of L. delanglei sp. nov. with already published sequences was Lycenchelys lenzeni with a sequence similarity of 98.47%, whereas the closest match of L. renatae sp. nov. with already published sequences was Lycenchelys jordani with a similarity of 98.62%. A new analysis of radiographs of the type specimens confirmed that L. birsteini should be considered as synonym of L. plicifera, especially due to similar numbers of free pterygiophores at the beginning of dorsal fin.},
}
@article {pmid40174087,
year = {2025},
author = {Luengo, E and Genis-Armero, R and Clark, PF and Palero, F},
title = {Final stage phyllosoma of Galearctus sp. (Decapoda: Scyllaridae) from the Coral Sea.},
journal = {Zootaxa},
volume = {5584},
number = {1},
pages = {101-112},
doi = {10.11646/zootaxa.5584.1.6},
pmid = {40174087},
issn = {1175-5334},
abstract = {Larval stages are known for only four out of eight Galearctus Holthuis, 2002 (Crustacea: Scyllaridae) species, a slipper lobster genus widely distributed throughout the Indo-Pacific region. DNA barcoding analyses of phyllosomae collected from the Coral Sea by the Australian Institute of Marine Science suggest the presence of two new genetic clades in the area, for which larvae cannot be discriminated morphologically. The last instar larva of an unknown species of Galearctus is described and illustrated in detail here. It is possible that this larval material may be assigned to G. umbilicatus, the only species of the genus lacking a DNA barcode. Morphological analyses and a literature review allowed the re-evaluation of previous Galearctus larval studies, identifying several misidentifications and inconsistencies. Further morphological and molecular revision of adult Galearctus species is required to confirm larval identities, but the results presented here indicate that the diversity of Galearctus may be underestimated.},
}
@article {pmid40174058,
year = {2025},
author = {Barrantes, EAB and Echavarria, MAZ and Bartlett, CR and Hendrix, SV and Helmick, EE and Bahder, BW},
title = {A new species of Cyclopoliarus (Hemiptera: Auchenorrhyncha: Fulgoromorpha: Cixiidae) from American oil palms (Elaeis oleifera) in Caño Negro, Costa Rica.},
journal = {Zootaxa},
volume = {5584},
number = {4},
pages = {523-538},
doi = {10.11646/zootaxa.5584.4.4},
pmid = {40174058},
issn = {1175-5334},
abstract = {Recent palm survey work in Costa Rica focusing on planthoppers has resulted in the discovery of several new taxa, primarily in Cixiidae and Derbidae. Here a new species of Cyclopoliarus Fennah, C. nigelwatsoni sp. nov., is described from Caño Negro, Limón Province, Costa Rica. The new species is compared with C. omani, the only other described Central American Cyclopoliarus. Supplemental molecular data is presented for the barcoding region (5' half) of the cytochrome c oxidase subunit I (COI) gene, 18S rRNA gene, and D9 to D10 expansion region of the 28S rRNA gene. A phylogeny is presented to place the new species relative to other available taxa.},
}
@article {pmid40174054,
year = {2025},
author = {Lukhtanov, VA and Makhov, IA and Gagarina, AV and Romanovich, AE},
title = {Taxonomy of the West Palaearctic butterfly genus Palaeophilotes Forster, 1938 (Lepidoptera: Lycaenidae) based on combined analysis of COI barcodes and multilocus nuclear markers.},
journal = {Zootaxa},
volume = {5584},
number = {4},
pages = {570-580},
doi = {10.11646/zootaxa.5584.4.8},
pmid = {40174054},
issn = {1175-5334},
abstract = {Based on molecular phylogenetic analysis of all relevant taxa, we propose to consider the species previously classified as members of Pseudophilotes, Palaeophilotes, Rubrapterus, and Inderskia as belonging to a single genus, the valid name of which is Palaeophilotes. This genus can be divided into two subgenera: Rubrapterus with species P. bavius and P. fatma, and Palaeophilotes sensu stricto. The latter subgenus includes four lineages and nine species: (1) the P. abencerragus lineage (single species P. abencerragus), (2) P. barbagiae lineage (single species P. barbagiae), (3) P. panope lineage (P. panope and P. triphysina), and (4) P. baton lineage (P. panoptes, P. baton, P. vicrama, P. jacuticus and P. sinaicus). The name Borisinia Korb, 2013, syn. nov. is shown to be an objective synonym of Palaeophilotes Forster, 1938. The previously proposed synonymy of P. svetlana and P. marina with P. panope is supported by the identity of their DNA-barcodes. Palaeophilotes panope is reported for the Kazakhstan part of the Altai mountains for the first time. Palaeophilotes jacuticus is confirmed for the Lake Baikal region in Siberia.},
}
@article {pmid40174049,
year = {2025},
author = {Serbina, L&#x160; and Malenovský, I and Queiroz, DL and Burckhardt, D},
title = {Jumping plant-lice of the tribe Paurocephalini (Hemiptera: Psylloidea: Liviidae) in Brazil.},
journal = {Zootaxa},
volume = {5585},
number = {1},
pages = {1-164},
doi = {10.11646/zootaxa.5585.1.1},
pmid = {40174049},
issn = {1175-5334},
abstract = {The predominantly tropical tribe Paurocephalini of jumping plant-lice currently consists of seven genera and 94 described species worldwide, of which the genera Klyveria Burckhardt et al. and Melanastera Serbina et al. have been recorded from Brazil with two and one species, respectively. Here we review the taxonomy of the Brazilian species based on material collected from extensive fieldwork carried out in 15 states over the last decade. One species of Klyveria and 59 species of Melanastera are newly described, bringing the number of extant Klyveria spp. to three (both in Brazil and worldwide) and that of extant Melanastera spp. to 69 (60 in Brazil, 67 in the Neotropical region and one each in the Afrotropical and Oriental regions). The new species are described and illustrated, and identification keys for the Brazilian species are provided for adults and last instar immatures. The most diagnostically important structures are the distal segment of the aedeagus and the paramere, the forewing (shape, venation, surface spinules and colour pattern) and the female terminalia in the adults, and the chaetotaxy, tarsal arolium and shape of the additional pore fields on the caudal plate in the last instar immatures. The species descriptions are complemented by mitochondrial DNA barcodes (COI and cytB) and information on host plants. Klyveria spp. are restricted to Luehea (Malvaceae), while in Brazil 28 Melanastera spp. develop or are likely to develop on Melastomataceae, 18 spp. on Annonaceae, four spp. each on Asteraceae and Myristicaceae, and one species on Cannabaceae. Only three of the 63 species of Paurocephalini reported here from Brazil, are also known from other countries: two from Paraguay and one from Trinidad. Probably many more species of Melanastera are yet to be discovered and described. Priority in fieldwork should be given to areas that are at high risk of destruction or degradation by human activities, such as the Amazon rainforest, the Atlantic Forest and the Cerrado.},
}
@article {pmid40174044,
year = {2024},
author = {Borkent, A and Spinelli, GR and Díaz, F and Steinke, D and Perez, KHJ and Stur, E and Hallwachs, W and Janzen, DH},
title = {Looking Into the Abyss-How Many Species of Biting Midges (Diptera: Ceratopogonidae) Are There? Their Remarkable Diversity in Costa Rica and Elsewhere.},
journal = {Zootaxa},
volume = {5555},
number = {3},
pages = {331-384},
doi = {10.11646/zootaxa.5555.3.3},
pmid = {40174044},
issn = {1175-5334},
abstract = {The biting midges (Ceratopogonidae) are one of the most species-rich families of insects on the planet with over 6,200 named species. However, their true diversity is unknown and this paper is the first to address the question. Our systematic study of the family in Costa Rica indicates that 192 species were present in a four hectare area of cloudforest at Zurquí de Moravia, at 1,600 m after a year of intensive sampling. Combined with a collection from a single Malaise trap at Tapantí for one year, about 40 kms away and also at 1,600 m, the total was 245 species with significant differences between the two areas and with the strong majority unnamed. This compares to 430 named species for all of Costa Rica and 1,314 for the entire Neotropical Region. Barcoding of 221,407 specimens from Costa Rica similarly indicates large numbers of unnamed species with 4,023 BINs present. On this basis, we project at least 5,000 species in Costa Rica and using ratios of named species here and elsewhere, we suggest that nearly 73,000 are present worldwide. Details from Malaise traps in the Área de Conservación Guanacaste also indicate various levels of endemism. Samples from Bolivia support an interpretation of high diversity. The diversification of the family was examined by comparing phyletic lineages, rather than merely comparing numbers of species in various genera, providing insight as to why some lineages are more diverse than others. Zoogeographic patterns of named species suggest stronger southern connections for Costa Rican Ceratopogonidae in both cloudforest habitats as well as the country as a whole, although many are also more broadly distributed north and south of the country. Comparisons between various collecting methods at Zurquí de Moravia indicate the efficacy of Malaise traps but also the importance of light traps and other methods in sampling adults of Ceratopogonidae. Phenological data from the Malaise traps in the Área de Conservación Guanacaste suggest some patterns of emergence of adults in Costa Rica, the first for any tropical country anywhere.},
}
@article {pmid40173973,
year = {2025},
author = {Huber, BA and Meng, G},
title = {Like grains of sand: Ninetis spiders on the Arabian Peninsula (Araneae, Pholcidae).},
journal = {Zootaxa},
volume = {5563},
number = {1},
pages = {290-335},
doi = {10.11646/zootaxa.5563.1.19},
pmid = {40173973},
issn = {1175-5334},
abstract = {Ninetinae is a group of small to tiny, short-legged daddy-longlegs spiders (Pholcidae) that has its highest diversity in the New World. Only two genera are known to occur in the Old World: the nominotypical genus Ninetis Simon, 1890 on the Arabian Peninsula and in Africa, and the monotypic genus Magana Huber, 2019 in Oman. Here we redescribe the type species of Ninetis, N. subtilissima Simon, 1890, and describe three new species from the Arabian Peninsula: N. amoud sp. nov. from Saudi Arabia, N. marnif sp. nov. and N. samail sp. nov. from Oman. All species descriptions are based on males and females, supported by CO1 barcodes, and accompanied by SEM photographs. While N. amoud sp. nov. is morphologically and genetically similar to N. subtilissima (and to the known African species, of which no CO1 barcodes are available), the two new Omani species are morphologically very distinct. Intraspecific genetic (K2P) distances are partly very high, in particular in N. amoud sp. nov. (up to 17%) and N. marnif sp. nov. (up to 13%). An exploratory species delimitation analysis suggests that these two nominal species might in fact represent several cryptic species each. No corresponding morphological variation was detected.},
}
@article {pmid40173932,
year = {2025},
author = {Zuñiga, R and Valerio, AA and Hanson, P and Hallwachs, W and Janzen, DH},
title = {Endoparasitoid wasps of the genus Cubus (Hymenoptera, Ichneumonidae, Metopiinae) reared from caterpillars of Área de Conservación Guanacaste, Costa Rica.},
journal = {Zootaxa},
volume = {5590},
number = {3},
pages = {365-385},
doi = {10.11646/zootaxa.5590.3.4},
pmid = {40173932},
issn = {1175-5334},
abstract = {As a result of COI barcoding over 200 reared specimens of what appeared to be Cubus validus from northwestern Costa Rica, and matching them with their host caterpillars and morphological traits, we describe eleven new sympatric species. All are endoparasitoids of leaf-rolling Crambidae (Lepidoptera). The new species, authored by Zúñiga, Valerio &amp; Hanson, are: Cubus alanflemingi, C. christhompsoni, C. curtsabrowskyi, C. duvalierbricenoi, C. gracewoodae, C. jeffcummingi, C. jimoharai, C. johnstiremani, C. manuelzumbadoi, C. montywoodi, and C. normwoodleyi. We also provide an illustrated key, a table of key morphological characters of each species, and a table of host records.},
}
@article {pmid40173915,
year = {2025},
author = {Brodin, Y},
title = {Procladius (Diptera, Chironomidae) of Europe and a global view.},
journal = {Zootaxa},
volume = {5591},
number = {1},
pages = {1-127},
doi = {10.11646/zootaxa.5591.1.1},
pmid = {40173915},
issn = {1175-5334},
abstract = {A project initiated in 1991 to untangle species-taxonomy of European Procladius (Chironomidae) has been accomplished. Increasing amount of material, loans and especially the development of barcodes and the BIN-system of BOLD, made finalization possible after about 33 years. An iterative process based on detailed studies of male morphology and barcode clusters, BINs, resulted in identification of 27 species present in Europe, most of them also in Asia (China, Japan, Mongolia and Russia) and North America (Canada and the United States). One hundred morphological characters were adopted for species identification of which the 30 most important ones were used to construct a species key and an additional helpdesk. The key contains three characters for each species separation as this is frequently needed for reliable identification. The ratio GspR, the outer length of the gonostylus process versus length of outer margin in gonostylus, proved to be the most important character for species identification. All but two of the 27 species have barcodes and BINs. All but one BIN contained only one species. The exception is a BIN that previously was divided into two BINs each containing one morphologically distinct species. Intraspecific divergence within the species ranged from 0‒3.3% and interspecific divergence from 2.0‒8.8%. Four new species are presented. These are P. exilis Brodin, new species, P. gemma Brodin, new species, P. saeticubitus Brodin, new species and P. tenebricosus Brodin &amp; Hellberg, new species. The other 23 species presented are as follows with new synonyms within brackets: P. appropinquatus (Lundström, 1916) [P. ruris Roback, 1971], P. bellus (Loew, 1866) [Tanypus rufovittatus van der Wulp, 1874, P. latifrons Kieffer, 1922, P. leucocoma Kieffer, 1922, P. profundorum Kieffer, 1923], P. breviatus Remmert, 1953, P. choreus (Meigen, 1804) [Chironomus incomptus Walker, 1856], P. clavus Roback, 1971, P. crassinervis (Zetterstedt, 1838) [Tanypus pectinatus Kieffer, 1909, P. bifasciatus Goetghebuer, 1936, P. cinereus Goetghebuer, 1936, P. abetus Roback, 1971], P. culiciformis (Linnaeus, 1767) [Tanypus sagittalis Kieffer, 1909, Trichotanypus scapularis Kieffer, 1924, P. freemani Sublette, 1964 in part], P. dentus Roback, 1971, P. ferrugineus (Kieffer, 1918) [Trichotanypus parvulus Kieffer, 1918, Trichotanypus fulvus Kieffer, 1924, Trichotanypus profundorum Kieffer, 1924, P. rugulosus Saether 2010], P. fimbriatus Wülker, 1959, P. flavifrons Edwards, 1929, P. floralis Kieffer, 1915, P. frigidus (Holmgren, 1869) [P. gretis Roback, 1971], P. imicola Kieffer, 1922 [P. bathyphilus Kieffer, 1922, P. nietus Roback, 1971], P. islandicus (Goetghebuer, 1931) [P. fuscus Brundin, 1949, P. vesus Roback, 1971], P. longistilus (Kieffer, 1916) [P. suecicus Brundin, 1949], P. lugens Kieffer, 1915 [P. macrotrichus Roback, 1971], P. lugubris (Zetterstedt, 1850) [P. barbatus Brundin, 1949, P. johnsoni Roback, 1980], P. nudipennis Brundin, 1947, P. pruinosus (Kieffer, 1924), P. signatus (Zetterstedt, 1850) [Trichotanypus nigriventris Kieffer, 1924, P. denticulatus Sublette, 1964 in part], P. simplicistilus Freeman, 1948, P. tatrensis Gowin, 1944. In addition, 12 species of Procladius not found in Europe are briefly described and it is indicated where they appear in the species-key. Species of Procladius have been reported from 133 countries or autonomies worldwide. As many as 12 species have been found in extreme cold places of the northern hemisphere, with mean annual temperature ‒10 C or more. Altitude records are at 4 730 m above sea level in the Himalayas. Larvae of most European species are known to be omnivorous, although predation might be more beneficial for growth. Synonyms and dubious names reduce the number of valid (accepted) species of Procladius according to Catalogue of Life and Systema Dipterorum with 34% worldwide. After the inclusion of four new species of the present study and two others from Asia the number or valid species of Procladius worldwide land on 69.},
}
@article {pmid40173762,
year = {2025},
author = {Wang, M and Lai, Y and Liu, X},
title = {The green lacewing genus Kuwayamachrysa Tsukaguchi &amp; Tago, 2018 from China, with description of two new species based on morphological and molecular evidence.},
journal = {Zootaxa},
volume = {5570},
number = {1},
pages = {138-150},
doi = {10.11646/zootaxa.5570.1.6},
pmid = {40173762},
issn = {1175-5334},
abstract = {Previously, Kuwayamachrysa Tsukaguchi &amp; Tago, 2018 (Neuroptera: Chrysopidae: Chrysopinae) was known as a monotypic green lacewing genus from the Palearctic region. Here we described two new species of Kuwayamachrysa from China: Kuwayamachrysa wujiaoensis sp. nov. and Kuwayamachrysa neptuna sp. nov. Also, Mallada qinlingensis Yang, 1989, currently named as Apertochrysa qinlingensis (Yang, 1989), is recognized as a junior synonym of Kuwayamachrysa kichijoi (Kuwayama, 1936). A key to the Kuwayamachrysa species is provided. The standard DNA barcoding region of cytochrome c oxidase subunit I (COI) of these species was sequenced for the verification of the new species.},
}
@article {pmid40173760,
year = {2025},
author = {Słomczyński, K and Matera, T and Brodecki, J and Gadawski, P and Płóciennik, M},
title = {The first report from Poland and larvae description of Eukiefferiella dittmari Lehmann, 1972 (Diptera: Chironomidae) based on morphological and molecular characteristics.},
journal = {Zootaxa},
volume = {5570},
number = {1},
pages = {169-178},
doi = {10.11646/zootaxa.5570.1.8},
pmid = {40173760},
issn = {1175-5334},
abstract = {Eukiefferiella is a large genus in the family Chironomidae with over 50 species worldwide. Their immature stages have so far been described in many species in the western Palearctic. Nevertheless, some species are still known only from adult males. Presented below is a description of Eukiefferiella dittmari Lehmann, 1972 larvae first recorded in Poland in the pristine river Rawka. The larvae were collected from water moss and identified to the species level using a DNA barcode from BOLD database. E. dittmari larvae belong to E. ilkleyensis group having bifid SIII seta, and mentum with wide central tooth and four pairs of lateral teeth. At the genetic and morphological level, E. dittmari is a sister species to Nearctic E. endobryonia, also an aquatic moss dweller. The phylogenetic relation of these two species should be further investigated.},
}
@article {pmid40173718,
year = {2025},
author = {Verdone, CJ and Williams, BW and Beaty, SR and Holland, VB and Grubbs, SA and Dewalt, RE},
title = {The adults, larvae, and systematics of the Nearctic Oemopteryx Klapálek, 1902 (Plecoptera: Taeniopterygidae).},
journal = {Zootaxa},
volume = {5595},
number = {1},
pages = {1-94},
doi = {10.11646/zootaxa.5595.1.1},
pmid = {40173718},
issn = {1175-5334},
abstract = {The adult and larval life stages of the Nearctic species of Oemopteryx Klapálek, 1902 (Plecoptera: Taeniopterygidae) are reviewed using color images, scanning electron microscopy photomicrographs, variation in the barcode region of the mitochondrial DNA cytochrome c oxidase subunit I (COI) gene, and distributional information. Two new species are described from the southeast Nearctic region. Adult and larval keys to Oemopteryx species are presented in addition to revised keys to genera for Nearctic Taeniopterygidae.},
}
@article {pmid40173671,
year = {2024},
author = {Eiseman, CS and Feldman, TS and Palmer, MW},
title = {New larval host records, parasitoid records, and DNA barcoding data for North American leaf-mining leaf beetles (Coleoptera: Chrysomeloidea).},
journal = {Zootaxa},
volume = {5549},
number = {1},
pages = {1-60},
doi = {10.11646/zootaxa.5549.1.1},
pmid = {40173671},
issn = {1175-5334},
abstract = {We discuss 46 species of North American leaf-mining leaf beetles (Coleoptera: Chrysomelidae, Megalopodidae), plus one external feeder observed to spin its cocoon within the leaf mine of another insect. For each species, we review previous records of larval and adult hosts and associated hymenopteran parasitoids, augmenting these with our own observations, including the first accounts of oviposition and larval habits for many species. We present the first rearing records for 12 of these species: Anisostena californica Van Dyke, A. funesta (Baly), A. lecontii (Baly), A. perspicua (Horn), Microrhopala excavata (Olivier), Odontota floridana Butte, Stenopodius lateralis (Schaeffer), Altica lazulina LeConte, Dibolia obscura Parry, Monoxia inornata Blake, Zeugophora puberula Crotch, and Z. varians Crotch; as well as 18 new state and provincial records for chrysomeloids, although some of these are based on tentative identifications. We also present original DNA barcoding data showing intra- and interspecific variation among 18 species of hispines (Chrysomelidae: Chalepini). Our data do not provide evidence for cryptic species within Baliosus nervosus (Panzer), Sumitrosis inaequalis (Weber), and S. rosea (Weber) hypothesized based on differences in larval hosts and leaf mines. However, they do suggest the possibility of cryptic species within Tilia-feeding B. nervosus, as well as within S. ancoroides (Schaeffer) and perhaps Microrhopala excavata and Odontota horni Smith. Our barcoding data also support the recognition of the Silphium-feeding M. laetula LeConte as distinct from the Solidago-feeding M. vittata (Fabricius).},
}
@article {pmid40173657,
year = {2024},
author = {Loh, KH and Poong, SW and DU, J and Ong, JJL and Zheng, X and Li, Y and Hu, W},
title = {First record of the blue-and-yellow grouper Epinephelus flavocaeruleus (Lacepède 1802) (Perciformes: Epinephelidae) from the Borneo waters, Malaysia.},
journal = {Zootaxa},
volume = {5550},
number = {1},
pages = {133-144},
doi = {10.11646/zootaxa.5550.1.14},
pmid = {40173657},
issn = {1175-5334},
abstract = {Groupers of the family Epinephelidae constitute a diverse and commercially valuable group of reef fishes globally. They comprise an assemblage of carnivorous marine fishes, comprising more than 177 species across 16 genera. The epinephelid genus Epinephelus, which consists of over 90 species, is found worldwide in the tropics and subtropics. To date, the ichthyofauna of Malaysia has documented a total of 43 epinephelid species. Apart from these, Epinephelus flavocaeruleus (Lacepède, 1802), commonly known as the blue-and-yellow grouper, is rarely reported in the Indo-Pacific Ocean. The present study extends the documented distribution range of E. flavocaeruleus eastwards from the Andaman Sea to the Borneo waters of Sabah, Malaysia. Five specimens of the blue-and-yellow grouper were collected from a local fish market. Species identification was confirmed by the color patterns and DNA barcoding of 630 base pairs of the cytochrome C oxidase I gene for all E. flavocaeruleus specimens, Epinephelus cyanopodus (Richardson, 1846), and 10 closely related Epinephelus species. The interspecies genetic distance ranged from 0.002-0.168. Results from the Templeton, Crandall, and Sing (TCS) haplotype network analysis and maximum likelihood phylogeny based on the COI marker indicate a close genetic relationship between E. flavocaeruleus and E. cyanopodus. However, we refrain from proposing any taxonomic revisions given that more in-depth studies using multiple molecular markers or phylogenomic analysis on a larger sample size are necessary to confirm the taxonomic status of both species. This study significantly contributes to a better understanding of the taxonomy, phylogenetic relationship, and genetic diversity of E. flavocaeruleus.},
}
@article {pmid40173619,
year = {2024},
author = {Leong, WI and Yu, JK and Tsai, IJ and Kaczmarek, &#x141; and Lee, YC and Lin, CP},
title = {Echiniscus gemmatussp. nov. (Heterotardigrada: Echiniscidae; the spinulosus morphogroup) from Macau, China.},
journal = {Zootaxa},
volume = {5551},
number = {2},
pages = {333-352},
doi = {10.11646/zootaxa.5551.2.5},
pmid = {40173619},
issn = {1175-5334},
abstract = {The study of tardigrades in urban environments, particularly in natural areas within cities, has been significantly overlooked. A recent discovery of a new species of tardigrade in lichens collected from Mong Há Hill Municipal Park in Macau provides new insights into the population of tardigrades within the city. Echiniscus gemmatus sp. nov. was identified based on distinct morphological characters, morphometric measurements, and DNA sequences of nuclear (18S rRNA, 28S rRNA, ITS-1, and ITS-2), as well as a mitochondrial (COI) markers. Our research indicates that Ech. gemmatus sp. nov. belongs to the Echiniscus spinulosus morphogroup and is most similar to Ech. tropicalis, as confirmed by both qualitative characters and DNA barcoding. Notably, Echiniscus gemmatus sp. nov. exhibits distinct characteristics that differentiate it from other members of the Ech. spinulosus morphogroup, including (1) often asymmetrical short spines B, C, Cd, Dd, and E, and (2) larger and more visible pores tend to be concentrated in the median and posterior portions of the first and second paired plates, with their visibility gradually decreasing towards the anterior and lateral suture regions.},
}
@article {pmid40173612,
year = {2024},
author = {Jiang, ZH and Li, T and Yan, M and Wang, JX and Zheng, XY and Hu, SJ},
title = {The life history of Smerinthus minor Mell, 1937, with a review of the East Asian species of the genus Smerinthus Latreille, 1802 (Lepidoptera: Sphingidae).},
journal = {Zootaxa},
volume = {5551},
number = {3},
pages = {453-478},
doi = {10.11646/zootaxa.5551.3.2},
pmid = {40173612},
issn = {1175-5334},
abstract = {The six species of the genus Smerinthus Latreille, 1802 known from China, namely S. caecus Ménétriés, 1857, S. kindermannii Lederer, 1853, S. minor Mell, 1937, S. ocellata (Linnaeus, 1758), S. planus Walker, 1856, and S. szechuanus (Clark, 1938) (Lepidoptera, Sphingidae, Smerinthinae, Smerinthini), are examined and illustrated, including the first description of the life history and female genitalia of S. minor. Diagnostic features and distribution maps of all Smerinthus species in East Asia are provided, together with a phylogenetic analysis based on DNA barcode sequences and a global checklist of all Smerinthus species.},
}
@article {pmid40173608,
year = {2024},
author = {Kodama, M and Kodama, N and Mukaida, Y and Hosoki, TK and Nakamoto, K and Tanita, I and Yamada, H},
title = {First record of the genus Cymadusa Savigny, 1816 (Crustacea: Amphipoda: Ampithoidae) from Japan, with redescription and DNA barcoding for C. imbroglio Rabindranath, 1972.},
journal = {Zootaxa},
volume = {5551},
number = {3},
pages = {556-568},
doi = {10.11646/zootaxa.5551.3.6},
pmid = {40173608},
issn = {1175-5334},
abstract = {The ampithoid amphipod Cymadusa imbroglio Rabindranath, 1972 was collected from Ishigaki Island, southwest Japan, as the first Japanese record of the genus. The specimens collected from Ishigaki Island also represent the northernmost record of the species. We herein provide a detailed description and illustration of the specimens from Ishigaki Island. Sequences of COI were determined from two specimens for DNA barcoding and future taxonomic studies.},
}
@article {pmid40173599,
year = {2024},
author = {Eiseman, CS and Lonsdale, O and Montgomery, GA and Jacobsen, JM and Kahn, EX and Rosati, MC and Hauser, M and Parikh, GR and Yu, D},
title = {Invasive Cape ivy (Asteraceae: Delairea odorata Lem.) confirmed as a host for the North American leafminer Liriomyza temperata Spencer (Diptera: Agromyzidae).},
journal = {Zootaxa},
volume = {5555},
number = {1},
pages = {24-34},
doi = {10.11646/zootaxa.5555.1.2},
pmid = {40173599},
issn = {1175-5334},
abstract = {A leafminer reared in California from Cape ivy (Asteraceae: Delairea odorata Lem.), an invasive plant introduced from South Africa, is identified as Liriomyza temperata Spencer (Diptera: Agromyzidae). This is believed to be a novel host association for a native Nearctic fly, which appears to have been introduced in Hawaii along with Cape ivy. Liriomyza tricornis Lonsdale syn. nov. is treated as a junior synonym of L. temperata. There are no previous host records for either taxon. We review previously published rearing records of North American Liriomyza spp. from other plants in the tribe Senecioneae, as well as observations of unidentified Liriomyza mines on these plants. We also discuss the leaf mine and DNA barcode of an undetermined Trypeta sp. (Diptera: Tephritidae) found mining leaves of Cape ivy in California.},
}
@article {pmid40173572,
year = {2025},
author = {Ps, FP and Arjunan, JK and Venu, S and Eranhottu, S and Ummath, A and Kalita, S and Pv, MR and Sadaka, S},
title = {Taxonomic redescription and molecular confirmation of Lutjanus rufolineatus (Acanthuriformes: Lutjanidae) from the Andaman Islands, India.},
journal = {Zootaxa},
volume = {5566},
number = {2},
pages = {370-380},
doi = {10.11646/zootaxa.5566.2.7},
pmid = {40173572},
issn = {1175-5334},
abstract = {We provide a detailed taxonomic redescription of Lutjanus rufolineatus, based on six specimens collected from the Andaman Islands, India. The species' taxonomic status and distribution have historically been misinterpreted within Indian waters due to close similarities with congeners, leading to frequent misidentification. To address this, we performed comprehensive morphological and molecular analyses, including DNA barcoding and phylogenetic reconstruction, to confirm the identity of L. rufolineatus and clarify its relationships with related species. Our findings emphasize the value of thorough taxonomic assessment in delineating species boundaries, particularly for understudied marine fauna. Additionally, this research fills critical gaps in the taxonomy of Indian marine fishes, addressing past ambiguities and enhancing regional biodiversity records. By integrating morphological and molecular data, this study underscores the importance of precise species identification for improved biodiversity conservation and management efforts in the Indo-Pacific.},
}
@article {pmid40173511,
year = {2025},
author = {Zaldívar-Riverón, A and Castañeda-Osorio, R and Shaw, SR},
title = {Three new species and phylogenetic affinity of the neotropical genus Sericobracon Shaw (Braconidae: Doryctinae).},
journal = {Zootaxa},
volume = {5613},
number = {1},
pages = {171-185},
doi = {10.11646/zootaxa.5613.1.9},
pmid = {40173511},
issn = {1175-5334},
abstract = {Sericobracon Shaw is a small doryctine genus which was erected based on two species from Trinidad and the U.S. Virgin Islands (St. Croix) in the Caribbean Sea (S. arimaensis Shaw and S. evansi Shaw). Its type species, S. arimaensis, was reported as endoparasitoid of an Embioptera species, which is a unique biology for known Braconidae. Here we describe three new species of Sericobracon from Costa Rica: S. paulmarshi Zaldívar-Riverón &amp; Shaw, S. puravida Zaldívar-Riverón &amp; Shaw, and S. zunigai Zaldívar-Riverón &amp; Shaw. The former species is characterized with DNA barcoding, providing the first such molecular data for any species in this genus. We also investigated the phylogenetic affinity of the genus within the subfamily Doryctinae based on nuclear UCE data. Sericobracon was recovered within the main Neotropical doryctine clade closely related to Bolivar Zaldívar-Riverón &amp; Rodríguez-Jiménez and Parallorhogas Marsh. We discuss the higher taxonomic classification of Sericobracon and the latter two genera within the Doryctinae based on these relationships recovered and their shared morphological features. A key to species and digital photographs of the five described species of Sericobracon are provided.},
}
@article {pmid40173502,
year = {2025},
author = {Jaroenchaiwattanachote, C and Pramual, P and Wangwasit, K and Bunchalee, P and Thanee, I},
title = {Integrative taxonomy and DNA barcoding of Thai Caddisflies (Trichoptera), with the description of a new Species.},
journal = {Zootaxa},
volume = {5613},
number = {2},
pages = {307-322},
doi = {10.11646/zootaxa.5613.2.6},
pmid = {40173502},
issn = {1175-5334},
abstract = {Caddisflies (Trichoptera) are abundant and diverse aquatic insects. Their immature stages inhabit a wide range of aquatic environments, making them ideal candidates for water quality biomonitoring. However, the limited morphological characteristics available for species identification in the immature stages pose a significant challenge to their application in biomonitoring. In this study, we evaluated the effectiveness of DNA barcoding, based on mitochondrial cytochrome c oxidase I (COI) sequences, for species identification of caddisflies in Thailand. A total of 1,487 adult specimens were collected and morphologically identified into 13 species across 8 genera and 4 families. From these taxa, 88 COI sequences were generated from representative specimens. Maximum intraspecific genetic divergence ranged from 0% to 3.08%. Only three species were successfully matched to COI sequences in the BOLD database, while nine species are reported here for the first time, and one species remained ambiguous. Integrating COI barcoding sequences with morphological data revealed that one species, morphologically similar to Triplectides indicus (Walker 1852), represents a novel species, Triplectides buengkanensis sp. nov. We provide a detailed description, illustrations, diagnostic features, and DNA barcoding sequences for this new species.},
}
@article {pmid40173501,
year = {2025},
author = {Kerkig, P and Quicke, DLJ and Latibari, MH and Butcher, BA},
title = {World checklist of the genus Lipolexis Förster (Hymenoptera, Braconidae, Aphidiinae) with description of a new species from Thailand.},
journal = {Zootaxa},
volume = {5613},
number = {2},
pages = {323-336},
doi = {10.11646/zootaxa.5613.2.7},
pmid = {40173501},
issn = {1175-5334},
abstract = {We describe and illustrate a new species of the aphidiine braconid genus Lipolexis Förster, Lipolexis khaoyaiensis sp. nov., from Thailand, using an integrative approach. Morphologically, the new species is similar to L. peregrinus Tomanović and Kocić, 2020, but molecular analysis showed clear separation of at least 27 independent Lipolexis lineages, only eight of which correspond to previously known species, plus the one which represents the new species described here. A molecular phylogeny based on all available barcodes support that the genus comprises two well supported clades, with L. khaoyaiensis sp. nov. being recovered in the gracilis species-group with strong support (100% ultrafast bootstrap). A modified section of the identification key to species of Lipolexis is added to include the new species. Reported host associations for each of the described species as well as a distribution map of all records of species plus provenances of all barcoded specimens is provided.},
}
@article {pmid40173486,
year = {2025},
author = {Lee, DJ and Roh, SJ},
title = {A new species of the genus Unilepidotricha (Lepidoptera, Meessiidae) from Ulleungdo island, Korea.},
journal = {Zootaxa},
volume = {5613},
number = {3},
pages = {585-592},
doi = {10.11646/zootaxa.5613.3.10},
pmid = {40173486},
issn = {1175-5334},
abstract = {In this study, we describe a new species, Unilepidotricha ulleungensis sp. nov., from Korea. All available information on U. ulleungensis is presented, including collecting locations and illustrations of adult and male genitalia. Additionally, DNA barcodes for the species are provided.},
}
@article {pmid40170826,
year = {2025},
author = {Liu, Y and Liu, K and Dong, W and Dong, S and Wang, Y and Xu, C and Li, E and Sun, J},
title = {Chloroplast Genome Evolution of Hamamelidaceae at Subfamily Level.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71141},
pmid = {40170826},
issn = {2045-7758},
abstract = {The Hamamelidaceae is significant for its contributions to construction, furniture making, and ornamental use, including 26 genera and 119 species. However, complete chloroplast genome sequences of Hamamelidaceae species have been reported less frequently. In this study, five species were newly sequenced, and seven others available complete chloroplast genomes were added to compare the chloroplast genome evolution in Hamamelidaceae at the subfamily level. The results indicated that the chloroplast genome size ranged from 158,116 to 159,941 bp, encoding 79 to 81 protein-coding genes, four ribosomal RNA genes, and 30 to 31 transfer RNA genes. A robust phylogenetic tree of Hamamelidaceae was obtained using complete chloroplast genomes, supporting that all Hamamelidaceae species formed a monophyletic group and divided into four subfamilies. Exbucklandioideae was the first diverged group within Hamamelidaceae, followed by Mytilarioideae, Disanthoideae, and Hamamelidoideae, which formed a clade. Furthermore, three new potential DNA barcodes were provided: trnH-psbA, psbJ-petA, and ycf1. This study confirms that the complete chloroplast genome data provide a more accurate and confident resolution of the phylogenetic relationships within the Hamamelidaceae. These new genomic data not only enhance the understanding of genome evolution but also provide a better understanding of the phylogenetic relationships of Hamamelidaceae.},
}
@article {pmid40170416,
year = {2025},
author = {Surmacz, B and Vecchi, M and Fontaneto, D and Budzik, K and Godziek, J and Matsko, Y and Stec, D},
title = {COI Metabarcoding With a Curated Reference Database and Optimized Protocol Provides a Reliable Species-Level Diversity Assessment of Tardigrades.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.12972},
pmid = {40170416},
issn = {1749-4877},
support = {2022/45/N/NZ8/01992//the National Science Centre, Poland/ ; 2022/44/C/NZ8/00050//the National Science Centre, Poland/ ; //the National Biodiversity Future Centre (NBFC)/ ; CN00000033//the Italian Ministry of University and Research, PNRR, Missione 4 Componente 2, "Dalla ricerca all'impresa," Investimento 1.4/ ; },
abstract = {DNA metabarcoding is revolutionizing biodiversity research by providing rapid and efficient ways of collecting species occurrence data. However, it has not yet been effectively applied to many taxonomic groups, mainly due to a significant lack of reference sequences and dedicated protocols. One such group is the tardigrades-a charismatic phylum of microinvertebrates known for their extremophilic and cryptobiotic capabilities. In this study, we provide the first curated database of 3194 tardigrade COI sequences sourced from public databases and supplemented with newly produced barcodes. We demonstrate tardigrade metabarcoding in action with optimized PCR primers and a sample processing protocol using 78 samples collected in Poland and Italy. The metabarcoding revealed the presence of more than a hundred operational taxonomic units classified as Tardigrada, representing 23 genera. We compared the metabarcoding results with a morphological survey, which revealed the presence of the same genera, but a lower number of species-level taxa identified morphologically. We observed congruent patterns of tardigrade species richness and taxonomic composition between metabarcoding and morphological surveys in both within-sample and regional fauna composition levels. The metabarcoding had a higher discriminatory power, revealing cryptic diversity, and distinguishing species belonging to taxonomically challenging species complexes. By combining metabarcoding with morphological study, we were able to find rare taxa, including novel biogeographic records and putative species new to science, showing also that this approach can be extremely powerful and effective in meiofauna research.},
}
@article {pmid40169572,
year = {2025},
author = {Martino, N and Yan, H and Abbott, G and Fahlberg, M and Forward, S and Kim, KH and Wu, Y and Zhu, H and Kwok, SJJ and Yun, SH},
title = {Large-scale combinatorial optical barcoding of cells with laser particles.},
journal = {Light, science &amp; applications},
volume = {14},
number = {1},
pages = {148},
doi = {10.1038/s41377-025-01809-x},
pmid = {40169572},
issn = {2047-7538},
support = {R01-EB033155//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01-EB034687//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R44CA281529//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
abstract = {The identification of individual cells is crucial for advancements in single-cell analysis. Optically readable barcodes provide a means to distinguish and track cells through repeated, non-destructive measurements. Traditional fluorophore-based methods are limited by the finite number of unique barcodes they can produce. Laser particles (LPs), which emit narrowband peaks over a wide spectral range, have emerged as a promising technology for single-cell barcoding. Here, we demonstrate the use of multiple LPs to generate combinatorial barcodes, enabling the identification of a vast number of live cells. We introduce a theoretical framework for estimating the number of LPs required for unique barcodes and the expected identification error rate. Additionally, we present an improved LP-tagging method that is highly effective across a variety of cell types and evaluate its biocompatibility. Our experimental results show successful barcoding of several million cells, closely matching our theoretical predictions. This research marks a significant step forward in the scalability of LP technology for single-cell tracking and analysis.},
}
@article {pmid40168522,
year = {2025},
author = {Men, J and Lv, S and Wang, Y and Wang, X and Bi, Y and Bi, S},
title = {Stimuli-Responsive Barcode Probe-Mediated Self-Powered Biosensor Enables Dual-Signal Amplification for Ultrasensitive Detection of Circulating Tumor Cells.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c00601},
pmid = {40168522},
issn = {1520-6882},
abstract = {Circulating tumor cells (CTCs) serve as valuable biomarkers for early cancer diagnosis in low abundance in the bloodstream. Therefore, the development of a biosensor for the ultrasensitive detection of CTCs is imperative. Herein, an enzymatic biofuel cell (EBFC)-based self-powered biosensor has been developed in which the recognition of CTCs with a stimuli-responsive barcode probe (SRBP) triggers the opening of a circuit "lock" and further activates the DNA dual-signal amplification, achieving ultrasensitive detection of CTCs. The SRBP is fabricated based on the hyaluronic acid (HA)-modified ZIF-8 framework, which is functionalized with Trigger and H2 at a certain ratio and further connected on magnetic beads via the hybridization between Trigger and the aptamer (Apt) of HepG2 cells. The specific recognition of target CTCs, hepatocellular carcinoma cell line G2 (HepG2) cells, by Apt results in the release of SRBP. Upon the stimuli of glutathione (GSH) under weakly acidic conditions (pH 5-6), ZIF-8 is disintegrated, leading to the releasing of Zn[2+], accompanied by the liberation of H2 and Trigger. As a result, the dual-signal amplification, that is, DNAzyme-mediated cyclic cleavage of substrate-linked SiO2 (Sub-SiO2) on the bioanode and catalytic hairpin assembly (CHA) on the biocathode, is activated. This self-powered biosensor achieves ultrasensitive detection of HepG2 cells with a detection limit as low as 3 cells/mL and excellent specificity, which exhibits substantial potential for early diagnosis of cancers.},
}
@article {pmid40166335,
year = {2025},
author = {Schaefer, NK and Pavlovic, BJ and Pollen, AA},
title = {CellBouncer, A Unified Toolkit for Single-Cell Demultiplexing and Ambient RNA Analysis, Reveals Hominid Mitochondrial Incompatibilities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.23.644821},
pmid = {40166335},
issn = {2692-8205},
abstract = {Pooled processing, in which cells from multiple sources are cultured or captured together, is an increasingly popular strategy for droplet-based single cell sequencing studies. This design allows efficient scaling of experiments, isolation of cell-intrinsic differences, and mitigation of batch effects. We present CellBouncer, a computational toolkit for demultiplexing and analyzing single-cell sequencing data from pooled experiments. We demonstrate that CellBouncer can separate and quantify multi-species and multi-individual cell mixtures, identify unknown mitochondrial haplotypes in cells, assign treatments from lipid-conjugated barcodes or CRISPR sgRNAs, and infer pool composition, outperforming existing methods. We also introduce methods to quantify ambient RNA contamination per cell, infer individual donors' contributions to the ambient RNA pool, and determine a consensus doublet rate harmonized across data types. Applying these tools to tetraploid composite cells, we identify a competitive advantage of human over chimpanzee mitochondria across 10 cell fusion lines and provide evidence for inter-mitochondrial incompatibility and mito-nuclear incompatibility between species.},
}
@article {pmid40166332,
year = {2025},
author = {Khalil, A and Dinh, T and Parks, M and Obeng, RC and Gryder, B and Kresak, A and Wang, Y and Maltas, J and Bedrock, M and Wei, X and Faber, Z and Rahm, M and Scott, J and LaFramboise, T and Wang, Z and McFarland, C},
title = {In Vivo Multiplexed Modeling Reveals Diverse Roles of the TBX2 Subfamily and Egr1 in Ras -Driven Lung Adenocarcinoma.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.15.642187},
pmid = {40166332},
issn = {2692-8205},
abstract = {The TBX2 subfamily of T-box transcription factors (including Tbx2 , Tbx3 , Tbx4 , Tbx5) plays an essential role in lung development. Downregulation of these genes in human Lung adenocarcinoma (LUAD) suggests that these genes may be tumor suppressive, however because downregulation appears to occur primarily via epigenetic change, it remains unclear if these changes causally drive tumor progression or are merely the consequence of upstream events. Herein, we developed the first multiplexed mouse model to study the impact of TBX2 subfamily loss, alongside associated signaling genes Egr1 , Chd2 , Tnfaip3a , and Atf3 , in Ras -driven lung cancer. Using TuBa-seq, a high-throughput tumor-barcoding system, we quantified the growth effects of these knockouts during early and late tumorigenesis. Chd2 loss consistently suppressed tumor progression, while Tbx2 loss exhibited stage-dependent effects. Notably, Egr1 emerged as a potent tumor suppressor, with its knockout increasing tumor size (∼5x) at 20 weeks, surpassing Rb1 loss. Transcriptomic analyses of Egr1 -deficient tumors suggested immune dysregulation, including heightened inflammation and potential markers of T cell exhaustion in the tumor microenvironment. These findings indicate that Egr1 may play a role in suppressing tumor growth through modulating immune dynamics, offering new insights into the interplay between tumor progression and immune regulation in LUAD.},
}
@article {pmid40166312,
year = {2025},
author = {Monge, M and Giovanetti, SM and Ravishankar, A and Sadhu, MJ},
title = {Highly replicated experiments studying complex genotypes using nested DNA barcodes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.18.643964},
pmid = {40166312},
issn = {2692-8205},
abstract = {Many biological experiments involve studying the differences caused by genetic modifications, including genotypes composed of modifications at more than one locus. However, as the number and complexity of the genotypes increases, independently generating and tracking the necessary number of biological replicate samples becomes a major challenge. We developed a barcode-based method to track large numbers of independent replicates of combinatorial genotypes in a pooled format, enabling robust detection of subtle phenotypic differences. To construct a plasmid library of combinatorial genotypes, we utilized a nested serial cloning process to combine gene variants of interest that have associated DNA barcodes. The final plasmids each contain variants of multiple genes of interest, and a combined barcode that specifies the genotype of all the genes while also encoding a random sequence for tracking individual replicates. Sequencing of the pool of barcodes by next-generation sequencing allows the whole population to be studied in a single flask, enabling a high degree of replication even for complex genotypes. Using this approach, we tested the functionality of combinations of yeast, human, and null orthologs of the nucleotide excision repair factor I (NEF-1) complex and found that cells expressing all three yeast NEF-1 subunits had superior growth in DNA-damaging conditions. We also assessed the sensitivity of our method by simulating downsampling of barcodes across different degrees of phenotypic differentiation. Our results demonstrate the utility of NICR barcodes for high-throughput combinatorial genetic screens and provide a scalable framework for exploring complex genotype-phenotype relationships.},
}
@article {pmid40166192,
year = {2025},
author = {Mazelis, I and Sun, H and Kulkarni, A and Torre, T and Klein, AM},
title = {Multi-step genomics on single cells and live cultures in sub-nanoliter capsules.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.14.642839},
pmid = {40166192},
issn = {2692-8205},
abstract = {Single-cell genomics encompasses a set of methods whereby hundreds to millions of cells are individually subjected to multiplexed assays including sequencing DNA, chromatin accessibility or modification, RNA, or combinations thereof [1,2] . These methods enable unbiased, systematic discovery of cellular phenotypes and their dynamics [1-3] . Many functional genomic methods, however, require multiple steps that cannot be easily scaled to high throughput, including assays on living cells. Here we develop capsules with amphiphilic gel envelopes (CAGEs), which selectively retain cells, mRNA, and gDNA, while allowing free diffusion of media, enzymes and reagents. CAGEs enable carrying out high-throughput assays that require multiple steps, including combining genomics with live-cell assays. We establish methods for barcoding CAGE DNA and RNA libraries, and apply them to measure persistence of gene expression programs by capturing the transcriptomes of tens of thousands of expanding clones in CAGEs. The compatibility of CAGEs with diverse enzymatic reactions will facilitate the expansion of the current repertoire of single-cell, high-throughput measurements and extend them to live-cell assays.},
}
@article {pmid40163932,
year = {2025},
author = {Richard Beaulieu, S and Ribéreau-Gayon, A and Devèze, T and Forbes, SL and Germain, H},
title = {Molecular identification of fungi associated with advanced decomposition at a human taphonomy facility in Canada.},
journal = {Forensic science international},
volume = {370},
number = {},
pages = {112451},
doi = {10.1016/j.forsciint.2025.112451},
pmid = {40163932},
issn = {1872-6283},
abstract = {Forensic taphonomy investigates the postmortem processes of human remains, focusing on the environmental factors that influence decomposition. Recent studies have highlighted the potential forensic relevance of fungi in this context, but the knowledge base remains limited. This study explored fungal communities associated with outdoor human decomposition at the REST[ES] facility in Quebec. Nested PCR amplification and Illumina MiSeq sequencing were used to identify fungal species on discolored patches of twelve samples of desiccated soft tissues from three donors. Twelve fungal species were putatively identified, some of which were previously unknown on human remains, including Leucosporidium yakuticum, Tausania pullulans, and Fusicolla species. These fungi may contribute to tissue discoloration and following longitudinal investigation, could serve as biomarkers for forensic reconstructions, including place and time of death. This study emphasizes the need for further research into the role of fungi in human decomposition processes and their applications in forensic science.},
}
@article {pmid40163300,
year = {2025},
author = {Umkehrer, C and Obenauf, A},
title = {Functional Lineage Tracing Using CaTCH.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2905},
number = {},
pages = {95-120},
pmid = {40163300},
issn = {1940-6029},
mesh = {*Cell Lineage/genetics ; *Flow Cytometry/methods ; Humans ; DNA Barcoding, Taxonomic/methods ; Animals ; Clone Cells ; },
abstract = {CaTCH is a functional lineage tracing tool using genetic barcodes to label and follow million of cell clones in a selection experiment. Furthermore, CaTCH allows to isolate specific cell clones from heterogeneous populations by their barcode. Thus, founding clones of a phenotype of interest can be retrospectively isolated alive using FACS (fluorescence-activated cell sorting), allowing to perform functional experiments. Example applications of this method are investigating the evolutionary selection of resistance to therapies or other evolutionary pressures.},
}
@article {pmid40162456,
year = {2024},
author = {Jose, AT and Kaur, T and Sarangi, S and Khan, S and Tripathi, S and Chandrasekaran, S and Kashwani, R},
title = {Innovations in denture marking: Forensic applications and clinical implications: A review.},
journal = {Bioinformation},
volume = {20},
number = {11},
pages = {1542-1548},
doi = {10.6026/9732063002001452},
pmid = {40162456},
issn = {0973-2063},
abstract = {Denture marking is a vital tool in forensic odontology and clinical practice, aiding in the identification of dental prostheses, especially in disaster victim identification and cases where traditional methods fail. Techniques are categorized into surface methods like engraving and laser etching and inclusion methods such as embedding RFID tags or barcodes. These markers provide reliable identification, assist in recovering lost prostheses and can be implemented at low cost in routine dental practice. Advancements like RFID technology have made denture marking more efficient and reliable. Overall, denture marking enhances patient safety, reduces redundancy and holds significant medico-legal value.},
}
@article {pmid40161029,
year = {2025},
author = {Mwamula, AO and Bae, CH and Kim, YS and Lee, DW},
title = {Description of Deladenus uljinensis n. sp., and additional DNA barcode data for Deladenus posteroporus (Nematoda: Neotylenchidae) from Korea.},
journal = {Journal of nematology},
volume = {57},
number = {1},
pages = {20250013},
doi = {10.2478/jofnem-2025-0013},
pmid = {40161029},
issn = {0022-300X},
abstract = {A new species of the genus Deladenus isolated from a dead red pine tree was characterized using morphometric and molecular DNA data. Deladenus uljinensis n. sp. is characterized by its lateral fields with six to seven lines, pharyngeal corpus without a distinct median bulb and lacking a chamber, esophageal-intestinal junction located immediately behind the nerve ring, hemizonid located posterior to nerve ring, excretory pore opening within the contour of hemizonid or just at the base of hemizonid, vulva with no lateral vulval flaps, post-uterine sac rudimentary or absent, vulva-anus distance ca. equal to tail length, tail conoid, gradually tapering to a broadly rounded terminus, and slender spicules, 18.5-21.5 μm long. The new species was compared with morphologically close species including D. gilanica, D. brevis, D. pakistanensis, D. oryzae, D. uteropinusus, D. aridus, and D. durus. Additionally, D. posteroporus was also characterized and the population represents the first record of the species outside its type locality. The phylogenetic relationships among species were reconstructed using 18S-rRNA, 28S-rRNA and COI gene sequences. Inferences from the more informative 28S-rRNA gene suggest that D. uljinensis n. sp. is a sister species to the morphologically close D. gilanica.},
}
@article {pmid40151624,
year = {2025},
author = {Sheng, W},
title = {The complete chloroplast genome of Gerbera piloselloides (L.) Cass., 1820 (Carduoideae, Asteraceae) and its phylogenetic analysis.},
journal = {Open life sciences},
volume = {20},
number = {1},
pages = {20251070},
pmid = {40151624},
issn = {2391-5412},
abstract = {Gerbera piloselloides (L.) Cass., 1820 of the genus Gerbera is of importance in Chinese ethnic medicine. In this research, the whole genome DNA of G. piloselloides was extracted and sequenced using the Illumina NovaSeq platform, its chloroplast genome was assembled and annotated, and its sequence characteristics were analyzed using bioinformatic methods. The results showed that its chloroplast genome has a length of 151,871 bp and contains 133 annotated genes, consisting of 88 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. In total, 202 simple sequence repeat sites and 43 long repeats were detected in G. piloselloides, mainly consisting of mono-nucleotide and tri-nucleotide repeats, with A/T as the major base composition. The chloroplast genome of G. piloselloides contains 22,772 codons, with leucine-coding codons being the most abundant. Comparative genomics showed that the genome structure, composition and variation were basically the same in the Asteraceae family. The phylogenetic tree analysis indicated a close relationship between the genus Atractylodes and Gerbera, consistent with the morphological classification. The research of the G. piloselloides chloroplast genome will lay a foundation for species discrimination, genetic evolution analysis, and DNA barcode construction in Gerbera plants.},
}
@article {pmid40151605,
year = {2025},
author = {Li, J and He, Q and Li, S and Yao, Z},
title = {Filling a zoogeographical gap in China: Taxonomic descriptions of six new spider species of the Pholcusphungiformes species group (Araneae, Pholcidae).},
journal = {ZooKeys},
volume = {1232},
number = {},
pages = {285-310},
pmid = {40151605},
issn = {1313-2989},
abstract = {The spiders of the Pholcusphungiformes species group in China are distributed across the Lüliang Mountains and the Yanshan-Taihang Mountains in northern China, and the Changbai Mountains, which border northeastern China and North Korea. This study presents the first collection of the P.phungiformes species group from mountainous regions situated between the Yanshan-Taihang and Changbai Mountains, revealing six new species: Pholcuschaoyang S. Li &amp; Yao, sp. nov., P.hebei S. Li &amp; Yao, sp. nov., P.huludao S. Li &amp; Yao, sp. nov., P.jinzhou S. Li &amp; Yao, sp. nov., P.liaoning S. Li &amp; Yao, sp. nov., and P.qin S. Li &amp; Yao, sp. nov. Detailed diagnoses, descriptions, photomicroscopy images, and DNA barcodes of new species are provided.},
}
@article {pmid40150400,
year = {2025},
author = {Tuncharoen, S and Panase, P and Panprommin, N and Wangkahart, E and Ruenkoed, S and Mongkolwit, K and Panprommin, D},
title = {New Data on Rhinogobius chiengmaiensis and Rhinogobius mekongianus in Thailand by DNA Barcoding and Morphological Methods.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/ani15060871},
pmid = {40150400},
issn = {2076-2615},
support = {Fundamental Fund 2025, Grant No. 5051/2567//University of Phayao and Thailand Science Research and Innovation Fund/ ; },
abstract = {A combination of morphological analysis and DNA barcoding (partial sequences of the cytochrome c oxidase I (COI) gene) was used to differentiate four gobiid fish species in the family Oxudercidae. Rhinogobius chiengmaiensis and Rhinogobius mekongianus were found in Thailand, while Eugnathogobius siamensis and Pseudogobiopsis oligactis were used for comparative purposes. Morphological identification relied on appearances, counts, and measurements. The 707-base pair COI sequences from eleven samples of four gobiid species were compared with reference sequences in public databases to confirm their scientific names. The average AT content was 51.8 ± 0.5% and the GC content was 48.2 ± 0.5%. Intraspecific genetic distances ranged from 0.00-0.28%, while interspecific genetic distances ranged from 0.86-16.63%. A neighbor-joining (NJ) phylogenetic tree depicted the relationships among the COI sequences of these species. Morphological analysis and COI sequences successfully distinguished the four gobiid species. Notably, the COI sequences of R. chiengmaiensis, R. mekongianus, and E. siamensis were previously unreported, hence, this study is the first report to add their sequences to public databases. These results can serve as valuable information for the management of aquatic resources, conservation, and aquaculture efforts.},
}
@article {pmid40149407,
year = {2025},
author = {Chatzoglou, E and Tsaousi, N and Spetsieri, A and Malandrakis, EE and Miliou, H},
title = {Rapid Detection of Epinephelus Species Substitution in the Greek Market Using High-Resolution Melting Analysis.},
journal = {Genes},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/genes16030255},
pmid = {40149407},
issn = {2073-4425},
mesh = {Animals ; Greece ; *Polymorphism, Single Nucleotide ; *DNA Barcoding, Taxonomic/methods ; *Seafood ; Bass/genetics/classification ; Endangered Species ; },
abstract = {Background/Objectives: Fish are vital in the Mediterranean diet, offering protein, nutrients, and ω-3 fatty acids. Greek consumers favor wild-caught, high-value fish like the dusky grouper (Epinephelus marginatus) classified as "vulnerable" and the white grouper (Epinephelus aeneus) classified as "near threatened" species, according to the IUCN Red List. Due to their premium prices and complex supply chains, these species are susceptible to fraud, especially through mislabeling. This practice not only deceives consumers but also poses health risks and encourages illegal fishing. DNA-based methods have shown effectiveness in accurately identifying species, even in processed samples. The aim of this study is to apply high-resolution melting analysis (HRM) as a rapid, effective method for monitoring the appropriate labeling of the two Epinephelus species in the Greek market. Methods: In this study, fresh fish from Greek catches as well as cooked, frozen, and filleted samples collected from the Greek market were identified using DNA barcoding. HRM analysis based on single nucleotide polymorphisms (SNPs) was used to differentiate between locally sourced E. marginatus and E. aeneus from their imported counterparts or from other species available in the Greek market that could be used in substitution incidents. Results: Using HRM analysis, cases of species mislabeling were identified and were also confirmed using sequencing. Conclusions: HRM analysis proved to be an accurate and cost-effective method for rapidly processing a large number of samples; therefore, it could serve as a valuable tool in extensive market controls as well as for bio-diversity conservation monitoring.},
}
@article {pmid40149301,
year = {2025},
author = {Arakelyan, A and Sirunyan, T and Khachatryan, G and Hakobyan, S and Minasyan, A and Nikoghosyan, M and Hakobyan, M and Chavushyan, A and Martirosyan, G and Hakobyan, Y and Binder, H},
title = {Assigning Transcriptomic Subtypes to Chronic Lymphocytic Leukemia Samples Using Nanopore RNA-Sequencing and Self-Organizing Maps.},
journal = {Cancers},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/cancers17060964},
pmid = {40149301},
issn = {2072-6694},
support = {21AG-1F021//State Committee of Science/ ; },
abstract = {Background/Objectives: Massively parallel sequencing technologies have advanced chronic lymphocytic leukemia (CLL) diagnostics and precision oncology. Illumina platforms, while offering robust performance, require substantial infrastructure investment and a large number of samples for cost-efficiency. Conversely, third-generation long-read nanopore sequencing from Oxford Nanopore Technologies (ONT) can significantly reduce sequencing costs, making it a valuable tool in resource-limited settings. However, nanopore sequencing faces challenges with lower accuracy and throughput than Illumina platforms, necessitating additional computational strategies. In this paper, we demonstrate that integrating publicly available short-read data with in-house generated ONT data, along with the application of machine learning approaches, enables the characterization of the CLL transcriptome landscape, the identification of clinically relevant molecular subtypes, and the assignment of these subtypes to nanopore-sequenced samples. Methods: Public Illumina RNA sequencing data for 608 CLL samples were obtained from the CLL-Map Portal. CLL transcriptome analysis, gene module identification, and transcriptomic subtype classification were performed using the oposSOM R package for high-dimensional data visualization with self-organizing maps. Eight CLL patients were recruited from the Hematology Center After Prof. R. Yeolyan (Yerevan, Armenia). Sequencing libraries were prepared from blood total RNA using the PCR-cDNA sequencing-barcoding kit (SQK-PCB109) following the manufacturer's protocol and sequenced on an R9.4.1 flow cell for 24-48 h. Raw reads were converted to TPM values. These data were projected into the SOMs space using the supervised SOMs portrayal (supSOM) approach to predict the SOMs portrait of new samples using support vector machine regression. Results: The CLL transcriptomic landscape reveals disruptions in gene modules (spots) associated with T cell cytotoxicity, B and T cell activation, inflammation, cell cycle, DNA repair, proliferation, and splicing. A specific gene module contained genes associated with poor prognosis in CLL. Accordingly, CLL samples were classified into T-cell cytotoxic, immune, proliferative, splicing, and three mixed types: proliferative-immune, proliferative-splicing, and proliferative-immune-splicing. These transcriptomic subtypes were associated with survival orthogonal to gender and mutation status. Using supervised machine learning approaches, transcriptomic subtypes were assigned to patient samples sequenced with nanopore sequencing. Conclusions: This study demonstrates that the CLL transcriptome landscape can be parsed into functional modules, revealing distinct molecular subtypes based on proliferative and immune activity, with important implications for prognosis and treatment that are orthogonal to other molecular classifications. Additionally, the integration of nanopore sequencing with public datasets and machine learning offers a cost-effective approach to molecular subtyping and prognostic prediction, facilitating more accessible and personalized CLL care.},
}
@article {pmid40148595,
year = {2025},
author = {Qian, N and Weinstein, JA},
title = {Spatial transcriptomic imaging of an intact organism using volumetric DNA microscopy.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40148595},
issn = {1546-1696},
support = {NIH-1R35GM143017-01//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; Moore Inventor Fellowship//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; Runyon-Rachleff Innovation Award//Damon Runyon Cancer Research Foundation (Cancer Research Fund of the Damon Runyon-Walter Winchell Foundation)/ ; NSF-2121044//National Science Foundation (NSF)/ ; },
abstract = {Lymphatic, nervous and tumor tissues exhibit complex physiology arising from three-dimensional interactions within genetically unique microenvironments. Here we develop a technology capable of volumetrically imaging transcriptomes, genotypes and morphologies in a single measurement, without relying on prior knowledge of spatial organization or genetic sequences. Our method extends DNA microscopy into three dimensions at scales involving 10[7] molecules by forming a distributed intermolecular network of proximal unique DNA barcodes tagging complementary DNA molecules inside the specimen. After sequencing the DNA-encoded network, an image of molecular positions is inferred using geodesic spectral embeddings, a dimensionality reduction approach that we show to be especially suitable for this data-inverse problem. Applying whole-transcriptome volumetric DNA microscopy to intact zebrafish embryos, we demonstrate that three-dimensional image inference recapitulates zebrafish morphology and known gene expression patterns, capturing the spatial organization of gene sequences. Our extension of spatial genetic measurements to three dimensions, independent of prior templates, opens the door to detailed joint resolution of genomics and morphology in biological tissues.},
}
@article {pmid40144949,
year = {2025},
author = {Pešić, V and Zawal, A and Gülle, P and Gülle, &#x130; and Jovanović, M and Bańkowska, A and Musielak, S and Smit, H},
title = {Water mite diversity from southwestern Türkiye through the lens of the DNA barcodes, with the description of one new species (Acari, Hydrachnidia).},
journal = {ZooKeys},
volume = {1232},
number = {},
pages = {205-236},
pmid = {40144949},
issn = {1313-2989},
abstract = {This study presents the molecular and morphological results from an analysis of water mites collected in southwestern Türkiye. 83 COI barcodes are provided, clustered into 40 BINs, with 23 BINs being unique and deposited for the first time in the Barcode of Life Data Systems (BOLD). The first DNA barcodes for eight water mite species are uploaded into the BOLD database. In total, 34 water mite species were identified and one of them, Iranothyasmarismortui (Gerecke, 1999) is newly reported from Türkiye. Iranothyasalhajarica Pešić, Gerecke &amp; Smit, 2009 is excluded from the fauna of Türkiye. Sperchonfundamentalis Bader &amp; Sepasgozarian, 1980, a species previously synonymized with S.glandulosus Koenike, 1886 is resurrected as a valid species. One species, Atractidesturani Pešić, Zawal, Gülle &amp; Smit, sp. nov. (Hygrobatidae), is described as new to science.},
}
@article {pmid40144381,
year = {2025},
author = {Kryukov, AA and Yurkov, AP and Gorbunova, AO and Kudriashova, TR and Gorenkova, AI and Kosulnikov, YV and Laktionov, YV},
title = {Evaluation of the biodiversity of arbuscular mycorrhizal fungi during regenerative succession in quarries.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {29},
number = {1},
pages = {72-78},
doi = {10.18699/vjgb-25-09},
pmid = {40144381},
issn = {2500-0462},
abstract = {Arbuscular mycorrhizal fungi (AMF) play a key role in the regenerative successions of plant communities after anthropogenic disturbances, particularly in quarries. AMF help plants with water and mineral nutrition, contributing to the restoration rate of vegetation cover. The research is aimed to study the biodiversity of AMF using molecular genetic methods at different stages of overgrowth of two quarries in the Leningrad region. Molecular genetic identification of fungi was carried out using Illumina MiSeq analysis of the ITS1 and ITS2 regions as barcodes for the identification of operational taxonomic units (OTUs) with species-level identification. An adapted and error-checked AMF genetic sequence database from NCBI was used as a reference. The study applied an optimized nucleic acid isolation technique for sandy soils. The results showed maximum AMF biodiversity at the initial stages of overgrowth - pioneer and grass stages - with minimum diversity observed at the shrub stage, where it decreased by five times. At the forest stage, the biodiversity of AMF was almost restored to the level seen at the grass stage. It has been shown that the biodiversity and species composition of AMF can vary greatly between the stages of regenerative succession and probably depends primarily on the biodiversity of grasses, with which AMF most effectively enter into symbiotic relationships. The analysis showed a reliable negative correlation between the number of AMF species and the number of woody plant species. Such studies can aid in understanding how plant-fungal symbiosis develops in regenerative successions and which AMF most effectively contribute to vegetation cover restoration.},
}
@article {pmid40144380,
year = {2025},
author = {Gokhman, VE and Ryabinin, AS and Bykov, RA and Ilinsky, YY},
title = {The lowest chromosome number in the family Pteromalidae (Hymenoptera: Chalcidoidea): the karyotype and other genetic features of Pachycrepoideus vindemmiae (Rondani, 1875).},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {29},
number = {1},
pages = {108-112},
doi = {10.18699/vjgb-25-12},
pmid = {40144380},
issn = {2500-0462},
abstract = {Various genetic features of the hitman strain of the widespread parasitoid of Drosophilidae (Diptera), Pachycrepoideus vindemmiae (Rondani, 1875) (Pteromalidae, Pachyneurinae) were studied. This strain was established and is maintained at the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences (Novosibirsk, Russia). An analysis of air-dried chromosome preparations from prepupae of this parasitoid showed that it has n = 4 and 2n = 8 in males and females, respectively, which is the lowest known chromosome number in the family Pteromalidae. All chromosomes in the karyotype of this species are metacentric. The first and second chromosomes are of similar size, the remaining ones are substantially shorter. The same results were obtained for an additional strain of this species kept at the Moscow State University (Moscow, Russia). A comparison of the DNA sequence of the barcoding region of the mitochondrial cytochrome c oxidase (COI) gene of the hitman strain of P. vindemmiae with those available from the GenBank and BoLD databases demonstrated that this strain clustered together with conspecifics originating from China, Turkey and Italy. Despite certain endosymbionts being previously reported for the genus Pachycrepoideus Ashmead, 1904 as well as for P. vindemmiae itself, the hitman strain turned out to be free of endosymbiotic bacteria in the genera Arsenophonus Gherna et al., 1991, Cardinium Zchori-Fein et al., 2004, Rickettsia da Rocha-Lima, 1916, Spiroplasma Saglio et al., 1973 and Wolbachia Hertig, 1936. The above-mentioned results improve our knowledge of various genetic features of parasitoids of the family Pteromalidae and those of P. vindemmiae in particular.},
}
@article {pmid40144376,
year = {2025},
author = {Smirnov, AV and Korablev, AN and Serova, IA and Yunusova, AM and Muravyova, AA and Valeev, ES and Battulin, NR},
title = {Studying concatenation of the Cas9-cleaved transgenes using barcodes.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {29},
number = {1},
pages = {26-34},
doi = {10.18699/vjgb-25-04},
pmid = {40144376},
issn = {2500-0462},
abstract = {In pronuclear microinjection, the Cas9 endonuclease is employed to introduce in vivo DNA double-strand breaks at the genomic target locus or within the donor vector, thereby enhancing transgene integration. The manner by which Cas9 interacts with DNA repair factors during transgene end processing and integration is a topic of considerable interest and debate. In a previous study, we developed a barcode-based genetic system for the analysis of transgene recombination following pronuclear microinjection in mice. In this approach, the plasmid library is linearized with a restriction enzyme or a Cas9 RNP complex at the site between a pair of barcodes. A pool of barcoded molecules is injected into the pronucleus, resulting in the generation of multicopy concatemers. In the present report, we compared the effects of in vivo Cas9 cleavage (RNP+ experiment) and in vitro production of Cas9- linearized transgenes (RNP- experiment) on concatenation. In the RNP+ experiment, two transgenic single-copy embryos were identified. In the RNP- experiment, six positive embryos were identified, four of which exhibited lowcopy concatemers. Next-generation sequencing (NGS) analysis of the barcodes revealed that 53 % of the barcoded ends had switched their initial library pairs, indicating the involvement of the homologous recombination pathway. Out of the 20 transgene-transgene junctions examined, 11 exhibited no mutations and were presumably generated through re-ligation of Cas9-induced blunt ends. The majority of mutated junctions harbored asymmetrical deletions of 2-4 nucleotides, which were attributed to Cas9 end trimming. These findings suggest that Cas9-bound DNA may present obstacles to concatenation. Conversely, clean DNA ends were observed to be joined in a manner similar to restriction-digested ends, albeit with distinctive asymmetry. Future experiments utilizing in vivo CRISPR/ Cas cleavage will facilitate a deeper understanding of how CRISPR-endonucleases influence DNA repair processes.},
}
@article {pmid40141343,
year = {2025},
author = {Cai, S and Liao, X and Xi, Y and Chu, Y and Liu, S and Su, H and Dou, D and Xu, J and Xiao, S},
title = {Screening and Application of DNA Markers for Novel Quality Consistency Evaluation in Panax ginseng.},
journal = {International journal of molecular sciences},
volume = {26},
number = {6},
pages = {},
doi = {10.3390/ijms26062701},
pmid = {40141343},
issn = {1422-0067},
support = {CI2023E002//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; 2023YFC3504000//National Key Research and Development Program of China/ ; ZZ13-YQ-047//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; },
mesh = {*Panax/genetics ; Genetic Markers ; *Quality Control ; Microsatellite Repeats/genetics ; Medicine, Chinese Traditional/standards ; Genetic Variation ; Genome, Chloroplast ; Polymorphism, Genetic ; DNA, Plant/genetics ; DNA Barcoding, Taxonomic/methods ; },
abstract = {Quality control remains a challenge in traditional Chinese medicine (TCM). This study introduced a novel genetic-based quality control method for TCM. Genetic variations in ginseng were evaluated across whole-genome, chloroplast genome, and ITS2 DNA barcode dimensions. Significant genetic variations were found in whole-genome comparison, leading to the use of inter-simple sequence repeat markers to assess the genetic diversity of ginseng decoction pieces (PG), garden ginseng (GG), and ginseng under forest (FG). Fingerprints of ginseng samples revealed instability within some batches. These evaluations were transformed into information entropy to calculate the size of Hardy-Weinberg equilibrium population (HWEP). FG had significantly higher genetic and chemical minimum HWEP than GG (p < 0.05). Notably, a significant positive correlation was observed between the minimum HWEP for genetics and for chemistry (r = 0.857, p = 0.014). Genetic polymorphism analysis of ginseng has the potential to evaluate chemical quality consistency, offering a new method to ensure quality consistency in TCM.},
}
@article {pmid40139723,
year = {2025},
author = {Singh, M and Zhang, M and Espinal-Ruiz, M and Rathnayake, S and Xue, J and Shi, J and Liu, X and Hanner, R and Corradini, MG},
title = {Maple Syrup Adulteration: Fluorescence Fingerprints as a Source of Information for Enhanced Detection.},
journal = {Journal of AOAC International},
volume = {},
number = {},
pages = {},
doi = {10.1093/jaoacint/qsaf029},
pmid = {40139723},
issn = {1944-7922},
abstract = {BACKGROUND: Maple syrup is often adulterated by dilution or substitution with other syrups due to its high demand and price. Fingerprinting techniques, e.g., DNA barcoding, detect adulteration in other foods. However, extensive processing during the transformation of sap into syrup degrades the genetic material, lowering the efficacy of this approach. In contrast, fluorescence fingerprints (EEMs) rely on a sample's intrinsic fluorophores to provide valuable information for detecting adulteration.<br><br>OBJECTIVE: This study evaluates the capabilities and limitations of EEMs to scout for adulteration markers and discriminate between pure and adulterated maple syrup samples.<br><br>METHODS: EEMs of pure amber and dark maple syrups and admixtures with common adulterants (beet, corn, and rice syrups at 1-50%) were obtained using a spectrophotometer (&#x3bb;ex=250-500&#x2009;nm, and &#x3bb;em=280-650&#x2009;nm).&#x202f;The major components of the EEMs were identified using PARAFAC and confirmed by LC-MS/MS. The ratio of intensities of the two most prevalent EEM features was calculated. An artificial neural network (ANN) and a convolutional neural network (CNN) were developed to analyze the EEMs based on emissions at two selected excitation wavelengths and the full EEM image, respectively, to discriminate presence and level of adulteration.<br><br>RESULTS: EEMs of the samples allowed identifying valuable discriminatory information. The efficacy of the ratio of the emission intensities at &#x3bb;em=350 and 425 (I425/I350) when &#x3bb;ex= 290&#x2009;nm to identify potential fraud (70-86% correct identifications) depended on the adulterant. This ratio was particularly effective for beet syrup adulteration, even at concentrations <2%. Applying machine learning algorithms improved detection for all adulterants. ANN correctly identified adulteration type and level (90 &amp; 82%). The CNN approach accurately classified 75-99% of adulterated syrups but required additional computational power and denser data sets.<br><br>CONCLUSION: This study aids in providing a quick, non-destructive and green monitoring tool for maple syrup adulteration based on its intrinsic fluorophores.<br><br>HIGHLIGHTS: Maple syrup is often adulterated with other syrups due to high demand and price. DNA barcoding is ineffective in detecting maple syrup adulteration due to DNA degradation. Fluorescence fingerprints or EEMs allow scouting for discriminatory markers in maple syrup. Machine learning algorithms (ANN and CNN) applied to EEM data can aid detection.},
}
@article {pmid40134468,
year = {2025},
author = {Ge, X and Wang, J and Chai, L and Yan, C},
title = {Descriptions of hitherto unknown larvae of the genus Hydropsyche Pictet, 1834 from China (Trichoptera, Hydropsychidae).},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e151321},
pmid = {40134468},
issn = {1314-2828},
abstract = {BACKGROUND: Hydropsyche Pictet, 1834 is the largest genus of Hydropsychinae. In China, larval descriptions exist for only about 20 species. Although the number of Hydropsyche larvae described in China has increased rapidly in recent years, larvae of more than 75% of Chinese Hydropsyche species remain unknown.<br><br>NEW INFORMATION: In this paper, we describe and illustrate the larvae of Hydropsychebriareus Malicky &amp; Chantaramongkol, 2000 and Hydropsychekozhantschikovi Martynov, 1924 for the first time. Neighbour-joining trees were reconstructed, based on known partial Hydropsyche species mtCOI barcodes.},
}
@article {pmid40134031,
year = {2025},
author = {Wang, X and Wang, K and Zhang, W and Tang, Z and Zhang, H and Cheng, Y and Zhou, D and Zhang, C and Zhong, WZ and Ma, Q and Xu, J and Hu, Z},
title = {Clonal expansion dictates the efficacy of mitochondrial lineage tracing in single cells.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {70},
pmid = {40134031},
issn = {1474-760X},
support = {32300493//National Natural Sciences Foundation of China/ ; 32070870//National Natural Sciences Foundation of China/ ; 32070644//National Natural Sciences Foundation of China/ ; 82241236//National Natural Sciences Foundation of China/ ; 2022M723301//China Postdoctoral Science Foundation/ ; 2021B1515020042//Guangdong Basic and Applied Basic Research Foundation/ ; },
mesh = {Humans ; *Cell Lineage ; *Single-Cell Analysis/methods ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics/metabolism ; Mutation ; Heteroplasmy ; },
abstract = {BACKGROUND: Mitochondrial DNA (mtDNA) variants hold promise as endogenous barcodes for tracking human cell lineages, but their efficacy as reliable lineage markers are hindered by the complex dynamics of mtDNA in somatic tissues.<br><br>RESULTS: Here, we use computational modeling and single-cell genomics to thoroughly interrogate the origin and clonal dynamics of mtDNA variants across various biological settings. Our findings reveal that the majority of mtDNA variants which are specifically present in a cell subpopulation, termed subpopulation-specific variants, are pre-existing heteroplasmies in the first cell instead of de novo somatic mutations during divisions. Moreover, subpopulation-specific variants demonstrate limited discriminatory power among different genuine lineages under weak clonal expansion; however, certain subpopulation-specific variants with consistently high frequencies among a subpopulation are capable of faithfully labeling cell lineages in scenarios of stringent clonal expansion, such as strongly expanded T cell populations in diseased conditions and clonal hematopoiesis in aged individuals. Inspired by our simulations, we introduce a lineage informative score, facilitating the identification of reliable mitochondrial lineage tracing markers across different modalities of single-cell genomic data.<br><br>CONCLUSIONS: Combining computational modeling and single-cell sequencing, our study reveals that the performance of mitochondrial lineage tracing is highly dependent on the extent of clonal expansion, which thus should be considered when applying mitochondrial lineage tracing.},
}
@article {pmid40133646,
year = {2025},
author = {Neurauter, M and Vinzelj, JM and Strobl, SFA and Kappacher, C and Schlappack, T and Badzoka, J and Podmirseg, SM and Huck, CW and Rainer, M},
title = {Application of MALDI TOF and DART mass spectrometry as novel tools for classification of anaerobic gut fungi strains.},
journal = {Analytical and bioanalytical chemistry},
volume = {},
number = {},
pages = {},
pmid = {40133646},
issn = {1618-2650},
support = {10.55776/I3808//Austrian Science Fund/ ; },
abstract = {Anaerobic gut fungi (AGF) have emerged as promising candidates for optimized biogas and biofuel production due to their unique repertoire of potent lignocellulose-degrading enzymes. However, identifying AGF strains through standard fungal DNA barcodes still poses challenges due to their distinct genomic features. This study explored the applicability of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI) and direct analysis in real-time (DART) mass spectrometry (MS) as alternative methods for AGF identification. Further, the capability of the methods to differentiate strains from different growth phases was investigated. The study found that both MALDI and DART were viable methods for AGF strain identification. MALDI proved to be a precise and robust technique for strain discrimination with prediction accuracies of 94% for unknown standard samples. Even at longer growth times (>3 weeks) MALDI achieved good prediction accuracies with 84%; however, younger cultures (72 h) were only predicted with 63% accuracy. The fast on-target lysis with minimal chemical demand yielded suitable spectra for strain differentiation. DART MS, while effective with prediction accuracies of samples with the same age of up to 93%, exhibited lower prediction accuracies for cultures of different ages, with 14% for young (72 h) and 71% for old (>3 weeks) samples. Further research could enhance the capabilities of these mass spectrometry methods for AGF identification and broaden their application to species-level discrimination and a wider range of AGF genera.},
}
@article {pmid40126103,
year = {2025},
author = {Warner, TC and Marando, VM and Santiago-Reyes, OA and Hart, EM and Smelyansky, SR and Carter, AW and Bernhardt, TG and Bryson, BD and Kim, DE and Kiessling, LL},
title = {Intercepting a Mycobacterial Biosynthetic Pathway with Covalent Labeling.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.4c17913},
pmid = {40126103},
issn = {1520-5126},
abstract = {The mycobacterial cell envelope plays both infectious and protective roles. Understanding its structure is crucial for unlocking the molecular basis underlying these functions. Studying glycans, the primary components of the cell envelope, is challenging due to their limited native functional handles for chemoselective modification. New labeling methods exploit biorthogonal chemistry, using small molecule mimics that intercept cellular metabolism or late-stage glycan biosynthesis. However, these strategies can have practical limitations, including probe delivery and effectiveness. An ideal small molecule probe should be easily deployed and exploit the critical enzyme-substrate relationships of natural substrates. To this end, we developed a "probegenic" strategy to label mycobacteria. Our approach eliminates the need for explicit substrate mimicry, as the relevant functionality is revealed by a target enzyme. Specifically, we synthesized an azide-substituted trans-β-lactone probe (AzLac), which adopts a substrate-like structure upon covalent enzyme labeling. This probe is incorporated by mycolyltransferases into a core mycobacterial cell envelope glycan, including in the pathogen Mycobacterium tuberculosis. Unlike other probes of the cell envelope, AzLac facilitates selective covalent labeling of the inner leaflet of the mycomembrane. Using Corynebacterium glutamicum mycolyltransferase deletion strains, we implicated Cmt2 as the primary mycolyltransferase target. We leveraged the ability to modify the cell envelope by demonstrating that AzLac could be used to attach a DNA barcode to mycobacteria, which would help track infection dynamics. Thus, we expect AzLac will be a valuable means of monitoring and tracking the mycobacterial cell envelope. Moreover, we anticipate masking and revealing recognition motifs in probes can be applied to diverse cellular targets.},
}
@article {pmid40125407,
year = {2025},
author = {Koffi, ADK and Babin, R and Delvare, G and Chérasse, S and Ouvrard, D and Shimbori, EM and Koigny, KJH and Kpangui, SK and Benoit, L and Galan, M and Yodé, CDV and Ouali N'goran, MS and Haran, JM},
title = {A barcode database for insects associated with the spread of the Cocoa Swollen Shoot Virus Disease in Côte d'Ivoire.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e144017},
pmid = {40125407},
issn = {1314-2828},
abstract = {Swollen Shoot is a viral disease affecting cocoa trees, transmitted by several species of mealybugs (Insecta, Hemiptera, Sternorrhyncha, Pseudococcidae). These insects maintain trophobiotic relationships with a complex and species-rich assemblage of ants protecting them and natural enemies controlling their populations. Here, we provide a curated DNA barcode database to characterise this insect community. Systematic observation of 7,500 cocoa trees was conducted, coupled with the collection of mealybug colonies and associated insect communities (parasitoids, predators and ants). Natural enemies were reared from mealybug colonies collected from 1,430 cocoa trees. Specimens were identified morphologically and sequenced for fragments of the standard DNA barcode region of the COI. We recovered 17 species of mealybugs from the family Pseudococcidae. Amongst these species, eight are new to the Ivorian cocoa orchard: Dysmicoccusneobrevipes Beardsley, Ferrisiadasylirii (Cockerell), Maconellicoccusugandae (Laing), Paracoccusmarginatus Williams &amp; Granara de Willink, Phenacoccussolenopsis Tinsley, Planococcusminor (Maskell), Pseudococcusconcavocerarii James and Pseudococcusocciduus De Lotto. Three of these species were identified for the first time in cocoa orchards in Africa: D.neobrevipes, Fe.dasylirii and Ph.solenopsis. A total of 54 ant species were identified and represented the first record of these species associated with mealybug colonies in cocoa in Côte d'Ivoire. Amongst the species associated with the mealybugs, 22 primary parasitoids, eight hyperparasitoids, 11 ladybirds beetles (Coccinellidae), seven gall midges (Cecidomyidae), one predatory lepidopteran species and four spider species were identified. Nine species of mealybugs parasitoids are newly recorded in the African cocoa orchards: Acerophagusaff.dysmicocci, Aloencyrtus sp., Anagyruskamali, Anagyrusaff.pseudococci, Aenasiusadvena, Clauseniaaff.corrugata, Gyranusoideaaff.tebygi, Zaplatycerusaff.natalensis (Encyrtidae) and Coccophaguspulvinariae (Aphelinidae) and one hyperparasitoid, Pachyneuronmuscarum (Pteromalidae). For Côte d'Ivoire in particular, besides the previously mentioned nine parasitoids and one hyperparasitoid, five additional species are recorded for the first time, including four primary parasitoids, Blepyrusinsularis (Encyrtidae), Clauseniacorrugata (Encyrtidae), Clausenia sp. (Encyrtidae), and Coccidoctonuspseudococci (Encyrtidae) and one hyperparasitoid, Cheiloneuruscyanonotus (Encyrtidae). These results significantly enhance the knowledge of the diversity of the entomofauna associated with Swollen Shoot disease and pave the way for developing control methods based on the natural regulation of its mealybug (Pseudococcidae) vectors.},
}
@article {pmid40124603,
year = {2025},
author = {de Sousa, VE and da Silva Cortinhas, MCF and Creed, JC and Batista, MGS and Proietti, MC and Copertino, M},
title = {Assessing morphological variations in the seagrass genus Halodule (Cymodoceaceae) along the Brazilian coast through genetic analyses.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19038},
pmid = {40124603},
issn = {2167-8359},
mesh = {Brazil ; *Phylogeny ; *Plant Leaves/anatomy &amp; histology ; Genetic Variation ; Alismatales/genetics/anatomy &amp; histology/classification ; },
abstract = {BACKGROUND: Seagrass meadows are distributed globally and provide critical ecological functions and ecosystem services, but seagrasses are still poorly studied compared with other coastal and marine foundation species. Species taxonomy is uncertain in various seagrass genera, such as the genus Halodule. Until recently, the morphological characteristics of leaves were the major criteria for species identification. In Brazil, three species of Halodule are recognized and separated solely using leaf morphology criteria by some authors; however, the leaves present high variability and plasticity, resulting in great uncertainty about species diversity. A review of seagrass species validation using both morphological and phylogenetic methods is needed. This includes examining the genus Halodule with the aim of better understanding its diversity and spatial distribution and consequently supporting management and conservation goals.<br><br>METHODS: Plant samples with the morphological forms of H. beaudettei and H. wrightii were collected at five sites across three Brazilian marine ecoregions. Leaf tip format and leaf width and length were compared among all the sites and between the two populations with different leaf tip forms. Molecular diversity and divergence indices and analyses were used to estimate the genetic distance between H. wrightii and H. beaudettei populations. To determine the phylogenetic relationship between the two morphologies, we sequenced two molecular markers, the internal transcribed spacer (ITS) fragment and the rbcL gene, to construct phylogenetic trees using Bayesian inference.<br><br>RESULTS: We identified H. beaudettei morphology at two sites in Northeast Brazil, while H. wrightii was found in all the ecoregions in the remaining areas, distinguished by the leaf tip shape that occurred at each site. Leaf width and length varied across the five sites, and leaf length differed between H. wrightii and H. beaudettei, with higher values observed in H. beaudettei. Variations in morphological measurements may be related to habitat conditions at each site studied. No divergence was observed for the DNA sequences of two molecular markers, except for a single base in the ITS region, resulting in the Brazilian specimens merging at a single node in the phylogenetic trees. AMOVA and genetic distance analysis revealed low genetic variation but high structuring within populations. The ITS marker showed insufficient genetic variance to delineate the two morphologies as different species which indicating H. wrightii and H. beaudettei are closely related. A genomic approach is needed to fully resolve this issue. This study represents the first step toward the complete determination of the Halodule genus on the Brazilian coast.},
}
@article {pmid40123593,
year = {2025},
author = {Silva, SE and Silva, LS and Eufrasio, LG and Cruz, GS and Lucini, F and Vechi, HT and Alves, MDM and Ribeiro, LRF and de Souza, KL and Moreira, JA and de Souza, JG and Morio, F and da Costa, GL and Baptista, BO and Tomé, LMR and Pedroso, SHSP and Iani, FCM and Adelino, T&#xc9;R and Castelo-Branco, D and Rossato, L and Peres, NTA and Santos, DA and Oliveira, MME and da Silva, KJG and Bastos, RW},
title = {Kodamaea ohmeri: An emergent yeast from a One Health perspective.},
journal = {Current research in microbial sciences},
volume = {8},
number = {},
pages = {100359},
pmid = {40123593},
issn = {2666-5174},
abstract = {Kodamaea ohmeri is an emerging and opportunistic yeast associated with a high mortality rate in humans. As it is commonly found in the environment, it is possible that environmental conditions and agricultural practices contribute to the adaptation of this yeast and the selection of antifungal resistance. During a multicentric study in Brazil, conducted under a One Health perspective, 14 isolates of K. ohmeri were identified from different sources: three from blood cultures, three from animals (swine and poultry), and eight from animal environments (swine and poultry). Yeasts were isolated using CHROmagar® Candida medium and identified by MALDI-TOF MS and ITS rDNA barcoding. Minimum inhibitory concentration (MIC) was determined using the broth microdilution method for clinical (azoles, echinocandins, pyrimidine analogs, and polyenes), and environmental antifungals (tebuconazole, pyraclostrobin, carbendazim, and mancozeb), and hospital disinfectants (quaternary ammonium compounds). Of note, color variations of K. ohmeri were noted on CHROmagar® depending on the incubation time, which is likely to complicate its identification. Following polyphasic identification and taxonomic confirmation, all isolates demonstrated low MIC values for clinical antifungals, disinfectants, and tebuconazole. However, all isolates were able to grow in the presence of carbendazim, mancozeb, and pyraclostrobin. Together, these findings highlight the risks associated with the use of environmental azoles, such as tebuconazole, as they may impact non-target fungi of medical importance, but other fungicides do not present the same risk. This is the first study to demonstrate that K. ohmeri, an important emerging yeast in human medicine, can be isolated from various sources, including patients. Although the isolates exhibited low MIC values for clinical antifungals, it is crucial to monitor changes in sensitivity patterns over time in emerging microorganisms to prevent the development of multidrug resistance, which may originate in the environment.},
}
@article {pmid40121084,
year = {2025},
author = {Zhao, A and Chan, MM},
title = {Cloning and validating systems for high throughput molecular recording.},
journal = {Methods in enzymology},
volume = {712},
number = {},
pages = {453-473},
doi = {10.1016/bs.mie.2025.01.015},
pmid = {40121084},
issn = {1557-7988},
mesh = {*CRISPR-Cas Systems ; *Cloning, Molecular/methods ; Humans ; *Gene Editing/methods ; Animals ; Single-Cell Analysis/methods ; Cell Lineage/genetics ; Mice ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Molecular recording technologies record and store information about cellular history. Lineage tracing is one form of molecular recording and produces information describing cellular trajectories during mammalian development, differentiation and maintenance of adult stem cell niches, and tumor evolution. Our molecular recorder technology utilizes CRISPR-Cas9 barcode editing to generate mutations in genomically integrated, engineered DNA cassettes, which are read out by single-cell RNA sequencing and used to produce high-resolution lineage trees. Here, we describe optimized cloning and validation procedures to construct the molecular recorder lineage tracing system. We include information on considerations of technology design, cloning procedures, the generation of lineage tracing cell lines, and time course experiments to assess their performance.},
}
@article {pmid40119005,
year = {2025},
author = {Li, H and Bao, S and Farzad, N and Qin, X and Fung, AA and Zhang, D and Bai, Z and Tao, B and Fan, R},
title = {Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&amp;Tag-RNA-seq.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {40119005},
issn = {1750-2799},
support = {U54AG076043//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U54AG079759//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; UG3CA257393//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; UH3CA257393//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01CA245313//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; RF1MH128876//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U54CA274509//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U01CA294514//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U54CA268083//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
abstract = {The epigenome of a cell is tightly correlated with gene transcription, which controls cell identity and diverse biological activities. Recent advances in spatial technologies have improved our understanding of tissue heterogeneity by analyzing transcriptomics or epigenomics with spatial information preserved, but have been mainly restricted to one molecular layer at a time. Here we present procedures for two spatially resolved sequencing methods, spatial-ATAC-RNA-seq and spatial-CUT&amp;Tag-RNA-seq, that co-profile transcriptome and epigenome genome wide. In both methods, transcriptomic readouts are generated through tissue fixation, permeabilization and in situ reverse transcription. In spatial-ATAC-RNA-seq, Tn5 transposase is used to probe accessible chromatin, and in spatial-CUT&amp;Tag-RNA-seq, the tissue is incubated with primary antibodies that target histone modifications, followed by Protein A-fused Tn5-induced tagmentation. Both methods leverage a microfluidic device that delivers two sets of oligonucleotide barcodes to generate a two-dimensional mosaic of tissue pixels at near single-cell resolution. A spatial-ATAC-RNA-seq or spatial-CUT&amp;Tag-RNA-seq library can be generated in 3-5 d, allowing researchers to simultaneously investigate the transcriptomic landscape and epigenomic landscape of an intact tissue section. This protocol is an extension of our previous spatially resolved epigenome sequencing protocol and provides opportunities in multimodal profiling.},
}
@article {pmid40119004,
year = {2025},
author = {Li, L and Bowling, S and Lin, H and Chen, D and Wang, SW and Camargo, FD},
title = {DARLIN mouse for in vivo lineage tracing at high efficiency and clonal diversity.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {40119004},
issn = {1750-2799},
support = {32470700//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; },
abstract = {Lineage tracing is a powerful tool to study cell history and cell dynamics during tissue development and homeostasis. An increasingly popular approach for lineage tracing is to generate high-frequent mutations at given genomic loci, which can serve as genetic barcodes to label different cell lineages. However, current lineage tracing mouse models suffer from low barcode diversity and limited single-cell lineage coverage. We recently developed the DARLIN mouse model by incorporating three barcoding arrays within defined genomic loci and combining Cas9 and terminal deoxynucleotidyl transferase (TdT) to improve editing diversity in each barcode array. We estimated that DARLIN generates 10[18] distinct lineage barcodes in theory, and enables the recovery of lineage barcodes in over 70% of cells in single-cell assays. In addition, DARLIN can be induced with doxycycline to generate stable lineage barcodes across different tissues at a defined stage. Here we provide a step-by-step protocol on applying the DARLIN system for in vivo lineage tracing, including barcode induction, estimation of induction efficiency, barcode analysis with bulk and single-cell sequencing, and computational analysis. The execution time of this protocol is ~1 week for experimental data collection and ~1 d for running the computational analysis pipeline. To execute this protocol, one should be familiar with sequencing library generation and Linux operation. DARLIN opens the door to study the lineage relationships and the underlying molecular regulations across various tissues at physiological context.},
}
@article {pmid40117582,
year = {2025},
author = {Catalano, R and Zhao, Y and Pecak, M and Korten, T and Diez, S},
title = {Barcoding Microtubules: Encoding Information onto Macromolecules by Photobleaching.},
journal = {Nano letters},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.nanolett.5c00105},
pmid = {40117582},
issn = {1530-6992},
abstract = {Kinesin-1-powered microtubules have emerged as versatile components in biocomputing and biosensing technologies. However, the inability to identify and track individual microtubules has constrained their applications to ensemble behaviors, limiting their potential for single-entity-based nanotechnologies. To address this challenge, we present a novel method for encoding digital information directly onto individual microtubules using photobleaching patterns. Binary numbers (1 to 15) were encoded within ∼12 μm segments of moving microtubules by photobleaching with a stationary pulsed laser, creating spatial frequency patterns corresponding to distinct bits of information. Fourier analysis enabled the accurate retrieval of the encoded data, demonstrating the feasibility of direct information storage and retrieval on macromolecular structures. This approach offers a transformative solution for recording microtubule trajectories within nanotechnological devices by encoding path information directly onto microtubules at branch points, obviating the need for video-based tracking. We anticipate that this innovation will advance the development of individualized microtubule-based technologies.},
}
@article {pmid40117330,
year = {2025},
author = {Abdel-Glil, MY and Brandt, C and Pletz, MW and Neubauer, H and Sprague, LD},
title = {High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy.},
journal = {Microbial genomics},
volume = {11},
number = {3},
pages = {},
pmid = {40117330},
issn = {2057-5858},
mesh = {*Nanopore Sequencing/methods ; Reproducibility of Results ; *Genome, Bacterial ; *Bacteria/genetics/classification ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Nanopore sequencing is a third-generation technology known for its portability, real-time analysis and ability to generate long reads. It has great potential for use in clinical diagnostics, but thorough validation is required to address accuracy concerns and ensure reliable and reproducible results. In this study, we automated an open-source workflow (freely available at https://gitlab.com/FLI_Bioinfo/nanobacta) for the assembly of Oxford Nanopore sequencing data and used it to investigate the reproducibility of assembly results under consistent conditions. We used a benchmark dataset of five bacterial reference strains and generated eight technical sequencing replicates of the same DNA using the Ligation and Rapid Barcoding kits together with the Flongle and MinION flow cells. We assessed reproducibility by measuring discrepancies such as substitution and insertion/deletion errors, analysing plasmid recovery results and examining genetic markers and clustering information. We compared the results of genome assemblies with and without short-read polishing. Our results show an average reproducibility accuracy of 99.999955% for nanopore-only assemblies and 99.999996% when the short reads were used for polishing. The genomic analysis results were highly reproducible for the nanopore-only assemblies without short read in the following areas: identification of genetic markers for antimicrobial resistance and virulence, classical MLST, taxonomic classification, genome completeness and contamination analysis. Interestingly, the clustering information results from the core genome SNP and core genome MLST analyses were also highly reproducible for the nanopore-only assemblies, with pairwise differences of up to two allele differences in core genome MLST and two SNPs in core genome SNP across replicates. After polishing the assemblies with short reads, the pairwise differences for cgMLST were 0 and for cgSNP were 0-1 SNP across replicates. These results highlight the advances in sequencing accuracy of nanopore data without the use of short reads.},
}
@article {pmid40115270,
year = {2025},
author = {Wu, Q and Xiang, P and Wang, C and Jing, C and Lin, X and Wang, Y and Chen, G and Lin, M and Xing, B},
title = {Diversity of lanternfish (Myctophidae) larvae along the Ninety East Ridge, Indian Ocean.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19144},
pmid = {40115270},
issn = {2167-8359},
mesh = {Animals ; Indian Ocean ; *Larva/genetics ; *Phylogeny ; Fishes/genetics/classification ; Biodiversity ; Haplotypes ; Salinity ; },
abstract = {Since the 19th century, the impact of seamounts on the distribution of plankton has been a topic of considerable interest. The influence of seamounts on the biogeographic patterns of marine organisms is complex, with some aspects still under debate. It is generally accepted that seamounts can drive the upwelling of nutrient-rich deep waters. Tidal amplification, flow acceleration, and internal waves can further enhance vertical mixing, leading to increased primary productivity near seamounts. Seamounts may also act as barriers to the migration of marine organisms, affecting gene flow. Research on Pacific seamounts suggests these features might serve as "stepping stones" for the dispersal of marine species across the ocean. However, investigations of seamounts in the eastern Indian Ocean remain limited. Focusing on the Ninety East Ridge region in the eastern Indian Ocean, this study collected zooplankton samples using horizontal (surface) and vertical (0-200 m) plankton nets and measured temperature and salinity profiles with a conductivity, temperature, and depth (CTD) sensor. A total of 544 fish larvae were identified, including 260 lanternfish larvae, representing 38 species across 12 genera, determined through COI DNA barcoding. Phylogenetic trees and haplotype networks were constructed to analyze genetic distances and population structures of lanternfish species. Among the samples, intra-specific genetic distances ranged from 0% to 2.99%, while inter-specific distances ranged from 1.88% to 25.71%. Except for Notolychnus valdiviae (Brauer, 1904), the maximum intra-specific distances were lower than the minimum inter-specific distances for all species. Haplotype analysis of nine species revealed significant variations in haplotype number, structure, and spatial distribution. Specifically, Ceratoscopelus warmingii (Lütken, 1892) and N. valdiviae exhibited a notable north-south divergence pattern, consistent with the temperature and salinity distribution of the region's water masses. This conclusion was supported by analysis of molecular variance analysis, suggesting that larval stages of certain lanternfish species may struggle to cross boundaries between water masses. However, the remaining species showed no significant north-south distribution differences, possibly due to their adaptive capabilities, vertical migration patterns, or the duration of their planktonic larval stages. These findings suggest that seamounts and water mass distribution have varying implications for lanternfish species, potentially influencing gene flow and horizontal distribution patterns, which could contribute to speciation. Global climate change-induced alterations in ocean currents may profoundly impact the genetic diversity of fish species. This study provides new insights into the diversity of lanternfish in the Ninety East Ridge region and offers valuable data for understanding the biogeography of seamounts.},
}
@article {pmid40114347,
year = {2025},
author = {Kefelegn, H and Couvreur, M and Meressa, BH and Wesemael, WML and Teklu, MG and Bert, W},
title = {First Report of the Root-Knot Nematode, Meloidogyne luci Parasitizing Chickpea (Cicer arietinum L.) in Ethiopia.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-01-25-0096-PDN},
pmid = {40114347},
issn = {0191-2917},
abstract = {Chickpea (Cicer arietinum L.) is a significant legume crop, with Ethiopia being the largest producer in Africa and the fifth globally (FAO 2022). However, various factors, including plant-parasitic nematodes, reduce its yield. Among these, root-knot nematodes (RKN; Meloidogyne spp.) pose a severe threat by causing root galling and stunted growth (Castillo et al. 2008). Despite the impact, research on plant-parasitic nematodes, their diversity and effect on chickpea yield in Ethiopia is limited (Kefelegn et al. 2024). In 2021, a survey was conducted to assess diversity of nematodes associated with chickpea in Ethiopia. Root-knot nematodes collected from galled chickpea roots of the 'Arerti' cultivar in the Minjar district, Ethiopia (8°54'21.1"N, 39°24'46.5"E), were identified as M. luci using multiple approaches. Esterase isozyme patterns of egg-laying females (n=10) were consistent with those described for M. luci by Carneiro et al. (2014) and Gerič Stare et al. (2017). PCR amplification with M. luci-specific primers (Maleita et al. 2021) confirmed its identity . Additionally, various sequences obtained from second-stage juveniles (J2), following the method described in Janssen et al. (2016) and Kefelegn et al. (2024): COX1 (PQ448335), Nad5 (PQ462657), COX2 (PQ619863) of mtDNA, and the D2-D3 region of 28S rDNA (PQ454017), were found identical to the M. luci sequences KU372172, KU372417, KU372211, and KX130766, respectively. Populations of M. luci were established from single egg masses and maintained on tomato plants (cv. 'Marmande'). To evaluate the pathogenicity of M. luci on the 'Arerti' chickpea cultivar, seedlings were inoculated with initial population densities (Pi) of 1000, 4000 and 8000 J2 (pot)-1 (2-liter capacity, n= 8) in a temperature controlled growth chamber in the Flanders Research Institute for Agriculture, Fisheries, and Food (ILVO), Belgium. After eight weeks, all inoculated plants exhibited stunted growth and visible root galling, consistent with typical field symptoms. The nematode reproduction factor (RF = final population (Pf) /initial population (Pi)) was calculated from the whole root and soil samples. Rf values were 31, 11.5 and 9.5 for Pi 1000, 4000 and 8000 J2 (pot)-1, respectively, corresponding to Pf values of 32000, 46000 and 76000 J2 (pot)-1, respectively. This clear pattern of increasing Pf with higher Pi levels, coupled with the declining RF trend, reflects the expected dynamics of a pathogenicity test. Nematodes extracted from the roots were reisolated and identified as M. luci using PCR amplification with M. luci-specific primers and esterase isozyme patterns analysis of egg-laying females (n = 10), confirming the species identity. These results confirmed that the 'Arerti' cultivar is a suitable host for M. luci. Meloidogyne luci has previously been reported in chickpea fields in Türkiye (Şen &amp; Aydinli 2021), in common bean and soybean in Brazil (Bellé et al. 2016), and various horticultural crops in Europe (Gerič Stare et al. 2017). This study marks the first report of M. luci parasitizing chickpea roots in Ethiopia and its first documented occurrence in Africa. Therefore, further investigations are essential to determine the distribution of M. luci and assess its damage potential on legumes and other crops in Ethiopia and across Africa.},
}
@article {pmid40114041,
year = {2025},
author = {Guo, X and Xie, P and Zhang, G and Wang, T and Li, J and Zhang, X and Su, W and Ji, Y},
title = {Complete plastomes serve as desirable molecular makers for precise identification of Asparagus cochinchinensis (Asparagaceae) and nine other congeneric species frequently utilized as its adulterants.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {366},
pmid = {40114041},
issn = {1471-2229},
support = {202305AT350001//Yunnan Revitalization Talent Support Program "Top Team" Project/ ; },
mesh = {*Asparagus Plant/genetics ; *Phylogeny ; *Genome, Plastid ; Drug Contamination/prevention &amp; control ; Plant Roots/genetics ; DNA, Plant/genetics ; DNA, Ribosomal/genetics ; Genetic Markers ; },
abstract = {BACKGROUD: The processed tuberous roots of Asparagus cochinchinensis (Asparagaceae), known as Asparagi Radix, have long been used in East Asia (particularly in China) as traditional medicines and play an indispensable role in the pharmaceutical industry. However, the frequent adulteration of Asparagi Radix with processed tuberous roots obtained from nine other congeneric species could potentially compromise the quality control measures for related pharmaceutical products, while also posing challenges to the conservation and rational exploitation of the nine adulterant congeneric species that are also used as traditional ethnomedicines. Given this issue, this study aims to develop a molecular authentication method for the accurate identification of A. cochinchinensis and the nine congeneric adulterants, employing the genome skimming approach to generate complete plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) arrays as the candidate molecular markers.<br><br>RESULTS: Through comprehensive phylogenetic and genetic distance analyses based on extensive sampling at both inter- and intra-specific levels, the efficacy of the two candidate molecular markers was assessed by investigating whether their inter-specific genetic divergences align with the taxonomically delineated species boundaries.<br><br>CONCLUSION: The results indicated that complete plastomes exhibit superior performance for accurately identifying A. cochinchinensis (the botanical source of Asparagi Radix) and the nine congeneric adulterants, thus can serve as the optimal molecular markers for effective authentication of Asparagi Radix. The desirable discriminative power demonstrated by complete plastomes suggests that the PCR-free molecular authentication method developed in this study will not only contribute to the quality control of pharmaceutical products derived from Asparagi Radix but also facilitate the conservation efforts and rational exploitation of the nine Asparagus species commonly used as adulterants.},
}
@article {pmid40109892,
year = {2025},
author = {Gastineau, R and Mianowicz, K and Dąbek, P and Otis, C and Stoyanova, V and Krawcewicz, A and Abramowski, T},
title = {Genomic investigation of benthic invertebrates from the Clarion-Clipperton fields of polymetallic nodules.},
journal = {ZooKeys},
volume = {1231},
number = {},
pages = {11-44},
pmid = {40109892},
issn = {1313-2989},
abstract = {The abyssal plains of the Clarion-Clipperton Zone (CCZ) are famous for their fields of polymetallic nodules, which are inhabited by benthic invertebrates. Ten specimens from the Interoceanmetal Joint Organisation (IOM) licence area in the CCZ were collected in 2014 and submitted to a short-read genome skimming sequencing. In total, mitochondrial genomes and nuclear ribosomal genes were retrieved for nine different organisms belonging to Ophiuroidea, Holothuroidea, Polychaeta, Bryozoa, Porifera, and Brachiopoda (assigned to these phyla immediately upon retrieval from the seafloor). As many of these samples were partial and physically deteriorated following their seven-year storage in IOM's collections, their morphology-based taxonomic identification could rarely be performed at the lowest possible level (species or genus) prior to preparing the samples for molecular or genomic investigations. Therefore, it was not possible to apply the reverse identification scheme recommended for such investigations. However, several of these specimens represent poorly studied groups for which few molecular references are available as of now. In two cases, the presence of introns in the mitochondrial genome questions the practicability of using the cox1 gene for further routine molecular barcoding of these organisms. These results might be useful in future DNA primers design, molecular barcoding, and phylogeny or population genetic studies when more samples are obtained.},
}
@article {pmid40106513,
year = {2025},
author = {Vielma-Puente, JE and Santos-Ordóñez, E and Cornejo, X and Chóez-Guaranda, I and Pacheco-Coello, R and Villao-Uzho, L and Moreno-Alvarado, C and Mendoza-Samaniego, N and Fonseca, Y},
title = {DNA Barcode, chemical analysis, and antioxidant activity of Psidium guineense from Ecuador.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0319524},
pmid = {40106513},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic ; Ecuador ; *Psidium/chemistry/genetics ; *Antioxidants/chemistry/pharmacology ; Plant Extracts/chemistry/pharmacology ; Flavonoids/analysis ; Plant Leaves/chemistry/genetics ; DNA, Plant/genetics ; Phenols/analysis ; },
abstract = {This study investigates the phytochemical, genetic, and antioxidant properties of Psidium guineense, a species native to the tropical dry forests of Ecuador. Leaves were collected, preserved in recognized herbaria, and subjected to Soxhlet extraction using polar and non-polar solvents. Phytochemical screening revealed the presence of secondary metabolites, while GC-MS analysis detected chemical compounds in the extracts. Antioxidant assays demonstrated high phenolic (54.34 ± 0.49 mg GAE/g) and flavonoid (6.43 ± 0.38 mg QE/g) content, with significant antioxidant activity in DPPH (0.57 ± 0.04 mg TE/g), FRAP (105.52 ± 6.85), and ABTS (1.25 ± 0.01 mg TE/g) assays. DNA barcoding of nine loci, (seven from the chloroplast genome and two nuclear genome) using a CTAB extraction protocol and PCR, provides the first genetic characterization of this species, contributing to genetic diversity assessments and phylogenetic studies. These findings underscore the importance of P. guineense as a source of potent bioactive compounds with significant antioxidant potential, highlighting its applicability in nutritional and pharmaceutical industries. Additionally, the genetic insights gained support efforts to expand DNA barcoding databases for tropical biodiversity conservation.},
}
@article {pmid40106335,
year = {2025},
author = {Chen, A and Nchinda, N and Cira, NJ},
title = {Scalable genotyping of microbial colonies.},
journal = {Microbial genomics},
volume = {11},
number = {3},
pages = {},
pmid = {40106335},
issn = {2057-5858},
mesh = {*RNA, Ribosomal, 16S/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; *Polymerase Chain Reaction/methods ; *Genotyping Techniques/methods ; Genotype ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Gene Library ; DNA Primers/genetics ; },
abstract = {The sequence of the 16S region is taxonomically informative and widely used for genotyping microbes. While it is easy and inexpensive to genotype several isolates by Sanger sequencing the 16S region, this method becomes quite costly if scaled to many isolates. High-throughput sequencing provides one potential avenue for obtaining 16S sequences at scale but presents additional challenges. First, DNA purification workflows for high-throughput sample preparation are labour-intensive and expensive. Second, cost-effective multiplexing and library preparation schemes are difficult to implement for many libraries on a single sequencing run. Therefore, we implemented a scalable protocol for isolate genotyping involving colony polymerase chain reaction (PCR) with simple cell lysis as well as a four-barcode indexing scheme that enables scalable multiplexing and streamlined library preparation by amplifying with four primers simultaneously in a single reaction. We tested this protocol on 93 colonies cultured from environmental samples, and we were able to ascertain the identity of ~90% of microbial isolates.},
}
@article {pmid40104553,
year = {2025},
author = {Cazal-Martínez, CC and Reyes-Caballero, YM and Chávez, AR and Pérez-Estigarribia, PE and Kohli, MM and Rojas, A and Arrua, AA and Moura-Mendes, J and Souza-Perera, R and Zúñiga Agilar, JJ and Gluck-Thaler, E and Lopez-Nicora, H and Iehisa, JCM},
title = {Pyricularia pennisetigena and Pyricularia oryzae isolates from Paraguay's wheat-growing regions and the impact on wheat.},
journal = {Current research in microbial sciences},
volume = {8},
number = {},
pages = {100361},
pmid = {40104553},
issn = {2666-5174},
abstract = {The Pyricularia genus includes species causing blast disease in monocots, posing significant challenges for disease management due to their ability to infect multiple hosts. This study aimed to identify the pathogenicity and species identity of Pyricularia isolates from 11 plant species in wheat-growing regions of Paraguay and assess their capacity to infect wheat. Twenty-four monosporic isolates were analyzed based on macroscopic and microscopic and phylogenetic characteristics. Three phylogenetic clades corresponding to P. oryzae, P. grisea, and P. pennisetigena were identified through five barcoding genes. For the first time, wheat blast was reported in San Pedro Department, and blast disease was observed in weeds in Cordillera and Central Departments. In greenhouse trials, P. oryzae isolates from wheat successfully infected both susceptible and resistant wheat cultivars, whereas isolates from non-wheat hosts did not elicit symptoms. Notably, P. pennisetigena isolates derived from Cenchrus echinatus were capable of infecting wheat spikes, producing typical blast symptoms, highlighting the potential for cross-species pathogen transmission. This finding suggests P. pennisetigena may pose an emerging threat to wheat in Paraguay, as its primary host is prevalent near wheat fields. These results highlight the critical importance of integrated disease management strategies, particularly the identification of inoculum sources, to mitigate cross-species pathogen transmission. This approach aligns with the One Health paradigm by addressing interconnected risks to plant health, food security, and environmental sustainability.},
}
@article {pmid40103772,
year = {2025},
author = {Al-Dhafer, HM and Balaji, R and Abdel-Dayem, MS and Rasool, I and Mohamed, A and Palanisamy, S},
title = {Simple DNA extraction for museum beetle specimens to unlock genetic data from historical collections.},
journal = {MethodsX},
volume = {14},
number = {},
pages = {103236},
pmid = {40103772},
issn = {2215-0161},
abstract = {Museum beetle specimens are valuable resources for genetic analyses; however, obtaining DNA from aged specimens remains challenging due to degradation, desiccation, and contamination. In this study, we present a simple, low-cost protocol for extracting DNA from museum beetles, optimized using cetyltrimethylammonium bromide (CTAB). This method effectively addresses common issues such as DNA fragmentation and contamination, enabling the recovery of DNA suitable for downstream applications such as PCR and next-generation sequencing. It provides a reproducible, non-destructive approach to extracting genetic material from fragile beetle specimens, thereby facilitating molecular investigations in fields such as taxonomy and conservation biology. The protocol is summarized as follows:•A method for DNA extraction is optimized for museum beetle specimens preserved for over 45 years.•The protocol is non-destructive and compatible with PCR and next-generation sequencing.•Multiple extractions can be pooled to increase yields, particularly when DNA concentrations are low. This method broadens the possibilities for genetic analysis of historical specimens, offering new insights into long-term ecological and evolutionary processes.},
}
@article {pmid40102722,
year = {2025},
author = {Luo, C and Peters, BA and Zhou, XM},
title = {Large indel detection in region-based phased diploid assemblies from linked-reads.},
journal = {BMC genomics},
volume = {26},
number = {Suppl 2},
pages = {263},
pmid = {40102722},
issn = {1471-2164},
support = {R35 GM146960/NH/NIH HHS/United States ; GET 300538//Complete Genomics/ ; },
mesh = {*INDEL Mutation ; *Diploidy ; Humans ; *Algorithms ; Haplotypes ; Sequence Analysis, DNA/methods ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Genome, Human ; },
abstract = {BACKGROUND: Linked-reads improve de novo assembly, haplotype phasing, structural variant (SV) detection, and other applications through highly-multiplexed genome partitioning and barcoding. Whole genome assembly and assembly-based variant detection based on linked-reads often require intensive computation costs and are not suitable for large population studies. Here we propose an efficient pipeline, RegionIndel, a region-based diploid assembly approach to characterize large indel SVs. This pipeline only focuses on target regions (50kb by default) to extract barcoded reads as input and then integrates a haplotyping algorithm and local assembly to generate phased diploid contiguous sequences (contigs). Finally, it detects variants in the contigs through a pairwise contig-to-reference comparison.<br><br>RESULTS: We applied RegionIndel on two linked-reads libraries of sample HG002, one using 10x and the other stLFR. HG002 is a well-studied sample and the Genome in a Bottle (GiaB) community provides a gold standard SV set for it. RegionIndel outperformed several assembly and alignment-based SV callers in our benchmark experiments.&#xa0;After assembling all indel SVs, RegionIndel achieved an overall F1 score of 74.8% in deletions and 61.8% in insertions for 10x linked-reads, and 64.3% in deletions and 36.7% in insertions for stLFR linked-reads, respectively. Furthermore, it achieved an overall genotyping accuracy of 83.6% and 80.8% for 10x and stLFR linked-reads, respectively.<br><br>CONCLUSIONS: RegionIndel can achieve diploid assembly and detect indel SVs in each target region. The phased diploid contigs can further allow us to investigate indel SVs with nearby linked single nucleotide polymorphism (SNPs) and small indels in the same haplotype.},
}
@article {pmid40102719,
year = {2025},
author = {Zhang, S and Ma, A and Xie, X and Lian, Z and Wang, Y},
title = {CacPred: a cascaded convolutional neural network for TF-DNA binding prediction.},
journal = {BMC genomics},
volume = {26},
number = {Suppl 2},
pages = {264},
pmid = {40102719},
issn = {1471-2164},
mesh = {*Neural Networks, Computer ; *Transcription Factors/metabolism/genetics ; *DNA/metabolism ; Chromatin Immunoprecipitation Sequencing/methods ; Binding Sites ; Computational Biology/methods ; Software ; Protein Binding ; Algorithms ; Humans ; },
abstract = {BACKGROUND: Transcription factors (TFs) regulate the genes' expression by binding to DNA sequences. Aligned TFBSs of the same TF are seen as cis-regulatory motifs, and substantial computational efforts have been invested to find motifs. In recent years, convolutional neural networks (CNNs) have succeeded in TF-DNA binding prediction, but existing DL methods' accuracy needs to be improved and convolution function in TF-DNA binding prediction should be further explored.<br><br>RESULTS: We develop a cascaded convolutional neural network model named CacPred to predict TF-DNA binding on 790 Chromatin immunoprecipitation-sequencing (ChIP-seq) datasets and seven ChIP-nexus (chromatin immunoprecipitation experiments with nucleotide resolution through exonuclease, unique barcode, and single ligation) datasets. We compare CacPred to six existing DL models across nine standard evaluation metrics. Our results indicate that CacPred outperforms all comparison models for TF-DNA binding prediction, and the average accuracy (ACC), matthews correlation coefficient (MCC), and the area of eight metrics radar (AEMR) are improved by 3.3%, 9.2%, and 6.4% on 790 ChIP-seq datasets. Meanwhile, CacPred improves the average ACC, MCC, and AEMR of 5.5%, 16.8%, and 12.9% on seven ChIP-nexus datasets. To explain the proposed method, motifs are used to show features CacPred learned. In light of the results, CacPred can find some significant motifs from input sequences.<br><br>CONCLUSIONS: This paper indicates that CacPred performs better than existing models on ChIP-seq data. Seven ChIP-nexus datasets are also analyzed, and they coincide with results that our proposed method performs the best on ChIP-seq data. CacPred only is equipped with the convolutional algorithm, demonstrating that pooling processing of the existing models leads to losing some sequence information. Some significant motifs are found, showing that CacPred can learn features from input sequences. In this study, we demonstrate that CacPred is an effective and feasible model for predicting TF-DNA binding. CacPred is freely available at https://github.com/zhangsq06/CacPred .},
}
@article {pmid40102641,
year = {2025},
author = {Kalvapalle, PB and Staubus, A and Dysart, MJ and Gambill, L and Reyes Gamas, K and Lu, LC and Silberg, JJ and Stadler, LB and Chappell, J},
title = {Information storage across a microbial community using universal RNA barcoding.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40102641},
issn = {1546-1696},
support = {2021-33522-35356//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; W911NF-24-2-0073//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; 1805901//National Science Foundation (NSF)/ ; 1828869//National Science Foundation (NSF)/ ; 2227526//National Science Foundation (NSF)/ ; 2237052//National Science Foundation (NSF)/ ; 2237512//National Science Foundation (NSF)/ ; FWP 78814//U.S. Department of Energy (DOE)/ ; A23-0202-004//Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation/ ; },
abstract = {Gene transfer can be studied using genetically encoded reporters or metagenomic sequencing but these methods are limited by sensitivity when used to monitor the mobile DNA host range in microbial communities. To record information about gene transfer across a wastewater microbiome, a synthetic catalytic RNA was used to barcode a highly conserved segment of ribosomal RNA (rRNA). By writing information into rRNA using a ribozyme and reading out native and modified rRNA using amplicon sequencing, we find that microbial community members from 20 taxonomic orders participate in plasmid conjugation with an Escherichia coli donor strain and observe differences in 16S rRNA barcode signal across amplicon sequence variants. Multiplexed rRNA barcoding using plasmids with pBBR1 or ColE1 origins of replication reveals differences in host range. This autonomous RNA-addressable modification provides information about gene transfer without requiring translation and will enable microbiome engineering across diverse ecological settings and studies of environmental controls on gene transfer and cellular uptake of extracellular materials.},
}
@article {pmid40102404,
year = {2025},
author = {Nadal-Ribelles, M and Solé, C and Díez-Villanueva, A and Stephan-Otto Attolini, C and Matas, Y and Steinmetz, L and de Nadal, E and Posas, F},
title = {A single-cell resolved genotype-phenotype map using genome-wide genetic and environmental perturbations.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2645},
pmid = {40102404},
issn = {2041-1723},
mesh = {*Single-Cell Analysis/methods ; *Saccharomyces cerevisiae/genetics ; *Genotype ; *Phenotype ; *Transcriptome/genetics ; Gene Expression Regulation, Fungal ; Genome, Fungal ; Mutation ; Gene Expression Profiling/methods ; },
abstract = {Heterogeneity is inherent to living organisms and it determines cell fate and phenotypic variability. Despite its ubiquity, the underlying molecular mechanisms and the genetic basis linking genotype to-phenotype heterogeneity remain a central challenge. Here we construct a yeast knockout library with a clone and genotype RNA barcoding structure suitable for genome-scale analyses to generate a high-resolution single-cell yeast transcriptome atlas of 3500 mutants under control and stress conditions. We find that transcriptional heterogeneity reflects the coordinated expression of specific gene programs, generating a continuous of cell states that can be responsive to external insults. Cell state plasticity can be genetically modulated with mutants that act as state attractors and disruption of state homeostasis results in decreased adaptive fitness. Leveraging on intra-genetic variability, we establish that regulators of transcriptional heterogeneity are functionally diverse and influenced by the environment. Our multimodal perturbation-based single-cell Genotype-to-Transcriptome Atlas in yeast provides insights into organism-level responses.},
}
@article {pmid40100602,
year = {2025},
author = {Ayala, LA and Nguyen, PU and Zhou, C and Hisoire, GL and Ahmedani, AH and Chen, X and Daud, A and Valdovinos, A and Varady, ES and Inlay, MA and Scarfone, VM},
title = {Mass Cytometry Immunophenotyping of Graft-Conditioned Cells Following Major Histocompatibility Complex Mismatched Murine Allograft.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2907},
number = {},
pages = {259-286},
pmid = {40100602},
issn = {1940-6029},
mesh = {Animals ; Mice ; *Immunophenotyping/methods ; *Flow Cytometry/methods ; *Graft vs Host Disease/immunology ; Hematopoietic Stem Cell Transplantation/methods/adverse effects ; Transplantation Conditioning/methods ; Major Histocompatibility Complex/immunology ; Transplantation, Homologous ; Allografts/immunology ; T-Lymphocytes/immunology/metabolism ; },
abstract = {Allogeneic hematopoietic cell transplantation (allo-HCT) is a potentially curative therapy for a variety of blood disorders but primarily reserved for blood cancer patients due to the life-threatening risk of acute graft-versus-host disease (aGVHD). Development of aGVHD is driven by alloreactive T cells that recognize the recipient's tissues as foreign and initiate a robust immune response causing severe tissue damage of the skin, liver, and gut. While methods to reduce aGVHD incidence and severity exist including posttransplant cyclophosphamide, relapse rates and transplantation-related mortality remain. We previously published a study using graft conditioning with glucocorticoids as a strategy to modify the immune repertoire in the donor grafts prior to transplantation to reduce aGVHD. Here, we describe a protocol to characterize the T-cell response in recipient mice given transplantation of graft-conditioned allogeneic donor cells via mass cytometry. Mass cytometry is a technology that uses heavy metal tags in place of fluorochromes to allow high-dimensional flow cytometric analysis. In this protocol, we include an antibody panel of 39 different antibodies conjugated to 41 different heavy metal tags that have been validated and titrated for barcoding and immunophenotyping by lineage markers, activation markers, cytokine secretion, and transcription factors. This chapter details the graft conditioning, transplantation, processing, barcoding, staining, and mass cytometric analysis of immune cells following murine allo-HCT.},
}
@article {pmid40097444,
year = {2025},
author = {Jin, W and Ma, J and Rong, L and Huang, S and Li, T and Jin, G and Zhou, Z},
title = {Semi-automated IT-scATAC-seq profiles cell-specific chromatin accessibility in differentiation and peripheral blood populations.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2635},
pmid = {40097444},
issn = {2041-1723},
mesh = {Animals ; Mice ; Humans ; *Chromatin/genetics/metabolism ; *Cell Differentiation/genetics ; *Leukocytes, Mononuclear/metabolism ; *Single-Cell Analysis/methods ; Chromatin Assembly and Disassembly ; High-Throughput Nucleotide Sequencing/methods ; Mouse Embryonic Stem Cells/metabolism ; Chromatin Immunoprecipitation Sequencing/methods ; Epigenomics/methods ; Sequence Analysis, DNA/methods ; Gene Library ; },
abstract = {Single-cell ATAC-seq (scATAC-seq) enables high-resolution mapping of chromatin accessibility but is often limited by throughput, cost, and equipment requirements. Here, we present indexed Tn5 tagmentation-based scATAC-seq (IT-scATAC-seq), a semi-automated, cost-effective, and scalable approach that leverages indexed Tn5 transposomes and a three-round barcoding strategy. This workflow prepares libraries for up to 10,000 cells in a single day, reduces the per-cell cost to approximately $0.01, and maintains high data quality. Comprehensive benchmarking demonstrates that IT-scATAC-seq achieves robust library complexity, high signal specificity, and improved cost-efficiency compared to existing methods. We apply IT-scATAC-seq to mouse embryonic stem cells, capturing chromatin remodelling during early differentiation, and to human peripheral blood mononuclear cells, resolving cell-type-specific regulatory programs. Here, we show that IT-scATAC-seq provides a robust and efficient approach for high-resolution single-cell epigenomic investigations, balancing scalability, data quality, and accessibility.},
}
@article {pmid40095752,
year = {2025},
author = {Suetsugu, K and Okada, H},
title = {Green, variegated, and albino Cremastra variabilis provide insight into mycoheterotrophic evolution associated with wood-decaying fungi.},
journal = {Plant biology (Stuttgart, Germany)},
volume = {},
number = {},
pages = {},
doi = {10.1111/plb.70014},
pmid = {40095752},
issn = {1438-8677},
support = {JPMJPR21D6//Precursory Research for Embryonic Science and Technology/ ; },
abstract = {With approximately 31,000 species, orchids begin life as mycoheterotrophs, relying on fungi to meet their carbon demands. Notably, some green orchids retain the ability to acquire carbon through fungal associations (partial mycoheterotrophy) and occasionally produce albino or, more rarely, variegated phenotypes. A linear relationship has been observed between leaf chlorophyll content and dependence on fungal-derived carbon, particularly in orchids associated with ectomycorrhizal (ECM) fungi, but whether such plasticity is similarly robust among orchids associated with non-ECM fungi remains underexplored. Here, we focused on the green, variegated, and albino forms of Cremastra variabilis, which likely lack ECM associations, to investigate (i) whether the degree of mycoheterotrophy, indicated by [13]C enrichment, correlates with chlorophyll content, and (ii) whether nutritional shifts align with changes in plant structure and mycorrhizal communities. Our results show that rhizoctonia fungi were dominant in green individuals with high chlorophyll levels and lacking coralloid rhizomes, whereas albino and most variegated individuals possessing coralloid rhizomes primarily associate with Psathyrellaceae fungi. Chlorophyll content and carbon stable isotope abundances were negatively correlated, indicating a gradient of increasing mycoheterotrophy from green to albino forms in individuals with coralloid rhizomes. In conclusion, C. variabilis maintains a flexible balance between photosynthesis and mycoheterotrophy, likely shaped by its subterranean morphology and fungal associations, with wood-decaying Psathyrellaceae fungi providing greater support for mycoheterotrophic nutrition than rhizoctonia fungi.},
}
@article {pmid40094434,
year = {2025},
author = {Mukherjee, A and Kar, O and Mukherjee, K and Mukherjee, B and Naskar, A and Banerjee, D},
title = {Molecular Identification of Onchocerciasis Vectors (Diptera: Simuliidae) from the Central Himalayan Landscape of India: A DNA Barcode Approach.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1089/vbz.2024.0123},
pmid = {40094434},
issn = {1557-7759},
abstract = {Background: Black flies (Diptera: Simuliidae) are a notorious group of blood-sucking insects acting as vectors of various diseases in humans and other animals, most notable being Onchocerciasis. Due to its medical and veterinary significance, accurate and quick species identification is of utmost importance in the field of black fly research. DNA barcoding is one such taxonomic tool, aiding in quick and efficient species identification using molecular methods. Despite sporadic reports of ocular and cutaneous Onchocerciasis, especially from North-East India, Indian Simuliidae has been understudied due to lack of expertise on morphological taxonomy and lack of genetic library. Materials and Methods: Blackflies were collected from eight distinct locations in the Central Himalayan region that are part of the West Bengal, India, districts of Kalimpong and Darjeeling. Various traps were used to collect the specimens, and they were kept it in 70% ethyl alcohol. Following the morphological identification of each fly specimen, genomic DNA was extracted from its dissected legs using the QIAmp DNA extraction kit (QIAGEN, Germany). The voucher specimen slide was deposited in the National Zoological collection, ZSI, Kolkata, India. Results: This is the first comprehensive DNA barcoding study of black flies (Feuerborni and Multistriatum species group) using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences along with morphological identification from the Central Himalayan region of West Bengal involving four species: Simulium dentatum, Simulium digitatum, Simulium praelargum, and Simulium senile. DNA barcode approach through ML tree clearly distinguished all the species with supporting PTP, ASAP, and GMYC analysis. Interspecific genetic distances were also calculated where S. dentatum and S. digitatum showed minimum distances in the study area. Conclusion: Coupled with a robust morpho-taxonomic framework, the DNA barcodes generated here will help with accurate species identification, which will lead to better management and control strategies for these harmful vector species at the study site.},
}
@article {pmid40093169,
year = {2025},
author = {Manian, KV and Ludwig, CH and Zhao, Y and Abell, N and Yang, X and Root, DE and Albert, ML and Comander, J},
title = {A comprehensive map of missense trafficking variants in rhodopsin and their response to pharmacologic correction.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40093169},
issn = {2692-8205},
support = {P30 EY014104/EY/NEI NIH HHS/United States ; R01 EY031036/EY/NEI NIH HHS/United States ; },
abstract = {Rhodopsin (RHO) missense variants are a leading cause of autosomal dominant retinitis pigmentosa (adRP), a progressive retinal degeneration with no currently approved therapies. Interpreting the pathogenicity of the growing number of identified RHO variants is a major clinical challenge, and understanding their disease mechanisms is essential for developing effective therapies. Here, we present a high-resolution map of RHO missense variant trafficking using two complementary deep mutational scanning (DMS) approaches based on a surface abundance immunoassay and a membrane proximity assay. We generated a comprehensive dataset encompassing all 6,612 possible single-residue missense variants, revealing a strong correlation between the two methods. Over 700 variants were identified with pathogenic trafficking scores, significantly expanding the number of RHO variants with functional evidence supporting pathogenicity. We demonstrate a high concordance between the trafficking scores and ClinVar pathogenicity classifications, highlighting this approach's utility in resolving variants of uncertain significance (VUS). The data also identified structurally clustered trafficking-deficient variants, predominantly within the N-terminal region and second extracellular loop, in and above the extracellular/intradiscal beta-plug region. Furthermore, we evaluated the efficacy of the non-retinoid pharmacological chaperone YC-001, observing significant rescue of trafficking defects in a majority of mistrafficking variants. This comprehensive functional map of RHO missense variants provides a valuable resource for pathogenicity assessment, genotype-phenotype correlations, and the development of targeted therapeutic strategies for RHO-adRP, paving the way for improved diagnosis and treatment for patients.},
}
@article {pmid40087979,
year = {2025},
author = {Van den Wyngaert, S and Cerbin, S and Garzoli, L and Grossart, HP and Gsell, AS and Kraberg, A and Lepère, C and Neuhauser, S and Stupar, M and Tarallo, A and Cunliffe, M and Gachon, C and Gavrilović, A and Masigol, H and Rasconi, S and Selmeczy, GB and Schmeller, DS and Scholz, B and Timoneda, N and Trbojević, I and Wilk-Woźniak, E and Reñé, A},
title = {ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14099},
doi = {10.1111/1755-0998.14099},
pmid = {40087979},
issn = {1755-0998},
support = {PID2020-112978GB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; CA20125//European Cooperation in Science and Technology/ ; 451-03-66/2024-03/200178//Ministarstvo Prosvete, Nauke i Tehnolo&#x161;kog Razvoja/ ; 239548-051//RANNIS Icelandic Research Fund/ ; 340659//Research Council of Finland/ ; 346387//Research Council of Finland/ ; 101086521//European Commission/ ; IR0000005//European Commission/ ; NKFIH KKP 144068//National Laboratory for Water Science and Water Security/ ; RRF-2.3.1-21-2022-00008//National Laboratory for Water Science and Water Security/ ; Y0801-B16//Austrian Science Fund/ ; //AXA Research Fund/ ; ANR-21-BIRE-0002-01//Agence Nationale de la Recherche/ ; 101052342//Biodiversa+/ ; CIR-01_00028//Italian Ministry of University and Research/ ; GR1540/33-1//Deutsche Forschungsgemeinschaft/ ; GR1540/47-1//Deutsche Forschungsgemeinschaft/ ; GR1540/48-1//Deutsche Forschungsgemeinschaft/ ; GR1540/51-1//Deutsche Forschungsgemeinschaft/ ; CEX2019-000928-S//AEI/ ; },
abstract = {Amplicon sequencing tools such as metabarcoding are commonly used for thorough characterisation of microbial diversity in natural samples. They mostly rely on the amplification of conserved universal markers, mainly ribosomal genes, allowing the taxonomic assignment of barcodes. However, linking taxonomic classification with functional traits is not straightforward and requires knowledge of each taxonomic group to confidently assign taxa to a given functional trait. Zoosporic parasites are highly diverse and yet understudied, with many undescribed species and host associations. However, they can have important impacts on host populations in natural ecosystems (e.g., controlling harmful algal blooms), as well as on industrial-scale algae production, e.g. aquaculture, causing their collapse or economic losses. Here, we present ParAquaSeq, a curated database of available molecular ribosomal sequences belonging to zoosporic parasites infecting aquatic vascular plants, macroalgae and photosynthetic microorganisms, i.e. microalgae and cyanobacteria. These sequences are aligned with ancillary data and other information currently available, including details on their hosts, occurrence, culture availability and associated bibliography. The database includes 1131 curated sequences from marine, freshwater and industrial or artificial environments, and belonging to 13 different taxonomic groups, including Chytridiomycota, Oomycota, Phytomyxea, and Syndiniophyceae. The curated database will allow a comprehensive analysis of zoosporic parasites in molecular datasets to answer questions related to their occurrence and distribution in natural communities. Especially through meta-analysis, the database serves as a valuable tool for developing effective mitigation and sustainable management strategies in the algae biomass industry, but it will also help to identify knowledge gaps for future research.},
}
@article {pmid40081365,
year = {2025},
author = {Vicario, R and Fragkogianni, S and Pokrovskii, M and Meyer, C and Lopez-Rodrigo, E and Hu, Y and Ogishi, M and Alberdi, A and Baako, A and Ay, O and Plu, I and Sazdovitch, V and Heritier, S and Cohen-Aubart, F and Shor, N and Miyara, M and Nguyen-Khac, F and Viale, A and Idbaih, A and Amoura, Z and Rosenblum, MK and Zhang, H and Karnoub, ER and Sashittal, P and Jakatdar, A and Iacobuzio-Donahue, CA and Abdel-Wahab, O and Tabar, V and Socci, ND and Elemento, O and Diamond, EL and Boisson, B and Casanova, JL and Seilhean, D and Haroche, J and Donadieu, J and Geissmann, F},
title = {Role of clonal inflammatory microglia in histiocytosis-associated neurodegeneration.},
journal = {Neuron},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuron.2025.02.007},
pmid = {40081365},
issn = {1097-4199},
abstract = {Langerhans cell histiocytosis (LCH) and Erdheim-Chester disease (ECD) are clonal myeloid disorders associated with mitogen-activated protein (MAP)-kinase-activating mutations and an increased risk of neurodegeneration. We found microglial mutant clones in LCH and ECD patients, whether or not they presented with clinical symptoms of neurodegeneration, associated with microgliosis, astrocytosis, and neuronal loss, predominantly in the rhombencephalon gray nuclei. Neurological symptoms were associated with PU.1[+] clone size (p = 0.0003) in patients with the longest evolution of the disease, indicating a phase of subclinical incipient neurodegeneration. Genetic barcoding analysis suggests that clones may originate from definitive or yolk sac hematopoiesis, depending on the patients. In a mouse model, disease topography was attributable to a local clonal proliferative advantage, and microglia depletion by a CSF1R-inhibitor limited neuronal loss and improved survival. These studies characterize a neurodegenerative disease associated with clonal proliferation of inflammatory microglia. The long preclinical stage represents a therapeutic window before irreversible neuronal depletion.},
}
@article {pmid40079026,
year = {2025},
author = {Ossowska, EA and Moncada, B and Lücking, R and Sérusiaux, E and Magain, N},
title = {Stictaflakusiorum and S.kukwae-two additional new species from the Neotropics (Peltigerales, Peltigeraceae).},
journal = {MycoKeys},
volume = {114},
number = {},
pages = {259-276},
pmid = {40079026},
issn = {1314-4049},
abstract = {Two additional species of Sticta are described as new to science based on material from Bolivia and Peru and supported by phylogenetic analysis of the fungal ITS barcoding marker. The two new species represent lineages within clade I on the global Sticta phylogeny. Stictaflakusiorum Ossowska, B. Moncada &amp; Lücking is a species in the S.humboldtii morphodeme and is characterized by lobes partly to entirely covered with white hairs, also covering the margins of submarginal and laminal apothecia, and the scabrid basal membrane of cyphellae, which is white to yellow, or partly brown, and when yellow K+ purple. The taxon was discovered at a single locality in Bolivia, but it is closely related to a potentially new Sticta species from Peru, which is here left undescribed. The other new species, S.kukwae Ossowska, Magain &amp; Sérus., belongs to the S.weigelii morphodeme. It has lobes with sinuous margins and dark, palmate to corymbose phyllidia. It was collected at several locations in Peru and a single locality in Bolivia.},
}
@article {pmid40078476,
year = {2025},
author = {Zhang, M and Zhai, X and He, L and Wang, Z and Cao, H and Wang, P and Ren, W and Ma, W},
title = {Morphological description and DNA barcoding research of nine Syringa species.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1544062},
pmid = {40078476},
issn = {1664-8021},
abstract = {INTRODUCTION: Syringa plants are highly valued for their ornamental qualities. However, traditional morphological identification methods are inefficient for discriminating Syringa species. DNA barcoding has emerged as a powerful alternative for species identification, but research on Syringa DNA barcodes is still limited.<br><br>METHODS: This study employed a multi-locus strategy, combining the nuclear ITS2 region with chloroplast genome regions psbA-trnH, trnL-trnF, and trnL to evaluate the effectiveness of Syringa DNA barcodes. The assessment involved genetic distance analysis, BLAST searches in NCBI, sequence character analysis, and phylogenetic tree construction, examining both individual and combined sequences.<br><br>RESULTS: The genetic distance analysis showed that the sequence combination of ITS2 + psbA-trnH + trnL-trnF exhibited a variation pattern where most interspecific genetic distances were greater than intraspecific genetic distances. The Wilcoxon signed-rank test results indicated that, except for psbA-trnH, the interspecific differences of the ITS2 + psbA-trnH + trnL-trnF sequence were greater than those of all single and combined sequences. BLAST analysis revealed that the identification rate for nine Syringa species using ITS2 + psbA-trnH + trnL-trnF could reach 98.97%. The trait-based method also demonstrated that ITS2 + psbA-trnH + trnL-trnF could effectively identify the nine Syringa species. Furthermore, the neighbor-joining (NJ) tree based on ITS2 + psbA-trnH + trnL-trnF clustered each of the nine Syringa species into distinct clades.<br><br>DISCUSSION: The study ultimately selected the barcode ITS2 + psbA-trnH + trnL-trnF, with an identification rate of 93.6%, as the optimal barcode for identifying nine species of Syringa trees. This combination proved to be highly effective in discriminating Syringa species, highlighting the potential of DNA barcoding as a reliable tool for species identification in Syringa. Future research could focus on expanding the sample size and exploring additional genetic markers to further enhance the accuracy and applicability of DNA barcoding in Syringa species identification.},
}
@article {pmid40078454,
year = {2025},
author = {Sterling, MJ and Price, BW and Lees, DC},
title = {A revision of the hitherto neglected genus Topiris Walker, 1863 (Lepidoptera, Xyloryctidae) with taxonomic notes on the genus Athrypsiastis Meyrick, 1910.},
journal = {ZooKeys},
volume = {1229},
number = {},
pages = {297-368},
pmid = {40078454},
issn = {1313-2989},
abstract = {The genus Topiris Walker, 1863 is revised. This genus, previously neglected or deemed unrecognisable, comprised only Walker's damaged and misrepaired type specimen of Topiriscandidella Walker, 1863. Evidence is provided that this specimen was collected by Alfred Russel Wallace in 1855-56 in Sarawak, Malaysian Borneo. The mitogenome of this specimen was assembled using low coverage whole genome sequencing (genome skimming). The COI-5P portion of this mitogenome (658 bp) differs by 1-3 bp from two haplotypes sequenced from early 1990's Brunei specimens. Another specimen recently discovered at NHMUK with an identical label to that of the type perfectly matches the Brunei specimens in its genitalia. Based on these four specimens, we present a fuller description of the morphology of T.candidella. Topiris includes the following additional species authored by Sterling and Lees: Topirisalbidella sp. nov., T.albogrisella sp. nov., T.cinderella sp. nov., T.digiticosta sp. nov., T.lacteella sp. nov., T.madonna sp. nov., T.meyricki sp. nov., T.ochrotincta sp. nov., T.schneeweissella sp. nov., T.sericella sp. nov., and T.thunbergella sp. nov. The following new combinations are also established: T.salva (Meyrick, 1932), comb. nov. and T.sampitella (Lvovsky, 2014), comb. nov. The type of Athrypsiastissalva Meyrick is confirmed as lost and so a neotype and paraneotype of this species are designated. A published mitogenome of "Linoclostisgonatias" is shown to be correctly identified as T.salva, and references to L.gonatias, identified in some literature as a pest of Theaceae, are likely misidentified. The genus Topiris is divided into three groups, the candidella group, the salva group, and the albidella group, based on characters in the male genitalia. The candidella group and albidella group are supported sub-clades of Topiris. The phylogenetic placement of Topiris and Athrypsiastis within 'core' Xyloryctidae (as subtended by its type species, X.luteotactella) is confirmed by analysis of COI and seven nuclear genes, whereas the genera Eumenodora Meyrick, 1906 and Izatha Walker, 1864 do not fall within this clade. The morphology of Athrypsiastisphaeoleuca Meyrick, 1910 (the type species of Athrypsiastis; Xyloryctidae) is more fully described. The following new species authored by Sterling and Lees are described: Athrypsiastischeesmanae sp. nov., A.edelweissella sp. nov., and A.penumbrella sp. nov. Two taxa are newly combined: Athrypsiastishalmaherella (Lvovsky, 2014), comb. nov. and Paralectarosiflora (Meyrick, 1930), comb. nov.},
}
@article {pmid40077453,
year = {2025},
author = {Wildbacher, M and Andronache, J and Pühringer, K and Dobrovolny, S and Hochegger, R and Cichna-Markl, M},
title = {Authentication of EU-Authorized Edible Insect Species in Food Products by DNA Barcoding and High-Resolution Melting (HRM) Analysis.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
pmid = {40077453},
issn = {2304-8158},
abstract = {The consumption of edible insects is a promising approach to meet the increasing global demand for food. Commercialization of edible insects in the EU is regulated by the Novel Food regulation. To date, the yellow mealworm (Tenebrio molitor larva), the migratory locust (Locusta migratoria), the house cricket (Acheta domesticus), and the buffalo worm (Alphitobius diaperinus larva) have been authorized in the EU for human consumption. We aimed to develop a method based on DNA barcoding and high-resolution melting (HRM) analysis for the identification and differentiation of these four EU-authorized edible insect species in food. A primer pair previously designed for DNA metabarcoding, targeting a ~200 bp sequence of mitochondrial 16S rDNA, allowed discrimination between the four insect species in highly processed food. However, house cricket and migratory locust could not unambiguously be differentiated from tropical house cricket, desert locust, superworm, cowpea weevil, and sago worm, respectively. This problem could be solved by designing primers specific for house cricket and migratory locust. By combining these primers with the insect primers, additional polymerase chain reaction (PCR) products for house cricket and migratory locust were obtained, resulting in more complex melt curves compared to the unauthorized insect species. The optimized PCR-HRM assay is a very cost-efficient screening tool for authentication of EU-authorized edible insect species in food.},
}
@article {pmid40076024,
year = {2025},
author = {Miller, C and Linzey, D and Hallerman, E},
title = {Morphological and Genetic Assessments of Coyote Diet in Qualla Boundary, North Carolina, Show Interaction with Humans.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {5},
pages = {},
pmid = {40076024},
issn = {2076-2615},
abstract = {Throughout the 20th century, coyotes (Canis latrans) expanded from their historical geographic range west of the Mississippi River to a current range of almost all of North America. Over the course of this expansion, coyotes have demonstrated diverse and variable omnivorous diets that change with the food resources available. This study examined the stomach contents of 25 coyotes in an area where they are relatively new, the Qualla Boundary in North Carolina, to better understand the diets of coyotes in this area. A combination of morphological identification and DNA barcoding was used to characterize the stomach contents of coyotes. Both plant and animal material were identified from anthropogenic and natural sources, the latter including native mammals. This study provides one example of the breadth and flexibility of coyote diets and helps build an understanding of how coyotes can adapt to new conditions.},
}
@article {pmid40075470,
year = {2025},
author = {Miao, K and Zhang, A and Yang, X and Zhang, Y and Lin, A and Wang, L and Zhang, X and Sun, H and Xu, J and Zhang, J and Feng, Y and Shao, F and Guo, S and Weng, Z and Luo, P and Wang, D and Gao, S and Zhao, XY and Xu, X and Deng, CX},
title = {Lymphatic system is the mainstream for breast cancer dissemination and metastasis revealed by single-cell lineage tracing.},
journal = {Molecular cancer},
volume = {24},
number = {1},
pages = {75},
pmid = {40075470},
issn = {1476-4598},
mesh = {*Breast Neoplasms/pathology/genetics/metabolism ; Female ; Humans ; *Tumor Microenvironment ; Animals ; *Single-Cell Analysis/methods ; Mice ; *Cell Lineage/genetics ; Lymphatic System/pathology ; Cell Line, Tumor ; Lymphatic Metastasis/pathology ; Neoplasm Metastasis ; },
abstract = {Cancer metastasis is the primary cause of cancer-related death, yet the forces that drive cancer cells through various steps and different routes to distinct target organs/tissues remain elusive. In this study, we applied a barcoding system based single-cell lineage tracing approach to study the metastasis rate and route of breast cancer cells and their interactions with the tumor microenvironment (TME) during metastasis. The results indicate that only a small fraction of cells, accounting for fewer than 3% of total barcodes, can intravasate from the primary site into the blood circulation, whereas more cells disseminate through the lymphatic system to different organs. Tumor cells derived from the same progenitor cell exhibit different gene expression patterns in different soils, and the cancer cell-TME communication paradigm varies significantly between primary and metastatic tumors. Furthermore, metastable cells require a prewired particular cytokine expression ability which may be specific for lymph metastasis route although the underlying mechanism requires further investigation. In summary, leveraging a single-cell lineage tracing system, we demonstrate that the crosstalk between tumor cells and the TME is the driving force controlling the preferential metastatic fate of cancer cells through the lymphatic system.},
}
@article {pmid40067649,
year = {2025},
author = {Cho, JM and Kang, M and Park, S and Oh, J and Ku, H and Shin, HY and Koh, JH and Cho, S and Kim, Y and Lee, S and Kim, YC and Han, SS and Joo, KW and Kim, YS and Yang, SH and Moon, KC and Lee, H and Kim, HJ and Kim, DK and , },
title = {Identification of conserved gene expression changes across common glomerular diseases by spatial transcriptomics.},
journal = {Journal of nephrology},
volume = {},
number = {},
pages = {},
pmid = {40067649},
issn = {1724-6059},
support = {RS-2024-00403375//Ministry of Health &amp; Welfare, Republic of Korea/ ; RS-2024-00345867//National Research Foundation of Korea (NRF)/ ; },
abstract = {BACKGROUND: Glomerular diseases encompass a group of kidney diseases that may share common gene expression pathways. Here, we analyzed glomerular-specific gene expression profiles across various glomerular diseases.<br><br>METHODS: We performed spatial transcriptomic profiling using formalin-fixed paraffin-embedded kidney biopsy specimens of controls and patients with five types of glomerular diseases using the GeoMx Digital Spatial Profiler. Disease-representative glomerular regions of interest (ROIs) were configured, probed with oligonucleotide barcodes linked with target complimentary sequence. The UV-cleaved barcodes were amplified to generate libraries and subsequently sequenced. Common differentially expressed genes across glomerular diseases were identified and Gene Ontology annotation was performed using the ToppGene suite.<br><br>RESULTS: The mean age of patients with glomerular diseases and kidney donors was 49.5&#x2009;&#xb1;&#x2009;12.2 and 49.5&#x2009;&#xb1;&#x2009;9.8&#xa0;years, respectively. A total of 35 differentially expressed genes were consistently downregulated in glomeruli across the disease compared to the control, while none of the differentially expressed genes were consistently upregulated. Twelve of 35 downregulated differentially expressed genes, including the two hub genes JUN and FOS, were annotated with molecular function Gene Ontology terms related to DNA-binding transcription factor activity. The annotated biological process Gene Ontology terms included response to lipid-related (17/35 differentially expressed genes), response to steroid hormone (12/35 differentially expressed genes), or cell cycle regulation (10/35 differentially expressed genes). Xenium and immunofluorescence staining confirmed the reduced expression of JUN, ZFP36, and KLF9 in intraglomerular cells of glomerular diseases.<br><br>CONCLUSIONS: Identifying common differentially expressed genes by spatial transcriptomic analysis provides insights into the underlying molecular mechanisms of glomerular diseases and may lead to novel assessment or therapeutic strategies.},
}
@article {pmid40066677,
year = {2025},
author = {Ascenzi, A and Wührl, L and Feng, V and Klug, N and Pylatiuk, C and Cerretti, P and Meier, R},
title = {EntoSieve: Automated Size-Sorting of Insect Bulk Samples to Aid Accurate Megabarcoding and Metabarcoding.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14097},
doi = {10.1111/1755-0998.14097},
pmid = {40066677},
issn = {1755-0998},
support = {B85F21005360001//Ministero dell'Universit&#xe0; e della Ricerca, Programma Operativo Nazionale/ ; },
abstract = {Widespread insect decline necessitates the development and use of standardized protocols for regular monitoring. These methods have to be rapid, efficient and cost-effective to allow for large-scale implementation. Many insect sampling and molecular methods have been developed. These include Malaise trapping, high-throughput DNA barcoding ('megabarcoding') and metabarcoding. The latter allows for assessing the species diversity in whole samples using few steps, but sample heterogeneity in terms of body size remains a challenge since large insects contribute disproportionately more mtDNA than small ones. This can potentially overwhelm the template DNA from small species that then go undetected. Size-sorting can mitigate this problem, but no satisfying automated, rapid and non-destructive solutions are available. We introduce the EntoSieve, a low-cost and DIY motorized instrument that disentangles and sorts abundant insect bulk samples into several body size fractions while minimizing damage to specimens, thus reducing the risk of DNA contamination across size fractions (e.g. legs of large specimens in small body size fraction). EntoSieve utilizes readily available components, 3D-printed parts and customizable meshes, thus enabling parallelization at low cost. We here show the efficiency of the EntoSieve for three samples with more than 10,000 specimens using three sieving protocols and assess the impact on specimen integrity. Efficiency ranged from 92% to 99%, achieved within 18-60 min, and specimen damage was not significant for subsamples. By facilitating rapid pre-processing, the device contributes to producing morphologically valuable vouchers for megabarcoding and is likely to improve compositional diversity accuracy across size classes when using metabarcoding.},
}
@article {pmid40066512,
year = {2025},
author = {Lv, Y and Liu, X and Liang, J and Dong, L and Zhang, Y and Lin, C and Xiang, S and Chen, B and Zhang, Z},
title = {Monochromatic Responsive HOF Heterostructures via VIA-Group-Based Framework Hybridization for Fully-Covert Photonic Barcode.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e2420486},
doi = {10.1002/adma.202420486},
pmid = {40066512},
issn = {1521-4095},
support = {22475047//National Natural Science Foundation of China/ ; 22373015//National Natural Science Foundation of China/ ; W2431013//National Natural Science Foundation of China/ ; 22271046//National Natural Science Foundation of China/ ; 22105039//National Natural Science Foundation of China/ ; 22425102//National Science Fund for Distinguished Young Scholars/ ; HFNKL2023WW04//Foundation of National Key Laboratory of Human Factors Engineering/ ; },
abstract = {Luminescent responsive heterostructures with region-domained emission and integrated responsiveness exhibit great potential in information security, but always suffer from the direct exposure of fingerprint information at the initial state, making it easy to decode the hidden confidential information. Herein, the first monochromatic responsive hydrogen-bonded organic framework (HOF) heterostructures are reported based on VIA-group-based framework hybridization toward fully-covert photonic barcodes. Designed HOF blocks with different VIA-group elements are integrated via a configuration-assimilation-based assembly method to generate the intrinsic monochromatic HOF heterostructures. Differentiated electronegativity of VIA-group elements endows each HOF block with distinct bonding stability, which triggers different responsive actions to the same stimuli, finally forming the multicolor emission mode at a responsive state. These monochromatic responsive HOF heterostructures can effectively hide the intrinsic fingerprint information, which further demonstrates the fully-covert photonic coding capability as high-security anti-counterfeiting labels. These findings offer novel insight on the exploitation of smart-responsive hetero-HOF systems for advanced information encryption and anticounterfeiting applications.},
}
@article {pmid40065744,
year = {2025},
author = {Marline, L and Ranaivoson, NAS and Smith, R and Ah-Peng, C and Hedderson, TAJ and Wilding, N and Antonelli, A},
title = {Advancing bryophyte research and conservation, a case study on Madagascar.},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcaf035},
pmid = {40065744},
issn = {1095-8290},
abstract = {BACKGROUND: Bryophytes are a group of plant that are ecologically important, diverse and include many undescribed species. Setting like Madagascar is well known for its charismatic species, less conspicuous groups, such as bryophytes, are virtually unknown to the public and the scientific community. Bryophyte diversity is a highly overlooked component of Madagascar's rich biodiversity, underlined by geographical sampling biases, sparse representation, and an evident research and conservation deficit as compared to more charismatic groups. With a significant bryophytes research gap and conservation, Madagascar can serve as model for addressing knowledge gaps and talking the global issue of bryophytes blindness. Here we first summarise historical research and current knowledge on the diversity and distribution of Malagasy bryophytes; address the issue of 'bryophyte blindness'; and propose future directions.<br><br>SCOPE: We give reason to think that to advance research and ensure the effective conservation of the bryophytes, it is crucial to build robust foundations for their study and appreciation. Investments on herbarium collections paired with leveraging technology and resources for identification, including an image bank and DNA barcodes, will facilitate taxonomic revisions, evolutionary biology and ecological research. Addressing geographical imbalances and fostering comprehensive research to elevate the scientific and public appreciation of bryophytes are key to advancing the integration of bryophytes into national, regional and global conservation initiatives. Key prospects also include research on ecosystems with high and/or endemic bryophyte diversity, facilitating the integration of bryophytes into conservation programs. Training the new generation of students and professionals on bryophytes is an imperative underlying all these initiatives. This is highly important to foster more equitable research and conservation in countries like Madagascar and help tackle bryophyte blindness in science and society, alongside with an urgently needed financial support for professional training to advance bryophytes research.<br><br>CONCLUSIONS: Overall, bryophytes need urgent research and conservation investments. Researchers, organisations, governments, and universities should collaborate to raise scientific and public awareness of their importance. Addressing key questions about bryophyte diversity, threats, and conservation requires a holistic, collaborative, and inclusive approach to bryophyte research.},
}
@article {pmid40063875,
year = {2025},
author = {Suzuki, M and Terada, R},
title = {DNA-based floristic survey of red algae (Rhodophyta) growing in the mesophotic coral ecosystems (MCEs) offshore of Tanegashima Island, northern Ryukyu Archipelago, Japan.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0316067},
pmid = {40063875},
issn = {1932-6203},
mesh = {*Rhodophyta/genetics ; Japan ; *Anthozoa/genetics ; *Ecosystem ; Animals ; Biodiversity ; Phylogeny ; DNA Barcoding, Taxonomic ; Islands ; DNA, Algal/genetics ; Coral Reefs ; },
abstract = {A molecular-based floristic survey of marine red algal biodiversity was conducted offshore Tanegashima Island, which is located at the northern end of mesophotic coral ecosystems (MCEs), in the Ryukyu Archipelago, Japan. This study provides the first comprehensive catalog of red algae comprising the sublittoral marine flora of offshore Tanegashima Island, Japan, and represents the first exhaustive molecular-assisted survey of red algal marine flora in Japan. Morphological and molecular analyses using plastid-encoded rbcL and mitochondrion-encoded cox1 genes revealed a total of 129 species, which included nine newly recognized species in Japan. Morphologically, 82 species were assigned to known species. Among the 82 species, 17 included cryptic species, and 25 appeared to have misapplied names. The remaining 47 species could not be identified to the species level, which indicates the necessity of a detailed reference library containing validated DNA barcodes and further taxonomic studies based on morpho-molecular analyses.},
}
@article {pmid40063774,
year = {2025},
author = {Trollip, C and Carnegie, A},
title = {First record of Graphium species associated with Euwallaceae perbrevis in Australia.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-02-25-0319-PDN},
pmid = {40063774},
issn = {0191-2917},
abstract = {In the wake of the detection of polyphagous shot hole borer (Euwallaceae fornicatus) in Perth, Western Australia, in 2021 (Cook and Broughton 2023), and ongoing surveillance for Fusarium dieback associated with ambrosia beetles in New South Wales (NSW) (Callaghan et al. (2024), there is a growing need to characterize fungal associates of already-established Euwallaceae species in Australia. Historically, plant health diagnostics targeting fungi vectored by tea shot hole borer, Euwallaceae perbrevis, in Australia has focused on Fusarium species, with only Fusarium obliquiseptatum and F. metavorans reported to date (Aoki et al. 2019; Callaghan et al. 2024). No other fungal associates have been reported from this vector in Australia despite the presence of key symbionts found in association with Euwallaceae beetles globally (Lynch et al. 2016, Na et al. 2018). In 2024, three cases of beetle infestation associated with dieback and tree mortality reported to forest biosecurity staff of NSW provided an opportunity for more detailed diagnostic investigations. The first was from Acer paxii at the Royal Botanic Garden of Sydney in April, the second from a stand of Cupaniopsis anacardioides at Lennox Head, northern NSW, in August, and the third from Ficus obliqua at the Royal Botanic Garden of Sydney in November. Isolations were performed from stained wood tissue, beetle galleries, and directly from beetle specimens, similar to described protocols (Lynch et al. 2016). Fusarium obliquiseptatum was confirmed in all cases (data not shown), however, Graphium spp. were readily observed in beetle galleries and in low abundance co-occuring with F. obliquiseptatum on isolation plates. Graphium isolates were recovered by picking conidial spore drops from synnemata and hyphal tipping to produce axenic cultures. Molecular identification was achieved by PCR and sequencing the internal transcribed spacer (ITS) and the translation elongation factor 1α barcoding regions using primers ITS1-ITS4 and EF2F-EF2R, respectively (Marincowitz et al. 2015). Three Graphium taxa were identified, viz. Graphium euwallaceae (DAR 86890) isolated from A. paxii in Sydney, the currently undescribed Graphium sp. II (DAR 86892) isolated from C. anacardioides in Lennox Head, and a putatively novel Graphium taxon, Graphium cf. basitruncatum (DAR 86894), isolated from F. obliqua in Sydney. These detections represent the first records of Graphium species associated with E. perbrevis in Australia. Graphium euwallaceae is a well-established fungal symbiont of E. fornicatus and E. perbrevis globally, previously reported in the United States, Vietnam and most recently in Perth, Western Australia (Lynch et al. 2016, Wright and Kehoe pers. comm.). In contrast, Graphium sp. II has only been previously recorded from a Durio sp. in Thailand (Na et al. 2018). The taxon identified as Graphium cf. basitruncatum is most closely related to G. basitruncatum, originally found in forest soils in the Solomon Islands and Japan (Okada et al. 2000). Graphium species are often regarded as saprobes or nutritional symbionts of ambrosia beetles, however their role in the lifecycle of Euwallaceae beetles and demonstrated pathogenic potential is arguably underappreciated in biosecurity (EPPO 2020, Lynch et al. 2016, Na et al. 2018). Future research in this regard might provide better assessment of the risks posed by fungal symbionts that goes beyond predetermined views of pathogenicity.},
}
@article {pmid40061916,
year = {2025},
author = {Arabeyyat, Z and Sweiss, M and Alajlouni, A and Al-Ajlouni, N and Mahmoud, M and Shartooh, S and Alsoqi, F and Kteifan, M},
title = {Identification and phylogenetic analysis of marine sponges in the Jordanian Gulf of Aqaba using DNA barcoding.},
journal = {Heliyon},
volume = {11},
number = {4},
pages = {e42771},
pmid = {40061916},
issn = {2405-8440},
abstract = {Sponges (Porifera) are the largest biomass component of coral reefs benthic fauna among marine organisms and are very morphologically diverse. In the present work, we aimed to identify marine sponges in the Jordanian Gulf of Aqaba using the partial 18S rRNA and the 28S rRNA genes as DNA barcoding markers. A total of nine morphologically different marine sponge samples from 6.6m to approximately 22m depth were collected. Sponge fragments were frozen at -80 °C prior to DNA extraction. The sponge's DNA was extracted using a commercial kit and subjected directly to PCR amplification for the 18S rRNA and 28S rRNA genes. The DNA sequences were analyzed using the Basic Local Alignment Search Tool (BLAST) to determine the sponge's identity, and phylogenetic trees were constructed to clarify the relationship among the samples. The results obtained revealed the presence of the following genera: Axinella, Negombata, Siphonochalina, Diacarnus, and an unidentified genus within the order Haplosclerida. Identification of sponge species was difficult due to the scarcity of diagnostic morphological characters. To our knowledge, this is the first study in the Jordanian Gulf of Aqaba that focuses on the morphological and molecular taxonomy of marine sponges using DNA barcoding markers.},
}
@article {pmid40060715,
year = {2025},
author = {Moura, CJ and Wirtz, P and Nhanquê, FT and Barbosa, C and Serrão, E},
title = {Hotspot of Exotic Benthic Marine Invertebrates Discovered in the Tropical East Atlantic: DNA Barcoding Insights From the Bijagós Archipelago, Guinea-Bissau.},
journal = {Ecology and evolution},
volume = {15},
number = {3},
pages = {e70964},
pmid = {40060715},
issn = {2045-7758},
abstract = {This study aimed to explore and document putative exotic marine benthic invertebrate species in the Bijagós Archipelago, Guinea-Bissau, to enhance understanding of marine biodiversity and address the extent of marine species introductions. The research was conducted in the Bijagós Archipelago, a UNESCO Biosphere Reserve located in Guinea-Bissau. The study involved the region's first scuba-diving survey of marine biodiversity. DNA barcoding was employed to assist in the identification of benthic invertebrate species. Molecular phylogenetic analyses were conducted with the available DNA barcodes to ensure accurate taxonomic assignments, detect cryptic species, and investigate the phylogeography of the taxa. The survey resulted in the discovery of 28 new species records for the Bijagós Archipelago, including octocorals, scleractinians, hydroids, bryozoans, barnacles, and ascidians. Among these, six species were documented for the first time in the East Atlantic: Stragulum bicolor, Nemalecium lighti, Diphasia sp., Amathia alternata, A. distans, and Symplegma rubra. Molecular analyses revealed pervasive cryptic diversity within species previously listed as exotic, suggesting that some, such as the hydroids Plumularia setacea, Obelia geniculata, and Dynamena disticha, are not exotic due to their restricted biogeographic distributions. Many other species reported as introduced present only a few genetic lineages capable of long-distance dispersal due to human activities. The study highlights considerable gaps in the knowledge of West African marine biodiversity and suggests a substantial underestimation of the anthropogenic trade in exotic marine species between the Tropical East Atlantic and the Americas, and between the Indo-Pacific, Mediterranean, and West Africa. Detailed taxonomic and genomic analyses are necessary for understanding marine exotic species' biogeography and adaptive traits. Our findings challenge current classifications of exotic species and underscore the need for improved monitoring and management to prevent the spread of non-native marine species.},
}
@article {pmid40060547,
year = {2025},
author = {Feldman, D and Sims, JN and Li, X and Johnson, R and Gerben, S and Kim, DE and Richardson, C and Koepnick, B and Eisenach, H and Hicks, DR and Yang, EC and Wicky, BIM and Milles, LF and Bera, AK and Kang, A and Brackenbrough, E and Joyce, E and Sankaran, B and Lubner, JM and Goreshnik, I and Vafeados, D and Allen, A and Stewart, L and MacCoss, MJ and Baker, D},
title = {Massively parallel assessment of designed protein solution properties using mass spectrometry and peptide barcoding.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40060547},
issn = {2692-8205},
support = {P30 GM133893/GM/NIGMS NIH HHS/United States ; U19 AG065156/AG/NIA NIH HHS/United States ; R01 AG063845/AG/NIA NIH HHS/United States ; R01 AI160052/AI/NIAID NIH HHS/United States ; R01 CA240339/CA/NCI NIH HHS/United States ; },
abstract = {Library screening and selection methods can determine the binding activities of individual members of large protein libraries given a physical link between protein and nucleotide sequence, which enables identification of functional molecules by DNA sequencing. However, the solution properties of individual protein molecules cannot be probed using such approaches because they are completely altered by DNA attachment. Mass spectrometry enables parallel evaluation of protein properties amenable to physical fractionation such as solubility and oligomeric state, but current approaches are limited to libraries of 1,000 or fewer proteins. Here, we improved mass spectrometry barcoding by co-synthesizing proteins with barcodes optimized to be highly multiplexable and minimally perturbative, scaling to libraries of >5,000 proteins. We use these barcodes together with mass spectrometry to assay the solution behavior of libraries of de novo-designed monomeric scaffolds, oligomers, binding proteins and nanocages, rapidly identifying design failure modes and successes.},
}
@article {pmid40060545,
year = {2025},
author = {Jang, J and Ko, KP and Zhang, J and Jun, S and Park, JI},
title = {Deciphering Precursor Cell Dynamics in Esophageal Preneoplasia via Genetic Barcoding and Single-Cell Transcriptomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40060545},
issn = {2692-8205},
support = {P30 CA016672/CA/NCI NIH HHS/United States ; R03 CA256207/CA/NCI NIH HHS/United States ; R01 CA278967/CA/NCI NIH HHS/United States ; K99 CA286761/CA/NCI NIH HHS/United States ; R03 CA279867/CA/NCI NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; R01 CA278971/CA/NCI NIH HHS/United States ; R01 CA193297/CA/NCI NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; },
abstract = {Cancer cells exhibit high heterogeneity and lineage plasticity, complicating studies of tumorigenesis and development of therapies. Recently, preneoplastic cells, although histologically normal, have been shown to possess high plasticity and early genetic alterations, yet their origins and lineage trajectories remain unclear. Herein, we introduce a lineage-tracing tool integrating genetic barcoding with single-cell RNA sequencing to map preneoplastic esophageal cell lineages. We identified preneoplastic precursor cells (PNPCs) as a distinct progenitor-like population with unique transcriptional profiles and high plasticity, contributing to proliferative and basal cell populations. To enhance lineage mapping, we developed the eXamined Ridge (XR) score, accurately identifying high-plasticity cells. Nfib and Qk emerged as conserved PNPC markers, peaking in early preneoplasia and declining after malignant transformation. These findings reveal PNPCs as key players in early tumorigenesis and highlight their potential as biomarkers for early cancer detection and therapeutic intervention, offering new strategies for preventing esophageal cancer progression.},
}
@article {pmid40058416,
year = {2025},
author = {Munir Ahamed, J and Dahms, HU and Schizas, NV and Rathinam, AJ and Ouddane, B and Huang, YL},
title = {Isolation of Pseudonocardia strains associated with the shallow water hydrothermal vent crab Xenograpsus testudinatus from a metal-rich environment: Biochemical characterization and enzymatic characterization, molecular identification, antibacterial, antibiofilm and antioxidant activity.},
journal = {Microbial pathogenesis},
volume = {203},
number = {},
pages = {107457},
doi = {10.1016/j.micpath.2025.107457},
pmid = {40058416},
issn = {1096-1208},
abstract = {A shallow hydrothermal vent at Kueishantao Island, Taiwan provides a challenging environment and has been less explored for its microbial communities, especially the actinomycetes and their antibacterial and antioxidant activity. Nine actinomycete strains were isolated from the endemic hydrothermal vent crab Xenograpsus testudinatus and were identified as belonging to the rare actinomycete genus Pseudonocardia sp. Physiochemical results showed that the optimum growth conditions of these nine isolates were at pH 7, 35 °C, and 0.5-2% NaCl. Biochemical characterization showed differences between the strains. These isolates were further characterized at genetic barcoding (16s rRNA sequencing) and phenotypic levels and identified at the species/strain level as Pseudonocardia alni SCSW01, Pseudonocardia yuanmonensis SCSW02, Pseudonocardia sp. strains SCSW03, SCSW04, SCSW05, SCSW06, BCSW29, ECSW09, and ECSW018. The morphology of the strains was analyzed using an environmental scanning electron microscope (ESEM). The nine isolates showed potential antibacterial activity against gram-positive and gram-negative pathogenic strains. The confocal laser scanning microscopy (CLSM) images show live and dead cells and biofilm/antibiofilm activity of the actinomycete supernatant and crude extracts against pathogenic bacterial strains. The crude extracts of SCSW02, SCSW06, BCSW29, ECSW09, and ECSW018 showed antibiofilm activity against P. aeruginosa, E. coli, and S. aureus. The antioxidant activity such as DPPH and H2O2 scavenging assay results showed that the nine actinomycetes crude extracts hold more substantial radical scavenging properties than supernatants. Our results marked the first report of Pseudonocardia genera from the vent crab Xenograpsus testudinatus of the HV region at Kueishantao island, Taiwan.},
}
@article {pmid40057837,
year = {2025},
author = {Zajta, E and Peskó, G and Knapp, GD and Vad, E and Bödör, C and Sinkó, J},
title = {[Opportunities offered by molecular diagnostics in the management of invasive fungal infections of oncohematological patients].},
journal = {Orvosi hetilap},
volume = {166},
number = {10},
pages = {363-376},
doi = {10.1556/650.2025.33241},
pmid = {40057837},
issn = {1788-6120},
mesh = {Humans ; *Invasive Fungal Infections/diagnosis ; Hematologic Neoplasms/complications/diagnosis ; Hungary ; Polymerase Chain Reaction/methods ; Molecular Diagnostic Techniques/methods ; Antifungal Agents/therapeutic use ; },
}
@article {pmid40056601,
year = {2025},
author = {Wu, SR and Sharpe, J and Tolliver, J and Groth, AJ and Chen, R and Guerra García, ME and Valentine, V and Williams, NT and Jacob, S and Reitman, ZJ},
title = {Combining the RCAS/tv-a retrovirus and CRISPR/Cas9 gene editing systems to generate primary mouse models of diffuse midline glioma.},
journal = {Neoplasia (New York, N.Y.)},
volume = {62},
number = {},
pages = {101139},
pmid = {40056601},
issn = {1476-5586},
mesh = {Animals ; *CRISPR-Cas Systems ; *Gene Editing ; Mice ; *Glioma/genetics/pathology/therapy ; *Disease Models, Animal ; *Brain Neoplasms/genetics/pathology/therapy ; Retroviridae/genetics ; Humans ; Tumor Suppressor Protein p53/genetics ; Mice, Transgenic ; Receptors, Virus ; Avian Proteins ; },
abstract = {Diffuse midline gliomas (DMGs) are lethal brain tumors that arise in children and young adults, resulting in a median survival of less than two years. Genetically engineered mouse models (GEMMs) are critical to studying tumorigenesis and tumor-immune interactions, which may inform new treatment approaches. However, current midline glioma GEMM approaches are limited in their ability to multiplex perturbations and/or target specific cell lineages in the brain for genetic manipulation. Here, we combined the RCAS/tv-a avian retrovirus system and CRISPR/Cas9 genetic engineering to drive midline glioma formation in mice. CRISPR/Cas9-based disruption of Trp53, a tumor suppressor that is frequently disrupted in midline gliomas, along with the oncogene PDGF-B resulted in high grade tumor formation with moderate latency (median time to tumor formation of 12 weeks). We confirmed CRISPR-mediated Trp53 disruption using next-generation sequencing (NGS) and immunohistochemistry (IHC). Next, we disrupted multiple midline glioma tumor suppressor genes (Trp53, Pten, Atm, Cdkn2a) in individual mouse brains. These mini-pooled in vivo experiments generated primary midline gliomas with decreased tumor latency (median time to tumor formation of 3.6 weeks, P < 0.0001, log-rank test compared to single-plex gRNA). Quantification of gRNA barcodes and CRISPR editing events revealed that all tumors contained cells with various disruptions of all target genes and suggested a multiclonal origin for the tumors as well as stronger selection for Trp53 disruption compared to disruption of the other genes. This mouse modeling approach will streamline midline glioma research and enable complex experiments to understand tumor evolution and therapeutics.},
}
@article {pmid40052334,
year = {2025},
author = {Lu, Y and Dong, Y and Zhang, M and Mao, L},
title = {Genome and Metagenome Skimming: Future Sequencing Methods for Environmental DNA (eDNA) Studies.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14095},
doi = {10.1111/1755-0998.14095},
pmid = {40052334},
issn = {1755-0998},
support = {2023YFF0805800//the National Key Research and Development Program of China/ ; BE2022792//Jiangsu Social Development Program/ ; },
abstract = {Genome skimming (GS), also referred to as low-coverage shotgun sequencing, is an efficient and cost-effective sequencing method that targets high-copy regions in genomes. It is most commonly used for species identification, phylogenetic analysis and expansion of reference libraries. GS can be applied to single species or composite DNA samples representing multiple species; the latter is termed metagenome skimming (MGS). GS/MGS shows promise as an effective approach for environmental DNA (eDNA) studies, but it is currently limited to ancient sedimentary samples. There is the potential to expand this methodology to other eDNA sources, including water, soil and airborne samples. In this paper, we introduce GS/MGS and briefly review its current applications. We also discuss the potential benefits and challenges of using GS/MGS to assay eDNA. eDNA GS/MGS is a promising technology that could broaden eDNA studies if some methodological challenges can be addressed.},
}
@article {pmid40052073,
year = {2025},
author = {Schnittler, M and Leontyev, D and Yatsiuk, I and Ronikier, A},
title = {Species descriptions in myxomycetes - can we settle on rules for good taxonomic practice?.},
journal = {IMA fungus},
volume = {16},
number = {},
pages = {e141199},
pmid = {40052073},
issn = {2210-6340},
abstract = {Myxomycetes are a unique branch of life, recognisable by sporophores showing a fungus-like dispersal biology. These structures bear nearly all diagnostic characters for species identification and develop by rapid transformation of plasmodia. During this short period of time, external factors can significantly influence the formation of morphological characters. Therefore, the description of a new species must be carried out with utmost care. Over the last 50 years, approximately 10-15 new species of myxomycetes have been described per year and only some of the latest publications underpin this with molecular data. In this paper, we discuss a set of recommendations for the description of myxomycete species new to science, striving for the following goals: (i) to minimise the number of erroneous descriptions of the species, whose names later have to be put into synonymy; (ii) to make all respective data easily accessible for the scientific community; and (iii) to comply with existing rules of nomenclature. We recommend (1) whenever possible not to describe a new taxon from a single specimen; however, an exception could be made only if supported by molecular data and by unique morphological characters which are unlikely to fall in the range of infraspecific variation of related species; (2) preparing detailed descriptions, including data on developmental stages, microhabitats, ecology, phenology and associated species; (3) providing at least two independent diagnostic characters that tell the new species apart from all others; (4) obtaining a molecular barcode and, whenever possible, providing proof for reproductive isolation of the new species from related taxa; and (5) depositing type specimens in public herbaria. To comply with nomenclatural rules, (6) the new name must be registered in a recognised repository, (7) all published names should be checked for usability before proposing a new name and (8) a unique name should be chosen, preferably highlighting a distinct character of the new species.},
}
@article {pmid40051454,
year = {2025},
author = {Zavala, E and Britzke, R and Siccha-Ramírez, Z and Ramirez, JL},
title = {DNA barcoding of marine rocky reef fishes from northern Peru suggests a parapatric speciation in the Tropical Eastern Pacific.},
journal = {Ecology and evolution},
volume = {15},
number = {3},
pages = {e70125},
pmid = {40051454},
issn = {2045-7758},
abstract = {Northern Peru marks the end of an extensive coastal marine region: The Panama province, which is characterized by predominantly tropical and equatorial features and is home to the only rocky reefs known in Peruvian territory. This unique ecosystem could explain the presence of a diverse range of fish species. However, due to the difficulty of sampling and accessing reef areas, our knowledge of this biodiversity is incomplete. To address this issue, we used DNA barcoding for the study of the fish biodiversity and revealed patterns that may have influenced their evolution throughout the Tropical Eastern Pacific (TEP). A fragment of Cytochrome oxidase subunit I (COI) of 177 samples of rocky reef fishes was sequenced. Intra and interspecific K2P distances were calculated and three species delimitation methods (GMYC, PTP, and bPTP) were used to obtain MOTUs. Both analyses support the conformation of additional MOTUs in samples of Mugil cephalus, Ophichthus zophochir, Malacoctenus tetranemus, Ariopsis seemanni and Halichoeres dispilus, species with a divergence above 2%. By comparing these sequences with public data, our analysis revealed the existence of COI lineages and suggested potential ecological parapatric speciation in the TEP. More studies using other markers and different approaches are required to confirm the existence of species complexes that could be related to the presence of cryptic species.},
}
@article {pmid40048560,
year = {2025},
author = {Bi, W and Cao, X and Li, J and Gao, Y and Song, Y and He, B},
title = {Ultrasensitive Detection of Extracellular Vesicles Based on Metal-Organic Framework DNA Biobarcodes Triggered G-Quadruplex Coupled with Rolling Circle Amplification Assay.},
journal = {ACS sensors},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssensors.4c03384},
pmid = {40048560},
issn = {2379-3694},
abstract = {Extracellular vesicles (EVs), as liquid biopsy markers for accurate tumor diagnosis, are considered to hold great promise. However, effectively isolating and sensitively detecting EVs with convenience still face challenges. Herein, we propose a highly sensitive and specific platform for EV detection by integrating a metal-organic framework (MOF)-based DNA biobarcodes strategy with a rolling circle amplification (RCA)/G-quadruplex system. In this study, first, Zr-MOFs act as signal converters by comodification with DNA barcodes and antibodies, converting and amplifying the abundance of EVs into DNA barcodes. Second, the released DNA can trigger RCA, followed by G-quadruplex formation to further amplify the signal. Consequently, this approach significantly enhances the sensitivity for EV biomarker detection, achieving a low limit of detection of 100 EVs mL[-1]. Furthermore, the strategy offers high sensitivity, specificity, accuracy, and simplicity, highlighting its potential for clinical applications in noninvasive EV detection.},
}
@article {pmid40047956,
year = {2025},
author = {Meghana, BN and Reshma, SV},
title = {DNA barcoding of geographical indication tagged Byadagi chilli and its cultivars using ITS2, matK and rbcL coding sequences.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {286},
pmid = {40047956},
issn = {1573-4978},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Phylogeny ; *Capsicum/genetics/classification ; DNA, Plant/genetics ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: Byadagi chilli, a Geographical Indication (GI)-tagged chilli variety known for its special aroma and bright red colour, was accorded the GI tag in February 2011 with the GI number 129. The two traditional varieties of Byadagi chilli, namely: Dabbi and Kaddi, are the GI-tagged varieties. In this study, GI-tagged Byadagi Dabbi, Byadagi Kaddi and other cultivars of Byadagi chilli, such as Byadagi Lali (BL), Byadagi HPH 2043 (B2), Byadagi BSS 355 (B3) and another popular GI-tagged chilli variety, Guntur Sannam, were analysed to assess their inter-relationships. Due to the high market value and demand, it is important to identify and differentiate the original variety of Byadagi chilli and its associated cultivars from the other chilli cultivars, which are sold under the name of Byadagi chilli. In this study, molecular assessment by DNA barcoding was performed to establish the identity of authentic Byadagi chilli varieties.<br><br>METHODS AND RESULTS: Five samples of Byadagi chilli and another GI-tagged chilli variety, Guntur Sannam, were analysed using three DNA barcodes: ITS2, matK and rbcL. The PCR products were sequenced, nucleotide BLAST was performed and ITS2 showed 97.7% identity, matK 99.1%, and rbcL 99.19% with Capsicum annuum at the genus and species levels. Phylogenetic analysis of the DNA sequences of all the six chilli samples was performed using ClustalW multiple sequence alignment in MEGA11. The genetic distance between the six samples was calculated using the maximum likelihood approach.<br><br>CONCLUSIONS: This study distinctly demonstrates that the chloroplast DNA barcodes matK and rbcL, along with the nuclear DNA barcode, ITS2, can be used for accurate identification of Byadagi chilli cultivars. This study offers significant molecular identification and establishes a robust barcoding foundation for Byadagi chilli. The phylogenetic trees generated from the barcode sequences clearly indicated the relationships among the selected cultivars.},
}
@article {pmid40046838,
year = {2025},
author = {Yang, G and Wang, W and Tong, Y and Zhou, Z},
title = {Species delimitation and DNA barcoding for Chinese Mantodea (Insecta, Dictyoptera).},
journal = {ZooKeys},
volume = {1229},
number = {},
pages = {25-42},
pmid = {40046838},
issn = {1313-2989},
abstract = {DNA barcoding has been proposed as a rapid and reliable tool for animal identification and species delineation. The 5' end of the mitochondrial cytochrome c oxidase I gene (COI-5P) was sequenced for 318 specimens of 55 mantis species. Of these, 44 species had not been sequenced before, thus being new COI-5P barcode sequences to science. Another 61 COI-5P barcode sequences comprising five species were retrieved from the Barcode of Life Database (BOLD; www.boldsystems.org). Five species delimitation algorithms were employed to sort barcode sequences into Molecular Operational Taxonomic Units (MOTUs), namely the distance-based Barcode Index Number (BIN) System, Generalized Mixed Yule Coalescent (GMYC), a Java program that uses an explicit, determinate algorithm to define Molecular Operational Taxonomic Unit (jMOTU), Assemble Species by Automatic Partitioning (ASAP), and Bayesian implementation of the Poisson Tree Processes model (bPTP). All species, except Hierodulachinensis Werner, 1929, were recovered as monophyletic on the neighbor-joining (NJ) tree. For the final dataset, 379 COI-5P barcode sequences were assigned to 68 BINs. Fifty-five out of 68 BINs obtained were new to BOLD. The low level of BIN overlap with other nations highlights the importance of constructing a regional DNA barcode reference library. The algorithms ASAP, jMOTU, bPTP, and GMYC clustered barcode sequences into 32, 58, 68, and 60 MOTUs, respectively. All species delimitation algorithms (except ASAP analysis) split Anaxarchasinensis Beier, 1933, Anaxarchazhengi Ren &amp; Wang, 1994, H.chinensis, Spilomantisoccipitalis (Westwood, 1889), Titanodulaformosana Giglio-Tos, 1912 into more than one MOTUs. All algorithms merged Hierodula sp. BCM-2019 and H.chinensis into the same MOTU, as for Tenoderaaridifolia Stoll, 1813 and Tenoderasinensis Saussure, 1871. More accurate identification results need to be supplemented by detailed morphological classification.},
}
@article {pmid40045661,
year = {2025},
author = {Chiyo, PI and King'ori, E},
title = {Genetic identification of Stephanofilaria sp. isolated from ulcerative dermal lesions in black rhinoceros.},
journal = {Journal of helminthology},
volume = {99},
number = {},
pages = {e42},
doi = {10.1017/S0022149X25000112},
pmid = {40045661},
issn = {1475-2697},
mesh = {Animals ; *Perissodactyla/parasitology ; *Phylogeny ; *Genetic Variation ; Electron Transport Complex IV/genetics ; DNA, Ribosomal Spacer/genetics ; Filarioidea/genetics/classification/isolation &amp; purification ; DNA Barcoding, Taxonomic ; Sequence Analysis, DNA ; DNA, Helminth/genetics ; Skin Ulcer/parasitology/veterinary ; },
abstract = {Stephanofilaria is a genus of nematodes that cause ulcerative dermal lesions in large mammals. However, there is a dearth of knowledge on the molecular genetics of Stephanofilaria species infecting critically endangered rhinoceros. This study employed genetic barcoding genes to identify Stephanofilaria species and to determine its genetic diversity and evolution. Phylogenetic analyses on partial genes of the second internal transcribed spacer Ribosomal DNA (ITS-2) and cytochrome c oxidase subunit 1 (Cox-1), revealed a 77% and 93% bootstrap support at the Cox-1 and ITS-2 loci respectively to a clade containing previously identified Stephanofilaria species. Morphological examination also confirmed features diagnostic of Stephanofilaria dinniki previously known to infect rhinoceros. Gene diversity of Cox-1 was 0.931 ± 0.030 and 0.579 ± 0.104 for the ITS-2, whereas nucleotide diversity was 0.008 ± 0.002 and 0.00197 ± 0.0016 for the Cox-1 and ITS-2 genes respectively. Neutrality tests (Fu and Li's D* and Fu and Li's F*) were significantly negative (p<0.05) at all loci, whereas Tajima D and Fu's FS were each statistically significant (p<0.05) at the Cox-1 and ITS-2 loci respectively. The high gene diversity, low nucleotide diversity and negative neutrality tests are consistent with positive selection at the Cox-1 gene. Stephanofilaria infection among rhinoceros is currently restricted to highland sanctuaries compared to a widespread distribution in both lowlands and highlands in the 1960s suggesting an adaptation to vectors thriving in cooler highland temperatures. This is the first genetic identification of S. dinniki, in rhinoceros and will aid in diagnosis, treatment, studies, and rhinoceros conservation.},
}
@article {pmid40045410,
year = {2025},
author = {Franco Martins, J and Dina Troco, A and Marques, C and Chipepa, V and Seixas, G and Pinto, J and Garcia, L and Pedro Jorge, C and Manuel, E and Alves, G},
title = {Asian tiger mosquito in the oil-producing city of Soyo: the first report of Aedes (Stegomyia) albopictus (Skuse, 1894) in Angola.},
journal = {Parasites &amp; vectors},
volume = {18},
number = {1},
pages = {90},
pmid = {40045410},
issn = {1756-3305},
mesh = {Animals ; Angola ; *Aedes/genetics/classification/physiology ; *Mosquito Vectors/genetics/classification/physiology ; *Phylogeny ; Larva/genetics ; Electron Transport Complex IV/genetics ; Humans ; DNA Barcoding, Taxonomic ; Introduced Species ; Cities ; Female ; },
abstract = {BACKGROUND: The Asian tiger mosquito, Aedes albopictus (Skuse, 1894), is a highly invasive species that has successfully colonized many tropical and temperate regions worldwide. Its rapid global spread is strongly associated with human activities and has created favorable conditions for the emergence of human arboviruses in new geographic areas.<br><br>METHODS: Mosquito larvae were collected by community health workers from different breeding sites and reared to adults in a field insectary. Adult mosquitoes were morphologically identified to species level. Species identification was confirmed by cytochrome oxidase subunit I DNA barcoding.<br><br>RESULTS: We report the first detection of Aedes albopictus in Angola during an Anopheles stephensi survey conducted in Soyo, Zaire Province. Phylogenetic analysis indicated that the Angolan Ae. albopictus population clusters with sequences from Central African countries, suggesting an introduction from within the continent.<br><br>CONCLUSIONS: The presence of Ae. albopictus in Angola highlights the need for enhanced vector surveillance and control measures to prevent the emergence of arboviral diseases. This finding emphasizes the relevance of collaboration between local health authorities, communities, and international organizations in monitoring the spread of invasive mosquito species.},
}
@article {pmid40043011,
year = {2025},
author = {Tineo, D and Bustamante, DE and Calderon, MS and Oliva, M},
title = {Comparative analyses of chloroplast genomes of Theobroma cacao from northern Peru.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0316148},
pmid = {40043011},
issn = {1932-6203},
mesh = {*Cacao/genetics ; Peru ; *Genome, Chloroplast ; *Phylogeny ; Evolution, Molecular ; DNA Barcoding, Taxonomic/methods ; Genotype ; },
abstract = {Theobroma cacao is the most economically important species within the genus Theobroma. Despite its importance, the intraspecific relationships of this species has not been fully elucidated due to insufficient molecular information. To facilitate a better understanding of the intraspecific evolutionary relationships of T. cacao, Sequencing technology has been to decode the plastid genomes, with the objective of identify potential DNA barcode genetic markers, explore intraspecific relationships, and infer divergence times. The plastid genome of the seven cocoa genotypes analyzed in this study, exhibited a typical angiosperm genomic structure. However, the structure of each plastid genome reflects notable changes in each genotype; for example, the infA gene was present in all the analyzed samples, unlike in previously published cocoa plastid genomes, while the complete ycf1 gene sequence has potential for use as DNA Barcoding in T. cacao. The estimated age of the node connecting T. cacao and T. grandiflorum, which was 10.11 Ma, supports this indication. It can be inferred that T. cacao diverged at approximately 7.55 Ma, and it is highly likely that T. cacao populations diversified during the Pliocene or Miocene. Therefore, it is crucial to perform mitochondrial and nuclear-based analyses on a broader spectrum of cocoa samples to validate these evolutionary mechanisms, including genetic estimates and divergence. This approach enables a deeper understanding of the evolutionary relationships among cocoa.},
}
@article {pmid40041862,
year = {2025},
author = {Amavet, P and Fernández, GP and Solís Neffa, V},
title = {Editorial: Challenges and prospects for conservation genetics at XXI century.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1554590},
pmid = {40041862},
issn = {1664-8021},
}
@article {pmid40041568,
year = {2025},
author = {Liu, Y and Chen, K and Wang, L and Yu, X and Xu, C and Suo, Z and Zhou, S and Shi, S and Dong, W},
title = {Assembly-free reads accurate identification (AFRAID) approach outperforms other methods of DNA barcoding in the walnut family (Juglandaceae).},
journal = {Plant diversity},
volume = {47},
number = {1},
pages = {115-126},
pmid = {40041568},
issn = {2468-2659},
abstract = {DNA barcoding has been extensively used for species identification. However, species identification of mixed samples or degraded DNA is limited by current DNA barcoding methods. In this study, we use plant species in Juglandaceae to evaluate an assembly-free reads accurate identification (AFRAID) method of species identification, a novel approach for precise species identification in plants. Specifically, we determined (1) the accuracy of DNA barcoding approaches in delimiting species in Juglandaceae, (2) the minimum size of chloroplast dataset for species discrimination, and (3) minimum amount of next generation sequencing (NGS) data required for species identification. We found that species identification rates were highest when whole chloroplast genomes were used, followed by taxon-specific DNA barcodes, and then universal DNA barcodes. Species identification of 100% was achieved when chloroplast genome sequence coverage reached 20% and the original sequencing data reached 500,000 reads. AFRAID accurately identified species for all samples tested after 500,000 clean reads, with far less computing time than common approaches. These results provide a new approach to accurately identify species, overcoming limitations of traditional DNA barcodes. Our method, which uses next generation sequencing to generate partial chloroplast genomes, reveals that DNA barcode regions are not necessarily fixed, accelerating the process of species identification.},
}
@article {pmid40038725,
year = {2025},
author = {Deng, LH and Li, MZ and Huang, XJ and Zhao, XY},
title = {Single-cell lineage tracing techniques in hematology: unraveling the cellular narrative.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {270},
pmid = {40038725},
issn = {1479-5876},
support = {No.82070184, 82350105, 82270228//National Natural Science Foundation of China/ ; No. 2023ZD0501200//National Major Science and Technology Projects of China/ ; No. 2023XACX0004//5511 Science and Technology Innovation Talent Project of Jiangxi Province/ ; JWZQ20240101001//Beijing Outstanding Young Scientists Project/ ; Z240019//Natural Science Foundation of Beijing Municipality/ ; },
mesh = {*Cell Lineage ; Humans ; *Single-Cell Analysis/methods ; Hematology/methods ; Animals ; Hematopoietic Stem Cells/cytology ; },
abstract = {Lineage tracing is a valuable technique that has greatly facilitated the exploration of cell origins and behavior. With the continuous development of single-cell sequencing technology, lineage tracing technology based on the single-cell level has become an important method to study biological development. Single-cell Lineage tracing technology plays an important role in the hematological system. It can help to answer many important questions, such as the heterogeneity of hematopoietic stem cell function and structure, and the heterogeneity of malignant tumor cells in the hematological system. Many studies have been conducted to explore the field of hematology by applying this technology. This review focuses on the superiority of the emerging single-cell lineage tracing technologies of Integration barcodes, CRISPR barcoding, and base editors, and summarizes their applications in the hematology system. These studies have suggested the vast potential in unraveling complex cellular behaviors and lineage dynamics in both normal and pathological contexts.},
}
@article {pmid40037839,
year = {2025},
author = {Chakravarty, S and Logsdon, G and Lonardi, S},
title = {RAmbler resolves complex repeats in human Chromosomes 8, 19, and X.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279308.124},
pmid = {40037839},
issn = {1549-5469},
abstract = {Repetitive regions in eukaryotic genomes often contain important functional or regulatory elements. Despite significant algorithmic and technological advancements in genome sequencing and assembly over the past three decades, modern de novo assemblers still struggle to accurately reconstruct highly repetitive regions. In this work, we introduce RAmbler (Repeat Assembler), a reference-guided assembler specialized for the assembly of complex repetitive regions exclusively from PacBio HiFi reads. RAmbler (i) identifies repetitive regions by detecting unusually high coverage regions after mapping HiFi reads to the draft genome assembly, (ii) finds single-copy k-mers from the HiFi reads, (i.e., k-mers that are expected to occur only once in the genome), (iii) uses the relative location of single-copy k-mers to barcode each HiFi read, (iv) clusters HiFi reads based on their shared bar-codes, (v) generates contigs by assembling the reads in each cluster, and (vi) generates a consensus assembly from the overlap graph of the assembled contigs. Here we show that RAmbler can reconstruct human centromeres and other complex repeats to a quality comparable to the manually-curated telomere-to-telomere human genome assembly. Across over 250 synthetic datasets, RAmbler outperforms hifiasm, LJA, HiCANU, and Verkko across various parameters such as repeat lengths, number of repeats, heterozygosity rates and depth of sequencing.},
}
@article {pmid40037039,
year = {2025},
author = {Osman, E and Saxena, S and Qian, S and L'Heureux-Hache, J and Li, P and Manek, J and Gu, J and Hoare, T and Li, Y and Soleymani, L},
title = {Electrochemical detection of Legionella pneumophila using DNAzymes and under continuous flow in cooling tower water.},
journal = {Biosensors &amp; bioelectronics},
volume = {278},
number = {},
pages = {117283},
doi = {10.1016/j.bios.2025.117283},
pmid = {40037039},
issn = {1873-4235},
abstract = {Rapid detection of Legionella pneumophila in cooling tower water is crucial to mitigate the fatal consequences of Legionnaires disease. This study presents a microfluidic system that employs RNA-cleaving DNAzymes (RCDs) for continuous real time monitoring of this pathogen directly in a single sample of cooling tower water without the need for lengthy bacterial culture. The RCDs, coupled to microgel magnetic beads, are programmed to release an electroactive DNA barcode in the presence of L. pneumophila, which is detected by a downstream electrochemical sensor in real time. Our system identifies key parameters such as peak current, slope of signal increase, and lag time that correlate with L. pneumophila concentration, achieving a limit of detection of 1.4 × 10[3] CFU/mL in buffer and 1.9 × 10[3] CFU/mL in cooling tower water, meeting regulatory requirements. This system was further used to identify different serotypes of L. pneumophila amongst other waterborne bacterial species including non pneumophila species of Legionella, creating a highly specific tool for identifying this high-risk pathogen.},
}
@article {pmid40036401,
year = {2025},
author = {Srisuka, W and Aupalee, K and Takaoka, H and Otsuka, Y and Saeung, A},
title = {Taxonomy and molecular phylogeny of a new species of black fly (Diptera: Simuliidae) in the Simulium striatum species-group from central Thailand.},
journal = {Journal of medical entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jme/tjaf016},
pmid = {40036401},
issn = {1938-2928},
support = {//National Research Council of Thailand/ ; N42A660464//Chiang Mai University/ ; },
abstract = {Generally, the DNA barcode relying on a short fragment of the cytochrome c oxidase I (COI) gene is a powerful tool for facilitating species discovery and taxonomic resolution in Diptera, including black flies. However, the COI barcode lacks sufficient resolution to identify several species or infer phylogenetic relationships of black flies in the Simulium striatum species-group, whereas the fast-evolving nuclear big zinc finger (BZF) gene has been suggested as a key marker for identifying the species. In this study, a new species of black fly in the S. striatum species-group from Kamphaeng Phet province, central Thailand, was discovered and characterized through an integrated method combining morphological analysis and molecular data based on the BZF gene. The new species, Simulium (Simulium) concitatum sp. nov., was morphologically described for all life stages, excluding the egg. It shares many morphological similarities with other species of the S. striatum species-group, particularly S. thilorsuense Takaoka, Srisuka &amp; Saeung, 2022 described from Tak province, western Thailand. Sequence analysis and phylogeny inferred from the BZF gene further confirmed that S. concitatum sp. nov. is a distinct species of the S. striatum species-group and revealed its close genetic relationship to S. wangkwaiense Takaoka, Srisuka &amp; Saeung, 2020. The morphological differences between the new species and all known species of the S. striatum species-group documented in Thailand and other countries are provided to assist in species identification. Furthermore, this study underscores the BZF gene as an effective genetic marker to differentiate the species.},
}
@article {pmid40035969,
year = {2025},
author = {Feng, Y and Liu, G and Li, H and Cheng, L},
title = {The landscape of cell lineage tracing.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40035969},
issn = {1869-1889},
abstract = {Cell fate changes play a crucial role in the processes of natural development, disease progression, and the efficacy of therapeutic interventions. The definition of the various types of cell fate changes, including cell expansion, differentiation, transdifferentiation, dedifferentiation, reprogramming, and state transitions, represents a complex and evolving field of research known as cell lineage tracing. This review will systematically introduce the research history and progress in this field, which can be broadly divided into two parts: prospective tracing and retrospective tracing. The initial section encompasses an array of methodologies pertaining to isotope labeling, transient fluorescent tracers, non-fluorescent transient tracers, non-fluorescent genetic markers, fluorescent protein, genetic marker delivery, genetic recombination, exogenous DNA barcodes, CRISPR-Cas9 mediated DNA barcodes, and base editor-mediated DNA barcodes. The second part of the review covers genetic mosaicism, genomic DNA alteration, TCR/BCR, DNA methylation, and mitochondrial DNA mutation. In the final section, we will address the principal challenges and prospective avenues of enquiry in the field of cell lineage tracing, with a particular focus on the sequencing techniques and mathematical models pertinent to single-cell genetic lineage tracing, and the value of pursuing a more comprehensive investigation at both the spatial and temporal levels in the study of cell lineage tracing.},
}
@article {pmid40034080,
year = {2025},
author = {Fan, S and Li, X and Liu, H and Ye, M and He, Y and Fu, W and Chen, F and Zhao, Y},
title = {Molecule Differentiation Encoding Microscopy to Dissect Dense Biomolecules in Cellular Nanoenvironments Below Spatial Resolution.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e202425136},
doi = {10.1002/anie.202425136},
pmid = {40034080},
issn = {1521-3773},
abstract = {Cellular biomolecules may exhibit dense distribution and organization at the nanoscale to govern vital biological processes. However, it remains a common challenge to digitize the spatially dense biomolecules under spatial resolution of microscopies. Here, we report a proof-of-principle method, molecule differentiation encoding microscopy by orthogonal tandem repeat DNA identifiers, to resolve the copy numbers of dense biomolecules in cellular nanoenvironments. The method encodes each copy of same biomolecules into different types of DNA barcodes based on stochastic multiplexed reactions. It can transform the overlap of the same spectrum into the overlap of different spectra. Furthermore, an algorithm is developed to automatically quantitate overlapping spots and individual spots. Using this method, we dissected RNAs in the cytoplasm, DNA epigenetic modifications in the cell nucleus, and glycans and glycoRNAs on the cell surface, respectively. We found that all these biomolecules presented dense distribution with diverse degrees in crowded cellular nanoenvironments. Especially, averaged 17% copies of U1 glycoRNA of single cells are gathered in various nanoenvironments on cell surface. Our strategy provides a powerful tool for digitally quantitative visualization of dense biomolecules below spatial resolution of microscopies, and could provide insights into underlying functions and mechanisms of the dense distribution information.},
}
@article {pmid40031227,
year = {2025},
author = {Tinarrage, R and Ponciano, JR and Linhares, CDG and Traina, AJM and Poco, J},
title = {ZigzagNetVis: Suggesting temporal resolutions for graph visualization using zigzag persistence.},
journal = {IEEE transactions on visualization and computer graphics},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/TVCG.2025.3528197},
pmid = {40031227},
issn = {1941-0506},
abstract = {Temporal graphs are commonly used to represent complex systems and track the evolution of their constituents over time. Visualizing these graphs is crucial as it allows one to quickly identify anomalies, trends, patterns, and other properties that facilitate better decision-making. In this context, selecting an appropriate temporal resolution is essential for constructing and visually analyzing the layout. The choice of resolution is particularly important, especially when dealing with temporally sparse graphs. In such cases, changing the temporal resolution by grouping events (i.e., edges) from consecutive timestamps - a technique known as timeslicing - can aid in the analysis and reveal patterns that might not be discernible otherwise. However, selecting an appropriate temporal resolution is a challenging task. In this paper, we propose ZigzagNetVis, a methodology that suggests temporal resolutions potentially relevant for analyzing a given graph, i.e., resolutions that lead to substantial topological changes in the graph structure. ZigzagNetVis achieves this by leveraging zigzag persistent homology, a well-established technique from Topological Data Analysis (TDA). To improve visual graph analysis, ZigzagNetVis incorporates the colored barcode, a novel timeline-based visualization inspired by persistence barcodes commonly used in TDA. We also contribute with a web-based system prototype that implements suggestion methodology and visualization tools. Finally, we demonstrate the usefulness and effectiveness of ZigzagNetVis through a usage scenario, a user study with 27 participants, and a detailed quantitative evaluation.},
}
@article {pmid40030848,
year = {2025},
author = {Pham, P and Bui, QT and Nguyen, NT and Kozma, R and Yu, PS and Vo, B},
title = {Topological Data Analysis in Graph Neural Networks: Surveys and Perspectives.},
journal = {IEEE transactions on neural networks and learning systems},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/TNNLS.2024.3520147},
pmid = {40030848},
issn = {2162-2388},
abstract = {For many years, topological data analysis (TDA) and deep learning (DL) have been considered separate data analysis and representation learning approaches, which have nothing in common. The root cause of this challenge comes from the difficulties in building, extracting, and integrating TDA constructs, such as barcodes or persistent diagrams, within deep neural network architectures. Therefore, the powers of these two approaches are still on their islands and have not yet combined to form more powerful tools for dealing with multiple complex data analysis tasks. Fortunately, we have witnessed several remarkable attempts to integrate DL-based architectures with topological learning paradigms in recent years. These topology-driven DL techniques have notably improved data-driven analysis and mining problems, especially within graph datasets. Recently, graph neural networks (GNNs) have emerged as a popular deep neural architecture, demonstrating significant performance in various graph-based analysis and learning problems. Explicitly, within the manifold paradigm, the graph is naturally considered as a topological object (e.g., the topological properties of the given graph can be represented by the edge weights). Therefore, integrating TDA and GNN is considered an excellent combination. Many well-known studies have recently presented the effectiveness of TDA-assisted GNN-based architectures in dealing with complex graph-based data representation analysis and learning problems. Motivated by the successes of recent research, we present systematic literature about this nascent and promising research direction in this article, which includes general taxonomy, preliminaries, and recently proposed state-of-the-art topology-driven GNN models and perspectives.},
}
@article {pmid40028202,
year = {2025},
author = {Silva-Morales, I and Carrera-Parra, LF},
title = {Redescription of Aspidosiphon (Paraspidosiphon) steenstrupii Diesing, 1859 (Sipuncula: Aspidosiphonidae) and the reinstatement of three species.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19003},
pmid = {40028202},
issn = {2167-8359},
mesh = {Animals ; *Phylogeny ; Male ; Female ; Trematoda/genetics/classification/anatomy &amp; histology ; Species Specificity ; },
abstract = {Sipuncula, specifically the family Aspidosiphonidae, faces taxonomic challenges due to brief original descriptions and the poor condition or loss of the type material. Detailed standardized redescriptions are essential to understanding the diversification in this group. Herein, a comprehensive redescription of Aspidosiphon (Paraspidosiphon) steenstrupii based on an extensive material collection from the tropical Western Atlantic is provided. Based on morphological data and the analysis of COI sequences, we delimited A. (P.) steenstrupii morphologically, restricting its distribution to the tropical Western Atlantic. Also, the redescriptions and proposals for reinstatement of A. (P.) exostomum, A. (P.) ochrus, and A. (P.) speculator, previously considered junior synonyms of A. (P.) steenstrupii, are included. Furthermore, a comprehensive discussion on diagnostic morphological features to recognize aspidosiphonid species and a detailed revision of synonyms of A. (P.) steenstrupii are included. Notable differences in morphology and genetic data suggest the need for revising the taxonomic status of several synonyms within the family, highlighting underestimated diversity in sipunculans.},
}
@article {pmid40027782,
year = {2025},
author = {Fukushima, T and Kristiansen, TA and Wong, LP and Keyes, S and Tanaka, Y and Mazzola, M and Zhao, T and He, L and Yagi, M and Hochedlinger, K and Yamazaki, S and Sadreyev, RI and Scadden, DT},
title = {Hematopoietic stem cells undergo bidirectional fate transitions in vivo.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40027782},
issn = {2692-8205},
support = {P01 HL131477/HL/NHLBI NIH HHS/United States ; P01 HL142494/HL/NHLBI NIH HHS/United States ; },
abstract = {Transitions between subsets of differentiating hematopoietic cells are widely regarded as unidirectional in vivo. Here, we introduce clonal phylogenetic tracer (CP-tracer) that sequentially introduces genetic barcodes, enabling high-resolution analysis of ~100,000 subclones derived from ~500 individual hematopoietic stem cells (HSC). This revealed previously uncharacterized HSC functional subsets and identified bidirectional fate transitions between myeloid-biased and lineage-balanced HSC. Contrary to the prevailing view that the more self-renewing My-HSCs unidirectionally transition to balanced-HSCs, phylogenetic tracing revealed durable lineage bidirectionality with the transition favoring My-HSC accumulation over time[1,2]. Further, balanced-HSCs mature through distinct intermediates-My-HSCs and lymphoid-biased-HSCs-with lymphoid competence here shown by CRISPR/Cas9 screening to be dependent on the homeobox gene, Hhex. Hhex enables Ly-HSC differentiation, but its expression declines with age. These findings establish HSC plasticity and Hhex as a determinant of myeloid-lymphoid balance with each changing over time to favor the age-related myeloid bias of the elderly.},
}
@article {pmid40027328,
year = {2025},
author = {Guo, P and Li, C and Liu, J and Wu, T and Chai, B},
title = {Contribution of environmental and biological factors to bacterial community structure and stability in a subalpine lake.},
journal = {Marine life science &amp; technology},
volume = {7},
number = {1},
pages = {176-186},
pmid = {40027328},
issn = {2662-1746},
abstract = {UNLABELLED: Bacterial community play an essential role in regulating water quality and the global biogeochemical cycle in aquatic ecosystems. However, how trophic interactions (i.e., biotic factors) regulate the diversity and composition of bacterial community in lake ecosystems remains unknown. Here, we employed DNA meta-barcoding of water samples to explore the impact of bacterivorous protozoans on the bacterial community. The results showed significant seasonal variations in the diversity and composition of both bacterial and protist communities. The composition of bacterivorous protozoans was identified as the primary predictor for the bacterial community alpha diversity in spring and summer, and for beta diversity in spring and autumn, indicating that biotic interactions play a greater role in driving the diversity of bacterial community across different seasons. Biological factors were more important than environmental factors for explaining the variations in the relative abundance of several bacterial genera (i.e., Pseudoxanthomonas, hgcI_clade, and Pseudorhodobacter). Network analyses showed that bacterial networks differed among seasons, and the autumn network exhibited the highest stability. Our findings indicated that the bacterial community stability was significantly affected by environmental factors, specifically SO4 [2-]and PO4 [3-], rather than bacterivorous protozoans. Overall, our findings provide new perspectives on the role of trophic interactions in maintaining the structure of bacterial community in different seasons, and enhance our understanding of the bacterial community assembly in lake ecosystems.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-024-00256-8.},
}
@article {pmid40027105,
year = {2025},
author = {Flores-Zambrano, K and Tapia, W and Castillejo, P},
title = {Microalgae strains isolated from piggery wastewater in Ecuador: Effective nitrogen compound removal and growth potential in extremophile conditions.},
journal = {Biotechnology reports (Amsterdam, Netherlands)},
volume = {45},
number = {},
pages = {e00883},
pmid = {40027105},
issn = {2215-017X},
abstract = {Effluents generated by anthropogenic activities are a significant source of pollution and eutrophication in natural water bodies. In Ecuador, the increase in pig production has exacerbated this issue due to the untreated discharge of pig effluents. This study focused on the characterization of native microalgae present in pig effluents and the evaluation of their capacity to remove nitrogenous compounds under various conditions, with the aim of identifying efficient strains for phycoremediation. Four microalgal strains were isolated and molecularly identified as Radiococcus polycoccus, Chlorolobion braunii, Micractinium sp., and Desmodesmus multivariabilis. The cultures were exposed to initial concentrations of 100 mg L[-1] N-NH4 and 49.97 mg L[-1] N-NO3 for 12 days to assess their cellular growth and nutrient removal rates. Growth kinetics were analyzed under conditions of 2000 mg L[-1] N-NH4 and extreme pH levels of 3 and 10. Chlorolobion braunii demonstrated the highest productivity, achieving a removal of 67.73 % of N-NH4 and 30.59 % of N-NO3, and reached the highest cellular density under extreme ammonium conditions, being the only strain capable of growing at acidic pH. Conversely, Micractinium sp. exhibited the highest growth under alkaline conditions. These results highlight the promising potential of native microalgae from pig effluents for wastewater remediation and their adaptation to environmental conditions.},
}
@article {pmid40026382,
year = {2025},
author = {Crabo, LG and Keegan, K},
title = {Revision of the North American genus Supralathosea Barnes &amp; Benjamin (Lepidoptera, Noctuidae, Oncocnemidinae) with description of two genera and three species.},
journal = {ZooKeys},
volume = {1228},
number = {},
pages = {197-223},
pmid = {40026382},
issn = {1313-2989},
abstract = {The noctuid genus Supralathosea Barnes &amp; Benjamin (Noctuidae, Oncocnemidinae) is revised to include three species for the United States of America, Supralathoseababoquivariensis Barnes &amp; Benjamin from southeast Arizona, Supralathoseayavapai sp. nov. from central Arizona, and Supralathoseasolastella sp. nov. from Texas. Two genera are described for species formerly included in Supralathosea. Infralathosea gen. nov. includes Infralathoseapronuba comb. nov. from Arizona and New Mexico and Infralathoseaunicornis sp. nov. from west Texas. Eulathosea gen. nov. contains only Eulathoseaobtusa Smith, comb. nov. from Arizona. A key to genera and species is presented and adults and genitalia of all taxa are illustrated. Infralathosea and Eulathosea are assigned to Oncocnemidinae based on molecular evidence.},
}
@article {pmid40023120,
year = {2025},
author = {Liu, D and Wang, X and Xu, L and Al-Delfi, ZNS and Mekonnen, ZA and Gao, S and Grubor-Bauk, B and Zhao, CX},
title = {Screening lipid nanoparticles using DNA barcoding and qPCR.},
journal = {Colloids and surfaces. B, Biointerfaces},
volume = {251},
number = {},
pages = {114598},
doi = {10.1016/j.colsurfb.2025.114598},
pmid = {40023120},
issn = {1873-4367},
abstract = {Quantifying the biodistribution of lipid nanoparticles (LNPs) is critical for optimizing mRNA delivery systems, yet current approaches have inherent limitations. This study introduces a cost-effective method utilizing double-stranded DNA (dsDNA) barcodes and quantitative polymerase chain reaction (qPCR) for rapid analysis of a small library of mRNA-LNPs biodistribution and functional delivery in vivo. Three unique 100-bp dsDNA barcodes were designed to represent for three FDA-approved LNP formulations. Concurrently, these three formulations carrying luciferase mRNA were mixed with DNA-barcoding LNPs as a pool. Following intravenous administration of the pooled LNPs in mice, qPCR analysis revealed the highest abundance of DNA barcodes and accumulation of luciferase mRNA in spleen, with positive correlation between barcodes presence and mRNA localization across organs, validating DNA barcodes as reliable indicators of mRNA-LNPs biodistribution in vivo. Bioluminescence imaging further confirmed successful delivery and protein translation of luciferase mRNA facilitated by the LNPs in vivo. Integrating DNA barcodes for biodistribution analysis and luciferase mRNA for assessing functional delivery enabled comprehensive evaluation of LNP performance. This robust methodology provides valuable insights into the localization patterns and mRNA delivery capabilities of different LNP formulations, paving the way for the development of more effective and targeted mRNA-based therapeutics.},
}
@article {pmid40019731,
year = {2025},
author = {Sinha, T and Shashank, PR},
title = {A Molecular Phylogeny of the Subfamily Plusiinae (Lepidoptera: Noctuidae) in India Inferred from Mitochondrial and Nuclear Ribosomal DNA Sequences.},
journal = {Molecular biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40019731},
issn = {1559-0305},
support = {DST-SERB (SB/YS/LS-126/2014)//DST-SERB (SB/YS/LS-126/2014)/ ; },
abstract = {The subfamily Plusiinae, an economically important moth pest group, belongs to the species-rich family Noctuidae (Lepidoptera). Despite their enormous economic importance, the evolutionary history of this subfamily has not been completely resolved. In India, they are represented by a species complex, but the taxonomic delineation among these organisms is unclear. This study represents an insight into the comprehensive phylogenetic relationship among species supported by molecular approach based on mitochondrial (Cytochrome Oxidase I) and nuclear gene markers (Ribosomal Protein S5), emphasizing tribal-level classification. A total of 125 plusiinae taxa were analysed from eight biogeographical zones of India. The results revealed that Plusiinae tribes were monophyletic and considered sister groups that shared many derived characteristics. The ML/MP cladogram based on the barcoding gene successfully separates all species but not all tribes. The nuclear gene marker RPS5, separated all the species according to their tribes. The combined analysis of both genes showed tribe resolution into distinct clades. This is the first comprehensive study on phylogenetic studies of 25 species of plusiinae from India that clarifies deep divergence and gives information about species position and arrangement within taxa.},
}
@article {pmid40018971,
year = {2025},
author = {Kartzinel, TR and Hoff, HK and Divoll, TJ and Littleford-Colquhoun, BL and Anderson, H and Burak, MK and Kuzmina, ML and Musili, PM and Rogers, H and Troncoso, AJ and Kartzinel, RY},
title = {Global Availability of Plant DNA Barcodes as Genomic Resources to Support Basic and Policy-Relevant Biodiversity Research.},
journal = {Molecular ecology},
volume = {34},
number = {7},
pages = {e17712},
doi = {10.1111/mec.17712},
pmid = {40018971},
issn = {1365-294X},
support = {1930820//Division of Environmental Biology/ ; 2026294//Division of Environmental Biology/ ; 2046797//Division of Environmental Biology/ ; 2033823//Office of Integrative Activities/ ; P22AC00332//National Park Service/ ; P23AC00378//National Park Service/ ; },
mesh = {*DNA Barcoding, Taxonomic ; *Biodiversity ; DNA, Plant/genetics ; Plants/genetics/classification ; Genomics ; Conservation of Natural Resources ; Embryophyta/genetics/classification ; },
abstract = {Genetic technologies such as DNA barcoding make it easier and less expensive to monitor biodiversity and its associated ecosystem services, particularly in biodiversity hotspots where traditional assessments are challenging. Successful use of these data-driven technologies, however, requires access to appropriate reference data. We reviewed the >373,584 reference plant DNA barcodes in public repositories and found that they cumulatively cover a remarkable quarter of the ~435,000 extant land plant species (Embryophyta). Nevertheless, coverage gaps in tropical biodiversity hotspots reflect well-documented biases in biodiversity science - most reference specimens originated in the Global North. Currently, at least 17% of plant families lack any reference barcode data whatsoever, affecting tropical and temperate regions alike. Investigators often emphasise the importance of marker choice and the need to ensure protocols are technically capable of detecting and identifying a broad range of taxa. Yet persistent geographic and taxonomic gaps in the reference datasets show that these protocols rely upon risk undermining all downstream applications of the strategy, ranging from basic biodiversity monitoring to policy-relevant objectives - such as the forensic authentication of materials in illegal trade. Future networks of investigators could work strategically to improve data coverage, which will be essential in global efforts to conserve biodiversity while advancing more fair and equitable access to benefits arising from genetic resources.},
}
@article {pmid40017781,
year = {2025},
author = {Aknine, N and Pelletier, R and Klymchenko, AS},
title = {Lipid-Directed Covalent Labeling of Plasma Membranes for Long-Term Imaging, Barcoding and Manipulation of Cells.},
journal = {JACS Au},
volume = {5},
number = {2},
pages = {922-936},
pmid = {40017781},
issn = {2691-3704},
abstract = {Fluorescent probes for cell plasma membranes (PM) generally exploit a noncovalent labeling mechanism, which constitutes a fundamental limitation in multiple bioimaging applications. Here, we report a concept of lipid-directed covalent labeling of PM, which exploits transient binding to the lipid membrane surface generating a high local dye concentration, thus favoring covalent ligation to random proximal membrane proteins. This concept yielded fluorescent probes for PM called MemGraft, which are built of a dye (cyanine Cy3 or Cy5) bearing a low-affinity membrane anchor and a reactive group: an activated ester or a maleimide. In contrast to specially designed control dyes and commercial Cy3-based labels of amino or thiol groups, MemGraft probes stain efficiently PM, revealing the crucial role of the membrane anchor combined with optimal reactivity of the activated ester or the maleimide. MemGraft probes overcome existing limitations of noncovalent probes, which makes them compatible with cell fixation, permeabilization, trypsinization, and the presence of serum. The latter allows long-term cell tracking and video imaging of cell PM dynamics without the signs of phototoxicity. The covalent strategy also enables staining and long-term tracking of cocultured cells labeled in different colors without exchange of probes. Moreover, the combination of MemGraft-Cy3 and MemGraft-Cy5 probes at different ratios enabled long-term cell barcoding in at least 5 color codes, important for tracking and visualizing multiple populations of cells. Ultimately, we found that the MemGraft strategy enables efficient biotinylation of the cell surface, opening the path to cell surface engineering and cell manipulation.},
}
@article {pmid40015720,
year = {2025},
author = {Gallina, M and Testagrossa, M and Provenzani, A},
title = {Unit dose drug dispensing systems in hospitals: a systematic review of medication error reduction and cost-effectiveness.},
journal = {European journal of hospital pharmacy : science and practice},
volume = {},
number = {},
pages = {},
doi = {10.1136/ejhpharm-2024-004444},
pmid = {40015720},
issn = {2047-9956},
abstract = {BACKGROUND: Medical errors pose significant risks to patient safety and public health. Automated unit dose drug dispensing systems (UDDSs) have emerged as valuable tools to reduce medication errors while optimising economic and logistical resources.<br><br>OBJECTIVES: This systematic review aims to evaluate studies specifically focused on the impact of automated UDDSs in reducing medication errors and streamlining processes.<br><br>METHODS: A literature search was performed on PubMed, Scopus, and Web of Science, focusing on peer-reviewed articles published between 2019 and 2024. The search, concluded on 24 September 2024, included studies conducted in inpatient hospital settings that assessed automated UDDS effects on medication errors, therapy management and inventory control. Outcomes examined included effects on patient safety, cost-effectiveness and inventory management. Results were synthesised qualitatively.<br><br>RESULTS: From 3346 references, four studies met the inclusion criteria: a cost-effectiveness analysis, an uncontrolled before-and-after study, and two observational studies. UDDS improved medication processes, reducing drug-related problems, medication handling and dispensing time by 50% per patient per day. Integrated with barcode scanning, UDDS lowered medication administration errors (MAEs) from 19.5% to 15.8% and harmful MAEs from 3.0% to 0.3%. Overall, medication errors dropped by 45-70%, enhancing safety and reducing manual handling risks. UDDS demonstrated cost-effectiveness by significantly reducing MAEs. The study estimated a reduction in MAEs, with a cost-effectiveness ratio of &#x20ac;17.69 per avoided MAE. For potentially harmful MAEs, the cost-effectiveness ratio was estimated at &#x20ac;30.23 per avoided error. These findings suggest substantial long-term savings potential, though the exact magnitude may vary depending on hospital size and implementation specifics CONCLUSIONS: Automated UDDSs improve patient safety by significantly reducing medication errors and delivering cost savings through better inventory management. Challenges such as high initial costs and workflow adjustments can be mitigated through gradual implementation and staff training. Further integration with other healthcare technologies, such as barcoding, real-time tracking, artificial intelligence (AI)-driven error prevention tools and fully automated restocking systems could enhance UDDS benefits and further support hospital processes.},
}
@article {pmid40015300,
year = {2025},
author = {Prakash, PS and Joshi, FM and Vogelsberg, E and Cremers, GAO and Gür, FN and Sato, Y and de Greef, TFA and Ader, M and Kurth, T and Nunes Gonçalves, DP and Schmidt, TL},
title = {DNA Origami Barcodes for Immunostaining.},
journal = {ACS applied materials &amp; interfaces},
volume = {17},
number = {10},
pages = {15813-15823},
doi = {10.1021/acsami.4c19153},
pmid = {40015300},
issn = {1944-8252},
mesh = {*Gold/chemistry ; *DNA/chemistry ; *Metal Nanoparticles/chemistry ; Animals ; Immunohistochemistry/methods ; Antibodies/chemistry/immunology ; Humans ; Mice ; Nanotechnology ; },
abstract = {In histology, immunostaining of biological samples is a gold standard for studying cellular processes, such as the expression of cell surface markers or the cellular uptake of proteins and drug molecules. Immuno-gold labeling is a commonly used technique to achieve nanometer spatial resolution, but simultaneous visualization of multiple antigens in parallel is an unresolved challenge. Herein, we demonstrate a DNA nanotechnology-based approach to label antigens in transmission electron microscopy images of tissue sections with high contrast patterns. For this, we attached gold nanoparticles to designated binding positions on DNA origami structures that act as visual "barcodes." These barcodes are then hybridized to complementary strands of DNA-modified antibodies that are bound to their respective antigens on ultrathin tissue resin sections. As a proof of concept, we demonstrate several types of barcodes and two different antibody labeling techniques that will expand the multiplexing abilities of immunostaining in a highly modular way.},
}
@article {pmid40013788,
year = {2025},
author = {Pfordt, A and Douanla-Meli, C and Schäfer, BC and Schrader, G and Tannen, E and Chandarana, MJ and von Tiedemann, A},
title = {Phylogenetic analysis of plant-pathogenic and non-pathogenic Trichoderma isolates on maize from plants, soil, and commercial bio-products.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {3},
pages = {e0193124},
pmid = {40013788},
issn = {1098-5336},
support = {FKZ2221NR014A//Bundesministerium f&#xfc;r Ern&#xe4;hrung und Landwirtschaft (BMEL)/ ; },
mesh = {*Zea mays/microbiology ; *Phylogeny ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Trichoderma/genetics/isolation &amp; purification/classification/pathogenicity/physiology ; },
abstract = {Fungi of the genus Trichoderma are primarily associated with the mycobiome of dead wood but can also be occasionally found in soil and plant rhizospheres. Several Trichoderma spp. are used in crop health management to promote growth and control plant diseases. Although widely considered beneficial to plants, some members have been reported to be pathogenic to maize, causing a disease called Trichoderma ear rot. Since 2018, Trichoderma afroharzianum has caused significant infections of maize cobs in Germany, France, and Italy. This study aimed to investigate the pathogenicity and phylogenetic relationships among different Trichoderma strains from diverse sources and geographical origins. While previous studies primarily identified T. afroharzianum as the main species causing Trichoderma ear rot, this study found that isolates of T. asperellum, T. atroviride, and T. guizhouense may also exhibit pathogenicity on maize cobs. Additionally, Trichoderma strains from commercial biocontrol products displayed unexpected pathogenicity inducing up to 92% disease severity on maize cobs. Most T. afroharzianum strains induced high levels of disease severity, although some isolates of the same species did not cause any disease, indicating a large heterogeneity in pathogenicity within the species. Notably, phylogeny reconstruction based on the tef1-α and rpb2 genes did not result in any discernible clustering between pathogenic and non-pathogenic isolates. A further novel finding is the isolation of pathogenic Trichoderma isolates from agricultural soil, demonstrating that soil can serve as a reservoir for pathogenic species. This study highlights the need for biosecurity assessment and monitoring of Trichoderma strains for agricultural use, considering their beneficial and pathogenic potential.IMPORTANCEIn this study, we explored the ability of different Trichoderma species to infect maize plants. Trichoderma is a group of fungi known for its beneficial role in agriculture, often used as a biological pesticide to control fungal plant diseases. However, some species within this genus can also act as pathogens, causing infections in crops like maize. We found that one species, T. afroharzianum, is particularly aggressive, capable of infecting maize without the plant being wounded first. This makes it a potentially serious threat to crop health. In contrast, other species, such as T. atroviride and T. asperellum, only caused infections when maize plants were injured before. Our research suggests that pathogenic Trichoderma species not only effectively infect plants but can also survive well in soil, making their control difficult. These findings highlight the need for better understanding of how these fungi operate in order to manage the risks they pose to important crops like maize, while still taking advantage of their beneficial uses in agriculture.},
}
@article {pmid40012563,
year = {2025},
author = {Kim, Y and Park, J and Hwang, UW and Park, JK},
title = {Taxonomic review of Korean Siphonaria species (Mollusca, Gastropoda, Siphonariidae).},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e139388},
pmid = {40012563},
issn = {1314-2828},
abstract = {BACKGROUND: Many molluscan species exhibit a high degree of shell morphological plasticity in their shape (including sculptures), size and colour patterns, which can vary significantly depending on environmental conditions. These shell morphological variations make it challenging to differentiate species, based on morphology alone, often resulting in various taxonomic errors, such as misidentifications, overlooking cryptic species diversity or a plethora of nominal species. The genus Siphonaria constitutes a significant component of the macrobenthic invertebrate fauna in intertidal habitats across temperate to tropical regions. Given the limited attention to shell variation in previous taxonomic studies on the Korean Siphonaria species, the extensive range of ecophenotypic shell variations documented in this group raises questions about the taxonomic validity of previously reported Siphonaria species in Korea.<br><br>NEW INFORMATION: The present study provides a comprehensive taxonomic review of Korean Siphonaria species using a combination of shell morphology, radula structure and phylogenetic analysis of the mtDNA cox1 sequences. This integrative analysis confirmed the validity of S.acmaeoides, S.japonica and S.sirius in Korea, highlighting differences in shell and siphonal groove morphology amongst these species. Detailed descriptions of shell and radula characteristics, along with mtDNA cox1 sequences as DNA barcodes, are also provided, which are very useful for the accurate identification of Siphonaria species. Unlike these three Siphonaria species, the taxonomic validity of the four other species (S.coreensis, S.javanica, S.laciniosa and S.rucuana) previously reported from Korean waters is questionable, given their documented geographic distribution ranges and the potential misidentification of shell variants in Korean malacofaunal studies.},
}
@article {pmid40012562,
year = {2025},
author = {Bergman, LA and Montenegro, J and Seid, CA and Bachtel, TS and Mann, F and Thuesen, EV and Lindsay, DJ and Drazen, JC},
title = {Checklist of ichthyoplankton of NORI-D polymetallic nodule exploration claim (eastern Clarion-Clipperton Zone) during winter 2021.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e137744},
pmid = {40012562},
issn = {1314-2828},
abstract = {BACKGROUND: There been increasing interest in polymetallic nodule mining within the Clarion-Clipperton Zone (CCZ). Polymetallic nodule mining within NORI-D will release a sediment plume within the water column and a previous mining collector test within the Nauru Ocean Resources Inc. (NORI-D) contract area released surface pollution from mining tailings. The mid-water plume, as well as accidental surface pollution, indicate that polymetallic nodule mining could impact surface plankton. Although the ichthyoplankton within the eastern tropical Pacific have been well-studied, recent data from within polymetallic nodule mining licence areas is lacking. Environmental Expedition C5e conducted an environmental baseline assessment of both pelagic and benthic fauna within the NORI-D region of the CCZ, which included the opportunistic collection of ichthyoplankton.<br><br>NEW INFORMATION: Ichthyoplankton were collected within NORI-D from November-December 2021 using two plankton nets and a Remotely Operated Vehicle (ROV). Here, we present a checklist of ichthyoplankton within the NORI-D licence area during this winter campaign. Eighteen samples were collected and identified through morphology, with a limited number identified through genetic sequencing. Specimens were from five orders, including Argentiniformes, Stomiiformes, Myctophiformes, Beloniformes and Scombriformes. This checklist will aid contractors and scientists conducting work within the CCZ to examine how wastewater discharge from polymetallic nodule mining could impact fish reproduction and ichthyoplankton survival.},
}
@article {pmid40011951,
year = {2025},
author = {Liu, LQ and Fu, WQ and Ma, YY and Liu, ZY and Ge, CF and Yang, YR and Qing, X and Zeng, QL},
title = {Draft genome of pin nematode Paratylenchus projectus recovered from rhizosphere of blueberry.},
journal = {Parasites &amp; vectors},
volume = {18},
number = {1},
pages = {77},
pmid = {40011951},
issn = {1756-3305},
support = {2023BCF01022//Key Research &amp; Development Project of Ningxia Autonomous Region, China/ ; },
mesh = {Animals ; *Blueberry Plants/parasitology ; *Phylogeny ; *Rhizosphere ; *Plant Roots/parasitology ; Plant Diseases/parasitology ; Genome, Helminth ; Tylenchoidea/genetics/classification ; },
abstract = {BACKGROUND: The pin nematode, belonging to the genus Paratylenchus, parasitizes higher plants, often causing reduced or inhibited root tip development.<br><br>METHODS: Pin nematodes were isolated from the roots and rhizosphere of blueberry plants and subsequently identified as representatives of Paratylenchus projectus based on morphological characteristics and molecular barcoding. The P. projectus draft genome was sequenced using the Illumina platform.<br><br>RESULTS: Phylogenetic analysis based on 18S, 28S and ITS rRNA placed this species in highly supported clades alongside other P. projectus specimens. The draft genome of P. projectus was sequenced and assembled, representing the first genomic data for both the genus Paratylenchus and the family Tylenchulidae. The assembled genome, though fragmented, had a total length of 191.36 Mb and an estimated genome size of 64.9 Mb. Protein-coding genes were predicted using four different databases, with particular focus on carbohydrate-active enzymes from the GH5 and GH18 families. The recovered GH5 genes were distributed among three distinct clades: one forming a basal group relative to other nematodes, one as a sister clade to the fungivorous nematode Aphelenchus avenae and one nested within a fungal clade. The GH18 chitinase genes were grouped into two clades: one closely related to sedentary plant-parasitic nematodes of the genera Heterodera and Globodera and the other closely related to the fungivorous nematode Ditylenchus.<br><br>CONCLUSIONS: The draft genome of Paratylenchus projectus was sequenced and assembled, representing the first genomic data for both the genus Paratylenchus and the family Tylenchulidae to our knowledge.},
}
@article {pmid40011622,
year = {2025},
author = {Eroğlu, M and Çelik, I and Düşükcan, M and Ünal, EM and Çoban, MZ and Gündüz, F and Keskin, E},
title = {Author Correction: DNA barcoding of invasive Gambusia holbrooki Girard, 1859 and Atherina boyeri Risso, 1810 inhabiting Upper Euphrates River Basin, Türkiye.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {6886},
doi = {10.1038/s41598-025-91131-8},
pmid = {40011622},
issn = {2045-2322},
}
@article {pmid40010350,
year = {2025},
author = {Singh, I and Fernandez-Perez, D and Sanchez, PS and Rodriguez-Fraticelli, AE},
title = {Pre-existing stem cell heterogeneity dictates clonal responses to the acquisition of leukemic driver mutations.},
journal = {Cell stem cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.stem.2025.01.012},
pmid = {40010350},
issn = {1875-9777},
abstract = {Cancer cells display wide phenotypic variation even across patients with the same mutations. Differences in the cell of origin provide a potential explanation, but traditional assays lack the resolution to distinguish clonally heterogeneous subsets of stem and progenitor cells. To address this challenge, we developed simultaneous tracking of recombinase activation and clonal kinetics (STRACK), a method to trace clonal dynamics and gene expression before and after the acquisition of cancer mutations. Using mouse models, we studied two leukemic mutations, Dnmt3a-R878H and Npm1c, and found that their effect was highly variable across different stem cell states. Specifically, a subset of differentiation-primed stem cells, which normally becomes outcompeted with time, expands with both mutations. Intriguingly, Npm1c mutations reversed the intrinsic bias of the clone of origin, with differentiation-primed stem cells giving rise to more primitive malignant states. Thus, we highlight the relevance of single-cell lineage tracing to unravel early events in cancer evolution and posit that different cellular histories carry distinct cancer phenotypic potential.},
}
@article {pmid40009639,
year = {2025},
author = {Huang, R and Ting, AY},
title = {Directed evolution of a sequence-specific covalent protein tag for RNA labeling.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {9},
pages = {e2422085122},
pmid = {40009639},
issn = {1091-6490},
support = {2330686//National Science Foundation (NSF)/ ; N/A//Chan Zuckerberg Biohub - San Francisco/ ; N/A//Stanford University (SU)/ ; },
mesh = {*RNA/metabolism/genetics/chemistry ; *Directed Molecular Evolution/methods ; Circovirus/genetics/metabolism ; Animals ; Humans ; Viral Proteins/metabolism/genetics/chemistry ; RNA-Binding Proteins/metabolism/genetics/chemistry ; },
abstract = {Efficient methods for conjugating proteins to RNA are needed for RNA delivery, imaging, editing, interactome mapping, and barcoding applications. Noncovalent coupling strategies using viral RNA binding proteins such as MS2/MCP have been widely applied but are limited by tag size, sensitivity, and dissociation over time. We took inspiration from a sequence-specific, covalent protein-DNA conjugation method based on the Rep nickase of a porcine circovirus called "HUH tag". Though wild-type HUH protein has no detectable activity toward an RNA probe, we engineered an RNA-reactive variant, called "rHUH", through 7 generations of yeast display-based directed evolution. Our 13.4 kD rHUH has 12 mutations relative to HUH and forms a covalent tyrosine-phosphate ester linkage with a 10-nucleotide RNA recognition sequence ("rRS") within minutes. We engineered the sensitivity down to 1 nM of target RNA, shifted the metal ion requirement from Mn[2+] toward Mg[2+], and demonstrated efficient labeling in mammalian cell lysate. This work paves the way toward a potentially powerful methodology for sequence-specific covalent protein-RNA conjugation in biological systems.},
}
@article {pmid40009600,
year = {2025},
author = {Tursky, ML and Artuz, CM and Rapadas, M and Wittert, GA and Molloy, TJ and Ma, DD},
title = {Error-corrected ultradeep next-generation sequencing for detection of clonal haematopoiesis and haematological neoplasms - sensitivity, specificity and accuracy.},
journal = {PloS one},
volume = {20},
number = {2},
pages = {e0318300},
pmid = {40009600},
issn = {1932-6203},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Clonal Hematopoiesis/genetics ; *Hematologic Neoplasms/genetics/diagnosis ; *Sensitivity and Specificity ; Reproducibility of Results ; Gene Frequency ; },
abstract = {Clonal haematopoiesis of indeterminate potential (CHIP) is an aging-associated phenomenon that has recently been correlated with a broad spectrum of human diseases, including haematological malignancy, cytopenia, coronary heart disease, stroke, and overall mortality. CHIP is defined as a somatic variant in blood cells with an allele frequency (VAF) ≥ 0.02, however recent reports show smaller clones are associated with poorer clinical outcome. Error-corrected ultradeep next-generation sequencing (NGS) assays detecting variants < 0.02 VAF also have clinical value for monitoring measurable residual disease (MRD) for myeloid neoplasms. However, limited data are available on optimal parameters, limits of detection, and accuracy of ultra-sensitive detection. We investigated parameters to improve accuracy of Illumina sequencing-by-synthesis method, including read depth, input DNA quantity, and molecular barcoding-based data filtering, while adhering to clinical accreditation criteria. Validation data were generated from reference standards and reference samples from a clinically accredited pathology laboratory. Analytical range measurements included linearity and bias, and precision included repeatability, reproducibility and detection rate. The lower limit of detection was ≥ 0.004 (0.4%) at depth > 3,000 × . Trueness measured using reference standards demonstrated a sensitivity, specificity, positive and negative predictive values, and accuracy of 100%, including FLT3-ITD, and 100% concordance was achieved with reference samples for reported variants and absence of variants. Sequencing blood samples from 383 community-dwelling adults (mean depth 3758×) revealed 2,190 somatic variants/sample, > 99.9% were < 0.02 VAF. Our data including cost-benefit analysis enables pathology and research laboratories to make informed decisions for detection of CHIP (VAF ≥ 0.02), sub-CHIP (VAF 0.01-0.02) and MRD (VAF ≥ 0.004).},
}
@article {pmid40006878,
year = {2025},
author = {Peng, Y and Chen, Y and Ding, H and Liu, X and Cao, F and Xu, L},
title = {From Phenotypes to Genotypes: Enhancing the Identification of Cymbidium Species with DNA Barcoding.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40006878},
issn = {2223-7747},
support = {No. 2019JJ50232//Hunan Provincial Science and Technology Department/ ; },
abstract = {The genus Cymbidium, with its intricate floral elements, pronounced endemicity, and patchy distribution, evolves a rich diversity of morphological forms and a wide variety of species while causing an indistinctness in the classification of its species. To elucidate the phylogenetic relationships among Cymbidium species and enhance their taxonomic classification by DNA barcoding, this study conducted amplification and sequence results of nuclear (ITS) and chloroplast genes (matK, rbcL, trnL-F, psbA-trnH) with phenotypic genetic diversity analysis, genetic distance analysis, and phylogenetic analysis from 48 samples of Cymbidium species. The comparison of genetic distance variations showed that psbA-trnH, ITS + psbA-trnH, and ITS + matK + psbA-trnH exhibit minimal overlap and significant genetic variation within Cymbidium species. The phylogenetic analysis indicated that the combination, ITS + matK + psbA-trnH, has the highest identification rate. Notably, both the phylogenetic analysis and the genetic diversity analysis of phenotypic traits consistently indicated a clear divergence between epiphytic and terrestrial orchids, with epiphytic orchids forming a distinct clade. This provides reference evidence for studying the ecological adaptations and evolutionary differences between epiphytic and terrestrial orchids, as well as a scientific basis for the classification and identification, germplasm conservation, resource utilization, and phylogenetic evolution of orchids.},
}
@article {pmid40005642,
year = {2025},
author = {Chittavichai, T and Sathitnaitham, S and Utthiya, S and Prompichai, W and Prommarit, K and Vuttipongchaikij, S and Wonnapinij, P},
title = {Limitations of 18S rDNA Sequence in Species-Level Classification of Dictyostelids.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
pmid = {40005642},
issn = {2076-2607},
support = {//Kasetsart University through the Graduate School Fellowship Program/ ; FF(KU)13.64//Kasetsart University Research and Development Institute (KURDI)/ ; N42A650286//The National Research Council of Thailand (NRCT) and Kasetsart University Research and Development Institute (KURDI)/ ; },
abstract = {Dictyostelid species classification has traditionally relied on morphology, a time-intensive method requiring expert knowledge. This study evaluated the potential and limitations of using the 18S rDNA sequence for species-level classification. 18S rDNA sequences of 16 samples from the Dicty stock center, including 14 samples found in Thailand, were analyzed. Signature sequence analyses confirmed genus-level identification with high accuracy. These sequences were analyzed alongside 309 database entries retrieved from the GenBank database. The analyses confirmed genus-level identification accuracy but highlighted challenges in distinguishing species due to overlapping intraspecific and interspecific variations, negative barcoding gaps, and incorrectly grouped samples to putative taxa by species delimitation analyses. Species delimitation methods, including maximum likelihood (ML) phylogenetic analysis, achieved limited success, with ML showing the highest accuracy but not exceeding 50%. However, species with high barcoding gaps, such as Raperostelium and Rostrostelium, demonstrated potential for accurate classification. These findings support using 18S rDNA for genus-level identification and suggest its possible application for certain species. Expanded sampling is needed to improve species-level classification and to identify more robust DNA markers for dictyostelid diversity studies.},
}
@article {pmid40003852,
year = {2025},
author = {Jiang, ZH and Kitching, IJ and Xu, XD and Xu, ZB and Yan, M and Yu, WB and Liu, CQ and Hu, SJ},
title = {A Review of the Genus Ambulyx Westwood, 1847 (Lepidoptera: Sphingidae) from China Based on Morphological and Phylogenetic Analyses, with the Description of a New Species.},
journal = {Insects},
volume = {16},
number = {2},
pages = {},
pmid = {40003852},
issn = {2075-4450},
support = {202305AF150037//Academician (Expert) Working Station (202305AF150037), Yunnan Provincial De-partment of Science, Technology/ ; Grant No. 2019FY101800//National Science &amp; Technology Fundamental Resources Investigation Program of Chi-na/ ; Grant Nos. 32100352&#xff0c;32100355//National Natural Science Foundation of China/ ; },
abstract = {The taxonomy of genus Ambulyx Westwood, 1847 from China is reviewed based on analysis of wing morphology, male and female genitalia and phylogenetic relationships derived from DNA barcodes. A new species, Ambulyx wukong sp. nov. is described from NW Yunnan, China. A male of the rare species, A. zhejiangensis from Yintiaoling Nature Reserve, Chongqing, China is examined and its male genitalia illustrated for the first time. Two taxa are newly recorded from China, A. tattina tattina from Xishuangbanna, Yunnan, and A. semiplacida montana from Pingbian, Yunnan. Distribution maps, biological notes, and ecological records are also given.},
}
@article {pmid40003849,
year = {2025},
author = {Gwiazdowska, A and Rutkowski, R and Sielezniew, M},
title = {Conservation Genetics of the Endangered Danube Clouded Yellow Butterfly Colias myrmidone (Esper, 1780) in the Last Central European Stronghold: Diversity, Wolbachia Infection and Balkan Connections.},
journal = {Insects},
volume = {16},
number = {2},
pages = {},
pmid = {40003849},
issn = {2075-4450},
support = {EZ.271.3.7.2021//General Directorate of the Polish State Forests/ ; },
abstract = {The Danube Clouded Yellow (Colias myrmidone) has experienced one of the most dramatic declines among European butterflies. To estimate genetic diversity in the last population in Poland that has survived in the Knyszyn Forest (KF), we analyzed mitochondrial (COI) and nuclear (EF-1α) polymorphisms in individuals sampled in 2014 and 2022. The results were compared with genetic data obtained in 2014 from a recently extirpated nearby population (Czerwony Bór, CB). Because mtDNA polymorphisms in insects can be modulated by endosymbionts, the samples were screened for Wolbachia. The polymorphism of EF-1α indicated that diversity was gradually decreasing. The KF experienced rapid demographic processes, manifested by a significant change in allele frequency. The small differentiation in nuclear markers between the KF and CB in 2014 suggests that the regional population used to be genetically uniform. Four COI haplotypes that were identified in this study probably belong to two different haplogroups. Wolbachia was detected only in individuals with one specific haplotype, and the prevalence was female-biased, suggesting the induction of two reproductive manipulations. The most common COI haplotype found in Poland was the same as that reported from other parts of Europe, not only for C. myrmidone but also C. caucasica. These results allow us to question the distinctiveness of each taxa.},
}
@article {pmid40003799,
year = {2025},
author = {Ricupero, M and Porcu, E and Russo, A and Zappalà, L and Siscaro, G},
title = {New Records of Phenacoccus solenopsis Natural Enemies in Europe and Taxonomic Additions on Anagyrus matritensis.},
journal = {Insects},
volume = {16},
number = {2},
pages = {},
pmid = {40003799},
issn = {2075-4450},
support = {CN00000022//the European Union Next-Generation EU (PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 - D.D. 1032 17/06/2022/ ; E73C22000240006//Agroecology-inspired Strategies and Tools to Enhance Resilience and ecosystem services in to-mato crop" (ASTER), PRIMA SECTION 2 2021 - MULTI-TOPIC/ ; 101136611//the European Union's Horizon Europe research and innovation programme (NextGenBioPest project)/ ; },
abstract = {The cotton mealybug Phenacoccus solenopsis (Hemiptera: Pseudococcidae) is a polyphagous invasive species native to America and considered one of the major cotton pests in Asia. It is currently threatening horticultural and ornamental protected crops in Mediterranean countries. Due to ecological and environmental concerns, the conventional chemical control of P. solenopsis in new areas of introduction is being replaced by exploring the potential of indigenous natural enemies as a sustainable biological control tool. After P. solenopsis introduction in Sicily (Italy), field surveys were conducted on native natural enemies attacking the mealybug to select promising biocontrol agents for field applications. For the first time, Aenasius arizonensis (Hymenoptera: Encyrtidae) was reported in Europe, and the native Anagyrus matritensis (Hymenoptera: Encyrtidae) was recorded in association with P. solenopsis. The two parasitoid species were identified by morphological features and molecularly using a portion of the mitochondrial cytochrome oxidase subunit I (mtCOI) gene. Because of missing information, additional morphological features were provided for the morphological identification of A. matritensis. In addition, the generalist predators Cryptolaemus montrouzieri, Hippodamia variegata and Parexochomus nigripennis (Coleoptera: Coccinellidae) were also recorded attacking the invasive mealybug.},
}
@article {pmid40003760,
year = {2025},
author = {Qian, P and Fan, J and Zhang, X and Zeng, M and Han, X and Li, Y and Luo, X},
title = {Morphogenetic Identification of a New Record Condica capensis (Lepidoptera: Noctuidae) in Yunnan, China.},
journal = {Insects},
volume = {16},
number = {2},
pages = {},
pmid = {40003760},
issn = {2075-4450},
support = {202301BD070001-185//Joint Agricultural Project of Yunnan Province/ ; },
abstract = {Condica capensis (Lepidoptera: Noctuidae), a newly identified pest in Yunnan Province, China, poses a threat to safflower crops. Discovered in Nanhua County in November 2023, the pest damages safflower at multiple life stages, especially during its larval stage, when it feeds on leaves, tender stems, and flower filaments, sometimes causing the entire plant to die. Morphological and molecular analyses, including mitochondrial cytochrome C oxidase I (COI) gene sequencing, confirmed its identity as C. capensis, a new species record for Yunnan. The study also documented the pest's life cycle, reproductive behavior, and natural enemies, highlighting the potential for biological control using parasitic wasps such as Cotesia sp. This research emphasizes the need for accurate pest identification and monitoring to develop effective, sustainable pest management strategies. As safflower cultivation grows in Yunnan, managing C. capensis is critical to safeguarding local agriculture and preventing broader agricultural threats.},
}
@article {pmid40002052,
year = {2025},
author = {Jiang, Y and Wei, S and Ge, H and Zhang, Y and Wang, H and Wen, X and Guo, C and Wang, S and Chen, Z and Li, P},
title = {Advances in the Identification Methods of Food-Medicine Homologous Herbal Materials.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40002052},
issn = {2304-8158},
support = {(No. 61975053, No. 62271191)//National Natural Science Foundation of China/ ; No. 222300420040//Natural Science Foundation of Henan Province/ ; (No. 22HASTIT017, No. 23HASTIT024)//Program for Science and Technology Innovation Talents in Universities of Henan Province/ ; No. CSKFJJ-2024-26//Open Project of Institute for Complexity Science, Henan University of Technology/ ; No. 201300210100//Major public welfare projects of Henan Province/ ; No. 2021ZKCJ04//Innovative Funds Plan of Henan University of Technology/ ; },
abstract = {As a key component of both traditional medicine and modern healthcare, Food-Medicine Homologous Herbal Materials have attracted considerable attention in recent years. However, issues related to the quality and authenticity of medicinal materials on the market often arise, not only compromising their efficacy but also presenting potential risks to consumer health. Therefore, the establishment of accurate and efficient identification methods is crucial for ensuring the safety and quality of Food-Medicine Homologous Herbal Materials. This paper provides a systematic review of the research progress on the identification methods for Food-Medicine Homologous Herbal Materials, starting with traditional methods such as morphological and microscopic identification, and focusing on the applications of modern techniques, including biomimetic recognition, chromatography, mass spectrometry, chromatography-mass spectrometry coupling, hyperspectral imaging, near-infrared spectroscopy, terahertz spectroscopy, and DNA barcoding. Moreover, it provides a comprehensive analysis of the fundamental principles, advantages, and limitations of these methods. Finally, the paper outlines the current challenges faced by identification methods and suggests future directions for improvement, aiming to offer a comprehensive technical perspective on identifying Food-Medicine Homologous Herbal Materials and foster further development in this field.},
}
@article {pmid39997428,
year = {2025},
author = {Motta, BDS and Almeida-Silva, F and Teixeira, MM and Bernardes-Engemann, AR and Almeida-Paes, R and de Macedo, PM and Zancopé-Oliveira, RM},
title = {Paracoccidioides Species Circulating in the Endemic Area of Rio de Janeiro, Brazil: Updates into Their Genetic Diversity.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {2},
pages = {},
pmid = {39997428},
issn = {2309-608X},
support = {001//CAPES/ ; E-26/211.430/2021//FAPERJ/ ; 308315/2021-9//CNPq/ ; E-26/200.381/2023//FAPERJ/ ; },
abstract = {Paracoccidiodomycosis (PCM) is the most important systemic mycosis in Brazil, and is usually associated with rural work. PCM is caused by inhalation of infective propagules of thermodimorphic fungi from the genus Paracoccidioides. In the past, it was believed that Paracoccidioides brasiliensis was the single species responsible for PCM cases. However, recent advances in molecular methods allowed the description of several new species, using phylogenetic concordance as the gold standard. Aside from P. brasiliensis sensu stricto, Paracoccidioides americana is also endemic in Rio de Janeiro state, Brazil. This study aimed to evaluate intraspecific genetic variability of Paracoccidioides isolates from patients diagnosed with PCM at a reference center for endemic mycoses in Rio de Janeiro state, from 2015 to 2021. Among the sixteen retrieved isolates, three (18.75%) were identified as P. americana and thirteen (81.25%) as P. brasiliensis sensu stricto. No intraspecific genetic variation was observed by the M-13 primer in P. americana isolates from this geographic region. However, P. brasiliensis sensu stricto isolates were clustered into two distinct molecular profiles, despite being grouped in a single clade in the phylogenetic tree after partial sequencing of arf and gp43 genes. The results suggest a single P. americana lineage and two P. brasiliensis populations causing PCM in Rio de Janeiro, Brazil.},
}
@article {pmid39997392,
year = {2025},
author = {Zuleta, MC and Gómez, OM and Misas, E and Torres, S and Rúa-Giraldo, &#xc1;L and McEwen, JG and Garcia, AM and Borges, CL and Hernández, O and López, AM},
title = {Species Identification and Orthologous Allergen Prediction and Expression in the Genus Aspergillus.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {2},
pages = {},
pmid = {39997392},
issn = {2309-608X},
support = {221384467683//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; },
abstract = {The genus Aspergillus comprises a diverse group of fungi that can cause a range of health issues, including systemic infections and allergic reactions. In this regard, A. fumigatus has been recognized as the most prevalent allergen-producing species. This genus taxonomic classification has been subject to frequent updates, which has generated considerable difficulties for its classification when traditional identification methodologies are employed. To demonstrate the feasibility of this approach, we sequenced the whole genomes of 81 Aspergillus isolates and evaluated a WGS-based pipeline for precise species identification. This pipeline employed two methodologies: (i) BLASTn web using four barcode genes and (ii) species tree inference by OrthoFinder. Furthermore, we conducted a prediction of allergenic capacity based on a homology analysis across all the isolated species and confirmed by RT-qPCR the expression of three orthologous allergens (Asp f 1, Asp f 3 and Asp f 22) in fifteen different Aspergillus species. The species-level identification rate with the barcoding and the species tree were calculated at 64.2% and 100%, respectively. The results demonstrated that A. fumigatus, A. flavus and A. niger were the most prevalent species. The species A. hortae, A. uvarum, A. spinulosporus, A. sydowii, A. westerdijkiae, A. amoenus and A. rhizopodus identified in this study represent the inaugural report of their presence in our region. The results of the homology analysis indicated the presence of orthologous allergens in a wide range of non-fumigatus species. This study presents a novel approach based on WGS that enables the classification of new species within the genus Aspergillus and reports the genomic sequences of a great diversity of species isolated in our geographic area that had never been reported before. Additionally, this approach enables the prediction of allergens in species other than A. fumigatus and demonstrates their genetic expression, thereby contributing to the understanding of the allergenic potential of different species within this fungal genus.},
}
@article {pmid39997216,
year = {2025},
author = {Chovanec, P and Yin, Y},
title = {Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility.},
journal = {Nucleic acids research},
volume = {53},
number = {4},
pages = {},
pmid = {39997216},
issn = {1362-4962},
support = {R35 GM142511/GM/NIGMS NIH HHS/United States ; R35GM142511/GF/NIH HHS/United States ; 5R35GM142511/GM/NIGMS NIH HHS/United States ; DFS-43-20/DRCRF/Damon Runyon Cancer Research Foundation/United States ; },
mesh = {*Chromatin/genetics/metabolism/chemistry ; *Single-Cell Analysis/methods ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; RNA/genetics/metabolism ; Sequence Analysis, RNA/methods ; Nucleic Acid Amplification Techniques/methods ; },
abstract = {Single-cell combinatorial indexing (sci) methods have addressed major limitations of throughput and cost for many single-cell modalities. With the incorporation of linear amplification and three-level barcoding in our suite of methods called sci-L3, we further addressed the limitations of uniformity in single-cell genome amplification. Here, we build on the generalizability of sci-L3 by extending it to template strand sequencing (sci-L3-Strand-seq), genome conformation capture (sci-L3-Hi-C), and the joint profiling of RNA and chromatin accessibility (sci-L3-RNA/ATAC). We demonstrate the ease of adapting sci-L3 to these new modalities by only requiring a single-step modification of the original protocol. As a proof of principle, we show our ability to detect sister chromatid exchanges, genome compartmentalization, and cell state-specific features in thousands of single cells. We anticipate sci-L3 to be compatible with additional modalities, including DNA methylation (sci-MET) and chromatin-associated factors (CUT&amp;Tag), and ultimately enable a multi-omics readout of them.},
}
@article {pmid39997191,
year = {2025},
author = {Turner, AD and Maskrey, BH and Stone, D and Mudge, EM and Robertson, A},
title = {First Confirmed Occurrence of Ciguatera Poisoning in the UK from Imported Pinjalo Snapper (Pinjalo pinjalo).},
journal = {Marine drugs},
volume = {23},
number = {2},
pages = {},
pmid = {39997191},
issn = {1660-3397},
support = {P01 ES028949/ES/NIEHS NIH HHS/United States ; Atlantic Area Program project Alertox-Net (EAPA-317-2016//Interreg Atlantic Area/ ; },
mesh = {*Ciguatera Poisoning ; Animals ; Humans ; *Ciguatoxins/toxicity ; Mice ; United Kingdom ; Perciformes ; Male ; Seafood ; Food Contamination/analysis ; Female ; Adult ; },
abstract = {Three people in England consumed fish steaks labeled as Red Snapper (Lutjanus bohar) originating from the Indian Ocean. Within 12 h, all three experienced sickness including nausea, vomiting, diarrhea, as well as myalgia and paresthesia. Three steaks from a single package of fish obtained from a grocery store were consumed, leaving one uneaten, which was submitted for analysis. Cytotoxicity testing via the mouse neuroblastoma assay confirmed the presence of sodium channel specific activity consistent with a ciguatoxin standard, and the levels detected were above established guidance limits for safe consumption. Chemical detection using liquid chromatography coupled with high-resolution mass spectrometry of both intact toxins and periodate oxidation products was used to confirm the presence of chromatographic peaks consistent with tri- and di-hydroxylated Pacific ciguatoxin 3C congeners. Taking the shared medical symptoms of patients, the recent dietary history, and the known potential for ciguatera poisoning to occur in snapper species, the subsequent evidence for CTX-like activity and CTXs in the same fish sample provides very strong evidence that the fish steaks consumed were similarly contaminated with CTXs. Furthermore, given the levels reported, such toxicity would be expected to cause intoxication in humans. Fish species identification based on DNA barcoding confirmed that the fish products were mislabeled, with the tissues instead being the Pinjalo snapper, Pinjalo pinjalo. This is the first confirmed ciguatera poisoning incident in both the UK and from the Pinjalo snapper and highlights the need for monitoring of these emerging toxins in reef fish imports to prevent future human intoxication.},
}
@article {pmid39996828,
year = {2025},
author = {Zhu, H and Yue, C and Li, H},
title = {Mitochondrial Genome Characteristics and Comparative Genomic Analysis of Spartina alterniflora.},
journal = {Current issues in molecular biology},
volume = {47},
number = {2},
pages = {},
pmid = {39996828},
issn = {1467-3045},
support = {2024C02002//"Leading Goose"R&amp;D Program of Zhejiang/ ; 2022SY06//Zhejiang Forestry Science and Technology Project/ ; },
abstract = {The mitochondrial genome of Spartina alterniflora, an invasive species with significant ecological and economic impacts, was analyzed to provide a theoretical basis for understanding its phylogenetic relationships and molecular biology. Mitochondrial genome sequences of S. alterniflora and 23 related species from NCBI were utilized for bioinformatics and comparative genomic analyses. A sliding window analysis identified three genes (rps2, atp9, and nad6) as potential DNA barcodes for species identification. Intracellular gene transfer (IGT) events between mitochondrial and chloroplast genome were detected, highlighting the dynamic nature of genomic evolution. A selective pressure analysis revealed that most protein-coding genes (PCGs) underwent purifying selection (Ka/Ks < 1), while the nad2 and ccmB genes showed signs of positive selection pressure (Ka/Ks > 1), indicating their role in adaptation. A phylogenetic analysis demonstrated a close relationship between S. alterniflora and Eleusine indica, supported by a collinearity analysis, which suggests environmental convergence. This study provides novel insights into the structural and evolutionary characteristics of the S. alterniflora mitochondrial genome, offering valuable genomic resources for future research on invasive species management and evolutionary biology.},
}
@article {pmid39995615,
year = {2025},
author = {Changbunjong, T and Weluwanarak, T and Laojun, S and Chaiphongpachara, T},
title = {Species classification of Tabanus (Diptera: Tabanidae) in Western Thailand: Integrating DNA barcoding and modern morphometrics.},
journal = {Current research in parasitology &amp; vector-borne diseases},
volume = {7},
number = {},
pages = {100243},
pmid = {39995615},
issn = {2667-114X},
abstract = {The species of Tabanus, commonly known as horse flies, are remarkable ectoparasites capable of transmitting various pathogens to animals and humans. Given their role in disease transmission, accurate identification of horse fly species is critical but traditionally relies on morphological characteristics, requiring significant expertise and posing a high potential for error, especially with damaged specimens. To address the limitations of traditional morphological identification, this study highlights the importance of alternative techniques, including DNA barcoding and geometric morphometrics (GM). To enhance the reliability of species identification, DNA barcoding was employed to analyze 30 cytochrome c oxidase subunit 1 (cox1) gene sequences from 15 horse fly species, which were then compared with sequences in the GenBank and BOLD databases. Most cox1 sequences aligned with existing data, with similarity percentages ranging from 96% to 100%. However, discrepancies were noted, including Tabanus helvinus, misidentified as Tabanus aurilineatus, and Tabanus minimus, whose sequences matched those of both Tabanus minimus and Tabanus mesogaeus. Besides DNA barcoding, GM analyses were conducted to enhance species classification accuracy. Our GM analyses employed the landmark-based method for the entire wing and the outline-based method for the first submarginal cell. While shape-based GM analyses demonstrated high reliability, with adjusted total accuracy scores of 97% and 96%, size-based GM analyses yielded significantly lower accuracy, with scores of only 27% and 23%, respectively. These findings provide a foundation for refining horse fly species classification by integrating DNA barcoding and GM approaches, offering valuable advances in species identification and developing targeted control measures.},
}
@article {pmid39994544,
year = {2025},
author = {Wu, Y and Sun, Z and Liu, Z and Qiu, T and Li, X and Leng, L and Chen, S},
title = {Assembly and analysis of stephania japonica mitochondrial genome provides new insights into its identification and energy metabolism.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {185},
pmid = {39994544},
issn = {1471-2164},
support = {030040016/030//This work is supported by the talented person scientific research start funds subsidization project of Chengdu University of Traditional Chinese Medicine/ ; },
mesh = {*Genome, Mitochondrial ; *Energy Metabolism/genetics ; *Phylogeny ; *Stephania/genetics/metabolism ; Electron Transport Complex IV/genetics/metabolism ; Genome, Plant ; Plant Proteins/genetics/metabolism ; },
abstract = {Stephania japonica, a popular indoor ornamental and medicinal plant widely found in southern China, contains many natural compounds with potential medicinal value. S. japonica is also favored by researchers for its ability to produce catharanthine. Energy metabolism functions in plant development, and the composition of mitochondrial genome is regarded as the foundation for understanding energy metabolism and getting insights into plant environmental adaptation. In present investigation, the whole mitochondrial genome of S. japonica was assembled from both second- and third-generation sequencing data. The mitochondrial genome size of S. japonica is 555,117 bp. It is depicted as a complex polycyclic structure. In addition, we conducted an in-depth study of the cytochrome c oxidase (cox) gene, of which expression levels in different tissues of S. japonica were measured by real-time quantification PCR. Two phylogenetic trees were established in the light of sequences concerning 19 conserved mitochondrial protein-coding genes and cox gene, respectively. Both phylogenetic trees show that S. japonica is more closely related to Aconitum kusnezoffii. The result showed that the cox genes were the most highly expressed in the roots. A high-quality mitochondrial genome exhibits potential application value for the progress of molecular markers, identification of species as super DNA barcoding, and resolve mitochondrial energy metabolism mechanisms in response to the environment using genomic information. With the recognition of the medicinal value of Stephania plants, the genomic information of S. japonica has been thoroughly studied and the comprehensive analysis of its mitochondrial genome in this investigation can offer valuable insights for the breeding of new plant varieties.},
}
@article {pmid39991452,
year = {2025},
author = {Ziganira, M and Downs, CT},
title = {Significant Progress in the Study of African Freshwater Snails Over the Past 260 Years.},
journal = {Ecology and evolution},
volume = {15},
number = {2},
pages = {e71031},
pmid = {39991452},
issn = {2045-7758},
abstract = {Globally, freshwater ecosystems are threatened. Research progress concerning African freshwater snails was reviewed using a systematic review process. Since 1757, the number of publications produced has increased, particularly in the last decade. In the first 50 years (1757-1800), 0.1% of publications on freshwater snails in Africa were conducted, followed by 0% (1801-1850), 3.3% (1851-1900), 3.5% (1901-1950) and 48.7% (1951-2000). The last 23 years (2001-2024) exhibited a large increase (44.3%) in publications of the total conducted. Studies on freshwater snails varied in number across the 10 major African water basins, with the majority of studies in the Nile (21.7%), followed by the Congo Basin (17.6%) and Niger (12.4%). The Orange Basin and Lake Tanganyika also received a high number of studies (10.9%) and (7.2%), respectively. Most freshwater snail study objectives related to conservation and taxonomy (70%), followed by disease vector (20.5%), with genetics/genomic/DNA barcoding/eDNA receiving significant focus as well (5.2%). Studies focusing on geology and palaeontology (2.5%), followed by climate change (1.5%) and machine learning (0.4%). The modern phase in the study of African freshwater snails came around the early 20th century with the discovery of Bulinus truncatus and Biomphalaria alexandrina as intermediate hosts for the parasites causing human schistosomiasis. African freshwater malacology has since then benefited from African and overseas malacologists based at universities and medical laboratories across Africa and overseas. In addition to taxonomic studies, there was a steady rise in contributions relating to ecology, disease vectors, palaeontology and genetics. These contributed knowledge on local endemism and speciation, invasive species, species origins and distribution across African water basins, as well as the spread of infectious diseases and impacts of climate change. In the last decade, there have been shifts in methods with the application of DNA barcoding, genomics, environmental DNA and, most recently, machine learning approaches.},
}
@article {pmid39990951,
year = {2025},
author = {Wang, KC and Young, TL and Chen, J and Tsai, SN and Xu, Y and Varley, AJ and Solek, NC and Gong, F and Lu, RXZ and Hubbard, BP and Li, B},
title = {A Reverse Transcription Nucleic-Acid-Based Barcoding System for In Vivo Measurement of Lipid Nanoparticle mRNA Delivery.},
journal = {ACS bio &amp; med chem Au},
volume = {5},
number = {1},
pages = {35-41},
pmid = {39990951},
issn = {2694-2437},
abstract = {Lipid nanoparticles (LNPs) are the most extensively validated clinical delivery vehicles for mRNA therapeutics, exemplified by their widespread use in the mRNA COVID-19 vaccines. The pace of lipid nanoparticle (LNP) development for mRNA therapeutics is restricted by the limitations of existing methods for large-scale LNP screening. To address this challenge, we developed Quantitative Analysis of Reverse Transcribed Barcodes (QuART), a novel nucleic-acid-based system for measuring LNP functional delivery in vivo. QuART uses a bacterial retron reverse transcription system to couple functional mRNA delivery into the cytoplasm with a cDNA barcode readout. Our results demonstrate that QuART can be used to identify functional mRNA delivery both in vitro in cell culture and in vivo in mice. Multiplexing of QuART could enable high-throughput screening of LNP formulations, facilitating the rapid discovery of promising LNP candidates for mRNA therapeutics.},
}
@article {pmid39990434,
year = {2025},
author = {Kinsler, G and Fagan, C and Li, H and Kaster, J and Dunne, M and Vander Velde, RJ and Boe, RH and Shaffer, S and Herlyn, M and Raj, A and Heyman, Y},
title = {SpaceBar enables clone tracing in spatial transcriptomic data.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39990434},
issn = {2692-8205},
support = {T32 CA009140/CA/NCI NIH HHS/United States ; T32 GM007170/GM/NIGMS NIH HHS/United States ; T32 HG000046/HG/NHGRI NIH HHS/United States ; },
abstract = {We report a cellular barcoding strategy, SpaceBar, that enables simultaneous clone tracing and spatial transcriptomics profiling. Our approach uses a library of 96 synthetic barcode sequences that can be robustly detected by imaging based spatial transcriptomics (seqFISH), delivered such that each cell is labeled with a combination of barcodes. We used these barcodes to label melanoma cells in a tumor xenograft model and profiled both clone identity and spatial gene expression in situ. We developed a gene scoring metric that quantifies how strongly gene expression is driven by intrinsic cellular cues or extrinsic environmental signals. Our framework distinguishes between clonal dynamics and environmentally-driven transcriptional regulation in complex tissue contexts.},
}
@article {pmid39990189,
year = {2025},
author = {Faltlhauser, AC and Cabrera, N and Hernández, MC and Sánchez Restrepo, AF and Hill, M and Sosa, AJ},
title = {Lysathiaflavipes and Lysathiacilliersae Cabrera sp. nov. (Coleoptera, Chrysomelidae): genetic and morphological unravelling of biocontrol agents for two invasive aquatic plants.},
journal = {ZooKeys},
volume = {1228},
number = {},
pages = {11-52},
pmid = {39990189},
issn = {1313-2989},
abstract = {In the search for specific natural enemies to control two invasive aquatic plants (IAP) from South America, Ludwigiagrandiflorasubsp.hexapetala (Onagraceae) and Myriophyllumaquaticum (Haloragaceae), taxonomic challenges associated with two Lysathia Bechyné, 1959 (Chrysomelidae; Alticini) species had to be resolved. Lysathiaflavipes (Boheman, 1859) exhibits significant morphological variation, causes heavy damage to both IAPs, and may represent more than one species due to the phylogenetic gap between hosts. Additionally, an undescribed Lysathia species (previously published as Lysathia sp.), sourced from Brazil, has been successfully used as a control agent for M.aquaticum in South Africa since 1994. An integrative taxonomic approach combining genetic and morphological analyses was employed. A lectotype and paralectotypes for Graptoderaflavipes Boheman, 1859 are here designated. Phylogenetic studies revealed that L.flavipes had greater genetic and morphological variation than originally described, and no evidence suggested that L.flavipes represented a species complex associated with its host plants. As a result, the species description was expanded. On the other hand, genetic and morphological differences such as body size, colouration, and genital structures further supported the description of Lysathiacilliersae Cabrera, sp. nov. and its differentiation from other closely related species, including L.flavipes and L.ludoviciana (Fall, 1910). Specimens of L.cilliersae sp. nov. collected in Misiones, Argentina, matched those from South Africa. Genetic sequences correlated with morphological vouchers, images, and illustrations of morphology and genitalia, as well as new distribution records, are provided. This research contributes to the taxonomic knowledge of the Lysathia genus and supports accurate species identification in applied entomological contexts, such as biological control programmes.},
}
@article {pmid39985775,
year = {2025},
author = {Xiong, EH and Zhang, X and Robbins, N and Myers, CL and Cowen, LE},
title = {Protocol to identify genes important for Candida albicans fitness in diverse environmental conditions using pooled bar-seq screening approach.},
journal = {STAR protocols},
volume = {6},
number = {1},
pages = {103645},
pmid = {39985775},
issn = {2666-1667},
mesh = {*Candida albicans/genetics ; Genetic Fitness/genetics ; DNA, Fungal/genetics ; Genomics/methods ; Sequence Analysis, DNA/methods ; DNA Barcoding, Taxonomic/methods ; Humans ; Gene Library ; },
abstract = {Identifying genes important for fitness in Candida albicans advances our understanding of this important pathogen of humans. Here, we present a functional genomics approach for assessing fitness through the quantification of strain-specific barcodes. We describe steps for library preparation, propagation of strains, genomic DNA extraction, amplification of barcodes, and sequencing. We then detail the computational analysis of data to determine effect size and statistical significance. For complete details on the use and execution of this protocol, please refer to Xiong et al.[1].},
}
@article {pmid39984340,
year = {2025},
author = {Nishimura, M and Takahashi, K and Hosokawa, M},
title = {Recent advances in single-cell RNA sequencing of Bacteria: Techniques, challenges, and applications.},
journal = {Journal of bioscience and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jbiosc.2025.01.008},
pmid = {39984340},
issn = {1347-4421},
abstract = {Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular heterogeneity in complex biological systems. While this technology has been widely applied to eukaryotic cells, its adaptation to bacterial systems has been challenging due to the unique characteristics of bacterial transcripts. This review surveys the recent developments in bacterial scRNA-seq techniques, highlighting the technical challenges, methodological innovations, and emerging applications in microbiology. We discuss the key differences between eukaryotic and bacterial RNA-seq approaches, focusing on the strategies to overcome limitations such as the lack of poly-A tails in bacterial mRNAs and the low RNA content in individual bacterial cells. The review covers various bacterial scRNA-seq methods, including plate-based, split-pool barcoding, and droplet-based techniques, comparing their strengths and limitations in terms of sensitivity, throughput, and applicability to different bacterial species. Furthermore, we explore the biological insights gained from these techniques, such as identifying rare cell states, characterization of antibiotic responses, and analysis of bacterial communities. Finally, we discuss future perspectives and potential applications of bacterial scRNA-seq in understanding microbial physiology, host-pathogen interactions, and complex microbial ecosystems. This comprehensive overview aims to provide researchers with a clear understanding of the current state and future directions of single-cell transcriptomics in bacteria.},
}
@article {pmid39984010,
year = {2025},
author = {Ya'cob, Z and Mintara, R and Belabut, DM and Halim, MRA and Pramual, P},
title = {DNA barcoding and host blood meal identification of Culicoides Latreille (Diptera, Ceratopogonidae) from Malaysia.},
journal = {Acta tropica},
volume = {263},
number = {},
pages = {107564},
doi = {10.1016/j.actatropica.2025.107564},
pmid = {39984010},
issn = {1873-6254},
mesh = {Animals ; *Ceratopogonidae/genetics/classification/anatomy &amp; histology ; Malaysia ; *DNA Barcoding, Taxonomic ; *Phylogeny ; *Electron Transport Complex IV/genetics ; *Genetic Variation ; Sequence Analysis, DNA ; Feeding Behavior ; Cluster Analysis ; },
abstract = {Mitochondrial cytochrome oxidase I (COI) sequences were used to determine the genetic diversity and species identification efficacy of Culicoides from Malaysia. In total, 100 COI sequences were obtained from 13 morphologically identified species. Intraspecific genetic divergence varied from 0.48 % in C. parahumeralis to 14.88 % in C. palpifer. However, most (8 of 13) had low (<3 %) intraspecific genetic divergence. Identification of these species based on best match (BM) and best close match (BCM) methods revealed a high efficiency of the COI sequences with 100 % and 99 % success for BM and BCM, respectively. Identification in the BOLD database revealed that 10 species were successfully determined and agreed with morphological identifications. There remained three taxa which were ambiguous (C. jacobsoni) or had no species level identity match (C. palpifer and C. flavescens). Phylogenetic analyses found that all Malaysian specimens were clustered with conspecifics except C. palpifer. Specimens of this taxon separated into two divergent clades, one with members of a BIN (BOLD:ADT9601) of C. palpifer whereas the other formed a novel genetic lineage. Molecular species delimitation identified the morphologically identified species of the Malaysian Culicoides in the respective species. The exceptions were two divergent lineages found in C. palpifer because they were treated as two different taxa. Molecular identification of the host blood meal source revealed that all were from water buffalo (Bubalus bubalis).},
}
@article {pmid39982940,
year = {2025},
author = {Talaga, S and Guidez, A and de Thoisy, B and Lavergne, A and Carinci, R and Gaborit, P and Issaly, J and Dusfour, I and Duchemin, JB},
title = {A DNA barcode library for Culex mosquitoes (Diptera: Culicidae) of South America with the description of two cryptic species of subgenus Melanoconion.},
journal = {PloS one},
volume = {20},
number = {2},
pages = {e0310571},
pmid = {39982940},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Culex/genetics/classification/anatomy &amp; histology ; *Phylogeny ; *Electron Transport Complex IV/genetics ; South America ; Male ; Female ; French Guiana ; Gene Library ; Species Specificity ; },
abstract = {Among mosquitoes (Diptera: Culicidae), the genus Culex Linnaeus is one of the most diverse in the world and includes numerous known vector species of parasites and viruses to humans. Morphological identification of Culex species is notoriously difficult and relies mostly on the examination of properly dissected male genitalia which largely prevents female and immature identification during entomological, ecological or arboviral surveys. The aims of this study were (i) to establish a DNA barcode library for Culex mosquitoes of French Guiana based on the mitochondrial gene cytochrome c oxidase I (COI) marker, (ii) to compare three approaches of molecular delimitation of species to morphological identification, (iii) to test the effectiveness of the COI marker at a broader geographical scale across South America, and (iv) to discuss the internal classification of the genus Culex as regard to our phylogenetic analysis. Mosquitoes used in this study were sampled in French Guiana between 2013 and 2023. We provide 246 COI sequences for 90 morphologically identified species of Culex, including five new country records and two newly described species. Overall, congruence between morphological identification and molecular delimitations using the COI barcode was high. The Barcode of Life Data clustering approach into Barcode Index Numbers gives the best result in terms of species delimitation. Inconsistencies between morphological identification and molecular delimitation can be explained by introgression, incomplete lineage sorting, imperfect taxonomy or the effect of geographical gap in sampling. This increases by almost two-fold the number of mosquito species for which a DNA barcode is available in French Guiana, including 75% of the Culex species currently known in the territory. Finally, this study confirms the usefulness of the COI barcode in identifying Culex of South America, but also points the limits of this marker for some groups of species within the subgenera Culex and Melanoconion.},
}
@article {pmid39982486,
year = {2025},
author = {Yadav, A and Nimi, C and Kapoor, M and Singh, R},
title = {A quick and non-destructive approach to combat timber adulteration using attenuated total reflectance Fourier transform infrared spectroscopy and chemometrics.},
journal = {Die Naturwissenschaften},
volume = {112},
number = {2},
pages = {21},
pmid = {39982486},
issn = {1432-1904},
support = {200510156051//University Grants Commission/ ; },
mesh = {Spectroscopy, Fourier Transform Infrared/methods ; Discriminant Analysis ; *Chemometrics/methods ; Principal Component Analysis ; Least-Squares Analysis ; Magnolia/chemistry ; },
abstract = {Timber adulteration, illegal harvesting, and logging of legally protected timber species are a major threat to biodiversity. Identifying and differentiating low-value timber species from high-grade ones is a prerequisite to combat timber-related crimes. Timber adulteration can be detected by techniques such as DNA barcoding. However, these techniques have some drawbacks as they are time-consuming and destructive. To address all these issues, in this study, a quick and non-destructive approach has been used to detect timber adulteration by identifying and discriminating selective timber species using vibrational spectroscopy along chemometric methods such as principal component analysis (PCA), linear discriminant analysis (LDA), and partial least square discriminant analysis (PLS-DA) that successfully differentiated Tectona grandis (teak) from Magnolia champaca (champ) with 96.25% accuracy, Swietenia macrophylla (mahogany) from Magnolia champaca with 97.5% accuracy, and Artocarpus heterophyllus (Jack) from Mangifera indica (mango) with 100% PCA LDA training accuracies. Partial least square discriminant analysis successfully differentiated the timber species with 100% accuracy. ATR-FTIR spectroscopy and chemometric tools proved to be effective in detecting timber adulteration, which will help the investigating agencies combat timber-related crimes.},
}
@article {pmid39982230,
year = {2025},
author = {Ding, S and Lu, N and Abolhassani, H},
title = {Assessing the Influence of Selected Permeabilization Methods on Lymphocyte Single-Cell Multi-Omics.},
journal = {Antibodies (Basel, Switzerland)},
volume = {14},
number = {1},
pages = {},
pmid = {39982230},
issn = {2073-4468},
support = {HA//Jonas S&#xf6;derquist scholarship/ ; },
abstract = {(1) Background: Single-cell multi-omics is a powerful method for the dissection and detection of complicated immunologic functions and synapses. However, most currently available technologies merge datasets of different omics from separate portions of the same sample to generate combined multi-omics. This process is a source of bias, mainly in the field of immunology on cells originating from pluripotent hematopoietic stem cells with high flexibility during maturation. (2) Methods: Although new multi-omics approaches have been developed to use the advantages of cellular and molecular barcoding and next-generation sequencing to solve this issue, one of the main current challenges is intracellular proteomics, which should be combined with other omics data with high importance for immune system studies. We designed this study to evaluate previously recommended minimal permeabilization and fixation methods on the quality and quantity of transcriptomics and proteomics data generated by the BD Rhapsody™ Single-Cell Analysis System. (3) Results: Our findings showed that high-throughput sequencing with advanced quality and read-out is required for the combination of multi-omics outcomes from a permeabilized single cell. Therefore, the HiseqX platform was selected for further analysis. The effect of immune stimulation was observed clearly as the separated clusters of helper and cytotoxic T cells using unsupervised clustering. Importantly, fixation and permeabilization did not affect the general expression profile of unstimulated cells. However, fixation and permeabilization were proved to negatively impact the detection of the whole transcriptome for single-cell assay. Nevertheless, about 60% of the transcriptomic signature of the stimulation was detected. If the measurement of combined surface and intracellular markers is required to be achieved, the modified fixation and permeabilization method is recommended because of a lower transcriptomic loss and more precise proteomic fingerprint detected. (4) Conclusions: The findings of this study support the potential possibility for integrating intracellular proteomics, which needs to be optimized and tested with newly designed oligonucleotide-tagged antibodies targeting intracellular proteins.},
}
@article {pmid39981117,
year = {2025},
author = {González, MA and López-de-Felipe, M and Magallanes, S and Alarcón-Elbal, PM and Barceló, C and Martínez-Barciela, Y and Polina, A and García-López, AM and Blanco-Sierra, L and Peláez Guerra, MA and Delacour, S and Figuerola, J and Ruiz-Arrondo, I and Bravo-Barriga, D},
title = {Distribution, identification and ecology of Phortica genus (Diptera: Drosophilidae) in Spain.},
journal = {International journal of veterinary science and medicine},
volume = {13},
number = {1},
pages = {1-11},
pmid = {39981117},
issn = {2314-4599},
abstract = {The genus Phortica (Diptera: Drosophilidae) includes five species of small flies in Europe. Phortica variegata, the zoophilic fruit fly, is the main vector of Thelazia callipaeda, a zoonotic parasite that is rapidly spreading througout Europe. Despite extensive studies on thelaziosis in animals and humans, there is limited knowledge about the geographical distribution and hovering activity of these vector flies. In 2023, 1,462 Phortica flies were sampled across 12 Spanish provinces, providing new records of Phortica variegata and Phortica oldenbergi. Surprisingly, P. oldenbergi, previously considered a rare Afrotropical species, was prevalent in most regions sampled in Spain. However, Phortica semivirgo was not collected. The abundance of Phortica spp. correlated positively with altitude and certain tree species. Rural oak-wooded areas in central and northern Spain showed the highest densities of P. variegata. Both drosophilid species were analysed morphologically and molecularly, providing new morphological descriptors and sequence barcodes for species identification. Phylogenetic analysis based on COI sequences, showed P. oldenbergi grouped with Asian origin Phortica species, while P. variegata in America was closer to Spanish sequences than those from other European countries. The hovering activity of P. variegata causes significant discomfort to humans during outdoor activities. This paper also reviews the historic records of P. variegata, P. semivirgo and P. oldenbergi in Spain over the last 90 years. This study enhances the understanding of the distribution, identification, ecology, and behaviour of these zoophilic flies in Europe.},
}
@article {pmid39981057,
year = {2025},
author = {Slater-Baker, MR and Fagan-Jeffries, EP and Oestmann, KJ and Portmann, OG and Bament, TM and Howe, AG and Guzik, MT and Bradford, TM and McClelland, AR and Woodward, A and Clarke, S and Ducker, N and Fernández-Triana, J},
title = {DNA barcoding, integrative taxonomy, citizen science, and Bush Blitz surveys combine to reveal 34 new species of Apanteles (Hymenoptera, Braconidae, Microgastrinae) in Australia.},
journal = {ZooKeys},
volume = {1227},
number = {},
pages = {1-128},
pmid = {39981057},
issn = {1313-2989},
abstract = {Microgastrinae is a megadiverse subfamily of wasps in the family Braconidae. As parasitoids of caterpillars, members of the subfamily play important roles in regulating native caterpillar populations, and several species are used commercially as biological control agents. The genus Apanteles comprises a large portion of total microgastrine diversity, however it has not been studied in Australia for more than 30 years, with only nine described species previously known from the continent. We explore the diversity and systematics of Apanteles in Australia, using cytochrome c oxidase subunit I (COI) and Wingless (wg) DNA barcodes from more than 400 Australian Apanteles specimens. Using molecular species delimitation in combination with reduced morphological diagnoses, at least 48 distinct molecular lineages of Apanteles are confirmed in Australia, and 34 new species are formally described, all authored by Slater-Baker, Fagan-Jeffries, Fernández-Triana, Portmann &amp; Oestmann: A.adustus, A.aeternus, A.alatomicans, A.allapsus, A.amicalis, A.apollo, A.apricus, A.artemis, A.aurantius, A.auroralis, A.banrock, A.breviflagellarius, A.brockhedgesi, A.cuprum, A.darthvaderi, A.doreenwatlerae, A.ethanbeaveri, A.fenestrinus, A.ferripulvis, A.focusalis, A.hades, A.insulanus, A.kelpiellus, A.lamingtonensis, A.ligdus, A.magicus, A.margaritarius, A.pellucidus, A.phantasmatus, A.pharusalis, A.ramsaris, A.rufiterra, A.sinusulus, and A.translucentis.},
}
@article {pmid39981046,
year = {2025},
author = {Borsato, ND and Lunn, K and Garrett, NR and Biganzoli-Rangel, AJ and Marquina, D and Steinke, D and Floyd, R and Clare, EL},
title = {Identification of potential insect ecological interactions using a metabarcoding approach.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18906},
pmid = {39981046},
issn = {2167-8359},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Bees/microbiology/genetics ; *Moths/genetics/microbiology ; Insecta/microbiology/genetics ; Wasps/genetics/microbiology ; },
abstract = {Species interactions are challenging to quantify, particularly when they happen cryptically. Molecular methods have become a key tool to uncover these interactions when they leave behind a DNA trace from the interacting organism (e.g., pollen on a bee) or when the taxa are still present but morphologically challenging to identify (e.g., microbial or fungal interactions). The decreasing costs of sequencing makes the mass analysis of thousands of target species possible. However, the challenge has shifted to selecting molecular markers which maximize information recovery while analyzing these data at broad biological scales. In this manuscript we use model arthropod groups to compare molecular markers and their analysis across life stages. We develop protocols for two ecologically and economically devastating pests, the spongy moth (Lymantria dispar dispar) and the emerald ash borer (Agrilus planipennis), and a group of pollinators including bees and wasps which regularly deposit eggs in "bee hotels" where the larvae develop. Using Illumina MiSeq and Oxford Nanopore MinION platforms we evaluate seven primer pairs for five molecular markers which target plants, fungi, microbes, insects, and parasitic phyla (e.g., nematodes). Our data reveals hundreds of potential ecological interactions and establishes generalized methods which can be applied across arthropod host taxa with recommendations on the appropriate markers in different systems. However, we also discuss the challenge of differentiating co-occurring DNA signals and true ecological interactions, a problem only starting to be recognized as eDNA from the environment accumulates on living organisms.},
}
@article {pmid39980701,
year = {2025},
author = {Park, SY and Sohee, K and Eunjin, K and Eo, JK and Lee, H},
title = {Taxonomic Revision of Korean Saddle Fungi (Helvella, Helvellaceae).},
journal = {Mycobiology},
volume = {53},
number = {1},
pages = {79-112},
pmid = {39980701},
issn = {1229-8093},
abstract = {Helvella, commonly known as saddle fungi, is a genus in the Helvellaceae family and is distributed globally. Recent comprehensive studies on Helvella have revealed that some Helvella species exhibit endemic traits and that many morphologically similar, cryptic species are phylogenetically distant. In this study, 202 Korean Helvella specimens collected between 1986 and 2023 were reevaluated through morphological analysis and phylogenetic characterization using barcode sequences, including nrLSU (nuclear Large Subunit Ribosomal DNA), hsp90 (Heat Shock Protein 90), and ITS (Internal Transcribed Spacer). The investigation confirmed the presence of at least 35 phylogenetic species in Korea. Among these, eight species (H. atroides, H. fistulosa, H. liquii, H. lobata, H. rugosa, H. subglabroides, H. sublactea, H. varia) were identified as previously unrecorded species in Korea, and seven new species (H. densipila, H. flavopus, H. macrospora, H. griseobrunnea, H. pseudolobata, H. parviflava, H. suborentitomentosa) were discovered. Of the 13 previously recorded Korean Helvella species, only three (H. ephippioides, H. macropus, H. orienticripsa) were confirmed, while the remaining ten species (H. acetabulum, H. atra, H. compressa, H. costifera, H. crispa, H. elastica, H. sublicia, H. fibrosa, H. lacunosa, H. pezizoides) were not detected in the samples studied. This study enhances our understanding of the distribution of Helvella species of Korea, revealing significant discrepancies between historical records and current findings. The discovery of new species and previously un-recorded species underscores the importance of continuous monitoring and reevaluation of fungal biodiversity.},
}
@article {pmid39980019,
year = {2025},
author = {Miyamoto, AT and Shimagami, H and Kumanogoh, A and Nishide, M},
title = {Spatial transcriptomics in autoimmune rheumatic disease: potential clinical applications and perspectives.},
journal = {Inflammation and regeneration},
volume = {45},
number = {1},
pages = {6},
pmid = {39980019},
issn = {1880-9693},
support = {JP24K11596//Japan Society for the Promotion of Science/ ; JP18H05282//Japan Society for the Promotion of Science/ ; JPMJFR235B//Fusion Oriented REsearch for disruptive Science and Technology/ ; 223fa627002h0001//Japan Agency for Medical Research and Development/ ; },
abstract = {Spatial transcriptomics is a cutting-edge technology that analyzes gene expression at the cellular level within tissues while integrating spatial location information. This concept, which combines high-plex RNA sequencing with spatial data, emerged in the early 2010s. Spatial transcriptomics has rapidly expanded with the development of technologies such as in situ hybridization, in situ sequencing, in situ spatial barcoding, and microdissection-based methods. Each technique offers advanced mapping resolution and precise spatial assessments at the single-cell level. Over the past decade, the use of spatial transcriptomics on clinical samples has enabled researchers to identify gene expressions in specific diseased foci, significantly enhancing our understanding of cellular interactions and disease processes. In the field of rheumatology, the complex and elusive pathophysiology of diseases such as rheumatoid arthritis, systemic lupus erythematosus, and Sjögren's syndrome remains a challenge for personalized treatment. Spatial transcriptomics provides insights into how different cell populations interact within disease foci, such as the synovial tissue, kidneys, and salivary glands. This review summarizes the development of spatial transcriptomics and current insights into the pathophysiology of autoimmune rheumatic diseases, focusing on immune cell distribution and cellular interactions within tissues. We also explore the potential of spatial transcriptomics from a clinical perspective and discuss the possibilities for translating this technology to the bedside.},
}
@article {pmid39979460,
year = {2025},
author = {Langerman, J and Baghdasarian, S and Cheng, RY and James, RG and Plath, K and Di Carlo, D},
title = {Linking single-cell transcriptomes with secretion using SEC-seq.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {39979460},
issn = {1750-2799},
support = {2023-332386//Silicon Valley Community Foundation (SVCF)/ ; 2023-332386//Silicon Valley Community Foundation (SVCF)/ ; },
abstract = {Cells secrete numerous proteins and other biomolecules into their surroundings to achieve critical functions-from communicating with other cells to blocking the activity of pathogens. Secretion of cytokines, growth factors, extracellular vesicles and even recombinant biologic drugs defines the therapeutic potency of many cell therapies. However, gene expression states that drive specific secretory phenotypes are largely unknown. We provide a protocol that enables the secretion amount of a target protein encoded (SEC) by oligonucleotide barcodes to be linked with transcriptional sequencing (seq) for thousands of single cells. SEC-seq leverages microscale hydrogel particles called Nanovials to isolate cells and capture their secretions in close proximity, oligonucleotide-labeled antibodies to tag secretions on Nanovials and flow cytometry and single-cell RNA-sequencing (scRNA-seq) platforms for readout. Cells on Nanovials can be sorted on the basis of viability, secretion amount or other surface markers without fixation or permeabilization, and cell- and secretion-containing Nanovials are directly introduced into microfluidic droplets-in-oil emulsions for single-cell barcoding of cell transcriptomes and secretions. We have used SEC-seq to link T cell receptor sequences to the relative amount of associated cytokine secretions, surface marker gene expression with a highly secreting and potential regenerative population of mesenchymal stromal cells and the transcriptome with high immunoglobulin secretion from plasma cells. Nanovial modification and cell loading takes <4 h, and once the desired incubation time is over, staining, cell sorting and emulsion generation for scRNA-seq can also be completed in <4 h. Compared to related techniques that link secretions to a cell's surface, SEC-seq provides a general solution across any secretion target because of the ease with which biotinylated Nanovials can be modified. By linking gene expression and secretory strength, SEC-seq can expand our understanding of cell secretion, how it is regulated and how it can be engineered to make better therapies.},
}
@article {pmid39979452,
year = {2025},
author = {Wu, HC and Chiu, YT and Wu, IC and Liou, CH and Cheng, HW and Kuo, SC and Lauderdale, TL and Sytwu, HK and Liao, YC and Chen, FJ},
title = {Streamlining whole genome sequencing for clinical diagnostics with ONT technology.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {6270},
pmid = {39979452},
issn = {2045-2322},
support = {IV-111-PP-11//National Health Research Institutes/ ; PH-112-PP-05//National Health Research Institutes/ ; IV-111-PP-23//National Health Research Institutes/ ; 111-2314-B-400-033//Ministry of Science and Technology, Taiwan/ ; },
mesh = {*Whole Genome Sequencing/methods ; Humans ; Software ; Genome, Bacterial ; Computational Biology/methods ; Workflow ; Bacteria/genetics/isolation &amp; purification/classification ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Recent advances in whole-genome sequencing (WGS) have increased the accessibility of this tool, offering substantial potential for pathogen surveillance, outbreak response, and diagnostics. However, the routine clinical adoption of WGS is hindered by factors such as high costs, technical complexity, and the requirement for bioinformatics expertise for data analysis. To address these challenges, we propose RapidONT, a workflow designed for cost-effective and accessible WGS-based pathogen analysis. RapidONT employs a mechanical shearing-based DNA extraction protocol, followed by library construction by using a multiplexing Oxford nanopore technologies (ONT) rapid barcoding kit. Flye software is used for de novo assembly without manual intervention, followed by basic assembly polishing using Medaka and Homopolish. The polished assemblies are then analyzed using the user-friendly web-based platform Pathogenwatch, which facilitates species identification, molecular typing, and antimicrobial resistance (AMR) prediction, all while requiring minimal bioinformatics expertise. The efficacy of RapidONT was evaluated using nine clinically relevant pathogens, encompassing a total of 90 gram-positive and gram-negative bacterial strains. The workflow demonstrated high accuracy in critical tasks such as multilocus sequence typing (MLST) and AMR identification, using only ONT R9.4.1 flowcell data. Notably, limitations were observed with Salmonella spp. and Neisseria gonorrhoeae. Furthermore, RapidONT enabled the generation of genomic information for 48 bacterial isolates by using a single flow cell, significantly reducing sequencing costs. This approach eliminates the need for extensive experimentation in obtaining crucial genomic information. This workflow facilitates broader WGS implementation in clinical pathogen analysis and diagnostics.},
}
@article {pmid39977545,
year = {2025},
author = {Gandin, V and Kim, J and Yang, LZ and Lian, Y and Kawase, T and Hu, A and Rokicki, K and Fleishman, G and Tillberg, P and Castrejon, AA and Stringer, C and Preibisch, S and Liu, ZJ},
title = {Deep-tissue transcriptomics and subcellular imaging at high spatial resolution.},
journal = {Science (New York, N.Y.)},
volume = {},
number = {},
pages = {eadq2084},
doi = {10.1126/science.adq2084},
pmid = {39977545},
issn = {1095-9203},
abstract = {Limited color channels in fluorescence microscopy have long constrained spatial analysis in biological specimens. Here, we introduce cycle Hybridization Chain Reaction (HCR), a method that integrates multicycle DNA barcoding with HCR to overcome this limitation. cycleHCR enables highly multiplexed imaging of RNA and proteins using a unified barcode system. Whole-embryo transcriptomics imaging achieved precise three-dimensional gene expression and cell fate mapping across a specimen depth of ~310 μm. When combined with expansion microscopy, cycleHCR revealed an intricate network of 10 subcellular structures in mouse embryonic fibroblasts. In mouse hippocampal slices, multiplex RNA and protein imaging uncovered complex gene expression gradients and cell-type-specific nuclear structural variations. cycleHCR provides a quantitative framework for elucidating spatial regulation in deep tissue contexts for research and potentially diagnostic applications.},
}
@article {pmid39975614,
year = {2025},
author = {Bhowmik, B and Dey, B and Das, S and Barman, GD and Chanda, S and Mondal, R},
title = {Morphological, ultrastructure and molecular characterization of Unionicola chelata (Acari: Hydrachnida: Unionicolidae) isolated from Bellamya bengalensis, West Bengal, India.},
journal = {Journal of parasitic diseases : official organ of the Indian Society for Parasitology},
volume = {49},
number = {1},
pages = {37-44},
pmid = {39975614},
issn = {0971-7196},
abstract = {Unionicola spp. is a parasitic aquatic mite known to infect freshwater aquatic organisms, especially the marine and freshwater molluscs and few species of sponges. Unionicola chelata (Acari: Hydrachnida: Unionicolidae) generally infect the freshwater bivalves of the Genus Unio sp. They are usually facultative in nature and can be parasitic at any stage of their life cycle. They cause damage to the gills of the host which harms their normal respiration process. The present work portraits the morphological characters, ultrastructure and DNA barcoding of its mitochondrial gene Cytochrome Oxidase I (COI)(mtCOI), and its taxonomic position was justified by obtaining a phylogenetic tree. The description regarding its morphological characters, ultrastructure and molecular characterization has been presented here. This paper holds the report of a parasitic aquatic mite Unionicola chelata for the first time from a gastropod molluscan host Bellamya bengalensis (Lamarck, 1882), from Diamond Harbour, South 24 Parganas, West Bengal, India.},
}
@article {pmid39975479,
year = {2024},
author = {Sadler, JM and Simkin, A and Tchuenkam, VPK and Gerdes Gyuricza, I and Fola, AA and Wamae, K and Assefa, A and Niaré, K and Thwai, K and White, SJ and Moss, WJ and Dinglasan, RR and Nsango, SE and Tume, CB and Parr, JB and Ali, IM and Bailey, JA and Juliano, JJ},
title = {Application of a new highly multiplexed amplicon sequencing tool to evaluate Plasmodium falciparum antimalarial resistance and relatedness in individual and pooled samples from Dschang, Cameroon.},
journal = {Frontiers in parasitology},
volume = {3},
number = {},
pages = {1509261},
pmid = {39975479},
issn = {2813-2424},
support = {R01 AI165537/AI/NIAID NIH HHS/United States ; R01 AI177791/AI/NIAID NIH HHS/United States ; U19 AI089680/AI/NIAID NIH HHS/United States ; R01 AI155730/AI/NIAID NIH HHS/United States ; R01 AI156267/AI/NIAID NIH HHS/United States ; K24 AI134990/AI/NIAID NIH HHS/United States ; },
abstract = {BACKGROUND: Resistance to antimalarial drugs remains a major obstacle to malaria elimination. Multiplexed, targeted amplicon sequencing is being adopted for surveilling resistance and dissecting the genetics of complex malaria infections. Moreover, genotyping of parasites and detection of molecular markers drug resistance in resource-limited regions requires open-source protocols for processing samples, using accessible reagents, and rapid methods for processing numerous samples including pooled sequencing.<br><br>METHODS: Plasmodium falciparum Streamlined Multiplex Antimalarial Resistance and Relatedness Testing (Pf-SMARRT) is a PCR-based amplicon panel consisting of 15 amplicons targeting antimalarial resistance mutations and 9 amplicons targeting hypervariable regions. This assay uses oligonucleotide primers in two pools and a non-proprietary library and barcoding approach.<br><br>RESULTS: We evaluated Pf-SMARRT using control mocked dried blood spots (DBS) at varying levels of parasitemia and a mixture of 3D7 and Dd2 strains at known frequencies, showing the ability to genotype at low parasite density and recall within-sample allele frequencies. We then piloted Pf-SMARRT to genotype 100 parasite isolates collected from uncomplicated malaria cases at three health facilities in Dschang, Western Cameroon. Antimalarial resistance genotyping showed high levels of sulfadoxine-pyrimethamine resistance mutations, including 31% prevalence of the DHPS A613S mutation. No K13 candidate or validated artemisinin partial resistance mutations were detected, but one low-level non-synonymous change was observed. Pf-SMARRT's hypervariable targets, used to assess complexity of infections and parasite diversity and relatedness, showed similar levels and patterns compared to molecular inversion probe (MIP) sequencing. While there was strong concordance of antimalarial resistance mutations between individual samples and pools, low-frequency variants in the pooled samples were often missed.<br><br>CONCLUSION: Overall, Pf-SMARRT is a robust tool for assessing parasite relatedness and antimalarial drug resistance markers from both individual and pooled samples. Control samples support that accurate genotyping as low as 1 parasite per microliter is routinely possible.},
}
@article {pmid39973970,
year = {2024},
author = {Yang, Z and Chen, J and Xiao, Y and Yang, C and Zhao, CX and Chen, D and Weitz, DA},
title = {Digital Barcodes for High-Throughput Screening.},
journal = {Chem &amp; bio engineering},
volume = {1},
number = {1},
pages = {2-12},
pmid = {39973970},
issn = {2836-967X},
abstract = {High-throughput screening is an indispensable technology in drug discovery, cancer therapy, and disease diagnosis, and it could greatly reduce time cost, reagent consumption, and labor expense. Here, four high-throughput screening methods with high sensitivity and accessibility are discussed in detail. Fluorescence, DNA, heavy metal, and nonmetal isotope barcodes, which generally label antibodies, proteins, and saccharides to identify cells, are detected by flow cytometry, second-generation DNA sequencing, mass cytometry, and second-ion mass spectrometry, respectively. Encoding binary information in barcodes, labeling individual cells by barcodes, performing the characterization of cells together, and identifying the result belonging to individual cells via barcodes are the main steps for high-throughput screening. Applications of the four digital barcodes in high-throughput screening for both in vitro and in vivo tests are described in detail, and their advantages and disadvantages are also summarized. High-throughput screening has provided a powerful platform widely accessible for multidisciplinary studies and has greatly sped up the progress of drug discovery, disease diagnosis, and cancer therapy.},
}
@article {pmid39972899,
year = {2025},
author = {Mohanta, D and Dvirnas, A and Ambjörnsson, T},
title = {Random sampling of ligand arrangements on a one-dimensional lattice.},
journal = {Physical review. E},
volume = {111},
number = {1-1},
pages = {014412},
doi = {10.1103/PhysRevE.111.014412},
pmid = {39972899},
issn = {2470-0053},
abstract = {We introduce a transfer-matrix-based sequential sampling scheme for generating random samples of ligand arrangements on one-dimensional templates. The number of ligand types is arbitrary, the binding constants can have positional dependence, and cooperativity parameters are included. From the random arrangements, any (linear or nonlinear) observable can be calculated using sample averaging. As an example case study, we investigate the competitive binding of three ligand types (the sequence-specific binder netropsin, YOYO-1, and ethidium bromide) to a DNA molecule. We also employ our random sampling method of ligands to determine the quality of synthetically generated DNA barcodes as a function of concentration of a ligand (e.g., netropsin) in optical DNA mapping (ODM) experiments. We provide publically available softwares, with a computational time that scales linearly with the lattice size, for generating random ligand arrangements and for generating synthetic barcodes.},
}
@article {pmid39972011,
year = {2025},
author = {Marsh, WA and Hall, A and Barnes, I and Price, B},
title = {Facilitating high throughput collections-based genomics: a comparison of DNA extraction and library building methods.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {6013},
pmid = {39972011},
issn = {2045-2322},
mesh = {*DNA/genetics/isolation &amp; purification ; *Genomics/methods ; *Gene Library ; *High-Throughput Nucleotide Sequencing/methods ; *Museums ; DNA Barcoding, Taxonomic/methods ; },
abstract = {While DNA barcoding methods are an increasingly important tool in biological conservation, the resource requirements of constructing reference libraries frequently reduce their efficacy. One efficient way of sourcing taxonomically validated DNA for reference libraries is to use museum collections. However, DNA degradation intrinsic to historical museum specimens can, if not addressed in the wet lab, lead to low quality data generation and severely limit scientific output. Several DNA extraction and library build methods that are designed to work with degraded DNA have been developed, although the ability to implement these methods at scale and at low cost has yet to be formally addressed. Here, the performance of widely used DNA extraction and library build methods are compared using museum specimens. We find that while our selected DNA extraction methods do not significantly differ in DNA yield, the Santa Cruz Reaction (SCR) library build method is not only the most effective at retrieving degraded DNA from museum specimens but also easily implemented at high throughput for low cost. Results highlight the importance of lab protocol on data yield. An optimised "sample to sequencing" high-throughput protocol which incorporates SCR is included to allow for easy uptake by the wider scientific community.},
}
@article {pmid39970179,
year = {2025},
author = {Yang, J and Kim, SC},
title = {Hosta clausa (Asparagaceae) in East Asia: Intraspecific chloroplast genome variation and its phylogenomic implications.},
journal = {PloS one},
volume = {20},
number = {2},
pages = {e0317884},
pmid = {39970179},
issn = {1932-6203},
mesh = {*Genome, Chloroplast ; *Phylogeny ; *Genetic Variation ; Hosta/genetics ; Asia, Eastern ; },
abstract = {Hosta species are abundant in northeastern Asia, offering significant ornamental and horticultural value due to their diverse foliage colors and textures, as well as their showy, fragrant flowers. Among the eight taxa naturally distributed in Korea, H. clausa is found in central and northern Korea, as well as northeastern China, providing valuable resources for developing and improving new varieties. Currently, four intraspecific taxa of H. clausa are recognized at the variety level based on reproductive (opened vs. closed perianth), vegetative (leaf shape), and habitat characteristics: var. clausa, var. normalis, var. ensata, and var. geumgangensis. Despite its horticultural and taxonomic importance, little is known about the degree of intraspecific chloroplast genome variation and relationships among the varieties of H. clausa. This could provide some valuable information for marker-assisted breeding programs and molecular cultivar identification. In this study, we investigated the complete plastid genome of 14 accessions of H. clausa, covering its native distribution range. We characterized genome size and features and performed comparative plastome analyses (frequency of codon usage, nucleotide diversity, mutation hotspots). Our analysis revealed highly conserved structures and gene content organization in H. clausa, along with significantly (two to three times) lower nucleotide diversity compared to intraspecific herbaceous and woody species. The phylogenetic analysis did not support the recognition of intraspecific taxa as currently delimited, and a broad-scale geographical structure of complete plastomes was not apparent. The asexual reproductive mode of H. clausa appears to contribute to the low plastome genetic diversity. A total of 72 polymorphic sites identified among 14 accessions of H. clausa and their phylogenetic relationships, in conjunction with their geographical distribution and morphological characteristics, will be a valuable resource for barcoding study, marker-assisted breeding programs, and developing conservation strategies for hosta species in East Asia.},
}
@article {pmid39970170,
year = {2025},
author = {Almuteri, JS and Al Wahaibi, MS and Mustafa, AEM and Alshaqhaa, MA and Afzal, M and Alshehri, MD},
title = {Morphological characterization and DNA barcoding of Ruellia sp. in Saudi Arabia.},
journal = {PloS one},
volume = {20},
number = {2},
pages = {e0315827},
pmid = {39970170},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic ; Saudi Arabia ; DNA, Plant/genetics ; Phylogeny ; },
abstract = {The genus Ruellia L. belongs to this family and its plants are herbs or shrubs. This genus was first detected in the tropical and subtropical regions. The primary objective this study is to identify the various species within the genus Ruellia using both morphological characteristics and DNA barcoding methods. For this purpose, plant samples were meticulously collected from eight distinct natural habitats across the region. All vegetative and floral parts were examined using a binocular microscope. All parts are measured and photographed. To ensure accurate identification and characterization, four molecular barcoding markers were employed: Psbk-psbi, trnH-psbA, rbcL, and AtpF-AtpH. Eight Ruellia species were identified from different regions: Abha, Aseer (24651), Jazan (24652), Malacosperma, Patula, Taif (24650 rose), Taif (24650 violet), and Taif (24650 white). The species were confirmed using specimens from the King Saud University herbarium. Notably, the samples collected from Taif, which had flowers of different colors, were determined to represent a single species with different genotypes. The use of four DNA barcode markers (Psbk-psbi, trnH-psbA, rbcL, and AtpF-AtpH) facilitated the identification of five distinct species: R. tweediana, R. sp. SH2010, R. carolinensis, R. simplex, and R. patula. These findings confirmed the dominant Ruellia species in Saudi Arabia and demonstrated the reliability of DNA barcode markers for species identification. Further assessment of these species' adaptability, molecular genetics, and functional genomics is necessary for their commercial utilization in the region. These species are recorded for the first time in Saudi Arabia and represent the first record.},
}
@article {pmid39968047,
year = {2024},
author = {Ling, M and Szarvas, J and Kurmauskaitė, V and Kiseliovas, V and Žilionis, R and Avot, B and Munk, P and Aarestrup, FM},
title = {High throughput single cell metagenomic sequencing with semi-permeable capsules: unraveling microbial diversity at the single-cell level in sewage and fecal microbiomes.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1516656},
pmid = {39968047},
issn = {1664-302X},
abstract = {Single-cell sequencing may serve as a powerful complementary technique to shotgun metagenomics to study microbiomes. This emerging technology allows the separation of complex microbial communities into individual bacterial cells, enabling high-throughput sequencing of genetic material from thousands of singular bacterial cells in parallel. Here, we validated the use of microfluidics and semi-permeable capsules (SPCs) technology (Atrandi) to isolate individual bacterial cells from sewage and pig fecal samples. Our method involves extracting and amplifying single bacterial DNA within individual SPCs, followed by combinatorial split-and-pool single-amplified genome (SAG) barcoding and short-read sequencing. We tested two different sequencing approaches with different numbers of SPCs from the same sample for each sequencing run. Using a deep sequencing approach, we detected 1,796 and 1,220 SAGs, of which 576 and 599 were used for further analysis from one sewage and one fecal sample, respectively. In shallow sequencing data, we aimed for 10-times more cells and detected 12,731 and 17,909 SAGs, of which we used 2,456 and 1,599 for further analysis for sewage and fecal samples, respectively. Additionally, we identified the top 10 antimicrobial resistance genes (ARGs) in both sewage and feces samples and linked them to their individual host bacterial species.},
}
@article {pmid39967725,
year = {2025},
author = {Islam, S},
title = {Commentary on "Preliminary Species Hypotheses" in Entomological Taxonomy: A Global Data and FAIR Infrastructure Perspective.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e141562},
pmid = {39967725},
issn = {1314-2828},
abstract = {What if early taxonomic findings were treated like preprints, open to iterative improvement or managed with practices from the open-source community, such as Git branching, merging and patch management? Prompted by Buckley's article Charting a Future for Entomological Taxonomy in New Zealand (2024), this commentary explores these possibilities in the context of biodiversity informatics. In response to the need for rapid, scalable biodiversity monitoring, Buckley introduces preliminary species hypotheses (PSH) as a bridge between quick identification tools and the rigorous Linnaean system, leveraging DNA barcoding and AI-assisted image recognition to produce provisional classifications that can later be validated. Expanding on Buckley's framework, this commentary emphasises the critical role of data linking, versioning and integration to support evolving taxonomic data. Borrowing from software and open-source practices, I explore the idea of managing PSH with an infrastructure that treats each taxonomic update as a versioned "commit", which can be tracked, refined and integrated over time. Drawing insights from FAIR (Findable, Accessible, Interoperable, Reusable) principles and Digital Extended Specimens, I identify infrastructure requirements for PSH, including robust data standards, persistent identifiers and interoperability to support global biodiversity repositories. Additionally, Taxonomic Data Objects offer a model for dynamically integrating PSH into adaptable taxonomies that can evolve with new data and tools. By positioning PSH within an open, infrastructure-focused framework, this commentary advocates for scalable, hypothesis-driven biodiversity data that meets modern conservation needs, bridging traditional and emerging practices in taxonomy.},
}
@article {pmid39966379,
year = {2025},
author = {Schubert, C and Nguyen, BD and Sichert, A and Näpflin, N and Sintsova, A and Feer, L and Näf, J and Daniel, BBJ and Steiger, Y and von Mering, C and Sauer, U and Hardt, WD},
title = {Monosaccharides drive Salmonella gut colonization in a context-dependent or -independent manner.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1735},
pmid = {39966379},
issn = {2041-1723},
support = {10.001.588//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 51NF40_180575//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 310030_19256//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 51NF40_180575//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; SCHU 3606/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Animals ; Mice ; *Salmonella typhimurium/genetics/pathogenicity ; *Monosaccharides/metabolism ; Gastrointestinal Microbiome/physiology ; Fructose/metabolism ; Glucose/metabolism ; Cecum/microbiology ; Salmonella Infections/microbiology ; Mice, Inbred C57BL ; Female ; Galactose/metabolism ; Mutation ; Disease Models, Animal ; Mannose/metabolism ; },
abstract = {The carbohydrates that fuel gut colonization by S. Typhimurium are not fully known. To investigate this, we designed a quality-controlled mutant pool to probe the metabolic capabilities of this enteric pathogen. Using neutral genetic barcodes, we tested 35 metabolic mutants across five different mouse models with varying microbiome complexities, allowing us to differentiate between context-dependent and context-independent nutrient sources. Results showed that S. Typhimurium uses D-mannose, D-fructose and likely D-glucose as context-independent carbohydrates across all five mouse models. The utilization of D-galactose, N-acetylglucosamine and hexuronates, on the other hand, was context-dependent. Furthermore, we showed that D-fructose is important in strain-to-strain competition between Salmonella serovars. Complementary experiments confirmed that D-glucose, D-fructose, and D-galactose are excellent niches for S. Typhimurium to exploit during colonization. Quantitative measurements revealed sufficient amounts of carbohydrates, such as D-glucose or D-galactose, in the murine cecum to drive S. Typhimurium colonization. Understanding these key substrates and their context-dependent or -independent use by enteric pathogens will inform the future design of probiotics and therapeutics to prevent diarrheal infections such as non-typhoidal salmonellosis.},
}
@article {pmid39965776,
year = {2025},
author = {Wang, K and Xu, Y and Lin, R and Yang, S and Wang, Z and Cui, K and Chen, S and Wang, Z and Chen, S and Wang, Z and Zhang, W and Zhu, C and Gao, Z},
title = {Spatiotemporal Control of Photoisomerization Dynamics via Domino Barriers for Programmatically Responsive Heterostructures.},
journal = {ACS nano},
volume = {19},
number = {8},
pages = {7718-7727},
doi = {10.1021/acsnano.4c12005},
pmid = {39965776},
issn = {1936-086X},
abstract = {Controlling the photoisomerization reaction at the micro-/nanoscale is important for the realization of high-end photonic components. Unfortunately, spatiotemporal manipulation of the photoisomerization dynamics still faces a significant challenge. Here, we propose an effective strategy to control the photoisomerization reaction spatiotemporally through introducing a steric-hindrance effect by the aid of alloy engineering. The external guest molecules behave like domino barriers and efficiently regulate the photoisomerization dynamics. Moreover, the flexible assembly of the organic heterostructures with different steric-hindrance degrees enabled us to spatiotemporally modulate the photoisomerization dynamics in 1D, 2D, and even annular morphologies. Interestingly, the photoisomerization reaction exhibits anisotropic change characteristics in 2D microcrystals. Our work provides deep insight into the modulation of the photoisomerization reaction and would promote the development of smart responsive barcodes with improved security level toward advanced anti-counterfeiting applications.},
}
@article {pmid39963517,
year = {2025},
author = {Wang, C and Lu, Z and She, G and Chen, K and Zhou, H and Zhan, X and Yu, H and Pi, L and Zuo, L and Che, D},
title = {The Identification of FN1 as an Early Diagnostic Marker for Recurrent Abortion by Single-Exosome Profiling.},
journal = {International journal of general medicine},
volume = {18},
number = {},
pages = {691-702},
pmid = {39963517},
issn = {1178-7074},
abstract = {PURPOSE: Recurrent abortion(RA) is a prevalent adverse pregnancy event. Exosomes, secreted by various body fluids, are known to play a role in disease diagnosis and serve as biomarkers through intercellular communication. This study aims to analyze single exosomes in patients with recurrent abortion to identify new biomarkers that may significantly contribute to recurrent abortion, providing new directions for its treatment.<br><br>PATIENTS AND METHODS: A total of 244 serum exosomes were collected, including 216 patients with recurrent abortion of varying outcomes and 28 normal pregnancies. We performed the proximity barcoding assay (PBA) to analyze single exosome surface proteins, which allowed us to identify individual exosomes related to the development of RA as well as the major subpopulations of exosomes. After PBA treatment, samples were analyzed for single exosomes, and exosomes from each group were compared using volcano plots, dot plots, and ROC curves.<br><br>RESULTS: By intersecting all significantly differentially expressed genes obtained from comparisons between the normal pregnancy control group and the recurrent abortion group, including the RA before abortion, RA after abortion, and RA non-pregnancy groups, we identified seven shared differential genes: FN1, APIPOQ, CDH13, DSG1, CLDN4, CD36, and ULBP3. Among these, FN1 was the most significantly differentially expressed gene in exosomes, with FN1 | log2 (fold change) |>1.5 and an AUC of 0.7414. In addition, exosome subpopulation analyses showed that cluster 11 accounted for the largest proportion of the total 16 subpopulations, and FN1 was the marker with the highest concentration of cluster 11.<br><br>CONCLUSION: Single-exosome profiling and exosome subpopulations of RA by PBA yielded significant differential gene FN1, which provides new possibilities for diagnostic screening of RA.},
}
@article {pmid39963510,
year = {2025},
author = {Corvalán, LCJ and de Melo-Ximenes, AA and Carvalho, LR and E Silva-Neto, CM and Diniz-Filho, JAF and Telles, MPC and Nunes, R},
title = {Is There a Key Primer for Amplification of Core Land Plant DNA Barcode Regions (rbcL and matK)?.},
journal = {Ecology and evolution},
volume = {15},
number = {2},
pages = {e70961},
pmid = {39963510},
issn = {2045-7758},
abstract = {The DNA barcode is a technique for molecular identification of species. Two core genes, matK and rbcL, are widely used for land plants. In this technique, the selection of primers is a fundamental step for the success of amplification. Then, we aim to evaluate the primer amplification capability for the DNA barcode regions rbcL and matK. We extracted primer sequences from DNA barcode studies in the Web of Science and used chloroplast genome sequences from NCBI for in silico PCR tests using OpenprimeR. Physicochemical properties of in silico PCR were evaluated using OpenprimeR. Our literature review resulted in 366 and 489 different rbcL and matK primers. These were tested in 8665 sequences, 8463 species from 98 orders. Evaluating only the primer and sequence match, the primers with the highest number of sequences covered were 96.39% and 93.81% forward and reverse for rbcL, and 91.56% and 61.62% forward and reverse for matK. No universal primer for all land plants was found, but two rbcL primer pairs could amplify > 99% of the sequences. In contrast to the results obtained for the matK region, the 10 pairs optimized for the greatest coverage of sequences were not covered by > 85% of the sequences. Therefore, it is advisable to pay attention when selecting primers for the matK region and the need to develop new primers. Here, we recommend a set of primers to cover the largest number of sequences and orders.},
}
@article {pmid39963041,
year = {2025},
author = {Lima-Cordón, R and Mohabir, JT and Sooklall, M and Zurita, AM and Shieh, M and Knox, C and Gobran, S and Johnson, Z and Laws, M and Panchal, R and Niles-Robin, R and Cox, H and Grillet, ME and Moreno, JE and Herrera, S and Quinones, M and Early, AM and Tennessen, JA and Neafsey, DE},
title = {A Short-Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14088},
doi = {10.1111/1755-0998.14088},
pmid = {39963041},
issn = {1755-0998},
support = {U19 AI110818/AI/NIAID NIH HHS/United States ; U19AI110818//National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services/ ; INV-009416/GATES/Bill &amp; Melinda Gates Foundation/United States ; },
abstract = {Vector control remains an important strategy worldwide to prevent human infection with pathogens transmitted by arthropods. Vector control strategies rely on accurate identification of vector taxa along with vector-specific biological indicators such as feeding ecology, infection prevalence and insecticide resistance. Multiple 'DNA barcoding' protocols have been published over the past several decades to support these applications, generally relying on informal manual approaches such as BLAST to assign taxonomic identity to the resulting sequences. We present a standardised informatic pipeline for analysis of DNA barcoding data from dipteran vectors, VecTreeID, that uses short-read amplicon sequencing (AmpSeq) coupled with sequence similarity assessment (BLAST) and an evolutionary placement algorithm (EPA-ng) to achieve vector taxonomic identification, capture bionomic features (blood and plant meal sources), determine Plasmodium infection status (for anopheline mosquitoes) and detect target-site insecticide resistance mutations. The VecTreeID pipeline provides uncertainty in assignment through identifications at varying levels of taxonomic rank, a feature missing from many approaches to DNA barcoding, but important given gaps and labelling problems in public sequence databases. We validated an Illumina-based implementation of VecTreeID on laboratory and field samples, and find that the blood meal amplicons can detect vertebrate DNA sequences up to 36 h post-feeding, and that short-read sequencing data are capable of sensitively detecting minor sequences in DNA mixtures representing multi-species blood or nectar meals. This high-throughput VecTreeID approach empowers researchers and public health professionals to survey and control arthropod disease vectors consistently and effectively.},
}
@article {pmid39961041,
year = {2025},
author = {Kim, IK and Kim, CJ and Choi, JH and Kang, HJ and Choi, MB},
title = {Stylopization by Xenos spp. (Xenidae, Strepsiptera) in invasive alien hornet, Vespa velutina, in South Korea.},
journal = {Parasite (Paris, France)},
volume = {32},
number = {},
pages = {10},
pmid = {39961041},
issn = {1776-1042},
support = {KNA1-2-44-23-2//Korea National Arboretum/ ; },
mesh = {Animals ; Republic of Korea ; *Wasps/classification/anatomy &amp; histology/physiology ; Male ; *Introduced Species ; *Pupa/parasitology/anatomy &amp; histology ; *Larva/anatomy &amp; histology/classification/growth &amp; development ; Female ; Host-Parasite Interactions ; },
abstract = {The invasive hornet Vespa velutina Lepeletier, which first invaded South Korea in 2003, has spread throughout the country, significantly affecting apiaries, ecosystems, and human health. Xenos spp. (Xenidae, Strepsiptera) are primarily parasitic to social wasps, with V. analis being the only known host in Korea. Until recently, no parasites or parasitoids on V. velutina had been discovered. In 2020, strepsipteran parasites were discovered on 11 hornet workers in Andong City, South Korea. These parasites, comprising four larvae and seven pupae, were all male, except for one individual of an undetermined sex. Molecular analysis and morphological examination identified the parasites as Xenos moutoni (du Buysson, 1903) and X. oxyodontes Nakase &amp; Kato, 2013. This marks the first recorded instance of strepsipteran parasites on V. velutina in regions invaded by this hornet. Although the exact infection rate of these parasites could not be determined, it appears that native strepsipteran parasites have adapted to a non-native Vespa species. Stylopization, the condition caused by these parasites, is known to negatively affect hornet colonies: infected workers do not contribute to nest activities, hindering nest development, and infected reproductive individuals (males and new queens) do not mate, which impedes the establishment of new colonies. However, due to the hornet's high reproductive rate and compensatory mechanisms, the overall control effect of the parasites is likely to be minor.},
}
@article {pmid39959867,
year = {2025},
author = {Hernández, M and Michel, M and García, J and Dueñas, G and Moncada, M and Amaya, K and Yánez, Y and Pinto, A and Matamoros, G and Zamora, A and Fontecha, G},
title = {Diversity of beetles (Arthropoda, Insecta, Coleoptera) associated with coniferous forests in Honduras.},
journal = {ZooKeys},
volume = {1226},
number = {},
pages = {101-119},
pmid = {39959867},
issn = {1313-2989},
abstract = {Bark beetles are among the primary drivers of tree mortality in coniferous forests worldwide. Individuals belonging to the order Coleoptera were identified across different forest areas in Honduras. Descriptive statistics were used to calculate the number of families, subfamilies, genera, and species collected per department. Moreover, the barcoding approach was used by amplifying and sequencing the mitochondrial COI gene. The intraspecific genetic diversity of Ipsapache was also analyzed. 1,131 individuals were examined and 27 genera were identified. Most of the specimens were identified as belonging to the genus Ips, accounting for 53.2% of the total. Xyleborus accounted for 16.5% and Temnoscheila accounted for 10%. Fewer than four individuals were found for fifteen genera. 68% of the specimens were identified to the species level, and all the specimens were identified to the genus level. Ips, Temnoscheila, Xyleborus, Hypothenemus, and Pityophthorus exhibited the most extensive geographic distribution among the sampled sites. At the genus level, Olancho, El Paraíso, and Copán displayed the highest diversity. This study also marks the first report of the genera Xylomeira and Stephanopachys in Honduran pine forests. Within I.apache, evidence of intraspecific genetic diversity was observed, although no population structure was detected. While this research provides an updated inventory of beetle species associated with Honduran coniferous forests, further taxonomic surveys and ecological studies are essential to better understand the spread and impact of bark beetles in pine ecosystems.},
}
@article {pmid39959861,
year = {2025},
author = {Betancourth-Cundar, M and Ríos-Orjuela, JC and Crawford, AJ and Cannatella, DC and Tarvin, RD},
title = {Honoring the Afro-Colombian musical culture with the naming of Epipedobatescurrulao sp. nov. (Anura, Dendrobatidae), a frog from the Pacific rainforests.},
journal = {ZooKeys},
volume = {1226},
number = {},
pages = {139-170},
pmid = {39959861},
issn = {1313-2989},
abstract = {The number of amphibian species described yearly shows no signs of slowing down, especially in tropical regions, implying that the biodiversity of amphibians remains woefully underestimated. A new species of poison frog is described from the Pacific lowlands of southwestern Colombia: Epipedobatescurrulao sp. nov., named for the Pacific music and dance genre known as "currulao" or "bambuco viejo". This species inhabits lowland forests from 0-260 m a.s.l. This taxon differs from congeners by having a combination of bright yellow blotches in the dorsal anterior region of the thigh and upper arm, homogenous dark-brown dorsal coloration, and advertisement calls of long duration and many pulses. We also describe the courtship call of E.currulao sp. nov., which is lower in frequency and shorter in duration than its advertisement call. Molecular phylogenetic analyses confirm the monophyly of the populations sampled and its position as the sister species of Epipedobatesnarinensis, which occurs in southwestern Colombia. Among species of Epipedobates, the new species has been previously confused with E.boulengeri, but the two species are allopatric and represent two divergent clades (1.77% divergent for 12S-16S and 5.39% for CYTB). These species can be distinguished by the presence of a bright yellow blotch on the dorsal anterior region of the thigh and on the upper arm of E.currulao sp. nov., blotches that are either more white than yellow or absent in E.boulengeri. In addition, the advertisement calls are distinct, with E.currulao sp. nov. having a single but long call in each call series while E.boulengeri has 2-6 calls in a series with each call being much shorter in length. Epipedobatescurrulao sp. nov. is the most northern species of Epipedobates, which extends southwards along the western edge of the Andes. Known as the Chocó, this biogeographic region has been largely converted to agriculture in Ecuador and is experiencing widespread transformation in Colombia, which may endanger E.currulao sp. nov. and biodiversity in the region. A Spanish translation of the main text is available in Suppl. material 8.},
}
@article {pmid39958907,
year = {2025},
author = {Liang, Y and Liu, J and Yin, H and Xu, X},
title = {On new spider species of the genus Episinus (Araneae, Theridiidae) from China and proposal of five species groups.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e144222},
pmid = {39958907},
issn = {1314-2828},
abstract = {BACKGROUND: Currently, the genus Episinus Walckenaer, 1809 includes 64 described species mainly being distributed in Asia, Africa and the Americas, with 16 described species in China. During the recent surveys across various regions of China, we found three previously undescribed species which have been identified as belonging to Episinus.<br><br>NEW INFORMATION: Three new species of Episinus Walckenaer, 1809 are described: Episinusanfu sp. nov. (&#x2640;) from Jiangxi Province, E.implicatus sp. nov. (&#x2640;) from Yunnan Province and E.pseudonubilus sp. nov. (&#x2642;&#x2640;) from Shaanxi Province. Based on morphological characteristics and previous studies, we further propose five species groups to accommodate the Chinese Episinus, including two species groups proposed by Liu et al. (2022). Detailed descriptions, photographs, hand drawings, DNA barcodes and a distribution map of the three new species are provided.},
}
@article {pmid39956942,
year = {2025},
author = {Meier, R and Srivathsan, A and Oliveira, SS and Balbi, MIPA and Ang, Y and Yeo, D and Kjærandsen, J and Amorim, DS},
title = {"Dark taxonomy": A new protocol for overcoming the taxonomic impediments for dark taxa and broadening the taxon base for biodiversity assessment.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {41},
number = {2},
pages = {223-238},
pmid = {39956942},
issn = {1096-0031},
mesh = {*Biodiversity ; *Classification/methods ; Fungi/classification/genetics ; Singapore ; Phylogeny ; DNA Barcoding, Taxonomic ; Extinction, Biological ; },
abstract = {We are entering the sixth mass extinction with little data for "dark taxa", although they comprise most species. Much of the neglect is due to the fact that conventional taxonomic methods struggle with handling thousands of specimens belonging to hundreds of species. We thus here propose a new strategy that we call "dark taxonomy". It addresses (i) taxonomic impediments, (ii) the lack of biodiversity baselines and (iii) the low impact of revisionary research. Taxonomic impediments are reduced by carrying out revisions at small geographic scales to keep the number of specimens low. The risk of taxonomic error is reduced by delimiting species based on two types of data. We furthermore show that dark taxonomy can yield important biodiversity baseline data by using samples obtained with biomonitoring traps. Lastly, we argue that the impact of revisionary research can be improved by publishing two papers addressing different readerships. The principles of dark taxonomy are illustrated by our taxonomic treatment of Singapore's fungus gnats (Mycetophilidae) based only on Malaise trap samples. We show that a first batch of specimens (N = 1454) contains 120 species, of which 115 are new to science, thus reducing taxonomic impediments by increasing the number of described Oriental species by 25%. Species delimitation started with using DNA barcodes to estimate the number of Molecular Operational Taxonomic Units (MOTUs) before "LIT" (Large-scale Integrative Taxonomy) was used to obtain the species boundaries for the 120 species by integrating morphological and molecular data. To test the taxonomic completeness of the revision, we next analysed a second batch of 1493 specimens and found that >97% belonged to the 120 species delimited based on the first batch. Indeed, the second batch only contained 18 new and rare MOTUs, i.e. our study suggests that a single revision can simultaneously yield the names for all important species and relevant biodiversity baseline data. Overall, we believe that "dark taxonomy" can quickly ready a large unknown taxon for biomonitoring.},
}
@article {pmid39955482,
year = {2025},
author = {Wang, M and Yang, J and Hou, Z and Li, C and Niu, Z and Zhang, B and Xue, Q and Liu, W and Ding, X},
title = {The multi-chromosomal structure of mitogenomes provided new insights into the accurate authentication of medicinal Dendrobium species.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {202},
pmid = {39955482},
issn = {1471-2229},
support = {32070353//National Natural Science Foundation of China/ ; 32070353//National Natural Science Foundation of China/ ; 32070353//National Natural Science Foundation of China/ ; 32070353//National Natural Science Foundation of China/ ; 32070353//National Natural Science Foundation of China/ ; 32070353//National Natural Science Foundation of China/ ; 32070353//National Natural Science Foundation of China/ ; 32070353//National Natural Science Foundation of China/ ; 32070353//National Natural Science Foundation of China/ ; (LYKJ[2021]12//Forestry Science and Technology Innovation and Promotion Project of Jiangsu Province/ ; (LYKJ[2021]12//Forestry Science and Technology Innovation and Promotion Project of Jiangsu Province/ ; (LYKJ[2021]12//Forestry Science and Technology Innovation and Promotion Project of Jiangsu Province/ ; (LYKJ[2021]12//Forestry Science and Technology Innovation and Promotion Project of Jiangsu Province/ ; (LYKJ[2021]12//Forestry Science and Technology Innovation and Promotion Project of Jiangsu Province/ ; (LYKJ[2021]12//Forestry Science and Technology Innovation and Promotion Project of Jiangsu Province/ ; (LYKJ[2021]12//Forestry Science and Technology Innovation and Promotion Project of Jiangsu Province/ ; (LYKJ[2021]12//Forestry Science and Technology Innovation and Promotion Project of Jiangsu Province/ ; (LYKJ[2021]12//Forestry Science and Technology Innovation and Promotion Project of Jiangsu Province/ ; 2024QL061//Youth Science and Technology Innovation Leading Talent Project of Ningbo, China/ ; 2024S110//the Public Welfare Project of Ningbo, China/ ; },
mesh = {*Dendrobium/genetics/classification ; *Plants, Medicinal/genetics ; *Genome, Mitochondrial ; *Phylogeny ; DNA, Mitochondrial/genetics ; Genetic Variation ; Chromosomes, Plant/genetics ; DNA Barcoding, Taxonomic/methods ; },
abstract = {BACKGROUND: The global prevalence of herbal-based health care rapidly promoted requirements for medicinal plant resources. Accurate classification and identification are crucial to assuring the safety of these herbal sources.<br><br>RESULTS: Here, we took Dendrobium (Orchidaceae), a famous horticultural and medicinal plant taxon, as the study focus to establish an effective authentication approach for medicinal plants based on new mtDNA barcodes. We first de novo assembled three complete mitogenomes using Illumina and Nanopore data. These three mitogenomes were 635,454&#xa0;bp-831,745&#xa0;bp long with multichromosomal structures. Moreover, the three mitogenomes were compared to the other four published Dendrobium mitogenomes. The results revealed great variations of the structure and repeat contents among these mitogenomes, while gene contents and genomic sequences were relatively conserved. The analysis of mutational hotspots showed eight mitochondrial DNA regions with high sequence variability (>&#x2009;5%) at the interspecific level, which could provide abundant informatic loci for phylogeny, genetic diversity, and identification analyses. We also newly obtained mitochondrial sequences of 45 individuals from 15 Dendrobium species for authentication analysis. These 15 Dendrobium species were successfully identified by the whole mitogenome sequences and the isoform combination (Mt17&#x2009;+&#x2009;Mt19) respectively.<br><br>CONCLUSIONS: Our findings revealed that mitochondrial isoforms (chromosomes) could be used as super-barcodes for Dendrobium species authentication. The multi-chromosomal structure of mitogenomes provided new insights into the accurate authentication of medical plants.},
}
@article {pmid39955017,
year = {2025},
author = {Diekmann, I and Krücken, J and Kuzmina, TA and Bredtmann, CM and Louro, M and Kharchenko, VA and Tzelos, T and Matthews, JB and Madeira de Carvalho, LM and von Samson-Himmelstjerna, G},
title = {Comparative phylogenetic and sequence identity analysis of internal transcribed spacer 2 and cytochrome c oxidase subunit I as DNA barcode markers for the most common equine Strongylidae species.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {129},
number = {},
pages = {105729},
doi = {10.1016/j.meegid.2025.105729},
pmid = {39955017},
issn = {1567-7257},
mesh = {Animals ; *Phylogeny ; *DNA Barcoding, Taxonomic/methods ; *Electron Transport Complex IV/genetics ; Horses ; *Horse Diseases/parasitology ; DNA, Ribosomal Spacer/genetics ; Strongylida Infections/parasitology/veterinary ; Genetic Markers ; Strongyloidea/genetics/classification ; Sequence Analysis, DNA ; },
abstract = {Morphologically, 64 strongylid species have been described in equines. Co-infections are common, with up to 29 species reported in a single horse. Morphological identification of these species is time consuming and requires expert knowledge due to their similar appearance. Therefore, non-invasive identification methods are needed. DNA barcoding offers a rapid and reliable tool for species identification and the discovery of cryptic species for these most common parasitic nematodes of equines. In total, 269 cytochrome c oxidase subunit I (COI) gene and 312 internal transcribed spacer 2 (ITS-2) sequences from 27 equine Strongylidae species, including sequences from two uncharacterised species, Coronocyclus sagittatus and Triodontophorus tenuicollis, were generated and combined with COI and ITS-2 sequences data from six Cyathostominae species from previous studies. This study represents a comprehensive DNA barcoding analysis of 22 Cyathostominae and six Strongylinae species using mitochondrial COI gene and ITS-2 sequences. Maximum likelihood phylogenetic trees were constructed and the intra- and interspecific genetic distances for both markers were compared. Analysis revealed complex phylogenetic relationships. Para- and polyphyletic relationships were observed among most genera within Strongylinae and Cyathostominae. This challenges current morphological classifications. Although both markers showed overlapping pairwise identities in intra- and inter-species comparisons, COI had higher discriminatory power than ITS-2. Expanding the COI and ITS-2 reference database, including the first sequences for Coronocyclus sagittatus and Triodontophorus tenuicollis, improve a reliable species identification and advanced studies on Strongylinae and Cyathostominae diversity using barcoding and metabarcoding.},
}
@article {pmid39953951,
year = {2025},
author = {Ametrano, CG and Jensen, J and Lumbsch, HT and Grewe, F},
title = {UnFATE: A Comprehensive Probe Set and Bioinformatics Pipeline for Phylogeny Reconstruction and Multilocus Barcoding of Filamentous Ascomycetes (Ascomycota, Pezizomycotina).},
journal = {Systematic biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/sysbio/syaf011},
pmid = {39953951},
issn = {1076-836X},
abstract = {The subphylum Pezizomycotina (filamentous ascomycetes) is the largest clade within Ascomycota. Despite the importance of this group of fungi, our understanding of their evolution is still limited due to insufficient taxon sampling. Although next-generation sequencing technology allows us to obtain complete genomes for phylogenetic analyses, generating complete genomes of fungal species can be challenging, especially when fungi occur in symbiotic relationships or when the DNA of rare herbarium specimens is degraded or contaminated. Additionally, assembly, annotation, and gene extraction of whole-genome sequencing data require bioinformatics skills and computational power, resulting in a substantial data burden. To overcome these obstacles, we designed a universal target enrichment probe set to reconstruct the phylogenetic relationships of filamentous ascomycetes at different phylogenetic levels. From a pool of single-copy orthologous genes extracted from available Pezizomycotina genomes, we identified the smallest subset of genetic markers that can reliably reconstruct a robust phylogeny. We used a clustering approach to identify a sequence set that could provide an optimal trade-off between potential missing data and probe set cost. We incorporated this probe set into a user-friendly wrapper script named UnFATE (https://github.com/claudioametrano/UnFATE) that allows phylogenomic inferences without requiring expert bioinformatics knowledge. In addition to phylogenetic results, the software provides a powerful multilocus alternative to ITS-based barcoding. Phylogeny and barcoding approaches can be complemented by an integrated, pre-processed, and periodically updated database of all publicly available Pezizomycotina genomes. The UnFATE pipeline, using the 195 selected marker genes, consistently performed well across various phylogenetic depths, generating trees consistent with the reference phylogenomic inferences. The topological distance between the reference trees from literature and the best tree produced by UnFATE ranged between 0.10 and 0.14 (nRF) for phylogenies from family to subphylum level. We also tested the in vitro success of the universal baits set in a target capture approach on 25 herbarium specimens from ten representative classes in Pezizomycotina, which recovered a topology congruent with recent phylogenomic inferences for this group of fungi. The discriminating power of our gene set was also assessed by the multilocus barcoding approach, which outperformed the barcoding approach based on ITS. With these tools, we aim to provide a framework for a collaborative approach to build robust, conclusive phylogenies of this important fungal clade.},
}
@article {pmid39952916,
year = {2025},
author = {Zhang, TH and Shi, Y and Komarova, NL and Wordaz, D and Kostelny, M and Gonzales, A and Abbaali, I and Chen, H and Bresson-Tan, G and Dimapasoc, M and Harvey, W and Oh, C and Carmona, C and Seet, C and Du, Y and Sun, R and Zack, JA and Kim, JT},
title = {Barcoded HIV-1 reveals viral persistence driven by clonal proliferation and distinct epigenetic patterns.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1641},
pmid = {39952916},
issn = {2041-1723},
support = {UM1 AI164568/AI/NIAID NIH HHS/United States ; R01 AI161803/AI/NIAID NIH HHS/United States ; AI155232//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; AI164568//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; UL1TR001881//U.S. Department of Health &amp; Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)/ ; AI127410//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; UL1 TR001881/TR/NCATS NIH HHS/United States ; 2152155//National Science Foundation (NSF)/ ; P30 AI152501/AI/NIAID NIH HHS/United States ; K08 AI155232/AI/NIAID NIH HHS/United States ; },
mesh = {*HIV-1/genetics/physiology ; Animals ; *Proviruses/genetics ; *Epigenesis, Genetic ; *HIV Infections/virology/drug therapy ; Humans ; Mice ; *Cell Proliferation ; *Virus Latency/genetics ; RNA, Viral/genetics ; Viremia/virology ; DNA, Viral/genetics ; Virus Integration/genetics ; High-Throughput Nucleotide Sequencing ; Genome, Viral/genetics ; Genetic Variation ; Viral Load ; CD4-Positive T-Lymphocytes/virology ; },
abstract = {The HIV reservoir consists of infected cells in which the HIV-1 genome persists as provirus despite effective antiretroviral therapy (ART). Studies exploring HIV cure therapies often measure intact proviral DNA levels, time to rebound after ART interruption, or ex vivo stimulation assays of latently infected cells. This study utilizes barcoded HIV to analyze the reservoir in humanized mice. Using bulk PCR and deep sequencing methodologies, we retrieve 890 viral RNA barcodes and 504 proviral barcodes linked to 15,305 integration sites at the single RNA or DNA molecule in vivo. We track viral genetic diversity throughout early infection, ART, and rebound. The proviral reservoir retains genetic diversity despite cellular clonal proliferation and viral seeding by rebounding virus. Non-proliferated cell clones are likely the result of elimination of proviruses associated with transcriptional activation and viremia. Elimination of proviruses associated with viremia is less prominent among proliferated cell clones. Proliferated, but not massively expanded, cell clones contribute to proviral expansion and viremia, suggesting they fuel viral persistence. This approach enables comprehensive assessment of viral levels, lineages, integration sites, clonal proliferation and proviral epigenetic patterns in vivo. These findings highlight complex reservoir dynamics and the role of proliferated cell clones in viral persistence.},
}
@article {pmid39952465,
year = {2025},
author = {Godfrey, TE and Kintsurashvili, E and Rasic, G and Kaur, J and D'Amato, C and Meltzer, RH},
title = {Single-Tube, Switched Temperature Amplicon Barcoding for Multiplex Detection of Rare Mutations in Circulating Tumor DNA.},
journal = {The Journal of molecular diagnostics : JMD},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jmoldx.2025.01.004},
pmid = {39952465},
issn = {1943-7811},
abstract = {Detection and analysis of circulating tumor DNA (ctDNA) is a promising biomarker for cancer. Applications for ctDNA analysis include screening, diagnosis, treatment selection, treatment monitoring, minimal residual disease detection, and recurrence monitoring. Detection of ctDNA is challenging and requires highly sensitive methods. Approaches such as digital PCR are appropriate when only a small number of targets is being interrogated, whereas next-generation sequencing (NGS) is typically used when more targets are required. There are several NGS methods available, some of which are published and can be implemented in laboratories with the required expertise while other, commercial approaches are proprietary and are only available as a service. Of the published methods, most use some kind of unique molecular identifiers (or barcodes) to facilitate NGS error correction and detection of rare mutations at mutant allele frequencies of <0.1%. However, incorporation of barcodes and amplification of the resulting libraries are not trivial and typically require multiple steps and considerable hands-on time by an experienced molecular biologist. We report a novel approach for switched temperature amplicon barcoding, in which barcoding and library amplification are performed in the same tube using a two-stage PCR protocol with no additional manipulation. Total hands-on time is approximately 15 minutes for reaction setup, and the library is then cleaned and is ready for sequencing.},
}
@article {pmid39951365,
year = {2025},
author = {Fernandes, MB and Bitencourt, JA and Da Silva, AT and Vicari, MR and Azambuja, M and Affonso, PRAM},
title = {Small Fishes, Big Issues: Species Delimitation in Hemigrammus Marginatus, Gill, 1958 (Acestrorhamphidae: Pristellinae) from Brazilian Coastal Basins Based on Integrative Genetics.},
journal = {Zebrafish},
volume = {},
number = {},
pages = {},
doi = {10.1089/zeb.2024.0174},
pmid = {39951365},
issn = {1557-8542},
abstract = {The small characins represent a systematic puzzle in the Neotropical ichthyofauna as a result of independent miniaturization processes, adaptive convergence and lack of diagnostic characters for several genera. In order to diminish the taxonomic uncertainties and the evolutionary pathways in Hemigrammus, we carried out an integrative genetic analysis in the putatively widespread Hemigrammus marginatus Ellis, 1958 by combining cytogenetic and molecular data based on the mitochondrial Cytochrome C Oxidase subunit I (COI). Specimens of H. marginatus from the type locality in Itapicuru River basin and other two populations from coastal rivers in northeastern Brazil were analyzed and compared with the available data from other regions in South America. Conspicuous macro and microkaryotypic differences were detected between the samples from northeastern and southern Brazil (Upper Paraná River basin). Likewise, the DNA barcoding and species delimitation analyses recovered distinct Molecular Operational Taxonomical Units within H. marginatus. Therefore, the population from the type locality should be referred to as H. marginatus stricto sensu, representing a restricted characin taxon from coastal drainages (including the São Francisco River basin) along northeastern Brazil, while other populations of this small characin fish need to be taxonomically revised and managed as unique lineages.},
}
@article {pmid39951198,
year = {2025},
author = {Senggagau, B and Bond, MM and Saputra, S and Pantjara, B and Sholichah, L},
title = {Evaluation of antioxidant activity of brown macroalgae found in Lampung Bay, Indonesia and molecular identification using DNA barcode cox1 BLAST.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {231},
pmid = {39951198},
issn = {1573-4978},
support = {B-3840/II.7.5/FR.06.00/11/2023//RIIM-LPDP/ ; B-3840/II.7.5/FR.06.00/11/2023//RIIM-LPDP/ ; B-3840/II.7.5/FR.06.00/11/2023//RIIM-LPDP/ ; B-3840/II.7.5/FR.06.00/11/2023//RIIM-LPDP/ ; },
mesh = {Indonesia ; *Antioxidants/pharmacology/metabolism ; *Phaeophyceae/genetics/chemistry ; *Seaweed/genetics/metabolism ; *DNA Barcoding, Taxonomic/methods ; Bays ; Sargassum/chemistry ; Biphenyl Compounds ; Picrates ; },
abstract = {BACKGROUND: The study on identifying of brown macroalgae species, particularly those on the southern coast of Lampung Bay-Indonesia, at the molecular level and their antioxidant activity has never been conducted, so we examined it as our purpose study.<br><br>METHOD AND RESULTS: The research uses DPPH free radical scavenging activity and molecular identification using DNA barcode cox1 BLAST. Fifteen samples of fresh brown macroalgae with five samples, respectively, were collected from Sebalang Beach, Kalianda and Pesawaran, South Lampung. The DNA was first purified, and then the gene product was amplified using specific primers, cox1F1 primer and cox1R1 primer. The DNA sequence was checked and traced using the Basic Local Alignment Search Tool (BLAST). The three most dominant species of brown macroalgae were identified, namely Sargassum plagiophyllum, Sargassum ilicifolium and Hormophysa cuneiformis. The base length obtained ranged from 1164 to 1212&#xa0;bp, with a similarity percentage of 98.36% to 100%. The three types of brown macroalgae have the ability to scavenge DPPH free radicals. Ethanol solvent and extract fractions significantly influence the reduction of DPPH free radicals. The ethanolic extract fraction of S. ilicifolium exhibited the lowest EC50 value (64.17&#x2009;&#xb1;&#x2009;1.23&#xa0;mg L[-1]) and has the strongest antioxidant activity, followed by H. cuneiformis (75.88&#x2009;&#xb1;&#x2009;0.34&#xa0;mg L[-1]), and S. plagiophyllum (82.97&#x2009;&#xb1;&#x2009;1.30&#xa0;mg L[-1]).<br><br>CONCLUSION: The difference in species of brown macroalgae had no significant effect on the EC50 activity, and all three had robust antioxidant activity because their concentrations ranged between 50 and 100&#xa0;mg L[-1].},
}
@article {pmid39949805,
year = {2025},
author = {Xiang, R and Wan, H and Sun, W and Duan, B and Chen, W and Cao, X and Wang, S and Song, C and Chen, S and Wang, Y and Wahab, AT and Iqbal Choudhary, M and Meng, X},
title = {TPMGD: A genomic database for the traditional medicines in Pakistan.},
journal = {Chinese herbal medicines},
volume = {17},
number = {1},
pages = {87-93},
pmid = {39949805},
issn = {2589-3610},
abstract = {OBJECTIVE: In Pakistan, traditional medicines are an important component of the medical system, with numerous varieties and great demands. However, due to the scattered resources and the lack of systematic collection and collation, adulteration of traditional Pakistani medicine (TPM) is common, which severely affects the safety of their medicinal use and the import and export trades. Therefore, it is urgent to systematically organize and unify the management of TPM and establish a set of standards and operable methods for the identification of TPM.<br><br>METHODS: We collected and organized the information on 128 TPMs with regard to their medicinal parts, efficacy, usage, and genetic material, based on Pakistan Hamdard Pharmacopoeia of Eastern Medicine: Pharmaceutical Codex. The genetic information of TPM is summarized from national center for biotechnology information (NCBI) and global pharmacopoeia genome database (GPGD). Furthermore, we utilized bioinformatics technology to supplement the chloroplast genome (cp-genome) data of 12 TPMs. To build the web server, we used the Linux&#xa0;+&#xa0;Apache&#xa0;+&#xa0;MySQL&#xa0;+&#xa0;PHP (LAMP) system and constructed the webpage on a PHP: Hypertext Preprocessor (PHP) model view controller (MVC) framework.<br><br>RESULTS: We constructed a new genomic database, the traditional Pakistani medicine genomic database (TPMGD). This database comprises five entries, namely homepage, medicinal species, species identification, basic local alignment search tool (BLAST), and download. Currently, TPMGD contains basic profiles of 128 TPMs and genetic information of 102 TPMs, including 140 cytochrome c oxidase subunit I (COI) sequences and 119 mitochondrial genome sequences from Bombyx mori, 1 396 internal transcribed spacer 2 (ITS2) sequences and 1 074 intergenic region (psbA-trnH) sequences specific to 92 and 83 plant species, respectively. Additionally, TPMGD includes 199 cp-genome sequences of 82 TPMs.<br><br>CONCLUSION: TPMGD is a multifunctional database that integrates species description, functional information inquiry, genetic information storage, molecular identification of TPM, etc. The database not only provides convenience for TPM information queries but also establishes the scientific basis for the medication safety, species identification, and resource protection of TPM.},
}
@article {pmid39949130,
year = {2025},
author = {Titus, M and Varetto, I and Grosser, C and Russo, E and Davinack, A},
title = {First molecular characterization of Proctoeces maculatus (Looss, 1901) (Digenea: Fellodistomidae) infecting blue mussels (Mytilus edulis) from the northeastern USA.},
journal = {Journal of helminthology},
volume = {99},
number = {},
pages = {e25},
doi = {10.1017/S0022149X25000021},
pmid = {39949130},
issn = {1475-2697},
mesh = {Animals ; *Trematoda/genetics/classification/isolation &amp; purification ; *Mytilus edulis/parasitology ; New England ; *Phylogeny ; *Haplotypes ; *RNA, Ribosomal, 28S/genetics ; *Genetic Variation ; Trematode Infections/parasitology/veterinary ; DNA, Helminth/genetics ; Phylogeography ; },
abstract = {The digenetic trematode Proctoeces maculatus is a cosmopolitan parasite that infects various invertebrates and fish hosts, including the blue mussel, Mytilus edulis, along the northeastern U.S. coast. Despite its impact on mussel fitness and the region's aquaculture, little is known about the genetic diversity and connectivity of P. maculatus in this region. This study provides the first genetic characterization of P. maculatus populations in New England using the D1-D3 region of the 28S ribosomal RNA gene. Bayesian phylogenetic analysis and a haplotype network were used to assess genetic variation and connectivity across six localities in Maine, New York, and southern New England, and to compare these populations to global samples. Our results revealed distinct geographic structuring of P. maculatus haplotypes. The ME1 haplotype, unique to Maine, reflects either recent range expansion or isolation driven by environmental and biogeographic factors, such as Cape Cod's role as a phylogeographic barrier. The most common haplotype, US1, was shared by populations in southern New England, New York, and a single specimen from Tunisia, indicating possible historical or anthropogenic connectivity. Two divergent haplotypes from Mississippi and Chile likely represent misidentifications or cryptic species. These findings support the hypothesis that P. maculatus is likely a cryptic species complex. Molecular evidence suggests connectivity across distant regions, emphasizing the role of host movement in parasite dispersal. Continued genetic studies, particularly from under-sampled regions, are needed to unravel the diversity and biogeography of P. maculatus and its potential impact on declining mussel populations.},
}
@article {pmid39948460,
year = {2025},
author = {Keukeleire, P and Rosen, JD and Göbel-Knapp, A and Salomon, K and Schubach, M and Kircher, M},
title = {Using individual barcodes to increase quantification power of massively parallel reporter assays.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {52},
pmid = {39948460},
issn = {1471-2105},
support = {UM1 HG011966/HG/NHGRI NIH HHS/United States ; 1UM1HG011966//Impact of Genomic Variation on Function (IGVF)/ ; 1UM1HG012003//Impact of Genomic Variation on Function (IGVF)/ ; },
mesh = {*Genes, Reporter ; *High-Throughput Nucleotide Sequencing/methods ; Software ; Humans ; },
abstract = {BACKGROUND: Massively parallel reporter assays (MPRAs) are an experimental technology for measuring the activity of thousands of candidate regulatory sequences or their variants in parallel, where the activity of individual sequences is measured from pools of sequence-tagged reporter genes. Activity is derived from the ratio of transcribed RNA to input DNA counts of associated tag sequences in each reporter construct, so-called barcodes. Recently, tools specifically designed to analyze MPRA data were developed that attempt to model the count data, accounting for its inherent variation. Of these tools, MPRAnalyze and mpralm are most widely used. MPRAnalyze models barcode counts to estimate the transcription rate of each sequence. While it has increased statistical power and robustness against outliers compared to mpralm, it is slow and has a high false discovery rate. Mpralm, a tool built on the R package Limma, estimates log fold-changes between different sequences. As opposed to MPRAnalyze, it is fast and has a low false discovery rate but is susceptible to outliers and has less statistical power.<br><br>RESULTS: We propose BCalm, an MPRA analysis framework aimed at addressing the limitations of the existing tools. BCalm is an adaptation of mpralm, but models individual barcode counts instead of aggregating counts per sequence. Leaving out the aggregation step increases statistical power and improves robustness to outliers, while being fast and precise. We show the improved performance over existing methods on both simulated MPRA data and a lentiviral MPRA library of 166,508 target sequences, including 82,258 allelic variants. Further, BCalm adds functionality beyond the existing mpralm package, such as preparing count input files from MPRAsnakeflow, as well as an option to test for sequences with enhancing or repressing activity. Its built-in plotting functionalities allow for easy interpretation of the results.<br><br>CONCLUSIONS: With BCalm, we provide a new tool for analyzing MPRA data which is robust and accurate on real MPRA datasets. The package is available at https://github.com/kircherlab/BCalm .},
}
@article {pmid39946438,
year = {2025},
author = {Somma, E and Costantini, M and Pennesi, C and Ruocco, N and De Castro, O and Terlizzi, A and Zupo, V},
title = {Identification of Cocconeis neothumensis var. marina using a polyphasic approach including ultrastructure and gene annotation.},
journal = {PloS one},
volume = {20},
number = {2},
pages = {e0317360},
pmid = {39946438},
issn = {1932-6203},
mesh = {*Diatoms/genetics/ultrastructure/classification ; *DNA Barcoding, Taxonomic/methods ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; Molecular Sequence Annotation ; Alismatales/genetics ; Plant Leaves ; Ribulose-Bisphosphate Carboxylase/genetics ; Microscopy, Electron, Scanning ; },
abstract = {Several microalgae, including marine diatoms, significantly contribute to the global primary production and play a vital role in the food webs of benthic and planktonic ecosystems. Diatoms of the genus Cocconeis frequently inhabit benthic substrates, including the leaves of seagrasses. They are seasonally dominant in the leaf epiphytic layer of the Mediterranean seagrass Posidonia oceanica L. Delile, and have been proposed as model organisms for chemical ecology studies. However, the genome of Cocconeis spp. has not been sequenced. Consequently, their low-level molecular identification is currently impossible, besides a few examples. To address this gap, a polyphasic identification of C. neothumensis has been employed, combining ultra-morphological data with DNA barcoding markers. A strain of diatoms was isolated from P. oceanica leaves. It has been cultured in the laboratory and examined under Scanning Electron Microscopy (SEM). The 18S ribosomal RNA gene (18S rRNA, nrDNA) and the ribulose 1,5-biphosphate carboxylase (rbcL, cpDNA) gene were analysed for DNA barcoding characterisation. Since ultra-morphology data unambiguously identified the isolated strain as C. neothumensis Krammer, 1991, the molecular sequences herein reported will facilitate its rapid and accurate identification. In addition, our comparative analyses will facilitate the evaluation of these molecular markers for identification of closely related benthic diatoms.},
}
@article {pmid39945940,
year = {2025},
author = {Celante, GL and Domahovski, AC and Jahyny, BJB and Martins, AL},
title = {Taxonomy and Biological Aspects of Gonatopus Ljungh (Hymenoptera: Dryinidae): Description of a New Species, Sexual Association and Record of Host from Northeast Brazil.},
journal = {Neotropical entomology},
volume = {54},
number = {1},
pages = {38},
pmid = {39945940},
issn = {1678-8052},
support = {A.L.M. (process 151844/2022-4)//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; and G.L.C. (process n&#xba;130692/2023-9)//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; ACD (FAPERJ//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; proc. E-26/204.206/2021)//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; },
mesh = {Animals ; Brazil ; Female ; Male ; *Hemiptera/classification ; *Wasps/classification ; Nymph ; Larva ; Hymenoptera/classification ; Host-Parasite Interactions ; Sex Characteristics ; },
abstract = {Gonatopus Ljungh is recognized as the third most diverse genus within Dryinidae (Hymenoptera: Aculeata) and exhibits a pronounced sexual dimorphism. Due to its extensive diversity, species recognition for both sexes are challenging without the use of specimens obtained through rearing or the application of molecular techniques such as DNA barcoding. In Brazil, the knowledge of Gonatopus fauna is limited, with the Northeast region being particularly under-studied. The objective of this study was to gather comprehensive information about the biology of Gonatopus through the rearing of parasitized leafhoppers (Hemiptera: Cicadellidae). This approach allowed for the recognition and description of a new species, G. cambitos Martins &amp; Celante sp. nov. Furthermore, the study facilitated the association of sexes through the parasitism performed by females of the new species on nymphs of Frequenamia confusa (Linnavuori) (Cicadellidae, Deltocephalinae). Additionally, the research provided insights into predation and parasitism behavior, detailing the developmental stages from larva to adult and we provided a discussion about the distribution of Gonatopus in the Northeast Region of Brazil. In addition to these findings, is provided a discussion about the previous of Gonatopus in the Northeast region of Brazil, based on distribution records.},
}
@article {pmid39945845,
year = {2025},
author = {Dubey, S and Pellaud, S and Furrer, S and Dufresnes, C},
title = {Unsuspected diversity and multiple origins of the frog legs imported to Switzerland for human consumption, as determined by DNA barcoding and morphology.},
journal = {Die Naturwissenschaften},
volume = {112},
number = {2},
pages = {17},
pmid = {39945845},
issn = {1432-1904},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Anura/genetics/classification/anatomy &amp; histology ; Switzerland ; Humans ; Biodiversity ; Commerce ; },
abstract = {The frog leg industry relies on a global, largely underregulated market with potentially important ecological impact such as the uncontrolled harvest of declining wild populations and the introduction of invasive species. Here, we inferred the taxonomic nature and geographic origins of frog legs imported to Switzerland by DNA barcoding. Out of 34 samples, we retrieved eight distinct lineages attributed to five species from four genera, namely Hoplobatrachus rugulosus from Vietnam, Fejervarya cancrivora from Indonesia (invasive on several Pacific islands), two phylogeographic lineages of Limnonectes macrodon from Western and Central Java, L. kadarsani from eastern Indonesia, and three phylogeographic lineages of Pelophylax ridibundus from northern and central southern Turkey (invasive in Western Europe). Only the first two species were correctly declared, which is particularly problematic to track down harvests of the declining and geographically restricted Limnonectes taxa. In this respect, we show that the three Asian genera can be reliably distinguished by basic measurements of the frog legs, which could be used in future forensic controls. Our study calls for more stringent international regulations of the frog trade, including shipment monitoring to document the relative abundance of harvested species and ensure the sustainability of their wild populations.},
}
@article {pmid39945742,
year = {2025},
author = {Hotinger, JA and Campbell, IW and Hullahalli, K and Osaki, A and Waldor, MK},
title = {Quantification of Salmonella enterica serovar Typhimurium population dynamics in murine infection using a highly diverse barcoded library.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {39945742},
issn = {2050-084X},
support = {R01 AI042347/AI/NIAID NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; F31 AI156949/AI/NIAID NIH HHS/United States ; T32 DK007477/DK/NIDDK NIH HHS/United States ; P30 CA006516/CA/NCI NIH HHS/United States ; T32 DK007477-37/DK/NIDDK NIH HHS/United States ; },
mesh = {*Salmonella enterica/classification/drug effects/genetics/growth &amp; development ; *Serogroup ; *Salmonella Infections, Animal/microbiology ; Animals ; *DNA Barcoding, Taxonomic ; *Gene Library ; *Genetic Variation ; Streptomycin/pharmacology ; Intestines/microbiology/pathology ; Bile/microbiology ; Gallbladder/microbiology/pathology ; Male ; Female ; Mice, Inbred C57BL ; },
abstract = {Murine models are often used to study the pathogenicity and dissemination of the enteric pathogen Salmonella enterica serovar Typhimurium. Here, we quantified S. Typhimurium population dynamics in mice using the STAMPR analytic pipeline and a highly diverse S. Typhimurium barcoded library containing ~55,000 unique strains distinguishable by genomic barcodes by enumerating S. Typhimurium founding populations and deciphering routes of spread in mice. We found that a severe bottleneck allowed only one in a million cells from an oral inoculum to establish a niche in the intestine. Furthermore, we observed compartmentalization of pathogen populations throughout the intestine, with few barcodes shared between intestinal segments and feces. This severe bottleneck widened and compartmentalization was reduced after streptomycin treatment, suggesting the microbiota plays a key role in restricting the pathogen's colonization and movement within the intestine. Additionally, there was minimal sharing between the intestine and extraintestinal organ populations, indicating dissemination to extraintestinal sites occurs rapidly, before substantial pathogen expansion in the intestine. Bypassing the intestinal bottleneck by inoculating mice via intravenous or intraperitoneal injection revealed that Salmonella re-enters the intestine after establishing niches in extraintestinal sites by at least two distinct pathways. One pathway results in a diverse intestinal population. The other re-seeding pathway is through the bile, where the pathogen is often clonal, leading to clonal intestinal populations and correlates with gallbladder pathology. Together, these findings deepen our understanding of Salmonella population dynamics.},
}
@article {pmid39943127,
year = {2025},
author = {Klimov, PB and Kolesnikov, VB and Khaustov, AA and Khaustov, VA and Merckx, J and Duarte, MVA and Vangansbeke, D and Geudens, I and Pepato, A},
title = {Typification of the Economically Important Species Thyreophagus entomophagus (Acari: Astigmata: Acaridae) Used for the Industrial Production of Predatory Mites: The Designation of a Neotype with Detailed Morphological and DNA Sequence Data.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {3},
pages = {},
pmid = {39943127},
issn = {2076-2615},
support = {&#x2116; 075-15-2021-1345, unique identifier RF-193021X0012//Ministry of Science and Higher Education of the Russian Federation within the framework of the Federal Scientific and Technical Program for the Development of Genetic Technologies for 2019-2027/ ; },
abstract = {The mite Thyreophagus entomophagus is a cosmopolitan species of significant economic importance in biocontrol applications, serving as a factitious prey for the mass rearing of predatory mites. This species has been reported from a variety of habitats. However, the taxonomic reliability of its name is questionable due to inconsistencies in historical species identifications, the absence of type specimens, and misidentified GenBank sequences. Here, to address these issues and to standardize the nomenclature, we redescribe Thyreophagus entomophagus based on a commercial culture with known COX1 barcoding sequence data and designate a neotype from this culture. As part of delimiting the species boundaries of Th. entomophagus, the question of whether this species forms heteromorphic deutonymphs is particularly important. While the literature suggests that most populations lack them, at least one population in Germany has been reported to produce heteromorphic deutonymphs. However, after careful examination, we identified this population as a new species, Thyreophagus holda, indicating that previous identifications of this population as Th. entomophagus were incorrect. The absence of the heteromorphic deutonymphal stage is a beneficial trait for mass production, as it simplifies the life cycle by eliminating the energetically costly heteromorphic deutonymph. Our preliminary molecular phylogenetic analyses of Th. entomophagus and other species of Thyreophagus indicate that the loss of heteromorphic deutonymphs and the emergence of asexual reproduction (another beneficial trait for mass production) are derived traits that arose after the divergence of the most recent common ancestor of Thyreophagus. These insights enhance our understanding of the evolutionary traits that increase the effectiveness of Th. entomophagus and related species in biocontrol settings. Our study points to the need for additional bioprospecting efforts to identify new candidate species for biocontrol that possess both asexual reproduction and the absence of heteromorphic deutonymphs.},
}
@article {pmid39941137,
year = {2025},
author = {Xu, J and Zhang, H and Yang, F and Zhu, W and Li, Q and Cao, Z and Song, Y and Xin, P},
title = {Phylogeny of Camphora and Cinnamomum (Lauraceae) Based on Plastome and Nuclear Ribosomal DNA Data.},
journal = {International journal of molecular sciences},
volume = {26},
number = {3},
pages = {},
pmid = {39941137},
issn = {1422-0067},
support = {123456789//Yunnan Province landscape architecture first-class discipline construction fund/ ; No. 202302AE090018//Key Technologies Research for the Germplasm of Important Woody Flowers in Yunnan Province/ ; Nos. 32260060//National Natural Science Foundation of China/ ; Nos. 32060710//National Natural Science Foundation of China/ ; },
mesh = {*Phylogeny ; *DNA, Ribosomal/genetics ; *Cinnamomum/genetics/classification ; Plastids/genetics ; Lauraceae/genetics/classification ; DNA, Plant/genetics ; Cell Nucleus/genetics ; Base Composition ; Microsatellite Repeats/genetics ; },
abstract = {Camphora Fabr. is a genus in the family Lauraceae, comprising over 20 tropical and subtropical tree species. Since the genera Camphora and Cinnamomum Schaeff. were described, there has been a long-lasting controversy regarding the phylogenetic relationships among taxa in both genera. In particular, phylogenetic inferences derived from plastid data remain debated, with varying hypotheses proposed and occasional disputes concerning the monophyly of Camphora taxa. To further investigate the relationships, We analyzed plastomes and nuclear ribosomal cistron sequences (nrDNA) of 22 Camphora taxa, 15 Cinnamomum taxa, and 13 representative taxa of related genera. The Camphora plastomes range from 152,745 to 154,190 bp, with a GC content of 39.1% to 39.2%. A total of 128 genes were identified in the Camphora plastomes, including 84 protein-coding genes, 8 rRNA genes, and 36 tRNA genes. A total of 1130 SSR loci were detected from plastomes of Camphora, and A/T base repeats looked like the most common. Comparative analyses revealed that the plastomes of Camphora exhibit high similarity in overall structure. The loci ycf1, ycf2, trnK (UUU), psbJ-psbL, and ccsA-ndhD were identified as candidate DNA barcodes for these taxa. Plastome phylogenetic analysis revealed that Camphora is not monophyletic, whereas the nrDNA dataset supported the monophyly of Camphora. We propose that intergeneric hybridization may underlie the observed discordance between plastid and nuclear data in Camphora, and we recommend enhanced taxonomic sampling and precise species identification to improve phylogenetic resolution and accuracy.},
}
@article {pmid39939719,
year = {2025},
author = {Olsen, TR and Talla, P and Sagatelian, RK and Furnari, J and Bruce, JN and Canoll, P and Zha, S and Sims, PA},
title = {Scalable co-sequencing of RNA and DNA from individual nuclei.},
journal = {Nature methods},
volume = {22},
number = {3},
pages = {477-487},
pmid = {39939719},
issn = {1548-7105},
support = {U54CA274506//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; R01CA275184//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; R01NS103473//U.S. Department of Health &amp; Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS)/ ; },
mesh = {Humans ; *Cell Nucleus/genetics ; *DNA/genetics ; *Nucleosomes/genetics ; Single-Cell Analysis/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, RNA/methods ; Sequence Analysis, DNA/methods ; RNA/genetics ; RNA, Messenger/genetics ; Polymorphism, Single Nucleotide ; Gene Library ; },
abstract = {The ideal technology for directly investigating the relationship between genotype and phenotype would analyze both RNA and DNA genome-wide and with single-cell resolution; however, existing tools lack the throughput required for comprehensive analysis of complex tumors and tissues. We introduce a highly scalable method for jointly profiling DNA and expression following nucleosome depletion (DEFND-seq). In DEFND-seq, nuclei are nucleosome-depleted, tagmented and separated into individual droplets for messenger RNA and genomic DNA barcoding. Once nuclei have been depleted of nucleosomes, subsequent steps can be performed using the widely available 10x Genomics droplet microfluidic technology and commercial kits. We demonstrate the production of high-complexity mRNA and gDNA sequencing libraries from thousands of individual nuclei from cell lines, fresh and archived surgical specimens for associating gene expression with both copy number and single-nucleotide variants.},
}
@article {pmid39939455,
year = {2025},
author = {Suetsugu, K and Yagi, R and Okada, H and Matsubayashi, J},
title = {The tiny-leaved orchid Disperis neilgherrensis primarily obtains carbon from decaying litter via saprotrophic Ceratobasidium.},
journal = {Mycorrhiza},
volume = {35},
number = {1},
pages = {9},
pmid = {39939455},
issn = {1432-1890},
support = {JPMJPR21D6//Precursory Research for Embryonic Science and Technology/ ; 21H04784//Japan Society for the Promotion of Science/ ; },
mesh = {*Orchidaceae/microbiology ; *Carbon/metabolism ; *Mycorrhizae/physiology ; *Basidiomycota/metabolism/physiology/genetics ; Plant Leaves/microbiology ; Japan ; Carbon Isotopes/analysis/metabolism ; },
abstract = {While most green orchids establish associations with non-ectomycorrhizal rhizoctonias belonging to Ceratobasidiaceae, Tulasnellaceae, and Serendipitaceae, fully mycoheterotrophic orchids-excluding albino mutants-primarily depend on either ectomycorrhizal fungi or saprotrophic non-rhizoctonia fungi. This suggests that non-ectomycorrhizal rhizoctonias may be unable to meet the carbon demands of adult orchids that exhibit a high degree of mycoheterotrophy. To understand the physiological ecology of Disperis neilgherrensis, an orchid species with reduced leaves growing in decaying litter from non-ectomycorrhizal trees, we employed molecular and stable isotope analyses to identify its mycorrhizal partners and ultimate nutritional sources at two populations on Ishigaki Island, Japan. Molecular barcoding techniques revealed that D. neilgherrensis forms exclusive associations with non-ectomycorrhizal Ceratobasidiaceae fungi. The Disperis specimens exhibited δ[13]C and δ[15]N isotopic values similar to those found in fully mycoheterotrophic orchids that exploit litter-decaying fungi. Furthermore, the pelotons of D. neilgherrensis showed significantly elevated δ[13]C values similar to saprotrophic non-rhizoctonia fungi. Our findings indicate that D. neilgherrensis primarily obtains its carbon from decaying litter through a specialized relationship with non-ECM Ceratobasidiaceae. Given that saprotrophic Ceratobasidiaceae facilitate nearly fully mycoheterotrophic growth in D. neilgherrensis, at least under warm and humid conditions, it is plausible that other (nearly) fully mycoheterotrophic tropical orchids also meet their carbon requirements through associations with saprotrophic rhizoctonias.},
}
@article {pmid39939320,
year = {2025},
author = {Kim, W and Chon, M and Koh, Y and Choi, H and Choi, E and Park, H and Jung, Y and Ryu, T and Kwon, S and Choi, Y},
title = {Oligonucleotide subsets selection by single nucleotide resolution barcode identification.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1586},
pmid = {39939320},
issn = {2041-1723},
support = {RS-2024-00440370//National Research Foundation of Korea (NRF)/ ; NRF-2022M3C1A3081366//National Research Foundation of Korea (NRF)/ ; RS-2023-00302766//National Research Foundation of Korea (NRF)/ ; },
mesh = {*Oligonucleotides/genetics ; *Nucleotides/genetics ; *Gene Library ; DNA Barcoding, Taxonomic/methods ; Polymerase Chain Reaction/methods ; DNA Primers/genetics ; },
abstract = {Effective subset selection from complex oligonucleotide libraries is crucial for genomics, synthetic biology, and DNA data storage. The polymerase chain reaction, foundational for amplifying target subsets is limited by primer design and length for specificity, which constrains the scalability of oligo libraries and increases the synthesis burden for primers. We introduce an oligo subset selection methodology that utilizes sequence-specific cyclic nucleotide synthesis and blocking of the template oligos. This approach eliminates the need for primers for selective hybridization and enables the encoding and selection of hundreds of subsets with barcode lengths of fewer than five nucleotides. Moreover, cyclic selection enables a hierarchical data structure in the oligo library, enhancing the programmability. This advancement offers a scalable and cost-effective solution for handling complex oligo libraries.},
}
@article {pmid39937412,
year = {2025},
author = {Liu, G and Wang, X and Su, X and Ji, S and Ma, Z and Gao, Y and Song, X},
title = {The Development Potential of AuNPs-Based Lateral Flow Technology Combined with Other Advanced Technologies in POCT.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {39937412},
issn = {1559-0291},
support = {No.20240304070SF//Science and Technology Development Plan Project of Jilin Province/ ; },
abstract = {Currently, there is a demand for rapid, sensitive, low-cost, portable, and visualized testing technologies for point-of-care testing (POCT). However, most traditional testing methods face challenges such as long testing times, complicated operations, and high costs, limiting their implementation in resource-limited areas and hindering the fulfillment of POCT demands. Lateral flow assay (LFA) has emerged as an ideal detection technique for POCT, particularly when utilizing gold nanoparticles (AuNPs) as labels. This approach not only enables visualization with the naked eye but also reduces the need for expensive reading instruments. The technologies reviewed in this paper encompass integrated detection technology utilizing amplification technique and LFA, integrated detection technology utilizing clustered regularly interspaced short palindromic repeats (CRISPR) system and LFA, the utilization of surface-enhanced Raman spectroscopy (SERS) in LFA detection technique, the utilization of aptamers in LFA detection technique, and the utilization of DNA barcodes in LFA detection technique. By integrating these advanced techniques, there is significant potential to overcome the limitations of LFA, including low sensitivity, poor specificity, inability to quantify, and false positives, thereby enabling broader applications in resource-constrained settings. Additionally, this article comprehensively evaluates the strengths and weaknesses of each approach, underscoring the immense developmental potential of AuNPs-based LFA in point-of-care testing (POCT).},
}
@article {pmid39929864,
year = {2025},
author = {Khan, MA and Latif, M and Mansha, M and Hussain, T and Bin Jardan, YA and Metouekel, A and Dauelbait, M and Belkahia, H and Iqbal, F and Said, MB},
title = {Genetic characterization and phylogenetic analysis of common house crows (Corvus splendens).},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {4871},
pmid = {39929864},
issn = {2045-2322},
mesh = {Animals ; *Phylogeny ; *Crows/genetics ; Pakistan ; Electron Transport Complex IV/genetics ; Genetic Variation ; DNA Barcoding, Taxonomic/methods ; },
abstract = {The Common House Crow (Corvus splendens) exhibits remarkable ecological adaptability, enabling its rapid expansion across continents. However, despite its wide distribution, there is a need for genetic studies to clarify its evolutionary history and population structure. This research employs DNA barcoding, focusing on the mitochondrial gene cytochrome oxidase subunit I (Cox1), which is effective for species identification and phylogenetic analysis. Blood samples were collected from 70 C. splendens specimens across seven cities in Punjab, Pakistan: Lahore, Kasur, Sialkot, Narowal, Pakpattan, Gujranwala, and Bahawalpur. Genomic DNA extraction was performed, and a partial sequence of the COX1 gene was amplified using PCR techniques. Sequencing of the Cox1 marker from 10 randomly selected specimens revealed nine distinct genetic variants. Interspecific analysis positioned our C. splendens sequences alongside various Corvus species available in GenBank, while intraspecific analysis identified a total of 15 genetic variants. These variants showed nucleotide identity rates ranging from 98.7 to 99.8%, with genetic distances between 0.002 and 0.013. The analysis indicated that the C. splendens group consists of a single heterogeneous clade with variants from multiple countries, including Pakistan, Tanzania, Nepal, South Africa, Malaysia, Sri Lanka, Bangladesh, Kenya, Australia, and Singapore. This study significantly enhances our understanding of genetic diversity and evolutionary relationships within C. splendens populations, highlighting the necessity of genetic research to inform conservation strategies. Further research employing advanced molecular techniques and broader geographic sampling is essential to assess the genetic diversity and population dynamics of this adaptable species.},
}
@article {pmid39924908,
year = {2025},
author = {Gao, Y and Ang, YS and Yung, LL},
title = {CRISPR-Cas12a-Assisted DNA Circuit for Nonmicroscopic Detection of Cell Surface Receptor Clustering.},
journal = {ACS sensors},
volume = {10},
number = {2},
pages = {977-985},
doi = {10.1021/acssensors.4c02770},
pmid = {39924908},
issn = {2379-3694},
mesh = {Humans ; *CRISPR-Cas Systems ; DNA/chemistry ; Cell Line, Tumor ; Receptor, ErbB-3/metabolism ; Receptor, ErbB-2/metabolism ; CRISPR-Associated Proteins/metabolism/chemistry ; Bacterial Proteins/chemistry/metabolism/genetics ; Endodeoxyribonucleases/chemistry/metabolism ; ErbB Receptors/metabolism/genetics ; },
abstract = {Protein-protein interactions (PPIs) on the cell surface have been of great interest due to their high clinical relevance and significance; however, the methods for detecting PPIs heavily rely on microscopic instruments. In this work, we designed a Cas12a-assisted DNA circuit for detecting cell surface receptor clustering events without a dependence on microscopy. This nonmicroscopic approach is based on the proximity principle, where localized protein-protein interactions such as receptor clustering are converted into DNA barcodes. These barcodes can then be identified by Cas12a for signal generation in the bulk. The compatibility of the circuit with Cas12a was first experimentally verified. Several leak reactions were identified and minimized. Lastly, we implemented this design in human breast cancer cell line models to distinguish the different levels of human epidermal growth factor receptor 2 (HER2) homodimers and heterodimers with HER1 and HER3 semiquantitatively without the use of a microscope. Overall, our proposed Cas12a-assisted DNA circuit for detecting cell surface receptor clustering shows the potential for fast screening in diagnostic applications and drug discovery, demonstrating the promising use of enzymatic DNA circuits in biological applications.},
}
@article {pmid39922091,
year = {2025},
author = {Zhu, Q and Wang, H and Hu, Y and Wei, Y and Wang, Y and Hou, T and Shan, T and Zhang, X and Yang, C and Cai, Y and Wang, Y and Zhang, J},
title = {Investigation into the genotyping performance of a unique molecular identifier based microhaplotypes MPS panel in complex DNA mixture.},
journal = {Forensic science international. Genetics},
volume = {76},
number = {},
pages = {103236},
doi = {10.1016/j.fsigen.2025.103236},
pmid = {39922091},
issn = {1878-0326},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *DNA/genetics ; *Haplotypes ; Genotype ; DNA Fingerprinting/methods ; Sequence Analysis, DNA ; Alleles ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; },
abstract = {In forensic science, genotyping mixed DNA is a critical and complex task. Sequencing errors and allele sharing complicate the analysis, particularly in cases involving unbalanced mixtures, multiple contributors, and kinship relationships. Massively parallel sequencing (MPS) panels comprising highly polymorphic microhaplotypes (MHs) offer a promising approach for detecting unique alleles in mixtures with a mixture ratio greater than 10:1, involving more than two contributors or contributors with kinship. However, sequencing errors such as base substitution and InDels on the MPS platform remain a significant challenge in genotyping complex mixed DNA. The barcoding approach has been introduced to MPS to distinguish true alleles from sequencing errors. This method employs unique molecular identifiers (UMIs) to tag individual DNA molecules, allowing for the identification and correction of random sequencing errors. By generating consensus sequences from read replicates associated with the same UMI, this approach enhances the accuracy of allele detection. In this study, UMIs were incorporated into developing a highly polymorphic panel consisting of 105 MHs, with an average effective number of alleles (Ae) of 6.9. Various types of mixed DNA samples were prepared, including unbalanced mixtures with ratios ranging from 1:1-160:1, multi-contributor mixtures with 2-6 contributors, and kinship-involved mixtures with parent-offspring to fourth-degree relatives contributors. Unique alleles were quantified, and mixture proportions (Mx) were calculated separately using sequencing reads and the number of UMI families with more than 10 members. The results demonstrated that UMI played a critical role in identifying sequencing errors and enhancing the accuracy of allele genotyping in unbalanced mixtures. A strong correlation (R[2] = 0.96) between UMI count and DNA template amount demonstrated that DNA template amount could be inferred from UMI count. Mx values derived from the number of UMIs were consistent across loci and showed a high correlation with mixture ratios (R[2] = 0.85). Additionally, the panel efficiently detected unique alleles across all three types of complex DNA mixtures. Overall, this study underscores the importance of UMIs in mitigating PCR and sequencing biases, thereby improving the performance of the MH-MPS panel for genotyping complex DNA mixtures. UMIs represent a valuable tool for mixed DNA genotyping and hold potential for boarder applications in probabilistic genotyping.},
}
@article {pmid39921565,
year = {2025},
author = {Harris, DT and Jan, CH},
title = {CRISPuRe-seq: pooled screening of barcoded ribonucleoprotein reporters reveals regulation of RNA polymerase III transcription by the integrated stress response via mTOR.},
journal = {Nucleic acids research},
volume = {53},
number = {4},
pages = {},
pmid = {39921565},
issn = {1362-4962},
support = {//Calico Life Sciences LLC/ ; },
mesh = {*TOR Serine-Threonine Kinases/metabolism/genetics ; *RNA Polymerase III/metabolism/genetics ; Humans ; *Ribonucleoproteins/metabolism/genetics ; *Transcription, Genetic ; *Stress, Physiological/genetics ; *RNA, Transfer/metabolism/genetics ; Mechanistic Target of Rapamycin Complex 1/metabolism/genetics ; HEK293 Cells ; Genes, Reporter ; CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; },
abstract = {Genetic screens using CRISPR (Clustered Regularly Interspaced Palindromic Repeats) provide valuable information about gene function. Nearly all pooled screening technologies rely on the cell to link genotype to phenotype, making it challenging to assay mechanistically informative, biochemically defined phenotypes. Here, we present CRISPuRe-seq (CRISPR PuRification), a novel pooled screening strategy that expands the universe of accessible phenotypes through the purification of ribonucleoprotein complexes that link genotypes to expressed RNA barcodes. While screening for regulators of the integrated stress response (ISR), we serendipitously discovered that the ISR represses transfer RNA (tRNA) production under conditions of reduced protein synthesis. This regulation is mediated through inhibition of mTORC1 and corresponding activation of the RNA polymerase III inhibitor MAF1. These data demonstrate that coherent downregulation of tRNA expression and protein synthesis is achieved through cross-talk between the ISR and mTOR, two master integrators of cell state.},
}
@article {pmid39920599,
year = {2025},
author = {Kalumbilo, M and Chuba, D and Banda, A and Smid, EJ and Schoustra, SE and De Deyn, GB},
title = {Characterization and DNA barcoding of Zambian plant species used as inoculum in the traditional fermentation of Munkoyo; a cereal-based beverage.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {166},
pmid = {39920599},
issn = {1471-2229},
mesh = {Zambia ; *DNA Barcoding, Taxonomic ; Fermentation ; Beverages ; Edible Grain/genetics ; Phylogeny ; Plant Roots/genetics ; Vigna/genetics ; DNA, Plant/genetics ; Soil/chemistry ; },
abstract = {BACKGROUND: Munkoyo, a non-alcoholic fermented beverage, is traditionally prepared in Zambia and neighbouring countries using cooked grains and the uncooked roots of wild plant species, collectively called 'Munkoyo' plants. The drink, valued for its refreshing taste and nutritional contribution, is made using roots of several wild plant species resulting in variations in the taste and quality of the beverage. However, comprehensive information on the specific plant species used in different regions of Zambia, as well as their occurrence in terms of habitat and soil type, is missing. This gap limits our understanding of the factors contributing to Munkoyo's heterogeneity. The present study sought to identify the Zambian plant species used as an inoculum in Munkoyo fermentation and to characterize the soil in which they occur.<br><br>RESULTS: Plant and soil samples were collected from four districts in Zambia known for Munkoyo production. Using morphological taxonomy, three Fabaceae species were identified as commonly used Munkoyo plants: Rhynchosia insignis (O.Hoffm.) R.E.Fr., Rhynchosia heterophylla Hauman, and Eminia holubii (Hemsl.) Taub. Root colour differed among these species, with the Rhynchosia species having yellowish roots and E. holubii having whitish roots. To validate their identification, we evaluated three DNA barcoding markers (matK, rbcL, and ITS2) for species discrimination. All markers showed 100% PCR amplification and sequencing success rates, with ITS2 displaying the highest genetic variability and species-level resolution. Phylogenetic analyses further confirmed ITS2 as the most effective marker. Validation using samples from a fifth district reaffirmed ITS2's suitability for species-level discrimination. Soil analysis revealed significant associations between soil texture and plant occurrence: R. insignis and E. holubii were prevalent in sandy soils, while R. heterophylla was more prevalent in soils with lower sand content.<br><br>CONCLUSIONS: This study identified three common Munkoyo plant species and demonstrated ITS2 as a robust DNA barcode for their identification. It also established the influence of soil texture on the distribution of these plants, contributing to the understanding of Munkoyo production's biological and environmental determinants.},
}
@article {pmid39915438,
year = {2025},
author = {van der Horst, SC and Kollenstart, L and Batté, A and Keizer, S and Vreeken, K and Pandey, P and Chabes, A and van Attikum, H},
title = {Replication-IDentifier links epigenetic and metabolic pathways to the replication stress response.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1416},
pmid = {39915438},
issn = {2041-1723},
support = {Vici 182.052//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; },
mesh = {*DNA Replication ; *Saccharomyces cerevisiae/genetics/metabolism ; *Saccharomyces cerevisiae Proteins/metabolism/genetics ; *Epigenesis, Genetic ; *Hydroxyurea/pharmacology ; *DNA Polymerase II/metabolism/genetics ; Metabolic Networks and Pathways/genetics ; Gene Expression Regulation, Fungal ; DNA Damage ; Stress, Physiological/genetics ; Ubiquitination ; Histones/metabolism ; },
abstract = {Perturbation of DNA replication, for instance by hydroxyurea-dependent dNTP exhaustion, often leads to stalling or collapse of replication forks. This triggers a replication stress response that stabilizes these forks, activates cell cycle checkpoints, and induces expression of DNA damage response genes. While several factors are known to act in this response, the full repertoire of proteins involved remains largely elusive. Here, we develop Replication-IDentifier (Repli-ID), which allows for genome-wide identification of regulators of DNA replication in Saccharomyces cerevisiae. During Repli-ID, the replicative polymerase epsilon (Pol ε) is tracked at a barcoded origin of replication by chromatin immunoprecipitation (ChIP) coupled to next-generation sequencing of the barcode in thousands of hydroxyurea-treated yeast mutants. Using this approach, 423 genes that promote Pol ε binding at replication forks were uncovered, including LGE1 and ROX1. Mechanistically, we show that Lge1 affects replication initiation and/or fork stability by promoting Bre1-dependent H2B mono-ubiquitylation. Rox1 affects replication fork progression by regulating S-phase entry and checkpoint activation, hinging on cellular ceramide levels via transcriptional repression of SUR2. Thus, Repli-ID provides a unique resource for the identification and further characterization of factors and pathways involved in the cellular response to DNA replication perturbation.},
}
@article {pmid39912668,
year = {2025},
author = {Weigl, S and Dabernig-Heinz, J and Granitz, F and Lipp, M and Ostermann, L and Harmsen, D and Trinh, TT and Steinmetz, I and Wagner, GE and Lichtenegger, S},
title = {Improving Nanopore sequencing-based core genome MLST for global infection control: a strategy for GC-rich pathogens like Burkholderia pseudomallei.},
journal = {Journal of clinical microbiology},
volume = {63},
number = {3},
pages = {e0156924},
pmid = {39912668},
issn = {1098-660X},
support = {"Individual Research Grant", 2024//European Society of Clinical Microbiology and Infectious Diseases (ESCMID)/ ; },
mesh = {*Burkholderia pseudomallei/genetics/classification ; *Multilocus Sequence Typing/methods ; *Nanopore Sequencing/methods ; Humans ; *Genome, Bacterial/genetics ; *Melioidosis/microbiology/diagnosis ; },
abstract = {UNLABELLED: Genomic surveillance of pathogens is essential to trace infections and analyze resistance markers. Core genome multilocus sequence typing (cgMLST) facilitates genomic surveillance by simplified analysis and standardization. However, its application is limited by the poor cost-efficiency of short-read (SR) sequencing. Oxford Nanopore long-read sequencing (ONT-LR), which allows fast on-site analysis with comparatively low costs, could provide an alternative. Despite ONT-LR raw read accuracy improvement, evidence for methylation-based errors accumulates. PCR-based library preparation, suggested as a solution, presumably poses difficulties for GC-rich bacteria. We challenged ONT-LR-based cgMLST using the highly GC-rich pathogen Burkholderia pseudomallei to develop a clinically applicable workflow. Our B. pseudomallei cgMLST scheme was applied to ONT-LR data, and the results were validated against SR data. Native, rapid, and PCR-based library preparation was performed and combined with different basecalling models (SUP@bacterial-methylation, SUP@v4.2, SUP@v4.3, and SUP@v5.0) and polishing strategies (medaka_consensus, medaka_variant, r103_min_high_g360). To ensure reliability across genotypes, we included 14 sequence types and 27 genotypes. The recommended ONT-LR workflow at study initiation (SUP@v4.2, medaka_consensus) showed nearly 200 allele differences compared with the reference for specific strains. PCR-based library preparation resulted in missing targets and typing errors of up to 21 alleles. Native barcoding with SUP@v5.0 basecalling and r103_min_high_g360 polishing outperformed the PCR-based approach in all parameters reducing the error rate to a maximum of two allele differences. The optimized ONT-LR-based cgMLST workflow for B. pseudomallei integrates high resolution and ease of implementation with enhanced cost-efficiency for rapid diagnostics. The developed protocol might serve as a guideline for other GC-rich pathogens.<br><br>IMPORTANCE: This study highlights a significant advancement in genomic surveillance of bacterial pathogens, specifically addressing the challenges posed by the GC-rich species Burkholderia pseudomallei. Core genome multilocus sequence typing (cgMLST) is widely used for bacterial typing as it combines high resolution with simple implementation and standardization. To improve cost efficiency and thus accessibility, we changed the sequencing approach from Illumina short-read (SR) to Oxford Nanopore long-read sequencing (ONT-LR). ONT-LR-based cgMLST showed a very high error rate compared with SR-based cgMLST, most likely due to methylation-associated errors. PCR-based library preparation, which is proposed to correct these errors, did not achieve the required accuracy. In contrast, native barcoding with advanced basecalling and polishing strategies massively reduces allelic differences. This optimized ONT-LR cgMLST workflow provides a transformative solution for cost-efficient, high-resolution typing of B. pseudomallei. Furthermore, this study can serve as a guide for similarly challenging bacteria.},
}
@article {pmid39912533,
year = {2025},
author = {Emerson, BC},
title = {Delimiting Species-Prospects and Challenges for DNA Barcoding.},
journal = {Molecular ecology},
volume = {34},
number = {5},
pages = {e17677},
pmid = {39912533},
issn = {1365-294X},
support = {PID2020-116788GB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Arthropods/genetics/classification ; *Biodiversity ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Discovering, describing and cataloguing global species diversity remains a fundamental challenge both for biodiversity research and for the management and conservation of biodiversity. Among animals, the challenge is particularly acute within the arthropods, which comprise approximately 85% of all described animals, with approximately 1 million described species. The true number of arthropod species is estimated to be in excess of 10 million species. This estimate is likely to be revised upward in the light of global DNA barcode sequencing initiatives that are cataloguing unprecedented levels of cryptic or overlooked diversity. The scale of diversity that is being recovered with barcode sequencing places further strain on a taxonomic system confronted by ever-limited global taxonomic capacity to verify and describe new species. It is predicted that the number of novel operational taxonomic units delimited by barcode sequencing is likely to eclipse the number of species described by Linnean taxonomy by as early as 2029. Unless addressed, this may see an increasing proportion of arthropod species falling outside of protective legislative frameworks as a consequence of their lack of formal description. Confronted with this challenge, there is increasing, but controversial, acceptance of species delimitation and species description based on barcode sequence clustering thresholds. In response to the evolving controversy surrounding this issue, it is both timely and important to identify and clarify prospects and challenges for DNA barcoding, with a specific focus on species delimitation to address important shortfalls and impediments in biodiversity research.},
}
@article {pmid39908076,
year = {2025},
author = {Blanco Mendana, J and Donovan, M and O'Brien, LG and Auch, B and Garbe, J and Gohl, DM},
title = {Deterministic genetic barcoding for multiplexed behavioral and single-cell transcriptomic studies.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {39908076},
issn = {2050-084X},
support = {P40 OD018537/OD/NIH HHS/United States ; },
mesh = {Animals ; *Single-Cell Analysis/methods ; *DNA Barcoding, Taxonomic/methods ; *Transcriptome/genetics ; Drosophila melanogaster/genetics ; Gene Expression Profiling/methods ; Behavior, Animal ; High-Throughput Nucleotide Sequencing ; Drosophila/genetics ; },
abstract = {Advances in single-cell sequencing technologies have provided novel insights into the dynamics of gene expression and cellular heterogeneity within tissues and have enabled the construction of transcriptomic cell atlases. However, linking anatomical information to transcriptomic data and positively identifying the cell types that correspond to gene expression clusters in single-cell sequencing data sets remains a challenge. We describe a straightforward genetic barcoding approach that takes advantage of the powerful genetic tools in Drosophila to allow in vivo tagging of defined cell populations. This method, called Targeted Genetically-Encoded Multiplexing (TaG-EM), involves inserting a DNA barcode just upstream of the polyadenylation site in a Gal4-inducible UAS-GFP construct so that the barcode sequence can be read out during single-cell sequencing, labeling a cell population of interest. By creating many such independently barcoded fly strains, TaG-EM enables positive identification of cell types in cell atlas projects, identification of multiplet droplets, and barcoding of experimental timepoints, conditions, and replicates. Furthermore, we demonstrate that TaG-EM barcodes can be read out using next-generation sequencing to facilitate population-scale behavioral measurements. Thus, TaG-EM has the potential to enable large-scale behavioral screens in addition to improving the ability to multiplex and reliably annotate single-cell transcriptomic experiments.},
}
@article {pmid39908038,
year = {2025},
author = {Gevers, J and Beamish, E and Voorspoels, A and Botermans, W and Fauvart, M and Martens, K and Van Dorpe, P},
title = {Impact of Translocation Dynamics and Bandwidth on the Readout of DNA Structural Barcodes with Membrane-Based Solid-State Nanopores.},
journal = {ACS nano},
volume = {19},
number = {6},
pages = {6058-6068},
doi = {10.1021/acsnano.4c12111},
pmid = {39908038},
issn = {1936-086X},
mesh = {*Nanopores ; *DNA/chemistry ; Nucleic Acid Conformation ; Nanotechnology/methods ; },
abstract = {Recent advances in nanopore technology have promoted significant progress in single-molecule detection and analysis. In particular, membrane-based solid-state nanopores show promise as highly scalable readout platforms. This study explores the detection performance of this class of nanopores, with a focus on their application in molecular sensing schemes using DNA structural barcodes. The barcode structures, here specifically a series of dumbbell-shaped hairpins, encode information in a dumbbell-bit, which modulates the nanopore ionic current during translocation for readout. Our experiments evaluate the detection capabilities of membrane-based solid-state nanopores with a diameter of ∼15 nm. We investigate the detection success rates of individual dumbbell-bits with lengths ranging from 5 dumbbells (∼35 nm) to 29 dumbbells (∼195 nm) and with varying transmembrane potential. Longer dumbbell-bits exhibit a quasi-constant detection rate, whereas shorter bits show a significant decrease in the detection rate with increasing voltage. The observed dependencies are shown to be due to the increasing translocation velocity with voltage, in combination with the temporal resolution limit of the measurement system. Moreover, we show that a local increase of the effective charge at the dumbbell-bits leads to a proportionally increased local translocation velocity. This local velocity increase further degrades the detection success rate for dumbbell-bits. The findings in this study enhance our understanding of the fundamental limitations and capabilities of nanopore technology in high-throughput biosensing applications and have important implications for the design and optimization of future molecular assays and solid-state nanopore readout platforms.},
}
@article {pmid39905314,
year = {2025},
author = {Nguyen, PL and Jung, JK and Park, JS and Sim, SC},
title = {Low-density SNP marker sets for genetic variation analysis and variety identification in cultivated citrus.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {146},
pmid = {39905314},
issn = {1471-2229},
support = {320040052HD060//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries/ ; },
mesh = {*Polymorphism, Single Nucleotide ; *Citrus/genetics ; Genetic Variation ; Genetic Markers ; Genome, Plant ; Genotyping Techniques/methods ; Crops, Agricultural/genetics ; },
abstract = {BACKGROUND: The Citrus species are major fruit crops cultivated in the world and have complex genetic relationships due to sexual comparability between Citrus and related genera. Of these, satsuma mandarin (C. unshiu (Mak.) Marc.) and sweet orange (C. sinensis (L.) Osb.) are widely grown diploid species. In this study, genotyping by sequencing (GBS) was conducted to identify single nucleotide polymorphisms (SNPs) for investigating genetic variation in a citrus collection.<br><br>RESULTS: A total of 26,903 high-quality SNPs were detected across nine chromosomes in the 144 citrus varieties, consisting of 70 C. unshiu, 40 C. sinensis, 22 interspecific hybrids, and 12 others. Of these, a core set of 481 SNPs was filtered based on polymorphism information content and genome distribution. Both principal component analysis (PCA) and model-based clustering showed genetic differentiation between C. unshiu and C. sinensis. For interspecific hybrids, these were separated from two species in PCA, but were mixed with each species in model-based clustering. Significant genetic differentiations between three populations were also found using the pairwise Fst. In addition, interspecific hybrids showed higher level of genetic diversity relative to the C. unshiu and C. sinensis populations. With the 481 SNPs, four subsets (192, 96, 48, and 24 SNPs) were generated to evaluate their performance for variety identification. Both 192 and 96 SNP sets distinguished all 144 varieties, while the 48 and 24 SNP sets separated 134 (93.1%) and 110 (76.4%), respectively.<br><br>CONCLUSIONS: The GBS-based SNP discovery led to robust and cost-effective molecular marker sets to assess genetic variation in the cultivated citrus species with narrow genetic bases. The resulting SNP sets are a resource to enhance the phenotype-based DUS testing by developing a DNA barcode system and thus facilitate new variety breeding and protection in citrus.},
}
@article {pmid39905266,
year = {2025},
author = {Tan, JH and Fraser, AG},
title = {Quantifying metabolites using structure-switching aptamers coupled to DNA sequencing.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {39905266},
issn = {1546-1696},
support = {PJT183712//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; },
abstract = {Here we report a method, smol-seq (small-molecule sequencing), using structure-switching aptamers (SSAs) and DNA sequencing to quantify metabolites. In smol-seq, each SSA detects a single target molecule and releases a unique DNA barcode on target binding. Sequencing the released barcodes can, thus, read out metabolite levels. We show that SSAs are highly specific and can be multiplexed to detect multiple targets in parallel, bringing the power of DNA sequencing to metabolomics.},
}
@article {pmid39905157,
year = {2025},
author = {Yong, Q and Li, M and Li, Z and Luo, C and Zhang, J and Bai, X},
title = {Complete chloroplast genomes of 13 species of the Impatiens genus for genomic features and phylogenetic relationships studies.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {4258},
pmid = {39905157},
issn = {2045-2322},
support = {(2022-36)//Guizhou University Talent Introduction Research Project: Systematic Evolution and Genetic Diversity of Wild Impatiens in Guizhou/ ; [2023]25//Guizhou University Cultivation Project: Molecular Mechanism of Phylogenetic Development of Wild Impatiens in Karst Regions/ ; No.32201282//National Natural Science Foundation of China: Leaf photophobic drooping is a unique mechanism to avoid photooxidation against sunflecks in karst-dwelling Impatiens hainanensis/ ; No. 322QN249//National Natural Science Foundation of Hainan: Physiological and ecological mechanisms adapt to different water conditions in karst-dwelling of Impatiens hainanensis/ ; Qiankehe Foundation-ZK [2023] General 102//Guizhou Provincial Science and Technology Projects: Taxonomic studies of wild Impatiens L. in Guizhou Province/ ; Qiankehefuqi [2024.013]//the Special fund for innovation capacity construction of Guizhou research institution/ ; },
mesh = {*Phylogeny ; *Genome, Chloroplast/genetics ; *Impatiens/genetics/classification ; Genomics/methods ; Microsatellite Repeats/genetics ; China ; Codon Usage ; },
abstract = {Impatiens spp. are well-known ornamental and medicinal plants that are widely distributed in the highlands and mountains of southwestern China. This area is one of the hotspots for the distribution of Impatiens species, with typical karst landforms and abundant wild resources. Many of these species are endemic to a narrow distribution area, but their classification and relationships are relatively unclear because of insufficient field investigations, diverse morphological characteristics and lack of molecular information. In this study, chloroplast genome analysis of 13 species (including 2 synonyms) in karst habitats was conducted to study their characteristics and phylogenetic relationships. The results revealed that these chloroplast genomes all had double-stranded tetrad structures ranging in length from 151,284 bp to 152,421 bp, including a total of 113 genes, including 80 protein-coding genes, 29 transfer RNAs, and 4 ribosomal RNAs. SSRs mainly consist of A/T repeats and AT/AT repeats, while INEs mainly consist of positive repeats and palindromic repeats. The frequency of codon usage was essentially the same, with a total of 31 high-frequency codons detected, the vast majority ending in A/U. Five mutation hotspots were detected: rps16-trnQ-UUG, ndhF, ccsA-ndhD, ycf1, and trnN-GUU, among which ycf1 had the highest Pi value and the greatest potential as a DNA barcode marker. Our phylogenetic tree shows that all 13 species belong to Section Impatiens. And supported the classification of I. reptans and I. rhombifolia should as synonyms (BS = 100/PP = 1.00). This study comprehensively analyzed the cp genomes of different taxa, sheds light on the taxonomic intricacies of Impatiens species, provide valuable information into its phylogenetic and taxonomy.},
}
@article {pmid39903394,
year = {2025},
author = {Rodrigues, P and Teixeira, C and Guimarães, L and Ferreira, NGC},
title = {Barcoding the Caatinga biome bees: a practical review.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {196},
pmid = {39903394},
issn = {1573-4978},
mesh = {Bees/genetics/classification ; Animals ; *DNA Barcoding, Taxonomic/methods ; Brazil ; *Ecosystem ; Pollination/genetics ; Phylogeny ; Biodiversity ; },
abstract = {Bees play a critical role as pollinators in ecosystem services, contributing significantly to the sexual reproduction and diversity of plants. The Caatinga biome in Brazil, home to around 200 bee species, provides an ideal habitat for these species due to its unique climate conditions. However, this biome faces threats from anthropogenic processes, making it urgent to characterise the local bee populations efficiently. Traditional taxonomic surveys for bee identification are complex due to the lack of suitable keys and expertise required. As a result, molecular barcoding has emerged as a valuable tool, using genome regions to compare and identify bee species. However, little is known about Caatinga bees to develop these molecular tools further. This study addresses this gap, providing an updated list of 262 Caatinga bee species across 86 genera and identifying ~ 40 primer sets to aid in barcoding these species. The findings highlight the ongoing work needed to fully characterise the Caatinga biome's bee distribution and species or subspecies to support more effective monitoring and conservation efforts.},
}
@article {pmid39903046,
year = {2025},
author = {Pinder, MIM and Andersson, B and Blossom, H and Svensson, M and Rengefors, K and Töpel, M},
title = {Bamboozle: A Bioinformatic Tool for Identification and Quantification of Intraspecific Barcodes.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14067},
doi = {10.1111/1755-0998.14067},
pmid = {39903046},
issn = {1755-0998},
support = {2016-00594//Svenska Forskningsr&#xe5;det Formas/ ; 2017-00466//Svenska Forskningsr&#xe5;det Formas/ ; 2018-04555//Vetenskapsr&#xe5;det/ ; FO2018-0042//Stiftelsen Oscar och Lili Lamms Minne/ ; },
abstract = {Evolutionary changes in populations of microbes, such as microalgae, cannot be traced using conventional metabarcoding loci as they lack intraspecific resolution. Consequently, selection and competition processes among strains of the same species cannot be resolved without elaborate isolation, culturing, and genotyping efforts. Bamboozle, a new bioinformatic tool introduced here, scans the entire genome of a species and identifies allele-rich barcodes that enable direct identification of different genetic strains from a population using amplicon sequencing of a single DNA sample. We demonstrate its usefulness by identifying hypervariable barcoding loci (< 500 bp) from genomic data in two microalgal species, the diploid diatom Skeletonema marinoi and the haploid chlorophyte Chlamydomonas reinhardtii. Across the two genomes, four and twenty-two loci, respectively, were identified that could in silico resolve all analysed genotypes. All of the identified loci are within protein-coding genes with various metabolic functions. Single nucleotide polymorphisms (SNPs) provided the most reliable genetic markers, and among 54 strains of S. marinoi, three 500 bp loci contained, on average, 46 SNPs, 103 strain-specific alleles, and displayed 100% heterozygosity. This high level of heterozygosity was identified as a novel opportunity to improve strain quantification and detect false positive artefacts during denoising of amplicon sequences. Finally, we illustrate how metabarcoding of a single genetic locus can be used to track abundances of S. marinoi strains in an artificial selection experiment. As future genomic datasets become available and DNA sequencing technologies develop, Bamboozle has flexible user settings enabling optimal barcodes to be designed for other species and applications.},
}
@article {pmid39902320,
year = {2025},
author = {Maldonado-Carrizales, J and Valdez-Mondragón, A and Jiménez-Jiménez, ML and Ponce-Saavedra, J},
title = {Three new species of the spider genus Naphrys Edwards (Araneae, Salticidae) under morphology and molecular data with notes in the distribution of Naphrys acerba (Peckham &amp; Peckham) from Mexico.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18775},
pmid = {39902320},
issn = {2167-8359},
mesh = {Animals ; Mexico ; *Spiders/genetics/classification/anatomy &amp; histology ; *Phylogeny ; Female ; Male ; Bayes Theorem ; Electron Transport Complex IV/genetics ; },
abstract = {Herein, we describe three new species of the spider genus Naphrys Edwards, 2003 from Mexico: Naphrys echeri sp. nov., Naphrys tecoxquin sp. nov., and Naphrys tuuca sp. nov. An integrative taxonomic approach was applied, utilizing data from morphology, ultra-morphology, the mitochondrial gene COI, and distribution records. Four molecular methods for species delimitation were implemented under the corrected p-distance Neighbor-Joining (NJ) criteria: (1) Assemble Species by Automatic Partitioning (ASAP); (2) general mixed Yule coalescent (GMYC); (3) Bayesian Poisson tree process (bPTP); and (4) multi-rate Poisson tree process (mPTP). Both morphological and molecular data supported the delimitation and recognition of the three new species. The average interspecific genetic distance (p-distance) within the genus Naphrys is 14%, while the intraspecific genetic distances (p-distance) is <2% for most species. We demonstrate that the natural distribution of Naphrys is not restricted to the Nearctic region. Furthermore, the reported localities herein represent the first with precise locations in the country for Naphrys acerba. In addition, a taxonomic identification key is provided for the species in the genus.},
}
@article {pmid39902286,
year = {2024},
author = {Gurjão, L and Brito, L and Dias, O and Neto, J and Iñiguez, AM},
title = {Integrating paleoparasitological, paleogenetic, and archaeological data to understand the paleoecological scenario of pre-Columbian archaeological site Gruta do Gentio II, Brazil.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1505059},
pmid = {39902286},
issn = {1664-302X},
abstract = {Paleoparasitology and paleogenetics is the study parasites in ancient remains from latrines, mummified individuals, and coprolites, that is fossilized or desiccated feces. Paleoparasitological studies in Brazil began with analyses of coprolites from the Gruta do Gentio II (GGII) archaeological site, the oldest site related to the Una ceramist tradition (12,000 to 410 BP), Brazil. The GGII archaeological site contained numerous human burials, lithics, and cultural artifacts such as basketry, ceremonial ornaments, and unique pottery of the Una tradition. Coprolites of GGII were submitted to paleoparasitological, and paleogenetic analyses for parasite identification and coprolite origin. In addition, the archaeological characterization of the GGII site was integrated into paleo analyses for proposing a paleoecological scenario. Five taxa of parasites, including Ancylostomidae, Echinostoma sp., Spirometra sp., and Trichostrongylus sp., and three different morphotypes of Capillariidae were recognized in multiple coprolites that were distributed heterogeneously in several stratigraphical layers. The origin of coprolites was genetically defined as five species of mammals, humans, felines as Panthera onca and Leopardus pardalis, and marsupials as Didelphis albiventris and Philander opossum. This is the first study in Brazil that identified both, parasites and species of animals in Pleistocene/Holocene producers of coprolites with geographical and temporal information. The integration of paleoparasitology, paleogenetics, and archaeology is essential to propose paleoecological scenarios from the past of Brazil.},
}
@article {pmid39901058,
year = {2025},
author = {Richardson, M and Zhao, S and Lin, L and Sheth, RU and Qu, Y and Lee, J and Moody, T and Ricaurte, D and Huang, Y and Velez-Cortes, F and Urtecho, G and Wang, HH},
title = {SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.},
journal = {Nature microbiology},
volume = {10},
number = {2},
pages = {527-540},
pmid = {39901058},
issn = {2058-5276},
support = {MCB-2025515//National Science Foundation (NSF)/ ; DGE-1644869//National Science Foundation (NSF)/ ; DGE-1644869//National Science Foundation (NSF)/ ; DGE-1644869//National Science Foundation (NSF)/ ; 2R01AI132403, 1R01DK118044, 1R01EB031935, 1R21AI146817//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; N00014-18-1-2237//United States Department of Defense | United States Navy | ONR | Office of Naval Research Global (ONR Global)/ ; 1016691//Burroughs Wellcome Fund (BWF)/ ; HR0011-23-2-0001//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; W911NF-22-2-0210//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/methods ; Feces/microbiology ; Inulin/metabolism ; RNA, Ribosomal, 16S/genetics ; Metagenome ; },
abstract = {The local arrangement of microbes can profoundly impact community assembly, function and stability. However, our understanding of the spatial organization of the human gut microbiome at the micron scale is limited. Here we describe a high-throughput and streamlined method called Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) to capture spatial co-localization in a complex microbial consortium. The method obtains microbial composition of micron-scale subcommunities through split-and-pool barcoding. SAMPL-seq analysis of the healthy human gut microbiome identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These co-localized microbes organize into spatially distinct groups or 'spatial hubs' dominated by Bacteroidaceae, Ruminococcaceae and Lachnospiraceae families. Using inulin as a dietary perturbation, we observed reversible spatial rearrangement of the gut microbiome where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock insights into microbiomes at the micron scale.},
}
@article {pmid39896656,
year = {2025},
author = {Andrianiaina, AF and Andry, S and Kettenburg, G and Ranaivoson, HC and Lacoste, V and Dussart, P and Heraud, JM and Laverty, TM and Guth, S and Young, KI and Andrianarimisa, A and Brook, CE},
title = {Diversity and seasonality of ectoparasite burden on two species of Madagascar fruit bat, Eidolon dupreanum and Rousettus madagascariensis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39896656},
issn = {2692-8205},
support = {DP2 AI171120/AI/NIAID NIH HHS/United States ; R01 AI129822/AI/NIAID NIH HHS/United States ; },
abstract = {BACKGROUND: Bats are important reservoir hosts for a variety of microparasites, some of which are transmitted by ectoparasite vectors that include mites, fleas, lice, ticks, and bat flies (families Nycteribiidae and Streblidae). All of these ectoparasite taxa are known to parasitize two endemic fruit bats of Madagascar, Eidolon dupreanum and Rousettus madagascariensis. We aimed to describe the diversity of ectoparasite infestation for both bat species through morphological observation and DNA barcoding and elucidate ecological and climatic correlates of seasonal nycteribiid parasitism of these hosts.<br><br>METHODS: Live E. dupreanum and R. madagascariensis fruit bats were captured monthly in northern and central-eastern Madagascar from 2013-2020. Ectoparasites on all captured bats were counted and identified in the field, then collected into ethanol. Field identification of a subset of samples were confirmed via microscopy and DNA barcoding of the cytochrome C oxidase subunit 1 (COI) and 18S genes. The seasonal abundance of nycteribiid bat flies on both host bats was analyzed using generalized additive models, and the role of climate in driving this seasonality was assessed via cross-correlation analysis combined with generalized linear models. Phylogenetic trees were generated to compare COIand 18S sequences of Madagascar nycteribiid and streblid bat flies with available reference sequences from GenBank.<br><br>RESULTS: Ectoparasites corresponding to four broad taxa (mites, ticks, fleas, and bat flies) were recovered from 628 of 873 E. dupreanum and 831 of 862 R. madagascariensis. E. dupreanum were most commonly parasitized by Cyclopodia dubia nycteribiids and R. madagascariensis by Eucampsipoda madagascariensis nycteribiids or Megastrebla wenzeli streblids. We observed significant seasonality in nycteribiid abundance on both bat hosts, which varied by bat sex and was positively correlated with lagged temperature, precipitation, and humidity variables. Barcoding sequences recovered for all three bat fly species grouped with previously reported sequences, confirming morphological species identification. Our study contributes the first DNA barcodes of any kind reported for M. wenzeli and the first 18S barcodes for C. dubia.<br><br>CONCLUSION: This study explores the diversity and abundance of ectoparasite burdens in two Malagasy fruit bat species, highlighting the importance of seasonal ecology and the influence of climate variables on parasitism, which correlates with resource availability.},
}
@article {pmid39896473,
year = {2025},
author = {Gardner, AL and Zheng, L and Howland, K and Saunders, A and Ramirez, A and Parker, P and Iloegbunam, C and Morgan, D and Jost, TA and Brock, A},
title = {Mapping cell-cell fusion at single-cell resolution.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39896473},
issn = {2692-8205},
support = {F31 CA268833/CA/NCI NIH HHS/United States ; R01 CA226258/CA/NCI NIH HHS/United States ; R01 CA255536/CA/NCI NIH HHS/United States ; U01 CA253540/CA/NCI NIH HHS/United States ; },
abstract = {Cell-cell fusion is a tightly controlled process in the human body known to be involved in fertilization, placental development, muscle growth, bone remodeling, and viral response. Fusion between cancer cells results first in a whole-genome doubled state, which may be followed by the generation of aneuploidies; these genomic alterations are known drivers of tumor evolution. The role of cell-cell fusion in cancer progression and treatment response has been understudied due to limited experimental systems for tracking and analyzing individual fusion events. To meet this need, we developed a molecular toolkit to map the origins and outcomes of individual cell fusion events within a tumor cell population. This platform, ClonMapper Duo ('CMDuo'), identifies cells that have undergone cell-cell fusion through a combination of reporter expression and engineered fluorescence-associated index sequences paired to randomly generated nucleotide barcodes. scRNA-seq of the indexed barcodes enables the mapping of each set of parental cells and fusion progeny throughout the cell population. In triple-negative breast cancer cells CMDuo uncovered subclonal transcriptomic hybridization and unveiled distinct cell-states which arise in direct consequence of homotypic cell-cell fusion. CMDuo is a platform that enables mapping of cell-cell fusion events in high-throughput single cell data and enables the study of cell fusion in disease progression and therapeutic response.},
}
@article {pmid39896240,
year = {2025},
author = {Queirós, J and Silva, R and Pinho, CJ and Vale-Gonçalves, HM and Pita, R and Alves, PC and Beja, P and Paupério, J and Porto, M},
title = {The InBIO Barcoding Initiative Database: contribution to the knowledge of DNA barcodes of the vascular plants of north-eastern Portugal.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e142020},
pmid = {39896240},
issn = {1314-2828},
abstract = {BACKGROUND: Metabarcoding is invaluable for understanding trophic interactions, enabling high-resolution and rapid dietary assessments. However, it requires a robust DNA barcode reference library for accurate taxa identification. This dataset has been generated in the framework of the InBIO Barcoding Initiative (IBI) and Agrivole project. The integration of these two projects was crucial, as Agrivole aimed to investigate the trophic niche of small mammals in Trás-os-Montes Region through DNA metabarcoding, which required a reliable plant DNA barcode library for this same region. Given the large number of species not yet represented in international databases, a survey of local plants was essential to fill this gap. Thus, this study created an accurate DNA reference database for the plants of the Trás-os-Montes Region of Portugal.<br><br>NEW INFORMATION: The current DNA reference database contains 632 vascular plant samples, all morphologically identified and belonging to 435 species. This represents 14% and 38.7% of the total known plant species for Portugal and the study area, respectively.Of the 1781 barcode sequences provided in this dataset, 1099 contain new information (61.7%) at different levels: 254 (13.6%, ITS2: 41, trnL-ef: 126, trnL-gh: 87) are completely new to GenBank and/or BOLD databases at the time of publication, 438 (24.6%, ITS2: 59, trnL-ef: 173, trnL-gh: 206) are new records for a given species and 407 (22.9%, ITS2: 187, trnL-ef: 206, trnL-gh: 14) provide additional information (e.g. different bp length, intraspecific genetic variability); the remaining 682 sequences (38.3%) are equal (100% identity) to sequences already publicly available for the identified species. Overall, this dataset represents a significant contribution to the genetic knowledge of vascular plants represented in public libraries. This is one of the public releases of the IBI database, which provides genetic and distributional data for several taxa.All vouchers are deposited in the Herbarium of the Museum of Natural History and Science of the University of Porto (MHNC-UP) and their DNA barcodes are publicly available in the Barcode of Life Data System (BOLD), NCBI GenBank online databases and International Nucleotide Sequence Database Collaboration (INSDC).},
}
@article {pmid39895457,
year = {2025},
author = {Naranjo-Orrico, D and Ovaskainen, O and Furneaux, B and Purhonen, J and Arancibia, PA and Burg, S and Moser, N and Niku, J and Tikhonov, G and Zakharov, E and Monkhouse, N and Abrego, N},
title = {Wind Is a Primary Driver of Fungal Dispersal Across a Mainland-Island System.},
journal = {Molecular ecology},
volume = {34},
number = {5},
pages = {e17675},
doi = {10.1111/mec.17675},
pmid = {39895457},
issn = {1365-294X},
support = {856506//H2020 European Research Council/ ; 336212//Research Council of Finland/ ; 342374//Research Council of Finland/ ; 345110//Research Council of Finland/ ; 346492//Research Council of Finland/ ; //Department of Biological and Environmental Sciences, University of Jyv&#xe4;skyl&#xe4;/ ; },
mesh = {*Wind ; Finland ; *Fungi/genetics/classification ; Phylogeny ; Islands ; Lakes/microbiology ; DNA Barcoding, Taxonomic ; Spores, Fungal/genetics ; Mycobiome/genetics ; },
abstract = {Dispersal is one of the main processes shaping ecological communities. Yet, for species-rich communities in natural systems, the role of dispersal in community assembly remains relatively less studied compared to other processes. This is the case for fungal communities, for which predictable knowledge about where and how the dispersal propagules move across space is largely lacking. We sampled fungal communities at their dispersal stage in a lake mainland-island system in Finland, using a regular grid of 18 × 18 km, including sites on the mainland, islands and over the water. Fungal communities were screened by applying DNA barcoding to air samples. To assess the factors determining fungal dispersal, we modelled aerial fungal communities with a joint species distribution model, including spore traits, weather-related predictors, and spatial predictors. We found that the probability of occurrence of most species (and consequently species richness measured as the number of OTUs per sample) was lower in low-connectivity sites (water and isolated islands) compared to high-connectivity sites (mainland). There was a strong phylogenetic signal in how the fungal species responded to connectivity, indicating that some taxonomic groups are more dispersal limited than others, although such responses were not structured by their trophic guilds. Furthermore, wind speed influenced how species with different spore sizes responded to connectivity: in low-connectivity sites, species with large sexual spores were detected especially when wind was high, whereas, in high-connectivity sites, they were detected especially when wind was low. This study demonstrates that air fungal dispersal might be more predictable than previously considered and contributes to the mechanistic understanding of fungal air dispersal.},
}
@article {pmid39893778,
year = {2025},
author = {Shang, Y and Liu, S and Liang, C and Tuliebieke, T and Chen, S and Du, K and Tian, X and Li, J and He, J and Jin, H and Chang, Y},
title = {A strategy integrated DNA barcoding with metabolomics for screening distinguishable combinatorial chemical quality marker between Pheretima aspergillum and Pheretima vulgaris Chen.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {257},
number = {},
pages = {116716},
doi = {10.1016/j.jpba.2025.116716},
pmid = {39893778},
issn = {1873-264X},
mesh = {Animals ; *Metabolomics/methods ; *DNA Barcoding, Taxonomic/methods ; *Quality Control ; Medicine, Chinese Traditional ; Oligochaeta/genetics/metabolism ; Uridine/chemistry/analysis ; Phenylalanine/analysis/metabolism ; Adenine/metabolism ; Adenosine/analysis/metabolism/analogs &amp; derivatives ; Species Specificity ; },
abstract = {Pheretima is an animal-derived traditional Chinese medicines (TCMs). The chemical quality markers of Pheretima used to distinguish different species are still ambiguous. Under this premise, a strategy integrated DNA barcoding with metabolomics is promoted for identifying Pheretima and screening distinguishable combinatorial chemical quality marker (DCQ-marker) between Pheretima aspergillum (P. aspergillum) and Pheretima vulgaris Chen (P. vulgaris). As a result, adenosine, adenine, L-phenylalanine and uridine are successfully selected as DCQ-markers between P. aspergillum and P. vulgaris. This study provides convenient strategy for quickly screening DCQ-marker between P. aspergillum and P. vulgaris. It will be meaningful for further promoting quality control on Pheretima and providing a reference for the quality evaluation of other animal-derived TCMs.},
}
@article {pmid39890856,
year = {2025},
author = {Parihar, TJ and Naik, M and Mehraj, S and Inam Ul Haq, S and Perveen, M and Malla, IA and Abid, T and Gul, N and Masoodi, KZ},
title = {Emergence of Fusarium incarnatum and Fusarium avenaceum in wilt affected solanaceous crops of the Northern Himalayas.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {3855},
pmid = {39890856},
issn = {2045-2322},
support = {PURSE Grant- SR/PURSE/2022/124//Department of Science and Technology, Ministry of Science and Technology, India/ ; CRG/2022/000207//Anusandhan national research foundation/ ; },
mesh = {*Fusarium/genetics/pathogenicity/isolation &amp; purification ; *Plant Diseases/microbiology ; *Phylogeny ; *Crops, Agricultural/microbiology ; India ; Solanum lycopersicum/microbiology ; Himalayas ; },
abstract = {The objective of this study was to identify and characterize the fungal pathogens responsible for wilt diseases in solanaceous crops, specifically tomato, brinjal, and chili, in the Kashmir valley. Through both morphological and molecular analyses, including DNA barcoding of the ITS, TEF, RPB1, and RPB2 genomic regions, Fusarium incarnatum and Fusarium avenaceum were identified as the primary causal agents of wilt in tomato and brinjal, and chili, respectively. Pathogenicity tests confirmed the virulence of these pathogens, with typical wilt symptoms observed upon inoculation. This represents the first report of F. incarnatum and F. avenaceum as wilt pathogens in solanaceous crops in India. Phylogenetic analysis further confirmed the genetic variability of these pathogens, revealing their expanding host range. The findings underscore the growing adaptability of these Fusarium species to diverse agricultural systems and highlight the urgent need for targeted disease management strategies to mitigate the significant yield losses caused by Fusarium wilt in solanaceous vegetable production.},
}
@article {pmid39887239,
year = {2025},
author = {Chen, P-R and Wei, Y and Li, X and Yu, H-Y and Wang, S-G and Yuan, X-Z and Xia, P-F},
title = {Precision engineering of the probiotic Escherichia coli Nissle 1917 with prime editing.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {2},
pages = {e0003125},
pmid = {39887239},
issn = {1098-5336},
support = {22278246//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022HWYQ-017//Department of Science and Technology of Shandong Province/ ; ZR2021ME066//Natural Science Foundation of Shandong Province/ ; Qilu Young Scholar Program//Shandong University (SDU)/ ; NO. tstp20230604//Taishan Scholar Project of Shandong Province/ ; U20A20146, 22378233//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Escherichia coli/genetics ; *Probiotics ; *Gene Editing/methods ; *CRISPR-Cas Systems ; CRISPR-Associated Protein 9/genetics ; },
abstract = {CRISPR-Cas systems are transforming precision medicine with engineered probiotics as next-generation diagnostics and therapeutics. To promote human health and treat disease, engineering probiotic bacteria demands maximal versatility to enable non-natural functionalities while minimizing undesired genomic interferences. Here, we present a streamlined prime editing approach tailored for probiotic Escherichia coli Nissle 1917 utilizing only essential genetic modules, including Cas9 nickase from Streptococcus pyogenes, a codon-optimized reverse transcriptase, and a prime editing guide RNA, and an optimized workflow with longer induction. As a result, we achieved all types of prime editing in every individual round of experiments with efficiencies of 25.0%, 52.0%, and 66.7% for DNA deletion, insertion, and substitution, respectively. A comprehensive evaluation of off-target effects revealed a significant reduction in unintended mutations, particularly in comparison to two different base editing methods. Leveraging the prime editing system, we inserted a unique DNA sequence to barcode the edited strain and established an antibiotic-resistance-gene-free platform to enable non-natural functionalities. Our prime editing strategy presents a CRISPR-Cas system that can be readily implemented in any laboratories with the basic CRISPR setups, paving the way for future innovations in engineered probiotics.IMPORTANCEOne ultimate goal of gene editing is to introduce designed DNA variations at specific loci in living organisms with minimal unintended interferences in the genome. Achieving this goal is especially critical for creating engineered probiotics as living diagnostics and therapeutics to promote human health and treat diseases. In this endeavor, we report a customized prime editing system for precision engineering of probiotic Escherichia coli Nissle 1917. With such a system, we developed a barcoding system for tracking engineered strains, and we built an antibiotic-resistance-gene-free platform to enable non-natural functionalities. We provide not only a powerful gene editing approach for probiotic bacteria but also new insights into the advancement of innovative CRISPR-Cas systems.},
}
@article {pmid39887112,
year = {2025},
author = {Maduenyane, M and Dos Santos, QM and Avenant-Oldewage, A},
title = {Multifaceted taxonomy of two Dactylogyrus species on Enteromius paludinosus: Integrating light microscopy, scanning electron microscopy and molecular approaches.},
journal = {Parasite (Paris, France)},
volume = {32},
number = {},
pages = {5},
pmid = {39887112},
issn = {1776-1042},
support = {Doctoral grant//National Research Foundation, South Africa/ ; Post doctoral fellowship//Ernest Oppenheimer Memorial Trust/ ; SRUG22052013241//National Research Foundation, South Africa/ ; University Research Committee and Faculty Research Committee//University of Johannesburg/ ; },
mesh = {Animals ; *Microscopy, Electron, Scanning/veterinary ; *Phylogeny ; South Africa ; *Fish Diseases/parasitology ; Cyprinidae/parasitology ; Microscopy ; RNA, Ribosomal, 28S/genetics ; DNA, Mitochondrial ; Platyhelminths/classification/genetics/anatomy &amp; histology/ultrastructure ; RNA, Ribosomal, 18S/genetics ; Trematode Infections/parasitology/veterinary ; DNA, Helminth ; Electron Transport Complex IV/genetics ; },
abstract = {Dactylogyrus Diesing, 1850 is the most speciose genus of platyhelminths with more than 900 species, and over a hundred species recorded from Africa. Of the latter, six are from the straightfin barb, Enteromius paludinosus (Peters). Dactylogyrus teresae Mashego, 1983 and Dactylogyrus dominici Mashego, 1983 were collected from E. paludinosus in the Vaal River system, Gauteng, South Africa and their taxonomic data revised using standard protocols and modern approaches, alongside the type material. Whole worms were mounted on glass slides with glycerine ammonium picrate (GAP) and studied using light microscopy (LM). For scanning electron microscopy (SEM), whole worms were placed on concavity slides and the soft tissue digested to release the sclerotised copulatory organs and haptoral sclerites. A combination of these approaches (LM and SEM) was employed for the first time to study the sclerotised structures of GAP-mounted material. Soft tissues of SEM analysed specimens were genetically characterised using CO1 mtDNA, 18S-ITS1-5.8S rDNA and partial 28S rDNA fragments. Phylogenetic topologies were constructed using Bayesian inference. Results confirmed the morphologic and genetic distinctness of D. dominici and D. teresae, highlighting the importance of studying the varying orientations of specifically the vagina and transverse bar. This study presents a new locality record, the first SEM study of isolated sclerotised structures, as well as the first molecular data for the Dactylogyrus afrobarbae-like species. The multifaceted approaches applied to the same specimen in this study enabled improved resolution of individual specimens, showing promise for studies where limited specimens are available.},
}
@article {pmid39885425,
year = {2025},
author = {Yu, W and Li, XJ and Lv, Z and Yang, LE and Peng, DL},
title = {The complete chloroplast genome sequences of monotypic genus Pseudogalium, and comparative analyses with its relative genera.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {93},
pmid = {39885425},
issn = {1471-2164},
support = {GZY24006//the Project for Fundamental Research of Guangxi Institute of Botany/ ; 31900185, 32360057//National Natural Science Foundation of China/ ; 202001AU070092//Natural Science Foundation of Yunnan Province/ ; },
mesh = {*Genome, Chloroplast ; *Phylogeny ; Microsatellite Repeats ; Rosaceae/genetics/classification ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Pseudogalium is a new monotypic genus with two subspecies in China and one in Japan, which holds a distinctive phylogenetic position and ecological significance within the tribe Rubieae. Chloroplast genomes contain abundant information for resolving phylogenetic relationships. To investigate the phylogenetics of P. paradoxum and its related genera, we first sequenced, assembled, and annotated the chloroplast genome of two subspecies of P. paradoxum in China and reconstructed the phylogenetic trees. Due to the lack of samples of P. paradoxum subsp. franchetianum from Japan, this study only analyzed and discussed P. paradoxum subsp. paradoxum and P. paradoxum subsp. duthiei.<br><br>RESULTS: This study had shown that the complete chloroplast genomes of Pseudogalium ranged from 153,093&#xa0;bp to 153,333&#xa0;bp in length with 130 genes in total, all of which had typical circular structures consisting of a large single-copy region, a small single-copy region and a pair of inverted repeat regions. The comparative analysis showed that the chloroplast genome of P. paradoxum was conserved in the inverted repeat regions. Additionally, we identified 60 dispersed repeat sequences, 61-63 simple sequence repeats, and 30 codons within the 82 protein-coding genes that exhibited RSCU values greater than one. Furthermore, we detected highly divergent regions that hold potential as new DNA barcodes for species identification. Compared with Pseudogalium, the gene number, gene length, and GC content in the chloroplast genomes of Galium and Rubia exhibited differential characteristics, and the dispersed repeat sequences and SSRs in Galium and Rubia were significantly different. Phylogenetic analysis based on the whole chloroplast genomes showed that Pseudogalium can be treated as a new genus, with P. paradoxum subsp. paradoxum and P. paradoxum subsp. duthiei considered as two distinct subspecies of P. paradoxum.<br><br>CONCLUSIONS: The complete chloroplast genomes of P. paradoxum were first reported in this study, which provided a new insight into phylogeny and taxonomy of this genus. Phylogenetic analyses strongly supported the following proposals: (1) P. paradoxum can be isolated as a genus closely related to Galium; (2) P. paradoxum subsp. paradoxum and P. paradoxum subsp. duthiei form distinct clades, both of which can be considered as subspecies of P. paradoxum.},
}
@article {pmid39884748,
year = {2025},
author = {Munro, R and Payne, A and Holmes, N and Moore, C and Cahyani, I and Loose, M},
title = {Enhancing nanopore adaptive sampling for PromethION using readfish at scale.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279329.124},
pmid = {39884748},
issn = {1549-5469},
abstract = {A unique feature of Oxford Nanopore Technologies sequencers, adaptive sampling, allows precise DNA molecule selection from sequencing libraries. Here, we present enhancements to our tool, readfish, enabling all features for the industrial scale PromethION sequencer, including standard and "barcode-aware" adaptive sampling. We demonstrate effective coverage enrichment and assessment of multiple human genomes for copy number and structural variation on a single PromethION flow cell.},
}
@article {pmid39883237,
year = {2025},
author = {González, MA and Barceló, C and Rodríguez-López, A and Figuerola, J and Miranda, M&#xc1;},
title = {Human-biting behaviour of Leptoconops irritans (Diptera: Ceratopogonidae) in a touristic area of the Balearic Islands (Spain).},
journal = {Parasitology research},
volume = {124},
number = {2},
pages = {15},
pmid = {39883237},
issn = {1432-1955},
support = {HR22-00123//Fundaci&#xf3;n "La Caixa" through the project ARBOPREVENT/ ; },
mesh = {Animals ; Spain ; Humans ; *Ceratopogonidae/classification/physiology/parasitology/anatomy &amp; histology ; *Insect Bites and Stings/parasitology ; Female ; Male ; Feeding Behavior ; },
abstract = {Biting midges of genus Leptoconops Skuse 1889 are small blood-feeding insects recognized as highly irritating diurnal pests in certain regions around the globe. In Europe, their presence is poorly documented, except in France and Italy. Following reports of human discomfort in a tourist area of Menorca, Balearic Islands (Spain), a small-scale study was conducted to identify the biting species and assess their preferred biting sites using a human-landing assay along a habitat gradient in a coastal dune area. Leptoconops irritans (Noé, 1905) was identified based on morphological features and DNA barcoding. This species reached high densities (average rates of 3.3 landings/min), particularly near coastal dune vegetation. No statistically significant differences were found among the four main body sites for landings of L. irritans (F3,6.023 = 1.80, p = 0.250): head (n = 91, 53.8%), lower extremities (n = 39, 23.1%), upper extremities (n = 37, 21.9%), and other covered areas (n = 2, 1.2%). Landing preferences varied among the three volunteers, and bites progressed differently. This study represents the second documented case of Leptoconops midges causing human discomfort in Spain. We hope this research will stimulate further interest in this understudied genus, which has been largely overlooked across much of Europe.},
}
@article {pmid39881664,
year = {2025},
author = {Nečas, T and Badjedjea, G and Czurda, J and Gvoždík, V},
title = {An eastern Congolian endemic, or widespread but secretive? New data on the recently described Afrixaluslacustris (Anura, Hyperoliidae) from the Democratic Republic of the Congo.},
journal = {ZooKeys},
volume = {1224},
number = {},
pages = {55-68},
pmid = {39881664},
issn = {1313-2989},
abstract = {The Great Lakes spiny reed frog (Afrixaluslacustris) was recently described from transitional (submontane) forests at mid-elevations of the Albertine Rift mountains in the eastern Congolian region. Previously, because of its similarity, it had been understood to represent eastern populations of the unrelated A.laevis, which is known mainly from Cameroon. Based on DNA barcoding, we document the westward extension of the known range of A.lacustris within lowland rainforests in the Northeastern and Central Congolian Lowland Forests. One sample was represented by a larva found in a clutch in a folded leaf, a typical oviposition type for most Afrixalus species, contrary to oviposition on an unfolded leaf surface in the similar A.laevis and closely related A.dorsimaculatus and A.uluguruensis. Comparison of the advertisement call of A.lacustris from Salonga National Park, Democratic Republic of the Congo, indicates similarity to its sister species from montane areas of the Albertine Rift, the ghost spiny reed frog (A.phantasma). Phylogeographic analysis suggests that A.phantasma and A.lacustris speciated allopatrically during the Early Pleistocene, with the former having refugia in montane forests and the latter in transitional and also lowland forests. The lowland populations of A.lacustris represent distinct evolutionary lineages, which diversified probably in isolated forest refugia during the Middle Pleistocene.},
}
@article {pmid39881498,
year = {2025},
author = {Gião, T and Müller, MI and Yamada, F and Freitas, F and Leite, L and da Silva, RJ and de Azevedo, R and Abdallah, V},
title = {Morphological and molecular phylogeny of Clinostomum sp. (Digenea: Clinostomidae) metacercariae, using DNA barcode from a South American freshwater fish.},
journal = {Journal of helminthology},
volume = {99},
number = {},
pages = {e13},
doi = {10.1017/S0022149X24000993},
pmid = {39881498},
issn = {1475-2697},
support = {3005/2010//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 174814/2023-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Animals ; *Phylogeny ; *Trematoda/genetics/classification/anatomy &amp; histology ; *DNA Barcoding, Taxonomic ; *Metacercariae/genetics/anatomy &amp; histology/classification ; *Fish Diseases/parasitology ; *Fresh Water/parasitology ; Brazil ; *Trematode Infections/parasitology/veterinary ; *DNA, Helminth/genetics ; *Electron Transport Complex IV/genetics ; Fishes/parasitology ; },
abstract = {Here, we present a comprehensive morphological and molecular phylogenetic analysis of Clinostomum sp. (Digenea: Clinostomidae) metacercariae parasitizing two freshwater fish species from Southeast Brazil: Serrasalmus spilopleura (piranha) and Callichthys callichthys (tambuatá). The morphological examination revealed distinct characteristics of metacercariae in each host. Using the cytochrome c oxidase I (COI) gene barcode region, we obtained DNA sequences that allowed for accurate phylogenetic placement. Phylogenetic analyses revealed that Clinostomum sp. HM41 (metacercariae), isolated from S. spilopleura, exhibited 86% similarity to Ithyoclinostomum yamagutii, while Clinostomum sp. HM125 (metacercariae), from C. callichthys, showed 98.7% similarity to Clinostomum sp. Cr_Ha1. The phylogenetic trees constructed through Bayesian Inference and Maximum Likelihood methods indicated high biodiversity within the Clinostomum genus and strong support for distinct lineages. These findings enhance our understanding of the diversity and ecological distribution of Clinostomum species in South American freshwater environments.},
}
@article {pmid39880590,
year = {2025},
author = {Pryszcz, LP and Diensthuber, G and Llovera, L and Medina, R and Delgado-Tejedor, A and Cozzuto, L and Ponomarenko, J and Novoa, EM},
title = {Rapid and accurate demultiplexing of direct RNA nanopore sequencing data with SeqTagger.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279290.124},
pmid = {39880590},
issn = {1549-5469},
abstract = {Nanopore direct RNA sequencing (DRS) enables direct measurement of RNA molecules, including their native RNA modifications, without prior conversion to cDNA. However, commercial methods for molecular barcoding of multiple DRS samples are lacking, and community-driven efforts, such as DeePlexiCon, are not compatible with newer RNA chemistry flowcells and the latest-generation of graphics processing units (GPUs). To overcome these limitations, we introduce SeqTagger, a rapid and robust method that can demultiplex DRS data sets with 99% precision and 95% recall. We demonstrate the applicability of SeqTagger in both RNA002/R9.4 and RNA004/RNA chemistries and show its robust performance both for long and short RNA libraries, including custom libraries that do not contain standard poly(A) tails, such as Nano-tRNAseq libraries. Finally, we demonstrate that increasing the multiplexing up to 96 barcodes yields highly accurate demultiplexing models. SeqTagger can be executed in a standalone manner or through the MasterOfPores NextFlow workflow. The availability of an efficient and simple multiplexing strategy improves the cost-effectiveness of this technology and facilitates the analysis of low-input biological samples.},
}
@article {pmid39877676,
year = {2025},
author = {Vargas, HA},
title = {Keiferiaazapaensis sp. nov., the first representative of the New World micromoth genus Keiferia Busck (Lepidoptera, Gelechiidae) associated with a member of Asteraceae.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e141827},
pmid = {39877676},
issn = {1314-2828},
abstract = {BACKGROUND: The New World micromoth genus Keiferia Busck, 1939 (Lepidoptera, Gelechiidae, Gelechiinae, Gnorimoschemini) includes 21 described species, ten of which occur in South America. Like the tomato pinworm, K.lycopersicella (Walsingham, 1897), all the species of Keiferia, whose host plants have been documented, are associated exclusively with members of the family Solanaceae.<br><br>NEW INFORMATION: Keiferiaazapaensis sp. nov. is described and illustrated, based on adults reared from leaf miner larvae collected on the shrub Trixiscacalioides (Kunth) D. Don (Asteraceae) in the Atacama Desert, northern Chile. Despite this unusual host plant, a Maximum Likelihood analysis, based on mitochondrial DNA sequences, placed the new species within a well-supported Keiferia clade. The discovery of the trophic association between K.azapaensis sp. nov. and T.cacalioides represents the first record of a member of Asteraceae as a host plant for the micromoth genus Keiferia.},
}
@article {pmid39877055,
year = {2025},
author = {Seid, CA and Hiley, AS and McCowin, MF and Carvajal, JI and Cha, H and Ahyong, ST and Ashford, OS and Breedy, O and Eernisse, DJ and Goffredi, SK and Hendrickx, ME and Kocot, KM and Mah, CL and Miller, AK and Mongiardino Koch, N and Mooi, R and O'Hara, TD and Pleijel, F and Stiller, J and Tilic, E and Valentich-Scott, P and Warén, A and Wicksten, MK and Wilson, NG and Cordes, EE and Levin, LA and Cortés, J and Rouse, GW},
title = {A faunal inventory of methane seeps on the Pacific margin of Costa Rica.},
journal = {ZooKeys},
volume = {1222},
number = {},
pages = {1-250},
pmid = {39877055},
issn = {1313-2989},
abstract = {The methane seeps on the Pacific margin of Costa Rica support extensive animal diversity and offer insights into deep-sea biogeography. During five expeditions between 2009 and 2019, we conducted intensive faunal sampling via 63 submersible dives to 11 localities at depths of 300-3600 m. Based on these expeditions and published literature, we compiled voucher specimens, images, and 274 newly published DNA sequences to present a taxonomic inventory of macrofaunal and megafaunal diversity with a focus on invertebrates. In total 488 morphospecies were identified, representing the highest number of distinct morphospecies published from a single seep or vent region to date. Of these, 131 are described species, at least 58 are undescribed species, and the remainder include some degree of taxonomic uncertainty, likely representing additional undescribed species. Of the described species, 38 are known only from the Costa Rica seeps and their vicinity. Fifteen range extensions are also reported for species known from Mexico, the Galápagos seamounts, Chile, and the western Pacific; as well as 16 new depth records and three new seep records for species known to occur at vents or organic falls. No single evolutionary narrative explains the patterns of biodiversity at these seeps, as even morphologically indistinguishable species can show different biogeographic affinities, biogeographic ranges, or depth ranges. The value of careful molecular taxonomy and comprehensive specimen-based regional inventories is emphasized for biodiversity research and monitoring.},
}
@article {pmid39873746,
year = {2025},
author = {Nammoku, Y and Nikkeshi, A and Terai, Y and Ushimaru, A and Kinoshita, M},
title = {Morphological and DNA analysis of pollen grains on butterfly individuals reveal their flower visitation history.},
journal = {Die Naturwissenschaften},
volume = {112},
number = {1},
pages = {13},
pmid = {39873746},
issn = {1432-1904},
mesh = {Animals ; *Butterflies/physiology/genetics/anatomy &amp; histology/classification ; *Pollen ; *Pollination ; *Flowers/anatomy &amp; histology ; DNA Barcoding, Taxonomic ; },
abstract = {Many butterfly species are conspicuous flower visitors. However, understanding their flower visitation patterns in natural habitats remains challenging due to the difficulty of tracking individual butterflies. Therefore, we aimed at establishing a protocol to solve the problem using the Common five-ring butterfly, Ypthima argus (Nymphalidae: Satyrinae). Focusing on the pollen grains attached the butterfly's body surface, we examined validities of two pollen analyses based on pollen morphology and DNA markers (ITS1 and ITS2), in addition to the classical route census method. We captured thirty-nine butterflies from mid-April to early July and collected pollen grains from each individual. Morphological and DNA analyses of collected pollens identified eighteen and thirty-four taxa of insect pollinated plants respectively, including woody plants such as Castanopsis. The DNA analysis detected as many as thirteen plant taxa from a single butterfly, indicating its high sensitivity for detecting flower visitation. We detected more plant taxa in May when many individuals were flying. This is assumingly related to the post emergence days of the butterflies with more foraging experience. We also found that fluctuations of pollen grain numbers of Leucanthemum vulgare and Erigeron philadelphicus on individual butterflies depend on their flowering periods overlapping partly. Consequently, we conclude that pollen morphology and DNA barcoding analysis, and field observations are mutually complementary techniques, providing an integrated pollen analysis method to study the pollination ecology of butterflies.},
}
@article {pmid39872901,
year = {2025},
author = {Thurman, CL and McNamara, JC and Shih, HT and Capparelli, MV},
title = {Fiddler Crabs (Crustacea: Decapoda: Ocypodidae) From Coastal Ecuador and the Galápagos Islands: Species Descriptions and DNA Barcodes.},
journal = {Ecology and evolution},
volume = {15},
number = {1},
pages = {e70646},
pmid = {39872901},
issn = {2045-7758},
abstract = {Neotropical regions near the equator are recognized as speciation "hot spots" reflecting their abundant biodiversity. In western South America, the coasts of Panama, Colombia, Ecuador, the Galápagos Archipelago, and northern Peru form the Tropical Eastern Pacific biome. This area has the greatest heterogeneity of sympatric fiddler crab species of any portion of the planet. Since the coastal fauna has not been assessed for almost 50 years, we studied fiddler crab species diversity in Ecuador and on the Galápagos Archipelago. Preserved collecting records for various species were examined at the U.S. National Museum of Natural History, Washington, DC, the American Museum of Natural History, New York, and the Naturalis Biodiversity Center, Leiden, the Netherlands. During a field study, 51 locations were collected resulting in over 870 preserved specimens (120 lots) along the 2237-km (1390 mi) coast of Ecuador and on three Galápagos Islands. A neighbor-joining tree was constructed using the Kimura 2-parameter model with a partial DNA sequence of the cytochrome oxidase-subunit 1 gene (COI) for a barcoding study. Twenty-five taxa were collected during the surveys, while two more were noted from the literature and museum collections. Five published species are new to Ecuador. The species assemblage was divided among four genera: Uca, Leptuca, Minuca, and Petruca. Morphological definitions and photographic images are given for 27 species. COI sequences were obtained for 27 operational taxonomic units from Ecuador, with three morphologically indistinguishable cryptic or pseudocryptic taxa also revealed. Based on species distributions, it appears that the area between Cabo San Lorenzo and Punta Santa Elena serves as a weak barrier separating some "northern" from "southern" taxa. Since coastal Ecuador is undergoing rapid economic development, the construction of maricultural facilities and the deforestation of mangroves promote wholesale habitat destruction. As habitat diversity is reduced, it is expected that there will be, in general, a local decline in fiddler crab species diversity with some taxa becoming rare or extinct.},
}
@article {pmid39872206,
year = {2024},
author = {Dhyani, A and Kasana, S and Uniyal, PL},
title = {From barcodes to genomes: a new era of molecular exploration in bryophyte research.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1500607},
pmid = {39872206},
issn = {1664-462X},
abstract = {Bryophytes represent a diverse and species-rich group of plants, characterized by a remarkable array of morphological variations. Due to their significant ecological and economic roles worldwide, accurate identification of bryophyte taxa is crucial. However, the variability in morphological traits often complicates their proper identification and subsequent commercial utilization. DNA barcoding has emerged as a valuable tool for the precise identification of bryophyte taxa, facilitating comparisons at both interspecific and intraspecific levels. Recent research involving plastomes, mitogenomes, and transcriptomes of various bryophyte species has provided insights into molecular changes and gene expression in response to environmental stressors. Advances in molecular phylogenetics have shed light on the origin and evolutionary history of bryophytes, thereby clarifying their phylogenetic relationships. Despite these advancements, a comprehensive understanding of the systematic relationships within bryophytes is still lacking. This review synthesizes current molecular studies that have been instrumental in unraveling the complexity of bryophyte taxonomy and systematics. By highlighting key findings from recent genetic and genomic research, we underscore the importance of integrating molecular data with traditional morphological approaches. Such integration is essential for refining the classification systems of bryophytes and for understanding their adaptive strategies in various ecological niches. Future research should focus on expanding the molecular datasets across underrepresented bryophyte lineages and exploring the functional significance of genetic variations under different environmental conditions. This will not only enhance our knowledge of bryophyte evolution, but also inform conservation strategies and potential applications in biotechnology.},
}
@article {pmid39870862,
year = {2025},
author = {Ramezani, M and Weisbart, E and Bauman, J and Singh, A and Yong, J and Lozada, M and Way, GP and Kavari, SL and Diaz, C and Leardini, E and Jetley, G and Pagnotta, J and Haghighi, M and Batista, TM and Pérez-Schindler, J and Claussnitzer, M and Singh, S and Cimini, BA and Blainey, PC and Carpenter, AE and Jan, CH and Neal, JT},
title = {A genome-wide atlas of human cell morphology.},
journal = {Nature methods},
volume = {22},
number = {3},
pages = {621-633},
pmid = {39870862},
issn = {1548-7105},
support = {DP2 GM146252/GM/NIGMS NIH HHS/United States ; NNF21SA0072102//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 1DP2GM146252//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {Humans ; *Genome, Human ; CRISPR-Cas Systems ; Phenotype ; Genome-Wide Association Study/methods ; Genomics/methods ; Protein Interaction Maps ; Membrane Proteins/genetics/metabolism ; },
abstract = {A key challenge of the modern genomics era is developing empirical data-driven representations of gene function. Here we present the first unbiased morphology-based genome-wide perturbation atlas in human cells, containing three genome-wide genotype-phenotype maps comprising CRISPR-Cas9-based knockouts of >20,000 genes in >30 million cells. Our optical pooled cell profiling platform (PERISCOPE) combines a destainable high-dimensional phenotyping panel (based on Cell Painting) with optical sequencing of molecular barcodes and a scalable open-source analysis pipeline to facilitate massively parallel screening of pooled perturbation libraries. This perturbation atlas comprises high-dimensional phenotypic profiles of individual cells with sufficient resolution to cluster thousands of human genes, reconstruct known pathways and protein-protein interaction networks, interrogate subcellular processes and identify culture media-specific responses. Using this atlas, we identify the poorly characterized disease-associated TMEM251/LYSET as a Golgi-resident transmembrane protein essential for mannose-6-phosphate-dependent trafficking of lysosomal enzymes. In sum, this perturbation atlas and screening platform represents a rich and accessible resource for connecting genes to cellular functions at scale.},
}
@article {pmid39870610,
year = {2025},
author = {Schlüter, HM and Uhler, C},
title = {Integrating representation learning, permutation, and optimization to detect lineage-related gene expression patterns.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1062},
pmid = {39870610},
issn = {2041-1723},
support = {DP2 AT012345/AT/NCCIH NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; N00014-22-1-2116//United States Department of Defense | United States Navy | Office of Naval Research (ONR)/ ; 1DP2AT012345//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; },
mesh = {Animals ; *Caenorhabditis elegans/genetics ; Mice ; *Cell Lineage/genetics ; *Single-Cell Analysis/methods ; *Lung Neoplasms/genetics/pathology ; Embryonic Development/genetics ; Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; RNA-Seq/methods ; Gene Expression Regulation, Neoplastic ; },
abstract = {Recent barcoding technologies allow reconstructing lineage trees while capturing paired single-cell RNA-sequencing (scRNA-seq) data. Such datasets provide opportunities to compare gene expression memory maintenance through lineage branching and pinpoint critical genes in these processes. Here we develop Permutation, Optimization, and Representation learning based single Cell gene Expression and Lineage ANalysis (PORCELAN) to identify lineage-informative genes or subtrees where lineage and expression are tightly coupled. We validate our method using synthetic data and apply it to recent paired lineage and scRNA-seq data of lung cancer in a mouse model and embryogenesis of mouse and C. elegans. Our method pinpoints subtrees giving rise to metastases or new cell states, and genes identified as most informative about lineage overlap with known pathways involved in lung cancer progression. Furthermore, our method highlights differences in how gene expression memory is maintained through divisions in cancer and embryogenesis, thereby providing a tool for studying cell state memory through divisions across biological systems.},
}
@article {pmid39869770,
year = {2025},
author = {Katalinić, J and Richards, M and Auyang, A and Millett, JH and Kogenaru, M and Windbichler, N},
title = {Do the Shuffle: Expanding the Synthetic Biology Toolkit for Shufflon-like Recombination Systems.},
journal = {ACS synthetic biology},
volume = {14},
number = {2},
pages = {363-372},
pmid = {39869770},
issn = {2161-5063},
mesh = {*Synthetic Biology/methods ; *Escherichia coli/genetics ; *Recombination, Genetic/genetics ; Plasmids/genetics ; DNA Shuffling/methods ; },
abstract = {Naturally occurring DNA inversion systems play an important role in the generation of genetic variation and adaptation in prokaryotes. Shufflon invertase (SI) Rci from plasmid R64, recognizing asymmetric sfx sites, has been adopted as a tool for synthetic biology. However, the availability of a single enzyme with moderate rates of recombination has hampered the more widespread use of SIs. We identified 14 previously untested SI genes and their sfx sites in public databases. We established an assay based on single-molecule sequencing that allows the quantification of the inversion rates of these enzymes and determined cross-recognition to identify orthogonal SI/sfx pairs. We describe SI enzymes with substantially improved shuffling rates when expressed in an inducible manner in E. coli. Our findings will facilitate the use of SIs in engineering biology where synthetic shufflons enable the generation of millions of sequence variants in vivo for applications such as barcoding or experimental selection.},
}
@article {pmid39869133,
year = {2025},
author = {An, K and Yin, G and Wang, X and Shi, Y and Zhang, X and He, G and Amu, L and Chen, W and Wang, B and Hu, X and Wang, X and Wei, S},
title = {Intraspecific identification and genetic diversity analysis of Paeonia lactiflora based on chloroplast genes rpoB and psbK-psbI.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {165},
pmid = {39869133},
issn = {1573-4978},
support = {2020110031009381//molecular anti-counterfeiting technology of 2 precision medicinal materials of Atractylodes chinensis and P. lactiflora/ ; },
mesh = {*Paeonia/genetics ; *Genetic Variation/genetics ; *Haplotypes/genetics ; *Phylogeny ; *Chloroplasts/genetics ; China ; Genes, Chloroplast ; DNA Barcoding, Taxonomic/methods ; Genome, Chloroplast ; DNA-Directed RNA Polymerases/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: Paeonia lactiflora Pall., a member of Paeoniaceae family, is a medicinal herb widely used in traditional Chinese medicine. Chloroplasts are multifunctional organelles containing distinct genetic material. This study provides a foundation for identifying P. lactiflora, protecting and utilizing germplasm resources, and supporting molecular breeding efforts.<br><br>RESULTS AND CONCLUSION: In this study, five complete chloroplast genome sequences of P. lactiflora samples originating from different regions in China were sequenced using the Illumina NovaSeq 4000 platform. All five P. lactiflora chloroplasts had a typical cyclic tetrameric structure with 130 genes annotated. Comparative genomic analysis indicated that rpoB and psbK-psbI function as the&#xa0;potential specific DNA barcodes for intraspecific identification of P. lactiflora. PCR amplification of rpoB and psbK-psbI was performed on 246 samples from 7 production areas, achieving 100% amplification efficiency. Sequence analysis revealed that 5 and 10 haplotypes were identified based on rpoB and psbK-psbI, respectively. The joint analysis of two sequences identified 15 haplotypes named Hap1&#x2009;~&#x2009;Hap15. Hap5 emerged as the most prevalent and geographically widespread haplotype across China. Haplotypic diversity (Hd) was 0.786, and nucleotide diversity was 0.00281, suggesting that P. lactiflora had high genetic diversity at the species level. The Neighbor-Joining tree showed that the 15 haplotypes were clustered into two branches, indicating extensive genetic exchange between clusters. The introduction of new individuals or rare genes into different clusters through gene flow increased genetic variation within clusters, enriching P. lactiflora genetic diversity.},
}
@article {pmid39868307,
year = {2025},
author = {Adler, KM and Xu, H and Gladstein, AC and Irizarry-Negron, VM and Robertson, MR and Doerig, KR and Petrov, DA and Winslow, MM and Feldser, DM},
title = {Tumor suppressor genotype influences the extent and mode of immunosurveillance in lung cancer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.15.633175},
pmid = {39868307},
issn = {2692-8205},
abstract = {UNLABELLED: The impact of cancer driving mutations in regulating immunosurveillance throughout tumor development remains poorly understood. To better understand the contribution of tumor genotype to immunosurveillance, we generated and validated lentiviral vectors that create an epi-allelic series of increasingly immunogenic neoantigens. This vector system is compatible with autochthonous Cre-regulated cancer models, CRISPR/Cas9-mediated somatic genome editing, and tumor barcoding. Here, we show that in the context of KRAS-driven lung cancer and strong neoantigen expression, tumor suppressor genotype dictates the degree of immune cell recruitment, positive selection of tumors with neoantigen silencing, and tumor outgrowth. By quantifying the impact of 11 commonly inactivated tumor suppressor genes on tumor growth across neoantigenic contexts, we show that the growth promoting effects of tumor suppressor gene inactivation correlate with increasing sensitivity to immunosurveillance. Importantly, specific genotypes dramatically increase or decrease sensitivity to immunosurveillance independently of their growth promoting effects. We propose a model of immunoediting in which tumor suppressor gene inactivation works in tandem with neoantigen expression to shape tumor immunosurveillance and immunoediting such that the same neoantigens uniquely modulate tumor immunoediting depending on the genetic context.<br><br>ONE SENTENCE SUMMARY: Here we uncover an under-appreciated role for tumor suppressor gene inactivation in shaping immunoediting upon neoantigen expression.},
}
@article {pmid39867691,
year = {2025},
author = {Li, Q and Haqnawaz, M and Niazi, AR and Khalid, AN},
title = {Phylogenetic studies on the genus Candolleomyces (Psathyrellaceae, Basidiomycota) occurring in the bed of the Indus River, Punjab, Pakistan, reveal three new species.},
journal = {MycoKeys},
volume = {112},
number = {},
pages = {165-182},
pmid = {39867691},
issn = {1314-4049},
abstract = {During macrofungal surveys in 2019-2024, several specimens belonging to the family Psathyrellaceae were collected from the bed of the Indus River, Punjab, Pakistan. Phylogenetic analyses, based on ITS, LSU, and tef-1α sequences and morpho-anatomical study, confirmed the novelty and placement of three taxa in the genus Candolleomyces. They are described as Candolleomycescrenatus, C.undulatus, and C.virgatus. For distinguishing characters, C.crenatus has crenate cap margins, small basidiospores, and a marginate base of stipe. Candolleomycesundulatus has parabolic to campanulate, wavy margins, light purplish gray with a light brownish gray center of pileus, and an appendiculate, pendant annulus. Candolleomycesvirgatus has a parabolic to plane, distinct umbo, a virgate surface of pileus, 1-7 tiers, forking lamellae, and longitudinal striation on the surface of the stipe. Currently, Candolleomyces comprises 60 formally recognized species worldwide. However, with the inclusion of these three species, the total number rises to 63. Detailed descriptions, a phylogenetic estimate, morphological comparisons, and illustrations are provided.},
}
@article {pmid39867668,
year = {2025},
author = {Hu, H and Zhou, F and Ma, X and Brokstad, KA and Kolmar, L and Girardot, C and Benes, V and Cox, RJ and Merten, CA},
title = {Targeted barcoding of variable antibody domains and individual transcriptomes of the human B-cell repertoire using Link-Seq.},
journal = {PNAS nexus},
volume = {4},
number = {1},
pages = {pgaf006},
pmid = {39867668},
issn = {2752-6542},
abstract = {Here, we present Link-Seq, a highly efficient droplet microfluidic method for combined sequencing of antibody-encoding genes and the transcriptome of individual B cells at large scale. The method is based on 3' barcoding of the transcriptome and subsequent single-molecule PCR in droplets, which freely shift the barcode along specific gene regions, such as the antibody heavy- and light-chain genes. Using the immune repertoire of COVID-19 patients and healthy donors as a model system, we obtain up to 91.7% correctly paired immunoglobulin heavy and light chains. Furthermore, we map the V(D)J usage and obtain sensitivities comparable with the current gold-standard 10× Genomics commercial systems while offering full flexibility in experimental setup and significant cost savings. A further unique feature of Link-Seq is the possibility of barcoding multiple target genes in a site-specific manner. Based on the open character of the platform and its conceptual advantages, we expect Link-Seq to become a versatile tool for single-cell analysis, especially for applications requiring additional processing steps that cannot be implemented on commercially available platforms.},
}
@article {pmid39865877,
year = {2025},
author = {Venugopal Menon, N and Lee, J and Tang, T and Lim, CT},
title = {Microfluidics for morpholomics and spatial omics applications.},
journal = {Lab on a chip},
volume = {25},
number = {5},
pages = {752-763},
doi = {10.1039/d4lc00869c},
pmid = {39865877},
issn = {1473-0189},
mesh = {Humans ; *Single-Cell Analysis/instrumentation ; Microfluidic Analytical Techniques/instrumentation ; Animals ; Lab-On-A-Chip Devices ; },
abstract = {Creative designs, precise fluidic manipulation, and automation have supported the development of microfluidics for single-cell applications. Together with the advancements in detection technologies and artificial intelligence (AI), microfluidic-assisted platforms have been increasingly used for new modalities of single-cell investigations and in spatial omics applications. This review explores the use of microfluidic technologies for morpholomics and spatial omics with a focus on single-cell and tissue characterization. We emphasize how various fluid dynamic principles and unique design integrations enable highly precise fluid manipulation, enhancing sample handling in morpholomics. Additionally, we examine the use of microfluidics-assisted spatial barcoding with micrometer resolutions for the spatial profiling of tissue specimens. Finally, we discuss how microfluidics can serve as a bridge for integrating multiple unique fields in omics research and outline key challenges that these technologies may face in practical translation.},
}
@article {pmid39862392,
year = {2025},
author = {Biernat, B and Gładysz, P and Kuna, A and Sulima, M and Bykowska-Tumasz, M and Sontag, E},
title = {Myiasis by Cordylobia anthropophaga and C. rodhaini (Diptera: Calliphoridae) in Polish travelers to Africa with new molecular data.},
journal = {Journal of medical entomology},
volume = {62},
number = {2},
pages = {471-474},
pmid = {39862392},
issn = {1938-2928},
support = {//Division of Tropical Parasitology/ ; //Department of Tropical Medicine and Parasitology/ ; //Institute of Maritime and Tropical Medicine/ ; //Medical University of Gda&#x144;sk/ ; },
mesh = {Animals ; *Myiasis/parasitology/veterinary ; Poland ; *Larva/growth &amp; development/genetics ; Humans ; *Calliphoridae/growth &amp; development ; Electron Transport Complex IV/genetics/analysis ; Travel ; Male ; Insect Proteins/genetics ; Diptera/genetics ; Female ; },
abstract = {Myiasis is a parasitic infestation of soft vertebrate tissues by larval stages of Diptera. We briefly described the lesion-causing genus Cordylobia Grünberg (Diptera: Calliphoridae). Three Polish travelers to Uganda, Gambia, and Senegal returned with furuncular myiasis. To identify the third-instar larvae removed from their skin, we examined the morphological features of the 3 specimens and sequenced a 5' barcoding fragment of the cytochrome c oxidase subunit I gene (COI-5P). One larva was identified as C. rodhaini Gedoelst, and 2 larvae were identified as C. anthropophaga (Blanchard). We were the first to submit the COI-5P of C. rodhaini to GenBank and the Barcode of Life Database. This is the first record of the importation of C. anthropophaga and the second record of the importation of C. rodhaini to Poland.},
}
@article {pmid39861914,
year = {2025},
author = {Ranabhat, NB and Fellers, JP and Bruce, MA and Rupp, JLS},
title = {High-Throughput Oxford Nanopore Sequencing Unveils Complex Viral Population in Kansas Wheat: Implications for Sustainable Virus Management.},
journal = {Viruses},
volume = {17},
number = {1},
pages = {},
pmid = {39861914},
issn = {1999-4915},
support = {USDA-ARS CRIS, 3020-21000-011-000-D//United States Department of Agriculture/ ; startup fund//Kansas State University/ ; },
mesh = {*Triticum/virology ; *Plant Diseases/virology ; Kansas ; *Nanopore Sequencing/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Phylogeny ; *Genome, Viral/genetics ; Plant Viruses/genetics/isolation &amp; purification/classification ; RNA, Viral/genetics ; Plant Leaves/virology ; },
abstract = {Wheat viruses are major yield-reducing factors, with mixed infections causing substantial economic losses. Determining field virus populations is crucial for effective management and developing virus-resistant cultivars. This study utilized the high-throughput Oxford Nanopore sequencing technique (ONT) to characterize wheat viral populations in major wheat-growing counties of Kansas from 2019 to 2021. Wheat leaves exhibiting virus-like symptoms were collected, total RNA was extracted, and cDNA libraries were prepared using a PCR-cDNA barcoding kit, then loaded onto ONT MinION flow cells. Sequencing reads aligned with cereal virus references identified eight wheat virus species. Tritimovirus tritici (wheat streak mosaic virus, WSMV), Poacevirus tritici (Triticum mosaic virus, TriMV), Bromovirus BMV (brome mosaic virus, BMV), as well as Emaravirus tritici, Luteovirus pavhordei, L. sgvhordei, Bymovirus tritici, and Furovirus tritici. Mixed infections involving two to five viruses in a single sample were common, with the most prevalent being WSMV + TriMV at 16.7% and WSMV + TriMV + BMV at 11.9%. Phylogenetic analysis revealed a wide distribution of WSMV isolates, including European and recombinant variants. A phylogenetic analysis of Emaravirus tritici based on RNA 3A and 3B segments and whole-genome characterization of Furovirus tritici were also conducted. These findings advance understanding of genetic variability, phylogenetics, and viral co-infections, supporting the development of sustainable management practices through host genetic resistance.},
}
@article {pmid39859664,
year = {2025},
author = {Barták, M and Kozánek, M and Belcari, A and Tóthová, A&#x160;},
title = {New Species of Empidinae (Diptera) from San Rossore National Park, Italy, with the First Report on Leg Polymorphism in the Genus Hilara Meigen and Their DNA Barcoding Evidence.},
journal = {Insects},
volume = {16},
number = {1},
pages = {},
pmid = {39859664},
issn = {2075-4450},
abstract = {Altogether three species of Empidinae are described from San Rossore National Park, Italy: Empis (Euempis) sanrossorensis Barták sp. nov., Hilara polymorpha Barták sp. nov., and Rhamphomyia (Megacyttarus) sanrossorensis Barták sp. nov. Polymorphism in the shape of foreleg in Hilara is reported for the first time. The COI sequences for barcoding purposes and upcoming studies are provided.},
}
@article {pmid39859622,
year = {2025},
author = {Wu, J and Zhao, TT and Geng, H and Jin, GZ and Han, HL},
title = {Guium nebulum gen. et sp. nov., a New Cup Moth from Southern China Based on Morphological and Molecular Analysis (Lepidoptera: Zygaenoidea: Limacodidae).},
journal = {Insects},
volume = {16},
number = {1},
pages = {},
pmid = {39859622},
issn = {2075-4450},
support = {No. 31572294//National Nature Science Foundation of China/ ; No. 415486//the financial assistance under Heilongjiang Postdoctoral Fund/ ; No. 415895//Full-time Postdoctoral Support Program/ ; NABRI202303; 2572022DS09//Northeast Asia Biodiversity Research Center/ ; },
abstract = {A new genus and species of Limacodidae, Guium nebulum gen. et sp. nov., is described based on specimens collected from Guangxi Autonomous Region and Jiangxi Province in China. The new genus shares certain morphological features, such as a well-developed labial palpus, with related genera like Tanvia Solovyev &amp; Witt, 2009; Scopelodes Westwood, 1841; Hyphorma Walker, 1865; and Monema Walker, 1855. However, the new genus can be separated from them by the wing venation and the male genital characteristics. COI molecular marker analysis further supports the monophyly of this new genus, indicating a close relationship with Scopelodes.},
}
@article {pmid39859606,
year = {2024},
author = {Yang, F and Xiao, J and Zhang, X and Shang, Y and Guo, Y},
title = {First Report and Phylogenetic Analysis of Mitochondrial Genomes of Chrysomya villeneuvi and Sarcophaga genuforceps.},
journal = {Insects},
volume = {16},
number = {1},
pages = {},
pmid = {39859606},
issn = {2075-4450},
support = {82072114//National Natural Science Foundation of China/ ; },
abstract = {The mitochondrial genome, highly conserved across species, is crucial for species identification, phylogenetic analysis, and evolutionary research. Chrysomya villeneuvi and Sarcophaga genuforceps, two species with significant forensic value, have been understudied in terms of genetic data. In this study, the complete mitochondrial genomes of C. villeneuvi (15,623 bp) and S. genuforceps (15,729 bp) were sequenced and analyzed. All thirteen protein-coding genes (PCGs) exhibited Ka/Ks ratios below one, indicating purifying selection and supporting their utility as barcoding markers. Phylogenetic analysis and genetic distance calculations based on PCGs showed that C. villeneuvi is closely related to Chrysomya rufifacies and Chrysomya albiceps, and S. genuforceps aligns more closely with Sarcophaga kentejana and Sarcophaga schuetzei. This research is the first to provide mitochondrial genome data for C. villeneuvi and S. genuforceps, expanding the genetic resources available for Calliphoridae and Sarcophagidae and offering a foundation for further forensic and evolutionary studies.},
}
@article {pmid39858563,
year = {2024},
author = {Wang, M and Lin, H and Lin, H and Du, P and Zhang, S},
title = {From Species to Varieties: How Modern Sequencing Technologies Are Shaping Medicinal Plant Identification.},
journal = {Genes},
volume = {16},
number = {1},
pages = {},
pmid = {39858563},
issn = {2073-4425},
mesh = {*Plants, Medicinal/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *High-Throughput Nucleotide Sequencing/methods ; Genomics/methods ; Sequence Analysis, DNA/methods ; DNA, Plant/genetics ; },
abstract = {BACKGROUND/OBJECTIVES: Modern sequencing technologies have transformed the identification of medicinal plant species and varieties, overcoming the limitations of traditional morphological and chemical approaches. This review explores the key DNA-based techniques, including molecular markers, DNA barcoding, and high-throughput sequencing, and their contributions to enhancing the accuracy and reliability of plant identification. Additionally, the integration of multi-omics approaches is examined to provide a comprehensive understanding of medicinal plant identity.<br><br>METHODS: The literature search for this review was conducted across databases such as Google Scholar, Web of Science, and PubMed, using keywords related to plant taxonomy, genomics, and biotechnology. Inclusion criteria focused on peer-reviewed studies closely related to plant identification methods and techniques that contribute significantly to the field.<br><br>RESULTS: The review highlights that while sequencing technologies offer substantial improvements, challenges such as high costs, technical expertise, and the lack of standardized protocols remain barriers to widespread adoption. Potential solutions, including AI-driven data analysis and portable sequencers, are discussed.<br><br>CONCLUSIONS: This review provides a comprehensive overview of molecular techniques, their transformative impact, and future perspectives for more accurate and efficient medicinal plant identification.},
}
@article {pmid39856575,
year = {2025},
author = {Mitra, A and Mitra, P and Mahadani, P and Trivedi, S and Banerjee, D and Das, M},
title = {Application of character based DNA barcode: a novel approach towards identification of fruit fly (Diptera: Tephritidae) species from cucurbit crops.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {70},
pmid = {39856575},
issn = {1471-2164},
mesh = {Animals ; *Tephritidae/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Crops, Agricultural/genetics/parasitology ; Phylogeny ; Electron Transport Complex IV/genetics ; },
abstract = {BACKGROUND: The Tephritidae family, commonly referred to as true fruit flies, comprises of a substantial group within order Diptera. Numerous species within this family are major agricultural pests, with a tendency to infest a wide array of fruits and vegetables in tropical and sub- tropical regions, leading to considerable damage and consequent reductions in the market value of the crops.<br><br>METHODS AND RESULTS: The current study was aimed to propose a promising solution to the menace posed by fruit flies by offering rapid, accurate and reliable species identification by using character-based DNA barcode methodology. The Tephritid specimens were collected from Cucurbitaceous plants of southern parts of West Bengal, India, and a total of eight species from Tephritidae family were obtained belonging to three genera, namely Bactrocera (Macquart, 1835), Dacus (Fabricius, 1805) and Zeugodacus (Hendel, 1927). Their morphological features were meticulously studied based on available literature, along with genetic analysis based on mitochondrial COI and ND1 gene sequences. A total of 30 uniquely variable sites at nucleotide position 42,48,51,60,66,72, 105,111,144,198,207,243, 273,297,307,318,345,357, 375,378,381,387,399,400, 402,436,444,450,453 and 460 in COI gene were discerned among Tephritid species in the present study.<br><br>CONCLUSIONS: The character-based DNA barcode holds the potential to differentiate closely related species of fruit flies and morphologically look-a-like ones. The novel method will be very significant in terms of rapid, precise and reliable species identification and might be extremely essential for early detection during pest outbreaks by facilitating timely intervention strategies to mitigate crop damage.},
}
@article {pmid39853537,
year = {2025},
author = {Ramezankhani, R and De Smedt, J and Toprakhisar, B and van der Veer, BK and Tricot, T and Vanmarcke, G and Balaton, B and van Grunsven, L and Vosough, M and Chai, YC and Verfaillie, C},
title = {Identification of Cell Fate Determining Transcription Factors for Generating Brain Endothelial Cells.},
journal = {Stem cell reviews and reports},
volume = {},
number = {},
pages = {},
pmid = {39853537},
issn = {2629-3277},
support = {G0B5819N//Fonds Wetenschappelijk Onderzoek/ ; S001221N//Fonds Wetenschappelijk Onderzoek/ ; 1280923N//Fonds Wetenschappelijk Onderzoek/ ; 11E7920N//Fonds Wetenschappelijk Onderzoek/ ; PDMT2/23/083//KU Leuven postdoctoral mandate/ ; },
abstract = {Reliable models of the blood-brain barrier (BBB), wherein brain microvascular endothelial cells (BMECs) play a key role in maintenance of barrier function, are essential tools for developing therapeutics and disease modeling. Recent studies explored generating BMEC-like cells from human pluripotent stem cells (hPSCs) by mimicking brain-microenvironment signals or genetic reprogramming. However, due to the lack of comprehensive transcriptional studies, the exact cellular identity of most of these cells remains poorly defined. In this study we aimed to identify the most likely master transcription factors (TFs) for inducing brain endothelial cell (EC) fate and assess the transcriptomic changes following their introduction into immature ECs. Therefore, we first generated PSC-derived immature ECs by transient overexpression of the TF, ETV2. Subsequently, by performing an extensive meta-analysis of transcriptome studies of brain and non-brain ECs, 12 candidate TFs were identified, which might fate immature ECs towards cells with brain EC features. Following combinatorial overexpression of these 12 TFs tagged with unique barcodes, single cell transcriptomics identified a subset of transduced cells that resembled mid-gestational human brain ECs. Assessment of the TF barcodes present in these cells revealed significant enrichment of the TFs ZIC3, TFAP2C, TFAP2A, and DLX2. These TFs might be useful to fate PSC-EC to BMEC-like cells, which could be incorporated in human in vitro BBB models.},
}
@article {pmid39852453,
year = {2025},
author = {Psurtseva, NV and Kiyashko, AA and Senik, SV and Pham, THG},
title = {Ex Situ Conservation, DNA Barcoding and Enzymatic Potential Evaluation of Macrofungi (Basidiomycota, Ascomycota) from Vietnam.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {1},
pages = {},
pmid = {39852453},
issn = {2309-608X},
support = {075-15-2021-1056//Ministry of Education and Science of the Russian Federation/ ; 124013100829-3//State Assignment of BIN RAS/ ; E1.5//Joint Vietnam - Russia Tropical Science and Technology Research Centre/ ; },
abstract = {The diversity and resource potential of macroscopic fungi in tropical regions remain understudied. Vietnam, being in a biodiversity hotspot, has a large number of new fungal species that are of interest for biotechnology and medicine. The presence of a large number of protected areas in Vietnam creates favorable opportunities for the study and ex situ conservation of tropical biodiversity. From 2012 to 2023, 785 strains of macrofungi from National Parks of Vietnam were preserved in the LE-BIN collection, 327 of which were barcoded with the sequences deposited in the NCBI GenBank. A taxonomic analysis demonstrated that many of the preserved isolates are potentially new or poorly studied species, representing a useful resource for taxonomical studies and a search for new medicinal mushrooms. More than 180 strains were studied for the first time for growth rate and enzymatic activities. Of these, 53 strains showed high growth rate, 43-high cellulolytic activity, 73-high oxidative enzymes activity, and 27 showed high proteolytic activity, making them promising candidates for biotechnological and medical applications and opening new opportunities for sustainable biomass management, discovery of new enzymes and bioactive substances, development of new drugs and efficient plant waste treatment technologies. The results confirm the importance of the ex situ conservation of fungal diversity in tropical regions as a valuable source for scientific and commercial applications and suggest certain new active strains for biotechnological study.},
}
@article {pmid39849649,
year = {2025},
author = {Hornok, S and Kontschán, J and Keve, G and Takács, N and Van Nguyen, D and Ho, KNP and Görföl, T and Wang, Y and Farkas, R and Dao, TTH},
title = {First report of Haemaphysalis bispinosa, molecular-geographic relationships of Ixodes granulatus and a new Dermacentor species from Vietnam.},
journal = {Parasites &amp; vectors},
volume = {18},
number = {1},
pages = {21},
pmid = {39849649},
issn = {1756-3305},
support = {1500107//HUN-REN Office for Supported Research Groups/ ; FK137778//NKFIH/ ; 2019-2.1.12-T&#xc9;T VN-2020-00012//NKFIH/ ; },
mesh = {Animals ; Vietnam ; *Phylogeny ; *Ixodidae/classification/genetics/anatomy &amp; histology ; Female ; *Dermacentor/classification/genetics/anatomy &amp; histology ; Dogs ; RNA, Ribosomal, 16S/genetics ; Tick Infestations/veterinary/parasitology ; Dog Diseases/parasitology ; Lorisidae/parasitology/genetics/anatomy &amp; histology/classification ; Electron Transport Complex IV/genetics ; Ixodes/classification/genetics/anatomy &amp; histology ; Male ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Vietnam and its region are regarded as an ixodid tick biodiversity hotspot for at least two genera: Haemaphysalis and Dermacentor. To contribute to our knowledge on the tick fauna of this country, ticks from these two genera as well as an Ixodes species were analyzed morphologically and their molecular-phylogenetic relationships were examined in taxonomic and geographical contexts.<br><br>METHODS: For this study, seven Haemaphysalis sp. ticks were removed from dogs and collected from the vegetation. These showed morphological differences from congeneric species known to occur in Vietnam. In addition, three Ixodes sp. ticks were collected from pygmy slow lorises (Xanthonycticebus pygmaeus), and a Dermacentor female had been previously collected from the vegetation. After DNA extraction, these were molecularly or phylogenetically analyzed based on the cytochrome c oxidase subunit I (cox1) and 16S rRNA genes.<br><br>RESULTS: The three species were morphologically identified as (i) Ixodes granulatus, which had nearly or exactly 100% sequence identities to conspecific ticks reported from large (approximately 2000&#xa0;km) geographical distances but was more different (having lower, only 94.2% cox1 and 96.7% 16S rRNA sequence identity) from samples collected within 1000&#xa0;km of Vietnam in Southern China and Malaysia, respectively; (ii) Haemaphysalis bispinosa, which showed 100% sequence identity to samples reported within both narrow and broad geographical ranges; and (iii) a new species, Dermacentor pseudotamokensis Hornok sp. nov., described here morphologically and shown to be phylogenetically&#xa0;a sister species to Dermacentor tamokensis.<br><br>CONCLUSIONS: Haemaphysalis bispinosa shows genetic homogeneity in the whole of South and Southeast Asia, probably owing to its frequent association with domestic ruminants and dogs (i.e. frequently transported hosts). However, I. granulatus, the Asian rodent tick, has a mixed geographical pattern of haplotypes, probably because it may associate with either synanthropic or wild-living rodents as primary hosts. This tick species is recorded here, for the first time to our knowledge, as parasitizing lorises in Vietnam and its region. Based on phylogenetic analyses, D. pseudotamokensis Hornok&#xa0;sp. nov., recognized and described here for the first time, was almost certainly misidentified previously as Dermacentor steini, drawing attention to the need to barcode all Dermacentor spp. in Southern Asia.},
}
@article {pmid39845798,
year = {2024},
author = {He, G and Man, J and Chen, Y and Zhang, X and Wang, X and An, K and Amu, L and Chen, W and Wang, B and Shi, Y and Wang, X and Wei, S},
title = {Identification of Salvia miltiorrhiza germplasm resources based on metabolomics and DNA barcoding.},
journal = {Frontiers in pharmacology},
volume = {15},
number = {},
pages = {1518906},
pmid = {39845798},
issn = {1663-9812},
abstract = {INTRODUCTION: Salvia miltiorrhiza radix et rhizoma (Danshen) is a crucial medicinal material for treating cardiovascular and cerebrovascular diseases. However, the presence of adulterants and intraspecific variability poses challenges to its clinical safety.<br><br>METHODS: This study collected samples of S. miltiorrhiza from various regions and commonly encountered adulterants. The composition differences of S. miltiorrhiza radix and its adulterants were analyzed by fingerprint and broad-target metabolomics. Chloroplast genome was used to distinguish intra-genus species and DNA barcoding was used to identify germplasm sources.<br><br>RESULTS: The fingerprinting analysis proved that there is no chemical composition consistency between S. miltiorrhiza radix and its adulterants. Broad-targeted metabolomics can distinguish S. miltiorrhiza radix from Salvia yunnanensis radix, Dipsacus asperoides radix, and Arctium lappa radix. Additionally, comparative chloroplast genome analysis indicated that atpF and rps4-trnT-UGU were the potential DNA barcodes for S. miltiorrhiza. 259 samples from 13 provinces and 21 origins were amplified and sequenced, resulting in the identification of 62 haplotypes. The unique haplotypes found in Shanxi Luoyang, Shandong Qingdao and other places can be used as molecular geographic markers for the identification of the germplasm source of S. miltiorrhiza.<br><br>DISCUSSION: This study systematically differentiates S. miltiorrhiza from its adulterants and highlights the potential of unique haplotypes as markers for sourcing. The findings provide strong scientific evidence for the clinical safety of S. miltiorrhiza, emphasizing the importance of proper cultivation, selection, and breeding of varieties.},
}
@article {pmid39845644,
year = {2025},
author = {Yu, Z and Qi, Y and Wei, Y and Zhuang, G and Li, Y and Wang, B and Akbar, S and Xu, Y and Hua, X and Xu, Q and Deng, Z and Zhang, J and Huang, Y and Yu, F and Zhou, J},
title = {A cost-effective oligo-based barcode system for chromosome identification in longan and lychee.},
journal = {Horticulture research},
volume = {12},
number = {1},
pages = {uhae278},
pmid = {39845644},
issn = {2662-6810},
abstract = {Oligonucleotide (Oligo)-based fluorescence in situ hybridization (FISH) represents a highly effective methodology for identifying plant chromosomes. Longan is a commercially significant fruit species, yet lacking basic chromosomal markers has hindered its cytogenetic research. In this study, we developed a cost-effective oligo-based system for distinguishing chromosomes of longan (Dimocarpus longan Lour., 2n = 2x = 30). For this system, each synthesized oligo contained two chromosome-specific sequences that spanned a distance of over 200 kb, and a PCR-based flexible amplification method coupled with nested primers was used for probe labeling. The use of these oligo-based barcodes enabled the marking of 36 chromosomal regions, which allowed for the unambiguous distinction of all 15 chromosomes in both longan and lychee (Litchi chinensis Sonn., 2n = 2x = 30) species. Based on the identification of individual chromosomes, we constructed karyotypes and detected genome assembly errors involving the 35S ribosomal RNA gene (35S rDNA) in longan and lychee. Developing oligo-based barcodes offers considerable promise for advancing cytogenetic research in longan, lychee, and their related species. Furthermore, this cost-effective synthesis system can be referred to the development of new oligo libraries among other species.},
}
@article {pmid39845497,
year = {2025},
author = {Lee, DJ and Kim, J and Euo, SS and Lee, JS and Lee, H and Roh, SJ},
title = {A new species of the genus Oiketicoides Heylaerts, 1885 (Lepidoptera, Psychidae) from Korea with its natural parasitoid enemy.},
journal = {ZooKeys},
volume = {1223},
number = {},
pages = {311-317},
pmid = {39845497},
issn = {1313-2989},
abstract = {Oiketicoidesgohadoensis Roh &amp; Lee, sp. nov. is described as new to science. The morphology of male adult, including genitalia, is described, and DNA barcodes for precise identification of the species are provided. A parasitoid, Neophryxepsychidis Townsend, 1916 (Diptera, Tachinidae) of O.gohadoensis is also reported for the first time in Korea, together with its DNA barcode sequence.},
}
@article {pmid39843438,
year = {2025},
author = {Lin, C and Liu, C and Chen, L and Cheng, H and Ashfaq, M and Hebert, PDN and Gao, Y},
title = {Data on insect biodiversity in a Chinese potato agroecosystem from DNA metabarcoding.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {131},
pmid = {39843438},
issn = {2052-4463},
support = {59-0212-9-001-F//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; },
mesh = {*DNA Barcoding, Taxonomic ; Animals ; *Biodiversity ; *Solanum tuberosum/genetics ; *Insecta/classification/genetics ; China ; East Asian People ; },
abstract = {Potato (Solanum tuberosum) is a staple crop important in global food security. As a leading potato producer, China faces significant challenges from insect pest infestations that compromise yield and quality. However, insect communities within Chinese potato fields remain poorly characterized. This study aimed to explore insect diversity in potato fields in Yunnan Province. From autumn 2021 to summer 2022, five Malaise traps were strategically deployed to capture insect samples. In total, 245 samples were collected over 49 weeks, and DNA metabarcoding was performed on bulk samples. The generated sequences were curated and analyzed using the Barcode of Life Data System and the Multiplex Barcode Research and Visualization Environment. The analysis assigned sequences to 1,688 Barcode Index Numbers (BINs) as species proxies derived from the Global Insecta Library, along with 166 BINs from the China Insecta dataset. This research provides valuable insights for barcoding local biodiversity and developing regional reference libraries and presents a comprehensive dataset of insect biodiversity within potato agroecosystems, encompassing 1,707 BINs linked to known insect taxa.},
}
@article {pmid39838754,
year = {2025},
author = {Zhang, D and Zhou, Y and Li, X and Luan, Q},
title = {CRISPR/Cas13a-Enhanced Porous Hydrogel Encapsulated Photonic Barcodes for Multiplexed Detection of Virus.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {21},
number = {8},
pages = {e2408725},
doi = {10.1002/smll.202408725},
pmid = {39838754},
issn = {1613-6829},
support = {82102511//National Natural Science Foundation of China/ ; 82102181//National Natural Science Foundation of China/ ; BK20210021//National Natural Science Foundation of China/ ; BK20210009//National Natural Science Foundation of China/ ; M2021031//Research Project of&#xa0;Jiangsu Province Health Committee/ ; 2024-LCYJ-MS-15//Medical School of Nanjing University/ ; (YKK23068)//Nanjing Medical Science and Technique Development Foundation YKK23068/ ; },
mesh = {*CRISPR-Cas Systems ; *SARS-CoV-2/genetics/isolation &amp; purification ; *Hydrogels/chemistry ; Porosity ; Humans ; Photons ; COVID-19/diagnosis/virology ; RNA, Viral/genetics ; Nucleic Acid Hybridization ; },
abstract = {In this study, we present an ultrasensitive and specific multiplexed detection method for SARS-CoV-2 and influenza (Flu) utilizing CRISPR/Cas13a technology combined with a hydrogel-encapsulated photonic crystal (PhC) barcode integrated with hybridization chain reaction (HCR). The barcodes, characterized by core-shell structures, are fabricated through partial replication of periodically ordered hexagonally close-packed silicon dioxide beads. Consequently, the opal hydrogel shell of these barcodes features abundant interconnected pores that provide a substantial surface area for probe immobilization. Furthermore, the inherent structural colors remain stable during detection events due to the robust mechanical strength of the barcode cores. This integration of CRISPR/Cas13a and HCR leverages both the highly specific RNA recognition capabilities and trans-cleavage activity of Cas13a while employing HCR to enhance sensitivity. Upon encountering target RNA, Cas13a cleaves a hairpin probe, thereby initiating subsequent HCR amplification for enhanced detection sensitivity. Our method demonstrates high accuracy and sensitivity in multiplexed detection of SARS-CoV-2, Flu A and Flu B RNA with a limit-of-detection as low as 200 aM. Importantly, this assay also exhibits acceptable accuracy in repeated clinical sample testing. Thus, our platform represents a promising strategy for highly sensitive multiplexed virus detection in clinical.},
}
@article {pmid39837566,
year = {2025},
author = {Zhuoma, D and Tingyin, D and Jun, L and Pei, Q and Duoji, C and Feng, D and Fang, D and Yan, Z},
title = {Study on Quality Evaluation of Tibetan Dracocephali tangutici Herba Based on DNA Barcode and HPLC Fingerprinting.},
journal = {Phytochemical analysis : PCA},
volume = {},
number = {},
pages = {},
doi = {10.1002/pca.3503},
pmid = {39837566},
issn = {1099-1565},
support = {XZ202101ZD0024G//Project of Science and Technology Programme of Tibet Autonomous Region/ ; },
abstract = {OBJECTIVES: The quality of 30 batches of the Tibetan Dracocephali tangutici Herba was evaluated using HPLC fingerprinting and DNA sequences.<br><br>METHODS: Botanical identification of 30 batches of D. tangutici herba was conducted using the DNA barcoding approach, specifically analyzing the ITS and rbcL sequences. HPLC fingerprints of Tibetan Dracocephali tangutici Herba were established. The quality of 30 batches of D. tangutici herba was comprehensively evaluated using principal component analysis (PCA), orthogonal partial least squares discriminant analysis (OPLS-DA), and entropy weighting method (EWM) combined with grey relation analysis (GRA).<br><br>RESULTS: The botanical provenance of all 30 batches of herbs was proven to be Dracocephali tangutici Maxim. using DNA barcoding techniques, namely, ITS sequence and rbcL sequence testing. A total of 17 common peaks were chosen from the HPLC fingerprinting analysis. Among these, three peaks were recognized by comparing them with three reference standards: chlorogenic acid, cryptochlorogenic acid, and salvianolic acid B. The similarity scores of the 30 batches of D. tangutici herba varied between 0.846 and 0.991. The 30 batches of samples were categorized into two groups using PCA. The findings from OPLS-DA indicated that chlorogenic acid and four flavonoids could be the crucial components for evaluating the quality of D. tangutici herba. Additionally, the combined evaluation results of EWM and GRA suggested that the quality of the 30 batches of samples varied significantly.<br><br>CONCLUSION: The results of this study can provide a reference basis for the development of quality standards for D. tangutici herba in Tibet.},
}
@article {pmid39834682,
year = {2025},
author = {},
title = {Correction to "Species Identification of Livefood Flightless Fly (Torinido-Shoujoubae) Through DNA Barcoding".},
journal = {Ecology and evolution},
volume = {15},
number = {1},
pages = {e70864},
doi = {10.1002/ece3.70864},
pmid = {39834682},
issn = {2045-7758},
abstract = {[This corrects the article DOI: 10.1002/ece3.11622.].},
}
@article {pmid39831564,
year = {2025},
author = {Mariz, J and Nawaz, A and Bösch, Y and Wurzbacher, C},
title = {Exploring Environmental Microfungal Diversity Through Serial Single Cell Screening.},
journal = {Molecular ecology resources},
volume = {25},
number = {3},
pages = {e14055},
pmid = {39831564},
issn = {1755-0998},
support = {WU 890/2-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Fungi/genetics/classification/isolation &amp; purification ; *Biodiversity ; Single-Cell Analysis/methods ; DNA Barcoding, Taxonomic/methods ; Sequence Analysis, DNA/methods ; DNA, Fungal/genetics ; Phylogeny ; },
abstract = {Known for its remarkable diversity and ecological importance, the fungal kingdom remains largely unexplored. In fact, the number of unknown and undescribed fungi is predicted to exceed the number of known fungal species by far. Despite efforts to uncover these dark fungal taxa, we still face inherent sampling biases and methodological limitations. Here, we present a framework that combines taxonomic knowledge, molecular biology and data processing to explore the fungal biodiversity of enigmatic aquatic fungal lineages. Our work is based on serial screening of environmental fungal cells to approach unknown fungal taxa. Microscopic documentation is followed by DNA analysis of laser micro-dissected cells, coupled with a ribosomal operon barcoding step realised by long-read sequencing, followed by an optional whole genome sequencing step. We tested this approach on a range of aquatic fungal cells mostly belonging to the ecological group of aquatic hyphomycetes derived from environmental samples. From this initial screening, we were able to identify 60 potentially new fungal taxa in the target dataset. By extending this methodology to other fungal lineages associated with different habitats, we expect to increasingly characterise the molecular barcodes of dark fungal taxa in diverse environmental samples. This work offers a promising solution to the challenges posed by unknown and unculturable fungi and holds the potential to be applied to the diverse lineages of undescribed microeukaryotes.},
}
@article {pmid39831278,
year = {2025},
author = {Nguyen, AD and Vu, TTT and Nguyen, TT},
title = {Mountainous millipedes in Vietnam. III. Two new dragon millipedes from limestone mountains in northern Vietnam (Polydesmida, Paradoxosomatidae, Hylomus), with an identification key to Vietnamese Hylomus species.},
journal = {ZooKeys},
volume = {1223},
number = {},
pages = {247-262},
pmid = {39831278},
issn = {1313-2989},
abstract = {Two new species of the dragon millipede genus Hylomus Cook &amp; Loomis, 1924 are described from mountainous areas in northern Vietnam, namely Hylomuspiccolo sp. nov. and Hylomusborealis sp. nov. The COI barcodes are provided for these species, and an identification key is presented to all Vietnamese Hylomus species.},
}
@article {pmid39830292,
year = {2024},
author = {Crous, PW and Wingfield, MJ and Jurjević, &#x17d; and Balashov, S and Osieck, ER and Marin-Felix, Y and Luangsa-Ard, JJ and Mejía, LC and Cappelli, A and Parra, LA and Lucchini, G and Chen, J and Moreno, G and Faraoni, M and Zhao, RL and Weholt, &#xd8; and Borovička, J and Jansen, GM and Shivas, RG and Tan, YP and Akulov, A and Alfenas, AC and Alfenas, RF and Altés, A and Avchar, R and Barreto, RW and Catcheside, DEA and Chi, TY and Esteve-Raventós, F and Fryar, SC and Hanh, LTM and Larsbrink, J and Oberlies, NH and Olsson, L and Pancorbo, F and Raja, HA and Thanh, VN and Thuy, NT and Ajithkumar, K and Akram, W and Alvarado, P and Angeletti, B and Arumugam, E and Khalilabad, AA and Bandini, D and Baroni, TJ and Barreto, GG and Boertmann, D and Bose, T and Castañeda Ruiz, RF and Couceiro, A and Cykowska-Marzencka, B and Dai, YC and Darmostuk, V and da Silva, SBG and Dearnaley, JDW and de Azevedo Santiago, ALCM and Declercq, B and de Freitas, LWS and De la Peña-Lastra, S and Delgado, G and de Lima, CLF and Dhotre, D and Dirks, AC and Eisvand, P and Erhard, A and Ferro, LO and García, D and García-Martín, A and Garrido-Benavent, I and Gené, J and Ghobad-Nejhad, M and Gore, G and Gunaseelan, S and Gusmão, LFP and Hammerbacher, A and Hernández-Perez, AT and Hernández-Restrepo, M and Hofmann, TA and Hubka, V and Jiya, N and Kaliyaperumal, M and Keerthana, KS and Ketabchi, M and Kezo, K and Knoppersen, R and Kolarczyková, D and Kumar, TKA and Læssøe, T and Langer, E and Larsson, E and Lodge, DJ and Lynch, MJ and Maciá-Vicente, JG and Mahadevakumar, S and Mateos, A and Mehrabi-Koushki, M and Miglio, BV and Noor, A and Oliveira, JA and Pereira, OL and Piątek, M and Pinto, A and Ramírez, GH and Raphael, B and Rawat, G and Renuka, M and Reschke, K and Mateo, AR and Saar, I and Saba, M and Safi, A and Sánchez, RM and Sandoval-Denis, M and Savitha, AS and Sharma, A and Shelke, D and Sonawane, H and Souza, MGAP and Stryjak-Bogacka, M and Thines, M and Thomas, A and Torres-Garcia, D and Traba, JM and Vauras, J and Vermaas, M and Villarreal, M and Vu, D and Whiteside, EJ and Zafari, D and Starink-Willemse, M and Groenewald, JZ},
title = {Fungal Planet description sheets: 1697-1780.},
journal = {Fungal systematics and evolution},
volume = {14},
number = {},
pages = {325-577},
pmid = {39830292},
issn = {2589-3831},
support = {P01 CA125066/CA/NCI NIH HHS/United States ; },
abstract = {Novel species of fungi described in this study include those from various countries as follows: Antarctica, Leuconeurospora bharatiensis from accumulated snow sediment sample. Argentina, Pseudocercospora quetri on leaf spots of Luma apiculata. Australia, Polychaetomyces verrucosus on submerged decaying wood in sea water, Ustilaginoidea cookiorum on Scleria levis, Xylaria guardiae as endophyte from healthy leaves of Macaranga tanarius. Belgium, Iodophanus taxi on leaf of Taxus baccata. Belize, Hygrocybe mirabilis on soil. Brazil, Gongronella irregularis from soil, Linodochium splendidum on decaying sheath of Euterpe oleracea, Nothophysalospora agapanthi (incl. Nothophysalospora gen. nov.) on flower stalks of Agapanthus praecox, Phaeosphaeria tabebuiae on leaf of Tabebuia sp., Verrucohypha endophytica (incl. Verrucohypha gen. nov.) from healthy roots of Acrocomia aculeata. Estonia, Inosperma apricum on soil under Quercus robur. Greece, Monosporascus solitarius isolated from surface-sterilised, asymptomatic roots of Microthlaspi perfoliatum. India, Diaporthe neocapsici on young seedling stems of Capsicum annuum, Fuscoporia naditirana on dead wood, Sebacina spongicarpa on soil, Torula kanvae from the gut of a Copris signatus beetle. Iran, Sarcinomyces pruni from twig and petiole tissues of Prunus persica and Prunus armeniaca, Xenodidymella quercicola from leaf spots of Quercus brantii. Italy, Agaricus aereiceps on grass, Agaricus bellui in meadows, Agaricus fabrianensis in urban grasslands, Beaucarneamyces muscorum on moss growing in forest, Xenoanthostomella quercus on leaf litter of Quercus ilex. Netherlands, Alfaria neerlandica on stem lesions of Cortaderia selloana, Neodictyosporium juncicola on culms of Juncus maritimus, Penicillium geertdesnooi from soil under Papaver rhoeas, Russula abscondita on rich calcareous soil with Quercus, Russula multiseptata on rich clay soil with Quercus, Russula purpureopallescens on soil with Populus, Sarocladium caricicola on leaves of Carex riparia. Pakistan, Circinaria shimlaensis on limestone rocks. Panama, Acrocalymma philodendri on leaf spots of Philodendron sp., Caligospora panamaensis on leaf litter, Chlamydocillium simulans associated with a Xylaria sp., Corynesporina panamaensis on leaf litter, Cylindromonium panamaense on twig litter of angiosperm, Cyphellophora panamaensis on twig litter of angiosperm, Microcera panamensis on leaf litter of fern, Pseudotricholoma pusillum in tropical montane forest dominated by Quercus spp., Striaticonidium panamaense on leaf litter, Yunnanomyces panamaensis on leaf litter. Poland, Albocremella abscondita (incl. Albocremella gen. nov.) from rhizoids of liverwort Conocephalum salebrosum. Portugal, Agaricus occidualis in meadows. South Africa, Alternaria elsarustiae on culms of unidentified Poaceae, Capronia capensis on dead twig of unidentified angiosperm, Codinaeella bulbinicola on dead leaves of Bulbine frutescens, Cytospora carpobroticola on leaf of Carpobrotus quadrifidus, Neophaeomoniella watsoniae on leaf of Watsonia sp., Neoplatysporoides aloigena on leaf of Aloe khamiesensis, Nothodactylaria comitabilis on living leaf of Itea rhamnoides, Nothopenidiella beaucarneae (incl. Nothopenidiella gen. nov.) on dead leaves of Beaucarnea stricta, Orbilia kirstenboschensis on dead flower stalks of Agapanthus praecox, Phragmocephala agapanthi on dead flower stalks of Agapanthus praecox, Podocarpigena hagahagaensis (incl. Podocarpigena gen. nov.) on leaf spots of Podocarpus falcatus, Sporisorium enterogonipteri from the gut of Gonipterus sp., Synnemapestaloides searsiae on leaf of Searsia populifolia, Xenophragmocapnias diospyri (incl. Xenophragmocapnias gen. nov.) on leaf spots of Diospyros sp., Yunnanomyces hagahagaensis on leaf spots of Sideroxylon inerme. Spain, Agaricus basicinctus in meadows, Agaricus quercetorum among leaf litter in oak forests, Coprinopsis palaciosii on degraded woody debris, Inocybe complutensis in calcareous loamy soil, Inocybe tanitiae in calcareous sandy soil, Mycena subfragosa on dead leaves of Salix atrocinerea, Pseudobaeospora cortegadensis in laurel forests, Trichoderma sedimenticola from fluvial sediments. Sweden, Inocybe badjelanndana on calcareous soil. Ukraine, Beaucarneamyces lupini on overwintered stems of Lupinus polyphyllus, Protocreopsis globulosa on thallus and apothecia of Lecania cyrtella on bark of Populus sp., Thyridium tiliae on dead twigs of Tilia sp. USA, Cladosporium louisianense, Cyphellophora americana from a bedroom vent, Extremus massachusettsianus from lyse buffer, Myxotrichum tapetae on carpet in basement, Neospissiomyces floridanus (incl. Neospissiomyces gen. nov.) on swab from hospital, Polychaetomyces marinus (incl. Polychaetomyces gen. nov.) on submerged driftwood in sea water, Steccherinum fragrans on hardwood fallen on the beach, Steinbeckomyces carnegieae (incl. Steinbeckomyces gen. nov.) on Carnegiea gigantea, Tolypocladium pennsylvanicum from air sampled in basement. Vietnam, Acidomyces ducanhii from Aglaia flowers, Acidomyces paludis from dead bark of Acacia sp., Phakopsora sageretiae on Sageretia theezans, Puccinia stixis on Stixis scandens. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Wingfield MJ, Jurjević Ž, et al. (2024). Fungal Planet description sheets: 1697-1780. Fungal Systematics and Evolution 14: 325-577. doi: 10.3114/fuse.2024.14.19.},
}
@article {pmid39825896,
year = {2025},
author = {Ellisor, D and Gregg, M and Folz, A and Possolo, A},
title = {Robust discrimination between closely related species of salmon based on DNA fragments.},
journal = {Analytical and bioanalytical chemistry},
volume = {},
number = {},
pages = {},
pmid = {39825896},
issn = {1618-2650},
abstract = {Closely related species of Salmonidae, including Pacific and Atlantic salmon, can be distinguished from one another based on nucleotide sequences from the cytochrome c oxidase sub-unit 1 mitochondrial gene (COI), using ensembles of fragments aligned to genetic barcodes that serve as digital proxies for the relevant species. This is accomplished by exploiting both the nucleotide sequences and their quality scores recorded in a FASTQ file obtained via Next Generation (NextGen) Sequencing of mitochondrial DNA extracted from Coho salmon caught with hook and line in the Gulf of Alaska. The alignment is done using MUSCLE (Muscle 5.2) [1], applied to multiple versions of each fragment perturbed according to the nucleobase identification error probabilities underlying the quality scores. The Damerau-Levenshtein distance was used to determine the genetic barcode of the candidate species that is closest to each aligned, perturbed fragment. The "votes" that the sampled fragments cast for the different candidate species are then pooled and converted into identification probabilities, using weights determined by the entropy of the fragment-specific identification probability distributions. This novel approach to quantify the uncertainty associated with measurements made using NextGen Sequencing can be applied to discriminate closely related species, hence to value-assignment for reference materials supporting determinations of the authenticity of seafood, for example, NIST Reference Materials 8256 and 8257 (Coho salmon) [2].},
}
@article {pmid39824859,
year = {2025},
author = {Holmes, CL and Dailey, KG and Hullahalli, K and Wilcox, AE and Mason, S and Moricz, BS and Unverdorben, LV and Balazs, GI and Waldor, MK and Bachman, MA},
title = {Patterns of Klebsiella pneumoniae bacteremic dissemination from the lung.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {785},
pmid = {39824859},
issn = {2041-1723},
support = {K99 AI175481/AI/NIAID NIH HHS/United States ; R01 AI042347/AI/NIAID NIH HHS/United States ; AI042347//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R37 AI042347/AI/NIAID NIH HHS/United States ; K99A1175481//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {*Klebsiella pneumoniae/pathogenicity/isolation &amp; purification ; *Bacteremia/microbiology ; *Klebsiella Infections/microbiology ; *Lung/microbiology/pathology ; Animals ; Female ; Mice ; Humans ; Mice, Inbred C57BL ; Male ; },
abstract = {Bacteremia, a leading cause of death, generally arises after bacteria establish infection in a particular tissue and transit to secondary sites. Studying dissemination from primary sites by solely measuring bacterial burdens does not capture the movement of individual clones. By barcoding Klebsiella pneumoniae, a leading cause of bacteremia, we track pathogen dissemination following pneumonia. Variability in organ bacterial burdens is attributable to two distinct dissemination patterns distinguished by the degree of similarity between the lung and systemic sites. In metastatic dissemination, lung bacterial clones undergo heterogeneous expansion and the dominant clones spread to secondary organs, leading to greater similarity between sites. In direct dissemination, bacterial clones exit the lungs without clonal expansion, leading to lower burdens in systemic sites and more dissimilarity from the lung. We uncover bacterial and host factors that influence the dynamics of clonal sharing and expansion. Here, our data reveal unexpected heterogeneity in Klebsiella bacteremia dynamics and define a framework for understanding within-host bacterial dissemination.},
}
@article {pmid39823405,
year = {2025},
author = {Miller, D and Dziulko, A and Levy, S},
title = {Pooled PPIseq: Screening the SARS-CoV-2 and human interface with a scalable multiplexed protein-protein interaction assay platform.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0299440},
pmid = {39823405},
issn = {1932-6203},
support = {R01 AI164530/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *SARS-CoV-2/metabolism ; Protein Interaction Mapping/methods ; Host-Pathogen Interactions ; COVID-19/virology/metabolism ; Protein Interaction Maps ; Viral Proteins/metabolism ; High-Throughput Screening Assays/methods ; HEK293 Cells ; },
abstract = {Protein-Protein Interactions (PPIs) are a key interface between virus and host, and these interactions are important to both viral reprogramming of the host and to host restriction of viral infection. In particular, viral-host PPI networks can be used to further our understanding of the molecular mechanisms of tissue specificity, host range, and virulence. At higher scales, viral-host PPI screening could also be used to screen for small-molecule antivirals that interfere with essential viral-host interactions, or to explore how the PPI networks between interacting viral and host genomes co-evolve. Current high-throughput PPI assays have screened entire viral-host PPI networks. However, these studies are time consuming, often require specialized equipment, and are difficult to further scale. Here, we develop methods that make larger-scale viral-host PPI screening more accessible. This approach combines the mDHFR split-tag reporter with the iSeq2 interaction-barcoding system to permit massively-multiplexed PPI quantification by simple pooled engineering of barcoded constructs, integration of these constructs into budding yeast, and fitness measurements by pooled cell competitions and barcode-sequencing. We applied this method to screen for PPIs between SARS-CoV-2 proteins and human proteins, screening in triplicate >180,000 ORF-ORF combinations represented by >1,000,000 barcoded lineages. Our results complement previous screens by identifying 74 putative PPIs, including interactions between ORF7A with the taste receptors TAS2R41 and TAS2R7, and between NSP4 with the transmembrane KDELR2 and KDELR3. We show that this PPI screening method is highly scalable, enabling larger studies aimed at generating a broad understanding of how viral effector proteins converge on cellular targets to effect replication.},
}
@article {pmid39823165,
year = {2025},
author = {Ivanova, A and Chalupska, R and Louro, AF and Firth, M and González-King Garibotti, H and Hultin, L and Kohl, F and Lázaro-Ibáñez, E and Lindgren, J and Musa, G and Oude Blenke, E and Silva, AM and Szeponik, L and Taylor, A and Viken, I and Wang, X and Jennbacken, K and Wiseman, J and Dekker, N},
title = {Barcoded Hybrids of Extracellular Vesicles and Lipid Nanoparticles for Multiplexed Analysis of Tissue Distribution.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {12},
number = {10},
pages = {e2407850},
pmid = {39823165},
issn = {2198-3844},
support = {825828//European Union's Horizon 2020 Research and Innovation Programme/ ; },
mesh = {*Extracellular Vesicles/metabolism ; Animals ; Mice ; *Nanoparticles/chemistry/metabolism ; Tissue Distribution ; Cell Line ; Humans ; Drug Delivery Systems/methods ; Liposomes/pharmacokinetics ; },
abstract = {Targeted delivery of therapeutic agents is a persistent challenge in modern medicine. Recent efforts in this area have highlighted the utility of extracellular vesicles (EVs) as drug carriers, given that they naturally occur in bloodstream and tissues, and can be loaded with a wide range of therapeutic molecules. However, biodistribution and tissue tropism of EVs remain difficult to study systematically. Here, a multiplexed approach is developed for simultaneous tracking of EVs from various cell lines within a single in vivo experiment. EVs are used from 16 different cell lines, and through controlled fusion with lipid nanoparticles (LNPs) carrying single-stranded DNA barcodes, uniquely barcoded hybrid EV particle (hEV) library is generated. These hEVs are combined for a multiplexed in vivo biodistribution profiling in mice, and discovered that HAP1-derived hEVs demonstrated lung tropism, suggesting that these hEVs may be used for targeted drug delivery into lung tissue. To examine this possibility further, it is shown that HAP1 hEV loaded with Cre mRNA displayed functional delivery to the lungs. Overall, the barcoded hEV technology enables rapid profiling of biodistribution across EV cell sources, which is poised to improve throughput and extent of EV studies, while reducing the number of animals required for research.},
}
@article {pmid39821740,
year = {2025},
author = {Dou, HY and Huang, TS and Wu, HC and Hsu, CH and Chen, FJ and Liao, YC},
title = {Targeted sputum sequencing for rapid and broad drug resistance of Mycobacterium tuberculosis.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {39821740},
issn = {1439-0973},
support = {IV-111-PP-23//National Health Research Institutes, Taiwan/ ; PH-112-PP-05//National Health Research Institutes, Taiwan/ ; 110-2314-B-400-038//Ministry of Science and Technology, Taiwan/ ; },
abstract = {PURPOSE: Rapid detection of drug resistance in Mycobacterium tuberculosis (Mtb) from clinical samples facilitates the timely provision of optimal treatment regimens for tuberculosis (TB) patients.<br><br>METHODS: In November, 2023, the WHO released its second catalogue of resistance-conferring mutations in Mtb. Utilizing this information, we developed a single 17-plex PCR assay covering 16 key resistance genes and modified thermo-protection buffer to amplify 30 kbp DNA directly from sputum samples for nanopore sequencing. We implemented our protocol using rapid barcoding for sequencing with both a Flongle and a MinION flow cell.<br><br>RESULTS: The single multiplex PCR assay was successfully validated on clinical sputum samples using the thermo-protection buffer. The protocol was applied to both Flongle and MinION flow cells, analyzing 12 and 40 samples, respectively. Data analysis suggested that optimal performance could be achieved by processing 6 and 12 samples with similar microscope staining scores on these two platforms. This approach facilitated rapid antimicrobial resistance (AMR) predictions directly from sputum on the day of collection or the following day, with a cost of less than $35 per sample. Compared to AMR predictions based on whole-genome sequencing (WGS) using Mykrobe and TBProfiler, our amplicon-based analysis tool, ARapidTb, demonstrated superior resistance detection capabilities. When analyzing publicly available nanopore WGS datasets for 442 isolates, ARapidTb achieved agreement rates of 95.8% and 98.0%, outperforming Mykrobe (89.4% and 98.3%) and TBProfiler (75.6% and 89.8%).<br><br>CONCLUSIONS: Our study significantly reduces the time required for drug resistance detection, enabling quicker initiation of appropriate treatments and potentially improving patient outcomes and TB management.},
}
@article {pmid39821447,
year = {2025},
author = {Zhang, C and Li, J and Yan, F and Wang, Z and Zeng, X and Zhang, J},
title = {Comparative analysis of the complete chloroplast genome of seven Wikstroemia taxa (Thymelaeaceae) provides insights into the genome structure and phylogenetic relationships.},
journal = {Planta},
volume = {261},
number = {2},
pages = {40},
pmid = {39821447},
issn = {1432-2048},
support = {2022QB-153//Science Fund for Distinguished Young Scholars of Gansu Province/ ; KYQD2022013//Doctoral Start-up Foundation of Hexi University/ ; 22JR11RG225//the Natural Science Foundation of Gansu Province, China/ ; 202210740073//National College Students Innovation and Entrepreneurship Training Program/ ; 22CX8NA071//the Technology Innovation Guidance Program Project of Gansu Provincial "Research and Popularization of Ecological Planting Techniques for Economic Shrubs Daphne tangutica Maxim. in Qilian Mountains"/ ; No. 32260472//the National Natural Science Foundation of China/ ; },
mesh = {*Phylogeny ; *Genome, Chloroplast/genetics ; Wikstroemia/genetics ; Base Composition/genetics ; RNA, Transfer/genetics ; },
abstract = {New insights into the phylogeny of species in the family Thymelaeaceae and support of the recognition of D. genkwa and D. aurantiaca as species in the genus Wikstroemia are provided. Wikstroemia (Thymelaeaceae) is an economically important genus because some of its species are used in traditional medicine and also contribute to pulp production. The morphological characteristics of Wikstroemia species exhibit continuous natural variation, posing a challenge in accurately distinguishing this genus from its sister genera solely based on morphological traits. Consequently, the classification of, and phylogenetic relationships between, Wikstroemia and its sister genera, as inferred from morphological characteristics, remain contentious. Chloroplast genome information has proven to be a valuable tool in plant phylogeny. Here, we performed a comparative analysis of the chloroplast genomes of 15 species in the genus Wikstroemia, all of which exhibited typical quadripartite structures, with sizes ranging from 150,054 bp to 175,898bp. These genomes encoded 122-143 genes, including 79-95 protein-coding genes, 36-40 tRNA genes, and 8 rRNA genes. The overall GC content displayed minimal variation, ranging from 36.6% to 37.47%. The distributions of SSRs and codon bias exhibited similarities among Wikstroemia species. High variability hotspots were found in 15 intergenic spacers and 5 genes. Phylogenetic analyses consistently grouped all Wikstroemia species into a single clade. Notably, Daphne genkwa and D. aurantiaca were found to be nested within Wikstroemia, rather than being closely related to other Daphne species. Furthermore, phylogenetic analyses suggested that Wikstroemia is paraphyletic relative to Stellera chamaejasme. These findings provide new insights into the phylogeny of Wikstroemia and Daphne within the Thymelaeaceae, contributing to improved species identification and increasing the taxonomic and phylogenetic resolution of Wikstroemia.},
}
@article {pmid39821021,
year = {2025},
author = {Merle, C and Fre, S},
title = {Recording Lineage History with Cellular Barcodes in the Mammary Epithelium and in Breast Cancer.},
journal = {Advances in experimental medicine and biology},
volume = {1464},
number = {},
pages = {77-94},
pmid = {39821021},
issn = {0065-2598},
mesh = {*Breast Neoplasms/pathology/genetics/metabolism ; Humans ; *Cell Lineage/genetics ; Female ; Animals ; *Single-Cell Analysis/methods ; Mammary Glands, Human/pathology/cytology/metabolism ; Mammary Glands, Animal/pathology/metabolism/cytology ; Neoplastic Stem Cells/pathology/metabolism ; },
abstract = {Lineage tracing methods have extensively advanced our understanding of physiological cell behaviour in vivo and in situ and have vastly contributed to decipher the phylogeny and cellular hierarchies during normal and tumour development. In recent years, increasingly complex systems have been developed to track thousands of cells within a given tissue or even entire organisms. Cellular barcoding comprises all techniques designed to genetically label single cells with unique DNA sequences or with a combination of fluorescent proteins, in order to trace their history and lineage production in space and time. We distinguish these two types of cellular barcoding as genetic or optical barcodes. Furthermore, transcribed cellular barcodes can integrate the lineage information with single-cell profiling of each barcoded cell. This enables the potential identification of specific markers or signalling pathways defining distinct stem cell states during development, but also signals promoting tumour growth and metastasis or conferring therapy resistance.In this chapter, we describe recent advances in cellular barcoding technologies and outline experimental and computational challenges. We discuss the biological questions that can be addressed using single-cell dynamic lineage tracing, with a focus on the study of cellular hierarchies in the mammary epithelium and in breast cancer.},
}
@article {pmid39820073,
year = {2025},
author = {Yeh, YH and Kirschner, R},
title = {Study of endophytic fungi of Ipomoea pes-caprae reveals the superiority of in situ plant conservation over ex situ conservation from a mycological view.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {2040},
pmid = {39820073},
issn = {2045-2322},
support = {NSTC 110-2811-B-002-568//National Science and Technology Council/ ; NSTC 111-2811-B-002-092//National Science and Technology Council/ ; NSTC 112-2811-B-002-150//National Science and Technology Council/ ; MOST 108-2621-B-002-007//National Science and Technology Council/ ; 109-2621-B-002-004//National Science and Technology Council/ ; 110-2621-B-002-001-MY2//National Science and Technology Council/ ; },
mesh = {*Ipomoea/microbiology ; *Endophytes/genetics ; *Fungi/genetics/classification/isolation &amp; purification ; *Biodiversity ; Conservation of Natural Resources/methods ; Taiwan ; Phylogeny ; DNA Barcoding, Taxonomic ; },
abstract = {In nature conservation, ex situ and in situ conservation strategies are discussed for protecting endangered species of plants and animals. However, the impacts of these strategies on the microbes associated with these species are rarely considered. In our study, we chose the endophytic fungi of the pantropical creeping plant Ipomoea pes-caprae as representative coastal plant in two natural coastal populations and two botanical gardens in Taiwan as collection sites in order to investigate the potential effect of ex situ plantation on the biodiversity of microbes intimately associated with this plant. In a culture-dependent approach, endophytic fungi were isolated under axenic conditions and identified to species, genus, or higher taxonomic ranks with DNA barcodes and morphology. In addition to yielding ca. 800 strains and over 100 morphospecies, a principal component analysis (PCA) of the distribution of the dominant fungal species showed clear differences in the composition of endophytic fungal species depending on the sampling sites. We conclude that the endophytic fungi from the original site are replaced by other species in the ex situ plantations. Due to the limitations of ex situ conservation of microbes and from a mycological and microbial perspective, in situ conservation should outweigh ex situ approaches.},
}
@article {pmid39819888,
year = {2025},
author = {Sun, J and Philpott, M and Loi, D and Hoffman, G and Robson, J and Mehta, N and Calcutt, E and Gamble, V and Brown, T and Brown, T and Oppermann, U and Cribbs, AP},
title = {Enhancing single-cell transcriptomics using interposed anchor oligonucleotide sequences.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {67},
pmid = {39819888},
issn = {2399-3642},
support = {MR/V010182/1//RCUK | Medical Research Council (MRC)/ ; },
mesh = {*Single-Cell Analysis/methods ; *Oligonucleotides/genetics ; *Gene Expression Profiling/methods ; Humans ; Transcriptome ; RNA, Messenger/genetics/metabolism ; Sequence Analysis, RNA/methods ; },
abstract = {Single-cell transcriptomics, which utilises barcodes and unique molecular identifiers (UMIs) for polyA+ mRNA capture, is compromised by oligonucleotide synthesis errors. To address this, we modified the oligonucleotide capture design and integrated an interposed anchor between the barcode and the UMI. This design significantly reduces the need to discard reads due to synthesis inaccuracies. Our results demonstrate that this anchor-enhanced design substantially improves gene expression profiles in droplet-based single-cell sequencing analyses.},
}
@article {pmid39819789,
year = {2025},
author = {Chaumeau, V and Sawasdichai, S and Min, TZMMM and Kularbkeeree, T and Jaruwan, N and Gloria, N and Lee, NY and Trackoolchengkaew, M and Phanaphadungtham, M and Rongthong, P and Inta, A and Watthanaworawit, W and Nosten, F},
title = {Identification of Southeast Asian Anopheles mosquito species with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using a cross-correlation approach.},
journal = {Parasites &amp; vectors},
volume = {18},
number = {1},
pages = {8},
pmid = {39819789},
issn = {1756-3305},
support = {/WT_/Wellcome Trust/United Kingdom ; 220211/WT_/Wellcome Trust/United Kingdom ; OPP1177406//Bill and Melinda Gates Foundation/ ; },
mesh = {*Anopheles/classification/chemistry/genetics ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Animals ; Myanmar ; Southeast Asian People ; },
abstract = {BACKGROUND: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is proposed for mosquito species identification. The absence of public repositories sharing mass spectra and open-source data analysis pipelines for fingerprint matching to mosquito species limits the widespread use of this technology. The objective of this study was to develop a free open-source data analysis pipeline for Anopheles species identification with MALDI-TOF MS.<br><br>METHODS: Anopheles mosquitoes were captured in 33 villages in Karen (Kayin) state in Myanmar. A subset of 403 specimens was selected for inclusion in either the reference or the test panel (270 and 133 specimens, respectively). Three hundred fifty-nine specimens could be identified with DNA barcodes and were assigned to 21 sensu stricto species and five sibling species pairs or complexes. A total of 3584 mass spectra of the head of these specimens identified with DNA barcoding were acquired and the similarity between mass spectra was quantified using a cross-correlation approach adapted from the published literature. A reference mass spectra database was created using all spectra of the PCR-identified specimens assigned to the reference panel. A simulation experiment was carried out by querying the reference database with the spectra of the test panel to evaluate the performance of species identification with MALDI-TOF MS at varying thresholds of the cross-correlation index for the algorithm to output an identification result and with varying numbers of technical replicates for the tested specimens, considering PCR identification results as the reference.<br><br>RESULTS: With one spot and a threshold value of -14 for the cross-correlation index on the log scale, the sensitivity was 0.99 [95% credible interval (CrI): 0.98-1.00], the predictive positive value was 0.99 (95% CrI: 0.98-0.99), and the accuracy was 0.98 (95% CrI: 0.97-0.99). It was not possible to directly estimate the sensitivity and negative predictive value because there was no true negative (i.e., queries of species not referenced in the database) in the assessment.<br><br>CONCLUSIONS: The cross-correlation approach can be used to match mass spectral fingerprints to predefined taxa. MALDI-TOF MS is a valuable tool for rapid, accurate, and affordable identification of Anopheles species.},
}
@article {pmid39816673,
year = {2025},
author = {Marquisseau, A and Canale-Tabet, K and Labarthe, E and Pascal, G and Klopp, C and Pornon, A and Escaravage, N and Rudelle, R and Vignal, A and Ouin, A and Ollivier, M and Pichon, M},
title = {Building a reliable 16S mini-barcode library of wild bees from Occitania, south-west of France.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e137540},
pmid = {39816673},
issn = {1314-2828},
abstract = {BACKGROUND: DNA barcoding and metabarcoding are now powerful tools for studying biodiversity and especially the accurate identification of large sample collections belonging to diverse taxonomic groups. Their success depends largely on the taxonomic resolution of the DNA sequences used as barcodes and on the reliability of the reference databases. For wild bees, the barcode sequences coverage is consistently growing in volume, but some incorrect species annotations need to be cared for. The COI (Cytochrome Oxydase subunit 1) gene, the most used in barcoding/metabarcoding of arthropods, suffers from primer bias and difficulties for covering all wild bee species using the classical Folmer primers.<br><br>NEW INFORMATION: We present here a curated database for a 250 bp mini-barcode region of the 16S rRNA gene, suitable for low-cost metabarcoding wild bees in applications, such as eDNA analysis or for sequencing ancient or degraded DNA. Sequenced specimens were captured in Occitania (south-west of France) and morphologically identified by entomologists, with a total of 530 individuals belonging to 171 species and 19 genera. A customised workflow including distance-tree inferences and a second round of entomologist observations, when necessary, was used for the validation of 348 mini-barcodes covering 148 species. Amongst them, 93 species did not have any 16S reference barcode available before our contribution. This high-quality reference library data are freely available to the scientific community, with the aim of facilitating future large-scale characterisation of wild bee communities in a context of pollinators' decline.},
}
@article {pmid39814875,
year = {2025},
author = {Elzain, IA and Idris, AB and Karim, AA and Ahmed, NM and Elzaki, SG and Yılmaz, S and Hassan, MA and Abdalla, HS},
title = {Analysis of DNA cox1 barcoding revealed novel haplotype in Schistosoma haematobium isolated from Western Sudan.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {2062},
pmid = {39814875},
issn = {2045-2322},
mesh = {Humans ; Sudan/epidemiology ; *Haplotypes ; Child ; Animals ; *Schistosoma haematobium/genetics/isolation &amp; purification ; Adolescent ; Male ; *Schistosomiasis haematobia/parasitology/epidemiology/genetics ; Cross-Sectional Studies ; Female ; Young Adult ; *DNA Barcoding, Taxonomic/methods ; Child, Preschool ; Phylogeny ; Feces/parasitology ; Cyclooxygenase 1/genetics ; Genetic Variation ; Electron Transport Complex IV/genetics ; },
abstract = {Schistosomiasis poses a significant global health threat, particularly in tropical and subtropical regions like Sudan. Although numerous epidemiological studies have examined schistosomiasis in Sudan, the genetic diversity of Schistosoma haematobium populations, specifically through analysis of the mtcox1 gene, remains unexplored. This study aimed to investigate the risk factors associated with urogenital schistosomiasis among school pupils in El-Fasher, Western Sudan, as well as the mtcox1 genetic diversity of human S. haematobium in this region. A cross-sectional study was conducted among school pupils aged 4 to 19 years. In total, 196 urine samples and 196 fecal samples were collected from participants across schools, health centers, and refugee camps in El-Fasher. Samples were examined using simple centrifugation/sedimentation technique and formol-ether concentration method to detect S. haematobium and S. mansoni eggs, respectively. S. haematobium mtcox1 partial gene was amplified and sequenced by the Sanger technique. A neighbor-joining phylogenetic tree was generated by MEGA software, and a haplotype network was constructed using PopART v.1.7 with the median-joining network method. In this study, S. haematobium was detected in 6.1% (12/196) of the participants while no S. mansoni ova were observed in fecal samples. The infection was more common among those who relied on indirect water supply like tankers (6, 50%). No infection was observed among residents of refugee camps. Only eight samples were PCR-positive, which were successfully sequenced, and included in the genetic diversity analysis. A unique haplotype (Hap_1) with no sequence diversity was found among cox1 sequences from El-Fasher strains. Both El-Fasher S. haematobium haplotype (Hap_1) and Gezira haplotype (Hap_31) fall within the mainland Africa group (group 1). In conclusion, this study identified a novel S. haematobium strain and provides insights into the evolutionary history and phylogeography of S. haematobium in Sudan, particularly in the western region. This genetic data could help in the control and monitoring of urogenital schistosomiasis in this region. For the first time, we utilized the DNA mtcox1 barcoding to investigate S. haematobium haplotypes in Western Sudan.},
}
@article {pmid39814794,
year = {2025},
author = {Yassin, S and Elsohafy, SM and El-Hawiet, A and Abdel-Kader, MS and Ghareeb, DA and Darwish, FA and Amer, ME},
title = {Comparative phytochemical and pharmacological analysis of two cultivars of Annona squamosa L. cultivated in Egypt.},
journal = {NPJ science of food},
volume = {9},
number = {1},
pages = {8},
pmid = {39814794},
issn = {2396-8370},
abstract = {This study compared two Annona squamosa L. cultivars, Abdelrazik (Annona A.) and Balady (Annona B.), in terms of their chemical profile, in vitro cytotoxicity against HCT-116 and A549 cell lines, and total acetogenin. In addition, the two cultivars pulp were compared regarding carbohydrates and magnesium ions content and immunomodulating activity. The two cultivars were also differentiated genetically by DNA barcoding using the universal primer matK and the specific primer Annona squamosa matK. The results showed that Annona A. seeds had higher acetogenin content and exhibited more potent cytotoxic activity against the two cell lines. In contrast, Annona B. pulp had higher carbohydrate content and lower magnesium ions content. The splenic lymphocyte proliferation assay revealed that Annona A. pulp extract was slightly more active as an immunostimulant. The specific primer used for DNA barcoding was more effective for species identification, while the universal primer was better for cultivar differentiation. Overall, our findings indicate the potential for using active compounds of Annona squamosa L. cultivars to develop new therapeutic agents for cancer therapy and immune enhancement.},
}
@article {pmid39813480,
year = {2025},
author = {Câmara, PEAS and Pellizzari, FM and Lopes, FAC and Amorim, ET and Bones, FLV and Anjos, DA and Carvalho-Silva, M and Convey, P and Rosa, LH},
title = {DNA metabarcoding reveal hidden diversity of periphytic eukaryotes on marine Antarctic macroalgae.},
journal = {Anais da Academia Brasileira de Ciencias},
volume = {96},
number = {suppl 2},
pages = {e20240570},
doi = {10.1590/0001-3765202420240570},
pmid = {39813480},
issn = {1678-2690},
mesh = {Antarctic Regions ; *Seaweed/classification/genetics ; *DNA Barcoding, Taxonomic ; *Biodiversity ; Eukaryota/classification/genetics ; },
abstract = {Polar marine macroalgae thrive in extreme conditions, often displaying geographic isolation and high degree of endemism. The "phycosphere" refers to the zone around the algae inhabited by microrganisms. Our study used DNA metabarcoding to survey the eukaryotic communities associated with seven seaweed species obtained at King George Island (South Shetland Islands, maritime Antarctic), including two Rhodophyta, two Chlorophyta and three Phaeophyceae. The ITS2 region was used as a barcode and our analysis yielded 77 eukaryotic ASVs spanning five Kingdoms (Fungi, Metazoa, Chromista, Protozoa, and Viridiplantae) and ten phyla (Ascomycota, Basidiomycota, Cercozoa, Ciliophora, Ochrophyta, Amebozoa, Chlorophyta, Rhodophyta, Bryophyta and Cnidaria). Additionally, we identified 14 potential new occurrence records for Antarctica. Ciliates and green algae were the most species-rich groups. The most abundant assigned associated species was Monostroma angicava (Chrorophyta). Within the macroalgal, the Chlorophyceans Ulothrix sp. hosted the greatest number of taxa, followed by Monostroma hariotii. Our data suggested that Antarctic macroalgae host a rich diversity of associated organisms and the biodiversity associated with the phycosphere remains underestimated.},
}
@article {pmid39813353,
year = {2025},
author = {Trende, R and Darling, TL and Gan, T and Wang, D and Boon, ACM},
title = {Barcoded SARS-CoV-2 viruses define the impact of duration and route of exposure on the transmission bottleneck in a hamster model.},
journal = {Science advances},
volume = {11},
number = {3},
pages = {eads2927},
pmid = {39813353},
issn = {2375-2548},
support = {75N93021C00016/AI/NIAID NIH HHS/United States ; R01 AI169022/AI/NIAID NIH HHS/United States ; U01 AI151810/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; *SARS-CoV-2/physiology/genetics/pathogenicity ; *COVID-19/transmission/virology ; Cricetinae ; *Disease Models, Animal ; Lung/virology ; Humans ; Virus Shedding ; Trachea/virology ; },
abstract = {The transmission bottleneck, defined as the number of viruses shed from one host to infect another, is an important determinant of the rate of virus evolution and the level of immunity required to protect against virus transmission. Despite its importance, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission bottleneck remains poorly characterized. We adapted a SARS-CoV-2 reverse genetics system to generate a pool of >200 isogenic SARS-CoV-2 viruses harboring specific 6-nucleotide barcodes, infected donor hamsters with this pool, and exposed contact hamsters to paired infected donors, varying the duration and route of exposure. Following exposure, the nasal turbinates, trachea, and lungs were collected and the number of barcodes in each tissue was enumerated. We found that longer and more direct exposures increased the transmission bottleneck and that the upper airway is the primary source of transmitted virus in this model. Together, these findings highlight the utility of barcoded viruses as tools to rigorously study virus transmission.},
}
@article {pmid39811811,
year = {2024},
author = {Duan, HN and Jiang, YZ and Yang, JB and Cai, J and Zhao, JL and Li, L and Yu, XQ},
title = {Skmer approach improves species discrimination in taxonomically problematic genus Schima (Theaceae).},
journal = {Plant diversity},
volume = {46},
number = {6},
pages = {713-722},
pmid = {39811811},
issn = {2468-2659},
abstract = {Genome skimming has dramatically extended DNA barcoding from short DNA fragments to next generation barcodes in plants. However, conserved DNA barcoding markers, including complete plastid genome and nuclear ribosomal DNA (nrDNA) sequences, are inadequate for accurate species identification. Skmer, a recently proposed approach that estimates genetic distances among species based on unassembled genome skims, has been proposed to effectively improve species discrimination rate. In this study, we used Skmer to identify species based on genomic skims of 47 individuals representing 10 out of 13 species of Schima (Theaceae) from China. The unassembled reads identified six species, with a species identification rate of 60%, twice as high as previous efforts that used plastid genomes (27.27%). In addition, Skmer was able to identify Schima species with only 0.5× sequencing depth, as six species were well-supported with unassembled data sizes as small as 0.5 Gb. These findings demonstrate the potential for Skmer approach in species identification, where nuclear genomic data plays a crucial role. For taxonomically difficult taxa such as Schima, which have diverged recently and have low levels of genetic variation, Skmer is a promising alternative to next generation barcodes.},
}
@article {pmid39811021,
year = {2025},
author = {Mutafchiev, Y and Roman, Y and Griffiths, K and Kenderov, L and Michalski, ML},
title = {DNA-elucidated life cycle of a highly pathogenic avian nematode: Streptocara incognita (Spirurida: Acuariidae) and its morphological development from infective third-stage larva to adult.},
journal = {Current research in parasitology &amp; vector-borne diseases},
volume = {7},
number = {},
pages = {100238},
pmid = {39811021},
issn = {2667-114X},
abstract = {Streptocara incognita Gibson, 1968 is an acuariid nematode associated with lethal cases of streptocarosis of diverse aquatic birds in North America and Europe. This study reports S. incognita as an agent causing severe and fatal necrosis of the oesophagus and proventriculus of anatids, i.e. Somateria mollissima (L.), Marmaronetta angustirostris (Ménétriés), Tadorna tadorna (L.) and Spatula querquedula (L.), kept in open pens in the Zoological Park, Clères, France. Comparative analysis of 12S rRNA gene sequences revealed that third-stage infective nematode larvae found in the amphipod Gammarus pulex pulex (L.) in the river passing through the pens belong to S. incognita thus elucidating the life cycle of this species. A partial sequence of the cox1 gene was also generated. To complement the brief original description of S. incognita, a detailed morphological description of the adult stages is provided based on light and scanning electron microscopy. Additionally, morphological data on the developing third- and fourth-stage larvae found in the definitive host and third-stage infective nematode larvae found in G. pulex pulex are also provided. This is the first record of an intermediate host of S. incognita. Somateria mollissima, M. angustirostris and S. querquedula are new host records.},
}
@article {pmid39809848,
year = {2025},
author = {Kniesz, K and Hoffman, L and Martínez Arbizu, P and Kihara, TC},
title = {High genomic connectivity within Anatoma at hydrothermal vents along the Central and Southeast Indian Ridge.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1971},
pmid = {39809848},
issn = {2045-2322},
mesh = {*Hydrothermal Vents ; Animals ; *Gastropoda/genetics/classification ; India ; Ecosystem ; Phylogeny ; Gene Flow ; DNA Barcoding, Taxonomic ; Genomics/methods ; },
abstract = {Hydrothermal vents are ecosystems inhabited by a highly specialized fauna. To date, more than 30 gastropod species have been recorded from vent fields along the Central and Southeast Indian Ridge and all of them are assumed to be vent-endemic. During the INDEX project, 701 representatives of the genus Anatoma (Mollusca: Vetigastropoda) were sampled from six abyssal hydrothermal vent fields. Traditional morphology and COI barcoding of Hoffman et al. (Eur J Taxon 826:135-162, 2022) were combined with 2b-RAD sequencing to investigate the anatomid community structure and connectivity between the different vent fields. Consequently, 2b-RAD sequencing supported the primary species hypothesis (based on morphology) for 125 individuals of the recently described taxa A. discapex, A. declivis, A. laevapex and A. paucisculpta. We assigned 22 additional specimens to species with 2b-RAD sequencing and updated the community analyses that confirmed the pattern of expanding populations. Population structure and FST values indicated high connectivity along the six sampled vent fields for the three most abundant species. High levels of gene flow are suggested, pointing to high dispersal potential of the target species along the study area. However, low levels of heterozygosity revealed a small gene pool and therefore an increased vulnerability towards environmental change. Our results demonstrate that 2b-RAD sequencing, in combination with other molecular methods, can accurately characterise macrobenthic mollusc communities. Sequencing technology is an essential tool for ongoing monitoring. Furthermore, we highlight that the inferred molecular and ecological patterns provide valuable insights into hydrothermal vent ecosystems, which are crucial for the successful conservation of these ecosystems.},
}
@article {pmid39809825,
year = {2025},
author = {Eroğlu, M and Çelik, I and Düşükcan, M and Ünal, EM and Çoban, MZ and Gündüz, F and Keskin, E},
title = {DNA barcoding of invasive Gambusia holbrooki Girard, 1859 and Atherina boyeri Risso, 1810 inhabiting Upper Euphrates River Basin, Türkiye.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1907},
pmid = {39809825},
issn = {2045-2322},
support = {SUF-16.13//F&#x131;rat University Scientific Research Projects Coordination Office/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Introduced Species ; *Rivers ; *Cyprinodontiformes/genetics/classification ; Electron Transport Complex IV/genetics ; Turkey ; Phylogeny ; Lakes ; Biodiversity ; },
abstract = {The main contributor to Türkiye's abundant freshwater fish biodiversity is its geographic location. This fauna consists of endemic, native, and non-native fish species. The introduction of Gambusia holbrooki Girard, 1859 to Lake Amik in the 1920s for the biological control of malaria was the first introduction of nonnative species to Türkiye. Atherina boyeri Risso, 1810 and other nonnative fish species have recently been introduced to Türkiye's freshwaters. In this research, the first records of invasive Gambusia holbrooki (Keban Dam Lake, in Elazığ Province) and Atherina boyeri (Karakaya Dam Lake, in Elazığ Province) are cited from the Upper Euphrates River Basin in the Eastern Anatolia Region of Türkiye. In situ electrofishing equipment was used to gather the specimens. Fish muscle samples were used to extract genomic DNA, which was then used to barcode the mitochondrial cytochrome c oxidase subunit I (COI) gene to identify different species of fish. The identification of invasive fish species using DNA barcoding is an effective technique, as evidenced by the comparison of amplified COI sequences to the BLAST database.},
}
@article {pmid39807677,
year = {2025},
author = {Lin, YC and Lee, LR and Tsai, TH and Lin, J and Hsu, YS and Kesavan, M and Lin, YL and Chen, YF and Chen, JT},
title = {A Streamlined Approach to Anticounterfeiting Technologies: Patterned AAO Membranes Based on Photonic Crystal Effects with Tunable Color Shifts and pH Responsiveness.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {21},
number = {8},
pages = {e2409919},
pmid = {39807677},
issn = {1613-6829},
support = {//Center for Emergent Functional Matter Science of National Yang Ming Chiao Tung University/ ; NSTC 112-2628-E-A49-012//National Science and Technology Council/ ; NSTC 113-2628-E-A49-006//National Science and Technology Council/ ; NSTC113-2740-M-007-001//National Science and Technology Council/ ; },
abstract = {Anticounterfeiting technologies have become increasingly crucial due to the growing issue of counterfeit goods, particularly in high-value industries. Traditional methods such as barcodes and holograms are prone to replication, prompting the need for advanced, cost-effective, and efficient solutions. In this work, a practical application of anodic aluminum oxide (AAO) membranes are presented for anticounterfeiting, which addresses the challenges of high production costs and complex fabrication processes. Unlike previous approaches requiring metal coatings for color generation, this method uses commercial aluminum foils to produce colorful AAO membranes without metal layers. Elemental mapping suggests that impurities on the aluminum surface contribute to enhanced reflectivity, aiding photonic crystal formation. A two-step anodization process that creates patterned AAO membranes is further introduced, with the pattern clarity controlled by anodization time. Additionally, a pH-responsive film composed of 2-anilino-6-dibutylaminofluoran (ODB-2) and thermoplastic polyurethane (TPU) is integrated, enabling dynamic color changes under varying pH conditions, further enhancing the anticounterfeiting functionality. This streamlined approach provides a scalable and cost-effective solution for developing versatile AAO membranes for industrial anticounterfeiting applications.},
}
@article {pmid39805772,
year = {2024},
author = {Chen, ZY and Hua, ZY and Yuan, Y},
title = {[Establishment and application of chloroplast genome database with the largest number of species in world].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {49},
number = {23},
pages = {6257-6263},
doi = {10.19540/j.cnki.cjcmm.20240909.101},
pmid = {39805772},
issn = {1001-5302},
mesh = {*Genome, Chloroplast ; Databases, Genetic ; Phylogeny ; Microsatellite Repeats/genetics ; Plants/genetics/classification ; },
abstract = {The chloroplast genome is an important tool for studying plant classification, evolution, and the heterologous production of secondary metabolites and protein drugs. With advancements in sequencing technology and reductions in sequencing costs, chloroplast genome data have rapidly accumulated. However, existing chloroplast genome databases suffer from issues such as incomplete data, inadequate management, and inconsistent, inaccurate information, posing significant challenges for the development and utilization of the chloroplast genome. Therefore, it is urgently necessary to establish a database that provides comprehensive and reliable chloroplast genome information. This article provides a brief introduction to the Chloroplast Genome Information Resource(CGIR), the most comprehensive chloroplast genome database globally in terms of species coverage. The database, consisting of five modules, i.e.,(1) genomes,(2) genes,(3) simple sequence repeats(SSRs),(4) DNA barcodes, and(5) DNA signature sequences(DSSs), currently includes 34 923 chloroplast genome assemblies from 16 717 species. Based on the functionalities of these modules, the article systematically summarizes the progress in the application of the database in plant phylogenetic analysis, species identification, and chloroplast genetic engineering. The chloroplast genome database will be continuously updated in the future to provide a solid and reliable data foundation for chloroplast genome research, further promoting studies on traditional Chinese medicine(TCM)identification, resource conservation, and germplasm innovation.},
}
@article {pmid39805757,
year = {2024},
author = {Li, XY and Guo, H and Ma, MX and Xu, LW and Huang, YH and Zhang, Y and Yang, CP and He, F and Tian, XX},
title = {[Mini-barcode combined with ITS2 for identification of bulk Artemisiae Scopariae Herba].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {49},
number = {24},
pages = {6685-6691},
doi = {10.19540/j.cnki.cjcmm.20240912.101},
pmid = {39805757},
issn = {1001-5302},
mesh = {*Artemisia/genetics/chemistry/classification ; *DNA Barcoding, Taxonomic/methods ; *Phylogeny ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; },
abstract = {Artemisiae Scoporiae Herba is derived from Artemisia scoparia or A. capillaris. The accurate identification of the herbs, particularly when dealing with bulk samples, is critical for ensuring the quality and efficacy of the medicinal product. This study aimed to establish a comprehensive molecular approach by combining multiple markers for the precise identification of Artemisiae Scoporiae Herba. The ITS2 from A. scoparia, A. capillaris, and other common Artemisia species were retrieved from GenBank. MEGA was used to build a phylogenetic tree with these sequences, and the effectiveness of ITS2 in species identification was assessed. The analysis revealed that while ITS2 could distinguish Artemisiae Scoporiae Herba from other closely related species of Artemisia, it was insufficient to differentiate between A. scoparia and A. capillaris. To address this limitation, the chloroplast genome of A. capillaris was assembled and compared with the published chloroplast genomes of A. scoparia and A. capillaris, on the basis of which a DNA mini-barcode was developed. The rpoA-rps11 region was selected as the target for the development of mini-barcode due to its potential for distinguishing between these two species. Specific primers were designed to differentiate A. scoparia from A. capillaris. The ITS2 sequences and the newly developed mini-barcode were used together for Sanger sequencing to identify individual samples of Artemisiae Scoporiae Herba, while DNA metabarcoding was employed for the identification of bulk samples. The identification results of representative individual samples and bulk samples from different regions consistently confirmed A. capillaris. This study established a method that combined ITS2 and mini-barcode to identify bulk samples of Artemisiae Scoporiae Herba from different regions. This approach overcomes the limitations of morphological and chemical methods, enhancing species identification accuracy and supporting a stable supply of medicinal materials.},
}
@article {pmid39803186,
year = {2025},
author = {Yao, J and Zheng, Z and Xu, T and Wang, D and Pu, J and Zhang, Y and Zha, L},
title = {Chloroplast Genome Sequencing and Comparative Analysis of Six Medicinal Plants of Polygonatum.},
journal = {Ecology and evolution},
volume = {15},
number = {1},
pages = {e70831},
pmid = {39803186},
issn = {2045-7758},
abstract = {The genus Polygonatum boasts abundant germplasm resources and comprises numerous species. Among these, medicinal plants of this genus, which have a long history, have garnered attention of scholars. This study sequenced and analyzed the chloroplast genomes of six species of Polygonatum medicinal plants (P. zanlanscianense, P. kingianum, P. sibiricum, P. cyrtonema, P. filipes, and P. odoratum, respectively) to explore their interspecific relationships. The sequence length (154, 578-155, 807 bp) and genome structure were conserved among the six Polygonatum species, with a typical tetrad structure. Among the 127-131 genes contained in the genomes, 84-85 are protein-coding genes, 37-38 are transfer RNA genes, and 6-8 are ribosomal RNA genes. The genomes contained 64-76 simple sequence repeats (SSRs) and 36-62 long repetitive sequences. Codon bias patterns tended to use codons ending in A/T. In 30 types of codons with RSCU > 1, 93.3% ended in A/T of the six species. Twenty-one highly variable plastid regions were identified in the chloroplast genomes of the six medicinal plants. Furthermore, a phylogenetic analysis encompassing these and 53 other chloroplast genomes of Polygonatum species revealed that P. cyrtonema, P. odoratum, and P. filipes clustered together on one clade, whereas P. kingianum and P. zanlanscianense formed separate clades. Notably, P. sibiricum emerged as a standalone clade, and our phylogenetic tree reinforces the classification of P. sibiricum as forming a monophyly. This study provides a novel basis for intragenus taxonomy and DNA barcoding molecular identification within the genus Polygonatum medicinal plants.},
}
@article {pmid39802739,
year = {2025},
author = {Meng, Z and Zheng, Q and Wang, W and Zhu, Y and Li, Y and Dong, F and Luo, W and Zhang, Z and Wang, F and Shen, H and Xie, Q and Li, H},
title = {Oligo-FISH barcode chromosome identification system provides novel insights into the natural chromosome aberrations propensity in the autotetraploid cultivated alfalfa.},
journal = {Horticulture research},
volume = {12},
number = {1},
pages = {uhae266},
pmid = {39802739},
issn = {2662-6810},
abstract = {Alfalfa is one of the most economically valuable forage crops in the world. However, molecular cytogenetic studies in alfalfa lag far behind other cash crops and have reached a bottleneck. Here, we developed a novel chromosome identification system by designing 21 oligo probes in specific regions of each chromosome, which can be used as a barcode to simultaneously distinguish all chromosomes in a cell. Using this system, we revealed the chromosome karyotype features and evolutionary differences among 10 cultivated alfalfa varieties. Interestingly, we also found two chromosomal variation types, i.e. aneuploidy and large chromosomal segment deletions in the seeds of three alfalfa varieties. Variation frequency analysis showed that only 7/173 seeds in those three alfalfa varieties had chromosome aberrations, which indicated that the inheritance and meiosis of alfalfa had evolved to a relatively stable state. Remarkably, 4/7 variation seeds were chromosome 2 aberrations, suggesting that chromosome 2 appears to be more susceptible to natural chromosomal aberrations than other chromosomes during inheritance. DNA sequence variation analysis showed that the difference of presence and absence variations (PAVs) among homologous copies of chromosome 2 was larger than that of the other seven chromosomes. We suggest that such large PAV divergence among homologous copies may provide the physical basis for natural chromosome 2 aberrations propensity. Our study provides a valuable and efficient tool for alfalfa's molecular cytogenetics and sheds new insights into the propensity for natural chromosome aberrations during autopolyploid inheritance.},
}
@article {pmid39801509,
year = {2025},
author = {Hao, L and Yu, K and Zhang, F},
title = {Description of five new species from southern China, with note on the type species of Latouchia Pocock, 1901 (Araneae, Halonoproctidae).},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e137852},
pmid = {39801509},
issn = {1314-2828},
abstract = {BACKGROUND: The genus Latouchia Pocock, 1901 previously included 25 known species and one subspecies from Asia, 12 species and one subspecies were reported in China.<br><br>NEW INFORMATION: Five new species of Latouchia Pocock, 1901 from southern China are described: L.calcicola sp. nov. (&#x2642;&#x2640;) from Hainan, L.jinyun sp. nov. (&#x2642;&#x2640;) from Chongqing, L.linmufu sp. nov. (&#x2642;&#x2640;) from Hunan, L.wenchuan sp. nov. (&#x2642;) from Sichuan and L.yaoi sp. nov. (&#x2642;&#x2640;) from south part of Shaanxi. DNA barcodes of the new species described herein are provided. The potential error in the previous illustrations of the alleged male of L.fossoria Pocock, 1901 (type species of the genus) is pointed out.},
}
@article {pmid39799216,
year = {2025},
author = {Shi, C and Guo, Y and Yao, L and Xu, Y and Zhou, J and Hua, M},
title = {Development of a mitochondrial mini-barcode and its application in metabarcoding for identification of leech in traditional Chinese medicine.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1698},
pmid = {39799216},
issn = {2045-2322},
mesh = {Animals ; *Leeches/genetics ; *DNA Barcoding, Taxonomic/methods ; *Medicine, Chinese Traditional ; RNA, Ribosomal, 16S/genetics ; Genome, Mitochondrial ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Phylogeny ; },
abstract = {In Traditional Chinese Medicine (TCM), the medicinal leech is vital for treatments to promote blood circulation and eliminate blood stasis. However, the prevalence of counterfeit leech products in the market undermines the quality and efficacy of these remedies. Traditional DNA barcoding techniques, such as the COI barcode, have been limited in their application due to amplification challenges. This study identified high variability in the 16 S rRNA gene within the mitochondrial genome across five leech species, leading to the development of a novel 219 bp mini-barcode. Compared with the traditional COI barcode, our mini-barcode showed remarkable identification efficiency, classifying 142 out of 147 leech samples from fresh and processed materials. In contrast, the COI barcode could only successfully identify 79 out of the 147 samples. In the case of seven batches of leech decoction pieces, the mini-barcode identified six, whereas the COI barcode only recognized one. Additionally, the mini-barcode effectively discerned five leech species within Chinese patent medicines when combined with metabarcoding technology. These results confirm the mini-barcode's potential as a reliable tool for rapidly and precisely identifying leech species in TCM products.},
}
@article {pmid39795359,
year = {2025},
author = {Jiamahate, A and Bozorov, TA and Wang, J and Zhang, J and Zhang, H and Wang, X and Yang, H and Zhang, D},
title = {Insights from DNA Barcodes-Based Phylogenetic Analysis of Medicinal Plants and Estimation of Their Conservation Status: A Case Study in the Tianshan Wild Forest, China.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {1},
pages = {},
pmid = {39795359},
issn = {2223-7747},
support = {Grant No.2021xjkk0500//Third Xinjiang Scientific Expedition Program/ ; 2021-XBQNXZ-015//the West Light Talents Cultivation Program of the Chinese Academy of Sciences/ ; Grant No. 31700289//the National Natural Science Foundation of China/ ; 2022D01A354//the Natural Science Foundation of the Xinjiang Uygur Autonomous Region/ ; ZDBS-LY-SM009//Key Research Program of Frontier Sciences, Chinese Academy of Sciences/ ; 2022TSYCLJ0049//Leading Talents in Technological Innovation programme/ ; },
abstract = {The Tianshan wild fruit forest region is a vital repository of plant biodiversity, particularly rich in the unique genetic resources of endemic medicinal plants in this ecological niche. However, human activities such as unregulated mining and excessive grazing have led to a significant reduction in the diversity of these medicinal plants. This study represents the first application of DNA barcoding to 101 medicinal plants found in the Tianshan wild fruit forests, using three genetic loci along with morphological identification methods. A phylogenetic analysis was performed to delineate species relationships. The results indicate that the internal transcribed spacer (ITS) region has been identified as the most reliable barcode for species identification across different families, while combining data from multiple gene segments can improve species detection. Moreover, the Analytical Hierarchy Process (AHP) was employed to assess and prioritize the 101 medicinal plants, highlighting 23 species as candidates for urgent conservation efforts in the region. The approaches and insights from this study provide a significant benchmark for DNA barcoding studies on medicinal plants with local significance and establish an evaluative framework for the conservation of biodiversity and the surveillance of genetic resources among medicinal plants in the Tianshan wild fruit forest area.},
}
@article {pmid39794360,
year = {2025},
author = {Maulding, ND and Zou, J and Zhou, W and Metcalfe, C and Stuart, JM and Ye, X and Hafner, M},
title = {Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer.},
journal = {NPJ systems biology and applications},
volume = {11},
number = {1},
pages = {5},
pmid = {39794360},
issn = {2056-7189},
mesh = {Humans ; *Breast Neoplasms/genetics/drug therapy ; *Drug Resistance, Neoplasm/genetics ; Female ; Cell Line, Tumor ; Pyridines/pharmacology ; Gene Expression Regulation, Neoplastic/genetics ; Piperazines/pharmacology ; Single-Cell Analysis/methods ; },
abstract = {Understanding transcriptional heterogeneity in cancer cells and its implication for treatment response is critical to identify how resistance occurs and may be targeted. Such heterogeneity can be captured by in vitro studies through clonal barcoding methods. We present TraCSED (Transformer-based modeling of Clonal Selection and Expression Dynamics), a dynamic deep learning approach for modeling clonal selection. Using single-cell gene expression and the fitness of barcoded clones, TraCSED identifies interpretable gene programs and the time points at which they are associated with clonal selection. When applied to cells treated with either giredestrant, a selective estrogen receptor (ER) antagonist and degrader, or palbociclib, a CDK4/6 inhibitor, pathways dynamically associated with resistance are revealed. For example, ER activity is associated with positive selection around day four under palbociclib treatment and this adaptive response can be suppressed by combining the drugs. Yet, in the combination treatment, one clone still emerged. Clustering based on partial least squares regression found that high baseline expression of both SNHG25 and SNCG genes was the primary marker of positive selection to co-treatment and thus potentially associated with innate resistance - an aspect that traditional differential analysis methods missed. In conclusion, TraCSED enables associating features with phenotypes in a time-dependent manner from scRNA-seq data.},
}
@article {pmid39792883,
year = {2025},
author = {Park, JW and Park, K and Kwak, IS},
title = {First report of a major management target species, chironomid Paratanytarsus grimmii (Diptera: Chironomidae) larvae, in drinking water treatment plants (DWTPs) in South Korea.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0315390},
pmid = {39792883},
issn = {1932-6203},
mesh = {Animals ; *Chironomidae/genetics/classification ; *Larva/genetics ; Republic of Korea ; Drinking Water ; Water Purification ; Phylogeny ; },
abstract = {Ensuring the supply of safe and high-quality drinking water can be compromised by the presence of chironomid larvae in drinking water treatment plants (DWTPs), which may contaminate municipal water systems through freshwater resources. Chironomids are dominant species known for their resilience to a broad range of extreme aquatic environments. This study aimed to identify the morphological characteristics and obtain genetic information of the chironomid Paratanytarsus grimmii found in the water intake source and freshwater resource of DWTPs in Korea, highlighting the potential possibility of a parthenogenetic chironomid outbreak within DWTP networks. The distribution of chironomid larvae at the water intake source site (DY) of the Danyang DWTP and the freshwater resource (ND) of the Nakdong River was investigated. A total of 180 chironomid individuals, encompassing three subfamilies and six species from six 6 genera were identified at the DY site, with Procladius nigriventris being the dominant species. At the ND site, fifty chironomid individuals, encompassing two subfamilies and six species from six genera, were identified, with Cricotopus sylvestris being the dominant species. The morphological characteristics of the head capsule, mentum, mandible, and antennae of six P. grimmii larvae collected from the DY and ND sites were characterized. DNA barcoding and phylogenetic analysis revealed distinct mitochondrial diversities between the P. grimmii larvae from DY and those from ND. These results provide crucial information for the morphological identification and DNA barcoding of the key management target chironomid P. grimmii larvae, which can be used to detect the occurrence of this chironomid species in DWTPs.},
}
@article {pmid39791888,
year = {2025},
author = {Manmana, Y and Kinugasa, S and Hiruta, Y and Citterio, D},
title = {Development of a Semiquantitative Barcode Readout Approach for Paper-Based Analytical Devices (PADs) for Enzymatic H2O2 and Glucose Detection.},
journal = {Analytical chemistry},
volume = {97},
number = {3},
pages = {1500-1506},
pmid = {39791888},
issn = {1520-6882},
mesh = {*Hydrogen Peroxide/chemistry ; *Paper ; *Horseradish Peroxidase/chemistry/metabolism ; Glucose/analysis/metabolism ; 3,3'-Diaminobenzidine/chemistry ; Biosensing Techniques ; Smartphone ; Humans ; },
abstract = {The integration of barcode technology with smartphones on paper-based analytical devices (PADs) presents a promising approach to bridging manual detection with digital interpretation and data storage. However, previous studies of 1D barcode approaches have been limited to providing only a "yes/no" response for analyte detection. Herein, a method of using barcode readout for semiquantitative signal detection on PADs has been achieved through the integration of barcode technology with a distance-based measurement concept on PADs. To demonstrate the feasibility of this concept, a PAD fabrication strategy incorporating barcodes was explored, using the enzymatic reaction between horseradish peroxidase (HRP), 3,3'-diaminobenzidine (DAB), and H2O2 as a model system. The enzyme-catalyzed polymerization of DAB to polyDAB in the presence of hydrogen peroxide results in the appearance of color observable by the naked eye inside a paperfluidic channel, with the color-changed length depending on the H2O2 concentration. At the same time, the barcode pattern displayed as a result of this distance-based color evolution overlaid with a paper-based barcode layer can be read using a smartphone application. Parameters affecting the signal readout performance were studied. The developed device can be used to detect H2O2 concentrations in the range of 0.25 to 10 mM within 90 min with 79.6% of barcode signals correctly readable. Additionally, results from different smartphone models showed a consistent reading performance (78.4-79.6%). Finally, the quantification of glucose levels in artificial urine samples was demonstrated. This developed PAD signaling strategy offers end-users more simplicity and can be used as a standalone device or in conjunction with other digital devices.},
}
@article {pmid39789982,
year = {2025},
author = {Xu, Y and Chan, MTJ and Yang, M and Meng, H and Chen, CH},
title = {Time-resolved single-cell secretion analysis via microfluidics.},
journal = {Lab on a chip},
volume = {25},
number = {5},
pages = {1282-1295},
doi = {10.1039/d4lc00904e},
pmid = {39789982},
issn = {1473-0189},
mesh = {*Single-Cell Analysis/instrumentation ; Humans ; *Microfluidic Analytical Techniques/instrumentation ; Animals ; Time Factors ; },
abstract = {Revealing how individual cells alter their secretions over time is crucial for understanding their responses to environmental changes. Key questions include: When do cells modify their functions and states? What transitions occur? Insights into the kinetic secretion trajectories of various cell types are essential for unraveling complex biological systems. This review highlights seven microfluidic technologies for time-resolved single-cell secretion analysis: 1. Microwell real-time electrical detection: uses microelectrodes for precise, cell-specific, real-time measurement of secreted molecules. 2. Microwell real-time optical detection: employs advanced optical systems for real-time, multiplexed monitoring of cellular secretions. 3. Microvalve real-time optical detection: dynamically analyzes secretions under controlled in situ stimuli, enabling detailed kinetic studies at the single-cell level. 4. Droplet real-time optical detection: provides superior throughput by generating droplets containing single cells and sensors for high-throughput screening. 5. Microwell time-barcoded optical detection: utilizes sequential barcoding techniques to facilitate scalable assays for tracking multiple secretions over time. 6. Microvalve time-barcoded optical detection: incorporates automated time-barcoding via micro-valves for robust and scalable analysis. 7. Microwell time-barcoded sequencing: captures and labels secretions for sequencing, enabling multidimensional analysis, though currently limited to a few time points and extended intervals. This review specifically addresses the challenges of achieving high-resolution timing measurements with short intervals while maintaining scalability for single-cell screening. Future advancements in microfluidic devices, integrating innovative barcoding technologies, advanced imaging technologies, artificial intelligence-powered decoding and analysis, and automations are anticipated to enable highly sensitive, scalable, high-throughput single-cell dynamic analysis. These developments hold great promise for deepening our understanding of biosystems by exploring single-cell timing responses on a larger scale.},
}
@article {pmid39787166,
year = {2025},
author = {Guarniero, I and Stancampiano, L and Franch, R and Armaroli, E and Macchioni, F and Negrisolo, E},
title = {Genetic variability and population structure analysis of Protostrongylus oryctolagi (Nematoda: Protostrongylidae) in Lepus europaeus from Central and Northern Italy.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0313998},
pmid = {39787166},
issn = {1932-6203},
mesh = {Animals ; Italy ; *Genetic Variation ; *Haplotypes ; Hares/genetics/parasitology ; Phylogeny ; Genetics, Population ; },
abstract = {Nematodes are abundant and ubiquitous animals which are poorly known at intraspecific level. This work represents the first attempt to fill the gap on basic knowledge of genetic variability and differentiation in Protostrongylus oryctolagi, a nematode parasite of lagomorphs. 68 cox1 sequences were obtained from brown hares collected in five locations in Northern and Central Italy, highlighting the presence of a high amount of genetic variation inside this species. The eleven haplotypes identified (Haplotype diversity equal to 0.702) were split into two lineages: lineage A (comprising six different haplotypes, A1-A6) and lineage B (B1-B5). The mean intra-lineage amount of genetic variation was 0.3%, whereas the inter-lineage percentage of variation was ten-fold higher (3%). These two lineages were non-randomly distributed in the investigated areas. Lineage A showed a preference for Central Italy (Tuscany) even if it was sporadically found also in northern territories (Emilia-Romagna), while B-haplotypes were present exclusively in Emilia-Romagna. The analysis of molecular variance identified two main barriers to gene flow: (i) a strong major one which separate samples of Central Italy (PIA and GR7) from the northern ones (RE1, RE3 and MO1; ΦST = 0.750, P = 0.00); (ii) a secondary faint barrier which separates Pianosa island from Grosseto (ΦST = 0.133, P = 0.00). Any difference was found among northern samples (ΦST = 0.009, P = 0.00). The observed data may be explained by several factors ranging from the parasite's biology (presence of a narrow host spectrum), the final host's behaviour (small home range), the natural dispersion of the host-parasite dyad occurred in past or the recent passive men-mediated migration. Finally, the presence of unconventional shortened amplicons revealed the presence of NUMTs (nuclear copy of mitochondrial genes) in the P. oryctolagi nuclear genome, suggesting caution when using DNA barcode as unique marker for the identification of species belonging to this genus. "In short, if all the matter in the universe except the nematodes were swept away, our world would still be dimly recognizable". Nathan Augustus Cobb, from "Nematodes and Their Relationships", 1915.},
}
@article {pmid39781258,
year = {2025},
author = {Fernando, MATM and Fu, J and Adamowicz, SJ},
title = {Testing Phylogenetic Placement Accuracy of DNA Barcode Sequences on a Fish Backbone Tree: Implications of Backbone Tree Completeness and Species Representation.},
journal = {Ecology and evolution},
volume = {15},
number = {1},
pages = {e70817},
pmid = {39781258},
issn = {2045-7758},
abstract = {Advancements in DNA sequencing technology have facilitated the generation of a vast number of DNA sequences, posing opportunities and challenges for constructing large phylogenetic trees. DNA barcode sequences, particularly COI, represent extensive orthologous sequences suitable for phylogenetic analysis. Phylogenetic placement analysis offers a promising method to integrate COI data into tree-building efforts, yet the impacts of backbone tree completeness and species composition remain under-explored. Using a dataset comprising 27 genes and 4520 species of bony fishes, we assessed the accuracy of phylogenetic inference by "placing" COI sequences onto backbone trees. The backbone tree completeness was varied by subsampling 20%, 40%, 60%, 80%, and 99% of the total species separately, followed by placement of those missing species based on their COI sequences using software packages EPA-ng and APPLES. We also compared the effects of biased, random, and stratified sampling strategies; the latter ensured the representation of all major lineages (Family) of bony fish. Our findings indicate that the placement accuracy is consistently high across all levels of backbone tree completeness, where 70%-78% missing species are correctly placed (by EPA-ng) in the same locations as the reference tree derived from the complete data. High completeness produces slightly high placement accuracy, although in many cases the differences are nonsignificant. For example, at the 99% completeness level with stratified sampling, EPA-ng placed 78% missing species correctly, and when only considering placement with high confidence (LWR > 0.9), the percentage is 87%. Additionally, stratified sampling outperforms random sampling in most cases, and biased sampling has the worst performance. The likelihood-based EPA-ng consistently provide higher accurate placements than the distance-based APPLES. In conclusion, COI-based placement analysis represents a potential route of using the available vast barcoding data for building large phylogenetic trees.},
}
@article {pmid39776788,
year = {2025},
author = {Sander, PN and Gillen Miller, JT and Lairson, LL},
title = {Induced cell phenotype activity recording of DNA-tagged ligands.},
journal = {RSC chemical biology},
volume = {6},
number = {2},
pages = {273-280},
pmid = {39776788},
issn = {2633-0679},
abstract = {Based on their ability to canvas vast genetic or chemical space at low cost and high speed, DNA-encoded libraries (DEL) have served to enable both genomic and small molecule discovery. Current DEL chemical library screening approaches focus primarily on in vitro target-based affinity or activity. Here we describe an approach to record the phenotype-based activity of DNA-encoded small molecules on their cognate barcode in living cells. We transfected chloroalkane-derivatized DNA barcodes carrying photoreleasable small molecules into cells. Following photorelease, bioactive compounds induced expression of a reporter gene cassette containing self-labeling HaloTag protein that becomes covalently modified by encoding barcodes. We demonstrate that we can recover activity information from cells that received active compound following immunoprecipitation-based enrichment. This generalizable approach should enable future strategies that facilitate phenotype-based screens of DNA-encoded chemical libraries in complex cellular or organism level systems.},
}
@article {pmid39775746,
year = {2024},
author = {de Freitas, EA and Dos Santos, DB and Moraes Ferreira, CS and Silva-Oliveira, C and Evangelista-Gomes, GF and Veneza, IB},
title = {Integrative use of DNA barcode and morphology reveal high level of diversity in the ornamental fish on the lower Amazon basin.},
journal = {PloS one},
volume = {19},
number = {12},
pages = {e0316455},
pmid = {39775746},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Biodiversity ; Electron Transport Complex IV/genetics ; Brazil ; Phylogeny ; Rivers ; Lakes ; Characiformes/genetics/classification ; },
abstract = {The Amazon basin is the world's largest hydrographic basin, in terms of both its total area and its species diversity, with more than 2,700 species of fish. Despite this diversity, the data available on the fish fauna of the Amazon basin are still relatively scant and incomplete, in particular from the streams and floodplain lakes of the lower Amazon, which may contain a large proportion of the still undescribed species of the basin. Many of these species are expected to be of interest to the ornamental fish market. The investigation of the diversity of potential ornamental fish using molecular tools is even more limited. Given this scenario, the present study employed DNA barcoding to investigate the diversity of ornamental fish found in two streams and a floodplain lake of the lower Amazon. The mitochondrially encoded cytochrome c oxidase I (MT-CO1) molecular marker was used to identify the taxa, in combination with morphological keys. A total of 51 ornamental species were identified, representing 13 families and three orders. A majority of the species were found at only one of the sampling points, which indicates that the distribution of the species is influenced by ecological factors. The most speciose order was the Characiformes, followed by the Cichliformes and Siluriformes, while the family with the greatest diversity of species was the Acestrorhamphidae (31.3% of the total number of species), followed by the Cichlidae (27.4%), and the Lebiasinidae (9.8%). One specie was registered in the region of the lower Amazon for the first time, and evidence was found of the possible existence of species not formally described of Aphyocharax, Astyanax, Apareiodon and Hemigrammus.},
}
@article {pmid39774107,
year = {2025},
author = {Dufresnes, C and Jablonski, D and Ambu, J and Prasad, VK and Bala Gautam, K and Kamei, RG and Mahony, S and Hofmann, S and Masroor, R and Alard, B and Crottini, A and Edmonds, D and Ohler, A and Jiang, J and Khatiwada, JR and Gupta, SK and Borzée, A and Borkin, LJ and Skorinov, DV and Melnikov, DA and Milto, KD and Konstantinov, EL and Künzel, S and Suchan, T and Arkhipov, DV and Trofimets, AV and Nguyen, TV and Suwannapoom, C and Litvinchuk, SN and Poyarkov, NA},
title = {Speciation and historical invasions of the Asian black-spined toad (Duttaphrynus melanostictus).},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {298},
pmid = {39774107},
issn = {2041-1723},
support = {RFIS 3211101356//National Natural Science Foundation of China (National Science Foundation of China)/ ; SPP1991 VE247/19-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Animals ; *Bufonidae/genetics/classification ; *Introduced Species ; Phylogeny ; Genetic Speciation ; Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Madagascar ; Phylogeography ; Asia, Southeastern ; India ; },
abstract = {Animal translocations provide striking examples of the human footprint on biodiversity. Combining continental-wide genomic and DNA-barcoding analyses, we reconstructed the historical biogeography of the Asian black-spined toad (Duttaphrynus melanostictus), a toxic commensal amphibian that currently threatens two biodiversity hotspots through biological invasions (Wallacea and Madagascar). The results emphasize a complex diversification shaped by speciation and mitochondrial introgression that comprises two distinct species. One species (true D. melanostictus) is distributed in the Indian subcontinent and is invasive in Wallacea. The other species, whose nomenclature remains unsettled, diverged from D. melanostictus in the Miocene era (~7 Mya) and diversified across Southeast Asia, from where it was introduced to Madagascar. Remarkably, the Indonesian population of D. melanostictus was recently established from India, which suggests historical, possibly human-assisted dispersal across the Bay of Bengal, reflecting the centuries-old connection between these regions.},
}
@article {pmid39774015,
year = {2025},
author = {Appleyard, SA and Ward, RD and Pogonoski, JJ and Graham, A and Last, PR and Deagle, BE and Holmes, B and Gomon, MF and Bray, DJ and Johnson, JW and Hay, AC and Moore, GI and Hammer, MP and Russell, B and Graham, KJ},
title = {Australia's marine fishes DNA barcode reference library for integrated taxonomy, metabarcoding &amp; eDNA research.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {21},
pmid = {39774015},
issn = {2052-4463},
mesh = {Animals ; *Aquatic Organisms/genetics/classification ; Australia ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Fishes/genetics/classification ; *Gene Library ; },
abstract = {Over 15 000 species of fishes are found globally in the marine environment and DNA barcodes are used extensively to describe, catalogue, understand and manage this diversity. The dataset outlined here represents a DNA barcode reference library of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) from 9767 voucher specimens (representing at least 2220 species and 288 families) of marine fishes. This publicly available dataset in the Barcode of Life Data System (BOLD) represents 17 years (2005-2022) of barcoding of marine fishes identified from Australian territorial waters. Tissues targeted for sequencing with their matching physical specimens (and extracted DNA), obtained via a multi-agency sampling effort, are mostly maintained and curated by the CSIRO Australian National Fish Collection (ANFC) in Hobart, Australia. Species-level integrated taxonomy (assigned after combined morphological and genetic assessment) has been determined for 91% of the dataset. The library represents the most complete COI barcode reference dataset for marine fishes from Australian waters and is currently utilised for integrated taxonomy, (meta)barcoding and eDNA studies.},
}
@article {pmid39771256,
year = {2024},
author = {Fedosov, VE and Pisarenko, OY and Fedorova, AV and Afonina, OM and Ignatova, EA},
title = {On the Cryptic Speciation in the Mosses with East Asia-East North America Disjunction: A Case Study of Two Poorly Understood Mosses from the Southern Extremity of the Russian Far East.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {24},
pages = {},
pmid = {39771256},
issn = {2223-7747},
support = {23-14-00043//Russian scientific foundation/ ; },
abstract = {A survey of the moss flora of the southernmost part of the Russian Primorsky Territory yielded several intriguing taxa, whose identity is assessed herein based on an integrative morpho-molecular approach. Bellibarbula recurva was previously known in inland Asia only from the Sino-Himalayan region and the new locality is distant from the earlier known ones to ca. 3000 km. Despite the morphological uniformity, Russian specimens are remarkably distinct in sequences of all three obtained DNA markers, approaching an American specimen in the rps4 sequence. Another probable relic, Symblepharis cf. crispifolia, appeared to be fairly common in the southern part of the Primorsky Territory, where low mountains are covered with hard-leaved forests. Russian specimens of Symblepharis cf. crispifolia var. brevipes show significant divergence from S. crispifolia s.str., which also has complex phylogenetic structure, obscuring further taxonomic implications. The description and illustrations of both taxa based on Russian specimens are provided, and the area, where both species occur, is briefly characterized; it includes numerous thermophilous species, which are rare or do not occur northwards. Our case study uncovers the problem of cryptic speciation within species distributed in temperate climate and is considered to represent relics of Arcto-Tertiary flora.},
}
@article {pmid39771168,
year = {2024},
author = {Li, X and Jia, H and Liu, D and Zhou, X and Wu, K},
title = {Potential Regional Pollination Services of Spodoptera litura (Lepidoptera: Noctuidae) Migrants as Evidenced by the Identification of Attached Pollen.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {24},
pages = {},
pmid = {39771168},
issn = {2223-7747},
support = {2023FY100500//Science &amp; Technology Fundamental Resources Investigation Program/ ; },
abstract = {Many species of noctuid moths exhibit long-distance migratory behavior and have an important pollination service function in terrestrial ecosystems. Spodoptera litura (Fabricius) is a globally distributed insect; however, its role in pollination remains underexplored. In this study, the feeding preferences and inter regional pollination of S. litura adults were explored. We conducted pollen analysis on 1253 S. litura migrants captured from 2018 to 2021 on Beihuangcheng Island in the Bohai Strait of China, which is located in the East Asian insect migration path. The results show that an average of 51.1% of S. litura migrants carry plant pollen each year, and the carrying rate shows fluctuations based on sex, year, and season. By combining morphological identification and DNA barcoding, pollen species were identified from 40 species of plants, representing 21 families and 26 genera, mainly from angiosperms of Dicotyledoneae, with Asteraceae, Apocynaceae, and Amaranthaceae being the dominant taxa. The geographical distribution range of Chrysanthemum zawadskii and Adenophora trachelioides and a migration trajectory simulation analysis indicate that S. litura predominantly migrate from Liaoning Province in Northeast China to North China over the Bohai Sea in autumn. These findings indicate the potential pollination activities of S. litura in North China and Northeast China, enriching our understanding of the interaction between S. litura and the plants it pollinates.},
}
@article {pmid39769939,
year = {2024},
author = {Wu, Z and Yu, W and Luo, F and Jin, Y and Pan, L and Deng, Q and Wang, Q and Yu, M},
title = {Construction of Heterogeneous Aggregation-Induced Emission Microspheres with Enhanced Multi-Mode Information Encryption.},
journal = {Molecules (Basel, Switzerland)},
volume = {29},
number = {24},
pages = {},
pmid = {39769939},
issn = {1420-3049},
abstract = {Traditional organic light-emitting materials hinder their anti-counterfeiting application in solid state due to their aggregation-caused quenching effect. A facile and straightforward method was reported to introduce AIE molecules into microspheres and manipulate different reaction parameters to prepare AIE microspheres with different morphologies. In this strategy, fluorescent microspheres with spherical, apple-shaped, and hemoglobin-like types were synthesized. Driven by the photocyclization and oxidation of tetraphenylethene, microspheres can be used as an aqueous fluorescence ink with erasable properties. The fluorescent patterns printed by microsphere ink on paper can be irreversibly erased by prolonged exposure to ultraviolet light (365 nm, 60 mw/cm[2]). Moreover, the multi-morphology microspheres can be further arranged for multiple-information encryption and anti-counterfeiting of barcodes and two-dimensional codes, in which double validation was carried out through fluorescence spectroscopy and laser confocal microscopy. This approach provides a new method for more reliable anti-counterfeiting and information encryption.},
}
@article {pmid39769610,
year = {2024},
author = {Ye, C and Tang, X and Yang, F and Zhang, X and Shang, Y and Xia, Y and Wang, Y and Guo, S and Zha, L and Guo, Y and Wen, D},
title = {Rapid and Accurate Detection of Chrysomya megacephala (Diptera: Calliphoridae) Using Recombinase Polymerase Amplification Combined with Lateral Flow Dipstick.},
journal = {Insects},
volume = {15},
number = {12},
pages = {},
pmid = {39769610},
issn = {2075-4450},
support = {No. 82072114//National Natural Science Foundation of China/ ; },
abstract = {Estimating the postmortem interval (PMI) is critical in the field of forensic science, and necrophagous insects play a significant role in this process. Chrysomya megacephala (Fabricius) (Diptera: Calliphoridae) is a common necrophagous insect species, making its rapid and accurate identification essential. However, commonly used molecular biology methods, such as DNA barcode, still have some limitations in identifying necrophagous insects as they are often complex, time-consuming, and reliant on laboratory instruments. Therefore, in this study, we have developed an innovative detection system for the rapid and accurate identification of C. megacephala based on the Cytochrome b gene using recombinase polymerase amplification (RPA) and lateral flow dipstick (LFD) in combination. The developed RPA-LFD detection system achieved complete amplification in just 15 min at 37 °C with good sensitivity and specificity. Only 7.8 × 10[-4] ng or more of target DNA fragments were required, and a positive detection rate of 100% was achieved in 18 C. megacephala samples from actual cases. In addition, the ability of the developed RPA-LFD detection system in combination with rapid DNA extraction methods to enable on-site detection was preliminarily explored. The results suggested that when the RPA-LFD detection system was combined with the grinding ddH2O extraction method (a rapid DNA extraction method), the process from species acquisition to visualization of detection results could be completed in less than 20 min. In conclusion, this innovative RPA-LFD detection system outperforms commonly used molecular biology methods for C. megacephala identification in terms of speed, sensitivity and convenience, making it suitable for direct application at crime scenes, promising to provide important assistance in estimating PMI and expanding the impact of forensic entomological evidence.},
}
@article {pmid39769570,
year = {2024},
author = {Han, Y and Achterberg, KV and Chen, X},
title = {DNA Barcodes and Morphology Reveal Two New Species of the Genus Prochas Walkley, 1959 (Ichneumonidae, Campopleginae), from China.},
journal = {Insects},
volume = {15},
number = {12},
pages = {},
pmid = {39769570},
issn = {2075-4450},
support = {31920103005//the Key International Joint Research Program of the Na-325 tional Natural Science Foundation of China/ ; 32070467//the National Natural Science Founda-326 tion of China/ ; 2017YFD0200101//the National Key Research and Development Plan/ ; 2019YFD0300104//the National Key Research and Development Plan/ ; 2018R51004//the Fundamental Research Funds for the Central Universities, the Special Re-328 search Fund for Distinguished Scholars of Zhejiang Province, China/ ; 2023qd31//the Scien-329 tific Research Starting Foundation of Chuzhou University, China/ ; },
abstract = {DNA barcoding is an effective modern tool in taxonomy, evolutionary biology, and biodiversity research. Many new species have been discovered and described with DNA barcodes as part of their diagnostic features. We combined morphological examination and molecular species delimitation of the mitochondrial cytochrome c oxidase 1 (COI) gene using the automatic barcode gap discovery (ABGD) to investigate species boundaries. The genus Prochas Walkley (Hymenoptera, Ichneumonidae, Campopleginae) was first reported from China and is new for the Oriental and Eastern Palearctic regions. Using an integrative taxonomy method, two new species P. rugipunctata sp. nov. and P. striata sp. nov. are hereby described and illustrated. A key to the world species and a distribution map are provided.},
}
@article {pmid39769553,
year = {2024},
author = {Enguídanos García, A and Galià-Camps, C and Pérez-González, CM and Víquez, D and Mateos, E},
title = {Expanding Soil Invertebrate Knowledge in Panama: The Genus Lepidocyrtus (Collembola, Entomobryidae) in the Parque Natural Metropolitano as a Study Case.},
journal = {Insects},
volume = {15},
number = {12},
pages = {},
pmid = {39769553},
issn = {2075-4450},
support = {2023-GEBI-Panama//European Society of Evolutionary Biology/ ; 2023-Linn&#xe9;Sys-Panama//Linnean Society of London &amp; Systematics Association/ ; Internacionalitzaci&#xf3;UB-Panama//Universitat de Barcelona/ ; 2021SGR689//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; 2021SGR1271//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; },
abstract = {Panama, located in the heart of the Mesoamerican hotspot, harbors an extraordinary species diversity across the Tree of Life. The Collembola species of the genus Lepidocyrtus play an important role in soil biological processes such as decomposition, being used to monitor soil health and functional parameters. However, the limitation of morphological characters and molecular resources hampers the evaluation of local soil diversity. Here, using 30 Lepidocyrtus specimens collected in the Parque Natural Metropolitano (PNM), we unravel the diversity of this Panamanian protected area through molecular tools and new taxonomic traits. Our phylogenies, in combination with species delimitation analyses, indicate that the PNM harbors an extremely rich community of Lepidocyrtus species, two of them cited in Panama for the first time, and three of them potentially new to science. We highlight that the presence of the dental tubercle and pseudopores on the BP4 region are not monophyletic and, therefore, can be used as supplementary characters to morphologically resolve species complexes. Overall, this study sheds light on the Lepidocyrtus richness of the PNM, which acts as a shelter for Panamanian and the Mesoamerican hotspot species.},
}
@article {pmid39769528,
year = {2024},
author = {Chen, H and van Achterberg, C and Li, Y and Liu, Z and Wang, J and Luo, S},
title = {Parasitoids of Insect Pests Feeding on Scaevola taccada (Goodeniaceae) from Yongxing Island in South China Sea.},
journal = {Insects},
volume = {15},
number = {12},
pages = {},
pmid = {39769528},
issn = {2075-4450},
abstract = {Scaevola taccada (Goodeniaceae) is an important evergreen coastal plant on islands in the South China Sea, which shows excellent tolerance for salty and drought conditions. Nevertheless, the growth of S. taccada populations on these islands in the South China Sea has been threatened by a few serious insect pests. However, we know little about the biology of these pests. In this study, we surveyed and identified the parasitoids of two main pests (Herpetogramma submarginale (Swinhoe, 1901) and Ophiomyia scaevolana Shiao and Wu, 1996) of S. taccada communities on Yongxing Island in the South China Sea, with the aim to assess their potential in biological control. Dolichogenidea stantoni (Ashmead, 1904) is a gregarious endoparasitoid of the larva of H. submarginale and contributes an average 48.9% parasitism rate on H. submarginale. Opius biroi, Fischer, 1960 and Euderus albitarsis (Zetterstedt, 1838) are both solitary endoparasitoids of the larva of O. scaevolana, with a respective 5.8% and 64.4% parasitism rate on O. scaevolana. We summarize the species diagnosis, biology, and distribution of the three parasitoid species. The potential of these parasitoids used in biological control is also discussed.},
}
@article {pmid39769523,
year = {2024},
author = {Lei, T and Gu, J and Zhao, M and Chen, Y and Song, C and Qi, X},
title = {Seasonal Dynamics of Non-Biting Midges (Diptera: Chironomidae) and Relevant Environmental Factors.},
journal = {Insects},
volume = {15},
number = {12},
pages = {},
pmid = {39769523},
issn = {2075-4450},
support = {32070481//National Natural Science Foundation of China/ ; 32100353//National Natural Science Foundation of China/ ; LY22C040003//Zhejiang Provincial Natural Science Foundation/ ; },
abstract = {The family Chironomidae is speciose and is present in almost all freshwater habitats. Adult non-biting midges emerge from waterbodies and swarm in high numbers, occasionally disrupting people's outdoor activities. In order to understand the seasonal dynamics of species composition, a continuous observation of non-biting midge diversity was performed. Adult non-biting midges were collected using light traps from the autumn of 2022 to the summer of 2023 in an urban wetland park. Species were identified based on morphological characteristics and DNA barcodes. Alpha diversity was evaluated using Margalef, Pielou, and Shannon-Wiener indexes. Beta diversity was evaluated using unconstrained NMDS analysis and constrained CCA. The impacts of environmental factors, including barometric pressure, temperature, relative humidity, and wind speed, on the variation in species composition were estimated in the constrained analyses. A total of 42 species were identified, with 29 species belonging to Chironominae, 9 species belonging to Orthocladiinae, and 4 species belonging to Tanypodinae. The species composition varied across different seasons. Summer sites and autumn sites shared the highest similarity in diversity, and spring sites presented the lowest diversity. The variation was significantly correlated with environmental conditions. The results showed that seasonality is a factor influencing the diversity of adult non-biting midges.},
}
@article {pmid39765491,
year = {2024},
author = {Chen, H and Olmi, M and Wang, J and Sun, Q and Luo, S},
title = {DNA Barcoding Reveals Species Diversity and Host Associations of Dryinidae Wasps (Insecta, Hymenoptera): A Case Study from the Xisha Islands in the South China Sea.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {24},
pages = {},
pmid = {39765491},
issn = {2076-2615},
abstract = {Dryinidae is a cosmopolitan wasp family, with over 1900 species found worldwide [...].},
}
@article {pmid39764454,
year = {2024},
author = {Jiang, S and Zhao, G and Ding, Y and Ye, S and Li, Z and You, C and Yin, Y and Guo, X},
title = {Deciphering dengue: novel RNA barcoding segments for enhanced serotype-specific identification and global surveillance of dengue viruses.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1474406},
pmid = {39764454},
issn = {1664-302X},
abstract = {INTRODUCTION: Dengue viruses (DENVs), the causative agents of dengue hemorrhagic fever and dengue shock syndrome, undergo genetic mutations that result in new strains and lead to ongoing global re-infections.<br><br>OBJECTIVES: To address the growing complexity of identifying and tracking biological samples, this study screened RNA barcode segments for the four DENV serotypes, ensuring high specificity and recall rates for DENV identification using segments.<br><br>RESULTS: Through analyzing complete genome sequences of DENVs, we screened eight barcode segments for DENV, DENV-1, DENV-2, DENV-3, and DENV-4 identification. Comparing the screened barcode segments to sequences of known strains and determining the proportion of correctly or incorrectly identified nucleotides, these segments demonstrated an average recall rate at nucleotide level of 91.34% for four DENV serotypes, a specificity of 99.50% at species level within the Flaviviridae family, and a precision rate of 100% for identifying DENVs. For arboviruses, the nucleotide-level specificity was 63.58%. We designed and used the "Barcoding" software to streamline segment design, integrating automated sequence preprocessing, evaluation of barcode segments, and primer design, significantly reducing manual intervention and enhancing overall efficiency. We also established an online database called "Barcodes" for storing and preparing barcode segments.<br><br>CONCLUSION: This work established a standard framework for DENV identification and barcode segment selection, promising significant advancements in the real-time management and control of DENVs, thereby enhancing surveillance capabilities and facilitating targeted interventions in dengue outbreak-prone regions.},
}
@article {pmid39764013,
year = {2024},
author = {Comstock, WJ and Navarro, MV and Maybee, DV and Rho, Y and Wagner, M and Wang, Y and Smolka, MB},
title = {Proteomic Sensors for Quantitative, Multiplexed and Spatial Monitoring of Kinase Signaling.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.16.628391},
pmid = {39764013},
issn = {2692-8205},
support = {R35 GM141159/GM/NIGMS NIH HHS/United States ; },
abstract = {Understanding kinase action requires precise quantitative measurements of their activity in vivo . In addition, the ability to capture spatial information of kinase activity is crucial to deconvolute complex signaling networks, interrogate multifaceted kinase actions, and assess drug effects or genetic perturbations. Here we developed a proteomic kinase activity sensor platform (ProKAS) for the analysis of kinase signaling using mass spectrometry. ProKAS is based on a tandem array of peptide sensors with amino acid barcodes that allow multiplexed analysis for spatial, kinetic, and screening applications. We engineered a ProKAS module to simultaneously monitor the activities of the DNA damage response kinases ATR, ATM, and CHK1 in response to genotoxic drugs, while also uncovering differences between these signaling responses in the nucleus, cytosol, and replication factories. Furthermore, we developed an in silico approach for the rational design of specific substrate peptides expandable to other kinases. Overall, ProKAS is a novel versatile system for systematically and spatially probing kinase action in cells.},
}
@article {pmid39763829,
year = {2024},
author = {Feng, Y and Chen, D and Applegate, CC and Gonzalez Medina, NY and Kuo, CW and Arogundade, OH and Wright, CL and Xu, F and Drnevich, J and Smith, AM},
title = {Nanocoding: Lipid Nanoparticle Barcoding for Multiplexed Single-Cell RNA Sequencing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.16.628827},
pmid = {39763829},
issn = {2692-8205},
abstract = {Sample multiplexing is an emerging method in single-cell RNA sequencing (scRNA-seq) that addresses high costs and batch effects. Current multiplexing schemes use DNA labels to barcode cell samples but are limited in their stability and extent of labeling across heterogeneous cell populations. Here, we introduce Nanocoding using lipid nanoparticles (LNPs) for high barcode labeling density in multiplexed scRNA-seq. LNPs reduce dependencies on cell surface labeling mechanisms due to multiple controllable means of cell uptake, amplifying barcode loading 10-100-fold and allowing both protection and efficient release by dissolution. In cultured cell lines and heterogeneous cells from tissue digests, Nanocoding occurs in 40 minutes with stability after sample mixing and requires only commercially available reagents without novel chemical modifications. In spleen digests, 6-plex barcoded samples show minimal unlabeled cells, with all barcodes giving bimodal count distributions. Challenging samples containing lipid-rich debris and heterogeneous cells from adipose tissue of obese rodents show more than 95% labeling with all known subtypes identified. Using Nanocoding, we investigate gene expression changes related to aging in adipose tissue, profiling cells that could not be readily identified with current direct conjugate methods using lipid or antibody conjugates. This ease of generating and tuning these constructs may afford efficient and robust whole-sample multiplexing with minimal sample crosstalk.},
}
@article {pmid39762652,
year = {2025},
author = {Hong, SJ and Resnick, SJ and Iketani, S and Cha, JW and Albert, BA and Fazekas, CT and Chang, CW and Liu, H and Dagan, S and Abagyan, MR and Fajtová, P and Culbertson, B and Brace, B and Reddem, ER and Forouhar, F and Glickman, JF and Balkovec, JM and Stockwell, BR and Shapiro, L and O'Donoghue, AJ and Sabo, Y and Freundlich, JS and Ho, DD and Chavez, A},
title = {A multiplex method for rapidly identifying viral protease inhibitors.},
journal = {Molecular systems biology},
volume = {21},
number = {2},
pages = {158-172},
pmid = {39762652},
issn = {1744-4292},
support = {1U19AI1711401//HHS | National Institutes of Health (NIH)/ ; 1017195.01//Burroughs Wellcome Fund (BWF)/ ; N/A//jack ma foundation/ ; DGE-2038238//NSF | National Science Foundation Graduate Research Fellowship Program (GRFP)/ ; },
mesh = {*Protease Inhibitors/pharmacology ; *High-Throughput Screening Assays/methods ; Humans ; Antiviral Agents/pharmacology ; Viral Proteases/metabolism ; SARS-CoV-2/drug effects/enzymology ; Drug Discovery/methods ; Biosensing Techniques/methods ; Coronavirus 3C Proteases/antagonists &amp; inhibitors/metabolism ; },
abstract = {With current treatments addressing only a fraction of pathogens and new viral threats constantly evolving, there is a critical need to expand our existing therapeutic arsenal. To speed the rate of discovery and better prepare against future threats, we establish a high-throughput platform capable of screening compounds against 40 diverse viral proteases simultaneously. This multiplex approach is enabled by using cellular biosensors of viral protease activity combined with DNA-barcoding technology, as well as several design innovations that increase assay sensitivity and correct for plate-to-plate variation. Among >100,000 compound-target interactions explored within our initial screen, a series of broad-acting inhibitors against coronavirus proteases were uncovered and validated through orthogonal assays. A medicinal chemistry campaign was performed to improve one of the inhibitor's potency while maintaining its broad activity. This work highlights the power of multiplex screening to efficiently explore chemical space at a fraction of the time and costs of previous approaches.},
}
@article {pmid39758945,
year = {2024},
author = {Senofsky, SR and Zamudio, I and Pan, B and McFadden, CS},
title = {Efficacy of the 28S rDNA barcode in differentiating Caribbean octocorals.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e140454},
pmid = {39758945},
issn = {1314-2828},
abstract = {The ecological landscape of Caribbean reefs is rapidly changing as octocorals fill the void left by declining scleractinian populations. Effective molecular barcodes are necessary to accurately identify these octocorals and monitor this shifting ecosystem. We tested the efficacy of the 28S rDNA as a barcode compared to the most commonly used mtMutS barcode on a collection of octocorals from across the Caribbean. Based on pairwise genetic distance values, 28S appeared to be more effective at differentiating species within the families Plexauridae and Gorgoniidae, while mtMutS was slightly more effective at distinguishing species of Pterogorgiidae. However, the standard 28S rDNA primers did not amplify all species as effectively as mtMutS, especially those belonging to the genus Eunicea. A shorter 28S barcode developed for eDNA applications distinguished species as effectively as the complete 28S barcode.},
}
@article {pmid39758943,
year = {2024},
author = {Boóz, B and Kovács, Z and Bartalovics, B and Boda, P and Miliša, M and Pernecker, B and Pařil, P and Rewicz, T and Simon, AB and Csabai, Z and Móra, A},
title = {Chironomids (Diptera) from Central European stream networks: new findings and taxonomic issues.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e136241},
pmid = {39758943},
issn = {1314-2828},
abstract = {BACKGROUND: Chironomidae, with over 7,300 described species, are amongst the most diverse and abundant insect families in freshwater ecosystems worldwide. Chironomids are known for their widespread distribution from various water types. The level of documentation of chironomid fauna varies considerably amongst European countries, with more comprehensive knowledge for Western Europe compared to other regions. Despite the recent extensive sampling effort and the increasing number of available data, the chironomid fauna of Central European countries still remains poorly known.<br><br>NEW INFORMATION: This study contributes to the knowledge of chironomid fauna in three river catchments in Croatia, Hungary and Czechia. A combination of morphological and molecular techniques was employed, with a focus on larvae, although pupae and exuviae were also examined. We found 207 taxa, amongst which 170 were identified to species level. In Croatia, 14 species were recorded for the first time and two species were newly recorded in Czechia. DNA barcoding of 31 specimens resulted in 23 BINs, including eight new ones to BOLD. We provided detailed notes on taxa with taxonomic problems and/or morphological peculiarities. Our results highlight that extensive studies conducted in relatively small areas and a limited range of habitats (only streams in hilly regions) can remarkably contribute to the local and global knowledge on Chironomidae fauna, especially when the taxonomically difficult and often problematic larvae are investigated.},
}
@article {pmid39753672,
year = {2025},
author = {Acford-Palmer, H and Andrade, AO and Phelan, JE and Santana, RA and Lopes, SCP and Medeiros, JF and Clark, TG and Araujo, MS and Campino, S},
title = {Application of a targeted amplicon sequencing panel to screen for insecticide resistance mutations in Anopheles darlingi populations from Brazil.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {731},
pmid = {39753672},
issn = {2045-2322},
support = {no. 261868591//British Council, Newton Institutional Links Grant/ ; 304830/2022-4//CNPq productivity grant/ ; BB/X018156/1//UK Research and Innovation/ ; INV-003970/GATES/Bill &amp; Melinda Gates Foundation/United States ; 442653/2019-0//Brazilian Ministry of Health/DECIT/CNPq N&#xb0; 23/2019/ ; CON-80002357//ICEMR/ ; },
mesh = {Animals ; *Anopheles/genetics/drug effects ; *Insecticide Resistance/genetics ; Brazil ; *Mosquito Vectors/genetics/drug effects ; High-Throughput Nucleotide Sequencing/methods ; Insecticides/pharmacology ; Mutation ; Malaria/transmission/prevention &amp; control ; },
abstract = {Large-scale surveillance and informed vector control approaches are urgently needed to ensure that national malaria programs remain effective in reducing transmission and, ultimately, achieving malaria elimination targets. In South America, Anopheles darlingi is the primary malaria vector and is responsible for the majority of Plasmodium species transmission. However, little is known about the molecular markers associated with insecticide resistance in this species. In this study, we developed a low-cost, high throughput amplicon sequencing ("amp-seq") panel, consisting of 11 amplicons targeting genes linked to mosquito species identification (cox-1 and its2) and insecticide resistance (ace-1, GSTe2, vgsc and rdl). When used in tandem with dual-index barcoding of amplicons, this approach permits high numbers of loci and samples to be sequenced in single runs, thereby decreasing costs and increasing efficiency. By screening 200 An. darlingi mosquitoes collected in Brazil, our amp-seq approach identified 10 point mutations leading to amino acid changes in ace-1 (V243I, N294H, S673N, S674N/T) and GSTe2 genes (I114V, D128E, T166I, T179I, and T205A). Overall, our work has demonstrated the utility of amp-seq to provide insights into the genetic diversity of An. darlingi mosquitoes. The amp-seq approach can be applied as a wide-scale insecticide-resistance surveillance technique to better inform vector-control methods.},
}
@article {pmid39752373,
year = {2025},
author = {, },
title = {Correction: Mitochondrial DNA barcoding of mosquito species (Diptera: Culicidae) in Thailand.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0317172},
pmid = {39752373},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0275090.].},
}
@article {pmid39748949,
year = {2024},
author = {Cabrera-Sosa, L and Safarpour, M and Kattenberg, JH and Ramirez, R and Vinetz, JM and Rosanas-Urgell, A and Gamboa, D and Delgado-Ratto, C},
title = {Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1488109},
pmid = {39748949},
issn = {1664-8021},
support = {U19 AI089681/AI/NIAID NIH HHS/United States ; },
abstract = {INTRODUCTION: Malaria molecular surveillance (MMS) can provide insights into transmission dynamics, guiding national control programs. We previously designed AmpliSeq assays for MMS, which include different traits of interest (resistance markers and pfhrp2/3 deletions), and SNP barcodes to provide population genetics estimates of Plasmodium vivax and Plasmodium falciparum parasites in the Peruvian Amazon. The present study compares the genetic resolution of the barcodes in the AmpliSeq assays with widely used microsatellite (MS) panels to investigate population genetics of Amazonian malaria parasites.<br><br>METHODS: We analyzed 51&#xa0;P. vivax and 80&#xa0;P. falciparum samples from three distinct areas in the Loreto region of the Peruvian Amazon: Nueva Jerusal&#xe9;n (NJ), Mazan (MZ), and Santa Emilia (SE). Population genetics estimates and costs were compared using the SNP barcodes (P. vivax: 40 SNPs and P. falciparum: 28 SNPs) and MS panels (P. vivax: 16 MS and P. falciparum: 7 MS).<br><br>RESULTS: The P. vivax genetic diversity (expected heterozygosity, He) trends were similar for both markers: He MS = 0.68-0.78 (p > 0.05) and He SNP = 0.36-0.38 (p > 0.05). P. vivax pairwise genetic differentiation (fixation index, FST) was also comparable: FST-MS = 0.04-0.14 and FST-SNP = 0.03-0.12 (pairwise p > 0.05). In addition, P. falciparum genetic diversity trends (He MS = 0-0.48, p < 0.05; He SNP = 0-0.09, p < 0.05) and pairwise FST comparisons (FST-MS = 0.14-0.65, FST-SNP = 0.19-0.61, pairwise p > 0.05) were concordant between both panels. For P. vivax, no geographic clustering was observed with any panel, whereas for P. falciparum, similar population structure clustering was observed with both markers, assigning most parasites from NJ to a distinct subpopulation from MZ and SE. We found significant differences in detecting polyclonal infections: for P. vivax, MS identified a higher proportion of polyclonal infections than SNP (69% vs. 33%, p = 3.3 &#xd7; 10[-5]), while for P. falciparum, SNP and MS detected similar rates (46% vs. 31%, p = 0.21). The AmpliSeq assay had a higher estimated per-sample cost compared to MS ($183 vs. $27-49).<br><br>DISCUSSION: The SNP barcodes in the AmpliSeq assays offered comparable results to MS for investigating population genetics in P. vivax and P. falciparum populations, despite some discrepancies in determining polyclonality. Given both panels have their respective advantages and limitations, the choice between both should be guided by research objectives, costs, and resource availability.},
}
@article {pmid39747844,
year = {2025},
author = {Coulombe, P and Tomellini, E and Chagraoui, J and Mayotte, N and Sauvageau, G},
title = {Deciphering the effect of UM171 on human hematopoietic progenitor cell fate through clonal analysis.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {195},
pmid = {39747844},
issn = {2041-1723},
support = {PJT-178113//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; FDN-143286//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; HZN-C4R1-1//Stem Cell Network (Le R&#xe9;seau de cellules souches)/ ; },
mesh = {*Hematopoietic Stem Cells/cytology/metabolism ; Humans ; Animals ; *Cell Differentiation ; Mice ; *Mast Cells/cytology/metabolism/drug effects ; Cell Proliferation ; Cell Lineage ; Cell Self Renewal/drug effects ; Hematopoietic Stem Cell Transplantation ; Signal Transduction ; },
abstract = {Ex vivo expansion of hematopoietic stem cells (HSC) requires the maintenance of a stemness state while cells are proliferating. This can be achieved via exposure to UM171 which leads to the degradation of chromatin modifiers and prevents the loss of key epigenetic marks. However, the chromatin landscape varies across populations within the hematopoietic system and the effect of UM171 on self-renewal and differentiation potential of different hematopoietic progenitor cells is less characterized. To address this, we use the CellTag barcoding approach to track the fate of individual stem and progenitor cells during in vitro expansion. We show that, in addition to its HSC self-renewing property, UM171 specifically modulates cell fate of a precursor common to erythroid, megakaryocytic, and mast cells in favor of self-renewal and a mast-bias differentiation trajectory. This differentiation bias can be driven by pro-inflammatory signaling pathways that are activated downstream of UM171 and results in an abundant mast cell population that can be transplanted as part of the graft to populate mice tissues in xenotransplantation studies.},
}
@article {pmid39747602,
year = {2025},
author = {Cho, S and Martino, N and Yun, SH},
title = {Half-wave nanolasers and intracellular plasmonic lasing particles.},
journal = {Nature nanotechnology},
volume = {20},
number = {3},
pages = {404-410},
pmid = {39747602},
issn = {1748-3395},
support = {R01-EB033155//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01-EB034687//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; Fund for Medical Discovery fundamental research fellowship award//Massachusetts General Hospital (MGH)/ ; },
abstract = {The ultimate limit for laser miniaturization would be achieving lasing action in the lowest-order cavity mode within a device volume of ≤(λ/2n)[3], where λ is the free-space wavelength and n is the refractive index. Here we highlight the equivalence of localized surface plasmons and surface plasmon polaritons within resonant systems, introducing nanolasers that oscillate in the lowest-order localized surface plasmon or, equivalently, half-cycle surface plasmon polariton. These diffraction-limited single-mode emitters, ranging in size from 170 to 280 nm, harness strong coupling between gold and InxGa1-xAs1-yPy in the near-infrared (λ = 1,000-1,460 nm), away from the surface plasmon frequency. This configuration supports only the lowest-order dipolar mode within the semiconductor's broad gain bandwidth. A quasi-continuous-level semiconductor laser model explains the lasing dynamics under optical pumping. In addition, we fabricate isolated gold-coated semiconductor discs and demonstrate higher-order lasing within live biological cells. These plasmonic nanolasers hold promise for multi-colour imaging and optical barcoding in cellular applications.},
}
@article {pmid39745647,
year = {2025},
author = {Raj, B},
title = {Single-Cell Profiling of Lineages and Cell Types in the Vertebrate Brain.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2886},
number = {},
pages = {299-310},
pmid = {39745647},
issn = {1940-6029},
mesh = {Animals ; *Single-Cell Analysis/methods ; *Brain/cytology/metabolism ; *Zebrafish/genetics ; *CRISPR-Cas Systems ; *Cell Lineage/genetics ; *Gene Editing/methods ; Transcriptome ; Gene Expression Profiling/methods ; },
abstract = {CRISPR-Cas tools have recently been adapted for cell lineage tracing during development. Combined with single-cell RNA sequencing, these methods enable scalable lineage tracing with single-cell resolution. Here, I describe, scGESTALTv2, which combines cumulative CRISPR-Cas9 editing of a lineage barcode array with transcriptional profiling via droplet-based single-cell RNA sequencing (scRNA-seq). The technique is applied in developing zebrafish brains to generate mutations in the barcode array during development. The recorded lineages along with cellular transcriptomes are then extracted via scRNA-seq to define cell relationships among thousands of profiled brain cells and dozens of cell types.},
}
@article {pmid39745646,
year = {2025},
author = {Bowling, S and Camargo, FD},
title = {CARLIN: A Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2886},
number = {},
pages = {281-298},
pmid = {39745646},
issn = {1940-6029},
mesh = {Animals ; Mice ; *Cell Lineage/genetics ; *DNA Barcoding, Taxonomic/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Single-Cell Analysis/methods ; CRISPR-Cas Systems ; Gene Editing/methods ; Gene Expression/genetics ; },
abstract = {The CRISPR-activated repair lineage tracing (CARLIN) mouse line uses DNA barcoding to enable high-resolution tracing of cell lineages in vivo (Bowling et al, Cell 181, 1410-1422.e27, 2020). CARLIN mice contain expressed barcodes that allow simultaneous interrogation of lineage and gene expression information from single cells. Furthermore, barcode editing is fully inducible, resulting in cell lineage labeling that can be performed at any time point in development or adulthood. This chapter details the protocols followed for maintaining CARLIN mice, inducing barcoding, and amplifying the CARLIN barcode from DNA, RNA, and single-cell RNA-sequencing libraries for next-generation sequencing.},
}
@article {pmid39745644,
year = {2025},
author = {Spanjaard, B and Junker, JP},
title = {LINNAEUS: Simultaneous Single-Cell Lineage Tracing and Cell Type Identification.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2886},
number = {},
pages = {243-263},
pmid = {39745644},
issn = {1940-6029},
mesh = {*Single-Cell Analysis/methods ; *Cell Lineage/genetics ; Animals ; Gene Editing/methods ; Gene Expression Profiling/methods ; Computational Biology/methods ; Sequence Analysis, RNA/methods ; Humans ; },
abstract = {A key goal of biology is to understand the origin of the many cell types that can be observed during diverse processes such as development, regeneration, and disease. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ. However, organizing the resulting taxonomy of cell types into lineage trees to understand the origins of cell states and relationships between cells remains challenging. Here we present LINNAEUS (Spanjaard et al, Nat Biotechnol 36:469-473. https://doi.org/10.1038/nbt.4124 , 2018; Hu et al, Nat Genet 54:1227-1237. https://doi.org/10.1038/s41588-022-01129-5 , 2022) (LINeage tracing by Nuclease-Activated Editing of Ubiquitous Sequences)-a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes, generated by genome editing of transgenic reporter genes, LINNAEUS can be used to reconstruct organism-wide single-cell lineage trees. LINNAEUS provides a systematic approach for tracing the origin of novel cell types, or known cell types under different conditions.},
}
@article {pmid39745643,
year = {2025},
author = {Baron, CS and Alemany, A},
title = {Paired Single-Cell Transcriptome and DNA Barcode Detection in Zebrafish Using ScarTrace.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2886},
number = {},
pages = {221-241},
pmid = {39745643},
issn = {1940-6029},
mesh = {Animals ; *Zebrafish/genetics ; *Single-Cell Analysis/methods ; *DNA Barcoding, Taxonomic/methods ; *CRISPR-Cas Systems ; *Transcriptome/genetics ; Gene Expression Profiling/methods ; Embryo, Nonmammalian/metabolism ; },
abstract = {ScarTrace is a CRISPR/Cas9-based genetic lineage tracing method that allows for uniquely barcoding the DNA of single cells at a target GFP sequence during developing zebrafish embryos. Single cells from barcoded adult zebrafish can be isolated from various tissues (e.g., marrow, brain, eyes, fins), and their transcriptome and barcode sequences are captured by single-cell cDNA amplification and genomic DNA nested PCR, respectively. Computationally, cell type and barcode identification permit clone tracing and lineage tree reconstruction of tissues to unravel fate decisions during embryogenesis.},
}
@article {pmid39745641,
year = {2025},
author = {Fang, W and Yang, Y and Ji, H and Kalhor, R},
title = {Reconstructing Progenitor State Hierarchy and Dynamics Using Lineage Barcoding Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2886},
number = {},
pages = {177-199},
pmid = {39745641},
issn = {1940-6029},
support = {R01 HG012357/HG/NHGRI NIH HHS/United States ; U01 HL156056/HL/NHLBI NIH HHS/United States ; },
mesh = {*Cell Lineage/genetics ; *Algorithms ; Animals ; Phylogeny ; Cell Differentiation/genetics ; Stem Cells/cytology/metabolism ; Single-Cell Analysis/methods ; Computational Biology/methods ; DNA Barcoding, Taxonomic/methods ; Software ; Humans ; },
abstract = {Measurements of cell phylogeny based on natural or induced mutations, known as lineage barcodes, in conjunction with molecular phenotype have become increasingly feasible for a large number of single cells. In this chapter, we delve into Quantitative Fate Mapping (QFM) and its computational pipeline, which enables the interrogation of the dynamics of progenitor cells and their fate restriction during development. The methods described here include inferring cell phylogeny with the Phylotime model, and reconstructing progenitor state hierarchy, commitment time, population size, and commitment bias with the ICE-FASE algorithm. Evaluation of adequate sampling based on progenitor state coverage statistics is emphasized for interpreting the QFM results. Overall, this chapter describes a general framework for characterizing the dynamics of cell fate changes using lineage barcoding data.},
}
@article {pmid39745638,
year = {2025},
author = {Ratz, M and von Berlin, L},
title = {Clonal Tracking in the Mouse Brain with Single-Cell RNA-Seq.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2886},
number = {},
pages = {103-137},
pmid = {39745638},
issn = {1940-6029},
mesh = {Animals ; Mice ; *Single-Cell Analysis/methods ; *Brain/metabolism/cytology/embryology ; RNA-Seq/methods ; Cell Lineage/genetics ; Cell Tracking/methods ; Lentivirus/genetics ; Sequence Analysis, RNA/methods ; Single-Cell Gene Expression Analysis ; },
abstract = {Lineage tracing methods enable the identification of all progeny generated by a single cell. High-throughput lineage tracing in the mammalian brain involves parallel labeling of thousands of progenitor cells with genetic barcodes in vivo followed by single-cell RNA-seq of lineage relations and cell types. Here we describe the generation of barcoded lentivirus, microinjections into the embryonic day 9.5 mouse forebrain, dissociation of 2-week-old mouse brain tissue, single-cell RNA-seq library preparation, and data analysis using a custom software. Compared to traditional methods based on sparse fluorophore labeling of progenitor cells, lineage tracing with genetic barcodes and single-cell RNA-seq has a >100-fold higher throughput while using >10 times fewer mice.},
}
@article {pmid39745637,
year = {2025},
author = {Gentile, E and Maynard, A and He, Z and Treutlein, B},
title = {Lineage Recording in Human Brain Organoids with iTracer.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2886},
number = {},
pages = {85-101},
pmid = {39745637},
issn = {1940-6029},
mesh = {Humans ; *Organoids/cytology/metabolism ; *Brain/cytology ; *Induced Pluripotent Stem Cells/cytology/metabolism ; *Cell Lineage/genetics ; *Single-Cell Analysis/methods ; *CRISPR-Cas Systems ; Transcriptome ; Cell Differentiation ; },
abstract = {Induced pluripotent stem cell (iPSC)-derived organoids provide models to study human organ development. Single-cell transcriptomics enables highly resolved descriptions of cell states within these systems; however, approaches are needed to directly determine the lineage relationship between cells. Here we provide a detailed protocol (Fig. 1) for the application of iTracer (He Z, Maynard A, Jain A, et al., Nat Methods 19:90-99, 2022), a recently published lineage recorder that combines reporter barcodes with inducible CRISPR-Cas9 scarring and is compatible with single-cell and spatial transcriptomics. iTracer is used to explore clonality and lineage dynamics during brain organoid development. More broadly, iTracer can be adapted to any iPSC-derived culture system to dissect lineage dynamics during normal or perturbed development.},
}
@article {pmid39745636,
year = {2025},
author = {Rodriguez Fraticelli, AE and Sánchez, PS},
title = {Single-Cell Lineage Tracing and Clonal State-Fate Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2886},
number = {},
pages = {65-84},
pmid = {39745636},
issn = {1940-6029},
mesh = {*Single-Cell Analysis/methods ; *Cell Lineage/genetics ; Humans ; Cell Differentiation ; Animals ; Clone Cells/cytology ; DNA Barcoding, Taxonomic/methods ; Lentivirus/genetics ; Cell Tracking/methods ; },
abstract = {Lineage tracing has significantly advanced our comprehension in many areas of biology, such as development or immunity, by precisely measuring cellular processes like migration, division, or differentiation across labeled cells and their progeny. Traditional recombinase-based prospective lineage tracing is limited by the need for a priori cell type information and is constrained in the numbers of clones it can simultaneously track. In this sense, clonal lineage tracing with integrated random barcodes offers a robust alternative, enabling researchers to label and track a vast array of cells and their progeny over time. Moreover, clonal lineage tracing can be combined with single-cell omics technologies to study cell states and their maintenance over time. Key steps in these protocols include stable barcode integration, cell division to expand clones, and simultaneous capture of cellular properties with barcode information. Here, we comment on those steps and summarize important parameters to take into account during the design of single-cell lineage tracing experiments. Also, we present the main features for various available lentiviral libraries of expressed barcodes than can be captured alongside the transcriptome of individual cells. We cover other crucial aspects of experimental design, such as the optimization of cellular sampling, library diversity, and the minimization of clonal dropouts. Regarding sequencing data analysis, we provide some tips based on our experience, as well as available computational tools for the assignment of clonal identities and the identification of fate determinants. We finally discuss limitations of current methodologies and use an example step-by-step protocol to illustrate key points during the process. In sum, we provide a roadmap for considering and implementing single-cell lineage tracing studies to comprehensively explore fate determinants and their mechanisms.},
}
@article {pmid39745115,
year = {2025},
author = {González-Peña, R and Laredo-Tiscareño, SV and Huerta, H and Hernández-Triana, LM and De Luna-Santillana, EJ and Adame-Gallegos, JR and Rodríguez-Alarcón, CA and García-Rejón, JE and Hidalgo-Martínez, DO and Garza-Hernández, JA},
title = {FIRST STATE AND NATIONAL RECORDS OF CULICOIDES DEBILIPALPIS AND CULICOIDES REEVESI IN CHIHUAHUA, MEXICO.},
journal = {Journal of the American Mosquito Control Association},
volume = {},
number = {},
pages = {},
doi = {10.2987/24-7207},
pmid = {39745115},
issn = {1943-6270},
abstract = {In July 2022, adult female Culicoides were collected from San Buenaventura (54 specimens) and Urique (3 specimens) in Chihuahua, Mexico. Culicoides reevesi and Culicoides debilipalpis were new records for the state, with C. reevesi also being a first for Mexico. The study highlights DNA barcode identification challenges and emphasizes the need for ongoing surveillance along the Mexico-USA border.},
}
@article {pmid39745059,
year = {2025},
author = {Huang, Z and Xie, X and Wu, Y and Liu, R and Lv, Y},
title = {Breaking Barcode Limits: Metal Nanoparticle Lego Brick Self-Assembly for High-Throughput Screening.},
journal = {Journal of the American Chemical Society},
volume = {147},
number = {6},
pages = {4904-4914},
doi = {10.1021/jacs.4c13706},
pmid = {39745059},
issn = {1520-5126},
mesh = {*High-Throughput Screening Assays/methods ; *Metal Nanoparticles/chemistry ; Humans ; *Streptavidin/chemistry ; Biotin/chemistry ; Immunoassay/methods ; Biomarkers, Tumor/analysis ; },
abstract = {As precision medicine increasingly reveals the biological diversity among individuals, the demand for higher-throughput screening techniques, particularly suspension array technologies capable of more multiplexing from smaller samples in a single run, is intensifying. However, advancements in the multiplexing capability of current suspension platforms have lagged with limited alleviation, necessitating breakthroughs for innovative solutions that enable larger-scale measurements. Here, we introduce such a breakthrough with a novel mass-cytometric barcode engineering by metal nanoparticle-based "Lego Brick"-like self-assembly for high-throughput barcode design and capacity amplification. The suspension array capacity can be expanded to over 20,500 unique barcodes by flexibly assembling just 10 types of barcoding units (metal nanoparticles) onto the surface of the barcoding center (magnetic spheres) through a universal biotin-streptavidin binding template, significantly enhancing both throughput and versatility. Further multiplexed immunoassay, termed MassMAP, demonstrates high-throughput profiling of cancer biomarkers, highlighting the revolutionary potential of Lego Brick self-assembly in massive cytometric screening for higher-throughput applications.},
}
@article {pmid39742275,
year = {2024},
author = {Ado, S and Dong, C and Attaf, N and Moussa, M and Carrier, A and Milpied, P and Navarro, JM},
title = {FB5P-seq-mAbs: monoclonal antibody production from FB5P-seq libraries for integrative single-cell analysis of B cells.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1505971},
pmid = {39742275},
issn = {1664-3224},
mesh = {Animals ; *Single-Cell Analysis/methods ; *Antibodies, Monoclonal/immunology/genetics ; *B-Lymphocytes/immunology/metabolism ; Mice ; Receptors, Antigen, B-Cell/genetics/immunology ; Gene Library ; Flow Cytometry/methods ; Sequence Analysis, RNA/methods ; Humans ; Transcriptome ; },
abstract = {Parallel analysis of phenotype, transcriptome and antigen receptor sequence in single B cells is a useful method for tracking B cell activation and maturation during immune responses. However, in most cases, the specificity and affinity of the B cell antigen receptor cannot be inferred from its sequence. Antibody cloning and expression from single B cells is then required for functional assays. Here we propose a method that integrates FACS-based 5'-end single-cell RNA sequencing (FB5P-seq) and monoclonal antibody cloning for integrative analysis of single B cells. Starting from a cell suspension, single B cells are FACS-sorted into 96-well plates for reverse transcription, cDNA barcoding and amplification. A fraction of the single-cell cDNA is used for preparing 5'-end RNA-seq libraries that are sequenced for retrieving transcriptome-wide gene expression and paired BCR sequences. The archived cDNA of selected cells of interest is used as input for cloning heavy and light chain variable regions into antibody expression plasmid vectors. The corresponding monoclonal antibodies are produced by transient transfection of a eukaryotic producing cell line and purified for functional assays. We provide detailed step-by-step instructions and describe results obtained on ovalbumin-specific murine germinal center B cells after immunization. Our method is robust, flexible, cost-effective, and applicable to different B cell types and species. We anticipate it will be useful for mapping antigen specificity and affinity of rare B cell subsets characterized by defined gene expression and/or antigen receptor sequence.},
}
@article {pmid39741786,
year = {2024},
author = {Haverinen, R and Pototski, A and Mutanen, M and Mikalauskas, D and Yakovlev, RV and Müller, GC and Prozorov, AM and Saldaitis, A},
title = {Integrative review of Xylomoiastrix, X.retinax and X.stangelmaieri (Lepidoptera, Noctuidae, Xyleninae, Apameini).},
journal = {ZooKeys},
volume = {1221},
number = {},
pages = {309-342},
pmid = {39741786},
issn = {1313-2989},
abstract = {The relationship of Xylomoiastrix Mikkola, 1980; Xylomoiaretinax Mikkola, 1998; and Xylomoiastangelmaieri Mikkola, 1998 is reconsidered based on 59 genitalia slides (37 males and 22 females) and 40 barcodes of adults collected from the type localities and areas in-between. Due to lack of stable morphologic differences, apart from the wing coloration of X.retinax, and low genetic distance between the three, they are considered as three subspecies of X.strix: the nominotypical one X.strixstangelmaieri stat. nov. and X.strixretinax stat. nov. Included are photographs of all specimens covering 37 adults, and 28 male and 18 female genitalia, as well as a phylogenetic tree and a map showing collecting localities.},
}
@article {pmid39739757,
year = {2025},
author = {Ramaprasad, A and Blackman, MJ},
title = {A scaleable inducible knockout system for studying essential gene function in the malaria parasite.},
journal = {Nucleic acids research},
volume = {53},
number = {4},
pages = {},
pmid = {39739757},
issn = {1362-4962},
support = {CC2129/CRUK_/Cancer Research UK/United Kingdom ; 751865//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; CC2129/ARC_/Arthritis Research UK/United Kingdom ; 220318/A/20/Z/WT_/Wellcome Trust/United Kingdom ; CC2129/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; //European Society of Clinical Microbiology and Infectious Diseases/ ; },
mesh = {*Gene Knockout Techniques ; *Genes, Essential ; Frameshift Mutation ; Protozoan Proteins/genetics/metabolism ; Plasmodium falciparum/genetics ; Malaria/parasitology/genetics ; Genes, Protozoan ; Animals ; },
abstract = {The malaria parasite needs nearly half of its genes to propagate normally within red blood cells. Inducible ways to interfere with gene expression like the DiCre-lox system are necessary to study the function of these essential genes. However, existing DiCre-lox strategies are not well-suited to be deployed at scale to study several genes simultaneously. To overcome this, we have developed SHIFTiKO (frameshift-based trackable inducible knockout), a novel scaleable strategy that uses short, easy-to-construct, barcoded repair templates to insert loxP sites around short regions in target genes. Induced DiCre-mediated excision of the flanked region causes a frameshift mutation resulting in genetic ablation of gene function. Dual DNA barcodes inserted into each mutant enables verification of successful modification and induced excision at each locus and collective phenotyping of the mutants, not only across multiple replication cycles to assess growth fitness but also within a single cycle to identify specific phenotypic impairments. As a proof of concept, we have applied SHIFTiKO to screen the functions of malarial rhomboid proteases, successfully identifying their blood stage-specific essentiality. SHIFTiKO thus offers a powerful platform to conduct inducible phenotypic screens to study essential gene function at scale in the malaria parasite.},
}
@article {pmid39739202,
year = {2025},
author = {Bard, NW and Davies, TJ and Cronk, QCB},
title = {Teknonaturalist: A Snakemake Pipeline for Assessing Fungal Diversity From Plant Genome Bycatch.},
journal = {Molecular ecology resources},
volume = {25},
number = {3},
pages = {e14056},
pmid = {39739202},
issn = {1755-0998},
support = {RGPIN-2019-04041//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2020-04439//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Fungi/genetics/classification/isolation &amp; purification ; *Genome, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Plants/microbiology ; DNA, Fungal/genetics ; Endophytes/genetics/classification/isolation &amp; purification ; DNA Barcoding, Taxonomic/methods ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Relatively little is known of the host associations and compatibility of fungal plant pathogens and endophytes. Publicly available plant genomic DNA can be mined to detect incidental fungal DNA, but taxonomic assignment can be challenging due to short lengths and variable discriminative power among different genomic regions and taxa. Here, we introduce a computationally lightweight and accessible Snakemake pipeline for rapid detection and classification (identification and assignment to taxonomic rank) of pathogenic and endophytic fungi (and other fungi associated with plants) that targets the internal transcribed spacer (ITS) region, a fungal barcode standard. We include methods for maximising query sequence length, which gives higher support for ITS1 and ITS2 taxonomic classifications by extending to other fragments of the ITS region and providing taxon-specific local cut-off and confidence scores. We demonstrate our pipeline with a case study using public genomic sequence data for six diverse plant species, including four species within Betula, an ecologically and economically important broadleaved forest tree genus, a shrub and a grass. Our pipeline classified fungi within minutes to a few hours per host individual, with 204 different fungal genera identified at high confidence (≥ 70%). Our pipeline detected and classified pathogenic and endophytic genera known to associate with Betula, and many others with no prior record of association. Our pipeline, leveraging existing sequence data, has several potential applications, including detecting cryptic fungal pathogens and helping characterise the endophytic fungal microbiome, bioprospecting commercially useful fungal species, and determining the plant host range of fungi.},
}
@article {pmid39736908,
year = {2024},
author = {Nguyen, QH and Van Nguyen, T and Vi, TTX and Vu, TTT and Nguyen, LTN and Nguyen, YTH and Nguyen, HD and Tu, TQ and Chu, MH},
title = {Dataset on ITS and some chloroplast DNA regions of Boehmeria holosericea Blume in Vietnam.},
journal = {Data in brief},
volume = {57},
number = {},
pages = {111193},
pmid = {39736908},
issn = {2352-3409},
abstract = {Species of the Boehmeria genus have the potential to be natural medicines and have industrial fibre production uses. Many species of this genus are morphologically similar and are difficult to distinguish, especially when their morphology is distorted. This dataset includes sequence information of several DNA regions isolated from the genome of Boehmeria holosericea, namely ITS (from the nuclear genome), matK, trnL-trnF, trnH-psbA, and rpoC1 (from the chloroplast genome) and phylogenetic analysis results based on the isolated sequences. On the phylogenetic tree based on the matK gene sequence, B. holosericea is grouped with B. umbrosa, B. clidemioides, B. spicata, and B. macrophylla with a bootstrap coefficient of 100%. In the phylogenetic tree based on the trnH-psbA spacer region sequences, B. holosericea was grouped with B. clidemioides (a bootstrap coefficient of 96%). In the phylogenetic tree based on the rpoC1 gene sequences, B. holosericea was grouped with B. spicata (a bootstrap coefficient of 100%). In the phylogenetic tree based on the ITS region sequences, B. holosericea was grouped with B. macrophylla (a bootstrap coefficient of 73%), and based on the trnL-trnF spacer region, B. holosericea was grouped with B. pilociuscula (a bootstrap coefficient of 16%). Two genes, matK and rpoC1 and the trnH-psbA region from the chloroplast genome, are potential DNA barcode candidates that could aid in the species identification of B. holosericea. This dataset the first report on the ITS, matK, trnL-trnF, trnH-psbA, and rpoC1 sequences and the phylogeny of B. holosericea.},
}
@article {pmid39732835,
year = {2024},
author = {Eastburn, DJ and White, KS and Jayne, ND and Camiolo, S and Montis, G and Ha, S and Watson, KG and Yeakley, JM and McComb, J and Seligmann, B},
title = {High-throughput gene expression analysis with TempO-LINC sensitively resolves complex brain, lung and kidney heterogeneity at single-cell resolution.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {31285},
pmid = {39732835},
issn = {2045-2322},
support = {R43 GM140771/GM/NIGMS NIH HHS/United States ; R44 GM140771/GM/NIGMS NIH HHS/United States ; R44GM140771/GF/NIH HHS/United States ; },
mesh = {*Single-Cell Analysis/methods ; Animals ; *Brain/metabolism ; *Kidney/metabolism/cytology ; *Lung/metabolism/cytology ; *Gene Expression Profiling/methods ; Mice ; Transcriptome ; Humans ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {We report the development and performance of a novel genomics platform, TempO-LINC, for conducting high-throughput transcriptomic analysis on single cells and nuclei. TempO-LINC works by adding cell-identifying molecular barcodes onto highly selective and high-sensitivity gene expression probes within fixed cells, without having to first generate cDNA. Using an instrument-free combinatorial indexing approach, all probes within the same fixed cell receive an identical barcode, enabling the reconstruction of single-cell gene expression profiles across as few as several hundred cells and up to 100,000 + cells per sample. The TempO-LINC approach is easily scalable based on the number of barcodes and rounds of barcoding performed; however, for the experiments reported in this study, the assay utilized over 5.3 million unique barcodes. TempO-LINC offers a robust protocol for fixing and banking cells and displays high-sensitivity gene detection from multiple diverse sample types. We show that TempO-LINC has a multiplet rate of less than 1.1% and a cell capture rate of ~ 50%. Although the assay can accurately profile the whole transcriptome (19,683 human, 21,400 mouse and 21,119 rat genes), it can be targeted to measure only actionable/informative genes and molecular pathways of interest - thereby reducing sequencing requirements. In this study, we applied TempO-LINC to profile the transcriptomes of more than 90,000 cells across multiple species and sample types, including nuclei from mouse lung, kidney and brain tissues. The data demonstrated the ability to identify and annotate more than 50 unique cell populations and positively correlate expression of cell type-specific molecular markers within them. TempO-LINC is a robust new single-cell technology that is ideal for large-scale applications/studies with high data quality.},
}
@article {pmid39731283,
year = {2024},
author = {Nieto-Clavijo, C and Morales, L and Delgado-Aldana, A and Hernández, PC and Torres-Molina, I and Gonzalez-Cuiza, A and Cortés-Muñoz, F and Chaparro-Olaya, J},
title = {Enhanced Blastocystis subtyping from stool samples using semi-nested barcode PCR: validation with an NGS-based approach.},
journal = {BioTechniques},
volume = {76},
number = {12},
pages = {581-591},
doi = {10.1080/07366205.2024.2442835},
pmid = {39731283},
issn = {1940-9818},
mesh = {*Blastocystis/genetics/classification/isolation &amp; purification ; *Feces/parasitology ; Humans ; *Blastocystis Infections/parasitology/diagnosis ; *Polymerase Chain Reaction/methods ; *High-Throughput Nucleotide Sequencing/methods ; *RNA, Ribosomal, 18S/genetics ; *DNA, Protozoan/genetics ; DNA Barcoding, Taxonomic/methods ; },
abstract = {In 2006, a PCR method was introduced to subtype Blastocystis by Sanger sequencing of an ≈610 bp amplicon of the 18S rRNA gene. This method, known as barcoding-PCR, has become widespread, although the primer pair used can amplify non-Blastocystis sequences, which can result in false positives. Barcoding-PCR is most effective with DNA extracted from Blastocystis cultures, limiting its sensitivity when used directly with stool samples. As a result, barcoding-PCR can sometimes yield negative results for stool samples confirmed as Blastocystis-positive by microscopy. To improve subtyping from stool-derived DNA, we developed a Semi-Nested barcode PCR that amplifies the barcoding region in a second reaction. Our study shows that this Semi-Nested approach outperforms classical barcoding-PCR, detecting Blastocystis more reliably from stool samples with stronger gel signals and no false positives. This was confirmed by near-complete concordance (68/70 samples) with the Santin-PCR coupled to Next-Generation Sequencing (NGS) as reference standard for Blastocystis subtyping. Of particular interest, one amplicon matched the only previous report of ST35, marking this as the second global detection of ST35 and the first in Colombia. Overall, Semi-Nested barcoded PCR offers a more robust and sensitive alternative compared to classical barcoding-PCR for subtyping Blastocystis directly from stool samples.},
}
@article {pmid39730712,
year = {2024},
author = {Nurtaza, A and Dyussembekova, D and Islamova, S and Samatova, I and Zhanybekova, Z and Umirzakova, A and Magzumova, G and Muranets, A and Kakimzhanova, A},
title = {In Vitro conservation and genetic diversity analysis of rare species Ribes janczewskii.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {31117},
pmid = {39730712},
issn = {2045-2322},
support = {AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; },
mesh = {*Genetic Variation ; Genotype ; Fruit/genetics/growth &amp; development ; DNA Barcoding, Taxonomic ; Conservation of Natural Resources ; },
abstract = {Ribes janczewskii is a rare and valuable plant known for its resistance to spring frosts, pests, and diseases. It is used in hybridization to develop resistant currant varieties but is on the verge of extinction, listed in Kazakhstan Red Book. This study developed a micropropagation and slow-growth storage protocol for conservation. Genotypes were identified through DNA barcode analysis (rbcL, ITS, and matK) and sequences uploaded to the National Center for Biotechnology Information database. Genetic diversity was assessed using iPBS primers, generating 98 fragments with 88-94% polymorphic bands. Biochemical analysis of fruits showed vitamin C content from 4.64 to 5.61 mg/100 g, vitamin E from 2.26 to 3.16 mg/100 g, vitamin B5 from 3.18 to 4.93 mg/100 g, and quercetin up to 12.5 mg/100 g. Micropropagation stages were optimized with 12% hydrogen peroxide for surface sterilization, achieving up to 73.3% explant viability. Effective hormonal combinations for in vitro culture included WPM with BAP 0.2 mg L[-1] and GA 0.5 mg L[-1], and for propagation, BAP 0.25 mg L[-1], GA 0.5 mg L[-1], and IBA 0.5 mg L[-1]. Mannitol (20 g L[-1]) was used for slow-growth storage, keeping explants viable for 4 months without re-cultivation.},
}
@article {pmid39729996,
year = {2025},
author = {Park, J and Cook, S and Lee, D and Choi, J and Yoo, S and Bae, S and Im, HJ and Lee, D and Choi, H},
title = {Generation of super-resolution images from barcode-based spatial transcriptomics by deep image prior.},
journal = {Cell reports methods},
volume = {5},
number = {1},
pages = {100937},
pmid = {39729996},
issn = {2667-2375},
mesh = {*Algorithms ; *Image Processing, Computer-Assisted/methods ; Humans ; *Gene Expression Profiling/methods ; Transcriptome/genetics ; },
abstract = {Spatially resolved transcriptomics (ST) has revolutionized the field of biology by providing a powerful tool for analyzing gene expression in situ. However, current ST methods, particularly barcode-based methods, have limitations in reconstructing high-resolution images from barcodes sparsely distributed in slides. Here, we present SuperST, an algorithm that enables the reconstruction of dense matrices (higher-resolution and non-zero-inflated matrices) from low-resolution ST libraries. SuperST is based on deep image prior, which reconstructs spatial gene expression patterns as image matrices. Compared with previous methods, SuperST generated output images that more closely resembled immunofluorescence images for given gene expression maps. Furthermore, we demonstrated how one can combine images created by SuperST with computer vision algorithms. In this context, we proposed a method for extracting features from the images, which can aid in spatial clustering of genes. By providing a dense matrix for each gene in situ, SuperST can successfully address the resolution and zero-inflation issue.},
}
@article {pmid39729477,
year = {2024},
author = {Lee, M and Lee, HY and Kang, JS and Lee, H and Park, KJ and Park, JY and Yang, TJ},
title = {Correction: Authentication of Allium ulleungense, A. microdictyon and A. ochotense based on super-barcoding of plastid genome and 45S nrDNA.},
journal = {PloS one},
volume = {19},
number = {12},
pages = {e0316742},
pmid = {39729477},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0294457.].},
}
@article {pmid39729273,
year = {2025},
author = {Randall, E and Keillor, B and Cooke, DEL},
title = {The Use of eDNA Metabarcoding to Detect and Identify Phytophthora in Water Samples.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2892},
number = {},
pages = {117-138},
pmid = {39729273},
issn = {1940-6029},
mesh = {*Phytophthora/genetics/isolation &amp; purification ; *DNA Barcoding, Taxonomic/methods ; Water/chemistry ; Water Microbiology ; Metagenomics/methods ; },
abstract = {We describe a protocol to amplify DNA barcodes of known and unknown taxa of Phytophthora and related plant pathogenic oomycetes from a range of environments. The methods focus on sampling pathogen propagules from water using in situ sampling and filtration equipment and buffers that enable efficient storage and DNA extraction for later downstream processing.},
}
@article {pmid39728620,
year = {2024},
author = {Husted, AL and Sutton, VR and Presnar, LA and Blackburn, RK and Staton, JL and Borgianini, SA and D'Antonio, EL},
title = {The Multifunctional Catalytic Hemoglobin from Amphitrite ornata: Protocols on Isolation, Taxonomic Identification, Protein Extraction, Purification, and Characterization.},
journal = {Methods and protocols},
volume = {7},
number = {6},
pages = {},
pmid = {39728620},
issn = {2409-9279},
support = {n/a//Pritchards Island State Funding/ ; 17220-15-39011//University of South Carolina, Office of the Vice President for Research/ ; n/a//University of South Carolina, Office of Undergraduate Research/ ; },
abstract = {The multifunctional catalytic hemoglobin from the terebellid polychaete Amphitrite ornata, also named dehaloperoxidase (AoDHP), utilizes the typical oxygen transport function in addition to four observed activities involved in substrate oxidation. The multifunctional ability of AoDHP is presently a rare observation, and there exists a limitation for how novel dehaloperoxidases can be identified from macrobenthic infauna. In order to discover more infaunal DHP-bearing candidates, we have devised a facilitated method for an accurate taxonomic identification that places visual and molecular taxonomic approaches in parallel. Traditional visual taxonomic species identification by the non-specialist, at least for A. ornata or even for other marine worms, is a very difficult and time-consuming task since a large diversity is present and the method is restricted to adult worm specimens. The work herein aimed to describe a method that simplifies the taxonomic identification of A. ornata in particular through the assessment of its mitochondrial cytochrome c oxidase subunit I gene by employing the DNA barcoding technique. Furthermore, whole-worm specimens of A. ornata were used to extract and purify AoDHP followed by an H2O2-dependent peroxidase activity assay evaluation against substrate 2,4,6-trichlorophenol. AoDHP isoenzyme A was also overexpressed as the recombinant protein in Escherichia coli, and its peroxidase activity parameters were compared to AoDHP from the natural source. The activity assay assessment indicated a tight correlation for all Michaelis-Menten parameters evaluated. We conclude that the method described herein exhibits a streamlined approach to identify the polychaete A. ornata, which can be adopted by the non-specialist, and the full procedure is predicted to facilitate the discovery of novel dehaloperoxidases from other marine invertebrates.},
}
@article {pmid39725934,
year = {2024},
author = {Feng, W and Zhang, Z and Zhang, J and Nan, P and Song, Z and Zhang, W and Yang, J and Wang, Y},
title = {Comparative plastomic analysis of cultivated Dioscorea polystachya and its close relatives provides insights on the inter- and intraspecific phylogenies and potential wild origins of domestication.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {1255},
pmid = {39725934},
issn = {1471-2229},
mesh = {*Dioscorea/genetics/classification/growth &amp; development ; *Phylogeny ; *Genome, Chloroplast ; Domestication ; China ; },
abstract = {BACKGROUND: Dioscorea polystachya and its closely related species are original plants of the tuber crop "yam", which had been intensively use for medicinal and food purposes and widely cultivated in northern China and its surrounding areas with a long history. Many cultivars of these species are often confused with one another because of similar tuber morphology, however, conventional DNA barcoding faces practical limitations restricting the method to effectively identify closely related species. In addition, phylogenetic relationships among various cultivar groups of Chinese yam (D. polystachya) remains unclear. To solve these problems, genomic DNAs of 15 Dioscorea samples were sequenced to assemble and annotate chloroplast genomes, which were used for analyzing their structural characteristics and identifying phylogenetic relationships at the inter- and intraspecific levels.<br><br>RESULTS: The size of chloroplast genomes of the tested samples is about 153&#xa0;kb, and 79 protein-coding genes, 29 tRNA genes, and 4 rRNA genes are annotated. Phylogenetic analysis showed that D. polystachya were sister to Dioscorea japonica, and for Huaishan yams, Dioscorea persimilis did not cluster with Dioscorea alata and Dioscorea fordii. Four cultivar groups of Chinese yam were determined, namely Tiegun group, Anping group, Foshou group and Taihang complex group. Among these cultivar groups, Foshou and Taihang complex are clustered with different wild yams, respectively. Amino acid preferences are similar at the inter- and intraspecific levels, while synonymous codon usage reflects distinct patterns in the majority of cultivars of D. polystachya. There are distinct SSR variations among species, as well as four cultivar groups. Collinearity and SNP analyses show that nucleotide hypervariable regions among Dioscorea species are mainly concentrated in trnK-atpA, rps16-trnQ, atpA-atpH, rpoB-psbD, atpH-atpI, trnV-ndhC in the LSC region, and ccsA-ndhF in the SSC region, while intraspecific variation of Chinese yam is enriched in the intergenic spacers of rpoB-psbC, ndhD-ndhF, and trnQ-trnS, as well as the gene ycf1.<br><br>CONCLUSION: Phylogenetic analysis supports that Huaishan yams are not of monophyletic origin and the cultivated Chinese yam has at least two wild origins of domestication, which is consistent with the historical records of these wild yams from Mt. Dabie and Mt. Taihang. The identification efficiency of the newly developed barcodes for cultivar groups based on chloroplast genome SNP screening is significantly better than those of conventional barcodes. This approach to generate viable candidate markers based on the comparison from interspecific and intraspecific hypervariable regions of chloroplast genomes can be applied to conduct phylogenetic relationships of more important crop species and their close relatives, which are difficult to identify, as well as their wild origins of domestication.},
}
@article {pmid39719730,
year = {2025},
author = {Bergin, R and Samperton, K and Bronikowski, M and Hoar, E and Rolison, J and Shollenberger, Q and Marks, N and Wellons, M and Scott, S},
title = {Synthesis and characterization of isotopically barcoded nickel, molybdenum, and tungsten taggants for intentional nuclear forensics.},
journal = {Talanta},
volume = {285},
number = {},
pages = {127425},
doi = {10.1016/j.talanta.2024.127425},
pmid = {39719730},
issn = {1873-3573},
abstract = {Intentional nuclear forensics is a concept wherein the deliberate addition of benign and persistent material signatures to nuclear material can be used to reduce the time between the discovery of material outside of regulatory control and determination of its original provenance. One concept within intentional nuclear forensics involves the use of perturbed stable isotopes to generate unique isotope ratio "barcodes" to encode information (e.g., production batch, location, etc.) and track material throughout the nuclear fuel cycle. Synthesis of taggant species of nickel (Ni), molybdenum (Mo), and tungsten (W) was undertaken via a double-spike mechanism, wherein two highly enriched isotopes of interest per elemental taggant were mixed to form an enriched "double-spike" which was subsequently isotopically diluted with bulk material having a natural isotopic composition. Two taggant species perturbing isotopic ratios, alpha (α) and beta (β), for each of Ni, Mo, and W were synthesized. Independent measurements of double spikes and alpha and beta taggant species agreed within uncertainty and are clearly resolvable from natural compositions. High-precision analyses were independently performed by MC-ICP-MS at two U.S. National Laboratories, with consensus values and uncertainties calculated for all samples. Observed isotopic perturbations in the final taggant species measured on the order of hundreds to thousands of permille (‰) with respect to natural for isotope ratios of interest (e.g., [60]Ni/[58]Ni, [100]Mo/[98]Mo, [186] W/[183]W). Discrepancies between modeled and measured isotopic compositions were observed and are largely attributed to imprecise vendor assay values for starting materials. Using measured starting material compositions as inputs for the mixing model improved the level of agreement between predicted and measured α and β taggant isotope ratios. Overall, characterization of all taggant species demonstrates that this "barcode" concept could have viability for use in nuclear forensics. It is expected that for any two-isotope mixing array dozens of isotopic barcodes could be encoded into a material system and subsequently resolved utilizing modern mass spectrometric methods.},
}
@article {pmid39719062,
year = {2025},
author = {Long, Y and Mora, A and Li, FZ and Gürsoy, E and Johnston, KE and Arnold, FH},
title = {LevSeq: Rapid Generation of Sequence-Function Data for Directed Evolution and Machine Learning.},
journal = {ACS synthetic biology},
volume = {14},
number = {1},
pages = {230-238},
doi = {10.1021/acssynbio.4c00625},
pmid = {39719062},
issn = {2161-5063},
mesh = {*Machine Learning ; *Directed Molecular Evolution/methods ; *Protein Engineering/methods ; *Software ; },
abstract = {Sequence-function data provides valuable information about the protein functional landscape but is rarely obtained during directed evolution campaigns. Here, we present Long-read every variant Sequencing (LevSeq), a pipeline that combines a dual barcoding strategy with nanopore sequencing to rapidly generate sequence-function data for entire protein-coding genes. LevSeq integrates into existing protein engineering workflows and comes with open-source software for data analysis and visualization. The pipeline facilitates data-driven protein engineering by consolidating sequence-function data to inform directed evolution and provide the requisite data for machine learning-guided protein engineering (MLPE). LevSeq enables quality control of mutagenesis libraries prior to screening, which reduces time and resource costs. Simulation studies demonstrate LevSeq's ability to accurately detect variants under various experimental conditions. Finally, we show LevSeq's utility in engineering protoglobins for new-to-nature chemistry. Widespread adoption of LevSeq and sharing of the data will enhance our understanding of protein sequence-function landscapes and empower data-driven directed evolution.},
}
@article {pmid39718626,
year = {2024},
author = {Dhabal, S and Chakrabarty, AK and Banerjee, D and Katiyar, CK and Rai, RK and Dubey, SK},
title = {Internal transcribed spacer (ITS): The powerful DNA barcode and phylogenetic marker for successful authentication of Withania somnifera.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {77},
pmid = {39718626},
issn = {1573-4978},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Phylogeny ; *Withania/genetics/classification ; Genetic Markers ; *DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: Understanding the evolutionary history of plants and accurately identifying biologically important species and their families is crucial for the herbal and Ayurvedic industries. The genetic approach by DNA barcoding plays a pivotal role in accurate species identification, authentication and quality control. Due to various therapeutic properties, Withania somnifera has been used worldwide in traditional systems of medicine for centuries including Ayurveda and Unani. The increasing demand for W. somnifera products has led to concerns regarding the authenticity and quality of commercial herbal preparations. However, adulteration become major trouble for users and industry for safety reasons and authentication of the plant with proper DNA marker is a major concern.<br><br>METHODOLOGY: DNA barcoding techniques and Phylogenetic analysis were employed to authenticate W. somnifera plant species using universal genetic markers. The markers were PCR amplified, sequenced and analyzed using BLAST-based and phylogeny-based identification methods.<br><br>RESULTS: The BLAST result shows the percent identity (PI) of ITS1, ITS2, trnK, atpB, rbcL and matK was 100%, 100%, 100%, 97.59%, 100 and 99.20% respectively with the NCBI reference sequence. However, ITS1 and ITS2 show the maximum sequence similarity with W. somnifera of NCBI data. Phylogenetic analysis using NCBI data further supports the role of ITS in the discrimination of W. somnifera from closely related species.<br><br>CONCLUSION: Therefore, the ITS gene may be considered promising a candidate for DNA barcoding for discrimination of W. somnifera from other species, its authentication and quality control.},
}
@article {pmid39717638,
year = {2024},
author = {Palandačić, A and Reier, S and Diripasko, OA and Jelić, D and Stroj, A and Wanka, A and Marić, D and Bogutskaya, NG},
title = {Substygophily in Dinaric Karst: A Model Case of Locally Endemic Minnows Phoxinellus (Leuciscinae).},
journal = {Ecology and evolution},
volume = {14},
number = {12},
pages = {e70648},
pmid = {39717638},
issn = {2045-7758},
abstract = {The Dinaric Karst extends along the Adriatic coast of the Western Balkan Peninsula and is home to a group of "karst minnows" of the genera Delminichthys, Phoxinellus, and Telestes, which have adapted to the highly variable water conditions in the karst by spending up to several months underground, but require surface habitats for spawning, defining them as substygophiles. The three species of the genus Phoxinellus, P. alepidotus, P. pseudalepidotus, and P. dalmaticus, are defined by restricted ranges, making them vulnerable to pollution and extended draughts caused by the climate change. In this study, the phylogeny of Leusciscinae was reconstructed using 15 Phoxinellus and one Delminichthys adspersus, one Pelasgus epiroticus, and one Telestes polylepis complete mitochondrial genomes and the position of the genus Phoxinellus within the subfamily as sister species to the Chondrostoma clade was confirmed. The inter- and intrapopulation structure of the genus Phoxinellus was inferred using molecular (nuclear and mitochondrial data) and morphological analyses. For the molecular analysis, more than 150 historical specimens were analyzed for a short fragment of the cytochrome oxidase I (COI) barcoding region and 15 Phoxinellus specimens were subjected to single nucleotide polymorphism analysis. For morphological analysis, 121 Phoxinellus specimens were analyzed for 51 measurements and 8 counts. All analyses confirmed the clear delimitation of the three Phoxinellus species, but were insufficient to fully resolve the intrapopulation structure within the species. This study also included data from field surveys of Phoxinellus collected over the past 20 years, which showed that abundance is declining and ranges are shrinking. Phoxinellus are also threatened by invasive/introduced species. Based on cave observations/occurrence and morphological analysis, P. dalmaticus was classified as an advanced substygophile and P. alepidotus and P. pseudalepidotus were classified as basic stygophiles.},
}
@article {pmid39716438,
year = {2025},
author = {Liu, X and Yang, X and Xiang, S and Lv, Y and Zhang, Z},
title = {Coordination-Defect-Driven Construction of Responsive Pure-MOF Microspheres for Switchable Mode-Dependent Anticounterfeiting Labels.},
journal = {ACS applied materials &amp; interfaces},
volume = {17},
number = {1},
pages = {2063-2071},
doi = {10.1021/acsami.4c19719},
pmid = {39716438},
issn = {1944-8252},
abstract = {Luminescent metal-organic frameworks (MOFs) with exceptional dynamics and diverse active sites possess tremendous potential in information security and anticounterfeiting applications. However, traditional MOF systems are based on broadband spectral signals with spectrum overlap, which easily leads to low-resolution signal identification, compromising the overall security level. Here, we report the coordination-defect-induced amorphous pure-MOF microsphere with switchable whispering-gallery-mode (WGM) signals as a mode-dependent security platform. Amorphous MOF microspheres are prepared by a chlorine coordination-defect-driven growth strategy based on the aperiodic arrangement in coordinate networks. The as-prepared amorphous MOF microspheres with well-defined circular morphology display the typical WGM resonance with dimension-dependent character, permitting the creation of photonic barcodes with substantial encoding capacity. Furthermore, the amorphous MOF microspheres exhibit optical mode switching behavior due to reversible framework shrinkage, which enables the design of covert photonic barcodes as anticounterfeiting labels, finally demonstrating responsive coding property and enhanced information security. The results provide a novel strategy for exploring an MOF-based security platform for information encryption and optical anticounterfeiting.},
}
@article {pmid39714325,
year = {2025},
author = {Vaidya, K and Regan, MS and Lin, J and Houle, J and Gupta, A and Stopka, SA and Agar, NYR and Hammond, PT and Boehnke, N},
title = {Pooled Nanoparticle Screening Using a Chemical Barcoding Approach.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {64},
number = {5},
pages = {e202420052},
pmid = {39714325},
issn = {1521-3773},
support = {DMR-2011401//National Science Foundation/ ; P41EB028741/EB/NIBIB NIH HHS/United States ; K99 CA255844/CA/NCI NIH HHS/United States ; P30 CA014051/CA/NCI NIH HHS/United States ; ECCS-2025124//National Nanotechnology coordinated infrastructure/ ; P41 EB028741/EB/NIBIB NIH HHS/United States ; P30-CA14051/CA/NCI NIH HHS/United States ; K99CA255844/CA/NCI NIH HHS/United States ; R00CA255844/CA/NCI NIH HHS/United States ; R00 CA255844/CA/NCI NIH HHS/United States ; },
mesh = {*Nanoparticles/chemistry ; Humans ; Cell Line, Tumor ; Polylactic Acid-Polyglycolic Acid Copolymer/chemistry ; Small Molecule Libraries/chemistry ; Ovarian Neoplasms ; },
abstract = {We report the development of a small molecule-based barcoding platform for pooled screening of nanoparticle delivery. Using aryl halide-based tags (halocodes), we achieve high-sensitivity detection via gas chromatography coupled with mass spectrometry or electron capture. This enables barcoding and tracking of nanoparticles with minimal halocode concentrations and without altering their physicochemical properties. To demonstrate the utility of our platform for pooled screening, we synthesized a halocoded library of polylactide-co-glycolide (PLGA) nanoparticles and quantified uptake in ovarian cancer cells in a pooled manner. Our findings correlate with conventional fluorescence-based assays. Additionally, we demonstrate the potential of halocodes for spatial mapping of nanoparticles using mass spectrometry imaging (MSI). Halocoding presents an accessible and modular nanoparticle screening platform capable of quantifying delivery of pooled nanocarrier libraries in a range of biological settings.},
}
@article {pmid39714184,
year = {2025},
author = {Leitner, DR and Zingl, FG and Morano, AA and Zhang, H and Waldor, MK},
title = {The Mla pathway promotes Vibrio cholerae re-expansion from stationary phase.},
journal = {mBio},
volume = {16},
number = {2},
pages = {e0343324},
pmid = {39714184},
issn = {2150-7511},
support = {Zingl-2024HHMI//Life Sciences Research Foundation (LSRF)/ ; R01 AI042347/AI/NIAID NIH HHS/United States ; //Howard Hughes Medical Institute (HHMI)/ ; AI-042347//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R37 AI042347/AI/NIAID NIH HHS/United States ; },
mesh = {*Vibrio cholerae/genetics/metabolism/growth &amp; development ; Bacterial Proteins/genetics/metabolism ; DNA Transposable Elements ; Mutation ; Phospholipids/metabolism ; Mutagenesis, Insertional ; Gene Expression Regulation, Bacterial ; },
abstract = {UNLABELLED: Bacteria have evolved diverse strategies to ensure survival under nutrient-limited conditions, where rapid energy generation is not achievable. Here, we performed a transposon insertion site sequencing loss-of-function screen to identify Vibrio cholerae genes that promote pathogen fitness in stationary phase. We discovered that the maintenance of lipid asymmetry (Mla) pathway, which is crucial for transferring phospholipids from the outer to the inner membrane, is critical for stationary phase fitness. Competition experiments with barcoded and fluorophore labeled wild-type (WT) and mlaE mutant V. cholerae revealed that the Mla pathway promotes re-expansion from 48 h stationary phase cultures. The mutant defect in transitioning out of stationary phase into active growth (culturability) was also observed in monocultures at 48 h. However, by 96 h the culturability of the WT and mutant strains were equivalent. By monitoring the abundances of genomically barcoded libraries of WT and ∆mlaE strains, we observed that a few barcodes dominated the mutant culture at 96 h, suggesting that the similarity of the population sizes at this time was caused by expansion of a subpopulation containing a mutation that suppressed the defect of ∆mlaE. Whole genome sequencing revealed that mlaE suppressors inactivated flagellar biosynthesis. Additional mechanistic studies support the idea that the Mla pathway is critical for maintaining the culturability of V. cholerae because it promotes energy homeostasis, likely due to its role in regulating outer membrane vesicle shedding. Together our findings provide insights into the cellular processes that control re-expansion from stationary phase and demonstrate a previously undiscovered role for the Mla pathway.<br><br>IMPORTANCE: Bacteria regularly encounter conditions with nutrient scarcity, where cell growth and division are minimal. Knowledge of the pathways that enable re-growth following nutrient restriction is limited. Here, using the cholera pathogen, we uncovered a role for the Mla pathway, a system that enables phospholipid re-cycling, in promoting Vibrio cholerae re-expansion from stationary phase cultures. Cells labeled with DNA barcodes or fluorophores were useful to demonstrate that though the abundances of wild-type and Mla mutant cells were similar in stationary phase cultures, they had marked differences in their capacities to regrow on plates. Of note, Mla mutant cells lose cell envelope components including high-energy phospholipids due to OMV shedding. Our findings suggest that the defects in cellular energy homeostasis that emerge in the absence of the Mla pathway underlie its importance in maintaining V. cholerae culturability.},
}
@article {pmid39713585,
year = {2024},
author = {Wang, H and Wei, Z and Ren, G},
title = {A new species of Laena Dejean (Coleoptera, Tenebrionidae) from Sichuan Province, China, with an updated key.},
journal = {ZooKeys},
volume = {1221},
number = {},
pages = {165-173},
pmid = {39713585},
issn = {1313-2989},
abstract = {In this study, we describe and illustrate a new species of the genus Laena Dejean, 1821, Laenacostata sp. nov., which was collected in Micangshan Nature Reserve of Sichuan Province, China. Additionally, the COI mitochondrial gene was sequenced to provide additional evidence for this new species' validity. The results of phylogenetic analyses suggest that this new species is sister to L.maowenica Schawaller, 2008. Furthermore, an updated key to Laena species from Sichuan Province is provided.},
}
@article {pmid39713068,
year = {2024},
author = {Douglas, HB and Hammond, G and Smith, TW and Mutz, J and Konstantinov, AS},
title = {Palaearctic flea beetle Phyllotretaochripes (Curtis) (Coleoptera, Chrysomelidae, Galerucinae), herbivore of Alliariapetiolata (garlic mustard), new to North America.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e135576},
pmid = {39713068},
issn = {1314-2828},
abstract = {BACKGROUND: The univoltine leaf beetle Phyllotretaochripes (Curtis, 1837b) is native to the Palaearctic Region from Japan to western Europe.This species was previously evaluated as a potential biological control agent against invasive populations of the woodland weed Alliariapetiolata (Bieb.) Cavara &amp; Grande (Brassicaceae) in North America, but rejected because it could harm native and at-risk populations of Brassicaceae.<br><br>NEW INFORMATION: First North American records are presented for Phyllotretaochripes (Curtis, 1837). Specimens were examined from the USA: Illinois, Maryland, Michigan, Ohio and Pennsylvania. Internet photographs of apparent additional individuals from USA: Indiana, Michigan, Minnesota, Ohio, Pennsylvania, Tennessee, Wisconsin and Canada: Ontario were also examined. DNA barcoding analysis showed high genetic variability and possible cryptic species within European populations of P.ochripes. Diagnostic information is presented to distinguish P.ochripes. from other North American Chrysomelidae and a species distribution model to assess its potential spread in North America is presented.Phyllotretaochripes breeds on invasive garlic mustard, Alliariapetiolata (Bieb.) Cavara &amp; Grande (Brassicaceae) and also non-native Rorippaamphibia (L.) Besser and other species of Brassicaceae.A species distribution model and the range of its host plant A.petiolata, indicates the most suitable conditions for this species are in humid areas of eastern North America. However, most of the known records of this species were discovered in areas projected to have low suitability. This is likely a consequence of sampling bias towards western Europe and away from the eastern Asian portion of its native range. The United States of America and Canada are now known to be home to 72 or more species of adventive Chrysomelidae.},
}
@article {pmid39711595,
year = {2024},
author = {Harun, A and Song, S and You, X and Liu, H and Wen, X and Fang, Z and Cheng, Z and Chen, C},
title = {Comprehensive mapping of molecular cytogenetic markers in pitaya (Hylocereus undatus) and related species.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1493776},
pmid = {39711595},
issn = {1664-462X},
abstract = {Pitaya (Hylocereus undatus; 2n=22) is an important fruit crop from the Cactaceae family, originally domesticated in Mexico and the USA, and is now widely cultivated for its nutritional benefits. It is characterized by its distinctive triangular-shaped stems and large, showy flowers, thriving in arid and semi-arid environments, particularly in hot, dry climates. However, systematic chromosomal studies, including chromosomal mapping of cytogenetic markers in pitaya, are limited, presenting challenges for its cytogenetic improvement. To address this issue, we designed oligo-barcodes specific to thirty-three chromosome regions based on the pitaya reference genome and applied them to both pitaya and cactus (Selenicerus grandifloras; 2n=22) for oligo-barcodes mapping, karyotyping, and chromosome identification. We utilized FISH technology, employing oligo, rDNA, and tandem repeat probes for chromosomal mapping, identification, and karyotyping of pitaya and related species. We successfully localized oligo-barcodes on eleven pairs of chromosomes in both pitaya and cactus, demonstrating the effectiveness of the synthesized oligo-barcodes. We used two ribosomal DNA (rDNA) probes (45S and 5S) and two tandem repeat probes (GTR11 and STR3) in pitaya (both diploid and tetraploid) and two other Cactaceae species (S. grandifloras and Opuntia humifusa; 2n=40) for chromosomal mapping. The analysis of rDNA distribution and CMA (Chromomycin A3) banding across different chromosomes in pitaya and cacti highlights the concept of conserved rDNA. This study provides fundamental insights into cytogenetic markers and their localization across different chromosomes in pitaya and other Cactaceae species.},
}
@article {pmid39711562,
year = {2024},
author = {Enninful, A and Zhang, Z and Klymyshyn, D and Zong, H and Bai, Z and Farzad, N and Su, G and Baysoy, A and Nam, J and Yang, M and Lu, Y and Zhang, NR and Braubach, O and Xu, ML and Ma, Z and Fan, R},
title = {Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {39711562},
issn = {2693-5015},
support = {U54 AG079759/AG/NIA NIH HHS/United States ; U54 CA274509/CA/NCI NIH HHS/United States ; RF1 MH128876/MH/NIMH NIH HHS/United States ; UH3 CA257393/CA/NCI NIH HHS/United States ; U01 CA294514/CA/NCI NIH HHS/United States ; R01 CA245313/CA/NCI NIH HHS/United States ; U54 AG076043/AG/NIA NIH HHS/United States ; RM1 MH132648/MH/NIMH NIH HHS/United States ; },
abstract = {Spatially mapping the transcriptome and proteome in the same tissue section can significantly advance our understanding of heterogeneous cellular processes and connect cell type to function. Here, we present Deterministic Barcoding in Tissue sequencing plus (DBiTplus), an integrative multi-modality spatial omics approach that combines sequencing-based spatial transcriptomics and image-based spatial protein profiling on the same tissue section to enable both single-cell resolution cell typing and genome-scale interrogation of biological pathways. DBiTplus begins with in situ reverse transcription for cDNA synthesis, microfluidic delivery of DNA oligos for spatial barcoding, retrieval of barcoded cDNA using RNaseH, an enzyme that selectively degrades RNA in an RNA-DNA hybrid, preserving the intact tissue section for high-plex protein imaging with CODEX. We developed computational pipelines to register data from two distinct modalities. Performing both DBiT-seq and CODEX on the same tissue slide enables accurate cell typing in each spatial transcriptome spot and subsequently image-guided decomposition to generate single-cell resolved spatial transcriptome atlases. DBiTplus was applied to mouse embryos with limited protein markers but still demonstrated excellent integration for single-cell transcriptome decomposition, to normal human lymph nodes with high-plex protein profiling to yield a single-cell spatial transcriptome map, and to human lymphoma FFPE tissue to explore the mechanisms of lymphomagenesis and progression. DBiTplusCODEX is a unified workflow including integrative experimental procedure and computational innovation for spatially resolved single-cell atlasing and exploration of biological pathways cell-by-cell at genome-scale.},
}
@article {pmid39704725,
year = {2025},
author = {Wang, R and Hastings, WJ and Saliba, JG and Bao, D and Huang, Y and Maity, S and Kamal Ahmad, OM and Hu, L and Wang, S and Fan, J and Ning, B},
title = {Applications of Nanotechnology for Spatial Omics: Biological Structures and Functions at Nanoscale Resolution.},
journal = {ACS nano},
volume = {19},
number = {1},
pages = {73-100},
pmid = {39704725},
issn = {1936-086X},
support = {P20 GM109036/GM/NIGMS NIH HHS/United States ; R21 AI126361/AI/NIAID NIH HHS/United States ; S10 OD032453/OD/NIH HHS/United States ; },
mesh = {*Nanotechnology ; Humans ; *Proteomics/methods ; Metabolomics ; Animals ; DNA/chemistry/metabolism ; Nanostructures/chemistry ; Genomics ; Epigenomics ; },
abstract = {Spatial omics methods are extensions of traditional histological methods that can illuminate important biomedical mechanisms of physiology and disease by examining the distribution of biomolecules, including nucleic acids, proteins, lipids, and metabolites, at microscale resolution within tissues or individual cells. Since, for some applications, the desired resolution for spatial omics approaches the nanometer scale, classical tools have inherent limitations when applied to spatial omics analyses, and they can measure only a limited number of targets. Nanotechnology applications have been instrumental in overcoming these bottlenecks. When nanometer-level resolution is needed for spatial omics, super resolution microscopy or detection imaging techniques, such as mass spectrometer imaging, are required to generate precise spatial images of target expression. DNA nanostructures are widely used in spatial omics for purposes such as nucleic acid detection, signal amplification, and DNA barcoding for target molecule labeling, underscoring advances in spatial omics. Other properties of nanotechnologies include advanced spatial omics methods, such as microfluidic chips and DNA barcodes. In this review, we describe how nanotechnologies have been applied to the development of spatial transcriptomics, proteomics, metabolomics, epigenomics, and multiomics approaches. We focus on how nanotechnology supports improved resolution and throughput of spatial omics, surpassing traditional techniques. We also summarize future challenges and opportunities for the application of nanotechnology to spatial omics methods.},
}
@article {pmid39704499,
year = {2025},
author = {Wäneskog, M and Hoch-Schneider, EE and Garg, S and Kronborg Cantalapiedra, C and Schäfer, E and Krogh Jensen, M and Damgaard Jensen, E},
title = {Accurate phenotype-to-genotype mapping of high-diversity yeast libraries by heat-shock-electroporation (HEEL).},
journal = {mBio},
volume = {16},
number = {2},
pages = {e0319724},
pmid = {39704499},
issn = {2150-7511},
support = {//Wenner-Gren Stiftelserna (Wenner-Gren Foundations)/ ; NNF20SA0035588//Novo Nordisk Fonden (NNF)/ ; NNF210C0069089//Novo Nordisk Fonden (NNF)/ ; NNF20CC0035580//Novo Nordisk Fonden (NNF)/ ; },
mesh = {*Electroporation/methods ; *Saccharomyces cerevisiae/genetics ; *Gene Library ; *Phenotype ; *Genotype ; Transformation, Genetic ; Heat-Shock Response ; Plasmids/genetics ; },
abstract = {High-throughput DNA transformation techniques are invaluable when generating high-diversity mutant libraries, a cornerstone of successful protein engineering. However, transformation efficiencies have a direct correlation with the probability of introducing multiple DNA molecules into each cell, although reliable library screenings require cells that contain a single unique genotype. Thus, transformation methods that yield a high multiplicity of transformations are unsuitable for high-diversity library screenings. Here, we describe an innovative yeast library transformation method that is both simple and highly efficient. Our dual heat-shock and electroporation approach (HEEL) creates high-quality DNA libraries by increasing the fraction of mono-transformed yeast cells from 20% to over 70% of all transformed cells, thus allowing for near-perfect phenotype-to-genotype associations. HEEL also allows more than 10[7] yeast cells per reaction to be transformed with a circular plasmid molecule, which corresponds to an almost 100-fold improvement compared with current yeast transformation methods. To further refine our library screening approach, we integrated an automated yeast genotyping workflow with a dual-barcode design that employs both a single nucleotide polymorphism and a high-diversity region. This design allows for robust identification and quantification of unique genotypes within a heterogeneous population using standard Sanger sequencing. Our findings demonstrate that the longstanding trade-off between the size and quality of transformed yeast libraries can be overcome. By employing the HEEL method, large DNA libraries can be transformed into yeast with high-efficiency, while maintaining high library quality, essential for successful mutant screenings. This advancement holds significant promise for the fields of molecular biology and protein engineering.IMPORTANCEWith the recent expansion of artificial intelligence in the field of synthetic biology, there has never been a greater need for high-quality data and reliable measurements of phenotype-to-genotype relationships. However, one major obstacle to creating accurate computer-based models is the current abundance of low-quality phenotypic measurements originating from numerous high-throughput but low-resolution assays. Rather than increasing the quantity of measurements, new studies should aim to generate as accurate measurements as possible. The HEEL methodology presented here aims to address this issue by minimizing the problem of multi-plasmid uptake during high-throughput yeast DNA transformations, which leads to the creation of heterogeneous cellular genotypes. HEEL should enable highly accurate phenotype-to-genotype measurements going forward, which could be used to construct better computer-based models.},
}
@article {pmid39703419,
year = {2024},
author = {Chamberlin, JT and Gillen, AE and Quinlan, AR},
title = {Improved characterization of 3' single-cell RNA-seq libraries with paired-end avidity sequencing.},
journal = {NAR genomics and bioinformatics},
volume = {6},
number = {4},
pages = {lqae175},
pmid = {39703419},
issn = {2631-9268},
support = {S10 OD021644/OD/NIH HHS/United States ; T15 LM007124/LM/NLM NIH HHS/United States ; },
abstract = {Prevailing poly(dT)-primed 3' single-cell RNA-seq protocols generate barcoded cDNA fragments containing the reverse transcriptase priming site or in principle the polyadenylation site. Direct sequencing across this site was historically difficult because of DNA sequencing errors induced by the homopolymeric primer at the 'barcode' end. Here, we evaluate the capability of 'avidity base chemistry' DNA sequencing from Element Biosciences to sequence through the primer and enable accurate paired-end read alignment and precise quantification of polyadenylation sites. We find that the Element Aviti instrument sequences through the thymine homopolymer into the subsequent cDNA sequence without detectable loss of accuracy. The additional sequence enables direct and independent assignment of reads to polyadenylation sites, which bypasses the complexities and limitations of conventional approaches but does not consistently improve read mapping rates compared to single-end alignment. We also characterize low-level artifacts and demonstrate necessary adjustments to adapter trimming and sequence alignment regardless of platform, particularly in the context of extended read lengths. Our analyses confirm that Element avidity sequencing is an effective alternative to Illumina sequencing for standard single-cell RNA-seq, particularly for polyadenylation site measurement but do not rule out the potential for similar performance from other emerging platforms.},
}
@article {pmid39702735,
year = {2024},
author = {Fandrey, CI and Jentzsch, M and Konopka, P and Hoch, A and Blumenstock, K and Zackria, A and Maasewerd, S and Lovotti, M and Lapp, DJ and Gohr, FN and Suwara, P and Świeżewski, J and Rossnagel, L and Gobs, F and Cristodaro, M and Muhandes, L and Behrendt, R and Lam, MC and Walgenbach, KJ and Bald, T and Schmidt, FI and Latz, E and Schmid-Burgk, JL},
title = {NIS-Seq enables cell-type-agnostic optical perturbation screening.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {39702735},
issn = {1546-1696},
abstract = {Optical pooled screening offers a broader-scale alternative to enrichment-based perturbation screening, using fluorescence microscopy to correlate phenotypes and perturbations across single cells. Previous methods work well in large, transcriptionally active cell lines, because they rely on cytosolic detection of endogenously expressed barcoded transcripts; however, they are limited by reliable cell segmentation, cytosol size, transcriptional activity and cell density. Nuclear In-Situ Sequencing (NIS-Seq) expands this technology by creating bright sequencing signals directly from nuclear genomic DNA to screen nucleated cells at high density and high library complexity. By inserting an inverted phage promoter downstream of the single guide RNA (sgRNA), many RNA copies of the sgRNA can be generated and sequenced independently of cellular transcription. In this study, we benchmarked NIS-Seq across eight cell types from two species and performed four genome-scale optical perturbation screens, identifying key players of inflammation-related cellular pathways. Finally, we performed a small-scale pooled optical screen in primary human macrophages from blood of healthy donors and demonstrated barcode identification in lentivirally transduced human skin tissue.},
}
@article {pmid39701988,
year = {2024},
author = {Zhang, J and Ning, Y and Li, J and Deng, Y and Wang, L and Mao, S and Zhao, B},
title = {Comparative chloroplast genome analysis of Ardisia (Myrsinoideae, Primulaceae) in China and implications for phylogenetic relationships and adaptive evolution.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {1198},
pmid = {39701988},
issn = {1471-2229},
support = {[2022]-KJ019 and [2021]-KJ014//Science and technology plan project of Guangzhou Construction Group/ ; 32060090//National Natural Science Foundation of China/ ; 2021JJA130119//Natural Science Foundation of Guangxi Province/ ; },
mesh = {*Genome, Chloroplast ; *Phylogeny ; China ; *Ardisia/genetics ; Evolution, Molecular ; Microsatellite Repeats/genetics ; },
abstract = {BACKGROUND: Numerous species of Ardisia are widely used for their medicinal and ornamental values in China. However, accurately identifying Ardisia species at the molecular level remains a challenge due to the morphological similarities among different species, the complexity of interspecific variation, and the limited availability of genetic markers. In this study, we reported 20 chloroplast genomes of Ardisia species from China and combined them with 8 previously published chloroplast genomes to conduct a comprehensive analysis for phylogenetic relationships and adaptive evolution.<br><br>RESULTS: For the 28 Ardisia species analyzed in this study, the size of the chloroplast genomes ranged from 155,088&#xa0;bp to 156,999&#xa0;bp, and all exhibited a typical tetrad structure with conserved gene content and number. Each genome contained 85-88 protein-coding genes, 36-37 tRNA genes, and 8 rRNA genes. Comparative analysis showed that the genomic structures and gene order were relatively conserved with slight variations in the inverted repeat regions (IRs). Simple sequence repeats (SSRs) were predominantly single nucleotide repeats, while repeat sequences were mainly composed of palindromic and forward repeats. Twelve highly variable regions were identified as potential DNA barcodes for species identification and phylogenetic analysis of Ardisia. The phylogenetic tree supported the division of the subgenus Bladhia s.l. into two subgenera: Bladhia s.str. and Odontophylla (Yang) Huang. Further investigation revealed that two protein-coding genes (rbcL and rpoC2) were under positive selection and might be associated with the adaptation of Ardisia species to shaded environments.<br><br>CONCLUSION: Our study analyzed the chloroplast genomes of 20 Ardisia species from China to explore their phylogenetic relationships and adaptive evolution. By combining these results with data from eight previously published chloroplast genomes, the essential characteristics of Ardisia chloroplast genomes were clarified. The research establishes a theoretical basis for the classification, identification, and comprehension of the adaptive evolution of Ardisia species.},
}
@article {pmid39700063,
year = {2025},
author = {Munusamy, S and Zheng, H and Jahani, R and Zhou, S and Chen, J and Kong, J and Guan, X},
title = {DNA-Assisted CRISPR-Cas12a Enhanced Fluorescent Assay for Protein Detection in Complicated Matrices.},
journal = {ACS applied bio materials},
volume = {8},
number = {1},
pages = {754-762},
doi = {10.1021/acsabm.4c01600},
pmid = {39700063},
issn = {2576-6422},
mesh = {*CRISPR-Cas Systems/genetics ; Humans ; *DNA/chemistry ; Materials Testing ; Biocompatible Materials/chemistry ; Particle Size ; CRISPR-Associated Proteins/genetics/metabolism ; Endodeoxyribonucleases/metabolism/genetics ; Proteins/analysis/metabolism ; Bacterial Proteins ; },
abstract = {Proteins are important biological macromolecules that perform a wide variety of functions in the cell and human body, and can serve as important biomarkers for early diagnosis and prognosis of human diseases as well as monitoring the effectiveness of disease treatment. Hence, sensitive and accurate detection of proteins in human biospecimens is imperative. However, at present, there is no ideal method available for the detection of proteins in clinical samples, many of which are present at ultralow (less than 1 pM) concentrations and in complicated matrices. Herein, we report an ultrasensitive and selective DNA-assisted CRISPR-Cas12a enhanced fluorescent assay (DACEA) for protein detection with detection limits reaching as low as attomolar concentrations. The high assay sensitivity was accomplished through the combined DNA barcode amplification (by using dual-functionalized AuNPs) and CRISPR analysis, while the high selectivity and high resistance to the matrix effects of our method were accomplished via the formation of protein-antibody sandwich structure and the specific recognition of Cas12a (under the guidance of crRNA) toward the designed target ssDNA. Given its ability to accurately and sensitively detect trace amounts of proteins in complicated matrices, the DACEA protein assay platform pioneered in this work has a potential application in routine protein biomarker testing.},
}
@article {pmid39698230,
year = {2024},
author = {Huang, WC and Hibino, Y and Balisco, RA and Liao, TY},
title = {Description of a new uniformly brown estuarine moray eel (Anguilliformes, Muraenidae) from the Central Indo-Pacific Ocean.},
journal = {ZooKeys},
volume = {1220},
number = {},
pages = {15-34},
pmid = {39698230},
issn = {1313-2989},
abstract = {A new estuarine moray eel, Uropterygiushades sp. nov., is described based on 14 specimens from Japan, Taiwan, the Philippines, southern Indonesia, and Fiji. It is a small-bodied, slender, uniformly dark-brown moray separated from congeners within the U.concolor species complex. The new species can be distinguished from congeners by the anteriorly positioned small eyes (5.0-7.2% of head length), absence of branchial pores, and extended inner rows of teeth which reach the posterior end of the jaws. Uropterygiushades sp. nov. represents a rare species of moray eel that inhabits turbid estuarine environments, preferring soft, muddy substrates, and burrowing and hiding among rocks or in fallen mangrove leaves. Additionally, Uropterygiusmactanensis Huang, Balisco, Evacitas &amp; Liao, another species recently separated from the U.concolor species complex, is reported for the first time from Iriomote Island in the Ryukyu Archipelago based on two specimens; this new record expands the geographic range of U.mactanensis from the central Philippines to southern Japan.},
}
@article {pmid39696450,
year = {2024},
author = {Wang, YW and Tan, PC and Li, QF and Xu, XW and Zhou, SB},
title = {Adipose tissue protects against skin photodamage through CD151- and AdipoQ- EVs.},
journal = {Cell communication and signaling : CCS},
volume = {22},
number = {1},
pages = {594},
pmid = {39696450},
issn = {1478-811X},
mesh = {Animals ; *Adiponectin/metabolism ; *Skin/metabolism ; *Fibroblasts/metabolism ; Mice ; *Adipose Tissue/metabolism/cytology ; *Extracellular Vesicles/metabolism ; Humans ; Mice, Nude ; Cell Proliferation ; },
abstract = {To clarify the protective effects of subcutaneous adipose tissue (SAT) against photodamage, we utilized nude mouse skin with or without SAT. Skin and fibroblasts were treated with adipose tissue-derived extracellular vesicles (AT-EVs) or extracellular vesicles derived from adipose-derived stem cells (ADSC-EVs) to demonstrate that SAT protects the overlying skin from photodamage primarily through AT-EVs. Surprisingly, AT-EVs stimulated fibroblast proliferation more rapidly than ADSC-EVs did. The yield of AT-EVs from the same volume of AT was 200 times greater than that of ADSC-EVs. To compare the differences between AT-EVs and ADSC-EVs, we used a proximity barcoding assay (PBA) to analyze the surface proteins on individual particles of these two types of EVs. PBA analysis revealed that AT-EVs contain diverse subpopulations, with 83.42% expressing CD151, compared to only 1.98% of ADSC-EVs. Furthermore, AT-EVs are internalized more rapidly by cells than ADSC-EVs, as our study demonstrated that CD151-positive AT-EVs were endocytosed more quickly than their CD151-negative counterparts. Additionally, adiponectin in AT-EVs activated the AMPK pathway and inhibited the NF-κB pathway, enhancing fibroblast protection against photodamage. The significantly higher yield and faster acquisition of AT-EVs compared to ADSC-EVs underscore their potential for broader applications.},
}
@article {pmid39695811,
year = {2024},
author = {Jeon, J and Kim, HC and Donnelly, MJ and Choi, KS},
title = {Genetic diversity and Wolbachia infection in the Japanese encephalitis virus vector Culex tritaeniorhynchus in the Republic of Korea.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {518},
pmid = {39695811},
issn = {1756-3305},
mesh = {Animals ; *Culex/virology/microbiology ; *Wolbachia/genetics/isolation &amp; purification/classification ; *Genetic Variation ; *Mosquito Vectors/microbiology/virology ; Republic of Korea/epidemiology ; *Encephalitis Virus, Japanese/genetics/classification/isolation &amp; purification ; Phylogeny ; Encephalitis, Japanese/epidemiology/transmission/virology ; Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; },
abstract = {BACKGROUND: Culex tritaeniorhynchus, a major vector of Japanese encephalitis virus (JEV), is found across a broad geographical range, including Africa, Asia, Australia and Europe. Understanding the population structure and genetic diversity of pathogen vectors is increasingly seen as important for effective disease control. In China and Japan, two countries in close proximity to the Republic of Korea (ROK), Cx. tritaeniorhynchus has been categorized into two clades based on the DNA barcoding region of mitochondrial cytochrome c oxidase subunit I (COI), suggesting the presence of cryptic species. No comprehensive analysis of the genetic diversity in Cx. tritaeniorhynchus has been conducted in the ROK. To address this gap, we investigated the population structure of Cx. tritaeniorhynchus in the ROK.<br><br>METHODS: In Daegu, mosquito collections were conducted over a 2-year period from 2022 to 2023. For all other regions, Cx. tritaeniorhynchus specimens collected in 2023 were used. The COI barcoding region was analyzed to determine the genetic structure of the populations, supplemented with data from the 28S ribosomal DNA region. Each population was also examined for the eventual presence of Wolbachia infection. Finally, a back trajectory analysis was conducted to assess the possibility of international introduction of Cx. tritaeniorhynchus into the ROK.<br><br>RESULTS: The analysis of the COI region revealed the presence of two distinct clades within Cx. tritaeniorhynchus; these clades were the same as Cx. tritaeniorhynchus continental type (Ct-C) and C. tritaeniorhynchus Japanese type (Ct-J) previously reported. In contrast, the nuclear 28S region showed no significant genetic differentiation between these clades. Wolbachia infection was confirmed in some populations, but there was no evidence of an association with Wolbachia in Ct-C and Ct-J. It was also confirmed that the ROK is currently dominated by the Ct-J clade, with a possible introduction of Ct-C via air currents.<br><br>CONCLUSIONS: Determining the presence of cryptic species is important for preventing vector-borne diseases. The results of this study confirm the existence of two clades of Cx. tritaeniorhynchus in the ROK, with Ct-J being the dominant clade. Our findings enhance current understanding of the genetic diversity within Cx. tritaeniorhynchus and provide valuable insights for the prevention of JEV outbreaks and the effective management of Cx. tritaeniorhynchus populations in East Asia.},
}
@article {pmid39695748,
year = {2024},
author = {Aupalee, K and Srisuka, W and Limsopatham, K and Sanit, S and Takaoka, H and Saeung, A},
title = {Reliability of wing morphometrics for species identification of human-biting black flies (Diptera: Simuliidae) in Thailand.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {508},
pmid = {39695748},
issn = {1756-3305},
support = {106-2565//Faculty of Medicine, Chiang Mai University/ ; },
mesh = {Animals ; Thailand ; *Wings, Animal/anatomy &amp; histology ; *Phylogeny ; *Simuliidae/anatomy &amp; histology/classification/genetics ; Female ; *DNA Barcoding, Taxonomic/methods ; *Electron Transport Complex IV/genetics ; Humans ; Reproducibility of Results ; },
abstract = {BACKGROUND: Fast and reliable species identification of black flies is essential for research proposes and effective vector control. Besides traditional identification based on morphology, which is usually supplemented with molecular methods, geometric morphometrics (GM) has emerged as a promising tool for identification. Despite its potential, no specific GM techniques have been established for the identification of black fly species.<br><br>METHODS: Adult female black flies collected using human bait, as well as those reared from pupae, were used in this study. Here, landmark-based GM analysis of wings was assessed for the first time to identify human-biting black fly species in Thailand, comparing this approach with the standard morphological identification method and DNA barcoding based on the mitochondrial cytochrome c oxidase subunit I (COI) gene. To explore genetic relationships between species, maximum likelihood (ML) and neighbor-joining (NJ) phylogenetic trees were built. Additionally, three different methods of species delimitation, i.e., assemble species by automatic partitioning (ASAP), generalized mixed yule coalescent (GMYC), and single Poisson tree processes (PTP), were utilized to identify the morphologically defined species. The effectiveness of a COI barcode in identifying black fly species was further examined through the best match (BM) and best close match (BCM) methods.<br><br>RESULTS: Seven black fly species, namely Simulium tenebrosum Takaoka, Srisuka &amp; Saeung, 2018 (complex), S. doipuiense Takaoka &amp; Choochote, 2005 (complex), S. nigrogilvum Summers, 1911, S. nodosum Puri, 1933, S. asakoae Takaoka &amp; Davies, 1995, S. chamlongi Takaoka &amp; Suzuki, 1984, and S. umphangense Takaoka, Srisuka &amp; Saeung, 2017 were morphologically identified. Compared with the standard method, the GM analysis based on wing shape showed high success in separating species, achieving an overall accuracy rate of 88.54%. On the other hand, DNA barcoding surpassed wing GM for species identification with a correct identification rate of 98.57%. Species delimitation analyses confirmed the validity of most nominal species, with an exception for S. tenebrosum complex and S. doipuiense complex, being delimited as a single species. Moreover, the analyses unveiled hidden diversity within S. asakoae, indicating the possible existence of up to four putative species.<br><br>CONCLUSIONS: This study highlights the potential of wing GM as a promising and reliable complementary tool for species identification of human-biting black flies in Thailand.},
}
@article {pmid39695366,
year = {2024},
author = {Pere, K and Mburu, K and Muge, EK and Wagacha, JM and Nyaboga, EN},
title = {Molecular identification, genetic diversity, and secondary structure predictions of Physalis species using ITS2 DNA barcoding.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {1178},
pmid = {39695366},
issn = {1471-2229},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Physalis/genetics ; *Genetic Variation ; *Phylogeny ; Kenya ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Nucleic Acid Conformation ; },
abstract = {BACKGROUND: The genus Physalis belongs to the Solanaceae family and has different species with important nutritional and medicinal values. Species within this genus have limited morphological differences, a characteristic that hinders accurate identification, safe utilization and genetic conservation of promising genotypes. In addition, to prevent the perceived loss of Physalis diversity due to habitat destruction, species delimitation needs attention. In this study, we used the sequence and structural information of the internal transcribed spacer 2 (ITS2) barcode to efficiently identify and discriminate Physalis species from a collection of 34 Physalis accessions.<br><br>METHODOLOGY: Physalis plant samples were collected from eight Counties in Kenya based on the availability of the germplasm. The voucher specimens were identified using the botanical taxonomy method and were deposited in the University of Nairobi herbarium. A total of 34 Physalis accessions were identified and accessed for diversity based on the ITS2 barcode region. The sequence similarity of the ITS2 genes was analyzed through the Basic Local Alignment Search Tool (BLAST), the nearest Kimura-2-parameter (K2P) genetic distances were calculated and a phylogenetic tree was constructed using the Bayesian inference (BI) method in MrBayes 3.2.7a software. The differences in the ITS2 secondary structure between the species were analyzed.<br><br>RESULTS: The success rate of PCR amplification and sequencing was 75% and 67%, respectively. The analyzed ITS2 sequences displayed significant inter-specific divergences, clear DNA barcoding gaps and high species identification efficiency. Based on the constructed phylogenetic tree, three Physalis species (Physalis peruviana, Physalis purpurea and Physalis cordata) were identified and were clustered in a homogenized distribution. High genetic diversity (0.36923) and genetic distance (0.703) were observed between Physalis peruviana and Physalis cordata. The highest genetic nucleotide diversity (0.26324) and distance (0.46) within species was obtained for Physalis peruviana. The differences in the secondary structures generated from this study discriminated between the Physalis species.<br><br>CONCLUSIONS: Our study demonstrated that ITS2 is a potential DNA barcode for effective identification and discrimination of Physalis species. The results of this study provide insights into the scientific basis of species identification, safe utilization, genetic conservation and future breeding strategies for this important nutritional and medicinal plant species.},
}
@article {pmid39695327,
year = {2024},
author = {Schröder, LC and Hüttermann, L and Kliesow Remes, A and Voran, JC and Hille, S and Sommer, W and Lutter, G and Warnecke, G and Frank, D and Schade, D and Müller, OJ},
title = {AAV library screening identifies novel vector for efficient transduction of human aorta.},
journal = {Gene therapy},
volume = {},
number = {},
pages = {},
pmid = {39695327},
issn = {1476-5462},
abstract = {Targeted gene delivery to vascular smooth muscle cells (VSMCs) could prevent or improve a variety of diseases affecting the vasculature and particularly the aorta. Thus, we aimed to develop a delivery vector that efficiently targets VSMCs. We selected engineered adeno-associated virus (AAV) capsids from a random AAV capsid library and tested the top enriched motifs in parallel screening through individual barcoding. This approach allowed us to distinguish capsids that only transduce cells based on genomic DNA (gDNA) from those also mediating transgene expression based on transcribed cDNA reads. After three rounds of selection on primary murine VSMCs (mVSMCs), we identified a novel targeting motif (RFTEKPA) that significantly improved transduction and gene expression efficiency over AAV9-wild type (WT) and increased expression in mVSMCs by 70% compared to the previously identified SLRSPPS peptide. Further analysis showed that the novel motif also improved expression in human aortic smooth muscle cells (HAoSMCs) and human aortic tissue ex vivo up to threefold compared to SLRSPPS and approximately 70-fold to AAV9-WT. This high cross-species transduction efficiency makes the novel capsid motif a potential candidate for future clinical application in vascular diseases.},
}
@article {pmid39695009,
year = {2024},
author = {Herath, DR and Perera, HACC and Ranasinghe, VK and Amarakoon, AADG and Hettiarachchi, GHCM},
title = {Stomach content analysis of Euthynnus affinis, Auxis thazard and Auxis rochei of the coastal waters of Sri Lanka by DNA barcoding.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {63},
pmid = {39695009},
issn = {1573-4978},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Sri Lanka ; *Gastrointestinal Contents ; *Tuna/genetics ; Feeding Behavior/physiology ; Predatory Behavior ; Fishes/genetics/classification ; },
abstract = {BACKGROUND: Analysis of the content of the gut of fish helps in the understanding of their inter- and intra-specific interactions, fish behaviour, condition and energy intake. The stomach contents of the commercially important neritic tuna species of Sri Lanka, kawakawa (Euthynnus affinis), frigate tuna (Auxis thazard) and bullet tuna (Auxis rochei) were analysed to determine their feeding habits and to identify prey species.<br><br>METHODS AND RESULTS: The weighed stomachs of fish were dissected to reveal the types of prey found within. The prey was categorised into prey categories and each prey species was identified morphologically. Prey items which were partially digested were identified using DNA barcoding. The main prey category was small fish, followed by crustaceans and cephalopods. While the highest occurring prey category for E. affinis and A. rochei was fish, crustaceans dominated the A. thazard diet. DNA barcoding identified 11 prey items that were partially digested, which could not be identified to species-level morphologically. Of the prey items identified by DNA barcoding, four species of fish, three species of cephalopod and four species of crustaceans were identified. These prey item identifications confirmed that E. affinis, A. thazard and A. rochei are all nonspecific feeders.<br><br>CONCLUSIONS: This exhibits the value of molecular tools in the identification of species which have lost their distinguishable features due to digestion. Further, it illustrates the predator-prey relationships between these species, aiding in the management of prey and predator populations, ensuring that both populations remain stable, helping in the maintenance of the balance of the ecosystem.},
}
@article {pmid39693934,
year = {2025},
author = {Heo, EH and Abrol, R},
title = {Thermodynamic role of receptor phosphorylation barcode in cannabinoid receptor desensitization.},
journal = {Biochemical and biophysical research communications},
volume = {743},
number = {},
pages = {151100},
pmid = {39693934},
issn = {1090-2104},
support = {R16 GM153621/GM/NIGMS NIH HHS/United States ; SC2 GM130480/GM/NIGMS NIH HHS/United States ; },
mesh = {Phosphorylation ; *Thermodynamics ; *Receptor, Cannabinoid, CB2/metabolism/chemistry/genetics ; Humans ; beta-Arrestin 2/metabolism/genetics/chemistry ; Molecular Dynamics Simulation ; Protein Binding ; Signal Transduction ; Models, Molecular ; Protein Conformation ; },
abstract = {The endocannabinoid signaling system is comprised of CB1 and CB2 G protein-coupled receptors (GPCRs). CB2 receptor subtype is predominantly expressed in the immune cells and signals through its transducer proteins (Gi protein and β-arrestin-2). Arrestins are signaling proteins that bind to many GPCRs after receptor phosphorylation to terminate G protein signaling (desensitization) and to initiate specific G protein-independent arrestin-mediated signaling pathways via a "phosphorylation barcode", that captures sequence patterns of phosphorylated Ser/Thr residues in the receptor's intracellular domains and can lead to different signaling effects. The structural basis for how arrestins and G proteins compete with the receptor for biased signaling and how different barcodes lead to different signaling profiles is not well understood as there is a lack of phosphorylated receptor structures in complex with arrestins. In this work, structural models of β-arrestin-2 were built in complex with the phosphorylated and unphosphorylated forms of the CB2 receptor. The complex structures were relaxed in the lipid bilayer environment with molecular dynamics (MD) simulations and analyzed structurally and thermodynamically. The β-arrestin-2 complex with the phosphorylated receptor was more stable than the non-phosphorylated one, highlighting the thermodynamic role of the receptor phosphorylation. It was also more stable than any of the G protein complexes with CB2 suggesting that phosphorylation signals receptor desensitization (end of G protein signaling) and arrest of the receptor by arrestins. These models are beginning to provide the thermodynamic landscape of CB2 signaling, which can help bias signaling towards therapeutically beneficial pathways in drug discovery applications.},
}
@article {pmid39693656,
year = {2025},
author = {Eriksen, TE and Brittain, JE and Sandin, L and Friberg, N},
title = {Unveiling cryptic macroinvertebrate sentinels to enhance biomonitoring in tropical rivers: Bridging traditional approaches with DNA barcoding in the Indo-Burma biodiversity hotspot.},
journal = {The Science of the total environment},
volume = {958},
number = {},
pages = {178064},
doi = {10.1016/j.scitotenv.2024.178064},
pmid = {39693656},
issn = {1879-1026},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Rivers ; Animals ; *Biodiversity ; *Environmental Monitoring/methods ; *Invertebrates/genetics ; Myanmar ; *Biological Monitoring/methods ; Ecosystem ; Tropical Climate ; },
abstract = {Human activities present significant threats to tropical freshwater ecosystems, notably in many global biodiversity hotspots, threats that are further increased by inadequate taxonomic knowledge and the lack of appropriate biomonitoring tools. This study integrates globally validated biomonitoring approaches with DNA-based identification methods to create a macroinvertebrate-based tool for diagnosing ecosystem health and assessing the biodiversity of tropical river ecosystems in Myanmar (Indo-Burma bioregion). To evaluate river site degradation, comprehensive data on water and habitat quality, as well as land use information, were collected. Riverine macroinvertebrates were sampled by kick sampling, and subsequent DNA barcoding analysis was used to establish molecular taxonomic units (MTUs) for key bioindicator groups, including Ephemeroptera, Plecoptera, Trichoptera, Coleoptera, and Odonata (EPTCO) as species-level identification nomenclature was lacking. Tolerance scores for the local fauna were derived along an environmental degradation gradient to enable comparisons with widely adopted global assessment tools relying on macroinvertebrate metrics. In both study areas, the upper parts of the river networks were generally undisturbed by human activities while stressors associated with urban and agricultural land use were evident in the lower parts of the catchments. The highest precision for assessment of river health was found when establishing tolerance scores adjusted to local species composition in each study area separately. Although a family-level-based multimetric approach was significantly related to the main environmental degradation gradient, assessments utilizing cryptic species-level data (MTUs) emerged as the being most precise indicator in both areas. Our study highlights the synergistic benefits of merging traditional biomonitoring with DNA-based methods for species identification for biomonitoring in tropical river ecosystems. To halt biodiversity decline and curb the extent of the escalating nature crisis, such integrated approaches will be highly valuable in understudied and biodiversity-rich aquatic ecosystems.},
}
@article {pmid39688736,
year = {2024},
author = {Singha, D and Patidar, A and Pal, S and Tyagi, K and Kumar, V},
title = {Mitochondrial genetic diversity of pest and vector species, Frankliniella schultzei (Thripidae: Thripinae).},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {55},
pmid = {39688736},
issn = {1573-4978},
support = {CRG/2023/000498//Science and Engineering Research Board/ ; },
mesh = {Animals ; *Phylogeny ; *Genetic Variation/genetics ; *Haplotypes/genetics ; India ; *Thysanoptera/genetics/classification ; DNA Barcoding, Taxonomic/methods ; Australia ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Insect Vectors/genetics/classification ; Bayes Theorem ; Gene Flow ; },
abstract = {BACKGROUND: Frankliniella schultzei (Trybom) is a serious pest and a carrier of tospoviruses in major agricultural crops. This species is a historical and unresolved species complex that contains genetically different cryptic species across the globe.<br><br>METHODS AND RESULTS: DNA barcodes were generated from freshly collected specimens of F. schultzei from India and Australia using the sanger sequencing. Seventy-five COI sequences were generated from India and Australia. Moreover, 318 sequences were downloaded (India, Australia, Pakistan, and Africa) from the NCBI GenBank to explore the genetic diversity and phylogeny. The minimum and maximum mean interspecific distance between 393 sequences was found to be 7.97% and 21.50%, respectively. Bayesian and Neighbour joining clustering indicated the presence of five putative species within F. schultzei that had sympatry and allopatry. Moreover, 20 haplotypes and 140 polymorphic sites were identified. The African clade is unique; it does not share haplotypes with any other countries, suggesting it may represent the true F. schultzei. Haplotype network analysis showed shallow gene flow and deep genetic variation between the populations. Signatures of recent population history events were measured using Fu's Fs test and Tajima's D test. Morphometric analysis based on seven characters is also carried out.<br><br>CONCLUSION: Phylogeny and genetic distance revealed the presence of five putative species within F. schultzei. On the contrary, morphology does not unequivocally corroborate the phylogenetic results, as morphometric analysis showed overlap among these clades. To resolve F. schultzei species complex, whole genome-based sequencing data are very much necessitated.},
}
@article {pmid39687742,
year = {2024},
author = {Haile, S and Corbett, RD and O'Neill, K and Xu, J and Smailus, DE and Pandoh, PK and Bayega, A and Bala, M and Chuah, E and Coope, RJN and Moore, RA and Mungall, KL and Zhao, Y and Ma, Y and Marra, MA and Jones, SJM and Mungall, AJ},
title = {Adaptable and comprehensive approaches for long-read nanopore sequencing of polyadenylated and non-polyadenylated RNAs.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1466338},
pmid = {39687742},
issn = {1664-8021},
abstract = {The advent of long-read (LR) sequencing technologies has provided a direct opportunity to determine the structure of transcripts with potential for end-to-end sequencing of full-length RNAs. LR methods that have been described to date include commercial offerings from Oxford Nanopore Technologies (ONT) and Pacific Biosciences. These kits are based on selection of polyadenylated (polyA+) RNAs and/or oligo-dT priming of reverse transcription. Thus, these approaches do not allow comprehensive interrogation of the transcriptome due to their exclusion of non-polyadenylated (polyA-) RNAs. In addition, polyA + specificity also results in 3'-biased measurements of PolyA+ RNAs especially when the RNA input is partially degraded. To address these limitations of current LR protocols, we modified rRNA depletion protocols that have been used in short-read sequencing: one approach representing a ligation-based method and the other a template-switch cDNA synthesis-based method to append ONT-specific adaptor sequences and by removing any deliberate fragmentation/shearing of RNA/cDNA. Here, we present comparisons with poly+ RNA-specific versions of the two approaches including the ONT PCR-cDNA Barcoding kit. The rRNA depletion protocols displayed higher proportions (30%-50%) of intronic content compared to that of the polyA-specific protocols (5%-8%). In addition, the rRNA depletion protocols enabled ∼20-50% higher detection of expressed genes. Other metrics that were favourable to the rRNA depletion protocols include better coverage of long transcripts, and higher accuracy and reproducibility of expression measurements. Overall, these results indicate that the rRNA depletion-based protocols described here allow the comprehensive characterization of polyadenylated and non-polyadenylated RNAs. While the resulting reads are long enough to help decipher transcript structures, future endeavors are warranted to improve the proportion of individual reads representing end-to-end spanning of transcripts.},
}
@article {pmid39684314,
year = {2024},
author = {Domingo-Bretón, R and Moroni, F and Toxqui-Rodríguez, S and Belenguer, &#xc1; and Piazzon, MC and Pérez-Sánchez, J and Naya-Català, F},
title = {Moving Beyond Oxford Nanopore Standard Procedures: New Insights from Water and Multiple Fish Microbiomes.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684314},
issn = {1422-0067},
support = {871108//Horizon H2020/ ; PRTR-C17.I1//Ministerio de Ciencia e Innovaci&#xf3;n/ ; THINKINAZUL/2021/024//Generalitat Valenciana/ ; },
mesh = {Animals ; *Microbiota/genetics ; *Fishes/microbiology ; Nanopores ; Feces/microbiology ; Water Microbiology ; DNA Barcoding, Taxonomic/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Oxford Nanopore Technology (ONT) allows for the rapid profiling of aquaculture microbiomes. However, not all the experimental and downstream methodological possibilities have been benchmarked. Here, we aimed to offer novel insights into the use of different library preparation methods (standard-RAP and native barcoding-LIG), primers (V3-V4, V1-V3, and V1-V9), and basecalling models (fast-FAST, high-HAC, and super-accuracy-SUP) implemented in ONT to elucidate the microbiota associated with the aquatic environment and farmed fish, including faeces, skin, and intestinal mucus. Microbial DNA from water and faeces samples could be amplified regardless of the library-primer strategy, but only with LIG and V1-V3/V1-V9 primers in the case of skin and intestine mucus. Low taxonomic assignment levels were favoured by the use of full-length V1-V9 primers, though in silico hybridisation revealed a lower number of potential matching sequences in the SILVA database, especially evident with the increase in Actinobacteriota in real datasets. SUP execution allowed for a higher median Phred quality (24) than FAST (11) and HAC (17), but its execution time (6-8 h) was higher in comparison to the other models (0.6-7 h). Altogether, we optimised the use of ONT for water- and fish-related microbial analyses, validating, for the first time, the use of the LIG strategy. We consider that LIG-V1-V9-HAC is the optimal time/cost-effective option to amplify the microbial DNA from environmental samples. However, the use of V1-V3 could help to maximise the dataset microbiome diversity, representing an alternative when long amplicon sequences become compromised by microbial DNA quality and/or high host DNA loads interfere with the PCR amplification/sequencing procedures, especially in the case of gut mucus.},
}
@article {pmid39682398,
year = {2024},
author = {Zhou, J and Zhang, X and Wang, Y and Liang, H and Yang, Y and Huang, X and Deng, J},
title = {Contamination Survey of Insect Genomic and Transcriptomic Data.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {23},
pages = {},
pmid = {39682398},
issn = {2076-2615},
support = {2022FY100500, KFB23016//the Special Investigation Program for National Science and Technology Basic Resources, the Special Fund for Science and Technology Innovation of Fujian Agriculture and Forestry University/ ; },
abstract = {The rapid advancement of high-throughput sequencing has led to a great increase in sequencing data, resulting in a significant accumulation of contamination, for example, sequences from non-target species may be present in the target species' sequencing data. Insecta, the most diverse group within Arthropoda, still lacks a comprehensive evaluation of contamination prevalence in public databases and an analysis of potential contamination causes. In this study, COI barcodes were used to investigate contamination from insects and mammals in GenBank's genomic and transcriptomic data across four insect orders. Among the 2796 WGS and 1382 TSA assemblies analyzed, contamination was detected in 32 (1.14%) WGS and 152 (11.0%) TSA assemblies. Key findings from this study include the following: (1) TSA data exhibited more severe contamination than WGS data; (2) contamination levels varied significantly among the four orders, with Hemiptera showing 9.22%, Coleoptera 3.48%, Hymenoptera 7.66%, and Diptera 1.89% contamination rates; (3) possible causes of contamination, such as food, parasitism, sample collection, and cross-contamination, were analyzed. Overall, this study proposes a workflow for checking the existence of contamination in WGS and TSA data and some suggestions to mitigate it.},
}
@article {pmid39678441,
year = {2024},
author = {Hamdi, I and Benmansour, B and Ahmed, M and Gulsher, M and Bouguerche, C},
title = {A new genus and a new species of microcotylids (Polyopisthocotyla, Platyhelminthes), gill parasite of the pink dentex Dentex gibbosus (Teleostei, Sparidae) off Tunisia and notes on Polyopisthocotyla and Monopisthocotyla from Dentex spp.},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {25},
number = {},
pages = {101016},
pmid = {39678441},
issn = {2213-2244},
abstract = {The study of the polyopisthocotylan parasites of marine fishes in the western Mediterranean is carried on using an integrative approach combining morphology and DNA barcodes. Ktarius patrickbrueli n. gen. n. sp (Polyopisthocotyla, Microcotylidae), from the gills of the pink dentex Dentex gibbosus (Teleostei, Sparidae) from the western Mediterranean Sea off Tunisia, is described. Anatomical and morphological features of the new genus are described, and the molecular barcodes for nuclear and mitochondrial markers (28S rRNA and cox1) are generated. The new genus is closely related to Microcotyle by sharing a symmetrical haptor, inverted question mark-shaped ovary and unarmed vagina. However, Ktarius n. gen. can be distinguished from Microcotyle and other Microcotylinae taxa by an unarmed male copulatory organ, formed by a long muscular cirrus, a basal layer of concentric muscles, and an elongated thick-walled ejaculatory bulb. A partial 28S rDNA sequence of K. patrickbrueli n. gen. n. sp. was obtained and found to be distinct from all known microcotylid sequences, with a p-distance of 5-13%. A phylogenetic tree constructed from available microcotylid sequences revealed that K. patrickbrueli n. gen. n. sp. clustered in a strongly supported clade of Microcotylinae, containing species of Omanicotyle, Bivagina, and Microcotyle confirming its belonging to the Microcotylinae subfamily. The cox1 sequences of K. patrickbrueli n. gen. n. sp. were highly divergent from the closely related genus Pauciconfibula and confirmed its distinction. This new genus is the third polyopisthocotylan genus to be described from sparids of Dentex.},
}
@article {pmid39677764,
year = {2024},
author = {Cho, S and Moon, W and Martino, N and Yun, SH},
title = {Wideband Tuning and Deep-Tissue Spectral Detection of Indium Phosphide Nano-Laser Particles.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39677764},
issn = {2692-8205},
support = {R01 EB033155/EB/NIBIB NIH HHS/United States ; R01 EB034687/EB/NIBIB NIH HHS/United States ; },
abstract = {Laser particles (LPs) emitting narrowband spectra across wide spectral ranges are highly promising for high-multiplex optical barcoding. Here, we present LPs based on indium phosphide (InP) nanodisks, operating in the near-infrared wavelength range of 740-970 nm. Utilizing low-order whispering gallery resonance modes in size-tuned nanodisks, we achieved an ultrawide color palette with 27% bandwidth utilization and nanometer-scale linewidth. The minimum laser size was 430 nm in air and 560 nm within the cytoplasm, operating at mode order 4 or 5. We further demonstrated spectral detection of laser peaks with high signal-to-background ratios in highly-scattering media, including 1-cm-thick chicken breast tissue and blood vessels in live mice.},
}
@article {pmid39677603,
year = {2024},
author = {Twa, GM and Phillips, RA and Robinson, NJ and Day, JJ},
title = {Accurate sample deconvolution of pooled snRNA-seq using sex-dependent gene expression patterns.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39677603},
issn = {2692-8205},
support = {DP1 DA039650/DA/NIDA NIH HHS/United States ; R01 DA053743/DA/NIDA NIH HHS/United States ; R01 DA054714/DA/NIDA NIH HHS/United States ; R01 MH114990/MH/NIMH NIH HHS/United States ; },
abstract = {Single nucleus RNA sequencing (snRNA-seq) technology offers unprecedented resolution for studying cell type-specific gene expression patterns. However, snRNA-seq poses high costs and technical limitations, often requiring the pooling of independent biological samples and loss of individual sample-level data. Deconvolution of sample identity using inherent features would enable the incorporation of pooled barcoding and sequencing protocols, thereby increasing data throughput and analytical sample size without requiring increases in experimental sample size and sequencing costs. In this study, we demonstrate a proof of concept that sex-dependent gene expression patterns can be leveraged for the deconvolution of pooled snRNA-seq data. Using previously published snRNA-seq data from the rat ventral tegmental area, we trained a range of machine learning models to classify cell sex using genes differentially expressed in cells from male and female rats. Models that used sex-dependent gene expression predicted cell sex with high accuracy (90-92%) and outperformed simple classification models using only sex chromosome gene expression (69-89%). The generalizability of these models to other brain regions was assessed using an additional published data set from the rat nucleus accumbens. Within this data set, model performance remained highly accurate in cell sex classification (89-90% accuracy) with no additional re-training. This work provides a model for future snRNA-seq studies to perform sample deconvolution using a two-sex pooled sample sequencing design and benchmarks the performance of various machine learning approaches to deconvolve sample identification from inherent sample features.},
}
@article {pmid39675106,
year = {2025},
author = {Mutum, RS and Das, A and Ghosh, SK and Wangkheimayum, VD},
title = {The origins of "Kaunayen" game fowls of Manipur, India: Insights from mitochondrial D-loop sequence analysis.},
journal = {Poultry science},
volume = {104},
number = {1},
pages = {104667},
pmid = {39675106},
issn = {1525-3171},
mesh = {Animals ; India ; *Chickens/genetics ; *DNA, Mitochondrial/genetics/analysis ; Genetic Variation ; Phylogeny ; Sequence Analysis, DNA/veterinary ; Breeding ; },
abstract = {Notably, poultry animals-particularly chickens-are recognized globally for their valuable contributions to the food, ornamental, and game economies. Further, more robust local and regional breeds can be parental donors for these area-specific consumable breeds' resilient traits. Game birds that are locally significant economically or on a much smaller scale are frequently excluded from the procedure. One such breed is the fighting chicken of Manipur, India, known locally as the Kaunayen breed and listed as the 17th breed at the ICAR, the National Bureau of Animal Genetic Resources, India. When Kaunayen fowl from throughout Manipur are considered, they have anatomical characteristics and common behavioural traits despite the breed's extreme genetic heterogeneity. With this gap in mind, we attempted to use mitochondrial D-loop sequences to characterize Manipur's Kaunayen fowls concerning the global breeds of nearly similar molecular characteristics. We found that Kaunayen fowls share evolutionary traits such as a similar transition/transversion ratio with some Southeast Asian breeds, including a few red jungle fowls. Overall Kaunayen are also more closely related to Southeast Asian birds phylogenetically, after which with a few breeds from East Asian, Bangladesh, North-East India, and the Indian island of Nicobar. The global database including our query has 19 haplotypes, and majority of the Kaunayen fowls share haplotypes with North East Indian fowls; the remaining haplotypes are primarily associated with South East Asia and East Asia. The findings additionally indicated that Kaunayen's and the global breed's D-loop region tended to fixed neutral substitution, contributing to the distinct varieties. Further, migration research demonstrated that Kaunayen fowls originated from a substantial maternal genome influx from Southeast Asia, which may have later made a substantial contribution to East Asian and South Asian breeds. We also display a portion of the D-loop that demonstrates the majority of the substitution diversity across all breeds, and we suggest using sequence stretch to create miniature breed-specific identifying barcodes.},
}
@article {pmid39673434,
year = {2024},
author = {Krasilnikova, LA and Tomkins-Tinch, CH and Gayton, AC and Schaffner, SF and Dobbins, ST and Gladden-Young, A and Siddle, KJ and Park, DJ and Sabeti, PC},
title = {Polyphonia: detecting inter-sample contamination in viral genomic sequencing data.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {12},
pages = {},
pmid = {39673434},
issn = {1367-4811},
support = {U01 AI151812/AI/NIAID NIH HHS/United States ; //US National Institutes of Health/ ; U19AI110818//National Institute of Allergy and Infectious Diseases/ ; },
mesh = {*Genome, Viral ; *SARS-CoV-2/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; *Software ; COVID-19/virology ; Genomics/methods ; },
abstract = {SUMMARY: In viral genomic research and surveillance, inter-sample contamination can affect variant detection, analysis of within-host evolution, outbreak reconstruction, and detection of superinfections and recombination events. While sample barcoding methods exist to track inter-sample contamination, they are not always used and can only detect contamination in the experimental pipeline from the point they are added. The underlying genomic information in a sample, however, carries information about inter-sample contamination occurring at any stage. Here, we present Polyphonia, a tool for detecting inter-sample contamination directly from deep sequencing data without the need for additional controls, using intrahost variant frequencies. We apply Polyphonia to 1102 SARS-CoV-2 samples sequenced at the Broad Institute and already tracked using molecular barcoding for comparison.<br><br>Polyphonia is available as a standalone Docker image and is also included as part of viral-ngs, available in Dockstore. Full documentation, source code, and instructions for use are available at https://github.com/broadinstitute/polyphonia.},
}
@article {pmid39672980,
year = {2025},
author = {Garcia-Gonzalez, I and Gambera, S and Rocha, SF and Regano, A and Garcia-Ortega, L and Lytvyn, M and Diago-Domingo, L and Sanchez-Muñoz, MS and Garcia-Cabero, A and Zagorac, I and Luo, W and De Andrés-Laguillo, M and Fernández-Chacón, M and Casquero-Garcia, V and Lunella, FF and Torroja, C and Sánchez-Cabo, F and Benedito, R},
title = {iFlpMosaics enable the multispectral barcoding and high-throughput comparative analysis of mutant and wild-type cells.},
journal = {Nature methods},
volume = {22},
number = {2},
pages = {323-334},
pmid = {39672980},
issn = {1548-7105},
support = {101001814//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 638028//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; HR22-00316//"la Caixa" Foundation (Caixa Foundation)/ ; HR19-00120//"la Caixa" Foundation (Caixa Foundation)/ ; CX-SO-16-1//"la Caixa" Foundation (Caixa Foundation)/ ; CX_E-2015-01//"la Caixa" Foundation (Caixa Foundation)/ ; PRE2018-085283//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a (Ministerio de Econom&#xed;a, Industria y Competitividad)/ ; },
mesh = {Animals ; Mice ; *Mutation ; *Single-Cell Analysis/methods ; Flow Cytometry/methods ; Mosaicism ; DNA Barcoding, Taxonomic/methods ; Integrases/genetics/metabolism ; },
abstract = {To understand gene function, it is necessary to compare cells carrying the mutated target gene with normal cells. In most biomedical studies, the cells being compared are in different mutant and control animals and, therefore, do not experience the same epigenetic changes and tissue microenvironment. The experimental induction of genetic mosaics is essential to determine a gene cell-autonomous function and to model the etiology of diseases caused by somatic mutations. Current technologies used to induce genetic mosaics in mice lack either accuracy, throughput or barcoding diversity. Here we present the iFlpMosaics toolkit comprising a large set of new genetic tools and mouse lines that enable recombinase-dependent ratiometric induction and single-cell clonal tracking of multiple fluorescently labeled wild-type and Cre-mutant cells within the same time window and tissue microenvironment. The labeled cells can be profiled by multispectral imaging or by fluorescence-activated flow cytometry and single-cell RNA sequencing. iFlpMosaics facilitate the induction and analysis of genetic mosaics in any quiescent or progenitor cell, and for any given single or combination of floxed genes, thus enabling a more accurate understanding of how induced genetic mutations affect the biology of single cells during tissue development, homeostasis and disease.},
}
@article {pmid39672483,
year = {2025},
author = {Houpt, TA and Houpt, CE and Cassell Erquiaga, CB},
title = {BarTender: A system for recording intakes and body weights in ingestive behavior experiments.},
journal = {Physiology &amp; behavior},
volume = {290},
number = {},
pages = {114783},
doi = {10.1016/j.physbeh.2024.114783},
pmid = {39672483},
issn = {1873-507X},
mesh = {Animals ; *Body Weight/physiology ; *Feeding Behavior/physiology ; Eating/physiology ; Rats ; },
abstract = {A system is described for the semi-automated collection of fluid bottle, food jar, and rodent body weights. Items are labeled with barcodes, which are scanned by a Macintosh application connected via USB to a scale. Body weights are collected in the animal room by an iPad application connected to a Bluetooth scale. Simple summary statistics are automatically calculated, and data are stored with experiment metadata in a cloud database. Up-to-date graphs of the data are rendered by a web application from any browser, from which data can be downloaded for further analysis. Such a system makes ingestive behavior experiments more accurate, rapid, and higher throughput.},
}
@article {pmid39670108,
year = {2024},
author = {Díaz, JA and Ordines, F and Massutí, E and Cárdenas, P},
title = {From caves to seamounts: the hidden diversity of tetractinellid sponges from the Balearic Islands, with the description of eight new species.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e16584},
pmid = {39670108},
issn = {2167-8359},
mesh = {Animals ; *Porifera/classification/anatomy &amp; histology ; Spain ; Caves ; Phylogeny ; Biodiversity ; Ecosystem ; DNA Barcoding, Taxonomic ; },
abstract = {The sponge fauna of the Western Mediterranean stands as one of the most studied in the world. Yet sampling new habitats and a poorly studied region like the Balearic Islands highlights once again our limited knowledge of this group of animals. This work focused on demosponges of the order Tetractinellida collected in several research surveys (2016-2021) on a variety of ecosystems of the Balearic Islands, including shallow caves, seamounts and trawl fishing grounds, in a broad depth range (0-725 m). Tetractinellid material from the North Atlantic and more than twenty type specimens were also examined and, for some, re-described in this work. All species were barcoded with the traditional molecular markers COI (Folmer fragment) and 28S (C1-C2 or C1-D2 fragment). A total of 36 species were identified, mostly belonging to the family Geodiidae (15 species), thereby bringing the number of tetractinellids recorded in the Balearic Islands from 15 to 39. Eight species from this study are new: Stelletta mortarium sp. nov., Penares cavernensis sp. nov., Penares isabellae sp. nov., Geodia bibilonae sp. nov., Geodia microsphaera sp. nov. and Geodia matrix sp. nov. from the Balearic Islands; Geodia phlegraeioides sp. nov. and Caminus xavierae sp. nov. from the North East Atlantic. Stelletta dichoclada and Erylus corsicus are reported for the first time since their description in Corsica in 1983. Pachastrella ovisternata is documented for the first time in the Mediterranean Sea. Finally, after comparisons of type material, we propose new synonymies: Geodia anceps as a junior synonym of Geodia geodina, Erylus cantabricus as a junior synonym of Erylus discophorus and Spongosorites maximus as a junior synonym of Characella pachastrelloides.},
}
@article {pmid39664260,
year = {2024},
author = {Albaina, A and Garić, R and Yebra, L},
title = {Know your limits; miniCOI metabarcoding fails with key marine zooplankton taxa.},
journal = {Journal of plankton research},
volume = {46},
number = {6},
pages = {581-595},
pmid = {39664260},
issn = {0142-7873},
abstract = {Eleven years after the publication of the first work applying deoxyribonucleic acid (DNA) metabarcoding to zooplankton communities, the commonly known "miniCOI" barcode is widely used, becoming the marker of choice. However, several primer combinations co-exist for this barcode and a critical evaluation of their performance is needed. This article reviews the misperformance of miniCOI metabarcoding with marine zooplankton communities, comparing them to microscopy and/or other universal markers. In total, misperformances were reported for 26 zooplankton taxa, including 18 copepods and five tunicates. We report a detection failure with Class Appendicularia and contrasting performances for Oithona similis (from good correspondence to detection failure), two worldwide abundant taxa with a crucial role in the marine pelagic realm. A combination of forward primer mismatches, the presence of long poly-T inserts and a low number of reference sequences would explain the failure to detect appendicularians. However, the contrasting performance with O. similis would correspond to distinct numbers of mismatches in the forward primer in different lineages within this cryptic taxon. This is reinforced by the report of similar patterns with other locally abundant zooplankton taxa. Therefore, we strongly call for the use of miniCOI in combination with alternative methods capable of addressing these limitations.},
}
@article {pmid39663496,
year = {2024},
author = {Hu, M and Yang, L and Twarog, N and Ochoada, J and Li, Y and Vrettos, EI and Torres-Hernandez, AX and Martinez, JB and Bhatia, J and Young, BM and Price, J and McGowan, K and Nguyen, TH and Shi, Z and Anyanwu, M and Rimmer, MA and Mercer, S and Rankovic, Z and Shelat, AA and Blair, DJ},
title = {Continuous collective analysis of chemical reactions.},
journal = {Nature},
volume = {636},
number = {8042},
pages = {374-379},
pmid = {39663496},
issn = {1476-4687},
support = {R25 CA023944/CA/NCI NIH HHS/United States ; T32 GM132061/GM/NIGMS NIH HHS/United States ; },
abstract = {The automated synthesis of small organic molecules from modular building blocks has the potential to transform our capacity to create medicines and materials[1-3]. Disruptive acceleration of this molecule-building strategy broadly unlocks its functional potential and requires the integration of many new assembly chemistries. Although recent advances in high-throughput chemistry[4-6] can speed up the development of appropriate synthetic methods, for example, in selecting appropriate chemical reaction conditions from the vast range of potential options, equivalent high-throughput analytical methods are needed. Here we report a streamlined approach for the rapid, quantitative analysis of chemical reactions by mass spectrometry. The intrinsic fragmentation features of chemical building blocks generalize the analyses of chemical reactions, allowing sub-second readouts of reaction outcomes. Central to this advance was identifying that starting material fragmentation patterns function as universal barcodes for downstream product analysis by mass spectrometry. Combining these features with acoustic droplet ejection mass spectrometry[7,8] we could eliminate slow chromatographic steps and continuously evaluate chemical reactions in multiplexed formats. This enabled the assignment of reaction conditions to molecules derived from ultrahigh-throughput chemical synthesis experiments. More generally, these results indicate that fragmentation features inherent to chemical synthesis can empower rapid data-rich experimentation.},
}
@article {pmid39660837,
year = {2025},
author = {Lewin, GR},
title = {mSphere of Influence: How the single cell contributes to the collective.},
journal = {mSphere},
volume = {10},
number = {1},
pages = {e0043124},
pmid = {39660837},
issn = {2379-5042},
support = {DP2 AI184733/AI/NIAID NIH HHS/United States ; R00 DE031018/DE/NIDCR NIH HHS/United States ; },
mesh = {*Single-Cell Analysis/methods ; Humans ; *Bacteria/genetics/classification ; Microbiota/genetics ; Ecosystem ; },
abstract = {Gina Lewin works in the field of microbial ecology, with a focus on the human microbiota. In this mSphere of Influence article, she reflects on how two papers describing bacterial single-cell RNA-seq-"Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing" by S. B. Blattman, W. Jiang, P. Oikonomou, and S. Tavazoie (Nat Microbiol 5:1192-1201, 2020, https://doi.org/10.1038/s41564-020-0729-6) and "Microbial single-cell RNA sequencing by split-pool barcoding" by A. Kuchina, L. M. Brettner, L. Paleologu, C. M. Roco, et al. (Science 371:eaba5257, 2021, https://doi.org/10.1126/science.aba5257)-impacted her work by developing a new approach to study how single cells of bacteria contribute to ecosystem-level processes.},
}
@article {pmid39660352,
year = {2024},
author = {Yu, T and Ren, Z and Gao, X and Li, G and Han, R},
title = {Generating barcodes for nanopore sequencing data with PRO.},
journal = {Fundamental research},
volume = {4},
number = {4},
pages = {785-794},
pmid = {39660352},
issn = {2667-3258},
abstract = {DNA barcodes, short and unique DNA sequences, play a crucial role in sample identification when processing many samples simultaneously, which helps reduce experimental costs. Nevertheless, the low quality of long-read sequencing makes it difficult to identify barcodes accurately, which poses significant challenges for the design of barcodes for large numbers of samples in a single sequencing run. Here, we present a comprehensive study of the generation of barcodes and develop a tool, PRO, that can be used for selecting optimal barcode sets and demultiplexing. We formulate the barcode design problem as a combinatorial problem and prove that finding the optimal largest barcode set in a given DNA sequence space in which all sequences have the same length is theoretically NP-complete. For practical applications, we developed the novel method PRO by introducing the probability divergence between two DNA sequences to expand the capacity of barcode kits while ensuring demultiplexing accuracy. Specifically, the maximum size of the barcode kits designed by PRO is 2,292, which keeps the length of barcodes the same as that of the official ones used by Oxford Nanopore Technologies (ONT). We validated the performance of PRO on a simulated nanopore dataset with high error rates. The demultiplexing accuracy of PRO reached 98.29% for a barcode kit of size 2,922, 4.31% higher than that of Guppy, the official demultiplexing tool. When the size of the barcode kit generated by PRO is the same as the official size provided by ONT, both tools show superior and comparable demultiplexing accuracy.},
}
@article {pmid39659773,
year = {2024},
author = {Xue, XL and Lu, XQ and Du, XC},
title = {The new genus Purpurata (Lepidoptera, Crambidae, Spilomelinae), with descriptions of two new species from China.},
journal = {ZooKeys},
volume = {1219},
number = {},
pages = {175-194},
pmid = {39659773},
issn = {1313-2989},
abstract = {The male genitalia characters of four species, Botysiopasalis Walker, 1859, Pleuroptyaobfuscalis Yamanaka, 1998, Botysplagiatalis Walker, 1859 and Pataniashompen Singh et Ahmad, 2022, placed in the genus Patania Moore, 1888 before the present study, do not conform to the diagnosis of Patania. A new genus, Purpurata gen. nov., is established for these four species, and two new species, Purpuratadirecta sp. nov. and Purpuratalurida sp. nov. are described based on their external morphology and genitalia characters. Purpuratadirecta sp. nov. is designated as the type species of the new genus. Five species of the new genus were clearly separated from Patania species in the Maximum likelihood phylogenetic tree constructed based on COI sequence data. Compared to Patania, the new genus Purpurata exhibits distinctive characters in male genitalia: the uncus is short, broad, and arc-shaped posteriorly; the gnathos is present and setose, or reduced; and the fibula is very small and setose. In addition, Pataniaclava (Xu &amp; Du), syn. nov. is synonymized with Purpurataiopasalis comb. nov. An identification key to species of the new genus is presented based on morphological characters of habitus and genitalia. Images of the habitus and genitalia are provided.},
}
@article {pmid39659496,
year = {2024},
author = {Shih, HT and Cai, Y and Niwa, N and Yoshigou, H and Nakahara, Y},
title = {Integrative Taxonomy Reveals Freshwater Shrimp Diversity (Decapoda: Atyidae: Neocaridina) from Kyushu and Southern Honshu of Japan, with a Discussion on Introduced Species.},
journal = {Zoological studies},
volume = {63},
number = {},
pages = {e18},
pmid = {39659496},
issn = {1810-522X},
abstract = {Correct identification of species is crucial for invasion ecology and management, particularly in aquatic systems. In this study, specimens of the freshwater shrimp genus Neocaridina from Kyushu and southern Honshuof Japan were identified by using an integrative approach that combined DNA barcoding of mitochondrial cytochrome oxidase subunit I (COI) and morphological examination. Among the eight species detected, two are native, viz. N. denticulata and N. ikiensis. Four are regarded as non-indigenous, viz. N. davidi, N. koreana, N. palmata, N. aff. palmata, which are believed to have been introduced from other East Asian countries either by the aquarium trade or as live fish bait. The remaining two species are likely cryptic native species, which have either been mistaken for known species, e.g., N. aff. denticulata, or species that have not been discovered before, e.g., N. aff. fukiensis. While the four alien species have spread widely in central Honshu, northern Kyushu and Tsushima Island, their impacts on the native species and the overall ecology remain mostly unexplored. Problems associated with using DNA barcoding for species identification are highlighted for further research.},
}
@article {pmid39657551,
year = {2025},
author = {Zhang, D and Zhang, N and Zhao, J and Li, X and Bian, F and Zhang, Y and Ge, Y and Li, Z},
title = {Label-free multiplexed detection based on core-shell photonic barcodes integrated RCA.},
journal = {Biosensors &amp; bioelectronics},
volume = {271},
number = {},
pages = {117037},
doi = {10.1016/j.bios.2024.117037},
pmid = {39657551},
issn = {1873-4235},
mesh = {*Biosensing Techniques/methods/instrumentation ; Humans ; *SARS-CoV-2/isolation &amp; purification/genetics ; *Nucleic Acid Amplification Techniques/instrumentation/methods ; *Limit of Detection ; Influenza A Virus, H1N1 Subtype/isolation &amp; purification/genetics ; COVID-19/diagnosis/virology ; Spike Glycoprotein, Coronavirus/analysis/immunology ; Photons ; Hydrogels/chemistry ; },
abstract = {Multiplexed, rapid, and accurate virus quantification is of great value in biomedical detection. Herein, we proposed a label-free multiplexed virus screening quantitative biosensor based on color core-shell hydrogel photonic crystal (PhC) barcode integrated rolling circle amplification (RCA). The composite hydrogel shell was formed by acrylic acid and polyethylene glycol diacrylate, and the core silica photonic crystal was used as a detector. In addition, by adjusting the internal periodic structure, the PhC microcarrier was able to perform various color barcodes for the detection of different targets. Based on these excellent properties of the nanocomposite barcode, the biosensor not only demonstrated the ability to rapidly and accurately detect SARS-COV-2-N, SARS-COV-2-S, and H1N1 simultaneously in one tube, but also converting the signal of target protein to nucleic acid signal based on DNA decorated antibody complex combine with the blocked primer and RCA strategy. As a result, the platform achieved highly sensitive multiplexed quantitative detection with a detection limit in the range of 0.30 pg/mL. In addition, the platform we developed was validated by clinical sample analysis with acceptable accuracy and high specificity, demonstrating the good potential applicability of the proposed detection method in clinical screening and diagnosis.},
}
@article {pmid39654309,
year = {2024},
author = {Frankenburg, R and Oreg, A},
title = {"As long as they remember me, I am alive": Commemoration and memory through stickers.},
journal = {Death studies},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/07481187.2024.2435929},
pmid = {39654309},
issn = {1091-7683},
abstract = {This study explores the phenomenon of memorial stickers commemorating victims of the October 7, 2023, massacre and subsequent Israel-Hamas war. Analyzing 600 stickers collected across Israel, we examine how these artifacts shape personal and collective memory of these tragic events. Using content analysis, visual data analysis, and ethnography of texts, we investigate the stickers' distribution, textual content, and visual elements. Three key findings emerged: (1) The widespread distribution of stickers expands commemoration beyond cemeteries, creating a larger community of remembrance; (2) Diverse textual content, from personal traits to universal messages, aims to keep the deceased's values alive in social awareness; (3) Visual elements balance public recognition with private mourning through strategic use of photographs, colors, and barcodes. Drawing on theories of collective memory and continuing bonds, we argue that these stickers symbolically bring the deceased into daily life and public spaces, contributing to the processing of personal and national trauma.},
}
@article {pmid39653555,
year = {2024},
author = {Fuchs, KJ and Göransson, M and Kester, MGD and Ettienne, NW and van de Meent, M and de Jong, RCM and Koster, EAS and Halkes, CJM and Scheeren, F and Heemskerk, MHM and van Balen, P and Falkenburg, JHF and Hadrup, SR and Griffioen, M},
title = {DNA barcoded peptide-MHC multimers to measure and monitor minor histocompatibility antigen-specific T cells after allogeneic stem cell transplantation.},
journal = {Journal for immunotherapy of cancer},
volume = {12},
number = {12},
pages = {},
pmid = {39653555},
issn = {2051-1426},
mesh = {Humans ; *Minor Histocompatibility Antigens/immunology/metabolism ; *Transplantation, Homologous ; *Graft vs Host Disease/immunology ; Middle Aged ; Hematopoietic Stem Cell Transplantation/methods ; Male ; Female ; Adult ; Peptides/immunology ; CD8-Positive T-Lymphocytes/immunology/metabolism ; Stem Cell Transplantation/adverse effects ; Aged ; Graft vs Leukemia Effect/immunology ; },
abstract = {Allogeneic stem cell transplantation (alloSCT) provides a curative treatment option for hematological malignancies. After HLA-matched alloSCT, donor-derived T cells recognize minor histocompatibility antigens (MiHAs), which are polymorphic peptides presented by HLA on patient cells. MiHAs are absent on donor cells due to genetic differences between patient and donor. T cells targeting broadly expressed MiHAs induce graft-versus-leukemia (GvL) reactivity as well as graft-versus-host disease (GvHD), while T cells for MiHAs with restricted or preferential expression on hematopoietic or non-hematopoietic cells may skew responses toward GvL or GvHD, respectively. Besides tissue expression, overall strength of GvL and GvHD is also determined by T-cell frequencies against MiHAs.Here, we explored the use of DNA barcode-labeled peptide-MHC multimers to detect and monitor antigen-specific T cells for the recently expanded repertoire of HLA-I-restricted MiHAs. In 16 patients who experienced an immune response after donor lymphocyte infusion, variable T-cell frequencies up to 30.5% of CD8[+] T cells were measured for 49 MiHAs. High T-cell frequencies above 1% were measured in 12 patients for 19 MiHAs, with the majority directed against mismatched MiHAs, typically 6-8 weeks after donor lymphocyte infusion and at the onset of GvHD. The 12 patients included 9 of 10 patients with severe GvHD, 2 of 3 patients with limited GvHD and 1 of 3 patients without GvHD.In conclusion, we demonstrated that barcoded peptide-MHC multimers reliably detect and allow monitoring for MiHA-specific T cells during treatment to investigate the kinetics of immune responses and their impact on development of GvL and GvHD after HLA-matched alloSCT.},
}
@article {pmid39652422,
year = {2025},
author = {Ashkin, EL and Tang, YJ and Xu, H and Hung, KL and Belk, JA and Cai, H and Lopez, SS and Dolcen, DN and Hebert, JD and Li, R and Ruiz, PA and Keal, T and Andrejka, L and Chang, HY and Petrov, DA and Dixon, JR and Xu, Z and Winslow, MM},
title = {A STAG2-PAXIP1/PAGR1 axis suppresses lung tumorigenesis.},
journal = {The Journal of experimental medicine},
volume = {222},
number = {1},
pages = {},
pmid = {39652422},
issn = {1540-9538},
support = {F99CA284289/CA/NCI NIH HHS/United States ; F99 CA274692/CA/NCI NIH HHS/United States ; 28FT-0019//Tobacco-Related Disease Research Program/ ; //Stanford University/ ; K00 CA245784/CA/NCI NIH HHS/United States ; DGE-2146755//National Science Foundation Graduate Research Fellowship Program/ ; MFE-176568//Canadian Institute of Health Research/ ; R01 CA234349/CA/NCI NIH HHS/United States ; F99 CA284289/CA/NCI NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; GT14928/HHMI/Howard Hughes Medical Institute/United States ; R01 CA231253/CA/NCI NIH HHS/United States ; R01-CA231253/NH/NIH HHS/United States ; PF-21-112-01-MM//American Cancer Society/ ; },
mesh = {*Lung Neoplasms/pathology/metabolism/genetics ; Humans ; Animals ; *Cell Cycle Proteins/metabolism/genetics ; Cell Line, Tumor ; Mice ; *Carcinogenesis/genetics/metabolism ; Gene Expression Regulation, Neoplastic ; CRISPR-Cas Systems ; Antigens, Nuclear/metabolism/genetics ; Tumor Suppressor Proteins/metabolism/genetics ; Cohesins ; },
abstract = {The cohesin complex is a critical regulator of gene expression. STAG2 is the most frequently mutated cohesin subunit across several cancer types and is a key tumor suppressor in lung cancer. Here, we coupled somatic CRISPR-Cas9 genome editing and tumor barcoding with an autochthonous oncogenic KRAS-driven lung cancer model and showed that STAG2 is uniquely tumor-suppressive among all core and auxiliary cohesin components. The heterodimeric complex components PAXIP1 and PAGR1 have highly correlated effects with STAG2 in human lung cancer cell lines, are tumor suppressors in vivo, and are epistatic to STAG2 in oncogenic KRAS-driven lung tumorigenesis in vivo. STAG2 inactivation elicits changes in gene expression, chromatin accessibility, and 3D genome conformation that impact the cancer cell state. Gene expression and chromatin accessibility similarities between STAG2- and PAXIP1-deficient neoplastic cells further relate STAG2-cohesin to PAXIP1/PAGR1. These findings reveal a STAG2-PAXIP1/PAGR1 tumor-suppressive axis and uncover novel PAXIP1-dependent and PAXIP1-independent STAG2-cohesin-mediated mechanisms of lung tumor suppression.},
}
@article {pmid39649949,
year = {2024},
author = {Rocha, LA and Pinheiro, HT and Najeeb, A and Rocha, CR and Shepherd, B},
title = {Chromisabadhah (Teleostei, Pomacentridae), a new species of damselfish from mesophotic coral ecosystems of the Maldives.},
journal = {ZooKeys},
volume = {1219},
number = {},
pages = {165-174},
pmid = {39649949},
issn = {1313-2989},
abstract = {A new species of Chromis (Teleostei, Pomacentridae) is described from four specimens collected between 95 and 110 m depth in mesophotic coral ecosystems in the Maldives, Indian Ocean. Chromisabadhah sp. nov. can be distinguished from all of its congeners by the following combination of characters: dorsal-fin rays XIII, 12-13; anal-fin rays II,11-12; pectoral-fin rays 17-18; tubed lateral-line scales 17; gill rakers 7+17-18 = 24-25; pearly white body with a large black marking covering the anterior two-thirds of the anal fin. The closest DNA barcode sequence (5.1% average uncorrected genetic distance on the mitochondrial COI gene), among those available, is Chromiswoodsi, a similar mesophotic species known from the coastal western Indian Ocean (Somalia to South Africa). The new species is easily distinguished from C.woodsi by having 13 dorsal spines (versus 14 in C.woodsi), the absence of a black band on the base of the tail (present in C.woodsi), and by the genetic difference.},
}
@article {pmid39649948,
year = {2024},
author = {Lehr, E and Moravec, J and Wang, Y and Uvizl, M},
title = {A new species of Pristimantis (Amphibia, Anura, Strabomantidae) from a montane forest of the Pui Pui Protected Forest in central Peru.},
journal = {ZooKeys},
volume = {1219},
number = {},
pages = {143-163},
pmid = {39649948},
issn = {1313-2989},
abstract = {Herpetological inventories conducted in the Pui Pui Protected Forest in the central Peruvian Andes between 2012 and 2014 revealed unusually high local anuran richness and endemism. Herein, we describe a new species of Pristimantis discovered in the buffer zone of the protected area between 1550 and 1730 m a.s.l. The description is based on one subadult male (snout-vent length 14.4 mm), one adult female (snout-vent length 26.4 mm), and six juvenile specimens collected in the montane forest between 1550 and 1730 m a.s.l. DNA barcoding placed P.vrazi sp. nov. as the sister taxon to P.rhabdocnemus and in the clade also containing P.lindae, P.sinschi, P.quaquaversus, and one still unnamed Pristimantis species. Pristimantisvrazi sp. nov. differs from all these closely related species by the combination of the following characters: tuberculate dorsum, presence of the tympanum, presence of dentigerous processes on the vomer, absence of vocal slits, a red median horizontal streak across the iris, a narrow black median vertical streak on the lower half of the eye, cream to dark brown dorsal ground coloration, and cream to gray ventral ground coloration.},
}
@article {pmid39649432,
year = {2024},
author = {Ollivier, M and Rivers-Moore, J and Pichon, M and Andrieu, E and Carrié, R and Rudelle, R and Sarthou, JP and Ouin, A},
title = {Wild bees (Apoidea, Anthophila) of south-west France: more than 10 years of inventories in mosaic landscapes of "Vallées et Coteaux de Gascogne" (ZA-PYGAR).},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e135157},
pmid = {39649432},
issn = {1314-2828},
abstract = {BACKGROUND: The reported massive decline of arthropods and particularly of pollinators such as wild bees, in terms of abundance and richness, is a threat for crop production and wild plant biodiversity conservation. This decline is mainly explained by a combination of drivers at local- and landscape-scale related to intensive farming practices. Assessing the evolution of wild bee communities in agricultural ecosystems and their response to such practices is needed to address conservation purposes.<br><br>NEW INFORMATION: We provide here data for the 24,329 wild bee specimens held in the collection of DYNAFOR Lab (UMR 1201 INRAE, INP-ENSAT, EI PURPAN), located at INP-ENSAT (Toulouse, France). All bee specimens were collected from the long term socio-ecological research site, ZA-PYGAR, located in south-west France, for more than 10 years (2010 to 2022) within the framework of different research programmes conducted by the DYNAFOR Lab. At least 270 species, representative of the six wild bee families, were identified from this area. The identified specimens are considered reliable as identifications were performed or have been verified by community-recognised experts. In addition, ongoing DNA barcoding performed on certain specimens helped clarify questionable morphological characters and provided cross-validation of species identification.},
}
@article {pmid39648853,
year = {2024},
author = {Shi, R and Chen, H and Zhang, W and Leak, RK and Lou, D and Chen, K and Chen, J},
title = {Single-cell RNA sequencing in stroke and traumatic brain injury: Current achievements, challenges, and future perspectives on transcriptomic profiling.},
journal = {Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism},
volume = {},
number = {},
pages = {271678X241305914},
pmid = {39648853},
issn = {1559-7016},
support = {R15 NS130532/NS/NINDS NIH HHS/United States ; R01 NS124673/NS/NINDS NIH HHS/United States ; R21 NS141002/NS/NINDS NIH HHS/United States ; I01 BX003377/BX/BLRD VA/United States ; I01 BX002495/BX/BLRD VA/United States ; },
abstract = {Single-cell RNA sequencing (scRNA-seq) is a high-throughput transcriptomic approach with the power to identify rare cells, discover new cellular subclusters, and describe novel genes. scRNA-seq can simultaneously reveal dynamic shifts in cellular phenotypes and heterogeneities in cellular subtypes. Since the publication of the first protocol on scRNA-seq in 2009, this evolving technology has continued to improve, through the use of cell-specific barcodes, adoption of droplet-based systems, and development of advanced computational methods. Despite induction of the cellular stress response during the tissue dissociation process, scRNA-seq remains a popular technology, and commercially available scRNA-seq methods have been applied to the brain. Recent advances in spatial transcriptomics now allow the researcher to capture the positional context of transcriptional activity, strengthening our knowledge of cellular organization and cell-cell interactions in spatially intact tissues. A combination of spatial transcriptomic data with proteomic, metabolomic, or chromatin accessibility data is a promising direction for future research. Herein, we provide an overview of the workflow, data analyses methods, and pros and cons of scRNA-seq technology. We also summarize the latest achievements of scRNA-seq in stroke and acute traumatic brain injury, and describe future applications of scRNA-seq and spatial transcriptomics.},
}
@article {pmid39647154,
year = {2024},
author = {Liu, YX and Xue, HJ and Liu, GQ},
title = {Two new species of the brachypterous Scirtetellus (Hemiptera: Heteroptera: Miridae) from China.},
journal = {Zootaxa},
volume = {5497},
number = {2},
pages = {244-254},
doi = {10.11646/zootaxa.5497.2.4},
pmid = {39647154},
issn = {1175-5334},
mesh = {Animals ; Male ; China ; *Heteroptera/anatomy &amp; histology/classification ; Female ; *Animal Distribution ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; DNA Barcoding, Taxonomic ; Phylogeny ; },
abstract = {Two new species of the genus Scirtetellus Reuter, 1890 (Heteroptera: Miridae: Orthotylinae: Halticini) are described as new to science from China: Scirtetellus qinghaiensis sp. nov. and Scirtetellus shanxiensis sp. nov. Detailed morphological description, photographs of the dorsal habitus and male parameres, key to species of Scirtetellus from China and species list of Scirtetellus of the world are provided. The 658 bp long fragments of the mitochondrial gene COI (DNA barcode) are provided as a part of the diagnosis of the new species. The type specimens and the DNA sample were deposited in the Institute of Entomology, Nankai University, Tianjin, China.},
}
@article {pmid39647119,
year = {2024},
author = {Prieto, C and Pinilla, C and Lorenc-Brudecka, J and Balke, M},
title = {Integrative description of Thaeides ramoni sp. nov. (Lepidoptera: Lycaenidae), a sympatric sibling species of Thaeides theia (Hewitson, 1870) found in the Sierra Nevada de Santa Marta, Colombia.},
journal = {Zootaxa},
volume = {5501},
number = {1},
pages = {181-190},
doi = {10.11646/zootaxa.5501.1.9},
pmid = {39647119},
issn = {1175-5334},
mesh = {Animals ; Male ; Female ; Colombia ; *Animal Distribution ; *Butterflies/anatomy &amp; histology/classification ; Organ Size ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Sympatry ; Phylogeny ; Ecosystem ; },
abstract = {We present evidence from DNA barcodes, wing pattern and distribution to support the hypothesis that an entity flying in sympatry with Thaeides theia in the Sierra Nevada de Santa Marta, is an undescribed biological species named herein as Thaides ramoni Prieto, sp. nov. Adult specimens and genital structures are illustrated for both species along with molecular and morphological diagnostic characters. In addition, we present some considerations about the taxonomy of the species in the Thaeides muela group.},
}
@article {pmid39647095,
year = {2024},
author = {Makarchenko, EA and Semenchenko, AA and Palatov, DM and Lisanovskaya, EA},
title = {Morphological description and DNA barcoding of Thalassomya paraskevae sp. nov. (Diptera: Chironomidae: Telmatogetoninae) from coast of the Black Sea.},
journal = {Zootaxa},
volume = {5501},
number = {4},
pages = {524-530},
doi = {10.11646/zootaxa.5501.4.2},
pmid = {39647095},
issn = {1175-5334},
mesh = {Animals ; Male ; *DNA Barcoding, Taxonomic ; *Chironomidae/anatomy &amp; histology/classification/genetics ; Black Sea ; Female ; *Animal Distribution ; Organ Size ; Body Size ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; },
abstract = {Illustrated description of adult male, as well as DNA barcoding, of Thalassomya paraskevae sp. nov. in comparison with close related species T. frauenfeldi Schiner from coast of the Black Sea are provided. Interspecific p-distances using gene COI 5P between T. paraskevae sp. nov. and T. frauenfeldi from Madeira (Portugal) were 8.94%. Divergence between described species and T. frauenfeldi collected near the type locality (Friuli Venezia-Giulia, Italy) using COI 3P were 7.72%. Obtained values corresponds to species level.},
}
@article {pmid39647062,
year = {2024},
author = {Barrantes, EAB and Echavarria, MAZ and Bartlett, CR and Helmick, EE and Bahder, BW},
title = {A new species of planthopper in the genus Platocerella (Hemiptera: Auchenorrhyncha: Derbidae) from palms in Costa Rica, a key to the genus and an updated molecular phylogeny of available New World Otiocerinae.},
journal = {Zootaxa},
volume = {5512},
number = {2},
pages = {222-232},
doi = {10.11646/zootaxa.5512.2.6},
pmid = {39647062},
issn = {1175-5334},
mesh = {Animals ; *Hemiptera/classification/anatomy &amp; histology/genetics ; Costa Rica ; *Phylogeny ; Male ; Female ; Animal Distribution ; Arecaceae/parasitology ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Electron Transport Complex IV/genetics ; },
abstract = {The genus Platocerella is a monotypic otiocerine genus (Derbidae: Otiocerinae: Otiocerini) reported from Guyana. A new species of Platocerella associated with palms is herein described from Costa Rica. Molecular data for the barcoding region cytochrome c oxidase subunit I (COI), 18S rRNA gene, and D9-D10 expansion region of the 28S rRNA gene is provided to produce a preliminary phylogenetic tree including the new species and related taxa to place the new species relative to other otiocerine planthoppers.},
}
@article {pmid39647046,
year = {2024},
author = {Mukherjee, B and Ray, N and Mukherjee, A and Naskar, A and Banerjee, D},
title = {First report of acifer group of the subgenus Tripodura Townes (Diptera: Chironomidae: Polypedilum) from India, with a new species and updated world checklist.},
journal = {Zootaxa},
volume = {5512},
number = {4},
pages = {531-552},
doi = {10.11646/zootaxa.5512.4.4},
pmid = {39647046},
issn = {1175-5334},
mesh = {Animals ; Male ; India ; *Chironomidae/classification/anatomy &amp; histology/growth &amp; development ; *Animal Distribution ; *Checklist ; Phylogeny ; Female ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; },
abstract = {A new species of the acifer group of the subgenus Tripodura and genus Polypedilum Kieffer is described on the basis of adult male. The acifer species group is recorded firstly from India. The molecular barcoding of the new species is provided. Moreover, molecular phylogeny of all available species of the subgenus Tripodura, along with an Indian key based on adult males of this subgenus have been designed here. Additionally, a world checklist of the subgenus Tripodura has also been furnished in this study.},
}
@article {pmid39647038,
year = {2024},
author = {Godfray, HCJ and Achterberg, CV},
title = {Annotated Checklist of the European Dacnusini and the Dapsilarthra genus group of the Alysiini (Hymenoptera: Braconidae, Alysiinae).},
journal = {Zootaxa},
volume = {5513},
number = {1},
pages = {1-73},
doi = {10.11646/zootaxa.5513.1.1},
pmid = {39647038},
issn = {1175-5334},
mesh = {Animals ; Female ; Male ; *Wasps/classification/anatomy &amp; histology ; *Checklist ; *Animal Distribution ; Europe ; Hymenoptera/classification/anatomy &amp; histology ; Body Size ; DNA Barcoding, Taxonomic ; },
abstract = {An annotated checklist of the European Dacnusini (426 species) and the Dapsilarthra genus group of the Alysiini (16 species) (Hymenoptera: Braconidae, Alysiinae) is provided. In addition to a species list with synonymy, further details are given of: (i) intrageneric groupings; (ii) a reference to each species' treatment in the unindexed and multipart major revisions of Nixon &amp; Griffith as well as the long keys of Tobias; (iii) a hypothesis about host range for the 60% of species which have been reared, and the evidence upon which it is based; (iv) whether a DNA barcode sequence is available (30% of species); (v) for species published after Griffiths' revision a reference to similar species; (vi) any further relevant notes. One new synonym is established: Chorebus luzulae Griffiths syn. nov. is synonymised with Chorebus aphantus Marshall. Mesocrina Förster is excluded from the Dapsilartha genus group and whether Grandia Goidanich and Lodbrokia Hedqvist are in the Dacnusini is considered uncertain.},
}
@article {pmid39647031,
year = {2024},
author = {Nazarov, RA and Nabizadeh, H and Rajabizadeh, M and Melnikov, DA and Volkova, VR and Poyarkov, NA and Rastegar-Pouyani, E},
title = {Taxonomy of Iranian Asaccus (Squamata: Phyllodactylidae) with description of a new species from southern Iran.},
journal = {Zootaxa},
volume = {5514},
number = {2},
pages = {101-128},
doi = {10.11646/zootaxa.5514.2.1},
pmid = {39647031},
issn = {1175-5334},
mesh = {Animals ; Iran ; *Lizards/anatomy &amp; histology/classification/genetics ; *Phylogeny ; Female ; Male ; *Animal Distribution ; *Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; },
abstract = {We provide the first diversity assessment of Iranian species of the genus Asaccus based on COI DNA-barcoding. We analyzed 53 samples of Iranian Asaccus representing nine OTU corresponding to 10 currently recognzied nominal species, and evaluated both morphological and genetic data to support the recognition of a new species from Bandar-e Jask, Hormozgan Province, southern Iran-Asaccus authenticus sp. nov. The new species is characterized by medium body size (SVL max 55.5 mm), elongated limbs, and relatively small dorsal tubercles arranged in 12-14 regular rows. Morphologically Asaccus authenticus sp. nov. resembles both Arabian and Iranian representatives of the genus; phylogenetically it forms a highly divergent lineage with sister relationships to all other Iranian congeners. We applied the geometric morphometrics method to compare the position and shape of postmental plates for almost all members of Asaccus and evaluated the importance of this character in species diagnostics in this group. We also critically evaluate the recent phylogenetic data on Asaccus and discuss the most problematic questions on taxonomy of this genus. We also revalidate Asaccus ingae (Eiselt, 1973) as a full species; overall our work raises the total number of species of the genus Asaccus to 20.},
}
@article {pmid39647018,
year = {2024},
author = {Bahder, BW and Randretsiferana, SA and Randretsiferana, A and Stroiński, A and Łukasik, P and Bartlett, CR and Pilet, F and Hasinjaka, RH},
title = {A new species of planthopper in the genus Eumyndus (Hemiptera: Cixiidae) from palms in eastern Madagascar and molecular evidence for the synonymy of Eumyndus kraussi and Eumyndus metcalfi.},
journal = {Zootaxa},
volume = {5514},
number = {4},
pages = {338-352},
doi = {10.11646/zootaxa.5514.4.3},
pmid = {39647018},
issn = {1175-5334},
mesh = {Animals ; Madagascar ; *Hemiptera/anatomy &amp; histology/classification/genetics ; Male ; Female ; *Animal Distribution ; Phylogeny ; Organ Size ; Electron Transport Complex IV/genetics ; Arecaceae/parasitology ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; RNA, Ribosomal, 18S/genetics ; },
abstract = {A new species of Eumyndus Synave, 1956, a genus endemic to Madagascar, is here described as Eumyndus jeanjacquei sp. nov. The new species was collected from the palm Vonitra fibrosa (C.H.Wright) Becc., 1911. Molecular data are provided for the new species from the barcoding region (5' half) of the cytochrome c oxidase subunit I (COI) gene, 18S rRNA gene and D9-D10 expansion region of the 28S rRNA gene and support placement of the new species in Eumyndus. A new synonymy is proposed based on examination of type material: E. metcalfi Synave, 1956 equals E. kraussi Synave, 1956, new synonym.},
}
@article {pmid39646982,
year = {2024},
author = {Pyrcz, TW and Boyer, P and Petit, JC and Garlacz, R and Garlacz, KSZ and Espeland, M and Willmott, KR},
title = {Bedazzled: a new, striking species of Corades from the outskirts of Quito questions our knowledge of Andean cloud forest butterflies (Lepidoptera, Nymphalidae, Satyrinae).},
journal = {Zootaxa},
volume = {5453},
number = {2},
pages = {255-262},
doi = {10.11646/zootaxa.5453.2.6},
pmid = {39646982},
issn = {1175-5334},
mesh = {Animals ; *Butterflies/anatomy &amp; histology/classification ; Male ; Ecuador ; Female ; *Animal Distribution ; Body Size ; Organ Size ; Ecosystem ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Forests ; Phylogeny ; },
abstract = {A new butterfly species in the genus Corades, C. yanacocha Pyrcz, Boyer &amp; Petit sp. n., belonging to the diverse, predominantly Andean subtribe Pronophilina (Nymphalidae, Satyrinae), is described from the Yanacocha Reserve situated only a couple of kilometres west of Quito, Ecuador. This is an extremely surprising discovery in a region whose butterfly fauna was considered to be fairly well known, underlying the need to protect remnants of high elevation forests in such overpopulated regions of the Andes. Morphological characters, in particular male genitalia, indicate an affinity of C. yanacocha sp. n. with C. trimaculata from northern Peru. A preliminary molecular study using COI barcodes indicates, however, the widely distributed north Andean C. dymantis as the closest relative.},
}
@article {pmid39646949,
year = {2024},
author = {Riccardi, PR and Ang, Y},
title = {New species and new records of Chloropinae from Singapore (Diptera: Chloropidae).},
journal = {Zootaxa},
volume = {5458},
number = {1},
pages = {83-92},
doi = {10.11646/zootaxa.5458.1.4},
pmid = {39646949},
issn = {1175-5334},
mesh = {Animals ; Singapore ; Male ; Female ; *Diptera/classification/anatomy &amp; histology/genetics ; *Animal Distribution ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; DNA Barcoding, Taxonomic ; Organ Size ; Phylogeny ; Biodiversity ; },
abstract = {Chloropidae biodiversity in the Oriental region is remarkably diverse and yet poorly understood. In this study, we used integrative taxonomy to tackle the species diversity of the subfamily Chloropinae from Singapore. We describe the first Oriental species of Cryptonevra Lioy, C. argenteum Riccardi, sp. nov., a new species of Chloropsina Becker, C. flavipes Riccardi, sp. nov., provide the first record of Eutropha noctilux (Walker) from Singapore and DNA barcodes of Chloropsina minima (Becker), Ensiferella kanmiyai Nartshuk. In addition, we increased the number of Chloropinae records from Singapore from two (Anthracophagella Anderson and Chlorops Meigen) to nine (addition of Cerais van der Wulp, Chloropsina, Cryptonevra, Elliponeura Loew, Ensiferella Andersson, Eutropha Loew, and Thressa Walker) genera and from two to seven described species plus four morphospecies. The species were discovered using NGS barcodes and are part of an ongoing campaign to document the biodiversity of Singapore.},
}
@article {pmid39646947,
year = {2024},
author = {Béarez, P and Zavalaga, F and Miranda, J and Mennesson, MI and Campos-León, S and Jiménez-Prado, P},
title = {Aulopus chirichignoae, a new flagfin from the eastern Pacific Ocean (Teleostei, Aulopiformes, Aulopidae).},
journal = {Zootaxa},
volume = {5458},
number = {1},
pages = {108-118},
doi = {10.11646/zootaxa.5458.1.6},
pmid = {39646947},
issn = {1175-5334},
mesh = {Animals ; Male ; Female ; Pacific Ocean ; Ecuador ; *Animal Distribution ; *Body Size ; Peru ; Organ Size ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Ecosystem ; },
abstract = {A new species of the Aulopidae is described from the waters of southern Ecuador and northern Peru. Aulopus chirichignoae sp. nov. was previously confused with Aulopus bajacali Parin &amp; Kotlyar, 1984, but it differs from this species by a significantly marked elongation of the dorsal fin rays in males (absent in females), a smaller head, modal differences in dorsal and anal ray counts (15 vs 14 and 11 vs 12, respectively), a higher number of vertebrae (50-51 vs 47-49), and color differences, especially on the dorsal fin. DNA barcoding analysis supported the status of new species, evidencing a 4.2% and 2.8% divergence with Aulopus filamentosus (Bloch, 1792) and A. bajacali, respectively. A sequence of an Aulopus sp., collected in the Tropical Eastern Pacific, matches the new species with only a 0.4% divergence, indicating that Aulopus chirichignoae sp. nov. is distributed at least as far north as the Paramount Seamount at 3°20.35'N, ca. 400 km north of the Galápagos Islands.},
}
@article {pmid39646945,
year = {2024},
author = {Fitrian, T and Rahayu, DL and Ismet, MS},
title = {A new species of hermit crab genus Diogenes Dana, 1851 from Papua, Indonesia (Crustacea, Decapoda, Anomura, Diogenidae).},
journal = {Zootaxa},
volume = {5458},
number = {1},
pages = {130-140},
doi = {10.11646/zootaxa.5458.1.8},
pmid = {39646945},
issn = {1175-5334},
mesh = {Animals ; Indonesia ; *Anomura/anatomy &amp; histology/classification/genetics ; Male ; Female ; *Animal Distribution ; Body Size ; Organ Size ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; },
abstract = {A new species of hermit crab from the genus Diogenes Dana, 1851 is described on the basis of a specimen from Papua, Indonesia. Diogenes hawisi n. sp. is distinguished from the closest allied species, D. edwardsii (De Haan, 1849) and D. laevicarpus Rahayu, 1996, by the shape and armature of the left cheliped. Morphological differences of these three species are also supported by genetic analysis, through DNA barcoding using the CO1 gene marker.},
}
@article {pmid39646930,
year = {2024},
author = {Kaila, L},
title = {A review of Coelopoetinae (Lepidoptera, Gelechioidea, Pterolonchidae), a moth subfamily confined to western North America, with descriptions of seven new species.},
journal = {Zootaxa},
volume = {5458},
number = {3},
pages = {361-384},
doi = {10.11646/zootaxa.5458.3.3},
pmid = {39646930},
issn = {1175-5334},
mesh = {Animals ; Male ; Female ; *Moths/anatomy &amp; histology/classification ; *Animal Distribution ; North America ; Phylogeny ; Organ Size ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; },
abstract = {Systematics and taxonomy of the gelechioid subfamily Coelopoetinae are reviewed. Following the current classification, this group is considered to form its own monotypic subfamily in Pterolonchidae with one recognized genus, Coelopoeta, after a convoluted and, in part, arguably conjectural, historical systematic treatment. On morphological basis (appearance, male genitalia) and with support from DNA barcodes, the genus is divided into two discrete units probably meriting recognition as separate genera. The species groups are informally treated as the nominate C. glutinosi species group, and the C. fissurina species group. In the absence of knowledge of females or the biologies of any of the species of the C. fissurina group, species of both groups are here provisionally included in Coelopoeta. In total, 10 species are recognized, seven of which are here described as new: C. glutinosi species group: C. alboflava Kaila, sp. nov., C. aprica Kaila, sp. nov., C. aurora Kaila, sp. nov., C. fulminea Kaila, sp. nov. and C. sariae Kaila, sp. nov.; C. fissurina species group: C. fissurina Kaila, sp. nov. and C. valalbui Kaila, sp. nov. The three previously known species, C. glutinosi Walsingham, 1907, C. maiadella Kaila, 1995 and C. phaceliae Kaila, 1995 are redescribed. All three of these species belong to the glutinosi species group. A lectotype is designated for C. glutinosi Walsingham, 1907. Some southwestern Coelopoeta species are potentially under threat of decline or even extinction due to the apparently increasingly intense and frequent forest fires. This threat is significant as the species with known life histories spend their entire life cycles above ground in low vegetation.},
}
@article {pmid39646926,
year = {2024},
author = {Kim, J and Lee, T},
title = {A new species of Janiralata Menzies, 1951 (Isopoda: Asellota, Janiridae) from Korea.},
journal = {Zootaxa},
volume = {5458},
number = {3},
pages = {427-441},
doi = {10.11646/zootaxa.5458.3.7},
pmid = {39646926},
issn = {1175-5334},
mesh = {*Isopoda/classification/anatomy &amp; histology ; Animals ; Male ; Republic of Korea ; *Animal Distribution ; Female ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Phylogeny ; Electron Transport Complex IV/genetics ; },
abstract = {A new isopod species, Janiralata kwangsooi sp. nov., from Dokdo Island located in the East Sea off the Korean Peninsula is described here. This species is distinguished from its congeners by the number of antennular articles, setation of mouthparts and pereopods, length and width ratio of appendages, and shape of male pleopods I and II. To aid species identification, a taxonomic key to species of Janiralata Menzies, 1951 in the Japanese and Korean waters is provided. A partial sequence of mitochondrial cytochrome-c-oxidase (COI) of this new species is also provided for DNA barcoding and compared with those of congeners publicly available in GenBank.},
}
@article {pmid39646853,
year = {2024},
author = {Triberti, P and Staude, H and Sharp, I and Lopez-Vaamonde, C},
title = {Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species.},
journal = {Zootaxa},
volume = {5529},
number = {1},
pages = {1-51},
doi = {10.11646/zootaxa.5529.1.1},
pmid = {39646853},
issn = {1175-5334},
mesh = {Animals ; South Africa ; *DNA Barcoding, Taxonomic ; Male ; Female ; *Moths/anatomy &amp; histology/classification/genetics ; *Animal Distribution ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; Plants ; Biodiversity ; },
abstract = {Despite relatively extensive historical exploration being carried out on Lepidopteran fauna of South Africa, leaf-mining micromoths of the family Gracillariidae remain a source of discovery, with many new species awaiting description. In the present work, 32 gracillariid species from South Africa are treated. For each species, hostplant and distribution information is provided, supplemented by taxonomic and molecular analysis where necessary. Nine species are described here as new to science: Ectropina spirostachydis sp. nov., Leucocercops curatellifoliae sp. nov., Phodoryctis tephrosiella sp. nov., Telamoptilia cordati sp. nov., Phyllonorycter pseudogrewiella sp. nov., Cameraria melhaniella sp. nov., Phyllocnistis magalismontani sp. nov., P. allisonae sp. nov. and P. faureae sp. nov. Sixteen host plant species are reported for the first time for the family Gracillariidae: Searsia pyroides (Anacardiaceae), Parinari curatellifolia (Chrysobalanaceae), Combretum zeyheri, Terminalia sericea (Combretaceae), Euclea divinorum (Ebenaceae), Spirostachys africana (Euphorbiaceae), Peltophorum africanum, Tephrosia rhodesica, Schotia brachypetala (Fabaceae), Cryptocarya transvaalensis (Lauraceae), Melhania acuminata (Malvaceae), Syzygium guineense (Myrtaceae), Ochna pretoriensis (Ochnaceae), Protea rubropilosa, Faurea saligna (Proteaceae), Englerophytum magalismontanum (Sapotaceae). Caloptilia mwamba De Prins, 2015 is recorded for the first time in South Africa.},
}
@article {pmid39646830,
year = {2024},
author = {Orr, AGW and Dow, RA and Steinhoff, POM},
title = {Descriptions of larvae of four mainly DNA barcode-matched species of chlorocyphids from south-east Asia (Odonata: Chlorocyphidae) with notes on the generic and species level larval identification of Oriental region members of the family.},
journal = {Zootaxa},
volume = {5486},
number = {3},
pages = {301-337},
doi = {10.11646/zootaxa.5486.3.1},
pmid = {39646830},
issn = {1175-5334},
mesh = {Animals ; *Larva/anatomy &amp; histology/classification/growth &amp; development/genetics ; Female ; Male ; *DNA Barcoding, Taxonomic ; *Animal Distribution ; Asia, Southeastern ; *Odonata/anatomy &amp; histology/classification/genetics/growth &amp; development ; Phylogeny ; Ecosystem ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Body Size ; },
abstract = {The final stadium larvae of the following four species of south-east Asian Chlorocyphidae are described and compared: Aristocypha fenestrella (Rambur), Heliocypha biseriata (Selys), Libellago hyalina (Selys) and Sundacypha petiolata (Selys), including both sexes for the latter two species. Excepting one L. hyalina specimen from Brunei, identified by supposition based on habitat, all specimens were identified by comparing and matching the mitochondrial marker COI with that of known adult specimens from Sarawak, Brunei and several localities throughout tropical Asia. The specimens presented close matches with all adults in this gene. An assessment of the efficacy of this method of identification is provided, noting that in some cases close species cannot be separated by bar-code matching and ultimate determination is partially based on known distributions of adults. Some aspects of the relationships among genera revealed by the genetic analyses are also discussed. In addition, an exuvia of Libellago lineata (Burmeister) from northern Thailand, identified by supposition, is partially described for the purpose of comparison with L. hyalina. For the morphological analysis the unique features of chlorocyphid anatomy are discussed, and some new terminology is introduced. Overall, the morphological analysis revealed numerous clear differences between the four species studied, and comparisons with available literature suggest that some of these may be characteristic of their genera. It is also evident that in some cases clear interspecific differences occur within genera. It is however concluded that a generic level larval key for the Oriental region Chlorocyphidae based on morphology may never be attainable, although local generic or even species level keys addressing the fauna of limited geographic areas may be possible in many places, especially as the larvae of more species come to be known and described in detail.},
}
@article {pmid39646800,
year = {2024},
author = {Ahrens, D and Zhao, MZ and Pham, PV and Liu, WG},
title = {Taxonomic updates on Pachyserica Brenske, 1898 and Serica MacLeay, 1819 reveal 38 new species and new challenges of Sericini systematics regarding DNA barcodes and genus-level diagnostic key characters (Coleoptera: Scarabaeidae: Sericinae).},
journal = {Zootaxa},
volume = {5491},
number = {1},
pages = {1-89},
doi = {10.11646/zootaxa.5491.1.1},
pmid = {39646800},
issn = {1175-5334},
mesh = {Animals ; *Coleoptera/classification/anatomy &amp; histology/genetics ; *DNA Barcoding, Taxonomic ; Male ; Female ; *Animal Distribution ; Organ Size ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Phylogeny ; },
abstract = {Here we present updates on the taxonomy and distribution of the genera Pachyserica Brenske, 1898 and Serica MacLeay, 1819 from East Asia. Thirty eight new species are desribed from China, Myanmar, South Korea, and Vietnam: Pachyserica chenchangchini Ahrens, Zhao, Pham &amp; Liu, new species, P. dieuthuyae Ahrens, Zhao, Pham &amp; Liu, new species, P. hoabinhensis Ahrens, Zhao, Pham &amp; Liu, new species, P. motuo Ahrens, Zhao, Pham &amp; Liu, new species, P. natmatoung Ahrens, Zhao, Pham &amp; Liu, new species, P. sanqingshanensis Ahrens, Zhao, Pham &amp; Liu, new species, P. sunfengyii Ahrens, Zhao, Pham &amp; Liu, new species, P. tayyentu Ahrens, Zhao, Pham &amp; Liu, new species, P. tianxuani Ahrens, Zhao, Pham &amp; Liu, new species, P. wangzizhaoi Ahrens, Zhao, Pham &amp; Liu, new species, P. yaonani Ahrens, Zhao, Pham &amp; Liu, new species, P. yinhengi Ahrens, Zhao, Pham &amp; Liu, new species, P. zhanbaoxiangi Ahrens, Zhao, Pham &amp; Liu, new species, Serica (s. l.) anhua Ahrens, Zhao, Pham &amp; Liu, new species, S. (s. l.) camura Ahrens, Zhao, Pham &amp; Liu, new species, S. (s. l.) fengxue Ahrens, Zhao, Pham &amp; Liu, new species, S. (s. l.) nhiae Ahrens, Zhao, Pham &amp; Liu, new species, S. (s. l.) paracallosericoides Ahrens, Zhao, Pham &amp; Liu, new species, S. (s. l.) taythien Ahrens, Zhao, Pham &amp; Liu, new species, S. (s. l.) wuyishan Ahrens, Zhao, Pham &amp; Liu, new species, S. (s. l.) yuechengling Ahrens, Zhao, Pham &amp; Liu, new species, S. (Serica) assingi Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) bomi Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) christophreuteri Ahrens, Zhao, Pham &amp; Liu, Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) cuona Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) fansipan Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) gongtonggouensis Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) guangxiensis Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) gwangjuensis Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) hongyii Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) jiangda Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) jiulaoci Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) lushui Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) liyitengi Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) qizhihaoi Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) xizang Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) zhamu Ahrens, Zhao, Pham &amp; Liu, new species, and S. (Taiwanoserica) yexiaohani Ahrens, Zhao, Pham &amp; Liu, new species. The lectotype of Pachyserica scalaris Arrow, 1946 is designated and its male genitalia is illustrated. Additional records of 66 other species are provided.},
}
@article {pmid39646795,
year = {2024},
author = {Zhang, JY and Sun, XL and Wang, N and Hao, LI and Ma, CX and Zhao, NA and Li, HP and Zhao, M and Yang, ST},
title = {Tardigrades in the alpine region of Northeast China with an integrative description of Crenubiotus liangshuiensis sp. nov.},
journal = {Zootaxa},
volume = {5492},
number = {1},
pages = {96-108},
doi = {10.11646/zootaxa.5492.1.5},
pmid = {39646795},
issn = {1175-5334},
mesh = {Animals ; *Tardigrada/classification/anatomy &amp; histology ; China ; *Animal Distribution ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; DNA Barcoding, Taxonomic ; Ecosystem ; RNA, Ribosomal, 18S/genetics ; Female ; Male ; },
abstract = {A new species of tardigrade, Crenubiotus liangshuiensis sp. nov. (Eutardigrada: Parachela: Macrobiotoidea: Adorybiotidae), was identified by combining DNA barcoding and classical morphological analyses (including both light contrast microscopy and scanning electron microscopy) of animals and an egg found in moss Collected in Yichun Liangshui National Nature Reserve. Moreover, nucleotide sequences of the 18S rRNA and COI markers from used to analyse the diversity of the local tardigrade fauna indicated the presence of at least 16 species representing 11 genera.},
}
@article {pmid39646779,
year = {2024},
author = {Liang, QR and Shi, L},
title = {Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences.},
journal = {Zootaxa},
volume = {5492},
number = {3},
pages = {325-342},
doi = {10.11646/zootaxa.5492.3.2},
pmid = {39646779},
issn = {1175-5334},
mesh = {Animals ; *Lizards/classification/genetics/anatomy &amp; histology ; *Phylogeny ; *DNA, Mitochondrial/genetics ; *Animal Distribution ; Male ; Female ; China ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; DNA Barcoding, Taxonomic ; },
abstract = {The rock lizard genus Laudakia is representative agamid species from the arid zone, and its genus division has not been resolved yet. Laudakia stoliczkana, which occurs in both Xinjiang, China, and the Gobi Altai, Mongolia, is divided into two subspecies, Laudakia stoliczkana stoliczkana and Laudakia stoliczkana altaica, based on morphological differences, but little is known about the molecular genetic differences between the two subspecies. This study reconstructs the phylogenetic tree of Laudakia and analyses molecular differences between two subspecies of L. stoliczkana by DNA barcoding (COI and 16S). Our results show that: (1) Laudakia is monophyletic and the phylogenetic tree is broadly divided into three main branches, namely branch A (L. caucasia and L. stoliczkana), which occurs mainly in Central Asia and the Gobi Altai region to the north, branch B (L. stellio), which occurs in the Middle East, and branch C (L. tuberculata, L. papenfussi, L. himalayana, L. wui, L. stellio), which occurs mainly near the Himalayas; (2) The biogeographic analysis of Laudakia suggests that the genus probably originated at 43.72 Ma (95% confidence interval HPD: 23.53-66.12Ma) and is associated with the uplift of the Tibetan Plateau and the aridification of Central Asias subsequently; (3) Molecular genetic distances and morphological differences support the delimitation of the two subspecies of L. stoliczkana, with divergence between the two subspecies estimated to have occurred at 3.27 Ma (95% confidence interval HPD: 1.58-5.87Ma), in associated with the recent uplift of the Tian Shan Mountains. The results highlight the importance of the uplift of the Central Asian mountains and the Tibetan Plateau for the divergence of Laudakia.},
}
@article {pmid39646691,
year = {2024},
author = {Yu, T and Kallies, A and Arita, Y and He, J and Li, H and Yata, N and Li, X},
title = {Two new species of the genus Taikona Arita &amp; Gorbunov, 2001 (Lepidoptera, Sesiidae) from Yunnan, China.},
journal = {Zootaxa},
volume = {5443},
number = {1},
pages = {135-140},
doi = {10.11646/zootaxa.5443.1.8},
pmid = {39646691},
issn = {1175-5334},
mesh = {Animals ; Male ; China ; *Animal Distribution ; *Moths/anatomy &amp; histology/classification ; Female ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; },
abstract = {Two new species, Taikona gaoligongshana Yu, Arita &amp; Kallies, sp. nov. and Taikona extraordinaria Yu, Kallies &amp; Arita sp. nov. are described from Yunnan Province, China. Illustrations of the holotypes and the male genitalia are provided, along with a key to all currently known species of the genus. DNA barcoding sequences are also provided.},
}
@article {pmid39646654,
year = {2024},
author = {David, KJ and Hancock, DL and Salini, S and Ningthoujam, K and Khemrajji, HN and Abhishek, V and Gracy, RG and Sushil, SN},
title = {New species and new records of fruit flies of tribe Acanthonevrini (Diptera: Tephritidae: Phytalmiinae) from India.},
journal = {Zootaxa},
volume = {5506},
number = {3},
pages = {301-321},
doi = {10.11646/zootaxa.5506.3.1},
pmid = {39646654},
issn = {1175-5334},
mesh = {Animals ; India ; Female ; Male ; *Animal Distribution ; *Tephritidae/classification/anatomy &amp; histology ; *Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Phylogeny ; },
abstract = {Two new species of Phytalmiinae belonging to the tribe Acanthonevrini are described from India, namely Ptilona confracta David &amp; Hancock, sp. nov. from Arunachal Pradesh and Tritaeniopteron obscurum David, Salini &amp; Nikhil, sp. nov. from Karnataka. Tritaeniopteron de Meijere is recorded for the first time from India based on the new species T. obscurum; male and female syntypes of T. punctatipleurum (Senior-White) are dissected and illustrated. A female of Erectovena desperata (Hering), both sexes of Felderimyia gombakensis Hancock &amp; Drew and Phorelliosoma hilaratum Hering, recorded for the first time from India are dissected and illustrated. An illustrated key to 23 species of Acanthonevrini belonging to 12 genera from India is included. DNA barcode sequences of Felderimyia fuscipennis Hendel, Ptilona confracta, P. confinis (Walker), Rioxoptilona dunlopi (van der Wulp) and Themara yunnana Zia were obtained and reported.},
}
@article {pmid39646638,
year = {2024},
author = {Teslenko, VA and Palatov, DM and Semenchenko, AA},
title = {Overview of the Caucasian Perla Geoffroy, 1762 (Plecoptera: Perlidae) based on morphological and molecular data with description of two new species.},
journal = {Zootaxa},
volume = {5507},
number = {1},
pages = {1-56},
doi = {10.11646/zootaxa.5507.1.1},
pmid = {39646638},
issn = {1175-5334},
mesh = {Male ; Female ; Animals ; *Insecta/anatomy &amp; histology/classification/growth &amp; development/genetics ; Russia ; *Animal Distribution ; Organ Size ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Phylogeny ; },
abstract = {Six species of Caucasian Perla are reviewed, and diagnostic morphological characteristics of all stages of development (where possible) are described, supplemented, and illustrated in detail with comparative light microscope and scanning electron microscopy images. The DNA barcoding of five species is presented. Two new morphologically and genetically distinct species, Perla schapsugica sp. nov. and Perla palatovi sp. nov., are described for both sexes and all life stages in the North Caucasus, Russia, Krasnodar Kray. Reinstatement of Perla persica Zwick, 1975, as a valid species distinct from P. caucasica Guérin-Méneville, 1843, is proposed. A new record of P. persica is reported for the Greater Caucasus, Russia, North-Ossetia-Alania for the first time. Morphologically, these two latter species can be separated in male adults by the shape of the hemitergal hook on terga X, an additional ventral brush on the penis of P. caucasica, wing length, and color.},
}
@article {pmid39646583,
year = {2024},
author = {DU, H and Liu, J and Heller, K and Shah, B and Wang, Q and Huang, J},
title = {Morphology and DNA barcodes of four species of Bradysia hilaris group from China (Diptera, Sciaridae).},
journal = {Zootaxa},
volume = {5493},
number = {2},
pages = {129-140},
doi = {10.11646/zootaxa.5493.2.2},
pmid = {39646583},
issn = {1175-5334},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; China ; *Diptera/anatomy &amp; histology/classification/genetics ; *Phylogeny ; Male ; Female ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; },
abstract = {Four morphologically allied species of the Bradysia hilaris group were studied from China. In a DNA metabarcoding based dipteran diversity study in Zhejiang, eastern China, a hyper-abundant sciarid species was discovered. It was further recognized in this study to be new to science, Bradysia tianmuensis Du &amp; Huang sp. nov., as well as a morphologically similar species, Bradysia curvula Du &amp; Huang sp. nov. Both new species were found to be fairly similar morphologically to the holotype of Bradysia noduspina Yang, Zhang &amp; Yang, 1993 from Guizhou in western China. However, the paratype of B. noduspina appeared to be different from the holotype and determined to be new to science, Bradysia chikunae Du &amp; Huang sp. nov. A phylogenetic tree of all the available 31 COI sequences of the Bradysia hilaris group was provided. Molecular work conducted in the current study also supports Bradysia tianmuensis Du &amp; Huang sp. nov. and Bradysia curvula Du &amp; Huang sp. nov. as new to science thus the four species were described or redescribed accompanied by detailed imagery of habitus and other characters useful for determination.},
}
@article {pmid39646580,
year = {2024},
author = {Liu, WB and Wang, CY and Tang, YN and Pei, WX and Yan, CC},
title = {DNA barcodes and morphology reveal new species within the Cryptochironomus Kieffer from Oriental China (Diptera: Chironomidae).},
journal = {Zootaxa},
volume = {5493},
number = {2},
pages = {165-174},
doi = {10.11646/zootaxa.5493.2.5},
pmid = {39646580},
issn = {1175-5334},
mesh = {Animals ; *Chironomidae/classification/anatomy &amp; histology/genetics/growth &amp; development ; Male ; China ; *DNA Barcoding, Taxonomic ; Female ; Animal Distribution ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; },
abstract = {The genus Cryptochironomus has a cosmopolitan distribution including over 140 valid described species worldwide. The morphological characteristics and DNA barcode data of Cryptochironomus inflatus Liu, sp. nov. based on specimens collected from Oriental China. DNA barcode analysis including the partial COI sequences of species of genus Cryptochironomus is conducted. An updated key to adult males of the genus is provided.},
}
@article {pmid39646562,
year = {2024},
author = {Makarchenko, EA},
title = {Pseudokiefferiella ferringtoni sp. nov. (Diptera: Chironomidae: Diamesinae) from North America.},
journal = {Zootaxa},
volume = {5493},
number = {4},
pages = {446-450},
doi = {10.11646/zootaxa.5493.4.10},
pmid = {39646562},
issn = {1175-5334},
mesh = {Animals ; Male ; *Chironomidae/classification/anatomy &amp; histology/growth &amp; development/genetics ; North America ; Female ; *Animal Distribution ; *Body Size ; Organ Size ; Pupa/anatomy &amp; histology/classification/growth &amp; development ; Animal Structures/anatomy &amp; histology/growth &amp; development ; },
abstract = {In this article I continue to publish the data obtained as a result of the revision of the subfamily Diamesinae, namely of the genus Pseudokiefferiella Zavřel, 1941. As we noted earlier (Makarchenko &amp; Semenchenko 2023), before the start of molecular genetic study this genus was considered as monotypic, that is, with one species of Ps. parva (Edwards) in Holarctic region (Ashe &amp; O'Connor 2009). According to work of Stur and Ekrem (2020), as well as the results of our research and data of GenBank, there are at least 6 species in the genus Pseudokiefferiella that are well separated by DNA barcoding, while adult males poorly differ morphologically. However, species of this genus can be successfully identified by the morphological structures of the pupa, if it is associated with a male imago. As confirmation of this, below is provided a description of Pseudokiefferiella ferringtoni sp. nov. from North America based on the adult male and pupa, in which the originality of a new species is corroborated by the morphological structures of the pupa.},
}
@article {pmid39646561,
year = {2024},
author = {Saha, S and Bogorodsky, SV and Baki, MA and Gao, T and McKay, RJ and Alpermann, TJ and Song, NA},
title = {Assessment of the diversity of the family Sillaginidae in the Indian Ocean with emphasis on the taxonomic identity of Sillago sihama.},
journal = {Zootaxa},
volume = {5493},
number = {5},
pages = {451-485},
doi = {10.11646/zootaxa.5493.5.1},
pmid = {39646561},
issn = {1175-5334},
mesh = {Animals ; Indian Ocean ; *Phylogeny ; *Animal Distribution ; Male ; Female ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Biodiversity ; Ecosystem ; },
abstract = {The present study contributes to the taxonomy of the family Sillaginidae, with comments on the distribution of its species in the Indian Ocean and an emphasis on the taxonomy and distribution of Sillago sihama. Thirty described and putative species with Indian Ocean distribution are listed, and a distribution range for each species is provided based on published data and results from the present study. A comprehensive phylogenetic analysis of the barcoding portion of the mitochondrial COI gene is provided together with three approaches for molecular species delimitation, which includes 44 to 47 genetic lineages (depending on the species delimitation approach used) in the family Sillaginidae, 33 of them applying to described species and also 8 putative species, formerly misidentified as S. sihama. Inclusion of specimens from South Africa, Iran, Pakistan, India, Bangladesh and the southern Red Sea (type locality) reveals one genetic lineage representing the true Sillago sihama. Distribution of the species is confined to the Red Sea and the Indian Ocean, and other records under the name S. sihama are based on misidentifications. Several undescribed species identified as S. sihama are distributed in the Indo-West Pacific region and closely resemble S. sihama, but are not identical with this species and can be identified as members of different evolutionary lineages. Two species, S. sihama and S. soringa, reported from Bangladesh, represent the easternmost record of both species. These two species are described in detail, including swimbladder morphology. The study also shows that specimens from India identified as Sillago ingenuua McKay, 1985 are nested within a lineage previously referred to as S. ingenuua A, but are different from the lineage S. ingenuua B, representing a confirmed record of the clade S. ingenuua in the northern Indian Ocean. Comments on misidentifications of S. sihama from the Indian Ocean and western Pacific are provided. Furthermore, we propose that Sillago erythraea should be resurrected from its synonymy with S. sihama. As Sillago suezensis is identical with the former species, it becomes a junior synonym of S. erythraea.},
}
@article {pmid39646546,
year = {2024},
author = {Li, D and Xia, L and Wang, H},
title = {DNA barcodes and morphological evidence reveal a new genus of Nygmiini (Lepidoptera: Erebidae: Lymantriinae) from China.},
journal = {Zootaxa},
volume = {5496},
number = {1},
pages = {101-110},
doi = {10.11646/zootaxa.5496.1.5},
pmid = {39646546},
issn = {1175-5334},
mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; Male ; Female ; *Moths/anatomy &amp; histology/classification/genetics/growth &amp; development ; *Animal Distribution ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Body Size ; },
abstract = {A new genus Aurivalva Li &amp; Wang gen. nov. is proposed for Nygmiini to accommodate three species previously placed in Euproctis Hübner: A. yunnanpina (Chao, 1984) comb. nov., A. telephanes (Collenette, 1939) comb. nov. and A. conistica (Collenette, 1936) comb. nov.. The new genus is supported by DNA barcodes and morphological evidence. A key to all currently recognized Aurivalva species in China is provided, with illustrations of the adults, wing venations and genitalia, together with a barcode-based tree.},
}
@article {pmid39646525,
year = {2024},
author = {Shah, B and Shao, Y and DU, H and Wang, Y and Huang, J},
title = {Taxonomy and DNA barcoding of the dark-winged fungus gnat genus Zygoneura Meigen (Diptera: Sciaridae) from China, with revision of the type materials.},
journal = {Zootaxa},
volume = {5496},
number = {3},
pages = {377-400},
doi = {10.11646/zootaxa.5496.3.5},
pmid = {39646525},
issn = {1175-5334},
mesh = {Animals ; China ; Male ; *DNA Barcoding, Taxonomic ; Female ; *Diptera/classification/anatomy &amp; histology/genetics ; *Phylogeny ; Animal Distribution ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; },
abstract = {The genus Zygoneura Meigen is revised thoroughly from China, and 14 species are recognized and illustrated, including four new species: Zygoneura (Allozygoneura) xizangensis Shah &amp; Huang sp. nov., Zygoneura (Pharetratula) minuscula sp. nov., Zygoneura (Pharetratula) motuoensis sp. nov. and Zygoneura (Pharetratula) yangi sp. nov. In addition, Zygoneura (Pharetratula) divergens (Mamaev), Zygoneura (Pharetratula) flavicornis (Mamaev), and Zygoneura (Pharetratula) subdivergens (Mohrig &amp; Mamaev) are reported for the first time from China. The identification of these species is supported by both morphological characteristics and sequence data obtained from cytochrome oxidase subunit one (COI) in the DNA barcode analysis. Furthermore, a checklist of the known Zygoneura species in China is also provided, along with an identification key for males.},
}
@article {pmid39646519,
year = {2024},
author = {Almeida, LH and Duarte, T and Bispo, PDC},
title = {Complementary studies of the Perlidae (Insecta: Plecoptera) fauna from the Paranapiacaba Mountains using DNA barcode data.},
journal = {Zootaxa},
volume = {5496},
number = {4},
pages = {500-508},
doi = {10.11646/zootaxa.5496.4.2},
pmid = {39646519},
issn = {1175-5334},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Brazil ; Female ; Male ; *Animal Distribution ; Phylogeny ; Insecta/classification/anatomy &amp; histology/genetics ; Nymph/anatomy &amp; histology/classification/growth &amp; development/genetics ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; },
abstract = {The Paranapiacaba Mountains are a region of Brazil where the stonefly fauna is relatively well known. Despite this, there are still gaps in knowledge that need to be filled. In this study, through field sampling and molecular analyses, we have updated the taxonomic knowledge of Perlidae species in this region. Our study employed DNA barcoding methods to complement traditional morphological approaches, facilitating the association and description of the nymphs of Anacroneuria itajaimirim Bispo &amp; Froehlich 2004. Additionally, we generated DNA barcode sequences for Anacroneuria iporanga Bispo &amp; Froehlich 2004. Our results contributed to knowledge about Perlidae from the Paranapiacaba Mountains, highlighting the importance of DNA barcode data in the association of immature stages and species delimitations. Although the stoneflies of Paranapiacaba Mountains have been relatively well-studied, our results reveal that we still have deficits in knowledge of the fauna of this region.},
}
@article {pmid39646485,
year = {2024},
author = {Gordon, ML and Colville, JF and Engelbrecht, A and Couldridge, VCK},
title = {Ancient Grasshoppers: A revision of the genus Bullacris (Orthoptera: Pneumoridae).},
journal = {Zootaxa},
volume = {5474},
number = {4},
pages = {301-354},
doi = {10.11646/zootaxa.5474.4.1},
pmid = {39646485},
issn = {1175-5334},
mesh = {Animals ; Male ; Female ; *Grasshoppers/anatomy &amp; histology/classification/genetics ; *Phylogeny ; *Animal Distribution ; Body Size ; Organ Size ; South Africa ; Animal Structures/anatomy &amp; histology/growth &amp; development ; },
abstract = {The genus Bullacris in the family Pneumoridae was most recently revised by Dirsh in 1965 based on morphological comparisons between species. However, since that time, new information about the genus and the family has come to light, necessitating a revision of the genus. In addition, the species B. boschimana was originally described based on a single female specimen. Here we present and describe the male of the species for the first time. The aim of this study was to update the current species descriptions by including additional specimens and incorporating additional methods for a more comprehensive comparison. Analyses consisted of morphometric measurements from high-quality images of type specimens, existing South African museum specimens, as well as personally collected specimens. Acoustic signals are also presented and compared between species. In addition, phylogenetic analyses were conducted on the barcoding mitochondrial gene COI and two nuclear genes, namely ITS and 18S. Results show that according to morphological, acoustic and genetic data, B. discolor and B. serrata as well as B. intermedia and B. membracioides share notable similarities. Bullacris discolor and B. serrata share similar phenotypic traits, in which B. discolor can either appear uniform in colour or have a speckled variation that is very similar in appearance to B. serrata. Bullacris intermedia and B. membracioides have a 5% mitochondrial DNA pairwise distance, suggesting that they may have not be fully diverged; however, morphological analysis shows that these species are morphologically distinguishable. It is suggested that these species may have undergone spatial separation at one point; however, further investigation is required. Additional sampling across a wider geographic range is essential to clarify the relationships between B. discolor and B. serrata, as well as between B. intermedia and B. membracioides.},
}
@article {pmid39646451,
year = {2024},
author = {Jimenez, PJ and Chang, K and Shih, HT and Yasuhara, M},
title = {Confirming the occurrence of two fiddler crabs, Tubuca dussumieri (H. Milne Edwards, 1852) and T. coarctata (H. Milne Edwards, 1852) (Crustacea: Decapoda: Ocypodidae), in Hong Kong by DNA barcoding and morphology.},
journal = {Zootaxa},
volume = {5476},
number = {1},
pages = {177-191},
doi = {10.11646/zootaxa.5476.1.17},
pmid = {39646451},
issn = {1175-5334},
mesh = {Animals ; *Brachyura/classification/anatomy &amp; histology/genetics ; Male ; Female ; Hong Kong ; *DNA Barcoding, Taxonomic ; *Animal Distribution ; Body Size ; Ecosystem ; Organ Size ; Phylogeny ; Electron Transport Complex IV/genetics ; Animal Structures/anatomy &amp; histology/growth &amp; development ; },
abstract = {The Indo-West Pacific region has a rich fiddler crab fauna. In East Asia, some species of fiddler crabs, such as Tubuca coarctata (H. Milne Edwards, 1852) and T. dussumieri (H. Milne Edwards, 1852), are considered insular, being present in the Philippines, Taiwan, and Ryukyus, but with no consistent record on continental China. Although T. dussumieri has been previously recorded in continental China, these records were considered dubious or misidentified. The nature of the Kuroshio Current and the colder waters of the China Coastal Current, compared to the currents along the eastern coasts of the Philippines and Taiwan, are considered barriers to the entrance of larvae of these species into the region. Nonetheless, using the cytochrome oxidase subunit I (COI) gene and morphological evidence, we present the first record of T. coarctata and show the presence of a T. dussumieri population in Hong Kong SAR, China. We hypothesize that the newly found T. coarctata in Hong Kong may be related to water temperature increases due to anthropogenic climate change, which allows its larvae to survive in this region and develop into adult crabs. Furthermore, our findings corroborate previous records of T. dussumieri in continental China. The restricted distribution of T. dussumieri in China and the smaller size of individuals, however, may indicate suboptimal habitats for arriving larvae. The limited presence of the two crabs on Chinese shores indicates that the intense coastal development in the country, such as in Hong Kong, may destroy suitable habitats and render these species susceptible to local extinction.},
}
@article {pmid39646447,
year = {2024},
author = {Ma, L and Wu, Y and Li, XZ},
title = {A new species of the genus Porirualia Huys &amp; Mu, 2021 (Copepoda, Harpacticoida, Parastenheliidae) from the intertidal zone of Qingdao, China, with a key to species of the genus.},
journal = {Zootaxa},
volume = {5476},
number = {1},
pages = {241-252},
doi = {10.11646/zootaxa.5476.1.21},
pmid = {39646447},
issn = {1175-5334},
mesh = {Animals ; Female ; Male ; China ; *Animal Distribution ; *Copepoda/classification/anatomy &amp; histology/genetics ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Ecosystem ; Phylogeny ; },
abstract = {A new species belonging to the genus Porirualia Huys &amp; Mu, 2021 was identified and described here based on samples collected from No. 1 Bathing Beach, Qingdao, China. The new species differs from Porirualia pyriformis mainly in the following characteristics: P3 and P4 exp-3 with three inner setae (two inner setae in P. pyriformis), ratio of length to maximum width of female P5 3.83 (3.25 in P. pyriformis). The new species differs from Porirualia megarostrum by the characters including rostrum reaching to distal margin of third segment of antennule (reaching to distal margin of fifth segment of antennule in P. megarostrum), ratio of length to maximum width of female P5 3.83 (2.2 in P. megarostrum); male P2 and P3 two-segmented (three-segmented in P. megarostrum); male P5 bearing five elements (six in P. megarostrum). This is the first report of the genus Porirualia from the China Seas. The DNA barcode (COI) sequence of the new species was obtained and submitted to GenBank (PP761118), which is the first submission of COI sequence of the family Parastenheliidae to GenBank.},
}
@article {pmid39646433,
year = {2024},
author = {Wong, KJH and Meij, SETV and Chan, BKK},
title = {A new species of coral-dwelling crab (Decapoda: Brachyura: Cryptochiridae: Opecarcinus) from the West Pacific.},
journal = {Zootaxa},
volume = {5476},
number = {1},
pages = {474-504},
doi = {10.11646/zootaxa.5476.1.35},
pmid = {39646433},
issn = {1175-5334},
mesh = {Animals ; *Brachyura/classification/anatomy &amp; histology/genetics ; Female ; Male ; *Animal Distribution ; *Body Size ; *Anthozoa/classification/anatomy &amp; histology ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Taiwan ; Pacific Ocean ; Phylogeny ; },
abstract = {Based on material acquired from Green Island, Taiwan, using a combined approach of traditional morphology-based taxonomy and molecular barcoding, we describe a new species of coral-dwelling crab, Opecarcinus ngankeeae sp. nov., from the scleractinian hosts Pavona decussata and P. varians (family Agariciidae). The DNA sequences of the present species matched with O. sp. SET6, associated with plate-forming Leptoseris and Pavona corals, available on Genbank, provided by Xu et al. (2022). The geographical distribution of O. ngankeeae sp. nov. spans from the Coral Triangle and Taiwan to Japan in West Pacific.},
}
@article {pmid39646432,
year = {2024},
author = {Yang, CH and Kumar, AB and Chan, TY},
title = {On the differences between the two widely distributed and closely related rock shrimps Sicyonia japonica Balss, 1914 and S. parajaponica Crosnier, 2003 (Dendrobranchiata, Penaeoidea, Sicyoniidae), with a new record of S. japonica from Taiwan.},
journal = {Zootaxa},
volume = {5476},
number = {1},
pages = {505-513},
doi = {10.11646/zootaxa.5476.1.36},
pmid = {39646432},
issn = {1175-5334},
mesh = {Animals ; Taiwan ; Male ; Female ; *Animal Distribution ; Penaeidae/classification/anatomy &amp; histology ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; },
abstract = {The rock shrimp Sicyonia japonica Balss, 1914 is recorded from Taiwan for the first time. The availability of many fresh specimens of S. japonica and S. parajaponica Crosnier, 2003 from various localities in the Indo-West Pacific allowed a detailed comparison of the morphology, fresh coloration and genetics between these two closely related species. Their major differences are illustrated by line drawings, micro-computed tomography (micro-CT) images and color photographs. DNA barcoding comparison supports the specific status of these two species and reveals that the western Indian Ocean material of S. japonica may represent another cryptic taxon.},
}
@article {pmid39646412,
year = {2024},
author = {Radashevsky, VI and Al-Kandari, M and Malyar, VV and Pankova, VV},
title = {A twin of Polydora hoplura (Annelida: Spionidae) from the Arabian (Persian) Gulf, with review of primers used for barcoding of Spionidae.},
journal = {Zootaxa},
volume = {5529},
number = {2},
pages = {245-268},
doi = {10.11646/zootaxa.5529.2.2},
pmid = {39646412},
issn = {1175-5334},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Polychaeta/classification/genetics/anatomy &amp; histology ; *Phylogeny ; Male ; Indian Ocean ; Female ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Body Size ; },
abstract = {The spionid polychaete Polydora hoplura Claparède, 1868 has been widely recorded boring in shells of abalone, oysters, clams, barnacle tests and sponges in temperate and subtropical waters. Molecular studies have suggested conspecificity of individuals collected worldwide but showed high genetic variability of the species with the highest diversity of haplotypes in the South African population. We have compared the morphology and genetic data of shell-boring worms from Kuwait, which were previously assigned to P. hoplura, with American, Asian and European individuals, including those from the type locality in Italy. The Kuwaiti individuals share key diagnostic morphological characters with P. hoplura but differ in ochre pigment on the anterior chaetigers in life, pattern of pigmentation after fixation in formalin, and pattern of methyl green staining of fixed specimens. They also differ in the dimensions of mature spermatozoa. The analysis of sequence data of five gene fragments (total 3483 bp) showed that the intraspecific diversity of P. hoplura and the variability of Polydora individuals from Kuwait are less than the divergences in all studied genes, except for 28S rDNA, between these two groups. These data, as well as the absence of common cytochrome c oxidase subunit I (COI) and 16S haplotypes, and morphological differences between individuals from Kuwait and P. hoplura, allowed us to conclude that the Kuwaiti population is not conspecific with P. hoplura. This conclusion was confirmed by the results of the species delimitation analysis. In the Bayesian inference analysis of the sequence data individuals from Kuwait formed a well-supported clade sister to P. hoplura. These individuals are described and illustrated here as a new species, Polydora mohammadi sp. nov. Primers used for successful amplification of the mitochondrial COI gene in various species of Spionidae are reviewed and we suggest future studies on Polydora use a combination of two primer pairs (2F-spionid-LCO/1R-spionid-HCO and Dorid_COI.3F/Dorid_COI.1R) to target sequences that include the barcode fragments covered with "Folmer" and "Dorid" primers.},
}
@article {pmid39646401,
year = {2024},
author = {Wesener, T},
title = {Five new species and numerous locality records of Spirobolida millipedes from Madagascar (Diplopoda, Spirobolida, Pachybolidae).},
journal = {Zootaxa},
volume = {5529},
number = {3},
pages = {461-486},
doi = {10.11646/zootaxa.5529.3.3},
pmid = {39646401},
issn = {1175-5334},
mesh = {Madagascar ; Animals ; Male ; *Animal Distribution ; Female ; *Arthropods/classification/anatomy &amp; histology ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Ecosystem ; },
abstract = {Based mainly on the results of generalized American biodiversity inventory programmes, several samples of Malagasy Spirobolida millipedes became available to study. Based on this material, five new species of Spirobolida are described from Madagascar: four potential microendemic species, Aphistogoniulus amberivery sp. nov. from the Amberivery forest, A. manombo sp. nov., from the lowland rainforest of Manombo, Spiromimus endemicus sp. nov. from the Montagne des Français, and a species from the littoral forest of Tampolo, tentatively placed in the genus Eucarlia Brölemann, 1913, E. tampolo sp. nov.. A fifth species appears to be more widespread and is a morphologically unusual species of the genus Alluviobolus Wesener, 2009, A. omega sp. nov.. Aphistogoniulus manombo sp. nov. was previously described as a population of A. jeekeli Decker &amp; Wesener, 2011. One of the most enigmatic Malagasy millipede species, Spirobolus olympiacus Karsch, 1881, is redescribed based on topotypic material as Colossobolus olympiacus (Karsch, 1881) new combination. Additional locality data is provided for 14 other Spirobolida species, of which 11 are listed on the IUCN Red List: Aphistogoniulus aridus Wesener, 2009, A. diabolicus Wesener, 2009, A. erythrocephalus (Pocock, 1893), A. hova (de Saussure &amp; Zehntner, 1897), Colossobolus semicyclus Wesener, 2009, Spiromimus albipes Wesener &amp; Enghoff, 2009, S. litoralis Wesener &amp; Enghoff, 2009, S. simplex Wesener &amp; Enghoff, 2009, S. triaureus Wesener &amp; Enghoff, 2009, S. univirgatus deSaussure &amp; Zehntner, 1901, Flagellobolus pauliani Wesener, 2009, Dactylobolus bivirgatus (Karsch, 1881), Madabolus maximus Wesener &amp; Enghoff, 2008 and Hylekobolus rufus Wesener, 2009. Fourteen new genetic barcoding COI sequences are provided for nine species: Hylekobolus rufus, Colossobolus semicyclus, Aphistogoniulus amberivery sp. nov., A. aridus, A. diabolicus, A. erythrocephalus, A. hova, Spiromimus univirgatus and S. scapularis Wesener &amp; Enghoff, 2009.},
}
@article {pmid39646399,
year = {2024},
author = {Zuñiga, R and Valerio, AA and Hanson, P and Smith, MA and Hallwachs, W and Janzen, DH},
title = {Cryptic diversity of Leurus wasps (Hymenoptera: Ichneumonidae: Metopiinae), parasitoids of caterpillars in Area de Conservación Guanacaste, Costa Rica.},
journal = {Zootaxa},
volume = {5529},
number = {3},
pages = {511-531},
doi = {10.11646/zootaxa.5529.3.5},
pmid = {39646399},
issn = {1175-5334},
mesh = {Animals ; Costa Rica ; *Wasps/anatomy &amp; histology/classification ; Male ; Female ; *Larva/anatomy &amp; histology/growth &amp; development ; *Animal Distribution ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Moths/anatomy &amp; histology/parasitology ; Ecosystem ; },
abstract = {As a consequence of COI barcoding hundreds of reared specimens of what appeared to be Leurus caeruliventris, a parasitoid of leaf-rolling Crambidae (Lepidoptera) from the Area de Conservación Guanacaste, northwestern Costa Rica, and matching them with their host caterpillars and morphological traits, we describe ten new sympatric species and redescribe L. caeruliventris. The new species, authored by Zuñiga &amp; Valerio, are: Leurus billeberhardi, L. henrytownesi, L. hugokonsi, L. iangauldi, L. jesusugaldei, L. marjorietownesae, L. maryjanewestae, L. pammitchellae, L. sondrawardae, and L. wahli. We also provide an illustrated key to the eleven species and an ecological glimpse into the lives of these very similar wasp species.},
}
@article {pmid39646383,
year = {2024},
author = {Haÿ, V and Mennesson, MI and Dahruddin, H and Sauri, S and Limmon, G and Wowor, D and Hubert, N and Keith, P and Lord, C},
title = {A new freshwater pipefish species (Syngnathidae: Microphis) from the Sunda shelf islands, Indonesia.},
journal = {Zootaxa},
volume = {5536},
number = {1},
pages = {139-152},
doi = {10.11646/zootaxa.5536.1.5},
pmid = {39646383},
issn = {1175-5334},
mesh = {Animals ; Indonesia ; Male ; Female ; *Animal Distribution ; *Smegmamorpha/genetics/classification/anatomy &amp; histology ; Islands ; Phylogeny ; Organ Size ; Fresh Water ; Body Size ; Ecosystem ; Animal Structures/anatomy &amp; histology/growth &amp; development ; },
abstract = {A new species of freshwater pipefish, Microphis arrakisae sp. nov., is described from the West Indonesian Islands (Java, Bali and Lombok). This species is morphologically very close to Microphis retzii (Bleeker, 1856), which is found in the eastern Indonesian Islands (Sulawesi, Ceram, Ambon and Papua). However, it can be distinguished by its in vivo coloration. Furthermore, genetic analysis of the partial COI gene (barcoding) indicates that it represents a distinct genetic lineage in the Indonesian region.},
}
@article {pmid39646344,
year = {2024},
author = {Selis, M and Fateryga, AV and Cilia, G},
title = {The genus Euodynerus Dalla Torre in Europe and the Maghreb (Hymenoptera: Vespidae: Eumeninae).},
journal = {Zootaxa},
volume = {5537},
number = {2},
pages = {151-194},
doi = {10.11646/zootaxa.5537.2.1},
pmid = {39646344},
issn = {1175-5334},
mesh = {Animals ; Europe ; *Wasps/anatomy &amp; histology/classification ; Male ; Female ; *Animal Distribution ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Phylogeny ; DNA Barcoding, Taxonomic ; },
abstract = {The genus Euodynerus Dalla Torre, 1904 (= Extraepipona Gusenleitner, 2014, syn. nov.; Euodynerus occultus (Gusenleitner, 2014), comb. nov.) is revised in Europe and the Maghreb, combining morphological data and DNA barcoding. New synonymies are proposed for E. (Pareuodynerus) Blüthgen, 1938 (= E. (Incolepipona) Giordani Soika, 1994, syn. nov.), E. annae (Kostylev, 1937) (= Euodynerus shirazensis Giordani Soika, 1970, syn. nov.), E. caspicus (Morawitz, 1873) (= Euodynerus caspicus armeniacus Gusenleitner, 2016, syn. nov.), E. curictensis Blüthgen, 1940 (= Euodynerus curictensis sardous Borsato, 2006, syn. nov.), E. dantici (Rossi, 1790) (= Euodynerus dantici poggii Giordani Soika, 1986, syn. nov.; = Euodynerus minoricensis Sanza, 2003, syn. nov.), E. quadrifasciatus (Fabricius, 1793) (= Euodynerus quadrifasciatus atripes Giordani Soika, 1976, syn. nov.; = Euodynerus quadrifasciatus rufipes Gusenleitner, 1984, syn. nov.; = Euodynerus quadrifasciatus eburnus Yamane, 1987, syn. nov.), E. rubrosignatus Gusenleitner, 1984, stat. nov. (= Euodynerus notatus cyrenaicus Giordani Soika, 1986, syn. nov.) and E. variegatus (Fabricius, 1793) (= Odynerus crenatus kruegeri von Schulthess, 1928, syn. nov.). Euodynerus quadrifasciatus rubrosignatus Gusenleitner, 1984 is raised to species-level (E. rubrosignatus, stat. nov.), and E. bidentoides (Giordani Soika, 1953), sp. resurr. is removed from synonymy with E. bidentiformis (Giordani Soika, 1942). Euodynerus bidentatus (Lepeletier, 1841) is transferred from the subgenus Pareuodynerus to Euodynerus s. str. A key for the identification of the Euro-Maghrebi species of Euodynerus and reference photos for each species are provided.},
}
@article {pmid39646260,
year = {2024},
author = {Makarchenko, EA and Semenchenko, AA and Krasheninnikov, AB and Yanygina, LV and Yavorskaya, NM},
title = {Review of archaic nymphomyiids (Diptera, Nymphomyiidae) of the Russian Far East and bordering territories, with describing of new taxa and DNA barcoding of known species.},
journal = {Zootaxa},
volume = {5448},
number = {2},
pages = {183-211},
doi = {10.11646/zootaxa.5448.2.2},
pmid = {39646260},
issn = {1175-5334},
mesh = {Animals ; Male ; *DNA Barcoding, Taxonomic ; Female ; *Diptera/classification/anatomy &amp; histology/genetics ; *Animal Distribution ; Russia ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Body Size ; Ecosystem ; },
abstract = {Nymphomyiidae from the Russian Far East and bordering territories are revised, including data on taxonomy, redescriptions, and results of DNA barcoding. Nymphomyia orientalis sp. nov. with two subspecies N orientalis orientalis subsp. nov. and N. orientalis makcha subsp. nov. are described and information on biology, ecology and distribution are presented. Key of Nymphomyia species for adult males and females of the world is provided. Three species delimitation approaches (ASAP, mPTP, GMYC) using the mitochondrial gene cytochrome c oxidase I (COI) confirm validity of described taxa as well as available nymphomyiids in GenBank. Morphologically indistinguishable specimens of N. orientalis sp. nov. from Makcha and Polovinka rivers belongs to separate mOTUs with the lowest distances in the genus 1.99% that is the lower interspecific threshold.},
}
@article {pmid39646227,
year = {2024},
author = {Sanz-Veiga, PA and Leivas, FWT and Díaz-Grisales, V and Anzaldo, S and Rosado-Neto, GH and Lampert, S and Maggio, DH and Corrêa, AS and Savaris, M},
title = {Sympatric species of Heilipus Germar (Coleoptera: Curculionidae: Hylobiini) on fruits of Lauraceae: a new species from Brazil and redescription of Heilipus draco (Fabricius, 1801).},
journal = {Zootaxa},
volume = {5463},
number = {1},
pages = {63-83},
doi = {10.11646/zootaxa.5463.1.4},
pmid = {39646227},
issn = {1175-5334},
mesh = {Animals ; Brazil ; *Weevils/anatomy &amp; histology/classification ; Male ; Female ; *Animal Distribution ; *Fruit ; Lauraceae/classification ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Body Size ; Sympatry ; },
abstract = {The genus Heilipus Germar (Curculionidae: Hylobiini) is an American weevil group with 89 described species, of which 28 species are known from Brazil. Here, we describe a new species of Heilipus from Brazil and redescribe H. draco (Fabricius, 1801). Heilipus vividaensis Sanz-Veiga, Savaris &amp; Leivas, sp. nov. and H. draco are similar sympatric species, reared from fruits of Ocotea puberula (Rich.) Nees and Nectandra angustifolia (Schrad.) Nees &amp; Mart. (Lauraceae) in south and southeast Brazil. External morphological and genitalia descriptions, illustrations, distribution records, notes on the host plant, and a barcode DNA sequence are provided for both species.},
}
@article {pmid39646215,
year = {2024},
author = {Lee, I and Park, KH},
title = {A new species of Homidia (Collembola: Entomobridae) from Korea, with notes on its DNA data.},
journal = {Zootaxa},
volume = {5463},
number = {2},
pages = {262-272},
doi = {10.11646/zootaxa.5463.2.6},
pmid = {39646215},
issn = {1175-5334},
mesh = {Animals ; Republic of Korea ; *Arthropods/classification/anatomy &amp; histology/genetics ; Male ; Female ; *DNA Barcoding, Taxonomic ; Animal Distribution ; Phylogeny ; Organ Size ; Electron Transport Complex IV/genetics ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; },
abstract = {A new species, Homidia pseudokoreana sp. nov., from South Korea described based on morphological data and DNA barcodes. This species is morphologically characterized by the body color pattern with a longitudinal dark stripe on medial area of Th. II to Th. III, coxal macrochaetal formula as 3/4+1,3/4+2, and unguis III with three inner teeth. In this study, DNA sequences of mitochondrial cytochrome c oxidase subunit I (COI) gene were used as DNA barcode to distinguish species. It showed distinct differences in genetic distances between Homidia species. DNA barcoding was a useful tool when identifying morphologically closely related species in Homidia.},
}
@article {pmid39646203,
year = {2024},
author = {Bahder, BW and Myrie, W and Helmick, EE and Bartlett, CR},
title = {A new species of planthopper in the genus Patara (Hemiptera: Auchenorrhyncha: Fulgoroidea: Derbidae) from central Jamaica.},
journal = {Zootaxa},
volume = {5463},
number = {3},
pages = {429-440},
doi = {10.11646/zootaxa.5463.3.8},
pmid = {39646203},
issn = {1175-5334},
mesh = {Animals ; *Hemiptera/classification/anatomy &amp; histology/genetics ; Male ; Female ; Jamaica ; *Animal Distribution ; Body Size ; Organ Size ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; },
abstract = {During survey work for planthoppers associated with palms in Jamaica, one new species of Patara was collected at the Castleton Botanic Garden and is here described as Patara euryfrons sp. n. The species is unusual in having a much broader head than is normally found in members of the genus. Supplementary molecular data for the barcoding region (5' half) of the cytochrome c oxidase subunit I (COI), 18S rRNA gene and D9-D10 expansion region of the 28S rRNA gene is provided to support the placement of the novel taxon in Patara.},
}
@article {pmid39646164,
year = {2024},
author = {Lukhtanov, VA and Botman, RV and Gagarina, AV},
title = {DNA barcode based phylogeographic analysis of the Aricia anteros (Freyer, 1838) species complex (Lepidoptera: Lycaenidae) with description of a new subspecies from SE Europe.},
journal = {Zootaxa},
volume = {5468},
number = {3},
pages = {505-522},
doi = {10.11646/zootaxa.5468.3.5},
pmid = {39646164},
issn = {1175-5334},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Phylogeography ; Male ; *Animal Distribution ; Female ; Europe ; Butterflies/classification/genetics/anatomy &amp; histology ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; },
abstract = {The complex of taxa closely related to Aricia anteros includes the species A. anteros sensu stricto, A. crassipuncta, A. bassoni, and A. vandarbani. All of them are sometimes considered as subspecies of a single polytypic species. Representatives of this complex are found in the Balkan Peninsula, Asia Minor, the Levant, the Caucasus, Transcaucasia, and Northern and Western Iran. In addition, an isolated population of A. anteros occurs in the Northern Black Sea region. In this work, based on DNA barcodes of all species and main populations of the complex, we show the existence of seven differentiated mitochondrial lineages: anteros (predominant in the Balkans), crassipuncta (predominant in Asia Minor), bassoni (the Levant), vandarbani (Talysh Mts), varicolor (Zagros Mts), dombaiensis (the Caucasus) and kalmius (Kalmius River basin in the Northern Black Sea region). The taxa of the A. anteros species complex are allopatric, except for A. anteros s.s. and A. crassipuncta, which have a mosaic distribution in eastern Anatolia and Transcaucasia. On the Balkan Peninsula, within the species A. anteros s.s, both the anteros and the crassipuncta mitochondrial haplogroups are found. This pattern is likely a consequence of interspecific hybridization and mitochondrial introgression. Based on mitochondrial DNA, the taxon A. crassipuncta mehmetcik from SE Anatolia is indistinguishable from A. crassipuncta crassipuncta, and the taxon varicolor from Central Iran is closer to the geographically distant European A. anteros than to the Anatolian A. crassipuncta. The geographically isolated and genetically differentiated population from the Kalmius River basin in the Northern Black Sea region is described here as a new subspecies.},
}
@article {pmid39646142,
year = {2024},
author = {Wesener, T},
title = {Integrative redescription of Glomeris cingulata C. L. Koch, 1847, an almost forgotten microendemic pill millipede (Diplopoda, Glomerida, Glomeridae).},
journal = {Zootaxa},
volume = {5541},
number = {3},
pages = {326-338},
doi = {10.11646/zootaxa.5541.3.4},
pmid = {39646142},
issn = {1175-5334},
mesh = {Animals ; *Arthropods/classification/anatomy &amp; histology ; Male ; Female ; *Animal Distribution ; *Phylogeny ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Slovenia ; Ecosystem ; },
abstract = {Among the more than 80 species of the common pill millipede genus Glomeris Latreille, 1803, there are several microendemic species that have not been recorded for the last 80-120 years. To discover whether these species are colour morphs of widespread species or true local endemics is important from a conservation point of view as well as for understanding the biogeography and evolution of the group. The author received three specimens that were morphologically identical to C. L. Koch's 175-year-old first description of Glomeris cingulata Koch, 1847 from the Triglav Mountain in Slovenia, close to the border with Italy. No clear specimen-based records are available for G. cingulata and the type specimen is apparently lost. In order to clarify the taxonomy of this microendemic species, an integrative redescription was conducted, including scanning electron microscopy and DNA barcoding. Glomeris cingulata is a distinct species, with genetic distances of 12.6-15.5% compared to the seven syntopic and numerous other widespread Glomeris species. Based on characters of the first description and following other authors, the synonymy of Glomeris cingulata intercedens Latzel, 1884 under Glomeris transalpina Koch, 1836 is confirmed. The dark colour with posterior red bands closely resembles that of some other high-altitude Glomeris species like G. transalpina Koch, 1836, Glomeris aurita Koch, 1847 and Glomeris oropensis Verhoeff, 1936. Glomeris cingulata is genetically close to, but distant enough from the small-bodied and widespread taxa like Glomeris pustulata Latreille, 1804 and Glomeris tetrasticha Brandt, 1833.},
}
@article {pmid39646033,
year = {2024},
author = {Krupitsky, AV and Naderi, A and Hagen, WT and Lukhtanov, VA and Nazari, V},
title = {New data on distribution of Phoenicurusia transcaucasicus (Miller, 1923) (Lepidoptera, Lycaenidae) with description of a new subspecies from Iran.},
journal = {Zootaxa},
volume = {5481},
number = {3},
pages = {373-383},
doi = {10.11646/zootaxa.5481.3.6},
pmid = {39646033},
issn = {1175-5334},
mesh = {Animals ; Iran ; Male ; Female ; *Animal Distribution ; *Phylogeny ; Butterflies/anatomy &amp; histology/classification/genetics/growth &amp; development ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; },
abstract = {Distribution of Phoenicurusia transcaucasicus (Miller, 1923) in Iran and neighbouring territories is clarified based on analysis of DNA barcodes, the male genitalia and wing pattern of adults. Our study revealed the widespread distribution of Ph. transcaucasicus throughout northern, northeastern and central Iran. Based on integrative analysis, a new subspecies, Ph. transcaucasicus flamma ssp. n., is described from the Zagros Mountains, the Central Iranian Range and the Alborz Mountains. Compared to the nominotypical subspecies, the new subspecies differs in well-developed orange pattern both of dorsal and ventral sides of the wings, shape of the valva in the male genitalia and distinct COI haplotypes. Additionally, distinct phylogenetic lineage of Ph. transcaucasicus is reported from Kerman Province. Diagnostic characters of the species of Ph. phoenicurus (Lederer, 1870) group of Iran are illustrated.},
}
@article {pmid39646026,
year = {2024},
author = {Baldizzone, G and Huemer, P},
title = {Coleophora elea Baldizzone &amp; Huemer, new species of the Coleophora oriolella Zeller, 1849 species-group (Lepidoptera, Coleophoridae).},
journal = {Zootaxa},
volume = {5481},
number = {4},
pages = {463-470},
doi = {10.11646/zootaxa.5481.4.4},
pmid = {39646026},
issn = {1175-5334},
mesh = {Animals ; Male ; Female ; *Moths/anatomy &amp; histology/classification/genetics ; *Animal Distribution ; Organ Size ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; },
abstract = {Coleophora elea Baldizzone &amp; Huemer, sp. nov., is described based on specimens collected from the Peloponnese peninsula (Greece). This species is closely related to C. oriolella Zeller, 1849, but it differs in external appearance and in characters of the male and female genitalia. Additionally, the two species are genetically distinct as evidenced by a p-distance of approximately 4% between their DNA barcodes (cytochrome c-oxidase subunit 1). Adult specimens and the genitalia of both species are illustrated for comparative purposes.},
}
@article {pmid39646024,
year = {2024},
author = {Makarchenko, EA and Semenchenko, AA and Palatov, DM},
title = {Morphological description and DNA barcoding of Diamesa achipseensis sp. nov. (Diptera: Chironomidae: Diamesinae) from Southwestern Caucasus.},
journal = {Zootaxa},
volume = {5481},
number = {4},
pages = {477-482},
doi = {10.11646/zootaxa.5481.4.6},
pmid = {39646024},
issn = {1175-5334},
mesh = {Animals ; Male ; *DNA Barcoding, Taxonomic ; *Chironomidae/anatomy &amp; histology/classification/genetics/growth &amp; development ; Female ; Body Size ; Animal Distribution ; Phylogeny ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; },
abstract = {Illustrated description of adult male, as well as DNA barcoding, of Diamesa achipseensis sp. nov. in comparison with close related species D. caucasica Kownacki et Kownacka from Southwestern Caucasus are provided. Interspecific distances between D. achipseensis sp. nov. and D. caucasica are extremely low (0.64% in average) despite the identified morphological differences. High similarity of these species is new example of genetically indistinguishable of some species of the genus Diamesa Meigen.},
}
@article {pmid39645963,
year = {2024},
author = {Gebremeskel, A and Salnitska, M and Solodovnikov, A},
title = {DNA barcode polymorphism within a common widespread rove beetle Quedius molochinus (Coleoptera: Staphylinidae).},
journal = {Zootaxa},
volume = {5519},
number = {4},
pages = {538-548},
doi = {10.11646/zootaxa.5519.4.3},
pmid = {39645963},
issn = {1175-5334},
mesh = {Animals ; *Coleoptera/genetics/classification/anatomy &amp; histology ; *DNA Barcoding, Taxonomic ; Male ; Female ; *Phylogeny ; *Animal Distribution ; Body Size ; Polymorphism, Genetic ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; },
abstract = {Phylogenetic assessment of COI barcodes from 22 specimens identified as Q. molochinus based on external morphology and shape of the aedeagus revealed three non-sister clades within this recently revised species, with large molecular distance (6.3-7.8%) among them, suggesting their species status. On the contrary, preliminary study of the aedeagal internal sac (endophallus) of the available males from these clades and from the more numerous additional non-sequenced materials of Q. molochinus did not reveal notable variants. We report this case here because firstly, this goes against some cases observed in other beetles where endophallic characters may be the only morphological traits supporting molecular-based cryptic species, and secondly, these molecular clades are unexpected within a species we thought to be well-known. DNA barcoding, exploration of nuclear DNA markers and an in-depth examination of the fully everted endophallus for a wider sample of freshly collected specimens are required for further study and explanation of the detected molecular polymorphism of Q. molochinus. An illustration of the everted internal sac as a reference and new distributional data for this species are provided.},
}
@article {pmid39645938,
year = {2024},
author = {Ballon-Estacio, R and Alvarado, M},
title = {Three new species of parasitoid wasps of the genus Mnioes Townes, 1946 (Ichneumonidae: Banchinae) in a humid forest in Peru.},
journal = {Zootaxa},
volume = {5523},
number = {2},
pages = {269-283},
doi = {10.11646/zootaxa.5523.2.8},
pmid = {39645938},
issn = {1175-5334},
mesh = {Animals ; Peru ; Female ; Male ; *Forests ; *Animal Distribution ; *Wasps/anatomy &amp; histology/classification ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Ecosystem ; },
abstract = {Mnioes is a predominantly Neotropical genus of Banchinae (Ichneumonidae), currently including 26 species. Three new species of Mnioes are described, found in a humid montane forest in southern Peru, M. chunka sp. nov, M. chusaq sp. nov. and M. isqun sp. nov, and the male of M. huk Alvarado 2020 is also described. DNA barcoding for all the species treated here is included and provides information to match females with males, especially for M. chunka sp. nov., M. chusaq sp. nov., and M. soqta Alvarado 2020 where females are similar to each other and occur in sympatry. Additionally, an updated key to the Peruvian species is provided.},
}
@article {pmid39645925,
year = {2024},
author = {Jiang, ZH and Yan, M and Wang, JX and Hu, SJ},
title = {Review of the genus Pseudodolbina Rothschild, 1894, with the description of a new species from Yunnan, China (Lepidoptera: Sphingidae).},
journal = {Zootaxa},
volume = {5523},
number = {4},
pages = {423-436},
doi = {10.11646/zootaxa.5523.4.2},
pmid = {39645925},
issn = {1175-5334},
mesh = {Animals ; China ; Male ; Female ; *Animal Distribution ; *Phylogeny ; *Moths/anatomy &amp; histology/classification ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; },
abstract = {The two species currently included in the genus Pseudodolbina Rothschild, 1894, Pseudodolbina fo (Walker, 1856) and Pseudodolbina aequalis Rothschild &amp; Jordan, 1903, were studied and a new species, Pseudodolbina yunnana sp. nov., was described from Yunnan, China. The diagnostic features and a distribution map of three species are provided, with a phylogenetic analysis based on DNA barcodes.},
}
@article {pmid39645924,
year = {2024},
author = {Huemer, P and Özden, &#xd6;},
title = {Scrobipalpa chardonnayi Huemer and Özden, sp. nov.: a new presumably endemic species from Cyprus (Lepidoptera, Gelechiidae).},
journal = {Zootaxa},
volume = {5523},
number = {4},
pages = {437-447},
doi = {10.11646/zootaxa.5523.4.3},
pmid = {39645924},
issn = {1175-5334},
mesh = {Animals ; Cyprus ; Female ; Male ; *Animal Distribution ; *Moths/anatomy &amp; histology/classification ; *Phylogeny ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Ecosystem ; },
abstract = {Scrobipalpa chardonnayi Huemer &amp; Özden, sp. nov. is described from the limestone mountains of northern Cyprus and considered as a possible island endemism. The new species shows closer phylogenetic relationships to S. vasconiella (Rössler, 1877) and some related species, but differs phenotypically and in male and female genitalia, as well as through significant divergences in DNA barcode. Morphologically relevant diagnostic characters are compared and figured. Finally, S. vasconiella is reported from Kyrgyzstan for the first time.},
}
@article {pmid39645904,
year = {2024},
author = {Komai, T and Hanai, M},
title = {A new shallow water species of the palaemonid shrimp genus Palaemon Weber, 1795 (Decapoda: Caridea) from Japan.},
journal = {Zootaxa},
volume = {5443},
number = {3},
pages = {417-430},
doi = {10.11646/zootaxa.5443.3.6},
pmid = {39645904},
issn = {1175-5334},
mesh = {Animals ; *Palaemonidae/classification/anatomy &amp; histology/genetics ; Japan ; Male ; Female ; *Animal Distribution ; *Body Size ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; },
abstract = {During a survey of the shallow water decapod fauna in the Miura Peninsula, Kanagawa Prefecture, central Japan, four specimens of a new palaemonid shrimp, Palaemon parvibrachium n. sp., were collected from sea grass beds of Nanozostera japonica (Ascherson &amp; Graebner) Tomlinson &amp; Posluszny, 2001. The new species appears morphologically similar to P. serrifer (Stimpson, 1860), one of the most common representatives of Palaemon Weber, 1795 in Japanese waters, but the short carpus of the second pereopod and the different live colouration readily differentiate the new species from the latter. A DNA barcode (a partial fragment of the mitochondrial CO1 gene), as well as a partial fragment of the mitochondrial 16S rRNA gene, are provided to genetically characterize the new species.},
}
@article {pmid39645896,
year = {2024},
author = {Barrantes, EAB and Echavarria, MAZ and Bartlett, CR and Helmick, EE and Bahder, BW},
title = {A new species of planthopper in the genus Myconus (Hemiptera: Auchenorrhyncha: Fulgoroidea: Achilidae) from the Osa Peninsula in Costa Rica.},
journal = {Zootaxa},
volume = {5443},
number = {4},
pages = {580-590},
doi = {10.11646/zootaxa.5443.4.6},
pmid = {39645896},
issn = {1175-5334},
mesh = {Animals ; *Hemiptera/anatomy &amp; histology/classification ; Costa Rica ; Male ; Female ; *Animal Distribution ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Phylogeny ; },
abstract = {Recent surveys of palm-associated planthoppers in Costa Rica have revealed many new species, primarily in the families Derbidae and Cixiidae, but also Myconus jacquelinae Bahder &amp; Bartlett, in the Achilidae. Here a new species of Myconus from the the Osa peninsula is described as Myconus florae sp. n. with supplemental molecular data for the barcoding region (5'-half) of the cytochrome c oxidase subunit I (COI) gene, 18S rRNA gene, and histone 3 (H3) gene. A key to all species of Myconus is provided.},
}
@article {pmid39645882,
year = {2024},
author = {Samoh, A and Grootaert, P},
title = {New species and records of the genus Hercostomus Loew (Diptera: Dolichopodidae) from Thailand mangroves, with notes on the Hercostomus fauna of Singapore mangroves.},
journal = {Zootaxa},
volume = {5446},
number = {2},
pages = {179-204},
doi = {10.11646/zootaxa.5446.2.2},
pmid = {39645882},
issn = {1175-5334},
mesh = {Animals ; Thailand ; Female ; *Animal Distribution ; *Diptera/classification/anatomy &amp; histology/genetics ; Singapore ; Male ; *Ecosystem ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; Wetlands ; },
abstract = {The long-legged fly genus Hercostomus Loew, 1857 is reported for the first time from mangrove habitats in Thailand. Two new species, H. obtusus sp. nov. and H. squamatus sp. nov. are described based on external morphology and supported by NGS barcoding. Four described species, namely, H. brevicornis Zhang, Yang &amp; Grootaert, 2008, H. brevidigitalis Zhang, Yang &amp; Grootaert, 2008, H. lanceolatus Zhang, Yang &amp; Grootaert, 2008, and H. plumatus Zhang, Yang &amp; Grootaert, 2008, previously known only from Singapore mangroves, are recorded for the first time from Thailand mangroves. In addition, species distributions are mapped and taxonomic notes are provided.},
}
@article {pmid39645866,
year = {2024},
author = {Yagi, S and Goto, K and Sohn, JC},
title = {A new species of Caloptilia (Lepidoptera: Gracillariidae) from Japan and Korea.},
journal = {Zootaxa},
volume = {5446},
number = {3},
pages = {420-432},
doi = {10.11646/zootaxa.5446.3.6},
pmid = {39645866},
issn = {1175-5334},
mesh = {Animals ; Male ; Republic of Korea ; Japan ; *Moths/classification/anatomy &amp; histology/genetics/growth &amp; development ; Female ; *Animal Distribution ; Larva/growth &amp; development/anatomy &amp; histology/classification ; Body Size ; Organ Size ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; DNA Barcoding, Taxonomic ; },
abstract = {A new species of Caloptilia, C. rhynchosiae n. sp. is described, based on 16 specimens from Japan and Korea. The species is characterized by the presence of the saccular process in the male genitalia. A fabaceous vine, Rhynchosia tomentosa (L.) Hook. &amp; Arn. is reported as the larval host of C. rhynchosiae n. sp. Larval feeding preference, biology and pupation process are described for the species. The species turned out to be host-specific. Two sets of COI barcodes were generated for C. rhynchosiae n. sp. The genetic distances of COI barcodes between the new species and other congeners in the public databases are compared. The conclusion was made that C. rhynchosiae n. sp. was misidentified as C. soyella in the BOLD and GenBank DNA barcode depositories.},
}
@article {pmid39645854,
year = {2024},
author = {Xue, G and Xie, Y and Shen, G and Li, X and Li, M and Guo, Y},
title = {Study on the intraspecific variation of Capila lineata lineata Chou &amp; Gu, 1994, with some taxonomic notes on the related taxa (Hesperiidae, Pyrginae).},
journal = {Zootaxa},
volume = {5446},
number = {4},
pages = {573-580},
doi = {10.11646/zootaxa.5446.4.9},
pmid = {39645854},
issn = {1175-5334},
mesh = {Animals ; Male ; Female ; *Animal Distribution ; Organ Size ; Phylogeny ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; DNA Barcoding, Taxonomic ; },
abstract = {The history with regard to questions on Capila lineata lineata Chou &amp; Gu, 1994, C. lineata magna Devyatkin &amp; Monastyrskii, 1999, C. lineata irregularis Devyatkin &amp; Monastyrskii, 2002 and C. neolineata Fan, Wang &amp; Huang, 2003 was reviewed. The intraspecific variation of C. lineata lineata was explored by DNA barcoding and morphological comparison. The results revealed a remarkable variability in wing patterns and a slight variability in female genitalia, whereas characters of the male genitalia were uniform. C. lineata irregularis syn. n. and C. neolineata syn. n. are treated as junior subjective synonyms of C. lineata lineata because morphological characters of the two taxa fall into the range of individual variation of the latter.},
}
@article {pmid39645812,
year = {2024},
author = {Navarro-Rodríguez, CI and Valdez-Mondragón, A},
title = {Violins we see, species we don't… Species delimitation of the spider genus Loxosceles Heineken &amp; Lowe (Araneae: Sicariidae) from North America using morphological and molecular evidence.},
journal = {Zootaxa},
volume = {5428},
number = {4},
pages = {527-548},
doi = {10.11646/zootaxa.5428.4.4},
pmid = {39645812},
issn = {1175-5334},
mesh = {Animals ; *Spiders/anatomy &amp; histology/classification/genetics ; Male ; Female ; North America ; *Phylogeny ; DNA Barcoding, Taxonomic ; Animal Distribution ; Electron Transport Complex IV/genetics ; Organ Size ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; },
abstract = {In modern systematics, different sources of evidence are commonly used for the discovery, identification, and delimitation of species, especially when morphology fails to delineate between species or in underestimated species complexes or cryptic species. In this study, morphological data and two DNA barcoding markers-cytochrome c oxidase subunit I (COI) and internal transcribed spacer 2 (ITS2)-were used to delimit species in the spider genus Loxosceles from North America. The molecular species delimitation analyses were carried out using three different methods under the corrected p-distance Neighbor-Joining (NJ) criteria: 1) Assemble Species by Automatic Partitioning (ASAP), 2) General Mixed Yule Coalescent model (GMYC), and 3) Bayesian Poisson Tree Processes (bPTP). The analyses incorporated 192 terminals corresponding to 43 putative species of Loxosceles, of which 15 are newly recognized herein, as putative new species, based on morphology and congruence between molecular methods with COI. The average intraspecific genetic distance (p-distance) was <2%, whereas the average interspecific genetic distance was 15.6%. The GMYC and bPTP molecular methods recovered 65-79 and 69 species respectively, overestimating the diversity in comparison with morphology, whereas the ASAP method delimited 60 species. The morphology of primary sexual structures (males palps and female seminal receptacles) was congruent with most of the molecular methods mainly with COI, showing that they are robust characters for identification at the species level. For species delimitation COI was more informative than ITS2. The diversity of Loxosceles species is still underestimated for North America, particularly in Mexico which holds the highest diversity of this genus worldwide.},
}
@article {pmid39645769,
year = {2024},
author = {Jia, J and Zhao, X and Skarżyński, D and Wu, R and Cheng, L and An, J},
title = {Morphological description and DNA barcoding of Ceratophysella gracilimucronata sp. nov. (Collembola: Hypogastruridae) from China, with a key to species of the C. armata group of the Sino-Japanese Region.},
journal = {Zootaxa},
volume = {5432},
number = {4},
pages = {555-566},
doi = {10.11646/zootaxa.5432.4.5},
pmid = {39645769},
issn = {1175-5334},
mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; *Arthropods/anatomy &amp; histology/classification/genetics ; Female ; Male ; Phylogeny ; Animal Distribution ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; },
abstract = {A new species, Ceratophysella gracilimucronata sp. nov. from Nan Ling Mountains (Guangdong Province, China), is described. It resembles C. ainu (Yosii, 1972), C. glancei Hammer, 1953 and C. falcifer Cassagnau, 1959 due to the B type chaeotataxy and short and slender mucro. Mitochondrial COI gene sequence of C. gracilimucronata sp. nov. is provided. A key to species of the C. armata group of the Sino-Japanese Region is given.},
}
@article {pmid39645686,
year = {2024},
author = {Oh, JI and Lee, JY and Kim, SY and Jeong, JH and Song, YG and Byun, BK},
title = {Discovery of Bucculatrix koreana sp. nov. and newly recorded Bucculatrix duanwuia (Lepidoptera: Bucculatricidae) in Korea.},
journal = {Zootaxa},
volume = {5538},
number = {5},
pages = {485-491},
doi = {10.11646/zootaxa.5538.5.9},
pmid = {39645686},
issn = {1175-5334},
mesh = {Animals ; Republic of Korea ; Male ; Female ; *Moths/anatomy &amp; histology/classification ; *Animal Distribution ; *Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; DNA Barcoding, Taxonomic ; },
abstract = {In this study, we describe a new species, Bucculatrix koreana sp. nov., and report B. duanwuia Liu, 2020, for the first time in Korea. Adults and genitalia of both species are illustrated. Additionally, we provide and discuss DNA barcode sequences for Bucculatrix species known from Korea.},
}
@article {pmid39645681,
year = {2024},
author = {Röll, B and Pinto, PV and Lobón-Rovira, J},
title = {A new species of African diurnal dwarf geckos (Gekkonidae: Lygodactylus) from the Lower Guinea rainforest.},
journal = {Zootaxa},
volume = {5538},
number = {6},
pages = {561-574},
doi = {10.11646/zootaxa.5538.6.3},
pmid = {39645681},
issn = {1175-5334},
mesh = {Animals ; *Lizards/classification/anatomy &amp; histology/genetics ; Female ; Male ; *Animal Distribution ; *Phylogeny ; Rainforest ; Body Size ; Ecosystem ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Guinea ; },
abstract = {The genus Lygodactylus Gray is a species-rich group of small, diurnal geckos distributed in Africa, Madagascar, and South America. The genus is divided into several species groups based on morphological characters, biogeographical affinities and/or phylogenetic investigations. To date, some of these groups still contain candidate species. One of these candidate species, provisionally designed as L. sp. B (a single female from Cameroon), had been placed phylogenetically within the East African Lygodactylus scheffleri-group. Furthermore, it shares typical scale characters with all members of this group. However, L. fischeri Boulenger, eponym and member of the West/Central African L. fischeri-group, also shares these scale characters with the L. scheffleri-group and with L. sp. B. While it could be ruled out that L. sp. B was conspecific with any member of the L. scheffleri-group, it could not be ruled out that L. sp. B represents a female of L. fischeri, as there is no female type material nor a clear description of a female of L. fischeri. Only when a male of this taxon was discovered in Cabinda (Angola) in a case of barcoding, the problem could be solved. We here describe the female L. sp. B from Cameroon and the male from Cabinda as new species Lygodactylus lobeke sp. nov. It is a small nondescript species without any bold color markings, such as dark blotches above the shoulder and on the flanks, which mark the male L. fischeri. The male and the female do not differ in coloration. In captivity, the female showed distinct 'mood dependent' colorations, including a 'pyjamas' coloration. For phylogenetic analysis, only sequences of L. laterimaculatus Pasteur, L. gravis Pasteur and L. lobeke sp. nov. were available. Lygodactylus lobeke sp. nov. was recovered as an independent clade which differs greatly in 16S uncorrected pairwise distance (>10%) from these two congeners. The new species is known from two localities in the Lower Guinea rainforests, with a linear distance of about 850 km. Despite this great distance, both specimens of L. lobeke sp. nov. are genetically surprisingly similar (3.5%). Presumably, the species has a wide distribution within the Lower Guinea region and a continuous gene flow within the population.},
}
@article {pmid39645676,
year = {2024},
author = {Wu, J and Liu, X},
title = {Systematics of the green lacewing tribe Ankylopterygini Navás, 1910 (Neuroptera: Chrysopidae: Chrysopinae) from China.},
journal = {Zootaxa},
volume = {5540},
number = {1},
pages = {1-169},
doi = {10.11646/zootaxa.5540.1.1},
pmid = {39645676},
issn = {1175-5334},
mesh = {China ; Animals ; Male ; Female ; *Animal Distribution ; Insecta/anatomy &amp; histology/classification ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; },
abstract = {A systematic revision of the taxonomy of the green lacewing tribe Ankylopterygini (Neuroptera: Chrysopidae: Chrysopinae) from China is present. Sixty-six species belonging to six genera are recorded and described. Keys to genera, subgenera and species are provided. A total of 201 COI barcodes (partial sequence of cytochrome c oxidase subunit I (COI)) from 49 species of the tribe are provided and used for molecular species delimitation. Nineta Navás, 1912 is treated as a subgenus of Tumeochrysa Needham, 1909. Two new generic synonyms are proposed: Tibetochrysa Yang, 1988, junior synonym of Retipenna Brooks, 1986; Sencera Navás, 1925, junior synonym of Ankylopteryx Brauer, 1864. Sixteen new species are described: Ankylopteryx hainanensis sp. nov., A. montipunctata sp. nov., A. stena sp. nov., Chrysopidia arcta sp. nov., C. macrosterna sp. nov., C. abdominata sp. nov., Tumeochrysa acuta sp. nov., T. breva sp. nov., T. biloba sp. nov., T. minina sp. nov., T. yangi sp. nov., Retipenna interrupta sp. nov., R. triphlebia sp. nov., Semachrysa pura sp. nov., Se. triloba sp. nov. and Signochrysa jianfenglingensis sp. nov. Twelve specific synonyms are proposed: Ankylopteryx yangi Ma, Yang &amp; Liu, 2020, junior synonym of Ankylopteryx octopunctata candida (Fabricius, 1798), Chrysopidia yangi Yang &amp; Lin, 1977, junior synonym of Chrysopidia junbesiana Hölzel, 1973; Chrysopidia fuscata Navás, 1914 and Chrysopidia tjederi Ma, 2022, junior synonyms of Chrysopidia regulata Navás, 1914; Tumeochrysa hui Yang, 1987, junior synonym of Tumeochrysa praeclara Hölzel, 1973; Tumeochrysa nyingchiana Yang, 1987, junior synonym of Tumeochrysa yunica Yang, 1986; Retipenna inordinata, Yang, 1997, junior synonym of Retipenna dasyphlebia (McLachlan, 1894); Retipenna chione (Banks, 1942 [1940]), junior synonym of Retipenna grahami (Banks, 1942 [1940]); Retipenna chaoi Yang &amp; Yang, 1987, Retipenna guangdongana Yang &amp; Yang, 1987 and Retipenna huai Yang &amp; Yang, 1987, junior synonyms of Retipenna burmana Brooks, 1986; and Signochrysa hainanus (Yang &amp; Yang, 1991), junior synonym of Signochrysa ornatissima (Nakahara, 1955). Eight new combinations are proposed: Retipenna phanera (Yang, 1987) comb. nov., R. sinica (Yang, 1988) comb. nov., Tumeochrysa abunda (Yang &amp; Yang, 1989) comb. nov., T. dolichoptera (Navás, 1910) comb. nov., T. grandis (Navás, 1915) comb. nov., T. inpunctata (Reuter, 1894) comb. nov., T. shaanxiensis (Yang &amp; Yang, 1989) comb. nov. and T. vittata (Wesmael, 1841) comb. nov. Ten species are newly recorded from China: Chrysopidia junbesiana Hölzel, 1973, C. nigrata Navás, 1910, C. ciliata (Wesmael, 1841), C. orientalis (Hölzel, 1973), Tumeochrysa inpunctata (Reuter, 1894), T. praeclara Hölzel, 1973, T. magnifica Hölzel, 1973, Retipenna burmana Brooks, 1986, R. variegata Brooks, 1986, and Semachrysa contorta Brooks, 1983. One species is transferred from Ankylopterygini to Chrysopini: Chrysopa yananica (Yang &amp; Yang, 1989) comb. nov.},
}
@article {pmid39645675,
year = {2024},
author = {Kasparek, M},
title = {New species, new synonyms, and resurrected taxa: A review of West and Central Palaearctic members of the genus Pseudoanthidium (Apoidea: Megachilidae).},
journal = {Zootaxa},
volume = {5541},
number = {1},
pages = {1-50},
doi = {10.11646/zootaxa.5541.1.1},
pmid = {39645675},
issn = {1175-5334},
mesh = {*Bees/anatomy &amp; histology/classification/genetics ; *Terminology as Topic ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Genes, Insect/genetics ; DNA, Mitochondrial/genetics ; Male ; Female ; Animals ; Animal Distribution ; },
abstract = {Wool carder bees of the genus Pseudoanthidium comprise approximately 60-65 species, which are found in the Palaearctic, Indo-Malayan and Afrotropical realms. Their taxonomic relationships are little understood. Herein, I revised West and Central Palaearctic members of the genus. Four species are described as new, namely P. farsiense sp. nov. from Iran, P. microrubrum sp. nov. from Morocco, P. syriacum sp. nov. from Syria, and P. tajikistanicum sp. nov. from Tajikistan. The largely overlooked species Anthidium fulviventre Friese, 1917, described from Russia, and Anthidium ivanovi Mavromoustakis, 1954, described from Tajikistan, are recognized as members of the Pseudoanthidium genus, as P. fulviventre (Friese, 1917) comb. nov. and P. ivanovi (Mavromoustakis, 1954) stat. resurrect. &amp; comb. nov. Anthidium moricei Friese, 1911, from Jordan, and A. royoi Dusmet, 1915, from Morocco, are resurrected from synonymy with P. melanurum and suggested to be treated as P. moricei (Friese, 1911) stat. resurrect. and P. royoi (Dusmet, 1915) stat. resurrect. &amp; comb. nov. The hitherto unknown males of P. moricei (Friese, 1911) and P. rubellulum Pasteels, 1969 are described based on material from Jordan and Israel, respectively. Royanthidium bicoloripenne Pasteels, 1981 (syn. nov.) from Morocco, is revealed to be a junior synonym of P. octodentatum (Pérez, 1895). Morphological traits, along with DNA sequences of the mitochondrial COI gene ("barcoding gene"), allowed clustering the species in five polytypic and five monotypic species groups. As key character traits of the type species of nominate Pseudoanthidium largely fit the subgeneric characters of the subgenus Royanthidium Pasteels, 1969, Royanthidium is regarded as a junior synonym (syn. nov.) of nominate Pseudoanthidium. The species of the subgenus Exanthidium Pasteels, 1969 form a uniform clade both in terms of morphology and DNA marker. An examination of the non-Palaearctic Pseudoanthidium species is suggested to determine whether Exanthidium deserves subgenus status.},
}
@article {pmid39645672,
year = {2024},
author = {Wang, S and Jiang, J and Wei, C},
title = {A review of the cicada genus Mata Distant, 1906 (Hemiptera: Cicadidae) with description of one new species from China.},
journal = {Zootaxa},
volume = {5541},
number = {1},
pages = {73-83},
doi = {10.11646/zootaxa.5541.1.4},
pmid = {39645672},
issn = {1175-5334},
mesh = {Animals ; *Hemiptera/anatomy &amp; histology/classification/genetics ; China ; Male ; Female ; *Phylogeny ; *Animal Distribution ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; },
abstract = {The cicada genus Mata Distant, 1906 was reviewed based on the description of one new species, Mata uncinulata sp. nov., from China. Mata kama (Distant, 1881) and Mata meghalayana Sarkar, Mahapatra, Mohapatra, Nair &amp; Kunte, 2021 are reported for the first time in China. Morphological phylogenetic analysis reveals the relationships among related species of Mata. Partial mitochondrial COI gene (DNA barcoding) of M. uncinulata sp. nov. and M. kama rec. nov. are sequenced and uploaded to GenBank. A key to species of Mata is provided.},
}
@article {pmid39644641,
year = {2025},
author = {Leidenberger, S and Wiese, V and Schaumann, F and Pleiss, F and Langen, K and Bourlat, SJ},
title = {Freshwater mollusc community screening - Classical and eDNA monitoring methods to detect rare, indicator and invasive species.},
journal = {The Science of the total environment},
volume = {958},
number = {},
pages = {177763},
doi = {10.1016/j.scitotenv.2024.177763},
pmid = {39644641},
issn = {1879-1026},
mesh = {Animals ; Sweden ; *Environmental Monitoring/methods ; *Introduced Species ; Mollusca ; Fresh Water ; DNA Barcoding, Taxonomic/methods ; Ecosystem ; Biodiversity ; },
abstract = {Freshwater habitats and their quality have always been of utmost importance for human subsistence. Water quality assessment is an important tool, covering biological, chemical and hydromorphological aspects. Bioindicators such as the bivalves can be used as evidence for good water quality, but widespread groups such as species of the family Sphaeriidae Deshayes,1855 (1822) and genus Pisidium/Euglesa/Odhneripidisium also known as 'pea clams' are poorly known and lack taxonomic expertise. The situation is similar for many other benthic macroinvertebrate species used in biomonitoring. In this study, we tested if pea clams can be detected using eDNA metabarcoding methods applied to sediment and plankton samples from 15 lakes and rivers in Sweden. Additionally, we detected benthic macroinvertebrates, so-called indicator species used in freshwater monitoring, as well as rare or red-listed and invasive species. We created a COI reference barcode library of 22 species of Swedish freshwater molluscs, of which one species is new, and five species have less than five records on NCBI and BOLD. From 272 sediment and plankton samples, we detected 497 benthic macroinvertebrate indicator species, 20 mollusc species and 3 invasive species in 15 freshwater environments in Sweden using eDNA metabarcoding. We show that one of the sediment sampling methods (M42) can detect slightly more species in autumn compared to the plankton or sediment kick-net methods, or to collecting samples in spring. A clear advantage is that biological water quality indices formerly calculated using taxa identified to the family level can now be calculated using the species level, giving higher precision. We suggest that future freshwater monitoring efforts can be greatly improved and sped up through large-scale and strategic habitat screening using barcoding and metabarcoding methods to support decision-making and help fulfill the goals of the UN 2030 Agenda.},
}
@article {pmid39642167,
year = {2025},
author = {Buri, MC and Shoeb, MR and Bykov, A and Repiscak, P and Baik, H and Dupanovic, A and David, FO and Kovacic, B and Hall-Glenn, F and Dopa, S and Urbanus, J and Sippl, L and Stofner, S and Emminger, D and Cosgrove, J and Schinnerl, D and Poetsch, AR and Lehner, M and Koenig, X and Perié, L and Schumacher, TN and Gotthardt, D and Halbritter, F and Putz, EM},
title = {Natural Killer Cell-Mediated Cytotoxicity Shapes the Clonal Evolution of B-cell Leukemia.},
journal = {Cancer immunology research},
volume = {13},
number = {3},
pages = {430-446},
pmid = {39642167},
issn = {2326-6074},
support = {I 4649/FWF_/Austrian Science Fund FWF/Austria ; TAI 454/FWF_/Austrian Science Fund FWF/Austria ; P 32001/FWF_/Austrian Science Fund FWF/Austria ; TAI 732/FWF_/Austrian Science Fund FWF/Austria ; P 31563/FWF_/Austrian Science Fund FWF/Austria ; P 34832/FWF_/Austrian Science Fund FWF/Austria ; WKP 132/FWF_/Austrian Science Fund FWF/Austria ; 10.55776/P32001//Austrian Science Fund (FWF)/ ; 10.55776/TAI454//Austrian Science Fund (FWF)/ ; 10.55776/P31563//Austrian Science Fund (FWF)/ ; 20-17258//Alex's Lemonade Stand Foundation for Childhood Cancer (ALSF)/ ; #25905//&#xd6;sterreichischen Akademie der Wissenschaften (&#xd6;AW)/ ; //Fellinger Krebsforschung/ ; //St. Anna Kinderkrebsforschung/ ; //Dr. Mildred Scheel Stiftung f&#xfc;r Krebsforschung/ ; },
mesh = {*Killer Cells, Natural/immunology/metabolism ; Animals ; Mice ; *Clonal Evolution/immunology/genetics ; Humans ; *Cytotoxicity, Immunologic ; Leukemia, B-Cell/immunology/genetics/pathology ; Cell Line, Tumor ; Interferon-gamma/metabolism ; Tumor Escape/immunology ; },
abstract = {The term cancer immunoediting describes the dual role by which the immune system can suppress and promote tumor growth and is divided into three phases: elimination, equilibrium, and escape. The role of NK cells has mainly been attributed to the elimination phase. Here, we show that NK cells play a role in all three phases of cancer immunoediting. Extended co-culturing of DNA-barcoded mouse BCR/ABLp185+ B-cell acute lymphoblastic leukemia (B-ALL) cells with NK cells allowed for a quantitative measure of NK cell-mediated immunoediting. Although most tumor cell clones were efficiently eliminated by NK cells, a certain fraction of tumor cells harbored an intrinsic primary resistance. Furthermore, DNA barcoding revealed tumor cell clones with secondary resistance, which stochastically acquired resistance to NK cells. NK cell-mediated cytotoxicity put a selective pressure on B-ALL cells, which led to an outgrowth of primary and secondary resistant tumor cell clones, which were characterized by an IFNγ signature. Besides well-known regulators of immune evasion, our analysis of NK cell-resistant tumor cells revealed the upregulation of genes, including lymphocyte antigen 6 complex, locus A (Ly6a), which we found to promote leukemic cell resistance to NK cells. Translation of our findings to the human system showed that high expression of LY6E on tumor cells impaired their physical interaction with NK cells and led to worse prognosis in patients with leukemia. Our results demonstrate that tumor cells are actively edited by NK cells during the equilibrium phase and use different avenues to escape NK cell-mediated eradication.},
}
@article {pmid39641628,
year = {2024},
author = {Hossain, A and Cetnar, DP and LaFleur, TL and McLellan, JR and Salis, HM},
title = {Automated Design of Oligopools and Rapid Analysis of Massively Parallel Barcoded Measurements.},
journal = {ACS synthetic biology},
volume = {13},
number = {12},
pages = {4218-4232},
pmid = {39641628},
issn = {2161-5063},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Algorithms ; Oligonucleotides/genetics ; Software ; Gene Library ; Sequence Analysis, DNA/methods ; },
abstract = {Oligopool synthesis and next-generation sequencing enable the construction and characterization of large libraries of designed genetic parts and systems. As library sizes grow, it becomes computationally challenging to optimally design large numbers of primer binding sites, barcode sequences, and overlap regions to obtain efficient assemblies and precise measurements. We present the Oligopool Calculator, an end-to-end suite of algorithms and data structures that rapidly designs many thousands of oligonucleotides within an oligopool and rapidly analyzes many billions of barcoded sequencing reads. We introduce several novel concepts that greatly increase the design and analysis throughput, including orthogonally symmetric barcode design, adaptive decision trees for primer design, a Scry barcode classifier, and efficient read packing. We demonstrate the Oligopool Calculator's capabilities across computational benchmarks and real-data projects, including the design of over four million highly unique and compact barcodes in 1.2 h, the design of universal primer binding sites for one million 200-mer oligos in 15 min, and the analysis of about 500 million deep sequencing reads per hour, all on an 8-core desktop computer. Overall, the Oligopool Calculator accelerates the creative use of massively parallel experiments by eliminating the computational complexity of their design and analysis.},
}
@article {pmid39641617,
year = {2024},
author = {Jiang, H and Qian, C and Deng, Y and Lv, X and Liu, Y and Li, A and Li, X},
title = {Novel Multimode Assay Based on Asymmetrically Competitive CRISPR and Raman Barcode Spectra for Multiple Hepatocellular Carcinoma Biomarkers Detection.},
journal = {Analytical chemistry},
volume = {96},
number = {50},
pages = {20004-20014},
doi = {10.1021/acs.analchem.4c04593},
pmid = {39641617},
issn = {1520-6882},
mesh = {*Spectrum Analysis, Raman/methods ; *Carcinoma, Hepatocellular/diagnosis/genetics ; Humans ; *Liver Neoplasms/diagnosis/genetics ; *Biomarkers, Tumor/genetics ; *MicroRNAs/analysis ; Gold/chemistry ; Metal Nanoparticles/chemistry ; CRISPR-Cas Systems/genetics ; },
abstract = {Commercial pregnancy test strips (PTS) possess the advantages of lower price, higher stability, and better repeatability and have been popularized to integrate with novel sensing strategies to detect other disease biomarkers, which accelerates the commercialization process of those novel sensing strategies. However, the current integration of novel sensing strategies into commercial PTS still faced the problems of insufficient quantification, low sensitivity, and lack of multiple detection capabilities. Hence, we proposed the concept of "visual classification recognition, spectral signal subdivision" for multiple hepatocellular carcinoma biomarkers (miRNA122 and miRNA233) detection with dual signals based on asymmetric competitive CRISPR (acCRISPR) and surface-enhanced Raman spectroscopy coupling with PTS, named the acCRISPR-PTS-SERS assay. In this assay, acCRISPR was used as a nonamplified cascaded signal amplification method to improve the sensitivity of detection. Two AuNPs-based core-shell Raman tags, each corresponding to different miRNA biomarkers, were used to achieve both visual recognition and spectral segmentation to enhance the quantification of PTS detection and the capability for multiple detection. Under the optimal conditions, the LOD for miRNA122 and miRNA223 were 10.36 and 4.65 fM, respectively. The sensitivity was enhanced by nearly 2 orders of magnitude. In the future, simultaneous hand-held detection for fingerprint barcodes of different cancers can be achieved with the assistance of a microfluidic chip and smartphone.},
}
@article {pmid39640376,
year = {2024},
author = {Tabares-Medina, J and García-Blandón, K and García-Montoya, GM and Soto-Calderón, ID},
title = {Redefining infections with trypanosomatids in Neotropical primates: Case study of the white-footed tamarin (Oedipomidas leucopus).},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {25},
number = {},
pages = {101021},
pmid = {39640376},
issn = {2213-2244},
abstract = {Trypanosomes are blood parasites capable of infecting nearly any vertebrate. Many Neotropical primates frequently host trypanosomes and are considered potential reservoirs for Trypanosoma cruzi and other human-pathogenic trypanosomatids. However, diagnostic methods originally developed for detecting these trypanosomatids in humans and domestic species must be validated to reliably diagnose infections in non-human primates. Without such validation, taxonomic biases and incorrect assignments of wildlife reservoirs can occur. The white-footed tamarin (Oedipomidas leucopus), a primate endemic to northwestern Colombia, is classified by the World Health Organization as a reservoir of T. cruzi. However, this classification is based on studies with small sample sizes, ambiguous diagnostic methods, and questionable geographic records. In this study, the 18S ribosomal RNA gene was amplified via PCR and sequenced to estimate trypanosome infection rates and identify species in natural populations of O. leucopus across a wide geographic range, as well as in (ex situ) specimens. This molecular approach was also compared with traditional microscopy diagnosis using blood smears. The molecular diagnosis revealed that over 60% of the tested specimens were infected, whereas traditional microscopy resulted in 58% false negatives compared to the molecular method. A Bayesian phylogeny of the 18S gene identified T. minasense as the sole trypanosomatid species present in O. leucopus, with no detections of T. cruzi or other trypanosomatids of concern to human or domestic animal health. This study highlights the risk of overestimating the presence of human-infecting trypanosomes, such as T. cruzi, in tamarins and other vertebrates, and underscores the importance of validating diagnostic methods to accurately assess the zoonotic potential of wild species. Accurate identification of wildlife reservoirs is essential for understanding parasite life cycles and implementing effective management and conservation strategies for primates and other potential reservoirs.},
}
@article {pmid39638898,
year = {2024},
author = {Aggarwal, SD and Lokken-Toyli, KL and Weiser, JN},
title = {Pneumococcal pneumonia is driven by increased bacterial turnover due to bacteriocin-mediated intra-strain competition.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1628},
pmid = {39638898},
issn = {2399-3642},
support = {P30 CA016087/CA/NCI NIH HHS/United States ; R01 AI038446/AI/NIAID NIH HHS/United States ; R01 AI50893//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; },
mesh = {*Bacteriocins/metabolism/genetics ; *Streptococcus pneumoniae/genetics/metabolism ; Animals ; Mice ; *Pneumonia, Pneumococcal/microbiology/metabolism ; *Streptolysins/metabolism/genetics ; Bacterial Proteins/metabolism/genetics ; Lung/microbiology/metabolism/pathology ; Mice, Inbred C57BL ; Female ; Disease Models, Animal ; Quorum Sensing ; },
abstract = {Using chromosomal barcoding, we observed that >97% of the Streptococcus pneumoniae (Spn) population turns over in the lung within 2 days post-inoculation in a murine model. This marked collapse of diversity and bacterial turnover was associated with acute inflammation (severe pneumococcal pneumonia), high bacterial numbers in the lungs, bacteremia, and mortality. Intra-strain competition mediated by the blp locus, which expresses bacteriocins in a quorum-sensing-dependent manner, was required for each of these effects. Bacterial turnover from the activity of Blp-bacteriocins increased the release of the pneumococcal toxin, pneumolysin (Ply), which was sufficient to account for the lung pathology. The ability of Ply to evade complement, rather than its pore-forming activity, prevented opsonophagocytic clearance of Spn enabling its multiplication in the lung, facilitating the inflammatory response and subsequent invasion into the bloodstream. Thus, our study demonstrates how an appreciation for bacterial population dynamics during infection provides new insight into pathogenesis.},
}
@article {pmid39636545,
year = {2024},
author = {Dlauchy, D and Kachalkin, A and Glushakova, A and Buda, K and Fehér, C and Péter, G},
title = {Description of Wickerhamia europaea sp. nov. and revisitation of the ascospore number of W. fluorescens.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39636545},
issn = {1618-1905},
support = {075-15-2021-1396//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2021-1396//Ministry of Science and Higher Education of the Russian Federation/ ; TKP2021-EGA//Ministry of Culture and Innovation of Hungary from the National Research, Development and Innovation Fund/ ; TKP2021-EGA//Ministry of Culture and Innovation of Hungary from the National Research, Development and Innovation Fund/ ; },
abstract = {During the course of two independent studies, six conspecific yeast strains were recovered from flowers, soil, bird faeces and wood of different geographical origins. The six strains share identical DNA sequences in two barcoding regions, the D1/D2 domain of the LSU rRNA gene and the internal transcribed spacer (ITS) region (ITS1-5.8S rRNA gene-ITS2). According to sequence comparisons and phylogenetic analysis, they represent an undescribed Wickerhamia species. The novel species is not only genetically distinct from W. fluorescens, the single species of the genus but can also be distinguished from it by some phenotypic characters. We propose Wickerhamia europaea sp. nov. (holotype: NCAIM Y.01938; isotype: CBS 18675; MycoBank no.: 856571) to accommodate the above noted strains. Under certain fermentation conditions, we detected the production of phenyllactic acid, a potential broad-spectrum antimicrobial compound against food-borne pathogens, by the type strain of the novel species, although in smaller concentrations than in the case of W. fluorescens. Comparing our observations on the formation and properties of the ascospores of Wickerhamia europaea sp. nov. and the ambiguous data on the number of ascospores per ascus of W. fluorescens, we suggest a possible explanation to reconcile the different data regarding the number of ascospores per ascus formed by W. fluorescens.},
}
@article {pmid39636286,
year = {2024},
author = {Ayika, MG and Bansal, K and Chakrabarti, S and Gazis, R and Dhillon, B},
title = {Lasiodiplodia theobromae causes rachis blight on coconut palms (Cocos nucifera L.) in Florida.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-09-24-1925-PDN},
pmid = {39636286},
issn = {0191-2917},
abstract = {Lasiodiplodia, a genus in the family Botryosphaeriaceae, has a broad host range and causes dieback, root rot, fruit rot, leaf rot, and blights in many plant species across sub-tropical and tropical geographical areas (Alves et al., 2008). In palms, this fungal pathogen is known to cause fruit and heart rot, wood decay and leaf blight around the globe (Atallah et al., 2024; Santos et al., 2020). In field-grown coconut palms symptoms usually start on older fronds progressing to younger fronds. Symptoms including discoloration of internal tissue, profuse pathogen sporulation, fruiting body formation, and death of entire fronds, universally characterize rachis blight caused by Lasiodiplodia. In summer 2023, a disease incidence of 30% and severity ranging from 20% to 100% of the canopy was observed in Florida. Three diseased coconut palms were sampled from a five-acre plot and the symptomatic tissue (internal rachis discoloration) was excised at the margin of the advancing lesion, and surface sterilized (30s 75% EtOH, 1 min 3% sodium hypochlorite, 1 min rinse in sterile water). Six pieces were plated on one Potato Dextrose Agar (PDA, Difco) plate supplemented with three antibiotics, penicillin, streptomycin, and neomycin, each at 5mg/L (Gibco PSN), and a total of three PDA plates per sample were processed. Plates were incubated at 25°C under darkness and Lasiodiplodia-like colonies were consistently recovered from all 54 rachis pieces. Initially white in color, the fungal colony grew radially, turned gray, and eventually took on a darker shade, with an abundance of aerial mycelium and rare occurrence of conidiomata and conidia in older plates. Two morphologically similar isolates Las1A and Las1B were obtained from single spores and grown at 28°C in the dark for 7 days. DNA was extracted using the quick DNA extraction protocol (Liu et al., 2000) and regions from two fungal barcoding genes, nuclear ribosomal internal transcribed spacer (nrITS) and translation elongation factor 1-α (TEF1-α) were amplified using primers ITS1/ITS4 (White et al., 1990) and EF1-728F/EF1-986R (Carbone &amp; Kohn, 1999), respectively, and sequenced. The ITS (PQ282128 and PQ282129) and TEF1-α sequences from both isolates (PQ278132 and PQ278133) were 100% identical to Lasiodiplodia theobromae isolate G112-8 (OR453211 and OR482955, respectively). One-year-old seedlings of coconut palm (Cocos nucifera L.) were used for pathogenicity tests. Agar plugs from margins of actively growing cultures of Las1A and Las1B were placed on cut end of petioles from fronds close to the spear leaf and covered with parafilm. The control palms were treated with distilled water. The onset of disease symptoms was observed about 14 days post inoculation. The inoculated petioles were soft, listless, lost turgidity, and could be easily bent without snapping about 1 month following inoculation. In contrast, the palm control seedlings that were inoculated with water remained turgid, healthy and alive. Fruiting body development was observed on inoculated petioles, the pathogen was reisolated, and examination of its colony and spore morphology as well as presence of paraphyses was used to verify its identity. This is the first report of Lasiodiplodia theobromae causing disease on Cocos nucifera in Florida. This pathogen is a potential threat to coconut palm production in Florida and further research on pathogen diversity, pathogenicity, and distribution is needed to develop options for disease management.},
}
@article {pmid39633475,
year = {2024},
author = {Evasco, KL and Brockway, C and Falkingham, T and Hall, M and Wilson, NG and Potter, A},
title = {First detection of Culex tritaeniorhynchus in Western Australia using molecular diagnostics and morphological identification.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {500},
pmid = {39633475},
issn = {1756-3305},
mesh = {*Culex/virology/classification/genetics ; Animals ; Western Australia ; *Phylogeny ; *Mosquito Vectors/virology/classification/genetics ; Electron Transport Complex IV/genetics ; Female ; Encephalitis Virus, Japanese/genetics/isolation &amp; purification/classification ; Encephalitis, Japanese/virology/transmission/epidemiology ; },
abstract = {BACKGROUND: Culex tritaeniorhynchus has long been considered the primary vector of Japanese encephalitis virus (JEV), but until recently, it was considered exotic to Australia. When the species was detected in the country's Northern Territory (NT) for the first time, the Western Australia (WA) Department of Health was cognisant of the risk it posed to the State because of the shared border and continuous mosquito habitat adjoining the two jurisdictions. The aim of this study was to undertake intensive mosquito surveillance in the Kimberley region to ascertain whether Cx. tritaeniorhynchus was present in WA, define the extent of its distribution and undertake phylogenetic analysis of select specimens to support hypothesized routes of entry into the state.<br><br>METHODS: Carbon dioxide (CO2)-baited encephalitis virus surveillance (EVS) mosquito traps were deployed at various sites throughout the Kimberley region by surveillance officers within the Medical Entomology unit of the Western Australia (WA) Department of Health. Mosquitoes were then morphologically identified, and a subset of four specimens were confirmed as Cx. tritaeniorhynchus by molecular identification using Cytochrome Oxidase I (COI) DNA data and phylogenetic analysis.<br><br>RESULTS: From 31 March 2021 to 30 May 2024, a total of 211 female Cx. tritaeniorhynchus specimens were collected from 21 unique trap sites in the Kimberley's Shire of Wyndham-East Kimberley (SWEK). Four COI DNA barcode regions were amplified and successfully sequenced for analysis. These sequences fell within a clade recognised as Cx. tritaeniorhynchus and specifically all sequences were in a clade with other specimens from the NT and Timor-Leste.<br><br>CONCLUSIONS: This study represents the first detection of Cx. tritaeniorhynchus in WA. Given the widespread nature of trap sites that yielded the species and consecutive seasons over which it was observed, the authors surmise that Cx. tritaeniorhynchus is now established within the northeast Kimberley region. The findings are significant given the detection of the species coincides with the first significant outbreak of JEV activity on mainland Australia involving an estimated 45 human cases of Japanese encephalitis, 80 impacted commercial piggeries and widespread feral pig activity. Although the role that Cx. tritaeniorhynchus&#xa0;may play in JEV transmission into the future is not yet understood, it presents a potential risk to public health in the region.},
}
@article {pmid39632768,
year = {2024},
author = {Martínez-Sánchez, A and Szpila, K and Villet, MH and Ståhls, G and Thomas-Cabianca, A and Velásquez, Y and Parrott, JJ and Rojo, S},
title = {Morphology, biology and molecular characterisation of the endemic Canary Islands blowfly Calliphora splendens Macquart, 1838 (Diptera: Calliphoridae).},
journal = {Medical and veterinary entomology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mve.12777},
pmid = {39632768},
issn = {1365-2915},
support = {//Universidad de Alicante/ ; //Horizon 2020/ ; //Rhodes University/ ; },
abstract = {The Canary Islands are an excellent natural laboratory for understanding ecological and evolutionary processes such as biogeographical colonisation. The morphology of the larva, puparium and adult of the endemic Canarian copper fly, Calliphora splendens, is described, illustrated and contrasted with those of the other species of Calliphora that occur in Africa, the Iberian Peninsula and Macaronesia. Partial cytochrome oxidase I sequences show a connection between C. splendens, Calliphora vicina, Calliphora loewi and Calliphora croceipalpis, but more distant relationship with Calliphora vomitoria. Calliphora splendens produced unisexual offspring in captivity. This work confirms the relict character of the Canarian copper fly associated with the endemic laurel forest habitat.},
}
@article {pmid39629927,
year = {2025},
author = {Ma, W and Li, J and Qu, X and Sun, S and Zhou, Y and Liu, Y and Wang, P and Sha, Z},
title = {Liquid-Solid Triboelectric Nanogenerator-Based DNA Barcode Detection Biosensor for Species Identification.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {12},
number = {4},
pages = {e2408718},
pmid = {39629927},
issn = {2198-3844},
support = {2022LSL050102//Laoshan Laboratory/ ; No. 42276216//National Natural Science Foundation of China/ ; No. GuiKeAD24010036//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; SDCX-ZG-202400209//Shandong Postdoctoral Science Foundation/ ; },
mesh = {*Biosensing Techniques/methods/instrumentation ; *DNA Barcoding, Taxonomic/methods ; *Gold/chemistry ; Metal Nanoparticles/chemistry ; Animals ; DNA/genetics ; Equipment Design ; Nanotechnology/methods/instrumentation ; },
abstract = {DNA barcode detection method is widely applied for species identification, which is imperative to evaluate the effect of human economic activities on the biodiversity of ecosystem. However, the wide utilization of existing detection biosensors is limited by bulky and expensive instruments, such as Raman spectroscopy and electrochemical station. Herein, a liquid-solid triboelectric nanogenerator (TENG)-based DNA barcode detection biosensor is proposed, which consists of water flow, fluid channel, and PDMS film attached by specifically designed capture probe. Through sequentially combining capture probe, targeted DNA barcode, and signal probe with Au nanoparticles (NPs), the surface charge density of friction layer of TENG decreases under the effect of AuNPs, verified by the density functional theory (DFT) method. Consequently, the peak value of output current spike signal for targeted DNA is smaller than that for other DNA, which is the working mechanism of the present TENG-based biosensor. Such biosensor successfully recognizes Alvinocaris muricola among different types of Alvinocarididae shrimps, and its low limit detection can reach 1×10[-12] m. The present work provides a paradigm-shift way to develop an inexpensive and accurate technique to detect DNA barcode for species identification, and paves a novel way for the application of liquid-solid TENG.},
}
@article {pmid39628840,
year = {2024},
author = {Mukalel, AJ and Hamilton, AG and Billingsley, MM and Li, J and Thatte, AS and Han, X and Safford, HC and Padilla, MS and Papp, T and Parhiz, H and Weissman, D and Mitchell, MJ},
title = {Oxidized mRNA Lipid Nanoparticles for In Situ Chimeric Antigen Receptor Monocyte Engineering.},
journal = {Advanced functional materials},
volume = {34},
number = {27},
pages = {},
pmid = {39628840},
issn = {1616-301X},
support = {DP2 TR002776/TR/NCATS NIH HHS/United States ; },
abstract = {Chimeric antigen receptor (CAR) monocyte and macrophage therapies are promising solid tumor immunotherapies that can overcome the challenges facing conventional CAR T cell therapy. mRNA lipid nanoparticles (mRNA-LNPs) offer a viable platform for in situ engineering of CAR monocytes with transient and tunable CAR expression to reduce off-tumor toxicity and streamline cell manufacturing. However, identifying LNPs with monocyte tropism and intracellular delivery potency is difficult using traditional screening techniques. Here, ionizable lipid design and high-throughput in vivo screening are utilized to identify a new class of oxidized LNPs with innate tropism and mRNA delivery to monocytes. A library of oxidized (oLNPs) and unoxidized LNPs (uLNPs) is synthesized to evaluate mRNA delivery to immune cells. oLNPs demonstrate notable differences in morphology, ionization energy, and pKa, therefore enhancing delivery to human macrophages, but not T cells. Subsequently, in vivo library screening with DNA barcodes identifies an oLNP formulation, C14-O2, with innate tropism to monocytes. In a proof-of-concept study, the C14-O2 LNP is used to engineer functional CD19-CAR monocytes in situ for robust B cell aplasia (45%) in healthy mice. This work highlights the utility of oxidized LNPs as a promising platform for engineering CAR macrophages/monocytes for solid tumor CAR monocyte therapy.},
}
@article {pmid39626340,
year = {2025},
author = {Huang, Z and Wu, K and Ju, F and He, R and Tang, Y and Chen, Y and He, X and Zhang, J and Nie, L},
title = {Copper nanocluster based cascade amplified DNA electrochemical detection combining with bio-barcode assay and surface-initiated enzyme polymerization.},
journal = {Bioelectrochemistry (Amsterdam, Netherlands)},
volume = {163},
number = {},
pages = {108857},
doi = {10.1016/j.bioelechem.2024.108857},
pmid = {39626340},
issn = {1878-562X},
mesh = {*Copper/chemistry ; *Biosensing Techniques/methods ; Humans ; *Electrochemical Techniques/methods ; *Metal Nanoparticles/chemistry ; *Gold/chemistry ; *Polymerization ; Graphite/chemistry ; Limit of Detection ; DNA/chemistry ; Nucleic Acid Amplification Techniques/methods ; Stomach Neoplasms/diagnosis ; Silicon Dioxide/chemistry ; },
abstract = {Early cancer diagnosis is paramount for enhancing treatment efficacy, extending patient survival, and improving the quality of life. We developed a highly sensitive electrochemical biosensor for the detection of target DNA (tDNA) associated with gastric cancer. This advancement integrates dual signal amplification strategies: bio-barcode amplification (BCA) and surface-initiated enzyme polymerization (SIEP), with copper nanoclusters (CuNCs) serving as signal labels. Silica nanoparticles (SiO2) were covalently linked with polythymine (poly T) and complementary DNA to create bio-barcode probes. These probes, through hybridization, were immobilized on the reduced graphene oxide and Au nanoparticle (rGO-AuNPs) modified interface and marking the first amplification of the electrical signal. Subsequently, the extended poly T prompted by SIEP bound additional CuNCs through the combination of T-Cu[2+], leading to a second round of signal amplification. The biosensor demonstrated a minimum detection limit of 0.13 fmol/L over a linear response range from 1 fmol/L to 1 nmol/L. It also showcased excellent specificity, repeatability, and stability, making it a promising tool for the sensitive detection of gastric cancer biomarkers.},
}
@article {pmid39623507,
year = {2024},
author = {Chen, Y and Shentu, J and Lou, H and Xia, Y and Jiang, Y and Duan, S},
title = {Hematopoietic stem cell heterogeneity and age-related platelet bias: implications for bone marrow transplantation and blood disorders.},
journal = {Stem cell research &amp; therapy},
volume = {15},
number = {1},
pages = {459},
pmid = {39623507},
issn = {1757-6512},
support = {210000-581835//the Qiantang Scholars Fund in Hangzhou City University/ ; 20221JCGY010610//the Natural Science Foundation of Ningbo Municipality, Zhejiang Province/ ; },
mesh = {Animals ; Humans ; Aging ; Blood Platelets/metabolism ; *Bone Marrow Transplantation/methods ; Hematologic Diseases/therapy/pathology ; Hematopoietic Stem Cell Transplantation/methods ; *Hematopoietic Stem Cells/metabolism/cytology ; },
abstract = {Hematopoietic stem cells (HSCs) are critical for maintaining lifelong blood production and immune function, especially in the context of bone marrow transplantation, where their ability to reconstruct multiple blood lineages is essential. However, recent studies have revealed that certain HSCs exhibit a bias toward platelet differentiation, termed platelet-biased HSCs (P-HSCs). This lineage bias, particularly pronounced with aging, can lead to imbalances in post-transplant blood recovery, negatively affecting patient outcomes. Research by Claus Nerlov's team has provided key insights into the heterogeneity of HSCs, focusing on the age-related expansion of P-HSCs. Using advanced techniques such as single-cell RNA sequencing and molecular barcoding, their work highlights the evolutionary conservation of platelet bias in HSCs across species. This work delves into these findings, discussing their clinical implications for bone marrow transplantation, aging-related blood disorders, and potential therapeutic strategies. Moreover, we address limitations in current methodologies and propose future directions for research to optimize HSC-based therapies and improve clinical outcomes in hematological diseases.},
}
@article {pmid39622837,
year = {2024},
author = {Kuo, LY and Tang, SK and Huang, YH and Xie, PJ and Chen, CW and Chang, ZX and Hsu, TC and Chang, YH and Chao, YS and Chen, CW and Fawcett, S and Nitta, JH and Sundue, M and Kao, TT and Luu, HT and Mustapeng, AMA and Coritico, FP and Amoroso, VB and Thai, YK},
title = {A DNA barcode reference of Asian ferns with expert-identified voucher specimens and DNA samples.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1314},
pmid = {39622837},
issn = {2052-4463},
mesh = {*DNA Barcoding, Taxonomic ; *Ferns/genetics/classification ; *Biodiversity ; *Phylogeny ; DNA, Plant/genetics ; },
abstract = {Ferns belong to species-rich group of land plants, encompassing more than 11,000 extant species, and are crucial for reflecting terrestrial ecosystem changes. However, our understanding of their biodiversity hotspots, particularly in Southeast Asia, remains limited due to scarce genetic data. Despite harboring around one-third of the world's fern species, less than 6% of Southeast Asian ferns have been DNA-sequenced. In this study, we addressed this gap by sequencing 1,496 voucher-referenced and expert-identified fern samples from (sub)tropical Asia, spanning Malaysia, the Philippines, Taiwan, and Vietnam, to retrieve their rbcL and trnL-F sequences. This DNA barcode collection of Asian ferns encompasses 956 species across 152 genera and 34 families, filling major gaps in fern biodiversity understanding and advancing research in systematics, phylogenetics, ecology and conservation. This dataset significantly expands the Fern Tree of Life to over 6,000 species, serving as a pivotal and global reference for worldwide barcoding identification of ferns.},
}
@article {pmid39621694,
year = {2024},
author = {Mata-Somarribas, C and Cardoso das Graças, G and de Oliveira R Pereira, L and Côrtes Boité, M and Motta Cantanhêde, L and Braga Filgueira, CP and Fallas, A and Quirós-Rojas, L and Morelli, KA and Ferreira, GEM and Cupolillo, E},
title = {Applying a cytochrome c oxidase I barcode for Leishmania species typing.},
journal = {PloS one},
volume = {19},
number = {12},
pages = {e0309277},
pmid = {39621694},
issn = {1932-6203},
mesh = {*Electron Transport Complex IV/genetics ; *Leishmania/genetics/enzymology/classification ; *DNA Barcoding, Taxonomic/methods ; *Phylogeny ; Species Specificity ; },
abstract = {Species delimitation has always been a challenge for taxonomists and for Leishmania studies there is no exception. Herein we attempt to display the usefulness of the mitochondrial gene Cytochrome Oxidase I-coI in classical and barcode-based approaches for Leishmania characterization. A total of 228 samples were analyzed, comprising 28 Leishmania related taxa, mainly from cultures of the Oswaldo Cruz Foundation`s Leishmania Collection. Primers were designed for amplification of coI; sequences were analyzed by distance-based indicators and both the Neighbor Joining and NeighborNet as species grouping techniques. Automatic Barcode Gap Discovery was applied to define species delimitation while for the character-based analysis a software for Barcoding with Logic formulas was employed. Final sequences of 486 bp with 238 parsimonious sites were aligned and edited. Robust groups were formed for most of the genus species, distinctive nucleotide positions in the barcode sequence were observed for 11 of them. A good agreement between the techniques applied and the original characterization was observed. Few species were not distinguished by coI: (i) L. (V.) peruviana, L. (V.) lindenbergi, and L. (V.) utingensis; (ii) L. (L.) venezuelensis and (iii) L. colombiensis and L. equatorensis with identical sequences. Some of these taxa have been, at one time or another, classified as controversial and, for most of them, a higher number of isolates should be studied to properly infer their taxonomic status. CoI represents a mitochondrial target that stands out as a taxonomically important asset with multiple advantages over other genes. This paper corresponds to the first report of coI analysis in Leishmania, a potentially advantageous target for the characterization of this parasite.},
}
@article {pmid39619925,
year = {2024},
author = {Santanumurti, MB and Nugraha, MAR and Dewi, NR and Awaluddin, M and Tang, PW and Pardede, HI and Solami, LA and Sulmartiwi, L and El-Regal, MAA},
title = {Fish diversity assessment through conventional morphological identification and recent advances in Saudi Arabia: A review.},
journal = {Veterinary world},
volume = {17},
number = {10},
pages = {2267-2285},
pmid = {39619925},
issn = {0972-8988},
abstract = {Fish identification in the Red Sea, particularly in Saudi Arabia, has a long history. Because of the vast fish diversity in Saudi Arabia, proper species identification is required. Indeed, identifying fish species is critical for biodiversity conservation, food and drug safety, and sustainable fishery management. Numerous approaches have been used to identify fish species, including conventional morphological identification, next-generation sequencing (NGS), nanopore sequencing, DNA barcoding, and environmental DNA analysis. In this review, we collected as much scientific information as possible on species identification in Saudi Arabia. Our findings suggest that the identification process has advanced and spread rapidly and broadly, as evidenced by the discovery of new fish species in Saudi Arabia. The advantages and disadvantages of each method were discussed as part of a comprehensive comparison. This study aimed to provide further scientific knowledge to promote the growth of fish diversity worldwide.},
}
@article {pmid39619666,
year = {2024},
author = {Réblová, M and Nekvindová, J and Kolařík, M and Jurjević, &#x17d; and Kolář, M and Hubka, V},
title = {Re-evaluation of Ceratostomella and Xylomelasma with introduction of two new species (Sordariomycetes).},
journal = {MycoKeys},
volume = {110},
number = {},
pages = {319-360},
pmid = {39619666},
issn = {1314-4049},
abstract = {In this study, we assessed the phylogenetic relationships among members of Ceratostomella and the morphologically similar genus Xylomelasma, currently classified within the Sordariomycetes. Our phylogenetic analyses, utilising three and five gene markers, revealed that species from these two genera are congeneric, supporting the transfer of Xylomelasma to Ceratostomella. Consequently, we propose two new combinations: C.sordida comb. nov. and C.novae-zelandiae comb. nov. In addition, we identified two cryptic species within the C.sordida species complex, which are described as C.crypta sp. nov. and C.melanospora sp. nov. Traditional micromorphological characters have proven insufficient for differentiating these new species; however, they are clearly distinguishable by molecular data, particularly using the internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) of the nuclear rRNA cistron, and genes encoding the second largest subunit of RNA polymerase II (rpb2), and translation elongation factor 1-α (tef1-α) as primary and secondary barcodes. This study provides new insights into the morphological characteristics of Ceratostomella, identifying the ascogenous system as an important diagnostic trait at the generic level, which distinguishes Ceratostomella from morphologically similar fungi. Ceratostomella is currently recognised with eight species. We also investigated the relationship between Ceratostomella and the closely related Barbatosphaeria. The lack of statistical support in the Maximum likelihood analysis is discussed and the inclusion of Ceratostomella in Barbatosphaeriaceae is not supported. Ceratostomella is accepted as a genus incertae sedis, while Barbatosphaeriaceae remains a monotypic family. The global diversity of Ceratostomella is inferred from metabarcoding data and published field observations. Biogeographic analysis indicates that members of Ceratostomella are widespread, found in soil and decaying wood, as well as in air, dust, roots, shoots, and water across temperate, subtropical and tropical regions in both the Northern and Southern Hemispheres. We are concurrently publishing whole-genome analyses of three ex-type strains of Ceratostomella, i.e. C.crypta, C.melanospora and C.sordida. This effort aims to establish a new standard for high-quality taxonomic studies, which, in accordance with current trends, should incorporate whole-genome sequencing data for future research and application. Our findings underscore the importance of integrating morphological, biogeographic and molecular data for accurate species delineation and highlight the complexity within the genus Ceratostomella.},
}
@article {pmid39619289,
year = {2024},
author = {Iqbal, Z and Azad, R and Jin, X and Hassan, MA and Abbas, M and Nasir, MF and Bodlah, I and Ali, M and Szawaryn, K and Nie, RE},
title = {The review of the genus Coccinella (Coleoptera, Coccinellidae) from Pakistan.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e137417},
pmid = {39619289},
issn = {1314-2828},
abstract = {BACKGROUND: The genus Coccinella is reviewed with seven species found in Pakistan: C.luteopicta (Mulsant, 1866), C.marussii Kapur, 1973, C.iranica Dobzhansky, 1926, C.transversalis Fabricius, 1781, C.septempunctata Linnaeus, 1758, C.transversoguttatatransversoguttata Faldermann, 1835 and C.undecimpunctata Linnaeus, 1758. Information on prey, host plants, distribution and an identification key for Coccinella species in Pakistan is provided. Additionally, newly-sequenced partial COI (cytochrome-c-oxidase subunit I) for C.luteopicta and C.marussii were used to determine their phylogenetic positions within the genus Coccinella.<br><br>NEW INFORMATION: This study comprehensively reviews the genus Coccinella in Pakistan and highlights Coccinellaluteopicta as a new country record. Morphological features of adults, including male genital characters and an identification key to known species in Pakistan are presented. Records of prey, host plants and distributions for all identified species are included. The new data (COI-barcode) shows that C.luteopicta (Mulsant, 1866) was recorded first in Pakistan.},
}
@article {pmid39619181,
year = {2024},
author = {McCartin, L and Saso, E and Vohsen, SA and Pittoors, N and Demetriades, P and McFadden, CS and Quattrini, AM and Herrera, S},
title = {Nuclear eDNA metabarcoding primers for anthozoan coral biodiversity assessment.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e18607},
pmid = {39619181},
issn = {2167-8359},
mesh = {*Anthozoa/genetics/classification ; Animals ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *DNA, Environmental/genetics ; DNA Primers/genetics ; Gulf of Mexico ; RNA, Ribosomal, 28S/genetics ; Polymerase Chain Reaction/methods ; Coral Reefs ; },
abstract = {The distributions of anthozoan corals are undercharacterized due to their wide bathymetric ranges, occurrences in remote locales, and difficulties of identification from morphology alone. Environmental DNA (eDNA) sequencing promises to be a noninvasive strategy to complement conventional approaches for mapping and monitoring the distribution and biodiversity of coral communities. Primers for eDNA metabarcoding have been designed to amplify nuclear and mitochondrial DNA barcodes in shallow scleractinians and mitochondrial MutS in deep-sea octocorals. However, a comprehensive method for eDNA metabarcoding of all anthozoan corals, including black corals, has not been developed. We leveraged a sequence database of global coral collections, from shallow water to the deep sea, to design new PCR primers for coral eDNA sequencing that target the 28S rRNA gene (28S rDNA). We tested the performance of these primers by amplifying and sequencing eDNA from water samples collected in the Gulf of Mexico near mesophotic and deep-sea corals that were also imaged, sampled, and sequenced. Sequencing libraries produced using the primers were highly enriched in eDNA from octocorals, black corals and scleractinians, with up to 99.9% of the reads originating from these corals. Further, the 28S barcode amplified using the primers distinguished coral genera and species in many cases, like previously developed methods that target eDNA in only octocorals or scleractinians. We recovered amplicon sequencing variants (ASVs) identical to DNA barcodes derived from Sanger sequencing and genome skimming of corals sampled at the same field sites. This new eDNA metabarcoding strategy permits targeted eDNA sequencing of black corals, octocorals, and scleractinians at sites where they co-occur and expands our current toolkit for mapping and monitoring coral communities in shallow coral reefs and the deep sea.},
}
@article {pmid39616387,
year = {2024},
author = {Huang, G and Peng, X},
title = {Genus Bithynia: morphological classification to molecular identification.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {496},
pmid = {39616387},
issn = {1756-3305},
support = {82060376//National Natural Science Foundation of China/ ; No.2024GXNSFAA010039//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; },
mesh = {Animals ; *Snails/parasitology ; Trematode Infections/parasitology/veterinary ; Phylogeny ; Humans ; },
abstract = {Snails of the genus Bithynia, whose primary habitat is slow-flowing ponds and ditches, serve as the first intermediate hosts of liver fluke. Currently, approximately 200 million individuals worldwide are at risk of liver fluke infection, yet questions still persist regarding the taxonomic identification of Bithynia genus, a crucial player in the transmission of this disease. Accurate taxonomic classification of the Bithynia genus could significantly enhance current understanding of the disease's transmission mechanisms. In this article we comprehensively review the extensive research conducted on Bithynia genus, spanning past inquiries up to the latest findings. The primary emphasis is placed on exploring the taxonomic identification of this genus within various technological settings. We then present a consolidated analysis of the morphological taxonomic identification methods, highlighting their strengths and limitations. We also introduce a novel perspective on the future direction of identification and classification efforts for the members of this genus, emphasizing the crucial role Bithynia plays in the epidemiological cycle of liver fluke transmission. We conclude by urging researchers to prioritize the significance of the members of this genus in the epidemiological cycle of liver fluke transmission and in control measures for disease dissemination, within the context of the vector organisms.},
}
@article {pmid39615483,
year = {2024},
author = {Michaels, YS and Major, MC and Bonham-Carter, B and Zhang, J and Heydari, T and Edgar, JM and Siu, MM and Greenstreet, L and Vilarrasa-Blasi, R and Kim, S and Castle, EL and Forrow, A and Ibanez-Rios, MI and Zimmerman, C and Chung, Y and Stach, T and Werschler, N and Knapp, DJHF and Vento-Tormo, R and Schiebinger, G and Zandstra, PW},
title = {Tracking the gene expression programs and clonal relationships that underlie mast, myeloid, and T lineage specification from stem cells.},
journal = {Cell systems},
volume = {15},
number = {12},
pages = {1245-1263.e10},
doi = {10.1016/j.cels.2024.11.001},
pmid = {39615483},
issn = {2405-4720},
mesh = {Humans ; *Cell Lineage/genetics ; *Cell Differentiation/genetics ; *T-Lymphocytes/cytology/metabolism ; Myeloid Cells/metabolism ; Mast Cells/metabolism ; Gene Regulatory Networks/genetics ; Hematopoietic Stem Cells/metabolism/cytology ; Hematopoiesis/genetics ; },
abstract = {T cells develop from hematopoietic progenitors in the thymus and protect against pathogens and cancer. However, the emergence of human T cell-competent blood progenitors and their subsequent specification to the T lineage have been challenging to capture in real time. Here, we leveraged a pluripotent stem cell differentiation system to understand the transcriptional dynamics and cell fate restriction events that underlie this critical developmental process. Time-resolved single-cell RNA sequencing revealed that downregulation of the multipotent hematopoietic program, upregulation of >90 lineage-associated transcription factors, and cell-cycle exit all occur within a highly coordinated developmental window. Gene-regulatory network inference uncovered a role for YBX1 in T lineage specification. We mapped the differentiation cell fate hierarchy using transcribed lineage barcoding and discovered that mast and myeloid potential bifurcate from each other early in hematopoiesis, upstream of T lineage restriction. Our systems-level analyses provide a quantitative, time-resolved model of human T cell fate specification. A record of this paper's transparent peer review process is included in the supplemental information.},
}
@article {pmid39613881,
year = {2024},
author = {Ghauri, MSZ and Soomro, S and Novianto, D and Arnuphapprasert, A and Kaewthamasorn, M},
title = {Molecular detection and genetic characterization of hemotropic mycoplasmas in goats and fleas from Thailand.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {29702},
pmid = {39613881},
issn = {2045-2322},
mesh = {Animals ; *Goats/microbiology ; Thailand/epidemiology ; *Mycoplasma/genetics/isolation &amp; purification ; *Siphonaptera/microbiology ; Goat Diseases/microbiology/epidemiology ; Mycoplasma Infections/veterinary/epidemiology/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; },
abstract = {Arthropod vectors play a crucial role in the transmission of hemotropic mycoplasmas, small bacteria that infect red blood cells in a wide range of animals and humans globally, leading to intravascular infections. Traditional Giemsa-stained thin blood smears, used for diagnosing hemotropic mycoplasmas through microscopic examination, have low sensitivity and are effective only when bacteremia levels are high. This study aimed to employ molecular methods to detect and genetically characterize hemotropic mycoplasmas in goats as well as investigate the potential role of fleas as vectors. Blood and flea samples were collected concurrently from goats on 16 farms across seven provinces in Thailand from January 2017 to October 2023. The 16 S rRNA, 23 S rRNA, and rnpB genes of hemoplasmas were amplified and sequenced. All fleas were identified morphologically and molecularly through DNA barcoding of the cytochrome oxidase I gene. A total of 78 out of 500 goats (15.6%), three pooled flea samples (3/6, 50%), and one individual flea (1/49, 2.04%) tested positive for hemoplasmas and all fleas were identified as Ctenocephalides orientis. BLASTN searches utilizing the three genetic markers revealed that the hemoplasmas detected in this study showed 97.81-100% similarity to Mycoplasma ovis and Candidatus Mycoplasma haemovis, which have been previously reported in sheep, goats, and humans, suggesting their zoonotic potential. The sequences were grouped into 28 unique nucleotide sequence types (ntSTs) based on minor variations in the 16 S rRNA gene. Hemotropic mycoplasma infection was significantly associated with farm locations and seasonality of sample collection (p < 0.0001), indicating that farm management practices or environmental conditions may play a critical role in the epidemiology of these infections. This study represents the first report of hemotropic mycoplasmas in goats in Thailand, confirms their presence in fleas, and provides valuable insights for farm management, such as guiding the rational use of insecticides and antibiotics.},
}
@article {pmid39610807,
year = {2024},
author = {Wang, C and Gan, J and Mi, X},
title = {On two species of Phintella Strand, 1906 from Hainan, China (Araneae, Salticidae).},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e138400},
pmid = {39610807},
issn = {1314-2828},
abstract = {BACKGROUND: In our recent examination of the Phintella specimens collected from Hainan Tropical Rainforest National Park, a new species and the unknown female of P.liae Wang, Mi &amp; Peng, 2023 were recognised, based on the morphological characteristics and molecular evidence.<br><br>NEW INFORMATION: A new species of Phintella Strand, 1906 is described: P.hongkan sp. nov. (&#x2642;&#x2640;) from Hainan, China. The unknown female of P.liae Wang, Mi &amp; Peng, 2023 is also described for the first time. Diagnostic photos of both species are provided.},
}
@article {pmid39609739,
year = {2024},
author = {Li, JW and Li, RY and Chen, YM and Wu, YH and Zou, LH and Tang, SL and Zhai, JW},
title = {Comprehensive characterization and phylogenetic analysis of the complete plastomes of two ant-orchids, Caularthron bicornutum and Myrmecophila thomsoniana.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {1146},
pmid = {39609739},
issn = {1471-2229},
support = {2023YFD1600504//the National Key Research and Development Program of China/ ; KH230350A//the Construction and Management Program of the Research Center for the Protection and Utilization of Orchids in Motuo County, Xizang Autonomous Region, China/ ; },
mesh = {*Phylogeny ; Animals ; *Orchidaceae/genetics/classification ; Genome, Plastid ; Ants/genetics/classification ; Plastids/genetics ; Symbiosis ; Gryllidae ; },
abstract = {BACKGROUND: Myrmecophytes, characterized by specialized structures like hollow stems that facilitate mutualistic relationships with ants, serve as an important system for studying ant-plant interactions and the adaptation mechanisms. Caularthron and Myrmecophila are exemplary myrmecophytes within Orchidaceae. Previous studies suggested a genetic relationship between these two genera, placing them within Laeliinae (Epidendreae), yet the precise phylogenetic positioning remained uncertain. The absence of available plastome resources has hindered investigations into plastome evolution and phylogeny.<br><br>RESULTS: In this study, we sequenced and assembled the complete plastomes of Caularthron bicornutum and Myrmecophila thomsoniana to elucidate their plastome characteristics and phylogenetic relationships. The determined plastome sizes were 150,557&#xa0;bp for C. bicornutum and 156,905&#xa0;bp for M. thomsoniana, with GC contents of 37.3% and 37.1%, respectively. Notably, M. thomsoniana exhibited a distinctive IR expansion and SSC contraction, with the SSC region measuring only 4532&#xa0;bp and containing five genes (ccsA, ndhD, rpl32, psaC, and trnL-UAG), a unique feature observed for the first time in Epidendreae. Comparative analyses with species from the related genus Epidendrum revealed that C. bicornutum plastome exhibited conserved genome size, GC content, gene content, and gene order. A total of 32 and 33 long sequence repeats, 50 and 40 tandem repeats, and 99 and 109 SSRs were identified in the plastomes of C. bicornutum and M. thomsoniana, respectively. The RSCU analysis demonstrated a consistent pattern in both plastomes, with 29 out of 30 codons with RSCU values greater than 1 featuring A/U at the third codon position. Leucine was the most prevalent amino acid, while Cysteine was the least common. Four potential DNA barcoding regions with Pi values exceeding 0.07, namely ycf1, ccsA-psaC, petN-psbM, and accD-psaI, were identified for subsequent phylogenetic reconstructions within Laeliinae. Phylogenetic analysis underscored the close relationships among Caularthron, Epidendrum, and Myrmecophila.<br><br>CONCLUSIONS: This study represents the first comprehensive analysis of the plastome characteristics of Caularthron bicornutum and Myrmecophila thomsoniana. Through our characterization and phylogenetic analyses, we unveiled the unique IR expansion/SSC contraction and further elucidated their phylogenetic positions. Our research contributes significant data and insights into the dynamic evolution of ant-orchid plastomes and the phylogeny of the Laeliinae.},
}
@article {pmid39608688,
year = {2025},
author = {Devan, J and Sandalova, M and Bitterli, P and Herger, N and Mengis, T and Brender, K and Heggli, I and Distler, O and Dudli, S},
title = {Massively parallel flow-cytometry-based screening of hematopoietic lineage cell populations from up to 25 donors simultaneously.},
journal = {Methods (San Diego, Calif.)},
volume = {234},
number = {},
pages = {45-53},
doi = {10.1016/j.ymeth.2024.11.014},
pmid = {39608688},
issn = {1095-9130},
mesh = {Humans ; *Flow Cytometry/methods ; *Immunophenotyping/methods ; *Leukocyte Common Antigens/metabolism/genetics ; Antigens, CD/genetics ; Hematopoietic Stem Cells/metabolism/cytology ; Single-Cell Analysis/methods ; Machine Learning ; Cell Lineage/genetics ; Receptors, Transferrin/metabolism/genetics ; },
abstract = {This study aimed to develop a method allowing high-dimensional and technically uniform screening of surface markers on cells of hematopoietic origin. High-dimensional screening of cell phenotypes is primarily the domain of single-cell RNA sequencing (RNAseq), which allows simultaneous analysis of the expression of thousands of genes in several thousands of cells. However, rare cell populations can often substantially impact tissue homeostasis or disease pathogenesis, and dysregulation of rare populations can easily be missed when only a few thousand cells are analyzed. With the presented methodological approach, it is possible to screen hundreds of markers on millions of cells in a technically uniform manner and thus identify and characterize changes in rare populations. We utilize the highly expressed markers CD45 on immune cells and CD71 on erythroid progenitors to create unique fluorescent barcodes on each of the 25 samples. Double-barcoded samples are co-stained with a broad immunophenotyping panel. The panel is designed in such a way that allows the addition of PE-labelled antibody, which was used for screening purposes. Multiplexed samples are divided into hundreds of aliquots and co-stained, each aliquot with a different PE-labelled antibody. Utilizing a broad immunophenotyping panel and machine-learning algorithms, we can predict the co-expression of hundreds of screened markers with a high degree of precision. This technique is suitable for screening immune cells in bone marrow from different locations, blood specimens, or any tissue with a substantial presence of immune cells, such as tumors or inflamed tissue areas in autoimmune conditions. It represents an approach that can significantly improve our ability to recognize dysregulated immune cell populations and, if needed, precisely target subsequent experiments covering lower cell counts such as RNAseq.},
}
@article {pmid39606648,
year = {2024},
author = {Alvarez Rojas, CA and Bonacic, C and Salgado, R and Peters, L and Fredes, D and Rubio, AV and Muñoz-Leal, S and Oyarzún-Ruiz, P and Aguirre, AA},
title = {Genetic and biological insights into Hydatigera taeniaeformis in invasive black rats from southern Chile.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1466409},
pmid = {39606648},
issn = {2297-1769},
abstract = {INTRODUCTION: This study investigates the genetic variability of Hydatigera taeniaeformis in black rats (Rattus rattus), a common tapeworm that infects cats and rodents worldwide. Despite its widespread presence and zoonotic potential, little is known about the genetic diversity of this parasite in the Americas.<br><br>METHODS: We conducted DNA barcoding analysis using mitochondrial cox1 gene sequences using samples collected from 171 invasive wild black rats, captured in the temperate rainforest of Southern Chile. We also included two adult parasites isolated from road killed Kodkods (Leopardus guigna), a small felid species native to the Americas.<br><br>RESULTS: Our findings revealed only two haplotypes, suggesting low genetic variability in a parasite that arrived in the Americas with the Spanish colonization.<br><br>DISCUSSION: These haplotypes are more closely related to parasite populations from Peru, Africa, Australia, and Europe, suggesting an origin linked to the Spanish colonization, possibly from North Africa via the Canary Islands. The study also analyzed infection rates, parasite size, and their correlation with host body size, age, and weight, revealing significant patterns. These results provide new insights into the biogeography and genetic diversity of H. taeniaeformis in a new geographical area, enhancing our understanding of its evolutionary history.},
}
@article {pmid39606254,
year = {2024},
author = {Ding, M and Cheng, H and Li, X and Li, X and Zhang, M and Cui, D and Yang, Y and Tian, X and Wang, H and Yang, W},
title = {Phytochemistry, quality control and biosynthesis in ginseng research from 2021 to 2023: A state-of-the-art review concerning advances and challenges.},
journal = {Chinese herbal medicines},
volume = {16},
number = {4},
pages = {505-520},
pmid = {39606254},
issn = {2589-3610},
abstract = {Panax L. (Araliaceae) has a long history of medicinal and edible use due to its significant tonifying effects, and ginseng research has been a hot topic in natural products research and food science. In continuation of our recent ginseng review, we highlighted the advances in ginseng research from 2021 to 2023 with 157 citations, which exhibited the increasingly systematic, collaborative, and intelligent characteristics. In this review, we firstly updated the progress in phytochemistry involving the ginsenosides and polysaccharides and summarized the researches on the active components. Then, some specific applications by feat of the multidimensional chromatography, mass spectrometry imaging, DNA barcoding, and metabolomics, were analyzed, which could provide rich information supporting the multi-component characterization, authentication, and quality control of ginseng and the versatile products. Finally, the recent biosynthesis studies concerning ginsenosides were retrospected. Additionally, the current challenges and future trends with respect to ginseng research were discussed.},
}
@article {pmid39605649,
year = {2024},
author = {Diamond, B and Chahar, D and Jain, MD and Poos, AM and Durante, M and Ziccheddu, B and Kaddoura, M and Papadimitriou, M and Maclachlan, K and Jelinek, T and Davies, F and Figura, NB and Morgan, G and Mai, E and Weisel, KC and Fenk, R and Raab, MS and Usmani, S and Landgren, O and Locke, FL and Goldschmidt, H and Schatz, JH and Weinhold, N and Maura, F},
title = {Mutagenic impact and evolutionary influence of radiotherapy in hematologic malignancies.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39605649},
issn = {2692-8205},
support = {K12 CA226330/CA/NCI NIH HHS/United States ; P30 CA240139/CA/NCI NIH HHS/United States ; },
abstract = {Ionizing radiotherapy (RT) is a widely used palliative and curative treatment strategy for malignancies. In solid tumors, RT-induced double strand breaks lead to the accumulation of indels, and their repair by non-homologous end-joining has been linked to the ID8 mutational signature in resistant cells. However, the extent of RT-induced DNA damage in hematologic malignancies and its impact on their evolution and interplay with commonly used chemotherapies has not yet been explored. Here, we interrogated 580 whole genome sequencing (WGS) from patients with large B-cell lymphoma, multiple myeloma, and myeloid neoplasms and identified ID8 only in relapsed disease. Yet, it was detected after exposure to both RT and mutagenic chemotherapy (i.e., platinum). Using WGS of single-cell colonies derived from treated lymphoma cells, we revealed a dose-response relationship between RT and platinum and ID8. Finally, using ID8 as a genomic barcode we demonstrate that a single RT-resistant cell may seed systemic relapse.},
}
@article {pmid39605582,
year = {2024},
author = {Meleshko, D and Yang, R and Maharjan, S and Danko, DC and Korobeynikov, A and Hajirasouliha, I},
title = {Blackbird: structural variant detection using synthetic and low-coverage long-reads.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39605582},
issn = {2692-8205},
support = {R35 GM138152/GM/NIGMS NIH HHS/United States ; },
abstract = {MOTIVATION: Recent benchmarks of structural variant (SV) detection tools revealed that the majority of human genome structural variations (SVs), especially the medium-range (50-10,000 bp) SVs cannot be resolved with short-read sequencing, but long-read SV callers achieve great results on the same datasets. While improvements have been made, high-coverage long-read sequencing is associated with higher costs and input DNA requirements. To decrease the cost one can lower the sequence coverage, but the current long-read SV callers perform poorly with coverage below 10×. Synthetic long-read (SLR) technologies hold great potential for structural variant (SV) detection, although utilizing their long-range information for events smaller than 50 kbp has been challenging.<br><br>RESULTS: In this work, we propose a hybrid novel integrated alignment- and local-assembly-based algorithm, Blackbird, that uses SLR together with low-coverage long reads to improve SV detection and assembly. Without the need for a computationally expensive whole genome assembly, Blackbird uses a sliding window approach and barcode information encoded in SLR to accurately assemble small segments and use long reads for an improved gap closing and contig assembly. We evaluated Blackbird on simulated and real human genome datasets. Using the HG002 GIAB benchmark set, we demonstrated that in hybrid mode, Blackbird demonstrated results comparable to state-of-the-art long-read tools, while using less long-read coverage. Blackbird requires only 5&#xd7; coverage to achieve F1 scores (0.835 and 0.808 for deletions and insertions) similar to PBSV (0.856 and 0.812) and Sniffles2 (0.839 and 0.804) using 10&#xd7; Pacbio Hi-Fi long-read coverage.},
}
@article {pmid39605581,
year = {2024},
author = {Enninful, A and Zhang, Z and Klymyshyn, D and Zong, H and Bai, Z and Farzad, N and Su, G and Baysoy, A and Nam, J and Yang, M and Lu, Y and Zhang, NR and Braubach, O and Xu, ML and Ma, Z and Fan, R},
title = {Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39605581},
issn = {2692-8205},
support = {U54 AG079759/AG/NIA NIH HHS/United States ; U54 CA274509/CA/NCI NIH HHS/United States ; RF1 MH128876/MH/NIMH NIH HHS/United States ; UH3 CA257393/CA/NCI NIH HHS/United States ; U01 CA294514/CA/NCI NIH HHS/United States ; R01 CA245313/CA/NCI NIH HHS/United States ; U54 AG076043/AG/NIA NIH HHS/United States ; RM1 MH132648/MH/NIMH NIH HHS/United States ; },
abstract = {Spatially mapping the transcriptome and proteome in the same tissue section can significantly advance our understanding of heterogeneous cellular processes and connect cell type to function. Here, we present Deterministic Barcoding in Tissue sequencing plus (DBiTplus), an integrative multi-modality spatial omics approach that combines sequencing-based spatial transcriptomics and image-based spatial protein profiling on the same tissue section to enable both single-cell resolution cell typing and genome-scale interrogation of biological pathways. DBiTplus begins with in situ reverse transcription for cDNA synthesis, microfluidic delivery of DNA oligos for spatial barcoding, retrieval of barcoded cDNA using RNaseH, an enzyme that selectively degrades RNA in an RNA-DNA hybrid, preserving the intact tissue section for high-plex protein imaging with CODEX. We developed computational pipelines to register data from two distinct modalities. Performing both DBiT-seq and CODEX on the same tissue slide enables accurate cell typing in each spatial transcriptome spot and subsequently image-guided decomposition to generate single-cell resolved spatial transcriptome atlases. DBiTplus was applied to mouse embryos with limited protein markers but still demonstrated excellent integration for single-cell transcriptome decomposition, to normal human lymph nodes with high-plex protein profiling to yield a single-cell spatial transcriptome map, and to human lymphoma FFPE tissue to explore the mechanisms of lymphomagenesis and progression. DBiTplusCODEX is a unified workflow including integrative experimental procedure and computational innovation for spatially resolved single-cell atlasing and exploration of biological pathways cell-by-cell at genome-scale.},
}
@article {pmid39605504,
year = {2024},
author = {Yan, Y and Cheung, E and Verzier, LH and Appetecchia, F and March, S and Craven, AR and Du, E and Probst, AS and Rinvee, TA and de Vries, LE and Kauffman, J and Bhatia, SN and Nelson, E and Singh, N and Peng, D and Shaw, WR and Catteruccia, F},
title = {Mapping Plasmodium transitions and interactions in the Anopheles female.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.12.623125},
pmid = {39605504},
issn = {2692-8205},
support = {T32 AI049928/AI/NIAID NIH HHS/United States ; },
abstract = {The human malaria parasite, Plasmodium falciparum , relies on Anopheles mosquitoes for transmission. Once ingested during blood feeding, most parasites die in the mosquito midgut lumen or during epithelium traversal. How surviving ookinetes interact with midgut cells and form oocysts is unknown, yet these steps are essential to initiate a remarkable, similarly uncharacterized growth process culminating in the production of thousands of infectious sporozoites. Here, using single-cell RNA sequencing of both parasites and mosquito cells across four time points and two metabolic conditions, we unveil key processes shaping developmental transitions and mosquito-parasite interactions occurring in the midgut. In depth functional analyses reveal processes regulating oocyst growth and identify the transcription factor Pf SIP2 as essential for sporozoite infection of human hepatocytes. By combining the analysis of shared mosquito-parasite barcodes with confocal microscopy, we discover that parasites preferentially interact with midgut progenitor cells during epithelial crossing, potentially using their basal location as an exit landmark. Additionally, we unveil tight connections between extracellular late oocysts and surrounding muscle cells that may ensure parasites adhere to the midgut without damaging it. Ultimately, our study provides fundamental insight into the molecular events characterizing previously inaccessible biological transitions and mosquito-parasite interactions, and identifies candidates for transmission-blocking strategies.},
}
@article {pmid39605487,
year = {2025},
author = {Delamarre, A and Bailey, B and Yavid, J and Koche, R and Mohibullah, N and Whitehouse, I},
title = {Chromatin architecture mapping by multiplex proximity tagging.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.12.623258},
pmid = {39605487},
issn = {2692-8205},
abstract = {Chromatin plays a pivotal role in genome expression, maintenance, and replication. To better understand chromatin organization, we developed a novel proximity-tagging method which assigns unique DNA barcodes to molecules that associate in 3D space. Using this method - Proximity Copy Paste (PCP) - we mapped the connectivity of individual nucleosomes in Saccharomyces cerevisiae. By analyzing nucleosome positions and spacing on single molecule fibers, we show that chromatin is predominantly organized into regularly spaced nucleosome arrays that can be positioned or delocalized. Basic features of nucleosome arrays are generally explained by gene size and transcription. PCP can also map long-range, multi-way interactions and we provide the first direct evidence supporting a model that metaphase chromosomes are compacted by cohesin loop clustering. Analyzing single-molecule nuclease footprinting data we define distinct chromatin states within a mixed population to show that non-canonical nucleosomes, notably Overlapping-Di-Nucleosomes (OLDN) are a stable feature of chromatin. PCP is a versatile method allowing the detection of the connectivity of individual molecules locally and over large distance to be mapped at high-resolution in a single experiment.},
}
@article {pmid39604449,
year = {2024},
author = {Holzmann, M and Nguyen, NL and Angeles, IB and Pawlowski, J},
title = {BFR2: a curated ribosomal reference dataset for benthic foraminifera.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1292},
pmid = {39604449},
issn = {2052-4463},
support = {Exploring abyssal and hadal biodiversity of foraminifera in the North Pacific//Fondation Ernst et Lucie Schmidheiny (Ernst and Lucie Schmidheiny Foundation)/ ; 221959//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_179125//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_159709//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 316030_150817//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
mesh = {*Foraminifera/genetics/classification ; *DNA Barcoding, Taxonomic ; RNA, Ribosomal, 18S/genetics ; DNA, Ribosomal/genetics ; },
abstract = {Benthic foraminifera are one of the major groups of marine protists that also occur in freshwater and terrestrial habitats. They are widely used to monitor current and past environmental conditions. Over the last three decades, thousands of DNA sequences have been obtained from benthic foraminiferal isolates. The results of this long-term effort are compiled here in the form of the first curated benthic foraminiferal ribosomal reference dataset (BFR2). The present dataset contains over 5000 sequences of a fragment of the 18S rDNA gene, which is recognized as the DNA barcode of foraminifera. The sequences represent 279 species and 204 genera belonging to 91 families. Thirteen percent of these sequences have not been assigned to any morphologically described group and may represent species new to science. Furthermore, forty-five percent of the sequences have not been previously published. The BFR[2] dataset aims to collect all DNA barcodes of benthic foraminifera and to provide a much-needed reference dataset for the rapidly developing field of molecular foraminiferal studies.},
}
@article {pmid39604411,
year = {2024},
author = {Purushothaman, S and Meola, M and Roloff, T and Rooney, AM and Egli, A},
title = {Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {29531},
pmid = {39604411},
issn = {2045-2322},
support = {310030_192512//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Metagenomics/methods ; *Nanopore Sequencing/methods ; *Drug Resistance, Bacterial/genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; Humans ; Bacteria/genetics/isolation &amp; purification/classification ; },
abstract = {During a bacterial infection or colonization, the detection of antimicrobial resistance (AMR) is critical, but slow due to culture-based approaches for clinical and screening samples. Culture-based phenotypic AMR detection and confirmation require up to 72 hours (h) or even weeks for slow-growing bacteria. Direct shotgun metagenomics by long-read sequencing using Oxford Nanopore Technologies (ONT) may reduce the time for bacterial species and AMR gene identification. However, screening swabs for metagenomics is complex due to the range of Gram-negative and -positive bacteria, diverse AMR genes, and host DNA present in the samples. Therefore, DNA extraction is a critical initial step. We aimed to compare the performance of different DNA extraction protocols for ONT applications to reliably identify species and AMR genes using a shotgun long-read metagenomic approach. We included three different sample types: ZymoBIOMICS Microbial Community Standard, an in-house mock community of ESKAPE pathogens including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli (ESKAPE Mock), and anonymized clinical swab samples. We processed all sample types with four different DNA extraction kits utilizing different lysis (enzymatic vs. mechanical) and purification (spin-column vs. magnetic beads) methods. We used kits from Qiagen (QIAamp DNA Mini and QIAamp PowerFecal Pro DNA) and Promega (Maxwell RSC Cultured Cells and Maxwell RSC Buccal Swab DNA). After extraction, samples were subject to the Rapid Barcoding Kit (RBK004) for library preparation followed by sequencing on the GridION with R9.4.1 flow cells. The fast5 files were base called to fastq files using Guppy in High Accuracy (HAC) mode with the inbuilt MinKNOW software. Raw read quality was assessed using NanoPlot and human reads were removed using Minimap2 alignment against the Hg38 genome. Taxonomy identification was performed on the raw reads using Kraken2 and on assembled contigs using Minimap2. The AMR genes were identified using Minimap2 with alignment against the CARD database on both the raw reads and assembled contigs. We identified all bacterial species present in the Zymo Mock Community (8/8) and ESKAPE Mock (6/6) with Qiagen PowerFecal Pro DNA kit (chemical and mechanical lysis) at read and assembly levels. Enzymatic lysis retrieved fewer aligned bases for the Gram-positive species (Staphylococcus aureus and Enterococcus faecium) from the ESKAPE Mock on the assembly level compared to the mechanical lysis. We detected the AMR genes from Gram-negative and -positive species in the ESKAPE Mock with the QIAamp PowerFecal Pro DNA kit on reads level with a maximum median time of 1.9 h of sequencing. Long-read metagenomics with ONT may reduce the turnaround time in screening for AMR genes. Currently, the QIAamp PowerFecal Pro DNA kit (chemical and mechanical lysis) for DNA extraction along with the Rapid Barcoding Kit for the ONT sequencing captured the best taxonomy and AMR identification for our specific use case.},
}
@article {pmid39603810,
year = {2025},
author = {Gong, X and Zhang, H and Guo, Y and Yu, S and Tang, M},
title = {Chromosome-level genome assembly of Iodes seguinii and its metabonomic implications for rheumatoid arthritis treatment.},
journal = {The plant genome},
volume = {18},
number = {1},
pages = {e20534},
pmid = {39603810},
issn = {1940-3372},
support = {SH2023078//Science and Technology Plan Projects of Zhenjiang/ ; JDYY2023009//Medical Education Collaborative Innovation Fund of Jiangsu University/ ; 32002235//National Natural Science Foundation of China/ ; },
mesh = {*Arthritis, Rheumatoid/genetics/drug therapy ; *Genome, Plant ; Metabolomics ; Chromosomes, Plant ; Phylogeny ; },
abstract = {Iodes seguinii is a woody vine known for its potential therapeutic applications in treating rheumatoid arthritis (RA) due to its rich bioactive components. Here, we achieved the first chromosome-level assembly of the nuclear genome of I. seguinii using PacBio HiFi and chromatin conformation capture (Hi-C) sequencing data. The initial assembly with PacBio data produced contigs with an N50 length of 9.71 Mb, and Hi-C data anchored these contigs into 13 chromosomes, achieving a total length of 273.58 Mb, closely matching the estimated genome size. Quality assessments, including BUSCO, long terminal repeat assembly index, transcriptome mapping rates, and sequencing coverage, confirmed the high quality, completeness, and continuity of the assembly, identifying 115.28 Mb of repetitive sequences, 1062 RNA genes, and 25,270 protein-coding genes. Additionally, we assembled and annotated the 150,599 bp chloroplast genome using Illumina sequencing data, containing 121 genes including key DNA barcodes, with maturase K (matK) proving effective for species identification. Phylogenetic analysis positioned I. seguinii at the base of the Lamiales clade, identifying significant gene family expansions and contractions, particularly related to secondary metabolite synthesis and DNA damage repair. Metabolite analysis identified 84 active components in I. seguinii, including the discovery of luteolin, with 119 targets predicted for RA treatment, including core targets like AKT1, toll-like receptor 4 (TLR4), epidermal growth factor receptor (EGFR), tumor necrosis factor (TNF), TP53, NFKB1, janus kinase 2 (JAK2), BCL2, mitogen-activated protein kinase 1 (MAPK1), and spleen-associated tyrosine kinase (SYK). Key active components such as flavonoids and polyphenols with anti-inflammatory activities were highlighted. The discovery of luteolin, in particular, underscores its potential therapeutic role. These findings provide a valuable genomic resource and a scientific basis for the development and application of I. seguinii, addressing the genomic gap in the genus Iodes and the order Icacinales and underscoring the need for further research in genomics, transcriptomics, and metabolomics to fully explore its potential.},
}
@article {pmid39603754,
year = {2024},
author = {Maladan, Y and Retnaningrum, E and Daryono, BS and Sarassari, R and Sari, RF and Balqis, SA and Wahid, GA and Safari, D},
title = {A New Serotyping Method of Streptococcus pneumoniae Based on CRISPR/Cas9-Targeted Sequencing.},
journal = {The Journal of molecular diagnostics : JMD},
volume = {26},
number = {12},
pages = {1045-1054},
doi = {10.1016/j.jmoldx.2024.08.009},
pmid = {39603754},
issn = {1943-7811},
mesh = {*Streptococcus pneumoniae/genetics/classification ; *CRISPR-Cas Systems/genetics ; *Serotyping/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Pneumococcal Infections/microbiology/genetics ; Genome, Bacterial ; },
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) application for targeted sequencing has made a breakthrough in the genomic research era. High diversity in the capsular polysaccharide (cps) locus of Streptococcus pneumoniae has hampered identification of the serotype. This study developed a new serotyping method for S. pneumoniae using CRISPR/Cas9-targeted sequencing with the Oxford Nanopore Technologies platform. A probe was designed at the position of the cps locus using an excision approach on two sides flanking genes between the dexB and aliA genes with approximately 20 kb. A native barcoding method was used for multiplexing. The probe will attach to a specific side followed by attachment of CRISPR/Cas9 to cut the recognition area. The study used de novo assembly to reconstruct sequence reads, which were analyzed using PneumoCRISPR, a new serotyping pipeline for Oxford Nanopore Technologies sequencing data output. Four CRISPR/Cas9 probes have been designed and recognize the cps locus of S. pneumoniae. Serotyping results align precisely with serotyping data from whole-genome sequencing. This serotyping method also allows researchers to use multiple samples in a single run. The new serotyping method based on CRISPR/Cas9-targeted sequencing holds immense promise for serotype identification of S. pneumoniae.},
}
@article {pmid39603242,
year = {2024},
author = {Pahl, V and Lubrano, P and Troßmann, F and Petras, D and Link, H},
title = {Intact protein barcoding enables one-shot identification of CRISPRi strains and their metabolic state.},
journal = {Cell reports methods},
volume = {4},
number = {12},
pages = {100908},
pmid = {39603242},
issn = {2667-2375},
mesh = {*Mass Spectrometry/methods ; Ubiquitin/metabolism/genetics ; CRISPR-Cas Systems/genetics ; Escherichia coli/genetics/metabolism ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Metabolome ; },
abstract = {Detecting strain-specific barcodes with mass spectrometry can facilitate the screening of genetically engineered bacterial libraries. Here, we introduce intact protein barcoding, a method to measure protein-based library barcodes and metabolites using flow injection mass spectrometry (FI-MS). Protein barcodes are based on ubiquitin with N-terminal tags of six amino acids. We demonstrate that FI-MS detects intact ubiquitin proteins and identifies the mass of N-terminal barcodes. In the same analysis, we measured relative concentrations of primary metabolites. We constructed six ubiquitin-barcoded CRISPR interference (CRISPRi) strains targeting metabolic enzymes and analyzed their metabolic profiles and ubiquitin barcodes. FI-MS detected barcodes and distinct metabolome changes in CRISPRi-targeted pathways. We demonstrate the scalability of intact protein barcoding by measuring 132 ubiquitin barcodes in microtiter plates. These results show that intact protein barcoding enables fast and simultaneous detection of library barcodes and intracellular metabolites, opening up new possibilities for mass spectrometry-based barcoding.},
}
@article {pmid39602973,
year = {2025},
author = {Um, DH and Knowles, DA and Kaiser, GE},
title = {Vector embeddings by sequence similarity and context for improved compression, similarity search, clustering, organization, and manipulation of cDNA libraries.},
journal = {Computational biology and chemistry},
volume = {114},
number = {},
pages = {108251},
doi = {10.1016/j.compbiolchem.2024.108251},
pmid = {39602973},
issn = {1476-928X},
mesh = {*Gene Library ; Cluster Analysis ; Algorithms ; Data Compression ; },
abstract = {This paper demonstrates the utility of organized numerical representations of genes in research involving flat string gene formats (i.e., FASTA/FASTQ[5]). By assigning a unique vector embedding to each short sequence, it is possible to more efficiently cluster and improve upon compression performance for the string representations of cDNA libraries. Furthermore, by studying alternative coordinate vector embeddings trained on the context of codon triplets, we can demonstrate clustering based on amino acid properties. Employing this sequence embedding method to encode barcodes and cDNA sequences, we can improve the time complexity of similarity searches. By pairing vector embeddings with an algorithm that determines the vector proximity in Euclidean space, this approach enables quicker and more flexible sequence searches.},
}
@article {pmid39602792,
year = {2024},
author = {Lancioni, GE and Alberti, G and Filippini, C and Singh, NN and O'Reilly, MF and Sigafoos, J and Orlando, I and Desideri, L},
title = {A Technology System to Help People With Intellectual Disability and Blindness Find Room Destinations During Indoor Traveling: Case Series Study.},
journal = {JMIR rehabilitation and assistive technologies},
volume = {11},
number = {},
pages = {e65680},
pmid = {39602792},
issn = {2369-2529},
abstract = {BACKGROUND: People with severe or profound intellectual disability and visual impairment tend to have serious problems in orientation and mobility and need assistance for their indoor traveling. The use of technology solutions may be critically important to help them curb those problems and achieve a level of independence.<br><br>OBJECTIVE: This study aimed to assess a new technology system to help people with severe to profound intellectual disability and blindness find room destinations during indoor traveling.<br><br>METHODS: A total of 7 adults were included in the study. The technology system entailed a barcode reader, a series of barcodes marking the room entrances, a smartphone, and a special app that controlled the presentation of different messages (instructions) for the participants. The messages varied depending on whether the participants were (1) in an area between room entrances, (2) in correspondence with a room entrance to bypass, or (3) in correspondence with a room entrance representing the destination to enter. The intervention with the technology system was implemented according to a nonconcurrent multiple baseline design across participants. Sessions included 7 traveling trials, in each of which the participants were to reach and enter a specific room (1 of the 7 or 9 available) to deliver an object they had carried (transported) during their traveling.<br><br>RESULTS: The participants' mean frequency of traveling trials completed correctly was between zero and 2 per session during the baseline (without the system). Their mean frequency increased to between about 6 and nearly 7 per session during the intervention (with the system).<br><br>CONCLUSIONS: The findings suggest that the new technology system might be a useful support tool for people with severe to profound intellectual disability and blindness.},
}
@article {pmid39599554,
year = {2024},
author = {Morelli, M and D'Attoma, G and Saldarelli, P and Minafra, A},
title = {The Evolution of Wisteria Vein Mosaic Virus: A Case Study Approach to Track the Emergence of New Potyvirus Threats.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
pmid = {39599554},
issn = {2076-0817},
mesh = {*Potyvirus/genetics/isolation &amp; purification/classification ; *Phylogeny ; *Plant Diseases/virology ; Genome, Viral/genetics ; Evolution, Molecular ; Brassicaceae/virology ; Genetic Variation/genetics ; },
abstract = {Wisteria vein mosaic virus (WVMV, Potyvirus wisteriae), a virus belonging to the genus Potyvirus, is responsible for Wisteria vein mosaic disease (WMD), a severe disease that affects Wisteria, a genus of garden plants acclaimed worldwide. Although probably originating in the Far East, WVMV infection was first reported in the US, and subsequently in numerous countries. Following the first molecular detection of an Italian isolate, WVMV Bari, its full-length genome was achieved using NGS barcoding technology. A PhyML phylogenetic analysis, supported by clustering algorithm validation, identified a clear separation between two phylogroups. One major clade comprised WVMV strains isolated from Wisteria spp. A second clade grouped three highly divergent strains, at the borderline species threshold, all found in non-wisteria hosts. Relying on a Relative Time Dated Tips (RTDT) molecular clock, the first emergence of WVMV clades has been traced back to around the 17th century. A network inference analysis confirmed the sharp separation between the two host-related phylogroups, also highlighting the presence of potential intermediate variants. Inter-population genetic parameters revealed a very high genetic differentiation in both populations, which was made reliable by statistically significant permutation tests. The migrant number (Nm) and fixation index (FST) evidenced a restricted gene flow and strong population structures. According to the dN/dS ratio and negative neutrality tests, it was derived that purifying selection at the expense of non-silent variants is underway within WVMV populations. Targeting WVMV evolutionary traits, the present effort raised interesting questions about the underestimated potential of this culpably neglected species to spread in economically relevant crops. The main intention of our study is, therefore, to propose an evolution-based analysis approach that serves as a case study to investigate how other potyviruses or newly emerging viruses may spread.},
}
@article {pmid39599494,
year = {2024},
author = {Alkathiri, B and Lee, S and Ahn, K and Youn, SY and Yoo, MS and Lee, HS and Cho, YS and Jung, J and Seo, K and Kim, S and Umemiya-Shirafuji, R and Xuan, X and Kwak, D and Shin, S and Lee, SH},
title = {DNA Barcoding Using 18S rRNA Gene Fragments for Identification of Tick-Borne Protists in Ticks in the Republic of Korea.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
pmid = {39599494},
issn = {2076-0817},
support = {//Animal and Plant Quarantine Agency/ ; 2024//Chungbuk National University BK21 program/ ; },
mesh = {Animals ; *RNA, Ribosomal, 18S/genetics ; *DNA Barcoding, Taxonomic/methods ; Republic of Korea/epidemiology ; DNA, Protozoan/genetics ; Ticks/parasitology ; Theileria/genetics/isolation &amp; purification ; Phylogeny ; Ixodes/genetics/parasitology ; },
abstract = {The objective of this study was to evaluate the diversity and prevalence of tick-borne protists in the Republic of Korea via DNA barcoding using 18S rRNA gene fragments and PCR. Between 2021 and 2022, questing ticks were collected using the flagging method, with a total of 13,375 ticks collected and pooled into 1003 samples. Of these, 50 tick pools were selected for DNA barcoding targeting the V4 and V9 regions of 18S rRNA using the MiSeq platform. A taxonomic analysis of the amplicon sequence variants identified three genera of protozoa, namely Hepatozoon canis, Theileria luwenshuni, and Gregarine sp. However, the number and abundance of protists detected were different depending on the primer sets, and T. gondii was not identified in DNA barcoding. Furthermore, conventional PCR confirmed the presence of H. canis, Toxoplasma gondii, T. luwenshuni, and Theileria sp. in the collected ticks. This study identified H. canis and T. gondii in Ixodes nipponensis for the first time. It demonstrated that the results of DNA barcoding using 18S rRNA gene fragments can vary depending on the primer sets and further optimization is required for library construction to identify tick-borne protists in ticks. Despite these limitations, the findings highlight the potential of DNA barcoding using 18S rRNA gene fragments for screening the diversity of tick-borne protists in ticks.},
}
@article {pmid39599378,
year = {2024},
author = {De Luca, D and Del Guacchio, E and Cennamo, P and Minutillo, F and Bernardo, L and Caputo, P},
title = {Genetics and Distribution of the Italian Endemic Campanula fragilis Cirillo (Campanulaceae).},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {22},
pages = {},
pmid = {39599378},
issn = {2223-7747},
abstract = {Campanula fragilis Cirillo is a species distributed in central and southern Italy and includes two subspecies with uncertain taxonomic position and distribution. By means of nuclear and chloroplast markers, we attempted at testing the genetic distinctness of the two subspecies, as well as their possible correspondence with geographical or ecological patterns. After a revision of geographic occurrences based on herbarium data, we carried out species distribution modeling to assess the present and future distribution of this species under different ecological variables, also for conservation purposes. Our findings support the recognition of two weakly differentiated taxa, here accepted at subspecific rank, in agreement with the current taxonomic treatment. We found that C. fragilis subsp. cavolinii is monophyletic and limited to mountains and hills of central Italy. On the contrary, C. fragilis subsp. fragilis shows a higher genetic variability and a broader distribution in central and southern Italy, with a wider altitudinal range from coasts to mountain cliffs. We confirmed that both subspecies are narrowly calcicolous and have similar ecological requirements, but C. fragilis subsp. cavolinii occurs in colder habitats. Our results forecast a significant distribution contraction in the long term.},
}
@article {pmid39597591,
year = {2024},
author = {Chen, H and Yin, X and Chen, Y and Wang, Y and Li, Q and Ji, N and Zhou, L and Hu, G and Shen, X},
title = {Characterization of a Levanderina fissa Bloom in Aquaculture Ponds and Its Utilization of Dissolved Organic Phosphorus.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
pmid = {39597591},
issn = {2076-2607},
support = {SF2303//Lianyungang Key Research and Development Program/ ; },
abstract = {Harmful algal blooms (HABs) pose significant threats to ecosystems and human health worldwide, with their frequency and intensity increasing substantially. The present study reports an algal bloom observed in an aquaculture pond near Haizhou Bay in July 2022. The causative species, identified through morphological observation and DNA barcoding analysis, was the dinoflagellate Levanderina fissa (Levander) Moestrup, Hakanen, Gert Hansen, Daugbjerg &amp; M. Ellegaard, 2014, known for causing extensive HAB events in the coastal waters of China. A sharp decline in phytoplankton species diversity was observed during the transition from the pre-bloom to the bloom phase. Furthermore, the uptake of four types of dissolved organic phosphorus (DOP), including glucose-6-phosphate (G6P), adenosine-5-triphosphate (ATP), sodium tripolyphosphate (TPP), and glyphosate, by isolated L. fissa was investigated in the laboratory. The results showed that G6P, ATP, and TPP supported L. fissa growth as effectively as orthophosphate. Additionally, the elevated concentrations of dissolved inorganic phosphorus in the media of the three treatments indicated the involvement of extracellular hydrolysis. However, alkaline phosphatase was not responsible for the hydrolysis of these three forms of DOP. This study demonstrates that the ability of L. fissa to utilize DOP may confer a competitive advantage within phytoplankton communities, potentially leading to algal blooms in aquaculture ponds.},
}
@article {pmid39596906,
year = {2024},
author = {Ismailaj, M and Zangaro, F and Specchia, V and Sangiorgio, F and Marcucci, F and Kiçaj, H and Basset, A and Pinna, M},
title = {Biodiversity Patterns and DNA Barcode Gap Analysis of COI in Coastal Lagoons of Albania.},
journal = {Biology},
volume = {13},
number = {11},
pages = {},
pmid = {39596906},
issn = {2079-7737},
support = {101082327//EU commission/ ; },
abstract = {Aquatic biodiversity includes a variety of unique species, their habitats, and their interactions with each other. Albania has a large hydrographic network including rivers, lakes, wetlands and coastal marine areas, contributing to a high level of aquatic biodiversity. Currently, evaluating aquatic biodiversity relies on morphological species identification methods, but DNA-based taxonomic identification could improve the monitoring and assessment of aquatic ecosystems. This study aims to evaluate the coverage of COI DNA barcodes in the reference libraries for the known aquatic animal species present in the coastal lagoons of Albania. In this study, the six most studied coastal lagoons of Albania were selected. Species data were gathered from the scientific literature and publicly available sites and studies. The collected species lists were taxonomically standardised using global public taxonomic databases like WORMS. The standardised lists were used to analyse the barcode gap of COI based on two public DNA barcode libraries: Barcode of Life Data Systems (BOLD) and NCBI GenBank. The results show that the COI DNA barcode gap in the coastal lagoons of Albania ranges from 7% (Lagoon of Patok) to 33% (Karavasta Lagoon). Fishes and Amphibia represent the groups with the lowest barcode gap (8% each), while Annelida shows the highest (47%). In conclusion, the COI gene marker for DNA-based biodiversity assessments is reliable for the coastal lagoons of Albania.},
}
@article {pmid39596647,
year = {2024},
author = {Almerekova, S and Yermagambetova, M and Ivashchenko, A and Abugalieva, S and Turuspekov, Y},
title = {Assessment of Complete Plastid Genome Sequences of Tulipa alberti Regel and Tulipa greigii Regel Species from Kazakhstan.},
journal = {Genes},
volume = {15},
number = {11},
pages = {},
pmid = {39596647},
issn = {2073-4425},
support = {AP14870612//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
mesh = {*Phylogeny ; *Genome, Plastid ; Kazakhstan ; *Tulipa/genetics ; Microsatellite Repeats/genetics ; Plastids/genetics ; RNA, Transfer/genetics ; Whole Genome Sequencing/methods ; },
abstract = {BACKGROUND: Tulipa species are economically, culturally, scientifically, and ecologically important. Tulips present taxonomic complexities that cannot be adequately resolved by examining their morphological characteristics alone or by relying on a limited selection of genetic markers.<br><br>METHODS: In the present study, we assessed the complete plastid sequences of Tulipa alberti Regel and Tulipa greigii Regel collected from Kazakhstan. Additionally, 14 previously published plastomes were obtained from GenBank for comparison and phylogenetic analysis.<br><br>RESULTS: The plastid genome sizes of T. alberti and T. greigii were 152,359 bp and 152,242 bp, respectively. In the plastid genomes of T. alberti and T. greigii, 136 genes were annotated, 114 of which were unique. These unique genes comprised eighty protein-coding, thirty transfer RNA, and four ribosomal RNA genes. Additionally, 415 simple sequence repeats were identified, comprising 107 tandem, 40 forward, 49 palindromic, 8 reverse, and 1 complementary repeat. Notably, the region containing ycf1 exhibited high variability and may serve as an informative DNA barcode for this genus.<br><br>CONCLUSION: Phylogenetic analysis showed strong support for the relationships among Tulipa species, indicating the utility of plastid genome data for further taxonomic studies within the genus.},
}
@article {pmid39596617,
year = {2024},
author = {Sajjad, S and Islam, M and Muhammad, K and Ghafoor, SU and Ullah, I and Khan, A and Siraj, M and Alrefaei, AF and Shah, JA and Ali, S},
title = {Comprehensive Evaluation of Cryptic Juglans Genotypes: Insight from Molecular Markers and Phylogenetic Analysis.},
journal = {Genes},
volume = {15},
number = {11},
pages = {},
pmid = {39596617},
issn = {2073-4425},
mesh = {*Juglans/genetics/classification ; *Phylogeny ; *Genotype ; Genetic Markers/genetics ; DNA Barcoding, Taxonomic/methods ; Pakistan ; },
abstract = {Background/Objectives: The current research work aimed to evaluate the cryptic walnut genotypes of the Hazara region in Pakistan by using DNA barcoding and phylogenetic analysis. Methods: Based on morphological traits such as nut size, nut shape, and the number of leaflets, five genotypes were chosen and samples were collected for the current study. For molecular analysis, gDNA was isolated from the fresh leaves, and the five most effective angiosperm-specific markers, ITS2, rbcLa, rbcLc, rpoC1, and UBE3, were utilized. Based on amplification, sequencing, and identification success rates, ITS2 and UBE3 were recorded as the most efficient markers followed by rbcLa, rbcLc, and rpoC1. Results: During phylogenetic analysis, the query genotype-1 based on ITS2 and genotype-2 based on UBE3 clustered with (KF454101.1-Juglans regia) and (KC870919.1-J. regia) with bootstraps of 56 and 100, respectively. Genotype-3 based on rbcla clustered in a major clade with J. regia L., cultivars (MN397935.1 J. regia 'Vina') and (MN397934.1-J. regia 'Serr'), (MN397933.1 J. regia 'Pedro'), (MN397932.1 J. regia 'Lara'), (MN397931.1 J. regia 'Howard'), and (MN397930.1 J. regia 'Hartley') with bootstrap of 100. Meanwhile, genotype-4 and genotype-5 based on rbclc and rpoC1 clustered with (MN397935.1 J. regia 'Vina') and (MN397934.1 J. regia 'Serr'), across the database sequences. To clarify the taxonomic status of cryptic walnut genotypes, it is necessary to combine diverse DNA barcodes. The results of ITS2 and UBE3, followed by rbcL barcoding markers, are promising taxonomic tools for cryptic walnut genotypes in Pakistan. Conclusions: It has been determined that the genotypes of walnuts in the study area are both J. regia L. and its cultivars and that the accuracy of discrimination regarding the genus Juglans L. is greater than 90%. The reported DNA barcodes are recommended for the correct identification and genetic evaluation of Juglans taxa and its population.},
}
@article {pmid39596209,
year = {2024},
author = {Wang, X and Wang, Z and Yang, F and Lin, R and Liu, T},
title = {Assembly, Annotation, and Comparative Analysis of Mitochondrial Genomes in Trichoderma.},
journal = {International journal of molecular sciences},
volume = {25},
number = {22},
pages = {},
pmid = {39596209},
issn = {1422-0067},
support = {XTCX2022NYB12//Collaborative Innovation Center Project of Hainan University/ ; },
mesh = {*Genome, Mitochondrial ; *Phylogeny ; *Trichoderma/genetics ; *Molecular Sequence Annotation ; RNA, Transfer/genetics ; Base Composition/genetics ; Evolution, Molecular ; Introns/genetics ; },
abstract = {Trichoderma is a widely studied ascomycete fungal genus, including more than 400 species. However, genetic information on Trichoderma is limited, with most species reporting only DNA barcodes. Mitochondria possess their own distinct DNA that plays a pivotal role in molecular function and evolution. Here, we report 42 novel mitochondrial genomes (mitogenomes) combined with 18 published mitogenomes of Trichoderma. These circular mitogenomes exhibit sizes of 26,276-94,608 bp, typically comprising 15 core protein-coding genes (PCGs), 2 rRNAs, and 16-30 tRNAs; however, the number of endonucleases and hypothetical proteins encoded in the introns of PCGs increases with genome size enlargement. According to the result of phylogenetic analysis of the whole mitogenome, these strains diverged into six distinct evolutionary branches, supported by the phylogeny based on 2830 single-copy nuclear genes. Comparative analysis revealed that dynamic Trichoderma mitogenomes exhibited variations in genome size, gene number, GC content, tRNA copy, and intron across different branches. We identified three mutation hotspots near the regions encoding nad3, cox2, and nad5 that caused major changes in the mitogenomes. Evolutionary analysis revealed that atp9, cob, nad4L, nad5, and rps3 have been influenced by positive selection during evolution. This study provides a valuable resource for exploring the important roles of the genetic and evolutionary dynamics of Trichoderma mitogenome in the adaptive evolution of biocontrol fungi.},
}
@article {pmid39595947,
year = {2024},
author = {Hoffmann, M and Jang, JH and Tallent, SM and Gonzalez-Escalona, N},
title = {Single Laboratory Evaluation of the Q20+ Nanopore Sequencing Kit for Bacterial Outbreak Investigations.},
journal = {International journal of molecular sciences},
volume = {25},
number = {22},
pages = {},
pmid = {39595947},
issn = {1422-0067},
support = {FDA Foods Program Intramural Funds//United States Food and Drug Administration/ ; FDA Foods Program Intramural Funds//United States Food and Drug Administration/ ; },
mesh = {*Nanopore Sequencing/methods ; *Disease Outbreaks ; Humans ; Polymorphism, Single Nucleotide ; Genome, Bacterial ; Foodborne Diseases/microbiology ; Phylogeny ; High-Throughput Nucleotide Sequencing/methods ; DNA, Bacterial/genetics ; Shiga-Toxigenic Escherichia coli/genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology/epidemiology/diagnosis ; Sequence Analysis, DNA/methods ; Pilot Projects ; },
abstract = {Leafy greens are a significant source of produce-related Shiga toxin-producing Escherichia coli (STEC) outbreaks in the United States, with agricultural water often implicated as a potential source. Current FDA outbreak detection protocols are time-consuming and rely on sequencing methods performed in costly equipment. This study evaluated the potential of Oxford Nanopore Technologies (ONT) with Q20+ chemistry as a cost-effective, rapid, and accurate method for identifying and clustering foodborne pathogens. The study focuses on assessing whether ONT Q20+ technology could facilitate near real-time pathogen identification, including SNP differences, serotypes, and antimicrobial resistance genes. This pilot study evaluated different combinations of two DNA extraction methods (Maxwell RSC Cultured Cell DNA kit and Monarch high molecular weight extraction kits) and two ONT library preparation protocols (ligation and the rapid barcoding sequencing kit) using five well-characterized strains representing diverse foodborne pathogens. High-quality, closed bacterial genomes were obtained from all combinations of extraction and sequencing kits. However, variations in assembly length and genome completeness were observed, indicating the need for further optimization. In silico analyses demonstrated that Q20+ nanopore sequencing chemistry accurately identified species, genotype, and virulence factors, with comparable results to Illumina sequencing. Phylogenomic clustering showed that ONT assemblies clustered with reference genomes, though some indels and SNP differences were observed, likely due to sequencing and analysis methodologies rather than inherent genetic variation. Additionally, the study evaluated the impact of a change in the sampling rates from 4 kHz (260 bases pair second) to 5 kHz (400 bases pair second), finding no significant difference in sequencing accuracy. This evaluation workflow offers a framework for evaluating novel technologies for use in surveillance and foodborne outbreak investigations. Overall, the evaluation demonstrated the potential of ONT Q20+ nanopore sequencing chemistry to assist in identifying the correct strain during outbreak investigations. However, further research, validation studies, and optimization efforts are needed to address the observed limitations and fully realize the technology's potential for improving public health outcomes and enabling more efficient responses to foodborne disease threats.},
}
@article {pmid39595309,
year = {2024},
author = {Figura, A and Gryzinska, M and Jakubczak, A},
title = {Comparison of Universal mtDNA Primers in Species Identification of Animals in a Sample with Severely Degraded DNA.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {22},
pages = {},
pmid = {39595309},
issn = {2076-2615},
abstract = {Analysis of mitochondrial DNA, specifically the cytochrome b gene (cyt b), has become an essential tool for species identification. In the case of degraded samples, in which DNA is fractionated, universal primers, which are highly effective at amplifying the target region, are necessary. The material analysed in this study was a keychain made of bone, which was secured at a border crossing due to the suspicion that it was made of ivory. Due to processing of the bone and the likelihood of DNA degradation, five pairs of universal primers with different product lengths (from 148 to 990 base pairs) were used for species identification. Fragments of mtDNA from the cyt b and the 12S rRNA and 16S rRNA subunits were analysed. The analysis showed that only one pair of primers (L15601/H15748) enabled identification of the species, which is very common in samples with highly degraded DNA. The material was bone tissue belonging to the species Bos taurus (cattle). Species identification by molecular methods is extremely important in analysis of material when the species cannot be identified on the basis of morphological characteristics.},
}
@article {pmid39591964,
year = {2025},
author = {Lu, X and Zhang, Q and Wang, Z and Cheng, X and Yan, H and Cai, S and Zhang, H and Liu, Q},
title = {Development of an inducible DNA barcoding system to understand lineage changes in Arabidopsis regeneration.},
journal = {Developmental cell},
volume = {60},
number = {2},
pages = {305-319.e5},
doi = {10.1016/j.devcel.2024.10.023},
pmid = {39591964},
issn = {1878-1551},
mesh = {*Arabidopsis/genetics ; *Regeneration/genetics/physiology ; *DNA Barcoding, Taxonomic/methods ; *Cell Lineage/genetics ; },
abstract = {Plants demonstrate a high degree of developmental plasticity, capable of regenerating entire individuals from detached somatic tissues-a regenerative phenomenon rarely observed in metazoa. Consequently, elucidating the lineage relationship between somatic founder cells and descendant cells in regenerated plant organs has long been a pursuit. In this study, we developed and optimized both DNA barcode- and multi-fluorescence-based cell-lineage tracing toolsets, employing an inducible method to mark individual cells in Arabidopsis donor somatic tissues at the onset of regeneration. Utilizing these complementary methods, we scrutinized cell identities at the single-cell level and presented compelling evidence that all cells in the regenerated Arabidopsis plants, irrespective of their organ types, originated from a single progenitor cell in the donor somatic tissue. Our discovery suggests a single-cell passage directing the transition from multicellular donor tissue to regenerated plants, thereby creating opportunities for cell-cell competition during plant regeneration-a strategy for maximizing survival.},
}
@article {pmid39590688,
year = {2024},
author = {Chen, TQ and Yang, C and Xu, XL and Yang, L and He, HQ and Weng, MT and Ying, ZH and Shi, XK and Ding, MG},
title = {Comparative Mitogenomics Provides Valuable Insights for the Phylogeny and New DNA Barcodes of Ganoderma.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {10},
number = {11},
pages = {},
pmid = {39590688},
issn = {2309-608X},
support = {2023R1106//Science &amp; Technology Department of Fujian Province, the Public Welfare Competitive Research Project/ ; },
abstract = {Ganoderma is the most important genus in the family Ganodermataceae; many species have attracted much attention and widely cultivated because of their medicinal values, but so far, not a sequenced mitogenome derived from dikaryon strains has been explicitly recorded. Herein, four novel mitogenomes of commonly cultivated Ganoderma (G. leucocontextum H4, G. lucidum G6, G. sinense MZ96 and G. tsugae SS) were de novo assembled and given detail functional annotations. Collinearity analysis revealed that the four mitogenomes shared 82.93-92.02% similarity with their corresponding reference mitogenomes at the nucleotide level. A total of 15 core protein-coding genes (PCGs), along with rrnL and rrnS (mtLSU and mtSSU) were chosen as potential candidates for constructing their individual phylogenetic trees. These trees were compared with those derived from the concatenated sequences of 15 core PCGs. And finally, we found that the atp9 and nad4L were the most reliable markers for the phylogenetic analysis of Ganoderma and chosen as standard sequences to generate new DNA barcodes. This finding was further verified by comparing it against almost all available Ganoderma mitogenomes in the NCBI, with Trametes versicolor (Polyporaceae) and Rigidoporus microporus (Meripilaceae) as two outgroups. A total of 52 mitogenomes from three families were highly conserved, with identical gene lengths for atp9 (222 bp) and nad4L (267 bp). These genes were capable of distinguish distinctly different various species, which are grouped into separate clades within the phylogenetic trees. The closest related clades (I and II), including at least 30 samples of the three classical taxonomic species (G. lingzhi, G. sichuanense and G. lucidum), differed in only one SNP. The single base mutation rate increased with the evolutionary divergence of the phylogenetic clades, from two to three SNPs in earlier clades (e.g., clade IV containing G. leucocontextum) to five to six SNPs in later clades (e.g., clade X containing G. sinense). Despite these variations between species, the atp9 and nad4L genes of Ganoderma mitogenomes consistently encoded the same ATP synthase F0 subunit c (73 aa) and NADH dehydrogenase subunit 4L (88 aa). These two genes have been identified as reliable markers of new DNA barcodes, offering valuable insights and contributing significantly to understanding the evolutionary relationships and phylogeny of the Ganoderma genus and even the Ganodermataceae family.},
}
@article {pmid39590509,
year = {2024},
author = {Xie, TT and Wang, MQ and Li, Y and Su, CY and Zhang, D and Zhou, QS and Niu, ZQ and Yuan, F and Liu, XW and Ma, KP and Zhu, CD and Hao, JS and Chesters, D},
title = {Blue Vane and Pan Traps Are More Effective for Profiling Multiple Facets of Bee Diversity in Subtropical Forests.},
journal = {Insects},
volume = {15},
number = {11},
pages = {},
pmid = {39590509},
issn = {2075-4450},
abstract = {The choice of trap in entomological surveys affects the composition of captured insects, though previous comparative studies have been limited in the types of composition measured, and the effects of environmental context. We assessed the sampling bias of several traps commonly used in pollinator monitoring: blue, yellow, and white pan traps, and blue vane traps, towards different taxonomic and functional groups and their efficiency in measuring taxonomic, phylogenetic, and functional diversity. Analyses were performed in monoculture and mixed forests to understand the environmental context of trap efficiency. We found that blue pan traps generally outperformed other types in bee capture and exhibited a preference for Halictidae bees. Blue pan traps yielded the highest species richness and phylogenetic diversity, while blue vane traps captured the highest functional richness. Bias differences were frequently detected in mixed forests compared with monoculture forests. We also found the combination of blue vane and pan traps consistently correlated highest with a complete survey among two-method combinations. Based on our findings, we recommend a combination of blue vane and pan traps to obtain a more comprehensive bee collection in an efficient manner. Additionally, it is crucial to consider habitat type when designing bee trapping protocols to ensure an accurate representation of bee communities.},
}
@article {pmid39590449,
year = {2024},
author = {Schmid-Egger, C and Schmidt, S and Rosa, P and Niehuis, O},
title = {DNA Barcoding of German Cuckoo Wasps (Hymenoptera: Chrysididae) Suggests Cryptic Species in Several Widely Distributed Species.},
journal = {Insects},
volume = {15},
number = {11},
pages = {},
pmid = {39590449},
issn = {2075-4450},
support = {NI 1387/1-1, NI 1387/2-1, NI 1387/5-1, NI 1387/6-1/2//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Germany is home to a rich cuckoo wasp fauna (Hymenoptera: Chrysididae) with about 108 species. However, several nomenclatural changes, the lack of identification keys, and the discovery of cryptic species difficult to identify based on external morphology have made the identification of several species a challenge. COI barcoding has been instrumental in the identification of some cuckoo wasp species and could help alleviate some of the above problems, but a reliable large reference database containing the cuckoo wasp barcodes is lacking. We present the COI barcodes of more than 800 specimens of 101 cuckoo wasp species native to Germany to lay the foundation for the barcode-based identification of German species. An analysis of the COI barcode sequences suggested groups that are largely consistent with the current taxonomy of the group. We found a few cases of over- or undersplitting of taxa. In some common species, the high degree of barcode divergence suggests the presence of cryptic species that need to be further assessed by integrative approaches. Our library of cuckoo wasp reference barcodes will enhance researchers' ability to reliably identify species within this fascinating group of insects, in particular for identifying life stages that offer few or no morphological features for species-level identification.},
}
@article {pmid39590434,
year = {2024},
author = {Zhu, J and van Achterberg, C and Chen, X and Tang, P},
title = {New Records and New Species of Dacnusini (Hymenoptera: Braconidae, Alysiinae) Based on Morphological and Molecular Evidence.},
journal = {Insects},
volume = {15},
number = {11},
pages = {},
pmid = {39590434},
issn = {2075-4450},
support = {2023FY100200//Science &amp; Technology Fundamental Resources Investigation Program of China/ ; 31920103005//Key International Joint Research Program of National Natural Science Foundation of China/ ; 32070467//General Program of National Natural Science Foundation of China/ ; (32200355)//National Natural Science Foundation of China/ ; 226-2024-00095//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Dacnusini is a species-rich tribe in the subfamily Alysiinae, with most species exclusively serving as parasitoids of leaf-mining Diptera (Agromyzidae). The number of genera discovered in China remains limited, which is apparently insufficient considering the global diversity of species and genera within this tribe, particularly given the vast and ecologically diverse landscapes of China. In the present study, three new record genera, Victorovita Tobias, Coloneura Foerster, and Laotris Nixon, were documented for the first time in China. In addition, the species delimitation approach and haplotype network analyses based on the COI sequences, combined with morphological evidence, were employed to delimit species. The findings indicated three new species: Laotris glabella sp. nov., Laotris aethidentata sp. nov., and Victorovita aequalis sp. nov. Additionally, K2P divergences showed no overlap between intra- and interspecific genetic distances in the Laotris and Victorovita species. Detailed descriptions for new species and keys to the species of Laotris and Victorovita are provided in this paper, along with the documentation of two new species records for China: Victorovita caudata (Szépligeti, 1901) and Coloneura stylata Foerster, 1863.},
}
@article {pmid39590432,
year = {2024},
author = {Ramos-Lagunes, VH and Laredo-Tiscareño, SV and González-Peña, R and Adame-Gallegos, JR and Rodríguez-Alarcón, CA and de Jesús de Luna-Santillana, E and Hernández-Triana, LM and Velasco-Chino, LE and Laredo-Tiscareño, AG and Garza-Hernández, JA},
title = {Aedes (Georgecraigius) epactius from Zacatecas and Chihuahua Mexico: New Geographical Distribution and Altitude Records.},
journal = {Insects},
volume = {15},
number = {11},
pages = {},
pmid = {39590432},
issn = {2075-4450},
support = {740742, 769056, and 842817//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; UACJ-PTC-399 and UACJ-PTC-267//Programa para el Desarrollo Profesional Docente, para el Tipo Superior/ ; No. 419-24-23//CONAHCYT CIENCIA DE FRONTERA 2023/ ; 397-24-01//Proyectos de Investigaci&#xf3;n con Impacto Social (PIISO) UACJ/ ; SV3045//Department for Environment Food and Rural Affairs (DEFRA), Scottish Government and Welsh Government/ ; },
abstract = {Adults and immatures of Aedes epactius were collected in July and December 2022 at sites of high elevation in the states of Chihuahua (2300 masl) and Zacatecas (2182 and 2595 masl), Mexico, respectively. Mosquitoes were identified morphologically and sequenced for a DNA barcode of the cytochrome c oxidase I (COX1). This is the first distributional record of Ae. epactius in Zacatecas and provides evidence of the highest altitude in the Americas, including Mexico. The geographical distribution of Ae. epactius in Mexico was reviewed, and the COX1 analysis, using phylogenetic Bayesian analysis to confirm species identification, was performed.},
}
@article {pmid39589980,
year = {2024},
author = {Zhong, L and Chen, H and Cao, S and Hu, S},
title = {Single Nucleotide Recognition and Mutation Site Sequencing Based on a Barcode Assay and Rolling Circle Amplification.},
journal = {Biosensors},
volume = {14},
number = {11},
pages = {},
pmid = {39589980},
issn = {2079-6374},
support = {2021Y9014//innovation of science and Technology, Fujian province/ ; XRCZX2019024//Fujian Medical University's Research Foundation for Talented Scholars/ ; },
mesh = {*Nucleic Acid Amplification Techniques ; *Polymorphism, Single Nucleotide ; *Helicobacter pylori/genetics ; Mutation ; DNA Barcoding, Taxonomic ; Quantum Dots ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; Biosensing Techniques ; },
abstract = {Single nucleotide polymorphisms (SNPs) present significant challenges in microbial detection and treatment, further raising the demands on sequencing technologies. In response to these challenges, we have developed a novel barcode-based approach for highly sensitive single nucleotide recognition. This method leverages a dual-head folded complementary template probe in conjunction with DNA ligase to specifically identify the target base. Upon recognition, the system triggers rolling circle amplification (RCA) followed by the self-assembly of CdSe quantum dots onto polystyrene microspheres, enabling a single-particle fluorescence readout. This approach allows for precise base identification at individual loci, which are then analyzed using a bio-barcode array to screen for base changes across multiple sites. This method was applied to sequence a drug-resistant mutation site in Helicobacter pylori (H. pylori), demonstrating excellent accuracy and stability. Offering high precision, high sensitivity, and single nucleotide resolution, this approach shows great promise as a next-generation sequencing method.},
}
@article {pmid39589713,
year = {2024},
author = {Guo, P and Deng, Y},
title = {Spatial Omics: Navigating Neuroscience Research into the New Era.},
journal = {Advances in neurobiology},
volume = {41},
number = {},
pages = {133-149},
pmid = {39589713},
issn = {2190-5215},
mesh = {Humans ; *Neurosciences ; *Brain/metabolism ; Proteomics ; Transcriptome ; High-Throughput Nucleotide Sequencing ; Animals ; Genomics ; In Situ Hybridization, Fluorescence ; Neurons/metabolism ; Epigenomics ; },
abstract = {The human brain's complexity is underpinned by billions of neurons and trillions of synapses, necessitating coordinated activities across diverse cell types. Conventional techniques like in situ hybridization and immunohistochemistry, while valuable, face limitations in resolution and comprehensiveness when analyzing neuron types. Advances in spatial omics technologies, especially those integrating transcriptomics and proteomics, have revolutionized our understanding of brain tissue organization. These technologies, such as FISH-based, in situ sequencing-based (ISS), and next-generation sequencing (NGS)-based methods, provide detailed spatial context, overcoming previous limitations. FISH techniques, including smFISH and its variants like seqFISH and MERFISH, offer high-resolution spatial gene expression data. ISS approaches leverage padlock probes and rolling circle amplification to yield spatial transcriptome information. NGS-based methods, such as spatial transcriptomics and spatial-epigenomics, integrate spatial barcodes with single-cell sequencing, enabling comprehensive profiling of gene expression and epigenetic states in tissues. These innovations have propelled insights into neural development and disease, identifying cellular heterogeneity and molecular alterations in conditions like Alzheimer's and major depression. Despite challenges in cost, speed, and data analysis, spatial omics technologies continue to evolve, promising deeper insights into the molecular mechanisms of the brain and neurodegenerative diseases.},
}
@article {pmid39589617,
year = {2024},
author = {Argôlo, LA and Ramos, RTC and Bitencourt, JA and Galdino, JH and Sampaio, I and Affonso, PRAM},
title = {Hidden diversity revealed by DNA barcoding of paralichthyidae fish along the caribbean and brazilian coast.},
journal = {Genetica},
volume = {153},
number = {1},
pages = {4},
pmid = {39589617},
issn = {1573-6857},
support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; code 406489/2023-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Brazil ; *Electron Transport Complex IV/genetics ; *Phylogeny ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Caribbean Region ; Genetic Variation ; Fishes/genetics/classification ; },
abstract = {DNA barcoding based on COI sequences has been highly informative for the taxonomic assessment of many fish species due to its high rate of species identification. Accordingly, numerous studies have employed this method to encompass species checklists of different areas, assessment of cryptic diversity, biodiversity monitoring, and other applications. Furthermore, most of the success of COI DNA barcoding relies on a comprehensive database (BOLD Systems) that holds sequences and detailed records of millions of species and applies a system (BIN) that clusters short DNA barcodes to generate OTUs. Besides COI, the 16S rDNA has proven to be suitable for the molecular identification of several taxa, and the combination of both markers could be advantageous in investigating species composition in the Neotropics. The family Paralichthyidae comprises over 60 flatfish species. Most of them inhabit tropical areas and remain understudied. Here, we evaluated the diversity of Paralichthyidae species along the Brazilian coast through COI and 16S DNA barcodes. Combining our dataset with BOLD (COI) and GenBank (16S) public records, we conducted tree-based and genetic distance analyses along with BIN-based and species delimitation methods. Our results were consistent for both markers, and we identified eight species of paralichthyids among our samples with high confidence. Interestingly, our analyses indicate several cases where public records assigned to the same species might be sequences from multiple species. Therefore, we provide new records and occurrences and explore important issues regarding misidentification and putative cryptic diversity for several species.},
}
@article {pmid39588656,
year = {2024},
author = {Jiang, Y and Wang, Y and Luo, W and Luan, X and Zhang, Z and Pan, Y and He, B and Gao, Y and Song, Y},
title = {Detecting telomerase activity at the single-cell level using a CRISPR-Cas12a-based chip.},
journal = {Lab on a chip},
volume = {25},
number = {1},
pages = {49-56},
doi = {10.1039/d4lc00619d},
pmid = {39588656},
issn = {1473-0189},
mesh = {*Telomerase/metabolism ; *CRISPR-Cas Systems ; Humans ; *Single-Cell Analysis/instrumentation ; Lab-On-A-Chip Devices ; Bacterial Proteins ; Endodeoxyribonucleases ; CRISPR-Associated Proteins ; },
abstract = {The intimate association between telomerase activity and cancer has driven the exploration of diverse methodologies for its precise detection. However, detecting telomerase activity at the single-cell level remains a significant challenge. Herein, we present a MOF-DNA barcode-amplified CRISPR-Cas12a strategy integrated with a single-cell microfluidic chip for ultrasensitive detection of telomerase activity. DNA-functionalized UiO-66 nanoparticles act as signal transducers, effectively converting telomerase activity into DNA activation strands, which subsequently trigger the trans-cleavage activity of CRISPR-Cas12a. This amplification-based assay could be integrated with a microfluidic chip to enable highly sensitive detection of telomerase activity at the single-cell level, offering promising advancements in early cancer diagnosis.},
}
@article {pmid39587724,
year = {2024},
author = {Tebaldi, ND and Mota, LCBM and Corrêa, JL and Santos, ACC and Santos, ARD and Ueira-Vieira, C},
title = {First report of Kosakonia cowanii causing bacterial blight on Coffea arabica.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-07-24-1572-PDN},
pmid = {39587724},
issn = {0191-2917},
abstract = {From 2012 to 2019, 6-month to 2-year-old coffee (Coffea arabica) plants showing leaf blight, stem blackening, brownish, necrotic, irregular leaf spots and shoot tip dieback (Figure 1A, B, C, and D) symptoms were observed at the municipalities of Araguari, Indianópolis, Monte Carmelo, Nova Ponte and Romaria, Minas Gerais State, Brazil. Bacterial exudates from infected tissues, mainly from the shoot tip, were observed under microscopy; no bacterial exudates were found in leaf tissues. Bacterial colonies were isolated from symptomatic disinfested tissues (leaves and shoot tip) using medium 523 (Figure 1E). The isolated bacteria were facultative anaerobe, Gram-negative, cream-colored on YDC medium, growth at 37 [o]C, arginine and oxidase negative, catalase and asparagine positive (Schaad et al. 2002), and positive hypersensitivity reaction in tobacco leaves. Pathogenicity was confirmed by spraying coffee plants (at the three-leaf stage) until runoff, with a 1 × 108 CFU/mL bacterial suspension inoculate. The plants were kept in the moist chamber for 24 hours, before and after inoculation under greenhouse conditions. No symptoms were observed under the mock-inoculated plants. Disease symptoms on inoculated plants were observed 13 days after inoculation. The bacteria were then reisolated to satisfy Koch's postulates, the colony phenotypes were identical to the original ones. Bacterial genomic DNA of four isolates (UFU D1, UFU G119, UFU H1, and UFU I87) was extracted, and the 16S rRNA gene region was amplified using the 8F and 1492R universal primers, and then compared with sequences deposited in the GenBank. The results aligned closely with those of Kosakonia cowanii (GenBank NR_025566.1), with 99.4% similarity and 96% query coverage for the sequence. In addition to sequencing the 16S rRNA gene, which is considered the barcode for bacteria, other single-copy genes are necessary for species confirmation. In this study, to confirm the species and generate more data on these new isolates, 150 bp paired-end libraries were constructed and sequenced using DNBSEQ. A minimum of 1 gigabase was obtained for each isolate, and the genomes were assembled using the SPAdes genome assembler v3.15.4. Subsequently, the in-house developed algorithm SpM (Species Matching) was used to identify the species. The phylogenetic tree for the 16S gene was constructed using the maximum likelihood algorithm available in PhyML (v3.1/3.0 aLRT). The Phylogeny.fr platform was used to perform the phylogenetic reconstruction. This analysis revealed that our K. cowanii isolates (H1, D1, G119, and I87) from the coffee tree clustered with other K. cowanii strains isolated from different locations (Figure 2A). The Average Nucleotide Identity (ANI) analysis was performed using the fastANI program on all complete genomes of the Kosakonia genus obtained from the NCBI database. The results indicated that our K. cowanii isolates from the coffee tree clustered closely with other strains of the K. cowanii species (Figure 2B). Genomic analyses confirmed that all isolates belong to the species K. cowanii, corroborating the 16S rRNA gene analyses. The genomes have been deposited in NCBI with the accession numbers CP160410 (K. cowanii strain UFU H1, size 4,749,805 bp and coverage 36.21x), CP160412 (strain UFU G119, size 4,509,735 bp and coverage 31.26x), CP162577 (strain UFU D1, size 4,867,107 bp and coverage 19.0x), and CP162576 (strain UFU I87, size 4,552,151 bp and coverage 18.23x). These results are of great importance for better understanding the role of K. cowanii as a disease-causing pathogen of coffee plants. K. cowanii has already been described infecting Eucalyptus with symptoms of bacterial blight in Uruguay (Brady et al. 2009), causing disease in soybeans (Krawczyk and Borodynko-Filas 2020), also associated as endophytic in plants (Thomas et al. 2007), and as human pathogens (Yang et al. 2018). Thus, to our knowledge, this is the first report of bacterial blight caused by K. cowanii on coffee plants. The isolates are deposited in the phytopathogenic bacteria collection at Instituto de Ciências Agrárias, Universidade Federal de Uberlândia, Brazil, under the codes UFU D1, UFU G119, UFU H1 and UFU I87.},
}
@article {pmid39587617,
year = {2024},
author = {Landman, F and Jamin, C and de Haan, A and Witteveen, S and Bos, J and van der Heide, HGJ and Schouls, LM and Hendrickx, APA and , },
title = {Genomic surveillance of multidrug-resistant organisms based on long-read sequencing.},
journal = {Genome medicine},
volume = {16},
number = {1},
pages = {137},
pmid = {39587617},
issn = {1756-994X},
mesh = {*Drug Resistance, Multiple, Bacterial/genetics ; Humans ; *Genome, Bacterial ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Bacteria/genetics/drug effects/classification ; Whole Genome Sequencing/methods ; },
abstract = {BACKGROUND: Multidrug-resistant organisms (MDRO) pose a significant threat to public health worldwide. The ability to identify antimicrobial resistance determinants, to assess changes in molecular types, and to detect transmission are essential for surveillance and infection prevention of MDRO. Molecular characterization based on long-read sequencing has emerged as a promising alternative to short-read sequencing. The aim of this study was to characterize MDRO for surveillance and transmission studies based on long-read sequencing only.<br><br>METHODS: Genomic DNA of 356 MDRO was automatically extracted using the Maxwell-RSC48. The MDRO included 106 Klebsiella pneumoniae isolates, 85 Escherichia coli, 15 Enterobacter cloacae complex, 10 Citrobacter freundii, 34 Pseudomonas aeruginosa, 16 Acinetobacter baumannii, and 69 methicillin-resistant Staphylococcus aureus (MRSA), of which 24 were from an outbreak. MDRO were sequenced using both short-read (Illumina NextSeq 550) and long-read (Nanopore Rapid Barcoding Kit-24-V14, R10.4.1) whole-genome sequencing (WGS). Basecalling was performed for two distinct models using Dorado-0.3.2 duplex mode. Long-read data was assembled using Flye, Canu, Miniasm, Unicycler, Necat, Raven, and Redbean assemblers. Long-read WGS data with&#x2009;>&#x2009;40&#x2009;&#xd7;&#x2009;coverage was used for multi-locus sequence typing (MLST), whole-genome MLST (wgMLST), whole-genome single-nucleotide polymorphisms (wgSNP), in silico multiple locus variable-number of tandem repeat analysis (iMLVA) for MRSA, and identification of resistance genes (ABRicate).<br><br>RESULTS: Comparison of wgMLST profiles based on long-read and short-read WGS data revealed&#x2009;>&#x2009;95% of wgMLST profiles within the species-specific cluster cut-off, except for P. aeruginosa. The wgMLST profiles obtained by long-read and short-read WGS differed only one to nine wgMLST alleles or SNPs for K. pneumoniae, E. coli, E. cloacae complex, C. freundii, A. baumannii complex, and MRSA. For P. aeruginosa, differences were up to 27 wgMLST alleles between long-read and short-read wgMLST and 0-10 SNPs. MLST sequence types and iMLVA types were concordant between long-read and short-read WGS data and conventional MLVA typing. Antimicrobial resistance genes were detected in long-read sequencing data with high sensitivity/specificity (92-100%/99-100%). Long-read sequencing enabled analysis of an MRSA outbreak.<br><br>CONCLUSIONS: We demonstrate that molecular characterization of automatically extracted DNA followed by long-read sequencing is as accurate compared to short-read sequencing and suitable for typing and outbreak analysis as part of genomic surveillance of MDRO. However, the analysis of P. aeruginosa requires further improvement which may be obtained by other basecalling algorithms. The low implementation costs and rapid library preparation for long-read sequencing of MDRO extends its applicability to resource-constrained settings and low-income countries worldwide.},
}
@article {pmid39587359,
year = {2024},
author = {Ramani, V},
title = {Split-pool barcoding serves up an epigenomic smorgasbord.},
journal = {Nature genetics},
volume = {56},
number = {12},
pages = {2596-2597},
pmid = {39587359},
issn = {1546-1718},
support = {DP2-HG012442//U.S. Department of Health &amp; Human Services | NIH | NIH Office of the Director (OD)/ ; },
}
@article {pmid39585955,
year = {2024},
author = {Osborne, M and Chen, H and Kadhiresan, P and Mahbub, N and Malekjahani, A and Kozlowski, HN and Udugama, B and Nguyen, LNM and Perusini, S and Mubareka, S and Chan, WCW},
title = {QBox: An Automated Portable System for Multiplex Quantum Dot Barcode Diagnostics.},
journal = {ACS nano},
volume = {18},
number = {49},
pages = {33629-33642},
doi = {10.1021/acsnano.4c12306},
pmid = {39585955},
issn = {1936-086X},
mesh = {*Quantum Dots/chemistry ; Humans ; *COVID-19/diagnosis/virology ; *SARS-CoV-2/isolation &amp; purification/genetics ; Point-of-Care Systems ; Automation ; },
abstract = {The COVID-19 pandemic accelerated the development of automated systems for detecting molecular targets for the point-of-care. However, these systems have limited multiplexing capabilities because of the need to alter their hardware to accommodate additional targets and probes. Quantum dot barcodes address this multiplexing obstacle, but their assays have multiple steps that rely on extensive training and laboratory equipment. Here, we built a portable cartridge-and-instrument system that automates the extraction, reverse transcription, amplification, and detection steps of a quantum dot barcode assay. This entire workflow can be completed in 40 minutes. We clinically validated the system with SARS-CoV-2 patient samples (n = 50, 92% sensitivity, 100% specificity). We then demonstrated multiplexing with 4-barcode respiratory and 5-barcode bloodborne pathogen panels. Our portable system opens quantum dot barcodes for broad use in rapid multiplexed detection of infectious pathogens with the potential for detecting cancer and other genetic diseases.},
}
@article {pmid39585918,
year = {2024},
author = {Ambu, J and Dufresnes, C},
title = {Genomic and bioacoustic variation in a midwife toad hybrid zone: A role for reinforcement?.},
journal = {PloS one},
volume = {19},
number = {11},
pages = {e0314477},
pmid = {39585918},
issn = {1932-6203},
mesh = {Animals ; *Anura/genetics/physiology ; *Hybridization, Genetic ; Reproductive Isolation ; Vocalization, Animal/physiology ; Polymorphism, Single Nucleotide ; Genomics/methods ; Gene Flow ; France ; },
abstract = {Hybrid zones, i.e., geographic areas where diverging lineages meet, hybridize and eventually mix their genomes, offer opportunities to understand the mechanisms behind reproductive isolation and speciation. Hybrid zones are particularly well suited to study reinforcement, i.e., the process by which selection against hybridization increases reproductive barriers, which, in anuran amphibians, is typically expressed by increased divergence in advertisement calls-the main cue to assortative mating-in parapatric ranges. Using mitochondrial barcoding (16S sequences), population genomics (thousands of SNPs) and bioacoustic analyses (four call parameters), we examine the hybrid zone between two incipient species of midwife toads (Alytes obstetricans and A. almogavarii) in southern France, with the purposes of locating their transition, measuring genetic introgression, and documenting potential signatures of reinforcement. We map range boundaries in the Eastern Pyrenees and the southwestern foothills of the Massif Central, namely along the Ariège valley and the Montagne Noire area. Similarly to another transition between these species in Spain, we found the hybrid zone to be narrow, involving geographically restricted gene flow (~20 km wide allele frequency clines) and barrier loci (i.e., loci resisting introgression), both suggestive of partial post-zygotic isolation (hybrid incompatibilities). The calls of the species overlap less inside than outside the hybrid zone, due to a reduction of their standing variation rather than a shift towards distinctive variants. While neutral causes cannot be excluded, this pattern follows the general expectations of reinforcement, yet without reproductive character displacement. Our study highlights the potential of amphibian hybrid zones to assess the genetic and behavioral drivers of reproductive isolation in statu nascendi and under various evolutionary contexts.},
}
@article {pmid39582226,
year = {2024},
author = {Wu, X and Zhao, Z and Yu, W and Liu, S and Zhou, M and Jiang, N and Du, X and Yang, X and Chen, J and Guo, H and Yang, R},
title = {Single-Cell Multiomics Identifies Glycan Epitope LacNAc as a Potential Cell-Surface Effector Marker of Peripheral T Cells in Bladder Cancer Patients.},
journal = {ACS chemical biology},
volume = {19},
number = {12},
pages = {2535-2547},
pmid = {39582226},
issn = {1554-8937},
mesh = {Humans ; *Urinary Bladder Neoplasms/immunology/pathology ; *Polysaccharides/chemistry ; *T-Lymphocytes/immunology/metabolism ; *Single-Cell Analysis/methods ; Biomarkers, Tumor/immunology/blood/metabolism ; Epitopes/immunology/chemistry ; Receptors, Antigen, T-Cell/immunology/metabolism ; Glycosylation ; Multiomics ; },
abstract = {Cancer is a systemic disease continuously monitored and responded to by the human global immune system. Peripheral blood immune cells, integral to this surveillance, exhibit variable phenotypes during tumor progression. Glycosylation, as one of the most prevalent and significant post-translational modifications of proteins, plays a crucial role in immune system recognition and response. Glycan analysis has become a key method for biomarker discovery. LacNAc, a prominent glycosylation modification, regulates immune cell activity and function. Therefore, we applied our previously developed single-cell glycomic multiomics to analyze peripheral blood in cancer patients. This platform utilizes chemoenzymatic labeling with DNA barcodes for detecting and quantifying LacNAc levels at single-cell resolution without altering the transcriptional status of immune cells. For the first time, we systematically integrated single-cell transcriptome, T cell receptor (TCR) repertoire, and glycan epitope LacNAc analyses in tumor-patient-derived peripheral blood. Our integrated analysis reveals that lower-stage bladder cancer patients showed significantly higher levels of LacNAc in peripheral T cells, and peripheral T cells with high levels of cell-surface LacNAc exhibit higher cytotoxicity and TCR clonal expansion. In summary, we identified LacNAc as a potential cell-surface effector marker for peripheral T cells in bladder cancer patients, which enhances our understanding of peripheral immune cells and offers potential advancements in liquid biopsy.},
}
@article {pmid39582135,
year = {2024},
author = {Seo, Y and Fowler, K and Flick, LM and Withers, TA and Savoldo, B and McKinnon, K and Iannone, MA},
title = {Barcoding of viable peripheral blood mononuclear cells with selenium and tellurium isotopes for mass cytometry experiments.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {105},
number = {12},
pages = {899-908},
doi = {10.1002/cyto.a.24907},
pmid = {39582135},
issn = {1552-4930},
support = {//University Cancer Research Fund (UCRF)/ ; //UNC Cancer Center Core Support Grant #P30CA016086/ ; },
mesh = {Humans ; *Tellurium/chemistry ; *Leukocytes, Mononuclear/cytology/drug effects/metabolism ; *Flow Cytometry/methods ; *Selenium/chemistry/pharmacology ; Isotopes ; Staining and Labeling/methods ; Isotope Labeling/methods ; Cell Survival/drug effects ; },
abstract = {Barcoding viable cells combined with pooled sample staining is an effective technique that eliminates batch effects from serial cell staining and facilitates uninterrupted data acquisition. We describe three novel and isotopically pure selenium-containing compounds (SeMals) that are useful cellular labeling tools. The maleimide-functionalized selenophenes ([76]SeMal, [77]SeMal, and [78]SeMal) covalently react with cellular sulfhydryl groups and uniquely label cell samples. The SeMal reagents label viable and paraformaldehyde-fixed peripheral blood mononuclear cells (PBMC), are well resolved by the mass cytometer, and have little spill into adjacent channels. They appear non-toxic to viable cells at working concentrations. We used SeMal reagents in combination with four isotopically pure tellurium maleimide reagents ([124]TeMal, [126]TeMal, [128]TeMal, and [130]TeMal) to label 21 individual PBMC samples with unique combinations of selenium and tellurium isotopes (seven donors with three replicates using a 7 isotope pick 2 combinatorial schema). The individually barcoded samples were pooled, stained with an antibody cocktail as a pool, and acquired on the mass cytometer as a single suspension. The single-cell data were de-barcoded into separate sample-specific files after data acquisition, enabling an uninterrupted instrument run. Each donor sample retained its unique phenotypic profile with excellent replicate reproducibility. Unlike current live cell barcoding methods, this approach does not require antibodies to surface markers, allowing for the labeling of all cells regardless of surface antigen expression. Additionally, since selenium and tellurium isotopes are not currently utilized in CyTOF antibody panels, this method expands barcoding options and frees up commonly used isotopes for more detailed cell profiling.},
}
@article {pmid39581345,
year = {2025},
author = {Parmar, DR and Johnston, NP and Wallman, JF and Szpila, K},
title = {Blowfly genomics: current insights, knowledge gaps, and future perspectives.},
journal = {Current opinion in insect science},
volume = {68},
number = {},
pages = {101305},
doi = {10.1016/j.cois.2024.101305},
pmid = {39581345},
issn = {2214-5753},
mesh = {Animals ; *Genome, Insect ; *Genomics ; *Calliphoridae/genetics ; Phylogeny ; DNA Barcoding, Taxonomic ; Genome, Mitochondrial ; },
abstract = {Blowflies (Calliphoridae) form a diverse, species-rich group, yet publicly available genome assemblies are limited to only 16 species, despite recent genomic advances. This knowledge gap extends to mitogenomes and barcode databases, which mainly focus on medically and veterinary-important species. While blowfly phylogenetics has progressed, additional genome sequencing is crucial for various subfamilies, given their diverse life histories. This review presents a quantitative overview of available genetic information for blowflies, highlighting substantial gaps in public databases. DNA barcodes, mitogenomes, and genomes represent only 16.5% (342 species), ∼3% (53 species), and <1% (16 species) of known family diversity, respectively. While 183 genomics-related calliphorid BioProjects are recorded by NCBI, many subfamilies and genera have limited or no genomic representation, impacting studies on identification, systematics, phylogenetics, and evolution. We stress the urgent need for high-quality reference genomes and highlight target species representing all blowfly subfamilies to support a new era of rapid, low-cost genomic research.},
}
@article {pmid39579652,
year = {2025},
author = {Bates, SA and Budowle, B and Baker, L and Mittelman, K and Mittelman, D},
title = {A molecular framework for enhancing quality control and sample integrity in forensic genome sequencing.},
journal = {Forensic science international. Genetics},
volume = {75},
number = {},
pages = {103179},
doi = {10.1016/j.fsigen.2024.103179},
pmid = {39579652},
issn = {1878-0326},
mesh = {Humans ; *Quality Control ; *DNA Fingerprinting ; *Forensic Genetics/methods/standards ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; Genome, Human ; Oligonucleotides/genetics ; },
abstract = {DNA typing is essential for identifying crime scene evidence and missing and unknown persons. Molecular tags historically have been incorporated into DNA typing reactions to improve result interpretation. Molecular tags like barcodes and unique identifiers are integral to MPS, aiding in sample tracking and error detection. However, these tags do not fully leverage sequence variation to enhance quality control. To address this need, molecular etches, which are synthetic oligonucleotides that serve as an internal molecular information management system, are introduced. Molecular etches encode detailed sample information improving sample workflow history, tracking, contamination detection, and authenticity verification. Validation studies demonstrate the robustness of molecular etches in genomic sequencing, making them a valuable quality tool for forensic DNA analysis.},
}
@article {pmid39578906,
year = {2024},
author = {Schack, AK and Garrido-Navas, MC and Galevski, D and Madjarov, G and Krych, L},
title = {SCAN: a nanopore-based, cost effective decision-supporting tool for mass screening of aneuploidies.},
journal = {Human genomics},
volume = {18},
number = {1},
pages = {131},
pmid = {39578906},
issn = {1479-7364},
mesh = {Humans ; *Aneuploidy ; Cost-Benefit Analysis ; Infant, Newborn ; Klinefelter Syndrome/genetics/diagnosis ; Genetic Testing/economics/methods ; Nanopore Sequencing/methods ; Neonatal Screening/economics/methods ; Nanopores ; Mass Screening/economics/methods ; Machine Learning ; },
abstract = {In developed countries, Newborn Screening (NBS) programs aim to detect treatable yet clinically silent disorders. The selection of disorders to be included in NBS considers severity, treatment availability, prevalence, and analysis cost. However, numerous genetic disorders remain excluded from routine testing due to high expenses and specialized equipment requirements. Here we present SCAN, a novel, non-invasive, and cost-effective decision-support tool utilizing nanopore sequencing for estimating proportions of chromosomes responsible for the most common aneuploidies. SCAN combines DNA enrichment (amplification), barcoding, nanopore sequencing, and machine learning predictive modeling. In a proof-of-concept study for Klinefelter Syndrome, SCAN achieved 100% sensitivity, specificity, and accuracy, becoming the world's first IVD-certified genetic test utilising nanopore sequencing. Further model training shows promise in expanding this assay to detect other chromosomal aneuploidies included in the protocol.},
}
@article {pmid39577343,
year = {2025},
author = {Sanhueza, MI and Montes, CS and Sanhueza, I and Montoya-Gallardo, NI and Escalona, F and Luarte, D and Escribano, R and Torres, S and Godoy, SE and Amigo, JM and Castillo, RDP and Urbina, M},
title = {VIS-NIR hyperspectral imaging and multivariate analysis for direct characterization of pelagic fish species.},
journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy},
volume = {328},
number = {},
pages = {125451},
doi = {10.1016/j.saa.2024.125451},
pmid = {39577343},
issn = {1873-3557},
mesh = {Animals ; *Fishes/classification ; *Spectroscopy, Near-Infrared/methods ; Multivariate Analysis ; *Hyperspectral Imaging/methods ; *Principal Component Analysis ; Discriminant Analysis ; Least-Squares Analysis ; Support Vector Machine ; },
abstract = {The identification of fish species and their physical and chemical characterization play a crucial role in the fishing industry, fish-food research and the management of marine resources. Traditional methods for species identification, such as expert observation, DNA barcoding and meta-barcoding, though effective, require labor-intensive laboratory work. Consequently, there is a pressing need for more objective and efficient methodologies for accurate fish species identification and characterization. This study proposes the use of multivariate analysis and visible-near infrared hyperspectral imaging (HSI) for a rapid characterization of fish, including the evaluation of specific morphological regions of interest (ROIs) in fish images or intrasample spectral variability, species differentiation, and freshness assessment. The study involves three pelagic species: sardine (Strangomera bentincki), silverside (Odontesthes regia) and anchovy (Engraulis ringens). Principal component analysis (PCA), support vector machine regression (SVM-R), partial least squares regression (PLS-R), and partial least squares discriminant analysis (PLS-DA) were applied as multivariate techniques for these purposes. Comparative studies of morphological ROIs revealed significant differences between the spectral characteristics of various fish zones. A decrease in reflectance intensity due to freshness loss was detected, and the prediction of this freshness, quantified as "time after capture," was achievable using SVM-R, with a 9% relative error of prediction. Overall, VIS-NIR HSI, supported by multivariate analysis, enables differentiation between the studied species, highlighting its potential as a robust fish species identification and characterization tool.},
}
@article {pmid39575683,
year = {2024},
author = {Siniscalco, AM and Perera, RP and Greenslade, JE and Veeravenkatasubramanian, H and Masters, A and Doll, HM and Raj, B},
title = {Barcoding Notch signaling in the developing brain.},
journal = {Development (Cambridge, England)},
volume = {151},
number = {24},
pages = {},
pmid = {39575683},
issn = {1477-9129},
support = {R00 HD098298/HD/NICHD NIH HHS/United States ; DGE-2236662//National Science Foundation/ ; //University of Pennsylvania/ ; DP2 NS131787/NS/NINDS NIH HHS/United States ; R00HD098298/NH/NIH HHS/United States ; },
mesh = {Animals ; *Zebrafish/genetics/embryology/metabolism ; *Brain/metabolism/embryology/growth &amp; development ; *Signal Transduction/genetics ; *Receptors, Notch/metabolism/genetics ; *Zebrafish Proteins/genetics/metabolism ; CRISPR-Cas Systems/genetics ; Neurons/metabolism/cytology ; Gene Expression Regulation, Developmental ; Single-Cell Analysis ; },
abstract = {Developmental signaling inputs are fundamental for shaping cell fates and behavior. However, traditional fluorescent-based signaling reporters have limitations in scalability and molecular resolution of cell types. We present SABER-seq, a CRISPR-Cas molecular recorder that stores transient developmental signaling cues as permanent mutations in cellular genomes for deconstruction at later stages via single-cell transcriptomics. We applied SABER-seq to record Notch signaling in developing zebrafish brains. SABER-seq has two components: a signaling sensor and a barcode recorder. The sensor activates Cas9 in a Notch-dependent manner with inducible control, while the recorder obtains mutations in ancestral cells where Notch is active. We combine SABER-seq with an expanded juvenile brain atlas to identify cell types derived from Notch-active founders. Our data reveal rare examples where differential Notch activities in ancestral progenitors are detected in terminally differentiated neuronal subtypes. SABER-seq is a novel platform for rapid, scalable and high-resolution mapping of signaling activity during development.},
}
@article {pmid39574722,
year = {2024},
author = {Leitner, DR and Zingl, FG and Morano, AA and Zhang, H and Waldor, MK},
title = {The Mla pathway promotes Vibrio cholerae re-expansion from stationary phase.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39574722},
issn = {2692-8205},
support = {R01 AI042347/AI/NIAID NIH HHS/United States ; R37 AI042347/AI/NIAID NIH HHS/United States ; },
abstract = {Bacteria have evolved diverse strategies to ensure survival under nutrient-limited conditions, where rapid energy generation is not achievable. Here, we performed a transposon insertion site sequencing loss-of-function screen to identify Vibrio cholerae genes that promote the pathogen's fitness in stationary phase. We discovered that the Mla (maintenance of lipid asymmetry) pathway, which is crucial for transferring phospholipids from the outer to the inner membrane, is critical for stationary phase fitness. Competition experiments with barcoded and fluorophore labeled wild-type and mlaE mutant V. cholerae revealed that the Mla pathway promotes re-expansion from 48h stationary phase cultures. The mutant's defect in transitioning out of stationary phase into active growth (culturability) was also observed in monocultures at 48h. However, by 96h the culturability of the mutant and wild-type strains were equivalent. By monitoring the abundances of genomically barcoded libraries of wild-type and ∆mlaE strains, we observed that a few barcodes dominated the mutant culture at 96h, suggesting that the similarity of the population sizes at this time was caused by expansion of a subpopulation containing a mutation that suppressed the mlaE mutant's defect. Whole genome sequencing revealed that mlaE suppressors inactivated flagellar biosynthesis. Additional mechanistic studies support the idea that the Mla pathway is critical for the maintenance of V. cholerae's culturability as it promotes energy homeostasis, likely due to its role in regulating outer membrane vesicle shedding. Together our findings provide insights into the cellular processes that control re-expansion from stationary phase and demonstrate a previously undiscovered role for the Mla pathway.},
}
@article {pmid39574588,
year = {2024},
author = {Stevenson, ZC and Laufer, E and Estevez, AO and Robinson, K and Phillips, PC},
title = {Precise Lineage Tracking Using Molecular Barcodes Demonstrates Fitness Trade-offs for Ivermectin Resistance in Nematodes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39574588},
issn = {2692-8205},
support = {P40 OD010440/OD/NIH HHS/United States ; R35 GM131838/GM/NIGMS NIH HHS/United States ; T32 GM007413/GM/NIGMS NIH HHS/United States ; U24 AG056052/AG/NIA NIH HHS/United States ; },
abstract = {A fundamental tenet of evolutionary genetics is that the direction and strength of selection on individual loci varies with the environment. Barcoded evolutionary lineage tracking is a powerful approach for high-throughput measurement of selection within experimental evolution that to date has largely been restricted to studies within microbial systems, largely because the random integration of barcodes within animals is limited by physical and molecular protection of the germline. Here, we use the recently developed TARDIS barcoding system in Caenorhabditis elegans (Stevenson et al., 2023) to implement the first randomly inserted genomic-barcode experimental evolution animal model and use this system to precisely measure the influence of the concentration of the anthelmintic compound ivermectin on the strength of selection on an ivermectin resistance cassette. The combination of the trio of knockouts in neuronally expressed GluCl channels, avr-14, avr-15, and glc-1, has been previously demonstrated to provide resistance to ivermectin at high concentrations. Varying the concentration of ivermectin in liquid culture allows the strength of selection on these genes to be precisely controlled within populations of millions of individuals, yielding the largest animal experimental evolution study to date. The frequency of each barcode was determined at multiple time points via sequencing at deep coverage and then used to estimate the fitness of the individual lineages in the population. The mutations display a high cost to resistance at low concentrations, rapidly losing out to wildtype genotypes, but the balance tips in their favor when the ivermectin concentration exceeds 2nM. This trade-off in resistance is likely generated by a hindered rate of development in resistant individuals. Our results demonstrate that C. elegans can be used to generate high precision estimates of fitness using a high-throughput barcoding approach to yield novel insights into evolutionarily and economically important traits.},
}
@article {pmid39572229,
year = {2024},
author = {Zhang, X and Huang, Y and Yang, Y and Wang, QE and Li, L},
title = {Advancements in prospective single-cell lineage barcoding and their applications in research.},
journal = {Genome research},
volume = {34},
number = {12},
pages = {2147-2162},
pmid = {39572229},
issn = {1549-5469},
mesh = {*Cell Lineage/genetics ; *Single-Cell Analysis/methods ; Humans ; *DNA Barcoding, Taxonomic/methods ; Animals ; Neoplasms/genetics ; },
abstract = {Single-cell lineage tracing (scLT) has emerged as a powerful tool, providing unparalleled resolution to investigate cellular dynamics, fate determination, and the underlying molecular mechanisms. This review thoroughly examines the latest prospective lineage DNA barcode tracing technologies. It further highlights pivotal studies that leverage single-cell lentiviral integration barcoding technology to unravel the dynamic nature of cell lineages in both developmental biology and cancer research. Additionally, the review navigates through critical considerations for successful experimental design in lineage tracing and addresses challenges inherent in this field, including technical limitations, complexities in data analysis, and the imperative for standardization. It also outlines current gaps in knowledge and suggests future research directions, contributing to the ongoing advancement of scLT studies.},
}
@article {pmid39570762,
year = {2024},
author = {Wang, YC and Koster, J and Rooney-Latham, S and Blomquist, CL and Belisle, WH and Bourret, T},
title = {First report of Phytophthora taxon × salinaslettuce (Subclade 8b hybrid) causing stem and basal rot in lettuce in North America.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-10-24-2155-PDN},
pmid = {39570762},
issn = {0191-2917},
abstract = {More than 55% of U.S. lettuce (Lactuca sativa L.) production is in California, with Monterey Co. being the largest producer. Stunted mature romaine 'Valencia' and 'Stomper' and iceberg 'Frazier' lettuces with wilted outer leaves were collected from five commercial fields in Monterey Co. in spring 2023 and 2024. Brown internal stem and crown lesions progressed into sunken cavities and plant collapse. Incidence was approximately 5 to 75%. Margins of discolored stem and crown tissue were surface sterilized and plated on PARP-CMA (Jeffers and Martin 1986) and colonies resembling Phytophthora were recovered. Papillate sporangia ranged from 42 to 67.5 × 25 to 45 μm (avg. 56.1 × 37.0 μm, n = 30) and a length/breadth ratio of 1.4 to 1.7 (avg. 1.5). Globose, intercalary or terminal chlamydospores, 20 to 45 µm in diameter (avg. 32.6 µm, n = 30), and oospores, 17 to 29 μm in diameter (avg. 23.9 μm, n = 30) formed on 10 to 12-day-old cultures. Sequences from the two primary barcodes, ITS and COI (Robideau et al. 2011) were obtained from isolates collected from five different host cultivars and locations, finding identical multi-locus genotypes. ITS chromatograms contained six double-peaks, indicating interspecific hybridization. COI found the lettuce isolates forming a clade with the provisional P. taxon castitis, in Subclade 8b where hybrids are common (Bertier et al. 2013). If P. taxon castitis ITS is used as one parental ITS haplotype, the other haplotype is 1 bp different from P. lactucae and P. pseudolactucae ITS, suggesting one is the other parent of this hybrid taxon, provisionally introduced here as P. taxon ×salinaslettuce with accessions PQ427275-9 (ITS), and PQ424946-50 (COI). Pathogenicity assays were conducted on lettuce cultivars 'Bondi', 'El Guapo', and 'Valencia' (seven-week-old; 473-ml pots; 5 pots each for 'Bondi' and 'El Guapo', and 2 pots for 'Valencia'). Phytophthora inoculum of isolate 5411 was prepared as described in Hao et al. (2019) with oat seed replaced with long grain rice. Ten milliliter inoculum was added into two 6-cm-deep holes on opposite sides of the main stem. A non-colonized mixture was added to an equal number of control plants. All plants were maintained in a growth chamber with a 12-h photoperiod at 20°C/18°C. After one week, 'Bondi' and 'El Guapo' inoculated plants were stunted, and after two weeks, older leaves were chlorotic and wilted. After three weeks, 80% of the plants collapsed. Dark brown internal lesions were seen along the stem, crown, and tap roots of the collapsed plants after four weeks. 'Valencia' inoculated plants were stunted with no internal tissue discoloration observed over the same period. No symptoms were observed on any control plants; P. taxon ×salinaslettuce was reisolated and confirmed via ITS sequence from symptomatic stems, crowns, and tap roots of 'Bondi' and 'El Guapo', as well as non-symptomatic feeder roots of all three cultivars. No Phytophthora was recovered from the controls. This is the first report of P. taxon ×salinaslettuce detection on lettuce; P. taxon castitis has been isolated from strawberry and carrot in Sweden and Canada (Bertier et al. 2013), while P. lactucae and P. pseudolactucae have only been reported on lettuce in Greece and Japan (Elena et al. 2006; Rahman et al. 2015). Plans are underway to confirm the hybrid status and parentage of P. taxon ×salinaslettuce using genomics. This emerging pathogen may cause severe economic losses in CA lettuce production during the winter and spring growing seasons.},
}
@article {pmid39570496,
year = {2024},
author = {Dilrukshi, HAC and Ruklani, NCS and Rubasinghe, SCK},
title = {Cryptogams as bio-indicators for ecosystem monitoring in Sri Lanka: a comprehensive review and recommendations.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {12},
pages = {1231},
pmid = {39570496},
issn = {1573-2959},
support = {22-101//National Research Council/ ; 22-101//National Research Council/ ; 22-101//National Research Council/ ; },
mesh = {Sri Lanka ; *Environmental Monitoring/methods ; *Ecosystem ; *Fungi ; *Biodiversity ; Lichens ; Climate Change ; Bryophyta ; },
abstract = {Cryptogams, encompassing algae, fungi, lichens, bryophytes, and pteridophytes play essential roles in soil formation, nutrient cycling, and ecological stability. Sri Lanka faces numerous environmental challenges, including habitat loss, climate change, and pollution and there is an urgent need for effective monitoring programs to assess and mitigate these changes. This comprehensive review compiles existing literature on the importance of cryptogams and their responses to various environmental stressors and highlights the specific characteristics that make cryptogams valuable bio-indicators, such as their sensitivity to pollution, climate change, and land-use changes in habitats such as forests, agricultural lands, and urban areas, as well as their ability to accumulate and retain pollutants over time. The diversity of cryptogams is integral to their effectiveness as bio-indicators, providing a comprehensive picture of ecosystem health. Furthermore, recommendations for the development of monitoring programs are provided for different areas in the country. These recommendations include establishing baseline data for cryptogam diversity and abundance and incorporating the integration of modern molecular techniques such as DNA barcoding which are widely used in biodiversity monitoring programs to track the responses of cryptogams to environmental changes. This review seeks to emphasize the importance of cryptogams in ecosystem health assessment raising awareness among policymakers, researchers, and conservationists in Sri Lanka. Through the implementation of effective monitoring programs, we can enhance our understanding of local ecosystem dynamics, improve conservation efforts, and contribute to the sustainable management of Sri Lanka's natural resources in the face of ongoing environmental changes.},
}
@article {pmid39570169,
year = {2024},
author = {Oliveira, RCG and Silva, JLN and Silva, ACC and Sousa, PRS and Almeida, MS and Nascimento, MHS and Rodrigues-Filho, LFS and Barros, MC and Fraga, EC},
title = {DNA barcode reveals a new lineage of Astyanax bimaculatus (Linnaeus 1758) in the basins of the Western Northeast Atlantic Region, Brazil.},
journal = {Anais da Academia Brasileira de Ciencias},
volume = {96},
number = {4},
pages = {e20240161},
doi = {10.1590/0001-3765202420240161},
pmid = {39570169},
issn = {1678-2690},
mesh = {Animals ; Brazil ; *DNA Barcoding, Taxonomic ; *Genetic Variation/genetics ; *Characidae/genetics/classification ; *Haplotypes/genetics ; Phylogeny ; Bayes Theorem ; DNA, Mitochondrial/genetics ; },
abstract = {Astyanax bimaculatus are small characids known as piabas or lambaris that form a complex encompassing 18 species, including cryptic species. The present study aimed to use DNA barcode to analyze populations of A. bimaculatus found in Maranhão hydrographic basins, comparing molecular diversity indices between populations from the other Brazilian basins. The results revealed the formation of 32 haplotypes (h = 0.9289; π = 0.0523). Seven haplogroups were formed with intrapopulation genetic distance ranging from 0 to 2%. The Maranhão populations of the Western Northeast Atlantic Region basins separated from the other analyzed basins, corroborating with the groups generated in BAPS and with the Bayesian Inference tree. The occurrence of exclusive OTUs for the Maranhão populations of the Western Northeast Atlantic Region was confirmed through delimitation models. Thus, the data from this study provide information on the genetic diversity of the A. bimaculatus complex with the detection of a different lineage for the State of Maranhão, contributing to the understanding of the group's systematics.},
}
@article {pmid39568955,
year = {2024},
author = {Park, J and Yagi, S and Kobayashi, S and Hirowatari, T},
title = {A new species of the genus Dryadaula Meyrick (Lepidoptera, Dryadaulidae) from Japan, with a redescription of D.epischista (Meyrick, 1936).},
journal = {ZooKeys},
volume = {1217},
number = {},
pages = {327-342},
pmid = {39568955},
issn = {1313-2989},
abstract = {Dryadaulaepischista (Meyrick, 1936), initially described from a single male specimen in Japan, is herein redescribed based on newly collected specimens from the type locality. Furthermore, we describe Dryadaulaorientalis Park &amp; Yagi, sp. nov., a new species from Japan that closely resembles D.epischista. The adults and genitalia of the two species are illustrated. The genitalia of D.epischista from a specimen collected at the type locality are shown for the first time. DNA barcodes of the two Dryadaula species and the genetic distances of barcode regions among them and other congeners are provided.},
}
@article {pmid39567484,
year = {2024},
author = {Zhang, P and Tian, Z and Jin, K and Yang, K and Collyer, W and Rufo, J and Upreti, N and Dong, X and Lee, LP and Huang, TJ},
title = {Automating life science labs at the single-cell level through precise ultrasonic liquid sample ejection: PULSE.},
journal = {Microsystems &amp; nanoengineering},
volume = {10},
number = {1},
pages = {172},
pmid = {39567484},
issn = {2055-7434},
support = {UH3TR002978//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; UH3 TR002978/TR/NCATS NIH HHS/United States ; R01 GM141055/GM/NIGMS NIH HHS/United States ; R44 AG063643/AG/NIA NIH HHS/United States ; R01HD103727//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01GM141055//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R44 HL140800/HL/NHLBI NIH HHS/United States ; R44 OD024963/OD/NIH HHS/United States ; R01 HD103727/HD/NICHD NIH HHS/United States ; },
abstract = {Laboratory automation technologies have revolutionized biomedical research. However, the availability of automation solutions at the single-cell level remains scarce, primarily owing to the inherent challenges of handling cells with such small dimensions in a precise, biocompatible manner. Here, we present a single-cell-level laboratory automation solution that configures various experiments onto standardized, microscale test-tube matrices via our precise ultrasonic liquid sample ejection technology, known as PULSE. PULSE enables the transformation of titer plates into microdroplet arrays by printing nanodrops and single cells acoustically in a programmable, scalable, and biocompatible manner. Unlike pipetting robots, PULSE enables researchers to conduct biological experiments using single cells as anchoring points (e.g., 1 cell vs. 1000 cells per "tube"), achieving higher resolution and potentially more relevant data for modeling and downstream analyses. We demonstrate the ability of PULSE to perform biofabrication, precision gating, and deterministic array barcoding via preallocated droplet-addressable primers. Single cells can be gently printed at a speed range of 5-20 cell⋅s[-1] with an accuracy of 90.5-97.7%, which can then adhere to the substrate and grow for up to 72 h while preserving cell integrity. In the deterministic barcoding experiment, 95.6% barcoding accuracy and 2.7% barcode hopping were observed by comparing the phenotypic data with known genotypic data from two types of single cells. Our PULSE platform allows for precise and dynamic analyses by automating experiments at the single-cell level, offering researchers a powerful tool in biomedical research.},
}
@article {pmid39565827,
year = {2024},
author = {Nazari, V and Yen, SH and Hsu, YF and Shapoval, G and Shapoval, N and Todisco, V},
title = {Wiped out by an earthquake? The 'extinct' Taiwanese swallowtail butterfly (Lepidoptera, Papilionidae) was morphologically and genetically distinct.},
journal = {PloS one},
volume = {19},
number = {11},
pages = {e0310318},
pmid = {39565827},
issn = {1932-6203},
mesh = {Animals ; *Butterflies/genetics ; Taiwan ; *Earthquakes ; DNA Barcoding, Taxonomic ; Haplotypes ; Phylogeny ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Female ; Male ; },
abstract = {For the first time, we obtained for the first time a COI DNA barcode from museum specimens of the Old World swallowtail butterfly endemic to Taiwan, Papilio machaon ssp. sylvina, that has disappeared since the devastating Jiji earthquake in 1999 that shook Central Taiwan. We demonstrate that this population was not only phenotypically distinct, but also had a unique mitochondrial haplotype among all other Holarctic populations of P. machaon. The life history of P. m. sylvina from rearing experiments carried out in the 1990s is illustrated and discussed.},
}
@article {pmid39563389,
year = {2024},
author = {Jumpato, W and Wannasingha, W and Jaroenchaiwattanachote, C and Mintara, R and Wongpakam, K and Adler, PH and Pramual, P},
title = {Diversity and prevalence of Leucocytozoon in black flies (Diptera: Simuliidae) of Thailand.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {475},
pmid = {39563389},
issn = {1756-3305},
support = {6720001/2567//Mahasarakham University/ ; },
mesh = {Animals ; Thailand/epidemiology ; *Simuliidae/parasitology/classification ; *Haemosporida/isolation &amp; purification/classification/genetics ; Prevalence ; Phylogeny ; Cytochromes b/genetics ; Insect Vectors/parasitology/classification ; Female ; Genetic Variation ; Birds/parasitology ; Bird Diseases/parasitology/epidemiology ; Protozoan Infections, Animal/epidemiology/parasitology ; DNA Barcoding, Taxonomic ; },
abstract = {BACKGROUND: Leucocytozoonosis, a parasitic disease of birds, is caused by haemosporidian protozoan parasites of the genus Leucocytozoon, which infect diverse avian species, including poultry. These parasites are transmitted by several black fly species, but knowledge of the factors determining the diversity and prevalence in these vectors, which is crucial for fully understanding disease epidemiology, is largely unexplored. In this study, we investigated factors associated with the prevalence and diversity of Leucocytozoon species in black flies from Thailand.<br><br>METHODS: Adults of two black fly taxa (Simulium asakoae Takaoka and Davies complex and S. khelangense Takaoka, Srisuka and Saeung) were collected using sweep nets at nine locations in northern and northeastern regions of Thailand. Specimens were identified morphologically and the results corroborated by DNA barcoding. Molecular methods using specific primers for amplification of the mitochondrial cytochrome b (cyt b) gene of Leucocytozoon were used to detect the parasite in black flies. Species and lineages of Leucocytozoon were determined using the MalAvi database of malaria parasites and related haemosporidians in avian hosts. Regression analysis was used to examine relationships between Leucocytozoon diversity and prevalence, black fly abundance and habitat characteristics.<br><br>RESULTS: A total of 11,718 adult black flies were collected, of which 4367 were members of the S. asakoae complex and 7351 were S. khelangense. For molecular detection of Leucocytozoon, we randomly selected 300 individual female black flies of the S. asakoae complex and 850 females of S. khelangense pooled into groups of five individuals (= 170 pools). A total of 34 of the 300 specimens of the S. asakoae complex and 118 of the 170 pools of S. khelangense were positive for Leucocytozoon. Fifty-four lineages (haplotypes) were identified, all of which belonged to those reported in domestic chickens, Gallus gallus, with one exception that was identified in S. khelangense and found to be closely related to the Leucocytozoon lineages reported in owls; this is the first record of the latter lineage in Asian black flies. Among these haplotypes, nine and 45 were exclusively found in the S. asakoae complex and S. khelangense, respectively. No lineage was shared between these black fly taxa. Analysis of similarity (ANOSIM) revealed significant Leucocytozoon lineage composition between the two black flies. Phylogenetic analysis found that Leucocytozoon lineages in the S. asakoae complex and S. khelangense are largely isolated, agreeing with the ANOSIM result. The overall prevalence of Leucocytozoon in the S. asakoae complex was 11.3% and ranged from 9% to 13% in each collection. Leucocytozoon prevalence in S. khelangense was 21%, varying from 13% to 37% in each collection. The Shannon H' index indicated greater Leucocytozoon diversity in S. khelangense (H'&#x2009;=&#x2009;3.044) than in the S. asakoae complex (H'&#x2009;=&#x2009;1.920). Regression analysis revealed that Leucocytozoon diversity was positively related to black fly abundance and negatively related to maximum air temperature.<br><br>CONCLUSIONS: The results of this study show that the prevalence and diversity of Leucocytozoon lineages in the S. asakoae complex and S. khelangense from Thailand were associated with the abundance of these black flies and with air temperature. The Leucocytozoon lineages identified also showed some degree of black fly taxon specificity, possibly related to different abundance peaks of these vectors. The environmental conditions that favor the development of black flies are possibly a driver of Leucocytozoon prevalence, diversity and vector-parasite co-evolution.},
}
@article {pmid39562752,
year = {2025},
author = {Cipurko, D and Ueda, T and Mei, L and Chevrier, N},
title = {Repurposing large-format microarrays for scalable spatial transcriptomics.},
journal = {Nature methods},
volume = {22},
number = {1},
pages = {145-155},
pmid = {39562752},
issn = {1548-7105},
support = {DP2 AI145100/AI/NIAID NIH HHS/United States ; U01 AI160418/AI/NIAID NIH HHS/United States ; U01-AI160418//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; DP2-AI145100//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {Animals ; Mice ; *Gene Expression Profiling/methods ; *Oligonucleotide Array Sequence Analysis/methods ; Humans ; *Transcriptome ; *High-Throughput Nucleotide Sequencing/methods ; RNA, Messenger/genetics ; },
abstract = {Spatiomolecular analyses are key to study tissue functions and malfunctions. However, we lack profiling tools for spatial transcriptomics that are easy to adopt, low cost and scalable in terms of sample size and number. Here, we describe a method, Array-seq, to repurpose classical oligonucleotide microarrays for spatial transcriptomics profiling. We generate Array-seq slides from microarrays carrying custom-design probes that contain common sequences flanking unique barcodes at known coordinates. Then we perform a simple, two-step reaction that produces mRNA capture probes across all spots on the microarray. We demonstrate that Array-seq yields spatial transcriptomes with high detection sensitivity and localization specificity using histological sections from mouse tissues as test systems. Moreover, we show that the large surface area of Array-seq slides yields spatial transcriptomes (i) at high throughput by profiling multi-organ sections, (ii) in three dimensions by processing serial sections from one sample, and (iii) across whole human organs. Thus, by combining classical DNA microarrays and next-generation sequencing, we have created a simple and flexible platform for spatiomolecular studies of small-to-large specimens at scale.},
}
@article {pmid39562573,
year = {2024},
author = {Kunitake, K and Mizuno, T and Hattori, K and Oneyama, C and Kamiya, M and Ota, S and Urano, Y and Kojima, R},
title = {Barcoding of small extracellular vesicles with CRISPR-gRNA enables comprehensive, subpopulation-specific analysis of their biogenesis and release regulators.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9777},
pmid = {39562573},
issn = {2041-1723},
support = {24H00868//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JPMJPR17H5//MEXT | JST | Precursory Research for Embryonic Science and Technology (PRESTO)/ ; CDA-00008/2019-C//Human Frontier Science Program (HFSP)/ ; K05 DA000008/DA/NIDA NIH HHS/United States ; JPMJCR19H1, JPMJCR23B7//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; },
mesh = {*Extracellular Vesicles/metabolism/genetics ; Humans ; *CRISPR-Cas Systems ; *RNA, Guide, CRISPR-Cas Systems/genetics/metabolism ; *Tetraspanin 29/metabolism/genetics ; *Tetraspanin 30/metabolism/genetics ; HEK293 Cells ; Exosomes/metabolism/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; },
abstract = {Small extracellular vesicles (sEVs) are important intercellular information transmitters in various biological contexts, but their release processes remain poorly understood. Herein, we describe a high-throughput assay platform, CRISPR-assisted individually barcoded sEV-based release regulator (CIBER) screening, for identifying key players in sEV release. CIBER screening employs sEVs barcoded with CRISPR-gRNA through the interaction of gRNA and dead Cas9 fused with an sEV marker. Barcode quantification enables the estimation of the sEV amount released from each cell in a massively parallel manner. Barcoding sEVs with different sEV markers in a CRISPR pooled-screening format allows genome-wide exploration of sEV release regulators in a subpopulation-specific manner, successfully identifying previously unknown sEV release regulators and uncovering the exosomal/ectosomal nature of CD63[+]/CD9[+] sEVs, respectively, as well as the synchronization of CD9[+] sEV release with the cell cycle. CIBER should be a valuable tool for detailed studies on the biogenesis, release, and heterogeneity of sEVs.},
}
@article {pmid39559832,
year = {2024},
author = {Grasshoff, M and Kalmer, M and Chatain, N and Kricheldorf, K and Maurer, A and Weiskirchen, R and Koschmieder, S and Costa, IG},
title = {SIngle cell level Genotyping Using scRna Data (SIGURD).},
journal = {Briefings in bioinformatics},
volume = {25},
number = {6},
pages = {},
pmid = {39559832},
issn = {1477-4054},
support = {KO2155/7-1 and 7-2//German Research Foundation/ ; KO 2155/6-1//German Research Foundation/ ; //German Ministry of Education and Science/ ; },
mesh = {*Single-Cell Analysis/methods ; Humans ; Sequence Analysis, RNA/methods ; Genotype ; Genotyping Techniques/methods ; Computational Biology/methods ; Mitochondria/genetics/metabolism ; },
abstract = {MOTIVATION: By accounting for variants within measured transcripts, it is possible to evaluate the status of somatic variants using single-cell RNA-sequencing (scRNA-seq) and to characterize their clonality. However, the sparsity (very few reads per transcript) or bias in protocols (favoring 3' ends of the transcripts) makes the chance of capturing somatic variants very unlikely. This can be overcome by targeted sequencing or the use of mitochondrial variants as natural barcodes for clone identification. Currently, available computational tools focus on genotyping, but do not provide functionality for combined analysis of somatic and mitochondrial variants and functional analysis such as characterization of gene expression changes in detected clones.<br><br>RESULTS: Here, we propose SIGURD (SIngle cell level Genotyping Using scRna Data) (SIGURD), which is an R-based pipeline for the clonal analysis of scRNA-seq data. This allows the quantification of clones by leveraging both somatic and mitochondrial variants. SIGURD also allows for functional analysis after clonal detection: association of clones with cell populations, detection of differentially expressed genes across clones, and association of somatic and mitochondrial variants. Here, we demonstrate the power of SIGURD by analyzing single-cell data of colony-forming cells derived from patients with myeloproliferative neoplasms.},
}
@article {pmid39559559,
year = {2024},
author = {Lu, SC and Lee, YY and Andres, FGM and Moyer, DA and Barry, MA},
title = {FastAd: A versatile toolkit for rapid generation of single adenoviruses or diverse adenoviral vector libraries.},
journal = {Molecular therapy. Methods &amp; clinical development},
volume = {32},
number = {4},
pages = {101356},
pmid = {39559559},
issn = {2329-0501},
abstract = {Adenoviruses (Ads) are potent gene delivery vectors for in vitro and in vivo applications. However, current methods for their construction are time-consuming and inefficient, limiting their rapid production and utility in generating complex genetic libraries. Here, we introduce FastAd, a rapid and easy-to-use technology for inserting recombinant "donor" DNA directly into infectious "receiver" Ads in mammalian cells by the concerted action of two efficient recombinases: Cre and Bxb1. Subsequently, the resulting mixed recombinant Ad population is subjected to negative selections by flippase recombinase to remove viruses that missed the initial recombination. With this approach, recombinant Ad production time is reduced from 2 months to 10 days or less. FastAd can be applied for inserting complex genetic DNA libraries into Ad genomes, as demonstrated by the generation of barcode libraries with over 3 million unique clones from a T25 flask-scale transfection of 3 million cells. Furthermore, we leveraged FastAd to construct an Ad library containing a comprehensive genome-wide CRISPR-Cas9 guide RNA library and demonstrated its effectiveness in uncovering novel virus-host interactions. In summary, FastAd enables the rapid generation of single Ad vectors or complex genetic libraries, facilitating not only novel applications of Ad vectors but also research in foundamental virology.},
}
@article {pmid39557939,
year = {2024},
author = {Shah, HK and Fathima, PA and Ajithlal, PM and Kumar, A and Rawani, A and Thakur, MS and Mohanty, SS and Sarma, DK and Pandey, K and Kumar, A and Rahi, M and Saini, P},
title = {Nationwide cross-sectional surveillance of Leishmania donovani in phlebotomine sand flies and its impact on national kala-azar elimination in India.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {28455},
pmid = {39557939},
issn = {2045-2322},
support = {6/9-7(331)/2020/ECD-II//Indian Council of Medical Research/ ; },
mesh = {Animals ; *Leishmaniasis, Visceral/epidemiology/parasitology/prevention &amp; control/transmission ; *Leishmania donovani/genetics/isolation &amp; purification ; India/epidemiology ; Cross-Sectional Studies ; *Insect Vectors/parasitology ; Psychodidae/parasitology ; Phlebotomus/parasitology ; Humans ; Disease Eradication/methods ; },
abstract = {India is accelerating efforts to eliminate kala-azar by aligning its National Kala-Azar Elimination Program with the World Health Organization's (WHO) roadmap for Neglected Tropical Diseases (NTDs) 2021-2030. Elimination relies on comprehensive vector surveillance and integrated vector management. This study aimed to conduct nationwide entomological surveillance to detect Leishmania donovani in phlebotomine sand flies. A cross-sectional survey was conducted from January 2022 to December 2023 in five different biogeographical zones in India. Mechanical aspirator, light traps were used for sampling. The collected sand flies were identified to species level. Molecular xenomonitoring was conducted using kDNA qPCR, and parasite characterization targeting ITS1 gene sequencing and RFLP. Sand fly species was confirmed by DNA barcode. Molecular xenomonitoring revealed that Phlebotomus argentipes from Bihar, West Bengal, and Kerala exhibited high levels of L. donovani parasitic DNA. In Rajasthan, P. sergenti and P. papatasi and in Himachal Pradesh, P. longiductus, P. major, and P. bruneyi were positive. The high levels of L. donovani parasitic DNA detected in various Phlebotomus species, along with its presence in other sand fly species beyond the established vectors, underscore the urgent need for the National Kala-Azar Elimination Program to prioritize comprehensive and rigorous vector surveillance. Strengthening these efforts is crucial for achieving the program's goal of eliminating the disease.},
}
@article {pmid39555796,
year = {2024},
author = {Yang, S and Chen, S and Mo, J and Liu, J and Pan, Q and Song, C},
title = {Application of DNA Barcoding to Identify Medicinal Plants.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {213},
pages = {},
doi = {10.3791/66925},
pmid = {39555796},
issn = {1940-087X},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Plants, Medicinal/genetics/classification ; *DNA, Plant/genetics ; },
abstract = {Medicinal plants are valuable resources globally and are used worldwide to maintain health and treat disease; however, the presence of adulteration obstructs their development. DNA barcoding, a technique for species identification by standard DNA regions, facilitates prompt and accurate identification of traditional medicinal plants. The process of DNA barcoding entails six basic steps: 1) processing the medicinal plants, 2) extracting high-quality total DNA from the medicinal plants using centrifugal column method, 3) amplifying target DNA region internal transcribed spacer 2 (ITS2) with universal primers of plants and performing Sanger sequencing, 4) splicing and aligning sequence to obtain the target sequence, 5) matching the barcode sequence against the barcode library for identification, 6) aligning sequence, comparing intraspecific and interspecific variation, constructing phylogenetic neighbor-joining tree. As shown in the results, the universal primer can amplify the target region. Basic Local Alignment Search Tool (BLAST) demonstrates the percentage identified was 100%, and the neighbor-joining tree demonstrates that the splicing sequences were clustered with the A. sinensis OR879715.1 clade, and the clade support value is 100. This protocol provides a reference for applying DNA barcoding technology as an effective method to identify medicinal plants and adulterants.},
}
@article {pmid39552916,
year = {2024},
author = {Chen, HP and Chan, FT and Shiao, SF and Chiu, MC},
title = {New record of Carnidae (Diptera) from Taiwan and potential challenges in DNA barcode amplification due to pseudogene.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e137532},
pmid = {39552916},
issn = {1314-2828},
abstract = {BACKGROUND: The genus Carnus Nitzsch, 1818 comprises small ectoparasites that feed on the blood of juvenile avians. They are characterised by dealated adults with setose abdominal intersegmental membranes. Carnusorientalis Maa, 1968 was previously recorded in Malaysia and the Ryukyu Islands of Japan, parasitising two owl species: Ketupaketupu (Horsfield, 1821) and Otuselegans (Cassin, 1852). This study confirms the occurrence of C.orientalis in Taiwan and presents a new host record, along with COI barcode sequences. Additionally, the study also elucidates the difficulties posed by blood meal contamination and pseudogene amplification as confounding factors intrinsic to the molecular taxonomic delineation of C.orientalis via universal DNA barcoding primers.<br><br>NEW INFORMATION: The following new information regarding C.orientalis is provided in this study: Carnusorientalis is first recorded in Taiwan, filling the gap in its East Asian distribution. This is also the first record of Carnidae from Taiwan.Otuslettia (Hodgson, 1836) (Aves, Strigidae) is reported as a new host for C.orientalis, identified on a fallen fledgling.Co-amplification of the host's COI is reported in this study using the universal PCR primer set LCO1490/HCO2198. Additionally, the amplification of a COI-like pseudogene using a newly-designed primer set is detected through abnormal translated amino acid sequences and the occurrence of a stop codon.New specific primers for the COI gene of Carnus were designed in this study. The new distribution and ecological data of C.orientalis enhance our understanding of this species. The provision of new COI primers is anticipated to contribute to future studies employing DNA barcoding in bird-parasitic flies.},
}
@article {pmid39552768,
year = {2024},
author = {Jiang, YY and Zhao, H and Chen, Y},
title = {A new species of Proaphelinoides Girault (Hymenoptera, Aphelinidae) from China, with a phylogenetic analysis.},
journal = {ZooKeys},
volume = {1217},
number = {},
pages = {263-272},
pmid = {39552768},
issn = {1313-2989},
abstract = {A new species of Proaphelinoides Girault, Proaphelinoideshuangi Chen &amp; Jiang, sp. nov., is reported from China. A key to all species of the genus is provided. DNA standard barcode COI and partial nuclear ribosomal 28S-D2 from two individuals of Proaphelinoides were sequenced, and 28S-D2 rDNA was included in a phylogenetic analysis, confirming Proaphelinoides as the sister group to Aphytis.},
}
@article {pmid39552767,
year = {2024},
author = {Kits, JH},
title = {Boreolimnus, a new leafhopper genus from northern North America, with a review of Cribrus Oman (Hemiptera, Cicadellidae, Deltocephalinae).},
journal = {ZooKeys},
volume = {1217},
number = {},
pages = {273-290},
pmid = {39552767},
issn = {1313-2989},
abstract = {The poorly known leafhopper species described as Deltocephalus (Laevicephalus) concinnus var. incisurus DeLong, 1926 previously had no accepted generic placement. It is here redescribed and placed in Boreolimnus gen. nov. in the tribe Paralimnini, as Boreolimnusincisurus (DeLong) comb. nov. Cribrusmicmac Hamilton, 1987 is a junior syn. nov. of B.incisurus. Due to historic confusion, the species currently placed in Cribrus Oman, 1949 were also reviewed. Cribrusconcinnus (Sanders &amp; DeLong, 1917) is redescribed, and a lectotype is designated to clarify the application of the name. Deltocephalusplagus Ball &amp; DeLong, 1926 and Laevicephalusshingwauki Beamer &amp; Tuthill, 1934 are recognized as junior syn. nov. of C.concinnus, now the only recognized species in the genus.},
}
@article {pmid39549753,
year = {2024},
author = {Pogner, CE and Antunes, C and Apangu, GP and Bruffaerts, N and Celenk, S and Cristofori, A and González Roldán, N and Grinn-Gofroń, A and Lara, B and Lika, M and Magyar, D and Martinez-Bracero, M and Muggia, L and Muyshondt, B and O'Connor, D and Pallavicini, A and Marchã Penha, MA and Pérez-Badia, R and Ribeiro, H and Rodrigues Costa, A and Tischner, Z and Xhetani, M and Ambelas Skjøth, C},
title = {Airborne DNA: State of the art - Established methods and missing pieces in the molecular genetic detection of airborne microorganisms, viruses and plant particles.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177439},
doi = {10.1016/j.scitotenv.2024.177439},
pmid = {39549753},
issn = {1879-1026},
mesh = {Aerosols/analysis ; *Air Microbiology ; Air Pollutants/analysis ; Bacteria/genetics ; Biodiversity ; *DNA/analysis ; *Environmental Monitoring/methods ; Fungi/genetics ; Plants/genetics ; Pollen ; Viruses/genetics ; },
abstract = {Bioaerosol is composed of different particles, originating from organisms, or their fragments with different origin, shape, and size. Sampling, analysing, identification and describing this airborne diversity has been carried out for over 100 years, and more recently the use of molecular genetic tools has been implemented. However, up to now there are no established protocols or standards for detecting airborne diversity of bacteria, fungi, viruses, pollen, and plant particles. In this review we evaluated commonalities of methods used in molecular genetic based studies in the last 23 years, to give an overview of applicable methods as well as knowledge gaps in diversity assessment. Various sampling techniques show different levels of effectiveness in detecting airborne particles based on their DNA. The storage and processing of samples, as well as DNA processing, influences the outcome of sampling campaigns. Moreover, the decisions on barcode selection, method of analysis, reference database as well as negative and positive controls may severely impact the results obtained. To date, the chain of decisions, methodological biases and error propagation have hindered DNA based molecular sequencing from offering a holistic picture of the airborne biodiversity. Reviewing the available studies, revealed a great diversity in used methodology and many publications didn't state all used methods in detail, making comparisons with other studies difficult or impossible. To overcome these limitations and ensure genuine comparability across studies, it is crucial to standardize protocols. Publications need to include all necessary information to enable comparison among different studies and to evaluate how methodological choices can impacts the results. Besides standardization, implementing of automatic tools and combining of different analytical techniques, such as real-time evaluation combined with sampling and molecular genetic analysis, could assist in achieving the goal of accurately assessing the actual airborne biodiversity.},
}
@article {pmid39548171,
year = {2024},
author = {Raupach, MJ and Charzinski, N and Villastrigo, A and Gossner, MM and Niedringhaus, R and Schäfer, P and Schmelzle, S and Strauß, G and Hendrich, L},
title = {The discovery of an overseen pygmy backswimmer in Europe (Heteroptera, Nepomorpha, Pleidae).},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {28139},
pmid = {39548171},
issn = {2045-2322},
mesh = {Animals ; *Heteroptera/genetics/classification/anatomy &amp; histology ; *Phylogeny ; Europe ; Male ; Genome, Mitochondrial ; DNA Barcoding, Taxonomic ; Female ; },
abstract = {The Pleidae, or pygmy backswimmers, is a family of aquatic bugs (Hemiptera, Heteroptera, Nepomorpha) containing four genera. Here, we describe Plea cryptica sp. nov. and redescribe its sister species, Plea minutissima Leach, 1817. Whereas the morphological distinction of these closely related species is only possible for males, molecular data clearly separate them. As part of our taxonomic study, we provide comprehensive molecular data including more than 200 DNA barcodes from all over Europe, complete nuclear ribosomal DNA, full mitochondrial genome data, and 3D scans for both species. Furthermore, the same molecular markers are also presented for Neoplea striola (Fieber, 1844). We used Maximum Likelihood (ML) analyses to reconstruct the phylogeny of the Pleidae and Notonectoidea based on available mitogenomic data. Our study represents a successful implementation of the proposed concept of taxonomics, using data from high-throughput sequencing technologies for integrative taxonomic studies, and allowing high confidence for both biodiversity and ecological research.},
}
@article {pmid39544525,
year = {2024},
author = {López-Blanco, C and Tasevska, O and Kostoski, G and Vicente, E and Epp, LS and García-Alix, A},
title = {Ancient Endemic or Recent Invader? Phylogenetic Position and the Probable Origin of the Ccladoceran Diaphanosoma macedonicum (Diplostraca, Sididae) from the Ancient Lakes in the Balkans.},
journal = {Zoological studies},
volume = {62},
number = {},
pages = {e9},
pmid = {39544525},
issn = {1810-522X},
abstract = {Ancient lakes contain unique and very vulnerable fauna. Determining and understanding the origin of such biodiversity is a key factor in promoting conservation and management actions in some of the most singular ecosystems on the planet. Lake Ohrid in the Balkans is known as a natural laboratory for speciation, containing a high number of endemic species. However, the identity and origin of the planktonic cladoceran Diaphanosoma is uncertain. Representatives of the genus were long considered to have invaded the lake, but recent morphological studies have suggested that they belonged to the endemic taxon in the Balkans, D. macedonicum. Here, phylogenetic methods based on two mitochondrial gene fragments (COI and 16S) were used to identify Diaphanosoma specimens from the ancient Lake Ohrid and Lake Prespa in the Balkans and compare them with other species in Europe, including those living in nearby water bodies. Molecular evidence showed that D. macedonicum was constrained to the ancient lakes Ohrid, Prespa, and Mikri Prespa, which suggests reproductive isolation within the lakes. Phylogenetic analyses supported previous morphological assessments and situated D. macedonicum within the D. mongolianum species group, which contains three sibling species (D. mongolianum, D. lacustris, and D. macedonicum). Nuclear markers are needed to study intraspecific gene flow in these organisms and discard a potential formation of hybrids.},
}
@article {pmid39542856,
year = {2024},
author = {Valkiūnas, G and Iezhova, TA and Duc, M and Dunn, JC and Bensch, S},
title = {A new blood parasite of the accentor birds: description, molecular characterization, phylogenetic relationships and distribution.},
journal = {Parasitology},
volume = {151},
number = {10},
pages = {1163-1173},
pmid = {39542856},
issn = {1469-8161},
support = {RG170086//Royal Society/ ; },
mesh = {Animals ; *Phylogeny ; *Haemosporida/genetics/classification/isolation &amp; purification ; *Bird Diseases/parasitology/epidemiology ; *Protozoan Infections, Animal/parasitology/epidemiology ; Cytochromes b/genetics ; Passeriformes/parasitology ; Europe/epidemiology ; North America/epidemiology ; Genome, Mitochondrial ; },
abstract = {Haemoproteus bobricklefsi sp. nov. (Haemosporida, Haemoproteidae) was found in the dunnock Prunella modularis and represents the first blood parasite described in accentor birds of the Prunellidae. The description is based on the morphology of blood stages and includes information about a barcoding segment of the mitochondrial cytochrome b gene (lineage hDUNNO01) and the full mitochondrial genome, which can be used for identification and diagnosis of this infection. The new parasite can be readily distinguished from described species of haemoproteids parasitizing passeriform birds due to markedly variable position of nuclei in advanced and fully grown macrogametocytes. Illustrations of blood stages of the new species are given, and phylogenetic analyses based on partial mitochondrial cytochrome b gene sequences and the full mitochondrial genome identified the closely related lineages. DNA haplotype networks showed that transmission occurs in Europe and North America. This parasite was found in the dunnock in Europe and several species of the Passerellidae in North America. It is probably of Holarctic distribution, with the highest reported prevalence in the UK. The parasite distribution seems to be geographically patchy, with preference for areas of relatively cool climates. Phylogenetic analysis suggests that H. bobricklefsi sp. nov. belongs to the Parahaemoproteus subgenus and is probably transmitted by biting midges belonging to Culicoides (Ceratopogonidae). The available data on molecular occurrence indicate that this pathogen is prone to abortive development, so worth attention in regard of consequences for bird health.},
}
@article {pmid39541669,
year = {2024},
author = {Kusuda, K and Yamashita, K and Morishita, E and Ishibashi, N and Shiraishi, Y and Yamaguchi, H},
title = {Comparison of Reading Times of RFID-Tagged and Barcode-Engraved Surgical Instruments.},
journal = {The Journal of surgical research},
volume = {304},
number = {},
pages = {121-125},
doi = {10.1016/j.jss.2024.09.087},
pmid = {39541669},
issn = {1095-8673},
mesh = {*Radio Frequency Identification Device/methods ; Humans ; *Surgical Instruments/economics ; Time Factors ; Electronic Data Processing ; Clinical Competence/statistics &amp; numerical data ; Adult ; Male ; Patient Safety ; Female ; },
abstract = {INTRODUCTION: To improve patient safety and reduce burden on healthcare professionals and institutions, the individual management of surgical instruments is essential. There are two methods for individual item management: radio-frequency identification (RFID) and barcoding. However, there has been no examination of efficiency regarding reading times. Therefore, this study aimed to compare the reading times of RFID-tagged and barcode-engraved surgical instruments and evaluate the influence of operator proficiency.<br><br>METHODS: The participants included 8 individuals and 41 surgical instruments from a varicose vein set. RFID tags and barcodes were attached to the surgical instruments. Five trials were conducted for each, and the reading times were measured.<br><br>RESULTS: The reading times for RFID-tagged surgical instruments in the skilled and unskilled groups were 64.0&#xa0;&#xb1;&#xa0;9.0s and 79.4&#xa0;&#xb1;&#xa0;17.0&#xa0;s, respectively, whereas those for barcode-engraved surgical instruments were 190.4&#xa0;&#xb1;&#xa0;28.1&#xa0;s and 212.3&#xa0;&#xb1;&#xa0;40.3&#xa0;s, respectively. Barcodes took 3.0 and 2.7 times longer to read than RFID-tagged instruments for the skilled and unskilled groups, respectively. Additionally, skilled operators using barcodes required 2.4 times more time than unskilled operators using RFID. Even nonmedical individuals were able to achieve quick and accurate readings with RFID. The estimated labor hours per person were $24,146-$42,322 for RFID and $71,078-$110,898 for barcode scanning for a year (working 8&#xa0;h/d for 250&#xa0;d).<br><br>CONCLUSIONS: RFID-tagged surgical instruments impose a lighter workload and financial burden than barcode-engraved surgical instruments. RFID technology may also improve patient safety due to less dependency on operator proficiency.},
}
@article {pmid39538416,
year = {2024},
author = {Hua, J and Wang, K and Chen, Y and Xu, X and Dong, G and Li, Y and Liu, R and Xiong, Y and Ding, J and Zhang, T and Zeng, X and Li, Y and Sun, H and Gu, Y and Liu, S and Ouyang, W and Liu, C},
title = {Molecular characterization of human HSPCs with different cell fates in vivo using single-cell transcriptome analysis and lentiviral barcoding technology.},
journal = {Clinical and translational medicine},
volume = {14},
number = {11},
pages = {e70085},
pmid = {39538416},
issn = {2001-1326},
support = {No.31970816//National Natural Science Foundation of China (NSFC)/ ; No.BGIRSZ20210006//Open fund project of Shenzhen BGI Institute of Life Science/ ; No. KJZD20230923114911023//Science, Technology and Innovation Commission of Shenzhen Municipality/ ; No.SZSM202211033//Sanming Project of Medicine in Shenzen Municipality/ ; },
mesh = {Humans ; *Single-Cell Analysis/methods ; *Gene Expression Profiling/methods ; *Hematopoietic Stem Cells/metabolism/cytology ; Cell Differentiation/genetics ; Lentivirus/genetics ; Single-Cell Gene Expression Analysis ; },
abstract = {Hematopoietic stem and progenitor cells (HSPCs) possess the potential to produce all types of blood cells throughout their lives. It is well recognized that HSPCs are heterogeneous, which is of great significance for their clinical applications and the treatment of diseases associated with HSPCs. This study presents a novel technology called Single-Cell transcriptome Analysis and Lentiviral Barcoding (SCALeBa) to investigate the molecular mechanisms underlying the heterogeneity of human HSPCs in vivo. The SCALeBa incorporates a transcribed barcoding library and algorithm to analyze the individual cell fates and their gene expression profiles simultaneously. Our findings using SCALeBa reveal that HSPCs subset with stronger stemness highly expressed MYL6B, ATP2A2, MYO19, MDN1, ING3, and so on. The high expression of COA3, RIF1, RAB14, and GOLGA4 may contribute to the pluripotent-lineage differentiation of HSPCs. Moreover, the roles of the representative genes revealed in this study regarding the stemness of HPSCs were confirmed with biological experiments. HSPCs expressing MRPL23 and RBM4 genes may contribute to differentiation bias into myeloid and lymphoid lineage, respectively. In addition, transcription factor (TF) characteristics of lymphoid and myeloid differentiation bias HSPCs subsets were identified and linked to previously identified genes. Furthermore, the stemness, pluripotency, and differentiation-bias genes identified with SCALeBa were verified in another independent HSPCs dataset. Finally, this study proposes using the SCALeBa-generated tracking trajectory to improve the accuracy of pseudo-time analysis results. In summary, our study provides valuable insights for understanding the heterogeneity of human HSPCs in vivo and introduces a novel technology, SCALeBa, which holds promise for broader applications. KEY POINTS: SCALeBa and its algorithm are developed to study the molecular mechanism underlying human HSPCs identity and function. The human HSPCs expressing MYL6B, MYO19, ATP2A2, MDN1, ING3, and PHF20 may have the capability for high stemness. The human HSPCs expressing COA3, RIF1, RAB14, and GOLGA4 may have the capability for pluripotent-lineage differentiation. The human HSPCs expressing MRPL23 and RBM4 genes may have the capability to differentiate into myeloid and lymphoid lineage respectively in vivo. The legitimacy of the identified genes with SCALeBa was validated using biological experiments and a public human HSPCs dataset. SCALeBa improves the accuracy of differentiation trajectories in monocle2-based pseudo-time analysis.},
}
@article {pmid39538182,
year = {2024},
author = {Anwar, A and Wahab, H and Wahab, A and Afshan, NUS and Moussa, IM and Elhindi, KM and Ahmed, M and Malik, A and Singh, MP and Gaidhane, S and Uddin, S},
title = {Molecular and morphoanatomical characterization of Urocystis heteropogonis sp. nov.: a novel smut fungus infecting Heteropogon contortus.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {1070},
pmid = {39538182},
issn = {1471-2229},
mesh = {*Phylogeny ; DNA, Fungal/genetics ; Spores, Fungal/genetics ; Pakistan ; Animals ; },
abstract = {BACKGROUND: A new species of smut fungus, Urocystis heteropogonis, was discovered infecting Heteropogon contortus in Shawar Valley, Swat district, Khyber Pakhtunkhwa, Pakistan. The study aimed to characterize this fungus based on its morpho-anatomical and molecular features and clarify its phylogenetic position within the genus Urocystis.<br><br>RESULTS: Urocystis heteropogonis was identified as a novel species, distinct from other Urocystis species. Morphologically, it is characterized by larger spore balls (14-69&#x2009;&#xd7;&#x2009;11-45&#xa0;&#x3bc;m) and central spores that are 14-28&#x2009;&#xd7;&#x2009;11-20&#xa0;&#x3bc;m in size, with each spore containing1-8 central spores. The spore walls measure 0.9-2.5&#xa0;&#x3bc;m in thickness and the species differs in infection patterns compared to other Urocystis species. Phylogenetic analysis based on the ITS and LSU regions of nuclear ribosomal DNA (nrDNA) further confirmed the novelty of the species, placing it within a distinct clade alongside U. agropyri, U. occulta, U. piptatheri, and U. tritici.<br><br>CONCLUSIONS: The discovery of Urocystis heteropogonis adds to the diversity of smut fungi infecting grasses and highlights the need for further research into its ecological and agricultural implications. Future studies should focus on the disease's spread, management, and potential impact on host populations.},
}
@article {pmid39538137,
year = {2024},
author = {El-Demerdash, MM and El-Sayed, ASA and Teleb, SS and Sadek, AM and Elsehely, HH},
title = {DNA barcoding, micromorphology and metabolic traits of selected Ficus L. (Moraceae) species from Egypt.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {1067},
pmid = {39538137},
issn = {1471-2229},
mesh = {*DNA Barcoding, Taxonomic ; *Ficus/genetics/anatomy &amp; histology/classification ; Egypt ; Phylogeny ; DNA, Plant/genetics ; Plant Leaves/anatomy &amp; histology/genetics/metabolism ; Species Specificity ; },
abstract = {The genus Ficus of the family Moraceae, is one of the largest genera of angiosperms, with diverse pharmaceutical applications and biological activities. The traditional approaches based on the morphological traits have been frequently implemented for taxonomical identification of the different taxa of Ficus, however, encompassing these features are quite laborious, due to the dependence of these phenotypic traits on the environmental conditions. So, authenticating the taxonomical identity of the Ficus taxa with molecular barcoding and metabolic profiling, as relatively stable traits, could be a relevant approach for confirming the traditional phenotypic traits of this genus. Nine species of the genus Ficus namely F. amplissima Sm., F. benjamina L. F. binnendijkii, F. drupacea var. pubescens, F. elastica Roxb., F. microcarpa L., F. religiosa L., F. tinctoria subsp. gibbosa and F. virens var. sublancelata in Egypt, were selected for this study. From the anatomical features, three species of subsection Urostigma, F. religiosa, F. virens var. sublanceolata have cystoliths on the abaxial layer, whereas in F. amplissima it was on the adaxial layer. The UPGMA dendrogram of the studied Ficus taxa has been generated from the 21 anatomical characters, categorized the studied taxa into two clusters (I and II) of average distance ~ 3.5, each cluster has been further divided into subclusters I and II. The sub-cluster I includes F. religiosa, F. virens var. sublanceolata and F. tinctoria subsp. gibbosa were grouped together to subsection Urostigma, while the sub-cluster II of the cluster I includes F. benjamina and F. amplissima. From the DNA barcoding analysis, three clusters I, II and III were emerged, the cluster I includes F. benjamina, F. binnendjikee, and F. amplissima. The cluster II, F. virens var. sublanceolata and F. religiosa that belong to subsection Urostigma, while, the cluster III includes F. elastica and F. drupacea var. pubescens, F. microcarpa that belongs to subsection Conosycea. From the metabolic profiling of Ficus species, the major compounds; H-cycloprop-azulen-7-ol, 3,7,11,15-Tetramethyl-2-hexadecen-1-ol, 2-(9-octadecenyloxy), pentadecanoic acid, phytol, sitosterol and 9,12-octadecadienoic acid were the common among the taxa, with an obvious fluctuation, that could be a chemotaxonomic markers for these species of Ficus. Based on the metabolic profiling, two distinct clusters I and II were evolved, the cluster I involve F. elastica, F. benjamina, F. drupacea var. pubescens, F. amplissima, while, the cluster II had F. tinctoria subsp. gibbosa and F. religiosa. The fluctuation on the metabolites of the tested Ficus species could be a metabolic fingerprint for each species. So, the delamination of the tested plants based on their anatomical traits was typically matched to the separation based on the ITS sequence analysis.},
}
@article {pmid39537812,
year = {2024},
author = {Mingeot, D and Chavalle, S and Buhl, PN and Sonet, G and Dubois, B and Hautier, L},
title = {Molecular methods for the detection and identification of parasitoids within larval wheat midges.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {27770},
pmid = {39537812},
issn = {2045-2322},
mesh = {Animals ; *Larva/parasitology ; *Triticum/parasitology ; *Diptera/parasitology ; *DNA Barcoding, Taxonomic/methods ; Hymenoptera/genetics ; },
abstract = {Three species of cecidomyiid midges (Diptera: Cecidomyiidae) cause significant yield losses on wheat in Europe: Sitodiplosis mosellana (Géhin), Contarinia tritici (Kirby) and Haplodiplosis marginata (von Roser). Eggs and young larvae may be parasitised by a complex of hymenopteran parasitoids belonging to the Pteromalidae and Platygastridae families which contributes to natural pest control. We have developed molecular tools for detecting and identifying seven parasitoid species previously encountered in Belgium inside individual wheat midge larvae. Barcode DNA sequences from COI, 18S and 28S genes were obtained from the midges and parasitoid species. Each of the three genes allowed all the species to be distinguished although 18S was the only one displaying a barcoding gap, both between parasitoids and midges, and at the species level. Based on the 18S gene, we developed a TaqMan assay to assess parasitism in midge larvae, regardless of the midge and parasitoid species. Next, two group-specific PCR primer pairs were generated, allowing the separate amplification of midge DNA or parasitoid DNA in parasitised individuals and subsequent identification by Sanger sequencing. Finally, species-specific primers were designed to identify six parasitoid species by simple PCR amplification. These tools were successfully applied to assess the parasitism rate of S. mosellana larvae in seven Belgian fields.},
}
@article {pmid39535995,
year = {2024},
author = {Shah, SHA and Nisar, M and Ihsan, M and Zahoor, M and Ullah, R and Iqbal, Z and Shah, AB},
title = {Estimation of genetic polymorphism in quince (Cydonia oblonga Mill.) genotypes using morphological traits and molecular (DNA barcoding) characterizations.},
journal = {PloS one},
volume = {19},
number = {11},
pages = {e0310048},
pmid = {39535995},
issn = {1932-6203},
mesh = {*Rosaceae/genetics ; *Genotype ; *Polymorphism, Genetic ; *DNA Barcoding, Taxonomic/methods ; Fruit/genetics/anatomy &amp; histology ; Pakistan ; Phylogeny ; DNA, Plant/genetics ; },
abstract = {Quince (Cydonia oblonga) is a medicinal plant and a member of family Rosaceae. It is native plant of Asia Minor and Europe. It is used in production of jam and jellies and also as a remedy of several ailments. The present study was conducted to evaluate the genetic polymorphism based on morphological and molecular traits. Different varieties of Quince were collected from different ecological zones of Khyber Pakhtunkhwa Pakistan and a total of 26 different morphological traits were recorded among studied genotypes. Based on qualitative morphological trait study, the variety collected from Tindodag was unique one with highest fruit weight (328.82 g). The lowest fruit weight (68.38 g) was recorded for Talash genotype. The Charbagh and Tindodag genotypes showed highest seed length (10.6 mm) while genotypes of Chitral was recorded as lowest (8.4 mm). Statistically, significant level of variation was noted with coefficient of variance ranged from 2.23% to 30.38%. Based on correlation analysis, fruit length had strongly correlation with fruit weight (r = 0.89**), Average Fruit width was found significant with fruit weight (r = 0.90**). Similarly, the Core Width was found strongly significant with Core Length (r = 0.95**). ANOVA analysis indicated 10 quantitative characters to be highly significant, 2 significant and 1 insignificant. Principal component analysis was also computed for the 13 quantitative traits with Eigen value of 0.48 and a total variance of 97.78%. The first principal component shows total variation of 52.52%. In PC2 the total variation was 80.15%, PC3 94.06% while in PC4 it was 97.78%. The NCBI BLAST results shows that all the genotypes have similar origin except Tindodag genotype, which shows differences in its origin. Accession number for all other genotypes is MN216014.1, while accession number of Tindodag genotype is KF861967.1. Based on this study, it can be concluded that Tindodag genotype is unique out of the studied localities. NCBI BLAST have provided further support for the drawn conclusion.},
}
@article {pmid39534104,
year = {2024},
author = {Wang, L and Li, F and Zhao, K and Yang, J and Sun, H and Cui, X and Dong, W and Li, E and Wang, N},
title = {Comparative plastomes sheds light on phylogeny of Weigela.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1487725},
pmid = {39534104},
issn = {1664-462X},
abstract = {Weigela Thunb. is a genus in the family Caprifoliaceae. All species in this genus have high ornamental and medicinal value. However, the genetic divergence between species and the phylogeny within Weigela is still unclear. Therefore, we sequenced and analyzed four plastomes from four different Weigela species to reveal the genetic divergence among species of this genus, and the phylogeny within Weigela. The four plastomes from Weigela ranged from 156,909 bp to 157,739 bp in size, and presented a typical circular quadripartite structure. Each complete plastome contained a pair of inverted repeat regions (23,592~24,957 bp), a larger single-copy (LSC) region (89,922~90,229 bp), and a small single-copy (SSC) region (17,668~20,429 bp). We identified three types of repeats, corresponding to 268 forward repeats, 128 palindromic repeats, and 867 tandem repeats, for a total of 1,263 long repeats. A total of 352 SSRs were identified from the four plastomes, and most of them were concentrated in the LSC region and the noncoding regions. Mononucleotide repeat units were the most frequently detected types of repeats, of which A/T repeat units were the most abundant. Three mutational hotspots (trnH-psbA, trnR-ndhF, and trnN-ndhF) were identified as candidate barcodes for Weigela species. Weigela belongs to Diervilloideae located at an early diverging position in the Caprifoliaceae. Within Weigela, W. japonica and W. floribunda were sister with W. subsessilis and W. florida. This study revealed the plastome structure and variation of four well-known Weigela species, and found three candidate barcodes for further study of four well-known Weigela species. In addition, the phylogenetic location of Weigela within the Caprifoliaceae was identified.},
}
@article {pmid39528918,
year = {2024},
author = {Filippov, I and Philip, CS and Schauser, L and Peterson, P},
title = {Comparative transcriptomic analyses of thymocytes using 10x Genomics and Parse scRNA-seq technologies.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1069},
pmid = {39528918},
issn = {1471-2164},
support = {955321//Horizon 2020 Framework Programme/ ; 955321//Horizon 2020 Framework Programme/ ; PRG2011//Eesti Teadusagentuur/ ; },
mesh = {Animals ; *Thymocytes/metabolism/cytology ; *Single-Cell Analysis/methods ; Mice ; *Genomics/methods ; *Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; Transcriptome ; RNA-Seq/methods ; Single-Cell Gene Expression Analysis ; },
abstract = {BACKGROUND: Single-cell RNA sequencing experiments commonly use 10x Genomics (10x) kits due to their high-throughput capacity and standardized protocols. Recently, Parse Biosciences (Parse) introduced an alternative technology that uses multiple in-situ barcoding rounds within standard 96-well plates. Parse enables the analysis of more cells from multiple samples in a single run without the need for additional reagents or specialized microfluidics equipment. To evaluate the performance of both platforms, we conducted a benchmark study using biological and technical replicates of mouse thymus as a complex immune tissue.<br><br>RESULTS: We found that Parse detected nearly twice the number of genes compared to 10x, with each platform detecting a distinct set of genes. The comparison of multiplexed samples generated from 10x&#xa0;and Parse techniques showed 10x&#xa0;data to have lower technical variability and more precise annotation of biological states in the thymus compared to Parse.<br><br>CONCLUSION: Our results provide a comprehensive comparison of the suitability of both single-cell platforms for immunological studies.},
}
@article {pmid39526042,
year = {2024},
author = {Pešić, V and Zawal, A and Ferreira, S and Benitez-Bosco, L and Cruz-Oliveira, A and Girão, D and Padilha, A and Turaccio, P and Rossini, S and Ballini, L and Staffoni, G and Fratini, S and Ciofi, C and Iannucci, A and Ekrem, T and Stur, E},
title = {DNA barcode library of Portuguese water mites, with the descriptions of two new species (Acari, Hydrachnidia).},
journal = {ZooKeys},
volume = {1217},
number = {},
pages = {119-171},
pmid = {39526042},
issn = {1313-2989},
abstract = {This study presents the first results from the analysis of water mites collected in Portugal as part of the Biodiversity Genomics Europe project. 307 COI DNA barcodes clustered into 75 BINs are provided, with 38 BINs being unique and deposited for the first time in the Barcode of Life Data Systems (BOLD). 65 species have been identified, of which 36 are new to the water mite fauna of Portugal. Two species, Torrenticolasoniae Pešić, sp. nov. and T.elisabethae Pešić, sp. nov. (Torrenticolidae), are described as new to science. 47% of the water mite species currently known from Portugal now have reference barcodes in BOLD. High intraspecific distances were recorded for some species, suggesting the presence of cryptic diversity and species complexes that needs further study. Our results improve the DNA barcode reference database for Portuguese water mites, enhancing species identification accuracy and stimulating future investigation.},
}
@article {pmid39524431,
year = {2024},
author = {Kan, J and Nie, L and Mi, Z and Liu, X and Xu, D and Tembrock, LR and Wu, Z and Hong, Z},
title = {Insights into Aquilaria phylogenetics through comparative plastomic resources.},
journal = {Forestry research},
volume = {4},
number = {},
pages = {e030},
pmid = {39524431},
issn = {2767-3812},
abstract = {The plastid is an essential organelle for its role in photosynthesis and energy production and its genomic information is always employed as important evolutionary markers to explore the relationship among species. Agarwood (Aquilaria), prized for its aromatic blend, finds extensive use in various cultures as incense and perfume. Despite its high economic importance, the phylogenetic status among Aquilaria based on plastomes remains ambiguous due to the lack of available plastomic resources. To bridge this knowledge gap, 22 Aquilaria plastomes were newly sequenced, similar variation patterns in this genus were determined, including a shared 16 bp extension of the rps19 gene and seven highly variable regions. The analysis highlighted the highest prevalence of the A/T motif among simple sequence repeats in these plastomes. Further phylogenetic analysis revealed Aquilaria's phylogenetic implications with an expanded dataset. This comprehensive plastomic resource not only enhances our understanding of Aquilaria evolution but also presents potential molecular markers for DNA barcoding.},
}
@article {pmid39524315,
year = {2024},
author = {Lamichhane, B and Brockway, C and Evasco, K and Nicholson, J and Neville, PJ and Mackenzie, JS and Smith, D and Imrie, A},
title = {DNA Barcoding for the Identification of Adult Mosquitoes (Diptera: Culicidae) in Western Australia.},
journal = {Ecology and evolution},
volume = {14},
number = {11},
pages = {e70493},
pmid = {39524315},
issn = {2045-7758},
abstract = {Precise mosquito identification is integral to effective arbovirus surveillance. Nonetheless, the conventional morphological approach to identifying mosquito species is laborious, demands expertise and presents challenges when specimens are damaged. DNA barcoding offers a promising alternative, surmounting challenges inherent in morphological identification. To integrate DNA barcoding into arbovirus surveillance effectively, a robust dataset of mosquito barcode sequences is required. This study established a comprehensive repository of Cytochrome Oxidase I (COI) barcodes, encompassing 177 samples representing 45 mosquito species from southern and northern Western Australia (WA), including 16 species which have not been previously barcoded. The average intraspecific and interspecific genetic distances were 1% and 6.8%, respectively. Anopheles annulipes sensu lato had the highest intraspecific distance at 9.1%, signifying a genetically diverse species. While validating the potential of COI barcodes to accurately differentiate mosquito species, we identified that some species pairs have low COI divergence. This includes Aedes clelandi and Ae. hesperonotius, Tripteroides atripes and Tp. punctolaeralis and Ae. turneri and Ae. stricklandi. In addition, we observed ambiguity in identification of the members of Culex sitiens subgroup (Cx. annulirostris, Cx. palpalis and Cx. sitiens) and three members of Cx. pipiens complex (Cx. australicus, Cx. globocoxitus, Cx. quinquefasciatus). In summary, despite presenting challenges in the identification of some mosquito species, the COI barcode accurately identified most of the species and generated a valuable resource that will support the WA arbovirus surveillance program and enhance public health intervention strategies for mosquito-borne disease control.},
}
@article {pmid39535538,
year = {2024},
author = {Singh, Y and Farrelly, C and Hathaway, QA and Carlsson, G},
title = {Persistence barcodes: A novel approach to reducing bias in radiological analysis.},
journal = {Oncotarget},
volume = {15},
number = {},
pages = {784-786},
pmid = {39535538},
issn = {1949-2553},
mesh = {Humans ; *Bias ; Diagnostic Imaging/methods/standards ; Image Processing, Computer-Assisted/methods/standards ; Algorithms ; Neural Networks, Computer ; Radiology/methods/standards ; },
abstract = {Persistence barcodes emerge as a promising tool in radiological analysis, offering a novel approach to reduce bias and uncover hidden patterns in medical imaging. By leveraging topological data analysis, this technique provides a robust, multi-scale perspective on image features, potentially overcoming limitations in traditional methods and Graph Neural Networks. While challenges in interpretation and implementation remain, persistence barcodes show significant potential for improving diagnostic accuracy, standardization, and ultimately, patient outcomes in the evolving field of radiology.},
}
@article {pmid39534110,
year = {2024},
author = {Oeum, K and Suong, M and Uon, K and Jobert, L and Bellafiore, S and Comte, A and Thomas, E and Kuok, F and Moulin, L},
title = {Comparison of plant microbiota in diseased and healthy rice reveals methylobacteria as health signatures with biocontrol capabilities.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1468192},
pmid = {39534110},
issn = {1664-462X},
abstract = {INTRODUCTION: Rice (Oryza sativa) is a staple food worldwide, but its production is under constant pressure from both abiotic and biotic stresses, resulting in high use of agrochemicals. The plant microbiome harbours microorganisms that can benefit plant health and provide alternatives to the use of agrochemicals. The composition of plant microbiomes depends on many factors (soil composition, age, and health) and is considered a primary driver of future plant health. To identify plant microbiomes that protect against disease, we hypothesised that asymptomatic rice plants in fields under high pathogen pressure (i.e., healthy islands of plants among predominantly diseased plants) might harbour a microbiota that protects them from disease.<br><br>MATERIAL AND METHODS: We sampled healthy and leaf-diseased plants in rice fields with high disease incidence in Cambodia and profiled their microbiota at leaf, root, and rhizosphere levels using 16S V3V4 and 18S V4 amplicon barcoding sequencing.<br><br>RESULTS: Comparison of amplicon sequence variants (ASV) of the microbiota of healthy and diseased samples revealed both disease and healthy signatures (significant enrichment or depletion at ASV/species/genus level) in both fields. The genera Methylobacterium and Methylorubrum were identified health taxa signatures with several species significantly enriched in healthy leaf samples (Methylobacterium indicum, Methylobacterium komagatae, Methylobacterium aerolatum, and Methylorubrum rhodinum). A cultivation approach on rice samples led to the isolation of bacterial strains of these two genera, which were further tested as bioinoculants on rice leaves under controlled conditions, showing for some of them a significant reduction (up to 77%) in symptoms induced by Xanthomonas oryzae pv. oryzae infection.<br><br>DISCUSSION: We validated the hypothesis that healthy plants in fields under high disease occurrence can host specific microbiota with biocontrol capacities. This strategy could help identify new microbes with biocontrol potential for sustainable rice production.},
}
@article {pmid39532481,
year = {2025},
author = {Nazar, N and Saxena, A and Sebastian, A and Slater, A and Sundaresan, V and Sgamma, T},
title = {Integrating DNA Barcoding Within an Orthogonal Approach for Herbal Product Authentication: A Narrative Review.},
journal = {Phytochemical analysis : PCA},
volume = {36},
number = {1},
pages = {7-29},
pmid = {39532481},
issn = {1099-1565},
support = {//Daphne Jackson Trust/ ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Plants, Medicinal/genetics/chemistry/classification ; DNA, Plant/genetics ; Quality Control ; },
abstract = {INTRODUCTION: Existing methods for morphological, organoleptic, and chemical authentication may not adequately ensure the accurate identification of plant species or guarantee safety. Herbal raw material authentication remains a major challenge in herbal medicine. Over the past decade, DNA barcoding, combined with an orthogonal approach integrating various testing methods for quality assurance, has emerged as a new trend in plant authentication.<br><br>OBJECTIVE: The review evaluates DNA barcoding and common alternative testing in plant-related sectors to enhance quality assurance and accurate authentication.<br><br>METHOD: Studies were selected based on their relevance to the identification, quality assurance, and safety of herbal products. Inclusion criteria were peer-reviewed articles, systematic reviews, and relevant case studies from the last two decades focused on DNA barcoding, identification methods, and their applications. Exclusion criteria involved studies lacking empirical data, those not peer-reviewed, or those unrelated to the main focus. This ensured the inclusion of high-quality, pertinent sources while excluding less relevant studies.<br><br>RESULTS: An orthogonal approach refers to the use of multiple, independent methods that provide complementary information for more accurate plant identification and quality assurance. This reduces false positives or negatives by confirming results through different techniques, combining DNA barcoding with morphological analysis or chemical profiling. It enhances confidence in results, particularly in cases of potential adulteration or misidentification of plant materials.<br><br>CONCLUSION: This study highlights the persistent challenges in assuring the quality, purity, and safety of plant materials. Additionally, it stresses the importance of incorporating DNA-based authentication alongside traditional methods, to enhance plant material identification.},
}
@article {pmid39532139,
year = {2024},
author = {Calderón-Gutiérrez, F and Labonté, JM and Gonzalez, BC and Iliffe, TM and Mejía-Ortíz, LM and Borda, E},
title = {Cryptic diversity patterns of subterranean estuaries.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2034},
pages = {20241483},
pmid = {39532139},
issn = {1471-2954},
support = {//T3: Texas A&amp;M Triads for transformation/ ; //Texas A&amp;M University Galveston/ ; //Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; //CONACYT- Texas A&amp;M University/ ; //Mohamed bin Zayed Species Conservation Fund/ ; //National Science Foundation/ ; //Texas A&amp;M University San Antonio/ ; },
mesh = {*RNA, Ribosomal, 16S/analysis ; *Estuaries ; *Biodiversity ; Animals ; *Electron Transport Complex IV/genetics/analysis ; *DNA Barcoding, Taxonomic ; *Phylogeny ; Mexico ; Sequence Analysis, DNA ; Genetic Variation ; Invertebrates/genetics ; },
abstract = {Subterranean estuaries are coastal ecosystems characterized by vertically stratified groundwater. The biota within these ecosystems is relatively understudied due to the inherent difficulty of accessing such extreme environments. The fauna inhabiting these ecosystems is considered vulnerable to extinction, and the presence of cryptic species has major implications for research and conservation efforts. Most species lack molecular data; however, the evaluation of genetic data for some taxa has revealed that undocumented species are common. This study employs molecular species delimitation methods and DNA barcoding through the analysis of publicly and newly generated sequences, including individuals from type localities and non-crustacean phyla; the latter are typically overlooked in biodiversity assessments of subterranean estuaries. We analysed 376 cytochrome c oxidase subunit I (COI) gene sequences and 154 16S rRNA gene sequences. The COI sequences represented 32% of previously described species and 50% of stygobiont species from the Yucatan Peninsula and Cozumel Island, while sequences of the 16S rRNA represented 14% of described species and 22% of stygobionts. Our results revealed cryptic genetic lineages and taxonomic misidentification of species. As several species from these ecosystems are recognized as endangered, the use of molecular approaches will improve biodiversity estimates and highlight overlooked cryptic lineages in need of evaluation of conservation status.},
}
@article {pmid39529423,
year = {2024},
author = {Bustamante, MI and Elfar, K and Carachure, C and Adaskaveg, A and Kabashima, JN and Shogren, C and Eskalen, A and Lynch, SC},
title = {Etiology of Pine Ghost Canker in Southern California Urban Forests.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-08-24-1718-SR},
pmid = {39529423},
issn = {0191-2917},
abstract = {Pine ghost canker is a recently described disease affecting multiple pine species in urban forests of Southern California. Symptoms include wedged cankers with irregular margins and cryptic discoloration on cross-sections of branches, which can lead to severe dieback and potentially tree death. In this study, we identified and characterized five Neofusicoccum species (N. luteum, N. mediterraneum, N. parvum, N. stellenboschianum, and N. vitifusiforme) as the primary etiological agents of pine ghost canker. These pathogens were consistently isolated from multiple symptomatic pine samples (n = 41) and identified by morphology and phylogenetic analyses using four DNA barcodes (rDNA ITS, tef1, tub2, and rpb2). Pathogenicity was confirmed on healthy branches of 15-year-old Monterey pines, where the five Neofusicoccum species, caused vascular lesions that were not significantly different in length. Secondary fungi (Diaporthe, Diplodia, Neopestalotiopsis, and Pestalotiopsis spp.) were also recovered from symptomatic tissues but did not cause vascular lesions in pathogenicity tests. The optimal temperature for mycelial growth of N. luteum and N. parvum was 30 °C, whereas for N. mediterraneum, N. stellenboschianum and N. vitifusiforme, it was 25 °C. All five species were able to resume growth at room temperature (20 °C) after showing no growth during a 7-day exposure to 5 °C and 40 °C. This study constitutes the first report of N. luteum, N. stellenboschianum, and N. vitifusiforme causing pine ghost canker in California. Environmental factors such as warmer temperatures, irrigation, and pest infestations are discussed as drivers of disease expression in pine trees. Management practices are also proposed.},
}
@article {pmid39526732,
year = {2024},
author = {Soto-Serrano, A and Li, W and Panah, FM and Hui, Y and Atienza, P and Fomenkov, A and Roberts, RJ and Deptula, P and Krych, L},
title = {Matching excellence: Oxford Nanopore Technologies' rise to parity with Pacific Biosciences in genome reconstruction of non-model bacterium with high G+C content.},
journal = {Microbial genomics},
volume = {10},
number = {11},
pages = {},
pmid = {39526732},
issn = {2057-5858},
mesh = {*Genome, Bacterial ; *Base Composition ; Nanopores ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Nanopore Sequencing/methods ; },
abstract = {The reconstruction of complete bacterial genomes is essential for microbial research, offering insights into genetic content, ontology and regulation. While Pacific Biosciences (PacBio) provides high-quality genomes, its cost remains a limitation. Oxford Nanopore Technologies (ONT) offers long reads at a lower cost, yet its error rate raises scepticism. Recent ONT advancements, such as new Flow cells (R10.4.1), chemistry (V14) and duplex mode, improve data quality. Our study compares ONT with PacBio and Illumina, including hybrid data. We used Propionibacterium freudenreichii, a bacterium with a genome known for being difficult to reconstruct. By combining data from ONT's Native Barcoding and a custom-developed BARSEQ method, we achieved high-quality, near-perfect genome assemblies. Our findings demonstrate, for the first time, that the combination of nanopore-only long-native with shorter PCR DNA reads (~3 kb) results in high-quality genome reconstruction, comparable to hybrid data assembly from two sequencing platforms. This endorses ONT as a cost-effective, stand-alone strategy for bacterial genome reconstruction. Additionally, we compared methylated motif detection between PacBio and ONT R10.4.1 data, showing that results comparable to PacBio are achievable using ONT, especially when utilizing the advanced Nanomotif tool.},
}
@article {pmid39523608,
year = {2024},
author = {Hosuru, RV and Yang, J and Zhou, Y and Gin, A and Hayal, TB and Hong, SG and Dunbar, CE and Wu, C},
title = {Long-term tracking of haematopoietic clonal dynamics and mutations in non-human primate undergoing transplantation of lentivirally barcoded haematopoietic stem and progenitor cells.},
journal = {British journal of haematology},
volume = {205},
number = {6},
pages = {2487-2497},
pmid = {39523608},
issn = {1365-2141},
support = {/HI/NHLBI NIH HHS/United States ; /HI/NHLBI NIH HHS/United States ; },
mesh = {Animals ; *Macaca mulatta ; *Hematopoietic Stem Cells/metabolism/cytology ; *Hematopoietic Stem Cell Transplantation/methods ; *Mutation ; *Lentivirus/genetics ; Genetic Therapy/methods ; Genetic Vectors ; Cell Tracking/methods ; Humans ; Transplantation, Autologous ; },
abstract = {Haematopoietic stem and progenitor cell (HSPC) autologous gene therapies are promising treatment for a variety of blood disorders. Investigation of the long-term HSPC clonal dynamics and other measures of safety and durability following lentiviral-mediated gene therapies in predictive models are crucial for assessing risks and benefits in order to inform decisions regarding wider utilization. We established an autologous lentivirally barcoded HSPC transplantation model in rhesus macaque (RM), a model offering insights into haematopoiesis and gene therapies with direct relevance to human. Healthy young adult RMs underwent total body irradiation, followed by transplantation of autologous HSPCs transduced with a lentiviral vector containing a diverse genetic barcode library, uniquely labelling individual HSPCs and their progeny. With up to 131 months of follow-up, we now report quantitative clonal dynamics, characterizing the number, diversity, stability and lineage bias of hundreds of thousands of HSPC clones tracked in five RMs. We documented long-term stable and multi-lineage output from a highly polyclonal pool of HSPCs. Clonal succession after stable haematopoietic reconstitution was minimal. There was no evidence for accelerated acquisition of acquired somatic mutations following autologous lentivirally transduced HSPC transplantation. Our results provide relevant insights into long-term HSPC behaviours in vivo following transplantation and gene therapies.},
}
@article {pmid39521085,
year = {2024},
author = {Bálint, M and Tumusiime, J and Nakintu, J and Baranski, D and Schardt, L and Romahn, J and Dusabe, MC and Tolo, CU and Kagoro, GR and Ssenkuba, F and Junginger, A and Albrecht, C},
title = {Environmental DNA barcoding reveals general biodiversity patterns in the large tropical rift Lake Albert.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177308},
doi = {10.1016/j.scitotenv.2024.177308},
pmid = {39521085},
issn = {1879-1026},
mesh = {*Biodiversity ; *DNA Barcoding, Taxonomic ; *Lakes ; *Environmental Monitoring/methods ; DNA, Environmental/analysis/genetics ; Animals ; },
abstract = {Lake Albert, Africa's seventh-largest lake and a biodiversity hotspot, faces significant environmental challenges, including unregulated anthropogenic pressure and a lack of comprehensive biological studies. To address the scarcity of biodiversity data, we utilized environmental DNA (eDNA) metabarcoding to assess the lake's eukaryotic and metazoan communities. Surface water samples were collected at three distinct locations: close to the southern inflow of the Semliki River, the central part of the lake, and close to the northern inflow of the Victoria Nile and outflow of the Albert Nile. We aimed to study ecological patterns across the lake, focusing on sequence variant richness and community composition, testing for differences among locations and between shoreline and pelagic zones. Consistent with previous morphology-based observations, our results revealed differences in community composition among the three sites, with cyclopoid copepods dominating the communities. Distance from shore was a significant factor influencing community composition, confirming expectations about the effects of nutrient and oxygen availability gradients. However, the lack of comprehensive reference sequence data limited accurate taxonomic assignments. Despite these limitations, our study demonstrates that eDNA metabarcoding is highly useful for assessing biodiversity in underexplored tropical freshwater ecosystems. We advocate for urgent efforts to generate reference sequences from tropical regions to enhance the utility of eDNA for biodiversity monitoring and conservation. Our findings underscore the potential of eDNA in providing insights into ecological patterns of entire communities and emphasize the need for comprehensive studies addressing the full taxonomic spectrum in tropical freshwater ecosystems.},
}
@article {pmid39519959,
year = {2024},
author = {Pun, TB and Thapa Magar, R and Koech, R and Owen, KJ and Adorada, DL},
title = {Emerging Trends and Technologies Used for the Identification, Detection, and Characterisation of Plant-Parasitic Nematode Infestation in Crops.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {21},
pages = {},
pmid = {39519959},
issn = {2223-7747},
abstract = {Accurate identification and estimation of the population densities of microscopic, soil-dwelling plant-parasitic nematodes (PPNs) are essential, as PPNs cause significant economic losses in agricultural production systems worldwide. This study presents a comprehensive review of emerging techniques used for the identification of PPNs, including morphological identification, molecular diagnostics such as polymerase chain reaction (PCR), high-throughput sequencing, meta barcoding, remote sensing, hyperspectral analysis, and image processing. Classical morphological methods require a microscope and nematode taxonomist to identify species, which is laborious and time-consuming. Alternatively, quantitative polymerase chain reaction (qPCR) has emerged as a reliable and efficient approach for PPN identification and quantification; however, the cost associated with the reagents, instrumentation, and careful optimisation of reaction conditions can be prohibitive. High-throughput sequencing and meta-barcoding are used to study the biodiversity of all tropical groups of nematodes, not just PPNs, and are useful for describing changes in soil ecology. Convolutional neural network (CNN) methods are necessary to automate the detection and counting of PPNs from microscopic images, including complex cases like tangled nematodes. Remote sensing and hyperspectral methods offer non-invasive approaches to estimate nematode infestations and facilitate early diagnosis of plant stress caused by nematodes and rapid management of PPNs. This review provides a valuable resource for researchers, practitioners, and policymakers involved in nematology and plant protection. It highlights the importance of fast, efficient, and robust identification protocols and decision-support tools in mitigating the impact of PPNs on global agriculture and food security.},
}
@article {pmid39519254,
year = {2024},
author = {Tshiabuila, D and Choga, W and San, JE and Maponga, T and Van Zyl, G and Giandhari, J and Pillay, S and Preiser, W and Naidoo, Y and Baxter, C and Martin, DP and de Oliveira, T},
title = {An Oxford Nanopore Technology-Based Hepatitis B Virus Sequencing Protocol Suitable for Genomic Surveillance Within Clinical Diagnostic Settings.},
journal = {International journal of molecular sciences},
volume = {25},
number = {21},
pages = {},
pmid = {39519254},
issn = {1422-0067},
support = {U01 AI151698/AI/NIAID NIH HHS/United States ; },
mesh = {*Hepatitis B virus/genetics ; Humans ; *Genome, Viral ; *Genotype ; Nanopore Sequencing/methods ; Hepatitis B, Chronic/virology/diagnosis/epidemiology ; Phylogeny ; High-Throughput Nucleotide Sequencing/methods ; DNA, Viral/genetics ; Sequence Analysis, DNA/methods ; Genomics/methods ; Nanopores ; Drug Resistance, Viral/genetics ; Hepatitis B/diagnosis/virology/epidemiology ; Genetic Variation ; },
abstract = {Chronic Hepatitis B Virus (HBV) infection remains a significant public health concern, particularly in Africa, where the burden is substantial. HBV is an enveloped virus, classified into ten phylogenetically distinct genotypes (A-J). Tests to determine HBV genotypes are based on full-genome sequencing or reverse hybridization. In practice, both approaches have limitations. Whereas diagnostic sequencing, generally using the Sanger approach, tends to focus only on the S-gene and yields little or no information on intra-patient HBV genetic diversity, reverse hybridization detects only known genotype-specific mutations. To resolve these limitations, we developed an Oxford Nanopore Technology (ONT)-based HBV diagnostic sequencing protocol suitable for clinical virology that yields both complete genome sequences and extensive intra-patient HBV diversity data. Specifically, the protocol involves tiling-based PCR amplification of HBV sequences, library preparation using the ONT Rapid Barcoding Kit (Oxford nanopore Technologies, Oxford, OX4 4DQ, UK), ONT GridION sequencing, genotyping using genome detective software v1.132/1.133, a recombination analysis using jpHMM (26 October 2011 version) and RDP5.61 software, and drug resistance profiling using Geno2pheno v2.0 software. We prove the utility of our protocol by efficiently generating and characterizing high-quality near full-length HBV genomes from 148 residual diagnostic samples from HBV-infected patients in the Western Cape province of South Africa, providing valuable insights into the genetic diversity and epidemiology of HBV in this region of the world.},
}
@article {pmid39516507,
year = {2024},
author = {Rodrigues, BL and de Oliveira, AG and da Silva, LEH and Vasconcelos Dos Santos, T and de Oliveira, LNC and Rêgo, FD and de Andrade, AJ and Maia, GB and de Souza Pinto, I and Andrade Filho, JD and Galati, EAB},
title = {Hidden diversity in anthropophilic sand flies of the Monticola Series (Diptera, Psychodidae).},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {27215},
pmid = {39516507},
issn = {2045-2322},
support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 314260/2023-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2023/03715-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
mesh = {Animals ; *Phylogeny ; *Psychodidae/genetics/classification/anatomy &amp; histology ; *Electron Transport Complex IV/genetics ; *Haplotypes ; Brazil ; *Genetic Variation ; },
abstract = {The Monticola series comprises two anthropophilic and widely distributed species in Brazil: Pintomyia (Pifanomyia) monticola (Costa Lima, 1932) and Pintomyia (Pifanomyia) misionensis (Castro, 1959). They mainly occur in the Atlantic Rainforest, and it is known that Pi. monticola comprises at least two well-structured genetic lineages regarding a fragment of the cytochrome c oxidase subunit I (COI) gene. Here, we aim to elucidate the taxonomic status of this group using integrative taxonomy tools. Collections were performed in nine localities of four Brazilian states, and COI fragments were sequenced and merged with publicly available data. Several single-locus species delimitation algorithms, genetic distance metrics, phylogenetic trees, and haplotype networks were used to uncover cryptic diversity and population structure within Pi. monticola and Pi. misionensis. The resulting genetic clusters were then tested for morphological differences through linear and geometric morphometry of several characters. We analyzed 152 COI sequences, comprising 48 haplotypes. The maximum intraspecific p distances were 8.21% (mean 4.17%) and 9.12% (mean 4.4%) for Pi. monticola and Pi. misionensis, respectively, while interspecific ones ranged from 10.94 to 14.09% (mean 12.33%). Phylogenetic gene trees showed well-supported clades for both species, with clear structuring patterns within them. Species-delimitation algorithms split our dataset into at least three putative species for each taxon. Moreover, population structure analysis showed a strong correlation between Atlantic Forest areas of endemism as sources of molecular variation in Pi. monticola. Morphometric analyses were significant for wing shape variation and some linear measurements (mainly of the head) when comparing specimens of different genetic clusters for both taxa. These results indicate strong genetic structuring of Monticola series species, confirmed by morphometry, indicating two possible cryptic species complexes.},
}
@article {pmid39514381,
year = {2024},
author = {Barone, ML and Wilson, JD and Zapata, L and Soto, EM and Haddad, CR and Grismado, C and Izquierdo, M and Arias, E and Pizarro-Araya, J and Briones, R and Barriga, JE and Peralta, L and Ramírez, MJ},
title = {Genetic barcodes for species identification and phylogenetic estimation in ghost spiders (Araneae: Anyphaenidae: Amaurobioidinae).},
journal = {Invertebrate systematics},
volume = {38},
number = {},
pages = {},
doi = {10.1071/IS24053},
pmid = {39514381},
issn = {1447-2600},
mesh = {*Spiders/genetics/classification ; Animals ; *DNA Barcoding, Taxonomic/methods ; *Phylogeny ; *Electron Transport Complex IV/genetics ; Species Specificity ; Algorithms ; },
abstract = {The identification of spider species presents many challenges, since in most cases the characters used are from genital structures that are only fully developed in the adult stage, hence the identification of immatures is most often not possible. Additionally, these structures usually also present some intra-specific variability, which in some cases makes the identification of closely related species difficult. The genetic barcode technique (DNA barcodes), based on sequencing of the mitochondrial marker cytochrome c oxidase subunit I (COI), has proven a useful, complementary tool to overcome these limitations. In this work, the contribution of DNA barcoding to the taxonomy of the subfamily Amaurobioidinae is explored using the refined single linkage analysis (RESL) algorithm for the delimitation of operational taxonomic units (OTUs), in comparison with the assemble species by automatic partitioning (ASAP) algorithm, and presented in conjunction with an updated molecular phylogenetic analysis of three other markers (28S rRNA, 16S rRNA, Histone H3), in addition to COI . Of a total of 97 included species identified by morphology, 82 species were concordant with the operational taxonomic units obtained from RESL, representing an 85% correspondence between the two methods. Similar results were obtained using the ASAP algorithm. Previous observations of morphological variation within the same species are supported, and this technique provides new information on genetic structure and potentially cryptic species. Most of the discrepancies between DNA barcoding and morphological identification are explained by low geographic sampling or by divergent or geographically structured lineages. After the addition of many specimens with only COI data, the multi-marker phylogenetic analysis is consistent with previous results and the support is improved. The markers COI , closely followed by 28S , are the most phylogenetically informative. We conclude that the barcode DNA technique is a valuable source of data for the delimitation of species of Amaurobioidinae, in conjunction with morphological and geographic data, and it is also useful for the detection of cases that require a more detailed and meticulous study.},
}
@article {pmid39512489,
year = {2024},
author = {Rodrigues, IVB and de Souza, PGC and Nunes, RC and Nunes Godeiro, N and Bellini, BC},
title = {A century later: a new species of Mastigoceras Handschin, 1924 (Collembola, Orchesellidae), with morphological and systematic updates on the genus.},
journal = {ZooKeys},
volume = {1217},
number = {},
pages = {79-100},
pmid = {39512489},
issn = {1313-2989},
abstract = {Mastigocerascamponoti Handschin, the sole member of its genus and the Mastigocerini tribe, exhibits unusual dorsal chaetotaxy compared to other Orchesellidae. This includes a reduction in dorsal macrochaetotaxy and a secondary covering of fusiform scales intermixed with ciliate microchaetae. Despite three redescriptions, Mastigoceras chaetotaxy remains poorly understood, with no data on tergal sensilla patterns or dorsal macrochaetae homology. Here, the genus is revisited by describing a new Brazilian species a century after the original description of M.camponoti, based on morphological depiction combined with the use of DNA barcoding, Mastigocerashandschini Rodrigues, Souza &amp; Bellini, sp. nov. The two species are differentiated by a few and unusual aspects of the dorsal chaetotaxy, especially scales distribution, and may be considered as pseudocryptic taxa. Our study of tergal sensilla formula, scales morphology, and distribution in Mastigoceras reveals no clear morphological support for placing Mastigocerini within Heteromurinae.},
}
@article {pmid39512488,
year = {2024},
author = {Lewis, JH and Kojima, H and Suenaga, M and Petsopoulos, D and Fujisawa, Y and Truong, XL and Warren, DL},
title = {The era of cybertaxonomy: X-ray microtomography reveals cryptic diversity and concealed cuticular sculpture in Aphanerostethus Voss, 1957 (Coleoptera, Curculionidae).},
journal = {ZooKeys},
volume = {1217},
number = {},
pages = {1-45},
pmid = {39512488},
issn = {1313-2989},
abstract = {Weevils represent one of the most speciose and economically important animal clades, but remain poorly studied across much of the Oriental Region. Here, an integrative revision of the Oriental, flightless genus Aphanerostethus Voss, 1957 (Curculionidae: Molytinae) based on X-ray microtomography, multi-gene DNA barcoding (CO1, Cytb, 16S), and traditional morphological techniques (light microscopy, dissections) is presented. Twelve new species, namely, A.armatus Lewis &amp; Kojima, sp. nov., A.bifidus Kojima &amp; Lewis, sp. nov., A.darlingi Lewis, sp. nov., A.decoratus Lewis &amp; Kojima, sp. nov., A.falcatus Kojima, Lewis &amp; Fujisawa, sp. nov., A.incurvatus Kojima &amp; Lewis, sp. nov., A.japonicus Lewis &amp; Kojima, sp. nov., A.magnus Lewis &amp; Kojima, sp. nov., A.morimotoi Kojima &amp; Lewis, sp. nov., A.nudus Lewis &amp; Kojima, sp. nov., A.spinosus Lewis &amp; Kojima, sp. nov., and A.taiwanus Lewis, Fujisawa &amp; Kojima, sp. nov. are described from Japan, Taiwan, Vietnam, and Malaysia. A neotype is designated for A.vannideki Voss, 1957. The hitherto monotypic genus Darumazo Morimoto &amp; Miyakawa, 1985, syn. nov. is synonymized under Aphanerostethus based on new morphological data and Aphanerostethusdistinctus (Morimoto &amp; Miyakawa, 1985), comb. nov. is transferred accordingly. X-ray microtomography is successfully used to explore for stable interspecific differences in cuticular, internal and micro morphology. Remarkable species-specific sexual dimorphism in the metatibial uncus is described in seven of the newly described Aphanerostethus species and the evolution of this character is discussed.},
}
@article {pmid39502327,
year = {2024},
author = {Mao, H and Wang, Z and Shan, Y and Cheng, X and Yu, J},
title = {The complete genome sequence of the chloroplast of Bidens aurea.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {9},
number = {11},
pages = {1487-1491},
pmid = {39502327},
issn = {2380-2359},
abstract = {Bidens aurea (Asteraceae), a native of tropical America is now widespread in Asia and the Americas. We explored the B. aurea chloroplast genome and conducted a phylogenetic analysis. The chloroplast genome was circular, consisting of a large single copy (LSC) of 83,909 base pairs (bp), a small single copy (SSC) of 18,407 bp, and two inverted repeat regions (IR) of 24,729 bp each. Phylogenetic analysis showed that the 19 Bidens taxa were divided into five major clades, and B. aurea was most closely related to two species. Our findings offer a high-quality B. aurea chloroplast genome, aiding DNA barcode development and evolutionary history reconstruction.},
}
@article {pmid39501899,
year = {2024},
author = {Zhang, T and Dong, B and Wang, H and Zhang, S},
title = {An innovative electrohydrodynamics-driven SERS platform for molecular stratification and treatment monitoring of lung cancer.},
journal = {Journal of materials chemistry. B},
volume = {12},
number = {47},
pages = {12139-12140},
doi = {10.1039/d4tb01434k},
pmid = {39501899},
issn = {2050-7518},
mesh = {Humans ; Extracellular Vesicles/chemistry ; *Gold/chemistry ; *Lung Neoplasms/diagnosis ; Microelectrodes ; *Spectrum Analysis, Raman ; Surface Properties ; },
abstract = {The advancement of molecular diagnostics for lung cancer stratification and monitoring is essential for the strategic planning and prompt modification of treatments, aiming to enhance clinical results. To address this need, we suggest a nanocavity structure designed to sensitively analyze the protein signature on small extracellular vesicles (sEVs). This approach facilitates precise, noninvasive staging and treatment monitoring of lung cancer. The nanocavity is created through molecular recognition, involving the interaction of sEVs with nanobox-based core-shell surface-enhanced Raman scattering (SERS) barcodes and asymmetric, mirrorlike gold microelectrodes. By applying an alternating current to the gold microelectrodes, a nanofluidic shear force was generated, promoting the binding of sEVs and the effective assembly of the nanoboxes. This interaction induced a nanocavity between the nanobox and the gold microelectrode, which significantly amplified the electromagnetic field. This amplification enhanced Raman signals from four SERS barcodes simultaneously, allowing the generation of patient-specific molecular sEV signatures. When tested on a cohort of clinical samples (n = 76) using the nanocavity architecture, these patient-specific sEV molecular signatures accurately identified, stratified, and monitored lung cancer patients' treatment, demonstrating its potential for clinical application.},
}
@article {pmid39497575,
year = {2024},
author = {Velázquez-Urrieta, Y and García-Varela, M and Pérez-Ponce de León, G},
title = {Assessing the diversity of freshwater fish trematodes from Laguna Escondida, Los Tuxtlas tropical rainforest, Mexico, using morphology and 28S rDNA sequences as barcodes.},
journal = {Journal of helminthology},
volume = {98},
number = {},
pages = {e67},
doi = {10.1017/S0022149X2400049X},
pmid = {39497575},
issn = {1475-2697},
mesh = {Animals ; *Trematoda/genetics/classification/isolation &amp; purification/anatomy &amp; histology ; Mexico ; *Fishes/parasitology ; *RNA, Ribosomal, 28S/genetics ; *Phylogeny ; *DNA Barcoding, Taxonomic ; *Fresh Water/parasitology ; *DNA, Ribosomal/genetics ; *Rainforest ; Fish Diseases/parasitology ; Biodiversity ; Trematode Infections/parasitology/veterinary ; DNA, Helminth/genetics ; Lakes/parasitology ; },
abstract = {Despite a great effort made for almost 90 years, the diversity of freshwater fish trematodes in Mexico is still far from being fully known. The addition of molecular data to the description of trematode diversity in the last two decades added the potential to establish more robust species limits and a more accurate biodiversity estimation, but also led in some instances to the recognition of cryptic species complexes. Here, we used sequences of the large subunit of the nuclear ribosomal gene (28S rRNA) as barcodes, and morphological data, to assess the diversity of freshwater fish trematodes from a lake within a tropical rainforest. Eighty freshwater fish specimens of eight species were studied, and 120 trematode specimens were collected. Morphologically, specimens were allocated into nine genera; molecular phylogenetic analyses along with sequence divergence data provided evidence for recognising 11 trematode taxa, six adults and five metacercariae; six of them were identified to species level. Geographical distribution and host association patterns are briefly discussed for each trematode taxa.},
}
@article {pmid39497202,
year = {2024},
author = {Benallal, KE and Mefissel, M and Dib, Y and Depaquit, J and Kavan, D and Harrat, Z and Dvořák, V and Volf, P and Halada, P},
title = {Phlebotomine sand fly survey, blood meal source identification, and description of Sergentomyia imihra n. sp. in the central Sahara of Algeria.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {449},
pmid = {39497202},
issn = {1756-3305},
mesh = {Animals ; Algeria ; *Psychodidae/classification/physiology/anatomy &amp; histology ; Female ; Humans ; *Insect Vectors/classification/physiology/parasitology/anatomy &amp; histology ; *Feeding Behavior ; Phlebotomus/classification/anatomy &amp; histology/physiology/genetics ; Male ; Leishmaniasis/transmission ; Leishmania/genetics/physiology/classification ; Goats/parasitology ; },
abstract = {BACKGROUND: Phlebotomine sand flies (Diptera: Psychodidae) are important vectors of various pathogens, mainly Leishmania parasites. In the Old World, the most important genus in term of pathogens transmission is the genus Phlebotomus, which includes many proven or suspected vectors of several Leishmania species, while the genus Sergentomyia remains so far unproven as a vector of human pathogens. Algeria is one of the most affected countries by human leishmaniasis.<br><br>METHODS: In the present study, an entomological survey was carried out in two provinces, Gharda&#xef;a and Illizi, located in the north and central Sahara, respectively, where cases of human leishmaniasis are recorded. Our goal was to understand the role of the local sand fly species in the transmission of Leishmania parasites and to analyze their blood meal preferences. Collected sand flies were identified by a combination of morphological and molecular approaches that included DNA-barcoding and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) protein profiling. In addition, female blood meals were analyzed by peptide mass mapping using MALDI-TOF MS.<br><br>RESULTS: In total, 640 sand fly specimens belonging to Phlebotomus and Sergentomyia genera were collected in the two provinces. Sergentomyia antennata and Se.&#xa0;fallax were most abundant species in Gharda&#xef;a, and Ph.&#xa0;papatasi and Ph.&#xa0;alexandri in Illizi. In addition, a new sand fly species was described in Illizi named Sergentomyia (Sergentomyia) imihra n. sp. Blood meal analysis of the engorged females revealed various mammalian hosts, especially goats, but also humans for Phlebotomus papatasi and Ph.&#xa0;alexandri, suggesting that these vector species are opportunistic feeders.<br><br>CONCLUSIONS: Integrative approach that combined morphological analysis, sequencing of DNA markers, and protein profiling enabled the recognition and description of a new Sergentomyia species, raising the number of the Algerian sand fly fauna to 27 species. Further sand fly surveillance in the central Sahara is recommended to identify the thus-far unknown males of Se.&#xa0;imihra n. sp.},
}
@article {pmid39497190,
year = {2024},
author = {Qi, J and Li, Z and Zhang, YZ and Li, G and Gao, X and Han, R},
title = {TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {285},
pmid = {39497190},
issn = {1474-760X},
mesh = {*Nanopore Sequencing/methods ; *Software ; DNA Barcoding, Taxonomic/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Nanopores ; },
abstract = {Oxford Nanopore Technologies (ONT) offers ultrahigh-throughput multi-sample sequencing but only provides barcode kits that enable up to 96-sample multiplexing. We present TDFPS-Designer, a new toolkit for nanopore sequencing barcode design, which creates significantly more barcodes: 137 with a length of 20 base pairs, 410 at 24 bp, and 1779 at 30 bp, far surpassing ONT's offerings. It includes GPU-based acceleration for ultra-fast demultiplexing and designs robust barcodes suitable for high-error ONT data. TDFPS-Designer outperforms current methods, improving the demultiplexing recall rate by 20% relative to Guppy, without a reduction in precision.},
}
@article {pmid39497089,
year = {2024},
author = {Zhang, J and Zhou, D and Chen, W and Lin, P and Zhao, S and Wang, M and Wang, H and Shi, S and Mehmood, F and Ye, X and Meng, J and Zhuang, W},
title = {Comparison of the chloroplast genomics of nine endangered Habenaria species and phylogenetic analysis.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {1046},
pmid = {39497089},
issn = {1471-2229},
mesh = {*Phylogeny ; *Genome, Chloroplast ; *Endangered Species ; *Orchidaceae/genetics/classification ; Genomics ; Microsatellite Repeats/genetics ; Chloroplasts/genetics ; },
abstract = {BACKGROUND: Habenaria, a genus in the family Orchidaceae, are the nearly cosmopolitan orchids, and most species have significant medicinal and ornamental values. Despite the morphological and molecular data that have been studied in recent years, the phylogenetic relationship is still unclear.<br><br>RESULTS: We sequenced, assembled, and annotated the chloroplast (cp) genomes of two species (Habenaria aitchisonii Rchb.f. and Habenaria tibetica Schltr.ex Limpricht) of Habenaria grown on the Qinghai-Tibetan Plateau (QTP), and compared them with seven previously published cp genomes which may aid in the genomic profiling of these species. The two genomes ranged from 155,259-155,269&#xa0;bp in length and both included 132 genes, encoding 86 proteins, 38 tRNAs and 8 rRNAs. In the cp genomes, the tandem repeats (797), SSRs (2195) and diverse loci (3214) were identified. Comparative analyses of codon usage, amino frequency, microsatellite, oligo repeats and transition and transversion substitutions revealed similarities between the species. Moreover, we identified 16 highly polymorphic regions with a nucleotide diversity above 0.02, which may be suitable for robust authentic barcoding and inferring in the phylogeny of Habenaria species. Among the polymorphic regions, positive selection was significantly exerted on several genes, such as cemA, petA, and ycf1. This finding may suggest an important adaptation strategy for the two Habenaria species on the QTP. The phylogenetic relationship revealed that H. aitchisonii and H. tibetica were more closely related to each other than to the other species, and the other seven species were clustered in three groups. In addition, the estimated divergence time suggested that the two species separated from the others approximately 0.39 Mya in the Neogene period. Our findings also suggest that Habenaria can be divided into different sections.<br><br>CONCLUSIONS: The results of this study enriched the genomics resources of Habenaria, and SSR marker may aid in the conservation management of two endangered species.},
}
@article {pmid39494514,
year = {2024},
author = {Pradhan, R and Chimene, D and Ko, BS and Goncharov, A and Ozcan, A and McShane, MJ},
title = {Insertable Biomaterial-Based Multianalyte Barcode Sensor toward Continuous Monitoring of Glucose and Oxygen.},
journal = {ACS sensors},
volume = {9},
number = {11},
pages = {6060-6070},
pmid = {39494514},
issn = {2379-3694},
mesh = {*Oxygen/chemistry ; *Biosensing Techniques/methods/instrumentation ; *Hydrogels/chemistry ; *Biocompatible Materials/chemistry ; Animals ; Glucose/analysis ; Polyethylene Glycols/chemistry ; Blood Glucose/analysis ; Humans ; },
abstract = {Chronic diseases, including diabetes, cardiovascular diseases, and microvascular complications, contribute significantly to global morbidity and mortality. Current monitoring tools such as glucometers and continuous glucose monitors only measure one analyte; multiplexing technologies offer a promising approach for monitoring multiple biomarkers, enabling the management of comorbidities and providing more comprehensive disease insights. In this work, we describe a miniaturized optical "barcode" sensor with high biocompatibility for the continuous monitoring of glucose and oxygen. This enzymatic sensor relies on oxygen consumption in proportion to local glucose levels and the phosphorescence reporting of tissue oxygen with a lifetime-based probe. The sensor was specifically designed to operate in a tissue environment with low levels of dissolved oxygen. The barcode sensor consists of a poly(ethylene glycol) diacrylate (PEGDA) hydrogel with four discrete compartments separately filled with glucose- or oxygen-sensing phosphorescent microparticles. We evaluated the response of the barcode hydrogels to fluctuating glucose levels over the physiological range under low oxygen conditions, demonstrating the controlled tuning of dynamic range and sensitivity. Moreover, the barcode sensor exhibited remarkable storage stability over 12 weeks, along with full reversibility and excellent reproducibility (∼6% variability in the phosphorescence lifetime) over nearly 50 devices. Electron beam sterilization had a negligible effect on the glucose response of the barcode sensors. Furthermore, our investigation revealed minimal phosphorescence lifetime changes in oxygen compartments while exhibiting increased lifetime in glucose-responsive compartments when subjected to alternating glucose concentrations (0 and 200 mg/dL), showcasing the sensor's multianalyte sensing capabilities without crosstalk between compartments. Additionally, the evaluation of chronic tissue response to sensors inserted in pigs revealed the appropriate biocompatibility of the barcodes as well as excellent material stability over many months. These findings support further development of similar technologies for introducing optical assays for multiple biomarkers that can provide continuous or on-demand feedback to individuals to manage chronic conditions.},
}
@article {pmid39494108,
year = {2024},
author = {Yetchom Fondjo, JA and Nzoko Fiemapong, AR and Tindo, M and Duressa, TF and Ivković, S and Husemann, M},
title = {Taxonomic review of the grasshopper genus Pteropera Karsch, 1891 (Orthoptera, Acrididea, Catantopinae) with description of three new species and a preliminary phylogeny of the Cameroonian species.},
journal = {ZooKeys},
volume = {1216},
number = {},
pages = {219-264},
pmid = {39494108},
issn = {1313-2989},
abstract = {The Afrotropical grasshopper genus Pteropera Karsch, 1891, is reviewed. Some species present in Cameroon are described, Pteroperaaugustini Donskoff, 1981, is recorded for the first time in the country, and three new species are described from Cameroon, Pteroperakennei Yetchom &amp; Husemann, sp. nov., Pteroperamatzkei Yetchom &amp; Husemann, sp. nov. and Pteroperamissoupi Yetchom &amp; Husemann, sp. nov., increasing the number of Pteropera species in Cameroon from eight to 12, and overall to 30 species in Central Africa. An updated key of Pteropera is provided. Photographs with data on the distributions of all known species are given. In addition, a phylogenetic tree was constructed using maximum likelihood and Bayesian inference on the basis of a concatenated dataset of COI, 16S, and 12S markers of available Cameroonian species. The maximum likelihood and Bayesian inference analyses of the concatenated datasets resulted in a well-resolved phylogeny of the group and species of Pteropera were recovered as monophyletic, largely with high support. In all cases, the discrimination of all studied species based on barcode information was congruent with the species limits determined by traditional taxonomy. Our findings show the potential of integrative taxonomy to resolve the relationships among grasshoppers below the family level. Further analyses, including more comprehensive taxon sampling and additional nuclear markers, are needed, and the occurrence of several taxa still needs to be confirmed in African rainforests.},
}
@article {pmid39490742,
year = {2025},
author = {Surwase, SS and Zhou, XMM and Luly, KM and Zhu, Q and Anders, RA and Green, JJ and Tzeng, SY and Sunshine, JC},
title = {Highly Multiplexed Immunofluorescence PhenoCycler Panel for Murine Formalin-Fixed Paraffin-Embedded Tissues Yields Insight Into Tumor Microenvironment Immunoengineering.},
journal = {Laboratory investigation; a journal of technical methods and pathology},
volume = {105},
number = {1},
pages = {102165},
doi = {10.1016/j.labinv.2024.102165},
pmid = {39490742},
issn = {1530-0307},
support = {R37 CA246699/CA/NCI NIH HHS/United States ; P41 EB028239/EB/NIBIB NIH HHS/United States ; R01 CA228133/CA/NCI NIH HHS/United States ; P30 CA006973/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; *Tumor Microenvironment ; Mice ; *Paraffin Embedding ; *Formaldehyde ; *Fluorescent Antibody Technique/methods ; Mice, Inbred C57BL ; Tissue Fixation/methods ; Melanoma, Experimental/metabolism/immunology ; Female ; },
abstract = {Spatial proteomics profiling is an emerging set of technologies that has the potential to elucidate the cell types, interactions, and molecular signatures that make up complex tissue microenvironments, with applications in the study of cancer, immunity, and much more. An emerging technique in the field is CoDetection by indEXing, recently renamed as the PhenoCycler system. This is a highly multiplexed immunofluorescence imaging technology that relies on oligonucleotide-barcoded antibodies and cyclic immunofluorescence to visualize many antibody markers in a single specimen while preserving tissue architecture. Existing PhenoCycler panels are primarily designed for fresh frozen tissues. Formalin-fixed paraffin-embedded blocks offer several advantages in preclinical research, but few antibody clones have been identified in this setting for PhenoCycler imaging. Here, we present a novel PhenoCycler panel of 28 validated antibodies for murine formalin-fixed paraffin-embedded tissues. We describe our workflow for selecting and validating clones, barcoding antibodies, designing our panel, and performing multiplex imaging. We further detail our analysis pipeline for comparing marker expressions, clustering and phenotyping single-cell proteomics data, and quantifying spatial relationships. We then apply our panel and analysis protocol to profile the effects of 3 gene delivery nanoparticle formulations, in combination with systemic anti-PD1, on the murine melanoma tumor immune microenvironment. Intralesional delivery of genes expressing the costimulatory molecule 4-1BBL and the cytokine IL-12 led to a shift toward intratumoral M1 macrophage polarization and promoted closer associations between intratumoral CD8 T cells and macrophages. Delivery of interferon gamma, in addition to 4-1BBL and IL-12, not only further increased markers of antigen presentation on tumor cells and intratumoral antigen-presenting cells but also promoted greater expression of checkpoint marker PD-L1 and closer associations between intratumoral CD8 T cells and PD-L1-expressing tumor cells. These findings help explain the benefits of 4-1BBL and IL-12 delivery while offering additional mechanistic insights into the limitations of interferon gamma therapeutic efficacy.},
}
@article {pmid39484616,
year = {2024},
author = {Lu, X and Pritko, DJ and Abravanel, ME and Huggins, JR and Ogunleye, F and Biswas, T and Ashy, KC and Woods, SK and Livingston, MWT and Blenner, MA and Birtwistle, MR},
title = {Genetically-Encoded Fluorescence Barcodes for Single-Cell Analysis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39484616},
issn = {2692-8205},
support = {R35 GM141891/GM/NIGMS NIH HHS/United States ; },
abstract = {Genetically-encoded, single-cell barcodes are broadly useful for experimental tasks such as lineage tracing or genetic screens. For such applications, a barcode library would ideally have high diversity (many unique barcodes), non-destructive identification (repeated measurements in the same cells or population), and fast, inexpensive readout (many cells and conditions). Current nucleic acid barcoding methods generate high diversity but require destructive and slow/expensive readout, and current fluorescence barcoding methods are non-destructive, fast, and inexpensive to readout but lack high diversity. We recently proposed theory for how fluorescent protein combinations may generate a high-diversity barcode library with non-destructive, fast and inexpensive identification. Here, we present an initial experimental proof-of-concept by generating a library of ~150 barcodes from two-way combinations of 18 fluorescent proteins. We use a pooled cloning strategy to generate a barcode library that is validated to contain every possible combination of the 18 fluorescent proteins. Experimental results using single mammalian cells and spectral flow cytometry demonstrate excellent classification performance of individual fluorescent proteins, with the exception of mTFP1, and of most evaluated barcodes, with many true positive rates >99%. The library is compatible with genetic screening for hundreds of genes (or gene pairs) and lineage tracing hundreds of clones. This work lays a foundation for greater diversity libraries (potentially ~10[5] and more) generated from hundreds of spectrally-resolvable tandem fluorescent protein probes.},
}
@article {pmid39483244,
year = {2024},
author = {Dockerill, M and Sabale, PM and Russo, F and Barluenga, S and Winssinger, N},
title = {Translation of Deoxyribonucleic Acid into Synthetic Alpha Helical Peptides for Darwinian Evolution.},
journal = {JACS Au},
volume = {4},
number = {10},
pages = {4013-4022},
pmid = {39483244},
issn = {2691-3704},
abstract = {DNA-encoded libraries connect the phenotypes of synthetic molecules to a DNA barcode; however, most libraries do not tap into the potential of Darwinian evolution. Herein, we report a DNA-templated synthesis (DTS) architecture to make peptides that are stabilized into α-helical conformations via head-to-tail supramolecular cyclization. Using a pilot library targeting MDM2, we show that repeated screening can amplify a binder from the lowest abundance in the library to a ranking that correlates to binding affinity. The study also highlights the need to design libraries such that the chemistry avoids biases from the heterogeneous yield in DTS.},
}
@article {pmid39480818,
year = {2024},
author = {Ramesh, S and Rapp, S and Tapias Gomez, J and Levine, B and Tapias-Gomez, D and Chung, D and Truong, Z},
title = {Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases.},
journal = {PloS one},
volume = {19},
number = {10},
pages = {e0309707},
pmid = {39480818},
issn = {1932-6203},
mesh = {*User-Computer Interface ; *Software ; *DNA Barcoding, Taxonomic/methods ; Databases, Genetic ; Databases, Nucleic Acid ; Web Browser ; },
abstract = {Land managers, researchers, and regulators increasingly utilize environmental DNA (eDNA) techniques to monitor species richness, presence, and absence. In order to properly develop a biological assay for eDNA metabarcoding or quantitative PCR, scientists must be able to find not only reference sequences (previously identified sequences in a genomics database) that match their target taxa but also reference sequences that match non-target taxa. Determining which taxa have publicly available sequences in a time-efficient and accurate manner currently requires computational skills to search, manipulate, and parse multiple unconnected DNA sequence databases. Our team iteratively designed a Graphic User Interface (GUI) Shiny application called the Reference Sequence Browser (RSB) that provides users efficient and intuitive access to multiple genetic databases regardless of computer programming expertise. The application returns the number of publicly accessible barcode markers per organism in the NCBI Nucleotide, BOLD, or CALeDNA CRUX Metabarcoding Reference Databases. Depending on the database, we offer various search filters such as min and max sequence length or country of origin. Users can then download the FASTA/GenBank files from the RSB web tool, view statistics about the data, and explore results to determine details about the availability or absence of reference sequences.},
}
@article {pmid39485438,
year = {2024},
author = {Pham, NV and Nguyen, QN and Nguyen, TV and Nguyen, TA and Ta, VD},
title = {High quality factor, monodisperse micron-sized random lasers based on porous PLGA spheres.},
journal = {Optics letters},
volume = {49},
number = {21},
pages = {6165-6168},
doi = {10.1364/OL.538543},
pmid = {39485438},
issn = {1539-4794},
abstract = {Miniature random lasers with high quality factor are crucial for applications in barcoding, bioimaging, and on-chip technologies. However, achieving monodisperse and size-tunable biocompatible random lasers has been a significant challenge. In this study, we employed poly(lactic-co-glycolic) acid (PLGA), a biocompatible material approved for medical use, as the base material for random lasers. By integrating a dye-doped PLGA solution with a microfluidic system, we successfully fabricated monodisperse and miniature dye-doped PLGA spheres with tunable sizes ranging from 25 to 52 µm. Upon optical pulse excitation, these spheres exhibited strong random lasing emission at 610-640 nm with a threshold of approximately 22 µJ·mm[-2]. The lasing modes demonstrated a spectral linewidth of 0.2 nm, corresponding to a quality factor of 3100. Fourier transform analysis of the lasing emission revealed fundamental cavity lengths, providing insights into the properties of the random lasers.},
}
@article {pmid39482470,
year = {2025},
author = {Dini, A and Barker, H and Piki, E and Sharma, S and Raivola, J and Murumägi, A and Ungureanu, D},
title = {A multiplex single-cell RNA-Seq pharmacotranscriptomics pipeline for drug discovery.},
journal = {Nature chemical biology},
volume = {21},
number = {3},
pages = {432-442},
pmid = {39482470},
issn = {1552-4469},
support = {336449//Academy of Finland (Suomen Akatemia)/ ; 333583//Academy of Finland (Suomen Akatemia)/ ; 288475//Academy of Finland (Suomen Akatemia)/ ; 271845//Academy of Finland (Suomen Akatemia)/ ; 349787//Academy of Finland (Suomen Akatemia)/ ; },
mesh = {Humans ; *Single-Cell Analysis/methods ; *Drug Discovery/methods ; Female ; RNA-Seq/methods ; Antineoplastic Agents/pharmacology ; Ovarian Neoplasms/drug therapy/genetics/metabolism/pathology ; Cell Line, Tumor ; TOR Serine-Threonine Kinases/metabolism/genetics/antagonists &amp; inhibitors ; Caveolin 1/genetics/metabolism ; ErbB Receptors/genetics/antagonists &amp; inhibitors/metabolism ; Proto-Oncogene Proteins c-akt/metabolism/genetics ; Drug Screening Assays, Antitumor/methods ; Single-Cell Gene Expression Analysis ; },
abstract = {The gene-regulatory dynamics governing drug responses in cancer are yet to be fully understood. Here, we report a pipeline capable of producing high-throughput pharmacotranscriptomic profiling through live-cell barcoding using antibody-oligonucleotide conjugates. This pipeline combines drug screening with 96-plex single-cell RNA sequencing. We show the potential of this approach by exploring the heterogeneous transcriptional landscape of primary high-grade serous ovarian cancer (HGSOC) cells after treatment with 45 drugs, with 13 distinct classes of mechanisms of action. A subset of phosphatidylinositol 3-OH kinase (PI3K), protein kinase B (AKT) and mammalian target of rapamycin (mTOR) inhibitors induced the activation of receptor tyrosine kinases, such as the epithelial growth factor receptor (EGFR), and this was mediated by the upregulation of caveolin 1 (CAV1). This drug resistance feedback loop could be mitigated by the synergistic action of agents targeting PI3K-AKT-mTOR and EGFR for HGSOC with CAV1 and EGFR expression. Using this workflow could enable the personalized testing of patient-derived tumor samples at single-cell resolution.},
}
@article {pmid39480094,
year = {2024},
author = {Alexander, LM and Khalid, S and Gallego-Lopez, GM and Astmann, TJ and Oh, J-H and Heggen, M and Huss, P and Fisher, R and Mukherjee, A and Raman, S and Choi, IY and Smith, MN and Rogers, CJ and Epperly, MW and Knoll, LJ and Greenberger, JS and van Pijkeren, J-P},
title = {Development of a Limosilactobacillus reuteri therapeutic delivery platform with reduced colonization potential.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {11},
pages = {e0031224},
pmid = {39480094},
issn = {1098-5336},
support = {T32 GM007215/GM/NIGMS NIH HHS/United States ; 75N93021C00008/AI/NIAID NIH HHS/United States ; R01 GM135483/GM/NIGMS NIH HHS/United States ; 2021-67015-34316//U.S. Department of Agriculture (USDA)/ ; R01GM135483//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; U01 AI172885/AI/NIAID NIH HHS/United States ; //Louis and Elsa Thomsen Wisconsin Distinguished Graduate Fellowship from the UW-Madison College of Agricultural &amp; Life Sciences/ ; //Dissertation Completion Fellowship from the UW-Madison Graduate School/ ; U01-AI172885//HHS | National Institutes of Health (NIH)/ ; R41 AI157357/AI/NIAID NIH HHS/United States ; //SciMed Graduate Research Scholars Program at UW-Madison/ ; R21 AI146634/AI/NIAID NIH HHS/United States ; 1R41AI157357-01//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; MSN1856150//UW-Madison Food Research Institute/ ; },
mesh = {*Limosilactobacillus reuteri/genetics/physiology ; Animals ; Mice ; Humans ; Bacterial Adhesion ; HT29 Cells ; Adhesins, Bacterial/genetics ; Drug Delivery Systems ; Female ; },
abstract = {Bacterial biotherapeutic delivery vehicles have the potential to treat a variety of diseases. This approach obviates the need to purify the recombinant effector molecule, allows delivery of therapeutics in situ via oral or intranasal administration, and protects the effector molecule during gastrointestinal transit. Lactic acid bacteria have been broadly developed as therapeutic delivery vehicles though risks associated with the colonization of a genetically modified microorganism have so-far not been addressed. Here, we present an engineered Limosilactobacillus reuteri strain with reduced colonization potential. We applied a dual-recombineering scheme for efficient barcoding and generated mutants in genes encoding five previously characterized and four uncharacterized putative adhesins. Compared with the wild type, none of the mutants were reduced in their ability to survive gastrointestinal transit in mice. CmbA was identified as a key protein in L. reuteri adhesion to HT-29 and enteroid cells. The nonuple mutant, a single strain with all nine genes encoding adhesins inactivated, had reduced capacity to adhere to enteroid monolayers. The nonuple mutant producing murine IFN-β was equally effective as its wild-type counterpart in mitigating radiation toxicity in mice. Thus, this work established a novel therapeutic delivery platform that lays a foundation for its application in other microbial therapeutic delivery candidates and furthers the progress of the L. reuteri delivery system towards human use.IMPORTANCEOne major advantage to leverage gut microbes that have co-evolved with the vertebrate host is that evolution already has taken care of the difficult task to optimize survival within a complex ecosystem. The availability of the ecological niche will support colonization. However, long-term colonization of a recombinant microbe may not be desirable. Therefore, strategies need to be developed to overcome this potential safety concern. In this work, we developed a single strain in which we inactivated the encoding sortase, and eight genes encoding characterized/putative adhesins. Each individual mutant was characterized for growth and adhesion to epithelial cells. On enteroid cells, the nonuple mutant has a reduced adhesion potential compared with the wild-type strain. In a model of total-body irradiation, the nonuple strain engineered to release murine interferon-β performed comparable to a derivative of the wild-type strain that releases interferon-β. This work is an important step toward the application of recombinant L. reuteri in humans.},
}
@article {pmid39478489,
year = {2024},
author = {Jiang, LQ and Drew, BT and Arthan, W and Yu, GY and Wu, H and Zhao, Y and Peng, H and Xiang, CL},
title = {Comparative plastome analysis of Arundinelleae (Poaceae, Panicoideae), with implications for phylogenetic relationships and plastome evolution.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1016},
pmid = {39478489},
issn = {1471-2164},
support = {31110103911//National Natural Science Foundation of China/ ; },
mesh = {*Phylogeny ; *Poaceae/genetics/classification ; *Evolution, Molecular ; Genome, Plastid ; Base Composition ; },
abstract = {BACKGROUND: Arundinelleae is a small tribe within the Poaceae (grass family) possessing a widespread distribution that includes Asia, the Americas, and Africa. Several species of Arundinelleae are used as natural forage, feed, and raw materials for paper. The tribe is taxonomically cumbersome due to a paucity of clear diagnostic morphological characters. There has been scant genetic and genomic research conducted for this group, and as a result the phylogenetic relationships and species boundaries within Arundinelleae are poorly understood.<br><br>RESULTS: We compared and analyzed 11 plastomes of Arundinelleae, of which seven plastomes were newly sequenced. The plastomes range from 139,629 base pairs (bp) (Garnotia tenella) to 140,943&#xa0;bp (Arundinella barbinodis), with a standard four-part structure. The average GC content was 38.39%, but varied in different regions of the plastome. In all, 110 genes were annotated, comprising 76 protein-coding genes, 30 tRNA genes, and four rRNA genes. Furthermore, 539 simple sequence repeats, 519 long repeats, and 10 hyper-variable regions were identified from the 11 plastomes of Arundinelleae. A phylogenetic reconstruction of Panicoideae based on 98 plastomes demonstrated the monophyly of Arundinella and Garnotia, but the circumscription of Arundinelleae remains unresolved.<br><br>CONCLUSION: Complete chloroplast genome sequences can improve phylogenetic resolution relative to single marker approaches, particularly within taxonomically challenging groups. All phylogenetic analyses strongly support the monophyly of Arundinella and Garnotia, respectively, but the monophylly of Arundinelleae was not well supported. The intergeneric phylogenetic relationships within Arundinelleae require clarification, indicating that more data is necessary to resolve generic boundaries and evaluate the monophyly of Arundinelleae. A comprehensive taxonomic revision for the tribe is necessary. In addition, the identified hyper-variable regions could function as molecular markers for clarifying phylogenetic relationships and potentially as barcoding markers for species identification in the future.},
}
@article {pmid39478225,
year = {2024},
author = {Lu, Z and Mo, S and Xie, D and Zhai, X and Deng, S and Zhou, K and Wang, K and Kang, X and Zhang, H and Tong, J and Hou, L and Hu, H and Li, X and Zhou, D and Lee, LTO and Liu, L and Zhu, Y and Yu, J and Lan, P and Wang, J and He, Z and He, X and Hu, Z},
title = {Polyclonal-to-monoclonal transition in colorectal precancerous evolution.},
journal = {Nature},
volume = {636},
number = {8041},
pages = {233-240},
pmid = {39478225},
issn = {1476-4687},
mesh = {Animals ; Humans ; Male ; Mice ; Carcinogenesis/genetics/pathology ; *Cell Lineage ; Cell Transformation, Neoplastic/genetics/pathology ; *Clonal Evolution ; *Clone Cells/metabolism ; Colonic Polyps/pathology/genetics ; *Colorectal Neoplasms/genetics/pathology ; Disease Models, Animal ; DNA Barcoding, Taxonomic ; Exome Sequencing ; Genes, APC ; Inflammation/pathology/genetics ; *Precancerous Conditions/genetics/pathology ; *Single-Cell Analysis ; Single-Cell Gene Expression Analysis ; Whole Genome Sequencing ; Intestines/cytology/pathology ; },
abstract = {Unravelling the origin and evolution of precancerous lesions is crucial for effectively preventing malignant transformation, yet our current knowledge remains limited[1-3]. Here we used a base editor-enabled DNA barcoding system[4] to comprehensively map single-cell phylogenies in mouse models of intestinal tumorigenesis induced by inflammation or loss of the Apc gene. Through quantitative analysis of high-resolution phylogenies including 260,922 single cells from normal, inflamed and neoplastic intestinal tissues, we identified tens of independent cell lineages undergoing parallel clonal expansions within each lesion. We also found polyclonal origins of human sporadic colorectal polyps through bulk whole-exome sequencing and single-gland whole-genome sequencing. Genomic and clinical data support a model of polyclonal-to-monoclonal transition, with monoclonal lesions representing a more advanced stage. Single-cell RNA sequencing revealed extensive intercellular interactions in early polyclonal lesions, but there was significant loss of interactions during monoclonal transition. Therefore, our data suggest that colorectal precancer is often founded by many different lineages and highlight their cooperative interactions in the earliest stages of cancer formation. These findings provide insights into opportunities for earlier intervention in colorectal cancer.},
}
@article {pmid39472907,
year = {2024},
author = {Nguyen, TT and Nugraheni, YR and Nguyen, HLA and Arnuphapprasert, A and Pengsakul, T and Thong, LQ and Ampol, R and Siriyasatien, P and Kaewthamasorn, M},
title = {Survey of sand fly fauna in six provinces of Southern Vietnam with species identification using DNA barcoding.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {443},
pmid = {39472907},
issn = {1756-3305},
mesh = {Animals ; Vietnam/epidemiology ; *DNA Barcoding, Taxonomic ; *Psychodidae/classification/genetics ; *Phylogeny ; *Biodiversity ; Electron Transport Complex IV/genetics ; Cytochromes b/genetics ; Insect Vectors/classification/genetics ; Female ; Haplotypes ; Genetic Variation ; },
abstract = {BACKGROUND: Sand flies, belonging to the Psychodidae family, represent small, hairy insects that serve as significant vectors in various important medical and veterinary diseases. Despite being recognized by the World Health Organization as an endemic area for leishmaniasis, Southeast Asia lacks comprehensive information on the species composition and biology of sand flies. To address this, the current study aimed to survey sand fly biodiversity.<br><br>METHODS: Sand flies from six provinces in Southern Vietnam were collected using CDC light traps. Sand flies were subsequently identified morphologically and confirmed molecularly using mitochondrial cytochrome oxidase c subunit I (COI) and cytochrome b (cytb) sequences. BLASTN searches were conducted, and the species identity of sand flies was further confirmed through a Barcode of Life Database (BOLD) search utilizing COI sequences. Subsequently, nucleotide sequences were subjected to a panel of analyses including intraspecific variation, phylogenetic relationships and haplotype network. The average densities of collected sand flies (sand flies/trap/night) and species richness were also recorded.<br><br>RESULTS: A total of 753 sand flies were collected. After excluding damaged specimens, six sand fly species, namely Phlebotomus stantoni, Sergentomyia khawi, Se. silvatica, Se. barraudi, Se. bailyi and Grassomyia indica, were identified. All conspecific sand fly sequences, including Ph. stantoni, Se. barraudi, Gr. indica, Se. bailyi, Se. khawi and Se. silvatica, clustered with their reference sequences, corroborating the results of morphology-based identification, BLASTN analysis and BOLD search. For intraspecific variation of sand flies obtained from the current study, COI diversity indices were consistently higher than those of cytb.<br><br>CONCLUSIONS: This study provides the first updates on morphological and molecular characterization of sand flies in Southern Vietnam. This acquired knowledge on sand fly species composition is essential for controlling sand fly-borne diseases in this potentially endemic region.},
}
@article {pmid39470724,
year = {2025},
author = {Jiang, J and Ye, X and Kong, Y and Guo, C and Zhang, M and Cao, F and Zhang, Y and Pei, W},
title = {scLTdb: a comprehensive single-cell lineage tracing database.},
journal = {Nucleic acids research},
volume = {53},
number = {D1},
pages = {D1173-D1185},
pmid = {39470724},
issn = {1362-4962},
support = {2022YFA1105700//National Key R&amp;D Program of China/ ; 82270123//National Natural Science Foundation of China/ ; 2024SSYS0034 to W.P.//Key R&amp;D Program of Zhejiang Province/ ; //Westlake Education Foundation/ ; },
mesh = {*Cell Lineage/genetics ; *Single-Cell Analysis/methods ; Animals ; Humans ; Software ; Mice ; Databases, Genetic ; Cell Differentiation/genetics ; },
abstract = {Single-cell lineage tracing (scLT) is a powerful technique that integrates cellular barcoding with single-cell sequencing technologies. This new approach enables the simultaneous measurement of cell fate and molecular profiles at single-cell resolution, uncovering the gene regulatory program of cell fate determination. However, a comprehensive scLT database is not yet available. Here, we present the single-cell lineage tracing database (scLTdb, https://scltdb.com) containing 109 datasets that are manually curated and analyzed through a standard pipeline. The scLTdb provides interactive analysis modules for visualizing and re-analyzing scLT datasets, especially the comprehensive cell fate analysis and lineage relationship analysis. Importantly, scLTdb also allows users to identify fate-related gene signatures. In conclusion, scLTdb provides an interactive interface of scLT data exploration and analysis, and will facilitate the understanding of cell fate decision and lineage commitment in development and diseases.},
}
@article {pmid39468463,
year = {2024},
author = {Jiang, C and Liu, F and Qin, J and Hubert, N and Kang, B and Huang, L and Yan, Y},
title = {DNA barcode reference library of the fish larvae and eggs of the South China Sea: taxonomic effectiveness and geographic structure.},
journal = {BMC ecology and evolution},
volume = {24},
number = {1},
pages = {132},
pmid = {39468463},
issn = {2730-7182},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Larva/genetics/anatomy &amp; histology ; China ; Ovum ; Electron Transport Complex IV/genetics ; Gene Library ; },
abstract = {Fish early-stages constitute useful indicators of the states of marine ecosystems, as well as important fishery resources. Given the spectacular phenotypic changes during ontogeny, and the paucity of diagnostic morphological characters at the species level, the identification of fish early-stages is a challenging task. DNA barcoding, the use of the mitochondrial gene of the cytochrome c oxidase subunit I (COI) as an internal species tag, opened new perspectives for the identifications of both larval fish and fish eggs. However, the accuracy of the identifications assisted by DNA barcoding are dependent of the completeness of the DNA barcode reference libraries used to assigned unknown sequences to known species. Here, we built a DNA barcode reference library for 113 species of larval fish and 85 species of fish eggs involving the production of 741 newly generated DNA barcodes from South China Sea (63 localities). Together with 514 DNA barcodes mined from Genbank for 116 species from the South China Sea regions, a reference library including 1255 DNA barcodes for 308 species (248 locations) was assembled. The present study emphasizes the importance of integrating DNA barcoding to large scale inventories of early stages, as DNA-based species delimitation analyses delimited 305 molecular operational taxonomic units (MOTUs) and multiple cases of discordance with morphological identifications were detected. Cryptic diversity is detected with 14 species displaying two MOTUs and a total of 23 species were lumped into 11 MOTUs due to low interspecific divergence and/or mixed lineages.},
}
@article {pmid39467896,
year = {2024},
author = {Thakur, P and Khanal, S and Tapwal, A and Kumar, D and Verma, R and Chauhan, P and Sharma, N},
title = {Exploring Ganoderma lucidum: morphology, cultivation and market potential.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {40},
number = {11},
pages = {369},
pmid = {39467896},
issn = {1573-0972},
support = {CRG/2021/001815//DST, New Delhi/ ; CRG/2021/001815//DST, New Delhi/ ; CRG/2021/001815//DST, New Delhi/ ; },
mesh = {*Reishi/growth &amp; development/metabolism/genetics ; *Fermentation ; *Wood/microbiology ; *Phylogeny ; Biomass ; DNA Barcoding, Taxonomic ; },
abstract = {Ganoderma lucidum, known as the "mushroom of immortality," is a white rot fungus renowned for its medicinal properties, attributed to its bioactive compounds. Although species with similar morphological traits to G. lucidum are found across the globe, precise identification is made possible through DNA barcoding and molecular phylogenetic analysis. Global cultivation and wild harvesting of G. lucidum are both done in response to the growing market needs. Artificial cultivation is typically performed on sawdust, but other woody substrates and the wood log method are also employed. This cultivation leverages the fungus's ecological role in converting industrial and agricultural solid wastes into biomass, thereby producing functional food and potential pharmaceutical sources. The review consolidates research on various aspects of, including cultivation methods (sawdust, agricultural waste, wood logs, and submerged fermentation), and the current global market conditions.},
}
@article {pmid39467031,
year = {2024},
author = {Fahlberg, MD and Forward, S and Assita, ER and Mazzola, M and Kiem, A and Handley, M and Yun, SH and Kwok, SJJ},
title = {Overcoming fixation and permeabilization challenges in flow cytometry by optical barcoding and multi-pass acquisition.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {105},
number = {11},
pages = {838-848},
doi = {10.1002/cyto.a.24904},
pmid = {39467031},
issn = {1552-4930},
support = {R44-GM139504/NH/NIH HHS/United States ; R43-GM140527/NH/NIH HHS/United States ; R01-EB033155/NH/NIH HHS/United States ; F31HL158020-03/NH/NIH HHS/United States ; T32GM132089-01/NH/NIH HHS/United States ; 5T32GM007226-43/NH/NIH HHS/United States ; R44-GM139504/NH/NIH HHS/United States ; R43-GM140527/NH/NIH HHS/United States ; R01-EB033155/NH/NIH HHS/United States ; F31HL158020-03/NH/NIH HHS/United States ; T32GM132089-01/NH/NIH HHS/United States ; 5T32GM007226-43/NH/NIH HHS/United States ; },
mesh = {*Flow Cytometry/methods ; Humans ; *Fluorescent Dyes/chemistry ; Tissue Fixation/methods ; Biomarkers/metabolism ; Cell Line, Tumor ; },
abstract = {The fixation and permeabilization of cells are essential for labeling intracellular biomarkers in flow cytometry. However, these chemical treatments often alter fragile targets, such as cell surface and fluorescent proteins (FPs), and can destroy chemically-sensitive fluorescent labels. This reduces measurement accuracy and introduces compromises into sample workflows, leading to losses in data quality. Here, we demonstrate a novel multi-pass flow cytometry approach to address this long-standing problem. Our technique utilizes individual cell barcoding with laser particles, enabling sequential analysis of the same cells with single-cell resolution maintained. Chemically-fragile protein markers and their fluorochrome conjugates are measured prior to destructive sample processing and adjoined to subsequent measurements of intracellular markers after fixation and permeabilization. We demonstrate the effectiveness of our technique in accurately measuring intracellular FPs and methanol-sensitive antigens and fluorophores, along with various surface and intracellular markers. This approach significantly enhances assay flexibility, enabling accurate and comprehensive cellular analysis without the constraints of conventional one-time measurement flow cytometry. This innovation paves new avenues in flow cytometry for a wide range of applications in immuno-oncology, stem cell research, and cell biology.},
}
@article {pmid39466839,
year = {2024},
author = {Dlauchy, D and Álvarez-Pérez, S and Tóbiás, A and Péter, G},
title = {Vishniacozyma floricola sp. nov., a flower-related tremellomycetous yeast species from Europe.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {10},
pages = {},
doi = {10.1099/ijsem.0.006555},
pmid = {39466839},
issn = {1466-5034},
mesh = {*Phylogeny ; *DNA, Fungal/genetics ; *Flowers/microbiology ; *Sequence Analysis, DNA ; *DNA, Ribosomal Spacer/genetics ; *Basidiomycota/genetics/classification/isolation &amp; purification ; Hungary ; Spain ; Mycological Typing Techniques ; },
abstract = {During the course of two independent studies conducted in Hungary and Spain, four conspecific yeast strains were isolated from flowers of different plant species. DNA sequences of two barcoding regions, the D1/D2 domain of the LSU rRNA gene and the internal transcribed spacer (ITS) region (ITS1-5.8S rRNA gene-ITS2), revealed that the four strains represent an undescribed Vishniacozyma (family Bulleribasidiaceae, Basidiomycota) species. In terms of pairwise sequence similarities and according to our phylogenetic analyses of the concatenated DNA sequences of the ITS region and the D1/D2 domain of the LSU rRNA gene, the undescribed species is most closely related to Vishniacozyma melezitolytica, a yeast species of phylloplane origin. The novel species differs from the type strain of V. melezitolytica by 8 substitutions and 3 insertion/deletion (indels) and 11 substitutions and 5 indels along the D1/D2 domain of the LSU rRNA gene and the ITS region, respectively. In addition to the DNA sequence divergences, the two species differ in some physiological characters as well. We propose the species Vishniacozyma floricola sp. nov. to accommodate the above-noted strains (holotype, NCAIM Y.02320; isotype, CBS 18939; MycoBank number, 856028).},
}
@article {pmid39466790,
year = {2024},
author = {Reyes Hueros, RA and Gier, RA and Shaffer, SM},
title = {Non-genetic differences underlie variability in proliferation among esophageal epithelial clones.},
journal = {PLoS computational biology},
volume = {20},
number = {10},
pages = {e1012360},
pmid = {39466790},
issn = {1553-7358},
support = {DP5 OD028144/OD/NIH HHS/United States ; UL1 TR001878/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; *Cell Proliferation/genetics ; *Epithelial Cells/cytology ; *Esophagus/cytology ; Clone Cells/cytology ; Cell Line ; Single-Cell Analysis/methods ; Computational Biology ; },
abstract = {Individual cells grown in culture exhibit remarkable differences in their growth, with some cells capable of forming large clusters, while others are limited or fail to grow at all. While these differences have been observed across cell lines and human samples, the growth dynamics and associated cell states remain poorly understood. In this study, we performed clonal tracing through imaging and cellular barcoding of an in vitro model of esophageal epithelial cells (EPC2-hTERT). We found that about 10% of clones grow exponentially, while the remaining have cells that become non-proliferative leading to a halt in the growth rate. Using mathematical models, we demonstrate two distinct growth behaviors: exponential and logistic. Further, we discovered that the propensity to grow exponentially is largely heritable through four doublings and that the less proliferative clones can become highly proliferative through increasing plating density. Combining barcoding with single-cell RNA-sequencing (scRNA-seq), we identified the cellular states associated with the highly proliferative clones, which include genes in the WNT and PI3K pathways. Finally, we identified an enrichment of cells resembling the highly proliferative cell state in the proliferating healthy human esophageal epithelium.},
}
@article {pmid39465511,
year = {2025},
author = {White, OW and Hall, A and Price, BW and Williams, ST and Clark, MD},
title = {A Snakemake Toolkit for the Batch Assembly, Annotation and Phylogenetic Analysis of Mitochondrial Genomes and Ribosomal Genes From Genome Skims of Museum Collections.},
journal = {Molecular ecology resources},
volume = {25},
number = {1},
pages = {e14036},
pmid = {39465511},
issn = {1755-0998},
mesh = {*Phylogeny ; *Museums ; *Genome, Mitochondrial/genetics ; Animals ; Gastropoda/genetics/classification ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; Molecular Sequence Annotation/methods ; },
abstract = {Low coverage 'genome-skims' are often used to assemble organelle genomes and ribosomal gene sequences for cost-effective phylogenetic and barcoding studies. Natural history collections hold invaluable biological information, yet poor preservation resulting in degraded DNA often hinders polymerase chain reaction-based analyses. However, it is possible to generate libraries and sequence the short fragments typical of degraded DNA to generate genome-skims from museum collections. Here we introduce a snakemake toolkit comprised of three pipelines skim2mito, skim2rrna and gene2phylo, designed to unlock the genomic potential of historical museum specimens using genome skimming. Specifically, skim2mito and skim2rrna perform the batch assembly, annotation and phylogenetic analysis of mitochondrial genomes and nuclear ribosomal genes, respectively, from low-coverage genome skims. The third pipeline gene2phylo takes a set of gene alignments and performs phylogenetic analysis of individual genes, partitioned analysis of concatenated alignments and a phylogenetic analysis based on gene trees. We benchmark our pipelines with simulated data, followed by testing with a novel genome skimming dataset from both recent and historical solariellid gastropod samples. We show that the toolkit can recover mitochondrial and ribosomal genes from poorly preserved museum specimens of the gastropod family Solariellidae, and the phylogenetic analysis is consistent with our current understanding of taxonomic relationships. The generation of bioinformatic pipelines that facilitate processing large quantities of sequence data from the vast repository of specimens held in natural history museum collections will greatly aid species discovery and exploration of biodiversity over time, ultimately aiding conservation efforts in the face of a changing planet.},
}
@article {pmid39463700,
year = {2024},
author = {Recuero, E and Etzler, FE and Caterino, MS},
title = {Most soil and litter arthropods are unidentifiable based on current DNA barcode reference libraries.},
journal = {Current zoology},
volume = {70},
number = {5},
pages = {637-646},
pmid = {39463700},
issn = {1674-5507},
abstract = {We are far from knowing all species living on the planet. Understanding biodiversity is demanding and requires time and expertise. Most groups are understudied given problems of identifying and delimiting species. DNA barcoding emerged to overcome some of the difficulties in identifying species. Its limitations derive from incomplete taxonomic knowledge and the lack of comprehensive DNA barcode libraries for so many taxonomic groups. Here, we evaluate how useful barcoding is for identifying arthropods from highly diverse leaf litter communities in the southern Appalachian Mountains (USA). We used 3 reference databases and several automated classification methods on a data set including several arthropod groups. Acari, Araneae, Collembola, Coleoptera, Diptera, and Hymenoptera were well represented, showing different performances across methods and databases. Spiders performed the best, with correct identification rates to species and genus levels of ~50% across databases. Springtails performed poorly, no barcodes were identified to species or genus. Other groups showed poor to mediocre performance, from around 3% (mites) to 20% (beetles) correctly identified barcodes to species, but also with some false identifications. In general, BOLD-based identification offered the best identification results but, in all cases except spiders, performance is poor, with less than a fifth of specimens correctly identified to genus or species. Our results indicate that the soil arthropod fauna is still insufficiently documented, with many species unrepresented in DNA barcode libraries. More effort toward integrative taxonomic characterization is needed to complete our reference libraries before we can rely on DNA barcoding as a universally applicable identification method.},
}
@article {pmid39460611,
year = {2024},
author = {Burgos, HL and Mandel, MJ},
title = {Generation of Barcode-Tagged Vibrio fischeri Deletion Strains and Barcode Sequencing (BarSeq) for Multiplex Strain Competitions.},
journal = {Current protocols},
volume = {4},
number = {10},
pages = {e70024},
pmid = {39460611},
issn = {2691-1299},
support = {F32 GM140673/GM/NIGMS NIH HHS/United States ; R35 GM148385/GM/NIGMS NIH HHS/United States ; /NH/NIH HHS/United States ; },
mesh = {*Aliivibrio fischeri/genetics ; *DNA Barcoding, Taxonomic/methods ; Gene Deletion ; High-Throughput Nucleotide Sequencing/methods ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Gene Library ; },
abstract = {Vibrio fischeri is a model mutualist for studying molecular processes affecting microbial colonization of animal hosts. We present a detailed protocol for a barcode sequencing (BarSeq) approach that combines targeted gene deletion with short-read sequencing technology to enable studies of mixed bacterial populations. This protocol includes wet lab steps to plan and produce the deletions, approaches to scale up mutant generation, protocols to prepare and conduct the strain competition, library preparation for sequencing on an Illumina iSeq 100 instrument, and data analysis with the barseq python package. Aspects of this protocol could be readily adapted for tagging wild-type V. fischeri strains with a neutral barcode for examination of population dynamics or BarSeq analyses in other species. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Production of the erm-bar DNA Basic Protocol 2: Generation of a targeted and barcoded deletion strain of V. fischeri Alternate Protocol: Parallel generation of multiple barcode-tagged V. fischeri deletion strains Basic Protocol 3: Setting up mixed populations of barcode-tagged strains Basic Protocol 4: Performing a competitive growth assay Basic Protocol 5: Amplicon library preparation and equimolar pooling Basic Protocol 6: Sequencing on Illumina iSeq 100 Basic Protocol 7: BarSeq data analysis.},
}
@article {pmid39460509,
year = {2024},
author = {Yang, M and Wang, Y and Dai, P and Feng, D and Hughes, AC and Li, H and Zhang, A},
title = {Sympatric diversity pattern driven by the secondary contact of two deeply divergent lineages of the soybean pod borer Leguminivora glycinivorella.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.12917},
pmid = {39460509},
issn = {1749-4877},
abstract = {The soybean pod borer, Leguminivora glycinivorella (Matsumura), is an important tortricid pest species widely distributed in most parts of China and its adjacent regions. Here, we analyzed the genetic diversity and population differentiation of L. glycinivorella using diverse genetic information including the standard cox1 barcode sequences, mitochondrial genomes (mitogenomes), and single-nucleotide polymorphisms (SNPs) from genotyping-by-sequencing. Based on a comprehensive sampling (including adults or larvae of L. glycinivorella newly collected at 22 of the total 30 localities examined) that covers most of the known distribution range of this pest, analyses of 543 cox1 barcode sequences and 60 mitogenomes revealed that the traditionally recognized and widely distributed L. glycinivorella contains two sympatric and widely distributed genetic lineages (A and B) that were estimated to have diverged ∼1.14 million years ago during the middle Pleistocene. Moreover, low but statistically significant correlations were recognized between genetic differentiation and geographic or environmental distances, indicating the existence of local adaptation to some extent. Based on SNPs, phylogenetic inference, principal component analysis, fixation index, and admixture analysis all confirm the two divergent sympatric lineages. Compared with the stable demographic history of Lineage B, the expansion of Lineage A had possibly made the secondary contact of the two lineages probable, and this process may be driven by the climate fluctuation during the late Pleistocene as revealed by ecological niche modeling.},
}
@article {pmid39459593,
year = {2024},
author = {Xia, X},
title = {Phylogeographic Analysis for Understanding Origin, Speciation, and Biogeographic Expansion of Invasive Asian Hornet, Vespa velutina Lepeletier, 1836 (Hymenoptera, Vespidae).},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
pmid = {39459593},
issn = {2075-1729},
support = {RGPIN-2024-05641//Natural Sciences and Engineering Research Council/ ; },
abstract = {The Asian hornet, Vespa velutina, is an invasive species that has not only expanded its range in Asia but has also invaded European countries, and it incurs significant costs on local apiculture. This phylogeographic study aims to trace the evolutionary trajectory of V. velutina and its close relatives; it aims to identify features that characterize an invasive species. The last successful invasion of Vespa velutina into France occurred in late May, 2002, and into South Korea in early October, 2002, which were estimated by fitting a logistic equation to the number of observations over time. The instantaneous rate of increase is 1.3667 for V. velutina in France and 0.2812 in South Korea, which are consistent with the interpretation of little competition in France and strong competition from local hornet species in South Korea. The invasive potential of two sister lineages can be compared by their distribution area when proper statistical adjustments are made to account for differences in sample size. V. velutina has a greater invasive potential than its sister lineage. The ancestor of V. velutina split into two lineages, one found in Indonesia/Malaysia and the other colonizing the Asian continent. The second lineage split into a sedentary clade inhabiting Pakistan and India and an invasive lineage colonizing much of Southeast Asia. This latter lineage gave rise to the subspecies V. v. nigrithorax, which invaded France, South Korea, and Japan. My software PGT version 1.5, which generates geophylogenies and computes geographic areas for individual taxa, is useful for understanding biogeography in general and invasive species in particular. I discussed the conceptual formulation of an index of invasiveness for a comparison between sister lineages.},
}
@article {pmid39458823,
year = {2024},
author = {Tahir, S and Hassan, SS and Yang, L and Ma, M and Li, C},
title = {Detection Methods for Pine Wilt Disease: A Comprehensive Review.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {20},
pages = {},
pmid = {39458823},
issn = {2223-7747},
support = {2022ZD0401602//Biological Breeding-Major Projects/ ; },
abstract = {Pine wilt disease (PWD), caused by the nematode Bursaphelenchus xylophilus, is a highly destructive forest disease that necessitates rapid and precise identification for effective management and control. This study evaluates various detection methods for PWD, including morphological diagnosis, molecular techniques, and remote sensing. While traditional methods are economical, they are limited by their inability to detect subtle or early changes and require considerable time and expertise. To overcome these challenges, this study emphasizes advanced molecular approaches such as real-time polymerase chain reaction (RT-PCR), droplet digital PCR (ddPCR), and loop-mediated isothermal amplification (LAMP) coupled with CRISPR/Cas12a, which offer fast and accurate pathogen detection. Additionally, DNA barcoding and microarrays facilitate species identification, and proteomics can provide insights into infection-specific protein signatures. The study also highlights remote sensing technologies, including satellite imagery and unmanned aerial vehicle (UAV)-based hyperspectral analysis, for their capability to monitor PWD by detecting asymptomatic diseases through changes in the spectral signatures of trees. Future research should focus on combining traditional and innovative techniques, refining visual inspection processes, developing rapid and portable diagnostic tools for field application, and exploring the potential of volatile organic compound analysis and machine learning algorithms for early disease detection. Integrating diverse methods and adopting innovative technologies are crucial to effectively control this lethal forest disease.},
}
@article {pmid39455411,
year = {2024},
author = {He, M and Zhu, X and Chen, Z and Wang, C and Mi, L and Shang, Y and Zheng, J and Xiang, C and Song, H and Liu, X},
title = {Epitaxial Growth of Multicolor Lanthanide MOFs by Ultrasound for Photonic Barcodes.},
journal = {ACS applied materials &amp; interfaces},
volume = {16},
number = {44},
pages = {60884-60889},
doi = {10.1021/acsami.4c16625},
pmid = {39455411},
issn = {1944-8252},
abstract = {Epitaxially grown lanthanide metal-organic frameworks (Ln MOFs) exhibit multicolor and characteristic Ln emission with sharp emission bands, which are of great value in the field of information security and anti-counterfeiting. Epitaxial growth of Ln MOFs is generally achieved by solvothermal or hydrothermal methods, which suffer from challenges such as high reaction temperature and long growth time. Here, we report the fast epitaxial growth of multicolor lanthanide MOFs by an ultrasonic method at room temperature. The TbSmSQ shows a core-shell type structure with the Tb ion in the core and Sm in the shell within one crystal and exhibits the characteristic emission lines of Tb and Sm, respectively. The nonporous structure and large distance between lanthanide ions effectively avoid the influence of solvent vapor on the intensity and color of luminescence emission. Its application as photonic barcodes has been studied. This work demonstrates the feasibility of epitaxial growth of multicolor Ln MOFs by the ultrasonic method and its value for anti-counterfeiting and information security applications.},
}
@article {pmid39454580,
year = {2024},
author = {Lima, GM and Jame-Chenarboo, Z and Sojitra, M and Sarkar, S and Carpenter, EJ and Yang, CY and Schmidt, E and Lai, J and Atrazhev, A and Yazdan, D and Peng, C and Volker, EA and Ho, R and Monteiro, G and Lai, R and Mahal, LK and Macauley, MS and Derda, R},
title = {The liquid lectin array detects compositional glycocalyx differences using multivalent DNA-encoded lectins on phage.},
journal = {Cell chemical biology},
volume = {31},
number = {11},
pages = {1986-2001.e9},
doi = {10.1016/j.chembiol.2024.09.010},
pmid = {39454580},
issn = {2451-9448},
mesh = {*Glycocalyx/metabolism/chemistry ; *Lectins/chemistry/metabolism ; Humans ; Bacteriophages/chemistry/metabolism ; Animals ; DNA/chemistry/metabolism ; Mice ; Polysaccharides/chemistry/metabolism ; },
abstract = {Selective detection of disease-associated changes in the glycocalyx is an emerging field in modern targeted therapies. Detecting minor glycan changes on the cell surface is a challenge exacerbated by the lack of correspondence between cellular DNA/RNA and glycan structures. We demonstrate that multivalent displays of lectins on DNA-barcoded phages-liquid lectin array (LiLA)-detect subtle differences in density of glycans on cells. LiLA constructs displaying 73 copies of diCBM40 (CBM) lectin per virion (φ-CBM73) exhibit non-linear ON/OFF-like recognition of sialoglycans on the surface of normal and cancer cells. A high-valency φ-CBM290 display, or soluble CBM protein, cannot amplify the subtle differences detected by φ-CBM73. Similarly, multivalent displays of CBM and Siglec-7 detect differences in the glycocalyx between stem-like and non-stem populations in cancer. Multivalent display of lectins offer in situ detection of minor differences in glycocalyx in cells both in vitro and in vivo not feasible to currently available technologies.},
}
@article {pmid39453698,
year = {2024},
author = {Rodger, G and Lipworth, S and Barrett, L and Oakley, S and Crook, DW and Eyre, DW and Stoesser, N},
title = {Comparison of direct cDNA and PCR-cDNA Nanopore sequencing of RNA from Escherichia coli isolates.},
journal = {Microbial genomics},
volume = {10},
number = {10},
pages = {},
pmid = {39453698},
issn = {2057-5858},
mesh = {*Escherichia coli/genetics ; *Nanopore Sequencing/methods ; *DNA, Complementary/genetics ; Polymerase Chain Reaction/methods ; Humans ; Escherichia coli Infections/microbiology ; Sequence Analysis, RNA/methods ; RNA, Bacterial/genetics ; Gene Expression Profiling/methods ; High-Throughput Nucleotide Sequencing/methods ; Transcriptome ; },
abstract = {Whole-transcriptome (long-read) RNA sequencing (Oxford Nanopore Technologies, ONT) holds promise for reference-agnostic analysis of differential gene expression in pathogenic bacteria, including for antimicrobial resistance genes (ARGs). However, direct cDNA ONT sequencing requires large concentrations of polyadenylated mRNA, and amplification protocols may introduce technical bias. Here we evaluated the impact of direct cDNA- and cDNA PCR-based ONT sequencing on transcriptomic analysis of clinical Escherichia coli. Four E. coli bloodstream infection-associated isolates (n=2 biological replicates per isolate) were sequenced using the ONT Direct cDNA Sequencing SQK-DCS109 and PCR-cDNA Barcoding SQK-PCB111.24 kits. Biological and technical replicates were distributed over eight flow cells using 16 barcodes to minimize batch/barcoding bias. Reads were mapped to a transcript reference and transcript abundance was quantified after in silico depletion of low-abundance and rRNA genes. We found there were strong correlations between read counts using both kits and when restricting the analysis to include only ARGs. We highlighted that correlations were weaker for genes with a higher GC content. Read lengths were longer for the direct cDNA kit compared to the PCR-cDNA kit whereas total yield was higher for the PCR-cDNA kit. In this small but methodologically rigorous evaluation of biological and technical replicates of isolates sequenced with the direct cDNA and PCR-cDNA ONT sequencing kits, we demonstrated that PCR-based amplification substantially improves yield with largely unbiased assessment of core gene and ARG expression. However, users of PCR-based kits should be aware of a small risk of technical bias which appears greater for genes with an unusually high (>52%)/low (<44%) GC content.},
}
@article {pmid39452649,
year = {2024},
author = {Yang, J and Reyes Loaiciga, C and Yue, HR and Hou, YJ and Li, J and Li, CX and Li, J and Zou, Y and Zhao, S and Zhang, FL and Zhao, XQ},
title = {Genomic Characterization and Establishment of a Genetic Manipulation System for Trichoderma sp. (Harzianum Clade) LZ117.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {10},
number = {10},
pages = {},
pmid = {39452649},
issn = {2309-608X},
support = {No. 2022YFE0108500//the State Key Research and Development Program of China/ ; },
abstract = {Trichoderma species have been reported as masters in producing cellulolytic enzymes for the biodegradation of lignocellulolytic biomass and biocontrol agents against plant pathogens and pests. In our previous study, a novel Trichoderma strain LZ117, which shows potent capability in cellulase production, was isolated. Herein, we conducted multilocus phylogenetic analyses based on DNA barcodes and performed time-scaled phylogenomic analyses using the whole genome sequences of the strain, annotated by integrating transcriptome data. Our results suggest that this strain represents a new species closely related to T. atrobrunneum (Harzianum clade). Genes encoding carbohydrate-active enzymes (CAZymes), transporters, and secondary metabolites were annotated and predicted secretome in Trichoderma sp. LZ117 was also presented. Furthermore, genetic manipulation of this strain was successfully achieved using PEG-mediated protoplast transformation. A putative transporter gene encoding maltose permease (Mal1) was overexpressed, which proved that this transporter does not affect cellulase production. Moreover, overexpressing the native Cre1 homolog in LZ117 demonstrated a more pronounced impact of glucose-caused carbon catabolite repression (CCR), suggesting the importance of Cre1-mediated CCR in cellulase production of Trichoderma sp. LZ117. The results of this study will benefit further exploration of the strain LZ117 and related species for their applications in bioproduction.},
}
@article {pmid39450195,
year = {2024},
author = {Lee, HE and Lee, GH and Min, GS},
title = {A new species of Thoracophelia (Annelida, Opheliidae) from the Yellow Sea of South Korea.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e129526},
pmid = {39450195},
issn = {1314-2828},
abstract = {BACKGROUND: Thoracophelia Ehlers, 1897 is a genus of Opheliidae characterised by the body divided into three distinct regions, modified parapodia in chaetiger 10 and a ventral groove restricted to the posterior half of the body. To date, 18 species have been described in the genus. Amongst them, six species have been recorded in northeast Asia.<br><br>NEW INFORMATION: A new species, Thoracopheliafoliformis sp. nov., was discovered in the intertidal zone of the Yellow Sea, South Korea. This is the first Thoracophelia species report from the Yellow Sea. This new species is closely related to T.dillonensis (Hartman, 1938) from California and T.ezoensis Okuda, 1936 from Japan in having pectinate branchiae. However, the new species can be distinguished from the two species by the unique combination of the following characteristics: 15 pairs of wrinkled pectinate branchiae with 12-15 filaments at best development and a foliaceous mid-ventral plate in the pygidium instead of one or two thick ventral cirri. Detailed descriptions and illustrations of T.foliformis sp. nov. are provided. Sequences of the mitochondrial cytochrome c oxidase subunit I (COI), nuclear 18S ribosomal DNA (rDNA) and 28S rDNA of the new species were determined and analysed.},
}
@article {pmid39450043,
year = {2024},
author = {Likhitrakarn, N and Golovatch, SI and Srisonchai, R and Jirapatrasilp, P and Sapparojpattana, P and Jeratthitikul, E and Panha, S and Sutcharit, C},
title = {A new species of the pill millipede genus Rhopalomeris Verhoeff, 1906 (Diplopoda, Glomerida, Glomeridae) from Myanmar, and notes on Rhopalomeriscarnifex (Pocock, 1889).},
journal = {ZooKeys},
volume = {1215},
number = {},
pages = {235-257},
pmid = {39450043},
issn = {1313-2989},
abstract = {The taxonomy of the pill millipede genus Rhopalomeris Verhoeff, 1906, which is restricted to Indochina and currently comprises six described species, is refined and updated. An integrative taxonomic approach was employed that combines morphological examination with DNA barcoding using the cytochrome c oxidase subunit I (COI) gene for species identification and delineation. The first objective was to confirm the identity of Rhopalomeriscarnifex (Pocock, 1889), a charismatic species known as the "candy pill millipede" due to its vivid coloration, based on specimens collected near the type locality in Myanmar. The second objective was to describe a new species, Rhopalomerisnigroflava Likhitrakarn, sp. nov., discovered in Linno Gu, Kayin State, Myanmar. This new species is distinguished by its small body size (5.1-9.7 mm long) and yellow body with contrasting brown to blackish markings on certain terga. In addition, the position of the telopod syncoxital lobe relative to the lateral syncoxite horns separates it from other Rhopalomeris species. The interspecific divergence between R.nigroflava Likhitrakarn, sp. nov. and other congeners ranges from 10.85% to 16.13%, based on uncorrected COI p-distances, while the intraspecific divergence was 0%-7.44%. A distribution map of and a revised identification key to all known species of Rhopalomeris are also provided.},
}
@article {pmid39444847,
year = {2024},
author = {Mwamula, AO and Kim, YS and Lee, DW},
title = {Morphological and molecular characterization of Paractinolaimus uljinensis n. sp. (Nematoda: Actinolaimidae) from Korea, with an updated compendium of the genus.},
journal = {Journal of nematology},
volume = {56},
number = {1},
pages = {20240040},
pmid = {39444847},
issn = {0022-300X},
abstract = {A new species of the genus Paractinolaimus isolated from the bark of a dead red pine tree was characterized using morphometric data and molecular DNA barcodes. Paractinolaimus uljinensis n. sp. was characterized by its medium sized body 2.50 to 2.98 mm long; lip region truncate, angular and offset by a depression; odontostyle 23.5 to 27.0 μm long; basal shield of pharynx present; vulval opening wide and longitudinal, positioned slightly anteriorly (V = 42.5-47.7); several advulval papillae; female tail long and filiform (324.0-435.0 μm long, c' = 10.1-14.2); a clearly visible copulatory hump; spicules 60.0 to 70.5 μm long; 12 to 15 (mostly 12-14) large contiguous ventromedian supplements, and male tail conoid to broadly rounded. The new species was morphologically compared with P. intermedius, P. sahandi, P. decraemerae, P. acutus, P. macrolaimus, and P. tuberculatus. The phylogenetic relationships among species were reconstructed using 18S- and 28S-rRNA gene sequences. The phylogenies showed well-supported sister relations of Paractinolaimus uljinensis n. sp. with P. sahandi, P. macrolaimus, and P. decraemerae. In addition, the ITS-rRNA gene sequences of Paractinolaimus uljinensis n. sp. were supplied, representing the first characterization of the gene for the genus.},
}
@article {pmid39443484,
year = {2024},
author = {Wu, B and Bennett, HM and Ye, X and Sridhar, A and Eidenschenk, C and Everett, C and Nazarova, EV and Chen, HH and Kim, IK and Deangelis, M and Owen, LA and Chen, C and Lau, J and Shi, M and Lund, JM and Xavier-Magalhães, A and Patel, N and Liang, Y and Modrusan, Z and Darmanis, S},
title = {Overloading And unpacKing (OAK) - droplet-based combinatorial indexing for ultra-high throughput single-cell multiomic profiling.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9146},
pmid = {39443484},
issn = {2041-1723},
support = {R01 EY031209/EY/NEI NIH HHS/United States ; },
mesh = {*Single-Cell Analysis/methods ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; Cell Line, Tumor ; Melanoma/genetics/drug therapy/pathology ; Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; Transcriptome ; },
abstract = {Multiomic profiling of single cells by sequencing is a powerful technique for investigating cellular diversity. Existing droplet-based microfluidic methods produce many cell-free droplets, underutilizing bead barcodes and reagents. Combinatorial indexing on microplates is more efficient for barcoding but labor-intensive. Here we present Overloading And unpacKing (OAK), which uses a droplet-based barcoding system for initial compartmentalization followed by a second aliquoting round to achieve combinatorial indexing. We demonstrate OAK's versatility with single-cell RNA sequencing as well as paired single-nucleus RNA sequencing and accessible chromatin profiling. We further showcase OAK's performance on complex samples, including differentiated bronchial epithelial cells and primary retinal tissue. Finally, we examine transcriptomic responses of over 400,000 melanoma cells to a RAF inhibitor, belvarafenib, discovering a rare resistant cell population (0.12%). OAK's ultra-high throughput, broad compatibility, high sensitivity, and simplified procedures make it a powerful tool for large-scale molecular analysis, even for rare cells.},
}
@article {pmid39443100,
year = {2024},
author = {Oshiro, A and Sumi, T and Imai, H},
title = {[Identification of Fish Species Involved with Ciguatera Food Poisoning in Okinawan Waters by Using PCR-RFLP analysis].},
journal = {Shokuhin eiseigaku zasshi. Journal of the Food Hygienic Society of Japan},
volume = {65},
number = {4},
pages = {79-83},
doi = {10.3358/shokueishi.65.79},
pmid = {39443100},
issn = {0015-6426},
mesh = {Animals ; *Polymorphism, Restriction Fragment Length ; *Ciguatera Poisoning ; Japan ; *Polymerase Chain Reaction ; *RNA, Ribosomal, 16S/genetics ; *Fishes/genetics ; DNA, Mitochondrial/genetics/analysis ; Phylogeny ; },
abstract = {Ciguatera fish poisoning (CFP), known as a seafood-borne disease, is caused by consumption of fish contaminated with ciguatoxins in tropical and subtropical sea. The ciguatera fishes, Variola louti, Lutjanus monostigma and L. bohar have an absolute majority in the Ryukyu Archipelago, southwestern Japan. We developed the cluster analysis of phylogenetic tree by using mitochondrial (mt) DNA 16S rRNA sequences of V. louti, L. monostigma and L. bohar and differentiate them from morphologically similar species (L. fulviflamma, L. russellii, L. argentimaculatus, Plectropomus leopardus and V. albimarginata) in our previous study. The fish were acquired from the coastal waters of the Ryukyu Archipelago, and a polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) marker of the mtDNA 16S rRNA region was used, employing the restriction enzymes BmgT120 I, Dde I, and SnaB I, to identify the fish species responsible for CFP. These results showed that a PCR-RFLP marker can be obtained more easily than a nucleotide sequence.},
}
@article {pmid39441940,
year = {2024},
author = {Smitha Pillai, K and Laxton, O and Li, G and Lin, J and Karginova, O and Nanda, R and Olopade, OI and Tay, S and Moellering, RE},
title = {Single-cell chemoproteomics identifies metastatic activity signatures in breast cancer.},
journal = {Science advances},
volume = {10},
number = {43},
pages = {eadp2622},
pmid = {39441940},
issn = {2375-2548},
support = {R01 GM127527/GM/NIGMS NIH HHS/United States ; R35 GM148231/GM/NIGMS NIH HHS/United States ; T32 GM144290/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Breast Neoplasms/metabolism/pathology/genetics ; *Single-Cell Analysis/methods ; Female ; *Proteomics/methods ; Cell Line, Tumor ; *Neoplasm Metastasis ; },
abstract = {Protein activity state, rather than protein or mRNA abundance, is a biologically regulated and relevant input to many processes in signaling, differentiation, development, and diseases such as cancer. While there are numerous methods to detect and quantify mRNA and protein abundance in biological samples, there are no general approaches to detect and quantify endogenous protein activity with single-cell resolution. Here, we report the development of a chemoproteomic platform, single-cell activity-dependent proximity ligation, which uses automated, microfluidics-based single-cell capture and nanoliter volume manipulations to convert the interactions of family-wide chemical activity probes with native protein targets into multiplexed, amplifiable oligonucleotide barcodes. We demonstrate accurate, reproducible, and multiplexed quantitation of a six-enzyme (Ag-6) panel with known ties to cancer cell aggressiveness directly in single cells. We further identified increased Ag-6 enzyme activity across breast cancer cell lines of increasing metastatic potential, as well as in primary patient-derived tumor cells and organoids from patients with breast cancer.},
}
@article {pmid39438815,
year = {2024},
author = {Bastidas-Caldes, C and Hernández-Alomía, F and Almeida, M and Ormaza, M and Boada, J and Graham, J and Calvopiña, M and Castillejo, P},
title = {Molecular identification and antimicrobial resistance patterns of enterobacterales in community urinary tract infections among indigenous women in Ecuador: addressing microbiological misidentification.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {1195},
pmid = {39438815},
issn = {1471-2334},
mesh = {Humans ; *Urinary Tract Infections/microbiology/drug therapy/epidemiology ; Female ; Ecuador/epidemiology ; Cross-Sectional Studies ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Adult ; Microbial Sensitivity Tests ; Indigenous Peoples ; Drug Resistance, Bacterial/genetics ; Middle Aged ; Enterobacteriaceae/drug effects/genetics/isolation &amp; purification ; Young Adult ; Enterobacteriaceae Infections/microbiology/epidemiology/drug therapy ; Community-Acquired Infections/microbiology ; },
abstract = {BACKGROUND: Antibiotic resistance of Enterobacterales poses a major challenge in the treatment of urinary tract infections (UTIs). In low- and middle-income countries (LMICs), standard microbiological (i.e. urine culture and simple disk diffusion test) methods are considered the "gold standard" for bacterial identification and drug susceptibility testing, while PCR and DNA sequencing are less commonly used. In this study, we aimed to re-identifying Enterobacterales as the primary bacterial agents responsible for urinary tract infections (UTIs) by comparing the sensitivity and specificity of traditional microbiological methods with advanced molecular techniques for the detection of uropathogens in indigenous women from Otavalo, Ecuador.<br><br>METHODS: A facility-based cross-sectional study was conducted from October 2021 to February 2022 among Kichwa-Otavalo women. Pathogens from urine samples were identified using culture and biochemical typing. Morphological identification was doble-checked through PCR and DNA sequencing of 16S, recA, and rpoB molecular barcodes. The isolates were subjected to antimicrobial susceptibility-testing using disk diffusion test.<br><br>RESULTS: This study highlighted a 32% misidentification rate between biochemical and molecular identification. Using traditional methods, E. coli was 26.19% underrepresented meanwhile Klebsiella oxytoca was overrepresented by 92.86%. Furthermore, the genera Pseudomonas, Proteus, and Serratia were confirmed to be E. coli and Klebsiella spp. by molecular method, and one Klebsiella spp. was reidentified as Enterobacter spp. The susceptibility profile showed that 59% of the isolates were multidrug resistant strains and 31% produced extended spectrum beta-lactamases (ESBLs). Co-trimoxazole was the least effective antibiotic with 61% of the isolates resistant. Compared to previous reports, resistance to nitrofurantoin and fosfomycin showed an increase in resistance by 25% and 15%, respectively.<br><br>CONCLUSIONS: Community-acquired UTIs in indigenous women in Otavalo were primarily caused by E. coli and Klebsiella spp. Molecular identification (16S/rpoB/recA) revealed a high rate of misidentification by standard biochemical and microbiological techniques, which could lead to incorrect antibiotic prescriptions. UTI isolates in this population displayed higher levels of resistance to commonly used antibiotics compared with non-indigenous groups. Accurate identification of pathogens causing UTIs and their antibiotic susceptibility in local populations is important for local antibiotic prescribing guidelines.},
}
@article {pmid39434349,
year = {2024},
author = {Hamdan, NT},
title = {Molecular identification of Hypomyces chrysospermus mycoparasitic fungus isolated from mushrooms in a local market of Iraq.},
journal = {JPMA. The Journal of the Pakistan Medical Association},
volume = {74},
number = {10 (Supple-8)},
pages = {S398-S401},
doi = {10.47391/JPMA-BAGH-16-90},
pmid = {39434349},
issn = {0030-9982},
mesh = {Iraq ; *Phylogeny ; Agaricales/genetics/isolation &amp; purification ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; },
abstract = {In this study, mycoparasitic fungus was identified by using the rDNA internal transcribed spacer barcode marker, i.e. ITS rDNA gene. Amplicons were sequenced and identified by NCBI - BLAST (Basic local alignment search tool). The BLAST results revealed that NOOR strain matched 100% with accession numbers [MH854754.1]. The phylogenetic tree shows close relationship between NOOR strain and H. chrysospermus [MH854754-1], H. chrysospermus [MZ389105-1], H. chrysospermus [MK605327- 1], H. chrysospermus [MT595227-1], H. [EU816370-1], H. chrysospermus [MG685885-1]. The Iraqi isolate was recorded as NOOR strain in the National Centre for Biotechnology Information for the first time in Iraq.},
}
@article {pmid39434133,
year = {2024},
author = {Gąsiorek, P and Sørensen, MV and Lillemark, MR and Leerhøi, F and Tøttrup, AP},
title = {Massive citizen science sampling and integrated taxonomic approach unravel Danish cryptogam-dwelling tardigrade fauna.},
journal = {Frontiers in zoology},
volume = {21},
number = {1},
pages = {27},
pmid = {39434133},
issn = {1742-9994},
abstract = {Tardigrade diversity and distribution are enigmatic in most parts of the globe, and only some European countries can boast of a relatively well-studied water bear fauna. However, even these suffer from the lack of genetic data, which would substantiate faunistic data and make biogeographic comparisons easier. Denmark has never been intensively and systematically researched in this regard, thus a citizen science sampling of cryptogams (mosses, liverworts, and lichens) was launched in spring 2023, aiming at a comprehensive biodiversity survey across this insular country. Nearly 700 samples were selected out of 8.000 sent to NHMD, based on the quality of samples, representativeness of various regions of Denmark, and the type of substrate to allow unravelling of potential ecological associations between tardigrades and cryptogams. Importantly, a large fraction of morphological identifications was backed up by DNA barcode data based on ITS-2 (1001 sequences), and in some cases also on COI (93 sequences) and ITS-1 (22 sequences) molecular markers, which are recognised DNA fragments used in species delimitation. We quadruple the number of known Danish limno-terrestrial tardigrade species (55 spp. reported in this paper vs. 14 spp. reported in literature so far, most of which were contentious due to the insufficient knowledge on tardigrade taxonomy), demonstrating the power of integrative taxonomy. No fewer than nine spp. are new to science. This is the first case where tardigrade fauna of an entire country is examined both from morphological and DNA barcoding data perspective.},
}
@article {pmid39433876,
year = {2024},
author = {Simon, JJ and Fowler, DM and Maly, DJ},
title = {Multiplexed profiling of intracellular protein abundance, activity, interactions and druggability with LABEL-seq.},
journal = {Nature methods},
volume = {21},
number = {11},
pages = {2094-2106},
pmid = {39433876},
issn = {1548-7105},
support = {RM1HG010461//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; RM1 HG010461/HG/NHGRI NIH HHS/United States ; R01 GM086858/GM/NIGMS NIH HHS/United States ; R01GM145011//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01 GM145011/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Proto-Oncogene Proteins B-raf/genetics/metabolism ; Mutation ; Cell Line, Tumor ; Cell Proliferation/drug effects ; },
abstract = {Here we describe labeling with barcodes and enrichment for biochemical analysis by sequencing (LABEL-seq), an assay for massively parallel profiling of pooled protein variants in human cells. By leveraging the intracellular self-assembly of an RNA-binding domain (RBD) with a stable, variant-encoding RNA barcode, LABEL-seq facilitates the direct measurement of protein properties and functions using simple affinity enrichments of RBD protein fusions, followed by high-throughput sequencing of co-enriched barcodes. Measurement of ~20,000 variant effects for ~1,600 BRaf variants revealed that variation at positions frequently mutated in cancer minimally impacted intracellular abundance but could dramatically alter activity, protein-protein interactions and druggability. Integrative analysis identified networks of positions with similar biochemical roles and enabled modeling of variant effects on cell proliferation and small molecule-promoted degradation. Thus, LABEL-seq enables direct measurement of multiple biochemical properties in a native cellular context, providing insights into protein function, disease mechanisms and druggability.},
}
@article {pmid39432187,
year = {2024},
author = {Ben Ahmed, R and Gajda, &#x141; and Świątek, P},
title = {Morphological data and DNA barcoding reveal the presence of the alien freshwater leech Helobdella octatestisaca (Hirudinida: Glossiphoniformes) in North Africa (Tunisia).},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {1081},
pmid = {39432187},
issn = {1573-4978},
mesh = {Animals ; *Phylogeny ; *Leeches/genetics/anatomy &amp; histology/classification ; *DNA Barcoding, Taxonomic/methods ; Tunisia ; Fresh Water ; Introduced Species ; Electron Transport Complex IV/genetics ; },
abstract = {BACKGROUND: We hereby report the first occurrence of Helobdella octatestisaca in North Africa, specifically in Tunisia, as a likely introduced species from the Neotropical Region. Historically, leeches bearing a prominent chitinous scute on their dorsal surface were commonly diagnosed as H. stagnalis. Most probably, H. octatestisaca had previously been misidentified as H. stagnalis in Tunisia.<br><br>METHODS AND RESULTS: The identification was primarily based on morphological evidence, supplemented by genetic data obtained from COI DNA barcoding. The morphology of the examined specimens was consistent with the original species description, notably characterized by the presence of four pairs of testisacs. To support our findings, we conducted a phylogenetic analysis using the Maximum Likelihood method based on COI alignment constructed with the newly obtained sequence from Tunisian specimens and complete or nearly complete 'Folmer fragment' sequences of congeners sourced from the GenBank database.<br><br>CONCLUSIONS: This study highlights the first identification of H. octatestisaca in North Africa and suggests that previous records of H. stagnalis in Tunisia likely misidentified this species.},
}
@article {pmid39431921,
year = {2024},
author = {Sun, F and Liu, J and Su, Z and Wu, D and Qu, S and Wu, Y and Li, L and Li, G},
title = {Encodable DNA Hairpin Probes for Nanopore Multiplexed Target Detection.},
journal = {Analytical chemistry},
volume = {96},
number = {44},
pages = {17612-17619},
doi = {10.1021/acs.analchem.4c03469},
pmid = {39431921},
issn = {1520-6882},
mesh = {*Nanopores ; *DNA Probes/chemistry/genetics ; *Hemolysin Proteins/chemistry/genetics ; MicroRNAs/analysis ; Biosensing Techniques/methods ; Nucleic Acid Conformation ; Inverted Repeat Sequences ; DNA/chemistry/analysis ; },
abstract = {Owing to the co-occurrence of hazardous compounds, it is crucial to build multiple highly discriminative probe libraries for simultaneous determination. Drawing inspiration from nucleic acid barcodes, we developed a probe system that is exclusively based on the nucleic acid secondary structure's hairpin structure, which can be directly read by nanopores. The highly distinguishable hairpin probes were constructed, and a detailed explanation of the possible patterns in their design was provided. These probe-representative events measured through the α-hemolysin (α-HL) nanopores were both distinguished, either through visual observation or comparison of the nanopore parameters. Besides, the potential design pattern for probes with unique telegraphic switching between the two levels was also unveiled. Finally, these probes were utilized to realize simultaneous, ultrasensitive mycotoxin multiple-detection, and their prospective applications for the detection of proteins and microRNAs were presented, indicating their suitability for a wide range of sensing applications.},
}
@article {pmid39424732,
year = {2025},
author = {Holmes, AB and Corinaldesi, C and Basso, K},
title = {Single-Cell Transcriptomic Analysis of Normal and Malignant B Cells.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2865},
number = {},
pages = {347-374},
pmid = {39424732},
issn = {1940-6029},
mesh = {*Single-Cell Analysis/methods ; Humans ; *Gene Expression Profiling/methods ; *B-Lymphocytes/metabolism/immunology ; *Transcriptome ; Software ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {In the past decade, single-cell (sc) transcriptomics has overcome the limitations of bulk analysis by measuring gene expression in individual cells, not just a population average. This can identify diverse cell types and states within a sample with high resolution, even without prior purification. Various technologies exist, each with its own capture, barcoding, and library preparation methods. This chapter focuses on the analysis of normal and malignant mature B cells using the 10× Genomics 5' sc-gene expression in parallel with B cell immune repertoire profiling. By integrating the gene expression data from similar cells, the complete transcriptome for each population can be reconstructed, while the identification of the expressed immunoglobulin genes allows investigating clonotype evolution and the detection of tumor clones that share the same clonally rearranged B cell receptor sequence. Researchers are guided through both the experimental protocols and data analysis with a comprehensive, step-by-step walkthrough of how to use some of the more popular single-cell software tools.},
}
@article {pmid39422558,
year = {2024},
author = {Zhang, SJ and Wu, C and Walt, DR},
title = {A Multiplexed Digital Platform Enables Detection of Attomolar Protein Levels with Minimal Cross-Reactivity.},
journal = {ACS nano},
volume = {18},
number = {43},
pages = {29891-29901},
doi = {10.1021/acsnano.4c10340},
pmid = {39422558},
issn = {1936-086X},
support = {R01 EB032826/EB/NIBIB NIH HHS/United States ; R56 EB032826/EB/NIBIB NIH HHS/United States ; },
mesh = {Humans ; *Enzyme-Linked Immunosorbent Assay ; Cross Reactions ; Antibodies/immunology/chemistry ; },
abstract = {Protein-based biomarkers are essential for disease diagnostics, yet their low abundance in biofluids often presents significant detection challenges for traditional enzyme-linked immunosorbent assay (ELISA) techniques. While various ultrasensitive methods such as digital ELISA have improved sensitivity, multiplex assays still suffer from considerable cross-reactivities that can compromise result accuracies. To address this challenge, we have developed barcoded Molecular On-bead Signal Amplification for Individual Counting (barcoded MOSAIC), a multiplexed digital ELISA technology that markedly reduces cross-reactivity by pairing barcoded detection antibodies with specific bead types. This approach enables the simultaneous detection of eight analytes from less than 9 μL of blood, with sensitivities ranging from midpicomolar to low-attomolar levels and a collective dynamic range exceeding seven logs across multiple analytes within a single multiplex assay. Additionally, barcoded MOSAIC is compatible with standard immunoassay reagents and workflows, utilizing a rapid, automatable flow cytometric readout for quantification, which makes it a highly accessible benchtop platform that is readily adoptable by both research and clinical laboratories, setting the stage for future translation into point-of-care applications.},
}
@article {pmid39421424,
year = {2024},
author = {Subbiah, VK and Gomez, CR and Robben, DM and Subramaniam, R and Hearn, AJ},
title = {Characterization of the complete mitochondrial genome of the Sunda stink-badger (Mydaus javanensis) from the island of Borneo.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e18190},
pmid = {39421424},
issn = {2167-8359},
mesh = {*Genome, Mitochondrial/genetics ; Borneo ; Animals ; *Phylogeny ; *Mustelidae/genetics ; Sequence Analysis, DNA ; RNA, Transfer/genetics ; },
abstract = {BACKGROUND: The Mephitidae is a family of skunks and stink-badgers that includes 12 extant species in four genera, namely, Mydaus, Conepatus, Mephitis and Spilogale. Mydaus is the only genus within Mephitidae found outside the American continent, with its distribution limited to the islands of Borneo, Indonesia and Philippines. There are two extant species of Mydaus i.e., javanensis and marchei. Currently, complete mitogenomes are unavailable for either species. Here, we present the characterization of the first complete mitogenome for the Sunda stink-badger (Mydaus javanensis) from the island of Borneo.<br><br>METHODS: Muscle tissue was obtained and the DNA was sequenced using a combination of Illumina Barcode Tagged Sequence (BTSeq) and Sanger sequencing techniques. The genome was annotated with MITOS and manually checked for accuracy. A circular map of the mitogenome was constructed with Proksee. Relative synonymous codon usage (RSCU) and codon frequency were calculated using MEGA-X. The protein coding genes (PCGs) were aligned with reference sequences from GenBank and used for the construction of phylogenetic trees (maximum liklihood (ML) and Bayesian inference (BI)). Additionally, due to the lack of available complete genomes in public databases, we constructed another tree with the cyt b gene.<br><br>RESULTS: The complete circular mitogenome was 16,391 base pairs in length. It comprises the typical 13 protein-coding genes, 22 tRNAs, two ribosomal RNA genes, one control region (CR) and an L-strand replication origin (OL). The G+C content was 38.1% with a clear bias towards A and T nucleotides. Of the 13 PGCs, only ND6 was positioned in the reverse direction, along with five other tRNAs. Five PCGs had incomplete stop codons and rely on post-transcriptional polyadenylation (TAA) for termination. Based on the codon count, Leucine was the most common amino acid (589), followed by Threonine (332) and Isoleucine (325). The ML and BI phylogenetic trees, based on concatenated PCGs and the cyt b gene, respectively, correctly clustered the species with other members of the Mephitidae family but were unique enough to set it apart from Conepatus, Mephitis and Spilogale. The results confirm Mydaus as a member of the mephitids and the mitogenome will be useful for evolutionary analysis and conservation of the species.},
}
@article {pmid39418234,
year = {2024},
author = {Cherie, N and Berta, DM and Tamir, M and Yiheyis, Z and Angelo, AA and Mekuanint Tarekegn, A and Chane, E and Nigus, M and Teketelew, BB},
title = {Improving laboratory turnaround times in clinical settings: A systematic review of the impact of lean methodology application.},
journal = {PloS one},
volume = {19},
number = {10},
pages = {e0312033},
pmid = {39418234},
issn = {1932-6203},
mesh = {Humans ; *Laboratories, Clinical ; Efficiency, Organizational ; Laboratories/standards ; Time Factors ; Workflow ; },
abstract = {BACKGROUND: Lean methodology, originally developed in the manufacturing sector, is a process management philosophy focused on maximizing value by eliminating waste. Its application in laboratory settings, particularly concerning laboratory turnaround times (TAT), involves a systematic approach to identifying inefficiencies and optimizing processes to enhance value for end customers.<br><br>METHODS: This systematic review was registered in PROSPERO with identification number (CRD42024552350) and reported based on the 2020 PRISMA checklist. An extensive search strategy was performed using PubMed, Scopus, and Embase databases and gray literatures. Advanced searching was used using Boolean operators (AND &amp; OR). After articles were exported to endnote x8, duplications were removed and articles were selected based on titles, abstracts, and full texts. The illegibility of the articles was independently assessed by the three authors (NC, DMB, and BBT), and the disagreements were settled through scientific consensus. Methodological quality was assessed using JBI critical appraisal checklist.<br><br>DISCUSSION: In this review, electronic databases search yielded 1261 articles, of which 7 met the inclusion criteria. The review demonstrated, implementation of lean principle into the routine laboratory testing had an overall impact 76.1% on reducing laboratory TAT. Transportation, manual data processing, inefficient workflow, and the heavy workload were identified as the main wasteful procedures. To eliminate these non-value-added steps, several intervention techniques were implemented, including the use of a barcoding system, process redesign, workflow optimization, hiring additional staff, and relocating the sample collection room closer to the result distribution center. Lean implementation is crucial in the medical laboratory industry for optimizing processes, reducing TAT, and ultimately enhancing customer satisfaction. As a result, all clinical laboratories should adopt and implement lean principles in their routine testing processes. The medical laboratory industry should also proactively look for and apply lean tools, provide ongoing training, and foster awareness among laboratory staffs.},
}
@article {pmid39417120,
year = {2024},
author = {Sadler, JM and Simkin, A and Tchuenkam, VPK and Gyuricza, IG and Fola, AA and Wamae, K and Assefa, A and Niaré, K and Thwai, K and White, SJ and Moss, WJ and Dinglasan, RR and Nsango, S and Tume, CB and Parr, JB and Ali, IM and Bailey, JA and Juliano, JJ},
title = {Application of a new highly multiplexed amplicon sequencing tool to evaluate Plasmodium falciparum antimalarial resistance and relatedness in individual and pooled samples from Dschang, Cameroon.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {39417120},
support = {R01 AI165537/AI/NIAID NIH HHS/United States ; R01 AI177791/AI/NIAID NIH HHS/United States ; U19 AI089680/AI/NIAID NIH HHS/United States ; R01 AI155730/AI/NIAID NIH HHS/United States ; R01 AI156267/AI/NIAID NIH HHS/United States ; K24 AI134990/AI/NIAID NIH HHS/United States ; },
abstract = {BACKGROUND: Resistance to antimalarial drugs remains a major obstacle to malaria elimination. Multiplexed, targeted amplicon sequencing is being adopted for surveilling resistance and dissecting the genetics of complex malaria infections. Moreover, genotyping of parasites and detection of molecular markers drug resistance in resource-limited regions requires open-source protocols for processing samples, using accessible reagents, and rapid methods for processing numerous samples including pooled sequencing.<br><br>METHODS: P lasmodium f alciparum Streamlined Multiplex Antimalarial Resistance and Relatedness Testing (Pf-SMARRT) is a PCR-based amplicon panel consisting of 15 amplicons targeting antimalarial resistance mutations and 9 amplicons targeting hypervariable regions. This assay uses oligonucleotide primers in two pools and a non-proprietary library and barcoding approach.<br><br>RESULTS: We evaluated Pf-SMARRT using control mocked dried blood spots (DBS) at varying levels of parasitemia and a mixture of 3D7 and Dd2 strains at known frequencies, showing the ability to genotype at low parasite density and recall within-sample allele frequencies. We then piloted Pf-SMARRT to genotype 100 parasite isolates collected from uncomplicated malaria cases at three health facilities in Dschang, Western Cameroon. Antimalarial resistance genotyping showed high levels of sulfadoxine-pyrimethamine resistance mutations, including 31% prevalence of the DHPS A613S mutation. No K13 candidate or validated artemisinin partial resistance mutations were detected, but one low-level non-synonymous change was observed. Pf-SMARRT's hypervariable targets, used to assess complexity of infections and parasite diversity and relatedness, showed similar levels and patterns compared to molecular inversion probe (MIP) sequencing. While there was strong concordance of antimalarial resistance mutations between individual samples and pools, low-frequency variants in the pooled samples were often missed.<br><br>CONCLUSION: Overall, Pf-SMARRT is a robust tool for assessing parasite relatedness and antimalarial drug resistance markers from both individual and pooled samples. Control samples support that accurate genotyping as low as 1 parasite per microliter is routinely possible.},
}
@article {pmid39416120,
year = {2024},
author = {Richardson, M and Zhao, S and Sheth, RU and Lin, L and Qu, Y and Lee, J and Moody, T and Ricaurte, D and Huang, Y and Velez-Cortes, F and Urtecho, G and Wang, HH},
title = {SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39416120},
issn = {2692-8205},
support = {P30 DK132710/DK/NIDDK NIH HHS/United States ; R21 AI146817/AI/NIAID NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; R01 AI132403/AI/NIAID NIH HHS/United States ; R01 EB031935/EB/NIBIB NIH HHS/United States ; },
abstract = {The local arrangement of microbes can profoundly impact community assembly, function, and stability. To date, little is known about the spatial organization of the human gut microbiome. Here, we describe a high-throughput and streamlined method, dubbed SAMPL-seq, that samples microbial composition of micron-scale sub-communities with split-and-pool barcoding to capture spatial colocalization in a complex consortium. SAMPL-seq analysis of the gut microbiome of healthy humans identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These colocalized microbes organize into spatially distinct groups or "spatial hubs" dominated by Bacteroideceae, Ruminococceae, and Lachnospiraceae families. From a dietary perturbation using inulin, we observed reversible spatial rearrangement of the gut microbiome, where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock new insights to improve the study of microbial communities.},
}
@article {pmid39416107,
year = {2024},
author = {Chen, J and Nilsen, ED and Chitboonthavisuk, C and Mo, CY and Raman, S},
title = {Systematic, high-throughput characterization of bacteriophage gene essentiality on diverse hosts.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39416107},
issn = {2692-8205},
support = {R21 AI156785/AI/NIAID NIH HHS/United States ; T32 GM135066/GM/NIGMS NIH HHS/United States ; },
abstract = {Understanding core and conditional gene essentiality is crucial for decoding genotype-phenotype relationships in organisms. We present PhageMaP, a high-throughput method to create genome-scale phage knockout libraries for systematically assessing gene essentiality in bacteriophages. Using PhageMaP, we generate gene essentiality maps across hundreds of genes in the model phage T7 and the non-model phage Bas63, on diverse hosts. These maps provide fundamental insights into genome organization, gene function, and host-specific conditional essentiality. By applying PhageMaP to a collection of anti-phage defense systems, we uncover phage genes that either inhibit or activate eight defenses and offer novel mechanistic hypotheses. Furthermore, we engineer synthetic phages with enhanced infectivity by modular transfer of a PhageMaP-discovered defense inhibitor from Bas63 to T7. PhageMaP is generalizable, as it leverages homologous recombination, a universal cellular process, for locus-specific barcoding. This versatile tool advances bacteriophage functional genomics and accelerates rational phage design for therapy.},
}
@article {pmid39416026,
year = {2024},
author = {Sendinc, E and Yu, H and Hwang Fu, YH and Santos, J and Johnson, Z and Kirstein, JR and Niu, J and Chabot, MB and Cantu, VA and Džakula, &#x17d; and Lam, Q and Anmangandla, A and Burcham, TS and Davis, EM and Miles, ZD and Price, AD and Purse, BW and Gregory, RI and Stengel, G},
title = {Mapping multiple RNA modifications simultaneously by proximity barcode sequencing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39416026},
issn = {2692-8205},
support = {R35 CA232115/CA/NCI NIH HHS/United States ; R44 HG012170/HG/NHGRI NIH HHS/United States ; },
abstract = {RNA is subject to a multitude of different chemical modifications that collectively represent the epitranscriptome. Individual RNA modifications including N6-methyladenosine (m[6]A) on mRNA play essential roles in the posttranscriptional control of gene expression. Recent technological advances have enabled the transcriptome-wide mapping of certain RNA modifications, to reveal their broad relevance and characteristic distribution patterns. However, convenient methods that enable the simultaneous mapping of multiple different RNA marks within the same sample are generally lacking. Here we present EpiPlex RNA modification profiling, a bead-based proximity barcoding assay with sequencing readout that expands the scope of molecular recognition-based RNA modification detection to multiple targets, while providing relative quantification and enabling low RNA input. Measuring signal intensity against spike-in controls provides relative quantification, indicative of the RNA mod abundance at each locus. We report on changes in the modification status of HEK293T cells upon treatment with pharmacological inhibitors separately targeting METTL3, the dominant m[6]A writer enzyme, and the EIF4A3 component of the exon junction complex (EJC). The treatments resulted in decreased or increased m[6]A levels, respectively, without effect on inosine levels. Inhibiting the helicase activity of EIF4A3 and EIF4A3 knockdown both cause a significant increase of m[6]A sites near exon junctions, consistent with the previously reported role of EIF4A3 in shaping the m[6]A landscape. Thus, EpiPlex offers a reliable and convenient method for simultaneous mapping of multiple RNA modifications to facilitate epitranscriptome studies.},
}
@article {pmid39415074,
year = {2024},
author = {Sojitra, M and Schmidt, EN and Lima, GM and Carpenter, EJ and McCord, KA and Atrazhev, A and Macauley, MS and Derda, R},
title = {Measuring carbohydrate recognition profile of lectins on live cells using liquid glycan array (LiGA).},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {39415074},
issn = {1750-2799},
support = {RGPIN-2016-402511//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; RGPIN-2018-03815//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; CR-29//UAlberta | Canadian Glycomics Network (GlycoNet)/ ; TP-22//UAlberta | Canadian Glycomics Network (GlycoNet)/ ; },
abstract = {Glycans constitute a significant fraction of biomolecular diversity on cellular surfaces across all kingdoms of life. As the structure of glycans is not directly encoded by the organism's DNA, it is impossible to use high-throughput DNA technologies to study the role of cellular glycosylation or to understand how glycocalyx is recognized by glycan-binding proteins (GBPs). To address this gap, we recently described a liquid glycan array (LiGA) platform that allows profiling of glycan-GBP interactions on the surface of live cells in vitro and in vivo using next-generation sequencing. LiGA is a library of DNA-barcoded bacteriophages, where each clonal bacteriophage displays 5-1,500 copies of a glycan and the distinct DNA barcode inside each bacteriophage clone encodes the structure and density of the displayed glycans. Deep sequencing of the glycophages associated with live cells yields a glycan-binding profile of GBPs expressed on the surface of cells. This protocol provides detailed instructions for how to use LiGA to probe cell surface receptors and includes information on the preparation of glycophages, analysis by MALDI-TOF mass spectrometry, the assembly of a LiGA library and its deep sequencing. Using this protocol, we measure glycan-binding profiles of the immunomodulatory sialic acid-binding immunoglobulin-like lectins‑1, -2, -6, -7 and -9 expressed on the surface of different cell types. Compared with existing methods that require complex specialist equipment, this method allows users with basic molecular biology expertise to measure the precise glycan-binding profile of GBPs on the surface of any cell type expressing exogenous GBP within 2-3 d.},
}
@article {pmid39411212,
year = {2024},
author = {Sasaki, M and Fukumoto, N and Fukumoto, S},
title = {DNA barcoding of Anoplocephala perfoliata derived from a draft horse (Ban'ei horse) in Hokkaido, Japan.},
journal = {Journal of equine science},
volume = {35},
number = {3},
pages = {43-46},
pmid = {39411212},
issn = {1340-3516},
abstract = {A two-year-old male Japanese draft horse (known as a "Ban'ei horse") excreted eight cestodes. Based on their morphological features, they were identified as Anoplocephala perfoliata. The partial mitochondrial cytochrome c oxidase subunit 1 (COI) sequences of the worms were nearly identical to A. perfoliata isolated from horses in Europe. The results of phylogenetic analyses of COI revealed that our samples and the European isolates formed the same clade, which was separate from Chinese and Australian isolates. Ban'ei horses were developed by crossbreeding draft horses imported from European countries in the 1900s. Our results suggest that A. perfoliata was transported to Hokkaido with horses from Europe. To our knowledge, this is the first report of A. perfoliata infection in a Japanese draft horse.},
}
@article {pmid39410130,
year = {2024},
author = {Liu, J and Sun, J and He, R and Xia, J and He, P},
title = {The Situation of Counterfeited and Mislabeled Commercialized Edible Mushrooms in China and the Development of Possible Controls.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {19},
pages = {},
pmid = {39410130},
issn = {2304-8158},
abstract = {Edible mushroom products, encompassing both cultivated and wild varieties, are highly favored by consumers due to their rich nutritional profiles, including significant levels of proteins and amino acids. These mushrooms have extensive applications across the food, pharmaceutical, and cosmetic industries, making the edible mushroom industry a vital component of global poverty alleviation efforts. Taking China as an example, the country produces over 45 million tons of edible mushrooms annually, accounting for 94.01% of the world's total production, thereby establishing itself as the leading global producer of edible mushrooms. However, alongside the rapid expansion of this industry, concerns have emerged regarding counterfeit products and incidents of poisoning resulting from the consumption of toxic wild mushrooms. As follows, to advance the development and integrity of the mushroom production and processing industry: (1) This study presents the situation of counterfeit edible mushrooms and elucidates the factors contributing to the production of fraudulent products from both subjective and non-subjective perspectives. (2) We provide a detailed introduction to 22 varieties of freshly cultivated edible mushrooms and commonly encountered wild edible mushrooms in the Chinese consumer market, proposing the application of DNA barcoding, environmental DNA analysis, and other technologies for the future authentication of counterfeit mushroom products. (3) Concurrently, we present an overview of mushroom poisoning incidents in China from 2010 to 2023, emphasizing the challenges in mitigating the risks associated with wild mushroom consumption and preventing food poisoning, thereby necessitating heightened consumer caution. (4) Finally, we offer four recommendations aimed at ensuring the healthy, stable, and sustainable growth of the edible mushroom industry.},
}
@article {pmid39409790,
year = {2024},
author = {Altvater-Hughes, TE and Hodgins, HP and Hodgins, DC and Bauman, CA and Paibomesai, MA and Mallard, BA},
title = {Investigating the IgM and IgG B Cell Receptor Repertoires and Expression of Ultralong Complementarity Determining Region 3 in Colostrum and Blood from Holstein-Friesian Cows at Calving.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {19},
pages = {},
pmid = {39409790},
issn = {2076-2615},
support = {RGPIN04638//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {In cattle, colostral maternal immunoglobulins and lymphocytes transfer across the neonate's intestinal epithelium to provide protection against pathogens. This study aimed to compare repertoires of B cell populations in blood and colostrum in cows for the first time, with an emphasis on ultralong complementarity determining region 3 (CDR3, ≥40 amino acids). Blood mononuclear cells (BMCs, n= 7) and colostral cells (n = 7) were isolated from Holstein-Friesian dairy cows. Magnetic-activated cell sorting was used to capture IgM and IgG B cells from BMCs. Colostral cells were harvested by centrifugation. RNA was extracted and cDNA was produced; IgM and IgG transcripts were amplified using polymerase chain reactions. Amplicons were sequenced using the Nanopore Native barcoding kit 24 V14 and MinION with R10.4 flow cells. In colostrum, there was a significantly greater percentage of IgM B cells with ultralong CDR3s (8.09% ± 1.73 standard error of the mean) compared to blood (4.22% ± 0.70, p = 0.05). There was a significantly greater percentage of IgG B cells in colostrum with ultralong CDR3s (12.98% ± 1.98) compared to blood (6.61% ± 1.11, p = 0.05). A higher percentage of IgM and IgG B cells with ultralong CDR3s in colostrum may be indicative of a potential role in protecting the neonate.},
}
@article {pmid39409782,
year = {2024},
author = {Dinh-Hung, N and Mwamburi, SM and Dong, HT and Rodkhum, C and Meemetta, W and Linh, NV and Mai, HN and Dhar, AK and Hirono, I and Senapin, S and Chatchaiphan, S},
title = {Unveiling Insights into the Whole Genome Sequencing of Mycobacterium spp. Isolated from Siamese Fighting Fish (Betta splendens).},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {19},
pages = {},
pmid = {39409782},
issn = {2076-2615},
abstract = {This study aims to genomically elucidate six isolates of rapidly growing non-tuberculous mycobacteria (RGM) derived from Siamese fighting fish (Betta splendens). These isolates had previously undergone phenotypic and biochemical characterization, antibiotic susceptibility testing, and in vivo virulence assessment. Initial DNA barcoding using the 16S rRNA sequence assigned these six isolates to five different species, namely Mycobacterium chelonae (BN1983), M. cosmeticum (BN1984 and N041), M. farcinogenes (SNSK5), M. mucogenicum (BN1956), and M. senegalense (BN1985). However, the identification relied solely on the highest percent identity of the 16S rRNA gene, raising concerns about the taxonomic ambiguity of these species. Comprehensive whole genome sequencing (WGS) and extended genomic comparisons using multilocus sequence typing (MLST), average nucleotide identity (ANI), and digital DNA-DNA hybridization (dDDH) led to the reclassification of BN1985 and SNSK5 as M. conceptionense while confirming BN1983 as M. chelonae and BN1984 and N041 as M. cosmeticum. Notably, the analysis of the BN1956 isolate revealed a potential new species that is proposed here as M. mucogenicum subsp. phocaicum sp. nov. Common genes encoding "mycobacterial" virulence proteins, such as PE and PPE family proteins, MCE, and YrbE proteins, were detected in all six isolates. Two species, namely M. chelonae and M. cosmeticum, appear to have horizontally acquired T6SS-II (clpB), catalase (katA), GroEL (groel), and capsule (rmlb) from distantly related environmental bacteria such as Klebsiella sp., Neisseria sp., Clostridium sp., and Streptococcus sp. This study provides the first draft genome sequence of RGM isolates currently circulating in B. splendens and underscores the necessity of WGS for the identification and classification of mycobacterial species.},
}
@article {pmid39409767,
year = {2024},
author = {Mezzasalma, M and Odierna, G and Macirella, R and Brunelli, E},
title = {New Insights on Chromosome Diversification in Malagasy Chameleons.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {19},
pages = {},
pmid = {39409767},
issn = {2076-2615},
abstract = {In this work, we performed a preliminary molecular analysis and a comparative cytogenetic study on 5 different species of Malagasy chameleons of the genus Brookesia (B. superciliaris) and Furcifer (F. balteautus, F. petteri, F. major and F. minor). A DNA barcoding analysis was first carried out on the study samples using a fragment of the mitochondrial gene coding for the cytochrome oxidase subunit 1 (COI) in order to assess the taxonomic identity of the available biological material. Subsequently, we performed on the studied individuals a chromosome analysis with standard karyotyping (5% Giemsa solution at pH 7) and sequential C-banding + Giemsa, + CMA3, and + DAPI. The results obtained indicate that the studied species are characterized by a different chromosome number and a variable heterochromatin content and distribution, with or without differentiated sex chromosomes. In particular, B. superciliaris (2n = 36) and F. balteatus (2n = 34) showed a similar karyotype with 6 macro- and 12-11 microchromosome pairs, without differentiated sex chromosomes. In turn, F. petteri, F. major, and F. minor showed a karyotype with a reduced chromosome number (2n = 22-24) and a differentiated sex chromosome system with female heterogamety (ZZ/ZW). Adding our newly generated data to those available from the literature, we highlight that the remarkable chromosomal diversification of the genus Furcifer was likely driven by non-homologous chromosome fusions, including autosome-autosome, Z-autosome, and W-autosome fusions. The results of this process resulted in a progressive reduction in the chromosome number and partially homologous sex chromosomes of different shapes and sizes.},
}
@article {pmid39409561,
year = {2024},
author = {Mehmood, F and Li, M and Bertolli, A and Prosser, F and Varotto, C},
title = {Comparative Plastomics of Plantains (Plantago, Plantaginaceae) as a Tool for the Development of Species-Specific DNA Barcodes.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {19},
pages = {},
pmid = {39409561},
issn = {2223-7747},
support = {CN00000033, CUPD43C22001280006//European Union Next-GenerationEU (PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 - D.D. 1034 17/06/2022/ ; },
abstract = {Plantago (plantains, Plantaginaceae) is a cosmopolitan genus including over 250 species used as functional foods, forage, and traditional medicine. Among them, Plantago lanceolata is commonly used as an ingredient of herbal products, but the close similarity to other Plantago species can cause misidentifications with potentially serious consequences for product safety/quality. To test the possibility of developing species-specific barcoding markers, we de novo assembled plastome sequences of individuals of Plantago argentea, Plantago atrata, P. lanceolata, and Plantago maritima. These genomes were characterized in comparison with both previously sequenced conspecific accessions and other publicly available plastomes, thus providing an assessment of both intraspecific and interspecific genetic variation in Plantago plastomes. Additionally, molecular evolutionary analyses indicated that eleven protein-coding genes involved in different plastid functions in Plantago plastomes underwent positive selection, suggesting they might have contributed to enhancing species' adaptation during the evolutionary history of Plantago. While the most variable mutational hotspots in Plantago plastomes were not suitable for the development of species-specific molecular markers, species-specific polymorphisms could discriminate P. lanceolata from its closest relatives. Taken together, these results highlight the potential of plastome sequencing for the development of molecular markers to improve the identification of species with relevance in herbal products.},
}
@article {pmid39406839,
year = {2024},
author = {Shen, Y and Zhou, X and Zhang, Y and Zhang, J and Li, Q and Chen, Q and Liu, Z and Li, Y and Cheng, R and Luo, Y},
title = {Important fish diversity maintenance status of the tributaries in a hotspot fish conservation area in the upper Yangtze River revealed by eDNA metabarcoding.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {24128},
pmid = {39406839},
issn = {2045-2322},
support = {No. 32202939//National Natural Science Foundation of China/ ; No. CSTB2022NSCQ-MSX0793//Natural Science Foundation of Chongqing, China/ ; },
mesh = {Animals ; *Rivers ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Biodiversity ; China ; DNA, Environmental/genetics/analysis ; Conservation of Natural Resources ; Ecosystem ; Seasons ; },
abstract = {This study employed Environmental DNA (eDNA) barcoding technology to delve into the influence of the tributaries and mainstem on fish diversity and spatiotemporal distribution in a hotspot fish conservation area in the upper Yangtze River. A total of 123 fish species were detected, belonging to 7 orders, 19 families, and 77 genera. The composition of fish species in tributaries is similar to that in mainstem, with higher fish community diversity in tributaries during the spring and summer. Exploration of fish ecotypes revealed significant differences between mainstem and tributaries. The fish community is mainly influenced by key environmental factors such as water temperature, dissolved oxygen, electrical conductivity, and ammonia nitrogen, with a higher impact of these factors on tributaries than on mainstem. In conclusion, while tributaries and mainstem in the Jiangjin section exhibit similarities in fish community composition, there are notable differences in community structure and diversity. Therefore, the protection of not only mainstem but also tributaries and their associated fish habitats is crucial for promoting the overall health and sustainability.},
}
@article {pmid39406030,
year = {2025},
author = {Hymus, CM and Cooper, PL and Rye, MS},
title = {Demonstration of potential DNA contamination introduced by laboratory consumables using Fluorescein.},
journal = {Forensic science international. Genetics},
volume = {74},
number = {},
pages = {103157},
doi = {10.1016/j.fsigen.2024.103157},
pmid = {39406030},
issn = {1878-0326},
mesh = {Humans ; *DNA Contamination ; *Fluorescein ; DNA Fingerprinting ; Fluorescent Dyes ; DNA/analysis/genetics ; Polymerase Chain Reaction ; Specimen Handling/instrumentation ; },
abstract = {The development of increasingly efficient DNA extraction and profiling kits has increased the amount of allelic information obtained from trace DNA samples, but also inadvertently, increased the detection of DNA contamination. This study aimed to evaluate the potential of DNA transfer using fluorescein, fluorescent under an alternate light source, in the use of a range of forensically relevant DNA profiling consumables. An evaluation of two pre-lysis methods adopting three different sample tubes, some with deliberate seal damage, showed the PrepFiler™ Automated Forensic DNA Extraction Kit caused leakage and crusting when the rim of the PrepFiler™ LySep column was compromised, but no leakage was observed under the same conditions using the Investigator STAR Lyse&amp;Prep kit. The AutoLys tube showed minimal leakage using the PrepFiler™ chemistry. A DNA extract tube with an external thread, similar to the AutoLys tube, showed no leakage after fridge or freezer storage. However, it highlighted that a centrifugal spin does not guarantee all the DNA will pool at the base of the tube. A comparison of adhesive plate sealing films to 8-well strip caps for sealing 96-well PCR plates showed the adhesive plate sealing films presented a lower risk of DNA transfer, largely due to the adhesion of dispersed liquid on the sticky surface of the film. Overall, this study highlighted a number of variables that may be considered in the development of more refined contamination minimisation protocols in respect to increased sensitivities of DNA profiling.},
}
@article {pmid39405910,
year = {2024},
author = {Popović, L and Brankatschk, B and Palladino, G and Rossner, MJ and Wehr, MC},
title = {Polypharmacological profiling across protein target families and cellular pathways using the multiplexed cell-based assay platform safetyProfiler reveals efficacy, potency and side effects of drugs.},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {180},
number = {},
pages = {117523},
doi = {10.1016/j.biopha.2024.117523},
pmid = {39405910},
issn = {1950-6007},
mesh = {Humans ; *Polypharmacology ; HEK293 Cells ; Signal Transduction/drug effects ; Receptors, G-Protein-Coupled/metabolism/drug effects ; },
abstract = {Selectivity profiling is key for assessing the pharmacological properties of multi-target drugs. We have developed a cell-based and barcoded assay encompassing ten druggable targets, including G protein-coupled receptors (GPCRs), receptor tyrosine kinases (RTKs), nuclear receptors, a protease as well as their key downstream pathways and profiled 17 drugs in living cells for efficacy, potency, and side effects. Notably, this multiplex assay, termed safetyProfiler assay, enabled the simultaneous assessment of multiple target and pathway activities, shedding light on the polypharmacological profile of compounds. For example, the neuroleptics clozapine, paliperidone, and risperidone potently inhibited primary targets DRD2 and HTR2A as well as cAMP and calcium pathways. However, while paliperidone and risperidone also potently inhibited the secondary target ADRA1A and mitogen-activated protein kinase (MAPK) downstream pathways, clozapine only exhibited mild antagonistic effects on ADRA1A and lacked MAPK inhibition downstream of DRD2 and HTR2A. Furthermore, we present data on the selectivity for bazedoxifene, an estrogen receptor antagonist currently undergoing clinical phase 2 trials for breast cancer, on MAPK signaling. Additionally, precise potency data for LY2452473, an androgen receptor antagonist, that completed a phase 2 clinical trial for prostate cancer, are presented. The non-selective kinase inhibitor staurosporine was observed to potently inactivate the two RTKs EGFR and ERBB4 as well as MAPK signaling, while eliciting stress-related cAMP responses. Our findings underscore the value of comprehensive profiling in elucidating the pharmacological properties of established and novel therapeutics, thereby facilitating the development of novel multi-target drugs with enhanced efficacy and selectivity.},
}
@article {pmid39403482,
year = {2024},
author = {Zhou, QR and Ma, YY and Lv, HQ and Lu, ZC and Wang, LS and Liang, JS and Li, JJ},
title = {Chloroplast mini-barcodes combined with high resolution melting analysis to identify herbal medicine Difengpi (Illicium difengpi).},
journal = {Heliyon},
volume = {10},
number = {19},
pages = {e38700},
pmid = {39403482},
issn = {2405-8440},
abstract = {Difengpi, derived from the air-dried stem bark of Illicium difengpi and enlisted in the Chinese Pharmacopoeia for its therapeutic effect against common ailments, confronts challenges due to dwindling wild resources and intentional substitution with potentially harmful botanical relatives. The imperative need to authenticate this herbal remedy has led to the development of robust methods. Here, we integrated chloroplast mini-barcoding and high resolution melting (HRM) analysis to distinguish Difengpi from the reported adulterants. We assembled the complete chloroplast (cp) genomes of I. difengpi and substituted close relatives I. jiadifengpi and I. majus, and conducted an in-depth comparative analysis to screen divergent regions for exploiting as DNA mini-barcodes. Despite the conservativeness characterizing the whole cp genomes among these Illicium species, we identified some highly variable regions with promising potential as molecular markers for species identification. Subsequently, we designed DNA mini-barcodes and subjected them to HRM analysis to assess their efficacy in species discrimination. Melting profiles unveiled that mini-barcodes designed from four divergence regions trnL-trnF, trnF-ndhJ, ycf1-ndhF and rpl32-trnL exhibited substantial discriminatory power, distinctly differentiated I. difengpi from I. jiadifengpi, I. majus and I. verum. We tested ten commercially available Difengpi products from online stores and local traditional markets using these four mini-barcodes. All ten samples clustered closely with the reference I. difengpi with genotype confidence higher than 93 %, indicating the presence of the claimed species in these samples, sans any reported toxic adulterants. Consequently, we simulated Difengpi mimic samples utilizing I. jiadifengpi, I. majus and I. verum and subjected them to evaluate the practicability of these mini-barcodes. The outcomes confirmed the precision of the four mini-barcodes in accurately discerning the mimic samples. In conclusion, integrating taxon-specific DNA mini-barcodes with HRM analysis is an efficient strategy for the authentication of species identity within commercial herbal products.},
}
@article {pmid39402626,
year = {2024},
author = {Liu, Y and Li, N and Qi, J and Xu, G and Zhao, J and Wang, N and Huang, X and Jiang, W and Wei, H and Justet, A and Adams, TS and Homer, R and Amei, A and Rosas, IO and Kaminski, N and Wang, Z and Yan, X},
title = {SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {271},
pmid = {39402626},
issn = {1474-760X},
support = {R21 LM012884/LM/NLM NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; R01 LM014087/LM/NLM NIH HHS/United States ; R21LM012884//Foundation for the National Institutes of Health/ ; DMS1916246//National Science Foundation/ ; R01LM014087//Foundation for the National Institutes of Health/ ; },
mesh = {*Machine Learning ; *Single-Cell Analysis/methods ; *Transcriptome ; Humans ; Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; Software ; Animals ; Regression Analysis ; RNA-Seq/methods ; },
abstract = {Spatial barcoding-based transcriptomic (ST) data require deconvolution for cellular-level downstream analysis. Here we present SDePER, a hybrid machine learning and regression method to deconvolve ST data using reference single-cell RNA sequencing (scRNA-seq) data. SDePER tackles platform effects between ST and scRNA-seq data, ensuring a linear relationship between them while addressing sparsity and spatial correlations in cell types across capture spots. SDePER estimates cell-type proportions, enabling enhanced resolution tissue mapping by imputing cell-type compositions and gene expressions at unmeasured locations. Applications to simulated data and four real datasets showed SDePER's superior accuracy and robustness over existing methods.},
}
@article {pmid39400321,
year = {2025},
author = {Castellanos-Labarcena, J and Steinke, D and Adamowicz, SJ},
title = {Anomalous latitudinal gradients in parasitoid wasp diversity-Hotspots in regions with larger temperature range.},
journal = {The Journal of animal ecology},
volume = {94},
number = {3},
pages = {410-422},
pmid = {39400321},
issn = {1365-2656},
support = {//Arrell Food Institute/ ; //Natural Sciences and Engineering Research Council of Canada/ ; //Genome Canada/ ; //Ontario Ministry of Economic Development, Job Creation and Trade/ ; //Canada First Research Excellence Fund/ ; },
mesh = {Animals ; *Wasps/physiology/genetics ; *Biodiversity ; *Temperature ; Genetic Variation ; DNA, Mitochondrial/genetics ; DNA Barcoding, Taxonomic ; Climate Change ; },
abstract = {Knowledge of global patterns of genetic diversity is essential for biodiversity conservation as this parameter describes the ability of a species to respond to environmental changes. Ichneumonoids parasitoid wasps are among the few taxa showing an anomalous latitudinal diversity gradient. Using the largest georeferenced molecular dataset for this group, we used a macrogenetics approach to examine latitudinal patterns and predictors of intraspecific genetic diversity. We calculated the mean nucleotide diversity of mitochondrial DNA barcode sequences at three geographic levels: grid cells, latitudinal bands and climatic zones. Nucleotide diversity values were consistently higher at northern temperate latitudes, peaking at 50°. We found a positive but weak relationship between intraspecific diversity and the latitude, between intra- and interspecific diversity, and a positive effect of the temperature range. Examining the spatial relationship between different levels of biodiversity and its drivers is particularly relevant considering climate change and its impact on species distribution. Yet, in insects, it has been challenging to integrate ecological, evolutionary and geographical components when analysing the processes leading to species richness gradients.},
}
@article {pmid39395971,
year = {2024},
author = {Li, Z and Ran, Z and Xiao, X and Yan, C and Xu, J and Tang, M and An, M},
title = {Comparative analysis of the whole mitochondrial genomes of four species in sect. Chrysantha (Camellia L.), endemic taxa in China.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {955},
pmid = {39395971},
issn = {1471-2229},
support = {2022&#xff08;072&#xff09;//Guizhou Provincial Basic Research Program (Natural Science)/ ; 32360101//National Natural Science Foundation of China/ ; 31960043//National Natural Science Foundation of China/ ; },
mesh = {*Genome, Mitochondrial ; China ; *Camellia/genetics ; Phylogeny ; RNA Editing ; Genome, Plant ; Base Composition ; },
abstract = {BACKGROUND: The sect. Chrysantha Chang of plants with yellow flowers of Camellia species as the "Queen of the Tea Family", most of these species are narrowly distributed endemics of China and are currently listed Grde-II in National Key Protected Wild Plant of China. They are commercially important plants with horticultural medicinal and scientific research value. However, the study of the sect. Chrysantha species genetics are still in its infancy, to date, the mitochondrial genome in sect. Chrysantha has been still unexplored.<br><br>RESULTS: In this study, we provide a comprehensive assembly and annotation of the mitochondrial genomes for four species within the sect. Chrysantha. The results showed that the mitochondrial genomes were composed of closed-loop DNA molecules with sizes ranging from 850,836&#xa0;bp (C. nitidissima) to 1,098,121&#xa0;bp (C. tianeensis) with GC content of 45.71-45.78% and contained 48-58 genes, including 28-37 protein-coding genes, 17-20 tRNA genes and 2 rRNA genes. We also examined codon usage, sequence repeats, RNA editing and selective pressure in the four species. Then, we performed a comprehensive comparison of their basic structures, GC contents, codon preferences, repetitive sequences, RNA editing sites, Ka/Ks ratios, haplotypes, and RNA editing sites. The results showed that these plants differ little in gene type and number. C. nitidissima has the greatest variety of genes, while C. tianeensis has the greatest loss of genes. The Ka/Ks values of the atp6 gene in all four plants were greater than 1, indicating positive selection. And the codons ending in A and T were highly used. In addition, the RNA editing sites differed greatly in number, type, location, and efficiency. Twelve, six, five, and twelve horizontal gene transfer (HGT) fragments were found in C. tianeensis, Camellia huana, Camellia liberofilamenta, and C. nitidissima, respectively. The phylogenetic tree clusters the four species of sect. Chrysantha plants into one group, and C. huana and C. liberofilamenta have closer affinities.<br><br>CONCLUSIONS: In this study, the mitochondrial genomes of four sect. Chrysantha plants were assembled and annotated, and these results contribute to the development of new genetic markers, DNA barcode databases, genetic improvement and breeding, and provide important references for scientific research, population genetics, and kinship identification of sect. Chrysantha plants.},
}
@article {pmid39387679,
year = {2025},
author = {Hebert, PDN and Floyd, R and Jafarpour, S and Prosser, SWJ},
title = {Barcode 100K Specimens: In a Single Nanopore Run.},
journal = {Molecular ecology resources},
volume = {25},
number = {1},
pages = {e14028},
pmid = {39387679},
issn = {1755-0998},
support = {OGI-208//Genome Canada/ ; OGI-233//Ontario Genomics/ ; //Canada Foundation for Innovation/ ; NFRFT-2020-00073//New Frontiers in Research Fund/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Nanopores ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Polymerase Chain Reaction/methods ; },
abstract = {It is a global priority to better manage the biosphere, but action must be informed by comprehensive data on the abundance and distribution of species. The acquisition of such information is currently constrained by high costs. DNA barcoding can speed the registration of unknown animal species, the most diverse kingdom of eukaryotes, as the BIN system automates their recognition. However, inexpensive sequencing protocols are critical as the census of all animal species is likely to require the analysis of a billion or more specimens. Barcoding involves DNA extraction followed by PCR and sequencing with the last step dominating costs until 2017. By enabling the sequencing of highly multiplexed samples, the Sequel platforms from Pacific BioSciences slashed costs by 90%, but these instruments are only deployed in core facilities because of their expense. Sequencers from Oxford Nanopore Technologies provide an escape from high capital and service costs, but their low sequence fidelity has, until recently, constrained adoption. However, the improved performance of its latest flow cells (R10.4.1) erases this barrier. This study demonstrates that a MinION flow cell can characterise an amplicon pool derived from 100,000 specimens while a Flongle flow cell can process one derived from several thousand. At $0.01 per specimen, DNA sequencing is now the least expensive step in the barcode workflow.},
}
@article {pmid39394065,
year = {2024},
author = {Kan, S and Su, X and Yang, L and Zhou, H and Qian, M and Zhang, W and Li, C},
title = {From light into shadow: comparative plastomes in Petrocosmea and implications for low light adaptation.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {949},
pmid = {39394065},
issn = {1471-2229},
support = {32200187//National Natural Science Foundation of China/ ; 82173936//National Natural Science Foundation of China/ ; },
mesh = {*Genome, Plastid ; *Phylogeny ; Light ; Plastids/genetics ; Adaptation, Physiological/genetics ; },
abstract = {BACKGROUND: Plastids originated from an ancient endosymbiotic event and evolved into the photosynthetic organelles in plant cells. They absorb light energy and carbon dioxide, converting them into chemical energy and oxygen, which are crucial for plant development and adaptation. However, little is known about the plastid genome to light adaptation. Petrocosmea, a member of the Gesneriaceae family, comprises approximately 70 species with diverse light environment, serve as an ideal subject for studying plastomes adapt to light.<br><br>RESULTS: In this study, we selected ten representative species of Petrocosmea from diverse light environments, assembled their plastid genomes, and conducted a comparative genomic analysis. We found that the plastid genome of Petrocosmea is highly conserved in both structure and gene content. The phylogenetic relationships reconstructed based on the plastid genes were divided into five clades, which is consistent with the results of previous studies. The vast majority of plastid protein-coding genes were under purifying selection, with only the rps8 and rps16 genes identified under positive selection in different light environments. Notably, significant differences of evolutionary rate were observed in NADH dehydrogenase, ATPase ribosome, and RNA polymerase between Clade A and the other clades. Additionally, we identified ycf1 and several intergenic regions (trnH-psbA, trnK-rps16, rpoB-trnC, petA-psbJ, ccsA-trnL, rps16-trnQ, and trnS-trnG) as candidate barcodes for this emerging ornamental horticulture.<br><br>CONCLUSION: We newly assembled ten plastid genomes of Petrocosmea and identified several hypervariable regions, providing genetic resources and candidate markers for this promising emerging ornamental horticulture. Furthermore, our study suggested that rps8 and rps16 were under positive selection and that the evolutionary patterns of NADH dehydrogenase, ATPase ribosome, and RNA polymerase were related to the diversity light environment in Petrocosmea. This revealed an evolutionary scenario for light adaptation of the plastid genome in plants.},
}
@article {pmid39391540,
year = {2024},
author = {Selnekovič, D and Kodada, J and Gülperçin, N and Tezcan, S and Ruzzier, E},
title = {Morphological and molecular characterisation of Mordellistenapeloponnesensis Batten, 1980 (Coleoptera, Mordellidae), with first records from Italy and Turkey.},
journal = {ZooKeys},
volume = {1214},
number = {},
pages = {105-117},
pmid = {39391540},
issn = {1313-2989},
abstract = {Mordellistenapeloponnesensis Batten, 1980, previously known from Cyprus and Greece, is reported from Italy and Turkey for the first time. The species is redescribed based on type specimens and additional material from its entire known distributional range. Eighteen DNA barcoding sequences of M.peloponnesensis from Greece, Cyprus, and Italy were generated, and genetic variability across the sampling localities was examined. Three mitochondrial haplotypes were detected within M.peloponnesensis. Specimens from mainland Italy share the same haplotype as those from Rhodes and Cyprus, whereas Sardinian specimens exhibit a distinct haplotype. The third haplotype is represented by one specimen from Cyprus. The DNA barcoding sequences of M.peloponnesensis were compared with those of the morphologically allied M.gemellata Schilsky, 1898, and M.pyrenaea Ermisch, 1966, to reveal the phylogenetic relationships between the species.},
}
@article {pmid39388461,
year = {2024},
author = {Martoni, F and Rako, L and Jaroslow, D and Selleck, C and Kant, P and Nancarrow, N and Blacket, MJ},
title = {Diversity and composition of the bacterial communities associated with the Australian spittlebugs Bathyllus albicinctus and Philagra parva (Hemiptera: Aphrophoridae).},
journal = {PloS one},
volume = {19},
number = {10},
pages = {e0311938},
pmid = {39388461},
issn = {1932-6203},
mesh = {Animals ; *Hemiptera/microbiology ; Australia ; Xylella/genetics ; Bacteria/genetics/classification/isolation &amp; purification ; Microbiota ; Nymph/microbiology ; Plant Diseases/microbiology/parasitology ; Insect Vectors/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Spittlebugs and froghoppers (Hemiptera: Cercopoidea) are insects feeding on xylem, which potentially can cause significant economic damage worldwide by transmitting plant pathogenic bacteria such as Xylella fastidiosa. Australia and New Zealand are currently free from X. fastidiosa, but they are home to at least 45 native spittlebug species. Among these, the Australian natives Bathyllus albicinctus (Erichson, 1842) and Philagra parva (Donovan, 1805) are particularly widespread and can be found across southern and eastern Australia, with B. albicinctus also in New Zealand. The potential that both species might be capable of vectoring Xylella fastidiosa poses a substantial biosecurity risk if the bacterium were to invade these regions. In this study, we examined 87 spittlebug nymphs collected across 12 different host plant species, in five locations in Victoria, Australia. Our objective was to explore the factors influencing bacterial communities within and between these widespread spittlebug species, considering geographic location, insect phylogenetics, and host plant associations. We employed COI barcoding to assess insect genetic variation and 16S high throughput sequencing (HTS) metabarcoding to analyse bacterial microbiome diversity across various host plants. Our findings revealed minimal genetic divergence among spittlebug individuals in the same species, highlighting conspecificity despite conspicuous morphological divergences. On the other hand, we recorded significant variation in bacterial communities harboured by Bathyllus albicinctus nymphs feeding on different plants, even when these were collected within close proximity to each other. Therefore, host plant association appeared to shape the bacterial communities of spittlebugs more than insect genetic divergence or geographical location. These diverse bacterial communities could potentially facilitate transmission of plant pathogenic bacteria, underscoring the risk of widespread transmission among numerous plant hosts through insect-plant interactions. This study emphasizes the critical need to understand these complex interactions, particularly in the context of biosecurity.},
}
@article {pmid39386966,
year = {2024},
author = {Twyford, AD and Beasley, J and Barnes, I and Allen, H and Azzopardi, F and Bell, D and Blaxter, ML and Broad, G and Campos-Dominguez, L and Choonea, D and Crowley, L and Cuber, P and Cunliffe, M and Dombrowski, A and Douglas, B and Forrest, LL and Gaya, E and Greeves, C and Griffin, C and Harley, J and Hart, ML and Holland, PWH and Hollingsworth, PM and Januszczak, I and Jones, A and Kersey, P and Kilias, E and Lawniczak, MKN and Lewis, OT and Mian, S and Minotto, A and Misra, R and Mulhair, PO and Pereira da Conceicoa, L and Price, BW and Salatino, S and Shaw, F and Sivell, O and Sivess, L and Uhl, R and Woof, K and , },
title = {A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life Project.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {339},
pmid = {39386966},
issn = {2398-502X},
abstract = {Biodiversity genomics research requires reliable organismal identification, which can be difficult based on morphology alone. DNA-based identification using DNA barcoding can provide confirmation of species identity and resolve taxonomic issues but is rarely used in studies generating reference genomes. Here, we describe the development and implementation of DNA barcoding for the Darwin Tree of Life Project (DToL), which aims to sequence and assemble high quality reference genomes for all eukaryotic species in Britain and Ireland. We present a standardised framework for DNA barcode sequencing and data interpretation that is then adapted for diverse organismal groups. DNA barcoding data from over 12,000 DToL specimens has identified up to 20% of samples requiring additional verification, with 2% of seed plants and 3.5% of animal specimens subsequently having their names changed. We also make recommendations for future developments using new sequencing approaches and streamlined bioinformatic approaches.},
}
@article {pmid39386620,
year = {2024},
author = {Mays, JC and Mei, S and Kogenaru, M and Quysbertf, HM and Bosco, N and Zhao, X and Bianchi, JJ and Goldberg, A and Kidiyoor, GR and Holt, LJ and Fenyö, D and Davoli, T},
title = {KaryoTap Enables Aneuploidy Detection in Thousands of Single Human Cells.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39386620},
issn = {2692-8205},
support = {P30 CA016087/CA/NCI NIH HHS/United States ; R01 HG012590/HG/NHGRI NIH HHS/United States ; R37 CA240765/CA/NCI NIH HHS/United States ; R01 DK135089/DK/NIDDK NIH HHS/United States ; R37 CA248631/CA/NCI NIH HHS/United States ; },
abstract = {Investigating chromosomal instability and aneuploidy within tumors is essential for understanding tumorigenesis and developing diagnostic and therapeutic strategies. Single-cell DNA sequencing technologies have enabled such analyses, revealing aneuploidies specific to individual cells within the same tumor. However, it has been difficult to scale the throughput of these methods to detect rare aneuploidies while maintaining high sensitivity. To overcome this deficit, we developed KaryoTap, a method combining custom targeted DNA sequencing panels for the Tapestri platform with a computational framework to enable detection of chromosome- and chromosome arm-scale aneuploidy (gains or losses) and copy number neutral loss of heterozygosity in all human chromosomes across thousands of single cells simultaneously. KaryoTap allows detecting gains and losses with an average accuracy of 83% for arm events and 91% for chromosome events. Importantly, together with chromosomal copy number, our system allows us to detect barcodes and gRNAs integrated into the cells' genome, thus enabling pooled CRISPR- or ORF-based functional screens in single cells. As a proof of principle, we performed a small screen to expand the chromosomes that can be targeted by our recently described CRISPR-based KaryoCreate system for engineering aneuploidy in human cells. KaryoTap will prove a powerful and flexible approach for the study of aneuploidy and chromosomal instability in both tumors and normal tissues.},
}
@article {pmid39386543,
year = {2024},
author = {Vong, KI and Alvarez, YD and Noel, G and Barton, ST and Chung, C and Howarth, R and Meave, N and Zhang, Q and Jiwani, F and Barrows, C and Patel, A and Wang, JX and Chi, N and Kingsmore, SF and White, MD and Yang, X and Gleeson, JG},
title = {Genomic mosaicism reveals developmental organization of trunk neural crest-derived ganglia.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39386543},
issn = {2692-8205},
support = {U01 MH108898/MH/NIMH NIH HHS/United States ; R01 MH124890/MH/NIMH NIH HHS/United States ; P01 HD104436/HD/NICHD NIH HHS/United States ; K99 HD111686/HD/NICHD NIH HHS/United States ; R21 MH134401/MH/NIMH NIH HHS/United States ; S10 OD026929/OD/NIH HHS/United States ; S10 OD021644/OD/NIH HHS/United States ; },
abstract = {The neural crest generates numerous cell types, but conflicting results leave developmental origins unresolved. Here using somatic mosaic variants as cellular barcodes, we infer embryonic clonal dynamics of trunk neural crest, focusing on the sensory and sympathetic ganglia. From three independent adult neurotypical human donors, we identified 1,278 mosaic variants using deep whole-genome sequencing, then profiled allelic fractions in 187 anatomically dissected ganglia. We found a massive rostrocaudal spread of progenitor clones specific to sensory or sympathetic ganglia, which unlike in the brain, showed robust bilateral distributions. Computational modeling suggested neural crest progenitor fate specification preceded delamination from neural tube. Single-cell multiomic analysis suggested both neurons and glia contributed to the rostrocaudal clonal organization. CRISPR barcoding in mice and live imaging in quail embryos confirmed these clonal dynamics across multiple somite levels. Our findings reveal an evolutionarily conserved clonal spread of cells populating peripheral neural ganglia.},
}
@article {pmid39386478,
year = {2024},
author = {Vaidya, K and Regan, MS and Lin, J and Houle, J and Stopka, SA and Agar, NYR and Hammond, PT and Boehnke, N},
title = {Pooled nanoparticle screening using a chemical barcoding approach.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.24.614746},
pmid = {39386478},
issn = {2692-8205},
abstract = {We report the development of a small molecule-based barcoding platform for pooled screening of nanoparticle delivery. Using aryl halide-based tags (halocodes), we achieve high-sensitivity detection via gas chromatography coupled with mass spectrometry or electron capture. This enables barcoding and tracking of nanoparticles with minimal halocode concentrations and without altering their physicochemical properties. To demonstrate the utility of our platform for pooled screening, we synthesized a halocoded library of polylactide-co-glycolide (PLGA) nanoparticles and quantified uptake in ovarian cancer cells in a pooled manner. Our findings correlate with conventional fluorescence-based assays. Additionally, we demonstrate the potential of halocodes for spatial mapping of nanoparticles using mass spectrometry imaging (MSI). Halocoding presents an accessible and modular nanoparticle screening platform capable of quantifying delivery of pooled nanocarrier libraries in a range of biological settings.},
}
@article {pmid39386005,
year = {2024},
author = {Lin, X and Waring, K and Ghezzi, H and Tropini, C and Tyson, J and Ziels, RM},
title = {High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the Nanopore platform.},
journal = {PNAS nexus},
volume = {3},
number = {10},
pages = {pgae411},
pmid = {39386005},
issn = {2752-6542},
abstract = {Small subunit (SSU) ribosomal RNA (rRNA) gene amplicon sequencing is a foundational method in microbial ecology. Currently, short-read platforms are commonly employed for high-throughput applications of SSU rRNA amplicon sequencing, but at the cost of poor taxonomic classification due to limited fragment lengths. The Oxford Nanopore Technologies (ONT) platform can sequence full-length SSU rRNA genes, but its lower raw-read accuracy has so-far limited accurate taxonomic classification and de novo feature generation. Here, we present a sequencing workflow, termed ssUMI, that combines unique molecular identifier (UMI)-based error correction with newer (R10.4+) ONT chemistry and sample barcoding to enable high throughput near full-length SSU rRNA (e.g. 16S rRNA) amplicon sequencing. The ssUMI workflow generated near full-length 16S rRNA consensus sequences with 99.99% mean accuracy using a minimum subread coverage of 3×, surpassing the accuracy of Illumina short reads. The consensus sequences generated with ssUMI were used to produce error-free de novo sequence features with no false positives with two microbial community standards. In contrast, Nanopore raw reads produced erroneous de novo sequence features, indicating that UMI-based error correction is currently necessary for high-accuracy microbial profiling with R10.4+ ONT sequencing chemistries. We showcase the cost-competitive scalability of the ssUMI workflow by sequencing 87 time-series wastewater samples and 27 human gut samples, obtaining quantitative ecological insights that were missed by short-read amplicon sequencing. ssUMI, therefore, enables accurate and low-cost full-length 16S rRNA amplicon sequencing on Nanopore, improving accessibility to high-resolution microbiome science.},
}
@article {pmid39385931,
year = {2024},
author = {Da Silva, C and Mannise, N and Seguí, R and Iriarte, A and Bou, N and Bonifacino, JM and Mailhos, A and Anza, L and Chitaro, S and Ocampo, F and Gándaras, R and Arezo, F and Capurro, L and Iturburu, M and Nieto, N and Juan, H and Garrido, J and Platero, R and Gago, J and Lezama, F and Do Carmo, M and Cosse, M},
title = {Exploring biodiversity of Uruguayan vascular plants through DNA barcoding.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1435592},
pmid = {39385931},
issn = {1664-8021},
}
@article {pmid39385841,
year = {2024},
author = {Siedlecki, I and Kochanowski, M and Pawłowska, J and Reszotnik, G and Okrasińska, A and Wrzosek, M},
title = {Ant's Nest as a microenvironment: Distinct Mucoromycota (Fungi) community of the red wood ants' (Formica polyctena) mounds.},
journal = {Ecology and evolution},
volume = {14},
number = {10},
pages = {e70333},
pmid = {39385841},
issn = {2045-7758},
abstract = {Many social insect species build nests, which differ from the surrounding environment and are often occupied by specific organismal communities. These organisms may interact mutualistically or parasitically with the nest-builders, or simply co-occur, being able to survive in these microenvironments. In temperate forests, red wood ants (e.g. Formica polyctena) are known to create distinct, highly developed nests, which consist of large, above-ground mounds, built primarily out of plant matter collected from the forest litter. The microorganismal communities of such mounds remain understudied. As representatives of Mucoromycota fungi commonly engage in the decomposition process of the forest litter, they would be expected to occur in the mounds. However, it is still not known whether the Mucoromycota community of these ants' nests differ from the one of the surrounding forest litter. In order to distinguish mound-associated taxa, we characterized Mucoromycota communities of Formica polyctena mounds and the surrounding forest litter. We sampled four sites, twice in a season. Sampled material was plated on agar media and emerging Mucoromycota colonies were identified based on their morphology. Fungal identification was further confirmed using DNA barcoding. In order to compare described communities, PERMANOVA test and non-metric multidimensional scaling ordinations were used. To distinguish taxa associated with the mounds, multilevel pattern analysis was performed. Our results show that the Mucoromycota community of Formica polyctena's mound differs from the community of the surrounding forest litter. While representatives of Entomortierella lignicola and Absidia cylindrospora clade were found to be associated with the mound environment, representatives of Umbelopsis curvata and Podila verticillata-humilis clade were associated with forest litter, and were rarely present in the mounds. Our findings strongly suggest that the red wood ants' nest is a specific microenvironment in the temperate forest floor, which is a preferred microhabitat for the mound-associated Mucoromycota, possibly adapted to live in proximity to ants.},
}
@article {pmid39385531,
year = {2025},
author = {Nirchio, M and Oliveira, C and de Bello Cioffi, M and Sassi, FMC and Rizzi, FP and Benavides, SWN and Berrones, AJC and Romero, JFR and Deon, GA and Kuranaka, M and Valdiviezo-Rivera, JS and Carrión Olmedo, JC and Rossi, AR},
title = {Integrative morphological, cytogenetic and molecular characterization of the Andean climbing catfish Astroblepus mindoensis (Regan, 1916) (Siluriformes:Astroblepidae).},
journal = {Journal of fish biology},
volume = {106},
number = {2},
pages = {292-304},
doi = {10.1111/jfb.15924},
pmid = {39385531},
issn = {1095-8649},
support = {2020/UTMACH-GPR-155//Universidad T&#xe9;cnica de Machala/ ; DI-CONV-2017-009//Universidad Central del Ecuador/ ; 2020/13433-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2023/00955-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2023/08116-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; proc. 306054/2006-0//Consejo de Desarrollo Cient&#xed;fico, Human&#xed;stico, Tecnol&#xf3;gico y de las Artes, Universidad de Los Andes Venezuela/ ; 441128/2020-3//Consejo de Desarrollo Cient&#xed;fico, Human&#xed;stico, Tecnol&#xf3;gico y de las Artes, Universidad de Los Andes Venezuela/ ; RP12117A6764463C//Sapienza Universit&#xe0; di Roma/ ; },
mesh = {Animals ; *Catfishes/genetics/anatomy &amp; histology/classification ; *Phylogeny ; *Electron Transport Complex IV/genetics ; Male ; Female ; Karyotype ; Ecuador ; Cytogenetic Analysis ; Karyotyping ; },
abstract = {Astroblepus species, commonly known as Andean climbing catfish, exhibit a unique challenge in species delimitation, leading to ongoing taxonomic debates. Here we report data on Astroblepus mindoensis, a vulnerable species endemic to Ecuador, obtained by an integrative approach that includes cytogenetic analysis, molecular identification of the specimens, and recording of morphological and morphometric characters useful for species diagnosis. Thus, this study aimed to associate the karyotype data of the specimens analyzed with morphological and molecular characters, improving and expanding the existing taxonomic information, thus contributing to the systematics of the species. Our morphology results, unlike Regan's original description, which is brief and ambiguous, provide a more detailed morphometric and meristic description. Molecular phylogenetic reconstruction and genetic distance based on a fragment of the cytochrome c oxidase subunit I (COI) showed that our samples constitute a well-supported and monophyletic clade within the A. grixalvii species complex. The cytogenetic analysis identified distinct chromosomal markers, including a single cluster of major ribosomal genes (on chromosome pair 3) and of minor ribosomal genes (on chromosome pair 12) with their localization differing from those reported in other Astroblepus species analyzed. Additionally, the presence of a heteromorphic chromosome pair in males suggests the presence of an XX/XY sex-determination system that has not been identified in other congeneric species. Further investigation is necessary to determine if these chromosomes are associated with the accumulation of repeated sequences, as typically occurs with sex chromosomes, and to assess their presence in other species of the genus.},
}
@article {pmid39384703,
year = {2024},
author = {Araújo, KS and Alves, JL and Pereira, OL and de Queiroz, MV},
title = {Five new species of endophytic Penicillium from rubber trees in the Brazilian Amazon.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {55},
number = {4},
pages = {3051-3074},
pmid = {39384703},
issn = {1678-4405},
support = {Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
mesh = {*Hevea/microbiology ; *Penicillium/genetics/isolation &amp; purification/classification ; *Phylogeny ; Brazil ; *Endophytes/isolation &amp; purification/classification/genetics ; DNA, Fungal/genetics ; DNA Barcoding, Taxonomic ; Calmodulin/genetics ; Tubulin/genetics ; },
abstract = {The Amazon rainforest is the world's most diverse ecosystem, full of fauna and flora. Among the trees that make up the forest are the rubber trees of the genus Hevea (H. brasiliensis and H. guianensis), which stand out for the industrial use of latex. It was previously shown that endophytic fungi colonize the leaves, stems, and roots of Hevea spp. In this study, 47 Penicillium spp. and three Talaromyces spp. isolates were analyzed using specific DNA barcodes: internal transcribed spacers region (ITS), β-tubulin (BenA), calmodulin (CaM), and the DNA-dependent RNA polymerase II second largest subunit (RPB2) genes and additionally, for species delimitation, the genealogical concordance phylogenetic species recognition (GCPSR) criteria were applied. The phylogenetic analyses placed the Penicillium isolates into four sections Lanata-Divaricata, Sclerotiora, Citrina, and Fasciculata. The morphological and molecular characteristics resulted in the discovery of five new species (P. heveae sp. nov., P. acrean sp. nov., P. aquiri sp. nov., P. amazonense sp. nov., and P. pseudomellis sp. nov.). The five new species were also compared to closely related species, with observations on morphologically distinguishing features and colony appearances. Bayesian inference and maximum likelihood analysis have supported the placement of P. heveae sp. nov. as a sister group to P. globosum; P. acrean sp. nov. and P. aquiri sp. nov. as sister groups to P. sumatrense; P. amazonense sp. nov. closely related to isolates of P. rolfsii, and P. pseudomellis sp. nov. closely related to P. mellis. The study of endophytic Penicillium species of rubber trees and the description of five new taxa of Penicillium sect. Citrina, Lanata-Divaricata, and Sclerotiora as endophytes add to the fungal biodiversity knowledge in native rubber trees. Reports of fungi in native tropical plants may reveal taxonomic novelties, potential pathogen control agents, and producers of molecular bioactive compounds of medical and agronomic interest.},
}
@article {pmid39384034,
year = {2024},
author = {Martínez Del Río, J and Frutos-Beltrán, E and Sebastián-Martín, A and Lasala, F and Yasukawa, K and Delgado, R and Menéndez-Arias, L},
title = {HIV-1 Reverse Transcriptase Error Rates and Transcriptional Thresholds Based on Single-strand Consensus Sequencing of Target RNA Derived From In Vitro-transcription and HIV-infected Cells.},
journal = {Journal of molecular biology},
volume = {436},
number = {22},
pages = {168815},
doi = {10.1016/j.jmb.2024.168815},
pmid = {39384034},
issn = {1089-8638},
mesh = {*HIV Reverse Transcriptase/genetics/metabolism ; Humans ; *HIV-1/genetics ; *RNA, Viral/genetics ; Reverse Transcription/genetics ; High-Throughput Nucleotide Sequencing/methods ; HIV Infections/virology/genetics ; Transcription, Genetic ; },
abstract = {Nucleotide incorporation and lacZ-based forward mutation assays have been widely used to determine the accuracy of reverse transcriptases (RTs) in RNA-dependent DNA polymerization reactions. However, they involve quite complex and laborious procedures, and cannot provide accurate error rates. Recently, NGS-based methods using barcodes opened the possibility of detecting all errors introduced by the RT, although their widespread use is limited by cost, due to the large size of libraries to be sequenced. In this study, we describe a novel and relatively simple NGS assay based on single-strand consensus sequencing that provides robust results with a relatively small number of raw sequences (around 60 Mb). The method has been validated by determining the error rate of HIV-1 (BH10 strain) RT using the HIV-1 protease-coding sequence as target. HIV-1 reverse transcription error rates in standard conditions (37 °C/3 mM Mg[2+]) using an in vitro-transcribed RNA were around 7.3 × 10[-5]. In agreement with previous reports, an 8-fold increase in RT's accuracy was observed after reducing Mg[2+] concentration to 0.5 mM. The fidelity of HIV-1 RT was also higher at 50 °C than at 37 °C (error rate 1.5 × 10[-5]). Interestingly, error rates obtained with HIV-1 RNA from infected cells as template of the reverse transcription at 3 mM Mg[2+] (7.4 × 10[-5]) were similar to those determined with the in vitro-transcribed RNA, and were reduced to 1.8 × 10[-5] in the presence of 0.5 mM Mg[2+]. Values obtained at low magnesium concentrations were modestly higher than the transcription error rates calculated for human cells, thereby suggesting a realistic transcriptional threshold for our NGS-based error rate determinations.},
}
@article {pmid39383837,
year = {2024},
author = {Mansfield, KL and González, E and McKay, S and Apaa, T and Kent, AJ and Cropper, P and Berry, N and Hernández-Triana, LM and Johnson, N},
title = {Short Communication: Anaplasma phagocytophilum and Babesia spp. in ixodid ticks infesting red foxes (Vulpes vulpes) in Great Britain.},
journal = {Ticks and tick-borne diseases},
volume = {15},
number = {6},
pages = {102401},
doi = {10.1016/j.ttbdis.2024.102401},
pmid = {39383837},
issn = {1877-9603},
mesh = {Animals ; *Foxes/parasitology ; *Anaplasma phagocytophilum/isolation &amp; purification/genetics ; *Babesia/isolation &amp; purification/genetics ; United Kingdom/epidemiology ; *Tick Infestations/veterinary/epidemiology/parasitology ; *Nymph/microbiology/growth &amp; development ; Female ; Ixodes/microbiology/parasitology ; Ixodidae/microbiology/parasitology ; Male ; Ehrlichiosis/epidemiology/veterinary/microbiology ; Babesiosis/epidemiology/parasitology ; },
abstract = {Red foxes (Vulpes vulpes) are found throughout the United Kingdom (UK), and can reach high population densities in urban areas. They are often infested with ticks which may carry tick-borne pathogens, leading to a risk of transmission to domestic animals and humans. This study investigated the prevalence of tick-borne pathogens in ticks sourced from red fox carcasses across Great Britain between 2018 and 2022. Tick species were identified using morphological keys and molecular barcoding, followed by specific pathogen testing using PCR. In total, 227 ticks were collected from 93 foxes. Pooling (n = 2) was undertaken for unengorged nymphs from the same tick species and fox host, with 203 homogenates tested in total (24 pools and 179 individual ticks). Ixodes hexagonus was the most abundant tick species sampled (73 %), of which 59 % were nymphs and 41 % were females. Less common were Ixodes ricinus (12 %) and Ixodes canisuga (15 %), the majority of which were females (73 % and 91 %, respectively). One Ixodes sp. larva was identified. Babesia DNA was identified in seven individual ticks and once in pooled ticks (n = 2); seven detections were in I. hexagonus and one in I. canisuga, with an overall detection rate of 7 % (95 % CI: 6 - 8 %). Sequence analysis confirmed that all Babesia detections in I. hexagonus were Babesia vulpes, with detection of Babesia Badger Type A in I. canisuga. Screening for Anaplasma phagocytophilum DNA through amplification of the msp2 gene yielded an overall detection rate of 4 % (detected in I. hexagonus only). Louping ill virus was not detected by qRT-PCR in any tick RNA tested. The majority of pathogen detections were in ticks from red foxes in rural areas of the UK, although a small number of Babesia detections were in ticks collected from semi-rural or urban red foxes. Additionally, B. vulpes was detected in GB red fox tissues, suggesting a potential role as a reservoir host. This study confirms the detection of tick-borne pathogens in ticks infesting UK red foxes and highlights the involvement of GB tick species in animal or human disease transmission.},
}
@article {pmid39380764,
year = {2023},
author = {Kartiganer, Z and Rojas, G and Riccio, M and Tyree, A and Noronha, K and Wetzel, M and Barnett, J and McGann, J and Garbarino, J and Massucci, D and Chafi, NS and Decker, S and McDaniels, A and Sabina, J and Levchenko, D and Perez, J and Ng, C and Wang, K},
title = {Improved cell-type identification and comprehensive mapping of regulatory features with spatial epigenomics 96-channel microfluidic platform.},
journal = {GEN biotechnology},
volume = {2},
number = {6},
pages = {503-514},
pmid = {39380764},
issn = {2768-1556},
support = {R44 CA287890/CA/NCI NIH HHS/United States ; },
abstract = {Gene expression is subject to epigenetic regulation and is dependent upon cellular context. Spatial omics tools can provide insight into cellular context; however, development has centered on spatial transcriptomics and proteomics. Deterministic barcoding in tissue for spatial omics sequencing (DBiT-seq) was the first spatial epigenomics platform at the cellular level. Here we present a comparison of spatial epigenomic profiling on both 50-channel and 96-channel platforms. The new 96-channel microfluidics chip design greatly improved precision in cell typing and identification of regulatory elements by spatial-ATAC-seq. Spatial mapping reveals complexity of glial cell and neuronal localization within brain structures as well as cis-regulatory elements controlling cellular function. This technology streamlines spatial analysis of the epigenome and contributes a new layer of spatial omics to uncover the context dependent regulatory mechanisms underpinning development, disease, and normal cellular function.},
}
@article {pmid39380274,
year = {2024},
author = {Abdulrahman Ismael, K and Abdul-Qadir Ali, L},
title = {Morphological and molecular identification of freshwater eutardigrade Dactylobiotus parthenogeneticus (Bertolani, 1982) in the Greater Zab River of Kurdistan Region - Iraq.},
journal = {Cellular and molecular biology (Noisy-le-Grand, France)},
volume = {70},
number = {9},
pages = {86-90},
doi = {10.14715/cmb/2024.70.9.12},
pmid = {39380274},
issn = {1165-158X},
mesh = {Animals ; Iraq ; *Tardigrada/genetics/classification/anatomy &amp; histology ; *Rivers ; *Electron Transport Complex IV/genetics ; *Phylogeny ; DNA Barcoding, Taxonomic/methods ; Fresh Water ; },
abstract = {Dactylobiotus parthenogeneticus is one of the widespread species of tardigrade all over the world. Tardigrades of this species were collected from the Greater Zab River in Erbil City-Iraq by filtering water of the river through a plankton net with a mesh of 45 µm pore. The samples were mounted on a slide with a cover slip and examined under the microscope to determine morphological characteristics and measurements. Based on these characters the species identified to be D. parthenogeneticus. To support this diagnosis, DNA barcoding techniques were applied to do molecular analysis and sequencing on the cytochrome oxidase subunit I (COI) gene. The sequence was subjected to the GenBank database of NCBI and recorded with the accession number PP140905. The result of the sequencing and molecular analysis of the cytochrome oxidase subunit I (COI) gene confirmed to be the same species diagnosed by relying upon morphological characters. This study represents one of the pioneer researches and documents on tardigrades and found D. parthenogeneticus for the first time in the Greater Zab River in Kurdistan, North of Iraq. Tardigrades play a magnificent role in different trophic levels and can be utilized as an indicator of ecosystem health.},
}
@article {pmid39380264,
year = {2024},
author = {Khawaja Ghulam, R and Husain, M and Sharaf, MR and Muhammad Tufail, and Sutanto, KD and Alwaneen, WS and Aldawood, AS},
title = {Mitochondrial DNA sequence-based identification of two subterranean termite species, from Riyadh Province, Kingdom of Saudi Arabia.},
journal = {Cellular and molecular biology (Noisy-le-Grand, France)},
volume = {70},
number = {9},
pages = {189-197},
doi = {10.14715/cmb/2024.70.9.26},
pmid = {39380264},
issn = {1165-158X},
mesh = {Animals ; *Isoptera/genetics/classification ; *Phylogeny ; Saudi Arabia ; *DNA, Mitochondrial/genetics ; *Electron Transport Complex IV/genetics ; *DNA Barcoding, Taxonomic/methods ; Sequence Analysis, DNA ; Base Sequence ; },
abstract = {Termites are economically important wood-destroying and agricultural pests. The termite fauna almost consists of 2900 described species in 286 genera worldwide. In the present study, hundreds of termite samples from 42 different locations in the Riyadh province were collected. These samples were previously used for morphometric identification and reported two subterranean termite species, Coptotermes heimi and Psammotermes hypostoma, in the family Rhinotermitidae. In the present study, these samples were analysed using DNA barcoding with the mitochondrial cytochrome c oxidase subunit 1 gene to confirm the conventional taxonomical identification on a molecular basis. The obtained COI gene sequences of all 42 termite specimens were submitted to GenBank (accession numbers: ON529959-ON529969, OP825131-OP825132, and OP890882-OP890910). Eleven of the 42 samples were thus identified as C. heimi and the remaining 31 samples as P. hypostoma, which were phylogenetically analysed. All the 11 C. heimi sequences were grouped in a single clade, indicating close relatedness. While 31 sequences of P. hypostoma constituted two clades in the phylogenetic tree. Pairwise nucleotide sequence identity and divergence analysis showed that C. heimi sequences showed high nucleotide identities of 87.6-99.5% and less divergence ranging from 0.5% to 13.6%. Similarly, sequences of P. hypostoma also showed high nucleotide identity of 78.6-100% and low divergence among them ranging from 0-10.7%. A further application, significance, and shortcomings of COI-based DNA barcoding have been discussed. DNA barcoding using the COI gene is a reliable tool to distinguish C. heimi and P. hypostoma genotypes.},
}
@article {pmid39380090,
year = {2024},
author = {Amstler, S and Streiter, G and Pfurtscheller, C and Forer, L and Di Maio, S and Weissensteiner, H and Paulweber, B and Schönherr, S and Kronenberg, F and Coassin, S},
title = {Nanopore sequencing with unique molecular identifiers enables accurate mutation analysis and haplotyping in the complex lipoprotein(a) KIV-2 VNTR.},
journal = {Genome medicine},
volume = {16},
number = {1},
pages = {117},
pmid = {39380090},
issn = {1756-994X},
mesh = {Humans ; *Haplotypes ; *Minisatellite Repeats ; *Lipoprotein(a)/genetics ; *Nanopore Sequencing/methods ; DNA Mutational Analysis/methods ; Polymorphism, Single Nucleotide ; },
abstract = {BACKGROUND: Repetitive genome regions, such as variable number of tandem repeats (VNTR) or short tandem repeats (STR), are major constituents of the uncharted dark genome and evade conventional sequencing approaches. The protein-coding LPA kringle IV type-2 (KIV-2) VNTR (5.6 kb per unit, 1-40 units per allele) is a medically highly relevant example with a particularly intricate structure, multiple haplotypes, intragenic homologies, and an intra-VNTR STR. It is the primary regulator of plasma lipoprotein(a) [Lp(a)] concentrations, an important cardiovascular risk factor. Lp(a) concentrations vary widely between individuals and ancestries. Multiple variants and functional haplotypes in the LPA gene and especially in the KIV-2 VNTR strongly contribute to this variance.<br><br>METHODS: We evaluated the performance of amplicon-based nanopore sequencing with unique molecular identifiers (UMI-ONT-Seq) for SNP detection, haplotype mapping, VNTR unit consensus sequence generation, and copy number estimation via coverage-corrected haplotypes quantification in the KIV-2 VNTR. We used 15 human samples and low-level mixtures (0.5 to 5%) of KIV-2 plasmids as a validation set. We then applied UMI-ONT-Seq to extract KIV-2 VNTR haplotypes in 48 multi-ancestry 1000 Genome samples and analyzed at scale a poorly characterized STR within the KIV-2 VNTR.<br><br>RESULTS: UMI-ONT-Seq detected KIV-2 SNPs down to 1% variant level with high sensitivity, specificity, and precision (0.977&#x2009;&#xb1;&#x2009;0.018; 1.000&#x2009;&#xb1;&#x2009;0.0005; 0.993&#x2009;&#xb1;&#x2009;0.02) and accurately retrieved the full-length haplotype of each VNTR unit. Human variant levels were highly correlated with next-generation sequencing (R[2]&#x2009;=&#x2009;0.983) without bias across the whole variant level range. Six reads per UMI produced sequences of each KIV-2 unit with Q40 quality. The KIV-2 repeat number determined by coverage-corrected unique haplotype counting was in close agreement with droplet digital PCR (ddPCR), with 70% of the samples falling even within the narrow confidence interval of ddPCR. We then analyzed 62,679 intra-KIV-2 STR sequences and explored KIV-2 SNP haplotype patterns across five ancestries.<br><br>CONCLUSIONS: UMI-ONT-Seq accurately retrieves the SNP haplotype and precisely quantifies the VNTR copy number of each repeat unit of the complex KIV-2 VNTR region across multiple ancestries. This study utilizes the KIV-2 VNTR, presenting a novel and potent tool for comprehensive characterization of medically relevant complex genome regions at scale.},
}
@article {pmid39380014,
year = {2024},
author = {Liu, Z and Pei, Y and Chen, T and Yang, Z and Jiang, W and Feng, X and Li, X},
title = {Molecular quantification of fritillariae cirrhosae bulbus and its adulterants.},
journal = {Chinese medicine},
volume = {19},
number = {1},
pages = {138},
pmid = {39380014},
issn = {1749-8546},
support = {7244492//Beijing Natural Science Foundation/ ; 2019YFC1710600//National Key Research and Development Program of China/ ; CI2021A04106//The Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; ZZ15-YQ-033//Fundamental Research Funds for the Central public welfare research institutes of China/ ; ZXKT23004//Fundamental Research Funds for the Central public welfare research institutes of China/ ; CI2024C003YN//The Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; },
abstract = {BACKGROUND: Fritillariae Cirrhosae Bulbus (FCB) is frequently adulterated with its closely related species due to personal or non-man made factors, leading to alterations in the composition of its constituents and compromising the efficacy of its products.<br><br>METHODS: The specific single nucleotide polymorphisms (SNPs) were screened by comparing candidate barcodes of Fritillaria and verified by amplification and sequencing. Herb molecular quantification (Herb-Q) was established by detecting specific SNPs, and the methodological validation was performed. Quantitative standard curves were established for FCB mixed with each adulterated species, and the quantitative validity of this method was verified based on external standard substance. In addition, eight commercial Shedan Chuanbei capsules (SDCBs) randomly selected were detected.<br><br>RESULTS: FCB and its five adulterants can be distinguished based on the ITS 341 site. The methodological investigation of Herb-Q shows optimal accuracy, and repeatability, which exhibited good linearity with an R[2] of 0.9997 (>&#x2009;0.99). An average bias in quantitative validity was 5.973% between the measured and actual values. Four of eight commercial SDCBs were adulterated with F. ussuriensis or F. thunbergia with adulteration levels ranging from 9 to 15% of the total weight.<br><br>CONCLUSION: This study confirmed that Herb-Q can quantitatively detect both the mixed herbs and Chinese patent medicines (CPMs) containing FCB with high reproducibility and accuracy. This method provides technical support for market regulation and helps safeguard patient rights.},
}
@article {pmid39375852,
year = {2025},
author = {Morales-Pulido, JM and Galindo-Sánchez, CE and Jiménez-Rosenberg, SPA and Batta-Lona, PG and Herzka, SZ and Arteaga, MC},
title = {A molecular approach to identify parrotfish (Sparisoma) species during early ontogeny.},
journal = {Journal of fish biology},
volume = {106},
number = {2},
pages = {266-275},
doi = {10.1111/jfb.15921},
pmid = {39375852},
issn = {1095-8649},
support = {Fund Project 201441//Consejo Nacional de Ciencia y Tecnolog&#xed;a in Mexico (National Council for Science and Technology - Mexican Ministry of Energy - Hydrocarbon)/ ; 682136//Internal project: Environmental variations effects on mollusks: a genomic and transcriptomic approximation/ ; },
mesh = {Animals ; *Perciformes/genetics/classification/growth &amp; development/anatomy &amp; histology ; *Phylogeny ; *Larva/growth &amp; development/anatomy &amp; histology/genetics/classification ; *Electron Transport Complex IV/genetics ; *RNA, Ribosomal, 16S/genetics ; DNA, Mitochondrial/genetics ; Gulf of Mexico ; Sequence Analysis, DNA ; },
abstract = {Sparisoma species (parrotfish) comprise an important functional group contributing to coral-reef resilience. The morphological diagnostic characteristics for species identification are clearly described for adult forms but not for the early stages. Consequently, many taxonomical listings of Sparisoma larvae are restricted to the genus level. The aims of this study are to determine whether the morphological and molecular identification techniques are useful to assign the species taxonomic level to Sparisoma larvae occurring in the Gulf of Mexico and whether there is a set of diagnostic features that could be used to discriminate between species in larvae of different developmental stages. Morphological assignment of Sparisoma was performed based on morphological and meristic features for 30 larvae collected in the Gulf of Mexico from late August to mid-September 2015. To corroborate and complement the morphological assignments, molecular identification was carried out using DNA sequences from regions of two mitochondrial genes, mitochondrial cytochrome oxidase I (mtDNA COI) and mitochondrial 16S rRNA (mtDNA 16S rRNA). COI and 16S gene trees for Sparisoma and related fish taxa were constructed using sequences available in the NCBI (National Center for Biotechnology Information) GenBank and BOLD (Barcode of Life Data) databases. Two morphotypes were identified based on morphology, but no diagnostic characteristics for species discrimination were found. Molecular identification, in contrast, successfully discriminated four early development stages of Sparisoma atomarium, three stages of Sparisoma radians, and two stages of Sparisoma chrysopterum and Sparisoma aurofrenatum, therefore demonstrating the successful and necessary application of molecular taxonomic approaches for species-level identifications of Sparisoma larvae.},
}
@article {pmid39375541,
year = {2024},
author = {Biggs, BW and Price, MN and Lai, D and Escobedo, J and Fortanel, Y and Huang, YY and Kim, K and Trotter, VV and Kuehl, JV and Lui, LM and Chakraborty, R and Deutschbauer, AM and Arkin, AP},
title = {High-throughput protein characterization by complementation using DNA barcoded fragment libraries.},
journal = {Molecular systems biology},
volume = {20},
number = {11},
pages = {1207-1229},
pmid = {39375541},
issn = {1744-4292},
support = {S10 OD018174/OD/NIH HHS/United States ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; NIH S10 OD018174//HHS | National Institutes of Health (NIH)/ ; },
mesh = {*Escherichia coli/genetics/metabolism ; *Gene Library ; *DNA Barcoding, Taxonomic ; Bacillus subtilis/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Genetic Complementation Test ; High-Throughput Nucleotide Sequencing ; Escherichia coli Proteins/genetics/metabolism ; },
abstract = {Our ability to predict, control, or design biological function is fundamentally limited by poorly annotated gene function. This can be particularly challenging in non-model systems. Accordingly, there is motivation for new high-throughput methods for accurate functional annotation. Here, we used complementation of auxotrophs and DNA barcode sequencing (Coaux-Seq) to enable high-throughput characterization of protein function. Fragment libraries from eleven genetically diverse bacteria were tested in twenty different auxotrophic strains of Escherichia coli to identify genes that complement missing biochemical activity. We recovered 41% of expected hits, with effectiveness ranging per source genome, and observed success even with distant E. coli relatives like Bacillus subtilis and Bacteroides thetaiotaomicron. Coaux-Seq provided the first experimental validation for 53 proteins, of which 11 are less than 40% identical to an experimentally characterized protein. Among the unexpected function identified was a sulfate uptake transporter, an O-succinylhomoserine sulfhydrylase for methionine synthesis, and an aminotransferase. We also identified instances of cross-feeding wherein protein overexpression and nearby non-auxotrophic strains enabled growth. Altogether, Coaux-Seq's utility is demonstrated, with future applications in ecology, health, and engineering.},
}
@article {pmid39375449,
year = {2024},
author = {Kudo, T and Meireles, AM and Moncada, R and Chen, Y and Wu, P and Gould, J and Hu, X and Kornfeld, O and Jesudason, R and Foo, C and Höckendorf, B and Corrada Bravo, H and Town, JP and Wei, R and Rios, A and Chandrasekar, V and Heinlein, M and Chuong, AS and Cai, S and Lu, CS and Coelho, P and Mis, M and Celen, C and Kljavin, N and Jiang, J and Richmond, D and Thakore, P and Benito-Gutiérrez, E and Geiger-Schuller, K and Hleap, JS and Kayagaki, N and de Sousa E Melo, F and McGinnis, L and Li, B and Singh, A and Garraway, L and Rozenblatt-Rosen, O and Regev, A and Lubeck, E},
title = {Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {39375449},
issn = {1546-1696},
abstract = {Optical pooled screening (OPS) is a scalable method for linking image-based phenotypes with cellular perturbations. However, it has thus far been restricted to relatively low-plex phenotypic readouts in cancer cell lines in culture due to limitations associated with in situ sequencing of perturbation barcodes. Here, we develop PerturbView, an OPS technology that leverages in vitro transcription to amplify barcodes before in situ sequencing, enabling screens with highly multiplexed phenotypic readouts across diverse systems, including primary cells and tissues. We demonstrate PerturbView in induced pluripotent stem cell-derived neurons, primary immune cells and tumor tissue sections from animal models. In a screen of immune signaling pathways in primary bone marrow-derived macrophages, PerturbView uncovered both known and novel regulators of NF-κB signaling. Furthermore, we combine PerturbView with spatial transcriptomics in tissue sections from a mouse xenograft model, paving the way to in situ screens with rich optical and transcriptomic phenotypes. PerturbView broadens the scope of OPS to a wide range of models and applications.},
}
@article {pmid39375448,
year = {2024},
author = {Gu, J and Iyer, A and Wesley, B and Taglialatela, A and Leuzzi, G and Hangai, S and Decker, A and Gu, R and Klickstein, N and Shuai, Y and Jankovic, K and Parker-Burns, L and Jin, Y and Zhang, JY and Hong, J and Niu, X and Costa, JA and Pezet, MG and Chou, J and Chen, C' and Paiva, M and Snoeck, HW and Landau, DA and Azizi, E and Chan, EM and Ciccia, A and Gaublomme, JT},
title = {Mapping multimodal phenotypes to perturbations in cells and tissue with CRISPRmap.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {39375448},
issn = {1546-1696},
support = {1DP2CA281605//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01CA197774-04//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01CA227450-04//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 1R21HG012639-01A1//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; 1R01HG012875-01//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; Lloyd J. Old STAR award//Cancer Research Institute (CRI)/ ; },
abstract = {Unlike sequencing-based methods, which require cell lysis, optical pooled genetic screens enable investigation of spatial phenotypes, including cell morphology, protein subcellular localization, cell-cell interactions and tissue organization, in response to targeted CRISPR perturbations. Here we report a multimodal optical pooled CRISPR screening method, which we call CRISPRmap. CRISPRmap combines in situ CRISPR guide-identifying barcode readout with multiplexed immunofluorescence and RNA detection. Barcodes are detected and read out through combinatorial hybridization of DNA oligos, enhancing barcode detection efficiency. CRISPRmap enables in situ barcode readout in cell types and contexts that were elusive to conventional optical pooled screening, including cultured primary cells, embryonic stem cells, induced pluripotent stem cells, derived neurons and in vivo cells in a tissue context. We conducted a screen in a breast cancer cell line of the effects of DNA damage repair gene variants on cellular responses to commonly used cancer therapies, and we show that optical phenotyping pinpoints likely pathogenic patient-derived mutations that were previously classified as variants of unknown clinical significance.},
}
@article {pmid39372282,
year = {2024},
author = {Huber, BA and Meng, G},
title = {Old World Micropholcus spiders, with first records of acrocerid parasitoids in Pholcidae (Araneae).},
journal = {ZooKeys},
volume = {1213},
number = {},
pages = {95-182},
pmid = {39372282},
issn = {1313-2989},
abstract = {Micropholcus Deeleman-Reinhold &amp; Prinsen, 1987 is one of only two Pholcidae genera known to occur both in the Old and New Worlds. However, there are major morphological and ecological differences among geographically separate groups of species, and it was mainly molecular data that have resulted in our current view of uniting all these species into a single genus. In the Old World, only four species have previously been described. Here, current knowledge about Old World Micropholcus is reviewed, redescribing three of the four previously known species, and describing twelve new species, originating from Saudi Arabia (M.dhahran Huber, sp. nov., M.harajah Huber, sp. nov., M.alfara Huber, sp. nov., M.abha Huber, sp. nov., M.tanomah Huber, sp. nov., M.bashayer Huber, sp. nov., M.maysaan Huber, sp. nov.), Oman (M.darbat Huber, sp. nov., M.shaat Huber, sp. nov.), Morocco (M.ghar Huber, sp. nov., M.khenifra Huber, Lecigne &amp; Lips, sp. nov.), and the Philippines (M.bukidnon Huber, sp. nov.). We provide an exploratory species delimitation analysis based on CO1 barcodes, extensive SEM data, and first records of Acroceridae (Diptera) larvae in Pholcidae, extracted from book lungs.},
}
@article {pmid39371081,
year = {2024},
author = {Ward, DF},
title = {Building a DNA barcode reference collection of Hymenoptera in New Zealand.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e131701},
pmid = {39371081},
issn = {1314-2828},
abstract = {Molecular tools used for the identification of species are heavily reliant on reference DNA sequences and taxonomic annotation. Despite this, there are large gaps in the availability of DNA sequences for many taxonomic groups and for different parts of the globe. Here, a DNA barcode library for the Hymenoptera of New Zealand is presented, based on the COI region for 3,145 sequences assigned to 837 BINs and which represent 231 genera and 236 species. This study provides a DNA barcode for approximately 25% of species and 42% of genera of Hymenoptera in New Zealand. However, when combined with sequences previously deposited in BOLD (a further 170 genera), DNA barcodes are available for 73% of New Zealand Hymenopteran genera. To further increase coverage, future efforts need to focus predominantly on taxa from seven families (Encyrtidae, Pteromalidae s.l., Mymaridae, Eulophidae, Diapriidae, Braconidae and Platygastridae). This database facilitates DNA-based identification of taxa for use in both taxonomic revisions and biodiversity monitoring.},
}
@article {pmid39370741,
year = {2025},
author = {Mayo Ilodiri, W and Huyghe, CET and da Costa, LM and Mambo Baba, T and Danadu Mizani, C and Vreven, EJWMN},
title = {Hidden species diversity in the Enteromius Cope, 1867 (Teleostei: Cyprinidae) from the Aruwimi basin (Middle Congo) in the Okapi Wildlife Reserve (Democratic Republic of the Congo).},
journal = {Journal of fish biology},
volume = {106},
number = {2},
pages = {230-255},
doi = {10.1111/jfb.15883},
pmid = {39370741},
issn = {1095-8649},
support = {//DEA scholarship/ ; //Mbisa Congo II/ ; //BICS project/ ; //Royal Museum for Central Africa (RMCA)/ ; //Directorate-General for Development Cooperation and Humanitarian Aid (DGD)/ ; },
mesh = {Animals ; *Rivers ; *Cyprinidae/anatomy &amp; histology/physiology/classification ; Democratic Republic of the Congo ; Phylogeny ; Biodiversity ; DNA, Mitochondrial/genetics ; Male ; Female ; },
abstract = {Two new African minnow species, Enteromius cerinus sp. nov. and Enteromius ruforum sp. nov., are described for science from the Angadiko River, a left-bank sub-affluent of first order of the Nepoko River, draining the north-eastern part of the Okapi Wildlife Reserve (OWR). Both new species belong to the group of Enteromius for which the last unbranched dorsal-fin ray is flexible and underrated. Within this morphological group, both are most similar to Enteromius kamolondoensis, especially in life colour pattern characteristics. However, Enteromius cerinus sp. nov. differs from E. kamolondoensis by its low number of circumpeduncular scales, 10-11 (vs. 12), low maximum body depth, 22.8%-25.7% standard length (Ls) (vs. 26.1%-30.0%), and long anterior and posterior barbel lengths, 32.6%-35.3% head length (LH) (vs. 23.6%-27.2%) and 41.6%-43.9% LH (vs. 30.3%-34.9%), respectively. Further, E. ruforum sp. nov. is also easily distinguished from E. kamolondoensis by its high maximum body depth, 30.6%-33.3% Ls (vs. 26.1%-30.0%), and small, isometric, eye diameter, 26.2%-28.0% LH (vs. 29.1%-31.9%). A barcoding study (mtDNA, cytochrome oxidase subunit I [COI]) revealed that specimens of both new species form lineages well differentiated from those of other available species. As such, (i) E. cerinus sp. nov. diverges from E. kamolondoensis by a K2P genetic distance (GD) of 10.3% and (ii) E. ruforum sp. nov. by a K2P GD of 11.2%. To the present day, the fish fauna of the left-bank sub-affluents of the Nepoko River, in general, remains poorly known or undocumented. Unfortunately, at the same time, multiple anthropogenic impacts are affecting this fauna, such as (i) the destruction of habitats along the river banks for agriculture and fishing and (ii) the use of illegal fishing practices, such as fishing with plant-based ichthyotoxins during ecopage, which is combined with dam building. As a result of the demographic growth, this ecopage results in overfishing and thus is threatening both new species in particular, but all other co-occurring fish species as well. Both new species, E. cerinus sp. nov. and E. ruforum sp. nov., should thus be considered Vulnerable (VU) according to IUCN criterion D2. It is therefore hoped that their discovery highlights the urgent need for a better protection and further in situ exploration of the reserve's freshwater (fish) biodiversity, in general, and that of those small sub-affluents, in particular.},
}
@article {pmid39369928,
year = {2024},
author = {Chomphuphuang, N and Leamyongyai, C and Songsangchote, C and Piraonapicha, K and Pojprasat, N and Piyatrakulchai, P},
title = {Phylogenetics and species delimitation of the recluse spider, Loxosceles rufescens (Araneae: Sicariidae) populations invading Bangkok, Thailand.},
journal = {Acta tropica},
volume = {260},
number = {},
pages = {107424},
doi = {10.1016/j.actatropica.2024.107424},
pmid = {39369928},
issn = {1873-6254},
mesh = {Animals ; Thailand ; *Phylogeny ; *Spiders/classification/genetics ; *Electron Transport Complex IV/genetics ; *Sequence Analysis, DNA ; DNA, Mitochondrial/genetics ; Humans ; },
abstract = {The Mediterranean recluse spider, Loxosceles rufescens, has been discovered for the first time inhabiting human dwellings in Bangkok, Thailand. Expeditions across 39 localities revealed five establishments with L. rufescens populations. The highest density was recorded in a storage house on Yaowarat Road, located in the heart of Bangkok's Chinatown, where 315 individuals were found, including adults, juveniles, and spiderlings. This medically significant spider's presence in such a densely populated urban area raises concerns about potential envenomation risks. Thirteen specimens of L. rufescens were extracted for DNA and sequenced for molecular phylogenetic analyses. COI and ITS2 markers were used to investigate relationships within L. rufescens and across available Loxosceles species sequences. Results indicate COI is superior for resolving species-level genetic clusters compared to ITS2. Surprisingly, L. rufescens individuals from the same house were found in significantly distant COI lineages, suggesting mtDNA may not be suitable for studying intra-specific phylogeography in this case. Species delimitation methods ABGD and ASAP demonstrated promising results for both COI and ITS2, while bPTP and GMYC tended to overestimate species numbers. ITS2 exhibited high sequence similarity in L. rufescens, suggesting potential utility as a barcoding marker for identification of this globally distributed species. Genetic distance analyses revealed a potential barcoding gap (K2P) of 8-9 % for COI and <2 % for ITS2 in Loxosceles. This study contributes valuable sequence data for the medically important genus Loxosceles and highlights the need for integrative approaches in understanding its evolution and spread. The findings have important implications for pest management strategies and public health in urban environments.},
}
@article {pmid39369756,
year = {2025},
author = {Li, H and Shangqing, Z and Yae, Z and Fan, Y and Xinyue, Z and Shirui, L and Tianyi, Z and Dongling, N},
title = {Classification, identification, and DNA barcoding study for common cockroach species (Dictyoptera: Blattaria) from China.},
journal = {Gene},
volume = {933},
number = {},
pages = {148981},
doi = {10.1016/j.gene.2024.148981},
pmid = {39369756},
issn = {1879-0038},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; China ; *Phylogeny ; *Cockroaches/genetics/classification ; DNA, Mitochondrial/genetics ; Periplaneta/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {Cockroaches are well-known pests and quarantined organisms worldwide. Due to morphological diversity and a lack of molecular data, their classification and identification are facing challenges. This study performed classification, identification, and DNA barcoding for cockroaches collected from China. Seventy-six samples were morphologically identified as seven species of two superfamilies that included Blattella germanica, Eublaberus posticus and Blaptica dubia belonging to the superfamily Blaberoidea, and Periplaneta americana, Periplaneta lateralis, Periplaneta fuliginosa and Periplaneta australasiae belonging to the superfamily Blattoidea. Based on sequence alignments of nine ribosomal and mitochondrial genes across the order Blattaria retrieved from GenBank, rDNA ITS2-517 bp and mtDNA 16S-327 bp were screened as candidates for molecular identification. Universal primers were designed for PCR amplification, cloning, and sequencing of the 37 representative samples. Sequence alignments and phylogeny analysis showed that both ITS2 and 16S confirmed samples 1-9, 20-24, and 25-29 as B. germanica, P. americana, and P. lateralis, respectively; only 16S (not ITS2) confirmed samples 10-14, 15-19, 30-34, and 35-37 as E. posticus, Blap. dubia, P. fuliginosa, and P. australasiae, respectively, indicating that 16S was a better target than ITS2 for molecular identification of cockroaches. Conservative motif and divergence analysis further revealed that ITS2 sequences vary significantly among different taxa, whereas 16S sequences are relatively conserved. There is an obvious barcoding gap between maximum intraspecific divergence and minimum interspecific divergence (2.57 % vs. 5.62 %) for ITS2, but not for 16S (6.15 % vs. 2.63 %). Therefore, it was confirmed that ITS2 is an ideal DNA barcode for molecular identification of cockroaches at lower category.},
}
@article {pmid39365069,
year = {2024},
author = {Biggel, M and Cernela, N and Horlbog, JA and Stephan, R},
title = {Oxford Nanopore's 2024 sequencing technology for Listeria monocytogenes outbreak detection and source attribution: progress and clone-specific challenges.},
journal = {Journal of clinical microbiology},
volume = {62},
number = {11},
pages = {e0108324},
pmid = {39365069},
issn = {1098-660X},
mesh = {*Listeria monocytogenes/genetics/classification/isolation &amp; purification ; *Listeriosis/microbiology/epidemiology/diagnosis ; *Disease Outbreaks ; Humans ; *Whole Genome Sequencing ; Genome, Bacterial/genetics ; Nanopore Sequencing/methods ; Nanopores ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Whole genome sequencing is an essential cornerstone of pathogen surveillance and outbreak detection. Established sequencing technologies are currently being challenged by Oxford Nanopore Technologies (ONT), which offers an accessible and cost-effective alternative enabling gap-free assemblies of chromosomes and plasmids. Limited accuracy has hindered its use for investigating pathogen transmission, but recent technology updates have brought significant improvements. To evaluate its readiness for outbreak detection, we selected 78 Listeria monocytogenes isolates from diverse lineages or known epidemiological clusters for sequencing with ONT's V14 Rapid Barcoding Kit and R10.4.1 flow cells. The most accurate of several tested workflows generated assemblies with a median of one error (SNP or indel) per assembly. For 66 isolates, the cgMLST profiles from ONT-only assemblies were identical to those generated from Illumina data. Eight assemblies were of lower quality, with more than 20 erroneous sites each, primarily caused by methylations at the GAAGAC motif (5'-GAAG6mAC-3'/5'-GT4mCTTC-3'). This led to inaccurate clustering, failing to group isolates from a persistence-associated clone that carried the responsible restriction-modification system. Out of 50 methylation motifs detected among the 78 isolates, only the GAAGAC motif was linked to substantially increased error rates. Our study shows that most L. monocytogenes genomes assembled from ONT-only data are suitable for high-resolution genotyping, but further improvements of chemistries or basecallers are required for reliable routine use in outbreak and food safety investigations.},
}
@article {pmid39364681,
year = {2024},
author = {Stancheva, R and Cantonati, M and Manoylov, K and Furey, PC and Cahoon, AB and Jones, RC and Gillevet, P and Amsler, CD and Wehr, JD and Salerno, JL and Krueger-Hadfield, SA},
title = {The importance of integrating phycological research, teaching, outreach, and engagement in a changing world.},
journal = {Journal of phycology},
volume = {60},
number = {6},
pages = {1335-1348},
pmid = {39364681},
issn = {1529-8817},
support = {DEB-2141971//National Science Foundation/ ; DEB-2436117//National Science Foundation/ ; },
mesh = {*Research ; Teaching ; },
abstract = {The ecological, evolutionary, economic, and cultural importance of algae necessitates a continued integration of phycological research, education, outreach, and engagement. Here, we comment on several topics discussed during a networking workshop-Algae and the Environment-that brought together phycological researchers from a variety of institutions and career stages. We share some of our perspectives on the state of phycology by examining gaps in teaching and research. We identify action areas where we urge the phycological community to prepare itself to embrace the rapidly changing world. We emphasize the need for more trained taxonomists as well as integration with molecular techniques, which may be expensive and complicated but are important. An essential benefit of these integrative studies is the creation of high-quality algal reference barcoding libraries augmented with morphological, physiological, and ecological data that are important for studies of systematics and crucial for the accuracy of the metabarcoding bioassessment. We highlight different teaching approaches for engaging undergraduate students in algal studies and the importance of algal field courses, forays, and professional phycological societies in supporting the algal training of students, professionals, and citizen scientists.},
}
@article {pmid39364584,
year = {2025},
author = {Buchner, D and Sinclair, JS and Ayasse, M and Beermann, AJ and Buse, J and Dziock, F and Enss, J and Frenzel, M and Hörren, T and Li, Y and Monaghan, MT and Morkel, C and Müller, J and Pauls, SU and Richter, R and Scharnweber, T and Sorg, M and Stoll, S and Twietmeyer, S and Weisser, WW and Wiggering, B and Wilmking, M and Zotz, G and Gessner, MO and Haase, P and Leese, F},
title = {Upscaling biodiversity monitoring: Metabarcoding estimates 31,846 insect species from Malaise traps across Germany.},
journal = {Molecular ecology resources},
volume = {25},
number = {1},
pages = {e14023},
pmid = {39364584},
issn = {1755-0998},
support = {//Hessisches Landesamt f&#xfc;r Naturschutz, Umwelt und Geologie/ ; 871128//EU Horizon 2020 project eLTER PLUS/ ; //Landes-Offensive zur Entwicklung Wissenschaftlich-&#xf6;konomischer Exzellenz of the German federal State of Hesse/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Germany ; *Biodiversity ; *Insecta/classification/genetics/physiology ; },
abstract = {Mitigating ongoing losses of insects and their key functions (e.g. pollination) requires tracking large-scale and long-term community changes. However, doing so has been hindered by the high diversity of insect species that requires prohibitively high investments of time, funding and taxonomic expertise when addressed with conventional tools. Here, we show that these concerns can be addressed through a comprehensive, scalable and cost-efficient DNA metabarcoding workflow. We use 1815 samples from 75 Malaise traps across Germany from 2019 and 2020 to demonstrate how metabarcoding can be incorporated into large-scale insect monitoring networks for less than 50 € per sample, including supplies, labour and maintenance. We validated the detected species using two publicly available databases (GBOL and GBIF) and the judgement of taxonomic experts. With an average of 1.4 M sequence reads per sample we uncovered 10,803 validated insect species, of which 83.9% were represented by a single Operational Taxonomic Unit (OTU). We estimated another 21,043 plausible species, which we argue either lack a reference barcode or are undescribed. The total of 31,846 species is similar to the number of insect species known for Germany (~35,500). Because Malaise traps capture only a subset of insects, our approach identified many species likely unknown from Germany or new to science. Our reproducible workflow (~80% OTU-similarity among years) provides a blueprint for large-scale biodiversity monitoring of insects and other biodiversity components in near real time.},
}
@article {pmid39364448,
year = {2024},
author = {Zhou, R and Huang, L and Ma, YT},
title = {Smooth post-labial chaetae in Homidia (Collembola, Entomobryidae) and the description of four new species from China with the aid of DNA barcoding.},
journal = {ZooKeys},
volume = {1213},
number = {},
pages = {41-73},
pmid = {39364448},
issn = {1313-2989},
abstract = {Four new species of Homidia are described from the Guangxi Zhuang Autonomous Region, China. Homidialongiantenna sp. nov. is characterised by its long antenna and slightly expanded post-labial chaetae; H.guangxiensis sp. nov. by the presence of smooth chaetae on the post-labium and posterior face of the ventral tube; H.huapingensis sp. nov. by the presence of smooth post-labial chaetae and pointed tenent hairs; and H.oligoseta sp. nov. by the pointed tenent hairs and fewer macrochaetae on Abdomen IV. Additions to the original description of Homidiaacutus Jing &amp; Ma, 2022 are also provided.},
}
@article {pmid39364039,
year = {2024},
author = {Zheng, LL and Yu, D and Sun, N and Wang, C and Chen, WJ and Ding, ZF and He, SP and Yang, LD},
title = {DNA barcoding and cryptic diversity in fishes from the Ili River Valley in China, Xinjiang.},
journal = {Ecology and evolution},
volume = {14},
number = {10},
pages = {e70352},
pmid = {39364039},
issn = {2045-7758},
abstract = {The Ili River Valley, located in the northwest of China, serves as a vital repository for fish genetic resources. Its extensive water network and diverse climate have given rise to a unique fish composition and endemic species. In this study, we collected the cytochrome c oxidase subunit I (COI) sequences from 660 fish specimens in the Ili River Valley. The effectiveness of DNA barcoding in identifying fish species in the area was assessed by examining genetic distances, constructing phylogenetic trees, and performing ABGD (Automatic Barcode Gap Discovery) analyses, among other methods. In total, 20 species were identified, including one unidentified species (Silurus sp.). Except for Silurus asotus and Hypophthalmichthys molitrix (only one sample), the maximum intraspecific genetic distance among the remaining species was smaller than the minimum interspecific distance, which proves that the species exhibit obvious barcode gaps. In the Neighbor-Joining trees, 20 species formed separate monophyletic branches. According to ABGD analysis, 660 sequences were categorized into 19 Operational Taxonomic Units, with Silurus sp. and S. asotus grouped into a single OTU. The Silurus in this study exhibits shared haplotypes and significant genetic divergence, suggesting the potential presence of cryptic species. Furthermore, the nucleotide diversity across all species fell below the threshold level, indicating that the local fish population is gradually declining. In conclusion, this study has demonstrated the effectiveness of DNA barcoding in identifying fish species in the Ili River Valley, providing valuable data to support the conservation of local fish resources.},
}
@article {pmid39363107,
year = {2025},
author = {Kumar, B and Navarro, C and Yung, PYK and Lyu, J and Salazar Mantero, A and Katsori, AM and Schwämmle, H and Martin, M and Elsässer, SJ},
title = {Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors.},
journal = {Nature protocols},
volume = {20},
number = {3},
pages = {779-809},
pmid = {39363107},
issn = {1750-2799},
support = {2020-04313//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; },
mesh = {*Chromatin Immunoprecipitation Sequencing/methods ; *Histones/metabolism ; *Chromatin/metabolism/genetics ; Humans ; Protein Processing, Post-Translational ; Chromatin Immunoprecipitation/methods ; High-Throughput Nucleotide Sequencing/methods ; DNA/metabolism/genetics ; Histone Code ; DNA-Binding Proteins/metabolism/genetics ; },
abstract = {ChIP-seq is a widely used technique for studying histone post-translational modifications and DNA-binding proteins. DNA fragments associated with a specific protein or histone modification epitope are captured by using antibodies, sequenced and mapped to a reference genome. Albeit versatile and popular, performing many parallel ChIP-seq experiments to compare different conditions, replicates and epitopes is laborious, is prone to experimental variation and does not allow quantitative comparisons unless adequate spike-in chromatin is included. We present a detailed protocol for performing and analyzing a multiplexed quantitative chromatin immunoprecipitation-sequencing experiment (MINUTE-ChIP), in which multiple samples are profiled against multiple epitopes in a single workflow. Multiplexing not only dramatically increases the throughput of ChIP-seq experiments (e.g., profiling 12 samples against multiple histone modifications or DNA-binding proteins in a single experiment), but also enables accurate quantitative comparisons. The protocol consists of four parts: sample preparation (i.e., lysis, chromatin fragmentation and barcoding of native or formaldehyde-fixed material), pooling and splitting of the barcoded chromatin into parallel immunoprecipitation reactions, preparation of next-generation sequencing libraries from input and immunoprecipitated DNA and data analysis using our dedicated analysis pipeline. This pipeline autonomously generates quantitatively scaled ChIP-seq tracks for downstream analysis and visualization, alongside necessary quality control indicators. The entire workflow requires basic knowledge in molecular biology and bioinformatics and can be completed in 1 week. MINUTE-ChIP empowers biologists to perform every ChIP-seq experiment with an appropriate number of replicates and control conditions, delivering more statistically robust, exquisitely quantitative and biologically meaningful results.},
}
@article {pmid39363072,
year = {2025},
author = {Ramírez Rojas, AA and Brinkmann, CK and Schindler, D},
title = {Validation of Golden Gate Assemblies Using Highly Multiplexed Nanopore Amplicon Sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2850},
number = {},
pages = {171-196},
pmid = {39363072},
issn = {1940-6029},
mesh = {*Nanopore Sequencing/methods ; *Synthetic Biology/methods ; Cloning, Molecular/methods ; Gene Library ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Polymerase Chain Reaction/methods ; Nanopores ; Workflow ; },
abstract = {Golden Gate cloning has revolutionized synthetic biology. Its concept of modular, highly characterized libraries of parts that can be combined into higher order assemblies allows engineering principles to be applied to biological systems. The basic parts, typically stored in Level 0 plasmids, are sequence validated by the method of choice and can be combined into higher order assemblies on demand. Higher order assemblies are typically transcriptional units, and multiple transcriptional units can be assembled into multi-gene constructs. Higher order Golden Gate assembly based on defined and validated parts usually does not introduce sequence changes. Therefore, simple validation of the assemblies, e.g., by colony polymerase chain reaction (PCR) or restriction digest pattern analysis is sufficient. However, in many experimental setups, researchers do not use defined parts, but rather part libraries, resulting in assemblies of high combinatorial complexity where sequencing again becomes mandatory. Here, we present a detailed protocol for the use of a highly multiplexed dual barcode amplicon sequencing using the Nanopore sequencing platform for in-house sequence validation. The workflow, called DuBA.flow, is a start-to-finish procedure that provides all necessary steps from a single colony to the final easy-to-interpret sequencing report.},
}
@article {pmid39360178,
year = {2024},
author = {Fahldieck, M and Rulik, B and Thormann, J and Mengual, X},
title = {A DNA barcode reference library for the Tipulidae (Insecta, Diptera) of Germany.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e127190},
pmid = {39360178},
issn = {1314-2828},
abstract = {Tipulidae, commonly known as true crane flies, represent one of the most species-rich dipteran families, boasting approximately 4,500 known species globally. Their larvae serve as vital decomposers across diverse ecosystems, prompting their frequent and close observation in biomonitoring programs. However, traditional morphological identification methods are laborious and time-consuming, underscoring the need for a comprehensive DNA barcode reference library to speed up species determination. In this study, we present the outcomes of the German Barcode of Life initiative focused on Tipulidae. Our DNA barcode library comprises 824 high-quality cytochrome c oxidase I (COI) barcodes encompassing 76 crane fly species, counting for ca. 54% of the German tipulid fauna. Our results significantly increased the number of European tipulid species available in the Barcode of Life Data System (BOLD) by 14%. Additionally, the number of barcodes from European tipulid specimens more than doubled, with an increase of 118%, bolstering the DNA resource for future identification inquiries. Employing diverse species delimitation algorithms - including the multi-rate Poisson tree processes model (mPTP), Barcode Index Number assignments (BIN), Assemble Species by Automatic Partitioning (ASAP), and the TaxCI R-script - we successfully match 76-86% of the morphologically identified species. Further validation through neighbor-joining tree topology analysis and comparison with 712 additional European tipulid barcodes yield a remarkable 89% success rate for the species identification of German tipulids based on COI barcodes. This comprehensive DNA barcode dataset not only enhances species identification accuracy but also serves as a pivotal resource for ecological and biomonitoring studies, fostering a deeper understanding of crane fly diversity and distribution across terrestrial landscapes.},
}
@article {pmid39353738,
year = {2024},
author = {Tek, AL and Nagaki, K and Yıldız Akkamış, H and Tanaka, K and Kobayashi, H},
title = {Chromosome-specific barcode system with centromeric repeat in cultivated soybean and wild progenitor.},
journal = {Life science alliance},
volume = {7},
number = {12},
pages = {},
pmid = {39353738},
issn = {2575-1077},
mesh = {*Glycine max/genetics ; *Centromere/genetics ; *Chromosomes, Plant/genetics ; DNA Barcoding, Taxonomic/methods ; Domestication ; Genome, Plant/genetics ; Histones/genetics/metabolism ; Plant Breeding/methods ; DNA, Plant/genetics ; },
abstract = {Wild soybean Glycine soja is the progenitor of cultivated soybean Glycine max Information on soybean functional centromeres is limited despite extensive genome analysis. These species are an ideal model for studying centromere dynamics for domestication and breeding. We performed a detailed chromatin immunoprecipitation analysis using centromere-specific histone H3 protein to delineate two distinct centromeric DNA sequences with unusual repeating units with monomer sizes of 90-92 bp (CentGm-1) and 413-bp (CentGm-4) shorter and longer than standard nucleosomes. These two unrelated DNA sequences with no sequence similarity are part of functional centromeres in both species. Our results provide a comparison of centromere properties between a cultivated and a wild species under the effect of the same kinetochore protein. Possible sequence homogenization specific to each chromosome could highlight the mechanism for evolutionary conservation of centromeric properties independent of domestication and breeding. Moreover, a unique barcode system to track each chromosome is developed using CentGm-4 units. Our results with a unifying centromere composition model using CentGm-1 and CentGm-4 superfamilies could have far-reaching implications for comparative and evolutionary genome research.},
}
@article {pmid39353436,
year = {2024},
author = {Bai, Z and Zhang, D and Gao, Y and Tao, B and Zhang, D and Bao, S and Enninful, A and Wang, Y and Li, H and Su, G and Tian, X and Zhang, N and Xiao, Y and Liu, Y and Gerstein, M and Li, M and Xing, Y and Lu, J and Xu, ML and Fan, R},
title = {Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues.},
journal = {Cell},
volume = {187},
number = {23},
pages = {6760-6779.e24},
pmid = {39353436},
issn = {1097-4172},
support = {R01 GM138856/GM/NIGMS NIH HHS/United States ; R56 HG012310/HG/NHGRI NIH HHS/United States ; R33 CA246711/CA/NCI NIH HHS/United States ; U54 CA274509/CA/NCI NIH HHS/United States ; RF1 MH128876/MH/NIMH NIH HHS/United States ; U54 CA268083/CA/NCI NIH HHS/United States ; UH3 CA257393/CA/NCI NIH HHS/United States ; U54 DK106857/DK/NIDDK NIH HHS/United States ; U01 CA294514/CA/NCI NIH HHS/United States ; R01 HG013185/HG/NHGRI NIH HHS/United States ; R01 CA245313/CA/NCI NIH HHS/United States ; U54 AG079759/AG/NIA NIH HHS/United States ; UM1 MH130991/MH/NIMH NIH HHS/United States ; U54 AG076043/AG/NIA NIH HHS/United States ; RM1 MH132648/MH/NIMH NIH HHS/United States ; },
mesh = {Humans ; *Paraffin Embedding ; *Formaldehyde/chemistry ; *Tissue Fixation ; MicroRNAs/genetics/metabolism ; RNA/metabolism/genetics ; Transcriptome/genetics ; RNA Splicing/genetics ; Lymphoma/genetics/pathology ; Gene Expression Profiling/methods ; Polyadenylation ; },
abstract = {The capability to spatially explore RNA biology in formalin-fixed paraffin-embedded (FFPE) tissues holds transformative potential for histopathology research. Here, we present pathology-compatible deterministic barcoding in tissue (Patho-DBiT) by combining in situ polyadenylation and computational innovation for spatial whole transcriptome sequencing, tailored to probe the diverse RNA species in clinically archived FFPE samples. It permits spatial co-profiling of gene expression and RNA processing, unveiling region-specific splicing isoforms, and high-sensitivity transcriptomic mapping of clinical tumor FFPE tissues stored for 5 years. Furthermore, genome-wide single-nucleotide RNA variants can be captured to distinguish malignant subclones from non-malignant cells in human lymphomas. Patho-DBiT also maps microRNA regulatory networks and RNA splicing dynamics, decoding their roles in spatial tumorigenesis. Single-cell level Patho-DBiT dissects the spatiotemporal cellular dynamics driving tumor clonal architecture and progression. Patho-DBiT stands poised as a valuable platform to unravel rich RNA biology in FFPE tissues to aid in clinical pathology evaluation.},
}
@article {pmid39353093,
year = {2025},
author = {Meier, R and Lawniczak, MKN and Srivathsan, A},
title = {Illuminating Entomological Dark Matter with DNA Barcodes in an Era of Insect Decline, Deep Learning, and Genomics.},
journal = {Annual review of entomology},
volume = {70},
number = {1},
pages = {185-204},
doi = {10.1146/annurev-ento-040124-014001},
pmid = {39353093},
issn = {1545-4487},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Insecta/genetics ; *Deep Learning ; *Genomics ; Biodiversity ; Entomology/methods ; },
abstract = {Most insects encountered in the field are initially entomological dark matter in that they cannot be identified to species while alive. This explains the enduring quest for efficient ways to identify collected specimens. Morphological tools came first but are now routinely replaced or complemented with DNA barcodes. Initially too expensive for widespread use, these barcodes have since evolved into powerful tools for specimen identification and sorting, given that the evolution of sequencing approaches has dramatically reduced the cost of barcodes, thus enabling decentralized deployment across the planet. In this article, we review how DNA barcodes have become a key tool for accelerating biodiversity discovery and analyzing insect communities through both megabarcoding and metabarcoding in an era of insect decline. We predict that DNA barcodes will be particularly important for assembling image training sets for deep learning algorithms, global biodiversity genomics, and functional analysis of insect communities.},
}
@article {pmid39355103,
year = {2024},
author = {Truong, C and Gabbarini, LA and Moretto, A and Escobar, JM and Smith, ME},
title = {Ectomycorrhizal fungi and the nitrogen economy of Nothofagus in southern Patagonia.},
journal = {Ecology and evolution},
volume = {14},
number = {10},
pages = {e70299},
pmid = {39355103},
issn = {2045-7758},
abstract = {Subantarctic Nothofagus forests are the southernmost forests in the world, with negligible atmospheric nitrogen (N) deposition. Most paradigms about the role of ectomycorrhizal (ECM) fungi in N cycling and plant N uptake at high latitudes have been tested in boreal coniferous forests, while in the southern hemisphere, ECM hosts are primarily angiosperms. Using ITS1 meta-barcoding, we characterized ECM and saprotrophic fungal communities in evergreen and deciduous Nothofagus forests forming monodominant and mixed stands in the archipelago of Tierra del Fuego (Chile and Argentina). We assessed the N economy of Nothofagus by correlating host species with fungal relative abundances, edaphic variables, net N mineralization, microbial biomass N and the activity of eight extracellular soil enzymes activities. The N economy of deciduous N. pumilio forests was strikingly similar to boreal coniferous forests, with the lowest inorganic N availability and net N mineralization, in correlation to higher relative abundances of ECM fungi with enzymatic capacity for organic N mobilization (genus Cortinarius). In contrast, the N economy of evergreen N. betuloides forests was predominantly inorganic and correlated with ECM lineages from the family Clavulinaceae, in acidic soils with poor drainage. Grassy understory vegetation in deciduous N. antarctica forests likely promoted saprotrophic fungi (i.e., genus Mortierella) in correlation with higher activities of carbon-degrading enzymes. Differences between Nothofagus hosts did not persist in mixed forests, illustrating the range of soil fertility of these ECM angiosperms and the underlying effects of soil and climate on Nothofagus distribution and N cycling in southern Patagonia.},
}
@article {pmid39354174,
year = {2024},
author = {Ali, M and Dey, R and Das, M and Kumar, V and Chandra, K and Uniyal, VP and Gupta, SK},
title = {Unique among high passes: Insights into the genetic uniqueness among butterflies of Ladakh Trans-Himalaya through DNA barcoding.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {1033},
pmid = {39354174},
issn = {1573-4978},
mesh = {Animals ; *Butterflies/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Phylogeny ; Bayes Theorem ; Genetic Variation/genetics ; Genetics, Population ; },
abstract = {BACKGROUND: The butterfly assemblage of Ladakh Trans-Himalaya demands a thorough analysis of their population genetic structure owing to their typical biogeographic affinity and their adaptability to extreme cold-desert climates. No such effort has been taken till date, and in this backdrop, we created a COI barcode reference library of 60 specimens representing 23 species.<br><br>METHODS AND RESULTS: Barcodes were generated from freshly collected leg samples using the Sanger sequencing method, followed by phylogenetic clade analyses and divergence calculation. Our data represents 22% of Ladakh's Rhopaloceran fauna with the novel barcode submission for six species, including one Schedule II species, Paralasa mani. Contrary to the 3% threshold rule, the interspecific divergence between two species pairs of typical mountain genus Hyponephele and Karanasa was found to be 2.3% and 2.2%, respectively. The addition of conspecific global barcodes revealed that most species showed little increase in divergence value, while a two-fold increase was noted in a few species. Bayesian clade clustering outcomes largely aligned with current morphological classifications, forming monophyletic clades of conspecific barcodes, with only minor exceptions observed for the taxonomically complicated genus Polyommatus and misidentified records of Aulocera in the database. We also observed variations within the same phylogenetic clades forming nested lineages, which may be attributed to the taxonomic intricacies present at the subspecies level globally, mostly among Eurasian species.<br><br>CONCLUSIONS: Overall, our effort not only substantiated the effectiveness of DNA Barcoding for the identification and conservation of this climatically vulnerable assemblage but also highlighted the significance of deciphering the unique genetic composition among this geographically isolated population of Ladakh butterflies.},
}
@article {pmid39351591,
year = {2025},
author = {Bigirimana, A and Kisekelwa, T and da Costa, LM and Huyghe, CET and Banyankimbona, G and Vreven, EJWMN},
title = {Description of a new endemic Enteromius (Teleostei: Cyprinidae) from the upper Malagarazi in Burundi: Lessons for a protected area under implementation.},
journal = {Journal of fish biology},
volume = {106},
number = {2},
pages = {173-200},
doi = {10.1111/jfb.15652},
pmid = {39351591},
issn = {1095-8649},
mesh = {Animals ; *Conservation of Natural Resources ; *Electron Transport Complex IV/genetics/analysis ; *Cyprinidae/genetics ; Burundi ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Phylogeny ; },
abstract = {Recent collecting efforts in the upper Malagarazi basin (2013-2022) allowed for an integrative study based on qualitative (colour), quantitative (meristic and metric), and barcoding gene [mtDNA, cytochrome c oxidase (COI)] data of specimens similar to Enteromius sp. 'ascutelatus', being a previously identified, potentially, new species. Based on these data, the present study confirms its identification as a new species for science, which is here formally described as Enteromius nzigidaherai sp. nov. This new species belongs to the group of Enteromius species for which the last unbranched ray of the dorsal fin is flexible and devoid of serrations along its posterior edge. This species has a horizontal series of black spots at the midlateral level of the sides. Three congeneric species, known from the Congo basin sensu lato, with two of them also found in the upper Malagarazi basin, are most similar to it. However, E. nzigidaherai sp. nov. is distinguished from the two sympatric upper Malagarazi species, that is, E. quadrilineatus and E. lineomaculatus, at least by two meristics and two morphometrics. It is also distinguished from E. urostigma, known from the upper Congo basin, by two meristics and one, apparently related, morphometric. In addition, a barcoding (mtDNA, COI) study revealed that the specimens of E. nzigidaherai sp. nov. form a well-supported, separate lineage, with a K2P genetic distance of more than 10% with specimens identified as E. quadrilineatus and E. lineomaculatus, both originating from the upper Malagarazi basin and for which tissue samples were available. Finally, the new species was found to be endemic to the upper reaches of two left bank affluents of the upper Malagarazi basin: the Muyovozi and the Kinwa. However, both affluents are threatened by human activities, which seem to have resulted in its local disappearance as recent intensive collecting efforts in the latter affluent have remained unsuccessful. The species should thus be considered Critically Endangered (CR) according to IUCN criteria B1ab(ii,iv)c(i,iii). Therefore, it is hoped that the present description draws renewed attention to the importance of aquatic protection in the region by highlighting the need for the effective establishment of the Malagarazi Nature Reserve and concern for its optimal delimitation to efficiently protect the entire ichthyofauna of the upper Malagarazi, without excluding the fish species confined to its affluent rivers.},
}
@article {pmid39351291,
year = {2024},
author = {Mwamula, AO and Lee, SM and Jung, YH and Kim, YS and Lee, DW},
title = {Description and Molecular Characterization of a New Dorylaimid Nematode, Mesodorylaimus pini n. sp. (Nematoda: Dorylaimidae) from Korea.},
journal = {Journal of nematology},
volume = {56},
number = {1},
pages = {20240028},
pmid = {39351291},
issn = {0022-300X},
abstract = {Mesodorylaimus pini n. sp., a new species isolated from the bark and cambium layer of a dead black pine tree is characterized herein using integrative taxonomy, considering both morphological and molecular phylogenetic analyses of the 18S- and 28S-rRNA genes. Mesodorylaimus pini n. sp. is characterized by having a medium-sized body 1.50-1.89 mm long; lip region angular and offset by a depression; a relatively long odontostyle (17.0-19.0 μm); vulval opening a transverse slit, positioned slightly posteriorly; pars refringens vaginae with two elongated drop-shaped to spindle-shaped sclerotizations; an intestine-prerectum junction with a long anteriorly directed conical or tongue-like projection; a relatively long female tail (115-187 μm); spicules 48.0-57.0 μm long; and regularly spaced 7-8 ventromedian supplements. It is closest to M. subtilis, especially in having similar body length and number of ventromedian supplements but can be differentiated from M. subtilis by the longer odontostyle, tongue-like projection, and longer spicules. The phylogenies based on the 18S- and 28S-rRNA sequences showed a well-supported sister relation of M. pini n. sp. with M. subtilis, M. japonicus, M. bastiani, M. pseudobastiani, Calcaridorylaimus castaneae, C. heynsi, and other member species of the group.},
}
@article {pmid39349515,
year = {2024},
author = {Zhang, S and Liao, A and Wang, Y and Liu, Q and Ouyang, L and Peng, H and Yuan, L and Zhao, L and Yang, X and Chen, X and He, Y and Li, Z},
title = {Profiling expressing features of surface proteins on single-exosome in first-episode Schizophrenia patients: a preliminary study.},
journal = {Schizophrenia (Heidelberg, Germany)},
volume = {10},
number = {1},
pages = {84},
pmid = {39349515},
issn = {2754-6993},
support = {82101576//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Proximity barcoding assay, a high-throughput method for single-exosome analysis, was employed to profile surface proteins on individual exosomes of SCZ patients. This analysis identified five differentially expressed proteins (DEPs) between SCZ patients and healthy controls (HC) and six DEPs between antipsychotic responders and non-responders. Furthermore, two exosome clusters were found to be associated with SCZ, and certain DEPs were correlated with cognitive functions.},
}
@article {pmid39349404,
year = {2025},
author = {Villa, S and Magoga, G and Montagna, M and Pierce, S},
title = {Elevational shifts in reproductive ecology indicate the climate response of a model chasmophyte, Rainer's bellflower (Campanula raineri).},
journal = {Annals of botany},
volume = {135},
number = {1-2},
pages = {181-198},
pmid = {39349404},
issn = {1095-8290},
support = {PSR2019_DIP_014SPIER//Department of Agricultural and Environmental Sciences (DiSAA), University of Milan, Italy/ ; //Department of Agricultural and Environmental Sciences/ ; //Doctoral School of Agriculture, Environment and Bioenergy/ ; },
mesh = {*Campanulaceae/physiology ; *Pollination/physiology ; *Reproduction/physiology ; Animals ; *Seeds/physiology ; *Climate Change ; *Altitude ; Pollen/physiology ; Hymenoptera/physiology ; Climate ; },
abstract = {BACKGROUND AND AIMS: Elevation gradients provide 'natural experiments' for investigating plant climate change responses, advantageous for the study of protected species and life forms for which transplantation experiments are illegal or unfeasible, such as chasmophytes with perennial rhizomes pervading rock fissures. Elevational climatic differences impact mountain plant reproductive traits (pollen and seed quality, sexual vs. vegetative investment) and pollinator community composition; we investigated the reproductive ecology of a model chasmophyte, Campanula raineri Perp. (Campanulaceae), throughout its current elevational/climatic range to understand where sub-optimal conditions jeopardise survival. We hypothesised that: 1) reproductive fitness measures are positively correlated with elevation, indicative of the relationship between fitness and climate; 2) C. raineri, like other campanulas, is pollinated mainly by Hymenoptera; 3) potential pollinators shift with elevation.<br><br>METHODS: We measured pollen and seed quality, seed production, the relative investment in sexual vs. vegetative structures and vegetative (Grime's CSR) strategies at different elevations. Potential pollinators were assessed by combining molecular and morphological identification.<br><br>KEY RESULTS: Whereas CSR strategies were not linked to elevation, pollen and seed quality were positively correlated, as was seed production per fruit (Hypothesis 1 is supported). The main pollinators of C. raineri were Apidae, Andrenidae, Halictidae (Hymenoptera) and Syrphidae (Diptera), probably complemented by a range of occasional pollinators and visitors (Hypothesis 2 partially supported). Potential pollinator communities showed a taxonomic shift towards Diptera with elevation (particularly Anthomyiidae and Muscidae) and away from Hymenoptera (Hypothesis 3 was supported).<br><br>CONCLUSIONS: Pollinator availability is maintained at all elevations by taxon replacement. However, reduced pollen quality and seed production at lower elevations suggest an impact of climate change on reproduction (especially <1200 m a.s.l., where seed germination was limited). Aside from guiding targeted conservation actions for C. raineri, our results highlight problems that may be common to mountain chasmophytes worldwide.},
}
@article {pmid39348735,
year = {2025},
author = {Wang, S and Zhou, Y and Ding, K and Ding, ZQ and Zhang, W and Liu, Y},
title = {High-throughput and multimodal profiling of antigen-specific T cells with a droplet-based cell-cell interaction screening platform.},
journal = {Biosensors &amp; bioelectronics},
volume = {267},
number = {},
pages = {116815},
doi = {10.1016/j.bios.2024.116815},
pmid = {39348735},
issn = {1873-4235},
mesh = {Humans ; *Cell Communication ; *Biosensing Techniques/methods ; *T-Lymphocytes/immunology/cytology ; Antigen-Presenting Cells/immunology ; Single-Cell Analysis/methods ; High-Throughput Screening Assays/methods ; Animals ; Antigens/immunology/chemistry ; Click Chemistry ; },
abstract = {Identifying antigen-specific T cells from tumor-infiltrating lymphocytes is essential for designing effective T cell immunotherapies. Traditional methods can detect antigen-specific T cells but struggle with high-throughput screening and multimodal profiling simultaneously. To address this issue, we developed DropCCI, a new strategy that transfers antigen information to co-incubated T cells for high-throughput, non-contaminated multimodal profiling. In DropCCI, droplets encapsulated DNA barcodes and antigen-loaded antigen-presenting cells (APCs), while click chemistry-modified T cells were injected into these droplets to capture free barcodes and acquire the corresponding antigen information. Following cell-cell interaction, APCs were removed via streptavidin-biotin conjugation, to prevent contamination. The resulting T cells underwent single-cell omics sequencing for comprehensive profiling of their antigen specificity, transcriptome, and genomics accurately. This click-chemistry method allowed detection of antigen-specific T cells without lysing APCs, avoiding cross-cell contamination and enabling low-noise multimodal profiling of primary T cells. With a completion time within 12 h and no requirement for complex equipment, DropCCI provides unbiased single-cell sequencing results that offer a comprehensive understanding of anti-tumor T cell responses. The concept of DropCCI holds great promise not only for advancing the field of T cell immunotherapy but also for its potential application in studying other cell-cell interactions.},
}
@article {pmid39348593,
year = {2024},
author = {Ren, J and Zhang, R},
title = {Delimiting species, revealing cryptic diversity in Molytinae (Coleoptera: Curculionidae) weevil through DNA barcoding.},
journal = {Journal of insect science (Online)},
volume = {24},
number = {4},
pages = {},
pmid = {39348593},
issn = {1536-2442},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Weevils/genetics/classification ; *Electron Transport Complex IV/genetics ; Genetic Variation ; Phylogeny ; },
abstract = {The subfamily Molytinae (Coleoptera: Curculionidae), being the second largest group within the family Curculionidae, exhibits a diverse range of hosts and poses a serious threat to agricultural and forestry industries. We used 1,290 cytochrome c oxidase subunit I (COI) barcodes to assess the efficiency of COI barcodes in species differentiation and uncover cryptic species diversity within weevils of Molytinae. The average Kimura 2-parameter distances within species, genus, and subfamily were 2.90%, 11.0%, and 22.26%, respectively, indicating significant genetic differentiation at both levels. Moreover, there exists a considerable degree of overlap between intraspecific (0%-27.50%) and interspecific genetic distances (GDs; 0%-39.30%). The application of Automatic barcode gap discovery, Assemble Species by Automatic Partitioning, Barcode Index Number, Poisson Tree Processes (PTP), Bayesian Poisson Tree Processes (bPTP), and jMOTU resulted in the identification of 279, 275, 494, 322, 320, and 279 molecular operational taxonomic units, respectively. The integration of 6 methods successfully delimited species of Molytinae in 86.6% of all examined morphospecies, surpassing a threshold value of 3% GD (73.0%). A total of 28 morphospecies exhibiting significant intraspecific divergences were assigned to multiple MOTUs, respectively, suggesting the presence of cryptic diversity or population divergence. The identification of cryptic species within certain morphological species in this study necessitates further investigation through comprehensive taxonomic practices in the future.},
}
@article {pmid39347602,
year = {2024},
author = {Kamata, K and Birkholz, N and Ceelen, M and Fagerlund, RD and Jackson, SA and Fineran, PC},
title = {Repurposing an Endogenous CRISPR-Cas System to Generate and Study Subtle Mutations in Bacteriophages.},
journal = {The CRISPR journal},
volume = {7},
number = {6},
pages = {343-354},
doi = {10.1089/crispr.2024.0047},
pmid = {39347602},
issn = {2573-1602},
mesh = {*CRISPR-Cas Systems ; *Bacteriophages/genetics ; *Gene Editing/methods ; *Mutation ; Genome, Viral ; Plasmids/genetics ; Pectobacterium carotovorum/virology/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Homologous Recombination ; },
abstract = {While bacteriophage applications benefit from effective phage engineering, selecting the desired genotype after subtle modifications remains challenging. Here, we describe a two-phase endogenous CRISPR-Cas-based phage engineering approach that enables selection of small defined edits in Pectobacterium carotovorum phage ZF40. We designed plasmids containing sequences homologous to ZF40 and a mini-CRISPR array. The plasmids allowed genome editing through homologous recombination and counter-selection against non-recombinant phage genomes using an endogenous type I-E CRISPR-Cas system. With this technique, we first deleted target genes and subsequently restored loci with modifications. This two-phase approach circumvented major challenges in subtle phage modifications, including inadequate sequence distinction for CRISPR-Cas counter-selection and the requirement of a protospacer-adjacent motif, limiting sequences that can be modified. Distinct 20-bp barcodes were incorporated through engineering as differential target sites for programmed CRISPR-Cas activity, which allowed quantification of phage variants in mixed populations. This method aids studies and applications that require mixtures of similar phages.},
}
@article {pmid39345550,
year = {2024},
author = {Carlos, AJ and Yang, D and Thomas, DM and Huang, S and Harter, KI and Moellering, RE},
title = {Family-Wide Photoproximity Profiling of Integrin Protein Social Networks in Cancer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39345550},
issn = {2692-8205},
support = {DP2 GM128199/GM/NIGMS NIH HHS/United States ; R01 GM145852/GM/NIGMS NIH HHS/United States ; T32 CA009594/CA/NCI NIH HHS/United States ; },
abstract = {Integrin family transmembrane receptors mediate dynamic interactions between cells and their extracellular microenvironment. The heterogeneous interaction partners of integrins directly regulate cell adhesion, motility, proliferation, and intracellular signaling. Despite the recognized importance of protein-protein interactions and the formation of signaling hubs around integrins, the ability to detect and quantify these dynamic binding partners with high spatial and temporal resolution remains challenging. Here, we developed an integrin-family-directed quantitative photoproximity protein interaction (PhotoPPI) profiling method to detect and quantify native integrin-centered protein social networks on live cells and tissues without the need for genetic manipulation, antibodies, or non-physiologic cell culture conditions. We drafted quantitative maps of integrin-centered protein social networks, highlighting conserved and unique binding partners between different cell types and cellular microenvironments. Comparison of integrin social networks in cancer cell lines of diverse tissue of origin and disease state identified specific AND-gate binding partners involved cell migration, microenvironmental interactions and proliferation that serve as markers of tumor cell metastatic state. Finally, we identified unique combinations - or barcodes - of integrin-proximal proteins on the surface of pre- and post-metastatic triple negative breast cancer (TNBC) cells whose expression strongly correlate with both positive and negative disease progression and outcomes in TNBC patients. Taken together, these data provide the first family-wide high-resolution maps of native protein interactors on live cells and identify dynamic integrin-centered social networks as potential AND-gate markers of cell identity, microenvironmental context and disease state.},
}
@article {pmid39345539,
year = {2024},
author = {Ashkin, EL and Tang, YJ and Xu, H and Hung, KL and Belk, J and Cai, H and Lopez, S and Dolcen, DN and Hebert, JD and Li, R and Ruiz, PA and Keal, T and Andrejka, L and Chang, HY and Petrov, DA and Dixon, JR and Xu, Z and Winslow, MM},
title = {A STAG2-PAXIP1/PAGR1 axis suppresses lung tumorigenesis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.14.613043},
pmid = {39345539},
issn = {2692-8205},
abstract = {UNLABELLED: The cohesin complex is a critical regulator of gene expression. STAG2 is the most frequently mutated cohesin subunit across several cancer types and is a key tumor suppressor in lung cancer. Here, we coupled somatic CRISPR-Cas9 genome editing and tumor barcoding with an autochthonous oncogenic KRAS-driven lung cancer model and show that STAG2 is uniquely tumor suppressive among all core and auxiliary cohesin components. The heterodimeric complex components PAXIP1 and PAGR1 have highly correlated effects with STAG2 in human lung cancer cell lines, are tumor suppressors in vivo , and are epistatic to STAG2 in oncogenic KRAS-driven lung tumorigenesis in vivo . STAG2 inactivation elicits changes in gene expression, chromatin accessibility and 3D genome conformation that impact cancer cell state. Gene expression and chromatin accessibility similarities between STAG2- and PAXIP1-deficient neoplastic cells further relates STAG2-cohesin to PAXIP1/PAGR1. These findings reveal a STAG2-PAXIP1/PAGR1 tumor-suppressive axis and uncover novel PAXIP1-dependent and PAXIP1-independent STAG2-cohesin mediated mechanisms of lung tumor suppression.<br><br>SUMMARY: STAG2 is a frequently mutated cohesin subunit across several cancers and one of the most important functional suppressors of lung adenocarcinoma. Our findings underscore important roles of STAG2 in suppressing lung tumorigenesis and highlight a STAG2-PAXIP1/PAGR1 tumor-suppressive program that may transcend cancer type.},
}
@article {pmid39345444,
year = {2024},
author = {Boutelle, AM and Mabene, AR and Yao, D and Xu, H and Wang, M and Tang, YJ and Lopez, SS and Sinha, S and Demeter, J and Cheng, R and Benard, BA and Valente, LJ and Drainas, AP and Fischer, M and Majeti, R and Petrov, DA and Jackson, PK and Yang, F and Winslow, MM and Bassik, MC and Attardi, LD},
title = {Integrative multiomic approaches reveal ZMAT3 and p21 as conserved hubs in the p53 tumor suppression network.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.17.612743},
pmid = {39345444},
issn = {2692-8205},
abstract = {TP53 , the most frequently mutated gene in human cancer, encodes a transcriptional activator that induces myriad downstream target genes. Despite the importance of p53 in tumor suppression, the specific p53 target genes important for tumor suppression remain unclear. Recent studies have identified the p53-inducible gene Zmat3 as a critical effector of tumor suppression, but many questions remain regarding its p53-dependence, activity across contexts, and mechanism of tumor suppression alone and in cooperation with other p53-inducible genes. To address these questions, we used Tuba-seq [Ultra] somatic genome editing and tumor barcoding in a mouse lung adenocarcinoma model, combinatorial in vivo CRISPR/Cas9 screens, meta-analyses of gene expression and Cancer Dependency Map data, and integrative RNA-sequencing and shotgun proteomic analyses. We established Zmat3 as a core component of p53-mediated tumor suppression and identified Cdkn1a as the most potent cooperating p53-induced gene in tumor suppression. We discovered that ZMAT3/CDKN1A serve as near-universal effectors of p53-mediated tumor suppression that regulate cell division, migration, and extracellular matrix organization. Accordingly, combined Zmat3 - Cdkn1a inactivation dramatically enhanced cell proliferation and migration compared to controls, akin to p53 inactivation. Together, our findings place ZMAT3 and CDKN1A as hubs of a p53-induced gene program that opposes tumorigenesis across various cellular and genetic contexts.},
}
@article {pmid39345427,
year = {2024},
author = {Fang, C and Lindsey, J and Abbott, LF and Aronov, D and Chettih, S},
title = {Barcode activity in a recurrent network model of the hippocampus enables efficient memory binding.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39345427},
issn = {2692-8205},
support = {DP2 AG071918/AG/NIA NIH HHS/United States ; K99 NS136846/NS/NINDS NIH HHS/United States ; T32 NS064929/NS/NINDS NIH HHS/United States ; },
abstract = {Forming an episodic memory requires binding together disparate elements that co-occur in a single experience. One model of this process is that neurons representing different components of a memory bind to an "index" - a subset of neurons unique to that memory. Evidence for this model has recently been found in chickadees, which use hippocampal memory to store and recall locations of cached food. Chickadee hippocampus produces sparse, high-dimensional patterns ("barcodes") that uniquely specify each caching event. Unexpectedly, the same neurons that participate in barcodes also exhibit conventional place tuning. It is unknown how barcode activity is generated, and what role it plays in memory formation and retrieval. It is also unclear how a memory index (e.g. barcodes) could function in the same neural population that represents memory content (e.g. place). Here, we design a biologically plausible model that generates barcodes and uses them to bind experiential content. Our model generates barcodes from place inputs through the chaotic dynamics of a recurrent neural network and uses Hebbian plasticity to store barcodes as attractor states. The model matches experimental observations that memory indices (barcodes) and content signals (place tuning) are randomly intermixed in the activity of single neurons. We demonstrate that barcodes reduce memory interference between correlated experiences. We also show that place tuning plays a complementary role to barcodes, enabling flexible, contextually-appropriate memory retrieval. Finally, our model is compatible with previous models of the hippocampus as generating a predictive map. Distinct predictive and indexing functions of the network are achieved via an adjustment of global recurrent gain. Our results suggest how the hippocampus may use barcodes to resolve fundamental tensions between memory specificity (pattern separation) and flexible recall (pattern completion) in general memory systems.},
}
@article {pmid39342262,
year = {2024},
author = {Bisaglia, B and Castelli, M and Soresinetti, L and Negri, A and Arnoldi, I and Montarsi, F and Gobbo, F and Defilippo, F and Callegari, E and Di Luca, M and Calzolari, M and Mastrantonio, V and Porretta, D and Ficetola, GF and Sassera, D and Gabrieli, P and Bandi, C and Epis, S},
title = {Barcoding of Italian mosquitoes (BITMO): generation and validation of DNA barcoding reference libraries for native and alien species of Culicidae.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {407},
pmid = {39342262},
issn = {1756-3305},
support = {MUSA - Multilayered Urban Sustainability Action - project, funded by the European Union - NextGenerationEU, under the National Recovery and Resilience Plan (NRRP) Mission 4 Component 2 Investment Line 1.5: Strengthening of research structures and creation of R&amp;D "innovation ecosystems", set up of "territorial leaders in R&amp;D".//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; PNRR Project title "National Biodiversity Future Center - NBFC" Project code CN_00000033, Concession Decree No. 1034 of 17 June 2022//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; PNRR project PE-13, INF-ACT "One Health Basic and Translational Research Actions addressing Unmet Needs on Emerging Infectious Diseases"//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; MUSA - Multilayered Urban Sustainability Action - project, funded by the European Union - NextGenerationEU, under the National Recovery and Resilience Plan (NRRP) Mission 4 Component 2 Investment Line 1.5: Strengthening of research structures and creation of R&amp;D "innovation ecosystems", set up of "territorial leaders in R&amp;D".//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *RNA, Ribosomal, 16S/genetics ; *Culicidae/genetics/classification ; Italy ; *Introduced Species ; *Mosquito Vectors/genetics/classification ; *Phylogeny ; Gene Library ; Electron Transport Complex IV/genetics ; },
abstract = {BACKGROUND: Mosquitoes (Culicidae), as disease vectors, represent a risk for human health worldwide. Repeated introductions of alien mosquito species and the spread of invasive species have been recorded in different countries. Traditionally, identification of mosquitoes relies on morphological observation. However, morphology-based identification is associated with a number of potential disadvantages, such as the high level of specialisation of the operator and its limited applicability to damaged samples. In these cases, species identification is achieved through molecular methods based on DNA amplification. Molecular-based taxonomy has also enabled the development of techniques for the study of environmental DNA (eDNA). Previous studies indicated the 16S mitochondrial ribosomal RNA (rRNA) gene as a promising target for this application; however, 16S rRNA sequences are available for only a limited number of mosquito species. In addition, although primers for the 16S rRNA gene were designed years ago, they are based on limited numbers of mosquito sequences. Thus, the aims of this study were to: (i) design pan-mosquito 16S rRNA gene primers; (ii) using these primers, generate a 16S rRNA gene mosquito reference library (with a focus on mosquitoes present in Italy); and (iii) compare the discriminatory power of the 16S rRNA gene with two widely used molecular markers, cytochrome c oxidase subunit 1 mitochondrial gene (COI) and internal transcribed spacer 2 (ITS2).<br><br>METHODS: A total of six mosquito genera (28 mosquito species) were included in this study: Aedes (n = 16 species), Anopheles (5 species), Coquillettidia (1 species), Culex (3 species), Culiseta (2 species) and Uranotaenia (1 species). DNA was extracted from the whole mosquito body, and more than one specimen for each species was included in the analysis. Sanger sequencing was used to generate DNA sequences that were then analysed through the Barcode of Life Data Systems (BOLD). Phylogenetic analyses were also performed.<br><br>RESULTS: Novel 16S rDNA gene, COI and ITS2 sequences were generated. The 16S rRNA gene was shown to possess sufficient informativeness for the identification of mosquito species, with a discriminatory power equivalent to that of COI.<br><br>CONCLUSIONS: This study contributes to the generation of DNA barcode libraries, focussed on Italian mosquitoes, with a significant increase in the number of 16S rRNA gene sequences. We hope that these novel sequences will provide a resource for studies on the biodiversity, monitoring and metabarcoding of mosquitoes, including eDNA-based approaches.},
}
@article {pmid39339949,
year = {2024},
author = {Sartingen, N and Stürmer, V and Kaltenböck, M and Müller, TG and Schnitzler, P and Kreshuk, A and Kräusslich, HG and Merle, U and Mücksch, F and Müller, B and Pape, C and Laketa, V},
title = {Multiplex Microscopy Assay for Assessment of Therapeutic and Serum Antibodies against Emerging Pathogens.},
journal = {Viruses},
volume = {16},
number = {9},
pages = {},
pmid = {39339949},
issn = {1999-4915},
support = {TTU 04.710//German Center for Infection Research/ ; EXC 2067/1- 390729940//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Humans ; *SARS-CoV-2/immunology ; *COVID-19/diagnosis/immunology/virology ; *Antibodies, Viral/blood/immunology ; *Spike Glycoprotein, Coronavirus/immunology ; HeLa Cells ; Antigens, Viral/immunology ; Microscopy/methods ; Coronavirus Nucleocapsid Proteins/immunology ; Machine Learning ; Phosphoproteins ; },
abstract = {The emergence of novel pathogens, exemplified recently by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), highlights the need for rapidly deployable and adaptable diagnostic assays to assess their impact on human health and guide public health responses in future pandemics. In this study, we developed an automated multiplex microscopy assay coupled with machine learning-based analysis for antibody detection. To achieve multiplexing and simultaneous detection of multiple viral antigens, we devised a barcoding strategy utilizing a panel of HeLa-based cell lines. Each cell line expressed a distinct viral antigen, along with a fluorescent protein exhibiting a unique subcellular localization pattern for cell classification. Our robust, cell segmentation and classification algorithm, combined with automated image acquisition, ensured compatibility with a high-throughput approach. As a proof of concept, we successfully applied this approach for quantitation of immunoreactivity against different variants of SARS-CoV-2 spike and nucleocapsid proteins in sera of patients or vaccinees, as well as for the study of selective reactivity of monoclonal antibodies. Importantly, our system can be rapidly adapted to accommodate other SARS-CoV-2 variants as well as any antigen of a newly emerging pathogen, thereby representing an important resource in the context of pandemic preparedness.},
}
@article {pmid39339575,
year = {2024},
author = {Heo, JH and Yeon, J and Jung, JK and Shin, IS and Sim, SC},
title = {Development of Cost-Effective SNP Markers for Genetic Variation Analysis and Variety Identification in Cultivated Pears (Pyrus spp.).},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {18},
pages = {},
pmid = {39339575},
issn = {2223-7747},
support = {320040052HD060//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries (IPET)/ ; },
abstract = {Pear (Pyrus spp.) is a major fruit crop in the Rosaceae family, and extensive efforts have been undertaken to develop elite varieties. With advances in genome sequencing technologies, single-nucleotide polymorphisms (SNPs) are commonly used as DNA markers in crop species. In this study, a large-scale discovery of SNPs was conducted using genotyping by sequencing in a collection of 48 cultivated pear accessions. A total of 256,538 confident SNPs were found on 17 chromosomes, and 288 SNPs were filtered based on polymorphic information content, heterozygosity rate, and genome distribution. This subset of SNPs was used to genotype an additional 144 accessions, consisting of P. pyrifolia (53), P. ussuriensis (27), P. bretschneideri (19), P. communis (26), interspecific hybrids (14), and others (5). The 232 SNPs with reliable polymorphisms revealed genetic variations between and within species in the 192 pear accessions. The Asian species (P. pyrifolia, P. ussuriensis, and P. bretschneideri) and interspecific hybrids were genetically differentiated from the European species (P. communis). Furthermore, the P. pyrifolia population showed higher genetic diversity relative to the other populations. The 232 SNPs and four subsets (192, 96, 48, and 24 SNPs) were assessed for variety identification. The 192 SNP subset identified 173 (90.1%) of 192 accessions, which was comparable to 175 (91.1%) from the 232 SNPs. The other three subsets showed 81.8% (24 SNPs) to 87.5% (96 SNPs) identification rates. The resulting SNPs will be a useful resource to investigate genetic variations and develop an efficient DNA barcoding system for variety identification in cultivated pears.},
}
@article {pmid39338960,
year = {2024},
author = {Olszak-Przybyś, H and Korbecka-Glinka, G},
title = {The Diversity of Seed-Borne Fungi Associated with Soybean Grown in Southern Poland.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {9},
pages = {},
pmid = {39338960},
issn = {2076-0817},
mesh = {*Glycine max/microbiology ; Poland ; *Seeds/microbiology ; *Fungi/isolation &amp; purification/genetics/classification ; Fusarium/isolation &amp; purification/genetics ; Germination ; Biodiversity ; Aspergillus/isolation &amp; purification/genetics ; },
abstract = {Fungi have the potential to colonize soybean seeds in the field, during their maturation in the pods and after harvest, during storage. The aim of this study was to identify fungi inhabiting soybean seeds after storage with varying germination capacity and to evaluate their chemical composition. The research material consisted of twelve soybean seed lots collected from the fields in southern Poland and stored over winter. The germination percentage of these lots ranged between 20.67% and 81.33%. The seeds were subjected to analyses of the main chemical components and mycological analysis. Fungal isolates were subjected to taxonomic identification using microscopic methods and DNA sequencing (using internal transcribed spacer region and secondary barcoding regions). A total number of 355 fungal isolates from 16 genera were identified, with Aspergillus, Alternaria, and Fusarium being the most common. Species were successfully identified in 94% of isolates. Twelve examined seed lots varied significantly in the number of isolated fungal species (from 1 to 17). Moreover, they also differed in the isolated species composition. Highly significant positive correlation was found between the number of Aspergillus psedudoglaucus isolates and the content of free fatty acids. In turn, the number of Fusarium spp. isolates correlated negatively with protein and nitrogen content. Similarly, highly significant negative correlation was found between the number of all fungal isolates and the 1000-seed weight, indicating that smaller seeds are more vulnerable to fungal infection. The results obtained in this study identify species of fungi which may be responsible for lowering quality of the seeds obtained in southern Poland.},
}
@article {pmid39337711,
year = {2024},
author = {Noh, S and Kim, WJ and Cha, JM and Choi, G and Yang, S and Song, JH and Moon, BC},
title = {Rapid Diagnostic PCR Assay Method for Species Identification of Mantidis Ootheca (Sangpiaoxiao) Based on Cytochrom C Oxidase I (COI) Barcode Analysis.},
journal = {International journal of molecular sciences},
volume = {25},
number = {18},
pages = {},
pmid = {39337711},
issn = {1422-0067},
support = {KSN1823320//Korea Institute of Oriental Medicine/ ; },
mesh = {*Electron Transport Complex IV/genetics ; *DNA Barcoding, Taxonomic/methods ; Animals ; Polymerase Chain Reaction/methods ; Species Specificity ; Mantodea/genetics/classification ; Rapid Diagnostic Tests ; },
abstract = {Mantidis Ootheca (sangpiaoxiao), the egg case of the mantis, is a type of insect-derived traditional medicine widely used in East Asia. However, species identification based on egg morphology is challenging, leading to the distribution of counterfeit and adulterated products. The use of inauthentic ingredients can pose serious health risks to consumers. This study aimed to develop PCR markers that can rapidly and accurately differentiate between authentic and counterfeit Mantidis Ootheca. The mitochondrial cytochrome c oxidase I (COI) region was sequenced in thirteen samples from four mantis species: Tenodera angustipennis, Statilia maculata, Hierodula patellifera, and T. sinensis. Four sets of SCAR primers were designed based on species-specific nucleotide polymorphisms, and a multiplex SCAR assay was developed by combining all sets of the primers. The sequence-characterized amplified region (SCAR) primers successfully produced amplicons for each target species, even with low-DNA templates or templates containing DNA from multiple samples. No amplification was observed for nontarget species. This study presents a novel approach for identifying authentic Mantidis Ootheca species using DNA-based diagnostic marker assays, which enable rapid and precise species identification. The SCAR assays developed in this study will aid in maintaining quality control and promoting the standardization of commercial Mantidis Ootheca products.},
}
@article {pmid39337663,
year = {2024},
author = {Sikora, J and Celiński, K},
title = {Exploring Taxonomic and Genetic Relationships in the Pinus mugo Complex Using Genome Skimming Data.},
journal = {International journal of molecular sciences},
volume = {25},
number = {18},
pages = {},
pmid = {39337663},
issn = {1422-0067},
support = {"Diamond Grant" program No. DI2017003147//Ministry of Science and Higher Education of the Republic of Poland./ ; },
mesh = {*Pinus/genetics/classification ; *Phylogeny ; *Genome, Plant ; *Genetic Variation ; DNA Barcoding, Taxonomic/methods ; Haplotypes/genetics ; Genomics/methods ; },
abstract = {Genome skimming is a novel approach that enables obtaining large-scale genomic information based on high-copy DNA fractions from shallow whole-genome sequencing. The simplicity of this method, low analysis costs, and large amounts of generated data have made it widely used in plant research, including species identification, especially in the case of protected or endangered taxa. This task is particularly difficult in the case of closely related taxa. The Pinus mugo complex includes several dozen closely related taxa occurring in the most important mountain ranges in Europe. The taxonomic rank, origin, or distribution of many of these taxa have been debated for years. In this study, we used genome skimming and multilocus DNA barcoding approaches to obtain different sequence data sets and also to determine their genetic diversity and suitability for distinguishing closely related taxa in the Pinus mugo complex. We generated seven different data sets, which were then analyzed using three discrimination methods, i.e., tree based, distance based, and assembling species by automatic partitioning. Genetic diversity among populations and taxa was also investigated using haplotype network analysis and principal coordinate analysis. The proposed data set based on divergence hotspots is even twenty-times more variable than the other analyzed sets and improves the phylogenetic resolution of the Pinus mugo complex. In light of the obtained results, Pinus × rhaetica does not belong to the Pinus mugo complex and should not be identified with either Pinus uliginosa or Pinus rotundata. It seems to represent a fixed hybrid or introgressant between Pinus sylvestris and Pinus mugo. In turn, Pinus mugo and Pinus uncinata apparently played an important role in the origins of Pinus uliginosa and Pinus rotundata.},
}
@article {pmid39336651,
year = {2024},
author = {Pramatarova, M and Burckhardt, D and Malenovský, I and Gjonov, I and Schuler, H and Štarhová Serbina, L},
title = {Unravelling the Molecular Identity of Bulgarian Jumping Plant Lice of the Family Aphalaridae (Hemiptera: Psylloidea).},
journal = {Insects},
volume = {15},
number = {9},
pages = {},
pmid = {39336651},
issn = {2075-4450},
support = {80-10-5/2024//Scientific Research Fund of SU "St. Kliment Ohridski", FWF Austrian Science Fund, Province of Bolzano-Bozen/ ; },
abstract = {Psyllids (Hemiptera: Psylloidea) are plant sap-sucking insects whose identification is often difficult for non-experts. Despite the rapid development of DNA barcoding techniques and their widespread use, only a limited number of sequences of psyllids are available in the public databases, and those that are available are often misidentified. Here, we provide 80 sequences of two mitochondrial genes, cytochrome c oxidase I (COI) and cytochrome b (Cytb), for 25 species of Aphalaridae, mainly from Bulgaria. The DNA barcodes for 15 of these species are published for the first time. In cases where standard primers failed to amplify the target gene fragment, we designed new primers that can be used in future studies. The distance-based thresholds for the analysed species were between 0.0015 and 0.3415 for COI and 0.0771 and 0.4721 for Cytb, indicating that the Cytb gene has a higher interspecific divergence, compared to COI, and therefore allows for more accurate species identification. The species delimitation based on DNA barcodes is largely consistent with the differences resulting from morphological and host plant data, demonstrating that the use of DNA barcodes is suitable for successful identification of most aphalarid species studied. The phylogenetic reconstruction based on maximum likelihood and Bayesian inference analyses, while showing similar results at high taxonomic levels to previously published phylogenies, provides additional information on the placement of aphalarids at the species level. The following five species represent new records for Bulgaria: Agonoscena targionii, Aphalara affinis, Colposcenia aliena, Co. bidentata, and Craspedolepta malachitica. Craspedolepta conspersa is reported for the first time from the Czech Republic, while Agonoscena cisti is reported for the first time from Albania.},
}
@article {pmid39336619,
year = {2024},
author = {Costa, MM and Corbel, V and Ben Hamouda, R and Almeras, L},
title = {MALDI-TOF MS Profiling and Its Contribution to Mosquito-Borne Diseases: A Systematic Review.},
journal = {Insects},
volume = {15},
number = {9},
pages = {},
pmid = {39336619},
issn = {2075-4450},
support = {Grant no PDH-2-NBC 2-B-2201//Direction G&#xe9;n&#xe9;rale de l'Armement/ ; },
abstract = {Mosquito-borne diseases are responsible for hundreds of thousands of deaths per year. The identification and control of the vectors that transmit pathogens to humans are crucial for disease prevention and management. Currently, morphological classification and molecular analyses via DNA barcoding are the standard methods used for vector identification. However, these approaches have several limitations. In the last decade, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) profiling has emerged as an innovative technology in biological sciences and is now considered as a relevant tool for the identification of pathogens and arthropods. Beyond species identification, this tool is also valuable for determining various life traits of arthropod vectors. The purpose of the present systematic review was to highlight the contribution of MALDI-TOF MS to the surveillance and control of mosquito-borne diseases. Published articles from January 2003 to August 2024 were retrieved, focusing on different aspects of mosquito life traits that could be determinants in disease transmission and vector management. The screening of the scientific literature resulted in the selection of 54 published articles that assessed MALDI-TOF MS profiling to study various mosquito biological factors, such species identification, life expectancy, gender, trophic preferences, microbiota, and insecticide resistance. Although a large majority of the selected articles focused on species identification, the present review shows that MALDI-TOF MS profiling is promising for rapidly identifying various mosquito life traits, with high-throughput capacity, reliability, and low cost. The strengths and weaknesses of this proteomic tool for vector control and surveillance are discussed.},
}
@article {pmid39336609,
year = {2024},
author = {Stonis, JR and Remeikis, A and Diškus, A and Dobrynina, V and Orlovskytė, S},
title = {A Phenomenon: What Are the Minuscule Grey Moths Abundant in the Dry Season in the Tropical Dry Forests of the Pacific Coast of Honduras?.},
journal = {Insects},
volume = {15},
number = {9},
pages = {},
pmid = {39336609},
issn = {2075-4450},
abstract = {Our investigation centered on the tropical dry forests along the Pacific coast of Honduras, aiming to elucidate the presence and abundance of minuscule grey moths during the dry season. Through specimen dissections and the taxonomic identification of the collected material, we have described three new species: Acalyptris podenasi sp. nov., A. palpiformis sp. nov., and A. tortoris sp. nov. Additionally, we documented two species previously known from neighboring countries, A. lascuevella Puplesis &amp; Robinson and A. basicornis Remeikis &amp; Stonis. The females of A. lascuevella were previously unknown and are documented here for the first time. Morphological examinations were complemented by DNA barcoding, particularly highlighting variation in A. lascuevella. The paper's primary significance lies not only in the description of new species but also in uncovering their taxonomic, morphological, and molecular importance. We found that these species are unique and indicative of the previously unstudied dry forests as a distinct ecosystem. Our findings revealed several novel atypical morphological traits within the studied Nepticulidae, including unusually large signum cells in the female genitalia, a dorso-ventrally divided uncus, and asymmetrical valvae in the male genitalia. These discoveries underscore the morphological diversity of Acalyptris Meyrick and their significance in evolutionary biology. Consequently, the paper addresses a previously unknown phenomenon of the occurrence and astonishing abundance of minuscule plant-mining micromoths in dry deciduous forests during the peak of the dry season. We hope that this paper will encourage Lepidoptera taxonomists to explore micromoths in other tropical dry forests, which, while limited in distribution, hold global importance. The paper is extensively illustrated with photographs of Acalyptris adults and their genitalia, along with maps, habitats, and molecular phylogenetic trees.},
}
@article {pmid39335263,
year = {2024},
author = {Poonlaphdecha, S and Ribas, A and Chaisiri, K and Morand, S and Chan, AHE and Thaenkham, U},
title = {Genetic Characterization of the Co-Invasive Rodent Parasite Heterakis spumosa (Nematoda, Heterakidae).},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {18},
pages = {},
pmid = {39335263},
issn = {2076-2615},
support = {ANR BiodivHealthSEA , ANR-17-CE35-0003-02//Agence nationale de la recherche/ ; },
abstract = {Heterakis spumosa, a parasitic worm infecting rodents, is globally prevalent in black rats, brown rats, and house mice. It is hypothesized to originate from Asia due to its widespread presence in Southeast Asia in various Murinae. Previous molecular studies focused on European, African, and Japanese specimens, but none included samples from the putative native range. Rodents were collected between 2008 and 2015 across various localities in Southeast Asia and Europe, identified by morphology or genetic barcoding. Viscera were examined or preserved for later inspection. DNA was extracted from H. spumosa. PCR amplification targeting the mtCOI gene and ITS1 region was conducted in this study using newly designed primers (based on Heterakis reference sequences). PCR amplicons were subsequently sequenced and analyzed. In this study, the phylogenetic analysis using ITS1 sequences revealed that Heterakis samples from Thai and Laotian rodents belong to the species H. spumosa, exhibiting low genetic variation compared to samples from other regions. Genetic distance calculations using mtCOI sequences confirmed the marked distinction of H. spumosa from other Heterakis species. Our phylogenetic analyses using partial mtCOI and ITS1 sequences have significantly enhanced our comprehension of the genetic diversity and evolutionary history of the nematode H. spumosa.},
}
@article {pmid39334308,
year = {2024},
author = {Hartop, E and Lee, L and Srivathsan, A and Jones, M and Peña-Aguilera, P and Ovaskainen, O and Roslin, T and Meier, R},
title = {Resolving biology's dark matter: species richness, spatiotemporal distribution, and community composition of a dark taxon.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {215},
pmid = {39334308},
issn = {1741-7007},
support = {2016-203 4.3//Swedish Taxonomy Initiative/ ; ERC-synergy grant 856506-LIFEPLAN//H2020 European Research Council/ ; ERC-synergy grant 856506-LIFEPLAN//H2020 European Research Council/ ; 336212 and 345110//Academy of Finland/ ; },
mesh = {Animals ; *Diptera/physiology/genetics ; *Biodiversity ; Sweden ; *DNA Barcoding, Taxonomic ; Seasons ; Climate Change ; Animal Distribution ; },
abstract = {BACKGROUND: Zoology's dark matter comprises hyperdiverse, poorly known taxa that are numerically dominant but largely unstudied, even in temperate regions where charismatic taxa are well understood. Dark taxa are everywhere, but high diversity, abundance, and small size have historically stymied their study. We demonstrate how entomological dark matter can be elucidated using high-throughput DNA barcoding ("megabarcoding"). We reveal the high abundance and diversity of scuttle flies (Diptera: Phoridae) in Sweden using 31,800 specimens from 37 sites across four seasonal periods. We investigate the number of scuttle fly species in Sweden and the environmental factors driving community changes across time and space.<br><br>RESULTS: Swedish scuttle fly diversity is much higher than previously known, with 549 putative specie) detected, compared to 374 previously recorded species. Hierarchical Modelling of Species Communities reveals that scuttle fly communities are highly structured by latitude and strongly driven by climatic factors. Large dissimilarities between sites and seasons are driven by turnover rather than nestedness. Climate change is predicted to significantly affect the 47% of species that show significant responses to mean annual temperature. Results were robust regardless of&#xa0;whether haplotype diversity or species-proxies were used&#xa0;as response variables. Additionally, species-level models of common taxa adequately predict overall species richness.<br><br>CONCLUSIONS: Understanding the bulk of the diversity around us is imperative during an era of biodiversity change. We show that dark insect taxa can be efficiently characterised and surveyed with megabarcoding. Undersampling of rare taxa and choice of operational taxonomic units do not alter the main ecological inferences, making it an opportune time to tackle zoology's dark matter.},
}
@article {pmid39333158,
year = {2024},
author = {Yuan, L and Chen, X and Zhan, H and Henry, GL and Zador, AM},
title = {Massive multiplexing of spatially resolved single neuron projections with axonal BARseq.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8371},
pmid = {39333158},
issn = {2041-1723},
support = {RF1MH123403//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; RF1 MH123403/MH/NIMH NIH HHS/United States ; U19NS123716//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U19 NS123716/NS/NINDS NIH HHS/United States ; D16PC0008//ODNI | Intelligence Advanced Research Projects Activity (IARPA)/ ; },
mesh = {Animals ; *Axons/metabolism ; *Neurons/cytology ; Mice ; Male ; *Auditory Cortex/cytology/physiology ; Single-Cell Analysis/methods ; Sequence Analysis, RNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Mice, Inbred C57BL ; },
abstract = {Neurons in the cortex are heterogeneous, sending diverse axonal projections to multiple brain regions. Unraveling the logic of these projections requires single-neuron resolution. Although a growing number of techniques have enabled high-throughput reconstruction, these techniques are typically limited to dozens or at most hundreds of neurons per brain, requiring that statistical analyses combine data from different specimens. Here we present axonal BARseq, a high-throughput approach based on reading out nucleic acid barcodes using in situ RNA sequencing, which enables analysis of even densely labeled neurons. As a proof of principle, we have mapped the long-range projections of >8000 primary auditory cortex neurons from a single male mouse. We identified major cell types based on projection targets and axonal trajectory. The large sample size enabled us to systematically quantify the projections of intratelencephalic (IT) neurons, and revealed that individual IT neurons project to different layers in an area-dependent fashion. Axonal BARseq is a powerful technique for studying the heterogeneity of single neuronal projections at high throughput within individual brains.},
}
@article {pmid39333091,
year = {2024},
author = {O'Neill, MJ and Yang, T and Laudeman, J and Calandranis, ME and Harvey, ML and Solus, JF and Roden, DM and Glazer, AM},
title = {ParSE-seq: a calibrated multiplexed assay to facilitate the clinical classification of putative splice-altering variants.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8320},
pmid = {39333091},
issn = {2041-1723},
support = {R35 GM150465/GM/NIGMS NIH HHS/United States ; P30 DK058404/DK/NIDDK NIH HHS/United States ; F30 HL163923/HL/NHLBI NIH HHS/United States ; T32 GM007347/GM/NIGMS NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; R01 HL164675/HL/NHLBI NIH HHS/United States ; R00 HG010904/HG/NHGRI NIH HHS/United States ; S10 OD025281/OD/NIH HHS/United States ; R01 HL149826/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Induced Pluripotent Stem Cells/metabolism ; *Myocytes, Cardiac/metabolism/cytology ; *RNA Splicing/genetics ; *NAV1.5 Voltage-Gated Sodium Channel/genetics/metabolism ; Arrhythmias, Cardiac/genetics ; RNA Splice Sites/genetics ; CRISPR-Cas Systems/genetics ; Calibration ; High-Throughput Nucleotide Sequencing/methods ; Genetic Variation ; Introns/genetics ; HEK293 Cells ; },
abstract = {Interpreting the clinical significance of putative splice-altering variants outside canonical splice sites remains difficult without time-intensive experimental studies. To address this, we introduce Parallel Splice Effect Sequencing (ParSE-seq), a multiplexed assay to quantify variant effects on RNA splicing. We first apply this technique to study hundreds of variants in the arrhythmia-associated gene SCN5A. Variants are studied in 'minigene' plasmids with molecular barcodes to allow pooled variant effect quantification. We perform experiments in two cell types, including disease-relevant induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). The assay strongly separates known control variants from ClinVar, enabling quantitative calibration of the ParSE-seq assay. Using these evidence strengths and experimental data, we reclassify 29 of 34 variants with conflicting interpretations and 11 of 42 variants of uncertain significance. In addition to intronic variants, we show that many synonymous and missense variants disrupted RNA splicing. Two splice-altering variants in the assay also disrupt splicing and sodium current when introduced into iPSC-CMs by CRISPR-Cas9 editing. ParSE-seq provides high-throughput experimental data for RNA-splicing to support precision medicine efforts and can be readily adopted to study other loss-of-function genotype-phenotype relationships.},
}
@article {pmid39332616,
year = {2025},
author = {Lone, S and Narayan, S and Hussain, K and Malik, M and Yadav, SK and Khan, FA and Safa, A and Ahmad, A and Masoodi, KZ},
title = {Investigating the antioxidant and anticancer potential of Daucus spp. extracts against human prostate cancer cell line C4-2, and lung cancer cell line A549.},
journal = {Journal of ethnopharmacology},
volume = {337},
number = {Pt 2},
pages = {118855},
doi = {10.1016/j.jep.2024.118855},
pmid = {39332616},
issn = {1872-7573},
mesh = {Humans ; *Antioxidants/pharmacology/isolation &amp; purification ; *Plant Extracts/pharmacology/chemistry ; Male ; *Daucus carota/chemistry ; *Prostatic Neoplasms/drug therapy ; *Lung Neoplasms/drug therapy ; *Antineoplastic Agents, Phytogenic/pharmacology/isolation &amp; purification ; A549 Cells ; Cell Line, Tumor ; Cell Proliferation/drug effects ; },
abstract = {The study evaluated 297 carrot germplasm lines, focusing on 52 cultivars to explore their therapeutic potential and address challenges related to the accessibility and affordability of nutraceuticals and health promoting foods. The investigation explores the application of DNA barcoding using the ITS region for precise species identification, highlighting genetic diversity among the examined cultivars. Through ITS sequence-based analysis and phylogenetic examination, six diverse Daucus spp. genotypes were differentiated and classified into distinct groups, indicating the presence of vast genetic variation. Evaluation of antioxidant activities using the DPPH radical scavenging assay revealed varying degrees of scavenging ability among genotypes with SKAU-C-15, SKAU-C-17, and SKAU-C-16 exhibiting the highest activity, suggesting their potential for antioxidant-rich products. Thin Layer Chromatography (TLC) bioautography confirmed the presence of bioactive compounds in carrot extracts responsible for their antioxidant properties. In cell culture studies, specific carrot genotype extracts demonstrated potential anti-proliferative and anti-invasive effects on recurrent prostate cancer cell line - C4-2 (SKAU-C-30, SKAU-C-10, and SKAU-C-42) and non-small cell lung cancer cell line - A549 (SKAU-C-18 and SKAU-C-11) cancer cells, as indicated by MTT assay, wound healing assay, and Colony Forming Unit assay. These findings suggest the promising therapeutic potential of carrot genotypes for developing anti-cancer functional foods, nutraceuticals and health supplements.Therefore, the study contributes to the nutrition security, paving the way for advancements in functional foods and health applications, particularly in cancer treatment and prevention.},
}
@article {pmid39331360,
year = {2024},
author = {Foote, NE and Foote, GG and Comai, N and Ibarra Caballero, JR and Stewart, JE and Ambrose, AR and Baxter, WL and Davis, TS},
title = {Patterns of occurrence, phenology, and phylogeny of Phloeosinus punctatus LeConte (Coleoptera: Curculionidae, Scolytinae) in giant sequoia.},
journal = {Environmental entomology},
volume = {53},
number = {6},
pages = {1183-1196},
pmid = {39331360},
issn = {1938-2936},
support = {//Save the Redwoods League/ ; //National Park Service/ ; P21AC12281//Colorado Plateau Cooperative Ecosystem Studies Unit, Northern Arizona University/ ; },
mesh = {Animals ; *Phylogeny ; *Weevils/genetics/physiology ; Male ; Female ; Reproduction ; Flight, Animal ; },
abstract = {Here, we describe patterns of reproduction and flight phenology of putative Phloeosinus punctatus in giant sequoia groves and compare morphology and genotypes of beetles from sympatric giant sequoia (Sequoiadendron giganteum) and California incense-cedar (Calocedrus decurrens). Surveys conducted in 2022 revealed that numerous branches fall from giant sequoia crowns (on average ~30 branches/tree), with 20%-50% of trees per site shedding branches, depositing breeding material for beetles on the forest floor that subsequently becomes colonized. When noninfested branches cut from mature giant sequoias were placed at the ground surface, they were colonized by P. punctatus and produced an average of 28 beetles/kg branch. Climbing and examination of sequoia crowns in 2023 showed that 75% of mature trees across 11 groves showed evidence of adult beetle entrance holes in their crowns. In 2021, tests with sticky traps showed that beetles alighted on fallen branches from 20th May to 20th August (peak landing: 2nd July); a logistic model developed from emergence data in 2021 and 2022 predicts the emergence of F1 offspring from branches between 10th July and 1st September (peak emergence: 8th August). Beetles emerging from giant sequoia preferred to settle on giant sequoia, did not reproduce in incense-cedar, and diverged morphologically from beetles emerging from incense-cedar. However, phylogenetic analysis of three genes (28S, CAD, and COI) revealed no clear pattern of sequence divergence, suggesting a single species (P. punctatus) that colonizes both hosts, though cryptic speciation may not be detectable with standard barcoding genes. Ecological and potential management implications are discussed.},
}
@article {pmid39329134,
year = {2024},
author = {Andriienko, V and Buczek, M and Meier, R and Srivathsan, A and Łukasik, P and Kolasa, MR},
title = {Implementing high-throughput insect barcoding in microbiome studies: impact of non-destructive DNA extraction on microbiome reconstruction.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e18025},
pmid = {39329134},
issn = {2167-8359},
support = {R35 GM124701/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Microbiota/genetics ; *Insecta/microbiology/genetics ; *RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Bacteria/genetics/isolation &amp; purification/classification ; Polymerase Chain Reaction/methods ; Biodiversity ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {BACKGROUND: Symbiotic relationships with diverse microorganisms are crucial for many aspects of insect biology. However, while our understanding of insect taxonomic diversity and the distribution of insect species in natural communities is limited, we know much less about their microbiota. In the era of rapid biodiversity declines, as researchers increasingly turn towards DNA-based monitoring, developing and broadly implementing approaches for high-throughput and cost-effective characterization of both insect and insect-associated microbial diversity is essential. We need to verify whether approaches such as high-throughput barcoding, a powerful tool for identifying wild insects, would permit subsequent microbiota reconstruction in these specimens.<br><br>METHODS: High-throughput barcoding ("megabarcoding") methods often rely on non-destructive approaches for obtaining template DNA for PCR amplification by leaching DNA out of insect specimens using alkaline buffers such as HotSHOT. This study investigated the impact of HotSHOT on microbial abundance estimates and the reconstructed bacterial community profiles. We addressed this question by comparing quantitative 16S rRNA amplicon sequencing data for HotSHOT-treated or untreated specimens of 16 insect species representing six orders and selected based on the expectation of limited variation among individuals.<br><br>RESULTS: We find that in 13 species, the treatment significantly reduced microbial abundance estimates, corresponding to an estimated 15-fold decrease in amplifiable 16S rRNA template on average. On the other hand, HotSHOT pre-treatment had a limited effect on microbial community composition. The reconstructed presence of abundant bacteria with known significant effects was not affected. On the other hand, we observed changes in the presence of low-abundance microbes, those close to the reliable detection threshold. Alpha and beta diversity analyses showed compositional differences in only a few species.<br><br>CONCLUSION: Our results indicate that HotSHOT pre-treated specimens remain suitable for microbial community composition reconstruction, even if abundance may be hard to estimate. These results indicate that we can cost-effectively combine barcoding with the study of microbiota across wild insect communities. Thus, the voucher specimens obtained using megabarcoding studies targeted at characterizing insect communities can be used for microbiome characterizations. This can substantially aid in speeding up the accumulation of knowledge on the microbiomes of abundant and hyperdiverse insect species.},
}
@article {pmid39329133,
year = {2024},
author = {Morris, MRJ and Summers, MM and Kwan, M and Mee, JA and Rogers, SM},
title = {Mislabeled and ambiguous market names in invertebrate and finfish seafood conceal species of conservation concern in Calgary, Alberta, Canada.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e18113},
pmid = {39329133},
issn = {2167-8359},
mesh = {Animals ; Alberta ; *Seafood/analysis ; *DNA Barcoding, Taxonomic ; Food Labeling/legislation &amp; jurisprudence ; Invertebrates/classification ; Conservation of Natural Resources ; Fishes/genetics ; Endangered Species ; },
abstract = {BACKGROUND: The mislabeling of seafood, wherein a food product's marketed name does not match its contents, has the potential to mask species of conservation concern. Less discussed is the role of legally ambiguous market names, wherein a single name could be used to sell multiple species. Here we report the first study in Canada to examine mislabeling and ambiguous market names in both invertebrate (e.g., bivalve, cephalopod, shrimp) and finfish products.<br><br>METHODS: A total of 109 invertebrate and 347 finfish products were sampled in Calgary between 2014 and 2020. Market names were documented from the label or equivalent and determined to be precise (the name could apply to only one species) or ambiguous (multiple species could be sold under that name). A region of the cytochrome c oxidase I gene was sequenced and compared to reference sequences from boldsystems.org. Samples were considered mislabeled if the species identified through DNA barcoding did not correspond to the market name, as determined through the Canadian Food Inspection Agency Fish List. Mislabeling was further differentiated between semantic mislabeling, wherein the market name was not found on the Fish List but the barcode identity was in line with what a consumer could reasonably have expected to have purchased; invalid market names, wherein the market name was so unusual that no legitimate inferences as to the product's identity could be made; and product substitution, wherein the DNA barcode identified the product as a species distinct from that associated with the market name. Invalid market names and product substitutions were used to provide conservative estimates of mislabeling. The global conservation status of the DNA-identified invertebrate or finfish was determined through the International Union for the Conservation of Nature Red List. A logistic regression was used to determine the relationship between precision and accuracy in predicting conservation status of the sampled species.<br><br>RESULTS: There was no significant difference in mislabeling occurrence between invertebrates (33.9% total mislabeling occurrence, 20.2% product substitution) and finfish (32.3% total mislabeling occurrence, 21.3% product substitution/invalid market names). Product substitutions sometimes involved species of conservation concern, such as foods marketed as freshwater eel (Anguilla rostrata) that were determined through DNA barcoding to be European eel (Anguilla anguilla), or cuttlefish balls putatively identified as the Endangered threadfin porgy (Evynnis cardinalis). Product substitutions and ambiguous market names were significantly associated with the sale of species of conservation concern, but ambiguity was a more important predictor. Although preventing the mislabeling of seafoods can and must remain a priority in Canada, our work suggests that moving towards precise names for all seafood products will better support sustainable fisheries goals.},
}
@article {pmid39326961,
year = {2024},
author = {Khumalo, N and Ledwaba, MB and Labuschagne, K and Voster, I and Oosthuizen, M and Mwale, M and Chaisi, M},
title = {Identification of ticks and tick-borne pathogens of wildlife necropsy cases submitted to the SANBI National Zoological Gardens, South Africa.},
journal = {Veterinary parasitology, regional studies and reports},
volume = {55},
number = {},
pages = {101105},
doi = {10.1016/j.vprsr.2024.101105},
pmid = {39326961},
issn = {2405-9390},
mesh = {Animals ; South Africa/epidemiology ; *Animals, Wild/parasitology ; *Tick Infestations/veterinary/parasitology/epidemiology ; *Tick-Borne Diseases/veterinary/parasitology/epidemiology/microbiology ; *RNA, Ribosomal, 16S/analysis ; *Ticks/parasitology/microbiology ; Phylogeny ; Female ; DNA Barcoding, Taxonomic/veterinary ; Animals, Zoo/parasitology ; },
abstract = {Ticks are arachnid blood-feeding parasites, which infest livestock, wildlife, and humans, transmitting medically and veterinary significant pathogens. Their biodiversity and distribution in wild animals remains complex. This study analysed archived tick samples (n = 48) from the South African Biodiversity Institute (SANBI) Wildlife Biobank utilizing morphology and genetic analyses of the 16S rRNA and COI (DNA barcoding) mitochondrial genes to identify ticks collected among 13 vertebratesavian, reptilian, and mammalian host species. The specimens came from nine localities including nature reserves and captive facilities (zoological garden) in South Africa, Namibia, and Botswana. These ticks were also assessed for associated pathogens with the reverse line blot (RLB) hybridization assay. Seven tick genera, Amblyomma, Hyalomma, Haemaphysalis, Ixodes, Rhipicephalus, Rhipicentor, and Otobius were identified, with Amblyomma being the most prevalent (22.9 %) in our sample set. Obtained sequences were 95-100 % similar to published records of tick species collected from wild and domestic animals, as well as those collected from vegetation, from different southern African areas. However, tick specimens (n = 3) identified morphologically as Hyalomma truncatum, Rhipicephalus e. evertsi, and R. simus, were, on a molecularly level, more closely related to their sister taxa (H. glabrum, R. e. mimeticus, and R. gertrudae, respectively) suggesting a need for taxonomic verification. With the RLB hybridization assay, six samples reacted with the Ehrlichia/Anaplasma genus-specific probe, while two reacted with the Theileria/Babesia genus-specific probe. Sequencing of the RLB amplicons targeting the 18S rRNA gene (n = 2) indicated 100 % similarity to Hepatozoon fitzsimonsi, while one was closely related to He. ingwe with 99.39 % similarity. The results show that wildlife harbour different tick species, and pathogen detection identified novel genotypes, indicating wildlife as potential pathogens reservoirs. This study enhances our understanding of tick biodiversity, distribution and highlights wildlife's role in harbouring diverse tick species and novel pathogens.},
}
@article {pmid39326113,
year = {2025},
author = {Zhao, R and Niu, Q and Murtaza, G and Zhang, G and Yang, Y},
title = {Integrated identification and detection of hydration state and its evolution using terahertz technology.},
journal = {Talanta},
volume = {281},
number = {},
pages = {126943},
doi = {10.1016/j.talanta.2024.126943},
pmid = {39326113},
issn = {1873-3573},
abstract = {The accurate detection of dehydration processes in hydrated drugs can reveal various intermolecular vibration modes mediated by hydrogen bonds between water molecules and other components, which underpin the further development of pharmaceutical science, food safety and biophysics. Herein, terahertz (THz) technology is utilized to investigate the dehydration state of d(+)-Raffinose pentahydrate (Rf·5H2O), in conjunction with imaging-based point by point scanning data acquisition and barcodes methods, to establish an innovative platform integrated identification, trace detection, and application capabilities. Our study demonstrates that the dehydration process of Rf·5H2O can be dynamically monitored through the evolution of its THz absorption peaks, offering more precise results compared to XRD and Raman spectroscopies. Moreover, the absorbance spectra data collected at each individual pixel is utilized to build visualized THz images, achieving an ultralow minimum content required for detection of 0.032 μg/(50 μm)[2]. Additionally, we introduce a THz spectra-barcode conversion system that not only ensures efficient electronic recordkeeping but also enhances user readability, thereby facilitating the practical applications of THz technology.},
}
@article {pmid39323091,
year = {2024},
author = {Zhang, Y and Shen, C and Xia, K},
title = {Multi-Cover Persistence (MCP)-based machine learning for polymer property prediction.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {6},
pages = {},
pmid = {39323091},
issn = {1477-4054},
support = {//Nanyang Technological University SPMS Collaborative Research Award 2022/ ; MOE-T2EP20220-0010//Singapore Ministry of Education Academic Research/ ; },
mesh = {*Polymers/chemistry ; *Machine Learning ; Algorithms ; },
abstract = {Accurate and efficient prediction of polymers properties is crucial for polymer design. Recently, data-driven artificial intelligence (AI) models have demonstrated great promise in polymers property analysis. Even with the great progresses, a pivotal challenge in all the AI-driven models remains to be the effective representation of molecules. Here we introduce Multi-Cover Persistence (MCP)-based molecular representation and featurization for the first time. Our MCP-based polymer descriptors are combined with machine learning models, in particular, Gradient Boosting Tree (GBT) models, for polymers property prediction. Different from all previous molecular representation, polymer molecular structure and interactions are represented as MCP, which utilizes Delaunay slices at different dimensions and Rhomboid tiling to characterize the complicated geometric and topological information within the data. Statistic features from the generated persistent barcodes are used as polymer descriptors, and further combined with GBT model. Our model has been extensively validated on polymer benchmark datasets. It has been found that our models can outperform traditional fingerprint-based models and has similar accuracy with geometric deep learning models. In particular, our model tends to be more effective on large-sized monomer structures, demonstrating the great potential of MCP in characterizing more complicated polymer data. This work underscores the potential of MCP in polymer informatics, presenting a novel perspective on molecular representation and its application in polymer science.},
}
@article {pmid39322294,
year = {2024},
author = {Wang, D and He, Z and Yang, C and Lu, D and Sun, Y and Kou, Y and Qian, D and Zhang, H and Liu, Y},
title = {[Genetic polymorphisms of common sandflies in selected areas of Henan Province based on DNA barcoding].},
journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control},
volume = {36},
number = {4},
pages = {352-360},
doi = {10.16250/j.32.1374.2024036},
pmid = {39322294},
issn = {1005-6661},
support = {222102310722//Henan Provincial Science and Technology Research Project/ ; LHGJ20220171//Henan Provincial Medical Science and Technology Research Project/ ; LHGJ20230640//Henan Provincial Medical Science and Technology Research Project/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Polymorphism, Genetic ; China ; *Phylogeny ; *Psychodidae/genetics/classification ; *Electron Transport Complex IV/genetics ; },
abstract = {OBJECTIVE: To characterize the species of common sandflies in Henan Province using DNA barcoding with cytochrome c oxidase subunit I (COI) gene as the molecular marker, and to analyze the genetic polymorphisms of sandflies, so as to provide insights into visceral leishmaniasis prevention and control in Henan Province.<br><br>METHODS: Sandfly specimens were sampled from 13 sandflies surveillance sites from 2021 to 2023 in Anyang City, Zhengzhou, Luoyang and Xuchang cities (Zhengzhou-Luoyang-Xuchang areas) where visceral leishmaniasis cases were reported and in Jiaozuo and Xinxiang cities (Jiaozuo-Xinxiang areas) without visceral leishmaniasis cases reported. Genomic DNA was extracted from a single sandfly, and COI gene was amplified. The amplification product was subjected to bidirectional sequencing. Following sequence assembly, the species of sandflies was characterized through sequence alignment using the BLAST tool. The intra-specific and inter-specific genetic distances of sandflies were estimated among different areas using the software Mega 11, and phylogenetic trees were created. The polymorphisms of nucleotide sequences in the sandflies COI gene were estimated using the software DnaSP. The fixation index (FST) of different geographical isolates of sandflies was calculated using the Arlequin software, and the gene flow value (Nm) was used to measure the gene flow in the sandflies populations. In addition, the population genetic structure of different geographical populations of Phlebotomus chinensis was analyzed using the STRUCTURE software.<br><br>RESULTS: A total of 978 sandflies were collected from 13 sandflies surveillance sites in Zhengzhou-Luoyang-Xuchang areas, Jiaozuo-Xinxiang areas and Anyang City of Henan Province from 2021 to 2023, and 475 sandflies were randomly sampled for subsequent detections. A total of 304 Ph. chinensis, 162 Se. squamirostris and 9 Se. bailyi were identified based on molecular biological detection of the COI gene, and Se. bailyi was reported for the first time in Henan Province. The intraspecific genetic distances of sandflies were 0.000 to 0.040, and the inter-specific genetic distances ranged from 0.133 to 0.161. Phylogenetic analysis revealed that each of the three sandfly species was clustered into a clade. The genetic polymorphisms of Ph. chinensis populations varied among different areas, with the highest haplotype diversity (0.966 &#xb1; 0.007) and the greatest nucleotide diversity (0.011) in Zhengzhou-Luoyang-Xuchang areas, and the lowest haplotype diversity (0.720 &#xb1; 0.091) and nucleotide diversity (0.004) in Anyang City. The dominant haplotype of Ph. chinensis populations was Pch_Hap_2 in Anyang City and Jiaozuo-Xinxiang areas, with moderate genetic differentiation (0.05 < FST < 0.15) and frequent gene exchange (Nm value > 1) between Ph. chinensis populations sampled from Anyang City, and Jiaozuo-Xinxiang areas. Population genetic structure analysis showed that the dominant component of Ph. chinensis populations was K5 in Anyang City and Jiaozuo-Xinxiang areas. No obvious dominant haplotype was observed in Ph. chinensis populations sampled from Zhengzhou-Luoyang-Xuchang areas, which had very high genetic differentiation (FST > 0.25) and little gene exchange (Nm value < 1) with Ph. chinensis populations from Anyang City, and Jiaozuo-Xinxiang areas, with K3 as the dominant component. In addition, there was no significant difference in the genetic polymorphism level among Se. squamirostris populations from the three areas.<br><br>CONCLUSIONS: There are Ph. chinensis, Se. squamirostris and Se. bailyi in Henan Province, and S. bailyi is recorded for the first time in Henan Province by molecular biological assays. There are different levels of genetic differentiation and gene exchange among P. chinensis populations in different areas of Henan Province.},
}
@article {pmid39318677,
year = {2024},
author = {Kaila, L and Huemer, P},
title = {Elachistadimicatella sensu auctt.-a complex of neglected species diversity (Lepidoptera, Elachistidae) from European mountain systems.},
journal = {ZooKeys},
volume = {1212},
number = {},
pages = {179-194},
pmid = {39318677},
issn = {1313-2989},
abstract = {Elachistadimicatella Rebel, 1903, has so far been considered a species in Europe with restricted distribution from Ukraine to western France. The species occurs on mountainous regions. However, the in-depth analysis of a taxonomically uncertain species of Elachista from the Cottian Alps (Italy), especially through DNA barcoding and subsequent morphological studies, led to the realization that individuals previously identified as E.dimicatella from the Cottian Alps and the Pyrenees were misidentified. According to our research, a total of three species can be differentiated: E.dimicatella from Carpathians and its former junior synonym E.niphadophanes Meyrick, 1937, sp. rev., from the Pyrenees, as well as the newly described E.cottiella sp. nov. from southwestern Alps, hitherto incorrectly identified as E.dimicatella. Diagnostic features of the three species are discussed and illustrated. Elachistadimicatella and E.niphadophanes are redescribed.},
}
@article {pmid39318675,
year = {2024},
author = {Dettner, K and Kovács, Z and Rewicz, T and Csabai, Z},
title = {Age-dependent variation of aedeagal morphology in Agabusuliginosus and the status of A.lotti (Coleoptera, Dytiscidae).},
journal = {ZooKeys},
volume = {1212},
number = {},
pages = {153-177},
pmid = {39318675},
issn = {1313-2989},
abstract = {A doubt has arisen about the taxonomic status of Agabuslotti within the Agabusuliginosus species group due to morphological similarities and lack of molecular data. In this study, a comprehensive morphological and molecular analysis of specimens from Central Europe was conducted, focusing on the Hungarian population. Morphological comparisons of genital structures revealed age-dependent variations, suggesting a gradual transition from A.lotti to A.uliginosus. Molecular analysis of COI sequences further supported this hypothesis, showing minimal genetic differences among most specimens, with only one individual exhibiting distinctiveness. Therefore, A.lotti syn. nov. must be regarded as a junior synonym of A.uliginosus. Our findings also highlight the need for additional multi-marker studies covering a broader geographic range and including both molecular and morphological approaches to elucidate the taxonomic and phylogenetic relationships within this species group. The inclusion of Hungarian samples notably enriched the diversity of haplotypes, emphasizing the importance of expanding sampling efforts in future research.},
}
@article {pmid39318674,
year = {2024},
author = {Qian, X and Tang, C and Wang, N and Yang, D},
title = {Syntormon Loew (Diptera, Dolichopodidae) from Inner Mongolia, China, with the description of a new species.},
journal = {ZooKeys},
volume = {1212},
number = {},
pages = {143-152},
pmid = {39318674},
issn = {1313-2989},
abstract = {Previously, no records of Syntormon Loew, 1857 species were known from Inner Mongolia (China). The genus is reported here from Inner Mongolia for the first time, with the description of a new species, S.sinicum sp. nov., along with two previously described species, S.dukha Hollis, 1964 and S.henanense Yang &amp; Saigusa, 2000. Syntormonsinicum sp. nov. and S.dukha Hollis, 1964 are barcoded for the first time to support the species delimitation. A key to Syntormon species in China is provided.},
}
@article {pmid39318673,
year = {2024},
author = {Silva-Segundo, CA and Funes-Rodríguez, R and Anaya-Godínez, E and Gómez-Gutiérrez, J},
title = {Molecular and morphological identification of larvae of Carangidae (Teleostei, Carangiformes) species from southern Gulf of California.},
journal = {ZooKeys},
volume = {1212},
number = {},
pages = {195-215},
pmid = {39318673},
issn = {1313-2989},
abstract = {The description of diagnostic morphological characters and DNA barcoding of fish larvae from nine species of the carangid family are provided from specimens collected during a weekly zooplankton time-series (2016-2017) at Cabo Pulmo National Park, Gulf of California, Mexico. Five nominal species (Caranxsexfasciatus, C.caballus, Naucratesductor, Selarcrumenophthalmus, and Seleneperuviana) and three morphotypes of Decapterus spp. and one of Caranx spp. were identified and separated based on morphological, meristic, and pigmentary diagnostic characters. All larvae were genetically sequenced for a fragment of the cytochrome c oxidase subunit I mitochondrial gene. Sequences of larval Caranx and Decapterus showed high genetic similarity (> 99%), low intraspecific divergence (< 1%), and an interspecific divergence between 6% and 11%, allowing the discrimination of diagnostic pigmentation patterns of fish larvae among three sibling species from each genus: Caranx (C.caballus, C.caninus, and C.sexfasciatus) and Decapterus (D.macarellus, D.macrosoma, and D.muroadsi). DNA barcoding supported the presence of Caranxcaballus, C.caninus, C.sexfasciatus, Decapterusmacarellus, D.muroadsi, Selarcrumenophthalmus, and Seleneperuviana, and for the first time Naucratesductor and D.macrosoma at the CPNP. Abundance of these nine species (confirmed molecularly) was estimated throughout the 2016-2017 weekly time series. Decapterusmacarellus and Caranxcaninus were the most abundant species. The morphological and molecular taxonomic methods allowed us to infer the species number and abundance of these commercial species at the CPNP to improve conservation in protected areas and fishery management.},
}
@article {pmid39315963,
year = {2024},
author = {George, FM and Venkatesan, S and Srinivasan, V and Semalaiyappan, J and Kuttiatt, VS},
title = {DNA barcoding and phylogenetic analysis of the vector Culex gelidus and its global and public health significance.},
journal = {Journal of vector ecology : journal of the Society for Vector Ecology},
volume = {49},
number = {2},
pages = {S5-S9},
doi = {10.52707/1081-1710-49.2.S5},
pmid = {39315963},
issn = {1948-7134},
mesh = {Animals ; *Culex/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Phylogeny ; Public Health ; Mosquito Vectors/genetics ; },
}
@article {pmid39315814,
year = {2024},
author = {Loes, AN and Tarabi, RAL and Huddleston, J and Touyon, L and Wong, SS and Cheng, SMS and Leung, NHL and Hannon, WW and Bedford, T and Cobey, S and Cowling, BJ and Bloom, JD},
title = {High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains.},
journal = {Journal of virology},
volume = {98},
number = {10},
pages = {e0068924},
pmid = {39315814},
issn = {1098-5514},
support = {P30 CA015704/CA/NCI NIH HHS/United States ; S10 OD028685/OD/NIH HHS/United States ; T11-712/19-N//Research Grants Council, University Grants Committee ()/ ; U01AI153700//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; U01 AI153700/AI/NIAID NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; S10 OD020069/OD/NIH HHS/United States ; R01AI165821//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; Investigator Support//Howard Hughes Medical Institute (HHMI)/ ; R01 AI165821/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Antibodies, Neutralizing/immunology/blood ; *Influenza A Virus, H1N1 Subtype/immunology/genetics ; *Influenza Vaccines/immunology/administration &amp; dosage ; *Antibodies, Viral/blood/immunology ; *Influenza, Human/prevention &amp; control/immunology/virology ; *Neutralization Tests/methods ; *Vaccination ; *Hemagglutinin Glycoproteins, Influenza Virus/immunology/genetics ; Adult ; Female ; },
abstract = {UNLABELLED: The high genetic diversity of influenza viruses means that traditional serological assays have too low throughput to measure serum antibody neutralization titers against all relevant strains. To overcome this challenge, we developed a sequencing-based neutralization assay that simultaneously measures titers against many viral strains using small serum volumes using a workflow similar to traditional neutralization assays. The key innovation is to incorporate unique nucleotide barcodes into the hemagglutinin (HA) genomic segment, and then pool viruses with numerous different barcoded HA variants and quantify the infectivity of all of them simultaneously using next-generation sequencing. With this approach, a single researcher performed the equivalent of 2,880 traditional neutralization assays (80 serum samples against 36 viral strains) in approximately 1 month. We applied the sequencing-based assay to quantify the impact of influenza vaccination on neutralization titers against recent human H1N1 strains for individuals who had or had not also received a vaccine in the previous year. We found that the viral strain specificities of the neutralizing antibodies elicited by vaccination vary among individuals and that vaccination induced a smaller increase in titers for individuals who had also received a vaccine the previous year-although the titers 6 months after vaccination were similar in individuals with and without the previous-year vaccination. We also identified a subset of individuals with low titers to a subclade of recent H1N1 even after vaccination. We provide an experimental protocol (dx.doi.org/10.17504/protocols.io.kqdg3xdmpg25/v1) and computational pipeline (https://github.com/jbloomlab/seqneut-pipeline) for the sequencing-based neutralization assays to facilitate the use of this method by others.<br><br>IMPORTANCE: We describe a new approach that can rapidly measure how the antibodies in human serum inhibit infection by many different influenza strains. This new approach is useful for understanding how viral evolution affects antibody immunity. We apply the approach to study the effect of repeated influenza vaccination.},
}
@article {pmid39314939,
year = {2024},
author = {Shao, F and Hu, J and Zhang, P and Akarapipad, P and Park, JS and Lei, H and Hsieh, K and Wang, TH},
title = {Enhanced CRISPR/Cas-Based Immunoassay through Magnetic Proximity Extension and Detection.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.06.24313206},
pmid = {39314939},
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-associated systems have recently emerged as a focal point for developing next-generation molecular diagnosis, particularly for nucleic acid detection. However, the detection of proteins is equally critical across diverse applications in biology, medicine, and the food industry, especially for diagnosing and prognosing diseases like cancer, Alzheimer's and cardiovascular conditions. Despite recent efforts to adapt CRISPR/Cas systems for protein detection with immunoassays, these methods typically achieved sensitivity only in the femtomolar to picomolar range, underscoring the need for enhanced detection capabilities. To address this, we developed CRISPR-AMPED, an innovative CRISPR/Cas-based immunoassay enhanced by magnetic proximity extension and detection. This approach combines proximity extension assay (PEA) with magnetic beads that converts protein into DNA barcodes for quantification with effective washing steps to minimize non-specific binding and hybridization, therefore reducing background noise and increasing detection sensitivity. The resulting DNA barcodes are then detected through isothermal nucleic acid amplification testing (NAAT) using recombinase polymerase amplification (RPA) coupled with the CRISPR/Cas12a system, replacing the traditional PCR. This integration eliminates the need for thermocycling and bulky equipment, reduces amplification time, and provides simultaneous target and signal amplification, thereby significantly boosting detection sensitivity. CRISPR-AMPED achieves attomolar level sensitivity, surpassing ELISA by over three orders of magnitude and outperforming existing CRISPR/Cas-based detection systems. Additionally, our smartphone-based detection device demonstrates potential for point-of-care applications, and the digital format extends dynamic range and enhances quantitation precision. We believe CRISPR-AMPED represents a significant advancement in the field of protein detection.},
}
@article {pmid39314390,
year = {2024},
author = {Cabrera-Sosa, L and Safarpour, M and Kattenberg, JH and Ramirez, R and Vinetz, J and Rosanas-Urgell, A and Gamboa, D and Delgado-Ratto, C},
title = {Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.09.611954},
pmid = {39314390},
issn = {2692-8205},
abstract = {Malaria molecular surveillance (MMS) can provide insights into transmission dynamics, guiding national control/elimination programs. Considering the genetic differences among parasites from different areas in the Peruvian Amazon, we previously designed SNP barcode panels for Plasmodium vivax (Pv) and P. falciparum (Pf), integrated into AmpliSeq assays, to provide population genetics estimates of malaria parasites. These AmpliSeq assays are ideal for MMS: multiplexing different traits of interest, applicable to many use cases, and high throughput for large numbers of samples. The present study compares the genetic resolution of the SNP barcode panels in the AmpliSeq assays with widely used microsatellite (MS) panels to investigate Amazonian malaria parasites. Malaria samples collected in remote areas of the Peruvian Amazon (51 Pv &amp; 80 Pf samples) were characterized using the Ampliseq assays and MS. Population genetics estimates (complexity of infection, genetic diversity and differentiation, and population structure) were compared using the SNP barcodes (Pv: 40 SNPs &amp; Pf: 28 SNPs) and MS panels (Pv: 16 MS &amp; Pf: 7 MS). The genetic diversity of Pv (expected heterozygosity, He) was similar across the subpopulations for both makers: He MS = 0.68 - 0.78 (p = 0.23) and He SNP = 0.36 - 0.38 (p = 0.80). Pairwise genetic differentiation (fixation index, F ST) was also comparable: F ST-MS = 0.04 - 0.14 and F ST-SNP = 0.03 - 0.12 (p = 0.34 - 0.85). No geographic clustering was observed with any panel. In addition, Pf genetic diversity trends (He MS = 0 - 0.48 p = 0.03 - 1; He SNP = 0 - 0.09, p = 0.03 - 1) and pairwise F ST comparisons (F ST-MS = 0.14 - 0.65, F ST-SNP = 0.19 - 0.61, p = 0.24 - 0.83) were concordant between the panels. Similar population structure clustering was observed with both SNP and MS, highlighting one Pf subpopulation in an indigenous community. The SNP barcodes in the Pv AmpliSeq v2 Peru and Pf AmpliSeq v1 Peru assays offer comparable results to MS panels when investigating population genetics in Pv and Pv populations. Therefore, the AmpliSeq assays can efficiently characterize malaria transmission dynamics and population structure and support malaria elimination efforts in Peru.},
}
@article {pmid39314385,
year = {2024},
author = {Baron, CS and Mitchell, O and Avagyan, S and Menard, R and Yang, S and Robertson, AL and Potluri, R and Shendure, J and Madelaine, R and McKenna, A and Zon, LI},
title = {Leukemia-derived apelin selects endothelial niche clones to promote tumorigenesis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.09.612077},
pmid = {39314385},
issn = {2692-8205},
abstract = {Hematopoietic stem cells are regulated by endothelial and mesenchymal stromal cells in the marrow niche1-3. Leukemogenesis was long believed to be solely driven by genetic perturbations in hematopoietic cells but introduction of genetic mutations in the microenvironment demonstrated the ability of niche cells to drive disease progression4-8. The mechanisms by which the stem cell niche induces leukemia remain poorly understood. Here, using cellular barcoding in zebrafish, we found that clones of niche endothelial and stromal cells are significantly expanded in leukemic marrows. The pro-angiogenic peptide apelin secreted by leukemic cells induced sinusoidal endothelial cell clonal selection and transcriptional reprogramming towards an angiogenic state to promote leukemogenesis in vivo. Overexpression of apelin in normal hematopoietic stem cells led to clonal amplification of the niche endothelial cells and promotes clonal dominance of blood cells. Knock-out of apelin in leukemic zebrafish resulted in a significant reduction in disease progression. Our results demonstrate that leukemic cells remodel the clonal and transcriptional landscape of the marrow niche to promote leukemogenesis and provide a potential therapeutic opportunity for anti-apelin treatment.},
}
@article {pmid39310847,
year = {2024},
author = {Böning, S and Schneider, F and Huber, AK and Langhoff, D and Lin, H and Kaczorowski, A and Stenzinger, A and Hohenfellner, M and Duensing, S and Duensing, A},
title = {Region of interest localization, tissue storage time, and antibody binding density-a technical note on the GeoMx® Digital Spatial Profiler.},
journal = {Immuno-oncology technology},
volume = {23},
number = {},
pages = {100727},
pmid = {39310847},
issn = {2590-0188},
abstract = {BACKGROUND: Spatial biology is an emerging concept to interrogate tumor heterogeneity. The NanoString GeoMx® Digital Spatial Profiling (DSP) platform has become increasingly available. It combines high-plex analysis of protein or messenger RNA expression using barcoded antibodies or oligonucleotide probes with investigator-driven selection of regions of interest. Cell populations, e.g. immune cells, can be selectively analyzed via segmentation. A key advantage is the use of archived formalin-fixed, paraffin-embedded tissue, however, begging the question whether and to what extent tissue fixation and storage time affect the results.<br><br>MATERIALS AND METHODS: Antibody binding density (ABD), i.e. the number of barcodes/&#x3bc;m[2], is a key quality control measure for DSP spatial proteomics. To assess whether regional differences in tissue fixation have an influence on ABD, we compared 652 regions of interest selected from tumor center and periphery of 49 prostate cancer and 25 renal cell carcinoma (RCC) specimens. Moreover, the effect of tissue storage time on ABD was examined. Finally, we tested whether regional differences have an influence on ABD of segmented CD45+ or CD8+ cells.<br><br>RESULTS: No significant differences in ABD between tumor center and periphery were found in prostate cancer or RCC. However, ABD was significantly higher in recent specimens (&#x2264;5 years) when compared with those that were older (>5&#xa0;years; P&#xa0;= 0.027). There was a trend towards higher ABD in the tumor periphery of RCC specimens after segmentation for immune cells, albeit without reaching statistical significance.<br><br>CONCLUSIONS: The NanoString GeoMx&#xae; DSP platform delivers robust data to interrogate tumor heterogeneity, but tissue storage time should be considered when interpreting the results.},
}
@article {pmid39309168,
year = {2024},
author = {Mitchueachart, B and Sutcharit, C and Tongkerd, P and Panha, S},
title = {Morphological and molecular evidence uncovers hidden species diversity in the leatherleaf slug genus Valiguna (Systellommatophora, Veronicellidae) from Thailand.},
journal = {ZooKeys},
volume = {1212},
number = {},
pages = {79-107},
pmid = {39309168},
issn = {1313-2989},
abstract = {The poorly studied leatherleaf slug genus Valiguna in Thailand was carefully investigated. Members of this genus are phenotypically similar, making their identification very challenging. This study clarifies the taxonomic status of all Valiguna species in Thailand by combining morphological and anatomical studies with DNA barcoding. Monophyly of all Valiguna species was confirmed by analysis of the mitochondrial COI data and that all Valiguna species have the acropleurocaulis type of penis. Currently, three Valiguna species are recognised: V.siamensis, V.semicerina Mitchueachart &amp; Panha, sp. nov., and V.crispa Mitchueachart &amp; Panha, sp. nov. that are new to science. For distinct characteristics, V.siamensis is characterised by having a cylindrical penis and honeycomb-like glans, V.semicerina sp. nov. has a lanceolate penis with half honeycomb-like glans, and V.crispa sp. nov. has a cylindrical penis with wavy-like glans. In addition, more detailed descriptions of the radula and genitalia of all three species and their distribution are also carefully presented, enhancing the understanding of this leatherleaf slug genus in Thailand.},
}
@article {pmid39309166,
year = {2024},
author = {Srisonchai, R and Likhitrakarn, N and Sutcharit, C and Wesener, T},
title = {Integrative taxonomy reveals two new giant pill-millipedes of the genus Zephronia Gray, 1832 from eastern Thailand (Diplopoda, Sphaerotheriida, Zephroniidae).},
journal = {ZooKeys},
volume = {1212},
number = {},
pages = {29-64},
pmid = {39309166},
issn = {1313-2989},
abstract = {A large amount of material of the millipede genus Zephronia Gray, 1832 was collected during 2014-2023 from many parts of eastern Thailand. An integrative study of morphological characters and genetic data (COI gene) revealed two new species: Z.chantaburiensis Srisonchai &amp; Wesener, sp. nov. and Z.macula Srisonchai &amp; Wesener, sp. nov. The two new species clearly differ from other congeners by their unique characteristics, especially in their colour pattern and telopod shape. The interspecific genetic distances of the 658 bp COI gene barcoding fragment between these new species and all other species of giant pill-millipede from Thailand, Laos and Cambodia are 12.01-23.49% for Z.chantaburiensis sp. nov. and 17.93-25.13% for Z.macula sp. nov. While relationships among species remain preliminary, the phylogenetic tree shows that species of Zephronia are interspersed with species of Sphaerobelum Verhoeff, 1924 and Prionobelum Verhoeff, 1924. Phylogenetic analyses place both new species in a clade termed Zephronia s.s., which receives support also from morphological data, showing a unique position of the organ of Tömösváry. Z.macula sp. nov. appears to occur over a broad distribution whereas Z.chantaburiensis sp. nov. was found only at the type locality. Given that all known records are in the eastern part of Thailand, we thus regard both species as endemic. Morphological illustrations based on SEM micrographs and a distribution map are also provided.},
}
@article {pmid39308990,
year = {2024},
author = {Nocella, E and Fassio, G and Zuccon, D and Puillandre, N and Modica, MV and Oliverio, M},
title = {From coral reefs into the abyss: the evolution of corallivory in the Coralliophilinae (Neogastropoda, Muricidae).},
journal = {Coral reefs (Online)},
volume = {43},
number = {5},
pages = {1285-1302},
pmid = {39308990},
issn = {1432-0975},
abstract = {UNLABELLED: In this study, we delved into the interaction between corallivorous marine gastropods, the muricid Coralliophilinae Chenu, 1859, and their cnidarian food targets. Coralliophilinae is a subfamily of specialised corallivorous caenogastropods that feed by browsing on octocorals or hexacorals. Only sparse information is available on the phylogenetic relationships and the degree of specificity of the trophic relationships within this corallivorous lineage. To address these gaps, we generated the largest molecular dataset to date, comprising two mitochondrial (cox1 and 16S rDNA) and one nuclear gene (ITS2 rDNA) from 586 specimens collected worldwide. The coral hosts of coralliophilines were identified through an integrative approach, combining literature data with new records, employing morphological and/or molecular markers, and incorporating data from DNA barcoding of the snail stomach content. Our comprehensive approach unveiled the existence of numerous cryptic species in Coralliophilinae, while the phylogeny showed that most of the currently accepted genera are not monophyletic. The molecular dating confirmed the origin of the Coralliophilinae in Middle Eocene, with diversification of most lineages during the Miocene. Our results indicate that the subfamily's ancestor evolved in shallow waters in association with Scleractinia. Through the evolutionary history of Coralliophilinae, multiple host shifts to other cnidarian orders were observed, not correlated with changes in the depth range. The results of diversification analyses within the subfamily further suggest that the association with the host has influenced the evolutionary patterns of Coralliophilinae, but not vice versa.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00338-024-02537-1.},
}
@article {pmid39306191,
year = {2024},
author = {Seyedabadi, M and Gurevich, VV},
title = {Flavors of GPCR signaling bias.},
journal = {Neuropharmacology},
volume = {261},
number = {},
pages = {110167},
doi = {10.1016/j.neuropharm.2024.110167},
pmid = {39306191},
issn = {1873-7064},
mesh = {*Receptors, G-Protein-Coupled/metabolism ; Humans ; *Signal Transduction/physiology/drug effects ; Animals ; Ligands ; GTP-Binding Proteins/metabolism ; },
abstract = {GPCRs are inherently flexible molecules existing in an equilibrium of multiple conformations. Binding of GPCR agonists shifts this equilibrium. Certain agonists can increase the fraction of active-like conformations that predispose the receptor to coupling to a particular signal transducer or a select group of transducers. Such agonists are called biased, in contrast to balanced agonists that facilitate signaling via all transducers the receptor couples to. These biased agonists preferentially channel the signaling of a GPCR to particular G proteins, GRKs, or arrestins. Preferential activation of particular G protein or arrestin subtypes can be beneficial, as it would reduce unwanted on-target side effects, widening the therapeutic window. However, biasing GPCRs has two important limitations: a) complete bias is impossible due to inherent flexibility of GPCRs; b) receptor-independent functions of signal transducer proteins cannot be directly affected by GPCR ligands or differential receptor barcoding by GRK phosphorylation. This article is part of the Special Issue on "Ligand Bias".},
}
@article {pmid39303852,
year = {2025},
author = {Yanar, A and Kamanli, SA and Sönmez, S and Hamdi, &#x130; and Özak, AA and Boxshall, GA},
title = {Caligus minimus Otto, 1821 (Copepoda: Caligidae): A commercially important but poorly described parasite of cultured European Sea Bass, Dicentrarchus labrax (Linnaeus, 1758).},
journal = {Parasitology international},
volume = {104},
number = {},
pages = {102964},
doi = {10.1016/j.parint.2024.102964},
pmid = {39303852},
issn = {1873-0329},
mesh = {Animals ; *Bass/parasitology ; *Copepoda/classification/anatomy &amp; histology/ultrastructure/genetics ; *Fish Diseases/parasitology ; Female ; *Aquaculture ; Male ; *Ectoparasitic Infestations/parasitology/veterinary ; Microscopy, Electron, Scanning/veterinary ; Phylogeny ; },
abstract = {Caligus minimus Otto, 1821 has been known for over two centuries and it is the second oldest of the approximately 275 species of Caligus O. F. Müller, 1985. Despite the numerous records of this species from European waters, it has never been fully described to modern standards. The lack of a comprehensive modern description has resulted in numerous misidentifications, even in recently published reports, and this is especially problematic for a species that is known to have a significant economic impact in aquaculture. This study presents a detailed description of both sexes and documents newly observed features of C. minimus collected from the buccal cavity of farmed European Sea Bass (ESB), Dicentrarchus labrax (Linnaeus, 1758). The morphology of C. minimus was examined using light microscope (LM), scanning electron microscope (SEM), and confocal laser scanning microscope (CLSM), and new details are revealed regarding the structure and ornamentation of the marginal membrane of the cephalothorax, maxilliped, antenna, sternal furca, abdomen, and legs 1, 3, 4, and 6. The ornamentation of the marginal membrane of the cephalothorax is unique and its impact on the functioning of the cephalothoracic sucker requires further investigation. Additionally, partial COI gene region sequences were obtained from four individuals of C. minimus and provided for future references. A phylogenetic analysis was conducted in conjunction with Caligus sequences available in the NCBI GenBank database.},
}
@article {pmid39302606,
year = {2025},
author = {Krishnan, S and Ulagesan, S and Moon, JS and Choi, YH and Nam, TJ},
title = {Establishment, characterization, and sensory characteristics (taste and flavor) of an immortalized muscle cell line from the seven-band grouper Epinephelus septemfasciatus: implications for cultured seafood applications.},
journal = {In vitro cellular &amp; developmental biology. Animal},
volume = {61},
number = {1},
pages = {8-23},
pmid = {39302606},
issn = {1543-706X},
support = {201803932//Future Fisheries Food Research Centre' funded by the Korea Institute of Marine Science and Technology (KIMST) promotions, Ministry of Oceans and Fisheries, Republic of Korea/ ; },
mesh = {Animals ; *Seafood ; *Taste ; *Cell Differentiation ; *Satellite Cells, Skeletal Muscle/cytology/metabolism ; Cell Proliferation ; Cell Line ; Cell Survival ; Bass ; },
abstract = {Grouper muscle satellite cells (GMSCs) from the seven-band grouper (Epinephelus septemfasciatus) were isolated, and their growth conditions were optimized (10% fetal bovine serum, 24°C, 10 ng/mL bFGF). The cells were immortalized at passage 14 and designated as grouper immortalized muscle satellite cells (GIMSCs). DNA barcoding confirmed the grouper origin of both GMSC and GIMSC lines. GIMSCs exhibited enhanced proliferation, accelerated differentiation, and robust myotube formation compared to pre-crisis GMSCs. Western blot analysis showed upregulation of key myogenic factors (Pax7, MyoD, MyoG) and structural proteins (Desmin) in GIMSC, indicating the differentiation potential. The immortalized GIMSC line maintained consistent morphology, growth rates, and viability across multiple passages. Biocompatibility studies showed GIMSCs were compatible with bio-inks (sodium alginate, gelatin, κ-carrageenan) at 250 to 10,000 µg/mL, retaining ~ 80% viability at the highest concentration. Taste sensory analysis revealed GMSCs had the highest umami and lowest saltiness and sourness, contrasting with the muscle of the seven-band grouper, which had higher saltiness and sourness. Flavor analysis identified pronounced fishy, hot fat, and ethereal flavors in the cells at higher level than in the muscle. These findings suggest GMSCs and GIMSCs are promising for producing cultured meat with enhanced umami taste and flavors, advancing cellular agriculture and sustainable food production.},
}
@article {pmid39298427,
year = {2024},
author = {Saiperaki, JL and Materu, SF and Mkenda, PA and Ligate, EJ and Rumisha, C},
title = {Field and DNA-barcode based surveys reveal evidence of rare endemic fishes in the Rufiji River Basin.},
journal = {PloS one},
volume = {19},
number = {9},
pages = {e0310387},
pmid = {39298427},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Rivers ; *Fishes/genetics/classification ; Conservation of Natural Resources ; Fisheries ; Biodiversity ; },
abstract = {Endemic fish species have long supported the livelihoods of local communities in the Rufiji River Basin (RRB). However, destructive fishing practices have led to a concerning decline in endemic fish stocks. To assess these changes, this study employed key informant interviews, focus group discussions (FGDs), and fishery surveys to assess the historical and contemporary distribution of endemic fishes within the RRB. DNA barcoding was also used to verify species identities. Out of 37 reported fish species, 33 species (54.55% endemic and 45.45% exotic to RRB) were confirmed through DNA barcoding and morphological characteristics. About 5 species including, Heterobranchus longifilis, Citharinus congicus, Labeo congoro, Mormyrus longirostris, and Labeobarbus leleupanus were rarely found in the field, despite being classified as Least Concern by IUCN. Additionally, five species that were reported to be present in the RRB by experienced fishers were not captured during sampling. This highlights the need for validation of the existence of such species through eDNA metabarcoding. Moreover, due to the rarity of some species in the area, their IUCN assessment should be revisited.},
}
@article {pmid39296989,
year = {2024},
author = {Caboňová, M and Vadkertiová, R and Adamčík, S and Bacigálová, K and Slovák, M and Zaib, S and Caboň, M},
title = {Taxonomic reintroduction of Taphrinaviridis (Taphrinales, Ascomycota) associated with Alnusalnobetula as one of five well defined European species colonizing alders.},
journal = {MycoKeys},
volume = {108},
number = {},
pages = {249-267},
pmid = {39296989},
issn = {1314-4049},
abstract = {Phylogenetic analysis of four DNA regions (ITS, LSU, mtSSU and tef1α) supported the existence of five European Taphrina species which colonise Alnus in Europe. In addition to previously well-defined species, T.viridis is, for the first time recognised, by molecular study as a species related to T.sadebeckii. Analysis of publicly available sequences of barcoding regions suggested that T.viridis is only associated with A.alnobetula and no other Taphrina species colonize this host tree. Symptomatic, morphological, and physiological characterisation of T.viridis are provided together with the key for identification of Alnus associated Taphrina species in Europe and North America.},
}
@article {pmid39293535,
year = {2024},
author = {Rosenmai, AK and Svingen, T and Evrard, B and Nguyen, KH and Nielsen, C and Axelstad, M and Chalmel, F and Ramhøj, L},
title = {Distinct transcriptional profiles in rat thyroid glands after developmental exposure to three in vitro thyroperoxidase inhibiting chemicals.},
journal = {Genomics},
volume = {116},
number = {5},
pages = {110938},
doi = {10.1016/j.ygeno.2024.110938},
pmid = {39293535},
issn = {1089-8646},
mesh = {Animals ; *Thyroid Gland/metabolism/drug effects ; Rats ; *Iodide Peroxidase/genetics/metabolism ; Male ; *Transcriptome/drug effects ; Amitrole/pharmacology ; Enzyme Inhibitors/pharmacology ; Benzimidazoles/pharmacology ; },
abstract = {Thyroperoxidase (TPO) is central in thyroid hormone (TH) synthesis and inhibition can lead to TH deficiency. Many chemicals can inhibit TPO activity in vitro, but how this may manifest in the developing thyroid gland at the molecular level is unclear. Here, we characterized the thyroid gland transcriptome of male rats developmentally exposed to the in vitro TPO-inhibitors amitrole, 2-mercaptobenzimidazole (MBI), or cyanamide by use of Bulk-RNA-Barcoding (BRB) and sequencing. Amitrole exposure caused TH deficiency and 149 differentially expressed genes in the thyroid gland. The effects indicated an activated and growing thyroid gland. MBI caused intermittent changes to serum TH concentrations in a previous study and this was accompanied by 60 differentially expressed genes in the present study. More than half of these were also affected by amitrole, indicating that they could be early effect biomarkers of developmental TH system disruption due to TPO inhibition. Further work to validate the signature is needed, including assessment of substance independency and applicability domain.},
}
@article {pmid39293082,
year = {2024},
author = {Liu, B and Klatt, D and Zhou, Y and Manis, JP and Sauvageau, G and Pellin, D and Brendel, C and Williams, DA},
title = {UM171 enhances fitness and engraftment of gene-modified hematopoietic stem cells from patients with sickle cell disease.},
journal = {Blood advances},
volume = {8},
number = {22},
pages = {5885-5895},
pmid = {39293082},
issn = {2473-9537},
mesh = {Humans ; *Hematopoietic Stem Cells/metabolism/cytology ; *Anemia, Sickle Cell/therapy ; Animals ; *Hematopoietic Stem Cell Transplantation/methods ; Mice ; Antigens, CD34/metabolism ; Lentivirus/genetics ; Transduction, Genetic ; Genetic Vectors ; Indoles ; Pyrimidines ; },
abstract = {Hematopoietic stem cell (HSC) transplantation with lentiviral vector (LVV)-transduced autologous cells has proven an effective therapeutic strategy for sickle cell disease (SCD). However, ex vivo culture or proliferative stress associated with in vivo reconstitution may amplify any underlying genetic risk of leukemia. We aimed to minimize culture-induced stress and reduce genomic damage during ex vivo culture and enhance stem cell fitness and reconstitution of SCD CD34+ cells transduced with BCL11A shmiR-encoding LVV. UM171, a pyrimidoindole derivative, can expand normal HSCs during in vitro culture and has been shown to be safe and effective using umbilical cord blood. We examined the effect of UM171 during ex vivo LVV transduction of SCD HSCs. Culture of SCD CD34+ HSCs with UM171 during transduction reduced DNA damage and reactive oxygen species, decreased apoptosis, and was associated with increased numbers of immunophenotypically defined long-term HSCs. UM171 increased the engraftment of LVV-transduced human HSCs in immunodeficient mice and barcode tracing revealed increased clonal diversity of engrafting cells. In competitive transplantation assays, analysis of bone marrow showed that cells transduced in the presence of UM171 consistently outcompeted those transduced under control conditions. In summary, exposure of SCD peripheral blood CD34+ cells to UM171 during LVV transduction enhances stem cell fitness. These findings suggest manufacturing of genetically modified HSCs in the presence of UM171 may improve efficacy, safety, and sustainability of gene therapy using ex vivo approaches. BCL11A shmiR-encoding LVV is in clinical trials to treat SCD (NCT03282656), UM171 is in clinical trials to culture umbilical cord blood (NCT02668315).},
}
@article {pmid39290075,
year = {2024},
author = {Sato, H and Lain, A and Mizuno, T and Yamashita, S and Hassan, JB and Othman, KB and Itioka, T},
title = {Host preference explains the high endemism of ectomycorrhizal fungi in a dipterocarp rainforest.},
journal = {Molecular ecology},
volume = {33},
number = {21},
pages = {e17529},
doi = {10.1111/mec.17529},
pmid = {39290075},
issn = {1365-294X},
support = {JPMJSA190//Science and Technology Research Partnership for Sustainable Development/ ; 20K06796//Japan Society for the Promotion of Science/ ; },
mesh = {*Mycorrhizae/genetics/classification ; *Rainforest ; Malaysia ; Dipterocarpaceae/microbiology ; DNA Barcoding, Taxonomic ; Host Specificity ; Symbiosis/genetics ; Phylogeny ; Trees/microbiology ; },
abstract = {Ectomycorrhizal (ECM) fungi are important tree symbionts within forests. The biogeography of ECM fungi remains to be investigated because it is challenging to observe and identify species. Because most ECM plant taxa have a Holarctic distribution, it is difficult to evaluate the extent to which host preference restricts the global distribution of ECM fungi. To address this issue, we aimed to assess whether host preference enhances the endemism of ECM fungi that inhabit dipterocarp rainforests. Highly similar sequences of 175 operational taxonomic units (OTUs) for ECM fungi that were obtained from Lambir Hill's National Park, Sarawak, Malaysia, were searched for in a nucleotide sequence database. Using a two-step binomial model, the probability of presence for the query OTUs and the registration rate of barcode sequences in each country were simultaneously estimated. The results revealed that the probability of presence in the respective countries increased with increasing species richness of Dipterocarpaceae and decreasing geographical distance from the study site (i.e. Lambir). Furthermore, most of the ECM fungi were shown to be endemic to Malaysia and neighbouring countries. These findings suggest that not only dispersal limitation but also host preference are responsible for the high endemism of ECM fungi in dipterocarp rainforests. Moreover, host preference likely determines the areas where ECM fungi potentially expand and dispersal limitation creates distance-decay patterns within suitable habitats. Although host preference has received less attention than dispersal limitation, our findings support that host preference has a profound influence on the global distribution of ECM fungi.},
}
@article {pmid39287819,
year = {2024},
author = {Pachalil, VT and Gupta, B and Maile, A and Sunish, IP},
title = {Molecular characterization of anopheline species diversity in the Andaman and Nicobar archipelago, with a particular emphasis on Anopheles barbirostris.},
journal = {Parasitology research},
volume = {123},
number = {9},
pages = {325},
pmid = {39287819},
issn = {1432-1955},
mesh = {Animals ; *Anopheles/genetics/classification ; *RNA, Ribosomal, 28S/genetics ; *DNA, Ribosomal Spacer/genetics ; *Electron Transport Complex IV/genetics ; *Phylogeny ; *Genetic Variation ; Biodiversity ; Sequence Analysis, DNA ; Cluster Analysis ; Molecular Sequence Data ; DNA, Ribosomal/genetics ; Islands ; },
abstract = {This study investigates anopheline species diversity in the Andaman and Nicobar Islands, employing morphological and molecular methods, focusing on the D3 domain of 28S rRNA (D3) and second internal spacer (ITS2). Ten Anopheline species were identified morphologically and confirmed with molecular markers. While the D3 region demonstrated low level of inter- and intra-specific genetic distance in all the species, ITS2 revealed clear barcoding gap. Among the ten species, A. barbirostris exhibited significant diversity when compared with the sequences from other countries available in GenBank. Further analyses of additional samples of A. barbirostris were carried out using ITS2 and cytochrome oxidase I (COI) markers. Limited variations among the sequences from the islands were observed, suggesting a prevalent single molecular form. However, when compared with the GenBank sequences, our samples formed a separate cluster closely related to the A3 species. The genetic distance between our samples and the A3 cluster was 0.02 for COI but very high (0.104) for ITS2, suggesting a potentially new molecular form or species in the island region. This warrants a more comprehensive and detailed analysis of A. barbirostris in these islands at both genetic and morphometric levels. Overall, these observations added-up the new knowledge in the understanding of anopheline diversity in the Andaman and Nicobar archipelago and highlight the necessity for continuous molecular investigations to unravel complexities within mosquito population dynamics.},
}
@article {pmid39285627,
year = {2024},
author = {Salis, R and Sunde, J and Gubonin, N and Franzén, M and Forsman, A},
title = {Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity.},
journal = {Molecular ecology resources},
volume = {24},
number = {8},
pages = {e14018},
doi = {10.1111/1755-0998.14018},
pmid = {39285627},
issn = {1755-0998},
support = {//Crafoordska Stiftelsen/ ; 2020-03519//Vetenskapsr&#xe5;det/ ; 2018-02846//Svenska Forskningsr&#xe5;det Formas/ ; 2021-02142//Svenska Forskningsr&#xe5;det Formas/ ; },
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic/methods ; Electron Transport Complex IV/genetics ; *Insecta/genetics/classification/anatomy &amp; histology ; Wasps/genetics/classification/anatomy &amp; histology ; },
abstract = {For two decades, DNA barcoding and, more recently, DNA metabarcoding have been used for molecular species identification and estimating biodiversity. Despite their growing use, few studies have systematically evaluated these methods. This study aims to evaluate the efficacy of barcoding methods in identifying species and estimating biodiversity, by assessing their consistency with traditional morphological identification and evaluating how assignment consistency is influenced by taxonomic group, sequence similarity thresholds and geographic distance. We first analysed 951 insect specimens across three taxonomic groups: butterflies, bumblebees and parasitic wasps, using both morphological taxonomy and single-specimen COI DNA barcoding. An additional 25,047 butterfly specimens were identified by COI DNA metabarcoding. Finally, we performed a systematic review of 99 studies to assess average consistency between insect species identity assigned via morphology and COI barcoding and to examine the distribution of research effort. Species assignment consistency was influenced by taxonomic group, sequence similarity thresholds and geographic distance. An average assignment consistency of 49% was found across taxonomic groups, with parasitic wasps displaying lower consistency due to taxonomic impediment. The number of missing matches doubled with a 100% sequence similarity threshold and COI intraspecific variation increased with geographic distance. Metabarcoding results aligned well with morphological biodiversity estimates and a strong positive correlation between sequence reads and species abundance was found. The systematic review revealed an 89% average consistency and also indicated taxonomic and geographic biases in research effort. Together, our findings demonstrate that while problems persist, barcoding approaches offer robust alternatives to traditional taxonomy for biodiversity assessment.},
}
@article {pmid39285331,
year = {2024},
author = {Zhang, Y and Song, M and Tang, D and Li, X and Xu, N and Li, H and Qu, L and Wang, Y and Yin, C and Zhang, L and Zhang, Z},
title = {Comprehensive comparative analysis and development of molecular markers for Lasianthus species based on complete chloroplast genome sequences.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {867},
pmid = {39285331},
issn = {1471-2229},
support = {2021-I2M-1-032//Yunnan "Xingdian Talent Support Program " young talents special project and CAMS Innovation Fund for Medical Sciences (CIFMS)/ ; },
mesh = {*Genome, Chloroplast ; *Phylogeny ; Genetic Markers ; Base Composition ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Lasianthus species are widely used in traditional Chinese folk medicine with high medicinal value. However, source materials and herbarium specimens are often misidentified due to morphological characteristics and commonly used DNA barcode fragments are not sufficient for accurately identifying Lasianthus species. To improve the molecular methods for distinguishing among Lasianthus species, we report the complete chloroplast (CP) genomes of Lasianthus attenuatus, Lasianthus henryi, Lasianthus hookeri, Lasianthus sikkimensis, obtained via high-throughput Illumina sequencing.<br><br>RESULTS: These showed CP genomes size of 160164-160246&#xa0;bp and a typical quadripartite structure, including a large single-copy region (86675-86848&#xa0;bp), a small single-copy region (17177-17326&#xa0;bp), and a pair of inverted repeats (28089-28135&#xa0;bp). As a whole, the gene order, GC content and IR/SC boundary structure were remarkably similar among of the four Lasianthus CP genomes, the partial gene length and IR, LSC and SSC regions length are still different. The average GC content of the CP genomes was 36.71-36.75%, and a total of 129 genes were detected, including 83 different protein-coding genes, 8 different rRNA genes and 38 different tRNA genes. Furthermore, we compared our 4 complete CP genomes data with publicly available CP genome data from six other Lasianthus species, and we initially screened eleven highly variable region fragments were initially screened. We then evaluated the identification efficiency of eleven highly variable region fragments and 5 regular barcode fragments. Ultimately, we found that the optimal combination fragment' ITS2&#x2009;+&#x2009;psaI-ycf4' could authenticated the Lasianthus species well. Additionally, the results of genome comparison of Rubiaceae species showed that the coding region is more conservative than the non-coding region, and the ycf1 gene shows the most significant variation. Finally, 49 species of CP genome sequences belonging to 16 genera of the Rubiaceae family were used to construct phylogenetic trees.<br><br>CONCLUSIONS: Our research is the first to analyze the chloroplast genomes of four species of Lasianthus in detail and we ultimately determined that the combination fragment' ITS2&#x2009;+&#x2009;psaI-ycf4' is the optimal barcode combination for identifying the genus of Lasianthus. Meanwhile, we gathered the available CP genome sequences from the Rubiaceae and used them to construct the most comprehensive phylogenetic tree for the Rubiaceae family. These investigations provide an important reference point for further studies in the species identification, genetic diversity, and phylogenetic analyses of Rubiaceae species.},
}
@article {pmid39282932,
year = {2024},
author = {Sun, L and Liu, M and Gong, Y and Zhai, K and Lv, F and He, L and Xue, X and Liu, X and Wang, H and Fan, D and You, Y and Fang, M and Sun, L and Xu, J and Zhang, J},
title = {Rapid Antimicrobial Susceptibility Test of Helicobacter pylori to Metronidazole via Single-Cell Raman Spectrometry.},
journal = {Helicobacter},
volume = {29},
number = {5},
pages = {e13136},
doi = {10.1111/hel.13136},
pmid = {39282932},
issn = {1523-5378},
support = {//Financial&#x2009;Special&#x2009;Fund/ ; //Project for software development and expansive application of Chinese Helicobacter pylori antimicrobial resistance dynamic map/ ; //Project for new techniques exploration for bacterial pathogens laboratory detection/ ; //National Natural Science Foundation of China/ ; //Project for collaborative research on analysis of Helicobacter pylori infection and gut flora changes/ ; },
mesh = {*Helicobacter pylori/drug effects ; *Metronidazole/pharmacology ; *Spectrum Analysis, Raman/methods ; *Microbial Sensitivity Tests/methods ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Helicobacter Infections/microbiology/drug therapy/diagnosis ; Single-Cell Analysis/methods ; Drug Resistance, Bacterial ; },
abstract = {BACKGROUND: Metronidazole is a first-line antibiotic to treat Helicobacter pylori infections. However, the Clinical Laboratory Standards Institute guidelines recommend against using antimicrobial susceptibility test (AST) to test metronidazole resistance, due to the unreliable predictive power which can result in treatment failure.<br><br>OBJECTIVES: The aim of this study was to establish an 8-h, metabolic-phenotype based AST for H. pylori metronidazole susceptibility using D2O-probed Raman microspectroscopy.<br><br>METHODS: Minimal inhibitory concentration (MIC) measured by conventional AST (E-test) were compared with expedited MIC via metabolic activity (eMIC-MA) for 10 H. pylori isolates. Raman barcodes of cellular-response to stress (RBCS) incorporating protein and carbohydrate Raman bands, were utilized to identify a biomarker to distinguish metronidazole susceptibility.<br><br>RESULTS: Specifically, eMIC-MA produces metronidazole susceptibility results showing 100% agreement with E-test, and determines the bactericidal dosage for both high- and low-level resistant H. pylori strains. In addition, RBCS not just reliably distinguish between metronidazole-susceptible and -resistant strains, but reveal their distinct mechanisms in bacterial responses to metronidazole.<br><br>CONCLUSION: The speed, accuracy, low cost, and rich information content that reveals the mode-of-action of drugs suggest the method's value in guiding metronidazole prescriptions for H. pylori eradication and in rapid screening based on drug-resistance mechanism.},
}
@article {pmid39282286,
year = {2024},
author = {Wu, JW and Yang, JM and Chen, CC and Au, G and Wang, S and Chern, GW and Huang, CH},
title = {Calibration of FRET-based biosensors using multiplexed biosensor barcoding.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.04.610346},
pmid = {39282286},
issn = {2692-8205},
support = {P50 CA098252/CA/NCI NIH HHS/United States ; R01 GM136711/GM/NIGMS NIH HHS/United States ; },
abstract = {Förster resonance energy transfer (FRET) between fluorescent proteins (FPs) is widely used in the design of genetically encoded fluorescent biosensors, which are powerful tools for monitoring the dynamics of biochemical activities in live cells. FRET ratio, defined as the ratio between acceptor and donor signals, is often used as a proxy for the actual FRET efficiency, which must be corrected for signal crosstalk using donor-only and acceptor-only samples. However, the FRET ratio is highly sensitive to imaging conditions, making direct comparisons across different experiments and over time challenging. Inspired by a method for multiplexed biosensor imaging using barcoded cells, we reasoned that calibration standards with fixed FRET efficiency can be introduced into a subset of cells for normalization of biosensor signals. Our theoretical analysis indicated that the FRET ratio of high-FRET species relative to non-FRET species slightly decreases at high excitation intensity, suggesting the need for calibration using both high and low FRET standards. To test these predictions, we created FRET donor-acceptor pairs locked in "FRET-ON" and "FRET-OFF" conformations and introduced them into a subset of barcoded cells. Our results confirmed the theoretical predictions and showed that the calibrated FRET ratio is independent of imaging settings. We also provided a strategy for calculating the FRET efficiency. Together, our study presents a simple strategy for calibrated and highly multiplexed imaging of FRET biosensors, facilitating reliable comparisons across experiments and supporting long-term imaging applications.},
}
@article {pmid39281619,
year = {2024},
author = {Lee, YJ and Phang, GJ and Chen, CC and Ou, JH and Fan, YH and Huang, YT},
title = {Optimal liquid-based DNA preservation for DNA barcoding of field-collected fungal specimens.},
journal = {Heliyon},
volume = {10},
number = {17},
pages = {e36829},
pmid = {39281619},
issn = {2405-8440},
abstract = {Preserving fungal tissue DNA in the field is essential for molecular ecological research, enabling the study of fungal biodiversity and community dynamics. This study systematically compares two liquid-based preservation solutions, RNAlater and DESS, for their effectiveness in maintaining macrofungi DNA integrity during field collection and storage. The research encompasses both controlled experiments and real-world field collections. In the controlled experiments, two fungal species were preserved in RNAlater and DESS at different temperatures and durations. DNA extraction success rates were high, but DNA quality and quantity metrics exhibited variations across samples. However, both preservation solutions demonstrated their viability for preserving fungal DNA, with no significant differences between them. In the field-collected macrofungi experiment, 160 paired fungal specimens were preserved in RNAlater and DESS, respectively. Including a drying process to facilitate tissue lysis for DNA extraction significantly impacted the outcomes. RNAlater showed a higher success rate and better DNA quality and quantity compared to DESS. Statistical analysis, including paired and independent t-tests, confirmed significant differences in DNA quality and quantity between the two preservation methods for field-collected samples. This study evaluates RNAlater and DESS for preserving macrofungi DNA in field conditions. Both methods are effective, but RNAlater is superior when a drying step is included in DNA extraction. Researchers can choose based on their specific needs without compromising DNA integrity. These findings advance fungal molecular ecology and DNA preservation strategies in ecological and environmental studies.},
}
@article {pmid39279612,
year = {2024},
author = {Biswas, A and Cencillo-Abad, P and Chanda, D},
title = {Multispectral Molecular Chiral Barcoding.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {36},
number = {45},
pages = {e2409565},
doi = {10.1002/adma.202409565},
pmid = {39279612},
issn = {1521-4095},
support = {ECCS-1800845//National Science Foundation/ ; },
abstract = {More than half of pharmaceutical drugs in use are chiral, necessitating accurate techniques for their characterization. Enantiomers, molecules with mirrored symmetry, often exhibit similar physical traits but possess distinct chemical and biological implications. This study harnesses the strong light-matter interaction induced by "superchiral" light to perform Surface-Enhanced Infrared Absorption (SEIRA) induced vibrational circular dichroism measurements in the mid-infrared spectral region. Utilizing a nanopatterned pixelated array of achiral plasmonic nanostructures, the system allows unique identification of enantiomers and biomolecules. Tunability of plasmon resonance facilitates spectral variation of the optical chirality over a wide infrared range, enabling development of a unique chiral "barcoding" scheme to distinguish chiral molecules based on their infrared fingerprint. This simple, yet robust sensor presents a low-cost solution for chiral mapping of drugs and biomolecules.},
}
@article {pmid39278523,
year = {2024},
author = {Hoxha, I and Trájer, AJ and Dvorak, V and Halada, P and Šupić, J and Obwaller, AG and Poeppl, W and Walochnik, J and Alić, A and Kniha, E},
title = {Phlebotomine sand flies (Diptera: Psychodidae) of Bosnia and Herzegovina: distribution, ecology and environmental preferences.},
journal = {Acta tropica},
volume = {260},
number = {},
pages = {107393},
doi = {10.1016/j.actatropica.2024.107393},
pmid = {39278523},
issn = {1873-6254},
mesh = {Animals ; Bosnia and Herzegovina ; *Psychodidae/classification/physiology/parasitology ; *Insect Vectors/physiology/parasitology/classification/virology ; Female ; Animal Distribution ; Leishmania/genetics ; Male ; Phlebotomus/classification ; Leishmania infantum/genetics/isolation &amp; purification ; Phlebovirus/isolation &amp; purification/genetics ; Ecosystem ; },
abstract = {Sand flies (Diptera: Phlebotominae) are the principal vectors for the protozoan parasites Leishmania spp. and for phleboviruses. The sand fly fauna on the Balkan Peninsula, including Bosnia and Herzegovina (BIH), is diverse and the circulation of Leishmania infantum as well as phleboviruses has been proven. However, recent data on the sand fly fauna in BIH are scarce. In this study, we surveyed understudied regions in central and northeastern BIH to update the sand fly distribution and gain insights into the ecological and environmental factors shaping their appearance. CDC light trapping was conducted in 2022 and 2023 and a combination of morphological and molecular methods (cytochrome oxidase I barcoding) was performed for species identifications. We mapped the currently known distribution, modelled climatic suitability patterns and performed environmental analyses by applying machine learning methods. In addition, we analyzed blood meals by host gene sequencing and MALDI-TOF peptide mass mapping and screened for Leishmania spp. DNA and Phlebovirus RNA. Altogether, 591 sand flies of four species were trapped, predominantly Phlebotomus neglectus (97 %), but also Ph. balcanicus, Ph. mascittii, and Ph. papatasi. Records of seven sand fly species known to be endemic were plotted onto distribution maps based on 101 datapoints, identifying Ph. neglectus as the overall predominant species. The environmental analyses of sand fly species indicated variation in altitudinal, thermal, and precipitation conditions across the sand fly-positive sites. Phlebotomus simici, Phlebotomus tobbi, and Sergentomyia minuta are typically found exclusively in Mediterranean and subtropical climate zones, whereas other species typically inhabit continental regions. The Inverse Distance Weighted (IDW) interpolation of sand fly species numbers and Shannon entropy values suggested the southeastern coastal region of BIH as a primary focus for sand fly occurrence. This finding was corroborated by modeled average climatic suitability patterns for sand flies, depicting four distinct meso-regions for sand fly occurrence. The results of the ensemble method highlight the importance of annual precipitation to distinguish between positive and negative sand fly trapping sites in BIH. In total, 55 blood meals of two sand fly species, Ph. neglectus and Ph. balcanicus, were analyzed and five host species identified. Our comprehensive assessment of ecological and environmental preferences of sand flies in BIH may support further entomological surveys and help to better understand and evaluate potential hot spots of disease transmission in the country.},
}
@article {pmid39276821,
year = {2024},
author = {Katoh, TK and Chen, JM and Yang, JH and Zhang, G and Wang, L and Suwito, A and Ak Meleng, P and Toda, MJ and Zhang, YP and Gao, JJ},
title = {Molecular phylogeny and species diversity of the genus Dichaetophora Duda and related taxa (Diptera: Drosophilidae).},
journal = {Molecular phylogenetics and evolution},
volume = {201},
number = {},
pages = {108194},
doi = {10.1016/j.ympev.2024.108194},
pmid = {39276821},
issn = {1095-9513},
mesh = {Animals ; *Phylogeny ; *Drosophilidae/genetics/classification ; *DNA Barcoding, Taxonomic ; Male ; Electron Transport Complex IV/genetics ; Sequence Analysis, DNA ; Bayes Theorem ; },
abstract = {Our intensive surveys of wild drosophilids in East and Southeast Asia discovered a great species diversity (more than 100 putatively new species) of the genus Dichaetophora, which is currently comprised of 67 formally described species assigned into five species groups, i.e., agbo, tenuicauda, acutissima, sinensis and trilobita. In the present study, we delimited species from a huge amount of samples of Dichaetophora and allied taxa (the genus Mulgravea and the subgenus Dudaica of Drosophila) collected from a wide range of the Oriental and east Palearctic regions. We first sorted all specimens into morpho-species, and representative specimen(s) selected from each morpho-species were subjected to barcoding of COI (the cytochrome c oxidase subunit I gene) sequences. The applied ASAP (Assemble Species by Automatic Partitioning) analysis estimated a total of 166 to 168 MOTUs (molecular operational taxonomic units). Integrating this result with morphological evidence from re-examined, detailed structures of male terminalia, we recognized a total of 144 (109 new and 35 known) species in our sample. Out of them, 83 species representing the supraspecific taxa of Dichaetophora, Mulgravea and Dudaica were selected, along with 33 species from major genera and subgenera of Drosophila in the tribe Drosophilini, as in-group and four species from the tribe Colocasiomyini as out-group for phylogenetic reconstruction based on 12 nuclear gene markers. In the trees constructed by the maximum likelihood and Bayesian inference methods, the three focal taxa (i.e., Dichaetophora, Mulgravea and Dudaica) formed a clade provisionally called the "pan-Dichaetophora". Within this large clade, the agbo, tenuicauda, sinensis and trilobita groups of Dichaetophora, Mulgravea and Dudaica were recovered as monophyletic groups, but Dichaetophora and its acutissima group were regarded as paraphyletic. In addition, two clusters were recognized among ungrouped species of Dichaetophora. Thus, the present study has uncovered some issues concerning the taxonomy of the pan-Dichaetophora. Such issues will be addressed elsewhere in the phylogenetic reclassification of the pan-Dichaetophora, along with descriptions/redescriptions of a large number of new/known species delimited in the present study.},
}
@article {pmid39267427,
year = {2024},
author = {Nieto-Lugilde, M and Nieto-Lugilde, D and Piatkowski, B and Duffy, AM and Robinson, SC and Aguero, B and Schuette, S and Wilkens, R and Yavitt, J and Shaw, AJ},
title = {Ecological differentiation and sympatry of cryptic species in the Sphagnum magellanicum complex (Bryophyta).},
journal = {American journal of botany},
volume = {111},
number = {9},
pages = {e16401},
doi = {10.1002/ajb2.16401},
pmid = {39267427},
issn = {1537-2197},
mesh = {*Sympatry ; *Sphagnopsida/genetics ; Ecosystem ; Phylogeny ; North America ; DNA Barcoding, Taxonomic ; Climate ; Species Specificity ; },
abstract = {PREMISE: Sphagnum magellanicum (Sphagnaceae, Bryophyta) has been considered to be a single semi-cosmopolitan species, but recent molecular analyses have shown that it comprises a complex of at least seven reciprocally monophyletic groups, that are difficult or impossible to distinguish morphologically.<br><br>METHODS: Newly developed barcode markers and RADseq analyses were used to identify species among 808 samples from 119 sites. Molecular approaches were used to assess the geographic ranges of four North American species, the frequency at which they occur sympatrically, and ecological differentiation among them. Microhabitats were classified with regard to hydrology and shade. Hierarchical modelling of species communities was used to assess climate variation among the species. Climate niches were projected back to 22,000 years BP to assess the likelihood that the North American species had sympatric ranges during the late Pleistocene.<br><br>RESULTS: The species exhibited parallel morphological variation, making them extremely difficult to distinguish phenotypically. Two to three species frequently co-occurred within peatlands. They had broadly overlapping microhabitat and climate niches. Barcode- versus RADseq-based identifications were in conflict for 6% of the samples and always involved S. diabolicum vs. S. magniae.<br><br>CONCLUSIONS: These species co-occur within peatlands at scales that could permit interbreeding, yet they remain largely distinct genetically and phylogenetically. The four cryptic species exhibited distinct geographic and ecological patterns. Conflicting identifications from barcode vs. RADseq analyses for S. diabolicum versus S. magniae could reflect incomplete speciation or hybridization. They comprise a valuable study system for additional work on climate adaptation.},
}
@article {pmid39273486,
year = {2024},
author = {Lei, W and Zhou, P and Pei, Z and Liu, Y and Luo, Y and Xiang, X},
title = {Plastome Evolution and Comparative Analyses of a Recently Radiated Genus Vanda (Aeridinae, Orchidaceae).},
journal = {International journal of molecular sciences},
volume = {25},
number = {17},
pages = {},
pmid = {39273486},
issn = {1422-0067},
mesh = {*Orchidaceae/genetics/classification ; *Phylogeny ; *Evolution, Molecular ; Genome, Plastid ; Base Composition ; DNA Barcoding, Taxonomic ; },
abstract = {Vanda R.Br. is an epiphytic orchid genus with significant horticultural and ornamental value. Previous molecular studies expanded Vanda including some members from five other genera. However, the interspecific relationships of this recently radiated genus have remained unclear based on several DNA markers until now. In this study, the complete plastome has been used to infer the phylogenetic relationships of Vanda s.l. The five newly obtained plastomes ranged from 146,340 bp to 149,273 bp in length, with a GC content ranging from 36.5% to 36.7%. The five plastomes contained 74 protein-coding genes (CDSs), 38 tRNAs, and 8 rRNAs, and their ndh genes underwent loss or pseudogenization. Comparative plastome analyses of 13 Vanda species revealed high conservation in terms of genome size, structure, and gene order, except for a large inversion from trnG[GCC] to ycf3 in V. coerulea. Moreover, six CDSs and five non-CDSs were selected as candidate DNA barcodes. Our phylogenetic analyses demonstrated that Vanda s.l. is a monophyletic group with high supporting values based on five different datasets (complete plastome with one IR, 68 CDSs, LSC, five hypervariable non-CDSs, and six hypervariable CDSs), while the phylogenetic relationships among species were fully resolved based on the complete plastome with one IR dataset. Our results confirmed that the complete plastome has a great power in resolving the phylogenetic relationships of recently radiated lineages.},
}
@article {pmid39270602,
year = {2024},
author = {González, MA and Ruiz-Arrondo, I and Magallanes, S and Oboňa, J and Ruiz-López, MJ and Figuerola, J},
title = {Molecular and morphological analysis revealed a new Lipoptena species (Diptera: Hippoboscidae) in southern Spain harbouring Coxiella burnetii and bacterial endosymbionts.},
journal = {Veterinary parasitology},
volume = {332},
number = {},
pages = {110300},
doi = {10.1016/j.vetpar.2024.110300},
pmid = {39270602},
issn = {1873-2550},
mesh = {Animals ; Spain/epidemiology ; *Diptera/microbiology ; Female ; Male ; *Coxiella burnetii/genetics/isolation &amp; purification ; *Symbiosis ; Phylogeny ; Wolbachia/genetics/isolation &amp; purification/physiology ; DNA Barcoding, Taxonomic ; },
abstract = {Hippoboscid flies (Diptera: Hippoboscidae) are obligate bloodsucking ectoparasites of animals. In Europe, limited research has been conducted on this family until the recent introduction of the deer ked Lipoptena fortisetosa Maa, 1965. A new species of the genus Lipoptena, Lipoptena andaluciensis sp. nov., was found in southern Spain after extensive sampling with carbon-dioxide baited suction traps. A total of 52 females and 32 males were collected at 29 out of 476 sites examined over eight months in 2023. Lipoptena andaluciensis sp. nov. was characterized morphologically and molecularly. The new Lipoptena species can be differentiated from the closely related L. fortisetosa by size, chaetotaxy of the dorsal and ventral thorax, abdominal plates, and genitalia. Based on DNA-barcoding, our specimens showed the highest similarity with Melophagus ovinus (Linnaeus, 1758) (88.4 %) and with L. fortisetosa (86-88 %). Individual screening of Lipoptena specimens (n = 76) for seven important zoonotic pathogens such as bacteria (Anaplasmataceae family: Bartonella spp., Borrelia spp., Coxiella burnetii and Rickettsia spp.) and protozoans (Babesia spp. and Theileria spp.) by conventional PCR and RT-PCR was performed. DNA of C. burnetii was detected in one specimen, while two other specimens harboured Anaplasmataceae (Wolbachia spp., 100 % homology and another endosymbiont probably related to Arsenophonus sp., 95.3 % homology, respectively), all representing the first records of these bacteria in the Lipoptena spp. from Europe. Carbon dioxide traps probed its effectiveness as a reliable passive method for keds surveillance. Our study highlights the existence of a new Lipoptena species, presumably widely distributed in southern Spain. The role of this species in the transmission cycle of pathogens of medical-veterinary relevance needs to be considered in the area.},
}
@article {pmid39268009,
year = {2024},
author = {Lim, C and Minkina, &#x141;},
title = {A new species of genus Acrossus Mulsant, 1842 (Scarabaeidae, Aphodiinae, Aphodiini) from South Korea.},
journal = {ZooKeys},
volume = {1211},
number = {},
pages = {211-230},
pmid = {39268009},
issn = {1313-2989},
abstract = {A new species of the genus Acrossus Mulsant, 1842, Acrossusbaei sp. nov. from South Korea, is described and illustrated on the basis of morphology and mitochondrial COI sequences. The species was compared with four related species; Acrossusatratus (Waterhouse, 1875), A.humerospinosus (Petrovitz, 1958), A.luridus (Fabricius, 1775), and A.superatratus (Nomura &amp; Nakane, 1951). The taxonomic status and diagnostic characters of the new species are discussed. A key to species of the genus Acrossus in the Korean Peninsula is given.},
}
@article {pmid39267125,
year = {2024},
author = {Shah, HK and Fathima, PA and Jicksy, J and Saini, P},
title = {Report of a new species of sand fly, Phlebotomus (Anaphlebotomus) ajithii n. sp. (Diptera: Psychodidae), from Western Ghats, India.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {388},
pmid = {39267125},
issn = {1756-3305},
support = {6/9-7(331)/2020/ECD-II//Indian Council of Medical Research/ ; IM-1905//Indian Council of Medical Research- Vector Control Research Centre/ ; },
mesh = {Animals ; India ; *Phlebotomus/genetics/classification ; *Phylogeny ; *Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; Female ; Male ; },
abstract = {BACKGROUND: Western Ghats is a biodiversity treasure trove with reports of indigenous leishmaniasis cases. Hence, systematic sand fly surveillance was carried out among the tribal population. The present study reports a novel sand fly species, Phlebotomus (Anaphlebotomus) ajithii n. sp. (Diptera: Psychodidae), discovered in the Western Ghats of India.<br><br>METHODS: A comprehensive sand fly survey was conducted across the Kollam, Thrissur, Idukki, Kasaragod and Malappuram districts of Kerala, India. The survey spanned both indoor and outdoor habitats using standard collection methods over a 3-year, 3-month period. DNA barcoding of samples was performed targeting mitochondrial cytochrome c oxidase subunit I (COI) gene, and the sequence generated was subjected to phylogenetic analysis.<br><br>RESULTS: Phlebotomus (Anaphlebotomus) ajithii, a new sand fly species, is recorded and described in this communication. The morphological relationship of the new species to other members of the subgenus Anaphlebotomus is discussed. Mitochondrial COI barcode followed by phylogenetic analysis confirmed that specimens of Ph. ajithii belong to the same taxonomic group, while a genetic distance of 11.7% from congeners established it as a distinct species.<br><br>CONCLUSIONS: The Western Ghats, known for its rich biodiversity, has lacked systematic entomological surveys focusing on sand flies. This study aims to fill this gap and reports and describes a new species of sand fly.},
}
@article {pmid39266625,
year = {2024},
author = {Almeida-Silva, MA and Braga-Ferreira, RS and Targueta, CP and Corvalán, LCJ and Silva-Neto, CM and Franceschinelli, EV and Sobreiro, MB and Nunes, R and Telles, MPC},
title = {Chloroplast genomes of Simarouba Aubl., molecular evolution and comparative analyses within Sapindales.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21358},
pmid = {39266625},
issn = {2045-2322},
support = {#28/2018//MCTIC/CNPq/ ; 435477/2018-8//MCTIC/CNPq/ ; 441114/2023-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 202210267000536//TWRA/FAPEG/ ; },
mesh = {*Genome, Chloroplast/genetics ; *Phylogeny ; *Evolution, Molecular ; },
abstract = {Simarouba, a neotropical genus in the family Simaroubaceae, currently lacks comprehensive genomic data in existing databases. This study aims to fill this gap by providing genomic resources for three Simarouba species, S. amara, S. versicolor, and S. glauca. It also aims to perform comparative molecular evolutionary analyses in relation to other species within the order Sapindales. The analysis of these three Simarouba species revealed the presence of the typical quadripartite structure expected in plastomes. However, some pseudogenization events were identified in the psbC, infA, rpl22, and ycf1 genes. In particular, the CDS of the psbC gene in S. amara was reduced from 1422 bp to 584 bp due to a premature stop codon. Nucleotide diversity data pointed to gene and intergenic regions as promising candidates for species and family discrimination within the group, specifically matK, ycf1, ndhF, rpl32, petA-psbJ, and trnS-trnG. Selection signal analyses showed strong evidence for positive selection on the rpl23 gene. Phylogenetic analyses indicated that S. versicolor and S. glauca have a closer phylogenetic relationship than S. amara. We provide chloroplast genomes of three Simaruba species and use them to elucidate plastome evolution, highlight the presence of pseudogenization, and identify potential DNA barcode regions.},
}
@article {pmid39265309,
year = {2024},
author = {Hung, CC and Chang, JS and Liao, CH and Lee, TM},
title = {Exploring the impact of ocean warming and nutrient overload on macroalgal blooms and carbon sequestration in deep-sea sediments of the subtropical western North Pacific.},
journal = {Marine pollution bulletin},
volume = {208},
number = {},
pages = {116918},
doi = {10.1016/j.marpolbul.2024.116918},
pmid = {39265309},
issn = {1879-3363},
mesh = {*Seaweed ; *Carbon Sequestration ; *Geologic Sediments/chemistry ; Pacific Ocean ; Carbon/analysis ; Eutrophication ; Climate Change ; Nutrients/analysis ; Environmental Monitoring ; Nitrogen/analysis ; },
abstract = {The role of macroalgae as blue carbon (BC) under changing climate was investigated in the subtropical western North Pacific. Sea surface temperatures (SSTs) and nutrient influx increased over the past two decades (2001-2021). The proliferation of climate-resilient macroalgae was facilitated. Using Pterocladiella capillacea and Turbinaria ornata, outdoor laboratory experiments and elemental assays underscored the influence of nutrient enrichment on their resilience under ocean warming and low salinity. Macroalgal incorporation into marine sediments, indicated by environmental DNA barcoding, total organic carbon (TOC), and stable isotope analysis. Over time, an increase in δ[13]C and δ[15]N values, particularly at greater depths, suggests a tendency of carbon signature towards macroalgaeand nitrogen pollution or high tropic levels. eDNA analysis revealed selective deposition of these species. The species-dependent nature of macroalgae in deep-sea sediments highlights the role of nutrients on climate-resilient macroalgal blooms as carbon sinks in the western North Pacific.},
}
@article {pmid39262988,
year = {2024},
author = {Mousa, WK and Ghemrawi, R and Abu-Izneid, T and Al Ramadan, N and Al Sheebani, F},
title = {The design and development of EcoBiomes: Multi-species synthetic microbial consortia inspired by natural desert microbiome to enhance the resilience of climate-sensitive ecosystems.},
journal = {Heliyon},
volume = {10},
number = {16},
pages = {e36548},
pmid = {39262988},
issn = {2405-8440},
abstract = {Synthetic microbial communities, which simplify the complexity of natural ecosystems while retaining their key features, are gaining momentum in engineering and biotechnology applications. One potential application is the development of bioinoculants, offering an eco-friendly, sustainable solution to promote plant growth and increase resilience to abiotic stresses amidst climate change. A potential source for stress-tolerant microbes is those associated with desert plants, evolved and shaped by selective pressures to promote host health under harsh environmental conditions. In our research, we aim to design and develop synthetic microbial consortia inspired by the natural microbiota of four desert plants native to the Arabian Peninsula, inferred from our previous work identifying the structure and predicting the function of these microbial communities using high throughput eDNA barcoding. To obtain culturable microbes that are manageable and traceable yet still representative of natural microbial communities, we combined multiple experimental protocols coupled with compatibility and synergy assessments, along with in planta testing. We isolated a total of 75 bacteria and conducted detailed biological evaluations, revealing that an overwhelming majority (84 %) of all isolates produced indole acetic acid (IAA), with 73 % capable of solubilizing phosphate, 60 % producing siderophores, 47 % forming biofilms, and 35 % producing ACC deaminase, all contributing to plant growth and stress tolerance. We constructed four synthetic microbial consortia, named EcoBiomes, consisting of synergistic combinations of multiple species that can co-exist without significant antagonism. Our preliminary data indicate that EcoBiomes enhance the resilience of heterologous host plants under simulated environmental stresses, including drought, heat, and salinity. EcoBiomes offer a unique, sustainable, and eco-friendly solution to mitigate the impact of climate change on sensitive ecosystems, ultimately affecting global food security.},
}
@article {pmid39262866,
year = {2024},
author = {Mohtar, JA and Rahman, KHA and Nyanasilan, S and Abdullah, NAH and Mohamad, F},
title = {Discovery of Web-Building Spiders in Gua Kelam, Perlis State Park, Malaysia.},
journal = {Tropical life sciences research},
volume = {35},
number = {1},
pages = {87-106},
pmid = {39262866},
issn = {1985-3718},
abstract = {A cave represents a subterranean ecosystem that harbours a myriad of unique, peculiar, and secluded flora and fauna. These biotas have evolved with a wide range of ecological adaptations that allow them to thrive in harsh environments with limited light. Gua Kelam 1 constitutes part of the Gua Kelam limestone caves system in the Nakawan Range of Perlis State Park, Malaysia. Previous observations indicated that it harbours a plethora of spider species; however, their existence is still elusive as speleobiological studies remain unexplored. Herein, we identified the cavernicolous spiders found in the dark zone areas of Gua Kelam 1 through a complementary approach based on morphology and DNA barcoding. From the morphological analysis, we described three web-building spiders of JTKK2 and JTKK3 groups down to the species-level to belong to Nephilengys malabarensis, and Orsinome vethi except for Pholcus sp. from JTKK4 individuals. The molecular analysis of the cytochrome oxidase-I (COI) genes of JTKK2 and JTKK3 individuals showed that they exhibited a high degree similarity with N. malabarensis (98.3%), and O. vethi (100.0%), respectively except for JTKK4 individuals with only 91.4% homology with P. kuhapimuk. Phylogenetic analysis also generated a congruent tree, in which the identified species are well nested within the family Araneidae, Tetragnathidae, and Pholcidae. By this integral approach, the three spiders were determined as N. malabarensis, O. vethi, and Pholcus sp. These spiders are originally epigean in their habitat but uniquely thrive in Gua Kelam 1.},
}
@article {pmid39258880,
year = {2024},
author = {Xhekaj, B and Hoxha, I and Platzgummer, K and Stefanovska, J and Dvořák, V and Milchram, M and Obwaller, AG and Poeppl, W and Muja-Bajraktari, N and Walochnik, J and Trájer, AJ and Sherifi, K and Cvetkovikj, A and Kniha, E},
title = {A cross-sectional study on phlebotomine sand flies in relation to disease transmission in the Republic of Kosovo.},
journal = {Medical and veterinary entomology},
volume = {38},
number = {4},
pages = {573-585},
doi = {10.1111/mve.12758},
pmid = {39258880},
issn = {1365-2915},
support = {886318//Austrian defence research programme FORTE of the Federal Ministry of Finance/ ; RRF-2.3.1-21-2022-00014//National Multidisciplinary Laboratory for Climate Change/ ; //J&#xe1;nos Bolyai Research Scholarship of the Hungarian Academy of Sciences/ ; },
mesh = {Animals ; Kosovo ; *Insect Vectors/physiology/parasitology ; Cross-Sectional Studies ; *Animal Distribution ; *Phlebotomus/classification/physiology/parasitology ; Female ; Psychodidae/physiology/parasitology ; Male ; Dogs ; Leishmania infantum/physiology ; },
abstract = {Sand flies (Diptera: Psychodidae: Phlebotominae) are blood-feeding insects that transmit the protozoan parasites Leishmania spp. and various arboviruses. The Balkan region, including the Republic of Kosovo, harbours a diverse sand fly fauna. Vector species of Leishmania infantum as well as phleboviruses are endemic; however, recent data are scarce. We performed a cross-sectional study to update the current sand fly distribution in Kosovo and assess biological as well as environmental factors associated with sand fly presence. CDC light trapping was conducted at 46 locations in 2022 and 2023, specifically targeting understudied regions in Kosovo. Individual morphological species identification was supported by molecular barcoding. The occurrence data of sand flies was used to create distribution maps and perform environmental analyses, taking elevation, wind speed and climate-related factors into account. In addition, PCR-based blood meal analysis and pathogen screening were conducted. Overall, 303 specimens of six sand fly species were trapped, predominated by Phlebotomus neglectus (97%). Barcodes from eight of nine known endemic sand fly species were obtained. Combining our data with previous surveys, we mapped the currently known sand fly distribution based on more than 4000 specimens at 177 data points, identifying Ph. neglectus and Ph. perfiliewi as the predominant species. Environmental analyses depicted two geographical groups of sand flies in Kosovo, with notable differences between the species. In total, 223 blood meals of five sand fly species were analysed. Of seven identified host species, the predominant blood meal source was observed to be cattle, but the DNA of dogs and humans, among others, was also detected. This study assessed biological as well as ecological factors of sand fly occurrence, which should help better understand and evaluate potential hot spots of disease transmission in Kosovo.},
}
@article {pmid39258547,
year = {2024},
author = {Kristen, M and Lander, M and Kilz, LM and Gleue, L and Jörg, M and Bregeon, D and Hamdane, D and Marchand, V and Motorin, Y and Friedland, K and Helm, M},
title = {DORQ-seq: high-throughput quantification of femtomol tRNA pools by combination of cDNA hybridization and Deep sequencing.},
journal = {Nucleic acids research},
volume = {52},
number = {18},
pages = {e89},
pmid = {39258547},
issn = {1362-4962},
support = {TRR-319 TP A05//Deutsche Forschungsgemeinschaft/ ; //ANR PRCI D-Erase/ ; },
mesh = {*RNA, Transfer/genetics/metabolism ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; *DNA, Complementary/genetics ; *Nucleic Acid Hybridization/methods ; Alzheimer Disease/genetics ; Sequence Analysis, RNA/methods ; Brain/metabolism ; },
abstract = {Due to its high modification content tRNAs are notoriously hard to quantify by reverse transcription and RNAseq. Bypassing numerous biases resulting from concatenation of enzymatic treatments, we here report a hybrid approach that harnesses the advantages of hybridization-based and deep sequencing-based approaches. The method renders obsolete any RNAseq related workarounds and correction factors that affect accuracy, sensitivity, and turnaround time. Rather than by reverse transcription, quantitative information on the isoacceptor composition of a tRNA pool is transferred to a cDNA mixture in a single step procedure, thereby omitting all enzymatic conversations except for the subsequent barcoding PCR. As a result, a detailed tRNA composition matrix can be obtained from femtomolar amounts of total tRNA. The method is fast, low in cost, and its bioinformatic data workup surprisingly simple. These properties make the approach amenable to high-throughput investigations including clinical samples, as we have demonstrated by application to a collection of variegated biological questions, each answered with novel findings. These include tRNA pool quantification of polysome-bound tRNA, of tRNA modification knockout strains under stress conditions, and of Alzheimer patients' brain tissues.},
}
@article {pmid39256584,
year = {2024},
author = {Zhu, J and Pang, K and Hu, B and He, R and Wang, N and Jiang, Z and Ji, P and Zhao, F},
title = {Custom microfluidic chip design enables cost-effective three-dimensional spatiotemporal transcriptomics with a wide field of view.},
journal = {Nature genetics},
volume = {56},
number = {10},
pages = {2259-2270},
pmid = {39256584},
issn = {1546-1718},
support = {32025009//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Mice ; *Transcriptome ; *Gene Expression Profiling/methods ; Microfluidics/methods ; Brain/metabolism ; Single-Cell Analysis/methods ; Cost-Benefit Analysis ; Lab-On-A-Chip Devices ; Organogenesis/genetics ; },
abstract = {Spatial transcriptomic techniques offer unprecedented insights into the molecular organization of complex tissues. However, integrating cost-effectiveness, high throughput, a wide field of view and compatibility with three-dimensional (3D) volumes has been challenging. Here we introduce microfluidics-assisted grid chips for spatial transcriptome sequencing (MAGIC-seq), a new method that combines carbodiimide chemistry, spatial combinatorial indexing and innovative microfluidics design. This technique allows sensitive and reproducible profiling of diverse tissue types, achieving an eightfold increase in throughput, minimal cost and reduced batch effects. MAGIC-seq breaks conventional microfluidics limits by enhancing barcoding efficiency and enables analysis of whole postnatal mouse sections, providing comprehensive cellular structure elucidation at near single-cell resolution, uncovering transcriptional variations and dynamic trajectories of mouse organogenesis. Our 3D transcriptomic atlas of the developing mouse brain, consisting of 93 sections, reveals the molecular and cellular landscape, serving as a valuable resource for neuroscience and developmental biology. Overall, MAGIC-seq is a high-throughput, cost-effective, large field of view and versatile method for spatial transcriptomic studies.},
}
@article {pmid39255672,
year = {2024},
author = {Douard, M and Fernandez, S and Garcia-Vazquez, E and Planes, S},
title = {Rapid expansion and ecosystem health risk of invasive biopollutants dispersed by maritime traffic in French Polynesia.},
journal = {Marine pollution bulletin},
volume = {208},
number = {},
pages = {116927},
doi = {10.1016/j.marpolbul.2024.116927},
pmid = {39255672},
issn = {1879-3363},
mesh = {Polynesia ; *Introduced Species ; Animals ; *Ecosystem ; Biofouling ; Ships ; Environmental Monitoring ; },
abstract = {The introduction of biopollutant species challenge ecosystem health and economy in remote islands. Here we checked the advance of invasive fouling species in five French Polynesian islands. Expansion of invasive species (Acantophora spicifera, Bugula neritina, Chthamalus proteus, Dendostrea frons) was detected using individual barcoding (COI for animals, RBLC for algae), and metabarcoding on biofouling (COI and 18S sequences). They were especially abundant in Port Phaeton (Tahiti), Bora Bora and Rangiroa atoll. Chthamalus proteus is a vector of bacterial diseases and may harm native French Polynesian mollusks. Dendostrea frons is a vector of Perkinsus, a parasite to which black pearl oysters, the mainstay of the Polynesian economy, are susceptible. High ecological and epidemiological risks were estimated for C. proteus and D. frons, and ecological risks also for A. spicifera and especially for B. neritina. Strengthening marine biosecurity measures is highly recommended to conserve these unique ecosystems and their associated services.},
}
@article {pmid39254601,
year = {2024},
author = {De Rijk, P and Watzeels, T and Küçükali, F and Van Dongen, J and Faura, J and Willems, P and De Deyn, L and Duchateau, L and Grones, C and Eekhout, T and De Pooter, T and Joris, G and Rombauts, S and De Rybel, B and Rademakers, R and Van Breusegem, F and Strazisar, M and Sleegers, K and De Coster, W},
title = {Scywalker: scalable end-to-end data analysis workflow for long-read single-cell transcriptome sequencing.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {9},
pages = {},
pmid = {39254601},
issn = {1367-4811},
support = {//University of Antwerp/ ; AARG-20-683760/ALZ/Alzheimer's Association/United States ; },
mesh = {*Single-Cell Analysis/methods ; Humans ; *Software ; *Workflow ; Transcriptome/genetics ; Arabidopsis/genetics ; Brain/metabolism ; High-Throughput Nucleotide Sequencing/methods ; Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; },
abstract = {MOTIVATION: Existing nanopore single-cell data analysis tools showed severe limitations in handling current data sizes.<br><br>RESULTS: We introduce scywalker, an innovative and scalable package developed to comprehensively analyze long-read sequencing data of full-length single-cell or single-nuclei cDNA. We developed novel scalable methods for cell barcode demultiplexing and single-cell isoform calling and quantification and incorporated these in an easily deployable package. Scywalker streamlines the entire analysis process, from sequenced fragments in FASTQ format to demultiplexed pseudobulk isoform counts, into a single command suitable for execution on either server or cluster. Scywalker includes data quality control, cell type identification, and an interactive report. Assessment of datasets from the human brain, Arabidopsis leaves, and previously benchmarked data from mixed cell lines demonstrate excellent correlation with short-read analyses at both the cell-barcoding and gene quantification levels. At the isoform level, we show that scywalker facilitates the direct identification of cell-type-specific expression of novel isoforms.<br><br>Scywalker is available on github.com/derijkp/scywalker under the GNU General Public License (GPL) and at https://zenodo.org/records/13359438/files/scywalker-0.108.0-Linux-x86_64.tar.gz.},
}
@article {pmid39251911,
year = {2024},
author = {Chang, JJM and Ip, YCA and Neo, WL and Mowe, MAD and Jaafar, Z and Huang, D},
title = {Primed and ready: nanopore metabarcoding can now recover highly accurate consensus barcodes that are generally indel-free.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {842},
pmid = {39251911},
issn = {1471-2164},
support = {A-0008413-00-00//National Parks Board - Singapore/ ; MSRDP-P18//National Research Foundation Singapore/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Nanopores ; Animals ; *High-Throughput Nucleotide Sequencing/methods ; INDEL Mutation ; Nanopore Sequencing/methods ; Electron Transport Complex IV/genetics ; Zooplankton/genetics/classification ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: DNA metabarcoding applies high-throughput sequencing approaches to generate numerous DNA barcodes from mixed sample pools for mass species identification and community characterisation. To date, however, most metabarcoding studies employ second-generation sequencing platforms like Illumina, which are limited by short read lengths and longer turnaround times. While third-generation platforms such as the MinION (Oxford Nanopore Technologies) can sequence longer reads and even in real-time, application of these platforms for metabarcoding has remained limited possibly due to the relatively high read error rates as well as the paucity of specialised software for processing such reads.<br><br>RESULTS: We show that this is no longer the case by performing nanopore-based, cytochrome c oxidase subunit I (COI) metabarcoding on 34 zooplankton bulk samples, and benchmarking the results against conventional Illumina MiSeq sequencing. Nanopore R10.3 sequencing chemistry and super accurate (SUP) basecalling model reduced raw read error rates to ~&#x2009;4%, and consensus calling with amplicon_sorter (without further error correction) generated metabarcodes that were &#x2264;&#x2009;1% erroneous. Although Illumina recovered a higher number of molecular operational taxonomic units (MOTUs) than nanopore sequencing (589 vs. 471), we found no significant differences in the zooplankton communities inferred between the sequencing platforms. Importantly, 406 of 444 (91.4%) shared MOTUs between Illumina and nanopore were also found to be free of indel errors, and 85% of the zooplankton richness could be recovered after just 12-15&#xa0;h of sequencing.<br><br>CONCLUSION: Our results demonstrate that nanopore sequencing can generate metabarcodes with Illumina-like accuracy, and we are the first study to show that nanopore metabarcodes are almost always indel-free. We also show that nanopore metabarcoding is viable for characterising species-rich communities rapidly, and that the same ecological conclusions can be obtained regardless of the sequencing platform used. Collectively, our study inspires confidence in nanopore sequencing and paves the way for greater utilisation of nanopore technology in various metabarcoding applications.},
}
@article {pmid39250970,
year = {2024},
author = {Jakubska-Busse, A and Wysocki, A and Domagała, PJ and Brudzińska-Kosior, A and Sporek, M and Kosior, G},
title = {Expanding the boundaries in the face of global warming: A lesson from genetic and ecological niche studies of Centaurium erythraea in Europe.},
journal = {The Science of the total environment},
volume = {953},
number = {},
pages = {176134},
doi = {10.1016/j.scitotenv.2024.176134},
pmid = {39250970},
issn = {1879-1026},
mesh = {*Global Warming ; Europe ; *Centaurium/genetics ; *Ecosystem ; *Climate Change ; DNA, Chloroplast/genetics ; },
abstract = {Climate change affects plant species, especially those with restricted ecology and distribution. Centaurium erythraea is a flowering plant species in the Gentianaceae family, native to Europe, with its centre of diversity in the Mediterranean and western Asia. Of the 11 infraspecific taxa distinct from C. erythraea, only two are common in Europe: C. erythraea subsp. erythraea (widespread nominal subspecies) and C. erythraea subsp. majus (mainly distributed in the western Mediterranean region). Freshly collected samples of 36 plants from 11 localities across Lower Silesia (Central Europe) were utilised for taxonomic and genetic analysis. The barcode sequences of chloroplast DNA region matK were used for molecular analysis. Data deposited in GenBank was also used. Five haplotypes were identified among the analysed specimens. Species Distribution Modelling (SDM) techniques were applied to predict the current and future (short- and long-term projections) potential distribution of C. erythraea subsp. majus and to identify the most influential climatic factors. Despite the typical Mediterranean distribution, the presence of C. erythraea subsp. majus outside its natural range in SW Poland has been confirmed by morphological and genetic studies. The mean monthly precipitation of the wettest quarter and the mean daily temperatures of the warmest quarter were identified as the key climatic factors. Short-term scenarios suggest that C. erythraea subsp. majus will maintain most of its current suitable habitats and potentially expand into the lowlands of Central Europe. However, long-term projections indicate a potential reduction in its currently suitable areas, especially in the southern parts of its range, with a possible expansion into north-western Europe. The results of these studies provide clear evidence of the impact of ongoing climate change on species range changes. These findings suggest that climate change may create new opportunities for Mediterranean species to spread to new regions, using C. erythraea subsp. majus as an example.},
}
@article {pmid39250184,
year = {2024},
author = {Pallen, MJ},
title = {The dynamic history of prokaryotic phyla: discovery, diversity and division.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {9},
pages = {},
pmid = {39250184},
issn = {1466-5034},
mesh = {Archaea/genetics/classification ; *Bacteria/genetics/classification ; Classification/methods ; History, 20th Century ; History, 21st Century ; *Phylogeny ; Prokaryotic Cells/classification ; History, 19th Century ; },
abstract = {Here, I review the dynamic history of prokaryotic phyla. Following leads set by Darwin, Haeckel and Woese, the concept of phylum has evolved from a group sharing common phenotypes to a set of organisms sharing a common ancestry, with modern taxonomy based on phylogenetic classifications drawn from macromolecular sequences. Phyla came as surprising latecomers to the formalities of prokaryotic nomenclature in 2021. Since then names have been validly published for 46 prokaryotic phyla, replacing some established names with neologisms, prompting criticism and debate within the scientific community. Molecular barcoding enabled phylogenetic analysis of microbial ecosystems without cultivation, leading to the identification of candidate divisions (or phyla) from diverse environments. The introduction of metagenome-assembled genomes marked a significant advance in identifying and classifying uncultured microbial phyla. The lumper-splitter dichotomy has led to disagreements, with experts cautioning against the pressure to create a profusion of new phyla and prominent databases adopting a conservative stance. The Candidatus designation has been widely used to provide provisional status to uncultured prokaryotic taxa, with phyla named under this convention now clearly surpassing those with validly published names. The Genome Taxonomy Database (GTDB) has offered a stable, standardized prokaryotic taxonomy with normalized taxonomic ranks, which has led to both lumping and splitting of pre-existing phyla. The GTDB framework introduced unwieldy alphanumeric placeholder labels, prompting recent publication of over 100 user-friendly Latinate names for unnamed prokaryotic phyla. Most candidate phyla remain 'known unknowns', with limited knowledge of their genomic diversity, ecological roles, or environments. Whether phyla still reflect significant evolutionary and ecological partitions across prokaryotic life remains an area of active debate. However, phyla remain of practical importance for microbiome analyses, particularly in clinical research. Despite potential diminishing returns in discovery of biodiversity, prokaryotic phyla offer extensive research opportunities for microbiologists for the foreseeable future.},
}
@article {pmid39247893,
year = {2024},
author = {Zhu, L and Bau, T},
title = {Species clarification of fairy inkcap ("Coprinellus disseminatus") in China.},
journal = {Mycology},
volume = {15},
number = {3},
pages = {424-470},
pmid = {39247893},
issn = {2150-1203},
abstract = {Coprinellus disseminatus and other morphologically similar species are widely dispersed worldwide and are commonly referred to as "fairy inkcap". Based on the molecular phylogenetic study and morphological observation, a thorough investigation was carried out utilising 74 collections of related species that were gathered from seventeen provinces and five Chinese fungaria between 1998 and 2023 and revealed 11 lineages of "fairy inkcap", nine of which were found in China, and which belonged to the two genera Coprinellus and Tulosesus. In sect. Disseminati, genetic diversities (π), and fixation index (Fst) amongst lineages were computed, and a haplotype-based network was established to ascertain the relationships amongst each clade. A new section of Coprinellus, sect. Aureodisseminati, were discovered. In addition, four new species (C. aureodisseminatus, C. austrodisseminatus, C. parcus, and C. velutipes), a new subspecies of C. disseminatus, a new combination (Tulosesus pseudodisseminatus), the first discovery of epigamous type of C. magnoliae and a new record to China (T. subdisseminatus) were also identified and thoroughly described with accompanying illustrations. Their differences in macro- and micro-features, as well as their character sequence, were discussed.},
}
@article {pmid39247535,
year = {2024},
author = {Zhang, A and Liu, W and Qiu, S},
title = {Mitochondrial genetic variations in leukemia: a comprehensive overview.},
journal = {Blood science (Baltimore, Md.)},
volume = {6},
number = {4},
pages = {e00205},
pmid = {39247535},
issn = {2543-6368},
abstract = {Leukemias are a group of heterogeneous hematological malignancies driven by diverse genetic variations, and the advent of genomic sequencing technologies facilitates the investigation of genetic abnormalities in leukemia. However, these sequencing-based studies mainly focus on nuclear DNAs. Increasing evidence indicates that mitochondrial dysfunction is an important mechanism of leukemia pathogenesis, which is closely related to the mitochondrial genome variations. Here, we provide an overview of current research progress concerning mitochondrial genetic variations in leukemia, encompassing gene mutations and copy number variations. We also summarize currently accessible mitochondrial DNA (mtDNA) sequencing methods. Notably, somatic mtDNA mutations may serve as natural genetic barcodes for lineage tracing and longitudinal assessment of clonal dynamics. Collectively, these findings enhance our understanding of leukemia pathogenesis and foster the identification of novel therapeutic targets and interventions.},
}
@article {pmid39247285,
year = {2024},
author = {Lee, HT and Liao, CH and Hsu, TH},
title = {DNA metabarcoding unveils the hidden species composition in fish surimi: Implications for the management of unlabeled and mixed seafood products.},
journal = {Heliyon},
volume = {10},
number = {16},
pages = {e36287},
pmid = {39247285},
issn = {2405-8440},
abstract = {Fish surimi products are traditional foods primarily made from fish meat and may contain a complex species composition. In Taiwan, the abundant fishery resources and diverse fish species lead to local catches being widely used as ingredients in fish surimi products. However, due to growing market demand and increasingly scarce resources, some surimi products contain sensitive species, such as sharks, posing potential threats to the ecological environment and biodiversity. In this study, by applying metabarcoding techniques, we analyzed 120 fish surimi product samples from different brands and types throughout the four seasons in Taiwan's market. The main fish species identified included milkfish (Chanos chanos), dolphinfish (Coryphaena hippurus), Pomfret (Taractes rubescens), swordfish (Istiophorus spp.) and cartilaginous. Moreover, at least 37 species of cartilaginous fish, including 26 endangered species, were found. Through comprehensive and accurate species identification of surimi product ingredients, we unveiled the usage of sensitive species in products on the market. This finding is important for the surimi industry's quality control and market supervision. Furthermore, it can promote the sustainable use of Taiwan's fishery resources and protect biodiversity.},
}
@article {pmid39245155,
year = {2024},
author = {Telles-de-Deus, J and Guimarães, LO and Rocha, EC and Helfstein, VC and Reginato, SL and Mucci, LF and Bergo, ES and de Camargo-Neves, VLF and Kirchgatter, K},
title = {COI DNA barcoding to differentiate Haemagogus janthinomys and Haemagogus capricornii (Diptera: Culicidae) mosquitoes.},
journal = {Acta tropica},
volume = {259},
number = {},
pages = {107377},
doi = {10.1016/j.actatropica.2024.107377},
pmid = {39245155},
issn = {1873-6254},
mesh = {Animals ; *Electron Transport Complex IV/genetics ; *DNA Barcoding, Taxonomic/methods ; *Culicidae/classification/genetics ; *Phylogeny ; Male ; Female ; Brazil ; Sequence Analysis, DNA ; },
abstract = {The genus Haemagogus (Diptera: Culicidae) includes species that are important vectors of pathogens such as the yellow fever virus. The accurate identification of these species is essential for the control of zoonoses. Females of Hg. capricornii and Hg. janthinomys are morphologically indistinguishable, which makes the use of alternative identification techniques desirable. This study aimed to obtain sequences of the mitochondrial cytochrome c oxidase I (COI) gene, in the region widely used for DNA barcoding, of Haemagogus specimens from the state of São Paulo, Brazil, to evaluate the effectiveness of these sequences in the molecular identification of the species. A total of 37 female and 2 male mosquitoes were collected in various locations in the state of São Paulo, using methods such as hand-nets, Shannon traps, CDC light traps with CO2 bait and Nasci aspirators. The sequences of a 710 bp fragment of the COI gene were amplified by PCR and sequenced. A phylogenetic tree reconstruction was conducted using the Bayesian approach implemented in MrBayes v3.2.2, providing support values for taxa where genetic clusters may indicate the presence of new or cryptic species. We obtained 39 COI sequences representing three species: Haemagogus capricornii, Haemagogus leucocelaenus, and Haemagogus janthinomys. Bayesian analysis of the sequences produced clades that corroborate the morphological identification of the species. The separation of Hg. capricornii and Hg. janthinomys received 100 % statistical support and the Hg. capricornii was very well supported (91 %). The two sequences from male specimens, morphologically identified as Hg. capricornii, were grouped in the same clade, a sister clade of Hg. janthinomys. It is important to highlight that the Hg. janthinomys were positioned in several subclades, showing a polymorphism of this species within the state, a situation not observed for Hg. capricornii. For the first time, sequences of the mtCOI gene from Hg. capricornii were obtained and related to morphologically identified specimens. COI sequences proved effective in the molecular identification of Haemagogus species. This study contributes to the expansion of the GenBank database, providing the first sequences of Hg. capricornii and new sequences for Hg. janthinomys and Hg. leucocelaenus.},
}
@article {pmid39244012,
year = {2024},
author = {van Ingen-Buijs, VA and van Westerhoven, AC and Skiadas, P and Zuijdgeest, XCL and Haridas, S and Daum, C and Duffy, K and Guo, J and Hundley, H and LaButti, K and Lipzen, A and Pangilinan, J and Riley, R and Wang, J and Yan, M and Martin, F and Barry, K and Grigoriev, IV and Groenewald, JZ and Crous, PW and Seidl, MF},
title = {Phyllosticta paracitricarpa is synonymous with the EU quarantine fungus P. citricarpa based on phylogenomic analyses.},
journal = {Fungal genetics and biology : FG &amp; B},
volume = {175},
number = {},
pages = {103925},
doi = {10.1016/j.fgb.2024.103925},
pmid = {39244012},
issn = {1096-0937},
mesh = {*Phylogeny ; *Ascomycota/genetics/classification ; *Plant Diseases/microbiology ; Citrus/microbiology ; Genome, Fungal/genetics ; Genetic Variation ; Genomics ; },
abstract = {Phyllosticta citricarpa is an important citrus-pathogen and a quarantine organism in the European Union. Its recently described relative, P. paracitricarpa, is very closely related and not listed as a quarantine organism. P. paracitricarpa is very difficult to distinguish from P. citricarpa, since its morphological features overlap and the barcoding gene sequences that were originally used to delimit them as distinct species have a low number of species-specific polymorphisms that have subsequently been shown to overlap between the two clades. Therefore, we performed extensive genomic analyses to determine whether the genetic variation between P. citricarpa and P. paracitricarpa strains should be considered to represent infraspecific variation within P. citricarpa, or whether it is indicative of distinct species. Using a phylogenomic analysis with 3,000 single copy ortholog genes and whole-genome comparisons, we determined that the variation between P. citricarpa and P. paracitricarpa can be considered as infraspecies variation within P. citricarpa. We also determined the level of variation in mitochondrial assemblies of several Phyllosticta species and concluded there are only minimal differences between the assemblies of P. citricarpa and P. paracitricarpa. Thus, using several orthogonal approaches, we here demonstrate that variation within the nuclear and mitochondrial genomes of other Phyllosticta species is larger than variation between genomes obtained from P. citricarpa and P. paracitricarpa strains. Thus, P. citricarpa and P. paracitricarpa should be considered as conspecific.},
}
@article {pmid39243221,
year = {2024},
author = {Athey, KJ and Chapman, EG and Al-Khatri, S and Moktar, AM and Obrycki, JJ},
title = {Molecular identification of predation on the Dubas bug (Hemiptera: Tropiduchidae) in Oman date palms: density-dependent response to prey.},
journal = {Journal of insect science (Online)},
volume = {24},
number = {4},
pages = {},
pmid = {39243221},
issn = {1536-2442},
support = {TRC/SRG/DB/13/005//Research Council of Oman/ ; },
mesh = {Animals ; *Phoeniceae ; *Predatory Behavior ; Oman ; *Food Chain ; *Heteroptera/physiology ; Hemiptera/physiology ; Pest Control, Biological ; Population Density ; Ants/physiology ; Mites/physiology ; Seasons ; },
abstract = {The date palm (Phoenix dactylifera L.) (Arecales: Arecaceae) is the most economically important crop in Oman with an annual production of >360,000 tons of fruit. The Dubas bug (Ommatissus lybicus de Bergevin) (Hemiptera: Tropiduchidae) is one of the major pests of date palms, causing up to a 50% reduction in fruit production. Across the course of 2 seasons, a variety of arthropod predators living in the date palm canopy were investigated for possible biological control of Dubas bugs, given the growing interest in nonchemical insect pest control in integrated pest management. We collected ~6,900 arthropod predators directly from date palm fronds from 60 Omani date palm plantations and tested them for Dubas bug predation using PCR-based molecular gut content analysis. We determined that ≥56 species of arthropod predators feed on the Dubas bug. We found that predatory mites, ants, and the entire predator community combined showed a positive correlation between predation detection frequency and increasing Dubas bug density. Additionally, there was a significant impact of season on gut content positives, with the spring season having a significantly higher percentage of predators testing positive for Dubas bug, suggesting this season could be the most successful time to target conservation biological control programs utilizing a diverse suite of predators.},
}
@article {pmid39242726,
year = {2024},
author = {Rossouw, EI and Landschoff, J and Ndhlovu, A and Neef, G and Miya, M and Courtaillac, KL and Brokensha, R and von der Heyden, S},
title = {Detecting kelp-forest associated metazoan biodiversity with eDNA metabarcoding.},
journal = {npj biodiversity},
volume = {3},
number = {1},
pages = {4},
pmid = {39242726},
issn = {2731-4243},
support = {Keystone Grant 542 (1001 Seaforest Species)//Save Our Seas Foundation/ ; Keystone Grant 542 (1001 Seaforest Species)//Save Our Seas Foundation/ ; 105842//National Research Foundation/ ; },
abstract = {Environmental DNA (eDNA) metabarcoding is a promising tool for monitoring marine biodiversity, but remains underutilised in Africa. In this study, we evaluated the ability of aquatic eDNA metabarcoding as a tool for detecting biodiversity associated with a South African kelp forest, an ecosystem that harbours high diversity of species, many of which are endemic, but are also sensitive to changing environmental conditions and anthropogenic pressures. Using fine-scale spatial (1 m and 8 m) and temporal (every four hours for 24 h) sampling of aquatic environmental DNA and targeting two gene regions (mtDNA COI and 12S rRNA), metabarcoding detected 880 OTUs representing 75 families in the broader metazoan community with 44 OTUs representing 24 fish families. We show extensive variability in the eDNA signal across space and time and did not recover significant spatio-temporal structure in OTU richness and community assemblages. Metabarcoding detected a broad range of taxonomic groups, including arthropods, ascidians, cnidarians, echinoderms, ctenophores, molluscs, polychaetes, ichthyofauna and sponges, as well as Placozoa, previously not reported from South Africa. Fewer than 3% of OTUs could be identified to species level using available databases (COI = 19 OTUs, 12S = 11 OTUs). Our study emphasizes that kelp-forest associated biodiversity in South Africa is understudied, but that with careful consideration for sampling design in combination with increased barcoding efforts and the construction of regional databases, eDNA metabarcoding will become a powerful biomonitoring tool of kelp-forest associated biodiversity.},
}
@article {pmid39240088,
year = {2024},
author = {Wang, Y and Li, X and Lu, W and Li, F and Yao, L and Liu, Z and Shi, H and Zhang, W and Bai, Y},
title = {Full-length circRNA sequencing method using low-input RNAs and profiling of circRNAs in MPTP-PD mice on a nanopore platform.},
journal = {The Analyst},
volume = {149},
number = {20},
pages = {5118-5130},
doi = {10.1039/d4an00715h},
pmid = {39240088},
issn = {1364-5528},
mesh = {Animals ; *RNA, Circular/genetics ; Mice ; *Mice, Inbred C57BL ; *Parkinson Disease/genetics ; Sequence Analysis, RNA/methods ; Male ; Nanopores ; High-Throughput Nucleotide Sequencing/methods ; Nanopore Sequencing/methods ; 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine ; Gene Expression Profiling/methods ; },
abstract = {Considering the importance of accurate information of full-length (FL) transcripts in functional analysis, researchers prefer to develop new sequencing methods based on third-generation sequencing (TGS) rather than short-read sequencing. Several FL circRNA sequencing strategies have been developed. However, the current methods are inapplicable to low-biomass samples, since a large amount of total RNAs are acquired for circRNA enrichment before library preparation. In this work, we developed an effective method to detect FL circRNAs from a nanogram level (1-100 ng) of total RNAs based on a nanopore platform. Additionally, prior to the library preparation process, we added a series of 24 nt barcodes for each sample to reduce the cost and operating time. Using this method, we profiled circRNA expression in the striatum, hippocampus and cerebral cortex of a Parkinson's disease (PD) mouse model. Over 6% of reads were effective for FL circRNA identification in most datasets. Notably, a reduction in the RNA initial input resulted in a lower correlation between replicates and the detection efficiency for longer circRNA, but the lowest input (1 ng) was able to detect numerous FL circRNAs. Next, we systematically identified over 263 934 circRNAs in PD and healthy mice using the lower-input FL sequencing method, some of which came from 50.52% of PD-associated genes. Moreover, significant changes were observed in the circRNA expression pattern at an isoform level, and high-confidence protein translation evidence was predicted. Overall, we developed an effective method to characterize FL circRNAs from low-input samples and provide a comprehensive insight into the biological function of circRNAs in PD at an isoform level.},
}
@article {pmid39238034,
year = {2024},
author = {Srisuka, W and Takaoka, H and Taai, K and Maleewong, W and Aupalee, K and Saeung, A},
title = {Morphological description and genetic analysis of a new black fly species (Diptera: Simuliidae) in the subgenus Asiosimulium from central Thailand.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {379},
pmid = {39238034},
issn = {1756-3305},
support = {N42A670561//National Research Council of Thailand (NRCT): High-Potential Research Team Grant Program/ ; },
mesh = {Animals ; *Simuliidae/genetics/anatomy &amp; histology/classification ; Thailand ; Female ; Male ; *Pupa/anatomy &amp; histology/genetics/classification ; *Phylogeny ; *Larva/anatomy &amp; histology/genetics/classification ; Electron Transport Complex IV/genetics ; Insect Vectors/anatomy &amp; histology/genetics/classification ; },
abstract = {BACKGROUND: Black flies are among the most medically and veterinary important insects, as adult females of certain species are the sole vector of Onchocerca volvulus. Here, a new black fly species belonging to the subgenus Asiosimulium Takaoka &amp; Choochote, 2005, is described and formally named as Simulium (Asiosimulium) kittipati sp. nov.<br><br>METHODS: Pupae and larvae of black flies were collected from available substrates in the stream from central Thailand. Pupae were individually separated in plastic tubes and maintained until adult flies emerged. The emerged adult flies associated with their pupal exuviae and cocoon as well as mature larvae preserved in 85% ethanol were used to describe the new species based on an integrated approach of morphological examination and molecular analysis of the COI gene.<br><br>RESULTS: The new species is characterized in the female by the medium-long sensory vesicle with a medium-sized opening apically, scutum with three faint longitudinal vittae, and the ellipsoidal spermatheca; in the male by the number of upper-eye (large) facets in 20 vertical columns and 21 horizontal rows, hind basitarsus slender, nearly parallel-sided, and median sclerite much wider and upturned apically; in the pupa by the head and thoracic integument densely covered with tiny tubercles, and the pupal gill of arborescent type with 28-30 filaments; and in the larva by the postgenal cleft deep, nearly reaching the posterior margin of the hypostoma, and dark pigmented sheath of the subesophageal ganglion. The DNA barcode successfully differentiated the new species from its congeners with an interspecific genetic divergence of 1.74-18.72%, confirming the morphological identification that the species is a new member of the subgenus Asiosimulium. Phylogenetic analyses also indicated that the new species is genetically closely related to Simulium phurueaense Tangkawanit, Wongpakam &amp; Pramual, 2018, further supporting its morphological classification.<br><br>CONCLUSIONS: This is the ninth species assigned to the subgenus Asiosimulium within the genus Simulium Latreille, 1802. Taxonomic notes and identification keys are given to distinguish this new species from the eight known species members in its same subgenus. Additionally, a distribution map of all species members in this subgenus occurring in Thailand and other countries is provided.},
}
@article {pmid39237449,
year = {2024},
author = {Wallace, JG and Griffis, H},
title = {Preparation of Illumina 16s Amplicon Sequencing Libraries with Peptide Nucleic Acids (PNAs) for the Analysis of Maize-Associated Microbiomes.},
journal = {Cold Spring Harbor protocols},
volume = {},
number = {},
pages = {},
doi = {10.1101/pdb.prot108583},
pmid = {39237449},
issn = {1559-6095},
abstract = {One of the most common methods to survey bacterial communities is targeted amplification of the hypervariable regions of the 16s rRNA gene followed by sequencing. This protocol details Illumina library preparation of such amplicons from communities isolated from maize. We include both staggered PCR primers to improve Illumina base calling and peptide nucleic acids (PNAs) to reduce the presence of plant organelles. Primers are designed with Illumina adapter sequences for the addition of sample-specific indexes (barcodes). We also briefly discuss alternative primer sets, including ones that directly discriminate against plant organelles or that amplify different organisms (e.g., fungal internal transcribed spacer [ITS] sequences).},
}
@article {pmid39234150,
year = {2024},
author = {Fang, X and Xu, Z and Yao, Y and Fu, Y},
title = {Two new species of Macropelopia (Diptera, Chironomidae) from Oriental China, delineated with morphology and COI sequences.},
journal = {ZooKeys},
volume = {1210},
number = {},
pages = {287-298},
pmid = {39234150},
issn = {1313-2989},
abstract = {Two new species, Macropelopia (Macropelopia) excavata Xu &amp; Fu, sp. nov. and Macropelopia (Macropelopia) quadrimacula Xu &amp; Fu, sp. nov., are described as male adults. A key to identify the males of Macropelopia from China is provided. Furthermore, in order to ascertain the genetic distance between these species and their morphological characteristics, mitochondrial cytochrome c oxidase subunit I gene sequences were uploaded to the National Center for Biotechnology Information. These COI sequences were then utilized to infer the relationships between the species, employing the neighbor-joining method.},
}
@article {pmid39233723,
year = {2024},
author = {Saigal, M and Shueh Yi, HN and Rameez, NA and van Manen, S and Van Anh, BT and Arora, VP and Han, KDM and Lee, JQT and Syaddad, A and Tan, CK and Lim, EXY and Wainwright, BJ},
title = {Beneath the surface: DNA barcoding of shark fins in Singapore.},
journal = {Royal Society open science},
volume = {11},
number = {9},
pages = {240532},
pmid = {39233723},
issn = {2054-5703},
abstract = {The global decline of shark populations, largely driven by overfishing to supply the shark fin trade, poses a significant threat to marine ecosystems. Southeast Asia, and particularly Singapore, is a key hub for the transit and trade of shark fins that contribute to the exploitation of these apex predators. Through the use of DNA barcoding techniques, this study aimed to determine what species of shark are involved in the Singapore shark fin trade. Fins were collected from markets, dried goods shops and traditional Chinese medicine halls throughout Singapore. In total, DNA was extracted from 684 fins collected in January 2024 and PCR amplification targeted a fragment of the mitochondrial COI gene for species identification. Results revealed fins from 24 species across 16 genera, with 19 species listed on CITES Appendices II, and 16 listed as threatened on the IUCN Red List (critically endangered = 2, endangered = 4, vulnerable = 10). The top five most frequently identified species were Carcharhinus falciformis, Galeorhinus galeus, Rhizoprionodon oligolinx, Sphyrna lewini and Rhizoprionodon acutus. Of these, four are listed on CITES Appendix II and four are listed as threatened on the IUCN Red List.},
}
@article {pmid39232201,
year = {2025},
author = {Chen, F and Li, X and Bai, M and Zhao, Y},
title = {Visualizing epigenetic modifications and their spatial proximities in single cells using three DNA-encoded amplifying FISH imaging strategies: BEA-FISH, PPDA-FISH and Cell-TALKING.},
journal = {Nature protocols},
volume = {20},
number = {1},
pages = {220-247},
pmid = {39232201},
issn = {1750-2799},
support = {22125404//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92068118//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Humans ; 5-Methylcytosine/metabolism/analogs &amp; derivatives ; *DNA/genetics ; *Epigenesis, Genetic ; *In Situ Hybridization, Fluorescence/methods ; Nucleic Acid Amplification Techniques/methods ; *Single-Cell Analysis/methods ; },
abstract = {Epigenetic modifications and spatial proximities of nucleic acids and proteins play important roles in regulating physiological processes and disease progression. Currently available cell imaging methods, such as fluorescence in situ hybridization (FISH) and immunofluorescence, struggle to detect low-abundance modifications and their spatial proximities. Here we describe a step-by-step protocol for three DNA-encoded amplifying FISH-based imaging strategies to overcome these challenges for varying applications: base-encoded amplifying FISH (BEA-FISH), pairwise proximity-differentiated amplifying FISH (PPDA-FISH) and cellular macromolecules-tethered DNA walking indexing (Cell-TALKING). They all use the similar core principle of DNA-encoded amplification, which transforms different nonsequence molecular features into unique DNA barcodes for in situ rolling circle amplification and FISH analysis. This involves three key reactions in fixed cell samples: target labeling, DNA encoding and rolling circle amplification imaging. Using this protocol, these three imaging strategies achieve in situ counting of low-abundance modifications alone, the pairwise proximity-differentiated visualization of two modifications and the exploration of multiple modifications around one protein (one-to-many proximity), respectively. Low-abundance modifications, including 5-hydroxymethylcytosine, 5-formylcytosine, 5-hydroxymethyluracil and 5-formyluracil, are clearly visualized in single cells. Various combinatorial patterns of nucleic acid modifications and/or histone modifications are found. The whole protocol takes ~2-4 d to complete, depending on different imaging applications.},
}
@article {pmid39232051,
year = {2024},
author = {Kinya, F and Milugo, TK and Mutero, CM and Wondji, CS and Torto, B and Tchouassi, DP},
title = {Insights into malaria vectors-plant interaction in a dryland ecosystem.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {20625},
pmid = {39232051},
issn = {2045-2322},
support = {/WT_/Wellcome Trust/United Kingdom ; 222005/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; RAF-3058 KEN-18/0005//Norwegian Agency for Development Cooperation (Norad)/ ; },
mesh = {Animals ; *Mosquito Vectors/parasitology/genetics ; *Ecosystem ; *Anopheles/parasitology/genetics/metabolism ; Kenya ; *Plasmodium falciparum/genetics/metabolism ; *DNA Barcoding, Taxonomic ; Malaria/transmission/parasitology ; Acacia/metabolism/parasitology/genetics ; Feeding Behavior/physiology ; Ribulose-Bisphosphate Carboxylase/metabolism/genetics ; },
abstract = {Improved understanding of mosquito-plant feeding interactions can reveal insights into the ecological dynamics of pathogen transmission. In wild malaria vectors Anopheles gambiae s.l. and An. funestus group surveyed in selected dryland ecosystems of Kenya, we found a low level of plant feeding (2.8%) using biochemical cold anthrone test but uncovered 14-fold (41%) higher rate via DNA barcoding targeting the chloroplast rbcL gene. Plasmodium falciparum positivity was associated with either reduced or increased total sugar levels and varied by mosquito species. Gut analysis revealed the mosquitoes to frequently feed on acacia plants (~ 89%) (mainly Vachellia tortilis) in the family Fabaceae. Chemical analysis revealed 1-octen-3-ol (29.9%) as the dominant mosquito attractant, and the sugars glucose, sucrose, fructose, talose and inositol enriched in the vegetative parts, of acacia plants. Nutritional analysis of An. longipalpis C with high plant feeding rates detected fewer sugars (glucose, talose, fructose) compared to acacia plants. These results demonstrate (i) the sensitivity of DNA barcoding to detect plant feeding in malaria vectors, (ii) Plasmodium infection status affects energetic reserves of wild anopheline vectors and (iii) nutrient content and olfactory cues likely represent potent correlates of acacia preferred as a host plant by diverse malaria vectors. The results have relevance in the development of odor-bait control strategies including attractive targeted sugar-baits.},
}
@article {pmid39231998,
year = {2024},
author = {Ma, YX and Wang, XD},
title = {Directional self-assembly of organic vertically superposed nanowires.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7706},
pmid = {39231998},
issn = {2041-1723},
support = {52173177//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Organic crystal-based superimposed heterostructures with inherent multichannel characteristics demonstrate superior potential for manipulating excitons/photons at the micro/nanoscale for integrated optoelectronics. However, the precise construction of organic superimposed heterostructures with fixed superimposed sites remains challenging because of the random molecular nucleation process. Here, organic vertically superimposed heterostructures (OSHs) with fixed superimposed positions are constructed via semi-wrapped core/shell heterostructures with partially exposed cores, which provide preferential nucleation sites for further molecular epitaxial growth processes. Furthermore, the relative length ratio from 21.7% to 95.3% between interlayers is accurately adjusted by regulating the exposed area of the semi-wrapped core/shell heterostructures. Significantly, these OSHs with anisotropic optical characteristics demonstrate well regulation of excitation position-dependent waveguide behaviors and can function as photonic barcodes for information encryption. This strategy provides a facile approach for controlling the nucleation sites for the controllable preparation of organic heterostructures and advanced applications for integrated optoelectronics.},
}
@article {pmid39229105,
year = {2024},
author = {Williams, MJ and Vázquez-García, I and Tam, G and Wu, M and Varice, N and Havasov, E and Shi, H and Satas, G and Lees, HJ and Lee, JJ and Myers, MA and Zatzman, M and Rusk, N and Ali, E and Shah, RH and Berger, MF and Mohibullah, N and Lakhman, Y and Chi, DS and Abu-Rustum, NR and Aghajanian, C and McPherson, A and Zamarin, D and Loomis, B and Weigelt, B and Friedman, CF and Shah, SP},
title = {Tracking clonal evolution of drug resistance in ovarian cancer patients by exploiting structural variants in cfDNA.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39229105},
issn = {2692-8205},
support = {P30 CA008748/CA/NCI NIH HHS/United States ; U24 CA264028/CA/NCI NIH HHS/United States ; P50 CA247749/CA/NCI NIH HHS/United States ; K99 CA256508/CA/NCI NIH HHS/United States ; R01 CA281928/CA/NCI NIH HHS/United States ; R01 CA269382/CA/NCI NIH HHS/United States ; },
abstract = {Drug resistance is the major cause of therapeutic failure in high-grade serous ovarian cancer (HGSOC). Yet, the mechanisms by which tumors evolve to drug resistant states remains largely unknown. To address this, we aimed to exploit clone-specific genomic structural variations by combining scaled single-cell whole genome sequencing with longitudinally collected cell-free DNA (cfDNA), enabling clonal tracking before, during and after treatment. We developed a cfDNA hybrid capture, deep sequencing approach based on leveraging clone-specific structural variants as endogenous barcodes, with orders of magnitude lower error rates than single nucleotide variants in ctDNA (circulating tumor DNA) detection, demonstrated on 19 patients at baseline. We then applied this to monitor and model clonal evolution over several years in ten HGSOC patients treated with systemic therapy from diagnosis through recurrence. We found drug resistance to be polyclonal in most cases, but frequently dominated by a single high-fitness and expanding clone, reducing clonal diversity in the relapsed disease state in most patients. Drug-resistant clones frequently displayed notable genomic features, including high-level amplifications of oncogenes such as CCNE1, RAB25, NOTCH3, and ERBB2. Using a population genetics Wright-Fisher model, we found evolutionary trajectories of these features were consistent with drug-induced positive selection. In select cases, these alterations impacted selection of secondary lines of therapy with positive patient outcomes. For cases with matched single-cell RNA sequencing data, pre-existing and genomically encoded phenotypic states such as upregulation of EMT and VEGF were linked to drug resistance. Together, our findings indicate that drug resistant states in HGSOC pre-exist at diagnosis and lead to dramatic clonal expansions that alter clonal composition at the time of relapse. We suggest that combining tumor single cell sequencing with cfDNA enables clonal tracking in patients and harbors potential for evolution-informed adaptive treatment decisions.},
}
@article {pmid39228674,
year = {2024},
author = {Vanhoye, X and Mouty, P and Mouty, S and Bargues, N and Couprie, N and Fayolle, E and Géromel, V and Taoudi, M and Raymond, L and Taly, JF},
title = {Implementation of long-read sequencing for routine molecular diagnosis of familial mediterranean fever.},
journal = {Practical laboratory medicine},
volume = {41},
number = {},
pages = {e00423},
pmid = {39228674},
issn = {2352-5517},
abstract = {BACKGROUND: Long-read sequencing technology, widely used in research, is proving useful in clinical diagnosis, especially for infectious diseases. Despite recent advances, it hasn't been routinely applied to constitutional human diseases. Long-read sequencing detects intronic variants and phases variants, crucial for identifying recessive diseases.<br><br>METHODS: We integrated long-read sequencing into the clinical diagnostic workflow for the MEFV gene, responsible for familial Mediterranean fever (FMF), using a Nanopore-based workflow. This involved long-range PCR amplification, native barcoding kit library preparation, GridION sequencing, and in-house bioinformatics. We compared this new workflow against our validated method using 39 patient samples and 3 samples from an external quality assessment scheme to ensure compliance with ISO15189 standards.<br><br>RESULTS: Our evaluation demonstrated excellent performance, meeting ISO15189 requirements for reproducibility, repeatability, sensitivity, and specificity. Since October 2022, 150 patient samples were successfully analyzed with no failures. Among these samples, we identified 13 heterozygous carriers of likely pathogenic (LP) or pathogenic (P) variants, 1 patient with a homozygous LP/P variant in MEFV, and 4 patients with compound heterozygous variants.<br><br>CONCLUSION: This study represents the first integration of long-read sequencing for FMF clinical diagnosis, achieving 100&#xa0;% sensitivity and specificity. Our findings highlight its potential to identify pathogenic variants without parental segregation analysis, offering faster, cost-effective, and accurate clinical diagnosis. This successful implementation lays the groundwork for future applications in other constitutional human diseases, advancing precision medicine.},
}
@article {pmid39228134,
year = {2024},
author = {Chan, WWR and Chang, JJM and Tan, CZ and Ng, JX and Ng, MH and Jaafar, Z and Huang, D},
title = {Eyeing DNA barcoding for species identification of fish larvae.},
journal = {Journal of fish biology},
volume = {105},
number = {6},
pages = {1784-1799},
pmid = {39228134},
issn = {1095-8649},
support = {A-0008413-00-00//National Parks Board - Singapore/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Fishes/genetics/classification ; *Larva/genetics/classification ; Electron Transport Complex IV/genetics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; Eye/anatomy &amp; histology ; },
abstract = {Identification of fish larvae based on morphology is typically limited to higher taxonomic ranks (e.g., family or order), as larvae possess few morphological diagnostic characters for precise discrimination to species. When many samples are presented at any one time, the use of morphology to identify such specimens can be laborious and time-consuming. Using a reverse workflow for specimen sorting and identification leveraging high-throughput DNA sequencing, thousands of fish larvae can be DNA barcoded and sorted into molecular operational taxonomic units (mOTUs) in a single sequencing run with the nanopore sequencing technology (e.g., MinION). This process reduces the time and financial costs of morphology-based sorting and instead deploys experienced taxonomists for species taxonomic work where they are needed most. In this study, a total of 3022 fish larval specimens from plankton tows across four sites in Singapore were collected and sorted based on this workflow. Eye tissue from individual samples was used for DNA extraction and sequencing of cytochrome c oxidase subunit I. We generated a total of 2746 barcodes after quality filtering (90.9% barcoding success), identified 2067 DNA barcodes (75.3% identification success), and delimited 256 mOTUs (146 genera, 52 families). Our analyses identified specific challenges to species assignment, such as the potential misidentification of publicly available sequences used as reference barcodes. We highlighted how the conservative application and comparison of a local sequence database can help resolve identification conflicts. Overall, this proposed approach enables and expedites taxonomic identification of fish larvae, contributing to the enhancement of reference barcode databases and potentially better understanding of fish connectivity.},
}
@article {pmid39227484,
year = {2024},
author = {Oliveira Carvalho, C and Pazirgiannidi, M and Ravelomanana, T and Andriambelomanana, F and Schrøder-Nielsen, A and Stuart Ready, J and de Boer, H and Fusari, CE and Mauvisseau, Q},
title = {Multi-method survey rediscovers critically endangered species and strengthens Madagascar's freshwater fish conservation.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {20427},
pmid = {39227484},
issn = {2045-2322},
mesh = {Animals ; *Endangered Species ; *Conservation of Natural Resources/methods ; Madagascar ; *Fresh Water ; *Biodiversity ; *Fishes/genetics/classification ; DNA, Environmental/genetics/analysis ; Rivers ; Ecosystem ; },
abstract = {Freshwater ecosystems are crucial for global biodiversity through supporting plant and animal species and providing essential resources. These ecosystems are under significant threat, particularly in island environments such as Madagascar. Our study focuses on the Amboaboa River basin, home to the rare and endemic fish species Rheocles derhami, last recorded in 2013. To assess the status of this and other threatened fish species including Ptychochromis insolitus and Paretroplus gymnopreopercularis, and to understand freshwater fish population dynamics in this biodiversity hotspot, we conducted a comprehensive survey using both environmental DNA (eDNA) and traditional fishing methods. While traditional methods effectively captured a diverse range of species, including several invasive aliens and the critically endangered endemic species that were the focus of this study, the eDNA approach detected only a fraction of these introduced species and struggled to identify some critically endangered endemics at the species level. This highlights the value of combining methods to enhance species detection. We also investigated the trade-offs associated with multi-primer assessments in eDNA analysis, focusing on three different primer combinations targeting the 12S mitochondrial gene: MiFish, Tele02, and Riaz. Additionally, we provided 12S reference barcodes for 10 species across 9 genera of fishes from the region to increase the coverage of the public reference databases. Overall, our study elucidates the current state of freshwater biodiversity in the Amboaboa River basin and underscores the value of employing multiple methods for effective conservation strategies.},
}
@article {pmid39226784,
year = {2024},
author = {Xia, Z and Yang, Y and Zeng, Y and Sun, Y and Cui, Q and Chen, Z and Liu, J and Zhang, J and He, P},
title = {Temporal succession of micropropagules during accumulation and dissipation of green tide algae: A case study in Rudong coast, Jiangsu Province.},
journal = {Marine environmental research},
volume = {202},
number = {},
pages = {106719},
doi = {10.1016/j.marenvres.2024.106719},
pmid = {39226784},
issn = {1879-0291},
mesh = {China ; *Ulva/metabolism ; *Environmental Monitoring ; *Eutrophication ; Chlorophyta/genetics ; Seawater/chemistry ; Geologic Sediments ; },
abstract = {Over the past 18 years, green tides have persistently occurred in the Yellow Sea. Micropropagules of these algae are key to bloom formation, yet their species composition and succession during dissipation remain underexplored. During the dissipation process of accumulated green tide algae, a large number of micropropagules are released. This study monitored the dissipation of green tide algae at a coastal site, tracking micropropagules in water and sediment using an internal transcribed spacer (ITS) and 5S rDNA primers. Results showed that the dissipation lasted about one month, with significant micropropagule release. Initially, micropropagules matched 5S-II Ulva prolifera, but later species like Ulva torta, Ulva simplex, Ulva flexuosa, and Ulva meridionalis emerged. Ulva meridionalis dominated sediment in July and August, while U. torta was prevalent in water, and U. flexuosa was dominant in other months. Accumulated U. prolifera in the intertidal zone may not contribute to the seeding of the next year's bloom. This study sheds light on the dissipation process and succession patterns of micropropagules in coastal environments.},
}
@article {pmid39224985,
year = {2024},
author = {Isma, LM and Golightly, CG and Bracken-Grissom, HD},
title = {Under the Sea: Investigation of Telson Morphology and Cryptic Diversity within Eucopia sculpticauda, a Deep-Sea Lophogastrid from the Gulf of Mexico (Peracarida: Lophogastrida).},
journal = {Integrative and comparative biology},
volume = {64},
number = {4},
pages = {1154-1161},
doi = {10.1093/icb/icae141},
pmid = {39224985},
issn = {1557-7023},
support = {//Gulf of Mexico Research Initiative/ ; },
mesh = {Animals ; Gulf of Mexico ; *Phylogeny ; Gastropoda/genetics/anatomy &amp; histology/classification ; },
abstract = {The field of phylogenetics employs a variety of methods and techniques to study the evolution of life across the planet. Understanding evolutionary relationships is crucial to enriching our understanding of how genes and organisms have evolved throughout time and how they could possibly evolve in the future. Eucopia sculpticauda Faxon, 1893 is a deep-water peracarid in the order Lophogastrida Boas, 1883, which can often be found in high abundances in pelagic trawls. The species can be found along the Mariana Trench, in the Mid-Atlantic Ridge, west Atlantic and east Pacific Oceans, and in the Gulf of Mexico and as deep as 7526 m. Recent collections of E. sculpticauda in the Gulf of Mexico have revealed putative cryptic diversity within the species based on both molecular and morphological evidence. Previous studies have documented two different morphotypes of the telson: the terminal part of the pleon (abdomen) and part of the tail fan. In adults, the morphotypes can be distinguished by lateral constrictions in the telson. This evidence, combined with a previous barcoding study, led to the speculation that telson morphology may be a distinguishing character useful to define cryptic diversity within E. sculpticauda. This study presents additional molecular data from the mitochondrial genes cytochrome c oxidase subunit I, and the large ribosomal subunit (16S), and the nuclear histone 3 gene (H3) to investigate telson morphotypes in relation to evolutionary history within this species. Molecular data identified two strongly supported clades, lending support for potential cryptic diversification within the Gulf of Mexico. Investigations into telson morphology suggest that this character may be informative, but the morphotypes were sometimes ambiguous and additional characters could not be found that discriminate clades. At present, our data suggest early evidence for cryptic diversification within Gulf of Mexico populations, but additional morphological characters and geographic sampling are needed before a new species can be described.},
}
@article {pmid39223179,
year = {2024},
author = {Schmidt, LA and Brix, S and Rossel, S and Forster, S and Eichsteller, A},
title = {Unveiling ophiuroid biodiversity across North Atlantic habitats via an integrative perspective.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {20405},
pmid = {39223179},
issn = {2045-2322},
support = {MSM75,MerMet17-05; SO276 MerMet17-06//Germany Science Foundation/ ; MSM75,MerMet17-05; SO276 MerMet17-06//Germany Science Foundation/ ; MSM75,MerMet17-05; SO276 MerMet17-06//Germany Science Foundation/ ; MSM75,MerMet17-05; SO276 MerMet17-06//Germany Science Foundation/ ; },
mesh = {*Biodiversity ; Animals ; *DNA Barcoding, Taxonomic ; Atlantic Ocean ; *Ecosystem ; Echinodermata/genetics/classification ; Phylogeny ; Proteomics/methods ; },
abstract = {The depths of the North Atlantic Ocean host a species-rich fauna providing heterogeneous habitats from thermal vent fields to cold-water coral reefs. With the increasing threat of destruction of deep-sea habitats due to human impacts, such as demersal fishing and the beginning of deep-sea mining, an analysis of the diversity and distribution of species is crucial for conservation efforts. Brittle stars occur in high biomasses, contributing to the biodiversity of the seafloor. Specimens were collected during several scientific expeditions to gain a more detailed insight into the brittle star diversity in the North Atlantic Ocean. An integrative approach to identify the species with DNA barcoding (mtCOI) in combination with morphological studies revealed 24 species. Most species have been previously identified in the North Atlantic, but sequences for 13 species are newly added to public repositories. Additionally, the MALDI-TOF-MS proteomic analysis was successfully applied for 197 specimens with known COI barcodes. Results are congruent with other molecular species delimitations demonstrating the functionality of proteomics for the identification of brittle stars. This dataset significantly expands our understanding of the taxonomic and genetic diversity of brittle stars and contributes to publicly available data. It emphasizes the importance of considering habitat heterogeneity for large scale patterns of biodiversity.},
}
@article {pmid39222178,
year = {2025},
author = {Shaban, D and Najm, N and Droin, L and Nijnik, A},
title = {Hematopoietic Stem Cell Fates and the Cellular Hierarchy of Mammalian Hematopoiesis: from Transplantation Models to New Insights from in Situ Analyses.},
journal = {Stem cell reviews and reports},
volume = {21},
number = {1},
pages = {28-44},
pmid = {39222178},
issn = {2629-3277},
support = {Canadian Institutes of Health Research/CAPMC/CIHR/Canada ; Leukemia and Lymphoma Society of Canada//Leukemia and Lymphoma Society of Canada/ ; Canada Research Chairs//Canada Research Chairs/ ; Fonds de Recherche du Qu&#xe9;bec - Sant&#xe9;//Fonds de Recherche du Qu&#xe9;bec - Sant&#xe9;/ ; Canadian Institutes of Health Research/CAPMC/CIHR/Canada ; },
mesh = {Animals ; *Hematopoietic Stem Cells/metabolism/cytology ; Humans ; *Hematopoiesis ; Cell Differentiation/genetics ; Cell Lineage/genetics ; Hematopoietic Stem Cell Transplantation ; Mice ; },
abstract = {Hematopoiesis is the process that generates the cells of the blood and immune system from hematopoietic stem and progenitor cells (HSPCs) and represents the system with the most rapid cell turnover in a mammalian organism. HSPC differentiation trajectories, their underlying molecular mechanisms, and their dysfunctions in hematologic disorders are the focal research questions of experimental hematology. While HSPC transplantations in murine models are the traditional tool in this research field, recent advances in genome editing and next generation sequencing resulted in the development of many fundamentally new approaches for the analyses of mammalian hematopoiesis in situ and at single cell resolution. The current review will cover many recent developments in this field in murine models, from the bulk lineage tracing studies of HSPC differentiation to the barcoding of individual HSPCs with Cre-recombinase, Sleeping Beauty transposase, or CRISPR/Cas9 tools, to map hematopoietic cell fates, together with their transcriptional and epigenetic states. We also address studies of the clonal dynamics of human hematopoiesis, from the tracing of HSPC clonal behaviours based on viral integration sites in gene therapy patients to the recent analyses of unperturbed human hematopoiesis based on naturally accrued mutations in either nuclear or mitochondrial genomes. Such studies are revolutionizing our understanding of HSPC biology and hematopoiesis both under homeostatic conditions and in the response to various forms of physiological stress, reveal the mechanisms responsible for the decline of hematopoietic function with age, and in the future may advance the understanding and management of the diverse disorders of hematopoiesis.},
}
@article {pmid39221955,
year = {2024},
author = {Fang, J and Salinas, I and San Vicente, S and Zielinski, C and Sade-Feldman, M},
title = {Dissociation of Human and Mouse Tumor Tissue Samples for Single-cell RNA Sequencing.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {210},
pages = {},
doi = {10.3791/66766},
pmid = {39221955},
issn = {1940-087X},
mesh = {Humans ; *Single-Cell Analysis/methods ; Mice ; Animals ; *Sequence Analysis, RNA/methods ; Neoplasms/genetics ; },
abstract = {Human tumor samples hold a plethora of information about their microenvironment and immune repertoire. Effective dissociation of human tissue samples into viable cell suspensions is a required input for the single-cell RNA sequencing (scRNAseq) pipeline. Unlike bulk RNA sequencing approaches, scRNAseq enables us to infer the transcriptional heterogeneity in tumor specimens at the single-cell level. Incorporating this approach in recent years has led to many discoveries, such as identifying immune and tumor cellular states and programs associated with clinical responses to immunotherapies and other types of treatments. Moreover, single-cell technologies applied to dissociated tissues can be used to identify accessible chromatin regions T and B cell receptor repertoire, and the expression of proteins, using DNA barcoded antibodies (CITEseq). The viability and quality of the dissociated sample are critical variables when using these technologies, as these can dramatically affect the cross-contamination of single cells with ambient RNA, the quality of the data, and interpretation. Moreover, long dissociation protocols can lead to the elimination of sensitive cell populations and the upregulation of a stress response gene signature. To overcome these limitations, we devised a rapid universal dissociation protocol, which has been validated on multiple types of human and murine tumors. The process begins with mechanical and enzymatic dissociation, followed by filtration, red blood lysis, and live dead enrichment, suitable for samples with a low input of cells (e.g., needle core biopsies). This protocol ensures a clean and viable single-cell suspension paramount to the successful generation of Gel Bead-In Emulsions (GEMs), barcoding, and sequencing.},
}
@article {pmid39221281,
year = {2024},
author = {Lutz, &#xcd; and Martins, T and Santana, P and Ferreira, C and Miranda, J and Matos, S and Muhala, V and Sampaio, I and Vallinoto, M and Evangelista-Gomes, G},
title = {Marine catfishes (Ariidae-Siluriformes) from the Coastal Amazon: mitochondrial DNA barcode for a recent diversification group?.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17581},
pmid = {39221281},
issn = {2167-8359},
mesh = {Animals ; *Catfishes/genetics/classification ; *DNA Barcoding, Taxonomic ; *DNA, Mitochondrial/genetics ; Phylogeny ; Genetic Variation/genetics ; Brazil ; Electron Transport Complex IV/genetics ; },
abstract = {BACKGROUND: Ariidae species play a significant role as fishing resources in the Amazon region. However, the family's systematic classification is notably challenging, particularly regarding species delimitation within certain genera. This difficulty arises from pronounced morphological similarities among species, posing obstacles to accurate species recognition.<br><br>METHODS: Following morphological identification, mitochondrial markers (COI and Cytb) were employed to assess the diversity of Ariidae species in the Amazon.<br><br>RESULTS: Our sampling efforts yielded 12 species, representing 92% of the coastal Amazon region's diversity. Morphological identification findings were largely corroborated by molecular data, particularly for species within the Sciades and Bagre genera. Nonetheless, despite morphological support, Cathorops agassizii and Cathorops spixii displayed minimal genetic divergence (0.010). Similarly, Notarius quadriscutis and Notarius phrygiatus formed a single clade with no genetic divergence, indicating mitochondrial introgression. For the majority of taxa examined, both COI and Cytb demonstrated efficacy as DNA barcodes, with Cytb exhibiting greater polymorphism and resolution. Consequently, the molecular tools utilized proved highly effective for species discrimination and identification.},
}
@article {pmid39221104,
year = {2024},
author = {Mullin, PG and Harris, T and Higgins, R and Dutta, E and Porazinska, DL and Powers, K and Powers, T},
title = {Taxonomy of Tobrilidae species from the Alkaline Lakes of the western Nebraska Sandhills.},
journal = {Journal of nematology},
volume = {56},
number = {1},
pages = {20240025},
pmid = {39221104},
issn = {0022-300X},
abstract = {Six distinct COI mitochondrial Haplotype Groups (HG) are morphologically, ecologically, and genetically characterized from the aquatic nematode family Tobrilidae. Collection locations included the extreme habitats of the Alkaline Lakes in the western Nebraska Sandhills and the contaminated stream, Johnson Creek, bordering the AltEn 2021 catastrophic pesticide release near the village of Mead in eastern Nebraska. Maximum likelihood and genetic distance metrics supported the genetic integrity of the haplotype groups. Discriminant function analysis of COI haplotype group datasets of combined morphological characters and soil chemistry attributes for both male and female Tobrilidae were classified correctly in all but one case. Scanning electron microscopy revealed new details about amphid apertures, male supplements, and spicules. Partial 18S gene phylogeny suggests that the genus Semitobrilus may not be a member of the subfamily Neotobrilinae, and three specimens in the 226 tobrilid dataset provide evidence of incongruence between COI and 18S derived phylogenies. Given the strong signal provided by the environmental chemistry data, tobrilid mitochondrial haplotypes may well have value as environmental indicators.},
}
@article {pmid39220016,
year = {2024},
author = {Chen, L and Song, BN and Yang, L and Wang, Y and Wang, YY and Aou, X and He, XJ and Zhou, SD},
title = {Phylogeny, adaptive evolution, and taxonomy of Acronema (Apiaceae): evidence from plastid phylogenomics and morphological data.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1425158},
pmid = {39220016},
issn = {1664-462X},
abstract = {INTRODUCTION: The genus Acronema, belonging to Apiaceae, includes approximately 25 species distributed in the high-altitude Sino-Himalayan region from E Nepal to SW China. This genus is a taxonomically complex genus with often indistinct species boundaries and problematic generic delimitation with Sinocarum and other close genera, largely due to the varied morphological characteristics.<br><br>METHODS: To explore the phylogenetic relationships and clarify the limits of the genus Acronema and its related genera, we reconstructed a reliable phylogenetic framework with high support and resolution based on two molecular datasets (plastome data and ITS sequences) and performed morphological analyses.<br><br>RESULTS: Both phylogenetic analyses robustly supported that Acronema was a non-monophyletic group that fell into two clades: Acronema Clade and East-Asia Clade. We also newly sequenced and assembled sixteen Acronema complete plastomes and performed comprehensively comparative analyses for this genus. The comparative results showed that the plastome structure, gene number, GC content, codon bias patterns were high similarity, but varied in borders of SC/IR and we identified six different types of SC/IR border. The SC/IR boundaries of Acronema chienii were significantly different from the other Acronema members which was consistent with the type VI pattern in the genus Tongoloa. We also identified twelve potential DNA barcode regions (ccsA, matK, ndhF, ndhG, psaI, psbI, rpl32, rps15, ycf1, ycf3, psaI-ycf4 and psbM-trnD) for species identification in Acronema. The molecular evolution of Acronema was relatively conservative that only one gene (petG) was found to be under positive selection (&#x3c9; = 1.02489).<br><br>DISCUSSION: The gene petG is one of the genes involved in the transmission of photosynthetic electron chains during photosynthesis, which plays a crucial role in the process of photosynthesis in plants. This is also a manifestation of the adaptive evolution of plants in high-altitude areas to the environment. In conclusion, our study provides novel insights into the plastome adaptive evolution, phylogeny, and taxonomy of genus Acronema.},
}
@article {pmid39218175,
year = {2024},
author = {Hosseini, SA and Elahian, F and Mirzaei, SA},
title = {Innovative genetic scissor strategies and their applications in cancer treatment and prevention: CRISPR modules and challenges.},
journal = {International journal of biological macromolecules},
volume = {279},
number = {Pt 2},
pages = {135239},
doi = {10.1016/j.ijbiomac.2024.135239},
pmid = {39218175},
issn = {1879-0003},
mesh = {*Neoplasms/genetics/therapy/prevention &amp; control ; Humans ; *CRISPR-Cas Systems ; *Gene Editing/methods ; Animals ; Genetic Therapy/methods ; },
abstract = {There are lots of gene editing tools for targeting genome sequences. Some are almost known, and most are a complete mystery and undiscovered. CRISPR/Cas editing tools have brought about a major revolution in medicine. Researchers have shown that CRISPR can modify DNA much more accurately, economically and easily than previous methods. CRISPR has proven itself effective for the deletion, replacement and insertion of DNA fragments into cell types, tissues and organisms. Recently, combining CRISPR/Cas with factors (transcription factors/repressors, exonucleases, endonucleases, transposons, caspase, fluorescent proteins, oxidoreductive enzymes, DNA/RNA polymerases), and elements (aptamers, barcodes, fluorescent probes, Trigger) have provided genome, transcriptome, proteome and epigenome modification. These modules are being investigated for cancer prevention and therapy and this review focuses on such innovative combinations that hopefully will become a clinical reality in the near future.},
}
@article {pmid39208239,
year = {2024},
author = {Douch, JK and Vaughan, LJ and Cooper, JA and Holmes, GD and Robinson, R and Stefani, F and Idnurm, A and May, TW},
title = {Taxonomic revision of fleshy species of Hydnellum, Neosarcodon, and Sarcodon (Thelephorales) from Australasia.},
journal = {Mycologia},
volume = {116},
number = {6},
pages = {965-992},
doi = {10.1080/00275514.2024.2363211},
pmid = {39208239},
issn = {1557-2536},
mesh = {*Phylogeny ; *DNA, Fungal/genetics ; *Basidiomycota/classification/genetics/isolation &amp; purification ; *DNA, Ribosomal Spacer/genetics ; Australia ; New Zealand ; Sequence Analysis, DNA ; RNA, Ribosomal, 28S/genetics ; Australasia ; DNA, Ribosomal/genetics ; Forests ; Mycorrhizae/classification/genetics ; },
abstract = {Stipitate Thelephorales are basidiomycetous, mostly hydnoid, ectomycorrhizal fungi. Some species have declined considerably, and some are threat-listed as vulnerable or endangered. These ecological concerns require a well-resolved taxonomy to understand diversity in this group of fungi and facilitate conservation. However, phylogenetic studies have mostly neglected Southern Hemisphere representatives. This study examines the fleshy species of stipitate Thelephorales from native forests in Australia and New Zealand, using morphological analyses and phylogenetic analyses of nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode) and D1-D2 domains at the 5' end of nuc 28S rDNA (28S) sequences amplified from DNA isolated from fungarium collections and environmental DNA (eDNA) sequences from the Australian Microbiome initiative. Five new species, Sarcodon austrofibulatus, Hydnellum gatesiae, H. nothofagacearum, H. pseudoioeides, and H. variisporum, are described, Sarcodon carbonarius is transferred to Neosarcodon, and a key is provided for the six named species in the region. Boletopsis and Neosarcodon are reported from Australia for the first time based on detections from eDNA in soil samples taken from native forests. The Australasian species of Hydnellum occupy a highly derived position with the phylogeny of the genus, the members of which are otherwise all from the Northern Hemisphere, suggestive of a long-distance dispersal origin for the Australasian species.},
}
@article {pmid39204610,
year = {2024},
author = {Kali, B and Bekkuzhina, S and Tussipkan, D and Manabayeva, S},
title = {A First Approach for the In Vitro Cultivation, Storage, and DNA Barcoding of the Endangered Endemic Species Euonymus koopmannii.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {16},
pages = {},
pmid = {39204610},
issn = {2223-7747},
support = {BR21882180//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {Euonymus koopmannii is a rare and protected species in Kazakhstan, valued for its ecological role in soil stabilization and its ornamental properties. This study presents the first use of micropropagation and phylogenetic analysis for the endemic plant E. koopmannii. Seedlings of E. koopmannii proved to be more effective than internodes as primary explants for plant micropropagation of in vitro culture, with a multiplication coefficient of 28.5 from seedlings and 6.1 from internodes. On MSR I medium supplemented with 0.5 mg/L IBA and 0.05 mg/L IAA, a higher success rate of 67% was achieved for root formation of test tube-grown E. koopmannii plants. Using mannitol as an osmotic agent at a concentration of 8 mg/L prolonged the storage time of E. koopmannii under slow growth conditions when compared to CCC and abscisic acid. Phylogenetic relationships and species identification were analyzed using four DNA-barcoding markers, comparing E. koopmannii with species from NCBI. All candidate barcoding markers showed sufficient levels of interspecific genetic variation among Euonymus species. In addition, ITS region and rbcL gene sequences effectively distinguished E. koopmannii from other species. These results provide fundamental information that will be valuable for future biotechnological and molecular studies.},
}
@article {pmid39203564,
year = {2024},
author = {Kamberović, J and Gligora Udovič, M and Kulaš, A and Tapolczai, K and Orlić, S and Jusufović, A and Gajić, A and Žutinić, P and Ahmić, A and Kalamujić Stroil, B},
title = {The Diatom Diversity and Ecological Status of a Tufa-Depositing River through eDNA Metabarcoding vs. a Morphological Approach-A Case Study of the Una River (Bosnia and Herzegovina).},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
pmid = {39203564},
issn = {2076-2607},
abstract = {Tufa deposits in karst rivers are unique habitats created by mutual interactions between specific environmental and biotope features and inhabited by diatoms as a highly abundant and diverse algal group. This pilot study aimed to investigate the diversity of diatom communities on tufa depositing habitats and assess the Una River's ecological status using a comparative molecular and morphological approach for diatom identification. The 312 base pairs of the rbcL gene were barcoded and analyzed using MiSeq reads and amplicon sequence variants (ASVs) obtained by the DADA2 pipeline. The reference database Diat.barcode v7 was used for taxonomic assignment. The morphological identification of the diatoms was carried out in parallel. In total, the combined dataset revealed 46 taxa identified at genus rank, 125 on the subgenus, and 145 on combined taxonomy rank. The metabarcoding approach mostly leads to a lower number of identified taxa at species rank (58 in molecular vs. 119 in optical inventory), resulting in higher values of beta diversity and heterogeneity in diatom assemblages in samples obtained by morphological approach. Despite the high percentage of taxonomically not assigned diatom ASVs to the species rank, high Shannon diversity index values and a similar number of taxa per locations compared to the morphological approach were obtained. Taxa Achnanthidium minutissimum (Kützing) Czarnecki, Achnanthidium pyrenaicum (Hustedt) H.Kobayasi, Amphora pediculus (Kützing) Grunow, Diatoma vulgaris Bory, Navicula cryptotenella Lange-Bertalot, and Navicula tripunctata (O.F.Müller) Bory were identified at all locations in both inventories. Although limited consistency in the diatom abundances between the two inventory datasets was found, a similar grouping of samples was observed connected to the river's longitudinal gradient. The data obtained using molecular approach in most sites indicated a mostly lower ecological status (good or moderate) compared to the data obtained from the morphological approach (high, good, and moderate). The potential of environmental DNA (eDNA) diatom metabarcoding for water monitoring and diversity studies is undeniable, but to fully realize the benefits of these methods in the future, it is essential to standardize protocols and expand the reference database for species found in specific habitats, such as tufa deposits.},
}
@article {pmid39203446,
year = {2024},
author = {Darienko, T and Rad-Menéndez, C and Pröschold, T},
title = {The New Genus Caulinema Revealed New Insights into the Generic Relationship of the Order Ulotrichales (Ulvophyceae, Chlorophyta).},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
pmid = {39203446},
issn = {2076-2607},
support = {P 34416-B//FWF Austrian Science Fund/ ; },
abstract = {Traditionally, the order Ulotrichales comprised green algae of an unbranched, uniseriate, filamentous morphology. However, since the establishment of ultrastructural features, the circumscription of this order has dramatically changed. Some genera and species have been excluded from this order and others with different morphologies (sarcinoid, branched filaments or even parenchymatous taxa) have been included. Phylogenetic analyses have confirmed the monophyly of this order, but its differentiation from the Ulvales and Acrosiphoniales remains difficult because of the lack of synapomorphies at every level (morphology, molecular signatures). To demonstrate the difficulties of placement into genera and orders, we investigated two sarcinoid taxa with the absence of zoospore formation. SSU and ITS rDNA tree topology and the ITS-2/CBC approach revealed that both strains SAG 2661 and CCAP 312/1 belong to Ulosarcina terrestrica and the newly erected genus Caulinema, respectively. The species conception using this approach was evaluated by sequencing the plastid-coding gene tufA, a commonly used barcode marker for green algae. All three molecular markers resulted in similar topologies at the generic and species levels, which is consistent with the ITS-2/CBC approach and tufA for barcoding. The reevaluation of the ultrastructural features revealed that the presence of organic scales on the surfaces of motile cells is characteristic for the order Ulotrichales and can be used for separation from the closely related orders. As a consequence of our study, we propose the new genus Caulinema for strain CCAP 312/1.},
}
@article {pmid39201691,
year = {2024},
author = {Zhao, Y and Kipkoech, A and Li, ZP and Xu, L and Yang, JB},
title = {Deciphering the Plastome and Molecular Identities of Six Medicinal "Doukou" Species.},
journal = {International journal of molecular sciences},
volume = {25},
number = {16},
pages = {},
pmid = {39201691},
issn = {1422-0067},
support = {2021FY100204//Obtaining Super Barcodes of Important Wild Plants in Gaoligong Mountain/ ; },
mesh = {*Phylogeny ; *Plants, Medicinal/genetics/classification ; Sequence Analysis, DNA/methods ; Genome, Plastid ; },
abstract = {The genus Amomum includes over 111 species, 6 of which are widely utilized as medicinal plants and have already undergone taxonomic revision. Due to their morphological similarities, the presence of counterfeit and substandard products remains a challenge. Accurate plant identification is, therefore, essential to address these issues. This study utilized 11 newly sequenced samples and extensive NCBI data to perform molecular identification of the six medicinal "Doukou" species. The plastomes of these species exhibited a typical quadripartite structure with a conserved gene content. However, independent variation shifts of the SC/IR boundaries existed between and within species. The comprehensive set of genetic sequences, including ITS, ITS1, ITS2, complete plastomes, matK, rbcL, psbA-trnH, and ycf1, showed varying discrimination of the six "Doukou" species based on both distance and phylogenetic tree methods. Among these, the ITS, ITS1, and complete plastome sequences demonstrated the highest identification success rate (3/6), followed by ycf1 (2/6), and then ITS2, matK, and psbA-trnH (1/6). In contrast, rbcL failed to identify any species. This research established a basis for a reliable molecular identification method for medicinal "Doukou" plants to protect wild plant resources, promote the sustainable use of medicinal plants, and restrict the exploitation of these resources.},
}
@article {pmid39200507,
year = {2024},
author = {Zhao, G and Li, L and Shen, X and Zhong, R and Zhong, Q and Lei, H},
title = {DNA Barcoding Unveils Novel Discoveries in Authenticating High-Value Snow Lotus Seed Food Products.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {16},
pages = {},
pmid = {39200507},
issn = {2304-8158},
support = {2023M731143//China Postdoctoral Science Foundation/ ; 2022YFD1601712//National Key Research and Development Program of China/ ; 2023A1515110822//Guangdong Basic and Applied Basic Research Foundation/ ; },
abstract = {Snow Lotus Seed (SLS), esteemed for its nutritional and market value, faces challenges of authentication due to the absence of appropriate testing standards and methods. This results in frequent adulteration of SLS sourced from Gleditsia sinensis (G. sinensis) with other plant seeds endosperm. Traditional chloroplast DNA barcoding methods are inadequate for species identification due to the absence of chloroplasts in G. sinensis seeds endosperm. In this study, the homology of 11 ITS genes among 6 common Gleditsia species was analyzed. Universal primers suitable for these species were designed and screened. A DNA barcoding method for distinguishing SLS species was developed using Sanger sequencing technology, leveraging existing GenBank and Barcode of Life Data System (BOLD) databases. Optimized sample pretreatment facilitated effective DNA extraction from phytopolysaccharide-rich SLS. Through testing of commercial SLS products, the species origin has been successfully identified. Additionally, a novel instance of food fraud was uncovered, where the Caesalpinia spinosa endosperm was used to counterfeit SLS for the first time. The study established that the developed DNA barcoding method is effective for authenticating SLS species. It is of great significance for combating food fraud related to SLS, ensuring food safety, and promoting the healthy development of the SLS industry.},
}
@article {pmid39199868,
year = {2024},
author = {Shang, Z and Chen, K and Han, T and Bu, F and Sun, S and Zhu, N and Man, D and Yang, K and Yuan, S and Fu, H},
title = {Natural Foraging Selection and Gut Microecology of Two Subterranean Rodents from the Eurasian Steppe in China.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {16},
pages = {},
pmid = {39199868},
issn = {2076-2615},
support = {32060256//National Natural Science Foundation of China/ ; 32060395//National Natural Science Foundation of China/ ; 2021ZD0006//Major Science and Technology Project of Inner Mongolia Autonomous Region/ ; BR221307//Basic scientific research business expenses of universities directly under Inner Mongolia Autonomous Region/ ; BR221037//Basic scientific research business expenses of universities directly under Inner Mongolia Autonomous Region/ ; },
abstract = {As the most abundant group of mammals, rodents possess a very rich ecotype, which makes them ideal for studying the relationship between diet and host gut microecology. Zokors are specialized herbivorous rodents adapted to living underground. Unlike more generalized herbivorous rodents, they feed on the underground parts of grassland plants. There are two species of the genus Myospalax in the Eurasian steppes in China: one is Myospalax psilurus, which inhabits meadow grasslands and forest edge areas, and the other is M. aspalax, which inhabits typical grassland areas. How are the dietary choices of the two species adapted to long-term subterranean life, and what is the relationship of this diet with gut microbes? Are there unique indicator genera for their gut microbial communities? Relevant factors, such as the ability of both species to degrade cellulose, are not yet clear. In this study, we analyzed the gut bacterial communities and diet compositions of two species of zokors using 16S amplicon technology combined with macro-barcoding technology. We found that the diversity of gut microbial bacterial communities in M. psilurus was significantly higher than that in M. aspalax, and that the two species of zokors possessed different gut bacterial indicator genera. Differences in the feeding habits of the two species of zokors stem from food composition rather than diversity. Based on the results of Mantel analyses, the gut bacterial community of M. aspalax showed a significant positive correlation with the creeping-rooted type food, and there was a complementary relationship between the axis root-type-food- and the rhizome-type-food-dominated (containing bulb types and tuberous root types) food groups. Functional prediction based on KEGG found that M. psilurus possessed a stronger degradation ability in the same cellulose degradation pathway. Neutral modeling results show that the gut flora of the M. psilurus has a wider ecological niche compared to that of the M. aspalax. This provides a new perspective for understanding how rodents living underground in grassland areas respond to changes in food conditions.},
}
@article {pmid39196267,
year = {2024},
author = {King, AC and Kumar, N and Mellor, KC and Hawkins, PA and McGee, L and Croucher, NJ and Bentley, SD and Lees, JA and Lo, SW},
title = {Comparison of gene-by-gene and genome-wide short nucleotide sequence-based approaches to define the global population structure of Streptococcus pneumoniae.},
journal = {Microbial genomics},
volume = {10},
number = {8},
pages = {},
pmid = {39196267},
issn = {2057-5858},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Streptococcus pneumoniae/genetics/classification ; *Multilocus Sequence Typing/methods ; *Genome, Bacterial ; *Phylogeny ; Cluster Analysis ; Humans ; Genomics/methods ; },
abstract = {Defining the population structure of a pathogen is a key part of epidemiology, as genomically related isolates are likely to share key clinical features such as antimicrobial resistance profiles and invasiveness. Multiple different methods are currently used to cluster together closely related genomes, potentially leading to inconsistency between studies. Here, we use a global dataset of 26 306 Streptococcus pneumoniae genomes to compare four clustering methods: gene-by-gene seven-locus MLST, core genome MLST (cgMLST)-based hierarchical clustering (HierCC) assignments, life identification number (LIN) barcoding and k-mer-based PopPUNK clustering (known as GPSCs in this species). We compare the clustering results with phylogenetic and pan-genome analyses to assess their relationship with genome diversity and evolution, as we would expect a good clustering method to form a single monophyletic cluster that has high within-cluster similarity of genomic content. We show that the four methods are generally able to accurately reflect the population structure based on these metrics and that the methods were broadly consistent with each other. We investigated further to study the discrepancies in clusters. The greatest concordance was seen between LIN barcoding and HierCC (adjusted mutual information score=0.950), which was expected given that both methods utilize cgMLST, but have different methods for defining an individual cluster and different core genome schema. However, the existence of differences between the two methods shows that the selection of a core genome schema can introduce inconsistencies between studies. GPSC and HierCC assignments were also highly concordant (AMI=0.946), showing that k-mer-based methods which use the whole genome and do not require the careful selection of a core genome schema are just as effective at representing the population structure. Additionally, where there were differences in clustering between these methods, this could be explained by differences in the accessory genome that were not identified in cgMLST. We conclude that for S. pneumoniae, standardized and stable nomenclature is important as the number of genomes available expands. Furthermore, the research community should transition away from seven-locus MLST, whilst cgMLST, GPSC and LIN assignments should be used more widely. However, to allow for easy comparison between studies and to make previous literature relevant, the reporting of multiple clustering names should be standardized within the research.},
}
@article {pmid39195758,
year = {2024},
author = {Chiappa, G and Fassio, G and Modica, MV and Oliverio, M},
title = {Potential Ancestral Conoidean Toxins in the Venom Cocktail of the Carnivorous Snail Raphitoma purpurea (Montagu, 1803) (Neogastropoda: Raphitomidae).},
journal = {Toxins},
volume = {16},
number = {8},
pages = {},
pmid = {39195758},
issn = {2072-6651},
support = {B89J21032850001//Sapienza University of Rome/ ; RM12017276B846BB//Sapienza University of Rome/ ; SEED-3840974//Sapienza University of Rome/ ; },
mesh = {Animals ; *Mollusk Venoms/genetics ; *Snails/genetics ; Transcriptome ; Salivary Glands/metabolism ; },
abstract = {Venomous marine gastropods of the superfamily Conoidea possess a rich arsenal of toxins, including neuroactive toxins. Venom adaptations might have played a fundamental role in the radiation of conoideans; nevertheless, there is still no knowledge about the venom of the most diversified family of the group: Raphitomidae Bellardi, 1875. In this study, transcriptomes were produced from the carcase, salivary glands, and proximal and distal venom ducts of the northeastern Atlantic species Raphitoma purpurea (Montagu, 1803). Using a gut barcoding approach, we were also able to report, for the first time, molecular evidence of a vermivorous diet for the genus. Transcriptomic analyses revealed over a hundred putative venom components (PVC), including 69 neurotoxins. Twenty novel toxin families, including some with high levels of expansion, were discovered. No significant difference was observed between the distal and proximal venom duct secretions. Peptides related to cone snail toxins (Cerm06, Pgam02, and turritoxin) and other venom-related proteins (disulfide isomerase and elevenin) were retrieved from the salivary glands. These salivary venom components may constitute ancestral adaptations for venom production in conoideans. Although often neglected, salivary gland secretions are of extreme importance for understanding the evolutionary history of conoidean venom.},
}
@article {pmid39194872,
year = {2024},
author = {Tian, WH and Jin, Y and Liao, YC and Faraj, TK and Guo, XY and Maharachchikumbura, SSN},
title = {New and Interesting Pine-Associated Hyphomycetes from China.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {10},
number = {8},
pages = {},
pmid = {39194872},
issn = {2309-608X},
support = {A1098531023601245//Talent Introduction and Cultivation Project, University of Electronic Science and Tech-nology of China/ ; RSP2024R487//Researchers Supporting Project at King Saud University, Riyadh, Saudi Arabia/ ; },
abstract = {Pine trees play a crucial role in the forests of Sichuan Province, boasting rich species diversity and a lengthy evolutionary history. However, research and investigation on fungi associated with pine trees are insufficient. This study investigated the diversity of hyphomycetes fungi associated with pine trees in Sichuan Province, China. During the survey, we collected five specimens of hyphomycetes from branches and bark of species of Pinus. Five barcodes were selected for study and sequenced, including ITS, SSU, LSU, TEF1, and RPB2. Morphological examination and multi-locus phylogenetic analyses revealed three new species, viz. Catenulostroma pini sp. nov. within Teratosphaeriaceae, Kirschsteiniothelia longisporum sp. nov. within Kirschsteiniotheliaceae, Sporidesmiella sichuanensis sp. nov. within Junewangiaceae, and two known species, Paradictyoarthrinium diffractum and P. hydei within Paradictyoarthriniaceae, which are the new host records from Pinus species. Catenulostroma pini, distinguished from other species in the genus by its unique morphology, has three conidial morphologies: small terminal helicoconidia, scolecoconidia with many septa, and phragmoconidia conidia. Kirschsteiniothelia longisporum has longer spores when compared to the other species in the genus. According to phylogenetic analysis, Sporidesmiella sichuanensis formed an independent clade sister to S. aquatica and S. juncicola, distinguished by differences in conidial size.},
}
@article {pmid39194831,
year = {2024},
author = {Wang, C and He, J and Chen, X},
title = {Revision of the Genus Laelius (Hymenoptera, Chrysidoidea, Bethylidae) from China.},
journal = {Insects},
volume = {15},
number = {8},
pages = {},
pmid = {39194831},
issn = {2075-4450},
support = {31920103005//National Natural Science Foundation of China/ ; 2023YFD1400600//National Key Research and Development Program of China/ ; },
abstract = {The genus Laelius from China is revised for the first time and six species are recognized, including one new species as well as three new records. The new species, Laelius longus sp. nov., which is supported by both morphological and molecular analyses, is described and illustrated. Three new records, L. naniwaensis, L. nigrofemoratus, and L. yamatonis, are illustrated. A key to the Chinese species of Laelius is provided.},
}
@article {pmid39194771,
year = {2024},
author = {Dimitrov, R and Gouliamova, D and Guéorguiev, B and Smith, M and Groenewald, M and Boekhout, T},
title = {First DNA Barcoding Survey in Bulgaria Unveiled Huge Diversity of Yeasts in Insects.},
journal = {Insects},
volume = {15},
number = {8},
pages = {},
pmid = {39194771},
issn = {2075-4450},
abstract = {In this study, we conducted a comprehensive survey aimed at assessing the diversity of yeast species inhabiting the guts of various insect species collected mainly from two Bulgarian National Parks, namely, Rila, and Pirin. The insect specimens encompass a broad taxonomic spectrum, including representatives from Coleoptera, Orthoptera, Lepidoptera, Hymenoptera, Dermaptera, Isopoda, and Collembola. Yeast strains were identified with DNA barcoding using the ribosomal markers, specifically, the D1/D2 domains of the ribosomal large subunit (LSU) and the internal transcribed spacers regions ITS 1 + 2 (ITS). The analysis unveiled the presence of 89 ascomycetous and 18 basidiomycetous yeast isolates associated with the insect specimens. Furthermore, our study identified 18 hitherto unknown yeast species.},
}
@article {pmid39193858,
year = {2024},
author = {Gómez-Zapata, PA and Johnson, MA and Bonacci, T and Aime, MC},
title = {Phylogeny, biogeography, and host range of gall midges (Diptera: Cecidomyiidae) feeding on spores of rust fungi (Basidiomycota: Pucciniales).},
journal = {Journal of insect science (Online)},
volume = {24},
number = {4},
pages = {},
pmid = {39193858},
issn = {1536-2442},
support = {//U.S. National Science Foundation/ ; DEB-1458290//CSBR/ ; DEB-1502887//TCN/ ; //U.S. Department of Agriculture/ ; AP20PPQS//APHIS/ ; 1010662//NIFA Hatch/ ; 2021-07760//NIFA Specialty Crop Research Initiative/ ; },
mesh = {Animals ; *Basidiomycota/physiology/genetics ; *Host Specificity ; *Phylogeny ; *Larva/microbiology/growth &amp; development/physiology ; Diptera/microbiology ; Phylogeography ; Spores, Fungal/physiology ; },
abstract = {Rust fungi (Pucciniales) are plant pathogens that can cause devastating yield losses to economically important crops and threaten native plants with extinction. Rusts are usually controlled with fungicides when rust-resistant plant varieties are unavailable. However, natural enemies may offer an alternative to chemicals by acting as biological controls. The larvae of Mycodiplosis Rübsaamen (49 spp.) feed on the spores of rusts and powdery mildew fungi and have been suggested as a potential biocontrol candidate for disease-causing rusts. However, little is known about the phylogenetic relationships, biogeography, and host range of this genus. We screened 5,665 rust specimens from fungarium specimens and field collections and recovered a total of 363 larvae on 315 rust specimens from 17 countries. Three mitochondrial and 2 nuclear loci were amplified and sequenced for the phylogenetic reconstruction of 129 individuals. We recovered 12 clades, of which 12 and 10 were supported with maximum likelihood and Bayesian inference, respectively. Of the 12 clades, 7 comprised species from multiple continents and climatic regions, and 5 comprised species from a single region. Individuals forming clades were collected from 2 to 18 rust species, suggesting that Mycodiplosis species have a broad host range. In total, Mycodiplosis larvae were identified on 44 different rust species collected from 18 plant families. Future studies should focus on expanding field sampling efforts, including data from additional gene regions, and incorporating morphological data to further elucidate species diversity and distribution patterns.},
}
@article {pmid39193167,
year = {2024},
author = {Catanese, G and Vázquez-Luis, M and Giacobbe, S and García-March, JR and Zotou, M and Patricia, P and Papadakis, O and Tena-Medialdea, J and Katsanevakis, S and Grau, A},
title = {Internal transcribed spacer as effective molecular marker for the detection of natural hybridization between the bivalves Pinna nobilis and Pinna rudis.},
journal = {Ecology and evolution},
volume = {14},
number = {8},
pages = {e70227},
pmid = {39193167},
issn = {2045-7758},
abstract = {The Pinna nobilis, a Mediterranean mollusc, has suffered population declines due to a massive mortality event associated with various factors including the parasite Haplosporidium pinnae. Some populations show resilience, possibly due to local environmental conditions. In this study, a molecular multiplex PCR method was developed using species-specific primers targeting Internal Transcribed Spacer (ITS) regions of P. nobilis and P. rudis, allowing accurate species identification and hybrid detection. Samples from Mediterranean areas were analysed, including putative hybrids and individuals from five other bivalve species. DNA was isolated, ITS regions were amplified and sequenced, and phylogenetic analyses confirmed species differentiation and primer specificity. The multiplex-PCR successfully identified P. nobilis, P. rudis, and their hybrids based on distinct amplicon patterns. This study highlights the value of molecular tools in species conservation, especially for monitoring and managing hybridization, supporting effective biodiversity conservation strategies.},
}
@article {pmid39192093,
year = {2024},
author = {Baryshev, A and La Fleur, A and Groves, B and Michel, C and Baker, D and Ljubetič, A and Seelig, G},
title = {Massively parallel measurement of protein-protein interactions by sequencing using MP3-seq.},
journal = {Nature chemical biology},
volume = {20},
number = {11},
pages = {1514-1523},
pmid = {39192093},
issn = {1552-4469},
support = {R01GM120379//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 2312398//National Science Foundation (NSF)/ ; N00014-16-1-3189//United States Department of Defense | United States Navy | Office of Naval Research (ONR)/ ; },
mesh = {*High-Throughput Nucleotide Sequencing/methods ; Protein Interaction Mapping/methods ; Two-Hybrid System Techniques ; Protein Binding ; Proteins/metabolism/chemistry/genetics ; Humans ; },
abstract = {Protein-protein interactions (PPIs) regulate many cellular processes and engineered PPIs have cell and gene therapy applications. Here, we introduce massively parallel PPI measurement by sequencing (MP3-seq), an easy-to-use and highly scalable yeast two-hybrid approach for measuring PPIs. In MP3-seq, DNA barcodes are associated with specific protein pairs and barcode enrichment can be read by sequencing to provide a direct measure of interaction strength. We show that MP3-seq is highly quantitative and scales to over 100,000 interactions. We apply MP3-seq to characterize interactions between families of rationally designed heterodimers and to investigate elements conferring specificity to coiled-coil interactions. Lastly, we predict coiled heterodimer structures using AlphaFold-Multimer (AF-M) and train linear models on physics-based energy terms to predict MP3-seq values. We find that AF-M-based models could be valuable for prescreening interactions but experimentally measuring interactions remains necessary to rank their strengths quantitatively.},
}
@article {pmid39191105,
year = {2024},
author = {Song, SF and Zhang, XW and Chen, S and Shu, Y and Yu, YL and Wang, JH},
title = {CRISPR-based dual-aptamer proximity ligation coupled hybridization chain reaction for precise detection of tumor extracellular vesicles and cancer diagnosis.},
journal = {Talanta},
volume = {280},
number = {},
pages = {126780},
doi = {10.1016/j.talanta.2024.126780},
pmid = {39191105},
issn = {1873-3573},
mesh = {Humans ; *Extracellular Vesicles/chemistry ; *Aptamers, Nucleotide/chemistry ; *Neoplasms/diagnosis/genetics ; *Nucleic Acid Hybridization ; Limit of Detection ; CRISPR-Cas Systems/genetics ; Biomarkers, Tumor/blood/genetics ; },
abstract = {Tumor cell-derived extracellular vesicles (TEVs) contain numerous cellular molecules and are considered potential biomarkers for non-invasive liquid biopsy. However, due to the low abundance of TEVs secreted by tumor cells and their phenotypic heterogeneity, there is a lack of sensitive and specific methods to quantify TEVs. Here, we developed a dual-aptamer proximity ligation-coupled hybridization chain reaction (HCR) method for tracing TEVs, exploiting CRISPR to achieve highly sensitive detection. Taking advantage of the high binding affinity of aptamers, the two aptamers (AptEpCAM, AptHER2) exhibited the high selectivity for TEVs recognition. HCR generated long-repeated sequence containing multiple crRNA targetable barcodes, and the signals were further amplified by CRISPR upon recognizing the HCR sequences, thereby enhancing the sensitivity. Under optimal conditions, the developed method demonstrated a favorable linear relationship in the range of 2 × 10[3]-10[7] particles/μL, with a limit of detection (LOD) of 3.3 × 10[2] particles/μL. We directly applied our assay to clinical plasma analysis, achieving 100 % accuracy in cancer diagnosis, thus demonstrating the potential clinical applications of TEVs. Due to its simplicity and rapidity, excellent sensitivity and specificity, this method has broad applications in clinical medicine.},
}
@article {pmid39189753,
year = {2024},
author = {DeCurtis, EK and Machado, I and Kuss-Duerkop, SK and Wang, Y and Khare, R},
title = {MALDI-TOF mass spectrometry from nucleic acid: development and evaluation of a novel platform for identification of mycobacteria and detection of genetic markers of resistance.},
journal = {Microbiology spectrum},
volume = {12},
number = {10},
pages = {e0163824},
pmid = {39189753},
issn = {2165-0497},
support = {None//National Jewish Health (NJH)/ ; },
mesh = {*Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Humans ; *Nontuberculous Mycobacteria/genetics/isolation &amp; purification/classification ; *Drug Resistance, Bacterial/genetics ; Genetic Markers ; Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; DNA, Bacterial/genetics ; Mycobacterium tuberculosis/genetics/isolation &amp; purification/classification/drug effects ; Sensitivity and Specificity ; Polymerase Chain Reaction/methods ; },
abstract = {Complete identification methods are critical for evaluating nontuberculous mycobacteria (NTM). Here, we describe a novel diagnostic method for identification of eight NTM, Mycobacterium tuberculosis complex, and three drug resistance markers using PCR/matrix-assisted, laser-desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) from cultured organisms. With this technology, a multiplex end-point PCR is performed for targets of interest. Detection probes that are extended in the presence of a target are added. The extended probes have greater molecular weight and can be detected by MALDI-TOF MS. An AFB Primary Panel was designed to differentiate Mycobacterium avium; Mycobacterium intracellulare subsp. chimaera; Mycobacterium avium complex (other); Mycobacterium abscessus subsp. abscessus, bolletii, and massiliense; Mycobacterium kansasii, and M. tuberculosis complex. This design should cover 90% (3,483/3,691) of mycobacteria seen onsite. A development set of unblinded isolates (n = 217) was used to develop PCR primers, detection probes, and probe barcodes. It demonstrated 99.1% (215/217) agreement with reference methods. An evaluation set using blinded isolates (n = 320) showed an overall sensitivity of 94.3% (range by target: 90.0-100%). Overall specificity from negative media, non-target mycobacteria, and bacteria was 99.1% (108/109; range by target: 94.4-100%). Three drug resistance markers erm (41), rrl, and rrs demonstrated 100%, 91%, and 100% sensitivity, respectively, and >99% specificity. Limit of detection per target ranged from 2.2 × 10[3] to 9.9 × 10[6] CFU/mL. The AFB Primary Panel allows for mycobacterial speciation, subspeciation, and resistance mutation detection, which is essential for diagnosis, appropriate therapy, identifying outbreaks, and managing treatment-refractory disease. It can perform with high-throughput and high specificity and sensitivity from isolates.IMPORTANCEEven closely related mycobacteria can have unique treatment patterns, but differentiating these organisms is a challenge. Here, we tested an innovative platform that combines two commonly used technologies and creates something new: matrix-assisted, laser-desorption ionization time-of flight mass spectrometry was performed on PCR amplicons instead of on proteins. This created a robust system with the advantages of PCR (high discriminatory power, high throughput, detection of resistance) with the advantages of mass spectrometry (more targets, lower operational cost) in order to identify closely related mycobacterial organisms.},
}
@article {pmid39185194,
year = {2024},
author = {Fahlberg, MD and Forward, S and Assita, ER and Mazzola, M and Kiem, A and Handley, M and Yun, SH and Kwok, SJJ},
title = {Overcoming fixation and permeabilization challenges in flow cytometry by optical barcoding and multi-pass acquisition.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39185194},
issn = {2692-8205},
support = {T32 GM007226/GM/NIGMS NIH HHS/United States ; R43 GM140527/GM/NIGMS NIH HHS/United States ; T32 GM132089/GM/NIGMS NIH HHS/United States ; F31 HL158020/HL/NHLBI NIH HHS/United States ; R44 GM139504/GM/NIGMS NIH HHS/United States ; R01 EB033155/EB/NIBIB NIH HHS/United States ; },
abstract = {The fixation and permeabilization of cells are essential for labeling intracellular biomarkers in flow cytometry. However, these chemical treatments often alter fragile targets, such as cell surface and fluorescent proteins, and can destroy chemically-sensitive fluorescent labels. This reduces measurement accuracy and introduces compromises into sample workflows, leading to losses in data quality. Here, we demonstrate a novel multi-pass flow cytometry approach to address this long-standing problem. Our technique utilizes individual cell barcoding with laser particles, enabling sequential analysis of the same cells with single-cell resolution maintained. Chemically-fragile protein markers and their fluorochrome conjugates are measured prior to destructive sample processing and adjoined to subsequent measurements of intracellular markers after fixation and permeabilization. We demonstrate the effectiveness of our technique in accurately measuring intracellular fluorescent proteins and methanol-sensitive antigens and fluorophores, along with various surface and intracellular markers. This approach significantly enhances assay flexibility, enabling accurate and comprehensive cell analysis without the constraints of conventional one-time measurement flow cytometry. This innovation paves new avenues in flow cytometry for a wide range of applications in immuno-oncology, stem cell research, and cell biology.},
}
@article {pmid39185156,
year = {2024},
author = {Handler, JS and Li, Z and Dveirin, RK and Fang, W and Goodarzi, H and Fertig, EJ and Kalhor, R},
title = {Identifying a gene signature of metastatic potential by linking pre-metastatic state to ultimate metastatic fate.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39185156},
issn = {2692-8205},
support = {P30 EY001765/EY/NEI NIH HHS/United States ; R01 HG012357/HG/NHGRI NIH HHS/United States ; T32 CA009071/CA/NCI NIH HHS/United States ; },
abstract = {Identifying the key molecular pathways that enable metastasis by analyzing the eventual metastatic tumor is challenging because the state of the founder subclone likely changes following metastatic colonization. To address this challenge, we labeled primary mouse pancreatic ductal adenocarcinoma (PDAC) subclones with DNA barcodes to characterize their pre-metastatic state using ATAC-seq and RNA-seq and determine their relative in vivo metastatic potential prospectively. We identified a gene signature separating metastasis-high and metastasis-low subclones orthogonal to the normal-to-PDAC and classical-to-basal axes. The metastasis-high subclones feature activation of IL-1 pathway genes and high NF-κB and Zeb/Snail family activity and the metastasis-low subclones feature activation of neuroendocrine, motility, and Wnt pathway genes and high CDX2 and HOXA13 activity. In a functional screen, we validated novel mediators of PDAC metastasis in the IL-1 pathway, including the NF-κB targets Fos and Il23a, and beyond the IL-1 pathway including Myo1b and Tmem40. We scored human PDAC tumors for our signature of metastatic potential from mouse and found that metastases have higher scores than primary tumors. Moreover, primary tumors with higher scores are associated with worse prognosis. We also found that our metastatic potential signature is enriched in other human carcinomas, suggesting that it is conserved across epithelial malignancies. This work establishes a strategy for linking cancer cell state to future behavior, reveals novel functional regulators of PDAC metastasis, and establishes a method for scoring human carcinomas based on metastatic potential.},
}
@article {pmid39184369,
year = {2024},
author = {Yamamoto, T and Tachihara, K and Toda, M},
title = {Examination of sequence variations in partial mitochondrial 12S gene amongst damselfish species as references for DNA barcoding.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e126744},
pmid = {39184369},
issn = {1314-2828},
abstract = {Accurate species identification, based on DNA barcoding, can be achieved when sufficient sequence variations are present amongst species in the sampled marker. In general, the ability to discriminate species decreases with shorter sequences; however, shorter regions have a merit in amplification success by the polymerase chain reaction. In either case, it is important to investigate sequence variations amongst species before barcoding to understand its reliability and limitations. In this study, we investigate how accurately short, but hypervariable portion of the mitochondrial 12S ribosomal RNA (12S) gene (MiFish region with approximately 180 bp) is used to identify each species in diversified pomacentrid fishes compared with the longer region of the same gene (approximately 750 bp). We prepared three datasets with 301 sequences of the MiFish region for 150 species, the same 301 of sequences of the longer 12S region and 476 sequences of the MiFish region for 183 species. Neighbour-joining (NJ) analyses and genetic distance analyses revealed several indistinguishable pairs of species in these DNA regions. Although the number of such pairs was larger in the MiFish region, 83.6% (153 of 183) of species possessed respective unique sequences even in the MiFish region (versus 96.0% [144 of 150 species] in the longer 12S region). A part of indistinguishable pairs of species might have caused by mitochondrial DNA introgressions and taxonomically unresolved problems. Our analysis clarified the effectiveness and limitations of species identification using DNA barcoding for Pomacentridae and the sequences we provided here contribute to the expansion of references for pomacentrid mitochondrial 12S sequences.},
}
@article {pmid39179166,
year = {2024},
author = {Thipphet, K and Horpaopan, S and Jaturas, N and Thanchomnang, T and Moophayak, K and Chaiwong, T and Hongsrichan, N and Nakhonkam, W and Phuwanatsarunya, P and Dumidae, A and Bunthong, S and Kaewbungkord, T and Sanit, S and Ruankham, W and Vitta, A and Kurahashi, H and Sukontason, KL and Bunchu, N},
title = {Molecular identification and genetic variation of forensically important fly species (Order: Diptera) in Thailand using DNA barcoding.},
journal = {Acta tropica},
volume = {258},
number = {},
pages = {107366},
doi = {10.1016/j.actatropica.2024.107366},
pmid = {39179166},
issn = {1873-6254},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Thailand ; *Genetic Variation ; *Electron Transport Complex IV/genetics ; *Forensic Entomology ; Diptera/genetics/classification/anatomy &amp; histology ; Calliphoridae/genetics/classification ; Phylogeny ; Sarcophagidae/genetics/classification ; Muscidae/genetics/classification ; },
abstract = {Forensic entomology plays a crucial role in criminal investigations by providing vital insights into minimum postmortem interval (PMImin) and corpse relocation by identifying insect species that colonize in decomposing remains. This study aimed to identify and analyze the genetic variation of forensically significant fly species in Thailand, using DNA barcoding of the mitochondrial cytochrome c oxidase subunit I COI gene. A total of 3,220 fly specimens were collected from 18 provinces across six regions of Thailand from October 2017 to September 2022. These specimens were classified by morphological identification into 21 species among three Dipteran families: Calliphoridae, Muscidae, and Sarcophagidae, with Chrysomya megacephala Diptera: Calliphoridae being the most abundant species. DNA barcoding confirmed the morphological identifications with 100 % accuracy, showing low intraspecific K2P distances0.0 to 1.1 %) and significant interspecific K2P distances 2.5 % to 17.2 %. A Neighbour-Joining (NJ) analysis was conducted to assess the molecular identification capabilities of the barcoding region. This analysis successfully recovered nearly all species as distinct monophyletic groups. The species groupings obtained were generally consistent with both morphological and molecular identifications. These findings underscore the effectiveness of DNA barcoding for precise species identification and contribute to a comprehensive database of forensically important flies in Thailand, thus facilitating improved forensic investigations and biodiversity studies.},
}
@article {pmid39179112,
year = {2024},
author = {Wei, PS and Thota, N and John, G and Chang, E and Lee, S and Wang, Y and Ma, Z and Tsai, YH and Mei, KC},
title = {Enhancing RNA-lipid nanoparticle delivery: Organ- and cell-specificity and barcoding strategies.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {375},
number = {},
pages = {366-388},
doi = {10.1016/j.jconrel.2024.08.030},
pmid = {39179112},
issn = {1873-4995},
mesh = {Humans ; *Nanoparticles/chemistry ; Animals ; *Lipids/chemistry ; RNA/administration &amp; dosage ; Gene Transfer Techniques ; RNA, Small Interfering/administration &amp; dosage ; Organ Specificity ; },
abstract = {Recent advancements in RNA therapeutics highlight the critical need for precision gene delivery systems that target specific organs and cells. Lipid nanoparticles (LNPs) have emerged as key vectors in delivering mRNA and siRNA, offering protection against enzymatic degradation, enabling targeted delivery and cellular uptake, and facilitating RNA cargo release into the cytosol. This review discusses the development and optimization of organ- and cell-specific LNPs, focusing on their design, mechanisms of action, and therapeutic applications. We explore innovations such as DNA/RNA barcoding, which facilitates high-throughput screening and precise adjustments in formulations. We address major challenges, including improving endosomal escape, minimizing off-target effects, and enhancing delivery efficiencies. Notable clinical trials and recent FDA approvals illustrate the practical applications and future potential of LNP-based RNA therapies. Our findings suggest that while considerable progress has been made, continued research is essential to resolve existing limitations and bridge the gap between preclinical and clinical evaluation of the safety and efficacy of RNA therapeutics. This review highlights the dynamic progress in LNP research. It outlines a roadmap for future advancements in RNA-based precision medicine.},
}
@article {pmid39176612,
year = {2024},
author = {Svandova, K and Smutny, Z},
title = {What Technologies Based on Unique Patient Identifiers Are Used for Patient Identification in Healthcare?.},
journal = {Studies in health technology and informatics},
volume = {316},
number = {},
pages = {1264-1268},
doi = {10.3233/SHTI240642},
pmid = {39176612},
issn = {1879-8365},
mesh = {Humans ; *Patient Identification Systems ; Patient Safety ; Radio Frequency Identification Device ; },
abstract = {Ensuring the correct identification of the patient is key to matching the correct patients with the proper care (e.g. correct administration of medications and treatments), but it is also applied, for example, to monitoring the patient's movement in the hospital environment. This scoping review aims to find out what technologies based on unique patient identifiers are used to identify patients in healthcare facilities to increase patient safety and to identify future research trends. PRISMA-ScR guidelines were used, and the search focused on Web of Science and Scopus citation databases from 2000 to February 2024. Thirty-two papers dealing with patient identification methods from the point of view of person identification were found. The solutions found were built on the technologies (linear or 2D) of barcodes, RFID and NFC tags. None of the patient identification solutions found offer complete accuracy due to the human factor, and each solution targets a different problem context associated with a particular type of health facility. Future research can focus on the combination of multiple technologies, including biometric methods, to improve identification and tools to support decisions about the use of technology in a particular context and health facility (e.g. hospitals, medical nursing homes).},
}
@article {pmid39172488,
year = {2024},
author = {Majima, K and Kojima, Y and Minoura, K and Abe, K and Hirose, H and Shimamura, T},
title = {LineageVAE: reconstructing historical cell states and transcriptomes toward unobserved progenitors.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {10},
pages = {},
pmid = {39172488},
issn = {1367-4811},
support = {20H04281//Grants-in-Aid for Scientific Research/ ; },
mesh = {*Single-Cell Analysis/methods ; *Transcriptome/genetics ; Humans ; Cell Lineage ; Sequence Analysis, RNA/methods ; Hematopoiesis/genetics ; Deep Learning ; Animals ; Computational Biology/methods ; Stem Cells/metabolism/cytology ; },
abstract = {MOTIVATION: Single-cell RNA sequencing (scRNA-seq) enables comprehensive characterization of the cell state. However, its destructive nature prohibits measuring gene expression changes during dynamic processes such as embryogenesis or cell state divergence due to injury or disease. Although recent studies integrating scRNA-seq with lineage tracing have provided clonal insights between progenitor and mature cells, challenges remain. Because of their experimental nature, observations are sparse, and cells observed in the early state are not the exact progenitors of cells observed at later time points. To overcome these limitations, we developed LineageVAE, a novel computational methodology that utilizes deep learning based on the property that cells sharing barcodes have identical progenitors.<br><br>RESULTS: LineageVAE is a deep generative model that transforms scRNA-seq observations with identical lineage barcodes into sequential trajectories toward a common progenitor in a latent cell state space. This method enables the reconstruction of unobservable cell state transitions, historical transcriptomes, and regulatory dynamics at a single-cell resolution. Applied to hematopoiesis and reprogrammed fibroblast datasets, LineageVAE demonstrated its ability to restore backward cell state transitions and infer progenitor heterogeneity and transcription factor activity along differentiation trajectories.<br><br>The LineageVAE model was implemented in Python using the PyTorch deep learning library. The code is available on GitHub at https://github.com/LzrRacer/LineageVAE/.},
}
@article {pmid39172294,
year = {2024},
author = {Ikeda, S and Inoue, Y and Imada, Y},
title = {Unveiled species diversity of moss-feeding mites (Stigmaeidae: Eustigmaeus): a research on their distribution, habitat, and host plant use in Japan.},
journal = {Experimental &amp; applied acarology},
volume = {93},
number = {4},
pages = {721-741},
pmid = {39172294},
issn = {1572-9702},
support = {2023-5007//Japan Science Society/ ; 18H06077, JP20K15852, JP22H02684//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; Japan ; *Mites/physiology/genetics/classification ; *Bryophyta ; *DNA Barcoding, Taxonomic ; *Animal Distribution ; Electron Transport Complex IV/analysis ; Ecosystem ; Biodiversity ; Feeding Behavior ; Host Specificity ; },
abstract = {The genus Eustigmaeus Berlese, 1910 represents the unique phytophagous group within the superfamily Raphignathoidea. Four species within this genus have been known to inhabit mosses and feed on them as larvae, nymphs, and adults. However, the interactions with mosses have remained poorly understood. In order to reveal the diversity and host-plant use of the moss-feeding species, we conducted an extensive field study in Japan. This study revealed an array of moss-feeding species inhabiting various moss species, with 10 morphologically distinctive species newly documented in Japan. Through DNA barcoding based on cytochrome c oxidase subunit I (COI) sequences, these morphospecies were recovered as distinct entities. Notably, the host-plant use of four species was elucidated. Among these, Eustigmaeus sp. 9 exhibited polyphagy, while three species (Eustigmaeus spp. 1-3) demonstrated varying degrees of host specificity, each using moss species from the Hypnales, Philonotis, and Dicranidae, respectively. While a few moss-feeding species were frequently found in the same geographic area, more than one species rarely co-occurred within the same moss colonies. Eustigmaeus offers a unique study system, with its diverse moss-feeding species and indications of specific host plant use. Consequently, the moss-feeding Eustigmaeus serves as a valuable model for exploring the macroevolutionary patterns underlying diversification in moss-feeding arthropods.},
}
@article {pmid39164496,
year = {2024},
author = {Cui, X and Dong, X and Hu, M and Zhou, W and Shi, W},
title = {Large field of view and spatial region of interest transcriptomics in fixed tissue.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1020},
pmid = {39164496},
issn = {2399-3642},
support = {41676119//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41476120//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Mice ; *Gene Expression Profiling/methods ; *Transcriptome ; *Tissue Fixation/methods ; Paraffin Embedding ; Brain/metabolism ; Embryo, Mammalian/metabolism ; },
abstract = {Expression profiling in spatially defined regions is crucial for systematically understanding tissue complexity. Here, we report a method of photo-irradiation for in-situ barcoding hybridization and ligation sequencing, named PBHL-seq, which allows targeted expression profiling from the photo-irradiated region of interest in intact fresh frozen and formalin fixation and paraffin embedding (FFPE) tissue samples. PBHL-seq uses photo-caged oligodeoxynucleotides for in situ reverse transcription followed by spatially targeted barcoding of cDNAs to create spatially indexed transcriptomes of photo-illuminated regions. We recover thousands of differentially enriched transcripts from different regions by applying PBHL-seq to OCT-embedded tissue (E14.5 mouse embryo and mouse brain) and FFPE mouse embryo (E15.5). We also apply PBHL-seq to the subcellular microstructures (cytoplasm and nucleus, respectively) and detect thousands of differential expression genes. Thus, PBHL-seq provides an accessible workflow for expression profiles from the region of interest in frozen and FFPE tissue at subcellular resolution with areas expandable to centimeter scale, while preserving the sample intact for downstream analysis to promote the development of transcriptomics.},
}
@article {pmid39161647,
year = {2024},
author = {Padilla-Villavicencio, M and Corzo, G and Guillén-Navarro, K and Ibarra-Núñez, G and Arenas, I and Zamudio, F and Diego-García, E},
title = {Cupiennius spiders (Trechaleidae) from southern Mexico: DNA barcoding, venomics, and biological effect.},
journal = {The journal of venomous animals and toxins including tropical diseases},
volume = {30},
number = {},
pages = {e20230098},
pmid = {39161647},
issn = {1678-9199},
abstract = {BACKGROUND: Members of the genus Cupiennius Simon, 1891 are categorized as wandering spiders and are part of the family Trechaleidae. The genomics and proteomics of Cupiennius spiders from North America remain uncharacterized. The present study explores for the first time molecular data from the endemic species Cupiennius chiapanensis Medina, 2006, and also presents new data for Cupiennius salei (Keyserling, 1878), both collected in southern Mexico.<br><br>METHODS: In total, 88 Cupiennius specimens were collected from southern Mexico and morphologically identified. DNA was extracted and the mitochondrial COI fragment was amplified. COI sequences were analyzed, and a phylogenetic tree was inferred for species from the Americas. Genetic diversity was analyzed using haplotype networks and gene distances. Venom was obtained from C. chiapanensis and C. salei by electrostimulation. The venom was separated by HPLC, visualized using SDS-PAGE, and quantified for use in toxicity bioassays in mice and insects.<br><br>RESULTS: Analysis of COI sequences from C. chiapanensis showed 94% identity with C. salei, while C. salei exhibited 94-97% identity with sequences from Central and South American conspecifics. The venom from C. chiapanensis exhibited toxic activity against crickets. Venoms from C. chiapanensis and C. salei caused death in Anastrepha obliqua flies. Analysis of venom fractions from C. salei and C. chiapanensis revealed molecular masses of a similar size as some previously reported toxins and neurotoxic components. We determined the amino acid sequences of ChiaTx1 and ChiaTx2, toxins that are reported here for the first time and which showed toxicity against mice and insects.<br><br>CONCLUSION: Our work is the first to report COI-based DNA barcoding sequences from southern Mexican Cupiennius spiders. Compounds with toxic activity were identified in venom from both species.},
}
@article {pmid39161631,
year = {2024},
author = {Liu, F and Hu, ZD and Yurkov, A and Chen, XH and Bao, WJ and Ma, Q and Zhao, WN and Pan, S and Zhao, XM and Liu, JH and Wang, QM and Boekhout, T},
title = {Saccharomycetaceae: delineation of fungal genera based on phylogenomic analyses, genomic relatedness indices and genomics-based synapomorphies.},
journal = {Persoonia},
volume = {52},
number = {},
pages = {1-21},
pmid = {39161631},
issn = {0031-5850},
abstract = {A correct classification of fungi, including yeasts, is of prime importance to understand fungal biodiversity and to communicate about this diversity. Fungal genera are mainly defined based on phenotypic characteristics and the results of single or multigene-based phylogenetic analyses. However, because yeasts often have less phenotypic characters, their classification experienced a strong move towards DNA-based data, from short ribosomal sequences to multigene phylogenies and more recently to phylogenomics. Here, we explore the usefulness of various genomics-based parameters to circumscribe fungal genera more correctly taking the yeast domain as an example. Therefore, we compared the results of a phylogenomic analysis, average amino acid identity (AAI) values, the presence of conserved signature indels (CSIs), the percentage of conserved proteins (POCP) and the presence-absence patterns of orthologs (PAPO). These genome-based metrics were used to investigate their usefulness in demarcating 13 hitherto relatively well accepted genera in Saccharomycetaceae, namely Eremothecium, Grigorovia, Kazachstania, Kluyveromyces, Lachancea, Nakaseomyces, Naumovozyma, Saccharomyces, Tetrapisispora, Torulaspora, Vanderwaltozyma, Zygosaccharomyces and Zygotorulaspora. As a result, most of these genera are supported by the genomics-based metrics, but the genera Kazachstania, Nakaseomyces and Tetrapisispora were shown to be genetically highly diverse based on the above listed analyses. Considering the results obtained for the presently recognized genera, a range of 80-92 % POCP values and a range of 60-70 % AAI values might be valuable thresholds to discriminate genera in Saccharomycetaceae. Furthermore, the genus-specific genes identified in the PAPO analysis and the CSIs were found to be useful as synapomorphies to characterize and define genera in Saccharomycetaceae. Our results indicate that the combined monophyly-based phylogenomic analysis together with genomic relatedness indices and synapomorphies provide promising approaches to delineating yeast genera and likely those of filamentous fungi as well. The genera Kazachstania, Nakaseomyces and Tetrapisispora are revised and we propose eight new genera and 41 new combinations. Citation: Liu F, Hu Z-D, Yurkov A, et al. 2024. Saccharomycetaceae: delinaeation of fungal genera based on phylogenomic analyses, genomic relatedness indices and genomics-based synapomorphies. Persoonia 52: 1-21. https://doi.org/10.3767/persoonia.2024.52.01.},
}
@article {pmid39160260,
year = {2024},
author = {Gallego, R and Arias, MB and Corral-Lou, A and Díez-Vives, C and Neave, EF and Wang, C and Cárdenas, P and Steffen, K and Taboada, S and Villamor, A and Kenchington, E and Mariani, S and Riesgo, A},
title = {North Atlantic deep-sea benthic biodiversity unveiled through sponge natural sampler DNA.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1015},
pmid = {39160260},
issn = {2399-3642},
support = {NE/T007028/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/T007028/1//RCUK | Natural Environment Research Council (NERC)/ ; 679849//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; ID 100010434//"la Caixa" Foundation (Caixa Foundation)/ ; },
mesh = {*Porifera/genetics/classification ; Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic/methods ; Atlantic Ocean ; DNA, Environmental/analysis ; Ecosystem ; },
abstract = {The deep-sea remains the biggest challenge to biodiversity exploration, and anthropogenic disturbances extend well into this realm, calling for urgent management strategies. One of the most diverse, productive, and vulnerable ecosystems in the deep sea are sponge grounds. Currently, environmental DNA (eDNA) metabarcoding is revolutionising the field of biodiversity monitoring, yet complex deep-sea benthic ecosystems remain challenging to assess even with these novel technologies. Here, we evaluate the effectiveness of whole-community metabarcoding to characterise metazoan diversity in sponge grounds across the North Atlantic by leveraging the natural eDNA sampling properties of deep-sea sponges themselves. We sampled 97 sponge tissues from four species across four North-Atlantic biogeographic regions in the deep sea and screened them using the universal COI barcode region. We recovered unprecedented levels of taxonomic diversity per unit effort, especially across the phyla Chordata, Cnidaria, Echinodermata and Porifera, with at least 406 metazoan species found in our study area. These assemblages identify strong spatial patterns in relation to both latitude and depth, and detect emblematic species currently employed as indicators for these vulnerable habitats. The remarkable performance of this approach in different species of sponges, in different biogeographic regions and across the whole animal kingdom, illustrates the vast potential of natural samplers as high-resolution biomonitoring solutions for highly diverse and vulnerable deep-sea ecosystems.},
}
@article {pmid39160220,
year = {2024},
author = {Liu, F and Zhang, X and Yang, Y},
title = {Simulation of CRISPR-Cas9 editing on evolving barcode and accuracy of lineage tracing.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {19213},
pmid = {39160220},
issn = {2045-2322},
support = {R01 CA251950/CA/NCI NIH HHS/United States ; },
mesh = {*CRISPR-Cas Systems ; *Gene Editing/methods ; *Computer Simulation ; Algorithms ; DNA Barcoding, Taxonomic/methods ; Cell Lineage/genetics ; INDEL Mutation ; Mutation ; },
abstract = {We designed a simulation program that mimics the CRISPR-Cas9 editing on evolving barcode and double strand break repair procedure along with cell divisions. Emerging barcode mutations tend to build upon previously existing mutations, occurring sequentially with each generation. This process results in a unique mutation profile in each cell. We sample the barcodes in leaf cells and reconstruct the lineage, comparing it to the original lineage tree to test algorithm accuracy under different parameter settings. Our computational simulations validate the reasonable assumptions deduced from experimental observations, emphasizing that factors such as sampling size, barcode length, multiple barcodes, indel probabilities, and Cas9 activity are critical for accurate and successful lineage tracing. Among the many factors we found that sampling size and indel probabilities are two major ones that affect lineage tracing accuracy. Large segment deletions in early generations could greatly impact lineage accuracy. These simulation results offer insightful recommendations for enhancing the design and analysis of Cas9-mediated molecular barcodes in actual experiments.},
}
@article {pmid39159937,
year = {2024},
author = {Cavalcante, KS and Rodrigues, BL and Posada-López, L and Peniche, T and Saraiva, JF and Galardo, AKR and Galati, EAB},
title = {Description of Trichophoromyia jariensis, a new species of phlebotomine sand fly (Diptera: Psychodidae) from the eastern Amazon.},
journal = {Journal of medical entomology},
volume = {61},
number = {6},
pages = {1382-1390},
doi = {10.1093/jme/tjae095},
pmid = {39159937},
issn = {1938-2928},
mesh = {Animals ; Brazil ; Female ; Male ; *Psychodidae/classification/genetics/anatomy &amp; histology ; *DNA Barcoding, Taxonomic ; *Electron Transport Complex IV/genetics ; },
abstract = {A new sand fly species, Trichophoromyia jariensis n. sp. Cavalcante, Rodrigues, &amp; Galati, from the state of Amapá, Brazil, is described based on both male and female morphology and cytochrome c oxidase subunit I DNA barcodes. The DNA barcoding analysis clearly associated males and females of this new species.},
}
@article {pmid39158755,
year = {2024},
author = {Krivina, E and Sinetova, M and Zadneprovskaya, E and Ivanova, M and Starikov, A and Shibzukhova, K and Lobakova, E and Bukin, Y and Portnov, A and Temraleeva, A},
title = {The genus Coelastrella (Chlorophyceae, Chlorophyta): molecular species delimitation, biotechnological potential, and description of a new species Coelastrella affinis sp. nov., based on an integrative taxonomic approach.},
journal = {Antonie van Leeuwenhoek},
volume = {117},
number = {1},
pages = {113},
pmid = {39158755},
issn = {1572-9699},
support = {075-15-2021-1051//Ministry of Science and Higher Education of the Russian Federation/ ; 122042700045-3//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2021-1051//Ministry of Science and Higher Education of the Russian Federation/ ; 122042700045-3//Ministry of Science and Higher Education of the Russian Federation/ ; 122042700045-3//Ministry of Science and Higher Education of the Russian Federation/ ; 122050400128-1//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2021-1051//Ministry of Science and Higher Education of the Russian Federation/ ; 21-74-30003//Russian Science Foundation/ ; 21-74-30003//Russian Science Foundation/ ; },
mesh = {*Phylogeny ; *Chlorophyceae/classification/genetics ; *RNA, Ribosomal, 18S/genetics ; Fatty Acids/analysis ; Biotechnology ; DNA Barcoding, Taxonomic ; DNA, Algal/genetics/chemistry ; Cluster Analysis ; Sequence Analysis, DNA ; DNA, Ribosomal Spacer/genetics ; },
abstract = {Despite the long research history on the genus Coelastrella, its species diversity and biotechnological potential have not been fully explored. For the first time, cluster analysis of morphological characteristics was done in the representatives of the said genus. The results obtained have shown that morphological similarity does not necessarily indicate a molecular genetic relationship. It the light of it, the taxonomic status of species can reliably be determined using specific DNA region, such as 18S-ITS1-5.8S-ITS2. The V4 and V9 regions of gene 18S rRNA are relatively conservative fragments which are not suitable for species identification. The ITS2 can be used as a "short barcode". Among the advanced machine methods for delimitation species, the most effective algorithm for distinguishing Coelastrella species was the Generalized Mixed Yule Coalescent (GMYC) method. This paper represented for the first time our comprehensive review of the works devoted to the analysis of the biotechnological potential of representatives of the genus Coelastrella and shows that fatty acid composition of the three main chemogroups within the studied genus differs. In the future, this may form the basis for predicting the composition of the fatty acid profile of new strains, which is important while searching for organisms with specified biotechnological properties. In conclusion, an integrative approach was employed to describe Coelastrella affinis sp. nov., a new species of the genus Coelastrella with high biotechnological potential. Also, a new description of C. thermophila var. astaxanthina comb. nov. was proposed.},
}
@article {pmid39157088,
year = {2024},
author = {Hanna, VS and Abd El-Ghany, MN and Ibrahim, MIM and Abdel-Rahman, TM and Tallima, H},
title = {Novel Approaches to Mortierella alpina Identification and Arachidonic Acid Production Optimization.},
journal = {ACS omega},
volume = {9},
number = {32},
pages = {34456-34463},
pmid = {39157088},
issn = {2470-1343},
abstract = {Arachidonic acid (ARA) is an integral constituent of cell structures and is instrumental for the nervous, muscular, and immune systems' functions. The sore need for this nutrient may be fulfilled via production based on the fungus Mortierella alpina. The identity of the M. alpina culture obtained from Assiut University, Egypt, was confirmed based on internal transcribed spacer DNA barcoding and elongation enzyme RNA sequencing. Liquid media glucose and peptone as carbon and nitrogen sources, respectively, and diverse micronutritional factors were adjusted for optimal biomass and ARA production. Shake flask cultivation at 25 °C for 7 days produced around 0.570 g of ARA per liter of culture. M. alpina treatment using mutagen 5-fluorouracil and octyl gallate-supplemented glucose-yeast-agar screening plates and shake-flask incubation at 25 °C, then at 20 °C, followed by aging at 10 °C, led to >3 g ARA/liter culture, a yield considered suitable for potential commercial production.},
}
@article {pmid39152642,
year = {2024},
author = {Romeijn, L and Bernatavicius, A and Vu, D},
title = {MycoAI: Fast and accurate taxonomic classification for fungal ITS sequences.},
journal = {Molecular ecology resources},
volume = {24},
number = {8},
pages = {e14006},
doi = {10.1111/1755-0998.14006},
pmid = {39152642},
issn = {1755-0998},
mesh = {*Fungi/classification/genetics ; *DNA, Ribosomal Spacer/genetics/chemistry ; DNA Barcoding, Taxonomic/methods ; DNA, Fungal/genetics ; Neural Networks, Computer ; Deep Learning ; Computational Biology/methods ; },
abstract = {Efficient and accurate classification of DNA barcode data is crucial for large-scale fungal biodiversity studies. However, existing methods are either computationally expensive or lack accuracy. Previous research has demonstrated the potential of deep learning in this domain, successfully training neural networks for biological sequence classification. We introduce the MycoAI Python package, featuring various deep learning models such as BERT and CNN tailored for fungal Internal Transcribed Spacer (ITS) sequences. We explore different neural architecture designs and encoding methods to identify optimal models. By employing a multi-head output architecture and multi-level hierarchical label smoothing, MycoAI effectively generalizes across the taxonomic hierarchy. Using over 5 million labelled sequences from the UNITE database, we develop two models: MycoAI-BERT and MycoAI-CNN. While we emphasize the necessity of verifying classification results by AI models due to insufficient reference data, MycoAI still exhibits substantial potential. When benchmarked against existing classifiers such as DNABarcoder and RDP on two independent test sets with labels present in the training dataset, MycoAI models demonstrate high accuracy at the genus and higher taxonomic levels, with MycoAI-CNN being the fastest and most accurate. In terms of efficiency, MycoAI models can classify over 300,000 sequences within 5 min. We publicly release the MycoAI models, enabling mycologists to classify their ITS barcode data efficiently. Additionally, MycoAI serves as a platform for developing further deep learning-based classification methods. The source code for MycoAI is available under the MIT Licence at https://github.com/MycoAI/MycoAI.},
}
@article {pmid39150891,
year = {2024},
author = {},
title = {Correction to "Patient and specimen identification in a tertiary care pediatric hospital: Barcodes do not scan themselves".},
journal = {Transfusion},
volume = {64},
number = {9},
pages = {1806},
doi = {10.1111/trf.17945},
pmid = {39150891},
issn = {1537-2995},
}
@article {pmid39149389,
year = {2024},
author = {Voorhies, M and Joehnk, B and Uehling, J and Walcott, K and Dubin, C and Mead, HL and Homer, CM and Galgiani, JN and Barker, BM and Brem, RB and Sil, A},
title = {Inferring the composition of a mixed culture of natural microbial isolates by deep sequencing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39149389},
issn = {2692-8205},
support = {R21 AI172185/AI/NIAID NIH HHS/United States ; S10 OD028511/OD/NIH HHS/United States ; T32 AI007641/AI/NIAID NIH HHS/United States ; U19 AI166798/AI/NIAID NIH HHS/United States ; },
abstract = {Next generation sequencing has unlocked a wealth of genotype information for microbial populations, but phenotyping remains a bottleneck for exploiting this information, particularly for pathogens that are difficult to manipulate. Here, we establish a method for high-throughput phenotyping of mixed cultures, in which the pattern of naturally occurring single-nucleotide polymorphisms in each isolate is used as intrinsic barcodes which can be read out by sequencing. We demonstrate that our method can correctly deconvolute strain proportions in simulated mixed-strain pools. As an experimental test of our method, we perform whole genome sequencing of 66 natural isolates of the thermally dimorphic pathogenic fungus Coccidioides posadasii and infer the strain compositions for large mixed pools of these strains after competition at 37°C and room temperature. We validate the results of these selection experiments by recapitulating the temperature-specific enrichment results in smaller pools. Additionally, we demonstrate that strain fitness estimated by our method can be used as a quantitative trait for genome-wide association studies. We anticipate that our method will be broadly applicable to natural populations of microbes and allow high-throughput phenotyping to match the rate of genomic data acquisition.},
}
@article {pmid39149311,
year = {2024},
author = {Hu, C and Borji, M and Marrero, GJ and Kumar, V and Weir, JA and Kammula, SV and Macosko, EZ and Chen, F},
title = {Scalable imaging-free spatial genomics through computational reconstruction.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39149311},
issn = {2692-8205},
support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 HG010647/HG/NHGRI NIH HHS/United States ; U24 HG011735/HG/NHGRI NIH HHS/United States ; },
abstract = {Tissue organization arises from the coordinated molecular programs of cells. Spatial genomics maps cells and their molecular programs within the spatial context of tissues. However, current methods measure spatial information through imaging or direct registration, which often require specialized equipment and are limited in scale. Here, we developed an imaging-free spatial transcriptomics method that uses molecular diffusion patterns to computationally reconstruct spatial data. To do so, we utilize a simple experimental protocol on two dimensional barcode arrays to establish an interaction network between barcodes via molecular diffusion. Sequencing these interactions generates a high dimensional matrix of interactions between different spatial barcodes. Then, we perform dimensionality reduction to regenerate a two-dimensional manifold, which represents the spatial locations of the barcode arrays. Surprisingly, we found that the UMAP algorithm, with minimal modifications can faithfully successfully reconstruct the arrays. We demonstrated that this method is compatible with capture array based spatial transcriptomics/genomics methods, Slide-seq and Slide-tags, with high fidelity. We systematically explore the fidelity of the reconstruction through comparisons with experimentally derived ground truth data, and demonstrate that reconstruction generates high quality spatial genomics data. We also scaled this technique to reconstruct high-resolution spatial information over areas up to 1.2 centimeters. This computational reconstruction method effectively converts spatial genomics measurements to molecular biology, enabling spatial transcriptomics with high accessibility, and scalability.},
}
@article {pmid39149288,
year = {2024},
author = {Eastburn, DJ and White, KS and Jayne, ND and Camiolo, S and Montis, G and Ha, S and Watson, KG and Yeakley, JM and McComb, J and Seligmann, B},
title = {High-throughput gene expression analysis with TempO-LINC sensitively resolves complex brain, lung and kidney heterogeneity at single-cell resolution.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39149288},
issn = {2692-8205},
support = {R43 GM140771/GM/NIGMS NIH HHS/United States ; R44 GM140771/GM/NIGMS NIH HHS/United States ; },
abstract = {We report the development and performance of a novel genomics platform, TempO-LINC, for conducting high-throughput transcriptomic analysis on single cells and nuclei. TempO-LINC works by adding cell-identifying molecular barcodes onto highly selective and high-sensitivity gene expression probes within fixed cells, without having to first generate cDNA. Using an instrument-free combinatorial-indexing approach, all probes within the same fixed cell receive an identical barcode, enabling the reconstruction of single-cell gene expression profiles across as few as several hundred cells and up to 100,000+ cells per run. The TempO-LINC approach is easily scalable based on the number of barcodes and rounds of barcoding performed; however, for the experiments reported in this study, the assay utilized over 5.3 million unique barcodes. TempO-LINC has a robust protocol for fixing and banking cells and displays high-sensitivity gene detection from multiple diverse sample types. We show that TempO-LINC has an observed multiplet rate of less than 1.1% and a cell capture rate of ~50%. Although the assay can accurately profile the whole transcriptome (19,683 human or 21,400 mouse genes), it can be targeted to measure only actionable/informative genes and molecular pathways of interest - thereby reducing sequencing requirements. In this study, we applied TempO-LINC to profile the transcriptomes of 89,722 cells across multiple sample types, including nuclei from mouse lung, kidney and brain tissues. The data demonstrated the ability to identify and annotate at least 50 unique cell populations and positively correlate expression of cell type-specific molecular markers within them. TempO-LINC is a robust new single-cell technology that is ideal for large-scale applications/studies across thousands of samples with high data quality.},
}
@article {pmid39149271,
year = {2024},
author = {Liao, H and Kottapalli, S and Huang, Y and Chaw, M and Gehring, J and Waltner, O and Phung-Rojas, M and Daza, RM and Matsen, FA and Trapnell, C and Shendure, J and Srivatsan, S},
title = {Optics-free reconstruction of 2D images via DNA barcode proximity graphs.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39149271},
issn = {2692-8205},
support = {R01 AI146028/AI/NIAID NIH HHS/United States ; R01 HG010632/HG/NHGRI NIH HHS/United States ; },
abstract = {Spatial genomic technologies include imaging- and sequencing-based methods (1-3). An emerging subcategory of sequencing-based methods relies on a surface coated with coordinate-associated DNA barcodes, which are leveraged to tag endogenous nucleic acids or cells in an overlaid tissue section (4-7). However, the physical registration of DNA barcodes to spatial coordinates is challenging, necessitating either high density printing of coordinate-specific oligonucleotides or in situ sequencing/probing of randomly deposited, oligonucleotide-bearing beads. As a consequence, the surface areas available to sequencing-based spatial genomic methods are constrained by the time, labor, cost, and instrumentation required to either print, synthesize or decode a coordinate-tagged surface. To address this challenge, we developed SCOPE (Spatial reConstruction via Oligonucleotide Proximity Encoding), an optics-free, DNA microscopy (8) inspired method. With SCOPE, the relative positions of randomly deposited beads on a 2D surface are inferred from the ex situ sequencing of chimeric molecules formed from diffusing "sender" and tethered "receiver" oligonucleotides. As a first proof-of-concept, we apply SCOPE to reconstruct an asymmetric "swoosh" shape resembling the Nike logo (16.75 × 9.25 mm). Next, we use a microarray printer to encode a "color" version of the Snellen eye chart for visual acuity (17.18 × 40.97 mm), and apply SCOPE to achieve optics-free reconstruction of individual letters. Although these are early demonstrations of the concept and much work remains to be done, we envision that the optics-free, sequencing-based quantitation of the molecular proximities of DNA barcodes will enable spatial genomics in constant experimental time, across fields of view and at resolutions that are determined by sequencing depth, bead size, and diffusion kinetics, rather than the limitations of optical instruments or microarray printers.},
}
@article {pmid39148054,
year = {2024},
author = {Wen, J and Wu, BC and Li, HM and Zhou, W and Song, CF},
title = {Plastome structure and phylogenetic relationships of genus Hydrocotyle (apiales): provide insights into the plastome evolution of Hydrocotyle.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {778},
pmid = {39148054},
issn = {1471-2229},
support = {32200191//National Natural Science Foundation of China/ ; JSPKLB202214//Foundation of Jiangsu Key Laboratory for the Research and Utilization of Plant Resources/ ; },
mesh = {*Phylogeny ; Evolution, Molecular ; Genome, Plastid ; Apiaceae/genetics ; },
abstract = {BACKGROUND: The genus Hydrocotyle Tourn. ex L. is a key group for further study on the evolution of Apiales, comprising around 170 species globally. Previous studies mainly focused on separate sections and provided much information about this genus, but its infrageneric relationships are still confusing. In addition, the genetic basis of its adaptive evolution remains poorly understood. To investigate the phylogeny and evolution of the genus, we selected ten representative species covering two of three diversity distribution centers and exhibiting rich morphology diversity. Comparative plastome analysis was conducted to clarify the structural character of Hydrocotyle plastomes. Positive selection analyses were implemented to assess the evolution of the genus. Phylogenetic inferences with protein-coding sequences (CDS) of Hydrocotyle and 17 related species were also performed.<br><br>RESULTS: Plastomes within Hydrocotyle were generally conservative in structure, gene order, and size. A total of 14 regions (rps16-trnK, trnQ-rps16, atpI-atpH, trnC-petN-psbM, ycf3-trnS, accD-psaI-ycf4, petA-psbJ, rps12-rpl20, rpl16 intron, rps3-rpl16 intron, rps9-rpl22, ndhF-rpl32, ndhA intron, and ycf1a) were recognized as hotspot regions within the genus, which suggested to be promising DNA barcodes for global phylogenetic analysis of Hydrocotyle. The ycf15 gene was suggested to be a protein-coding gene for Hydrocotyle species, and it could be used as a DNA barcode to identify Hydrocotyle. In phylogenetic analysis, three monophyletic clades (Clade I, II, III) were identified with evidence of rapid radiation speciation within Clade I. The selective pressure analysis detected that six CDS genes (ycf1b, matK, atpF, accD, rps14, and psbB) of Hydrocotyle species were under positive selection. Within the genus, the last four genes were conservative, suggesting a relation to the unique evolution of the genus in Apiales. Seven genes (atpE, matK, psbH, ycf1a, ycf1b, rpoA, and ycf2) were detected to be under some degree of positive selection in different taxa within the genus Hydrocotyle, indicating their role in the adaptive evolution of species.<br><br>CONCLUSIONS: Our study offers new insights into the phylogeny and adaptive evolution of Hydrocotyle. The plastome sequences could significantly enhance phylogenetic resolution and provide genomic resources and potential DNA markers useful for future studies of the genus.},
}
@article {pmid39145191,
year = {2024},
author = {Feng, J and Liu, Y and Xie, A and Yang, Y and Lv, F and Wei, J},
title = {Successful development of molecular diagnostic technology combining mini-barcoding and high-resolution melting for traditional Chinese medicine agarwood species based on single-nucleotide polymorphism in the chloroplast genome.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1405168},
pmid = {39145191},
issn = {1664-462X},
abstract = {Agarwood is a valuable traditional medicine and fragrance. The production process is a typical injury-induced defense response. Currently, there are approximately 22 known species in the genus Aquilaria Lam., all of which can produce agarwood, whereas there are only two legal species of traditional Chinese medicinal agarwood, Aquilaria sinensis (Lour.) Spreng. and Aquilaria agallocha (Lour.) Roxb. The Taiwan herbal Pharmacopoeia of China stipulates that the medicinal agarwood species are A. sinensis and its relatives in the same genus. Moreover, there are five species of agarwood available for clinical medicinal use in Japan, including A. agallocha and A. sinensis, which are often confused with each other or used in a mixed way in the trade process. Therefore, accurate identification of traditional Chinese medicinal agarwood species is important to ensure the authenticity of traditional medicines and to guide the safety of clinical medication. In this study, 59 specific single-nucleotide polymorphism loci were screened and obtained from the chloroplast genomes of 12 species of the genus Aquilaria Lam. We established an identification method for traditional Chinese medicinal agarwood using mini-barcoding combined with high-resolution melting (HRM) and designed and validated 10 pairs of primers from the psbM-trnD, psbA, rps16, petN, ndhE-psaC, rps4, atpE, ycf1, rps15-trnN, and matK regions. The amplification products were all less than 200 bp, with a high success rate of amplification. The method was applied to successfully identify traditional Chinese medicinal agarwood species from commercial agarwood samples. Overall, the sensitivity of this method was sufficient to detect 1% of adulterants in medicinal agarwood products, proving that mini-barcoding HRM is a powerful and flexible tool. This method can be used as a fast and effective high-throughput method for authenticity testing of traditional Chinese medicinal agarwood and its raw materials containing agarwood-containing proprietary Chinese medicines and is recommended for industrial applications.},
}
@article {pmid39144078,
year = {2024},
author = {Framst, I and Wolking, RM and Schonfeld, J and Ricker, N and Beeler-Marfisi, J and Chalmers, G and Kamath, PL and Maboni, G},
title = {High-throughput rapid amplicon sequencing for multilocus sequence typing of Mycoplasma ovipneumoniae from archived clinical DNA samples.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1443855},
pmid = {39144078},
issn = {2297-1769},
abstract = {INTRODUCTION: Spillover events of Mycoplasma ovipneumoniae have devastating effects on the wild sheep populations. Multilocus sequence typing (MLST) is used to monitor spillover events and the spread of M. ovipneumoniae between the sheep populations. Most studies involving the typing of M. ovipneumoniae have used Sanger sequencing. However, this technology is time-consuming, expensive, and is not well suited to efficient batch sample processing.<br><br>METHODS: Our study aimed to develop and validate an MLST workflow for typing of M. ovipneumoniae using Nanopore Rapid Barcoding sequencing and multiplex polymerase chain reaction (PCR). We compare the workflow with Nanopore Native Barcoding library preparation and Illumina MiSeq amplicon protocols to determine the most accurate and cost-effective method for sequencing multiplex amplicons. A multiplex PCR was optimized for four housekeeping genes of M. ovipneumoniae using archived DNA samples (N = 68) from nasal swabs.<br><br>RESULTS: Sequences recovered from Nanopore Rapid Barcoding correctly identified all MLST types with the shortest total workflow time and lowest cost per sample when compared with Nanopore Native Barcoding and Illumina MiSeq methods.<br><br>DISCUSSION: Our proposed workflow is a convenient and effective method for strain typing of M. ovipneumoniae and can be applied to other bacterial MLST schemes. The workflow is suitable for diagnostic settings, where reduced hands-on time, cost, and multiplexing capabilities are important.},
}
@article {pmid39141231,
year = {2024},
author = {Ansari, SA and Uhlenhaut, NH},
title = {An Optimized High-Resolution Mapping Method for Glucocorticoid Receptor-DNA Binding in Mouse Primary Macrophages.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2846},
number = {},
pages = {91-107},
pmid = {39141231},
issn = {1940-6029},
mesh = {Animals ; *Receptors, Glucocorticoid/metabolism/genetics ; Mice ; *Macrophages/metabolism ; *DNA/metabolism/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Chromatin Immunoprecipitation/methods ; Protein Binding ; Binding Sites ; },
abstract = {ChIP-exo is a powerful tool for achieving enhanced sensitivity and single-base-pair resolution of transcription factor (TF) binding, which utilizes a combination of chromatin immunoprecipitation (ChIP) and lambda exonuclease digestion (exo) followed by high-throughput sequencing. ChIP-nexus (chromatin immunoprecipitation experiments with nucleotide resolution through exonuclease, unique barcode, and single ligation) is an updated and simplified version of the original ChIP-exo method, which has reported an efficient adapter ligation through the DNA circularization step. Building upon an established method, we present a protocol for generating NGS (next-generation sequencing) ready and high-quality ChIP-nexus library for glucocorticoid receptor (GR). This method is specifically optimized for bone marrow-derived macrophage (BMDM) cells. The protocol is initiated by the formation of DNA-protein cross-links in intact cells. This is followed by chromatin shearing, chromatin immunoprecipitation, ligation of sequencing adapters, digestion of adapter-ligated DNA using lambda exonuclease, and purification of single-stranded DNA for circularization and library amplification.},
}
@article {pmid39140204,
year = {2024},
author = {Davis, HR and Sanford, HT and Das, I and Nashriq, I and Leaché, AD},
title = {Establishing species boundaries in Bornean geckos.},
journal = {Biology letters},
volume = {20},
number = {8},
pages = {20240157},
pmid = {39140204},
issn = {1744-957X},
support = {//Heerensperger Award/ ; //Orians Award for Tropical Studies/ ; //Ministry of Higher Education, Malaysia/ ; //Society of Systematic Biologists/ ; },
mesh = {Animals ; *Lizards/genetics/classification ; *DNA, Mitochondrial/genetics ; Borneo ; Phylogeny ; Gene Flow ; Species Specificity ; Genetic Speciation ; Genetic Variation ; },
abstract = {Species delimitation using mitochondrial DNA (mtDNA) remains an important and accessible approach for discovering and delimiting species. However, delimiting species with a single locus (e.g. DNA barcoding) is biased towards overestimating species diversity. The highly diverse gecko genus Cyrtodactylus is one such group where delimitation using mtDNA remains the paradigm. In this study, we use genomic data to test putative species boundaries established using mtDNA within three recognized species of Cyrtodactylus on the island of Borneo. We predict that multi-locus genomic data will estimate fewer species than mtDNA, which could have important ramifications for the species diversity within the genus. We aim to (i) investigate the correspondence between species delimitations using mtDNA and genomic data, (ii) infer species trees for each target species, and (iii) quantify gene flow and identify migration patterns to assess population connectivity. We find that species diversity is overestimated and that species boundaries differ between mtDNA and nuclear data. This underscores the value of using genomic data to reassess mtDNA-based species delimitations for taxa lacking clear species boundaries. We expect the number of recognized species within Cyrtodactylus to continue increasing, but, when possible, genomic data should be included to inform more accurate species boundaries.},
}
@article {pmid39140100,
year = {2024},
author = {Crous, PW and Jurjević, &#x17d; and Balashov, S and De la Peña-Lastra, S and Mateos, A and Pinruan, U and Rigueiro-Rodríguez, A and Osieck, ER and Altés, A and Czachura, P and Esteve-Raventós, F and Gunaseelan, S and Kaliyaperumal, M and Larsson, E and Luangsa-Ard, JJ and Moreno, G and Pancorbo, F and Piątek, M and Sommai, S and Somrithipol, S and Asif, M and Delgado, G and Flakus, A and Illescas, T and Kezo, K and Khamsuntorn, P and Kubátová, A and Labuda, R and Lavoise, C and Lebel, T and Lueangjaroenkit, P and Maciá-Vicente, JG and Paz, A and Saba, M and Shivas, RG and Tan, YP and Wingfield, MJ and Aas, T and Abramczyk, B and Ainsworth, AM and Akulov, A and Alvarado, P and Armada, F and Assyov, B and Avchar, R and Avesani, M and Bezerra, JL and Bhat, JD and Bilański, P and Bily, DS and Boccardo, F and Bozok, F and Campos, JC and Chaimongkol, S and Chellappan, N and Costa, MM and Dalecká, M and Darmostuk, V and Daskalopoulos, V and Dearnaley, J and Dentinger, BTM and De Silva, NI and Dhotre, D and Carlavilla, JR and Doungsa-Ard, C and Dovana, F and Erhard, A and Ferro, LO and Gallegos, SC and Giles, CE and Gore, G and Gorfer, M and Guard, FE and Hanson, S&#xc5; and Haridev, P and Jankowiak, R and Jeffers, SN and Kandemir, H and Karich, A and Kisło, K and Kiss, L and Krisai-Greilhuber, I and Latha, KPD and Lorenzini, M and Lumyong, S and Manimohan, P and Manjón, JL and Maula, F and Mazur, E and Mesquita, NLS and Młynek, K and Mongkolsamrit, S and Morán, P and Murugadoss, R and Nagarajan, M and Nalumpang, S and Noisripoom, W and Nosalj, S and Novaes, QS and Nowak, M and Pawłowska, J and Peiger, M and Pereira, OL and Pinto, A and Plaza, M and Polemis, E and Polhorský, A and Ramos, DO and Raza, M and Rivas-Ferreiro, M and Rodriguez-Flakus, P and Ruszkiewicz-Michalska, M and Sánchez, A and Santos, A and Schüller, A and Scott, PA and Şen, I and Shelke, D and Śliwa, L and Solheim, H and Sonawane, H and Strašiftáková, D and Stryjak-Bogacka, M and Sudsanguan, M and Suwannarach, N and Suz, LM and Syme, K and Taşkın, H and Tennakoon, DS and Tomka, P and Vaghefi, N and Vasan, V and Vauras, J and Wiktorowicz, D and Villarreal, M and Vizzini, A and Wrzosek, M and Yang, X and Yingkunchao, W and Zapparoli, G and Zervakis, GI and Groenewald, JZ},
title = {Fungal Planet description sheets: 1614-1696.},
journal = {Fungal systematics and evolution},
volume = {13},
number = {},
pages = {183-440},
pmid = {39140100},
issn = {2589-3831},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Baobabopsis sabindy in leaves of Eragrostis spartinoides, Cortinarius magentiguttatus among deep leaf litter, Laurobasidium azarandamiae from uredinium of Puccinia alyxiae on Alyxia buxifolia, Marasmius pseudoelegans on well-rotted twigs and litter in mixed wet sclerophyll and subtropical rainforest. Bolivia, Favolaschia luminosa on twigs of Byttneria hirsuta, Lecanora thorstenii on bark, in savannas with shrubs and trees. Brazil, Asterina costamaiae on leaves of Rourea bahiensis, Purimyces orchidacearum (incl. Purimyces gen. nov.) as root endophyte on Cattleya locatellii. Bulgaria, Monosporascus bulgaricus and Monosporascus europaeus isolated from surface-sterilised, asymptomatic roots of Microthlaspi perfoliatum. Finland, Inocybe undatolacera on a lawn, near Betula pendula. France, Inocybe querciphila in humus of mixed forest. Germany, Arrhenia oblongispora on bare soil attached to debris of herbaceous plants and grasses. Greece, Tuber aereum under Quercus coccifera and Acer sempervirens. India, Alfoldia lenyadriensis from the gut of a Platynotus sp. beetle, Fulvifomes subramanianii on living Albizzia amara, Inosperma pavithrum on soil, Phylloporia parvateya on living Lonicera sp., Tropicoporus maritimus on living Peltophorum pterocarpum. Indonesia, Elsinoe atypica on leaf of Eucalyptus pellita. Italy, Apiotrichum vineum from grape wine, Cuphopyllus praecox among grass. Madagascar, Pisolithus madagascariensis on soil under Intsia bijuga. Netherlands, Cytosporella calamagrostidis and Periconia calamagrostidicola on old leaves of Calamagrostis arenaria, Hyaloscypha caricicola on leaves of Carex sp., Neoniesslia phragmiticola (incl. Neoniesslia gen. nov.) on leaf sheaths of standing dead culms of Phragmites australis, Neptunomyces juncicola on culms of Juncus maritimus, Zenophaeosphaeria calamagrostidis (incl. Zenophaeosphaeria gen. nov.) on culms of Calamagrostis arenaria. Norway, Hausneria geniculata (incl. Hausneria gen. nov.) from a gallery of Dryocoetes alni on Alnus incana. Pakistan, Agrocybe auriolus on leaf litter of Eucalyptus camaldulensis, Rhodophana rubrodisca in nutrient-rich loamy soil with Morus alba. Poland, Cladosporium nubilum from hypersaline brine, Entomortierella ferrotolerans from soil at mines and postmining sites, Pseudopezicula epiphylla from sooty mould community on Quercus robur, Quixadomyces sanctacrucensis from resin of Pinus sylvestris, Szafranskia beskidensis (incl. Szafranskia gen. nov.) from resin of Abies alba. Portugal, Ascocoryne laurisilvae on degraded wood of Laurus nobilis, Hygrocybe madeirensis in laurel forests, Hygrocybula terracocta (incl. Hygrocybula gen. nov.) on mossy areas of laurel forests planted with Cryptomeria japonica. Republic of Kenya, Penicillium gorferi from a sterile chicken feather embedded in a soil sample. Slovakia, Cerinomyces tatrensis on bark of Pinus mugo, Metapochonia simonovicovae from soil. South Africa, Acremonium agapanthi on culms of Agapanthus praecox, Alfaria elegiae on culms of Elegia ebracteata, Beaucarneamyces stellenboschensis (incl. Beaucarneamyces gen. nov.) on dead leaves of Beaucarnea stricta, Gardeniomyces kirstenboschensis (incl. Gardeniomyces gen. nov.) rotting fruit of Gardenia thunbergia, Knufia dianellae on dead leaves of Dianella caerulea, Lomaantha quercina on twigs of Quercus suber. Melanina restionis on dead leaves of Restio duthieae, Microdochium buffelskloofinum on seeds of Eragrostis cf. racemosa, Thamnochortomyces kirstenboschensis (incl. Thamnochortomyces gen. nov.) on culms of Thamnochortus fraternus, Tubeufia hagahagana on leaves of Hypoxis angustifolia, Wingfieldomyces cypericola on dead leaves of Cyperus papyrus. Spain, Geastrum federeri in soil under Quercus suber and Q. canariensis, Geastrum nadalii in calcareous soil under Juniperus, Quercus, Cupressus, Pinus and Robinia, Hygrocybe garajonayensis in laurel forests, Inocybe cistophila on acidic soil under Cistus ladanifer, Inocybe sabuligena in a mixed Quercus ilex subsp. ballota/Juniperus thurifera open forest, Mycena calongei on mossy bark base of Juniperus oxycedrus, Rhodophana ulmaria on soil in Ulmus minor forest, Tuber arriacaense in soil under Populus pyramidalis, Volvariella latispora on grassy soils in a Quercus ilex ssp. rotundifolia stand. Sweden, Inocybe iota in alpine heath on calcareous soil. Thailand, Craterellus maerimensis and Craterellus sanbuakwaiensis on laterite and sandy soil, Helicocollum samlanense on scale insects, Leptosporella cassiae on dead twigs of Cassia fistula, Oxydothis coperniciae on dead leaf of Copernicia alba, Russula mukdahanensis on soil, Trechispora sangria on soil, Trechispora sanpatongensis on soil. Türkiye, Amanita corylophila in a plantation of Corylus avellana. Ukraine, Pararthrophiala adonis (incl. Pararthrophiala gen. nov.) on dead stems of Adonis vernalis. USA, Cladorrhinum carnegieae from Carnegiea gigantea, Dematipyriformia americana on swab from basement wall, Dothiora americana from outside air, Dwiroopa aeria from bedroom air, Lithohypha cladosporioides from hospital swab, Macroconia verruculosa on twig of Ilex montana, associated with black destroyed ascomycetous fungus and Biatora sp., Periconia floridana from outside air, Phytophthora fagacearum from necrotic leaves and shoots of Fagus grandifolia, Queenslandipenidiella californica on wood in crawlspace. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Jurjević Z, Balashov S, De la Peña-Lastra S, Mateos A, Pinruan U, Rigueiro-Rodríguez A, Osieck ER, Altés A, Czachura P, Esteve-Raventós F, Gunaseelan S, Kaliyaperumal M, Larsson E, Luangsa-ard JJ, Moreno G, Pancorbo F, Piątek M, Sommai S, Somrithipol S, Asif M, Delgado G, Flakus A, Illescas T, Kezo K, Khamsuntorn P, Kubátová A, Labuda R, Lavoise C, Lebel T, Lueangjaroenkit P, Maciá-Vicente JG, Paz A, Saba M, Shivas RG, Tan YP, Wingfield MJ, Aas T, Abramczyk B, Ainsworth AM, Akulov A, Alvarado P, Armada F, Assyov B, Avchar R, Avesani M, Bezerra JL, Bhat JD, Bilański P, Bily DS, Boccardo F, Bozok F, Campos JC, Chaimongkol S, Chellappan N, Costa MM, Dalecká M, Darmostuk V, Daskalopoulos V, Dearnaley J, Dentinger BTM, De Silva NI, Dhotre D, Carlavilla JR, Doungsa-ard C, Dovana F, Erhard A, Ferro LO, Gallegos SC, Giles CE, Gore G, Gorfer M, Guard FE, Hanson S-A, Haridev P, Jankowiak R, Jeffers SN, Kandemir H, Karich A, Kisło K, Kiss L, Krisai-Greilhuber I, Latha KPD, Lorenzini M, Lumyong S, Manimohan P, Manjón JL, Maula F, Mazur E, Mesquita NLS, Młynek K, Mongkolsamrit S, Morán P, Murugadoss R, Nagarajan M, Nalumpang S, Noisripoom W, Nosalj S, Novaes QS, Nowak M, Pawłowska J, Peiger M, Pereira OL, Pinto A, Plaza M, Polemis E, Polhorský A, Ramos DO, Raza M, Rivas-Ferreiro M, Rodriguez-Flakus P, Ruszkiewicz-Michalska M, Sánchez A, Santos A, Schüller A, Scott PA, Şen İ, Shelke D, Śliwa L, Solheim H, Sonawane H, Strašiftáková D, Stryjak-Bogacka M, Sudsanguan M, Suwannarach N, Suz LM, Syme K, Taşkın H, Tennakoon DS, Tomka P, Vaghefi N, Vasan V, Vauras J, Wiktorowicz D, Villarreal M, Vizzini A, Wrzosek M, Yang X, Yingkunchao W, Zapparoli G, Zervakis GI, Groenewald JZ (2024). Fungal Planet description sheets: 1614-1696. Fungal Systematics and Evolution 13: 183-440. doi: 10.3114/fuse.2024.13.11.},
}
@article {pmid39138532,
year = {2024},
author = {Makhanthisa, TI and Guarido, MM and Kemp, A and Weyer, J and Rostal, MK and Karesh, WB and Thompson, PN},
title = {Characterization of mosquito host-biting networks of potential Rift Valley fever virus vectors in north-eastern KwaZulu-Natal province, South Africa.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {341},
pmid = {39138532},
issn = {1756-3305},
mesh = {Animals ; South Africa ; *Mosquito Vectors/virology/physiology ; *Rift Valley fever virus/genetics/isolation &amp; purification/physiology ; *Rift Valley Fever/transmission/virology/epidemiology ; *Aedes/virology/physiology/genetics/classification ; Humans ; Feeding Behavior ; Culex/virology/physiology ; Insect Bites and Stings ; Female ; Culicidae/virology/physiology/classification ; },
abstract = {BACKGROUND: Rift Valley fever virus (RVFV) is a zoonotic mosquito-borne virus with serious implications for livestock health, human health, and the economy in Africa, and is suspected to be endemic in north-eastern KwaZulu-Natal (KZN), South Africa. The vectors of RVFV in this area are poorly known, although several species, such as Aedes (Neomelaniconion) mcintoshi, Aedes (Neomelaniconion) circumluteolus, Aedes (Aedimorphus) durbanensis, and Culex (Lasioconops) poicilipes may be involved. The aim of the study was to determine the vertebrate blood meal sources of potential RVFV mosquito vectors in north-eastern KZN and to characterize the host-biting network.<br><br>METHODS: Blood-fed mosquitoes were collected monthly from November 2019 to February 2023 using a backpack aspirator, CO2-baited Centers for Disease Control and Prevention (CDC) miniature light traps and tent traps, in the vicinity of water bodies and livestock farming households. The mosquitoes were morphologically identified. DNA was extracted from individual mosquitoes and used as templates to amplify the vertebrate cytochrome c oxidase I (COI) and cytochrome b (cytb) genes using conventional polymerase chain reaction (PCR). Amplicons were sequenced and queried in GenBank and the Barcode of Life Data systems to identify the vertebrate blood meal sources and confirm mosquito identifications. All mosquitoes were screened for RVFV using real time reverse transcription (RT)-PCR.<br><br>RESULTS: We identified the mammalian (88.8%) and avian (11.3%) blood meal sources from 409 blood-fed mosquitoes. Aedes circumluteolus (n&#x2009;=&#x2009;128) made up the largest proportion of collected mosquitoes. Cattle (n&#x2009;=&#x2009;195) and nyala (n&#x2009;=&#x2009;61) were the most frequent domestic and wild hosts, respectively. Bipartite network analysis showed that the rural network consisted of more host-biting interactions than the reserve network. All mosquitoes tested negative for RVFV.<br><br>CONCLUSIONS: Several mosquito species, including Ae. circumluteolus, and vertebrate host species, including cattle and nyala, could play a central role in RVFV transmission. Future research in this region should focus on these species to better understand RVFV amplification.},
}
@article {pmid39137246,
year = {2024},
author = {Gareri, C and Pfeiffer, CT and Jiang, X and Paulo, JA and Gygi, SP and Pham, U and Chundi, A and Wingler, LM and Staus, DP and Stepniewski, TM and Selent, J and Lucero, EY and Grogan, A and Rajagopal, S and Rockman, HA},
title = {Phosphorylation patterns in the AT1R C-terminal tail specify distinct downstream signaling pathways.},
journal = {Science signaling},
volume = {17},
number = {849},
pages = {eadk5736},
pmid = {39137246},
issn = {1937-9145},
support = {T32 HL007101/HL/NHLBI NIH HHS/United States ; P01 HL075443/HL/NHLBI NIH HHS/United States ; R01 HL056687/HL/NHLBI NIH HHS/United States ; R01 GM122798/GM/NIGMS NIH HHS/United States ; R01 GM067945/GM/NIGMS NIH HHS/United States ; R01 GM132129/GM/NIGMS NIH HHS/United States ; },
mesh = {*Receptor, Angiotensin, Type 1/metabolism/chemistry/genetics ; *Signal Transduction ; Phosphorylation ; Humans ; *beta-Arrestins/metabolism/genetics ; HEK293 Cells ; Molecular Dynamics Simulation ; Angiotensin II/metabolism ; },
abstract = {Different ligands stabilize specific conformations of the angiotensin II type 1 receptor (AT1R) that direct distinct signaling cascades mediated by heterotrimeric G proteins or β-arrestin. These different active conformations are thought to engage distinct intracellular transducers because of differential phosphorylation patterns in the receptor C-terminal tail (the "barcode" hypothesis). Here, we identified the AT1R barcodes for the endogenous agonist AngII, which stimulates both G protein activation and β-arrestin recruitment, and for a synthetic biased agonist that only stimulates β-arrestin recruitment. The endogenous and β-arrestin-biased agonists induced two different ensembles of phosphorylation sites along the C-terminal tail. The phosphorylation of eight serine and threonine residues in the proximal and middle portions of the tail was required for full β-arrestin functionality, whereas phosphorylation of the serine and threonine residues in the distal portion of the tail had little influence on β-arrestin function. Similarly, molecular dynamics simulations showed that the proximal and middle clusters of phosphorylated residues were critical for stable β-arrestin-receptor interactions. These findings demonstrate that ligands that stabilize different receptor conformations induce different phosphorylation clusters in the C-terminal tail as barcodes to evoke distinct receptor-transducer engagement, receptor trafficking, and signaling.},
}
@article {pmid39137139,
year = {2024},
author = {Jansen van Rensburg, MJ and Berger, DJ and Yassine, I and Shaw, D and Fohrmann, A and Bray, JE and Jolley, KA and Maiden, MCJ and Brueggemann, AB},
title = {Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure.},
journal = {Microbial genomics},
volume = {10},
number = {8},
pages = {},
pmid = {39137139},
issn = {2057-5858},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Streptococcus pneumoniae/genetics/classification/isolation &amp; purification ; *Multilocus Sequence Typing/methods ; *Genome, Bacterial ; Humans ; *DNA Barcoding, Taxonomic/methods ; *Pneumococcal Infections/microbiology/epidemiology ; Phylogeny ; Gene Library ; Whole Genome Sequencing/methods ; },
abstract = {Investigating the genomic epidemiology of major bacterial pathogens is integral to understanding transmission, evolution, colonization, disease, antimicrobial resistance and vaccine impact. Furthermore, the recent accumulation of large numbers of whole genome sequences for many bacterial species enhances the development of robust genome-wide typing schemes to define the overall bacterial population structure and lineages within it. Using the previously published data, we developed the Pneumococcal Genome Library (PGL), a curated dataset of 30 976 genomes and contextual data for carriage and disease pneumococci recovered between 1916 and 2018 in 82 countries. We leveraged the size and diversity of the PGL to develop a core genome multilocus sequence typing (cgMLST) scheme comprised of 1222 loci. Finally, using multilevel single-linkage clustering, we stratified pneumococci into hierarchical clusters based on allelic similarity thresholds and defined these with a taxonomic life identification number (LIN) barcoding system. The PGL, cgMLST scheme and LIN barcodes represent a high-quality genomic resource and fine-scale clustering approaches for the analysis of pneumococcal populations, which support the genomic epidemiology and surveillance of this leading global pathogen.},
}
@article {pmid39135884,
year = {2024},
author = {Visagie, CM and Yilmaz, N and Allison, JD and Barreto, RW and Boekhout, T and Boers, J and Delgado, MA and Dewing, C and Fitza, KNE and Furtado, ECA and Gaya, E and Hill, R and Hobden, A and Hu, DM and Hülsewig, T and Khonsanit, A and Luangsa-Ard, JJ and Mthembu, A and Pereira, CM and Price, JL and Pringle, A and Qikani, N and Sandoval-Denis, M and Schumacher, RK and Seifert, KA and Slippers, B and Tennakoon, DS and Thanakitpipattana, D and van Vuuren, NI and Groenewald, JZ and Crous, PW},
title = {New and Interesting Fungi. 7.},
journal = {Fungal systematics and evolution},
volume = {13},
number = {},
pages = {441-494},
pmid = {39135884},
issn = {2589-3831},
abstract = {Two new genera, 17 new species, two epitypes, and six interesting new host and / or geographical records are introduced in this study. New genera include: Cadophorella (based on Cadophorella faginea) and Neosatchmopsis (based on Neosatchmopsis ogrovei). New species include: Alternaria halotolerans (from hypersaline sea water, Qatar), Amylostereum stillwellii (from mycangia of Sirex areolatus, USA), Angiopsora anthurii (on leaves of Anthurium andraeanum, Brazil), Anthracocystis zeae-maydis (from pre-stored Zea mays, South Africa), Bisifusarium solicola (from soil, South Africa), Cadophorella faginea (from dead capsule of Fagus sylvatica, Germany), Devriesia mallochii (from house dust, Canada), Fusarium kirstenboschense (from soil, South Africa), Macroconia podocarpi (on ascomata of ascomycete on twigs of Podocarpus falcatus, South Africa), Neosatchmopsis ogrovei (on Eucalyptus leaf litter, Spain), Ophiocordyceps kuchinaraiensis (on Coleoptera larva, Thailand), Penicillium cederbergense (from soil, South Africa), Penicillium pascuigraminis (from pasture mulch, South Africa), Penicillium viridipigmentum (from soil, South Africa), Pleurotheciella acericola (on stem, bark of living tree of Acer sp., Germany), Protocreopsis physciae (on Physcia caesia, Netherlands), and Talaromyces podocarpi (from soil, South Africa). Citation: Visagie CM, Yilmaz N, Allison JD, Barreto RW, Boekhout T, Boers J, Delgado MA, Dewing C, Fitza KNE, Furtado ECA, Gaya E, Hill R, Hobden A, Hu DM, Hülsewig T, Khonsanit A, Kolecka A, Luangsa-ard JJ, Mthembu A, Pereira CM, Price J-L, Pringle A, Qikani N, Sandoval-Denis M, Schumacher RK, Slippers B, Tennakoon DS, Thanakitpipattana D, van Vuuren NI, Groenewald JZ, Crous PW (2024). New and Interesting Fungi. 7. Fungal Systematics and Evolution 13: 441-494. doi: 10.3114/fuse.2024.13.12.},
}
@article {pmid39133743,
year = {2024},
author = {Ibalim, S and Toko, PS and Segar, ST and Sagata, K and Koane, B and Miller, SE and Novotny, V and Janda, M},
title = {Phylogenetic structure of moth communities (Geometridae, Lepidoptera) along a complete rainforest elevational gradient in Papua New Guinea.},
journal = {PloS one},
volume = {19},
number = {8},
pages = {e0308698},
pmid = {39133743},
issn = {1932-6203},
mesh = {Animals ; Papua New Guinea ; *Phylogeny ; *Moths/genetics/physiology/classification ; *Rainforest ; *Altitude ; *Biodiversity ; },
abstract = {We use community phylogenetics to elucidate the community assembly mechanisms for Geometridae moths (Lepidoptera) collected along a complete rainforest elevational gradient (200-3700 m a.s.l) on Mount Wilhelm in Papua New Guinea. A constrained phylogeny based on COI barcodes for 604 species was used to analyse 1390 species x elevation occurrences at eight elevational sites separated by 500 m elevation increments. We obtained Nearest Relatedness Index (NRI), Nearest Taxon Index (NTI) and Standardised Effect Size of Faith's Phylogenetic Diversity (SES.PD) and regressed these on temperature, plant species richness and predator abundance as key abiotic and biotic predictors. We also quantified beta diversity in the moth communities between elevations using the Phylogenetic Sorensen index. Overall, geometrid communities exhibited phylogenetic clustering, suggesting environmental filters, particularly at higher elevations at and above 2200 m a.s.l and no evidence of overdispersion. NRI, NTI and SES.PD showed no consistent trends with elevation or the studied biotic and abiotic variables. Change in community structure was driven by turnover of phylogenetic beta-diversity, except for the highest 2700-3200 m elevations, which were characterised by nested subsets of lower elevation communities. Overall, the elevational signal of geometrid phylogeny was weak-moderate. Additional insect community phylogeny studies are needed to understand this pattern.},
}
@article {pmid39129968,
year = {2024},
author = {Trollip, C and Carnegie, AJ and Anderson, C and Priest, MJ and Gorrie, B and Daly, A},
title = {Response to the detection of Rugonectria castaneicola and Rugonectria wingfieldii sp. nov. on Quercus in Australia.},
journal = {Fungal systematics and evolution},
volume = {13},
number = {},
pages = {123-130},
pmid = {39129968},
issn = {2589-3831},
abstract = {Here we report on the detection and surveillance response to two Rugonectria species found in Sydney, Australia, in 2015. Both Rugonectria castaneicola and R. wingfieldii sp. nov. were found in association with cankers on Quercus robur (English oak). The fungi were initially found to be localised on amenity trees in northern Sydney, New South Wales, and as they were new detections for Australia, eradication was considered. Ongoing surveillance across the Sydney basin, regional New South Wales, and the Australian Capital Territory, however, indicated that they were already well established. Species identities were confirmed through morphological examination and molecular barcoding, with the subsequent analysis undertaken to classify R. wingfieldii sp. nov. This study provides the first records of Rugonectria found in association with canker on Oak trees in Australia. Citation: Trollip C, Carnegie AJ, Anderson C, Priest MJ, Gorrie B, Daly A (2024). Response to the detection of Rugonectria castaneicola and Rugonectria wingfieldii sp. nov. on Quercus in Australia. Fungal Systematics and Evolution 13: 123-130. doi: 10.3114/fuse.2024.13.06.},
}
@article {pmid39126069,
year = {2024},
author = {Zhou, P and Lei, WS and Shi, YK and Liu, YZ and Luo, Y and Li, JH and Xiang, XG},
title = {Plastome Evolution, Phylogenomics, and DNA Barcoding Investigation of Gastrochilus (Aeridinae, Orchidaceae), with a Focus on the Systematic Position of Haraella retrocalla.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
pmid = {39126069},
issn = {1422-0067},
support = {32060056 and 32360063//National Natural Science Foundation of China/ ; },
mesh = {*Orchidaceae/genetics/classification ; *Phylogeny ; *DNA Barcoding, Taxonomic/methods ; *Evolution, Molecular ; Genome, Plastid ; },
abstract = {Gastrochilus is an orchid genus containing about 70 species in tropical and subtropical Asia with high morphological diversity. The phylogenetic relationships among this genus have not been fully resolved, and the plastome evolution has not been investigated either. In this study, five plastomes of Gastrochilus were newly reported, and sixteen plastomes of Gastrochilus were used to conduct comparative and phylogenetic analyses. Our results showed that the Gastrochilus plastomes ranged from 146,183 to 148,666 bp, with a GC content of 36.7-36.9%. There were 120 genes annotated, consisting of 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. No contraction and expansion of IR borders, gene rearrangements, or inversions were detected. Additionally, the repeat sequences and codon usage bias of Gastrochilus plastomes were highly conserved. Twenty hypervariable regions were selected as potential DNA barcodes. The phylogenetic relationships within Gastrochilus were well resolved based on the whole plastome, especially among main clades. Furthermore, both molecular and morphological data strongly supported Haraella retrocalla as a member of Gastrochilus (G. retrocallus).},
}
@article {pmid39125672,
year = {2024},
author = {Park, J and Shin, S and Kim, Y and Bu, Y and Choi, HY and Lee, K},
title = {Effect of Torilis japonica Fruit Extract for Endothelium-Independent Vasorelaxation and Blood Pressure Lowering in Rats.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
pmid = {39125672},
issn = {1422-0067},
mesh = {Animals ; Rats ; *Vasodilation/drug effects ; *Plant Extracts/pharmacology ; *Blood Pressure/drug effects ; Male ; *Fruit/chemistry ; *Rats, Sprague-Dawley ; *Endothelium, Vascular/drug effects/metabolism ; Antihypertensive Agents/pharmacology ; Vasodilator Agents/pharmacology ; Aorta, Thoracic/drug effects/metabolism ; Rats, Inbred SHR ; Muscle, Smooth, Vascular/drug effects/metabolism ; Hypertension/drug therapy/metabolism/physiopathology ; },
abstract = {Torilis japonica (TJ) fruit, is a herb that is traditionally used for erectile dysfunction (ED). Given the shared mechanisms of ED and hypertension through vascular smooth muscle, we hypothesized that TJ would be effective in vasodilation and blood pressure reduction. This study confirmed the authenticity of TJ samples via DNA barcoding and quantified the main active compound, torilin, using HPLC. TJ was extracted with distilled water (TJW) and 50% ethanol (TJE), yielding torilin contents of 0.35 ± 0.01% and 2.84 ± 0.02%, respectively. Ex vivo tests on thoracic aortic rings from Sprague-Dawley rats showed that TJE (3-300 µg/mL) induced endothelium-independent, concentration-dependent vasodilation, unlike TJW. Torilin caused concentration-dependent relaxation with an EC50 of 210 ± 1.07 µM. TJE's effects were blocked by a voltage-dependent K[+] channel blocker and alleviated contractions induced by CaCl2 and angiotensin II. TJE inhibited vascular contraction induced by phenylephrine or KCl via extracellular CaCl2 and enhanced inhibition with nifedipine, indicating involvement of voltage-dependent and receptor-operated Ca[2+] channels. Oral administration of TJE (1000 mg/kg) significantly reduced blood pressure in spontaneously hypertensive rats. These findings suggest TJ extract's potential for hypertension treatment through vasorelaxant mechanisms, though further research is needed to confirm its efficacy and safety.},
}
@article {pmid39123731,
year = {2024},
author = {Luo, Z and Pei, C and Zhang, H and Wang, Y and Zhang, B and Hu, D},
title = {Nutritional Partitioning among Sympatric Ungulates in Eastern Tibet.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {15},
pages = {},
pmid = {39123731},
issn = {2076-2615},
abstract = {Wild ungulates play crucial roles in maintaining the structure and function of local ecosystems. The alpine musk deer (Moschus chrysogaste), white-lipped deer (Przewalskium albirostris), and red serow (Capricornis rubidus) are widely distributed throughout the Nyenchen Tanglha Mountains of Tibet. However, research on the mechanisms underlying their coexistence in the same habitat remains lacking. This study aimed to investigate the mechanisms underlying the coexistence of these species based on their dietary preferences through DNA barcoding using the fecal samples of these animals collected from the study area. These species consume a wide variety of food types. Alpine musk deer, white-lipped deer, and red serow consume plants belonging to 74 families and 114 genera, 62 families and 122 genera, and 63 families and 113 genera, respectively. Furthermore, significant differences were observed in the nutritional ecological niche among these species, primarily manifested in the differentiation of food types and selection of food at the genus level. Owing to differences in social behavior, body size, and habitat selection, these three species further expand their differentiation in resource selection, thereby making more efficient use of environmental resources. Our findings indicate these factors are the primary reasons for the stable coexistence of these species.},
}
@article {pmid39120762,
year = {2024},
author = {Morales-Serna, FN and Camacho-Zepeda, S},
title = {Morphology, DNA barcoding and seasonal occurrence of Ergasilus lizae Krøyer, 1863 (Copepoda: Ergasilidae) parasitizing mullets from northwestern Mexico.},
journal = {Systematic parasitology},
volume = {101},
number = {5},
pages = {54},
pmid = {39120762},
issn = {1573-5192},
support = {IN215722//Programa de Apoyo a Proyectos de Investigaci&#xf3;n e Innovaci&#xf3;n Tecnol&#xf3;gica (PAPIIT, UNAM)/ ; },
mesh = {Animals ; *Copepoda/genetics/anatomy &amp; histology/classification ; Mexico ; *DNA Barcoding, Taxonomic ; *Seasons ; *Species Specificity ; Smegmamorpha/parasitology ; Phylogeny ; Electron Transport Complex IV/genetics ; },
abstract = {Ergasilus lizae Krøyer, 1863 is a parasitic copepod known to infect mullets (Mugilidae) in different parts of the world. It was originally reported from the east coast of North America, but the original description lacks enough detail, making identification with this information difficult. In this study, we provide a redescription of E. lizae found on Mugil curema Valenciennes and M. cephalus Linnaeus, caught in two coastal lagoons of northwestern Mexico during two climatic seasons: warm/rainy and cold/dry. The prevalence of this parasite was higher in the warm season than in the cold season. To facilitate the species identification, new sequences of the barcoding gene (COI mtDNA) of E. lizae were generated and compared against unpublished sequences of E. lizae available in the Barcode of Life Database (BOLD). Our results suggest that the sequences of BOLD possibly belong to a species misidentified as E. lizae.},
}
@article {pmid39119217,
year = {2024},
author = {Murcia-Moreno, D and Gálvez, D},
title = {Preliminary checklist of spiders (Araneae) from Coiba National Park, Panama.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e117642},
pmid = {39119217},
issn = {1314-2828},
abstract = {BACKGROUND: Coiba National Park is an offshore region on the Pacific side of Panama, which hosts several endemic species of animals and plants. It was declared a UNESCO World Heritage Site in 2005. Despite the title awarded to the Park, knowledge about basic elements of its biodiversity are still lacking, which are of vital relevance for management and conservation policies. For instance, until now, no study had ever monitored the araneofauna diversity of the Park.<br><br>NEW INFORMATION: Here, we provide the first checklist of spider species in Coiba National Park, including the main island and several surrounding islands. We sampled during several field trips carried out from August 2021 to August 2023. We identified at least 152 species (98 genera and 30 families) and we report three new spiders species for Panama, namely Ctenusnigrolineatus Berland (1913), Chapodagitae Zhang &amp; Maddison (2012) and Sarindanigra Peckham &amp; Peckham (1892). We discuss the implications of our results and recommend future lines of work that include DNA barcoding, monitoring of population and community dynamics, plus linkage of climatic data from the newly-installed meteorological station on the Island.},
}
@article {pmid39118362,
year = {2024},
author = {Everts, T and Van Driessche, C and Neyrinck, S and Haegeman, A and Ruttink, T and Jacquemyn, H and Brys, R},
title = {Phenological mismatches mitigate the ecological impact of a biological invader on amphibian communities.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {34},
number = {6},
pages = {e3017},
doi = {10.1002/eap.3017},
pmid = {39118362},
issn = {1051-0761},
support = {1S01822N//Fonds Wetenschappelijk Onderzoek/ ; 1S23822N//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Animals ; *Introduced Species ; *Rana catesbeiana/physiology ; Belgium ; DNA, Environmental ; },
abstract = {Horizon scans have emerged as a valuable tool to anticipate the incoming invasive alien species (IAS) by judging species on their potential impacts. However, little research has been conducted on quantifying actual impacts and assessing causes of species-specific vulnerabilities to particular IAS due to persistent methodological challenges. The underlying interspecific mechanisms driving species-specific vulnerabilities therefore remain poorly understood, even though they can substantially improve the accuracy of risk assessments. Given that interspecific interactions underlying ecological impacts of IAS are often shaped by phenological synchrony, we tested the hypothesis that temporal mismatches in breeding phenology between native species and IAS can mitigate their ecological impacts. Focusing on the invasive American bullfrog (Lithobates catesbeianus), we combined an environmental DNA (eDNA) quantitative barcoding and metabarcoding survey in Belgium with a global meta-analysis, and integrated citizen-science data on breeding phenology. We examined whether the presence of native amphibian species was negatively related to the presence or abundance of invasive bullfrogs and whether this relationship was affected by their phenological mismatches. The field study revealed a significant negative effect of increasing bullfrog eDNA concentrations on native amphibian species richness and community structure. These observations were shaped by species-specific vulnerabilities to invasive bullfrogs, with late spring- and summer-breeding species being strongly affected, while winter-breeding species remained unaffected. This trend was confirmed by the global meta-analysis. A significant negative relationship was observed between phenological mismatch and the impact of bullfrogs. Specifically, native amphibian species with breeding phenology differing by 6 weeks or less from invasive bullfrogs were more likely to be absent in the presence of bullfrogs than species whose phenology differed by more than 6 weeks with that of bullfrogs. Taken together, we present a novel method based on the combination of aqueous eDNA quantitative barcoding and metabarcoding to quantify the ecological impacts of biological invaders at the community level. We show that phenological mismatches between native and invasive species can be a strong predictor of invasion impact regardless of ecological or methodological context. Therefore, we advocate for the integration of temporal alignment between native and IAS's phenologies into invasion impact frameworks.},
}
@article {pmid39117628,
year = {2024},
author = {Siegel, SV and Trimarsanto, H and Amato, R and Murie, K and Taylor, AR and Sutanto, E and Kleinecke, M and Whitton, G and Watson, JA and Imwong, M and Assefa, A and Rahim, AG and Nguyen, HC and Tran, TH and Green, JA and Koh, GCKW and White, NJ and Day, N and Kwiatkowski, DP and Rayner, JC and Price, RN and Auburn, S},
title = {Lineage-informative microhaplotypes for recurrence classification and spatio-temporal surveillance of Plasmodium vivax malaria parasites.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6757},
pmid = {39117628},
issn = {2041-1723},
support = {R01AI137154//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 200909/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; R01 AI137154/AI/NIAID NIH HHS/United States ; 206194/Z17/Z//Wellcome Trust (Wellcome)/ ; APP2001083//Department of Health | National Health and Medical Research Council (NHMRC)/ ; /WT_/Wellcome Trust/United Kingdom ; INV-043618//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; 204911/WT_/Wellcome Trust/United Kingdom ; OPP1054404//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; 206194/WT_/Wellcome Trust/United Kingdom ; ICRG GR071614MA//Wellcome Trust (Wellcome)/ ; },
mesh = {*Plasmodium vivax/genetics ; *Malaria, Vivax/parasitology/epidemiology ; Humans ; *Recurrence ; Haplotypes/genetics ; Polymorphism, Single Nucleotide ; Genome, Protozoan/genetics ; Genotype ; },
abstract = {Challenges in classifying recurrent Plasmodium vivax infections constrain surveillance of antimalarial efficacy and transmission. Recurrent infections may arise from activation of dormant liver stages (relapse), blood-stage treatment failure (recrudescence) or reinfection. Molecular inference of familial relatedness (identity-by-descent or IBD) can help resolve the probable origin of recurrences. As whole genome sequencing of P. vivax remains challenging, targeted genotyping methods are needed for scalability. We describe a P. vivax marker discovery framework to identify and select panels of microhaplotypes (multi-allelic markers within small, amplifiable segments of the genome) that can accurately capture IBD. We evaluate panels of 50-250 microhaplotypes discovered in a global set of 615 P. vivax genomes. A candidate global 100-microhaplotype panel exhibits high marker diversity in the Asia-Pacific, Latin America and horn of Africa (median HE = 0.70-0.81) and identifies 89% of the polyclonal infections detected with genome-wide datasets. Data simulations reveal lower error in estimating pairwise IBD using microhaplotypes relative to traditional biallelic SNP barcodes. The candidate global panel also exhibits high accuracy in predicting geographic origin and captures local infection outbreak and bottlenecking events. Our framework is open-source enabling customised microhaplotype discovery and selection, with potential for porting to other species or data resources.},
}
@article {pmid39114565,
year = {2024},
author = {van Achterberg, C and Shaw, MR and Fernandez-Triana, J and Quicke, DLJ},
title = {Resolution of the Aleiodesseriatus (Herrich-Schäffer, 1838)-aggregate in the western Palaearctic (Hymenoptera, Braconidae, Rogadinae), with description of a new species.},
journal = {ZooKeys},
volume = {1208},
number = {},
pages = {241-258},
pmid = {39114565},
issn = {1313-2989},
abstract = {Two European species are recognised and characterised within the traditional Aleiodesseriatus species concept, based initially on DNA barcoding but with supporting, although slight and sometimes unreliable, morphological differences. Aleiodespseudoseriatus sp. nov. is described and a neotype is designated for Rogasseriatus Herrich-Schäffer, 1838. Specimens from the Russian Far East were also DNA barcoded and were found to belong to a new species distinct from the two European taxa. The two European species were found to use different lithosiine hosts.},
}
@article {pmid39113382,
year = {2024},
author = {Lu, Y and Su, J and Cheng, S and Hu, Y and Xia, Q},
title = {Molecular identification and genetic diversity of biting midges (Diptera: Ceratopogonidae) in the tropical environment on Hainan Island, China.},
journal = {Journal of vector borne diseases},
volume = {},
number = {},
pages = {},
doi = {10.4103/JVBD.JVBD_100_23},
pmid = {39113382},
issn = {0972-9062},
abstract = {BACKGROUND OBJECTIVES: Biting midges are hematophagous arthropods responsible for zoonotic infectious diseases and have a wide distribution in temperate and tropical latitudes of the world.<br><br>METHODS: The genomic DNA of midge samples was extracted using the Chelex method and the ITS1gene was amplified by PCR to identify the midge species via BLAST. The sequence characteristics and the genetic diversity were analyzed using ClustalOmega, DnaSP, Arlequin, PopART, and TCS software tool. The validity of the ITS1 gene as a DNA barcode marker was evaluated using DAMBE. The phylogenetic relationship was established in the MEGA software. The ABGD web determined the species boundary and the SDT software visualized the pairwise sequence comparisons.<br><br>RESULTS: A total of 39 midge samples possessed the range from 364 to 429 bp of the ITS1 sequences. The midge samples were identified as Culicoides imicola, Culicoides oxystoma, Culicoides peregrinus, Culicoides jacobsoni, Forcipomyia peregrinator, and Culicoides fulvus, respectively. The ITS1 sequences had 288 conserved sites (60.25%), 167 variable sites (34.94%), 141 parsimony-informative sites (29.50%), and 26 singleton sites (5.44%), with a considerable sequence variation with a high haplotype diversity. Populations in Lingao, Haikou, Tunchang were relatively independent, with a low level of gene flow. A separate population of Forcipomyia genus in Danzhou was observed.<br><br>INTERPRETATION CONCLUSION: The biting midges in Hainan, a tropical island, had abundant genetic diversity. Timely surveillance is a crucial control measure for the spread of midge-borne diseases.},
}
@article {pmid39113366,
year = {2024},
author = {Madpathi, S and Daravath, SS and Bannoth, RN},
title = {Molecular characterization of Armigeres Subalbatus from Hyderabad region of Telangana state, India.},
journal = {Journal of vector borne diseases},
volume = {},
number = {},
pages = {},
doi = {10.4103/JVBD.JVBD_13_24},
pmid = {39113366},
issn = {0972-9062},
abstract = {BACKGROUND OBJECTIVES: The mosquito Armigeres subalbatus (Coquillett, 1898) is a significant vector for Japanese encephalitis infection, and breeds in high organic polluted water. Understanding mosquito diversity and there abundance in relation to mosquito-borne diseases is an important component for public health managers. Though the conventional methods for systematic position of mosquito species by using morphological characteristics is a classical method, but it requires perfect expertise and well preserved specimen. Conversely, the molecular analysis of mitochondrial cytochrome C oxidase subunit I (COI) serves as a gene-centric DNA barcoding approach and offers a promising alternative method for mosquito species identification.<br><br>METHODS: The study at hand delves into the morphological characteristics of Armigeres subalbatus were compared with COI- gene to ensure a more dependable verification for identification of mosquito species found in Hyderabad region of Telangana.<br><br>RESULTS: The 489 base pair amplicons were acquired and deposited into the NCBI Gene Bank nucleotide database under the accession number MG686500. The maximum likelihood tree infers that, the Hyderabad species was diverged from USA and Japan species but had ancestral relationship with Tamil Nadu, Karnataka, Maharastra, Kerala and Goa species.<br><br>INTERPRETATION CONCLUSION: Mitochondrial gene (COI) based DNA barcoding is the most reliable and potential alternative technique to identify the mosquito species.},
}
@article {pmid39112930,
year = {2024},
author = {Liu, X and Luo, J and Chen, H and Li, T and Qu, T and Tang, M and Fu, Z},
title = {Comparative analysis of complete chloroplast genomes of Synotis species (Asteraceae, Senecioneae) for identification and phylogenetic analysis.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {769},
pmid = {39112930},
issn = {1471-2164},
support = {31500166//National Natural Science Foundation of China/ ; 32000158//National Natural Science Foundation of China/ ; 2021XJKK0702//National Science &amp; Technology Fundamental Resources Investigation Program of China/ ; 2020CXZYHJZX03//Foundation of Sustainable Development Research Center of Resources and Environment of Western Sichuan, Sichuan Normal University/ ; },
mesh = {*Genome, Chloroplast ; *Phylogeny ; *Asteraceae/genetics/classification ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: The Synotis (C. B. Clarke) C. Jeffrey &amp; Y. L. Chen is an ecologically important genus of the tribe Senecioneae, family Asteraceae. Because most species of the genus bear similar morphology, traditional morphological identification methods are very difficult to discriminate them. Therefore, it is essential to develop a reliable and effective identification method for Synotis species. In this study, the complete chloroplast (cp.) genomes of four Synotis species, S. cavaleriei (H.Lév.) C. Jeffrey &amp; Y.L. Chen, S. duclouxii (Dunn) C. Jeffrey &amp; Y.L. Chen, S. nagensium (C.B. Clarke) C. Jeffrey &amp; Y.L. Chen and S. erythropappa (Bureau &amp; Franch.) C. Jeffrey &amp; Y. L. Chen had been sequenced using next-generation sequencing technology and reported here.<br><br>RESULTS: These four cp. genomes exhibited a typical quadripartite structure and contained the large single-copy regions (LSC, 83,288 to 83,399&#xa0;bp), the small single-copy regions (SSC, 18,262 to 18,287&#xa0;bp), and the inverted repeat regions (IR, 24,837 to 24,842&#xa0;bp). Each of the four cp. genomes encoded 134 genes, including 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes (ycf1 and rps19). The highly variable regions (trnC-GCA-petN, ccsA-psaC, trnE-UUC-rpoB, ycf1, ccsA and petN) may be used as potential molecular barcodes. The complete cp. genomes sequence of Synotis could be used as the potentially effective super-barcode to accurately identify Synotis species. Phylogenetic analysis demonstrated that the four Synotis species were clustered into a monophyletic group, and they were closed to the Senecio, Crassocephalum and Dendrosenecio in tribe Senecioneae.<br><br>CONCLUSIONS: This study will be useful for further species identification, evolution, genetic diversity and phylogenetic studies within this genus Synotis and the tribe Senecioneae.},
}
@article {pmid39109773,
year = {2024},
author = {Dos Reis Júnior, MR and Caixeta, HC and Oliveira, C and Melo, MRS},
title = {New report of the rare Sciadonus alphacrucis Melo et al., 2022 (Teleostei, Ophidiiformes, Bythitidae), DNA barcoding, and range extension in the western South Atlantic.},
journal = {Journal of fish biology},
volume = {105},
number = {4},
pages = {1357-1361},
doi = {10.1111/jfb.15896},
pmid = {39109773},
issn = {1095-8649},
support = {CNPq 403380/2022-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 306054/2006-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 441128/2020-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CAPES 88887.644858/202100//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; FAPESP 2017/12909-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2020/134336//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2021/056195//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
mesh = {Animals ; Brazil ; *DNA Barcoding, Taxonomic ; *Electron Transport Complex IV/genetics ; Atlantic Ocean ; Phylogeny ; Animal Distribution ; Female ; Male ; Fishes/genetics/classification ; },
abstract = {Sciadonus alphacrucis Melo, Gomes, Møller &amp; Nielsen, 2022 is a rare deep-sea species, previously known from only two specimens collected off São Paulo State, southeastern Brazil, in the western South Atlantic. Herein, we report a new specimen of S. alphacrucis collected on the continental slope off Santa Catarina State, southern Brazil, thereby extending its known distribution by 420 km. Additionally, we provide the new meristic and morphometric data, the molecular identification using sequences of the cytochrome c oxidase subunit I (COI), an updated distribution map, and a discussion of troglomorphic traits.},
}
@article {pmid39109414,
year = {2024},
author = {You, G and Hou, F and Niu, L and Wang, S and Wang, L and Sun, L and Ren, X},
title = {Identification of Euphorbiae pekinensis Radix and its counterfeit and adulterated products based on DNA barcode, UPLC-Q-TOF-MS, UPLC fingerprint, and chemometrics.},
journal = {Biomedical chromatography : BMC},
volume = {38},
number = {10},
pages = {e5978},
doi = {10.1002/bmc.5978},
pmid = {39109414},
issn = {1099-0801},
support = {2021KJ124//Scientific Research Project of Tianjin Educational Committee/ ; },
mesh = {*Drugs, Chinese Herbal/chemistry/analysis ; Chromatography, High Pressure Liquid/methods ; *Drug Contamination ; *Counterfeit Drugs/analysis/chemistry ; *Mass Spectrometry/methods ; *DNA Barcoding, Taxonomic/methods ; Chemometrics/methods ; Tannins/analysis/chemistry ; },
abstract = {Euphorbiae pekinensis Radix (EPR) is a traditional Chinese herb commonly used to treat edema, pleural effusion, and ascites. However, counterfeit and adulterated products often appear in the market because of the homonym phenomenon, similar appearance, and artificial forgery of Chinese herbs. This study comprehensively evaluated the quality of EPR using multiple methods. The DNA barcode technique was used to identify EPR, while the UPLC-Q-TOF-MS technique was utilized to analyze the chemical composition of EPR. A total of 15 tannin and phenolic acid components were identified. Furthermore, UPLC fingerprints of EPR and its common counterfeit products were established, and unsupervised and supervised pattern recognition models were developed using these fingerprints. The backpropagation artificial neural network and counter-propagation artificial neural network models accurately identified counterfeit and adulterated products, with a counterfeit ratio of more than 25%. Finally, the contents of the chemical markers 3,3'-di-O-methyl ellagic acid-4'-O-β-D-glucopyranoside, ellagic acid, 3,3'-di-O-methyl ellagic acid-4'-O-β-d-xylopyranoside, and 3,3'-di-O-methyl ellagic acid were determined to range from 0.05% to 0.11%, 1.95% to 8.52%, 0.27% to 0.86%, and 0.10% to 0.42%, respectively. This proposed strategy offers a general procedure for identifying Chinese herbs and distinguishing between counterfeit and adulterated products.},
}
@article {pmid39109336,
year = {2024},
author = {Chen, X and Feng, Y and Qu, T and Chen, H and Liu, X and Pang, L and Chen, M and Fu, Z},
title = {Complete chloroplast genomes of two Ainsliaea species and the phylogenetic analysis in the tribe Pertyeae.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1408114},
pmid = {39109336},
issn = {1664-8021},
abstract = {The genus Ainsliaea DC. is one of the major groups within the tribe Pertyeae (Asteraceae). It comprises several important Chinese medicinal species. However, the phylogenetic position has undergone a long process of exploration. The complete chloroplast (cp) genome sequences data has not been employed in species identification and phylogeny of Ainsliaea. In this study, the complete cp genomes of two Ainsliaea species (A. gracilis and A. henryi) were reported, followed by structural, comparative, and phylogenetic analyses within the tribe Peryteae. Both cp genomes displayed a typical quadripartite circular structure, with the LSC and SSC regions separated by the IR regions. The genomes were 152,959 (A. gracilis) and 152,805 (A. henryi) base pairs (bp) long, with a GC content of 37.6%. They were highly conserved, containing 134 genes, including 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes (rps19 and ycf1). Moreover, thirteen highly polymorphic regions (e.g., trnK-UUU, trnG-UCC, trnT-GGU, accD-psaI, and rpl22-rps19) were identified, indicating their potential as DNA barcodes. The phylogenetic analysis confirmed the placement of Ainsliaea in the tribe Pertyeae, revealing close relationships with the genera Myripnois and Pertya. In comparison with Ainsliaea, Myripnois was more closely related to Pertya. This study lays a theoretical foundation for future research on species identification, population genetics, resource conservation, and sustainable utilization within Ainsliaea and Pertyeae.},
}
@article {pmid39108338,
year = {2024},
author = {Namayandeh, A and Guerra, S and Islam, N and James, T and Hudson, PL and Ghaderi, E and Yusuf, T and Vasquez, AA and Ram, JL},
title = {New species and a fascinating diversity of Chironomidae (Diptera, Insecta) in and around an overlooked urban vernal pool.},
journal = {ZooKeys},
volume = {1208},
number = {},
pages = {133-163},
pmid = {39108338},
issn = {1313-2989},
abstract = {In this study, the biodiversity of Chironomidae was investigated in Palmer Park Pond A, an urban vernal pond in Detroit, Michigan, USA. This study is developed as part of our ongoing Public Environmental Outreach Program at the Detroit Exploration and Nature Center in Palmer Park. Twenty-one Chironomidae species were discovered in and on the adjacent riparian vegetation of this pond using molecular and morphological methods. Three species Bryophaenocladiuspalmerparcum Namayandeh &amp; Hudson sp. nov., Limnophyesstagnum Namayandeh, Guerra &amp; Ram sp. nov., and Rheocricotopus (s. s.) angustus Namayandeh &amp; Hudson sp. nov. are new to science. Bryophaenocladiuspalmerparcum sp. nov. and L.stagnum sp. nov. are unusual Orthoclads, with B.palmerparcum sp. nov. possessing a setose, short, and wide anal point and L.stagnum sp. nov. lacking lanceolate setae on both sexes. Based on the shape of superior volsella, R.angustus sp. nov., belongs to the effusus group, which was also confirmed by DNA barcoding molecular analysis. In this study, a new faunistic record was also found for the Nearctic as well as four new faunistic records for the state of Michigan. Ephemeral aquatic habitats such as vernal pools are often overlooked or destroyed by urbanization activities, controlling vector species, creating groomed fields, and/or residential development. Therefore, finding these new species demonstrates the biodiversity value of vernal ponds as important habitats, further motivating us to preserve them.},
}
@article {pmid39105821,
year = {2024},
author = {Kobayashi, G and Abe, H},
title = {Cost-efficient PCR based DNA barcoding of marine invertebrate specimens with NovaSeq amplicon sequencing.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {887},
pmid = {39105821},
issn = {1573-4978},
support = {JP22K15174//JSPS KAKENHI/ ; JPMEERF20204R01//Environment Research and Technology Development Fund/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Aquatic Organisms/genetics ; *Phylogeny ; *Invertebrates/genetics ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods ; RNA, Ribosomal, 16S/genetics ; Electron Transport Complex IV/genetics ; High-Throughput Nucleotide Sequencing/methods ; Biodiversity ; Cost-Benefit Analysis ; },
abstract = {BACKGROUND: The marine environment harbors high biodiversity; however, it is poorly understood. Nucleotide sequence data of all marine organisms should be accumulated before natural and/or anthropogenic environmental changes jeopardize the marine environment. In this study, we report a cost-effective and easy DNA barcoding method. This method can be readily adopted without using library preparation kits. It includes multiplex PCR of short targets, indexing PCR, and outsourcing to a sequencing service using the NovaSeq system.<br><br>METHODS AND RESULTS: We targeted four mitochondrial genes [cytochrome c oxidase subunit I (COI), COIII, 16S rRNA (16S), and 12S rRNA (12S)] and three nuclear genes [18S rRNA (18S), 28S rRNA (28S), internal transcribed spacer 2 (ITS2)] in 95 marine invertebrate specimens, which were primarily annelids. The primers, including adapters and indices for NovaSeq sequencing, were newly designed. Two PCR runs were conducted. The 1st PCR amplified specific loci with universal primers and the 2nd added sequencing adapters and indices to the 1st PCR products. The gene sequences obtained from the FASTQ files were subjected to BLAST search and phylogenetic analyses. One run using 95 specimens yielded sequences averaging 2816&#xa0;bp per specimen for a total length of six loci. Nuclear genes were more successfully assembled compared with mitochondrial genes. A weak but significantly negative correlation was observed between the average length of each locus and success rate of the assembly. Some of the sequences were almost identical to the sequences obtained from specimens collected far from Japan, indicating the presence of potentially invasive species identified for the first time.<br><br>CONCLUSIONS: We obtained gene sequences efficiently using next-generation sequencing rather than Sanger sequencing. Although this method requires further optimization to increase the success rate for some loci, it is used as a first step to select specimens for further analyses by determining the specific loci of the targets.},
}
@article {pmid39099456,
year = {2024},
author = {Lee, H and Langseth, CM and Salas, SM and Sariyar, S and Metousis, A and Rueda-Alaña, E and Bekiari, C and Lundberg, E and Garcı A-Moreno, F and Grillo, M and Nilsson, M},
title = {Open-source, high-throughput targeted in situ transcriptomics for developmental and tissue biology.},
journal = {Development (Cambridge, England)},
volume = {151},
number = {16},
pages = {},
pmid = {39099456},
issn = {1477-9129},
support = {//Chan Zuckerberg Initiative/ ; //Familjen Erling-Perssons Stiftelse/ ; //Ikerbasque, Basque Foundation for Science/ ; //Ministerio de Ciencia e Innovacion/ ; //Eusko Jaurlaritza/ ; //EASI genomics TNA/ ; //Silicon Valley Community Foundation/ ; //Erling-Perssons Stiftelse/ ; KAW 2018.0172//Knut och Alice Wallenbergs Stiftelse/ ; 2019-01238//Vetenskapsr&#xe5;det/ ; CAN 2021/1726//Cancerfonden/ ; MICNN PGC2018-096173-A-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PIBA 2020\_1\_0057//Eusko Jaurlaritza/ ; PID14596//European Advanced infraStructure for Innovative Genomics/ ; //Stockholms Universitet/ ; },
mesh = {Animals ; *Gene Expression Profiling/methods ; RNA, Messenger/genetics/metabolism ; Transcriptome/genetics ; Humans ; In Situ Hybridization/methods ; Mice ; Developmental Biology/methods ; },
abstract = {Multiplexed spatial profiling of mRNAs has recently gained traction as a tool to explore the cellular diversity and the architecture of tissues. We propose a sensitive, open-source, simple and flexible method for the generation of in situ expression maps of hundreds of genes. We use direct ligation of padlock probes on mRNAs, coupled with rolling circle amplification and hybridization-based in situ combinatorial barcoding, to achieve high detection efficiency, high-throughput and large multiplexing. We validate the method across a number of species and show its use in combination with orthogonal methods such as antibody staining, highlighting its potential value for developmental and tissue biology studies. Finally, we provide an end-to-end computational workflow that covers the steps of probe design, image processing, data extraction, cell segmentation, clustering and annotation of cell types. By enabling easier access to high-throughput spatially resolved transcriptomics, we hope to encourage a diversity of applications and the exploration of a wide range of biological questions.},
}
@article {pmid39095717,
year = {2024},
author = {Nazari, V and Lukhtanov, V and Naderi, A and Bruna, CD and Zahiri, R and Cesaroni, D and Sbordoni, V and Todisco, V},
title = {COI Barcodes combined with multilocus data for representative Aporia taxa shed light on speciation in the high altitude Irano-Turanian mountain plateaus (Lepidoptera: Pieridae).},
journal = {BMC ecology and evolution},
volume = {24},
number = {1},
pages = {105},
pmid = {39095717},
issn = {2730-7182},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Iran ; *Phylogeny ; *Electron Transport Complex IV/genetics ; *Butterflies/genetics/classification ; Genetic Speciation ; Altitude ; Female ; Male ; },
abstract = {Even though the high plateaus of Qinghai-Tibet and Iran share many faunal elements, the historical biogeography of the species present in this area are not very well understood. We present a complete COI barcode library for Aporia Hübner and a first comprehensive phylogeny for the genus including all known species and majority of subspecies using ten available genes (COI-COII, ND1, ND5, Cytb, EF-1a, Wg, 16S, 28S-D2/D3 and 28S-D8). We then focus on A. leucodice (Eversmann, 1843) and related taxa in order to resolve some long-standing taxonomic issues in this species-group. Based on DNA sequence data as well as morphology, we raise Aporia illumina (Grum-Grshimailo 1890) stat. nov. (= pseudoillumina Tshikolovets 2021 syn. nov.) as a distinct species and designate a lectotype; synonymize Aporia leucodice leucodice Eversmann, 1843 (= A. l. morosevitshae Sheljuzhko, 1908 syn. nov.); and describe a new species, Aporia ahura sp. nov., from the Central Alborz Mountains in northern Iran.},
}
@article {pmid39095612,
year = {2024},
author = {Underwood, O and Fritzwanker, S and Glenn, J and Blum, NK and Batista-Gondin, A and Drube, J and Hoffmann, C and Briddon, SJ and Schulz, S and Canals, M},
title = {Key phosphorylation sites for robust β-arrestin2 binding at the MOR revisited.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {933},
pmid = {39095612},
issn = {2399-3642},
support = {AMSPR/1013/AMS_/Academy of Medical Sciences/United Kingdom ; BB/T013966/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; MRC IMPACT//RCUK | Medical Research Council (MRC)/ ; },
mesh = {Phosphorylation ; *beta-Arrestin 2/metabolism/genetics ; Humans ; *Receptors, Opioid, mu/metabolism/genetics ; HEK293 Cells ; Protein Binding ; Animals ; G-Protein-Coupled Receptor Kinases/metabolism/genetics ; },
abstract = {Desensitisation of the mu-opioid receptor (MOR) is proposed to underlie the initiation of opioid analgesic tolerance and previous work has shown that agonist-induced phosphorylation of the MOR C-tail contributes to this desensitisation. Moreover, phosphorylation is important for β-arrestin recruitment to the receptor, and ligands of different efficacies induce distinct phosphorylation barcodes. The C-tail [370]TREHPSTANT[379] motif harbours Ser/Thr residues important for these regulatory functions. [375]Ser is the primary phosphorylation site of a ligand-dependent, hierarchical, and sequential process, whereby flanking [370]Thr, [376]Thr and [379]Thr get subsequently and rapidly phosphorylated. Here we used GRK KO cells, phosphosite specific antibodies and site-directed mutagenesis to evaluate the contribution of the different GRK subfamilies to ligand-induced phosphorylation barcodes and β-arrestin2 recruitment. We show that both GRK2/3 and GRK5/6 subfamilies promote phosphorylation of [370]Thr and [375]Ser. Importantly, only GRK2/3 induce phosphorylation of [376]Thr and [379]Thr, and we identify these residues as key sites to promote robust β-arrestin recruitment to the MOR. These data provide insight into the mechanisms of MOR regulation and suggest that the cellular complement of GRK subfamilies plays an important role in determining the tissue responses of opioid agonists.},
}
@article {pmid39091743,
year = {2024},
author = {Bernadskaya, YY and Kuan, A and Tjärnberg, A and Brandenburg, J and Zheng, P and Wiechecki, K and Kaplan, N and Failla, M and Bikou, M and Madilian, O and Wang, W and Christiaen, L},
title = {Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39091743},
issn = {2692-8205},
support = {R01 HD096770/HD/NICHD NIH HHS/United States ; R01 HL108643/HL/NHLBI NIH HHS/United States ; },
abstract = {During development, stem and progenitor cells divide and transition through germ layer- and lineage-specific multipotent states to generate the diverse cell types that compose an animal. Defined changes in biomolecular composition underlie the progressive loss of potency and acquisition of lineage-specific characteristics. For example, multipotent cardiopharyngeal progenitors display multilineage transcriptional priming, whereby both the cardiac and pharyngeal muscle programs are partially active and coexist in the same progenitor cells, while their daughter cells engage in a cardiac or pharyngeal muscle differentiation path only after cell division. Here, using the tunicate Ciona, we studied the acquisition of multilineage competence and the coupling between fate decisions and cell cycle progression. We showed that multipotent cardiopharyngeal progenitors acquire the competence to produce distinct Tbx1/10(+) and (-) daughter cells shortly before mitosis, which is necessary for Tbx1/10 activation. By combining transgene-based sample barcoding with single cell RNA-seq (scRNA-seq), we uncovered transcriptome-wide dynamics in migrating cardiopharyngeal progenitors as cells progress through G1, S and G2 phases. We termed this process "transcriptome maturation", and identified candidate "mature genes", including the Rho GAP-coding gene Depdc1, which peak in late G2. Functional assays indicated that transcriptome maturation fosters cardiopharyngeal competence, in part through multilineage priming and proper oriented and asymmetric division that influences subsequent fate decisions, illustrating the concept of "behavioral competence". Both classic feedforward circuits and coupling with cell cycle progression drive transcriptome maturation, uncovering distinct levels of coupling between cell cycle progression and fateful molecular transitions. We propose that coupling competence and fate decision with the G2 and G1 phases, respectively, ensures the timely deployment of lineage-specific programs.},
}
@article {pmid39091496,
year = {2024},
author = {Hulen, TM and Friese, C and Kristensen, NP and Granhøj, JS and Borch, TH and Peeters, MJW and Donia, M and Andersen, MH and Hadrup, SR and Svane, IM and Met, &#xd6;},
title = {Corrigendum: Ex vivo modulation of intact tumor fragments with anti-PD-1 and anti-CTLA-4 influences the expansion and specificity of tumor-infiltrating lymphocytes.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1462081},
doi = {10.3389/fimmu.2024.1462081},
pmid = {39091496},
issn = {1664-3224},
abstract = {[This corrects the article DOI: 10.3389/fimmu.2023.1180997.].},
}
@article {pmid39091449,
year = {2024},
author = {Hübner, J and Chemyreva, V and Macek, J and Kolyada, V},
title = {A review of the genus Zygota (Hymenoptera, Diapriidae) in Germany with taxonomic notes on this genus and its distinction from Pantoclis.},
journal = {ZooKeys},
volume = {1207},
number = {},
pages = {325-353},
pmid = {39091449},
issn = {1313-2989},
abstract = {This study provides a comprehensive overview of the genus Zygota Förster combining DNA barcoding and current morphology. Nineteen species of Zygota were found throughout Germany, including the newly described species Zygotawalli sp. nov. First species records for Germany are: Zygotabalteata Macek, 1997; Z.comitans Macek, 1997; Z.spinosipes (Kieffer, 1908); Z.sordida Macek, 1997; Z.angularis Macek, 1997 and Z.vigil Nixon, 1957. We also clarify diagnoses for the two related genera, Pantoclis Förster and Zygota to designate the boundaries of the Zygota genus and propose new synonymies: Zygotacaligula Buhl, 1997 is a junior synonym of Z.congener (Zetterstedt, 1840); Z.reticulata Kozlov, 1978 is a junior synonym of Z.ruficornis (Curtis, 1831). Thirteen species of Zygota sensu Nixon (1957) are transferred to the genus Pantoclis with the following new combinations proposed: Zygotabrevinervis (Kieffer, 1908) (= Pantoclisbrevinervis (Kieffer, 1909), comb. nov.); Z.brevipennis (Kieffer, 1908) (= P.brevipennis (Kieffer, 1908), comb. nov.); Z.caecutiens (Kieffer, 1908) (= P.caecutiens (Kieffer, 1908), comb. nov.); Z.cursor (Kieffer, 1908) (= P.cursor (Kieffer, 1908), comb. nov.); Z.fossulata (Thomson, 1858) (=P.fossulata (Thomson, 1858), comb. nov.); Z.fuscata (Thomson, 1858) (= P.fuscata (Thomson, 1858), comb. nov.); Z.hemiptera (Thomson, 1858) (= P.hemiptera (Thomson, 1858), comb. nov.); Z.microtoma (Kieffer, 1909) (= P.microtoma (Kieffer, 1909), comb. nov.); Z.soluta (Kieffer, 1907) (= P.soluta (Kieffer, 1907), comb. nov.); Z.striata (Kieffer, 1909) (= P.striata (Kieffer, 1909), comb. nov.); Z.subaptera (Thomson, 1858) (= P.subaptera (Thomson, 1858), comb. nov.); Z.sulciventris (Kieffer, 1909) (= P.sulciventris (Kieffer, 1909), comb. nov.), and Z.unicolor (Kieffer, 1908) (= P.unicolor (Kieffer, 1908), comb. nov.).},
}
@article {pmid39090851,
year = {2024},
author = {Di Nunzio, M and Barrot-Feixat, C and Gangitano, D},
title = {Characterization and evaluation of nine Cannabis sativa chloroplast SNP markers for crop type determination and biogeographical origin on European samples.},
journal = {Forensic science international. Genetics},
volume = {68},
number = {},
pages = {102971},
doi = {10.1016/j.fsigen.2023.102971},
pmid = {39090851},
issn = {1878-0326},
mesh = {*Cannabis/genetics ; Genetic Markers ; *Polymorphism, Single Nucleotide ; *DNA, Chloroplast/genetics ; Mexico ; Polymerase Chain Reaction ; Europe ; Italy ; Chile ; Spain ; },
abstract = {Cannabis sativa can be classified in two main types, according to psychotropic cannabinoid ∆9-tetrahydrocannabinol (∆9-THC) content: the drug-type and the fiber-type. According to the European Monitoring Center for Drugs and Drug Addiction, most of the European Union countries consider the possession of cannabis, for personal use, a minor offense with possibility of incarceration. Despite of the model of legal supply (i.e., Spanish cannabis clubs, Netherlands coffee shops) or medical use (i.e., Italy), cannabis remains the most used and trafficked illicit plant in the European Union. Differentiating cannabis crops or tracing the biogeographical origin is crucial for law enforcement purposes. Chloroplast DNA (cpDNA) markers may assist to determine biogeographic origin and to differentiate hemp from marijuana. This research aims: to identify and to evaluate nine C. sativa cpDNA polymorphic SNP sites to differentiate crop type and to provide information about its biogeographical origin. Five SNaPshot™ assays for nine chloroplast markers were developed and conducted in marijuana samples seized in Chile, the USA-Mexico border and Spain, and hemp samples grown in Spain and in Italy. The SNapShot™ assays were tested on 122 cannabis samples, which included 16 blind samples, and were able to differentiate marijuana crop type from hemp crop type in all samples. Using phylogenetic analysis, genetic differences were observed between marijuana and hemp samples. Moreover, principal component analysis (PCA) supported the relationship among hemp samples, as well as for USA-Mexico border, Spanish, and Chilean marijuana samples. Genetic differences between groups based on the biogeographical origin and their crop type were observed. Increasing the number of genetic markers, including the most recently studied ones, and expanding the sample database will provide more accurate information about crop differentiation and biogeographical origin.},
}
@article {pmid39086104,
year = {2024},
author = {Macher, JN and Martínez, A and Çakir, S and Cholley, PE and Christoforou, E and Curini Galletti, M and van Galen, L and García-Cobo, M and Jondelius, U and de Jong, D and Leasi, F and Lemke, M and Rubio Lopez, I and Sánchez, N and Sørensen, MV and Todaro, MA and Renema, W and Fontaneto, D},
title = {Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna.},
journal = {Molecular ecology resources},
volume = {24},
number = {7},
pages = {e13997},
doi = {10.1111/1755-0998.13997},
pmid = {39086104},
issn = {1755-0998},
support = {T0206/37197/2021/kg//Stemmler Foundation/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Electron Transport Complex IV/genetics ; Netherlands ; Biodiversity ; North Sea ; Invertebrates/genetics/classification ; Bathing Beaches ; Ecosystem ; Metagenomics/methods ; },
abstract = {Molecular techniques like metabarcoding, while promising for exploring diversity of communities, are often impeded by the lack of reference DNA sequences available for taxonomic annotation. Our study explores the benefits of combining targeted DNA barcoding and morphological taxonomy to improve metabarcoding efficiency, using beach meiofauna as a case study. Beaches are globally important ecosystems and are inhabited by meiofauna, microscopic animals living in the interstitial space between the sand grains, which play a key role in coastal biodiversity and ecosystem dynamics. However, research on meiofauna faces challenges due to limited taxonomic expertise and sparse sampling. We generated 775 new cytochrome c oxidase I DNA barcodes from meiofauna specimens collected along the Netherlands' west coast and combined them with the NCBI GenBank database. We analysed alpha and beta diversity in 561 metabarcoding samples from 24 North Sea beaches, a region extensively studied for meiofauna, using both the enriched reference database and the NCBI database without the additional reference barcodes. Our results show a 2.5-fold increase in sequence annotation and a doubling of species-level Operational Taxonomic Units (OTUs) identification when annotating the metabarcoding data with the enhanced database. Additionally, our analyses revealed a bell-shaped curve of OTU richness across the intertidal zone, aligning more closely with morphological analysis patterns, and more defined community dissimilarity patterns between supralittoral and intertidal sites. Our research highlights the importance of expanding molecular reference databases and combining morphological taxonomy with molecular techniques for biodiversity assessments, ultimately improving our understanding of coastal ecosystems.},
}
@article {pmid39080687,
year = {2024},
author = {Modimo, MY and Bernt, MJ and Monsembula Iyaba, RJC and Mbimbi, JJMM and Liyandja, TLD},
title = {Parauchenoglanis stiassnyae (Siluriformes: Auchenoglanididae): A new species of giraffe catfish from Mfimi-Lukenie basin, central Africa, Democratic Republic of Congo.},
journal = {Journal of fish biology},
volume = {105},
number = {4},
pages = {1227-1239},
doi = {10.1111/jfb.15885},
pmid = {39080687},
issn = {1095-8649},
support = {1655227//National Science Foundation Graduate Research Fellowship Program/ ; //Axelrod Research curatorship (MJLS)/ ; },
mesh = {Animals ; *Catfishes/classification ; Democratic Republic of the Congo ; *Rivers ; Male ; Female ; Spine/anatomy &amp; histology ; },
abstract = {A new, distinctively short-bodied giraffe catfish of Parauchenoglanis is described from the Ndzaa River, a small left-bank tributary of the Mfimi-Lukenie basin in the Central basin of the Congo River in the Democratic Republic of the Congo. The new species can be distinguished from all congeners by having 29 or fewer (vs. 33 or more) total vertebrae. It can further be distinguished from all congeners, except Parauchenoglanis zebratus Sithole et al., 2023 and Parauchenoglanis ngamensis (Boulenger 1911), by having 13 or 14 (vs. 16 or more) pre-anal vertebrae. The species is endemic to the Mfimi River basin, where it has been collected mainly in blackwater tributaries.},
}
@article {pmid39080149,
year = {2024},
author = {Barman, M and Bhushan, S and Phukan, B and Kumar, AP and Jaiswar, AK and Talukdar, A and Kalita, R and S, S},
title = {Molecular identification and phylogenetic relationship of fishes belonging to the Family Danionidae from Brahmaputra Basin, Assam, Northeast India.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {875},
pmid = {39080149},
issn = {1573-4978},
support = {FISH/30/2017-FISHERY/27(eCFNo.43140)//SCoPIF, Government of Assam/ ; FISH/30/2017-FISHERY/27(eCFNo.43140)//SCoPIF, Government of Assam/ ; FISH/30/2017-FISHERY/27(eCFNo.43140)//SCoPIF, Government of Assam/ ; FISH/30/2017-FISHERY/27(eCFNo.43140)//SCoPIF, Government of Assam/ ; FISH/30/2017-FISHERY/27(eCFNo.43140)//SCoPIF, Government of Assam/ ; FISH/30/2017-FISHERY/27(eCFNo.43140)//SCoPIF, Government of Assam/ ; FISH/30/2017-FISHERY/27(eCFNo.43140)//SCoPIF, Government of Assam/ ; FISH/30/2017-FISHERY/27(eCFNo.43140)//SCoPIF, Government of Assam/ ; },
mesh = {Animals ; *Phylogeny ; India ; *Electron Transport Complex IV/genetics ; *DNA Barcoding, Taxonomic/methods ; Fishes/genetics/classification ; DNA, Mitochondrial/genetics ; Biodiversity ; },
abstract = {BACKGROUD: The Northeast India, being part of two global biodiversity hotspot namely the Indo-Burma and Eastern Himalayan Hotspots supports a wide variety of rich aquatic biodiversity including fishes. The family Danionidae is a widely diverse group inhabiting the upper colder stretches of river although few are abundant in the lower stretches. The persisting similarity in the morphological appearance and body colouration within the members of this family seeks an integrated method to identify the species correctly.<br><br>METHODS AND RESULTS: In the present study, the mt-DNA barcode was generated for correct identification and confirmation of the species. A total of nine mitochondrial cytochrome c oxidase subunit I gene sequences were generated for each species under the study. The pairwise distance values ranged from 0.09 to 9.11% within species and 9.06-32.71% between species. A neighbour-joining tree was constructed based on the Kimura 2 parameter model. Two major groups were observed where Danioninae formed a sister group to the Chedrinae and Rasborinae.<br><br>CONCLUSION: The present study is a preliminary work to document and identify the species under the family Danionidae from Brahmaputra basin, Assam, using molecular tools and establish the phylogenetic relationship.},
}
@article {pmid39076800,
year = {2024},
author = {Yoshimura, H and Hayakawa, T and Kikuchi, DM and Zhumabai Uulu, K and Qi, H and Sugimoto, T and Sharma, K and Kinoshita, K},
title = {Metabarcoding analysis provides insight into the link between prey and plant intake in a large alpine cat carnivore, the snow leopard.},
journal = {Royal Society open science},
volume = {11},
number = {5},
pages = {240132},
pmid = {39076800},
issn = {2054-5703},
abstract = {Species of the family Felidae are thought to be obligate carnivores. However, detection of plants in their faeces raises questions about the role of plants in their diet. This is particularly true for the snow leopard (Panthera uncia). Our study aimed to comprehensively identify the prey and plants consumed by snow leopards. We applied DNA metabarcoding methods on 90 faecal samples of snow leopards collected in Kyrgyzstan, employing one vertebrate and four plant markers. We found that argali (Ovis ammon) was detected only from male snow leopards. Myricaraia sp. was the most consumed among 77 plant operational taxonomic units found in snow leopard samples. It frequently appeared in samples lacking any prey animal DNA, indicating that snow leopards might have consumed this plant especially when their digestive tracts were empty. We also observed differences in the patterns of plant consumption between male and female snow leopards. Our comprehensive overview of prey and plants detected in the faeces of snow leopards and other sympatric mammals will help in formulating hypotheses and guiding future research to understand the adaptive significance of plant-eating behaviour in felids. This knowledge supports the enhancement of their captive environments and the conservation planning of their natural habitats.},
}
@article {pmid39075103,
year = {2024},
author = {Lovell, MS and Polito, MJ and Schuster, JA and Shallow, EE and Janosik, AM and Falterman, BJ and Dance, MA},
title = {Seasonal variability in the feeding ecology of an oceanic predator.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {17353},
pmid = {39075103},
issn = {2045-2322},
mesh = {Animals ; *Seasons ; *Predatory Behavior/physiology ; Food Chain ; Feeding Behavior/physiology ; Tuna/physiology ; Carbon Isotopes/analysis ; Diet ; DNA Barcoding, Taxonomic ; Gulf of Mexico ; Nitrogen Isotopes/analysis ; Ecosystem ; },
abstract = {Complementary approaches (stomach contents, DNA barcoding, and stable isotopes) were used to examine seasonal shifts in the feeding ecology of an oceanic predator, yellowfin tuna (Thunnus albacares, n = 577), in the northern Gulf of Mexico. DNA barcoding greatly enhanced dietary resolution and seasonally distinct prey assemblages were observed for both sub-adults and adults. In general, diet was characterized by ommastrephid squids and exocoetids in spring, juvenile fishes (i.e., carangids and scombrids) in summer, migratory coastal fishes during fall, and an increased consumption of planktonic prey (e.g., amphipods) in winter. Seasonal variability in bulk stable isotope values (δ[13]C, δ[15]N, and δ[34]S) was also observed, with low δ[15]N values and high δ[34]S values during late summer/early fall and high δ[15]N values (low δ[34]S) during late winter/early spring. Bayesian stable isotope mixing models corroborated seasonal diet shifts, highlighting the importance of oceanic nekton in spring/summer, coastal nekton during fall, and oceanic plankton during winter. Seasonal shifts in diet appeared to be influenced by prey reproductive cycles, habitat associations, and environmental conditions. Findings highlight the complex food web dynamics supporting an opportunistic oceanic predator and the importance of seasonal cycles in prey availability to predator resource utilization in open-ocean ecosystems.},
}
@article {pmid39071290,
year = {2024},
author = {Shibata, D},
title = {Human Brain Ancestral Barcodes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39071290},
issn = {2692-8205},
support = {P01 CA196569/CA/NCI NIH HHS/United States ; R01 CA271237/CA/NCI NIH HHS/United States ; },
abstract = {Dynamic CpG methylation "barcodes" were read from 15,000 to 21,000 single cells from three human male brains. To overcome sparse sequencing coverage, the barcode had ~31,000 rapidly fluctuating X-chromosome CpG sites (fCpGs), with at least 500 covered sites per cell and at least 30 common sites between cell pairs (average of ~48). Barcodes appear to start methylated and record mitotic ages because excitatory neurons and glial cells that emerge later in development were less methylated. Barcodes are different between most cells, with average pairwise differences (PWDs) of ~0.5 between cells. About 10 cell pairs per million were more closely related with PWDs < 0.05. Barcodes appear to record ancestry and reconstruct trees where more related cells had similar phenotypes, albeit some pairs had phenotypic differences. Inhibitory neurons showed more evidence of tangential migration than excitatory neurons, with related cells in different cortical regions. fCpG barcodes become polymorphic during development and can distinguish between thousands of human cells.},
}
@article {pmid39071121,
year = {2024},
author = {Pozzobon, APB and Ready, JS and Di Dario, F and Nunes-da-Fonseca, R},
title = {Identification of pre-flexion fish larvae from the western South Atlantic using DNA barcoding and morphological characters.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17791},
pmid = {39071121},
issn = {2167-8359},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Larva/anatomy &amp; histology/genetics/growth &amp; development ; *Fishes/anatomy &amp; histology/genetics ; Brazil ; *Electron Transport Complex IV/genetics ; Phylogeny ; Atlantic Ocean ; Species Specificity ; },
abstract = {Knowledge on species composition is the first step necessary for the proper conservation and management of biological resources and ecologically relevant species. High species diversity and a lack of diagnostic characters for some groups can impose difficulties for taxonomic identification through traditional methodologies, and ichthyoplankton (fish larvae and eggs) are a good example of such a scenario. With more than 35.000 valid species of fishes worldwide and overall similar anatomies in early developmental stages in closely related groups, fish larvae are often hard to be identified at the species or even more encompassing taxonomic levels. To overcome this situation, molecular techniques have been applied, with different markers tested over the years. Cytochrome c oxidase I (COI) is the most commonly used marker and now has the broadest public reference libraries, providing consistent results for species identification in different metazoan studies. Here we sequenced the mitochondrial COI-5P fragment of 89 fish larvae collected in the Campos Basin, coastal southeastern Brazil, and compared these sequences with references deposited in public databases to obtain taxonomic identifications. Most specimens identified are species of the Blenniiformes, with Parablennius and Labrisomus the most frequently identified genera. Parablennius included two species (P. marmoreus and P. pilicornis), while Labrisomus included three species (L. cricota, L. conditus and L. nuchipinnis). Anatomy of these molecularly identified specimens were then analyzed with the intention of finding anatomical characters that might be diagnostically informative amongst the early development stage (pre-flexion) larvae. Ventral pigmentation patterns are proposed as useful markers to identify Labrisomus species. However, additional specimens are needed to confirm if the character holds stability through the geographic distribution of the species.},
}
@article {pmid39070712,
year = {2024},
author = {Quek, ZBR and Yip, ZT and Jain, SS and Wong, HXV and Tan, Z and Joseph, AR and Huang, D},
title = {DNA barcodes are ineffective for species identification of Acropora corals from the aquarium trade.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e125914},
pmid = {39070712},
issn = {1314-2828},
abstract = {Species identification of stony corals (Scleractinia), which are regulated under the Convention on International Trade in Endangered Species of Wild Fauna and Flora, is critical for effective control of harvest quotas, enforcement of trade regulations and species conservation in general. DNA barcoding has the potential to enhance species identification success, depending on the specific taxon concerned and genetic markers used. For Acropora, DNA barcoding, based on the mitochondrial putative control region (mtCR) and the nuclear PaxC intron (PaxC), has been commonly used for species identification and delimitation, but the reliability and robustness of these loci remain contentious. Therefore, we sought to verify the applicability of this approach. In this study, we obtained 127 Acropora colonies from the aquarium trade to test the effectiveness of barcoding mtCR and PaxC for species identification. We were able to recover sequences for both loci in over half of the samples (n = 68), while gene amplification and sequencing of mtCR (n = 125) outperformed PaxC (n = 70). Amongst the 68 samples with both loci recovered, just a single sample could be unambiguously identified to species. Preliminary identities, based on only one gene, were assigned for 40 and 65 samples with mtCR and PaxC, respectively. Further analyses of 110 complete mitochondrial genomes obtained from GenBank showed that, despite the full length of the sequences, only eight species were delimited, of which only three species were correspondingly monophyletic. Therefore, we conclude that the commonly used DNA barcoding markers for Acropora are ineffective for accurate species assignments due to limited variability in both markers and even across the entire mitochondrial genome. Therefore, we propose that barcoding markers should generally not be the only means for identifying corals.},
}
@article {pmid39065533,
year = {2024},
author = {Tirrò, G and Conti Taguali, S and Pane, A and Riolo, M and Ezra, D and Cacciola, SO},
title = {Outbreak of Alternaria Black Spot of Pomegranate (Punica granatum L.) in Italy as a Consequence of Unusual Climatic Conditions.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {14},
pages = {},
pmid = {39065533},
issn = {2223-7747},
abstract = {Alternaria black spot of pomegranate (Punica granatum) was reported for the first time in Italy. In spring 2023, an outbreak of this disease was noticed in commercial pomegranate 'Wonderful' orchards of the municipality of Misterbianco (Sicily), following an unusually rainy period. A total of 30 randomly selected Alternaria isolates recovered from typical necrotic spots of leaves and fruits were characterized. Based on the colony morphology on solid agar media (PDA and MEA), isolates were separated into three distinct morphotypes (1, 2, and 3). The first two morphotypes comprised only isolates from fruits, while morphotype 3 comprised only isolates from leaves. Multigene phylogenetic analysis of four DNA regions, including internal transcribed spacer (ITS), translation elongation factor 1-α (EF-1α), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and a SCAR marker (OPA10-2), identified the isolates of morphotypes 1 and 2 as Alternaria alternata and morphotype 3 isolates as A. arborescens. In pathogenicity tests on unwounded leaves and fruit, the isolates of all three morphotypes produced symptoms on the leaves of three pomegranate cultivars, 'Acco', 'Wonderful', and 'Etna'. The symptoms on 'Acco' leaves were the least severe. Conversely, the fruits of 'Acco' were the most susceptible. The isolates of morphotypes 2 and 3 were not pathogenic on the fruits of 'Wonderful' and 'Etna'. This is the first report of Alternaria black spot in Italy and of A. arborescens associated with Alternaria black spot of pomegranate worldwide.},
}
@article {pmid39065505,
year = {2024},
author = {Sokoloff, DD and Degtjareva, GV and Valiejo-Roman, CM and Severova, EE and Barinova, S and Chepinoga, VV and Kuzmin, IV and Sennikov, AN and Shmakov, AI and Skaptsov, MV and Smirnov, SV and Remizowa, MV},
title = {Kazakhstan Has an Unexpected Diversity of Medicinal Plants of the Genus Acorus (Acoraceae) and Could Be a Cradle of the Triploid Species A. calamus.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {14},
pages = {},
pmid = {39065505},
issn = {2223-7747},
support = {075-15-2021-1064//Ministry of Science and Higher Education of Russia/ ; FZMW-2023-0008//State Assignment of the Altai State University/ ; BR18574062//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {The Acorus calamus group, or sweet flag, includes important medicinal plants and is classified into three species: A. americanus (diploid), A. verus (tetraploid), and A. calamus (sterile triploid of hybrid origin). Members of the group are famous as components of traditional Indian medicine, and early researchers suggested the origin of the sweet flag in tropical Asia. Subsequent research led to an idea of the origin of the triploid A. calamus in the Amur River basin in temperate Asia, because this was the only region where both diploids and tetraploids were known to co-occur and be capable of sexual reproduction. Contrary to this hypothesis, triploids are currently very rare in the Amur basin. Here, we provide the first evidence that all three species occur in Kazakhstan. The new records extend earlier data on the range of A. verus for c. 1800 km. Along the valley of the Irtysh River in Kazakhstan and the adjacent Omsk Oblast of Russia, A. verus is recorded in the south, A. americanus in the north, and A. calamus is common in between. We propose the Irtysh River valley as another candidate for a cradle of the triploid species A. calamus. It is possible that the range of at least one parent species (A. americanus) has contracted through competition with its triploid derivative species, for which the Irtysh River floods provide a tool for downstream range expansion. We refine our earlier data and show that the two parent species have non-overlapping ranges of variation in a quantitative metric of leaf aerenchyma structure.},
}
@article {pmid39065465,
year = {2024},
author = {Metouekel, A and Badrana, F and Kachkoul, R and Chebaibi, M and Akhazzane, M and El Moussaoui, A and Touil, N and El Amri, H and El Fahime, E and El Kazzouli, S and El Brahmi, N},
title = {Genetic Characterization and Chemical Identification of Moroccan Cannabis sativa (L.) Seeds: Extraction, and In Vitro and In Silico Biological Evaluation.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {14},
pages = {},
pmid = {39065465},
issn = {2223-7747},
abstract = {This study investigated the molecular, phytochemical, and biological aspects of ten local Moroccan traditional landrace Cannabis seeds. Genetic polymorphisms were analyzed using DNA barcode determination, revealing two distinct molecular profiles: "Cannabis, species sativa, subspecies indica" and "Cannabis, species sativa, subspecies sativa". Furthermore, a new sequence was identified by sequencing of the THCA synthase coding gene. Chemical profiling via HPLC-ESI-FULL-MS and GC-MS-MS of AMSD1 maceration extracts revealed 13 non-volatile chemicals, including 3 inactive cannabinoids and 3 polyphenols, and 24 intriguing volatile compounds, including 7 previously unreported in Cannabis seed extracts. Moreover, the in vitro/in silico analysis provision of biological activities through their antioxidant power, antimicrobial effect, and cytotoxicity potency, as well as antiviral activity, were realized. These results contribute to a thorough comprehension of Moroccan Cannabis seeds, illuminating their molecular, phytochemical, and biological features. Furthermore, they highlight the seeds as a potential source of nutritious components with antioxidant properties, offering valuable insights for future research.},
}
@article {pmid39062719,
year = {2024},
author = {Zheng, HZ and Dai, W and Xu, MH and Lin, YY and Zhu, XL and Long, H and Tong, LL and Xu, XG},
title = {Intraspecific Differentiation of Styrax japonicus (Styracaceae) as Revealed by Comparative Chloroplast and Evolutionary Analyses.},
journal = {Genes},
volume = {15},
number = {7},
pages = {},
pmid = {39062719},
issn = {2073-4425},
mesh = {*Genome, Chloroplast ; *Evolution, Molecular ; *Phylogeny ; Chloroplasts/genetics ; Acanthaceae/genetics ; Polymorphism, Genetic ; },
abstract = {Styrax japonicus is a medicinal and ornamental shrub belonging to the Styracaceae family. To explore the diversity and characteristics of the chloroplast genome of S. japonicus, we conducted sequencing and comparison of the chloroplast genomes of four naturally distributed S. japonicus. The results demonstrated that the four chloroplast genomes (157,914-157,962 bp) exhibited a typical quadripartite structure consisting of a large single copy (LSC) region, a small single copy (SSC) region, and a pair of reverse repeats (IRa and IRb), and the structure was highly conserved. DNA polymorphism analysis revealed that three coding genes (infA, psbK, and rpl33) and five intergene regions (petA-psbJ, trnC-petN, trnD-trnY, trnE-trnT, and trnY-trnE) were identified as mutation hotspots. These genetic fragments have the potential to be utilized as DNA barcodes for future identification purposes. When comparing the boundary genes, a small contraction was observed in the IR region of four S. japonicus. Selection pressure analysis indicated positive selection for ycf1 and ndhD. These findings collectively suggest the adaptive evolution of S. japonicus. The phylogenetic structure revealed conflicting relationships among several S. japonicus, indicating divergent evolutionary paths within this species. Our study concludes by uncovering the genetic traits of the chloroplast genome in the differentiation of S. japonicus variety, offering fresh perspectives on the evolutionary lineage of this species.},
}
@article {pmid39062644,
year = {2024},
author = {Hopkins, L and Yim, K and Rumora, A and Baykus, MF and Martinez, L and Jimenez, L},
title = {Genotypic Identification of Trees Using DNA Barcodes and Microbiome Analysis of Rhizosphere Microbial Communities.},
journal = {Genes},
volume = {15},
number = {7},
pages = {},
pmid = {39062644},
issn = {2073-4425},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Rhizosphere ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *RNA, Ribosomal, 16S/genetics ; *Quercus/microbiology/genetics ; *Trees/microbiology/genetics ; Soil Microbiology ; Fagus/microbiology/genetics ; Fungi/genetics/classification ; Genotype ; Phylogeny ; Acer/microbiology/genetics ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {DNA barcodes can provide accurate identification of plants. We used previously reported DNA primers targeting the internal transcribed spacer (ITS1) region of the nuclear ribosomal cistron, internal transcribed spacer (ITS2), and chloroplast trnL (UAA) intron to identify four trees at Bergen Community College. Two of the four trees were identified as Acer rubrum and Fagus sylvatica. However, Quercus was only identified at the genus level, and the fourth tree did not show similar identification between barcodes. Next-generation sequencing of 16S rRNA genes showed that the predominant bacterial communities in the rhizosphere mainly consisted of the Pseudomonadota, Actinomycetota, Bacteroidota, and Acidobacteriota. A. rubrum showed the most diverse bacterial community while F. sylvatica was less diverse. The genus Rhodoplanes showed the highest relative bacterial abundance in all trees. Fungal ITS sequence analysis demonstrated that the communities predominantly consisted of the Ascomycota and Basidiomycota. Quercus showed the highest fungi diversity while F. sylvatica showed the lowest. Russula showed the highest abundance of fungi genera. Average similarity values in the rhizosphere for fungi communities at the phylum level were higher than for bacteria. However, at the genus level, bacterial communities showed higher similarities than fungi. Similarity values decreased at lower taxonomical levels for both bacteria and fungi, indicating each tree has selected for specific bacterial and fungal communities. This study confirmed the distinctiveness of the microbial communities in the rhizosphere of each tree and their importance in sustaining and supporting viability and growth but also demonstrating the limitations of DNA barcoding with the primers used in this study to identify genus and species for some of the trees. The optimization of DNA barcoding will require additional DNA sequences to enhance the resolution and identification of trees at the study site.},
}
@article {pmid39059835,
year = {2024},
author = {Pei, Y and Liu, Z and Yu, D and Zhang, X and Sun, W and Chen, X and Feng, X and Li, X},
title = {Molecular quantification of herbs (Herb-Q): a pyrosequencing-based approach and its application in Pinellia ternata.},
journal = {Chinese journal of natural medicines},
volume = {22},
number = {7},
pages = {663-672},
doi = {10.1016/S1875-5364(24)60636-9},
pmid = {39059835},
issn = {1875-5364},
mesh = {*Pinellia/genetics/chemistry ; *DNA Barcoding, Taxonomic/methods ; Polymorphism, Single Nucleotide ; DNA, Plant/genetics ; Sequence Analysis, DNA/methods ; Drugs, Chinese Herbal/chemistry ; Drug Contamination ; Plants, Medicinal/genetics/chemistry/classification ; },
abstract = {Variations in herb dosage due to species adulteration and dosing inaccuracies can substantially affect clinical safety and efficacy. Accurate species quantification remains challenging, as current methods often yield inconsistent results. This study introduces a novel pyrosequencing-based technique, termed herb molecular quantification (Herb-Q), designed to precisely quantify herbal products. We evaluated its effectiveness using Pinellia ternata and five of its adulterants. Initially, we assessed commonly used DNA barcodes with sequences from a public database, identifying two candidate regions, Maturase K (matK) and internal transcribed spacer 2 (ITS2), for screening specific single nucleotide polymorphism (SNP) loci, allowing for species-specific identification. These loci were validated by amplifying and sequencing genomic material from collected samples. Our validation studies showed that Herb-Q demonstrated excellent linearity, accuracy, repeatability, and detection limits. We established quantitative standard curves with high R[2] values (> 0.99) to enable precise species quantification, which were combined with external standards to provide clear and accurate visual quantification results. The average bias in quantifying the tuber of P. ternata was 2.38%, confirming that Herb-Q can accurately identify and quantify herbal product constituents. Moreover, the entire quantification process took less than 4 h. This study presents a novel, rapid method for accurately quantifying species in herbal products and advances the application of DNA barcoding from species identification to quantitative detection.},
}
@article {pmid39057812,
year = {2024},
author = {Aytenov, IS and Bozorov, TA and Zhang, D and Samadiy, SA and Muhammadova, DA and Isokulov, MZ and Murodova, SM and Zakirova, OR and Chinikulov, BK and Sherimbetov, AG},
title = {Uncovering the Antifungal Potential of Plant-Associated Cultivable Bacteria from the Aral Sea Region against Phytopathogenic Fungi.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {39057812},
issn = {2076-0817},
support = {PZ-20200929166//Ministry of Innovative Development of Uzbekistan/ ; KFL-BRP-007-008//Biological resources programme, Chinese Academy of the Sciences/ ; },
mesh = {*Fungi/isolation &amp; purification/pathogenicity ; *Bacteria/isolation &amp; purification/drug effects/genetics ; *Rhizosphere ; Antifungal Agents/pharmacology ; Antibiosis/physiology ; Plant Diseases/microbiology/prevention &amp; control ; Plants/microbiology ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; },
abstract = {Two freshwater rivers, the Amu Darya and Syr Darya, flow into the Aral Sea, but they began to diminish in the early 1960s, and by the 1980s, the lake had nearly ceased to exist due to excessive water consumption for agriculture and the unsustainable management of water resources from rivers, which transformed the Aral Sea into a hypersaline lake. Despite this, the flora and fauna of the region began to evolve in the high-salinity seabed soil, which has received little attention in studies. In this study, we isolated approximately 1400 bacterial strains from the rhizosphere and phyllosphere of plant species of distinct families. Bacterial isolates were examined for antifungal activities against a range of pathogenic fungi such as Rhizoctonia gossypii, Trichothecium ovalisporum, Fusarium annulatum, F. oxysporum, F. culmorum, F. brachygibbosum, F. tricinctum, F. verticillioides, Alternaria alternata, A. terreus, Aspergillus niger, and As. flavus. Eighty-eight bacterial isolates exhibited varying antagonistic ability against pathogenic fungi. Furthermore, DNA barcoding of isolates using the 16S rRNA gene indicated that most antagonistic bacteria belonged to the Bacillus and Pseudomonas genera. The study also explored the activity of hydrolytic and cell-wall-degrading enzymes produced by antagonistic bacteria. The findings revealed that antagonistic bacteria can be utilized to widely protect seabed plants and plants growing in saline areas against pathogenic fungi, as well as agricultural crops.},
}
@article {pmid39057785,
year = {2024},
author = {Zheng, JX and Sun, XH and Wei, X and Wang, G and Yuan, CQ and Weng, XD and Zuo, QQ and Liu, JY and Mu, ZQ and Mao, TC and Ding, YZ and Wang, XM and Wang, X and Wang, ZH},
title = {Species Composition of a Small Mammal Community and Prevalence of Echinococcus spp. in the Alpine Pastoral Area of the Eastern Tibetan Plateau.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {39057785},
issn = {2076-0817},
support = {31071944//National Science Foundation of China/ ; 31470488//National Science Foundation of China/ ; 32071529//National Science Foundation of China/ ; },
mesh = {Animals ; Tibet/epidemiology ; *Echinococcosis/epidemiology/veterinary/parasitology ; Prevalence ; *Echinococcus/isolation &amp; purification/genetics ; *Rodentia/parasitology ; Lagomorpha/parasitology ; Mammals/parasitology ; },
abstract = {We aimed to investigate the species composition of a small mammal community and the prevalence of Echinococcus spp. in a typical endemic area of the Tibetan Plateau. One pika and five rodent species were identified based on the morphological characteristics of 1278 small mammal specimens collected during 2014-2019. Detection of Echinococcus DNA in tissue samples from small mammal specimens revealed that Ochotona curzoniae (pika, total prevalence: 6.02%, 26/432), Neodon fuscus (5.91%, 38/643), N. leucurus (2.50%, 3/120), and Alexandromys limnophilus (21.74%, 10/46) were infected by both E. multilocularis and E. shiquicus; Cricetulus longicaudatus (16.67%, 1/6) was infected by E. shiquicus; and no infection was detected in N. irene (0/15). Neodon fuscus and O. curzoniae were the two most abundant small mammal species. There was no significant difference in the prevalence of pika and the overall rodent species assemblage (6.26%, 53/846); however, the larger rodent populations suggested that more attention should be paid to their role in the transmission of echinococcosis in the wildlife reservoir, which has long been underestimated. Moreover, although DNA barcoding provides a more efficient method than traditional morphological methods for identifying large numbers of small mammal samples, commonly used barcodes failed to distinguish the three Neodon species in this study. The close genetic relationships between these species suggest the need to develop more powerful molecular taxonomic tools.},
}
@article {pmid39057752,
year = {2024},
author = {Zhang, J and Jiamahate, A and Feng, H and Bozorov, TA and Zhang, D and Guo, J and Yang, H and Zhang, D},
title = {Distribution and Pathogenicity Differentiation of Physiological Races of Verticillium dahliae from Cotton Stems in Western China.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {39057752},
issn = {2076-0817},
support = {31700289//National Natural Science Foundation of China/ ; ZDBS-LY-SM009//Key Research Program of Frontier Sciences, Chinese Academy of Sciences/ ; 2021-XBQNXZ-015//the West Light Talents Cultivation Program of the Chinese Academy of Sciences/ ; 2021xjkk0500//Third Xinjiang Scientific Expedition Program/ ; 2022D01A354//the Natural Science Foundation of the Xinjiang Uygur Autonomous Region/ ; },
mesh = {*Gossypium/microbiology ; China ; *Plant Diseases/microbiology ; Virulence/genetics ; *Ascomycota/genetics/pathogenicity/isolation &amp; purification ; Plant Stems/microbiology ; Genetic Variation/genetics ; Phylogeny ; Haplotypes ; Verticillium ; },
abstract = {Verticillium wilt, caused by the pathogenic fungus Verticillium dahliae, has emerged as a severe threat to cotton globally. However, little is known about the genetic diversity of this pathogen in an infected single cotton plant. In this study, we isolated three new V. dahliae strains from the disease stems of Gossypium hirsutum from the cotton field in Western China and assessed their pathogenicity to the cotton cultivar Xinnongmian-1 and its two transgenic lines, as well as two laboratory strains, VD592 and VD991. These three new V. dahliae strains were identified using DNA barcodes of tryptophan synthase (TS), actin (ACT), elongation factor 1-α (EF), and glyceraldehyde-3-phosphate dehydrogenase (GPD). Moreover, the haplotype analysis revealed that the three new races had distinct haplotypes at the TS locus. Furthermore, the results of culture features and genetic diversity of ISSR (inter-simple sequence repeat) revealed that there were separate V. dahliae strains, which were strong defoliating pathotypes belonging to race 2 type, as determined by particular DNA marker recognition. The identified strains demonstrated varied levels of pathogenicity by leaf disc and entire plant inoculation methods. Conservatively, these strains showed some pathogenicity on cotton lines, but were less pathogenic than the reference strains. The findings revealed that several strong defoliating V. dahliae pathotypes coexist on the same cotton plant. It indicats the importance of regular monitoring as an early warning system, as well as the detection and reporting of virulent pathogen strains and their effects on crop response.},
}
@article {pmid39057277,
year = {2024},
author = {Lukhtanov, VA and Dantchenko, AV},
title = {Cryptic Taxa Revealed through Combined Analysis of Chromosomes and DNA Barcodes: The Polyommatus ripartii Species Complex in Armenia and NW Iran.},
journal = {Insects},
volume = {15},
number = {7},
pages = {},
pmid = {39057277},
issn = {2075-4450},
support = {24-14-00047//Russian Science Foundation/ ; },
abstract = {The detection of cryptic species in complexes that have undergone recent speciation is often difficult, since many standard nuclear markers have not yet accumulated differences between closely related taxa, and differences in mitochondrial markers can be leveled out due to mitochondrial introgressions. In these cases, the use of derived chromosomal characters such as non-ancestral chromosomal numbers and/or unusual karyotype features may be a solution to the species delimitation problem. However, non-ancestral but similar karyotypes may arise secondarily as a result of homoplastic evolution, and their interpretation as homologies may lead to incorrect taxonomic conclusions. In our study, we show that the combined use of mitochondrial DNA barcodes and karyotypes helps to solve this problem and identifies cryptic species in situations where each of these markers does not work individually. Using this approach, we show that the fauna of Armenia and adjacent Iran includes the following cryptic taxa of the Polyommatus ripartii species complex (haploid chromosome number, n in parentheses): P. ripartii paralcestis (n = 90), P. ripartii kalashiani, subsp. nov (n close to 90), P. emmeli, sp. nov. (n = 77-79), P. keleybaricus, sp. nov. (n = 86), P. demavendi belovi (n = 73-75), P. demavendi antonius, subsp. nov. (n = 71-73), P. admetus anatoliensis (n = 79) and P. eriwanensis (n = 29-34). Polyommatus admetus yeranyani is synonymized with P. admetus anatoliensis.},
}
@article {pmid39057251,
year = {2024},
author = {Kocić, K and Mjǿs, AT and Čkrkić, J and Petrović, A and Popović, N and Paulsen, ES and Tomanović, &#x17d;},
title = {Uncovering Norway: Descriptions of Four New Aphidiinae Species (Hymenoptera, Braconidae) with Identification Key and Notes on Phylogenetic Relationships of the Subgenus Fovephedrus Chen.},
journal = {Insects},
volume = {15},
number = {7},
pages = {},
pmid = {39057251},
issn = {2075-4450},
support = {451-03-65/2024-03/200178//Ministry of Science, Technological Development and Innovation of Serbia/ ; F131//Serbian Academy of Sciences and Arts/ ; },
abstract = {With only 33 reported species, Norway ranks among the European countries with the lowest documented diversity of parasitoids from the subfamily Aphidiinae. The "MUST Malaise" project, carried out by Museum Stavanger in Norway, aimed to assess insect abundance and biodiversity and create a reference base for future studies. The preliminary results of our study revealed four species new to science, indicating that the current number of recorded species in Norway is significantly lower than the actual diversity. All species possess unique combinations of morphological characters, distinguishing them from other known Aphidiinae species. Molecular analysis of the barcoding region confirmed that these specimens all belong to the previously undescribed species. In this study, we describe Aphidius norvegicus sp.n., Praon breviantennalis sp.n., Ephedrus gardenforsi sp.n., and Ephedrus borealis sp.n., all collected in Norway. We also provide an identification key and discuss the phylogenetic relationships within the subgenus Fovephedrus Chen, 1986.},
}
@article {pmid39057241,
year = {2024},
author = {Liu, J and Xu, H and Wang, Z and Li, P and Yan, Z and Bai, M and Li, J},
title = {Phylogenetics, Molecular Species Delimitation and Geometric Morphometrics of All Reddish-Brown Species in the Genus Neotriplax Lewis, 1887 (Coleoptera: Erotylidae: Tritomini).},
journal = {Insects},
volume = {15},
number = {7},
pages = {},
pmid = {39057241},
issn = {2075-4450},
support = {No. 31750002//National Natural Science Foundation of China/ ; No. 22326507D//Special Project of Technological innovation for Rural Revitalization/ ; No. 2020GDASYL-20200102021//GDAS Special Project of Science and Technology Development/ ; No. C2023204114//Hebei Provincial Natural Science Foundation/ ; },
abstract = {To date, five species of reddish-brown Neotriplax have been described, but their highly similar body color and other phenotypic traits make accurate taxonomy challenging. To clarify species-level taxonomy and validate potential new species, the cytochrome oxidase subunit I (COI) was used for phylogenetic analysis and the geometric morphometrics of elytron, pronotum, and hind wing were employed to distinguish all reddish-brown Neotriplax species. Phylogenetic results using maximum likelihood and Bayesian analyses of COI sequences aligned well with the current taxonomy of the Neotriplax species group. Significant K2P divergences, with no overlap between intra- and interspecific genetic distances, were obtained in Neotriplax species. The automatic barcode gap discovery (ABGD), assemble species by automatic partitioning (ASAP), and generalized mixed Yule coalescent (GMYC) approaches concurred, dividing the similar species into eight molecular operational taxonomic units (MOTUs). Geometric morphometric analysis using pronotum, elytron, hind wing shape and wing vein patterns also validated the classification of all eight species. By integrating these analytical approaches with morphological evidence, we successfully delineated the reddish-brown species of Neotriplax into eight species with three new species: N. qinghaiensis sp. nov., N. maoershanensis sp. nov., and N. guangxiensis sp. nov. Furthermore, we documented the first record of N. lewisii in China. This study underscores the utility of an integrative taxonomy approach in species delimitation within Neotriplax and serves as a reference for the taxonomic revision of other morphologically challenging beetles through integrative taxonomy.},
}
@article {pmid39057230,
year = {2024},
author = {Xi, O and Zhang, S and Li, J and Hu, H and Bai, M},
title = {Geometric Morphometrics and Genetic Diversity Analysis of Chalcidoidea (Diglyphus and Pachyneuron) at Various Elevations.},
journal = {Insects},
volume = {15},
number = {7},
pages = {},
pmid = {39057230},
issn = {2075-4450},
support = {No. 31860612//National Key Research and Development Program of China/ ; No. 32070472//National Key Research and Development Program of China/ ; },
abstract = {Eulophidae and Pteromalidae are parasitic wasps with a global distribution and import for the biological control of pests. They can be distributed in different altitude regions, but their morphological and genetic adaptations to different altitudes are unclear. Here, we collected specimens that belong to Eulophidae and Pteromalidae from various altitudinal gradients, based on integrated taxonomic approaches to determine the species composition, and we analyzed their body shape and size from different altitudes using geometric morphometrics. Then, we performed an analysis of the D. isaea population's haplotype genes to illustrate their genetic diversity. As a result, eight species that belong to two genera, Diglyphus Walker (Eulophidae) and Pachyneuron Walker (Pteromalidae), were identified, including two newly recorded species from China (D. chabrias and D. sabulosus). Through a geometric morphometrics analysis of body shape, we found that a narrow forewing shape and a widened thorax are the significant characteristics of adaptation to high-altitude environments in D. isaea and P. aphidis. Additionally, the body size studies showed a principal relationship between centroid size and altitude; the size of the forewings and thorax increases at higher altitudes. Next, using haplotype analysis, 32 haplotypes were found in seven geographic populations with high genetic diversity of this species. Our research provides preliminary evidence for the morphological and genetic diversity adaptation of parasitic wasps to extreme environments, and these data can provide important references for investigations on the ecological adaptability of parasitic wasps.},
}
@article {pmid39055168,
year = {2024},
author = {Guo, W and Liu, Y and Han, Y and Tang, H and Fan, X and Wang, C and Chen, PR},
title = {Amplifiable protein identification via residue-resolved barcoding and composition code counting.},
journal = {National science review},
volume = {11},
number = {7},
pages = {nwae183},
pmid = {39055168},
issn = {2053-714X},
abstract = {Ultrasensitive protein identification is of paramount importance in basic research and clinical diagnostics but remains extremely challenging. A key bottleneck in preventing single-molecule protein sequencing is that, unlike the revolutionary nucleic acid sequencing methods that rely on the polymerase chain reaction (PCR) to amplify DNA and RNA molecules, protein molecules cannot be directly amplified. Decoding the proteins via amplification of certain fingerprints rather than the intact protein sequence thus represents an appealing alternative choice to address this formidable challenge. Herein, we report a proof-of-concept method that relies on residue-resolved DNA barcoding and composition code counting for amplifiable protein fingerprinting (AmproCode). In AmproCode, selective types of residues on peptides or proteins are chemically labeled with a DNA barcode, which can be amplified and quantified via quantitative PCR. The operation generates a relative ratio as the residue-resolved 'composition code' for each target protein that can be utilized as the fingerprint to determine its identity from the proteome database. We developed a database searching algorithm and applied it to assess the coverage of the whole proteome and secretome via computational simulations, proving the theoretical feasibility of AmproCode. We then designed the residue-specific DNA barcoding and amplification workflow, and identified different synthetic model peptides found in the secretome at as low as the fmol/L level for demonstration. These results build the foundation for an unprecedented amplifiable protein fingerprinting method. We believe that, in the future, AmproCode could ultimately realize single-molecule amplifiable identification of trace complex samples without further purification, and it may open a new avenue in the development of next-generation protein sequencing techniques.},
}
@article {pmid39054884,
year = {2024},
author = {Cilia, G and Caringi, V and Zavatta, L and Bortolotti, L},
title = {Pathogen occurrence in different developmental stages of the invasive Vespa velutina nigrithorax (Buysson, 1905).},
journal = {Pest management science},
volume = {80},
number = {11},
pages = {5909-5917},
doi = {10.1002/ps.8325},
pmid = {39054884},
issn = {1526-4998},
support = {2021/2115//Regulation (EU) of the European Parliament and of the Council/ ; },
mesh = {Animals ; *Wasps/virology/physiology/growth &amp; development ; *Introduced Species ; Nosema/physiology ; Bees/virology ; DNA, Mitochondrial/genetics ; Larva/virology/growth &amp; development ; Italy ; RNA Viruses/physiology/genetics ; Pupa/virology/growth &amp; development ; },
abstract = {BACKGROUND: The yellow-legged hornet (Vespa velutina nigrithorax) is a predatory species native to South-East Asia. The hornet is invasive in Europe, spreading to several countries and becoming a pest for Apis mellifera due to its behaviour of preying in front of apiaries. The aim of this study was (i) to investigate the presence of honey bee pathogens within the developmental stages of V. velutina after neutralizing a nest in Bologna province (Emilia-Romagna, Italy) and (ii) to analyze the mitochondrial DNA to determine if the population derived from the population initially introduced in Europe.<br><br>RESULTS: The results indicated that deformed wing virus (82.76%) and Nosema ceranae (67.28%) were the most prevalent pathogens. Deformed wing virus, N. ceranae and sacbrood virus were found in all investigated stages, while chronic bee paralysis virus and Kashmir bee virus were exclusively found in foraging adults. All detected viruses were found to be replicative, highlighting active infection in the hosts. The mtDNA analysis demonstrated that the origin derived from the invasive population arrived in France.<br><br>CONCLUSION: This study underscores the importance of further research to understand the effect of interspecific transmission, especially concerning the potential role of these pathogens as a biocontrol for the invasive V. velutina nigrithorax. &#xa9; 2024 Society of Chemical Industry.},
}
@article {pmid39052818,
year = {2024},
author = {Kawaoka, J and Lomvardas, S},
title = {Barcoding distinct neurons.},
journal = {Science (New York, N.Y.)},
volume = {385},
number = {6707},
pages = {370-371},
doi = {10.1126/science.adq5225},
pmid = {39052818},
issn = {1095-9203},
mesh = {Animals ; Humans ; Mice ; *Neurons/cytology/physiology ; *Gene Expression Regulation ; *Cohesins/genetics ; *Cadherins/genetics/metabolism ; },
abstract = {The genomic landscape of a cell surface protein reveals how neuron identity is displayed.},
}
@article {pmid39051761,
year = {2024},
author = {Feng, J and Ren, Q and Xie, A and Jiang, Z and Liu, Y},
title = {High-resolution melting analysis to authenticate deer-derived materials in processed products in China using a cytochrome oxidase I mini-barcode.},
journal = {Journal of the science of food and agriculture},
volume = {104},
number = {15},
pages = {9390-9398},
doi = {10.1002/jsfa.13761},
pmid = {39051761},
issn = {1097-0010},
support = {ZDKJ2021034//Hainan Province Science and Technology Special Fund Program/ ; 2022wnkj10//Wanning City Scientific Research Program/ ; },
mesh = {*Deer ; Animals ; China ; *Electron Transport Complex IV/genetics ; *DNA Barcoding, Taxonomic ; *Antlers/chemistry ; Transition Temperature ; Food Contamination/analysis ; DNA/analysis ; Bone and Bones/chemistry ; },
abstract = {BACKGROUND: Deer-derived materials (antler, venison, fetus, penis, bone, tail, and others) are some of the most valuable traditional animal-based medicinal and food materials in China. In production, processing, and trade, the quality of deer products varies. The market is confusing, and counterfeit and shoddy products are common. There is an urgent need to establish an accurate identification method.<br><br>RESULTS: Two pairs of primers suitable for identifying deer-derived medicinal materials were obtained by screening the cytochrome oxidase I (COI) sequences of 18 species from nine genera of the deer family. The two primers were used to identify the species and adulteration of 22 batches of commercially available deer-derived products with a mini-barcode combining high-resolution melting (HRM) technology and methodical investigation. Deer-derived materials (sika and red deer) were correctly identified by species using varying DNA amounts (1 to 500 ng). The two pairs of primers COI-1FR and COI-2FR yielded melting temperatures (Tm) of 80.55 to 81.00&#x2009;&#xb0;C and 82.00 to 82.50&#x2009;&#xb0;C for sika deer, and 81.00 to 82.00&#x2009;&#xb0;C and 81.40 to 82.00&#x2009;&#xb0;C for red deer. Twenty-two batches of commercially available samples were analyzed by HRM analysis and conventional amplification sequencing, and it was found that the species samples had an error rate of species labeling of 31.8%. Four batches of samples were identified as mixed (adulterated) in the HRM analysis.<br><br>CONCLUSION: The combination of DNA mini-barcode with HRM analysis facilitated the accurate identification of species of deer-derived materials, especially the identification of samples in an adulterated mixed state. &#xa9; 2024 Society of Chemical Industry.},
}
@article {pmid39051560,
year = {2024},
author = {Odunze, U and Rustogi, N and Devine, P and Miller, L and Pereira, S and Vashist, S and Snijder, HJ and Corkill, D and Sabirsh, A and Douthwaite, J and Bond, N and Desai, A},
title = {RNA encoded peptide barcodes enable efficient in vivo screening of RNA delivery systems.},
journal = {Nucleic acids research},
volume = {52},
number = {16},
pages = {9384-9396},
pmid = {39051560},
issn = {1362-4962},
support = {//AstraZeneca R&amp;D/ ; //AstraZeneca RNA Therapy/ ; },
mesh = {Animals ; *Peptides/chemistry ; Mice ; *Nanoparticles/chemistry ; RNA, Messenger/genetics/metabolism ; Humans ; Lipids/chemistry ; RNA/genetics/chemistry/metabolism ; Genes, Reporter ; Liposomes ; },
abstract = {Lipid nanoparticles (LNPs) have been demonstrated to hold great promise for the clinical advancement of RNA therapeutics. Continued exploration of LNPs for application in new disease areas requires identification and optimization of leads in a high throughput way. Currently available high throughput in vivo screening platforms are well suited to screen for cellular uptake but less so for functional cargo delivery. We report on a platform which measures functional delivery of LNPs using unique peptide 'barcodes'. We describe the design and selection of the peptide barcodes and the evaluation of these for the screening of LNPs. We show that proteomic analysis of peptide barcodes correlates with quantification and efficacy of barcoded reporter proteins both in vitro and in vivo and, that the ranking of selected LNPs using peptide barcodes in a pool correlates with ranking using alternative methods in groups of animals treated with individual LNPs. We show that this system is sensitive, selective, and capable of reducing the size of an in vivo study by screening up to 10 unique formulations in a single pool, thus accelerating the discovery of new technologies for mRNA delivery.},
}
@article {pmid39045589,
year = {2024},
author = {Arya, V and Narayana, S and Sinha, T and Kandan, A and Satyanarayana Raju, SV},
title = {A simple PCR-based quick detection of the economically important oriental fruit fly, Bactrocera dorsalis (Hendel) from India.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1399718},
pmid = {39045589},
issn = {1664-462X},
abstract = {The oriental fruit fly, Bactrocera dorsalis (Hendel), is a significant economic and quarantine pest due to its polyphagous nature. The accurate identification of B. dorsalis is challenging at the egg, maggot, and pupal stages, due to lack of distinct morphological characters and its similarity to other fruit flies. Adult identification requires specialized taxonomist. Existing identification methods are laborious, time consuming, and expensive. Rapid and precise identification is crucial for timely management. By analyzing the variations in the mitochondrial cytochrome oxidase-1 gene sequence (Insect barcoding gene), we developed a species-specific primer (SSP), DorFP1/DorRP1, for accurate identification of B. dorsalis. The optimal annealing temperature for the SSP was determined to be 66°C, with no cross-amplification or primer-dimer formation observed. The SSP was validated with B. dorsalis specimens from various locations in northern and eastern India and tested for cross-specificity with six other economically significant fruit fly species in India. The primer specificity was further confirmed by the analysis of critical threshold (Ct) value from a qPCR assay. Sensitivity analysis showed the primer could detect template DNA concentrations as low as 1 pg/µl, though sensitivity decreased at lower concentrations. Sequencing of the SSP-amplified product revealed over >99% similarity with existing B. dorsalis sequences in the NCBI GenBank. The developed SSP reliably identifies B. dorsalis across all developmental stages and sexes. This assay is expected to significantly impact pest identification, phytosanitary measures, and eradication programs for B. dorsalis.},
}
@article {pmid39045014,
year = {2024},
author = {Chien, YC and Valencia, CA and Lee, HY and Yoon, GM and Kim, D},
title = {DNA-encoded probe-based assay for profiling plant kinase activities.},
journal = {PNAS nexus},
volume = {3},
number = {7},
pages = {pgae281},
pmid = {39045014},
issn = {2752-6542},
abstract = {Elucidating kinase-substrate relationships is pivotal for deciphering cellular signaling mechanisms, yet it remains challenging due to the complexity of kinase networks. Herein, we report the development of a versatile DNA-based kinase assay platform for high-throughput profiling of plant protein kinase activities and substrate preferences. Our approach employs DNA-linked peptide substrates, facilitating quantitative and specific kinase activity detection through next-generation DNA sequencing. Leveraging DNA barcodes as quantitative readouts, our approach establishes a high-throughput, sensitive, and specific platform for dissecting kinase-substrate networks in plants, representing a powerful tool for elucidating signaling mechanisms in plants.},
}
@article {pmid39044181,
year = {2024},
author = {Askari, F and Paksa, A and Shahabi, S and Saeedi, S and Sofizadeh, A and Vahedi, M and Soltani, A},
title = {Population genetic structure and phylogenetic analysis of Anopheles hyrcanus (Diptera: Culicidae) inferred from DNA sequences of nuclear ITS2 and the mitochondrial COI gene in the northern part of Iran.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {724},
pmid = {39044181},
issn = {1471-2334},
support = {30181//Shiraz University of Medical Sciences/ ; },
mesh = {Animals ; Iran ; *Phylogeny ; *Anopheles/genetics/classification ; *Electron Transport Complex IV/genetics ; *Mosquito Vectors/genetics/classification ; Haplotypes ; Genetic Variation ; Genetics, Population ; Sequence Analysis, DNA ; DNA, Ribosomal Spacer/genetics ; },
abstract = {BACKGROUND: The Anopheles hyrcanus group is distributed throughout the Oriental and Palaearctic regions and can transmit diseases such as malaria, Japanese encephalitis virus, and filariasis. This investigation marks the inaugural comprehensive study to undertake a phylogenetic analysis of the constituents of this malaria vector group in the northeastern region of Iran, juxtaposed with documented occurrences from different areas within Iran and worldwide.<br><br>METHODS: Mosquitoes were collected using various methods from nine different locations in Golestan province from April to December 2023. The collected mosquitoes were identified morphologically using valid taxonomic keys. DNA was isolated using the Sambio&#x2122; Kit. COI and ITS2 primers were designed using Oligo7 and GeneRunner. PCR and purification were performed with the Qiagen kit. Subsequently, sequencing was carried out at the Mehr Mam GENE Center using an Applied Biosystems 3730XL sequencer. The nucleotide sequences were then analyzed and aligned with GenBank data using BioEdit. Kimura 2-parameter was Utilized for base substitutions. DNA models were selected based on AIC and BIC criteria. Bayesian and Maximum Likelihood trees were constructed, along with a haplotype network. Molecular diversity statistics computed using DnaSP software.<br><br>RESULTS: In this study, a total of 819 adult mosquitoes were collected. An. hyrcanus was the second most abundant species, predominantly found in Kalaleh and Turkman counties. The sequenced and edited COI and ITS2 sequences were deposited in GenBank under specific accession numbers. Phylogenetic analyses using ML, BI, and NJ methods confirmed a monophyletic lineage for An. hyrcanus with strong support. Molecular analysis of Iranian An. hyrcanus found 11 diverse haplotypes, with the COI gene displaying low diversity. The ITS2 gene revealed two clades - one associating with Iran, Europe, and Asia; the other originating from southwestern Iran. The haplotype network showed two main groups - one from southwest Iran and the other from north Iran. Iran exhibited six distinct haplotypes, while Turkey showcased the highest diversity.<br><br>CONCLUSIONS: An. hyrcanus in southwestern Iran exhibits a distinct haplogroup, suggesting possible subspecies differentiation. Additional studies are required to validate this phenomenon.},
}
@article {pmid39041315,
year = {2024},
author = {Titus, BM and Gibbs, HL and Simões, N and Daly, M},
title = {Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama.},
journal = {Systematic biology},
volume = {73},
number = {5},
pages = {758-768},
doi = {10.1093/sysbio/syae045},
pmid = {39041315},
issn = {1076-836X},
support = {DEB-1601645//National Science Foundation Doctoral Dissertation Improvement/ ; //Operation Wallacea, American Philosophical Society/ ; //International Society for Reef Studies Graduate Fellowship/ ; //PADI Foundation Grant/ ; //American Museum of Natural History Lerner Gray Funds/ ; CONACyTCB-2012-01-177293//The Ohio State University Presidential Fellowship/ ; //Trautman Fund of The OSU Museum of Biological Diversity/ ; //The Ohio State Universit/ ; DEB-1257796//National Science Foundation/ ; },
mesh = {Animals ; *Genetic Speciation ; Caribbean Region ; *Phylogeny ; Panama ; Gene Flow ; Decapoda/classification/genetics ; },
abstract = {Recent genomic analyses have highlighted the prevalence of speciation with gene flow in many taxa and have underscored the importance of accounting for these reticulate evolutionary processes when constructing species trees and generating parameter estimates. This is especially important for deepening our understanding of speciation in the sea where fast-moving ocean currents, expanses of deep water, and periodic episodes of sea level rise and fall act as soft and temporary allopatric barriers that facilitate both divergence and secondary contact. Under these conditions, gene flow is not expected to cease completely while contemporary distributions are expected to differ from historical ones. Here, we conduct range-wide sampling for Pederson's cleaner shrimp (Ancylomenes pedersoni), a species complex from the Greater Caribbean that contains three clearly delimited mitochondrial lineages with both allopatric and sympatric distributions. Using mtDNA barcodes and a genomic ddRADseq approach, we combine classic phylogenetic analyses with extensive topology testing and demographic modeling (10 site frequency replicates × 45 evolutionary models × 50 model simulations/replicate = 22,500 simulations) to test species boundaries and reconstruct the evolutionary history of what was expected to be a simple case study. Instead, our results indicate a history of allopatric divergence, secondary contact, introgression, and endemic hybrid speciation that we hypothesize was driven by the final closure of the Isthmus of Panama and the strengthening of the Gulf Stream Current ~3.5 Ma. The history of this species complex recovered by model-based methods that allow reticulation differs from that recovered by standard phylogenetic analyses and is unexpected given contemporary distributions. The geologically and biologically meaningful insights gained by our model selection analyses illuminate what is likely a novel pathway of species formation not previously documented that resulted from one of the most biogeographically significant events in Earth's history.},
}
@article {pmid39041198,
year = {2024},
author = {McGee, RS and Kinsler, G and Petrov, D and Tikhonov, M},
title = {Improving the Accuracy of Bulk Fitness Assays by Correcting Barcode Processing Biases.},
journal = {Molecular biology and evolution},
volume = {41},
number = {8},
pages = {},
pmid = {39041198},
issn = {1537-1719},
support = {R35 GM118165/GM/NIGMS NIH HHS/United States ; PHY-2310746//National Science Foundation/ ; R35GM118165/NH/NIH HHS/United States ; },
mesh = {*Genetic Fitness ; *DNA Barcoding, Taxonomic/methods ; High-Throughput Nucleotide Sequencing/methods ; Bias ; },
abstract = {Measuring the fitnesses of genetic variants is a fundamental objective in evolutionary biology. A standard approach for measuring microbial fitnesses in bulk involves labeling a library of genetic variants with unique sequence barcodes, competing the labeled strains in batch culture, and using deep sequencing to track changes in the barcode abundances over time. However, idiosyncratic properties of barcodes can induce nonuniform amplification or uneven sequencing coverage that causes some barcodes to be over- or under-represented in samples. This systematic bias can result in erroneous read count trajectories and misestimates of fitness. Here, we develop a computational method, named REBAR (Removing the Effects of Bias through Analysis of Residuals), for inferring the effects of barcode processing bias by leveraging the structure of systematic deviations in the data. We illustrate this approach by applying it to two independent data sets, and demonstrate that this method estimates and corrects for bias more accurately than standard proxies, such as GC-based corrections. REBAR mitigates bias and improves fitness estimates in high-throughput assays without introducing additional complexity to the experimental protocols, with potential applications in a range of experimental evolution and mutation screening contexts.},
}
@article {pmid39041008,
year = {2024},
author = {Allison, PF and Pickich, ET and Barnett, ZC and Garrick, RC},
title = {DNA barcoding is currently unreliable for species identification in most crayfishes.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e70050},
pmid = {39041008},
issn = {2045-7758},
abstract = {DNA barcoding is commonly used for species identification. Despite this, there has not been a comprehensive assessment of the utility of DNA barcoding in crayfishes (Decapoda: Astacidea). Here we examined the extent to which local barcoding gaps (used for species identification) and global barcoding gaps (used for species discovery) exist among crayfishes, and whether global gaps met a previously suggested 10× threshold (mean interspecific difference being 10× larger than mean intra specific difference). We examined barcoding gaps using publicly available mitochondrial COI sequence data from the National Center for Biotechnology Information's nucleotide database. We created two versions of the COI datasets used for downstream analyses: one focused on the number of unique haplotypes (N H) per species, and another that focused on total number of sequences (N S; i.e., including redundant haplotypes) per species. A total of 81 species were included, with 58 species and five genera from the family Cambaridae and 23 species from three genera from the family Parastacidae. Local barcoding gaps were present in only 30 species (20 Cambaridae and 10 Parastacidae species). We detected global barcoding gaps in only four genera (Cambarus, Cherax, Euastacus, and Tenuibranchiurus), which were all below (4.2× to 5.2×) the previously suggested 10× threshold. We propose that a ~5× threshold would be a more appropriate working hypothesis for species discovery. While the N H and N S datasets yielded largely similar results, there were some discrepant inferences. To understand why some species lacked a local barcoding gap, we performed species delimitation analyses for each genus using the N H dataset. These results suggest that current taxonomy in crayfishes may be inadequate for the majority of examined species, and that even species with local barcoding gaps present may be in need of taxonomic revisions. Currently, the utility of DNA barcoding for species identification and discovery in crayfish is quite limited, and caution should be exercised when mitochondrial-based approaches are used in place of taxonomic expertise. Assessment of the evidence for local and global barcoding gaps is important for understanding the reliability of molecular species identification and discovery, but outcomes are dependent on the current state of taxonomy. As this improves (e.g., via resolving species complexes, possibly elevating some subspecies to the species-level status, and redressing specimen misidentifications in natural history and other collections), so too will the utility of DNA barcoding.},
}
@article {pmid39040809,
year = {2024},
author = {Alojayri, G and Al-Quraishy, S and Al-Shaebi, E and Mohammed, OB and Abdel-Gaber, R},
title = {Morphological and genetic identification of the gill monogenean parasite (Diclidophora merlangi) that infects Twobar Seabream Fish (Acanthopagrus bifasciatus) in the Arabian Gulf, Saudi Arabia.},
journal = {Helminthologia},
volume = {61},
number = {2},
pages = {184-193},
pmid = {39040809},
issn = {0440-6605},
abstract = {Ectoparasites, particularly monogeneans, negatively affect fish health and growth. This study identified monogenean parasites in the twobar seabream, Acanthopagrus bifasciatus (Sparidae), inhabited the Arabian Gulf (Saudi Arabia). Following that, forty A. bifasciatus fish samples were visually examined for monogeneans. Parasite species were collected from the gills and then analyzed morphometrically, morphologically, and molecularly using the partial regions of the large subunit of ribosomal RNA (28S rRNA) and mitochondrial cytochrome C oxidase subunit I (COI) genes. Fish species were also identified using a DNA barcoding approach based on the COI gene. The monogenean species of Diclidophora merlangi (Diclidophoridae) were found in 45% of the fish species studied. The generic features of the Diclidophora genus distinguish this species. This species discriminated itself from congeners by having a muscular bulb with 17 grooved and recurved hooks, 218±10 (184-267) post-ovarian testes, and four pairs of pedunculated clamps of relative sizes. Partial 28S rRNA sequencing from monogeneans revealed that they grouped with members of the genus Diclidophora, forming a monophyletic group that supported the morphological descriptions. Molecular identification revealed that D. merlangi has a unique barcode made up of a COI sequence. The host identity was established as A. bifasciatus based on the COI gene sequences. Furthermore, a molecular phylogenetic study was performed to determine the phylogenetic affinity of parasite species and fish hosts. This study on Diclidophora species is considered the first record of this genus in the examined area.},
}
@article {pmid39037657,
year = {2024},
author = {Handly-Santana, A and Oren, Y},
title = {Characterizing Rare Dormant and Cycling Lineages Using the Watermelon System.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2811},
number = {},
pages = {165-175},
pmid = {39037657},
issn = {1940-6029},
mesh = {*Single-Cell Analysis/methods ; *Cell Lineage/genetics ; Humans ; Cell Proliferation/genetics ; Sequence Analysis, RNA/methods ; RNA, Messenger/genetics ; },
abstract = {Barcode-based lineage tracing approaches enable molecular characterization of clonal cell families. Barcodes that are expressed as mRNA can be used to deconvolve lineage identity from single-cell RNA sequencing transcriptional data. Here we describe the Watermelon system, which facilitates the simultaneous tracing of lineage, transcriptional, and proliferative state at a single cell level.},
}
@article {pmid39032368,
year = {2024},
author = {Kwon, YL and Shin, KJ},
title = {Unique molecular identifier-based amplicon sequencing of microhaplotypes for background noise mitigation.},
journal = {Forensic science international. Genetics},
volume = {72},
number = {},
pages = {103096},
doi = {10.1016/j.fsigen.2024.103096},
pmid = {39032368},
issn = {1878-0326},
mesh = {Humans ; *Polymorphism, Single Nucleotide ; *High-Throughput Nucleotide Sequencing ; *Polymerase Chain Reaction ; *Haplotypes ; Sequence Analysis, DNA ; DNA Fingerprinting/methods ; },
abstract = {Microhaplotypes (MHs), comprising two or more single-nucleotide polymorphisms in a short fragment, are promising forensic markers owing to their remarkable polymorphic nature. Several studies have demonstrated the utility of MHs through massively parallel sequencing (MPS). Nevertheless, the background noise level associated with MHs in MPS, which imposes a practical detection limit for the system, remains uninvestigated. Currently, unique molecular identifier (UMI) systems are known to effectively mitigate background noise by tracking original DNA molecules and facilitating PCR and MPS error corrections. Hence, this study aimed to design a UMI-based amplicon sequencing system, designated MH-UMIseq, which can amplify 46 MHs simultaneously and generate MPS libraries in four steps: barcoding PCR, nuclease reaction, boosting PCR, and indexing PCR. The performance of the MH-UMIseq system was evaluated using the Illumina NextSeq 550 and MiniSeq systems with 31 sets for 5 ng, 1 ng, and 200 pg of input DNA. The fgbio toolkit was used in conjunction with STRait Razor 3.0 and Visual Microhap to analyze the UMI data on MHs. The corresponding average not suppressed noise proportion of MH-UMIseq were 0.1 %, 0.3 %, and 0.7 % for 5 ng, 1 ng, and 200 pg of DNA, respectively, which substantially suppressed the background noise for more than 1 ng of DNA. Interestingly, the proportion of not suppressed noise in MH-UMIseq notably decreased as the amount of input DNA increased. The number of UMI families was proportional to the copy number of the template DNA and closely correlated with the system resolution. Therefore, the resolution of MH-UMIseq system is expected to be higher than that of conventional MPS for the deconvolution of mixtures containing more than 1 ng of DNA.},
}
@article {pmid39031987,
year = {2024},
author = {Wang, H and Zhan, Q and Ning, M and Guo, H and Wang, Q and Zhao, J and Bao, P and Xing, S and Chen, S and Zuo, S and Xia, X and Li, M and Wang, P and Lu, ZJ},
title = {Depletion-assisted multiplexed cell-free RNA sequencing reveals distinct human and microbial signatures in plasma versus extracellular vesicles.},
journal = {Clinical and translational medicine},
volume = {14},
number = {7},
pages = {e1760},
pmid = {39031987},
issn = {2001-1326},
support = {32170671//National Natural Science Foundation of China/ ; 82371855//National Natural Science Foundation of China/ ; 82341101//National Natural Science Foundation of China/ ; 81902384//National Natural Science Foundation of China/ ; CFH 2022-2-4075//Capital's Funds for Health Improvement and Research/ ; 2022ZD0117700//National Key Research and Development Plan of China/ ; 2021GQG1020//Tsinghua University Guoqiang Institute/ ; 2022ZLA003//Tsinghua University Initiative Scientific Research Program of Precision Medicine/ ; //Institute of Health and Medicine, Hefei Comprehensive National Science Center/ ; //Bayer Micro-funding/ ; //Bio-Computing Platform of Tsinghua University Branch of China National Center for Protein Sciences/ ; },
mesh = {Humans ; *Extracellular Vesicles/genetics/metabolism ; *Cell-Free Nucleic Acids/blood/analysis/genetics ; *Sequence Analysis, RNA/methods ; },
abstract = {BACKGROUND: Cell-free long RNAs in human plasma and extracellular vesicles (EVs) have shown promise as biomarkers in liquid biopsy, despite their fragmented nature.<br><br>METHODS: To investigate these fragmented cell-free RNAs (cfRNAs), we developed a cost-effective cfRNA sequencing method called DETECTOR-seq (depletion-assisted multiplexed cell-free total RNA sequencing). DETECTOR-seq utilised a meticulously tailored set of customised guide RNAs to remove large amounts of unwanted RNAs (i.e., fragmented ribosomal and mitochondrial RNAs) in human plasma. Early barcoding strategy was implemented to reduce costs and minimise plasma requirements.<br><br>RESULTS: Using DETECTOR-seq, we conducted a comprehensive analysis of cell-free transcriptomes in both whole human plasma and EVs. Our analysis revealed discernible distributions of RNA types in plasma and EVs. Plasma exhibited pronounced enrichment in structured circular RNAs, tRNAs, Y RNAs and viral RNAs, while EVs showed enrichment in messenger RNAs (mRNAs) and signal recognition particle RNAs (srpRNAs). Functional pathway analysis highlighted RNA splicing-related ribonucleoproteins (RNPs) and antimicrobial humoral response genes in plasma, while EVs demonstrated enrichment in transcriptional activity, cell migration and antigen receptor-mediated immune signals. Our study indicates the comparable potential of cfRNAs from whole plasma and EVs in distinguishing cancer patients (i.e., colorectal and lung cancer) from healthy donors. And microbial cfRNAs in plasma showed potential in classifying specific cancer types.<br><br>CONCLUSIONS: Our comprehensive analysis of total and EV cfRNAs in paired plasma samples provides valuable insights for determining the need for EV purification in cfRNA-based studies. We envision the cost effectiveness and efficiency of DETECTOR-seq will empower transcriptome-wide investigations in the fields of cfRNAs and liquid biopsy.<br><br>KEYPOINTS: DETECTOR-seq (depletion-assisted multiplexed cell-free total RNA sequencing) enabled efficient and specific depletion of sequences derived from fragmented ribosomal and mitochondrial RNAs in plasma. Distinct human and microbial cell-free RNA (cfRNA) signatures in whole Plasma versus extracellular vesicles (EVs) were revealed. Both Plasma and EV cfRNAs were capable of distinguishing cancer patients from normal individuals, while microbial RNAs in Plasma cfRNAs enabled better classification of cancer types than EV cfRNAs.},
}
@article {pmid39031978,
year = {2024},
author = {Bañón, R and de Carlos, A and Comesaña, &#xc1;S and Barreiro Vázquez, JD and Baldó, F},
title = {Second world record for Barathronus roulei Nielsen, 2019 (Ophidiiformes, Bythitidae), from the Porcupine Bank (Northeast Atlantic).},
journal = {Journal of fish biology},
volume = {105},
number = {4},
pages = {1348-1353},
doi = {10.1111/jfb.15878},
pmid = {39031978},
issn = {1095-8649},
support = {PORCUDEM-20233FMP001//European Maritime, Fisheries and Aquaculture Fund/ ; },
mesh = {Animals ; *RNA, Ribosomal, 16S/genetics ; *DNA Barcoding, Taxonomic ; *Electron Transport Complex IV/genetics ; Phylogeny ; Eels/genetics/anatomy &amp; histology ; Atlantic Ocean ; },
abstract = {Barathronus is a genus of blind cusk eels comprising 11 valid species. In this paper, we report the second specimen ever documented of Barathronus roulei (Bythitidae) obtained from the Porcupine Bank by R.V. Vizconde de Eza using a bottom trawl at a depth of 1349 m. Morphological description and illustrations, including a radiograph, are provided. In addition, three new sequences corresponding to three different genes, cytochrome c oxidase subunit I (COI)-DNA barcoding, 16S ribosomal RNA (16S), and recombination activating protein 1 (RAG1), have been added to the molecular repositories, representing the first sequences for the species.},
}
@article {pmid39031483,
year = {2024},
author = {Gil, F and Beroiz, B and Ballesteros, I and Horreo, JL},
title = {Can consumers avoid mislabelling? Genetic species identification provides recommendations for shrimp/prawn products.},
journal = {Journal of the science of food and agriculture},
volume = {104},
number = {15},
pages = {9486-9493},
doi = {10.1002/jsfa.13771},
pmid = {39031483},
issn = {1097-0010},
mesh = {Animals ; *Food Labeling ; *Penaeidae/genetics/classification ; Spain ; Shellfish/analysis/economics ; Humans ; Consumer Behavior ; DNA, Mitochondrial/genetics ; Food Contamination/analysis ; },
abstract = {BACKGROUND: Crustaceans of the superfamily Penaeoidea (e.g., shrimps and prawns) are among the most commercially available aquatic products worldwide. However, there are few studies regarding not only the presence but also the characteristics of mislabelling in these food products. Such information would be helpful for consumers in order to avoid the typical problems associated with mislabelling (e.g., health and economic issues). For this reason, this work considers Penaeoidea mislabelling by comparing different products (frozen, fresh, boiled), and sources (hypermarkets, supermarkets and fishmongers) from Spain (Europe).<br><br>RESULTS: A total of 94 samples from 55 different products were collected, representing 19 different species from 13 genera. Mitochondrial DNA (COI gene) was amplified, revealing mislabelling in almost 30% of supermarket products and almost exclusively found in frozen samples (95% of the total) regardless of its price. In addition, products from the Pacific Ocean seem to be particularly susceptible to mislabelling.<br><br>CONCLUSIONS: All in all, recommendations for the consumer in order to avoid mislabelling of prawns include purchasing them fresh from fishmongers; aquaculture products must not be avoided. This study represents, to our knowledge, the first attempt to provide recommendations to consumers based on DNA analyses in order to avoid mislabelling in food products. Further research is therefore required to provide such recommendations in different food products, particularly those that are processed, packaged and/or frozen. &#xa9; 2024 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley &amp; Sons Ltd on behalf of Society of Chemical Industry.},
}
@article {pmid39027082,
year = {2024},
author = {Changbunjong, T and Weluwanarak, T and Laojun, S and Duvallet, G and Chaiphongpachara, T},
title = {Genetic and morphometric differentiation between two morphs of Haematobosca sanguinolenta (Diptera: Muscidae) from Thailand.},
journal = {Current research in parasitology &amp; vector-borne diseases},
volume = {6},
number = {},
pages = {100186},
pmid = {39027082},
issn = {2667-114X},
abstract = {Haematobosca is a genus of biting fly within the subfamily Stomoxyinae of the family Muscidae. It is currently recognized to include 16 species worldwide. These species, acting as ectoparasites, are considered to have significant importance in the veterinary and medical fields. To address the color polymorphism related to the genus Haematobosca in Thailand, herein, we focused on the normal (legs mainly black) and yellow (legs mainly yellow) morphs of Haematobosca sanguinolenta and examined them for genetic differences using three molecular markers: the cytochrome c oxidase subunit 1 (cox1) and cytochrome b (cytb) genes from the mitochondrial genome as well as the internal transcribed spacer 2 (ITS2) region from the nuclear ribosomal DNA. In addition, we analyzed wing differences between the two morphs using geometric morphometrics (GM). The genetic divergences between the two morphs showed that cytb gene showed the greatest divergence, for which the average distance was 5.6%. This was followed by the combination of cox1-cytb-ITS2, exhibiting an average divergence of 4.5%, ITS2 with a divergence of 4.1%, and finally cox1, showing the lowest divergence of 3.5%. Phylogenetic analyses distinctly separated the two morphs of H. sanguinolenta; this separation was supported by high bootstrap values (97-100%). These results were further corroborated by three species delimitation methods, i.e. assemble species by automatic partitioning (ASAP), automated barcode gap discovery (ABGD), and Poisson tree processes (PTP), all of which suggested that the two morphs likely represent separate species. In addition, a GM study identified a statistically significant difference in wing shape between the two morphs of H. sanguinolenta (P < 0.05). This combination of genetic and morphometric results strongly supports the existence of two distinct species within H. sanguinolenta in Thailand.},
}
@article {pmid39027045,
year = {2024},
author = {Götz, TI and Cong, X and Rauber, S and Angeli, M and Lang, EW and Ramming, A and Schmidkonz, C},
title = {A novel Slide-seq based image processing software to identify gene expression at the single cell level.},
journal = {Journal of pathology informatics},
volume = {15},
number = {},
pages = {100384},
pmid = {39027045},
issn = {2229-5089},
abstract = {Analysis of gene expression at the single-cell level could help predict the effectiveness of therapies in the field of chronic inflammatory diseases such as arthritis. Here, we demonstrate an adopted approach for processing images from the Slide-seq method. Using a puck, which consists of about 50,000 DNA barcode beads, an RNA sequence of a cell is to be read. The pucks are repeatedly brought into contact with liquids and then recorded with a conventional epifluorescence microscope. The image analysis initially consists of stitching the partial images of a sequence recording, registering images from different sequences, and finally reading out the bases. The new method enables the use of an inexpensive epifluorescence microscope instead of a confocal microscope.},
}
@article {pmid39026955,
year = {2024},
author = {Worth, JRP and Kikuchi, S and Kanetani, S and Takahashi, D and Aizawa, M and Marchuk, EA and Choi, HJ and Polezhaeva, MA and Sheiko, VV and Ueno, S},
title = {Chloroplast genome-based genetic resources via genome skimming for the subalpine forests of Japan and adjacent regions.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e11584},
pmid = {39026955},
issn = {2045-7758},
abstract = {The Japanese subalpine zone is dominated by an ecologically important forest biome, subalpine coniferous forest, constituting a distinct assemblage of cold-tolerant angiosperm and conifer species. While being relatively intact compared to other forest biomes in Japan, subalpine coniferous forests are under significant threat from deer browsing, global warming and small population size effects. However, there is a severe lack of genetic resources available for this biome's major constituent plant species. This study aimed to develop chloroplast genome-based genetic resources for 12 widespread subalpine tree and shrub species (7 angiosperms and 5 conifers) via genome skimming of whole-genomic DNA using short reads (100-150 bp in length). For 10 species, whole chloroplast genomes were assembled via de novo-based methods from 4 to 10 individuals per species sampled from across their ranges in Japan and, for non-Japanese endemic species, elsewhere in northeast Asia. A total of 566 single nucleotide polymorphisms for Japanese samples and 768 for all samples (varying from 2 to 202 per species) were identified which were distributed in geographically restricted lineages in most species. In addition, between 9 and 58 polymorphic simple sequence repeat regions were identified per species. For two Ericaceae species (Rhododendron brachycarpum and Vaccinium vitis-idaea) characterised by large chloroplast genomes, de novo assembly failed, but single nucleotide polymorphisms could be identified using reference mapping. These data will be useful for genetic studies of species taxonomic relationships, investigating phylogeographic patterns within species, developing chloroplast-based markers for conservation genetic studies and has potential application for studies of environmental and ancient DNA.},
}
@article {pmid39026715,
year = {2024},
author = {Chamberlin, JT and Gillen, AE and Quinlan, AR},
title = {Improved characterization of single-cell RNA-seq libraries with paired-end avidity sequencing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39026715},
issn = {2692-8205},
support = {S10 OD021644/OD/NIH HHS/United States ; T15 LM007124/LM/NLM NIH HHS/United States ; },
abstract = {Prevailing poly(dT)-primed 3' single-cell RNA-seq protocols generate barcoded cDNA fragments containing the reverse transcriptase priming site, which is expected to be the poly(A) tail or a genomic adenine homopolymer. Direct sequencing across this priming site was historically difficult because of DNA sequencing errors induced by the homopolymeric primer at the 'barcode' end. Here, we evaluate the capability of "avidity base chemistry" DNA sequencing from Element Biosciences to sequence through this homopolymer accurately, and the impact of the additional cDNA sequence on read alignment and precise quantification of polyadenylation site usage. We find that the Element Aviti instrument sequences through the thymine homopolymer into the subsequent cDNA sequence without detectable loss of accuracy. The resulting paired-end alignments enable direct and independent assignment of reads to polyadenylation sites, which bypasses complexities and limitations of conventional approaches but does not consistently improve read mapping rates compared to single-end alignment. We also characterize low-level artifacts and arrive at an adjusted adapter trimming and alignment workflow that significantly improves the alignment of sequence data from Element and Illumina, particularly in the context of extended read lengths. Our analyses confirm that Element avidity sequencing is an effective alternative to Illumina sequencing for standard single-cell RNA-seq, particularly for polyadenylation site analyses but do not rule out the potential for similar performance from other emerging platforms.},
}
@article {pmid39024335,
year = {2024},
author = {Gul, A and Shah, SHJ and Faris, S and Qazi, J and Qazi, A and Dey, SK},
title = {An analysis of morphological and genetic diversity of mango fruit flies in Pakistan.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0304472},
pmid = {39024335},
issn = {1932-6203},
mesh = {Animals ; *Tephritidae/genetics/classification ; Pakistan ; *Mangifera/parasitology/genetics ; *Genetic Variation ; *DNA Barcoding, Taxonomic ; *Electron Transport Complex IV/genetics ; Phylogeny ; },
abstract = {Fruit flies of genus Bactrocera are important insect pests of commercially cultivated mangos in Pakistan limiting its successful production in the country. Despite the economic risk, the genetic diversity and population dynamics of this pest have remained unexplored. This study aimed to morphologically identify Bactrocera species infesting Mango in major production areas of the country and to confirm the results with insect DNA barcode techniques. Infested mango fruits from the crop of 2022, were collected from 46 locations of 11major production districts of Punjab and Sindh provinces, and first-generation flies were obtained in the laboratory. All 10,653 first generation flies were morphologically identified as two species of Bactrocera; dorsalis and zonata showing geography-based relative abundance in the two provinces; Punjab and Sindh. Morphological identification was confirmed by mitochondrial cytochrome oxidase gene subunit I (mt-COI) based DNA barcoding. Genetic analysis of mtCOI gene region of 61 selected specimens by the presence of two definite clusters and reliable intraspecific distances validated the results of morphological identification. This study by morphological identification of a large number of fruit fly specimens from the fields across Pakistan validated by insect DNA barcode reports two species of Bactrocera infesting mango in the country.},
}
@article {pmid39023176,
year = {2024},
author = {Zhang, LJ and Liu, Y and Wang, YL and Xie, LL and Wang, XY and Ma, YS},
title = {Population genetic diversity and structure of Tephritis angustipennis and Campiglossa loewiana (Diptera: Tephritidae) based on COI DNA barcodes in the three-river source region, China.},
journal = {Journal of insect science (Online)},
volume = {24},
number = {4},
pages = {},
pmid = {39023176},
issn = {1536-2442},
support = {2024-SF-101//Qinghai Science and Technology Department/ ; },
mesh = {Animals ; *Tephritidae/genetics ; China ; *Electron Transport Complex IV/genetics ; *Genetic Variation ; *DNA Barcoding, Taxonomic ; Haplotypes ; Phylogeny ; Insect Proteins/genetics ; },
abstract = {Tephritis angustipennis (Diptera: Tephritidae) and Campiglossa loewiana (Diptera: Tephritidae) are phytophagous pests in China. Their damage has significantly impacted the collection and cultivation of germplasm resources of native Asteraceae plants. However, the genetic characteristics and structure of their population are unclear. This study focused on the highly damaging species of T. angustipennis and C. loewiana collected from the three-river source region (TRSR). We amplified the mitochondrial cytochrome C oxidase subunit I (mtCOI) gene sequences of these pests collected from this area and compared them with COI sequences from GenBank. We also analyzed their genetic diversity and structure. In T. angustipennis, 5 haplotypes were identified from 5 geographic locations; the genetic differentiation between France population FRPY (from Nylandia, Uusimaa) and China populations GLJZ (from Dehe Longwa Village, Maqin County), GLDR (from Zhique Village, Dari County), and GLMQ (from Rijin Village, Maqin County) was the strongest. GLJZ exhibited strong genetic differentiation from GLDR and GLMQ, with relatively low gene flow. For C. loewiana, 11 haplotypes were identified from 5 geographic locations; the genetic differentiation between the Chinese population GLMQ-YY (from Yangyu Forest Farm, Maqin County) and Finnish population FDNL (from Nylandia, Uusimaa) was the strongest, with relatively low gene flow, possibly due to geographical barriers in the Qinghai-Tibet plateau. Only 1 haplotype was identified across GLDR, GLMQ, and GLBM. High gene flow between distant locations indicates that human activities or wind dispersal may facilitate the dispersal of fruit flies and across different geographic. Geostatistical analysis suggested a recent population expansion of these 2 species in TRSR. Our findings provide technical references for identifying pests in the TRSR region and theoretical support for managing resistance, monitoring pest occurrences, analyzing environmental adaptability, and formulating biological control strategies for Tephritidae pests on Asteraceae plants.},
}
@article {pmid39020177,
year = {2024},
author = {Chen, W and Choi, J and Li, X and Nathans, JF and Martin, B and Yang, W and Hamazaki, N and Qiu, C and Lalanne, JB and Regalado, S and Kim, H and Agarwal, V and Nichols, E and Leith, A and Lee, C and Shendure, J},
title = {Symbolic recording of signalling and cis-regulatory element activity to DNA.},
journal = {Nature},
volume = {632},
number = {8027},
pages = {1073-1081},
pmid = {39020177},
issn = {1476-4687},
support = {R01 HG010632/HG/NHGRI NIH HHS/United States ; UM1 HG011586/HG/NHGRI NIH HHS/United States ; F31 HG011576/HG/NHGRI NIH HHS/United States ; K99 HG012973/HG/NHGRI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Mice ; Cell Differentiation/genetics ; *DNA/genetics/metabolism ; Enhancer Elements, Genetic/genetics ; *Gene Editing/methods ; Genomics ; Mouse Embryonic Stem Cells/cytology ; NF-kappa B/metabolism ; Reproducibility of Results ; RNA, Guide, CRISPR-Cas Systems/genetics/metabolism ; *Signal Transduction/genetics ; Time Factors ; Transcription Factors/metabolism ; *Transcription, Genetic/genetics ; Wnt Signaling Pathway/genetics ; Nucleotide Motifs ; Consensus Sequence/genetics ; Developmental Biology ; Proof of Concept Study ; },
abstract = {Measurements of gene expression or signal transduction activity are conventionally performed using methods that require either the destruction or live imaging of a biological sample within the timeframe of interest. Here we demonstrate an alternative paradigm in which such biological activities are stably recorded to the genome. Enhancer-driven genomic recording of transcriptional activity in multiplex (ENGRAM) is based on the signal-dependent production of prime editing guide RNAs that mediate the insertion of signal-specific barcodes (symbols) into a genomically encoded recording unit. We show how this strategy can be used for multiplex recording of the cell-type-specific activities of dozens to hundreds of cis-regulatory elements with high fidelity, sensitivity and reproducibility. Leveraging signal transduction pathway-responsive cis-regulatory elements, we also demonstrate time- and concentration-dependent genomic recording of WNT, NF-κB and Tet-On activities. By coupling ENGRAM to sequential genome editing via DNA Typewriter[1], we stably record information about the temporal dynamics of two orthogonal signalling pathways to genomic DNA. Finally we apply ENGRAM to integratively record the transient activity of nearly 100 transcription factor consensus motifs across daily windows spanning the differentiation of mouse embryonic stem cells into gastruloids, an in vitro model of early mammalian development. Although these are proof-of-concept experiments and much work remains to fully realize the possibilities, the symbolic recording of biological signals or states within cells, to the genome and over time, has broad potential to complement contemporary paradigms for how we make measurements in biological systems.},
}
@article {pmid39018572,
year = {2024},
author = {Khumalo, N and Chaisi, M and Magoro, R and Mwale, M},
title = {An analysis of the gaps in the South African DNA barcoding library of ticks of veterinary and public health importance.},
journal = {Genome},
volume = {67},
number = {11},
pages = {392-402},
doi = {10.1139/gen-2024-0052},
pmid = {39018572},
issn = {1480-3321},
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; South Africa ; *Ticks/genetics/classification ; *Biodiversity ; Public Health ; Phylogeny ; },
abstract = {Ticks transmit pathogens of veterinary and public health importance. Understanding their diversity is critical as infestations lead to significant economic losses globally. To date, over 90 species across three families have been identified in South Africa. However, the taxonomy of most species has not been resolved due to morphological identification challenges. DNA barcoding through the Barcode of Life Data Systems (BOLD) is therefore a valuable tool for species verifications for biodiversity assessments. This study conducted an analysis of South African tick COI barcodes on BOLD by verifying species on checklists, literature, and other sequence databases. The compiled list represented 97 species, including indigenous (59), endemics (27), introduced (2), invasives (1), and eight that could not be classified. Analyses indicated that 31 species (32%) from 11 genera have verified COI barcodes. These are distributed across all nine provinces with the Eastern Cape having the highest species diversity, followed by Limpopo, with KwaZulu-Natal having the least diversity. Rhipicephalus, Hyalomma, and Argas species had multiple barcode index numbers, suggesting cryptic diversity or unresolved taxonomy. We identified 21 species of veterinary or zoonotic importance from the Argasidae and Ixodidae families that should be prioritised for barcoding. Coordinating studies and defining barcoding targets is necessary to ensure that tick checklists are updated to support decision-making for the control of vector-borne diseases and alien invasives.},
}
@article {pmid39018344,
year = {2024},
author = {Todisco, V and Basu, DN and Prosser, SWJ and Russell, S and Mutanen, M and Zilli, A and Huertas, B and Kunte, K and Vane-Wright, R},
title = {DNA barcodes from over-a-century-old type specimens shed light on the taxonomy of a group of rare butterflies (Lepidoptera: Nymphalidae: Calinaginae).},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0305825},
pmid = {39018344},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Butterflies/genetics/classification/anatomy &amp; histology ; *Phylogeny ; Wings, Animal/anatomy &amp; histology ; Electron Transport Complex IV/genetics ; },
abstract = {We analyzed COI barcode sequences from 138 over-a-century old specimens of Calinaga including 36 name-bearing type specimens stored at the Natural History Museum London. These new data, combined with previously available RPS5 sequences, divide the Calinaga samples into four well-supported mitochondrial lineages that together with a novel wing-pattern analysis, support the recognition of six species (lhatso, buddha, brahma, aborica, formosana and davidis), with all other names subsumed either as subspecies or synonyms. One new taxon is described, Calinaga aborica naima Vane-Wright, ssp. n.},
}
@article {pmid39018276,
year = {2024},
author = {de Almeida, LH and Gonçalves, MC and da Conceição Bispo, P},
title = {An integrative approach to the study of Kempnyia Klapálek, 1914 (Plecoptera: Perlidae) from Brazil: Support for the description of four new species and a basis for future studies.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0305824},
pmid = {39018276},
issn = {1932-6203},
mesh = {Animals ; Brazil ; *Phylogeny ; Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; Bayes Theorem ; Insecta/classification/genetics/anatomy &amp; histology ; Neoptera/genetics/classification/anatomy &amp; histology ; Species Specificity ; Female ; },
abstract = {Kempnyia (Plecoptera: Perlidae) is an endemic genus of Brazilian stoneflies that has 36 valid species and is distributed primarily in the Atlantic Forest and the mountainous areas of Central Brazil, particularly in Goiás and Tocantins states. Despite being the Brazilian genus with the most DNA sequences available on GenBank, integrative studies on the genus began only recently, in 2014. In this context, herein we studied the morphology and molecular data of Kempnyia specimens deposited in the Aquatic Biology Laboratory (UNESP, Assis) and the Entomology Museum of the Federal University of Viçosa (UFVB, Viçosa) collections. For the integrative approach adopted, in addition to studying the specimens morphologically, we used sequences of the COI mitochondrial gene combined with the following species delimitation methods: Automatic Barcode Gap Discovery (ABGD), both primary (ABGDp) and recursive (ABGDr) partitions; Assemble Species by Automatic Partitioning (ASAP); Poisson Tree Processes (PTP) and the Bayesian implementation of the Poisson Tree Processes (bPTP). As a result, we provided 28 new COI sequences of 21 species and support the description of four new species, namely, K. guarani sp. nov., K. tupiniquim sp. nov., K. una sp. nov., and K. zwickii sp. nov., consequently increasing the known diversity of the genus to 40 species. We also discuss the morphological variations observed in other species of the genus and provide several new geographic records. Therefore, our study brings new insights into the values of intra- and interspecific molecular divergence within Kempnyia, serving as a basis for new studies.},
}
@article {pmid39015799,
year = {2024},
author = {Xiaoqi, M and Zhang, T and Wang, C},
title = {Description of two species of the orb-weaver spider genus Argiope Audouin, 1826 (Araneae, Araneidae) from Xizang, China.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e125601},
pmid = {39015799},
issn = {1314-2828},
abstract = {BACKGROUND: The spider genus Argiope Audouin, 1826, comprises 88 species worldwide, including 23 species occurring in China. Two Argiope species were collected by the spider survey on Yarlung Zangbo Grand Canyon National Nature Reserve, Xizang, southwest China, conducted in 2023.<br><br>NEW INFORMATION: Two species of the orb-weaver spider genus Argiope from Xizang, China are described, including a new species, A.beibeng Mi &amp; Wang, sp. nov. (&#x2642;&#x2640;) and a known species, A.caesarea Thorell, 1897 (&#x2642;&#x2640;). The unknown male of A.caesarea is described for the first time.},
}
@article {pmid39015529,
year = {2024},
author = {Lee, S and Hwang, S and Lee, M and Seung, J and Choi, W and Bai, M},
title = {DNA barcoding reveals a taxonomic fraud: Note on validity of Propomacrusmuramotoae (Coleoptera, Scarabaeidae).},
journal = {ZooKeys},
volume = {1206},
number = {},
pages = {181-190},
pmid = {39015529},
issn = {1313-2989},
abstract = {Until the early 2000s, the genus Propomacrus was known to comprise two species, occurring in the Eastern Mediterranean and Southeast China. The discovery of Propomacrusmuramotoae Fujioka in Tibet and subsequently in Bhutan and Nepal, might play a crucial role in bridging the geographical distribution gap of the Euchirini tribe between the Mediterranean and Central China, offering profound insights into its evolution and biogeography. However, all specimens, including the holotype specimen, were sourced from a single insect vendor, with no further specimens found or catalogued in museum collections thereafter. During our examination of a P.muramotoae specimen from a private collection in South Korea, we found its COI gene sequence to be identical to that of P.bimucronatus (Pallas) from Turkey, a species known for its wide distribution and genetic variability across regional populations. This overlap in genetic identity raised significant doubts, further compounded by our detection of deliberate modifications in essential diagnostic features during morphological examination. All three specimens we examined showed crude modifications, including staining and artificial grinding. Despite our inability to access the P.muramotoae type specimens for direct examination-a challenge we attempted to overcome through various means-it is evident that significant fraudulent tampering has occurred with the P.muramotoae specimens. Therefore, a new synonymy is proposed: Propomacrusbimucronatus Pallas, 1781 = P.muramotoae Fujioka, 2007 (syn. nov.). We also advocate for a straightforward verification of the type specimen through molecular analysis of the COI barcode region and morphological re-examination under a microscope for those who have access to the type specimens.},
}
@article {pmid39014300,
year = {2024},
author = {Darabi, A and Sobhani, S and Aghdam, R and Eslahchi, C},
title = {AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {241},
pmid = {39014300},
issn = {1471-2105},
mesh = {*Metagenomics/methods ; *Algorithms ; Nucleotides/genetics ; High-Throughput Nucleotide Sequencing/methods ; Software ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Cluster Analysis ; Contig Mapping/methods ; Metagenome/genetics ; },
abstract = {BACKGROUND: Using next-generation sequencing technologies, scientists can sequence complex microbial communities directly from the environment. Significant insights into the structure, diversity, and ecology of microbial communities have resulted from the study of metagenomics. The assembly of reads into longer contigs, which are then binned into groups of contigs that correspond to different species in the metagenomic sample, is a crucial step in the analysis of metagenomics. It is necessary to organize these contigs into operational taxonomic units (OTUs) for further taxonomic profiling and functional analysis. For binning, which is synonymous with the clustering of OTUs, the tetra-nucleotide frequency (TNF) is typically utilized as a compositional feature for each OTU.<br><br>RESULTS: In this paper, we present AFIT, a new l-mer statistic vector for each contig, and AFITBin, a novel method for metagenomic binning based on AFIT and a matrix factorization method. To evaluate the performance of the AFIT vector, the t-SNE algorithm is used to compare species clustering based on AFIT and TNF information. In addition, the efficacy of AFITBin is demonstrated on both simulated and real datasets in comparison to state-of-the-art binning methods such as MetaBAT 2, MaxBin 2.0, CONCOT, MetaCon, SolidBin, BusyBee Web, and MetaBinner. To further analyze the performance of the purposed AFIT vector, we compare the barcodes of the AFIT vector and the TNF vector.<br><br>CONCLUSION: The results demonstrate that AFITBin shows superior performance in taxonomic identification compared to existing methods, leveraging the AFIT vector for improved results in metagenomic binning. This approach holds promise for advancing the analysis of metagenomic data, providing more reliable insights into microbial community composition and function.<br><br>AVAILABILITY: A python package is available at: https://github.com/SayehSobhani/AFITBin .},
}
@article {pmid39012608,
year = {2024},
author = {Albrecht, C and Bashtrykov, P and Jeltsch, A},
title = {Amplicon-Based Bisulfite Conversion-NGS DNA Methylation Analysis Protocol.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2842},
number = {},
pages = {405-418},
pmid = {39012608},
issn = {1940-6029},
mesh = {*DNA Methylation ; *Sulfites/chemistry ; *High-Throughput Nucleotide Sequencing/methods ; *Polymerase Chain Reaction/methods ; Humans ; DNA/genetics ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Epigenesis, Genetic ; Epigenomics/methods ; },
abstract = {DNA methylation is an important epigenetic modification that regulates chromatin structure and the cell-type-specific expression of genes. The association of aberrant DNA methylation with many diseases, as well as the increasing interest in modifying the methylation mark in a directed manner at genomic sites using epigenome editing for research and therapeutic purposes, increases the need for easy and efficient DNA methylation analysis methods. The standard approach to analyze DNA methylation with a single-cytosine resolution is bisulfite conversion of DNA followed by next-generation sequencing (NGS). In this chapter, we describe a robust, powerful, and cost-efficient protocol for the amplification of target regions from bisulfite-converted DNA, followed by a second PCR step to generate libraries for Illumina NGS. In the two consecutive PCR steps, first, barcodes are added to individual amplicons, and in the second PCR, indices and Illumina adapters are added to the samples. Finally, we describe a detailed bioinformatics approach to extract DNA methylation levels of the target regions from the sequencing data. Combining barcodes with indices enables a high level of multiplexing allowing to sequence multiple pooled samples in the same sequencing run. Therefore, this method is a robust, accurate, quantitative, and cheap approach for the readout of DNA methylation patterns at defined genomic regions.},
}
@article {pmid39011841,
year = {2024},
author = {Berteloot, OH and Peusens, G and Beliën, T and De Clercq, P and Van Leeuwen, T},
title = {Unveiling the diet of two generalist stink bugs, Halyomorpha halys and Pentatoma rufipes (Hemiptera: Pentatomidae), through metabarcoding of the ITS2 region from gut content.},
journal = {Pest management science},
volume = {80},
number = {11},
pages = {5694-5705},
doi = {10.1002/ps.8287},
pmid = {39011841},
issn = {1526-4998},
support = {LA-traject HBC.2018.2224//VLAIO (Flanders Innovation and Entrepreneurship)/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Heteroptera/physiology ; *Diet ; Gastrointestinal Contents ; Herbivory ; },
abstract = {BACKGROUND: The use of DNA metabarcoding has become an increasingly popular technique to infer feeding relationships in polyphagous herbivores and predators. Understanding host plant preference of native and invasive herbivore insects can be helpful in establishing effective integrated pest management (IPM) strategies. The invasive Halyomorpha halys and native Pentatoma rufipes are piercing-sucking stink bug pests that are known to cause economic damage in commercial fruit orchards.<br><br>RESULTS: In this study, we performed molecular gut content analysis (MGCA) on field-collected specimens of these two herbivorous pentatomids using next-generation amplicon sequencing (NGAS) of the internal transcribed spacer 2 (ITS2) barcode region. Additionally, a laboratory experiment was set up where H.&#x2009;halys was switched from a mixed diet to a monotypic diet, allowing us to determine the detectability of the initial diet in a time series of &#x2264;3&#x2009;days after the diet switch. We detected 68 unique plant species from 54 genera in the diet of two stink bug species, with fewer genera found per sample and a smaller diet breadth for P.&#x2009;rufipes than for H.&#x2009;halys. Both stink bug species generally prefer deciduous trees over gymnosperms and herbaceous plants. Landscape type significantly impacted the observed genera in the diet of both stink bug species, whereas season only had a significant effect on the diet of H.&#x2009;halys.<br><br>CONCLUSION: This study provides further insights into the dietary composition of two polyphagous pentatomid pests and illustrates that metabarcoding can deliver a relevant species-level resolution of host plant preference. &#xa9; 2024 Society of Chemical Industry.},
}
@article {pmid39008212,
year = {2024},
author = {Wengrat, APGS and Carvalho, LC and Pietrowski, V and Schoeninger, K and Costa, VA and Johnson, NF},
title = {First Record of Telenomus dilophonotae (Hymenoptera, Scelionidae), Parasitizing Eggs of Erinnyis ello (Lepidoptera, Sphingidae) in Western Paraná, Brazil, with Molecular Characterization and Records of Occurrences.},
journal = {Neotropical entomology},
volume = {53},
number = {5},
pages = {1162-1167},
pmid = {39008212},
issn = {1678-8052},
support = {152666/2022-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2020/16051-7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/50334-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2018/18965-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 65562/2014-0//Instituto Nacional de Ci&#xea;ncia e Tecnologia de Hymenoptera Parasitoides/ ; 2018/02317-5//S&#xe3;o Paulo Advanced Research Center for Biological Control/ ; },
mesh = {Animals ; Brazil ; *Wasps/classification ; *Ovum/parasitology ; Lepidoptera/parasitology ; DNA Barcoding, Taxonomic ; Female ; Manihot/parasitology ; Hymenoptera/classification ; Hevea/parasitology ; },
abstract = {There are few records for Telenomus dilophonotae Cameron, 1913 (Hymenoptera, Scelionidae) from South America. In Brazil, the first occurrence was reported in Bahia in rubber crops, Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell. - Arg., there parasitizing eggs of Erinnyis ello Linnaeus, 1758 (Lepidoptera, Sphingidae). It was also found parasitizing the same host in cassava, Manihot esculenta Crantz (Euphorbiaceae). This is the first record of occurrence of T. dilophonotae in the state of Paraná, parasitizing eggs of E. ello in areas of cassava production in the western region of Paraná, this being the southernmost record of the species. Here, photographs, the first sequence of DNA barcode of this species of parasitoid wasp, and a distribution map are provided.},
}
@article {pmid39007612,
year = {2024},
author = {Bomidi, C and Zeng, XL and Poplaski, V and Coarfa, C and Estes, MK and Blutt, SE},
title = {Using Human Intestinal Organoids to Understand the Small Intestine Epithelium at the Single Cell Transcriptional Level.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {208},
pages = {},
doi = {10.3791/66749},
pmid = {39007612},
issn = {1940-087X},
support = {U19 AI144297/AI/NIAID NIH HHS/United States ; U19 AI116497/AI/NIAID NIH HHS/United States ; P01 AI057788/AI/NIAID NIH HHS/United States ; U01 DK103168/DK/NIDDK NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Organoids/cytology/metabolism ; *Intestine, Small/cytology/metabolism ; *Single-Cell Analysis/methods ; *Intestinal Mucosa/cytology/metabolism ; Gene Expression Profiling/methods ; Transcriptome/genetics ; },
abstract = {Single cell transcriptomics has revolutionized our understanding of the cell biology of the human body. State-of-the-art human small intestinal organoid cultures provide ex vivo model systems that bridge the gap between animal models and clinical studies. The application of single cell transcriptomics to human intestinal organoid (HIO) models is revealing previously unrecognized cell biology, biochemistry, and physiology of the GI tract. The advanced single cell transcriptomics platforms use microfluidic partitioning and barcoding to generate cDNA libraries. These barcoded cDNAs can be easily sequenced by next generation sequencing platforms and used by various visualization tools to generate maps. Here, we describe methods to culture and differentiate human small intestinal HIOs in different formats and procedures for isolating viable cells from these formats that are suitable for use in single-cell transcriptional profiling platforms. These protocols and procedures facilitate the use of small intestinal HIOs to obtain an increased understanding of the cellular response of human intestinal epithelium at the transcriptional level in the context of a variety of different environments.},
}
@article {pmid39006907,
year = {2024},
author = {Kantelinen, A and Svensson, M and Malíček, J and Vondrák, J and Thor, G and Palice, Z and Svoboda, S and Myllys, L},
title = {A phylogenetic study of Micareamelaeniza and similar-looking species (Pilocarpaceae) unveils hidden diversity and clarifies species boundaries and reproduction modes.},
journal = {MycoKeys},
volume = {106},
number = {},
pages = {327-354},
pmid = {39006907},
issn = {1314-4049},
abstract = {Micarea (Ascomycota, Pilocarpaceae) is a large cosmopolitan genus of crustose lichens. We investigated molecular systematics and taxonomy of the poorly known Micareamelaeniza group focussing on M.melaeniza, M.nigella and M.osloensis. A total of 54 new sequences were generated and using Bayesian and maximum likelihood analysis of two markers (nuITS and mtSSU), we discovered two previously unrecognized phylogenetic lineages, one of which is described here as Micareaeurasiatica Kantelinen &amp; G. Thor, sp. nov., morphologically characterized by pycnidia that are sessile to emergent, cylindrically shaped, with greenish-black K+ olive green, wall pigmentation and containing large mesoconidia up to 6 µm in length. The species is known from Japan and Finland. In addition, we show that the reproduction biology of M.osloensis has been poorly understood and that the species often occurs as an anamorph with stipitate pycnidia. We present a species synopsis and notes on pigments. Our research supports previous results of asexuality being an important reproductive strategy of species growing on dead wood.},
}
@article {pmid39005645,
year = {2024},
author = {Wattanasatja, V and Phisutrattanaporn, J and Doenphai, N and Sirinual, S and Kanjanabuch, T},
title = {Peritoneal dialysis-associated peritonitis due to infected umbilicus.},
journal = {Medical mycology case reports},
volume = {45},
number = {},
pages = {100654},
pmid = {39005645},
issn = {2211-7539},
abstract = {We provide the first case report of peritoneal dialysis (PD)-associated peritonitis due to Lasiodiplodia theobromae, a known plant pathogen causing rotting and dieback in post-harvest citrus fruit, in immunocompetent patient with fungal colonization inside the PD catheter lumen. A root cause analysis suspected the patient's umbilical infection as the source of contamination. The fungal infection was established through microscopic examination of the PD catheter lumen and galactomannan testing in both serum and effluent. The species of pathogen was confirmed by DNA barcoding. The patient responded well to timely PD catheter removal and a 2-week course of oral voriconazole. Preventive strategies should prioritize hygiene practices, including umbilical care, to mitigate the risk of contamination and subsequent infections of fungal pathogens.},
}
@article {pmid39000014,
year = {2024},
author = {Kartavtsev, YP and Masalkova, NA},
title = {Structure, Evolution, and Mitochondrial Genome Analysis of Mussel Species (Bivalvia, Mytilidae).},
journal = {International journal of molecular sciences},
volume = {25},
number = {13},
pages = {},
pmid = {39000014},
issn = {1422-0067},
mesh = {Animals ; *Genome, Mitochondrial/genetics ; *Phylogeny ; *Evolution, Molecular ; Mytilidae/genetics/classification ; RNA, Transfer/genetics ; Bivalvia/genetics/classification ; Mytilus/genetics/classification ; },
abstract = {Based on the nucleotide sequences of the mitochondrial genome (mitogenome) of specimens taken from two mussel species (Arcuatula senhousia and Mytilus coruscus), an investigation was performed by means of the complex approaches of the genomics, molecular phylogenetics, and evolutionary genetics. The mitogenome structure of studied mussels, like in many other invertebrates, appears to be much more variable than in vertebrates and includes changing gene order, duplications, and deletions, which were most frequent for tRNA genes; the mussel species' mitogenomes also have variable sizes. The results demonstrate some of the very important properties of protein polypeptides, such as hydrophobicity and its determination by the purine and pyrimidine nucleotide ratio. This fact might indirectly indicate the necessity of purifying natural selection for the support of polypeptide functionality. However, in accordance with the widely accepted and logical concept of natural cutoff selection for organisms living in nature, which explains its action against deleterious nucleotide substitutions in the nonsynonymous codons (mutations) and its holding of the active (effective) macromolecules of the polypeptides in a population, we were unable to get unambiguous evidence in favor of this concept in the current paper. Here, the phylogeny and systematics of mussel species from one of the largest taxons of bivalve mollusks are studied, the family known as Mytilidae. The phylogeny for Mytilidae (order Mytilida), which currently has no consensus in terms of systematics, is reconstructed using a data matrix of 26-27 mitogenomes. Initially, a set of 100 sequences from GenBank were downloaded and checked for their gender: whether they were female (F) or male (M) in origin. Our analysis of the new data confirms the known drastic differences between the F/M mitogenome lines in mussels. Phylogenetic reconstructions of the F-lines were performed using the combined set of genetic markers, reconstructing only protein-coding genes (PCGs), only rRNA + tRNA genes, and all genes. Additionally, the analysis includes the usage of nucleotide sequences composed of other data matrices, such as 20-68 mitogenome sequences. The time of divergence from MRCA, estimated via BEAST2, for Mytilidae is close to 293 Mya, suggesting that they originate in the Silurian Period. From all these data, a consensus for the phylogeny of the subfamily of Mytilinae and its systematics is suggested. In particular, the long-debated argument on mussel systematics was resolved as to whether Mytilidae, and the subfamily of Mytilinae, are monophyletic. The topology signal, which was strongly resolved in this paper and in the literature, has refuted the theory regarding the monophyly of Mytilinae.},
}
@article {pmid38997781,
year = {2024},
author = {Jiang, K and Liu, T and Kales, S and Tewhey, R and Kim, D and Park, Y and Jarvis, JN},
title = {A systematic strategy for identifying causal single nucleotide polymorphisms and their target genes on Juvenile arthritis risk haplotypes.},
journal = {BMC medical genomics},
volume = {17},
number = {1},
pages = {185},
pmid = {38997781},
issn = {1755-8794},
support = {UL1 TR001412/TR/NCATS NIH HHS/United States ; UL1TR001412/TR/NCATS NIH HHS/United States ; R21 AR076948/AR/NIAMS NIH HHS/United States ; R21-AR071878//National Institutes of Health (USA)/ ; R21 AR071878/AR/NIAMS NIH HHS/United States ; R21 AR076948/NH/NIH HHS/United States ; },
mesh = {Humans ; *Polymorphism, Single Nucleotide ; *Haplotypes ; *Arthritis, Juvenile/genetics ; K562 Cells ; *Genetic Predisposition to Disease ; Genome-Wide Association Study ; },
abstract = {BACKGROUND: Although genome-wide association studies (GWAS) have identified multiple regions conferring genetic risk for juvenile idiopathic arthritis (JIA), we are still faced with the task of identifying the single nucleotide polymorphisms (SNPs) on the disease haplotypes that exert the biological effects that confer risk. Until we identify the risk-driving variants, identifying the genes influenced by these variants, and therefore translating genetic information to improved clinical care, will remain an insurmountable task. We used a function-based approach for identifying causal variant candidates and the target genes on JIA risk haplotypes.<br><br>METHODS: We used a massively parallel reporter assay (MPRA) in myeloid K562 cells to query the effects of 5,226 SNPs in non-coding regions on JIA risk haplotypes for their ability to alter gene expression when compared to the common allele. The assay relies on 180&#xa0;bp oligonucleotide reporters ("oligos") in which the allele of interest is flanked by its cognate genomic sequence. Barcodes were added randomly by PCR to each oligo to achieve&#x2009;>&#x2009;20 barcodes per oligo to provide a quantitative read-out of gene expression for each allele. Assays were performed in both unstimulated K562 cells and cells stimulated overnight with interferon gamma (IFNg). As proof of concept, we then used CRISPRi to demonstrate the feasibility of identifying the genes regulated by enhancers harboring expression-altering SNPs.<br><br>RESULTS: We identified 553 expression-altering SNPs in unstimulated K562 cells and an additional 490 in cells stimulated with IFNg. We further filtered the SNPs to identify those plausibly situated within functional chromatin, using open chromatin and H3K27ac ChIPseq peaks in unstimulated cells and open chromatin plus H3K4me1 in stimulated cells. These procedures yielded 42 unique SNPs (total&#x2009;=&#x2009;84) for each set. Using CRISPRi, we demonstrated that enhancers harboring MPRA-screened variants in the TRAF1 and LNPEP/ERAP2 loci regulated multiple genes, suggesting complex influences of disease-driving variants.<br><br>CONCLUSION: Using MPRA and CRISPRi, JIA risk haplotypes can be queried to identify plausible candidates for disease-driving variants. Once these candidate variants are identified, target genes can be identified using CRISPRi informed by the 3D chromatin structures that encompass the risk haplotypes.},
}
@article {pmid38996389,
year = {2024},
author = {Baxter, JR and Kotze, A and de Bruyn, M and Matlou, K and Labuschagne, K and Mwale, M},
title = {DNA barcoding of southern African mammal species and construction of a reference library for forensic application.},
journal = {Genome},
volume = {67},
number = {10},
pages = {378-391},
doi = {10.1139/gen-2023-0050},
pmid = {38996389},
issn = {1480-3321},
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Mammals/genetics/classification ; Electron Transport Complex IV/genetics ; Phylogeny ; Cytochromes b/genetics ; South Africa ; Species Specificity ; Forensic Genetics/methods ; Gene Library ; Endangered Species ; Conservation of Natural Resources ; },
abstract = {Combating wildlife crimes in South Africa requires accurate identification of traded species and their products. Diagnostic morphological characteristics needed to identify species are often lost when specimens are processed and customs officials lack the expertise to identify species. As a potential solution, DNA barcoding can be used to identify morphologically indistinguishable specimens in forensic cases. However, barcoding is hindered by the reliance on comprehensive, validated DNA barcode reference databases, which are currently limited. To overcome this limitation, we constructed a barcode library of cytochrome c oxidase subunit 1 and cytochrome b sequences for threatened and protected mammals exploited in southern Africa. Additionally, we included closely related or morphologically similar species and assessed the database's ability to identify species accurately. Published southern African sequences were incorporated to estimate intraspecific and interspecific variation. Neighbor-joining trees successfully discriminated 94%-95% of the taxa. However, some widespread species exhibited high intraspecific distances (>2%), suggesting geographic sub-structuring or cryptic speciation. Lack of reliable published data prevented the unambiguous discrimination of certain species. This study highlights the efficacy of DNA barcoding in species identification, particularly for forensic applications. It also highlights the need for a taxonomic re-evaluation of certain widespread species and challenging genera.},
}
@article {pmid38993689,
year = {2024},
author = {Shim, J and Song, JH},
title = {A taxonomic review of the order Mantodea in Korea based on morphology and DNA barcodes.},
journal = {ZooKeys},
volume = {1206},
number = {},
pages = {1-43},
pmid = {38993689},
issn = {1313-2989},
abstract = {A taxonomic study of Korean Mantodea using morphological and molecular characters (COI) is presented. Eight species [Amantisnawai (Shiraki, 1908), Acromantisjaponica Westwood, 1889, Mantisreligiosasinica Bazyluk, 1960, Statiliamaculata (Thunberg, 1784), Tenoderaangustipennis Saussure, 1869, T.sinensis Saussure, 1871, Hierodulachinensis Werner, 1929, H.patellifera (Audinet-Serville, 1838)] belonging to six genera in three families are recognized. Interspecific genetic divergence of COI using uncorrected p-distance ranged from 6.7% to 22.4%, while intraspecific divergence ranged from 0% to 2.2% among eight Korean Mantodea species. All eight species were each strongly supported as a single lineage using COI on both neighbor-joining and parsimony trees. An illustrated key, redescriptions, habitus photographs, and illustrations of diagnostic characters of the species of Korean Mantodea are provided to facilitate identification.},
}
@article {pmid38989842,
year = {2024},
author = {Slusher, EK and Cottrell, T and Gariepy, T and Acebes-Doria, A and Querejeta Coma, M and Toledo, PFS and Schmidt, JM},
title = {A molecular approach to unravel trophic interactions between parasitoids and hyperparasitoids associated with pecan aphids.},
journal = {Journal of insect science (Online)},
volume = {24},
number = {4},
pages = {},
pmid = {38989842},
issn = {1536-2442},
mesh = {Animals ; *Aphids/parasitology/genetics ; *Food Chain ; *Host-Parasite Interactions ; Carya/parasitology ; DNA Barcoding, Taxonomic ; Wasps/physiology/genetics ; },
abstract = {Advances in molecular ecology can overcome many challenges in understanding host-parasitoid interactions. Genetic characterization of the key-players in systems helps to confirm species and identify trophic linkages essential for ecological service delivery by biological control agents; however, relatively few agroecosystems have been explored using this approach. Pecan production consists of a large tree perennial system containing an assortment of seasonal pests and natural enemies. As a first step to characterizing host-parasitoid associations in pecan food webs, we focus on aphid species and their parasitoids. Based on DNA barcoding of field-collected and reared specimens, we confirmed the presence of 3 species of aphid, one family of primary parasitoids, and 5 species of hyperparasitoids. By applying metabarcoding to field-collected aphid mummies, we were able to identify multiple species within each aphid mummy to unravel a complex food web of 3 aphids, 2 primary parasitoids, and upward of 8 hyperparasitoid species. The results of this study demonstrate that multiple hyperparasitoid species attack a single primary parasitoid of pecan aphids, which may have negative consequences for successful aphid biological control. Although further research is needed on a broader spatial scale, our results suggest multiple species exist in this system and may suggest a complex set of interactions between parasitoids, hyperparasitoids, and the 3 aphid species. This was the first time that many of these species have been characterized and demonstrates the application of novel approaches to analyze the aphid-parasitoid food webs in pecans and other tree crop systems.},
}
@article {pmid38989789,
year = {2024},
author = {Ansai, E and Nitta, M and Saito, T and Kojima, Y and Waki, T},
title = {The first intermediate host of the invasive frog trematode Glypthelmins quieta in Japan.},
journal = {Diseases of aquatic organisms},
volume = {159},
number = {},
pages = {9-14},
doi = {10.3354/dao03799},
pmid = {38989789},
issn = {0177-5103},
mesh = {Animals ; Japan ; *Trematoda/genetics ; *Snails/parasitology ; Introduced Species ; Host-Parasite Interactions ; RNA, Ribosomal, 28S/genetics ; },
abstract = {Glypthelmins quieta is a frog trematode native to North and Central America. This trematode was recently detected in Japan in the American bullfrog Lithobates catesbeianus, which was introduced from North America to Japan. As the first intermediate host of G. quieta, typically a snail, has not yet been identified in Japan, we conducted a snail survey in eastern Japan to screen for an intermediate host using DNA barcoding based on the nuclear 28S ribosomal RNA and mitochondrial cytochrome c oxidase subunit 1. We sampled 3 different snail species, Orientogalba ollula, Physella acuta, and Sinotaia quadrata histrica (157 individuals in total), and only the freshwater snail Physella acuta, which is also believed to have been introduced from North America to Japan, had sporocysts of G. quieta in its hepatopancreas. The introduction of the intermediate and definitive hosts from North America may have facilitated the invasion of G. quieta into Japan.},
}
@article {pmid38988805,
year = {2024},
author = {, and Bragard, C and Baptista, P and Chatzivassiliou, E and Di Serio, F and Gonthier, P and Jaques Miret, JA and Justesen, AF and Magnusson, CS and Milonas, P and Navas-Cortes, JA and Parnell, S and Potting, R and Reignault, PL and Stefani, E and Thulke, HH and Van der Werf, W and Vicent Civera, A and Yuen, J and Zappalà, L and Grégoire, JC and Malumphy, C and Gobbi, A and Golic, D and Kertesz, V and Sfyra, O and MacLeod, A},
title = {Pest categorisation of Monema flavescens.},
journal = {EFSA journal. European Food Safety Authority},
volume = {22},
number = {7},
pages = {e8831},
pmid = {38988805},
issn = {1831-4732},
abstract = {The EFSA Panel on Plant Health performed a pest categorisation of Monema flavescens (Lepidoptera, Limacodidae), following the commodity risk assessment of Acer palmatum plants grafted on A. davidii from China, in which M. flavescens was identified as a pest of possible concern to the European Union. This species can be identified by morphological taxonomic keys and by barcoding. The adults of the overwintering generation emerge from late June to late August. The eggs are laid in groups on the underside of the host-plant leaves, on which the larvae feed throughout their six to eight larval instars. Pupation occurs in ovoid cocoons at the junction between twigs and branches, or on the trunk. Overwintering occurs as fully grown larvae or prepupae in their cocoon. There are one or two generations per year. M. flavescens is polyphagous and feeds on broadleaves; it has been reported on 51 plant species belonging to 24 families. It mainly occurs in Asia (Bhutan, China, the Democratic People's Republic of Korea, Japan, Nepal, the Republic of Korea), Russia (Eastern Siberia) and Taiwan. It is also present in the USA (Massachusetts). The pest's flight capacities are unknown. The main pathway for entry and spread is plants for planting with cocoons attached. This is partially closed by prohibition of some hosts. In several EU member states climatic conditions are conducive for establishment and many host plants are widespread. Introduction of M. flavescens may result in defoliations influencing tree health and forest diversity. The caterpillars also have urticating spines affecting human health. Phytosanitary measures are available to reduce the likelihood of entry, establishment and spread, and there is a definite potential for classical biological control. Recognising that natural enemies prevent M. flavescens being regarded as a pest in Asia, there is uncertainty regarding the magnitude of potential impact in EU depending on the influence of natural enemies. All criteria assessed by EFSA for consideration as a potential quarantine pest are met.},
}
@article {pmid38988182,
year = {2025},
author = {Chen, MY and Tu, YC and Shyu, HY and Lin, TA and Juan, CP and Wu, FC},
title = {Using rDNA ITS2 barcoding to identify kratom (Mitragyna speciosa) from the genus Mitragyna and Neolamarckia cadamba.},
journal = {Electrophoresis},
volume = {46},
number = {3-4},
pages = {192-197},
doi = {10.1002/elps.202400003},
pmid = {38988182},
issn = {1522-2683},
mesh = {*Mitragyna/genetics/chemistry ; *DNA Barcoding, Taxonomic/methods ; *DNA, Plant/genetics/analysis ; *DNA, Ribosomal Spacer/genetics ; Polymerase Chain Reaction/methods ; },
abstract = {This study collected 80 samples of suspected kratom plant powder. A polymerase chain reaction sequence analysis was conducted using two sets of DNA barcode primers for plant ribosomal (r)DNA internal transcribed spacers (ITSs), namely, ITS3/ITS4 and ITS-p3/ITS-u4. Among the 80 samples, 40 were analyzed using the ITS3/ITS4 primer pair, and then DNA sequences were subjected to a National Center for Biotechnology Information-Basic Local Alignment Search Tool (NCBI-BLAST) comparison. Results showed that 29 samples had a 100% match (364/364) with Mitragyna speciosa (kratom), and 6 samples had a 99.73% match (363/364) with M. speciosa, whereas 5 samples had disordered and unreadable sequences. The 5 unreadable samples and an additional 40 suspected kratom samples were then analyzed using the ITS-p3/ITS-u4 primer pair, followed by an NCBI-BLAST comparison. Among these, 32 samples had a 100% match (404/404) with M. speciosa, and 11 samples had a 99.75% match (403/404) with M. speciosa. Among the samples with sequences matching M. speciosa, three distinct types were observed (no variance/404, 287M/404, and 287A/404). One sample had a 99.51% match (404/406) with Neolamarckia cadamba, and another sample had a sequencing length of 305 bp, with 25 positions showing mixed base pairs, indicating a mixture of different species. Analysis of the mixed base pair pattern suggested a possible mixture of M. speciosa and N. cadamba. Actually, M. speciosa and N. cadamba have very similar external morphologies. This indicates that the ITS-p3/ITS-u4 primer pair is effective in distinguishing mixtures of M. speciosa and N. cadamba and is thus more suitable than ITS3/ITS4 for identifying and analyzing samples of suspected kratom plant powder.},
}
@article {pmid38987689,
year = {2024},
author = {Wu, X and Wang, M and Li, X and Chen, Y and Liao, Z and Zhang, D and Wen, Y and Wang, S},
title = {Identification and characterization of a new species of Taxus - Taxus qinlingensis by multiple taxonomic methods.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {658},
pmid = {38987689},
issn = {1471-2229},
support = {CX2018B435//Hunan Provincial Innovation Foundation for Postgraduate/ ; 31470666//National Natural Science Foundation of China/ ; },
mesh = {*Taxus/genetics/anatomy &amp; histology/classification ; *Phylogeny ; *Plant Leaves/anatomy &amp; histology/genetics ; *DNA Barcoding, Taxonomic ; China ; DNA, Plant/genetics ; Phenotype ; },
abstract = {BACKGROUND: The taxonomy of Taxus Linn. remains controversial due to its continuous phenotypic variation and unstable topology, thus adversely affecting the formulation of scientific conservation strategies for this genus. Recently, a new ecotype, known as Qinling type, is mainly distributed in the Qinling Mountains and belongs to a monophyletic group. Here, we employed multiple methods including leaf phenotype comparison (leaf shapes and microstructure), DNA barcoding identification (ITS + trnL-trnF + rbcL), and niche analysis to ascertain the taxonomic status of the Qinling type.<br><br>RESULTS: Multiple comparisons revealed significant differences in the morphological characters (length, width, and length/width ratio) among the Qinling type and other Taxus species. Leaf anatomical analysis indicated that only the Qinling type and T. cuspidata had no papilla under the midvein or tannins in the epicuticle. Phylogenetic analysis of Taxus indicated that the Qinling type belonged to a monophyletic group. Moreover, the Qinling type had formed a relatively independent niche, it was mainly distributed around the Qinling Mountains, Ta-pa Mountains, and Taihang Mountains, situated at an elevation below 1500&#xa0;m.<br><br>CONCLUSIONS: Four characters, namely leaf curvature, margin taper, papillation on midvein, and edges were put forward as primary indexes for distinguishing Taxus species. The ecotype Qingling type represented an independent evolutionary lineage and formed a unique ecological niche. Therefore, we suggested that the Qingling type should be treated as a novel species and named it Taxus qinlingensis Y. F. Wen &amp; X. T. Wu, sp. nov.},
}
@article {pmid38985195,
year = {2024},
author = {Corradini, B and Gianfreda, D and Ferri, G and Ferrari, F and Borciani, I and Santunione, AL and Cecchi, R},
title = {Forensic species identification: practical guide for animal and plant DNA analysis.},
journal = {International journal of legal medicine},
volume = {138},
number = {6},
pages = {2271-2280},
pmid = {38985195},
issn = {1437-1596},
mesh = {Animals ; Humans ; DNA/analysis ; DNA Fingerprinting/methods ; *DNA, Plant/genetics ; *Forensic Genetics/methods ; Microsatellite Repeats ; Species Specificity ; Specimen Handling/methods ; },
abstract = {The importance of non-human DNA in the forensic field has increased greatly in recent years, together with the type of applications. The molecular species identification of animal and botanical material may be crucial both for wildlife trafficking and crime scene investigation. However, especially for forensic botany, several challenges slow down the implementation of the discipline in the routine.Although the importance of molecular analysis of animal origin samples is widely recognized and the same value is acknowledged to the botanical counterpart, the latter does not find the same degree of application.The availability of molecular methods, especially useful in cases where the material is fragmented, scarce or spoiled preventing the morphological identification, is not well known. This work is intended to reaffirm the relevance of non-human forensic genetics (NHFG), highlighting differences, benefits and pitfalls of the current most common molecular analysis workflow for animal and botanical samples, giving a practical guide. A flowchart describing the analysis paths, divided in three major working areas (inspection and sampling, molecular analysis, data processing and interpretation), is provided. More real casework examples of the utility of non-human evidence in forensic investigations should be shared by the scientific community, especially for plants. Moreover, concrete efforts to encourage initiatives in order to promote quality and standardization in the NHFG field are also needed.},
}
@article {pmid38984293,
year = {2024},
author = {Ollinger, N and Malachova, A and Sulyok, M and Krska, R and Weghuber, J},
title = {Mycotoxin contamination in moldy slices of bread is mostly limited to the immediate vicinity of the visible infestation.},
journal = {Food chemistry: X},
volume = {23},
number = {},
pages = {101563},
pmid = {38984293},
issn = {2590-1575},
abstract = {Bread is an important staple food that is susceptible to spoilage, making it one of the most wasted foods. To determine the safety of partially moldy bread, five types of bread were inoculated with common mold species. After incubation, the metabolite profile was determined in and under the inoculation spot, as well as at a lateral distance of 3 cm from the moldy spot. The result showed that the metabolites were exclusively concentrated in the inoculation area and directly below the inoculation area. The only exception was citrinin, a mycotoxin produced by Penicillia such as Penicillium citrinum, which was detected in almost all tested bread areas when inoculated with the corresponding strains. The results of our study suggest that the removal of moldy parts may be a solution to reduce food waste if the remaining bread is to be used, for example for insect farming to produce animal feed.},
}
@article {pmid38982951,
year = {2024},
author = {Yang, S and Xu, Y and Lin, R and Feng, X and Wang, K and Wang, Z and Cui, K and Chen, S and Wang, Z and Wang, X and Chen, S and Zhang, W and Zhu, C and Gao, Z},
title = {Conformation-Driven Responsive 1D and 2D Lanthanide-Metal-Organic Framework Heterostructures for High-Security Photonic Barcodes.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {20},
number = {44},
pages = {e2402890},
doi = {10.1002/smll.202402890},
pmid = {38982951},
issn = {1613-6829},
support = {22275104//National Natural Science Foundation of China/ ; ZR2021YQ06//Shandong Provincial Natural Science Foundation/ ; tsqn202306255//Taishan Scholar Program of Shandong Province/ ; kq2206026//The Training Program for Excellent Young Innovators of Changsha/ ; },
abstract = {Development of luminescent segmented heterostructures featuring multiple spatial-responsive blocks is important to achieve miniaturized photonic barcodes toward anti-counterfeit applications. Unfortunately, dynamic manipulation of the spatial color at micro/nanoscale still remains a formidable challenge. Here, a straightforward strategy is proposed to construct spatially varied heterostructures through amplifying the conformation-driven response in flexible lanthanide-metal-organic frameworks (Ln-MOFs), where the thermally induced minor conformational changes in organic donors dramatically modulate the photoluminescence of Ln acceptors. Notably, compositionally and structurally distinct heterostructures (1D and 2D) are further constructed through epitaxial growth of multiple responsive MOF blocks benefiting from the isomorphous Ln-MOF structures. The thermally controlled emissive colors with distinguishable spectra carry the fingerprint information of a specific heterostructure, thus allowing for the effective construction of smart photonic barcodes with spatially responsive characteristics. The results will deepen the understanding of the conformation-driven responsive mechanism and also provide guidance to fabricate complex stimuli-responsive hierarchical microstructures for advanced optical recording and high-security labels.},
}
@article {pmid38979326,
year = {2024},
author = {Hotinger, JA and Campbell, IW and Hullahalli, K and Osaki, A and Waldor, MK},
title = {Quantification of Salmonella enterica serovar Typhimurium Population Dynamics in Murine Infection Using a Highly Diverse Barcoded Library.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38979326},
issn = {2692-8205},
support = {R01 AI042347/AI/NIAID NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; F31 AI156949/AI/NIAID NIH HHS/United States ; T32 DK007477/DK/NIDDK NIH HHS/United States ; P30 CA006516/CA/NCI NIH HHS/United States ; },
abstract = {Murine models are often used to study the pathogenicity and dissemination of the enteric pathogen Salmonella enterica serovar Typhimurium. Here, we quantified S. Typhimurium population dynamics in mice using the STAMPR analytic pipeline and a highly diverse S. Typhimurium barcoded library containing [~]55,000 unique strains distinguishable by genomic barcodes by enumerating S. Typhimurium founding populations and deciphering routes of spread in mice. We found that a severe bottleneck allowed only one in a million cells from an oral inoculum to establish a niche in the intestine. Furthermore, we observed compartmentalization of pathogen populations throughout the intestine, with few barcodes shared between intestinal segments and feces. This severe bottleneck widened and compartmentalization was reduced after streptomycin treatment, suggesting the microbiota plays a key role in restricting the pathogen's colonization and movement within the intestine. Additionally, there was minimal sharing between the intestine and extraintestinal organ populations, indicating dissemination to extraintestinal sites occurs rapidly, before substantial pathogen expansion in the intestine. Bypassing the intestinal bottleneck by inoculating mice via intravenous or intraperitoneal injection revealed that Salmonella re-enters the intestine after establishing niches in extraintestinal sites by at least two distinct pathways. One pathway results in a diverse intestinal population. The other re-seeding pathway is through the bile, where the pathogen is often clonal, leading to clonal intestinal populations and correlates with gallbladder pathology. Together, these findings deepen our understanding of Salmonella population dynamics.},
}
@article {pmid38979006,
year = {2024},
author = {Ren, J and Ren, L and Zhang, R},
title = {Delimiting species, revealing cryptic diversity, and population divergence in Qinghai-Tibet Plateau weevils through DNA barcoding.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e11592},
pmid = {38979006},
issn = {2045-7758},
abstract = {The Leptomias group represents one of the most diverse taxonomic group of weevils in the Qinghai-Tibet Plateau and its adjacent areas. Despite the potential of hidden diversity, relatively few comprehensive studies have been conducted on species diversity in this taxonomic group. In this study, we performed DNA barcoding analysis for species of the Leptomias group using a comprehensive DNA barcode dataset that included 476 sequences representing 54 morphospecies. Within the dataset, our laboratory contributed 474 sequences, and 390 sequences were newly generated for this study. The average Kimura 2-parameter distances among morphospecies and genera were 0.76% and 19.15%, respectively. In 94.4% of the species, the minimum interspecific distances exceeded the maximum intraspecific distances, indicating the presence of barcode gaps in most species of Leptomias group. The application of Automatic Barcode Gap Discovery, Assemble Species by Automatic Partitioning, Barcode Index Number, Bayesian Poisson tree processes, jMOTU, and Neighbor-joining tree methods revealed 45, 45, 63, 54, and 55 distinct clusters representing single species, respectively. Additionally, a total of four morphospecies, Leptomias kangmarensis, L. midlineatus, L. siahus, and L. sp.9RL, were found to be assigned to multiple subclade each, indicating the geographical divergences and the presence of cryptic diversity. Our findings of this study demonstrate that Qinghai-Tibet Plateau exhibits a higher species diversity of the Leptomias group, and it is imperative to investigate cryptic species within certain morphospecies using integrative taxonomic approaches in future studies. Moreover, the construction of a DNA barcode reference library presented herein establishes a robust foundational dataset to support forthcoming research on weevil taxonomy, phylogenetics, ecology, and evolution.},
}
@article {pmid38979002,
year = {2024},
author = {Nakagawa, K and Ogino, K and Katoh, TK and Kono, N},
title = {Species identification of livefood flightless fly (Torinido-shoujoubae) through DNA barcoding.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e11622},
pmid = {38979002},
issn = {2045-7758},
abstract = {Torinido-shoujoubae, as it is called in Japanese, is a flightless Drosophila sp. that is sold commercially in Japan. This Drosophila sp. is often used as feeds for model organisms such as reptiles and spiders. There is no scientific name provided for the fruit fly that is known as Torinido-shoujoubae, as well as any historical background or data behind this species. There has been a previous study that was conducted through morphological characteristics analysis of the body as well as the male copulatory organ and has been estimated as Drosophila hydei. The objective of this study was to determine the species of this unidentified fly known as Torinido-shoujoubae based on a molecular evidence with a DNA barcoding. Samples were purchased from four separate suppliers to examine whether there are any differences between them. COI regions were amplified using PCR and the sequenced results were aligned against two databases, NCBI and BOLD. Torinido-shoujoubae samples provided from all suppliers were confirmed to be D. hydei.},
}
@article {pmid38973066,
year = {2024},
author = {Kumano, S and Tanaka, K and Akahori, R and Yanagiya, A and Nojima, A},
title = {Using peptide barcodes for simultaneous profiling of protein expression from mRNA.},
journal = {Rapid communications in mass spectrometry : RCM},
volume = {38},
number = {18},
pages = {e9867},
doi = {10.1002/rcm.9867},
pmid = {38973066},
issn = {1097-0231},
support = {//Hitachi Ltd/ ; //ARCALIS Inc./ ; },
mesh = {*RNA, Messenger/genetics/analysis ; *Green Fluorescent Proteins/genetics/chemistry/metabolism ; *Peptides/chemistry/analysis/genetics/metabolism ; Humans ; Mass Spectrometry/methods ; Gene Expression Profiling/methods ; },
abstract = {RATIONALE: mRNA technology has begun to play a significant role in the areas of therapeutic intervention and vaccine development. However, optimizing the mRNA sequence that influences protein expression levels is a resource-intensive and time-consuming process. This study introduces a new method to accelerate the selection of sequences of mRNA for optimal protein expression.<br><br>METHODS: We designed the mRNA sequences in such a way that a unique peptide barcode, corresponding to each mRNA sequence, is attached to the expressed protein. These barcodes, cleaved off by a protease and simultaneously quantified by mass spectrometry, reflect the protein expression, enabling a parallel analysis. We validated this method using two mRNAs, each with different untranslated regions (UTRs) but encoding enhanced green fluorescence protein (eGFP), and investigated whether the peptide barcodes could analyze the differential eGFP expression levels.<br><br>RESULTS: The fluorescence intensity of eGFP, a marker of its expression level, has shown noticeable changes between the two UTR sequences in mRNA-transfected cells when measured using flow cytometry. This suggests alterations in the expression level of eGFP due to the influence of different UTR sequences. Furthermore, the quantified amount of peptide barcodes that were released from eGFP showed consistent patterns with these changes.<br><br>CONCLUSIONS: The experimental findings suggest that peptide barcodes serve as a valuable tool for assessing protein expression levels. The process of mRNA sequence selection, aimed at maximizing protein expression, can be enhanced by the parallel analysis of peptide barcodes using mass spectrometry.},
}
@article {pmid38972989,
year = {2024},
author = {Ng, DYM and Sun, W and Sit, THC and Brackman, CJ and Tse, ACN and Bui, CHT and Tang, AWY and Wong, ANC and Tsang, ATL and Koo, JCT and Cheng, SMS and Peiris, M and Chin, AWH and Poon, LLM},
title = {Genetic diversity of astroviruses detected in wild aquatic birds in Hong Kong.},
journal = {Virology journal},
volume = {21},
number = {1},
pages = {153},
pmid = {38972989},
issn = {1743-422X},
support = {U01 AI151810/AI/NIAID NIH HHS/United States ; U01AI151810//Division of Microbiology and Infectious Diseases/ ; T11-705/21-N//Research Grants Council, University Grants Committee/ ; },
mesh = {Animals ; Hong Kong ; *Phylogeny ; *Genetic Variation ; *Birds/virology ; *Genome, Viral ; *Feces/virology ; *Astroviridae Infections/veterinary/virology ; Animals, Wild/virology ; Bird Diseases/virology ; High-Throughput Nucleotide Sequencing ; Avastrovirus/genetics/classification/isolation &amp; purification ; RNA, Viral/genetics ; Open Reading Frames ; Astroviridae/genetics/isolation &amp; purification/classification ; },
abstract = {Wild waterfowl serve as a reservoir of some astroviruses. Fecal samples from wild waterfowl collected at Hong Kong's Marshes were tested using pan-astrovirus reverse transcription-PCR. Positive samples underwent subsequent host identification using DNA barcoding. Based on deduced partial sequences, noteworthy samples from three astrovirus groups (mammalian, avian and unclassified astroviruses) were further analyzed by next-generation sequencing. One sample of Avastrovirus 4 clade, MP22-196, had a nearly complete genome identified. The results of ORF2 phylogenetic analysis and genetic distance analysis indicate that Avastrovirus 4 is classified as a distinct subclade within Avastrovirus. MP22-196 has typical astrovirus genome characteristics. The unique characteristics and potential differences of this genome, compared to other avian astrovirus sequences, involve the identification of a modified sgRNA sequence situated near the ORF2 start codon, which precedes the ORF1b stop codon. Additionally, the 3' UTR of MP22-196 is shorter than other avian astroviruses. This study expands our understanding of the Avastrovirus 4 clade.},
}
@article {pmid38972540,
year = {2024},
author = {Mizuno, T and Tokoro, M and Yagi, T and Wada, E and Yamadori, I and Arai, M},
title = {Infant gastrointestinal canthariasis caused by cigarette beetle (Lasioderma serricorne).},
journal = {Parasitology international},
volume = {103},
number = {},
pages = {102921},
doi = {10.1016/j.parint.2024.102921},
pmid = {38972540},
issn = {1873-0329},
mesh = {Animals ; Male ; *Coleoptera/parasitology ; *Larva/growth &amp; development ; Child, Preschool ; Humans ; Polymerase Chain Reaction ; },
abstract = {Diseases caused by beetle larvae infestation are known as intestinal canthariasis. Canthariasis from the cigarette beetle, Lasioderma serricorne, is quite rare; however, with the accumulation of genetic references, such cases of accidental pseudo-parasitism have been increasingly recognized. Here, we describe a case of asymptomatic gastrointestinal passage of L. serricorne in a 4-year-old male. Larval identification was conducted by PCR-sequencing targeting cytochrome c oxidase subunit 1 using DNA extracted from the larvae. Due to the difficulty of differential identification of beetles using larval morphology, DNA barcoding is essential.},
}
@article {pmid38969342,
year = {2024},
author = {Serio, RN and Scheben, A and Lu, B and Gargiulo, DV and Patruno, L and Buckholtz, CL and Chaffee, RJ and Jibilian, MC and Persaud, SG and Staklinski, SJ and Hassett, R and Brault, LM and Ramazzotti, D and Barbieri, CE and Siepel, AC and Nowak, DG},
title = {Clonal Lineage Tracing with Somatic Delivery of Recordable Barcodes Reveals Migration Histories of Metastatic Prostate Cancer.},
journal = {Cancer discovery},
volume = {14},
number = {10},
pages = {1990-2009},
doi = {10.1158/2159-8290.CD-23-1332},
pmid = {38969342},
issn = {2159-8290},
support = {R35-GM127070//National Institutes of Health (NIH)/ ; Research Scholar Grant//American Cancer Society (ACS)/ ; 22790//Cancer Research UK (CRUK)/ ; T32 GM141949/GM/NIGMS NIH HHS/United States ; T32CA203702//National Cancer Institute (NCI)/ ; 1T32GM141949//National Institutes of Health (NIH)/ ; W81XWH-22-1-0068//Department of Defense Education Activity (DoDEA)/ ; 22790//Fondazione AIRC per la ricerca sul cancro ETS (AIRC)/ ; 5T32GM141949//National Institutes of Health (NIH)/ ; R01-CA272466//National Cancer Institute (NCI)/ ; R01 CA272466/CA/NCI NIH HHS/United States ; Centennial Scholarship//Starr Foundation (TSF)/ ; },
mesh = {Male ; *Prostatic Neoplasms/pathology/genetics ; Animals ; Mice ; Humans ; *Neoplasm Metastasis ; Cell Movement ; Disease Models, Animal ; },
abstract = {The patterns by which primary tumors spread to metastatic sites remain poorly understood. Here, we define patterns of metastatic seeding in prostate cancer using a novel injection-based mouse model-EvoCaP (Evolution in Cancer of the Prostate), featuring aggressive metastatic cancer to bone, liver, lungs, and lymph nodes. To define migration histories between primary and metastatic sites, we used our EvoTraceR pipeline to track distinct tumor clones containing recordable barcodes. We detected widespread intratumoral heterogeneity from the primary tumor in metastatic seeding, with few clonal populations instigating most migration. Metastasis-to-metastasis seeding was uncommon, as most cells remained confined within the tissue. Migration patterns in our model were congruent with human prostate cancer seeding topologies. Our findings support the view of metastatic prostate cancer as a systemic disease driven by waves of aggressive clones expanding their niche, infrequently overcoming constraints that otherwise keep them confined in the primary or metastatic site. Significance: Defining the kinetics of prostate cancer metastasis is critical for developing novel therapeutic strategies. This study uses CRISPR/Cas9-based barcoding technology to accurately define tumor clonal patterns and routes of migration in a novel somatically engineered mouse model (EvoCaP) that recapitulates human prostate cancer using an in-house developed analytical pipeline (EvoTraceR).},
}
@article {pmid38968228,
year = {2024},
author = {Chaumeau, V and Piarroux, M and Kulabkeeree, T and Sawasdichai, S and Inta, A and Watthanaworawit, W and Nosten, F and Piarroux, R and Nabet, C},
title = {Identification of Southeast Asian Anopheles mosquito species using MALDI-TOF mass spectrometry.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0305167},
pmid = {38968228},
issn = {1932-6203},
mesh = {Animals ; *Anopheles/genetics/classification ; Asia, Southeastern ; DNA Barcoding, Taxonomic/methods ; Malaria/transmission ; Mosquito Vectors/genetics/classification ; Species Specificity ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Thailand ; },
abstract = {Malaria elimination in Southeast Asia remains a challenge, underscoring the importance of accurately identifying malaria mosquitoes to understand transmission dynamics and improve vector control. Traditional methods such as morphological identification require extensive training and cannot distinguish between sibling species, while molecular approaches are costly for extensive screening. Matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and cost-effective tool for Anopheles species identification, yet its current use is limited to few specialized laboratories. This study aimed to develop and validate an online reference database for MALDI-TOF MS identification of Southeast Asian Anopheles species. The database, constructed using the in-house data analysis pipeline MSI2 (Sorbonne University), comprised 2046 head mass spectra from 209 specimens collected at the Thailand-Myanmar border. Molecular identification via COI and ITS2 DNA barcodes enabled the identification of 20 sensu stricto species and 5 sibling species complexes. The high quality of the mass spectra was demonstrated by a MSI2 median score (min-max) of 61.62 (15.94-77.55) for correct answers, using the best result of four technical replicates of a test panel. Applying an identification threshold of 45, 93.9% (201/214) of the specimens were identified, with 98.5% (198/201) consistency with the molecular taxonomic assignment. In conclusion, MALDI-TOF MS holds promise for malaria mosquito identification and can be scaled up for entomological surveillance in Southeast Asia. The free online sharing of our database on the MSI2 platform (https://msi.happy-dev.fr/) represents an important step towards the broader use of MALDI-TOF MS in malaria vector surveillance.},
}
@article {pmid38966247,
year = {2024},
author = {Turanov, SV and Koltsova, MA and Rutenko, OA},
title = {Experimental evaluation of genetic variability based on DNA metabarcoding from the aquatic environment: Insights from the Leray COI fragment.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e11631},
pmid = {38966247},
issn = {2045-7758},
abstract = {Intraspecific genetic variation is important for the assessment of organisms' resistance to changing environments and anthropogenic pressures. Aquatic DNA metabarcoding provides a non-invasive method in biodiversity research, including investigations at the within-species level. Through the analysis of eDNA samples collected from the Peter the Great Gulf of the Japan Sea, in this study, we aimed to evaluate the identification of Amplicon Sequence Variants (ASVs) in marine eDNA among abundant species of the Zostera sp. community: Hexagrammos octogrammus, Pholidapus dybowskii (Teleostei: Perciformes), and Pandalus latirostris (Arthropoda: Decapoda). These species were collected from two distant locations to produce mock communities and gather aquatic eDNA both on the community and individual level. Our approach highlights the efficacy of eDNA metabarcoding in capturing haplotypic diversity and the potential for this methodology to track genetic diversity accurately, contributing to conservation efforts and ecosystem management. Additionally, our results elucidate the impact of nuclear mitochondrial DNA segments (NUMTs) on the reliability of metabarcoding data, indicating the necessity for cautious interpretation of such data in ecological studies. Moreover, we analyzed 83 publicly available COI sequence datasets from common groups of multicellular organisms (Mollusca, Echinodermata, Crustacea, Polychaeta, and Actinopterygii). The results reflect the decrease in population diversity that arises from using the metabarcode compared to the COI barcode.},
}
@article {pmid38965520,
year = {2024},
author = {, },
title = {Retraction Note: DNA barcoding detects contamination and substitution in North American herbal products.},
journal = {BMC medicine},
volume = {22},
number = {1},
pages = {279},
doi = {10.1186/s12916-024-03504-x},
pmid = {38965520},
issn = {1741-7015},
}
@article {pmid38965405,
year = {2024},
author = {LeSavage, BL and Zhang, D and Huerta-López, C and Gilchrist, AE and Krajina, BA and Karlsson, K and Smith, AR and Karagyozova, K and Klett, KC and Huang, MS and Long, C and Kaber, G and Madl, CM and Bollyky, PL and Curtis, C and Kuo, CJ and Heilshorn, SC},
title = {Engineered matrices reveal stiffness-mediated chemoresistance in patient-derived pancreatic cancer organoids.},
journal = {Nature materials},
volume = {23},
number = {8},
pages = {1138-1149},
pmid = {38965405},
issn = {1476-4660},
support = {DP1CA238296//U.S. Department of Health Human Services | National Institutes of Health (NIH)/ ; U01 DK127395/DK/NIDDK NIH HHS/United States ; CBET 2033302//National Science Foundation (NSF)/ ; R01 EB027171/EB/NIBIB NIH HHS/United States ; U01CA217851//U.S. Department of Health Human Services | National Institutes of Health (NIH)/ ; U54CA224081//U.S. Department of Health Human Services | National Institutes of Health (NIH)/ ; },
mesh = {Humans ; *Drug Resistance, Neoplasm ; *Organoids/metabolism/pathology/drug effects ; *Pancreatic Neoplasms/metabolism/pathology/drug therapy/genetics ; *Carcinoma, Pancreatic Ductal/metabolism/pathology/genetics/drug therapy ; *Extracellular Matrix/metabolism ; Hyaluronic Acid/metabolism/chemistry ; Antineoplastic Agents/pharmacology/therapeutic use ; },
abstract = {Pancreatic ductal adenocarcinoma (PDAC) is characterized by its fibrotic and stiff extracellular matrix. However, how the altered cell/extracellular-matrix signalling contributes to the PDAC tumour phenotype has been difficult to dissect. Here we design and engineer matrices that recapitulate the key hallmarks of the PDAC tumour extracellular matrix to address this knowledge gap. We show that patient-derived PDAC organoids from three patients develop resistance to several clinically relevant chemotherapies when cultured within high-stiffness matrices mechanically matched to in vivo tumours. Using genetic barcoding, we find that while matrix-specific clonal selection occurs, cellular heterogeneity is not the main driver of chemoresistance. Instead, matrix-induced chemoresistance occurs within a stiff environment due to the increased expression of drug efflux transporters mediated by CD44 receptor interactions with hyaluronan. Moreover, PDAC chemoresistance is reversible following transfer from high- to low-stiffness matrices, suggesting that targeting the fibrotic extracellular matrix may sensitize chemoresistant tumours. Overall, our findings support the potential of engineered matrices and patient-derived organoids for elucidating extracellular matrix contributions to human disease pathophysiology.},
}
@article {pmid38963889,
year = {2024},
author = {Wu, R and Liu, L and Zhang, L and Bogan, AE and Niu, G and Jin, D and Wu, X and Liu, X},
title = {Taxonomic revision of two species in the genus Ptychorhynchus Simpson, 1900 (Bivalvia: Unionidae: Gonideinae), with description of a new species.},
journal = {Invertebrate systematics},
volume = {38},
number = {},
pages = {},
doi = {10.1071/IS24014},
pmid = {38963889},
issn = {1447-2600},
mesh = {Animals ; *Phylogeny ; *Unionidae/genetics/classification/anatomy &amp; histology ; *Species Specificity ; Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; },
abstract = {Accurate identification and precise classification of freshwater mussel species that are among the most threatened freshwater taxa in the world, play a crucial role in informing conservation and management efforts for these organisms. However, due to the variability in shell morphology, relying solely on shell characteristics for species taxonomy poses significant challenges, thereby impeding effective conservation planning and management. The freshwater mussel genus Ptychorhynchus Simpson, 1900 is one such group in need of study. We integrate molecular phylogeny, shell morphology and soft-body anatomy to examine the classification of Ptychorhynchus denserugata (Haas, 1910) and Ptychorhynchus resupinatus (von Martens, 1902). The COI barcoding data support the clustering of P. denserugata and Nodularia douglasiae within a single clade, and P. denserugata shares the diagnostic feature of the genus Nodularia , i.e. knobs or bumps on the inner mantle surface in the excurrent aperture. Therefore, by integrating molecular data and anatomical characteristics, we confirm that the nominal species P. denserugata syn. nov. is a new synonym for N. douglasiae . The multi-locus (COI + ND1 + 16S rRNA + 18S rRNA + 28S rRNA) phylogeny and mitochondrial phylogenomics support the transfer of P. resupinatus from Ptychorhynchus to the newly elevated genus Cosmopseudodon stat. rev., as Cosmopseudodon resupinatus stat. rev. that is still considered the designated type species. We also describe a new species based on integrative taxonomy, i.e. Cosmopseudodon wenshanensis sp. nov. The comprehensive understanding of the taxonomy and diversity of the revised Cosmopseudodon species, and shell heteromorphism of N. douglasiae (=P. denserugata syn. nov.), will serve as a crucial foundation for further scientific assessment and conservation strategies pertaining to these taxa. ZooBank: urn:lsid:zoobank.org:pub:E48968B1-DF0F-42AD-8F31-B8C95F23CE57.},
}
@article {pmid38962025,
year = {2024},
author = {Mamadashvili, G and Brin, A and Chumak, M and Diedus, V and Drössler, L and Förster, B and Georgiev, KB and Ghrejyan, T and Hleb, R and Kalashian, M and Kamburov, I and Karagyan, G and Kevlishvili, J and Khutsishvili, Z and Larrieu, L and Mazmanyan, M and Petrov, PI and Tabunidze, L and Bässler, C and Müller, J},
title = {Drivers of wood-inhabiting fungal diversity in European and Oriental beech forests.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e11660},
pmid = {38962025},
issn = {2045-7758},
abstract = {The hyperdiverse wood-inhabiting fungi play a crucial role in the global carbon cycle, but often are threatened by deadwood removal, particularly in temperate forests dominated by European beech (Fagus sylvatica) and Oriental beech (Fagus orientalis). To study the impact of abiotic drivers, deadwood factors, forest management and biogeographical patterns in forests of both beech species on fungal composition and diversity, we collected 215 deadwood-drilling samples in 18 forests from France to Armenia and identified fungi by meta-barcoding. In our analyses, we distinguished the patterns driven by rare, common, and dominant species using Hill numbers. Despite a broad overlap in species, the fungal composition with focus on rare species was determined by Fagus species, deadwood type, deadwood diameter, precipitation, temperature, and management status in decreasing order. Shifting the focus on common and dominant species, only Fagus species, both climate variables and deadwood type remained. The richness of species within the deadwood objects increased significantly only with decay stage. Gamma diversity in European beech forests was higher than in Oriental beech forests. We revealed the highest gamma diversity for old-growth forests of European beech when focusing on dominant species. Our results implicate that deadwood retention efforts, focusing on dominant fungi species, critical for the decay process, should be distributed across precipitation and temperature gradients and both Fagus species. Strategies focusing on rare species should additionally focus on different diameters and on the conservation of old-growth forests.},
}
@article {pmid38962021,
year = {2024},
author = {Ma, Y and López-Pujol, J and Yan, D and Zhou, Z and Deng, Z and Niu, J},
title = {Complete chloroplast genomes of the hemiparasitic genus Cymbaria: Insights into comparative analysis, development of molecular markers, and phylogenetic relationships.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e11677},
pmid = {38962021},
issn = {2045-7758},
abstract = {The hemiparasitic tribe Cymbarieae (Orobanchaceae) plays a crucial role in elucidating the initial stage of the transition from autotrophism to heterotrophism. However, the complete chloroplast genome of the type genus Cymbaria has yet to be reported. In addition, the traditional Mongolian medicine Cymbaria daurica is frequently subjected to adulteration or substitution because of the minor morphological differences with Cymbaria mongolica. In this study, the complete chloroplast genomes of the two Cymbaria species were assembled and annotated, and those of other published 52 Orobanchaceae species were retrieved for comparative analyses. We found that the Cymbaria chloroplast genomes are characterized by pseudogenization or loss of stress-relevant genes (ndh) and a unique rbcL-matK inversion. Unlike the high variability observed in holoparasites, Cymbaria and other hemiparasites exhibit high similarity to autotrophs in genome size, guanine-cytosine (GC) content, and intact genes. Notably, four pairs of specific DNA barcodes were developed and validated to distinguish the medicinal herb from its adulterants. Phylogenetic analyses revealed that the genus Cymbaria and the Schwalbea-Siphonostegia clade are grouped into the tribe Cymbarieae, which forms a sister clade to the remaining Orobanchaceae parasitic lineages. Moreover, the diversification of monophyletic Cymbaria occurred during the late Miocene (6.72 Mya) in the Mongol-Chinese steppe region. Our findings provide valuable genetic resources for studying the phylogeny of Orobanchaceae and plant parasitism, and genetic tools to validate the authenticity of the traditional Mongolian medicine "Xinba.".},
}
@article {pmid38959129,
year = {2024},
author = {Luo, J and Walsh, E and Faulborn, A and Gao, K and White, J and Zhang, N},
title = {Pinibarreniales, a new order of Sordariomycetes from pine barrens ecosystem.},
journal = {Mycologia},
volume = {116},
number = {5},
pages = {835-847},
doi = {10.1080/00275514.2024.2363084},
pmid = {38959129},
issn = {1557-2536},
support = {DEB 2224067//US National Science Foundation/ ; },
mesh = {*Phylogeny ; *Ecosystem ; *Plant Roots/microbiology ; *Ascomycota/classification/genetics/isolation &amp; purification ; DNA, Fungal/genetics ; New Jersey ; Arabidopsis/microbiology ; Blueberry Plants/microbiology ; Plant Diseases/microbiology ; Sequence Analysis, DNA ; Pinus/microbiology ; DNA Barcoding, Taxonomic ; },
abstract = {Pinibarrenia chlamydospora, sp. nov. isolated from the roots of highbush blueberry in the New Jersey Pine Barrens, is described and illustrated. Based on multigene phylogenetic analysis, as well as morphological and ecological characteristics, Pinibarreniales and Pinibarreniaceae are established to accommodate this novel lineage in Sordariomycetidae, Sordariomycetes. Pinibarreniales, Tracyllalales, and Vermiculariopsiellales are proposed to be included in the subclass Sordariomycetidae. Pinibarreniales likely have a wide distribution and forms association with Ericaceae plants that live in acidic and oligotrophic environments because its DNA barcode matches with environmental sequences from other independent ecological studies. The plant-fungal interaction experiment revealed negative impacts on Arabidopsis, indicating its pathogenicity. This uncovered new fungal lineage will contribute to a better understanding of the diversity and systematics of Sordariomycetes.},
}
@article {pmid38958078,
year = {2024},
author = {Xu, Z and Chen, L and Lin, X and Lyu, Y and Zhou, M and Chen, H and Zhang, H and Zhang, T and Chen, Y and Suo, Y and Liang, Q and Qin, Z and Wang, Y},
title = {Single Nucleus Total RNA Sequencing of Formalin-Fixed Paraffin-Embedded Gliomas.},
journal = {Small methods},
volume = {8},
number = {10},
pages = {e2301801},
doi = {10.1002/smtd.202301801},
pmid = {38958078},
issn = {2366-9608},
support = {32200073//National Natural Science Foundation of China/ ; 32250710678//National Natural Science Foundation of China/ ; 82200977//National Natural Science Foundation of China/ ; 2021R01012//Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang/ ; 2024C03005//"Pioneer" R&amp;D programs of Zhejiang Province/ ; 2024SSYS0022//Key R&amp;D Program of Zhejiang/ ; Y-zai2021/qn-0204//Beijing Xisike Clinical Oncology Research Foundation/ ; Y-zai2021/zd-0207//Beijing Xisike Clinical Oncology Research Foundation/ ; },
mesh = {Humans ; *Glioma/genetics/pathology ; *Paraffin Embedding ; *Formaldehyde/chemistry ; *Brain Neoplasms/genetics/pathology ; *Single-Cell Analysis/methods ; *Sequence Analysis, RNA/methods ; Tissue Fixation ; Cell Nucleus/genetics ; High-Throughput Nucleotide Sequencing ; RNA, Untranslated/genetics ; },
abstract = {Gliomas, the predominant form of brain cancer, comprise diverse malignant subtypes with limited curative therapies available. The insufficient understanding of their molecular diversity and evolutionary processes hinders the advancement of new treatments. Technical complexities associated with formalin-fixed paraffin-embedded (FFPE) clinical samples hinder molecular-level analyses of gliomas. Current single-cell RNA sequencing (scRNA-seq) platforms are inadequate for large-scale clinical applications. In this study, automated snRandom-seq is developed, a high-throughput single-nucleus total RNA sequencing platform optimized for archival FFPE samples. This platform integrates automated single-nucleus isolation and droplet barcoding systems with the random primer-based scRNA-seq chemistry, accommodating a broad spectrum of sample types. The automated snRandom-seq is applied to analyze 116 492 single nuclei from 17 FFPE samples of various glioma subtypes, including rare clinical samples and matched primary-recurrent glioblastomas (GBMs). The study provides comprehensive insights into the molecular characteristics of gliomas at the single-cell level. Abundant non-coding RNAs (ncRNAs) with distinct expression profiles across different glioma clusters and uncovered promising recurrence-related targets and pathways in primary-recurrent GBMs are identified. These findings establish automated snRandom-seq as a robust tool for scRNA-seq of FFPE samples, enabling exploration of molecular diversities and tumor evolution. This platform holds significant implications for large-scale integrative and retrospective clinical research.},
}
@article {pmid38956928,
year = {2024},
author = {Doorenweerd, C and San Jose, M and Leblanc, L and Barr, N and Geib, SM and Chung, AYC and Dupuis, JR and Ekayanti, A and Fiegalan, E and Hemachandra, KS and Aftab Hossain, M and Huang, CL and Hsu, YF and Morris, KY and Maryani A Mustapeng, A and Niogret, J and Pham, TH and Thi Nguyen, N and Sirisena, UGAI and Todd, T and Rubinoff, D},
title = {Towards a better future for DNA barcoding: Evaluating monophyly- and distance-based species identification using COI gene fragments of Dacini fruit flies.},
journal = {Molecular ecology resources},
volume = {24},
number = {6},
pages = {e13987},
doi = {10.1111/1755-0998.13987},
pmid = {38956928},
issn = {1755-0998},
support = {8130-0565//United States Department of Agriculture/ ; 8130-0665//United States Department of Agriculture/ ; 8130-0893//United States Department of Agriculture/ ; HAW00942-H//United States Department of Agriculture/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Electron Transport Complex IV/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Tephritidae/genetics/classification ; },
abstract = {The utility of a universal DNA 'barcode' fragment (658 base pairs of the Cytochrome C Oxidase I [COI] gene) has been established as a useful tool for species identification, and widely criticized as one for understanding the evolutionary history of a group. Large amounts of COI sequence data have been produced that hold promise for rapid species identification, for example, for biosecurity. The fruit fly tribe Dacini holds about a thousand species, of which 80 are pests of economic concern. We generated a COI reference library for 265 species of Dacini containing 5601 sequences that span most of the COI gene using circular consensus sequencing. We compared distance metrics versus monophyly assessments for species identification and although we found a 'soft' barcode gap around 2% pairwise distance, the exceptions to this rule dictate that a monophyly assessment is the only reliable method for species identification. We found that all fragments regularly used for Dacini fruit fly identification >450 base pairs long provide similar resolution. 11.3% of the species in our dataset were non-monophyletic in a COI tree, which is mostly due to species complexes. We conclude with recommendations for the future generation and use of COI libraries. We revise the generic assignment of Dacus transversus stat. rev. Hardy 1982, and Dacus perpusillus stat. rev. Drew 1971 and we establish Dacus maculipterus White 1998 syn. nov. as a junior synonym of Dacus satanas Liang et al. 1993.},
}
@article {pmid38955202,
year = {2024},
author = {Nath, A and Gangopadhayya, A and Ghuge, O and Kumar, S and Ramdasi, A and Karlekar, S and Sudeep, AB and Lole, KS},
title = {Determination of Species Identity and Genetic Diversity of Aedes aegypti and Other Medically Important Mosquitoes of India Using DNA Barcoding.},
journal = {The American journal of tropical medicine and hygiene},
volume = {111},
number = {2},
pages = {324-332},
pmid = {38955202},
issn = {1476-1645},
mesh = {Animals ; India ; *Aedes/genetics/classification/virology ; *DNA Barcoding, Taxonomic ; *Genetic Variation ; *Phylogeny ; *Mosquito Vectors/genetics/classification ; Electron Transport Complex IV/genetics ; Culex/genetics/classification/virology ; Anopheles/genetics/classification ; Species Specificity ; },
abstract = {Aedes aegypti-borne viruses (i.e., dengue, chikungunya, and Zika) have become endemic to India, posing a severe threat to public health. Vector control remains the mainstay of disease management due to nonavailability of licensed vaccines/therapeutics. Conventional morpho-taxonomical methods cannot differentiate between closely related sibling species or species complexes, and hence we evaluated two molecular markers, mitochondrial cytochrome c oxidase subunit 1 (Cox1) and nuclear DNA internal transcribed spacer 2 (-2) gene sequences, to characterize seven populations of Ae. aegypti and four medically important mosquito species (Aedes albopictus, Anopheles stephensi, Culex tritaeniorhyncus, and Culex murrelli). DNA extracted from the 11 mosquito populations (two mosquitoes per population) was polymerase chain reaction amplified, sequenced, and analyzed. Molecular characterization was found to be congruent with morphological identification, suggesting no variants or cryptic species exist in Ae. aegypti and the other mosquitoes studied. Phylogenetic analysis with sequences obtained with Cox1 gene of Ae. aegypti and other Aedes and non-Aedes mosquito species showed clustering of sequences from different species representing different clades, distinctly separating one taxon from the other, whereas ITS-2 sequences of Aedes aegypti from across the world clustered tightly. Nucleotide divergence values revealed a low percentage of intraspecies variation and a higher percentage of interspecies variation. The present study authenticates the applicability of Cox1 and ITS-2 in the precise identification of Ae. aegypti mosquitoes against cryptic or sibling species. Cox1 appeared to be a more reliable marker because it showed distinct clustering of mosquito species, and some sequence variations to represent genetic diversity.},
}
@article {pmid38949306,
year = {2024},
author = {Higgins, SA and Kara Murdoch, F and Clifton, JM and Brooks, JH and Fillinger, KL and Middleton, JK and Heater, BS},
title = {CRISPR-Cas9-mediated barcode insertion into Bacillus thuringiensis for surrogate tracking.},
journal = {Microbiology spectrum},
volume = {12},
number = {8},
pages = {e0000324},
pmid = {38949306},
issn = {2165-0497},
support = {FA8075-14-D-0003-FA807518F1414//DOD | OSD | Defense Technical Information Center (DTIC)/ ; 70RSAT19KPM0000470001//U.S. Department of Homeland Security (DHS)/ ; },
mesh = {*Bacillus thuringiensis/genetics ; *CRISPR-Cas Systems ; *DNA Barcoding, Taxonomic/methods ; Genome, Bacterial/genetics ; Bacillus anthracis/genetics ; Whole Genome Sequencing/methods ; Plasmids/genetics ; Gene Editing/methods ; },
abstract = {UNLABELLED: The use of surrogate organisms can enable researchers to safely conduct research on pathogens and in a broader set of conditions. Being able to differentiate between the surrogates used in the experiments and background contamination as well as between different experiments will further improve research efforts. One effective approach is to introduce unique genetic barcodes into the surrogate genome and track their presence using the quantitative polymerase chain reaction (qPCR). In this report, we utilized the CRISPR-Cas9 methodology, which employs a single plasmid and a transformation step to insert five distinct barcodes into Bacillus thuringiensis, a well-established surrogate for Bacillus anthracis when Risk Group 1 organisms are needed. We subsequently developed qPCR assays for barcode detection and successfully demonstrated the stability of the barcodes within the genome through five cycles of sporulation and germination. Additionally, we conducted whole-genome sequencing on these modified strains and analyzed 187 potential Cas9 off-target sites. We found no correlation between the mutations observed in the engineered strains and the predicted off-target sites, suggesting this genome engineering strategy did not directly result in off-target mutations in the genome. This simple approach has the potential to streamline the creation of barcoded B. thuringiensis strains for use in future studies on surrogate genomes.<br><br>IMPORTANCE: The use of Bacillus anthracis as a biothreat agent poses significant challenges for public health and national security. Bacillus anthracis surrogates, like Bacillus thuringiensis, are invaluable tools for safely understanding Bacillus anthracis properties without the safety concerns that would arise from using a virulent strain of Bacillus anthracis. We report a simple method for barcode insertion into Bacillus thuringiensis using the CRISPR-Cas9 methodology and subsequent tracking by quantitative polymerase chain reaction (qPCR). Moreover, whole-genome sequencing data and CRISPR-Cas9 off-target analyses in Bacillus thuringiensis suggest that this gene-editing method did not directly cause unwanted mutations in the genome. This study should assist in the facile development of barcoded Bacillus thuringiensis surrogate strains, among other biotechnological applications in Bacillus species.},
}
@article {pmid38949302,
year = {2024},
author = {Kramara, J and Kim, M-J and Ollinger, TL and Ristow, LC and Wakade, RS and Zarnowski, R and Wellington, M and Andes, DR and Mitchell, AG and Krysan, DJ},
title = {Systematic analysis of the Candida albicans kinome reveals environmentally contingent protein kinase-mediated regulation of filamentation and biofilm formation in vitro and in vivo.},
journal = {mBio},
volume = {15},
number = {8},
pages = {e0124924},
pmid = {38949302},
issn = {2150-7511},
support = {R01 AI133409/AI/NIAID NIH HHS/United States ; R21AI157341//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01AI133409//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01 AI177254/AI/NIAID NIH HHS/United States ; R21 AI157341/AI/NIAID NIH HHS/United States ; },
mesh = {*Candida albicans/genetics/enzymology/pathogenicity/physiology ; *Biofilms/growth &amp; development ; *Protein Kinases/genetics/metabolism ; Virulence ; Animals ; Fungal Proteins/genetics/metabolism ; Candidiasis/microbiology ; Gene Expression Regulation, Fungal ; Mice ; Hyphae/growth &amp; development/genetics ; },
abstract = {Protein kinases are critical regulatory proteins in both prokaryotes and eukaryotes. Accordingly, protein kinases represent a common drug target for a wide range of human diseases. Therefore, understanding protein kinase function in human pathogens such as the fungus Candida albicans is likely to extend our knowledge of its pathobiology and identify new potential therapies. To facilitate the study of C. albicans protein kinases, we constructed a library of 99 non-essential protein kinase homozygous deletion mutants marked with barcodes in the widely used SN genetic background. Here, we describe the construction of this library and the characterization of the competitive fitness of the protein kinase mutants under 11 different growth and stress conditions. We also screened the library for protein kinase mutants with altered filamentation and biofilm formation, two critical virulence traits of C. albicans. An extensive network of protein kinases governs these virulence traits in a manner highly dependent on the specific environmental conditions. Studies on specific protein kinases revealed that (i) the cell wall integrity MAPK pathway plays a condition-dependent role in filament initiation and elongation; (ii) the hyper-osmolar glycerol MAPK pathway is required for both filamentation and biofilm formation, particularly in the setting of in vivo catheter infection; and (iii) Sok1 is dispensable for filamentation in hypoxic environments at the basal level of a biofilm but is required for filamentation in normoxia. In addition to providing a new genetic resource for the community, these observations emphasize the environmentally contingent function of C. albicans protein kinases.IMPORTANCECandida albicans is one of the most common causes of fungal disease in humans for which new therapies are needed. Protein kinases are key regulatory proteins and are increasingly targeted by drugs for the treatment of a wide range of diseases. Understanding protein kinase function in C. albicans pathogenesis may facilitate the development of new antifungal drugs. Here, we describe a new library of 99 protein kinase deletion mutants to facilitate the study of protein kinases. Furthermore, we show that the function of protein kinases in two virulence-related processes, filamentation and biofilm formation, is dependent on the specific environmental conditions.},
}
@article {pmid38948916,
year = {2024},
author = {Dreyling, L and Boch, S and Lumbsch, HT and Schmitt, I},
title = {Surveying lichen diversity in forests: A comparison of expert mapping and eDNA metabarcoding of bark surfaces.},
journal = {MycoKeys},
volume = {106},
number = {},
pages = {153-172},
pmid = {38948916},
issn = {1314-4049},
abstract = {Lichens are an important part of forest ecosystems, contributing to forest biodiversity, the formation of micro-niches and nutrient cycling. Assessing the diversity of lichenised fungi in complex ecosystems, such as forests, requires time and substantial skills in collecting and identifying lichens. The completeness of inventories thus largely depends on the expertise of the collector, time available for the survey and size of the studied area. Molecular methods of surveying biodiversity hold the promise to overcome these challenges. DNA barcoding of individual lichen specimens and bulk collections is already being applied; however, eDNA methods have not yet been evaluated as a tool for lichen surveys. Here, we assess which species of lichenised fungi can be detected in eDNA swabbed from bark surfaces of living trees in central European forests. We compare our findings to an expert floristic survey carried out in the same plots about a decade earlier. In total, we studied 150 plots located in three study regions across Germany. In each plot, we took one composite sample based on six trees, belonging to the species Fagussylvatica, Piceaabies and Pinussylvestris. The eDNA method yielded 123 species, the floristic survey 87. The total number of species found with both methods was 167, of which 48% were detected only in eDNA, 26% only in the floristic survey and 26% in both methods. The eDNA contained a higher diversity of inconspicuous species. Many prevalent taxa reported in the floristic survey could not be found in the eDNA due to gaps in molecular reference databases. We conclude that, currently, eDNA has merit as a complementary tool to monitor lichen biodiversity at large scales, but cannot be used on its own. We advocate for the further development of specialised and more complete databases.},
}
@article {pmid38948467,
year = {2024},
author = {Shen, L and Zhang, M and Qiu, Y and Yang, L and Lu, Y and Li, H and Zhang, L and Tang, F and Wang, F and Zhu, C and Bao, H and Ding, Y},
title = {DNA barcoding combined with high-resolution melting analysis to discriminate rhubarb species and its traditional Chinese patent medicines.},
journal = {Frontiers in pharmacology},
volume = {15},
number = {},
pages = {1371890},
pmid = {38948467},
issn = {1663-9812},
abstract = {Introduction: Rhubarb is a frequently used and beneficial traditional Chinese medicine. Wild resources of these plants are constantly being depleted, meaning that rhubarb products have been subjected to an unparalleled level of adulteration. Consequentially, reliable technology is urgently required to verify the authenticity of rhubarb raw materials and commercial botanical drugs. Methods: In this study, the barcode-DNA high-resolution melting (Bar-HRM) method was applied to characterize 63 rhubarb samples (five Polygonaceae species: Rheum tanguticum, Rh. palmatum, Rh. officinale, Rumex japonicus and Ru. sp.) and distinguish the rhubarb contents of 24 traditional Chinese patent medicine (TCPM) samples. Three markers, namely ITS2, rbcL and psbA-trnH, were tested to assess the candidate DNA barcodes for their effectiveness in distinguishing rhubarb from its adulterants. A segment from ITS2 was selected as the most suitable mini-barcode to identify the botanical drug rhubarb in TCPMs. Then, rhubarbs and TCPM samples were subjected to HRM analysis based on the ITS2 barcode. Results: Among the tested barcoding loci, ITS2 displayed abundant sites of variation and was effective in identifying Polygonaceae species and their botanical origins. HRM analysis based on the ITS2 mini-barcode region successfully distinguished the authenticity of five Polygonaceae species and eight batches of TCPMs. Of the 18 TCPM samples, 66.7 % (12 samples) were identified as containing Rh. tanguticum or Rh. officinale. However, 33.3 % were shown to consist of adulterants. Conclusions: These results demonstrated that DNA barcoding combined with HRM is a specific, suitable and powerful approach for identifying rhubarb species and TCPMs, which is crucial to guaranteeing the security of medicinal plants being traded internationally.},
}
@article {pmid38947432,
year = {2024},
author = {Frigerio, J and Campone, L and Giustra, MD and Buzzelli, M and Piccoli, F and Galimberti, A and Cannavacciuolo, C and Ouled Larbi, M and Colombo, M and Ciocca, G and Labra, M},
title = {Convergent technologies to tackle challenges of modern food authentication.},
journal = {Heliyon},
volume = {10},
number = {11},
pages = {e32297},
pmid = {38947432},
issn = {2405-8440},
abstract = {The authentication process involves all the supply chain stakeholders, and it is also adopted to verify food quality and safety. Food authentication tools are an essential part of traceability systems as they provide information on the credibility of origin, species/variety identity, geographical provenance, production entity. Moreover, these systems are useful to evaluate the effect of transformation processes, conservation strategies and the reliability of packaging and distribution flows on food quality and safety. In this manuscript, we identified the innovative characteristics of food authentication systems to respond to market challenges, such as the simplification, the high sensitivity, and the non-destructive ability during authentication procedures. We also discussed the potential of the current identification systems based on molecular markers (chemical, biochemical, genetic) and the effectiveness of new technologies with reference to the miniaturized systems offered by nanotechnologies, and computer vision systems linked to artificial intelligence processes. This overview emphasizes the importance of convergent technologies in food authentication, to support molecular markers with the technological innovation offered by emerging technologies derived from biotechnologies and informatics. The potential of these strategies was evaluated on real examples of high-value food products. Technological innovation can therefore strengthen the system of molecular markers to meet the current market needs; however, food production processes are in profound evolution. The food 3D-printing and the introduction of new raw materials open new challenges for food authentication and this will require both an update of the current regulatory framework, as well as the development and adoption of new analytical systems.},
}
@article {pmid38946964,
year = {2024},
author = {Rossouw, L and Ngcobo, N and Clouse, K and Nattey, C and Technau, KG and Maskew, M},
title = {Augmenting maternal clinical cohort data with administrative laboratory dataset linkages: a validation study.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {38946964},
support = {R01 HD103466/HD/NICHD NIH HHS/United States ; U01 AI069924/AI/NIAID NIH HHS/United States ; U01 HD080441/HD/NICHD NIH HHS/United States ; },
abstract = {BACKGROUND: The use of big data and large language models in healthcare can play a key role in improving patient treatment and healthcare management, especially when applied to large-scale administrative data. A major challenge to achieving this is ensuring that patient confidentiality and personal information is protected. One way to overcome this is by augmenting clinical data with administrative laboratory dataset linkages in order to avoid the use of demographic information.<br><br>METHODS: We explored an alternative method to examine patient files from a large administrative dataset in South Africa (the National Health Laboratory Services, or NHLS), by linking external data to the NHLS database using specimen barcodes associated with laboratory tests. This offers us with a deterministic way of performing data linkages without accessing demographic information. In this paper, we quantify the performance metrics of this approach.<br><br>RESULTS: The linkage of the large NHLS data to external hospital data using specimen barcodes achieved a 95% success. Out of the 1200 records in the validation sample, 87% were exact matches and 9% were matches with typographic correction. The remaining 5% were either complete mismatches or were due to duplicates in the administrative data.<br><br>CONCLUSIONS: The high success rate indicates the reliability of using barcodes for linking data without demographic identifiers. Specimen barcodes are an effective tool for deterministic linking in health data, and may provide a method of creating large, linked data sets without compromising patient confidentiality.},
}
@article {pmid38943817,
year = {2024},
author = {Piersanti, S and Rebora, M and Turchetti, B and Salerno, G and Ruscetta, M and Zucconi, L and D'Alò, F and Buzzini, P and Sannino, C},
title = {Microplastics in the diet of Hermetia illucens: Implications for development and midgut bacterial and fungal microbiota.},
journal = {Waste management (New York, N.Y.)},
volume = {186},
number = {},
pages = {259-270},
doi = {10.1016/j.wasman.2024.06.021},
pmid = {38943817},
issn = {1879-2456},
mesh = {Animals ; *Larva/microbiology ; *Diptera/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Microplastics ; Polyvinyl Chloride ; Fungi/metabolism ; Bacteria/classification/metabolism ; Diet ; Mycobiome ; },
abstract = {In a world with a population exceeding 8 billion people and continuing to grow, pollution from food and plastic waste is causing long-term issues in ecosystems. Potential solutions may be found by exploiting insect-based bioconversion. In this context, we investigated the impact of polyvinyl chloride microparticles (PVC-MPs) on the development of Hermetia illucens (black soldier fly; BSF) and its midgut bacterial and fungal microbiota. The impact of PVC-MPs was evaluated feeding BSF larvae with a PVC-MPs-supplemented diet. The larvae exposed to different PVC-MPs concentrations (2.5%, 5%, 10% and 20% w/w) developed into adults with no significant increase in pupal mortality. Faster development and smaller pupae were observed when 20% PVC-MPs was provided. The BSF larvae ingest PVC-MPs, resulting in a reduction in MPs size. Larvae exposed to PVC-MPs did not exhibit differences in gut morphology. Regarding the impact of PVC-MPs on the structure of both bacterial and fungal communities, the overall alpha- and beta-diversity did not exhibit significant changes. However, the presence of PVC-MPs significantly affected the relative abundances of Enterobacteriaceae and Paenibacillaceae among the bacteria and of Dipodascaceae and Plectospharellaceae among the fungi (including yeast and filamentous life forms), suggesting that PVC-MP contamination has a taxa-dependent impact. These results indicate that BSF larvae can tolerate PVC-MPs in their diet, supporting the potential use of these insects in organic waste management, even in the presence of high levels of PVC-MP contamination.},
}
@article {pmid38943640,
year = {2024},
author = {Xiao, S and Yadav, S and Jayant, K},
title = {Probing multiplexed basal dendritic computations using two-photon 3D holographic uncaging.},
journal = {Cell reports},
volume = {43},
number = {7},
pages = {114413},
doi = {10.1016/j.celrep.2024.114413},
pmid = {38943640},
issn = {2211-1247},
support = {R21 EB029740/EB/NIBIB NIH HHS/United States ; },
mesh = {*Dendrites/metabolism/physiology ; Animals ; *Holography/methods ; Pyramidal Cells/metabolism/physiology ; Synapses/metabolism/physiology ; Action Potentials/physiology ; Receptors, N-Methyl-D-Aspartate/metabolism ; Photons ; Mice ; Male ; },
abstract = {Basal dendrites of layer 5 cortical pyramidal neurons exhibit Na[+] and N-methyl-D-aspartate receptor (NMDAR) regenerative spikes and are uniquely poised to influence somatic output. Nevertheless, due to technical limitations, how multibranch basal dendritic integration shapes and enables multiplexed barcoding of synaptic streams remains poorly mapped. Here, we combine 3D two-photon holographic transmitter uncaging, whole-cell dynamic clamp, and biophysical modeling to reveal how synchronously activated synapses (distributed and clustered) across multiple basal dendritic branches are multiplexed under quiescent and in vivo-like conditions. While dendritic regenerative Na[+] spikes promote millisecond somatic spike precision, distributed synaptic inputs and NMDAR spikes regulate gain. These concomitantly occurring dendritic nonlinearities enable multiplexed information transfer amid an ongoing noisy background, including under back-propagating voltage resets, by barcoding the axo-somatic spike structure. Our results unveil a multibranch dendritic integration framework in which dendritic nonlinearities are critical for multiplexing different spatial-temporal synaptic input patterns, enabling optimal feature binding.},
}
@article {pmid38943021,
year = {2024},
author = {Farzad, N and Enninful, A and Bao, S and Zhang, D and Deng, Y and Fan, R},
title = {Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue.},
journal = {Nature protocols},
volume = {19},
number = {11},
pages = {3389-3425},
pmid = {38943021},
issn = {1750-2799},
mesh = {Animals ; *Transposases/genetics/metabolism ; Mice ; *Epigenome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Epigenomics/methods ; DNA Barcoding, Taxonomic/methods ; Sequence Analysis, DNA/methods ; Epigenesis, Genetic ; },
abstract = {Spatial epigenetic mapping of tissues enables the study of gene regulation programs and cellular functions with the dependency on their local tissue environment. Here we outline a complete procedure for two spatial epigenomic profiling methods: spatially resolved genome-wide profiling of histone modifications using in situ cleavage under targets and tagmentation (CUT&amp;Tag) chemistry (spatial-CUT&amp;Tag) and transposase-accessible chromatin sequencing (spatial-ATAC-sequencing) for chromatin accessibility. Both assays utilize in-tissue Tn5 transposition to recognize genomic DNA loci followed by microfluidic deterministic barcoding to incorporate spatial address codes. Furthermore, these two methods do not necessitate prior knowledge of the transcription or epigenetic markers for a given tissue or cell type but permit genome-wide unbiased profiling pixel-by-pixel at the 10 μm pixel size level and single-base resolution. To support the widespread adaptation of these methods, details are provided in five general steps: (1) sample preparation; (2) Tn5 transposition in spatial-ATAC-sequencing or antibody-controlled pA-Tn5 tagmentation in CUT&amp;Tag; (3) library preparation; (4) next-generation sequencing; and (5) data analysis using our customed pipelines available at: https://github.com/dyxmvp/Spatial_ATAC-seq and https://github.com/dyxmvp/spatial-CUT-Tag . The whole procedure can be completed on four samples in 2-3 days. Familiarity with basic molecular biology and bioinformatics skills with access to a high-performance computing environment are required. A rudimentary understanding of pathology and specimen sectioning, as well as deterministic barcoding in tissue-specific skills (e.g., design of a multiparameter barcode panel and creation of microfluidic devices), are also advantageous. In this protocol, we mainly focus on spatial profiling of tissue region-specific epigenetic landscapes in mouse embryos and mouse brains using spatial-ATAC-sequencing and spatial-CUT&amp;Tag, but these methods can be used for other species with no need for species-specific probe design.},
}
@article {pmid38940749,
year = {2024},
author = {Nolan, DJ and DaRoza, J and Brody, R and Ganta, K and Luzuriaga, K and Huston, C and Rosenthal, S and Lamers, SL and Rose, R},
title = {Comparing Gold-Standard Sanger Sequencing with Two Next-Generation Sequencing Platforms of HIV-1 gp160 Single Genome Amplicons.},
journal = {AIDS research and human retroviruses},
volume = {40},
number = {11},
pages = {659-669},
pmid = {38940749},
issn = {1931-8405},
support = {R43 FD008039/FD/FDA HHS/United States ; UL1 TR001453/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods/standards ; *HIV-1/genetics/classification ; *Sequence Analysis, DNA/methods ; HIV Envelope Protein gp160/genetics ; HIV Infections/virology ; Consensus Sequence ; Genome, Viral ; },
abstract = {Our goal was to assess the accuracy of next generation sequencing (NGS) compared with Sanger. We performed single genome amplification (SGA) of HIV-1 gp160 on extracted tissue DNA from two HIV+ individuals. Amplicons (n = 30) were sequenced with Sanger or reamplified with barcoded primers and pooled before sequencing using Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PB). For each amplicon, a consensus sequence for NGS reads was obtained by (1) mapping reads to the Sanger sequence when available ("reference-based") or (2) mapping reads to a "pseudo-reference" sequence, i.e., a consensus sequence of a subset of NGS reads ("reference-free"). PB reads were clustered based on genetic similarity. A Sanger consensus sequence was obtained for 23/30 amplicons, for which all NGS consensus sequences were identical (n = 9) or nearly identical (n = 14) compared with Sanger. For the nine mismatches between Sanger/NGS, the nucleotide in the NGS sequence matched all other sequences from that patient. Of the 7/30 amplicons without a Sanger sequence, NGS sequences had ≥35 ambiguous calls in five amplicons and 0 ambiguities in two amplicons. Analysis of the electropherograms showed failure of a single sequencing primer for the latter two amplicons (consistent with a single template) and overlapping peaks for the other five (consistent with multiple templates). Clustering results closely followed the Sanger/NGS consensus results, where amplicons derived from a single template also had a single cluster and vice versa (with one exception, which could be the result of barcode misidentification). Representative sequences from the clusters contained 2-13 differences compared with Sanger/NGS. In summary, we show that both ONT and PB can produce amplicon consensus sequences with similar or higher accuracy compared with Sanger and, importantly, without the need for a known reference sequence. Clustering could be useful in some circumstances to predict or confirm the presence of multiple starting templates.},
}
@article {pmid38935254,
year = {2024},
author = {Saathoff, S and Goodman, CL and Haas, E and Mettelmann, I and Stanley, D},
title = {A cell line derived from the black soldier fly, Hermetia illucens (Diptera: Stratiomyidae).},
journal = {In vitro cellular &amp; developmental biology. Animal},
volume = {},
number = {},
pages = {},
pmid = {38935254},
issn = {1543-706X},
support = {5070-22000-038-000-D//Agricultural Research Service/ ; },
abstract = {Insect cell lines are effective tools used in industry and academia. For example, they are used in screening potential insecticides, in making certain proteins for biomedical applications, and in basic research into insect biology. So far, there are no cell lines derived from the black soldier fly, Hermetia illucens (BSF). This may become an issue because BSFs are employed in a range of industrial and household processes. BSFs are used in producing biodiesel, in developing cosmetics and skin creams, and in the production of some medicines and animal feeds. BSF larvae process waste streams from a variety of sources into food for some animals and are also used in household composting. Our BSF cell line, designated BCIRL-HiE0122021-SGS, was developed from eggs using the medium CLG#2 (50% L-15 + 50% EX-CELL 420, with 9% FBS and antibiotics), with many other media being tested. This cell line consists of attached cells with a variety of morphologies and its identity was authenticated using CO1 barcoding. A growth curve was generated and the resulting doubling time was 118 h. We quantified the fatty acid methyl esters (FAMES) and recorded the expected range of saturated, monounsaturated, and polyunsaturated FAMEs, with only trace levels of lauric acid being noted. The BSF cell line is available free of charge by request.},
}
@article {pmid38933488,
year = {2024},
author = {Kurata, S and Mano, S and Nakahama, N and Hirota, SK and Suyama, Y and Ito, M},
title = {Development of mitochondrial DNA cytochrome c oxidase subunit I primer sets to construct DNA barcoding library using next-generation sequencing.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e117014},
pmid = {38933488},
issn = {1314-2828},
abstract = {Insects are one of the most diverse eukaryotic groups on the planet, with one million or more species present, including those yet undescribed. The DNA barcoding system has been developed, which has aided in the identification of cryptic species and undescribed species. The mitochondrial cytochrome c oxidase I region (mtDNA COI) has been utilised for the barcoding analysis of insect taxa. Thereafter, next-generation sequencing (NGS) technology has been developed, allowing for rapid acquisition of massive amounts of sequence data for genetic analyses. Although NGS-based PCR primers designed to amplify the mtDNA COI region have been developed, their target regions were only a part of COI region and/or there were taxonomic bias for PCR amplification. As the mtDNA COI region is a traditional DNA marker for the DNA barcoding system, modified primers for this region would greatly contribute to taxonomic studies. In this study, we redesigned previously developed PCR primer sets that targetted the mtDNA COI barcoding region to improve amplification efficiency and to enable us to conduct sequencing analysis on NGS. As a result, the redesigned primer sets achieved a high success rate (> 85%) for species examined in this study, covering four insect orders (Coleoptera, Lepidoptera, Orthoptera and Odonata). Thus, by combining the primers with developed primer sets for 12S or 16S rRNA regions, we can conduct more detailed taxonomic, phylogeographic and conservation genetic studies using NGS.},
}
@article {pmid38927697,
year = {2024},
author = {Kim, JE and Kim, KM and Kim, YS and Chung, GY and Che, SH and Na, CS},
title = {Chloroplast Genomes of Vitis flexuosa and Vitis amurensis: Molecular Structure, Phylogenetic, and Comparative Analyses for Wild Plant Conservation.},
journal = {Genes},
volume = {15},
number = {6},
pages = {},
pmid = {38927697},
issn = {2073-4425},
support = {2021400B10-2425-CA02//Korea Forestry Promotion Institute/ ; },
mesh = {*Vitis/genetics ; *Genome, Chloroplast/genetics ; *Phylogeny ; Evolution, Molecular ; Genetic Variation ; Republic of Korea ; Chloroplasts/genetics ; Genome, Plant ; },
abstract = {The chloroplast genome plays a crucial role in elucidating genetic diversity and phylogenetic relationships. Vitis vinifera L. (grapevine) is an economically important species, prompting exploration of wild genetic resources to enhance stress resilience. We meticulously assembled the chloroplast genomes of two Korean Vitis L. species, V. flexuosa Thunb. and V. amurensis Rupr., contributing valuable data to the Korea Crop Wild Relatives inventory. Through exhaustive specimen collection spanning diverse ecological niches across South Korea, we ensured comprehensive representation of genetic diversity. Our analysis, which included rigorous codon usage bias assessment and repeat analysis, provides valuable insights into amino acid preferences and facilitates the identification of potential molecular markers. The assembled chloroplast genomes were subjected to meticulous annotation, revealing divergence hotspots enriched with nucleotide diversity, thereby presenting promising candidates for DNA barcodes. Additionally, phylogenetic analysis reaffirmed intra-genus relationships and identified related crops, shedding light on evolutionary patterns within the genus. Comparative examination with chloroplast genomes of other crops uncovered conserved sequences and variable regions, offering critical insights into genetic evolution and adaptation. Our study advances the understanding of chloroplast genomes, genetic diversity, and phylogenetic relationships within Vitis species, thereby laying a foundation for enhancing grapevine genetic diversity and resilience to environmental challenges.},
}
@article {pmid38927627,
year = {2024},
author = {Li, H and Miao, X and Wang, R and Liao, Y and Wen, Y and Zhang, R and Lin, L},
title = {Biodiversity of Demersal Fish Communities in the Cosmonaut Sea Revealed by DNA Barcoding Analyses.},
journal = {Genes},
volume = {15},
number = {6},
pages = {},
pmid = {38927627},
issn = {2073-4425},
support = {IRASCC01-02-02&amp;02-02//Chinese Arctic and Antarctic Administration, Ministry of Natural Resources of the People's Republic of China/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Biodiversity ; Antarctic Regions ; *Electron Transport Complex IV/genetics ; Phylogeny ; Oceans and Seas ; },
abstract = {The Cosmonaut Sea is one of the least accessed regions in the Southern Ocean, and our knowledge about the fish biodiversity in the region is sparse. In this study, we provided a description of demersal fish diversity in the Cosmonaut Sea by analysing cytochrome oxidase I (COI) barcodes of 98 fish samples that were hauled by trawling during the 37th and 38th Chinese National Antarctic Research Expedition (CHINARE) cruises. Twenty-four species representing 19 genera and 11 families, namely, Artedidraconidae, Bathydraconidae, Bathylagidae, Channichthyidae, Liparidae, Macrouridae, Muraenolepididae, Myctophidae, Nototheniidae, Paralepididae and Zoarcidae, were discriminated and identified, which were largely identical to local fish occurrence records and the general pattern of demersal fish communities at high Antarctic shelf areas. The validity of a barcoding gap failed to be detected and confirmed across all species due to the indicative signals of two potential cryptic species. Nevertheless, DNA barcoding still demonstrated to be a very efficient and sound method for the discrimination and classification of Antarctic fishes. In the future, various sampling strategies that cover all geographic sections and depth strata of the Cosmonaut Sea are encouraged to enhance our understanding of local fish communities, within which DNA barcoding can play an important role in either molecular taxonomy or the establishment of a dedicated local reference database for eDNA metabarcoding analyses.},
}
@article {pmid38927625,
year = {2024},
author = {Karbarz, M and Szlachcikowska, D and Zapał, A and Leśko, A},
title = {Unlocking the Genetic Identity of Endangered Paphiopedilum Orchids: A DNA Barcoding Approach.},
journal = {Genes},
volume = {15},
number = {6},
pages = {},
pmid = {38927625},
issn = {2073-4425},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Orchidaceae/genetics/classification ; *Endangered Species ; Phylogeny ; DNA, Plant/genetics ; },
abstract = {Orchids of the genus Paphiopedilum, also called slippers, are among the most valued representatives of the Orchidaceae family due to their aesthetic qualities. Due to overexploitation, deforestation, and illegal trade in these plants, especially in the vegetative phase, Paphiopedilum requires special protection. This genus is listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora. Their precise identification is of great importance for the preservation of genetic resources and biodiversity of the orchid family (Orchidaceae). Therefore, the main objective of the study was to investigate the usefulness of the DNA barcoding technique for the identification of endangered orchids of the genus Paphiopedilum and to determine the effectiveness of five loci: matK, rbcL, ITS2, atpF-atpH and trnH-psbA as potential molecular markers for species of this genus. Among single locus barcodes, matK was the most effective at identifying species (64%). Furthermore, matK, ITS2, matK + rbcL, and matK + trnH-psbA barcodes can be successfully used as a complementary tool to identify Paphiopedilum orchids while supporting morphological data provided by taxonomists.},
}
@article {pmid38927245,
year = {2024},
author = {Sutula, M and Kakanay, A and Tussipkan, D and Dzhumanov, S and Manabayeva, S},
title = {Phylogenetic Analysis of Rare and Endangered Tulipa Species (Liliaceae) of Kazakhstan Based on Universal Barcoding Markers.},
journal = {Biology},
volume = {13},
number = {6},
pages = {},
pmid = {38927245},
issn = {2079-7737},
support = {BR18574125//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; OR11465422//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {In Kazakhstan, the genus Tulipa is represented by 35 species, 18 of which are listed in the Red Data Book of Kazakhstan and protected by the state. Recent studies of tulip specimens from regions bordering Kazakhstan emphasize the significance of species inventory and report the discovery of several hybrids. In this study, eight tulip species were identified based on morphological characteristics and using DNA barcoding methods. Molecular genetic markers, including nrDNA (ITS) and cpDNA markers (rbcL, matK), of the studied species were sequenced and analyzed using the Bayesian inference and maximum likelihood phylogenetic analysis methods. Our work demonstrates that DNA barcodes based on the ITS, rbcL, and matK marker regions have successful practical applicability, with ITS being the most informative at the intragenic level. However, for distinguishing closely related taxa, the most effective approach would be to use a combined dataset of sequences from multiple DNA markers. The results showed discrepancies in the placement of several taxa (T. kaufmanniana, T. patens), likely due to introgression and natural spontaneous hybridization. The molecular phylogenetic analysis suggests the existence of a previously undescribed hybrid between T. patens and T. alberti. Further detailed population studies are needed to validate this hypothesis.},
}
@article {pmid38926630,
year = {2024},
author = {Liu, H},
title = {Bacterial barcoding facilitates plant microbiome studies.},
journal = {Nature reviews. Microbiology},
volume = {22},
number = {8},
pages = {459},
pmid = {38926630},
issn = {1740-1534},
mesh = {*Microbiota/genetics ; *Plants/microbiology ; *DNA Barcoding, Taxonomic/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; },
}
@article {pmid38926392,
year = {2024},
author = {Li, S and Xv, Y and Sun, Y and Shen, Z and Hao, R and Yan, J and Liu, M and Liu, Z and Jing, T and Li, X and Zhang, X},
title = {Macrophage-derived CD36 + exosome subpopulations as novel biomarkers of Candida albicans infection.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {14723},
pmid = {38926392},
issn = {2045-2322},
mesh = {*Exosomes/metabolism ; *Candida albicans ; *Biomarkers/metabolism ; *Macrophages/metabolism/microbiology/immunology ; *CD36 Antigens/metabolism ; *Candidiasis/diagnosis/microbiology/metabolism/immunology ; Humans ; Animals ; Mice ; },
abstract = {Invasive candidiasis (IC) is a notable healthcare-associated fungal infection, characterized by high morbidity, mortality, and substantial treatment costs. Candida albicans emerges as a principal pathogen in this context. Recent academic advancements have shed light on the critical role of exosomes in key biological processes, such as immune responses and antigen presentation. This burgeoning body of research underscores the potential of exosomes in the realm of medical diagnostics and therapeutics, particularly in relation to fungal infections like IC. The exploration of exosomal functions in the pathophysiology of IC not only enhances our understanding of the disease but also opens new avenues for innovative therapeutic interventions. In this investigation, we focus on exosomes (Exos) secreted by macrophages, both uninfected and those infected with C. albicans. Our objective is to extract and analyze these exosomes, delving into the nuances of their protein compositions and subgroups. To achieve this, we employ an innovative technique known as Proximity Barcoding Assay (PBA). This methodology is pivotal in our quest to identify novel biological targets, which could significantly enhance the diagnostic and therapeutic approaches for C. albicans infection. The comparative analysis of exosomal contents from these two distinct cellular states promises to yield insightful data, potentially leading to breakthroughs in understanding and treating this invasive fungal infection. In our study, we analyzed differentially expressed proteins in exosomes from macrophages and C. albicans -infected macrophages, focusing on proteins such as ACE2, CD36, CAV1, LAMP2, CD27, and MPO. We also examined exosome subpopulations, finding a dominant expression of MPO in the most prevalent subgroup, and a distinct expression of CD36 in cluster14. These findings are crucial for understanding the host response to C. albicans and may inform targeted diagnostic and therapeutic approaches. Our study leads us to infer that MPO and CD36 proteins may play roles in the immune escape mechanisms of C. albicans. Additionally, the CD36 exosome subpopulations, identified through our analysis, could serve as potential biomarkers and therapeutic targets for C. albicans infection. This insight opens new avenues for understanding the infection's pathology and developing targeted treatments.},
}
@article {pmid38925122,
year = {2024},
author = {Zhang, Z and Melzer, ME and Arun, KM and Sun, H and Eriksson, CJ and Fabian, I and Shaashua, S and Kiani, K and Oren, Y and Goyal, Y},
title = {Synthetic DNA barcodes identify singlets in scRNA-seq datasets and evaluate doublet algorithms.},
journal = {Cell genomics},
volume = {4},
number = {7},
pages = {100592},
pmid = {38925122},
issn = {2666-979X},
mesh = {*Algorithms ; *Single-Cell Analysis/methods ; *DNA Barcoding, Taxonomic/methods ; Humans ; Machine Learning ; Sequence Analysis, RNA/methods ; Animals ; Single-Cell Gene Expression Analysis ; },
abstract = {Single-cell RNA sequencing (scRNA-seq) datasets contain true single cells, or singlets, in addition to cells that coalesce during the protocol, or doublets. Identifying singlets with high fidelity in scRNA-seq is necessary to avoid false negative and false positive discoveries. Although several methodologies have been proposed, they are typically tested on highly heterogeneous datasets and lack a priori knowledge of true singlets. Here, we leveraged datasets with synthetically introduced DNA barcodes for a hitherto unexplored application: to extract ground-truth singlets. We demonstrated the feasibility of our framework, "singletCode," to evaluate existing doublet detection methods across a range of contexts. We also leveraged our ground-truth singlets to train a proof-of-concept machine learning classifier, which outperformed other doublet detection algorithms. Our integrative framework can identify ground-truth singlets and enable robust doublet detection in non-barcoded datasets.},
}
@article {pmid38922410,
year = {2024},
author = {Sakae, K and Kawai, S and Kitagami, Y and Matsuo, N and Selosse, MA and Tanikawa, T and Matsuda, Y},
title = {Effects of fungicide treatments on mycorrhizal communities and carbon acquisition in the mixotrophic Pyrola japonica (Ericaceae).},
journal = {Mycorrhiza},
volume = {34},
number = {4},
pages = {293-302},
pmid = {38922410},
issn = {1432-1890},
support = {2023-4099//Japan Science Society/ ; 25304026//Japan Society for the Promotion of Science/ ; },
mesh = {*Mycorrhizae/physiology/drug effects ; *Fungicides, Industrial/pharmacology ; *Carbon/metabolism ; Japan ; *Pyrola/microbiology/metabolism ; Plant Roots/microbiology ; Benomyl/pharmacology ; Soil Microbiology ; Plant Leaves/microbiology ; },
abstract = {Pyrola japonica, a member of the family Ericaceae, is a mixotroph that grows on forest floors and obtains carbon (C) from both its photosynthesis and its mycorrhizal fungi. Its mycorrhizal community is dominated by Russulaceae. However, the mechanism of its C acquisition and its flexibility are not well understood. Our aim was to assess the impact of disturbance of the mycorrhizal fungal communities on C acquisition by P. japonica. We repeatedly applied a fungicide (Benomyl) to soils around P. japonica plants in a broad-leaved forest of central Japan, in order to disturb fungal associates near roots. After fungicide treatment, P. japonica roots were collected and subjected to barcoding by next-generation sequencing, focusing on the ITS2 region. The rate of mycorrhizal formation and α-diversity did not significantly change upon fungicide treatments. Irrespective of the treatments, Russulaceae represented more than 80% of the taxa. Leaves and seeds of the plants were analysed for [13]C stable isotope ratios that reflect fungal C gain. Leaf and seed δ[13]C values with the fungicide treatment were significantly lower than those with the other treatments. Thus the fungicide did not affect mycorrhizal communities in the roots, but disturbed mycorrhizal fungal pathways via extraradical hyphae, and resulted in a more photosynthetic behaviour of P. japonica for leaves and seeds.},
}
@article {pmid38921121,
year = {2024},
author = {Ganbaatar, B and Li, Q and Xi, O and Cao, H and Zhu, C},
title = {One Step beyond Species Description: Unveiling a Fine-Scale Diversity within the Genus Dzhanokmenia Kostjukov (Hymenoptera: Eulophidae).},
journal = {Insects},
volume = {15},
number = {6},
pages = {},
pmid = {38921121},
issn = {2075-4450},
support = {32330013//the National Natural Science Foundation of China/ ; 2008DP173354//the Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences/ ; },
abstract = {Although Chalcidoidea is one of the megadiverse superfamilies in Hymenoptera, numerous species are still being discovered and described. However, the difficulties in delimiting intra- and interspecific variation hinder this process. In this study, DNA barcoding methods using the COI gene were employed to investigate the morphological variation within Dzhanokmenia Kostjukov, 1977. The nuclear locus, 28S D2, was used to infer a phylogeny to gain an understanding of the relationship of Dzhanokmenia with other potentially close genera. Through a preliminary DNA barcode library established here, including eight species, we calibrated the intraspecific variation in certain diagnostic characters for the new species described here, D. brevifunis Ganbaatar &amp; Cao sp. nov. Maximum likelihood results show that Dzhanokmenia is clustered with the genera associated with Tetrastichus, such as Chaenotetrastichus Graham, 1987, Baryscapus Förster, 1856, Tetrastichus Haliday, 1844, and Oomyzus Rondani, 1870 involved in this study. Our results indicate that the species diversity of Dzhanokmenia is understudied and tentatively confirm that Dzhanokmenia has a potential close relationship with Baryscapus. Along with the DNA barcode library, the referenced phylogeny datasets improve the understanding of the systematic position of Dzhanokmenia within the subfamily Tetrastichinae and the definition of this genus in terms of morphology, thereby facilitating species delimitation, discovery, and description within Dzhanokmenia.},
}
@article {pmid38920364,
year = {2024},
author = {Mau, RL and Hayer, M and Purcell, AM and Geisen, S and Hungate, BA and Schwartz, E},
title = {Measurements of soil protist richness and community composition are influenced by primer pair, annealing temperature, and bioinformatics choices.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {7},
pages = {e0080024},
pmid = {38920364},
issn = {1098-5336},
support = {DE-AC52-07NA27344//U.S. Department of Energy (DOE)/ ; DE-SC0020172//U.S. Department of Energy (DOE)/ ; DE-SC0023126//U.S. Department of Energy (DOE)/ ; },
mesh = {*RNA, Ribosomal, 18S/genetics ; *Computational Biology/methods ; *Eukaryota/genetics/classification ; *DNA Primers/genetics ; *Soil Microbiology ; Biodiversity ; Temperature ; Soil/parasitology/chemistry ; Polymerase Chain Reaction ; },
abstract = {Protists are a diverse and understudied group of microbial eukaryotic organisms especially in terrestrial environments. Advances in molecular methods are increasing our understanding of the distribution and functions of these creatures; however, there is a vast array of choices researchers make including barcoding genes, primer pairs, PCR settings, and bioinformatic options that can impact the outcome of protist community surveys. Here, we tested four commonly used primer pairs targeting the V4 and V9 regions of the 18S rRNA gene using different PCR annealing temperatures and processed the sequences with different bioinformatic parameters in 10 diverse soils to evaluate how primer pair, amplification parameters, and bioinformatic choices influence the composition and richness of protist and non-protist taxa using Illumina sequencing. Our results showed that annealing temperature influenced sequencing depth and protist taxon richness for most primer pairs, and that merging forward and reverse sequencing reads for the V4 primer pairs dramatically reduced the number of sequences and taxon richness of protists. The data sets of primers that targeted the same 18S rRNA gene region (e.g., V4 or V9) had similar protist community compositions; however, data sets from primers targeting the V4 18S rRNA gene region detected a greater number of protist taxa compared to those prepared with primers targeting the V9 18S rRNA region. There was limited overlap of protist taxa between data sets targeting the two different gene regions (80/549 taxa). Together, we show that laboratory and bioinformatic choices can substantially affect the results and conclusions about protist diversity and community composition using metabarcoding.IMPORTANCEEcosystem functioning is driven by the activity and interactions of the microbial community, in both aquatic and terrestrial environments. Protists are a group of highly diverse, mostly unicellular microbes whose identity and roles in terrestrial ecosystem ecology have been largely ignored until recently. This study highlights the importance of choices researchers make, such as primer pair, on the results and conclusions about protist diversity and community composition in soils. In order to better understand the roles protist taxa play in terrestrial ecosystems, biases in methodological and analytical choices should be understood and acknowledged.},
}
@article {pmid38919770,
year = {2024},
author = {Vogel, J and Sauren, J and Peters, RS},
title = {New evidence on the identity of the European Helorus species (Hymenoptera, Proctotrupoidea, Heloridae).},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e122523},
pmid = {38919770},
issn = {1314-2828},
abstract = {BACKGROUND: Species of Helorus Latreille 1802 are rarely collected endoparasitoids of Chrysopidae larvae (Neuroptera). Previous work on the limits between the European species of this species-poor genus, based on morphology only, has left some uncertainties. Here, we approach these cases and revisit previous taxonomic decisions using freshly collected and museum material.<br><br>NEW INFORMATION: We generated the first large-scale Heloridae DNA barcode dataset, combined these with morphological data in an integrative taxonomic approach, and added information from studying all relevant type material. We found five species, Helorusanomalipes (Panzer, 1798), H.coruscus Haliday, 1857 stat. rev., H.nigripes F&#xf6;rster, 1856, H.ruficornis F&#xf6;rster, 1856, and H.striolatus Cameron, 1906, for which we provide an updated identification key. DNA barcode data are added to publicly available DNA barcode reference databases, for all species, except H.nigripes.},
}
@article {pmid38918858,
year = {2024},
author = {Cardoso, SF and Guesser, JVC and Rodrigues, AAF and Brazil, RP and Rona, LDP and Pitaluga, AN},
title = {Leishmania infantum detection in Nyssomyia neivai and dogs in Southern Brazil.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {269},
pmid = {38918858},
issn = {1756-3305},
support = {16/2014//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Animals ; Dogs ; *Leishmania infantum/genetics/isolation &amp; purification ; Brazil/epidemiology ; *Psychodidae/parasitology/classification ; *Dog Diseases/parasitology/epidemiology ; *Leishmaniasis, Visceral/veterinary/epidemiology/parasitology/transmission ; Female ; *Insect Vectors/parasitology ; Polymerase Chain Reaction ; Male ; },
abstract = {BACKGROUND: The sand fly Nyssomyia neivai is one of the most abundant species in Southern Brazil. It is frequently found in areas that are foci of visceral leishmaniasis in the state of Santa Catarina, caused by Leishmania infantum. In this region, the main vector of L. infantum, Lutzomyia longipalpis, has not been detected. In the absence of L. longipalpis, this study aimed to identify the sand fly fauna and diagnose any potential Leishmania spp. infection in sand flies and in dogs in a region of Southern Brazil that experienced a recent canine visceral leishmaniasis outbreak.<br><br>METHODS: This report includes a survey of the sand fly fauna at the Zoonosis Control Center of the Municipality of Tubar&#xe3;o (Santa Catarina, Brazil). Molecular tests were conducted to investigate Leishmania spp. natural infection in sand flies using polymerase chain reaction (PCR). In positive females, in addition to morphological identification, molecular analysis through DNA barcoding was performed to determine the sand fly species. Additionally, the dogs were tested for the presence of Leishmania spp. using a non-invasive technique for the collection of biological material, to be assessed by PCR.<br><br>RESULTS: A total of 3419 sand flies, belonging to five genera, were collected. Nyssomyia neivai was the most abundant species (85.8%), followed by Migonemyia migonei (13.3%), Pintomyia fischeri (0.8%), Evandromyia edwardsi (<&#x2009;0.1%), and species of the genus Brumptomyia. (0.1%). Out of the 509 non-engorged females analyzed by PCR, two (0.4%) carried L. infantum DNA. The naturally infected females were identified as Ny. neivai, in both morphological and molecular analysis. In addition, two out of 47 conjunctival swabs from dogs tested positive for L. infantum, yielding an infection rate of 4.2%.<br><br>CONCLUSIONS: These results confirm the presence of Ny. neivai naturally infected with L. infantum in an area where dogs were also infected by the parasite, suggesting its potential role as a vector in Southern Brazil.},
}
@article {pmid38918509,
year = {2024},
author = {Bauer, N and Oberist, C and Poth, M and Stingele, J and Popp, O and Ausländer, S},
title = {Genomic barcoding for clonal diversity monitoring and control in cell-based complex antibody production.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {14587},
pmid = {38918509},
issn = {2045-2322},
mesh = {CHO Cells ; *Cricetulus ; Animals ; *DNA Barcoding, Taxonomic/methods ; *Clone Cells ; Genomics/methods ; Antibodies, Monoclonal/genetics ; },
abstract = {Engineered mammalian cells are key for biotechnology by enabling broad applications ranging from in vitro model systems to therapeutic biofactories. Engineered cell lines exist as a population containing sub-lineages of cell clones that exhibit substantial genetic and phenotypic heterogeneity. There is still a limited understanding of the source of this inter-clonal heterogeneity as well as its implications for biotechnological applications. Here, we developed a genomic barcoding strategy for a targeted integration (TI)-based CHO antibody producer cell line development process. This technology provided novel insights about clone diversity during stable cell line selection on pool level, enabled an imaging-independent monoclonality assessment after single cell cloning, and eventually improved hit-picking of antibody producer clones by monitoring of cellular lineages during the cell line development (CLD) process. Specifically, we observed that CHO producer pools generated by TI of two plasmids at a single genomic site displayed a low diversity (< 0.1% RMCE efficiency), which further depends on the expressed molecules, and underwent rapid population skewing towards dominant clones during routine cultivation. Clonal cell lines from one individual TI event demonstrated a significantly lower variance regarding production-relevant and phenotypic parameters as compared to cell lines from distinct TI events. This implies that the observed cellular diversity lies within pre-existing cell-intrinsic factors and that the majority of clonal variation did not develop during the CLD process, especially during single cell cloning. Using cellular barcodes as a proxy for cellular diversity, we improved our CLD screening workflow and enriched diversity of production-relevant parameters substantially. This work, by enabling clonal diversity monitoring and control, paves the way for an economically valuable and data-driven CLD process.},
}
@article {pmid38918059,
year = {2024},
author = {Belford, SG},
title = {Combining Morphological Characteristics and DNA Barcoding Techniques Confirm Sea Urchins of the Genus Echinometra (Echinodermata: Echinoidea) in Marine Habitat Located at Extreme Regions of the Caribbean Sea.},
journal = {Integrative and comparative biology},
volume = {64},
number = {4},
pages = {1078-1086},
doi = {10.1093/icb/icae083},
pmid = {38918059},
issn = {1557-7023},
support = {//University of Tennessee/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Sea Urchins/genetics/anatomy &amp; histology ; Caribbean Region ; *Electron Transport Complex IV/genetics ; Phylogeny ; Ecosystem ; Trinidad and Tobago ; },
abstract = {Echinometra spp. are pantropical echinoids found in benthic marine habitat throughout the Caribbean, Atlantic, and Indo-West Pacific oceanic regions. Currently, morphology and molecular data are sparse for echinoids observed along the northeastern coast of Toco, Trinidad, where they are relatively common. Additionally, accurate species identity for Echinometra spp. remains dynamic at both northernmost and southernmost parts of the Caribbean Sea. Although distribution of sea urchins in the genus Echinometra have extensively been studied throughout the Atlantic and Indo-West Pacific, information on its range of distribution at the edge of the Caribbean Sea is lacking. In this study, the mitochondrial Cytochrome c Oxidase subunit I (mt COI) gene was amplified using polymerase chain reaction, then sequenced. Based on successfully obtained gene sequences for 581 base pairs, the echinoid species Echinometra lucunter and Echinometra viridis were identified for black and red color morphotypes from Trinidad (n = 23) and Key Largo, Florida (n = 6), respectively. Furthermore, these specimens were genetically identical to species identified in other studies for Puerto Rico, Panamá, Honduras, and Belize. Although morphological variations, such as spine and test color occur throughout Echinometra spp., molecular identification using the barcoding technique confirmed E. lucunter color morphs for the first time in Trinidad. Since the status of E. lucunter populations, specifically at the most northern and southern regions of the Caribbean Sea is dynamic, further studies using gene markers are essential in determining species distribution, in light of current trends in climate change.},
}
@article {pmid38915710,
year = {2024},
author = {Trende, R and Darling, TL and Gan, T and Wang, D and Boon, ACM},
title = {Barcoded SARS-CoV-2 viruses define the impact of time and route of transmission on the transmission bottleneck in a Syrian hamster model.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38915710},
issn = {2692-8205},
support = {75N93021C00016/AI/NIAID NIH HHS/United States ; R01 AI169022/AI/NIAID NIH HHS/United States ; U01 AI070374/AI/NIAID NIH HHS/United States ; U01 AI151810/AI/NIAID NIH HHS/United States ; },
abstract = {The transmission bottleneck, defined as the number of viruses that transmit from one host to infect another, is an important determinant of the rate of virus evolution and the level of immunity required to protect against virus transmission. Despite its importance, SARS-CoV-2's transmission bottleneck remains poorly characterized, in part due to a lack of quantitative measurement tools. To address this, we adapted a SARS-CoV-2 reverse genetics system to generate a pool of >200 isogenic SARS-CoV-2 viruses harboring specific 6-nucleotide barcodes inserted in ORF10, a non-translated ORF. We directly inoculated donor Syrian hamsters intranasally with this barcoded virus pool and exposed a paired naïve contact hamster to each donor. Following exposure, the nasal turbinates, trachea, and lungs were collected, viral titers were measured, and the number of barcodes in each tissue were enumerated to quantify the transmission bottleneck. The duration and route (airborne, direct contact, and fomite) of exposure were varied to assess their impact on the transmission bottleneck. In airborne-exposed hamsters, the transmission bottleneck increased with longer exposure durations. We found that direct contact exposure produced the largest transmission bottleneck (average 27 BCs), followed by airborne exposure (average 16 BCs) then fomite exposure (average 8 BCs). Interestingly, we detected unique BCs in both the upper and lower respiratory tract of contact animals from all routes of exposure, suggesting that SARS-CoV-2 can directly infect hamster lungs. Altogether, these findings highlight the utility of barcoded viruses as tools to rigorously study virus transmission. In the future, barcoded SARS-CoV-2 will strengthen studies of immune factors that influence virus transmission.},
}
@article {pmid38912975,
year = {2024},
author = {Zahn, FE and Jiang, H and Lee, YI and Gebauer, G},
title = {Mode of carbon gain and fungal associations of Neuwiedia malipoensis within the evolutionarily early-diverging orchid subfamily Apostasioideae.},
journal = {Annals of botany},
volume = {134},
number = {3},
pages = {511-520},
pmid = {38912975},
issn = {1095-8290},
mesh = {*Orchidaceae/microbiology/growth &amp; development/physiology ; *Mycorrhizae/physiology ; *Carbon/metabolism ; Symbiosis ; Biological Evolution ; Seedlings/microbiology/growth &amp; development ; Phylogeny ; },
abstract = {BACKGROUND AND AIMS: The earliest-diverging orchid lineage, Apostasioideae, consists only of two genera: Apostasia and Neuwiedia. Previous reports of Apostasia nipponica indicated a symbiotic association with an ectomycorrhiza-forming Ceratobasidiaceae clade and partial utilization of fungal carbon during the adult stage. However, the trophic strategy of Neuwiedia throughout its development remains unidentified. To further improve our understanding of mycoheterotrophy in the Apostasioideae, this study focused on Neuwiedia malipoensis examining both the mycorrhizal association and the physiological ecology of this orchid species across various development stages.<br><br>METHODS: We identified the major mycorrhizal fungi of N. malipoensis protocorm, leafy seedling and adult stages using molecular barcoding. To reveal nutritional resources utilized by N. malipoensis, we compared stable isotope natural abundances (&#x3b4;13C, &#x3b4;15N, &#x3b4;2H, &#x3b4;18O) of different developmental stages with those of autotrophic reference plants.<br><br>KEY RESULTS: Protocorms exhibited an association with saprotrophic Ceratobasidiaceae rather than ectomycorrhiza-forming Ceratobasidiaceae and the 13C signature was characteristic of their fully mycoheterotrophic nutrition. Seedlings and adults were predominantly associated with saprotrophic fungi belonging to the Tulasnellaceae. While 13C and 2H stable isotope data revealed partial mycoheterotrophy of seedlings, it is unclear to what extent the fungal carbon supply is reduced in adult N. malipoensis. However, the 15N enrichment of mature N. malipoensis suggests partially mycoheterotrophic nutrition. Our data indicated a transition in mycorrhizal partners during ontogenetic development with decreasing dependency of N. malipoensis on fungal nitrogen and carbon.<br><br>CONCLUSIONS: The divergence in mycorrhizal partners between N. malipoensis and A. nipponica indicates different resource acquisition strategies and allows various habitat options in the earliest-diverging orchid lineage, Apostasioideae. While A. nipponica relies on the heterotrophic carbon gain from its ectomycorrhizal fungal partner and thus on forest habitats, N. malipoensis rather relies on own photosynthetic carbon gain as an adult, allowing it to establish in habitats as widely distributed as those where Rhizoctonia fungi occur.},
}
@article {pmid38911824,
year = {2024},
author = {Nassiri, I and Kwok, AJ and Bhandari, A and Bull, KR and Garner, LC and Klenerman, P and Webber, C and Parkkinen, L and Lee, AW and Wu, Y and Fairfax, B and Knight, JC and Buck, D and Piazza, P},
title = {Demultiplexing of single-cell RNA-sequencing data using interindividual variation in gene expression.},
journal = {Bioinformatics advances},
volume = {4},
number = {1},
pages = {vbae085},
pmid = {38911824},
issn = {2635-0041},
abstract = {MOTIVATION: Pooled designs for single-cell RNA sequencing, where many cells from distinct samples are processed jointly, offer increased throughput and reduced batch variation. This study describes expression-aware demultiplexing (EAD), a computational method that employs differential co-expression patterns between individuals to demultiplex pooled samples without any extra experimental steps.<br><br>RESULTS: We use synthetic sample pools and show that the top interindividual differentially co-expressed genes provide a distinct cluster of cells per individual, significantly enriching the regulation of metabolism. Our application of EAD to samples of six isogenic inbred mice demonstrated that controlling genetic and environmental effects can solve interindividual variations related to metabolic pathways. We utilized 30 samples from both sepsis and healthy individuals in six batches to assess the performance of classification approaches. The results indicate that combining genetic and EAD results can enhance the accuracy of assignments (Min. 0.94, Mean 0.98, Max. 1). The results were enhanced by an average of 1.4% when EAD and barcoding techniques were combined (Min. 1.25%, Median 1.33%, Max. 1.74%). Furthermore, we demonstrate that interindividual differential co-expression analysis within the same cell type can be used to identify cells from the same donor in different activation states. By analysing single-nuclei transcriptome profiles from the brain, we demonstrate that our method can be applied to nonimmune cells.<br><br>EAD workflow is available at https://isarnassiri.github.io/scDIV/ as an R package called scDIV (acronym for single-cell RNA-sequencing data demultiplexing using interindividual variations).},
}
@article {pmid38909361,
year = {2024},
author = {Fei, L and Zhang, K and Hautaniemi, S and Sahu, B},
title = {Protocol to identify defined reprogramming factor expression using a factor-indexing single-nuclei multiome sequencing approach.},
journal = {STAR protocols},
volume = {5},
number = {3},
pages = {103148},
pmid = {38909361},
issn = {2666-1667},
mesh = {Humans ; *Cellular Reprogramming/genetics ; *Transcription Factors/genetics/metabolism ; Fibroblasts/metabolism/cytology ; Cell Nucleus/genetics/metabolism ; },
abstract = {Ectopic expression of lineage-specific transcription factors (TFs) of another cell type can induce cell fate reprogramming. However, the heterogeneity of reprogramming cells has been a challenge for data interpretation and model evaluation. Here, we present a protocol to characterize cells expressing defined factors during direct cell reprogramming using a factor-indexing approach based on single-nuclei multiome sequencing (FI-snMultiome-seq). We describe the steps for barcoding TFs, converting human fibroblasts to pancreatic ductal-like cells using defined TFs, and preparing library for FI-snMultiome-seq analysis. For complete details on the use and execution of this protocol, please refer to Fei et al.[1].},
}
@article {pmid38907922,
year = {2024},
author = {Bell, CM},
title = {Single-Cell Sequencing of 3' RNA Transcripts.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2822},
number = {},
pages = {227-243},
pmid = {38907922},
issn = {1940-6029},
mesh = {*Single-Cell Analysis/methods ; Humans ; *3' Untranslated Regions ; *RNA, Messenger/genetics ; *Sequence Analysis, RNA/methods ; Gene Expression Profiling/methods ; Animals ; High-Throughput Nucleotide Sequencing/methods ; Poly A/genetics ; Transcriptome/genetics ; },
abstract = {Single-cell RNA sequencing (scRNA-seq) enables the measurement of RNA expressed from individual cells within a tissue or population. RNA expression profiles may be used to draw conclusions about cellular states, cell subtypes within the population, responses to perturbations, and cellular behavior in the context of disease. Here we describe a method for scRNA-seq via single-cell encapsulation and capture of the polyadenosine tails at the 3' end of mRNA transcripts combined with cell and molecular barcoding, allowing for the sequencing of 3' untranslated regions in order to identify expressed genes from a cell.},
}
@article {pmid38907921,
year = {2024},
author = {Orzolek, LD},
title = {Sequencing: 10X Genomics 3' HT Assay for Gene Expression.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2822},
number = {},
pages = {207-226},
pmid = {38907921},
issn = {1940-6029},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Genomics/methods ; *Gene Library ; *Single-Cell Analysis/methods ; Sequence Analysis, RNA/methods ; Gene Expression Profiling/methods ; DNA, Complementary/genetics ; },
abstract = {Single-cell RNA sequencing supports the isolation of individual cells and barcoding of cDNA, specific to each cell of origin. Subsequent sequencing of the generated library yields both the gene expression sequences and the cellular barcode, allowing distinction of gene expression patterns across individual cells. The 10X Genomics 3' HT assay uses a droplet-based method to isolate individual cells within oil emulsions, combined with a gel bead coated in uniquely barcoded primers, specific to each bead. The high-throughput, HT, assay is similar to its predecessor (3' v3.1) in reaction chemistry but utilizes (a) higher numbers of cellular barcodes, (b) a new, proprietary chip designed to target up to 60,000 cells per lane, and (c) captures up to 16 samples per run. The 3' HT assay supports whole cells and nuclei as input, with an approximate 60% capture rate. Here we describe the methods for sample quality control (QC) assays, loading and operation of the Chromium X instrument for cell capture, and cDNA synthesis and library preparation for downstream Illumina sequencing.},
}
@article {pmid38906909,
year = {2024},
author = {Wang, T and Li, X and Tang, C and Cao, Z and He, H and Ma, X and Li, Y and De, K},
title = {Complete chloroplast genomes and phylogenetic relationships of Pedicularis chinensis and Pedicularis kansuensis.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {14357},
pmid = {38906909},
issn = {2045-2322},
support = {LHZX-2022-01//The Chinese Academy of Sciences - People's Government of Qinghai Province on Sanjiangyuan National Park/ ; 2021-SF-A4//The major science and technology projects of Qinghai Province/ ; },
mesh = {*Phylogeny ; *Genome, Chloroplast ; *Pedicularis/genetics/classification ; *Microsatellite Repeats/genetics ; RNA, Transfer/genetics ; },
abstract = {The complete cp genomes of Pedicularis chinensis (GenBank accession number: OQ587614) and Pedicularis kansuensis (GenBank accession number: OQ587613) were sequenced, assembled, and annotated. Their chloroplast (cp) genome lengths were 146,452 bp, and 146,852 bp, respectively; 120 and 116 genes were identified, comprising 75 and 72 protein-coding genes (PCGs), 37 and 36 transfer RNA (tRNA) genes, and 8 and 8 ribosomal RNA (rRNA) genes, for P. chinensis and P. kansuensis, respectively. A simple sequence repeat (SSR) analysis revealed that the repetitive sequences were mainly composed of mononucleotide repeats (A/T motif) and dinucleotide repeats (AT/TA motif). Comparative genomics identified several variant genes (rpl22, rps19, rpl12, ycf1, trnH, psbA, and ndhH) and variant regions (trnS-GGA, trnV-UAC, ndhJ-trnV, ycf4-cemA, ndhE-nhdG, and rpl32-trnL) with a high Pi, indicating the potential to serve as deoxyribo nucleic acid (DNA) barcodes for Pedicularis species identification. The results show that the cp genomes of P. chinensis and P. kansuensis were the same as those of other plants in Pedicularis, with different degrees of AT preference for codons. Large differences in the number of SSRs and the expansion of the inverted repeat (IR) region showed strong variability and interspecific differentiation between these two species and other species represented in the genus Pedicularis. A phylogenetic analysis showed that P. kansuensis had the closest relationship with P. oliveriana, and P. chinensis had the closest relationship with P. aschistorhyncha. These results will facilitate the study of the phylogenetic classification and interspecific evolution of Pedicularis plants.},
}
@article {pmid38903959,
year = {2024},
author = {Ferreira, S and Corley, MFV and Nunes, J and Rosete, J and Vasconcelos, S and Mata, VA and Veríssimo, J and Silva, TL and Sousa, P and Andrade, R and Grosso-Silva, JM and Pinho, CJ and Chaves, C and Martins, FM and Pinto, J and Puppo, P and Muñoz-Mérida, A and Archer, J and Pauperio, J and Beja, P},
title = {The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese moths.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e117169},
pmid = {38903959},
issn = {1314-2828},
abstract = {BACKGROUND: The InBIO Barcoding Initiative (IBI) Dataset - DS-IBILP08 contains records of 2350 specimens of moths (Lepidoptera species that do not belong to the superfamily Papilionoidea). All specimens have been morphologically identified to species or subspecies level and represent 1158 species in total. The species of this dataset correspond to about 42% of mainland Portuguese Lepidoptera species. All specimens were collected in mainland Portugal between 2001 and 2022. All DNA extracts and over 96% of the specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources.<br><br>NEW INFORMATION: The authors enabled "The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese moths" in order to release the majority of data of DNA barcodes of Portuguese moths within the InBIO Barcoding Initiative. This dataset increases the knowledge on the DNA barcodes of 1158 species from Portugal belonging to 51 families. There is an increase in DNA barcodes of 205% in Portuguese specimens publicly available. The dataset includes 61 new Barcode Index Numbers. All specimens have their DNA barcodes publicly accessible through BOLD online database and the distribution data can be accessed through the Global Biodiversity Information Facility (GBIF).},
}
@article {pmid38901752,
year = {2024},
author = {Negi, N and Ramkrishna, and Meena, RK and Bhandari, MS and Pandey, S},
title = {Discovery of Botryosphaeria eucalypti sp. nov. from blighted Eucalyptus leaves in India.},
journal = {Microbial pathogenesis},
volume = {193},
number = {},
pages = {106756},
doi = {10.1016/j.micpath.2024.106756},
pmid = {38901752},
issn = {1096-1208},
mesh = {*Eucalyptus/microbiology ; *Plant Diseases/microbiology ; *Ascomycota/genetics/isolation &amp; purification/classification ; *Plant Leaves/microbiology ; India ; *Phylogeny ; *DNA, Fungal/genetics ; *Tubulin/genetics ; *Sequence Analysis, DNA ; Peptide Elongation Factor 1/genetics ; Spores, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; },
abstract = {Eucalyptus spp. are undoubtedly one of the most favored plantation trees globally. Accurately identifying Eucalyptus pathogens is therefore crucial for timely disease prevention and control. Recently, symptoms of a leaf blight disease were observed on Eucalyptus trees in plantations at Jhajjar and Karnal in the state of Haryana, northern India. Asexual morphs resembling the features of the Botryosphaeriaceae were consistently isolated from the symptomatic leaves. Morphological features coupled with DNA sequence analysis confirmed a novel species, which is described and illustrated here as Botryosphaeria eucalypti sp. nov. Conidia of the new taxon are longer and wider than those of its phylogenetic neighbors. A distinct phylogenetic position for the new taxon was established through combined analysis of the internal transcribed spacer (ITS), partial translation elongation factor-1α (tef1) and partial β-tubulin (tub2) regions. Recombination analysis provided additional support for the new species hypothesis. The pathogenicity of the novel species was proved on Eucalyptus leaves, and Koch's postulates were fulfilled. The discovery of new Botryosphaeria species is important because it will help in understanding the species diversity, host range, possible threats and disease control in the long run.},
}
@article {pmid38900825,
year = {2024},
author = {Rewicz, A and Monzalvo, R and Myśliwy, M and Tończyk, G and Desiderato, A and Ruchisansakun, S and Rewicz, T},
title = {Pollination biology of Impatiens capensis Meerb. in non-native range.},
journal = {PloS one},
volume = {19},
number = {6},
pages = {e0302283},
pmid = {38900825},
issn = {1932-6203},
mesh = {*Pollination/physiology ; Animals ; *Impatiens/physiology/genetics ; *Introduced Species ; Diptera/physiology/anatomy &amp; histology ; Poland ; DNA Barcoding, Taxonomic ; Hymenoptera/physiology ; },
abstract = {Pollination biology in the widespread species Impatiens capensis Meerb. has only been studied in America, specifically in zones of the U.S.A. and Canada. In this study, we investigated the pollination biology of I. capensis using an integrative identification approach using morphological and molecular tools in four populations of Northwest Poland. We also determined and compared the functional characteristics of the pollinators of the introduced species from the study sites and the native ones reported, for the latter collecting information from bibliographic sources. Visitors were identified using standard morphological keys, including identifying and classifying insect mouthparts. Molecular identification was carried out using mitochondrial DNA's cytochrome oxidase subunit I (COI). We morphologically identified 20 species of visitors constituted by 17 pollinators and three nectar robbers. DNA barcoding of 59 individuals proved the identification of 18 species (also 18 BINs). The frequency of pollinator species was primarily made up of representatives of both Hymenoptera (75%) and Diptera (21%). The morphological traits, such as the chewing and sucking mouthparts, small and big body height, and robber and pollinator behavior explained mainly the native and introduced visitors' arrangements that allow pollination success. However, to understand the process comprehensively, further investigation of other causalities in pollination success and understanding the diversity of pollinators in outer native ranges are necessary.},
}
@article {pmid38900631,
year = {2024},
author = {Li, H and Humphreys, BD},
title = {Protocol for multimodal profiling of human kidneys with simultaneous high-throughput ATAC and RNA expression with sequencing.},
journal = {STAR protocols},
volume = {5},
number = {3},
pages = {103049},
pmid = {38900631},
issn = {2666-1667},
mesh = {Humans ; *Kidney/metabolism ; *High-Throughput Nucleotide Sequencing/methods ; Gene Expression Profiling/methods ; Chromatin Immunoprecipitation Sequencing/methods ; Sequence Analysis, RNA/methods ; Transposases/genetics/metabolism ; Single-Cell Analysis/methods ; Gene Library ; Chromatin/genetics/metabolism ; },
abstract = {Simultaneous high-throughput ATAC and RNA expression with sequencing (SHARE-seq) profiles transcriptomics and chromatin accessibility in the same cells at high throughput. Here, we present a protocol for multimodal profiling of human kidneys with SHARE-seq. We describe steps for processing fixed nuclei for SHARE-seq split-pool barcoding and library preparation. We also detail how to determine the optimal working concentration of Tn5 transposase for transposition and tagmentation. This protocol allows researchers to generate large-scale single-cell multiomics data at low reagent cost. For complete details on the use and execution of this protocol, please refer to Li et al.[1].},
}
@article {pmid38899721,
year = {2024},
author = {Veltman, MA and Anthoons, B and Schrøder-Nielsen, A and Gravendeel, B and de Boer, HJ},
title = {Orchidinae-205: A new genome-wide custom bait set for studying the evolution, systematics, and trade of terrestrial orchids.},
journal = {Molecular ecology resources},
volume = {24},
number = {6},
pages = {e13986},
doi = {10.1111/1755-0998.13986},
pmid = {38899721},
issn = {1755-0998},
support = {765000//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; },
mesh = {*Orchidaceae/genetics/classification ; *Phylogeny ; Genetic Markers/genetics ; Sequence Analysis, DNA/methods ; Asia ; Mediterranean Region ; Genome, Plant/genetics ; },
abstract = {Terrestrial orchids are a group of genetically understudied, yet culturally and economically important plants. The Orchidinae tribe contains many species that produce edible tubers that are used for the production of traditional delicacies collectively called 'salep'. Overexploitation of wild orchids in the Eastern Mediterranean and Western Asia threatens to drive many of these species to extinction, but cost-effective tools for monitoring their trade are currently lacking. Here we present a custom bait kit for target enrichment and sequencing of 205 novel genetic markers that are tailored to phylogenomic applications in Orchidinae s.l. A subset of 31 markers capture genes putatively involved in the production of glucomannan, a water-soluble polysaccharide that gives salep its distinctive properties. We tested the kit on 73 taxa native to the area, demonstrating universally high locus recovery irrespective of species identity, that exceeds the total sequence length obtained with alternative kits currently available. Phylogenetic inference with concatenation and coalescent approaches was robust and showed high levels of support for most clades, including some which were previously unresolved. Resolution for hybridizing and recently radiated lineages remains difficult, but could be further improved by analysing multiple haplotypes and the non-exonic sequences captured by our kit, with the promise to shed new light on the evolution of enigmatic taxa with a complex speciation history. Offering a step-up from traditional barcoding and universal markers, the genome-wide custom loci targeted by Orchidinae-205 are a valuable new resource to study the evolution, systematics and trade of terrestrial orchids.},
}
@article {pmid38899428,
year = {2025},
author = {Laifi-Necibi, N and Amor, N and Merella, P and Mohammed, OB and Medini, L},
title = {DNA barcoding reveals cryptic species in the sea slater Ligia italica (Crustacea, Isopoda) from Tunisia.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {35},
number = {1-2},
pages = {1-11},
doi = {10.1080/24701394.2024.2363350},
pmid = {38899428},
issn = {2470-1408},
mesh = {Animals ; *Isopoda/genetics/classification ; Tunisia ; *Phylogeny ; *DNA Barcoding, Taxonomic/methods ; *Electron Transport Complex IV/genetics ; DNA, Mitochondrial/genetics ; Mediterranean Sea ; },
abstract = {Barcoding studies have provided significant insights into phylogenetic relationships among species belonging to the genus Ligia (Crustacea, Isopoda). Herein the diversity of the Italian sea slater Ligia italica from Tunisia is studied for the first time. Samples were collected from 18 localities in Tunisia, and the analysis included previously published sequences from Italy and Greece available in GenBank. Bayesian and Maximum Likelihood phylogenetic analyses were carried out using a fragment of the mitochondrial COI gene. Putative cryptic species were explored using the 'barcode gap' approach in the software ASAP. A genetic landscape shape analysis was carried out using the program Alleles in Space. The analyses revealed highly divergent and well-supported clades of L. italica dispersed across Tunisia (Clades A1 and A2), Greece (Clade B) and Italy (Clades C1 and C2). High genetic dissimilarity among clades suggested that L. italica constitute a cryptic species complex. Divergence among different L. italica lineages (Clades A, B and C) occurred around 7-4.5 Ma. The detected high genetic distances among clades did not result from atypical mitochondrial DNAs or intracellular infection by Wolbachia bacteria. The complex history of the Mediterranean Sea appears to have played a significant role in shaping the phylogeographic pattern of Ligia italica. Additional morphological and molecular studies are needed to confirm the existence of cryptic species in Ligia italica in Mediterranean.},
}
@article {pmid38898172,
year = {2024},
author = {Liu, Y and Sundah, NR and Ho, NRY and Shen, WX and Xu, Y and Natalia, A and Yu, Z and Seet, JE and Chan, CW and Loh, TP and Lim, BY and Shao, H},
title = {Bidirectional linkage of DNA barcodes for the multiplexed mapping of higher-order protein interactions in cells.},
journal = {Nature biomedical engineering},
volume = {8},
number = {7},
pages = {909-923},
pmid = {38898172},
issn = {2157-846X},
support = {MOH-000564; MOH-000541; MOH-000206//MOH | National Medical Research Council (NMRC)/ ; NRF-CRP29-2022-0001//National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)/ ; DTC-RGC-09//National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)/ ; T2EP20121-0040//Ministry of Education - Singapore (MOE)/ ; },
mesh = {Humans ; *Breast Neoplasms/genetics/metabolism/pathology ; *DNA Barcoding, Taxonomic/methods ; Protein Interaction Mapping/methods ; Cell Line, Tumor ; DNA/chemistry/metabolism/genetics ; Female ; },
abstract = {Capturing the full complexity of the diverse hierarchical interactions in the protein interactome is challenging. Here we report a DNA-barcoding method for the multiplexed mapping of pairwise and higher-order protein interactions and their dynamics within cells. The method leverages antibodies conjugated with barcoded DNA strands that can bidirectionally hybridize and covalently link to linearize closely spaced interactions within individual 3D protein complexes, encoding and decoding the protein constituents and the interactions among them. By mapping protein interactions in cancer cells and normal cells, we found that tumour cells exhibit a larger diversity and abundance of protein complexes with higher-order interactions. In biopsies of human breast-cancer tissue, the method accurately identified the cancer subtype and revealed that higher-order protein interactions are associated with cancer aggressiveness.},
}
@article {pmid38898081,
year = {2024},
author = {Goudarzi, MH and Robinson, SD and Cardoso, FC and Mitchell, ML and Cook, LG and King, GF and Walker, AA},
title = {Phylogeny, envenomation syndrome, and membrane permeabilising venom produced by Australia's electric caterpillar Comana monomorpha.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {14172},
pmid = {38898081},
issn = {2045-2322},
support = {DP200102867//Australian Research Council/ ; CE200100012//Australian Research Council/ ; DP200102867//Australian Research Council/ ; APP2017461//National Health and Medical Research Council/ ; },
mesh = {Animals ; Australia ; *Phylogeny ; Larva ; Proteomics/methods ; Arthropod Venoms/genetics/metabolism ; Moths/genetics ; Cell Membrane Permeability ; Humans ; Bites and Stings ; Proteome ; },
abstract = {Zygaenoidea is a superfamily of lepidopterans containing many venomous species, including the Limacodidae (nettle caterpillars) and Megalopygidae (asp caterpillars). Venom proteomes have been recently documented for several species from each of these families, but further data are required to understand the evolution of venom in Zygaenoidea. In this study, we examined the 'electric' caterpillar from North-Eastern Australia, a limacodid caterpillar densely covered in venomous spines. We used DNA barcoding to identify this caterpillar as the larva of the moth Comana monomorpha (Turner, 1904). We report the clinical symptoms of C. monomorpha envenomation, which include acute pain, and erythema and oedema lasting for more than a week. Combining transcriptomics of venom spines with proteomics of venom harvested from the spine tips revealed a venom markedly different in composition from previously examined limacodid venoms that are rich in peptides. In contrast, the venom of C. monomorpha is rich in aerolysin-like proteins similar to those found in venoms of asp caterpillars (Megalopygidae). Consistent with this composition, the venom potently permeabilises sensory neurons and human neuroblastoma cells. This study highlights the diversity of venom composition in Limacodidae.},
}
@article {pmid38896378,
year = {2024},
author = {Akhter, G and Ahmed, I and Ahmad, SM},
title = {Comparative Study of Two Himalayan Snow Trouts, Schizothorax esocinus and Schizothorax curvifrons Within the Schizothoracinae and Other Nearest Relatives of Cyprinidae, Inferred from Mitochondrial Sequences of Cytochrome b (Cyt-b) and Cytochrome Oxidase I (Co-I) Gene.},
journal = {Biochemical genetics},
volume = {},
number = {},
pages = {},
pmid = {38896378},
issn = {1573-4927},
abstract = {The Himalayan region encompasses varied aquatic ecosystems, characterized by the presence of diverse ichthyofauna, particularly represented by members of the Schizothorax genus, commonly referred to as snow trout. The primary objective of this work was to examine the molecular phylogeny of Schizothoracinae, specifically focusing on the two species, Schizothorax esocinus and Schizothorax curvifrons, which are known to inhabit the northern and north-eastern regions of the Himalayas. This investigation was conducted by analyzing the entire mitochondrial Cyt-b and Co-I gene sequences. The aligned Cyt-b and Co-I sequences for S. esocinus, S. curvifrons, and related members within the subfamily Schizothoracinae, spanned 1130 to 1141 and 1536 to 1551 base pairs, respectively. Using these gene, phylogenetic trees were created to compare Schizothoracinae species to other subfamilies of the family Cyprinidae (Barbinae, Alburninae, Leuciscinae, Xenocyprinae, Cyprininae, and Cultrinae). Genetic distances for Cyt-b and Co-I sequence at three hierarchical levels shows significant disparities in their average score. For Cyt-b, average p-distances for intraspecies, intragenus, and intrafamily were 2.13%, 4.1%, and 15.23%, respectively. Similarly, for Co-I, average p-distances were 1.19%, 3.6%, and 13.8% for intraspecies, intragenus, and intrafamily, respectively. Total number of haplotypes (h) based on Cyt-b and Co-I gene were 6 and 12 within the target Schizothorax spp. In the present study, the observed range of haplotype diversity (hd) for the Cyt-b gene varied from 0.00 to 0.847, with an average haplotype diversity of 0.847 ± 0.034. Similarly, for the Co-I gene, the observed haplotype diversity ranged from 0.00 to 0.931, with an average value of haplotype diversity estimated to be 0.931 ± 0.024. The results of the present study clearly shows that the representative species exhibited close affinities with members of Barbinae and Cyprininae, while other subfamilies formed distinct groups. The findings of the study also indicated that the Cyt-b and Co-I gene exhibits polymorphism and has the potential to serve as a marker for identifying genetic differentiation among populations based on ecological habitats. Mitochondrial Cyt-b and Co-I have been established as a universally accepted and validated genetic marker within a comprehensive bio-identification system at the species level.},
}
@article {pmid38895703,
year = {2023},
author = {Hou, LW and Giraldo, A and Groenewald, JZ and Rämä, T and Summerbell, RC and Huang, GZ and Cai, L and Crous, PW},
title = {Redisposition of acremonium-like fungi in Hypocreales.},
journal = {Studies in mycology},
volume = {105},
number = {},
pages = {23-203},
pmid = {38895703},
issn = {0166-0616},
abstract = {Acremonium is acknowledged as a highly ubiquitous genus including saprobic, parasitic, or endophytic fungi that inhabit a variety of environments. Species of this genus are extensively exploited in industrial, commercial, pharmaceutical, and biocontrol applications, and proved to be a rich source of novel and bioactive secondary metabolites. Acremonium has been recognised as a taxonomically difficult group of ascomycetes, due to the reduced and high plasticity of morphological characters, wide ecological distribution and substrate range. Recent advances in molecular phylogenies, revealed that Acremonium is highly polyphyletic and members of Acremonium s. lat. belong to at least three distinct orders of Sordariomycetes, of which numerous orders, families and genera with acremonium-like morphs remain undefined. To infer the phylogenetic relationships and establish a natural classification for acremonium-like taxa, systematic analyses were conducted based on a large number of cultures with a global distribution and varied substrates. A total of 633 cultures with acremonium-like morphology, including 261 ex-type cultures from 89 countries and a variety of substrates including soil, plants, fungi, humans, insects, air, and water were examined. An overview phylogenetic tree based on three loci (ITS, LSU, rpb2) was generated to delimit the orders and families. Separate trees based on a combined analysis of four loci (ITS, LSU, rpb2, tef-1α) were used to delimit species at generic and family levels. Combined with the morphological features, host associations and ecological analyses, acremonium-like species evaluated in the present study are currently assigned to 63 genera, and 14 families in Cephalothecales, Glomerellales and Hypocreales, mainly in the families Bionectriaceae, Plectosphaerellaceae and Sarocladiaceae and five new hypocrealean families, namely Chrysonectriaceae, Neoacremoniaceae, Nothoacremoniaceae, Pseudoniessliaceae and Valsonectriaceae. Among them, 17 new genera and 63 new combinations are proposed, with descriptions of 65 new species. Furthermore, one epitype and one neotype are designated to stabilise the taxonomy and use of older names. Results of this study demonstrated that most species of Acremonium s. lat. grouped in genera of Bionectriaceae, including the type A. alternatum. A phylogenetic backbone tree is provided for Bionectriaceae, in which 183 species are recognised and 39 well-supported genera are resolved, including 10 new genera. Additionally, rpb2 and tef-1α are proposed as potential DNA barcodes for the identification of taxa in Bionectriaceae. Taxonomic novelties: New families: Chrysonectriaceae L.W. Hou, L. Cai &amp; Crous, Neoacremoniaceae L.W. Hou, L. Cai &amp; Crous, Nothoacremoniaceae L.W. Hou, L. Cai &amp; Crous, Pseudoniessliaceae L.W. Hou, L. Cai &amp; Crous, Valsonectriaceae L.W. Hou, L. Cai &amp; Crous. New genera: Bionectriaceae: Alloacremonium L.W. Hou, L. Cai &amp; Crous, Gossypinidium L.W. Hou, L. Cai &amp; Crous, Monohydropisphaera L.W. Hou, L. Cai &amp; Crous, Musananaesporium L.W. Hou, L. Cai &amp; Crous, Paragliomastix L.W. Hou, L. Cai &amp; Crous, Proliferophialis L.W. Hou, L. Cai &amp; Crous, Proxiovicillium L.W. Hou, L. Cai &amp; Crous, Ramosiphorum L.W. Hou, L. Cai &amp; Crous, Verruciconidia L.W. Hou, L. Cai &amp; Crous, Waltergamsia L.W. Hou, L. Cai &amp; Crous; Clavicipitaceae: Subuliphorum L.W. Hou, L. Cai &amp; Crous; Neoacremoniaceae: Neoacremonium L.W. Hou, L. Cai &amp; Crous; Nothoacremoniaceae: Nothoacremonium L.W. Hou, L. Cai &amp; Crous; Plectosphaerellaceae: Allomusicillium L.W. Hou, L. Cai &amp; Crous, Parafuscohypha L.W. Hou, L. Cai &amp; Crous; Pseudoniessliaceae: Pseudoniesslia L.W. Hou, L. Cai &amp; Crous; Sarocladiaceae: Polyphialocladium L.W. Hou, L. Cai &amp; Crous. New species: Bionectriaceae: Alloacremonium ferrugineum L.W. Hou, L. Cai &amp; Crous, Al. humicola L.W. Hou, L. Cai &amp; Crous, Acremonium aerium L.W. Hou, L. Cai &amp; Crous, A. brunneisporum L.W. Hou, L. Cai &amp; Crous, A. chlamydosporium L.W. Hou, L. Cai &amp; Crous, A. ellipsoideum L.W. Hou, Rämä, L. Cai &amp; Crous, A. gamsianum L.W. Hou, L. Cai &amp; Crous, A. longiphialidicum L.W. Hou, L. Cai &amp; Crous, A. multiramosum L.W. Hou, Rämä, L. Cai &amp; Crous, A. mycoparasiticum L.W. Hou, L. Cai &amp; Crous, A. stroudii K. Fletcher, F.C. Küpper &amp; P. van West, A. subulatum L.W. Hou, L. Cai &amp; Crous, A. synnematoferum L.W. Hou, Rämä, L. Cai &amp; Crous, Bulbithecium ammophilae L.W. Hou, L. Cai &amp; Crous, B. ellipsoideum L.W. Hou, L. Cai &amp; Crous, B. truncatum L.W. Hou, L. Cai &amp; Crous, Emericellopsis brunneiguttula L.W. Hou, L. Cai &amp; Crous, Gliomastix musae L.W. Hou, L. Cai &amp; Crous, Gossypinidium sporodochiale L.W. Hou, L. Cai &amp; Crous, Hapsidospora stercoraria L.W. Hou, L. Cai &amp; Crous, H. variabilis L.W. Hou, L. Cai &amp; Crous, Mycocitrus odorus L.W. Hou, L. Cai &amp; Crous, Nectriopsis ellipsoidea L.W. Hou, L. Cai &amp; Crous, Paracylindrocarpon aurantiacum L.W. Hou, L. Cai &amp; Crous, Pn. foliicola Lechat &amp; J. Fourn., Paragliomastix rosea L.W. Hou, L. Cai &amp; Crous, Proliferophialis apiculata L.W. Hou, L. Cai &amp; Crous, Protocreopsis finnmarkica L.W. Hou, L. Cai, Rämä &amp; Crous, Proxiovicillium lepidopterorum L.W. Hou, L. Cai &amp; Crous, Ramosiphorum echinoporiae L.W. Hou, L. Cai &amp; Crous, R. polyporicola L.W. Hou, L. Cai &amp; Crous, R. thailandicum L.W. Hou, L. Cai &amp; Crous, Verruciconidia erythroxyli L.W. Hou, L. Cai &amp; Crous, Ve. infuscata L.W. Hou, L. Cai &amp; Crous, Ve. quercina L.W. Hou, L. Cai &amp; Crous, Ve. siccicapita L.W. Hou, L. Cai &amp; Crous, Ve. unguis L.W. Hou, L. Cai &amp; Crous, Waltergamsia alkalina L.W. Hou, L. Cai &amp; Crous, W. catenata L.W. Hou, L. Cai &amp; Crous, W. moroccensis L.W. Hou, L. Cai &amp; Crous, W. obpyriformis L.W. Hou, L. Cai &amp; Crous; Chrysonectriaceae: Chrysonectria crystallifera L.W. Hou, L. Cai &amp; Crous; Nectriaceae: Xenoacremonium allantoideum L.W. Hou, L. Cai &amp; Crous; Neoacremoniaceae: Neoacremonium distortum L.W. Hou, L. Cai &amp; Crous, N. flavum L.W. Hou, L. Cai &amp; Crous; Nothoacremoniaceae: Nothoacremonium subcylindricum L.W. Hou, L. Cai &amp; Crous, No. vesiculophorum L.W. Hou, L. Cai &amp; Crous; Myrotheciomycetaceae: Trichothecium hongkongense L.W. Hou, L. Cai &amp; Crous; Plectosphaerellaceae: Brunneomyces polyphialidus L.W. Hou, L. Cai &amp; Crous, Parafuscohypha proliferata L.W. Hou, L. Cai &amp; Crous; Sarocladiaceae: Chlamydocillium acaciae L.W. Hou, L. Cai &amp; Crous, C. antarcticum L.W. Hou, L. Cai &amp; Crous, C. guttulatum L.W. Hou, L. Cai &amp; Crous, C. lolii L.W. Hou, L. Cai &amp; Crous, C. soli L.W. Hou, L. Cai &amp; Crous, C. terrestre L.W. Hou, L. Cai &amp; Crous, Parasarocladium chondroidum L.W. Hou, L. Cai &amp; Crous,Polyphialocladium fusisporum L.W. Hou, L. Cai &amp; Crous, Sarocladium agarici L.W. Hou, L. Cai &amp; Crous, S. citri L.W. Hou, L. Cai &amp; Crous, S. ferrugineum L.W. Hou, L. Cai &amp; Crous, S. fuscum L.W. Hou, L. Cai &amp; Crous,S. theobromae L.W. Hou, L. Cai &amp; Crous; Valsonectriaceae: Valsonectria crystalligena L.W. Hou, L. Cai &amp; Crous, V. hilaris L.W. Hou, L. Cai &amp; Crous. New combinations: Bionectriaceae: Acremonium purpurascens (Sukapure &amp; Thirum.) L.W. Hou, L. Cai &amp; Crous, Bulbithecium arxii (Malloch) L.W. Hou, L. Cai &amp; Crous, Bu. borodinense (Tad. Ito et al.) L.W. Hou, L. Cai &amp; Crous, Bu. pinkertoniae (W. Gams) L.W. Hou, L. Cai &amp; Crous, Bu. spinosum (Negroni) L.W. Hou, L. Cai &amp; Crous, Emericellopsis exuviara (Sigler et al.) L.W. Hou, L. Cai &amp; Crous, E. fimetaria (Pers.) L.W. Hou, L. Cai &amp; Crous, E. fuci (Summerb. et al.) L.W. Hou, L. Cai &amp; Crous, E. moniliformis (A. Giraldo et al.) L.W. Hou, L. Cai &amp; Crous, E. salmonea (W. Gams &amp; Lodha) L.W. Hou, L. Cai &amp; Crous, E. tubakii (Gams) L.W. Hou, L. Cai &amp; Crous, Fusariella arenula (Berk. &amp; Broome) L.W. Hou, L. Cai &amp; Crous, Hapsidospora chrysogena (Thirum. &amp; Sukapure) L.W. Hou, L. Cai &amp; Crous, H. flava (W. Gams) L.W. Hou, L. Cai &amp; Crous, H. globosa (Malloch &amp; Cain) L.W. Hou, L. Cai &amp; Crous, H. inversa (Malloch &amp; Cain) L.W. Hou, L. Cai &amp; Crous, Hydropisphaera aurantiaca (C.A. Jørg.) L.W. Hou, L. Cai &amp; Crous, Lasionectria atrorubra (Lechat &amp; J. Fourn.) L.W. Hou, L. Cai &amp; Crous, L. bisepta (W. Gams) L.W. Hou, L. Cai &amp; Crous, L. castaneicola (Lechat &amp; Gardiennet) L.W. Hou, L. Cai &amp; Crous, L. cerealis (P. Karst.) L.W. Hou, L. Cai &amp; Crous, L. olida (W. Gams) L.W. Hou, L. Cai &amp; Crous, Lasionectriopsis dentifera (Samuels) L.W. Hou, L. Cai &amp; Crous, Lasionectriella arenuloides (Samuels) L.W. Hou, L. Cai &amp; Crous, La. marigotensis (Lechat &amp; J. Fourn.) L.W. Hou, L. Cai &amp; Crous, Monohydropisphaera fusigera (Berk. &amp; Broome) L.W. Hou, L. Cai &amp; Crous, Musananaesporium tectonae (R.F. Castañeda) L.W. Hou, L. Cai &amp; Crous, Mycocitrus zonatus (Sawada) L.W. Hou, L. Cai &amp; Crous, Nectriopsis microspora (Jaap) L.W. Hou, L. Cai &amp; Crous, Ovicillium asperulatum (A. Giraldo et al.) L.W. Hou, L. Cai &amp; Crous, O. variecolor (A. Giraldo et al.) L.W. Hou, L. Cai &amp; Crous, Paracylindrocarpon multiloculatum (Samuels) L.W. Hou, L. Cai &amp; Crous, Pn. multiseptatum (Samuels)L.W. Hou, L. Cai &amp; Crous, Paragliomastix chiangraiensis (J.F. Li et al.) L.W. Hou, L. Cai &amp; Crous, Px. luzulae (Fuckel) L.W. Hou, L. Cai &amp; Crous, Px. znieffensis (Lechat &amp; J. Fourn.) L.W. Hou, L. Cai &amp; Crous, Protocreopsis rutila (W. Gams) L.W. Hou, L. Cai &amp; Crous, Proxiovicillium blochii (Matr.)L.W. Hou, L. Cai &amp; Crous, Stanjemonium dichromosporum (Gams &amp; Sivasith.) L.W. Hou, L. Cai &amp; Crous, Verruciconidia persicina (Nicot) L.W. Hou, L. Cai &amp; Crous, Ve. verruculosa (W. Gams &amp; Veenb.-Rijks) L.W. Hou, L. Cai &amp; Crous, Waltergamsia citrina (A. Giraldo et al.) L.W. Hou, L. Cai &amp; Crous, W. dimorphospora (A. Giraldo et al.) L.W. Hou, L. Cai &amp; Crous, W. epimycota (Samuels) L.W. Hou, L. Cai &amp; Crous, W. fusidioides (Nicot) L.W. Hou, L. Cai &amp; Crous, W. hennebertii (W. Gams) L.W. Hou, L. Cai &amp; Crous, W. parva (A. Giraldo et al.) L.W. Hou, L. Cai &amp; Crous, W. pilosa (A. Giraldo et al.) L.W. Hou, L. Cai &amp; Crous, W. zeylanica (Petch) L.W. Hou, L. Cai &amp; Crous; Cephalothecaceae: Phialemonium thermophilum (W. Gams &amp; J. Lacey) L.W. Hou, L. Cai &amp; Crous; Clavicipitaceae: Subuliphorum camptosporum (W. Gams) L.W. Hou, L. Cai &amp; Crous; Coniochaetaceae: Coniochaeta psammospora (W. Gams) L.W. Hou, L. Cai &amp; Crous; Nothoacremoniaceae: Nothoacremonium exiguum (W. Gams) L.W. Hou, L. Cai &amp; Crous; Neoacremoniaceae: Neoacremonium minutisporum (Sukapure &amp; Thirum.) L.W. Hou, L. Cai &amp; Crous; Ne. taiwanense (K.L. Pang et al.) L.W. Hou, L. Cai &amp; Crous; Ne. vitellinum (W. Gams) L.W. Hou, L. Cai &amp; Crous; Plectosphaerellaceae: Allomusicillium domschii (W. Gams) L.W. Hou, L. Cai &amp; Crous, Brunneomyces pseudozeylanicus (W. Gams) L.W. Hou, L. Cai &amp; Crous; Pseudoniessliaceae: Pseudoniesslia minutispora (W. Gams et al.) L.W. Hou, L. Cai &amp; Crous; Sarocladiaceae: Chlamydocillium curvulum (W. Gams) L.W. Hou, L. Cai &amp; Crous, Parasarocladium funiculosum (Sukapure &amp; Thirum.) L.W. Hou, L. Cai &amp; Crous; Valsonectriaceae: Valsonectria inflata (C.H. Dickinson) L.W. Hou, L. Cai &amp; Crous, V. roseola (G. Sm.) L.W. Hou, L. Cai &amp; Crous. Epitype (basionym): Sphaeria violacea J.C. Schmidt ex Fr. Neotype (basionym): Mastigocladium blochii Matr. Citation: Hou LW, Giraldo A, Groenewald JZ, Rämä T, Summerbell RC, Zang P, Cai L, Crous PW (2023). Redisposition of acremonium-like fungi in Hypocreales. Studies in Mycology 105: 23-203. doi: 10.3114/sim.2023.105.02.},
}
@article {pmid38895212,
year = {2024},
author = {Totty, M and Hicks, SC and Guo, B},
title = {SpotSweeper: spatially-aware quality control for spatial transcriptomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38895212},
issn = {2692-8205},
support = {F32 MH135620/MH/NIMH NIH HHS/United States ; R01 MH126393/MH/NIMH NIH HHS/United States ; },
abstract = {Quality control (QC) is a crucial step to ensure the reliability and accuracy of the data obtained from RNA sequencing experiments, including spatially-resolved transcriptomics (SRT). Existing QC approaches for SRT that have been adopted from single-nucleus RNA sequencing (snRNA-seq) methods are confounded by spatial biology and are inappropriate for SRT data. In addition, no methods currently exist for identifying histological tissue artifacts unique to SRT. Here, we introduce SpotSweeper, spatially-aware QC methods for identifying local outliers and regional artifacts in SRT. SpotSweeper evaluates the quality of individual spots relative to their local neighborhood, thus minimizing bias due to biological heterogeneity, and uses multiscale methods to detect regional artifacts. Using SpotSweeper on publicly available data, we identified a consistent set of Visium barcodes/spots as systematically low quality and demonstrate that SpotSweeper accurately identifies two distinct types of regional artifacts, resulting in improved downstream clustering and marker gene detection for spatial domains.},
}
@article {pmid38895104,
year = {2024},
author = {Nath, S and VanSlambrouck, JT and Yao, JW and Gullapalli, A and Razi, F and Lu, Y},
title = {DNA barcoding of terrestrial invasive plant species in Southwest Michigan.},
journal = {Plant direct},
volume = {8},
number = {6},
pages = {e615},
pmid = {38895104},
issn = {2475-4455},
abstract = {Because of the detrimental effects of terrestrial invasive plant species (TIPS) on native species, ecosystems, public health, and the economy, many countries have been actively looking for strategies to prevent the introduction and minimize the spread of TIPS. Fast and accurate detection of TIPS is essential to achieving these goals. Conventionally, invasive species monitoring has relied on morphological attributes. Recently, DNA-based species identification (i.e., DNA barcoding) has become more attractive. To investigate whether DNA barcoding can aid in the detection and management of TIPS, we visited multiple nature areas in Southwest Michigan and collected a small piece of leaf tissue from 91 representative terrestrial plant species, most of which are invasive. We extracted DNA from the leaf samples, amplified four genomic loci (ITS, rbcL, matK, and trnH-psbA) with PCR, and then purified and sequenced the PCR products. After careful examination of the sequencing data, we were able to identify reliable DNA barcode regions for most species and had an average PCR-and-sequencing success rate of 87.9%. We found that the species discrimination rate of a DNA barcode region is inversely related to the ease of PCR amplification and sequencing. Compared with rbcL and matK, ITS and trnH-psbA have better species discrimination rates (80.6% and 63.2%, respectively). When ITS and trnH-psbA are simultaneously used, the species discrimination rate increases to 97.1%. The high species/genus/family discrimination rates of DNA barcoding indicate that DNA barcoding can be successfully employed in TIPS identification. Further increases in the number of DNA barcode regions show little or no additional increases in the species discrimination rate, suggesting that dual-barcode approaches (e.g., ITS + trnH-psbA) might be the efficient and cost-effective method in DNA-based TIPS identification. Close inspection of nucleotide sequences at the four DNA barcode regions among related species demonstrates that DNA barcoding is especially useful in identifying TIPS that are morphologically similar to other species.},
}
@article {pmid38891833,
year = {2024},
author = {Weber, B and Ritter, A and Han, J and Schaible, I and Sturm, R and Relja, B and Huber-Lang, M and Hildebrand, F and Pallas, C and Widera, M and Henrich, D and Marzi, I and Leppik, L},
title = {Development of a Sampling and Storage Protocol of Extracellular Vesicles (EVs)-Establishment of the First EV Biobank for Polytraumatized Patients.},
journal = {International journal of molecular sciences},
volume = {25},
number = {11},
pages = {},
pmid = {38891833},
issn = {1422-0067},
support = {465409392//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Humans ; *Extracellular Vesicles/metabolism ; *Biological Specimen Banks ; *Multiple Trauma/metabolism/blood ; Specimen Handling/methods ; Chromatography, Gel/methods ; Male ; Ultracentrifugation/methods ; MicroRNAs/blood/genetics ; Adult ; Female ; },
abstract = {In the last few years, several studies have emphasized the existence of injury-specific EV "barcodes" that could have significant importance for the precise diagnosis of different organ injuries in polytrauma patients. To expand the research potential of the NTF (network trauma research) biobank of polytraumatized patients, the NTF research group decided to further establish a biobank for EVs. However, until now, the protocols for the isolation, characterization, and storage of EVs for biobank purposes have not been conceptualized. Plasma and serum samples from healthy volunteers (n = 10) were used. Three EV isolation methods of high relevance for the work with patients' samples (ultracentrifugation, size exclusion chromatography, and immune magnetic bead-based isolation) were compared. EVs were quantified using nanoparticle tracking analysis, EV proteins, and miRNAs. The effects of different isolation solutions; the long storage of samples (up to 3 years); and the sensibility of EVs to serial freezing-thawing cycles and different storage conditions (RT, 4/-20/-80 °C, dry ice) were evaluated. The SEC isolation method was considered the most suitable for EV biobanking. We did not find any difference in the quantity of EVs between serum and plasma-EVs. The importance of particle-free PBS as an isolation solution was confirmed. Plasma that has been frozen for a long time can also be used as a source of EVs. Serial freezing-thawing cycles were found to affect the mean size of EVs but not their amount. The storage of EV samples for 5 days on dry ice significantly reduced the EV protein concentration.},
}
@article {pmid38887455,
year = {2024},
author = {Wang, J and Kan, J and Wang, J and Yan, X and Li, Y and Soe, T and Tembrock, LR and Xing, G and Li, S and Wu, Z and Jia, M},
title = {The pan-plastome of Prunus mume: insights into Prunus diversity, phylogeny, and domestication history.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1404071},
pmid = {38887455},
issn = {1664-462X},
abstract = {BACKGROUNDS: Prunus mume in the Rosaceae and commonly referred to as mei or Chinese plum is widely used as a traditional ornamental flowering plant and fruit tree in China. Although some population and genetic analyses have been conducted for this species, no extensive comparisons of genetic variation from plastomes have yet been investigated.<br><br>METHODS: We de novo assembled a total of 322 complete P. mume plastomes in this study and did a series of comparative analyses to better resolve pan-plastomic patterns of P. mume. To determine the phylogeny and domestication history of this species, we reconstructed the phylogenetic tree of Prunus genus, and resolved the population structure of P. mume. We also examined the nucleotide variation of P. mume to find potential DNA barcodes.<br><br>RESULTS: The assembled plastomes exhibited a typical quadripartite structure and ranged from 157,871 bp to 158,213 bp in total size with a GC content ranging from 36.73 to 36.75%. A total of 112 unique genes were identified. Single nucleotide variants (SNVs) were the most common variants found among the plastomes, followed by nucleotide insertions/deletions (InDels), and block substitutions with the intergenic spacer (IGS) regions containing the greatest number of variants. From the pan-plastome data six well-supported genetic clusters were resolved using multiple different population structure analyses. The different cultivars were unevenly distributed among multiple clades. We also reconstructed a phylogeny for multiple species of Prunus to better understand genus level diversity and history from which a complex introgressive relationship between mei and other apricots/plums was resolved.<br><br>CONCLUSION: This study constructed the pan-plastome of P. mume, which indicated the domestication of P. mume involved multiple genetic origins and possible matrilineal introgression from other species. The phylogenetic analysis in Prunus and the population structure of P. mume provide an important maternal history for Prunus and the groundwork for future studies on intergenomic sequence transfers, cytonuclear incompatibility, and conservation genetics.},
}
@article {pmid38886529,
year = {2024},
author = {Gaisser, KD and Skloss, SN and Brettner, LM and Paleologu, L and Roco, CM and Rosenberg, AB and Hirano, M and DePaolo, RW and Seelig, G and Kuchina, A},
title = {High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding.},
journal = {Nature protocols},
volume = {19},
number = {10},
pages = {3048-3084},
pmid = {38886529},
issn = {1750-2799},
support = {DE-SC0023091//U.S. Department of Energy (DOE)/ ; R21 DE032890/DE/NIDCR NIH HHS/United States ; R35GM150994//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R21DE032890//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; R35 GM150994/GM/NIGMS NIH HHS/United States ; },
mesh = {*Single-Cell Analysis/methods ; *High-Throughput Nucleotide Sequencing/methods ; Bacteria/genetics/classification ; Gene Expression Profiling/methods ; DNA Barcoding, Taxonomic/methods ; Transcriptome/genetics ; Gene Library ; },
abstract = {Microbial split-pool ligation transcriptomics (microSPLiT) is a high-throughput single-cell RNA sequencing method for bacteria. With four combinatorial barcoding rounds, microSPLiT can profile transcriptional states in hundreds of thousands of Gram-negative and Gram-positive bacteria in a single experiment without specialized equipment. As bacterial samples are fixed and permeabilized before barcoding, they can be collected and stored ahead of time. During the first barcoding round, the fixed and permeabilized bacteria are distributed into a 96-well plate, where their transcripts are reverse transcribed into cDNA and labeled with the first well-specific barcode inside the cells. The cells are mixed and redistributed two more times into new 96-well plates, where the second and third barcodes are appended to the cDNA via in-cell ligation reactions. Finally, the cells are mixed and divided into aliquot sub-libraries, which can be stored until future use or prepared for sequencing with the addition of a fourth barcode. It takes 4 days to generate sequencing-ready libraries, including 1 day for collection and overnight fixation of samples. The standard plate setup enables single-cell transcriptional profiling of up to 1 million bacterial cells and up to 96 samples in a single barcoding experiment, with the possibility of expansion by adding barcoding rounds. The protocol requires experience in basic molecular biology techniques, handling of bacterial samples and preparation of DNA libraries for next-generation sequencing. It can be performed by experienced undergraduate or graduate students. Data analysis requires access to computing resources, familiarity with Unix command line and basic experience with Python or R.},
}
@article {pmid38886157,
year = {2025},
author = {Guarneri, I and Bozzo, M and Perez Criado, N and Serafini, E and Manfè, G and Tagliapietra, D and Fiorin, R and Scapin, L and Povero, P and Bellitto, D and Ferrando, S and Amaroli, A and Castellano, L and Pestarino, M and Schubert, M and Candiani, S},
title = {Amphioxus (Branchiostoma lanceolatum) in the North Adriatic Sea: ecological observations and spawning behavior.},
journal = {Integrative zoology},
volume = {20},
number = {2},
pages = {331-343},
pmid = {38886157},
issn = {1749-4877},
support = {FRA2023//Universit&#xe0; di Genova/ ; //CNRS/ ; ANR-21-CE34-0006-02//ANR/ ; },
mesh = {Animals ; *Lancelets/genetics/physiology ; *Ecosystem ; *Reproduction/physiology ; Seasons ; Mediterranean Sea ; Sexual Behavior, Animal/physiology ; Female ; Male ; },
abstract = {The European amphioxus (Branchiostoma lanceolatum) is a member of the chordate subphylum Cephalochordata, and, as such, a key model organism for providing insights into the origin and evolution of vertebrates. Despite its significance and global distribution, detailed characterizations of natural populations of cephalochordates are still very limited. This study investigates the abundance, habitat, and spawning behavior of amphioxus in the North Adriatic Sea. Across 32 sampled sites, adult amphioxus were consistently present, reaching densities exceeding 300 individuals m[-] [2]. DNA barcoding confirmed the species as B. lanceolatum, and environmental analyses revealed an amphioxus preference for slightly gravelly sand with low silt content and a correlation between amphioxus density and the presence of specific macroinvertebrate taxa. Remarkably, the amphioxus population was breeding in early spring and possibly late fall, in contrast to the typical late spring/early summer spawning season described for other populations of European amphioxus. Amphioxus adults kept in captivity maintained the spawning seasonality of their place of origin, suggesting the possibility of extending the overall spawning season of European amphioxus in laboratory settings by exploiting populations from diverse geographic origins. This study thus expands our understanding of B. lanceolatum ecology and reproduction in the Mediterranean Sea, emphasizing the role of the North Adriatic Sea as a substantial reservoir.},
}
@article {pmid38885824,
year = {2024},
author = {Oliveira, HFM and Freire-Jr, GB and Silva, DC and Mata, VA and Abra, FD and Camargo, NF and Araujo Goebel, LG and Longo, GR and Silva, JM and Colli, GR and Domingos, FMCB},
title = {Barcoding Brazilian mammals to monitor biological diversity and threats: Trends, perspectives, and knowledge gaps.},
journal = {Environmental research},
volume = {258},
number = {},
pages = {119374},
doi = {10.1016/j.envres.2024.119374},
pmid = {38885824},
issn = {1096-0953},
mesh = {Animals ; Brazil ; *Mammals/genetics/classification ; *DNA Barcoding, Taxonomic ; *Biodiversity ; Conservation of Natural Resources ; Environmental Monitoring/methods ; },
abstract = {DNA barcoding and environmental DNA (eDNA) represent significant advances for biomonitoring the world's biodiversity and its threats. However, these methods are highly dependent on the presence of species sequences on molecular databases. Brazil is one of the world's largest and most biologically diverse countries. However, many knowledge gaps still exist for describing, identifying, and monitoring of mammalian biodiversity using molecular methods. We aimed to unravel the patterns of the presence of Brazilian mammal species on molecular databases to improve our understanding of how effectively it would be to monitor them using DNA barcoding and environmental DNA, and contribute to mammalian conservation. We foundt many gaps in molecular databases, with many taxa being poorly represented, particularly from Amazonia, the order Lagomorpha, and arboreal, gomivorous, near extinct, and illegally traded species. Moreover, our analyses revealed that species description year was the most important factor determining the probability of a species to being sequenced. Primates are the group with the highest number of species considered a priority for sequencing due to their high level of combined threats. We highlight where investments are needed to fill knowledge gaps and increase the representativity of species on molecular databases to enable a better monitoring ability of Brazilian mammals encompassing different traits using DNA barcoding and environmental DNA.},
}
@article {pmid38884656,
year = {2024},
author = {Xing, RR and Bai, WM and Hu, D and Deng, TT and Zhang, JK and Chen, Y},
title = {Using a DNA mini-barcode within the ITS region to identify toxic Amanita in mushroom poisoning cases.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {376},
pmid = {38884656},
issn = {1432-0614},
support = {2022YFF1101000//Key Technologies Research and Development Program/ ; 2023YFF1104700//Key Technologies Research and Development Program/ ; },
mesh = {*Mushroom Poisoning/diagnosis ; *Amanita/genetics ; *DNA Barcoding, Taxonomic ; *Phylogeny ; *DNA, Fungal/genetics ; DNA Primers/genetics ; DNA, Ribosomal Spacer/genetics ; Sequence Analysis, DNA ; Humans ; },
abstract = {Mushroom poisoning contributes significantly to global foodborne diseases and related fatalities. Amanita mushrooms frequently cause such poisonings; however, identifying these toxic species is challenging due to the unavailability of fresh and intact samples. It is often necessary to analyze residues, vomitus, or stomach extracts to obtain DNA sequences for the identification of species responsible for causing food poisoning. This usually proves challenging to obtain usable DNA sequences that can be analyzed using conventional molecular biology techniques. Therefore, this study aimed to develop a DNA mini-barcoding method for the identification of Amanita species. Following the evaluation and optimization of universal primers for DNA mini-barcoding in Amanita mushrooms, we found that the internal transcribed spacer (ITS) gene sequence primer ITS-a was the most suitable DNA barcode primer for identifying Amanita species. Forty-three Amanita samples were subsequently amplified and sequenced. The sequences obtained were analyzed for intra- and inter-species genetic distances, and a phylogenetic tree was constructed. The findings indicated that the designed primers had strong universality among the Amanita samples and could accurately identify the target gene fragment with a length of 290 bp. Notably, the DNA mini-barcode accurately identified the 43 Amanita samples, demonstrating high consistency with the conventional DNA barcode. Furthermore, it effectively identified DNA from digested samples. In summary, this DNA mini-barcode is a promising tool for detecting accidental ingestion of toxic Amanita mushrooms. It may be used as an optimal barcode for species identification and traceability in events of Amanita-induced mushroom poisoning. KEY POINTS: • Development of a DNA mini-barcoding method for Amanita species identification without fresh samples. • The ITS-a primer set was optimized for robust universality in Amanita samples. • The mini-barcode is suitable for screening toxic mushroom species in mushroom poisoning cases.},
}
@article {pmid38884110,
year = {2024},
author = {Rathgeber, AC and Ludwig, LS and Penter, L},
title = {Single-cell genomics-based immune and disease monitoring in blood malignancies.},
journal = {Clinical hematology international},
volume = {6},
number = {2},
pages = {62-84},
pmid = {38884110},
issn = {2590-0048},
support = {UM1 HG012076/HG/NHGRI NIH HHS/United States ; },
abstract = {Achieving long-term disease control using therapeutic immunomodulation is a long-standing concept with a strong tradition in blood malignancies. Besides allogeneic hematopoietic stem cell transplantation that continues to provide potentially curative treatment for otherwise challenging diagnoses, recent years have seen impressive progress in immunotherapies for leukemias and lymphomas with immune checkpoint blockade, bispecific monoclonal antibodies, and CAR T cell therapies. Despite their success, non-response, relapse, and immune toxicities remain frequent, thus prioritizing the elucidation of the underlying mechanisms and identifying predictive biomarkers. The increasing availability of single-cell genomic tools now provides a system's immunology view to resolve the molecular and cellular mechanisms of immunotherapies at unprecedented resolution. Here, we review recent studies that leverage these technological advancements for tracking immune responses, the emergence of immune resistance, and toxicities. As single-cell immune monitoring tools evolve and become more accessible, we expect their wide adoption for routine clinical applications to catalyze more precise therapeutic steering of personal immune responses.},
}
@article {pmid38884003,
year = {2024},
author = {Chieochanthanakij, R and Wattanasatja, V and Passorn, P and Wannigama, DL and Kanjanabuch, T},
title = {Caregiver skin infection causing peritoneal dialysis-associated peritonitis.},
journal = {Medical mycology case reports},
volume = {44},
number = {},
pages = {100653},
pmid = {38884003},
issn = {2211-7539},
abstract = {We present the first case report of peritoneal dialysis (PD)-associated peritonitis due to Gibellulopsis nigrescens, with the same pathogen detected in her caregiver's tinea capitis. This confirms that touch contamination from the caregiver's infection was the primary source of this rare organism. The species of pathogen causing peritonitis and her caregiver's scalp lesions were identified by DNA barcoding. The patient responded well to timely PD catheter removal and a 2-week course of systemic amphotericin B deoxycholate. Preventive strategies should prioritize hygiene practices, including maintaining adequate personal hygiene and practicing thorough hand washing, to mitigate the risk of touch contamination and subsequent infection with fungal pathogens.},
}
@article {pmid38883207,
year = {2024},
author = {Valsecchi, E and Gabbiadini, A},
title = {An Observatory to monitor range extension of the Mediterranean monk seal based on its eDNA traces: collecting data and delivering results in the "Open Science" era.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e120201},
pmid = {38883207},
issn = {1314-2828},
abstract = {The monk seal is the most endangered pinniped in the world and the only one found in the Mediterranean, where its distribution and abundance have suffered a drastic decline in the last few decades. Data on its status are scattered due to both its rarity and evasiveness and records are biased towards occasional, mostly coastal encounters. Nowadays, molecular techniques allow us to detect and quantify minute amounts of DNA traces released into the environment (eDNA) by any organism. A species-specific molecular assay is now available for detecting the recent presence of the monk seal in the water column through the analysis of sea-water samples collected from the sea surface. The project "Spot the Monk" uses this non-invasive detection tool to monitor monk seal occurrence in Mediterranean waters by means of eDNA analysis. The simplicity in the acquisition of samples together with the need to collect samples in multiple points simultaneously made the project well suited to the involvement of the general public. Up to today, about 350 samples have been collected and analysed in the central-western Mediterranean by researchers and a multifarious range of citizen scientists - from recreational sailing organisations, both amateur and competitive sportsmen, to fishermen. This work announces the launch of an open-source Observatory (https://www.spot-the-monk-observatory.com/) where the project outcomes are publicly accessible as soon as they are produced. Embracing the principles of Open Science, we believe that such an approach can contribute to filling the knowledge gap about the distribution of this charismatic species in our seas, providing, at the same time, a proof of concept on how data collected by a variety of actors can be returned to the scientific and non-scientific communities in an innovative format for immediate consultation.},
}
@article {pmid38883206,
year = {2024},
author = {Jaume-Schinkel, S and Müller, B and Avila-Calero, S and Kukowka, S and Rduch, V and Mengual, X},
title = {Preserving morphology while extracting DNA: a non-destructive field-to-museum protocol for slide-mounted specimens.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e119448},
pmid = {38883206},
issn = {1314-2828},
abstract = {Our study aimed to develop an optimised laboratory protocol ensuring the preservation of morphological structures and extraction of high-quality DNA sequences from Psychodidae (Insecta, Diptera) specimens. With 310 analysed specimens, we investigated the impact of distinct laboratory treatments by employing two shaking categories (constant and interrupted) with five different incubation periods (16, 12, 8, 4 and 2 hours) during the DNA extraction process. Notably, 80.65% of the specimens exhibited morphological changes during DNA extraction. Our results indicated no statistical difference between constant and interrupted shaking for the total of morphological structures lost. However, within each shaking category, the loss of structures was influenced significantly by the incubation period. Prolonged incubation correlated with increased structural losses, whereas shorter incubation periods caused minor alterations in structures lost. In addition, our results showed a significant difference between constant and interrupted shaking treatments for DNA concentration. Likewise, the incubation period showed differences within each shaking category. Successful COI sequencing was achieved in 89.6% of specimens, with negligible differences in DNA fragment lengths across treatments. Our findings underscore the importance of an optimised protocol and its potential in systematic research involving nematoceran dipteran specimens by balancing morphological integrity and DNA extraction efficiency.},
}
@article {pmid38882565,
year = {2024},
author = {Li, SL and Liu, P and Peng, XJ},
title = {Three new species of jumping spiders (Araneae, Salticidae) from Hunan, China.},
journal = {ZooKeys},
volume = {1204},
number = {},
pages = {301-312},
pmid = {38882565},
issn = {1313-2989},
abstract = {Three new species of the genera Thiania C. L. Koch, 1846 and Yaginumaella Prószyński, 1979 are described and named as T.bamian sp. nov. (♂♀), T.flacata sp. nov. (♀) and Y.curvata sp. nov. (♂♀), from Hunan Province, China. Detailed descriptions, photos of somatic features and copulatory organs, as well as a distribution map are provided. Nucleotide data for the barcoding gene, cytochrome c oxidase subunit I (COI) of T.bamian sp. nov. (♂♀) and Y.curvata sp. nov. (♀) are provided.},
}
@article {pmid38879694,
year = {2024},
author = {Siddika, MA and Ahmed, KA and Alam, MS and Bushra, J and Begum, RA},
title = {Complete mitogenome and intra-family comparative mitogenomics showed distinct position of Pama Croaker Otolithoides pama.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {13820},
pmid = {38879694},
issn = {2045-2322},
support = {NST Fellowship for Masters Thesis Research//Ministry of Science and Technology, Government of the People's Republic of Bangladesh/ ; Post Doctoral Research Fund//CSIRO, Australia/ ; 2022-23/23//University Grants Commission of Bangladesh/ ; },
mesh = {Animals ; *Genome, Mitochondrial/genetics ; *Phylogeny ; *Perciformes/genetics/classification ; Codon Usage ; Gene Order ; },
abstract = {The Pama Croaker, Otolithoides pama, is an economically important fish species in Bangladesh. Intra-family similarities in morphology and typical barcode sequences of cox1 create ambiguities in its identification. Therefore, morphology and the complete mitochondrial genome of O. pama, and comparative mitogenomics within the family Sciaenidae have been studied. Extracted genomic DNA was subjected to Illumina-based short read sequencing for De-Novo mitogenome assembly. The complete mitogenome of O. pama (Accession: OQ784575.1) was 16,513 bp, with strong AC biasness and strand asymmetry. Relative synonymous codon usage (RSCU) among 13 protein-coding genes (PCGs) of O. pama was also analyzed. The studied mitogenomes including O. pama exhibited consistent sizes and gene orders, except for the genus Johnius which possessed notably longer mitogenomes with unique gene rearrangements. Different genetic distance metrics across 30 species of Sciaenidae family demonstrated 12S rRNA and the control region (CR) as the most conserved and variable regions, respectively, while most of the PCGs undergone a purifying selection. Different phylogenetic trees were congruent with one another, where O. pama was distinctly placed. This study would contribute to distinguishing closely related fish species of Sciaenidae family and can be instrumental in conserving the genetic diversity of O. pama.},
}
@article {pmid38877523,
year = {2024},
author = {De Silva, S and Cagliero, C and Gostel, MR and Johnson, G and Anderson, JL},
title = {Versatile DNA extraction from diverse plant taxa using ionic liquids and magnetic ionic liquids: a methodological breakthrough for enhanced sample utility.},
journal = {Plant methods},
volume = {20},
number = {1},
pages = {91},
pmid = {38877523},
issn = {1746-4811},
support = {CHE-2203891//U.S. National Science Foundation/ ; },
abstract = {BACKGROUND: There is a growing demand for fast and reliable plant biomolecular analyses. DNA extraction is the major bottleneck in plant nucleic acid-based applications especially due to the complexity of tissues in different plant species. Conventional methods for plant cell lysis and DNA extraction typically require extensive sample preparation processes and large quantities of sample and chemicals, elevated temperatures, and multiple sample transfer steps which pose challenges for high throughput applications.<br><br>RESULTS: In a prior investigation, an ionic liquid (IL)-based modified vortex-assisted matrix solid phase dispersion approach was developed using the model plant, Arabidopsis thaliana (L.) Heynh. Building upon this foundational study, the present study established a simple, rapid and efficient protocol for DNA extraction from milligram fragments of plant tissue representing a diverse range of taxa from the plant Tree of Life including 13 dicots and 4 monocots. Notably, the approach was successful in extracting DNA from a century old herbarium sample. The isolated DNA was of sufficient quality and quantity for sensitive molecular analyses such as qPCR. Two plant DNA barcoding markers, the plastid rbcL and nuclear ribosomal internal transcribed spacer (nrITS) regions were selected for DNA amplification and Sanger sequencing was conducted on PCR products of a representative dicot and monocot species. Successful qPCR amplification of the extracted DNA up to 3 weeks demonstrated that the DNA extracted using this approach remains stable at room temperature for an extended time period prior to downstream analysis.<br><br>CONCLUSIONS: The method presented here is a rapid and simple approach enabling cell lysis and DNA extraction from 1.5&#xa0;mg of plant tissue across a broad range of plant taxa. Additional purification prior to DNA amplification is not required due to the compatibility of the extraction solvents with qPCR. The method has tremendous potential for applications in plant biology that require DNA, including barcoding methods for agriculture, conservation, ecology, evolution, and forensics.},
}
@article {pmid38876979,
year = {2024},
author = {Sullivan, DK and Pachter, L},
title = {Flexible parsing, interpretation, and editing of technical sequences with splitcode.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {6},
pages = {},
pmid = {38876979},
issn = {1367-4811},
support = {T32 GM008042/GM/NIGMS NIH HHS/United States ; UM1 HG012077/HG/NHGRI NIH HHS/United States ; U19MH114830/NH/NIH HHS/United States ; },
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Software ; Sequence Analysis, DNA/methods ; Gene Library ; },
abstract = {MOTIVATION: Next-generation sequencing libraries are constructed with numerous synthetic constructs such as sequencing adapters, barcodes, and unique molecular identifiers. Such sequences can be essential for interpreting results of sequencing assays, and when they contain information pertinent to an experiment, they must be processed and analyzed.<br><br>RESULTS: We present a tool called splitcode, that enables flexible and efficient parsing, interpreting, and editing of sequencing reads. This versatile tool facilitates simple, reproducible preprocessing of reads from libraries constructed for a large array of single-cell and bulk sequencing assays.<br><br>The splitcode program is available at http://github.com/pachterlab/splitcode.},
}
@article {pmid38874640,
year = {2024},
author = {Bhendarkar, M and Rodriguez-Ezpeleta, N},
title = {Exploring uncharted territory: new frontiers in environmental DNA for tropical fisheries management.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {7},
pages = {617},
pmid = {38874640},
issn = {1573-2959},
mesh = {*Fisheries ; *Biodiversity ; *Conservation of Natural Resources/methods ; Animals ; *Environmental Monitoring/methods ; *DNA, Environmental/analysis ; *Tropical Climate ; Ecosystem ; Fishes/genetics ; },
abstract = {Tropical ecosystems host a significant share of global fish diversity contributing substantially to the global fisheries sector. Yet their sustainable management is challenging due to their complexity, diverse life history traits of tropical fishes, and varied fishing techniques involved. Traditional monitoring techniques are often costly, labour-intensive, and/or difficult to apply in inaccessible sites. These limitations call for the adoption of innovative, sensitive, and cost-effective monitoring solutions, especially in a scenario of climate change. Environmental DNA (eDNA) emerges as a potential game changer for biodiversity monitoring and conservation, especially in aquatic ecosystems. However, its utility in tropical settings remains underexplored, primarily due to a series of challenges, including the need for a comprehensive barcode reference library, an understanding of eDNA behaviour in tropical aquatic environments, standardized procedures, and supportive biomonitoring policies. Despite these challenges, the potential of eDNA for sensitive species detection across varied habitats is evident, and its global use is accelerating in biodiversity conservation efforts. This review takes an in-depth look at the current state and prospects of eDNA-based monitoring in tropical fisheries management research. Additionally, a SWOT analysis is used to underscore the opportunities and threats, with the aim of bridging the knowledge gaps and guiding the more extensive and effective use of eDNA-based monitoring in tropical fisheries management. Although the discussion applies worldwide, some specific experiences and insights from Indian tropical fisheries are shared to illustrate the practical application and challenges of employing eDNA in a tropical context.},
}
@article {pmid38873813,
year = {2024},
author = {McNamara, LE and Boyn, JN and Anferov, SW and Filatov, AS and Maloney, MW and Mazziotti, DA and Schaller, RD and Anderson, JS},
title = {Variable Peripheral Ligand Donation Tunes Electronic Structure and NIR II Emission in Tetrathiafulvalene Tetrathiolate Diradicaloids.},
journal = {Journal of the American Chemical Society},
volume = {146},
number = {25},
pages = {17285-17295},
doi = {10.1021/jacs.4c04032},
pmid = {38873813},
issn = {1520-5126},
abstract = {Near-infrared (NIR) lumiphores are promising candidates for numerous imaging, communication, and sensing applications, but they typically require large, conjugated scaffolds to achieve emission in this low-energy region. Due to the extended conjugation and synthetic complexity required, it is extremely difficult to tune the photophysical properties of these systems for desired applications. Here, we report facile tuning of deep NIR-emitting diradicaloid complexes through simple modification of peripheral ligands. These new lumiphores are rare examples of air-, acid-, and water-stable emissive diradicaloids. We apply a simple Hammett parameter-based strategy to tune the electron donation of the capping ligand across a series of commercially available triarylphosphines. This minor peripheral modification significantly alters the electronic structure, and consequently, the electrochemical, photophysical, and magnetic properties of the tetrathiafulvalene tetrathiolate (TTFtt)-based lumiphores. The resultant ∼100 nm absorption and emission range spans common laser lines and the desirable telecom region (ca. 1260-1550 nm). Furthermore, these lumiphores are sensitive to local dielectrics, distinguishing them as promising candidates for ratiometric imaging and/or barcoding in the deep NIR region.},
}
@article {pmid38869148,
year = {2024},
author = {Yang, C and Zhang, Z and Huang, Y and Xie, X and Liao, H and Xiao, J and Veldsman, WP and Yin, K and Fang, X and Zhang, L},
title = {LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome.},
journal = {GigaScience},
volume = {13},
number = {},
pages = {},
pmid = {38869148},
issn = {2047-217X},
support = {518000//BGI-Shenzhen, Shenzhen/ ; //Hong Kong Research Grant Council Early Career Scheme/ ; 22201419//HKBU/ ; C2004-23Y//Young Collaborative Research/ ; 11221026//Health and Medical Research Fund/ ; RC-SGT2/19-20/SCI/007//HKBU Start-up Grant Tier 2/ ; IRCMS/19-20/D02//HKBU IRCMS/ ; 2021A1515012226//Guangdong Basic and Applied Basic Research Foundation/ ; SGDX20190919142801722//Science Technology and Innovation Committee of Shenzhen Municipality, China/ ; },
mesh = {Humans ; *Genome, Human ; *Metagenome ; *Software ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; },
abstract = {BACKGROUND: Linked-read sequencing technologies generate high-base quality short reads that contain extrapolative information on long-range DNA connectedness. These advantages of linked-read technologies are well known and have been demonstrated in many human genomic and metagenomic studies. However, existing linked-read analysis pipelines (e.g., Long Ranger) were primarily developed to process sequencing data from the human genome and are not suited for analyzing metagenomic sequencing data. Moreover, linked-read analysis pipelines are typically limited to 1 specific sequencing platform.<br><br>FINDINGS: To address these limitations, we present the Linked-Read ToolKit (LRTK), a unified and versatile toolkit for platform agnostic processing of linked-read sequencing data from both human genome and metagenome. LRTK provides functions to perform linked-read simulation, barcode sequencing error correction, barcode-aware read alignment and metagenome assembly, reconstruction of long DNA fragments, taxonomic classification and quantification, and barcode-assisted genomic variant calling and phasing. LRTK has the ability to process multiple samples automatically and provides users with the option to generate reproducible reports during processing of raw sequencing data and at multiple checkpoints throughout downstream analysis. We applied LRTK on linked reads from simulation, mock community, and real datasets for both human genome and metagenome. We showcased LRTK's ability to generate comparative performance results from preceding benchmark studies and to report these results in publication-ready HTML document plots.<br><br>CONCLUSIONS: LRTK provides comprehensive and flexible modules along with an easy-to-use Python-based workflow for processing linked-read sequencing datasets, thereby filling the current gap in the field caused by platform-centric genome-specific linked-read data analysis tools.},
}
@article {pmid38865431,
year = {2024},
author = {Tedersoo, L and Hosseyni Moghaddam, MS and Mikryukov, V and Hakimzadeh, A and Bahram, M and Nilsson, RH and Yatsiuk, I and Geisen, S and Schwelm, A and Piwosz, K and Prous, M and Sildever, S and Chmolowska, D and Rueckert, S and Skaloud, P and Laas, P and Tines, M and Jung, JH and Choi, JH and Alkahtani, S and Anslan, S},
title = {EUKARYOME: the rRNA gene reference database for identification of all eukaryotes.},
journal = {Database : the journal of biological databases and curation},
volume = {2024},
number = {},
pages = {},
pmid = {38865431},
issn = {1758-0463},
support = {Distinguished Scientist Fellowship Programme//King Saud University/ ; MOBERC66 MOBTP198//European Regional Development Fund/ ; //LOEWE Zentrum AdRIA/ ; Distinguished Scientist Fellowship Programme//King Saud University/ ; MOBERC66 MOBTP198//European Regional Development Fund/ ; //LOEWE Zentrum AdRIA/ ; },
mesh = {*Eukaryota/genetics ; RNA, Ribosomal, 18S/genetics ; Databases, Genetic ; Databases, Nucleic Acid ; Animals ; Genes, rRNA/genetics ; Phylogeny ; },
abstract = {Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers-ITS1, ITS2, 18S V4-V5 and 28S D1-D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding-a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.},
}
@article {pmid38864889,
year = {2024},
author = {Yu, KY and Lam, YH and Ng, SW and Cheung, YT and Tseung, JS and Tong, HF and Ching, CK and Chong, YK},
title = {Plant-origin rotenone poisoning - a rare cause of metabolic acidosis with hyperlactatemia diagnosed with DNA barcoding of gastric contents.},
journal = {Clinical toxicology (Philadelphia, Pa.)},
volume = {62},
number = {6},
pages = {407-408},
doi = {10.1080/15563650.2024.2350597},
pmid = {38864889},
issn = {1556-9519},
mesh = {Humans ; *Acidosis/chemically induced ; *Rotenone/toxicity ; *Hyperlactatemia/chemically induced ; *Gastrointestinal Contents/chemistry ; Male ; Adult ; },
}
@article {pmid38863065,
year = {2024},
author = {Van Caenegem, W and Haelewaters, D},
title = {New insights into the DNA extraction and PCR amplification of minute ascomycetes in the genus Laboulbenia (Pezizomycotina, Laboulbeniales).},
journal = {IMA fungus},
volume = {15},
number = {1},
pages = {14},
pmid = {38863065},
issn = {2210-6340},
support = {DEB-2127290//Directorate for Biological Sciences/ ; Senior Postdoctoral Fellowship 1206024N//Research Foundation Flanders/ ; },
abstract = {Molecular studies of fungi within the order Laboulbeniales (Ascomycota, Pezizomycotina) have been hampered for years because of their minute size, inability to grow in axenic culture, and lack of reliable and cost-efficient DNA extraction protocols. In particular, the genus Laboulbenia is notorious for low success with DNA extraction and polymerase chain reaction (PCR) amplification. This is attributed to the presence of melanin, a molecule known to inhibit PCR, in the cells. We evaluated the efficacy of a standard single cell-based DNA extraction protocol by halving the recommended amount of reagents to reduce the cost per extraction and adding bovine serum albumin (BSA) during the multiple displacement amplification step to reverse the effect of melanin. A total of 196 extractions were made, 111 of which were successful. We found that halving the reagents used in the single cell-based extraction kit did not significantly affect the probability of successful DNA extraction. Using the halved protocol reduces cost and resource consumption. Moreover, there was no significant difference in the probability of successfully extracting DNA based on whether BSA was added or not, suggesting that the amount of melanin present in cells of the thallus has no major inhibitory effect on PCR. We generated 277 sequences from five loci, but amplification of the internal transcribed spacer region, the mitochondrial small subunit rDNA, and protein-coding genes remains challenging. The probability of successfully extracting DNA from Laboulbeniales was also impacted by specimen storage methods, with material preserved in > 95% ethanol yielding higher success rates compared to material stored in 70% ethanol and dried material. We emphasize the importance of proper preservation of material and propose the design of Laboulbeniales-specific primers to overcome the problems of primer mismatches and contaminants. Our new insights apply not only to the genus Laboulbenia; Laboulbeniales generally are understudied, and the vast majority of species remain unsequenced. New and approachable molecular developments will benefit the study of Laboulbeniales, helping to elucidate the true diversity and evolutionary relationships of these peculiar microfungi.},
}
@article {pmid38861479,
year = {2024},
author = {Hamilton, AG and Swingle, KL and Thatte, AS and Mukalel, AJ and Safford, HC and Billingsley, MM and El-Mayta, RD and Han, X and Nachod, BE and Joseph, RA and Metzloff, AE and Mitchell, MJ},
title = {High-Throughput In Vivo Screening Identifies Differential Influences on mRNA Lipid Nanoparticle Immune Cell Delivery by Administration Route.},
journal = {ACS nano},
volume = {18},
number = {25},
pages = {16151-16165},
doi = {10.1021/acsnano.4c01171},
pmid = {38861479},
issn = {1936-086X},
mesh = {Animals ; *Nanoparticles/chemistry ; *RNA, Messenger/genetics ; Mice ; *Lipids/chemistry ; *Mice, Inbred C57BL ; High-Throughput Screening Assays ; Female ; Injections, Intramuscular ; Dendritic Cells/immunology/metabolism ; Injections, Intravenous ; Immunotherapy ; Liposomes ; },
abstract = {Immune modulation through the intracellular delivery of nucleoside-modified mRNA to immune cells is an attractive approach for in vivo immunoengineering, with applications in infectious disease, cancer immunotherapy, and beyond. Lipid nanoparticles (LNPs) have come to the fore as a promising nucleic acid delivery platform, but LNP design criteria remain poorly defined, making the rate-limiting step for LNP discovery the screening process. In this study, we employed high-throughput in vivo LNP screening based on molecular barcoding to investigate the influence of LNP composition on immune tropism with applications in vaccines and systemic immunotherapies. Screening a large LNP library under both intramuscular (i.m.) and intravenous (i.v.) injection, we observed differential influences on LNP uptake by immune populations across the two administration routes, gleaning insight into LNP design criteria for in vivo immunoengineering. In validation studies, the lead LNP formulation for i.m. administration demonstrated substantial mRNA translation in the spleen and draining lymph nodes with a more favorable biodistribution profile than LNPs formulated with the clinical standard ionizable lipid DLin-MC3-DMA (MC3). The lead LNP formulations for i.v. administration displayed potent immune transfection in the spleen and peripheral blood, with one lead LNP demonstrating substantial transfection of splenic dendritic cells and another inducing substantial transfection of circulating monocytes. Altogether, the immunotropic LNPs identified by high-throughput in vivo screening demonstrated significant promise for both locally- and systemically-delivered mRNA and confirmed the value of the LNP design criteria gleaned from our screening process, which could potentially inform future endeavors in mRNA vaccine and immunotherapy applications.},
}
@article {pmid38859300,
year = {2024},
author = {Xu, B and Ji, Y and Xu, C and Zhang, B and Liu, K and Li, J},
title = {Simple modulation of Lissajous MEMS laser beam scanning with reconfigurable structured light patterns for 3D imaging.},
journal = {Optics express},
volume = {32},
number = {8},
pages = {13249-13265},
doi = {10.1364/OE.518283},
pmid = {38859300},
issn = {1094-4087},
abstract = {Structured light 3D imaging systems commonly employ panel-based projectors or 1-axis MEMS mirrors with beam expander lens to project multi-frame barcodes or dot clouds, addressing challenges posed by objects with multi-scale feature sizes. However, these methods often result in large system volumes due to the required projection multi-lens modules, high hardware costs, or limited light pattern generation capabilities that hindering measurement precision enhancement. This paper introduces an innovative approach to reconfigurable spatial light pattern projection using a single bi-axial MEMS mirror with Lissajous scanning. In contrast to the pixel-by-pixel pre-defined image patterns encoding of conventional 2D laser beam scanning, the proposed method simply aligns the MEMS bi-axial resonance frequencies with laser pulse modulation, enabling the projection of diverse structured light patterns such as stripes, lines, dot matrices, and random dot clouds, which can adapt to different 3D imaging algorithms demands. It eliminates the need for multi-frame encoding and streamlines data caching, simplifies digital logic hardware. A prototype 3D imaging system was developed to demonstrate the mathematical model for laser modulation and the technical feasibility based on the proposed principle. Beyond its lens-free essence, the system supports focal-free optics and a compact projection form factor, which accommodates to a broad range of projection distances and field-of-views based on object's location. 3D depth map of polynomial surface and blocks objects are extracted through single-frame pattern projection with a relative high accuracy. The presented modulation theory for diverse structured light pattern generation opens avenues for versatile and compact 3D imaging applications of LiDAR and robotic 3D vision.},
}
@article {pmid38853940,
year = {2024},
author = {Willimann, M and Tiyaboonchai, A and Adachi, K and Li, B and Waldburger, L and Nakai, H and Grompe, M and Thöny, B},
title = {AAV Capsid Screening for Translational Pig Research Using a Mouse Xenograft Liver Model.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38853940},
issn = {2692-8205},
support = {U01 DK123608/DK/NIDDK NIH HHS/United States ; },
abstract = {In gene therapy, delivery vectors are a key component for successful gene delivery and safety, based on which adeno-associated viruses (AAVs) gained popularity in particular for the liver, but also for other organs. Traditionally, rodents have been used as animal models to develop and optimize treatments, but species and organ specific tropism of AAV desire large animal models more closely related to humans for preclinical in-depth studies. Relevant AAV variants with the potential for clinical translation in liver gene therapy were previously evolved in vivo in a xenogeneic mouse model transplanted with human hepatocytes. Here, we selected and evaluated efficient AAV capsids using chimeric mice with a >90% xenografted pig hepatocytes. The pig is a valuable preclinical model for therapy studies due to its anatomic and immunological similarities to humans. Using a DNA-barcoded recombinant AAV library containing 47 different capsids and subsequent Illumina sequencing of barcodes in the AAV vector genome DNA and transcripts in the porcine hepatocytes, we found the AAVLK03 and AAVrh20 capsid to be the most efficient delivery vectors regarding transgene expression in porcine hepatocytes. In attempting to validate these findings with primary porcine hepatocytes, we observed capsid-specific differences in cell entry and transgene expression efficiency where the AAV2, AAVAnc80, and AAVDJ capsids showed superior efficiency to AAVLK03 and AAVrh20. This work highlights intricacies of in vitro testing with primary hepatocytes and the requirements for suitable pre-clinical animal models but suggests the chimeric mouse to be a valuable model to predict AAV capsids to transduce porcine hepatocytes efficiently.},
}
@article {pmid38853931,
year = {2024},
author = {Choudhury, S and Sivankutty, I and Jung, Y and Huang, A and Araten, S and Kenny, C and An, Z and Doan, R and Foijer, F and Matsu, E and Rosen, I and Marciano, J and Jain, A and Sun, L and Hilal, N and Lee, E and Walsh, C and Chen, M},
title = {Single-nucleus multi-omic profiling of polyploid heart nuclei identifies fusion-derived cardiomyocytes in the human heart.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {38853931},
issn = {2693-5015},
support = {R56 AG079857/AG/NIA NIH HHS/United States ; P50 HD105351/HD/NICHD NIH HHS/United States ; DP2 AG072437/AG/NIA NIH HHS/United States ; S10 OD016453/OD/NIH HHS/United States ; UG3 NS132144/NS/NINDS NIH HHS/United States ; R01 HL152063/HL/NHLBI NIH HHS/United States ; R01 AG070921/AG/NIA NIH HHS/United States ; },
abstract = {Understanding the mechanisms of polyploidization in cardiomyocytes is crucial for advancing strategies to stimulate myocardial regeneration. Although endoreplication has long been considered the primary source of polyploid human cardiomyocytes, recent animal work suggests the potential for cardiomyocyte fusion. Moreover, the effects of polyploidization on the genomic-transcriptomic repertoire of human cardiomyocytes have not been studied previously. We applied single-nuclei whole genome sequencing, single nuclei RNA sequencing, and multiome ATAC + gene expression (from the same nuclei) techniques to nuclei isolated from 11 healthy hearts. Utilizing post-zygotic non-inherited somatic mutations occurring during development as "endogenous barcodes," to reconstruct lineage relationships of polyploid cardiomyocytes. Of 482 cardiomyocytes from multiple healthy donor hearts 75.7% can be sorted into several developmental clades marked by one or more somatic single-nucleotide variants (SNVs). At least ~10% of tetraploid cardiomyocytes contain cells from distinct clades, indicating fusion of lineally distinct cells, whereas 60% of higher-ploidy cardiomyocytes contain fused cells from distinct clades. Combined snRNA-seq and snATAC-seq revealed transcriptome and chromatin landscapes of polyploid cardiomyocytes distinct from diploid cardiomyocytes, and show some higher-ploidy cardiomyocytes with transcriptional signatures suggesting fusion between cardiomyocytes and endothelial and fibroblast cells. These observations provide the first evidence for cell and nuclear fusion of human cardiomyocytes, raising the possibility that cell fusion may contribute to developing or maintaining polyploid cardiomyocytes in the human heart.},
}
@article {pmid38853372,
year = {2024},
author = {Landers, E and Claridge, B and Kuhn, W and Seymour, V and Peek, H and Fluet, S and Ramgren, J and Phelps, J and Paulk, B and Cordner, L and Blaschke, J},
title = {Using DNA barcoding to identify high-priority taxa (Hymenoptera: Ichneumonidae) from Great Smoky Mountains National Park.},
journal = {Environmental entomology},
volume = {53},
number = {4},
pages = {730-739},
doi = {10.1093/ee/nvae058},
pmid = {38853372},
issn = {1938-2936},
mesh = {Biodiversity ; *DNA Barcoding, Taxonomic/standards ; *Hymenoptera/anatomy &amp; histology/classification/genetics ; *Parks, Recreational ; Species Specificity ; Animals ; },
abstract = {The All Taxa Biodiversity Inventory (ATBI) in Great Smoky Mountains National Park (GSMNP) seeks to document every species of living thing in the park. The ATBI is decades in progress, yet some taxa remain virtually untouched by taxonomists. Such "high priority" taxa include the hyper-diverse parasitoid wasp family Ichneumonidae. Despite the positive and multifaceted effects ichneumonids have on their environment, only a small percentage of those collected in the park have been identified as species, mostly to their complex morphology and overwhelming diversity. Recently, DNA barcoding has transformed biodiversity inventories, streamlining the process to be more rapid and efficient. To test the effectiveness of barcoding 20 + year-old specimens of Ichneumonidae and catalog new records for GSMNP, COI was amplified from 95 ichneumonid morphospecies collected from Andrew's Bald, NC. Species identifications were confirmed morphologically. Eighty-one ichneumonids generated sequence data, representing 16 subfamilies and 44 genera. The subfamily Oxytorinae is newly recorded from GSMNP, along with 10 newly recorded genera and 23 newly recorded species across Ichneumonidae. These results contribute significantly to the ATBI by adding new park records for a high-priority taxon and demonstrate the effectiveness of applying DNA barcoding to samples in long-term storage or those lacking immediate taxonomic expertise.},
}
@article {pmid38853364,
year = {2024},
author = {Byrne, GW and McGregor, CGA},
title = {Anti-pig antibodies in swine veterinarian serum: Implications for clinical xenotransplantation.},
journal = {Xenotransplantation},
volume = {31},
number = {3},
pages = {e12865},
doi = {10.1111/xen.12865},
pmid = {38853364},
issn = {1399-3089},
support = {//Experimental Surgical Services/ ; },
mesh = {Animals ; *Transplantation, Heterologous/methods ; Humans ; Swine ; *Graft Rejection/immunology ; HEK293 Cells ; Veterinarians ; Polysaccharides/immunology ; Animals, Genetically Modified ; Antibodies, Heterophile/immunology/blood ; Heterografts/immunology ; Immunoglobulin M/immunology/blood ; },
abstract = {Recent clinical xenotransplantation and human decedent studies demonstrate that clinical hyperacute rejection of genetically engineered porcine organs can be reliably avoided but that antibody mediated rejection (AMR) continues to limit graft survival. We previously identified porcine glycans and proteins which are immunogenic after cardiac xenotransplantation in non-human primates, but the clinical immune response to antigens present in glycan depleted triple knockout (TKO) donor pigs is poorly understood. In this study we use fluorescence barcoded human embryonic kidney cells (HEK) and HEK cell lines expressing porcine glycans (Gal and SDa) or proteins (tetraspanin-29 [CD9], membrane cofactor protein [CD46], protectin, membrane attack complex inhibition factor [CD59], endothelial cell protein C receptor, and Annexin A2) to screen antibody reactivity in human serum from 160 swine veterinarians, a serum source with potential occupational immune challenge from porcine tissues and pathogens. High levels of anti-Gal IgM were present in all samples and lower levels of anti-SDa IgM were present in 41% of samples. IgM binding to porcine proteins, primarily CD9 and CD46, previously identified as immunogenic in pig to non-human primate cardiac xenograft recipients, was detected in 28 of the 160 swine veterinarian samples. These results suggest that barcoded HEK cell lines expressing porcine protein antigens can be useful for screening human patient serum. A comprehensive analysis of sera from clinical xenotransplant recipients to define a panel of commonly immunogenic porcine antigens will likely be necessary to establish an array of porcine non-Gal antigens for effective monitoring of patient immune responses and allow earlier therapies to reverse AMR.},
}
@article {pmid38852495,
year = {2024},
author = {Hii, KS and Abdul Manaff, AHN and Gu, H and Lim, PT and Leaw, CP},
title = {A comparative analysis of real-time quantitative PCR and metabarcoding methods for eDNA-based detection of the toxic dinophyte Alexandrium tamiyavanichii (Dinophyceae).},
journal = {Marine environmental research},
volume = {199},
number = {},
pages = {106593},
doi = {10.1016/j.marenvres.2024.106593},
pmid = {38852495},
issn = {1879-0291},
mesh = {*Dinoflagellida/genetics ; *Real-Time Polymerase Chain Reaction/methods ; *DNA Barcoding, Taxonomic/methods ; *Environmental Monitoring/methods ; DNA, Environmental ; China ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {The marine dinophyte Alexandrium tamiyavanichii is a toxigenic species that produces a group of neurotoxins that is responsible for paralytic shellfish poisoning in humans. Early detection of the species is essential for efficient monitoring. Harmful microalgal monitoring systems have evolved over the years with the advent of environmental DNA (eDNA)-based species detection techniques. In this study, eDNA samples were collected from a large-scale sampling covering the southern South China Sea. The sensitivity and specificity of metabarcoding of the V4 and V9 18S ribosomal DNA barcodes by high-throughput sequencing (HTS) were compared to the species-specific real-time qPCR targeting the A. tamiyavanichii ITS2 region. Environmental samples were screened for A. tamiyavanichii by qPCR (n = 43) and analyzed with metabarcoding (n = 30). Our results revealed a high occupancy profile across samples for both methods; 88% by qPCR, and 80-83% by HTS. When comparing the consistency between the two approaches, only two samples out of 30 were discordant. The V4 and V9 molecular units detected in each sample were positively correlated with the qPCR ITS2 gene copies (V4, rs = 0.67, p < 0.0001; V9, rs = 0.65, p < 0.0001), indicating that metabarcoding could be used as a useful tool for early detection of the species. Our results also revealed that the estimation of A. tamiyavanichii cell abundances based on the HTS read abundances was comparable to that of the qPCR quantification. For long-term monitoring, metabarcoding could serve as a cost-effective screening of detecting not only single HAB species but also simultaneously detecting a multitude of potentially harmful species, which is valuable in informing the subsequent implementation of species-specific monitoring strategies.},
}
@article {pmid38851103,
year = {2024},
author = {Liu, Q and Dai, J and Chen, J and Liu, Z and Lin, Y and Qiu, G and Gao, X and Zhang, R and Zhu, S},
title = {Comparative analysis the chloroplast genomes of Celastrus (Celastraceae) species: Provide insights into molecular evolution, species identification and phylogenetic relationships.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {131},
number = {},
pages = {155770},
doi = {10.1016/j.phymed.2024.155770},
pmid = {38851103},
issn = {1618-095X},
mesh = {*Celastrus/genetics/classification ; *Genome, Chloroplast ; *Phylogeny ; *Evolution, Molecular ; Base Composition ; Plants, Medicinal/genetics/classification ; China ; Introns ; },
abstract = {BACKGROUND: The genus Celastrus is an important medicinal plant resource. The similarity of morphology and the lack of complete chloroplast genome analysis have significantly impeded the exploration of species identification, molecular evolution and phylogeny of Celastrus.<br><br>PURPOSE: In order to resolve the phylogenic controversy of Celastrus species, the chloroplast genome comparative analysis was performed to provide genetic evidence.<br><br>METHODS: In this study, we collected and sequenced ten chloroplast genomes of Celastrus species from China and downloaded three chloroplast genomes from the databases. The chloroplast genomes were compared and analyzed to explore their characteristics and evolution. Furthermore, the phylogenetic relationships of Celastrus species were inferred based on the whole chloroplast genomes and protein-coding genes.<br><br>RESULTS: All the 13 Celastrus species chloroplast genomes showed a typical quadripartite structure with genome sizes ranging from 155,113 to 157,366&#x2009;bp. The intron loss of the rps16 gene occurred in all the 13 Celastrus species. The GC content, gene sequence, repeat types and codon bias pattern were highly conserved. Ten highly variation regions were identified, which can be used as potential DNA markers in molecular identification of Celastrus species. Eight genes, including accD, atp4, ndhB, rpoC1, rbcL, rpl2, rpl20 and ycf1, were detected to experience positive selection. Phylogenetic analysis showed that Celastrus was a monophyletic group and Tripterygium was the closest sister-group. Noteworthy, C. gemmatus Loes. and C. orbiculatus Thunb. can be discriminated using the chloroplast genome as a super barcode. The comparative and phylogenetic analysis results proposed that C. tonkinensis Pitard. was the synonym of C. hindsii Benth.<br><br>CONCLUSION: The comparative analysis of the Celastrus chloroplast genomes can provide comprehensive genetic evidence for molecular evolution, species identification and phylogenetic relationships.},
}
@article {pmid38849559,
year = {2024},
author = {Gowri, G and Sheng, K and Yin, P},
title = {Scalable design of orthogonal DNA barcode libraries.},
journal = {Nature computational science},
volume = {4},
number = {6},
pages = {423-428},
pmid = {38849559},
issn = {2662-8457},
support = {R01GM124401//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01HG012926//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; DP1GM133052//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; DP1 GM133052/GM/NIGMS NIH HHS/United States ; R01 GM124401/GM/NIGMS NIH HHS/United States ; R01 HG012926/HG/NHGRI NIH HHS/United States ; RF1MH128861//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; RF1 MH128861/MH/NIMH NIH HHS/United States ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Gene Library ; Algorithms ; DNA/genetics/chemistry ; },
abstract = {Orthogonal DNA barcode library design is an essential task in bioengineering. Here we present seqwalk, an efficient method for designing barcode libraries that satisfy a sequence symmetry minimization (SSM) heuristic for orthogonality, with theoretical guarantees of maximal or near-maximal library size under certain design constraints. Seqwalk encodes SSM constraints in a de Bruijn graph representation of sequence space, enabling the application of recent advances in discrete mathematics[1] to the problem of orthogonal sequence design. We demonstrate the scalability of seqwalk by designing a library of >10[6] SSM-satisfying barcode sequences in less than 20 s on a standard laptop.},
}
@article {pmid38844664,
year = {2024},
author = {Hugel, T},
title = {New dimensions for fluorescence-based barcoding in complex mixtures.},
journal = {Nature nanotechnology},
volume = {19},
number = {8},
pages = {1081-1082},
pmid = {38844664},
issn = {1748-3395},
support = {390951807//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
}
@article {pmid38844553,
year = {2024},
author = {Liao, H and Choi, J and Shendure, J},
title = {Molecular recording using DNA Typewriter.},
journal = {Nature protocols},
volume = {19},
number = {10},
pages = {2833-2862},
pmid = {38844553},
issn = {1750-2799},
mesh = {Humans ; *DNA/genetics ; *Gene Editing/methods ; HEK293 Cells ; RNA, Guide, CRISPR-Cas Systems/genetics ; CRISPR-Cas Systems ; },
abstract = {Recording molecular information to genomic DNA is a powerful means of investigating topics ranging from multicellular development to cancer evolution. With molecular recording based on genome editing, events such as cell divisions and signaling pathway activity drive specific alterations in a cell's DNA, marking the genome with information about a cell's history that can be read out after the fact. Although genome editing has been used for molecular recording, capturing the temporal relationships among recorded events in mammalian cells remains challenging. The DNA Typewriter system overcomes this limitation by leveraging prime editing to facilitate sequential insertions to an engineered genomic region. DNA Typewriter includes three distinct components: DNA Tape as the 'substrate' to which edits accrue in an ordered manner, the prime editor enzyme, and prime editing guide RNAs, which program insertional edits to DNA Tape. In this protocol, we describe general design considerations for DNA Typewriter, step-by-step instructions on how to perform recording experiments by using DNA Typewriter in HEK293T cells, and example scripts for analyzing DNA Typewriter data (https://doi.org/10.6084/m9.figshare.22728758). This protocol covers two main applications of DNA Typewriter: recording sequential transfection events with programmed barcode insertions by using prime editing and recording lineage information during the expansion of a single cell to many. Compared with other methods that are compatible with mammalian cells, DNA Typewriter enables the recording of temporal information with higher recording capacities and can be completed within 4-6 weeks with basic expertise in molecular cloning, mammalian cell culturing and DNA sequencing data analysis.},
}
@article {pmid38843225,
year = {2024},
author = {Zavadska, D and Henry, N and Auladell, A and Berney, C and Richter, DJ},
title = {Diverse patterns of correspondence between protist metabarcodes and protist metagenome-assembled genomes.},
journal = {PloS one},
volume = {19},
number = {6},
pages = {e0303697},
pmid = {38843225},
issn = {1932-6203},
mesh = {*Metagenome ; *DNA Barcoding, Taxonomic/methods ; Eukaryota/genetics/classification ; RNA, Ribosomal, 18S/genetics ; Metagenomics/methods ; },
abstract = {Two common approaches to study the composition of environmental protist communities are metabarcoding and metagenomics. Raw metabarcoding data are usually processed into Operational Taxonomic Units (OTUs) or amplicon sequence variants (ASVs) through clustering or denoising approaches, respectively. Analogous approaches are used to assemble metagenomic reads into metagenome-assembled genomes (MAGs). Understanding the correspondence between the data produced by these two approaches can help to integrate information between the datasets and to explain how metabarcoding OTUs and MAGs are related with the underlying biological entities they are hypothesised to represent. MAGs do not contain the commonly used barcoding loci, therefore sequence homology approaches cannot be used to match OTUs and MAGs. We made an attempt to match V9 metabarcoding OTUs from the 18S rRNA gene (V9 OTUs) and MAGs from the Tara Oceans expedition based on the correspondence of their relative abundances across the same set of samples. We evaluated several metrics for detecting correspondence between features in these two datasets and developed controls to filter artefacts of data structure and processing. After selecting the best-performing metrics, ranking the V9 OTU/MAG matches by their proportionality/correlation coefficients and applying a set of selection criteria, we identified candidate matches between V9 OTUs and MAGs. In some cases, V9 OTUs and MAGs could be matched with a one-to-one correspondence, implying that they likely represent the same underlying biological entity. More generally, matches we observed could be classified into 4 scenarios: one V9 OTU matches many MAGs; many V9 OTUs match many MAGs; many V9 OTUs match one MAG; one V9 OTU matches one MAG. Notably, we found some instances in which different OTU-MAG matches from the same taxonomic group were not classified in the same scenario, with all four scenarios possible even within the same taxonomic group, illustrating that factors beyond taxonomic lineage influence the relationship between OTUs and MAGs. Overall, each scenario produces a different interpretation of V9 OTUs, MAGs and how they compare in terms of the genomic and ecological diversity they represent.},
}
@article {pmid38841282,
year = {2024},
author = {Wei, M and Tian, Y and Zang, E and Tsambaa, B and Liu, J and Shi, L and Borjigidai, A},
title = {Species identification of biological ingredients in herbal product, Gurigumu-7, based on DNA barcoding and shotgun metagenomics.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1358136},
pmid = {38841282},
issn = {1664-462X},
abstract = {Accurate identification the species composition in mixtures poses a significant challenge, especially in processed mixtures comprising multiple species, such as those found in food and pharmaceuticals. Therefore, we have attempted to utilize shotgun metabarcoding technology to tackle this issue. In this study, the method was initially established using two mock samples of the Mongolian compound preparation Gurigumu-7 (G-7), which was then applied to three pharmaceutical products and 12 hospital-made preparations. A total of 119.72 Gb of raw data sets were obtained through shotgun metagenomic sequencing. By combining ITS2, matK, and rbcL, all the labeled bio-ingredients specified in the G-7 prescription can be detected, although some species may not be detectable in all samples. The prevalent substitution of Akebia quinata can be found in all the pharmaceutical and hospital samples, except for YN02 and YN12. The toxic alternative to Akebia quinata, Aristolochia manshuriensis, was exclusively identified in the YN02 sample. To further confirm this result, we validated it in YN02 using HPLC and real-time PCR with TaqMan probes. The results showed that aristolochic acid A (AAA) was detected in YN02 using HPLC, and the ITS2 sequence of Aristolochia manshuriensis has been validated in YN02 through qPCR and the use of a TaqMan probe. This study confirms that shotgun metabarcoding can effectively identify the biological components in Mongolian medicine compound preparation G-7. It also demonstrates the method's potential to be utilized as a general identification technique for mixtures containing a variety of plants.},
}
@article {pmid38841135,
year = {2024},
author = {Recuero, E and Caterino, MS},
title = {Molecular diversity of Diplura in southern High Appalachian leaf litter.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e125162},
pmid = {38841135},
issn = {1314-2828},
abstract = {The fauna of Diplura, the two-pronged bristletails (Hexapoda), of the southern Appalachians has received little focused systematic attention. Existing literature suggests the fauna to comprise around a dozen species. Based on a broader DNA barcode-based survey of high elevation litter arthropods in the region, we suggest the fauna to be much richer, with automated species delimitation methods hypothesising as many as 35 species, most highly restricted to single or closely proximate localities. Such a result should not be very surprising for such small, flightless arthropods, although it remains to be seen if other markers or morphology support such high diversity. The region still remains sparsely sampled for these more cryptic elements of the arthropod fauna and much larger numbers of species undoubtedly remain to be discovered.},
}
@article {pmid38838190,
year = {2024},
author = {Shirali, H and Hübner, J and Both, R and Raupach, M and Reischl, M and Schmidt, S and Pylatiuk, C},
title = {Image-based recognition of parasitoid wasps using advanced neural networks.},
journal = {Invertebrate systematics},
volume = {38},
number = {},
pages = {},
doi = {10.1071/IS24011},
pmid = {38838190},
issn = {1447-2600},
mesh = {Animals ; *Wasps/genetics/anatomy &amp; histology ; *Neural Networks, Computer ; DNA Barcoding, Taxonomic ; Image Processing, Computer-Assisted/methods ; Female ; Classification/methods ; Species Specificity ; Male ; },
abstract = {Hymenoptera has some of the highest diversity and number of individuals among insects. Many of these species potentially play key roles as food sources, pest controllers and pollinators. However, little is known about the diversity and biology and ~80% of the species have not yet been described. Classical taxonomy based on morphology is a rather slow process but DNA barcoding has already brought considerable progress in identification. Innovative methods such as image-based identification and automation can further speed up the process. We present a proof of concept for image data recognition of a parasitic wasp family, the Diapriidae (Hymenoptera), obtained as part of the GBOL III project. These tiny (1.2-4.5mm) wasps were photographed and identified using DNA barcoding to provide a solid ground truth for training a neural network. Taxonomic identification was used down to the genus level. Subsequently, three different neural network architectures were trained, evaluated and optimised. As a result, 11 different genera of diaprids and one mixed group of 'other Hymenoptera' can be classified with an average accuracy of 96%. Additionally, the sex of the specimen can be classified automatically with an accuracy of >97%.},
}
@article {pmid38837405,
year = {2024},
author = {Kutsokon, Y and Bielikova, O and Pekárik, L and Roman, A and Shcherbatiuk, M and Čiamporová-Zaťovičová, Z and Čiampor, F},
title = {The expansion of invasive species to the East: new sites of the bullheads (genus Ameiurus Rafinesque 1820) in Ukraine with morphological and genetic identification.},
journal = {Journal of fish biology},
volume = {105},
number = {3},
pages = {708-720},
doi = {10.1111/jfb.15778},
pmid = {38837405},
issn = {1095-8649},
support = {09I03-03-V01-00004//European Union NextGeneration EU/ ; 09I03-03-V01-00075//European Union NextGeneration EU/ ; },
mesh = {Ukraine ; Animals ; *Introduced Species ; *Electron Transport Complex IV/genetics ; Phylogeny ; DNA Barcoding, Taxonomic ; Cyprinidae/genetics/anatomy &amp; histology/classification ; Animal Distribution ; },
abstract = {This study confirms the extended distribution of two invasive species of the genus Ameiurus in Ukraine. Specifically, A. melas is recorded for the first time in the Southern Buh basin and A. nebulosus has expanded further eastward within the Dnipro basin. Material collected in 2019 and 2022 was identified by morphological features and confirmed by molecular genetic analysis. The most reliable morphological characters for distinguishing these two species include anal-fin membrane pigmentation (light or black), gill raker count (fewer or more than 16), and serrations on the pectoral-fin spine (well-developed along the full length or small, absent near the tip). The analysis of the cytochrome oxidase subunit I barcoding marker identified all samples from the Dnipro Basin (Tnia and Velykyi Luh localities) as A. nebulosus, while all specimens from the Vinnytsia region within the Southern Buh basin (Sotskoho and Vyshenske lakes) were attributed to A. melas. The maximum-likelihood analysis revealed clearly separated clades with high bootstrap support (>75%), strongly supporting the presence of the two separate species. This study suggests the potential for further eastward expansion of both species within Ukraine: A. nebulosus in the northern direction and A. melas in the southern direction.},
}
@article {pmid40028488,
year = {2023},
author = {Dhar, R and Devi, A},
title = {Exosomes Barcoding: A smart approach for cancer liquid biopsy.},
journal = {The journal of liquid biopsy},
volume = {2},
number = {},
pages = {100129},
pmid = {40028488},
issn = {2950-1954},
abstract = {Cancer is an unsolved health crisis worldwide. Extracellular vesicles (EVs) address this problem in a new way. In cancer, early detection is highly challenging, exosomes (a subpopulation of EVs, originating from endosomes) overcomes this limitation. In cancer, tumor-derived exosomes (TEXs) play a role as signaling molecules in cancer development and progression. TEXs provide detailed investigation for specific cancer biomarkers research. Exosomes heterogeneity (variation in exosomes size, exosomes origin, and inner molecular diversity) has led to complications in understanding and studying cancer liquid biopsies. Single exosome profiling and exosomes barcoding has helped in supporting and overcoming this limitation and has played a significant role in precision oncology. Exosomes barcoding is a promising interdisciplinary approach for screening cancers more specifically.},
}
@article {pmid39711846,
year = {2023},
author = {Adams, SJ and Walker, AK},
title = {Diversity of fungi from marine inundated wood from the Bay of Fundy, Nova Scotia, Canada.},
journal = {Botanica marina},
volume = {66},
number = {4},
pages = {319-329},
pmid = {39711846},
issn = {0006-8055},
abstract = {Marine fungi play an integral role in the decomposition of intertidal organic substrata but remain understudied in cold-water habitats including Atlantic Canada. Marine inundated wood from the intertidal zone was sampled from 30 sites along the Bay of Fundy coastline in Nova Scotia, Canada. Wood types studied included attached and loose intertidal wood, and driftwood. Emergent fungi were cultured and identified using ITS (internal transcribed spacers) rDNA barcoding. Two hundred and twenty cultures representing 86 fungi are reported. Sixty-one fungi were new records for the Bay of Fundy, 41 are first records from the marine environment, and 19 fungi are potentially new to science. Fungi identified included eight obligate marine fungi, with the remaining fungi being facultatively marine. Eight ascomycetes were soft rot fungi; this ecological strategy for decaying woody material in cold-water marine environments is discussed. Historical records and roles of wood type and site on fungal colonization are discussed.},
}
@article {pmid39635013,
year = {2022},
author = {Liu, Y and Li, X and Chen, Y and Geng, G and Li, J and Wang, Y and Huang, L},
title = {Imaging-based optical barcoding for relative humidity sensing based on meta-tip.},
journal = {Nanophotonics (Berlin, Germany)},
volume = {11},
number = {1},
pages = {111-118},
pmid = {39635013},
issn = {2192-8614},
abstract = {In a wide range of applications such as healthcare treatment, environmental monitoring, food processing and storage, and semiconductor chip manufacturing, relative humidity (RH) sensing is required. However, traditional fiber-optic humidity sensors face the challenges of miniaturization and indirectly obtaining humidity values. Here, we propose and demonstrate an optical barcode technique by cooperating with RH meta-tip, which can predict the humidity values directly. Such RH meta-tip is composed of fiber-optic sensor based on surface plasmon resonance (SPR) effect and graphene oxide film as humidity sensitizer. While SPR sensor is composed of multimode fiber (MMF) integrated with metallic metasurface. Dynamic time warping (DTW) algorithm is used to obtain the warp path distance (WPD) sequence between the measured reflection spectrum and the spectra of the precalibrated database. The distance sequence is transformed into a pseudo-color barcode, and the humidity value is corresponded to the lowest distance, which can be read by human eyes. The RH measurement depends on the collective changes of the reflection spectrum rather than tracking a single specific resonance peak/dip. This work can open up new doors to the development of a humidity sensor with direct RH recognition by human eyes.},
}
@article {pmid39440195,
year = {2022},
author = {Shepherd, LD and Ann Smith, C and Lowe, BJ and Campbell, D and Ngarimu, R},
title = {The identification of plants used to make tapa artefacts: development of a reference DNA database and trial of non-destructive DNA extraction methods.},
journal = {Journal of the Royal Society of New Zealand},
volume = {52},
number = {5},
pages = {491-507},
pmid = {39440195},
issn = {1175-8899},
abstract = {Tapa (barkcloth) is a non-woven textile made from the inner bark of some plant species. Tapa manufacture was once widespread throughout the Pacific and tapa from the eighteenth and nineteenth century form part of Pacific collections in many museums. Here we examined the feasibility of DNA identification of the plants used to make tapa artefacts by developing and testing a DNA reference database of chloroplast trnL intron P6 loop sequences from many of the plant species used to make tapa, as well as other New Zealand textile plants. This database enabled identification to genus for most species but many species shared identical sequences. Despite the lack of species-level resolution, this technique will still aid with identifying the origins of tapa artefacts made from plants with restricted distributions, such as endemic New Zealand and Hawaiian Islands plants. A second aim was to test a number of DNA extraction methods, including non-destructive methods of interest to the heritage sector, on tapa samples. Only one of the non-destructive sampling methods produced amplifiable DNA. However, we did find variation in the success of the destructive methods tested, with the Qiagen DNeasy Plant Mini Kit having the highest success rate.},
}
@article {pmid38834513,
year = {2024},
author = {Latif, H and Pazra, DF and Basri, C and Wibawan, IWT and Rahayu, P},
title = {Whole genome sequencing analysis on antibiotic-resistant Escherichia coli isolated from pig farms in Banten Province, Indonesia.},
journal = {Journal of veterinary science},
volume = {25},
number = {3},
pages = {e44},
pmid = {38834513},
issn = {1976-555X},
support = {102/E5/PG.02.00.PL/2023/MECRT/Kementerian Pendidikan, Kebudayaan, Riset, dan Teknologi/Indonesia ; },
mesh = {Animals ; *Escherichia coli/genetics/drug effects/isolation &amp; purification ; Swine ; Indonesia/epidemiology ; *Swine Diseases/microbiology/epidemiology ; *Escherichia coli Infections/veterinary/microbiology/epidemiology ; *Whole Genome Sequencing/veterinary ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {IMPORTANCE: The emergence and rapid increase in the incidence of multidrug-resistant (MDR) bacteria in pig farms has become a serious concern and reduced the choice of effective antibiotics.<br><br>OBJECTIVE: This study analyzed the phylogenetics and diversity of antibiotic resistance genes (ARGs) and molecularly identified the source of ARGs in antibiotic-resistant Escherichia coli isolated from pig farms in Banten Province, Indonesia.<br><br>METHODS: Forty-four antibiotic-resistant E. coli isolates from fecal samples from 44 pig farms in Banten Province, Indonesia, were used as samples. The samples were categorized into 14 clusters. Sequencing was performed using the Oxford Nanopore Technologies MinION platform, with barcoding before sequencing with Nanopore Rapid sequencing gDNA-barcoding (SQK-RBK110.96) according to manufacturing procedures. ARG detection was conducted using ResFinder, and the plasmid replicon was determined using PlasmidFinder.<br><br>RESULTS: Three phylogenetic leaves of E. coli were identified in the pig farming cluster in Banten Province. The E. coli isolates exhibited potential resistance to nine classes of antibiotics. Fifty-one ARGs were identified across all isolates, with each cluster carrying a minimum of 10 ARGs. The ant(3'')-Ia and qnrS1 genes were present in all isolates. ARGs in the E. coli pig farming cluster originated mainly from plasmids, accounting for an average of 89.4%.<br><br>CONCLUSIONS AND RELEVANCE: The elevated potential for MDR events, coupled with the dominance of ARGs originating from plasmids, increases the risk of ARG spread among bacterial populations in animals, humans, and the environment.},
}
@article {pmid38832046,
year = {2024},
author = {Samreen, KB and Manzoor, F},
title = {Assessing arthropod biodiversity with DNA barcoding in Jinnah Garden, Lahore, Pakistan.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17420},
pmid = {38832046},
issn = {2167-8359},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Pakistan ; *Biodiversity ; *Arthropods/genetics/classification ; Gardens ; },
abstract = {Previous difficulties in arthropod taxonomy (such as limitations in conventional morphological approaches, the possibility of cryptic species and a shortage of knowledgeable taxonomists) has been overcome by the powerful tool of DNA barcoding. This study presents a thorough analysis of DNA barcoding in regards to Pakistani arthropods, which were collected from Lahore's Jinnah Garden. The 88 % (9,451) of the 10,792 specimens that were examined were able to generate DNA barcodes and 83% (8,974) of specimens were assigned 1,361 barcode index numbers (BINs). However, the success rate differed significantly between the orders of arthropods, from 77% for Thysanoptera to an astounding 93% for Diptera. Through morphological exams, DNA barcoding, and cross-referencing with the Barcode of Life Data system (BOLD), the Barcode Index Numbers (BINs) were assigned with a high degree of accuracy, both at the order (100%) and family (98%) levels. Though, identifications at the genus (37%) and species (15%) levels showed room for improvement. This underscores the ongoing need for enhancing and expanding the DNA barcode reference library. This study identified 324 genera and 191 species, underscoring the advantages of DNA barcoding over traditional morphological identification methods. Among the 17 arthropod orders identified, Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera from the class Insecta dominated, collectively constituting 94% of BINs. Expected malaise trap Arthropod fauna in Jinnah Garden could contain approximately 2,785 BINs according to Preston log-normal species distribution, yet the Chao-1 Index predicts 2,389.74 BINs. The Simpson Index of Diversity (1-D) is 0.989, signaling high species diversity, while the Shannon Index is 5.77, indicating significant species richness and evenness. These results demonstrated that in Pakistani arthropods, DNA barcoding and BOLD are an invaluable tool for improving taxonomic understanding and biodiversity assessment, opening the door for further eDNA and metabarcoding research.},
}
@article {pmid38827149,
year = {2024},
author = {Atavliyeva, S and Auganova, D and Tarlykov, P},
title = {Genetic diversity, evolution and drug resistance of Mycobacterium tuberculosis lineage 2.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1384791},
pmid = {38827149},
issn = {1664-302X},
abstract = {Mycobacterium tuberculosis causes a chronic infectious disease called tuberculosis. Phylogenetic lineage 2 (L2) of M. tuberculosis, also known as the East Asian lineage, is associated with high virulence, increased transmissibility, and the spread of multidrug-resistant strains. This review article examines the genomic characteristics of the M. tuberculosis genome and M. tuberculosis lineage 2, such as the unique insertion sequence and spoligotype patterns, as well as MIRU-VNTR typing, and SNP-based barcoding. The review describes the geographical distribution of lineage 2 and its history of origin. In addition, the article discusses recent studies on drug resistance and compensatory mechanisms of M. tuberculosis lineage 2 and its impact on the pathogen's transmissibility and virulence. This review article discusses the importance of establishing a unified classification for lineage 2 to ensure consistency in terminology and criteria across different studies and settings.},
}
@article {pmid38826425,
year = {2024},
author = {Ali, M and Dey, R and Das, M and Kumar, V and Chandra, K and Uniyal, VP and Gupta, SK},
title = {Unique among high passes: Phylogenetic inferences from DNA barcoding of the butterfly fauna of Ladakh Trans-Himalaya, India.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {38826425},
issn = {2693-5015},
abstract = {The butterfly assemblage of Ladakh Trans-Himalaya demands a thorough analysis of their population genetic structure owing to their typical biogeographic affinity and their adaptability to extreme cold-desert climates. No such effort has been taken till date, and in this backdrop, we created a barcode reference library of 60 specimens representing 23 species. Barcodes were generated from freshly collected leg samples using the Sanger sequencing method, followed by phylogenetic clade analyses and divergence calculation. Our data represents 22% of Ladakh's Rhopaloceran fauna with the novel barcode submission for six species, including one Schedule II species, Paralasa mani. Contrary to the 3% threshold rule, the interspecific divergence between two species pairs of typical mountain genus Hyponephele and Karanasa was found to be 2.3% and 2.2%, respectively. The addition of conspecific global barcodes revealed that most species showed little increase in divergence value, while a two-fold increase was noted in a few species. Bayesian clade clustering outcomes largely aligned with current morphological classifications, forming monophyletic clades of conspecific barcodes, with only minor exceptions observed for the taxonomically complicated genus Polyommatus and misidentified records of Aulocera in the database. We also observed variations within the same phylogenetic clades forming nested lineages, which may be attributed to the taxonomic intricacies present at the subspecies level globally, mostly among Eurasian species. Overall, our effort not only substantiated the effectiveness of DNA Barcoding for the identification and conservation of this climatically vulnerable assemblage but also highlighted the significance of deciphering the unique genetic composition among this geographically isolated population of Ladakh butterflies.},
}
@article {pmid38826396,
year = {2024},
author = {Papadimitriou, M and Ahn, S and Diamond, B and Lee, H and McIntyre, J and Truger, M and Durante, M and Ziccheddu, B and Landgren, O and Rasche, L and Bahlis, NJ and Neri, P and Maura, F},
title = {Timing antigenic escape in multiple myeloma treated with T-cell redirecting immunotherapies.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38826396},
issn = {2692-8205},
support = {P30 CA240139/CA/NCI NIH HHS/United States ; },
abstract = {Recent data highlight genomic events driving antigen escape as a recurring cause of chimeric antigen receptor T-cell (CAR-T) and bispecific T-cell engager (TCE) resistance in multiple myeloma (MM). Yet, it remains unclear if these events, leading to clonal dominance at progression, result from acquisition under treatment selection or selection of pre-existing undetectable clones. This differentiation gains importance as these immunotherapies progress to earlier lines of treatment, prompting the need for innovative diagnostic testing to detect these events early on. By reconstructing phylogenetic trees and exploring chemotherapy mutational signatures as temporal barcodes in 11 relapsed refractory MM patients with available whole genome sequencing data before and after CART/TCE treatment, we demonstrated that somatic antigen escape mechanisms for BCMA- and GPRC5D-targeting therapies are acquired post-diagnosis, likely during CART/TCE treatment. Longitudinal tracking of these mutations using digital PCR in 4 patients consistently showed that genomic events promoting antigen escape were not detectable during the initial months of therapy but began to emerge nearly 1 year post therapy initiation. This finding reduces the necessity for a diagnostic panel to identify these events before CART/TCE. Instead, it underscores the importance of surveillance and identifying patients at higher risk of acquiring these events.},
}
@article {pmid38826163,
year = {2024},
author = {Onyango, B and Copeland, R and Mbogholi, J and Wamalwa, M and Kibet, C and Tonnang, HEZ and Senagi, K},
title = {WiPFIM: A digital platform for interlinking biocollections of wild plants, fruits, associated insects, and their molecular barcodes.},
journal = {Ecology and evolution},
volume = {14},
number = {6},
pages = {e11457},
pmid = {38826163},
issn = {2045-7758},
abstract = {The current knowledge on insects feeding on fruits is limited, and some of the scarce existing data on the fruit-associated insects are secluded within the host institutions. Consequently, their value is not fully realized. Moreover, in countries like Kenya, the integration of biocollections data within a digital framework has not been fully exploited. To address these gaps, this article presents a description of the development of a web-based platform for data sharing and integrating biodiversity historical data of wild plants, fruits, associated insects, and their molecular barcodes (WiPFIM) while leveraging data science technologies. The barcodes corresponding to the biocollections data were retrieved from BOLD database. The platform is an online resource about fruit-insect interactions that can be of interest to a worldwide community of users and can be useful in building innovative tools. The platform is accessible online at https://test-dmmg.icipe.org/wpfhi.},
}
@article {pmid38821971,
year = {2024},
author = {Zhang, Z and Xiao, J and Wang, H and Yang, C and Huang, Y and Yue, Z and Chen, Y and Han, L and Yin, K and Lyu, A and Fang, X and Zhang, L},
title = {Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4631},
pmid = {38821971},
issn = {2041-1723},
mesh = {Humans ; *Metagenome/genetics ; *Algorithms ; *Genome, Microbial ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Deep Learning ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; Genome, Bacterial ; },
abstract = {Although long-read sequencing enables the generation of complete genomes for unculturable microbes, its high cost limits the widespread adoption of long-read sequencing in large-scale metagenomic studies. An alternative method is to assemble short-reads with long-range connectivity, which can be a cost-effective way to generate high-quality microbial genomes. Here, we develop Pangaea, a bioinformatic approach designed to enhance metagenome assembly using short-reads with long-range connectivity. Pangaea leverages connectivity derived from physical barcodes of linked-reads or virtual barcodes by aligning short-reads to long-reads. Pangaea utilizes a deep learning-based read binning algorithm to assemble co-barcoded reads exhibiting similar sequence contexts and abundances, thereby improving the assembly of high- and medium-abundance microbial genomes. Pangaea also leverages a multi-thresholding algorithm strategy to refine assembly for low-abundance microbes. We benchmark Pangaea on linked-reads and a combination of short- and long-reads from simulation data, mock communities and human gut metagenomes. Pangaea achieves significantly higher contig continuity as well as more near-complete metagenome-assembled genomes (NCMAGs) than the existing assemblers. Pangaea also generates three complete and circular NCMAGs on the human gut microbiomes.},
}
@article {pmid38820740,
year = {2024},
author = {An, HE and Mun, MH and Malik, A and Kim, CB},
title = {Development of a two-layer machine learning model for the forensic application of legal and illegal poppy classification based on sequence data.},
journal = {Forensic science international. Genetics},
volume = {71},
number = {},
pages = {103061},
doi = {10.1016/j.fsigen.2024.103061},
pmid = {38820740},
issn = {1878-0326},
mesh = {*Machine Learning ; *Papaver/genetics ; *DNA, Plant/genetics ; Genetic Markers ; *DNA Barcoding, Taxonomic ; Sequence Analysis, DNA ; Forensic Genetics/methods ; },
abstract = {Poppies are beneficial plants with a variety of applications, including medicinal, edible, ornamental, and industrial purposes. Some Papaver species are forensically significant plants because they contain opium, a narcotic substance. Internationally trafficked species of illegal poppies are being identified by DNA barcoding employing multiple markers in response to their forensic value. However, effective markers for precise species identification of legal and illegal poppies are still under discussion, with research on illegal poppies focusing on Papaver somniferum L., and species identification studies of Papaver bracteatum and Papaver setigerum DC. still lacking. As a result, in order to evaluate the performance of genetic markers and classify their DNA sequences in the genus Papaver, this study developed the first machine learning-based two-layer model, in which the first layer classifies legal and illegal poppies from the given sequence and the second layer identifies species of illegal poppies using their sequences. We constructed the dataset and investigated biological features from four markers, internal transcribed spacer 1 (ITS1), internal transcribed spacer 2 (ITS2), transfer RNA Leucine (trnL), transfer RNA Leucine - transfer RNA Phenylalanine intergenic spacer (trnL-trnF intergenic spacer) and their combination, using four machine learning algorithms, K-nearest neighbor (KNN), Naïve Bayes (NB), extreme gradient boost (XGBoost) and Random Forest (RF). According to our findings, for Layer 1 to classify legal and illegal poppies, KNN-based models using combined ITS region achieved the greatest performance of accuracy 0.846 and 0.889 using training and test sets, respectively. Additionally, for Layer 2 to identify illegal poppy species, KNN-based models using combined ITS region achieved the best performance of 0.833 and 1.000 for using training and test sets, respectively. To validate the model, the combined ITS region, which includes ITS 1 and 2 sequences, from blind poppy samples were used as a case study, with the Layer 1 correctly classifying legal and illegal poppies with over 0.830 accuracy. Layer 2 correctly identified P. setigerum DC., however, only one of the three P. somniferum L. species was accurately identified. Nevertheless, our research shows that machine learning can be used to classify and identify legal and illegal poppy species using DNA barcodes which can then be used as an efficient and effective forensic tool for improved law enforcement and a safer society.},
}
@article {pmid38820192,
year = {2024},
author = {Smiley, AT and Babilonia-Díaz, NS and Hughes, AJ and Lemmex, ACD and Anderson, MJM and Tompkins, KJ and Gordon, WR},
title = {HUHgle: An Interactive Substrate Design Tool for Covalent Protein-ssDNA Labeling Using HUH-Tags.},
journal = {ACS synthetic biology},
volume = {13},
number = {6},
pages = {1669-1678},
doi = {10.1021/acssynbio.4c00188},
pmid = {38820192},
issn = {2161-5063},
support = {R35 GM119483/GM/NIGMS NIH HHS/United States ; },
mesh = {*Software ; *DNA, Single-Stranded/metabolism/chemistry/genetics ; Proteins/metabolism/chemistry/genetics ; },
abstract = {HUH-tags have emerged as versatile fusion partners that mediate sequence specific protein-ssDNA bioconjugation through a simple and efficient reaction. Here we present HUHgle, a python-based interactive tool for the visualization, design, and optimization of substrates for HUH-tag mediated covalent labeling of proteins of interest with ssDNA substrates of interest. HUHgle streamlines design processes by integrating an intuitive plotting interface with a search function capable of predicting and displaying protein-ssDNA bioconjugate formation efficiency and specificity in proposed HUH-tag/ssDNA sequence combinations. Validation demonstrates that HUHgle accurately predicts product formation of HUH-tag mediated bioconjugation for single- and orthogonal-labeling reactions. In order to maximize the accessibility and utility of HUHgle, we have implemented it as a user-friendly Google Colab notebook which facilitates broad use of this tool, regardless of coding expertise.},
}
@article {pmid38818076,
year = {2024},
author = {Shi, W and Zhang, J and Huang, S and Fan, Q and Cao, J and Zeng, J and Wu, L and Yang, C},
title = {Next-Generation Sequencing-Based Spatial Transcriptomics: A Perspective from Barcoding Chemistry.},
journal = {JACS Au},
volume = {4},
number = {5},
pages = {1723-1743},
pmid = {38818076},
issn = {2691-3704},
abstract = {Gene expression profiling of tissue cells with spatial context is in high demand to reveal cell types, locations, and intercellular or molecular interactions for physiological and pathological studies. With rapid advances in barcoding chemistry and sequencing chemistry, spatially resolved transcriptome (SRT) techniques have emerged to quantify spatial gene expression in tissue samples by correlating transcripts with their spatial locations using diverse strategies. These techniques provide both physical tissue structure and molecular characteristics and are poised to revolutionize many fields, such as developmental biology, neuroscience, oncology, and histopathology. In this context, this Perspective focuses on next-generation sequencing-based SRT methods, particularly highlighting spatial barcoding chemistry. It delves into optically manipulated spatial indexing methods and DNA array-barcoded spatial indexing methods by exploring current advances, challenges, and future development directions in this nascent field.},
}
@article {pmid38817114,
year = {2024},
author = {Borbee, EM and Puspa, IA and Gelis, ERE and Setiawan, F and Maduppa, H and Humphries, AT and Lane, CE},
title = {Surface currents shape protist community structure across the Indo-Pacific.},
journal = {Journal of phycology},
volume = {60},
number = {4},
pages = {816-833},
doi = {10.1111/jpy.13465},
pmid = {38817114},
issn = {1529-8817},
support = {1541510//Division of Environmental Biology/ ; AID-497-A-16-00004//United States Agency for International Development/ ; },
mesh = {Indonesia ; Pacific Ocean ; *Biodiversity ; Eukaryota/genetics/classification/physiology ; },
abstract = {Biogeographic structure in marine protist communities is shaped by a combination of dispersal potential and environmental selection. High-throughput sequencing and global sampling efforts have helped better resolve the composition and functions of these communities in the world's oceans using both molecular and visual methods. However, molecular barcoding data are critically lacking across the Indo-Pacific, a region widely considered the epicenter of marine biodiversity. To fill this gap, we characterized protist communities in four sampling regions across Indonesia that represent the latitudinal, longitudinal, and human population gradients of the region: Lombok, Wakatobi, Misool, and Waigeo. We show high spatial structuring in marine protist communities across Indonesia, and biotic factors appear to play little role in driving this observed structure. Our results appear to be driven by abiotic factors linked to surface current patterns across the Indo-Pacific as a result of: (1) a choke point in circulation at the Indonesian Throughflow leading to low diatom diversity in Lombok, Wakatobi, and Misool; (2) an increase in nutrient availability at the edge of the Halmahera Eddy in Waigeo, leading to an increase in diatom diversity; and/or (3) seasonal variations in protist communities in line with shifts in velocity of the Indonesian Throughflow. Overall, our results highlight the importance of abiotic factors in shaping protist communities on broad geographic scales over biotic, top-down pressures, such as grazing from higher trophic levels.},
}
@article {pmid38816489,
year = {2024},
author = {Nagakubo, Y and Hirotsu, Y and Yoshino, M and Amemiya, K and Saito, R and Kakizaki, Y and Tsutsui, T and Miyashita, Y and Goto, T and Omata, M},
title = {Comparison of diagnostic performance between Oncomine Dx target test and AmoyDx panel for detecting actionable mutations in lung cancer.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {12480},
pmid = {38816489},
issn = {2045-2322},
support = {JP18K16292//Japan Society for the Promotion of Science/ ; 21K08894//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; *Lung Neoplasms/genetics/diagnosis ; *Mutation ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Male ; ErbB Receptors/genetics ; Middle Aged ; Proto-Oncogene Proteins c-ret/genetics ; Biomarkers, Tumor/genetics ; Aged ; Proto-Oncogene Proteins c-met/genetics ; Protein-Tyrosine Kinases/genetics ; Proto-Oncogene Proteins/genetics ; Multiplex Polymerase Chain Reaction/methods ; },
abstract = {Companion diagnostic (CDx) tests play important roles in identifying oncogenic driver genes and tailoring effective molecularly targeted therapies for lung cancer patients. In Japan, the Oncomine Dx target test (ODxTT) and the AmoyDx pan lung cancer PCR panel (AmoyDx) are prominent CDx tests and only one of these tests is covered by the domestic insurance system. However, these CDx tests cover different target regions and apply different technologies (ODxTT is amplicon-based next-generation sequencing and AmoyDx is multiplex PCR-based assay), which may lead to missing of actionable mutations affecting patient prognosis. Here, we performed a direct comparison analysis of 1059 genetic alterations of eight driver genes from 131 samples and evaluated the concordance between two CDx tests for detecting actionable variants and fusions. When excluding the eight uncovered variants (ODxTT: two variants, AmoyDx: six variants), the overall percent agreement was 97.6% (1026/1051) with 89.0% of overall positive percent agreement (89/100) and 98.5% of overall negative percent agreement (937/951). Of the 25 discordant genetic alterations, two were undetected despite being covered in the AmoyDx (one EGFR variant and one ROS1 fusion). Furthermore, there were potential false positives in the ODxTT (nine MET exon 14 skippings) and in the AmoyDx (five variants, six ROS1 and three RET fusions). These potential false positives in the AmoyDx likely due to non-specific amplification, which was validated by the unique molecular barcoding sequencing. The ODxTT missed two uncovered EGFR rare variants, which was visually confirmed in the raw sequencing data. Our study provides insights into real-world performance of CDx tests for lung cancer and ensures reliability to advance precision medicine.},
}
@article {pmid38814962,
year = {2024},
author = {Niu, M and Liu, Y and Xue, L and Cai, B and Zhao, Q and Wei, J},
title = {Improving DNA barcoding library of armored scale insects (Hemiptera: Diaspididae) in China.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0301499},
pmid = {38814962},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; China ; *Hemiptera/genetics/classification ; *Phylogeny ; Electron Transport Complex IV/genetics ; Genetic Variation ; Gene Library ; Bayes Theorem ; },
abstract = {DNA barcoding is used to identify cryptic species, survey environmental samples, and estimate phyletic and genetic diversity. Armored scale insects are phytophagous insects and are the most species-rich taxa in the Coccoidea superfamily. This study developed a DNA barcode library for armored scale insect species collected from southern China during 2021-2022. We sequenced a total of 239 specimens, recognized as 50 morphological species, representing two subfamilies and 21 genera. Sequencing analysis revealed that the average G + C content of the cytochrome oxidase subunit I (COI) gene sequence was very low (~18.06%) and that the average interspecific divergence was 10.07% while intraspecific divergence was 3.20%. The intraspecific divergence value was inflated by the high intraspecific divergence in ten taxa, which may indicate novel species overlooked by current taxonomic treatments. All the Automated Barcode Gap Discovery, Assemble Species by Automatic Partitioning, Taxon DNA analysis and Bayesian Poisson Tree Process methods yielded largely consistent results, indicating a robust and credible species delimitation. Based on these results, an intergeneric distance threshold of ≤ 5% was deemed appropriate for the differentiation of armored scale insect species in China. This study establishes a comprehensive barcode library for the identification of armored scale insects, future research, and application.},
}
@article {pmid38813184,
year = {2024},
author = {Wachananawat, B and Kong, BL and Shaw, PC and Bongcheewin, B and Sangvirotjanapat, S and Prombutara, P and Pornputtapong, N and Sukrong, S},
title = {Characterization and phylogenetic analysis of the complete chloroplast genome of Curcuma comosa and C. latifolia.},
journal = {Heliyon},
volume = {10},
number = {10},
pages = {e31248},
pmid = {38813184},
issn = {2405-8440},
abstract = {Members of the Curcuma genus, a crop in the Zingiberaceae, are widely utilized rhizomatous herbs globally. There are two distinct species, C. comosa Roxb. and C. latifolia Roscoe, referred to the same vernacular name "Wan Chak Motluk" in Thai. C. comosa holds economic importance and is extensively used as a Thai traditional medicine due to its phytoestrogenic properties. However, its morphology closely resembles that of C. latifolia, which contains zederone, a compound known for its hepatotoxic effects. They are often confused, which may affect the quality, efficacy and safety of the derived herbal materials. Thus, DNA markers were developed for discriminating C. comosa from C. latifolia. This study focused on analyzing core DNA barcode regions, including rbcL, matK, psbA-trnH spacer and ITS2, of the authentic C. comosa and C. latifolia species. As a result, no variable nucleotides in core DNA barcode regions were observed. The complete chloroplast (cp) genome was introduced to differentiate between the two species. The comparison revealed that the cp genomes of C. comosa and C. latifolia were 162,272 and 162,289 bp, respectively, with a total of 133 identified genes. The phylogenetic analysis revealed that C. comosa and C. latifolia exhibited a very close relationship with other Curcuma species. The cp genome of C. comosa and C. latifolia were identified for the first time, providing valuable insights for species identification and evolutionary research within the Zingiberaceae family.},
}
@article {pmid38811654,
year = {2024},
author = {Sundebo Meldgaard, T and Viborg, N and Suarez Hernandez, S and Vazquez Albacete, D and Tamhane, T and Reker Hadrup, S},
title = {Validation of novel conditional ligands and large-scale detection of antigen-specific T cells for H-2D[d] and H-2K[d].},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {12292},
pmid = {38811654},
issn = {2045-2322},
mesh = {Animals ; Ligands ; Mice ; *CD8-Positive T-Lymphocytes/immunology/metabolism ; *Peptides/immunology/chemistry ; Mice, Inbred C57BL ; H-2 Antigens/immunology/metabolism/genetics ; Mice, Inbred BALB C ; },
abstract = {The UV-mediated peptide exchange has enabled the generation of multiple different MHC multimer specificities in parallel, surpassing tedious individual refolding of MHC molecules with peptide ligands. Murine models are acknowledged as an effective tool for preclinical research to advance our understanding of immunological mechanisms, with the potential translatability of key learnings from mouse models to the clinic. The common inbred mouse strain BALB/c is frequently used in immunological research. However, for the BALB/c histocompatibility (H)-2 alleles availability of conditional ligand has been limited. To overcome this challenge, we design and experimentally validate conditional ligands restricted to murine MHC class I alleles H2D[d] and H2K[d]. In addition, we demonstrate the ability of the three H2[d] molecules and two additional C57BL/6 H2[b] molecules folded in-house with conditional ligands to generate fluorescently labeled peptide-H2 tetramers that allow staining of antigen-specific CD8+ T cells in splenocyte samples. Finally, we generate large peptide-H-2 multimer libraries with a DNA-barcode labeling system for high-throughput interrogation of CD8+ T cell specificity in murine splenocyte samples. Consequently, the described techniques will contribute to our understanding of the antigen-specific CD8+ T cell repertoire in murine preclinical models of various diseases.},
}
@article {pmid38811354,
year = {2024},
author = {Kar, C and Raghavan, R and Ummath, A and Puthiyaalikom, N and Idreesbabu, KK and Sureshkumar, S},
title = {Resolving fusilier puzzles: The identity of Squamosicaesio marri and Pterocaesio flavifasciata, and a new record of Flavicaesio suevica from the Western Indian Ocean.},
journal = {Journal of fish biology},
volume = {105},
number = {3},
pages = {993-997},
doi = {10.1111/jfb.15808},
pmid = {38811354},
issn = {1095-8649},
support = {200510341520//University Grants Commission/ ; CRG/2020/004498//Department of Science and Technology/ ; },
mesh = {Indian Ocean ; Animals ; *Phylogeny ; Electron Transport Complex IV/genetics ; DNA, Mitochondrial/genetics ; },
abstract = {A phylogenetic analysis incorporating mitochondrial cox1 gene sequences of members of the family Caesionidae revealed the conspecificity of Pterocaesio flavifasciata and Squamosicaesio marri, which was also supported by the absence of any clear morphological diagnostic characters and meristic counts to separate the two species. Additionally, we provide the first record of the Suez fusilier, Flavicaesio suevica, from outside the Red Sea, based on specimens collected from the Laccadive archipelago, Western Indian Ocean. Together, these results show that the taxonomy, diversity, and distribution of members of the family Caesionidae continue to be poorly known, necessitating a comprehensive range-wide study.},
}
@article {pmid38809447,
year = {2024},
author = {Laojun, S and Chaiphongpachara, T},
title = {Island mosquitoes of Thailand: an update on species diversity and DNA barcoding.},
journal = {Parasitology research},
volume = {123},
number = {5},
pages = {224},
pmid = {38809447},
issn = {1432-1955},
mesh = {Animals ; Thailand ; *DNA Barcoding, Taxonomic ; *Culicidae/classification/genetics ; Islands ; Biodiversity ; Mosquito Vectors/genetics/classification ; Genetic Variation ; Phylogeny ; Electron Transport Complex IV/genetics ; },
abstract = {Mosquitoes (Diptera: Culicidae) are among the most medically significant insects, with several species acting as vectors for human pathogens. Although there are frequent reports of mosquito-borne diseases in the border island areas of Thailand, comprehensive data on the diversity and DNA barcoding of these mosquito species remain limited. This study investigated mosquito diversity in two main archipelagos in Thailand-the Trat archipelago (comprising Chang Island and Kood Island) and the Ranong archipelago (comprising Chang Island and Phayam Island)-and generated DNA barcode data from the mosquitoes found there. The survey across these islands discovered a total of 41 species, highlighting the presence of several species known to be vectors for human diseases. Thirty-seven mosquito species from the island areas were documented to provide reference DNA barcode sequences for mosquitoes in Thailand's island regions. Two species, Aedes fumidus and Finlaya flavipennis, have been added as new COI sequence records in the database. DNA barcoding was highly effective in classifying almost all species by identifying barcoding gaps, except for Anopheles baimaii and Anopheles dirus, which could not be distinguished. Additionally, the study noted that geographical variations might influence certain mosquito species, such as Anopheles barbirostris A3 and Mansonia dives, causing them to be split into two distinct subgroups. The findings of this study are crucial, as they aid in classifying mosquito species using molecular techniques and expand our knowledge of disease vectors in these biodiverse regions.},
}
@article {pmid38808126,
year = {2024},
author = {Vogel, J and Peters, RS and Selfa, J and Ferrer-Suay, M},
title = {Characterising the north-western European species of Phaenoglyphis Förster, 1869 (Hymenoptera: Figitidae: Charipinae) with novel insights from DNA barcode data.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e120950},
pmid = {38808126},
issn = {1314-2828},
abstract = {BACKGROUND: The taxonomy of the hymenopteran parasitoid subfamily Charipinae (Hymenoptera: Cynipoidea: Figitidae) has, until recently, been in a state of chaos. While this situation has improved significantly in recent years, most of the efforts were focused on morphological data of typically old specimens. Here, we present the first integrative approach to describe the diversity of the genus Phaenoglyphis Förster, 1869 from north-western Europe.<br><br>NEW INFORMATION: For seven (of a total of 17) species, we provide DNA barcode data. Phaenoglyphisbelizini Pujade-Villar, 2018 and Phaenoglyphisevenhuisi Pujade-Villar &amp; Paretas-Mart&#xed;nez, 2006 are recorded for the first time from Germany. All DNA barcodes and specimen data were added to the publicly available GBOL and BOLD reference database. The presence of a 6 bp long deletion in the CO1 barcode region that is characteristic to the genus and unique amongst Figitidae supports the monophyly of Phaenoglyphis.},
}
@article {pmid38805929,
year = {2024},
author = {Sharma, R and Nath, PC and Lodh, BK and Mukherjee, J and Mahata, N and Gopikrishna, K and Tiwari, ON and Bhunia, B},
title = {Rapid and sensitive approaches for detecting food fraud: A review on prospects and challenges.},
journal = {Food chemistry},
volume = {454},
number = {},
pages = {139817},
doi = {10.1016/j.foodchem.2024.139817},
pmid = {38805929},
issn = {1873-7072},
mesh = {*Food Contamination/analysis ; Fraud/prevention &amp; control ; Food Analysis/methods ; Food Safety ; Mass Spectrometry ; },
abstract = {Precise and reliable analytical techniques are required to guarantee food quality in light of the expanding concerns regarding food safety and quality. Because traditional procedures are expensive and time-consuming, quick food control techniques are required to ensure product quality. Various analytical techniques are used to identify and detect food fraud, including spectroscopy, chromatography, DNA barcoding, and inotrope ratio mass spectrometry (IRMS). Due to its quick findings, simplicity of use, high throughput, affordability, and non-destructive evaluations of numerous food matrices, NI spectroscopy and hyperspectral imaging are financially preferred in the food business. The applicability of this technology has increased with the development of chemometric techniques and near-infrared spectroscopy-based instruments. The current research also discusses the use of several multivariate analytical techniques in identifying food fraud, such as principal component analysis, partial least squares, cluster analysis, multivariate curve resolutions, and artificial intelligence.},
}
@article {pmid38803273,
year = {2024},
author = {Wang, Y and Yang, Y and Liu, Y and Liu, C and Xu, M and Fang, M and Mu, X},
title = {CoSFISH: a comprehensive reference database of COI and 18S rRNA barcodes for fish.},
journal = {Database : the journal of biological databases and curation},
volume = {2024},
number = {},
pages = {},
pmid = {38803273},
issn = {1758-0463},
support = {2022SBH00001//Guangdong Rural Revitalization Strategy Special Provincial Organization/ ; 2023KJ134 2023KJ150//Modern Agriculture Industry Technology Innovation Team/ ; CAMC-2018F//China-ASEAN Maritime Cooperation Fund/ ; FGRC18537//National Freshwater Genetic Resource Center/ ; 2022SBH00001//Guangdong Rural Revitalization Strategy Special Provincial Organization/ ; 2023KJ134 2023KJ150//Modern Agriculture Industry Technology Innovation Team/ ; CAMC-2018F//China-ASEAN Maritime Cooperation Fund/ ; FGRC18537//National Freshwater Genetic Resource Center/ ; },
mesh = {Animals ; *Fishes/genetics/classification ; *RNA, Ribosomal, 18S/genetics ; *Electron Transport Complex IV/genetics ; *DNA Barcoding, Taxonomic/methods ; Databases, Genetic ; Phylogeny ; Databases, Nucleic Acid ; },
abstract = {Fish, being a crucial component of aquatic ecosystems, holds significant importance from both economic and ecological perspectives. However, the identification of fish at the species level remains challenging, and there is a lack of a taxonomically complete and comprehensive reference sequence database for fish. Therefore, we developed CoSFISH, an online fish database. Currently, the database contains 21 535 cytochrome oxidase I sequences and 1074 18S rRNA sequences of 21 589 species, belonging to 8 classes and 90 orders. We additionally incorporate online analysis tools to aid users in comparing, aligning and analyzing sequences, as well as designing primers. Users can upload their own data for analysis, in addition to using the data stored in the database directly. CoSFISH offers an extensive fish database and incorporates online analysis tools, making it a valuable resource for the study of fish diversity, phylogenetics and biological evolution. Database URL: http://210.22.121.250:8888/CoSFISH/home/indexPage.},
}
@article {pmid38798722,
year = {2024},
author = {Li, ZZ and Xu, Z and Wu, S and Yuan, LX and Zou, CY and Liu, Y and Lin, JY and Liang, SC},
title = {Molecular analyses display the increasing diversity of Podostemaceae in China.},
journal = {Plant diversity},
volume = {46},
number = {3},
pages = {421-424},
pmid = {38798722},
issn = {2468-2659},
abstract = {•Four newly recorded species of Podostemaceae from southern China were identified by molecular and morphological evidence.•17 plastomes of Podostemaceae were newly sequenced and two novel polymorphic barcodes (ccsA and ndhA) detected.•Our findings reveal greater species richness (15 species from five genera) of Podostemaceae in China and supply molecular resources for research on taxonomy and phylogenomics of this enigmatic aquatic family.},
}
@article {pmid38797438,
year = {2024},
author = {Meadow, ME and Broas, S and Hoare, M and Alimohammadi, F and Welle, KA and Swovick, K and Hryhorenko, JR and Martinez, JC and Biashad, SA and Seluanov, A and Gorbunova, V and Buchwalter, A and Ghaemmaghami, S},
title = {Proteome Birthdating Reveals Age-Selectivity of Protein Ubiquitination.},
journal = {Molecular &amp; cellular proteomics : MCP},
volume = {23},
number = {7},
pages = {100791},
pmid = {38797438},
issn = {1535-9484},
support = {P01 AG047200/AG/NIA NIH HHS/United States ; P01 AG051449/AG/NIA NIH HHS/United States ; R01 AG027237/AG/NIA NIH HHS/United States ; R37 AG046320/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; *Ubiquitination ; *Proteome/metabolism ; *Proteasome Endopeptidase Complex/metabolism ; *Ubiquitinated Proteins/metabolism ; Proteomics/methods ; Proteolysis ; Ubiquitin/metabolism ; },
abstract = {Within a cell, proteins have distinct and highly variable half-lives. As a result, the molecular ages of proteins can range from seconds to years. How the age of a protein influences its environmental interactions is a largely unexplored area of biology. To investigate the age-selectivity of cellular pathways, we developed a methodology termed "proteome birthdating" that barcodes proteins based on their time of synthesis. We demonstrate that this approach provides accurate measurements of protein turnover kinetics from a single biological sample encoding multiple labeling time-points. As a first application of the birthdated proteome, we investigated the age distribution of the human ubiquitinome. Our results indicate that the vast majority of ubiquitinated proteins in a cell consist of newly synthesized proteins and that these young proteins constitute the bulk of the degradative flux through the proteasome. Rapidly ubiquitinated nascent proteins are enriched in cytosolic subunits of large protein complexes. Conversely, proteins destined for the secretory pathway and vesicular transport have older ubiquitinated populations. Our data also identify a smaller subset of older ubiquitinated cellular proteins that do not appear to be targeted to the proteasome for rapid degradation. Together, our data provide an age census of the human ubiquitinome and establish proteome birthdating as a robust methodology for investigating the protein age-selectivity of diverse cellular pathways.},
}
@article {pmid38794403,
year = {2024},
author = {Almerekova, S and Yermagambetova, M and Osmonali, B and Vesselova, P and Abugalieva, S and Turuspekov, Y},
title = {Characterization of the Plastid Genomes of Four Caroxylon Thunb. Species from Kazakhstan.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {10},
pages = {},
pmid = {38794403},
issn = {2223-7747},
support = {AP14869593//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {The family Chenopodiaceae Vent. (Amaranthaceae s.l.) is known for its taxonomic complexity, comprising species of significant economic and ecological importance. Despite its significance, the availability of plastid genome data for this family remains limited. This study involved assembling and characterizing the complete plastid genomes of four Caroxylon Thunb. species within the tribe Salsoleae s.l., utilizing next-generation sequencing technology. We compared genome features, nucleotide diversity, and repeat sequences and conducted a phylogenetic analysis of ten Salsoleae s.l. species. The size of the plastid genome varied among four Caroxylon species, ranging from 150,777 bp (C. nitrarium) to 151,307 bp (C. orientale). Each studied plastid genome encoded 133 genes, including 114 unique genes. This set of genes includes 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Eight divergent regions (accD, atpF, matK, ndhF-ndhG, petB, rpl20-rpl22, rpoC2, and ycf3) were identified in ten Salsoleae s.l. plastid genomes, which could be potential DNA-barcoding markers. Additionally, 1106 repeat elements were detected, consisting of 814 simple sequence repeats, 92 tandem repeats, 88 forward repeats, 111 palindromic repeats, and one reverse repeat. The phylogenetic analysis provided robust support for the relationships within Caroxylon species. These data represent a valuable resource for future phylogenetic studies within the genus.},
}
@article {pmid38792756,
year = {2024},
author = {Abdillah, A and Kodio, A and Ranque, S},
title = {Malian Children's Core Gut Mycobiome.},
journal = {Microorganisms},
volume = {12},
number = {5},
pages = {},
pmid = {38792756},
issn = {2076-2607},
support = {M&#xe9;diterran&#xe9;e Infection 10-IAHU-03//M&#xe9;diterran&#xe9;e Infection Foundation/ ; },
abstract = {Because data on the fungal gut community structure of African children are scarce, we aimed to describe it by reanalysing rRNA ITS1 and ITS2 metabarcoding data from a study designed to assess the influence of microbiota in malaria susceptibility in Malian children from the Dogon country. More specifically, we aimed to establish the core gut mycobiome and compare the gut fungal community structure of breastfed children, aged 0-2 years, with other age groups. Briefly, DNA was extracted from 296 children's stool samples. Both rRNA ITS1 and ITS2 genomic barcodes were amplified and subjected to Illumina MiSeq sequencing. The ITS2 barcode generated 1,975,320 reads and 532 operational taxonomic units (OTUs), while the ITS1 barcode generated 647,816 reads and 532 OTUs. The alpha diversity was significantly higher by using the ITS1 compared to the ITS2 barcode (p < 0.05); but, regardless of the ITS barcode, we found no significant difference between breastfed children, aged 0-2 years, compared to the other age groups. The core gut mycobiome of the Malian children included Saccharomyces cerevisiae, Candida albicans, Pichia kudriavzevii, Malassezia restricta, Candida tropicalis and Aspergillus section Aspergillus, which were present in at least 50% of the 296 children. Further studies in other African countries are warranted to reach a global view of African children's core gut mycobiome.},
}
@article {pmid38791964,
year = {2024},
author = {Zhu, Y and Koleilat, MKI and Roszik, J and Kwong, MK and Wang, Z and Maru, DM and Kopetz, S and Kwong, LN},
title = {A Gold Standard-Derived Modular Barcoding Approach to Cancer Transcriptomics.},
journal = {Cancers},
volume = {16},
number = {10},
pages = {},
pmid = {38791964},
issn = {2072-6694},
support = {1R01CA251608-01, 1R01HG011356-01/NH/NIH HHS/United States ; 1R01CA251608-01 and 1R01HG011356-01/NH/NIH HHS/United States ; },
abstract = {A challenge with studying cancer transcriptomes is in distilling the wealth of information down into manageable portions of information. In this resource, we develop an approach that creates and assembles cancer type-specific gene expression modules into flexible barcodes, allowing for adaptation to a wide variety of uses. Specifically, we propose that modules derived organically from high-quality gold standards such as The Cancer Genome Atlas (TCGA) can accurately capture and describe functionally related genes that are relevant to specific cancer types. We show that such modules can: (1) uncover novel gene relationships and nominate new functional memberships, (2) improve and speed up analysis of smaller or lower-resolution datasets, (3) re-create and expand known cancer subtyping schemes, (4) act as a "decoder" to bridge seemingly disparate established gene signatures, and (5) efficiently apply single-cell RNA sequencing information to other datasets. Moreover, such modules can be used in conjunction with native spreadsheet program commands to create a powerful and rapid approach to hypothesis generation and testing that is readily accessible to non-bioinformaticians. Finally, we provide tools for users to create and interpret their own modules. Overall, the flexible modular nature of the proposed barcoding provides a user-friendly approach to rapidly decoding transcriptome-wide data for research or, potentially, clinical uses.},
}
@article {pmid38791511,
year = {2024},
author = {Wu, Y and Jensen, N and Rossner, MJ and Wehr, MC},
title = {Exploiting Cell-Based Assays to Accelerate Drug Development for G Protein-Coupled Receptors.},
journal = {International journal of molecular sciences},
volume = {25},
number = {10},
pages = {},
pmid = {38791511},
issn = {1422-0067},
mesh = {*Receptors, G-Protein-Coupled/metabolism ; Humans ; Signal Transduction/drug effects ; Drug Development/methods ; Drug Discovery/methods ; Animals ; Bioluminescence Resonance Energy Transfer Techniques/methods ; Biological Assay/methods ; },
abstract = {G protein-coupled receptors (GPCRs) are relevant targets for health and disease as they regulate various aspects of metabolism, proliferation, differentiation, and immune pathways. They are implicated in several disease areas, including cancer, diabetes, cardiovascular diseases, and mental disorders. It is worth noting that about a third of all marketed drugs target GPCRs, making them prime pharmacological targets for drug discovery. Numerous functional assays have been developed to assess GPCR activity and GPCR signaling in living cells. Here, we review the current literature of genetically encoded cell-based assays to measure GPCR activation and downstream signaling at different hierarchical levels of signaling, from the receptor to transcription, via transducers, effectors, and second messengers. Singleplex assay formats provide one data point per experimental condition. Typical examples are bioluminescence resonance energy transfer (BRET) assays and protease cleavage assays (e.g., Tango or split TEV). By contrast, multiplex assay formats allow for the parallel measurement of multiple receptors and pathways and typically use molecular barcodes as transcriptional reporters in barcoded assays. This enables the efficient identification of desired on-target and on-pathway effects as well as detrimental off-target and off-pathway effects. Multiplex assays are anticipated to accelerate drug discovery for GPCRs as they provide a comprehensive and broad identification of compound effects.},
}
@article {pmid38790191,
year = {2024},
author = {Ciborowski, K and Szczecińska, M and Maździarz, M and Sawicki, J and Paukszto, &#x141;},
title = {Decoding Evolution of Rubioideae: Plastomes Reveal Sweet Secrets of Codon Usage, Diagnostides, and Superbarcoding.},
journal = {Genes},
volume = {15},
number = {5},
pages = {},
pmid = {38790191},
issn = {2073-4425},
support = {N304 364438//National Science Center/ ; },
mesh = {*Codon Usage ; *Phylogeny ; *Genome, Chloroplast/genetics ; *Evolution, Molecular ; *Rubiaceae/genetics ; Codon/genetics ; DNA Barcoding, Taxonomic/methods ; },
abstract = {Galium genus belongs to the Rubiaceae family, which consists of approximately 14,000 species. In comparison to its well-known relatives, the plastomes of the Galium genus have not been explored so far. The plastomes of this genus have a typical, quadripartite structure, but differ in gene content, since the infA gene is missing in Galium palustre and Galium trfidum. An evaluation of the effectiveness of using entire chloroplast genome sequences as superbarcodes for accurate plant species identification revealed the high potential of this method for molecular delimitation within the genus and tribe. The trnE-UUC-psbD region showed the biggest number of diagnostides (diagnostic nucleotides) which might be new potential barcodes, not only in Galium, but also in other closely related genera. Relative synonymous codon usage (RSCU) appeared to be connected with the phylogeny of the Rubiaceae family, showing that during evolution, plants started preferring specific codons over others.},
}
@article {pmid38789603,
year = {2024},
author = {Scholtz, L and Eckert, JG and Graf, RT and Kunst, A and Wegner, KD and Bigall, NC and Resch-Genger, U},
title = {Correlating semiconductor nanoparticle architecture and applicability for the controlled encoding of luminescent polymer microparticles.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {11904},
pmid = {38789603},
issn = {2045-2322},
abstract = {Luminophore stained micro- and nanobeads made from organic polymers like polystyrene (PS) are broadly used in the life and material sciences as luminescent reporters, for bead-based assays, sensor arrays, printable barcodes, security inks, and the calibration of fluorescence microscopes and flow cytometers. Initially mostly prepared with organic dyes, meanwhile luminescent core/shell nanoparticles (NPs) like spherical semiconductor quantum dots (QDs) are increasingly employed for bead encoding. This is related to their narrower emission spectra, tuneability of emission color, broad wavelength excitability, and better photostability. However, correlations between particle architecture, morphology, and photoluminescence (PL) of the luminescent nanocrystals used for encoding and the optical properties of the NP-stained beads have been rarely explored. This encouraged us to perform a screening study on the incorporation of different types of luminescent core/shell semiconductor nanocrystals into polymer microparticles (PMPs) by a radical-induced polymerization reaction. Nanocrystals explored include CdSe/CdS QDs of varying CdS shell thickness, a CdSe/ZnS core/shell QD, CdSe/CdS quantum rods (QRs), and CdSe/CdS nanoplatelets (NPLs). Thereby, we focused on the applicability of these NPs for the polymerization synthesis approach used and quantified the preservation of the initial NP luminescence. The spectroscopic characterization of the resulting PMPs revealed the successful staining of the PMPs with luminescent CdSe/CdS QDs and CdSe/CdS NPLs. In contrast, usage of CdSe/CdS QRs and CdSe QDs with a ZnS shell did not yield luminescent PMPs. The results of this study provide new insights into structure-property relationships between NP stained PMPs and the initial luminescent NPs applied for staining and underline the importance of such studies for the performance optimization of NP-stained beads.},
}
@article {pmid38787488,
year = {2024},
author = {Kumari, A and Sidhu, MC},
title = {Morphological and molecular characterization of two species of genus Ageratum.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {668},
pmid = {38787488},
issn = {1573-4978},
mesh = {*Phylogeny ; *DNA Barcoding, Taxonomic/methods ; *Ageratum/genetics ; DNA, Plant/genetics ; Plant Leaves/genetics ; Sequence Analysis, DNA/methods ; India ; },
abstract = {BACKGROUND: The species of genus Ageratum (family Asteraceae) are distributed in various parts of the world. Ageratum conyzoides and A. houstonianum are the most commonly occurring species in India. These species are quite similar in their morphology thus creating a challenge in identification during the field survey and taxonomic validation. The accurate identification of the species is highly significant especially when those are of medicinal interest. To overcome the barriers in morphological based identification, DNA barcoding has been employed during the present investigation.<br><br>METHODS AND RESULTS: Morphological and DNA barcodes matK and ITS genes, were employed to differentiate between Ageratum conyzoides and A. houstonianum. The obtained matK and ITS gene sequences were submitted to GenBank and BOLD system to obtain accession numbers. The DNA sequences were aligned with database sequences using BLAST and phylogenetic trees were constructed through neighbor-joining algorithm in MEGA 11 software. The distinguish features of A. conyzoides include ovate to elliptic-oblong leaves with a cuneate base and inflorescence heads forming domed to flat-topped clusters. However, A. houstonianum has triangular to ovate leaves with a cordate to truncate base, cymose clusters in the inflorescence and stipulate glandular involucre bracts. The matK gene has shown the highest identity percentages (100%) for A. houstonianum and 99.87% for A. conyzoides. The phylogenetic tree analysis has demonstrated a close association of A. conyzoides and A. houstonianum with their respective species, supported by bootstrap values in the matK and ITS trees.<br><br>CONCLUSION: This study revealed that morphological and molecular data can be successfully utilized in the identification of A. conyzoides and A. houstonianum. The matK and ITS barcodes provide promising results in the identification of Ageratum species, with their phylogeny supporting classification within the family asteraceae.},
}
@article {pmid38786915,
year = {2024},
author = {Jiang, ZH and Wang, JX and Xu, ZB and Kitching, IJ and Huang, CL and Hu, SJ and Xiao, YL},
title = {Revision of the Genus Rhagastis Rothschild &amp; Jordan, 1903 (Lepidoptera: Sphingidae) from China, Based on Morphological and Phylogenetic Analyses.},
journal = {Insects},
volume = {15},
number = {5},
pages = {},
pmid = {38786915},
issn = {2075-4450},
support = {2019FY101800//National Science &amp; Technology Fundamental Resources Investigation Program of China (Grant No. 2019FY101800)/ ; 202305AF150037//Academician (Expert) Working Station (202305AF150037), Yunnan Provincial Department of Science/ ; },
abstract = {Here, the taxonomy of the genus Rhagastis Rothschild &amp; Jordan, 1903 (Lepidoptera, Sphingidae, Macroglossinae, Macroglossini) from China is revised based on differences in wing morphology, male and female genitalia, and the phylogenetic relationship of the DNA barcodes. Subspecies of Rhagastis albomarginatus (Rothschild, 1894) and R. castor (Walker, 1856) are treated as "good" species, namely Rhagastis dichroae Mell, 1922 stat. nov.; R. everetti Rothschild &amp; Jordan, 1903 stat. nov.; R. aurifera (Butler, 1875) stat. rev.; R. chinensis Mell, 1922 stat. nov.; R. formosana Clark, 1925 stat. nov.; and R. jordani Oberthür, 1904 stat. rev. The distribution maps, biological notes, and ecological records of the genus Rhagastis Rothschild &amp; Jordan, 1903 from China are given, and a species inventory of genus Rhagastis in the world is also included.},
}
@article {pmid38785505,
year = {2024},
author = {Matoute, A and Maestri, S and Saout, M and Laghoe, L and Simon, S and Blanquart, H and Hernandez Martinez, MA and Pierre Demar, M},
title = {Meat-Borne-Parasite: A Nanopore-Based Meta-Barcoding Work-Flow for Parasitic Microbiodiversity Assessment in the Wild Fauna of French Guiana.},
journal = {Current issues in molecular biology},
volume = {46},
number = {5},
pages = {3810-3821},
pmid = {38785505},
issn = {1467-3045},
support = {PARALIM project (Synergie n&#xb0; GY0012553)//European funding (ERDF/FEDER)/ ; CEBA: ANR-10-LABEX-25-01//Investissement d'Avenir 358 grants of the the Agence Nationale de la Recherche/ ; },
abstract = {French Guiana, located in the Guiana Shield, is a natural reservoir for many zoonotic pathogens that are of considerable medical or veterinary importance. Until now, there has been limited data available on the description of parasites circulating in this area, especially on protozoan belonging to the phylum Apicomplexa; conversely, the neighbouring countries describe a high parasitic prevalence in animals and humans. Epidemiological surveillance is necessary, as new potentially virulent strains may emerge from these forest ecosystems, such as Amazonian toxoplasmosis. However, there is no standard tool for detecting protozoa in wildlife. In this study, we developed Meat-Borne-Parasite, a high-throughput meta-barcoding workflow for detecting Apicomplexa based on the Oxford Nanopore Technologies sequencing platform using the 18S gene of 14 Apicomplexa positive samples collected in French Guiana. Sequencing reads were then analysed with MetONTIIME pipeline. Thanks to a scoring rule, we were able to classify 10 samples out of 14 as Apicomplexa positive and reveal the presence of co-carriages. The same samples were also sequenced with the Illumina platform for validation purposes. For samples identified as Apicomplexa positive by both platforms, a strong positive correlation at up to the genus level was reported. Overall, the presented workflow represents a reliable method for Apicomplexa detection, which may pave the way for more comprehensive biomonitoring of zoonotic pathogens.},
}
@article {pmid38784157,
year = {2024},
author = {Pina, S and Pauperio, J and Barros, F and Chaves, C and Martins, FM and Pinto, J and Veríssimo, J and Mata, VA and Beja, P and Ferreira, S},
title = {The InBIO Barcoding Initiative Database: DNA barcodes of Orthoptera from Portugal.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e118010},
pmid = {38784157},
issn = {1314-2828},
abstract = {BACKGROUND: The InBIO Barcoding Initiative (IBI) Orthoptera dataset contains records of 420 specimens covering all the eleven Orthoptera families occurring in Portugal. Specimens were collected in continental Portugal from 2005 to 2021 and were morphologically identified to species level by taxonomists. A total of 119 species were identified corresponding to about 77% of all the orthopteran species known from continental Portugal.<br><br>NEW INFORMATION: DNA barcodes of 54 taxa were made public for the first time at the Barcode of Life Data System (BOLD). Furthermore, the submitted sequences were found to cluster in 129 BINs (Barcode Index Numbers), 35 of which were new additions to the Barcode of Life Data System (BOLD). All specimens have their DNA barcodes publicly accessible through BOLD online database. Stenobothruslineatus is recorded for the first time for continental Portugal. This dataset greatly increases the knowledge on the DNA barcodes and distribution of Orthoptera from Portugal. All DNA extractions and most specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources.},
}
@article {pmid38781750,
year = {2024},
author = {Bouchali, R and Mandon, C and Danty-Berger, E and Géloën, A and Marjolet, L and Youenou, B and Pozzi, ACM and Vareilles, S and Galia, W and Kouyi, GL and Toussaint, JY and Cournoyer, B},
title = {Runoff microbiome quality assessment of a city center rainwater harvesting zone shows a differentiation of pathogen loads according to human mobility patterns.},
journal = {International journal of hygiene and environmental health},
volume = {260},
number = {},
pages = {114391},
doi = {10.1016/j.ijheh.2024.114391},
pmid = {38781750},
issn = {1618-131X},
mesh = {*Rain ; Humans ; *Microbiota ; *Water Microbiology ; *Cities ; *Bacteria/isolation &amp; purification/classification/genetics ; *Environmental Monitoring/methods ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; },
abstract = {The hygienic quality of urban surfaces can be impaired by multiple sources of microbiological contaminants. These surfaces can trigger the development of multiple bacterial taxa and favor their spread during rain events through the circulation of runoff waters. These runoff waters are commonly directed toward sewer networks, stormwater infiltration systems or detention tanks prior a release into natural water ways. With water scarcity becoming a major worldwide issue, these runoffs are representing an alternative supply for some usage like street cleaning and plant watering. Microbiological hazards associated with these urban runoffs, and surveillance guidelines must be defined to favor these uses. Runoff microbiological quality from a recently implemented city center rainwater harvesting zone was evaluated through classical fecal indicator bacteria (FIB) assays, quantitative PCR and DNA meta-barcoding analyses. The incidence of socio-urbanistic patterns on the organization of these urban microbiomes were investigated. FIB and DNA from Human-specific Bacteroidales and pathogens such as Staphylococcus aureus were detected from most runoffs and showed broad distribution patterns. 16S rRNA DNA meta-barcoding profilings further identified core recurrent taxa of health concerns like Acinetobacter, Mycobacterium, Aeromonas and Pseudomonas, and divided these communities according to two main groups of socio-urbanistic patterns. One of these was highly impacted by heavy traffic, and showed recurrent correlation networks involving bacterial hydrocarbon degraders harboring significant virulence properties. The tpm-based meta-barcoding approach identified some of these taxa at the species level for more than 30 genera. Among these, recurrent pathogens were recorded such as P. aeruginosa, P. paraeruginosa, and Aeromonas caviae. P. aeruginosa and A. caviae tpm reads were found evenly distributed over the study site but those of P. paraeruginosa were higher among sub-catchments impacted by heavy traffic. Health risks associated with these runoff P. paraeruginosa emerging pathogens were high and associated with strong cytotoxicity on A549 lung cells. Recurrent detections of pathogens in runoff waters highlight the need of a microbiological surveillance prior allowing their use. Good microbiological quality can be obtained for certain typologies of sub-catchments with good hygienic practices but not all. A reorganization of Human mobility and behaviors would likely trigger changes in these bacterial diversity patterns and reduce the occurrences of the most hazardous groups.},
}
@article {pmid38781285,
year = {2024},
author = {Govorov, V and Shcherbakov, E and Janšta, P and Černá Bolfiková, B},
title = {First assessment of the biodiversity of praying mantises (Insecta: Mantodea) in Cameroon with DNA barcoding.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0304163},
pmid = {38781285},
issn = {1932-6203},
mesh = {Cameroon ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Animals ; *Mantodea/genetics/classification ; *Phylogeny ; },
abstract = {Praying mantises are the apex insect predators in many ecosystems, nevertheless they receive relatively less recognition in biodiversity reviews. We report a first survey of diversity of praying mantises in Cameroon, which is situated in the Congo Basin region, one of the richest biodiversity hotspots. Combination of light trapping with manual collecting resulted in 495 specimens representing 62 species. A total of eight species are novel for the country, at least five species are likely undescribed. DNA barcodes of 72 specimens representing every collected species were obtained, curated, and submitted to NCBI database. For eight species, barcodes are published for the first time. A maximum likelihood phylogenetic tree was created using all available barcodes of Mantodea of Central African subregion. The results obtained during this study stress the importance of combining traditional and molecular approaches during biodiversity assessments of often neglected taxa, the latter aiding in uncovering new species, resolving unknown morphological divergencies and assigning conspecifics.},
}
@article {pmid38778277,
year = {2024},
author = {Fu, N and Xu, Y and Jin, L and Xiao, TW and Song, F and Yan, HF and Chen, YS and Ge, XJ},
title = {Testing plastomes and nuclear ribosomal DNA sequences as the next-generation DNA barcodes for species identification and phylogenetic analysis in Acer.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {445},
pmid = {38778277},
issn = {1471-2229},
support = {No. XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; No. XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; No. XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; No. XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; No. XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; No. XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
mesh = {*Acer/genetics ; *Phylogeny ; *DNA Barcoding, Taxonomic/methods ; *DNA, Ribosomal/genetics ; *DNA, Plant/genetics ; Plastids/genetics ; Species Specificity ; Cell Nucleus/genetics ; },
abstract = {BACKGROUND: Acer is a taxonomically intractable and speciose genus that contains over 150 species. It is challenging to distinguish Acer species only by morphological method due to their abundant variations. Plastome and nuclear ribosomal DNA (nrDNA) sequences are recommended as powerful next-generation DNA barcodes for species discrimination. However, their efficacies were still poorly studied. The current study will evaluate the application of plastome and nrDNA in species identification and perform phylogenetic analyses for Acer.<br><br>RESULT: Based on a collection of 83 individuals representing 55 species (c. 55% of Chinese species) from 13 sections, our barcoding analyses demonstrated that plastomes exhibited the highest (90.47%) species discriminatory power among all plastid DNA markers, such as the standard plastid barcodes matK&#x2009;+&#x2009;rbcL&#x2009;+&#x2009;trnH-psbA (61.90%) and ycf1 (76.19%). And the nrDNA (80.95%) revealed higher species resolution than ITS (71.43%). Acer plastomes show abundant interspecific variations, however, species identification failure may be due to the incomplete lineage sorting (ILS) and chloroplast capture resulting from hybridization. We found that the usage of nrDNA contributed to identifying those species that were unidentified by plastomes, implying its capability to some extent to mitigate the impact of hybridization and ILS on species discrimination. However, combining plastome and nrDNA is not recommended given the cytonuclear conflict caused by potential hybridization. Our phylogenetic analysis covering 19 sections&#xa0;(95% sections of Acer) and 128 species (over 80% species of this genus) revealed pervasive inter- and intra-section cytonuclear discordances, hinting that hybridization has played an important role in the evolution of Acer.<br><br>CONCLUSION: Plastomes and nrDNA can significantly improve the species resolution in Acer. Our phylogenetic analysis uncovered the scope and depth of cytonuclear conflict in Acer, providing important insights into its evolution.},
}
@article {pmid38776430,
year = {2024},
author = {Wang, N and Mcneer, NA and Eton, E and Fass, J and Kentsis, A},
title = {Proteomic Barcoding Platform for Macromolecular Screening and Delivery.},
journal = {Journal of proteome research},
volume = {23},
number = {6},
pages = {2067-2077},
pmid = {38776430},
issn = {1535-3907},
support = {R01 CA204396/CA/NCI NIH HHS/United States ; U54 CA243124/CA/NCI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; R21 CA235285/CA/NCI NIH HHS/United States ; //Commonwealth Foundation for Cancer Research the Center for Experimental Therapeutics/ ; R01 CA214812/CA/NCI NIH HHS/United States ; /DDCF/Doris Duke Charitable Foundation/United States ; //Starr Cancer Consortium/ ; },
mesh = {Humans ; *Proteomics/methods ; *Cell-Penetrating Peptides/chemistry ; Algorithms ; Mass Spectrometry/methods ; Peptide Library ; High-Throughput Screening Assays/methods ; Macromolecular Substances/chemistry/analysis ; },
abstract = {Engineered macromolecules offer compelling means for the therapy of conventionally undruggable interactions in human disease. However, their efficacy is limited by barriers to tissue and intracellular delivery. Inspired by recent advances in molecular barcoding and evolution, we developed BarcodeBabel, a generalized method for the design of libraries of peptide barcodes suitable for high-throughput mass spectrometry proteomics. Combined with PeptideBabel, a Monte Carlo sampling algorithm for the design of peptides with evolvable physicochemical properties and sequence complexity, we developed a barcoded library of cell penetrating peptides (CPPs) with distinct physicochemical features. Using quantitative targeted mass spectrometry, we identified CPPS with improved nuclear and cytoplasmic delivery exceeding hundreds of millions of molecules per human cell while maintaining minimal membrane disruption and negligible toxicity in vitro. These studies provide a proof of concept for peptide barcoding as a homogeneous high-throughput method for macromolecular screening and delivery. BarcodeBabel and PeptideBabel are available open-source from https://github.com/kentsisresearchgroup/.},
}
@article {pmid38775954,
year = {2024},
author = {Liu, Y and Chen, J and Lin, C and Ke, R},
title = {Multiplexed in situ RNA imaging by combFISH.},
journal = {Analytical and bioanalytical chemistry},
volume = {416},
number = {16},
pages = {3765-3774},
pmid = {38775954},
issn = {1618-2650},
support = {2021Y4001//Natural Science Foundation of Fujian Province/ ; 2022J06022//Natural Science Foundation of Fujian Province/ ; ZQN-1123//Fundamental Research Funds for the Central Universities/ ; 3502Z20234012//Xiamen Municipal Bureau of Science and Technology/ ; },
mesh = {*In Situ Hybridization, Fluorescence/methods ; *RNA/analysis ; Humans ; Animals ; Fluorescent Dyes/chemistry ; Gene Expression Profiling/methods ; },
abstract = {Multiplexed in situ RNA imaging offers new opportunities for gene expression profiling by providing high-throughput spatial information. In this work, we present a cyclic combinatorial fluorescent in situ hybridization (combFISH) assay to achieve multiplexed detection of RNA in cell cultures and tissues. Specifically, multiplexing is achieved through cyclic interrogation of barcode sequences on the rolling circle amplicons generated from the padlock probe assay by using sets of combinatorial detection probes. Theoretically, combFISH can detect 64 genes in three hybridization cycles by combinatorial barcoding using 12 fluorescently labeled detection probes. Our method eliminates sequencing-by-ligation (SBL) chemistry in the in situ sequencing protocol and directly uses RNA as targets for ligation, making it more straightforward. We showed that our method works in fresh-frozen and formalin-fixed paraffin-embedded tissue sections. With its straightforward protocols, we expect our method to be adopted by the scientific community and extended to clinical settings.},
}
@article {pmid38775145,
year = {2024},
author = {Graham, K and Cantu, C and Houston, R},
title = {Sequence variation of commercially available kratom products at universal DNA barcode regions.},
journal = {Journal of forensic sciences},
volume = {69},
number = {4},
pages = {1421-1428},
doi = {10.1111/1556-4029.15547},
pmid = {38775145},
issn = {1556-4029},
mesh = {*Mitragyna/genetics/chemistry ; *DNA Barcoding, Taxonomic ; *DNA, Plant/genetics ; Humans ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Polymorphism, Genetic ; Genetic Variation ; DNA, Chloroplast/genetics ; },
abstract = {Mitragyna speciosa, commonly known as kratom, is a narcotic plant that is used for its unique mood-enhancing and pain-relieving effects. It is marketed throughout the United States as a 'legal high' and has gained popularity as an alternative to opioids. However, kratom's increasing involvement in accidental overdoses, especially among polydrug users, has prompted warnings from the Drug Enforcement Agency (DEA) and the Food and Drug Administration (FDA). Despite these warnings, kratom remains legal federally, although it is banned in six states. This legal disparity complicates monitoring and enforcement efforts in states where kratom is illegal. Common forensic techniques using morphology or chemical analysis are beneficial in some instances but are not useful in source attribution because most seized kratom is powdered and the alkaloid content of samples can vary within products, making sourcing unreliable. This study focused on developing a DNA barcoding method to access sequence variation in commercial kratom products. It evaluated the utility of one nuclear barcode region (ITS) and three chloroplast barcode regions (matK, rbcL, and trnH-psbA) in assessing sequence variation across commercially available kratom products. Novel polymorphisms were discovered, and the ITS region showed the greatest variation between samples. Among the 15 kratom products tested, only two haplotypes were identified across the four barcoding regions. The findings highlight the potential of DNA barcoding as a forensic tool in the traceability and enforcement against illegal kratom distribution. Nonetheless, the limited haplotypic diversity points to a need for further development and expansion of the M. speciosa DNA sequence database.},
}
@article {pmid38774420,
year = {2024},
author = {Parker, TB and Meiklejohn, KA and Dahlem, GA and Eagle, RC and Heersink, MJ},
title = {Ophthalmomyiasis Case Caused by Two Blow Fly (Diptera: Calliphoridae) Species in North America.},
journal = {TheScientificWorldJournal},
volume = {2024},
number = {},
pages = {2209301},
pmid = {38774420},
issn = {1537-744X},
mesh = {Animals ; *Calliphoridae/genetics ; Male ; Humans ; *Larva ; Myiasis/parasitology/diagnosis ; North America ; Phylogeny ; Diptera/parasitology ; Genome, Mitochondrial ; },
abstract = {Ophthalmomyiasis is the result of fly larvae feeding on the tissues of the eye. Commonly associated with poor hygiene and open wounds, this condition is rare and often stigmatized. Treatment can be straightforward, and full recovery is common. Identifying the species responsible for ophthalmomyiasis is important for the medical, forensic, and entomological communities. Here, we present a case of ophthalmomyiasis where 30-40 blow fly (Diptera: Calliphoridae) larvae were removed from the eye of a human male. A representative subsample of five larvae was used for taxonomic identification via two approaches (a) DNA analysis, via sequencing of the complete mitochondrial genome (mtGenome) and comparison of the mtGenome and mitochondrial COI barcode region to GenBank, and (b) morphology, examination of the posterior spiracles using microscopy, and comparison to published larval descriptions of blow flies. Two species of blow flies were identified from the DNA analysis: Lucilia coeruleiviridis and Phormia regina. Morphological examination could only confirm L. coeruleiviridis as being present. To our knowledge, finding two blow fly species causing ophthalmomyiasis in a single individual has not been previously reported in the scientific literature. Neither P. regina nor L. coeruleiviridis prefers living tissue for larva development, but since they fill similar ecological niches, perhaps this was a show of competition rather than a normal feeding habit. Knowing these blow fly species can resort to this behavior, and that it can affect human populations, is valuable to the education of patients and providers.},
}
@article {pmid38774237,
year = {2024},
author = {Hoang, CV and Tu, TQ and Lo, TTM and Chu, MH},
title = {Dataset on intergenic spacer regions of chloroplast genome and potential DNA barcode of Hoya varticillata var varticillata in Vietnam.},
journal = {Data in brief},
volume = {54},
number = {},
pages = {110471},
pmid = {38774237},
issn = {2352-3409},
abstract = {Hoya verticillata var verticillata, an epiphytic plant, is both an ornamental and a valuable medicinal plant. However, H. verticillata has a similar morphology to other species belonging to the Hoya genus, so it is challenging to distinguish the H. verticillata var verticillata, plant accurately. Alternatively, if H. verticillata var verticillata, is deformed or powdered, it is more challenging to identify. This dataset includes information on H. verticillata var verticillata, samples collected from the natural environment and four chloroplast DNA markers to support H. verticillata var verticillata, species identification. Phylogenetic analysis based on sequences of intergenic spacer regions (trnK-rps16, rps16-trnQ, psbI-atpA, and ndhC-trnV) shows that H. verticilata var verticillata, is very closely related and distributed in the same group as Hoya carnosa with a Bootstrap coefficient of 99-100 %. Four intergenic spacer region sequences, trnK-rps16, rps16-trnQ, psbI-atpA, and ndhC-trnV from the chloroplast genome are potential DNA barcoding candidates to distinguish H. verticilata var verticillata, from different species in the Hoya genus.},
}
@article {pmid38773773,
year = {2024},
author = {Yoon, CJ and Nam, CH and Kim, T and Lee, JS and Kim, R and Yi, K and Koh, JY and Kim, J and Won, H and Oh, JW and Griffith, OL and Griffith, M and Sung, J and Kim, TY and Cho, D and Choi, JS and Ju, YS},
title = {Whole-genome sequences reveal zygotic composition in chimeric twins.},
journal = {HGG advances},
volume = {5},
number = {3},
pages = {100301},
pmid = {38773773},
issn = {2666-2477},
support = {F30 HD106744/HD/NICHD NIH HHS/United States ; },
mesh = {Humans ; Female ; *Twins, Dizygotic/genetics ; *Zygote/metabolism ; *Whole Genome Sequencing ; Pregnancy ; Chimerism ; Placenta/metabolism ; Male ; Chimera/genetics ; Twins, Monozygotic/genetics ; },
abstract = {While most dizygotic twins have a dichorionic placenta, rare cases of dizygotic twins with a monochorionic placenta have been reported. The monochorionic placenta in dizygotic twins allows in utero exchange of embryonic cells, resulting in chimerism in the twins. In practice, this chimerism is incidentally identified in mixed ABO blood types or in the presence of cells with a discordant sex chromosome. Here, we applied whole-genome sequencing to one triplet and one twin family to precisely understand their zygotic compositions, using millions of genomic variants as barcodes of zygotic origins. Peripheral blood showed asymmetrical contributions from two sister zygotes, where one of the zygotes was the major clone in both twins. Single-cell RNA sequencing of peripheral blood tissues further showed differential contributions from the two sister zygotes across blood cell types. In contrast, buccal tissues were pure in genetic composition, suggesting that in utero cellular exchanges were confined to the blood tissues. Our study illustrates the cellular history of twinning during human development, which is critical for managing the health of chimeric individuals in the era of genomic medicine.},
}
@article {pmid38773521,
year = {2024},
author = {Mudavanhu, A and Schols, R and Goossens, E and Nhiwatiwa, T and Manyangadze, T and Brendonck, L and Huyse, T},
title = {One Health monitoring reveals invasive freshwater snail species, new records, and undescribed parasite diversity in Zimbabwe.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {234},
pmid = {38773521},
issn = {1756-3305},
mesh = {Animals ; Zimbabwe/epidemiology ; *Snails/parasitology ; *Trematoda/genetics/classification/isolation &amp; purification/physiology ; Cross-Sectional Studies ; *Introduced Species ; *Fresh Water/parasitology ; One Health ; Humans ; Trematode Infections/parasitology/veterinary/epidemiology ; Biodiversity ; Prevalence ; Schistosomiasis/epidemiology/parasitology/veterinary ; },
abstract = {BACKGROUND: Snail-borne trematodes afflict humans, livestock, and wildlife. Recognizing their zoonotic potential and possible hybridization, a One Health approach is essential for effective control. Given the dearth of knowledge on African trematodes, this study aimed to map snail and trematode diversity, focusing on (i) characterizing gastropod snail species and their trematode parasites, (ii) determining infection rates of snail species as intermediate hosts for medically, veterinary, and ecologically significant trematodes, and (iii) comparing their diversity across endemic regions.<br><br>METHODS: A cross-sectional study conducted in 2021 in Chiredzi and Wedza districts in Zimbabwe, known for high human schistosomiasis prevalence, involved malacological surveys at 56 sites. Trematode infections in snails were detected through shedding experiments and multiplex rapid diagnostic polymerase chain reactions (RD-PCRs). Morphological and molecular analyses were employed to identify snail and trematode species.<br><br>RESULTS: Among 3209 collected snail specimens, 11 species were identified, including schistosome and fasciolid competent snail species. We report for the first time the invasive exotic snail Tarebia granifera in Zimbabwe, which was highly abundant, mainly in Chiredzi, occurring at 29 out of 35 sites. Shedding experiments on 1303 snails revealed a 2.24% infection rate, with 15 trematode species identified through molecular genotyping. Five species were exclusive to Chiredzi: Bolbophorus sp., Schistosoma mansoni, Schistosoma mattheei, Calicophoron sp., and Uvulifer sp. Eight were exclusive to Wedza, including Trichobilharzia sp., Stephanoprora amurensis, Spirorchid sp., and Echinostoma sp. as well as an unidentified species of the Plagiorchioidea superfamily. One species, Tylodelphys mashonensis, was common to both regions. The RD-PCR screening of 976 non-shedding snails indicated a 35.7% trematode infection rate, including&#xa0;the presence of schistosomes (1.1%) Fasciola nyanzae (0.6%). In Chiredzi, Radix natalensis had the highest trematode infection prevalence (33.3%), while in Wedza, R. natalensis (55.4%) and Bulinus tropicus (53.2%) had the highest infection prevalence.<br><br>CONCLUSIONS: Our xenomonitoring approach unveiled 15 trematode species, including nine new records in Zimbabwe. Schistosoma mansoni persists in the study region despite six mass deworming rounds. The high snail and parasite diversity, including the presence of exotic snail species&#xa0;that can impact endemic species and biomedically important trematodes, underscores the need for increased monitoring.},
}
@article {pmid38773413,
year = {2024},
author = {Richardson, MA and Nenadic, N and Wingfield, M and McDougall, C},
title = {The development of multiplex PCR assays for the rapid identification of multiple Saccostrea species, and their practical applications in restoration and aquaculture.},
journal = {BMC ecology and evolution},
volume = {24},
number = {1},
pages = {67},
pmid = {38773413},
issn = {2730-7182},
mesh = {Animals ; *Multiplex Polymerase Chain Reaction/methods ; *Aquaculture/methods ; *DNA Barcoding, Taxonomic/methods ; *Electron Transport Complex IV/genetics ; *Ostreidae/genetics ; Queensland ; Species Specificity ; Conservation of Natural Resources/methods ; },
abstract = {BACKGROUND: The ecology and biology of oysters (Ostreidae) across the tropics is poorly understood. Morphological plasticity and shared characteristics among oysters have resulted in the misidentification of species, creating challenges for understanding basic species-specific biological information that is required for restoration and aquaculture. Genetic barcoding has proven essential for accurate species identification and understanding species geographic ranges. To reduce the costs of molecular species identification we developed multiplex assays using the cytochrome c oxidase subunit I (COI or cox1) barcoding gene for the rapid identification of five species of oysters within the genus Saccostrea that are commonly found in Queensland, Australia: Saccostrea glomerata, Saccostrea lineage B, Saccostrea lineage F, Saccostrea lineage G, and Saccostrea spathulata (lineage J).<br><br>RESULTS: Multiplex assays were successful in species-specific amplification of targeted species. The practical application of these primers was tested on wild spat collected from a pilot restoration project in Moreton Bay, Queensland, with identified species (S. glomerata, lineage B and lineage G) validated by Sanger sequencing. DNA sampling by extraction of oyster pallial fluid was also tested on adult oysters collected from the Noosa estuary in Queensland to assess whether oysters were able to be identified non-destructively. DNA concentrations as low as 1 ng/ &#x3bc;L still amplified in most cases, allowing for identification, and mortality at 6 weeks post pallial fluid collection was low (3 out of 104 sampled oysters).<br><br>CONCLUSION: These multiplex assays will be essential tools for species identification in future studies, and we successfully demonstrate their practical application in both restoration and aquaculture contexts in Queensland. The multiplex assays developed in this study outline easily replicable methods for the development of additional species-specific primer sets for the rapid identification of other species of Saccostrea found across the Indo-Pacific, which will be instrumental in unravelling the taxonomic ambiguities within this genus in tropical regions.},
}
@article {pmid38769096,
year = {2024},
author = {Hermansen, JU and Yin, Y and Rein, ID and Skånland, SS},
title = {Immunophenotyping with (phospho)protein profiling and fluorescent cell barcoding for single-cell signaling analysis and biomarker discovery.},
journal = {NPJ precision oncology},
volume = {8},
number = {1},
pages = {107},
pmid = {38769096},
issn = {2397-768X},
support = {322898//Norges Forskningsr&#xe5;d (Research Council of Norway)/ ; 19//Stiftelsen Kristian Gerhard Jebsen (Kristian Gerhard Jebsen Foundation)/ ; 328827//Kreftforeningen (Norwegian Cancer Society)/ ; },
abstract = {The microenvironment of hematologic cancers contributes to tumor cell survival and proliferation, as well as treatment resistance. Understanding tumor- and drug-induced changes to the immune cell composition and functionality is therefore critical for implementing optimal treatment strategies and for the development of novel cancer therapies. The liquid nature of peripheral blood makes this organ uniquely suited for single-cell studies by flow cytometry. (Phospho)protein profiles detected by flow cytometry analyses have been shown to correlate with ex vivo drug sensitivity and to predict treatment outcomes in hematologic cancers, demonstrating that this method is suitable for pre-clinical studies. Here, we present a flow cytometry protocol that combines multi-parameter immunophenotyping with single-cell (phospho)protein profiling. The protocol makes use of fluorescent cell barcoding, which means that multiple cell samples, either collected from different donors or exposed to different treatment conditions, can be combined and analyzed as one experiment. This reduces variability between samples, increases the throughput of the experiment, and lowers experimental costs. This protocol may serve as a guide for the use and further development of assays to study immunophenotype and cell signaling at single-cell resolution in normal and malignant cells. The read-outs may provide biological insight into cancer pathogenesis, identify novel drug targets, and ultimately serve as a biomarker to guide clinical decision-making.},
}
@article {pmid38768238,
year = {2024},
author = {Shukla, N and Roelle, SM and Snell, JC and DelSignore, O and Bruchez, AM and Matreyek, KA},
title = {Pseudotyped virus infection of multiplexed ACE2 libraries reveals SARS-CoV-2 variant shifts in receptor usage.},
journal = {PLoS pathogens},
volume = {20},
number = {5},
pages = {e1012044},
pmid = {38768238},
issn = {1553-7374},
support = {R21 AI169561/AI/NIAID NIH HHS/United States ; S10 OD021559/OD/NIH HHS/United States ; R21 AI161275/AI/NIAID NIH HHS/United States ; P30 CA043703/CA/NCI NIH HHS/United States ; R21 AI178151/AI/NIAID NIH HHS/United States ; R35 GM142886/GM/NIGMS NIH HHS/United States ; R21 AI156907/AI/NIAID NIH HHS/United States ; },
mesh = {*Angiotensin-Converting Enzyme 2/metabolism/genetics/chemistry ; Humans ; *SARS-CoV-2/genetics ; *Spike Glycoprotein, Coronavirus/genetics/metabolism/chemistry ; *COVID-19/virology/transmission ; Virus Internalization ; Receptors, Virus/metabolism/genetics ; HEK293 Cells ; Viral Pseudotyping ; Mutation ; },
abstract = {Pairwise compatibility between virus and host proteins can dictate the outcome of infection. During transmission, both inter- and intraspecies variabilities in receptor protein sequences can impact cell susceptibility. Many viruses possess mutable viral entry proteins and the patterns of host compatibility can shift as the viral protein sequence changes. This combinatorial sequence space between virus and host is poorly understood, as traditional experimental approaches lack the throughput to simultaneously test all possible combinations of protein sequences. Here, we created a pseudotyped virus infection assay where a multiplexed target-cell library of host receptor variants can be assayed simultaneously using a DNA barcode sequencing readout. We applied this assay to test a panel of 30 ACE2 orthologs or human sequence mutants for infectability by the original SARS-CoV-2 spike protein or the Alpha, Beta, Gamma, Delta, and Omicron BA1 variant spikes. We compared these results to an analysis of the structural shifts that occurred for each variant spike's interface with human ACE2. Mutated residues were directly involved in the largest shifts, although there were also widespread indirect effects altering interface structure. The N501Y substitution in spike conferred a large structural shift for interaction with ACE2, which was partially recreated by indirect distal substitutions in Delta, which does not harbor N501Y. The structural shifts from N501Y greatly influenced the set of animal orthologs the variant spike was capable of interacting with. Out of the thirteen non-human orthologs, ten exhibited unique patterns of variant-specific compatibility, demonstrating that spike sequence changes during human transmission can toggle ACE2 compatibility and potential susceptibility of other animal species, and cumulatively increase overall compatibilities as new variants emerge. These experiments provide a blueprint for similar large-scale assessments of protein compatibility during entry by diverse viruses. This dataset demonstrates the complex compatibility relationships that occur between variable interacting host and virus proteins.},
}
@article {pmid38766256,
year = {2024},
author = {Siniscalco, A and Perera, RP and Greenslade, JE and Masters, A and Doll, H and Raj, B},
title = {Barcoding Notch signaling in the developing brain.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38766256},
issn = {2692-8205},
support = {DP2 NS131787/NS/NINDS NIH HHS/United States ; R00 HD098298/HD/NICHD NIH HHS/United States ; },
abstract = {Developmental signaling inputs are fundamental for shaping cell fates and behavior. However, traditional fluorescent-based signaling reporters have limitations in scalability and molecular resolution of cell types. We present SABER-seq, a CRISPR-Cas molecular recorder that stores transient developmental signaling cues as permanent mutations in cellular genomes for deconstruction at later stages via single-cell transcriptomics. We applied SABER-seq to record Notch signaling in developing zebrafish brains. SABER-seq has two components: a signaling sensor and a barcode recorder. The sensor activates Cas9 in a Notch-dependent manner with inducible control while the recorder accumulates mutations that represent Notch activity in founder cells. We combine SABER-seq with an expanded juvenile brain atlas to define cell types whose fates are determined downstream of Notch signaling. We identified examples wherein Notch signaling may have differential impact on terminal cell fates. SABER-seq is a novel platform for rapid, scalable and high-resolution mapping of signaling activity during development.},
}
@article {pmid38766101,
year = {2024},
author = {Toledo-Rodriguez, DA and Veglia, A and Jimenez Marrero, NM and Gomez-Samot, JM and McFadden, CS and Weil, E and Schizas, NV},
title = {Shadows over Caribbean reefs: Identification of a new invasive soft coral species, Xenia umbellata, in southwest Puerto Rico.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38766101},
issn = {2692-8205},
support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; },
abstract = {In October 2023, several colonies of an alien soft coral species were reported on shallow reefs in southwest Puerto Rico. The soft coral was identified as a xeniid octocoral (species undetermined), resembling the octocoral Unomia stolonifera, which has invaded and overgrown reefs in Venezuela in recent years. To conclusively characterize the species of the invading xeniid, we employed multilocus barcoding targeting four genes (ND2, mtMutS, COI, and 28S) of three separate colonies across three locations in southwest Puerto Rico. Sequence comparisons with xeniid sequences from GenBank, including those from the genera Xenia and Unomia, indicated a 100% sequence identity (>3,000 bp combined) with the species Xenia umbellata (Octocorallia : Malacalcyonacea : Xeniidae). Xenia umbellata is native to the Red Sea and to our knowledge, this represents the first confirmed case of this species as an invader on Caribbean reefs. Similar to U. stolonifera, X. umbellata is well known for its ability to rapidly overgrow substrate as well as tolerate environmental extremes. In addition, X. umbellata has recently been proposed as a model system for tissue regeneration having the ability to regenerate completely from a single tentacle. These characteristics greatly amplify X. umbellata's potential to adversely affect any reef it invades. Our findings necessitate continued collaborative action between local management agencies and stakeholders in Puerto Rico, as well as neighboring islands, to monitor and control this invasion prior to significant ecological perturbation.},
}
@article {pmid38762544,
year = {2024},
author = {Hale, JJ and Matsui, T and Goldstein, I and Mullis, MN and Roy, KR and Ville, CN and Miller, D and Wang, C and Reynolds, T and Steinmetz, LM and Levy, SF and Ehrenreich, IM},
title = {Genome-scale analysis of interactions between genetic perturbations and natural variation.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4234},
pmid = {38762544},
issn = {2041-1723},
support = {R01 AI164530/AI/NIAID NIH HHS/United States ; R01 HG010378/HG/NHGRI NIH HHS/United States ; R35 GM130381/GM/NIGMS NIH HHS/United States ; 1R35GM130381//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*Saccharomyces cerevisiae/genetics ; *Epistasis, Genetic ; *Genome, Fungal ; Genetic Variation ; Genetic Fitness ; CRISPR-Cas Systems ; Phenotype ; DNA Barcoding, Taxonomic ; },
abstract = {Interactions between genetic perturbations and segregating loci can cause perturbations to show different phenotypic effects across genetically distinct individuals. To study these interactions on a genome scale in many individuals, we used combinatorial DNA barcode sequencing to measure the fitness effects of 8046 CRISPRi perturbations targeting 1721 distinct genes in 169 yeast cross progeny (or segregants). We identified 460 genes whose perturbation has different effects across segregants. Several factors caused perturbations to show variable effects, including baseline segregant fitness, the mean effect of a perturbation across segregants, and interacting loci. We mapped 234 interacting loci and found four hub loci that interact with many different perturbations. Perturbations that interact with a given hub exhibit similar epistatic relationships with the hub and show enrichment for cellular processes that may mediate these interactions. These results suggest that an individual's response to perturbations is shaped by a network of perturbation-locus interactions that cannot be measured by approaches that examine perturbations or natural variation alone.},
}
@article {pmid38761946,
year = {2024},
author = {Múrria, C and Wangensteen, OS and Somma, S and Väisänen, L and Fortuño, P and Arnedo, MA and Prat, N},
title = {Taxonomic accuracy and complementarity between bulk and eDNA metabarcoding provides an alternative to morphology for biological assessment of freshwater macroinvertebrates.},
journal = {The Science of the total environment},
volume = {935},
number = {},
pages = {173243},
doi = {10.1016/j.scitotenv.2024.173243},
pmid = {38761946},
issn = {1879-1026},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Invertebrates/genetics/classification ; *Fresh Water ; *Environmental Monitoring/methods ; *Biodiversity ; DNA, Environmental ; Ecosystem ; Biological Monitoring/methods ; },
abstract = {Determining biological status of freshwater ecosystems is critical for ensuring ecosystem health and maintaining associated services to such ecosystems. Freshwater macroinvertebrates respond predictably to environmental disturbances and are widely used in biomonitoring programs. However, many freshwater species are difficult to capture and sort from debris or substrate and morphological identification is challenging, especially larval stages, damaged specimens, or hyperdiverse groups such as Diptera. The advent of high throughput sequencing technologies has enhanced DNA barcoding tools to automatise species identification for whole communities, as metabarcoding is increasingly used to monitor biodiversity. However, recent comparisons have revealed little congruence between morphological and molecular-based identifications. Using broad range universal primers for DNA barcode marker cox1, we compare community composition captured between morphological and molecular-based approaches from different sources - tissue-based (bulk benthic and bulk drift samples) and environmental DNA (eDNA, filtered water) metabarcoding - for samples collected along a gradient of anthropogenic disturbances. For comparability, metabarcoding taxonomic assignments were filtered by taxa included in the standardised national biological metric IBMWP. At the family level, bulk benthic metabarcoding showed the highest congruence with morphology, and the most abundant taxa were captured by all techniques. Richness captured by morphology and bulk benthic metabarcoding decreased along the gradient, whereas richness recorded by eDNA remained constant and increased downstream when sequencing bulk drift. Estimates of biological metrics were higher using molecular than morphological identification. At species level, diversity captured by bulk benthic samples were higher than the other techniques. Importantly, bulk benthic and eDNA metabarcoding captured different and complementary portions of the community - benthic versus water column, respectively - and their combined use is recommended. While bulk benthic metabarcoding can likely replace morphology using similar benthic biological indices, water eDNA will require new metrics because this technique sequences a different portion of the community.},
}
@article {pmid38757413,
year = {2024},
author = {Tiono, YV and Prasetyo, AH and Wulanjati, MP and Wink, M and Nurcahyanti, ADR},
title = {Inhibition of oxidative stress of Biancaea sappan (L) Tod. from Java.},
journal = {Natural product research},
volume = {},
number = {},
pages = {1-7},
doi = {10.1080/14786419.2024.2355585},
pmid = {38757413},
issn = {1478-6427},
abstract = {Increased reactive oxygen species and advanced glycation end products are often associated with human ageing and degenerative diseases. Biancaea sappan L serves as a medicinal plant and a healthy drinks ingredient in Java. However, the pharmacological investigation of the plant native to this island is still lacking in depth. In the current study, DNA barcoding using the marker gene maturase K (matK), evaluation of the chemical composition, total phenolic content (TPC) and antioxidant properties, antiglycation, anti-β-amyloid, anti-inflammatory, and selective cytotoxic activities were performed. B. sappan shares well-known phytoconstituents with other members of the genus Biancaea. The heartwood ethanol extract possesses the most prominent antioxidant, anti-inflammatory, and anti-β-amyloid effects. The aqueous extract demonstrated a most substantial anti-glycation activity and was rich in phenolics. The ethanol extract from heartwood exhibited the highest cytotoxicity against SW-48, indicating B. sappan heartwood from Java holds promise as antioxidants and may selectively inhibit colorectal cancer.},
}
@article {pmid38756345,
year = {2024},
author = {Crabo, LG},
title = {A new noctuid genus and species (Lepidoptera, Noctuidae, Amphipyrinae, Psaphidini, Triocnemidina) from New Mexico and Texas, United States of America.},
journal = {ZooKeys},
volume = {1200},
number = {},
pages = {199-213},
pmid = {38756345},
issn = {1313-2989},
abstract = {Pooleagen. nov. is described for two noctuid species from southwestern United States: Pooleagrandimacula Barnes &amp; McDunnough, comb. nov., previously in Oxycnemis Grote, and Pooleapsaphidoidessp. nov.Poolea is compared to Oxycnemis (Amphipyrinae, Psaphidini, Triocnemidina) and is retained in the same subtribe. Adult moths and male and female genitalia of Poolea species are illustrated along with those of Oxycnemisadvena Grote, the genus type species. Pertinent recent taxonomic changes to Amphipyrinae classification are reviewed.},
}
@article {pmid38751964,
year = {2024},
author = {Li, Z and Zhang, F},
title = {Two new species of the genus Cheiracanthium C. L. Koch, 1839 (Araneae, Cheiracanthiidae) from China.},
journal = {ZooKeys},
volume = {1200},
number = {},
pages = {145-157},
pmid = {38751964},
issn = {1313-2989},
abstract = {Two species of the long-legged sac spider genus Cheiracanthium C. L. Koch, 1839 collected from China are diagnosed and described as new to science: Cheiracanthiumbannaensissp. nov. (♂♀) from Yunnan Province and C.bifurcatumsp. nov. (♂♀) from Xinjiang Uyger Autonomous Region. Photos of the habitus and copulatory organs are given. In addition, DNA barcode information of the two new species is provided.},
}
@article {pmid38750233,
year = {2024},
author = {Karras, P and Black, JRM and McGranahan, N and Marine, JC},
title = {Decoding the interplay between genetic and non-genetic drivers of metastasis.},
journal = {Nature},
volume = {629},
number = {8012},
pages = {543-554},
pmid = {38750233},
issn = {1476-4687},
mesh = {Animals ; Humans ; *Neoplasm Metastasis/drug therapy/genetics ; *Neoplasms/drug therapy/genetics/pathology ; Single-Cell Analysis ; Multiomics ; Molecular Typing ; Cellular Reprogramming ; },
abstract = {Metastasis is a multistep process by which cancer cells break away from their original location and spread to distant organs, and is responsible for the vast majority of cancer-related deaths. Preventing early metastatic dissemination would revolutionize the ability to fight cancer. Unfortunately, the relatively poor understanding of the molecular underpinnings of metastasis has hampered the development of effective anti-metastatic drugs. Although it is now accepted that disseminating tumour cells need to acquire multiple competencies to face the many obstacles they encounter before reaching their metastatic site(s), whether these competencies are acquired through an accumulation of metastasis-specific genetic alterations and/or non-genetic events is often debated. Here we review a growing body of literature highlighting the importance of both genetic and non-genetic reprogramming events during the metastatic cascade, and discuss how genetic and non-genetic processes act in concert to confer metastatic competencies. We also describe how recent technological advances, and in particular the advent of single-cell multi-omics and barcoding approaches, will help to better elucidate the cross-talk between genetic and non-genetic mechanisms of metastasis and ultimately inform innovative paths for the early detection and interception of this lethal process.},
}
@article {pmid38746545,
year = {2024},
author = {Quattrini, AM and McCartin, LJ and Easton, EE and Horowitz, J and Wirshing, HH and Bowers, H and Mitchell, K and González-García, MDP and Sei, M and McFadden, CS and Herrera, S},
title = {Skimming genomes for systematics and DNA barcodes of corals.},
journal = {Ecology and evolution},
volume = {14},
number = {5},
pages = {e11254},
pmid = {38746545},
issn = {2045-7758},
abstract = {Numerous genomic methods developed over the past two decades have enabled the discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa and scales. Genome skimming (or low-coverage genome sequencing) is a promising method to not only extract high-copy loci but also 100s to 1000s of phylogenetically informative nuclear loci (e.g., ultraconserved elements [UCEs] and exons) from contemporary and museum samples. The subphylum Anthozoa, including important ecosystem engineers (e.g., stony corals, black corals, anemones, and octocorals) in the marine environment, is in critical need of phylogenetic resolution and thus might benefit from a genome-skimming approach. We conducted genome skimming on 242 anthozoan corals collected from 1886 to 2022. Using existing target-capture baitsets, we bioinformatically obtained UCEs and exons from the genome-skimming data and incorporated them with data from previously published target-capture studies. The mean number of UCE and exon loci extracted from the genome skimming data was 1837 ± 662 SD for octocorals and 1379 ± 476 SD loci for hexacorals. Phylogenetic relationships were well resolved within each class. A mean of 1422 ± 720 loci was obtained from the historical specimens, with 1253 loci recovered from the oldest specimen collected in 1886. We also obtained partial to whole mitogenomes and nuclear rRNA genes from >95% of samples. Bioinformatically pulling UCEs, exons, mitochondrial genomes, and nuclear rRNA genes from genome skimming data is a viable and low-cost option for phylogenetic studies. This approach can be used to review and support taxonomic revisions and reconstruct evolutionary histories, including historical museum and type specimens.},
}
@article {pmid38746196,
year = {2024},
author = {Andriienko, V and Buczek, M and Meier, R and Srivathsan, A and Łukasik, P and Kolasa, MR},
title = {Implementing high-throughput insect barcoding in microbiome studies: impact of non-destructive DNA extraction on microbiome reconstruction.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38746196},
issn = {2692-8205},
support = {R35 GM124701/GM/NIGMS NIH HHS/United States ; },
abstract = {BACKGROUND: Symbiotic relationships with diverse microorganisms are crucial for many aspects of insect biology. However, while our understanding of insect taxonomic diversity and the distribution of insect species in natural communities is limited, we know much less about their microbiota. In the era of rapid biodiversity declines, as researchers increasingly turn towards DNA-based monitoring, developing and broadly implementing approaches for high-throughput and cost-effective characterization of both insect and insect-associated microbial diversity is essential. We need to verify whether approaches such as high-throughput barcoding, a powerful tool for identifying wild insects, would permit subsequent microbiota reconstruction in these specimens.<br><br>METHODS: High-throughput barcoding ("megabarcoding") methods often rely on non-destructive approaches for obtaining template DNA for PCR amplification by leaching DNA out of insect specimens using alkaline buffers such as HotSHOT. This study investigated the impact of HotSHOT on microbial abundance estimates and the reconstructed bacterial community profiles. We addressed this question by comparing quantitative 16S rRNA amplicon sequencing data for HotSHOT-treated or untreated specimens of 16 insect species representing six orders and selected based on the expectation of limited variation among individuals.<br><br>RESULTS: We find that in 13 species, the treatment significantly reduced microbial abundance estimates, corresponding to an estimated 15-fold decrease in amplifiable 16S rRNA template on average. On the other hand, HotSHOT pre-treatment had a limited effect on microbial community composition. The reconstructed presence of abundant bacteria with known significant effects was not affected. On the other hand, we observed changes in the presence of low-abundance microbes, those close to the reliable detection threshold. Alpha and beta diversity analyses showed compositional differences in only a few species.<br><br>CONCLUSION: Our results indicate that HotSHOT pre-treated specimens remain suitable for microbial community composition reconstruction, even if abundance may be hard to estimate. These results indicate that we can cost-effectively combine barcoding with the study of microbiota across wild insect communities. Thus, the voucher specimens obtained using megabarcoding studies targeted at characterizing insect communities can be used for microbiome characterizations. This can substantially aid in speeding up the accumulation of knowledge on the microbiomes of abundant and hyperdiverse insect species.},
}
@article {pmid38746155,
year = {2024},
author = {Su, C and Chandradoss, KR and Malachowski, T and Boya, R and Ryu, HS and Brennand, KJ and Phillips-Cremins, JE},
title = {MASTR-seq: Multiplexed Analysis of Short Tandem Repeats with sequencing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.29.591790},
pmid = {38746155},
issn = {2692-8205},
support = {R01 MH120269/MH/NIMH NIH HHS/United States ; DP1 MH129957/MH/NIMH NIH HHS/United States ; U01 DA052715/DA/NIDA NIH HHS/United States ; F31 NS129317/NS/NINDS NIH HHS/United States ; U01 DK127405/DK/NIDDK NIH HHS/United States ; },
abstract = {UNLABELLED: More than 60 human disorders have been linked to unstable expansion of short tandem repeat (STR) tracts. STR length and the extent of DNA methylation is linked to disease pathology and can be mosaic in a cell type-specific manner in several repeat expansion disorders. Mosaic phenomenon have been difficult to study to date due to technical bias intrinsic to repeat sequences and the need for multi-modal measurements at single-allele resolution. Nanopore long-read sequencing accurately measures STR length and DNA methylation in the same single molecule but is cost prohibitive for studies assessing a target locus across multiple experimental conditions or patient samples. Here, we describe MASTR-seq, M ultiplexed A nalysis of S hort T andem R epeats, for cost-effective, high-throughput, accurate, multi-modal measurements of DNA methylation and STR genotype at single-allele resolution. MASTR-seq couples long-read sequencing, Cas9-mediated target enrichment, and PCR-free multiplexed barcoding to achieve a >ten-fold increase in on-target read mapping for 8-12 pooled samples in a single MinION flow cell. We provide a detailed experimental protocol and computational tools and present evidence that MASTR-seq quantifies tract length and DNA methylation status for CGG and CAG STR loci in normal-length and mutation-length human cell lines. The MASTR-seq protocol takes approximately eight days for experiments and one additional day for data processing and analyses.<br><br>KEY POINTS: We provide a protocol for MASTR-seq: M ultiplexed A nalysis of S hort T andem R epeats using Cas9-mediated target enrichment and PCR-free, multiplexed nanopore sequencing. MASTR-seq achieves a >10-fold increase in on-target read proportion for highly repetitive, technically inaccessible regions of the genome relevant for human health and disease.MASTR-seq allows for high-throughput, efficient, accurate, and cost-effective measurement of STR length and DNA methylation in the same single allele for up to 8-12 samples in parallel in one Nanopore MinION flow cell.},
}
@article {pmid38744526,
year = {2024},
author = {Dreyer, N and Olesen, J and Grygier, MJ and Eibye-Jacobsen, D and Savchenko, AS and Fujita, Y and Kolbasov, GA and Machida, RJ and Chan, BKK and Palero, F},
title = {Novel molecular resources for single-specimen barcoding of enigmatic crustacean y-larvae.},
journal = {Invertebrate systematics},
volume = {38},
number = {},
pages = {},
doi = {10.1071/IS23018},
pmid = {38744526},
issn = {1447-2600},
mesh = {Animals ; *Crustacea/classification/genetics ; *DNA Barcoding, Taxonomic/methods ; Larva/genetics ; Phylogeny ; },
abstract = {Despite discovery more than 100years ago and documented global occurrence from shallow waters to the deep sea, the life cycle of the enigmatic crustacean y-larvae isincompletely understood and adult forms remain unknown. To date, only 2 of the 17 formally described species, all based on larval stages, have been investigated using an integrative taxonomic approach. This approach provided descriptions of the morphology of the naupliar and cyprid stages, and made use of exuvial voucher material and DNA barcodes. To improve our knowledge about the evolutionary history and ecological importance of y-larvae, we developed a novel protocol that maximises the amount of morpho-ecological and molecular data that can be harvested from single larval specimens. This includes single-specimen DNA barcoding and daily imaging of y-nauplii reared in culture dishes, mounting of the last naupliar exuviae on a slide as a reference voucher, live imaging of the y-cyprid instar that follows, and fixation, DNA extraction, amplification and sequencing of the y-cyprid specimen. Through development and testing of a suite of new primers for both nuclear and mitochondrial protein-coding and ribosomal genes, we showcase how new sequence data can be used to estimate the phylogeny of Facetotecta. We expect that our novel procedure will help to unravel the complex systematics of y-larvae and show how these fascinating larval forms have evolved. Moreover, we posit that our protocols should work on larval specimens from a diverse array of moulting marine invertebrate taxa.},
}
@article {pmid38742850,
year = {2024},
author = {Neven, LG and Walker, WB and Gowton, C and Carrillo, J},
title = {Using eDNA to play whack-a-mole with invasive species in green yard waste.},
journal = {Journal of economic entomology},
volume = {117},
number = {3},
pages = {918-927},
doi = {10.1093/jee/toae090},
pmid = {38742850},
issn = {1938-291X},
support = {K2530//Washington State Department of Agriculture/ ; },
mesh = {*Introduced Species ; Animals ; *DNA, Environmental/analysis ; Washington ; Insecta/genetics ; British Columbia ; Waste Disposal Facilities ; DNA Barcoding, Taxonomic ; },
abstract = {As large cities begin to overrun their landfill capacities, they begin to look for alternative locations to handle the waste stream. Seeing an opportunity to bring in revenue, rural communities offer to handle municipal waste in their landfills. However, many rural communities are also places of agricultural production, which are vulnerable to attacks by invasive insect species, which could be present in green yard waste, the component of municipal waste most likely to contain agriculturally harmful insect species. We used environmental DNA (eDNA) to determine whether green yard waste could be a pathway for invasive insect species to enter and establish in the landfill-receiving agricultural community. We identified several target species that could be in green yard waste coming from Vancouver, BC, Canada, to Central Washington State, USA. We sampled green yard waste from 3 sites every 2 weeks from June to October in 2019 and 2020. DNA was extracted from the nearly 400 samples and subjected to amplification with COI barcoding primers followed by sequencing to identify target insects in the samples. Sequence analyses identified 3 species from the target list: 2 species that are pests of deciduous tree fruits and a generalist root-feeding crop pest. This eDNA technique was useful in identifying potential invasive species in green yard waste and may prove to be an important tool informing policy on the movement of biological material across borders and stemming the spread of invasive species.},
}
@article {pmid38742184,
year = {2024},
author = {Tarkhnishvili, D and Seropian, A and Erhardt, C and Kachlishvili, N and Krammer, HJ and Hein, N},
title = {How dispersal rates depend on the prey capture strategy: A case study of Georgia's spiders.},
journal = {Ecology and evolution},
volume = {14},
number = {5},
pages = {e11372},
pmid = {38742184},
issn = {2045-7758},
abstract = {Large-scale barcoding projects help to aggregate information on genetic variability of multiple species throughout their ranges. Comparing DNA sequences of both non-conspecific and conspecific individuals from distant parts of their ranges helps to compare level of genetic isolation-by-distance patterns in different species and adaptive types. We compared mitochondrial CO1 gene sequences of 223 spiders from Georgia (Caucasus), representing 124 species and eight families, with 3097 homological sequences from spiders mostly from Europe, but also from other parts of the World. In most families, a significant isolation-by distance pattern was observed on family level. On species level, a significant isolation-by-distance was observed in 40 species, although this low proportion is most likely related to a lack of data. Simultaneously, remarkable differences in spatial structure were shown for different species. Although the majority of the studied species have a broad western Palearctic range, web-building spiders from families Araneidae, Theridiidae, and Linyphiidae are less isolated spatially than flower spiders (Thomisidae), jumping spiders (Salticidae), wolf spiders (Lycosidae), sac spiders (Clubionidae), and ground spiders (Gnaphosidae). This pattern is related with more common ballooning in web building than in actively hunting spiders, which commonly remain isolated since preglacial time. Ground spiders build the most isolated populations in the Caucasus.},
}
@article {pmid38741893,
year = {2024},
author = {Musa, S and Hemberle, T and Bensch, S and Palinauskas, V and Baltrūnaitė, L and Woog, F and Mackenstedt, U},
title = {Raising the bar: genus-specific nested PCR improves detection and lineage identification of avian haemosporidian parasites.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1385599},
pmid = {38741893},
issn = {2235-2988},
mesh = {Animals ; *Haemosporida/genetics/isolation &amp; purification/classification ; *Polymerase Chain Reaction/methods ; *Protozoan Infections, Animal/diagnosis/parasitology ; Bird Diseases/parasitology/diagnosis ; Birds/parasitology ; Phylogeny ; Sensitivity and Specificity ; Passeriformes/parasitology ; DNA, Protozoan/genetics ; },
abstract = {Avian haemosporidian parasites are useful model organisms to study the ecology and evolution of parasite-host interactions due to their global distribution and extensive biodiversity. Detection of these parasites has evolved from microscopic examination to PCR-based methods, with the mitochondrial cytochrome b gene serving as barcoding region. However, standard PCR protocols used for screening and identification purposes have limitations in detecting mixed infections and generating phylogenetically informative data due to short amplicon lengths. To address these issues, we developed a novel genus-specific nested PCR protocol targeting avian haemosporidian parasites. The protocol underwent rigorous testing utilizing a large dataset comprising blood samples from Malagasy birds of three distinct Passeriformes families. Furthermore, validation was done by examining smaller datasets in two other laboratories employing divergent master mixes and different bird species. Comparative analyses were conducted between the outcomes of the novel PCR protocol and those obtained through the widely used standard nested PCR method. The novel protocol enables specific identification of Plasmodium, Haemoproteus (Parahaemoproteus), and Leucocytozoon parasites. The analyses demonstrated comparable sensitivity to the standard nested PCR with notable improvements in detecting mixed infections. In addition, phylogenetic resolution is improved by amplification of longer fragments, leading to a better understanding of the haemosporidian biodiversity and evolution. Overall, the novel protocol represents a valuable addition to avian haemosporidian detection methodologies, facilitating comprehensive studies on parasite ecology, epidemiology, and evolution.},
}
@article {pmid38740284,
year = {2024},
author = {Qin, T and Hernandez, SER and Shiers, J and Crittall, M and Novak, A and Smith, CS},
title = {A decentralized solid compound storage facility managed by a centralized electronic platform at a growing drug discovery company.},
journal = {SLAS technology},
volume = {29},
number = {3},
pages = {100143},
doi = {10.1016/j.slast.2024.100143},
pmid = {38740284},
issn = {2472-6311},
mesh = {*Drug Discovery ; *Drug Storage ; Drug Industry ; },
abstract = {Within a growing drug discovery company, scientists acquire (either through in house synthesis or purchase) then store, retrieve, and ship solid compound samples daily between multiple locations. The efficient management and tracking of this entire process to support drug discovery is a significant challenge. This article describes a decentralized and cost-effective inventory facility that simplifies the solid compound storage and retrieval process. Standardized storage cabinets from the market are utilized, providing a cost-effective physical infrastructure. The cabinets can be distributed across storage rooms at multiple sites and arranged into spaces with a variety of dimensions, allowing the system to be retrofitted into existing facilities and scaled up easily. We can provide storage close to work areas at each location, minimizing both unnecessary movement of staff and transportation of substances. We have applied a systematic barcoding method to the compound batch identifier that correlates with its compound location. This simplifies the compound registration process as well as the process of finding and returning compounds. Additionally, a centralized electronic platform has been employed to store, update and track solid compound information, such as properties, location and quantity. Compound shipment may be initiated from different sites, and a centralized electronic platform assists the information retrieval process, ensuring each location possesses up-to-date information. The electronic platform we present streamlines the management of compound registration, location tracking, weight updates and shipment information, facilitating seamless record sharing among all stakeholders. Every step of the process can be tracked in real time by the project team. The platform can be flexibly configured to adapt to an evolving set of storage locations, with all information and processes being audited.},
}
@article {pmid38739854,
year = {2024},
author = {Dos Santos, EL and Xavier, JKAM and Galvão, PLN and Carneiro Nunes, AR and Alegria, OVC and Moreira, ECO and Maia, JGS and Setzer, WN and Figueiredo, PLB and da Silva, JKR},
title = {Volatile Profiles and DNA Barcodes of Myrtaceae Species with Occurrence in the Brazilian Amazon.},
journal = {Chemistry &amp; biodiversity},
volume = {21},
number = {7},
pages = {e202400388},
doi = {10.1002/cbdv.202400388},
pmid = {38739854},
issn = {1612-1880},
support = {//Aromatic Plant Research Center/ ; },
mesh = {*DNA Barcoding, Taxonomic ; Brazil ; *Oils, Volatile/chemistry ; *Myrtaceae/chemistry/genetics ; Plant Leaves/chemistry ; DNA, Plant/genetics ; },
abstract = {Myrtaceae family includes many species with taxonomic challenges, making it one of the most complex families to identify. This study used DNA barcoding to find molecular markers for species authentication based on the Myrtaceae family's chemical composition and genetic diversity. Essential oils and genetic material were extracted from the leaves of six different species: Eugenia uniflora, E. patrisii, Myrcia splendens, Psidium guajava, P. guineense, and Psidium sp. The samples were analyzed based on compound classes and grouped into two categories. Group I included samples with high amounts of oxygenated sesquiterpenes (3.69-76.05 %) and fatty acid derivatives (0.04-43.59 %), such as E. uniflora, Myrcia splendens, and E. patrisii. Group II included samples P. guajava, P. guineense, and Psidium sp., which had a significant content of monoterpene hydrocarbons (0.69-72.35 %), oxygenated sesquiterpenes (8.06-68.1 %), phenylpropanoids (0.45-22.59 %), and sesquiterpene hydrocarbons (0.27-21.84 %). The PsbA-trnH gene sequences had a high genetic variability, allowing the species to be distinguished. A phylogenetic analysis showed two main clusters with high Bootstrap values corresponding to the subtribes Eugeniineae, Myrciinae, and Pimentinae. The results suggest a weak correlation between genetic and chemical data in these Myrtaceae species.},
}
@article {pmid38737823,
year = {2024},
author = {Wang, T and Shen, H and Xu, B and Yang, W and Chen, S and Chen, J},
title = {Genome Analysis of Plasmodium falciparum: A Preliminary Observation - Sierra Leone, 2022-2023.},
journal = {China CDC weekly},
volume = {6},
number = {17},
pages = {368-373},
pmid = {38737823},
issn = {2096-7071},
abstract = {Sierra Leone, with a gross domestic product (GDP) per capita below $300 and significant poverty, ranks among the world's least developed countries (LDCs). Despite its modest population of 8.6 million, the nation reports approximately 2.6 million malaria cases annually. Previously, there has been no reporting on the malaria genome data from this country.<br><br>WHAT IS ADDED BY THIS REPORT?: In this study, we present the first reported whole-genome sequence analysis of 19 high parasite-density Plasmodium falciparum isolates from Sierra Leone, providing insights into the genomic epidemiology of this high-prevalence area. We found a high degree of relatedness among infections and substantial genetic diversity, consistent with the gradual reduction in overall case numbers. Moreover, our whole-genome analysis revealed that, beyond drug-resistance genes, gene families related to blood cell invasion, immune evasion, and others are undergoing directional selection. This suggests that the population in Sierra Leone has developed a relatively strong acquired immunity.<br><br>The genomic data not only facilitate the creation of single nucleotide polymorphism barcodes for case tracking but also enable the analysis of evolving transmission dynamics and selection pressures. Additionally, the samples from Sierra Leone exhibited higher selective pressures on resistance genes compared to those from Asia, a trend not commonly observed in other African samples. This suggests that less stringent healthcare systems and inconsistent treatment strategies can subject parasites to increased drug pressure, thereby accelerating the development of resistant strains.},
}
@article {pmid38734639,
year = {2024},
author = {Bušić, N and Klobučar, A and Landeka, N and Žitko, T and Vignjević, G and Turić, N and Sudarić Bogojević, M and Merdić, E and Kučinić, M and Bruvo Mađarić, B},
title = {A DNA barcode reference library of Croatian mosquitoes (Diptera: Culicidae): implications for identification and delimitation of species, with notes on the distribution of potential vector species.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {216},
pmid = {38734639},
issn = {1756-3305},
support = {IP-2016-06-9988//Croatian Science Foundation/ ; IP-2016-06-9988//Croatian Science Foundation/ ; IP-2016-06-9988//Croatian Science Foundation/ ; IP-2016-06-9988//Croatian Science Foundation/ ; IP-2016-06-9988//Croatian Science Foundation/ ; IP-2016-06-9988//Croatian Science Foundation/ ; IP-2016-06-9988//Croatian Science Foundation/ ; ZUP-2018-55, 3105-5//Josip Juraj Strossmayer University of Osijek/ ; ZUP-2018-55, 3105-5//Josip Juraj Strossmayer University of Osijek/ ; ZUP-2018-55, 3105-5//Josip Juraj Strossmayer University of Osijek/ ; ZUP-2018-55, 3105-5//Josip Juraj Strossmayer University of Osijek/ ; },
mesh = {*Culicidae/anatomy &amp; histology/classification/genetics ; Mosquito Vectors/anatomy &amp; histology/classification/genetics ; *DNA Barcoding, Taxonomic/methods ; Cyclooxygenase 1/genetics ; DNA, Ribosomal Spacer/genetics ; Phylogeny ; },
abstract = {BACKGROUND: Mosquitoes pose a risk to human health worldwide, and correct species identification and detection of cryptic species are the most important keys for surveillance and control of mosquito vectors. In addition to traditional identification based on morphology, DNA barcoding has recently been widely used as a complementary tool for reliable identification of mosquito species. The main objective of this study was to create a reference DNA barcode library for the Croatian mosquito fauna, which should contribute to more accurate and faster identification of species, including cryptic species, and recognition of relevant vector species.<br><br>METHODS: Sampling was carried out in three biogeographical regions of Croatia over six years (2017-2022). The mosquitoes were morphologically identified; molecular identification was based on the standard barcoding region of the mitochondrial COI gene and the nuclear ITS2 region, the latter to identify species within the Anopheles maculipennis complex. The BIN-RESL algorithm assigned the COI sequences to the corresponding BINs (Barcode Index Number clusters) in BOLD, i.e. to putative MOTUs (Molecular Operational Taxonomic Units). The bPTP and ASAP species delimitation methods were applied to the genus datasets in order to verify/confirm the assignment of specimens to specific MOTUs.<br><br>RESULTS: A total of 405 mosquito specimens belonging to six genera and 30 morphospecies were collected and processed. Species delimitation methods assigned the samples to 31 (BIN-RESL), 30 (bPTP) and 28 (ASAP) MOTUs, with most delimited MOTUs matching the morphological identification. Some species of the genera Culex, Aedes and Anopheles were assigned to the same MOTUs, especially species that are difficult to distinguish morphologically and/or represent species complexes. In total, COI barcode sequences for 34 mosquito species and ITS2 sequences for three species of the genus Anopheles were added to the mosquito sequence database for Croatia, including one individual from the Intrudens Group, which represents a new record for the Croatian mosquito fauna.<br><br>CONCLUSION: We present the results of the first comprehensive study combining morphological and molecular identification of most mosquito species present in Croatia, including several invasive and vector species. With the exception of some closely related species, this study confirmed that DNA barcoding based on COI provides a reliable basis for the identification of mosquito species in Croatia.},
}
@article {pmid38734030,
year = {2024},
author = {Stanley, S and Spaulding, CN and Liu, Q and Chase, MR and Ha, DTM and Thai, PVK and Lan, NH and Thu, DDA and Quang, NL and Brown, J and Hicks, ND and Wang, X and Marin, M and Howard, NC and Vickers, AJ and Karpinski, WM and Chao, MC and Farhat, MR and Caws, M and Dunstan, SJ and Thuong, NTT and Fortune, SM},
title = {Identification of bacterial determinants of tuberculosis infection and treatment outcomes: a phenogenomic analysis of clinical strains.},
journal = {The Lancet. Microbe},
volume = {5},
number = {6},
pages = {e570-e580},
pmid = {38734030},
issn = {2666-5247},
support = {75N93019C00071/AI/NIAID NIH HHS/United States ; T32 AI049928/AI/NIAID NIH HHS/United States ; T32 AI007535/AI/NIAID NIH HHS/United States ; T32 GM135014/GM/NIGMS NIH HHS/United States ; U19 AI142793/AI/NIAID NIH HHS/United States ; P01 AI132130/AI/NIAID NIH HHS/United States ; P01 AI143575/AI/NIAID NIH HHS/United States ; T32 HD040128/HD/NICHD NIH HHS/United States ; U19 AI107774/AI/NIAID NIH HHS/United States ; T32 AI132120/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Mycobacterium tuberculosis/genetics/drug effects ; *Tuberculosis/drug therapy/microbiology ; Vietnam/epidemiology ; *Antitubercular Agents/therapeutic use/pharmacology ; Genome-Wide Association Study ; Treatment Outcome ; Phenotype ; Phylogeny ; Mutation ; Phenomics ; Genotype ; Female ; Adult ; Male ; },
abstract = {BACKGROUND: Bacterial diversity could contribute to the diversity of tuberculosis infection and treatment outcomes observed clinically, but the biological basis of this association is poorly understood. The aim of this study was to identify associations between phenogenomic variation in Mycobacterium tuberculosis and tuberculosis clinical features.<br><br>METHODS: We developed a high-throughput platform to define phenotype-genotype relationships in M tuberculosis clinical isolates, which we tested on a set of 158 drug-sensitive M tuberculosis strains sampled from a large tuberculosis clinical study in Ho Chi Minh City, Viet Nam. We tagged the strains with unique genetic barcodes in multiplicate, allowing us to pool the strains for in-vitro competitive fitness assays across 16 host-relevant antibiotic and metabolic conditions. Relative fitness was quantified by deep sequencing, enumerating output barcode read counts relative to input normalised values. We performed a genome-wide association study to identify phylogenetically linked and monogenic mutations associated with the in-vitro fitness phenotypes. These genetic determinants were further associated with relevant clinical outcomes (cavitary disease and treatment failure) by calculating odds ratios (ORs) with binomial logistic regressions. We also assessed the population-level transmission of strains associated with cavitary disease and treatment failure using terminal branch length analysis of the phylogenetic data.<br><br>FINDINGS: M tuberculosis clinical strains had diverse growth characteristics in host-like metabolic and drug conditions. These fitness phenotypes were highly heritable, and we identified monogenic and phylogenetically linked variants associated with the fitness phenotypes. These data enabled us to define two genetic features that were associated with clinical outcomes. First, mutations in Rv1339, a phosphodiesterase, which were associated with slow growth in glycerol, were further associated with treatment failure (OR 5&#xb7;34, 95% CI 1&#xb7;21-23&#xb7;58, p=0&#xb7;027). Second, we identified a phenotypically distinct slow-growing subclade of lineage 1 strains (L1.1.1.1) that was associated with cavitary disease (OR 2&#xb7;49, 1&#xb7;11-5&#xb7;59, p=0&#xb7;027) and treatment failure (OR 4&#xb7;76, 1&#xb7;53-14&#xb7;78, p=0&#xb7;0069), and which had shorter terminal branch lengths on the phylogenetic tree, suggesting increased transmission.<br><br>INTERPRETATION: Slow growth under various antibiotic and metabolic conditions served as in-vitro intermediate phenotypes underlying the association between M tuberculosis monogenic and phylogenetically linked mutations and outcomes such as cavitary disease, treatment failure, and transmission potential. These data suggest that M&#xa0;tuberculosis growth regulation is an adaptive advantage for bacterial success in human populations, at least in some circumstances. These data further suggest markers for the underlying bacterial processes that contribute to these clinical outcomes.<br><br>FUNDING: National Health and Medical Research Council/A&#x2217;STAR, National Institutes of Allergy and Infectious Diseases, National Institute of Child Health and Human Development, and the Wellcome Trust Fellowship in Public Health and Tropical Medicine.},
}
@article {pmid38732467,
year = {2024},
author = {Kim, JH and Doh, EJ and Kim, HY and Lee, G},
title = {Chemical Relationship among Genetically Authenticated Medicinal Species of Genus Angelica.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {9},
pages = {},
pmid = {38732467},
issn = {2223-7747},
support = {NRF-2021R1A2C1095558//the National Research Foundation of Korea/ ; },
abstract = {The genus Angelica comprises various species utilized for diverse medicinal purposes, with differences attributed to the varying levels or types of inherent chemical components in each species. This study employed DNA barcode analysis and HPLC analysis to genetically authenticate and chemically classify eight medicinal Angelica species (n = 106) as well as two non-medicinal species (n = 14) that have been misused. Nucleotide sequence analysis of the nuclear internal transcribed spacer (ITS) region revealed differences ranging from 11 to 117 bp, while psbA-trnH showed variances of 3 to 95 bp, respectively. Phylogenetic analysis grouped all samples except Angelica sinensis into the same cluster, with some counterfeits forming separate clusters. Verification using the NCBI database confirmed the feasibility of species identification. For chemical identification, a robust quantitative HPLC analysis method was developed for 46 marker compounds. Subsequently, two A. reflexa-specific and seven A. biserrata-specific marker compounds were identified, alongside non-specific markers. Moreover, chemometric clustering analysis reflecting differences in chemical content between species revealed that most samples formed distinct clusters according to the plant species. However, some samples formed mixed clusters containing different species. These findings offer crucial insights for the standardization and quality control of medicinal Angelica species.},
}
@article {pmid38731365,
year = {2024},
author = {Ricardo, F and Lopes, ML and Mamede, R and Domingues, MR and Ferreira da Silva, E and Patinha, C and Calado, R},
title = {Combined Use of Fatty Acid Profiles and Elemental Fingerprints to Trace the Geographic Origin of Live Baits for Sports Fishing: The Solitary Tube Worm (Diopatra neapolitana, Annelida, Onuphidae) as a Case Study.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {9},
pages = {},
pmid = {38731365},
issn = {2076-2615},
support = {TC-C10-i01//Desenvolvimento do Projeto de Refor&#xe7;o do Polo de Aveiro (H4)", framed within Measure 10 of Investment TC-C10-i01 - Hub Azul - Rede de Infraestruturas para a Economia Azul, financed by the Recovery and Resilience Plan (PRR) and supported by Fundo Azul of t/ ; + UIDB/50017/2020+ LA/P/0094/2020 + UIDB/50006/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; },
abstract = {Diopatra neapolitana Delle Chiaje, 1841 (Annelida, Onuphidae) is one of the most exploited polychaete species in European waters, particularly in Ria de Aveiro, a coastal lagoon in mainland Portugal, where the overexploitation of this resource has led to a generalized decline of local populations. In an attempt to reduce the impact of harvesting, several management actions were implemented, but illegal poaching still fuels a parallel economy that threatens the sustainable use of this marine resource. The present study evaluated the combination of fatty acid profiles and elemental fingerprints of the whole body and jaws, respectively, of D. neapolitana collected from four harvesting locations within Ria de Aveiro in order to determine if their geographic origin could be correctly assigned post-harvesting. Results showed that both fatty acid profiles and elemental fingerprints differ significantly among locations, discriminating the geographic origin with higher accuracy when combining these two natural barcodes than when employing each individually. The present work can, therefore, contribute to the implementation of an effective management plan for the sustainable use of this marine resource, making it possible to detect if D. neapolitana was sourced from no-take zones and if it was collected from the place of origin claimed by live bait traders.},
}
@article {pmid38729950,
year = {2024},
author = {Cheng, C and Wang, G and Zhu, Y and Wu, H and Zhang, L and Liu, Z and Huang, Y and Zhang, J},
title = {Multiplexed bulk and single-cell RNA-seq hybrid enables cost-efficient disease modeling with chimeric organoids.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3946},
pmid = {38729950},
issn = {2041-1723},
support = {31871453//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Organoids/metabolism ; *Single-Cell Analysis/methods ; *Induced Pluripotent Stem Cells/metabolism/cytology ; Humans ; *Cell Differentiation/genetics ; *RNA-Seq/methods ; Sequence Analysis, RNA/methods ; Macrophages/metabolism/cytology ; Animals ; Single-Cell Gene Expression Analysis ; },
abstract = {Disease modeling with isogenic Induced Pluripotent Stem Cell (iPSC)-differentiated organoids serves as a powerful technique for studying disease mechanisms. Multiplexed coculture is crucial to mitigate batch effects when studying the genetic effects of disease-causing variants in differentiated iPSCs or organoids, and demultiplexing at the single-cell level can be conveniently achieved by assessing natural genetic barcodes. Here, to enable cost-efficient time-series experimental designs via multiplexed bulk and single-cell RNA-seq of hybrids, we introduce a computational method in our Vireo Suite, Vireo-bulk, to effectively deconvolve pooled bulk RNA-seq data by genotype reference, and thereby quantify donor abundance over the course of differentiation and identify differentially expressed genes among donors. Furthermore, with multiplexed scRNA-seq and bulk RNA-seq, we demonstrate the usefulness and necessity of a pooled design to reveal donor iPSC line heterogeneity during macrophage cell differentiation and to model rare WT1 mutation-driven kidney disease with chimeric organoids. Our work provides an experimental and analytic pipeline for dissecting disease mechanisms with chimeric organoids.},
}
@article {pmid38729384,
year = {2024},
author = {Dufresnes, C and Ghielmi, S and Halpern, B and Martínez-Freiría, F and Mebert, K and Jelić, D and Crnobrnja-Isailović, J and Gippner, S and Jablonski, D and Joger, U and Laddaga, L and Petrovan, S and Tomović, L and Vörös, J and İğci, N and Kariş, M and Zinenko, O and Ursenbacher, S},
title = {Phylogenomic insights into the diversity and evolution of Palearctic vipers.},
journal = {Molecular phylogenetics and evolution},
volume = {197},
number = {},
pages = {108095},
doi = {10.1016/j.ympev.2024.108095},
pmid = {38729384},
issn = {1095-9513},
mesh = {*Phylogeny ; Animals ; *Viperidae/genetics/classification ; Genetic Variation ; Genome, Mitochondrial/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; },
abstract = {Despite decades of molecular research, phylogenetic relationships in Palearctic vipers (genus Vipera) still essentially rely on a few loci, such as mitochondrial barcoding genes. Here we examined the diversity and evolution of Vipera with ddRAD-seq data from 33 representative species and subspecies. Phylogenomic analyses of ∼ 1.1 Mb recovered nine major clades corresponding to known species/species complexes which are generally consistent with the mitochondrial phylogeny, albeit with a few deep discrepancies that highlight past hybridization events. The most spectacular case is the Italian-endemic V. walser, which is grouped with the alpine genetic diversity of V. berus in the nuclear tree despite carrying a divergent mitogenome related to the Caucasian V. kaznakovi complex. Clustering analyses of SNPs suggest potential admixture between diverged Iberian taxa (V. aspis zinnikeri and V. seoanei), and confirm that the Anatolian V. pontica corresponds to occasional hybrids between V. (ammodytes) meridionalis and V. kaznakovi. Finally, all analyzed lineages of the V. berus complex (including V. walser and V. barani) form vast areas of admixture and may be delimited as subspecies. Our study sets grounds for future taxonomic and phylogeographic surveys on Palearctic vipers, a group of prime interest for toxinological, ecological, biogeographic and conservation research.},
}
@article {pmid38728918,
year = {2024},
author = {Luo, Y and Yang, H and Tao, G},
title = {Systematic review on fingerprinting development to determine adulteration of Chinese herbal medicines.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {129},
number = {},
pages = {155667},
doi = {10.1016/j.phymed.2024.155667},
pmid = {38728918},
issn = {1618-095X},
mesh = {*Drugs, Chinese Herbal/chemistry/analysis ; *Drug Contamination ; *Quality Control ; Chromatography, High Pressure Liquid/methods ; DNA Barcoding, Taxonomic ; },
abstract = {BACKGROUND: It has been a current research hospots using fingerprinting technology for quality control of Chinese herbal medicines (CHMs), which provides a scientific basis for establishment of overall quality control in accordance with the characteristics of CHMs. The fingerprinting technology for CHMs is diverse, and the research field covers many disciplines, such as analytical chemistry, pharmacology, pharmaceutics, biochemistry, and molecular biology.<br><br>PURPOSE: To effectively understand the key areas and future directions of research regarding the fingerprint and adulteration of CHMs.<br><br>METHODS/RESULTS: this paper analyzed 879 articles in this field in the Web of Science Core Collection from 2000 to 2023 with CiteSpace and VOSviewer, and systematically assessed the research process, hotspots, topic distribution among disciplines, etc. The most prominent contributors of fingerprint and adulteration of CHMs research are mainly from China, India, the United States, England, and Brazil. The knowledge domains of fingerprint and adulteration of CHMs research focus mainly on the topics of molecular authentication, DNA barcoding, HPLC, near-infrared spectroscopy, manage data, chemometrics, and electrochemical fingerprinting. Most countries have recognized the pharmaceutical potential of natural products, and have paid more attention to the fingerprint and adulteration of CHMs in the past decade. Future the research tends to focus more on molecular identification and authentication, and electrochemical and chromatographic fingerprinting in controlling the adulteration of CHMs.<br><br>CONCLUSION: This research provides a valuable reference for scholars in related fields to analyze existing research results, understand the development trend, and explore new research directions.},
}
@article {pmid38727924,
year = {2024},
author = {Niu, J and Wang, X and Zhou, S and Yue, J and Liu, Z and Zhou, J},
title = {Molecular authentication of commercial "Qian-hu" through the integration of nrDNA internal transcribed spacer 2 and nucleotide signature.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {639},
pmid = {38727924},
issn = {1573-4978},
support = {202205AM070006//Gaoligong Mountain, Forest Ecosystem, Observation and Research Station of Yunnan Province/ ; 31960048//National Natural Science Foundation of China/ ; YNWRQNBJ-2019-208//Ten Thousand Talents Program of Yunnan/ ; 202201AT070118//Department of Science and Technology of Yunnan Province/ ; },
mesh = {*DNA, Plant/genetics ; *DNA Barcoding, Taxonomic/methods ; Drugs, Chinese Herbal/standards ; Apiaceae/genetics/classification ; Medicine, Chinese Traditional/standards ; DNA, Ribosomal Spacer/genetics ; Drug Contamination ; Plants, Medicinal/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Polymerase Chain Reaction/methods ; Nucleotides/genetics/analysis ; },
abstract = {BACKGROUND: Peucedani Radix, also known as "Qian-hu" is a traditional Chinese medicine derived from Peucedanum praeruptorum Dunn. It is widely utilized for treating wind-heat colds and coughs accompanied by excessive phlegm. However, due to morphological similarities, limited resources, and heightened market demand, numerous substitutes and adulterants of Peucedani Radix have emerged within the herbal medicine market. Moreover, Peucedani Radix is typically dried and sliced for sale, rendering traditional identification methods challenging.<br><br>MATERIALS AND METHODS: We initially examined and compared 104 commercial "Qian-hu" samples from various Chinese medicinal markets and 44 species representing genuine, adulterants or substitutes, utilizing the mini barcode ITS2 region to elucidate the botanical origins of the commercial "Qian-hu". The nucleotide signature specific to Peucedani Radix was subsequently developed by analyzing the polymorphic sites within the aligned ITS2 sequences.<br><br>RESULTS: The results demonstrated a success rate of 100% and 93.3% for DNA extraction and PCR amplification, respectively. Forty-five samples were authentic "Qian-hu", while the remaining samples were all adulterants, originating from nine distinct species. Peucedani Radix, its substitutes, and adulterants were successfully identified based on the neighbor-joining tree. The 24-bp nucleotide signature (5'-ATTGTCGTACGAATCCTCGTCGTC-3') revealed distinct differences between Peucedani Radix and its common substitutes and adulterants. The newly designed specific primers (PR-F/PR-R) can amplify the nucleotide signature region from commercial samples and processed materials with severe DNA degradation.<br><br>CONCLUSIONS: We advocate for the utilization of ITS2 and nucleotide signature for the rapid and precise identification of herbal medicines and their adulterants to regulate the Chinese herbal medicine industry.},
}
@article {pmid38722810,
year = {2024},
author = {Marshall, WF and Fung, JC},
title = {Modeling homologous chromosome recognition via nonspecific interactions.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {20},
pages = {e2317373121},
pmid = {38722810},
issn = {1091-6490},
support = {R01 GM137126/GM/NIGMS NIH HHS/United States ; R35 GM130327/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Models, Genetic ; Chromosome Pairing ; Drosophila melanogaster/genetics ; Chromosomes ; Drosophila/genetics ; Computer Simulation ; Chromosomes, Insect/genetics/metabolism ; },
abstract = {In many organisms, most notably Drosophila, homologous chromosomes associate in somatic cells, a phenomenon known as somatic pairing, which takes place without double strand breaks or strand invasion, thus requiring some other mechanism for homologs to recognize each other. Several studies have suggested a "specific button" model, in which a series of distinct regions in the genome, known as buttons, can associate with each other, mediated by different proteins that bind to these different regions. Here, we use computational modeling to evaluate an alternative "button barcode" model, in which there is only one type of recognition site or adhesion button, present in many copies in the genome, each of which can associate with any of the others with equal affinity. In this model, buttons are nonuniformly distributed, such that alignment of a chromosome with its correct homolog, compared with a nonhomolog, is energetically favored; since to achieve nonhomologous alignment, chromosomes would be required to mechanically deform in order to bring their buttons into mutual register. By simulating randomly generated nonuniform button distributions, many highly effective button barcodes can be easily found, some of which achieve virtually perfect pairing fidelity. This model is consistent with existing literature on the effect of translocations of different sizes on homolog pairing. We conclude that a button barcode model can attain highly specific homolog recognition, comparable to that seen in actual cells undergoing somatic homolog pairing, without the need for specific interactions. This model may have implications for how meiotic pairing is achieved.},
}
@article {pmid38721629,
year = {2024},
author = {Waki, T and Kumagai, T and Nishino, Y},
title = {Identification of Lepidapedon oregonense as the current world's deepest trematode.},
journal = {Journal of helminthology},
volume = {98},
number = {},
pages = {e38},
doi = {10.1017/S0022149X24000269},
pmid = {38721629},
issn = {1475-2697},
mesh = {Animals ; *Trematoda/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 28S/genetics ; *Phylogeny ; *DNA, Helminth/genetics ; *DNA, Ribosomal/genetics ; Gastropoda/parasitology ; Sequence Analysis, DNA ; Fishes/parasitology ; Fish Diseases/parasitology ; Trematode Infections/parasitology/veterinary ; },
abstract = {The deepest recorded depth for trematodes currently stands at approximately 6200 m. This depth record was achieved solely through sequence datasets of Lepidapedon sp. obtained from a gastropod. Given that trematodes of this genus typically use fish as definitive hosts, the origin of the trematode sequence was thought to be larval stages. However, the specific species remained unclear owing to the absence of reported adult-stage sequences. In the present study, we definitively identified the deepest trematode as Lepidapedon oregonense by comparing 28S ribosomal DNA sequences from adult worms from the macrourid fish Coelorinchus gilberti with data from the gastropod in the previous study.},
}
@article {pmid38718049,
year = {2024},
author = {Lokken-Toyli, KL and Aggarwal, SD and Bee, GCW and de Steenhuijsen Piters, WAA and Wu, C and Chen, KZM and Loomis, C and Bogaert, D and Weiser, JN},
title = {Impaired upper respiratory tract barrier function during postnatal development predisposes to invasive pneumococcal disease.},
journal = {PLoS pathogens},
volume = {20},
number = {5},
pages = {e1012111},
pmid = {38718049},
issn = {1553-7374},
mesh = {Animals ; *Pneumococcal Infections/microbiology/immunology ; Mice ; *Streptococcus pneumoniae ; Humans ; Animals, Newborn ; Disease Models, Animal ; Mice, Inbred C57BL ; Respiratory Mucosa/microbiology/metabolism ; Female ; Nasopharynx/microbiology ; },
abstract = {Infants are highly susceptible to invasive respiratory and gastrointestinal infections. To elucidate the age-dependent mechanism(s) that drive bacterial spread from the mucosa, we developed an infant mouse model using the prevalent pediatric respiratory pathogen, Streptococcus pneumoniae (Spn). Despite similar upper respiratory tract (URT) colonization levels, the survival rate of Spn-infected infant mice was significantly decreased compared to adults and corresponded with Spn dissemination to the bloodstream. An increased rate of pneumococcal bacteremia in early life beyond the newborn period was attributed to increased bacterial translocation across the URT barrier. Bacterial dissemination in infant mice was independent of URT monocyte or neutrophil infiltration, phagocyte-derived ROS or RNS, inflammation mediated by toll-like receptor 2 or interleukin 1 receptor signaling, or the pore-forming toxin pneumolysin. Using molecular barcoding of Spn, we found that only a minority of bacterial clones in the nasopharynx disseminated to the blood in infant mice, indicating the absence of robust URT barrier breakdown. Rather, transcriptional profiling of the URT epithelium revealed a failure of infant mice to upregulate genes involved in the tight junction pathway. Expression of many such genes was also decreased in early life in humans. Infant mice also showed increased URT barrier permeability and delayed mucociliary clearance during the first two weeks of life, which corresponded with tighter attachment of bacteria to the respiratory epithelium. Together, these results demonstrate a window of vulnerability during postnatal development when altered mucosal barrier function facilitates bacterial dissemination.},
}
@article {pmid38715571,
year = {2024},
author = {Murwani, R and Anggraeni, R and Setiawan, GNA and Astari, PD and Cahyani, NKD and Sibero, MT and Ambariyanto, A},
title = {Lactic Acid Bacteria Isolates and the Microbiome of Cincalok, Tempoyak, and Mandai: A Traditional Fermented Food from Kalimantan Island, Indonesia.},
journal = {International journal of food science},
volume = {2024},
number = {},
pages = {6589766},
pmid = {38715571},
issn = {2314-5765},
abstract = {Indonesia has abundant traditional fermented food with various lactic acid bacteria (LAB), which can be developed into probiotics for pharmaceutical and functional food and feed products. This research is aimed at (1) obtaining and identifying LAB isolates and (2) studying the microbiome (bacterial diversity and abundance) of spontaneously-fermented traditional foods of Kalimantan Island, Cincalok, Tempoyak, and Mandai. To obtain LAB isolates, food samples were serially diluted and inoculated on MRS agar that contained 1% CaCO3 (MRSA). Isolates forming clear zones were purified and identified by DNA barcoding. The microbiome was studied using genomic-sequencing techniques and analysed for taxonomic composition. Seven pure isolates were obtained from Cincalok, two Tempoyak, and one Mandai. DNA barcoding revealed that the Cincalok seven isolates were Staphylococcus carnosus (strain HSP-S16), Tetragenococcus halophilus (FSB201), Corynebacterium phoceense, Vagococcus vulneris (SS1995), Enterococcus faecalis (S11-6), Pisciglobus halotolerans (C01), and Priestia filamentosa (P3.1); two from Tempoyak, Levilactobacillus brevis (E1D3BL1) and Lactiplantibacillus plantarum (UMCC-2996); and one from Mandai, Staphylococcus cohnii (XAAS.x13; non-LAB). The T. halophilus, E. faecalis, P. halotolerans, L. brevis, and L. plantarum belong to LAB. The P. halotolerans from Cincalok and non-LAB in these three fermented foods were the first documented report. The microbiome revealed the dominance of Firmicutes phyla in the fermented foods, with 93% in Cincalok, 89.94% in Tempoyak, and 60.32% in Mandai. On the genus level, Cincalok was dominated by Tetragenococcus 40.33%, Anaerococcus 23.29%, Vagococcus 9.27%, and Lactobacillus 6.84%. Meanwhile, Tempoyak was dominated only by Lactobacillus 89.94%. Mandai were dominated by Lactobacillus 31.97%, Proteus 17.14%, Aerococcus 16.85%, Mangrovibacter 15.15%, and Vagococcus 6.2%. However, Mandai's microbiome LAB was not culturable/isolated on MRSA. The plausibility is that those unculturable LAB require coculturing with other bacteria and additional media components to grow on MRSA. This study is the first report regarding the microbiome of Cincalok, Tempoyak, and Mandai, along with their culturable LAB isolates.},
}
@article {pmid38714853,
year = {2024},
author = {Lindenhofer, D and Haendeler, S and Esk, C and Littleboy, JB and Brunet Avalos, C and Naas, J and Pflug, FG and van de Ven, EGP and Reumann, D and Baffet, AD and von Haeseler, A and Knoblich, JA},
title = {Cerebral organoids display dynamic clonal growth and tunable tissue replenishment.},
journal = {Nature cell biology},
volume = {26},
number = {5},
pages = {710-718},
pmid = {38714853},
issn = {1476-4679},
support = {DOC 72/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {*Organoids/cytology/metabolism ; Humans ; *Cell Lineage ; *Neural Stem Cells/metabolism/cytology ; Brain/cytology/growth &amp; development/metabolism ; Cell Differentiation ; Cell Proliferation ; Clone Cells ; Neurogenesis/genetics ; DNA Barcoding, Taxonomic ; Animals ; },
abstract = {During brain development, neural progenitors expand through symmetric divisions before giving rise to differentiating cell types via asymmetric divisions. Transition between those modes varies among individual neural stem cells, resulting in clones of different sizes. Imaging-based lineage tracing allows for lineage analysis at high cellular resolution but systematic approaches to analyse clonal behaviour of entire tissues are currently lacking. Here we implement whole-tissue lineage tracing by genomic DNA barcoding in 3D human cerebral organoids, to show that individual stem cell clones produce progeny on a vastly variable scale. By using stochastic modelling we find that variable lineage sizes arise because a subpopulation of lineages retains symmetrically dividing cells. We show that lineage sizes can adjust to tissue demands after growth perturbation via chemical ablation or genetic restriction of a subset of cells in chimeric organoids. Our data suggest that adaptive plasticity of stem cell populations ensures robustness of development in human brain organoids.},
}
@article {pmid38714828,
year = {2024},
author = {Sipiczki, M and Czentye, K and Kállai, Z},
title = {High intragenomic, intergenomic, and phenotypic diversity in pulcherrimin-producing Metschnikowia yeasts indicates a special mode of genome evolution.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {10521},
pmid = {38714828},
issn = {2045-2322},
mesh = {*Metschnikowia/genetics ; *Genome, Fungal ; *Evolution, Molecular ; *Phylogeny ; Genetic Variation ; Phenotype ; DNA, Mitochondrial/genetics ; },
abstract = {In molecular systematics, the delimitation of yeast species is based on the notion that the barcode differences are smaller within species than between them. The most widely used barcodes are segments of the chromosomal repeats coding for ribosomal RNAs that are homogenised in yeasts. The analysis of these segments of the type strains of ten species recently merged in Metschnikowia pulcherrima and 37 new isolates demonstrated that this is not the case in this species. The intragenomic diversity significantly exceeded the threshold gaps used to differentiate related yeast species. Large segments of the D1/D2 domains were not diverse within the genomes and could therefore be used to determine the taxonomic affiliation of the isolates. The genome structures of the isolates were compared by RAPD and the RFLP of the mitochondrial DNA. Both patterns were highly heterogeneous. The sequence analysis of the PUL4 gene (a member of the PUL gene cluster involved in pulcherrimin production) revealed very high intragenomic differences, suggesting that the genomes may be chimerised. Three phenotypic traits related to the antimicrobial antagonism characteristic of the species were also highly diverse and prone to reversible segregation resembling epigenetic processes (silencing and reactivation of regulators) rather than mutations and back-mutations. These features make M. pulcherrima unique among yeasts and indicate that it evolves in a non-standard way.},
}
@article {pmid38712508,
year = {2024},
author = {Voorspoels, A and Gevers, J and Santermans, S and Akkan, N and Martens, K and Willems, K and Van Dorpe, P and Verhulst, AS},
title = {Design Principles of DNA-Barcodes for Nanopore-FET Readout, Based on Molecular Dynamics and TCAD Simulations.},
journal = {The journal of physical chemistry. A},
volume = {128},
number = {19},
pages = {3926-3933},
doi = {10.1021/acs.jpca.4c01772},
pmid = {38712508},
issn = {1520-5215},
mesh = {*Molecular Dynamics Simulation ; *DNA/chemistry ; *Nanopores ; *Transistors, Electronic ; },
abstract = {Nanopore field-effect transistor (NP-FET) devices hold great promise as sensitive single-molecule sensors, which provide CMOS-based on-chip readout and are also highly amenable to parallelization. A plethora of applications will therefore benefit from NP-FET technology, such as large-scale molecular analysis (e.g., proteomics). Due to its potential for parallelization, the NP-FET looks particularly well-suited for the high-throughput readout of DNA-based barcodes. However, to date, no study exists that unravels the bit-rate capabilities of NP-FET devices. In this paper, we design DNA-based barcodes by labeling a piece of double-stranded DNA with dumbbell-like DNA structures. We explore the impact of both the size of the dumbbells and their spacing on achievable bit-rates. The conformational fluctuations of this DNA-origami, as observed by molecular dynamics (MD) simulation, are accounted for when selecting label sizes. An experimentally informed 3D continuum nanofluidic-nanoelectronic device model subsequently predicts both the ionic current and FET signals. We present a barcode design for a conceptually generic NP-FET, with a 14 nm diameter pore, operating in conditions corresponding to experiments. By adjusting the spacing between the labels to half the length of the pore, we show that a bit-rate of 78 kbit·s[-1] is achievable. This lies well beyond the state-of-the-art of ≈40 kbit·s[-1], with significant headroom for further optimizations. We also highlight the advantages of NP-FET readout based on the larger signal size and sinusoidal signal shape.},
}
@article {pmid38712231,
year = {2024},
author = {Yang, L and Liu, F and Hahm, H and Okuda, T and Li, X and Zhang, Y and Kalyanaraman, V and Heitmeier, MR and Samineni, VK},
title = {Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38712231},
issn = {2692-8205},
support = {P30 CA091842/CA/NCI NIH HHS/United States ; R01 DA056829/DA/NIDA NIH HHS/United States ; R01 DK128475/DK/NIDDK NIH HHS/United States ; R01 DK139386/DK/NIDDK NIH HHS/United States ; },
abstract = {Single-cell multiomic techniques have sparked immense interest in developing a comprehensive multi-modal map of diverse neuronal cell types and their brain wide projections. However, investigating the spatial organization, transcriptional and epigenetic landscapes of brain wide projection neurons is hampered by the lack of efficient and easily adoptable tools. Here we introduce Projection-TAGs, a retrograde AAV platform that allows multiplex tagging of projection neurons using RNA barcodes. By using Projection-TAGs, we performed multiplex projection tracing of the mouse cortex and high-throughput single-cell profiling of the transcriptional and epigenetic landscapes of the cortical projection neurons. Projection-TAGs can be leveraged to obtain a snapshot of activity-dependent recruitment of distinct projection neurons and their molecular features in the context of a specific stimulus. Given its flexibility, usability, and compatibility, we envision that Projection-TAGs can be readily applied to build a comprehensive multi-modal map of brain neuronal cell types and their projections.},
}
@article {pmid38709890,
year = {2024},
author = {Li, W and Miller, D and Liu, X and Tosi, L and Chkaiban, L and Mei, H and Hung, PH and Parekkadan, B and Sherlock, G and Levy, SF},
title = {Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries.},
journal = {Nucleic acids research},
volume = {52},
number = {10},
pages = {e47},
pmid = {38709890},
issn = {1362-4962},
support = {R01 AI164530/AI/NIAID NIH HHS/United States ; R01 HG011676/HG/NHGRI NIH HHS/United States ; R01HG011676/NH/NIH HHS/United States ; },
mesh = {*Plasmids/genetics ; *Gene Library ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; DNA/genetics ; DNA Barcoding, Taxonomic/methods ; Nanopore Sequencing/methods ; },
abstract = {Sequence verification of plasmid DNA is critical for many cloning and molecular biology workflows. To leverage high-throughput sequencing, several methods have been developed that add a unique DNA barcode to individual samples prior to pooling and sequencing. However, these methods require an individual plasmid extraction and/or in vitro barcoding reaction for each sample processed, limiting throughput and adding cost. Here, we develop an arrayed in vivo plasmid barcoding platform that enables pooled plasmid extraction and library preparation for Oxford Nanopore sequencing. This method has a high accuracy and recovery rate, and greatly increases throughput and reduces cost relative to other plasmid barcoding methods or Sanger sequencing. We use in vivo barcoding to sequence verify >45 000 plasmids and show that the method can be used to transform error-containing dispersed plasmid pools into sequence-perfect arrays or well-balanced pools. In vivo barcoding does not require any specialized equipment beyond a low-overhead Oxford Nanopore sequencer, enabling most labs to flexibly process hundreds to thousands of plasmids in parallel.},
}
@article {pmid38709485,
year = {2024},
author = {Wang, S and Chi, WY and Au, G and Huang, CC and Yang, JM and Huang, CH},
title = {Reconstructing Signaling Networks Using Biosensor Barcoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2800},
number = {},
pages = {189-202},
pmid = {38709485},
issn = {1940-6029},
support = {P50 CA098252/CA/NCI NIH HHS/United States ; R01 GM136711/GM/NIGMS NIH HHS/United States ; S10 OD016374/OD/NIH HHS/United States ; },
mesh = {*Biosensing Techniques/methods ; *Signal Transduction ; Humans ; ErbB Receptors/metabolism/genetics ; },
abstract = {Understanding how signaling networks are regulated offers valuable insights into how cells and organisms react to internal and external stimuli and is crucial for developing novel strategies to treat diseases. To achieve this, it is necessary to delineate the intricate interactions between the nodes in the network, which can be accomplished by measuring the activities of individual nodes under perturbation conditions. To facilitate this, we have recently developed a biosensor barcoding technique that enables massively multiplexed tracking of numerous signaling activities in live cells using genetically encoded fluorescent biosensors. In this chapter, we detail how we employed this method to reconstruct the EGFR signaling network by systematically monitoring the activities of individual nodes under perturbations.},
}
@article {pmid38705596,
year = {2024},
author = {Schulz, AR and Rademacher, J and Bockhorn, V and Mei, HE},
title = {Harmonized analysis of PBMC by mass cytometry.},
journal = {Methods in cell biology},
volume = {186},
number = {},
pages = {107-130},
doi = {10.1016/bs.mcb.2024.02.015},
pmid = {38705596},
issn = {0091-679X},
mesh = {Humans ; *Leukocytes, Mononuclear/cytology/immunology ; *Flow Cytometry/methods/standards ; Immunophenotyping/methods ; Single-Cell Analysis/methods ; },
abstract = {Mass cytometry permits the high dimensional analysis of cellular systems at single-cell resolution with high throughput in various areas of biomedical research. Here, we provide a state-of-the-art protocol for the analysis of human peripheral blood mononuclear cells (PBMC) by mass cytometry. We focus on the implementation of measures promoting the harmonization of large and complex studies to aid robustness and reproducibility of immune phenotyping data.},
}
@article {pmid38705192,
year = {2024},
author = {van Klink, R},
title = {Delivering on a promise: futureproofing automated insect monitoring methods.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1904},
pages = {20230105},
pmid = {38705192},
issn = {1471-2970},
mesh = {Animals ; Automation/methods ; *Biodiversity ; Entomology/methods/instrumentation/trends ; *Insecta/physiology ; },
abstract = {Due to rapid technological innovations, the automated monitoring of insect assemblages comes within reach. However, this continuous innovation endangers the methodological continuity needed for calculating reliable biodiversity trends in the future. Maintaining methodological continuity over prolonged periods of time is not trivial, since technology improves, reference libraries grow and both the hard- and software used now may no longer be available in the future. Moreover, because data on many species are collected at the same time, there will be no simple way of calibrating the outputs of old and new devices. To ensure that reliable long-term biodiversity trends can be calculated using the collected data, I make four recommendations: (1) Construct devices to last for decades, and have a five-year overlap period when devices are replaced. (2) Construct new devices to resemble the old ones, especially when some kind of attractant (e.g. light) is used. Keep extremely detailed metadata on collection, detection and identification methods, including attractants, to enable this. (3) Store the raw data (sounds, images, DNA extracts, radar/lidar detections) for future reprocessing with updated classification systems. (4) Enable forward and backward compatibility of the processed data, for example by in-silico data 'degradation' to match the older data quality. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.},
}
@article {pmid38705187,
year = {2024},
author = {Meier, R and Hartop, E and Pylatiuk, C and Srivathsan, A},
title = {Towards holistic insect monitoring: species discovery, description, identification and traits for all insects.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1904},
pages = {20230120},
pmid = {38705187},
issn = {1471-2970},
mesh = {*Insecta/physiology/classification/genetics ; Animals ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; },
abstract = {Holistic insect monitoring needs scalable techniques to overcome taxon biases, determine species abundances, and gather functional traits for all species. This requires that we address taxonomic impediments and the paucity of data on abundance, biomass and functional traits. We here outline how these data deficiencies could be addressed at scale. The workflow starts with large-scale barcoding (megabarcoding) of all specimens from mass samples obtained at biomonitoring sites. The barcodes are then used to group the specimens into molecular operational taxonomic units that are subsequently tested/validated as species with a second data source (e.g. morphology). New species are described using barcodes, images and short diagnoses, and abundance data are collected for both new and described species. The specimen images used for species discovery then become the raw material for training artificial intelligence identification algorithms and collecting trait data such as body size, biomass and feeding modes. Additional trait data can be obtained from vouchers by using genomic tools developed by molecular ecologists. Applying this pipeline to a few samples per site will lead to greatly improved insect monitoring regardless of whether the species composition of a sample is determined with images, metabarcoding or megabarcoding. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.},
}
@article {pmid38705185,
year = {2024},
author = {Łukasik, P and Kolasa, MR},
title = {With a little help from my friends: the roles of microbial symbionts in insect populations and communities.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1904},
pages = {20230122},
pmid = {38705185},
issn = {1471-2970},
mesh = {Animals ; *Insecta/microbiology/physiology ; *Symbiosis ; *Microbiota/physiology ; Biodiversity ; },
abstract = {To understand insect abundance, distribution and dynamics, we need to understand the relevant drivers of their populations and communities. While microbial symbionts are known to strongly affect many aspects of insect biology, we lack data on their effects on populations or community processes, or on insects' evolutionary responses at different timescales. How these effects change as the anthropogenic effects on ecosystems intensify is an area of intense research. Recent developments in sequencing and bioinformatics permit cost-effective microbial diversity surveys, tracking symbiont transmission, and identification of functions across insect populations and multi-species communities. In this review, we explore how different functional categories of symbionts can influence insect life-history traits, how these effects could affect insect populations and their interactions with other species, and how they may affect processes and patterns at the level of entire communities. We argue that insect-associated microbes should be considered important drivers of insect response and adaptation to environmental challenges and opportunities. We also outline the emerging approaches for surveying and characterizing insect-associated microbiota at population and community scales. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.},
}
@article {pmid38705180,
year = {2024},
author = {Li, R and Ratnasingham, S and Zarubiieva, I and Somervuo, P and Taylor, GW},
title = {PROTAX-GPU: a scalable probabilistic taxonomic classification system for DNA barcodes.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1904},
pages = {20230124},
pmid = {38705180},
issn = {1471-2970},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Algorithms ; Classification/methods ; Computer Graphics ; Animals ; },
abstract = {DNA-based identification is vital for classifying biological specimens, yet methods to quantify the uncertainty of sequence-based taxonomic assignments are scarce. Challenges arise from noisy reference databases, including mislabelled entries and missing taxa. PROTAX addresses these issues with a probabilistic approach to taxonomic classification, advancing on methods that rely solely on sequence similarity. It provides calibrated probabilistic assignments to a partially populated taxonomic hierarchy, accounting for taxa that lack references and incorrect taxonomic annotation. While effective on smaller scales, global application of PROTAX necessitates substantially larger reference libraries, a goal previously hindered by computational barriers. We introduce PROTAX-GPU, a scalable algorithm capable of leveraging the global Barcode of Life Data System (>14 million specimens) as a reference database. Using graphics processing units (GPU) to accelerate similarity and nearest-neighbour operations and the JAX library for Python integration, we achieve over a 1000 × speedup compared with the central processing unit (CPU)-based implementation without compromising PROTAX's key benefits. PROTAX-GPU marks a significant stride towards real-time DNA barcoding, enabling quicker and more efficient species identification in environmental assessments. This capability opens up new avenues for real-time monitoring and analysis of biodiversity, advancing our ability to understand and respond to ecological dynamics. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.},
}
@article {pmid38705177,
year = {2024},
author = {Li, Y and Devenish, C and Tosa, MI and Luo, M and Bell, DM and Lesmeister, DB and Greenfield, P and Pichler, M and Levi, T and Yu, DW},
title = {Combining environmental DNA and remote sensing for efficient, fine-scale mapping of arthropod biodiversity.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1904},
pages = {20230123},
pmid = {38705177},
issn = {1471-2970},
mesh = {*Arthropods/classification ; *Biodiversity ; Animals ; *DNA, Environmental/analysis ; *Remote Sensing Technology/methods ; Forests ; Animal Distribution ; DNA Barcoding, Taxonomic/methods ; },
abstract = {Arthropods contribute importantly to ecosystem functioning but remain understudied. This undermines the validity of conservation decisions. Modern methods are now making arthropods easier to study, since arthropods can be mass-trapped, mass-identified, and semi-mass-quantified into 'many-row (observation), many-column (species)' datasets, with homogeneous error, high resolution, and copious environmental-covariate information. These 'novel community datasets' let us efficiently generate information on arthropod species distributions, conservation values, uncertainty, and the magnitude and direction of human impacts. We use a DNA-based method (barcode mapping) to produce an arthropod-community dataset from 121 Malaise-trap samples, and combine it with 29 remote-imagery layers using a deep neural net in a joint species distribution model. With this approach, we generate distribution maps for 76 arthropod species across a 225 km[2] temperate-zone forested landscape. We combine the maps to visualize the fine-scale spatial distributions of species richness, community composition, and site irreplaceability. Old-growth forests show distinct community composition and higher species richness, and stream courses have the highest site-irreplaceability values. With this 'sideways biodiversity modelling' method, we demonstrate the feasibility of biodiversity mapping at sufficient spatial resolution to inform local management choices, while also being efficient enough to scale up to thousands of square kilometres. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.},
}
@article {pmid38705075,
year = {2024},
author = {Li, X and Liu, R and Zhang, N and Zhao, J and Zhou, Y and Zhou, Q and Gu, Z and Zhang, D},
title = {Carbon nanotubes integrated photonic barcodes in Herringbone Microfluidics for Multiplex Biomarker Quantification.},
journal = {Biosensors &amp; bioelectronics},
volume = {258},
number = {},
pages = {116350},
doi = {10.1016/j.bios.2024.116350},
pmid = {38705075},
issn = {1873-4235},
mesh = {*Nanotubes, Carbon/chemistry ; Humans ; *Biosensing Techniques/instrumentation ; *Biomarkers ; *Lab-On-A-Chip Devices ; Equipment Design ; Aptamers, Nucleotide/chemistry ; Silicon Dioxide/chemistry ; Photons ; Nanoparticles/chemistry ; Microfluidic Analytical Techniques/instrumentation ; },
abstract = {Early monitoring of cardiovascular disease (CVD) is crucial for its treatment and prognosis. Hence, highly specific and sensitive detection method is urgently needed. In this study, we propose a novel herringbone microfluid chip with aptamer functionalized core-shell photonic crystal (PhC) barcode integration for high throughput multiplex CVD detection. Based on the PhC derived from co-assembled carboxylated single-wall carbon nanotubes and silicon dioxide nanoparticles, we obtain core-shell PhC barcodes by hydrogel replicating and partially etching. These core-shell PhC barcodes not only retain the original structural colors coding element, but also fully expose a large number of carboxyl elements in the ore for the probe immobilization. We further combine the functionalized barcodes with herringbone groove microfluidic chip to elucidate its acceptability in testing clinical sample. It is demonstrated that the special design of microfluidic chip can significantly enhance fluid vortex resistance and contact frequency, improving the sample capture efficiency and detection sensitivity. These features indicate that our core-shell PhC barcodes-integrated herringbone microfluidic system possesses great potential for multiplex biomarker detection in clinical application.},
}
@article {pmid38703100,
year = {2024},
author = {Molero-Baltanás, R and Mitchell, A and Gaju-Ricart, M and Robla, J},
title = {Worldwide revision of synanthropic silverfish (Insecta: Zygentoma: Lepismatidae) combining morphological and molecular data.},
journal = {Journal of insect science (Online)},
volume = {24},
number = {3},
pages = {},
pmid = {38703100},
issn = {1536-2442},
support = {//the Australian Museum Research Institute/ ; //University of C&#xf3;rdoba/ ; },
mesh = {Animals ; *Phylogeny ; *Insecta/genetics/anatomy &amp; histology/classification ; Female ; Male ; Animal Distribution ; },
abstract = {Synanthropic silverfish are the best-known and most widely distributed insects of the order Zygentoma. However, there is a great gap in the knowledge and confusion about the geographic distribution and the diagnostic characteristics that allow their identification. In this work, we provide an exhaustive and deep analysis of the most common 9 synanthropic silverfish of the world, combining previously published and newly derived morphological and molecular data. Updated descriptions of Ctenolepisma calvum (Ritter, 1910) and Ctenolepisma (Sceletolepisma) villosum (Fabricius, 1775) are included, and morphological remarks, illustrations, and photographs of the remaining synanthropic species are provided to clarify their diagnosis and differentiation among them and from other free-living species. In addition, Ctenolepisma targionii (Grassi and Rovelli, 1889) is synonymized with C. villosum. A molecular phylogeny is presented based on the COI sequences of all the synanthropic species deposited in BOLD and GenBank, with 15 new sequences provided by this study. This has allowed us to detect and correct a series of identification errors based on the lack of morphological knowledge of several species. Moreover, 2 different lineages of Ctenolepisma longicaudatumEscherich, 1905 have also been detected. To help future studies, we also provide a taxonomic interpretation guide for the most important diagnostic characters of the order Zygentoma, as well as an identification key for all the Synanthropic studied species. Finally, an approximation of the global distribution of synanthropic silverfish is discussed. Several new records indicate that the expansion of these species, generally associated with the transport of goods and people, is still far from over.},
}
@article {pmid38703052,
year = {2024},
author = {Burg, S and Ovaskainen, O and Furneaux, B and Ivanova, N and Abrahamyan, A and Niittynen, P and Somervuo, P and Abrego, N},
title = {Experimental evidence that root-associated fungi improve plant growth at high altitude.},
journal = {Molecular ecology},
volume = {33},
number = {12},
pages = {e17376},
doi = {10.1111/mec.17376},
pmid = {38703052},
issn = {1365-294X},
support = {101057437//H2020 European Research Council/ ; 101059492//H2020 European Research Council/ ; 856506//H2020 European Research Council/ ; 30865//Research Council of Finland/ ; 336212//Research Council of Finland/ ; 342374//Research Council of Finland/ ; 345110//Research Council of Finland/ ; 346492//Research Council of Finland/ ; },
mesh = {*Altitude ; *Plant Roots/microbiology/growth &amp; development ; *Symbiosis/genetics ; Fungi/genetics ; Plant Development/genetics ; DNA Barcoding, Taxonomic ; Mycorrhizae/genetics/physiology ; },
abstract = {Unravelling how species communities change along environmental gradients requires a dual understanding: the direct responses of the species to their abiotic surroundings and the indirect variation of these responses through biotic interactions. Here, we focus on the interactive relationships between plants and their symbiotic root-associated fungi (RAF) along stressful abiotic gradients. We investigate whether variations in RAF community composition along altitudinal gradients influence plant growth at high altitudes, where both plants and fungi face harsher abiotic conditions. We established a translocation experiment between pairs of Bistorta vivipara populations across altitudinal gradients. To separate the impact of shifting fungal communities from the overall influence of changing abiotic conditions, we used a root barrier to prevent new colonization by RAF following translocation. To characterize the RAF communities, we applied DNA barcoding to the root samples. Through the utilization of joint species distribution modelling, we assessed the relationship between changes in plant functional traits resulting from experimental treatments and the corresponding changes in the RAF communities. Our findings indicate that RAF communities influence plant responses to stressful abiotic conditions. Plants translocated from low to high altitudes grew more when they were able to associate with the resident high-altitude RAF compared to those plants that were not allowed to associate with the resident RAF. We conclude that interactions with RAF impact how plants respond to stressful abiotic conditions. Our results provide experimental support that interactions with RAF improve plant stress tolerance to altitudinal stressors such as colder temperatures and less nutrient availability.},
}
@article {pmid38701091,
year = {2024},
author = {Aggarwal, S and Walker, FC and Weagley, JS and McCune, BT and Wu, X and Schriefer, LA and Makimaa, H and Lawrence, D and Sridhar, P and Baldridge, MT},
title = {Interferons and tuft cell numbers are bottlenecks for persistent murine norovirus infection.},
journal = {PLoS pathogens},
volume = {20},
number = {5},
pages = {e1011961},
pmid = {38701091},
issn = {1553-7374},
support = {R01 AI139314/AI/NIAID NIH HHS/United States ; R01 AI127552/AI/NIAID NIH HHS/United States ; F32 AI138392/AI/NIAID NIH HHS/United States ; R25 GM103757/GM/NIGMS NIH HHS/United States ; T32 AI007172/AI/NIAID NIH HHS/United States ; T32 GM007067/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Norovirus/physiology ; *Caliciviridae Infections/virology/immunology ; Mice ; *Interferons/metabolism ; Persistent Infection/virology/immunology ; Mice, Inbred C57BL ; Intestinal Mucosa/virology/immunology ; Gastroenteritis/virology ; Virus Replication ; Mice, Knockout ; Immunity, Innate ; Virus Shedding ; },
abstract = {Noroviruses (NoVs) are a leading cause of viral gastroenteritis. Despite global clinical relevance, our understanding of how host factors, such as antiviral cytokines interferons (IFNs), modulate NoV population dynamics is limited. Murine NoV (MNoV) is a tractable in vivo model for the study of host regulation of NoV. A persistent strain of MNoV, CR6, establishes a reservoir in intestinal tuft cells for chronic viral shedding in stool. However, the influence of host innate immunity and permissive cell numbers on viral population dynamics is an open question. We generated a pool of 20 different barcoded viruses (CR6BC) by inserting 6-nucleotide barcodes at the 3' position of the NS4 gene and used this pool as our viral inoculum for in vivo infections of different mouse lines. We found that over the course of persistent CR6 infection, shed virus was predominantly colon-derived, and viral barcode richness decreased over time irrespective of host immune status, suggesting that persistent infection involves a series of reinfection events. In mice lacking the IFN-λ receptor, intestinal barcode richness was enhanced, correlating with increased viral intestinal replication. IL-4 treatment, which increases tuft cell numbers, also increased barcode richness, indicating the abundance of permissive tuft cells to be a bottleneck during CR6 infection. In mice lacking type I IFN signaling (Ifnar1-/-) or all IFN signaling (Stat1-/-), barcode diversity at extraintestinal sites was dramatically increased, implicating different IFNs as critical bottlenecks at specific tissue sites. Of interest, extraintestinal barcodes were overlapping but distinct from intestinal barcodes, indicating that disseminated virus represents a distinct viral population than that replicating in the intestine. Barcoded viruses are a valuable tool to explore the influence of host factors on viral diversity in the context of establishment and maintenance of infection as well as dissemination and have provided important insights into how NoV infection proceeds in immunocompetent and immunocompromised hosts.},
}
@article {pmid38699326,
year = {2024},
author = {Zhuang, X and Vo, V and Moshi, MA and Dhede, K and Ghani, N and Akbar, S and Chang, CL and Young, AK and Buttery, E and Bendik, W and Zhang, H and Afzal, S and Moser, D and Cordes, D and Lockett, C and Gerrity, D and Kan, HY and Oh, EC},
title = {Early Detection of Novel SARS-CoV-2 Variants from Urban and Rural Wastewater through Genome Sequencing and Machine Learning.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.18.24306052},
pmid = {38699326},
abstract = {Genome sequencing from wastewater has emerged as an accurate and cost-effective tool for identifying SARS-CoV-2 variants. However, existing methods for analyzing wastewater sequencing data are not designed to detect novel variants that have not been characterized in humans. Here, we present an unsupervised learning approach that clusters co-varying and time-evolving mutation patterns leading to the identification of SARS-CoV-2 variants. To build our model, we sequenced 3,659 wastewater samples collected over a span of more than two years from urban and rural locations in Southern Nevada. We then developed a multivariate independent component analysis (ICA)-based pipeline to transform mutation frequencies into independent sources with co-varying and time-evolving patterns and compared variant predictions to >5,000 SARS-CoV-2 clinical genomes isolated from Nevadans. Using the source patterns as data-driven reference "barcodes", we demonstrated the model's accuracy by successfully detecting the Delta variant in late 2021, Omicron variants in 2022, and emerging recombinant XBB variants in 2023. Our approach revealed the spatial and temporal dynamics of variants in both urban and rural regions; achieved earlier detection of most variants compared to other computational tools; and uncovered unique co-varying mutation patterns not associated with any known variant. The multivariate nature of our pipeline boosts statistical power and can support accurate and early detection of SARS-CoV-2 variants. This feature offers a unique opportunity for novel variant and pathogen detection, even in the absence of clinical testing.},
}
@article {pmid38695131,
year = {2025},
author = {Ramos, SC and Culver, M},
title = {Integration of Indigenous Research Methodologies, Traditional Ecological Knowledge and molecular scatology in an assessment of mesocarnivore presence, diet and habitat use on Yurok Ancestral Lands.},
journal = {Molecular ecology resources},
volume = {25},
number = {2},
pages = {e13963},
doi = {10.1111/1755-0998.13963},
pmid = {38695131},
issn = {1755-0998},
support = {2010-3-03//The University of Arizona/Sloan Indigenous Graduate Partnership Program/ ; 1906338//National Science Foundation/ ; },
mesh = {Animals ; *Ecosystem ; *Diet ; DNA Barcoding, Taxonomic/methods ; Lynx/genetics/classification/physiology ; Ecology/methods ; Foxes/genetics/classification ; Feeding Behavior ; },
abstract = {Partnerships between Tribes and researchers in wildlife monitoring and application of Traditional Ecological Knowledge (TEK) have taken a variety of forms, and some scholars have noted a need for culturally sensitive approaches. Guided by Indigenous Research Methodologies, this research is coupled with Yurok TEK, or hlkelonah 'ue-megetohl ('to take care of the earth'), enabling an applied, culturally sensitive approach in partnership with the Yurok Tribe. We present results from a molecular scatology study of wildlife within the ancestral territory of the Yurok Tribe. Scats were collected opportunistically on road transects. All samples (N = 132) were analysed via DNA barcoding and results matched to documented 'Oohl 'we-toh (Yurok language) names to determine the depositor species (N = 8). Though there were four focal mesocarnivore species in our study, only bobcat (Chmuuek; Lynx rufus) and gray fox (Wergers; Urocyon cinereoargenteus) were detected as depositor species. Post hoc analyses were conducted to explore distribution, habitat use and selection in a use-availability context, and food habits of these two species. We found almost complete separation of bobcat and gray fox use of transects, as well as indication of partitioning of vegetation cover types and food. We demonstrate an integrated framework of Western and Indigenous sciences that allows the Indigenous researcher to transcend structured academic disciplinary boundaries. Our approach can be modified for partnerships between Tribes, agencies, academics and students for wildlife monitoring in broader geographic regions in various research applications.},
}
@article {pmid38694266,
year = {2024},
author = {Ossowska, EA and Moncada, B and Lücking, R and Flakus, A and Rodriguez-Flakus, P and Olszewska, S and Kukwa, M},
title = {Additional new species and new records of the genus Sticta (lichenised Ascomycota, lobarioid Peltigeraceae) from Bolivia.},
journal = {MycoKeys},
volume = {105},
number = {},
pages = {21-47},
pmid = {38694266},
issn = {1314-4049},
abstract = {Four species of the genus Sticta are described as new from Bolivia, based on morphological examination and phylogenetic analysis of the fungal ITS barcoding marker. Additionally, two species are reported as new to Bolivia (their identification confirmed by molecular data) and one previously reported species is confirmed by molecular data for the first time. Detailed morphological and anatomical descriptions are provided for all new species. Two of the new species, S.isidiolobulata Ossowska, B. Moncada, Lücking &amp; Kukwa and S.madidiensis Ossowska, B. Moncada, Lücking &amp; Kukwa belong to clade I, as defined in previous studies. In contrast, S.montepunkuensis Ossowska, B. Moncada, Lücking &amp; Kukwa and S.macrolobata Ossowska, B. Moncada, Lücking &amp; Kukwa, also described here as new to science, belong to clade III. Stictaisidiolobulata has an irregular to suborbicular thallus of medium size, with isidia developing into spathulate lobules, cyanobacterial photobiont and apothecia with entire to weakly-crenate margins. The large irregular thallus of the cyanobacteria-associated S.macrolobata has broad lobes, apothecia with verrucous to tomentose margins and cyphellae with raised margins, whereas S.madidiensis has a medium-sized, palmate to irregular thallus with a stipe, but without vegetative propagules and apothecia. Stictamontepunkuensis has large and irregular thalli with green algae as photobiont, apothecia with crenate to verrucous margins and urceolate cyphellae with a wide pore and a scabrid basal membrane. Two species, S.beauvoisii Delise and S.riparia Merc.-Díaz are reported as new to Bolivia (the latter also as new to South America) and belong to clade III. Stictatomentosa (Sw.) Ach., species confirmed from Bolivia by molecular data, belongs to clade II. Stictabeauvoisii is characterised by a smooth yellowish-brown upper surface with darker apices and abundant, marginal isidia and a brown lower surface with golden-chocolate brown primary tomentum and sparse, golden-brown rhizines. Stictariparia has a strongly branched thallus, with undulate lobes and abundant, marginal, palmate, grey to dark brown phyllidia and greyish-brown lower surface with the primary tomentum absent towards the margins. Stictatomentosa has palmate, bluish thalli with white cilia and abundant, submarginal apothecia and creamy-white lower surface with a sparse, white primary tomentum.},
}
@article {pmid38693183,
year = {2024},
author = {Moustafa, MAM and Mohamed, WMA and Chatanga, E and Naguib, D and Matsuno, K and Gofton, AW and Barker, SC and Nonaka, N and Nakao, R},
title = {Unraveling the phylogenetics of genetically closely related species, Haemaphysalis japonica and Haemaphysalis megaspinosa, using entire tick mitogenomes and microbiomes.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9961},
pmid = {38693183},
issn = {2045-2322},
support = {16H06431//Japan Society for the Promotion of Science/ ; 19H03118//Japan Society for the Promotion of Science/ ; 19F19097//Japan Society for the Promotion of Science/ ; 20K21358//Japan Society for the Promotion of Science/ ; 20KK0151//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *Phylogeny ; *Ixodidae/microbiology/genetics ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Genome, Mitochondrial ; Genetic Variation ; },
abstract = {Ticks have a profound impact on public health. Haemaphysalis is one of the most widespread genera in Asia, including Japan. The taxonomy and genetic differentiation of Haemaphysalis spp. is challenging. For instance, previous studies struggled to distinguish Haemaphysalis japonica and Haemaphysalis megaspinosa due to the dearth of nucleotide sequence polymorphisms in widely used barcoding genes. The classification of H. japonica japonica and its related sub-species Haemaphysalis japonica douglasi or Haemaphysalis jezoensis is also confused due to their high morphological similarity and a lack of molecular data that support the current classification. We used mitogenomes and microbiomes of H. japonica and H. megaspinosa to gain deeper insights into the phylogenetic relationships and genetic divergence between two species. Phylogenetic analyses of concatenated nucleotide sequences of protein-coding genes and ribosomal DNA genes distinguished H. japonica and H. megaspinosa as monophyletic clades, with further subdivision within the H. japonica clade. The 16S rRNA and NAD5 genes were valuable markers for distinguishing H. japonica and H. megaspinosa. Population genetic structure analyses indicated that genetic variation within populations accounted for a large proportion of the total variation compared to variation between populations. Microbiome analyses revealed differences in alpha and beta diversity between H. japonica and H. megaspinosa: H. japonica had the higher diversity. Coxiella sp., a likely endosymbiont, was found in both Haemaphysalis species. The abundance profiles of likely endosymbionts, pathogens, and commensals differed between H. japonica and H. megaspinosa: H. megaspinosa was more diverse.},
}
@article {pmid38690989,
year = {2024},
author = {Li, J and Li, M and Wuethrich, A and Guan, R and Zhao, L and Hu, C and Trau, M and Sun, Y},
title = {Molecular Stratification and Treatment Monitoring of Lung Cancer Using a Small Extracellular Vesicle-Activated Nanocavity Architecture.},
journal = {Analytical chemistry},
volume = {96},
number = {19},
pages = {7651-7660},
doi = {10.1021/acs.analchem.4c00558},
pmid = {38690989},
issn = {1520-6882},
mesh = {*Extracellular Vesicles/chemistry/metabolism ; *Lung Neoplasms/metabolism ; Humans ; *Spectrum Analysis, Raman ; *Gold/chemistry ; Microelectrodes ; },
abstract = {Development of molecular diagnostics for lung cancer stratification and monitoring is crucial for the rational planning and timely adjustment of treatments to improve clinical outcomes. In this regard, we propose a nanocavity architecture to sensitively profile the protein signature on small extracellular vesicles (sEVs) to enable accurate, noninvasive staging and treatment monitoring of lung cancer. The nanocavity architecture is formed by molecular recognition through the binding of sEVs with the nanobox-based core-shell surface-enhanced Raman scattering (SERS) barcodes and mirrorlike, asymmetric gold microelectrodes. By imposing an alternating current on the gold microelectrodes, a nanofluidic shear force was stimulated that supported the binding of sEVs and the efficient assembly of the nanoboxes. The binding of sEVs further induced a nanocavity between the nanobox and the gold microelectrode that significantly amplified the electromagnetic field to enable the simultaneous enhancement of Raman signals from four SERS barcodes and generate patient-specific molecular sEV signatures. Importantly, evaluated on a cohort of clinical samples (n = 76) on the nanocavity architecture, the acquired patient-specific sEV molecular signatures achieved accurate identification, stratification, and treatment monitoring of lung cancer patients, highlighting its potential for transition to clinical utility.},
}
@article {pmid38688969,
year = {2024},
author = {Blanc-Benigeri, A and Poirier, V and Narango, D and Elliott, KH and Frei, B},
title = {Diet of moulting Swainson's Thrushes (Catharus ustulatus) and Tennessee Warblers (Leiothlypis peregrina) at a stopover site during fall migration measured with fecal DNA metabarcoding.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9913},
pmid = {38688969},
issn = {2045-2322},
support = {#522431//Natural Sciences and Engineering Research Council of Canada-Undergraduate Student Research Award (NSERC USRA)/ ; #320544//Graduate Scholarship-Master's (CGS M) award, a Fonds de recherche du Qu&#xe9;bec-Nature et technologies (FRQNT)/ ; },
mesh = {Animals ; *Animal Migration/physiology ; *Songbirds/physiology ; *Diet ; *Feces/chemistry ; DNA Barcoding, Taxonomic/methods ; Seasons ; },
abstract = {Moult and migration are energetically demanding and require adequate nutrition. In some species, individuals may interrupt their fall migration to moult at discrete stopover locations outside of their breeding grounds (i.e., moult-migration) leading to competing nutritional demands for moult and migration. Here, we use DNA barcoding of fecal samples to compare the diet of moulting and actively migrating (post-moult) Swainson's Thrushes (Catharus ustulatus) and Tennessee Warblers (Leiothlypis peregrina) during their fall migration stopover at a large urban greenspace in Montreal, Canada. Diet differed according to moult status, species, and seasonality. Swainson's Thrushes had a broad diet with frequent detections of both insects and berry-producing shrubs; while detections in Tennessee Warblers' diets were mainly arthropods. For both species, more actively migrating individuals consumed fleshy-fruiting plants than moulting individuals. A higher proportion of moulting birds consumed arthropods compared to active migrants, due to either arthropod availability or a dietary preference for proteinaceous foods to grow feathers. Both species and moult classes consumed more native plants than non-native plants later in the season. We show the importance of managing urban greenspaces with native plants and diverse food sources that can provide for the different dietary needs of migratory birds.},
}
@article {pmid38684618,
year = {2024},
author = {Wang, X and Zhang, Z and Shi, Y and Man, J and Huang, Y and Zhang, X and Liu, S and He, G and An, K and Amu, L and Chen, W and Liu, Z and Wang, X and Wei, S},
title = {Population identification and genetic diversity analysis of Fritillaria ussuriensis (Fritillaria) based on chloroplast genes atpF and petB.},
journal = {Journal of applied genetics},
volume = {65},
number = {3},
pages = {453-462},
pmid = {38684618},
issn = {2190-3883},
support = {20221156//study on breeding and cultivation technology of precision medicine Bupleurum bupleurum based on molecular anti-counterfeiting technology/ ; 2020110031009385//research project on molecular anti-counterfeiting technology of 4 precision medicinal materials such as Platycodon grandiflorus/ ; 2022YFC3501505//National Key Research and Development Program of China/ ; },
mesh = {*Fritillaria/genetics/classification ; *Haplotypes/genetics ; *Genetic Variation ; Genetics, Population ; DNA Barcoding, Taxonomic ; Genome, Chloroplast/genetics ; Genes, Chloroplast/genetics ; Phylogeny ; DNA, Chloroplast/genetics ; Chloroplasts/genetics ; Evolution, Molecular ; },
abstract = {The chloroplast genomes of five Fritillaria ussuriensis materials from different production areas were comparatively analyzed, atpF and petB were screened as specific DNA barcodes, and the population identification and genetic diversity of F. ussuriensis were analyzed based on them. The F. ussuriensis chloroplast genome showed a total length of 151 515-151 548 bp with a typical tetrad structure and encoded 130 genes. atpF and petB were used to amplify 183 samples from 13 populations, and they could identify 6 and 9 haplotypes, respectively. Joint analysis of the two sequences revealed 18 haplotypes, named H1-H18, with the most widely distributed and most abundant being H4. Ten haplotypes were unique for 7 populations that they could be used to distinguish from others. Haplotype diversity and nucleotide diversity were 0.99 and 2.09 × 10[-3], respectively, indicating the genetic diversity was relatively rich. The results of the intermediary adjacency network showed that H5 was the oldest haplotype, and stellate radiation was centered around it, indicating that population expansion occurred in genuine production areas. This study lays a theoretical foundation for the population identification, genetic evolution, and breed selection of F. ussuriensis.},
}
@article {pmid38683343,
year = {2024},
author = {Vences, M and Miralles, A and DeSalle, R},
title = {A Glossary of DNA Barcoding Terms.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {561-572},
pmid = {38683343},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; Terminology as Topic ; DNA/genetics ; Humans ; },
abstract = {This chapter provides a reference glossary for the protocols in this volume. We have chosen only the very basic terms in the DNA barcode lexicon to include, and provide clear and concise definitions of these terms. We hope the reader finds this glossary useful.},
}
@article {pmid38683342,
year = {2024},
author = {Williams, J and Nash, B and Ghiban, C and Khalfan, M and Hilgert, U and Lauter, S and Yang, CH and Micklos, DA},
title = {Analysis of DNA Barcodes Using DNA Subway.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {551-560},
pmid = {38683342},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; *Computational Biology/methods ; Phylogeny ; DNA/genetics ; Workflow ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {DNA Subway makes bioinformatic analysis of DNA barcodes classroom friendly, eliminating the need for software installations or command line tools. Subway bundles research-grade bioinformatics software into workflows with an easy-to-use interface. This chapter covers DNA Subway's DNA barcoding analysis workflow (Blue Line) starting with one or more Sanger sequence reads. During analysis, users can view trace files and sequence quality, pair and align forward and reverse reads, create and trim consensus sequences, perform BLAST searches, select reference data, align multiple sequences, and compute phylogenetic trees. High-quality sequences with the required metadata can also be submitted as barcode sequences to NCBI GenBank.},
}
@article {pmid38683341,
year = {2024},
author = {Shumskaya, M},
title = {DNA Barcoding for an Undergraduate Class.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {537-550},
pmid = {38683341},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Students ; Universities ; DNA/genetics/analysis ; Humans ; Curriculum ; Polymerase Chain Reaction/methods ; },
abstract = {DNA technique is a topic mandatorily covered in a biology and biochemistry undergraduate curriculum. Inquiry-based pedagogy is proven to be the most effective way of learning, and DNA barcoding method allows to merge necessary-to-study experimental techniques such as DNA isolation and purification, PCR, and basic BLAST search into a two- or three-week inquiry-based student project. It also provides a research-based experience to the students, who, when organized in groups, can design their own DNA-barcoding project if they wish. Here, we describe how DNA barcoding can be offered in an undergraduate college or advanced high school settings. This chapter is intended to help college and high school instructors to include DNA barcoding in their classes.},
}
@article {pmid38683340,
year = {2024},
author = {Wright, L and Garbarino, J and Marizzi, C},
title = {Engaging Students and Teachers as Community Scientists in DNA Barcoding Initiatives.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {525-535},
pmid = {38683340},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Students ; Humans ; Curriculum ; Faculty ; },
abstract = {Historically, contributions to scientific knowledge have been perceived as something that only professional scientists have the ability to affect. This has led to the belief that scientific pursuits are done not by everyday people but by individuals who have no connection to the communities that their discoveries might impact. DNA barcoding initiatives have the potential to bridge this gap. Community leaders, students, teachers, and other community members can come together with engaged scientists to solve relevant issues that affect them. Over the last 20 years, DNA barcoding has been used successfully in a variety of educational contexts to incorporate original research into school curricula and informal outreach and education programs. DNA barcoding is especially suitable for educational settings because it is conceptually and technically straightforward, the workflow is adaptable to a variety of situations, and free and open-access online tools exist that allow participants to contribute high-quality data to international research efforts. DNA barcoding also offers a unique service-learning opportunity, where participants gain both knowledge and confidence in science. This is important because a growing body of evidence suggests that actively conducting research increases student and teacher engagement and retention of students in science. Here, we describe a framework and case studies in different educational settings that can be modeled and adapted to various educational contexts.},
}
@article {pmid38683339,
year = {2024},
author = {Pepenella, S and Hackett, J and Fernandez-Marco, C and Petracca, J and Marizzi, C and Nash, B and Micklos, DA},
title = {A Rapid, Equipment-Free DNA Isolation Method for DNA Barcoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {517-523},
pmid = {38683339},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; DNA/isolation &amp; purification/genetics ; DNA, Plant/genetics/isolation &amp; purification ; Plants/genetics ; Chromatography/methods ; Lichens/genetics ; },
abstract = {This rapid, equipment-free DNA isolation procedure using chromatography paper is a simple method that can be performed in less than 30 min and requires no wet lab experience. With minimal expense, it offers an affordable alternative for anyone wanting to explore biodiversity. It also provides an excellent option for use in classrooms or other activities that are time limited. The method works best for plants or lichens, producing stable DNA on Whatman® chromatography paper at room temperature, which can be eluted as needed.},
}
@article {pmid38683338,
year = {2024},
author = {Wangh, LJ and Rice, JE and Sanchez, JA},
title = {Recent Applications of FastFish-ID.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {503-514},
pmid = {38683338},
issn = {1940-6029},
mesh = {Animals ; *Fishes ; *Sharks ; *DNA Barcoding, Taxonomic/methods ; Animal Fins ; },
abstract = {FastFish-ID via Closed-Tube barcoding is a portable platform for rapid and accurate identification of fish species that was conceived at Brandeis University, commercialized at Thermagenix, Inc., and further improved at Ecologenix, LLC (see Chap. 17 in this volume). This chapter focuses on the use of FastFish-ID for (1) identification of intraspecies variants, (2) quantitative use of FastFish-ID to measure the decay of fresh fish, and (3) use of FastFish-ID for the identification of dried and processed shark fins.},
}
@article {pmid38683337,
year = {2024},
author = {Gwiazdowski, R},
title = {Principles for Constructing DNA Barcode Reference Libraries.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {491-502},
pmid = {38683337},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Gene Library ; Reference Standards ; DNA/genetics ; Humans ; },
abstract = {All DNA barcode methods rely on reference sequences linked to well-curated voucher specimens. Definitions for and locations of DNA barcode reference libraries are not standardized, and vary throughout the literature. Standardizing, and centralizing reference specimens would provide an unambiguous source, analogous to reference genomes, to reproduce identifications and improve a library. This chapter proposes a working definition of a DNA barcode reference library, consistent with DNA barcode data standards, along with principles and methods to consider when producing or using such a library. These methods allow explicit traceback to sequence-sources which elevate the value of voucher specimens, and create a potential for community curation.},
}
@article {pmid38683336,
year = {2024},
author = {O'Brien, TD and Blanco-Bercial, L and Questel, JM and Batta-Lona, PG and Bucklin, A},
title = {MetaZooGene Atlas and Database: Reference Sequences for Marine Ecosystems.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {475-489},
pmid = {38683336},
issn = {1940-6029},
mesh = {Animals ; *Aquatic Organisms/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Ecosystem ; Databases, Genetic ; Databases, Nucleic Acid ; },
abstract = {The MetaZooGene Atlas and Database (MZGdb; https://metazoogene.org/mzgdb/) is an open-access data and metadata portal synchronized with the NCBI GenBank and BOLD data repositories. The MZGdb includes sequences for genes used for the classification and identification of marine organisms based on DNA barcoding and metabarcoding. The focus of the MZGdb is biodiversity of marine ecosystems, including phytoplankton and microbes, zooplankton and invertebrates, fish, and other marine vertebrates (pinnipeds, cetaceans, and sea turtles). DNA sequences currently included are mitochondrial cytochrome oxidase I (COI), 12S, and 16S rRNA, and nuclear 18S and 28S rRNA. The MZGdb provides data and mapping tools for assembling and downloading compilations of reference sequence data that are specific to selected genes, taxonomic groups, and/or ocean regions. An additional feature of the MZGdb is the Atlas which summarizes data coverage and proportional completeness based on statistics of species with available sequences versus species commonly found in each ocean region.This chapter is a collaborative effort of the Scientific Committee for Ocean Research (SCOR) Working Group WG157: MetaZooGene: Toward a new global view of marine zooplankton biodiversity based on DNA metabarcoding and reference DNA sequence databases (https://metazoogene.org).},
}
@article {pmid38683335,
year = {2024},
author = {Whitley, BS and Li, Z and Jones, L and de Vere, N},
title = {Mega-Barcoding Projects: Delivering National DNA Barcoding Initiatives for Plants.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {445-473},
pmid = {38683335},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Plants/genetics ; *DNA, Plant/genetics ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods ; Gene Library ; },
abstract = {Plant DNA barcoding has a multitude of applications ranging from species detection and biomonitoring to investigating ecological networks and checking food quality. The ability to accurately identify species, using DNA barcoding, depends on the quality and comprehensiveness of the reference library that is used. This chapter describes how to create plant reference libraries using the rbcL, matK, and ITS2 DNA barcode regions. It covers the creation of species lists, the collection of specimens from the field and herbarium, DNA extraction, PCR amplification, and DNA sequencing. This methodology gives special attention to using samples from herbaria, as they represent important collections of easily accessible, taxonomically verified plant material.},
}
@article {pmid38683334,
year = {2024},
author = {Ratnasingham, S and Wei, C and Chan, D and Agda, J and Agda, J and Ballesteros-Mejia, L and Boutou, HA and El Bastami, ZM and Ma, E and Manjunath, R and Rea, D and Ho, C and Telfer, A and McKeowan, J and Rahulan, M and Steinke, C and Dorsheimer, J and Milton, M and Hebert, PDN},
title = {BOLD v4: A Centralized Bioinformatics Platform for DNA-Based Biodiversity Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {403-441},
pmid = {38683334},
issn = {1940-6029},
mesh = {*Biodiversity ; *DNA Barcoding, Taxonomic/methods ; *Computational Biology/methods ; Software ; DNA/genetics ; },
abstract = {BOLD, the Barcode of Life Data System, supports the acquisition, storage, validation, analysis, and publication of DNA barcodes, activities requiring the integration of molecular, morphological, and distributional data. Its pivotal role in curating the reference library of DNA barcodes, coupled with its data management and analysis capabilities, makes it a central resource for biodiversity science. It enables rapid, accurate identification of specimens and also reveals patterns of genetic diversity and evolutionary relationships among taxa.Launched in 2005, BOLD has become an increasingly powerful tool for advancing the understanding of planetary biodiversity. It currently hosts 17 million specimen records and 14 million barcodes that provide coverage for more than a million species from every continent and ocean. The platform has the long-term goal of providing a consistent, accurate system for identifying all species of eukaryotes.BOLD's integrated analytical tools, full data lifecycle support, and secure collaboration framework distinguish it from other biodiversity platforms. BOLD v4 brought enhanced data management and analysis capabilities as well as novel functionality for data dissemination and publication. Its next version will include features to strengthen its utility to the research community, governments, industry, and society-at-large.},
}
@article {pmid38683333,
year = {2024},
author = {Damaso, N and Elwick, KE and Robertson, JM},
title = {Guidelines for the Analysis of DNA Barcoding/Metabarcoding Sequencing Data and Interpretation of Publicly Available Databases.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {391-402},
pmid = {38683333},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Databases, Nucleic Acid ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; Databases, Genetic ; Software ; },
abstract = {This chapter describes procedures for the use of DNA sequence data to obtain and compare taxonomic identification using the public databases GenBank and Barcode of Life Data System (BOLD). The chapter begins by describing procedures used to prepare quality sequences for uploading into GenBank and BOLD. Next, steps used to query the DNA sequences against the public databases are described using GenBank BLAST and BOLD identification engines. Interpretation guidelines for the taxonomic identification assignments are presented. Finally, a procedure for evaluating the accuracy and reliability of sequences from GenBank and BOLD is provided.},
}
@article {pmid38683332,
year = {2024},
author = {Phillips, JD and Griswold, CK and Young, RG and Hubert, N and Hanner, RH},
title = {A Measure of the DNA Barcode Gap for Applied and Basic Research.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {375-390},
pmid = {38683332},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; Coleoptera/genetics/classification ; DNA/genetics/analysis ; Species Specificity ; },
abstract = {DNA barcoding has largely established itself as a mainstay for rapid molecular taxonomic identification in both academic and applied research. The use of DNA barcoding as a molecular identification method depends on a "DNA barcode gap"-the separation between the maximum within-species difference and the minimum between-species difference. Previous work indicates the presence of a gap hinges on sampling effort for focal taxa and their close relatives. Furthermore, both theory and empirical work indicate a gap may not occur for related pairs of biological species. Here, we present a novel evaluation approach in the form of an easily calculated set of nonparametric metrics to quantify the extent of proportional overlap in inter- and intraspecific distributions of pairwise differences among target species and their conspecifics. The metrics are based on a simple count of the number of overlapping records for a species falling within the bounds of maximum intraspecific distance and minimum interspecific distance. Our approach takes advantage of the asymmetric directionality inherent in pairwise genetic distance distributions, which has not been previously done in the DNA barcoding literature. We apply the metrics to the predatory diving beetle genus Agabus as a case study because this group poses significant identification challenges due to its morphological uniformity despite both relative sampling ease and well-established taxonomy. Results herein show that target species and their nearest neighbor species were found to be tightly clustered and therefore difficult to distinguish. Such findings demonstrate that DNA barcoding can fail to fully resolve species in certain cases. Moving forward, we suggest the implementation of the proposed metrics be integrated into a common framework to be reported in any study that uses DNA barcoding for identification. In so doing, the importance of the DNA barcode gap and its components for the success of DNA-based identification using DNA barcodes can be better appreciated.},
}
@article {pmid38683331,
year = {2024},
author = {Mahmoud, MAB},
title = {Classification of DNA Sequence Based on a Non-gradient Algorithm: Pseudoinverse Learners.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {359-373},
pmid = {38683331},
issn = {1940-6029},
mesh = {*Algorithms ; *Neural Networks, Computer ; DNA/genetics ; Computational Biology/methods ; DNA Barcoding, Taxonomic/methods ; Sequence Analysis, DNA/methods ; Humans ; Deep Learning ; },
abstract = {This chapter proposes a prototype-based classification approach for analyzing DNA barcodes that uses a spectral representation of DNA sequences and a non-gradient neural network. Biological sequences can be viewed as data components with higher non-fixed dimensions, which correspond to the length of the sequences. Through computational procedures such as one-hot encoding, numerical encoding plays an important role in DNA sequence evaluation (OHE). However, the OHE method has some disadvantages: (1) It does not add any details that could result in an additional predictive variable, and (2) if the variable has many classes, OHE significantly expands the feature space. To address these shortcomings, this chapter proposes a computationally efficient framework for classifying DNA sequences of living organisms in the image domain. A multilayer perceptron trained by a pseudoinverse learning autoencoder (PILAE) algorithm is used in the proposed strategy. The learning control parameters and the number of hidden layers do not have to be specified during the PILAE training process. As a result, the PILAE classifier outperforms other deep neural network (DNN) strategies such as the VGG-16 and Xception models.},
}
@article {pmid38683330,
year = {2024},
author = {Bergmann, T},
title = {CAOS-R: Character-Based Barcoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {347-357},
pmid = {38683330},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; },
abstract = {CAOS-Barcoding is a culmination of traditional taxonomy and modern DNA barcoding. CAOS identifies taxa by diagnostic characters as is done in traditional taxonomy and produces an identification matrix for taxon discrimination similar to DNA barcoding distance matrices. Here, I describe how to set up the CAOS-Barcoder and CAOS-Classifier software, which input data is needed, and how to interpret the output data. With the CAOS-Barcoder, single marker or concatenated data can be processed into diagnostic barcodes for taxon discrimination. The CAOS-Classifier can use the diagnostic barcodes for specimen identification.},
}
@article {pmid38683329,
year = {2024},
author = {Ramanan, V and Sarkar, IN},
title = {Characteristic Attribute Organization System (CAOS): Identifying Classification Rules Based on Phylogenetically Organized Sequences.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {335-345},
pmid = {38683329},
issn = {1940-6029},
mesh = {*Phylogeny ; *Software ; Computational Biology/methods ; Algorithms ; Sequence Alignment/methods ; },
abstract = {Classification is a technique that labels subjects based on the characteristics of the data. It often includes using prior learned information from preexisting data drawn from the same distribution or data type to make informed decisions per each given subject. The method presented here, the Characteristic Attribute Organization System (CAOS), uses a character-based approach to molecular sequence classification. Using a set of aligned sequences (either nucleotide or amino acid) and a maximum parsimony tree, CAOS will generate classification rules for the sequences based on tree structure and provide more interpretable results than other classification or sequence analysis protocols. The code is accessible at https://github.com/JuliaHealth/CAOS.jl/ .},
}
@article {pmid38683328,
year = {2024},
author = {Puillandre, N and Miralles, A and Brouillet, S and Fedosov, A and Fischell, F and Patmanidis, S and Vences, M},
title = {Species Delimitation and Exploration of Species Partitions with ASAP and LIMES.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {313-334},
pmid = {38683328},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; *Computational Biology/methods ; Biodiversity ; Phylogeny ; Species Specificity ; Animals ; Genetic Speciation ; },
abstract = {DNA barcoding plays an important role in exploring undescribed biodiversity and is increasingly used to delimit lineages at the species level (see Chap. 4 by Miralles et al.). Although several approaches and programs have been developed to perform species delimitation from datasets of single-locus DNA sequences, such as DNA barcodes, most of these were not initially provided as user-friendly GUI-driven executables. In spite of their differences, most of these tools share the same goal, i.e., inferring de novo a partition of subsets, potentially each representing a distinct species. More recently, a proposed common exchange format for the resulting species partitions (SPART) has been implemented by several of these tools, paving the way toward developing an interoperable digital environment entirely dedicated to integrative and comparative species delimitation. In this chapter, we provide detailed protocols for the use of two bioinformatic tools, one for single locus molecular species delimitation (ASAP) and one for statistical comparison of species partitions resulting from any kind of species delimitation analyses (LIMES).},
}
@article {pmid38683327,
year = {2024},
author = {Fedosov, A and Puillandre, N and Fischell, F and Patmanidis, S and Miralles, A and Vences, M},
title = {DNA Barcode-Based Species Diagnosis with MolD.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {297-311},
pmid = {38683327},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; *Computational Biology/methods ; Phylogeny ; Biodiversity ; },
abstract = {Rapid biodiversity loss sets new requirements for taxonomic research, prompting updating some long-established practices to maximize timely documentation of species before they have gone extinct. One of the crucial procedures associated with the description of new taxa in Linnean taxonomy is assigning them a diagnosis, which is an account of the specific features of the taxon, differentiating it from already described species. Traditionally, diagnostic characters have been morphological, but especially in the case of morphologically cryptic species, molecular diagnoses become increasingly important. In this chapter, we provide detailed protocols for molecular taxon diagnosis with the bioinformatic tool MolD which is available as open-source Python code, command-line driven binary, GUI-driven executable for Windows and Mac, and Galaxy implementation. MolD identifies diagnostic combinations of nucleotides (DNCs) in addition to single (pure) diagnostic sites, enabling users to base DNA diagnoses on a minimal number of diagnostic sites necessary for reliable differentiation of taxa.},
}
@article {pmid38683326,
year = {2024},
author = {Vences, M and Patmanidis, S and Fedosov, A and Miralles, A and Puillandre, N},
title = {iTaxoTools 1.0: Improved DNA Barcode Exploration with TaxI2.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {281-296},
pmid = {38683326},
issn = {1940-6029},
mesh = {*Software ; *DNA Barcoding, Taxonomic/methods ; Computational Biology/methods ; DNA/genetics ; },
abstract = {The overall availability of user-friendly software tools tailored to the analysis of DNA barcodes is limited. Several obvious functions such as detecting and visualizing the DNA barcode gap, the calculation of matrices of pairwise distances at the level of species, or the filtering and decontaminating of sets of sequences based on comparisons with reference databases can typically be carried out only by complex procedures that involve various programs and/or a substantial manual work of formatting. The iTaxoTools project aims at contributing user-friendly software solutions to improve the speed and quality of the workflow of alpha-taxonomy. In this chapter, we provide detailed protocols for the use of a substantially improved version of the tool TaxI2 for distance-based exploration of DNA barcodes. The program calculates genetic distances from prealigned data sets, or based on pairwise alignments, or with an alignment-free approach. Sequence and metadata input can be formatted as tab-delimited files and TaxI2 then computes tables, matrices and graphs of distances, and distance summary statistics within and between species and genera. TaxI2 also includes modes to compare a set of sequences against one or two reference data sets and output lists of best matches or filter data according to thresholds or reciprocal matches. Here, detailed step-by-step protocols are provided for the use of TaxI2, as well as for the interpretation of the program's output.},
}
@article {pmid38683325,
year = {2024},
author = {Sanchez, JA and Rice, JE and Wangh, LJ},
title = {Recent Advances in Closed-Tube Barcoding for FastFish-ID.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {267-278},
pmid = {38683325},
issn = {1940-6029},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; Seafood ; Polymerase Chain Reaction/methods ; DNA, Mitochondrial/genetics ; Fisheries ; },
abstract = {FastFish-ID for rapid and accurate identification of fish species was conceived at Brandeis University based on pioneering work on Closed-Tube Barcoding (Rice et al., Mitochondrial DNA Part A 27(2):1358-1363, 2016; Sirianni et al., Genome 59:1049-1061, 2016). FastFish-ID was subsequently validated and commercialized at Thermagenix, Inc. using a portable device and high-precision PCR (Naaum et al., Food Res Int 141:110035, 2021). The motivation for these efforts was the pressing need for a technology that could be widely used throughout the seafood supply chain to combat IUU Fishing (Helyar et al., PLOS ONE 9, 2014) and overfishing (FAO, State of the World Fisheries and Aquaculture 2018. http://www.fao.org/documents/card/en/c/I9540EN/ , 2018), along with seafood fraud and mislabeling (Watson et al., Fish Fish 17:585-595, 2015). These destructive practices are wasting fish stocks, frustrating attempts to achieve seafood sustainability, endangering oceanic ecosystems, and causing consumers billions of dollars each year (Porterfield et al., Oceana: February, 2022). During the past three Covid19 pandemic years, EcologeniX, LLC has taken over further development and optimization of FastFish-ID. The present chapter provides an overview of the improvements introduced throughout the FastFish-ID process.},
}
@article {pmid38683323,
year = {2024},
author = {Liu, R and Wang, Y and Yao, X and Liu, C},
title = {Generating 2D Barcode for DNA Barcode Sequences.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {239-246},
pmid = {38683323},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; DNA/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {DNA barcode sequence is a short DNA sequence representing a sample from a particular species. The commonly used DNA barcodes are at least 200 bps long. This large number of characters cannot be encoded in two-dimensional codes for sample recognition and tracking. In the present study, we described a method that can be used to compress the DNA sequences and then generate the corresponding QR code. With the large numbers of software and hardware, the QR code can be used efficiently for printing, labeling, and scanning.},
}
@article {pmid38683322,
year = {2024},
author = {Srivathsan, A and Meier, R},
title = {Scalable, Cost-Effective, and Decentralized DNA Barcoding with Oxford Nanopore Sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {223-238},
pmid = {38683322},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods/economics ; *Nanopore Sequencing/methods ; Cost-Benefit Analysis ; High-Throughput Nucleotide Sequencing/methods/economics ; Software ; Gene Library ; Sequence Analysis, DNA/methods/economics ; Workflow ; DNA/genetics ; },
abstract = {DNA barcodes are useful in biodiversity research, but sequencing barcodes with dye termination methods ("Sanger sequencing") has been so time-consuming and expensive that DNA barcodes are not as widely used as they should be. Fortunately, MinION sequencers from Oxford Nanopore Technologies have recently emerged as a cost-effective and efficient alternative for barcoding. MinION barcodes are now suitable for large-scale species discovery and enable specimen identification when the target species are represented in barcode databases. With a MinION, it is possible to obtain 10,000 barcodes from a single flow cell at a cost of less than 0.10 USD per specimen. Additionally, a Flongle flow cell can be used for small projects requiring up to 300 barcodes (0.50 USD per specimen). We here describe a cost-effective laboratory workflow for obtaining tagged amplicons, preparing ONT libraries, sequencing amplicon pools, and analyzing the MinION reads with the software ONTbarcoder. This workflow has been shown to yield highly accurate barcodes that are 99.99% identical to Sanger barcodes. Overall, we propose that the use of MinION for DNA barcoding is an attractive option for all researchers in need of a cost-effective and efficient solution for large-scale species discovery and specimen identification.},
}
@article {pmid38683321,
year = {2024},
author = {Ivanov, V and Lee, KM and Mutanen, M},
title = {ddRAD Sequencing and DNA Barcoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {213-221},
pmid = {38683321},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Polymorphism, Single Nucleotide ; *Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; DNA/genetics ; Gene Library ; Humans ; },
abstract = {Double-digest restriction site-associated DNA sequencing is a library preparation protocol that enables capturing variable sites across the genome including single-nucleotide polymorphisms (SNPs). These SNPs can be utilized to gain evolutionary insights into patterns observed in DNA barcodes, to infer population structure and phylogenies, to detect gene flow and introgression, and to perform species delimitation analyses. The protocol includes chemically shearing genomic DNA with restriction enzymes, unique tagging, size selection, and amplification of the resulting DNA fragments. Here we provide a detailed description of each step of the protocol, as well as information on essential equipment and common issues encountered during laboratory work.},
}
@article {pmid38683320,
year = {2024},
author = {Seth, S and Bhattacharya, A},
title = {DNA Barcodes Using a Dual Nanopore Device.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {197-211},
pmid = {38683320},
issn = {1940-6029},
support = {R21 HG011236/HG/NHGRI NIH HHS/United States ; },
mesh = {*Nanopores ; *DNA Barcoding, Taxonomic/methods ; *Algorithms ; DNA/chemistry/genetics ; },
abstract = {We report a novel method based on the current blockade (CB) characteristics obtained from a dual nanopore device that can determine DNA barcodes with near-perfect accuracy using a Brownian dynamics simulation strategy. The method supersedes our previously reported velocity correction algorithm (S. Seth and A. Bhattacharya, RSC Advances, 11:20781-20787, 2021), taking advantage of the better measurement of the time-of-flight (TOF) protocol offered by the dual nanopore setup. We demonstrate the efficacy of the method by comparing our simulation data from a coarse-grained model of a polymer chain consisting of 2048 excluded volume beads of diameter 𝜎 = 24 bp using with those obtained from experimental CB data from a 48,500 bp λ-phage DNA, providing a 48500 2400 ≅ 24 base pair resolution in simulation. The simulation time scale is compared to the experimental time scale by matching the simulated time-of-flight (TOF) velocity distributions with those obtained experimentally (Rand et al., ACS Nano, 16:5258-5273, 2022). We then use the evolving coordinates of the dsDNA and the molecular features to reconstruct the current blockade characteristics on the fly using a volumetric model based on the effective van der Waal radii of the species inside and in the immediate vicinity of the pore. Our BD simulation mimics the control-zoom-in-logic to understand the origin of the TOF distributions due to the relaxation of the out-of-equilibrium conformations followed by a reversal of the electric fields. The simulation algorithm is quite general and can be applied to differentiate DNA barcodes from different species.},
}
@article {pmid38683319,
year = {2024},
author = {Sethi, S and Wijesinghe, KM and Dhakal, S},
title = {Single-Molecule FRET-Based Multiplexed Detection.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {183-195},
pmid = {38683319},
issn = {1940-6029},
mesh = {*Fluorescence Resonance Energy Transfer/methods ; *Single Molecule Imaging/methods ; *Fluorescent Dyes/chemistry ; Biosensing Techniques/methods ; Humans ; },
abstract = {Single-molecule multiplexed detection is a high-promise toolkit for the expanding field of biosensing and molecular diagnostics. Among many single-molecule techniques available today for biomarker sensing including fluorescence, force, electrochemical, spectroscopic, barcoding, and other techniques, fluorescence-based approaches are arguably the most widely used methods due to their high sensitivity, selectivity, and readily available fluorophore-labeling schemes for a wide variety of biomolecules. However, multiplexed imaging using fluorescence techniques has proven to be challenging due to the sophisticated labeling schemes often requiring multiple FRET (fluorescence resonance energy transfer) pairs and/or excitation sources, which lead to overlapping signals and complicate data analysis. Here, we describe a single-molecule FRET method that enables multiplexed analysis while still using only one FRET pair, and thus the described approach is a significant step forward from conventional FRET methods.},
}
@article {pmid38683317,
year = {2024},
author = {Elwick, KE and Damaso, N and Robertson, JM},
title = {DNA Barcoding and Metabarcoding Protocols for Species Identification.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {155-169},
pmid = {38683317},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *High-Throughput Nucleotide Sequencing/methods ; Animals ; *Plants/genetics ; Insecta/genetics/classification ; Fungi/genetics/classification ; Sequence Analysis, DNA/methods ; Gene Library ; DNA/genetics ; },
abstract = {The article presents the several steps to be performed on a plant, fungal, insect, or soil sample to obtain DNA sequences for DNA barcode analysis. The chapter begins with a description of sample preparation including procedures for cleaning and proceeds to DNA extraction with methods adapted for the specific type of sample. Next, DNA quantification is described so the proper amount is used for the amplification of the selected barcode regions. Information is provided for reaction mixes and amplification conditions for several referenced barcode primer pairs tuned for the individual sample of interest. This is followed by a description of procedures to access the success of amplification, cleanup, and quantification of the product ready for either Sanger sequencing or library preparation for massive parallel sequencing (MPS). Finally, procedures are provided for Sanger sequencing, library preparation, and MPS sequencing. The chapter provides several references of barcode regions for different sample types.},
}
@article {pmid38683316,
year = {2024},
author = {David, A and Deepa Arul Priya, J and Gautam, A},
title = {DNA Sequencing Technologies and DNA Barcoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {139-154},
pmid = {38683316},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Biodiversity ; DNA/genetics ; Animals ; },
abstract = {DNA barcodes are short, standardized DNA segments that geneticists can use to identify all living taxa. On the other hand, DNA barcoding identifies species by analyzing these specific regions against a DNA barcode reference library. In its initial years, DNA barcodes sequenced by Sanger's method were extensively used by taxonomists for the characterization and identification of species. But in recent years, DNA barcoding by next-generation sequencing (NGS) has found broader applications, such as quality control, biomonitoring of protected species, and biodiversity assessment. Technological advancements have also paved the way to metabarcoding, which has enabled massive parallel sequ.encing of complex bulk samples using high-throughput sequencing techniques. In future, DNA barcoding along with high-throughput techniques will show stupendous progress in taxonomic classification with reference to available sequence data.},
}
@article {pmid38683315,
year = {2024},
author = {Hyman, O and Cass, A and Enke, R and Storm, A and Nash, B},
title = {Cost-Effective DNA Extraction for DNA Barcoding Diverse Biological Samples.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {129-137},
pmid = {38683315},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *DNA/genetics/isolation &amp; purification ; *Cost-Benefit Analysis ; Polymerase Chain Reaction/methods ; Plants/genetics ; },
abstract = {DNA barcoding employs standard molecular techniques (e.g., DNA extraction, PCR, and Sanger sequencing) to taxonomically identify biological samples. While DNA barcoding is a useful experimental workflow for in-class active learning exercises, extracting DNA from diverse sample types in a time and cost-effective manner can be challenging in a classroom setting. Here, we provide two time and cost-effective methods that have been used by novice students to successfully extract DNA from a variety of animal, fungal, algal, and plant tissues for DNA barcoding.},
}
@article {pmid38683314,
year = {2024},
author = {Hackett, J and Pepenella, S and Marco, CF and Bodt, L and Grajales, LR and Petracca, J and Burke, J and Mayle, A and Nash, B and Micklos, DA},
title = {Simple, Robust Invertebrate DNA Barcoding: Chelex-Based DNA Extraction and Optimized COI Amplification.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {119-127},
pmid = {38683314},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Electron Transport Complex IV/genetics ; *Polymerase Chain Reaction/methods ; Invertebrates/genetics/classification ; DNA/genetics/isolation &amp; purification ; },
abstract = {Chelex-based DNA extractions are well suited for student DNA barcoding research because they are simple, safe, and inexpensive and can be performed without specialized laboratory equipment, allowing them to be performed in classrooms or at home. Extracted DNA is stable in Chelex solution for at least a week at ambient temperature, allowing collection of DNA samples from remote students. These extractions provide quality DNA for many taxa and are optimal for barcoding invertebrates, especially in combination with novel cytochrome c oxidase I (COI) primer cocktails and PCR cycling conditions.},
}
@article {pmid38683313,
year = {2024},
author = {Brower, AVZ and DeSalle, R},
title = {DNA Barcodes in Taxonomic Descriptions.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {105-115},
pmid = {38683313},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; Software ; DNA/genetics ; Animals ; Phylogeny ; },
abstract = {This chapter discusses methods for incorporating DNA barcode information into formal taxonomic descriptions. We first review what a formal description entails and then discuss previous attempts to incorporate barcode information into taxonomic descriptions. Several computer programs are listed that extract diagnostics from DNA barcode data. Finally, we examine a test case (Astraptes taxonomy).},
}
@article {pmid38683312,
year = {2024},
author = {Miralles, A and Puillandre, N and Vences, M},
title = {DNA Barcoding in Species Delimitation: From Genetic Distances to Integrative Taxonomy.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {77-104},
pmid = {38683312},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; Classification/methods ; Phylogeny ; Animals ; Species Specificity ; },
abstract = {Over the past two decades, DNA barcoding has become the most popular exploration approach in molecular taxonomy, whether for identification, discovery, delimitation, or description of species. The present contribution focuses on the utility of DNA barcoding for taxonomic research activities related to species delimitation, emphasizing the following aspects:(1) To what extent DNA barcoding can be a valuable ally for fundamental taxonomic research, (2) its methodological and theoretical limitations, (3) the conceptual background and practical use of pairwise distances between DNA barcode sequences in taxonomy, and (4) the different ways in which DNA barcoding can be combined with complementary means of investigation within a broader integrative framework. In this chapter, we recall and discuss the key conceptual advances that have led to the so-called renaissance of taxonomy, elaborate a detailed glossary for the terms specific to this discipline (see Glossary in Chap. 35), and propose a newly designed step-by-step species delimitation protocol starting from DNA barcode data that includes steps from the preliminary elaboration of an optimal sampling strategy to the final decision-making process which potentially leads to nomenclatural changes.},
}
@article {pmid38683311,
year = {2024},
author = {Hubert, N and Phillips, JD and Hanner, RH},
title = {Delimiting Species with Single-Locus DNA Sequences.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {53-76},
pmid = {38683311},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Phylogeny ; *Algorithms ; Software ; Biodiversity ; Sequence Analysis, DNA/methods ; Haplotypes/genetics ; },
abstract = {DNA sequences are increasingly used for large-scale biodiversity inventories. Because these genetic data avoid the time-consuming initial sorting of specimens based on their phenotypic attributes, they have been recently incorporated into taxonomic workflows for overlooked and diverse taxa. Major statistical developments have accompanied this new practice, and several models have been proposed to delimit species with single-locus DNA sequences. However, proposed approaches to date make different assumptions regarding taxon lineage history, leading to strong discordance whenever comparisons are made among methods. Distance-based methods, such as Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP), rely on the detection of a barcode gap (i.e., the lack of overlap in the distributions of intraspecific and interspecific genetic distances) and the associated threshold in genetic distances. Network-based methods, as exemplified by the REfined Single Linkage (RESL) algorithm for the generation of Barcode Index Numbers (BINs), use connectivity statistics to hierarchically cluster-related haplotypes into molecular operational taxonomic units (MOTUs) which serve as species proxies. Tree-based methods, including Poisson Tree Processes (PTP) and the General Mixed Yule Coalescent (GMYC), fit statistical models to phylogenetic trees by maximum likelihood or Bayesian frameworks.Multiple webservers and stand-alone versions of these methods are now available, complicating decision-making regarding the most appropriate approach to use for a given taxon of interest. For instance, tree-based methods require an initial phylogenetic reconstruction, and multiple options are now available for this purpose such as RAxML and BEAST. Across all examined species delimitation methods, judicious parameter setting is paramount, as different model parameterizations can lead to differing conclusions. The objective of this chapter is to guide users step-by-step through all the procedures involved for each of these methods, while aggregating all necessary information required to conduct these analyses. The "Materials" section details how to prepare and format input files, including options to align sequences and conduct tree reconstruction with Maximum Likelihood and Bayesian inference. The Methods section presents the procedure and options available to conduct species delimitation analyses, including distance-, network-, and tree-based models. Finally, limits and future developments are discussed in the Notes section. Most importantly, species delimitation methods discussed herein are categorized based on five indicators: reliability, availability, scalability, understandability, and usability, all of which are fundamental properties needed for any approach to gain unanimous adoption within the DNA barcoding community moving forward.},
}
@article {pmid38683310,
year = {2024},
author = {Ahrens, D},
title = {Species Diagnosis and DNA Taxonomy.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {33-52},
pmid = {38683310},
issn = {1940-6029},
mesh = {*DNA/genetics ; DNA Barcoding, Taxonomic/methods ; Classification/methods ; Phylogeny ; Species Specificity ; },
abstract = {The use of DNA has helped to improve and speed up species identification and delimitation. However, it also provides new challenges to taxonomists. Incongruence of outcome from various markers and delimitation methods, bias from sampling and skewed species distribution, implemented models, and the choice of methods/priors may mislead results and also may, in conclusion, increase elements of subjectivity in species taxonomy. The lack of direct diagnostic outcome from most contemporary molecular delimitation approaches and the need for a reference to existing and best sampled trait reference systems reveal the need for refining the criteria of species diagnosis and diagnosability in the current framework of nomenclature codes and good practices to avoid nomenclatorial instability, parallel taxonomies, and consequently more and new taxonomic impediment.},
}
@article {pmid38683309,
year = {2024},
author = {Schindel, DE and Page, RMP},
title = {Creating Virtuous Cycles for DNA Barcoding: A Case Study in Science Innovation, Entrepreneurship, and Diplomacy.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2744},
number = {},
pages = {7-32},
pmid = {38683309},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Entrepreneurship ; Humans ; Inventions ; },
abstract = {This chapter on the history of the DNA barcoding enterprise attempts to set the stage for the more scholarly contributions in this volume by addressing the following questions. How did the DNA barcoding enterprise begin? What were its goals, how did it develop, and to what degree are its goals being realized? We have taken a keen interest in the barcoding movement and its relationship to taxonomy, collections, and biodiversity informatics more broadly considered. This chapter integrates our two different perspectives on barcoding. DES was the Executive Secretary of the Consortium for the Barcode of Life from 2004 to 2017, with the mission to support the success of DNA barcoding without being directly involved in generating barcode data. RDMP viewed barcoding as an important entry into the landscape of biodiversity data, with many potential linkages to other components of that landscape. We also saw it as a critical step toward the era of international genomic research that was sure to follow. Like the Mercury Program that paved the way for lunar landings by the Apollo Program, we saw DNA barcoding as the proving grounds for the interdisciplinary and international cooperation that would be needed for success of whole-genome research.},
}
@article {pmid38681421,
year = {2024},
author = {Halue, G and Chieochanthanakij, R and Kittipanyaworakun, T and Passorn, P and Kaewboonsert, D and Tharavichitkul, T and Banjongjit, A and Kanjanabuch, T and Eiam-Ong, S},
title = {Peritonitis Caused by Various Species of Diaporthe in Peritoneal Dialysis Patients: A Plant Pathogen to Human Infection.},
journal = {Cureus},
volume = {16},
number = {3},
pages = {e57016},
pmid = {38681421},
issn = {2168-8184},
abstract = {Peritonitis caused by dematiaceous molds is uncommon but poses a significant threat to patients undergoing peritoneal dialysis (PD), leading to high mortality and morbidity. This report highlights three cases of peritonitis caused by three distinct species of Diaporthe (D. amygdali, D. eucalyptorum, and D. phaseolorum), initially unidentified through conventional culture methods. The nucleotide sequences of internal transcribed spacer regions (ITS), 18S nuclear ribosomal small subunit (SSU), and 28S nuclear ribosomal large subunit (LSU) of the ribosomal DNA gene correctly identified the isolates. Despite early catheter removal and administration of appropriate antifungal medications, all patients experienced fatal outcomes. DNA barcoding emerges as a valuable tool for accurately diagnosing species within the genus of pathogenic microbes, aiding in identifying the root causes of infections. It emphasizes the importance of strict adherence to aseptic techniques during PD exchanges to prevent peritonitis caused by plant-borne pathogens.},
}
@article {pmid38680524,
year = {2024},
author = {Kermek, D and Pischiutta, N and Hlebec, D and Sivec, I and Kučinić, M},
title = {Utilising public sequence databases to investigate genetic diversity of stoneflies in Medvednica Nature Park.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e121398},
pmid = {38680524},
issn = {1314-2828},
abstract = {In Medvednica Nature Park, near Croatia's capital Zagreb, urbanisation significantly impacts the fauna. Comprehensive field research has never been conducted in this area, despite the presence of diverse microhabitats and the discovery of several rare species previously unknown in the Croatian fauna. This study provides the Park with first insight into the genetic and morphological diversity of stoneflies, one of the most endangered groups of organisms. Phylogenetic reconstructions and species delineation methods revealed intraspecific haplotype variation in most species (e.g. Brachypteraseticornis, Isoperlagrammatica and Leuctrabraueri), except for Leuctraprima. Additionally, our study has identified isolated populations that merit further in-depth investigation concerning morphology, genetics and ecology.},
}
@article {pmid38678568,
year = {2024},
author = {Gallaccio, G and Wang, M and Schlickeiser, S and Kunkel, D and Böttcher, C and Fernández-Zapata, C},
title = {Protocol to characterize immune cell subpopulations in cerebrospinal fluid of patients with neuroinflammatory diseases using mass cytometry.},
journal = {STAR protocols},
volume = {5},
number = {2},
pages = {103038},
pmid = {38678568},
issn = {2666-1667},
mesh = {Humans ; *Flow Cytometry/methods ; *Neuroinflammatory Diseases/cerebrospinal fluid/immunology ; Single-Cell Analysis/methods ; Biomarkers/cerebrospinal fluid ; Cerebrospinal Fluid/cytology/immunology ; },
abstract = {Phenotypic and compositional changes of immune cells in cerebrospinal fluid (CSF) can be used as biomarkers to help diagnose and track disease activity for neuroinflammatory and neurodegenerative diseases. Here, we present a workflow to perform high-dimensional immune profiling at single-cell resolution using cytometry by time-of-flight (CyTOF) on cells isolated from the CSF of patients with neuroinflammation. We describe steps for sample collection and preparation, barcoding to allow for multiplexing, and downstream data analysis using R. For complete details on the use and execution of this protocol, please refer to Fernández-Zapata et al.[1].},
}
@article {pmid38676334,
year = {2024},
author = {Rong, Q and Deng, Y and Chen, F and Yin, Z and Hu, L and Su, X and Zhou, D},
title = {Polymerase-Based Signal Delay for Temporally Regulating DNA Involved Reactions, Programming Dynamic Molecular Systems, and Biomimetic Sensing.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {20},
number = {35},
pages = {e2400142},
doi = {10.1002/smll.202400142},
pmid = {38676334},
issn = {1613-6829},
support = {32141003//National Natural Science Foundation of China/ ; },
mesh = {*DNA/chemistry/metabolism ; *DNA-Directed DNA Polymerase/metabolism ; *Biomimetics/methods ; Molecular Dynamics Simulation ; Biosensing Techniques/methods ; Nanotechnology/methods ; },
abstract = {Complex temporal molecular signals play a pivotal role in the intricate biological pathways of living organisms, and cells exhibit the ability to transmit and receive information by intricately managing the temporal dynamics of their signaling molecules. Although biomimetic molecular networks are successfully engineered outside of cells, the capacity to precisely manipulate temporal behaviors remains limited. In this study, the catalysis activity of isothermal DNA polymerase (DNAP) through combined use of molecular dynamics simulation analysis and fluorescence assays is first characterized. DNAP-driven delay in signal strand release ranged from 10[0] to 10[2] min, which is achieved through new strategies including the introduction of primer overhangs, utilization of inhibitory reagents, and alteration of DNA template lengths. The results provide a deeper insight into the underlying mechanisms of temporal control DNAP-mediated primer extension and DNA strand displacement reactions. Then, the regulated DNAP catalysis reactions are applied in temporal modulation of downstream DNA-involved reactions, the establishment of dynamic molecular signals, and the generation of barcodes for multiplexed detection of target genes. The utility of DNAP-based signal delay as a dynamic DNA nanotechnology extends beyond theoretical concepts and achieves practical applications in the fields of cell-free synthetic biology and bionic sensing.},
}
@article {pmid38674379,
year = {2024},
author = {Zhang, S and Han, S and Bi, D and Yang, J and Ge, W and Ye, Y and Gao, J and Dai, C and Kan, X},
title = {Intraspecific and Intrageneric Genomic Variation across Three Sedum Species (Crassulaceae): A Plastomic Perspective.},
journal = {Genes},
volume = {15},
number = {4},
pages = {},
pmid = {38674379},
issn = {2073-4425},
support = {BK20211078//the Basic Research Program of Natural Science Foundation of Jiangsu Province of China/ ; NEL&amp;MARA-003//the Opening Foundation of National Engineering Laboratory of Soil Pollution Control and Remediation Technologies, and Key Laboratory of Heavy Metal Pollution Prevention &amp; Control, Ministry of Agriculture and Rural Affairs/ ; },
mesh = {*Phylogeny ; *Sedum/genetics ; Genome, Plastid ; Evolution, Molecular ; Genetic Variation ; Codon Usage ; Genome, Plant ; Base Composition/genetics ; },
abstract = {Sedum is the largest succulent genus in Crassulaceae. Because of predominant maternal inheritance, little recombination, and slow evolution, plastomes can serve as powerful super barcodes for inter- or intra-species phylogenetic analyses. While previous research has focused on plastomes between Sedum species, intra-species studies are scarce. Here, we sequenced plastomes from three Sedum species (Sedum alfredii, Sedum plumbizincicola, and Sedum japonicum) to understand their evolutionary relationships and plastome structural evolution. Our analyses revealed minimal size and GC content variation across species. However, gene distribution at IR boundaries, repeat structures, and codon usage patterns showed diversity at both inter-specific and intra-specific levels. Notably, an rps19 gene expansion and a bias toward A/T-ending codons were observed. Codon aversion motifs also varied, potentially serving as markers for future studies. Phylogenetic analyses confirmed the non-monophyly of Sedum and divided the Acre clade into two groups. Individuals from the same species clustered together, with strong support for the relationships between S. alfredii, S. tricarpum, and S. plumbizincicola. Additionally, S. japonicum clearly affiliates with the Acre clade. This study provides valuable insights into both intra-specific and intra-generic plastome variation in Sedum, as well as overall plastome evolution within the genus.},
}
@article {pmid38674377,
year = {2024},
author = {Kan, J and Zhang, S and Wu, Z and Bi, D},
title = {Exploring Plastomic Resources in Sempervivum (Crassulaceae): Implications for Phylogenetics.},
journal = {Genes},
volume = {15},
number = {4},
pages = {},
pmid = {38674377},
issn = {2073-4425},
support = {BK20211078//the Basic Research Program (Natural Science Foundation) of Jiangsu Province (Grant no. BK20211078)/ ; RCYX20200714114538196//the Science Technology and Innovation Commission of Shenzhen Municipality/ ; JCYJ20220818103212025//the Shenzhen Fundamental Research Program/ ; 2021QN02N792//the Guangdong Pearl River Talent Program/ ; },
mesh = {*Phylogeny ; *Plastids/genetics ; Codon Usage ; Genome, Plastid/genetics ; Evolution, Molecular ; },
abstract = {The plastid organelle is vital for photosynthesis and energy production. Advances in sequencing technology have enabled the exploration of plastomic resources, offering insights into plant evolution, diversity, and conservation. As an important group of horticultural ornamentals in the Crassulaceae family, Sempervivum plants are known for their unique rosette-like structures and reproduction through offsets. Despite their popularity, the classification status of Sempervivum remains uncertain, with only a single plastome sequence currently available. Furthermore, codon usage bias (CUB) is a widespread phenomenon of the unbalanced usage of synonymous codons in the coding sequence (CDS). However, due to the limited available plastid data, there has been no research that focused on the CUB analysis among Sempervivum until now. To address these gaps, we sequenced and released the plastomes of seven species and one subspecies from Sempervivum, revealing several consistent patterns. These included a shared 110 bp extension of the rps19 gene, 14 hypervariable regions (HVRs) with distinct nucleotide diversity (π: 0.01173 to 0.02702), and evidence of selective pressures shaping codon usage. Notably, phylogenetic analysis robustly divided the monophyletic clade into two sections: Jovibarba and Sempervivum. In conclusion, this comprehensive plastomic resource provides valuable insights into Sempervivum evolution and offers potential molecular markers for DNA barcoding.},
}
@article {pmid38672767,
year = {2024},
author = {Vankova, L and Vanek, D},
title = {Capillary-Electrophoresis-Based Species Barcoding of Big Cats: CR-mtDNA-Length Polymorphism.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {38672767},
issn = {2075-1729},
support = {VJ01010026//Ministry of Interior Czech Republic/ ; },
abstract = {This study aimed to provide an overview of the methodological approach used for the species determination of big cats. The molecular system described herein employs mitochondrial DNA control region (CR-mtDNA)-length polymorphism in combination with highly sensitive and precise capillary electrophoresis. We demonstrated that the described CR-mtDNA barcoding system can be utilized for species determination where the presence of biological material from big cats is expected or used as a confirmatory test alongside Sanger or massive parallel sequencing (MPS). We have also addressed the fact that species barcoding, when based on the analysis of mtDNA targets, can be biased by nuclear inserts of the mitochondrial genome (NUMTs). The CR-mtDNA barcoding system is suitable even for problematic and challenging samples, such as hair. CR-mtDNA-length polymorphisms can also distinguish hybrids from pure breeds.},
}
@article {pmid38671234,
year = {2024},
author = {Rios-Willars, E and Chirinos-Arias, MC},
title = {Mfind: a tool for DNA barcode analysis in angiosperms and its relationship with microsatellites using a sliding window algorithm.},
journal = {Planta},
volume = {259},
number = {6},
pages = {134},
pmid = {38671234},
issn = {1432-2048},
mesh = {*Microsatellite Repeats/genetics ; *DNA Barcoding, Taxonomic/methods ; *Algorithms ; *Magnoliopsida/genetics ; DNA, Plant/genetics ; },
abstract = {Mfind is a tool to analyze the impact of microsatellite presence on DNA barcode specificity. We found a significant correlation between barcode entropy and microsatellite count in angiosperm. Genetic barcodes and microsatellites are some of the identification methods in taxonomy and biodiversity research. It is important to establish a relationship between microsatellite quantification and genetic information in barcodes. In order to clarify the association between the genetic information in barcodes (expressed as Shannon's Measure of Information, SMI) and microsatellites count, a total of 330,809 DNA barcodes from the BOLD database (Barcode of Life Data System) were analyzed. A parallel sliding-window algorithm was developed to compute the Shannon entropy of the barcodes, and this was compared with the quantification of microsatellites like (AT)n, (AC)n, and (AG)n. The microsatellite search method utilized an algorithm developed in the Java programming language, which systematically examined the genetic barcodes from an angiosperm database. For this purpose, a computational tool named Mfind was developed, and its search methodology is detailed. This comprehensive study revealed a broad overview of microsatellites within barcodes, unveiling an inverse correlation between the sumz of microsatellites count and barcodes information. The utilization of the Mfind tool demonstrated that the presence of microsatellites impacts the barcode information when considering entropy as a metric. This effect might be attributed to the concise length of DNA barcodes and the repetitive nature of microsatellites, resulting in a direct influence on the entropy of the barcodes.},
}
@article {pmid38670414,
year = {2024},
author = {Lattos, A and Makri, V and Papadopoulos, DK and Gourzioti, E and Pagonis, C and Georgoulis, I and Karagiannis, D and Theodorou, JA and Michaelidis, B and Giantsis, IA and Feidantsis, K},
title = {Molecular characterization of Lernathropus kroyeri from intensive aquaculture and pathophysiology of infested sea bass.},
journal = {Fish &amp; shellfish immunology},
volume = {149},
number = {},
pages = {109576},
doi = {10.1016/j.fsi.2024.109576},
pmid = {38670414},
issn = {1095-9947},
mesh = {Animals ; *Bass/immunology ; *Copepoda/physiology/genetics ; *Fish Diseases/immunology/parasitology ; *Aquaculture ; *Phylogeny ; Greece ; Ectoparasitic Infestations/veterinary/parasitology/immunology ; },
abstract = {The copepod Lernathropus kroyeri constitutes one of the major parasites for the Mediterranean aquaculture, infesting the sea bass Dicentrarchus labrax causing thus disruptions of growth performance and occasionally mortalities. Despite the large spread and the high frequency of this parasite in mariculture farms of Eastern Mediterranean, L. kroyeri genetic profile from aquaculture as well as the pathophysiological response of D. labrax have not been studied so far. Keeping this in mind, in the present study we investigated the L. kroyeri infestation on D. labrax from two farms in Greece, examining both healthy and heavy parasitized individuals. Assays included histopathology, phylogenetic reconstruction of the parasite and physiological response of the fish by the means of antioxidant, inflammatory metabolic and stress related gene expression analysis at both mRNA and protein levels. Genetic analysis indicated that L. kroyeri composes a monophyletic group, highly phylogenetically distant from other congeneric groups. Heavy infested D. labrax witnessed a significantly increased immune response that further led to oxidative stress and metabolic alterations. Overall, our results demonstrate the, seasonally independent, high infestation of this parasitic copepods, which continue to affect Mediterranean intensive aquaculture systems.},
}
@article {pmid38670101,
year = {2024},
author = {Holze, H and Talarmain, L and Fennell, KA and Lam, EY and Dawson, MA and Vassiliadis, D},
title = {Analysis of synthetic cellular barcodes in the genome and transcriptome with BARtab and bartools.},
journal = {Cell reports methods},
volume = {4},
number = {5},
pages = {100763},
pmid = {38670101},
issn = {2667-2375},
mesh = {*Transcriptome ; *Single-Cell Analysis/methods ; Humans ; *High-Throughput Nucleotide Sequencing ; Software ; DNA Barcoding, Taxonomic/methods ; Genome/genetics ; Cell Lineage/genetics ; Gene Expression Profiling/methods ; Computational Biology/methods ; Animals ; },
abstract = {Cellular barcoding is a lineage-tracing methodology that couples heritable synthetic barcodes to high-throughput sequencing, enabling the accurate tracing of cell lineages across a range of biological contexts. Recent studies have extended these methods by incorporating lineage information into single-cell or spatial transcriptomics readouts. Leveraging the rich biological information within these datasets requires dedicated computational tools for dataset pre-processing and analysis. Here, we present BARtab, a portable and scalable Nextflow pipeline, and bartools, an open-source R package, designed to provide an integrated end-to-end cellular barcoding analysis toolkit. BARtab and bartools contain methods to simplify the extraction, quality control, analysis, and visualization of lineage barcodes from population-level, single-cell, and spatial transcriptomics experiments. We showcase the utility of our integrated BARtab and bartools workflow via the analysis of exemplar bulk, single-cell, and spatial transcriptomics experiments containing cellular barcoding information.},
}
@article {pmid38667952,
year = {2024},
author = {Guerra-Mateo, D and Cano-Lira, JF and Fernández-Bravo, A and Gené, J},
title = {Sunken Riches: Ascomycete Diversity in the Western Mediterranean Coast through Direct Plating and Flocculation, and Description of Four New Taxa.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {10},
number = {4},
pages = {},
pmid = {38667952},
issn = {2309-608X},
support = {PID2021-128068NB-100//Ministeri de Ci&#xe8;ncia Innovaci&#xf3; i Universitats/ ; },
abstract = {The Mediterranean Sea stands out as a hotspot of biodiversity, whose fungal composition remains underexplored. Marine sediments represent the most diverse substrate; however, the challenge of recovering fungi in culture hinders the precise identification of this diversity. Concentration techniques like skimmed milk flocculation (SMF) could represent a suitable solution. Here, we compare the effectiveness in recovering filamentous ascomycetes of direct plating and SMF in combination with three culture media and two incubation temperatures, and we describe the fungal diversity detected in marine sediments. Sediments were collected at different depths on two beaches (Miracle and Arrabassada) on the Spanish western Mediterranean coast between 2021 and 2022. We recovered 362 strains, and after a morphological selection, 188 were identified primarily with the LSU and ITS barcodes, representing 54 genera and 94 species. Aspergillus, Penicillium, and Scedosporium were the most common genera, with different percentages of abundance between both beaches. Arrabassada Beach was more heterogeneous, with 42 genera representing 60 species (Miracle Beach, 28 genera and 54 species). Although most species were recovered with direct plating (70 species), 20 species were exclusively obtained using SMF as a sample pre-treatment, improving our ability to detect fungi in culture. In addition, we propose three new species in the genera Exophiala, Nigrocephalum, and Queenslandipenidiella, and a fourth representing the novel genus Schizochlamydosporiella. We concluded that SMF is a useful technique that, in combination with direct plating, including different culture media and incubation temperatures, improves the chance of recovering marine fungal communities in culture-dependent studies.},
}
@article {pmid38667369,
year = {2024},
author = {Aguado-Aranda, P and Ricarte, A and Nedeljković, Z and Hauser, M and Kelso, S and Sainz-Escudero, L and Skevington, JH and Marcos-García, M&#xc1;},
title = {Unveiling the Mainland vs. Insular Variability of the Eumerus barbarus Species Group (Diptera: Syrphidae) in the Western Mediterranean Basin.},
journal = {Insects},
volume = {15},
number = {4},
pages = {},
pmid = {38667369},
issn = {2075-4450},
support = {PRE2019-087508//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades (Spain)/ ; PGC2018-095851-A-C65//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades (Spain)/ ; IME 2022//Institut Menorqu&#xed; d'Estudis (Spain)/ ; },
abstract = {Comprising nearly 300 described species, Eumerus Meigen, 1822, is one of the most speciose syrphid genera worldwide, and its taxonomic diversity is remarkable in the Mediterranean basin. The Eumerus barbarus (Coquebert, 1804) group consists of four species in the western Mediterranean. Although the phenotypic variability of this species group has been commented on in previous studies, it has never been contrasted with molecular data. In the present work, the morphological variation found in 300+ specimens of this species group from the western Mediterranean is explored and tested against the COI mitochondrial DNA (mtDNA). The highest phenotypic disparity was found in E. barbarus and Eumerus sulcitibius Rondani 1868. The integrative approach has not revealed cryptic diversity within the species E. barbarus but in E. sulcitibius. As a result, a new species close to E. sulcitibius was discovered, Eumerus sardus Aguado-Aranda, Ricarte &amp; Hauser sp. n., from Sardinia, Italy. The new insular species is here described, illustrated, and discussed. A total of twenty-three haplotypes of COI mtDNA were identified amongst the analyzed Mediterranean specimens of E. barbarus, whereas two and five haplotypes were distinguished in the Iberian specimens of E. sulcitibius and Eumerus gibbosus van Steenis, Hauser &amp; van Zuijen, 2017, respectively. Moreover, the first known barcodes of E. gibbosus and Eumerus schmideggeri van Steenis, Hauser &amp; van Zuijen, 2017 were obtained, and the distribution ranges of all species are mapped. An updated dichotomous key to the males of the E. barbarus group from the western Mediterranean is provided.},
}
@article {pmid38667358,
year = {2024},
author = {Wang, L and Wu, H and He, W and Lai, G and Li, J and Liu, S and Zhou, Q},
title = {Diversity of Parasitoid Wasps and Comparison of Sampling Strategies in Rice Fields Using Metabarcoding.},
journal = {Insects},
volume = {15},
number = {4},
pages = {},
pmid = {38667358},
issn = {2075-4450},
support = {2023KJ113//the Agricultural Science and Technology Innovative and Promotion Program of Guangdong Province/ ; },
abstract = {A comprehensive and precise evaluation of Arthropoda diversity in agricultural landscapes can enhance biological pest control strategies. We used Malaise traps and sweep nets to collect insects from three double-cropping paddy fields. DNA was extracted from the ethanol preservative of the Malaise traps and from tissue samples of selected parasitoid wasps. This was followed by amplification using DNA barcoding primers to prepare high-throughput sequencing libraries. We annotated a total of 4956 operational taxonomic units (OTUs), encompassing 174 genera and 32 families of parasitoid wasps. The ethanol filter method efficiently captured a wide range of information. However, the method has low resolution and may result in a reduced estimate of species abundance. Additional insect species were also identified in the parasitoid samples. This suggests that high throughput sequencing from adult parasitoid wasps can also detect host species, enabling a better understanding of host species and providing insights into food webs.},
}
@article {pmid38666586,
year = {2024},
author = {Wang, J and Zhang, T and Gao, Z and Wei, M and Jia, Y and Tong, X and Hu, F and Zhao, YS},
title = {Two-Dimensional Lanthanide Metal-Organic Framework Heterostructures for Noninvasively Photoresponsive High-Security Photonic Barcodes.},
journal = {ACS applied materials &amp; interfaces},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsami.4c02440},
pmid = {38666586},
issn = {1944-8252},
abstract = {Stimuli-responsive micro/nanoscale photonic barcodes show great capacity for encryption and anticounterfeiting technologies due to multiple authentications, yet their application is commonly restricted by invasive stimuli. Herein, we report noninvasive light-stimulated high-security photonic barcodes based on spatially assembled photoresponsive two-dimensional (2D) 1,3,5-benzenetribenzoate (BTB)@Ln-MOF host-guest heterostructures. The photoluminescence (PL) spectra information on BTB@Ln-MOF heterostructures could be precisely controlled by the different wavelengths of ultraviolet (UV) light trigger. By using the PL properties and 2D heterostructures as cryptographic primitives, spatially resolved smart photonic barcodes based on both spectral and graphical coding are realized in BTB@Ln-MOF host-guest materials. These results will pave an avenue for the development of smart stimuli-responsive photonic barcodes for anticounterfeiting applications.},
}
@article {pmid38665980,
year = {2023},
author = {Li, GS and Leal-Dutra, CA and Cuesta-Maté, A and Conlon, BH and Peereboom, N and Beemelmanns, C and Aanen, DK and Rosendahl, S and de Beer, ZW and Poulsen, M},
title = {Resolution of eleven reported and five novel Podaxis species based on ITS phylogeny, phylogenomics, morphology, ecology, and geographic distribution.},
journal = {Persoonia},
volume = {51},
number = {},
pages = {257-279},
pmid = {38665980},
issn = {0031-5850},
abstract = {The genus Podaxis was first described from India by Linnaeus in 1771, but several revisions of the genus have left the taxonomy unclear. Forty-four Podaxis species names and nine intraspecific varieties are currently accepted, but most fungarium specimens are labelled Podaxis pistillaris. Recent molecular analyses based on barcoding genes suggest that the genus comprises several species, but their status is largely unresolved. Here we obtained basidiospores and photographs from 166 fungarium specimens from around the world and generated a phylogeny based on rDNA internal transcribed spacer ITS1,5.8S and ITS2 (ITS), and a phylogenomic analysis of 3 839 BUSCO genes from low-coverage genomes for a subset of the specimens. Combining phylogenetics, phylogenomics, morphology, ecology, and geographical distribution, spanning 250 years of collections, we propose that the genus includes at least 16 unambiguous species. Based on 10 type specimens (holotype, paratype, and syntype), four recorded species were confirmed, P. carcinomalis, P. deflersii, P. emerici, and P. farlowii. Comparing phylogenetic analysis with described species, including morphology, ecology, and distribution, we resurrected P. termitophilus and designated neotypes, epitypes, or lectotypes for five previously described species, P. aegyptiacus, P. africana, P. beringamensis, P. calyptratus, and P. perraldieri. Lastly, based on phylogenies and morphology of type material, we synonymized three reported species, P. algericus, P. arabicus, and P. rugospora with P. pistillaris, and described five new species that we named P. desolatus, P. inyoensis, P. mareebaensis, P. namaquensis, and P. namibensis. Citation: Li GS, Leal-Dutra CA, Cuesta-Maté A, et al. 2023. Resolution of eleven reported and five novel Podaxis species based on ITS phylogeny, phylogenomics, morphology, ecology, and geographic distribution. Persoonia 51: 257-279. doi: 10.3767/persoonia.2023.51.07.},
}
@article {pmid38665977,
year = {2023},
author = {Crous, PW and Costa, MM and Kandemir, H and Vermaas, M and Vu, D and Zhao, L and Arumugam, E and Flakus, A and Jurjević, &#x17d; and Kaliyaperumal, M and Mahadevakumar, S and Murugadoss, R and Shivas, RG and Tan, YP and Wingfield, MJ and Abell, SE and Marney, TS and Danteswari, C and Darmostuk, V and Denchev, CM and Denchev, TT and Etayo, J and Gené, J and Gunaseelan, S and Hubka, V and Illescas, T and Jansen, GM and Kezo, K and Kumar, S and Larsson, E and Mufeeda, KT and Piątek, M and Rodriguez-Flakus, P and Sarma, PVSRN and Stryjak-Bogacka, M and Torres-Garcia, D and Vauras, J and Acal, DA and Akulov, A and Alhudaib, K and Asif, M and Balashov, S and Baral, HO and Baturo-Cieśniewska, A and Begerow, D and Beja-Pereira, A and Bianchinotti, MV and Bilański, P and Chandranayaka, S and Chellappan, N and Cowan, DA and Custódio, FA and Czachura, P and Delgado, G and De Silva, NI and Dijksterhuis, J and Dueñas, M and Eisvand, P and Fachada, V and Fournier, J and Fritsche, Y and Fuljer, F and Ganga, KGG and Guerra, MP and Hansen, K and Hywel-Jones, N and Ismail, AM and Jacobs, CR and Jankowiak, R and Karich, A and Kemler, M and Kisło, K and Klofac, W and Krisai-Greilhuber, I and Latha, KPD and Lebeuf, R and Lopes, ME and Lumyong, S and Maciá-Vicente, JG and Maggs-Kölling, G and Magistà, D and Manimohan, P and Martín, MP and Mazur, E and Mehrabi-Koushki, M and Miller, AN and Mombert, A and Ossowska, EA and Patejuk, K and Pereira, OL and Piskorski, S and Plaza, M and Podile, AR and Polhorský, A and Pusz, W and Raza, M and Ruszkiewicz-Michalska, M and Saba, M and Sánchez, RM and Singh, R and Śliwa, L and Smith, ME and Stefenon, VM and Strasiftáková, D and Suwannarach, N and Szczepańska, K and Telleria, MT and Tennakoon, DS and Thines, M and Thorn, RG and Urbaniak, J and van der Vegte, M and Vasan, V and Vila-Viçosa, C and Voglmayr, H and Wrzosek, M and Zappelini, J and Groenewald, JZ},
title = {Fungal Planet description sheets: 1550-1613.},
journal = {Persoonia},
volume = {51},
number = {},
pages = {280-417},
pmid = {38665977},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Argentina, Neocamarosporium halophilum in leaf spots of Atriplex undulata. Australia, Aschersonia merianiae on scale insect (Coccoidea), Curvularia huamulaniae isolated from air, Hevansia mainiae on dead spider, Ophiocordyceps poecilometigena on Poecilometis sp. Bolivia, Lecanora menthoides on sandstone, in open semi-desert montane areas, Sticta monlueckiorum corticolous in a forest, Trichonectria epimegalosporae on apothecia of corticolous Megalospora sulphurata var. sulphurata, Trichonectria puncteliae on the thallus of Punctelia borreri. Brazil, Catenomargarita pseudocercosporicola (incl. Catenomargarita gen. nov.) hyperparasitic on Pseudocercospora fijiensis on leaves of Musa acuminata, Tulasnella restingae on protocorms and roots of Epidendrum fulgens. Bulgaria, Anthracoidea umbrosae on Carex spp. Croatia, Hymenoscyphus radicis from surface-sterilised, asymptomatic roots of Microthlaspi erraticum, Orbilia multiserpentina on wood of decorticated branches of Quercus pubescens. France, Calosporella punctatispora on dead corticated twigs of Aceropalus. French West Indies (Martinique), Eutypella lechatii on dead corticated palm stem. Germany, Arrhenia alcalinophila on loamy soil. Iceland, Cistella blauvikensis on dead grass (Poaceae). India, Fulvifomes maritimus on living Peltophorum pterocarpum, Fulvifomes natarajanii on dead wood of Prosopis juliflora, Fulvifomes subazonatus on trunk of Azadirachta indica, Macrolepiota bharadwajii on moist soil near the forest, Narcissea delicata on decaying elephant dung, Paramyrothecium indicum on living leaves of Hibiscus hispidissimus, Trichoglossum syamviswanathii on moist soil near the base of a bamboo plantation. Iran, Vacuiphoma astragalicola from stem canker of Astragalus sarcocolla. Malaysia, Neoeriomycopsis fissistigmae (incl. Neoeriomycopsidaceae fam. nov.) on leaf spots on flower Fissistigma sp. Namibia, Exophiala lichenicola lichenicolous on Acarospora cf. luederitzensis. Netherlands, Entoloma occultatum on soil, Extremus caricis on dead leaves of Carex sp., Inocybe pseudomytiliodora on loamy soil. Norway, Inocybe guldeniae on calcareous soil, Inocybe rupestroides on gravelly soil. Pakistan, Hymenagaricus brunneodiscus on soil. Philippines, Ophiocordyceps philippinensis parasitic on Asilus sp. Poland, Hawksworthiomyces ciconiae isolated from Ciconia ciconia nest, Plectosphaerella vigrensis from leaf spots on Impatiens noli-tangere, Xenoramularia epitaxicola from sooty mould community on Taxus baccata. Portugal, Inocybe dagamae on clay soil. Saudi Arabia, Diaporthe jazanensis on branches of Coffea arabica. South Africa, Alternaria moraeae on dead leaves of Moraea sp., Bonitomyces buffels-kloofinus (incl. Bonitomyces gen. nov.) on dead twigs of unknown tree, Constrictochalara koukolii on living leaves of Itea rhamnoides colonised by a Meliola sp., Cylindromonium lichenophilum on Parmelina tiliacea, Gamszarella buffelskloofina (incl. Gamszarella gen. nov.) on dead insect, Isthmosporiella africana (incl. Isthmosporiella gen. nov.) on dead twigs of unknown tree, Nothoeucasphaeria buffelskloofina (incl. Nothoeucasphaeria gen. nov.), on dead twigs of unknown tree, Nothomicrothyrium beaucarneae (incl. Nothomicrothyrium gen. nov.) on dead leaves of Beaucarnea stricta, Paramycosphaerella proteae on living leaves of Protea caffra, Querciphoma foliicola on leaf litter, Rachicladosporium conostomii on dead twigs of Conostomium natalense var. glabrum, Rhamphoriopsis synnematosa on dead twig of unknown tree, Waltergamsia mpumalanga on dead leaves of unknown tree. Spain, Amanita fulvogrisea on limestone soil, in mixed forest, Amanita herculis in open Quercus forest, Vuilleminia beltraniae on Cistus symphytifolius. Sweden, Pachyella pulchella on decaying wood on sand-silt riverbank. Thailand, Deniquelata cassiae on dead stem of Cassia fistula, Stomiopeltis thailandica on dead twigs of Magnolia champaca. Ukraine, Circinaria podoliana on natural limestone outcrops, Neonematogonum carpinicola (incl. Neonematogonum gen. nov.) on dead branches of Carpinus betulus. USA, Exophiala wilsonii water from cooling tower, Hygrophorus aesculeticola on soil in mixed forest, and Neocelosporium aereum from air in a house attic. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Costa MM, Kandemir H, et al. 2023. Fungal Planet description sheets: 1550-1613. Persoonia 51: 280-417. doi: 10.3767/persoonia.2023.51.08.},
}
@article {pmid38665369,
year = {2024},
author = {Sun, W and Wei, Z and Gu, Y and Wang, T and Liu, B and Yan, Y},
title = {Chloroplast genome structure analysis of Equisetum unveils phylogenetic relationships to ferns and mutational hotspot region.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1328080},
pmid = {38665369},
issn = {1664-462X},
abstract = {Equisetum is one of the oldest extant group vascular plants and is considered to be the key to understanding vascular plant evolution. Equisetum is distributed almost all over the world and has a high degree of adaptability to different environments. Despite the fossil record of horsetails (Equisetum, Equisetaceae) dating back to the Carboniferous, the phylogenetic relationship of this genus is not well, and the chloroplast evolution in Equisetum remains poorly understood. In order to fill this gap, we sequenced, assembled, and annotated the chloroplast genomes of 12 species of Equisetum, and compared them to 13 previously published vascular plants chloroplast genomes to deeply examine the plastome evolutionary dynamics of Equisetum. The chloroplast genomes have a highly conserved quadripartite structure across the genus, but these chloroplast genomes have a lower GC content than other ferns. The size of Equisetum plastomes ranges from 130,773 bp to 133,684 bp and they encode 130 genes. Contraction/expansion of IR regions and the number of simple sequences repeat regions underlie large genomic variations in size among them. Comparative analysis revealed we also identified 13 divergence hotspot regions. Additionally, the genes accD and ycf1 can be used as potential DNA barcodes for the identification and phylogeny of the genus Equisetum. Twelve photosynthesis-related genes were specifically selected in Equisetum. Comparative genomic analyses implied divergent evolutionary patterns between Equisetum and other ferns. Phylogenomic analyses and molecular dating revealed a relatively distant phylogenetic relationship between Equisetum and other ferns, supporting the division of pteridophyte into Lycophytes, Equisetaceae and ferns. The results show that the chloroplast genome can be used to solve phylogenetic problems within or between Equisetum species, and also provide genomic resources for the study of Equisetum systematics and evolution.},
}
@article {pmid38661214,
year = {2024},
author = {Ylagan, M and Xu, Q and Kowalski, J},
title = {TTSBBC: triplex target site biomarkers and barcodes in cancer.},
journal = {Nucleic acids research},
volume = {52},
number = {W1},
pages = {W547-W555},
pmid = {38661214},
issn = {1362-4962},
support = {//University of Texas Dell Medical School Research Funds/ ; },
mesh = {Humans ; *DNA/chemistry/genetics/metabolism ; *Neoplasms/genetics/metabolism ; Software ; Biomarkers, Tumor/genetics/metabolism ; Oligonucleotides/chemistry ; Binding Sites ; Nucleic Acid Conformation ; DNA Barcoding, Taxonomic/methods ; },
abstract = {The technology of triplex-forming oligonucleotides (TFOs) provides an approach to manipulate genes at the DNA level. TFOs bind to specific sites on genomic DNA, creating a unique intermolecular triple-helix DNA structure through Hoogsteen hydrogen bonding. This targeting by TFOs is site-specific and the locations TFOs bind are referred to as TFO target sites (TTS). Triplexes have been observed to selectively influence gene expression, homologous recombination, mutations, protein binding, and DNA damage. These sites typically feature a poly-purine sequence in duplex DNA, and the characteristics of these TTS sequences greatly influence the formation of the triplex. We introduce TTSBBC, a novel analysis and visualization platform designed to explore features of TTS sequences to enable users to design and validate TTSs. The web server can be freely accessed at https://kowalski-labapps.dellmed.utexas.edu/TTSBBC/.},
}
@article {pmid38660246,
year = {2024},
author = {Lin, T and Liu, D and Guan, Z and Zhao, X and Li, S and Wang, X and Hou, R and Zheng, J and Cao, J and Shi, M},
title = {CRISPR screens in mechanism and target discovery for AML.},
journal = {Heliyon},
volume = {10},
number = {8},
pages = {e29382},
pmid = {38660246},
issn = {2405-8440},
abstract = {CRISPR-based screens have discovered novel functional genes involving in diverse tumor biology and elucidated the mechanisms of the cancer pathological states. Recently, with its randomness and unbiasedness, CRISPR screens have been used to discover effector genes with previously unknown roles for AML. Those novel targets are related to AML survival resembled cellular pathways mediating epigenetics, synthetic lethality, transcriptional regulation, mitochondrial and energy metabolism. Other genes that are crucial for pharmaceutical targeting and drug resistance have also been identified. With the rapid development of novel strategies, such as barcodes and multiplexed mosaic CRISPR perturbation, more potential therapeutic targets and mechanism in AML will be discovered. In this review, we present an overview of recent progresses in the development of CRISPR-based screens for the mechanism and target identification in AML and discuss the challenges and possible solutions in this rapidly growing field.},
}
@article {pmid38659825,
year = {2024},
author = {Simon, JJ and Fowler, DM and Maly, DJ},
title = {Multiplexed, multimodal profiling of the intracellular activity, interactions, and druggability of protein variants using LABEL-seq.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38659825},
issn = {2692-8205},
support = {R01 GM086858/GM/NIGMS NIH HHS/United States ; R01 GM145011/GM/NIGMS NIH HHS/United States ; },
abstract = {Multiplexed assays of variant effect are powerful tools for assessing the impact of protein sequence variation, but are limited to measuring a single protein property and often rely on indirect readouts of intracellular protein function. Here, we developed LAbeling with Barcodes and Enrichment for biochemicaL analysis by sequencing (LABEL-seq), a platform for the multimodal profiling of thousands of protein variants in cultured human cells. Multimodal measurement of ~20,000 variant effects for ~1,600 BRaf variants using LABEL-seq revealed that variation at positions that are frequently mutated in cancer had minimal effects on folding and intracellular abundance but could dramatically alter activity, protein-protein interactions, and druggability. Integrative analysis of our multimodal measurements identified networks of positions with similar roles in regulating BRaf's signaling properties and enabled predictive modeling of variant effects on complex processes such as cell proliferation and small molecule-promoted degradation. LABEL-seq provides a scalable approach for the direct measurement of multiple biochemical effects of protein variants in their native cellular context, yielding insight into protein function, disease mechanisms, and druggability.},
}
@article {pmid38656593,
year = {2024},
author = {Al-Sarar, AS and Abobakr, Y and Alzabib, AA and Saleh, AA},
title = {First Report on Banana Weevil, Cosmopolites sordidus (Germar 1823) (Coleoptera: Curculionidae), an Exotic Economically Important Pest from Saudi Arabia.},
journal = {Neotropical entomology},
volume = {53},
number = {3},
pages = {461-468},
pmid = {38656593},
issn = {1678-8052},
support = {2-17-04-001-0040//National Plan for Science, Technology and Innovation/ ; },
mesh = {Animals ; *Weevils/classification ; Saudi Arabia ; *Musa/parasitology ; Female ; Male ; },
abstract = {We report the first record of the occurrence of the banana weevil, Cosmopolites sordidus (Germar, 1823) (Coleoptera: Curculionidae), an economically important pest of bananas (Musa spp.), from Fifa Mountains in Saudi Arabia. Moreover, we recorded the first observation of damage caused to bananas by C. sordidus in a banana farm in Jazan Province, southwestern Saudi Arabia, in March 2022. Molecular characterization using DNA sequences of the mitochondrial COI gene confirmed the morphological identification of C. sordidus. This discovery is considered a warning notice to prevent the potential establishment and spread of this dangerous pest in the banana cultivation regions in Saudi Arabia. Therefore, it is recommended that detection and monitoring of banana weevil should be undertaken in Saudi banana farms in order to restrict the dissemination of this weevil to other banana cultivation areas.},
}
@article {pmid38656472,
year = {2024},
author = {Yuan, JM and Su, J and Zhang, ZH and Sun, B and Jiao, XL and Zhang, X and Zhai, YP and Chen, YJ},
title = {Initial study and phylogenetic analysis of hard ticks (Acari: Ixodidae) in Nantong, China along the route of avian migration.},
journal = {Experimental &amp; applied acarology},
volume = {92},
number = {4},
pages = {871-883},
pmid = {38656472},
issn = {1572-9702},
support = {MS2023092//Research Project Foundation of Nantong Health Commission/ ; },
mesh = {Animals ; China ; *Ixodidae/genetics/classification/physiology ; *Phylogeny ; *Electron Transport Complex IV/genetics/analysis ; *Animal Migration ; *Birds ; RNA, Ribosomal/genetics/analysis ; Nymph/growth &amp; development/classification/genetics/physiology ; Arthropod Proteins/genetics/analysis ; DNA, Ribosomal Spacer/analysis ; },
abstract = {The growing concern about migratory birds potentially spreading ticks due to global warming has become a significant issue. The city of Nantong in this study is situated along the East Asia-Australasian Flyway (EAAF), with numerous wetlands serving as roosting sites for migratory birds. We conducted an investigation of hard ticks and determined the phylogenetic characteristics of tick species in this city. We utilized three different genes for our study: the mitochondrial cytochrome oxidase subunit 1 (COX1) gene, the second internal transcribed spacer (ITS2), and the mitochondrial small subunit rRNA (12 S rRNA) gene. The predominant tick species were Haemaphysalis flava (H. flava) and Haemaphysalis longicornis (H. longicornis). Additionally, specimens of Haemaphysalis campanulata (H. campanulata) and Rhipicephalus sanguineus (R. sanguineus) were collected. The H. flava specimens in this study showed a close genetic relationship with those from inland provinces of China, as well as South Korea and Japan. Furthermore, samples of H. longicornis exhibited a close genetic relationship with those from South Korea, Japan, Australia, and the USA, as well as specific provinces in China. Furthermore, R. sanguineus specimens captured in Nantong showed genetic similarities with specimens from Egypt, Nigeria, and Argentina.},
}
@article {pmid38656420,
year = {2024},
author = {Oyuntsetseg, D and Nyamgerel, N and Baasanmunkh, S and Oyuntsetseg, B and Urgamal, M and Yoon, JW and Bayarmaa, GA and Choi, HJ},
title = {The complete chloroplast genome and phylogentic results support the species position of Swertia banzragczii and Swertia marginata (Gentianaceae) in Mongolia.},
journal = {Botanical studies},
volume = {65},
number = {1},
pages = {11},
pmid = {38656420},
issn = {1817-406X},
support = {P2023-4591//National University of Mongolia/ ; KNA1-2-42, 22-2//Korea National Arboretum/ ; 2023R1A6C101B022//Korea Basic Science Institute/ ; },
abstract = {BACKGROUND: Swertia banzragczii and S. marginata are important medicinal species in Mongolia. However, their taxonomic positions and genetic backgrounds remain unknown. In this study, we explored the complete chloroplast genomes and DNA barcoding of these species and compared them with those of closely related species within the subgenus to determine their taxonomic positions and phylogenetic relationships.<br><br>RESULT: The chloroplast genomes of S. banzragczii and S. marginata encoded 114 genes, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Among them, 16 genes contained a single intron, and 2 genes had two introns. Closely related species had a conserved genome structure and gene content. Only differences in genome length were noticed, which were caused by the expansion and contraction of the inverted repeat (IR) region and loss of exons in some genes. The trnH-GUG-psbA and trnD-GUC-trnY-GUA intergenic regions had high genetic diversity within Swertia plastomes. Overall, S. banzragczii and S. marginata are true species and belong to the subgenus Swertia.<br><br>CONCLUSIONS: These results provide valuable genetic and morphological information on rare and subendemic Swertia species in Mongolia, which can be used for further advanced studies on the Swertia genus.},
}
@article {pmid38655012,
year = {2024},
author = {Ståhls, G},
title = {Pelecocera (Pelecocera) tricincta and Pelecocera (Chamaesyrphus) caledonica (Diptera, Syrphidae) reared from Rhizopogon fungal host in Finland.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e118563},
pmid = {38655012},
issn = {1314-2828},
abstract = {MtDNA COI barcodes have frequently been used in identification to associate an unknown life stage in insects with a known species. This study reports the discovery of hoverfly larvae in the fungal fruit bodies of Rhizopogonluteolus Fr. &amp; Nordholm, 1817 in Finland. The identity of the larvae was firstly resolved using mtDNA COI barcodes generated from the larvae and tree-based identification confirming the species Pelecocera (Pelecocera) tricincta Meigen, 1822 and Pelecocera (Chamaesyrphus) caledonica (Collin, 1940) (Diptera, Syrphidae). Obtained pupae were reared into adult flies and produced the same two species. The morphological features of these mycophagous larvae are compared with those of other fungus-feeding hoverfly species. This study confirms Rhizopogonluteolus as fungal host for these Pelecocera species in the Western Palaearctic Region.},
}
@article {pmid38655011,
year = {2024},
author = {Kim, S and Čkrkić, J and Tomanović, &#x17d; and Sohn, JH and Lim, J and Kim, H},
title = {A new species of genus Monoctonus (Hymenoptera, Braconidae, Aphidiinae) from South Korea.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e119476},
pmid = {38655011},
issn = {1314-2828},
abstract = {BACKGROUND: The genus Monoctonus Haliday, 1833 is a small group which consists of 24 species worldwide. In South Korea, Chang and Youn (1983) recorded one species, M.similis Starý &amp; Schlinger, 1967, but the evidence for identification of this species is doubtful and further confirmation is required (personal communication with Prof. Jong-Cheol Paik).<br><br>NEW INFORMATION: An additional Monoctonus species is recorded as new to science from South Korea. Descriptions and illustrations of the new species -Monoctonuskoreanus sp. nov. - are provided, together with its mitochondrial cytochrome c oxidase subunit I (COI) data and phylogenetic position. A key to the female of the two species present in Korea is provided.},
}
@article {pmid38652658,
year = {2024},
author = {Cheng, YL and Banu, MA and Zhao, W and Rosenfeld, SS and Canoll, P and Sims, PA},
title = {Multiplexed single-cell lineage tracing of mitotic kinesin inhibitor resistance in glioblastoma.},
journal = {Cell reports},
volume = {43},
number = {5},
pages = {114139},
pmid = {38652658},
issn = {2211-1247},
support = {R01 NS103473/NS/NINDS NIH HHS/United States ; R01 NS118513/NS/NINDS NIH HHS/United States ; U01 CA168426/CA/NCI NIH HHS/United States ; U01 CA272610/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Glioblastoma/pathology/genetics/metabolism/drug therapy ; *Kinesins/metabolism/antagonists &amp; inhibitors/genetics ; *Drug Resistance, Neoplasm/drug effects/genetics ; Animals ; *Single-Cell Analysis ; *Cell Lineage/drug effects ; Mice ; Brain Neoplasms/pathology/genetics/drug therapy/metabolism ; Cell Line, Tumor ; Mitosis/drug effects ; },
abstract = {Glioblastoma (GBM) is a deadly brain tumor, and the kinesin motor KIF11 is an attractive therapeutic target with roles in proliferation and invasion. Resistance to KIF11 inhibitors, which has mainly been studied in animal models, presents significant challenges. We use lineage-tracing barcodes and single-cell RNA sequencing to analyze resistance in patient-derived GBM neurospheres treated with ispinesib, a potent KIF11 inhibitor. Similar to GBM progression in patients, untreated cells lose their neural lineage identity and become mesenchymal, which is associated with poor prognosis. Conversely, cells subjected to long-term ispinesib treatment exhibit a proneural phenotype. We generate patient-derived xenografts and show that ispinesib-resistant cells form less aggressive tumors in vivo, even in the absence of drug. Moreover, treatment of human ex vivo GBM slices with ispinesib demonstrates phenotypic alignment with in vitro responses, underscoring the clinical relevance of our findings. Finally, using retrospective lineage tracing, we identify drugs that are synergistic with ispinesib.},
}
@article {pmid38646932,
year = {2024},
author = {Saranholi, BH and França, FM and Vogler, AP and Barlow, J and Vaz de Mello, FZ and Maldaner, ME and Carvalho, E and Gestich, CC and Howes, B and Banks-Leite, C and Galetti, PM},
title = {Testing and optimizing metabarcoding of iDNA from dung beetles to sample mammals in the hyperdiverse Neotropics.},
journal = {Molecular ecology resources},
volume = {24},
number = {5},
pages = {e13961},
doi = {10.1111/1755-0998.13961},
pmid = {38646932},
issn = {1755-0998},
support = {1989427//University of Bristol (PolicyBristol, SYNPAM)/ ; ProjectBIOCLIMATE//BNP Paribas Foundation (Climate and Biodiversity Initiative)/ ; 2258319//Cabot Seedcorn 2023 (Voices of Amazonia)/ ; 303524/2019-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 406767/2022-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 420254/2018-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 441257/2023-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 441573/2020-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 441659/2016-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 1777136//University of Bristol (Liv Sidse Jansen Memorial Foundation, FOR-TRAITS)/ ; NE/S011811/1//Natural Environment Research Council/ ; 170839//Climate and Net Zero Impact Awards (Scaling-up TAOCA)/ ; MR/X032949/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; *Coleoptera/genetics/classification ; *Mammals/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA/methods ; Biodiversity ; Metagenomics/methods ; DNA/genetics ; Feces/chemistry ; },
abstract = {Over the past few years, insects have been used as samplers of vertebrate diversity by assessing the ingested-derived DNA (iDNA), and dung beetles have been shown to be a good mammal sampler given their broad feeding preference, wide distribution and easy sampling. Here, we tested and optimized the use of iDNA from dung beetles to assess the mammal community by evaluating if some biological and methodological aspects affect the use of dung beetles as mammal species samplers. We collected 403 dung beetles from 60 pitfall traps. iDNA from each dung beetle was sequenced by metabarcoding using two mini-barcodes (12SrRNA and 16SrRNA). We assessed whether dung beetles with different traits related to feeding, nesting and body size differed in the number of mammal species found in their iDNA. We also tested differences among four killing solutions in preserving the iDNA and compared the effectiveness of each mini barcode to recover mammals. We identified a total of 50 mammal OTUs (operational taxonomic unit), including terrestrial and arboreal species from 10 different orders. We found that at least one mammal-matching sequence was obtained from 70% of the dung beetle specimens. The number of mammal OTUs obtained did not vary with dung beetle traits as well as between the killing solutions. The 16SrRNA mini-barcode recovered a higher number of mammal OTUs than 12SrRNA, although both sets were partly non-overlapping. Thus, the complete mammal diversity may not be achieved by using only one of them. This study refines the methodology for routine assessment of tropical mammal communities via dung beetle 'samplers' and its universal applicability independently of the species traits of local beetle communities.},
}
@article {pmid38646006,
year = {2024},
author = {Banerjee, P and Dey, G and Maity, JP and Stewart, KA and Sharma, RK and Chan, MWY and Lee, K and Chen, CY},
title = {The unseen invaders: Tracking phylogeographic dynamics and genetic diversity of cryptic Pomacea canaliculata and P. maculata (Golden apple snails) across Taiwan.},
journal = {Ecology and evolution},
volume = {14},
number = {4},
pages = {e11268},
pmid = {38646006},
issn = {2045-7758},
abstract = {The cryptic invasion of golden apple snails (Pomacea canaliculata and P. maculata) in Taiwan has caused significant ecological and economical damage over the last few decades, however, their management remains difficult due to inadequate taxonomic identification, complex phylogeny, and limited population genetic information. We aim to understand the current distribution, putative population of origin, genetic diversity, and potential path of cryptic invasion of Pomacea canaliculata and P. maculata across Taiwan to aid in improved mitigation approaches. The present investigation conducted a nationwide survey with 254 samples collected from 41 locations in 14 counties or cities across Taiwan. We identified P. canaliculata and P. maculata based on mitochondrial COI and compared their genetic diversity across Taiwan, as well as other introduced and native countries (based on publicly available COI data) to understand the possible paths of invasion to Taiwan. Based on mitochondrial COI barcoding, sympatric and heterogeneous distributions of invasive P. canaliculata and P. maculata were noted. Our haplotype analysis and mismatch distribution results suggested multiple introductions of P. canaliculata in Taiwan was likely originated directly from Argentina, whereas P. maculata was probably introduced from a single, or a few, introduction event(s) from Argentina and Brazil. Our population genetic data further demonstrated a higher haplotype and genetic diversity for P. canaliculata and P. maculata in Taiwan compared to other introduced regions. Based on our current understanding, the establishment of P. canaliculata and P. maculata is alarming and widespread beyond geopolitical borders, requiring a concerted and expedited national and international invasive species mitigation program.},
}
@article {pmid38645306,
year = {2024},
author = {Lammertse, E and Li, S and Kendall, J and Kim, C and Morris, P and Ranade, N and Levy, D and Wigler, M and Brouzes, E},
title = {Magnetically functionalized hydrogels for high-throughput genomic applications.},
journal = {Advanced materials technologies},
volume = {9},
number = {2},
pages = {},
pmid = {38645306},
issn = {2365-709X},
support = {R01 CA181595/CA/NCI NIH HHS/United States ; },
abstract = {Single-cell genomics has revolutionized tissue analysis by revealing the genetic program of individual cells. The key aspect of the technology is the use of barcoded beads to unambiguously tag sequences originating from a single cell. The generation of unique barcodes on beads is mainly achieved by split-pooling methods, which are labor-intensive due to repeated washing steps. Towards the automation of the split-pooling method, we developed a simple method to magnetize hydrogel beads. We show that these hydrogel beads provide increased yields and washing efficiencies for purification procedures. They are also fully compatible with single-cell sequencing using the BAG-Seq workflow. Our work opens the automation of the split-pooling technique, which will improve single-cell genomic workflows.},
}
@article {pmid38643988,
year = {2024},
author = {Nathans, JF and Ayers, JL and Shendure, J and Simpson, CL},
title = {Genetic Tools for Cell Lineage Tracing and Profiling Developmental Trajectories in the Skin.},
journal = {The Journal of investigative dermatology},
volume = {144},
number = {5},
pages = {936-949},
pmid = {38643988},
issn = {1523-1747},
support = {K08 AR075846/AR/NIAMS NIH HHS/United States ; },
mesh = {Humans ; *Cell Lineage ; Animals ; *Cell Differentiation ; Skin/cytology ; Stem Cells/cytology ; Cell Proliferation ; Regeneration/physiology ; },
abstract = {The epidermis is the body's first line of protection against dehydration and pathogens, continually regenerating the outermost protective skin layers throughout life. During both embryonic development and wound healing, epidermal stem and progenitor cells must respond to external stimuli and insults to build, maintain, and repair the cutaneous barrier. Recent advances in CRISPR-based methods for cell lineage tracing have remarkably expanded the potential for experiments that track stem and progenitor cell proliferation and differentiation over the course of tissue and even organismal development. Additional tools for DNA-based recording of cellular signaling cues promise to deepen our understanding of the mechanisms driving normal skin morphogenesis and response to stressors as well as the dysregulation of cell proliferation and differentiation in skin diseases and cancer. In this review, we highlight cutting-edge methods for cell lineage tracing, including in organoids and model organisms, and explore how cutaneous biology researchers might leverage these techniques to elucidate the developmental programs that support the regenerative capacity and plasticity of the skin.},
}
@article {pmid38642645,
year = {2024},
author = {Alloun, W and Berkani, M and Shavandi, A and Beddiar, A and Pellegrini, M and Garzia, M and Lakhdari, D and Ganachari, SV and Aminabhavi, TM and Vasseghian, Y and Muddapur, U and Chaouche, NK},
title = {Harnessing artificial intelligence-driven approach for enhanced indole-3-acetic acid from the newly isolated Streptomyces rutgersensis AW08.},
journal = {Environmental research},
volume = {252},
number = {Pt 3},
pages = {118933},
doi = {10.1016/j.envres.2024.118933},
pmid = {38642645},
issn = {1096-0953},
mesh = {*Streptomyces/genetics/metabolism ; *Artificial Intelligence ; *Indoleacetic Acids/metabolism ; *RNA, Ribosomal, 16S/genetics ; Algeria ; Phylogeny ; },
abstract = {Indole-3-acetic acid (IAA) derived from Actinobacteria fermentations on agro-wastes constitutes a safer and low-cost alternative to synthetic IAA. This study aims to select a high IAA-producing Streptomyces-like strain isolated from Lake Oubeira sediments (El Kala, Algeria) for further investigations (i.e., 16S rRNA gene barcoding and process optimization). Subsequently, artificial intelligence-based approaches were employed to maximize IAA bioproduction on spent coffee grounds as high-value-added feedstock. The specificity was the novel application of the Limited-Memory Broyden-Fletcher-Goldfarb-Shanno Box (L-BFGS-B) optimization algorithm. The new strain AW08 was a significant producer of IAA (26.116 ± 0.61 μg/mL) and was identified as Streptomyces rutgersensis by 16S rRNA gene barcoding and phylogenetic inquiry. The empirical data involved the inoculation of AW08 in various cultural conditions according to a four-factor Box Behnken Design matrix (BBD) of Response surface methodology (RSM). The input parameters and regression equation extracted from the RSM-BBD were the basis for implementing and training the L-BFGS-B algorithm. Upon training the model, the optimal conditions suggested by the BBD and L-BFGS-B algorithm were, respectively, L-Trp (X1) = 0.58 %; 0.57 %; T° (X2) = 26.37 °C; 28.19 °C; pH (X3) = 7.75; 8.59; and carbon source (X4) = 30 %; 33.29 %, with the predicted response IAA (Y) = 152.8; 169.18 μg/mL). Our findings emphasize the potential of the multifunctional S. rutgersensis AW08, isolated and reported for the first time in Algeria, as a robust producer of IAA. Validation investigations using the bioprocess parameters provided by the L-BFGS-B and the BBD-RSM models demonstrate the effectiveness of AI-driven optimization in maximizing IAA output by 5.43-fold and 4.2-fold, respectively. This study constitutes the first paper reporting a novel interdisciplinary approach and providing insights into biotechnological advancements. These results support for the first time a reasonable approach for valorizing spent coffee grounds as feedstock for sustainable and economic IAA production from S. rutgersensis AW08.},
}
@article {pmid38641660,
year = {2024},
author = {Reicher, A and Reiniš, J and Ciobanu, M and Růžička, P and Malik, M and Siklos, M and Kartysh, V and Tomek, T and Koren, A and Rendeiro, AF and Kubicek, S},
title = {Pooled multicolour tagging for visualizing subcellular protein dynamics.},
journal = {Nature cell biology},
volume = {26},
number = {5},
pages = {745-756},
pmid = {38641660},
issn = {1476-4679},
support = {ERC-CoG-772437//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; LS21-01//Vienna Science and Technology Fund (Wiener Wissenschafts-, Forschungs- und Technologiefonds)/ ; },
mesh = {Humans ; *Proteomics/methods ; Machine Learning ; Microscopy, Fluorescence/methods ; Cell Line, Tumor ; },
abstract = {Imaging-based methods are widely used for studying the subcellular localization of proteins in living cells. While routine for individual proteins, global monitoring of protein dynamics following perturbation typically relies on arrayed panels of fluorescently tagged cell lines, limiting throughput and scalability. Here, we describe a strategy that combines high-throughput microscopy, computer vision and machine learning to detect perturbation-induced changes in multicolour tagged visual proteomics cell (vpCell) pools. We use genome-wide and cancer-focused intron-targeting sgRNA libraries to generate vpCell pools and a large, arrayed collection of clones each expressing two different endogenously tagged fluorescent proteins. Individual clones can be identified in vpCell pools by image analysis using the localization patterns and expression level of the tagged proteins as visual barcodes, enabling simultaneous live-cell monitoring of large sets of proteins. To demonstrate broad applicability and scale, we test the effects of antiproliferative compounds on a pool with cancer-related proteins, on which we identify widespread protein localization changes and new inhibitors of the nuclear import/export machinery. The time-resolved characterization of changes in subcellular localization and abundance of proteins upon perturbation in a pooled format highlights the power of the vpCell approach for drug discovery and mechanism-of-action studies.},
}
@article {pmid38637345,
year = {2024},
author = {Patil, GS and Pinto, N and Nath, R and Goswami, M},
title = {Decoding the molecular phylogenetics of ornamental catfishes (siluriformes) of North East India using DNA barcoding approach.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {528},
pmid = {38637345},
issn = {1573-4978},
support = {BT/PR16430/NER/95/201/2015//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR16430/NER/95/201/2015//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR16430/NER/95/201/2015//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR16430/NER/95/201/2015//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {Animals ; Humans ; *Catfishes/genetics ; DNA Barcoding, Taxonomic/methods ; Phylogeny ; DNA ; India ; },
abstract = {BACKGROUND: Catfishes (order Siluriformes) are among the most diverse and widely distributed fish groups in the world. They are not only used for human consumption but are also a major part of the ornamental fish trade. Being a Biodiversity Hotspot, the North Eastern Region of India is home to a diverse population of ornamental fishes. Catfishes contain a humongous number of species; in this study, the authors have tried to elucidate the phylogenetic relationship of some important ornamental catfishes found in North East India using DNA barcodes.<br><br>METHODS AND RESULTS: In this study, we have tried to explore the phylogenetic history of 13 species (41 specimens) of ornamental catfishes spanning 12 genera and 9 families of Siluriformes using DNA barcoding. Pairwise genetic distances using Kimura 2-Parameter (K2P) were calculated at intra-specific and inter-specific levels. A Neighbor-Joining tree was constructed to understand the phylogenetic relationship among the nine different catfish families. All the specimens under this study clustered with their respective species under the same family and formed three sub-clades. However, Olyra longicaudata, belonging to the Bagridae family, did not cluster with other species from the same family. In this study, the authors have suggested a revision of the classification of O. longicaudata back to its original family, Olyridae.<br><br>CONCLUSIONS: In this study, the maximum intraspecific genetic distance of 0.03 and the minimum interspecific genetic distance of 0.14 were observed among the species. Therefore, it is evident that there is a barcoding gap among the species, which helped in the correct identification of the species. Thus, DNA barcoding helped complement the phenetic approach and also revealed a different phylogenetic relationship among the catfishes belonging to the Bagridae family.},
}
@article {pmid38635627,
year = {2024},
author = {Chevée, V and Hullahalli, K and Dailey, KG and Güereca, L and Zhang, C and Waldor, MK and Portnoy, DA},
title = {Temporal and spatial dynamics of Listeria monocytogenes central nervous system infection in mice.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {17},
pages = {e2320311121},
pmid = {38635627},
issn = {1091-6490},
support = {R25 GM140276/GM/NIGMS NIH HHS/United States ; R01 AI042347/AI/NIAID NIH HHS/United States ; R01 AI027655/AI/NIAID NIH HHS/United States ; F31 AI156949/AI/NIAID NIH HHS/United States ; P01 AI063302/AI/NIAID NIH HHS/United States ; },
mesh = {Mice ; Animals ; *Listeria monocytogenes/physiology ; *Listeriosis/microbiology ; Brain/microbiology ; *Central Nervous System Infections ; },
abstract = {Listeria monocytogenes is a bacterial pathogen that can cause life-threatening central nervous system (CNS) infections. While mechanisms by which L. monocytogenes and other pathogens traffic to the brain have been studied, a quantitative understanding of the underlying dynamics of colonization and replication within the brain is still lacking. In this study, we used barcoded L. monocytogenes to quantify the bottlenecks and dissemination patterns that lead to cerebral infection. Following intravenous (IV) inoculation, multiple independent invasion events seeded all parts of the CNS from the blood, however, only one clone usually became dominant in the brain. Sequential IV inoculations and intracranial inoculations suggested that clones that had a temporal advantage (i.e., seeded the CNS first), rather than a spatial advantage (i.e., invaded a particular brain region), were the main drivers of clonal dominance. In a foodborne model of cerebral infection with immunocompromised mice, rare invasion events instead led to a highly infected yet monoclonal CNS. This restrictive bottleneck likely arose from pathogen transit into the blood, rather than directly from the blood to the brain. Collectively, our findings provide a detailed quantitative understanding of the L. monocytogenes population dynamics that lead to CNS infection and a framework for studying the dynamics of other cerebral infections.},
}
@article {pmid38634956,
year = {2024},
author = {Chakraborty, M and Kaur, J and Gunjan, and Kathpalia, M and Kaur, N},
title = {Clinical relevance of glycosylation in triple negative breast cancer: a review.},
journal = {Glycoconjugate journal},
volume = {41},
number = {2},
pages = {79-91},
pmid = {38634956},
issn = {1573-4986},
mesh = {Female ; Humans ; Biomarkers, Tumor/metabolism ; Clinical Relevance ; Glycosylation ; *Triple Negative Breast Neoplasms/metabolism ; },
abstract = {Glycosylation alterations in TNBC have significant implications for tumor behavior, diagnosis, prognosis, and therapeutic strategies. Dysregulated glycosylation affects cell adhesion, signaling, immune recognition, and response to therapy in TNBC. Different types of glycosylation, including N-linked glycosylation, O-linked glycosylation, glycosphingolipid glycosylation, mucin-type glycosylation, and sialylation, play distinct roles in TNBC. The "barcoding" method based on glycosylation sites of the membrane type mannose receptor (MR) shows promise in accurately distinguishing breast cancer subtypes, including TNBC. Alpha-L-fucosidase 1 (FUCA1) and Monocarboxylate transporter 4 (MCT4) have been identified as potential diagnostic and prognostic markers for TNBC. The glycosylation status of PD-L1 impacts the response to immune checkpoint blockade therapy in TNBC. Inhibiting fucosylation of B7H3 enhances immune responses and improves anti-tumor effects. Targeting glycosylated B7H4 and modulating estrogen metabolism through glycosylation-related mechanisms are potential therapeutic strategies for TNBC. Understanding the role of glycosylation in TNBC provides insights into disease mechanisms, diagnosis, and potential therapeutic targets. Further research in this field may lead to personalized treatment approaches and improved outcomes for TNBC patients.},
}
@article {pmid38633369,
year = {2024},
author = {Kang, S and Choi, P and Maile-Moskowitz, A and Brown, CL and Gonzalez, RA and Pruden, A and Vikesland, PJ},
title = {Highly Multiplexed Reverse-Transcription Loop-Mediated Isothermal Amplification and Nanopore Sequencing (LAMPore) for Wastewater-Based Surveillance.},
journal = {ACS ES&amp;T water},
volume = {4},
number = {4},
pages = {1629-1636},
pmid = {38633369},
issn = {2690-0637},
abstract = {Wastewater-based surveillance (WBS) has gained attention as a strategy to monitor and provide an early warning for disease outbreaks. Here, we applied an isothermal gene amplification technique, reverse-transcription loop-mediated isothermal amplification (RT-LAMP), coupled with nanopore sequencing (LAMPore) as a means to detect SARS-CoV-2. Specifically, we combined barcoding using both an RT-LAMP primer and the nanopore rapid barcoding kit to achieve highly multiplexed detection of SARS-CoV-2 in wastewater. RT-LAMP targeting the SARS-CoV-2 N region was conducted on 96 reactions including wastewater RNA extracts and positive and no-target controls. The resulting amplicons were pooled and subjected to nanopore sequencing, followed by demultiplexing based on barcodes that differentiate the source of each SARS-CoV-2 N amplicon derived from the 96 RT-LAMP products. The criteria developed and applied to establish whether SARS-CoV-2 was detected by the LAMPore assay indicated high consistency with polymerase chain reaction-based detection of the SARS-CoV-2 N gene, with a sensitivity of 89% and a specificity of 83%. We further profiled sequence variations on the SARS-CoV-2 N amplicons, revealing a number of mutations on a sample collected after viral variants had emerged. The results demonstrate the potential of the LAMPore assay to facilitate WBS for SARS-CoV-2 and the emergence of viral variants in wastewater.},
}
@article {pmid38632506,
year = {2024},
author = {Alkathiry, HA and Alghamdi, SQ and Sinha, A and Margos, G and Stekolnikov, AA and Alagaili, AN and Darby, AC and Makepeace, BL and Khoo, JJ},
title = {Microbiome and mitogenomics of the chigger mite Pentidionis agamae: potential role as an Orientia vector and associations with divergent clades of Wolbachia and Borrelia.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {380},
pmid = {38632506},
issn = {1471-2164},
mesh = {Animals ; *Borrelia/genetics ; DNA ; *Microbiota ; Multilocus Sequence Typing ; Orientia ; *Orientia tsutsugamushi/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rodentia/genetics ; Saudi Arabia ; *Scrub Typhus/epidemiology/microbiology ; *Trombiculidae/genetics/microbiology ; *Wolbachia/genetics ; },
abstract = {BACKGROUND: Trombiculid mites are globally distributed, highly diverse arachnids that largely lack molecular resources such as whole mitogenomes for the elucidation of taxonomic relationships. Trombiculid larvae (chiggers) parasitise vertebrates and can transmit bacteria (Orientia spp.) responsible for scrub typhus, a zoonotic febrile illness. Orientia tsutsugamushi causes most cases of scrub typhus and is endemic to the Asia-Pacific Region, where it is transmitted by Leptotrombidium spp. chiggers. However, in Dubai, Candidatus Orientia chuto was isolated from a case of scrub typhus and is also known to circulate among rodents in Saudi Arabia and Kenya, although its vectors remain poorly defined. In addition to Orientia, chiggers are often infected with other potential pathogens or arthropod-specific endosymbionts, but their significance for trombiculid biology and public health is unclear.<br><br>RESULTS: Ten chigger species were collected from rodents in southwestern Saudi Arabia. Chiggers were pooled according to species and screened for Orientia DNA by PCR. Two species (Microtrombicula muhaylensis and Pentidionis agamae) produced positive results for the htrA gene, although Ca. Orientia chuto DNA was confirmed by Sanger sequencing only in P. agamae. Metagenomic sequencing of three pools of P. agamae provided evidence for two other bacterial associates: a spirochaete and a Wolbachia symbiont. Phylogenetic analysis of 16S rRNA and multi-locus sequence typing genes placed the spirochaete in a clade of micromammal-associated Borrelia spp. that are widely-distributed globally with no known vector. For the Wolbachia symbiont, a genome assembly was obtained that allowed phylogenetic localisation in a novel, divergent clade. Cytochrome c oxidase I (COI) barcodes for Saudi Arabian chiggers enabled comparisons with global chigger diversity, revealing several cases of discordance with classical taxonomy. Complete mitogenome assemblies were obtained for the three P. agamae pools and almost 50 SNPs were identified, despite a common geographic origin.<br><br>CONCLUSIONS: P. agamae was identified as a potential vector of Ca. Orientia chuto on the Arabian Peninsula. The detection of an unusual Borrelia sp. and a divergent Wolbachia symbiont in P. agamae indicated links with chigger microbiomes in other parts of the world, while COI barcoding and mitogenomic analyses greatly extended our understanding of inter- and intraspecific relationships in trombiculid mites.},
}
@article {pmid38631624,
year = {2024},
author = {Hu, H and Liu, L and Wei, XY and Duan, JJ and Deng, JY and Pei, DS},
title = {Revolutionizing aquatic eco-environmental monitoring: Utilizing the RPA-Cas-FQ detection platform for zooplankton.},
journal = {The Science of the total environment},
volume = {929},
number = {},
pages = {172414},
doi = {10.1016/j.scitotenv.2024.172414},
pmid = {38631624},
issn = {1879-1026},
mesh = {*Zooplankton ; *Environmental Monitoring/methods ; Animals ; CRISPR-Cas Systems ; DNA, Environmental/analysis ; Nucleic Acid Amplification Techniques/methods ; Recombinases/metabolism ; },
abstract = {The integration of recombinase polymerase amplification (RPA) with CRISPR/Cas technology has revolutionized molecular diagnostics and pathogen detection due to its unparalleled sensitivity and trans-cleavage ability. However, its potential in the ecological and environmental monitoring scenarios for aquatic ecosystems remains largely unexplored, particularly in accurate qualitative/quantitative detection, and its actual performance in handling complex real environmental samples. Using zooplankton as a model, we have successfully optimized the RPA-CRISPR/Cas12a fluorescence detection platform (RPA-Cas-FQ), providing several crucial "technical tips". Our findings indicate the sensitivity of CRISPR/Cas12a alone is 5 × 10[9] copies/reaction, which can be dramatically increased to 5 copies/reaction when combined with RPA. The optimized RPA-Cas-FQ enables reliable qualitative and semi-quantitative detection within 50 min, and exhibits a good linear relationship between fluorescence intensity and DNA concentration (R[2] = 0.956-0.974***). Additionally, we developed a rapid and straightforward identification procedure for single zooplankton by incorporating heat-lysis and DNA-barcode techniques. We evaluated the platform's effectiveness using real environmental DNA (eDNA) samples from the Three Gorges Reservoir, confirming its practicality. The eDNA-RPA-Cas-FQ demonstrated strong consistency (Kappa = 0.43***) with eDNA-Metabarcoding in detecting species presence/absence in the reservoir. Furthermore, the two semi-quantitative eDNA technologies showed a strong positive correlation (R[2] = 0.58-0.87***). This platform also has the potential to monitor environmental pollutants by selecting appropriate indicator species. The novel insights and methodologies presented in this study represent a significant advancement in meeting the complex needs of aquatic ecosystem protection and monitoring.},
}
@article {pmid38629445,
year = {2024},
author = {Fiedler, S and Frenzel, F and Würth, C and Tavernaro, I and Grüne, M and Schweizer, S and Engel, A and Resch-Genger, U},
title = {Interlaboratory Comparison on Absolute Photoluminescence Quantum Yield Measurements of Solid Light Converting Phosphors with Three Commercial Integrating Sphere Setups.},
journal = {Analytical chemistry},
volume = {96},
number = {17},
pages = {6730-6737},
pmid = {38629445},
issn = {1520-6882},
abstract = {Scattering luminescent materials dispersed in liquid and solid matrices and luminescent powders are increasingly relevant for fundamental research and industry. Examples are luminescent nano- and microparticles and phosphors of different compositions in various matrices or incorporated into ceramics with applications in energy conversion, solid-state lighting, medical diagnostics, and security barcoding. The key parameter to characterize the performance of these materials is the photoluminescence/fluorescence quantum yield (Φf), i.e., the number of emitted photons per number of absorbed photons. To identify and quantify the sources of uncertainty of absolute measurements of Φf of scattering samples, the first interlaboratory comparison (ILC) of three laboratories from academia and industry was performed by following identical measurement protocols. Thereby, two types of commercial stand-alone integrating sphere setups with different illumination and detection geometries were utilized for measuring the Φf of transparent and scattering dye solutions and solid phosphors, namely, YAG:Ce optoceramics of varying surface roughness, used as converter materials for blue light emitting diodes. Special emphasis was dedicated to the influence of the measurement geometry, the optical properties of the blank utilized to determine the number of photons of the incident excitation light absorbed by the sample, and the sample-specific surface roughness. While the Φf values of the liquid samples matched between instruments, Φf measurements of the optoceramics with different blanks revealed substantial differences. The ILC results underline the importance of the measurement geometry, sample position, and blank for reliable Φf data of scattering the YAG:Ce optoceramics, with the blank's optical properties accounting for uncertainties exceeding 20%.},
}
@article {pmid38629305,
year = {2024},
author = {Fening, KO and Okyere, SO and Forchibe, EE and Layodé, BFR and Richmond, TE and Agboyi, LKBA and Afreh-Nuamah, K and Wamonje, FO},
title = {First report of Leucinodes africensis and Leucinodes laisalis on Solanum aethiopicum and Solanum melongena in farmer's fields in southern Ghana.},
journal = {Bulletin of entomological research},
volume = {114},
number = {3},
pages = {359-373},
doi = {10.1017/S0007485324000154},
pmid = {38629305},
issn = {1475-2670},
mesh = {Animals ; Ghana ; *Moths/physiology ; *Solanum ; Male ; *Solanum melongena/parasitology ; },
abstract = {The eggplant fruit and shoot borer (EFSB) is a devastating pest of eggplants (Solanum aethiopicum L. and Solanum melongena L.) in Ghana, causing significant economic losses. Although initially thought to be the Leucinodes orbonalis Guenee species found in Asia, recent European and Mediterranean Plant Protection Organization reports suggest its absence in Africa. However, eight Leucinodes species have been recently described in Africa, including two new species, Leucinodes africensis sp. n. and Leucinodes laisalis Walker, which were intercepted in eggplant fruits exported from Ghana to the United Kingdom. Despite the reported absence of L. orbonalis in Africa, it remains on the pest list of Ghana as a species known to attack eggplants. To accurately determine the identity of the EFSB complex occurring on eggplant in Southern Ghana, molecular and morphological taxonomic tools were employed, and adult male populations were monitored in on-farm conditions. Our results revealed the presence of two EFSB species, L. africensis and L. laisalis, in the shoot and fruits of eggplants, with L. africensis being the dominant species and widely distributed in Southern Ghana. Notably, L. africensis males were attracted to the pheromone lure of L. orbonalis despite the two species being biologically distinct. This study provides crucial information on correctly identifying the EFSB species attacking eggplants in Southern Ghana and has significant implications for developing management interventions against these pests and their effects on international eggplant trade.},
}
@article {pmid38621699,
year = {2024},
author = {Grisendi, A and Calzolari, M and Defilippo, F and Torri, D and Marzani, K and Dottori, M and Bonilauri, P and Maioli, G},
title = {MORPHOLOGICAL AND MOLECULAR CHARACTERIZATION OF AMBLYOMMA SCUTATUM (ACARI: IXODIDAE) ACCIDENTALLY INTRODUCED IN ITALY.},
journal = {The Journal of parasitology},
volume = {110},
number = {2},
pages = {155-158},
doi = {10.1645/20-69},
pmid = {38621699},
issn = {1937-2345},
mesh = {Animals ; *Ixodidae/genetics ; Amblyomma ; *Tick Infestations/epidemiology/veterinary ; *Ticks ; Italy ; *Lizards ; },
abstract = {Eight ticks were found in Comacchio (FE), Italy parasitizing a young black iguana (Ctenosaura similis) that had been accidentally transported in a commercial plant container from Costa Rica. Specimens were identified morphologically as Amblyomma scutatum and then confirmed by the barcoding of the mitochondrial cytochrome c oxidase subunit 1 gene. Amblyomma scutatum is a common tick known to infest reptiles in Central America, Mexico, and Venezuela, but not in Europe. In Italy, the possibility for this tick to become endemic is unlikely because of the absence of its principal hosts. Nevertheless, this finding confirms the high risk of introducing exotic species that is linked with global commerce and therefore the need for veterinary control of shipments.},
}
@article {pmid38621643,
year = {2024},
author = {Liu, Z and Zeng, H and Xiang, H and Deng, S and He, X},
title = {Achieving single-cell-resolution lineage tracing in zebrafish by continuous barcoding mutations during embryogenesis.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {51},
number = {9},
pages = {947-956},
doi = {10.1016/j.jgg.2024.04.004},
pmid = {38621643},
issn = {1673-8527},
mesh = {Animals ; *Zebrafish/genetics/embryology ; *Cell Lineage/genetics ; *Single-Cell Analysis/methods ; *Embryonic Development/genetics ; *Mutation/genetics ; Phylogeny ; DNA Barcoding, Taxonomic ; Germ Cells/cytology/metabolism ; Embryo, Nonmammalian/cytology ; },
abstract = {Unraveling the lineage relationships of all descendants from a zygote is fundamental to advancing our understanding of developmental and stem cell biology. However, existing cell barcoding technologies in zebrafish lack the resolution to capture the majority of cell divisions during embryogenesis. A recently developed method, a substitution mutation-aided lineage-tracing system (SMALT), successfully reconstructed high-resolution cell phylogenetic trees for Drosophila melanogaster. Here, we implement the SMALT system in zebrafish, recording a median of 14 substitution mutations on a one-kilobase-pair barcoding sequence for one-day post-fertilization embryos. Leveraging this system, we reconstruct four cell lineage trees for zebrafish fin cells, encompassing both original and regenerated fin. Each tree consists of hundreds of internal nodes with a median bootstrap support of 99%. Analysis of the obtained cell lineage trees reveals that regenerated fin cells mainly originate from cells in the same part of the fins. Through multiple times sampling germ cells from the same individual, we show the stability of the germ cell pool and the early separation of germ cell and somatic cell progenitors. Our system offers the potential for reconstructing high-quality cell phylogenies across diverse tissues, providing valuable insights into development and disease in zebrafish.},
}
@article {pmid38617833,
year = {2024},
author = {Ge, X and Wang, C and Pei, W and Tang, Y and Liu, W and Yan, C},
title = {New descriptions of the larval and pupal stages of Orthocladiusnitidoscutellatus and Psectrocladiusnevalis from Xizang, China (Diptera, Chironomidae).},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e121952},
pmid = {38617833},
issn = {1314-2828},
abstract = {BACKGROUND: Tibetan Plateau is one of the most typical areas of biodiversity in the world because of its unique environmental and regional units, which breed unique biological communities and concentrate on many unique and rare wild animals and plants. Research on Chironomidae in the Tibetan Plateau is relatively weak. At present, the identification of Chironomidae species mainly depends on male adults, while identification of larvae and pupae is relatively difficult and there is less research on them.<br><br>NEW INFORMATION: During the investigations of insect diversity in the Tibetan Plateau, larval and pupal stages of Orthocladiusnitidoscutellatus Lundstr&#xf6;m, 1915 and Psectrocladiusnevalis Akhrorov, 1977 were described and illustrated. Matching and identification of larval and pupal stages were based on DNA barcodes. Neighbour-joining trees were reconstructed, based on known Orthocladius and Psectrocladius COI DNA barcodes, respectively.},
}
@article {pmid38617287,
year = {2024},
author = {Scherer, M and Singh, I and Braun, M and Szu-Tu, C and Kardorff, M and Rühle, J and Frömel, R and Beneyto-Calabuig, S and Raffel, S and Rodriguez-Fraticelli, A and Velten, L},
title = {Somatic epimutations enable single-cell lineage tracing in native hematopoiesis across the murine and human lifespan.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38617287},
issn = {2692-8205},
support = {K99 HL146983/HL/NHLBI NIH HHS/United States ; },
abstract = {Current approaches to lineage tracing of stem cell clones require genetic engineering or rely on sparse somatic DNA variants, which are difficult to capture at single-cell resolution. Here, we show that targeted single-cell measurements of DNA methylation at single-CpG resolution deliver joint information about cellular differentiation state and clonal identities. We develop EPI-clone, a droplet-based method for transgene-free lineage tracing, and apply it to study hematopoiesis, capturing hundreds of clonal trajectories across almost 100,000 single-cells. Using ground-truth genetic barcodes, we demonstrate that EPI-clone accurately identifies clonal lineages throughout hematopoietic differentiation. Applied to unperturbed hematopoiesis, we describe an overall decline of clonal complexity during murine ageing and the expansion of rare low-output stem cell clones. In aged human donors, we identified expanded hematopoietic clones with and without genetic lesions, and various degrees of clonal complexity. Taken together, EPI-clone enables accurate and transgene-free single-cell lineage tracing at scale.},
}
@article {pmid38615893,
year = {2024},
author = {Merivaara, A and Puranen, J and Sadeghi, A and Zashikhina, N and Pirskanen, L and Lajunen, T and Terasaki, T and Auriola, S and Vellonen, KS and Urtti, A},
title = {Barcode lipids for absolute quantitation of liposomes in ocular tissues.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {370},
number = {},
pages = {1-13},
doi = {10.1016/j.jconrel.2024.04.023},
pmid = {38615893},
issn = {1873-4995},
mesh = {Animals ; *Liposomes ; *Vitreous Body/metabolism ; *Aqueous Humor/metabolism ; *Lipids/chemistry ; *Retina/metabolism ; Male ; Rats ; Eye/metabolism ; Mass Spectrometry ; Chromatography, Liquid ; Rats, Sprague-Dawley ; Tissue Distribution ; },
abstract = {Lipid-based drug formulations are promising systems for improving delivery of drugs to ocular tissues, such as retina. To develop lipid-based systems further, an improved understanding of their pharmacokinetics is required, but high-quality in vivo experiments require a large number of animals, raising ethical and economic questions. In order to expedite in vivo kinetic testing of lipid-based systems, we propose a barcode approach that is based on barcoding liposomes with non-endogenous lipids. We developed and evaluated a liquid-chromatography-mass spectrometry method to quantify many liposomes simultaneously in aqueous humor, vitreous, and neural retina at higher than ±20% precision and accuracy. Furthermore, we showed in vivo suitability of the method in pharmacokinetic evaluation of six different liposomes after their simultaneous injection into the rat vitreal cavity. We calculated pharmacokinetic parameters in vitreous and aqueous humor, quantified liposome concentrations in the retina, and quantitated retinal distribution of the liposomes in the rats. Compared to individual injections of the liposome formulations, the barcode-based study design enabled reduction of animal numbers from 72 to 12. We believe that the proposed approach is reliable and will reduce and refine ocular pharmacokinetic experiments with liposomes and other lipid-based systems.},
}
@article {pmid38614287,
year = {2024},
author = {Lu, Q and Tian, Q and Gu, W and Yang, CX and Wang, DJ and Yi, TS},
title = {Comparative genomics on chloroplasts of Rubus (Rosaceae).},
journal = {Genomics},
volume = {116},
number = {3},
pages = {110845},
doi = {10.1016/j.ygeno.2024.110845},
pmid = {38614287},
issn = {1089-8646},
mesh = {*Phylogeny ; *Rubus/genetics ; *Genomics ; Genome, Chloroplast ; Chloroplasts/genetics ; Microsatellite Repeats ; Evolution, Molecular ; RNA, Transfer/genetics ; Codon Usage ; },
abstract = {Rubus, the largest genus in Rosaceae, contains over 1400 species that distributed in multiple habitats across the world, with high species diversity in the temperate regions of Northern Hemisphere. Multiple Rubus species are cultivated for their valuable fruits. However, the intrageneric classification and phylogenetic relationships are still poorly understood. In this study, we sequenced, assembled, and characterized 17 plastomes of Rubus, and conducted comparative genomics integrating with 47 previously issued plastomes of this genus. The 64 plastomes of Rubus exhibited typical quadripartite structure with sizes ranging from 155,144 to 156,700 bp, and contained 132 genes including 87 protein-coding genes, 37 tRNA genes and eight rRNA genes. All plastomes are conservative in the gene order, the frequency of different types of long repeats and simple sequence repeats (SSRs), the codon usage, and the selection pressure of protein-coding genes. However, there are also some differences in the Rubus plastomes, including slight contraction and expansion of the IRs, a variation in the numbers of SSRs and long repeats, and some genes in certain clades undergoing intensified or relaxed purifying selection. Phylogenetic analysis based on whole plastomes showed that the monophyly of Rubus was strongly supported and resolved it into six clades corresponding to six subgenera. Moreover, we identified 12 highly variable regions that could be potential molecular markers for phylogenetic, population genetic, and barcoding studies. Overall, our study provided insight into plastomic structure and sequence diversification of Rubus, which could be beneficial for future studies on identification, evolution, and phylogeny in this genus.},
}
@article {pmid38613982,
year = {2024},
author = {Zhang, J and Zheng, T and Helalat, SH and Yesibolati, MN and Sun, Y},
title = {Synthesis of eco-friendly multifunctional dextran microbeads for multiplexed assays.},
journal = {Journal of colloid and interface science},
volume = {666},
number = {},
pages = {603-614},
doi = {10.1016/j.jcis.2024.04.061},
pmid = {38613982},
issn = {1095-7103},
mesh = {*Dextrans/chemistry ; *Microspheres ; Particle Size ; Surface Properties ; Humans ; Cytokines/analysis ; Click Chemistry ; Porosity ; Mice ; Animals ; Green Chemistry Technology ; },
abstract = {There has been an increasing demand for simultaneous detection of multiple analytes in one sample. Microbead-based platforms have been developed for multiplexed assays. However, most of the microbeads are made of non-biodegradable synthetic polymers, leading to environmental and human health concerns. In this study, we developed an environmentally friendly dextran microbeads as a new type of multi-analyte assay platform. Biodegradable dextran was utilized as the primary material. Highly uniform magnetic dextran microspheres were successfully synthesized using the Shirasu porous glass (SPG) membrane emulsification technique. To enhance the amount of surface functional groups for ligand conjugation, we coated the dextran microbeads with a layer of dendrimers via a simple electrostatic adsorption process. Subsequently, a unique and efficient click chemistry coupling technique was developed for the fluorescence encoding of the microspheres, enabling multiplexed detection. The dextran microbeads were tested for 3-plex cytokine analysis, and exhibited excellent biocompatibility, stable coding signals, low background noise and high sensitivity.},
}
@article {pmid38612346,
year = {2024},
author = {Vella, A and Vella, N},
title = {The First Report of Pennella (Crustacea: Copepoda) Infesting Stenella coeruleoalba Stranded in Malta: Morphological and Genetic Analyses.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {7},
pages = {},
pmid = {38612346},
issn = {2076-2615},
support = {I18LU06-01//University of Malta/ ; },
abstract = {Here, we document the stranding of a striped dolphin Stenella coeruleoalba (Meyen, 1833) (Mammalia: Delphinidae), which was found dead in Maltese waters in July 2020. The stranded dolphin exhibited a severe infestation of the mesoparasitic copepod, Pennella balaenoptera Koren and Danielssen, 1877 (Copepoda: Pennelidae). Parasites of this genus represent the largest known mesoparasites to infest cetaceans. Under normal circumstances, cetaceans may have a few P. balaenoptera individuals attached to them, but cetaceans with compromised health are more prone to heavy infestations. The identification of the parasite was accomplished through morphological and genetic analyses. This incident highlights the significance of monitoring mesoparasitic infestations, offering valuable insights into the health of cetacean populations and emphasizing the potential implications for conservation efforts in the region.},
}
@article {pmid38612257,
year = {2024},
author = {Graziosi, G and Lupini, C and Gobbo, F and Zecchin, B and Quaglia, G and Pedrazzoli, S and Lizzi, G and Dosa, G and Martini, G and Terregino, C and Catelli, E},
title = {Genetic Diversity of Avian Influenza Viruses Detected in Waterbirds in Northeast Italy Using Two Different Sampling Strategies.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {7},
pages = {},
pmid = {38612257},
issn = {2076-2615},
support = {Project no. PE00000007, INF-ACT//Ministero dell'Universit&#xe0; e della Ricerca/ ; },
abstract = {Avian influenza viruses (AIVs), which circulate endemically in wild aquatic birds, pose a significant threat to poultry and raise concerns for their zoonotic potential. From August 2021 to April 2022, a multi-site cross-sectional study involving active AIV epidemiological monitoring was conducted in wetlands of the Emilia-Romagna region, northern Italy, adjacent to densely populated poultry areas. A total of 129 cloacal swab samples (CSs) and 407 avian faecal droppings samples (FDs) were collected, with 7 CSs (5.4%) and 4 FDs (1%) testing positive for the AIV matrix gene through rRT-PCR. A COI-barcoding protocol was applied to recognize the species of origin of AIV-positive FDs. Multiple low-pathogenic AIV subtypes were identified, and five of these were isolated, including an H5N3, an H1N1, and three H9N2 in wild ducks. Following whole-genome sequencing, phylogenetic analyses of the hereby obtained strains showed close genetic relationships with AIVs detected in countries along the Black Sea/Mediterranean migratory flyway. Notably, none of the analyzed gene segments were genetically related to HPAI H5N1 viruses of clade 2.3.4.4b isolated from Italian poultry during the concurrent 2021-2022 epidemic. Overall, the detected AIV genetic diversity emphasizes the necessity for ongoing monitoring in wild hosts using diverse sampling strategies and whole-genome sequencing.},
}
@article {pmid38609853,
year = {2024},
author = {Kuijpers, L and Hornung, B and van den Hout-van Vroonhoven, MCGN and van IJcken, WFJ and Grosveld, F and Mulugeta, E},
title = {Split Pool Ligation-based Single-cell Transcriptome sequencing (SPLiT-seq) data processing pipeline comparison.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {361},
pmid = {38609853},
issn = {1471-2164},
mesh = {*Transcriptome ; *Computational Biology ; Data Analysis ; },
abstract = {BACKGROUND: Single-cell sequencing techniques are revolutionizing every field of biology by providing the ability to measure the abundance of biological molecules at a single-cell resolution. Although single-cell sequencing approaches have been developed for several molecular modalities, single-cell transcriptome sequencing is the most prevalent and widely applied technique. SPLiT-seq (split-pool ligation-based transcriptome sequencing) is one of these single-cell transcriptome techniques that applies a unique combinatorial-barcoding approach by splitting and pooling cells into multi-well plates containing barcodes. This unique approach required the development of dedicated computational tools to preprocess the data and extract the count matrices. Here we compare eight bioinformatic pipelines (alevin-fry splitp, LR-splitpipe, SCSit, splitpipe, splitpipeline, SPLiTseq-demultiplex, STARsolo and zUMI) that have been developed to process SPLiT-seq data. We provide an overview of the tools, their computational performance, functionality and impact on downstream processing of the single-cell data, which vary greatly depending on the tool used.<br><br>RESULTS: We show that STARsolo, splitpipe and alevin-fry splitp can all handle large amount of data within reasonable time. In contrast, the other five pipelines are slow when handling large datasets. When using smaller dataset, cell barcode results are similar with the exception of SPLiTseq-demultiplex and splitpipeline. LR-splitpipe that is originally designed for processing long-read sequencing data is the slowest of all pipelines. Alevin-fry produced different down-stream results that are difficult to interpret. STARsolo functions nearly identical to splitpipe and produce results that are highly similar to each other. However, STARsolo lacks the function to collapse random hexamer reads for which some additional coding is required.<br><br>CONCLUSION: Our comprehensive comparative analysis aids users in selecting the most suitable analysis tool for efficient SPLiT-seq data processing, while also detailing the specific prerequisites for each of these pipelines. From the available pipelines, we recommend splitpipe or STARSolo for SPLiT-seq data analysis.},
}
@article {pmid38608184,
year = {2024},
author = {Laojun, S and Changbunjong, T and Abdulloh, A and Chaiphongpachara, T},
title = {Geometric morphometrics to differentiate species and explore seasonal variation in three Mansonia species (Diptera: Culicidae) in central Thailand and their association with meteorological factors.},
journal = {Medical and veterinary entomology},
volume = {38},
number = {3},
pages = {325-340},
doi = {10.1111/mve.12720},
pmid = {38608184},
issn = {1365-2915},
support = {//Suan Sunandha Rajabhat University/ ; },
mesh = {Animals ; Thailand ; *Seasons ; *Culicidae/anatomy &amp; histology/classification ; Male ; DNA Barcoding, Taxonomic ; Female ; Species Specificity ; },
abstract = {Mansonia mosquito species are recognised as a significant vector of human pathogens, primarily transmitting the filarial nematode, Brugia malayi. In central Thailand, the three most prevalent Mansonia species are Mansonia annulifera, Mansonia indiana and Mansonia uniformis. This study explored the influence of seasonal changes on the phenotypic variation of these Mansonia species in central Thailand using the geometric morphometrics (GM). To ensure accurate species identification, we integrated GM techniques with DNA barcoding, examining distinctions in both phenotype and genotype among the species. The intraspecific genetic divergence ranged from 0.00% to 1.69%, whereas the interspecific genetic divergence ranged from 10.52% to 16.36%. The clear distinction between intra- and interspecific distances demonstrated the presence of a barcoding gap, confirming the successful differentiation of the three Mansonia mosquito species through DNA barcoding. Similarly, the interspecies GM assessment for classifying Mansonia species demonstrated a high degree of accuracy, with an overall performance of 98.12%. Exploring seasonal variation in the three Mansonia species revealed wing variations across different seasons, and pronounced variations appearing in the cool season. Regarding their association with meteorological factors, Ma. annulifera and Ma. uniformis showed significant positive correlations with temperature (p < 0.05), and Ma. uniformis also displayed a significant negative correlation with atmospheric pressure (p < 0.05). The insights from this study will deepen our understanding of the adaptive patterns of Mansonia mosquitoes in Thailand's central region, paving the way for enhanced disease surveillance related to these vectors.},
}
@article {pmid38607945,
year = {2024},
author = {Cai, L and Lin, L and Lin, S and Wang, X and Chen, Y and Zhu, H and Zhu, Z and Yang, L and Xu, X and Yang, C},
title = {Highly Multiplexing, Throughput and Efficient Single-Cell Protein Analysis with Digital Microfluidics.},
journal = {Small methods},
volume = {8},
number = {12},
pages = {e2400375},
doi = {10.1002/smtd.202400375},
pmid = {38607945},
issn = {2366-9608},
support = {21927806//National Natural Science Foundation of China/ ; 22204132//National Natural Science Foundation of China/ ; 22293031//National Natural Science Foundation of China/ ; 2022YFB3205600//National Key Research and Development Program of China/ ; 20720210001//Fundamental Research Funds for the Central Universities/ ; 20720220005//Fundamental Research Funds for the Central Universities/ ; SSMU-ZLCX20180701//Innovative research team of high-level local universities in Shanghai/ ; },
mesh = {*Single-Cell Analysis/methods ; Humans ; Microfluidics/methods/instrumentation ; Proteins/analysis/chemistry ; Microfluidic Analytical Techniques/instrumentation/methods ; Lab-On-A-Chip Devices ; },
abstract = {Proteins as crucial components of cells are responsible for the majority of cellular processes. Sensitive and efficient protein detection enables a more accurate and comprehensive investigation of cellular phenotypes and life activities. Here, a protein sequencing method with high multiplexing, high throughput, high cell utilization, and integration based on digital microfluidics (DMF-Protein-seq) is proposed, which transforms protein information into DNA sequencing readout via DNA-tagged antibodies and labels single cells with unique cell barcodes. In a 184-electrode DMF-Protein-seq system, ≈1800 cells are simultaneously detected per experimental run. The digital microfluidics device harnessing low-adsorbed hydrophobic surface and contaminants-isolated reaction space supports high cell utilization (>90%) and high mapping reads (>90%) with the input cells ranging from 140 to 2000. This system leverages split&amp;pool strategy on the DMF chip for the first time to overcome DMF platform restriction in cell analysis throughput and replace the traditionally tedious bench-top combinatorial barcoding. With the benefits of high efficiency and sensitivity in protein analysis, the system offers great potential for cell classification and drug monitoring based on protein expression at the single-cell level.},
}
@article {pmid38607148,
year = {2024},
author = {Cheng, H and Qu, J and Mao, W and Chen, S and Dong, H},
title = {Continuous-Wave Pumped Monolayer WS2 Lasing for Photonic Barcoding.},
journal = {Nanomaterials (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
pmid = {38607148},
issn = {2079-4991},
support = {61925506, 12374297, 62305078//National Natural Science Foundation of China/ ; TD2020002//Hangzhou Science and Technology Bureau of Zhejiang Province/ ; 23XD1404500//Academic/Technology Research Leader Program of Shanghai/ ; },
abstract = {Micro/nano photonic barcoding has emerged as a promising technology for information security and anti-counterfeiting applications owing to its high security and robust tamper resistance. However, the practical application of conventional micro/nano photonic barcodes is constrained by limitations in encoding capacity and identification verification (e.g., broad emission bandwidth and the expense of pulsed lasers). Herein, we propose high-capacity photonic barcode labels by leveraging continuous-wave (CW) pumped monolayer tungsten disulfide (WS2) lasing. Large-area, high-quality monolayer WS2 films were grown via a vapor deposition method and coupled with external cavities to construct optically pumped microlasers, thus achieving an excellent CW-pumped lasing with a narrow linewidth (~0.39 nm) and a low threshold (~400 W cm[-2]) at room temperature. Each pixel within the photonic barcode labels consists of closely packed WS2 microlasers of varying sizes, demonstrating high-density and nonuniform multiple-mode lasing signals that facilitate barcode encoding. Notably, CW operation and narrow-linewidth lasing emission could significantly simplify detection. As proof of concept, a 20-pixel label exhibits a high encoding capacity (2.35 × 10[108]). This work may promote the advancement of two-dimensional materials micro/nanolasers and offer a promising platform for information encoding and security applications.},
}
@article {pmid38606447,
year = {2024},
author = {Mwamula, AO and Kwon, OG and Kwon, C and Kim, YS and Kim, YH and Lee, DW},
title = {A Revision of the Phylogeny of Helicotylenchus Steiner, 1945 (Tylenchida: Hoplolaimidae) as Inferred from Ribosomal and Mitochondrial DNA.},
journal = {The plant pathology journal},
volume = {40},
number = {2},
pages = {171-191},
pmid = {38606447},
issn = {1598-2254},
support = {//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries/ ; 321001-03//Ministry of Agriculture, Food and Rural Affairs/ ; },
abstract = {Identification of Helicotylenchus species is very challenging due to phenotypic plasticity and existence of cryptic species complexes. Recently, the use of rDNA barcodes has proven to be useful for identification of Helicotylenchus. Molecular markers are a quick diagnostic tool and are crucial for discriminating related species and resolving cryptic species complexes within this speciose genus. However, DNA barcoding is not an error-free approach. The public databases appear to be marred by incorrect sequences, arising from sequencing errors, mislabeling, and misidentifications. Herein, we provide a comprehensive analysis of the newly obtained, and published DNA sequences of Helicotylenchus, revealing the potential faults in the available DNA barcodes. A total of 97 sequences (25 nearly full-length 18S-rRNA, 12 partial 28S-rRNA, 16 partial internal transcribed spacer [ITS]-rRNA, and 44 partial cytochrome c oxidase subunit I [COI] gene sequences) were newly obtained in the present study. Phylogenetic relationships between species are given as inferred from the analyses of 103 sequences of 18S-rRNA, 469 sequences of 28S-rRNA, 183 sequences of ITS-rRNA, and 63 sequences of COI. Remarks on suggested corrections of published accessions in GenBank database are given. Additionally, COI gene sequences of H. dihystera, H. asiaticus and the contentious H. microlobus are provided herein for the first time. Similar to rDNA gene analyses, the COI sequences support the genetic distinctness and validity of H. microlobus. DNA barcodes from type material are needed for resolving the taxonomic status of the unresolved taxonomic groups within the genus.},
}
@article {pmid38605363,
year = {2024},
author = {Pellecchia, S and Franchini, M and Viscido, G and Arnese, R and Gambardella, G},
title = {Single cell lineage tracing reveals clonal dynamics of anti-EGFR therapy resistance in triple negative breast cancer.},
journal = {Genome medicine},
volume = {16},
number = {1},
pages = {55},
pmid = {38605363},
issn = {1756-994X},
support = {23162//My First AIRC grant/ ; },
mesh = {Humans ; *Triple Negative Breast Neoplasms/drug therapy/genetics/metabolism ; Afatinib/pharmacology/therapeutic use ; Cell Lineage ; ErbB Receptors ; Signal Transduction ; Protein Kinase Inhibitors/pharmacology/therapeutic use ; Cell Line, Tumor ; },
abstract = {BACKGROUND: Most primary Triple Negative Breast Cancers (TNBCs) show amplification of the Epidermal Growth Factor Receptor (EGFR) gene, leading to increased protein expression. However, unlike other EGFR-driven cancers, targeting this receptor in TNBC yields inconsistent therapeutic responses.<br><br>METHODS: To elucidate the underlying mechanisms of this variability, we employ cellular barcoding and single-cell transcriptomics to reconstruct the subclonal dynamics of EGFR-amplified TNBC cells in response to afatinib, a tyrosine kinase inhibitor (TKI) that irreversibly inhibits EGFR.<br><br>RESULTS: Integrated lineage tracing analysis revealed a rare pre-existing subpopulation of cells with distinct biological signature, including elevated expression levels of Insulin-Like Growth Factor Binding Protein 2 (IGFBP2). We show that IGFBP2 overexpression is sufficient to render TNBC cells tolerant to afatinib treatment by activating the compensatory insulin-like growth factor I receptor (IGF1-R) signalling pathway. Finally, based on reconstructed mechanisms of resistance, we employ deep learning techniques to predict the afatinib sensitivity of TNBC cells.<br><br>CONCLUSIONS: Our strategy proved effective in reconstructing the complex signalling network driving EGFR-targeted therapy resistance, offering new insights for the development of individualized treatment strategies in TNBC.},
}
@article {pmid38602321,
year = {2024},
author = {Cai, Y and Chen, T and Cai, Y and Liu, J and Yu, B and Fan, Y and Su, J and Zeng, Y and Xiao, X and Ren, L and Tang, Y},
title = {Surface protein profiling and subtyping of extracellular vesicles in body fluids reveals non-CSF biomarkers of Alzheimer's disease.},
journal = {Journal of extracellular vesicles},
volume = {13},
number = {4},
pages = {e12432},
pmid = {38602321},
issn = {2001-3078},
support = {82171776//National Natural Science Foundation of China/ ; 82101429//National Natural Science Foundation of China/ ; 81971300//National Natural Science Foundation of China/ ; JCYJ20180228162815750//Science, Technology and Innovation Commission of Shenzhen Municipality/ ; JCYJ20190806164203496//Science, Technology and Innovation Commission of Shenzhen Municipality/ ; JCYJ20210324103213037//Science, Technology and Innovation Commission of Shenzhen Municipality/ ; KCXFZ20201221173213036//Science, Technology and Innovation Commission of Shenzhen Municipality/ ; ZDSYS20190902093401689//Science, Technology and Innovation Commission of Shenzhen Municipality/ ; },
mesh = {Humans ; Mice ; Animals ; *Alzheimer Disease/diagnosis/metabolism ; *Extracellular Vesicles/metabolism ; Biomarkers/metabolism ; Mice, Transgenic ; Membrane Proteins/metabolism ; *Body Fluids/metabolism ; },
abstract = {Noninvasive and effortless diagnosis of Alzheimer's disease (AD) remains challenging. Here we report the multiplexed profiling of extracellular vesicle (EV) surface proteins at the single EV level in five types of easily accessible body fluids using a proximity barcoding assay (PBA). A total of 183 surface proteins were detected on the EVs from body fluids collected from APP/PS1 transgenic mice and patients with AD. The AD-associated differentially expressed EV proteins could discriminate between the control and AD/AD model samples with high accuracy. Based on machine learning predictive models, urinary EV proteins exhibited the highest diagnostic potential compared to those on other biofluid EVs, both in mice and humans. Single EV analysis further revealed AD-associated EV subpopulations in the tested body fluids, and a urinary EV subpopulation with the signature proteins PLAU, ITGAX and ANXA1 could diagnose patients with AD in blinded datasets with 88% accuracy. Our results suggest that EVs and their subpopulations from noninvasive body fluids, particularly urine, are potential diagnostic biomarkers for AD.},
}
@article {pmid38601700,
year = {2024},
author = {Adao, DEV and Rivera, WL},
title = {Subtype-host patterns and genetic differentiation of Blastocystis sp. in the Philippines.},
journal = {Heliyon},
volume = {10},
number = {7},
pages = {e29019},
pmid = {38601700},
issn = {2405-8440},
abstract = {Blastocystis sp. is a gastrointestinal protozoan commonly encountered in humans and animals. Specificity to certain hosts may be associated with 38 known subtypes (STs) and 8 nonmammalian and avian STs (NMASTs). This can be determined by analyzing ST-host associations, ST-allele data, genetic variability analyses, and fixation index (FST) with sufficient data present. Thus, newly acquired and previously published data on Blastocystis sp. STs and NMASTs from the Philippines were compiled to determine the following: (1) ST-host associations, (2) ST-allele diversity per ST in certain hosts/sources, (3) intrasubtype diversity of certain STs found in different hosts using genetic variability analysis, and (4) comparison of similarities between specific ST populations to determine if these are the same circulating populations using FST. A total of 448 samples subtyped using both sequence-tagged site primers and the 600-bp barcoding region of the Blastocystis sp. SSU rRNA gene were analyzed in this study. Patterns of association for the Philippine samples were similar to those from neighboring Southeast Asian countries and around the world: ST1-ST4 were found in humans but ST3 was the most common, ST5 were found in pigs, and ST6 and ST7 were found in poultry. Blastocystis sp. from humans are mostly the same ST alleles (ST3 allele 34 and ST1 allele 4) while 3-5 ST alleles were found in the most common STs in pigs, macaques, and poultry. Also, ST1, ST3, ST5, and NMAST I are undergoing population expansion according to genetic variability analyses through possible addition of new alleles based on ST-allele diversity. Moreover, FST shows the same circulating population of ST1 in humans, pigs, and water indicating a possible waterborne route of cross-transmission. In contrast, ST3 found in humans possibly come from the same circulating population and is genetically distinct from those in nonhuman sources.},
}
@article {pmid38601032,
year = {2024},
author = {Cardinali, I and Ceccarelli, M},
title = {Molecular and cytogenetic analyses in Geranium macrorrhizum L. wild Italian plants.},
journal = {Royal Society open science},
volume = {11},
number = {4},
pages = {240035},
pmid = {38601032},
issn = {2054-5703},
abstract = {Geranium macrorrhizum L. is a herbaceous species native to southern Europe and was introduced in central Europe and North America. It is also widely distributed in Italy. In this study, molecular and cytogenetic analyses were carried out on 22 wild plants, collected in central and southern Italy, compared with five cultivated plants, with the main purpose to identify those living near the Marmore waterfalls in central Italy, recently described as the new species Geranium lucarinii. Four barcoding markers (rbcL, matK, trnH-psbA intergenic spacer and internal transcribed spacer region) were sequenced and their variability among the plants was evaluated. Chromosome numbers were determined and 45S rDNA was physically mapped by fluorescence in situ hybridization. Moreover, genomic affinity between wild and cultivated plants was evaluated by genomic in situ hybridization. The results of this study supported that all the plants belong to G. macrorrhizum, including the Marmore population. Barcoding analyses showed a close similarity among the wild plants, and a differentiation, although not significant, between the wild plants on one hand and the cultivated plants on the other. Integrated studies focusing on morphological, genetic and ecological characterization of a larger number of wild populations would allow us to know the extent of the variability within the species.},
}
@article {pmid38600958,
year = {2024},
author = {Visagie, CM and Yilmaz, N and Kocsubé, S and Frisvad, JC and Hubka, V and Samson, RA and Houbraken, J},
title = {A review of recently introduced Aspergillus, Penicillium, Talaromyces and other Eurotiales species.},
journal = {Studies in mycology},
volume = {107},
number = {},
pages = {1-66},
pmid = {38600958},
issn = {0166-0616},
abstract = {The order Eurotiales is diverse and includes species that impact our daily lives in many ways. In the past, its taxonomy was difficult due to morphological similarities, which made accurate identification of species difficult. This situation improved and stabilised with recent taxonomic and nomenclatural revisions that modernised Aspergillus, Penicillium and Talaromyces. This was mainly due to the availability of curated accepted species lists and the publication of comprehensive DNA sequence reference datasets. This has also led to a sharp increase in the number of new species described each year with the accepted species lists in turn also needing regular updates. The focus of this study was to review the 160 species described between the last list of accepted species published in 2020 until 31 December 2022. To review these species, single-gene phylogenies were constructed and GCPSR (Genealogical Concordance Phylogenetic Species Recognition) was applied. Multi-gene phylogenetic analyses were performed to further determine the relationships of the newly introduced species. As a result, we accepted 133 species (37 Aspergillus, two Paecilomyces, 59 Penicillium, two Rasamsonia, 32 Talaromyces and one Xerochrysium), synonymised 22, classified four as doubtful and created a new combination for Paraxerochrysium coryli, which is classified in Xerochrysium. This brings the number of accepted species to 453 for Aspergillus, 12 for Paecilomyces, 535 for Penicillium, 14 for Rasamsonia, 203 for Talaromyces and four for Xerochrysium. We accept the newly introduced section Tenues (in Talaromyces), and series Hainanici (in Aspergillus sect. Cavernicolarum) and Vascosobrinhoana (in Penicillium sect. Citrina). In addition, we validate the invalidly described species Aspergillus annui and A. saccharicola, and series Annuorum (in Aspergillus sect. Flavi), introduce a new combination for Dichlaena lentisci (type of the genus) and place it in a new section in Aspergillus subgenus Circumdati, provide an updated description for Rasamsonia oblata, and list excluded and recently synonymised species that were previously accepted. This study represents an important update of the accepted species lists in Eurotiales. Taxonomic novelties: New sections: Aspergillus section Dichlaena Visagie, Kocsubé &amp; Houbraken. New series: Aspergillus series Annuorum J.J. Silva, B.T. Iamanaka, Frisvad. New species: Aspergillus annui J.J. Silva, M.H.P. Fungaro, Frisvad, M.H. Taniwaki &amp; B.T. Iamanaka; Aspergillus saccharicola J.J. Silva, Frisvad, M.H.P. Fungaro, M.H. Taniwaki &amp; B.T. Iamanaka. New combinations: Aspergillus lentisci (Durieu &amp; Mont.) Visagie, Malloch, L. Kriegsteiner, Samson &amp; Houbraken; Xerochrysium coryli (Crous &amp; Decock) Visagie &amp; Houbraken. Citation: Visagie CM, Yilmaz N, Kocsubé S, Frisvad JC, Hubka V, Samson RA, Houbraken J (2024). A review of recently introduced Aspergillus, Penicillium, Talaromyces and other Eurotiales species. Studies in Mycology 107: 1-66. doi: 10.3114/sim.2024.107.01.},
}
@article {pmid38599628,
year = {2024},
author = {Diver, P and Ward, BA and Cunliffe, M},
title = {Physiological and morphological plasticity in response to nitrogen availability of a yeast widely distributed in the open ocean.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {5},
pages = {},
pmid = {38599628},
issn = {1574-6941},
support = {772584/ERC_/European Research Council/International ; },
mesh = {*Nitrogen/metabolism ; *Seawater/microbiology ; *Nitrates/metabolism ; Atlantic Ocean ; Yeasts/metabolism/genetics/growth &amp; development ; Ammonium Compounds/metabolism ; Urea/metabolism ; },
abstract = {Yeasts are prevalent in the open ocean, yet we have limited understanding of their ecophysiological adaptations, including their response to nitrogen availability, which can have a major role in determining the ecological potential of other planktonic microbes. In this study, we characterized the nitrogen uptake capabilities and growth responses of marine-occurring yeasts. Yeast isolates from the North Atlantic Ocean were screened for growth on diverse nitrogen substrates, and across a concentration gradient of three environmentally relevant nitrogen substrates: nitrate, ammonium, and urea. Three strains grew with enriched nitrate while two did not, demonstrating that nitrate utilization is present but not universal in marine yeasts, consistent with existing knowledge of nonmarine yeast strains. Naganishia diffluens MBA_F0213 modified the key functional trait of cell size in response to nitrogen concentration, suggesting yeast cell morphology changes along chemical gradients in the marine environment. Meta-analysis of the reference DNA barcode in public databases revealed that the genus Naganishia has a global ocean distribution, strengthening the environmental applicability of the culture-based observations. This study provides novel quantitative understanding of the ecophysiological and morphological responses of marine-derived yeasts to variable nitrogen availability in vitro, providing insight into the functional ecology of yeasts within pelagic open ocean environments.},
}
@article {pmid38598919,
year = {2024},
author = {Sidstedt, M and Gynnå, AH and Kiesler, KM and Jansson, L and Steffen, CR and Håkansson, J and Johansson, G and Österlund, T and Bogestål, Y and Tillmar, A and Rådström, P and Ståhlberg, A and Vallone, PM and Hedman, J},
title = {Ultrasensitive sequencing of STR markers utilizing unique molecular identifiers and the SiMSen-Seq method.},
journal = {Forensic science international. Genetics},
volume = {71},
number = {},
pages = {103047},
doi = {10.1016/j.fsigen.2024.103047},
pmid = {38598919},
issn = {1878-0326},
mesh = {Humans ; *Microsatellite Repeats ; *High-Throughput Nucleotide Sequencing ; *DNA Fingerprinting/methods ; Alleles ; Multiplex Polymerase Chain Reaction ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Machine Learning ; Genetic Markers ; },
abstract = {Massively parallel sequencing (MPS) is increasingly applied in forensic short tandem repeat (STR) analysis. The presence of stutter artefacts and other PCR or sequencing errors in the MPS-STR data partly limits the detection of low DNA amounts, e.g., in complex mixtures. Unique molecular identifiers (UMIs) have been applied in several scientific fields to reduce noise in sequencing. UMIs consist of a stretch of random nucleotides, a unique barcode for each starting DNA molecule, that is incorporated in the DNA template using either ligation or PCR. The barcode is used to generate consensus reads, thus removing errors. The SiMSen-Seq (Simple, multiplexed, PCR-based barcoding of DNA for sensitive mutation detection using sequencing) method relies on PCR-based introduction of UMIs and includes a sophisticated hairpin design to reduce unspecific primer binding as well as PCR protocol adjustments to further optimize the reaction. In this study, SiMSen-Seq is applied to develop a proof-of-concept seven STR multiplex for MPS library preparation and an associated bioinformatics pipeline. Additionally, machine learning (ML) models were evaluated to further improve UMI allele calling. Overall, the seven STR multiplex resulted in complete detection and concordant alleles for 47 single-source samples at 1 ng input DNA as well as for low-template samples at 62.5 pg input DNA. For twelve challenging mixtures with minor contributions of 10 pg to 150 pg and ratios of 1-15% relative to the major donor, 99.2% of the expected alleles were detected by applying the UMIs in combination with an ML filter. The main impact of UMIs was a substantially lowered number of artefacts as well as reduced stutter ratios, which were generally below 5% of the parental allele. In conclusion, UMI-based STR sequencing opens new means for improved analysis of challenging crime scene samples including complex mixtures.},
}
@article {pmid38598453,
year = {2024},
author = {Hussain, A and Kakar, A and Naseem, M and Kamran, K and Ullah, Z and Shehla, S and Obaid, MK and Ahmed, N and Khan, Q and Liaqat, I},
title = {Molecular identification of Hymenopteran insects collected by using Malaise traps from Hazarganji Chiltan National Park Quetta, Pakistan.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0300903},
pmid = {38598453},
issn = {1932-6203},
mesh = {Humans ; Animals ; Bees/genetics ; Pakistan ; *Parks, Recreational ; DNA Barcoding, Taxonomic/methods ; Insecta/genetics ; *Hymenoptera/genetics ; Plants/genetics ; },
abstract = {The order Hymenoptera holds great significance for humans, particularly in tropical and subtropical regions, due to its role as a pollinator of wild and cultivated flowering plants, parasites of destructive insects and honey producers. Despite this importance, limited attention has been given to the genetic diversity and molecular identification of Hymenopteran insects in most protected areas. This study provides insights into the first DNA barcode of Hymenopteran insects collected from Hazarganji Chiltan National Park (HCNP) and contributes to the global reference library of DNA barcodes. A total of 784 insect specimens were collected using Malaise traps, out of which 538 (68.62%) specimens were morphologically identified as Hymenopteran insects. The highest abundance of species of Hymenoptera (133/538, 24.72%) was observed during August and least in November (16/538, 2.97%). Genomic DNA extraction was performed individually from 90/538 (16.73%) morphologically identified specimens using the standard phenol-chloroform method, which were subjected separately to the PCR for their molecular confirmation via the amplification of cytochrome c oxidase subunit 1 (cox1) gene. The BLAST analyses of obtained sequences showed 91.64% to 100% identities with related sequences and clustered phylogenetically with their corresponding sequences that were reported from Australia, Bulgaria, Canada, Finland, Germany, India, Israel, and Pakistan. Additionally, total of 13 barcode index numbers (BINs) were assigned by Barcode of Life Data Systems (BOLD), out of which 12 were un-unique and one was unique (BOLD: AEU1239) which was assigned for Anthidium punctatum. This indicates the potential geographical variation of Hymenopteran population in HCNP. Further comprehensive studies are needed to molecularly confirm the existing insect species in HCNP and evaluate their impacts on the environment, both as beneficial (for example, pollination, honey producers and natural enemies) and detrimental (for example, venomous stings, crop damage, and pathogens transmission).},
}
@article {pmid38590889,
year = {2024},
author = {Askari, H and Soleimanian-Zad, S and Kadivar, M and Shahbazi, S},
title = {Creating a novel genetic diversity of Trichoderma afroharzianum by γ-radiation for xylanase-cellulase production.},
journal = {Heliyon},
volume = {10},
number = {7},
pages = {e28349},
pmid = {38590889},
issn = {2405-8440},
abstract = {Creating novel sources of a microbial strain using induced mutation can increase enzyme production for industrial use. According to this, we have developed a mutant strain of Trichoderma afroharzianum by Co[60] gamma irradiation. Trichoderma mutants were isolated from an optimum dose of 250 Gy. The qualitative and quantitative screening were used for evaluating their enzyme production and the DNA barcoding method was used to identify the best Trichoderma mutant isolates. The highest cellulase (exo-glucanase, endoglucanase, β-glucosidase, and total cellulase) and xylanase activities were observed in superior mutant isolates of Trichoderma afroharzianum NAS107-M44 and Trichoderma afroharzianum NAS107-M82, which is approximately 1.6-2.5 times higher than its parent strain, respectively. The electrophoretic pattern of proteins showed that the exo-glucanase I, endo-glucanase III, and the xylanase I enzymes hydrolyzed the corn bran, synergistically. Overall, gamma irradiation-induced mutation could be an expedient technique to access such superior mutants for the bioconversion of corn bran wastes.},
}
@article {pmid38589809,
year = {2024},
author = {Stelbrink, B and von Rintelen, T and Marwoto, RM and Salzburger, W},
title = {Mitogenomes do not substantially improve phylogenetic resolution in a young non-model adaptive radiation of freshwater gastropods.},
journal = {BMC ecology and evolution},
volume = {24},
number = {1},
pages = {42},
pmid = {38589809},
issn = {2730-7182},
mesh = {Humans ; Animals ; Phylogeny ; *Genome, Mitochondrial/genetics ; *Gastropoda/genetics ; Ecosystem ; Lakes ; },
abstract = {BACKGROUND: Species flocks in ancient lakes, and particularly those arising from adaptive radiation, make up the bulk of overall taxonomic and morphological diversity in these insular ecosystems. For these mostly young species assemblages, classical mitochondrial barcoding markers have so far been key to disentangle interspecific relationships. However, with the rise and further development of next-generation sequencing (NGS) methods and mapping tools, genome-wide data have become an increasingly important source of information even for non-model groups.<br><br>RESULTS: Here, we provide, for the first time, a comprehensive mitogenome dataset of freshwater gastropods endemic to Sulawesi and thus of an ancient lake invertebrate species flock in general. We applied low-coverage whole-genome sequencing for a total of 78 individuals including 27 out of the 28 Tylomelania morphospecies from the Malili lake system as well as selected representatives from Lake Poso and adjacent catchments. Our aim was to assess whether mitogenomes considerably contribute to the phylogenetic resolution within this young species flock. Interestingly, we identified a high number of variable and parsimony-informative sites across the other 'non-traditional' mitochondrial loci. However, although the overall support was very high, the topology obtained was largely congruent with previously published single-locus phylogenies. Several clades remained unresolved and a large number of species was recovered polyphyletic, indicative of both rapid diversification and mitochondrial introgression.<br><br>CONCLUSIONS: This once again illustrates that, despite the higher number of characters available, mitogenomes behave like a single locus and thus can only make a limited contribution to resolving species boundaries, particularly when introgression events are involved.},
}
@article {pmid38588740,
year = {2024},
author = {Rund, H and Wanzenböck, J and Dobrovolny, S and Kurmayer, R},
title = {Relating target fish DNA concentration to community composition analysis in freshwater fish via metabarcoding.},
journal = {The Science of the total environment},
volume = {927},
number = {},
pages = {172281},
doi = {10.1016/j.scitotenv.2024.172281},
pmid = {38588740},
issn = {1879-1026},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Fishes/genetics ; *Fresh Water ; *Biodiversity ; Environmental Monitoring/methods ; DNA/analysis ; },
abstract = {Metabarcoding has been widely accepted as a useful tool for biodiversity assessment based on eDNA. The method allows for the detection of entire groups of organisms in a single sample, making it particularly applicable in aquatic habitats. The high sensitivity of the molecular approaches is especially beneficial in detecting elusive and rare fish species, improving biodiversity assessments. Numerous biotic and abiotic factors that affect the persistence and availability of fish DNA in surface waters and therefore affecting species detectability, have been identified. However, little is known about the relationship between the total fish DNA concentration and the detectability of differential abundant species. In this study three controlled mock-community DNA samples (56 individual samples) were analyzed by (i) metabarcoding (MiSeq) of 12S rDNA (175 bp) and by (ii) total freshwater fish DNA quantification (via qPCR of 12S rDNA). We show that the fish DNA quantity affects the relative abundance of species-specific sequences and the detectability of rare species. In particular we found that samples with a concentration between 1000 pg/μL down to 10 pg/μL of total fish DNA revealed a stable relative frequency of DNA sequences obtained for a specific fish species, as well as a low variability between replicates. Additionally, we observed that even in complex mock-community DNA samples, a total fish DNA concentration of 23 pg/μL was sufficient to reliably detect all species in every replicate, including three rare species with proportions of ≤0.5 %. We also found that the DNA barcode similarity between species can affect detectability, if evenness is low. Our data suggest that the total DNA concentration of fish is an important factor to consider when analyzing and interpreting relative sequence abundance data. Therefore, the workflow proposed here will contribute to an ecologically and economically efficient application of metabarcoding in fish biodiversity assessment.},
}
@article {pmid38588628,
year = {2024},
author = {Xue, W and Wang, L and Yi, K and Sun, L and Ren, H and Bian, F},
title = {Hepatocellular carcinoma biomarkers screening based on hydrogel photonic barcodes with tyramine deposition amplified ELISA.},
journal = {Biosensors &amp; bioelectronics},
volume = {255},
number = {},
pages = {116270},
doi = {10.1016/j.bios.2024.116270},
pmid = {38588628},
issn = {1873-4235},
mesh = {Humans ; Hydrogels/chemistry ; *Carcinoma, Hepatocellular/diagnosis ; *Biosensing Techniques/methods ; *Liver Neoplasms/diagnosis ; Biomarkers, Tumor ; Enzyme-Linked Immunosorbent Assay ; Tyramine ; },
abstract = {Hepatocellular carcinoma (HCC), as one of the most lethal cancers, significantly impacts human health. Attempts in this area tends to develop novel technologies with sensitive and multiplexed detection properties for early diagnosis. Here, we present novel hydrogel photonic crystal (PhC) barcodes with tyramine deposition amplified enzyme-linked immunosorbent assay (ELISA) for highly sensitive and multiplexed HCC biomarker screening. Because of the abundant amino groups of acrylic acid (AA) component, the constructed hydrogel PhC barcodes with inverse opal structure could facilitate the loading of antibody probes for subsequent detection of tumor markers. By integrating tyramine deposition amplified ELISA on the barcode, the detection signal of tumor markers has been enhanced. Based on these features, it is demonstrated that the hydrogel PhC barcodes with tyramine deposition amplified ELISA could realize highly sensitive and multiplexed detection of HCC-related biomarkers. It was found that this method is flexible, sensitive and accurate, suitable for multivariate analysis of low abundance tumor markers and future cancer diagnosis. These features make the newly developed PhC barcodes an innovation platform, which possesses tremendous potential for practical application of low abundance targets.},
}
@article {pmid38587185,
year = {2024},
author = {Saunders, SH and Ahmed, AM},
title = {ORBIT for E. coli: kilobase-scale oligonucleotide recombineering at high throughput and high efficiency.},
journal = {Nucleic acids research},
volume = {52},
number = {8},
pages = {e43},
pmid = {38587185},
issn = {1362-4962},
mesh = {*Escherichia coli/genetics ; *Oligonucleotides/genetics ; *Plasmids/genetics ; Integrases/genetics/metabolism ; Genome, Bacterial/genetics ; Genetic Engineering/methods ; Gene Knockout Techniques ; Transcription Factors/genetics/metabolism ; },
abstract = {Microbiology and synthetic biology depend on reverse genetic approaches to manipulate bacterial genomes; however, existing methods require molecular biology to generate genomic homology, suffer from low efficiency, and are not easily scaled to high throughput. To overcome these limitations, we developed a system for creating kilobase-scale genomic modifications that uses DNA oligonucleotides to direct the integration of a non-replicating plasmid. This method, Oligonucleotide Recombineering followed by Bxb-1 Integrase Targeting (ORBIT) was pioneered in Mycobacteria, and here we adapt and expand it for Escherichia coli. Our redesigned plasmid toolkit for oligonucleotide recombineering achieved significantly higher efficiency than λ Red double-stranded DNA recombineering and enabled precise, stable knockouts (≤134 kb) and integrations (≤11 kb) of various sizes. Additionally, we constructed multi-mutants in a single transformation, using orthogonal attachment sites. At high throughput, we used pools of targeting oligonucleotides to knock out nearly all known transcription factor and small RNA genes, yielding accurate, genome-wide, single mutant libraries. By counting genomic barcodes, we also show ORBIT libraries can scale to thousands of unique members (>30k). This work demonstrates that ORBIT for E. coli is a flexible reverse genetic system that facilitates rapid construction of complex strains and readily scales to create sophisticated mutant libraries.},
}
@article {pmid38586055,
year = {2024},
author = {Franco-Enzástiga, &#xda; and Inturi, NN and Natarajan, K and Mwirigi, JM and Mazhar, K and Schlachetzki, JCM and Schumacher, M and Price, TJ},
title = {Epigenomic landscape of the human dorsal root ganglion: sex differences and transcriptional regulation of nociceptive genes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38586055},
issn = {2692-8205},
support = {R01 NS111929/NS/NINDS NIH HHS/United States ; U19 NS130608/NS/NINDS NIH HHS/United States ; },
abstract = {Gene expression is influenced by chromatin architecture via controlled access of regulatory factors to DNA. To better understand gene regulation in the human dorsal root ganglion (hDRG) we used bulk and spatial transposase-accessible chromatin technology followed by sequencing (ATAC-seq). Using bulk ATAC-seq, we detected that in females diverse differentially accessible chromatin regions (DARs) mapped to the X chromosome and in males to autosomal genes. EGR1/3 and SP1/4 transcription factor binding motifs were abundant within DARs in females, and JUN, FOS and other AP-1 factors in males. To dissect the open chromatin profile in hDRG neurons, we used spatial ATAC-seq. The neuron cluster showed higher chromatin accessibility in GABAergic, glutamatergic, and interferon-related genes in females, and in Ca[2+]- signaling-related genes in males. Sex differences in transcription factor binding sites in neuron-proximal barcodes were consistent with the trends observed in bulk ATAC-seq data. We validated that EGR1 expression is biased to female hDRG compared to male. Strikingly, XIST, the long-noncoding RNA responsible for X inactivation, hybridization signal was found to be highly dispersed in the female neuronal but not non-neuronal nuclei suggesting weak X inactivation in female hDRG neurons. Our findings point to baseline epigenomic sex differences in the hDRG that likely underlie divergent transcriptional responses that determine mechanistic sex differences in pain.},
}
@article {pmid38585983,
year = {2024},
author = {Shepherdson, JL and Granas, DM and Li, J and Shariff, Z and Plassmeyer, SP and Holehouse, AS and White, MA and Cohen, BA},
title = {Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38585983},
issn = {2692-8205},
support = {DP2 CA290639/CA/NCI NIH HHS/United States ; F30 EY033640/EY/NEI NIH HHS/United States ; R01 GM092910/GM/NIGMS NIH HHS/United States ; R21 HG012146/HG/NHGRI NIH HHS/United States ; },
abstract = {Cone-Rod Homeobox, encoded by CRX, is a transcription factor (TF) essential for the terminal differentiation and maintenance of mammalian photoreceptors. Structurally, CRX comprises an ordered DNA-binding homeodomain and an intrinsically disordered transcriptional effector domain. Although a handful of human variants in CRX have been shown to cause several different degenerative retinopathies with varying cone and rod predominance, as with most human disease genes the vast majority of observed CRX genetic variants are uncharacterized variants of uncertain significance (VUS). We performed a deep mutational scan (DMS) of nearly all possible single amino acid substitution variants in CRX, using an engineered cell-based transcriptional reporter assay. We measured the ability of each CRX missense variant to transactivate a synthetic fluorescent reporter construct in a pooled fluorescence-activated cell sorting assay and compared the activation strength of each variant to that of wild-type CRX to compute an activity score, identifying thousands of variants with altered transcriptional activity. We calculated a statistical confidence for each activity score derived from multiple independent measurements of each variant marked by unique sequence barcodes, curating a high-confidence list of nearly 2,000 variants with significantly altered transcriptional activity compared to wild-type CRX. We evaluated the performance of the DMS assay as a clinical variant classification tool using gold-standard classified human variants from ClinVar, and determined that activity scores could be used to identify pathogenic variants with high specificity. That this performance could be achieved using a synthetic reporter assay in a foreign cell type, even for a highly cell type-specific TF like CRX, suggests that this approach shows promise for DMS of other TFs that function in cell types that are not easily accessible. Per-position average activity scores closely aligned to a predicted structure of the ordered homeodomain and demonstrated position-specific residue requirements. The intrinsically disordered transcriptional effector domain, by contrast, displayed a qualitatively different pattern of substitution effects, following compositional constraints without specific residue position requirements in the peptide chain. The observed compositional constraints of the effector domain were consistent with the acidic exposure model of transcriptional activation. Together, the results of the CRX DMS identify molecular features of the CRX effector domain and demonstrate clinical utility for variant classification.},
}
@article {pmid38585727,
year = {2024},
author = {Sarhan, MS and Filosi, M and Maixner, F and Fuchsberger, C},
title = {Taxonize-gb: A tool for filtering GenBank non-redundant databases based on taxonomy.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38585727},
issn = {2692-8205},
support = {R01 HG009976/HG/NHGRI NIH HHS/United States ; },
abstract = {Analyzing taxonomic diversity and identification in diverse ecological samples has become a crucial routine in various research and industrial fields. While DNA barcoding marker-gene approaches were once prevalent, the decreasing costs of next-generation sequencing have made metagenomic shotgun sequencing more popular and feasible. In contrast to DNA-barcoding, metagenomic shotgun sequencing offers possibilities for in-depth characterization of structural and functional diversity. However, analysis of such data is still considered a hurdle due to absence of taxa-specific databases. Here we present taxonize-gb, a command-line software tool to extract GenBank non-redundant nucleotide and protein databases, related to one or more input taxonomy identifier. Our tool allows the creation of taxa-specific reference databases tailored to specific research questions, which reduces search times and therefore represents a practical solution for researchers analyzing large metagenomic data on regular basis. Taxonize-gb is an open-source command-line Python-based tool freely available for installation at https://pypi.org/project/taxonize-gb/ and on GitHub https://github.com/msabrysarhan/taxonize_genbank. It is released under Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0).},
}
@article {pmid38583817,
year = {2024},
author = {Afifi, MAM and Azab, AM and Ali, E and Ghazy, A and El-Tabakh, MAM},
title = {DNA barcoding, phylogeography and evolutionary dynamics of Chrysichthys auratus.},
journal = {Gene},
volume = {917},
number = {},
pages = {148448},
doi = {10.1016/j.gene.2024.148448},
pmid = {38583817},
issn = {1879-0038},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Phylogeography ; *Phylogeny ; *Haplotypes ; Evolution, Molecular ; Genetic Variation ; Goldfish/genetics/classification ; Gene Flow ; Electron Transport Complex IV/genetics ; },
abstract = {This study embarked on an exploration into the genetic structure and evolutionary history of the Chrysichthys auratus species, leveraging PCR amplification, phylogenetic trees, and haplotype networks. Specific DNA segments were successfully amplified and visualized through electrophoresis. Newly obtained sequences were Bank into GenBank and given accession numbers (OR730807-OR730808-OR730809). The Neighbor-Joining method provided insights into the evolutionary relationships among taxa, further augmented by bootstrap values and the Tamura 3-parameter method. A comprehensive geographical haplotype network showcased pronounced genetic differentiation, especially between remote populations. Nonetheless, shared haplotypes between proximate regions indicated either ancestral genetic connections or ongoing gene flow. Employing the COI-DNA barcodes, an in-depth understanding of intra- and inter-populational genetic diversity was achieved. The study's findings unravel the intricate genetic landscape and evolutionary dynamics of C. auratus, offering novel perspectives into its demographic history across its vast native habitat.},
}
@article {pmid38580715,
year = {2024},
author = {Mikhaylova, V and Rzepka, M and Kawamura, T and Xia, Y and Chang, PL and Zhou, S and Paasch, A and Pham, L and Modi, N and Yao, L and Perez-Agustin, A and Pagans, S and Boles, TC and Lei, M and Wang, Y and Garcia-Bassets, I and Chen, Z},
title = {Targeted phasing of 2-200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {7988},
pmid = {38580715},
issn = {2045-2322},
mesh = {Humans ; Sequence Analysis, DNA/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Genomics ; DNA/genetics ; Genome, Human ; },
abstract = {In the human genome, heterozygous sites refer to genomic positions with a different allele or nucleotide variant on the maternal and paternal chromosomes. Resolving these allelic differences by chromosomal copy, also known as phasing, is achievable on a short-read sequencer when using a library preparation method that captures long-range genomic information. TELL-Seq is a library preparation that captures long-range genomic information with the aid of molecular identifiers (barcodes). The same barcode is used to tag the reads derived from the same long DNA fragment within a range of up to 200 kilobases (kb), generating linked-reads. This strategy can be used to phase an entire genome. Here, we introduce a TELL-Seq protocol developed for targeted applications, enabling the phasing of enriched loci of varying sizes, purity levels, and heterozygosity. To validate this protocol, we phased 2-200 kb loci enriched with different methods: CRISPR/Cas9-mediated excision coupled with pulse-field electrophoresis for the longest fragments, CRISPR/Cas9-mediated protection from exonuclease digestion for mid-size fragments, and long PCR for the shortest fragments. All selected loci have known clinical relevance: BRCA1, BRCA2, MLH1, MSH2, MSH6, APC, PMS2, SCN5A-SCN10A, and PKI3CA. Collectively, the analyses show that TELL-Seq can accurately phase 2-200 kb targets using a short-read sequencer.},
}
@article {pmid38578268,
year = {2024},
author = {Quail, MA and Corton, C and Uphill, J and Keane, J and Gu, Y},
title = {Identifying the best PCR enzyme for library amplification in NGS.},
journal = {Microbial genomics},
volume = {10},
number = {4},
pages = {},
pmid = {38578268},
issn = {2057-5858},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Polymerase Chain Reaction/methods ; *Saccharomyces cerevisiae ; Gene Library ; *DNA ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Background. PCR amplification is a necessary step in many next-generation sequencing (NGS) library preparation methods [1, 2]. Whilst many PCR enzymes are developed to amplify single targets efficiently, accurately and with specificity, few are developed to meet the challenges imposed by NGS PCR, namely unbiased amplification of a wide range of different sizes and GC content. As a result PCR amplification during NGS library prep often results in bias toward GC neutral and smaller fragments. As NGS has matured, optimized NGS library prep kits and polymerase formulations have emerged and in this study we have tested a wide selection of available enzymes for both short-read Illumina library preparation and long fragment amplification ahead of long-read sequencing.We tested over 20 different hi-fidelity PCR enzymes/NGS amplification mixes on a range of Illumina library templates of varying GC content and composition, and find that both yield and genome coverage uniformity characteristics of the commercially available enzymes varied dramatically. Three enzymes Quantabio RepliQa Hifi Toughmix, Watchmaker Library Amplification Hot Start Master Mix (2X) 'Equinox' and Takara Ex Premier were found to give a consistent performance, over all genomes, that mirrored closely that observed for PCR-free datasets. We also test a range of enzymes for long-read sequencing by amplifying size fractionated S. cerevisiae DNA of average size 21.6 and 13.4 kb, respectively.The enzymes of choice for short-read (Illumina) library fragment amplification are Quantabio RepliQa Hifi Toughmix, Watchmaker Library Amplification Hot Start Master Mix (2X) 'Equinox' and Takara Ex Premier, with RepliQa also being the best performing enzyme from the enzymes tested for long fragment amplification prior to long-read sequencing.},
}
@article {pmid38577158,
year = {2024},
author = {Veselovsky, VA and Boldyreva, DI and Olekhnovich, EI and Klimina, KM and Babenko, VV and Zakharevich, NV and Larin, AK and Morozov, MD and Zoruk, PY and Sergiev, PV and Dontsova, OA and Maev, IV and Novik, TS and Kotlobay, AA and Lazarev, VN and Lagarkova, MA},
title = {Effect of the consumption of brazzein and monellin, two recombinant sweet-tasting proteins, on rat gut microbiota.},
journal = {Frontiers in nutrition},
volume = {11},
number = {},
pages = {1362529},
pmid = {38577158},
issn = {2296-861X},
abstract = {Sweet-tasting proteins (SPs) are proteins of plant origin initially isolated from tropical fruits. They are thousands of times sweeter than sucrose and most artificial sweeteners. SPs are a class of proteins capable of causing a sweet taste sensation in humans when interacting with the T1R2/T1R3 receptor. SP thaumatin has already been introduced in the food industry in some countries. Other SPs, such as monellin and brazzein, are promising products. An important stage in researching SPs, in addition to confirming the absence of toxicity, mutagenicity, oncogenicity, and allergenic effects, is studying their influence on gut microbiota. In this paper we describe changes in the composition of rat gut microbiota after six months of consuming one of two recombinant SPs-brazzein or monellin. A full length 16S gene sequencing method was used for DNA library barcoding. The MaAsLin2 analysis results showed noticeable fluctuations in the relative abundances of Anaerocella delicata in brazzein-fed rat microbiota, and of Anaerutruncus rubiinfantis in monellin-fed rat microbiota, which, however, did not exceed the standard deviation. The sucrose-fed group was associated with an increase in the relative abundance of Faecalibaculum rodentium, which may contribute to obesity. Overall, prolonged consumption of the sweet proteins brazzein and monellin did not significantly change rat microbiota and did not result in the appearance of opportunistic microbiota. This provides additional evidence for the safety of these potential sweeteners.},
}
@article {pmid38575088,
year = {2024},
author = {Li, P and Zhao, Z and Li, Z and Zeng, R and Li, W},
title = {Distinguishing features of Prunus humilis, P. japonica, P. pedunculata seeds and their adulterant based on DNA barcoding, morphological characterization, and chemical profiles.},
journal = {Fitoterapia},
volume = {175},
number = {},
pages = {105942},
doi = {10.1016/j.fitote.2024.105942},
pmid = {38575088},
issn = {1873-6971},
mesh = {*Seeds/chemistry ; *DNA Barcoding, Taxonomic ; *Prunus/chemistry/classification/genetics ; *Phylogeny ; Amygdalin ; Flavonoids/analysis ; Drug Contamination ; China ; Phytochemicals ; },
abstract = {Pruni Semen, the dried ripe seed of Prunus humilis, P. japonica, or P. pedunculata as recorded in the Chinese Pharmacopoeia, has been widely used in pharmaceutical and food industries. The adulteration of the marketed product with morphologically similar plants of the same genus has led to variable product quality and clinical effectiveness. This study systematically investigated the phylogenetic relationships, morphological traits, and chemical profiles of 37 Pruni Semen samples from planting bases, markets, and fields. DNA barcoding could successfully distinguish the genuine and counterfeit Pruni Semen, and the results indicated that there was almost no authentic Pruni Semen available in the market. The samples were divided into "big seed" (P. pedunculata and P. salicina seeds) and "small seed" (P. humilis, P. japonica, P. tomentosa, and P. avium seeds) categories based on morphology results. The notable discrepancy in the chemical characteristics of "big seed" and "small seed" was that "small seeds" were rich in flavonoids and low in amygdalin, whereas "big seeds" were the opposite. Furthermore, principal component analysis and clustered heatmap analysis verified the distinguishing features of "big seed" and "small seed" based on morphological and chemical characteristics. This study suggested that a combination of DNA barcoding and morphological and chemical characteristics can aid in the identification and quality evaluation of authentic and adulterated Pruni Semen. These findings may help standardize Pruni Semen available in the market and protect the rights and interests of customers.},
}
@article {pmid38574082,
year = {2024},
author = {Tiktak, GP and Gabb, A and Brandt, M and Diz, FR and Bravo-Vásquez, K and Peñaherrera-Palma, C and Valdiviezo-Rivera, J and Carlisle, A and Melling, LM and Cain, B and Megson, D and Preziosi, R and Shaw, KJ},
title = {Genetic identification of three CITES-listed sharks using a paper-based Lab-on-a-Chip (LOC).},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0300383},
pmid = {38574082},
issn = {1932-6203},
mesh = {Animals ; *Sharks/genetics ; Endangered Species ; Seafood ; Meat ; DNA/genetics ; },
abstract = {Threatened shark species are caught in large numbers by artisanal and commercial fisheries and traded globally. Monitoring both which shark species are caught and sold in fisheries, and the export of CITES-restricted products, are essential in reducing illegal fishing. Current methods for species identification rely on visual examination by experts or DNA barcoding techniques requiring specialist laboratory facilities and trained personnel. The need for specialist equipment and/or input from experts means many markets are currently not monitored. We have developed a paper-based Lab-on-a-Chip (LOC) to facilitate identification of three threatened and CITES-listed sharks, bigeye thresher (Alopias superciliosus), pelagic thresher (A. pelagicus) and shortfin mako shark (Isurus oxyrinchus) at market source. DNA was successfully extracted from shark meat and fin samples and combined with DNA amplification and visualisation using Loop Mediated Isothermal Amplification (LAMP) on the LOC. This resulted in the successful identification of the target species of sharks in under an hour, with a working positive and negative control. The LOC provided a simple "yes" or "no" result via a colour change from pink to yellow when one of the target species was present. The LOC serves as proof-of-concept (PoC) for field-based species identification as it does not require specialist facilities. It can be used by non-scientifically trained personnel, especially in areas where there are suspected high frequencies of mislabelling or for the identification of dried shark fins in seizures.},
}
@article {pmid38572806,
year = {2024},
author = {Ang, YS and Yung, LL},
title = {Protein-to-DNA Converter with High Signal Gain.},
journal = {ACS nano},
volume = {18},
number = {15},
pages = {10454-10463},
doi = {10.1021/acsnano.3c11435},
pmid = {38572806},
issn = {1936-086X},
mesh = {*DNA/genetics/chemistry ; Nucleic Acid Amplification Techniques/methods ; *Biosensing Techniques/methods ; },
abstract = {DNA isothermal amplification techniques have been applied extensively for evaluating nucleic acid inputs but cannot be implemented directly on other types of biomolecules. In this work, we designed a proximity activation mechanism that converts protein input into DNA barcodes for the DNA exponential amplification reaction, which we termed PEAR. Several design parameters were identified and experimentally verified, which included the choice of enzymes, sequences of proximity probes and template strand via the NUPACK design tool, and the implementation of a hairpin lock on the proximity probe structure. Our PEAR system was surprisingly more robust against nonspecific DNA amplification, which is a major challenge faced in existing formats of the DNA-based exponential amplification reaction. The as-designed PEAR exhibited good target responsiveness for three protein models with a dynamic range of 4-5 orders of magnitude down to femtomolar input concentration. Overall, our proposed protein-to-DNA converter module led to the development of a stable and robust configuration of the DNA exponential amplification reaction to achieve high signal gain. We foresee this enabling the use of protein inputs for more complex molecular evaluation as well as ultrasensitive protein detection.},
}
@article {pmid38569896,
year = {2024},
author = {Weile, J and Ferra, G and Boyle, G and Pendyala, S and Amorosi, C and Yeh, CL and Cote, AG and Kishore, N and Tabet, D and van Loggerenberg, W and Rayhan, A and Fowler, DM and Dunham, MJ and Roth, FP},
title = {Pacybara: accurate long-read sequencing for barcoded mutagenized allelic libraries.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {4},
pages = {},
pmid = {38569896},
issn = {1367-4811},
support = {R01 GM132162/GM/NIGMS NIH HHS/United States ; R01 HL164675/HL/NHLBI NIH HHS/United States ; RM1 HG010461/HG/NHGRI NIH HHS/United States ; /NH/NIH HHS/United States ; },
mesh = {Sequence Analysis, DNA/methods ; *High-Throughput Nucleotide Sequencing/methods ; Gene Library ; Genotype ; Cluster Analysis ; *Software ; },
abstract = {MOTIVATION: Long-read sequencing technologies, an attractive solution for many applications, often suffer from higher error rates. Alignment of multiple reads can improve base-calling accuracy, but some applications, e.g. sequencing mutagenized libraries where multiple distinct clones differ by one or few variants, require the use of barcodes or unique molecular identifiers. Unfortunately, sequencing errors can interfere with correct barcode identification, and a given barcode sequence may be linked to multiple independent clones within a given library.<br><br>RESULTS: Here we focus on the target application of sequencing mutagenized libraries in the context of multiplexed assays of variant effects (MAVEs). MAVEs are increasingly used to create comprehensive genotype-phenotype maps that can aid clinical variant interpretation. Many MAVE methods use long-read sequencing of barcoded mutant libraries for accurate association of barcode with genotype. Existing long-read sequencing pipelines do not account for inaccurate sequencing or nonunique barcodes. Here, we describe Pacybara, which handles these issues by clustering long reads based on the similarities of (error-prone) barcodes while also detecting barcodes that have been associated with multiple genotypes. Pacybara also detects recombinant (chimeric) clones and reduces false positive indel calls. In three example applications, we show that Pacybara identifies and correctly resolves these issues.<br><br>Pacybara, freely available at https://github.com/rothlab/pacybara, is implemented using R, Python, and bash for Linux. It runs on GNU/Linux HPC clusters via Slurm, PBS, or GridEngine schedulers. A single-machine simplex version is also available.},
}
@article {pmid38568891,
year = {2024},
author = {D'Ercole, J and Dapporto, L and Opler, P and Schmidt, CB and Ho, C and Menchetti, M and Zakharov, EV and Burns, JM and Hebert, PDN},
title = {A genetic atlas for the butterflies of continental Canada and United States.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0300811},
pmid = {38568891},
issn = {1932-6203},
mesh = {Animals ; United States ; *Butterflies/genetics ; Phylogeography ; DNA, Mitochondrial/genetics/chemistry ; Mitochondria/genetics ; Haplotypes ; Genetic Variation ; DNA Barcoding, Taxonomic ; Phylogeny ; },
abstract = {Multi-locus genetic data for phylogeographic studies is generally limited in geographic and taxonomic scope as most studies only examine a few related species. The strong adoption of DNA barcoding has generated large datasets of mtDNA COI sequences. This work examines the butterfly fauna of Canada and United States based on 13,236 COI barcode records derived from 619 species. It compiles i) geographic maps depicting the spatial distribution of haplotypes, ii) haplotype networks (minimum spanning trees), and iii) standard indices of genetic diversity such as nucleotide diversity (π), haplotype richness (H), and a measure of spatial genetic structure (GST). High intraspecific genetic diversity and marked spatial structure were observed in the northwestern and southern North America, as well as in proximity to mountain chains. While species generally displayed concordance between genetic diversity and spatial structure, some revealed incongruence between these two metrics. Interestingly, most species falling in this category shared their barcode sequences with one at least other species. Aside from revealing large-scale phylogeographic patterns and shedding light on the processes underlying these patterns, this work also exposed cases of potential synonymy and hybridization.},
}
@article {pmid38567263,
year = {2023},
author = {Crous, PW and Osieck, ER and Shivas, RG and Tan, YP and Bishop-Hurley, SL and Esteve-Raventós, F and Larsson, E and Luangsa-Ard, JJ and Pancorbo, F and Balashov, S and Baseia, IG and Boekhout, T and Chandranayaka, S and Cowan, DA and Cruz, RHSF and Czachura, P and De la Peña-Lastra, S and Dovana, F and Drury, B and Fell, J and Flakus, A and Fotedar, R and Jurjević, &#x17d; and Kolecka, A and Mack, J and Maggs-Kölling, G and Mahadevakumar, S and Mateos, A and Mongkolsamrit, S and Noisripoom, W and Plaza, M and Overy, DP and Piątek, M and Sandoval-Denis, M and Vauras, J and Wingfield, MJ and Abell, SE and Ahmadpour, A and Akulov, A and Alavi, F and Alavi, Z and Altés, A and Alvarado, P and Anand, G and Ashtekar, N and Assyov, B and Banc-Prandi, G and Barbosa, KD and Barreto, GG and Bellanger, JM and Bezerra, JL and Bhat, DJ and Bilański, P and Bose, T and Bozok, F and Chaves, J and Costa-Rezende, DH and Danteswari, C and Darmostuk, V and Delgado, G and Denman, S and Eichmeier, A and Etayo, J and Eyssartier, G and Faulwetter, S and Ganga, KGG and Ghosta, Y and Goh, J and Góis, JS and Gramaje, D and Granit, L and Groenewald, M and Gulden, G and Gusmão, LFP and Hammerbacher, A and Heidarian, Z and Hywel-Jones, N and Jankowiak, R and Kaliyaperumal, M and Kaygusuz, O and Kezo, K and Khonsanit, A and Kumar, S and Kuo, CH and Læssøe, T and Latha, KPD and Loizides, M and Luo, SM and Maciá-Vicente, JG and Manimohan, P and Marbach, PAS and Marinho, P and Marney, TS and Marques, G and Martín, MP and Miller, AN and Mondello, F and Moreno, G and Mufeeda, KT and Mun, HY and Nau, T and Nkomo, T and Okrasińska, A and Oliveira, JPAF and Oliveira, RL and Ortiz, DA and Pawłowska, J and Pérez-De-Gregorio, M&#xc0; and Podile, AR and Portugal, A and Privitera, N and Rajeshkumar, KC and Rauf, I and Rian, B and Rigueiro-Rodríguez, A and Rivas-Torres, GF and Rodriguez-Flakus, P and Romero-Gordillo, M and Saar, I and Saba, M and Santos, CD and Sarma, PVSRN and Siquier, JL and Sleiman, S and Spetik, M and Sridhar, KR and Stryjak-Bogacka, M and Szczepańska, K and Taşkın, H and Tennakoon, DS and Thanakitpipattana, D and Trovão, J and Türkekul, I and van Iperen, AL and van 't Hof, P and Vasquez, G and Visagie, CM and Wingfield, BD and Wong, PTW and Yang, WX and Yarar, M and Yarden, O and Yilmaz, N and Zhang, N and Zhu, YN and Groenewald, JZ},
title = {Fungal Planet description sheets: 1478-1549.},
journal = {Persoonia},
volume = {50},
number = {},
pages = {158-310},
pmid = {38567263},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Aschersonia mackerrasiae on whitefly, Cladosporium corticola on bark of Melaleuca quinquenervia, Penicillium nudgee from soil under Melaleuca quinquenervia, Pseudocercospora blackwoodiae on leaf spot of Persoonia falcata, and Pseudocercospora dalyelliae on leaf spot of Senna alata. Bolivia, Aspicilia lutzoniana on fully submersed siliceous schist in high-mountain streams, and Niesslia parviseta on the lower part and apothecial discs of Erioderma barbellatum on a twig. Brazil, Cyathus bonsai on decaying wood, Geastrum albofibrosum from moist soil with leaf litter, Laetiporus pratigiensis on a trunk of a living unknown hardwood tree species, and Scytalidium synnematicum on dead twigs of unidentified plant. Bulgaria, Amanita abscondita on sandy soil in a plantation of Quercus suber. Canada, Penicillium acericola on dead bark of Acer saccharum, and Penicillium corticola on dead bark of Acer saccharum. China, Colletotrichum qingyuanense on fruit lesion of Capsicum annuum. Denmark, Helminthosphaeria leptospora on corticioid Neohypochnicium cremicolor. Ecuador (Galapagos), Phaeosphaeria scalesiae on Scalesia sp. Finland, Inocybe jacobssonii on calcareous soils in dry forests and park habitats. France, Cortinarius rufomyrrheus on sandy soil under Pinus pinaster, and Periconia neominutissima on leaves of Poaceae. India, Coprinopsis fragilis on decaying bark of logs, Filoboletus keralensis on unidentified woody substrate, Penicillium sankaranii from soil, Physisporinus tamilnaduensis on the trunk of Azadirachta indica, and Poronia nagaraholensis on elephant dung. Iran, Neosetophoma fici on infected leaves of Ficus elastica. Israel, Cnidariophoma eilatica (incl. Cnidariophoma gen. nov.) from Stylophora pistillata. Italy, Lyophyllum obscurum on acidic soil. Namibia, Aureobasidium faidherbiae on dead leaf of Faidherbia albida, and Aureobasidium welwitschiae on dead leaves of Welwitschia mirabilis. Netherlands, Gaeumannomycella caricigena on dead culms of Carex elongata, Houtenomyces caricicola (incl. Houtenomyces gen. nov.) on culms of Carex disticha, Neodacampia ulmea (incl. Neodacampia gen. nov.) on branch of Ulmus laevis, Niesslia phragmiticola on dead standing culms of Phragmites australis, Pseudopyricularia caricicola on culms of Carex disticha, and Rhodoveronaea nieuwwulvenica on dead bamboo sticks. Norway, Arrhenia similis half-buried and moss-covered pieces of rotting wood in grass-grown path. Pakistan, Mallocybe ahmadii on soil. Poland, Beskidomyces laricis (incl. Beskidomyces gen. nov.) from resin of Larix decidua ssp. polonica, Lapidomyces epipinicola from sooty mould community on Pinus nigra, and Leptographium granulatum from a gallery of Dendroctonus micans on Picea abies. Portugal, Geoglossum azoricum on mossy areas of laurel forest areas planted with Cryptomeria japonica, and Lunasporangiospora lusitanica from a biofilm covering a biodeteriorated limestone wall. Qatar, Alternaria halotolerans from hypersaline sea water, and Alternaria qatarensis from water sample collected from hypersaline lagoon. South Africa, Alfaria thamnochorti on culm of Thamnochortus fraternus, Knufia aloeicola on Aloe gariepensis, Muriseptatomyces restionacearum (incl. Muriseptatomyces gen. nov.) on culms of Restionaceae, Neocladosporium arctotis on nest of cases of bag worm moths (Lepidoptera, Psychidae) on Arctotis auriculata, Neodevriesia scadoxi on leaves of Scadoxus puniceus, Paraloratospora schoenoplecti on stems of Schoenoplectus lacustris, Tulasnella epidendrea from the roots of Epidendrum × obrienianum, and Xenoidriella cinnamomi (incl. Xenoidriella gen. nov.) on leaf of Cinnamomum camphora. South Korea, Lemonniera fraxinea on decaying leaves of Fraxinus sp. from pond. Spain, Atheniella lauri on the bark of fallen trees of Laurus nobilis, Halocryptovalsa endophytica from surface-sterilised, asymptomatic roots of Salicornia patula, Inocybe amygdaliolens on soil in mixed forest, Inocybe pityusarum on calcareous soil in mixed forest, Inocybe roseobulbipes on acidic soils, Neonectria borealis from roots of Vitis berlandieri × Vitis rupestris, Sympoventuria eucalyptorum on leaves of Eucalyptus sp., and Tuber conchae from soil. Sweden, Inocybe bidumensis on calcareous soil. Thailand, Cordyceps sandindaengensis on Lepidoptera pupa, buried in soil, Ophiocordyceps kuchinaraiensis on Coleoptera larva, buried in soil, and Samsoniella winandae on Lepidoptera pupa, buried in soil. Taiwan region (China), Neophaeosphaeria livistonae on dead leaf of Livistona rotundifolia. Türkiye, Melanogaster anatolicus on clay loamy soils. UK, Basingstokeomyces allii (incl. Basingstokeomyces gen. nov.) on leaves of Allium schoenoprasum. Ukraine, Xenosphaeropsis corni on recently dead stem of Cornus alba. USA, Nothotrichosporon aquaticum (incl. Nothotrichosporon gen. nov.) from water, and Periconia philadelphiana from swab of coil surface. Morphological and culture characteristics for these new taxa are supported by DNA barcodes. Citation: Crous PW, Osieck ER, Shivas RG, et al. 2023. Fungal Planet description sheets: 1478-1549. Persoonia 50: 158- 310. https://doi.org/10.3767/persoonia.2023.50.05.},
}
@article {pmid38567073,
year = {2024},
author = {Wojciechowska, D and Salamon, S and Wróblewska-Seniuk, K},
title = {It's time to shed some light on the importance of fungi in neonatal intensive care units: what do we know about the neonatal mycobiome?.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1355418},
pmid = {38567073},
issn = {1664-302X},
abstract = {The 21st century, thanks to the development of molecular methods, including DNA barcoding, using Sanger sequencing, and DNA metabarcoding, based on next-generation sequencing (NGS), is characterized by flourishing research on the human microbiome. Microbial dysbiosis is perceived as a new pathogenetic factor for neonatal diseases. Fungi are crucial, but neglected, components of the neonatal microbiome, which, despite their low abundance, significantly impact morbidity and mortality rates of premature infants hospitalized in Neonatal Intensive Care Units (NICUs). The neonatal mycobiome's composition and effect on health remain poorly studied research areas. Our knowledge about neonatal mycobiome, composed of limited genera, is mainly based on research on the bacterial microbiome. We presume it is influenced by clinical factors, including prematurity, antibiotic therapy, and type of delivery. Understanding these risk factors may be useful in prevention strategies against dysbiosis and invasive fungal infections. Despite the methodological challenges resulting from the biology of the fungal cell, this topic is an attractive area of research that may contribute to more effective treatment, especially of newborns from risk groups. In this mini review, we discuss the current state of knowledge, research gaps, study difficulties, and future research directions on the neonatal mycobiome, concerning potential future clinical applications.},
}
@article {pmid38566915,
year = {2024},
author = {Moreno, K and Rico, DM and Middlebrooks, M and Medrano, S and Valdés, &#xc1;A and Krug, PJ},
title = {A cryptic radiation of Caribbean sea slugs revealed by integrative analysis: Cyerce 'antillensis' (Sacoglossa: Caliphyllidae) is six distinct species.},
journal = {Zoological journal of the Linnean Society},
volume = {200},
number = {4},
pages = {940-979},
pmid = {38566915},
issn = {0024-4082},
abstract = {Integrative studies have revealed cryptic radiations in several Caribbean lineages of heterobranch sea slugs, raising questions about the evolutionary mechanisms that promote speciation within the tropical Western Atlantic. Cyerce Bergh, 1871 is a genus comprising 12 named species in the family Caliphyllidae that lack the photosynthetic ability of other sacoglossans but are noted for vibrant colours on the large cerata (dorsal leaf-like appendages) that characterize many species. Two species are widely reported from the Caribbean: Cyerce cristallina (Trinchese, 1881) and Cyerce antillensis Engel, 1927. Here, we present an integrative assessment of diversity in Caribbean Cyerce. Four methods of molecular species delimitation supported seven species in samples from the Caribbean and adjacent subtropical Western Atlantic. Six delimited species formed a monophyletic lineage in phylogenetic analyses but were > 9% divergent at the barcoding COI locus and could be differentiated using ecological, reproductive and/or morphological traits. We redescribe C. antillensis, a senior synonym for the poorly known Cyerce habanensis Ortea &amp; Templado, 1988, and describe five new species. Evolutionary shifts in algal host use, penial armature and larval life history might have acted synergistically to promote the rapid divergence of endemic species with restricted distributions in this radiation, substantially increasing global diversity of the genus.},
}
@article {pmid38566888,
year = {2024},
author = {Khan, Q and Kakar, A and Kamran, K},
title = {New faunistic data on Diptera (Hexapoda, Insecta) from the Ziarat Juniperus forest ecosystem (Pakistan).},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e114414},
pmid = {38566888},
issn = {1314-2828},
abstract = {BACKGROUND: This study presents the first faunistic record and DNA barcoding for some Diptera species recorded from the Juniperus forest ecosystem of Balochistan, Pakistan. DNA barcoding was used to explore species diversity of Dipterans and collections carried out using a Malaise trap between December 2018 to December 2019. This process involved sequencing the 658 bp Cytochrome Oxidase I (COI) gene.<br><br>NEW INFORMATION: Amongst the collected Diptera specimens, nine families were identified, representing 13 genera. These species include Atherigonasoccata (Rondani, 1871), Atherigonavaria (Schiner, 1868), Chironomusdorsalis (Meigen, 1818), Eupeodescorollae (Linnaeus, 1758), Eristalistenax (Linnaeus,1758), Goniaornata (Meigen, 1826), Luciliasericata (Meigen, 1826), Paragusquadrifasciatus (Linnaeus, 1758), Polleniarudis (Fabricius, 1794), Raviniapernix (Thompson, 1869), Sarcophagadux (Thompson, 1869), Trupaneaamoena (Schiner, 1868) and Wohlfahrtiabella (Linnaeus, 1758). The families Syrphidae and Sarcophagidae exhibited the highest representation, each comprising three genera and three species. They were followed by the family Muscidae, which had a single genus and two species. Anthomyiidae, Chironomidae, Calliphoridae, Polleniidae, Tachinidae and Tephritidae were represented by only one genus and one species. A nique Barcode Index Number (BIN) was allotted to Tachinidae (specie i.e Goniaornata). The results indicated that barcoding through cytochrome oxidase I is an effective approach for the accurate identification and genetic studies of Diptera species. This discovery highlights the significant diversity of this insect order in study region. Furthermore, a comprehensive list of other Diptera species remains elusive because of difficulties in distinguishing them, based on morphology and a lack of professional entomological knowledge.},
}
@article {pmid38566239,
year = {2024},
author = {Reichl, J and Prossegger, C and Petutschnig, S and Unterköfler, MS and Bakran-Lebl, K and Markowicz, M and Indra, A and Fuehrer, HP},
title = {Comparison of a multiplex PCR with DNA barcoding for identification of container breeding mosquito species.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {171},
pmid = {38566239},
issn = {1756-3305},
support = {FFG 901442//Austrian Climate Research Program/ ; FFG 901442//Austrian Climate Research Program/ ; },
mesh = {Female ; Animals ; *DNA Barcoding, Taxonomic ; Multiplex Polymerase Chain Reaction ; Ovum ; *Aedes/genetics ; Mosquito Vectors/genetics ; },
abstract = {BACKGROUND: Identification of mosquitoes greatly relies on morphological specification. Since some species cannot be distinguished reliably by morphological methods, it is important to incorporate molecular techniques into the diagnostic pipeline. DNA barcoding using Sanger sequencing is currently widely used for identification of mosquito species. However, this method does not allow detection of multiple species in one sample, which would be important when analysing mosquito eggs. Detection of container breeding Aedes is typically performed by collecting eggs using ovitraps. These traps consist of a black container filled with water and a wooden spatula inserted for oviposition support. Aedes mosquitoes of different species might lay single or multiple eggs on the spatula. In contrast to Sanger sequencing of specific polymerase chain reaction (PCR) products, multiplex PCR protocols targeting specific species of interest can be of advantage for detection of multiple species in the same sample.<br><br>METHODS: For this purpose, we adapted a previously published PCR protocol for simultaneous detection of four different Aedes species that are relevant for Austrian monitoring programmes, as they can be found in ovitraps: Aedes albopictus, Aedes japonicus, Aedes koreicus, and Aedes geniculatus. For evaluation of the multiplex PCR protocol, we analysed 2271 ovitrap mosquito samples from the years 2021 and 2022, which were collected within the scope of an Austrian nationwide monitoring programme. We compared the results of the multiplex PCR to the results of DNA barcoding.<br><br>RESULTS: Of 2271 samples, the multiplex PCR could identify 1990 samples, while species determination using DNA barcoding of the mitochondrial cytochrome c oxidase subunit I gene was possible in 1722 samples. The multiplex PCR showed a mixture of different species in 47 samples, which could not be detected with DNA barcoding.<br><br>CONCLUSIONS: In conclusion, identification of Aedes species in ovitrap samples was more successful when using the multiplex PCR protocol as opposed to the DNA barcoding protocol. Additionally, the multiplex PCR allowed us to detect multiple species in the same sample, while those species might have been missed when using DNA barcoding with Sanger sequencing alone. Therefore, we propose that the multiplex PCR protocol is highly suitable and of great advantage when analysing mosquito eggs from ovitraps.},
}
@article {pmid38562907,
year = {2024},
author = {Wang, J and Suh, JM and Woo, BJ and Navickas, A and Garcia, K and Yin, K and Fish, L and Cavazos, T and Hänisch, B and Markett, D and Yu, S and Hirst, G and Brown-Swigart, L and Esserman, LJ and van 't Veer, LJ and Goodarzi, H},
title = {Systematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic drivers.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38562907},
issn = {2692-8205},
support = {P01 CA210961/CA/NCI NIH HHS/United States ; R01 CA240984/CA/NCI NIH HHS/United States ; R01 CA244634/CA/NCI NIH HHS/United States ; S10 OD028511/OD/NIH HHS/United States ; },
abstract = {From extrachromosomal DNA to neo-peptides, the broad reprogramming of the cancer genome leads to the emergence of molecules that are specific to the cancer state. We recently described orphan non-coding RNAs (oncRNAs) as a class of cancer-specific small RNAs with the potential to play functional roles in breast cancer progression[1]. Here, we report a systematic and comprehensive search to identify, annotate, and characterize cancer-emergent oncRNAs across 32 tumor types. We also leverage large-scale in vivo genetic screens in xenografted mice to functionally identify driver oncRNAs in multiple tumor types. We have not only discovered a large repertoire of oncRNAs, but also found that their presence and absence represent a digital molecular barcode that faithfully captures the types and subtypes of cancer. Importantly, we discovered that this molecular barcode is partially accessible from the cell-free space as some oncRNAs are secreted by cancer cells. In a large retrospective study across 192 breast cancer patients, we showed that oncRNAs can be reliably detected in the blood and that changes in the cell-free oncRNA burden captures both short-term and long-term clinical outcomes upon completion of a neoadjuvant chemotherapy regimen. Together, our findings establish oncRNAs as an emergent class of cancer-specific non-coding RNAs with potential roles in tumor progression and clinical utility in liquid biopsies and disease monitoring.},
}
@article {pmid38562884,
year = {2024},
author = {Lee, E and Zhang, Z and Chen, CC and Choi, D and Rivera, ACA and Linton, E and Ho, YJ and Love, J and LaClair, J and Wongvipat, J and Sawyers, CL},
title = {Timing of treatment shapes the path to androgen receptor signaling inhibitor resistance in prostate cancer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.03.18.585532},
pmid = {38562884},
issn = {2692-8205},
support = {F99 CA223063/CA/NCI NIH HHS/United States ; P01 CA265768/CA/NCI NIH HHS/United States ; },
abstract = {There is optimism that cancer drug resistance can be addressed through appropriate combination therapy, but success requires understanding the growing complexity of resistance mechanisms, including the evolution and population dynamics of drug-sensitive and drug-resistant clones over time. Using DNA barcoding to trace individual prostate tumor cells in vivo , we find that the evolutionary path to acquired resistance to androgen receptor signaling inhibition (ARSI) is dependent on the timing of treatment. In established tumors, resistance occurs through polyclonal adaptation of drug-sensitive clones, despite the presence of rare subclones with known, pre-existing ARSI resistance. Conversely, in an experimental setting designed to mimic minimal residual disease, resistance occurs through outgrowth of pre-existing resistant clones and not by adaptation. Despite these different evolutionary paths, the underlying mechanisms responsible for resistance are shared across the two evolutionary paths. Furthermore, mixing experiments reveal that the evolutionary path to adaptive resistance requires cooperativity between subclones. Thus, despite the presence of pre-existing ARSI-resistant subclones, acquired resistance in established tumors occurs primarily through cooperative, polyclonal adaptation of drug-sensitive cells. This tumor ecosystem model of resistance has new implications for developing effective combination therapy.},
}
@article {pmid38560094,
year = {2024},
author = {Li, S and Wang, S and Mi, X and Wang, C},
title = {Four new species of Anyphaena Sundevall, 1833 from Xizang, China (Araneae, Anyphaenidae).},
journal = {ZooKeys},
volume = {1196},
number = {},
pages = {1-14},
pmid = {38560094},
issn = {1313-2989},
abstract = {Four new species of the genus Anyphaena Sundevall, 1833 collected from Xizang, China, are described: A.cibagou Wang &amp; Mi, sp. nov. (♂♀), A.linzhi Wang &amp; Mi, sp. nov. (♂♀), A.shufui Wang &amp; Mi, sp. nov. (♀) and A.yejiei Wang &amp; Mi, sp. nov. (♀). Diagnostic photos of the habitus and copulatory organs and a distributional map are provided.},
}
@article {pmid38560091,
year = {2024},
author = {Kim, CJ and Tan, JL and Kim, JK and Choi, MB},
title = {Confirmation of the valid specific status of Dolichovespulakuami Kim &amp; Yoon, 1996 (Hymenoptera, Vespidae) based on molecular and morphological evidence.},
journal = {ZooKeys},
volume = {1196},
number = {},
pages = {111-119},
pmid = {38560091},
issn = {1313-2989},
abstract = {The taxonomic validity of Dolichovespulakuami, especially in relation to D.flora, has been the subject of a long-term debate. Herein, the valid specific status of the former was supported through an integrated analysis of morphological characters and DNA barcodes. The pronotal rugae and male genitalia of the two species are different, and partial mitochondrial genes (cytochrome oxidase subunit I, COI) indicate that they form significantly distinct lineages. The hitherto unknown male of D.kuami is described for the first time, and a brief discussion of the D.maculata species group is provided.},
}
@article {pmid38558968,
year = {2024},
author = {Walton, RT and Qin, Y and Blainey, PC},
title = {CROPseq-multi: a versatile solution for multiplexed perturbation and decoding in pooled CRISPR screens.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38558968},
issn = {2692-8205},
support = {K00 CA264422/CA/NCI NIH HHS/United States ; R61 CA278536/CA/NCI NIH HHS/United States ; },
abstract = {Forward genetic screens seek to dissect complex biological systems by systematically perturbing genetic elements and observing the resulting phenotypes. While standard screening methodologies introduce individual perturbations, multiplexing perturbations improves the performance of single-target screens and enables combinatorial screens for the study of genetic interactions. Current tools for multiplexing perturbations are incompatible with pooled screening methodologies that require mRNA-embedded barcodes, including some microscopy and single cell sequencing approaches. Here, we report the development of CROPseq-multi, a CROPseq[1]-inspired lentiviral system to multiplex Streptococcus pyogenes (Sp) Cas9-based perturbations with mRNA-embedded barcodes. CROPseq-multi has equivalent per-guide activity to CROPseq and low lentiviral recombination frequencies. CROPseq-multi is compatible with enrichment screening methodologies and optical pooled screens, and is extensible to screens with single-cell sequencing readouts. For optical pooled screens, an optimized and multiplexed in situ detection protocol improves barcode detection efficiency 10-fold, enables detection of recombination events, and increases decoding efficiency 3-fold relative to CROPseq. CROPseq-multi is a widely applicable multiplexing solution for diverse SpCas9-based genetic screening approaches.},
}
@article {pmid38558363,
year = {2024},
author = {Montes-Herrera, JC and Cimoli, E and Cummings, VJ and D'Archino, R and Nelson, WA and Lucieer, A and Lucieer, V},
title = {Quantifying pigment content in crustose coralline algae using hyperspectral imaging: A case study with Tethysphytum antarcticum (Ross Sea, Antarctica).},
journal = {Journal of phycology},
volume = {60},
number = {3},
pages = {695-709},
doi = {10.1111/jpy.13449},
pmid = {38558363},
issn = {1529-8817},
support = {SR140300001//Australian Research Council's Special Research Initiative for the Antarctic Gateway Partnership/ ; },
mesh = {*Rhodophyta ; Antarctic Regions ; *Phycobilins/analysis/metabolism ; Hyperspectral Imaging/methods ; Pigments, Biological/analysis/metabolism ; DNA Barcoding, Taxonomic ; },
abstract = {Crustose coralline algae (CCA) are a highly diverse group of habitat-forming, calcifying red macroalgae (Rhodophyta) with unique adaptations to diverse irradiance regimes. A distinctive CCA phenotype adaptation, which allows them to maximize photosynthetic performance in low light, is their content of a specific group of light-harvesting pigments called phycobilins. In this study, we assessed the potential of noninvasive hyperspectral imaging (HSI) in the visible spectrum (400-800 nm) to describe the phenotypic variability in phycobilin content of an Antarctic coralline, Tethysphytum antarcticum (Hapalidiales), from two distinct locations. We validated our measurements with pigment extractions and spectrophotometry analysis, in addition to DNA barcoding using the psbA marker. Targeted spectral indices were developed and correlated with phycobilin content using linear mixed models (R[2] = 0.64-0.7). Once applied to the HSI, the models revealed the distinct phycoerythrin spatial distribution in the two site-specific CCA phenotypes, with thin and thick crusts, respectively. This study advances the capabilities of hyperspectral imaging as a tool to quantitatively study CCA pigmentation in relation to their phenotypic plasticity, which can be applied in laboratory studies and potentially in situ surveys using underwater hyperspectral imaging systems.},
}
@article {pmid38554991,
year = {2024},
author = {Yoon, B and Kim, H and Jung, SW and Park, J},
title = {Single-cell lineage tracing approaches to track kidney cell development and maintenance.},
journal = {Kidney international},
volume = {105},
number = {6},
pages = {1186-1199},
doi = {10.1016/j.kint.2024.01.045},
pmid = {38554991},
issn = {1523-1755},
mesh = {*Cell Lineage ; *Single-Cell Analysis/methods ; Animals ; Humans ; *Kidney/cytology ; Cell Differentiation ; CRISPR-Cas Systems ; Cell Tracking/methods ; DNA Transposable Elements/genetics ; },
abstract = {The kidney is a complex organ consisting of various cell types. Previous studies have aimed to elucidate the cellular relationships among these cell types in developing and mature kidneys using Cre-loxP-based lineage tracing. However, this methodology falls short of fully capturing the heterogeneous nature of the kidney, making it less than ideal for comprehensively tracing cellular progression during kidney development and maintenance. Recent technological advancements in single-cell genomics have revolutionized lineage tracing methods. Single-cell lineage tracing enables the simultaneous tracing of multiple cell types within complex tissues and their transcriptomic profiles, thereby allowing the reconstruction of their lineage tree with cell state information. Although single-cell lineage tracing has been successfully applied to investigate cellular hierarchies in various organs and tissues, its application in kidney research is currently lacking. This review comprehensively consolidates the single-cell lineage tracing methods, divided into 4 categories (clustered regularly interspaced short palindromic repeat [CRISPR]/CRISPR-associated protein 9 [Cas9]-based, transposon-based, Polylox-based, and native barcoding methods), and outlines their technical advantages and disadvantages. Furthermore, we propose potential future research topics in kidney research that could benefit from single-cell lineage tracing and suggest suitable technical strategies to apply to these topics.},
}
@article {pmid38554707,
year = {2024},
author = {Chettih, SN and Mackevicius, EL and Hale, S and Aronov, D},
title = {Barcoding of episodic memories in the hippocampus of a food-caching bird.},
journal = {Cell},
volume = {187},
number = {8},
pages = {1922-1935.e20},
pmid = {38554707},
issn = {1097-4172},
support = {DP2 AG071918/AG/NIA NIH HHS/United States ; F32 MH123015/MH/NIMH NIH HHS/United States ; K99 NS131256/NS/NINDS NIH HHS/United States ; },
mesh = {Animals ; *Birds/physiology ; Feeding Behavior ; Food ; *Hippocampus/cytology/physiology ; *Memory, Episodic ; Neurons/cytology ; },
abstract = {The hippocampus is critical for episodic memory. Although hippocampal activity represents place and other behaviorally relevant variables, it is unclear how it encodes numerous memories of specific events in life. To study episodic coding, we leveraged the specialized behavior of chickadees-food-caching birds that form memories at well-defined moments in time whenever they cache food for subsequent retrieval. Our recordings during caching revealed very sparse, transient barcode-like patterns of firing across hippocampal neurons. Each "barcode" uniquely represented a caching event and transiently reactivated during the retrieval of that specific cache. Barcodes co-occurred with the conventional activity of place cells but were uncorrelated even for nearby cache locations that had similar place codes. We propose that animals recall episodic memories by reactivating hippocampal barcodes. Similarly to computer hash codes, these patterns assign unique identifiers to different events and could be a mechanism for rapid formation and storage of many non-interfering memories.},
}
@article {pmid38551122,
year = {2024},
author = {Lima, RC and de Lima, SR and Rocha, MS and Dos Anjos, HDB and Dantas, YCA and Benites, IDN and Queiroz, CDCS and Fraga, EDC and Batista, JDS},
title = {Identification of fish specimens of the Tocantins River, Brazil, using DNA barcoding.},
journal = {Journal of fish biology},
volume = {104},
number = {6},
pages = {1924-1939},
doi = {10.1111/jfb.15721},
pmid = {38551122},
issn = {1095-8649},
support = {//FAPEMA/ ; //FAPEAM/ ; //CAPES/ ; //CNPq/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Rivers ; Brazil ; *Fishes/genetics/classification ; *Electron Transport Complex IV/genetics ; Haplotypes ; Phylogeny ; },
abstract = {The fish fauna of the Tocantins River possesses many endemic species; however, it is little studied in molecular terms and is quite threatened by the construction of several hydroelectric dams. Therefore, the objective of this study was to identify the ichthyofauna of the Tocantins River using DNA barcoding. For this, collections were carried out in five points of this river, which resulted in the capture of 725 individuals from which partial sequences of the cytochrome oxidase subunit I (COI) gene were obtained for genetic analysis. A total of 443 haplotypes were recovered with the mean intraspecific K2P genetic distance of 1.82%. Altogether, 138 species were identified based on morphological criteria, which was a quantity that was much lower than that indicated by the four molecular methods (assemble species by automatic partitioning [ASAP], barcode index number [BIN], generalized mixed Yule coalescent (GMYC), and Bayesian Poisson tree processes [bPTP]) through which 152-157 molecular entities were identified. In all, 41 unique BINs were obtained based on the data generated in the BOLDSystems platform. According to the result indicated by ASAP (species delimitation approach considered the most appropriate in the present study), there was an increase of 17 molecular entities (12.32%), when compared to the number of species identified through their morphological criteria, as it can show cryptic diversity, candidates for new species, and misidentifications. There were 21 incongruities indicated between the different identification approaches for species. Therefore, it is suggested that these taxonomic problems be cautiously evaluated by experts to solve such taxonomic issues.},
}
@article {pmid38550579,
year = {2024},
author = {Früh, SP and Früh, MA and Kaufer, BB and Göbel, TW},
title = {Unraveling the chicken T cell repertoire with enhanced genome annotation.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1359169},
pmid = {38550579},
issn = {1664-3224},
mesh = {Animals ; *T-Lymphocytes ; *Chickens/genetics ; Receptors, Antigen, T-Cell, alpha-beta/genetics ; DNA, Complementary ; Genome ; },
abstract = {T cell receptor (TCR) repertoire sequencing has emerged as a powerful tool for understanding the diversity and functionality of T cells within the host immune system. Yet, the chicken TCR repertoire remains poorly understood due to incomplete genome annotation of the TCR loci, despite the importance of chickens in agriculture and as an immunological model. Here, we addressed this critical issue by employing 5' rapid amplification of complementary DNA ends (5'RACE) TCR repertoire sequencing with molecular barcoding of complementary DNA (cDNA) molecules. Simultaneously, we enhanced the genome annotation of TCR Variable (V), Diversity (D, only present in β and δ loci) and Joining (J) genes in the chicken genome. To enhance the efficiency of TCR annotations, we developed VJ-gene-finder, an algorithm designed to extract VJ gene candidates from deoxyribonucleic acid (DNA) sequences. Using this tool, we achieved a comprehensive annotation of all known chicken TCR loci, including the α/δ locus on chromosome 27. Evolutionary analysis revealed that each locus evolved separately by duplication of long homology units. To define the baseline TCR diversity in healthy chickens and to demonstrate the feasibility of the approach, we characterized the splenic α/β/γ/δ TCR repertoire. Analysis of the repertoires revealed preferential usage of specific V and J combinations in all chains, while the overall features were characteristic of unbiased repertoires. We observed moderate levels of shared complementarity-determining region 3 (CDR3) clonotypes among individual birds within the α and γ chain repertoires, including the most frequently occurring clonotypes. However, the β and δ repertoires were predominantly unique to each bird. Taken together, our TCR repertoire analysis allowed us to decipher the composition, diversity, and functionality of T cells in chickens. This work not only represents a significant step towards understanding avian T cell biology, but will also shed light on host-pathogen interactions, vaccine development, and the evolutionary history of avian immunology.},
}
@article {pmid38548880,
year = {2024},
author = {Moraes Zenker, M and Portella, TP and Pessoa, FAC and Bengtsson-Palme, J and Galetti, PM},
title = {Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {7432},
pmid = {38548880},
issn = {2045-2322},
support = {101450/2022-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 303524/2019-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2017/23548-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
mesh = {Animals ; *Culicidae/genetics ; DNA Barcoding, Taxonomic/methods ; Mosquito Vectors ; Australia ; DNA/genetics ; Biodiversity ; },
abstract = {Mosquitoes (Culicidae) represent the main vector insects globally, and they also inhabit many of the terrestrial and aquatic habitats of the world. DNA barcoding and metabarcoding are now widely used in both research and routine practices involving mosquitoes. However, these methodologies rely on information available in databases consisting of barcode sequences representing taxonomically identified voucher specimens. In this study, we assess the availability of public data for mosquitoes in the main online databases, focusing specifically on the two most widely used DNA barcoding markers in Culicidae: COI and ITS2. In addition, we test hypotheses on possible factors affecting species coverage (i.e., the percentage of species covered in the online databases) for COI in different countries and the occurrence of the DNA barcode gap for COI. Our findings showed differences in the data publicly available in the repositories, with a taxonomic or species coverage of 28.4-30.11% for COI in BOLD + GenBank, and 12.32% for ITS2 in GenBank. Afrotropical, Australian and Oriental biogeographic regions had the lowest coverages, while Nearctic, Palearctic and Oceanian had the highest. The Neotropical region had an intermediate coverage. In general, countries with a higher diversity of mosquitoes and higher numbers of medically important species had lower coverage. Moreover, countries with a higher number of endemic species tended to have a higher coverage. Although our DNA barcode gap analyses suggested that the species boundaries need to be revised in half of the mosquito species available in the databases, additional data must be gathered to confirm these results and to allow explaining the occurrence of the DNA barcode gap. We hope this study can help guide regional species inventories of mosquitoes and the completion of a publicly available reference library of DNA barcodes for all mosquito species.},
}
@article {pmid38545457,
year = {2023},
author = {Crous, PW and Akulov, A and Balashov, S and Boers, J and Braun, U and Castillo, J and Delgado, MA and Denman, S and Erhard, A and Gusella, G and Jurjević, &#x17d; and Kruse, J and Malloch, DW and Osieck, ER and Polizzi, G and Schumacher, RK and Slootweg, E and Starink-Willemse, M and van Iperen, AL and Verkley, GJM and Groenewald, JZ},
title = {New and Interesting Fungi. 6.},
journal = {Fungal systematics and evolution},
volume = {11},
number = {},
pages = {109-156},
pmid = {38545457},
issn = {2589-3831},
abstract = {Three new genera, six new species, three combinations, six epitypes, and 25 interesting new host and / or geographical records are introduced in this study. New genera: Neoleptodontidium (based on Neoleptodontidium aquaticum), and Nothoramularia (based on Nothoramularia ragnhildianicola). New species: Acremonium aquaticum (from cooling pad water, USA, Cladophialophora laricicola (on dead wood of Larix sp., Netherlands), Cyphellophora neerlandica (on lichen on brick wall, Netherlands), Geonectria muralis (on moss growing on a wall, Netherlands), Harposporium illinoisense (from rockwool, USA), and Neoleptodontidium aquaticum (from hydroponic water, USA). New combinations: Cyphellophora deltoidea (based on Anthopsis deltoidea), Neoleptodontidium aciculare (based on Leptodontidium aciculare), and Nothoramularia ragnhildianicola (based on Ramularia ragnhildianicola). Epitypes: Cephaliophora tropica (from water, USA), Miricatena prunicola (on leaves of Prunus serotina, Netherlands), Nothoramularia ragnhildianicola (on Ragnhildiana ferruginea, parasitic on Artemisia vulgaris, Germany), Phyllosticta multicorniculata (on needles of Abietis balsamea, Canada), Thyronectria caraganae (on twigs of Caragana arborescens, Ukraine), and Trichosphaeria pilosa (on decayed Salix branch, Netherlands). Furthermore, the higher order phylogeny of three genera regarded as incertae sedis is resolved, namely Cephaliophora (Ascodesmidaceae, Pezizales), Miricatena (Helotiales, Leotiomycetes), and Trichosphaeria (Trichosphaeriaceae, Trichosphaeriales), with Trichosphaeriaceae being an older name for Plectosphaerellaceae. Citation: Crous PW, Akulov A, Balashov S, Boers J, Braun U, Castillo J, Delgado MA, Denman S, Erhard A, Gusella G, Jurjević Ž, Kruse J, Malloch DW, Osieck ER, Polizzi G, Schumacher RK, Slootweg E, Starink-Willemse M, van Iperen AL, Verkley GJM, Groenewald JZ (2023). New and Interesting Fungi. 6. Fungal Systematics and Evolution 11: 109-156. doi: 10.3114/fuse.2023.11.09.},
}
@article {pmid38542477,
year = {2024},
author = {Wu, T and Sima, YK and Chen, SY and Fu, YP and Ma, HF and Hao, JB and Zhu, YF},
title = {Comparative Analysis of the Chloroplast Genomes of Eight Species of the Genus Lirianthe Spach with Its Generic Delimitation Implications.},
journal = {International journal of molecular sciences},
volume = {25},
number = {6},
pages = {},
pmid = {38542477},
issn = {1422-0067},
support = {31760180//China National Natural Science Foundation/ ; 202203AK140005//the Identification of international science and technology commissioners (Yong-Kang Sima) of Yunnan Province/ ; the Yunnan Fundamental Research Projects//202201BC070001/ ; },
mesh = {Phylogeny ; *Magnolia ; *Genome, Chloroplast ; Molecular Sequence Annotation ; Plants/genetics ; },
abstract = {Based on Sima and Lu's system of the family Magnoliaceae, the genus Lirianthe Spach s. l. includes approximately 25 species, each with exceptional landscaping and horticultural or medical worth. Many of these plants are considered rare and are protected due to their endangered status. The limited knowledge of species within this genus and the absence of research on its chloroplast genome have greatly impeded studies on the relationship between its evolution and systematics. In this study, the chloroplast genomes of eight species from the genus Lirianthe were sequenced and analyzed, and their phylogenetic relationships with other genera of the family Magnoliaceae were also elucidated. The results showed that the chloroplast genome sizes of the eight Lirianthe species ranged from 159,548 to 159,833 bp. The genomes consisted of a large single-copy region, a small single-copy region, and a pair of inverted repeat sequences. The GC content was very similar across species. Gene annotation revealed that the chloroplast genomes contained 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, totaling 130 genes. Codon usage analysis indicated that codon usage was highly conserved among the eight Lirianthe species. Repeat sequence analysis identified 42-49 microsatellite sequences, 16-18 tandem repeats, and 50 dispersed repeats, with microsatellite sequences being predominantly single-nucleotide repeats. DNA polymorphism analysis revealed 10 highly variable regions located in the large single-copy and small single-copy regions, among which rpl32-trnL, petA-psbJ, and trnH-psbA were the recommended candidate DNA barcodes for the genus Lirianthe species. The inverted repeat boundary regions show little variation between species and are generally conserved. The result of phylogenetic analysis confirmed that the genus Lirianthe s. l. is a monophyletic taxon and the most affinal to the genera, Talauma and Dugandiodendron, in Sima and Lu's system and revealed that the genus Lirianthe s. s. is paraphyletic and the genus Talauma s. l. polyphyletic in Xia's system, while Magnolia subsection Gwillimia is paraphyletic and subsection Blumiana polyphyletic in Figlar and Nooteboom's system. Morphological studies found noticeable differences between Lirianthe species in aspects including leaf indumentum, stipule scars, floral orientation, tepal number, tepal texture, and fruit dehiscence. In summary, this study elucidated the chloroplast genome evolution within Lirianthe and laid a foundation for further systematic and taxonomic research on this genus.},
}
@article {pmid38541732,
year = {2024},
author = {Ruzycka-Ayoush, M and Prochorec-Sobieszek, M and Cieszanowski, A and Glogowski, M and Szumera-Cieckiewicz, A and Podgorska, J and Targonska, A and Sobczak, K and Mosieniak, G and Grudzinski, IP},
title = {Extracellular Vesicles as Next-Generation Biomarkers in Lung Cancer Patients: A Case Report on Adenocarcinoma and Squamous Cell Carcinoma.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
pmid = {38541732},
issn = {2075-1729},
support = {NOR/POLNOR/TEPCAN/0057/2019-00//National Centre for Research and Development/ ; },
abstract = {Extracellular vesicles (EVs) released from primary cell lines, originating from resected tissues during biopsies in patients with non-small cell lung cancer (NSCLC) revealing adenocarcinoma and squamous cell carcinoma subtypes, were examined for membrane proteomic fingerprints using a proximity barcoding assay. All the collected EVs expressed canonical tetraspanins (CD9, CD63, and CD81) highly coexpressed with molecules such as lysosome-associated membrane protein-1 (LAMP1-CD107a), sialomucin core protein 24 (CD164), Raph blood group (CD151), and integrins (ITGB1 and ITGA2). This representation of the protein molecules on the EV surface may provide valuable information on NSCLC subtypes and offer new diagnostic opportunities as next-generation biomarkers in personalized oncology.},
}
@article {pmid38541609,
year = {2024},
author = {Freeman, A and Xia, X},
title = {Phylogeographic Reconstruction to Trace the Source Population of Asian Giant Hornet Caught in Nanaimo in Canada and Blaine in the USA.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
pmid = {38541609},
issn = {2075-1729},
support = {RGPIN/2018-03878//Natural Sciences and Engineering Research Council/ ; },
abstract = {The Asian giant hornet, Vespa mandarinia, is an invasive species that could potentially destroy the local honeybee industry in North America. It has been observed to nest in the coastal regions of British Columbia in Canada and Washington State in the USA. What is the source population of the immigrant hornets? The identification of the source population can shed light not only on the route of immigration but also on the similarity between the native habitat and the potential new habitat in the Pacific Northwest. We analyzed mitochondrial COX1 sequences of specimens sampled from multiple populations in China, the Republic of Korea, Japan, and the Russian Far East. V. mandarinia exhibits phylogeographic patterns, forming monophyletic clades for 16 specimens from China, six specimens from the Republic of Korea, and two specimens from Japan. The two mitochondrial COX1 sequences from Nanaimo, British Columbia, are identical to the two sequences from Japan. The COX1 sequence from Blaine, Washington State, clustered with those from the Republic of Korea and is identical to one sequence from the Republic of Korea. Our geophylogeny, which allows visualization of genetic variation over time and space, provides evolutionary insights on the evolution and speciation of three closely related vespine species (V. tropica, V. soror, and V. mandarinia), with the speciation events associated with the expansion of the distribution to the north.},
}
@article {pmid38540360,
year = {2024},
author = {Yang, J and Zhang, X and Hua, Z and Jia, H and Li, K and Ling, C},
title = {High-Quality Assembly and Analysis of the Complete Mitogenomes of German Chamomile (Matricaria recutita) and Roman Chamomile (Chamaemelum nobile).},
journal = {Genes},
volume = {15},
number = {3},
pages = {},
pmid = {38540360},
issn = {2073-4425},
support = {00011702//Biology &amp; Medicine/ ; },
mesh = {*Matricaria/genetics ; Chamaemelum/genetics ; Phylogeny ; *Genome, Mitochondrial/genetics ; *Oils, Volatile ; *Asteraceae/genetics ; },
abstract = {German chamomile (Matricaria chamomilla L.) and Roman chamomile (Chamaemelum nobile) are the two well-known chamomile species from the Asteraceae family. Owing to their essential oils and higher medicinal value, these have been cultivated widely across Europe, Northwest Asia, North America, and Africa. Regarding medicinal applications, German chamomile is the most commonly utilized variety and is frequently recognized as the "star among medicinal species". The insufficient availability of genomic resources may negatively impact the progression of chamomile industrialization. Chamomile's mitochondrial genome is lacking in extensive empirical research. In this study, we achieved the successful sequencing and assembly of the complete mitochondrial genome of M. chamomilla and C. nobile for the first time. An analysis was conducted on codon usage, sequence repeats within the mitochondrial genome of M. chamomilla and C. nobile. The phylogenetic analysis revealed a consistent positioning of M. chamomilla and C. nobile branches within both mitochondrial and plastid-sequence-based phylogenetic trees. Furthermore, the phylogenetic analysis also showed a close relationship between M. chamomilla and C. nobile within the clade comprising species from the Asteraceae family. The results of our analyses provide valuable resources for evolutionary research and molecular barcoding in chamomile.},
}
@article {pmid38540077,
year = {2024},
author = {Rajasegaran, P and Koosakulnirand, S and Tan, KK and Khoo, JJ and Suliman, Y and Mansor, MS and Ahmad Khusaini, MKS and AbuBakar, S and Chaisiri, K and Morand, S and Ya'cob, Z and Makepeace, BL},
title = {Multi-Locus Sequence Analysis Indicates Potential Cryptic Speciation in the Chigger Mite Neoschoengastia gallinarum (Hatori, 1920) Parasitising Birds in Asia.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {6},
pages = {},
pmid = {38540077},
issn = {2076-2615},
support = {ICA\R1\191058//Royal Society/ ; ANR-17-CE35-0003-01//Agence Nationale de la Recherche/ ; },
abstract = {Neoschoengastia gallinarum is widely distributed in Asia, preferentially parasitising birds, and heavy infestations have clinical impacts on domestic fowl. In common with other trombiculid mites, the genetic diversity and potential variation in host preferences or pathology induced by N. gallinarum are poorly understood. This study aimed to unravel the geographical variation and population structure of N. gallinarum collected from galliform birds in Peninsular Malaysia and Thailand by inference from concatenated mitochondrial-encoded cytochrome c oxidase subunit I (COI), and nuclear-encoded internal transcribed spacer 2 (ITS2) and 18S ribosomal DNA gene sequences, including a comparison with previously published data from southeastern China. Our multi-locus sequence analysis revealed three monophyletic clades comprising (A) specimens from Peninsular Malaysia, (B) the samples from Thailand together with a minority of Chinese sequences, and (C) the majority of sequences from China. Similarly, most species delimitation approaches divided the specimens into three operational taxonomic units. Analysis of molecular variance revealed 96.41% genetic divergence between Malaysian and Thai populations, further supported by the absence of gene flow (Nm = 0.01). In conclusion, despite the two countries sharing a land border, populations of N. gallinarum from Peninsular Malaysia and Thailand appear to be genetically segregated and may represent distinct cryptic species.},
}
@article {pmid38539155,
year = {2024},
author = {Dalilah, D and Syafruddin, D and Saleh, I and Ghiffari, A and Vernadesly, L and Syahrani, L and Irdayanti, I and Anwar, C},
title = {A systematic review: is Anopheles vagus a species complex?.},
journal = {Malaria journal},
volume = {23},
number = {1},
pages = {88},
pmid = {38539155},
issn = {1475-2875},
mesh = {Animals ; Phylogeny ; *Anopheles ; Genotype ; Mosquito Vectors/genetics ; *Malaria ; },
abstract = {BACKGROUND: Anopheles vagus (subgenus Cellia) has been identified as a vector for malaria, filariasis, and Japanese encephalitis in Asia. Sporozoites of Plasmodium falciparum and Plasmodium vivax have been found in this zoophilic mosquito in Asia and Indonesia. This study systematically reviews publications regarding An. vagus species, variation, bio-ecology, and malaria transmission in various localities in Asia, especially Indonesia, to determine whether the current data support An. vagus as a species complex.<br><br>METHODS: The databases Pubmed, Scopus, Europe PMC, and Proquest were searched to identify information regarding the morphology, karyotypes, polytene chromosome, cross-mating, ecology, and molecular identification of An. vagus was then evaluated to determine whether there were possible species complexes.<br><br>RESULTS: Of the 1326 articles identified, 15 studies were considered for synthesis. The Anopheles spp. samples for this study came from Asia. Eleven studies used morphology to identify An. vagus, with singular studies using each of karyotype identification, chromosomal polytene identification, and cross-breeding experiments. Ten studies used molecular techniques to identify Anopheles spp., including An. vagus. Most studies discovered morphological variations of An. vagus either in the same or different areas and ecological settings. In this review, the members of An. vagus sensu lato grouped based on morphology (An. vagus, An. vagus vagus, An. vagus limosus, and An. limosus), karyotyping (form A and B), and molecular (An. vagus genotype A and B, An. vagus AN4 and AN5). Genetic analysis revealed a high conservation of the ITS2 fragment among members except for the An. vagus genotype B, which was, in fact, Anopheles sundaicus. This review also identified that An. vagus limosus and An. vagus vagus were nearly identical to the ITS2 sequence.<br><br>CONCLUSION: Literature review studies revealed that An. vagus is conspecific despite the distinct morphological characteristic of An. vagus and An. limosus. Further information using another barcoding tool, such as mitochondrial COI and ND6 and experimental cross-mating between the An. vagus and An. limosus may provide additional evidence for the status of An. vagus as a species complex.},
}
@article {pmid38536748,
year = {2024},
author = {Koo, D and Mao, Z and Dimatteo, R and Noguchi, M and Tsubamoto, N and McLaughlin, J and Tran, W and Lee, S and Cheng, D and de Rutte, J and Burton Sojo, G and Witte, ON and Di Carlo, D},
title = {Defining T cell receptor repertoires using nanovial-based binding and functional screening.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {14},
pages = {e2320442121},
pmid = {38536748},
issn = {1091-6490},
support = {P50 CA092131/CA/NCI NIH HHS/United States ; R21 CA256084/CA/NCI NIH HHS/United States ; },
mesh = {*Receptors, Antigen, T-Cell ; *T-Lymphocytes ; Peptides/chemistry ; Histocompatibility Antigens/chemistry ; Antigens ; },
abstract = {The ability to selectively bind to antigenic peptides and secrete effector molecules can define rare and low-affinity populations of cells with therapeutic potential in emerging T cell receptor (TCR) immunotherapies. We leverage cavity-containing hydrogel microparticles, called nanovials, each coated with peptide-major histocompatibility complex (pMHC) monomers to isolate antigen-reactive T cells. T cells are captured and activated by pMHCs inducing the secretion of effector molecules including IFN-γ and granzyme B that are accumulated on nanovials, allowing sorting based on both binding and function. The TCRs of sorted cells on nanovials are sequenced, recovering paired αβ-chains using microfluidic emulsion-based single-cell sequencing. By labeling nanovials having different pMHCs with unique oligonucleotide-barcodes and secretions with oligo-barcoded detection antibodies, we could accurately link TCR sequences to specific targets and rank each TCR based on the corresponding cell's secretion level. Using the technique, we identified an expanded repertoire of functional TCRs targeting viral antigens with high specificity and found rare TCRs with activity against cancer-specific splicing-enhanced epitopes.},
}
@article {pmid38536613,
year = {2024},
author = {Ru, SS and Cheng, C and Jiang, P and Zhang, X},
title = {Identification of a Clinical Spirometra mansoni Plerocercoid Isolate Using Molecular and Morphological Data.},
journal = {Acta parasitologica},
volume = {69},
number = {2},
pages = {1304-1308},
pmid = {38536613},
issn = {1896-1851},
support = {NPRC-2019-194-30//the National Parasitic Resources Center, and the Ministry of Science and Technology fund/ ; 24ZX003//the Fundamental Research Project of key scientific research in Henan Province/ ; },
mesh = {Animals ; *Spirometra/genetics/isolation &amp; purification/classification ; *Sparganosis/parasitology/diagnosis ; Humans ; China ; Electron Transport Complex IV/genetics ; Female ; Phylogeny ; },
abstract = {Sparganosis has been a neglected parasitic zoonosis for a long time. The accurate identification of Spirometra tapeworms in clinical practice is poorly understood. A case of breast sparganosis was reported in Henan Province of central China. One plerocercoid approximately 3.5 cm in length was collected from the patient. The clinical isolate was identified as Spirometra mansoni based on the barcoding sequences of mitochondrial cytochrome c oxidase subunit 1 (cox1). Finally, the epidemiology of sparganosis in central China was reviewed. Comprehensive public health education should be carried out, and the risky habit of eating live tadpoles must be discouraged in Henan Province.},
}
@article {pmid38536151,
year = {2024},
author = {Li, X and Li, R and Rao, F and An, R and Li, J and Zhang, Z and Li, Y and Liu, D},
title = {Genetic characterization of 2 Ceutorhynchus (Coleoptera: Curculionidae) weevils with mitogenomes and insights into the phylogeny and evolution of related weevils.},
journal = {Journal of insect science (Online)},
volume = {24},
number = {2},
pages = {},
pmid = {38536151},
issn = {1536-2442},
support = {2022NY-131//Key R&amp;D Project in Shaanxi Province/ ; },
mesh = {Animals ; *Weevils ; *Coleoptera ; Phylogeny ; Bayes Theorem ; *Genome, Mitochondrial ; Larva ; *Brassica rapa ; },
abstract = {The rape stem weevil (Ceutorhynchus asper Roel.) and its close relatives primarily breed on cruciferous plants and cause severe damage to rapeseed production. However, their genetic and molecular information is still scarce. Here, we generated mitogenomes for both C. asper and Ceutorhynchus albosuturalis. The lengths of the 2 mitochondrial genomes are 14,207 bp (C. asper) and 15,373 bp (C. albosuturalis), and both weevils exhibit identical numbers of protein-coding genes with the absence of trnI. A + T contents for both mitogenomes are high (80% and 79.9%, respectively). Haplotype and genetic distance analyses showed that the genetic differentiation of C. asper populations in northwestern China is low. Based on 5 datasets from mitogenomes, phylogenetic analyses with maximum-likelihood and Bayesian methods show that both species (C. asper and C. albosuturalis) fall in the CCCMS clade (Curculioninae, Conoderinae, Cossoninae, Molytinae, and Scolytinae) of Curculionidae and belong to clades H and I of the genus Ceutorhynchus, respectively. Larvae of the clade H weevils mainly are borers in petioles or stems of cruciferous plants, while larvae of the clade I weevils mainly inhabit the fruits of the same plants, suggesting that ecological niche specialization can play a critical role in the diversification of Ceutorhynchus species. This study generates baseline molecular and genetic information for future research of Ceutorhynchus-related taxa and provides insights into the phylogeny and evolution of Curculionidae.},
}
@article {pmid38535374,
year = {2024},
author = {Song, C and Chen, G and Wang, L and Lei, T and Qi, X},
title = {DNA Barcoding Supports "Color-Pattern''-Based Species of Stictochironomus from China (Diptera: Chironomidae).},
journal = {Insects},
volume = {15},
number = {3},
pages = {},
pmid = {38535374},
issn = {2075-4450},
support = {32070481,32100353//National Natural Science Foundation of China/ ; LY22C040003//Zhejiang Provincial Natural Science Foundation of China/ ; 2023R474004//The Science and Technology Innovation Activities of College Students in Zhejiang Province/ ; },
abstract = {The genus Stictochironomus (Diptera: Chironomidae) has an almost worldwide distribution, with more than 30 species. However, species delimitation and identification based on the markings on the wings and legs are controversial and uncertain. In this study, we focused on color patterns to review the adults of the genus from China, and two new species (S. trifuscipes sp. nov. and S. quadrimaculatus sp. nov.) are described and figured. DNA barcodes can accurately separate the two new species with specific color patterns. However, heterospecific individuals form a monophyletic cluster in the phylogeny tree. For example, S. maculipennis (Meigen) and S. pictulus (Meigen), which have a lower interspecific genetic divergence, form a single clade. Sequences with the same species name but with high intraspecific distance form more than one phylogenetic clade, such as S. sticticus (Fabricius) of three clades, S. pictulus of four clades, S. akizukii (Tokunaga) and S. juncaii Qi, Shi, and Wang of two clades, might have potential cryptic species diversity. Species delimitation analysis using ASAP, PTP, and GMYC clearly delineated them as separate species. Consequently, color patterns are a good diagnostic characteristic for species delimitation in Stictochironomus. The distance-based analysis shows that a threshold of 4.5-7.7% is appropriate for species delimitation in Stictochironomus. Additionally, an updated key including color pattern variation for male adults of known Stictochironomus species from China is provided.},
}
@article {pmid38535361,
year = {2024},
author = {Zhao, P and Chen, S and Liu, Y and Wang, J and Chen, Z and Li, H and Cai, W},
title = {Review of the Genus Sycanus Amyot &amp; Serville, 1843 (Heteroptera: Reduviidae: Harpactorinae), from China Based on DNA Barcoding and Morphological Evidence.},
journal = {Insects},
volume = {15},
number = {3},
pages = {},
pmid = {38535361},
issn = {2075-4450},
support = {32270474//National Natural Science Foundation of China/ ; 2021GXNSFAA220106//Guangxi Natural Science Foundation/ ; 1630042020002//Central Public-interest Scientific Institution Basal Research Fund of Chinese Academy of Tropical Agricultural Sciences/ ; HXQT2020120701//Project of Biological Resources Survey in Wuyishan National Park/ ; SYND-4222022-04//Sanya Yazhou Bay Science and Technology City/ ; NNNU-KLOP-X2002//Opening Foundation of Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Nanning Normal University/ ; 602021239295//Nanning Normal University/ ; },
abstract = {Due to the variability of body coloration and morphological similarity among closely related species, unresolved issues and debates still persist in the taxonomic study of the genus Sycanus from China. In this study, we conducted phylogenetic analyses and species delimitation for Sycanus in China based on a COI DNA barcoding dataset comprising 81 samples. The results revealed that all the samples could be classified into 12 species by integrating molecular analyses with morphological comparison. This paper provides a comprehensive systematic review of the Sycanus species found in China, including descriptions of three new species: S. taiwanensis Zhao &amp; Cai sp. nov., S. flavicorius Li &amp; Cai sp. nov., and S. hainanensis Wang &amp; Cai sp. nov. Furthermore, it is proposed that S. croceovittatus Dohrn, 1859, S. leucomesus Walker, 1873, and S. villicus Stål, 1863, are three synonyms of S. bifidus (Fabricius, 1787); S. bicolor Hsiao, 1979, is a synonym of S. versicolor Dohrn, 1859; and S. hsiaoi Maldonado-Capriles, 1990, is a synonym of S. marginellus Putshkov, 1987. Additionally, brief biological information is provided for two species, S. falleni Stål, 1863, and S. croceus Hsiao, 1979.},
}
@article {pmid38534459,
year = {2024},
author = {Yaish, MW and Al-Busaidi, A and Glick, BR and Ahmed, T and Alatalo, JM},
title = {The Effects of Salinity and Genotype on the Rhizospheric Mycobiomes in Date Palm Seedlings.},
journal = {Biology},
volume = {13},
number = {3},
pages = {},
pmid = {38534459},
issn = {2079-7737},
support = {IG/SCI/BIOL/24/03//Sultan Qaboos University/ ; },
abstract = {Salinity severely affects the health and productivity of plants, with root-associated microbes, including fungi, potentially playing a crucial role in mitigating this effect and promoting plant health. This study employed metagenomics to investigate differences in the structures of the epiphyte mycobiomes in the rhizospheres of seedlings of two distinct date palm cultivars with contrasting salinity tolerances, the susceptible cultivar, 'Zabad', and the tolerant cultivar, 'Umsila'. Next-generation sequencing (NGS) of the internal transcribed spacer (ITS) rRNA was utilized as a DNA barcoding tool. The sequencing of 12 mycobiome libraries yielded 905,198 raw sequences of 268,829 high-quality reads that coded for 135 unique and annotatable operational taxonomic units (OTUs). An OTU analysis revealed differences in the rhizofungal community structures between the treatments regardless of genotype, and non-metric dimensional scaling (N-MDS) analyses demonstrated distinct separations between the cultivars under saline stress. However, these differences were not detected under the control environmental conditions, i.e., no salinity. The rhizospheric fungal community included four phyla (Ascomycota, Basidiomycota, Chytridiomycota, and Mucoromycota), with differences in the abundances of Aspergillus, Clonostachys, and Fusarium genera in response to salinity, regardless of the genotype. Differential pairwise comparisons showed that Fusarium falciforme-solani and Aspergillus sydowii-versicolor increased in abundance under saline conditions, providing potential future in vitro isolation guidelines for plant growth-promoting fungi. This study highlights the intricate dynamics of the rhizosphere microbial communities in date palms and their responses to salt stress. Additionally, we found no support for the hypothesis that indigenous epiphytic fungal communities are significantly involved in salinity tolerance in date palms.},
}
@article {pmid38534432,
year = {2024},
author = {Limeira Filho, D and França, ERR and Costa, DKP and Lima, RC and Nascimento, MHSD and Batista, JDS and Barros, MC and Fraga, EDC},
title = {Molecular Evidence Reveals Taxonomic Uncertainties and Cryptic Diversity in the Neotropical Catfish of the Genus Pimelodus (Siluriformes: Pimelodidae).},
journal = {Biology},
volume = {13},
number = {3},
pages = {},
pmid = {38534432},
issn = {2079-7737},
support = {03633/13, 00775/13, and 01374/2018//the Maranh&#xe3;o State Foundation for Research and Scientific and Technological Develop-ment-FAPEMA/ ; },
abstract = {Pimelodus is the most speciose genus of the family Pimelodidae, and is amply distributed in the Neotropical region. The species-level taxonomy and phylogenetic relationships within this genus are still poorly resolved, however. These taxonomic problems and the general lack of data have generated major uncertainties with regard to the identification of specimens from different localities. In the present study, we applied a single-locus species delimitation approach to identify the MOTUs found within the genus Pimelodus and provide sound evidence for the evaluation of the species richness of this genus in the different river basins of the Neotropical region. The study was based on the analysis of sequences of the mitochondrial COI gene of 13 nominal species, which resulted in the identification of 24 consensus MOTUs. Only six nominal species were recovered as well-defined molecular entities by both the traditional barcoding analysis and the molecular delimitation methods, while the other seven presented cryptic diversity or persistent taxonomic uncertainties. The lineages identified from the Parnaíba ecoregions, Amazonas Estuary and Coastal Drainages may represent a much greater diversity of Pimelodus species than that recognized currently, although a more detailed study of this diversity will be necessary to provide a more definitive classification of the genus.},
}
@article {pmid38527998,
year = {2024},
author = {Uechi, L and Vasudevan, S and Vilenski, D and Branciamore, S and Frankhouser, D and O'Meally, D and Meshinchi, S and Marcucci, G and Kuo, YH and Rockne, R and Kravchenko-Balasha, N},
title = {Transcriptome free energy can serve as a dynamic patient-specific biomarker in acute myeloid leukemia.},
journal = {NPJ systems biology and applications},
volume = {10},
number = {1},
pages = {32},
pmid = {38527998},
issn = {2056-7189},
support = {P30 CA033572/CA/NCI NIH HHS/United States ; U01 CA250046/CA/NCI NIH HHS/United States ; U01CA250067 S1//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 1961/19//Israel Science Foundation (ISF)/ ; },
mesh = {Adult ; Animals ; Mice ; Humans ; Child ; *Transcriptome/genetics ; Gene Expression Profiling ; *Leukemia, Myeloid, Acute/genetics ; Biomarkers, Tumor/genetics ; Phenotype ; },
abstract = {Acute myeloid leukemia (AML) is prevalent in both adult and pediatric patients. Despite advances in patient categorization, the heterogeneity of AML remains a challenge. Recent studies have explored the use of gene expression data to enhance AML diagnosis and prognosis, however, alternative approaches rooted in physics and chemistry may provide another level of insight into AML transformation. Utilizing publicly available databases, we analyze 884 human and mouse blood and bone marrow samples. We employ a personalized medicine strategy, combining state-transition theory and surprisal analysis, to assess the RNA transcriptome of individual patients. The transcriptome is transformed into physical parameters that represent each sample's steady state and the free energy change (FEC) from that steady state, which is the state with the lowest free energy.We found the transcriptome steady state was invariant across normal and AML samples. FEC, representing active molecular processes, varied significantly between samples and was used to create patient-specific barcodes to characterize the biology of the disease. We discovered that AML samples that were in a transition state had the highest FEC. This disease state may be characterized as the most unstable and hence the most therapeutically targetable since a change in free energy is a thermodynamic requirement for disease progression. We also found that distinct sets of ongoing processes may be at the root of otherwise similar clinical phenotypes, implying that our integrated analysis of transcriptome profiles may facilitate a personalized medicine approach to cure AML and restore a steady state in each patient.},
}
@article {pmid38526726,
year = {2024},
author = {Wang, Y and Zhao, J and Jiang, Z and Ma, Y and Zhang, R},
title = {Single-Cell Proteomics by Barcoded Phage-Displayed Screening via an Integrated Microfluidic Chip.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2793},
number = {},
pages = {101-112},
pmid = {38526726},
issn = {1940-6029},
mesh = {Humans ; Microfluidics ; Cell Separation ; Proteomics ; Cell Line, Tumor ; *Neoplastic Cells, Circulating/pathology ; *Microfluidic Analytical Techniques ; },
abstract = {Recent advancements in the profiling of proteomes at the single-cell level necessitate the development of quantitative and versatile platforms, particularly for analyzing rare cells like circulating tumor cells (CTCs). In this chapter, we present an integrated microfluidic chip that utilizes magnetic nanoparticles to capture single tumor cells with exceptional efficiency. This chip enables on-chip incubation and facilitates in situ analysis of cell-surface protein expression. By combining phage-based barcoding with next-generation sequencing technology, we successfully monitored changes in the expression of multiple surface markers induced by CTC adherence. This innovative platform holds significant potential for comprehensive screening of multiple surface antigens simultaneously in rare cells, offering single-cell resolution. Consequently, it will contribute valuable insights into biological heterogeneity and human disease.},
}
@article {pmid38526661,
year = {2024},
author = {Arulvendhan, V and Saravana Bhavan, P and Rajaganesh, R},
title = {Molecular Identification and Phytochemical Analysis and Bioactivity Assessment of Catharanthus roseus Leaf Extract: Exploring Antioxidant Potential and Antimicrobial Activities.},
journal = {Applied biochemistry and biotechnology},
volume = {196},
number = {11},
pages = {7614-7641},
pmid = {38526661},
issn = {1559-0291},
mesh = {*Catharanthus/chemistry ; *Plant Leaves/chemistry ; *Antioxidants/pharmacology/chemistry ; *Plant Extracts/pharmacology/chemistry ; *Phytochemicals/pharmacology/chemistry ; Anti-Infective Agents/pharmacology/chemistry ; Microbial Sensitivity Tests ; },
abstract = {Plants have long been at the main focus of the medical industry's attention due to their extensive list of biological and therapeutic properties and ethnobotanical applications. Catharanthus roseus, sometimes referred to as Nithyakalyani in Tamil, is an Apocynaceae family member used in traditional Indian medicine. It also examines the plant's potential antimicrobial and antioxidant activities as well as its preliminary phytochemical makeup. Leaf material from C. roseus was analyzed and found to include a variety of phytochemicals including alkaloids, terpenoids, flavonoids, tannins, phenols, saponins, glycosides, quinones, and steroids. Four of the seven secondary metabolic products discovered in C. roseus leaves showed bioactive principles: 3-methylmannoside, squalene, pentatriacontane, and 2,4,4-trimethyl-3-hydroxymethyl-5a-(3-methyl-but-2-enyl)-cyclohexene. Catharanthus roseus is rich in the anticancer compounds vinblastine and vincristine. Whole DNA was isolated from fresh leaves, then amplified, sequenced, and aligned to find prospective DNA barcode candidates. One DNA marker revealed the restricted genetic relationship among C. roseus based on genetic distance and phylogenetic analysis. The antioxidant activity of the plant extract was evaluated using the DPPH, ABTS, phosphomolybdenum, FRAP, and superoxide radical scavenging activity assays, while the antibacterial potential was evaluated using the agar well diffusion assay. The ethanol extract of C. roseus was found to have the highest reducing power. In addition, a 4- to 21-mm-wide zone of inhibition was seen when the C. roseus extract was tested against bacterial and fungal stains. In conclusion, C. roseus has the most promise as an antibacterial and antioxidant agent.},
}
@article {pmid38526308,
year = {2024},
author = {Park, S and Kim, M and Lee, JW},
title = {Optimizing Nucleic Acid Delivery Systems through Barcode Technology.},
journal = {ACS synthetic biology},
volume = {13},
number = {4},
pages = {1006-1018},
doi = {10.1021/acssynbio.3c00602},
pmid = {38526308},
issn = {2161-5063},
mesh = {*Nucleic Acids/genetics ; Technology ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Conventional biological experiments often focus on in vitro assays because of the inherent limitations when handling multiple variables in vivo, including labor-intensive and time-consuming procedures. Often only a subset of samples demonstrating significant efficacy in the in vitro assays can be evaluated in vivo. Nonetheless, because of the low correlation between the in vitro and in vivo tests, evaluation of the variables under examination in vivo and not solely in vitro is critical. An emerging approach to achieve high-throughput in vivo tests involves using a barcode system consisting of various nucleotide combinations. Unique barcodes for each variant enable the simultaneous testing of multiple entities, eliminating the need for separate individual tests. Subsequently, to identify crucial parameters, samples were collected and analyzed using barcode sequencing. This review explores the development of barcode design and its applications, including the evaluation of nucleic acid delivery systems and the optimization of gene expression in vivo.},
}
@article {pmid38525354,
year = {2024},
author = {Vargas, HA},
title = {On Ypsolopha micromoths (Lepidoptera, Ypsolophidae) associated with Adesmia shrubs (Fabaceae) in the arid western slope of the central Andes.},
journal = {ZooKeys},
volume = {1195},
number = {},
pages = {131-138},
pmid = {38525354},
issn = {1313-2989},
abstract = {Ypsolopha Latreille, 1796 (Lepidoptera, Ypsolophidae) is a genus comprised mostly of Holarctic micromoth species with a fairly broad range of larval hosts (e.g. Aceraceae, Rosaceae, and Fagaceae). The only previous record of herbivory on a representative of the South American genus Adesmia DC. (Fabaceae) was based on the discovery of Ypsolophamoltenii Vargas, 2018 larvae feeding on Adesmiaverrucosa Meyen in the Andes of northern Chile. Further surveys revealed Adesmiaatacamensis Phil. as another host for Y.moltenii, and Adesmiaspinosissima Meyen as the single host of Ypsolopha sp. The genetic distance between DNA barcodes of the two micromoth species was 7.9-8.1% (K2P). These results suggest narrow host ranges for Adesmia-feeding Ypsolopha and highlight the need to further explore the taxonomic diversity of these micromoths in other South American environments.},
}
@article {pmid38524900,
year = {2024},
author = {Kim, S and Sohn, J and Kim, H},
title = {Two new records of the genus Trioxys (Hymenoptera, Braconidae, Aphidiinae) parasitic on bamboo aphids from South Korea.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e118599},
pmid = {38524900},
issn = {1314-2828},
abstract = {BACKGROUND: The genus Trioxys Haliday, 1833 consists of more than 80 species worldwide with three species being recorded in South Korea. In this study, we report the first observation of the two additional species, T.liui Chou &amp; Chou, 1993 from Takecallisarundinariae (Essig, 1917) on Phyllostachysbambusoides Siebold &amp; Zucc., 1843 and T.remaudierei Starý &amp; Rakhshani, 2017 from T.taiwana (Takahashi, 1926) on Sasaborealis (Hack.) Makino &amp; Shibata, 1901.<br><br>NEW INFORMATION: Trioxysliui and T.remaudierei are described and reported with phototographs of the diagnostic morphological characters and the mitochondrial cytochrome c oxidase subunit I (COI) data (barcode region) and Bayesian tree of the phylogenetic analysis amongst the closely-related taxa are provided.},
}
@article {pmid38524763,
year = {2024},
author = {Pellitier, PT and Van Nuland, M and Salamov, A and Grigoriev, IV and Peay, KG},
title = {Potential for functional divergence in ectomycorrhizal fungal communities across a precipitation gradient.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae031},
pmid = {38524763},
issn = {2730-6151},
abstract = {Functional traits influence the assembly of microbial communities, but identifying these traits in the environment has remained challenging. We studied ectomycorrhizal fungal (EMF) communities inhabiting Populus trichocarpa roots distributed across a precipitation gradient in the Pacific Northwest, USA. We profiled these communities using taxonomic (meta-barcoding) and functional (metagenomic) approaches. We hypothesized that genes involved in fungal drought-stress tolerance and fungal mediated plant water uptake would be most abundant in drier soils. We were unable to detect support for this hypothesis; instead, the abundance of genes involved in melanin synthesis, hydrophobins, aquaporins, trehalose-synthases, and other gene families exhibited no significant shifts across the gradient. Finally, we studied variation in sequence homology for certain genes, finding that fungal communities in dry soils are composed of distinct aquaporin and hydrophobin gene sequences. Altogether, our results suggest that while EMF communities exhibit significant compositional shifts across this gradient, coupled functional turnover, at least as inferred using community metagenomics is limited. Accordingly, the consequences of these distinct EMF communities on plant water uptake remain critically unknown, and future studies targeting the expression of genes involved in drought stress tolerance are required.},
}
@article {pmid38523561,
year = {2024},
author = {Janko, &#x160; and Rok, &#x160; and Blaž, K and Danilo, B and Andrej, G and Denis, K and Klemen, &#x10c; and Matjaž, G},
title = {DNA barcoding insufficiently identifies European wild bees (Hymenoptera, Anthophila) due to undefined species diversity, genus-specific barcoding gaps and database errors.},
journal = {Molecular ecology resources},
volume = {24},
number = {5},
pages = {e13953},
doi = {10.1111/1755-0998.13953},
pmid = {38523561},
issn = {1755-0998},
support = {V1-1938//Ministry of Agriculture, Forestry and Food/ ; V1-1938//Ministry of Natural Resources and Spatial Planning/ ; J1-1703//Slovenian Research and Innovation Agency/ ; P1-0236//Slovenian Research and Innovation Agency/ ; P1-0255//Slovenian Research and Innovation Agency/ ; P4-0407//Slovenian Research and Innovation Agency/ ; V1-1938//Slovenian Research and Innovation Agency/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Bees/genetics/classification ; Europe ; Biodiversity ; },
abstract = {Recent declines in insect abundances, especially populations of wild pollinators, pose a threat to many natural and agricultural ecosystems. Traditional species monitoring relies on morphological character identification and is inadequate for efficient and standardized surveys. DNA barcoding has become a standard approach for molecular identification of organisms, aiming to overcome the shortcomings of traditional biodiversity monitoring. However, its efficacy depends on the completeness of reference databases. Large DNA barcoding efforts are (almost entirely) lacking in many European countries and such patchy data limit Europe-wide analyses of precisely how to apply DNA barcoding in wild bee identification. Here, we advance towards an effective molecular identification of European wild bees. We conducted a high-effort survey of wild bees at the junction of central and southern Europe and DNA barcoded all collected morphospecies. For global analyses, we complemented our DNA barcode dataset with all relevant European species and conducted global analyses of species delimitation, general and genus-specific barcoding gaps and examined the error rate in DNA data repositories. We found that (i) a sixth of all specimens from Slovenia could not be reliably identified, (ii) species delimitation methods show numerous systematic discrepancies, (iii) there is no general barcoding gap across all bees and (iv) the barcoding gap is genus specific, but only after curating for errors in DNA data repositories. Intense sampling and barcoding efforts in underrepresented regions and strict curation of DNA barcode repositories are needed to enhance the use of DNA barcoding for the identification of wild bees.},
}
@article {pmid38522492,
year = {2024},
author = {Sun, Y and Nan, H and Zhang, C and Yang, X and Zhao, Y and Feng, G and Ma, L},
title = {Genetic characteristics of Blastocystis sp. in cattle from Hebei Province, China.},
journal = {Microbial pathogenesis},
volume = {190},
number = {},
pages = {106629},
doi = {10.1016/j.micpath.2024.106629},
pmid = {38522492},
issn = {1096-1208},
mesh = {Animals ; Cattle ; *Blastocystis/genetics/classification/isolation &amp; purification ; China/epidemiology ; *Blastocystis Infections/epidemiology/parasitology/veterinary ; *Cattle Diseases/parasitology/epidemiology ; *Genetic Variation ; *Feces/parasitology ; *Phylogeny ; Prevalence ; DNA, Protozoan/genetics ; Genotype ; Polymerase Chain Reaction ; },
abstract = {Blastocystis sp. is a protozoan parasite that infects the intestines of humans and animals, causing chronic diseases such as skin rashes, abdominal pain, and irritable bowel syndrome. A survey was conducted to determine the prevalence and genetic diversity of Blastocystis sp. infection in cattle, in Hebei Province, China. 2746 cattle fecal samples were collected from 11 cities in Hebei Province and analyzed using polymerase chain reaction targeting the Blastocystis sp. barcoding gene. MEGA, PhyloSuite, and PopART were used to analyze the subtype, sequence signature, pairwise genetic distance, and genetic diversity indices. The results showed that the Blastocystis sp. detection rate was 12.60% (346/2746). The infection rate in different herds was affected by region, age, breeding mode, and variety; that is, the infection rates in areas of southern Hebei, cattle under one year old, intensive raising, and dairy cattle were higher than the infection rates in northern Hebei, cattle over one year old, scatter feeding, and beef cattle. Seven Blastocystis subtypes were identified, namely, ST1, ST2, ST5, ST10, ST14, ST21, and ST26; ST10 was the dominant subtype, and ST14 was the second most common subtype. A total of 374 polymorphic and conserved sites were obtained, including 273 invariable (monomorphic) sites and 101 variable (polymorphic) sites, accounting for 27.01% of all nucleotides. The nucleotide diversity index (Pi) was 0.07749, and the haplotype (gene) diversity index (Hd) was 0.946. This study provides the first comprehensive information on the epidemiological situation of Blastocystis sp. infection in cattle from Hebei Province, China, and revealed rich genetic diversity of Blastocystis sp.},
}
@article {pmid38520554,
year = {2024},
author = {Suetsugu, K and Ohta, T and Tayasu, I},
title = {Partial mycoheterotrophy in the leafless orchid Eulophia zollingeri specialized on wood-decaying fungi.},
journal = {Mycorrhiza},
volume = {34},
number = {1-2},
pages = {33-44},
pmid = {38520554},
issn = {1432-1890},
support = {17H05016//Japan Society for the Promotion of Science/ ; 16H02524//Japan Society for the Promotion of Science/ ; JPMJPR21D6//Precursory Research for Embryonic Science and Technology/ ; },
mesh = {*Mycorrhizae/physiology ; Carbon Isotopes/analysis ; Wood/chemistry/metabolism ; Symbiosis ; Carbon/metabolism ; *Agaricales ; *Orchidaceae/microbiology ; },
abstract = {Although the absence of normal leaves is often considered a sign of full heterotrophy, some plants remain at least partially autotrophic despite their leafless habit. Leafless orchids with green stems and capsules probably represent a late evolutionary stage toward full mycoheterotrophy and serve as valuable models for understanding the pathways leading to this nutritional strategy. In this study, based on molecular barcoding and isotopic analysis, we explored the physiological ecology of the leafless orchid Eulophia zollingeri, which displays green coloration, particularly during its fruiting phase. Although previous studies had shown that E. zollingeri, in its adult stage, is associated with Psathyrellaceae fungi and exhibits high [13]C isotope signatures similar to fully mycoheterotrophic orchids, it remained uncertain whether this symbiotic relationship is consistent throughout the orchid's entire life cycle and whether the orchid relies exclusively on mycoheterotrophy for its nutrition during the fruiting season. Our study has demonstrated that E. zollingeri maintains a specialized symbiotic relationship with Psathyrellaceae fungi throughout all life stages. However, isotopic analysis and chlorophyll data have shown that the orchid also engages in photosynthesis to meet its carbon needs, particularly during the fruiting stage. This research constitutes the first discovery of partial mycoheterotrophy in leafless orchids associated with saprotrophic non-rhizoctonia fungi.},
}
@article {pmid38520175,
year = {2024},
author = {Macko, P and Derka, T and Čiamporová-Zaťovičová, Z and Grabowski, M and Čiampor, F},
title = {Detailed DNA barcoding of mayflies in a small European country proved how far we are from having comprehensive barcode reference libraries.},
journal = {Molecular ecology resources},
volume = {24},
number = {5},
pages = {e13954},
doi = {10.1111/1755-0998.13954},
pmid = {38520175},
issn = {1755-0998},
support = {VEGA1/0127/20//Vedeck&#xe1; Grantov&#xe1; Agent&#xfa;ra M&#x160;VVa&#x160; SR a SAV/ ; VEGA2/0084/21//Vedeck&#xe1; Grantov&#xe1; Agent&#xfa;ra M&#x160;VVa&#x160; SR a SAV/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Ephemeroptera/genetics/classification ; Europe ; *Phylogeny ; Genetic Variation ; Biodiversity ; Sequence Analysis, DNA/methods ; },
abstract = {Mayflies (Ephemeroptera) are among the crucial water and habitat quality bioindicators. However, despite their intensive long-term use in various studies, more reliable mayfly DNA barcode data have been produced in a negligible number of countries, and only ~40% of European species had been barcoded with less than 50% of families covered. Despite being carried out in a small area, our study presents the second-most species-rich DNA reference library of mayflies from Europe and the first comprehensive view from an important biodiversity hotspot such as the Western Carpathians. Within 1153 sequences, 76 morphologically determined species were recorded and added to the Barcode of Life Data System (BOLD) database. All obtained sequences were assigned to 97 BINs, 11 of which were unique and three represented species never barcoded before. Sequences of 16 species with high intraspecific variability were divided into 40 BINs, confirming the presence of cryptic lineages. Due to the low interspecific divergence and the non-existing barcoding gap, sequences of six species were assigned to three shared BINs. Delimitation analyses resulted in 79 and 107 putative species respectively. Bayesian and maximum-likelihood phylogenies confirmed the monophyly of almost all species and complexes of cryptic taxa and proved that DNA barcoding distinguishes almost all studied mayfly species. We have shown that it is still sufficient to thoroughly investigate the fauna of a small but geographically important area to enrich global databases greatly. In particular, the insights gained here transcend the local context and may have broader implications for advancing barcoding efforts.},
}
@article {pmid38519979,
year = {2024},
author = {Zhang, H and Mulqueen, RM and Iannuzo, N and Farrera, DO and Polverino, F and Galligan, JJ and Ledford, JG and Adey, AC and Cusanovich, DA},
title = {txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {78},
pmid = {38519979},
issn = {1474-760X},
support = {R35GM137910/GM/NIGMS NIH HHS/United States ; R35 GM137896/GM/NIGMS NIH HHS/United States ; T32 ES007091/ES/NIEHS NIH HHS/United States ; R35GM137896/GM/NIGMS NIH HHS/United States ; P30 ES006694/ES/NIEHS NIH HHS/United States ; R01 HL142769/HL/NHLBI NIH HHS/United States ; RF1MH128842/MH/NIMH NIH HHS/United States ; RF1 MH128842/MH/NIMH NIH HHS/United States ; R01HL142769/HL/NHLBI NIH HHS/United States ; R35 GM137910/GM/NIGMS NIH HHS/United States ; T32ES007091/ES/NIEHS NIH HHS/United States ; R35 GM124704/GM/NIGMS NIH HHS/United States ; R35GM124704/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Mice ; Humans ; *Chromatin/metabolism ; *Chromatin Immunoprecipitation Sequencing ; Cell Nucleus/genetics ; Regulatory Sequences, Nucleic Acid ; },
abstract = {We develop a large-scale single-cell ATAC-seq method by combining Tn5-based pre-indexing with 10× Genomics barcoding, enabling the indexing of up to 200,000 nuclei across multiple samples in a single reaction. We profile 449,953 nuclei across diverse tissues, including the human cortex, mouse brain, human lung, mouse lung, mouse liver, and lung tissue from a club cell secretory protein knockout (CC16[-/-]) model. Our study of CC16[-/-] nuclei uncovers previously underappreciated technical artifacts derived from remnant 129 mouse strain genetic material, which cause profound cell-type-specific changes in regulatory elements near many genes, thereby confounding the interpretation of this commonly referenced mouse model.},
}
@article {pmid38519193,
year = {2024},
author = {Wang, G and Ren, Y and Su, Y and Zhang, H and Li, J and Zhao, H and Zhang, H and Han, J},
title = {Identification of toxic Gelsemium elegans in processed food and honey based on real-time PCR analysis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {182},
number = {},
pages = {114188},
doi = {10.1016/j.foodres.2024.114188},
pmid = {38519193},
issn = {1873-7145},
mesh = {Bees ; Animals ; *Honey/analysis ; Real-Time Polymerase Chain Reaction ; *Gelsemium ; Food, Processed ; Plants ; *Foodborne Diseases ; },
abstract = {Gelsemium elegans (GE) is a widely distributed hypertoxic plant that has caused many food poisoning incidents. Its pollen can also be collected by bees to produce toxic honey, posing a great threat to the health and safety of consumers. However, for the complex matrices such as cooked food and honey, it is challenging to perform composition analysis. It is necessary to establish more effective strategies for investigating GE contamination. In this study, the real-time PCR (qPCR) analysis combined with DNA barcode matK was proposed for the identification and detection of GE. Fifteen honey samples along with twenty-eight individuals of GE and the common confusable objects Lonicera japonica, Ficus hirta, Stellera chamaejasme and Chelidonium majus were gathered. Additionally, the food mixtures treated with 20-min boiling and 30-min digestion were prepared. Specific primers were designed, and the detection capability and sensitivity of qPCR in honey and boiled and digested food matrices were tested. The results demonstrated that the matK sequence with sufficient mutation sites was an effective molecular marker for species differentiation. GE and the confusable species could be clearly classified by the fluorescence signal of qPCR assay with a high sensitivity of 0.001 ng/μl. In addition, this method was successfully employed for the detection of deeply processed food materials and honey containing GE plants which even accounted for only 0.1 %. The sequencing-free qPCR approach undoubtedly can serve as a robust support for the quality supervision of honey industry and the prevention and diagnosis of food poisoning.},
}
@article {pmid38519172,
year = {2024},
author = {Zhao, S and Zhang, H and Zhao, Z and Zhang, Y and Yu, J and Tang, Y and Zhou, C},
title = {Integrated DNA barcoding methods to identify species in the processed fish products from Chinese market.},
journal = {Food research international (Ottawa, Ont.)},
volume = {182},
number = {},
pages = {114140},
doi = {10.1016/j.foodres.2024.114140},
pmid = {38519172},
issn = {1873-7145},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *DNA/genetics ; Fish Products/analysis ; DNA Primers ; Fishes/genetics ; },
abstract = {DNA-based methods are reliable for a precise identification of species in processed products. In this study, we assessed five typical DNA extraction methods from multiple aspects. Full-length and mini-length DNA barcoding were performed to detect the species substitution and mislabeling of 305 processed fish products from the Chinese market covering six processed fish products. The salt extraction method that exhibited the best overall performance was applied. All samples were successfully extracted; however, only 19.3 % of samples could be amplified using the full-DNA barcode primer set, and 90.2 % of samples could be amplified using the newly designed mini-DNA barcode primer sets (401 and 320 bp). Overall, the molecular identification results revealed that 36.4 % (111/305) of the samples were inconsistent with the labels, with commercial fraud observed in all six types of processed fish products. The survey findings provide technical references for effective fish authentication monitoring, offering insights into the seafood safety in markets.},
}
@article {pmid38514444,
year = {2024},
author = {Urbina, H and Jones, C and Moore, M and Hansen, J},
title = {Southern blight of water lily: The first host record of Agroathelia rolfsii on Nelumbo nucifera discovered in Florida, USA.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-01-24-0020-PDN},
pmid = {38514444},
issn = {0191-2917},
abstract = {Nelumbo nucifera Gaertn. (Nelumbonaceae, Eudicots), also known as water lily or sacred lotus, is a nonnative and invasive plant commonly found in artificial ponds and natural lakes throughout Florida (UF-IFAS 2023; Wunderlin et al. 2023). In August 2020, a single sample of water lily plants showing large leaf spots were collected at a residence in Dunnellon, Marion County, Florida (80% disease prevalence with 40% leaf coverage). Symptoms and signs of the disease were necrotized adaxial leaf spots only, bordered by whitish mycelia and hyphae with clamp connections, and whitish to light brown sclerotia formed in the center (<0.7 mm diameter). Symptomatic tissue was plated on acid potato dextrose agar (APDA) amended with chloramphenicol (100 mg/L) and ampicillin (30mg/L), and incubated at 20 °C for one week. Data supporting the molecular identification of this putative pathogen were gathered by PCR amplification and Sanger sequencing of the complete internal transcribed spacer (ITS) and a fragment of the large subunit (LSU) of the rRNA gene (~1.5 kb) using primers ITS1F and LR5 (FDACS-DPI PPST 2020-105211, GenBank OR492009) (White et al. 1990). The identification of the host was confirmed by Sanger sequencing of three plant barcode fragments: ITS2 (ITS2-S2F/ITS4, OR492008), ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) (rbcLa-F/rbcLa-R, GenBank OR502388), and Maturase K (matK) (matK-KIM1R/matK-KIM3F, GenBank OR502389) (Fazekas et al. 2012). MegaBLAST queries of the ITS/LSU sequence obtained here recovered a 99.61% match to the fungal pathogen Agroathelia (=Athelia) rolfsii (Sacc.) Redhead &amp; Mullineux. (Redhead and Mullineux 2023) (Amylocorticiaceae, Agaricomycotina) strain GP3 (GenBank JABRWF010000005) (Yan et al. 2021). MegaBLAST queries of three host plant DNA barcodes recovered matches of greater than 99.62% similarity to N. nucifera sequences. After diagnosis, symptomatic dried leaf samples were deposited at Plant Industry Herbarium Gainesville (PIHG 17807) and an axenic culture was deposited at the Agricultural Research Services Culture Collection (NRRL 66964). Koch's postulates were fulfilled by the inoculation of sclerotia (as in Terrones-Salgado et al. 2022) on adaxial leaf surface of four-week- old water lily transplants obtained from an artificial pond on campus (two plants with five leaves each). One additional transplant was not inoculated and served as a control; this plant remained asymptomatic during the experimentation period. Each transplant was kept in a 27-gallon plastic container (21W × 30L × 14H in) filled with tap water containing one tablespoon of 20-20-20 all-purpose-water-soluble plant fertilizer (VPG, TX, USA) in a plant biosafety level 2 greenhouse (23 °C, >50% relative humidity, and a 12-h/12-h photoperiod). All inoculated leaves showed necrotized areas after one week and new sclerotia were observed floating on the water surface after three weeks. Fungal pathogen was reisolated and reidentified subsequently. Agroathelia rolfsii is the causal agent of southern blight, also known as grey rot, and is reported from at least in 260 plant genera, including specialty crops such as citrus, cucumber, pepper, peanuts, pumpkin, and strawberry (Farr and Rossman 2018). Agroathelia rolfsii usually causes lower stem, crown, and root rots; consequently, leaf spots are a noteworthy presentation of symptoms for this fungus.},
}
@article {pmid38513288,
year = {2024},
author = {Bañón, R and Barros-García, D and Baldó, F and Cojan, M and de Carlos, A},
title = {Unveiling taxonomic diversity in the deep-sea fish genus Notacanthus (Notacanthiformes: Notacanthidae) with description of Notacanthus arrontei n. sp.},
journal = {Journal of fish biology},
volume = {104},
number = {6},
pages = {1910-1923},
doi = {10.1111/jfb.15734},
pmid = {38513288},
issn = {1095-8649},
support = {PORCUDEM-20233FMP001//European Maritime, Fisheries and Aquaculture Fund/ ; UIDB/04423/2020//Foundation for Science and Technology (FCT)/ ; UIDP/04423/2020//Foundation for Science and Technology (FCT)/ ; 2020.04364.CEECIND//Foundation for Science and Technology (FCT)/ ; ED431C 2019/28//Foundation for Science and Technology (FCT)/ ; },
mesh = {Animals ; *Phylogeny ; *Biodiversity ; DNA Barcoding, Taxonomic ; Fishes/classification/genetics ; Spain ; },
abstract = {Notacanthid fishes constitute a common part of benthopelagic deep-sea fish communities on seamounts and continental slopes around the world. However, their highly conserved morphology and the usual lack of information on deep-water organisms make it difficult to appropriately address their biodiversity. A multidisciplinary approach combining morphological data with a DNA-based species delimitation analyses was used to explore the taxonomy of Notacanthus species. For this purpose, morphological and molecular data were obtained from 43 individuals, and the resulting information was combined with the available data. The results showed the occurrence of Notacanthus arrontei n. sp. from the Iberian Peninsula and highlighted several taxonomic conundrums regarding the Notacanthus genus. For instance, no significant differences were found between Notacanthus indicus and the recently described Notacanthus laccadiviensis, questioning its taxonomic status. Similarly, the result of the species delimitation molecular analysis coincided with previous DNA barcoding studies supporting the snubnosed spiny eel Notacanthus chemnitzii as a species complex that requires further research. Moreover, two unidentified records from the Indian Ocean were confirmed to belong to an unknown species pending formal description, and barcoding data show for the first time the occurrence of the shortfin spiny eel Notacanthus bonaparte in the Australia-New Zealand area. This research confirms the existence of important gaps in the knowledge of notacanthid fishes and represents a step forward toward a better understanding of their biological diversity.},
}
@article {pmid38509571,
year = {2024},
author = {Cavalluzzo, B and Viuff, MC and Tvingsholm, SA and Ragone, C and Manolio, C and Mauriello, A and Buonaguro, FM and Tornesello, ML and Izzo, F and Morabito, A and Hadrup, SR and Tagliamonte, M and Buonaguro, L},
title = {Cross-reactive CD8[+] T cell responses to tumor-associated antigens (TAAs) and homologous microbiota-derived antigens (MoAs).},
journal = {Journal of experimental &amp; clinical cancer research : CR},
volume = {43},
number = {1},
pages = {87},
pmid = {38509571},
issn = {1756-9966},
support = {"Ricerca Corrente" Project L2/3//Ministero della Salute/ ; "Ricerca Corrente" Project L2/13//Ministero della Salute/ ; POR FESR 2014/2020 "Campania OncoTerapie"//Regione Campania/ ; },
mesh = {Humans ; *Epitopes, T-Lymphocyte ; CD8-Positive T-Lymphocytes ; Antigens, Neoplasm ; *Neoplasms ; Peptides/chemistry ; },
abstract = {BACKGROUND: We have recently shown extensive sequence and conformational homology between tumor-associated antigens (TAAs) and antigens derived from microorganisms (MoAs). The present study aimed to assess the breadth of T-cell recognition specific to MoAs and the corresponding TAAs in healthy subjects (HS) and patients with cancer (CP).<br><br>METHOD: A library of&#x2009;>&#x2009;100 peptide-MHC (pMHC) combinations was used to generate DNA-barcode labelled multimers. Homologous peptides were selected from the Cancer Antigenic Peptide Database, as well as Bacteroidetes/Firmicutes-derived peptides. They were incubated with CD8&#x2009;+&#x2009;T cells from the peripheral blood of HLA-A*02:01 healthy individuals (n&#x2009;=&#x2009;10) and cancer patients (n&#x2009;=&#x2009;16). T cell recognition was identified using tetramer-staining analysis. Cytotoxicity assay was performed using as target cells TAP-deficient T2 cells loaded with MoA or the paired TuA.<br><br>RESULTS: A total of 66 unique pMHC recognized by CD8+ T cells across all groups were identified. Of these, 21 epitopes from microbiota were identified as novel immunological targets. Reactivity against selected TAAs was observed for both HS and CP. pMHC tetramer staining confirmed CD8+ T cell populations cross-reacting with CTA SSX2 and paired microbiota epitopes. Moreover, PBMCs activated with the MoA where shown to release IFN&#x3b3; as well as to exert cytotoxic activity against cells presenting the paired TuA.<br><br>CONCLUSIONS: Several predicted microbiota-derived MoAs are recognized by T cells in HS and CP. Reactivity against TAAs was observed also in HS, primed by the homologous bacterial antigens. CD8+ T cells cross-reacting with MAGE-A1 and paired microbiota epitopes were identified in three subjects. Therefore, the microbiota can elicit an extensive repertoire of natural memory T cells to TAAs, possibly able to control tumor growth ("natural anti-cancer vaccination"). In addition, non-self MoAs can be included in preventive/therapeutic off-the-shelf cancer vaccines with more potent anti-tumor efficacy than those based on TAAs.},
}
@article {pmid38508195,
year = {2024},
author = {Lee, BC and Gin, A and Wu, C and Singh, K and Grice, M and Mortlock, R and Abraham, D and Fan, X and Zhou, Y and AlJanahi, A and Choi, U and DeRavin, SS and Shin, T and Hong, S and Dunbar, CE},
title = {Impact of CRISPR/HDR editing versus lentiviral transduction on long-term engraftment and clonal dynamics of HSPCs in rhesus macaques.},
journal = {Cell stem cell},
volume = {31},
number = {4},
pages = {455-466.e4},
pmid = {38508195},
issn = {1875-9777},
support = {Z01 HL002339/ImNIH/Intramural NIH HHS/United States ; ZIA HL006063/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Animals ; Macaca mulatta/genetics ; *Hematopoietic Stem Cell Transplantation/methods ; Lentivirus/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; Hematopoietic Stem Cells ; Gene Editing/methods ; CRISPR-Cas Systems/genetics ; },
abstract = {For precise genome editing via CRISPR/homology-directed repair (HDR), effective and safe editing of long-term engrafting hematopoietic stem cells (LT-HSCs) is required. The impact of HDR on true LT-HSC clonal dynamics in a relevant large animal model has not been studied. To track the output and clonality of HDR-edited cells and to provide a comparison to lentivirally transduced HSCs in vivo, we developed a competitive rhesus macaque (RM) autologous transplantation model, co-infusing HSCs transduced with a barcoded GFP-expressing lentiviral vector (LV) and HDR edited at the CD33 locus. CRISPR/HDR-edited cells showed a two-log decrease by 2 months following transplantation, with little improvement via p53 inhibition, in comparison to minimal loss of LV-transduced cells long term. HDR long-term clonality was oligoclonal in contrast to highly polyclonal LV-transduced HSCs. These results suggest marked clinically relevant differences in the impact of current genetic modification approaches on HSCs.},
}
@article {pmid38507736,
year = {2024},
author = {Heimlich, JB and Bhat, P and Parker, AC and Jenkins, MT and Vlasschaert, C and Ulloa, J and Van Amburg, JC and Potts, CR and Olson, S and Silver, AJ and Ahmad, A and Sharber, B and Brown, D and Hu, N and van Galen, P and Savona, MR and Bick, AG and Ferrell, PB},
title = {Multiomic profiling of human clonal hematopoiesis reveals genotype and cell-specific inflammatory pathway activation.},
journal = {Blood advances},
volume = {8},
number = {14},
pages = {3665-3678},
pmid = {38507736},
issn = {2473-9537},
support = {DP5 OD029586/OD/NIH HHS/United States ; K23 HL138291/HL/NHLBI NIH HHS/United States ; R00 CA218832/CA/NCI NIH HHS/United States ; R01 CA262287/CA/NCI NIH HHS/United States ; U01 OH012271/OH/NIOSH CDC HHS/United States ; },
mesh = {Humans ; *Clonal Hematopoiesis ; *Inflammation/genetics ; Genotype ; Mutation ; Gene Expression Profiling ; Dioxygenases ; DNA Methyltransferase 3A/metabolism ; Male ; Female ; DNA-Binding Proteins/genetics/metabolism ; },
abstract = {Clonal hematopoiesis (CH) is an age-associated phenomenon that increases the risk of hematologic malignancy and cardiovascular disease. CH is thought to enhance disease risk through inflammation in the peripheral blood.1 Here, we profile peripheral blood gene expression in 66 968 single cells from a cohort of 17 patients with CH and 7 controls. Using a novel mitochondrial DNA barcoding approach, we were able to identify and separately compare mutant Tet methylcytosine dioxygenase 2 (TET2) and DNA methyltransferase 3A (DNMT3A) cells with nonmutant counterparts. We discovered the vast majority of mutated cells were in the myeloid compartment. Additionally, patients harboring DNMT3A and TET2 CH mutations possessed a proinflammatory profile in CD14+ monocytes through previously unrecognized pathways such as galectin and macrophage inhibitory factor. We also found that T cells from patients with CH, although mostly unmutated, had decreased expression of GTPase of the immunity associated protein genes, which are critical to T-cell development, suggesting that CH impairs T-cell function.},
}
@article {pmid38506394,
year = {2024},
author = {Tsuchida, A and Kaneko, T and Nishikawa, K and Kawasaki, M and Yokokawa, R and Shintaku, H},
title = {Opto-combinatorial indexing enables high-content transcriptomics by linking cell images and transcriptomes.},
journal = {Lab on a chip},
volume = {24},
number = {8},
pages = {2287-2297},
doi = {10.1039/d3lc00866e},
pmid = {38506394},
issn = {1473-0189},
mesh = {Humans ; *Transcriptome ; HeLa Cells ; *Gene Expression Profiling/methods ; High-Throughput Nucleotide Sequencing/methods ; Hydrogels ; Single-Cell Analysis/methods ; Sequence Analysis, RNA/methods ; },
abstract = {We introduce a simple integrated analysis method that links cellular phenotypic behaviour with single-cell RNA sequencing (scRNA-seq) by utilizing a combination of optical indices from cells and hydrogel beads. With our method, the combinations, referred to as joint colour codes, enable the link via matching the optical combinations measured by conventional epi-fluorescence microscopy with the concatenated DNA molecular barcodes created by cell-hydrogel bead pairs and sequenced by next-generation sequencing. We validated our approach by demonstrating an accurate link between the cell image and scRNA-seq with mixed species experiments, longitudinal cell tagging by electroporation and lipofection, and gene expression analysis. Furthermore, we extended our approach to multiplexed chemical transcriptomics, which enabled us to identify distinct phenotypic behaviours in HeLa cells treated with various concentrations of paclitaxel, and determine the corresponding gene regulation associated with the formation of a multipolar spindle.},
}
@article {pmid38503974,
year = {2024},
author = {Ordon, J and Thouin, J and Nakano, RT and Ma, KW and Zhang, P and Huettel, B and Garrido-Oter, R and Schulze-Lefert, P},
title = {Chromosomal barcodes for simultaneous tracking of near-isogenic bacterial strains in plant microbiota.},
journal = {Nature microbiology},
volume = {9},
number = {4},
pages = {1117-1129},
pmid = {38503974},
issn = {2058-5276},
support = {390686111//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SPP 2125//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Humans ; Bacteria/genetics ; *Microbiota/genetics ; *Arabidopsis/genetics/microbiology ; Genes, Bacterial ; Symbiosis ; },
abstract = {DNA-amplicon-based microbiota profiling can estimate species diversity and abundance but cannot resolve genetic differences within individuals of the same species. Here we report the development of modular bacterial tags (MoBacTags) encoding DNA barcodes that enable tracking of near-isogenic bacterial commensals in an array of complex microbiome communities. Chromosomally integrated DNA barcodes are then co-amplified with endogenous marker genes of the community by integrating corresponding primer binding sites into the barcode. We use this approach to assess the contributions of individual bacterial genes to Arabidopsis thaliana root microbiota establishment with synthetic communities that include MoBacTag-labelled strains of Pseudomonas capeferrum. Results show reduced root colonization for certain mutant strains with defects in gluconic-acid-mediated host immunosuppression, which would not be detected with traditional amplicon sequencing. Our work illustrates how MoBacTags can be applied to assess scaling of individual bacterial genetic determinants in the plant microbiota.},
}
@article {pmid38503940,
year = {2024},
author = {Wong, KH and Zheng, T and Yue, GG and Li, MC and Wu, HY and Tong, MH and Zhao, XL and Chen, HB and Lau, CB and Shaw, PC and Lau, DT},
title = {A systematic approach for authentication of medicinal Patrinia species using an integration of morphological, chemical and molecular methods.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {6566},
pmid = {38503940},
issn = {2045-2322},
mesh = {*Patrinia/chemistry ; *Plants, Medicinal/genetics/chemistry ; },
abstract = {Four common Patrinia species, including P. heterophylla, P. monandra, P. scabiosifolia and P. villosa, have been documented as herbal medicines with various clinical applications, such as anti-cancer, anti-diarrhea and sedative. However, the authentication of medicinal Patrinia species poses a problem, particularly with the processed herbal materials. This study aimed to systematically authenticate the four medicinal Patrinia species in the market using morphological and chemical characterization, as well as DNA markers. We found the species identity authenticated by traditional morphologies were in good agreement with both chemical and molecular results. The four species showed species-specific patterns in chromatographic profiles with distinct chemical markers. We also revealed the power of complete chloroplast genomes in species authentication. The sequences of targeted loci, namely atpB, petA, rpl2-rpl23 and psaI-ycf4, contained informative nucleotides for the species differentiation. Our results also facilitate authentication of medicinal Patrinia species using new DNA barcoding markers. To the best of our knowledge, this is the first report on the application of morphology, chemical fingerprinting, complete chloroplast genomes and species-specific Insertion-Deletions (InDels) in differentiating Patrinia species. This study reported on the power of a systematic, multidisciplinary approach in authenticating medicinal Patrinia species.},
}
@article {pmid38501855,
year = {2024},
author = {Cassone, BJ and Pilling, BG and Borrego-Benjumea, A and LeMoine, CMR},
title = {Identification of nectar sources foraged by female mosquitoes in Canada.},
journal = {Journal of insect science (Online)},
volume = {24},
number = {2},
pages = {},
pmid = {38501855},
issn = {1536-2442},
support = {//Public Health Agency of Canada/ ; //Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Female ; Animals ; *Culicidae/genetics ; Plant Nectar ; Feeding Behavior ; Canada ; Dietary Supplements ; *Aedes ; Mosquito Vectors ; *Culex ; },
abstract = {For many mosquito species, the females must obtain vertebrate blood to complete a gonotrophic cycle. These blood meals are frequently supplemented by feeding on sugary plant nectar, which sustains energy reserves needed for flight, mating, and overall fitness. Our understanding of mosquito nectar foraging behaviors is mostly limited to laboratory experiments and direct field observations, with little research into natural mosquito-host plant relationships done in North America. In this study, we collected nectar-fed female mosquitoes over a 2-year period in Manitoba, Canada, and amplified a fragment of the chloroplast rbcL gene to identify the plant species fed upon. We found that mosquitoes foraged from diverse plant families (e.g., grasses, trees, ornamentals, and legumes), but preferred certain species, most notably soybean and Kentucky blue grass. Moreover, there appeared to be some associations between plant feeding preferences and mosquito species, date of collection, landscape, and geographical region. Overall, this study implemented DNA barcoding to identify nectar sources forage by mosquitoes in the Canadian Prairies.},
}
@article {pmid38500531,
year = {2024},
author = {Pedersen, KM and von Beeren, C and Oggioni, A and Blüthgen, N},
title = {Mammal dung-dung beetle trophic networks: an improved method based on gut-content DNA.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e16627},
pmid = {38500531},
issn = {2167-8359},
mesh = {Animals ; *Coleoptera/genetics ; DNA, Ribosomal ; *Ecosystem ; Feces ; Mammals ; },
abstract = {BACKGROUND: Dung beetles provide many important ecosystem services, including dung decomposition, pathogen control, soil aeration, and secondary seed dispersal. Yet, the biology of most dung beetles remains unknown. Natural diets are poorly studied, partly because previous research has focused on choice or attraction experiments using few, easily accessible dung types from zoo animals, farm animals, or humans. This way, many links within natural food webs have certainly been missed. In this work, we aimed to establish a protocol to analyze the natural diets of dung beetles using DNA gut barcoding.<br><br>METHODS: First, the feasibility of gut-content DNA extraction and amplification of 12s rDNA from six different mammal dung types was tested in the laboratory. We then applied the method to beetles caught in pitfall traps in Ecuador and Germany by using 12s rDNA primers. For a subset of the dung beetles caught in the Ecuador sampling, we also used 16s rDNA primers to see if these would improve the number of species we could identify. We predicted the likelihood of amplifying DNA using gut fullness, DNA concentration, PCR primer, collection method, and beetle species as predictor variables in a dominance analysis. Based on the gut barcodes, we generated a dung beetle-mammal network for both field sites (Ecuador and Germany) and analyzed the levels of network specificity.<br><br>RESULTS: We successfully amplified mammal DNA from dung beetle gut contents for 128 specimens, which included such prominent species as Panthera onca (jaguar) and Puma concolor (puma). The overall success rate of DNA amplification was 53%. The best predictors for amplification success were gut fullness and DNA concentration, suggesting the success rate can be increased by focusing on beetles with a full gut. The mammal dung-dung beetle networks differed from purely random network models and showed a moderate degree of network specialization (H2': Ecuador = 0.49; Germany = 0.41).<br><br>CONCLUSION: We here present a reliable method of extracting and amplifying gut-content DNA from dung beetles. Identifying mammal dung via DNA reference libraries, we created mammal dung-dung beetle trophic networks. This has benefits over previous methods because we inventoried the natural mammal dung resources of dung beetles instead of using artificial mammal baits. Our results revealed higher levels of specialization than expected and more rodent DNA than expected in Germany, suggesting that the presented method provides more detailed insights into mammal dung-dung beetle networks. In addition, the method could have applications for mammal monitoring in many ecosystems.},
}
@article {pmid38499663,
year = {2024},
author = {Ben Romdhane, W and Al-Doss, A and Hassairi, A},
title = {The newly assembled chloroplast genome of Aeluropus littoralis: molecular feature characterization and phylogenetic analysis with related species.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {6472},
pmid = {38499663},
issn = {2045-2322},
support = {2-17-04-001-0046//National Plan for Science, Technology and Innovation (MAARIFAH), King Abdul Aziz City for Science and Technology, Kingdom of Saudi Arabia/ ; },
mesh = {Phylogeny ; *Genome, Chloroplast/genetics ; Poaceae/genetics ; Chloroplasts/genetics ; Photosynthesis ; },
abstract = {Aeluropus littoralis, a halophyte grass, is widely distributed from the Mediterranean to the Indian subcontinent through the Mongolian Gobi. This model halophyte has garnered increasing attention owing to its use as forage and its high tolerance to environmental stressors. The chloroplast genomes of many plants have been extensively examined for molecular, phylogenetic and transplastomic applications. However, no published research on the A. littoralis chloroplast (cp) genome was discovered. Here, the entire chloroplast genome of A. littoralis was assembled implementing accurate long-read sequences. The entire chloroplast genome, with an estimated length of 135,532 bp (GC content: 38.2%), has a quadripartite architecture and includes a pair of inverted repeat (IR) regions, IRa and IRb (21,012 bp each), separated by a large and a small single-copy regions (80,823 and 12,685 bp, respectively). The features of A. littoralis consist of 133 genes that synthesize 87 peptides, 38 transfer RNAs, and 8 ribosomal RNAs. Of these genes, 86 were unique, whereas 19 were duplicated in IR regions. Additionally, a total of forty-six simple sequence repeats, categorized into 32-mono, four-di, two-tri, and eight-tetranucleotides, were discovered. Furthermore, ten sets of repeats greater than 20 bp were located primarily in the LSC region. Evolutionary analysis based on chloroplast sequence data revealed that A. littoralis with A. lagopoides and A. sinensis belong to the Aeluropodinae subtribe, which is a sister to the Eleusininae in the tribe Cynodonteae and the subfamily Chloridoideae. This subfamily belongs to the PACMAD clade, which contains the majority of the C4 photosynthetic plants in the Poaceae. The newly constructed A. littoralis cp genome offers valuable knowledge for DNA barcoding, phylogenetic, transplastomic research, and other biological studies.},
}
@article {pmid38496800,
year = {2024},
author = {van Nieukerken, EJ and Davis, DR and Swain, SV and Epstein, ME},
title = {A new North American species of Etainia (Lepidoptera, Nepticulidae), feeding on Arbutus and Arctostaphylos species (Ericaceae).},
journal = {ZooKeys},
volume = {1193},
number = {},
pages = {195-218},
pmid = {38496800},
issn = {1313-2989},
abstract = {Etainiathoraceleuca van Nieukerken, Epstein &amp; Davis, sp. nov. is the second native American species of Etainia Beirne, 1945, and the second known Etainia species feeding on Ericaceae. The species is known from light-collected adults in the USA (California, Arizona) and Canada (Ontario). These were linked via DNA barcodes to larvae that make short leafmines on Arbutus and Arctostaphylos species, then continue feeding in stems and branches, causing damage in nurseries and planted trees in Sonoma and Marin Counties, California. The holotype was accidentally reared from Arbutusarizonica, without observing the damage. Life history and damage are described in detail. Damage in Arctostaphylosuva-ursi found in Washington State probably belongs to E.thoraceleuca, which is a sister species to the European E.albibimaculella (Larsen, 1927).},
}
@article {pmid38496577,
year = {2024},
author = {Loes, AN and Tarabi, RAL and Huddleston, J and Touyon, L and Wong, SS and Cheng, SMS and Leung, NHL and Hannon, WW and Bedford, T and Cobey, S and Cowling, BJ and Bloom, JD},
title = {High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38496577},
issn = {2692-8205},
support = {P30 CA015704/CA/NCI NIH HHS/United States ; S10 OD028685/OD/NIH HHS/United States ; U01 AI153700/AI/NIAID NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; S10 OD020069/OD/NIH HHS/United States ; R01 AI165821/AI/NIAID NIH HHS/United States ; },
abstract = {The high genetic diversity of influenza viruses means that traditional serological assays have too low throughput to measure serum antibody neutralization titers against all relevant strains. To overcome this challenge, we have developed a sequencing-based neutralization assay that simultaneously measures titers against many viral strains using small serum volumes via a workflow similar to traditional neutralization assays. The key innovation is to incorporate unique nucleotide barcodes into the hemagglutinin (HA) genomic segment, and then pool viruses with numerous different barcoded HA variants and quantify infectivity of all of them simultaneously using next-generation sequencing. With this approach, a single researcher performed the equivalent of 2,880 traditional neutralization assays (80 serum samples against 36 viral strains) in approximately one month. We applied the sequencing-based assay to quantify the impact of influenza vaccination on neutralization titers against recent human H1N1 strains for individuals who had or had not also received a vaccine in the previous year. We found that the viral strain specificities of the neutralizing antibodies elicited by vaccination vary among individuals, and that vaccination induced a smaller increase in titers for individuals who had also received a vaccine the previous year-although the titers six months after vaccination were similar in individuals with and without the previous-year vaccination. We also identified a subset of individuals with low titers to a subclade of recent H1N1 even after vaccination. This study demonstrates the utility of high-throughput sequencing-based neutralization assays that enable titers to be simultaneously measured against many different viral strains. We provide a detailed experimental protocol (DOI: https://dx.doi.org/10.17504/protocols.io.kqdg3xdmpg25/v1) and a computational pipeline (https://github.com/jbloomlab/seqneut-pipeline) for the sequencing-based neutralization assays to facilitate the use of this method by others.},
}
@article {pmid38496463,
year = {2024},
author = {Hebert, JD and Xu, H and Tang, YJ and Ruiz, PA and Detrick, CR and Wang, J and Hughes, NW and Donosa, O and Andrejka, L and Karmakar, S and Aboiralor, I and Tang, R and Sage, J and Cong, L and Petrov, DA and Winslow, MM},
title = {Efficient and multiplexed somatic genome editing with Cas12a mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.03.07.583774},
pmid = {38496463},
issn = {2692-8205},
abstract = {Somatic genome editing in mouse models has increased our understanding of the in vivo effects of genetic alterations in areas ranging from neuroscience to cancer biology and beyond. However, existing models are limited in their ability to create multiple targeted edits. Thus, our understanding of the complex genetic interactions that underlie development, homeostasis, and disease remains incomplete. Cas12a is an RNA-guided endonuclease with unique attributes that enable simple targeting of multiple genes with crRNA arrays containing tandem guides. To accelerate and expand the generation of complex genotypes in somatic cells, we generated transgenic mice with Cre-regulated and constitutive expression of enhanced Acidaminococcus sp. Cas12a (enAsCas12a). In these mice, enAsCas12a-mediated somatic genome editing robustly generated compound genotypes, as exemplified by the initiation of diverse cancer types driven by homozygous inactivation of trios of tumor suppressor genes. We further integrated these modular crRNA arrays with clonal barcoding to quantify the size and number of tumors with each array, as well as the efficiency of each crRNA. These Cas12a alleles will enable the rapid generation of disease models and broadly facilitate the high-throughput investigation of coincident genomic alterations in somatic cells in vivo .},
}
@article {pmid38495438,
year = {2024},
author = {Xue, Y and Su, Z and Lin, X and Ho, MK and Yu, KHO},
title = {Single-cell lineage tracing with endogenous markers.},
journal = {Biophysical reviews},
volume = {16},
number = {1},
pages = {125-139},
pmid = {38495438},
issn = {1867-2450},
abstract = {Resolving lineage relationships between cells in an organism provides key insights into the fate of individual cells and drives a fundamental understanding of the process of development and disease. A recent rapid increase in experimental and computational advances for detecting naturally occurring somatic nuclear and mitochondrial mutation at single-cell resolution has expanded lineage tracing from model organisms to humans. This review discusses the advantages and challenges of experimental and computational techniques for cell lineage tracing using somatic mutation as endogenous DNA barcodes to decipher the relationships between cells during development and tumour evolution. We outlook the advantages of spatial clonal evolution analysis and single-cell lineage tracing using endogenous genetic markers.},
}
@article {pmid38495311,
year = {2024},
author = {Juhász, A and Nkolokosa, C and Kambewa, E and Jones, S and Cunningham, LJ and Chammudzi, P and Kapira, D and Namacha, G and Lally, D and Kayuni, SA and Makaula, P and Musaya, J and Stothard, JR},
title = {An alien intermediate snail host in Malawi - Orientogalba viridis (Quoy and Gaimard, 1832) - A new concern for schistosomiasis transmission in Africa?.},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {23},
number = {},
pages = {100919},
pmid = {38495311},
issn = {2213-2244},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {The freshwater amphibious snail Orientogalba viridis commonly occurs in eastern Asia, on certain Pacific islands and more importantly has recently dispersed into Europe. Since this snail is now considered an invasive species, its distribution is of growing parasitological interest as an alien intermediate host for various trematodes, particularly liver flukes. As part of ongoing surveillance for snail-borne diseases in Malawi, a population of O. viridis was first observed in May 2023, alongside an alarming presence of a human schistosome cercaria. This snail population later underwent detailed morphological characterisation with both snail and parasite identities confirmed upon DNA barcoding. This seminal observation triggered more extensive local snail surveys, finding 3 further populations in separated rice paddies, with further field-caught snails (n = 465) screened for infection and a selection used for repeated experimental challenges with miracidia from Schistosoma haematobium and Schistosoma mattheei. Although no field-caught (and experimentally exposed) snail was seen to shed schistosome cercariae, molecular xenomonitoring for schistosomiasis provided tangible evidence of putative transmission potential. Our first report of O. viridis here in Malawi, and more broadly in Africa, flags a need for increased vigilance for this invasive species alongside local clarification(s) of its transmission potential for trematodiases of either medical and/or veterinary importance.},
}
@article {pmid38494250,
year = {2024},
author = {Arisuryanti, T and Waskito Aji, K and Nur Shabrina, F and Febriyanti, D and Setiadi Daryono, B and Sendi Priyono, D},
title = {Phylogenetic and genetic variation of common mudskippers (Periophthalmus kalolo Lesson, 1831) from the southern coast of Java, Indonesia inferred from the COI mitochondrial gene.},
journal = {Journal, genetic engineering &amp; biotechnology},
volume = {22},
number = {1},
pages = {100335},
pmid = {38494250},
issn = {2090-5920},
abstract = {BACKGROUND: The common mudskipper (Periophthalmus kalolo Lesson, 1831) belongs to a group of fish species that exhibit amphibious lifestyles during specific daily periods. However, identifying this species poses a challenge due to its morphological similarities with other mudskipper species. These similarities have occasionally caused misidentifications of mudskippers. In Indonesia, previous studies have examined the genetic variation of common mudskippers, but these investigations have been limited to a few specific areas, particularly along the southern coast of Java. As a result, the available data remain fragmented, and no comprehensive genetic population analysis of common mudskippers on the southern coast of Java has been conducted. Therefore, our study aimed to establish DNA barcodes of COI mtDNA and explore the genetic variation and relationship among these common mudskipper populations from the southern coast of Java. We collected nine specimens from two populations, Cilacap Mangrove Forest and Kondang Bandung Beach, and supplemented our dataset with 38 previously collected COI sequences of common mudskippers from three different populations from the southern coast of Java (Pasir Mendit Beach, Bogowonto Lagoon, and Baros Beach).<br><br>RESULTS: The study revealed that 47 common mudskippers from five different populations are separated into three genetically distinct clades (A, B, and C). These clades display genetic divergences ranging from 0.97% to 1.91%. Each clade exhibits high levels of haplotype diversity but relatively low nucleotide diversity, suggesting a previous bottleneck in population followed by a fast expansion. However, the phylogeny, haplotype network, and principal coordinate analysis indicate overlapping populations with no geographic separation within these clades. This suggests the potential occurrence of gene flow among these populations, which might have been facilitated by past geological events.<br><br>CONCLUSIONS: These results enhance our understanding of common mudskipper biodiversity in Indonesia. Further studies involving common mudskipper populations from various geographical sites in Indonesia are required to further enrich our understanding of the variation and evolution of this species.},
}
@article {pmid38493661,
year = {2024},
author = {González, MA and Ruiz-Arrondo, I and Bravo-Barriga, D and Cervera-Acedo, C and Santibáñez, P and Oteo, JA and Miranda, M&#xc1; and Barceló, C},
title = {Surveillance and screening of Stomoxyinae flies from Mallorca Island (Spain) reveal the absence of selected pathogens but confirm the presence of the endosymbiotic bacterium Wolbachia pipientis.},
journal = {Research in veterinary science},
volume = {171},
number = {},
pages = {105206},
doi = {10.1016/j.rvsc.2024.105206},
pmid = {38493661},
issn = {1532-2661},
mesh = {Animals ; *Wolbachia/genetics ; Spain ; RNA, Ribosomal, 16S/genetics ; *Muscidae/genetics/microbiology/parasitology ; Bacteria/genetics ; },
abstract = {Adult brachycera biting flies can significantly impact livestock through both direct effects (reduction of food intake, disturbance, painful bites, and blood loss) and indirect effects (pathogen transmission), leading to substantial economic losses and production damage. This study aimed to assess the presence of blood-sucking flies in six mixed-animal farm environments on the island of Mallorca (Balearic Islands, Spain) by employing multiple trapping methods. Additionally, distribution maps of brachycera biting fly species recorded in Spain were created, based on data extracted thorough review of scientific literature and citizen digital databases. Investigation of several pathogens, including equine infectious anemia virus (EIAV), Anaplasmataceae bacteria, and piroplasm protozoa, was carried out using different PCR targets (18S rRNA, 16S rRNA, groESL, and tat genes). Citizen science databases and literature review corroborated the consistent distribution trend for two Stomoxyinae species, underscoring the importance of citizen collaboration as a complement to traditional entomological surveillance. Our study confirmed the presence of two biting Stomoxyinae species: the prevalent stable fly Stomoxys calcitrans across all sampled farms, and the horn fly Haematobia irritans, which turned out to be less abundant. DNA barcoding techniques validated the identification of the two species. Neither EIAV nor bacterial/protozoan pathogens were detected using the selected PCR targets in either fly species. However, Wolbachia pipientis (clustered in the supergroup A together with the only sequence of W. pipientis from the USA) was identified through PCR targeting 16S rRNA, groESL and wsp genes in all pools of H. irritans (n = 13) collected from two of the examined farms. This study represents the first attempt to investigate pathogens in Stomoxyinae biting flies in Spain. The discovery of the endosymbiotic Wolbachia organism in H. irritans represents the first record in Spain and the second from Europe. This finding holds significant implications for future research on the applications of this bacterium in biocontrol programs.},
}
@article {pmid38491512,
year = {2024},
author = {Chan, KT and Wu, HY and Tin, WY and But, PP and Cheung, SC and Shaw, PC},
title = {Ethnopharmacology of five flowers herbal tea, a popular traditional beverage in Hong Kong and South China.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {20},
number = {1},
pages = {36},
pmid = {38491512},
issn = {1746-4269},
mesh = {Ethnopharmacology ; *Teas, Herbal ; Hong Kong ; China ; Beverages ; Flowers ; Tea ; },
abstract = {BACKGROUND: It has been a long-standing tradition of using herbal tea for preventive and therapeutic healthcare in Hong Kong and South China and Five Flowers Tea is one of the most popular herbal teas. Based on the principle of traditional Chinese medicine, the pharmacological functions are to clear heat and dispel dampness in the body. Heat and dampness are thought to contribute to a range of health problems, especially during the hot and humid season in South China and Hong Kong. The most prevalent herbs in the formula contain bioactive compounds including flavonoids, alkaloids and terpenoids, which have a wide range of pharmacological properties including anti-inflammation, antivirus, antidiarrhoea, antibacteria, and antioxidation. However, with the composition varies widely, the ethnopharmacological benefits described may not be delivered uniformly. This study is to provide a comprehensive analysis on the composition of the Five Flowers Tea sold in Hong Kong and investigate the rationale behind the selection of herbs used in the formula. This study also provides information on the variation and quality of the Five Flowers Tea in the market.<br><br>METHODS: Thirty-three Five Flowers Tea samples were collected from various locations in Hong Kong. The size, texture, colour and organoleptic properties were documented. Macroscopic and molecular authentication methods were employed to identify the individual components.<br><br>RESULTS: Macroscopic identification&#xa0;revealed there were 23 herbs belonging to 18 plant families. The most prevalent herb was Bombax ceiba L., followed by Chrysanthemum morifolium. Ten adulterants and the existence of insect Lasioderma serricorne were confirmed by&#xa0;DNA barcoding techniques.<br><br>CONCLUSION: This study employed a comprehensive approach to authenticate the herbs in Five&#xa0;Flowers Tea samples&#xa0;collected from various locations in Hong Kong. Macroscopic and&#xa0;molecular methods&#xa0;were used to identify the herbs and adulterants. The findings revealed the varied composition in Five Flowers Tea and the occurrence of adulterants in some samples. This shows that quality assurance of Five Flowers Tea is essential for the effective use of this popular folk medicine.},
}
@article {pmid38491157,
year = {2024},
author = {Vuataz, L and Reding, JP and Reding, A and Roesti, C and Stoffel, C and Vinçon, G and Gattolliat, JL},
title = {A comprehensive DNA barcoding reference database for Plecoptera of Switzerland.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {6322},
pmid = {38491157},
issn = {2045-2322},
mesh = {Animals ; *Insecta/genetics ; Switzerland ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; Ecosystem ; },
abstract = {DNA barcoding is an essential tool in modern biodiversity sciences. Despite considerable work to barcode the tree of life, many groups, including insects, remain partially or totally unreferenced, preventing barcoding from reaching its full potential. Aquatic insects, especially the three orders Ephemeroptera, Plecoptera, and Trichoptera (EPT), are key freshwater quality indicators worldwide. Among them, Plecoptera (stoneflies), which are among the most sensitive aquatic insects to habitat modification, play a central role in river monitoring surveys. Here, we present an update of the Plecoptera reference database for (meta)barcoding in Switzerland, now covering all 118 species known from this country. Fresh specimens, mostly from rare or localized species, were collected, and 151 new CO1 barcodes were generated. These were merged with the 422 previously published sequences, resulting in a dataset of 573 barcoded specimens. Our CO1 dataset was delimited in 115 CO1 clusters based on a priori morphological identifications, of which 17% are newly reported for Switzerland, and 4% are newly reported globally. Among the 115 CO1 clusters, 85% showed complete congruence with morphology. Distance-based analysis indicated local barcoding gaps in 97% of the CO1 clusters. This study significantly improves the Swiss reference database for stoneflies, enhancing future species identification accuracy and biodiversity monitoring. Additionally, this work reveals cryptic diversity and incongruence between morphology and barcodes, both presenting valuable opportunities for future integrative taxonomic studies. Voucher specimens, DNA extractions and reference barcodes are available for future developments, including metabarcoding and environmental DNA surveys.},
}
@article {pmid38489863,
year = {2024},
author = {Wittwer, CT and Hemmert, AC and Kent, JO and Rejali, NA},
title = {DNA melting analysis.},
journal = {Molecular aspects of medicine},
volume = {97},
number = {},
pages = {101268},
doi = {10.1016/j.mam.2024.101268},
pmid = {38489863},
issn = {1872-9452},
mesh = {*Nucleic Acid Denaturation ; Humans ; *DNA/genetics/chemistry ; Polymerase Chain Reaction/methods ; },
abstract = {Melting is a fundamental property of DNA that can be monitored by absorbance or fluorescence. PCR conveniently produces enough DNA to be directly monitored on real-time instruments with fluorescently labeled probes or dyes. Dyes monitor the entire PCR product, while probes focus on a specific locus within the amplicon. Advances in amplicon melting include high resolution instruments, saturating DNA dyes that better reveal multiple products, prediction programs for domain melting, barcode taxonomic identification, high speed microfluidic melting, and highly parallel digital melting. Most single base variants and small insertions or deletions can be genotyped by high resolution amplicon melting. High resolution melting also enables heterozygote scanning for any variant within a PCR product. A web application (uMelt, http://www.dna-utah.org) predicts amplicon melting curves with multiple domains, a useful tool for verifying intended products. Additional applications include methylation assessment, copy number determination and verification of sequence identity. When amplicon melting does not provide sufficient detail, unlabeled probes or snapback primers can be used instead of covalently labeled probes. DNA melting is a simple, inexpensive, and powerful tool with many research applications that is beginning to make its mark in clinical diagnostics.},
}
@article {pmid38489348,
year = {2024},
author = {Razo-Mejia, M and Mani, M and Petrov, D},
title = {Bayesian inference of relative fitness on high-throughput pooled competition assays.},
journal = {PLoS computational biology},
volume = {20},
number = {3},
pages = {e1011937},
pmid = {38489348},
issn = {1553-7358},
support = {R01 CA230025/CA/NCI NIH HHS/United States ; R01 CA263715/CA/NCI NIH HHS/United States ; R35 GM118165/GM/NIGMS NIH HHS/United States ; U01 AG077922/AG/NIA NIH HHS/United States ; },
mesh = {Bayes Theorem ; Sequence Analysis, DNA ; *Software ; *High-Throughput Screening Assays ; Gene Library ; },
abstract = {The tracking of lineage frequencies via DNA barcode sequencing enables the quantification of microbial fitness. However, experimental noise coming from biotic and abiotic sources complicates the computation of a reliable inference. We present a Bayesian pipeline to infer relative microbial fitness from high-throughput lineage tracking assays. Our model accounts for multiple sources of noise and propagates uncertainties throughout all parameters in a systematic way. Furthermore, using modern variational inference methods based on automatic differentiation, we are able to scale the inference to a large number of unique barcodes. We extend this core model to analyze multi-environment assays, replicate experiments, and barcodes linked to genotypes. On simulations, our method recovers known parameters within posterior credible intervals. This work provides a generalizable Bayesian framework to analyze lineage tracking experiments. The accompanying open-source software library enables the adoption of principled statistical methods in experimental evolution.},
}
@article {pmid38487668,
year = {2024},
author = {Hou, JW and Xu, Y and Hu, TH and Zhang, ZH and Wu, SY and Gong, P and He, ZQ},
title = {A new species of Svistella Gorochov, 1987 from Xizang, China (Orthoptera, Trigonidiidae, Trigonidiinae).},
journal = {ZooKeys},
volume = {1193},
number = {},
pages = {145-160},
pmid = {38487668},
issn = {1313-2989},
abstract = {The genus Svistella Gorochov, 1987 includes 10 species from Asia, with nine documented in China. In this study, a new species, Svistellayayun He, sp. nov., is described from Xizang, China. Morphologically, it resembles S.rufonotata (Chopard, 1932) but can be distinguished by a smaller inner tympanum, dark-brown setae on the 5[th] segment of the maxillary palp, and a rounded apex on the ectoparamere. To validate our morphological inferences and support the description of S.yayunsp. nov. as a new species, we performed a PCA based on bioacoustics parameters and molecular analysis. All Svistella species documented in China are distinguished by integrating their songs and DNA barcoding.},
}
@article {pmid38485107,
year = {2024},
author = {Heine, HLA and Derkarabetian, S and Morisawa, R and Fu, PA and Moyes, NHW and Boyer, SL},
title = {Machine learning approaches delimit cryptic taxa in a previously intractable species complex.},
journal = {Molecular phylogenetics and evolution},
volume = {195},
number = {},
pages = {108061},
doi = {10.1016/j.ympev.2024.108061},
pmid = {38485107},
issn = {1095-9513},
mesh = {Animals ; Phylogeny ; *Arachnida ; Machine Learning ; *Spiders ; New Zealand ; },
abstract = {Cryptic species are not diagnosable via morphological criteria, but can be detected through analysis of DNA sequences. A number of methods have been developed for identifying species based on genetic data; however, these methods are prone to over-splitting taxa with extreme population structure, such as dispersal-limited organisms. Machine learning methodologies have the potential to overcome this challenge. Here, we apply such approaches, using a large dataset generated through hybrid target enrichment of ultraconserved elements (UCEs). Our study taxon is the Aoraki denticulata species complex, a lineage of extremely low-dispersal arachnids endemic to the South Island of Aotearoa New Zealand. This group of mite harvesters has been the subject of previous species delimitation studies using smaller datasets generated through Sanger sequencing and analytical approaches that rely on multispecies coalescent models and barcoding gap discovery. Those analyses yielded a number of putative cryptic species that seems unrealistic and extreme, based on what we know about species' geographic ranges and genetic diversity in non-cryptic mite harvesters. We find that machine learning approaches, on the other hand, identify cryptic species with geographic ranges that are similar to those seen in other morphologically diagnosable mite harvesters in Aotearoa New Zealand's South Island. We performed both unsupervised and supervised machine learning analyses, the latter with training data drawn either from animals broadly (vagile and non-vagile) or from a custom training dataset from dispersal-limited harvesters. We conclude that applying machine learning approaches to the analysis of UCE-derived genetic data is an effective method for delimiting species in complexes of low-vagility cryptic species, and that the incorporation of training data from biologically relevant analogues can be critically informative.},
}
@article {pmid38484921,
year = {2024},
author = {Martin, C and Evrard, B and Percevault, F and Ryder, K and Darde, T and Lardenois, A and Zhadobov, M and Sauleau, R and Chalmel, F and Le Dréan, Y and Habauzit, D},
title = {Transcriptional landscape of human keratinocyte models exposed to 60-GHz millimeter-waves.},
journal = {Toxicology in vitro : an international journal published in association with BIBRA},
volume = {97},
number = {},
pages = {105808},
doi = {10.1016/j.tiv.2024.105808},
pmid = {38484921},
issn = {1879-3177},
mesh = {Humans ; *Keratinocytes/metabolism ; Cell Line ; },
abstract = {The use of millimeter waves (MMW) will exponentially grow in the coming years due to their future utilization in 5G/6G networks. The question of possible biological effects at these frequencies has been raised. In this present study, we aimed to investigate gene expression changes under exposure to MMW using the Bulk RNA Barcoding and sequencing (BRB-seq) technology. To address this issue, three exposure scenarios were performed aiming at: i) comparing the cellular response of two primary culture of keratinocytes (HEK and NHEK) and one keratinocyte derivate cell line (HaCaT) exposed to MMW; ii) exploring the incident power density dose-effect on gene expression in HaCaT cell line; and, iii) studying the exposure duration at the new ICNIRP exposure limit for the general population. With the exception of heat effect induced by high power MMW (over 10 mW/cm[2]), those exposure scenarios have not enabled us to demonstrate important gene expression changes in the different cell populations studied. Very few differentially genes were observed between MMW exposed samples and heat shock control, and most of them were significantly associated with heat shock response that may reflect small differences in the heat generation. Together these results show that acute exposure to MMW has no effects on the transcriptional landscape of human keratinocyte models under athermal conditions.},
}
@article {pmid38484189,
year = {2024},
author = {Vo, DN and Yuan, O and Kanaya, M and Telliam-Dushime, G and Li, H and Kotova, O and Caglar, E and Honnens de Lichtenberg, K and Rahman, SH and Soneji, S and Scheding, S and Bryder, D and Malmberg, KJ and Sitnicka, E},
title = {A temporal developmental map separates human NK cells from noncytotoxic ILCs through clonal and single-cell analysis.},
journal = {Blood advances},
volume = {8},
number = {11},
pages = {2933-2951},
pmid = {38484189},
issn = {2473-9537},
mesh = {Humans ; *Killer Cells, Natural/immunology/metabolism ; *Single-Cell Analysis/methods ; Cell Lineage ; Immunity, Innate ; Cell Differentiation ; },
abstract = {Natural killer (NK) cells represent the cytotoxic member within the innate lymphoid cell (ILC) family that are important against viral infections and cancer. Although the NK cell emergence from hematopoietic stem and progenitor cells through multiple intermediate stages and the underlying regulatory gene network has been extensively studied in mice, this process is not well characterized in humans. Here, using a temporal in vitro model to reconstruct the developmental trajectory of NK lineage, we identified an ILC-restricted oligopotent stage 3a CD34-CD117+CD161+CD45RA+CD56- progenitor population, that exclusively gave rise to CD56-expressing ILCs in vitro. We also further investigated a previously nonappreciated heterogeneity within the CD56+CD94-NKp44+ subset, phenotypically equivalent to stage 3b population containing both group-1 ILC and RORγt+ ILC3 cells, that could be further separated based on their differential expression of DNAM-1 and CD161 receptors. We confirmed that DNAM-1hi S3b and CD161hiCD117hi ILC3 populations distinctively differed in their expression of effector molecules, cytokine secretion, and cytotoxic activity. Furthermore, analysis of lineage output using DNA-barcode tracing across these stages supported a close developmental relationship between S3b-NK and S4-NK (CD56+CD94+) cells, whereas distant to the ILC3 subset. Cross-referencing gene signatures of culture-derived NK cells and other noncytotoxic ILCs with publicly available data sets validated that these in vitro stages highly resemble transcriptional profiles of respective in vivo ILC counterparts. Finally, by integrating RNA velocity and gene network analysis through single-cell regulatory network inference and clustering we unravel a network of coordinated and highly dynamic regulons driving the cytotoxic NK cell program, as a guide map for future studies on NK cell regulation.},
}
@article {pmid38481855,
year = {2024},
author = {Wood, TJ and Gaspar, H and Le Divelec, R and Penado, A and Silva, TL and Mata, VA and Veríssimo, J and Michez, D and Castro, S and Loureiro, J and Beja, P and Ferreira, S},
title = {The InBIO Barcoding Initiative Database: DNA barcodes of Iberian Bees.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e117172},
pmid = {38481855},
issn = {1314-2828},
abstract = {BACKGROUND: Bees are important actors in terrestrial ecosystems and are recognised for their prominent role as pollinators. In the Iberian Peninsula, approximately 1,100 bee species are known, with nearly 100 of these species being endemic to the Peninsula. A reference collection of DNA barcodes, based on morphologically identified bee specimens, representing 514 Iberian species, was constructed. The "InBIO Barcoding Initiative Database: DNA Barcodes of Iberian bees" dataset contains records of 1,059 sequenced specimens. The species of this dataset correspond to about 47% of Iberian bee species diversity and 21% of endemic species diversity. For peninsular Portugal only, the corresponding coverage is 71% and 50%. Specimens were collected between 2014 and 2022 and are deposited in the research collection of Thomas Wood (Naturalis Biodiversity Center, The Netherlands), in the FLOWer Lab collection at the University of Coimbra (Portugal), in the Andreia Penado collection at the Natural History and Science Museum of the University of Porto (MHNC-UP) (Portugal) and in the InBIO Barcoding Initiative (IBI) reference collection (Vairão, Portugal).<br><br>NEW INFORMATION: Of the 514 species sequenced, 75 species from five different families are new additions to the Barcode of Life Data System (BOLD) and 112 new BINs were added. Whilst the majority of species were assigned to a single BIN (94.9%), 27 nominal species were assigned to multiple BINs. Although the placement into multiple BINs may simply reflect genetic diversity and variation, it likely also represents currently unrecognised species-level diversity across diverse taxa, such as Amegillaalbigena Lepeletier, 1841, Andrenarussula Lepeletier, 1841, Lasioglossumleucozonium (Schrank, 1781), Nomadafemoralis Morawitz, 1869 and Sphecodesalternatus Smith, 1853. Further species pairs of Colletes, Hylaeus and Nomada were placed into the same BINs, emphasising the need for integrative taxonomy within Iberia and across the Mediterranean Basin more broadly. These data substantially contribute to our understanding of bee genetic diversity and DNA barcodes in Iberia and provide an important baseline for ongoing taxonomic revisions in the West Palaearctic biogeographical region.},
}
@article {pmid38481352,
year = {2024},
author = {Schols, R and Smitz, N and Vanderheyden, A and Huyse, T},
title = {Expanding the swimmer's itch pool of the Benelux: a first record of the neurotropic Trichobilharzia regenti and potential link to human infection.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {126},
pmid = {38481352},
issn = {1756-3305},
support = {B2/191/P1/MicroResist//Belgische Federale Overheidsdiensten/ ; BOPCO//Belgische Federale Overheidsdiensten/ ; BOPCO//Belgische Federale Overheidsdiensten/ ; },
mesh = {Animals ; Humans ; *Trematode Infections/parasitology ; *Schistosomiasis/epidemiology ; *Schistosomatidae/genetics ; *Dermatitis/parasitology ; Zoonoses ; *Skin Diseases, Parasitic/epidemiology ; Snails/parasitology ; Birds/parasitology ; Mammals ; },
abstract = {BACKGROUND: Swimmer's itch, an allergic contact dermatitis caused by avian and mammalian blood flukes, is a parasitic infection affecting people worldwide. In particular, avian blood flukes of the genus Trichobilharzia are infamous for their role in swimmer's itch cases. These parasites infect waterfowl as a final host, but incidental infections by cercariae in humans are frequently reported. Upon accidental infections of humans, parasite larvae will be recognized by the immune system and destroyed, leading to painful itchy skin lesions. However, one species, Trichobilharzia regenti, can escape this response in experimental animals and reach the spinal cord, causing neuroinflammation. In the last few decades, there has been an increase in case reports across Europe, making it an emerging zoonosis.<br><br>METHODS: Following a reported case of swimmer's itch in Kampenhout in 2022 (Belgium), the transmission site consisting of a private pond and an adjacent creek was investigated through a malacological and parasitological survey.<br><br>RESULTS: Six snail species were collected, including the widespread Ampullaceana balthica, a well-known intermediate host for Trichobilharzia parasites. Shedding experiments followed by DNA barcoding revealed a single snail specimen to be infected with T. regenti, a new species record for Belgium and by extension the Benelux. Moreover, it is the most compelling case to date of the link between this neurotropic parasite and cercarial dermatitis. Additionally, an Echinostomatidae sp. and Notocotylus sp. were isolated from two other specimens of A.&#xa0;balthica. However, the lack of reference DNA sequences for these groups in the online repositories prevented genus- and species-level identification, respectively.<br><br>CONCLUSIONS: The presence of T.&#xa0;regenti in Belgium might have severe clinical implications and its finding highlights the need for increased vigilance and diagnostic awareness among medical professionals. The lack of species-level identification of the other two parasite species showcases the barcoding void for trematodes. Overall, these findings demonstrate the need for a Belgian framework to rapidly detect and monitor zoonotic outbreaks of trematode parasites within the One Health context.},
}
@article {pmid38480448,
year = {2024},
author = {Watung, JF and Tairas, RW and Kaligis, JB and Darmawan, D and Suwito, A and Narakusumo, RP and Encilia, E and Dwibadra, D and Dharmayanthi, AB and Sutrisno, H},
title = {A new endemic clove tree pest of Cryptophasa Lewin, from Sangihe Island, Indonesia (Lepidoptera: Xyloryctidae).},
journal = {Zootaxa},
volume = {5403},
number = {1},
pages = {141-150},
doi = {10.11646/zootaxa.5403.1.10},
pmid = {38480448},
issn = {1175-5334},
mesh = {Male ; Female ; Animals ; *Lepidoptera ; Indonesia ; *Syzygium ; Trees ; Australia ; Animal Distribution ; *Moths ; Genitalia ; },
abstract = {A novel endemic pest of clove tree, Cryptophasa warouwi sp. nov., has been discovered on Sangihe Island. This new species can be distinguished from its closest relative species, C. watungi Sutrisno &amp; Suwito, 2015 which is found in North Sulawesi, by its dark brown straw-coloured wings in both males and females. The most distinctive diagnostic characters of this new species are observed in its genitalia structure: a bent-downward uncus with a strongly sclerotized finger-shaped apex, a bent phallus gradually widened towards coecum, and a double, membranous corpus bursae branching off at mid-ductus corpus bursae of female genitalia. Additionally, DNA barcodes revealed this new species to be embedded among Australian Cryptophasa species despite having fasciculated male antennae that have been considered diagnostic of the genus Paralecta. This suggests that the male antennae may not be a reliable character for separating Cryptophasa from Paralecta. A more comprehensive study including all Cryptophasa and Paralecta will be required to elucidate the definition of each genus. Images depicting both adults and genitalia are provided for this newly recognized species.},
}
@article {pmid38480431,
year = {2024},
author = {Sohn, JC and Shih, LC and Wu, S},
title = {Review of Microleon Butler, 1885 (Lepidoptera: Limacodidae) from Taiwan with description of a new species based on morphology and DNA barcoding.},
journal = {Zootaxa},
volume = {5403},
number = {3},
pages = {377-384},
doi = {10.11646/zootaxa.5403.3.7},
pmid = {38480431},
issn = {1175-5334},
mesh = {Male ; Animals ; *Lepidoptera/genetics ; Taiwan ; DNA Barcoding, Taxonomic ; Genitalia, Male ; DNA ; },
abstract = {The Taiwanese species of Microleon are reviewed with morphological and DNA data. Our review recognized two congeners, including a new species, M. taiwanensis n. sp. and one known species, M. longipalpis Butler, 1885. The findings from this study request a reconsideration of the previous records of Microleon from Taiwan. The minor differences in external appearance among the species of Microleon pose a challenge for reliable identification. Our study shows that examination of the male genitalia and COI barcoding helps distinguish the species. A checklist of the world species of Microleon with their distributional range is provided.},
}
@article {pmid38480372,
year = {2024},
author = {Selis, M and Cilia, G and Wood, TJ and Soon, V},
title = {Taxonomic revision of the Stenodynerus fastidiosissimus species-group in Western Europe and North Africa (Hymenoptera: Vespidae: Eumeninae).},
journal = {Zootaxa},
volume = {5418},
number = {1},
pages = {34-56},
doi = {10.11646/zootaxa.5418.1.2},
pmid = {38480372},
issn = {1175-5334},
mesh = {Animals ; *Hymenoptera/genetics ; *Wasps/genetics/anatomy &amp; histology ; Africa, Northern ; Europe ; Animal Distribution ; },
abstract = {The fastidiosissimus species-group of Stenodynerus de Saussure, 1863 is revised in Western Europe and North Africa, combining morphological data and DNA barcoding. Six species are recognized: S. difficilis (Morawitz, 1867) stat. resurr. (= S. fastidiosissimus auct.), S. fastidiosissimus (de Saussure, 1855), S. laborans (Costa, 1882) stat. resurr., S. montanus Selis, sp. nov., S. muelleri (Dusmet, 1917) (= Stenodynerus gusenleitneri Giordani Soika, 1986 syn. nov.), and S. rufescens Giordani Soika, 1977 stat. nov. Lectotypes are designated for Odynerus fastidiosissimus de Saussure, 1855 and Odynerus insularis Andr, 1883 non Smith, 1859. A key for the identification of members of this species-group is provided. DNA barcodes are published for every species, representing the first available sequences for the fastidiosissimus species-group.},
}
@article {pmid38480365,
year = {2024},
author = {Ordines, F and Ramrez-Amaro, S and Calero, B and Farriols, MT and Massut, E},
title = {A new species of the genus Ophiomyxa (Echinodermata: Ophiuroidea: Ophiomyxidae) from the Mallorca Channel seamounts in the western Mediterranean.},
journal = {Zootaxa},
volume = {5418},
number = {2},
pages = {159-171},
doi = {10.11646/zootaxa.5418.2.3},
pmid = {38480365},
issn = {1175-5334},
mesh = {Animals ; *Echinodermata ; *Ecosystem ; Biodiversity ; },
abstract = {A new species belonging to the ophiuroid genus Ophiomyxa is described from the Mallorca Channel seamount, in the western Mediterranean Sea. It can be distinguished from other Ophiomyxa species by the lack of interradial marginal plates, three arm spines, the presence of two thin, transparent and completely perforated dorsal arm plates on each arm segment, the separate heptagonal ventral arm plates, the disk integument full of transparent rounded scales with scattered perforated ossicles, and a characteristic coloration of the disk, which in the living specimen is brown with abundant scattered bright white spots. Molecular analyses based on cytochrome c Oxidase subunit I (DNA barcode) clearly support the assignment of the new species to Ophiomyxa. This discovery highlights the importance of the Mallorca Channel seamounts for the Mediterranean biodiversity conservation, as they seem to provide a suitable habitat for several invertebrate species, including recent descriptions of species and new Mediterranean records, which apparently have not established permanent populations along the closest continental margin.},
}
@article {pmid38480309,
year = {2024},
author = {Donworth, P and Wesener, T},
title = {The first record of the giant pill-millipede genus Prionobelum Verhoeff, 1924 from Thailand, with the integrative description of two species (Diplopoda, Sphaerotheriida, Zephroniidae).},
journal = {Zootaxa},
volume = {5419},
number = {4},
pages = {545-562},
doi = {10.11646/zootaxa.5419.4.4},
pmid = {38480309},
issn = {1175-5334},
mesh = {Animals ; Thailand ; *Arthropods/genetics ; Microscopy, Electron, Scanning ; },
abstract = {Thailand hosts a very rich but underexplored giant pill-millipede (Sphaerotheriida) fauna, with 11 of its 13 species described in the last three years. Currently, all known Thai giant pill-millipedes belong to the genera Zephronia Gray, 1832 (nine species) and Sphaerobelum Verhoeff, 1924 (four species). Here we describe the first two species of the genus Prionobelum Verhoeff, 1924 (previously restricted to Vietnam and China), Prionobelum inthanonense n. sp. and P. naevium n. sp. from Thailand. The species occur at Thailands highest mountain (2500 m) Doi Inthanon and the lowland rainforests at Bang Lang National Park touching the border with Malaysia. Both species are described integratively, utilizing light microscopy, scanning electron microscopy as well as DNA barcoding. Both new species of Prionobelum differ from other Zephroniidae species, as well as from one another, by more than 20% p-distance in the COI barcoding gene suggesting that potential closer related species are still awaiting discovery.},
}
@article {pmid38480291,
year = {2024},
author = {Tsvetkov, E and Trofimova, T},
title = {Description of two new species of the genus Repetekiodes Amsel, 1961 (Lepidoptera: Pyralidae: Phycitinae) from Central Asia with faunal notes on the genus.},
journal = {Zootaxa},
volume = {5424},
number = {2},
pages = {176-188},
doi = {10.11646/zootaxa.5424.2.2},
pmid = {38480291},
issn = {1175-5334},
mesh = {Animals ; *Lepidoptera ; Animal Distribution ; *Moths/genetics ; Asia, Central ; Genitalia ; *Songbirds ; },
abstract = {Two new species, Repetekiodes serratalis sp. nov. and Repetekiodes turanella sp. nov. are described from Central Asia. The described species are well distinguished from their congeners by the genitalia and forewing pattern. A brief overview of the genus Repetekiodes Amsel, 1961 is given and original data on the distribution of Repetekiodes species are provided. DNA barcode data are presented for several species of the genus.},
}
@article {pmid38480202,
year = {2024},
author = {Ruiz-Garca, A and Lara-Rodrguez, A and Garzn, A},
title = {Description of the full-grown larva and barcode of Athripsodes taounate taounate Dakki &amp; Malicky 1980 (Trichoptera: Leptoceridae), an Iberic-Maghrebian endemic.},
journal = {Zootaxa},
volume = {5415},
number = {2},
pages = {309-320},
doi = {10.11646/zootaxa.5415.2.5},
pmid = {38480202},
issn = {1175-5334},
mesh = {Animals ; *Holometabola ; *Insecta/anatomy &amp; histology ; Larva/anatomy &amp; histology ; Africa, Northern ; Mediterranean Region ; },
abstract = {In this paper we describe the main morphological characteristics that distinguish the full-grown larva of Athripsodes taounate taounate, an Iberic-Maghrebian endemic. The conspecificity of the larva and adult was confirmed by DNA analysis. Morphological features that discriminate it from the described Iberian-Maghrebian species of Athripsodes are given.},
}
@article {pmid38480182,
year = {2024},
author = {Makarchenko, EA and Semenchenko, AA and Palatov, DM},
title = {Smittia solominae sp. nov. (Diptera: Chironomidae: Orthocladiinae), living on ice of high mountain glaciers of the Elbrus Region (North Caucasus).},
journal = {Zootaxa},
volume = {5415},
number = {4},
pages = {561-569},
doi = {10.11646/zootaxa.5415.4.5},
pmid = {38480182},
issn = {1175-5334},
mesh = {Male ; Animals ; *Diptera ; *Chironomidae/genetics ; Ice Cover ; Larva ; Pupa ; Altitude ; },
abstract = {Illustrated morphological description with a study of DNA barcoding and biology of adult male, pupa and larva of Smittia solominae sp. nov., living on the ice surface of glaciers at an altitude of about 3000 m above sea level in the Elbrus region of the North Caucasus is given. DNA barcoding provided support that the new species unique within genus Smittia. The average interspecific distances between S. solominae sp. nov. and other Smittia from BOLD above 12% that correspond to species level.},
}
@article {pmid38480169,
year = {2024},
author = {Saito, N and Moritaki, T and Minakata, K and Wakabayashi, K},
title = {Three new species of sea star parasite Dendrogaster (Crustacea: Thecostraca) from Japan.},
journal = {Zootaxa},
volume = {5405},
number = {4},
pages = {577-590},
doi = {10.11646/zootaxa.5405.4.6},
pmid = {38480169},
issn = {1175-5334},
mesh = {Animals ; *Starfish ; *Parasites ; Japan ; Crustacea ; },
abstract = {Three new species of ascothoracidan crustaceans, Dendrogaster danni sp. nov., Dendrogaster tanabensis sp. nov., and Dendrogaster jinshomaruae sp. nov. are described from the sea around the Kii Peninsula on the Pacific coast of central Japan. They are found in the coelomic cavities of the sea stars, Neoferdina japonica Oguro &amp; Misaki, 1986., Henricia sp., and Coronaster volsellatus (Sladen, 1889), respectively. Morphological examinations and DNA barcoding analyses of these new species are reported in this study. The emergence of Dendrogaster from their host sea stars is also noted. These findings represent the 11th to 13th species of Dendrogaster that infest Japanese sea stars.},
}
@article {pmid38478046,
year = {2024},
author = {Klesser, R and Blick, T and Fritze, MA and Marten, A and Hemauer, M and Kastner, L and Höfer, H and Jäger, G and Husemann, M},
title = {Ice cage: new records and cryptic, isolated lineages in wingless snow flies (Diptera, Limoniidae: Chionea spp.) in German lower mountain ranges.},
journal = {Die Naturwissenschaften},
volume = {111},
number = {2},
pages = {15},
pmid = {38478046},
issn = {1432-1904},
mesh = {Male ; Animals ; Phylogeny ; *Diptera/genetics ; Ice ; Genetic Variation ; Snow ; },
abstract = {In Earth's history warm and cold periods have alternated. Especially, during the Pleistocene, the alternation between these different climatic conditions has led to frequent range expansions and retractions of many species: while thermophilic species dispersed during warm periods, cold adapted species retracted to cold refugia and vice versa. After the last Pleistocene cycle many cold adapted taxa found refuges in relict habitats in mountain ranges. One example for such a cold adapted relict is the flightless snow fly Chionea araneoides (Dalman, 1816). It can be found in lower mountain ranges of Central Europe exclusively in stone runs and stony accumulations which provide cold microclimates. Imagines develop only in winter. They have strongly restricted ranges and hence experienced strong isolation predicting that local populations may show local adaptation and hence also genetic differentiation. We investigated this for several middle mountain ranges of Germany using the COI barcoding gene. Our analyses revealed two distinct lineages, one in the Bavarian Forest and a second one in all other more northern locations up to Scandinavia. These lineages likely go back to post-Pleistocene isolation and should be studied in more detail in the future, also to confirm the taxonomic status of both lineages. Further, we confirmed former records of the species for Germany and report new records for the federal states of Saxony, Lower Saxony, Saxony-Anhalt and Thuringia. Finally, we provide the first evidence of two types of males for the species, a small and a larger male type.},
}
@article {pmid38477062,
year = {2024},
author = {Baldó, F and De Carlos, A and Bañón, R},
title = {On the occurrence of a post-larval specimen of Brosme brosme (Gadiformes: Lotidae) on Porcupine Bank (west Ireland).},
journal = {Journal of fish biology},
volume = {104},
number = {6},
pages = {2086-2089},
doi = {10.1111/jfb.15724},
pmid = {38477062},
issn = {1095-8649},
support = {PORCUDEM-20233FMP001//European Maritime, Fisheries and Aquaculture Fund/ ; },
mesh = {Animals ; *Gadiformes/anatomy &amp; histology/genetics/classification ; DNA Barcoding, Taxonomic ; Ireland ; Ecosystem ; },
abstract = {The occurrence of a small specimen of Brosme brosme (Gadiformes: Lotidae) from the Porcupine Bank is reported. A single specimen with a total length of 73.2 mm was caught with bottom trawl at a depth of 322 m depth in 2017. The specimen was identified morphologically and confirmed by molecular taxonomy using DNA barcoding. Based on the size and ontogenetic characters found, the specimen was identified as a post-larval individual, and a pelagic habitat of the specimen seems more likely.},
}
@article {pmid38472358,
year = {2024},
author = {Ruggiero, MV and Buffoli, M and Wolf, KKE and D'Alelio, D and Di Tuccio, V and Lombardi, E and Manfellotto, F and Vitale, L and Margiotta, F and Sarno, D and John, U and Ferrante, MI and Montresor, M},
title = {Multiannual patterns of genetic structure and mating type ratios highlight the complex bloom dynamics of a marine planktonic diatom.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {6028},
pmid = {38472358},
issn = {2045-2322},
support = {Grant number 7978//Gordon and Betty Moore Foundation/ ; Grant number 7978//Gordon and Betty Moore Foundation/ ; Grant number 7978//Gordon and Betty Moore Foundation/ ; Grant number 7978//Gordon and Betty Moore Foundation/ ; Grant number 7978//Gordon and Betty Moore Foundation/ ; Grant number 7978//Gordon and Betty Moore Foundation/ ; Grant number 7978//Gordon and Betty Moore Foundation/ ; Grant number 7978//Gordon and Betty Moore Foundation/ ; LTER-MC program//Stazione Zoologica Anton Dohrn (SZN), Naples (Italy)/ ; LTER-MC program//Stazione Zoologica Anton Dohrn (SZN), Naples (Italy)/ ; LTER-MC program//Stazione Zoologica Anton Dohrn (SZN), Naples (Italy)/ ; LTER-MC program//Stazione Zoologica Anton Dohrn (SZN), Naples (Italy)/ ; LTER-MC program//Stazione Zoologica Anton Dohrn (SZN), Naples (Italy)/ ; LTER-MC program//Stazione Zoologica Anton Dohrn (SZN), Naples (Italy)/ ; LTER-MC program//Stazione Zoologica Anton Dohrn (SZN), Naples (Italy)/ ; LTER-MC program//Stazione Zoologica Anton Dohrn (SZN), Naples (Italy)/ ; LTER-MC program//Stazione Zoologica Anton Dohrn (SZN), Naples (Italy)/ ; },
mesh = {*Diatoms/genetics ; Plankton/genetics ; Reproduction/genetics ; Cell Communication ; Genetic Structures ; },
abstract = {Understanding the genetic structure of populations and the processes responsible for its spatial and temporal dynamics is vital for assessing species' adaptability and survival in changing environments. We investigate the genetic fingerprinting of blooming populations of the marine diatom Pseudo-nitzschia multistriata in the Gulf of Naples (Mediterranean Sea) from 2008 to 2020. Strains were genotyped using microsatellite fingerprinting and natural samples were also analysed with Microsatellite Pool-seq Barcoding based on Illumina sequencing of microsatellite loci. Both approaches revealed a clonal expansion event in 2013 and a more stable genetic structure during 2017-2020 compared to previous years. The identification of a mating type (MT) determination gene allowed to assign MT to strains isolated over the years. MTs were generally at equilibrium with two notable exceptions, including the clonal bloom of 2013. The populations exhibited linkage equilibrium in most blooms, indicating that sexual reproduction leads to genetic homogenization. Our findings show that P. multistriata blooms exhibit a dynamic genetic and demographic composition over time, most probably determined by deeper-layer cell inocula. Occasional clonal expansions and MT imbalances can potentially affect the persistence and ecological success of planktonic diatoms.},
}
@article {pmid38469542,
year = {2023},
author = {Tembrock, LR and Wilson, CR and Zink, FA and Timm, AE and Gilligan, TM and Konstantinov, AS and Tishechkin, AK},
title = {CO1 barcodes resolve an asymmetric biphyletic clade for Diabrotica undecimpunctata subspecies and provide nucleotide variants for differentiation from related lineages using real-time PCR.},
journal = {Frontiers in insect science},
volume = {3},
number = {},
pages = {1168586},
pmid = {38469542},
issn = {2673-8600},
abstract = {Diabrotica undecimpunctata is a multivoltine polyphagous beetle species that has long been documented as a significant agricultural pest throughout its native range in North America. This beetle can vector bacterial and viral plant pathogens that result in major losses to crops such as cucumber and soybean. Many countries outside the Americas treat D. undecimpunctata as a species of quarantine importance, while in the USA only the subspecies D. u. duodecimnotata is subject to quarantine, to prevent introduction from Mexico. Identification of D. undecimpunctata on the basis of morphology alone can be complicated given the use of conflicting characters in the description of some subspecific taxa. To better understand relationships among D. undecimpunctata subspecies and other related species, we sequenced mitochondrial cytochrome oxidase 1 (CO1) and nuclear internal transcribed spacer 2 (ITS2) DNA from individuals in different subspecific taxa and across different parts of the species range using museum samples and interceptions. When our data were combined with publicly available Diabrotica data, no pattern of divergence consistent with the currently recognized subspecific designations was found. In addition, we compared phylogenetic patterns in CO1 data from the congener D. virgifera to demonstrate the utility of mitochondrial data in resolving subspecies. From the CO1 data, a diagnostic real-time PCR assay was developed that could successfully identify all haplotypes within the large D. undecimpunctata clade for use in surveys and identification at ports of entry. These findings underscore the need to resolve molecular and morphological datasets into cogent, lineage-based groupings. Such efforts will provide an evolutionary context for the study of agriculturally important attributes of Diabrotica such as host preferences, xenobiotic metabolism, and natural and anthropogenic patterns of dispersal.},
}
@article {pmid38469226,
year = {2024},
author = {Leontyev, D and Yatsiuk, I},
title = {Dataset of barcoded Reticulariaceae: ten years of DNA sequencing.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e115630},
pmid = {38469226},
issn = {1314-2828},
abstract = {BACKGROUND: As a result of the ten years (2012-2022) work under the critical revision of the genera of Reticulariaceae, a set of papers was published. Collection data of hundreds of specimens, used as a material for these studies, were provided as supplements of corresponding papers, but remained unpublished in biodiversity databases.<br><br>NEW INFORMATION: Here, we represent an occurrence dataset "Barcoded Reticulariaceae of the World", published in GBIF. It includes data on 523 myxomycete collections (including 36 types) gathered from five continents and spanning 24 countries. The dataset encompasses 43 distinct species and one subspecies of myxomycetes, including rare, endemic, and recently-described taxa. Species included to the database mainly belong to the genera Alwisia, Lycogala, Reticularia, Siphoptychium, Thecotubifera and Tubifera (Reticulariaceae), but as well Lindbladia and Licaethalium (Cribrariaceae). Nearly all of the research material, with the exception of several old collections, underwent molecular barcoding, primarily involving the 18S rDNA gene, but also the elongation factor 1&#x3b1; gene and mitochondrial cytochrome oxidase subunit I gene. For those sequences that are stored in the NCBI GenBank, accession numbers are provided in the dataset. Newly-described species make up a significant part of the studied herbarium collections; many of them can be characterised as common for their region. A particularly high level of taxonomic novelty is observed in Australia, which may be explained by the endemism of the local myxomycete biota.},
}
@article {pmid38469225,
year = {2024},
author = {McMullin, RT and Simon, ADF and Brodo, IM and Wickham, SB and Bell-Doyon, P and Kuzmina, M and Starzomski, BM},
title = {DNA barcoding aids in generating a preliminary checklist of the lichens and allied fungi of Calvert Island, British Columbia: Results from the 2018 Hakai Terrestrial BioBlitz.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e120292},
pmid = {38469225},
issn = {1314-2828},
abstract = {BACKGROUND: Bioblitzes are a tool for the rapid appraisal of biodiversity and are particularly useful in remote and understudied regions and for understudied taxa. Lichens are an example of an often overlooked group, despite being widespread in virtually all terrestrial ecosystems and having many important ecological functions.<br><br>NEW INFORMATION: We report the lichens and allied fungi collected during the 2018 terrestrial bioblitz conducted on Calvert Island on the Central Coast of British Columbia, Canada. We identified 449 specimens belonging to 189 species in 85 genera, increasing the total number of species known from Calvert Island to 194, and generated Internal Transcribed Spacer (ITS) sequences for 215 specimens from 121 species. Bryoriafurcellata, Chaenothecopsislecanactidis and C.nigripunctata were collected for the first time in British Columbia. We also found Pseudocyphellariarainierensis, which is listed as Special Concern on the federal Species at Risk Act, and other rarely reported species in British Columbia including Opegraphasphaerophoricola, Protomicarealimosa, Raesaeneniahuuskonenii and Sareadifformis. We demonstrate that DNA barcoding improves the scope and accuracy of expert-led bioblitzes by facilitating the detection of cryptic species and allowing for consistent identification of chemically and morphologically overlapping taxa. Despite the spatial and temporal limitations of our study, the results highlight the value of intact forest ecosystems on the Central Coast of British Columbia for lichen biodiversity, education and conservation.},
}
@article {pmid38468197,
year = {2024},
author = {Jiang, Y and Yang, J and Folk, RA and Zhao, J and Liu, J and He, Z and Peng, H and Yang, S and Xiang, C and Yu, X},
title = {Species delimitation of tea plants (Camellia sect. Thea) based on super-barcodes.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {181},
pmid = {38468197},
issn = {1471-2229},
mesh = {Humans ; *Camellia ; DNA Barcoding, Taxonomic/methods ; *Camellia sinensis/genetics ; Tea/genetics ; DNA ; Phylogeny ; },
abstract = {BACKGROUND: The era of high throughput sequencing offers new paths to identifying species boundaries that are complementary to traditional morphology-based delimitations. De novo species delimitation using traditional or DNA super-barcodes serve as efficient approaches to recognizing putative species (molecular operational taxonomic units, MOTUs). Tea plants (Camellia sect. Thea) form a group of morphologically similar species with significant economic value, providing the raw material for tea, which is the most popular nonalcoholic caffeine-containing beverage in the world. Taxonomic challenges have arisen from vague species boundaries in this group.<br><br>RESULTS: Based on the most comprehensive sampling of C. sect. Thea by far (165 individuals of 39 morphospecies), we applied three de novo species delimitation methods (ASAP, PTP, and mPTP) using plastome data to provide an independent evaluation of morphology-based species boundaries in tea plants. Comparing MOTU partitions with morphospecies, we particularly tested the congruence of MOTUs resulting from different methods. We recognized 28 consensus MOTUs within C. sect. Thea, while tentatively suggesting that 11 morphospecies be discarded. Ten of the 28 consensus MOTUs were uncovered as morphospecies complexes in need of further study integrating other evidence. Our results also showed a strong imbalance among the analyzed MOTUs in terms of the number of molecular diagnostic characters.<br><br>CONCLUSION: This study serves as a solid step forward for recognizing the underlying species boundaries of tea plants, providing a needed evidence-based framework for the utilization and conservation of this economically important plant group.},
}
@article {pmid38468096,
year = {2024},
author = {Feng, H and Zhou, Y and Zhang, C},
title = {Encoding Genetic Circuits with DNA Barcodes Paves the Way for High-Throughput Profiling of Dose-Response Curves of Metabolite Biosensors.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2760},
number = {},
pages = {309-318},
pmid = {38468096},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic ; *Biosensing Techniques/methods ; Transcription Factors/metabolism ; Gene Regulatory Networks ; Saccharomyces cerevisiae/genetics/metabolism ; DNA/genetics/metabolism ; },
abstract = {Metabolite biosensors, through which the intracellular metabolite concentrations could be converted to changes in gene expression, are widely used in a variety of applications according to the different output signals. However, it remains challenging to fine-tune the dose-response relationships of biosensors to meet the needs of various scenarios. On the other hand, the short read length of next-generation sequencing (NGS) has greatly limited the design capability of sequence libraries. To address these issues, we describe a DNA trackable assembly method, coupled with fluorescence-activated cell sorting and NGS (Sort-Seq), to achieve the characterization of dose-response curves in a massively parallel manner. As a proof of the concept, we constructed a malonyl-CoA biosensor library containing 5184 combinations with six levels of transcription factor dosage, four different operator positions, and 216 possible upstream enhancer sequence (UAS) designs in Saccharomyces cerevisiae BY4700. By using Sort-Seq and machine learning approach, we obtained comprehensive dose-response relationships of the combinatorial sequence space. Therefore, our pipeline provides a platform for the design, tuning, and profiling of biosensor response curves and shows great potential to facilitate the rational design of genetic circuits.},
}
@article {pmid38466749,
year = {2024},
author = {Schattanek-Wiesmair, B and Huemer, P and Wieser, C and Stark, W and Hausmann, A and Koblmüller, S and Sefc, KM},
title = {A DNA barcode library of Austrian geometridae (Lepidoptera) reveals high potential for DNA-based species identification.},
journal = {PloS one},
volume = {19},
number = {3},
pages = {e0298025},
pmid = {38466749},
issn = {1932-6203},
mesh = {Animals ; *Lepidoptera/genetics ; DNA Barcoding, Taxonomic/methods ; Austria ; Ecosystem ; Biodiversity ; *Moths/genetics ; DNA ; },
abstract = {Situated in the Eastern section of the European Alps, Austria encompasses a great diversity of different habitat types, ranging from alpine to lowland Pannonian ecosystems, and a correspondingly high level of species diversity, some of which has been addressed in various DNA barcoding projects. Here, we report a DNA barcode library of all the 476 species of Geometridae (Lepidoptera) that have been recorded in Austria. As far as possible, species were sampled from different Austrian regions in order to capture intraspecific genetic variation. In total, 2500 DNA barcode sequences, representing 438 species, were generated in this study. For complete coverage of Austrian geometrid species in the subsequent analyses, the dataset was supplemented with DNA barcodes from specimens of non-Austrian origin. Species delimitations by ASAP, BIN and bPTP methods yielded 465, 510 and 948 molecular operational taxonomic units, respectively. Congruency of BIN and ASAP partitions with morphospecies assignments was reasonably high (85% of morphospecies in unique partitions), whereas bPTP appeared to overestimate the number of taxonomic units. The study furthermore identified taxonomically relevant cases of morphospecies splitting and sharing in the molecular partitions. We conclude that DNA barcoding and sequence analysis revealed a high potential for accurate DNA-based identification of the Austrian Geometridae species. Additionally, the study provides an updated checklist of the geometrid moths of Austria.},
}
@article {pmid38465701,
year = {2024},
author = {Dufresnes, C and Monod-Broca, B and Bellati, A and Canestrelli, D and Ambu, J and Wielstra, B and Dubey, S and Crochet, PA and Denoël, M and Jablonski, D},
title = {Piecing the barcoding puzzle of Palearctic water frogs (Pelophylax) sheds light on amphibian biogeography and global invasions.},
journal = {Global change biology},
volume = {30},
number = {3},
pages = {e17180},
doi = {10.1111/gcb.17180},
pmid = {38465701},
issn = {1365-2486},
support = {3211101356//National Natural Science Foundation of China/ ; T.0070.19//Fonds De La Recherche Scientifique-FNRS/ ; },
mesh = {Animals ; *Anura/genetics ; Europe ; Phylogeny ; Phylogeography ; *Ranidae ; },
abstract = {Palearctic water frogs (genus Pelophylax) are an outstanding model in ecology and evolution, being widespread, speciose, either threatened or threatening to other species through biological invasions, and capable of siring hybrid offspring that escape the rules of sexual reproduction. Despite half a century of genetic research and hundreds of publications, the diversity, systematics and biogeography of Pelophylax still remain highly confusing, in no small part due to a lack of correspondence between studies. To provide a comprehensive overview, we gathered >13,000 sequences of barcoding genes from >1700 native and introduced localities and built multigene mitochondrial (~17 kb) and nuclear (~10 kb) phylogenies. We mapped all currently recognized taxa and their phylogeographic lineages (>40) to get a grasp on taxonomic issues, cyto-nuclear discordances, the genetic makeup of hybridogenetic hybrids, and the origins of introduced populations. Competing hypotheses for the molecular calibration were evaluated through plausibility tests, implementing a new approach relying on predictions from the anuran speciation continuum. Based on our timetree, we propose a new biogeographic paradigm for the Palearctic since the Paleogene, notably by attributing a prominent role to the dynamics of the Paratethys, a vast paleo-sea that extended over most of Europe. Furthermore, our results show that distinct marsh frog lineages from Eastern Europe, the Balkans, the Near East, and Central Asia (P. ridibundus ssp.) are naturally capable of inducing hybridogenesis with pool frogs (P. lessonae). We identified 14 alien lineages (mostly of P. ridibundus) over ~20 areas of invasions, especially in Western Europe, with genetic signatures disproportionally pointing to the Balkans and Anatolia as the regions of origins, in line with exporting records of the frog leg industry and the stocks of pet sellers. Pelophylax thus emerges as one of the most invasive amphibians worldwide, and deserves much higher conservation concern than currently given by the authorities fighting biological invasions.},
}
@article {pmid38463243,
year = {2024},
author = {Maslennikov, O and Perc, M and Nekorkin, V},
title = {Topological features of spike trains in recurrent spiking neural networks that are trained to generate spatiotemporal patterns.},
journal = {Frontiers in computational neuroscience},
volume = {18},
number = {},
pages = {1363514},
pmid = {38463243},
issn = {1662-5188},
abstract = {In this study, we focus on training recurrent spiking neural networks to generate spatiotemporal patterns in the form of closed two-dimensional trajectories. Spike trains in the trained networks are examined in terms of their dissimilarity using the Victor-Purpura distance. We apply algebraic topology methods to the matrices obtained by rank-ordering the entries of the distance matrices, specifically calculating the persistence barcodes and Betti curves. By comparing the features of different types of output patterns, we uncover the complex relations between low-dimensional target signals and the underlying multidimensional spike trains.},
}
@article {pmid38462101,
year = {2024},
author = {Al-Qahtani, SD and Al-Senani, GM},
title = {Immobilization of rare-earth doped aluminate nanoparticles encapsulated with silica into polylactic acid-based color-tunable smart plastic window.},
journal = {International journal of biological macromolecules},
volume = {264},
number = {Pt 2},
pages = {130766},
doi = {10.1016/j.ijbiomac.2024.130766},
pmid = {38462101},
issn = {1879-0003},
mesh = {Silicon Dioxide ; *Metals, Rare Earth ; *Nanoparticles ; Polyesters ; Aluminum Oxide ; Aluminum ; },
abstract = {An inorganic/organic nanocomposite was used to develop an afterglow and color-tunable smart window. A combination of polylactic acid (PLA) plastic waste as an environmentally-friendly hosting agent, and lanthanide-activated strontium aluminum oxide nanoparticles (SAON) encapsulated with silica nanoparticles (SAON@Silica) as a photoluminescent efficient agent resulted in a smart organic/inorganic nanocomposite. In order to prepare SAON-encapsulated silica nanoparticles (SAON@Silica), the SAON nanoparticles were coated with silica using the heterogeneous precipitation method. By using transmission electron microscopy (TEM), SAON showed a diameter range of 5-12 nm, while the SAON@Silica nanoparticles showed a diameter range of 50-100 nm. In order to ensure the development of a colorless plastic film, a homogeneous dispersion of the phosphorescent Phosphor@Silica nanoparticles throughout the plastic bulk was confirmed. CIE Lab coordinates and luminescence spectra were used to study the color shift characteristics. Under visible light conditions, the plastic films were transparent. The photoluminescent films emitted green light at 525 nm when excited at 375 nm. The hydrophobicity and ultraviolet protection were enhanced without altering the fundamental physico-mechanical performance of the plastic sheet. The current color-tunable plastic can be used in many potential applications, such as warning signs, anti-counterfeiting barcodes, smart windows, and protective apparel.},
}
@article {pmid38462022,
year = {2024},
author = {Tuliebieke, T and Abdullah, and Zhang, H and Yan, R and Li, H and Zhang, Y and Zhang, T and Ahmed, I and Li, T and Tian, X},
title = {Exploring the biological diversity and source species of medicinal horseflies through metabarcoding.},
journal = {Gene},
volume = {913},
number = {},
pages = {148356},
doi = {10.1016/j.gene.2024.148356},
pmid = {38462022},
issn = {1879-0038},
mesh = {Humans ; Animals ; *Diptera/genetics ; Biodiversity ; China ; DNA Barcoding, Taxonomic ; },
abstract = {Horseflies from the Tabanidae family play a significant role in traditional Chinese medicine to treat various health conditions, including coronary heart disease, stroke, headaches, liver cirrhosis, psoriasis, and hepatic carcinoma. There are 27 species of Tabaninae (Tabanidae) used as medicine, and they showed high morphological similarities with those for which medicinal properties have not been reported. Nonetheless, there have been reports suggesting that medicinal crude drugs sometimes contain irrelevant or false species, impacting the drug's efficacy. In this current study, we collected 14 batches, totaling 13,528 individuals, from various provinces in China. Instead of "classic" DNA barcoding strategy, we employed a high-throughput metabarcoding approach to assess the biological composition of crude drug mixtures derived from horseflies. Our analysis identified 40 Amplicon Sequence Variants (ASVs) with similarity percentages ranging from 92% to 100% with 12 previously reported species. Species delimitation methods revealed the presence of 11 Molecular Operational Taxonomic Units (MOTUs), with ten belonging to the Tabanus genus and one to Hybomitra. Tabanus sp6 displayed the highest relative abundance, and its ASVs showed close resemblance to Tabanus pleski. Our investigations revealed that the medicinal batches were biologically composed of 6 to 12 species. Some batches contained ASVs that closely resembled species previously associated with false Tabanus species. In conclusion, our findings offer valuable insights into the biological composition of crude drugs derived from horseflies and have the potential to enhance the quality of these traditional medicines.},
}
@article {pmid38460806,
year = {2024},
author = {Yuan, L and Ni, Y and Chen, H and Li, J and Lu, Q and Wang, L and Zhang, X and Yue, J and Yang, H and Liu, C},
title = {Comparative chloroplast genomes study of five officinal Ardisia Species: Unraveling interspecific diversity and evolutionary insights in Ardisia.},
journal = {Gene},
volume = {912},
number = {},
pages = {148349},
doi = {10.1016/j.gene.2024.148349},
pmid = {38460806},
issn = {1879-0038},
mesh = {*Ardisia ; *Genome, Chloroplast ; Phylogeny ; China ; Plant Leaves ; },
abstract = {Ardisia S.W. (Primulaceae), naturally distributed in tropical and subtropical regions, has edible and medicinal values and is prevalent in clinical and daily use in China. More genetic information for distinct species delineation is needed to support the development and utilization of the genus Ardisia. We sequenced, annotated, and compared the chloroplast genomes of five Ardisia species: A. brunnescens, A. pusilla, A. squamulosa, A. crenata, and A. brevicaulis in this study. We found a typical quadripartite structure in all five chloroplast genomes, with lengths ranging from 155,045 to 156,943 bp. Except for A. pusilla, which lacked the ycf15 gene, the other four Ardisia species contained 114 unique genes, including 79 protein-coding genes, 30 tRNAs, and four rRNAs. In addition, the rps19 pseudogene gene was present only in A. brunnescens. Five highly variable DNA barcodes were identified for five Ardisia species, including trnT-GGU-psbD, trnT-UGU-trnL-UAA, rps4-trnT-UGU, rpl32-trnL-UAG, and rpoB-trnC-GAA. The RNA editiing sites of protein-coding genes in the five Ardisia plastome were characterized and compared, and 274 (A. crenata)-288 (A. brevicaulis) were found. The results of the phylogenetic analysis were consistent with the morphological classification. Sequence alignment and phylogenetic analysis showed that ycf15 genes were highly divergent in Primulaceae. Reconstructions of ancestral character states indicated that leaf margin morphology is critical for classifying the genus Ardisia, with a rodent-like character being the most primitive. These results provide valuable information on the taxonomy and evolution of Ardisia plants.},
}
@article {pmid38460210,
year = {2024},
author = {Tang, M and Zhu, KJ and Sun, W and Yuan, X and Wang, Z and Zhang, R and Ai, Z and Liu, K},
title = {Ultrasimple size encoded microfluidic chip for rapid simultaneous multiplex detection of DNA sequences.},
journal = {Biosensors &amp; bioelectronics},
volume = {253},
number = {},
pages = {116172},
doi = {10.1016/j.bios.2024.116172},
pmid = {38460210},
issn = {1873-4235},
mesh = {Microfluidics ; Base Sequence ; *Microfluidic Analytical Techniques/methods ; *Biosensing Techniques ; Oligonucleotide Array Sequence Analysis/methods ; },
abstract = {Simultaneous multiplexed analysis can provide comprehensive information for disease diagnosis. However, the current multiplex methods rely on sophisticated barcode technology, which hinders its wider application. In this study, an ultrasimple size encoding method is proposed for multiplex detection using a wedge-shaped microfluidic chip. Driving by negative pressure, microparticles are naturally arranged in distinct stripes based on their sizes within the chip. This size encoding method demonstrates a high level of precision, allowing for accuracy in distinguishing 3-5 sizes of microparticles with a remarkable accuracy rate of up to 99%, even the microparticles with a size difference as small as 0.5 μm. The entire size encoding process is completed in less than 5 min, making it ultrasimple, reliable, and easy to operate. To evaluate the function of this size encoding microfluidic chip, three commonly co-infectious viruses' nucleic acid sequences (including complementary DNA sequences of HIV and HCV, and DNA sequence of HBV) are employed for multiplex detection. Results indicate that all three DNA sequences can be sensitively detected without any cross-interference. This size-encoding microfluidic chip-based multiplex detection method is simple, rapid, and high-resolution, its successful application in serum samples renders it highly promising for potential clinical promotion.},
}
@article {pmid38457426,
year = {2024},
author = {Escobar Camacho, D and Barragán, KS and Guayasamin, JM and Gavilanes, G and Encalada, AC},
title = {New records of native and introduced fish species in a river basin of Western Ecuador, the Chocó-Darien Ecoregion, using DNA barcoding.},
journal = {PloS one},
volume = {19},
number = {3},
pages = {e0298970},
pmid = {38457426},
issn = {1932-6203},
mesh = {Humans ; Animals ; *Rivers ; Introduced Species ; DNA Barcoding, Taxonomic/methods ; Phylogeny ; Ecuador ; Electron Transport Complex IV/genetics ; Fishes ; DNA/genetics ; *Catfishes/genetics ; Biodiversity ; },
abstract = {DNA barcoding, based on mitochondrial markers, is widely applied in species identification and biodiversity studies. The aim of this study was to establish a barcoding reference database of fishes inhabiting the Cube River from Western Ecuador in the Chocó-Darien Global Ecoregion (CGE), a threatened ecoregion with high diversity and endemism, and evaluate the applicability of using barcoding for the identification of fish species. Barcode sequences were obtained from seven orders, 17 families, 23 genera and 26 species, which were validated through phylogenetic analysis, morphological measurements, and literature review. Our results showed that 43% of fish species in this region are endemic, confirmed the presence of known species in the area, and included the addition of three new records of native (Hoplias microlepis, Rhamdia guatemalensis and Sicydium salvini) and an introduced species (Xiphophorus maculatus) to Ecuador. In addition, eight species were barcoded for the first time. Species identification based on barcoding and morphology showed discrepancy with species lists from previous studies in the CGE, suggesting that the current baseline of western fishes of Ecuador is still incomplete. Because this study analyzed fishes from a relatively small basin (165 km2), more molecular-based studies focusing on fish are needed to achieve a robust sequence reference library of species inhabiting Western Ecuador. The new sequences of this study will be useful for future comparisons and biodiversity monitoring, supporting the application of barcoding tools for studying fish diversity in genetically unexplored regions and to develop well-informed conservation programs.},
}
@article {pmid38457335,
year = {2024},
author = {Fernandes, DS and Horikoshi, RJ and Dourado, PM and Ovejero, RFL and Berger, GU and Savaris, M and Brown, JW and Corrêa, AS},
title = {Molecular characterization and demographic insights into soybean bud borer (Lepidoptera: Tortricidae) in Brazil.},
journal = {Journal of insect science (Online)},
volume = {24},
number = {2},
pages = {},
pmid = {38457335},
issn = {1536-2442},
support = {//Bayer Crop Science/ ; },
mesh = {Male ; Animals ; *Lepidoptera/genetics ; Brazil ; Glycine max/genetics ; *Moths/genetics ; Phylogeography ; Demography ; },
abstract = {The soybean bud borer, a soybean pest in Brazil, was initially identified as Crocidosema aporema (Walsingham 1914) (Lepidoptera: Tortricidae). Outbreaks of this species have recently increased, but identification of this pest remains uncertain, and the historical factors associated with its geographic distribution in Brazil are little known. Here, we conducted a species characterization and phylogeographic analysis based on molecular and morphological evidence. Ninety individuals of bud-borers Lepidoptera were collected in different regions of Brazil. We sequenced COI and COII mitochondrial genes and examined wing patterns and male genital morphology. DNA barcoding approach revealed that 10 individuals were Argyrotaenia sphaleropa (Meyrick 1909) (Lepidoptera: Tortricidae) and 80 were a species of the genus Crocidosema Zeller. The morphology of the adult genitalia and wings proved to be insufficient to confirm the identification of Brazilian individuals as C. aporema, a species originally described from a high-elevation site in Costa Rica. Furthermore, the genetic distance between putative C. aporema specimens from Brazil and Costa Rica (ranging from 5.2% to 6.4%) supports the hypothesis that the Brazilian specimens are not referable to C. aporema. Our analysis revealed a single genetic strain (i.e., species) with low genetic diversity on soybean crops. We found no indication that the genetic structure was related to geographic distance among populations or edaphoclimatic regions. The population expansion of the soybean bud borer coincides with the increase in the area of soybean production in Brazil, suggesting that expanded soybean farming has allowed a significant increase in the effective population size of this pest.},
}
@article {pmid38455575,
year = {2024},
author = {Wang, D and Wei, J and Yuan, X and Chen, Z and Wang, L and Geng, Y and Zhang, J and Wang, Y},
title = {Transcriptome and comparative chloroplast genome analysis of Taxus yunnanensis individuals with high and low paclitaxel yield.},
journal = {Heliyon},
volume = {10},
number = {5},
pages = {e27223},
pmid = {38455575},
issn = {2405-8440},
abstract = {Paclitaxel is a potent anti-cancer drug that is mainly produced through semi-synthesis, which still requires plant materials as precursors. The content of paclitaxel and 10-deacetyl baccatin III (10-DAB) in Taxus yunnanensis has been found to differ from that of other Taxus species, but there is little research on the mechanism underlying the variation in paclitaxel content in T. yunnanensis of different provenances. In this experiment, the contents of taxoids and precursors in twigs between a high paclitaxel-yielding individual (TG) and a low paclitaxel-yielding individual (TD) of T. yunnanensis were compared, and comparative analyses of transcriptomes as well as chloroplast genomes were performed. High-performance liquid chromatography (HPLC) detection showed that 10-DAB and baccatin III contents in TG were 18 and 47 times those in TD, respectively. Transcriptomic analysis results indicated that genes encoding key enzymes in the paclitaxel biosynthesis pathway, such as taxane 10-β-hydroxylase (T10βH), 10-deacetylbaccatin III 10-O-acetyltransferase (DBAT), and debenzoyl paclitaxel N-benzoyl transferase (DBTNBT), exhibited higher expression levels in TG. Additionally, qRT-PCR showed that the relative expression level of T10βH and DBAT in TG were 29 and 13 times those in TD, respectively. In addition, six putative transcription factors were identified that may be involved in paclitaxel biosynthesis from transcriptome data. Comparative analysis of plastid genomes showed that the TD chloroplast contained a duplicate of rps12, leading to a longer plastid genome length in TD relative to TG. Fifteen mutation hotspot regions were identified between the two plastid genomes that can serve as candidate DNA barcodes for identifying high-paclitaxel-yield individuals. This experiment provides insight into the difference in paclitaxel accumulation among different provenances of T. yunnanensis individuals.},
}
@article {pmid38452550,
year = {2024},
author = {Jankowska, K and Łukomska-Kowalczyk, M and Milanowski, R and Fells, A and Zakryś, B},
title = {Biodiversity of autotrophic euglenids based on the group specific DNA metabarcoding approach.},
journal = {Protist},
volume = {175},
number = {3},
pages = {126024},
doi = {10.1016/j.protis.2024.126024},
pmid = {38452550},
issn = {1618-0941},
mesh = {*DNA Barcoding, Taxonomic ; *Biodiversity ; *Euglenida/genetics/classification ; Poland ; RNA, Ribosomal, 18S/genetics ; Phylogeny ; DNA, Protozoan/genetics ; Autotrophic Processes ; DNA, Ribosomal/genetics ; },
abstract = {This study reports a comprehensive analysis of photoautotrophic euglenids' distribution and biodiversity in 16 small water bodies of various types (including fish ponds, field ponds, rural ponds and park ponds) located in three regions of Poland: Masovia, Masuria and Pomerania during a period of three years. By employing a euglenid specific barcode marker and a curated database of V2 18S rDNA sequences it was possible to identify 97.7 % of euglenid reads at species level. A total of 152 species classified in 13 genera were identified. The number of euglenid species found in one pond varied from 40 to 102. The most common species were Euglena agilis and Euglenaria caudata, found in every analysed waterbody. The highest number of observed species belonged to Trachelomonas and Phacus. Certain species exhibited a tendency to coexist, suggesting the presence of distinct species assemblages. Among them, the most distinctive cluster was associated with water bodies located in the Masuria region, characterized also by the greatest species richness, including many very rare species: Euglenaformis chlorophoenicea, Lepocinclis autumnalis, L. marssonii, Trachelomonas eurystoma, T. manschurica, T. mucosa, T. zuberi, T. zuberi var. nepos.},
}
@article {pmid38450097,
year = {2024},
author = {Abraham, JS and Somasundaram, S and Maurya, S and Sood, U and Lal, R and Toteja, R and Makhija, S},
title = {Insights into freshwater ciliate diversity through high throughput DNA metabarcoding.},
journal = {FEMS microbes},
volume = {5},
number = {},
pages = {xtae003},
pmid = {38450097},
issn = {2633-6685},
abstract = {The freshwater bodies of India are highly biodiverse but still understudied, especially concerning ciliates. Ciliates constitute a significant portion of eukaryotic diversity and play crucial roles in microbial loops, nutrient recycling, and ecosystem maintenance. The present study aimed to elucidate ciliate diversity in three freshwater sites in the Delhi region of India: Okhla Bird Sanctuary (OBS), Sanjay Lake (SL), and Raj Ghat pond (RJ). This study represents the first investigation into the taxonomic diversity and richness of freshwater ciliates in India using a high-throughput DNA metabarcoding approach. For the analysis, total environmental DNA was extracted from the three freshwater samples, followed by sequencing of the 18S V4 barcode region and subsequent phylogenetic analyses. Operational taxonomic units (OTU) analyses revealed maximum species diversity in OBS (106), followed by SL (104) and RJ (99) sites. Ciliates from the classes Oligohymenophorea, Prostomatea, and Spirotrichea were dominant in the three sites. The study discusses the ability of the metabarcoding approach to uncover unknown and rare species. The study highlights the need for refined reference databases and cautious interpretation of the high-throughput sequencing-generated data while emphasizing the complementary nature of molecular and morphological approaches in studying ciliate diversity.},
}
@article {pmid38443405,
year = {2024},
author = {Ho, CW and Chen, PY and Liao, YT and Cheng, YF and Tsou, HH and Liu, TY and Liang, KH},
title = {Uncovering the microbiome landscape in sashimi delicacies.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {5454},
pmid = {38443405},
issn = {2045-2322},
support = {V113E-002-4//Taipei Veterans General Hospital/ ; },
mesh = {Animals ; Phylogeny ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Salmon ; Tuna/genetics ; Seafood ; Photobacterium ; Pseudomonas ; },
abstract = {It is widely believed that a significant portion of the gut microbiota, which play crucial roles in overall health and disease, originates from the food we consume. Sashimi is a type of popular raw seafood cuisine. Its microbiome, however, remained to be thoroughly explored. The objective of this study is to explore the microbiome composition in sashimi at the time when it is served and ready to be eaten. Specifically, our tasks include investigating the diversity and characteristics of microbial profiles in sashimi with respect to the fish types. We utilized the Sanger-sequencing based DNA barcoding technology for fish species authentication and next-generation sequencing for sashimi microbiome profiling. We investigated the microbiome profiles of amberjack, cobia, salmon, tuna and tilapia sashimi, which were all identified using the MT-CO1 DNA sequences regardless of their menu offering names. Chao1 and Shannon indexes, as well as Bray-Curtis dissimilarity index were used to evaluate the alpha and beta diversities of sashimi microbiome. We successfully validated our previous observation that tilapia sashimi has a significantly higher proportions of Pseudomonas compared to other fish sashimi, using independent samples (P = 0.0010). Salmon sashimi exhibited a notably higher Chao1 index in its microbiome in contrast to other fish species (P = 0.0031), indicating a richer and more diverse microbial ecosystem. Non-Metric Multidimensional Scaling (NMDS) based on Bray-Curtis dissimilarity index revealed distinct clusters of microbiome profiles with respect to fish types. Microbiome similarity was notably observed between amberjack and tuna, as well as cobia and salmon. The relationship of microbiome similarity can be depicted as a tree which resembles partly the phylogenetic tree of host species, emphasizing the close relationship between host evolution and microbial composition. Moreover, salmon exhibited a pronounced relative abundance of the Photobacterium genus, significantly surpassing tuna (P = 0.0079), observed consistently across various restaurant sources. In conclusion, microbiome composition of Pseudomonas is significantly higher in tilapia sashimi than in other fish sashimi. Salmon sashimi has the highest diversity of microbiome among all fish sashimi that we analyzed. The level of Photobacterium is significantly higher in salmon than in tuna across all the restaurants we surveyed. These findings provide critical insights into the intricate relationship between the host evolution and the microbial composition. These discoveries deepen our understanding of sashimi microbiota, facilitating our decision in selecting raw seafood.},
}
@article {pmid38440750,
year = {2024},
author = {Sarlin, PJ and Morris, S and Geethambika, SB and Gopi, L and Muraleedharan, M and Thomas, JA and Savitha, G and Joseph, P},
title = {Halocercus lagenorhynchi infection in a stranded striped dolphin Stenella coeruleoalba (Meyen, 1833) on the Southwest coastline of India.},
journal = {Journal of parasitic diseases : official organ of the Indian Society for Parasitology},
volume = {48},
number = {1},
pages = {168-179},
pmid = {38440750},
issn = {0971-7196},
abstract = {Necropsy on a striped dolphin Stenella coeruleoalba (Meyen, 1833) entangled in ghost fishing net and dead while rescuing yielded some helminth parasites, later identified as Halocercus lagenorhynchi. DNA barcoding of the host and parasite and the phylogenetic analysis of the parasite was conducted. This study provides valuable information towards establishing basal data of marine mammal parasite diversity and distribution in the Indian waters. We believe this is the first report of the occurrence of Halocercus lagenorhynchi in marine mammals in India.},
}
@article {pmid38438232,
year = {2024},
author = {Xiao, X and Lin, X and Ting, CL and Huang, X and Zeng, B and Liu, T and Zeng, T},
title = {Extraction-free, immuno-RPA-CRISPR/Cas13a-based one-pot detection of glypican-3 directly from extracellular vesicles.},
journal = {Analytica chimica acta},
volume = {1297},
number = {},
pages = {342385},
doi = {10.1016/j.aca.2024.342385},
pmid = {38438232},
issn = {1873-4324},
mesh = {Adult ; Humans ; Recombinases ; *Carcinoma, Hepatocellular/diagnosis ; Clustered Regularly Interspaced Short Palindromic Repeats ; Glypicans/genetics ; *Liver Neoplasms/diagnosis ; *Extracellular Vesicles ; },
abstract = {BACKGROUND: Glypican-3 (GPC3) is a heparan sulfate proteoglycan (HSPG) that binds to the cell membrane via glycosylphosphatidylinositol (GPI). It is not found in healthy adult liver but is overexpressed in human hepatocellular carcinoma (HCC). The protein marker GPC3 on extracellular vesicles (GPC3[+] EVs) is also useful for HCC detection. Nevertheless, the absence of practical and dependable quantitative techniques to evaluate EVs proteins prevents their clinical implementation.<br><br>RESULTS: Here, using an immuno-recombinase polymerase amplification (immuno-RPA) process and dual amplification of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas13a, we firstly create an extraction-free one-pot immuno-RPA-CRISPR (opiCRISPR) for the direct and extremely sensitive detection of EVs proteins. The EVs protein-targeted detection probe is amplified by RPA to generate a long repetitive sequence containing multiple CRISPR RNA (crRNA) targeting barcodes, and the signal is further amplified by the CRISPR-Cas13a side-chain cleavage activity to generate a fluorescent signal. The results show that circulating extracellular vesicle GPC3 (eGPC3) levels are a reliable marker for GPC3 expression in tumor, opening up new avenues for tumor diagnosis.<br><br>SIGNIFICANCE AND NOVELTY: We created an eGPC3 assay based on the CRISPR-Cas13a system, and successfully study the significance of extracellular vesicle GPC3 markers in hepatocellular carcinoma.},
}
@article {pmid38437570,
year = {2024},
author = {Eygeris, Y and Gupta, M and Kim, J and Jozic, A and Gautam, M and Renner, J and Nelson, D and Bloom, E and Tuttle, A and Stoddard, J and Reynaga, R and Neuringer, M and Lauer, AK and Ryals, RC and Sahay, G},
title = {Thiophene-based lipids for mRNA delivery to pulmonary and retinal tissues.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {11},
pages = {e2307813120},
pmid = {38437570},
issn = {1091-6490},
support = {P51 OD011092/OD/NIH HHS/United States ; P30 EY010572/EY/NEI NIH HHS/United States ; P51 OD011092/CD/ODCDC CDC HHS/United States ; R01 EY033423/EY/NEI NIH HHS/United States ; S10 RR024585/RR/NCRR NIH HHS/United States ; },
mesh = {Animals ; Mice ; Tissue Distribution ; *Retina ; RNA, Messenger/genetics ; *Lung ; Lipids ; },
abstract = {Lipid nanoparticles (LNPs) largely rely on ionizable lipids to yield successful nucleic acid delivery via electrostatic disruption of the endosomal membrane. Here, we report the identification and evaluation of ionizable lipids containing a thiophene moiety (Thio-lipids). The Thio-lipids can be readily synthesized via the Gewald reaction, allowing for modular lipid design with functional constituents at various positions of the thiophene ring. Through the rational design of ionizable lipid structure, we prepared 47 Thio-lipids and identified some structural criteria required in Thio-lipids for efficient mRNA (messenger RNA) encapsulation and delivery in vitro and in vivo. Notably, none of the tested lipids have a pH-response profile like traditional ionizable lipids, potentially due to the electron delocalization in the thiophene core. Placement of the tails and localization of the ionizable headgroup in the thiophene core can endow the nanoparticles with the capability to reach various tissues. Using high-throughput formulation and barcoding techniques, we optimized the formulations to select two top lipids-20b and 29d-and investigated their biodistribution in mice. Lipid 20b enabled LNPs to transfect the liver and spleen, and 29d LNP transfected the lung and spleen. Unexpectedly, LNP with lipid 20b was especially potent in mRNA delivery to the retina with no acute toxicity, leading to the successful delivery to the photoreceptors and retinal pigment epithelium in non-human primates.},
}
@article {pmid38437539,
year = {2024},
author = {Radmand, A and Kim, H and Beyersdorf, J and Dobrowolski, CN and Zenhausern, R and Paunovska, K and Huayamares, SG and Hua, X and Han, K and Loughrey, D and Hatit, MZC and Del Cid, A and Ni, H and Shajii, A and Li, A and Muralidharan, A and Peck, HE and Tiegreen, KE and Jia, S and Santangelo, PJ and Dahlman, JE},
title = {Cationic cholesterol-dependent LNP delivery to lung stem cells, the liver, and heart.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {11},
pages = {e2307801120},
pmid = {38437539},
issn = {1091-6490},
support = {R35 GM124846/GM/NIGMS NIH HHS/United States ; UG3 TR002855/TR/NCATS NIH HHS/United States ; UH3 TR002855/TR/NCATS NIH HHS/United States ; },
mesh = {*Liver ; *Stem Cells ; Heart ; Cations ; Cholesterol ; RNA, Messenger ; },
abstract = {Adding a cationic helper lipid to a lipid nanoparticle (LNP) can increase lung delivery and decrease liver delivery. However, it remains unclear whether charge-dependent tropism is universal or, alternatively, whether it depends on the component that is charged. Here, we report evidence that cationic cholesterol-dependent tropism can differ from cationic helper lipid-dependent tropism. By testing how 196 LNPs delivered mRNA to 22 cell types, we found that charged cholesterols led to a different lung:liver delivery ratio than charged helper lipids. We also found that combining cationic cholesterol with a cationic helper lipid led to mRNA delivery in the heart as well as several lung cell types, including stem cell-like populations. These data highlight the utility of exploring charge-dependent LNP tropism.},
}
@article {pmid38436023,
year = {2024},
author = {Victor, BC and Frable, BW and Ludt, WB},
title = {Halichoeres sanchezi n. sp., a new wrasse from the Revillagigedo Archipelago of Mexico, tropical eastern Pacific Ocean (Teleostei: Labridae).},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e16828},
pmid = {38436023},
issn = {2167-8359},
mesh = {Male ; Animals ; Mexico ; Pacific Ocean ; *Perciformes ; Fishes/genetics ; *Abdominal Cavity ; },
abstract = {A new labrid fish species, Halichoeres sanchezi n. sp., is described from eight specimens collected in the Revillagigedo Archipelago in the tropical eastern Pacific Ocean, off the coast of Mexico. The new species belongs to the Halichoeres melanotis species complex that is found throughout the region, differing by 2.4% in the mtDNA cytochrome c oxidase I sequence from its nearest relative, H. melanotis from Panama, and 2.9% from Halichoeres salmofasciatus from Cocos Island, off Costa Rica. The complex is distinguished from others in the region by having a black spot on the opercular flap and a prominent black area on the caudal fin of males. The juveniles and initial phase of the new species closely resemble those of H. salmofasciatus and Halichoeres malpelo from Malpelo Island of Colombia, differing in having an oblong black spot with a yellow dorsal margin on the mid-dorsal fin of initial-phase adults as well as on juveniles. In contrast, the terminal-phase male color pattern is distinct from other relatives, being vermilion to orangish brown with dark scale outlines, a white patch on the upper abdomen, and a prominent black band covering the posterior caudal peduncle and base of the caudal fin. The new species adds to the list of endemic fish species for the isolated archipelago and is an interesting case of island endemism in the region. The discovery was made during the joint 2022 collecting expedition to the archipelago, which featured a pioneering collaborative approach to an inventory of an island ichthyofauna, specifically including expert underwater photographers systematically documenting specimens in situ, before hand-collection, and then photographed fresh, tissue-sampled, and subsequently vouchered in museum collections.},
}
@article {pmid38435688,
year = {2024},
author = {Baños-Quintana, AP and Gershenzon, J and Kaltenpoth, M},
title = {The Eurasian spruce bark beetle Ips typographus shapes the microbial communities of its offspring and the gallery environment.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1367127},
pmid = {38435688},
issn = {1664-302X},
abstract = {The Eurasian spruce bark beetle (Ips typographus) is currently the most economically relevant pest of Norway spruce (Picea abies). Ips typographus associates with filamentous fungi that may help it overcome the tree's chemical defenses. However, the involvement of other microbial partners in this pest's ecological success is unclear. To understand the dynamics of the bark beetle-associated microbiota, we characterized the bacterial and fungal communities of wild-collected and lab-reared beetles throughout their development by culture-dependent approaches, meta-barcoding, and quantitative PCR. Gammaproteobacteria dominated the bacterial communities, while the fungal communities were mainly composed of yeasts of the Saccharomycetales order. A stable core of microbes is shared by all life stages, and is distinct from those associated with the surrounding bark, indicating that Ips typographus influences the microbial communities of its environment and offspring. These findings coupled with our observations of maternal behavior, suggest that Ips typographus transfers part of its microbiota to eggs via deposition of an egg plug treated with maternal secretions, and by inducing an increase in abundance of a subset of taxa from the adjacent bark.},
}
@article {pmid38434835,
year = {2024},
author = {Ruppeka-Rupeika, E and Abakumov, S and Engelbrecht, M and Chen, X and do Carmo Linhares, D and Bouwens, A and Leen, V and Hofkens, J},
title = {Optical Mapping: Detecting Genomic Resistance Cassettes in MRSA.},
journal = {ACS omega},
volume = {9},
number = {8},
pages = {8862-8873},
pmid = {38434835},
issn = {2470-1343},
abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) is a multidrug-resistant bacterium with a global presence in healthcare facilities as well as community settings. The resistance of MRSA to beta-lactam antibiotics can be attributed to a mobile genetic element called the staphylococcal cassette chromosome mec (SCCmec), ranging from 23 to 68 kilobase pairs in length. The mec gene complex contained in SCCmec allows MRSA to survive in the presence of penicillin and other beta-lactam antibiotics. We demonstrate that optical mapping (OM) is able to identify the bacterium as S. aureus, followed by an investigation of the presence of kilobase pair range SCCmec elements by examining the associated OM-generated barcode patterns. By employing OM as an alternative to traditional DNA sequencing, we showcase its potential for the detection of complex genetic elements such as SCCmec in MRSA. This approach holds promise for enhancing our understanding of antibiotic resistance mechanisms and facilitating the development of targeted interventions against MRSA infections.},
}
@article {pmid38430432,
year = {2025},
author = {Lonare, N and Patil, G and Waghmare, S and Bhor, R and Hardikar, H and Tembe, S},
title = {DNA Barcoding of Invasive Terrestrial Plant Species in India.},
journal = {Molecular biotechnology},
volume = {67},
number = {3},
pages = {1027-1034},
pmid = {38430432},
issn = {1559-0305},
mesh = {*DNA Barcoding, Taxonomic/methods ; India ; *Introduced Species ; *Phylogeny ; *Plants/genetics/classification ; DNA, Plant/genetics ; Genetic Markers ; Biodiversity ; },
abstract = {Invasive plants are known to cause biodiversity loss and pose a major risk to human health and environment. Identification of invasive plants and distinguishing them from native species has been relied on morphological examination. Stringent requirement of floral characters and decreasing number of expert taxonomists are making conventional morphology-based identification system tedious and resource-intensive. DNA barcoding may help in quick identification of invasive species if distinct sequence divergence pattern at various taxonomic levels is observed. The present work evaluates the utility of four molecular markers; rbcL, matK, their combination (rbcL + matK), and psbA-trnH for identification of 37 invasive plant species from India and also in distinguishing them from 97 native species. A psbA-trnH locus was found to be of restricted utility in this work as it was represented by the members of a single family. A hierarchical increase in K2P mean divergence across different taxonomic levels was found to be the maximum for matK alone followed by rbcL + matK and rbcL alone, respectively. NJ clustering analysis, however, confirmed the suitability of combined locus (rbcL + matK) over individual rbcL and matK as the DNA barcode. RbcL showed the lowest resolution power among the three markers studied. MatK exhibited much better performance compared to rbcL alone in identifying most of the species accurately although it failed to show monophyly of genus Dinebra. Two families; Asteraceae and Poaceae, remained polyphyletic in the trees constructed by all three markers. Combined locus (rbcL + matK) was found to be the most suitable marker as it raised the resolution power of both the markers and could identify more than 90% of genera correctly. Phylogenetic tree constructed by Maximum-Parsimony method using combined locus as a molecular marker exhibited the best resolution, thus, supporting the significance of two-locus combination of rbcL + matK for barcoding invasive plant species from India. Present study contributes to the global barcode data of invasive plant species by adding fifty-one new sequences to it. Effective barcoding of additional number of native as well as invasive plant species from India is possible using this dual locus if it is combined with one or more new molecular plastid markers. Expansion of barcode database with a focus on barcode performance optimisation to improve discrimination ability at species level can be undertaken in future.},
}
@article {pmid38427209,
year = {2024},
author = {Minami, M and Tanaka, R and Mori, T and Fujii, T and Tsuchida, T},
title = {Identification of Angelica acutiloba, A. sinensis, and other Chinese medicinal Apiaceae plants by DNA barcoding.},
journal = {Journal of natural medicines},
volume = {78},
number = {3},
pages = {792-798},
pmid = {38427209},
issn = {1861-0293},
support = {22212K//Chubu University Grant (K)/ ; },
mesh = {*DNA Barcoding, Taxonomic ; *Angelica/genetics/chemistry/classification ; *Angelica sinensis/genetics ; *Plant Roots/genetics ; Apiaceae/genetics/classification ; DNA, Plant/genetics ; Plants, Medicinal/genetics/classification ; Drugs, Chinese Herbal/chemistry ; Phylogeny ; China ; },
abstract = {Crude drug Angelicae acutilobae radix is one of the most important crude drugs in Japanese traditional medicine and is used mainly for the treatment of gynecological disorders. In the listing in the Japanese Pharmacopoeia XVIII, Angelicae acutilobae radix is defined as the root of Angelica acutiloba (Apiaceae), which has long been produced on an industrial scale in Japan. With the aging of farmers and depopulation of production areas, the domestic supply has recently declined and the majority of the supply is now imported from China. Due to having only slightly different morphological and chemical characteristics for the Apiaceae roots used to produce dried roots for Chinese medicines, the plant species originating the crude drug Apiaceae roots may be incorrectly identified. In particular, Angelicae sinensis radix, which is widely used in China, and Angelicae acutilobae radix are difficult to accurately identify by morphology and chemical profiles. Thus, in order to differentiate among Angelicae acutilobae radix and other radixes originated from Chinese medicinal Apiaceae plants, we established DNA markers. Using DNA sequences for the chloroplast psbA-trnH intergenic spacer and nuclear internal transcribed spacer regions, Angelicae acutilobae radix and other Chinese Apiaceae roots, including Angelicae sinensis radix, can be definitively identified.},
}
@article {pmid38424061,
year = {2024},
author = {Xue, L and Hamilton, AG and Zhao, G and Xiao, Z and El-Mayta, R and Han, X and Gong, N and Xiong, X and Xu, J and Figueroa-Espada, CG and Shepherd, SJ and Mukalel, AJ and Alameh, MG and Cui, J and Wang, K and Vaughan, AE and Weissman, D and Mitchell, MJ},
title = {High-throughput barcoding of nanoparticles identifies cationic, degradable lipid-like materials for mRNA delivery to the lungs in female preclinical models.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {1884},
pmid = {38424061},
issn = {2041-1723},
support = {DP2 TR002776/TR/NCATS NIH HHS/United States ; R01 HL153539/HL/NHLBI NIH HHS/United States ; },
mesh = {Female ; Animals ; Mice ; RNA, Messenger/genetics ; *DNA ; *Nanoparticles ; Lung ; Lipids ; },
abstract = {Lipid nanoparticles for delivering mRNA therapeutics hold immense promise for the treatment of a wide range of lung-associated diseases. However, the lack of effective methodologies capable of identifying the pulmonary delivery profile of chemically distinct lipid libraries poses a significant obstacle to the advancement of mRNA therapeutics. Here we report the implementation of a barcoded high-throughput screening system as a means to identify the lung-targeting efficacy of cationic, degradable lipid-like materials. We combinatorially synthesize 180 cationic, degradable lipids which are initially screened in vitro. We then use barcoding technology to quantify how the selected 96 distinct lipid nanoparticles deliver DNA barcodes in vivo. The top-performing nanoparticle formulation delivering Cas9-based genetic editors exhibits therapeutic potential for antiangiogenic cancer therapy within a lung tumor model in female mice. These data demonstrate that employing high-throughput barcoding technology as a screening tool for identifying nanoparticles with lung tropism holds potential for the development of next-generation extrahepatic delivery platforms.},
}
@article {pmid38422290,
year = {2024},
author = {Wahyuni, DK and Indriati, DT and Ilham, M and Murtadlo, AAA and Purnobasuki, H and Junairiah, and Purnama, PR and Ikram, NKK and Samian, MZ and Subramaniam, S},
title = {Morpho-anatomical characterization and DNA barcoding of Artemesia vulgaris L.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {84},
number = {},
pages = {e278393},
doi = {10.1590/1519-6984.278393},
pmid = {38422290},
issn = {1678-4375},
mesh = {*DNA Barcoding, Taxonomic/methods ; DNA, Plant/genetics ; Phylogeny ; *Plants, Medicinal/genetics ; Plant Leaves/genetics ; },
abstract = {Artemisia vulgaris L. belongs to Asteraceae, is a herbal plant that has various benefits in the medical field, so that its use in the medical field can be explored optimally, the plant must be thoroughly identified. This study aims to identify A. vulgaris both in terms of descriptive morpho-anatomy and DNA barcoding using BLAST and phylogenetic tree reconstruction. The morpho-anatomical character was observed on root, stem, and leaf. DNA barcoding analysis was carried out through amplification and alignment of the rbcL and matK genes. All studies were conducted on three samples from Taman Husada (Medicinal Plant Garden) Graha Famili Surabaya, Indonesia. The anatomical slide was prepared by the paraffin method. Morphological studies revealed that the leaves of A. vulgaris both on the lower-middle part and on the upper part of the stem have differences, especially in the character of the stipules, petioles, and incisions they have. Meanwhile, from the study of anatomy, A. vulgaris has an anomocytic type of stomata and its distribution is mostly on the ventral part of the leaves. Through the BLAST process and phylogenetic tree reconstruction, the plant sequences being studied are closely related to several species of the genus Artemisia as indicated by a percentage identity above 98% and branch proximity between taxa in the reconstructed phylogenetic tree.},
}
@article {pmid38421005,
year = {2024},
author = {Sakpuntoon, V and Srathongporn, N and Pontes, A and Khunnamwong, P and Aires, A and Limtong, S and Gonçalves, C and Gonçalves, P and Sampaio, JP and Srisuk, N},
title = {Phylogenomic delineation of two new species of ascomycetous yeasts, Wickerhamiella koratensis sp. nov. and Wickerhamiella limtongiae sp. nov., and proposal of two synonyms, Wickerhamiella infanticola and Wickerhamiella tropicalis.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {2},
pages = {},
doi = {10.1099/ijsem.0.006282},
pmid = {38421005},
issn = {1466-5034},
mesh = {Phylogeny ; Food ; Sequence Analysis, DNA ; DNA, Fungal/genetics ; Mycological Typing Techniques ; Base Composition ; *Refuse Disposal ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Fatty Acids/chemistry ; *Saccharomycetales ; Thailand ; },
abstract = {Two novel ascomycetous yeast species of the genus Wickerhamiella are proposed based on isolates obtained in Thailand from food waste and the fruiting body of a polypore fungus, and on a combination of conventional DNA-barcode sequence analyses and whole-genome phylogenies. We focus on a particular subclade of the genus Wickerhamiella that contains species found in anthropic environments and describe Wickerhamiella limtongiae sp. nov. (DMKU-FW31-5[T]=PYCC 9022[T]=TBRC 15055[T]), found on food waste samples. In an adjacent clade, we describe Wickerhamiella koratensis sp. nov. (DMKU-KO16[T]=PYCC 8908[T]=TBRC 14869[T]), which represents the closest relative of Wickerhamiella slavikovae and was isolated from the fruiting body of Bjerkandera sp. In the subclade of W. limtongiae sp. nov., we propose that Wickerhamiella infanticola should be regarded as a synonym of Wickerhamiella sorbophila and that Wickerhamiella tropicalis should be regarded as a synonym of Wickerhamiella verensis.},
}
@article {pmid38420748,
year = {2025},
author = {Zhang, X and Li, P and Gan, Y and Xiang, S and Gu, L and Zhou, J and Zhou, X and Wu, P and Zhang, B and Deng, D},
title = {Driving effect of P16 methylation on telomerase reverse transcriptase-mediated immortalization and transformation of normal human fibroblasts.},
journal = {Chinese medical journal},
volume = {138},
number = {3},
pages = {332-342},
pmid = {38420748},
issn = {2542-5641},
mesh = {Humans ; *Telomerase/genetics/metabolism ; *DNA Methylation/genetics ; *Fibroblasts/metabolism ; *Cyclin-Dependent Kinase Inhibitor p16/genetics/metabolism ; Cell Transformation, Neoplastic/genetics ; Cell Line ; },
abstract = {BACKGROUND: P16 inactivation is frequently accompanied by telomerase reverse transcriptase (TERT) amplification in human cancer genomes. P16 inactivation by DNA methylation often occurs automatically during immortalization of normal cells by TERT . However, direct evidence remains to be obtained to support the causal effect of epigenetic changes, such as P16 methylation, on cancer development. This study aimed to provide experimental evidence that P16 methylation directly drives cancer development.<br><br>METHODS: A zinc finger protein-based P16 -specific DNA methyltransferase (P16-Dnmt) vector containing a "Tet-On" switch was used to induce extensive methylation of P16 CpG islands in normal human fibroblast CCD-18Co cells. Battery assays were used to evaluate cell immortalization and transformation throughout their lifespan. Cell subcloning and DNA barcoding were used to track the diversity of cell evolution.<br><br>RESULTS: Leaking P16-Dnmt expression (without doxycycline-induction) could specifically inactivate P16 expression by DNA methylation. P16 methylation only promoted proliferation and prolonged lifespan but did not induce immortalization of CCD-18Co cells. Notably, cell immortalization, loss of contact inhibition, and anchorage-independent growth were always prevalent in P16-Dnmt&amp;TERT cells, indicating cell transformation. In contrast, almost all TERT cells died in the replicative crisis. Only a few TERT cells recovered from the crisis, in which spontaneous P16 inactivation by DNA methylation occurred. Furthermore, the subclone formation capacity of P16-Dnmt&amp;TERT cells was two-fold that of TERT cells. DNA barcoding analysis showed that the diversity of the P16-Dnmt&amp;TERT cell population was much greater than that of the TERT cell population.<br><br>CONCLUSION: P16 methylation drives TERT -mediated immortalization and transformation of normal human cells that may contribute to cancer development.},
}
@article {pmid38419597,
year = {2024},
author = {Zhou, G and Li, T and Du, J and Wu, M and Lin, D and Pu, W and Zhang, J and Gu, Z},
title = {Harnessing HetHydrogel: A Universal Platform to Dropletize Single-Cell Multiomics.},
journal = {Small methods},
volume = {8},
number = {7},
pages = {e2301631},
doi = {10.1002/smtd.202301631},
pmid = {38419597},
issn = {2366-9608},
support = {2020YFA0803800//National Key Research and Development Program of China/ ; SL2022A04J00717//Guangzhou Basic and Applied Basic Research Special Program/ ; 32070948//National Natural Science Foundation of China/ ; 61904105//National Natural Science Foundation of China/ ; 91942313//National Natural Science Foundation of China/ ; 32293210//National Natural Science Foundation of China/ ; 19PJ1401600//Shanghai Pujiang Talent Program/ ; },
mesh = {*Single-Cell Analysis ; *Hydrogels/chemistry ; *DNA, Mitochondrial/genetics ; Humans ; Animals ; Mutation ; Multiomics ; },
abstract = {A universal platform is developed for dropletizing single cell plate-based multiomic assays, consisting of three main pillars: a miniaturized open Heterogeneous Hydrogel reactor (abbreviated HetHydrogel) for multi-step biochemistry, its tunable permeability that allows Tn5 tagmentation, and single cell droplet barcoding. Through optimizing the HetHydrogel manufacturing procedure, the chemical composition, and cell permeation conditions, simultaneous high-throughput mitochondrial DNA genotyping and chromatin profiling at the single-cell level are demonstrated using a mixed-species experiment. This platform offers a powerful way to investigate the genotype-phenotype relationships of various mtDNA mutations in biological processes. The HetHydrogel platform is believed to have the potential to democratize droplet technologies, upgrading a whole range of plate-based single cell assays to high throughput format.},
}
@article {pmid38416278,
year = {2024},
author = {Boder-Pasche, S and Demir, M and Heub, S and Garzuel, M and Ischer, R and Migliozzi, D and Graf, S and Schmid, N and Atakan, HB and Gudkova, D and Alpern, D and Dainese, R and Deplancke, B and Weder, G},
title = {Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing.},
journal = {Biomedical microdevices},
volume = {26},
number = {2},
pages = {18},
pmid = {38416278},
issn = {1572-8781},
support = {38445.1 IP-LS//Innosuisse - Schweizerische Agentur f&#xfc;r Innovationsf&#xf6;rderung/ ; 38445.1 IP-LS//Innosuisse - Schweizerische Agentur f&#xfc;r Innovationsf&#xf6;rderung/ ; 38445.1 IP-LS//Innosuisse - Schweizerische Agentur f&#xfc;r Innovationsf&#xf6;rderung/ ; 38445.1 IP-LS//Innosuisse - Schweizerische Agentur f&#xfc;r Innovationsf&#xf6;rderung/ ; 38445.1 IP-LS//Innosuisse - Schweizerische Agentur f&#xfc;r Innovationsf&#xf6;rderung/ ; 38445.1 IP-LS//Innosuisse - Schweizerische Agentur f&#xfc;r Innovationsf&#xf6;rderung/ ; 38445.1 IP-LS//Innosuisse - Schweizerische Agentur f&#xfc;r Innovationsf&#xf6;rderung/ ; 38445.1 IP-LS//Innosuisse - Schweizerische Agentur f&#xfc;r Innovationsf&#xf6;rderung/ ; 38445.1 IP-LS//Innosuisse - Schweizerische Agentur f&#xfc;r Innovationsf&#xf6;rderung/ ; 38445.1 IP-LS//Innosuisse - Schweizerische Agentur f&#xfc;r Innovationsf&#xf6;rderung/ ; 38445.1 IP-LS//Innosuisse - Schweizerische Agentur f&#xfc;r Innovationsf&#xf6;rderung/ ; 38445.1 IP-LS//Innosuisse - Schweizerische Agentur f&#xfc;r Innovationsf&#xf6;rderung/ ; 38445.1 IP-LS//Innosuisse - Schweizerische Agentur f&#xfc;r Innovationsf&#xf6;rderung/ ; 38445.1 IP-LS//Innosuisse - Schweizerische Agentur f&#xfc;r Innovationsf&#xf6;rderung/ ; BRIDGE 40B2-0_187102//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; BRIDGE 40B2-0_187102//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; BRIDGE 40B2-0_187102//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; BRIDGE 40B2-0_187102//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; BRIDGE 40B2-0_187102//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; BRIDGE 40B2-0_187102//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; BRIDGE 40B2-0_187102//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; BRIDGE 40B2-0_187102//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; BRIDGE 40B2-0_187102//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; BRIDGE 40B2-0_187102//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; BRIDGE 40B2-0_187102//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; BRIDGE 40B2-0_187102//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; BRIDGE 40B2-0_187102//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; BRIDGE 40B2-0_187102//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; },
mesh = {*High-Throughput Nucleotide Sequencing ; Feces ; *RNA ; },
abstract = {High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatments. Focusing on gene expression, the transcriptomic market exploits the benefits of next-generation sequencing (NGS), leveraging RNA sequencing (RNA-seq) as standard for measuring genome-wide gene expression in biological samples. The cumbersome sample preparation, including RNA extraction, conversion to cDNA and amplification, prevents high-throughput translation of RNA-seq technologies. Bulk RNA barcoding and sequencing (BRB-seq) addresses this limitation by enabling sample preparation in multi-well plate format. Sample multiplexing combined with early pooling into a single tube reduces reagents consumption and manual steps. Enabling simultaneous pooling of all samples from the multi-well plate into one tube, our technology relies on smart labware: a pooling lid comprising fluidic features and small pins to transport the liquid, adapted to standard 96-well plates. Operated with standard fluidic tubes and pump, the system enables over 90% recovery of liquid in a single step in less than a minute. Large scale manufacturing of the lid is demonstrated with the transition from a milled polycarbonate/steel prototype into an injection molded polystyrene lid. The pooling lid demonstrated its value in supporting high-throughput barcode-based sequencing by pooling 96 different DNA barcodes directly from a standard 96-well plate, followed by processing within the single sample pool. This new pooling technology shows great potential to address medium throughput needs in the BRB-seq workflow, thereby addressing the challenge of large-scale and cost-efficient sample preparation for RNA-seq.},
}
@article {pmid38414433,
year = {2024},
author = {Tan, Y and Zhang, L and Deng, S},
title = {Programmable DNA barcode-encoded exponential amplification reaction for the multiplex detection of miRNAs.},
journal = {Analytical methods : advancing methods and applications},
volume = {16},
number = {11},
pages = {1649-1658},
doi = {10.1039/d3ay02215c},
pmid = {38414433},
issn = {1759-9679},
mesh = {*DNA Barcoding, Taxonomic ; *MicroRNAs/genetics/analysis ; Nucleic Acid Amplification Techniques/methods ; Temperature ; },
abstract = {Multiple analysis of miRNAs is essential for the early diagnosis and monitoring of diseases. Here, a programmable, multiplex, and sensitive approach was developed for one-pot detection of miRNAs by melting temperature encoded sequences and exponential isothermal amplification (E-EXPAR). In the presence of target miRNAs, the corresponding templates initiate the cycles of nicking and polymerization/displacement, generating numerous barcode strands with unique encoding sequences. Subsequently, generated barcode strands hybridize with fluorescent probes and quench the fluorophore by a triplet of G base through a photo-induced electron transfer mechanism. Finally, a melting curve analysis is performed to quantify miRNAs by calculating the rate of fluorescence change at the corresponding melting temperature. Based on this, miRNA-21, miRNA-9, and miRNA-122 were detected with the detection limits of 3.3 fM, 2.9 fM, and 1.7 fM, respectively. This E-EXPAR was also employed to simultaneously detect three miRNAs in biological samples, showing consistent results with RT-qPCR. Overall, this study provides a programmable and universal platform for multiplex analysis of miRNAs, and holds great promise as an alternative to the multiplex analysis in clinical diagnostics and prognostics for nucleic acid detection.},
}
@article {pmid38414030,
year = {2024},
author = {Whelpley, MJ and Zhou, LH and Rascon, J and Payne, B and Moehn, B and Young, KI and Mire, CE and Peters, DPC and Rodriguez, LL and Hanley, KA},
title = {Community composition of black flies during and after the 2020 vesicular stomatitis virus outbreak in Southern New Mexico, USA.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {93},
pmid = {38414030},
issn = {1756-3305},
support = {NACA 58-8064-9-012//U.S. Department of Agriculture/ ; },
mesh = {Animals ; *Simuliidae ; *Vesicular Stomatitis/epidemiology ; New Mexico/epidemiology ; Insect Vectors ; Vesiculovirus ; Larva ; Disease Outbreaks ; },
abstract = {BACKGROUND: Vesicular stomatitis virus (VSV), a vector-borne pathogen of livestock, emerges periodically in the western US. In New Mexico (NM), US, most cases occur close to the Rio Grande River, implicating black flies (Simulium spp.) as a possible vector. In 2020, VS cases were reported in NM from April to May, although total black fly abundance remained high until September. We investigated the hypothesis that transience of local VSV transmission results from transient abundance of key, competent black fly species. Additionally, we investigated whether irrigation canals in southern NM support a different community of black flies than the main river. Lastly, to gain insight into the source of local black flies, in 2023 we collected black fly larvae prior to the release of water into the Rio Grande River channel.<br><br>METHODS: We randomly sub-sampled adult black flies collected along the Rio Grande during and after the 2020 VSV outbreak. We also collected black fly adults along the river in 2021 and 2022 and at southern NM farms and irrigation canals in 2022. Black fly larvae were collected from dams in the area in 2023. All collections were counted, and individual specimens were subjected to molecular barcoding for species identification.<br><br>RESULTS: DNA barcoding of adult black flies detected four species in 2020: Simulium meridionale&#x2009;(N = 158),&#x2009;S. mediovittatum (N&#x2009;= 83),&#x2009;S. robynae&#x2009;(N =&#x2009;26) and S. griseum/notatum&#x2009;(N =&#x2009;1). Simulium robynae was only detected during the VSV outbreak period, S. meridionale showed higher relative abundance, but lower absolute abundance, during the outbreak than post-outbreak period, and S. mediovittatum was rare during the outbreak period but predominated later in the summer. In 2022, relative abundance of black fly species did not differ significantly between the Rio Grande sites and farm and irrigation canals. Intriguingly, 63 larval black flies comprised 56% Simulium vittatum, 43% S. argus and 1% S. encisoi species that were either extremely rare or not detected in previous adult collections.<br><br>CONCLUSIONS: Our results suggest that S. robynae and S. meridionale could be shaping patterns of VSV transmission in southern NM. Thus, field studies of the source of these species as well as vector competence studies are warranted.},
}
@article {pmid38411607,
year = {2024},
author = {Holeva, MC and Glynos, PE and Reppa, C and Karafla, CD},
title = {First report of Ralstonia pseudosolanacearum causing bacterial wilt on Rosa sp. in Greece.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-11-23-2279-PDN},
pmid = {38411607},
issn = {0191-2917},
abstract = {In March 2021, a sample of nine-month-old, non-grafted, diseased rose (Rosa sp.) plants was sent by a grower to the Benaki Phytopathological Institute for examination. The plants exhibited symptoms of dieback with black necrosis of pruned shoots, brown discoloration of shoot and root vascular tissues, and whitish slime exudation on cutting wounds of the shoots. The symptoms resembled those caused by Ralstonia pseudosolanacearum (Tjou-Tam-Sin et al. 2016). According to the sample's information sheet, the sample had been collected in a commercial greenhouse rose crop for cut flowers with a 10% disease incidence in the area of Troizinia-Methana (Regional Unit of Islands, Greece). Microscopic examination of symptomatic shoot and root vascular tissues revealed masses of bacterial cells streaming out of them. Sections of symptomatic tissues were suspended in water and in the resulting suspension, bacteria of the R. solanacearum species complex (RSSC) were detected by an indirect immunofluorescence (IF) assay using polyclonal antibodies (Plant Research International, the Netherlands) and a qPCR assay (RS-I-F/RS-II-R primers, RSP-55T probe) (Vreeburg et al. 2016). Furthermore, colonies with typical characteristics of RSSC were isolated from vascular tissues of shoots and roots on non-selective (NA) and semi-selective (mSMSA) media (EPPO 2022), and their identification as RSSC was confirmed by the above-mentioned IF and qPCR assays. Also, the isolates were assigned to: i) biovar 3, based on their ability to metabolize three disaccharides (maltose, lactose, D(+) cellobiose) and three hexose alcohols (mannitol, sorbitol, dulcitol) producing acid (EU 2006) and ii) phylotype I, by multiplex conventional PCR (Opina et al. 1997; Fegan and Prior 2005). A representative isolate was selected for sequencing part of the genes: 16S rDNA (1464bp), mutS (729bp) and egl (795bp) with GenBank Accession Nos. OR102443, OR683617 and OR702781, respectively. Blast analysis of these sequences showed 100% identity with those of various RSSC strains (e.g. GenBank Ac. Nos. CP025741.1, CP021762.1, MF141029.1, respectively). The obtained egl sequence conforms with the characteristics of phylotype I based on the DNA barcoding tool (EPPO 2021) and is 100% identical to that of the Dutch strain PD7216 (MF141029.1) reported to be sequevar I-33 (Bergsma-Vlami et al. 2018). The pathogenicity of two isolates was tested by inoculating: i) tomato seedlings (cv. 'Belladona') at their stem between the cotyledons and the first true leaf (EU 2006) and b) rose plants (cv. 'Aqua' and 'Papa Meilland') at their shoot base (Tjou-Tam-Sin et al. 2016), with bacterial suspensions in water (10[8] cfu/ml). The inoculated plants were maintained at a day/night temperature about 28/20°C with tomato plants exhibiting leaf wilting (7-17 dpi) and rose plants exhibiting chlorosis and necrosis of leaves (17 dpi). The pathogen was re-isolated on mSMSA from both artificially infected plant species and identified by the IF assay described above, thus fulfilling Koch's postulates. This is the first diagnosis in Greece of: i) rose plants infected by a Ralstonia species and ii) a crop infected by R. solanacearum phylotype I that corresponds to the R. pseudosolanacearum species (EPPO 2022). Official phytosanitary measures imposed in the affected area include an annual survey of rose crops for the presence of this pathogen, aiming at an early detection and prevention of its spread in such a highly valued ornamental crop.},
}
@article {pmid38406290,
year = {2024},
author = {Wang, YC and Liu, SH and Ho, HC and Su, HY and Chang, CH},
title = {DNA mini-barcoding reveals the mislabeling rate of canned cat food in Taiwan.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e16833},
pmid = {38406290},
issn = {2167-8359},
mesh = {Humans ; Cats ; Animals ; RNA, Ribosomal, 16S/genetics ; *Animal Feed ; Taiwan ; *DNA ; Seafood ; Proteins ; },
abstract = {BACKGROUND: Domestic cats are important companion animals in modern society that live closely with their owners. Mislabeling of pet food can not only harm pets but also cause issues in areas such as religious beliefs and natural resource management. Currently, the cat food market is booming. However, despite the risk that mislabeling poses to cats and humans, few studies have focused on species misrepresentation in cat food products.<br><br>METHODS: To address this issue, we used DNA barcoding, a highly effective identification methodology that can be applied to even highly processed products. We targeted a short segment (~85 basepairs) of the mitochondrial 16S rRNA (16S) gene as a barcode and employed Sanger or next generation sequencing (NGS) to inspect 138 canned cat food products in the Taiwanese market.<br><br>RESULTS: We discovered that the majority of mislabeling incidents were related to replacement of tuna with other species. Moreover, our metabarcoding revealed that numerous undeclared ingredients were present in all examined canned products. One product contained CITES Appendix II-listed shortfin mako shark (Isurus oxyrinchus). Overall, we uncovered a mislabeling rate of at least 28.99%. To verify cases of mislabeling, an official standardized list of vernacular names, along with the corresponding scientific species names, as well as a dependable barcoding reference sequence database are necessary.},
}
@article {pmid38405830,
year = {2024},
author = {Pinglay, S and Lalanne, JB and Daza, RM and Koeppel, J and Li, X and Lee, DS and Shendure, J},
title = {Multiplex generation and single cell analysis of structural variants in a mammalian genome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38405830},
issn = {2692-8205},
support = {DP5 OD036167/OD/NIH HHS/United States ; R01 HG010632/HG/NHGRI NIH HHS/United States ; RM1 HG009491/HG/NHGRI NIH HHS/United States ; },
abstract = {The functional consequences of structural variants (SVs) in mammalian genomes are challenging to study. This is due to several factors, including: 1) their numerical paucity relative to other forms of standing genetic variation such as single nucleotide variants (SNVs) and short insertions or deletions (indels); 2) the fact that a single SV can involve and potentially impact the function of more than one gene and/or cis regulatory element; and 3) the relative immaturity of methods to generate and map SVs, either randomly or in targeted fashion, in in vitro or in vivo model systems. Towards addressing these challenges, we developed Genome-Shuffle-seq, a straightforward method that enables the multiplex generation and mapping of several major forms of SVs (deletions, inversions, translocations) throughout a mammalian genome. Genome-Shuffle-seq is based on the integration of "shuffle cassettes" to the genome, wherein each shuffle cassette contains components that facilitate its site-specific recombination (SSR) with other integrated shuffle cassettes (via Cre-loxP), its mapping to a specific genomic location (via T7-mediated in vitro transcription or IVT), and its identification in single-cell RNA-seq (scRNA-seq) data (via T7-mediated in situ transcription or IST). In this proof-of-concept, we apply Genome-Shuffle-seq to induce and map thousands of genomic SVs in mouse embryonic stem cells (mESCs) in a single experiment. Induced SVs are rapidly depleted from the cellular population over time, possibly due to Cre-mediated toxicity and/or negative selection on the rearrangements themselves. Leveraging T7 IST of barcodes whose positions are already mapped, we further demonstrate that we can efficiently genotype which SVs are present in association with each of many single cell transcriptomes in scRNA-seq data. Finally, preliminary evidence suggests our method may be a powerful means of generating extrachromosomal circular DNAs (ecDNAs). Looking forward, we anticipate that Genome-Shuffle-seq may be broadly useful for the systematic exploration of the functional consequences of SVs on gene expression, the chromatin landscape, and 3D nuclear architecture. We further anticipate potential uses for in vitro modeling of ecDNAs, as well as in paving the path to a minimal mammalian genome.},
}
@article {pmid38405739,
year = {2024},
author = {Shukla, N and Roelle, SM and Snell, JC and DelSignore, O and Bruchez, AM and Matreyek, KA},
title = {Pseudotyped virus infection of multiplexed ACE2 libraries reveals SARS-CoV-2 variant shifts in receptor usage.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38405739},
issn = {2692-8205},
support = {R21 AI169561/AI/NIAID NIH HHS/United States ; S10 OD021559/OD/NIH HHS/United States ; R21 AI161275/AI/NIAID NIH HHS/United States ; P30 CA043703/CA/NCI NIH HHS/United States ; R21 AI178151/AI/NIAID NIH HHS/United States ; R35 GM142886/GM/NIGMS NIH HHS/United States ; R21 AI156907/AI/NIAID NIH HHS/United States ; },
abstract = {Pairwise compatibility between virus and host proteins can dictate the outcome of infection. During transmission, both inter- and intraspecies variabilities in receptor protein sequences can impact cell susceptibility. Many viruses possess mutable viral entry proteins and the patterns of host compatibility can shift as the viral protein sequence changes. This combinatorial sequence space between virus and host is poorly understood, as traditional experimental approaches lack the throughput to simultaneously test all possible combinations of protein sequences. Here, we created a pseudotyped virus infection assay where a multiplexed target-cell library of host receptor variants can be assayed simultaneously using a DNA barcode sequencing readout. We applied this assay to test a panel of 30 ACE2 orthologs or human sequence mutants for infectability by the original SARS-CoV-2 spike protein or the Alpha, Beta, Gamma, Delta, and Omicron BA1 variant spikes. We compared these results to an analysis of the structural shifts that occurred for each variant spike's interface with human ACE2. Mutated residues were directly involved in the largest shifts, although there were also widespread indirect effects altering interface structure. The N501Y substitution in spike conferred a large structural shift for interaction with ACE2, which was partially recreated by indirect distal substitutions in Delta, which does not harbor N501Y. The structural shifts from N501Y greatly influenced the set of animal orthologs the variant spike was capable of interacting with. Out of the thirteen non-human orthologs, ten exhibited unique patterns of variant-specific compatibility, demonstrating that spike sequence changes during human transmission can toggle ACE2 compatibility and potential susceptibility of other animal species, and cumulatively increase overall compatibilities as new variants emerge. These experiments provide a blueprint for similar large-scale assessments of protein compatibility during entry by diverse viruses. This dataset demonstrates the complex compatibility relationships that occur between variable interacting host and virus proteins.},
}
@article {pmid38405678,
year = {2024},
author = {Li, QQ and Yao, WW and Zhang, K and Wang, ZQ and Che, YL},
title = {Six new species of Margattea Shelford, 1911 (Blaberoidea, Pseudophyllodromiidae, Neoblattellini) from China.},
journal = {ZooKeys},
volume = {1191},
number = {},
pages = {339-367},
pmid = {38405678},
issn = {1313-2989},
abstract = {Six Margattea species are established and described: three are cryptic species, namely, M.parabisignata Li &amp; Che, sp. nov., M.semicircularis Li &amp; Che, sp. nov., and M.forcipata Li &amp; Che, sp. nov. They are distinguished from known species M.bisignata, M.spinifera, and M.paratransversa by their male genitalia with the aid of molecular species delimitation method (ABGD) using COI as the molecular marker. The other three new species are M.pedata Li &amp; Che, sp. nov., M.undulata Li &amp; Che, sp. nov., and M.bisphaerica Li &amp; Che, sp. nov. Morphological and genitalia photographs of these new species of Margattea, as well as a key to the species of Margattea from China, are provided.},
}
@article {pmid38405380,
year = {2024},
author = {Cornalba, M and Quaranta, M and Selis, M and Flaminio, S and Gamba, S and Mei, M and Bonifacino, M and Cappellari, A and Catania, R and Niolu, P and Tempesti, S and Biella, P},
title = {Exploring the hidden riches: Recent remarkable faunistic records and range extensions in the bee fauna of Italy (Hymenoptera, Apoidea, Anthophila).},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e116014},
pmid = {38405380},
issn = {1314-2828},
abstract = {BACKGROUND: The area sourrounding the Mediterranean basin is recognised as a major biodiversity hotspot for bees, and Italy is amongst the European countries with the highest bee species richness. Detailed knowledge of bee distribution is crucial for understanding bee biology and designing tailored conservation strategies, but is still insufficient in southern European countries, especially in Italy.<br><br>NEW INFORMATION: We report recent finds of 48 bee species that yield significant novelties for the Italian bee fauna. Eight species, namely Andrenaconfinis St&#xf6;ckhert, Anthidiellumbreviusculum P&#xe9;rez, Coelioxysalatus Foerster, Lasioglossumalgericolellum Strand, Megachilelapponica Thomson, Megachileopacifrons P&#xe9;rez, Megachilesemicircularis auct. nec Zanden and Trachusaintegra Eversmann are reported as new for Italy. In addition, Andrenabinominata Smith, Andrenacompta Lepeletier, Colletesacutus P&#xe9;rez, Lasioglossumstrictifrons Vachal, Rhodanthidiumsiculum Spinola and Rhodanthidiumsticticum Fabricius are newly recorded from mainland Italy, Osmiaheteracantha P&#xe9;rez from Sardegna and Nomadaflavopicta Kirby from Sicilia. We also report significant range extensions for other bee species and recent records of species that had long gone unrecorded in Italy. The combination of morphology and DNA barcoding provided reliable identifications even for the most challenging specimens. As several of our records come from areas neglected by bee experts in the past, this study stands out as a key indicator of a bee faunistic richness still awaiting discovery and hopefully it will stimulate the interest of taxonomists and stakeholders in pursuing bee research in Italy in the near future.},
}
@article {pmid38403342,
year = {2024},
author = {Dou, XM and Zhang, JH and Wang, X and Liu, SH and Shi, Y and Huang, YY and Zhang, XQ and He, GJ and An, KL and Qi, Y and Wang, XH and Wei, SL and Zhang, Y},
title = {[DNA barcode screening, identification of germplasm resources, and analysis of genetic diversity of Anemarrhena asphodeloides].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {49},
number = {1},
pages = {88-99},
doi = {10.19540/j.cnki.cjcmm.20231122.101},
pmid = {38403342},
issn = {1001-5302},
mesh = {*Anemarrhena/chemistry ; DNA Barcoding, Taxonomic ; Genetic Variation ; China ; Phylogeny ; },
abstract = {Anemarrhena asphodeloides is a common medicinal material used in clinical prescriptions and Chinese patent medicine. In this study, the Illumina platform was used to obtain the chloroplast genome sequences of seven kinds of A. asphodeloides from different areas. The specific DNA barcodes were screened by comparative genomics analysis, and the DNA barcodes were used to identify the germplasm resources and analyze the genetic diversity of A. asphodeloides samples from different areas in China. All the seven chloroplast genomes had a ring structure. The total length was 156 801-156 930 bp, and 113 genes were annotated, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The comparative genomics analysis showed that rps16, trnG-GCC, atpF, rpoB, ycf3, rpl16, ndhF, trnS-GCU＿trnG-GCC, petN-psbM, and ndhF-rpl32 were potential candidates for specific DNA barcodes of A. asphodeloides. In this study, the second intron of ycf3 and atpF intron sequences with a sequence length of 700-800 bp and easy amplification were selected for polymerase chain reaction(PCR) amplification and sequencing of 594 samples from 26 areas. The sequence analysis showed that six and eight haplotypes of ycf3 and atpF sequences could be identified, respectively, and 17 haplotypes could be identified by combined analysis of the two sequences, which were named Hap1-Hap17. The haplotype diversity(H_d), nucleotide diversity(P_i), and genetic distance of A. asphodeloides in 26 populations were 0.68, 0.93×10~(-3), and 0-0.003 1, respectively, indicating that the genetic diversity within the species of A. asphodeloides is rich. The intermediary adjacent network analysis showed that Hap5 was the oldest haplotype, which was mainly distributed in Yixian county of Baoding, Hebei province, Hequ county of Xinzhou, Shanxi province, and Xiangfen county of Linfen, Shanxi province. This study has important guiding significance for the identification of A. asphodeloides species, the protection and development of germplasm resources, and the identification of production areas, and it provides a research basis for further revealing the genetic evolution law of A. asphodeloides.},
}
@article {pmid38402196,
year = {2024},
author = {Kaishian, P and Layug, CRK and Anderson, M and Berg, DR and Aime, MC},
title = {Rust HUBB: DNA barcode-based identification of Pucciniales.},
journal = {IMA fungus},
volume = {15},
number = {1},
pages = {3},
pmid = {38402196},
issn = {2210-6340},
support = {APHIS AP20PPQS//U.S. Department of Agriculture/ ; T00C077//U.S. Department of Agriculture/ ; NIFA Hatch project 1010662//U.S. Department of Agriculture/ ; (CSBR program: DEB-1458290//National Science Foundation/ ; TCN program: DEB-1502887//National Science Foundation/ ; Pursuit program: DEB-2018098//National Science Foundation/ ; },
abstract = {Rust fungi (Pucciniales, Basidiomycota) are a species-rich (ca. 8000 species), globally distributed order of obligate plant pathogens. Rust species are host-specific, and as a group they cause disease on many of our most economically and/or ecologically significant plants. As such, the ability to accurately and rapidly identify these fungi is of particular interest to mycologists, botanists, agricultural scientists, farmers, quarantine officials, and associated stakeholders. However, the complexities of the rust life cycle, which may include production of up to five different spore types and alternation between two unrelated host species, have made standard identifications, especially of less-documented spore states or alternate hosts, extremely difficult. The Arthur Fungarium (PUR) at Purdue University is home to one of the most comprehensive collections of rust fungi in the world. Using material vouchered in PUR supplemented with fresh collections we generated DNA barcodes of the 28S ribosomal repeat from > 3700 rust fungal specimens. Barcoded material spans 120 genera and > 1100 species, most represented by several replicate sequences. Barcodes and associated metadata are hosted in a publicly accessible, BLAST searchable database called Rust HUBB (Herbarium-based Universal Barcode Blast) and will be continuously updated.},
}
@article {pmid38401539,
year = {2024},
author = {Schaff, DL and Fasse, AJ and White, PE and Vander Velde, RJ and Shaffer, SM},
title = {Clonal differences underlie variable responses to sequential and prolonged treatment.},
journal = {Cell systems},
volume = {15},
number = {3},
pages = {213-226.e9},
pmid = {38401539},
issn = {2405-4720},
support = {DP5 OD028144/OD/NIH HHS/United States ; P50 CA174523/CA/NCI NIH HHS/United States ; P50 CA261608/CA/NCI NIH HHS/United States ; R01 GM149671/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Neoplasms/genetics/pathology ; Clone Cells/pathology ; Single-Cell Analysis/methods ; Exome Sequencing ; },
abstract = {Cancer cells exhibit dramatic differences in gene expression at the single-cell level, which can predict whether they become resistant to treatment. Treatment perpetuates this heterogeneity, resulting in a diversity of cell states among resistant clones. However, it remains unclear whether these differences lead to distinct responses when another treatment is applied or the same treatment is continued. In this study, we combined single-cell RNA sequencing with barcoding to track resistant clones through prolonged and sequential treatments. We found that cells within the same clone have similar gene expression states after multiple rounds of treatment. Moreover, we demonstrated that individual clones have distinct and differing fates, including growth, survival, or death, when subjected to a second treatment or when the first treatment is continued. By identifying gene expression states that predict clone survival, this work provides a foundation for selecting optimal therapies that target the most aggressive resistant clones within a tumor. A record of this paper's transparent peer review process is included in the supplemental information.},
}
@article {pmid38399639,
year = {2024},
author = {Simin, S and Tomanović, S and Sukara, R and Stefanov, M and Savović, M and Gajić, B and Lalošević, V},
title = {Long Time No Hear, Magnificent Wohlfahrtia! Morphological and Molecular Evidence of Almost Forgotten Flesh Fly in Serbia and Western Balkans.},
journal = {Microorganisms},
volume = {12},
number = {2},
pages = {},
pmid = {38399639},
issn = {2076-2607},
abstract = {The "beautiful viviparous fly", Wohlfahrtia magnifica, may have a magnificent appearance due to its striking morphology; however, it is a potentially deadly agent of obligate traumatic myiasis in humans and animals, with a serious impact on welfare and economics. The fly is found across the Palearctic realm, including the Western Balkan region, with reports from former Yugoslavian countries from the first half of the 20th century. In this paper, a recent case of wohlfahrtiosis recorded in Northern Serbia is evidenced using morphological and molecular techniques. Larvae were collected from two adult sheep with severe hoof myiasis and two young sheep with genital and interdigital myiasis. Morphological identification was performed for adults bred from the infested vulva and third-stage larvae (L3) collected from the hoof wounds, supported with barcoding sequences of the COI gene obtained from larval pairs from the hoof wounds of older and the genitalia of younger sheep. W. magnifica was identified according to the appearance of male fly terminalia and the morphology of L3, which was confirmed after the comparison of representative sequences of the COI gene (deposited in GenBank™ under accession numbers MT027108-MT027114) to those available in GenBank™. This finding represents the first reported case of wohlfahrtiosis in the Western Balkans in 80 years, highlighting the need to re-inform relevant stakeholders to achieve adequate disease control.},
}
@article {pmid38398777,
year = {2024},
author = {Kirichenko, NI and Ageev, AA and Astapenko, SA and Golovina, AN and Kasparyan, DR and Kosheleva, OV and Timokhov, AV and Tselikh, EV and Zakharov, EV and Musolin, DL and Belokobylskij, SA},
title = {The Diversity of Parasitoids and Their Role in the Control of the Siberian Moth, Dendrolimus sibiricus (Lepidoptera: Lasiocampidae), a Major Coniferous Pest in Northern Asia.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {2},
pages = {},
pmid = {38398777},
issn = {2075-1729},
support = {22-16-00075//Russian Science Foundation/ ; FWES-2024-0029//Basic project of the Sukachev Institute of Forest SB RAS/ ; },
abstract = {The Siberian moth, Dendrolimus sibiricus Tschetv., 1908 (Lepidoptera: Lasiocampidae) is a conifer pest that causes unprecedented forest mortality in Northern Asia, leading to enormous ecological and economic losses. This is the first study summarizing data on the parasitoid diversity and parasitism of this pest over the last 118 years (1905-2022). Based on 860 specimens of freshly reared and archival parasitoids, 16 species from two orders (Hymenoptera and Diptera) were identified morphologically and/or with the use of DNA barcoding. For all of them, data on distribution and hosts and images of parasitoid adults are provided. Among them, the braconid species, Meteorus versicolor (Wesmael, 1835), was documented as a parasitoid of D. sibiricus for the first time. The eastern Palaearctic form, Aleiodes esenbeckii (Hartig, 1838) dendrolimi (Matsumura, 1926), status nov., was resurrected from synonymy as a valid subspecies, and a key for its differentiation from the western Palaearctic subspecies Aleiodes esenbeckii ssp. esenbecki is provided. DNA barcodes of 11 parasitoid species from Siberia, i.e., nine hymenopterans and two dipterans, represented novel records and can be used for accurate molecular genetic identification of species. An exhaustive checklist of parasitoids accounting for 93 species associated with D. sibirisus in northern Asia was compiled. Finally, the literature and original data on parasitism in D. sibiricus populations for the last 83 years (1940-2022) were analysed taking into account the pest population dynamics (i.e., growth, outbreak, decline, and depression phases). A gradual time-lagged increase in egg and pupal parasitism in D. sibiricus populations was detected, with a peak in the pest decline phase. According to long-term observations, the following species are able to cause significant mortality of D. sibiricus in Northern Asia: the hymenopteran egg parasitoids Telenomus tetratomus and Ooencyrtus pinicolus; the larval parasitoids Aleiodes esenbeckii sp. dendrolimi, Cotesia spp., and Glyptapanteles liparidis; and the dipteran pupal parasitoids Masicera sphingivora, Tachina sp., and Blepharipa sp. Their potential should be further explored in order to develop biocontrol programs for this important forest pest.},
}
@article {pmid38396871,
year = {2024},
author = {Zhao, S and Gao, X and Yu, X and Yuan, T and Zhang, G and Liu, C and Li, X and Wei, P and Li, X and Liu, X},
title = {Comparative Analysis of Chloroplast Genome of Meconopsis (Papaveraceae) Provides Insights into Their Genomic Evolution and Adaptation to High Elevation.},
journal = {International journal of molecular sciences},
volume = {25},
number = {4},
pages = {},
pmid = {38396871},
issn = {1422-0067},
support = {XZ202001YD0028C, XZ202102YD0031C//the Local Development Funds of Science and Technology Department of Tibet/ ; },
mesh = {Sequence Analysis, DNA ; *Genome, Chloroplast ; Phylogeny ; Genomics/methods ; *Papaveraceae/genetics ; Evolution, Molecular ; },
abstract = {The Meconopsis species are widely distributed in the Qinghai-Tibet Plateau, Himalayas, and Hengduan Mountains in China, and have high medicinal and ornamental value. The high diversity of plant morphology in this genus poses significant challenges for species identification, given their propensity for highland dwelling, which makes it a question worth exploring how they cope with the harsh surroundings. In this study, we recently generated chloroplast (cp) genomes of two Meconopsis species, Meconopsis paniculata (M. paniculata) and M. pinnatifolia, and compared them with those of ten Meconopsis cp genomes to comprehend cp genomic features, their phylogenetic relationships, and what part they might play in plateau adaptation. These cp genomes shared a great deal of similarities in terms of genome size, structure, gene content, GC content, and codon usage patterns. The cp genomes were between 151,864 bp and 154,997 bp in length, and contain 133 predictive genes. Through sequence divergence analysis, we identified three highly variable regions (trnD-psbD, ccsA-ndhD, and ycf1 genes), which could be used as potential markers or DNA barcodes for phylogenetic analysis. Between 22 and 38 SSRs and some long repeat sequences were identified from 12 Meconopsis species. Our phylogenetic analysis confirmed that 12 species of Meconopsis clustered into a monophyletic clade in Papaveraceae, which corroborated their intrageneric relationships. The results indicated that M. pinnatifolia and M. paniculata are sister species in the phylogenetic tree. In addition, the atpA and ycf2 genes were positively selected in high-altitude species. The functions of these two genes might be involved in adaptation to the extreme environment in the cold and low CO2 concentration conditions at the plateau.},
}
@article {pmid38396790,
year = {2024},
author = {Ishino, T and Oda, T and Kawasumi, T and Takemoto, K and Nishida, M and Horibe, Y and Chikuie, N and Taruya, T and Hamamoto, T and Ueda, T and Takeno, S},
title = {Severe Type 2 Inflammation Leads to High Platelet-Activating-Factor-Associated Pathology in Chronic Rhinosinusitis with Nasal Polyps-A Hierarchical Cluster Analysis Using Bulk RNA Barcoding and Sequencing.},
journal = {International journal of molecular sciences},
volume = {25},
number = {4},
pages = {},
pmid = {38396790},
issn = {1422-0067},
support = {22K09668//the Japan Society for the Promotion of Science KAKENHI/ ; H30-Nanchitou (Nan)-Ippan- 016//a Health Labor Sciences Research grant/ ; 0G20KA7383//Research Collaboration Fund with Universal Sound Design Inc/ ; },
mesh = {Humans ; *Rhinitis/pathology ; Platelet Activating Factor/genetics/metabolism ; Nasal Mucosa/metabolism ; RNA/metabolism ; *Nasal Polyps/pathology ; *Rhinosinusitis ; *Sinusitis/metabolism ; Inflammation/metabolism ; Chronic Disease ; Cluster Analysis ; Eosinophils/metabolism ; },
abstract = {Platelet-activating factor (PAF) is a phospholipid-derived inflammatory mediator that triggers various inflammatory conditions, including eosinophil activation and recruitment. This study aimed to evaluate the expressions of PAF-metabolism-associated genes, namely genes coding the enzymes involved in PAF synthesis (LPCAT1, LPCAT2, LPCAT3, and LPCAT4), PAF degradation (PAFAH1B2, PAFAH1B3, and PAFAH2), and the gene for the PAF receptor (PTAFR) in subtypes of CRSwNP classified by clinical- or hierarchal-analysis-based classifications. Transcriptomic analysis using bulk RNA barcoding and sequencing (BRB-seq) was performed with CRSwNP, including eosinophilic CRS (ECRS) (n = 9), nonECRS (n = 8), ECRS with aspirin-exacerbated respiratory disease (Asp) (n = 3), and controls with a normal uncinate process mucosa (n = 6). PTAFR was only upregulated in ECRS and nonECRS. In the hierarchical cluster analysis with clusters 1 and 2 reflecting patients with low-to-moderate and high levels of type 2 inflammation, respectively, cluster 1 exhibited a significant downregulation of LPCAT2 and an upregulation of PTAFR expression, while cluster 2 showed an upregulation of LPCAT1, PAFAH1B2, and PTAFR and downregulation of PAFAH2 expression. Understanding this strong PAF-associated pathophysiology in the severe type 2 inflammation group could provide valuable insights into the treatment and management of CRSwNP.},
}
@article {pmid38396506,
year = {2024},
author = {Seniczak, S and Seniczak, A and Jordal, BH},
title = {Morphological Ontogeny, Ecology, and Biogeography of Fuscozetes fuscipes (Acari, Oribatida, Ceratozetidae).},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {4},
pages = {},
pmid = {38396506},
issn = {2076-2615},
support = {6-20, 70184243//Norwegian Taxonomy Initiative/ ; 9-21, 70184244//Norwegian Taxonomy Initiative/ ; },
abstract = {The systematic status of Fuscozetes Sellnick, 1928, is not clear in the literature. Therefore, the morphological ontogeny of F. fuscipes (C.L. Koch, 1844), the type species of this genus, was investigated and compared with its congeners in this study, and a new diagnosis of Fuscozetes is given. The juveniles of F. fuscipes are light brown, with a brown prodorsum, sclerites, epimeres, and legs. In all juveniles, a humeral organ and a humeral macrosclerite are present. The gastronotum of the larva has 12 pairs of setae (h3 is present), whereas the nymphs have 15 pairs. In the larva, the gastronotal shield is weakly developed, and most gastronotal setae are short except for a slightly longer h2. Most of the gastronotal setae are inserted on the microsclerites except for h3, and several other macrosclerites and many microsclerites are present on the hysterosoma. In the nymphs, the gastronotal shield is well developed, with 10 pairs of setae (d-, l-, and h-series, and p1), and setae p2 and p3 are located on a large posteroventral macrosclerite. In all the instars, femora I and II are oval in cross-section, without a large ventral carina. Mitochondrial COI sequence data revealed a deep split between the Nearctic and Palearctic populations of F. fuscipes, and a less, but significant, divergence within each continent. These strong geographical barriers were contrasted with multiple cases of shared haplotypes over long distances in the Palearctic, indicating high migration rates in modern times.},
}
@article {pmid38396041,
year = {2024},
author = {Coorens, THH and Spencer Chapman, M and Williams, N and Martincorena, I and Stratton, MR and Nangalia, J and Campbell, PJ},
title = {Reconstructing phylogenetic trees from genome-wide somatic mutations in clonal samples.},
journal = {Nature protocols},
volume = {19},
number = {6},
pages = {1866-1886},
pmid = {38396041},
issn = {1750-2799},
support = {21777/CRUK_/Cancer Research UK/United Kingdom ; ALTF 172-2022//European Molecular Biology Organization (EMBO)/ ; },
mesh = {Humans ; *Phylogeny ; *Mutation ; Software ; Genome, Human/genetics ; Whole Genome Sequencing/methods ; },
abstract = {Phylogenetic trees are a powerful means to display the evolutionary history of species, pathogens and, more recently, individual cells of the human body. Whole-genome sequencing of laser capture microdissections or expanded stem cells has allowed the discovery of somatic mutations in clones, which can be used as natural barcodes to reconstruct the developmental history of individual cells. Here we describe Sequoia, our pipeline to reconstruct lineage trees from clones of normal cells. Candidate somatic mutations are called against the human reference genome and filtered to exclude germline mutations and artifactual variants. These filtered somatic mutations form the basis for phylogeny reconstruction using a maximum parsimony framework. Lastly, we use a maximum likelihood framework to explicitly map mutations to branches in the phylogenetic tree. The resulting phylogenies can then serve as a basis for many subsequent analyses, including investigating embryonic development, tissue dynamics in health and disease, and mutational signatures. Sequoia can be readily applied to any clonal somatic mutation dataset, including single-cell DNA sequencing datasets, using the commands and scripts provided. Moreover, Sequoia is highly flexible and can be easily customized. Typically, the runtime of the core script ranges from minutes to an hour for datasets with a moderate number (50,000-150,000) of variants. Competent bioinformatic skills, including in-depth knowledge of the R programming language, are required. A high-performance computing cluster (one that is capable of running mutation-calling algorithms and other aspects of the analysis at scale) is also required, especially if handling large datasets.},
}
@article {pmid38392777,
year = {2024},
author = {Ali, S and Wright, AH and Tanney, JB and Renaud, JB and Sumarah, MW},
title = {Fungal Endophytes: Discovering What Lies within Some of Canada's Oldest and Most Resilient Grapevines.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {10},
number = {2},
pages = {},
pmid = {38392777},
issn = {2309-608X},
support = {J-001742 and J-002358//Agriculture and Agri-Food Canada A-base projects/ ; },
abstract = {Plant diseases and pests reduce crop yields, accounting for global crop losses of 30% to 50%. In conventional agricultural production systems, these losses are typically controlled by applying chemical pesticides. However, public pressure is mounting to curtail agrochemical use. In this context, employing beneficial endophytic microorganisms is an increasingly attractive alternative to the use of conventional chemical pesticides in agriculture. A multitude of fungal endophytes are naturally present in plants, producing enzymes, small peptides, and secondary metabolites due to their bioactivity, which can protect hosts from pathogens, pests, and abiotic stresses. The use of beneficial endophytic microorganisms in agriculture is an increasingly attractive alternative to conventional pesticides. The aim of this study was to characterize fungal endophytes isolated from apparently healthy, feral wine grapes in eastern Canada that have grown without agrochemical inputs for decades. Host plants ranged from unknown seedlings to long-lost cultivars not widely propagated since the 1800s. HPLC-MS was used to identify unique endophyte-derived chemical compounds in the host plants, while dual-culture competition assays showed a range in endophytes' ability to suppress the mycelial growth of Botrytis, which is typically controlled in viticulture with pesticides. Twelve of the most promising fungal endophytes isolated were identified using multilocus sequencing and morphology, while DNA barcoding was employed to identify some of their host vines. These fungal endophyte isolates, which consisted of both known and putative novel strains, belonged to seven genera in six families and five orders of Ascomycota. Exploring the fungal endophytes in these specimens may yield clues to the vines' survival and lead to the discovery of novel biocontrol agents.},
}
@article {pmid38392547,
year = {2024},
author = {Kock, LS and Körs, E and Husemann, M and Davaa, L and Dey, LS},
title = {Barcoding Fails to Delimit Species in Mongolian Oedipodinae (Orthoptera, Acrididae).},
journal = {Insects},
volume = {15},
number = {2},
pages = {},
pmid = {38392547},
issn = {2075-4450},
abstract = {Mongolia, a country in central Asia, with its vast grassland areas represents a hotspot for Orthoptera diversity, especially for the Acrididae. For Mongolia, 128 Acrididae species have been documented so far, of which 41 belong to the subfamily Oedipodinae (band-winged grasshoppers). Yet, few studies concerning the distribution and diversity of Oedipodinae have been conducted in this country. Molecular genetic data is almost completely absent, despite its value for species identification and discovery. Even, the simplest and most used data, DNA barcodes, so far have not been generated for the local fauna. Therefore, we generated the first DNA barcode data for Mongolian band-winged grasshoppers and investigated the resolution of this marker for species delimitation. We were able to assemble 105 DNA barcode (COI) sequences of 35 Oedipodinae species from Mongolia and adjacent countries. Based on this data, we reconstructed maximum likelihood and Bayesian inference phylogenies. We, furthermore, conducted automatic barcode gap discovery and used the Poisson tree process (PTP) for species delimitation. Some resolution was achieved at the tribe and genus level, but all delimitation methods failed to differentiate species by using the COI region. This lack of resolution may have multiple possible reasons, which likely differ between taxa: the lack of resolution in the Bryodemini may be partially explained by their massive genomes, implying the potential presence of large numbers of pseudogenes, while within the Sphingonotini incomplete lineage sorting and incorrect taxonomy are more likely explanations for the lack of signal. Further studies based on a larger number of gene fragments, including nuclear DNA, are needed to distinguish the species also at the molecular level.},
}
@article {pmid38392526,
year = {2024},
author = {Khatun, MF and Hwang, HS and Kang, JH and Lee, KY and Kil, EJ},
title = {Genetic Diversity and DNA Barcoding of Thrips in Bangladesh.},
journal = {Insects},
volume = {15},
number = {2},
pages = {},
pmid = {38392526},
issn = {2075-4450},
support = {//Andong National University/ ; },
abstract = {Thrips are economically important pests, and some species transmit plant viruses that are widely distributed and can damage vegetables and cash crops. Although few studies on thrips species have been conducted in Bangladesh, the variation and genetic diversity of thrips species remain unknown. In this study, we collected thrips samples from 16 geographical locations throughout the country and determined the nucleotide sequences of the mitochondrial cytochrome c oxidase subunit 1 (mtCOI) gene in 207 thrips individuals. Phylogenetic analysis revealed ten genera (Thrips, Haplothrips, Megalothrips, Scirtothrips, Frankliniella, Dendrothripoides, Astrothrips, Microcephalothrips, Ayyaria, and Bathrips) and 19 species of thrips to inhabit Bangladesh. Among these, ten species had not been previously reported in Bangladesh. Intraspecific genetic variation was diverse for each species. Notably, Thrips palmi was the most genetically diverse species, containing 14 haplotypes. The Mantel test revealed no correlation between genetic and geographical distances. This study revealed that thrips species are expanding their host ranges and geographical distributions, which provides valuable insights into monitoring the diversity of and control strategies for these pests.},
}
@article {pmid38389997,
year = {2024},
author = {Li, D and Jin, XH and Li, Y and Wang, YC and He, HY and Zhang, HB},
title = {Fungal communities associated with early immature tubers of wild Gastrodia elata.},
journal = {Ecology and evolution},
volume = {14},
number = {2},
pages = {e11004},
pmid = {38389997},
issn = {2045-7758},
abstract = {Full myco-heterotrophic orchid Gastrodia elata Bl. is widely distributed in Northeast Asia, and previous research has not fully investigated the symbiotic fungal community of its early immature tubers. This study utilized Illumina sequencing to compare symbiotic fungal communities in natural G. elata immature tubers and their habitats. LEfSe (Linear Discriminant Analysis Effect Size) was used to screen for Biomarkers that could explain variations among different fungal communities, and correlation analyses were performed among Biomarkers and other common orchid mycorrhizal fungi. Our results illustrate that the symbiotic fungal communities of immature G. elata tubers cannot be simply interpreted as subsets of the environmental fungal communities because some key members cannot be traced back to the environment. The early growth of G. elata was related to a small group of fungi, such as Sebacina, Thelephora, and Inocybe, which were also common mycorrhizal fungi from other orchids. In addition, Mycena, Auricularia, and Cryptococcus were unique fungal partners of G. elata, and many new species have yet to be discovered. Possible symbiotic Mycena should be M. plumipes and its sibling species in this case. Our results provide insight into the symbiotic partner switch and trophic pattern change during the development and maturation of G. elata.},
}
@article {pmid38387000,
year = {2024},
author = {Braglia, L and Ceschin, S and Iannelli, MA and Bog, M and Fabriani, M and Frugis, G and Gavazzi, F and Gianì, S and Mariani, F and Muzzi, M and Pelella, E and Morello, L},
title = {Characterization of the cryptic interspecific hybrid Lemna×mediterranea by an integrated approach provides new insights into duckweed diversity.},
journal = {Journal of experimental botany},
volume = {75},
number = {10},
pages = {3092-3110},
pmid = {38387000},
issn = {1460-2431},
support = {//European Commission/ ; //National Research Council/ ; },
mesh = {*Araceae/genetics ; *Hybridization, Genetic ; *Phylogeny ; Genetic Variation ; Polyploidy ; Genome, Plant ; Biodiversity ; },
abstract = {Lemnaceae taxonomy is challenged by the particular morphology of these tiny free-floating angiosperms. Although molecular taxonomy has helped clarify the phylogenetic history of this family, some inconsistency with morphological data leads to frequent misclassifications in the genus Lemna. Recently, the finding that Lemna japonica is an interspecific hybrid between Lemna minor and Lemna turionifera provided a clear explanation for one such taxonomic question. Here we demonstrated that L. minor is also capable of hybridizing with Lemna gibba, generating a cryptic but widespread taxon in the Mediterranean area. The nothotaxon Lemna ×mediterranea is described and compared with clones of the putative parental species L. minor and L. gibba. Genetic analysis by nuclear and plastid markers, as well as genome size measurement, revealed that two different cytotypes, diploid and triploid, originated by at least two independent hybridization events. Despite high overall similarity, morphometrical, physiological, and biochemical analyses showed an intermediate position of L. ×mediterranea between its parental species in most qualitative and quantitative characters, and also separation of the two hybrid cytotypes by some criteria. These data provide evidence that hybridization and polyploidization, driving forces of terrestrial plant evolution, contribute to duckweed genetic diversity and may have shaped the phylogenetic history of these mainly asexual, aquatic plants.},
}
@article {pmid38386133,
year = {2024},
author = {Zheng, Z and Zeng, W and Wang, S and Tan, W and Lu, X and Kairullayev, K and Mi, L and Hazihan, W and Liu, G and Yang, M and Wang, Y},
title = {Application of DNA barcodes in the genetic diversity of hard ticks (Acari: Ixodidae) in Kazakhstan.},
journal = {Experimental &amp; applied acarology},
volume = {92},
number = {3},
pages = {547-554},
pmid = {38386133},
issn = {1572-9702},
support = {RCZK202369//High-Level Talent Initiative Foundation of Shihezi University/ ; KX019303/0305//High-Level Talent Initiative Foundation of Shihezi University/ ; 2022B03014//Natural Science Key Project of Xinjiang Uygur Autonomous Region/ ; 2022YFC2304004//National Key Research and Development Program of China/ ; 82260399 and 81960379//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Kazakhstan ; *Ixodidae/genetics/classification ; *Genetic Variation ; *Electron Transport Complex IV/genetics ; *DNA Barcoding, Taxonomic ; *Phylogeny ; Haplotypes ; Arthropod Proteins/genetics ; },
abstract = {Forty-five tick species have been recorded in Kazakhstan. However, their genetic diversity and evolutionary relationships, particularly when compared to ticks in neighbouring countries, remain unclear. In the present study, 148 mitochondrial cytochrome c oxidase subunit I (COI) sequence data from our laboratory and NCBI (National Center for Biotechnology Information; https://www.ncbi.nlm.nih.gov/) data were used to address this knowledge gap. Phylogenetic analyses showed that i) Hyalomma anatolicum anatolicum (Koch, 1844) ticks from Jambyl Oblast (southeastern Kazakhstan) and Gansu Province (northwestern China) constituted a newly deviated clade; and ii) Dermacentor reticulatus (Fabricius, 1974) ticks from South Kazakhstan Oblast were closer to those in Romania and Turkey. The network diagram of haplotypes showed that i) the H-1 and H-2 haplotypes of Dermacentor marginatus (Sulzer, 1776) ticks from Zhetisu and Almaty were all newly evolved; and ii) the H-3 haplotypes of Haemaphysalis erinacei (Pavesi, 1884) from Almaty Oblast and Xinjiang Uygur Autonomous Region (northwestern China) were evolved from the H-1 haplotype from Italy. In the future, more COI data from different tick species, especially from Kazakhstan and neighbouring countries, should be employed in the field of tick DNA barcoding.},
}
@article {pmid38384757,
year = {2024},
author = {Mata-Sucre, Y and Parteka, LM and Ritz, CM and Gatica-Arias, A and Félix, LP and Thomas, WW and Souza, G and Vanzela, ALL and Pedrosa-Harand, A and Marques, A},
title = {Oligo-barcode illuminates holocentric karyotype evolution in Rhynchospora (Cyperaceae).},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1330927},
pmid = {38384757},
issn = {1664-462X},
abstract = {Holocentric karyotypes are assumed to rapidly evolve through chromosome fusions and fissions due to the diffuse nature of their centromeres. Here, we took advantage of the recent availability of a chromosome-scale reference genome for Rhynchospora breviuscula, a model species of this holocentric genus, and developed the first set of oligo-based barcode probes for a holocentric plant. These probes were applied to 13 additional species of the genus, aiming to investigate the evolutionary dynamics driving the karyotype evolution in Rhynchospora. The two sets of probes were composed of 27,392 (green) and 23,968 (magenta) oligonucleotides (45-nt long), and generated 15 distinct FISH signals as a unique barcode pattern for the identification of all five chromosome pairs of the R. breviuscula karyotype. Oligo-FISH comparative analyzes revealed different types of rearrangements, such as fusions, fissions, putative inversions and translocations, as well as genomic duplications among the analyzed species. Two rounds of whole genome duplication (WGD) were demonstrated in R. pubera, but both analyzed accessions differed in the complex chain of events that gave rise to its large, structurally diploidized karyotypes with 2n = 10 or 12. Considering the phylogenetic relationships and divergence time of the species, the specificity and synteny of the probes were maintained up to species with a divergence time of ~25 My. However, karyotype divergence in more distant species hindered chromosome mapping and the inference of specific events. This barcoding system is a powerful tool to study chromosomal variations and genomic evolution in holocentric chromosomes of Rhynchospora species.},
}
@article {pmid38383946,
year = {2024},
author = {Zhang, D and Luo, M and Guan, W and Ding, X and Liao, B and Su, H and Huang, J and Bai, J and Qiu, X and Huang, Z and Gong, L},
title = {Conservation Strategies for Aquilaria sinensis: Insights from DNA Barcoding and ISSR Markers.},
journal = {Plant foods for human nutrition (Dordrecht, Netherlands)},
volume = {79},
number = {2},
pages = {425-431},
pmid = {38383946},
issn = {1573-9104},
support = {002009/2019KT1261/2020ZDB25//Quality standard system construction for the whole industry chain of Chinese medicinal detection pieces/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Microsatellite Repeats ; *Thymelaeaceae/genetics/classification ; *Genetic Variation ; *Conservation of Natural Resources ; DNA, Plant/genetics ; Genetic Markers ; Phylogeny ; },
abstract = {The evergreen tree species Aquilaria sinensis holds significant economic importance due to its specific medicinal values and increasing market demand. However, the unrestricted illegal exploitation of its wild population poses a threat to its survival. This study aims to contribute to the conservation efforts of A. sinensis by constructing a library database of DNA barcodes, including two chloroplast genes (psbA-trnH and matK) and two nuclear genes (ITS and ITS2). Additionally, the genetic diversity and structure were estimated using inter-simple sequence repeats (ISSR) markers. Four barcodes of 57 collections gained 194 sequences, and 1371 polymorphic bands (98.63%) were observed using DNA ISSR fingerprinting. The Nei's gene diversity (H) of A. sinensis at the species level is 0.2132, while the Shannon information index (I) is 0.3128. The analysis of molecular variance revealed a large significant proportion of total genetic variations and differentiation among populations (Gst = 0.4219), despite a relatively gene flow (Nm = 0.6853) among populations, which were divided into two groups by cluster analysis. There was a close genetic relationship among populations with distances of 0.0845 to 0.5555. This study provides evidence of the efficacy and dependability of establishing a DNA barcode database and using ISSR markers to assess the extent of genetic diversity A. sinensis. Preserving the genetic resources through the conservation of existing populations offers a valuable proposition. The effective utilization of these resources will be further deliberated in subsequent breeding endeavors, with the potential to breed agarwood commercial lines.},
}
@article {pmid38381588,
year = {2024},
author = {Cambronero-Heinrichs, JC and Rojas-Gätjens, D and Baizán, M and Alvarado-Ocampo, J and Rojas-Jimenez, K and Loaiza, R and Chavarría, M and Calderón-Arguedas, &#xd3; and Troyo, A},
title = {Highly abundant bacteria in the gut of Triatoma dimidiata (Hemiptera: Reduviidae) can inhibit the growth of Trypanosoma cruzi (Kinetoplastea: Trypanosomatidae).},
journal = {Journal of medical entomology},
volume = {61},
number = {6},
pages = {1333-1344},
doi = {10.1093/jme/tjae012},
pmid = {38381588},
issn = {1938-2928},
support = {//Vicerectory of Research of Universidad de Costa Rica/ ; //National Center of Biotechnological Innovations/ ; },
mesh = {Animals ; *Triatoma/growth &amp; development/microbiology ; *Gastrointestinal Microbiome ; *Trypanosoma cruzi ; Bacteria/isolation &amp; purification/classification ; Insect Vectors/microbiology ; RNA, Ribosomal, 16S/analysis ; Costa Rica ; },
abstract = {Chagas disease, caused by the protozoan Trypanosoma cruzi, is a zoonosis primarily found in rural areas of Latin America. It is considered a neglected tropical disease, and Triatoma dimidiata is the main vector of the parasite in Central America. Despite efforts, Chagas disease continues to be a public health concern, and vector control remains a primary tool to reduce transmission. In this study, we tested the hypothesis that highly abundant bacteria in the gut of T. dimidiata inhibit the growth of T. cruzi. To achieve this, bacterial diversity in the gut of T. dimidiata specimens from Costa Rica was characterized by metabarcoding of the 16S rRNA, microbial isolation was performed, and the effect of freeze-dried supernatants of the isolates on T. cruzi was investigated. Metabarcoding showed that the most abundant genera in the gut were Corynebacterium, Tsukamurella, Brevibacterium, and Staphylococcus. Barcoding and sequences comparison confirmed that 8 of the 30 most abundant amplicon sequence variants (ASVs) were isolated, and 2 of them showed an inhibitory effect on the growth of T. cruzi epimastigotes. These bacteria correspond to isolates of Tsukamurella and Brevibacterium, which were respectively the second and sixth most abundant ASVs in the gut of T. dimidiata. Notably, only the isolate of Brevibacterium showed a significant difference in growth inhibition against epimastigotes of both T. cruzi strains tested. These findings suggest that the gut microbiota of T. dimidiata may play an active role in modulating parasite development.},
}
@article {pmid38379414,
year = {2024},
author = {Cheng, O and Ling, MH and Wang, C and Wu, S and Ritchie, ME and Göke, J and Amin, N and Davidson, NM},
title = {Flexiplex: a versatile demultiplexer and search tool for omics data.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {3},
pages = {},
pmid = {38379414},
issn = {1367-4811},
support = {GNT2016547//NHMRC/ ; },
mesh = {*Software ; Sequence Analysis, DNA ; *Search Engine ; High-Throughput Nucleotide Sequencing ; Electronic Data Processing ; },
abstract = {MOTIVATION: The process of analyzing high throughput sequencing data often requires the identification and extraction of specific target sequences. This could include tasks, such as identifying cellular barcodes and UMIs in single-cell data, and specific genetic variants for genotyping. However, existing tools, which perform these functions are often task-specific, such as only demultiplexing barcodes for a dedicated type of experiment, or are not tolerant to noise in the sequencing data.<br><br>RESULTS: To overcome these limitations, we developed Flexiplex, a versatile and fast sequence searching and demultiplexing tool for omics data, which is based on the Levenshtein distance and thus allows imperfect matches. We demonstrate Flexiplex's application on three use cases, identifying cell-line-specific sequences in Illumina short-read single-cell data, and discovering and demultiplexing cellular barcodes from noisy long-read single-cell RNA-seq data. We show that Flexiplex achieves an excellent balance of accuracy and computational efficiency compared to leading task-specific tools.<br><br>Flexiplex is available at https://davidsongroup.github.io/flexiplex/.},
}
@article {pmid38375033,
year = {2024},
author = {Mück, F and Scotti, F and Mauvisseau, Q and Thorbek, BLG and Wangensteen, H and de Boer, HJ},
title = {Three-tiered authentication of herbal traditional Chinese medicine ingredients used in women's health provides progressive qualitative and quantitative insight.},
journal = {Frontiers in pharmacology},
volume = {15},
number = {},
pages = {1353434},
pmid = {38375033},
issn = {1663-9812},
abstract = {Traditional Chinese Medicine (TCM) herbal products are increasingly used in Europe, but prevalent authentication methods have significant gaps in detection. In this study, three authentication methods were tested in a tiered approach to improve accuracy on a collection of 51 TCM plant ingredients obtained on the European market. We show the relative performance of conventional barcoding, metabarcoding and standardized chromatographic profiling for TCM ingredients used in one of the most diagnosed disease patterns in women, endometriosis. DNA barcoding using marker ITS2 and chromatographic profiling are methods of choice reported by regulatory authorities and relevant national pharmacopeias. HPTLC was shown to be a valuable authentication tool, combined with metabarcoding, which gives an increased resolution on species diversity, despite dealing with highly processed herbal ingredients. Conventional DNA barcoding as a recommended method was shown to be an insufficient tool for authentication of these samples, while DNA metabarcoding yields an insight into biological contaminants. We conclude that a tiered identification strategy can provide progressive qualitative and quantitative insight in an integrative approach for quality control of processed herbal ingredients.},
}
@article {pmid38374415,
year = {2024},
author = {Furusawa, H and Waki, T},
title = {A description of a new species of the genus Brachydistomum (Trematode, Dicrocoeliidae) from the Eurasian Tree Sparrow Passer montanus (Linnaeus) (Passeriformes) in Japan, with a report on the first intermediate host.},
journal = {Systematic parasitology},
volume = {101},
number = {2},
pages = {22},
pmid = {38374415},
issn = {1573-5192},
mesh = {Animals ; *Sparrows/genetics ; *Dicrocoeliidae ; Japan ; Phylogeny ; Species Specificity ; *Trematoda ; },
abstract = {The trematode Brachydistomum suzume n. sp. (Dicrocoeliidae) was detected in the Eurasian Tree Sparrow Passer montanus, and described as a new species in Japan. This new species can be distinguished from the other members of the genus on the basis of morphological characters of suckers and reproductive organs. A partial sequence of adult mitochondrial cytochrome c oxidase subunit 1 (COI) was used as a DNA barcode, and dicrocoeliid sporocysts and cercariae detected from four camaenid land snail species, Bradybaena pellucida, Brad. similaris, Acusta sieboldiana and Euhadra brandtii, were molecularly identified as the new species. Phylogenetic trees of nuclear 28S ribosomal DNA and COI also showed the new species to be distinct from the other trematode species, including Brachydistomum spp.},
}
@article {pmid38374363,
year = {2024},
author = {Sun, W and Perkins, M and Huyghe, M and Faraldo, MM and Fre, S and Perié, L and Lyne, AM},
title = {Extracting, filtering and simulating cellular barcodes using CellBarcode tools.},
journal = {Nature computational science},
volume = {4},
number = {2},
pages = {128-143},
pmid = {38374363},
issn = {2662-8457},
support = {FSER20200211117//Schlumberger Foundation/ ; ARCPGA2021120004232_4874//Fondation ARC pour la Recherche sur le Cancer (ARC Foundation for Cancer Research)/ ; ERC StG 758170-Microbar//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; ATIPAvenir//Centre National de la Recherche Scientifique (National Center for Scientific Research)/ ; },
mesh = {Reproducibility of Results ; Sequence Analysis, DNA/methods ; *DNA Barcoding, Taxonomic/methods ; *DNA/genetics ; Polymerase Chain Reaction ; },
abstract = {Identifying true DNA cellular barcodes among polymerase chain reaction and sequencing errors is challenging. Current tools are restricted in the diversity of barcode types supported or the analysis strategies implemented. As such, there is a need for more versatile and efficient tools for barcode extraction, as well as for tools to investigate which factors impact barcode detection and which filtering strategies to best apply. Here we introduce the package CellBarcode and its barcode simulation kit, CellBarcodeSim, that allows efficient and versatile barcode extraction and filtering for a range of barcode types from bulk or single-cell sequencing data using a variety of filtering strategies. Using the barcode simulation kit and biological data, we explore the technical and biological factors influencing barcode identification and provide a decision tree on how to optimize barcode identification for different barcode settings. We believe that CellBarcode and CellBarcodeSim have the capability to enhance the reproducibility and interpretation of barcode results across studies.},
}
@article {pmid38371866,
year = {2024},
author = {Vanderpool, DD and Wilcox, TM and Young, MK and Pilgrim, KL and Schwartz, MK},
title = {Simultaneous species detection and discovery with environmental DNA metabarcoding: A freshwater mollusk case study.},
journal = {Ecology and evolution},
volume = {14},
number = {2},
pages = {e11020},
pmid = {38371866},
issn = {2045-7758},
support = {P20 GM103546/GM/NIGMS NIH HHS/United States ; },
abstract = {Environmental DNA (eDNA) sampling is a powerful tool for rapidly characterizing biodiversity patterns for specious, cryptic taxa with incomplete taxonomies. One such group that are also of high conservation concern are North American freshwater gastropods. In particular, springsnails of the genus Pyrgulopsis (Family: Hydrobiidae) are prevalent throughout the western United States where >140 species have been described. Many of the described species are narrow endemics known from a single spring or locality, and it is believed that there are likely many additional species which have yet to be described. The distribution of these species across the landscape is of interest because habitat loss and degradation, climate change, groundwater mining, and pollution have resulted in springsnail imperilment rates as high as 92%. Determining distributions with conventional sampling methods is limited by the fact that these snails are often <5 mm in length with few distinguishing morphological characters, making them both difficult to detect and to identify. We developed an eDNA metabarcoding protocol that is both inexpensive and capable of rapid, accurate detection of all known Pyrgulopsis species. When compared with conventional collection techniques, our pipeline consistently resulted in detection at sites previously known to contain Pyrgulopsis springsnails and at a cost per site that is likely to be substantially less than the conventional sampling and individual barcoding that has been done historically. Additionally, because our method uses eDNA extracted from filtered water, it is non-destructive and suitable for the detection of endangered species where "no take" restrictions may be in effect. This effort represents both a tool which is immediately applicable to taxa of high conservation concern across western North America and a case study in the broader application of eDNA sampling for landscape assessments of cryptic taxa of conservation concern.},
}
@article {pmid38370872,
year = {2024},
author = {Curd, EE and Gal, L and Gallego, R and Silliman, K and Nielsen, S and Gold, Z},
title = {rCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R.},
journal = {Environmental DNA (Hoboken, N.J.)},
volume = {6},
number = {1},
pages = {},
pmid = {38370872},
issn = {2637-4943},
support = {P20 GM103449/GM/NIGMS NIH HHS/United States ; },
abstract = {The sequencing revolution requires accurate taxonomic classification of DNA sequences. Key to making accurate taxonomic assignments are curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given the large and continuously growing volumes of both DNA sequence data and novel reference barcode targets. Monitoring and research applications require a greater diversity of specialized gene regions and targeted taxa then are currently curated by professional staff. Thus there is a growing need for an easy to implement computational tool that can generate comprehensive metabarcoding reference libraries for any bespoke locus. We address this need by reimagining CRUX from the Anacapa Toolkit and present the rCRUX package in R which, like it's predecessor, relies on sequence homology and PCR primer compatibility instead of keyword-searches to avoid limitations of user-defined metadata. The typical workflow involves searching for plausible seed amplicons (get_seeds_local() or get_seeds_remote()) by simulating in silico PCR to acquire a set of sequences analogous to PCR products containing a user-defined set of primer sequences. Next, these seeds are used to iteratively blast search seed sequences against a local copy of the National Center for Biotechnology Information (NCBI) formatted nt database using a taxonomic-rank based stratified random sampling approach (blast_seeds()). This results in a comprehensive set of sequence matches. This database is dereplicated and cleaned (derep_and_clean_db()) by identifying identical reference sequences and collapsing the taxonomic path to the lowest taxonomic agreement across all matching reads. This results in a curated, comprehensive database of primer-specific reference barcode sequences from NCBI. Databases can then be compared (compare_db()) to determine read and taxonomic overlap. We demonstrate that rCRUX provides more comprehensive reference databases for the MiFish Universal Teleost 12S, Taberlet trnl, fungal ITS, and Leray CO1 loci than CRABS, MetaCurator, RESCRIPt, and ecoPCR reference databases. We then further demonstrate the utility of rCRUX by generating 24 reference databases for 20 metabarcoding loci, many of which lack dedicated reference database curation efforts. The rCRUX package provides a simple to use tool for the generation of curated, comprehensive reference databases for user-defined loci, facilitating accurate and effective taxonomic classification of metabarcoding and DNA sequence efforts broadly.},
}
@article {pmid38370833,
year = {2024},
author = {Bai, Z and Zhang, D and Gao, Y and Tao, B and Bao, S and Enninful, A and Zhang, D and Su, G and Tian, X and Zhang, N and Xiao, Y and Liu, Y and Gerstein, M and Li, M and Xing, Y and Lu, J and Xu, ML and Fan, R},
title = {Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38370833},
issn = {2692-8205},
support = {R01 GM138856/GM/NIGMS NIH HHS/United States ; R56 HG012310/HG/NHGRI NIH HHS/United States ; R33 CA246711/CA/NCI NIH HHS/United States ; U54 CA274509/CA/NCI NIH HHS/United States ; RF1 MH128876/MH/NIMH NIH HHS/United States ; U54 CA268083/CA/NCI NIH HHS/United States ; UH3 CA257393/CA/NCI NIH HHS/United States ; U54 DK106857/DK/NIDDK NIH HHS/United States ; R01 CA245313/CA/NCI NIH HHS/United States ; U54 AG079759/AG/NIA NIH HHS/United States ; UM1 MH130991/MH/NIMH NIH HHS/United States ; U54 AG076043/AG/NIA NIH HHS/United States ; RM1 MH132648/MH/NIMH NIH HHS/United States ; },
abstract = {Spatial transcriptomics has emerged as a powerful tool for dissecting spatial cellular heterogeneity but as of today is largely limited to gene expression analysis. Yet, the life of RNA molecules is multifaceted and dynamic, requiring spatial profiling of different RNA species throughout the life cycle to delve into the intricate RNA biology in complex tissues. Human disease-relevant tissues are commonly preserved as formalin-fixed and paraffin-embedded (FFPE) blocks, representing an important resource for human tissue specimens. The capability to spatially explore RNA biology in FFPE tissues holds transformative potential for human biology research and clinical histopathology. Here, we present Patho-DBiT combining in situ polyadenylation and deterministic barcoding for spatial full coverage transcriptome sequencing, tailored for probing the diverse landscape of RNA species even in clinically archived FFPE samples. It permits spatial co-profiling of gene expression and RNA processing, unveiling region-specific splicing isoforms, and high-sensitivity transcriptomic mapping of clinical tumor FFPE tissues stored for five years. Furthermore, genome-wide single nucleotide RNA variants can be captured to distinguish different malignant clones from non-malignant cells in human lymphomas. Patho-DBiT also maps microRNA-mRNA regulatory networks and RNA splicing dynamics, decoding their roles in spatial tumorigenesis trajectory. High resolution Patho-DBiT at the cellular level reveals a spatial neighborhood and traces the spatiotemporal kinetics driving tumor progression. Patho-DBiT stands poised as a valuable platform to unravel rich RNA biology in FFPE tissues to study human tissue biology and aid in clinical pathology evaluation.},
}
@article {pmid38368650,
year = {2024},
author = {Shchepin, ON and López Villalba, &#xc1; and Inoue, M and Prikhodko, IS and Erastova, DA and Okun, MV and Woyzichovski, J and Yajima, Y and Gmoshinskiy, VI and Moreno, G and Novozhilov, YK and Schnittler, M},
title = {DNA barcodes reliably differentiate between nivicolous species of Diderma (Myxomycetes, Amoebozoa) and reveal regional differences within Eurasia.},
journal = {Protist},
volume = {175},
number = {2},
pages = {126023},
doi = {10.1016/j.protis.2024.126023},
pmid = {38368650},
issn = {1618-0941},
mesh = {*Myxomycetes ; DNA Barcoding, Taxonomic/methods ; Bayes Theorem ; Phylogeny ; DNA, Ribosomal/genetics ; },
abstract = {The nivicolous species of the genus Diderma are challenging to identify, and there are several competing views on their delimitation. We analyzed 102 accessions of nivicolous Diderma spp. that were sequenced for two or three unlinked genes to determine which of the current taxonomic treatments is better supported by molecular species delimitation methods. The results of a haplotype web analysis, Bayesian species delimitation under a multispecies coalescent model, and phylogenetic analyses on concatenated alignments support a splitting approach that distinguishes six taxa: Diderma alpinum, D. europaeum, D. kamchaticum, D. meyerae, D. microcarpum and D. niveum. The first two approaches also support the separation of Diderma alpinum into two species with allopatric distribution. An extended dataset of 800 specimens (mainly from Europe) that were barcoded with 18S rDNA revealed only barcode variants similar to those in the species characterized by the first data set, and showed an uneven distribution of these species in the Northern Hemisphere: Diderma microcarpum and D. alpinum were the only species found in all seven intensively sampled mountain regions. Partial 18S rDNA sequences serving as DNA barcodes provided clear signatures that allowed for unambiguous identification of the nivicolous Diderma spp., including two putative species in D. alpinum.},
}
@article {pmid38359907,
year = {2024},
author = {Han, S and Zhang, S and Yi, R and Bi, D and Ding, H and Yang, J and Ye, Y and Xu, W and Wu, L and Zhuo, R and Kan, X},
title = {Phylogenomics and plastomics offer new evolutionary perspectives on Kalanchoideae (Crassulaceae).},
journal = {Annals of botany},
volume = {133},
number = {4},
pages = {585-604},
pmid = {38359907},
issn = {1095-8290},
support = {//Opening Foundation of National Engineering Laboratory of Soil Pollution Control and Remediation Technologies/ ; NEL&amp;MARA-003//Key Laboratory of Heavy Metal Pollution Prevention &amp; Control, Ministry of Agriculture and Rural Affairs/ ; BK20211078//Basic Research Program of Natural Science Foundation of Jiangsu Province of China/ ; BS2101//Doctoral Enhancement Program of Suzhou Polytechnic Institute of Agriculture/ ; },
mesh = {*Phylogeny ; *Crassulaceae/genetics ; Plastids/genetics ; Biological Evolution ; Evolution, Molecular ; Genome, Plastid ; },
abstract = {BACKGROUND AND AIMS: Kalanchoideae is one of three subfamilies within Crassulaceae and contains four genera. Despite previous efforts, the phylogeny of Kalanchoideae remains inadequately resolved with persistent issues including low support, unstructured topologies and polytomies. This study aimed to address two central objectives: (1) resolving the pending phylogenetic questions within Kalanchoideae by using organelle-scale 'barcodes' (plastomes) and nuclear data; and (2) investigating interspecific diversity patterns among Kalanchoideae plastomes.<br><br>METHODS: To explore the plastome evolution in Kalanchoideae, we newly sequenced 38 plastomes representing all four constituent genera (Adromischus, Cotyledon, Kalanchoe and Tylecodon). We performed comparative analyses of plastomic features, including GC and gene contents, gene distributions at the IR (inverted repeat) boundaries, nucleotide divergence, plastomic tRNA (pttRNA) structures and codon aversions. Additionally, phylogenetic inferences were inferred using both the plastomic dataset (79 genes) and nuclear dataset (1054 genes).<br><br>KEY RESULTS: Significant heterogeneities were observed in plastome lengths among Kalanchoideae, strongly correlated with LSC (large single copy) lengths. Informative diversities existed in the gene content at SSC/IRa (small single copy/inverted repeat a), with unique patterns individually identified in Adromischus leucophyllus and one major Kalanchoe clade. The ycf1 gene was assessed as a shared hypervariable region among all four genera, containing nine lineage-specific indels. Three pttRNAs exhibited unique structures specific to Kalanchoideae and the genera Adromischus and Kalanchoe. Moreover, 24 coding sequences revealed a total of 41 lineage-specific unused codons across all four constituent genera. The phyloplastomic inferences clearly depicted internal branching patterns in Kalanchoideae. Most notably, by both plastid- and nuclear-based phylogenies, our research offers the first evidence that Kalanchoe section Eukalanchoe is not monophyletic.<br><br>CONCLUSIONS: This study conducted comprehensive analyses on 38 newly reported Kalanchoideae plastomes. Importantly, our results not only reconstructed well-resolved phylogenies within Kalanchoideae, but also identified highly informative unique markers at the subfamily, genus and species levels. These findings significantly enhance our understanding of the evolutionary history of Kalanchoideae.},
}
@article {pmid38359055,
year = {2024},
author = {Combosch, DJ and Burdick, D and Primov, K and Rios, D and Rios, K and Fernandez, J},
title = {Barcoding and mitochondrial phylogenetics of Porites corals.},
journal = {PloS one},
volume = {19},
number = {2},
pages = {e0290505},
pmid = {38359055},
issn = {1932-6203},
mesh = {Animals ; *Anthozoa/genetics ; Phylogeny ; Ecosystem ; Coral Reefs ; DNA, Mitochondrial ; },
abstract = {Coral reefs are the most diverse ecosystem on the planet based on the abundance and diversity of phyla and higher taxa. However, it is still difficult to assess the diversity of lower taxa, especially at the species level. One tool for improving the identification of lower taxa are genetic markers that can distinguish cryptic species and assess species boundaries. Here, we present one such approach for an important and challenging group of reef-building corals. Porites corals are the main reef-builders of many coral reefs in the Indo-Pacific, owing to the massive growth forms of some species. The current number of valid Porites species is controversial, inflated with many synonymies, and often based on gross colony morphology although several morphospecies believed to be widespread and common can only be distinguished based on detailed microstructure analyses by taxonomic experts. Here, we test the suitability of multiple regions of mtDNA as genetic barcodes to identify suitable markers for species differentiation and unambiguous identification. Resulting sequencing data was further used for the first phylogenetic analysis of Guam's Porites species. We tested eight different mitochondrial markers and analyzed four in detail for 135 Porites specimens: mtDNA markers were amplified for 67 Porites specimens from Guam, representing 12 nominal Porites species, and combined with 69 mitochondrial genomes, mostly from Hawaii. The combination of all 4 markers distinguished 10 common and 7 uncommon Central-West Pacific Porites species. Most clades separate species along taxonomic boundaries, which is uncommon for Porites corals and testifies to the suitability of our multi-marker approach, and a combination of the two most promising barcodes distinguished 8/10 common species. These barcodes are thus suitable to distinguish virtually cryptic species in one of the most important and challenging coral genera. They offer a cheap, fast and reliable way to identify Porites species for species-level research, monitoring and conservation.},
}
@article {pmid38358970,
year = {2024},
author = {Dvorak, M and Dittmann, IL and Pedrini-Martha, V and Hamerlík, L and Bitušík, P and Stuchlik, E and Vondrák, D and Füreder, L and Lackner, R},
title = {Molecular and morphological characterisation of larvae of the genus Diamesa Meigen, 1835 (Diptera: Chironomidae) in Alpine streams (Ötztal Alps, Austria).},
journal = {PloS one},
volume = {19},
number = {2},
pages = {e0298367},
pmid = {38358970},
issn = {1932-6203},
mesh = {Animals ; *Chironomidae/genetics ; *Diptera/genetics ; Ecosystem ; Larva/anatomy &amp; histology ; Rivers ; Austria ; DNA Barcoding, Taxonomic ; },
abstract = {Diamesa species (Diptera, Chironomidae) are widely distributed in freshwater ecosystems, and their life cycles are closely linked to environmental variables such as temperature, water quality, and sediment composition. Their sensitivity to environmental changes, particularly in response to pollution and habitat alterations, makes them valuable indicators of ecosystem health. The challenges associated with the morphological identification of larvae invoke the use of DNA barcoding for species determination. The mitochondrial cytochrome oxidase subunit I (COI) gene is regularly used for species identification but faces limitations, such as similar sequences in closely related species. To overcome this, we explored the use of the internal transcribed spacers (ITS) region in addition to COI for Diamesa larvae identification. Therefore, this study employs a combination of molecular markers alongside traditional morphological identification to enhance species discrimination. In total, 129 specimens were analysed, of which 101 were sampled from a glacier-fed stream in Rotmoostal, and the remaining 28 from spring-fed streams in the neighbouring valleys of Königstal and Timmelstal. This study reveals the inadequacy of utilizing single COI or ITS genes for comprehensive species differentiation within the genus Diamesa. However, the combined application of COI and ITS markers significantly enhances species identification resolution, surpassing the limitations faced by traditional taxonomists. Notably, this is evident in cases involving morphologically indistinguishable species, such as Diamesa latitarsis and Diamesa modesta. It highlights the potential of employing a multi-marker approach for more accurate and reliable Diamesa species identification. This method can be a powerful tool for identifying Diamesa species, shedding light on their remarkable adaptations to extreme environments and the impacts of environmental changes on their populations.},
}
@article {pmid38357418,
year = {2023},
author = {Schütte, A and Stüben, PE and Astrin, JJ},
title = {Molecular Weevil Identification Project: A thoroughly curated barcode release of 1300 Western Palearctic weevil species (Coleoptera, Curculionoidea).},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e96438},
pmid = {38357418},
issn = {1314-2828},
abstract = {The Molecular Weevil Identification project (MWI) studies the systematics of Western Palearctic weevils (superfamily Curculionoidea) in an integrative taxonomic approach of DNA barcoding, morphology and ecology. This barcode release provides almost 3600 curated CO1 sequences linked to morphological vouchers in about 1300 weevil species. The dataset is presented in statistical distance tables and as a Neighbour-Joining tree. Bayesian Inference trees are computed for the subfamilies Cryptorhynchinae, Apioninae and Ceutorhynchinae. Altogether, 18 unresolved taxonomic issues are discussed. A new barcode primer set is presented. Finally, we establish group-specific genetic distances for many weevil genera to serve as a tool in species delineation. These values are statistically based on distances between "good species" and their congeners. With this morphologically calibrated approach, we could resolve most alpha-taxonomic questions within the MWI project.},
}
@article {pmid38357249,
year = {2024},
author = {Li, BL and Hu, PH and Guo, L and Che, YL and Wang, ZQ},
title = {Discovery of five new species of Allacta from Yunnan and Hainan, China (Blattodea, Pseudophyllodromiidae).},
journal = {ZooKeys},
volume = {1191},
number = {},
pages = {1-21},
pmid = {38357249},
issn = {1313-2989},
abstract = {We examined new Allacta materials from Yunnan and Hainan Province, China, and discovered new species using both morphological and molecular species delimitation (ABGD) methods. Five new species are described: A.bifolium Li &amp; Wang, sp. nov., A.hemiptera Li &amp; Wang, sp. nov., A.lunulara Li &amp; Wang, sp. nov., A.redacta Li &amp; Wang, sp. nov., and A.unicaudata Li &amp; Wang, sp. nov. All five species are placed under the hamifera species group. An updated key and checklist of Allacta species from China are provided.},
}
@article {pmid38354391,
year = {2024},
author = {Lerminiaux, N and Fakharuddin, K and Mulvey, MR and Mataseje, L},
title = {Do we still need Illumina sequencing data? Evaluating Oxford Nanopore Technologies R10.4.1 flow cells and the Rapid v14 library prep kit for Gram negative bacteria whole genome assemblies.},
journal = {Canadian journal of microbiology},
volume = {70},
number = {5},
pages = {178-189},
doi = {10.1139/cjm-2023-0175},
pmid = {38354391},
issn = {1480-3275},
mesh = {*Genome, Bacterial ; *High-Throughput Nucleotide Sequencing/methods ; Gram-Negative Bacteria/genetics ; Whole Genome Sequencing/methods ; beta-Lactamases/genetics ; Nanopore Sequencing/methods ; Gene Library ; Sequence Analysis, DNA/methods ; },
abstract = {The best whole genome assemblies are currently built from a combination of highly accurate short-read sequencing data and long-read sequencing data that can bridge repetitive and problematic regions. Oxford Nanopore Technologies (ONT) produce long-read sequencing platforms and they are continually improving their technology to obtain higher quality read data that is approaching the quality obtained from short-read platforms such as Illumina. As these innovations continue, we evaluated how much ONT read coverage produced by the Rapid Barcoding Kit v14 (SQK-RBK114) is necessary to generate high-quality hybrid and long-read-only genome assemblies for a panel of carbapenemase-producing Enterobacterales bacterial isolates. We found that 30× long-read coverage is sufficient if Illumina data are available, and that more (at least 100× long-read coverage is recommended for long-read-only assemblies. Illumina polishing is still improving single nucleotide variants (SNVs) and INDELs in long-read-only assemblies. We also examined if antimicrobial resistance genes could be accurately identified in long-read-only data, and found that Flye assemblies regardless of ONT coverage detected >96% of resistance genes at 100% identity and length. Overall, the Rapid Barcoding Kit v14 and long-read-only assemblies can be an optimal sequencing strategy (i.e., plasmid characterization and AMR detection) but finer-scale analyses (i.e., SNV) still benefit from short-read data.},
}
@article {pmid38352648,
year = {2024},
author = {Jacob, C and Student, J and Bridges, DF and Chu, W and Porwollik, S and McClelland, M and Melotto, M},
title = {Intraspecies competition among Salmonella enterica isolates in the lettuce leaf apoplast.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1302047},
pmid = {38352648},
issn = {1664-462X},
abstract = {Multiple Salmonella enterica serovars and strains have been reported to be able to persist inside the foliar tissue of lettuce (Lactuca sativa L.), potentially resisting washing steps and reaching the consumer. Intraspecies variation of the bacterial pathogen and of the plant host can both significantly affect the outcome of foliar colonization. However, current understanding of the mechanisms underlying this phenomenon is still very limited. In this study, we evaluated the foliar fitness of 14 genetically barcoded S. enterica isolates from 10 different serovars, collected from plant and animal sources. The S. enterica isolates were vacuum-infiltrated individually or in pools into the leaves of three- to four-week-old lettuce plants. To estimate the survival capacity of individual isolates, we enumerated the bacterial populations at 0- and 10- days post-inoculation (DPI) and calculated their net growth. The competition of isolates in the lettuce apoplast was assessed through the determination of the relative abundance change of barcode counts of each isolate within pools during the 10 DPI experimental period. Isolates exhibiting varying apoplast fitness phenotypes were used to evaluate their capacity to grow in metabolites extracted from the lettuce apoplast and to elicit the reactive oxygen species burst immune response. Our study revealed that strains of S. enterica can substantially differ in their ability to survive and compete in a co-inhabited lettuce leaf apoplast. The differential foliar fitness observed among these S. enterica isolates might be explained, in part, by their ability to utilize nutrients available in the apoplast and to evade plant immune responses in this niche.},
}
@article {pmid38352467,
year = {2024},
author = {Roy, KR and Smith, JD and Li, S and Vonesch, SC and Nguyen, M and Burnett, WT and Orsley, KM and Lee, CS and Haber, JE and St Onge, RP and Steinmetz, LM},
title = {Dissecting quantitative trait nucleotides by saturation genome editing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38352467},
issn = {2692-8205},
support = {R01 GM121932/GM/NIGMS NIH HHS/United States ; R01 HG012446/HG/NHGRI NIH HHS/United States ; },
abstract = {Genome editing technologies have the potential to transform our understanding of how genetic variation gives rise to complex traits through the systematic engineering and phenotypic characterization of genetic variants. However, there has yet to be a system with sufficient efficiency, fidelity, and throughput to comprehensively identify causal variants at the genome scale. Here we explored the ability of templated CRISPR editing systems to install natural variants genome-wide in budding yeast. We optimized several approaches to enhance homology-directed repair (HDR) with donor DNA templates, including donor recruitment to target sites, single-stranded donor production by bacterial retrons, and in vivo plasmid assembly. We uncovered unique advantages of each system that we integrated into a single superior system named MAGESTIC 3.0. We used MAGESTIC 3.0 to dissect causal variants residing in 112 quantitative trait loci across 32 environmental conditions, revealing an enrichment for missense variants and loci with multiple causal variants. MAGESTIC 3.0 will facilitate the functional analysis of the genome at single-nucleotide resolution and provides a roadmap for improving template-based genome editing systems in other organisms.},
}
@article {pmid38351434,
year = {2024},
author = {Morard, R and Darling, KF and Weiner, AKM and Hassenrück, C and Vanni, C and Cordier, T and Henry, N and Greco, M and Vollmar, NM and Milivojevic, T and Rahman, SN and Siccha, M and Meilland, J and Jonkers, L and Quillévéré, F and Escarguel, G and Douady, CJ and de Garidel-Thoron, T and de Vargas, C and Kucera, M},
title = {The global genetic diversity of planktonic foraminifera reveals the structure of cryptic speciation in plankton.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {99},
number = {4},
pages = {1218-1241},
doi = {10.1111/brv.13065},
pmid = {38351434},
issn = {1469-185X},
support = {390741603//Deutsche Forschungsgemeinschaft/ ; FJC2021-047494-I/MCIN/AEI/10.13039/501100011033//Juan de la Cierva-formaci&#xf3;n 2021/ ; NER/J/S/2000/00860//Natural Environment Research Council of the United Kingdom/ ; NE/D009707/1//Natural Environment Research Council of the United Kingdom/ ; },
mesh = {*Foraminifera/genetics/classification ; *Genetic Variation ; *Plankton/genetics/classification ; Genetic Speciation ; DNA Barcoding, Taxonomic ; },
abstract = {The nature and extent of diversity in the plankton has fascinated scientists for over a century. Initially, the discovery of many new species in the remarkably uniform and unstructured pelagic environment appeared to challenge the concept of ecological niches. Later, it became obvious that only a fraction of plankton diversity had been formally described, because plankton assemblages are dominated by understudied eukaryotic lineages with small size that lack clearly distinguishable morphological features. The high diversity of the plankton has been confirmed by comprehensive metabarcoding surveys, but interpretation of the underlying molecular taxonomies is hindered by insufficient integration of genetic diversity with morphological taxonomy and ecological observations. Here we use planktonic foraminifera as a study model and reveal the full extent of their genetic diversity and investigate geographical and ecological patterns in their distribution. To this end, we assembled a global data set of ~7600 ribosomal DNA sequences obtained from morphologically characterised individual foraminifera, established a robust molecular taxonomic framework for the observed diversity, and used it to query a global metabarcoding data set covering ~1700 samples with ~2.48 billion reads. This allowed us to extract and assign 1 million reads, enabling characterisation of the structure of the genetic diversity of the group across ~1100 oceanic stations worldwide. Our sampling revealed the existence of, at most, 94 distinct molecular operational taxonomic units (MOTUs) at a level of divergence indicative of biological species. The genetic diversity only doubles the number of formally described species identified by morphological features. Furthermore, we observed that the allocation of genetic diversity to morphospecies is uneven. Only 16 morphospecies disguise evolutionarily significant genetic diversity, and the proportion of morphospecies that show genetic diversity increases poleward. Finally, we observe that MOTUs have a narrower geographic distribution than morphospecies and that in some cases the MOTUs belonging to the same morphospecies (cryptic species) have different environmental preferences. Overall, our analysis reveals that even in the light of global genetic sampling, planktonic foraminifera diversity is modest and finite. However, the extent and structure of the cryptic diversity reveals that genetic diversification is decoupled from morphological diversification, hinting at different mechanisms acting at different levels of divergence.},
}
@article {pmid38351222,
year = {2024},
author = {Zhang, X and Gao, Y and Zhang, Y and Li, F and Li, H and Lei, F},
title = {Identification of Autism Spectrum Disorder Using Topological Data Analysis.},
journal = {Journal of imaging informatics in medicine},
volume = {37},
number = {3},
pages = {1023-1037},
pmid = {38351222},
issn = {2948-2933},
support = {12071051//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Autism Spectrum Disorder/diagnosis/epidemiology ; Magnetic Resonance Imaging ; Databases, Factual ; Brain/pathology/diagnostic imaging ; Child ; Algorithms ; },
abstract = {Autism spectrum disorder (ASD) is a pervasive brain development disease. Recently, the incidence rate of ASD has increased year by year and posed a great threat to the lives and families of individuals with ASD. Therefore, the study of ASD has become very important. A suitable feature representation that preserves the data intrinsic information and also reduces data complexity is very vital to the performance of established models. Topological data analysis (TDA) is an emerging and powerful mathematical tool for characterizing shapes and describing intrinsic information in complex data. In TDA, persistence barcodes or diagrams are usually regarded as visual representations of topological features of data. In this paper, the Regional Homogeneity (ReHo) data of subjects obtained from Autism Brain Imaging Data Exchange (ABIDE) database were used to extract features by using TDA. The average accuracy of cross validation on ABIDE I database was 95.6% that was higher than any other existing methods (the highest accuracy among existing methods was 93.59%). The average accuracy for sampling with the same resolutions with the ABIDE I on the ABIDE II database was 96.5% that was also higher than any other existing methods (the highest accuracy among existing methods was 75.17%).},
}
@article {pmid38346458,
year = {2024},
author = {Cao, Z and Qu, Y and Song, Y and Xin, P},
title = {Comparative genomics and phylogenetic analysis of chloroplast genomes of Asian Caryodaphnopsis taxa (Lauraceae).},
journal = {Gene},
volume = {907},
number = {},
pages = {148259},
doi = {10.1016/j.gene.2024.148259},
pmid = {38346458},
issn = {1879-0038},
mesh = {Humans ; Phylogeny ; *Genome, Chloroplast ; *Lauraceae/genetics ; Genomics ; Biological Evolution ; },
abstract = {The genus Caryodaphnopsis, a member of the Lauraceae family, is characterized by seeds that are rich in oil, as well as highly exploitable fruits and wood. The Asian taxa within this genus exhibit complex morphological variations, posing challenges to their accurate classification and impeding their effective use and development as a resource. In this study, we sequenced the chloroplast genomes of 31 individuals representing nine Asian taxa within the Caryodaphnopsis genus. Our primary objectives were to reveal structural variations in these chloroplast genomes through comparative analyses and to infer the species' phylogenetic relationships. Our findings revealed that all chloroplast genomes had a tetrad structure, ranged in length from 148,828 to 154,946 bp, and harbored 128-131 genes. Notably, contraction of the IR region led to the absence of some genes in eight taxa. A comprehensive analysis identified 1267 long repetitive sequences and 2176 SSRs, 286 SNPs, and 135 indels across the 31 chloroplast genomes. The Ka/Ks ratio analysis indicated potential positive selection on the matK, rpl22, and rpoC2 genes. Furthermore, we identified six variable regions as promising barcode regions. Phylogenetic analysis grouped the nine Asian taxa into six branches, with C. henryi forming the basal group from which three distinct complexes emerged. This study contributes significantly to the current understanding of the evolutionary dynamics and phylogenetic relationships within the genus Caryodaphnopsis. Furthermore, the identified molecular markers hold potential for molecular barcoding applications in population genetics, providing valuable tools for future research and conservation efforts within this diverse genus.},
}
@article {pmid38343574,
year = {2024},
author = {Liu, K and Sun, H and Zhao, X and Wang, C and An, C and Li, A and Liu, S and Zhuang, Z},
title = {DNA barcoding, identification, and validation of the pufferfish (Order: Tetraodontiformes) in China coastal waters.},
journal = {Ecology and evolution},
volume = {14},
number = {2},
pages = {e10944},
pmid = {38343574},
issn = {2045-7758},
abstract = {The order Tetraodontiformes are one of the most unique groups of teleostean fish, exhibiting highly derived and greatly diversified phenotypes. It is a difficult task for both professionals and nonprofessionals to accurately identify these species only according to morphological characteristics. DNA barcoding can identify species at the molecular level to overcome the limitations of morphological classification. In this study, we collected 616 specimens of pufferfish from the coastal waters of China. According to the morphological characteristics, they were preliminarily identified as 50 species. Further analysis using DNA barcodes identified these specimens as 46 species, belonging to 23 genera, 6 families. According to the species classification results of DNA barcoding, the three species identified by morphology as Takifugu pseudommus, Takifugu chinensis, and Takifugu rubripes should be the same species. Similarly, Lagocephalus wheeleri is the synonym of Lagocephalus spadiceus. Another important discovery of DNA barcoding analysis is that there are closer interspecific genetic distances within the genus Takifugu. If T. rubripes, T. pseudommus, and T. chinensis are taken as one species, the average interspecific to intraspecific genetic distance ratio of Takifugu is only 6.21 times, which does not reach the DNA barcoding threshold of more than 10 times proposed previously. Although the interspecific genetic distance in the genus Takifugu is relatively small, each species can be clustered into independent clades in the NJ tree. In conclusion, this study not only found that there are synonymous phenomena in the order Tetraodontiformes but also provided molecular evidence for the valid species names of Takifugu rubripes and Lagocephalus Spadiceus. The results can provide reliable DNA barcoding information for the identification of pufferfish species, help solve the problem of classification confusion in this order, and provide technical support for the identification of the original components of related commodities on the aquatic product market.},
}
@article {pmid38342898,
year = {2024},
author = {Liu, LJ and Liu, CK and Cai, J and Deng, JJ and He, XJ and Zhou, SD},
title = {The complete plastomes of thirteen Libanotis (Apiaceae, Apioideae) plants: comparative and phylogenetic analyses provide insights into the plastome evolution and taxonomy of Libanotis.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {106},
pmid = {38342898},
issn = {1471-2229},
support = {32070221//National Natural Science Foundation of China/ ; 32070221//National Natural Science Foundation of China/ ; 32070221//National Natural Science Foundation of China/ ; 32070221//National Natural Science Foundation of China/ ; 32070221//National Natural Science Foundation of China/ ; 32070221//National Natural Science Foundation of China/ ; 510101202200376//Survey on the Background Resources of Chengdu Area of Giant Panda National Park/ ; 510101202200376//Survey on the Background Resources of Chengdu Area of Giant Panda National Park/ ; 510101202200376//Survey on the Background Resources of Chengdu Area of Giant Panda National Park/ ; 510101202200376//Survey on the Background Resources of Chengdu Area of Giant Panda National Park/ ; 510101202200376//Survey on the Background Resources of Chengdu Area of Giant Panda National Park/ ; 510101202200376//Survey on the Background Resources of Chengdu Area of Giant Panda National Park/ ; },
mesh = {Phylogeny ; *Apiaceae ; Evolution, Molecular ; Plastids/genetics ; Plants ; },
abstract = {BACKGROUND: The genus Libanotis Haller ex Zinn, nom. cons., a contentious member of Apiaceae, encompasses numerous economically and medicinally significant plants, comprising approximately 30 species distributed across Eurasia. Despite many previous taxonomic insights into it, phylogenetic studies of the genus are still lacking. And the establishment of a robust phylogenetic framework remains elusive, impeding advancements and revisions in the taxonomic system for this genus. Plastomes with greater variability in their genetic characteristics hold promise for building a more robust Libanotis phylogeny.<br><br>RESULTS: During our research, we sequenced, assembled, and annotated complete plastomes for twelve Libanotis species belong to three sections and two closely related taxa. We conducted a comprehensive comparative analysis through totally thirteen Libanotis plastomes for the genus, including an additional plastome that had been published. Our results suggested that Libanotis plastome was highly conserved between different subclades, while the coding regions were more conserved than the non-coding regions, and the IR regions were more conserved than the single copy regions. Nevertheless, eight mutation hotspot regions were identified among plastomes, which can be considered as candidate DNA barcodes for accurate species identification in Libanotis. The phylogenetic analyses generated a robustly framework for Libanotis and revealed that Libanotis was not a monophyletic group and their all three sections were polygenetic. Libanotis schrenkiana was sister to L. sibirica, type species of this genus, but the remainders scattered within Selineae.<br><br>CONCLUSION: The plastomes of Libanotis exhibited a high degree of conservation and was effective in enhancing the support and resolution of phylogenetic analyses within this genus. Based on evidence from both phylogeny and morphology, we propose the recognition of "Libanotis sensu stricto" and provide taxonomic recommendations for other taxa that previously belonged to Libanotis. In conclusion, our study not only revealed the phylogenetic position and plastid evolution of Libanotis, but also provided new insights into the phylogeny of the family Apiaceae and phylogenetic relationships within the tribe Selineae.},
}
@article {pmid38342699,
year = {2024},
author = {Luo, B and Zhou, J and Zhan, X and Ying, B and Lan, F and Wu, Y},
title = {Smartphone-Based Free-to-Total Prostate Specific Antigen Ratio Detection System Using a Colorimetric Reaction Integrated with Proximity-Induced Bio-Barcode and CRISPR/Cas12a Assay.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {20},
number = {28},
pages = {e2310212},
doi = {10.1002/smll.202310212},
pmid = {38342699},
issn = {1613-6829},
support = {31872749//National Natural Science Foundation of China/ ; 32271394//National Natural Science Foundation of China/ ; //Fundamental Research Funds for the Central Universities/ ; //Sichuan Province Innovative Talent Funding Project/ ; },
mesh = {*Colorimetry/methods ; *Prostate-Specific Antigen ; *Smartphone ; Humans ; Male ; *CRISPR-Cas Systems ; *Metal Nanoparticles/chemistry ; Prostatic Neoplasms/diagnosis ; Benzidines/chemistry ; Silver/chemistry ; Hydrogen Peroxide/chemistry ; Platinum/chemistry ; Biosensing Techniques/methods ; },
abstract = {The free-to-total prostate-specific antigen (f/t-PSA) ratio is of great significance in the accurate diagnosis of prostate cancer. Herein, a smartphone-based detection system is reported using a colorimetric reaction integrated with proximity-induced bio-barcode and the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a assay for f/t-PSA ratio detection. DNA/antibody recognition probes are designed to bind f-PSA or t-PSA and induce the release of the DNA bio-barcode. The CRISPR/Cas12a system is activated by the DNA bio-barcode to release Ag+ from the C-Ag+-C structure of the hairpin DNA. The released Ag+ is used to affect the tetramethylbenzidine (TMB)-H2O2-based colorimetric reaction catalyzed by Pt nanoparticles (NPs), as the peroxidase-like activity of the Pt NPs can be efficiently inhibited by Ag+. A smartphone with a self-developed app is used as an image reader and analyzer to analyze the colorimetric reaction and provide the results. A limit of detection of 0.06 and 0.04 ng mL[-1] is achieved for t-PSA and f-PSA, respectively. The smartphone-based method showed a linear response between 0.1 and 100 ng mL[-1] of t-PSA or f-PSA. In tests with clinical samples, the smartphone-based method successfully diagnosed prostate cancer patients from benign prostatic hyperplasia patients and healthy cases with high sensitivity and specificity.},
}
@article {pmid38341646,
year = {2024},
author = {Sintsova, A and Ruscheweyh, HJ and Field, CM and Feer, L and Nguyen, BD and Daniel, B and Hardt, WD and Vorholt, JA and Sunagawa, S},
title = {mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {2},
pages = {},
pmid = {38341646},
issn = {1367-4811},
support = {//NCCR Microbiomes/ ; },
mesh = {*DNA Barcoding, Taxonomic ; *Software ; DNA ; Computational Biology ; },
abstract = {MOTIVATION: DNA barcoding has become a powerful tool for assessing the fitness of strains in a variety of studies, including random transposon mutagenesis screens, attenuation of site-directed mutants, and population dynamics of isogenic strain pools. However, the statistical analysis, visualization, and contextualization of the data resulting from such experiments can be complex and require bioinformatic skills.<br><br>RESULTS: Here, we developed mBARq, a user-friendly tool designed to simplify these steps for diverse experimental setups. The tool is seamlessly integrated with an intuitive web app for interactive data exploration via the STRING and KEGG databases to accelerate scientific discovery.<br><br>The tool is implemented in Python. The source code is freely available (https://github.com/MicrobiologyETHZ/mbarq) and the web app can be accessed at: https://microbiomics.io/tools/mbarq-app.},
}
@article {pmid38339166,
year = {2024},
author = {Paschalidis, K and Fanourakis, D and Tsaniklidis, G and Tsichlas, I and Tzanakakis, VA and Bilias, F and Samara, E and Ipsilantis, I and Grigoriadou, K and Samartza, I and Matsi, T and Tsoktouridis, G and Krigas, N},
title = {DNA Barcoding and Fertilization Strategies in Sideritis syriaca subsp. syriaca, a Local Endemic Plant of Crete with High Medicinal Value.},
journal = {International journal of molecular sciences},
volume = {25},
number = {3},
pages = {},
pmid = {38339166},
issn = {1422-0067},
mesh = {*DNA Barcoding, Taxonomic ; *Sideritis/genetics ; Phylogeny ; Greece ; Fertilizers ; Plants/genetics ; Chlorophyll ; Soil ; Fertilization ; DNA, Plant/genetics ; },
abstract = {Herein, we applied DNA barcoding for the genetic characterization of Sideritis syriaca subsp. syriaca (Lamiaceae; threatened local Cretan endemic plant) using seven molecular markers of cpDNA. Five fertilization schemes were evaluated comparatively in a pilot cultivation in Crete. Conventional inorganic fertilizers (ChFs), integrated nutrient management (INM) fertilizers, and two biostimulants were utilized (foliar and soil application). Plant growth, leaf chlorophyll fluorescence, and color were assessed and leaf content of chlorophyll, key antioxidants (carotenoids, flavonoids, phenols), and nutrients were evaluated. Fertilization schemes induced distinct differences in leaf shape, altering quality characteristics. INM-foliar and ChF-soil application promoted yield, without affecting tissue water content or biomass partitioning to inflorescences. ChF-foliar application was the most stimulatory treatment when the primary target was enhanced antioxidant contents while INM-biostimulant was the least effective one. However, when the primary target is yield, INM, especially by foliar application, and ChF, by soil application, ought to be employed. New DNA sequence datasets for the plastid regions of petB/petD, rpoC1, psbK-psbI, and atpF/atpH were deposited in the GenBank for S. syriaca subsp. syriaca while the molecular markers rbcL, trnL/trnF, and psbA/trnH were compared to those of another 15 Sideritis species retrieved from the GenBank, constructing a phylogenetic tree to show their genetic relatedness.},
}
@article {pmid38335955,
year = {2024},
author = {Jain, N and Goyal, Y and Dunagin, MC and Cote, CJ and Mellis, IA and Emert, B and Jiang, CL and Dardani, IP and Reffsin, S and Arnett, M and Yang, W and Raj, A},
title = {Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells.},
journal = {Cell systems},
volume = {15},
number = {2},
pages = {109-133.e10},
pmid = {38335955},
issn = {2405-4720},
support = {T32 DK007780/DK/NIDDK NIH HHS/United States ; R01 CA238237/CA/NCI NIH HHS/United States ; F30 CA236129/CA/NCI NIH HHS/United States ; T32 GM007170/GM/NIGMS NIH HHS/United States ; R01 CA232256/CA/NCI NIH HHS/United States ; F30 HD103378/HD/NICHD NIH HHS/United States ; T32 HG000046/HG/NHGRI NIH HHS/United States ; F30 HG010822/HG/NHGRI NIH HHS/United States ; U01 DK127405/DK/NIDDK NIH HHS/United States ; R01 GM137425/GM/NIGMS NIH HHS/United States ; F30 NS100595/NS/NINDS NIH HHS/United States ; },
mesh = {Humans ; *Cellular Reprogramming ; *Induced Pluripotent Stem Cells/metabolism ; Kruppel-Like Factor 4 ; Retrospective Studies ; Fibroblasts ; },
abstract = {Pluripotency can be induced in somatic cells by the expression of OCT4, KLF4, SOX2, and MYC. Usually only a rare subset of cells reprogram, and the molecular characteristics of this subset remain unknown. We apply retrospective clone tracing to identify and characterize the rare human fibroblasts primed for reprogramming. These fibroblasts showed markers of increased cell cycle speed and decreased fibroblast activation. Knockdown of a fibroblast activation factor identified by our analysis increased the reprogramming efficiency. We provide evidence for a unified model in which cells can move into and out of the primed state over time, explaining how reprogramming appears deterministic at short timescales and stochastic at long timescales. Furthermore, inhibiting the activity of LSD1 enlarged the pool of cells that were primed for reprogramming. Thus, even homogeneous cell populations can exhibit heritable molecular variability that can dictate whether individual rare cells will reprogram or not.},
}
@article {pmid38335055,
year = {2024},
author = {Chen, B and Sultan, MM and Karaletsos, T},
title = {Compositional Deep Probabilistic Models of DNA-Encoded Libraries.},
journal = {Journal of chemical information and modeling},
volume = {64},
number = {4},
pages = {1123-1133},
doi = {10.1021/acs.jcim.3c01699},
pmid = {38335055},
issn = {1549-960X},
mesh = {*Small Molecule Libraries/chemistry ; *DNA/chemistry ; Models, Statistical ; Gene Library ; },
abstract = {DNA-encoded library (DEL) has proven to be a powerful tool that utilizes combinatorially constructed small molecules to facilitate highly efficient screening experiments. These selection experiments, involving multiple stages of washing, elution, and identification of potent binders via unique DNA barcodes, often generate complex data. This complexity can potentially mask the underlying signals, necessitating the application of computational tools, such as machine learning, to uncover valuable insights. We introduce a compositional deep probabilistic model of DEL data, DEL-Compose, which decomposes molecular representations into their monosynthon, disynthon, and trisynthon building blocks and capitalizes on the inherent hierarchical structure of these molecules by modeling latent reactions between embedded synthons. Additionally, we investigate methods to improve the observation models for DEL count data, such as integrating covariate factors to more effectively account for data noise. Across two popular public benchmark data sets (CA-IX and HRP), our model demonstrates strong performance compared to count baselines, enriches the correct pharmacophores, and offers valuable insights via its intrinsic interpretable structure, thereby providing a robust tool for the analysis of DEL data.},
}
@article {pmid38334685,
year = {2024},
author = {Harl, J and Fauchois, A and Puech, MP and Gey, D and Ariey, F and Izac, B and Weissenböck, H and Chakarov, N and Iezhova, T and Valkiūnas, G and Duval, L},
title = {Novel phylogenetic clade of avian Haemoproteus parasites (Haemosporida, Haemoproteidae) from Accipitridae raptors, with description of a new Haemoproteus species.},
journal = {Parasite (Paris, France)},
volume = {31},
number = {},
pages = {5},
pmid = {38334685},
issn = {1776-1042},
mesh = {Animals ; *Haemosporida/genetics ; *Raptors ; Phylogeny ; *Parasites ; *Bird Diseases/epidemiology/parasitology ; Birds ; *Protozoan Infections, Animal/epidemiology/parasitology ; },
abstract = {Avian haemosporidian parasites (order Haemosporida, phylum Apicomplexa) are blood and tissue parasites transmitted by blood-sucking dipteran insects. Three genera (Plasmodium, Haemoproteus and Leucocytozoon) have been most often found in birds, with over 270 species described and named in avian hosts based mainly on the morphological characters of blood stages. A broad diversity of Haemoproteus parasites remains to be identified and characterized morphologically and molecularly, especially those infecting birds of prey, an underrepresented bird group in haemosporidian parasite studies. The aim of this study was to investigate and identify Haemoproteus parasites from a large sample comprising accipitriform raptors of 16 species combining morphological and new molecular protocols targeting the cytb genes of this parasite group. This study provides morphological descriptions and molecular characterizations of two Haemoproteus species, H. multivacuolatus n. sp. and H. nisi Peirce and Marquiss, 1983. Haemoproteus parasites of this group were so far found in accipitriform raptors only and might be classified into a separate subgenus or even genus. Cytb sequences of these parasites diverge by more than 15% from those of all others known avian haemosporidian genera and form a unique phylogenetic clade. This study underlines the importance of developing new diagnostic tools to detect molecularly highly divergent parasites that might be undetectable by commonly used conventional tools.},
}
@article {pmid38333669,
year = {2024},
author = {Liu, B and Stüning, D},
title = {Review of the genus Prochasma Warren (Geometridae, Ennominae, Boarmiini), with description of a new species from Hainan, South China.},
journal = {ZooKeys},
volume = {1190},
number = {},
pages = {303-317},
pmid = {38333669},
issn = {1313-2989},
abstract = {The few already published generic features of the genus Prochasma Warren, 1897 are reviewed and new-found characters are added to make the generic description more comprehensive. A new species, Prochasmadiaoluoensis Liu &amp; Stüning, sp. nov. is described from Hainan Province, China. It is the only Prochasma species found on this island and exceptional for its conspicuous pattern, vivid coloration and some morphological characters not observed in other species before. Descriptions and illustrations of adults, their venation, and male and female genitalia are presented. An identification key and an annotated checklist of all presently known species of Prochasma are provided. In addition, a DNA barcode sequence is given for the new species, and preliminary phylogenetic estimations of the genus Prochasma are discussed.},
}
@article {pmid38333190,
year = {2023},
author = {Anđelić Dmitrović, B and Ivanković Tatalović, L and Kos, T and Crnčan, P and Gajski, D and Jelić, M and Šerić Jelaska, L},
title = {Mediterranean vineyards and olive groves in Croatia harbour some rare and endemic invertebrates.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e100963},
pmid = {38333190},
issn = {1314-2828},
abstract = {The Mediterranean is characterised by high biodiversity and numerous endemic species. These species are not only present in natural habitats, but also inhabit areas under human influence, such as agricultural lands. In the biodiversity assessment of Mediterranean vineyards and olive orchards within Zadar County, in Croatia, we identified eight endemic species with Mediterranean distribution, six with a Balkan Peninsula distribution, four with Dinaric Alps distribution and three species rare and endangered in Europe. Alongside these species, we have recorded five new species for Croatian fauna, many of those identified by combining morphological characteristics and the DNA barcoding tool. Araneae and Coleoptera contributed the highest number of endemic species and groups with new record were the following: Coleoptera, Diptera and Araneae. Compared to other sites, an olive orchard with ecological pest management (EPM), surrounded by natural ecosystems, had the highest ratio of endemic and rare species. Our findings emphasise that agricultural lands in the Mediterranean can be habitats for endemic and rare species and that future biodiversity research of these habitats is highly important, to monitor potential biodiversity changes and motivate future species and ecosystem conservation.},
}
@article {pmid38328460,
year = {2024},
author = {Harefa, T and Chen, IS},
title = {Complete mitochondrial genome of larged-eye pygmy goby Trimma macrophthalmus (Teleostei, Gobiidae) and its phylogenetic implications.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {9},
number = {2},
pages = {247-251},
pmid = {38328460},
issn = {2380-2359},
abstract = {Trimma macrophthalmus is a colorful pygmy goby that is widely associated with coral and distributed in the Indo-Pacific Ocean. Here, the complete mitochondrial genome of T. macrophthalmus was first sequenced and annotated. The entire mitogenome is a typical circular molecule (16,943 bp in total length) containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region (CR). The overall base composition is 29.6% for A, 15.6% for G, 27.9% for C and 26.9% for T. Phylogenetic tree was reconstructed using concatenated 13 protein coding genes sequences of the 38 related taxa. The phylogenetic analysis indicated that T. macrophthalmus was most closely related to T. okinawae. These findings will contribute for further genetic studies such as evolution, DNA barcoding and molecular phylogeny of genus Trimma and related gobiid fishes.},
}
@article {pmid38327380,
year = {2023},
author = {Chen, X and Kuang, J and Tao, W and Xiong, Z and Mao, K},
title = {A new species of Megastigmus (Hymenoptera, Megastigmidae) from China.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e102828},
pmid = {38327380},
issn = {1314-2828},
abstract = {BACKGROUND: Most species of Megastigmus are considered important economic pests that grow in seeds, especially of conifers. Accurate identification of species is a crucial step for the biological research of parasitic pests and the further application of biological control. However, their large variety, small size, similar morphology and different growth and development stages have brought great challenges to taxonomic research. Traditional morphological identification often takes a long time and this requires us to seek a new method for rapid and accurate identification. Therefore, the better identification of Megastigmus urgently needs to be combined with molecular methods to help taxonomic development.<br><br>NEW INFORMATION: Here, Megastigmusdaduheensis sp. n. (Chalcidoidea: Megastigmidae) was identified, based on morphology and molecular markers, such as COI and Cytb. M.daduheensis sp. n. is distinct from other known species of the same genus in the morphology. The results of the molecular phylogenetic tree, similarity alignment and genetic distance indicate that the COI and Cytb sequences of M.daduheensis sp. n. are highly similar to M.sobinae and M.duclouxiana, but there are some genetic differences. The genetic distances of M.daduheensis sp. nov. with M.duclouxiana and M.sabinae were 0.34 and 0.33 and the percentages of shared base pairs were 76.3% and 76.8%, respectively. Both morphological and molecular data classified M.daduheensis sp. n. as a new species. The obtained COI and Cytb sequences of M.daduheensis sp. n. can be used as DNA barcodes, providing molecular data for rapid and accurate identification of this species in the future.},
}
@article {pmid38327368,
year = {2023},
author = {Rosa, P and Wood, T and Silva, TLL and Veríssimo, J and Mata, VA and Michez, D and Beja, P and Ferreira, S},
title = {The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of cuckoo wasps, with the description of new species from the Iberian Peninsula (Hymenoptera, Chrysididae).},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e98743},
pmid = {38327368},
issn = {1314-2828},
abstract = {BACKGROUND: DNA barcoding technologies have provided a powerful tool for the fields of ecology and systematics. Here, we present a part of the InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of cuckoo wasps (Hymenoptera, Chrysididae) dataset representing 144 specimens and 103 species, covering approximately 44% of the Iberian and 21% of the European fauna. The InBIO Barcoding Initiative (IBI - DNA Barcoding Portuguese terrestrial invertebrate biodiversity) aims to fill the barcoding gap for the terrestrial invertebrate taxa. All DNA extractions are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources and specimens are deposited in the University of Mons collection (Belgium) and in the Natur-Museum in Lucerne (Switzerland).<br><br>NEW INFORMATION: This dataset increases the knowledge on the DNA barcodes and distribution of 102 species of cuckoo wasps. A total of 52 species, from 11 different genera, were new additions to the Barcode of Life Data System (BOLD), with DNA barcodes for another 44 species added from under-represented taxa in BOLD. All specimens have their DNA barcodes publicly accessible through the BOLD online database. Nine cuckoo wasp species are newly recorded for Portugal. Additionally, two new species for science are described: Chrysiscrossi Rosa, sp. nov. from southern Portugal and Hedychridiumcalcarium Rosa, sp. nov. from eastern Spain. Several taxonomic changes are proposed and Hedychrumrutilans Dahlbom, 1845 is found to consist of two different taxa that can be found in sympatry, Hedychrumrutilans s. str. and Hedychrumviridaureum Tournier, 1877 stat. nov. Stilbumwestermanni Dahlbom, 1845 stat. nov. is confirmed as distinct from Stilbumcalens (Fabricius, 1781), with the latter species not confirmed as present in Iberia; barcoded Stilbum material from Australia is distinct and represents Stilbumamethystium (Fabricius, 1775) sp. resurr.; Portuguese material identified as Hedychridiumchloropygum Buysson, 1888 actually belongs to Hedychridiumcaputaureum Trautmann &amp; Trautmann, 1919, the first confirmed record of this species from Iberia. Philoctetesparvulus (Dahlbom, 1845) is confirmed to be a synonym of Philoctetespunctulatus (Dahlbom, 1845). Chrysislusitanica Bischoff, 1910 is confirmed as a valid species. Chrysishebraeica Linsenmaier, 1959 stat. nov. is raised to species status.},
}
@article {pmid38327336,
year = {2023},
author = {Wiklund, H and Rabone, M and Glover, AG and Bribiesca-Contreras, G and Drennan, R and Stewart, ECD and Boolukos, CM and King, LD and Sherlock, E and Smith, CR and Dahlgren, TG and Neal, L},
title = {Checklist of newly-vouchered annelid taxa from the Clarion-Clipperton Zone, central Pacific Ocean, based on morphology and genetic delimitation.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e86921},
pmid = {38327336},
issn = {1314-2828},
abstract = {BACKGROUND: We present a checklist of annelids from recent United Kingdom Seabed Resources (UKSR) expeditions (Abyssal Baseline - ABYSSLINE project) to the eastern abyssal Pacific Clarion-Clipperton Zone (CCZ) polymetallic nodule fields, based on DNA species delimitation, including imagery of voucher specimens, Darwin Core (DwC) data and links to vouchered specimen material and new GenBank sequence records. This paper includes genetic and imagery data for 129 species of annelids from 339 records and is restricted to material that is, in general, in too poor a condition to describe formally at this time, but likely contains many species new to science. We make these data available both to aid future taxonomic studies in the CCZ that will be able to link back to these genetic data and specimens and to better underpin ongoing ecological studies of potential deep-sea mining impacts using the principles of FAIR (Findable, Accessible, Interoperable, Reusuable) data and specimens that will be available for all.<br><br>NEW INFORMATION: We include genetic, imagery and all associated metadata in Darwin Core format for 129 species of annelids from the Clarion-Clipperton Zone, eastern abyssal Pacific, with 339 records.},
}
@article {pmid38327333,
year = {2023},
author = {Levesque-Beaudin, V and Miller, ME and Dikow, T and Miller, SE and Prosser, SWJ and Zakharov, EV and McKeown, JTA and Sones, JE and Redmond, NE and Coddington, JA and Santos, BF and Bird, J and deWaard, JR},
title = {A workflow for expanding DNA barcode reference libraries through 'museum harvesting' of natural history collections.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e100677},
pmid = {38327333},
issn = {1314-2828},
abstract = {Natural history collections are the physical repositories of our knowledge on species, the entities of biodiversity. Making this knowledge accessible to society - through, for example, digitisation or the construction of a validated, global DNA barcode library - is of crucial importance. To this end, we developed and streamlined a workflow for 'museum harvesting' of authoritatively identified Diptera specimens from the Smithsonian Institution's National Museum of Natural History. Our detailed workflow includes both on-site and off-site processing through specimen selection, labelling, imaging, tissue sampling, databasing and DNA barcoding. This approach was tested by harvesting and DNA barcoding 941 voucher specimens, representing 32 families, 819 genera and 695 identified species collected from 100 countries. We recovered 867 sequences (> 0 base pairs) with a sequencing success of 88.8% (727 of 819 sequenced genera gained a barcode > 300 base pairs). While Sanger-based methods were more effective for recently-collected specimens, the methods employing next-generation sequencing recovered barcodes for specimens over a century old. The utility of the newly-generated reference barcodes is demonstrated by the subsequent taxonomic assignment of nearly 5000 specimen records in the Barcode of Life Data Systems.},
}
@article {pmid38327328,
year = {2023},
author = {Phillips, JD and Athey, TBT and McNicholas, PD and Hanner, RH},
title = {VLF: An R package for the analysis of very low frequency variants in DNA sequences.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e96480},
pmid = {38327328},
issn = {1314-2828},
abstract = {Here, we introduce VLF, an R package to determine the distribution of very low frequency variants (VLFs) in nucleotide and amino acid sequences for the analysis of errors in DNA sequence records. The package allows users to assess VLFs in aligned and trimmed protein-coding sequences by automatically calculating the frequency of nucleotides or amino acids in each sequence position and outputting those that occur under a user-specified frequency (default of p = 0.001). These results can then be used to explore fundamental population genetic and phylogeographic patterns, mechanisms and processes at the microevolutionary level, such as nucleotide and amino acid sequence conservation. Our package extends earlier work pertaining to an implementation of VLF analysis in Microsoft Excel, which was found to be both computationally slow and error prone. We compare those results to our own herein. Results between the two implementations are found to be highly consistent for a large DNA barcode dataset of bird species. Differences in results are readily explained by both manual human error and inadequate Linnean taxonomy (specifically, species synonymy). Here, VLF is also applied to a subset of avian barcodes to assess the extent of biological artifacts at the species level for Canada goose (Branta canadensis), as well as within a large dataset of DNA barcodes for fishes of forensic and regulatory importance. The novelty of VLF and its benefit over the previous implementation include its high level of automation, speed, scalability and ease-of-use, each desirable characteristics which will be extremely valuable as more sequence data are rapidly accumulated in popular reference databases, such as BOLD and GenBank.},
}
@article {pmid38327313,
year = {2023},
author = {Schilthuizen, M and Berenyi, S and Ezzwan, NSMN and Hamdani, NIAA and Wu, H and De Antoni, L and Vincenzi, L and de Gier, W and van Peursen, ADP and Njunjić, I and Delledonne, M and Slik, F and Grafe, U and Cicuzza, D},
title = {A new semi-slug of the genus Microparmarion from Brunei, discovered, described and DNA-barcoded on citizen-science 'taxon expeditions' (Gastropoda, Stylommatophora, Ariophantidae).},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e101579},
pmid = {38327313},
issn = {1314-2828},
abstract = {BACKGROUND: During citizen-science expeditions to the Ulu Temburong National Park, Brunei, several individuals were collected of a semi-slug species of the genus Microparmarion that, based on morphology and in-the-field DNA-barcoding, was found to be an undescribed species.<br><br>NEW INFORMATION: In this paper, we describe Microparmarionsallehi Wu, Ezzwan &amp; Hamdani, n. sp., after field centre supervisor Md Salleh Abdullah Bat. We provide details on the external and internal reproductive morphology, the shell and the ecology of the type locality, as well as a diagnosis comparing it with related species. DNA barcodes were generated for five individuals and used for a phylogenetic reconstruction. Microparmarionsallehi sp. n. and M.exquadratus Schilthuizen et al., 2019 so far are the only Bornean species of the genus that live in lowland forest; other species are found in montane forests.},
}
@article {pmid38327295,
year = {2023},
author = {Pauperio, J and Gonzalez, LM and Martinez, J and González, MA and Martins, FM and Veríssimo, J and Puppo, P and Pinto, J and Chaves, C and Pinho, CJ and Grosso-Silva, JM and Quaglietta, L and Silva, TLL and Sousa, P and Alves, PC and Fonseca, N and Beja, P and Ferreira, S},
title = {The InBIO barcoding initiative database: DNA barcodes of Iberian Trichoptera, documenting biodiversity for freshwater biomonitoring in a Mediterranean hotspot.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e97484},
pmid = {38327295},
issn = {1314-2828},
abstract = {BACKGROUND: The Trichoptera are an important component of freshwater ecosystems. In the Iberian Peninsula, 380 taxa of caddisflies are known, with nearly 1/3 of the total species being endemic in the region. A reference collection of morphologically identified Trichoptera specimens, representing 142 Iberian taxa, was constructed. The InBIO Barcoding Initiative (IBI) Trichoptera 01 dataset contains records of 438 sequenced specimens. The species of this dataset correspond to about 37% of Iberian Trichoptera species diversity. Specimens were collected between 1975 and 2018 and are deposited in the IBI collection at the CIBIO (Research Center in Biodiversity and Genetic Resources, Portugal) or in the collection Marcos A. González at the University of Santiago de Compostela (Spain).<br><br>NEW INFORMATION: Twenty-nine species, from nine different families, were new additions to the Barcode of Life Data System (BOLD). A success identification rate of over 80% was achieved when comparing morphological identifications and DNA barcodes for the species analysed. This encouraging step advances incorporation of informed Environmental DNA tools in biomonitoring schemes, given the shortcomings of morphological identifications of larvae and adult Caddis&#xfb02;ies in such studies. DNA barcoding was not successful in identifying species in six Trichoptera genera: Hydropsyche (Hydropsychidae), Athripsodes (Leptoceridae), Wormaldia (Philopotamidae), Polycentropus (Polycentropodidae) Rhyacophila (Rhyacophilidae) and Sericostoma (Sericostomatidae). The high levels of intraspecific genetic variability found, combined with a lack of a barcode gap and a challenging morphological identification, rendered these species as needing additional studies to resolve their taxonomy.},
}
@article {pmid38327291,
year = {2023},
author = {Kjærandsen, J and Kerr, PH and Lindemann, JP and Kurina, O},
title = {When details matter: Integrative revision of Holarctic Coelophthinia Edwards (Diptera, Mycetophilidae), including mapping of its mitogenome, leads to the description of four new pseudocryptic species.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e98741},
pmid = {38327291},
issn = {1314-2828},
abstract = {BACKGROUND: The small genus Coelophthinia Edwards, 1941 of the subfamily Gnoristinae (Diptera, Mycetophilidae) is so far known to harbour four species from the Palaearctic, Nearctic and Neotropical Regions. Extensive DNA barcoding of fungus gnats of the family Mycetophilidae through the International Barcode of Life project (iBOL) have initiated integrative studies resulting in taxonomic upgrades and a better understanding of many species and their delimitation. The opportunity was also taken to describe the mitogenome of a member of Coelophthinia for the first time.<br><br>NEW INFORMATION: The integrative studies give evidence for splitting the European species C.thoracica Edwards, 1941 into three different species. Four new species are described from the USA, Japan and the Nordic Region in Europe, Coelophthiniacirra Kerr sp. n., Coelophthiniaitoae Kurina sp. n., Coelophthinialata Kjaerandsen sp. n. and Coelophthinialoraasi Kjaerandsen sp. n., raising the number of Holarctic species from two to six. The mitogenome of Coelophthinialoraasi sp. n. is described and analysed.},
}
@article {pmid38327288,
year = {2023},
author = {Santos, BF and Miller, ME and Miklasevskaja, M and McKeown, JTA and Redmond, NE and Coddington, JA and Bird, J and Miller, SE and Smith, A and Brady, SG and Buffington, ML and Chamorro, ML and Dikow, T and Gates, MW and Goldstein, P and Konstantinov, A and Kula, R and Silverson, ND and Solis, MA and deWaard, SL and Naik, S and Nikolova, N and Pentinsaari, M and Prosser, SWJ and Sones, JE and Zakharov, EV and deWaard, JR},
title = {Enhancing DNA barcode reference libraries by harvesting terrestrial arthropods at the Smithsonian's National Museum of Natural History.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e100904},
pmid = {38327288},
issn = {1314-2828},
abstract = {The use of DNA barcoding has revolutionised biodiversity science, but its application depends on the existence of comprehensive and reliable reference libraries. For many poorly known taxa, such reference sequences are missing even at higher-level taxonomic scales. We harvested the collections of the Smithsonian's National Museum of Natural History (USNM) to generate DNA barcoding sequences for genera of terrestrial arthropods previously not recorded in one or more major public sequence databases. Our workflow used a mix of Sanger and Next-Generation Sequencing (NGS) approaches to maximise sequence recovery while ensuring affordable cost. In total, COI sequences were obtained for 5,686 specimens belonging to 3,737 determined species in 3,886 genera and 205 families distributed in 137 countries. Success rates varied widely according to collection data and focal taxon. NGS helped recover sequences of specimens that failed a previous run of Sanger sequencing. Success rates and the optimal balance between Sanger and NGS are the most important drivers to maximise output and minimise cost in future projects. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, the Global Genome Biodiversity Network Data Portal and the NMNH data portal.},
}
@article {pmid38327265,
year = {2024},
author = {Nguyen, AD and Vu, TTT and Eguchi, K},
title = {The millipede family Polydesmidae Leach, 1816 (Diplopoda, Polydesmida) from Vietnam, with a description of a new cavernicolous species.},
journal = {ZooKeys},
volume = {1190},
number = {},
pages = {259-280},
pmid = {38327265},
issn = {1313-2989},
abstract = {The millipede family Polydesmidae Leach, 1816 is reviewed in the scope of the Vietnamese fauna. The distribution of the species, Polydesmusvietnamicus Nguyen, 2009 is extended northward to Ha Giang Province. A new cavernicolous polydesmid, Pacidesmustuachuasp. nov., is described from two caves in northwestern Vietnam, representing the first record of the genus from Vietnam. Extensive illustrations and DNA barcodes are provided for both species, a revised key is presented to all 12 species of Pacidesmus Golovatch, 1991, as well as a key to all eight genera of Asian Polydesmidae.},
}
@article {pmid38323085,
year = {2023},
author = {Recuero, E and Caterino, MS},
title = {A second species of the pill millipede genus Nearctomeris Wesener, 2012 (Diplopoda, Glomerida) from the Great Smoky Mountains, USA.},
journal = {ZooKeys},
volume = {1166},
number = {},
pages = {333-349},
pmid = {38323085},
issn = {1313-2989},
abstract = {We describe a second species of Nearctomeris Wesener, 2012, a genus of pill millipede endemic to the southern Appalachians, based on morphological and molecular evidence. The fauna of Glomerida in America is characterized by its low diversity, and Nearctomerissmokysp. nov. is only the fifth species of the order known from the eastern United States. Our phylogenetic analyses based on COI sequences recover a tentatively monophyletic lineage including both eastern American genera Onomeris Cook, 1896 and Nearctomeris, with a common ancestor in the Late Cretaceous to Mid Eocene and extant diversity within genera dating back to the Miocene. Our results suggest that the observed low diversity of the group in the eastern US is likely caused by extinction events, but it is also possible that new species are yet to be found. We provide new records for Nearctomerisinexpectata Wesener, 2012, Onomerisunderwoodi Cook, 1896 and O.australora Hoffman, 1950; the latter is here reported for the first time from South Carolina. We also present DNA barcoding data for all species of Glomerida present in the US that are not yet publicly available.},
}
@article {pmid38319915,
year = {2024},
author = {Muhala, V and Guimarães-Costa, A and Macate, IE and Rabelo, LP and Bessa-Silva, AR and Watanabe, L and Dos Santos, GD and Sambora, L and Vallinoto, M and Sampaio, I},
title = {DNA barcoding for the assessment of marine and coastal fish diversity from the Coast of Mozambique.},
journal = {PloS one},
volume = {19},
number = {2},
pages = {e0293345},
pmid = {38319915},
issn = {1932-6203},
mesh = {Humans ; Animals ; *DNA Barcoding, Taxonomic/methods ; Mozambique ; *Biodiversity ; Phylogeny ; Fishes/genetics ; DNA/genetics ; Endangered Species ; },
abstract = {The ichthyological provinces of Mozambique are understudied hotspots of global fish diversity. In this study, we applied DNA barcoding to identify the composition of the fish fauna from the coast of Mozambique. A total of 143 species belonging to 104 genera, 59 families, and 30 orders were identified. The overall K2P distance of the COI sequences within species ranged from 0.00% to 1.51%, while interspecific distances ranged from 3.64% to 24.49%. Moreover, the study revealed 15 threatened species according to the IUCN Red List of Threatened Species, with elasmobranchs being the most represented group. Additionally, the study also uncovered four new species that were not previously recorded in this geographic area, including Boleophthalmus dussumieri, Maculabatis gerrardi, Hippocampus kelloggi, and Lethrinus miniatus. This study represents the first instance of utilizing molecular references to explore the fish fauna along the Mozambican coast. Our results indicate that DNA barcoding is a dependable technique for the identification and delineation of fish species in the waters of Mozambique. The DNA barcoding library established in this research will be an invaluable asset for advancing the understanding of fish diversity and guiding future conservation initiatives.},
}
@article {pmid38319817,
year = {2024},
author = {Pitt, WJ and Cooper, WR and Pouchnik, D and Headrick, H and Nachappa, P},
title = {High-throughput molecular gut content analysis of aphids identifies plants relevant for potato virus Y epidemiology.},
journal = {Insect science},
volume = {31},
number = {5},
pages = {1489-1502},
doi = {10.1111/1744-7917.13327},
pmid = {38319817},
issn = {1744-7917},
mesh = {Animals ; *Aphids/virology/genetics ; *Potyvirus/genetics/physiology ; *High-Throughput Nucleotide Sequencing ; Plant Diseases/virology ; Gastrointestinal Contents/virology ; Colorado ; Insect Vectors/virology/genetics ; Solanum tuberosum/virology ; },
abstract = {Aphids are phloem-feeding insects that reduce crop productivity due to feeding and transmission of plant viruses. When aphids disperse across the landscape to colonize new host plants, they will often probe on a wide variety of nonhost plants before settling on a host suitable for feeding and reproduction. There is limited understanding of the diversity of plants that aphids probe on within a landscape, and characterizing this diversity can help us better understand host use patterns of aphids. Here, we used gut content analysis (GCA) to identify plant genera that were probed by aphid vectors of potato virus Y (PVY). Aphids were trapped weekly near potato fields during the growing seasons of 2020 and 2021 in San Luis Valley in Colorado. High-throughput sequencing of plant barcoding genes, trnF and ITS2, from 200 individual alate (i.e., winged) aphids representing nine vector species of PVY was performed using the PacBio sequencing platform, and sequences were identified to genus using NCBI BLASTn. We found that 34.7% of aphids probed upon presumed PVY host plants and that two of the most frequently detected plant genera, Solanum and Brassica, represent important crops and weeds within the study region. We found that 75% of aphids frequently probed upon PVY nonhosts including many species that are outside of their reported host ranges. Additionally, 19% of aphids probed upon more than one plant species. This study provides the first evidence from high-throughput molecular GCA of aphids and reveals host use patterns that are relevant for PVY epidemiology.},
}
@article {pmid38319699,
year = {2024},
author = {Zhang, A and Jin, L and Yao, S and Matsuyama, M and van Velthoven, CTJ and Sullivan, HA and Sun, N and Kellis, M and Tasic, B and Wickersham, I and Chen, X},
title = {Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {38319699},
issn = {2050-084X},
support = {DP2 MH132940/MH/NIMH NIH HHS/United States ; RF1 MH120017/MH/NIMH NIH HHS/United States ; RF1 MH132596/MH/NIMH NIH HHS/United States ; 1DP2MH132940/NH/NIH HHS/United States ; },
mesh = {Animals ; Mice ; *Rabies virus/genetics ; Neuroanatomy ; Neurons ; Sequence Analysis, RNA ; RNA ; },
abstract = {Mapping the connectivity of diverse neuronal types provides the foundation for understanding the structure and function of neural circuits. High-throughput and low-cost neuroanatomical techniques based on RNA barcode sequencing have the potential to map circuits at cellular resolution and a brain-wide scale, but existing Sindbis virus-based techniques can only map long-range projections using anterograde tracing approaches. Rabies virus can complement anterograde tracing approaches by enabling either retrograde labeling of projection neurons or monosynaptic tracing of direct inputs to genetically targeted postsynaptic neurons. However, barcoded rabies virus has so far been only used to map non-neuronal cellular interactions in vivo and synaptic connectivity of cultured neurons. Here we combine barcoded rabies virus with single-cell and in situ sequencing to perform retrograde labeling and transsynaptic labeling in the mouse brain. We sequenced 96 retrogradely labeled cells and 295 transsynaptically labeled cells using single-cell RNA-seq, and 4130 retrogradely labeled cells and 2914 transsynaptically labeled cells in situ. We found that the transcriptomic identities of rabies virus-infected cells can be robustly identified using both single-cell RNA-seq and in situ sequencing. By associating gene expression with connectivity inferred from barcode sequencing, we distinguished long-range projecting cortical cell types from multiple cortical areas and identified cell types with converging or diverging synaptic connectivity. Combining in situ sequencing with barcoded rabies virus complements existing sequencing-based neuroanatomical techniques and provides a potential path for mapping synaptic connectivity of neuronal types at scale.},
}
@article {pmid38319598,
year = {2024},
author = {Kavčič, A and Podlipec, R and Krišelj, A and Jelen, A and Vella, D and Humar, M},
title = {Intracellular biocompatible hexagonal boron nitride quantum emitters as single-photon sources and barcodes.},
journal = {Nanoscale},
volume = {16},
number = {9},
pages = {4691-4702},
pmid = {38319598},
issn = {2040-3372},
abstract = {Color centers in hexagonal boron nitride (hBN) have been emerging as a multifunctional platform for various optical applications including quantum information processing, quantum computing and imaging. Simultaneously, due to its biocompatibility and biodegradability hBN is a promising material for biomedical applications. In this work, we demonstrate single-photon emission from hBN color centers embedded inside live cells and their application to cellular barcoding. The generation and internalization of multiple color centers into cells was performed via simple and scalable procedure while keeping the cells unharmed. The emission from live cells was observed as multiple diffraction-limited spots, which exhibited excellent single-photon characteristics with high single-photon purity of 0.1 and superb emission stability without photobleaching or spectral shifts over several hours. Due to different emission wavelengths and peak widths of the color centers, they were employed as barcodes. We term them Quantum Photonic Barcodes (QPBs). Each QPB can exist in one out of 470 possible distinguishable states and a combination of a few QPBs per cell can be used to uniquely tag virtually an unlimited number of cells. The barcodes developed here offer some excellent properties, including ease of production by a single-step procedure, biocompatibility and biodegradability, emission stability, no photobleaching, small size and a huge number of unique barcodes. This work provides a basis for the use of hBN color centers for robust barcoding of cells and due to the single photon emission, presented concepts could in future be extended to quantum-limited sensing and super-resolution imaging.},
}
@article {pmid38318523,
year = {2023},
author = {Lugo, D and Suárez, D and Martín, S and Afonso, &#xd3;M and Martín, A and Ruiz, C},
title = {First record of Leptoglossusoccidentalis Heidemann, 1910 (Hemiptera, Coreidae) in the Canary Islands, a novel pine pest detected through citizen science in an oceanic archipelago.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e109851},
pmid = {38318523},
issn = {1314-2828},
abstract = {BACKGROUND: The 'western seed bug', known as Leptoglossusoccidentalis, is considered a global invasive species that has experienced a recent rapid expansion worldwide, becoming an important pest species for coniferous forests.<br><br>NEW INFORMATION: With the 'Canary Islands early-warning network for the detection and intervention of invasive exotic species' (RedEXOS), this species was detected for the first time in the Canarian archipelago in an urban area in the eastern part of the island of Gran Canaria. This early detection is crucial for understanding the potential damage in one of the islands with the highest surface area of natural endemic pine forest.},
}
@article {pmid38318520,
year = {2023},
author = {Grižančić, L and Baričević, A and Smodlaka Tanković, M and Vlašiček, I and Knjaz, M and Podolšak, I and Kogovšek, T and Pfannkuchen, MA and Marić Pfannkuchen, D},
title = {A metabarcode based (species) inventory of the northern Adriatic phytoplankton.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e106947},
pmid = {38318520},
issn = {1314-2828},
abstract = {BACKGROUND: The northern Adriatic is characterised as the coldest and most productive marine area of the Mediterranean, which is due to high nutrient levels introduced by river discharges, the largest of which is the Italian Po River (at the same time also the largest freshwater input into the Mediterranean). The northern Adriatic is a very shallow marine ecosystem with ocean current patterns that result in long retention times of plankton in the area. The northern Adriatic phytoplankton biodiversity and abundance are well-studied, through many scientific and long-term monitoring reports. These datasets were based on phytoplankton morphological traits traditionally obtained with light microscopy. The most recent comprehensive eastern Adriatic phytoplankton checklist was published more than 20 years ago and is still valuable today. Since phytoplankton taxonomy and systematics are constantly being reviewed (partly also due to new molecular methods of species identification that complement classical methodologies), checklists need to be updated and complemented. Today, metabarcoding of molecular markers gains more and more importance in biodiversity research and monitoring. Here, we report the use of high throughput sequencing methods to re-examine taxonomic richness and provide updated knowledge of phytoplankton diversity in the eastern northern Adriatic to complement the standardised light microscopy method.<br><br>NEW INFORMATION: This study aimed to report an up-to-date list of the phytoplankton taxonomic richness and phylogenetic relationships in the eastern northern Adriatic, based on sequence variability of barcoding genes resolved with advanced molecular tools, namely metabarcoding. Here, metabarcoding is used to complement standardised light microscopy to advance conventional monitoring and research of phytoplankton communities for the purpose of assessing biodiversity and the status of the marine environments. Monthly two-year net sampling targeted six phytoplankton groups including Bacillariophyceae (diatoms) and Chrysophyceae (golden algae) belonging to Ochrophyta, Dinophyceae (dinoflagellates), Cryptophyceae (cryptophytes), Haptophyta (mostly coccolithophorids) and Chlorophyta with Prasinophyceae (prasinophytes) and Chlorophyceae (protist green algae). Generated sequence data were taxonomically assigned and redistributed in two kingdoms, five classes, 32 orders, 49 families and 67 genera. The most diverse group were dinoflagellates, comprising of 34 found genera (48.3%), following by diatoms with 23 (35.4%) and coccolithophorids with three genera (4.0%). In terms of genetic diversity, results were a bit different: a great majority of sequences with one nucleotide tolerance (ASVs, Amplicon sequence variants) assigned to species or genus level were dinoflagellates (83.8%), 13.7% diatoms and 1.6% Chlorophyta, respectively. Although many taxa have not been detected that have been considered as common in this area, metabarcoding revealed five diatoms and 20 dinoflagellate genera that were not reported in previous checklists, along with a few species from other targeted groups that have been reported previously. We here describe the first comprehensive 18S metabarcode inventory for the northern Adriatic Sea.},
}
@article {pmid38318513,
year = {2023},
author = {Yang, W and Zhou, Y and Gu, D and Yu, H},
title = {Pancoriusguiyang sp. nov., a new species of jumping spiders (Araneae, Salticidae) from Guizhou Province, China.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e108159},
pmid = {38318513},
issn = {1314-2828},
abstract = {BACKGROUND: Pancorius Simon, 1902 is a relatively large genus of jumping spider family Salticidae and currently contains 42 valid species that are mainly distributed in South East Asia, 11 of which are recorded from China.<br><br>NEW INFORMATION: A new spider species of the genus Pancorius from Guiyang City in southwest China, is described under the name of P.guiyang Yang, Gu &amp; Yu, sp. nov. Detailed descriptions and photographs are provided. DNA barcodes (a partial fragment of the mitochondrial cytochrome oxidase subunit I gene, COI) of the species were obtained to confirm matching of the sexes and for future use in molecular studies.},
}
@article {pmid38318508,
year = {2023},
author = {Kamimura, Y and Nishikawa, M and Yamasako, J},
title = {DNA barcoding of Japanese earwig species (Insecta, Dermaptera), with sequence diversity analyses of three species of Anisolabididae.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e107001},
pmid = {38318508},
issn = {1314-2828},
abstract = {Dermaptera is a polyneopteran insect order that includes more than 2,000 described species, commonly known as earwigs, that mainly inhabit tropical, subtropical and warm temperate regions. Although 40 species have been found in Japan, their distribution and habitat preferences have remained ambiguous due to sample misidentification, particularly amongst immature specimens. To overcome this problem, we sequenced and analysed the DNA barcoding region of the mitochondrial cytochrome oxidase I gene (cox1) of dermapteran species recorded from Japan. Including publicly available data, 72.5% of known Japanese dermapteran species were subjected to molecular identification. We extensively sampled three wingless species of subfamily Anisolabidinae (Anisolabididae): Anisolabismaritima, Anisolabellamarginalis and Euborelliapallipes. Although these species exhibit similar habitat preferences as semi-synanthropes, A.maritima, a cosmopolitan species with the highest affinity to seashore, had significantly higher sequence diversity than the latter two species, which are considered endemic to East Asia. A similar trend was observed for (at least partly) winged cosmopolitan species of other families. Introgression with the congener Anisolabisseirokui is also suggested for A.maritima. Possible causes of the varying levels of sequence diversity are discussed.},
}
@article {pmid38318285,
year = {2023},
author = {Huang, X and Gan, Y and Wang, L and Xu, Y and Wei, Z and Shi, A},
title = {The larval, pupal and mitogenomic characteristics of Agrilusadelphinus Kerremans, 1895 (Coleoptera, Buprestidae) from China.},
journal = {ZooKeys},
volume = {1174},
number = {},
pages = {15-33},
pmid = {38318285},
issn = {1313-2989},
abstract = {In this study, the larva and pupa of Agrilusadelphinus are described and illustrated. DNA barcoding (COI gene) was used to associate the larval and pupal stages with adults based on the maximum-likelihood method. In the resulting phylogenetic tree, species from the same species-group were found to be clustered on a branch with high support value. To better understand A.adelphinus, the complete mitochondrial genome of this species was also sequenced and annotated. Comparing this genome to the known mitogenomes of Agrilus species, the newly sequenced genome is shorter, with 15,732 bp. However, its whole mitogenome composition and gene orientation were consistent with that of most species of Buprestidae. In the mitogenome of A.adelphinus, the ATGATAG sequence was observed between ATP8 and ATP6, which is ATGATAA in other insect mitogenomes. Leu2, Phe, Ile, Gly, and Ser2 were the five most frequently encoded amino acids. The results further prove that DNA barcoding can remove the limitation of traditional taxonomy which cannot identify to species all developmental stages. This study also provides valuable molecular and morphological data for species identification and phylogenetic analyses of the genus Agrilus.},
}
@article {pmid38317009,
year = {2024},
author = {},
title = {Homotrimer barcodes enable accurate counting of RNA molecules during high-throughput RNA sequencing.},
journal = {Nature methods},
volume = {21},
number = {3},
pages = {379-380},
pmid = {38317009},
issn = {1548-7105},
mesh = {*High-Throughput Nucleotide Sequencing ; *DNA Barcoding, Taxonomic ; RNA/genetics ; Sequence Analysis, RNA ; },
}
@article {pmid38315121,
year = {2024},
author = {Han, K and Li, J and Yang, D and Zhuang, Q and Zeng, H and Rong, C and Yue, J and Li, N and Gu, C and Chen, L and Chen, C},
title = {Detecting horizontal gene transfer with metagenomics co-barcoding sequencing.},
journal = {Microbiology spectrum},
volume = {12},
number = {3},
pages = {e0360223},
pmid = {38315121},
issn = {2165-0497},
support = {2021YFF0703805//MOST | National Key Research and Development Program of China (NKPs)/ ; 82102447//MOST | National Natural Science Foundation of China (NSFC)/ ; DFL20191801//Beijing Hospital Authority/ ; Z201100005520040//Beijing Municipal Science and Technology Commission, Adminitrative Commission of Zhongguancun Science Park/ ; QML20230701//Beijing Hospitals Authority Youth Programme/ ; },
mesh = {Animals ; Humans ; Mice ; *Gene Transfer, Horizontal ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; Bacteria/genetics ; DNA ; },
abstract = {Horizontal gene transfer (HGT) is the process through which genetic information is transferred between different genomes and that played a crucial role in bacterial evolution. HGT can enable bacteria to rapidly acquire antibiotic resistance and bacteria that have acquired resistance is spreading within the microbiome. Conventional methods of characterizing HGT patterns include short-read metagenomic sequencing (short-reads mNGS), long-read sequencing, and single-cell sequencing. These approaches present several limitations, such as short-read fragments, high amounts of input DNA, and sequencing costs, respectively. Here, we attempt to circumvent present limitations to detect HGT by developing a metagenomics co-barcode sequencing workflow (MECOS) and applying it to the human and mouse gut microbiomes. In addition to that, we have over 10-fold increased contig length compared to short-reads mNGS; we also obtained exceeding 30 million paired reads with co-barcode information. Applying the novel bioinformatic pipeline, we integrated this co-barcoding information and the context information from long reads, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Specifically, we detected approximately 3,000 HGT blocks in individual samples, encompassing ~6,000 genes and ~100 taxonomic groups, including loci conferring tetracycline resistance through ribosomal protection. MECOS provides a valuable tool for investigating HGT and advance our understanding on the evolution of natural microbial communities within hosts.IMPORTANCEIn this study, to better identify horizontal gene transfer (HGT) in individual samples, we introduce a new co-barcoding sequencing system called metagenomics co-barcoding sequencing (MECOS), which has three significant improvements: (i) long DNA fragment extraction, (ii) a special transposome insertion, (iii) hybridization of DNA to barcode beads, and (4) an integrated bioinformatic pipeline. Using our approach, we have over 10-fold increased contig length compared to short-reads mNGS, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Our results indicate the presence of approximately 3,000 HGT blocks, involving roughly 6,000 genes and 100 taxonomic groups in individual samples. Notably, these HGT events are predominantly enriched in genes that confer tetracycline resistance via ribosomal protection. MECOS is a useful tool for investigating HGT and the evolution of natural microbial communities within hosts, thereby advancing our understanding of microbial ecology and evolution.},
}
@article {pmid38314328,
year = {2023},
author = {Yamada, A and Nguyen, DD and Eguchi, K},
title = {First discovery of the ant genus Eburopone Borowiec, 2016 (Hymenoptera, Formicidae, Dorylinae) in the Oriental realm, with description of a new species from Vietnam.},
journal = {ZooKeys},
volume = {1184},
number = {},
pages = {1-17},
pmid = {38314328},
issn = {1313-2989},
abstract = {The doryline ant genus Eburopone Borowiec, 2016 currently contains only one valid species, E.wroughtoni (Forel, 1910) from southern Africa, with a considerable number of undescribed species awaiting formal description in the Afrotropical and Malagasy regions. In the present paper, Eburoponeeasoanasp. nov. is described based on workers and dealate queens from a colony series collected in an evergreen forest on the Dak Lak Plateau of Vietnam (Ea So Nature Reserve, Dak Lak Province). The worker of the new species is morphologically clearly distinguished from E.wroughtoni by the combination of following characteristics: i) frontal line distinct, extending a little beyond mid-length of cranium; ii) anterior (frontoclypeal) margins of torulo-posttorular complex not forming conspicuous lobes protruding over anterior clypeal margin in full-face view; iii) mandibles when closed in full-face view forming only a little space between anterior clypeal margin and mandibles; iv) promesonotal suture faint and inconspicuous; v) abdominal segment III in dorsal view distinctly wider than long, with lateral margins only feebly convex. This represents the first discovery of the genus Eburopone in the Oriental realm, revealing the disjunct distribution of the genus. A partial sequence of the mitochondrial COI gene (658 bp) is provided as a DNA barcode for the new species. A worker-based key to the doryline genera of the Oriental realm is also provided.},
}
@article {pmid38314123,
year = {2024},
author = {Santos-Perdomo, I and Suárez, D and Moraza, ML and Arribas, P and Andújar, C},
title = {Towards a Canary Islands barcode database for soil biodiversity: revealing cryptic and unrecorded mite species diversity within insular soils.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e113301},
pmid = {38314123},
issn = {1314-2828},
abstract = {Soil arthropod diversity contributes to a high proportion of the total biodiversity on Earth. However, most soil arthropods are still undescribed, hindering our understanding of soil functioning and global biodiversity estimations. Inventorying soil arthropods using conventional taxonomical approaches is particularly difficult and costly due to the great species richness, abundance and local-scale heterogeneity of mesofauna communities and the poor taxonomic background knowledge of most lineages. To alleviate this situation, we have designed and implemented a molecular barcoding framework adapted to soil fauna. This pipeline includes different steps, starting with a morphology-based selection of specimens which are imaged. Then, DNA is extracted non-destructively. Both images and voucher specimens are used to assign a taxonomic identification, based on morphology that is further checked for consistency with molecular information. Using this procedure, we studied 239 specimens of mites from the Canary Islands including representatives of Mesostigmata, Sarcoptiformes and Trombidiformes, of which we recovered barcode sequences for 168 specimens that were morphologically identified to 49 species, with nine specimens that could only be identified at the genus or family levels. Multiple species delimitation analyses were run to compare molecular delimitations with morphological identifications, including ASAP, mlPTP, BINs and 3% and 8% genetic distance thresholds. Additionally, a species-level search was carried out at the Biodiversity Databank of the Canary Islands (BIOTA) to evaluate the number of species in our dataset that were not previously recorded in the archipelago. In parallel, a sequence-level search of our sequences was performed against BOLD Systems. Our results reveal that multiple morphologically identified species correspond to different molecular lineages, which points to significant levels of unknown cryptic diversity within the archipelago. In addition, we evidenced that multiple species in our dataset constituted new records for the Canary Islands fauna and that the information for these lineages within online genetic repositories is very incomplete. Our study represents the first systematic effort to catalogue the soil arthropod mesofauna of the Canary Islands and establishes the basis for the Canary Islands Soil Biodiversity barcode database. This resource will constitute a step forward in the knowledge of these arthropods in a region of special interest.},
}
@article {pmid38314115,
year = {2024},
author = {Vargas, HA},
title = {Argyrotaeniasocoromaensis sp. nov. (Lepidoptera, Tortricidae), a sexually dimorphic micromoth with polyphagous larvae from the arid Andes of northern Chile.},
journal = {ZooKeys},
volume = {1189},
number = {},
pages = {327-336},
pmid = {38314115},
issn = {1313-2989},
abstract = {Argyrotaeniasocoromaensissp. nov. (Lepidoptera, Tortricidae, Tortricinae, Archipini) from the arid Andes of northern Chile is described and illustrated. Adults are sexually dimorphic, with differences in wing size, shape and pattern. The larvae feed on Steviaphilippiana Hieron. (Asteraceae) and Lupinusoreophilus Phil. (Fabaceae). Genetic distance between DNA barcodes of male and female adults reared from larvae collected on the two hosts was 0-0.2% (K2P). The discovery of A.socoromaensissp. nov. represents the first record of the genus Argyrotaenia Stephens, 1852 and the tribe Archipini for the Chilean fauna of Tortricidae.},
}
@article {pmid38314107,
year = {2024},
author = {Betters, MJ and Cordes, EE},
title = {New records of Provanna (Gastropoda, Provannidae) from the Costa Rica Margin and an identification key for the genus.},
journal = {ZooKeys},
volume = {1189},
number = {},
pages = {1-32},
pmid = {38314107},
issn = {1313-2989},
abstract = {Consistent species identification is foundational to biological research and requires coordination among a diversity of researchers and institutions. However, such consistency may be hindered for rare organisms where specimens, identification resources, and taxonomic experts are few. This is often the case for deep-sea taxonomic groups. For example, the deep-sea gastropod genus Provanna Dall, 1918 is common at chemosynthetic sites throughout the world's oceans, yet no formal guide to these species has yet been produced. Recent exploration has recovered new specimens of Provanna from hydrocarbon seeps off the Pacific Costa Rica Margin. The current work assesses the species identity of these specimens using shell morphology, radular morphology, and genetic barcoding (mitochondrial CO1 and nuclear H3). Records of occurrence for P.laevis Warén &amp; Ponder, 1991, P.ios Warén &amp; Bouchet, 1986, and P.pacifica Warén &amp; Bouchet, 1986 are herein presented from the Costa Rica Margin. A critical taxonomic review of the 29 extant species within this genus was conducted and their genetic, morphological, and biogeographical distinction assessed. In this review, genetic and morphological support was found for nearly all current species delineations except for P.glabraOkutani et al., 1992, syn. nov. and P.laevis, syn. nov., which are herein synonymized to P.laevis, and for P.ios, syn. nov. and P.goniata Warén &amp; Bouchet, 1986, syn. nov., which are synonymized to P.ios. Finally, the first species identification key for the extant species in this genus is presented. This work clarifies the taxonomy and systematics of this deep-sea gastropod genus and contributes a novel polytomous key for use in future research.},
}
@article {pmid38312343,
year = {2023},
author = {Caterino, M and Recuero, E},
title = {Molecular diversity of Protura in southern High Appalachian leaf litter.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e113342},
pmid = {38312343},
issn = {1314-2828},
abstract = {The higher elevations of the southern Appalachian Mountains, U.S.A., host a rich, but little-studied fauna of Proturan hexapods. Here, we publish 117 Proturan barcode sequences from this region, estimated by automated species delimitation methods to represent 72 distinct species, whereas only nine species have previously been reported from the region. Two families, Eosentomidae and Acerentomidae, co-occur at most sampling sites, with as many as five species occurring in sympatry. Most populations exhibit very low haplotype diversity, but divergences amongst populations and amongst closely-related species are very high, a finding common to other phylogeographic studies of Proturans. Though we were unable to identify any of the barcodes to species, they form a useful, if preliminary, glimpse of southern Appalachian Proturan diversity.},
}
@article {pmid38312335,
year = {2023},
author = {Andersen, T and Höcherl, A and Hübner, J and Chimeno, C and Lin, X and Baranov, VA},
title = {New species and records of Pseudochironomini Sæther, 1977 (Diptera, Chironomidae) from the Dominican Republic.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e111925},
pmid = {38312335},
issn = {1314-2828},
abstract = {BACKGROUND: Pseudochironomini is a relatively small and poorly-studied tribe of subfamily Chironominae (Diptera, Chironomidae).<br><br>NEW INFORMATION: Pseudochironomusruthae Andersen &amp; Baranov sp. nov. is described and figured, based on a single male collected in a light trap at Matadero, Dominican Republic. The species can be separated from its congeners by the combination of the following characters: wing without dark bands, dorsocentrals in partly double row and apex of superior volsella rounded. The species is the first Pseudochironomus species to be formally recorded and described from the Caribbean. In addition, a new record of Manoapahayokeensis Jacobsen &amp; Perry, 2002 from the Dominican Republic is given. One specimen was DNA-barcoded and the barcode is given.},
}
@article {pmid38311607,
year = {2024},
author = {Liu, ZW and Zhou, J},
title = {DNA barcoding of Notopterygii Rhizoma et Radix (Qiang-huo) and identification of adulteration in its medicinal services.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {2879},
pmid = {38311607},
issn = {2045-2322},
support = {31960048//National Natural Science Foundation of China/ ; 202201AT070118//Foundation of Yunnan Science and Technology Department/ ; YNWRQNBJ-2019-208//Ten Thousand Talents Program of Yunnan/ ; 60118260127//Hundred-Talent Program of Kunming Medical University/ ; },
mesh = {*Drugs, Chinese Herbal ; DNA Barcoding, Taxonomic/methods ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Phylogeny ; },
abstract = {Safety concerns, stemming from the presence of complex and unpredictable adulterants, permeate the entire industrial chain of traditional Chinese medicines (TCMs). The Notopterygii Rhizoma et Radix (NReR) from the Apiaceae family, commonly known as "Qiang-huo", is a widely used herbal medicine. The recent surge in its demand has given rise to a proliferation of counterfeit and substituted products in the market. Traditional identification presents inherent limitations, while DNA mini-barcoding, reliant on sequencing a short-standardized region, has received considerable attention as a new potential means to identify processed medicinal materials. In this study, we constructed a comprehensive Internal Transcribed Spacer 2 (ITS2) matrix encompassing genuine NReR and their commonly found adulterants for the first time. Leveraging this matrix, we conducted a thorough assessment of the genetic profiles and sources of NReR available in the Chinese herbal medicine market. Following established DNA barcoding protocols, the intra-specific genetic divergences within NReR species were found to be lower than the inter-specific genetic divergences from other species. Among the 120 samples that were successfully amplified, ITS2 exhibits an outstanding species-level identification efficiency of 100% when evaluated using both the BLASTN and neighbor-joining (NJ) tree methods. We concluded that ITS2 is a mini-barcode that has shown its potential and may become a universal mini-barcode for the quality control of "Qiang-huo", thereby ensuring the safety of clinical medication.},
}
@article {pmid38307873,
year = {2024},
author = {Modeel, S and Negi, RK and Sharma, M and Dolkar, P and Yadav, S and Siwach, S and Yadav, P and Negi, T},
title = {A comprehensive DNA barcoding of Indian freshwater fishes of the Indus River system, Beas.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {2763},
pmid = {38307873},
issn = {2045-2322},
support = {F. No. EEQ/2019/000214//Science and Engineering Research Board/ ; },
mesh = {Humans ; Animals ; *Rivers ; *DNA Barcoding, Taxonomic/methods ; Bayes Theorem ; Electron Transport Complex IV/genetics ; Fishes/genetics ; Fresh Water ; DNA ; Phylogeny ; Biodiversity ; },
abstract = {The Beas River is one of the important rivers of the Indus River system located in Himachal Pradesh, India, that harbors a diverse range of freshwater fish species. The present study employed COI gene to investigate the ichthyofaunal diversity of river Beas. Through the sequencing of 203 specimens from Beas River, we identified 43 species, belonging to 31 genera, 16 families, and 10 orders. To analyze the genetic divergence and phylogeny of identified species, 485 sequences of Indian origin were retrieved from BOLD, resulting in a dataset of 688 sequences. Our findings consistently revealed a hierarchical increase in the mean K2P genetic divergence within species (0.80%), genus (9.06%), and families (15.35%). Automated Barcode Gap discovery, Neighbour Joining, and Bayesian inference consensus tree methodologies were employed to determine the putative species and their phylogeny, successfully delimiting most of the species with only a few exceptions. The results unveiled six species exhibiting high intra-species divergence (> 2%), suggesting the presence of sibling species and falsely identified sequences on online databases. The present study established the first DNA barcoding-based inventory of freshwater fish species in the Beas River providing comprehensive insights into economically exploited endangered and vulnerable species. In order to ensure the sustainable use of aquatic resources in the Beas River, we recommend the implementation of species measures to protect biodiversity and genetic resources.},
}
@article {pmid38306450,
year = {2024},
author = {Jamonneau, T and Dahruddin, H and Limmon, G and Sukmono, T and Busson, F and Nurjirana, and Gani, A and Patikawa, J and Wuniarto, E and Sauri, S and Nurhaman, U and Wowor, D and Steinke, D and Keith, P and Hubert, N},
title = {Jump dispersal drives the relationship between micro- and macroevolutionary dynamics in the Sicydiinae (Gobiiformes: Oxudercidae) of Sundaland and Wallacea.},
journal = {Journal of evolutionary biology},
volume = {37},
number = {12},
pages = {1458-1473},
doi = {10.1093/jeb/voae017},
pmid = {38306450},
issn = {1420-9101},
support = {//Institut de Recherche pour le D&#xe9;veloppement/ ; },
mesh = {Animals ; *Animal Distribution ; Male ; Genetic Variation ; Female ; Biological Evolution ; Phylogeny ; Bayes Theorem ; Electron Transport Complex IV/genetics ; },
abstract = {Insular biodiversity hotspots of Southeast Asia are remarkable for their biodiverse faunas. With a marine larval phase lasting up to several months, the freshwater fish subfamily Sicydiinae has colonized most islands of these hotspots. However, Sicydiinae diversity is still poorly understood in Southeast Asia. With the objective of estimating intraspecific genetic diversity and inferring past demography, we conducted the molecular inventory of Sicydiinae species in Sundaland and Wallacea using 652 bp of the mitochondrial cytochrome oxidase I gene, species delimitation methods, and Bayesian Skyline plot reconstructions. In total, 24 Molecular Operational Taxonomic Units are delimited among the 603 sequences belonging to 27 species and 5 genera. Two cases of discordance between morphology and mitochondrial sequence are observed, suggesting ongoing speciation and/or introgression in 2 genera. Multiple new occurrences are reported, either for a single biodiversity hotspot or both, some of which correspond to observations of a few individuals far from the range distribution of their conspecifics. Among the 10 species or species groups whose intraspecific diversity was examined, high levels of genetic diversity and past population expansion are revealed by Tajima's D tests and Bayesian Skyline Plot reconstructions. Together, these results indicate that long-distance dispersal is common and suggest that most endemic species originated through founder events followed by population expansion. Patterns of sexual dimorphism and males' coloration among diverging species pairs seem to point to sexual selection as an important mechanism contributing to speciation in the Sicydiinae of Sundaland and Wallacea.},
}
@article {pmid38306182,
year = {2024},
author = {Ali, R and Lezcano, RD and Jayaraman, J and Mohammed, A and Carrington, CVF and Daniel, B and Lovin, DD and Cunningham, JM and Severson, DW and Ramsubhag, A},
title = {DNA Barcoding Analysis of Trinidad Haemagogus Mosquitoes Reveals Evidence for Putative New Species.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {24},
number = {4},
pages = {237-244},
doi = {10.1089/vbz.2023.0031},
pmid = {38306182},
issn = {1557-7759},
mesh = {Animals ; Female ; *Culicidae ; DNA Barcoding, Taxonomic/veterinary ; Mosquito Vectors/genetics/anatomy &amp; histology ; Phylogeny ; Trinidad and Tobago ; },
abstract = {Background: Haemagogus janthinomys is a primary sylvan vector of yellow fever virus and the emerging Mayaro virus. However, despite its medical importance, there is a dearth of data on the molecular taxonomy of this mosquito species. Methods: In this study, DNA barcoding analysis was performed on 64 adult female mosquitoes from Trinidad morphologically identified as Hg. janthinomys. The mitochondrial cytochrome c oxidase I (COI) gene and ribosomal DNA internal transcribed spacer 2 (ITS2) region of the mosquitoes were PCR amplified and sequenced, and molecular phylogenies inferred. Results: The BLASTN analysis showed that only 20% (n = 13/66) of COI sequences had high similarity (>99% identity) to Hg. janthinomys and the remaining sequences had low similarity (<90% identity) to reference GenBank sequences. Phylogenetic analysis of COI sequences revealed the presence of four strongly supported groups, with one distinct clade that did not align with any reference sequences. Corresponding ITS2 sequences for samples in this distinct COI group clustered into three clades. Conclusions: These molecular findings suggest the existence of a putative new Haemagogus mosquito species and underscore the need for further, more in-depth investigations into the taxonomy and classification of the Haemagogus genus.},
}
@article {pmid38304893,
year = {2024},
author = {Wei, Z and Ren, G},
title = {Review of the genus Laena Dejean, 1821 (Coleoptera, Tenebrionidae) from Gansu Province, China, with the description of a new species.},
journal = {ZooKeys},
volume = {1190},
number = {},
pages = {121-130},
pmid = {38304893},
issn = {1313-2989},
abstract = {A new species of the genus Laena from Xiaolongshan in Gansu Province, China is described as Laenahuisp. nov. All Laena species known to occur in Gansu Province are reviewed, and an identification key is provided. The mitochondrial gene COI to confirm the identity of the new species, which is morphologically most similar and phylogenetically close to L.fengileana. The new species can be recognized by features of elytra and tibiae.},
}
@article {pmid38304272,
year = {2024},
author = {Jing, W and Niu, Z and Ma, S and Yu, H},
title = {New species and new record of Statherotmantis Diakonoff, 1973 from China (Lepidoptera: Tortricidae: Olethreutinae).},
journal = {Ecology and evolution},
volume = {14},
number = {2},
pages = {e10906},
pmid = {38304272},
issn = {2045-7758},
abstract = {In China, six species of Statherotmantis Diakonoff, 1973 were previously recorded. In the present study, four other species were recognized using morphology and DNA barcording analysis. Among these, three of which, S. miniscula sp. n., S. calva sp. n., and S. longiuscula sp. n., are described as new. In addition, one species, S. laetana Kuznetzov, 1988, is a new record for China. Adults and genitalia are illustrated, and keys to identify the Chinese species of Statherotmantis are provided.},
}
@article {pmid38304271,
year = {2024},
author = {Hartvig, I and Kosawang, C and Rasmussen, H and Kjær, ED and Nielsen, LR},
title = {Co-occurring orchid species associated with different low-abundance mycorrhizal fungi from the soil in a high-diversity conservation area in Denmark.},
journal = {Ecology and evolution},
volume = {14},
number = {2},
pages = {e10863},
pmid = {38304271},
issn = {2045-7758},
abstract = {Plant-fungal interactions are ubiquitous across ecosystems and contribute significantly to plant ecology and evolution. All orchids form obligate symbiotic relationships with specific fungi for germination and early growth, and the distribution of terrestrial orchid species has been linked to occurrence and abundance of specific orchid mycorrhizal fungi (OMF) in the soil. The availability of OMF can therefore be a habitat requirement that is relevant to consider when establishing management and conservation strategies for threatened orchid species, but knowledge on the spatial distribution of OMF in soil is limited. We here studied the mycorrhizal associations of three terrestrial orchid species (Anacamptis pyramidalis, Orchis purpurea and Platanthera chlorantha) found in a local orchid diversity hotspot in eastern Denmark, and investigated the abundance of the identified mycorrhizal fungi in the surrounding soil. We applied ITS metabarcoding to samples of orchid roots, rhizosphere soil and bulk soil collected at three localities, supplemented with standard barcoding of root samples with OMF specific primers, and detected 22 Operational Taxonomic Units (OTUs) putatively identified as OMF. The three orchid species displayed different patterns of OMF associations, supporting the theory that association with specific fungi constitutes part of an orchid's ecological niche allowing co-occurrence of many species in orchid-rich habitats. The identified mycorrhizal partners in the basidiomycete families Tulasnellaceae and Ceratobasidiaceae (Cantharallales) were detected in low abundance in rhizosphere soil, and appeared almost absent from bulk soil at the localities. This finding highlights our limited knowledge of the ecology and trophic mode of OMF outside orchid tissues, as well as challenges in the detection of specific OMF with standard methods. Potential implications for management and conservation strategies are discussed.},
}
@article {pmid38301093,
year = {2023},
author = {Nasibi, S and Mojarrab, S and Lashkarizadeh, MR and Shafiei, M and Saedi Dezaki, E and Mahmoudvand, H and Alizadeh, A and Mohammadzadeh, A and Adnani Sadati, SJ and Mirbadie, SR and Keighobadi, M and Gholami, S and Raeghi, S and Abbasi, M and Mohtasham, F and Ravari, MS and Dabirzadeh, M and Mosavi Anari, SA and Mirjalali, H and Aliakbarian, M and Abbasifard, M and Fasihi Harandi, M},
title = {Iranian Hydatid Disease Registry: Establishment and Implementation of a Neglected Tropical Disease Registry.},
journal = {Archives of Iranian medicine},
volume = {26},
number = {7},
pages = {358-364},
pmid = {38301093},
issn = {1735-3947},
mesh = {Humans ; Iran/epidemiology ; *Neglected Diseases/epidemiology ; *Echinococcosis/epidemiology/parasitology ; Public Health ; Registries ; },
abstract = {BACKGROUND: Cystic echinococcosis (CE) or hydatid disease is a global public health concern which imposes considerable economic costs on the communities in endemic regions. CE surveillance data are not adequately reliable. The present study reports the development and outcomes of a CE registry in Iran.<br><br>METHODS: Hydatid Registry (HydatidReg) was initially established as a single-center registry in 2014 after the ethical approval of KMU. Following a call from MoHME to promote registry of different diseases and health outcomes, a call for participation was announced and all the Iranian Universities of Medical Sciences were requested to contribute to the registry. Subsequently, a nation-wide registry of hydatid disease was established in 2016. With a global perspective, HydatidReg joined the European Register of Cystic Echinococcosis (ERCE). A data collection form based on minimum dataset was designed and standard operating procedures (SOPs) were prepared to ensure standardized patient enrolment in the registry. A biobank system with two-dimensional barcoding was established along with HydatidReg for management and organization of biological specimens.<br><br>RESULTS: As of March 2021, a total of 690 patients were enrolled in the registry. HydatidReg registered 362 (17.3%) out of the total 2097 patients enrolled in ERCE. Quality control (QC) of the data demonstrated 91.2% completeness and 80% timeliness. In the biobank, 322 biological specimens from 184 CE patients have been deposited including 70 blood, 96 sera and 156 parasite materials.<br><br>CONCLUSION: High-quality data in the HydatidReg registry provided opportunities for health professionals to improve quality of care and organize meaningful research.},
}
@article {pmid38297649,
year = {2024},
author = {Rosenbaum, P and Barhom, H and Inberg, A and Lapsker, I and Rosenman, G and Apter, B},
title = {Hidden imaging in thin polymer films with embedded fluorescent peptide nanodots.},
journal = {Optics express},
volume = {32},
number = {3},
pages = {4485-4497},
doi = {10.1364/OE.511152},
pmid = {38297649},
issn = {1094-4087},
mesh = {Polymers ; *Nanoparticles/chemistry ; *Quantum Dots/chemistry ; Peptides ; Coloring Agents ; Fluorescent Dyes/chemistry ; },
abstract = {Fluorescent (FL) encrypting nanostructures, such as quantum dots, carbon dots, organic dyes, lanthanide nanocrystals, DNA, and more, are effective tools for advanced applications in high-resolution hidden imaging. These applications include tracking, labeling, security printing, and anti-counterfeiting drug technology. In this work, what we believe to be a new FL encoding nanostructures has been proposed, which consists of recently discovered nanometer-scale peptide dots. When refolded into a beta-sheet peptide secondary structure, these biocompatible nanoparticles exhibit a strong and tunable FL effect. The biophotonic FL covers the entire visible spectrum, making the peptide dots next-generation nanoscale light sources with a quantum yield of 30%. Our studies demonstrate that these FL bio-nanodots also exhibit a significant irreversible photo-bleaching effect associated with the light-induced destruction of noncovalent intermolecular hydrogen bonds of the peptide dots' highly stable beta-sheet secondary structure. We present what we believe is a new approach for achieving high-resolution long-term optical memory by tailoring various hidden images in the developed thin polyvinyl alcohol (PVA) polymer films with an embedded dense array of FL peptide nanodots. The technology enables recording photo-bleached patterns, barcodes, and high-resolution images.},
}
@article {pmid38296555,
year = {2024},
author = {Osawa, T and Obika, S},
title = {Synthesis of Coumarin-Conjugated Oligonucleotides via Knoevenagel Condensation to Prepare an Oligonucleotide Library.},
journal = {Chemical &amp; pharmaceutical bulletin},
volume = {72},
number = {2},
pages = {143-148},
doi = {10.1248/cpb.c23-00295},
pmid = {38296555},
issn = {1347-5223},
mesh = {*Oligonucleotides ; *Coumarins/chemistry ; DNA/chemistry ; Cyclization ; },
abstract = {DNA-encoded libraries (DELs) are attracting attention as a screening tool in the early stages of drug discovery. In the development of DELs, drug candidate compounds are chemically synthesized on barcode DNA. Therefore, it is important to perform the synthesis under mild conditions so as to not damage the DNA. On the other hand, coumarins are gaining increasing research focus not only because they possess excellent fluorescence properties, but also because many medicines contain a coumarin skeleton. Among the various reactions developed for the synthesis of coumarins thus far, Knoevenagel condensation followed by intramolecular cyclization under mild conditions can yield coumarins. In this study, we developed a new synthetic method for preparing a coumarin-conjugated oligonucleotide library via Knoevenagel condensation. The results showed that coumarins substituted at the 5-, 6-, 7-, or 8-positions could be constructed on DNA to afford a total of 26 coumarin-conjugated DNAs. Moreover, this method was compatible with enzymatic ligation, demonstrating its utility in DEL synthesis. The developed strategy for the construction of coumarin scaffolds based on Knoevenagel condensation may contribute to the use of DELs in drug discovery and medicinal chemistry.},
}
@article {pmid38295293,
year = {2024},
author = {Ramírez Rojas, AA and Brinkmann, CK and Köbel, TS and Schindler, D},
title = {DuBA.flow─A Low-Cost, Long-Read Amplicon Sequencing Workflow for the Validation of Synthetic DNA Constructs.},
journal = {ACS synthetic biology},
volume = {13},
number = {2},
pages = {457-465},
pmid = {38295293},
issn = {2161-5063},
mesh = {Workflow ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Plasmids/genetics ; *DNA/genetics ; },
abstract = {Modern biological science, especially synthetic biology, relies heavily on the construction of DNA elements, often in the form of plasmids. Plasmids are used for a variety of applications, including the expression of proteins for subsequent purification, the expression of heterologous pathways for the production of valuable compounds, and the study of biological functions and mechanisms. For all applications, a critical step after the construction of a plasmid is its sequence validation. The traditional method for sequence determination is Sanger sequencing, which is limited to approximately 1000 bp per reaction. Here, we present a highly scalable in-house method for rapid validation of amplified DNA sequences using long-read Nanopore sequencing. We developed two-step amplicon and transposase strategies to provide maximum flexibility for dual barcode sequencing. We also provide an automated analysis pipeline to quickly and reliably analyze sequencing results and provide easy-to-interpret results for each sample. The user-friendly DuBA.flow start-to-finish pipeline is widely applicable. Furthermore, we show that construct validation using DuBA.flow can be performed by barcoded colony PCR amplicon sequencing, thus accelerating research.},
}
@article {pmid38293072,
year = {2024},
author = {Hale, JJ and Matsui, T and Goldstein, I and Mullis, MN and Roy, KR and Ville, CN and Miller, D and Wang, C and Reynolds, T and Steinmetz, LM and Levy, SF and Ehrenreich, IM},
title = {Genome-scale analysis of interactions between genetic perturbations and natural variation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38293072},
issn = {2692-8205},
support = {R01 AI164530/AI/NIAID NIH HHS/United States ; R01 HG010378/HG/NHGRI NIH HHS/United States ; R35 GM130381/GM/NIGMS NIH HHS/United States ; },
abstract = {Interactions between genetic perturbations and segregating loci can cause perturbations to show different phenotypic effects across genetically distinct individuals. To study these interactions on a genome scale in many individuals, we used combinatorial DNA barcode sequencing to measure the fitness effects of 7,700 CRISPRi perturbations targeting 1,712 distinct genes in 169 yeast cross progeny (or segregants). We identified 460 genes whose perturbation has different effects across segregants. Several factors caused perturbations to show variable effects, including baseline segregant fitness, the mean effect of a perturbation across segregants, and interacting loci. We mapped 234 interacting loci and found four hub loci that interact with many different perturbations. Perturbations that interact with a given hub exhibit similar epistatic relationships with the hub and show enrichment for cellular processes that may mediate these interactions. These results suggest that an individual's response to perturbations is shaped by a network of perturbation-locus interactions that cannot be measured by approaches that examine perturbations or natural variation alone.},
}
@article {pmid38293032,
year = {2024},
author = {Tshiabuila, D and Choga, W and James, SE and Maponga, T and Preiser, W and van Zyl, G and Moir, M and van Wyk, S and Giandhari, J and Pillay, S and Anyaneji, UJ and Lessells, RJ and Naidoo, Y and Sanko, TJ and Wilkinson, E and Tegally, H and Baxter, C and Martin, DP and de Oliveira, T},
title = {An Oxford Nanopore Technology-Based Hepatitis B Virus Sequencing Protocol Suitable For Genomic Surveillance Within Clinical Diagnostic Settings.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {38293032},
support = {U01 AI151698/AI/NIAID NIH HHS/United States ; U54 TW012041/TW/FIC NIH HHS/United States ; },
abstract = {Chronic hepatitis B virus (HBV) infection remains a significant public health concern, particularly in Africa, where there is a substantial burden. HBV is an enveloped virus, with isolates being classified into ten phylogenetically distinct genotypes (A - J) determined based on full-genome sequence data or reverse hybridization-based diagnostic tests. In practice, limitations are noted in that diagnostic sequencing, generally using Sanger sequencing, tends to focus only on the S-gene, yielding little or no information on intra-patient HBV genetic diversity with very low-frequency variants and reverse hybridization detects only known genotype-specific mutations. To resolve these limitations, we developed an Oxford Nanopore Technology (ONT)-based HBV genotyping protocol suitable for clinical virology, yielding complete HBV genome sequences and extensive data on intra-patient HBV diversity. Specifically, the protocol involves tiling-based PCR amplification of HBV sequences, library preparation using the ONT Rapid Barcoding Kit, ONT GridION sequencing, genotyping using Genome Detective software, recombination analysis using jpHMM and RDP5 software, and drug resistance profiling using Geno2pheno software. We prove the utility of our protocol by efficiently generating and characterizing high-quality near full-length HBV genomes from 148 left-over diagnostic Hepatitis B patient samples obtained in the Western Cape province of South Africa, providing valuable insights into the genetic diversity and epidemiology of HBV in this region of the world.},
}
@article {pmid38291503,
year = {2024},
author = {Zhu, Q and Conrad, DN and Gartner, ZJ},
title = {deMULTIplex2: robust sample demultiplexing for scRNA-seq.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {37},
pmid = {38291503},
issn = {1474-760X},
support = {CRI5054/CRI/Cancer Research Institute/United States ; R01GM135462/GM/NIGMS NIH HHS/United States ; R01 GM135462/GM/NIGMS NIH HHS/United States ; R33CA247744/CA/NCI NIH HHS/United States ; R33 CA247744/CA/NCI NIH HHS/United States ; U01 DK103147/DK/NIDDK NIH HHS/United States ; U01CA199315/CA/NCI NIH HHS/United States ; R01DK126376/DK/NIDDK NIH HHS/United States ; U01DK103147/DK/NIDDK NIH HHS/United States ; U01 CA199315/CA/NCI NIH HHS/United States ; R01 DK126376/DK/NIDDK NIH HHS/United States ; },
mesh = {*Single-Cell Gene Expression Analysis ; *Single-Cell Analysis/methods ; Algorithms ; Sequence Analysis, RNA/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Sample multiplexing enables pooled analysis during single-cell RNA sequencing workflows, thereby increasing throughput and reducing batch effects. A challenge for all multiplexing techniques is to link sample-specific barcodes with cell-specific barcodes, then demultiplex sample identity post-sequencing. However, existing demultiplexing tools fail under many real-world conditions where barcode cross-contamination is an issue. We therefore developed deMULTIplex2, an algorithm inspired by a mechanistic model of barcode cross-contamination. deMULTIplex2 employs generalized linear models and expectation-maximization to probabilistically determine the sample identity of each cell. Benchmarking reveals superior performance across various experimental conditions, particularly on large or noisy datasets with unbalanced sample compositions.},
}
@article {pmid38288484,
year = {2024},
author = {Zhang, P and Cai, Y and Ma, L and Chai, J and Zhou, Z},
title = {DNA barcoding of the genus Gampsocleis (Orthoptera, Tettigoniidae) from China.},
journal = {Archives of insect biochemistry and physiology},
volume = {115},
number = {1},
pages = {e22070},
doi = {10.1002/arch.22070},
pmid = {38288484},
issn = {1520-6327},
support = {C2021201002//Natural Science Foundation of Hebei Province/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Bayes Theorem ; *Orthoptera/genetics ; Phylogeny ; DNA ; },
abstract = {DNA barcoding is a useful addition to the traditional morphology-based taxonomy. A ca. 650 bp fragment of the 5' end of mitochondrial cytochrome c oxidase subunit I (hereafter COI-5P) DNA barcoding was sued as a practical tool for Gampsocleis species identification. DNA barcodes from 889 specimens belonging to 8 putative Gampsocleis species was analyzed, including 687 newly generated DNA barcodes. These barcode sequences were clustered/grouped into Operational Taxonomic Units (OTUs) using the criteria of five algorithms, namely Barcode Index Number (BIN) System, Assemble Species by Automatic Partitioning (ASAP), a Java program uses an explicit, determinate algorithm to define Molecular Operational Taxonomic Unit (jMOTU), Generalized Mixed Yule Coalescent (GMYC), and Bayesian implementation of the Poisson Tree Processes model (bPTP). The Taxon ID Tree grouped sequences of morphospecies and almost all MOTUs in distinct nonoverlapping clusters. Both long- and short-winged Gampsocleis species are reciprocally monophyletic in the Taxon ID Tree. In BOLD, 889 barcode sequences are assigned to 17 BINs. The algorithms ASAP, jMOTU, bPTP and GMYC clustered the barcode sequences into 6, 13, 10, and 23 MOTUs, respectively. BIN, ASAP, and bPTP algorithm placed three long-winged species, G. sedakovii, G. sinensis and G. ussuriensis within the same MOTU. All species delimitation algorithms split two short-winged species,G. fletcheri and G. gratiosa into at least two MOTUs each, except for ASAP algorithm. More detailed molecular and morphological integrative studies are required to clarify the status of these MOTUs in the future.},
}
@article {pmid38288374,
year = {2024},
author = {Gezelius, H and Enblad, AP and Lundmark, A and Åberg, M and Blom, K and Rudfeldt, J and Raine, A and Harila, A and Rendo, V and Heinäniemi, M and Andersson, C and Nordlund, J},
title = {Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening.},
journal = {NAR genomics and bioinformatics},
volume = {6},
number = {1},
pages = {lqae001},
pmid = {38288374},
issn = {2631-9268},
abstract = {Functional precision medicine (FPM) aims to optimize patient-specific drug selection based on the unique characteristics of their cancer cells. Recent advancements in high throughput ex vivo drug profiling have accelerated interest in FPM. Here, we present a proof-of-concept study for an integrated experimental system that incorporates ex vivo treatment response with a single-cell gene expression output enabling barcoding of several drug conditions in one single-cell sequencing experiment. We demonstrate this through a proof-of-concept investigation focusing on the glucocorticoid-resistant acute lymphoblastic leukemia (ALL) E/R+ Reh cell line. Three different single-cell transcriptome sequencing (scRNA-seq) approaches were evaluated, each exhibiting high cell recovery and accurate tagging of distinct drug conditions. Notably, our comprehensive analysis revealed variations in library complexity, sensitivity (gene detection), and differential gene expression detection across the methods. Despite these differences, we identified a substantial transcriptional response to fludarabine, a highly relevant drug for treating high-risk ALL, which was consistently recapitulated by all three methods. These findings highlight the potential of our integrated approach for studying drug responses at the single-cell level and emphasize the importance of method selection in scRNA-seq studies. Finally, our data encompassing 27 327 cells are freely available to extend to future scRNA-seq methodological comparisons.},
}
@article {pmid38288251,
year = {2024},
author = {Wang, Y and Hu, B and Peng, J and Zhou, Q},
title = {The complete chloroplast genome of Sinosenecio globigerus (C. C. Chang) B. Nordenstam (Asteraceae).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {9},
number = {1},
pages = {204-208},
pmid = {38288251},
issn = {2380-2359},
abstract = {The genus Sinosenecio B. Nordenstam is a group of perennial or sometimes annual or biennial herbs in the family Asteraceae. Here, we have successfully assembled and characterized the complete chloroplast (cp) genome of S. globigerus, which shows a typical quadratic structure with an overall GC content of 37.4%, comprising a pair of inverted repeat regions (IRs) of 24,848 bp, a large single-copy region (LSC) of 83,379 bp and a small single-copy region (SSC) of 18,180 bp. 133 genes were annotated, including 88 protein-coding genes, 37 tRNA genes and eight rRNA genes. Further nucleotide diversity analysis indicated that three genomic regions (accD-psaI, trnK-rps16, and ycf1) exhibited sufficient variability and thus could be recommended as valuable barcodes for the delimitation and identification of Sinosenecio species. Phylogenetic reconstruction presented clear interspecific relationships within Sinosenecio, which were supported to some extent by cytology, morphology and geographic distributions. Our study will provide valuable and high-quality genetic information to further elucidate the diversified mechanisms in Sinosenecio.},
}
@article {pmid38287974,
year = {2023},
author = {Balz, K and Grange, M and Pegel, U and Karamya, ZA and Mello, M and Zhou, X and Berger, T and Bloch, K and Dunham, D and Chinthrajah, S and Nadeau, K and Luche, H and Skevaki, C},
title = {A novel mass cytometry protocol optimized for immunophenotyping of low-frequency antigen-specific T cells.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1336489},
pmid = {38287974},
issn = {2235-2988},
mesh = {Humans ; Animals ; Mice ; Flow Cytometry/methods ; Immunophenotyping ; *Antigens ; *T-Lymphocytes ; Staining and Labeling ; CD8-Positive T-Lymphocytes ; },
abstract = {Understanding antigen-specific T-cell responses, for example, following virus infections or allergen exposure, is of high relevance for the development of vaccines and therapeutics. We aimed on optimizing immunophenotyping of T cells after antigen stimulation by improving staining procedures for flow and mass cytometry. Our method can be used for primary cells of both mouse and human origin for the detection of low-frequency T-cell response using a dual-barcoding system for individual samples and conditions. First, live-cell barcoding was performed using anti-CD45 antibodies prior to an in vitro T-cell stimulation assay. Second, to discriminate between stimulation conditions and prevent cell loss, sample barcoding was combined with a commercial barcoding solution. This dual-barcoding approach is cell sparing and, therefore, particularly relevant for samples with low cell numbers. To further reduce cell loss and to increase debarcoding efficiency of multiplexed samples, we combined our dual-barcoding approach with a new centrifugation-free washing system by laminar flow (Curiox™). Finally, to demonstrate the benefits of our established protocol, we assayed virus-specific T-cell response in SARS-CoV-2-vaccinated and SARS-CoV-2-infected patients and compared with healthy non-exposed individuals by a high-parameter CyTOF analysis. We could reveal a heterogeneity of phenotypes among responding CD4, CD8, and gd-T cells following antigen-specific stimulations. Our protocol allows to assay antigen-specific responses of minute populations of T cells to virus-derived peptides, allergens, or other antigens from the same donor sample, in order to investigate qualitative and quantitative differences.},
}
@article {pmid38286429,
year = {2024},
author = {Reza, F and Jones, C and Reed, JH},
title = {Improving Immunization Health Care Data Quality using Two-Dimensional Barcoding and Barcode Scanning Practices.},
journal = {Applied clinical informatics},
volume = {15},
number = {2},
pages = {265-273},
pmid = {38286429},
issn = {1869-0327},
mesh = {Humans ; *Data Accuracy ; COVID-19 Vaccines ; Immunization ; *Vaccines ; Ambulatory Care Facilities ; Delivery of Health Care ; },
abstract = {BACKGROUND: Manual data entry is time-consuming, inefficient, and error prone. In contrast, leveraging two-dimensional (2D) barcodes and barcode scanning tools is a rapid and effective practice for automatically entering vaccine data accurately and completely. CDC pilots documented clinical and public health impacts of 2D barcode scanning practices on data quality and completeness, time savings, workflow efficiencies, and staff experience.<br><br>OBJECTIVES: &#x2003;Data entry practices and entered records from routine and mass vaccination settings were analyzed. Data quality improvement opportunities were identified.<br><br>METHODS: &#x2003;A sample of 50 million emergency use authorization (EUA) coronavirus disease 2019 (COVID-19) vaccine records were analyzed for accuracy and completeness across three data fields: lot number, expiration date, and National Drug Code (NDC). The EUA COVID-19 vaccines lacked a 2D barcode containing these data fields, which necessitated manual data entry at administration. A CDC pilot at clinic compared scanned and manually entered data for routine vaccines across these same data fields.<br><br>RESULTS: &#x2003;Analysis of 50 million manually entered EUA COVID-19 vaccine administration records indicated significant gaps in data accuracy and completeness across three data fields. Over half of the analyzed EUA vaccine NDCs (53%) and one-third of the expiration dates (35%) had missing or inaccurate data recorded. Pilot data also showed many errors when manually entered. However, when the pilot's routine vaccines were scanned (out of 71,969 records), nearly all entries were complete and accurate across all three data fields (ranging from 99.7% to 99.999% accurate).<br><br>CONCLUSION: &#x2003;Vaccine 2D barcode scanning practices increased data accuracy and completeness (up to 99.999% accurate) across data fields assessed. When used consistently, vaccine 2D barcode scanning can resolve issues demonstrated in manually entered data. To realize these benefits, the immunization community should widely use scanning practices. To increase use, CDC developed a Vaccine 2D Barcode National Adoption Strategy and implementation resources.},
}
@article {pmid38284970,
year = {2024},
author = {Sultana, S and Azlan, A and Mohd Desa, MN and Mahyudin, NA and Anburaj, A},
title = {A review of CRISPR-Cas and PCR-based methods for the detection of animal species in the food chain-current challenges and future prospects.},
journal = {Food additives &amp; contaminants. Part A, Chemistry, analysis, control, exposure &amp; risk assessment},
volume = {41},
number = {3},
pages = {213-227},
doi = {10.1080/19440049.2024.2304577},
pmid = {38284970},
issn = {1944-0057},
mesh = {Animals ; *CRISPR-Cas Systems ; *Food Chain ; Cell Line ; DNA/genetics ; Polymerase Chain Reaction ; },
abstract = {Regular testing and systematic investigation play a vital role to ensure product safety. Until now, the existing food authentication techniques have been based on proteins, lipids, and nucleic acid-based assays. Among various deoxyribonucleic acid (DNA)-based methods, the recently developed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) based bio-sensing is an innovative and fast-expanding technology. The CRISPR/Cas-9 is known as Clustered Regularly Interspaced Short Palindromic Repeats due to the flexibility and simplicity of the CRISPR/Cas9 site-specific editing tool has been applied in many biological research areas such as Gene therapy, cell line development, discovering mechanisms of disease, and drug discovery. Nowadays, the CRISPR-Cas system has also been introduced into food authentication via detecting DNA barcodes of poultry and livestock both in processed and unprocessed food samples. This review documents various DNA based approaches, in an accessible format. Future CRISPR technologies are forecast while challenges are outlined.},
}
@article {pmid38284609,
year = {2024},
author = {Giusti, A and Malloggi, C and Magagna, G and Filipello, V and Armani, A},
title = {Is the metabarcoding ripe enough to be applied to the authentication of foodstuff of animal origin? A systematic review.},
journal = {Comprehensive reviews in food science and food safety},
volume = {23},
number = {1},
pages = {e13256},
doi = {10.1111/1541-4337.13256},
pmid = {38284609},
issn = {1541-4337},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Food ; Quality Control ; },
abstract = {Food authentication using molecular techniques is of great importance to fight food fraud. Metabarcoding, based on the next-generation sequencing (NGS) technologies, allowing large-scale taxonomic identification of complex samples via massive parallel sequencing of fragments (called DNA barcodes) simultaneously, has become increasingly popular in many scientific fields. A systematic review to answer the question "Is the metabarcoding ripe enough to be applied to the authentication of foodstuff of animal origin?" is presented. The inclusion criteria were focused on the selection of scientific papers (SPs) only applying metabarcoding to foodstuff of animal origin collected on the market. The 23 included SPs were first analyzed with respect to the metabarcoding phases: library preparation (target genes, primer pairs, and fragment length), sequencing (NGS platforms), and final data analysis (bioinformatic pipelines). Given the importance of primer selection, the taxonomic coverage of the used primers was also evaluated. In addition, the SPs were scored based on the use of quality control measures (procedural blanks, positive controls, replicates, curated databases, and thresholds to filter the data). A lack of standardized protocols, especially with respect to the target barcode/s and the universal primer/s, and the infrequent application of the quality control measures, leads to answer that metabarcoding is not ripe enough for authenticating foodstuff of animal origin. However, the observed trend of the SP quality improvement over the years is encouraging. Concluding, a proper protocol standardization would allow a wider use of metabarcoding by both official and private laboratories, enabling this method to become the primary for the authentication of foodstuffs of animal origin.},
}
@article {pmid38282716,
year = {2024},
author = {Schmid-Egger, C and Schmidt, S and Bogusch, P},
title = {DNA Barcoding of Central European Gasteruptiidae and the rarely-collected families Evaniidae, Stephanidae, Trigonalidae, and Aulacidae (Hymenoptera, Apocrita).},
journal = {ZooKeys},
volume = {1189},
number = {},
pages = {275-286},
pmid = {38282716},
issn = {1313-2989},
abstract = {The study presents DNA barcoding results of five families of Hymenoptera in Germany. DNA barcodes are provided for 24 of the 25 species of Gasteruption occurring in Central Europe, including 18 of the 19 species recorded from Germany. The genetic diversity was higher than expected, with five species exhibiting two or more Barcode Index Number (BINs), whereas BIN sharing occurred in four species. Gasteruptionfoveiceps Semenov, 1892, stat. nov. is removed from synonymy with G.nigrescens Schletterer, 1885 and treated as a distinct species.},
}
@article {pmid38282715,
year = {2024},
author = {Zograf, JK and Semenchenko, AA and Mordukhovich, VV},
title = {New deep-sea species of Aborjinia (Nematoda, Leptosomatidae) from the North-Western Pacific: an integrative taxonomy and phylogeny.},
journal = {ZooKeys},
volume = {1189},
number = {},
pages = {231-256},
pmid = {38282715},
issn = {1313-2989},
abstract = {Marimermithid nematodes parasitising invertebrates are mainly found in the deep-sea environments. Several adult and juvenile specimens marimermithids of the genus Aborjinia have been found in bottom sediments and inside Polychaeta during recent cruises to the Kuril-Kamchatka trench and the Kuril Basin (the Sea of Okhotsk). New species are described based on integrative study. Aborjiniaprofundasp. nov. differs from A.eulagiscae by the location of the ventral gland cell bodies (posterior to the nerve ring vs posterior to the cardia), by the smaller body size (23-28 mm vs 103-132 mm) and shorter tail (193-263 µm vs 500-850 µm). BI and ML phylogenetic analyses based on 18S and 28S rDNA suggest that genus Aborjinia belongs to the family Leptosomatidae. Based on molecular and morphological characters the new genus Paraborjiniagen. nov. is proposed for A.corallicola. Within the family Leptosomatidae the new genus differs from all genera except Aborjinia by its endoparasitic lifestyle and hologonic ovaries. Paraborjiniagen. nov. differs from Aborjinia by the position of cephalic sensitive organs (outer labial and cephalic papillae in two separate circles vs outer labial and cephalic papillae in one circle) and by the parasitic adult (vs free-living in Aborjinia).},
}
@article {pmid38282330,
year = {2024},
author = {Brettner, L and Eder, R and Schmidlin, K and Geiler-Samerotte, K},
title = {An ultra high-throughput, massively multiplexable, single-cell RNA-seq platform in yeasts.},
journal = {Yeast (Chichester, England)},
volume = {41},
number = {4},
pages = {242-255},
pmid = {38282330},
issn = {1097-0061},
support = {R35 GM133674/GM/NIGMS NIH HHS/United States ; R35GM133674/NH/NIH HHS/United States ; },
mesh = {*Gene Expression Profiling/methods ; *Single-Cell Gene Expression Analysis ; Saccharomyces cerevisiae/genetics ; Transcriptome ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Yeasts are naturally diverse, genetically tractable, and easy to grow such that researchers can investigate any number of genotypes, environments, or interactions thereof. However, studies of yeast transcriptomes have been limited by the processing capabilities of traditional RNA sequencing techniques. Here we optimize a powerful, high-throughput single-cell RNA sequencing (scRNAseq) platform, SPLiT-seq (Split Pool Ligation-based Transcriptome sequencing), for yeasts and apply it to 43,388 cells of multiple species and ploidies. This platform utilizes a combinatorial barcoding strategy to enable massively parallel RNA sequencing of hundreds of yeast genotypes or growth conditions at once. This method can be applied to most species or strains of yeast for a fraction of the cost of traditional scRNAseq approaches. Thus, our technology permits researchers to leverage "the awesome power of yeast" by allowing us to survey the transcriptome of hundreds of strains and environments in a short period of time and with no specialized equipment. The key to this method is that sequential barcodes are probabilistically appended to cDNA copies of RNA while the molecules remain trapped inside of each cell. Thus, the transcriptome of each cell is labeled with a unique combination of barcodes. Since SPLiT-seq uses the cell membrane as a container for this reaction, many cells can be processed together without the need to physically isolate them from one another in separate wells or droplets. Further, the first barcode in the sequence can be chosen intentionally to identify samples from different environments or genetic backgrounds, enabling multiplexing of hundreds of unique perturbations in a single experiment. In addition to greater multiplexing capabilities, our method also facilitates a deeper investigation of biological heterogeneity, given its single-cell nature. For example, in the data presented here, we detect transcriptionally distinct cell states related to cell cycle, ploidy, metabolic strategies, and so forth, all within clonal yeast populations grown in the same environment. Hence, our technology has two obvious and impactful applications for yeast research: the first is the general study of transcriptional phenotypes across many strains and environments, and the second is investigating cell-to-cell heterogeneity across the entire transcriptome.},
}
@article {pmid38278818,
year = {2024},
author = {Piccinno, R and Tatti, A and Avosani, S and Galla, G and Lazazzara, V and Pedrazzoli, F and Zadra, N and Rodeghiero, M and Seljak, G and Özgen, &#x130; and Hauffe, HC and Verrastro, V and Stacconi, MVR and Mazzoni, V and Rota-Stabelli, O},
title = {A multidisciplinary approach to tackling invasive species: barcoding, morphology, and metataxonomy of the leafhopper Arboridia adanae.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {2229},
pmid = {38278818},
issn = {2045-2322},
mesh = {Humans ; Animals ; *Introduced Species ; *Hemiptera ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Greece ; },
abstract = {The leafhopper genus Arboridia includes several species that feed on Vitis vinifera and cause leaf chlorosis. We report the first alien Arboridia infestation in Italy in 2021 in an Apulian vineyard. To confirm the taxonomic status of the species responsible for crop damage, and reconstruct its demographic history, we barcoded individuals from Apulia together with Arboridia spp. from Crete (Greece), A. adanae from Central Turkey and other specimens of the presumed sister species, A. dalmatina from Dalmatia (Croatia). Molecular phylogenies and barcoding gap analysis identified clades not associated with sampling locations. This result is incongruent with classical specimen assignment and is further supported by morphological analyses, which did not reveal significant differences among the populations. Therefore, we propose A. dalmatina as a junior synonym of A. adanae, which would become the only grapevine-related Arboridia species in the eastern Mediterranean. To further characterise A. adanae evolution, we performed a molecular clock analysis that suggested a radiation during the Pleistocene glaciations. Finally, to assess whether the Apulian individuals carried microorganisms of agricultural relevance, we sequenced their bacterial microbiota using 16S rRNA amplicon sequencing identifying three phytopathogens not generally associated with Arboridia activities as well as Wolbachia in one Apulian haplogroup. We discuss the agricultural implications of this infestation.},
}
@article {pmid38276828,
year = {2024},
author = {Kim, S and Jung, JK and Park, I and Lee, BW and Kim, YH},
title = {Integrated Identification and Genetic Diversity of Potentially Invasive Clearwing Moths (Lepidoptera: Cossoidea: Sesiidae) in Korea.},
journal = {Insects},
volume = {15},
number = {1},
pages = {},
pmid = {38276828},
issn = {2075-4450},
support = {none//research funds for newly appointed professors of Jeonbuk National University in 2021/ ; MAFRA no. 32100103//Korean Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry/ ; NIBR202304203//National Institute of Biological Resources/ ; 2019151D10-2323-0301//Korea Forest Service/ ; },
abstract = {The populations of clearwing moth borers in Korea have recently caused extensive and severe damage to pin oaks (Quercus palustris Munchh.). We conducted field monitoring and molecular analyses to identify them in an integrated manner. Morphological examination and molecular analyses of the COI gene, based on intra- and interspecific genetic divergences (GDs), revealed that the borers were identified as two invasive species, Sphecodoptera sheni and Paranthrenella pinoakula sp. nov. The maximum intraspecific GD was found to be 1.9%, whereas the minimum interspecific GD was confirmed as 8.1%, indicating a distinct barcoding gap. Both the MJ network and NJ tree also showed that 18 haplotypes (Hs) were detected from the 52 COI sequences. The borers revealed a total of 17 Hs: (i) H1-H7 were detected in all seven regions with S. sheni; (ii) Wonju and Goyang populations of S. sheni revealed more than three Hs; (iii) H7 was closely connected with H8 of the Chinese population of S. sheni; (iv) H9-H10 were detected in other samples from the Wonju population with P. pinoakula sp. n. and were closely located with congeneric species. A maximum likelihood tree also revealed that P. pinoacula sp. n. nested within the congeneric species, genetically separating from S. sheni.},
}
@article {pmid38276823,
year = {2024},
author = {Gomontean, B and Jumpato, W and Wongpakam, K and Tangkawanit, U and Wannasingha, W and Thanee, I and Ya'cob, Z and Pramual, P},
title = {Diversity, Distribution and Host Blood Meal Analysis of Adult Black Flies (Diptera: Simuliidae) from Thailand.},
journal = {Insects},
volume = {15},
number = {1},
pages = {},
pmid = {38276823},
issn = {2075-4450},
support = {6601002/2566//Mahasarakham University/ ; },
abstract = {Understanding the factors associated with the species diversity and distribution of insect vectors is critically important for disease epidemiology. Black flies (Diptera: Simuliidae) are significant hematophagous insects, as many species are pests and vectors that transmit pathogens to humans and other animals. Ecological factors associated with black fly species distribution have been extensively examined for the immature stages but are far less well explored for the adult stage. In this study, we collected a total of 7706 adult black fly specimens from various locations in forests, villages and animal shelters in Thailand. The integration of morphology and DNA barcoding revealed 16 black fly taxa, including Simulium yvonneae, a species first found in Vietnam, which is a new record for Thailand. The most abundant species was the Simulium asakoae complex (n = 5739, 74%), followed by S. chumpornense Takaoka and Kuvangkadilok (n = 1232, 16%). The Simulium asakoae complex was dominant in forest (3786 of 4456; 85%) and village (1774 of 2077; 85%) habitats, while S. chumpornense predominated (857 of 1175; 73%) in animal shelter areas. The Simulium asakoae complex and S. nigrogilvum Summers, which are significant pests and vectors in Thailand, occurred at a wide range of elevations, although the latter species was found mainly in high (>1000 m) mountain areas. Simulium chumpornense, S. nodosum Puri and the S. siamense Takaoka and Suzuki complex occurred predominately in low (<800 m)-elevation areas. Simulium furvum Takaoka and Srisuka; S. phurueaense Tangkawanit, Wongpakam and Pramual; and S. nr. phurueaense were only found in high (>1000 m) mountain areas. A host blood meal analysis revealed that the S. asakoae; S. chamlongi Takaoka and Suzuki; S. nigrogilvum; S. chumpornense; and the S. striatum species group were biting humans. This is the first report of the latter two species biting humans. We also found that S. chumpornense was biting turkeys, and S. chamlongi was biting chickens, which are new host blood sources recorded for these species. In addition, we found that the S. feuerborni Edwards complex was biting water buffalo, which is the first report on the biting habits of this species.},
}
@article {pmid38272945,
year = {2024},
author = {Quaresma, A and Ankenbrand, MJ and Garcia, CAY and Rufino, J and Honrado, M and Amaral, J and Brodschneider, R and Brusbardis, V and Gratzer, K and Hatjina, F and Kilpinen, O and Pietropaoli, M and Roessink, I and van der Steen, J and Vejsnæs, F and Pinto, MA and Keller, A},
title = {Semi-automated sequence curation for reliable reference datasets in ITS2 vascular plant DNA (meta-)barcoding.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {129},
pmid = {38272945},
issn = {2052-4463},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Phylogeny ; Plants/genetics ; Sequence Analysis, DNA ; *Tracheophyta ; },
abstract = {One of the most critical steps for accurate taxonomic identification in DNA (meta)-barcoding is to have an accurate DNA reference sequence dataset for the marker of choice. Therefore, developing such a dataset has been a long-term ambition, especially in the Viridiplantae kingdom. Typically, reference datasets are constructed with sequences downloaded from general public databases, which can carry taxonomic and other relevant errors. Herein, we constructed a curated (i) global dataset, (ii) European crop dataset, and (iii) 27 datasets for the EU countries for the ITS2 barcoding marker of vascular plants. To that end, we first developed a pipeline script that entails (i) an automated curation stage comprising five filters, (ii) manual taxonomic correction for misclassified taxa, and (iii) manual addition of newly sequenced species. The pipeline allows easy updating of the curated datasets. With this approach, 13% of the sequences, corresponding to 7% of species originally imported from GenBank, were discarded. Further, 259 sequences were manually added to the curated global dataset, which now comprises 307,977 sequences of 111,382 plant species.},
}
@article {pmid38271463,
year = {2024},
author = {Almerekova, S and Yermagambetova, M and Jumanov, S and Abugalieva, S and Turuspekov, Y},
title = {Comparative analysis of chloroplast genomes of seven Juniperus species from Kazakhstan.},
journal = {PloS one},
volume = {19},
number = {1},
pages = {e0295550},
pmid = {38271463},
issn = {1932-6203},
mesh = {*Genome, Chloroplast/genetics ; *Juniperus/genetics ; Phylogeny ; Kazakhstan ; Ecosystem ; Microsatellite Repeats/genetics ; },
abstract = {Juniperus species are shrubs or trees in the family Cupressaceae that play an important role in forest ecosystems. In this study, we report the complete sequences of the plastid (pt) genomes of five Juniperus species collected in Kazakhstan (J. communis, J. sibirica, J. pseudosabina, J. semiglobosa, and J. davurica). The sequences of the pt genomes of the five species were annotated in addition to two full pt genome sequences from J. sabina and J. seravschanica, which we have previously reported. The pt genome sequences of these seven species were compared to the pt genomes of Juniperus species available in the public NCBI database. The total length of the pt genomes of Juniperus species, including previously published pt genome data, ranged from 127,469 bp (J. semiglobosa) to 128,097 bp (J. communis). Each Juniperus plastome consisted of 119 genes, including 82 protein-coding genes, 33 transfer RNA and 4 ribosomal RNA genes. Among the identified genes, 16 contained one or two introns, and 2 tRNA genes were duplicated. A comparative assessment of pt genome sequences suggested the identification of 1145 simple sequence repeat markers. A phylogenetic tree of 26 Juniperus species based on the 82 protein-coding genes separated the Juniperus samples into two major clades, corresponding to the Juniperus and Sabina sections. The analysis of pt genome sequences indicated that accD and ycf2 were the two most polymorphic genes. The phylogenetic evaluation of 26 Juniperus species using these two genes confirmed that they can be efficiently used as DNA barcodes for phylogenetic analyses in the genus. The sequenced plastomes of these Juniperus species have provided a large amount of genetic data that will be valuable for future genomic studies of this genus.},
}
@article {pmid38268108,
year = {2024},
author = {Santos, GKN and Navarro, DMDAF and Maia, ACD},
title = {Cuticular lipid profiles of selected species of cyclocephaline beetles (Melolonthidae, Cyclocephalini).},
journal = {Bulletin of entomological research},
volume = {114},
number = {1},
pages = {124-133},
doi = {10.1017/S0007485323000664},
pmid = {38268108},
issn = {1475-2670},
mesh = {Animals ; *Coleoptera/genetics ; Ecosystem ; Hydrocarbons ; Pheromones/chemistry ; Lipids/analysis ; },
abstract = {Neotropical cyclocephaline beetles, a diverse group of flower-loving insects, significantly impact natural and agricultural ecosystems. In particular, the genus Cyclocephala, with over 350 species, displays polymorphism and cryptic complexes. Lacking a comprehensive DNA barcoding framework, accessible tools for species differentiation are needed for research in taxonomy, ecology, and crop management. Moreover, cuticular hydrocarbons are believed to be involved in sexual recognition mechanisms in these beetles. In the present study we examined the cuticular chemical profiles of six species from the genus Cyclocephala and two populations of Erioscelis emarginata and assessed their efficiency in population, species, and sex differentiation. Overall we identified 74 compounds in cuticular extracts of the selected taxa. Linear alkanes and unsaturated hydrocarbons were prominent, with ten compounds between them explaining 85.6% of species dissimilarity. Although the cuticular chemical profiles efficiently differentiated all investigated taxa, only C. ohausiana showed significant cuticular profile differences between sexes. Our analysis also revealed two E. emarginata clades within a larger group of 'Cyclocephala' species, but they were not aligned with the two studied populations. Our research underscores the significance of cuticular lipid profiles in distinguishing selected cyclocephaline beetle species and contemplates their potential impact as contact pheromones on sexual segregation and speciation.},
}
@article {pmid38268047,
year = {2024},
author = {Piccoli, C and Muñoz-Mérida, A and Crottini, A},
title = {PARSID: a Python script for automatic analysis of local BLAST results for a rapid molecular taxonomic identification.},
journal = {BMC research notes},
volume = {17},
number = {1},
pages = {35},
pmid = {38268047},
issn = {1756-0500},
support = {SFRH/BD/144342/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2020.00823.CEECIND/CP1601/CT0003//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
mesh = {Humans ; *Databases, Nucleic Acid ; Gene Library ; *Publications ; Research Personnel ; Workflow ; },
abstract = {OBJECTIVE: A reliable taxonomic identification of species from molecular samples is the first step for many studies. For researchers unfamiliar with programming, running a BLAST analysis, filtering, and organizing results for hundreds of sequences through the BLAST web interface can be difficult. Additionally, sequences deposited in GenBank can have outdated taxonomic identification. The use of reliable Reference Sequences Library (RSL) containing accurate taxonomically-identified sequences facilitates this task. Pending the availability of a RSL with the user, we developed a tool that automates the molecular taxonomic identification of sequences.<br><br>RESULTS: We developed PARSID, a Python script running through the command-line that automates the routine workflow of blasting an input sequence file against the user's RSL, and retrieves the matches with the highest percentage of identity in five steps. PARSID accepts cut-off parameters and supplementary information in a.csv file for filtering the results. The final output is visualized in a spreadsheet. We tested its functioning using 10 input sequences simulating different situations of the molecular taxonomic identification of sequences against an example RSL containing 25 sequences. Step-by-step instructions and test files are publicly available at https://github.com/kokinide/PARSID.git .},
}
@article {pmid38263700,
year = {2025},
author = {Cheng, R and Luo, A and Orr, M and Ge, D and Hou, Z and Qu, Y and Guo, B and Zhang, F and Sha, Z and Zhao, Z and Wang, M and Shi, X and Han, H and Zhou, Q and Li, Y and Liu, X and Shao, C and Zhang, A and Zhou, X and Zhu, C},
title = {Cryptic diversity begets challenges and opportunities in biodiversity research.},
journal = {Integrative zoology},
volume = {20},
number = {1},
pages = {33-49},
doi = {10.1111/1749-4877.12809},
pmid = {38263700},
issn = {1749-4877},
support = {NGSB20211405//Ningxia Hui Autonomous Region Agricultural Science and Technology Independent Innovation Fund/ ; 2008DP173354//Key Laboratory of the Zoological Systematics and Evolution of the Chinese Academy of Sciences/ ; ZL202203601//Survey of Wildlife Resources in Key Areas of Tibet/ ; },
mesh = {*Biodiversity ; Animals ; Classification/methods ; Biological Evolution ; Research ; },
abstract = {How many species of life are there on Earth? This is a question that we want to know but cannot yet answer. Some scholars speculate that the number of species may reach 2.2 billion when considering cryptic diversity and that each morphology-based insect species may contain an average of 3.1 cryptic species. With nearly two million described species, such high estimates of cryptic diversity would suggest that cryptic species are widespread. The development of molecular species delimitation has led to the discovery of a large number of cryptic species, and cryptic biodiversity has gradually entered our field of vision and attracted more attention. This paper introduces the concept of cryptic species, how they evolve, and methods by which they may be discovered and confirmed, and provides theoretical and methodological guidance for the study of hidden species. A workflow of how to confirm cryptic species is provided. In addition, the importance and reliability of multi-evidence-based integrated taxonomy are reaffirmed as a way to better standardize decision-making processes. Special focus on cryptic diversity and increased funding for taxonomy is needed to ensure that cryptic species in hyperdiverse groups are discoverable and described. An increased focus on cryptic species in the future will naturally arise as more difficult groups are studied, and thereby, we may finally better understand the rules governing the evolution and maintenance of cryptic biodiversity.},
}
@article {pmid38263006,
year = {2024},
author = {Song, BN and Liu, CK and Zhao, AQ and Tian, RM and Xie, DF and Xiao, YL and Chen, H and Zhou, SD and He, XJ},
title = {Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {70},
pmid = {38263006},
issn = {1471-2229},
support = {Project No.: 510101202200376//Survey on the Background Resources of Chengdu Area of Giant Panda National Park/ ; Project No.: 510101202200376//Survey on the Background Resources of Chengdu Area of Giant Panda National Park/ ; Project No.: 510101202200376//Survey on the Background Resources of Chengdu Area of Giant Panda National Park/ ; Project No.: 510101202200376//Survey on the Background Resources of Chengdu Area of Giant Panda National Park/ ; Project No.: 510101202200376//Survey on the Background Resources of Chengdu Area of Giant Panda National Park/ ; Project No.: 510101202200376//Survey on the Background Resources of Chengdu Area of Giant Panda National Park/ ; Project No.: 510101202200376//Survey on the Background Resources of Chengdu Area of Giant Panda National Park/ ; Project No.: 510101202200376//Survey on the Background Resources of Chengdu Area of Giant Panda National Park/ ; Project No.: 510101202200376//Survey on the Background Resources of Chengdu Area of Giant Panda National Park/ ; },
mesh = {*Sanicula ; *Apiaceae ; Phylogeny ; Plastids ; Chloroplasts ; },
abstract = {BACKGROUND: The genus Sanicula L. is a unique perennial herb that holds important medicinal values. Although the previous studies on Sanicula provided us with a good research basis, its taxonomic system and interspecific relationships have not been satisfactorily resolved, especially for those endemic to China. Moreover, the evolutionary history of this genus also remains inadequately understood. The plastid genomes possessing highly conserved structure and limited evolutionary rate have proved to be an effective tool for studying plant phylogeny and evolution.<br><br>RESULTS: In the current study, we newly sequenced and assembled fifteen Sanicula complete plastomes. Combined with two previously reported plastomes, we performed comprehensively plastid phylogenomics analyses to gain novel insights into the evolutionary history of this genus. The comparative results indicated that the seventeen plastomes exhibited a high degree of conservation and similarity in terms of their structure, size, GC content, gene order, IR borders, codon bias patterns and SSRs profiles. Such as all of them displayed a typical quadripartite structure, including a large single copy region (LSC: 85,074-86,197&#xa0;bp), a small single copy region (SSC: 17,047-17,132&#xa0;bp) separated by a pair of inverted repeat regions (IRs: 26,176-26,334&#xa0;bp). And the seventeen plastomes had similar IR boundaries and the adjacent genes were identical. The rps19 gene was located at the junction of the LSC/IRa, the IRa/SSC junction region was located between the trnN gene and ndhF gene, the ycf1 gene appeared in the SSC/IRb junction and the IRb/LSC boundary was located between rpl12 gene and trnH gene. Twelve specific mutation hotspots (atpF, cemA, accD, rpl22, rbcL, matK, ycf1, trnH-psbA, ycf4-cemA, rbcL-accD, trnE-trnT and trnG-trnR) were identified that can serve as potential DNA barcodes for species identification within the genus Sanicula. Furthermore, the plastomes data and Internal Transcribed Spacer (ITS) sequences were performed to reconstruct the phylogeny of Sanicula. Although the tree topologies of them were incongruent, both provided strong evidence supporting the monophyly of Saniculoideae and Apioideae. In addition, the sister groups between Saniculoideae and Apioideae were strongly suggested. The Sanicula species involved in this study were clustered into a clade, and the Eryngium species were also clustered together. However, it was clearly observed that the sections of Sanicula involved in the current study were not respectively recovered as monophyletic group. Molecular dating analysis explored that the origin of this genus was occurred during the late Eocene period, approximately 37.84&#xa0;Ma (95% HPD: 20.33-52.21&#xa0;Ma) years ago and the diversification of the genus was occurred in early Miocene 18.38&#xa0;Ma (95% HPD: 10.68-25.28&#xa0;Ma).<br><br>CONCLUSION: The plastome-based tree and ITS-based tree generated incongruences, which may be attributed to the event of hybridization/introgression, incomplete lineage sorting (ILS) and chloroplast capture. Our study highlighted the power of plastome data to significantly improve the&#xa0;phylogenetic supports and resolutions, and to efficiently explore the evolutionary history of this genus. Molecular dating analysis explored that the diversification of the genus occurred in the early Miocene, which was largely influenced by the prevalence of the East Asian monsoon and the uplift of the Hengduan Mountains (HDM). In summary, our study provides novel insights into the plastome evolution, phylogenetic relationships, taxonomic framework and evolution of genus Sanicula.},
}
@article {pmid38262257,
year = {2024},
author = {Asghari, A and Yousefi, A and Mohammadi, MR and Badali, R and Shamsi, L and Köseoğlu, AE and Abbaszadeh, A and Shams, M and Mohammadi-Ghalehbin, B},
title = {Comparative molecular epidemiology, subtype distribution, and zoonotic potential of Blastocystis sp. in Equus animals (horses, donkeys, and mules) in northwestern Iran.},
journal = {Comparative immunology, microbiology and infectious diseases},
volume = {106},
number = {},
pages = {102124},
doi = {10.1016/j.cimid.2024.102124},
pmid = {38262257},
issn = {1878-1667},
mesh = {Humans ; Animals ; Horses ; Female ; Male ; *Blastocystis ; *Blastocystis Infections/epidemiology/veterinary ; Equidae/genetics ; Iran/epidemiology ; Molecular Epidemiology ; Genetic Variation ; DNA, Protozoan/genetics ; Feces ; Prevalence ; Phylogeny ; },
abstract = {A total of 500 fecal samples were collected from Equus animals in six different cities (Ardabil, Namin, Nir, Meshginshahr, Germi, and Khalkhal) of Ardabil Province, northwestern Iran, with 200 samples from horses, 200 from donkeys, and 100 from mules. Of the horse samples, 100 were from racing horses under special monitoring and care, while the remaining 100 were from non-racing horses, including those used for herding or in rural areas. All fecal samples were examined for the presence of Blastocystis sp. using PCR amplification of the SSU rRNA gene's barcode region after DNA extraction. The molecular prevalence of Blastocystis infection in Equus animals was 7.6% (38/500). Blastocystis was more common in horses [11.5% (23/200)] than in donkeys [5.5% (11/200)] and mules [4% (4/100)] (P > 0.05). Compared to racing horses [3% (3/100)], non-racing/rural horses [20% (20/100)] exhibited a substantially higher prevalence of Blastocystis (P < 0.05). The prevalence of Blastocystis in diarrheal samples and younger animals was remarkably higher than in formed samples and older animals, respectively (P < 0.05). No significant difference in Blastocystis infection prevalence was found between the genders of examined animals (P > 0.05). In Equus animals, 38 Blastocystis isolates included eight STs: ST10 [31.6% (12/38)], ST1 [21.1% (8/38)], ST2 [15.8% (6/38)], ST3 [10.5% (4/38)], ST4 [7.9% (3/38)], ST7 [5.2% (2/38)], ST14 [5.2% (2/38)], and ST6 [2.6% (1/38)]. These results suggest that Equus animals act as a proper reservoir for numerous Blastocystis STs, consequently playing a crucial part in the spread of this protozoan infection to humans, animals, and water reservoirs.},
}
@article {pmid38254910,
year = {2023},
author = {Ma, L and Zhou, CY and Chen, JL and Liu, DK and Lan, S and Liu, ZJ},
title = {Comparative Analysis of Luisia (Aeridinae, Orchidaceae) Plastomes Shed Light on Plastomes Evolution and Barcodes Investigation.},
journal = {Genes},
volume = {15},
number = {1},
pages = {},
pmid = {38254910},
issn = {2073-4425},
support = {E0117G1001//the Project of National Plant Specimen Resource Center/ ; MWY2023-5-02//the Launch of High-level Talent Research Project/ ; },
mesh = {*Orchidaceae/genetics ; Phylogeny ; Codon Usage ; Cysteine ; Exons ; },
abstract = {Luisia, a genus of the subtribe Aeridinae of Orchidaceae, comprises ca. 40 species. Members of Luisia exhibit unique morphological characteristics and represent a valuable ornamental orchid genus. However, due to the scarcity of distinct morphological characters, species identification within this genus is ambiguous and controversial. In the present study, next-generation sequencing (NGS) methods were used to assemble the plastomes of five Luisia species and compare them with one publicly available Luisia plastid genome data. The plastomes of Luisia possessed a quadripartite structure, with sizes ranging from 146,243 bp to 147,430 bp. The plastomes of six Luisia species contained a total of 120 genes, comprising 74 protein-coding genes, 38 tRNA genes and eight rRNA genes. Notably, all ndh genes were pseudogenized or lost. An analysis of codon usage bias showed that leucine (Leu) exhibited the highest frequency, while cysteine (Cys) exhibited the lowest frequency. A total of 57 to 64 SSRs and 42 to 49 long repeats were identified. Five regions and five coding sequences were identified for DNA barcodes, based on the nucleotide diversity (Pi) analysis. The species of Luisia constituted a monophyletic group and were sister to Paraphalaenopsis with strong support. Our study deepens the understanding of species identification, plastome evolution and the phylogenetic positions of Luisia.},
}
@article {pmid38253266,
year = {2024},
author = {Weng, C and Yu, F and Yang, D and Poeschla, M and Liggett, LA and Jones, MG and Qiu, X and Wahlster, L and Caulier, A and Hussmann, JA and Schnell, A and Yost, KE and Koblan, LW and Martin-Rufino, JD and Min, J and Hammond, A and Ssozi, D and Bueno, R and Mallidi, H and Kreso, A and Escabi, J and Rideout, WM and Jacks, T and Hormoz, S and van Galen, P and Weissman, JS and Sankaran, VG},
title = {Deciphering cell states and genealogies of human haematopoiesis.},
journal = {Nature},
volume = {627},
number = {8003},
pages = {389-398},
pmid = {38253266},
issn = {1476-4687},
support = {R01 CA265726/CA/NCI NIH HHS/United States ; RM1 HG009490/HG/NHGRI NIH HHS/United States ; T32 GM144273/GM/NIGMS NIH HHS/United States ; R01 DK103794/DK/NIDDK NIH HHS/United States ; R01 HL146500/HL/NHLBI NIH HHS/United States ; R33 CA278393/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Cell Lineage ; Chromatin/genetics/metabolism ; Clone Cells/classification/cytology/metabolism ; DNA, Mitochondrial/genetics ; *Hematopoiesis ; *Hematopoietic Stem Cells/classification/cytology/metabolism ; Mutation ; Single-Cell Analysis ; Transcription, Genetic ; Aging ; },
abstract = {The human blood system is maintained through the differentiation and massive amplification of a limited number of long-lived haematopoietic stem cells (HSCs)[1]. Perturbations to this process underlie diverse diseases, but the clonal contributions to human haematopoiesis and how this changes with age remain incompletely understood. Although recent insights have emerged from barcoding studies in model systems[2-5], simultaneous detection of cell states and phylogenies from natural barcodes in humans remains challenging. Here we introduce an improved, single-cell lineage-tracing system based on deep detection of naturally occurring mitochondrial DNA mutations with simultaneous readout of transcriptional states and chromatin accessibility. We use this system to define the clonal architecture of HSCs and map the physiological state and output of clones. We uncover functional heterogeneity in HSC clones, which is stable over months and manifests as both differences in total HSC output and biases towards the production of different mature cell types. We also find that the diversity of HSC clones decreases markedly with age, leading to an oligoclonal structure with multiple distinct clonal expansions. Our study thus provides a clonally resolved and cell-state-aware atlas of human haematopoiesis at single-cell resolution, showing an unappreciated functional diversity of human HSC clones and, more broadly, paving the way for refined studies of clonal dynamics across a range of tissues in human health and disease.},
}
@article {pmid38253258,
year = {2024},
author = {You, C and Jiang, S and Ding, Y and Ye, S and Zou, X and Zhang, H and Li, Z and Chen, F and Li, Y and Ge, X and Guo, X},
title = {RNA barcode segments for SARS-CoV-2 identification from HCoVs and SARSr-CoV-2 lineages.},
journal = {Virologica Sinica},
volume = {39},
number = {1},
pages = {156-168},
pmid = {38253258},
issn = {1995-820X},
mesh = {Humans ; *SARS-CoV-2/genetics ; *COVID-19/diagnosis ; RNA ; Reproducibility of Results ; Base Sequence ; },
abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen responsible for coronavirus disease 2019 (COVID-19), continues to evolve, giving rise to more variants and global reinfections. Previous research has demonstrated that barcode segments can effectively and cost-efficiently identify specific species within closely related populations. In this study, we designed and tested RNA barcode segments based on genetic evolutionary relationships to facilitate the efficient and accurate identification of SARS-CoV-2 from extensive virus samples, including human coronaviruses (HCoVs) and SARSr-CoV-2 lineages. Nucleotide sequences sourced from NCBI and GISAID were meticulously selected and curated to construct training sets, encompassing 1733 complete genome sequences of HCoVs and SARSr-CoV-2 lineages. Through genetic-level species testing, we validated the accuracy and reliability of the barcode segments for identifying SARS-CoV-2. Subsequently, 75 main and subordinate species-specific barcode segments for SARS-CoV-2, located in ORF1ab, S, E, ORF7a, and N coding sequences, were intercepted and screened based on single-nucleotide polymorphism sites and weighted scores. Post-testing, these segments exhibited high recall rates (nearly 100%), specificity (almost 30% at the nucleotide level), and precision (100%) performance on identification. They were eventually visualized using one and two-dimensional combined barcodes and deposited in an online database (http://virusbarcodedatabase.top/). The successful integration of barcoding technology in SARS-CoV-2 identification provides valuable insights for future studies involving complete genome sequence polymorphism analysis. Moreover, this cost-effective and efficient identification approach also provides valuable reference for future research endeavors related to virus surveillance.},
}
@article {pmid38250578,
year = {2023},
author = {, },
title = {Erratum: Community dynamics and co-occurrence relationships of pelagic ciliates and their potential prey at a coastal and an offshore station in the ultra-oligotrophic Eastern Mediterranean Sea.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1358985},
doi = {10.3389/fgene.2023.1358985},
pmid = {38250578},
issn = {1664-8021},
abstract = {[This corrects the article DOI: 10.3389/fgene.2023.1219085.].},
}
@article {pmid38250474,
year = {2024},
author = {Höcherl, A and Shaw, MR and Boudreault, C and Rabl, D and Haszprunar, G and Raupach, MJ and Schmidt, S and Baranov, V and Fernández-Triana, J},
title = {Scratching the tip of the iceberg: integrative taxonomy reveals 30 new species records of Microgastrinae (Braconidae) parasitoid wasps for Germany, including new Holarctic distributions.},
journal = {ZooKeys},
volume = {1188},
number = {},
pages = {305-386},
pmid = {38250474},
issn = {1313-2989},
abstract = {Substantial parts of the European and German insect fauna still remain largely unexplored, the so-called "dark taxa". In particular, midges (Diptera) and parasitoid wasps (Hymenoptera) are abundant and species-rich throughout Europe, yet are often neglected in biodiversity research. One such dark taxon is Microgastrinae wasps (Hymenoptera: Braconidae), a group of parasitoids of lepidopteran caterpillars with 252 species reported in Germany so far. As part of the German Barcode of Life Project GBOL III: Dark Taxa, reverse DNA barcoding and integrative taxonomic approaches were used to shed some light on the German Fauna of Microgastrinae wasps. In our workflow, DNA barcoding was used for molecular clustering of our specimens in a first step, morphological examination of the voucher specimens in a second step, and host data compared in a third step. Here, 30 species are reported for the first time in Germany, adding more than 10% to the known German fauna. Information for four species is provided in a new Holarctic context, reporting them for the Nearctic or, respectively, Palaearctic region, and 26 additional country records are added from sequenced material available in the collections accessible to us. Molecular clusters that show signs of discrepancies are discussed. Results show that we are just scratching the tip of the iceberg of the unexplored Microgastrinae diversity in Germany.},
}
@article {pmid38249569,
year = {2024},
author = {Recuero, E and Caterino, MS},
title = {Molecular diversity of Pseudoscorpiones in southern High Appalachian leaf litter.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e115928},
pmid = {38249569},
issn = {1314-2828},
abstract = {The Pseudoscorpiones fauna of North America is diverse, but in regions like the southern Appalachian Mountains, they are still poorly documented with respect to their species diversity, distributions and ecology. Several families have been reported from these mountains and neighbouring areas. Here we analyse barcoding data of 136 specimens collected in leaf litter, most of them from high-elevation coniferous forest. We used ASAP as a species delimitation method to obtain an estimation of the number of species present in the region. For this and based on interspecific genetic distance values previously reported in Pseudoscorpions, we considered three different genetic Kimura two-parameter distance thresholds (3%/5%/8%), to produce more or less conservative estimates. These distance thresholds resulted in 64/47/27 distinct potential species representing the families Chthoniidae (33/22/12 species) and Neobisiidae (31/25/15) and at least six different genera within them. The diversity pattern seems to be affected by the Asheville Depression, a major biogeographic barrier in this area, with a higher diversity to the west of this geographic feature, particularly within the family Neobisiidae. The absence of representatives from other families amongst our studied samples may be explained by differences in their ecological requirements and occupation of different microhabitats.},
}
@article {pmid38249470,
year = {2023},
author = {Ogola, EO and Bastos, ADS and Slothouwer, I and Getugi, C and Osalla, J and Omoga, DCA and Ondifu, DO and Sang, R and Torto, B and Junglen, S and Tchouassi, DP},
title = {Viral diversity and blood-feeding patterns of Afrotropical Culicoides biting midges (Diptera: Ceratopogonidae).},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1325473},
pmid = {38249470},
issn = {1664-302X},
abstract = {INTRODUCTION: Culicoides biting midges (Diptera: Ceratopogonidae) are vectors of arboviral pathogens that primarily affect livestock represented by Schmallenberg virus (SBV), epizootic hemorrhagic disease virus (EHDV) and bluetongue virus (BTV). In Kenya, studies examining the bionomic features of Culicoides including species diversity, blood-feeding habits, and association with viruses are limited.<br><br>METHODS: Adult Culicoides were surveyed using CDC light traps in two semi-arid ecologies, Baringo and Kajiado counties, in Kenya. Blood-fed specimens were analysed through polymerase chain reaction (PCR) and sequencing of cytochrome oxidase subunit 1 (cox1) barcoding region. Culicoides pools were screened for virus infection by generic RT-PCR and next-generation sequencing (NGS).<br><br>RESULTS: Analysis of blood-fed specimens confirmed that midges had fed on cattle, goats, sheep, zebra, and birds. Cox1 barcoding of the sampled specimens revealed the presence of known vectors of BTV and epizootic hemorrhagic disease virus (EHDV) including species in the Imicola group (Culicoides imicola) and Schultzei group (C. enderleni, C. kingi, and C. chultzei). Culicoides leucostictus and a cryptic species distantly related to the Imicola group were also identified. Screening of generated pools (11,006 individuals assigned to 333 pools) by generic RT-PCR revealed presence of seven phylogenetically distinct viruses grouping in the genera Goukovirus, Pacuvirus and Orthobunyavirus. The viruses showed an overall minimum infection rate (MIR) of 7.0% (66/333, 95% confidence interval (CI) 5.5-8.9). In addition, full coding sequences of two new iflaviruses, tentatively named Oloisinyai_1 and Oloisinyai_2, were generated by next-generation sequencing (NGS) from individual homogenate of Culicoides pool.<br><br>CONCLUSION: The results indicate a high genetic diversity of viruses in Kenyan biting midges. Further insights into host-vector-virus interactions as well as investigations on the potential clinical significance of the detected viruses are warranted.},
}
@article {pmid38249024,
year = {2023},
author = {Chen, H and Olmi, M and Ødegaard, F and Capradossi, L and Liu, J},
title = {DNA Barcoding Unveils New Species of the Sexually Dimorphic Genus Anteon Jurine (Hymenoptera, Dryinidae) from China.},
journal = {Insects},
volume = {15},
number = {1},
pages = {},
pmid = {38249024},
issn = {2075-4450},
support = {31472027//National Natural Science Foundation of China/ ; },
abstract = {Species of Anteon Jurine, 1807 are a large group of parasitoids attacking leafhoppers, which are important insect pests. Despite their great potential in pest biological control, the taxonomy and biology of these parasitoids are far from clear. Sexual dimorphism is extreme in Anteon species and has hampered the taxonomy of these parasitoids, resulting in many species described based on a single sex. In this paper, we employed an integrated taxonomic approach for delimitating species, combining morphological examinations with DNA barcoding, to investigate Anteon species from China. In total, 53 COI sequences representing 29 species of Anteon were obtained and analyzed. On the basis of both morphology and DNA barcoding, five new species of Anteon were discovered and described: A. clariclypeum sp. nov., A. maguanense sp. nov., A. parafidum sp. nov., A. shaanxianum sp. nov., and A. shandonganum sp. nov. The neotype of A. claricolle Kieffer is designated. The sexual association of six species was confirmed by DNA barcoding, which led to the synonymy of Anteon liui Xu, Olmi &amp; He 2010, new syn., under Anteon meifenganum Olmi, 1991. Keys to species of Anteon from the Oriental and Eastern Palaearctic are updated to contain the five new species. Our study demonstrates that DNA barcoding is a potent tool for tackling the taxonomic challenges in parasitoids with extreme sexual dimorphism.},
}
@article {pmid38248921,
year = {2023},
author = {Yurkov, AP and Kryukov, AA and Gorbunova, AO and Kudriashova, TR and Kovalchuk, AI and Gorenkova, AI and Bogdanova, EM and Laktionov, YV and Zhurbenko, PM and Mikhaylova, YV and Puzanskiy, RK and Bagrova, TN and Yakhin, OI and Rodionov, AV and Shishova, MF},
title = {Diversity of Arbuscular Mycorrhizal Fungi in Distinct Ecosystems of the North Caucasus, a Temperate Biodiversity Hotspot.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {10},
number = {1},
pages = {},
pmid = {38248921},
issn = {2309-608X},
support = {22-16-00064//Russian Science Foundation/ ; },
abstract = {BACKGROUND: Investigations that are focused on arbuscular mycorrhizal fungus (AMF) biodiversity is still limited. The analysis of the AMF taxa in the North Caucasus, a temperate biodiversity hotspot, used to be limited to the genus level. This study aimed to define the AMF biodiversity at the species level in the North Caucasus biotopes.<br><br>METHODS: The molecular genetic identification of fungi was carried out with ITS1 and ITS2 regions as barcodes via sequencing using Illumina MiSeq, the analysis of phylogenetic trees for individual genera, and searches for operational taxonomic units (OTUs) with identification at the species level. Sequences from MaarjAM and NCBI GenBank were used as references.<br><br>RESULTS: We analyzed >10 million reads in soil samples for three biotopes to estimate fungal biodiversity. Briefly, 50 AMF species belonging to 20 genera were registered. The total number of the AM fungus OTUs for the "Subalpine Meadow" biotope was 171/131, that for "Forest" was 117/60, and that for "River Valley" was 296/221 based on ITS1/ITS2 data. The total number of the AM fungus species (except for virtual taxa) for the "Subalpine Meadow" biotope was 24/19, that for "Forest" was 22/13, and that for "River Valley" was 28/24 based on ITS1/ITS2 data. Greater AMF diversity, as well as number of OTUs and species, in comparison with that of forest biotopes, characterized valley biotopes (disturbed ecosystems; grasslands). The correlation coefficient between "Percentage of annual plants" and "Glomeromycota total reads" r = 0.76 and 0.81 for ITS1 and ITS2, respectively, and the correlation coefficient between "Percentage of annual plants" and "OTUs number (for total species)" was r = 0.67 and 0.77 for ITS1 and ITS2, respectively.<br><br>CONCLUSION: High AMF biodiversity for the river valley can be associated with a higher percentage of annual plants in these biotopes and the active development of restorative successional processes.},
}
@article {pmid38245987,
year = {2024},
author = {Kleinnijenhuis, AJ and van Holthoon, FL},
title = {Convergent analysis of food products using molecular barcodes, based on LC-HRMS data.},
journal = {Food chemistry},
volume = {442},
number = {},
pages = {138466},
doi = {10.1016/j.foodchem.2024.138466},
pmid = {38245987},
issn = {1873-7072},
mesh = {*Food Analysis ; },
abstract = {There are various analytical techniques available to address the growing interest in the composition of food products. LC-HRMS(/MS) is the most comprehensive technique, providing detailed information at the molecular level. However, given the vast number of different molecules encountered in food products, it is important to obtain a global overview of the dataset before focusing on similarities and differences. Therefore, a convergent strategy was employed, going from non-targeted to targeted analysis, with insightful data representations, most notably Molecular Barcode. Additionally an intermediate, semi-targeted analysis was defined, aimed at the specific detection of animal tissue in food products, using pG[+] and related fragments after all ion fragmentation. The use of Molecular Barcode as a starting point to obtain relevant molecular data was also demonstrated. In conclusion, the convergent approach facilitates the design of suitable targeted methods, either to discriminate between samples or to find a generic target.},
}
@article {pmid38241246,
year = {2024},
author = {Li, W and Ren, Q and Feng, J and Lee, SY and Liu, Y},
title = {DNA barcoding for the identification and authentication of medicinal deer (Cervus sp.) products in China.},
journal = {PloS one},
volume = {19},
number = {1},
pages = {e0297164},
pmid = {38241246},
issn = {1932-6203},
mesh = {Male ; Cattle ; Female ; Animals ; Sheep/genetics ; Swine/genetics ; *DNA Barcoding, Taxonomic ; Phylogeny ; *Deer/genetics ; DNA/analysis ; Sequence Analysis, DNA ; },
abstract = {Deer products from sika deer (Cervus nippon) and red deer (C. elaphus) are considered genuine and used for Traditional Chinese Medicine (TCM) materials in China. Deer has a very high economic and ornamental value, resulting in the formation of a characteristic deer industry in the prescription preparation of traditional Chinese medicine, health food, cosmetics, and other areas of development and utilization. Due to the high demand for deer products, the products are expensive and have limited production, but the legal use of deer is limited to only two species of sika deer and red deer; other wild deer are prohibited from hunting, so there are numerous cases of mixing and adulteration of counterfeit products and so on. There have been many reports that other animal (pig, cow, sheep, etc.) tissues or organs are often used for adulteration and confusion, resulting in poor efficacy of deer traditional medicine and trade fraud in deer products. To authenticate the deer products in a rapid and effective manner, the analysis used 22 deer products (antler, meat, bone, fetus, penis, tail, skin, and wool) that were in the form of blind samples. Total DNA extraction using a modified protocol successfully yielded DNA from the blind samples that was useful for PCR. Three candidate DNA barcoding loci, cox1, Cyt b, and rrn12, were evaluated for their discrimination strength through BLAST and phylogenetic clustering analyses. For the BLAST analysis, the 22 blind samples obtained 100% match identity across the three gene loci tested. It was revealed that 12 blind samples were correctly labeled for their species of origin, while three blind samples that were thought to originate from red deer were identified as C. nippon, and seven blind samples that were thought to originate from sika deer were identified as C. elaphus, Dama dama, and Rangifer tarandus. DNA barcoding analysis showed that all three gene loci were able to distinguish the two Cervus species and to identify the presence of adulterant species. The DNA barcoding technique was able to provide a useful and sensitive approach in identifying the species of origin in deer products.},
}
@article {pmid38240642,
year = {2024},
author = {Mirza, JD and de Oliveira Guimarães, L and Wilkinson, S and Rocha, EC and Bertanhe, M and Helfstein, VC and de-Deus, JT and Claro, IM and Cumley, N and Quick, J and Faria, NR and Sabino, EC and Kirchgatter, K and Loman, NJ},
title = {Tracking arboviruses, their transmission vectors and potential hosts by nanopore sequencing of mosquitoes.},
journal = {Microbial genomics},
volume = {10},
number = {1},
pages = {},
pmid = {38240642},
issn = {2057-5858},
support = {MC_PC_15100/MRC_/Medical Research Council/United Kingdom ; MR/S019510/1/MRC_/Medical Research Council/United Kingdom ; MR/S035362/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/M501621/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; Humans ; *Culicidae/genetics ; *Arboviruses/genetics ; *Nanopore Sequencing ; Mosquito Vectors ; Brazil ; DNA ; },
abstract = {The risk to human health from mosquito-borne viruses such as dengue, chikungunya and yellow fever is increasing due to increased human expansion, deforestation and climate change. To anticipate and predict the spread and transmission of mosquito-borne viruses, a better understanding of the transmission cycle in mosquito populations is needed. We present a pathogen-agnostic combined sequencing protocol for identifying vectors, viral pathogens and their hosts or reservoirs using portable Oxford Nanopore sequencing. Using mosquitoes collected in São Paulo, Brazil, we extracted RNA for virus identification and DNA for blood meal and mosquito identification. Mosquitoes and blood meals were identified by comparing cytochrome c oxidase I (COI) sequences against a curated Barcode of Life Data System (BOLD). Viruses were identified using the SMART-9N protocol, which allows amplified DNA to be prepared with native barcoding for nanopore sequencing. Kraken 2 was employed to detect viral pathogens and Minimap2 and BOLD identified the contents of the blood meal. Due to the high similarity of some species, mosquito identification was conducted using blast after generation of consensus COI sequences using RACON polishing. This protocol can simultaneously uncover viral diversity, mosquito species and mosquito feeding habits. It also has the potential to increase understanding of mosquito genetic diversity and transmission dynamics of zoonotic mosquito-borne viruses.},
}
@article {pmid38240168,
year = {2024},
author = {Vasilita, C and Feng, V and Hansen, AK and Hartop, E and Srivathsan, A and Struijk, R and Meier, R},
title = {Express barcoding with NextGenPCR and MinION for species-level sorting of ecological samples.},
journal = {Molecular ecology resources},
volume = {24},
number = {3},
pages = {e13922},
doi = {10.1111/1755-0998.13922},
pmid = {38240168},
issn = {1755-0998},
support = {//Bundesministerium f&#xfc;r Bildung und Forschung/ ; //Carlsbergfondet/ ; },
mesh = {Humans ; *DNA Barcoding, Taxonomic/methods ; Sequence Analysis, DNA/methods ; *Biodiversity ; DNA ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {The use of DNA barcoding is well established for specimen identification and large-scale biodiversity discovery, but remains underutilized for time-sensitive applications such as rapid species discovery in field stations, identifying pests, citizen science projects, and authenticating food. The main reason is that existing express barcoding workflows are either too expensive or can only be used in very well-equipped laboratories by highly-trained staff. We here show an alternative workflow combining rapid DNA extraction with HotSHOT, amplicon production with NextGenPCR thermocyclers, and sequencing with low-cost MinION sequencers. We demonstrate the power of the approach by generating 250 barcodes for 285 specimens within 6 h including specimen identification through BLAST. The workflow required only the following major equipment that easily fits onto a lab bench: Thermocycler, NextGenPCR, microplate sealer, Qubit, and MinION. Based on our results, we argue that simplified barcoding workflows for species-level sorting are now faster, more accurate, and sufficiently cost-effective to replace traditional morpho-species sorting in many projects.},
}
@article {pmid38239385,
year = {2024},
author = {McFadden, CS and Benayahu, Y and Samimi-Namin, K},
title = {A new genus of soft coral (Octocorallia, Malacalcyonacea, Cladiellidae) and three new species from Indo-Pacific coral reefs.},
journal = {ZooKeys},
volume = {1188},
number = {},
pages = {275-304},
pmid = {38239385},
issn = {1313-2989},
abstract = {Molecular systematic studies of the anthozoan class Octocorallia have revealed widespread incongruence between phylogenetic relationships and taxonomic classification at all levels of the Linnean hierarchy. Among the soft coral taxa in order Malacalcyonacea, the family Alcyoniidae and its type genus Alcyonium have both been recognised to be highly polyphyletic. A recent family-level revision of Octocorallia established a number of new families for genera formerly considered to belong to Alcyoniidae, but revision of Alcyonium is not yet complete. Previous molecular studies have supported the placement of Alcyoniumverseveldti (Benayahu, 1982) in family Cladiellidae rather than Alcyoniidae, phylogenetically distinct from the other three genera in that family. Here we describe a new genus, Ofwegenumgen. nov. to accommodate O.verseveldticomb. nov. and three new species of that genus, O.coronalucissp. nov., O.kloogisp. nov., and O.collisp. nov., bringing the total number of species in this genus to four. Ofwegenumgen. nov. is a rarely encountered genus so far known from only a few locations spanning the Indian and western Pacific Oceans. We present the morphological characters of each species and use molecular data from both DNA barcoding and target-enrichment of conserved elements to explore species boundaries and phylogenetic relationships within the genus.},
}
@article {pmid38238774,
year = {2024},
author = {Máquina, M and Opiyo, MA and Cuamba, N and Marrenjo, D and Rodrigues, M and Armando, S and Nhate, S and Luis, F and Saúte, F and Candrinho, B and Lobo, NF and Paaijmans, KP},
title = {Multiple Anopheles species complicate downstream analysis and decision-making in a malaria pre-elimination area in southern Mozambique.},
journal = {Malaria journal},
volume = {23},
number = {1},
pages = {23},
pmid = {38238774},
issn = {1475-2875},
support = {Inv-009959/GATES/Bill &amp; Melinda Gates Foundation/United States ; Inv-009652/GATES/Bill &amp; Melinda Gates Foundation/United States ; },
mesh = {Animals ; Female ; *Anopheles/genetics ; Mozambique ; Mosquito Vectors ; *Malaria/epidemiology ; DNA, Ribosomal ; Electron Transport Complex IV/genetics ; },
abstract = {BACKGROUND: Different anopheline species (even within a species group/complex) can differ in their feeding and resting behaviours, which impact both malaria transmission patterns as well as the efficacy of vector control interventions. While morphological identification of sampled specimens is an important first step towards understanding species diversity and abundance, misidentification can result in the implementation of less effective vector control measures, and consequently smaller reductions in the number of local malaria cases. Focusing on southern Mozambique, a malaria pre-elimination area where malaria remains persistent, the aims of this preliminary study were to use molecular identification (CO1 and ITS2 barcoding) to (1) validate the results from the morphological identification (with a particular focus on Anopheles pharoensis and Anopheles squamosus), and (2) have a closer look at the Anopheles coustani group (which includes Anopheles tenebrosus and Anopheles ziemanni).<br><br>METHODS: Female anopheline mosquitoes (n&#x2009;=&#x2009;81) were identified morphologically and subsequently sequenced at the ribosomal DNA internal transcribed spacer region 2 (ITS2) and/or cytochrome oxidase subunit 1 (CO1) loci towards species determination.<br><br>RESULTS: Out of the 62 specimens that were identified morphologically to species, 4 (6.5%) were misidentified. Regarding the An. coustani group, morphological identification showed that several members are present in southern Mozambique, including An. coustani sensu lato (s.l.), An. ziemanni and An. tenebrosus. However, based on both ITS2 and CO1 sequences, the exact species remains unknown for the latter two members until voucher sequences are available for comparison.<br><br>CONCLUSION: The reason(s) for morphological misidentification of anopheline mosquitoes need to be mitigated. This is usually related to both the capacity (i.e. training) of the microscopist to identify anopheline species, and the information provided in the dichotomous identification key. As the An. coustani complex contributes to (residual) malaria transmission in sub-Saharan Africa, it may play a role in the observed persistent malaria in southern Mozambique. A better baseline characterizing of the local anophelines species diversity and behaviours will allow us to improve entomological surveillance strategies, better understand the impact of vector control on each local vector species, and identify new approaches to target those vector species.},
}
@article {pmid38236339,
year = {2024},
author = {Ibrahim, M and Detroja, A and Sheth, BP and Bhadja, P and Sanghvi, G and Bishoyi, AK},
title = {Existing status and future advancements of adulteration detection techniques in herbal products.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {151},
pmid = {38236339},
issn = {1573-4978},
mesh = {Chromatography, High Pressure Liquid ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Mass Spectrometry ; *Metabolomics ; Plant Extracts ; },
abstract = {BACKGROUND: Herbal products have been commonly used all over the world for centuries. Its products have gained remarkable acceptance as therapeutic agents for a variety of disorders. However, following recent research disclosing discrepancies between labeling and actual components of herbal products, there is growing concern about the efficacy, quality and safety of the products. The admixture and adulteration of herbal medicinal products pose a risk of serious health compromise and the well-being of the consumers. To prevent adulteration in raw ingredients and final herbal products, it is necessary to use approaches to assess both genomes as well as metabolomics of the products; this offers quality assurance in terms of product identification and purity. The combinations of molecular and analytical methods are inevitable for thorough verification and quality control of herbal medicine.<br><br>METHODS AND RESULTS: This review discusses the combination of DNA barcoding, DNA metabarcoding, mass spectroscopy as well as HPLC for the authentication of herbal medicine and determination of the level of adulteration. It also discusses the roles of PCR and real-time PCR techniques in validating and ensuring the quality, purity and identity of the herbal products.<br><br>CONCLUSIONS: In conclusion, each technique has its own pros and cons, but the cumulative of both the chemical and molecular methods is proven to be the best strategy for adulteration detection. Moreover, CRISPR diagnosis tools equipped with multiplexing techniques may be implemented for screening adulteration from herbal drugs, this will play a crucial role in herbal product authentication in the future.},
}
@article {pmid38236331,
year = {2024},
author = {Saran, C and Genç, HY},
title = {Genetic diversity of diamondback moth, Plutella xylostella L. (Lepidoptera: Plutellidae) populations in Türkiye.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {146},
pmid = {38236331},
issn = {1573-4978},
support = {Grant number: FYL-2020/Project no: 3351//&#xc7;anakkale Onsekiz Mart &#xdc;niversitesi/ ; },
mesh = {Animals ; *Moths/genetics ; Turkey ; *Brassicaceae ; DNA, Mitochondrial/genetics ; Genetic Variation/genetics ; },
abstract = {BACKGROUND: Diamondback moth (DBM), Plutella xylostella (L.) (Lepidoptera: Plutellidae), is an important worldwide pest of plants belonging to the Brassicaceae family. In this study, we investigated genetic diversity of DBM populations in Brassicaceae production areas in Türkiye using the partial mtDNA CO1 gene region.<br><br>METHODS: We determined 43 samples from 11 different populations for haplotype variations using the partial mitochondrial DNA sequences a 684&#xa0;bp fragment of the CO1 gene.<br><br>RESULTS: The results indicated that, the average haplotype diversity (Hd) was determined as 0.962 and nucleotide diversity (&#x3c0;) was determined as 0.557%. In neutrality tests, negative values were obtained in Tajima's D and Fu' Fs tests (Fu' Fs=-0.40, Tajima's D=-0.01). Tajima's D test was not found significant (p&#x2009;>&#x2009;0.05). Fst value among DBM population estimates ranged from 0 to 0.631. Barcode gap distance was determined as 1.6%, but the intraspecies of genetic distance were found to be 0.15%.<br><br>CONCLUSION: In conclusion, the presented study provided detailed and fundamental information about the genetic diversity of DBM populations in T&#xfc;rkiye. Further studies are needed to develop alternative pest management strategies for DBM populations integrating genetic approaches.},
}
@article {pmid38235186,
year = {2024},
author = {Lecca, M and Lecca, P},
title = {A dataset for illuminant- and device- invariant colour barcode decoding with cameras.},
journal = {Data in brief},
volume = {52},
number = {},
pages = {109960},
doi = {10.1016/j.dib.2023.109960},
pmid = {38235186},
issn = {2352-3409},
abstract = {Barcodes are visual representations of data widely used in commerce and administration to compactly codify information about objects, services, and people. Specifically, a barcode is an image composed of parallel lines, with different widths, spacing and sizes. Generally, the lines are dark (usually black) on a bright background (usually white) or vice-versa. Thanks to this representation, barcodes can be detected and decoded in a way robust to changes of light and noise. However, using barcodes with several colours for the lines is quite intriguing because it enables boosting the barcode's data capacity. Colour barcodes still pose a challenge today, even though numerous studies on the topic were conducted between 1990 and 2022. The main issue that needs to be solved is the creation of an optical technology able to decode colour sequences regardless of the ambient light, the acquisition and printing or visualisation device, and the physical support on which the barcode is printed or displayed. To the best of our knowledge, the studies currently available in literature do not provide the experimental data on which they are based, nor are there online databases that can be used for further studies or for training data analysis procedures based on artificial intelligence techniques. To fill this gap and push further research in this technology, we built COCO-10, a public dataset of colour barcode images, that would like to become a testbench for the development and testing of colour barcode decoding algorithms, taking into account the colour variability due to the light, to the printer and camera gamuts and to the quality of the paper on which the barcode is printed. COCO-10 contains 5400 images of 150 colour barcodes, each of one printed on two white papers with different density and printers and acquired under six illuminations by three smartphones' cameras. For each colour barcode image, a mask identifying the region occupied by the barcode is released too. The 150 colour barcodes have been generated by colouring the lines of black &amp; white barcodes with colours randomly selected from a palette of ten colours including both warm and colour hues. The name COCO-10 just refers to the fact that the dataset contains COlor BarCOdes with 10 possible colours for each line. We also provide a set of 300 images created as follows. The 150 COCO-10 colour barcodes were synthetically superimposed on 150 cluttered backgrounds, resulting in 150 images. The first 75 (group 1) were printed on thick paper, the others (group 2) on plain paper. Each group was further subdivided into subsets of 25 images, resulting in 3 subgroups, each of which was captured by 2 smartphones' cameras under one of the 6 illuminants mentioned above. We also provide masks for these images. These images would like to be a benchmark for testing the accuracy of barcode decoding algorithms, bearing in mind that the performance of these algorithms may be influenced by the accuracy of the previous detection of the barcodes themselves in the background. The total number of images in COCO-10 is 11700, including the 300 synthetic images of the colour barcodes displayed on white and cluttered background, the 5700 real-world images of the colour barcodes printed on white papers and with cluttered backgrounds and their corresponding 5700 masks. We finally highlight that COCO-10 can be also used for developing and testing algorithms for gamut and tone mapping, machine colour constancy, and colour correction.},
}
@article {pmid38234835,
year = {2023},
author = {Gu, J and Iyer, A and Wesley, B and Taglialatela, A and Leuzzi, G and Hangai, S and Decker, A and Gu, R and Klickstein, N and Shuai, Y and Jankovic, K and Parker-Burns, L and Jin, Y and Zhang, JY and Hong, J and Niu, S and Chou, J and Landau, DA and Azizi, E and Chan, EM and Ciccia, A and Gaublomme, JT},
title = {CRISPRmap: Sequencing-free optical pooled screens mapping multi-omic phenotypes in cells and tissue.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38234835},
issn = {2692-8205},
support = {R01 CA227450/CA/NCI NIH HHS/United States ; DP2 CA281605/CA/NCI NIH HHS/United States ; R01 CA197774/CA/NCI NIH HHS/United States ; R21 HG012639/HG/NHGRI NIH HHS/United States ; R01 HG012875/HG/NHGRI NIH HHS/United States ; },
abstract = {Pooled genetic screens are powerful tools to study gene function in a high-throughput manner. Typically, sequencing-based screens require cell lysis, which limits the examination of critical phenotypes such as cell morphology, protein subcellular localization, and cell-cell/tissue interactions. In contrast, emerging optical pooled screening methods enable the investigation of these spatial phenotypes in response to targeted CRISPR perturbations. In this study, we report a multi-omic optical pooled CRISPR screening method, which we have named CRISPRmap. Our method combines a novel in situ CRISPR guide identifying barcode readout approach with concurrent multiplexed immunofluorescence and in situ RNA detection. CRISPRmap barcodes are detected and read out through combinatorial hybridization of DNA oligos, enhancing barcode detection efficiency, while reducing both dependency on third party proprietary sequencing reagents and assay cost. Notably, we conducted a multi-omic base-editing screen in a breast cancer cell line on core DNA damage repair genes involved in the homologous recombination and Fanconi anemia pathways investigating how nucleotide variants in those genes influence DNA damage signaling and cell cycle regulation following treatment with ionizing radiation or DNA damaging agents commonly used for cancer therapy. Approximately a million cells were profiled with our multi-omic approach, providing a comprehensive phenotypic assessment of the functional consequences of the studied variants. CRISPRmap enabled us to pinpoint likely-pathogenic patient-derived mutations that were previously classified as variants of unknown clinical significance. Furthermore, our approach effectively distinguished barcodes of a pooled library in tumor tissue, and we coupled it with cell-type and molecular phenotyping by cyclic immunofluorescence. Multi-omic spatial analysis of how CRISPR-perturbed cells respond to various environmental cues in the tissue context offers the potential to significantly expand our understanding of tissue biology in both health and disease.},
}
@article {pmid38234383,
year = {2022},
author = {Tan, YP and Bishop-Hurley, SL and Shivas, RG and Cowan, DA and Maggs-Kölling, G and Maharachchikumbura, SSN and Pinruan, U and Bransgrove, KL and De la Peña-Lastra, S and Larsson, E and Lebel, T and Mahadevakumar, S and Mateos, A and Osieck, ER and Rigueiro-Rodríguez, A and Sommai, S and Ajithkumar, K and Akulov, A and Anderson, FE and Arenas, F and Balashov, S and Bañares, &#xc1; and Berger, DK and Bianchinotti, MV and Bien, S and Bilański, P and Boxshall, AG and Bradshaw, M and Broadbridge, J and Calaça, FJS and Campos-Quiroz, C and Carrasco-Fernández, J and Castro, JF and Chaimongkol, S and Chandranayaka, S and Chen, Y and Comben, D and Dearnaley, JDW and Ferreira-Sá, AS and Dhileepan, K and Díaz, ML and Divakar, PK and Xavier-Santos, S and Fernández-Bravo, A and Gené, J and Guard, FE and Guerra, M and Gunaseelan, S and Houbraken, J and Janik-Superson, K and Jankowiak, R and Jeppson, M and Jurjević, &#x17d; and Kaliyaperumal, M and Kelly, LA and Kezo, K and Khalid, AN and Khamsuntorn, P and Kidanemariam, D and Kiran, M and Lacey, E and Langer, GJ and López-Llorca, LV and Luangsa-Ard, JJ and Lueangjaroenkit, P and Lumbsch, HT and Maciá-Vicente, JG and Mamatha Bhanu, LS and Marney, TS and Marqués-Gálvez, JE and Morte, A and Naseer, A and Navarro-Ródenas, A and Oyedele, O and Peters, S and Piskorski, S and Quijada, L and Ramírez, GH and Raja, K and Razzaq, A and Rico, VJ and Rodríguez, A and Ruszkiewicz-Michalska, M and Sánchez, RM and Santelices, C and Savitha, AS and Serrano, M and Leonardo-Silva, L and Solheim, H and Somrithipol, S and Sreenivasa, MY and Stępniewska, H and Strapagiel, D and Taylor, T and Torres-Garcia, D and Vauras, J and Villarreal, M and Visagie, CM and Wołkowycki, M and Yingkunchao, W and Zapora, E and Groenewald, JZ and Crous, PW},
title = {Fungal Planet description sheets: 1436-1477.},
journal = {Persoonia},
volume = {49},
number = {},
pages = {261-350},
pmid = {38234383},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Argentina, Colletotrichum araujiae on leaves, stems and fruits of Araujia hortorum. Australia, Agaricus pateritonsus on soil, Curvularia fraserae on dying leaf of Bothriochloa insculpta, Curvularia millisiae from yellowing leaf tips of Cyperus aromaticus, Marasmius brunneolorobustus on well-rotted wood, Nigrospora cooperae from necrotic leaf of Heteropogon contortus, Penicillium tealii from the body of a dead spider, Pseudocercospora robertsiorum from leaf spots of Senna tora, Talaromyces atkinsoniae from gills of Marasmius crinis-equi and Zasmidium pearceae from leaf spots of Smilaxglyciphylla. Brazil, Preussia bezerrensis from air. Chile, Paraconiothyrium kelleni from the rhizosphere of Fragaria chiloensis subsp. chiloensis f. chiloensis. Finland, Inocybe udicola on soil in mixed forest with Betula pendula, Populus tremula, Picea abies and Alnus incana. France, Myrmecridium normannianum on dead culm of unidentified Poaceae. Germany, Vexillomyces fraxinicola from symptomless stem wood of Fraxinus excelsior. India, Diaporthe limoniae on infected fruit of Limonia acidissima, Didymella naikii on leaves of Cajanus cajan, and Fulvifomes mangroviensis on basal trunk of Aegiceras corniculatum. Indonesia, Penicillium ezekielii from Zea mays kernels. Namibia, Neocamarosporium calicoremae and Neocladosporium calicoremae on stems of Calicorema capitata, and Pleiochaeta adenolobi on symptomatic leaves of Adenolobus pechuelii. Netherlands, Chalara pteridii on stems of Pteridium aquilinum, Neomackenziella juncicola (incl. Neomackenziella gen. nov.) and Sporidesmiella junci from dead culms of Juncus effusus. Pakistan, Inocybe longistipitata on soil in a Quercus forest. Poland, Phytophthora viadrina from rhizosphere soil of Quercus robur, and Septoria krystynae on leaf spots of Viscum album. Portugal (Azores), Acrogenospora stellata on dead wood or bark. South Africa, Phyllactinia greyiae on leaves of Greyia sutherlandii and Punctelia anae on bark of Vachellia karroo. Spain, Anteaglonium lusitanicum on decaying wood of Prunus lusitanica subsp. lusitanica, Hawksworthiomyces riparius from fluvial sediments, Lophiostoma carabassense endophytic in roots of Limbarda crithmoides, and Tuber mohedanoi from calcareus soils. Spain (Canary Islands), Mycena laurisilvae on stumps and woody debris. Sweden, Elaphomyces geminus from soil under Quercus robur. Thailand, Lactifluus chiangraiensis on soil under Pinus merkusii, Lactifluus nakhonphanomensis and Xerocomus sisongkhramensis on soil under Dipterocarpus trees. Ukraine, Valsonectria robiniae on dead twigs of Robinia hispida. USA, Spiralomyces americanus (incl. Spiralomyces gen. nov.) from office air. Morphological and culture characteristics are supported by DNA barcodes. Citation: Tan YP, Bishop-Hurley SL, Shivas RG, et al. 2022. Fungal Planet description sheets: 1436-1477. Persoonia 49: 261-350. https://doi.org/10.3767/persoonia.2022.49.08.},
}
@article {pmid38234382,
year = {2022},
author = {Reschke, K and Morozova, OV and Dima, B and Cooper, JA and Corriol, G and Biketova, AY and Piepenbring, M and Noordeloos, ME},
title = {Phylogeny, taxonomy, and character evolution in Entoloma subgenus Nolanea.},
journal = {Persoonia},
volume = {49},
number = {},
pages = {136-170},
pmid = {38234382},
issn = {0031-5850},
abstract = {Nolanea is a well-known and long-established subgenus of the genus Entoloma traditionally defined mainly by the mycenoid basidiocarps of the included species. Until now, revisions of this subgenus including molecular data exist only on a regional scale. In this study, the phylogeny of species of Nolanea is analysed based on multi-gene DNA sequences including data of specimens from all continents. New primers are designed for the mitochondrial small subunit and RPB2. The performance of the DNA loci in reconstructing the phylogeny in subg. Nolanea is evaluated. An ancestral state reconstruction is used to infer the character state evolution as well as the importance and reliability of morphological characters used to define subclades below subgeneric rank. Based on the results, seven sections are recognised in Nolanea: the sections Holoconiota, Infularia, Mammosa, Nolanea, Papillata, Staurospora, and the newly described sect. Elegantissima. A large phylogeny based on the fungal barcode rDNA ITS with numerous type sequences is used to evaluate current species concepts. Several names are revealed to be synonyms of older names. Four species new to science are described, namely E. altaicum, E. argillaceum, E. cornicolor, and E. incognitum. Lectotypes, epitypes or neotypes are designated for E. cetratum, E. clandestinum, E. conferendum, E. cuspidiferum, E. hebes, E. minutum, E. nitens, and E. rhodocylix. The re-evaluation of the limits of subg. Nolanea leads to an altered concept excluding species with distinct, lageniform cheilocystidia. The section Ameides is placed in subg. Leptonia. For several species formerly accommodated in Nolanea, but excluded now, viz., E. lepiotoides, E. rhombisporum, E. subelegans, and E. velenovskyi the taxonomic position remains unclear, because of the yet unresolved phylogeny of the whole genus Entoloma. Citation: Reschke K, Morozova OV, Dima B, et al. 2022. Phylogeny, taxonomy, and character evolution in Entoloma subgenus Nolanea. Persoonia 49: 136-170. https://doi.org/10.3767/persoonia.2022.49.04.},
}
@article {pmid38232459,
year = {2024},
author = {Rama-Garda, R and Martin-Ortega, MD and Sánchez, AJ and Priego, J and de Blas, J and Torrado, A and Domínguez, E and Haro, R and Rivera-Sagredo, A and Román, JP and Lorite, MJ and Johansson, HE and Loza, MI and Amigo, J and Sobrino, B and Lallena, MJ and Toledo, M&#xc1;},
title = {Design, synthesis and validation of a new Crimped Head-Piece for DNA-Encoded libraries generation.},
journal = {Bioorganic &amp; medicinal chemistry},
volume = {99},
number = {},
pages = {117596},
doi = {10.1016/j.bmc.2024.117596},
pmid = {38232459},
issn = {1464-3391},
mesh = {*Drug Discovery/methods ; *Small Molecule Libraries/chemistry ; DNA/chemistry ; Gene Library ; DNA, Single-Stranded ; },
abstract = {Codification of DNA Encoded Libraries (DELs) is critical for successful ligand identification of molecules that bind a protein of interest (POI). There are different encoding strategies that permit, for instance, the customization of a DEL for testing single or dual pharmacophores (single strand DNA) or for producing and screening large diversity libraries of small molecules (double strand DNA). Both approaches challenges, either from the synthetic and encoding point of view, or from the selection methodology to be utilized for the screening. The Head-Piece contains the DNA sequence that is attached to a chemical compound, allowing the encoding of each molecule with a unique DNA tag. Designing the Head-Piece for a DNA-encoded library involves careful consideration of several key aspects including DNA barcode identity, sequence length and attachment chemistry. Here we describe a double stranded DNA versatile Head-Piece that can be used for the generation of single or dual pharmacophore libraries, but also shows other advanced DEL functionalities, stability and enlarged encoding capacity.},
}
@article {pmid38231602,
year = {2023},
author = {Khamnuan, S and Phrutivorapongkul, A and Pitchakarn, P and Buacheen, P and Karinchai, J and Chittasupho, C and Na Takuathung, M and Theansungnoen, T and Thongkhao, K and Intharuksa, A},
title = {The Identification and Cytotoxic Evaluation of Nutmeg (Myristica fragrans Houtt.) and Its Substituents.},
journal = {Foods (Basel, Switzerland)},
volume = {12},
number = {23},
pages = {},
pmid = {38231602},
issn = {2304-8158},
support = {//Research supporting scholarship for graduate students of Faculty of Pharmacy, Chiang Mai University/ ; //Research Administration, Chiang Mai University/ ; },
abstract = {The aril and seed of nutmeg, Myristica fragrans Houtt. (Myristicaceae), hold significant value in various industries globally. Our preliminary research found two morphological variations: a globose shape and an oval shape. Due to these different characteristics, the safety of consumers is of primary concern. Thus, authentication and comparative pharmacological and toxicity analyses are necessary. In this study, pharmacognostic and advanced phytochemical analyses, DNA barcoding, cytotoxicity, and the anti-nitric oxide production of commercial Thai nutmeg were examined. Via morphologic examinations and TLC fingerprinting, all the sampled aril and seed were categorized into globose and oval-shaped groups. The results of HPLC, GC-MS, and LC-MS/MS experiments revealed distinct differences between these groups. The DNA barcoding of the trnH-psbA region using the BLAST method and neighbor-joining tree analyses confirmed the globose nutmeg as M. fragrans and the oval-shaped variant as M. argentea. A comparison was then carried out between the potential toxicity and anti-inflammatory capabilities of M. fragrans and M. argentea. Cytotoxicity tests on HaCaT, 3T3-L1, Caco-2, HEK293, and RAW264.7 were performed using both methanolic extracts and volatile oil from the arils and seeds of both species. This study concludes that blending or substituting these two species maintains their therapeutic integrity without posing safety concerns.},
}
@article {pmid38230309,
year = {2024},
author = {Hübner, JJ and Chemyreva, V},
title = {Review of German Spilomicrus Westwood (Hymenoptera, Diapriidae, Spilomicrini).},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e114515},
pmid = {38230309},
issn = {1314-2828},
abstract = {BACKGROUND: This study provides an integrative taxonomy-based review for the genus Spilomicrus Westwood in Germany using DNA barcoding and classic morphology.<br><br>NEW INFORMATION: Spilomicrussimplex Tomsik, 1947 is placed in synonymy with S.antennatus Jurine, 1807; Spilomicrusthomsoni Kieffer, 1911 is removed from synonymy with S.hemipterus Marshall, 1868. A lectotype is designated for Spilomicrusnigripes Thomson, 1858. Newly recorded for Germany are the following species: S.thomsoni Kieffer, 1911, S.crassiclavis Marshall, 1868, S.lusitanicus Kieffer, 1910 and S.diversus Chemyreva, 2021. Three species, Spilomicrusbrevimalaris sp. nov., S.flavecorpus sp. nov. and S.politus sp. nov. are described as new to science. The 23 DNA-barcodes with species identification present a substantial addition over the previous German checklist. This study aims to update the number of nationwide known Spilomicrus species from fifteen to twenty. Furthermore, a new key to identify all European Spilomicrus species is provided.},
}
@article {pmid38228777,
year = {2024},
author = {Cao, J and Zheng, Z and Sun, D and Chen, X and Cheng, R and Lv, T and An, Y and Zheng, J and Song, J and Wu, L and Yang, C},
title = {Decoder-seq enhances mRNA capture efficiency in spatial RNA sequencing.},
journal = {Nature biotechnology},
volume = {42},
number = {11},
pages = {1735-1746},
pmid = {38228777},
issn = {1546-1696},
support = {22293031; 21927806//National Natural Science Foundation of China (National Science Foundation of China)/ ; 22104080//National Natural Science Foundation of China (National Science Foundation of China)/ ; 22004083//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2021M702167//China Postdoctoral Science Foundation/ ; },
mesh = {*RNA, Messenger/genetics/metabolism ; Animals ; Mice ; Humans ; *Sequence Analysis, RNA/methods ; Carcinoma, Renal Cell/genetics/pathology ; Receptors, Odorant/genetics/metabolism ; Olfactory Bulb/metabolism ; Gene Expression Profiling/methods ; Single-Cell Analysis/methods ; Kidney Neoplasms/genetics/pathology ; Tumor Microenvironment ; },
abstract = {Spatial transcriptomics technologies with high resolution often lack high sensitivity in mRNA detection. Here we report a dendrimeric DNA coordinate barcoding design for spatial RNA sequencing (Decoder-seq), which offers both high sensitivity and high resolution. Decoder-seq combines dendrimeric nanosubstrates with microfluidic coordinate barcoding to generate spatial arrays with a DNA density approximately ten times higher than previously reported methods while maintaining flexibility in resolution. We show that the high RNA capture efficiency of Decoder-seq improved the detection of lowly expressed olfactory receptor (Olfr) genes in mouse olfactory bulbs and contributed to the discovery of a unique layer enrichment pattern for two Olfr genes. The near-cellular resolution provided by Decoder-seq has enabled the construction of a spatial single-cell atlas of the mouse hippocampus, revealing dendrite-enriched mRNAs in neurons. When applying Decoder-seq to human renal cell carcinomas, we dissected the heterogeneous tumor microenvironment across different cancer subtypes and identified spatial gradient-expressed genes related to epithelial-mesenchymal transition with the potential to predict tumor prognosis and progression.},
}
@article {pmid38227649,
year = {2024},
author = {Feng, J and Jang, G and Esteva, E and Adams, NM and Jin, H and Reizis, B},
title = {Clonal barcoding of endogenous adult hematopoietic stem cells reveals a spectrum of lineage contributions.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {4},
pages = {e2317929121},
pmid = {38227649},
issn = {1091-6490},
support = {R01 HL152637/HL/NHLBI NIH HHS/United States ; R21 HL113678/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Cell Differentiation ; *Hematopoietic Stem Cells ; Hematopoiesis/genetics ; *Adult Stem Cells ; Cell Lineage/genetics ; },
abstract = {The hierarchical model of hematopoiesis posits that self-renewing, multipotent hematopoietic stem cells (HSCs) give rise to all blood cell lineages. While this model accounts for hematopoiesis in transplant settings, its applicability to steady-state hematopoiesis remains to be clarified. Here, we used inducible clonal DNA barcoding of endogenous adult HSCs to trace their contribution to major hematopoietic cell lineages in unmanipulated animals. While the majority of barcodes were unique to a single lineage, we also observed frequent barcode sharing between multiple lineages, specifically between lymphocytes and myeloid cells. These results suggest that both single-lineage and multilineage contributions by HSCs collectively drive continuous hematopoiesis, and highlight a close relationship of myeloid and lymphoid development.},
}
@article {pmid38227156,
year = {2024},
author = {Erban, T and Sopko, B and Klimov, PB and Hubert, J},
title = {Mixta mediterraneensis as a novel and abundant gut symbiont of the allergen-producing domestic mite Blomia tropicalis.},
journal = {Experimental &amp; applied acarology},
volume = {92},
number = {2},
pages = {161-181},
pmid = {38227156},
issn = {1572-9702},
support = {MZE-RO0423//Ministerstvo Zem&#x11b;d&#x11b;lstv&#xed;/ ; LUAUS23082//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; RF 193021X0012//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {Humans ; Animals ; *Allergens ; *Mites ; },
abstract = {Blomia tropicalis is an allergen-producing mite in the human environment in tropical regions. The microbiome of B. tropicalis was described using the barcode sequencing region of V4 16S rDNA and genome assemblage. Mixta mediterraneensis, previously isolated from human skin swabs, was identified as a B. tropicalis gut symbiont based on genome assembly. The microbiome contains two bacteria, Staphylococcus and M. mediterraneensis. The number of M. mediterraneensis 16S DNA copies was 10[6] per mite and 10[9] per feces in the rearing chamber based on qPCR quantification. The profile of this bacterium reached 50% of reads in the mite gut and feces. Genomic analyses revealed that the bacterium has several metabolic pathways that suggest metabolic cooperation with the mite host in vitamin and amino acid synthesis, nitrogen recycling, and antimicrobial defense. Lysozyme is present in the symbiotic bacterium but absent in the mite. The B. tropicalis microbiome contained Staphylococcus, which accelerates mite population growth. Mites can digest Staphylococcus by using specific enzymes with hydrolytic functions against bacterial cell walls (chitinases and cathepsin D), leading to endocytosis of bacteria and their degradation in lysosomes and phagosomes. Gene expression analysis of B. tropicalis indicated that phagocytosis was mediated by the PI3-kinase/Akt pathway interacting with the invasins produced by M. mediterraneensis. Moreover, the symbiont had metabolic pathways that allowed it to recycle the mite metabolic waste product guanine, known as a mite attractant. The mite host symbiont enhances mite aggregation in the feces, and the fecal-oral transmission route is excepted.},
}
@article {pmid38225696,
year = {2024},
author = {Harris, CM and Kim, DY and Jordan, CR and Miranda, MI and Hellberg, RS},
title = {DNA barcoding of herbal supplements on the US commercial market associated with the purported treatment of COVID-19.},
journal = {Phytochemical analysis : PCA},
volume = {35},
number = {4},
pages = {664-677},
doi = {10.1002/pca.3320},
pmid = {38225696},
issn = {1099-1565},
support = {N/A//Chapman University/ ; NSF-EAR #1757991//National Science Foundation/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Dietary Supplements/analysis ; United States ; Plants, Medicinal/chemistry/genetics ; Medicine, Ayurvedic/methods ; COVID-19 Drug Treatment ; Humans ; Drug Contamination ; DNA, Plant/genetics ; SARS-CoV-2/genetics ; Plant Preparations/therapeutic use ; },
abstract = {INTRODUCTION: The COVID-19 pandemic was associated with an increased global use of traditional medicines, including Ayurvedic herbal preparations. Due to their growing demand, their processed nature, and the complexity of the global supply chain, there is an increased risk of adulteration in these products.<br><br>OBJECTIVES: The objective of this study was to assess the use of DNA barcoding for species identification in herbal supplements on the US market associated with the Ayurvedic treatment of respiratory symptoms.<br><br>METHODS: A total of 54 commercial products containing Ayurvedic herbs were tested with four DNA barcoding regions (i.e., rbcL, matK, ITS2, and mini-ITS2) using two composite samples per product. Nine categories of herbs were targeted: amla, ashwagandha, cinnamon, ginger, guduchi, tribulus, tulsi, turmeric, and vacha.<br><br>RESULTS: At least one species was identified in 64.8% of products and the expected species was detected in 38.9% of products. Undeclared plant species, including other Ayurvedic herbs, rice, and pepper, were detected in 19 products, and fungal species were identified in 12 products. The presence of undeclared plant species may be a result of intentional substitution or contamination during harvest or processing, while fungal DNA was likely associated with the plant material or the growing environment. The greatest sequencing success (42.6-46.3%) was obtained with the matK and rbcL primers.<br><br>CONCLUSION: The results of this study indicate that a combination of genetic loci should be used for DNA barcoding of herbal supplements. Due to the limitations of DNA barcoding in identification of these products, future research should incorporate chemical characterization techniques.},
}
@article {pmid38224796,
year = {2024},
author = {Schmidt, R and Dufresnes, C and Krištín, A and Künzel, S and Vences, M and Hawlitschek, O},
title = {Phylogenetic insights into Central European Chorthippus and Pseudochorthippus (Orthoptera: Acrididae) species using ddRADseq data.},
journal = {Molecular phylogenetics and evolution},
volume = {193},
number = {},
pages = {108012},
doi = {10.1016/j.ympev.2024.108012},
pmid = {38224796},
issn = {1095-9513},
mesh = {Animals ; *Grasshoppers/genetics ; Phylogeny ; Chromosomes ; DNA, Mitochondrial/genetics ; Sequence Analysis, DNA ; },
abstract = {The evolution of several orthopteran groups, especially within the grasshopper family Acrididae, remains poorly understood. This is particularly true for the subfamily Gomphocerinae, which comprises cryptic sympatric and syntopic species. Previous mitochondrial studies have highlighted major discrepancies between taxonomic and phylogenetic hypotheses, thereby emphasizing the necessity of genome-wide approaches. In this study, we employ double-digest restriction site-associated DNA sequencing (ddRADseq) to reconstruct the evolution of Central European Chorthippus and Pseudochorthippus species, especially C.smardai, P.tatrae and the C.biguttulus group. Our phylogenomic analyses recovered deep discordance with mitochondrial DNA barcoding, emphasizing its unreliability in Gomphocerinae grasshoppers. Specifically, our data robustly distinguished the C.biguttulus group and confirmed the distinctiveness of C.eisentrauti, also shedding light on its presence in the Berchtesgaden Alps. Moreover, our results support the reclassification of C.smardai to the genus Pseudochorthippus and of P.tatrae to the genus Chorthippus. Our study demonstrates the efficiency of high-throughput genomic methods such as RADseq without prior optimization to elucidate the complex evolution of grasshopper radiations with direct taxonomic implications. While RADseq has predominantly been utilized for population genomics and within-genus phylogenomics, its application extends to resolve relationships between deeply-diverged clades representative of distinct genera.},
}
@article {pmid38222481,
year = {2024},
author = {Huang, MC and Bruce, NL},
title = {DNA barcoding of the supergiant isopods from Bathynomuskensleyi Lowry &amp; Dempsey, 2006 (Cirolanidae) and a molecular biology comparison of B.jamesi Kou, Chen &amp; Li, 2017.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e111046},
pmid = {38222481},
issn = {1314-2828},
abstract = {DNA was extracted from tissue samples from specimens of newly-collected Bathynomuskensleyi from Queensland and subsequently the COI and 16S rRNA sequences were successfully cloned. The holotype of B.kensleyi was also sampled for COI only. Comparison of the sequences showed that, for the COI sequences, B.jamesi and B.kensleyi have more than 59 different DNA positions amongst 596 known reading sequences. The Kimura two parameter (K2P) distance analysis confirmed that B.jamesi and B.kensleyi are two species. Indian records of Bathynomus are reviewed and three of the four identified species from India are shown to be misidentifications. Bathynomusdecemspinosus, B.doederlini and B.kensleyi are found to not occur in India and the only accepted record is that of Bathynomuskeablei Lowry &amp; Dempsey, 2006. We conclude that, based on molecular analysis and morphological comparisons, the correct species identity of Indian species other than Bathynomuskeablei remains unknown.},
}
@article {pmid38222294,
year = {2024},
author = {Macpherson, E and Rodríguez-Flores, PC and Machordom, A},
title = {DNA barcoding and morphology revealed the existence of seven new species of squat lobsters in the family Munididae (Decapoda, Galatheoidea) in the southwestern Pacific.},
journal = {ZooKeys},
volume = {1188},
number = {},
pages = {91-123},
pmid = {38222294},
issn = {1313-2989},
abstract = {Specimens of squat lobsters belonging to the family MunididaeAhyong et al., 2010, representing the genera Garymunida Macpherson &amp; Baba, 2022, Trapezionida Macpherson &amp; Baba, 2022 and Typhlonida Macpherson &amp; Baba, 2022, were collected during several cruises around New Caledonia and Papua New Guinea, Southwest Pacific. The integrative study of these specimens revealed the presence of one new species in Garymunida, five in Trapezionida and one in Typhlonida. We describe and illustrate these new species, providing some new data on the taxonomy of several rare or scarcely studied species of Trapezionida. Molecular data from different markers (mitochondrial and nuclear) was also included, based on data availability, to support the taxonomic status of different species. Finally, a key to species for each genus is also provided.},
}
@article {pmid38221992,
year = {2024},
author = {Dutta, M and Sharma, P and Raturi, V and Bhargava, B and Zinta, G},
title = {SarCTAB: an efficient and cost-effective DNA isolation protocol from geophytes.},
journal = {3 Biotech},
volume = {14},
number = {2},
pages = {36},
pmid = {38221992},
issn = {2190-572X},
abstract = {Geophytes are herbaceous plants that grow anew from underground buds and are excellent models to study storage organ formation. However, molecular studies involving geophytes are constrained due to the presence of a wide spectrum of polysaccharides and polyphenols that contaminate the genomic DNA. At present, several protocols exist for the extraction of genomic DNA from different plant species; however, isolating high-quality DNA from geophytes is challenging. Such challenges are further complexed by longer incubation time and multiple precipitation steps involved in existing DNA isolation methods. To overcome such problems, we aimed to establish a DNA extraction method (SarCTAB) which is an economical, quick, and sustainable way of DNA isolation from geophytes. We improved the traditional CTAB method by optimizing key ingredients such as sarcosine, β-mercaptoethanol, and high molar concentration of sodium chloride (NaCl), which resulted in high concentration and good-quality DNA with lesser polysaccharides, proteins, and polyphenols. This method was evaluated to extract DNA from storage organs of six different geophytes. The SarCTAB method provides an average yield of 1755 ng/µl of high-quality DNA from 100 mg of underground storage tissues with an average standard purity of 1.86 (260/280) and 1.42 (260/230). The isolated genomic DNA performed well with Inter-simple sequence repeat (ISSR) amplification, restriction digestion with EcoRI, and PCR amplification of plant barcode genes viz. matK and rbcL. Also, the cost involved in DNA isolation was low when compared to that with commercially available kits. Overall, SarCTAB method works effectively to isolate high-quality genomic DNA in a cost-effective manner from the underground storage tissues of geophytes, and can be applied for next-generation sequencing, DNA barcoding, and whole genome bisulfite sequencing.},
}
@article {pmid38221502,
year = {2023},
author = {Liao, CQ and Hirowatari, T and Yagi, S and Wang, M and Wang, X and Huang, GH},
title = {The fauna of the family Adelidae (Insecta, Lepidoptera, Adeloidea) from China.},
journal = {Zootaxa},
volume = {5348},
number = {1},
pages = {1-152},
doi = {10.11646/zootaxa.5348.1.1},
pmid = {38221502},
issn = {1175-5334},
mesh = {Animals ; *Lepidoptera ; Phylogeny ; Animal Distribution ; *Moths/genetics ; Genitalia ; China ; },
abstract = {Ninety-eight species of the family Adelidae, belonging to three genera in two subfamilies, were recorded and described in China, with illustrations of the adults and their genitalia. Keys to subfamilies, genera and species are also provided. Twenty-four new species are described, nine species are newly recorded from China, and four new combinations are made. Ecological photos and DNA barcodes of some species are provided, and the phylogenetic analysis based on cytochrome c oxidase subunit I (COI) sequences are conducted. The new taxa are as follows: Nemophora pseudalbiantennella Liao, Hirowatari &amp; Huang, sp. nov., N. badagongshana Liao, Hirowatari &amp; Huang, sp. nov., N. longlabiae Liao, Hirowatari &amp; Huang, sp. nov., N. quadrata Liao, Hirowatari &amp; Huang, sp. nov., N. basalistriata Liao, Hirowatari &amp; Huang, sp. nov., N. digitata Liao, Hirowatari &amp; Huang, sp. nov., N. duplicifascia Liao, Hirowatari &amp; Huang, sp. nov., N. hunanensis Liao, Hirowatari &amp; Huang, sp. nov., N. purpurata Liao, Hirowatari &amp; Huang, sp. nov., N. arcuatifasciata Liao, Hirowatari &amp; Huang, sp. nov., N. caeruliantenna Liao, Hirowatari &amp; Huang, sp. nov., N. xizangensis Liao, Hirowatari &amp; Huang, sp. nov., N. caerulea Liao, Hirowatari &amp; Huang, sp. nov., N. songgangensis Liao, Hirowatari &amp; Huang, sp. nov., N. conjugata Liao, Hirowatari &amp; Huang, sp. nov., N. latilobula Liao, Hirowatari &amp; Huang, sp. nov., N. longispina Liao, Hirowatari &amp; Huang, sp. nov., N. ganziensis Liao, Hirowatari &amp; Huang, sp. nov., N. jiajinshana Liao, Hirowatari &amp; Huang, sp. nov., N. litangensis Liao, Hirowatari &amp; Huang, sp. nov., N. tianpingshana Liao, Hirowatari &amp; Huang, sp. nov., N. triangulifascia Liao, Hirowatari &amp; Huang, sp. nov., N. yajiagengensis Liao, Hirowatari &amp; Huang, sp. nov., and N. bispina Liao, Hirowatari &amp; Huang, sp. nov. The newly recorded taxa from China are: Nematopogon distinctus Yasuda, 1957, Adela nobilis Christoph, 1882, A. praepilosa Hirowatari, 1997, Nemophora albiantennella Issiki, 1930, N. chionites (Meyrick, 1907), N. smaragdaspis (Meyrick, 1924), N. trimetrella Stringer, 1930, N. optima (Butler, 1878), and N. bifasciatella Issikii, 1930. The new combinations are N. servata (Meyrick, 1925) com. nov., N. diplophragma (Meyrick, 1938) com. nov., N. chionella (Caradja, 1935) com. nov., and N. chrysocharis (Caradja, 1938) com. nov.},
}
@article {pmid38221496,
year = {2023},
author = {Echavarria, MAZ and Barrantes, EAB and Helmic, EE and Bartlett, CR and Bahder, BW},
title = {A new species of planthopper in the genus Cobacella (Hemiptera: Auchenorrhyncha: Derbidae) from oil palm (Elaeis guineensis) in Costa Rica.},
journal = {Zootaxa},
volume = {5351},
number = {1},
pages = {107-121},
doi = {10.11646/zootaxa.5351.1.4},
pmid = {38221496},
issn = {1175-5334},
mesh = {Animals ; *Hemiptera/genetics ; Costa Rica ; *Arecaceae/genetics ; Surveys and Questionnaires ; *Expeditions ; },
abstract = {Recent survey work in Costa Rica has revealed a high diversity of planthoppers in the family Derbidae on palms (Arecaceae). During an expedition to Costa Rica in 2021, specimens were collected from African oil palm (Elaeis guineensis) along the pacific coast and determined to represent a new species of derbid in the genus Cobacella. Herein, the novel taxon, Cobacella palmensis sp. n., is described and compared with the two other species in the genus. Supplemental molecular data for the cytochrome c oxidase subunit I (COI) barcoding region, 18S rRNA gene and D9-D10 expansion region of the 28S rRNA gene are provided to test the placement of the novel taxon relative to available otiocerine planthoppers. We also present a preliminary key to the species of Cobacella and review all available specimen records of the genus.},
}
@article {pmid38221403,
year = {2023},
author = {Makarchenko, EA and Semenchenko, AA},
title = {Two new chironomid species of the genus Pseudokiefferiella Zavel (Diptera: Chironomidae: Diamesinae) from the Amur River basin of Russia.},
journal = {Zootaxa},
volume = {5339},
number = {5},
pages = {481-491},
doi = {10.11646/zootaxa.5339.5.5},
pmid = {38221403},
issn = {1175-5334},
mesh = {Male ; Animals ; *Chironomidae/genetics ; *Diptera/genetics ; Rivers ; Russia ; Larva/anatomy &amp; histology ; Pupa/anatomy &amp; histology ; DNA Barcoding, Taxonomic ; },
abstract = {The adult male, pupa, larva with DNA barcoding of Ps. matafonovi sp. nov. and the adult male of Ps. silinka sp. nov. from Amur River basin of Russia are described and illustrated. Ps. matafonovi sp. nov. is genetically distant from other Pseudokiefferiella showing uncorrected p-distances of >6.8 %. The results of species delimitation show that genus Pseudokiefferiella includes 10 (mPTP), 13 (ASAP, GMYC) or 14 (BOLD) distinct molecular taxonomic units (mOTUs) that requires a revision of this genus using both morphological and molecular approaches.},
}
@article {pmid38221399,
year = {2023},
author = {Echavarria, MAZ and Barrantes, EAB and Bartlett, CR and Helmick, EE and Bahder, BW},
title = {A new species of Oecleus (Hemiptera: Auchenorrhyncha: Fulgoromorpha: Cixiidae) from the Osa Peninsula in Costa Rica.},
journal = {Zootaxa},
volume = {5339},
number = {6},
pages = {533-546},
doi = {10.11646/zootaxa.5339.6.3},
pmid = {38221399},
issn = {1175-5334},
mesh = {Animals ; *Hemiptera/genetics ; Costa Rica ; *Arecaceae ; Surveys and Questionnaires ; },
abstract = {Recent palm survey work in Costa Rica focusing on planthoppers has resulted in the discovery of several new taxa, primarily in Cixiidae and Derbidae. In addition to sampling palms directly, light trapping has been utilized to collect a broader range of planthoppers that may not be found on palms. During a light trapping event at the Cotinga Biological station on the Osa peninsula in Costa Rica, a cixiid was collected and subsequently determined to be an unidentified species in the genus Oecleus Stl. Herein, the novel taxon, Oecleus urru sp. n., is described. Supplemental molecular data for the barcoding region (5 half) of the cytochrome c oxidase subunit I (COI) gene, 18S rRNA gene, and histone 3 (H3) gene is provided to support the placement of the novel taxon in the genus Oecleus.},
}
@article {pmid38221379,
year = {2023},
author = {Ortiz, AS and Rubio, RM and Guerrero, JJ and Garre, M and Yela, JL},
title = {DNA barcoding of the genus Apaidia Hampson, 1900 for species delimitation from Western Mediterranean fauna (Lepidoptera, Erebidae).},
journal = {Zootaxa},
volume = {5343},
number = {2},
pages = {193-200},
doi = {10.11646/zootaxa.5343.2.5},
pmid = {38221379},
issn = {1175-5334},
mesh = {Animals ; Phylogeny ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; *Moths/genetics ; },
abstract = {The genus Apaidia Hampson, 1900 is a relict Western Mediterranean genus in the South-western part of Europe and the North-western areas of the Mediterranean Africa comprising so far three species, Apaidia rufeola (Rambur, 1832), Apaidia mesogona (Godart, [1824]) and Apaidia barbarica Legrand, 1939. According to the examined material, COI mitochondrial DNA sequences and adult morphology integration supports the existence of three main lineages of Apaidia with sequence divergence rates of approximately 4.5%, which are within the range reported for other well-defined insect species. In addition, we recovered three different BINS, suggesting the presence of different species with unique and specific identifier for A. mesogona (AEC6797), A. rufeola (AEI9539), and the Iberian-Balearic A. barbarica (AEI9540). This study contributes to a better understanding of the taxonomy of the genus Apaidia and challenges future revision of this genus in Northern Africa, as well as the presence of the Apaidia species in Western Mediterranean islands and populations located in Italy.},
}
@article {pmid38221354,
year = {2023},
author = {Hoare, RJB and Patrick, BH and Buckley, TR and Brav-Cubitt, T},
title = {Wing pattern variation and DNA barcodes defy taxonomic splitting in the New Zealand Pimelea Looper Notoreas perornata (Walker) (Lepidoptera: Geometridae: Larentiinae): the importance of populations as conservation units.},
journal = {Zootaxa},
volume = {5346},
number = {1},
pages = {1-27},
doi = {10.11646/zootaxa.5346.1.1},
pmid = {38221354},
issn = {1175-5334},
mesh = {Animals ; *Lepidoptera/genetics ; DNA Barcoding, Taxonomic ; New Zealand ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; *Moths/genetics/anatomy &amp; histology ; Phylogeny ; },
abstract = {The endemic Notoreas perornata (Walker, 1863) complex (Lepidoptera: Geometridae: Larentiinae) from the North Island and northern South Island of New Zealand is reviewed. Larvae feed on Pimelea spp. (Thymelaeaceae), frequently in highly fragmented and threatened shrubland habitats. Allopatric populations tend to differ in size and wing pattern characteristics, but not in genitalia; moreover extensive variation renders recognition of subspecies / allopatric species based on any species concept problematic. A mitochondrial DNA gene tree is not congruent with morphology and indicates rapid recent divergence that has not settled into diagnosable lineages. Based on our results, we synonymise Notoreas simplex Hudson, 1898 with N. perornata (Walker, 1863), and retain N. perornata as a single, highly diverse but monotypic species. All known populations are illustrated to display variation. For conservation purposes, we recommend the continued recognition within the species of 10 populations or groups of populations that appear to be on the way to diverging at subspecific level based on morphological and/or DNA data. The conservation status of all these populations is reviewed. One conservation unit, comprising the populations from Westland, has not been seen since 1998 and is feared possibly extinct.},
}
@article {pmid38221347,
year = {2023},
author = {Hui, P and Mukherjee, B and Hazra, N},
title = {Coriophagus chaudhuri sp. n. (Strepsiptera: Halictophagidae: Coriophaginae): a male strepsipteran from Jharkhand, India with a tentative phylogeny and world key to known males.},
journal = {Zootaxa},
volume = {5346},
number = {2},
pages = {131-150},
doi = {10.11646/zootaxa.5346.2.2},
pmid = {38221347},
issn = {1175-5334},
mesh = {Animals ; Male ; Phylogeny ; *Holometabola ; India ; Wings, Animal ; },
abstract = {A new species of the genus Coriophagus Kinzelbach is described from the state of Jharkhand, India raising two in number from India. The new species, Coriophagus chaudhuri differs from other members of the genus in wing venation with base of R3 touching the subapex of R4, and flattened, oval-shaped foretarsomere I. The DNA barcoding of the new species has also been attempted here. An attempt is made to hypothesise the possible phylogenetic relationship of the males of the genus. A world key to known males of the genus is provided.},
}
@article {pmid38221346,
year = {2023},
author = {Silva, FLD},
title = {Connecting the dots: DNA barcoding and lectotype designation shedding light on Labrundinia longipalpis (Goetghebuer, 1921), an intriguing non-biting midge (Chironomidae, Tanypodinae).},
journal = {Zootaxa},
volume = {5346},
number = {2},
pages = {151-162},
doi = {10.11646/zootaxa.5346.2.3},
pmid = {38221346},
issn = {1175-5334},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Chironomidae ; Phylogeny ; DNA ; },
abstract = {Accurate taxonomic classification is deemed paramount for gaining an understanding of the diversity and distribution of insect species. In this study, an essential stride was made towards advancing the taxonomy of the non-biting midge Labrundinia longipalpis (Chironomidae, Tanypodinae), which serves as the type species of the genus. The distribution of L. longipalpis is particularly intriguing as it contrasts with the predominantly tropical distribution of the genus, with this species being found across the Holarctic region. The main goal of this investigation was to designate a lectotype and several paralectotypes, which was achieved through a comprehensive reexamination of the original material, alongside additional specimens obtained from the type-locality in Flanders. Furthermore, the distribution of L. longipalpis across Europe and North America was examined, and the proposed synonymization of L. maculata with the latter was challenged using the analysis of molecular data. Through the comparison of DNA barcodes, it was revealed that the North American population of L. longipalpis clustered together with the European population, which alludes to a considerable level of genetic similarity between these two populations. These results provide valuable insights into the behavior, ecological dynamics and biogeography of L. longipalpis, while also raising interesting questions about colonization and distribution patterns attributed to its adaptability and potential for long-distance dispersal.},
}
@article {pmid38221322,
year = {2023},
author = {Kasparek, M and Fateryga, AV},
title = {DNA barcoding confirms the validity of Anthidium melanopygum Friese, 1917 stat. nov. (Hymenoptera: Megachilidae) as a distinct species of Western Asia.},
journal = {Zootaxa},
volume = {5346},
number = {5},
pages = {567-580},
doi = {10.11646/zootaxa.5346.5.4},
pmid = {38221322},
issn = {1175-5334},
mesh = {Bees/genetics ; Animals ; *Hymenoptera ; DNA Barcoding, Taxonomic ; DNA ; Asia, Western ; },
abstract = {Heinrich Friese described Anthidium spiniventris [sic] from Palestine in 1899, and A. melanopygum as a variety of it from Turkey in 1917. While A. melanopygum was subsequently recognized as a subspecies of A. spiniventre, a morphological examination of new material of both taxa suggests that these taxa represent distinct species. This was also confirmed by genetic barcoding of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene, which revealed the two taxa form distinct clades with an average genetic distance of 5.69%, while the genetic within-group distance of these two taxa was only 0.14% for A. melanopygum and 0% for A. spiniventre. Anthidium melanopygum has a wide distribution that extends from Greece and Bulgaria in the west across Turkey and Iran to Turkmenistan in the east. By contrast, A. spiniventre has a restricted, disjunct distribution with isolated populations in the southern Levant and Iran.},
}
@article {pmid38221298,
year = {2023},
author = {Periasamy, R and Crdenas, P and Kurian, PJ and Ingole, B and Samaai, T},
title = {Is the North Atlantic Geodia barretti (Porifera, Tetractinellida, Geodiidae) present on the Southwest Indian Ridge?.},
journal = {Zootaxa},
volume = {5380},
number = {5},
pages = {461-474},
doi = {10.11646/zootaxa.5380.5.3},
pmid = {38221298},
issn = {1175-5334},
mesh = {Animals ; *Geodia ; *Porifera ; },
abstract = {There are currently 163 species of Geodia Lamarck, 1815 described worldwide, many of which are found in deep waters, but none of which have been recorded from the Southwest Indian Ridge (SWIR). Spicule morphology and barcodes (Folmer COI, 28S (C2D2), partial 18S) suggest that a specimen of Geodia collected on the SWIR at a depth of 2236 m is closely comparable to Geodia barretti Bowerbank, 1858. Geodia barretti is the most studied and thus well-known deep-sea Geodia species, due to its wide North Atlantic distribution and key role in boreal sponge grounds. This unexpected and markedly disjunct record would extend the distribution range of this species considerably, consequently challenging our knowledge about interoceanic deep-sea sponges.},
}
@article {pmid38221276,
year = {2023},
author = {Yin, JD and Bu, WJ and Xie, Q},
title = {Heissophila macrotheleae Schuh, 2006, the first record of the subfamily Heissophilinae from China (Hemiptera: Heteroptera: Plokiophilidae).},
journal = {Zootaxa},
volume = {5382},
number = {1},
pages = {55-61},
doi = {10.11646/zootaxa.5382.1.8},
pmid = {38221276},
issn = {1175-5334},
mesh = {Animals ; *Heteroptera/genetics ; *Hemiptera ; China ; Animal Distribution ; *Spiders ; },
abstract = {Heissophila Schuh, 2006, a monotypic genus of Heissophilinae (Hemiptera: Plokiophilidae), is newly recorded from Oriental China based on Heissophila macrotheleae Schuh, 2006 collected from Yunnan Province, China. The diagnosis of the species is expanded based on the newly collected materials. In addition, a DNA barcode of H. macrotheleae and host spider are provided. Photographs of the co-existing web-loving bugs and the natural habitat are also present.},
}
@article {pmid38221179,
year = {2024},
author = {Antoniolli, HRM and Carvalho, TL and Gottschalk, MS and Loreto, ELS and Robe, LJ and Depr, M},
title = {Systematics and spatio-temporal evolutionary patterns of the flavopilosa group of Drosophila (Diptera, Drosophilidae).},
journal = {Zootaxa},
volume = {5399},
number = {1},
pages = {1-18},
doi = {10.11646/zootaxa.5399.1.1},
pmid = {38221179},
issn = {1175-5334},
mesh = {Animals ; *Drosophila/genetics ; Phylogeny ; *Plant Breeding ; Biological Evolution ; Mitochondria/genetics ; },
abstract = {The Drosophila flavopilosa group comprises morphologically cryptic species that are ecologically restricted to feeding, breeding and ovipositing on flowers of Cestrum and Sessea (Solanaceae). Previous studies confirmed the monophyly of the group and the success of DNA barcoding in identifying a subset of its species, but several others remain yet to be evaluated. Furthemore, the taxonomy of the group remains incomplete, with only nine of the 17 species assigned to subgroups. Here, we accessed the phylogenetic relationships and spatio-temporal evolutionary patterns of the flavopilosa group based on a mitochondrial and two nuclear genes, providing the first molecular support to the subdivision of the group and suggesting a new taxonomic scheme for its species. Barcoding proved to be an effective tool, as all species were reciprocally monophyletic and different analyses of species delimitation yielded congruent results. The close relationship of D. flavopilosa with D. cestri and D. cordeiroi was strongly supported, suggesting that the latter should be placed in the flavopilosa subgroup together with the first. Furthermore, D. mariaehelenae was positioned as sister to D. incompta, supporting its inclusion in the nesiota subgroup. Despite new taxonomic assignments, the synapomorphic status of the diagnostic characters proposed for both subgroups was supported. Based on them, each of the remaining species were placed into one of both subgroups. Divergence time estimates suggest that their diversification coincided with the divergence of Sessea and Cestrum, providing an interesting case of coevolution.},
}
@article {pmid38221096,
year = {2023},
author = {Yang, H and Teng, K and Liu, T},
title = {A new species and new record of the leaf-mining genus Dactylotula Cockerell (Lepidoptera: Gelechiidae) from China.},
journal = {Zootaxa},
volume = {5336},
number = {2},
pages = {259-270},
doi = {10.11646/zootaxa.5336.2.7},
pmid = {38221096},
issn = {1175-5334},
mesh = {Female ; Animals ; *Lepidoptera ; China ; Plants ; *Wasps ; Poaceae ; *Moths ; },
abstract = {Until recently, only two species of Dactylotula Cockerell, 1888 have been known. Dactylotula kinkerella (Snellen, 1876), feeding on Calamagrostis arenaria (L.) Roth (Poaceae), is distributed in Europe and the Asian part of Russia, while D. altithermella (Walsingham, 1903) was only recorded in Europe with host plant unknown. Here, we report Dactylotula for the first time in China represented by a new leaf-mining species described herein as D. phragmitella, sp. n., feeding on Phragmites australis (Cav.) Steud. (Poaceae). Most of the specimens were collected in the Yellow River Delta. Photos of the adult, wing venation, male and female genitalia, host plant, leaf mines and parasitoid wasps of the new species are provided. Additionally, DNA barcodes of the new species are provided and discussed along sequences of the other two congeneric species.},
}
@article {pmid38221078,
year = {2023},
author = {Pyrcz, TW and Fhraeus, C and Boyer, P and Mahecha-J, O and Lorenc-Brudecka, J and Zajc, KS and Willmott, KR and Padrn, S},
title = {The sunny butterflies: new species of high montane pierids of the Catasticta poujadei group from the Peruvian Andes (Pieridae, Pierinae, Aporiina).},
journal = {Zootaxa},
volume = {5336},
number = {4},
pages = {530-542},
doi = {10.11646/zootaxa.5336.4.4},
pmid = {38221078},
issn = {1175-5334},
mesh = {Animals ; *Butterflies ; Peru ; },
abstract = {The Catasticta poujadei group, within the subgenus Hesperochoia Reissinger, is revised. Two new species, C. copernicus Pyrcz &amp; Fhraeus sp. nov., and C. buszkoi Boyer &amp; Pyrcz sp. nov. occurring near the timberline in Junn and Apurmac are described. Catasticta eximia Rber is reinstated as a species separate from C. poujadei, and a new subspecies, C. eximia tapuna ssp. nov., is described. The affinities of the species of the C. poujadei group are evaluated based on COI barcodes. Their distribution and habitats are described.},
}
@article {pmid38221073,
year = {2023},
author = {Rosa, JS and Martnez, JJ and Benites, P and Hernndez-Cumplido, J and Zaldvar-Rivern, A},
title = {A new species of Bracon (Braconidae: Braconinae) from central Mexico, probable parasitoid of a weevil that feeds on roots of Argemone ochroleuca Sweet (Papaveraceae).},
journal = {Zootaxa},
volume = {5336},
number = {4},
pages = {590-596},
doi = {10.11646/zootaxa.5336.4.9},
pmid = {38221073},
issn = {1175-5334},
mesh = {Animals ; *Weevils/genetics ; *Wasps ; *Argemone ; Mexico ; *Papaveraceae ; },
abstract = {A new species of the braconine genus Bracon (subgenus Bracon), B. hidalguensis sp. nov., is described from the locality of Tasquillo in the state of Hidalgo, central Mexico. The new species was reared from roots of Argemone ochroleuca Sweet (Papaveraceae), where specimens of the weevil species Conotrachelus leucophaeus (Champion) (Curculionidae) were also obtained and thus probably it represents its host. The new Bracon species was characterised molecularly with DNA barcoding (COI) and a fragment of the variable D23 region of the nuclear ribosomal 28S gene.},
}
@article {pmid38221058,
year = {2023},
author = {Yang, W and Deng, L and Yu, H and Zhong, Y},
title = {A new species of Jacaena Thorell, 1897 (Araneae: Liocranidae) from Guiyang, southwestern China.},
journal = {Zootaxa},
volume = {5339},
number = {2},
pages = {185-195},
doi = {10.11646/zootaxa.5339.2.5},
pmid = {38221058},
issn = {1175-5334},
mesh = {Animals ; China ; *Spiders/genetics ; },
abstract = {A new species belonging to the liocranid genus Jacaena Thorell, 1897, J. guiyang sp. nov., is described from southwestern China. A detailed description, diagnosis, photographs, and distribution map of the new species are given. DNA barcodes of the species were obtained and confirmed matching of the sexes, and are available for future use.},
}
@article {pmid38221049,
year = {2023},
author = {Fiebig, R and Lszl, GM and Volynkin, AV and Taberer, TR},
title = {Integrative taxonomic revision of the Metarctia Walker, 1855 subgenus HebenaWalker, 1856, with descriptions of six new species and one new subspecies(Lepidoptera: Erebidae: Arctiinae: Syntomini).},
journal = {Zootaxa},
volume = {5339},
number = {4},
pages = {301-354},
doi = {10.11646/zootaxa.5339.4.1},
pmid = {38221049},
issn = {1175-5334},
mesh = {Animals ; Bayes Theorem ; *Moths/genetics ; Genitalia ; Ecosystem ; },
abstract = {A revision of the subgenus Hebena Walker, 1856 of the syntomine genus Metarctia Walker, 1855 is given based on integrative taxonomic analyses. Six new species (Metarctia (Hebena) manfredi sp. n., M. (H.) elleni sp. n., M. (H.) brigitta sp. n., M. (H). lukaszi sp. n., M. (H.) smithi sp. n., and M. (H.) haraldsulaki sp.n.) and one new subspecies (M. (H.) smithi transvallesiana ssp. n.) are described. Metarctia (H.) kelleni (Snellen, 1886) stat. rev. is reinstated from synonymy with M. (H.) rubra (Walker, 1856) and Metarctia (H.) subincarnata Kiriakoff, 1954 syn. n. is synonymised with M. (H.) henrardi Kiriakoff, 1953 and Metarctia cinnamomea (Wallengren, 1860) syn. n. with M. (H.) rubra (Walker, 1856). DNA barcodes were obtained for 116 specimens representing 7 taxa, and genetic analyses were performed using Maximum Likelihood and Bayesian Inference approaches; a DNA barcode tree resulting from the latter is illustrated. Pairwise distances of barcodes between taxa are provided where available. The adults and genitalia of all taxa, their habitats and distribution are illustrated in 19 colour plates and 5 distribution maps.},
}
@article {pmid38221015,
year = {2023},
author = {Hoang, QD and Tran, HMT and LE, STT},
title = {A new synonymy and combination in Vietnamese agelenids (Araneae: Agelenidae: Coelotinae), supported by both morphology and DNA barcoding.},
journal = {Zootaxa},
volume = {5389},
number = {3},
pages = {393-395},
doi = {10.11646/zootaxa.5389.3.7},
pmid = {38221015},
issn = {1175-5334},
mesh = {Animals ; Vietnam ; *DNA Barcoding, Taxonomic ; *Spiders/genetics ; Animal Distribution ; },
}
@article {pmid38220889,
year = {2023},
author = {Werner, MJ and Hausmann, A and Kostjuk, I and Wanke, D and Rajaei, H},
title = {Integrative taxonomic revision of the genus Phaselia Guene, [1858] (Geometridae: Ennominae) in the Middle East and Central Asia.},
journal = {Zootaxa},
volume = {5326},
number = {1},
pages = {1-66},
doi = {10.11646/zootaxa.5326.1.1},
pmid = {38220889},
issn = {1175-5334},
mesh = {Female ; Male ; Animals ; Animal Distribution ; Middle East ; *Genitalia ; DNA ; *Moths ; },
abstract = {In the past, the high intraspecific variation of wing pattern within the genus Phaselia Guene, [1858] repeatedly led to misidentifications. In this study, we applied an integrative approach using external and internal morphological characters, along with DNA barcoding and distribution data to review the taxonomy of the genus Phaselia in the Middle East and Central Asia. For this study, 710 specimens, including type specimens and 242 genitalia slides were prepared and examined. As a result, P. phaeoleucaria (Lederer, 1855) stat. rev. is reinstated from synonymy of P. serrularia; P. phaeoleucaria shurensis Wehrli 1941 comb. nov. is regarded as a subspecies of P. phaeoleucaria stat. rev. instead of a subspecies of P. serrularia; P. serrularia catharia Wehrli, 1941 syn. nov. is regarded as a junior synonym of P. phaeoleucaria shurensis comb. nov.; P. narynaria Oberthr, 1913 syn. nov. is regarded as a junior synonym of P. serrularia (Eversmann, 1847); P. pithana Wehrli, 1941 bona sp. is raised to species level from subspecies of P. serrularia. Furthermore, two species and two subspecies are described as new to science: P. smettboi sp. nov., P. sihvoneni sp. nov., P. erika jonubi ssp. nov. and P. erika sindhi ssp. nov. Wing pattern, and both male and female genitalia of all discussed taxa are illustrated, their distribution patterns are shown on a map and CO1 data is evaluated to confirm our taxonomic decisions.},
}
@article {pmid38220865,
year = {2023},
author = {Tabell, J and Kullberg, J and Mutanen, M and Tokr, Z and Sihvonen, P},
title = {New and little known Coleophora Hbner, 1822 species from Morocco. Part I. (Lepidoptera, Coleophoridae).},
journal = {Zootaxa},
volume = {5374},
number = {2},
pages = {151-195},
doi = {10.11646/zootaxa.5374.2.1},
pmid = {38220865},
issn = {1175-5334},
mesh = {Male ; Female ; Animals ; *Lepidoptera ; Morocco ; *Moths/genetics ; Genitalia ; *Expeditions ; Animal Distribution ; },
abstract = {Altogether, 64 Coleophora (Lepidoptera: Coleophoridae) species from Morocco are reported, based on recent collecting expeditions. Twelve new species are described: C. retusa Tabell, sp. nov., C. afrofrischella Tabell, sp. nov., C. olei Tabell, sp. nov., C. carsteni Tabell, sp. nov., C. ifranensis Tabell &amp; Kullberg, sp. nov., C. jaskai Tabell, sp. nov., C. submendica Tabell, sp. nov., C. adipella Tabell, sp. nov., C. antiatlasella Tabell, sp. nov., C. dikeratella Tabell &amp; Kullberg, sp. nov., C. afrodianthi Tabell, sp. nov. and C. knudi Tabell, sp. nov. Of the previously described species, 20 are collected for the first time from Morocco, of which nine are also new to Africa. Adult males and females and their genitalia are illustrated. DNA barcodes of the presented species, if existing, are compared with those of all other Coleophoridae available on the BOLD database. Each of the barcoded new species has a unique BIN (Barcode Index Number). The female genitalia of C. arefactella Staudinger, 1859, C. stenidella Toll, 1952 and C. griseomixta Toll, 1960 are illustrated for the first time.},
}
@article {pmid38220826,
year = {2023},
author = {Lszl, GM and Volynkin, AV},
title = {A new species of Karschiola Gaede from Mozambique and Zimbabwe (Lepidoptera: Erebidae: Arctiinae) with updated information on the distribution of the genus.},
journal = {Zootaxa},
volume = {5375},
number = {2},
pages = {214-226},
doi = {10.11646/zootaxa.5375.2.3},
pmid = {38220826},
issn = {1175-5334},
mesh = {Animals ; Zimbabwe ; Mozambique ; *Moths/genetics ; Genitalia ; },
abstract = {The present paper provides the description of a new species of the genus Karschiola Gaede, 1926 from central Mozambique and Zimbabwe: K. ndzou sp. n. The pairwise genetic distance between the two Karschiola species is calculated and a neighbour-joining tree based on DNA barcodes of two K. holoclera and five K. ndzou sp. n. specimens is provided. The paper is illustrated with eight colour photos of adults and 18 genitalia images, a distribution map and two habitat photos.},
}
@article {pmid38220808,
year = {2023},
author = {Mukherjee, K and Pramanik, D and Naskar, A and Banerjee, D},
title = {A new species of Thinophilus Wahlberg (Diptera: Dolichopodidae: Hydrophorinae) from coastal India with re-description of Thinophilus tesselatus Becker (Diptera: Dolichopodidae: Hydrophorinae).},
journal = {Zootaxa},
volume = {5375},
number = {4},
pages = {478-494},
doi = {10.11646/zootaxa.5375.4.2},
pmid = {38220808},
issn = {1175-5334},
mesh = {Male ; Animals ; *Diptera ; India ; },
abstract = {A new peculiar species of marine dolichopodid fly from West Bengal, India is described: Thinophilus maritimus Mukherjee &amp; Pramanik sp. nov. COI barcodes of the new species were compared to other available Thinophilus sequences. Despite the lack of lateral setae on its hind coxa, this species clusters within the Thinophilus group. Males of Thinophilus tesselatus Becker, 1922 were also obtained from the same area, and a detailed redescription of the species is presented here. A checklist of 70 Oriental Thinophilus species is also provided.},
}
@article {pmid38220760,
year = {2023},
author = {Yuan, ZM and Jiang, W and Sha, ZL},
title = {A new species of the coral-symbiont crab genus Cymo de Haan, 1833 (Decapoda, Brachyura, Xanthidae) from Nansha Islands, the South China Sea.},
journal = {Zootaxa},
volume = {5361},
number = {2},
pages = {275-286},
doi = {10.11646/zootaxa.5361.2.8},
pmid = {38220760},
issn = {1175-5334},
mesh = {Animals ; *Brachyura ; *Anthozoa ; Animal Shells ; DNA, Mitochondrial/genetics ; China ; },
abstract = {A new species of coral-symbiont crab, Cymo mazu sp. nov., is described from the Nansha Islands in the South China Sea. The new species is distinguished from its congeners by several unique morphological characteristics, including a smooth carapace armed with isolated spiny granules, chelipeds featuring large spines and granules, and a strongly concave endopodite of the first maxilliped. Molecular analysis using mitochondrial cytochrome oxidase I DNA barcodes provides further support for the identification of the new species. The relationships between the new species and its congeners were elucidated through a combination of morphological and molecular evidence. Diagnostic characteristics for differentiation among species of Cymo are discussed, and an updated key to the species of the genus is provided.},
}
@article {pmid38220746,
year = {2023},
author = {Zlatkov, B and Huemer, P},
title = {Eucosma subvittana (Staudinger 1892) stat. rev., a Mediterranean species resurrected by DNA barcodes and morphology (Lepidoptera, Tortricidae).},
journal = {Zootaxa},
volume = {5361},
number = {4},
pages = {451-462},
doi = {10.11646/zootaxa.5361.4.1},
pmid = {38220746},
issn = {1175-5334},
mesh = {Female ; Male ; Animals ; *Lepidoptera/genetics ; DNA Barcoding, Taxonomic ; *Moths ; Genitalia ; Genitalia, Female ; },
abstract = {Eucosma subvittana is resurrected from synonymy with E. cana (Haworth, 1811) and redescribed from extensive material collected in Greece (Crete) and Tunisia. It is distinguished from the similar E. cana by constant differences in wing pattern and the female genitalia, whereas the male genitalia are inseparable. A lectotype of E. subvittana is designated in order to fix the identity of this species. Adults and genitalia of both species are figured extensively. Furthermore, the DNA barcodes (cytochrome c-oxidase subunit 1) of both species are clearly divergent. In comparison, several cryptic taxa of related species-groups are genetically inseparable.},
}
@article {pmid38220743,
year = {2023},
author = {Zahniser, JN and Halbert, SE and Moore, MR and Mottern, JL and Beuzelin, JM},
title = {Balclutha jafara (Hemiptera: Cicadellidae): integrative identification of a species introduced in the Western Hemisphere, and notes on other Balclutha.},
journal = {Zootaxa},
volume = {5361},
number = {4},
pages = {526-554},
doi = {10.11646/zootaxa.5361.4.4},
pmid = {38220743},
issn = {1175-5334},
mesh = {Animals ; *Hemiptera ; Phylogeny ; *Oryza ; *Magnoliopsida ; },
abstract = {Leafhopper specimens of the genus Balclutha Kirkaldy, found in southern Florida (Palm Beach and Collier Counties), United States, beginning in 2020, and in shipments of plant products originating from Colombia and entering the United States beginning in 2019, are identified as B. jafara Webb. This species was previously known only from the Seychelles and Aldabra Islands, which are parts of the Seychelles archipelago in the Indian Ocean east of mainland Africa. Identifications were made by comparison with type specimens, both morphologically and through molecular analysis. Specimens in Palm Beach Co. were swept from commercial rice (Oryza sativa L.) paddies. Mitochondrial cytochrome c oxidase I (COI) barcodes of specimens from Florida and Colombia were closely matched to each other and to partial barcodes obtained from paratype specimens of B. jafara. The COI barcodes also closely matched sequences from previously unidentified Balclutha specimens in the Barcode of Life Data Systems (BOLD) from Kenya and South Africa, several of which were confirmed later morphologically as B. jafara. Previously unidentified museum specimens from South Sudan, Zambia, and Zimbabwe were determined as B. jafara. Together, these specimens show that B. jafara has a more widespread African distribution than was known previously, and that it arrived in the Western Hemisphere by 2019. Balclutha jafara is redescribed and illustrated. Further studies on the Balclutha fauna of Florida were performed. COI barcode data were generated for Floridian specimens of B. caldwelli Blocker, B. curvata Caldwell, B. flavescens (Baker), B. frontalis (Ferrari), B. incisa (Matsumura), and B. lucida (Butler). A phylogenetic analysis of COI data was conducted using publicly available sequences and those generated here. A key to the Balclutha species known from Florida is provided. The names that have been applied and mis-applied to Western Hemisphere species are discussed. To clarify the identity of some species, illustrations are given for: the female holotype and a male paratype of Eugnathodus virescens Osborn (=B. flavescens); the holotype of Nesosteles robustus Caldwell (=B. robusta); and the holotype of Balclutha curvata Caldwell. Additional barcoded specimens of Balclutha from Kenya and Pakistan were provided for examination by the BOLD research group and determined as B. sujawalensis Ahmed, previously known only from India and Pakistan, and this species is also illustrated here.},
}
@article {pmid38220708,
year = {2023},
author = {Huemer, P and Karsholt, O},
title = {Klimeschiopsis terroris auctt. from Spaina further case of cryptic diversity in European Lepidoptera (Lepidoptera, Gelechiidae, Gelechiinae).},
journal = {Zootaxa},
volume = {5369},
number = {3},
pages = {400-412},
doi = {10.11646/zootaxa.5369.3.4},
pmid = {38220708},
issn = {1175-5334},
mesh = {Female ; Male ; Animals ; *Lepidoptera ; Animal Distribution ; Genitalia ; *Moths/genetics ; },
abstract = {A new species of Gnorimoschemini (Gelechiidae), Klimeschiopsis arnoldfransorum sp. nov., is described from specimens collected in Spain. The species is most closely related to Klimeschiopsis terroris (Hartig, 1938), with which it was hitherto mixed, but differs particularly by its small size with reduced yellowish-white forewing markings, the characters of the male and female genitalia, and the highly divergent DNA barcode (cytochrome c-oxidase subunit 1). Adult and genitalia of both sexes are figured. Finally, a checklist of the genus is provided.},
}
@article {pmid38220653,
year = {2023},
author = {Liu, S and Liu, T and Yu, J and Xu, J and Teng, K},
title = {The leaf-mining genus Lyonetia Hbner from China, with descriptions of two new species (Lepidoptera: Yponomeutoidea: Lyonetiidae).},
journal = {Zootaxa},
volume = {5357},
number = {1},
pages = {100-120},
doi = {10.11646/zootaxa.5357.1.4},
pmid = {38220653},
issn = {1175-5334},
mesh = {Female ; Animals ; *Lepidoptera ; *Moths ; China ; Plants ; Genitalia ; Animal Distribution ; },
abstract = {So far, only five species of the genus Lyonetia Hbner, 1825 have been recorded in China. In this paper, we describe two new species: L. (Lyonetiola) blasta T. Liu, sp. n., and L. (Lyonetiola) duplistriata T. Liu, sp. n., and report a newly recorded species, L. (Lyonetia) ledi Wocke, 1859 from China. Autumnal forms, manifesting darker forewings, of L. (Lyonetia) clerkella (Linnaeus, 1758) were collected from Xizang at an altitude of 3650 m in summer. The distribution and host plants of L. (Lyonetia) clerkella (Linnaeus, 1758) and L. (Lyonetia) prunifoliella (Hbner, 1796) in China are summarized. Photos of adults, male and female genitalia are provided. Host plants, leaf mines and DNA barcodes are also provided when available.},
}
@article {pmid38220649,
year = {2023},
author = {Makarchenko, EA and Semenchenko, AA},
title = {Morphological redescription and DNA barcoding of Diamesa parancysta Serra-Tosio (Diptera: Chironomidae: Diamesinae).},
journal = {Zootaxa},
volume = {5357},
number = {1},
pages = {144-150},
doi = {10.11646/zootaxa.5357.1.8},
pmid = {38220649},
issn = {1175-5334},
mesh = {Animals ; *Diptera/genetics ; *Chironomidae/genetics ; DNA Barcoding, Taxonomic ; Larva/anatomy &amp; histology ; DNA ; },
}
@article {pmid38220630,
year = {2023},
author = {Huang, SY and Hou, YX and Zhu, LJ and Chen, LS},
title = {First record of the family Neopseustidae from Yunnan, China with description of a new species (Lepidoptera, Neopseustidae).},
journal = {Zootaxa},
volume = {5357},
number = {4},
pages = {587-594},
doi = {10.11646/zootaxa.5357.4.6},
pmid = {38220630},
issn = {1175-5334},
mesh = {Animals ; *Lepidoptera ; China ; Genitalia ; Phylogeny ; },
abstract = {The family Neopseustidae is reported from Yunnan Province, Southwest China, for the first time, with a new species, N. gaoligongensis Huang &amp; Chen, sp. n., described from Mt. Gaoligong, West Yunnan, based on molecular and morphological evidence. The new species was found to belong to the N. bicornuta species-group and is closely related to N. fanjingshana Yang, 1988, but can be distinguished from it by the differences in morphology and a 3.2% COI distance. Adults and genitalia of the new species and N. fanjingshana are illustrated, and the molecular phylogeny based on COI barcoding of the genus Neopseustis is also updated.},
}
@article {pmid38220627,
year = {2023},
author = {Wanke, D and Hausmann, A and Lee, KM and Murillo-Ramos, L and Sihvonen, P and Rajaei, H},
title = {Systematics and integrative taxonomic revision of the tribe Scopulini Duponchel, 1845 in Iran (Lepidoptera: Geometridae: Sterrhinae).},
journal = {Zootaxa},
volume = {5359},
number = {1},
pages = {1-96},
doi = {10.11646/zootaxa.5359.1.1},
pmid = {38220627},
issn = {1175-5334},
mesh = {Female ; Male ; Animals ; *Lepidoptera ; Iran ; Animal Distribution ; Genitalia ; Mitochondria ; *Moths/genetics ; },
abstract = {The Iranian taxa of the tribe Scopulini are taxonomically revised. The systematic positions of the genera Cinglis Guene, 1858, Glossotrophia Prout, 1913, Pseudocinglis Hausmann, 1994 and Scopuloides Hausmann, 1994, with uncertain validity and/or position within the tribe Scopulini Duponchel, 1845 (Lepidoptera: Sterrhinae), are further elucidated by use of one mitochondrial and up to nine protein-coding nuclear gene regions. Available type specimens of the described species and more than 2,600 additional specimens were morphologically investigated. In addition, over 400 genitalia preparations were made and examined together with distribution data and DNA barcodes. As a result of the multi-gene analysis, the genera Cinglis stat. rev. and Scopuloides stat. rev. are re-validated at the genus level. The genus Pseudocinglis syn. nov. is regarded as a junior synonym of the genus Cinglis stat. rev. and Glossotrophia syn. nov. is regarded as a junior synonym of the genus Scopula. Cinglis eurata (Prout, 1913) comb. nov. and Cinglis benigna (Brandt, 1941) comb. nov. are combined with the genus Cinglis. Additionally, Cinglis benigna amseli (Wiltshire, 1967) syn. nov. is regarded as a synonym of C. benigna. Scopula adulteraria (Erschov, 1874) stat. nov. is raised from subspecies to species rank; Scopula iranaria Bytinski-Salz &amp; Brandt, 1937 syn. nov. is synonymized with S. flaccidaria (Zeller, 1852); S. transcaspica taftanica Brandt, 1941 syn. nov. is synonymized with S. transcaspica Prout, 1935; S. diffinaria asiatica (Brandt, 1938) syn. nov. is synonymized with S. diffinaria (Prout, 1913) and Glossotrophia bullata Vojnits, 1986 syn. nov. is synonymized with Scopula sacraria ariana (Ebert, 1965). The female genitalia of Scopula lactarioides Brandt, 1941 are described and illustrated for the first time. In total, the presence of 33 species of Scopulini in Iran is confirmed. Wing patterns, male and female genitalia and diagnostic characters of most Iranian Scopulini species are depicted and their distribution ranges are mapped.},
}
@article {pmid38220624,
year = {2023},
author = {Bang, WJ and Shin, S},
title = {A new species of the Chaoborus flavicans complex (Diptera, Chaoboridae) in South Korea.},
journal = {Zootaxa},
volume = {5360},
number = {1},
pages = {57-81},
doi = {10.11646/zootaxa.5360.1.3},
pmid = {38220624},
issn = {1175-5334},
mesh = {Animals ; *Diptera/genetics ; Larva/genetics ; Republic of Korea ; },
abstract = {Using reverse taxonomy and morphological analyses, this study describes a new species belonging to the C. flavicans species complex in the Korean Peninsula, Chaoborus pseudoflavicans Bang &amp; Shin sp. nov. Descriptions of the new species from larvae to adults are provided, and the key to the C. flavicans species complex is updated accordingly. DNA barcodes (COI partial sequences) are shown to be sufficient for molecular identification in the C. flavicans species complex. Finally, the taxonomic accounts of all species in the C. flavicans complex are completely resolved for the first time.},
}
@article {pmid38220615,
year = {2023},
author = {Kovai, M and Ztrk, DS and Innal, D},
title = {The morphology and mitochondrial DNA barcode of Knipowitschia caucasica (Berg, 1916) (Gobiiformes: Gobiidae) from Karpuzay, Levantine Sea, the easternmost record of Knipowitschia species in the Mediterranean Sea.},
journal = {Zootaxa},
volume = {5360},
number = {2},
pages = {219-238},
doi = {10.11646/zootaxa.5360.2.3},
pmid = {38220615},
issn = {1175-5334},
mesh = {Humans ; Animals ; *DNA, Mitochondrial/genetics ; Mediterranean Sea ; *Perciformes/genetics ; Fishes/genetics ; Phylogeny ; },
abstract = {Knipowitschia is a sand-goby genus historically comprising 17 species. The congeneric Knipowitschia species show discordance between morphology and genetics in two ways: the morphologically similar species that are clearly distinct by genetics and the morphologically and ecologically distinct populations that are similar by genetics. A sample of Knipowitschia individuals has been collected from Karpuzay Creek on the Levantine Sea coast. It is the easternmost Mediterranean record of any Knipowitschia, and a number of arguments suggest it is native. Among the presently valid Knipowitschia species, the population was identified by both genetics and morphology as K. caucasica. The detailed morphological description and genetics are provided for this population. The morphology of the present sample fits within the highly variable morphology of east Aegean populations presently recognized as K. caucasica, although with the extreme values of the already known morphological and coloration variability.},
}
@article {pmid38220607,
year = {2023},
author = {Luo, HR and Kong, XY and Munroe, TA},
title = {Re-evaluation of the taxonomic status of four nominal, western Pacific species of tongue soles (Pleuronectoidei: Cynoglossidae: Cynoglossus), with redescription of C. joyneri Gnther, 1878.},
journal = {Zootaxa},
volume = {5360},
number = {3},
pages = {385-408},
doi = {10.11646/zootaxa.5360.3.3},
pmid = {38220607},
issn = {1175-5334},
mesh = {Animals ; *DNA, Mitochondrial ; *Fishes ; },
abstract = {Striking similarities in morphological characters and significant overlap in meristic features have resulted in different hypotheses regarding the taxonomic status of several nominal species of northwestern Pacific tongue soles of the genus Cynoglossus, including C. joyneri Gnther, 1878, C. lighti Norman, 1925, C. tenuis (Oshima, 1927), and C. tshusanensis Chabanaud, 1951. Previous hypotheses have proposed that each taxon is a valid species; or that C. lighti and C. tshusanensis are junior subjective synonyms of C. joyneri; or that C. tenuis is a junior subjective synonym of either C. joyneri or C. lighti. Although several previous investigations concluded that C. lighti is a synonym of C. joyneri, names of both nominal species still appear in contemporary literature indicating that taxonomic status of these nominal species remains unresolved. To clarify the taxonomic status of these four nominal species, detailed study of morphological characters of 138 specimens collected from 22 localities in Japan and China, and re-examination of type specimens of three of these nominal species was conducted. The molecular barcodes of mitochondrial DNA from six representative specimens featuring morphological variation purportedly useful for distinguishing C. lighti from C. joyneri were also analyzed and then compared with sequences reported for C. joyneri in the literature. Lectotypes of C. joyneri and C. lighti differed in only two morphological characters (body depth and position of posterior tip of rostral hook relative to anterior margin of lower eye). However, when these two characters were examined in 138 recently collected non-type specimens, no differences were found among these nominal species. Our results do not support recognizing these as separate species. Results from genetic analyses also support recognizing only a single species among the material examined. Furthermore, overall similarities in morphological features between the holotype of C. tshusanensis and specimens of C. joyneri support recognizing C. tshusanensis as a junior subjective synonym of C. joyneri. Likewise, values for morphological features of C. joyneri examined in the present study also encompass the range of values reported in the original description of C. tenuis. This finding supports conclusions of previous studies that this nominal species is also a junior synonym of C. joyneri. Based on morphological and genetic evidence, we conclude that only a single species, C. joyneri, should be recognized among the four nominal species included in this study. Cynoglossus joyneri is re-described based on data from 492 specimens collected throughout nearly the entire range of the species.},
}
@article {pmid38218052,
year = {2024},
author = {Halvarsson, P and Grandi, G and Hägglund, S and Höglund, J},
title = {Gastrointestinal parasite community structure in horses after the introduction of selective anthelmintic treatment strategies.},
journal = {Veterinary parasitology},
volume = {326},
number = {},
pages = {110111},
doi = {10.1016/j.vetpar.2023.110111},
pmid = {38218052},
issn = {1873-2550},
mesh = {Horses ; Animals ; *Parasites ; *Strongyle Infections, Equine/drug therapy/epidemiology/parasitology ; *Anthelmintics/therapeutic use ; Strongyloidea/genetics ; Strongylus ; Feces/parasitology ; Larva ; *Intestinal Diseases, Parasitic/veterinary ; *Horse Diseases/drug therapy/epidemiology/parasitology ; Parasite Egg Count/veterinary ; },
abstract = {A relatively new method to study the species richness and diversity of nematode parasites in grazing animals is to perform deep sequencing on composite samples containing a mixture of parasites. In this work, we compared species composition of strongyles in two groups of horses as a function of egg count and age, based on a DNA barcoding approach. Faecal egg counts and larval cultures were obtained from nearly 300 horses, i.e., domestic horses (n = 167) and trotters (n = 130) sampled nationwide. The second internal transcribed spacer region (ITS2) of strongyle nematodes in the larval cultures was first amplified using barcoded universal primers and then sequenced on the PacBio platform. Subsequently, bioinformatic sequence analysis was performed using SCATA to assign operational taxonomic units (OTU). Finally, species occurrence and composition were assessed using R. ITS2 sequences were found in the majority (89%) of larval samples. Sequencing yielded an average of 140 (26 to 503) reads per sample. The OTUs were assigned to 28 different taxa, of which all but three could be identified as species. The average relative abundance of the seven most abundant species (all Cyathostominae) accounted for 87% of the combined data set. The three species with the highest prevalence in both horse groups were Cyathostomum catinatum, Cylicocyclus nassatus and Cylicostephanus calicatus, and they were frequently found in different combinations with other species regardless of horse group. Interestingly, this result is largely consistent with a previous Swedish study based on morphological analysis of adult worms. In addition, two migratory strongylids (Strongylus vulgaris and S. edentatus) occurred in few domestic horses and trotters. Except for C. minutus and C. nassatus, which decreased with age, and C. catinatum and S. vulgaris, which increased, no specific trends were observed with respect to horse age. Taken together, these results are broadly consistent with data obtained before the introduction of selective targeted treatment in Sweden in 2007. All in all, our results suggest that this treatment strategy has not led to a significant change in strongyle nematode community structure in Swedish horses. The study also confirms that nemabiome analysis in combination with diversity index analysis is an objective method to study strongyle communities in horses.},
}
@article {pmid38215838,
year = {2024},
author = {Nicolosi Gelis, MM and Canino, A and Bouchez, A and Domaizon, I and Laplace-Treyture, C and Rimet, F and Alric, B},
title = {Assessing the relevance of DNA metabarcoding compared to morphological identification for lake phytoplankton monitoring.},
journal = {The Science of the total environment},
volume = {914},
number = {},
pages = {169774},
doi = {10.1016/j.scitotenv.2023.169774},
pmid = {38215838},
issn = {1879-1026},
mesh = {*Phytoplankton/genetics ; Lakes ; DNA Barcoding, Taxonomic ; Genetic Markers ; *Diatoms/genetics ; DNA ; },
abstract = {Phytoplankton is a key biological group used to assess the ecological status of lakes. The classical monitoring approach relies on microscopic identification and counting of phytoplankton species, which is time-consuming and requires high taxonomic expertise. High-throughput sequencing, combined with metabarcoding, has recently demonstrated its potential as an alternative approach for plankton surveys. Several studies have confirmed the relevance of the diatom metabarcoding approach to calculate biotic indices based on species ecology. However, phytoplankton communities have not yet benefited from such validation. Here, by comparing the results obtained with the two methods (molecular and microscopic counting), we evaluated the relevance of metabarcoding approach for phytoplankton monitoring by considering different metrics: alpha diversity, taxonomic composition, community structure and a phytoplankton biotic index used to assess the trophic level of lakes. For this purpose, 55 samples were collected in four large alpine lakes (Aiguebelette, Annecy, Bourget, Geneva) during the year 2021. For each sample, a metabarcoding analysis based on two genetic markers (16S and 23S rRNA) was performed, in addition to the microscopic count. Regarding the trophic level of lakes, significant differences were found between index values obtained with the two approaches. The main hypothesis to explain these differences comes from the incompleteness, particularly at the species level, of the barcode reference library for the two genetic markers. It is therefore necessary to complete reference libraries for using such species-based biotic indices with metabarcoding data. Besides this, species richness and diversity were higher in the molecular inventories than in the microscopic ones. Moreover, despite differences in taxonomic composition of the floristic lists obtained by the two approaches, their community structures were similar. These results support the possibility of using metabarcoding for phytoplankton monitoring but in a different way. We suggest exploring alternative approaches to index development, such as a taxonomy-free approach.},
}
@article {pmid38213823,
year = {2024},
author = {Booeshaghi, AS and Min, KHJ and Gehring, J and Pachter, L},
title = {Quantifying orthogonal barcodes for sequence census assays.},
journal = {Bioinformatics advances},
volume = {4},
number = {1},
pages = {vbad181},
pmid = {38213823},
issn = {2635-0041},
abstract = {SUMMARY: Barcode-based sequence census assays utilize custom or random oligonucloetide sequences to label various biological features, such as cell-surface proteins or CRISPR perturbations. These assays all rely on barcode quantification, a task that is complicated by barcode design and technical noise. We introduce a modular approach to quantifying barcodes that achieves speed and memory improvements over existing tools. We also introduce a set of quality control metrics, and accompanying tool, for validating barcode designs.<br><br>https://github.com/pachterlab/kb_python, https://github.com/pachterlab/qcbc.},
}
@article {pmid38213697,
year = {2023},
author = {Yarinich, LA and Ogienko, AA and Pindyurin, AV and Omelina, ES},
title = {Analysis of the transcriptional activity of model piggyBac transgenes stably integrated into different loci of the genome of CHO cells in the absence of selection pressure.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {27},
number = {7},
pages = {906-915},
doi = {10.18699/VJGB-23-105},
pmid = {38213697},
issn = {2500-0462},
abstract = {CHO cells are most commonly used for the synthesis of recombinant proteins in biopharmaceutical production. When stable producer cell lines are obtained, the locus of transgene integration into the genome has a great influence on the level of its expression. Therefore, the identification of genomic loci ensuring a high level of protein production is very important. Here, we used the TRIP assay to study the influence of the local chromatin environment on the activity of transgenes in CHO cells. For this purpose, reporter constructs encoding eGFP under the control of four promoters were stably integrated into the genome of CHO cells using the piggyBac transposon. Each individual transgene contained a unique tag, a DNA barcode, and the resulting polyclonal cell population was cultured for almost a month without any selection. Next, using the high-throughput sequencing, genomic localizations of barcodes, as well as their abundances in the population and transcriptional activities were identified. In total, ~640 transgenes more or less evenly distributed across all chromosomes of CHO cells were characterized. More than half of the transgenes were completely silent. The most active transgenes were identified to be inserted in gene promoters and 5' UTRs. Transgenes carrying Chinese hamster full-length promoter of the EF-1α gene showed the highest activity. Transgenes with a truncated version of the same promoter and with the mouse PGK gene promoter were on average 10 and 19 times less active, respectively. In total, combinations of genomic loci of CHO cells and transgene promoters that together provide different levels of transcriptional activity of the model reporter construct were described.},
}
@article {pmid38206671,
year = {2024},
author = {Piernas, C and Lee, C and Hobson, A and Harmer, G and Payne Riches, S and Noreik, M and Jebb, SA},
title = {A Behaviorally Informed Mobile App to Improve the Nutritional Quality of Grocery Shopping (SwapSHOP): Feasibility Randomized Controlled Trial.},
journal = {JMIR mHealth and uHealth},
volume = {12},
number = {},
pages = {e45854},
pmid = {38206671},
issn = {2291-5222},
mesh = {Adult ; Humans ; Feasibility Studies ; *Food ; *Mobile Applications ; *Nutritive Value ; Sodium Chloride, Dietary ; Sugars ; Supermarkets ; },
abstract = {BACKGROUND: Interventions targeting the nutritional quality of grocery shopping have the potential to help improve diet and health outcomes.<br><br>OBJECTIVE: This study aims to assess the feasibility and acceptability of receiving advice on healthier food purchases through SwapSHOP, a behaviorally informed smartphone app that allows users to scan barcodes of grocery products from the United Kingdom, providing nutritional information and personalized swap suggestions to encourage healthier purchases.<br><br>METHODS: We randomized adult volunteers in a 6-arm parallel-group controlled feasibility trial. Participants used the SwapSHOP app to record their grocery shopping during a 2-week run-in period and were individually randomized in a 3:1 ratio to either intervention or control arms within 3 strata related to a nutrient of concern of their choice: saturated fat (SFA), sugar, or salt. Participants randomized to the intervention received the SwapSHOP app with a healthier swap function, goal setting, and personalized feedback. Participants in the control group were instructed to use a simpler version of the app to log all their food purchases without receiving any guidance or advice. The primary outcome was the feasibility of progression to a full trial, including app use and follow-up rates at 6 weeks. The secondary outcomes included other feasibility outcomes, process and qualitative measures, and exploratory effectiveness outcomes to assess changes in the nutrient content of the purchased foods.<br><br>RESULTS: A total of 112 participants were randomized into 3 groups: SFA (n=38 intervention and n=13 control), sugar (n=40 intervention and n=15 control), and salt (n=5 intervention and n=1 control, not analyzed). The 2 progression criteria were met for SFA and sugar: 81% (30/37) and 87% (34/39) of intervention participants in the SFA and sugar groups, respectively, used the app to obtain healthier swaps, and 89% (68/76) of intervention participants and 96% (23/24) of control participants completed follow-up by scanning all purchases over the follow-up period. The process and qualitative outcomes suggested that the intervention was acceptable and has the potential to influence shopping behaviors. There were reductions of -0.56 g per 100 g (95% CI -1.02 to -0.19) in SFA and -1 g per 100 g (95% CI -1.97 to -0.03) in total sugars across all food purchases in the intervention groups.<br><br>CONCLUSIONS: People were willing to use the SwapSHOP app to help reduce sugar and SFA (but not salt) in their grocery shopping. Adherence and follow-up rates suggest that a full trial is feasible. Given the suggestive evidence indicating that the intervention resulted in reductions in sugars and SFA, a definitive trial is necessary to target improvements in health outcomes.<br><br>TRIAL REGISTRATION: International Standard Randomised Controlled Trial Number ISRCTN13022312; https://doi.org/10.1186/ISRCTN13022312.},
}
@article {pmid38206129,
year = {2024},
author = {Derelle, R and Verdonck, R and Jacob, S and Huet, M and Akerman, I and Philippe, H and Legrand, D},
title = {The macronuclear genomic landscape within Tetrahymena thermophila.},
journal = {Microbial genomics},
volume = {10},
number = {1},
pages = {},
pmid = {38206129},
issn = {2057-5858},
mesh = {*Tetrahymena thermophila/genetics ; Ecosystem ; Genomics ; Eukaryota ; Laboratories ; },
abstract = {The extent of intraspecific genomic variation is key to understanding species evolutionary history, including recent adaptive shifts. Intraspecific genomic variation remains poorly explored in eukaryotic micro-organisms, especially in the nuclear dimorphic ciliates, despite their fundamental role as laboratory model systems and their ecological importance in many ecosystems. We sequenced the macronuclear genome of 22 laboratory strains of the oligohymenophoran Tetrahymena thermophila, a model species in both cellular biology and evolutionary ecology. We explored polymorphisms at the junctions of programmed eliminated sequences, and reveal their utility to barcode very closely related cells. As for other species of the genus Tetrahymena, we confirm micronuclear centromeres as gene diversification centres in T. thermophila, but also reveal a two-speed evolution in these regions. In the rest of the genome, we highlight recent diversification of genes coding for extracellular proteins and cell adhesion. We discuss all these findings in relation to this ciliate's ecology and cellular characteristics.},
}
@article {pmid38203529,
year = {2023},
author = {Lu, Z and Lin, Q and Zhang, H},
title = {Characterization of the Complete Mitochondrial Genome of Agelas nakamurai from the South China Sea.},
journal = {International journal of molecular sciences},
volume = {25},
number = {1},
pages = {},
pmid = {38203529},
issn = {1422-0067},
support = {2021YFF0502803//National Key Research and Development Program of China/ ; 41825013, 41976116//National Natural Science Foundation of China/ ; 2021A1515011393//Guangdong Basic and Applied Basic Research Foundation/ ; },
mesh = {Animals ; *Agelas ; *Genome, Mitochondrial ; Phylogeny ; Bandages ; China ; },
abstract = {The Agelas genus sponges are widely distributed and provide shelter for organisms that inhabit reefs. However, there is a lack of research on the genetic diversity of the Agelas sponges. Additionally, only one Agelas mitochondrial genome has been documented, leaving the characteristics of the Agelas genus's mitogenome in need of further clarification. To address this research gap, we utilized Illumina HiSeq4000 sequencing and de novo assembly to ascertain the complete mitochondrial genome of Agelas sp. specimens, sourced from the South China Sea. Our analysis of the cox1 barcoding similarity and phylogenetic relationship reveals that taxonomically, the Agelas sp. corresponds to Agelas nakamurai. The mitogenome of Agelas nakamurai is 20,885 bp in length, encoding 14 protein-coding genes, 24 transfer RNA genes, and 2 ribosomal RNA genes. Through a comparison of the mitochondrial genes, we discovered that both Agelas nakamurai and Agelas schmidti have an identical gene arrangement. Furthermore, we observed a deletion in the trnD gene and duplication and remodeling of the trnL gene in the Agelas nakamurai's mitogenome. Our evolutionary analysis also identified lineage-specific positive selection sites in the nad3 and nad5 genes of the Agelas sponges' mitogenome. These findings shed light on the gene rearrangement events and positive selection sites in the mitogenome of Agelas nakamurai, providing valuable molecular insights into the evolutionary processes of this genus.},
}
@article {pmid38203355,
year = {2023},
author = {Zhou, CY and Lin, WJ and Li, R and Wu, Y and Liu, ZJ and Li, MH},
title = {Characterization of Angraecum (Angraecinae, Orchidaceae) Plastomes and Utility of Sequence Variability Hotspots.},
journal = {International journal of molecular sciences},
volume = {25},
number = {1},
pages = {},
pmid = {38203355},
issn = {1422-0067},
support = {XJQ202005//Outstanding Youth Scientific Fund of Fujian Agriculture and Forestry University/ ; 2021J01134//Nature Science Foundation of Fujian Province, China/ ; 72202200205//Forestry Peak Discipline Construction Project of Fujian Agriculture and Forestry University/ ; },
mesh = {*Orchidaceae/genetics ; Phylogeny ; Codon Usage ; Nucleotides ; Phototherapy ; },
abstract = {Angraecum, commonly known as Darwin's orchid, is the largest genus of Angraecinae (Orchidaceae). This genus exhibits a high morphological diversity, making it as a good candidate for macroevolutionary studies. In this study, four complete plastomes of Angraecum were firstly reported and the potential variability hotspots were explored. The plastomes possessed the typical quadripartite structure and ranged from 150,743 to 151,818 base pair (bp), with a guanine-cytosine (GC) content of 36.6-36.9%. The plastomes all contained 120 genes, consisting of 74 protein-coding genes (CDS), 38 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes; all ndh genes were pseudogenized or lost. A total of 30 to 46 long repeats and 55 to 63 SSRs were identified. Relative synonymous codon usage (RSCU) analysis indicated a high degree of conservation in codon usage bias. The Ka/Ks ratios of most genes were lower than 1, indicating that they have undergone purifying selection. Based on the ranking of Pi (nucleotide diversity) values, five regions (trnS[GCU]-trnG[GCC], ycf1-trnN[GGU], trnN[GUU]-rpl32, psaC-ndhE and trnS[GCU]-trnG[GCC]) and five protein-coding genes (rpl32, rps16, psbK, rps8, and ycf1) were identified. The consistent and robust phylogenetic relationships of Angraecum were established based on a total of 40 plastomes from the Epidendroideae subfamily. The genus Angraecum was strongly supported as a monophyletic group and sister to Aeridinae. Our study provides an ideal system for investigating molecular identification, plastome evolution and DNA barcoding for Angraecum.},
}
@article {pmid38203228,
year = {2023},
author = {Mshiywa, FM and Edwards, S and Bradley, G},
title = {Rhodophyta DNA Barcoding: Ribulose-1, 5-Bisphosphate Carboxylase Gene and Novel Universal Primers.},
journal = {International journal of molecular sciences},
volume = {25},
number = {1},
pages = {},
pmid = {38203228},
issn = {1422-0067},
mesh = {DNA Barcoding, Taxonomic ; DNA ; DNA Primers/genetics ; *Carboxy-Lyases ; *Rhodophyta/genetics ; *Seaweed ; *Pentoses ; },
abstract = {Red algae (Rhodophyta) are a heterogeneous group of marine algal species that have served as a source of high-value molecules, including antioxidants and scaffolds, for novel drug development. However, it is challenging to identify Rhodophytes through morphological features alone, and in most instances, that has been the prevailing approach to identification. Consequently, this study undertook the identification of red algae species in Kenton-on-Sea, South Africa, as a baseline for future research on red algae biodiversity and conservation. The identification was achieved by designing, analysing, and using a set of universal primers through DNA barcoding of the rbcL gene. The PCR products of the rbcL gene were sequenced, and 96% of the amplicons were successfully sequenced from this set and matched with sequences on BOLD, which led to these species being molecularly described. Amongst these species are medicinally essential species, such as Laurencia natalensis and Hypnea spinella, and potential cryptic species. This calls for further investigation into the biodiversity of the studied region. Meanwhile, the availability of these primers will ease the identification process of red algae species from other coastal regions.},
}
@article {pmid38201231,
year = {2023},
author = {Kim, IS},
title = {DNA Barcoding Technology for Lineage Recording and Tracing to Resolve Cell Fate Determination.},
journal = {Cells},
volume = {13},
number = {1},
pages = {},
pmid = {38201231},
issn = {2073-4409},
support = {NRF-2021R1A5A2030333//National Research Foundation of Korea/ ; SSTF-BA2102-08//Samsung Science and Technology Foundation/ ; },
mesh = {*DNA Barcoding, Taxonomic ; Phylogeny ; Cell Differentiation ; *DNA ; Technology ; },
abstract = {In various biological contexts, cells receive signals and stimuli that prompt them to change their current state, leading to transitions into a future state. This change underlies the processes of development, tissue maintenance, immune response, and the pathogenesis of various diseases. Following the path of cells from their initial identity to their current state reveals how cells adapt to their surroundings and undergo transformations to attain adjusted cellular states. DNA-based molecular barcoding technology enables the documentation of a phylogenetic tree and the deterministic events of cell lineages, providing the mechanisms and timing of cell lineage commitment that can either promote homeostasis or lead to cellular dysregulation. This review comprehensively presents recently emerging molecular recording technologies that utilize CRISPR/Cas systems, base editing, recombination, and innate variable sequences in the genome. Detailing their underlying principles, applications, and constraints paves the way for the lineage tracing of every cell within complex biological systems, encompassing the hidden steps and intermediate states of organism development and disease progression.},
}
@article {pmid38195805,
year = {2024},
author = {Shamsi, S and Nelson, L and Gordon, A and Markham, K and Francis, N and Suthar, J and Zhu, X},
title = {Multidisciplinary approach to the diagnosis of Contracaecum magnipapillatum infections in Australian black noddies, Anous minutus (Charadriiformes: Laridae).},
journal = {Parasitology research},
volume = {123},
number = {1},
pages = {90},
pmid = {38195805},
issn = {1432-1955},
mesh = {Animals ; *Charadriiformes ; Australia ; Birds ; *Ascaridoidea/genetics ; Queensland ; },
abstract = {We provide the incidental necropsy findings associated with anisakid nematode infections of black noddy terns, Anous minutus Boie, 1844 (Charadriiformes: Laridae), from offshore islands in the southern Great Barrier Reef, Queensland, Australia. Specimens collected from the proventriculi were identified morphologically as Contracaecum magnipapillatum Chapin, 1925 (Rhabditida: Anisakidae), using light and scanning electron microscopy (SEM). The entire nuclear ribosomal DNA internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) was amplified by polymerase chain reaction (PCR) and sequenced to provide reference sequences for morphologically well-identified voucher specimens. Interestingly, after an alignment with closely related taxa using BLAST, sequences of the ITS1 and ITS2 were 100% identical to the sequences assigned to Contracaecum septentrionale Kreis, 1955, from a razorbill, Alca torda Linnaeus, 1758 (Charadriiformes: Alcidae), from Spain. These results either raise questions about the ITS as a genetic marker for some members of Contracaecum, or the identity of the specimens assigned to C. septentrionale, given that no supporting morphological data was associated with them. We highlight the need for a combined morphological and molecular approach to parasite diagnostics and the use of multiple genetic loci to resolve the molecular taxonomy of cryptic species. Morphological identifications should be taxonomically robust, transparent and precede the deposition of molecular barcodes in public repositories. The gross and histopathological findings of our investigation concur with previous reports of widespread Contracaecum infections in black noddies and support the contention that Contracaecum spp. are an unlikely primary cause of mortality.},
}
@article {pmid38195670,
year = {2024},
author = {Jeon, J and Lee, DY and Jo, Y and Ryu, J and Kim, E and Choi, KS},
title = {Wing geometric morphometrics and COI barcoding of Culex pipiens subgroup in the Republic of Korea.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {878},
pmid = {38195670},
issn = {2045-2322},
support = {2020R1I1A2066186//National Research Foundation of Korea/ ; },
mesh = {Culex ; Republic of Korea ; Aedes ; *Mosquito Vectors ; Animals ; },
abstract = {Two members of the Culex pipiens subgroup, Culex pallens and Culex pipiens f. molestus, are known to occur in the Republic of Korea (ROK). These species exhibit morphologically similar features and are challenging to distinguish below the species level. Therefore, this study utilized wing geometric morphometrics (GM) on the right wing of the Culex pipiens subgroup, alongside sequencing of the cytochrome c oxidase subunit I (COI) region. Mosquitoes were collected from 11 locations between June and October (2020-2022) to minimize regional and seasonal variations. Additionally, Culex pipiens f. pipiens, which is not native to the ROK, was included in the analysis. Culex tritaeniorhynchus, Aedes albopictus, and Anopheles sinensis, the primary vectors in the ROK, were used as outgroups for comparison. All three taxa in the Culex pipiens subgroup could be identified with an 82.4%-97.0% accuracy using GM. However, a comparison of the COI regions of the Culex pipiens subgroup revealed no clear differences between the taxa. These data can be used for accurate identification, contributing to effective mosquito control, in addition to providing a foundation for evolutionary and ecological studies on wing shape differences.},
}
@article {pmid38195557,
year = {2024},
author = {Owens, LA and Friant, S and Martorelli Di Genova, B and Knoll, LJ and Contreras, M and Noya-Alarcon, O and Dominguez-Bello, MG and Goldberg, TL},
title = {VESPA: an optimized protocol for accurate metabarcoding-based characterization of vertebrate eukaryotic endosymbiont and parasite assemblages.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {402},
pmid = {38195557},
issn = {2041-1723},
support = {R01 AG049395/AG/NIA NIH HHS/United States ; R21 AI163592/AI/NIAID NIH HHS/United States ; R37 AG049395/AG/NIA NIH HHS/United States ; T32 AI007414/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; *Parasites/genetics ; *Wasps ; Archaea/genetics ; *Microbiota/genetics ; Vertebrates/genetics ; },
abstract = {Protocols for characterizing taxonomic assemblages by deep sequencing of short DNA barcode regions (metabarcoding) have revolutionized our understanding of microbial communities and are standardized for bacteria, archaea, and fungi. Unfortunately, comparable methods for host-associated eukaryotes have lagged due to technical challenges. Despite 54 published studies, issues remain with primer complementarity, off-target amplification, and lack of external validation. Here, we present VESPA (Vertebrate Eukaryotic endoSymbiont and Parasite Analysis) primers and optimized metabarcoding protocol for host-associated eukaryotic community analysis. Using in silico prediction, panel PCR, engineered mock community standards, and clinical samples, we demonstrate VESPA to be more effective at resolving host-associated eukaryotic assemblages than previously published methods and to minimize off-target amplification. When applied to human and non-human primate samples, VESPA enables reconstruction of host-associated eukaryotic endosymbiont communities more accurately and at finer taxonomic resolution than microscopy. VESPA has the potential to advance basic and translational science on vertebrate eukaryotic endosymbiont communities, similar to achievements made for bacterial, archaeal, and fungal microbiomes.},
}
@article {pmid38194998,
year = {2024},
author = {Min, Y and Deng, W and Yuan, H and Zhu, D and Zhao, R and Zhang, P and Xue, J and Yuan, Z and Zhang, T and Jiang, Y and Xu, K and Wu, D and Cai, Y and Suo, C and Chen, X},
title = {Single extracellular vesicle surface protein-based blood assay identifies potential biomarkers for detection and screening of five cancers.},
journal = {Molecular oncology},
volume = {18},
number = {3},
pages = {743-761},
pmid = {38194998},
issn = {1878-0261},
support = {2019FY101103//National Science &amp; Technology Fundamental Resources Investigation Program of China/ ; GWV-10.2-YQ32//Three-Year Action Plan for Strengthening Public Health System in Shanghai/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; 2017YFC0907000//National Key Research and Development Program of China/ ; 2019YFC1315804//National Key Research and Development Program of China/ ; 2022YFC3400700//National Key Research and Development Program of China/ ; 82073637//National Natural Science Foundation of China/ ; 82122060//National Natural Science Foundation of China/ ; 91846302//National Natural Science Foundation of China/ ; 20ZR1405600//Innovation Grant from Science and Technology Commission of Shanghai Municipality/ ; },
mesh = {Humans ; Early Detection of Cancer ; Membrane Proteins ; Case-Control Studies ; *Lung Neoplasms ; Biomarkers ; *Extracellular Vesicles ; Biomarkers, Tumor ; },
abstract = {Extracellular vesicles (EVs) and EV proteins are promising biomarkers for cancer liquid biopsy. Herein, we designed a case-control study involving 100 controls and 100 patients with esophageal, stomach, colorectal, liver, or lung cancer to identify common and type-specific biomarkers of plasma-derived EV surface proteins for the five cancers. EV surface proteins were profiled using a sequencing-based proximity barcoding assay. In this study, five differentially expressed proteins (DEPs) and eight differentially expressed protein combinations (DEPCs) showed promising performance (area under curve, AUC > 0.900) in pan-cancer identification [e.g., TENM2 (AUC = 0.982), CD36 (AUC = 0.974), and CD36-ITGA1 (AUC = 0.971)]. Our classification model could properly discriminate between cancer patients and controls using DEPs (AUC = 0.981) or DEPCs (AUC = 0.965). When distinguishing one cancer from the other four, the accuracy of the classification model using DEPCs (85-92%) was higher than that using DEPs (78-84%). We validated the performance in an additional 14 cancer patients and 14 controls, and achieved an AUC value of 0.786 for DEPs and 0.622 for DEPCs, highlighting the necessity to recruit a larger cohort for further validation. When clustering EVs into subpopulations, we detected cluster-specific proteins highly expressed in immune-related tissues. In the context of colorectal cancer, we identified heterogeneous EV clusters enriched in cancer patients, correlating with tumor initiation and progression. These findings provide epidemiological and molecular evidence for the clinical application of EV proteins in cancer prediction, while also illuminating their functional roles in cancer physiopathology.},
}
@article {pmid38194793,
year = {2024},
author = {Kompoura, V and Karapantzou, I and Mitropoulou, G and Parisis, NA and Gkalpinos, VK and Anagnostou, VA and Tsiailanis, AD and Vasdekis, EP and Koutsaliaris, IK and Tsouka, AN and Karapetsi, L and Madesis, P and Letsiou, S and Florou, D and Koukkou, AI and Barbouti, A and Tselepis, AD and Kourkoutas, Y and Tzakos, AG},
title = {Exploiting the beneficial effects of Salvia officinalis L. extracts in human health and assessing their activity as potent functional regulators of food microbiota.},
journal = {Food chemistry},
volume = {441},
number = {},
pages = {138175},
doi = {10.1016/j.foodchem.2023.138175},
pmid = {38194793},
issn = {1873-7072},
mesh = {Humans ; *Salvia officinalis/chemistry ; Hydrogen Peroxide ; Plant Extracts/chemistry ; Phytochemicals/analysis ; Antioxidants/chemistry ; },
abstract = {Salvia officinalis L. has attracted scientific and industrial interest due to its pharmacological properties. However, its detailed phytochemical profile and its correlation with beneficial effects in the human microbiome and oxidative stress remained elusive. To unveil this, S. officinalis was collected from the region of Epirus and its molecular identity was verified with DNA barcoding. Phytochemical profile for both aqueous and ethanol-based extracts was determined by high-pressure liquid chromatography-tandem mass spectrometry and 103 phytochemicals were determined. The effect of S. officinalis extracts as functional regulators of food microbiota by stimulating the growth of Lacticaseibacillus rhamnosus strains and by suppressing evolution of pathogenic bacteria was verified. Furthermore, we recorded that both extracts exhibited a significant cellular protection against H2O2-induced DNA damage. Finally, both extracts exhibited strong inhibitory effect towards LDL oxidation. This study provides a comprehensive characterization of S. officinalis on its phytochemical components as also its potential impact in human microbiome and oxidative stress.},
}
@article {pmid38192741,
year = {2023},
author = {Wang, Z and Liu, F and Shi, S and Xia, S and Peng, F and Wang, L and Ai, S and Xu, Z},
title = {Automatic epileptic seizure detection based on persistent homology.},
journal = {Frontiers in physiology},
volume = {14},
number = {},
pages = {1227952},
pmid = {38192741},
issn = {1664-042X},
abstract = {Epilepsy is a prevalent brain disease, which is quite difficult-to-treat or cure. This study developed a novel automatic seizure detection method based on the persistent homology method. In this study, a Vietoris-Rips (VR) complex filtration model was constructed based on the EEG data. And the persistent homology method was applied to calculate the VR complex filtration barcodes to describe the topological changes of EEG recordings. Afterward, the barcodes as the topological characteristics of EEG signals were fed into the GoogLeNet for classification. The persistent homology is applicable for multi-channel EEG data analysis, where the global topological information is calculated and the features are extracted by considering the multi-channel EEG data as a whole, without the multiple calculations or the post-stitching. Three databases were used to evaluate the proposed approach and the results showed that the approach had high performances in the epilepsy detection. The results obtained from the CHB-MIT Database recordings revealed that the proposed approach can achieve a segment-based averaged accuracy, sensitivity and specificity values of 97.05%, 96.71% and 97.38%, and achieve an event-based averaged sensitivity value of 100% with 1.22 s average detection latency. In addition, on the Siena Scalp Database, the proposed method yields averaged accuracy, sensitivity and specificity values of 96.42%, 95.23% and 97.6%. Multiple tasks of the Bonn Database also showed achieved accuracy of 99.55%, 98.63%, 98.28% and 97.68%, respectively. The experimental results on these three EEG databases illustrate the efficiency and robustness of our approach for automatic detection of epileptic seizure.},
}
@article {pmid38190930,
year = {2024},
author = {Almeida, CE and Máximo, MM and Pires-Silva, D and Takiya, DM and Valença-Barbosa, C and Viana, MC and Reigada, C and Iñiguez, AM and Harry, M and Folly-Ramos, E},
title = {From molecules to ecosystems: Insights into a network of interactions for a Chagas disease outbreak using Triatoma brasiliensis as natural samplers.},
journal = {Acta tropica},
volume = {251},
number = {},
pages = {107107},
doi = {10.1016/j.actatropica.2023.107107},
pmid = {38190930},
issn = {1873-6254},
mesh = {Humans ; Animals ; Cats ; *Triatoma/genetics/parasitology ; Ecosystem ; *Chagas Disease ; *Trypanosoma cruzi/genetics ; Disease Outbreaks ; Rodentia/parasitology ; *Didelphis/parasitology ; },
abstract = {Exploring the dynamics of disease transmission involves an understanding of complex interactions within the eco-epidemiologic framework. In the context of Chagas disease (CD), elements are mainly represented by the interactions among the pathogen, insect vector, host, humans and the environment. We performed quantitative and qualitative analyses on a dataset derived from 98 Triatoma brasiliensis infected by trypanosomatids, which were linked to a CD outbreak in the semi-arid region of northeastern Brazil. We extracted invertebrate-derived DNA (iDNA) from these insects, comprising 18 populations around the outbreak area, each indicative of various strata of anthropogenic influence. Food source (FS) diversity, representing potential parasite reservoirs, was determined through mitochondrial gene (cyt b) sequencing of vertebrates, and parasite genotyping was accessed using fluorescent amplified fragment barcodes (FFLB) of trypanosomatids. We also assessed the residents' awareness of breeding sites for CD vectors in the inspected houses. The quantification of Trypanosoma cruzi was estimated via real-time PCR and is denominated here as the average parasite load (PL) per insect (T. cruzi/intestinal unit). We aimed to address vector-parasite-host-environment interactions that were discussed based on their significance among the components. Notably, among the significant interactions, we observed that the PL in the insects was significantly influenced by FS. Infected insects that fed on the classic reservoir, Didelphis albiventris, and Galea spixii exhibited higher PLs, compared to those that fed on Kerodon rupestris (p < 0.04)-a primary host. While D. albiventris is already recognized as a synanthropic species, we propose that G. spixii may also be undergoing a synanthropic process. Conversely, domestic cats are frequently identified as FS in infected insects from the sylvatic environment, suggesting a possible change in their behavior towards a wild state. Therefore, we propose that neglected anthropogenic actions have facilitated the reciprocal (sylvatic-peridomestic) circulation of T. cruzi-especially noted for TcI because it was predominant in insects found in peridomestic environments. Residents are often unaware of the existence of insect breeding grounds near their homes, particularly when it involves the storage of materials without planning for use, such as piles of tiles, bricks and wood. Although indirect inferences about the interaction among vector-parasite-host-environment are still incipient, we highlight the potential use of vectors as natural samplers of biological and ecological components in transmitting the disease.},
}
@article {pmid38189499,
year = {2023},
author = {Moraes Cabé, C and Novault, S and Jeemin Choi, A and Seffer, V and Barrio Cano, L and Libri, V and Hasan, M},
title = {High-Quality Brain and Bone Marrow Nuclei Preparation for Single Nuclei Multiome Assays.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {202},
pages = {},
doi = {10.3791/65715},
pmid = {38189499},
issn = {1940-087X},
mesh = {*Bone Marrow ; *Brain ; Cell Nucleus ; RNA, Small Nuclear ; Biological Assay ; },
abstract = {Single-cell analysis has become the approach of choice for unraveling the complexity of biological processes that require assessing the variability of individual cellular responses to treatment or infection with single-cell resolution. Many techniques for single-cell molecular profiling have been developed over the past 10 years, and several dedicated technologies have been commercialized. The 10X Genomics droplet-based single-cell profiling is a widespread technology that offers ready-to-use reagents for transcriptomic and multi-omic single-cell profiling. The technology includes workflows for single-cell and single-nuclei RNA sequencing (scRNA-Seq and snRNA-Seq, respectively), scATAC-Seq, single-cell immune profiling (BCR/TCR sequencing), and multiome. The latter combines transcriptional (scRNA-Seq) and epigenetic information (scATAC-Seq) coming from the same cell. The quality (viability, integrity, purity) of single-cell or single-nuclei suspensions isolated from tissues and analyzed by any of these approaches is critical for generating high-quality data. Therefore, the sample preparation protocols should be adapted to the particularities of each biological tissue and ensure the generation of high-quality cell and nuclei suspensions. This article describes two protocols for preparing brain and bone marrow samples for the downstream multiome 10X Genomics pipeline. The protocols are performed stepwise and cover tissue dissociation, cell sorting, nuclei isolation, and quality control of prepared nuclei suspension that is used as starting material for cell partitioning and barcoding, library preparation, and sequencing. These standardized protocols produce high-quality nuclei libraries and robust and reliable data.},
}
@article {pmid38188538,
year = {2024},
author = {Salam, MR and Ezaouine, A and Zekhnini, H and El Messal, M and El Mellouli, F and Chegdani, F and Bennis, F},
title = {Morphological, molecular identification and evaluation of antioxidant activity of seahorses from the Moroccan coasts.},
journal = {Saudi journal of biological sciences},
volume = {31},
number = {2},
pages = {103898},
pmid = {38188538},
issn = {1319-562X},
abstract = {Seahorses, part of the small marine teleost fish family Syngnathidae, are increasingly under threat due to habitat degradation and overfishing. Notably used in traditional Chinese medicine, these fish have demonstrated significant pharmacological and cosmetic properties. In Morocco, however, seahorses are minimally exploited. This study aims to explore the biodiversity of Moroccan seahorses, focusing on identifying species from the Atlantic and Mediterranean coasts both morphologically and molecularly, and evaluating their antioxidant activity. The research involved collecting 62 dried seahorses from local fishermen. These specimens were subjected to detailed morphological and molecular identification through the DNA barcoding method, concentrating on the mitochondrial marker Cytochrome Oxidase I (COI) gene. Following DNA extraction and amplification, the sequences were analyzed for species identification and phylogenetic relationships. Additionally, the antioxidant activities of the seahorses were quantified using assays such as ABTS, reducing power, phosphomolybdenum, and β-carotene-linoleic acid. The combined morphological and molecular analyses consistently identified all specimens as Hippocampus hippocampus, and phylogenetic trees suggested a close relation with European and Turkish counterparts. Furthermore, the antioxidant assays revealed significant activity, with the ABTS assay showing an IC50 of 14.571 mg/mL ± 0.334, and the β-carotene-linoleic acid assay showing an IC50 of 1.273 mg/mL ± 0.166. The reducing power and phosphomolybdenum assays recorded EC50 values of 1.868 mg/mL ± 0.033 and 1.156 mg/mL ± 0.112, respectively. These results confirm the high antioxidant potential of Moroccan seahorses, suggesting their therapeutic value and necessitating measures for their biodiversity preservation at a national level.},
}
@article {pmid38188178,
year = {2024},
author = {Selena Shen, KL and Cheow, JJ and Cheung, AB and Koh, RJR and Koh Xiao Mun, A and Lee, YN and Lim, YZ and Namatame, M and Peng, E and Vintenbakh, V and Lim, EXY and Wainwright, BJ},
title = {DNA barcoding continues to identify endangered species of shark sold as food in a globally significant shark fin trade hub.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e16647},
pmid = {38188178},
issn = {2167-8359},
mesh = {Animals ; *Endangered Species ; *Sharks/genetics ; Conservation of Natural Resources ; DNA Barcoding, Taxonomic ; Fisheries ; Seafood ; DNA ; Heavy Metal Poisoning ; },
abstract = {Shark fins are a delicacy consumed throughout Southeast Asia. The life history characteristics of sharks and the challenges associated with regulating fisheries and the fin trade make sharks particularly susceptible to overfishing. Here, we used DNA barcoding techniques to investigate the composition of the shark fin trade in Singapore, a globally significant trade hub. We collected 505 shark fin samples from 25 different local seafood and Traditional Chinese Medicine shops. From this, we identified 27 species of shark, three species are listed as Critically Endangered, four as Endangered and ten as Vulnerable by the International Union for Conservation of Nature (IUCN). Six species are listed on CITES Appendix II, meaning that trade must be controlled in order to avoid utilization incompatible with their survival. All dried fins collected in this study were sold under the generic term "shark fin"; this vague labelling prevents accurate monitoring of the species involved in the trade, the effective implementation of policy and conservation strategy, and could unwittingly expose consumers to unsafe concentrations of toxic metals. The top five most frequently encountered species in this study are Rhizoprionodon acutus, Carcharhinus falciformis, Galeorhinus galeus, Sphyrna lewini and Sphyrna zygaena. Accurate labelling that indicates the species of shark that a fin came from, along with details of where it was caught, allows consumers to make an informed choice on the products they are consuming. Doing this could facilitate the avoidance of species that are endangered, and similarly the consumer can choose not to purchase species that are documented to contain elevated concentrations of toxic metals.},
}
@article {pmid38184675,
year = {2024},
author = {So, WL and Chong, TK and Lee, IHT and So, MTW and Liu, AMY and Leung, STC and Ching, W and Yip, HY and Shaw, PC and Hui, JHL},
title = {Cytochrome oxidase I DNA barcodes of crocodilians meat selling in Hong Kong.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {46},
pmid = {38184675},
issn = {2052-4463},
mesh = {Animals ; *Alligators and Crocodiles/genetics ; DNA ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Hong Kong ; *Meat ; Phylogeny ; },
abstract = {The crocodilians include true crocodiles, alligators, caimans, and gharial, and the trade of crocodilian products is regulated in accordance with the Convention of Wild Fauna and Flora (CITES). Hong Kong does not have her own wild crocodilians; thus, all crocodilians meat available is presumably imported with proper license. Here, we obtained a dataset of cytochrome oxidase I (COI) gene markers of 114 crocodilian meat samples (including frozen and dried crocodilian meat products) available in the contemporary market. We have also validated these barcodes in a phylogenetic approach with other data deposited on the GenBank, and detected 112 samples belonging to four crocodile species Crocodylus siamensis, C. porosus, C. niloticus and Alligator mississippiensis, and 2 samples belonging to snake Malayopython reticulatus. The dataset generated in this study will be useful for further studies including meat inspection, illegal trading, and enhancement of international and local legislations on illegal reptile importation.},
}
@article {pmid38184292,
year = {2024},
author = {Matute, DR and Cooper, BS},
title = {Aedes albopictus is present in the lowlands of southern Zambia.},
journal = {Acta tropica},
volume = {251},
number = {},
pages = {107115},
pmid = {38184292},
issn = {1873-6254},
support = {R35 GM124701/GM/NIGMS NIH HHS/United States ; R35 GM148244/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Animals ; Zambia ; *Aedes/genetics ; *Chikungunya Fever ; Mozambique ; *Zika Virus ; *Zika Virus Infection ; Mosquito Vectors/genetics ; },
abstract = {Identifying the current geographic range of disease vectors is a critical first step towards determining effective mechanisms for controlling and potentially eradicating them. This is particularly true given that historical vector ranges may expand due to changing climates and human activity. The Aedes subgenus Stegomyia contains over 100 species, and among them, Ae. aegypti and Ae. albopictus mosquitoes represent the largest concern for public health, spreading dengue, chikungunya, and zika viruses. While Ae. aegypti has been observed in the country of Zambia for decades, Ae. albopictus has not. In 2015 we sampled four urban and three rural areas in Zambia for Aedes species. Using DNA barcoding, we confirmed the presence of immature and adult Ae. albopictus at two sites: Siavonga and Livingstone. These genotypes seem most closely related to specimens previously collected in Mozambique based on mtDNA barcoding. We resampled Siavonga and Livingstone sites in 2019, again observing immature and adult Ae. albopictus at both sites. Relative Ae. albopictus frequencies were similar between sites, with the exception of immature life stages, which were higher in Siavonga than in Livingstone in 2019. While Ae. albopictus frequencies did not vary through time in Livingstone, both immature and adult frequencies increased through time in Siavonga. This report serves to document the presence of Ae. albopictus in Zambia, which will contribute to understanding the potential public health implications of this disease vector in southern Africa.},
}
@article {pmid38181517,
year = {2024},
author = {Zhao, X and Xu, Y and Chen, Z and Tang, C and Mi, X},
title = {Encoding fluorescence intensity with tetrahedron DNA nanostructure based FRET effect for bio-detection.},
journal = {Biosensors &amp; bioelectronics},
volume = {248},
number = {},
pages = {115994},
doi = {10.1016/j.bios.2023.115994},
pmid = {38181517},
issn = {1873-4235},
mesh = {Fluorescence Resonance Energy Transfer/methods ; *Biosensing Techniques ; DNA/chemistry ; *MicroRNAs/analysis ; *Nanostructures ; Biomarkers ; *Carbocyanines ; },
abstract = {Biocoding technology constructed by readable tags with distinct signatures is a brand-new bioanalysis method to realize multiplexed identification and bio-information decoding. In this study, a novel fluorescence intensity coding technology termed Tetra-FICT was reported based on tetrahedron DNA nanostructure (TDN) carrier and Főrster Resonance Energy Transfer (FRET) effect. By modulating numbers and distances of Cy3 and Cy5 at four vertexes of TDN, different fluorescence intensities of twenty-six samples were produced at ∼565.0 nm (FICy3) and ∼665.0 nm (FICy5) by detecting fluorescence spectra. By developing an error correction mechanism, eleven codes were established based on divided intensity ranges of the final FICy3 together with FICy5 (Final-FICy3&amp;FICy5). These resulting codes were used to construct barcode probes, with three miRNA biomarkers (miRNA-210, miRNA-199a and miRNA-21) as cases for multiplexed bio-assay. The high specificity and sensitivity were also demonstrated for the detection of miRNA-210. Overall, the proposed Tetra-FICT enriched the toolbox of fluorescence coding, which could be applied to multiplexing biomarkers detection.},
}
@article {pmid38181080,
year = {2024},
author = {Zhong, Q and Tan, EKW and Martin-Alonso, C and Parisi, T and Hao, L and Kirkpatrick, JD and Fadel, T and Fleming, HE and Jacks, T and Bhatia, SN},
title = {Inhalable point-of-care urinary diagnostic platform.},
journal = {Science advances},
volume = {10},
number = {1},
pages = {eadj9591},
pmid = {38181080},
issn = {2375-2548},
support = {P30 CA014051/CA/NCI NIH HHS/United States ; P30 ES002109/ES/NIEHS NIH HHS/United States ; },
mesh = {Animals ; Mice ; Point-of-Care Systems ; *Lung Neoplasms/diagnosis ; *Adenocarcinoma of Lung ; Disease Models, Animal ; DNA ; },
abstract = {Although low-dose computed tomography screening improves lung cancer survival in at-risk groups, inequality remains in lung cancer diagnosis due to limited access to and high costs of medical imaging infrastructure. We designed a needleless and imaging-free platform, termed PATROL (point-of-care aerosolizable nanosensors with tumor-responsive oligonucleotide barcodes), to reduce resource disparities for early detection of lung cancer. PATROL formulates a set of DNA-barcoded, activity-based nanosensors (ABNs) into an inhalable format. Lung cancer-associated proteases selectively cleave the ABNs, releasing synthetic DNA reporters that are eventually excreted via the urine. The urinary signatures of barcoded nanosensors are quantified within 20 min at room temperature using a multiplexable paper-based lateral flow assay. PATROL detects early-stage tumors in an autochthonous lung adenocarcinoma mouse model with high sensitivity and specificity. Tailoring the library of ABNs may enable not only the modular PATROL platform to lower the resource threshold for lung cancer early detection tools but also the rapid detection of chronic pulmonary disorders and infections.},
}
@article {pmid38175654,
year = {2024},
author = {Dhillon, JS and Rawat, K and Duhan, D and Chugh, RK and Ranebennur, H},
title = {First report of a 'Candidatus phytoplasma asteris' related strain (16SrI) associated with phyllody and witches'-broom symptom in Pisum sativum in Hisar, India.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-10-23-2035-PDN},
pmid = {38175654},
issn = {0191-2917},
abstract = {Pea (Pisum sativum L.) is a leguminous vegetable crop, and India holds the fourth position in the production, primarily contributed by three major states: Uttar Pradesh, Madhya Pradesh, and Punjab (Anonymous, 2022). However, a survey conducted in February 2023 at the National Seed Corporation Farm (15 hectares) in Hisar, Haryana, revealed deformities in the growth of some pea plants. Approximately 10% of these plants exhibited a distinct bushy appearance, accompanied by phyllody and witches'-broom symptoms, characterized by deformed leaves and short internodes (Fig. 1). In response to these observed anomalies, a detailed molecular analysis was conducted at the Plant Pathology Laboratory, IARI, New Delhi. The investigation involved the collection of ten samples each from symptomatic and asymptomatic plants, and DNA was extracted from 100 mg leaf midribs using the CTAB method (Ahrens and Seemüller, 1992). The extracted DNA (100 ng/µl) along with one positive (Catharanthus roseus from glass house, 16SrII-D group) and one negative (without template DNA), served as a template for PCR reactions targeting the 16Sr RNA and secA genes. Universal primers P1/P7 and secAfor1/secArev3 were employed in the first round of PCR for the respective genes. Subsequently, the product from the 1st round was diluted and used as a template for the 2nd round of PCR with primers R16F2n/R16R2 for 16Sr RNA and secAfor2/secArev3 for the secA gene (Gundersen and Lee 1996; Deng and Hiruki 1991; Hodgetts et al. 2008). This nested-PCR approach yielded distinct bands, approximately 1.2 kb (16Sr RNA) and 480 bp (secA), from the DNA of all ten symptomatic plants and positive sample, while no bands were observed in any of the asymptomatic plants. The nested PCR products were sequenced by BBS labs (Barcode biosciences, Bengaluru). The 16Sr RNA gene sequences, showing 100% similarity, were submitted to NCBI as representative sequences (Acc. No. OQ690013, OQ690014, OQ709133, OQ709134). Similarly, secA gene sequences were submitted with Acc. Nos. OR604283-86. BLAST analysis revealed a maximum 99.76% identity with Onion yellows phytoplasma and 'Ca. P. asteris' reference strain for 16Sr RNA gene, and a maximum 100% identity with 'Elaeis guineensis' stunt phytoplasma for secA gene. The phylogenetic tree constructed using the 16S rRNA and secA gene sequences indicated that the pea phytoplasma strains of this study clustered with 'Ca. P. asteris' (16SrI-B) related strains (Fig 2a and 2b). Additionally, the 16S rRNA sequences from this study, when subjected to Virtual RFLP using iPhyclassifier (Zhao et al. 2009), exhibited a pattern (Fig. 3) matching the reference pattern of the 16S group I, subgroup B (GenBank accession: M30790), with a similarity coefficient of 1.0. Previously, Rao et al. (2021) reported several crops associated with the 16SrI ribosomal group, including eight sub-groups from India. However, this report represents the first instance of a phytoplasma 16SrI-B group associated with phyllody and witches'-broom symptoms in pea, both in India and globally. Considering the economic importance of pea as a vegetable crop, the observed disease incidence and affected area are significant. Urgent attention is required to conduct additional research and implement preventive measures to avert the potential outbreak of this disease in the near future.},
}
@article {pmid38175298,
year = {2024},
author = {Choudhary, A and Shekhawat, D and Pathania, J and Sita, K and Sharma, S and Chawla, A and Jaiswal, V},
title = {Exploring DNA barcode for accurate identification of threatened Aconitum L. species from Western Himalaya.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {75},
pmid = {38175298},
issn = {1573-4978},
support = {JRF//Council of Scientific and Industrial Research, India/ ; MLP-172//Council of Scientific and Industrial Research, India/ ; MLP-172//Council of Scientific and Industrial Research, India/ ; MLP-172//Council of Scientific and Industrial Research, India/ ; MLP-172//Council of Scientific and Industrial Research, India/ ; MLP-172//Council of Scientific and Industrial Research, India/ ; MLP-172//Council of Scientific and Industrial Research, India/ ; },
mesh = {Animals ; *Aconitum/genetics ; DNA Barcoding, Taxonomic ; Himalayas ; DNA ; Endangered Species ; },
abstract = {BACKGROUND: Aconitum species, belonging to Ranunculaceae, have high medicinal importance but due to their overexploitation come under IUCN (International Union for Conservation of Nature) red list. The precise identification of the Aconitum species is equally important because they are used in herbal formulations. The present study aimed to develop an efficient DNA barcode system for the authentic identification of Aconitum species.<br><br>METHODS AND RESULTS: A set of 92 barcode gene sequences (including 12 developed during the present study and 80 retrieved from NCBI) of 5 Aconitum species (A. heterophyllum, A. vialoceum, A. japonicum, A. napellus, and A. stapfianum) were analyzed using three methods (tree-based, distance-based, and similarity-based) for species discrimination. The PWG-distance method was found most effective for species discrimination. The discrimination rate of PWG- distance ranged from 33.3% (rbcL&#x2009;+&#x2009;trnH-psbA) to 100% (ITS, rbcL&#x2009;+&#x2009;ITS, ITS&#x2009;+&#x2009;trnH-psbA and rbcL&#x2009;+&#x2009;ITS&#x2009;+&#x2009;trnH-psbA). Among DNA barcodes and their combinations, the ITS marker had the highest degree of species discrimination (NJ-40%, PWG-100% and BLAST-40%), followed by trnH-psbA (NJ-20%, PWG-60% and BLAST-20%). ITS also had higher barcoding gap as compared to other individual barcodes and their combinations. Further, we also analyzed six Aconitum species (A. balfourii, A. ferox, A. heterophyllum, A. rotundifolium, A. soongaricum and A. violaceum) existing in Western Himalaya. These species were distinguished clearly through tree-based method using the ITS barcode gene with 100% species resolution.<br><br>CONCLUSION: ITS showed the best species discrimination power and was used to develop species-specific barcodes for Aconitum species. DNA barcodes developed during the present study can be used to identify Aconitum species.},
}
@article {pmid38174322,
year = {2024},
author = {Ullrich, V and Ertmer, S and Baginska, A and Dorsch, M and Gull, HH and Cima, I and Berger, P and Dobersalske, C and Langer, S and Meyer, L and Dujardin, P and Kebir, S and Glas, M and Blau, T and Keyvani, K and Rauschenbach, L and Sure, U and Roesch, A and Grüner, BM and Scheffler, B},
title = {KDM5B predicts temozolomide-resistant subclones in glioblastoma.},
journal = {iScience},
volume = {27},
number = {1},
pages = {108596},
pmid = {38174322},
issn = {2589-0042},
abstract = {Adaptive plasticity to the standard chemotherapeutic temozolomide (TMZ) leads to glioblastoma progression. Here, we examine early stages of this process in patient-derived cellular models, exposing the human lysine-specific demethylase 5B (KDM5B) as a prospective indicator for subclonal expansion. By integration of a reporter, we show its preferential activity in rare, stem-like ALDH1A1+ cells, immediately increasing expression upon TMZ exposure. Naive, genetically unmodified KDM5B[high] cells phosphorylate AKT (pAKT) and act as slow-cycling persisters under TMZ. Knockdown of KDM5B reverses pAKT levels, simultaneously increasing PTEN expression and TMZ sensitivity. Pharmacological inhibition of PTEN rescues the effect. Interference with KDM5B subsequent to TMZ decreases cellular vitality, and clonal tracing with DNA barcoding demonstrates high individual levels of KDM5B to predict subclonal expansion already before TMZ exposure. Thus, KDM5B[high] treatment-naive cells preferentially contribute to the dynamics of drug resistance under TMZ. These findings may serve as a cornerstone for future biomarker-assisted clinical trials.},
}
@article {pmid38173494,
year = {2024},
author = {Karimifard, S and Saberi-Pirooz, R and Ahmadzadeh, F and Aghamir, F},
title = {Investigating the impacts of agricultural land use on soil earthworm communities: A case study of northern Zagros Mountains of Iran.},
journal = {Heliyon},
volume = {10},
number = {1},
pages = {e23523},
pmid = {38173494},
issn = {2405-8440},
abstract = {Earthworms play a crucial role in the invertebrate community of soil by contributing to the belowground biomass and biogeochemical cycle. Environmental stresses, such as human activities and land use changes, have been found to negatively affect their abundance and diversity. To investigate the impact of agricultural land use and pastures on earthworms' genetic diversity in the Northern Zagros Mountains, we used COI molecular marker and DNA barcoding approaches. We collected earthworm specimens from four farmland sites and six pastures and assessed the abundance and species composition of earthworm communities across the two land uses using quadrat sampling. Using the barcoding method, we identified 13 molecular operational taxonomic units (MOTUs) among the captured earthworms. Our results showed that the number of total MOTUs, density, and earthworm communities differed significantly between the two land uses. We also found that pastures had more abundant earthworms, while farmlands had greater diversity. The diversity of OTUs in the Lumbricidae family was dominant in the agricultural system. Overall, the population of invasive earthworm species in cultivation systems is influenced by chemical inputs and organic materials from plant residues, cover crops, manure, or organic fertilizers. Given the rapid rate of land use change worldwide, especially in Iran, it is crucial to understand the impact of disturbances on earthworms.},
}
@article {pmid38170774,
year = {2024},
author = {Xiong, H and Wang, Q and Li, CC and He, A},
title = {Single-cell joint profiling of multiple epigenetic proteins and gene transcription.},
journal = {Science advances},
volume = {10},
number = {1},
pages = {eadi3664},
pmid = {38170774},
issn = {2375-2548},
mesh = {Humans ; *DNA Methylation ; *Epigenomics/methods ; Gene Expression Regulation ; Transcriptome ; Epigenesis, Genetic ; },
abstract = {Sculpting the epigenome with a combination of histone modifications and transcription factor occupancy determines gene transcription and cell fate specification. Here, we first develop uCoTarget, utilizing a split-pool barcoding strategy for realizing ultrahigh-throughput single-cell joint profiling of multiple epigenetic proteins. Through extensive optimization for sensitivity and multimodality resolution, we demonstrate that uCoTarget enables simultaneous detection of five histone modifications (H3K27ac, H3K4me3, H3K4me1, H3K36me3, and H3K27me3) in 19,860 single cells. We applied uCoTarget to the in vitro generation of hematopoietic stem/progenitor cells (HSPCs) from human embryonic stem cells, presenting multimodal epigenomic profiles in 26,418 single cells. uCoTarget reveals establishment of pairing of HSPC enhancers (H3K27ac) and promoters (H3K4me3) and RUNX1 engagement priming for H3K27ac activation along the HSPC path. We then develop uCoTargetX, an expansion of uCoTarget to simultaneously measure transcriptome and multiple epigenome targets. Together, our methods enable generalizable, versatile multimodal profiles for reconstructing comprehensive epigenome and transcriptome landscapes and analyzing the regulatory interplay at single-cell level.},
}
@article {pmid38170141,
year = {2023},
author = {Yang, J and Fan, S and Guo, M and Xie, Z and Cheng, Q and Gao, P and Cheng, C},
title = {DNA barcoding and comparative RNA-Seq analysis provide new insights into leaf formation using a novel resource of high-yielding Epimedium koreanum.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1290836},
pmid = {38170141},
issn = {1664-462X},
abstract = {Epimedium koreanum Nakai, a well-known traditional Chinese medicinal herb, has been widely used to treat osteoporosis and sexual dysfunction for thousands of years. However, due to the decreasing population of East Asian natural resources, yearly output of Epimedium crude herb has been in low supply year by year. In this study, an unusual variety of E. koreanum was discovered in Dunhua, Jilin Province, the northernmost area where this variety was found containing 6 individuals, with three branches that had 27 leaflets, which is much more than the typical leaflet number of 9. Firstly, the novel E. koreanum varety was identified using DNA barcodes. Then, 1171 differentially expressed genes (DEGs) were discovered through parallel RNA-seq analysis between the newly discovered variety and wild type (WT) E. koreanum plant. Furthermore, the results of bioinformatics investigation revealed that 914 positively and 619 negatively correlated genes associated with the number of leaflets. Additionally, based on RNA-Seq and qRT-PCR analysis, two homologous hub TCP genes, which were commonly implicated in plant leaf development, and shown to be up regulated and down regulated in the discovered newly variety, respectively. Thus, our study discovered a novel wild resource for leaf yield rewarding medicinal Epimedium plant breeding, provided insights into the relationship between plant compound leaf formation and gene expression of TCPs transcription factors and other gene candidates, providing bases for creating high yield cultivated Epimedium variety by using further molecular selection and breeding techniques in the future.},
}
@article {pmid38169973,
year = {2023},
author = {Shen, W and Hu, F and Lei, P and Tang, Y},
title = {Applications of CRISPR screening to lung cancer treatment.},
journal = {Frontiers in cell and developmental biology},
volume = {11},
number = {},
pages = {1295555},
pmid = {38169973},
issn = {2296-634X},
abstract = {Lung cancer is an extremely aggressive and highly prevalent disease worldwide, and it is one of the leading causes of cancer death. Deciphering intrinsic genetic mechanism, finding new targets, and overcoming drug resistance are the key to lung cancer treatment. High-throughput CRISPR screening has been extensively used to obtain the genes related to cancers including lung cancer. This review describes CRISPR/Cas9 or CRISPR/dCas9-based technologies for high-throughput screening. We summarize the applications of CRISPR screening technology in exploring the mechanism of lung cancer development in vivo or in vitro, overcoming drug resistance, improving the effect of immunotherapy, and discovering new therapeutic targets. This review highlights the potential of CRISPR screening in combination with tumor barcoding and high-throughput sequencing (Tuba-seq) to precisely quantify the impact of alterations in many tumor suppressor genes on lung cancer.},
}
@article {pmid38168153,
year = {2023},
author = {Lee, BC and Gin, A and Wu, C and Singh, K and Grice, M and Mortlock, R and Abraham, D and Fan, X and Zhou, Y and AlJanahi, A and Choi, U and de Ravin, SS and Shin, T and Hong, S and Dunbar, CE},
title = {Impact of CRISPR/HDR-editing versus lentiviral transduction on long-term engraftment and clonal dynamics of HSPCs in rhesus macaques.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.12.13.571396},
pmid = {38168153},
issn = {2692-8205},
abstract = {For precise genome editing via CRISPR/homology-directed repair (HDR), effective and safe editing of long-term engrafting hematopoietic stem cells (LT-HSCs) requires both sufficient HDR efficiency and protection of LT-HSC function and number. The impact of HDR on true LT-HSCs clonal dynamics in a relevant large animal model has not previously been studied. To track the HDR-edited cells, autologous rhesus macaque (RM) CD34 [+] cells were electroporated with the gRNA/Cas9 ribonucleoprotein (RNP) and HDR cassette barcode library structure and reinfused into RMs following myeloablation. For competitive model animals, fractionated CD34 [+] cells were transduced with a barcoded GFP-expressing lentiviral vector (LV) and electroporated via HDR machinery, respectively. CD33 knockout (KO) neutrophils were prevalent early following engraftment and then rapidly decreased, resulting in less than 1% total editing efficiency. Interestingly, in competitive animals, a higher concentration of i53 mRNA result in a less steep reduction in CD33 KO cells, presented a modest decrease in HDR rate (0.1-0.2%) and total indels (1.5-6.5%). In contrast, the drop off of LV-transduced GFP [+] cells stabilized at 20% after 2 months. We next retrieved embedded barcodes and revealed that various clones contributed to early hematopoietic reconstitution, then after dominant clones appeared at steady state throughout the animals. In conclusion, CRISPR/HDR edited cells disappeared rapidly after the autologous transplantation in RM despite substantial gene editing outcome, whereas LV-transduced cells were relatively well maintained. Clonality of HDR-edited cells drastically shrank at early stage and then relied on several dominant clones, which can be mildly mitigated by the introduction of i53 mRNA.},
}
@article {pmid38167959,
year = {2024},
author = {Baygin, RC and Yilmaz, KC and Acar, A},
title = {Characterization of dabrafenib-induced drug insensitivity via cellular barcoding and collateral sensitivity to second-line therapeutics.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {286},
pmid = {38167959},
issn = {2045-2322},
support = {118C197//T&#xfc;rkiye Bilimsel ve Teknolojik Ara&#x15f;t&#x131;rma Kurumu/ ; },
mesh = {Humans ; *Drug Collateral Sensitivity ; Oxaliplatin ; Capecitabine ; *Proto-Oncogene Proteins B-raf/genetics ; Oximes/pharmacology/therapeutic use ; Mutation ; },
abstract = {Drug insensitivity is arguably one of the biggest challenges in cancer therapeutics. Although effective therapeutic solutions in cancer are limited due to the emergence of drug insensitivity, exploiting evolutionary understanding in this context can provide potential second-line therapeutics sensitizing the drug insensitive populations. Targeted therapeutic agent dabrafenib is used to treat CRC patients with BRAF V600E genotype and insensitivity to dabrafenib is often observed. Understanding underlying clonal architecture of dabrafenib-induced drug insensitivity and identification of potential second-line therapeutics that could sensitize dabrafenib insensitive populations remain to be elucidated. For this purpose, we utilized cellular barcoding technology to decipher dabrafenib-induced clonal evolution in BRAF V600E mutant HT-29 cells. This approach revealed the detection of both pre-existing and de novo barcodes with increased frequencies as a result of dabrafenib insensitivity. Furthermore, our longitudinal monitoring of drug insensitivity based on barcode detection from floating DNA within used medium enabled to identify temporal dynamics of pre-existing and de novo barcodes in relation to dabrafenib insensitivity in HT-29 cells. Moreover, whole-exome sequencing analysis exhibited possible somatic CNVs and SNVs contributing to dabrafenib insensitivity in HT-29 cells. Last, collateral drug sensitivity testing demonstrated oxaliplatin and capecitabine, alone or in combination, as successful second-like therapeutics in inducing collateral sensitivity in dabrafenib-insensitive HT-29 cells. Overall, our findings demonstrate clonal dynamics of dabrafenib-insensitivity in HT-29 cells. In addition, oxaliplatin and capecitabine, alone or in combination, were successful second-line therapeutics in inducing collateral sensitivity in dabrafenib-insensitive HT-29 cells.},
}
@article {pmid38167266,
year = {2024},
author = {Jiang, G and Zhang, Y and Chen, M and Ramoneda, J and Han, L and Shi, Y and Peyraud, R and Wang, Y and Shi, X and Chen, X and Ding, W and Jousset, A and Hikichi, Y and Ohnishi, K and Zhao, FJ and Xu, Y and Shen, Q and Dini-Andreote, F and Zhang, Y and Wei, Z},
title = {Effects of plant tissue permeability on invasion and population bottlenecks of a phytopathogen.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {62},
pmid = {38167266},
issn = {2041-1723},
support = {7006279//USDA/ ; },
mesh = {Virulence ; *Ralstonia solanacearum/genetics ; Permeability ; Plant Diseases ; Plant Roots ; },
abstract = {Pathogen genetic diversity varies in response to environmental changes. However, it remains unclear whether plant barriers to invasion could be considered a genetic bottleneck for phytopathogen populations. Here, we implement a barcoding approach to generate a pool of 90 isogenic and individually barcoded Ralstonia solanacearum strains. We used 90 of these strains to inoculate tomato plants with different degrees of physical permeability to invasion (intact roots, wounded roots and xylem inoculation) and quantify the phytopathogen population dynamics during invasion. Our results reveal that the permeability of plant roots impacts the degree of population bottleneck, genetic diversity, and composition of Ralstonia populations. We also find that selection is the main driver structuring pathogen populations when barriers to infection are less permeable, i.e., intact roots, the removal of root physical and immune barriers results in the predominance of stochasticity in population assembly. Taken together, our study suggests that plant root permeability constitutes a bottleneck for phytopathogen invasion and genetic diversity.},
}
@article {pmid38167262,
year = {2024},
author = {Penter, L and Borji, M and Nagler, A and Lyu, H and Lu, WS and Cieri, N and Maurer, K and Oliveira, G and Al'Khafaji, AM and Garimella, KV and Li, S and Neuberg, DS and Ritz, J and Soiffer, RJ and Garcia, JS and Livak, KJ and Wu, CJ},
title = {Integrative genotyping of cancer and immune phenotypes by long-read sequencing.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {32},
pmid = {38167262},
issn = {2041-1723},
support = {P01 CA229092/CA/NCI NIH HHS/United States ; P50 CA101942/CA/NCI NIH HHS/United States ; UM1 CA186709/CA/NCI NIH HHS/United States ; U24 CA224316/CA/NCI NIH HHS/United States ; P01 CA066996/CA/NCI NIH HHS/United States ; U24 CA224331/CA/NCI NIH HHS/United States ; U24 CA224285/CA/NCI NIH HHS/United States ; R01 CA155010/CA/NCI NIH HHS/United States ; R50 CA251956/CA/NCI NIH HHS/United States ; U24 CA224309/CA/NCI NIH HHS/United States ; U24 CA224319/CA/NCI NIH HHS/United States ; K08 CA245209/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Genotype ; *High-Throughput Nucleotide Sequencing/methods ; *Leukemia, Myeloid, Acute/genetics/pathology ; Phenotype ; Gene Expression Profiling/methods ; },
abstract = {Single-cell transcriptomics has become the definitive method for classifying cell types and states, and can be augmented with genotype information to improve cell lineage identification. Due to constraints of short-read sequencing, current methods to detect natural genetic barcodes often require cumbersome primer panels and early commitment to targets. Here we devise a flexible long-read sequencing workflow and analysis pipeline, termed nanoranger, that starts from intermediate single-cell cDNA libraries to detect cell lineage-defining features, including single-nucleotide variants, fusion genes, isoforms, sequences of chimeric antigen and TCRs. Through systematic analysis of these classes of natural 'barcodes', we define the optimal targets for nanoranger, namely those loci close to the 5' end of highly expressed genes with transcript lengths shorter than 4 kB. As proof-of-concept, we apply nanoranger to longitudinal tracking of subclones of acute myeloid leukemia (AML) and describe the heterogeneous isoform landscape of thousands of marrow-infiltrating immune cells. We propose that enhanced cellular genotyping using nanoranger can improve the tracking of single-cell tumor and immune cell co-evolution.},
}
@article {pmid38166527,
year = {2022},
author = {Zhang, C and Sui, L and Han, X},
title = {DNA barcoding of Schizothoracinae fishes from the Yarlung Zangbo River in Tibet.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {33},
number = {1-8},
pages = {24-28},
pmid = {38166527},
issn = {2470-1408},
abstract = {The nine endemic species of the genus Schizothorax from the Yarlung Zangbo River, Tibet comprise a putative cyprinid species flock. In this study, the effectiveness of the COI DNA barcode for Schizothoracinae species identification was verified by using 45 COI sequences covering nine species in four genera of Schizothoracinae fishes. The average Kimura two parameter (K2P) genetic distances within and among species were 0.13% and 8.57%, respectively. The results revealed that most of the species were clearly discriminated by their estimated genetic distances and monophyletic clustering in a maximum likelihood tree. However, insignificant genetic distances were noticed in two reportedly valid species: Schizothorax molesworthi and S. integrilabiatus (0.1%), and the monophyly of S. macropogon could not be recovered in the schizothoracine group. The fishes of S.curilabiatus living in the lower course of Yalung Zangbo River were clustered together with three species from the upper course, which is inconsistent with the geographical distribution of the populations.},
}
@article {pmid38165899,
year = {2024},
author = {Arana, A and Arana, C and Watsa, M and Tobler, MW and Pacheco, V and Esteves, J and Mena, JL and Salinas, L and Ramirez, JL},
title = {Lack of local genetic representation in one of the regions with the highest bird species richness, the Peruvian Amazonia.},
journal = {PloS one},
volume = {19},
number = {1},
pages = {e0296305},
pmid = {38165899},
issn = {1932-6203},
mesh = {Animals ; Peru ; *Biodiversity ; *Birds/genetics ; Brazil ; },
abstract = {Peru ranks among the three countries with the highest bird species diversity globally and a majority of those species are found in the Peruvian Amazon. However, birds in this area are currently facing serious anthropogenic threats. Genetic and genomic methods are becoming important tools for avian biodiversity monitoring and conservation planning. Comprehensive molecular libraries that are publicly available are key to the effective deployment of these tools. We analyze the information gaps for four molecular markers in the most important genetic sequence databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, for bird species of the Peruvian Amazonia. We found that 64% of Peruvian Amazonian bird species have gene sequences for COI, 59.5% have CYTB sequences, 16.4% have 12S sequences, and only 0.6% have 18S sequences. However, these numbers decrease drastically to 4.3% for COI sequences when we only consider specimens sampled in Peru. Our data also showed that 43.8% of Peruvian Amazonian endemic species (n = 32) are missing sequences of any screened marker uploaded to GenBank or BOLD. Our results will encourage and guide efforts of the scientific community to complete reference libraries for Peruvian avian species that will be useful for future DNA-based monitoring projects that include birds.},
}
@article {pmid38165582,
year = {2024},
author = {Mozafari, M},
title = {Biomaterials barcoding: a high-throughput breakthrough.},
journal = {Molecular biomedicine},
volume = {5},
number = {1},
pages = {2},
pmid = {38165582},
issn = {2662-8651},
mesh = {Humans ; *Biocompatible Materials ; High-Throughput Screening Assays/methods ; },
abstract = {In the world of biomedical breakthroughs, Rice University bioengineer Omid Veiseh and his team are making waves with their recent publication in Nature Biomedical Engineering (2023) (Mukherjeeet al., Nat Biomed Eng. 7:867–886, 2023). This study is a pivotal step in our fight against fibrosis, an issue that has long hindered medical progress. Their pioneering research isn’t just a scientific milestone; it’s a game-changer in how we tackle tissue scarring. Veiseh and his team have introduced an innovative method that allows for rapid testing of various materials within living organisms. By employing cellular barcoding and cutting-edge sequencing techniques, they’ve accelerated the assessment of multiple hydrogels. As we delve deeper into the specifics of this groundbreaking study, we uncover not just scientific insights, but the potential to revolutionize how we conceptualize and utilize biomaterials. This discussion isn’t merely about research methods; it’s about the ray of hope and boundless opportunities this study illuminates across the spectrum of biomaterials science.},
}
@article {pmid38165474,
year = {2024},
author = {Alshegaihi, RM},
title = {The complete chloroplast genome of the halophyte flowering plant Suaeda monoica from Jeddah, Saudi Arabia.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {60},
pmid = {38165474},
issn = {1573-4978},
support = {UJ-23-FR-89//University of Jeddah/ ; },
mesh = {*Magnoliopsida ; *Genome, Chloroplast/genetics ; Salt-Tolerant Plants/genetics ; Saudi Arabia ; Phylogeny ; *Chenopodiaceae/genetics ; },
abstract = {The complete chloroplast genome (plastome) of the annual flowering halophyte herb Suaeda monoica Forssk. ex J. F. Gmel. family (Amaranthaceae) that grows in Jeddah, Saudi Arabia, was identified for the first time in this study. Suaeda monoica is a medicinal plant species whose taxonomic classification remains controversial. Further, studying the species is useful for current conservation and management efforts. In the current study, the full chloroplast genome S. monoica was reassembled using whole-genome next-generation sequencing and compared with the previously published chloroplast genomes of Suaeda species. The chloroplast genome size of Suaeda monoica was 151,789 bp, with a single large copy of 83,404 bp, a small single copy of 18,007 bp and two inverted repeats regions of 25,189 bp. GC content in the whole genome was 36.4%. The cp genome included 87 genes that coded for proteins, 37 genes coding for tRNA, 8 genes coding for rRNA and one non-coding pseudogene. Five chloroplast genome features were compared between S. monoica and S. japonica, S. glauca, S. salsa, S. malacosperma and S. physophora. Among Suaeda genus and equal to most angiosperms chloroplast genomes, the RSCU values were conservative. Two pseudogenes (accD and ycf1), rpl16 intron and ndhF-rpl32 intergenic spacer, were highlighted as suitable DNA barcodes for different Suaeda species. Phylogenetic analyses show Suaeda cluster into three main groups; one in which S. monoica was closer to S. salsa. The obtained result provided valuable information on the characteristics of the S. monoica chloroplast genome and the phylogenetic relationships.},
}
@article {pmid38164633,
year = {2022},
author = {Chuhila, YJ and Chibwana, FD and Katandukila, JV and Mwita, CJ},
title = {DNA barcoding and delimitation of critically endangered indigenous and introduced tilapias (pisces cichlidae) of Pangani catchment, Northern Tanzania.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {33},
number = {1-8},
pages = {40-52},
pmid = {38164633},
issn = {2470-1408},
abstract = {The Pangani catchment of Northern Tanzania harbours the critically endangered endemic tilapias of the genus Oreochromis. The introduction of non-native congenerics and consequent hybridization complicates taxa identification and phylogeny based on morphological systematics. We therefore morphologically and molecularly identified these tilapias and delimited their Molecular Operational Taxonomic Units (MOTUs) based on Cytochrome Oxidase Subunit I (CO1) gene for future management and conservation. A total of 132 indigenous and introduced tilapia specimens were morphologically identified, barcoded using the CO1 gene and delimited by Kimura 2 Parameter distance approaches, Automatic Barcode Gap Discovery (ABGD), Neighbour Joining (NJ) tree and haplotype analysis. Theoverall mean conspecific, congeneric and confamillial genetic distances based on the K2P model were 0.54%, 5.32% and 13.29% respectively. All taxa had a mean K2P distance < 2% and 90% (n = 10), were clearly delimited by the ABGD method. The NJ tree delimited tilapia taxa commensurate to the genetic distances depicted by DNA barcoding. However, DNA barcoding and NJ tree coherently failed to discriminate the morphologically distinct allopatric Oreochromis jipe and Oreochromis hunteri taxa. Moreover, the two methods depicted lack of monophyly in Oreochromis korogwe MOTUs implying that the taxon could consist of at least one MOTU. We conclude that the integration of morphological-based taxonomy and DNA barcoding among ichthyofaunal taxa herein will be invaluable in conservation and management of native tilapias in Pangani basin.},
}
@article {pmid38164547,
year = {2022},
author = {Torres, SKM and Santos, BS},
title = {Genetic diversity and population structure of giant trevallies (Caranx ignobilis Forsskål, 1775) in the Philippines with implications to management.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {33},
number = {1-8},
pages = {10-23},
pmid = {38164547},
issn = {2470-1408},
abstract = {The giant trevallies (Caranx ignobilis) is a globally important fish species that is at risk from overexploitation. In this study, 150 C. ignobilis from six provinces in the Philippines were collected for genetic analyses. For each province, five representative specimens of C. ignobilis were subjected to DNA barcoding and revealed high interspecific K2P distances of 9.58% and 17.29% when compared to other species of Caranx and Carangoides, respectively. On the other hand, all 150 C. ignobilis specimens were subjected to population genetic analysis using the mitochondrial cytochrome b region. In the studied population of C. ignobilis, 33 unique haplotypes were observed, and the population exhibited high haplotype (h = 0.831) and nucleotide (π=0.930%) diversity. Pairwise FST values between the six study sites indicated limited genetic differentiation among the studied populations. The limited genetic differentiation may be due to the oceanic currents in the Philippines facilitating larval dispersal as observed in the results of the Lagrangian dispersion model. Data from neutrality tests, mismatch distribution, and Bayesian skyline plot revealed that the population may have undergone demographic expansion. This study provides valuable genetic information on C. ignobilis that can be used for formulating sustainable fishery management strategies.},
}
@article {pmid38161716,
year = {2023},
author = {Jing, MD and Ding, YH and Ма, YT},
title = {Description of three new species of Callyntrura (Japonphysa) (Collembola, Entomobryidae) from China with the aid of DNA barcoding.},
journal = {ZooKeys},
volume = {1187},
number = {},
pages = {237-260},
pmid = {38161716},
issn = {1313-2989},
abstract = {Callyntrura(s.l.) Börner, 1906 is the largest genus of the subfamily Salininae and contains 11 subgenera and 98 species from all over the world (mainly Asia), with eight species recorded from China. In the present paper, three new species of Callyntrura(s.l.) are described from China: C. (Japonphysa) xinjianensissp. nov.; C. (J.) tongguensissp. nov. and C. (J.) raoisp. nov. Their differences in colour pattern, chaetotaxy and other characters are slight, however distances of COI mtDNA support their validation as three new distinct species. A key to the Chinese Callyntrura(s.l.) is provided.},
}
@article {pmid38161489,
year = {2023},
author = {Krivosheeva, V and Solodovnikov, A and Shulepov, A and Semerikova, D and Ivanova, A and Salnitska, M},
title = {Assessment of the DNA barcode libraries for the study of the poorly-known rove beetle (Staphylinidae) fauna of West Siberia.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e115477},
pmid = {38161489},
issn = {1314-2828},
abstract = {Staphylinidae, or rove beetles, are one of the mega-diverse and abundant families of the ground-living terrestrial arthropods that is taxonomically poorly known even in the regions adjacent to Europe where the fauna has been investigated for the longest time. Since DNA barcoding is a tool to accelerate biodiversity research, here we explored if the currently-available COI barcode libraries are representative enough for the study of rove beetles of West Siberia. This is a vast region adjacent to Europe with poorly-known fauna of rove beetles and from where not a single DNA barcode has hitherto been produced for Staphylinidae. First, we investigated the faunal similarity between the rove beetle faunas of the climatically compatible West Siberia in Asia, Fennoscandia in Europe and Canada and Alaska in North America. Second, we investigated barcodes available for Staphylinidae from the latter two regions in BOLD and GenBank, the world's largest DNA barcode libraries. We conclude that the rather different rove beetle faunas of Fennoscandia, on the one hand and Canada and Alaska on the other hand, are well covered in both barcode libraries that complement each other. We also find that even without any barcodes originating from specimens collected in West Siberia, this coverage is helpful for the study of rove beetles there due to the significant number of widespread species shared between West Siberia and Fennoscandia and due to the even larger number of shared genera amongst all three investigated regions. For the first time, we compiled a literature-based checklist for 726 species of the West Siberian Staphylinidae supplemented by their occurrence dataset submitted to GBIF. Our script written for mining unique (i.e. not redundant) barcodes for a given geographic area across global libraries is made available here and can be adopted for any other regions.},
}
@article {pmid38159778,
year = {2024},
author = {Kelly, MG and Mann, DG and Taylor, JD and Juggins, S and Walsh, K and Pitt, JA and Read, DS},
title = {Maximising environmental pressure-response relationship signals from diatom-based metabarcoding in rivers.},
journal = {The Science of the total environment},
volume = {914},
number = {},
pages = {169445},
doi = {10.1016/j.scitotenv.2023.169445},
pmid = {38159778},
issn = {1879-1026},
mesh = {*Rivers ; *Diatoms ; Fresh Water ; Biodiversity ; Databases, Factual ; Environmental Monitoring ; Ecosystem ; },
abstract = {DNA metabarcoding has been performed on a large number of river phytobenthos samples collected from the UK, using rbcL primers optimised for diatoms. Within this dataset the composition of non-diatom sequence reads was studied and the effect of including these in models for evaluating the nutrient gradient was assessed. Whilst many non-diatom taxonomic groups were detected, few contained the full diversity expected in riverine environments. This may be due to the performance of the current primers in characterising the wider phytobenthic community and influenced by the sampling method employed, as both were developed specifically for diatoms. Nevertheless, the study identified considerable diversity in some groups, e.g. Eustigmatophyceae and a wider distribution than previously thought for freshwater Phaeophyceae. These results offer a strong case for the benefits of metabarcoding for expanding knowledge of aquatic biodiversity in the UK and elsewhere. Many of the ASVs associated with non-diatoms showed significant pressure responses; however, models that included non-diatoms had similar predictive strength to those based on diatoms alone. Whilst limitations of the primers for assessing non-diatoms may play a role in explaining these results, the diatoms provide a strong signal along the nutrient gradient and other algae, therefore, add little unique information. We recommend that future developments should use ASVs to calculate metrics, with links to reference databases made as a final step to generate lists of taxa to support interpretation. Any further exploration of the potential of non-diatoms would benefit from access to a well-curated reference database, similar to diat.barcode. Such a database does not yet exist, and we caution against the indiscriminate use of NCBI GenBank as a taxonomic resource as many rbcL sequences deposited have not been curated.},
}
@article {pmid38158426,
year = {2023},
author = {Reichl, J and Prossegger, C and Eichholzer, B and Plauder, P and Unterköfler, MS and Bakran-Lebl, K and Indra, A and Fuehrer, HP},
title = {A citizen science report-Tiger mosquitoes (Aedes albopictus) in allotment gardens in Graz, Styria, Austria.},
journal = {Parasitology research},
volume = {123},
number = {1},
pages = {79},
pmid = {38158426},
issn = {1432-1955},
mesh = {Animals ; *Aedes/genetics ; Gardens ; Austria ; *Citizen Science ; *Zika Virus ; *Zika Virus Infection ; Mosquito Vectors/genetics ; },
abstract = {Aedes albopictus, the Asian tiger mosquito, is an invasive species not native to Europe. Due to its ability to transmit pathogens, such as dengue, chikungunya and Zika viruses, Ae. albopictus is considered a major health threat. In Austria, it was first reported in 2012 in the Western province of Tyrol and was documented in the metropolitan area of Vienna in 2020, demonstrating its ability to colonize urban areas. In July 2021, a garden owner from Graz, Styria, Austria, contacted experts because of the possible presence of tiger mosquitoes in an allotment garden complex. Accordingly, citizen scientists collected adult mosquitoes and set up ovitraps. Adults and eggs were sent to the laboratory for morphological examination and molecular DNA barcoding within the mitochondrial cytochrome c oxidase subunit I gene. In total, 217 eggs of Ae. albopictus were found at the allotment garden as well as at a second location in the city of Graz. In addition, 14 adult Ae. albopictus specimens, of which 7 were molecularly identified as an identical haplotype, were collected at the allotment garden. With its mild climate and numerous parks and gardens, Graz provides the perfect environment for reproduction of tropical/subtropical alien Aedes mosquitoes. The presence of eggs and adult specimens in the current study period indicates that Ae. albopictus is already breeding in Graz. However, monitoring efforts need to be continued to determine whether stable populations of Ae. albopictus can survive there.},
}
@article {pmid38156032,
year = {2023},
author = {Touray, AO and Sternlieb, T and Isebe, T and Cestari, I},
title = {Identifying Antigenic Switching by Clonal Cell Barcoding and Nanopore Sequencing in Trypanosoma brucei.},
journal = {Bio-protocol},
volume = {13},
number = {24},
pages = {e4904},
pmid = {38156032},
issn = {2331-8325},
abstract = {Many organisms alternate the expression of genes from large gene sets or gene families to adapt to environmental cues or immune pressure. The single-celled protozoan pathogen Trypanosoma brucei spp. periodically changes its homogeneous surface coat of variant surface glycoproteins (VSGs) to evade host antibodies during infection. This pathogen expresses one out of ~2,500 VSG genes at a time from telomeric expression sites (ESs) and periodically changes their expression by transcriptional switching or recombination. Attempts to track VSG switching have previously relied on genetic modifications of ES sequences with drug-selectable markers or genes encoding fluorescent proteins. However, genetic modifications of the ESs can interfere with the binding of proteins that control VSG transcription and/or recombination, thus affecting VSG expression and switching. Other approaches include Illumina sequencing of the VSG repertoire, which shows VSGs expressed in the population rather than cell switching; the Illumina short reads often limit the distinction of the large set of VSG genes. Here, we describe a methodology to study antigenic switching without modifications of the ES sequences. Our protocol enables the detection of VSG switching at nucleotide resolution using multiplexed clonal cell barcoding to track cells and nanopore sequencing to identify cell-specific VSG expression. We also developed a computational pipeline that takes DNA sequences and outputs VSGs expressed by cell clones. This protocol can be adapted to study clonal cell expression of large gene families in prokaryotes or eukaryotes. Key features • This protocol enables the analysis of variant surface glycoproteins (VSG) switching in T. brucei without modifying the expression site sequences. • It uses a streamlined computational pipeline that takes fastq DNA sequences and outputs expressed VSG genes by each parasite clone. • The protocol leverages the long reads sequencing capacity of the Oxford nanopore sequencing technology, which enables accurate identification of the expressed VSGs. • The protocol requires approximately eight to nine days to complete.},
}
@article {pmid38155711,
year = {2023},
author = {Yu, QF and Tan, YH and Yu, WB and Yang, ST and Huang, JP and Caraballo-Ortiz, MA and Liu, C and Song, Y},
title = {Comparative analyses of eight complete plastid genomes of two hemiparasitic Cassytha vines in the family Lauraceae.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1192170},
pmid = {38155711},
issn = {1664-8021},
abstract = {Cassytha is the sole genus of hemiparasitic vines (ca. 20 spp.) belonging to the Cassytheae tribe of the Lauraceae family. It is extensively distributed in tropical and subtropical regions. In this study, we determined the complete plastid genome sequences of C. filiformis and C. larsenii, which do not possess the typical quadripartite structure. The length of C. filiformis plastomes ranged from 114,215 to 114,618 bp, whereas that of C. larsenii plastomes ranged from 114,900 to 114,988 bp. Comparative genomic analysis revealed 1,013 mutation sites, four large intragenomic deletions, and five highly variable regions in the eight plastome sequences. Phylogenetic analyses based on 61 complete plastomes of Laurales species, 19 ITS sequences, and trnK barcodes from 91 individuals of Cassytha spp. confirmed a non-basal group comprising individuals of C. filiformis, C. larsenii, and C. pubescens in the family Lauraceae and proposed a sister relationship between C. filiformis and C. larsenii. Further morphological comparisons indicated that the presence or absence of hairs on the haustoria and the shape or size of fruits were useful traits for differentiating C. filiformis and C. larsenii.},
}
@article {pmid38155211,
year = {2023},
author = {Olou, BA and Hègbè, ADMT and Piepenbring, M and Yorou, NS},
title = {Genetic diversity and population differentiation in Earliella scabrosa, a pantropical species of Polyporales.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {23020},
pmid = {38155211},
issn = {2045-2322},
support = {91651629//Deutscher Akademischer Austauschdienst/ ; 2225290065//Mohamed bin Zayed Species Conservation Fund/ ; 01D20015//German Federal Ministry of Education and Research/ ; },
mesh = {*Polyporales ; Genetic Variation ; Phylogeny ; *Polyporaceae ; },
abstract = {Earliella scabrosa is a pantropical species of Polyporales (Basidiomycota) and well-studied concerning its morphology and taxonomy. However, its pantropical intraspecific genetic diversity and population differentiation is unknown. We initiated this study to better understand the genetic variation within E. scabrosa and to test if cryptic species are present. Sequences of three DNA regions, the nuclear ribosomal internal transcribed spacer (ITS), the large subunit ribosomal DNA (LSU), and the translation elongation factor (EF1α) were analysed for 66 samples from 15 geographical locations. We found a high level of genetic diversity (haplotype diversity, Hd = 0.88) and low nucleotide diversity (π = 0.006) across the known geographical range of E. scabrosa based on ITS sequences. The analysis of molecular variance (AMOVA) indicates that the genetic variability is mainly found among geographical populations. The results of Mantel tests confirmed that the genetic distance among populations of E. scabrosa is positively correlated with the geographical distance, which indicates that geographical isolation is an important factor for the observed genetic differentiation. Based on phylogenetic analyses of combined dataset ITS-LSU-EF1α, the low intraspecific divergences (0-0.3%), and the Automated Barcode Gap Discovery (ABGD) analysis, E. scabrosa can be considered as a single species with five different geographical populations. Each population might be in the process of allopatric divergence and in the long-term they may evolve and become distinct species.},
}
@article {pmid38153939,
year = {2023},
author = {da Silva, TF and Sampaio, I and Angulo, A and Domínguez-Domínguez, O and Andrade-Santos, J and Guimarães-Costa, A and Santos, S},
title = {Species delimitation by DNA barcoding reveals undescribed diversity in Stelliferinae (Sciaenidae).},
journal = {PloS one},
volume = {18},
number = {12},
pages = {e0296335},
pmid = {38153939},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Bayes Theorem ; DNA ; Phylogeny ; *Perciformes/genetics ; },
abstract = {Stelliferinae is the third most speciose subfamily of Sciaenidae, with 51 recognized species arranged in five genera. Phylogenies derived from both morphological and molecular data support the monophyly of this subfamily, although there is no general consensus on the intergeneric relationships or the species diversity of this group. We used the barcoding region of the cytochrome oxidase C subunit I (COI) gene to verify the delimitation of Stelliferinae species based on the Automatic Barcode Gap Discovery (ABGD), Generalized Mixed Yule Coalescence (GMYC), and Bayesian Poisson Tree Process (bPTP) methods. In general, the results of these different approaches were congruent, delimiting 30-32 molecular operational taxonomic units (MOTUs), most of which coincided with valid species. Specimens of Stellifer menezesi and Stellifer gomezi were attributed to a single species, which disagrees with the most recent review of this genus. The evidence also indicated that Odontoscion xanthops and Corvula macrops belong to a single MOTU. In contrast, evidence also indicates presence of distinct lineages in both Odontoscion dentex and Bairdiella chrysoura. Such results are compatible with the existence of cryptic species, which is supported by the genetic divergence and haplotype genealogy. Therefore, the results of the present study indicate the existence of undescribed diversity in the Stelliferinae, which reinforces the need for an ample taxonomic review of the fish in this subfamily.},
}
@article {pmid38153158,
year = {2024},
author = {Littleford-Colquhoun, B and Kartzinel, TR},
title = {A CRISPR-based strategy for targeted sequencing in biodiversity science.},
journal = {Molecular ecology resources},
volume = {24},
number = {3},
pages = {e13920},
doi = {10.1111/1755-0998.13920},
pmid = {38153158},
issn = {1755-0998},
support = {//Institute at Brown for Environment and Society seed award/ ; NSF DEB-2046797//National Science Foundation/ ; },
mesh = {*RNA, Guide, CRISPR-Cas Systems ; *Biodiversity ; Sequence Analysis, DNA/methods ; DNA Barcoding, Taxonomic/methods ; DNA, Plant ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Many applications in molecular ecology require the ability to match specific DNA sequences from single- or mixed-species samples with a diagnostic reference library. Widely used methods for DNA barcoding and metabarcoding employ PCR and amplicon sequencing to identify taxa based on target sequences, but the target-specific enrichment capabilities of CRISPR-Cas systems may offer advantages in some applications. We identified 54,837 CRISPR-Cas guide RNAs that may be useful for enriching chloroplast DNA across phylogenetically diverse plant species. We tested a subset of 17 guide RNAs in vitro to enrich plant DNA strands ranging in size from diagnostic DNA barcodes of 1,428 bp to entire chloroplast genomes of 121,284 bp. We used an Oxford Nanopore sequencer to evaluate sequencing success based on both single- and mixed-species samples, which yielded mean chloroplast sequence lengths of 2,530-11,367 bp, depending on the experiment. In comparison to mixed-species experiments, single-species experiments yielded more on-target sequence reads and greater mean pairwise identity between contigs and the plant species' reference genomes. But nevertheless, these mixed-species experiments yielded sufficient data to provide ≥48-fold increase in sequence length and better estimates of relative abundance for a commercially prepared mixture of plant species compared to DNA metabarcoding based on the chloroplast trnL-P6 marker. Prior work developed CRISPR-based enrichment protocols for long-read sequencing and our experiments pioneered its use for plant DNA barcoding and chloroplast assemblies that may have advantages over workflows that require PCR and short-read sequencing. Future work would benefit from continuing to develop in vitro and in silico methods for CRISPR-based analyses of mixed-species samples, especially when the appropriate reference genomes for contig assembly cannot be known a priori.},
}
@article {pmid38152695,
year = {2023},
author = {Vargas, HA},
title = {A new distribution record, first host plant record and DNA barcoding of the Neotropical micromoth Astrotischeriakarsholti Puplesis &amp; Diškus (Lepidoptera, Tischeriidae).},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e115397},
pmid = {38152695},
issn = {1314-2828},
abstract = {BACKGROUND: Astrotischeria Puplesis &amp; Diškus, 2003 (Lepidoptera, Tischeriidae) is a New World genus of micromoths whose larvae are leaf miners associated mainly with plants of the family Asteraceae. The original description of the type species Astrotischeriakarsholti Puplesis &amp; Diškus, 2003 was based on adults from central Peru. No additional distribution records, host plants or DNA barcodes have been documented for this species.<br><br>NEW INFORMATION: Astrotischeriakarsholti is reported for the first time from Chile, based on adults obtained from leaf mines of Ambrosiacumanensis Kunth (Asteraceae) collected in the transverse valleys of the Atacama Desert. This discovery expands the distribution range of this micromoth nearly 900 km to the southeast and represents its first host plant record. Divergence between DNA barcodes of A.karsholti and the nearest congeneric was 6% (K2P). A Maximum Likelihood analysis, based on DNA barcodes, raises questions about the monophyly of Astrotischeria.},
}
@article {pmid38150417,
year = {2023},
author = {Asrar, R and Masood, M and Bodlah, I and Rasool, G and Suleman, N and Yousaf, S},
title = {Molecular characterization of mitochondrial COI gene sequences in Micraspis allardi from Pakistan.},
journal = {PloS one},
volume = {18},
number = {12},
pages = {e0294034},
pmid = {38150417},
issn = {1932-6203},
mesh = {Animals ; *Electron Transport Complex IV/genetics ; Phylogeny ; Pakistan ; Biological Control Agents ; DNA, Mitochondrial/genetics ; *Coleoptera/genetics ; DNA Barcoding, Taxonomic ; },
abstract = {The Coccinellidae is a highly diversified family of order Coleoptera. Coccinellid ladybirds are well known for their role as biological control agent against varied range of agricultural pests. The samples of coccinellid ladybird collected from Pakistan were identified and characterized as Micraspis allardi (Mulsant, 1866). This is one of the least-studied ladybird species with limited work on its ecological distribution as a biological control agent. The genus Micraspis has vast genetic diversity with a possible presence of unknown number of cryptic species. Sequence information of some species of the genus Micraspis are present in NCBI database. However, least molecular data or sequences describing M. allardi could be available from database. Therefore, morphological and molecular characterization was imperative for this species. Here, the samples collected from sugarcane field of Faisalabad District of Pakistan and were identified by using morphological and molecular protocols. For molecular identification, two different regions of mitochondrial cytochrome c oxidase I (COI) gene (COI-5' and COI- 3') were used as molecular markers for the identification of the species. Morphological appearance, DNA sequence similarity searches and phylogenetic analysis collectively indicated it as M. allardi. To the best of our knowledge, this is the first report providing molecular evidence of M. allardi using mitochondrial DNA barcode region (658bp) as well as mtCOI-3' sequences (817bp). The study will help in understanding population genetics through diversity analysis, ecological role, and phenotypic structures associated with the geographic range of this species.},
}
@article {pmid38149878,
year = {2024},
author = {Shao, X and Zhang, H and Zhu, Z and Ji, F and He, Z and Yang, Z and Xia, Y and Cai, Z},
title = {Response to the Comment on "DpCoA tagSeq: Barcoding dpCoA-Capped RNA for Direct Nanopore Sequencing via Maleimide-Thiol Reaction".},
journal = {Analytical chemistry},
volume = {96},
number = {1},
pages = {610-613},
doi = {10.1021/acs.analchem.3c05281},
pmid = {38149878},
issn = {1520-6882},
mesh = {*Sulfhydryl Compounds ; *Nanopore Sequencing ; Maleimides ; RNA ; },
}
@article {pmid38149875,
year = {2024},
author = {Vinther, J},
title = {Comment on "DpCoA tagSeq: Barcoding dpCoA-Capped RNA for Direct Nanopore Sequencing via Maleimide-Thiol Reaction".},
journal = {Analytical chemistry},
volume = {96},
number = {1},
pages = {606-609},
pmid = {38149875},
issn = {1520-6882},
mesh = {*Sulfhydryl Compounds ; *Nanopore Sequencing ; Maleimides ; RNA ; },
}
@article {pmid38147298,
year = {2023},
author = {Talaga, S and Duchemin, JB},
title = {Mosquitoes (Diptera: Culicidae) of the Amazonian savannas of French Guiana with a description of two new species.},
journal = {Journal of vector ecology : journal of the Society for Vector Ecology},
volume = {49},
number = {1},
pages = {15-27},
doi = {10.52707/1081-1710-49.1.15},
pmid = {38147298},
issn = {1948-7134},
mesh = {Animals ; Male ; *Culicidae ; French Guiana ; Grassland ; *Culex ; },
abstract = {Amazonian savannas are among the most noteworthy landscape components of the coastal plain of French Guiana. Although they cover only 0.22% of the territory, they bring together a large part of the animal and plant diversity of this overseas region of France. This article outlines the results of the first study dedicated to mosquitoes (Diptera: Culicidae) of Amazonian savannas. Samplings were conducted in eight independent savannas evenly distributed along a transect of 170 km on the coastal plain of French Guiana. A total of 50 mosquito species were recorded, which is about 20% of the culicid fauna currently known in French Guiana. Among them, Culex (Melanoconion) organaboensis sp. nov. and Cx. (Mel.) zabanicus sp. nov. are newly described based on both morphological features of the male genitalia and a DNA barcode obtained from type specimens. Diagnostic characters to assist their identification are provided and their placement within the infrasubgeneric classification of the subgenus Melanoconion is discussed.},
}
@article {pmid38146909,
year = {2024},
author = {Dietz, L and Mayer, C and Stolle, E and Eberle, J and Misof, B and Podsiadlowski, L and Niehuis, O and Ahrens, D},
title = {Metazoa-level USCOs as markers in species delimitation and classification.},
journal = {Molecular ecology resources},
volume = {24},
number = {3},
pages = {e13921},
doi = {10.1111/1755-0998.13921},
pmid = {38146909},
issn = {1755-0998},
support = {AH175/6-1, 6-2//Deutsche Forschungsgemeinschaft/ ; MA 3684/5-2//Deutsche Forschungsgemeinschaft/ ; MI 649/18-2//Deutsche Forschungsgemeinschaft/ ; NI1387/6-1, 6-2//Deutsche Forschungsgemeinschaft/ ; PO 765/12-2//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; Phylogeny ; *Butterflies/genetics ; DNA ; Genome ; Hybridization, Genetic ; },
abstract = {Metazoa-level universal single-copy orthologs (mzl-USCOs) are universally applicable markers for DNA taxonomy in animals that can replace or supplement single-gene barcodes. Previously, mzl-USCOs from target enrichment data were shown to reliably distinguish species. Here, we tested whether USCOs are an evenly distributed, representative sample of a given metazoan genome and therefore able to cope with past hybridization events and incomplete lineage sorting. This is relevant for coalescent-based species delimitation approaches, which critically depend on the assumption that the investigated loci do not exhibit autocorrelation due to physical linkage. Based on 239 chromosome-level assembled genomes, we confirmed that mzl-USCOs are genetically unlinked for practical purposes and a representative sample of a genome in terms of reciprocal distances between USCOs on a chromosome and of distribution across chromosomes. We tested the suitability of mzl-USCOs extracted from genomes for species delimitation and phylogeny in four case studies: Anopheles mosquitos, Drosophila fruit flies, Heliconius butterflies and Darwin's finches. In almost all instances, USCOs allowed delineating species and yielded phylogenies that corresponded to those generated from whole genome data. Our phylogenetic analyses demonstrate that USCOs may complement single-gene DNA barcodes and provide more accurate taxonomic inferences. Combining USCOs from sources that used different versions of ortholog reference libraries to infer marker orthology may be challenging and, at times, impact taxonomic conclusions. However, we expect this problem to become less severe as the rapidly growing number of reference genomes provides a better representation of the number and diversity of organismal lineages.},
}
@article {pmid38145378,
year = {2023},
author = {Van Heest, AE and Deng, F and Zhao, RT and Harzallah, NS and Fleming, HE and Bhatia, SN and Hao, L},
title = {CRISPR-Cas-mediated Multianalyte Synthetic Urine Biomarker Test for Portable Diagnostics.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {202},
pages = {},
pmid = {38145378},
issn = {1940-087X},
support = {T32 GM130546/GM/NIGMS NIH HHS/United States ; P30 CA014051/CA/NCI NIH HHS/United States ; P30 ES002109/ES/NIEHS NIH HHS/United States ; T32 EB006359/EB/NIBIB NIH HHS/United States ; R00 CA237861/CA/NCI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; Mice ; *CRISPR-Cas Systems ; Urinalysis ; *Body Fluids ; Biomarkers ; DNA/genetics ; },
abstract = {Creating synthetic biomarkers for the development of precision diagnostics has enabled detection of disease through pathways beyond those used for traditional biofluid measurements. Synthetic biomarkers generally make use of reporters that provide readable signals in the biofluid to reflect the biochemical alterations in the local disease microenvironment during disease incidence and progression. The pharmacokinetic concentration of the reporters and biochemical amplification of the disease signal are paramount to achieving high sensitivity and specificity in a diagnostic test. Here, a cancer diagnostic platform is built using one format of synthetic biomarkers: activity-based nanosensors carrying chemically stabilized DNA reporters that can be liberated by aberrant proteolytic signatures in the tumor microenvironment. Synthetic DNA as a disease reporter affords multiplexing capability through its use as a barcode, allowing for the readout of multiple proteolytic signatures at once. DNA reporters released into the urine are detected using CRISPR nucleases via hybridization with CRISPR RNAs, which in turn produce a fluorescent or colorimetric signal upon enzyme activation. In this protocol, DNA-barcoded, activity-based nanosensors are constructed and their application is exemplified in a preclinical mouse model of metastatic colorectal cancer. This system is highly modifiable according to disease biology and generates multiple disease signals simultaneously, affording a comprehensive understanding of the disease characteristics through a minimally invasive process requiring only nanosensor administration, urine collection, and a paper test which enables point-of-care diagnostics.},
}
@article {pmid38143577,
year = {2023},
author = {Krawczyk, K and Paukszto, &#x141; and Maździarz, M and Sawicki, J},
title = {The low level of plastome differentiation observed in some lineages of Poales hinders molecular species identification.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1275377},
pmid = {38143577},
issn = {1664-462X},
abstract = {Chloroplast genomes are a source of information successfully used in various fields of plant genetics, including molecular species identification. However, recent studies indicate an extremely low level of interspecific variability in the plastomes of some taxonomic groups of plants, including the genus Stipa L., which is a representative of the grass family. In this study we aimed to analyze the level of chloroplast genome diversity within particular genera as well as the effectiveness of identifying plant species in the Poaceae family and the other representatives of Poales order. Analysis of complete plastid genome alignments created for 96 genera comprising 793 species and 1707 specimens obtained from the GenBank database allowed defining and categorizing molecular diagnostic characters distinguishing the analyzed species from the other representatives of the genus. The results also demonstrate which species do not have any species-specific mutations, thereby they cannot be identified on the basis of differences between the complete chloroplast genomes. Our research showed a huge diversity of the analyzed species in terms of the number of molecular diagnostic characters and indicated which genera pose a particular challenge in terms of molecular species identification. The results show that a very low level of genetic diversity between plastomes is not uncommon in Poales. This is the first extensive research on super-barcoding that tests this method on a large data set and illustrates its effectiveness against the background of phylogenetic relationships.},
}
@article {pmid38142412,
year = {2024},
author = {Lee, S and Povey, A and van Tongeren, M},
title = {The application of the mobile application for the assessment of cleaning workers' exposure to cleaning products: a pilot study.},
journal = {Annals of work exposures and health},
volume = {68},
number = {2},
pages = {211-216},
pmid = {38142412},
issn = {2398-7316},
mesh = {Humans ; *Occupational Exposure/adverse effects ; Pilot Projects ; *Mobile Applications ; Hazardous Substances ; *Asthma ; },
abstract = {BACKGROUND: Cleaning product use has been associated with adverse respiratory health effects such as asthma in cleaning staff and healthcare workers. Research in health effects from cleaning products has largely depended upon collecting exposure information by questionnaires which has limitations such as recall bias and underestimation of exposure. The aim of this study was to develop a Cleaning and Hazardous Products Exposure Logging (CHaPEL) app with a barcode scanner and to test the feasibility of this app with university cleaners.<br><br>METHODS: The CHaPEL app was developed to collect information on demographics, individual product information, and exposure information. It also included an ease-of-use survey. A pilot study with university cleaning workers was undertaken in which cleaning workers scanned each product after use and answered the survey. Respiratory hazards of cleaning substances in the scanned cleaning products were screened by safety data sheets, a Quantitative Structure-Activity Relationship model and an asthmagen list established by an expert group in the US.<br><br>RESULTS: Eighteen university cleaners participated in this study over a period of 5 weeks. In total, 77 survey responses and 6 cleaning products were collected and all reported that using the app was easy. The most frequently used product was a multi-surface cleaner followed by a disinfectant. Out of 14 substances in cleaning products, ethanolamine and Alkyl (C12-16) dimethyl benzyl ammonium chloride were found as respiratory hazardous substances.<br><br>CONCLUSION: The CHaPEL app is a user-friendly immediate way to successfully collect exposure information using the barcodes of cleaning products. This tool could be useful for future epidemiological studies focused on exposure assessment with less interruption to the workers.},
}
@article {pmid38141036,
year = {2024},
author = {Lee, I and Kwon, SJ and Heeger, P and Dordick, JS},
title = {Ultrasensitive ImmunoMag-CRISPR Lateral Flow Assay for Point-of-Care Testing of Urinary Biomarkers.},
journal = {ACS sensors},
volume = {9},
number = {1},
pages = {92-100},
pmid = {38141036},
issn = {2379-3694},
support = {U01 AI063594/AI/NIAID NIH HHS/United States ; U01 AI170424/AI/NIAID NIH HHS/United States ; },
mesh = {Biomarkers/urine ; *Point-of-Care Testing ; },
abstract = {Rapid, accurate, and noninvasive detection of biomarkers in saliva, urine, or nasal fluid is essential for the identification, early diagnosis, and monitoring of cancer, organ failure, transplant rejection, vascular diseases, autoimmune disorders, and infectious diseases. We report the development of an Immuno-CRISPR-based lateral flow assay (LFA) using antibody-DNA barcode complexes with magnetic enrichment of the target urinary biomarkers CXCL9 and CXCL10 for naked eye detection (ImmunoMag-CRISPR LFA). An intermediate approach involving a magnetic bead-based Immuno-CRISPR assay (ImmunoMag-CRISPR) resulted in a limit of detection (LOD) of 0.6 pg/mL for CXCL9. This value surpasses the detection limits achieved by previously reported assays. The highly sensitive detection method was then re-engineered into an LFA format with an LOD of 18 pg/mL for CXCL9, thereby enabling noninvasive early detection of acute kidney transplant rejection. The ImmunoMag-CRISPR LFA was tested on 42 clinical urine samples from kidney transplant recipients, and the assay could determine 11 positive and 31 negative urinary samples through a simple visual comparison of the test line and the control line of the LFA strip. The LFA system was then expanded to quantify the CXCL9 and CXCL10 levels in clinical urine samples from images. This approach has the potential to be extended to a wide range of point-of-care tests for highly sensitive biomarker detection.},
}
@article {pmid38136915,
year = {2023},
author = {Glowska, E and Laniecka, I and Ostrowska, K and Gebhard, CA and Olechnowicz, J and Dabert, M},
title = {Evaluation of Genetic Diversity in Quill Mites of the Genus Syringophiloidus Kethley, 1970 (Prostigmata: Syringophilidae) with Six New-to-Science Species.},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {24},
pages = {},
pmid = {38136915},
issn = {2076-2615},
support = {2015/19/D/NZ8/00191//National Science Center/ ; },
abstract = {Quill mites (Acariformes: Syringophilidae) are poorly explored bird parasites. Syringophiloidus Kethley, 1970, is the most specious and widespread genus in this family. It is believed to contain mono-, steno- and poly-xenous parasites and thus seems to be an exemplary for studies on biodiversity and host associations. In this work, we applied the DNA barcode marker (mitochondrial cytochrome c oxidase subunit I gene fragment, COI) to analyze the species composition and host specificity of representatives of fifteen Syringophiloidus populations parasitizing fifteen bird species. The neighbor joining analyses distinguished thirteen monophyletic lineages, almost completely corresponding to seven previously known species recognized based on morphological features, and six new-to-science species. The only exception is S. amazilia Skoracki, 2017, which is most likely conspecific with Syringophiloidus stawarczyki Skoracki, 2004. The intraspecific distances of all species were not higher than 0.9%, whilst the interspecific diversity ranged from 5.9% to 19.2% and 6.3-22.4%, inferred as the distances p and K2P, respectively. Although all putative species (except S. amazilia) are highly supported, the relationships between them have not been fully resolved and only faintly indicate that both host phylogeny and distributions influence the phylogenetic structure of quill mite taxa.},
}
@article {pmid38134194,
year = {2023},
author = {Tolley-Jordan, LR and Chadwick, MA and Triplett, JK},
title = {DNA barcoding indicates multiple invasions of the freshwater snail Melanoides tuberculata sensu lato in Florida.},
journal = {PloS one},
volume = {18},
number = {12},
pages = {e0292164},
pmid = {38134194},
issn = {1932-6203},
mesh = {Animals ; Female ; Phylogeny ; Florida ; *DNA Barcoding, Taxonomic ; *Snails/genetics ; DNA ; Fresh Water ; },
abstract = {Melanoides tuberculata sensu lato (Thiaridae) are polymorphic female-clonal snails of Asian and African origins that have invaded freshwaters worldwide, including those in Florida. Although the snails have been documented in Florida for at least 70 years, no studies have investigated whether the observed distribution is due to a single introduction or multiple independent invasions. Here, cytochrome oxidase I was used to measure genetic diversity within and among sites in Florida and compare genetic diversity between Florida and other regions of the world. We also examined the relationship between shell morphology and haplotype diversity to determine if shell morphs can serve as a proxy for haplotypes. In total, we recovered 8 haplotypes randomly distributed across populations in Florida. Phylogenetic reconstruction supported the hypothesis of multiple invasions by diverse representatives of the M. tuberculata species complex. In contrast, shell morphology was not found to be a useful phylogeographic character, with divergent haplotypes represented by similar shell forms. These results suggest that the observed invasion patterns in Florida are best explained by serial introductions, and that shell morphology cannot be used to predict haplotypes or reconstruct invasion history of Melanoides tuberculata s.l. and that extensive taxonomic revisions are needed to investigate invasion dynamics.},
}
@article {pmid38132616,
year = {2023},
author = {Shapoval, NA and Kir'yanov, AV and Krupitsky, AV and Yakovlev, RV and Romanovich, AE and Zhang, J and Cong, Q and Grishin, NV and Kovalenko, MG and Shapoval, GN},
title = {Phylogeography of Two Enigmatic Sulphur Butterflies, Colias mongola Alphéraky, 1897 and Colias tamerlana Staudinger, 1897 (Lepidoptera, Pieridae), with Relations to Wolbachia Infection.},
journal = {Insects},
volume = {14},
number = {12},
pages = {},
pmid = {38132616},
issn = {2075-4450},
support = {22-24-01086//Russian Science Foundation/ ; },
abstract = {The genus Colias Fabricius, 1807 includes numerous taxa and forms with uncertain status and taxonomic position. Among such taxa are Colias mongola Alphéraky, 1897 and Colias tamerlana Staudinger, 1897, interpreted in the literature either as conspecific forms, as subspecies of different but morphologically somewhat similar Colias species or as distinct species-level taxa. Based on mitochondrial and nuclear DNA markers, we reconstructed a phylogeographic pattern of the taxa in question. We recover and include in our analysis DNA barcodes of the century-old type specimens, the lectotype of C. tamerlana deposited in the Natural History Museum (Museum für Naturkunde), Berlin, Germany (ZMHU) and the paralectotype of C. tamerlana and the lectotype of C. mongola deposited in the Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia (ZISP). Our analysis grouped all specimens within four (HP_I-HP_IV) deeply divergent but geographically poorly structured clades which did not support nonconspecifity of C. mongola-C. tamerlana. We also show that all studied females of the widely distributed haplogroup HP_II were infected with a single Wolbachia strain belonging to the supergroup B, while the males of this haplogroup, as well as all other investigated specimens of both sexes, were not infected. Our data highlight the relevance of large-scale sampling dataset analysis and the need for testing for Wolbachia infection to avoid erroneous phylogenetic reconstructions and species misidentification.},
}
@article {pmid38132615,
year = {2023},
author = {Lukhtanov, VA and Zakharov, EV},
title = {Taxonomic Structure and Wing Pattern Evolution in the Parnassius mnemosyne Species Complex (Lepidoptera, Papilionidae).},
journal = {Insects},
volume = {14},
number = {12},
pages = {},
pmid = {38132615},
issn = {2075-4450},
support = {19-14-00202//Russian Science Foundation/ ; },
abstract = {In our study, using the analysis of DNA barcodes and morphology (wing color, male genitalia, and female sphragis shape), we show that the group of species close to P. mnemosyne comprises the western and eastern phylogenetic lineages. The eastern lineage includes P. stubbendorfii, P. glacialis, and P. hoenei. The western lineage includes three morphologically similar species: P. mnemosyne (Western Eurasia), P. turatii (southwestern Europe), and P. nubilosusstat. nov. (Turkmenistan and NE Iran), as well as the morphologically differentiated P. ariadne (Altai). The latter species differs from the rest of the group in the presence of red spots on the wings. Parnassius mnemosyne s.s. is represented by four differentiated mitochondrial clusters that show clear association with specific geographic regions. We propose to interpret them as subspecies: P. mnemosyne mnemosyne (Central and Eastern Europe, N Caucasus, N Turkey), P. mnemosyne adolphi (the Middle East), P. mnemosyne falsa (Tian Shan), and P. mnemosyne gigantea (Gissar-Alai in Central Asia). We demonstrate that in P. ariadne, the red spots on the wing evolved as a reversion to the ancestral wing pattern. This reversion is observed in Altai, where the distribution areas of the western lineage, represented by P. ariadne, and the eastern lineage, represented by P. stubbendorfii, overlap. These two species hybridize in Altai, and we hypothesize that the color change in P. ariadne is the result of reinforcement of prezygotic isolation in the contact zone. The lectotype of Parnassius mnemosyne var. nubilosus Christoph, 1873, is designated.},
}
@article {pmid38132578,
year = {2023},
author = {Zadra, N and Tatti, A and Silverj, A and Piccinno, R and Devilliers, J and Lewis, C and Arnoldi, D and Montarsi, F and Escuer, P and Fusco, G and De Sanctis, V and Feuda, R and Sánchez-Gracia, A and Rizzoli, A and Rota-Stabelli, O},
title = {Shallow Whole-Genome Sequencing of Aedes japonicus and Aedes koreicus from Italy and an Updated Picture of Their Evolution Based on Mitogenomics and Barcoding.},
journal = {Insects},
volume = {14},
number = {12},
pages = {},
pmid = {38132578},
issn = {2075-4450},
support = {PRIN 2022 Prot. n 2022YNL8ZH//Partially funded by the European Union under NextGenerationEU/ ; },
abstract = {Aedes japonicus and Aedes koreicus are two invasive mosquitoes native to East Asia that are quickly establishing in temperate regions of Europe. Both species are vectors of arboviruses, but we currently lack a clear understanding of their evolution. Here, we present new short-read, shallow genome sequencing of A. japonicus and A. koreicus individuals from northern Italy, which we used for downstream phylogenetic and barcode analyses. We explored associated microbial DNA and found high occurrences of Delftia bacteria in both samples, but neither Asaia nor Wolbachia. We then assembled complete mitogenomes and used these data to infer divergence times estimating the split of A. japonicus from A. koreicus in the Oligocene, which was more recent than that previously reported using mitochondrial markers. We recover a younger age for most other nodes within Aedini and other Culicidae. COI barcoding and phylogenetic analyses indicate that A. japonicus yaeyamensis, A. japonicus amamiensis, and the two A. koreicus sampled from Europe should be considered as separate species within a monophyletic species complex. Our studies further clarify the evolution of A. japonicus and A. koreicus, and indicate the need to obtain whole-genome data from putative species in order to disentangle their complex patterns of evolution.},
}
@article {pmid38131272,
year = {2023},
author = {Karakas, E and Ferrante, P and Schafleitner, R and Giuliano, G and Fernie, AR and Alseekh, S},
title = {Plant Sample Collection and Shipment for Multi-omic Analyses and Phytosanitary Evaluation.},
journal = {Current protocols},
volume = {3},
number = {12},
pages = {e952},
doi = {10.1002/cpz1.952},
pmid = {38131272},
issn = {2691-1299},
mesh = {*Multiomics ; *Metabolomics/methods ; Metabolome ; Specimen Handling ; DNA, Plant/genetics ; Plants/genetics ; },
abstract = {Plant sample preparation for analyses is a fundamental step in high-throughput omics strategies. Especially for plant metabolomics, quenching of hydrolytic enzymes able to affect metabolite concentrations is crucial for the accuracy of results. Given that DNA is usually less labile than metabolites, most sampling and shipment procedures able to preserve the metabolome are also suitable for preventing the degradation of plant DNA or of DNA of pathogens in the plant tissue. In this article, we describe all the steps of sample collection, shipment (including the phytosanitary issues of moving plant samples), and processing for combined genomics and metabolomics from a single sample, as well as the protocols used in our laboratories for downstream approaches for crop plants, allowing collection of multi-omic datasets in large experimental setups. The protocols have been adjusted to apply to both freeze-dried and fresh-frozen material to allow the processing of crop plant samples that will require long-distance transport. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of freeze-dried leaf disks for multiplexed PCR or DArT-Seq genotyping Basic Protocol 2: Medium-throughput preparation of pathogen-free nucleic acids for most genotyping-resequencing applications or pathogen detection Alternate Protocol: Low-throughput extraction of high-quality DNA for resequencing using commercial kits Support Protocol: DNA quality control Basic Protocol 3: Preparation of freeze-dried plant material for metabolomics Basic Protocol 4: Preparation of fresh-frozen plant material for metabolomics Basic Protocol 5: Preparation and shipment of metabolite extracts for metabolomic analyses Basic Protocol 6: Sample shipping and long-term storage.},
}
@article {pmid38128795,
year = {2024},
author = {Sgarlata, GM and Rasolondraibe, E and Salmona, J and Le Pors, B and Ralantoharijaona, T and Rakotonanahary, A and Jan, F and Manzi, S and Iribar, A and Zaonarivelo, JR and Volasoa Andriaholinirina, N and Rasoloharijaona, S and Chikhi, L},
title = {The genomic diversity of the Eliurus genus in northern Madagascar with a putative new species.},
journal = {Molecular phylogenetics and evolution},
volume = {193},
number = {},
pages = {107997},
doi = {10.1016/j.ympev.2023.107997},
pmid = {38128795},
issn = {1095-9513},
mesh = {Rats ; Animals ; Phylogeny ; Madagascar ; *Ecosystem ; *Biodiversity ; Forests ; Rodentia/genetics ; DNA, Mitochondrial/genetics ; Genomics ; },
abstract = {Madagascar exhibits extraordinarily high level of species richness and endemism, while being severely threatened by habitat loss and fragmentation (HL&amp;F). In front of these threats to biodiversity, conservation effort can be directed, for instance, in the documentation of species that are still unknown to science, or in investigating how species respond to HL&amp;F. The tufted-tail rats genus (Eliurus spp.) is the most speciose genus of endemic rodents in Madagascar, with 13 described species, which occupy two major habitat types: dry or humid forests. The large species diversity and association to specific habitat types make the Eliurus genus a suitable model for investigating species adaptation to new environments, as well as response to HL&amp;F (dry vs humid). In the present study, we investigated Eliurus spp. genomic diversity across northern Madagascar, a region covered by both dry and humid fragmented forests. From the mitochondrial DNA (mtDNA) and nuclear genomic (RAD-seq) data of 124 Eliurus individuals sampled in poorly studied forests of northern Madagascar, we identified an undescribed Eliurus taxon (Eliurus sp. nova). We tested the hypothesis of a new Eliurus species using several approaches: i) DNA barcoding; ii) phylogenetic inferences; iii) species delimitation tests based on the Multi-Species Coalescent (MSC) model, iv) genealogical divergence index (gdi); v) an ad-hoc test of isolation-by-distance within versus between sister-taxa, vi) comparisons of %GC content patterns and vii) morphological analyses. All analyses support the recognition of the undescribed lineage as a putative distinct species. In addition, we show that Eliurus myoxinus, a species known from the dry forests of western Madagascar, is, surprisingly, found mostly in humid forests in northern Madagascar. In conclusion, we discuss the implications of such findings in the context of Eliurus species evolution and diversification, and use the distribution of northern Eliurus species as a proxy for reconstructing past changes in forest cover and vegetation type in northern Madagascar.},
}
@article {pmid38127267,
year = {2024},
author = {Sandberg, E and Demirbay, B and Kulkarni, A and Liu, H and Piguet, J and Widengren, J},
title = {Fluorescence Bar-Coding and Flowmetry Based on Dark State Transitions in Fluorescence Emitters.},
journal = {The journal of physical chemistry. B},
volume = {128},
number = {1},
pages = {125-136},
pmid = {38127267},
issn = {1520-5207},
mesh = {Spectrometry, Fluorescence/methods ; Carbocyanines/chemistry ; Rhodamines ; *Fluorescent Dyes/chemistry ; *Microfluidics ; },
abstract = {Reversible dark state transitions in fluorophores represent a limiting factor in fluorescence-based ultrasensitive spectroscopy, are a necessary basis for fluorescence-based super-resolution imaging, but may also offer additional, largely orthogonal fluorescence-based readout parameters. In this work, we analyzed the blinking kinetics of Cyanine5 (Cy5) as a bar-coding feature distinguishing Cy5 from rhodamine fluorophores having largely overlapping emission spectra. First, fluorescence correlation spectroscopy (FCS) solution measurements on mixtures of free fluorophores and fluorophore-labeled small unilamellar vesicles (SUVs) showed that Cy5 could be readily distinguished from the rhodamines by its reversible, largely excitation-driven trans-cis isomerization. This was next confirmed by transient state (TRAST) spectroscopy measurements, determining the fluorophore dark state kinetics in a more robust manner, from how the time-averaged fluorescence intensity varies upon modulation of the applied excitation light. TRAST was then combined with wide-field imaging of live cells, whereby Cy5 and rhodamine fluorophores could be distinguished on a whole cell level as well as in spatially resolved, multiplexed images of the cells. Finally, we established a microfluidic TRAST concept and showed how different mixtures of free Cy5 and rhodamine fluorophores and corresponding fluorophore-labeled SUVs could be distinguished on-the-fly when passing through a microfluidic channel. In contrast to FCS, TRAST does not rely on single-molecule detection conditions or a high time resolution and is thus broadly applicable to different biological samples. Therefore, we expect that the bar-coding concept presented in this work can offer an additional useful strategy for fluorescence-based multiplexing that can be implemented on a broad range of both stationary and moving samples.},
}
@article {pmid38126902,
year = {2024},
author = {Wu, Z and Zheng, Y and Lin, L and Lin, Y and Xie, T and Lin, J and Xing, G and Lin, JM},
title = {Fabrication and Performance of Bubble-Containing Multicompartmental Particles: Novel Self-Orienting Carriers.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {20},
number = {17},
pages = {e2306814},
doi = {10.1002/smll.202306814},
pmid = {38126902},
issn = {1613-6829},
support = {82073816//National Natural Science Foundation of China/ ; 22034005//National Natural Science Foundation of China/ ; 22322401//National Natural Science Foundation of China/ ; 20220484055//Beijing Nova Program/ ; },
abstract = {In this work, a class of bubble-containing multicompartmental particles with self-orienting capability is developed, where a single bubble is enclosed at the top of the super-segmented architecture. Such bubbles, driven by potential energy minimization, cause the particles to have a bubble-upward preferred orientation in liquid, enabling efficient decoding of their high-density signals in an interference-resistant manner. The particle preparation involves bubble encapsulation via the impact of a multicompartmental droplet on the liquid surface and overall stabilization via rational crosslinking. The conditions for obtaining these particles are systematically investigated. Methodological compatibility with materials is demonstrated by different hydrogel particles. Finally, by encapsulating cargoes of interest, these particles have found broad applications in actuators, multiplexed detection, barcodes, and multicellular systems.},
}
@article {pmid38126630,
year = {2023},
author = {Wahyuni, DK and Yoku, BF and Mukarromah, SR and Purnama, PR and Ilham, M and Rakashiwi, GA and Indriati, DT and Junairiah, and Wacharasindhu, S and Prasongsuk, S and Subramaniam, S and Purnobasuki, H},
title = {Unraveling the secrets of Eclipta alba (L.) Hassk.: a comprehensive study of morpho-anatomy and DNA barcoding.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {83},
number = {},
pages = {e274315},
doi = {10.1590/1519-6984.274315},
pmid = {38126630},
issn = {1678-4375},
mesh = {*Eclipta ; DNA Barcoding, Taxonomic ; Phylogeny ; Plant Leaves/anatomy &amp; histology ; Flowers ; },
abstract = {Safety regarding herbal products is very necessary; therefore, routine identification of raw materials should be performed to ensure that the raw materials used in pharmaceutical products are suitable for their intended use. In order for the identification-related data obtained to be accurate, the identification of various kinds of markers is also very necessary. The purpose of this study was to describe the characteristics of Eclipta alba (L.) Hassk. based on qualitative morpho-anatomical markers and quantitative DNA coding. The morphology of this plant has herbaceous habit with a taproot and a stem with branches that appear from the middle. Leaves are single type imperfectly arranged oppositely, lanceolatus, finely serrated on the edges, tapered at the base, pointed at the end, and have a pinnate and hairy leaf surface. The flowers consist of ray flowers and tube flowers with a cup shape. Meanwhile, in terms of anatomy, E. alba has aerenchyma, which are scattered in the cortex of the root and stem. In addition, there are anisocytic stomata, glandular trichomes, and non-glandural trichomes with an elongated shape accompanied by ornamentation found on the leaf epidermis. The results of sequence alignment and phylogenetic tree reconstruction show that the sample plants are closely related to species in the genus Eclipta.},
}
@article {pmid38125953,
year = {2023},
author = {Tadmor-Levi, R and Feldstein-Farkash, T and Milstein, D and Golani, D and Leader, N and Goren, M and David, L},
title = {Revisiting the species list of freshwater fish in Israel based on DNA barcoding.},
journal = {Ecology and evolution},
volume = {13},
number = {12},
pages = {e10812},
pmid = {38125953},
issn = {2045-7758},
abstract = {Israel's region forms a continental bridge; hence, the freshwater fish fauna in Israel consists of unique populations of species that originated from Africa, Asia, or Europe and are often endemic or at the edge of their distribution range. Worldwide, fish biodiversity suffers significantly from pressures and disturbances of freshwater habitats, especially in arid regions, such as in parts of Israel. Biodiversity conservation requires efficient tools for monitoring changes in populations. DNA barcoding, by complementing and enhancing species identification, provides such monitoring tools. In this study, over 200 specimens representing over 28 species were DNA barcoded and together with previously available records, a DNA barcoding database for freshwater fish of Israel was established. Of the 71 distinct barcodes generated, 37% were new, attesting to the uniqueness of fish populations in Israel. For most species, morphological and molecular species identifications agreed. However, discrepancies were found for five genera. Based on DNA barcoding, we propose Acanthobrama telavivensis as a junior synonym for Acanthobrama lissneri. In Garra spp., we propose splitting Garra nana into two species and assigning Garra rufa in the region to Garra jordanica, or possibly to two species. Israeli Pseudophoxinus kervillei is not the same species as in Syria and Lebanon. However, Pseudophoxinus syriacus might not be endangered since it is genetically very similar to Pseudophoxinus drusensis. In Israel, instead of five reported Oxynoemacheilus species, combining DNA barcoding with morphology suggests only three. Genetic and geographic separation suggested that Aphanius mento is likely a species complex. The study provides a thorough barcoding database, suggests significant species reconsiderations in the region, and highlights the Sea of Galilee and the Beit She'an valley streams as biodiversity "hotspots." This study will therefore promote further studying of the fish species in the region and their ecology, as well as the monitoring and conservation of freshwater fish biodiversity in Israel and the region.},
}
@article {pmid38124090,
year = {2023},
author = {Bleich, RM and Li, C and Sun, S and Ahn, JH and Dogan, B and Barlogio, CJ and Broberg, CA and Franks, AR and Bulik-Sullivan, E and Carroll, IM and Simpson, KW and Fodor, AA and Arthur, JC},
title = {A consortia of clinical E. coli strains with distinct in vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {277},
pmid = {38124090},
issn = {2049-2618},
support = {P40 OD010995/OD/NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; P30DK034987/NH/NIH HHS/United States ; K12 GM000678/GM/NIGMS NIH HHS/United States ; R21 AI159786/AI/NIAID NIH HHS/United States ; K01 DK103952/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Humans ; Mice ; Young Adult ; Dysbiosis/complications ; Escherichia coli/genetics ; *Escherichia coli Infections/microbiology ; *Gastrointestinal Microbiome ; Inflammation/metabolism ; Interleukin-10 ; Intestinal Mucosa/microbiology ; RNA, Ribosomal, 16S/genetics/metabolism ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) patients experience recurrent episodes of intestinal inflammation and often follow an unpredictable disease course. Mucosal colonization with adherent-invasive Escherichia coli (AIEC) are believed to perpetuate intestinal inflammation. However, it remains unclear if the 24-year-old AIEC in vitro definition fully predicts mucosal colonization in vivo. To fill this gap, we have developed a novel molecular barcoding approach to distinguish strain variants in the gut and have integrated this approach to explore mucosal colonization of distinct patient-derived E. coli isolates in gnotobiotic mouse models of colitis.<br><br>RESULTS: Germ-free inflammation-susceptible interleukin-10-deficient (Il10[-/-]) and inflammation-resistant WT mice were colonized with a consortium of AIEC and non-AIEC strains, then given a murine fecal transplant to provide niche competition. E. coli strains isolated from human intestinal tissue were each marked with a unique molecular barcode that permits identification and quantification by barcode-targeted sequencing. 16S rRNA sequencing was used to evaluate the microbiome response to E. coli colonization. Our data reveal that specific AIEC and non-AIEC strains reproducibly colonize the intestinal mucosa of WT and Il10[-/-] mice. These E. coli expand in Il10[-/-] mice during inflammation and induce compositional dysbiosis to the microbiome in an inflammation-dependent manner. In turn, specific microbes co-evolve in inflamed mice, potentially diversifying E. coli colonization patterns. We observed no selectivity in E. coli colonization patterns in the fecal contents, indicating minimal selective pressure in this niche from host-microbe and interbacterial interactions. Because select AIEC and non-AIEC strains colonize the mucosa, this suggests the in vitro AIEC definition may not fully predict in vivo colonization potential. Further comparison of seven E. coli genomes pinpointed unique genomic features contained only in highly colonizing strains (two AIEC and two non-AIEC). Those colonization-associated features may convey metabolic advantages (e.g., iron acquisition and carbohydrate consumption) to promote efficient mucosal colonization.<br><br>CONCLUSIONS: Our findings establish the in vivo mucosal colonizer, not necessarily AIEC, as a principal dysbiosis driver through crosstalk with host and associated microbes. Furthermore, we highlight the utility of high-throughput screens to decode the in vivo colonization dynamics of patient-derived bacteria in murine models. Video Abstract.},
}
@article {pmid38114145,
year = {2023},
author = {Liu, QZ and Dai, JP and Zhu, PJ and Lin, YX and Gao, XX and Zhu, S},
title = {[Characterization and phylogenetic analysis of complete chloroplast genome of cultivated Qinan agarwood].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {48},
number = {20},
pages = {5531-5539},
doi = {10.19540/j.cnki.cjcmm.20230617.101},
pmid = {38114145},
issn = {1001-5302},
mesh = {Phylogeny ; *Genome, Chloroplast ; Codon ; Molecular Sequence Annotation ; *Thymelaeaceae/genetics ; },
abstract = {"Tangjie" leaves of cultivated Qinan agarwood were used to obtain the complete chloroplast genome using high-throughput sequencing technology. Combined with 12 chloroplast genomes of Aquilaria species downloaded from NCBI, bioinformatics method was employed to determine the chloroplast genome characteristics and phylogenetic relationships. The results showed that the chloroplast genome sequence length of cultivated Qinan agarwood "Tangjie" leaves was 174 909 bp with a GC content of 36.7%. A total of 136 genes were annotated, including 90 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Sequence repeat analysis detected 80 simple sequence repeats(SSRs) and 124 long sequence repeats, with most SSRs composed of A and T bases. Codon preference analysis revealed that AUU was the most frequently used codon, and codons with A and U endings were preferred. Comparative analysis of Aquilaria chloroplast genomes showed relative conservation of the IR region boundaries and identified five highly variable regions: trnD-trnY, trnT-trnL, trnF-ndhJ, petA-cemA, and rpl32, which could serve as potential DNA barcodes specific to the Aquilaria genus. Selection pressure analysis indicated positive selection in the rbcL, rps11, and rpl32 genes. Phylogenetic analysis revealed that cultivated Qinan agarwood "Tangjie" and Aquilaria agallocha clustered together(100% support), supporting the Chinese origin of Qinan agarwood from Aquilaria agallocha. The chloroplast genome data obtained in this study provide a foundation for studying the genetic diversity of cultivated Qinan agarwood and molecular identification of the Aquilaria genus.},
}
@article {pmid38113555,
year = {2024},
author = {Ohyama, H and Hirotsu, Y and Amemiya, K and Mikata, R and Amano, H and Hirose, S and Oyama, T and Iimuro, Y and Kojima, Y and Mochizuki, H and Kato, N and Omata, M},
title = {Development of a molecular barcode detection system for pancreaticobiliary malignancies and comparison with next-generation sequencing.},
journal = {Cancer genetics},
volume = {280-281},
number = {},
pages = {6-12},
doi = {10.1016/j.cancergen.2023.12.002},
pmid = {38113555},
issn = {2210-7762},
mesh = {Humans ; *Neoplasms ; Liquid Biopsy ; Mutation/genetics ; High-Throughput Nucleotide Sequencing ; DNA ; },
abstract = {BACKGROUND: Obtaining sufficient tumor tissue for genomic profiling is challenging in pancreaticobiliary cancer (PBCA). We determined the utility of molecular barcoding (MB) of liquid biopsies (bile, duodenal fluid, and plasma) for highly sensitive genomic diagnosis and detection of druggable mutations for PBCA.<br><br>METHODS: Two in-house panels of 60 genes (non-MB panel) and 21 genes using MB (MB panel) were used for the genomic analysis of 112 DNA samples from 20 PBCA patients. We measured the yield of DNA and compared the genomic profiles of liquid samples obtained using the non-MB panel and the MB panel. The utility of the panels in detecting druggable mutations was investigated.<br><br>RESULTS: A significantly greater amount of DNA was obtained from bile supernatants and precipitates compared to tumor samples (P < 0.001 and P&#xa0;=&#xa0;0.001, respectively). The number of mutations per patient was significantly higher using the MB panel than using the non-MB panel (2.8&#xa0;vs. 1.3, P&#xa0;=&#xa0;0.002). Tumor-derived mutations were detected more frequently using the MB panel than the non-MB panel (P&#xa0;=&#xa0;0.023). Five drug-matched mutations were detected in liquid samples.<br><br>CONCLUSIONS: Liquid biopsy with MB may have utility in providing genomic information for the prognosis of patients with PBCA.},
}
@article {pmid38110579,
year = {2024},
author = {Russell, AJC and Weir, JA and Nadaf, NM and Shabet, M and Kumar, V and Kambhampati, S and Raichur, R and Marrero, GJ and Liu, S and Balderrama, KS and Vanderburg, CR and Shanmugam, V and Tian, L and Iorgulescu, JB and Yoon, CH and Wu, CJ and Macosko, EZ and Chen, F},
title = {Publisher Correction: Slide-tags enables single-nucleus barcoding for multimodal spatial genomics.},
journal = {Nature},
volume = {625},
number = {7994},
pages = {E11},
doi = {10.1038/s41586-023-06961-1},
pmid = {38110579},
issn = {1476-4687},
}
@article {pmid38110100,
year = {2024},
author = {Augusto, AM and Raposeira, H and Horta, P and Mata, VA and Aizpurua, O and Alberdi, A and Jones, G and Razgour, O and Santos, SAP and Russo, D and Rebelo, H},
title = {Bat diversity boosts ecosystem services: Evidence from pine processionary moth predation.},
journal = {The Science of the total environment},
volume = {912},
number = {},
pages = {169387},
doi = {10.1016/j.scitotenv.2023.169387},
pmid = {38110100},
issn = {1879-1026},
mesh = {Animals ; Ecosystem ; *Chiroptera ; Predatory Behavior ; *Moths ; Forests ; },
abstract = {Coniferous forests contribute to the European economy; however, they have experienced a decline since the late 1990s due to an invasive pest known as the pine processionary moth, Thaumetopoea pityocampa. The impacts of this pest are increasingly exacerbated by climate change. Traditional control strategies involving pesticides have had negative effects on public health and the environment. Instead, forest managers seek a more ecological and sustainable approach to management that promotes the natural actions of pest control agents. This study aims to evaluate the role of bats in suppressing pine processionary moths in pine forests and examine how the bat community composition and abundance influence pest consumption. Bats were sampled in the mountainous environment of the Serra da Estrela in central Portugal to collect faecal samples for DNA meta-barcoding analysis. We assessed the relationship between a) bat richness, b) bat relative abundance, c) bat diet richness, and the frequency of pine processionary moth consumption. Our findings indicate that sites with the highest bat species richness and abundance exhibit the highest levels of pine processionary moth consumption. The intensity of pine processionary moth consumption is independent of insect diversity within the site. The highest occurrence of pine processionary moth presence in bat diets is primarily observed in species that forage in cluttered habitats. A typical predator of pine processionary moths among bats is likely to be a forest-dwelling species that specialises in consuming Lepidoptera. These species primarily use short-range echolocation calls, which are relatively inaudible to tympanate moths, suitable for locating prey in cluttered environments, employing a gleaning hunting strategy. Examples include species from the genera Plecotus, Myotis, and Rhinolophus. This study enhances our understanding of the potential pest consumption services provided by bats in pine forests. The insights gained from this research can inform integrated pest management practices in forestry.},
}
@article {pmid38104156,
year = {2023},
author = {Pan, X and Li, H and Putta, P and Zhang, X},
title = {LinRace: cell division history reconstruction of single cells using paired lineage barcode and gene expression data.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {8388},
pmid = {38104156},
issn = {2041-1723},
support = {R35 GM143070/GM/NIGMS NIH HHS/United States ; },
mesh = {*CRISPR-Cas Systems ; *Gene Editing/methods ; Cell Lineage/genetics ; Cell Division/genetics ; Gene Expression ; },
abstract = {Lineage tracing technology using CRISPR/Cas9 genome editing has enabled simultaneous readouts of gene expressions and lineage barcodes in single cells, which allows for inference of cell lineage and cell types at the whole organism level. While most state-of-the-art methods for lineage reconstruction utilize only the lineage barcode data, methods that incorporate gene expressions are emerging. Effectively incorporating the gene expression data requires a reasonable model of how gene expression data changes along generations of divisions. Here, we present LinRace (Lineage Reconstruction with asymmetric cell division model), which integrates lineage barcode and gene expression data using asymmetric cell division model and infers cell lineages and ancestral cell states using Neighbor-Joining and maximum-likelihood heuristics. On both simulated and real data, LinRace outputs more accurate cell division trees than existing methods. With inferred ancestral states, LinRace can also show how a progenitor cell generates a large population of cells with various functionalities.},
}
@article {pmid38101696,
year = {2024},
author = {Mulder, KP and Savage, AE and Gratwicke, B and Longcore, JE and Bronikowski, E and Evans, M and Longo, AV and Kurata, NP and Walsh, T and Pasmans, F and McInerney, N and Murray, S and Martel, A and Fleischer, RC},
title = {Sequence capture identifies fastidious chytrid fungi directly from host tissue.},
journal = {Fungal genetics and biology : FG &amp; B},
volume = {170},
number = {},
pages = {103858},
doi = {10.1016/j.fgb.2023.103858},
pmid = {38101696},
issn = {1096-0937},
mesh = {Animals ; Phylogeny ; *Chytridiomycota/genetics ; Amphibians/genetics/microbiology ; Biological Evolution ; DNA ; },
abstract = {The chytrid fungus Batrachochytrium dendrobatidis (Bd) was discovered in 1998 as the cause of chytridiomycosis, an emerging infectious disease causing mass declines in amphibian populations worldwide. The rapid population declines of the 1970s-1990s were likely caused by the spread of a highly virulent lineage belonging to the Bd-GPL clade that was introduced to naïve susceptible populations. Multiple genetically distinct and regional lineages of Bd have since been isolated and sequenced, greatly expanding the known biological diversity within this fungal pathogen. To date, most Bd research has been restricted to the limited number of samples that could be isolated using culturing techniques, potentially causing a selection bias for strains that can grow on media and missing other unculturable or fastidious strains that are also present on amphibians. We thus attempted to characterize potentially non-culturable genetic lineages of Bd from distinct amphibian taxa using sequence capture technology on DNA extracted from host tissue and swabs. We focused our efforts on host taxa from two different regions that likely harbored distinct Bd clades: (1) wild-caught leopard frogs (Rana) from North America, and (2) a Japanese Giant Salamander (Andrias japonicus) at the Smithsonian Institution's National Zoological Park that exhibited signs of disease and tested positive for Bd using qPCR, but multiple attempts failed to isolate and culture the strain for physiological and genetic characterization. We successfully enriched for and sequenced thousands of fungal genes from both host clades, and Bd load was positively associated with number of recovered Bd sequences. Phylogenetic reconstruction placed all the Rana-derived strains in the Bd-GPL clade. In contrast, the A. japonicus strain fell within the Bd-Asia3 clade, expanding the range of this clade and generating additional genomic data to confirm its placement. The retrieved ITS locus matched public barcoding data from wild A. japonicus and Bd infections found on other amphibians in India and China, suggesting that this uncultured clade is widespread across Asia. Our study underscores the importance of recognizing and characterizing the hidden diversity of fastidious strains in order to reconstruct the spatiotemporal and evolutionary history of Bd. The success of the sequence capture approach highlights the utility of directly sequencing pathogen DNA from host tissue to characterize cryptic diversity that is missed by culture-reliant approaches.},
}
@article {pmid38100368,
year = {2023},
author = {Zhao, C and Gao, Y and Qiu, J},
title = {Achieving Multicolor Emitting of Antimony-Doped Indium-Based Halide Perovskite via Monovalent Metal Induced Phase Engineering.},
journal = {ACS applied materials &amp; interfaces},
volume = {15},
number = {51},
pages = {59610-59617},
doi = {10.1021/acsami.3c14670},
pmid = {38100368},
issn = {1944-8252},
abstract = {Lead-free metal halide perovskites have attracted attention because of their excellent optical properties and nontoxicity. Here, we report the synthesis of Sb[3+]-doped indium halide perovskite Cs2InCl5·H2O:Sb[3+] by an improved solution coprecipitation method. The treatment of the Sb[3+]-doped indium halide perovskite with selected monovalent cation halides led to Cs2MInCl6 (Ag[+], K[+], Na[+]) in different crystal structures or phases. Sb[3+] has an isolated ns[2] electron, and Sb[3+]-doped metal halide acts as the luminescence center and exhibits bright broadband emission that originated from self-trapped excitons. Under UV light excitation, these phosphors with different crystal structures emitted multicolored luminescence ranging from blue, green, yellow, and red depending on whether or not or which monovalent metal ion was used. The phosphor samples were used to print high-resolution 2D color barcodes for security and anticounterfeiting applications. The study presented here provides a new approach for the design and synthesis of lead-free metal halide perovskites with different crystal structures and unique optical properties.},
}
@article {pmid38099308,
year = {2023},
author = {Hu, H and Wang, Q and Hao, G and Zhou, R and Luo, D and Cao, K and Yan, Z and Wang, X},
title = {Insights into the phylogenetic relationships and species boundaries of the Myricaria squamosa complex (Tamaricaceae) based on the complete chloroplast genome.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16642},
pmid = {38099308},
issn = {2167-8359},
mesh = {Phylogeny ; *Genome, Chloroplast/genetics ; *Tamaricaceae/genetics ; DNA, Chloroplast/genetics ; *Genome, Plastid ; },
abstract = {Myricaria plants are widely distributed in Eurasia and are helpful for windbreak and embankment protection. Current molecular evidence has led to controversy regarding species boundaries within the Myricaria genus and interspecific phylogenetic relationships between three specific species-M. bracteata, M. paniculata and M. squamosa-which have remained unresolved. This study treated these three unresolved taxa as a species complex, named the M. squamosa complex. The genome skimming approach was used to determine 35 complete plastome sequences and nuclear ribosomal DNA sequences for the said complex and other closely related species, followed by de novo assembly. Comparative analyses were conducted across Myricaria to identify the genome size, gene content, repeat type and number, SSR (simple sequence repeat) abundance, and codon usage bias of chloroplast genomes. Tree-based species delimitation results indicated that M. bracteata, M. paniculata and M. squamosa could not be distinguished and formed two monophyletic lineages (P1 and P2) that were clustered together. Compared to plastome-based species delimitation, the standard nuclear DNA barcode had the lowest species resolution, and the standard chloroplast DNA barcode and group-specific barcodes delimitated a maximum of four out of the five species. Plastid phylogenomics analyses indicated that the monophyletic M. squamosa complex is comprised of two evolutionarily significant units: one in the western Tarim Basin and the other in the eastern Qinghai-Tibet Plateau. This finding contradicts previous species discrimination and promotes the urgent need for taxonomic revision of the threatened genus Myricaria. Dense sampling and plastid genomes will be essential in this effort. The super-barcodes and specific barcode candidates outlined in this study will aid in further studies of evolutionary history.},
}
@article {pmid38098497,
year = {2023},
author = {Xin, ZB and Monro, AK and Wang, RF and Fu, LF},
title = {An integrative approach to species delimitation sinks three Chinese limestone karst Elatostema (Urticaceae) species.},
journal = {PhytoKeys},
volume = {236},
number = {},
pages = {83-96},
pmid = {38098497},
issn = {1314-2011},
abstract = {Elatostema is recognized as a taxonomically difficult group due to the reduced nature of the tiny flowers and inflorescences, also the large number of species (ca 650 to 700). Different opinions on morphological species delimitation have resulted in instability, which is problematic in such a speciose group. In this paper, the taxonomic status of three putative species, E.robustipes, E.scaposum, E.conduplicatum and their hypothetical closest relatives, was revised using morphological and molecular observations. Morphological comparison suggested high similarity between E.robustipes &amp; E.retrohirtum, E.scaposum &amp; E.oblongifolium, E.conduplicatum &amp; E.coriaceifolium, respectively. Phylogenetic analyses of four universal DNA barcodes (ITS, trnH-psbA, matK and rbcL) suggested that each species pair represents a single evolutionary lineage. Taking these two findings together, we propose E.robustipes to be a synonym of E.retrohirtum, E.scaposum a synonym of E.oblongifolium, and E.conduplicatum a synonym of E.coriaceifolium. Our results recover the number, shape and size of the bracts and bracteoles to be relatively stable characters, and the disposition of the male inflorescences on modified stems to be an unstable character, unsuitable for species delimitation in Elatostema.},
}
@article {pmid38097946,
year = {2023},
author = {Fu, QL and Mo, ZQ and Xiang, XG and Milne, RI and Jacquemyn, H and Burgess, KS and Sun, YN and Yan, H and Qiu, L and Yang, BY and Tan, SL},
title = {Plastome phylogenomics and morphological traits analyses provide new insights into the phylogenetic position, species delimitation and speciation of Triplostegia (Caprifoliaceae).},
journal = {BMC plant biology},
volume = {23},
number = {1},
pages = {645},
pmid = {38097946},
issn = {1471-2229},
mesh = {Humans ; Adult ; Phylogeny ; *Caprifoliaceae/genetics ; *Genome, Plastid/genetics ; Phenotype ; DNA, Ribosomal ; },
abstract = {BACKGROUND: The genus Triplostegia contains two recognized species, T. glandulifera and T. grandiflora, but its phylogenetic position and species delimitation remain controversial. In this study, we assembled plastid genomes and nuclear ribosomal DNA (nrDNA) cistrons sampled from 22 wild Triplostegia individuals, each from a separate population, and examined these with 11 recently published Triplostegia plastomes. Morphological traits were measured from herbarium specimens and wild material, and ecological niche models were constructed.<br><br>RESULTS: Triplostegia is a monophyletic genus within the subfamily Dipsacoideae comprising three monophyletic species, T. glandulifera, T. grandiflora, and an unrecognized species Triplostegia sp. A, which occupies much higher altitude than the other two. The new species had previously been misidentified as T. glandulifera, but differs in taproot, leaf, and other characters. Triplotegia is an old genus, with stem age 39.96&#x2009;Ma, and within it T. glandulifera diverged 7.94&#x2009;Ma. Triplostegia grandiflora and sp. A diverged 1.05&#x2009;Ma, perhaps in response to Quaternary climate fluctuations. Niche overlap between Triplostegia species was positively correlated with their phylogenetic relatedness.<br><br>CONCLUSIONS: Our results provide new insights into the species delimitation of Triplostegia, and indicate that a taxonomic revision of Triplostegia is needed. We also identified that either rpoB-trnC or ycf1 could serve as a DNA barcode for Triplostegia.},
}
@article {pmid38097660,
year = {2023},
author = {Zhu, X and Gopurenko, D and Holloway, JC and Duff, JD and Malipatil, MB},
title = {Two independent LAMP assays for rapid identification of the serpentine leafminer, Liriomyza huidobrensis (Blanchard, 1926) (Diptera: Agromyzidae) in Australia.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {22286},
pmid = {38097660},
issn = {2045-2322},
support = {MT20005//Hort Innovation/ ; },
mesh = {Animals ; Male ; *Diptera/genetics ; DNA ; Australia ; },
abstract = {Liriomyza huidobrensis is a leafminer fly and significant horticultural pest. It is a quarantine listed species in many countries and is now present as an established pest in Australia. Liriomyza huidobrensis uses a broad range of host plants and has potential for spread into various horticultural systems and regions of Australia. Rapid in-field identification of the pest is critically needed to assist efforts to manage this pest. Morphological identification of the pest is effectively limited to specialist examinations of adult males. Generally, molecular methods such as qPCR and DNA barcoding for identification of Liriomyza species require costly laboratory-based hardware. Herein, we developed two independent and rapid LAMP assays targeted to independently inherited mitochondrial and nuclear genes. Both assays are highly sensitive and specific to L. huidobrensis. Positive signals can be detected within 10 min on laboratory and portable real-time amplification fluorometers. Further, we adapted these assays for use with colorimetric master mixes, to allow fluorometer free in-field diagnostics of L. huidobrensis. Our LAMP assays can be used for stand-alone testing of query specimens and are likely to be essential tools used for rapid identification and monitoring of L. huidobrensis.},
}
@article {pmid38097151,
year = {2024},
author = {Rodrigues, BL and Galati, EAB},
title = {New sand fly (Diptera, Psychodidae) records and COI DNA barcodes in the state of Maranhão, Eastern Amazon, Brazil.},
journal = {Acta tropica},
volume = {250},
number = {},
pages = {107095},
doi = {10.1016/j.actatropica.2023.107095},
pmid = {38097151},
issn = {1873-6254},
mesh = {Animals ; *Psychodidae/genetics ; DNA Barcoding, Taxonomic ; Brazil ; Phylogeny ; *Phlebotomus ; DNA ; },
abstract = {The sand fly fauna and the usefulness of the DNA barcoding fragment of the cytochrome c oxidase subunit I (COI) gene were accessed in a forest fragment in the municipality of Governador Newton Bello, state of Maranhão, Brazil. We performed entomological collections in three independent campaigns in May and October 2021, and January 2023. Sand flies were morphologically-identified and then DNA barcoded. Sequences were deposited and analyzed in the BOLD System Database, and various species delimitation algorithms, to assess whether DNA sequences merge into taxonomic units in accordance with nominal species. In total, 1,524 sand flies were collected, comprising 32 nominal species. Nyssomyia antunesi was the most abundant species (31.5 %), followed by Psychodopygus davisi (27 %). We reported for the first time in the state of Maranhão, the presence of Lutzomyia evangelistai, Lutzomyia sherlocki, Pressatia equatorialis, and Psathyromyia barrettoi. We amplified and analyzed 67 COI barcodes of 23 species, which were merged with conspecific sequences extracted from GenBank. The maximum intraspecific p distances ranged from 0.0 % to 14.74 %, while the distances to the nearest neighbor varied from 1.67 % to 13.64 %. The phylogenetic gene tree and species delimitation tools clustered sequences into well-supported clades/clusters for each nominal species, except for Pressatia choti/Pr. equatorialis, which have the lowest interspecific genetic distance (1.67 %). We sequenced for the first time COI barcodes of Brumptomyia brumpti, Evandromyia monstruosa, Micropygomyia rorotaensis, Micropygomyia pilosa, Pintomyia christenseni, Pintomyia pacae, Pr. equatorialis, Pa. barrettoi, and Psathyromyia hermanlenti, which will be useful for further molecular identification and classification proposals of Neotropical species. This study updated the current list of the sand fly fauna for the state of Maranhão to 97, and demonstrated that COI barcodes are useful for specific identification.},
}
@article {pmid38096567,
year = {2023},
author = {Shrestha, P and Yang, D and Ward, A and Shih, WM and Wong, WP},
title = {Mapping Single-Molecule Protein Complexes in 3D with DNA Nanoswitch Calipers.},
journal = {Journal of the American Chemical Society},
volume = {145},
number = {51},
pages = {27916-27921},
pmid = {38096567},
issn = {1520-5126},
support = {R35 GM119537/GM/NIGMS NIH HHS/United States ; },
mesh = {Streptavidin/chemistry ; *Biotin/chemistry ; *Nanotechnology/methods ; Binding Sites ; DNA ; },
abstract = {The ability to accurately map the 3D geometry of single-molecule complexes in trace samples is a challenging goal that would lead to new insights into molecular mechanics and provide an approach for single-molecule structural proteomics. To enable this, we have developed a high-resolution force spectroscopy method capable of measuring multiple distances between labeled sites in natively folded protein complexes. Our approach combines reconfigurable nanoscale devices, we call DNA nanoswitch calipers, with a force-based barcoding system to distinguish each measurement location. We demonstrate our approach by reconstructing the tetrahedral geometry of biotin-binding sites in natively folded streptavidin, with 1.5-2.5 Å agreement with previously reported structures.},
}
@article {pmid38093010,
year = {2024},
author = {Russell, AJC and Weir, JA and Nadaf, NM and Shabet, M and Kumar, V and Kambhampati, S and Raichur, R and Marrero, GJ and Liu, S and Balderrama, KS and Vanderburg, CR and Shanmugam, V and Tian, L and Iorgulescu, JB and Yoon, CH and Wu, CJ and Macosko, EZ and Chen, F},
title = {Slide-tags enables single-nucleus barcoding for multimodal spatial genomics.},
journal = {Nature},
volume = {625},
number = {7993},
pages = {101-109},
pmid = {38093010},
issn = {1476-4687},
support = {UH3 CA246632/CA/NCI NIH HHS/United States ; UG3 NS132135/NS/NINDS NIH HHS/United States ; R01 HG010647/HG/NHGRI NIH HHS/United States ; T32 GM008313/GM/NIGMS NIH HHS/United States ; R01 CA276865/CA/NCI NIH HHS/United States ; UM1 MH130966/MH/NIMH NIH HHS/United States ; },
mesh = {Animals ; Humans ; Mice ; Brain/cytology/metabolism ; Chromatin/genetics/metabolism ; *DNA Barcoding, Taxonomic/methods ; Epigenesis, Genetic ; Gene Expression Profiling ; *Genomics/methods ; Melanoma/genetics/pathology ; Palatine Tonsil/cytology/metabolism ; Receptors, Antigen, T-Cell/genetics ; RNA/genetics ; Single-Cell Analysis/methods ; Transcriptome/genetics ; Tumor Microenvironment ; Hippocampus/cytology/metabolism ; Single-Cell Gene Expression Analysis ; Organ Specificity ; Ligands ; Response Elements/genetics ; Transcription Factors/metabolism ; },
abstract = {Recent technological innovations have enabled the high-throughput quantification of gene expression and epigenetic regulation within individual cells, transforming our understanding of how complex tissues are constructed[1-6]. However, missing from these measurements is the ability to routinely and easily spatially localize these profiled cells. We developed a strategy, Slide-tags, in which single nuclei within an intact tissue section are tagged with spatial barcode oligonucleotides derived from DNA-barcoded beads with known positions. These tagged nuclei can then be used as an input into a wide variety of single-nucleus profiling assays. Application of Slide-tags to the mouse hippocampus positioned nuclei at less than 10 μm spatial resolution and delivered whole-transcriptome data that are indistinguishable in quality from ordinary single-nucleus RNA-sequencing data. To demonstrate that Slide-tags can be applied to a wide variety of human tissues, we performed the assay on brain, tonsil and melanoma. We revealed cell-type-specific spatially varying gene expression across cortical layers and spatially contextualized receptor-ligand interactions driving B cell maturation in lymphoid tissue. A major benefit of Slide-tags is that it is easily adaptable to almost any single-cell measurement technology. As a proof of principle, we performed multiomic measurements of open chromatin, RNA and T cell receptor (TCR) sequences in the same cells from metastatic melanoma, identifying transcription factor motifs driving cancer cell state transitions in spatially distinct microenvironments. Slide-tags offers a universal platform for importing the compendium of established single-cell measurements into the spatial genomics repertoire.},
}
@article {pmid38092771,
year = {2023},
author = {Upshur, IF and Fehlman, M and Parikh, V and Vinauger, C and Lahondère, C},
title = {Sugar feeding by invasive mosquito species on ornamental and wild plants.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {22121},
pmid = {38092771},
issn = {2045-2322},
support = {2020-68018-30674//National Institute of Food and Agriculture/ ; VA-160160//National Institute of Food and Agriculture/ ; },
mesh = {Humans ; Animals ; Sugars ; Mosquito Vectors ; *Aedes ; *Chikungunya Fever ; *Zika Virus Infection ; *Zika Virus ; Plants ; },
abstract = {Feeding on plant-derived sugars is an essential component of mosquito biology, affecting key aspects of their lives such as survival, metabolism, and reproduction. Among mosquitoes, Aedes aegypti and Aedes albopictus are two invasive mosquito species in the US, and are vectors of diseases such as dengue fever, chikungunya, and Zika. These species live in heavily populated, urban areas, where they have high accessibility to human hosts as well as to plants in backyards and public landscapes. However, the range of plants that are suitable sugar hosts for these species remains to be described, despite the importance of understanding what plants may attract or repel mosquitoes to inform citizens and municipal authorities accordingly. Here, we tested whether Ae. aegypti and Ae. albopictus would sugar-feed on eleven commonly planted ornamental plant species. We confirmed feeding activity using the anthrone method and identified the volatile composition of plant headspace using gas-chromatography mass-spectroscopy. These chemical analyses revealed that a broad range of olfactory cues are associated with plants that mosquitoes feed on. This prompted us to use plant DNA barcoding to identify plants that field-caught mosquitoes feed on. Altogether, results show that native and invasive mosquito species can exploit a broader range of plants than originally suspected, including wild and ornamental plants from different phyla throughout the Spring, Summer and Fall seasons.},
}
@article {pmid38091499,
year = {2024},
author = {Taniguchi, K and Miyaguchi, H},
title = {COL1A2 Barcoding: Bone Species Identification via Shotgun Proteomics.},
journal = {Journal of proteome research},
volume = {23},
number = {1},
pages = {377-385},
doi = {10.1021/acs.jproteome.3c00615},
pmid = {38091499},
issn = {1535-3907},
mesh = {Animals ; *Proteomics/methods ; *Proteins/analysis ; Peptides/analysis ; Amino Acid Sequence ; Databases, Protein ; },
abstract = {Species identification of fragmentary bones remains a challenging task in archeology and forensics. A species identification method for such fragmentary bones that has recently attracted interest is the use of bone collagen proteins. Here, we describe a method similar to DNA barcoding that reads collagen protein sequences in bone and automatically determines the species by performing sequence database searches. The method is almost identical to conventional shotgun proteomics analysis of bone samples, except that the database used by the SEQUEST search engine consisted only of entries for collagen type 1 alpha 2 (COL1A2) proteins from various vertebrates. Accordingly, the COL1A2 peptides that differ in sequence among species act as species marker peptides. In SEQUEST-based shotgun proteomics, the protein entries that contain more marker peptide sequences are assigned higher scores; therefore, the highest-scoring protein entry will be the COL1A2 entry for the species from which the analyzed bone was derived. We tested our method using bone samples from 30 vertebrate species and found that all species were correctly identified. In conclusion, COL1A2 can be used as a bone protein barcode and can be read through shotgun proteomics, allowing for automatic bone species identification. Data are available via ProteomeXchange with the identifier PXD045402.},
}
@article {pmid38091409,
year = {2023},
author = {Solis-Leal, A and Boby, N and Mallick, S and Cheng, Y and Wu, F and De La Torre, G and Dufour, J and Alvarez, X and Shivanna, V and Liu, Y and Fennessey, CM and Lifson, JD and Li, Q and Keele, BF and Ling, B},
title = {Lymphoid tissues contribute to plasma viral clonotypes early after antiretroviral therapy interruption in SIV-infected rhesus macaques.},
journal = {Science translational medicine},
volume = {15},
number = {726},
pages = {eadi9867},
pmid = {38091409},
issn = {1946-6242},
support = {R01 MH130193/MH/NIMH NIH HHS/United States ; 75N91019D00024/CA/NCI NIH HHS/United States ; U42 OD024282/OD/NIH HHS/United States ; R01 MH116844/MH/NIMH NIH HHS/United States ; R01 AI093307/AI/NIAID NIH HHS/United States ; HHSN261201500003I/CA/NCI NIH HHS/United States ; P51 OD011133/OD/NIH HHS/United States ; R01 NS104016/NS/NINDS NIH HHS/United States ; S10 OD028732/OD/NIH HHS/United States ; U42 OD010442/OD/NIH HHS/United States ; P51 RR000164/RR/NCRR NIH HHS/United States ; S10 OD028653/OD/NIH HHS/United States ; P51 OD011104/OD/NIH HHS/United States ; HHSN261201500003C/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; *Simian Immunodeficiency Virus/genetics ; Macaca mulatta ; *HIV Infections/drug therapy ; *Simian Acquired Immunodeficiency Syndrome ; Anti-Retroviral Agents/therapeutic use/pharmacology ; Lymphoid Tissue ; Virus Replication ; RNA, Viral ; Viral Load ; CD4-Positive T-Lymphocytes ; },
abstract = {The rebound-competent viral reservoir, composed of a virus that is able to persist during antiretroviral therapy (ART) and mediate reactivation of systemic viral replication and rebound viremia after ART interruption (ATI), remains the biggest obstacle to treating HIV infection. A better understanding of the cellular and tissue origins and the dynamics of viral populations that initiate rebound upon ATI could help develop therapeutic strategies for reducing the rebound-competent viral reservoir. In this study, barcoded simian immunodeficiency virus (SIV), SIVmac239M, was used to infect rhesus macaques to enable monitoring of viral barcode clonotypes contributing to virus detectable in plasma after ATI. Blood and tissues from secondary lymphoid organs (spleen, mesenteric lymph nodes, and inguinal lymph nodes) and from the colon, ileum, lung, liver, and brain were analyzed using viral barcode sequencing, intact proviral DNA assay, single-cell RNA sequencing, and combined CODEX and RNAscope in situ hybridization. Four of seven animals had viral barcodes detectable by deep sequencing of plasma at necropsy, although plasma viral RNA remained below 22 copies per milliliter. Among the tissues studied, mesenteric lymph nodes, inguinal lymph nodes, and spleen contained viral barcodes detected in plasma. CD4[+] T cells were the main cell type harboring viral RNA after ATI. Furthermore, T cell zones in lymphoid tissues showed higher viral RNA abundance than B cell zones for most animals. These findings are consistent with lymphoid tissues contributing to the virus present in plasma early after ATI.},
}
@article {pmid38091117,
year = {2023},
author = {Doi, M and Nakagawa, T and Asano, M},
title = {A practical workflow for forensic species identification using direct sequencing of real-time PCR products.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {17},
pmid = {38091117},
issn = {1573-4978},
mesh = {Animals ; Humans ; Real-Time Polymerase Chain Reaction/methods ; Workflow ; *DNA ; DNA Primers/genetics ; *DNA Fingerprinting/methods ; Mammals ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Forensic scientists are often required to identify species of unknown biological samples. Although methods based on sequencing of DNA barcode regions are the gold standard for species identification in single-source forensic samples, they are cumbersome to implement as routine work in forensic laboratories that perform many tests, including human DNA typing. We have developed a species identification workflow that incorporates direct sequencing with real-time PCR products (real-time PCR-direct sequencing) as the technical trick for easy testing in forensic practice.<br><br>METHOD AND RESULTS: Following our workflow, DNA samples from vertebrates, such as mammals, amphibians, reptiles, birds, and fish, were subjected to species identification using vertebrate universal primers targeting each of the four DNA barcode regions. In real-time PCR melting curve analysis, humans and animals (nonhuman) could be differentiated by comparing melting temperatures, and subsequent real-time PCR-direct sequencing contributed to simplified sequencing. Searches against public DNA databases using the obtained sequences were compatible with the origin of the samples, indicating that this method might be used to identify animal species at the genus level. Furthermore, this workflow was effective in actual casework, which provided rapid test results according to the needs of the investigating agencies.<br><br>CONCLUSIONS: The species identification workflow will simply sequence as much as possible and can be integrated into routine forensic practice. The real-time PCR-direct sequencing used in this workflow might be beneficial not only for species identification but also for DNA sequencing by using the Sanger method for a variety of life sciences.},
}
@article {pmid38089891,
year = {2023},
author = {Jiang, C and Yi, M and Luo, Z and He, X and Lin, HD and Hubert, N and Yan, Y},
title = {DNA barcoding the ichthyofauna of the Beibu Gulf: Implications for fisheries management in a seafood market hub.},
journal = {Ecology and evolution},
volume = {13},
number = {12},
pages = {e10822},
pmid = {38089891},
issn = {2045-7758},
abstract = {The Beibu Gulf in China is situated in the tropics, in the western Pacific Ocean. It is an emblematic region combining proximity to a marine biodiversity hotspot and a major seafood hub. Intensification of marine fishing and ocean warming led to a drastic decline in fish populations in the Beibu Gulf during the last decades. This situation urges the development of molecular resources of the Beibu Gulf fish fauna in order to enable automated molecular identifications at the species level for next-generation monitoring. With this objective, we present the results of a large-scale campaign to DNA barcode fishes of the Beibu Gulf. We successfully generated 789 new DNA barcodes corresponding to 263 species which, together with 291 sequences mined from Genbank and BOLD, resulted in a reference library of 1080 sequences from 285 species. Based on the use of four DNA-based species delimitation methods (BIN, ASAP, mPTP, mGMYC), a total of 285 Molecular Operational Taxonomical Units (MOTUs). A single case of cryptic diversity was detected in Scomberomorus guttatus and a single species pair was not captured by delimitation methods. Intraspecific K2P genetic distances averaged 0.36% among sequences within species, whereas K2P genetic distances among species within genera averaged 6.96%. The most speciose families in open water trawling differ from those at fish market, and discrepancies with historical data are discussed in the light of recently documented stock collapses.},
}
@article {pmid38086895,
year = {2023},
author = {Kim, D and Burkett-Cadena, ND and Reeves, LE},
title = {Changes in mosquito species and blood meal composition associated with adulticide applications.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {22087},
pmid = {38086895},
issn = {2045-2322},
support = {27472//Florida Department of Agriculture and Consumer Services/ ; },
mesh = {Animals ; Humans ; Female ; *Ecosystem ; *Vertebrates/genetics ; Animals, Wild ; Meals ; },
abstract = {Although adulticide application is a pillar in the integrated management of nuisance and vector mosquitoes, non-target effects of adulticide applications within ecosystems are a substantial concern. However, the impacts of adulticide applications on non-target organisms are not necessarily detrimental, and in some cases, may provide benefits to certain organisms or wildlife. Here, we hypothesized that adulticide applications have beneficial non-target impacts on vertebrate wildlife through reduced biting pressure. To test this, we collected mosquitoes from ultra-low volume Permanone-treated (intervention) and untreated (reference) areas and assessed mosquito abundance and diversity, and abundance of blood-engorged female mosquitoes. We performed DNA barcoding analysis on mosquito blood meals to identify host species. Our results demonstrated a significant reduction in mosquito abundance by 58.9% in the intervention areas, taking into account the reduction in reference areas. Consequently, this decline led to a 64.5% reduction in the abundance of blood-engorged females. We also found a temporal dynamic of mosquito composition driven by mosquito control actions in which different mosquito species became dominant at treated sites while composition at reference areas remained similar during the same period. The present study suggests that the beneficial effects of mosquito control treatments for humans extend to other vertebrates, which represents an unstudied and rarely recognized non-target impact.},
}
@article {pmid38085667,
year = {2023},
author = {Barki, N and Jenkins, L and Marsango, S and Dedeo, D and Bolognini, D and Dwomoh, L and Abdelmalik, AM and Nilsen, M and Stoffels, M and Nagel, F and Schulz, S and Tobin, AB and Milligan, G},
title = {Phosphorylation bar-coding of free fatty acid receptor 2 is generated in a tissue-specific manner.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {38085667},
issn = {2050-084X},
support = {BB/X001814/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S000453/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Humans ; Mice ; Cell Line ; *Fatty Acids, Nonesterified ; Fatty Acids, Volatile/metabolism ; Mice, Transgenic ; Phosphorylation ; *Receptors, G-Protein-Coupled/metabolism ; },
abstract = {Free fatty acid receptor 2 (FFAR2) is activated by short-chain fatty acids and expressed widely, including in white adipocytes and various immune and enteroendocrine cells. Using both wild-type human FFAR2 and a designer receptor exclusively activated by designer drug (DREADD) variant we explored the activation and phosphorylation profile of the receptor, both in heterologous cell lines and in tissues from transgenic knock-in mouse lines expressing either human FFAR2 or the FFAR2-DREADD. FFAR2 phospho-site-specific antisera targeting either pSer[296]/pSer[297] or pThr[306]/pThr[310] provided sensitive biomarkers of both constitutive and agonist-mediated phosphorylation as well as an effective means to visualise agonist-activated receptors in situ. In white adipose tissue, phosphorylation of residues Ser[296]/Ser[297] was enhanced upon agonist activation whilst Thr[306]/Thr[310] did not become phosphorylated. By contrast, in immune cells from Peyer's patches Thr[306]/Thr[310] become phosphorylated in a strictly agonist-dependent fashion whilst in enteroendocrine cells of the colon both Ser[296]/Ser[297] and Thr[306]/Thr[310] were poorly phosphorylated. The concept of phosphorylation bar-coding has centred to date on the potential for different agonists to promote distinct receptor phosphorylation patterns. Here, we demonstrate that this occurs for the same agonist-receptor pairing in different patho-physiologically relevant target tissues. This may underpin why a single G protein-coupled receptor can generate different functional outcomes in a tissue-specific manner.},
}
@article {pmid38079451,
year = {2023},
author = {de Jong-Bolm, D and Sadeghi, M and Bogaciu, CA and Bao, G and Klaehn, G and Hoff, M and Mittelmeier, L and Basmanav, FB and Opazo, F and Noé, F and Rizzoli, SO},
title = {Protein nanobarcodes enable single-step multiplexed fluorescence imaging.},
journal = {PLoS biology},
volume = {21},
number = {12},
pages = {e3002427},
pmid = {38079451},
issn = {1545-7885},
mesh = {*Single-Domain Antibodies ; DNA ; Antibodies ; Optical Imaging ; Protein Isoforms ; },
abstract = {Multiplexed cellular imaging typically relies on the sequential application of detection probes, as antibodies or DNA barcodes, which is complex and time-consuming. To address this, we developed here protein nanobarcodes, composed of combinations of epitopes recognized by specific sets of nanobodies. The nanobarcodes are read in a single imaging step, relying on nanobodies conjugated to distinct fluorophores, which enables a precise analysis of large numbers of protein combinations. Fluorescence images from nanobarcodes were used as input images for a deep neural network, which was able to identify proteins with high precision. We thus present an efficient and straightforward protein identification method, which is applicable to relatively complex biological assays. We demonstrate this by a multicell competition assay, in which we successfully used our nanobarcoded proteins together with neurexin and neuroligin isoforms, thereby testing the preferred binding combinations of multiple isoforms, in parallel.},
}
@article {pmid38077427,
year = {2023},
author = {Noll, NW and Scherber, C and Schäffler, L},
title = {taxalogue: a toolkit to create comprehensive CO1 reference databases.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16253},
pmid = {38077427},
issn = {2167-8359},
mesh = {*DNA Barcoding, Taxonomic/methods ; *DNA/genetics ; Databases, Factual ; Software ; Ecosystem ; },
abstract = {BACKGROUND: Taxonomic identification through DNA barcodes gained considerable traction through the invention of next-generation sequencing and DNA metabarcoding. Metabarcoding allows for the simultaneous identification of thousands of organisms from bulk samples with high taxonomic resolution. However, reliable identifications can only be achieved with comprehensive and curated reference databases. Therefore, custom reference databases are often created to meet the needs of specific research questions. Due to taxonomic inconsistencies, formatting issues, and technical difficulties, building a custom reference database requires tremendous effort. Here, we present taxalogue, an easy-to-use software for creating comprehensive and customized reference databases that provide clean and taxonomically harmonized records. In combination with extensive geographical filtering options, taxalogue opens up new possibilities for generating and testing evolutionary hypotheses.<br><br>METHODS: taxalogue collects DNA sequences from several online sources and combines them into a reference database. Taxonomic incongruencies between the different data sources can be harmonized according to available taxonomies. Dereplication and various filtering options are available regarding sequence quality or metadata information. taxalogue is implemented in the open-source Ruby programming language, and the source code is available at https://github.com/nwnoll/taxalogue. We benchmark four reference databases by sequence identity against eight queries from different localities and trapping devices. Subsamples from each reference database were used to compare how well another one is covered.<br><br>RESULTS: taxalogue produces reference databases with the best coverage at high identities for most tested queries, enabling more accurate, reliable predictions with higher certainty than the other benchmarked reference databases. Additionally, the performance of taxalogue is more consistent while providing good coverage for a variety of habitats, regions, and sampling methods. taxalogue simplifies the creation of reference databases and makes the process reproducible and transparent. Multiple available output formats for commonly used downstream applications facilitate the easy adoption of taxalogue in many different software pipelines. The resulting reference databases improve the taxonomic classification accuracy through high coverage of the query sequences at high identities.},
}
@article {pmid38074911,
year = {2023},
author = {Wang, LY and Peng, XJ and Zhang, ZS},
title = {The first record of Tricholathys Chamberlin &amp; Ivie, 1935 (Araneae, Dictynidae) from China, with a new combination and descriptions of seven new species.},
journal = {ZooKeys},
volume = {1185},
number = {},
pages = {255-267},
pmid = {38074911},
issn = {1313-2989},
abstract = {The genus Tricholathys, found for the first time in China, is surveyed and seven new species, T.burangensissp. nov. (♂♀, Thibet), T.chenzhenningisp. nov. (♂♀, Qinghai), T.hebeiensissp. nov. (♀, Hebei), T.lhunzeensissp. nov. (♂♀, Tibet), Tricholathysrelictoidessp. nov. (♂♀, Xinjiang), T.serratasp. nov. (♂♀, Tibet), and T.xizangensissp. nov. (♂♀, Tibet), are described. A new combination is proposed for Tricholathysalxa (Tang, 2011) comb. nov., ex. Argenna Thorell, 1870. Descriptions of all new species are provided, together with digital images, illustrations, and a distribution map. The DNA barcode information of four recently collected species is also provided.},
}
@article {pmid38074292,
year = {2024},
author = {Tnah, LH and Lee, SL and Lee, CT and Ng, KKS and Ng, CH and Zawiah, N},
title = {DNA barcode identification of cultivated and wild tropical fruit species.},
journal = {3 Biotech},
volume = {14},
number = {1},
pages = {7},
pmid = {38074292},
issn = {2190-572X},
abstract = {UNLABELLED: With the rapid growth of the fruit industry worldwide, it is important to assess adulteration to ensure the authenticity and the safety of fruit products. The DNA barcoding approach offers a quick and accurate way of identifying and authenticating species. In this study, we developed reference DNA barcodes (rbcL, ITS2, and trnH-psbA) for 70 cultivated and wild tropical fruit species, representing 43 genera and 26 families. In terms of species recoverability, rbcL has a greater recoverability (100%) than ITS2 (95.7%) and trnH-psbA (88.6%). We evaluated the performance of these barcodes in species discrimination using similarity BLAST, phylogenetic tree, and barcoding gap analyses. The efficiency of rbcL, ITS2, and trnH-psbA in discriminating species was 80%, 100%, and 93.6%, respectively. We employed a multigene-tiered approach for species identification, with the rbcL region used for primary differentiation and ITS2 or trnH-psbA used for secondary differentiation. The two-locus barcodes rbcL + ITS2 and rbcL + trnH-psbA demonstrated robustness, achieving species discrimination rates of 100% and 94.3% respectively. Beyond the conventional species identification method based on plant morphology, the developed reference barcodes will aid the fruit agroindustry and trade, by making fruit-based product authentication possible.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-023-03848-w.},
}
@article {pmid38073427,
year = {2023},
author = {Martínez-Aquino, A and García-Teh, JG and Ceccarelli, FS and Aguirre-Macedo, ML and Vidal-Martínez, VM},
title = {Integrative taxonomy of Serrasentis gibsoni n. sp. (Acanthocephala: Isthmosacanthidae) from flatfishes in the Gulf of Mexico.},
journal = {Journal of helminthology},
volume = {97},
number = {},
pages = {e96},
doi = {10.1017/S0022149X23000822},
pmid = {38073427},
issn = {1475-2697},
support = {A1-S-15134//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 400/1/C/23/23//Universidad Aut&#xf3;noma de Baja California/ ; },
mesh = {Animals ; *Acanthocephala/genetics ; *Flatfishes/genetics/parasitology ; Phylogeny ; Gulf of Mexico ; Bayes Theorem ; Mexico ; },
abstract = {The Isthmosacanthidae acanthocephalan species of the genus Serrasentis are parasites of marine teleosts and an elasmobranch. In this study, Serrasentis gibsoni n. sp. is described from the intestines of four flatfish species (Paralichthyidae), namely Ancyclopsetta quadrocellata, Cyclopsetta chittendeni, Syacium gunteri, and S. papillosum from 10 oceanic sites in the Gulf of Mexico (GoM). Twenty sequences of the 'barcoding' region of cytochrome C oxidase subunit I gene were obtained from 20 adults of Serrasentis gibsoni n. sp. Additionally, five sequences of the barcoding region were obtained from five adults of rhadinorhynchid Gorgorhynchus lepidus from C. chittendeni, S. papillosum and one species of Haemulidae, Haemulom aurolineatum, from five oceanic sites from the GoM. Two phylogenetic approaches were followed: Bayesian inference and maximum likelihood. In both phylogenetic reconstructions, the sequences of Serrasentis gibsoni n. sp. were recovered as a monophyletic group within the genus Serrasentis and placed as a sister group to G. lepidus. However, due to the lack of molecular data for species of the Isthmosacanthidae and Rhadinorhynchidea, these phylogenetic inferences must be taken with caution. Serrasentis gibsoni n. sp. is the first species of Serrasentis described from Paralichthyidae flatfish species from marine waters of the Americas and from the GoM. Based on the barcoding data set analyzed, Serrasentis gibsoni n. sp. appears to have high intraspecific genetic variation; thus, it is necessary to continue exploring the genetic diversity of this species to infer its intraspecific evolutionary patterns.},
}
@article {pmid38072140,
year = {2024},
author = {Gajski, D and Wolff, JO and Melcher, A and Weber, S and Prost, S and Krehenwinkel, H and Kennedy, SR},
title = {Facilitating taxonomy and phylogenetics: An informative and cost-effective protocol integrating long amplicon PCRs and third-generation sequencing.},
journal = {Molecular phylogenetics and evolution},
volume = {192},
number = {},
pages = {107988},
doi = {10.1016/j.ympev.2023.107988},
pmid = {38072140},
issn = {1095-9513},
mesh = {Humans ; Phylogeny ; Cost-Benefit Analysis ; *DNA/chemistry ; Sequence Analysis, DNA/methods ; *DNA Barcoding, Taxonomic/methods ; },
abstract = {Phylogenetic inference has become a standard technique in integrative taxonomy and systematics, as well as in biogeography and ecology. DNA barcodes are often used for phylogenetic inference, despite being strongly limited due to their low number of informative sites. Also, because current DNA barcodes are based on a fraction of a single, fast-evolving gene, they are highly unsuitable for resolving deeper phylogenetic relationships due to saturation. In recent years, methods that analyse hundreds and thousands of loci at once have improved the resolution of the Tree of Life, but these methods require resources, experience and molecular laboratories that most taxonomists do not have. This paper introduces a PCR-based protocol that produces long amplicons of both slow- and fast-evolving unlinked mitochondrial and nuclear gene regions, which can be sequenced by the affordable and portable ONT MinION platform with low infrastructure or funding requirements. As a proof of concept, we inferred a phylogeny of a sample of 63 spider species from 20 families using our proposed protocol. The results were overall consistent with the results from approaches based on hundreds and thousands of loci, while requiring just a fraction of the cost and labour of such approaches, making our protocol accessible to taxonomists worldwide.},
}
@article {pmid38070383,
year = {2024},
author = {Laojun, S and Changbunjong, T and Sumruayphol, S and Pimsuka, S and Chaiphongpachara, T},
title = {Wing geometric morphometrics and DNA barcoding to distinguish three closely related species of Armigeres mosquitoes (Diptera: Culicidae) in Thailand.},
journal = {Veterinary parasitology},
volume = {325},
number = {},
pages = {110092},
doi = {10.1016/j.vetpar.2023.110092},
pmid = {38070383},
issn = {1873-2550},
mesh = {Humans ; Animals ; *Culicidae/genetics/parasitology ; DNA Barcoding, Taxonomic/methods/veterinary ; Thailand ; Mosquito Vectors ; },
abstract = {Armigeres subalbatus, a mosquito species widely found in Thailand and other Asian countries, serves as a vector for filarial parasites, affecting both humans and animals. However, the surveillance of this vector is complicated because of its morphological similarity to two other species, Armigeres dohami and Armigeres kesseli. To differentiate these morphologically similar species, our study employed both wing geometric morphometrics (GM) and DNA barcoding, offering a comprehensive approach to accurately identify these closely related Armigeres species in Thailand. Our GM analyses based on shape demonstrated significant accuracy in differentiating Armigeres species. Specifically, the outline-based GM method focusing on the 3rd posterior cell exhibited an accuracy rate of 82.61%, closely followed by the landmark-based GM method with 81.54%. Both these GM techniques effectively distinguished Ar. subalbatus from Ar. dohami and Ar. kesseli. Regarding DNA barcoding, our investigation of pairwise intra- and interspecific divergences revealed a "barcoding gap". Furthermore, the results of species confirmation using both species delimitation methods including the automatic barcode gap discovery method (ABGD) and the Multi-rate Poisson tree process (mPTP) were consistent with those of morphological identification, sequence comparisons with the GenBank and Barcode of Life Data System (BOLD) databases, and the neighbor-joining tree construction. These consistent results emphasize the efficacy of DNA barcoding in the precise identification of Armigeres species.},
}
@article {pmid38063564,
year = {2023},
author = {Deligios, M and Mazzarello, V and Fiamma, M and Barac, A and Diana, L and Ferrari, M and Murgia, M and Paglietti, B and Rubino, S},
title = {Seasonal Variation in Fungi in Beach Sand in Summertime: Stintino (Italy).},
journal = {International journal of environmental research and public health},
volume = {20},
number = {23},
pages = {},
pmid = {38063564},
issn = {1660-4601},
mesh = {*Sand ; *Water Microbiology ; Seasons ; Bacteria/genetics ; Fungi/genetics ; Bathing Beaches ; Environmental Monitoring/methods ; },
abstract = {BACKGROUND: The goal of this study was to monitor the microbial biodiversity in beach sand that is heavily visited by tourists during the summer, and to determinate whether the high presence of bathers (around 5000 per day) can modify sand microbial composition.<br><br>METHODS: Between 2016 and 2020, 150 sand samples were collected from nine different points at La Pelosa beach in Sardinia, Italy. Non-culturing methods were used; DNA extraction and meta-barcode sequencing were performed. All samples were analyzed with sequencing methods for 16S and ITS sequences.<br><br>RESULTS: Fungal genera differ on the three beaches and in the winter/summer zones. The ITS sequence showed the most common presence of Candida during summer and Paradendryphiella in the winter. The greatest diversity was found in the dune during winter, while in other parts of the beach, there are differences between bacteria and fungi, particularly in the wash zone during the winter, with high diversity for 16S sequences but low diversity for ITS sequences.<br><br>CONCLUSIONS: It appears reasonable that the sands, even on non-urban beaches, should be included in health monitoring programs in addition to the waters, and that access to them should be regulated by limiting the number of bathers with the aim of reducing the presence of pathogenic fungal species.},
}
@article {pmid38062249,
year = {2024},
author = {Xi, H and Liang, X and Huang, G and Liang, J and Li, D and Wen, Q and Zhang, Y and Xiao, X and Zhu, W},
title = {Enzyme-free electrochemical biosensor based on bio-barcode amplification for ultra-sensitive detection of microRNA.},
journal = {Analytical sciences : the international journal of the Japan Society for Analytical Chemistry},
volume = {40},
number = {2},
pages = {285-290},
pmid = {38062249},
issn = {1348-2246},
support = {GuikeZY20198006//Central Government-Guided Local Science and Technology Development Project/ ; },
mesh = {*MicroRNAs/genetics ; Gold/chemistry ; *Metal Nanoparticles/chemistry ; DNA/chemistry ; *Biosensing Techniques ; Electrochemical Techniques ; Limit of Detection ; },
abstract = {The rapid and accurate detection of miRNAs is of great significance for early diagnosis and treatment of cancer. Hence, a novel enzyme-free and label-free electrochemical biosensor based on bio-barcode amplification for detecting miRNAs was presented. Sandwich structures constructed of magnetic nanoparticles modified with DNA probes, gold nanoparticles with numerous barcoded DNA strands that hybridized with target miRNAs were fabricated as the amplifier. The released barcoded DNA strands then acted as the secondary targets and triggered the electrochemical sensor with a significant electrochemical response. A highly sensitive (detection limit of 0.24 fM) and selective electrochemical miRNA detection was realized, which has great potential for application in miRNA-related clinical diagnosis and biochemical research.},
}
@article {pmid38061816,
year = {2023},
author = {von Dassow, P and Mikhno, M and Percopo, I and Orellana, VR and Aguilera, V and Álvarez, G and Araya, M and Cornejo-Guzmán, S and Llona, T and Mardones, JI and Norambuena, L and Salas-Rojas, V and Kooistra, WHCF and Montresor, M and Sarno, D},
title = {Diversity and toxicity of the planktonic diatom genus Pseudo-nitzschia from coastal and offshore waters of the Southeast Pacific, including Pseudo-nitzschia dampieri sp. nov.},
journal = {Harmful algae},
volume = {130},
number = {},
pages = {102520},
doi = {10.1016/j.hal.2023.102520},
pmid = {38061816},
issn = {1878-1470},
mesh = {*Diatoms/chemistry ; Plankton ; Oceans and Seas ; DNA, Ribosomal ; Chile ; },
abstract = {To expand knowledge of Pseudo-nitzschia species in the Southeast Pacific, we isolated specimens from coastal waters of central Chile (36°S-30°S), the Gulf of Corcovado, and the oceanic Robinson Crusoe Island (700 km offshore) and grew them into monoclonal strains. A total of 123 Pseudo-nitzschia strains were identified to 11 species based on sequencing of the ITS region of the nuclear rDNA and on ultrastructural and morphometric analyses of the frustule in selected representatives of each clade: P. australis, P. bucculenta, P. cf. chiniana, P. cf. decipiens, P. fraudulenta, P. hasleana, P. multistriata, P. plurisecta, P. cf. sabit, the new species P. dampieri sp. nov., and one undescribed species. Partial 18S and 28S rDNA sequences, including the hypervariable V4 and D1-D3 regions used for barcoding, were gathered from representative strains of each species to facilitate future metabarcoding studies. Results showed different levels of genetic, and at times ultrastructural, diversity among the above-mentioned entities, suggesting morphological variants (P. bucculenta), rapidly radiating complexes with ill-defined species boundaries (P. cf. decipiens and P. cf. sabit), and the presence of new species (P. dampieri sp. nov., Pseudo-nitzschia sp. 1, and probably P. cf. chiniana). Domoic acid (DA) was detected in 18 out of 82 strains tested, including those of P. australis, P. plurisecta, and P. multistriata. Toxicity varied among species mostly corresponding to expectations from previous reports, with the prominent exception of P. fraudulenta; DA was not detected in any of its 10 strains tested. In conclusion, a high diversity of Pseudo-nitzschia exists in Chilean waters, particularly offshore.},
}
@article {pmid38060129,
year = {2024},
author = {Tarquini, G and Maestri, S and Ermacora, P and Martini, M},
title = {The Oxford Nanopore MinION as a Versatile Technology for the Diagnosis and Characterization of Emerging Plant Viruses.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2732},
number = {},
pages = {235-249},
pmid = {38060129},
issn = {1940-6029},
mesh = {*Nanopores ; DNA, Complementary ; Sequence Analysis, DNA ; Technology ; High-Throughput Nucleotide Sequencing/methods ; RNA ; *Plant Viruses/genetics ; },
abstract = {The emergence of novel viral epidemics that could affect major crops represents a serious threat to global food security. The early and accurate identification of the causative viral agent is the most important step for a rapid and effective response to disease outbreaks. Over the last years, the Oxford Nanopore Technologies (ONT) MinION sequencer has been proposed as an effective diagnostic tool for the early detection and identification of emerging viruses in plants, providing many advantages compared with different high-throughput sequencing (HTS) technologies. Here, we provide a step-by-step protocol that we optimized to obtain the virome of "Lamon bean" plants (Phaseolus vulgaris L.), an agricultural product with Protected Geographical Indication (PGI) in North-East of Italy, which is frequently subjected to multiple infections caused by different RNA viruses. The conversion of viral RNA in ds-cDNA enabled the use of Genomic DNA Ligation Sequencing Kit and Native Barcoding DNA Kit, which have been originally developed for DNA sequencing. This allowed the simultaneous diagnosis of both DNA- and RNA-based pathogens, providing a more versatile alternative to the use of direct RNA and/or direct cDNA sequencing kits.},
}
@article {pmid38057701,
year = {2023},
author = {Liu, DK and Zhou, CY and Tu, XD and Zhao, Z and Chen, JL and Gao, XY and Xu, SW and Zeng, MY and Ma, L and Ahmad, S and Li, MH and Lan, S and Liu, ZJ},
title = {Comparative and phylogenetic analysis of Chiloschista (Orchidaceae) species and DNA barcoding investigation based on plastid genomes.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {749},
pmid = {38057701},
issn = {1471-2164},
support = {72202200205//Forestry Peak Discipline Construction Project of Fujian Agriculture and Forestry University/ ; 2019YFD1000400//National Key Research and Development Program of China/ ; },
mesh = {Phylogeny ; DNA Barcoding, Taxonomic ; *Orchidaceae/genetics ; *Genome, Plastid ; Nucleotides ; *Genome, Chloroplast ; },
abstract = {BACKGROUND: Chiloschista (Orchidaceae, Aeridinae) is an epiphytic leafless orchid that is mainly distributed in tropical or subtropical forest canopies. This rare and threatened orchid lacks molecular resources for phylogenetic and barcoding analysis. Therefore, we sequenced and assembled seven complete plastomes of Chiloschista to analyse the plastome characteristics and phylogenetic relationships and conduct a barcoding investigation.<br><br>RESULTS: We are the first to publish seven Chiloschista plastomes, which possessed the typical quadripartite structure and ranged from 143,233&#xa0;bp to 145,463&#xa0;bp in size. The plastomes all contained 120 genes, consisting of 74 protein-coding genes, 38 tRNA genes and eight rRNA genes. The ndh genes were pseudogenes or lost in the genus, and the genes petG and psbF were under positive selection. The seven Chiloschista plastomes displayed stable plastome structures with no large inversions or rearrangements. A total of 14 small inversions (SIs) were identified in the seven Chiloschista plastomes but were all similar within the genus. Six noncoding mutational hotspots (trnN[GUU]-rpl32&#x2009;>&#x2009;rpoB-trnC[GCA] > psbK-psbI&#x2009;>&#x2009;psaC-rps15&#x2009;>&#x2009;trnE[UUC]-trnT[GGU] > accD-psaI) and five coding sequences (ycf1&#x2009;>&#x2009;rps15&#x2009;>&#x2009;matK&#x2009;>&#x2009;psbK&#x2009;>&#x2009;ccsA) were selected as potential barcodes based on nucleotide diversity and species discrimination analysis, which suggested that the potential barcode ycf1 was most suitable for species discrimination. A total of 47-56 SSRs and 11-14 long repeats (>&#x2009;20&#xa0;bp) were identified in Chiloschista plastomes, and they were mostly located in the large single copy intergenic region. Phylogenetic analysis indicated that Chiloschista was monophyletic. It was clustered with Phalaenopsis and formed the basic clade of the subtribe Aeridinae with a moderate support value. The results also showed that seven Chiloschista species were divided into three major clades with full support.<br><br>CONCLUSION: This study was the first to analyse the plastome characteristics of the genus Chiloschista in Orchidaceae, and the results showed that Chiloschista plastomes have conserved plastome structures. Based on the plastome hotspots of nucleotide diversity, several genes and noncoding regions are suitable for phylogenetic and population studies. Chiloschista may provide an ideal system to investigate the dynamics of plastome evolution and DNA barcoding investigation for orchid studies.},
}
@article {pmid38057622,
year = {2024},
author = {Liao, M and Gao, X and Chen, C and Li, Q and Guo, Q and Huang, H and Zhang, E and Ju, D},
title = {Integrated neural tracing and in-situ barcoded sequencing reveals the logic of SCN efferent circuits in regulating circadian behaviors.},
journal = {Science China. Life sciences},
volume = {67},
number = {3},
pages = {518-528},
pmid = {38057622},
issn = {1869-1889},
mesh = {*Suprachiasmatic Nucleus/metabolism ; *Circadian Rhythm/genetics ; Hypothalamus ; Neurons/physiology ; Synaptic Transmission ; },
abstract = {The circadian clock coordinates rhythms in numerous physiological processes to maintain organismal homeostasis. Since the suprachiasmatic nucleus (SCN) is widely accepted as the circadian pacemaker, it is critical to understand the neural mechanisms by which rhythmic information is transferred from the SCN to peripheral clocks. Here, we present the first comprehensive map of SCN efferent connections and suggest a molecular logic underlying these projections. The SCN projects broadly to most major regions of the brain, rather than solely to the hypothalamus and thalamus. The efferent projections from different subtypes of SCN neurons vary in distance and intensity, and blocking synaptic transmission of these circuits affects circadian rhythms in locomotion and feeding to different extents. We also developed a barcoding system to integrate retrograde tracing with in-situ sequencing, allowing us to link circuit anatomy and spatial patterns of gene expression. Analyses using this system revealed that brain regions functioning downstream of the SCN receive input from multiple neuropeptidergic cell types within the SCN, and that individual SCN neurons generally project to a single downstream brain region. This map of SCN efferent connections provides a critical foundation for future investigations into the neural circuits underlying SCN-mediated rhythms in physiology. Further, our new barcoded tracing method provides a tool for revealing the molecular logic of neuronal circuits within heterogeneous brain regions.},
}
@article {pmid38052482,
year = {2024},
author = {Reeves, MQ and Balmain, A},
title = {Mutations, Bottlenecks, and Clonal Sweeps: How Environmental Carcinogens and Genomic Changes Shape Clonal Evolution during Tumor Progression.},
journal = {Cold Spring Harbor perspectives in medicine},
volume = {14},
number = {3},
pages = {},
pmid = {38052482},
issn = {2157-1422},
support = {CGCATF-2021/100007/CRUK_/Cancer Research UK/United Kingdom ; R21 CA264599/CA/NCI NIH HHS/United States ; P30 CA042014/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Animals ; Mice ; *Carcinogens, Environmental ; Neoplastic Processes ; Genomics ; Mutation ; Clonal Evolution ; Disease Models, Animal ; },
abstract = {The transition from a single, initiated cell to a full-blown malignant tumor involves significant genomic evolution. Exposure to carcinogens-whether directly mutagenic or not-can drive progression toward malignancy, as can stochastic acquisition of cancer-promoting genetic events. Mouse models using both carcinogens and germline genetic manipulations have enabled precise inquiry into the evolutionary dynamics that take place as a tumor progresses from benign to malignant to metastatic stages. Tumor progression is characterized by changes in somatic point mutations and copy-number alterations, even though any single tumor can itself have a high or low burden of genomic alterations. Further, lineage-tracing, single-cell analyses and CRISPR barcoding have revealed the distinct clonal dynamics within benign and malignant tumors. Application of these tools in a range of mouse models can shed unique light on the patterns of clonal evolution that take place in both mouse and human tumors.},
}
@article {pmid38049699,
year = {2024},
author = {Lochs, SJA and van der Weide, RH and de Luca, KL and Korthout, T and van Beek, RE and Kimura, H and Kind, J},
title = {Combinatorial single-cell profiling of major chromatin types with MAbID.},
journal = {Nature methods},
volume = {21},
number = {1},
pages = {72-82},
pmid = {38049699},
issn = {1548-7105},
support = {101002885//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {Mice ; Animals ; *Chromatin/genetics ; *Histones/metabolism ; Chromatin Immunoprecipitation/methods ; Histone Code ; Protein Processing, Post-Translational ; Epigenesis, Genetic ; },
abstract = {Gene expression programs result from the collective activity of numerous regulatory factors. Studying their cooperative mode of action is imperative to understand gene regulation, but simultaneously measuring these factors within one sample has been challenging. Here we introduce Multiplexing Antibodies by barcode Identification (MAbID), a method for combinatorial genomic profiling of histone modifications and chromatin-binding proteins. MAbID employs antibody-DNA conjugates to integrate barcodes at the genomic location of the epitope, enabling combined incubation of multiple antibodies to reveal the distributions of many epigenetic markers simultaneously. We used MAbID to profile major chromatin types and multiplexed measurements without loss of individual data quality. Moreover, we obtained joint measurements of six epitopes in single cells of mouse bone marrow and during mouse in vitro differentiation, capturing associated changes in multifactorial chromatin states. Thus, MAbID holds the potential to gain unique insights into the interplay between gene regulatory mechanisms, especially for low-input samples and in single cells.},
}
@article {pmid38049447,
year = {2023},
author = {Shankar, M and Shetty, A and N S, M and C G, S and A, K and Tennankore, K},
title = {Urinary exosomal miRNA signature of IgA nephropathy: a case-control study.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {21400},
pmid = {38049447},
issn = {2045-2322},
support = {20MED2076//Rajiv Gandhi University of Health Sciences/ ; },
mesh = {Humans ; Adult ; *Glomerulonephritis, IGA/diagnosis/genetics ; Case-Control Studies ; *MicroRNAs/genetics/metabolism ; Biomarkers ; Proteinuria ; },
abstract = {IgA nephropathy is the most common primary glomerulonephritis worldwide and can progress to end-stage kidney disease (ESKD). The current "gold standard" for diagnosis is kidney biopsy, which is invasive and associated with morbidity. miRNAs are small, non-coding endogenous RNA that may serve as non-invasive biomarkers, and that are found in urinary exosomes. Thus far, there is a paucity of studies of the miRNA profile for the diagnosis of IgA nephropathy. Hence, we aimed to study the urinary exosomal miRNA signature of Indian patients with IgA nephropathy. Fifty biopsy-proven IgA nephropathy patients, 50 healthy controls and 25 patients with ESKD (IgA nephropathy) were recruited over 2 years (2020-2022). Urinary exosomes were isolated from which miRNA was extracted . Analysis of urinary exosomal miRNA was done using the digital multiplexed nCounter® human v3 miRNA Expression Assay which contains 799 unique miRNA barcodes. Candidate miRNAs were identified using Lasso regression and consensus clustering. The mean age of IgA nephropathy patients was 36.32 ± 3.067 years, mean creatinine was 2.26 ± 0.318 mg/dl and mean proteinuria was 2.69 ± 0.64 g/day. Compared to healthy controls, the majority (N = 150) of miRNAs were significantly downregulated. Five candidate miRNAs (hsa.miR.146b.3p, hsa.miR.599, hsa.miR.4532, hsa.miR.664b.5p and hsa.miR.221.5p) were able to differentiate between IgA nephropathy cases and controls (AUC > 0.90); the presence of all 5 was associated with 100% specificity and sensitivity for diagnosing IgA nephropathy cases. This study of Indian patients identified that there was a significant difference in the urinary exosomal miRNA profile between IgA nephropathy cases and healthy controls, suggesting that miRNAs may be valuable in the non-invasive diagnosis of IgA nephropathy.},
}
@article {pmid38048388,
year = {2024},
author = {Rahmberg, AR and Wu, C and Shin, T and Hong, SG and Pei, L and Markowitz, TE and Hickman, HD and Dunbar, CE and Brenchley, JM},
title = {Ongoing production of tissue-resident macrophages from hematopoietic stem cells in healthy adult macaques.},
journal = {Blood advances},
volume = {8},
number = {3},
pages = {523-537},
pmid = {38048388},
issn = {2473-9537},
mesh = {Humans ; Animals ; Mice ; *Macaca ; *Hematopoietic Stem Cells ; Macrophages ; Monocytes ; Bone Marrow ; },
abstract = {Macrophages orchestrate tissue immunity from the initiation and resolution of antimicrobial immune responses to the repair of damaged tissue. Murine studies demonstrate that tissue-resident macrophages are a heterogenous mixture of yolk sac-derived cells that populate the tissue before birth, and bone marrow-derived replacements recruited in adult tissues at steady-state and in increased numbers in response to tissue damage or infection. How this translates to species that are constantly under immunologic challenge, such as humans, is unknown. To understand the ontogeny and longevity of tissue-resident macrophages in nonhuman primates (NHPs), we use a model of autologous hematopoietic stem progenitor cell (HSPC) transplantation with HSPCs genetically modified to be marked with clonal barcodes, allowing for subsequent analysis of clonal ontogeny. We study the contribution of HSPCs to tissue macrophages, their clonotypic profiles relative to leukocyte subsets in the peripheral blood, and their transcriptomic and epigenetic landscapes. We find that HSPCs contribute to tissue-resident macrophage populations in all anatomic sites studied. Macrophage clonotypic profiles are dynamic and overlap significantly with the clonal hierarchy of contemporaneous peripheral blood monocytes. Epigenetic and transcriptomic landscapes of HSPC-derived macrophages are similar to tissue macrophages isolated from NHPs that did not undergo transplantation. We also use in vivo bromodeoxyuridine infusions to monitor tissue macrophage turnover in NHPs that did not undergo transplantation and find evidence for macrophage turnover at steady state. These data demonstrate that the life span of most tissue-resident macrophages is limited and can be replenished continuously from HSPCs.},
}
@article {pmid38048319,
year = {2023},
author = {Piya, D and Nolan, N and Moore, ML and Ramirez Hernandez, LA and Cress, BF and Young, R and Arkin, AP and Mutalik, VK},
title = {Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages.},
journal = {PLoS biology},
volume = {21},
number = {12},
pages = {e3002416},
pmid = {38048319},
issn = {1545-7885},
support = {R35 GM136396/GM/NIGMS NIH HHS/United States ; },
mesh = {*Bacteriophages/genetics ; DNA ; Genes, Essential/genetics ; },
abstract = {Phages are one of the key ecological drivers of microbial community dynamics, function, and evolution. Despite their importance in bacterial ecology and evolutionary processes, phage genes are poorly characterized, hampering their usage in a variety of biotechnological applications. Methods to characterize such genes, even those critical to the phage life cycle, are labor intensive and are generally phage specific. Here, we develop a systematic gene essentiality mapping method scalable to new phage-host combinations that facilitate the identification of nonessential genes. As a proof of concept, we use an arrayed genome-wide CRISPR interference (CRISPRi) assay to map gene essentiality landscape in the canonical coliphages λ and P1. Results from a single panel of CRISPRi probes largely recapitulate the essential gene roster determined from decades of genetic analysis for lambda and provide new insights into essential and nonessential loci in P1. We present evidence of how CRISPRi polarity can lead to false positive gene essentiality assignments and recommend caution towards interpreting CRISPRi data on gene essentiality when applied to less studied phages. Finally, we show that we can engineer phages by inserting DNA barcodes into newly identified inessential regions, which will empower processes of identification, quantification, and tracking of phages in diverse applications.},
}
@article {pmid38047014,
year = {2023},
author = {Kobayashi, G},
title = {Buried treasure in a public repository: Mining mitochondrial genes of 32 annelid species from sequence reads deposited in the Sequence Read Archive (SRA).},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16446},
pmid = {38047014},
issn = {2167-8359},
mesh = {Humans ; Animals ; Genes, Mitochondrial ; Phylogeny ; *Annelida ; DNA, Mitochondrial/genetics ; *Polychaeta/genetics ; },
abstract = {BACKGROUND: The mitochondrial genomes (mitogenomes) of metazoans generally include the same set of protein-coding genes, which ensures the homology of mitochondrial genes between species. The mitochondrial genes are often used as reference data for species identification based on genetic data (DNA barcoding). The need for such reference data has been increasing due to the application of environmental DNA (eDNA) analysis for environmental assessments. Recently, the number of publicly available sequence reads obtained with next-generation sequencing (NGS) has been increasing in the public database (the NCBI Sequence Read Archive, SRA). Such freely available NGS reads would be promising sources for assembling mitochondrial protein-coding genes (mPCGs) of organisms whose mitochondrial genes are not available in GenBank. The present study aimed to assemble annelid mPCGs from raw data deposited in the SRA.<br><br>METHODS: The recent progress in the classification of Annelida was briefly introduced. In the present study, the mPCGs of 32 annelid species of 19 families in clitellates and allies in Sedentaria (echiurans and polychaetes) were newly assembled from the reads deposited in the SRA. Assembly was performed with a recently published pipeline mitoRNA, which includes cycles of Bowtie2 mapping and Trinity assembly. Assembled mPCGs were deposited in GenBank as Third Party Data (TPA) data. A phylogenetic tree was reconstructed with maximum likelihood (ML) analysis, together with other mPCGs deposited in GenBank.<br><br>RESULTS AND DISCUSSION: mPCG assembly was largely successful except for Travisia forbesii; only four genes were detected from the assembled contigs of the species probably due to the reads targeting its parasite. Most genes were largely successfully obtained, whereas atp8, nad2, and nad4l were only successful in 22-24 species. The high nucleotide substitution rates of these genes might be relevant to the failure in the assembly although nad6, which showed a similarly high substitution rate, was successfully assembled. Although the phylogenetic positions of several lineages were not resolved in the present study, the phylogenetic relationships of some polychaetes and leeches that were not inferred by transcriptomes were well resolved probably due to a more dense taxon sampling than previous phylogenetic analyses based on transcriptomes. Although NGS data are generally better sources for resolving phylogenetic relationships of both higher and lower classifications, there are ensuring needs for specific loci of the mitochondrial genes for analyses that do not require high resolutions, such as DNA barcoding, eDNA, and phylogenetic analysis among lower taxa. Assembly from publicly available NGS reads would help design specific primers for the mitochondrial gene sequences of species, whose mitochondrial genes are hard to amplify by Sanger sequencing using universal primers.},
}
@article {pmid38046786,
year = {2023},
author = {Shih, HT and Chang, K and Pramono, FA and Malay, MCMD},
title = {Morphological and Molecular Evidence for the Identity of Two Land Hermit Crabs Coenobita longitarsis De Man, 1902 and C. pseudorugosus Nakasone, 1988 (Crustacea: Decapoda: Anomura: Coenobitidae).},
journal = {Zoological studies},
volume = {62},
number = {},
pages = {e52},
pmid = {38046786},
issn = {1810-522X},
abstract = {Two species of land hermit crabs, Coenobita longitarsis De Man, 1902 and C. pseudorugosus Nakasone, 1988 were described based on female specimens from Maluku, Indonesia and specimens from Cebu, the Philippines, respectively. However, no confirmed records of either species have been reported since their original descriptions. In this study, we examined specimens with typical morphological characters of C. longitarsis from Papua New Guinea and C. pseudorugosus from the Philippines and Indonesia, further supported by the analyses of the DNA barcoding marker, cytochrome oxidase subunit I (COI). The characters of male C. longitarsis are provided for the first time, with coxae of male fifth pereiopods subequal, without sexual tubes developed. Their slender morphology is suggested to be an adaptation to utilize native terrestrial snail shells in inland forests, which may also explain its rarity. Coenobita pseudorugosus is very similar to C. rugosus H. Milne Edwards, 1837, but can be distinguished by the adult sizes, as well as the morphology of sexual tubes of male fifth pereiopods and propodus of left third pereiopod. Morphological variation and the fresh coloration of C. longitarsis and C. pseudorugosus are also provided in this study.},
}
@article {pmid38043901,
year = {2024},
author = {Tegart, LJ and Schiro, G and Dickinson, JL and Green, BJ and Barberán, A and Marthick, JR and Bissett, A and Johnston, FH and Jones, PJ},
title = {Decrypting seasonal patterns of key pollen taxa in cool temperate Australia: A multi-barcode metabarcoding analysis.},
journal = {Environmental research},
volume = {243},
number = {},
pages = {117808},
doi = {10.1016/j.envres.2023.117808},
pmid = {38043901},
issn = {1096-0953},
mesh = {Humans ; Seasons ; *Pollen ; *Rhinitis, Allergic, Seasonal ; Allergens/analysis ; Poaceae ; Australia ; RNA, Transfer ; },
abstract = {Pollen allergies pose a considerable global public health concern. Allergy risk can vary significantly within plant families, yet some key pollen allergens can only be identified to family level by current optical methods. Pollen information with greater taxonomic resolution is therefore required to best support allergy prevention and self-management. We used environmental DNA (eDNA) metabarcoding to deepen taxonomic insights into the seasonal composition of airborne pollen in cool temperate Australia, a region with high rates of allergic respiratory disease. In Hobart, Tasmania, we collected routine weekly air samples from December 2018 until October 2020 and sequenced the internal transcribed spacer 2 (ITS2) and chloroplastic tRNA-Leucine tRNA-Phenylalanine intergenic spacer (trnL-trnF) regions in order to address the following questions: a) What is the genus-level diversity of known and potential aeroallergens in Hobart, in particular, in the families Poaceae, Cupressaceae and Myrtaceae? b) How do the atmospheric concentrations of these taxa change over time, and c) Does trnL-trnF enhance resolution of biodiversity when used in addition to ITS2? Our results suggest that individuals in the region are exposed to temperate grasses including Poa and Bromus in the peak grass pollen season, however low levels of exposure to the subtropical grass Cynodon may occur in autumn and winter. Within Cupressaceae, both metabarcodes showed that exposure is predominantly to pollen from the introduced genera Cupressus and Juniperus. Only ITS2 detected the native genus, Callitris. Both metabarcodes detected Eucalyptus as the major Myrtaceae genus, with trnL-trnF exhibiting primer bias for this family. These findings help refine our understanding of allergy triggers in Tasmania and highlight the utility of multiple metabarcodes in aerobiome studies.},
}
@article {pmid38041646,
year = {2024},
author = {Srivathsan, A and Feng, V and Suárez, D and Emerson, B and Meier, R},
title = {ONTbarcoder 2.0: rapid species discovery and identification with real-time barcoding facilitated by Oxford Nanopore R10.4.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {40},
number = {2},
pages = {192-203},
doi = {10.1111/cla.12566},
pmid = {38041646},
issn = {1096-0031},
support = {CGL2017-85718-P//Ministerio de Ciencia e Innovaci&#xf3;n/ ; },
mesh = {*Nanopores ; Sequence Analysis, DNA/methods ; DNA Barcoding, Taxonomic/methods ; Software ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Most arthropod species are undescribed and hidden in specimen-rich samples that are difficult to sort to species using morphological characters. For such samples, sorting to putative species with DNA barcodes is an attractive alternative, but needs cost-effective techniques that are suitable for use in many laboratories around the world. Barcoding using the portable and inexpensive MinION sequencer produced by Oxford Nanopore Technologies (ONT) could be useful for presorting specimen-rich samples with DNA barcodes because it requires little space and is inexpensive. However, similarly important is user-friendly and reliable software for analysis of the ONT data. It is here provided in the form of ONTbarcoder 2.0 that is suitable for all commonly used operating systems and includes a Graphical User Interface (GUI). Compared with an earlier version, ONTbarcoder 2.0 has three key improvements related to the higher read quality obtained with ONT's latest flow cells (R10.4), chemistry (V14 kits) and basecalling model (super-accuracy model). First, the improved read quality of ONT's latest flow cells (R10.4) allows for the use of primers with shorter indices than those previously needed (9 bp vs. 12-13 bp). This decreases the primer cost and can potentially improve PCR success rates. Second, ONTbarcoder now delivers real-time barcoding to complement ONT's real-time sequencing. This means that the first barcodes are obtained within minutes of starting a sequencing run; i.e. flow cell use can be optimized by terminating sequencing runs when most barcodes have already been obtained. The only input needed by ONTbarcoder 2.0 is a demultiplexing sheet and sequencing data (raw or basecalled) generated by either a Mk1B or a Mk1C. Thirdly, we demonstrate that the availability of R10.4 chemistry for the low-cost Flongle flow cell is an attractive option for users who require only 200-250 barcodes at a time.},
}
@article {pmid38041142,
year = {2023},
author = {El-Tabakh, MAM and Elhawary, EA and Hwihy, HM and Darweesh, KF and Shaapan, RM and Ghazala, EA and Mokhtar, MM and Waheeb, HO and Emam, DEM and Bakr, NA and Shehata, AZI},
title = {UPLC/ESI/MS profiling of red algae Galaxaura rugosa extracts and its activity against malaria mosquito vector, Anopheles pharoensis, with reference to Danio rerio and Daphnia magna as bioindicators.},
journal = {Malaria journal},
volume = {22},
number = {1},
pages = {368},
pmid = {38041142},
issn = {1475-2875},
mesh = {Animals ; Humans ; *Anopheles ; Zebrafish ; Daphnia ; Environmental Biomarkers ; Mosquito Vectors ; Methanol/analysis/pharmacology ; Acetylcholinesterase/analysis ; Ecosystem ; Plant Extracts/pharmacology ; Solvents/analysis/pharmacology ; Larva ; *Malaria ; *Rhodophyta ; *Insecticides/pharmacology ; Plant Leaves/chemistry ; *Culex ; },
abstract = {BACKGROUND: Anopheles pharoensis has a major role in transmitting several human diseases, especially malaria, in Egypt?. Controlling Anopheles is considered as an effective strategy to eliminate the spread of malaria worldwide. Galaxaura rugosa is a species of red algae found in tropical to subtropical marine environments. The presence of G. rugosa is indicative of the ecosystem's overall health. The current work aims to investigate UPLC/ESI/MS profile of G. rugosa methanol and petroleum ether extracts and its activity against An. pharoensis and non-target organisms, Danio rerio and Daphnia magna.<br><br>METHODS: Galaxaura rugosa specimens have been identified using DNA barcoding for the COI gene and verified as G. rugosa. The UPLC/ESI/MS profiling of G. rugosa collected from Egypt was described. The larvicidal and repellent activities of G. rugosa methanol and petroleum ether extracts against An. pharoensis were evaluated, as well as the toxicity of tested extracts on non-target organisms, Dan. rerio and Dap. magna.<br><br>RESULTS: The UPLC/ESI/MS analysis of methanol and petroleum ether extracts led to the tentative identification of 57 compounds belonging to different phytochemical classes, including flavonoids, tannins, phenolic acids, phenyl propanoids. Larval mortality was recorded at 93.33% and 90.67% at 80 and 35&#xa0;ppm of methanol and petroleum ether extracts, respectively, while pupal mortality recorded 44.44 and 22.48% at 35 and 30&#xa0;ppm, respectively. Larval duration was recorded at 5.31 and 5.64&#xa0;days by methanol and petroleum ether extracts at 80 and 35&#xa0;ppm, respectively. A decrease in acetylcholinesterase (AChE) level and a promotion in Glutathione-S-transferase (GST) level of An. pharoensis 3rd instar larvae were recorded by tested extracts. The petroleum ether extract was more effective against An. pharoensis starved females than methanol extract. Also, tested extracts recorded LC50 of 1988.8, 1365.1, and 11.65, 14.36&#xa0;&#xb5;g/mL against Dan. rerio, and Dap. magna, respectively.<br><br>CONCLUSIONS: Using red algae derivatives in An. pharoensis control could reduce costs and environmental impact and be harmless to humans and other non-target organisms.},
}
@article {pmid38039317,
year = {2023},
author = {Wu, M and Guo, H and Zhao, M and Yan, Y and Zheng, Y and Sun, H and Ma, D},
title = {DNA barcoding identification of grafted Semen Ziziphi Spinosae and transcriptome study of wild Semen Ziziphi Spinosae.},
journal = {PloS one},
volume = {18},
number = {12},
pages = {e0294944},
pmid = {38039317},
issn = {1932-6203},
mesh = {*Transcriptome ; DNA Barcoding, Taxonomic ; Seeds/genetics ; Plant Extracts ; *Ziziphus/genetics ; Chromatography, High Pressure Liquid/methods ; },
abstract = {Semen Ziziphi Spinosae (SZS) is the dried and ripe seeds of Ziziphus jujuba var. spinosa. Currently, the yield of naturally grown SZS is unstable owing to environmental factors. Grafting high-quality sour jujube scions onto sour jujube or jujube tree stocks can result in a greater yield. However, the effects of grafting on the quality and gene expression of SZS have rarely been reported. This study used a DNA barcoding technique, high-performance liquid phase-evaporative luminescence detector (HPLC-ELSD), and transcriptomics to investigate the origin and genetic differences between grafted and wild jujube seeds. DNA barcoding identified all samples as Ziziphus jujuba var. spinosa. HPLC-ELSD analysis revealed a higher content of grafted SZS compared to that of the wild SZS. Transcriptome analysis of the metabolic pathways in SZS showed that 22 and 19 differentially expressed gene sequences encoded enzymes related to flavonoids and saponin synthesis, respectively. Weighted correlation network analysis (WGCNA) identified 15 core genes governing the differences in medicinal components between grafted and wild SZS. This study demonstrated the use of DNA barcoding and fingerprint methods to identify jujube seed species and effectively capture ingredient information of medicinal materials. Additionally, transcriptome technology provided data for identifying core differential genes, facilitating studies on quality differences between grafted and wild SZS.},
}
@article {pmid38038692,
year = {2024},
author = {Shipman, A and Tian, M},
title = {Combined Use of Phenotype-Based and Genome-Informed Approaches Identified a Unique Fusarium oxysporum f. sp. cubense Isolate in Hawaii.},
journal = {Phytopathology},
volume = {114},
number = {6},
pages = {1305-1319},
doi = {10.1094/PHYTO-07-23-0257-R},
pmid = {38038692},
issn = {0031-949X},
mesh = {*Fusarium/genetics/pathogenicity ; *Musa/microbiology ; Hawaii ; *Plant Diseases/microbiology ; *Phylogeny ; *Phenotype ; *Genome, Fungal/genetics ; Virulence/genetics ; Polymorphism, Single Nucleotide ; },
abstract = {Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense (Foc), is a serious disease that threatens banana production worldwide. It is a long-standing problem in Hawaii, but previously, there was little knowledge of the causal pathogen. We isolated a strain of Foc, named Foc-UH, from a field experiencing the disease epidemic in Hawaii. Infection assays of a diverse panel of 26 banana clones, including varieties used for differentiating pathogen races and fruit production, revealed that Foc-UH has a race 1 pathogenic phenotype with an intermediate race 2 virulence and revealed the differential resistance of varieties to infection. Separate phylogenetic analyses using the barcoding regions of three nuclear genes, seven complete nuclear genes, and single-nucleotide polymorphisms within conserved whole-genome protein coding sequences placed Foc-UH into recently proposed taxonomic frameworks relevant to Foc and the F. oxysporum species complex. Screening of the 99.7% complete draft genome identified five secreted in xylem (SIX) gene homologs: SIX1d, SIX1f, SIX9a, SIX9b, and SIX13a. This profile is similar to that of several race 1 isolates except for the absence of SIX4 and SIX6. Foc-UH was morphologically dissimilar to the nearest related isolates. Altogether, this study identified a unique isolate that causes banana Fusarium wilt, which represents the first characterization of the causal pathogen in Hawaii. The findings and genomic resources generated in this study are expected to guide banana breeding and cultivar deployment in Hawaii and beyond and contribute to further understanding of the pathogenicity and evolutionary systematics of Foc.},
}
@article {pmid38036616,
year = {2024},
author = {Kwok, SJJ and Forward, S and Fahlberg, MD and Assita, ER and Cosgriff, S and Lee, SH and Abbott, GR and Zhu, H and Minasian, NH and Vote, AS and Martino, N and Yun, SH},
title = {High-dimensional multi-pass flow cytometry via spectrally encoded cellular barcoding.},
journal = {Nature biomedical engineering},
volume = {8},
number = {3},
pages = {310-324},
pmid = {38036616},
issn = {2157-846X},
support = {DP1 EB024242/EB/NIBIB NIH HHS/United States ; R01 EB033155/EB/NIBIB NIH HHS/United States ; R43 GM140527/GM/NIGMS NIH HHS/United States ; R44 GM139504/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Flow Cytometry/methods ; *Leukocytes, Mononuclear ; *Light ; },
abstract = {Advances in immunology, immuno-oncology, drug discovery and vaccine development demand improvements in the capabilities of flow cytometry to allow it to measure more protein markers per cell at multiple timepoints. However, the size of panels of fluorophore markers is limited by overlaps in fluorescence-emission spectra, and flow cytometers typically perform cell measurements at one timepoint. Here we describe multi-pass high-dimensional flow cytometry, a method leveraging cellular barcoding via microparticles emitting near-infrared laser light to track and repeatedly measure each cell using more markers and fewer colours. By using live human peripheral blood mononuclear cells, we show that the method enables the time-resolved characterization of the same cells before and after stimulation, their analysis via a 10-marker panel with minimal compensation for spectral spillover and their deep immunophenotyping via a 32-marker panel, where the same cells are analysed in 3 back-to-back cycles with 10-13 markers per cycle, reducing overall spillover and simplifying marker-panel design. Cellular barcoding in flow cytometry extends the utility of the technique for high-dimensional multi-pass single-cell analyses.},
}
@article {pmid38031549,
year = {2023},
author = {Ghansah, A and Tiedje, KE and Argyropoulos, DC and Onwona, CO and Deed, SL and Labbé, F and Oduro, AR and Koram, KA and Pascual, M and Day, KP},
title = {Comparison of molecular surveillance methods to assess changes in the population genetics of Plasmodium falciparum in high transmission.},
journal = {Frontiers in parasitology},
volume = {2},
number = {},
pages = {},
pmid = {38031549},
issn = {2813-2424},
support = {R01 AI149779/AI/NIAID NIH HHS/United States ; R01 TW009670/TW/FIC NIH HHS/United States ; },
abstract = {A major motivation for developing molecular methods for malaria surveillance is to measure the impact of control interventions on the population genetics of Plasmodium falciparum as a potential marker of progress towards elimination. Here we assess three established methods (i) single nucleotide polymorphism (SNP) barcoding (panel of 24-biallelic loci), (ii) microsatellite genotyping (panel of 12-multiallelic loci), and (iii) varcoding (fingerprinting var gene diversity, akin to microhaplotyping) to identify changes in parasite population genetics in response to a short-term indoor residual spraying (IRS) intervention. Typical of high seasonal transmission in Africa, multiclonal infections were found in 82.3% (median 3; range 1-18) and 57.8% (median 2; range 1-12) of asymptomatic individuals pre- and post-IRS, respectively, in Bongo District, Ghana. Since directly phasing multilocus haplotypes for population genetic analysis is not possible for biallelic SNPs and microsatellites, we chose ~200 low-complexity infections biased to single and double clone infections for analysis. Each genotyping method presented a different pattern of change in diversity and population structure as a consequence of variability in usable data and the relative polymorphism of the molecular markers (i.e., SNPs < microsatellites < var). Varcoding and microsatellite genotyping showed the overall failure of the IRS intervention to significantly change the population structure from pre-IRS characteristics (i.e., many diverse genomes of low genetic similarity). The 24-SNP barcode provided limited information for analysis, largely due to the biallelic nature of SNPs leading to a high proportion of double-allele calls and a view of more isolate relatedness compared to microsatellites and varcoding. Relative performance, suitability, and cost-effectiveness of the methods relevant to sample size and local malaria elimination in high-transmission endemic areas are discussed.},
}
@article {pmid38027658,
year = {2023},
author = {Haque, MA and Rashid, J and Mia, ML and Rahman, MK and Ali, MA and Bhadra, A and Mahmud, Y},
title = {The first report on a new Tor species, Tor barakae Arunkumar &amp; Basudha 2003, from Bangladesh using DNA barcoding technique.},
journal = {Heliyon},
volume = {9},
number = {11},
pages = {e21764},
pmid = {38027658},
issn = {2405-8440},
abstract = {Mahseer are large-scale fish of the Cyprinidae family that inhabit South and Southeast Asian mountainous streams, rivers, and reservoirs. Tor tor and Tor putitora, two species of the Tor genus, were reportedly found in Bangladesh. This study aimed to confirm the species level of specimens collected from the Sangu River. The collected samples were identified using the DNA barcoding technique, followed by amplifying 645 bp of the cytochrome oxidase c subunit 1 gene (COI) using the FishF1/FishR1 universal primer. The sequence similarity was conducted using BOLD and NCBI databases which showed 99.85-100 % similarity to the reference genome. The genetic divergence between T. putitora vs. SRI, BT, and ST was found to be 0.0239, 0.0239, and 0.0238, respectively. The genetic divergence between T. tor vs. SRI, BT, and ST was 0.0272, 0.0272, and 0.0270, respectively. In the phylogenetic tree, two clusters were formed where collected specimens (SRI, BT, and ST) formed a subcluster with the reference genome (NC_056296.1 T. barakae) with 100 % bootstrap support. This study's findings revealed the presence of a new Tor species named Tor barakae in the Sangu River basin in Bangladesh.},
}
@article {pmid38026223,
year = {2023},
author = {Liu, X and Du, W and Wang, C and Wu, Y and Chen, W and Zheng, Y and Wang, M and Liu, H and Yang, Q and Qian, S and Chen, L and Liu, C},
title = {A multilocus DNA mini-barcode assay to identify twenty vertebrate wildlife species.},
journal = {iScience},
volume = {26},
number = {11},
pages = {108275},
pmid = {38026223},
issn = {2589-0042},
abstract = {The world faces significant challenges in preserving the diversity of vertebrate species due to wildlife crimes. DNA barcoding, an effective molecular marker for insufficient nuclear DNA, is an authentic and quick identification technique to trace the origin of seized samples in forensic investigations. Here, we present a multiplex assay capable of identifying twenty vertebrate wildlife species utilizing twenty species-specific primers that target short fragments of the mitochondrial Cyt b, COI, 16S rRNA, and 12S rRNA genes. The assay achieved strong species specificity and sensitivity with a detection limit as low as 5 pg of DNA input. Additionally, it effectively discriminated a minor contributor (≥1%) from binary mixtures and successfully identified of noninvasive samples, inhibited DNA samples, artificially degraded DNA samples, and case samples, demonstrating a sensitive, robust, practical and easily interpretable tool in screening, and investigating forensic wildlife crimes.},
}
@article {pmid38025745,
year = {2023},
author = {Khemira, H and Mahdhi, M and Afzal, M and Oteef, MDY and Tounekti, T and Al-Faifi, Z and Alsolami, W},
title = {Assessment of genetic diversity and phylogenetic relationship of local coffee populations in southwestern Saudi Arabia using DNA barcoding.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16486},
pmid = {38025745},
issn = {2167-8359},
mesh = {Phylogeny ; *Coffee ; *DNA Barcoding, Taxonomic ; Saudi Arabia ; Plant Breeding ; Genetic Variation/genetics ; Nucleotides ; },
abstract = {The genetic diversity of local coffee populations is crucial to breed new varieties better adapted to the increasingly stressful environment due to climate change and evolving consumer preferences. Unfortunately, local coffee germplasm conservation and genetic assessment have not received much attention. Molecular tools offer substantial benefits in identifying and selecting new cultivars or clones suitable for sustainable commercial utilization. New annotation methods, such as chloroplast barcoding, are necessary to produce accurate and high-quality phylogenetic analyses. This study used DNA barcoding techniques to examine the genetic relationships among fifty-six accessions collected from the southwestern part of Saudi Arabia. PCR amplification and sequence characterization were used to investigate the effectiveness of four barcoding loci: atpB-rbcl, trnL-trnF, trnT-trnL, and trnL. The maximum nucleotide sites, nucleotide diversity, and an average number of nucleotide differences were recorded for atpB-rbcl, while trnT-trnL had the highest variable polymorphic sites, segregating sites, and haploid diversity. Among the four barcode loci, trnT-trnL recorded the highest singleton variable sites, while trnL recorded the highest parsimony information sites. Furthermore, the phylogenetic analysis clustered the Coffea arabica genotypes into four different groups, with three genotypes (KSA31, KSA38, and KSA46) found to be the most divergent genotypes standing alone in the cluster and remained apart during the analysis. The study demonstrates the presence of considerable diversity among coffee populations in Saudi Arabia. Furthermore, it also shows that DNA barcoding is an effective technique for identifying local coffee genotypes, with potential applications in coffee conservation and breeding efforts.},
}
@article {pmid38025712,
year = {2023},
author = {Wang, WY and Yamada, A},
title = {Scrutinising an inscrutable bark-nesting ant: Exploring cryptic diversity in the Rhopalomastix javana (Hymenoptera: Formicidae) complex using DNA barcodes, genome-wide MIG-seq and geometric morphometrics.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16416},
pmid = {38025712},
issn = {2167-8359},
mesh = {Animals ; Phylogeny ; *Ants/genetics ; DNA Barcoding, Taxonomic/methods ; Ecosystem ; Plant Bark ; DNA/chemistry ; },
abstract = {Overlooking cryptic species diversity has grave implications on assessments of climate change impacts on biodiversity, ecosystems and organismal populations. Discriminating between cryptic species has long been challenging even for seasoned taxonomists, as interspecies morphological differences are often indiscernible by visual observation. Multi-disciplinary methods involving genetic analyses in conjunction with quantitative morphological data, should therefore be used to investigate boundaries between cryptic species. We adopted an integrated approach combining analyses of mitochondrial COI barcodes, a genome-wide dataset obtained via multiplexed inter-simple sequence repeats (ISSRs) genotyping by sequencing (MIG-seq), and geometric morphometrics to investigate species divergences in the inscrutable Rhopalomastix javana species complex. Objective clustering of COI suggested five putative molecular species units divergent from each other by thresholds within 4.2-10.6% uncorrected pairwise distance. Phylogenetic analyses based on concatenated MIG-seq data also recovered and strongly supported the monophyly of five major lineages in agreement with COI clusters. Co-ancestry analyses based on MIG-seq data using fineRADstructure resolved variable patterns of admixture linked to geography, and potential genetic drift within some putative species. Geometric morphometric analyses of specimen images further detected statistically significant differences in at least one of three anatomical aspects (Head, Meso, Profile) between all pairs of putative species. Head shape (full-face view) was determined to be the most informative character for species diagnosis, with relatively high classification accuracy. Thin-plate spline deformation grids highlighted areas of high variation between species in each shape for deeper taxonomic scrutiny. The presence of species from multiple distinct lineages existing in near-sympatry firmly demonstrates that R. javana comprises more than one closely-related species, but exact species boundaries are difficult to ascertain. Differences in elevation and its associated abiotic effects on ant adaptations and reproductive phenology may contribute to restricting gene flow and maintaining species boundaries between sympatric populations of the R. javana complex. We further assess the advantages and limitations of geometric morphometrics as a taxonomic tool. Despite its drawbacks, our combined approach has helped draw important insights on cryptic diversity in R. javana, and also identified gaps of knowledge that await address. Results from this study will inform and prime future in-depth taxonomic investigation on the R. javana complex, including formal descriptions and establishment of the five putative species.},
}
@article {pmid38025048,
year = {2023},
author = {Kavaliauskaite, G and Madsen, JGS},
title = {Automatic quality control of single-cell and single-nucleus RNA-seq using valiDrops.},
journal = {NAR genomics and bioinformatics},
volume = {5},
number = {4},
pages = {lqad101},
pmid = {38025048},
issn = {2631-9268},
abstract = {Single-cell and single-nucleus RNA-sequencing (sxRNA-seq) measures gene expression in individual cells or nuclei enabling comprehensive characterization of cell types and states. However, isolation of cells or nuclei for sxRNA-seq releases contaminating RNA, which can distort biological signals, through, for example, cell damage and transcript leakage. Thus, identifying barcodes containing high-quality cells or nuclei is a critical analytical step in the processing of sxRNA-seq data. Here, we present valiDrops, an automated method to identify high-quality barcodes and flag dead cells. In valiDrops, barcodes are initially filtered using data-adaptive thresholding on community-standard quality metrics, and subsequently, valiDrops uses a novel clustering-based approach to identify barcodes with distinct biological signals. We benchmark valiDrops and show that biological signals from cell types and states are more distinct, easier to separate and more consistent after filtering by valiDrops compared to existing tools. Finally, we show that valiDrops can predict and flag dead cells with high accuracy. This novel classifier can further improve data quality or be used to identify dead cells to interrogate the biology of cell death. Thus, valiDrops is an effective and easy-to-use method to improve data quality and biological interpretation. Our method is openly available as an R package at www.github.com/madsen-lab/valiDrops.},
}
@article {pmid38023848,
year = {2023},
author = {Wanke, S and Wicke, S},
title = {Editorial: Phylogenomic discordance in plant systematics.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1308126},
doi = {10.3389/fpls.2023.1308126},
pmid = {38023848},
issn = {1664-462X},
}
@article {pmid38016629,
year = {2024},
author = {Muzarabani, KC and Carolus, H and Schols, R and Hammoud, C and Barson, M and Huyse, T},
title = {An update on snail and trematode communities in the Sanyati Basin of Lake Kariba: New snail and trematode species but no human schistosomes.},
journal = {Parasitology international},
volume = {99},
number = {},
pages = {102830},
doi = {10.1016/j.parint.2023.102830},
pmid = {38016629},
issn = {1873-0329},
mesh = {Animals ; Lakes ; *Trematoda/genetics ; Bulinus ; *Schistosomiasis/epidemiology ; Schistosoma/genetics ; },
abstract = {BACKGROUND: The construction of Lake Kariba brought about a rise in the incidence of schistosomiasis in its surrounding towns of Kariba (Zimbabwe) and Siavonga (Zambia). After extensive control programs in Kariba, schistosomiasis prevalence dropped significantly. The objective of this study was to revisit the same localities sampled by Chimbari et al. (2003), and provide an update on the snail community and prevalence of trematodes in the Northern shore of Lake Kariba while focusing on planorbid species.<br><br>METHODS: Monthly sampling of snails at 16 sites along the Northern shoreline of Lake Kariba, near Kariba town, was undertaken for one year. Minimum one specimen per morphotype was identified using molecular barcoding (sequencing a fragment of cytochrome c oxidase I subunit (COI)). The infection status of snails was assessed by Rapid Diagnostic PCRs (RD-PCR), and trematode infections were genotyped by sequencing COI and 18S rDNA markers.<br><br>RESULTS: We collected and identified seven snail species: Bulinus truncatus, Bulinus forskalii, Gyraulus sp., Physella acuta, Bellamya sp., Radix affinis plicatula and Pseudosuccinea columella. Physella acuta was the most abundant snail species (comprising 56.95% of the total snail count) and present at all sites. The B. truncatus population was found to be infected with the stomach fluke Carmyerius cruciformis, a Petasiger sp. and a trematode species belonging to the family Notocotylidae. No Schistosoma sp. infections were detected in our collected snail specimens.<br><br>CONCLUSIONS: We report B. truncatus as an intermediate snail host for Carmyerius cruciformis, and the presence of three non-schistosome trematode species that have not been reported in Lake Kariba before. Furthermore, we detect a possible shift in the snail community when compared to the report by Chimbari et al. (2003): this is the first record of Gyraulus sp. in Lake Kariba, and we did not observe the previously reported B. pfeifferi, B. globosus and Radix natalensis. Although this shift in snail communities might have contributed to the absence of Schistosoma spp. detection in this study, further monitoring of final and intermediate hosts across the Kariba basin is essential to prove a decrease of schistosomiasis in the area.},
}
@article {pmid38015008,
year = {2023},
author = {Doliwa, A and Grabner, D and Sures, B and Dunthorn, M},
title = {Comparing Microsporidia-targeting primers for environmental DNA sequencing.},
journal = {Parasite (Paris, France)},
volume = {30},
number = {},
pages = {52},
pmid = {38015008},
issn = {1776-1042},
support = {CRC 1439/1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; *DNA, Environmental ; *Microsporidia/genetics ; Sequence Analysis, DNA ; Phylogeny ; },
abstract = {Metabarcoding is a powerful tool to detect classical, and well-known "long-branch" Microsporidia in environmental samples. Several primer pairs were developed to target these unique microbial parasites, the majority of which remain undetected when using general metabarcoding primers. Most of these Microsporidia-targeting primer pairs amplify fragments of different length of the small subunit ribosomal RNA (SSU-rRNA) gene. However, we lack a broad comparison of the efficacy of those primers. Here, we conducted in silico PCRs with three short-read (which amplify a few-hundred base pairs) and two long-read (which amplify over a thousand base pairs) metabarcoding primer pairs on a variety of publicly available Microsporidia sensu lato SSU-rRNA gene sequences to test which primers capture most of the Microsporidia diversity. Our results indicate that the primer pairs do result in slight differences in inferred richness. Furthermore, some of the reverse primers are also able to bind to microsporidian subtaxa beyond the classical Microsporidia, which include the metchnikovellidan Amphiamblys spp., the chytridiopsid Chytridiopsis typographi and the "short-branch" microsporidian Mitosporidium daphniae.},
}
@article {pmid38014933,
year = {2024},
author = {Xie, Y and Tong, Z and Xia, T and Worch, JC and Rho, JY and Dove, AP and O'Reilly, RK},
title = {2D Hierarchical Microbarcodes with Expanded Storage Capacity for Optical Multiplex and Information Encryption.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {36},
number = {8},
pages = {e2308154},
doi = {10.1002/adma.202308154},
pmid = {38014933},
issn = {1521-4095},
support = {22205133//National Natural Science Foundation of China/ ; 22273087//National Natural Science Foundation of China/ ; },
abstract = {The design of nanosegregated fluorescent tags/barcodes by geometrical patterning with precise dimensions and hierarchies could integrate multilevel optical information within one carrier and enhance microsized barcoding techniques for ultrahigh-density optical data storage and encryption. However, precise control of the spatial distribution in micro/nanosized matrices intrinsically limits the accessible barcoding applications in terms of material design and construction. Here, crystallization forces are leveraged to enable a rapid, programmable molecular packing and rapid epitaxial growth of fluorescent units in 2D via crystallization-driven self-assembly. The fluorescence encoding density, scalability, information storage capacity, and decoding techniques of the robust 2D polymeric barcoding platform are explored systematically. These results provide both a theoretical and an experimental foundation for expanding the fluorescence storage capacity, which is a longstanding challenge in state-of-the-art microbarcoding techniques and establish a generalized and adaptable coding platform for high-throughput analysis and optical multiplexing.},
}
@article {pmid38014182,
year = {2023},
author = {Holmes, KE and VanInsberghe, D and Ferreri, LM and Elie, B and Ganti, K and Lee, CY and Lowen, AC},
title = {Viral expansion after transfer is a primary driver of influenza A virus transmission bottlenecks.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38014182},
issn = {2692-8205},
support = {75N93021C00017/AI/NIAID NIH HHS/United States ; R01 AI165644/AI/NIAID NIH HHS/United States ; },
abstract = {For many viruses, narrow bottlenecks acting during transmission sharply reduce genetic diversity in a recipient host relative to the donor. Since genetic diversity represents adaptive potential, such losses of diversity are though to limit the opportunity for viral populations to undergo antigenic change and other adaptive processes. Thus, a detailed picture of evolutionary dynamics during transmission is critical to understanding the forces driving viral evolution at an epidemiologic scale. To advance this understanding, we used a novel barcoded virus library and a guinea pig model of transmission to decipher where in the transmission process diversity is lost for influenza A viruses. In inoculated guinea pigs, we show that a high level of viral genetic diversity is maintained across time. Continuity in the barcodes detected furthermore indicates that stochastic effects are not pronounced within inoculated hosts. Importantly, in both aerosol-exposed and direct contact-exposed animals, we observed many barcodes at the earliest time point(s) positive for infectious virus, indicating robust transfer of diversity through the environment. This high viral diversity is short-lived, however, with a sharp decline seen 1-2 days after initiation of infection. Although major losses of diversity at transmission are well described for influenza A virus, our data indicate that events that occur following viral transfer and during the earliest stages of natural infection have a predominant role in this process. This finding suggests that immune selection may have greater opportunity to operate during influenza A transmission than previously recognized.},
}
@article {pmid38012397,
year = {2024},
author = {Jin, J and Yamamoto, R and Shiroguchi, K},
title = {High-throughput identification and quantification of bacterial cells in the microbiota based on 16S rRNA sequencing with single-base accuracy using BarBIQ.},
journal = {Nature protocols},
volume = {19},
number = {1},
pages = {207-239},
pmid = {38012397},
issn = {1750-2799},
support = {JPMJPR15F3//MEXT | JST | Precursory Research for Embryonic Science and Technology (PRESTO)/ ; 26115719//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; P17389//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
mesh = {Animals ; Mice ; RNA, Ribosomal, 16S/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; Bacteria/genetics ; Sequence Analysis, DNA/methods ; Mouth/microbiology ; DNA, Bacterial/genetics ; Phylogeny ; },
abstract = {Bacteria often function as a community, called the microbiota, consisting of many different bacterial species. The accurate identification of bacterial types and the simultaneous quantification of the cells of each bacterial type will advance our understanding of microbiota; however, this cannot be performed by conventional 16S rRNA sequencing methods as they only identify and quantify genes, which do not always represent cells. Here, we present a protocol for our developed method, barcoding bacteria for identification and quantification (BarBIQ). In BarBIQ, the 16S rRNA genes of single bacterial cells are amplified and attached to a unique cellular barcode in a droplet. Sequencing the tandemly linked cellular barcodes and 16S rRNA genes from many droplets (representing many cells with unique cellular barcodes) and clustering the sequences using the barcodes determines both the bacterial type for each cell based on 16S rRNA gene and the number of cells for each bacterial type based on the quantity of barcode types sequenced. Single-base accuracy for 16S rRNA sequencing is achieved via the barcodes and by avoiding chimera formation from 16S rRNA genes of different bacteria using droplets. For data processing, an easy-to-use bioinformatic pipeline is available (https://github.com/Shiroguchi-Lab/BarBIQ_Pipeline_V1_2_0). This protocol allows researchers with experience in molecular biology but without bioinformatics experience to perform the process in ~2 weeks. We show the application of BarBIQ in mouse gut microbiota analysis as an example; however, this method is also applicable to other microbiota samples, including those from the mouth and skin, marine environments, soil and plants, as well as those from other terrestrial environments.},
}
@article {pmid38008858,
year = {2023},
author = {Cahyani, NKD and Kasanah, N and Kurnia, DS and Hamann, MT},
title = {Profiling Prokaryotic Communities and Aaptamines of Sponge Aaptos suberitoides from Tulamben, Bali.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {25},
number = {6},
pages = {1158-1175},
pmid = {38008858},
issn = {1436-2236},
support = {R01 AT007318/AT/NCCIH NIH HHS/United States ; R01 GM145845/GM/NIGMS NIH HHS/United States ; Hibah Postdoc no 15734/IT3/ TU.00.01/ M/B/2021//Universitas Gadjah Mada/ ; },
mesh = {Animals ; *Porifera/genetics/chemistry ; Indonesia ; RNA, Ribosomal, 16S/genetics ; DNA ; },
abstract = {Sponges (Porifera) harbor a diversity of microorganisms that contribute largely to the production a vast array of bioactive compounds. The microorganisms associated with sponge have an important impact on the chemical diversity of the natural products. Herein, our study focuses on an Aaptos suberitoides commonly found in Indonesia. The objective of this study was to investigate the profile of prokaryotic community and the presence of aaptamine metabolites in sponge Aaptos suberitoides. Sponges were collected from two site locations (Liberty Wreck and Drop Off) in Tulamben, Bali. The sponges were identified by barcoding DNA cytochrome oxidase subunit I (COI) gene. The profile of prokaryotic composition was investigated by amplifying the 16S rRNA gene using primers 515f and 806r to target the V4 region. The metabolites were analyzed using LC-MS, and dereplication was done to identify the aaptamines and its derivates. The barcoding DNA of the sponges confirmed the identity of samples as Aaptos suberitoides. The prokaryotic communities of samples A. suberitoides were enriched and dominated by taxa Proteobacteria, Chloroflexi, Actinobacteria, and Acidobacteria. The chemical analysis showed that all sponges produce aaptamine and isoaaptamine except A. suberitoides S2421 produce analog of aaptamines. This is the first report on the profile of prokaryotic community and the aaptamine of tropical marine sponges, A. suberitoides, from Tulamben, Bali.},
}
@article {pmid38007006,
year = {2024},
author = {Zaharias, P and Kantor, YI and Fedosov, AE and Puillandre, N},
title = {Coupling DNA barcodes and exon-capture to resolve the phylogeny of Turridae (Gastropoda, Conoidea).},
journal = {Molecular phylogenetics and evolution},
volume = {191},
number = {},
pages = {107969},
doi = {10.1016/j.ympev.2023.107969},
pmid = {38007006},
issn = {1095-9513},
mesh = {Animals ; Phylogeny ; *DNA Barcoding, Taxonomic ; *Snails/genetics ; DNA ; Exons ; },
abstract = {Taxon sampling in most phylogenomic studies is often based on known taxa and/or morphospecies, thus ignoring undescribed diversity and/or cryptic lineages. The family Turridae is a group of venomous snails within the hyperdiverse superfamily Conoidea that includes many undescribed and cryptic species. Therefore 'traditional' taxon sampling could constitute a strong risk of undersampling or oversampling Turridae lineages. To minimize potential biases, we establish a robust sampling strategy, from species delimitation to phylogenomics. More than 3,000 cox-1 "barcode" sequences were used to propose 201 primary species hypotheses, nearly half of them corresponding to species potentially new to science, including several cryptic species. A 110-taxa exon-capture tree, including species representatives of the diversity uncovered with the cox-1 dataset, was build using up to 4,178 loci. Our results show the polyphyly of the genus Gemmula, that is split into up to 10 separate lineages, of which half would not have been detected if the sampling strategy was based only on described species. Our results strongly suggest that the use of blind, exploratory and intensive barcode sampling is necessary to avoid sampling biases in phylogenomic studies.},
}
@article {pmid38006330,
year = {2024},
author = {Legault, S and James, PMA},
title = {Spatial patterns of hyperparasitism along a latitudinal gradient of forest genus diversity: insights from the spruce budworm-parasitoids community.},
journal = {Environmental entomology},
volume = {53},
number = {1},
pages = {116-126},
doi = {10.1093/ee/nvad110},
pmid = {38006330},
issn = {1938-2936},
support = {174142//FRQNT Team grant/ ; //NSERC PGS-D scholarship/ ; 174142//FRQNT Team/ ; //NSERC PGS-D/ ; },
mesh = {Animals ; Ecosystem ; Forests ; Insecta ; Food Chain ; *Picea ; *Moths ; },
abstract = {High-order mobile predators are generally thought to increase ecosystem stability and resilience to natural perturbations. In many insect food-webs, higher trophic positions are occupied by parasitoids, which are themselves hosts for hyperparasitoids that can reduce primary parasitoids' efficiency in controlling insect pests. Hyperparasitoids can thus provide ecosystem disservices by facilitating pest outbreaks, or ecosystem services by stabilizing food web fluctuations over longer time periods. To better understand how hyperparasitism affects multitrophic forest systems, we examined for the first time spatial variations in hyperparasitism associated with the spruce budworm. We examined 2 common primary parasitoids of the spruce budworm during outbreaks (Apanteles fumiferanae and Glypta fumiferanae), and estimated their true and pseudohyperparasitism rates in 2014-2015 from 28 locations across a latitudinal gradient (over 450 km) of forest genus diversity. Hyperparasitoid cryptic diversity was also quantified using DNA-barcoding. We found that A. fumiferanae and G. fumiferanae share at least 2 of 5 common hyperparasitoid species, confirming the connected nature of the spruce budworm-parasitoid food web. Moreover, hyperparasitism is modulated by spatial context as we observed a positive correlation between forest genus diversity and hyperparasitism for A. fumiferanae, but not for G. fumiferanae. Further monitoring hyperparasitism holds significant potential to provide new insights into how forest composition affects multitrophic interactions and spatio-temporal outbreak dynamics.},
}
@article {pmid38005450,
year = {2023},
author = {Sueker, M and Daghighi, A and Akhbardeh, A and MacKinnon, N and Bearman, G and Baek, I and Hwang, C and Qin, J and Tabb, AM and Roungchun, JB and Hellberg, RS and Vasefi, F and Kim, M and Tavakolian, K and Kashani Zadeh, H},
title = {A Novel Machine-Learning Framework Based on a Hierarchy of Dispute Models for the Identification of Fish Species Using Multi-Mode Spectroscopy.},
journal = {Sensors (Basel, Switzerland)},
volume = {23},
number = {22},
pages = {},
pmid = {38005450},
issn = {1424-8220},
support = {NA21OAR0210305//National Oceanic and Atmospheric Administration/ ; },
mesh = {Animals ; *Artificial Intelligence ; *Dissent and Disputes ; Machine Learning ; Spectrum Analysis ; Fishes ; },
abstract = {Seafood mislabeling rates of approximately 20% have been reported globally. Traditional methods for fish species identification, such as DNA analysis and polymerase chain reaction (PCR), are expensive and time-consuming, and require skilled technicians and specialized equipment. The combination of spectroscopy and machine learning presents a promising approach to overcome these challenges. In our study, we took a comprehensive approach by considering a total of 43 different fish species and employing three modes of spectroscopy: fluorescence (Fluor), and reflectance in the visible near-infrared (VNIR) and short-wave near-infrared (SWIR). To achieve higher accuracies, we developed a novel machine-learning framework, where groups of similar fish types were identified and specialized classifiers were trained for each group. The incorporation of global (single artificial intelligence for all species) and dispute classification models created a hierarchical decision process, yielding higher performances. For Fluor, VNIR, and SWIR, accuracies increased from 80%, 75%, and 49% to 83%, 81%, and 58%, respectively. Furthermore, certain species witnessed remarkable performance enhancements of up to 40% in single-mode identification. The fusion of all three spectroscopic modes further boosted the performance of the best single mode, averaged over all species, by 9%. Fish species mislabeling not only poses health-related risks due to contaminants, toxins, and allergens that could be life-threatening, but also gives rise to economic and environmental hazards and loss of nutritional benefits. Our proposed method can detect fish fraud as a real-time alternative to DNA barcoding and other standard methods. The hierarchical system of dispute models proposed in this work is a novel machine-learning tool not limited to this application, and can improve accuracy in any classification problem which contains a large number of classes.},
}
@article {pmid38004803,
year = {2023},
author = {Bartholomew, HP and Luciano-Rosario, D and Bradshaw, MJ and Gaskins, VL and Peng, H and Fonseca, JM and Jurick, WM},
title = {Avirulent Isolates of Penicillium chrysogenum to Control the Blue Mold of Apple Caused by P. expansum.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004803},
issn = {2076-2607},
support = {N/A//United States Department of Agriculture/ ; DE-SC0014664//Oak Ridge Associated Universities/ ; },
abstract = {Blue mold is an economically significant postharvest disease of pome fruit that is primarily caused by Penicillium expansum. To manage this disease and sustain product quality, novel decay intervention strategies are needed that also maintain long-term efficacy. Biocontrol organisms and natural products are promising tools for managing postharvest diseases. Here, two Penicillium chrysogenum isolates, 404 and 413, were investigated as potential biocontrol agents against P. expansum in apple. Notably, 404 and 413 were non-pathogenic in apple, yet they grew vigorously in vitro when compared to the highly aggressive P. expansum R19 and Pe21 isolates. Whole-genome sequencing and species-specific barcoding identified both strains as P. chrysogenum. Each P. chrysogenum strain was inoculated in apple with the subsequent co-inoculation of R19 or Pe21 simultaneously, 3, or 7 days after prior inoculation with 404 or 413. The co-inoculation of these isolates showed reduced decay incidence and severity, with the most significant reduction from the longer establishment of P. chrysogenum. In vitro growth showed no antagonism between species, further suggesting competitive niche colonization as the mode of action for decay reduction. Both P. chrysogenum isolates had incomplete patulin gene clusters but tolerated patulin treatment. Finally, hygromycin resistance was observed for both P. chrysogenum isolates, yet they are not multiresistant to apple postharvest fungicides. Overall, we demonstrate the translative potential of P. chrysogenum to serve as an effective biocontrol agent against blue mold decay in apples, pending practical optimization and formulation.},
}
@article {pmid38003002,
year = {2023},
author = {Sertić Kovačević, M and Baričević, A and Kružić, P and Maurić Maljković, M and Hamer, B},
title = {Barcoding (COI) Sea Cucumber Holothuria mammata Distribution Analysis: Adriatic Rare or Common Species?.},
journal = {Genes},
volume = {14},
number = {11},
pages = {},
pmid = {38003002},
issn = {2073-4425},
mesh = {Animals ; *Sea Cucumbers/genetics ; *Holothuria/genetics ; Pacific Ocean ; },
abstract = {The overexploitation of the western Pacific Ocean has expanded the sea cucumber fishery into new regions to supply the Asian market. In 2013, sea cucumbers were removed from the Croatian marine protected species list, and commercial fishery took place for a short period (2017-2018) in the Eastern Adriatic Sea. However, holothuroid species are difficult to distinguish. Holothuria mammata is a species that has rarely been reported in this region and strongly resembles the common species Holothuria tubulosa. This is the first study to assess the genetic diversity of sea cucumbers in the Adriatic Sea using genetic barcoding of the mitochondrial gene cytochrome c oxidase subunit 1 (COI). Specimens for barcoding were collected from the northern and central Adriatic, along with a specimen that had been previously identified as H. sp. cf. mammata based on its morphological characteristics. While genetic analyses showed identified this specimen as H. tubulosa, 30% of the collected specimens were genetically identified as H. mammata. These results call into question the historically accepted sea cucumber assemblage in the Adriatic Sea, which regarded H. mammata as a rare species and generally disregarded its presence in large census studies. Such species distribution data are extremely important in developing and monitoring a sustainable fishery.},
}
@article {pmid38002986,
year = {2023},
author = {Gao, T and Shi, Y and Xiao, J},
title = {Comparative Mitogenomics Reveals Cryptic Species in Sillago ingenuua McKay, 1985 (Perciformes: Sillaginidae).},
journal = {Genes},
volume = {14},
number = {11},
pages = {},
pmid = {38002986},
issn = {2073-4425},
support = {41976083//National Natural Science Foundation of China/ ; 41776171//National Natural Science Foundation of China/ ; 2021C0204//the Province Key Research and Development Program of Zhejiang/ ; },
mesh = {Animals ; Phylogeny ; Thailand ; *Fishes/genetics ; *Perciformes/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {It is unreliable to identify marine fishes only by external morphological features. Species misidentification brings great challenges to fishery research, resource monitoring and ecomanagement. Sillago ingenuua is an important part of commercial marine fishes, and in which, the morphological differences between different groups are not obvious. Here, we compared different geographical groups of S. ingenuua which were collected from Xiamen, Dongshan, Keelung, Songkhla and Java. The results showed that all samples of S. ingenuua were similar in external morphological characteristics and the shape of the swim bladder, but there were two distinctive lineages which were flagged as cryptic species based on DNA barcoding. The comparative mitogenomic results showed that S. ingenuua A and S. ingenuua B were identical in structural organization and gene arrangement. Their nucleotide composition and codon usage were also similar. A phylogenetic analysis was performed based on 13 concatenated PCGs from eight Sillago species. The results showed that the genetic distance between S. ingenuua A and S. ingenuua B was large (D = 0.069), and this genetic distance was large enough to reveal that S. ingenuua A and S. ingenuua B might be different species.},
}
@article {pmid38002314,
year = {2023},
author = {Demir, &#xd6; and Zeng, H and Schulz, B and Schrey, H and Steinert, M and Stadler, M and Surup, F},
title = {Bioactive Compounds from an Endophytic Pezicula sp. Showing Antagonistic Effects against the Ash Dieback Pathogen.},
journal = {Biomolecules},
volume = {13},
number = {11},
pages = {},
pmid = {38002314},
issn = {2218-273X},
support = {2219WK22F4//Fachagentur Nachwachsende Rohstoffe/ ; Stipend to &#xd6;.D.//Republic of T&#xfc;rkiye Ministry of National Education/ ; },
mesh = {*Staphylococcus aureus ; *Antifungal Agents ; Pyrrolidinones/pharmacology ; Ascomycota ; },
abstract = {A fungal endophyte originating from the Canary Islands was identified as a potent antagonist against the fungal phytopathogen Hymenoscyphus fraxineus, which causes the devastating ash dieback disease. This endophyte was tentatively identified as Pezicula cf. ericae, using molecular barcoding. Isolation of secondary metabolites by preparative high-performance liquid chromatography (HPLC) yielded the known compounds CJ-17,572 (1), mycorrhizin A (3) and cryptosporioptides A-C (4-6), besides a new N-acetylated dihydroxyphenylalanin derivative 2, named peziculastatin. Planar structures were elucidated by NMR and HRMS data, while the relative stereochemistry of 2 was assigned by H,H and C,H coupling constants. The assignment of the unknown stereochemistry of CJ-17,572 (1) was hampered by the broadening of NMR signals. Nevertheless, after semisynthetic conversion of 1 into its methyl derivatives 7 and 8, presumably preventing tautomeric effects, the relative configuration could be assigned, whereas comparison of ECD data to those of related compounds determined the absolute configuration. Metabolites 1 and 3 showed significant antifungal effects in vitro against H. fraxineus. Furthermore, 4-6 exhibited significant dispersive effects on preformed biofilms of S. aureus at concentrations up to 2 µg/mL, while the biofilm formation of C. albicans was also inhibited. Thus, cryptosporioptides might constitute a potential source for the development of novel antibiofilm agents.},
}
@article {pmid37999093,
year = {2023},
author = {Evangelou, V and Lytra, I and Krokida, A and Antonatos, S and Georgopoulou, I and Milonas, P and Papachristos, DP},
title = {Insights into the Diversity and Population Structure of Predominant Typhlocybinae Species Existing in Vineyards in Greece.},
journal = {Insects},
volume = {14},
number = {11},
pages = {},
pmid = {37999093},
issn = {2075-4450},
abstract = {Insects of the subfamily Typhlocybinae (Hemiptera: Cicadellidae) are pests of economically important agricultural and horticultural crops. They damage the plants directly or indirectly by transmitting plant pathogens, resulting in significant yield loss. Several leafhoppers of this subfamily use vines as hosts. Accurate and rapid identification is the key to their successful management. The aim of this study is to determine the Typhlocybinae species that exist in vineyards all over Greece and investigate the relationship between them. For this purpose, yellow sticky traps were placed, morphological and molecular data were collected, and phylogenetic models were analyzed. The mitochondrial marker Cytochrome Oxidase Subunit I (mtCOI) was applied for the DNA and phylogenetic analysis. The combination of morphological and molecular data resulted in identifying the existence of six different species all over Greece: Arboridia adanae, Asymmetrasca decedens, Hebata decipiens, Hebata vitis, Jacobiasca lybica and Zygina rhamni. Forty-eight different haplotypes were found to exist in the different regions of the country.},
}
@article {pmid37993967,
year = {2023},
author = {Chong, SQY and Yeo, D and Aidil, NI and Ong, JLY and Chan, AHJ and Fernandez, CJ and Lim, BTM and Khoo, MDY and Wong, AMS and Chang, SF and Yap, HH},
title = {Detection of a novel Babesia sp. in Amblyomma javanense, an ectoparasite of Sunda pangolins.},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {432},
pmid = {37993967},
issn = {1756-3305},
mesh = {Animals ; Humans ; *Babesia/genetics ; Pangolins ; Amblyomma ; Phylogeny ; Animals, Wild ; *Ticks ; *Parasites ; },
abstract = {BACKGROUND: Babesia is a protozoal, tick-borne parasite that can cause life-threatening disease in humans, wildlife and domestic animals worldwide. However, in Southeast Asia, little is known about the prevalence and diversity of Babesia species present in wildlife and the tick vectors responsible for its transmission. Recently, a novel Babesia species was reported in confiscated Sunda pangolins (Manis javanica) in Thailand. To investigate the presence of this parasite in Singapore, we conducted a molecular survey of Babesia spp. in free-roaming Sunda pangolins and their main ectoparasite, the Amblyomma javanense tick.<br><br>METHODS: Ticks and tissue samples were opportunistically collected from live and dead Sunda pangolins and screened using a PCR assay targeting the 18S rRNA gene of Babesia spp. DNA barcoding of the cytochrome oxidase subunit I (COI) mitochondrial gene was used to confirm the species of ticks that were Babesia positive.<br><br>RESULTS: A total of 296 ticks and 40 tissue samples were obtained from 21 Sunda pangolins throughout the 1-year study period. Babesia DNA was detected in five A. javanense ticks (minimum infection rate&#x2009;=&#x2009;1.7%) and in nine different pangolins (52.9%) located across the country. Phylogenetic analysis revealed that the Babesia 18S sequences obtained from these samples grouped into a single monophyletic clade together with those derived from Sunda pangolins in Thailand and that this evolutionarily distinct species is basal to the Babesia sensu stricto clade, which encompasses a range of Babesia species that infect both domestic and wildlife vertebrate hosts.<br><br>CONCLUSIONS: This is the first report documenting the detection of a Babesia species in A. javanense ticks, the main ectoparasite of Sunda pangolins. While our results showed that A. javanense can carry this novel Babesia sp., additional confirmatory studies are required to demonstrate vector competency. Further studies are also necessary to investigate the role of other transmission pathways given the low infection rate of ticks in relation to the high infection rate of Sunda pangolins. Although it appears that this novel Babesia sp. is of little to no pathogenicity to Sunda pangolins, its potential to cause disease in other animals or humans cannot be ruled out.},
}
@article {pmid37993453,
year = {2023},
author = {Jin, L and Shi, HY and Li, T and Zhao, N and Xu, Y and Xiao, TW and Song, F and Ma, CX and Li, QM and Lin, LX and Shao, XN and Li, BH and Mi, XC and Ren, HB and Qiao, XJ and Lian, JY and Du, H and Ge, XJ},
title = {A DNA barcode library for woody plants in tropical and subtropical China.},
journal = {Scientific data},
volume = {10},
number = {1},
pages = {819},
pmid = {37993453},
issn = {2052-4463},
mesh = {China ; *DNA Barcoding, Taxonomic ; Forests ; Phylogeny ; *Plants/genetics ; Wood ; },
abstract = {The application of DNA barcoding has been significantly limited by the scarcity of reliable specimens and inadequate coverage and replication across all species. The deficiency of DNA barcode reference coverage is particularly striking for highly biodiverse subtropical and tropical regions. In this study, we present a comprehensive barcode library for woody plants in tropical and subtropical China. Our dataset includes a standard barcode library comprising the four most widely used barcodes (rbcL, matK, ITS, and ITS2) for 2,520 species from 4,654 samples across 49 orders, 144 families, and 693 genera, along with 79 samples identified at the genus level. This dataset also provides a super-barcode library consisting of 1,239 samples from 1,139 species, 411 genera, 113 families, and 40 orders. This newly developed library will serve as a valuable resource for DNA barcoding research in tropical and subtropical China and bordering countries, enable more accurate species identification, and contribute to the conservation and management of tropical and subtropical forests.},
}
@article {pmid37986859,
year = {2023},
author = {Goshia, T and Aralar, A and Wiederhold, N and Jenks, JD and Mehta, SR and Sinha, M and Karmakar, A and Sharma, A and Shrivastava, R and Sun, H and White, PL and Hoenigl, M and Fraley, SI},
title = {Universal Digital High Resolution Melt for the detection of pulmonary mold infections.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37986859},
issn = {2692-8205},
support = {R01 AI134982/AI/NIAID NIH HHS/United States ; },
abstract = {BACKGROUND: Invasive mold infections (IMIs) such as aspergillosis, mucormycosis, fusariosis, and lomentosporiosis are associated with high morbidity and mortality, particularly in immunocompromised patients, with mortality rates as high as 40% to 80%. Outcomes could be substantially improved with early initiation of appropriate antifungal therapy, yet early diagnosis remains difficult to establish and often requires multidisciplinary teams evaluating clinical and radiological findings plus supportive mycological findings. Universal digital high resolution melting analysis (U-dHRM) may enable rapid and robust diagnosis of IMI. This technology aims to accomplish timely pathogen detection at the single genome level by conducting broad-based amplification of microbial barcoding genes in a digital polymerase chain reaction (dPCR) format, followed by high-resolution melting of the DNA amplicons in each digital reaction to generate organism-specific melt curve signatures that are identified by machine learning.<br><br>METHODS: A universal fungal assay was developed for U-dHRM and used to generate a database of melt curve signatures for 19 clinically relevant fungal pathogens. A machine learning algorithm (ML) was trained to automatically classify these 19 fungal melt curves and detect novel melt curves. Performance was assessed on 73 clinical bronchoalveolar lavage (BAL) samples from patients suspected of IMI. Novel curves were identified by micropipetting U-dHRM reactions and Sanger sequencing amplicons.<br><br>RESULTS: U-dHRM achieved an average of 97% fungal organism identification accuracy and a turn-around-time of 4hrs. Pathogenic molds (Aspergillus, Mucorales, Lomentospora and Fusarium) were detected by U-dHRM in 73% of BALF samples suspected of IMI. Mixtures of pathogenic molds were detected in 19%. U-dHRM demonstrated good sensitivity for IMI, as defined by current diagnostic criteria, when clinical findings were also considered.<br><br>CONCLUSIONS: U-dHRM showed promising performance as a separate or combination diagnostic approach to standard mycological tests. The speed of U-dHRM and its ability to simultaneously identify and quantify clinically relevant mold pathogens in polymicrobial samples as well as detect emerging opportunistic pathogens may provide information that could aid in treatment decisions and improve patient outcomes.},
}
@article {pmid37985545,
year = {2024},
author = {Jaito, W and Sonongbua, J and Panthum, T and Wattanadilokcahtkun, P and Ariyaraphong, N and Thong, T and Singchat, W and Ahmad, SF and Kraichak, E and Muangmai, N and Han, K and Antunes, A and Sitdhibutr, R and Koga, A and Duengkae, P and Kasorndorkbua, C and Srikulnath, K},
title = {Disclosing the hidden nucleotide sequences: a journey into DNA barcoding of raptor species in public repositories.},
journal = {Genes &amp; genomics},
volume = {46},
number = {1},
pages = {95-112},
pmid = {37985545},
issn = {2092-9293},
support = {6417400239//The Graduate grants scholarship of the Faculty of Science, Kasetsart University/ ; 6514400931//The Higher Education for Industry Consortium (Hi-FI)/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Base Sequence ; *DNA ; Genes, Mitochondrial ; Electron Transport Complex IV/genetics ; Cytochromes b/genetics ; },
abstract = {BACKGROUND: In nucleotide public repositories, studies discovered data errors which resulted in incorrect species identification of several accipitrid raptors considered for conservation. Mislabeling, particularly in cases of cryptic species complexes and closely related species, which were identified based on morphological characteristics, was discovered. Prioritizing accurate species labeling, morphological taxonomy, and voucher documentation is crucial to rectify spurious data.<br><br>OBJECTIVE: Our study aimed to identify an effective DNA barcoding tool that accurately reflects the efficiency status of barcodes in raptor species (Accipitridae).<br><br>METHODS: Barcode sequences, including 889 sequences from the mitochondrial cytochrome c oxidase I (COI) gene and 1052 sequences from cytochrome b (Cytb), from 150 raptor species within the Accipitridae family were analyzed.<br><br>RESULTS: The highest percentage of intraspecific nearest neighbors from the nearest neighbor test was 88.05% for COI and 95.00% for Cytb, suggesting that the Cytb gene is a more suitable marker for accurately identifying raptor species and can serve as a standard region for DNA barcoding. In both datasets, a positive barcoding gap representing the difference between inter-and intra-specific sequence divergences was observed. For COI and Cytb, the cut-off score sequence divergences for species identification were 4.00% and 3.00%, respectively.<br><br>CONCLUSION: Greater accuracy was demonstrated for the Cytb gene, making it the preferred primary DNA barcoding marker for raptors.},
}
@article {pmid37985161,
year = {2024},
author = {Pandit, S and Duchow, M and Chao, W and Capasso, A and Samanta, D},
title = {DNA-Barcoded Plasmonic Nanostructures for Activity-Based Protease Sensing.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {63},
number = {2},
pages = {e202310964},
doi = {10.1002/anie.202310964},
pmid = {37985161},
issn = {1521-3773},
support = {IRG-21-135-01-IRG//American Cancer Society/ ; RR 160093//Cancer Prevention and Research Institute of Texas/ ; },
mesh = {Humans ; Peptide Hydrolases ; Gold/chemistry ; *Metal Nanoparticles ; *Nanostructures ; Peptides/chemistry ; Endopeptidases ; DNA ; *Biosensing Techniques ; },
abstract = {We report the development of a new class of protease activity sensors called DNA-barcoded plasmonic nanostructures. These probes are comprised of gold nanoparticles functionalized with peptide-DNA conjugates (GPDs), where the peptide is a substrate of the protease of interest. The DNA acts as a barcode identifying the peptide and facilitates signal amplification. Protease-mediated peptide cleavage frees the DNA from the nanoparticle surface, which is subsequently measured via a CRISPR/Cas12a-based assay as a proxy for protease activity. As proof-of-concept, we show activity-based, multiplexed detection of the SARS-CoV-2-associated protease, 3CL, and the apoptosis marker, caspase 3, with high sensitivity and selectivity. GPDs yield >25-fold turn-on signals, 100-fold improved response compared to commercial probes, and detection limits as low as 58 pM at room temperature. Moreover, nanomolar concentrations of proteases can be detected visually by leveraging the aggregation-dependent color change of the gold nanoparticles. We showcase the clinical potential of GPDs by detecting a colorectal cancer-associated protease, cathepsin B, in three different patient-derived cell lines. Taken together, GPDs detect physiologically relevant concentrations of active proteases in challenging biological samples, require minimal sample processing, and offer unmatched multiplexing capabilities (mediated by DNA), making them powerful chemical tools for biosensing and disease diagnostics.},
}
@article {pmid37984157,
year = {2024},
author = {Chan, AHJ and Gardner, MG and Linacre, A},
title = {Visualisation and detection of latent DNA deposited by pangolin scales onto plastic packaging materials.},
journal = {Forensic science international. Genetics},
volume = {68},
number = {},
pages = {102975},
doi = {10.1016/j.fsigen.2023.102975},
pmid = {37984157},
issn = {1878-0326},
mesh = {Animals ; Humans ; *Pangolins/genetics ; *Mammals/genetics ; Animals, Wild/genetics ; DNA, Mitochondrial/genetics ; Polymerase Chain Reaction ; },
abstract = {We report on the detection and visualisation of latent DNA from pangolin scales deposited onto a plastic packaging material through the use of a nucleic acid staining dye. This latent DNA deposited by pangolin scales was subsequently isolated and analysed using DNA barcoding method. Pangolins are the most illegally traded mammalian species due to the demand for their scales and meat. The demand for their scales were mostly fuelled by its use in traditional medicines. The scales are usually packed into bags and transported globally via sea routes. This is the first report detailing the detection of trace latent DNA from processed wildlife products, on surfaces of bags that they were packaged in. Prior to this report, it was not known if the dried pangolin scales contained transferable quantities of biological material for DNA analyses. To address this, scales were removed from a roadkill Sunda pangolin (Manis javanica), processed by drying and packaged into one of five plastic bags. The presence of pangolin latent DNA was detected on the surface of the plastic bags and visualised using Diamond™ nucleic acid dye. Swabs were then used to recover the stained biological material from various locations in the five bags. The DNA was isolated and quantified using a newly designed quantitative PCR (qPCR) specific to M. javanica to amplify a fragment of the mitochondrial DNA cytochrome b gene. There was a positive correlation between the number of stained particles and DNA quantity, and a greater number of stained particles were found at the bottom of the bag than were found at the top. Conventional PCR targeting part of the cyt b gene amplified a product from all 30 samples taken from the bags and in all cases, sequence data generated matched that of the Sunda pangolin, as expected. All negative controls yielded no results. The method described here is the very first use of a nucleic acid staining dye to detect latent DNA from a mammalian species, other than humans, and highlights the opportunity for further use of Diamond™ nucleic acid dye in wildlife forensic science. It is anticipated that this method will be invaluable in retrieving latent DNA deposited by wildlife products from the environment in which they were contained, to determine the presence of these illegal wildlife products even when previously hidden, inaccessible, or no longer present physically. Further research is required to understand if the use on non-human mammalian wildlife species is feasible.},
}
@article {pmid37983242,
year = {2023},
author = {Lee, M and Lee, HY and Kang, JS and Lee, H and Park, KJ and Park, JY and Yang, TJ},
title = {Authentication of Allium ulleungense, A. microdictyon and A. ochotense based on super-barcoding of plastid genome and 45S nrDNA.},
journal = {PloS one},
volume = {18},
number = {11},
pages = {e0294457},
pmid = {37983242},
issn = {1932-6203},
mesh = {Phylogeny ; *Allium/genetics ; *Genome, Plastid ; Base Sequence ; DNA, Ribosomal/genetics ; },
abstract = {Allium ulleungense (AU) and A. microdictyon (AM) are valuable medicinal and edible vegetables, referred to as mountain garlic in Korea. The identification of AU, AM and a neighboring species A. ochotense (AO) is difficult because of their morphological similarities. We collected samples from three species and 46 cultivated collections to understand the genetic diversity of these valuable Allium species. Among them, we sequenced six collections, including three species and three cultivating collections to obtain data from the plastid genome (plastome) and nuclear 45S ribosomal DNA (nrDNA) for super-barcoding. The AM and AO showed around 60 single nucleotide polymorphisms (SNPs) and 39 Insertion/Deletion (InDels) in the plastome but no variations in the nrDNA sequences. Conversely, the AU and AM showed more than 170 SNPs and 80 InDels in the plastomes, and 20 SNPs and 1 InDel were found in the 45S nrDNA sequences. Among the three cultivating collections, one TB collection was determined to be the AU type in both plastome and nrDNA sequences. However, the other two collections, JB and SA, showed the AM type plastome but were heterozygous in the 45S nrDNA sequences, indicating both AU and AM types (putative AM x AU hybrid). Ten molecular markers were developed based on sequence variations to identify these three species and assess their genetic diversity. A total of 49 collections were genotyped using the ten developed markers and classified into five groups: 14 AU, 22 AM, 1 AO, 3 putative AM x AU hybrids, and 9 putative AU x AM hybrid collections. Super-barcoding with plastomes and nrDNAs revealed the genetic diversity of the three Allium species and putative hybrids between species. The newly developed markers will facilitate species and hybrid identification, thereby benefiting marker-assisted molecular breeding of Allium species.},
}
@article {pmid37983141,
year = {2025},
author = {Chen, Y and Wang, Y and Ma, C and Li, Y and Zuo, D and Huang, X and Tian, X and Wang, W},
title = {Advances in the authentication of collagen products based on DNA technology.},
journal = {Critical reviews in food science and nutrition},
volume = {65},
number = {5},
pages = {884-895},
doi = {10.1080/10408398.2023.2283278},
pmid = {37983141},
issn = {1549-7852},
mesh = {*Collagen/chemistry/genetics ; *Polymerase Chain Reaction/methods ; *DNA/analysis ; Animals ; DNA Barcoding, Taxonomic/methods ; Gelatin/chemistry ; Cytochromes b/genetics ; },
abstract = {Collagenous products are making their way into consumer markets such as foods, nutraceuticals, cosmetics and pharmaceuticals increasingly. Collagen in a large family of proteins is ubiquitous in metazoan. The most effective way to identify biological samples including collagen is DNA technology indisputably. However, the DNA content of collagen mostly derived from connective tissue is relatively less, and commercial collagen products are usually subjected to some harsh treatments in the production process, which makes DNA damage more serious, thus tracing their origin becomes a huge challenge. At present, DNA enrichment mainly relies on silica based centrifugal columns after extraction by classical phenol chloroform method. For improving the amplification of DNA fragments, small amplicons are designed based on more stable mitochondrial genes, such as cytochrome b gene (cytb). In addition to conventional PCR for DNA amplification, some new PCR techniques have also been developed, such as DNA barcoding techniques, PCR-Southern hybridization and fluorescent PCR. These PCR techniques have their pros and cons, and are mainly used in the identification of gelatin at present. The development of a complete set of DNA authentication is of great significance for the control of collagen products quality and will contribute to sustainable development of collagen industry.},
}
@article {pmid37982803,
year = {2023},
author = {Alpsoy, L and Sedeky, AS and Rehbein, U and Thedieck, K and Brandstetter, T and Rühe, J},
title = {Particle ID: A Multiplexed Hydrogel Bead Platform for Biomedical Applications.},
journal = {ACS applied materials &amp; interfaces},
volume = {15},
number = {48},
pages = {55346-55357},
pmid = {37982803},
issn = {1944-8252},
mesh = {Humans ; *Hydrogels ; Enzyme-Linked Immunosorbent Assay ; },
abstract = {We present a new platform based on hydrogel beads for multiplex analysis that can be fabricated, barcoded, and functionalized in a single step using a simple microfluidic assembly and a photo-cross-linking process. The beads are generated in a two-phase flow fluidic system and photo-cross-linking of the polymer in the aqueous phase by C,H insertion cross-linking (CHic). The size and shape of the hydrogel particles can be controlled over a wide range by fluidic parameters. During the fabrication of the beads, they are barcoded by using physical and optical barcoding strategies. Magnetic beads and fluorescent particles, which allow identification of the production batch number, are added simultaneously as desired, resulting in complex, multifunctional beads in a one-step reaction. As an example of biofunctionalization, Borrelia antigens were immobilized on the beads. Serum samples that originated from infected and non-infected patients could be clearly distinguished, and the sensitivity was as good as or even better than ELISA, the state of the art in clinical diagnostics. The ease of the one-step production process and the wide range of barcoding parameters offer strong advantages for multiplexed analytics in the life sciences and medical diagnostics.},
}
@article {pmid37975907,
year = {2023},
author = {Saini, A and Pandey, S},
title = {Calonectria populi sp. nov., causing leaf blight of Populus deltoides in India.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {40},
number = {1},
pages = {15},
pmid = {37975907},
issn = {1573-0972},
support = {Scheme no. 13-28/2018-CAMPA, dated 02.01.2020//Compensatory Afforestation Fund Management and Planning Authority (CAMPA), Ministry of Environment, Forest and Climate Change (MoEF&amp;CC), Government of India, New Delhi/ ; },
mesh = {*Populus ; Phylogeny ; Actins ; Biological Assay ; *Hypocreales ; India ; },
abstract = {Populus deltoides is one of the most favored cash crops in northern India. Thus, accurate identification of pathogens affecting P. deltoides is a critical step in finding or developing effective control measures. In June 2020, symptoms of a leaf blight disease were observed on P. deltoides trees planted at Forest Research Institute, Dehradun, India. Calonectria-like fungal isolates were consistently isolated from the infected leaf samples. Morphological features coupled with phylogenetic analysis of combined partial actin (act), calmodulin (cmdA), histone (his3), translation elongation factor 1-alpha (tef1) and β-tubulin (tub2) gene regions of two fungal isolates confirmed a novel species, which is described and illustrated here as Calonectria populi sp. nov. Symptoms similar to those observed in natural conditions were caused by both the isolates on P. deltoides clone AM109 in detached leaf assays and glasshouse inoculation experiments. Finally, Koch's postulates were established by re-isolation and re-identification of the pathogen from the inoculated leaves. This work is the first to confirm a new leaf blight disease of P. deltoides caused by C. populi sp. nov. in India and worldwide.},
}
@article {pmid37974618,
year = {2023},
author = {Wang, H and Zhao, G and Zhang, T and Li, Y and Zhang, G and Li, Y},
title = {Comparative Study of DNA Barcode Integrity Evaluation Approaches in the Early-Stage Development of DNA-Compatible Chemical Transformation.},
journal = {ACS pharmacology &amp; translational science},
volume = {6},
number = {11},
pages = {1724-1733},
pmid = {37974618},
issn = {2575-9108},
abstract = {DNA-encoded libraries (DEL) have emerged as an important drug discovery technical platform for target-based compound library selection. The success rate of DEL depends on both the chemical diversity of combinatorial libraries and the accuracy of DNA barcoding. Therefore, it is critical that the chemistry applied to library construction should efficiently transform on a wide range of substrates while preserving the integrity of DNA tags. Although several analytical methods have been developed to measure DNA damage caused by DEL chemical reactions, efficient and cost-effective evaluation criteria for DNA damage detection are still demanding. Herein, we set standards for evaluating the DNA compatibility of chemistry development at the laboratory level. Based on four typical DNA damage models of three different DEL formats, we evaluated the detection capabilities of four analytical methods, including ultraperformance liquid chromatography (UPLC-MS), electrophoresis, quantitative polymerase chain reaction (qPCR), and Sanger sequencing. This work systematically revealed the scope and capability of different analytical methods in assessing DNA damages caused by chemical transformation. Based on the results, we recommended UPLC-MS and qPCR as efficient methods for DNA barcode integrity analysis in the early-stage development of DNA-compatible chemistry. Meanwhile, we identified that Sanger sequencing was unreliable to assess DNA damage in this application.},
}
@article {pmid37972287,
year = {2023},
author = {Sandler, SE and Horne, RI and Rocchetti, S and Novak, R and Hsu, NS and Castellana Cruz, M and Faidon Brotzakis, Z and Gregory, RC and Chia, S and Bernardes, GJL and Keyser, UF and Vendruscolo, M},
title = {Multiplexed Digital Characterization of Misfolded Protein Oligomers via Solid-State Nanopores.},
journal = {Journal of the American Chemical Society},
volume = {145},
number = {47},
pages = {25776-25788},
pmid = {37972287},
issn = {1520-5126},
mesh = {Humans ; alpha-Synuclein/metabolism ; *Nanopores ; *Parkinson Disease/metabolism ; },
abstract = {Misfolded protein oligomers are of central importance in both the diagnosis and treatment of Alzheimer's and Parkinson's diseases. However, accurate high-throughput methods to detect and quantify oligomer populations are still needed. We present here a single-molecule approach for the detection and quantification of oligomeric species. The approach is based on the use of solid-state nanopores and multiplexed DNA barcoding to identify and characterize oligomers from multiple samples. We study α-synuclein oligomers in the presence of several small-molecule inhibitors of α-synuclein aggregation as an illustration of the potential applicability of this method to the development of diagnostic and therapeutic methods for Parkinson's disease.},
}
@article {pmid37971927,
year = {2023},
author = {Kota, PK and Vu, HA and LeJeune, D and Han, M and Syed, S and Baraniuk, RG and Drezek, RA},
title = {Expanded Multiplexing on Sensor-Constrained Microfluidic Partitioning Systems.},
journal = {Analytical chemistry},
volume = {95},
number = {48},
pages = {17458-17466},
pmid = {37971927},
issn = {1520-6882},
support = {T15 LM007093/LM/NLM NIH HHS/United States ; },
mesh = {*Microfluidics ; Polymerase Chain Reaction/methods ; *Bacteria/genetics ; },
abstract = {Microfluidics can split samples into thousands or millions of partitions, such as droplets or nanowells. Partitions capture analytes according to a Poisson distribution, and in diagnostics, the analyte concentration is commonly inferred with a closed-form solution via maximum likelihood estimation (MLE). Here, we present a new scalable approach to multiplexing analytes. We generalize MLE with microfluidic partitioning and extend our previously developed Sparse Poisson Recovery (SPoRe) inference algorithm. We also present the first in vitro demonstration of SPoRe with droplet digital PCR (ddPCR) toward infection diagnostics. Digital PCR is intrinsically highly sensitive, and SPoRe helps expand its multiplexing capacity by circumventing its channel limitations. We broadly amplify bacteria with 16S ddPCR and assign barcodes to nine pathogen genera by using five nonspecific probes. Given our two-channel ddPCR system, we measured two probes at a time in multiple groups of droplets. Although individual droplets are ambiguous in their bacterial contents, we recover the concentrations of bacteria in the sample from the pooled data. We achieve stable quantification down to approximately 200 total copies of the 16S gene per sample, enabling a suite of clinical applications given a robust upstream microbial DNA extraction procedure. We develop a new theory that generalizes the application of this framework to many realistic sensing modalities, and we prove scaling rules for system design to achieve further expanded multiplexing. The core principles demonstrated here could impact many biosensing applications with microfluidic partitioning.},
}
@article {pmid37969875,
year = {2023},
author = {Simpson, AC and Tighe, S and Wong, S and Leo, P and Parker, C and Chander, AM and Williams, M and Wu, HW and Venkateswaran, K and Singh, NK},
title = {Analysis of Microbiomes from Ultra-Low Biomass Surfaces Using Novel Surface Sampling and Nanopore Sequencing.},
journal = {Journal of biomolecular techniques : JBT},
volume = {34},
number = {3},
pages = {},
pmid = {37969875},
issn = {1943-4731},
mesh = {Humans ; Biomass ; *Nanopore Sequencing ; *Microbiota/genetics ; Sequence Analysis, DNA/methods ; DNA ; Indicators and Reagents ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {The rapid assessment of microbiomes from ultra-low biomass environments such as cleanrooms or hospital operating rooms has a number of applications for human health and spacecraft manufacturing. Current techniques often employ lengthy protocols using short-read DNA sequencing technology to analyze amplified DNA and have the disadvantage of a longer analysis time and lack of portability. Here, we demonstrate a rapid (~24 hours) on-site nanopore-based sequencing approach to characterize the microbiome of a NASA Class 100K cleanroom where spacecraft components are assembled. This approach employs a modified protocol of Oxford Nanopore's Rapid PCR Barcoding Kit in combination with the recently developed Squeegee-Aspirator for Large Sampling Area (SALSA) surface sampling device. Results for these ultra-low biomass samples revealed DNA amplification ~1 to 2 orders of magnitude above process control samples and were dominated primarily by Paracoccus and Acinetobacter species. Negative control samples were collected to provide critical data on background contamination, including Cutibacerium acnes, which most likely originated from the sampling reagents-associated microbiome (kitome). Overall, these results provide data on a novel approach for rapid low-biomass DNA profiling using the SALSA sampler combined with modified nanopore sequencing. These data highlight the critical need for employing multiple negative controls, along with using DNA-free reagents and techniques, to enable a proper assessment of ultra-low biomass samples.},
}
@article {pmid37969756,
year = {2023},
author = {Jeon, H and Son, H and Min, K},
title = {Detailed Protocol to Perform Direct PCR Using Filamentous Fungal Biomass-Tips and Considerations.},
journal = {Bio-protocol},
volume = {13},
number = {21},
pages = {e4889},
pmid = {37969756},
issn = {2331-8325},
abstract = {The precise and rapid detection of fungi is important in various fields, including clinics, industry, and agriculture. While sequencing universal DNA barcodes remains the standard method for species identification and phylogenetic analysis, a significant bottleneck has been the labor-intensive and time-consuming sample preparation for genomic DNA extraction. To address this, we developed a direct PCR method that bypasses the DNA extraction steps, facilitating efficient target DNA amplification. Instead of extracting genomic DNA from fungal mycelium, our method involves adding a small quantity of mycelium directly to the PCR mixture, followed by a heat shock and vortexing. We found these simple adjustments to be sufficient to lyse many filamentous fungal cells, enabling target DNA amplification. This paper presents a comprehensive protocol for executing direct PCR in filamentous fungi. Beyond species identification, this direct PCR approach holds promise for diverse applications, such as diagnostic PCR for genotype screening without fungal DNA extraction. We anticipate that direct PCR will expedite research on filamentous fungi and diagnosis of fungal diseases. Key features • Eliminates the time-consuming genomic DNA extraction step for PCR, enhancing the speed of molecular identification. • Adds a small quantity of mycelium directly into the PCR mix. • Emphasizes the crucial role of heat shock and vortexing in achieving efficient target DNA amplification. • Accelerates the molecular identification of filamentous fungi and rapid diagnosis of fungal diseases.},
}
@article {pmid37968331,
year = {2023},
author = {de Alcantara Viana, JV and Campos Duarte, R and Vieira, C and Augusto Poleto Antiqueira, P and Bach, A and de Mello, G and Silva, L and Rabelo Oliveira Leal, C and Quevedo Romero, G},
title = {Crypsis by background matching and disruptive coloration as drivers of substrate occupation in sympatric Amazonian bark praying mantises.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {19985},
pmid = {37968331},
issn = {2045-2322},
support = {88887.817249/2023-00//Capes/ ; 2019/01934-3 and 2022/00946-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/26243-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2018/12225-0 and 2019/08474-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 88887.686421/2022-00//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; 88887.675494/2022-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 88887.609466/2021-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; NAF/R2/180791//Royal Society, Newton Advanced Fellowship/ ; },
mesh = {Animals ; Humans ; *Mantodea ; Plant Bark ; Sympatry ; Color ; Vision, Ocular ; Predatory Behavior ; Pigmentation ; },
abstract = {Background matching and disruptive coloration are common camouflage strategies in nature, but few studies have accurately measured their protective value in living organisms. Amazon's Bark praying mantises exhibit colour patterns matching whitish and greenish-brown tree trunks. We tested the functional significance of background matching and disruptive coloration of different praying mantis morphospecies (white, grey and green) detected by DNA barcoding. Through image analysis, avian visual models and field experiments using humans as potential predators, we explored whether the background occupation of mantises provides camouflage against predation. Data were obtained for individuals against their occupied tree trunks (whitish or greenish-brown) and microhabitats (lichen or bryophyte patches), compared to non-occupied trunks. White and grey mantises showed lower colour contrasts against occupied trunks at the scale of tree trunk, with no differences in luminance contrasts. Conversely, green mantises showed lower colour and luminance contrasts against microhabitats and also exhibited high edge disruption against greenish-brown trunks. The camouflage of white and green mantis models against colour-matching trunks increased search time and reduced encounter distance of human predators. We highlight the importance of camouflage strategies at different spatial scales to enhance individual survival against predators. Specifically, we present a stunning study system to investigate the relationship of phylogenetically related species that use camouflage in sympatry.},
}
@article {pmid37967132,
year = {2023},
author = {Schweikle, S and Häser, A and Wetters, S and Raisin, M and Greiner, M and Rigbers, K and Fischer, U and Pietsch, K and Suntz, M and Nick, P},
title = {DNA barcoding as new diagnostic tool to lethal plant poisoning in herbivorous mammals.},
journal = {PloS one},
volume = {18},
number = {11},
pages = {e0292275},
pmid = {37967132},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; DNA/genetics ; Plants, Toxic ; *Plant Poisoning/diagnosis/genetics/veterinary ; Forensic Medicine ; Genetic Markers ; DNA, Plant/genetics ; Mammals/genetics ; },
abstract = {Reliable identification of plant species in the digestive tract of a deceased animal often represents the major key to diagnose a lethal intoxication with poisonous plants in veterinary pathology. In many cases, identification of the species is challenging or even impossible because the diagnostic morphological features have been degraded, and because the interpretation of such features requires a considerable expertise in plant anatomy and biodiversity. The use of DNA barcoding markers can support or even replace classical morphological assessment. While these markers have been widely used for plant taxonomy, their forensic application to clarify causes of animal poisoning is novel. In addition, we use specific single-nucleotide polymorphisms as fingerprints. This allows for a clear decision even in cases, where the conventionally used statistical e-values remain ambiguous. In the current work, we explore the feasibility of this strategy in a couple of exemplary cases, either in concert with anatomical diagnostics, or in cases where visual species identification is not possible, or where chemical toxin detection methods are not well established, complex, time consuming and expensive.},
}
@article {pmid37965298,
year = {2023},
author = {Duong, TY and Pham, LTK and Le, XTK and Nguyen, NTT and Nor, AM and Le, TH},
title = {Mitophylogeny of Pangasiid Catfishes and its Taxonomic Implications for Pangasiidae and the Suborder Siluroidei.},
journal = {Zoological studies},
volume = {62},
number = {},
pages = {e48},
pmid = {37965298},
issn = {1810-522X},
abstract = {Pangasiidae (catfish order: Siluriformes) comprises 30 valid catfish species in four genera: Pangasius, Pangasianodon, Helicophagus, and Pseudolais. Their systematics are frequently revised due to the addition of newly described species. Although Pangasiidae is known to be a monophyletic family, the generic and phylogenetic relationships among the taxa are poorly resolved. This study characterized three newly obtained complete mitogenomes of Mekong River catfishes from Vietnam (Pangasius mekongensis, Pangasius krempfi, and Pangasianodon hypophthalmus), as well as the inter-and intrafamilial relationships of the Pangasiidae and catfish families in Siluroidei. The genomic features of their mitogenomes were similar to those of previously reported pangasiids, including all regulatory elements, extended terminal associated sequences (ETAS), and conserved sequence blocks (CSBs) (CSB-1, CSB-2, CSB-3, and CSBs, A to F) in the control region. A comprehensive phylogeny constructed from datasets of multiple 13 PCG sequences from 117 complete mitogenomes of 32 recognized siluriform families established Pangasiidae as monophyletic and a sister group of Austroglanididae. The [Pangasiidae + Austroglanididae] + (Ictaluridae + Cranoglanididae) + Ariidae] clade is a sister to the "Big Africa" major clade of Siluriformes. Furthermore, both phylogenies constructed from the single barcodes (83 partial cox1 and 80 partial cytB, respectively) clearly indicate genus relationships within Pangasiidae. Pangasianodon was monophyletic and a sister to the (Pangasius + Helicophagus + Pseudolais) group. Within the genus Pangasius, P. mekongensis was placed as a sister taxon to P. pangasius. Pangasius sanitwongsei was found to be related to and grouped with Pangasianodon, but in single-gene phylogenies, it was assigned to the Pangasius + Helicophagus + Pseudolais group. The datasets in this study are useful for studying pangasiid systematics, taxonomy and evolution.},
}
@article {pmid37964203,
year = {2023},
author = {Niu, Z and Lin, Z and Tong, Y and Chen, X and Deng, Y},
title = {Complete plastid genome structure of 13 Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses.},
journal = {BMC plant biology},
volume = {23},
number = {1},
pages = {564},
pmid = {37964203},
issn = {1471-2229},
support = {31970208//National Natural Science Foundation of China/ ; XDA13020500//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
mesh = {*Justicia/genetics ; *Acanthaceae/genetics ; Phylogeny ; *Genome, Chloroplast/genetics ; Genomics ; *Genome, Plastid ; },
abstract = {BACKGROUND: Justicia L. is the largest genus in Acanthaceae Juss. and widely distributed in tropical and subtropical regions of the world. Previous phylogenetic studies have proposed a general phylogenetic framework for Justicia based on several molecular markers. However, their studies were mainly focused on resolution of phylogenetic issues of Justicia in Africa, Australia and South America due to limited sampling from Asia. Additionally, although Justicia plants are of high medical and ornamental values, little research on its genetics was reported. Therefore, to improve the understanding of its genomic structure and relationships among Asian Justicia plants, we sequenced complete chloroplast (cp.) genomes of 12 Asian plants and combined with the previously published cp. genome of Justicia leptostachya Hemsl. for further comparative genomics and phylogenetic analyses.<br><br>RESULTS: All the cp. genomes exhibit a typical quadripartite structure without genomic rearrangement and gene loss. Their sizes range from 148,374 to 151,739&#xa0;bp, including a large single copy (LSC, 81,434-83,676&#xa0;bp), a small single copy (SSC, 16,833-17,507&#xa0;bp) and two inverted repeats (IR, 24,947-25,549&#xa0;bp). GC contents range from 38.1 to 38.4%. All the plastomes contain 114 genes, including 80 protein-coding genes, 30 tRNAs and 4 rRNAs. IR variation and repetitive sequences analyses both indicated that Justicia grossa C. B. Clarke is different from other Justicia species because its lengths of ndhF and ycf1 in IRs are shorter than others and it is richest in SSRs and dispersed repeats. The ycf1 gene was identified as the candidate DNA barcode for the genus Justicia. Our phylogenetic results showed that Justicia is a polyphyletic group, which is consistent with previous studies. Among them, J. grossa belongs to subtribe Tetramerinae of tribe Justicieae while the other Justicia members belong to subtribe Justiciinae. Therefore, based on morphological and molecular evidence, J. grossa should be undoubtedly recognized as a new genus. Interestingly, the evolutionary history of Justicia was discovered to be congruent with the morphology evolution.<br><br>CONCLUSION: Our study not only elucidates basic features of Justicia whole plastomes, but also sheds light on interspecific relationships of Asian Justicia plants for the first time.},
}
@article {pmid37963457,
year = {2023},
author = {Terekhova, M and Swain, A and Bohacova, P and Aladyeva, E and Arthur, L and Laha, A and Mogilenko, DA and Burdess, S and Sukhov, V and Kleverov, D and Echalar, B and Tsurinov, P and Chernyatchik, R and Husarcikova, K and Artyomov, MN},
title = {Single-cell atlas of healthy human blood unveils age-related loss of NKG2C[+]GZMB[-]CD8[+] memory T cells and accumulation of type 2 memory T cells.},
journal = {Immunity},
volume = {56},
number = {12},
pages = {2836-2854.e9},
doi = {10.1016/j.immuni.2023.10.013},
pmid = {37963457},
issn = {1097-4180},
mesh = {Humans ; Adult ; Middle Aged ; Aged ; Aged, 80 and over ; *CD8-Positive T-Lymphocytes ; *Memory T Cells ; T-Lymphocyte Subsets ; Aging ; Receptors, Antigen, T-Cell/metabolism ; Granzymes/metabolism ; },
abstract = {Extensive, large-scale single-cell profiling of healthy human blood at different ages is one of the critical pending tasks required to establish a framework for the systematic understanding of human aging. Here, using single-cell RNA/T cell receptor (TCR)/BCR-seq with protein feature barcoding, we profiled 317 samples from 166 healthy individuals aged 25-85 years old. From this, we generated a dataset from ∼2 million cells that described 55 subpopulations of blood immune cells. Twelve subpopulations changed with age, including the accumulation of GZMK[+]CD8[+] T cells and HLA-DR[+]CD4[+] T cells. In contrast to other T cell memory subsets, transcriptionally distinct NKG2C[+]GZMB[-]CD8[+] T cells counterintuitively decreased with age. Furthermore, we found a concerted age-associated increase in type 2/interleukin (IL)4-expressing memory subpopulations across CD4[+] and CD8[+] T cell compartments (CCR4[+]CD8[+] Tcm and Th2 CD4[+] Tmem), suggesting a systematic functional shift in immune homeostasis with age. Our work provides novel insights into healthy human aging and a comprehensive annotated resource.},
}
@article {pmid37962704,
year = {2023},
author = {Bevilaqua, DR and Batista, JS and da Mota, AJ and da Silva, ACV and da Mota, AMS and Formiga, KM and de Carvalho Freitas, CE},
title = {FishDNAIDs: DNA barcoding as a tool in the development and validation in silico and in vitro of detection systems to four species of Characiformes of commercial importance in the Brazilian Amazon.},
journal = {Molecular biology reports},
volume = {50},
number = {12},
pages = {10657-10662},
pmid = {37962704},
issn = {1573-4978},
support = {RH-INTERIORIZA&#xc7;&#xc3;O/Call 003/2014//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Amazonas/ ; 062.01350/2018//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Amazonas/ ; },
mesh = {Humans ; Animals ; *Characiformes/genetics ; DNA Barcoding, Taxonomic/methods ; Brazil ; DNA ; DNA Primers ; Phylogeny ; },
abstract = {BACKGROUND: The COI mitochondrial gene has been chosen as the "DNA barcode in animals" and the large quantity of genetic information in public databanks gives solid support for the use of DNA barcoding as a promising tool for the development of a specific molecular detection system.<br><br>METHODS AND RESULTS: The present study aimed to develop a Specific Molecular Detection System (SMDS: FishDNAIDs) (primers and probe sets) for the following four target species: Prochilodus nigricans, Potamorhina altamazonica, Psectrogaster rutiloides and Triportheus angulatus, in qPCR assays. In silico and in vitro tests (using gDNA) were performed to test these sets. The database generated contained the cytochrome c oxidase subunit I (COI) nucleotide sequence for 183 specimens of Characiformes, distributed in 34 species representing eight families. In silico, primers designed for the target species amplified different species from the same genus, except for P. rutiloides, which amplified only the target species. In the in vitro test, using the SYBRGreen[tm] and TaqMan&#xae; fluorescence systems, both sets detected the respective target species (P. nigricans, P. altamazonica, P. rutiloides and T. angulatus). In the qPCR assays using SYBRGreen[tm], species considered to be related were also detected, in addition to the target species, with the exception of P. amazonica and P. essequibensis (correlated to P. rutiloides). All target species were detected in the qPCR assays using the TaqMan&#xae; system; however, with the SMDS PALT, the target species P. altamazonica was detected with low CT values (22.21&#x2009;&#xb1;&#x2009;0.17) as well as the correlates of P. latior and P. pristigaster, though with high CT values (23.51&#x2009;&#xb1;&#x2009;0.19 and 30.21&#x2009;&#xb1;&#x2009;0.95). This assay uniquely identifies known adult tissue samples from all four species.<br><br>CONCLUSIONS: The primers and probe sets developed can act as powerful tools for detecting the target Characiformes species.},
}
@article {pmid37957204,
year = {2023},
author = {Santana, P and Martins, T and Lutz, &#xcd; and Miranda, J and da Silva, R and Mesquita, D and Martins, R and Veneza, I and Vallinoto, M and Sampaio, I and Evangelista-Gomes, G},
title = {DNA barcode reveals occurrence of threatened species and hidden diversity on Teleost fish trade in the Coastal Amazon.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {19749},
pmid = {37957204},
issn = {2045-2322},
mesh = {Animals ; *Endangered Species ; DNA Barcoding, Taxonomic ; Phylogeny ; DNA ; *Perciformes ; },
abstract = {This study aimed to identify the teleost fish species sold in Bragança, a major fishing hub on the north coast of Brazil. The COI gene analysis was performed for the identification of fish species. The local market uses common names that are not accurate and do not reflect the diversity of the species. 204 sequences were obtained, with 119 haplotypes. 83 species were identified by comparing with public databases and constructing phylogenetic trees, with Carangidae being the most prevalent family. The study also found Haemulon atlanticus, Menticirrhus cuiaranensis and Hoplias misioneira, a newly described species from the Amazon basin, among the samples. Additionally, 73 commercial names were recorded, including 10 categories, and the illegal trade of Epinephelus itajara was detected. The DNA Barcode method proved to be effective for discriminating the species. The study highlights that common and commercial names are vague and underestimate the fish diversity, and that Brazil needs to revise its regulations for commercial and scientific names.},
}
@article {pmid37954288,
year = {2023},
author = {Lagare, A and Faye, M and Issa, M and Hamidou, O and Bienvenu, B and Mohamed, A and Aoula, B and Moumouni, K and Hassane, F and Otto, YA and Tambwe, DDK and Tassiou, EI and Seini, H and Faye, O and Jambou, R},
title = {First identification of the SARS-COV-2/XBB.1.5 sublineage among indigenous COVID-19 cases through the influenza sentinel surveillance system in Niger.},
journal = {Heliyon},
volume = {9},
number = {11},
pages = {e20916},
pmid = {37954288},
issn = {2405-8440},
support = {001/WHO_/World Health Organization/International ; },
abstract = {The emergence of the Omicron variant in November 2021, has caused panic worldwide due to the rapid evolution and the ability of the virus to escape the immune system. Since, several Omicron sublineages (BA.1 to BA.5) and their descendent recombinant lineages have been circulating worldwide. Furthermore, in December 2022, a new Omicron subvariant XBB.1.5 characterized by an unusual mutation in the spike protein evolved in the United States and rapidly spread to the other continents. Our study reports on the first cases of XBB.1.5 sublineage among indigenous Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-COV-2) positive cases detected through the influenza sentinel surveillance system in Niger. All influenza suspected cases were tested for both influenza and SARS-COV-2 using the Centre for Disease Control and prevention (CDC) Influenza SARS-COV-2 Multiplex quantitative Reverse-Transcription Polymerase Chain Reaction (qRT-PCR) Assay. SARS-COV-2 positive samples with cycle threshold ≤28 were selected for whole genome sequencing subsequently using the Oxford Nanopore Midnight protocol with rapid barcoding on a MinIon MK1B device. A total of 51 SARS-COV-2 positive samples were confirmed between December 2022 and March 2023. We successfully obtained 19 sequences with a predominance of the XBB.1/XBB.1.5 sublineages (73.7 %). In addition, a recombinant XBD sequence was also first-ever identified in early March 2023. Our findings support the need to strengthen the influenza sentinel surveillance for routine Coronavirus Disease 2019 (COVID-19) surveillance and SARS-COV-2 variants monitoring in Niger.},
}
@article {pmid37953749,
year = {2023},
author = {Hausmann, A and László, GM and Mayr, T and Huemer, P},
title = {Surprising discovery of an enigmatic geometrid in Croatia: Mirlatiaarcuata, gen. nov., sp. nov. (Lepidoptera, Geometridae).},
journal = {ZooKeys},
volume = {1183},
number = {},
pages = {99-110},
pmid = {37953749},
issn = {1313-2989},
abstract = {A new monotypic genus of Geometridae, Mirlatiagen. nov., and a new species, M.arcuatasp. nov., are described from Croatia. Based on external and genitalia characters, the new genus is tentatively placed in the subfamily Larentiinae. However, the new genus takes a highly isolated position by having unique characters of the tympanum and showing an unusually long pectination of female antennae. Genetic analysis of a fragmented DNA barcode (mtDNA; cytochrome c oxidase 1) did not result in a clear assignation to any geometrid subfamily or tribe. Adults, male and female genitalia, and habitat photos of the type locality of the new species are illustrated.},
}
@article {pmid37953748,
year = {2023},
author = {Gastineau, R and Dąbek, P and Mianowicz, K and Stoyanova, V and Krawcewicz, A and Abramowski, T},
title = {Complete mitochondrial genome of the abyssal coral Abyssoprimnoagemina Cairns, 2015 (Octocorallia, Primnoidae) from the Clarion-Clipperton Zone, Pacific Ocean.},
journal = {ZooKeys},
volume = {1183},
number = {},
pages = {81-98},
pmid = {37953748},
issn = {1313-2989},
abstract = {The Clarion-Clipperton Zone (CCZ) in the tropical East Pacific is a region of interest for deep-sea mining due to its underwater deposits of polymetallic nodules containing economically important metals such as nickel, copper, and cobalt. It is also a region of extensive baseline studies aiming to describe the state of the environment, including the biodiversity of the benthic fauna. An abundant component of the abyssal plain ecosystem consists of sessile fauna which encrusts polymetallic nodules and are vulnerable to potential impacts arising from exploitation activities, particularly removal of substrate. Therefore, this fauna is often considered to have key species whose genetic connectivity should be studied to assess their ecological resilience. One such species is Abyssoprimnoagemina Cairns, 2015, a deep-sea coral from the CCZ whose presence in the Interoceanmetal Joint Organization (IOM) claim area has been confirmed during samplings. In this study, we used next-generation sequencing (NGS) to obtain the 18S nuclear rRNA gene and the complete mitochondrial genome of A.gemina from IOM exploration area. The mitogenome is 18,825 bp long and encodes for 14 protein coding genes, 2 rRNAs, and a single tRNA. The two phylogeny reconstructions derived from these data confirm previous studies and display A.gemina within a highly supported cluster of seven species whose mitogenomes are all colinear and of comparable size. This study also demonstrates the suitability of NGS for DNA barcoding of the benthic megafauna of the CCZ, which could become part of the IOM protocol for the assessment of population diversity and genetic connectivity in its claim area.},
}
@article {pmid37953586,
year = {2023},
author = {Sagbas, HI and Ercisli, S and Aydin, M and Ilhan, E and Aydinyurt, R and Kasapoglu, AG and Muslu, S and Polat, Y},
title = {Evaluation of genetic diversity using iPBS-SCoT marker methods in native hawthorn genetic resources and species ıdentification by using DNA barcoding method.},
journal = {Cellular and molecular biology (Noisy-le-Grand, France)},
volume = {69},
number = {10},
pages = {43-55},
doi = {10.14715/cmb/2023.69.10.6},
pmid = {37953586},
issn = {1165-158X},
mesh = {Humans ; *Genetic Variation ; *Crataegus/genetics ; DNA Barcoding, Taxonomic ; Polymorphism, Genetic ; DNA ; Phylogeny ; },
abstract = {Hawthorn is an important medicinal plant that spreads around the world and is used in traditional Chinese medicine. Its flowers and leaves contain flavonoids, vitamins, organic acids and essential oils. Its fruit is consumed as fresh and dried and is an important plant for human health. In this study, iPBS (Inter Primer Binding Site) and SCoT (Start Codon Target Polymorphism) markers were used to analyze genetic variation among 101 hawthorn genotypes collected from Çoruh Valley, Türkiye and ITS markers were used for DNA barcoding. Ten iPBS primers were used and a total of 400 alleles were identified from ten iPBS primers with an average of 40 alleles. PIC values ranged from 0.239 (iPBS 2387) to 0.272 (iPBS 2244). Twenty SCoT primers were used and have an average of 50.05 alleles. The PIC values of the primers ranged from 0.251 (SCoT 2) to 0.297 (SCoT 34). For the DNA barcoding study, it was confirmed that the correct region was amplified and sequenced. The genotypes we used in the study matched 14 different accession numbers by searching a BLASTN in the NCBI. NCBI similarity rates of hawthorn genotypes are between 90.83% and 100%. The study emphasizes the genetic diversity of hawthorn grown from seed and the importance of preserving plant genetic resources.},
}
@article {pmid37951847,
year = {2023},
author = {Hendrick, GC and Nicholson, MD and Pagan, JA and Artim, JM and Dolan, MC and Sikkel, PC},
title = {Blood meal identification reveals extremely broad host range and host-bias in a temporary ectoparasite of coral reef fishes.},
journal = {Oecologia},
volume = {203},
number = {3-4},
pages = {349-360},
pmid = {37951847},
issn = {1432-1939},
support = {NSF OCE 1536794//Division of Ocean Sciences/ ; },
mesh = {Humans ; Animals ; Coral Reefs ; Host Specificity ; *Fish Diseases/parasitology ; Fishes ; Meals ; *Isopoda/parasitology ; },
abstract = {Appreciation for the role of cryptofauna in ecological systems has increased dramatically over the past decade. The impacts blood-feeding arthropods, such as ticks and mosquitos, have on terrestrial communities are the subject of hundreds of papers annually. However, blood-feeding arthropods have been largely ignored in marine environments. Gnathiid isopods, often referred to as "ticks of the sea", are temporary external parasites of fishes. They are found in all marine environments and have many consequential impacts on host fitness. Because they are highly mobile and only associated with their hosts while obtaining a blood meal, their broader trophic connections are difficult to discern. Conventional methods rely heavily on detecting gnathiids on wild-caught fishes. However, this approach typically yields few gnathiids and does not account for hosts that avoid capture. To overcome this limitation, we sequenced blood meals of free-living gnathiids collected in light traps to assess the host range and community-dependent exploitation of Caribbean gnathiid isopods. Using fish-specific COI (cox1) primers, sequencing individual blood meals from 1060 gnathiids resulted in the identification of 70 host fish species from 27 families. Comparisons of fish assemblages to blood meal identification frequencies at four collection sites indicated that fishes within the families Haemulidae (grunts) and Lutjanidae (snappers) were exploited more frequently than expected based on their biomass, and Labrid parrotfishes were exploited less frequently than expected. The broad host range along with the biased exploitation of diel-migratory species has important implications for the role gnathiid isopods play in Caribbean coral reef communities.},
}
@article {pmid37951606,
year = {2023},
author = {Cembella, A and Klemm, K and John, U and Karlson, B and Arneborg, L and Clarke, D and Yamanaka, T and Cusack, C and Naustvoll, L and Bresnan, E and Šupraha, L and Lundholm, N},
title = {Emerging phylogeographic perspective on the toxigenic diatom genus Pseudo-nitzschia in coastal northern European waters and gateways to eastern Arctic seas: Causes, ecological consequences and socio-economic impacts.},
journal = {Harmful algae},
volume = {129},
number = {},
pages = {102496},
doi = {10.1016/j.hal.2023.102496},
pmid = {37951606},
issn = {1878-1470},
mesh = {Humans ; *Diatoms ; Ecosystem ; Oceans and Seas ; Harmful Algal Bloom ; Socioeconomic Factors ; },
abstract = {The diatom Pseudo-nitzschia H. Peragallo is perhaps the most intensively researched genus of marine pennate diatoms, with respect to species diversity, life history strategies, toxigenicity, and biogeographical distribution. The global magnitude and consequences of harmful algal blooms (HABs) of Pseudo-nitzschia are particularly significant because of the high socioeconomic impacts and environmental and human health risks associated with the production of the neurotoxin domoic acid (DA) among populations of many (although not all) species. This has led to enhanced monitoring and mitigation strategies for toxigenic Pseudo-nitzschia blooms and their toxins in recent years. Nevertheless, human adaptive actions based on future scenarios of bloom dynamics and proposed shifts in biogeographical distribution under climate-change regimes have not been implemented on a regional scale. In the CoCliME (Co-development of climate services for adaptation to changing marine ecosystems) program these issues were addressed with respect to past, current and anticipated future status of key HAB genera such as Pseudo-nitzschia and expected benefits of enhanced monitoring. Data on the distribution and frequency of Pseudo-nitzschia blooms in relation to DA occurrence and associated amnesic shellfish toxin (AST) events were evaluated in a contemporary and historical context over the past several decades from key northern CoCliME Case Study areas. The regional studies comprised the greater North Sea and adjacent Kattegat-Skagerrak and Norwegian Sea, eastern North Atlantic marginal seas and Arctic gateways, and the Baltic Sea. The first evidence of possible biogeographical expansion of Pseudo-nitzschia taxa into frontier eastern Arctic gateways was provided from DNA barcoding signatures. Key climate change indicators, such as salinity, temperature, and water-column stratification were identified as drivers of upwelling and advection related to the distribution of regional Pseudo-nitzschia blooms. The possible influence of changing variables on bloom dynamics, magnitude, frequency and spatial and temporal distribution were interpreted in the context of regional ocean climate models. These climate change indicators may play key roles in selecting for the occurrence and diversity of Pseudo-nitzschia species within the broader microeukaryote communities. Shifts to higher temperature and lower salinity regimes predicted for the southern North Sea indicate the potential for high-magnitude Pseudo-nitzschia blooms, currently absent from this area. Ecological and socioeconomic impacts of Pseudo-nitzschia blooms are evaluated with reference to effects on fisheries and mariculture resources and coastal ecosystem function. Where feasible, effective adaptation strategies are proposed herein as emerging climate services for the northern CoCLiME region.},
}
@article {pmid37948378,
year = {2023},
author = {Ruiz-Arrondo, I and Veiga, J and Adler, PH and Collantes, F and Oteo, JA and Valera, F},
title = {Integrated taxonomy of black flies (Diptera: Simuliidae) reveals unexpected diversity in the most arid ecosystem of Europe.},
journal = {PloS one},
volume = {18},
number = {11},
pages = {e0293547},
pmid = {37948378},
issn = {1932-6203},
mesh = {Animals ; *Simuliidae/genetics ; Phylogeny ; Ecosystem ; Ecology ; Europe ; },
abstract = {The family Simuliidae includes more than 2000 species of black flies worldwide. Their morphological uniformity creates difficulty for species identification, which limits our knowledge of their ecology and vectorial role. We investigated the systematics of black flies in a semi-arid area of the Iberian Peninsula, an ecologically harsh environment for these organisms. Sampling adult black flies in three different habitats (by means of CDC traps) and in avian nest boxes and collecting immature stages in high-salinity rills provided a representative sample of the component species. A combination of approaches, including morphological, chromosomal, and molecular (based on the mitochondrial cytochrome C oxidase subunit I (COI) and internal transcribed spacer 2 (ITS2) genes) revealed five species: four common species (Simulium intermedium, S. petricolum, S. pseudequinum, and S. rubzovianum) and the first European record for S. mellah. Barcoding gap and phylogenetic analyses revealed that ITS2 is a key marker to identify the species, whereas the COI marker does not provide enough resolution to identify some species or infer their phylogenetic relationships. Morphological and chromosomal features are also provided to identify S. mellah unequivocally. Our study highlights the need for integrated studies of black flies in ecologically extreme habitats to increase our knowledge of their distribution, ecology, and potential risks for public health.},
}
@article {pmid37947881,
year = {2023},
author = {Reiter, N and Dimon, R and Arifin, A and Linde, C},
title = {Culture age of Tulasnella affects symbiotic germination of the critically endangered Wyong sun orchid Thelymitra adorata (Orchidaceae).},
journal = {Mycorrhiza},
volume = {33},
number = {5-6},
pages = {409-424},
pmid = {37947881},
issn = {1432-1890},
support = {LP200200264//Australian Research Council/ ; },
mesh = {*Mycorrhizae ; *Orchidaceae/microbiology ; Germination ; Phylogeny ; Symbiosis ; *Basidiomycota ; },
abstract = {Orchids (Orchidaceae) are dependent on mycorrhizal fungi for germination and to a varying extent as adult plants. We isolated fungi from wild plants of the critically endangered terrestrial orchid Thelymitra adorata and identified them using a multi-region barcoding approach as two undescribed Tulasnella species, one in each of phylogenetic group II and III (OTU1) of the Tulasnellaceae. Using symbiotic propagation methods, we investigated the role of Tulasnella identity (species and isolate) and age post isolation, on the fungus's ability and efficacy in germinating T. adorata. The group II isolate did not support germination. Seed germination experiments were conducted using either (i) three different isolates of OTU1, (ii) 4- and 12-week-old fungal cultures (post isolation) of a single isolate of OTU1, and (iii) T. subasymmetrica which is widespread and known to associate with other species of Thelymitra. Culture age and fungal species significantly (P < 0.05) affected the time to germination and percentage of seed germination, with greater and faster germination with 4-week-old cultures. Tulasnella subasymmetrica was able to germinate T. adorata to leaf stage, although at slightly lower germination percentages than OTU1. The ability of T. adorata to germinate with T. subasymmetrica may allow for translocation sites to be considered outside of its native range. Our findings on the age of Tulasnella culture affecting germination may have applications for improving the symbiotic germination success of other orchids. Furthermore, storage of Tulasnella may need to take account of the culture age post-isolation, with storage at - 80 °C as soon as possible recommended, post isolation.},
}
@article {pmid37944758,
year = {2024},
author = {Lwande, OW and Näslund, J and Sjödin, A and Lantto, R and Luande, VN and Bucht, G and Ahlm, C and Agwanda, B and Obanda, V and Evander, M},
title = {Novel strains of Culex flavivirus and Hubei chryso-like virus 1 from the Anopheles mosquito in western Kenya.},
journal = {Virus research},
volume = {339},
number = {},
pages = {199266},
pmid = {37944758},
issn = {1872-7492},
mesh = {Animals ; *Culex ; *Anopheles/genetics ; *Flavivirus ; Phylogeny ; Kenya ; *Insect Viruses/genetics ; RNA ; },
abstract = {Surveillance of mosquito vectors is critical for early detection, prevention and control of vector borne diseases. In this study we used advanced molecular tools, such as DNA barcoding in combination with novel sequencing technologies to discover new and already known viruses in genetically identified mosquito species. Mosquitoes were captured using BG sentinel traps in Western Kenya during May and July 2019, and homogenized individually before pooled into groups of ten mosquitoes. The pools and individual samples were then used for molecular analysis and to infect cell cultures. Of a total of fifty-four (54) 10-pools, thirteen (13) showed cytopathic effect (CPE) on VeroB4 cells, eighteen (18) showed CPE on C6/36 cells. Eight (8) 10-pools out of the 31 CPE positive pools showed CPE on both VeroB4 and C6/36 cells. When using reverse transcriptase polymerase chain reaction (RT-PCR), Sanger sequencing and Twist Comprehensive Viral Research Panel (CVRP) (Twist Biosciences), all pools were found negative by RT-PCR when using genus specific primers targeting alphaviruses, orthobunyaviruses and virus specific primers towards o'nyong-nyong virus, chikungunya virus and Sindbis virus (previously reported to circulate in the region). Interestingly, five pools were RT-PCR positive for flavivirus. Two of the RT-PCR positive pools showed CPE on both VeroB4 and C6/36 cells, two pools showed CPE on C6/36 cells alone and one pool on VeroB4 cells only. Fifty individual mosquito homogenates from the five RT-PCR positive 10-pools were analyzed further for flavivirus RNA. Of these, 19 out of the 50 individual mosquito homogenates indicated the presence of flavivirus RNA. Barcoding of the flavivirus positive mosquitoes revealed the mosquito species as Aedes aegypti (1), Mansonia uniformis (6), Anopheles spp (3), Culex pipiens (5), Culex spp (1), Coquilletidia metallica (2) and Culex quinquefasciatus (1). Of the 19 flavivirus positive individual mosquitoes, five (5) virus positive homogenates were sequenced. Genome sequences of two viruses were completed. One was identified as the single-stranded RNA Culex flavivirus and the other as the double-stranded RNA Hubei chryso-like virus 1. Both viruses were found in the same Anopheles spp. homogenate extracted from a sample that showed CPE on both VeroB4 and C6/36 cells. The detection of both viruses in a single mosquito homogenate indicated coinfection. Phylogenetic analyses suggested that the Culex flavivirus sequence detected was closely related to a Culex flavivirus isolated from Uganda in 2008. All four Hubei chryso-like virus 1 segments clusters closely to Hubei chryso-like virus 1 strains isolated in Australia, China and USA. Two novel strains of insect-specific viruses in Anopheles mosquitoes were detected and characterized.},
}
@article {pmid37944134,
year = {2023},
author = {Cero, C and Shu, W and Reese, AL and Douglas, D and Maddox, M and Singh, AP and Ali, SL and Zhu, AR and Katz, JM and Pierce, AE and Long, KT and Nilubol, N and Cypess, RH and Jacobs, JL and Tian, F and Cypess, AM},
title = {Standardized In Vitro Models of Human Adipose Tissue Reveal Metabolic Flexibility in Brown Adipocyte Thermogenesis.},
journal = {Endocrinology},
volume = {164},
number = {12},
pages = {},
pmid = {37944134},
issn = {1945-7170},
support = {R01 DK075112/DK/NIDDK NIH HHS/United States ; },
mesh = {Male ; Mice ; Animals ; Humans ; Adult ; *Adipocytes, Brown/metabolism ; *Adipose Tissue, Brown/metabolism ; Obesity/metabolism ; Adipose Tissue, White/metabolism ; Thermogenesis/genetics ; Adrenergic Agents/metabolism ; Uncoupling Protein 1/genetics/metabolism ; },
abstract = {Functional human brown and white adipose tissue (BAT and WAT) are vital for thermoregulation and nutritional homeostasis, while obesity and other stressors lead, respectively, to cold intolerance and metabolic disease. Understanding BAT and WAT physiology and dysfunction necessitates clinical trials complemented by mechanistic experiments at the cellular level. These require standardized in vitro models, currently lacking, that establish references for gene expression and function. We generated and characterized a pair of immortalized, clonal human brown (hBA) and white (hWA) preadipocytes derived from the perirenal and subcutaneous depots, respectively, of a 40-year-old male individual. Cells were immortalized with hTERT and confirmed to be of a mesenchymal, nonhematopoietic lineage based on fluorescence-activated cell sorting and DNA barcoding. Functional assessments showed that the hWA and hBA phenocopied primary adipocytes in terms of adrenergic signaling, lipolysis, and thermogenesis. Compared to hWA, hBA were metabolically distinct, with higher rates of glucose uptake and lactate metabolism, and greater basal, maximal, and nonmitochondrial respiration, providing a mechanistic explanation for the association between obesity and BAT dysfunction. The hBA also responded to the stress of maximal respiration by using both endogenous and exogenous fatty acids. In contrast to certain mouse models, hBA adrenergic thermogenesis was mediated by several mechanisms, not principally via uncoupling protein 1 (UCP1). Transcriptomics via RNA-seq were consistent with the functional studies and established a molecular signature for each cell type before and after differentiation. These standardized cells are anticipated to become a common resource for future physiological, pharmacological, and genetic studies of human adipocytes.},
}
@article {pmid37941478,
year = {2024},
author = {Jiang, M and Wang, Y and Yu, X and He, Y and Zheng, X and Qin, J and Gu, Y and Li, X and Shi, Y and Ma, X and Li, J and Pu, K},
title = {An image-based Abplex method for high-throughput GPCRs antibody discovery.},
journal = {Biotechnology journal},
volume = {19},
number = {1},
pages = {e2300336},
doi = {10.1002/biot.202300336},
pmid = {37941478},
issn = {1860-7314},
support = {81602252//National Natural Science Foundation of China/ ; },
mesh = {*Receptors, G-Protein-Coupled/chemistry/metabolism ; *Membrane Proteins ; },
abstract = {As the field of antibody therapeutics advances rapidly, membrane proteins, particularly G protein-coupled receptors (GPCRs), have emerged as highly sought-after drug targets. However, the challenges associated with extracting membrane proteins have created a demand for effective antibody screening systems targeting these proteins. In this study, we propose developing an innovative antibody screening strategy (Abplex) based on high-content imaging. This approach leverages intact cells that express target membrane proteins, facilitating the presentation of proteins in their native conformation. Furthermore, it acquires both specific and non-specific binding signals in a single well, thereby bolstering the robustness of the outcomes. The technique involves just one step and can be completed within 50 min, enabling the analysis of a single sample in just one second. The amalgamation of dependable experimental findings, a simplified workflow, reduced hands-on time, and a swift analytical pace positions our method for superior throughput and precision when juxtaposed with traditional techniques such as CbELISA and FACS. Moreover, we introduce the concept of cell barcoding, wherein cells are labeled with different fluorescence spatial patterns. This feature allows for multiplexed detection to meet the needs of various experiments. The characteristics of Abplex promise to expedite GPCR-targeting antibody discovery, advance therapeutics and enable new disease treatments.},
}
@article {pmid37941426,
year = {2023},
author = {Gálico, DA and Murugesu, M},
title = {Dual-signalled magneto-optical barcodes with lanthanide-based molecular cluster-aggregates.},
journal = {Nanoscale},
volume = {15},
number = {45},
pages = {18198-18202},
doi = {10.1039/d3nr03838f},
pmid = {37941426},
issn = {2040-3372},
abstract = {A proof-of-concept for magneto-optical barcodes is demonstrated for the first time. The dual-signalled spectrum observed via magnetic circular dichroism spectroscopy can be used to develop anti-counterfeiting materials with extra layers of security when compared with the widely studied luminescent barcodes.},
}
@article {pmid37941142,
year = {2023},
author = {Höjer, P and Frick, T and Siga, H and Pourbozorgi, P and Aghelpasand, H and Martin, M and Ahmadian, A},
title = {BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies.},
journal = {Nucleic acids research},
volume = {51},
number = {22},
pages = {e114},
pmid = {37941142},
issn = {1362-4962},
support = {191-0475//Erling Persson Family Foundation, Olle Engkvist Foundation/ ; 2018-06228//Swedish Research Council/ ; 20190989//Stockholm County Council/ ; //KTH-SFO SciLifeLab/ ; //Knut and Alice Wallenberg Foundation/ ; //National Bioinformatics Infrastructure Sweden/ ; },
mesh = {Humans ; *Genome, Human ; *Genomics/methods ; *Haplotypes ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Linked-read sequencing promises a one-method approach for genome-wide insights including single nucleotide variants (SNVs), structural variants, and haplotyping. We introduce Barcode Linked Reads (BLR), an open-source haplotyping pipeline capable of handling millions of barcodes and data from multiple linked-read technologies including DBS, 10× Genomics, TELL-seq and stLFR. Running BLR on DBS linked-reads yielded megabase-scale phasing with low (<0.2%) switch error rates. Of 13616 protein-coding genes phased in the GIAB benchmark set (v4.2.1), 98.6% matched the BLR phasing. In addition, large structural variants showed concordance with HPRC-HG002 reference assembly calls. Compared to diploid assembly with PacBio HiFi reads, BLR phasing was more continuous when considering switch errors. We further show that integrating long reads at low coverage (∼10×) can improve phasing contiguity and reduce switch errors in tandem repeats. When compared to Long Ranger on 10× Genomics data, BLR showed an increase in phase block N50 with low switch-error rates. For TELL-Seq and stLFR linked reads, BLR generated longer or similar phase block lengths and low switch error rates compared to results presented in the original publications. In conclusion, BLR provides a flexible workflow for comprehensive haplotype analysis of linked reads from multiple platforms.},
}
@article {pmid37941051,
year = {2023},
author = {Bastin, S and Percy, DM and Siverio, F},
title = {Establishing reliable DNA barcoding primers for jumping plant lice (Psylloidea, Hemiptera).},
journal = {BMC research notes},
volume = {16},
number = {1},
pages = {322},
pmid = {37941051},
issn = {1756-0500},
support = {2019-2023 PhD//Agencia Canaria de Investigaci&#xf3;n, Innovaci&#xf3;n y Sociedad de la Informaci&#xf3;n (ACIISI)/ ; CUARENTAGRI (MAC2/1.1a/231)//PROGRAMA MAC 2014-2020 - INTERREG/ ; },
mesh = {Animals ; DNA Barcoding, Taxonomic/methods ; *Hemiptera/genetics ; *Aphids/genetics ; DNA Primers/genetics ; Electron Transport Complex IV/genetics ; },
abstract = {OBJECTIVES: DNA Barcoding has proven to be a reliable method for rapid insect identification. The success of this method is based on the amplification of a specific region, the 'Folmer' barcode region at the 5´ start of the cytochrome c oxidase 1 gene (cox1), with universal primers. Previous studies showed failures of standard "universal" primers to amplify this region in psyllids. The aim of the study was the design of a new alternative more reliable primer combination for taxa of the superfamily Psylloidea and its comparison with the performance of the standard "universal" Folmer-primers.<br><br>RESULTS: A newly designed degenerate forward primer LCOP-F was developed following comparison of the sequence alignment of the priming site of "universal" primer LCO1490 and the standard insect forward primer LepF1. When combined with the "universal" reverse primer, HCO2198, this new primer pairing was able to generate barcode sequence for all 36 species in 20 genera across the five families of psyllids tested in this study, and these primers were found to be more universally reliable across psyllid taxa than other primer pairs tested.},
}
@article {pmid37940706,
year = {2023},
author = {Gondard, M and Lane, M and Barratt, J and Talundzic, E and Qvarnstrom, Y},
title = {Simultaneous targeted amplicon deep sequencing and library preparation for a time and cost-effective universal parasite diagnostic sequencing approach.},
journal = {Parasitology research},
volume = {122},
number = {12},
pages = {3243-3256},
pmid = {37940706},
issn = {1432-1955},
support = {CC999999/ImCDC/Intramural CDC HHS/United States ; },
mesh = {Animals ; Humans ; *Parasites/genetics ; Cost-Benefit Analysis ; *Plasmodium/genetics ; Plasmodium falciparum/genetics ; DNA, Ribosomal/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Babesia/genetics ; },
abstract = {We recently described a targeted amplicon deep sequencing (TADS) strategy that utilizes a nested PCR targeting the 18S rDNA gene of blood-borne parasites. The assay facilitates selective digestion of host DNA by targeting enzyme restriction sites present in vertebrates but absent in parasites. This enriching of parasite-derived amplicon drastically reduces the proportion of host-derived reads during sequencing and results in the sensitive detection of several clinically important blood parasites including Plasmodium spp., Babesia spp., kinetoplastids, and filarial nematodes. Despite these promising results, high costs and the laborious nature of metagenomics sequencing are prohibitive to the routine use of this assay in most laboratories. We describe and evaluate a new metagenomic approach that utilizes a set of primers modified from our original assay that incorporates Illumina barcodes and adapters during the PCR steps. This modification makes amplicons immediately compatible with sequencing on the Illumina MiSeq platform, removing the need for a separate library preparation, which is expensive and time-consuming. We compared this modified assay to our previous nested TADS assay in terms of preparation speed, limit of detection (LOD), and cost. Our modifications reduced assay turnaround times from 7 to 5 days. The cost decreased from approximately $40 per sample to $11 per sample. The modified assay displayed comparable performance in the detection and differentiation of human-infecting Plasmodium spp., Babesia spp., kinetoplastids, and filarial nematodes in clinical samples. The LOD of this modified approach was determined for malaria parasites and remained similar to that previously reported for our earlier assay (0.58 Plasmodium falciparum parasites/µL of blood). These modifications markedly reduced costs and turnaround times, making the assay more amenable to routine diagnostic applications.},
}
@article {pmid37940688,
year = {2023},
author = {Hua, Y and Cai, D and Shirley, CA and Mo, S and Chen, R and Gao, F and Chen, F},
title = {A prognostic model for ovarian neoplasms established by an integrated analysis of 1580 transcriptomic profiles.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {19429},
pmid = {37940688},
issn = {2045-2322},
mesh = {Female ; Humans ; Neoplasm Recurrence, Local/genetics/pathology ; Neoplasm Staging ; *Ovarian Neoplasms/pathology ; Prognosis ; Sulfur Compounds ; *Transcriptome ; },
abstract = {Even after debulking surgery combined with chemotherapy or new adjuvant chemotherapy paired with internal surgery, the average year of disease free survival in advanced ovarian cancer was approximately 1.7 years[1]. The development of a molecular predictor of early recurrence would allow for the identification of ovarian cancer (OC) patients with high risk of relapse. The Ovarian Cancer Disease Free Survival Predictor (ODFSP), a predictive model constructed from a special set of 1580 OC tumors in which gene expression was assessed using both microarray and sequencing platforms, was created by our team. To construct gene expression barcodes that were resistant to biases caused by disparate profiling platforms and batch effects, we employed a meta-analysis methodology that was based on the binary gene pair technique. We demonstrate that ODFSP is a reliable single-sample predictor of early recurrence (1 year or less) using the largest pool of OC transcriptome data sets available to date. The ODFSP model showed significantly high prognostic value for binary recurrence prediction unaffected by clinicopathologic factors, with a meta-estimate of the area under the receiver operating curve of 0.64 (P = 4.6E-05) and a D-index (robust hazard ratio) of 1.67 (P = 9.2E-06), respectively. GO analysis of ODFSP's 2040 gene pairs (collapsed to 886 distinct genes) revealed the involvement in small molecular catabolic process, sulfur compound metabolic process, organic acid catabolic process, sulfur compound biosynthetic process, glycosaminoglycan metabolic process and aminometabolic process. Kyoto encyclopedia of genes and genomes pathway analysis of ODFSP's signature genes identified prominent pathways that included cAMP signaling pathway and FoxO signaling pathway. By identifying individuals who might benefit from a more aggressive treatment plan or enrolment in a clinical trial but who will not benefit from standard surgery or chemotherapy, ODFSP could help with treatment decisions.},
}
@article {pmid37936815,
year = {2023},
author = {Hu, HS and Mao, JY and Wang, X and Liang, YZ and Jiang, B and Zhang, DQ},
title = {Plastid phylogenomics and species discrimination in the "Chinese" clade of Roscoea (Zingiberaceae).},
journal = {Plant diversity},
volume = {45},
number = {5},
pages = {523-534},
pmid = {37936815},
issn = {2468-2659},
abstract = {Roscoea is an alpine or subalpine genus from the pan-tropical family Zingiberaceae, which consists of two disjunct groups in geography, namely the "Chinese" clade and the "Himalayan" clade. Despite extensive research on the genus, Roscoea species remain poorly defined and relationships between these species are not well resolved. In this study, we used plastid genomes of nine species and one variety to resolve phylogenetic relationships within the "Chinese" clade of Roscoea and as DNA super barcodes for species discrimination. We found that Roscoea plastid genomes ranged in length from 163,063 to 163,796 bp, and encoded 113 genes, including 79 protein-coding genes, 30 tRNA genes, four rRNA genes. In addition, expansion and contraction of the IR regions showed obvious infraspecific conservatism and interspecific differentiation. Plastid phylogenomics revealed that species belonging to the "Chinese" clade of Roscoea can be divided into four distinct subclades. Furthermore, our analysis supported the independence of R. cautleoides var. pubescens, the recovery of Roscoea pubescens Z.Y. Zhu, and a close relationship between R. humeana and R. cautloides. When we used the plastid genome as a super barcode, we found that it possessed strong discriminatory power (90%) with high support values. Intergenic regions provided similar resolution, which was much better than that of protein-coding regions, hypervariable regions, and DNA universal barcodes. However, plastid genomes could not completely resolve Roscoea phylogeny or definitively discriminate species. These limitations are likely related to the complex history of Roscoea speciation, poorly defined species within the genus, and the maternal inheritance of plastid genomes.},
}
@article {pmid37936056,
year = {2023},
author = {Wang, W and Chen, B and Ma, R and Qiao, M and Fu, Y},
title = {The DNA barcode identification of Dalbergia odorifera T. Chen and Dalbergia tonkinensis Prain.},
journal = {BMC plant biology},
volume = {23},
number = {1},
pages = {546},
pmid = {37936056},
issn = {1471-2229},
support = {31870540//National Natural Science Foundation of China/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Dalbergia/genetics ; DNA, Plant/genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Dalbergia odorifera is a precious tree species with unique economic and medicinal values, which is difficult to distinguish from Dalbergia tonkinensis by traditional identification methods such as morphological characteristics and wood structure characteristics. It has been demonstrated that the identification of tree species can be effectively achieved using DNA barcoding, but there is a lack of study of the combined sequences used as DNA barcodes in the two tree species. In this study, 10 single sequences and 4 combined sequences were selected for analysis, and the identification effect of each sequence was evaluated by the distance-based method, BLAST-based search, character-based method, and tree-based method.<br><br>RESULTS: Among the single sequences and the combined sequences, the interspecies distance of trnH-psbA and ITS2&#x2009;+&#x2009;trnH-psbA was greater than the intraspecies distance, and there was no overlap in their frequency distribution plots. The results of the Wilcoxon signed-rank test for the interspecies distance of each sequence showed that the interspecies differences of the single sequences except trnL-trnF, trnH-psbA, and ycf3 were significantly smaller than those of the combined sequences. The results of BLAST analysis showed that trnH-psbA could accurately identify D. odorifera and D. tonkinensis at the species level. In the character-based method, single sequences of trnL-trnF, trnH-psbA with all the combined sequences can be used for the identification of D. odorifera and D. tonkinensis. In addition, the neighbor-joining (NJ) trees constructed based on trnH-psbA and ITS2&#x2009;+&#x2009;trnH-psbA were able to cluster D. odorifera and D. tonkinensis on two clades.<br><br>CONCLUSIONS: The results showed that the character-based method with the BLOG algorithm was the most effective among all the evaluation methods, and the combined sequences can improve the ability to identify tree species compared with single sequences. Finally, the trnH-psbA and ITS2&#x2009;+&#x2009;trnH-psbA were proposed as DNA barcodes to identify D. odorifera and D. tonkinensis.},
}
@article {pmid37936052,
year = {2024},
author = {Lee, EL and Harrison, J and Barnes, J},
title = {Exploring the Use of Traditional Medicines, Natural Health Products and Conventional Medicines: Development and Testing of the New Zealand 'All-Medicines' Questionnaire.},
journal = {Drugs - real world outcomes},
volume = {11},
number = {1},
pages = {13-32},
pmid = {37936052},
issn = {2199-1154},
abstract = {INTRODUCTION: Traditional, complementary and alternative medicine (TCAM) are popular healthcare choices among consumers globally. The latest national data on the use of TCAM practitioners in New Zealand (NZ) were collected over a decade ago. Robust data on the use of natural health products (NHPs) and TCAM practices alongside conventional medicines are not yet available in NZ.<br><br>OBJECTIVES: This study aimed to develop and test a bespoke questionnaire (All-MedsNZ) that included comprehensive data collection elements exploring NHPs' and conventional medicines' use.<br><br>METHODS: This was a questionnaire design study involving expert panel feedback, and engagement with TCAM users, in the development process. This work comprised questionnaire development (stage 1) followed by a questionnaire-testing study (stage 2). The questionnaire was developed on the basis of literature review findings and the research team's expertise. The questionnaire content was then validated by an expert panel comprising practitioners in TCAM and conventional medicine. Then, a two-phase study was utilised to test the questionnaire. Phase 1 involved participants (NHP users) completing the web-based questionnaire and providing feedback by answering probing questions added throughout the questionnaire to evaluate users' comprehension of the questions and to&#xa0;identify issues with the questionnaire. In phase 2, selected participants were interviewed online to gain in-depth insights into issues identified in phase one. Based on these findings, the questionnaire was revised.<br><br>RESULTS: The expert panel (n = 9) confirmed the questionnaire had high face and content validity; most original questions were retained. In the questionnaire-testing study, 95 and 27 participants completed the phase 1 and 2 studies, respectively. Most questions achieved a high response rate of &#x2265;&#xa0;90%, and participants had no major issues understanding and answering the questionnaire. Problematic questions were those relating to providing product barcodes and photographs, and information on product costs. Most of the NHPs data entered by participants included the brand/generic name, manufacturer/company name, main ingredient(s) and dose form. Generally, these NHP-related data were of acceptable quality. However, information on the main ingredient(s) of products entered by participants was less satisfactory: approximately one-third of the 143 NHPs recorded in the study had the main ingredient(s) missing or incorrectly stated. Interviews with participants reiterated the issues identified in the phase 1 study. The low response rates for some of the questions were partly due to participants' unpreparedness (i.e. not having NHPs/medicines on hand) to complete the questionnaire. In addition, a lack of clarity for the term 'natural health practitioner' led to confusion among some participants.<br><br>CONCLUSION: Overall, no major design-, method- or questionnaire-related issues were identified in this development and testing work. The questionnaire demonstrated adequate face and content validity and acceptability among participants. The data collected were reasonably complete and of sufficient quality for analysis. Future studies should pilot the revised All-MedsNZ questionnaire with a larger, nationally representative sample to ascertain its feasibility and utility.},
}
@article {pmid37935964,
year = {2024},
author = {Janssens, DH and Greene, JE and Wu, SJ and Codomo, CA and Minot, SS and Furlan, SN and Ahmad, K and Henikoff, S},
title = {Scalable single-cell profiling of chromatin modifications with sciCUT&amp;Tag.},
journal = {Nature protocols},
volume = {19},
number = {1},
pages = {83-112},
pmid = {37935964},
issn = {1750-2799},
support = {R01 HG010492/HG/NHGRI NIH HHS/United States ; R44 GM140536/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Histones/genetics/metabolism ; *Leukocytes, Mononuclear/metabolism ; Chromatin/genetics ; Protein Processing, Post-Translational ; Histone Code ; Single-Cell Analysis/methods ; },
abstract = {Cleavage under targets and tagmentation (CUT&amp;Tag) is an antibody-directed in situ chromatin profiling strategy that is rapidly replacing immune precipitation-based methods, such as chromatin immunoprecipitation-sequencing. The efficiency of the method enables chromatin profiling in single cells but is limited by the numbers of cells that can be profiled. Here, we describe a combinatorial barcoding strategy for CUT&amp;Tag that harnesses a nanowell dispenser for simple, high-resolution, high-throughput, single-cell chromatin profiling. In this single-cell combinatorial indexing CUT&amp;Tag (sciCUT&amp;Tag) protocol, lightly cross-linked nuclei are bound to magnetic beads and incubated with primary and secondary antibodies in bulk and then arrayed in a 96-well plate for a first round of cellular indexing by antibody-directed Tn5 tagmentation. The sample is then repooled, mixed and arrayed across 5,184 nanowells at a density of 12-24 nuclei per well for a second round of cellular indexing during PCR amplification of the sequencing-ready library. This protocol can be completed in 1.5 days by a research technician, and we illustrate the optimized protocol by profiling histone modifications associated with developmental gene repression (H3K27me3) as well as transcriptional activation (H3K4me1-2-3) in human peripheral blood mononuclear cells and use single-nucleotide polymorphisms to facilitate collision removal. We have also used sciCUT&amp;Tag for simultaneous profiling of multiple chromatin epitopes in single cells. The reduced cost, improved resolution and scalability of sciCUT&amp;Tag make it an attractive platform to profile chromatin features in single cells.},
}
@article {pmid37934387,
year = {2024},
author = {Zhu, H and Li, H},
title = {Comprehensive Analysis of the Complete Chloroplast Genome of Cinnamomum daphnoides (Lauraceae), An Endangered Island Endemic Plant.},
journal = {Molecular biotechnology},
volume = {66},
number = {12},
pages = {3514-3525},
pmid = {37934387},
issn = {1559-0305},
support = {2022F1068-3//Scientific Research Institution Support Special Project of Zhejiang Province, China/ ; 2021F1065-6//Scientific Research Institution Support Special Project of Zhejiang Province, China/ ; 2022C02038//the "Pioneer" and "Leading Goose" R&amp;D Program of Zhejiang/ ; },
mesh = {*Genome, Chloroplast ; *Endangered Species ; *Phylogeny ; *Cinnamomum/genetics/classification ; Base Composition ; Codon Usage ; High-Throughput Nucleotide Sequencing ; },
abstract = {Cinnamomum daphnoides (Siebold &amp; Zucc 1846) is a rare and endangered island species with a unique Sino-Japanese distribution pattern. However, inormation regarding the species' chloroplast (cp) genome, structural features, and the phylogenetic relationship is still lacking. We utilized high-throughput sequencing technology to assemble and annotate the first cp genome of C. daphnoides (GenBank OR654104), followed by genomic characterization and phylogenetic analysis to fill the gaps in this species' cp genome. Our analysis showed that the cp genome has a quadripartite structure spanning 152,765 bp with a GC content of 39.15%. The genome encodes 126 genes, which include 36 tRNA genes, 8 rRNA genes, and 82 mRNA genes. Specifically, 44 genes are related to photosynthesis, 59 are associated with self-replication, six are other genes, and four have unknown functionality. The Codon usage bias in the genome exhibits a preference for A/U bases. We identified 29 interspaced repeat sequences that belonging to three types of repeat sequences. A total of 217 cpSSR loci were detected with single nucleotide repeats (59.91%) being the most frequent loci, mainly composed of A/T repeats. Our selection pressure analysis revealed that the ycf2 gene experienced strong positive selection (Ka/Ks = 1.81, P > 0.844). Further, we identified three highly variable fragments (psbM, psbT, and ycf1) that can be utilized as specific DNA barcoding markers for species definition and population genetic studies. We conducted boundary analysis, which showed that the structure and gene sequence of the two species were highly conserved. Finally, our phylogenetic analysis supports that C. daphnoides is close to C. cassia in the Cinnamomum genes, indicating that the two species share a common ancestry. Overall, providing genomic information on C. daphnoides will be beneficial for the conservation and utilization of endangered plant genetic resources. It will also serve as a reference for the identification of species and the phylogenetic analysis of Cinnamomum. This information will be useful in future research.},
}
@article {pmid37933260,
year = {2023},
author = {Uh-Navarrete, AE and Valdez-Moreno, M and Callejas-Jiménez, ME and Vásquez-Yeomans, L},
title = {Discovering the fish fauna of a lagoon from the southeast of the Yucatan Peninsula, Mexico, using DNA barcodes.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16285},
pmid = {37933260},
issn = {2167-8359},
mesh = {Humans ; Animals ; *Ecosystem ; Mexico ; *DNA Barcoding, Taxonomic ; Fishes ; Larva ; DNA ; },
abstract = {BACKGROUND: Aquatic ecosystems in the tropics are typically environments with a high species richness of fishes. These systems are also among the most vulnerable in the world, threatening the overall biodiversity of tropical regions. As a first step, it is important to enumerate the species in any ecosystem to promote its conservation. This study aims to inventory the ichthyofauna in the Chile Verde Lagoon, Quintana Roo, on the Yucatan Peninsula, a system fortunately well protected in Mexico, based on faunal surveys backed up with mtDNA barcodes.<br><br>METHODS: We collected larvae, juveniles, and adults of fishes in the lagoon with a variety of sampling gear targeting various life stages. Species were identified using both morphology and DNA barcodes. The abundance of species and ichthyoplankton biomass (wet weight, suction technique) were calculated from 43 samples.<br><br>RESULTS: We collected 197 adult and juvenile fishes and 3,722 larvae, of which 306 specimens were DNA-sequenced with a success rate of 96.7%. We identified 13 families, 24 genera, and 27 species in our inventory. The species number was estimated to comprise 75% of the potential total richness using the Chao 1 richness estimator. Clupeids and gobiids accounted for 87.9% of the total abundance of fishes, and, together with cyprinodontids, also accounted for the highest ichthyoplankton biomass.<br><br>CONCLUSION: Adult and juvenile fishes were identified by morphology and meristic values, however larvae required DNA barcoding to identify species. The high biomass and abundance of larvae of clupeids, gobiids and cyprinodontids suggests that the Chile Verde Lagoon may be important for reproduction of these species in the region. Microgobius microlepis, a marine goby species, is reported for the first time in an inland oligohaline system. This study provides a basis for future environmental assessment and biomonitoring of the Chile Verde Lagoon in the Yucatan Peninsula of Mexico.},
}
@article {pmid37932792,
year = {2023},
author = {Olyaiee, A and Yadegar, A and Mirsamadi, ES and Sadeghi, A and Mirjalali, H},
title = {Profiling of the fecal microbiota and circulating microRNA-16 in IBS subjects with Blastocystis infection : a case-control study.},
journal = {European journal of medical research},
volume = {28},
number = {1},
pages = {483},
pmid = {37932792},
issn = {2047-783X},
mesh = {Humans ; *Irritable Bowel Syndrome ; *Blastocystis Infections/microbiology ; *Circulating MicroRNA ; Case-Control Studies ; *Blastocystis ; *Microbiota ; *MicroRNAs ; },
abstract = {Irritable bowel syndrome (IBS) is a prevalent gastrointestinal (GI) tract disorder. Although the main reason for IBS is not clear, the interaction between intestinal microorganisms and the gut barrier seems to play an important role in pathogenesis of IBS. The current study aimed to investigate the effect of Blastocystis on the gut microbiota profile and the circulation levels of microRNA (mir)-16 of IBS patients compared to healthy subjects. Stool and blood samples were collected from 80 participants including 40 samples from each IBS and healthy group. Upon DNA extraction from stool samples, barcoding region and quantitative real-time PCR were analyzed to investigate Blastocystis and the microbiota profile, respectively. RNA was extracted from serum samples of included subjects and the expression of mir-16 was evaluated using stem-loop protocol and qreal-time PCR. Significant changes between IBS patients and healthy controls was observed in Firmicutes, Actinobacteria, Faecalibacterium, and Alistipes. In IBS patients, the relative abundance of Bifidobacteria was directly correlated with the presence of Blastocystis, while Alistipes was decreased with Blastocystis. Lactobacillus was significantly increased in Blastocystis carriers. In healthy subjects, the relative abundance of Bifidobacteria was decreased, but Alistipes was increased in Blastocystis carriers. The changes in the Firmicutes/Bacteroidetes ratio was not significant in different groups. The relative expression of mir-16 in Blastocystis-negative IBS patients and healthy carriers was significantly overexpressed compared to control group. The presence of Blastocystis, decreased the relative expression of mir-16 in IBS patients compared to Blastocystis-negative IBS patients. The present study revealed that Blastocystis has the ability to change the abundance of some phyla/genera of bacteria in IBS and healthy subjects. Moreover, Blastocystis seems to modulate the relative expression of microRNAs to control the gut atmosphere, apply its pathogenicity, and provide a favor niche for its colonization.},
}
@article {pmid37929970,
year = {2023},
author = {Tulloch, LB and Carvalho, S and Lima, M and Wall, RJ and Tinti, M and Pinto, EG and MacLean, L and Wyllie, S},
title = {RES-Seq-a barcoded library of drug-resistant Leishmania donovani allowing rapid assessment of cross-resistance and relative fitness.},
journal = {mBio},
volume = {14},
number = {6},
pages = {e0180323},
pmid = {37929970},
issn = {2150-7511},
support = {/WT_/Wellcome Trust/United Kingdom ; 218448/Z/19/Z, 203134/Z/16/Z//Wellcome Trust (WT)/ ; },
mesh = {*Leishmania donovani/drug effects/genetics ; *Drug Resistance/genetics ; *Antiprotozoal Agents/pharmacology ; Leishmaniasis, Visceral/parasitology/drug therapy ; Genetic Fitness ; Humans ; DNA Barcoding, Taxonomic ; Gene Library ; High-Throughput Nucleotide Sequencing ; },
abstract = {Visceral leishmaniasis (VL) remains the third largest parasitic killer worldwide, responsible for 20,000-30,000 deaths each year. Control and ultimate elimination of VL will require a range of therapeutic options with diverse mechanisms of action to combat drug resistance. One approach to ensure that compounds in development exploit diverse mechanisms of action is to screen them against highly curated cell lines resistant to drugs already in the VL pipeline. The identification of cross-resistant cell lines indicates that test compounds are likely acting via previously established mechanisms. Current cross-resistance screens are limited by the requirement to profile individual resistant cell lines one at a time. Here, we introduce unique DNA barcodes into multiple resistant cell lines to facilitate parallel profiling. Utilizing the power of Illumina sequencing, growth kinetics and relative fitness under compound selection can be monitored revolutionizing our ability to identify and prioritize compounds acting via novel mechanisms.},
}
@article {pmid37926385,
year = {2024},
author = {Rodríguez-Rojas, JJ and Lozano-Sardaneta, YN and Fernández-Salas, I and Sánchez-Casas, RM and Becker, I},
title = {Species diversity, barcode, detection of pathogens and blood meal pattern in Phlebotominae (Diptera: Psychodidae) from northeastern Mexico.},
journal = {Acta tropica},
volume = {249},
number = {},
pages = {107064},
doi = {10.1016/j.actatropica.2023.107064},
pmid = {37926385},
issn = {1873-6254},
mesh = {Animals ; Male ; Female ; Humans ; *Psychodidae/parasitology ; Mexico ; Insect Vectors/parasitology ; *Leishmania/genetics ; *Leishmaniasis ; Feeding Behavior ; },
abstract = {More than 90 species of phlebotomines are vectors of parasites, bacteria, and viruses, which cause disease in animals and humans. Therefore, their study is necessary to establish prevention and control strategies. Mexico is an endemic country for leishmaniasis, mostly in the center and southern regions of the country, yet only few studies have been conducted in the northern part of the country. The present study aims to: (a) assess the alpha diversity of Phlebotominae in an annual cycle, (b) to correlate climatic variables with abundance, (c) to generate barcodes of these insects as part of the integrative taxonomy, and (d) to detect Leishmania, Wolbachia and blood sources in an area close to where a case of autochthonous leishmaniasis has been detected in Nuevo Leon, Mexico. A systematic sampling was conducted during three consecutive nights from 17:00 to 22:00 h., placing Shannon traps, CDC traps with incandescent light, and BG Sentinel 2 + BG Lure traps. A total catch effort of 660 nights/traps/hours was achieved, in which a total number of 707 phlebotomines (58% female and 42% male) of six species were collected and identified. The most abundant species were Psathyromyia cratifer (57%) and Psathyromyia shannoni sensu stricto (26%). The highest abundance (72%; 507/707) was collected during March, April and May 2021. Barcodes were generated for four species of phlebotomines, which represent new records for Mexico. For the molecular detection of microorganisms, 302 specimens were analyzed, although no specimens were positive for Leishmania spp. Wolbachia strains were detected in phlebotomines with an infection rate of 1.32% (4/302) and found in Pa. cratifer and Lu. cruciata. Likewise, human DNA was identified in female Lu. cruciata and Pa. cratifer phlebotomines. These findings indicate the presence of potential vector species of the parasite Leishmania spp. This result shows the need for further entomological surveillance to elucidate the transmission mechanisms in these northern areas of the country.},
}
@article {pmid37922517,
year = {2024},
author = {Bhooma, V and Vassou, SL and Kaliappan, I and Parani, M},
title = {Identification of adulteration in the market samples of saffron using morphology, HPLC, HPTLC, and DNA barcoding methods.},
journal = {Genome},
volume = {67},
number = {2},
pages = {43-52},
doi = {10.1139/gen-2022-0059},
pmid = {37922517},
issn = {1480-3321},
mesh = {Humans ; *Crocus/genetics/chemistry ; Chromatography, High Pressure Liquid ; Chromatography, Thin Layer ; DNA Barcoding, Taxonomic ; Drug Contamination ; Plants/genetics ; },
abstract = {Saffron, the stigma of Crocus sativus L., is the most expensive spice used for culinary, medicinal, dye, and cosmetics purposes. It is highly adulterated because of its limited production and high commercial value. In this study, 104 saffron market samples collected from 16 countries were tested using morphology, high-performance liquid chromatography (HPLC), high-performance thin-layer chromatography (HPTLC), and deoxyribonucleic acid (DNA) barcoding. Overall, 45 samples (43%) were adulterated. DNA barcoding identified the highest number of adulterated saffron (44 samples), followed by HPTLC (39 samples), HPLC (38 samples), and morphology (32 samples). Only DNA barcoding identified the adulterated samples containing saffron and other plants' parts as bulking agents. In addition, DNA barcoding identified 20 adulterant plant species, which will help develop quality control methods and market surveillance. Some of the adulterant plants are unsafe for human consumption. The HPLC method helped identify the saffron samples adulterated with synthetic safranal. HPLC and HPTLC methods will help identify the samples adulterated with other parts of the saffron plant (auto-adulteration).},
}
@article {pmid37919838,
year = {2023},
author = {Li, SY and Yao, Y and Sun, L and Ling, HN and Jin, WD and Lin, XL},
title = {DNA barcodes and morphology reveal new species within the Rheotanytarsus guineensis species group from China (Diptera: Chironomidae).},
journal = {Archives of insect biochemistry and physiology},
volume = {114},
number = {4},
pages = {e22060},
doi = {10.1002/arch.22060},
pmid = {37919838},
issn = {1520-6327},
support = {2018M640227//China Postdoctoral Science Foundation/ ; A2-2006-23-200303//Shanghai Ocean University/ ; 31900344//National Natural Science Foundation of China/ ; },
mesh = {Male ; Animals ; *Chironomidae/genetics ; *Diptera ; DNA Barcoding, Taxonomic ; China ; },
abstract = {The Rheotanytarsus guineensis species group (Diptera: Chironomidae) is a species diverse and taxonomically difficult group. Using DNA barcodes, we found five new species within the R. guineensis species group and reviewed the species group based on adult males from China. Rheotanytarsus guoae Lin &amp; Yao sp. n., Rheotanytarsus miaoae Lin &amp; Yao sp. n., Rheotanytarsus qiangi Lin &amp; Yao sp. n., Rheotanytarsus yueqingensis Lin &amp; Yao sp. n., and Rheotanytarsus yui Lin &amp; Yao sp. n. are all described and figured. A key to known adult males of the R. guineensis species group worldwide is provided for the first time.},
}
@article {pmid37919743,
year = {2023},
author = {Tumusiime, J and Kagoro-Rugunda, G and Tolo, CU and Namirembe, D and Schols, R and Hammoud, C and Albrecht, C and Huyse, T},
title = {An accident waiting to happen? Exposing the potential of urogenital schistosomiasis transmission in the Lake Albert region, Uganda.},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {398},
pmid = {37919743},
issn = {1756-3305},
support = {B2/191/P1/MicroResist//BRAIN-be 2.0 under the MicroResist project/ ; },
mesh = {Animals ; Humans ; *Schistosomiasis haematobia ; Lakes ; Uganda/epidemiology ; Schistosoma haematobium/genetics ; Bulinus/parasitology ; },
abstract = {BACKGROUND: Urogenital schistosomiasis caused by the parasitic blood fluke Schistosoma haematobium is the most common form of that constitutes a majority of over 240 million schistosomiasis cases. The enigmatic absence of urogenital schistosomiasis in Uganda has, until now, been attributed to the absence of substantial populations of suitable snail intermediate hosts.<br><br>METHODS: Malacological surveys were carried out in 73 sites southeast of Lake Albert, Uganda in October and November 2020. Collected snails were transported to the laboratory for identification. The snails were identified using partial mitochondrial cytochrome c oxidase subunit one and nuclear internal transcribed spacer barcoding. Schistosome infections in snails were also assessed using cercarial shedding and rapid diagnostic PCR techniques.<br><br>RESULTS: We found&#xa0;Bulinus globosus and Bulinus nasutus productus, the main intermediate species in the transmission of S. haematobium in mainland East Africa. In this survey, B. globosus was more common than B. nasutus productus, with the former reported at four sites (total count&#x2009;=&#x2009;188) and the latter reported at one site (total count&#x2009;=&#x2009;79). Molecular testing revealed a high prevalence of Schistosoma bovis in B. nasutus productus (16%), but no S. haematobium infections were found.<br><br>CONCLUSIONS: Given the abundance of snail hosts and the risky human water contact behaviours observed, we highlight the potential for urogenital schistosomiasis transmission in the region.},
}
@article {pmid37919549,
year = {2024},
author = {Mason, JW and Chow, YT and Hudson, L and Tutter, A and Michaud, G and Westphal, MV and Shu, W and Ma, X and Tan, ZY and Coley, CW and Clemons, PA and Bonazzi, S and Berst, F and Briner, K and Liu, S and Zécri, FJ and Schreiber, SL},
title = {DNA-encoded library-enabled discovery of proximity-inducing small molecules.},
journal = {Nature chemical biology},
volume = {20},
number = {2},
pages = {170-179},
pmid = {37919549},
issn = {1552-4469},
support = {R35 GM127045/GM/NIGMS NIH HHS/United States ; },
mesh = {*Von Hippel-Lindau Tumor Suppressor Protein/chemistry/metabolism ; *Nuclear Proteins/metabolism ; Transcription Factors ; Ubiquitin-Protein Ligases/metabolism ; DNA ; },
abstract = {Small molecules that induce protein-protein associations represent powerful tools to modulate cell circuitry. We sought to develop a platform for the direct discovery of compounds able to induce association of any two preselected proteins, using the E3 ligase von Hippel-Lindau (VHL) and bromodomains as test systems. Leveraging the screening power of DNA-encoded libraries (DELs), we synthesized ~1 million DNA-encoded compounds that possess a VHL-targeting ligand, a variety of connectors and a diversity element generated by split-and-pool combinatorial chemistry. By screening our DEL against bromodomains in the presence and absence of VHL, we could identify VHL-bound molecules that simultaneously bind bromodomains. For highly barcode-enriched library members, ternary complex formation leading to bromodomain degradation was confirmed in cells. Furthermore, a ternary complex crystal structure was obtained for our most enriched library member with BRD4[BD1] and a VHL complex. Our work provides a foundation for adapting DEL screening to the discovery of proximity-inducing small molecules.},
}
@article {pmid37916676,
year = {2021},
author = {Domingos, AR and Carvalho-Batista, A and Robles, R and Arcifa, MS and Mantelatto, FL},
title = {Evaluating food web interactions among microcrustaceans and insect in a tropical shallow lake using DNA-based protocol.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {32},
number = {5-8},
pages = {202-211},
pmid = {37916676},
issn = {2470-1408},
abstract = {We developed species-specific primers of five microcrustacean preys, Ceriodaphnia richardi, Diaphanosoma cf. brevireme, Daphnia gessneri, Simocephalus serrulatus, Thermocyclops decipiens and Mesocyclops sp., to analyze food-web interactions involving their two insect predators Rheumatobates crassifemur and Martarega uruguayensis distributed in a tropical shallow lake. We designed internal primers of the COI gene (177-282 bp), and tested them, by means of PCR, for specificity and sensitivity. In our tests for specificity, all primers successfully amplified the DNA target but were species-specific failing to amplify the biomarker from any of the other species tested, even in a mixed DNA sample, including predators' DNA. In tests for sensitivity, primers successfully amplified zooplankton biomarkers from low concentration of DNA extractions and also from digestive tract of predators, even after many hours of ingestion. This technique provides a framework as an efficient tool for evaluation of food-web research in natural aquatic environments, where it is impossible to observe if predation occurs. Furthermore, this technique provides an effective solution for the identification of zooplankton species from the predator's digestive tract, where morphological identification alone is sometimes difficult because predators do not consume the prey but feeds using extra-oral digestion, such is the case of heteropterans.},
}
@article {pmid37915996,
year = {2023},
author = {Hübner, J and Chemyreva, VG and Notton, DG},
title = {Taxonomic and nomenclatural notes on Geodiaprialongiceps Kieffer, 1911 (Hymenoptera, Diapriidae) and synonymy of the genus Geodiapria Kieffer, 1910.},
journal = {ZooKeys},
volume = {1183},
number = {},
pages = {1-11},
pmid = {37915996},
issn = {1313-2989},
abstract = {This paper reviews the status of Geodiapria and its nominotypical and only included species G.longiceps. Geodiapria was previously understood to be very similar to, and doubtfully separated from the genus Basalys. We use integrative taxonomy (morphology, DNA-barcoding, phylogenetic tree building) to show that the valid name for what was G.longiceps Kieffer, 1911 is now Basalysrufocinctus (Kiefer, 1911) and that Geodiapria is consequently a junior synonym of Basalyssyn. nov. The following taxa are new synonyms of B.rufocinctus: Loxotropalongiceps Wasmann, 1909, syn. nov., G.longiceps Kieffer, 1911, syn. nov., L.rufosignata Kieffer, 1911, syn. nov. Basalysrufocinctus is newly reported from Corsica, Germany, Norway and Spain.},
}
@article {pmid37915621,
year = {2023},
author = {Zhang, K and Zhang, D and Yang, Q and Long, L and Xie, J and Wang, Y and Yao, Q and Wu, F and Liu, S},
title = {Integrated widely targeted metabolomics and network pharmacology revealed quality disparities between Guizhou and conventional producing areas of Codonopsis Radix.},
journal = {Frontiers in nutrition},
volume = {10},
number = {},
pages = {1271817},
pmid = {37915621},
issn = {2296-861X},
abstract = {INTRODUCTION: With the internationalization of traditional Chinese medicine, the demand for medicinal and edible Codonopsis Radix (CR) has increased, and its medicinal resources have attracted attention. CR is a well-known traditional Chinese medicine with a long pharmaceutical and edible history. The Guizhou province in China has abundant CR resources, but in the absence of systematic studies on species identification and chemical compositions, the capacity of the capacity of the province to CR resource has not been fully utilized.<br><br>METHODOLOGY: We used plant morphology and DNA barcoding techniques to identify Luodang (LD) and Weidang (WD) species. To investigate the differences in metabolites between LD and WD, as well as three Chinese Pharmacopeia CRs, and to predict pharmacological mechanisms of action for the dominant differential metabolites, we utilized widely targeted metabolomics and network pharmacology. The results also revealed the material basis for the excellent food properties of both LD and WD.<br><br>RESULTS: The plant traits and DNA barcoding molecular identification results indicated that Luodang and Weidang from Guizhou were Codonopsis tangshen and Codonopsis pilosula, respectively. Widely targeted metabolomics analysis revealed that a total of 1,116 metabolites from 14 categories, including phenolic acids, lipids, flavonoids, were found in five CRs and shared 1,054 (94.4%) metabolites. LD and WD each contained 3 and 10 dominant differential metabolites, respectively, which were primarily flavonoids and amino acids. Amino acids, phenolic acids, and organic acids play important roles in their excellent food attributes. In CR, eight dominant differential metabolites were discovered for the first time, including isoorientin-7-O-(6&#x2033;-feruloyl) glucoside, N-formyl-L-methionine, and cyclo (Phe-Glu), among others. Network pharmacology analyses showed that, in LD, dominant differential metabolites were closely related to anti-tumor, cardiovascular disease improvement, nervous system protection, and metabolic disease treatment, whereas in WD, they were closely related to nervous system protection and cardiovascular disease improvement.<br><br>CONCLUSION: The species of LD and WD were included in the Chinese Pharmacopeia, and their metabolite profiles were remarkably similar to CR from traditional producing areas. Therefore, LD and WD can be used and promoted medicinally as CR, and they have potential value for new drug development. This study enriched the database of CR compounds and provided a reference for quality control, resource development, and new drug development of CR.},
}
@article {pmid37915430,
year = {2023},
author = {Weaver, WN and Smith, SA},
title = {From leaves to labels: Building modular machine learning networks for rapid herbarium specimen analysis with LeafMachine2.},
journal = {Applications in plant sciences},
volume = {11},
number = {5},
pages = {e11548},
pmid = {37915430},
issn = {2168-0450},
abstract = {PREMISE: Quantitative plant traits play a crucial role in biological research. However, traditional methods for measuring plant morphology are time consuming and have limited scalability. We present LeafMachine2, a suite of modular machine learning and computer vision tools that can automatically extract a base set of leaf traits from digital plant data sets.<br><br>METHODS: LeafMachine2 was trained on 494,766 manually prepared annotations from 5648 herbarium images obtained from 288 institutions and representing 2663 species; it employs a set of plant component detection and segmentation algorithms to isolate individual leaves, petioles, fruits, flowers, wood samples, buds, and roots. Our landmarking network automatically identifies and measures nine pseudo-landmarks that occur on most broadleaf taxa. Text labels and barcodes are automatically identified by an archival component detector and are prepared for optical character recognition methods or natural language processing algorithms.<br><br>RESULTS: LeafMachine2 can extract trait data from at least 245 angiosperm families and calculate pixel-to-metric conversion factors for 26 commonly used ruler types.<br><br>DISCUSSION: LeafMachine2 is a highly efficient tool for generating large quantities of plant trait data, even from occluded or overlapping leaves, field images, and non-archival data sets. Our project, along with similar initiatives, has made significant progress in removing the bottleneck in plant trait data acquisition from herbarium specimens and shifted the focus toward the crucial task of data revision and quality control.},
}
@article {pmid37915315,
year = {2023},
author = {Melo, M and Covas, R and de Lima, RF and Veiga da Horta, O and do Bom Jesus, C and Barros da Veiga, M and Samba, S and Fonseca, R and Cabinda, G and Viegas, L and Silva, TL and Mata, VA and Beja, P and Ferreira, S},
title = {DNA Barcode library of the endemic-rich avifauna of the oceanic islands of the Gulf of Guinea.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e110428},
pmid = {37915315},
issn = {1314-2828},
abstract = {BACKGROUND: The BioSTP: DNA Barcoding of endemic birds from oceanic islands of the Gulf of Guinea dataset contains records of 155 bird specimens belonging to 56 species in 23 families, representing over 80% of the diversity of the breeding landbird community. All specimens were collected on Príncipe, São Tomé and Annobón Islands between 2002 and 2021 and morphologically identified to species or subspecies level by qualified ornithologists. The dataset includes all endemic species and 3/4 of the extant endemic subspecies of the islands. This dataset is the second release by BioSTP and it greatly increases the knowledge on the DNA barcodes of Gulf of Guinea birds. All DNA extractions are deposited at Associação BIOPOLIS - CIBIO, Research Center in Biodiversity and Genetic Resources.<br><br>NEW INFORMATION: The dataset includes DNA barcodes for all 29 endemic bird species and for 11 of the 15 extant endemic bird subspecies from the oceanic islands of the Gulf of Guinea. This is the first major DNA barcode set of African birds. The three endemic subspecies of Crithagrarufobrunnea, an island endemic with three allopatric populations within the Archipelago, are also represented. Additionally, we obtained DNA barcodes for 16 of the 21 non-endemic landbirds and for one vagrant (Sylviacommunis). In total, forty-one taxa were new additions to the Barcode of Life Data System (BOLD), with another 11 corresponding to under-represented taxa in BOLD. Furthermore, the submitted sequences were found to cluster in 55 Barcode Index Numbers (BINs), 37 of which were new to BOLD. All specimens have their DNA barcodes publicly accessible through BOLD online database and GenBank.},
}
@article {pmid37914761,
year = {2023},
author = {Huang, D and An, Q and Huang, S and Tan, G and Quan, H and Chen, Y and Zhou, J and Liao, H},
title = {Biomod2 modeling for predicting the potential ecological distribution of three Fritillaria species under climate change.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {18801},
pmid = {37914761},
issn = {2045-2322},
mesh = {*Climate Change ; *Fritillaria/genetics ; Ecosystem ; China ; Temperature ; },
abstract = {The Fritillaria species ranked as a well-known traditional medicine in China and has become rare due to excessive harvesting. To find reasonable strategy for conservation and cultivation, identification of new ecological distribution of Fritillaria species together with prediction of those responses to climate change are necessary. In terms of current occurrence records and bioclimatic variables, the suitable habitats for Fritillaria delavayi, Fritillaria taipaiensis, and Fritillaria wabuensis were predicted. In comparison with Maxent and GARP, Biomod2 obtained the best AUC, KAPPA and TSS values of larger than 0.926 and was chosen to construct model. Temperature seasonality was indicated to put the greatest influence on Fritillaria taipaiensis and Fritillaria wabuensis, while isothermality was of most importance for Fritillaria delavayi. The current suitable areas for three Fritillaria species were distributed in south-west China, accounting for approximately 17.72%, 23.06% and 20.60% of China's total area, respectively. During 2021-2100 period, the suitable habitats of F. delavayi and F. wabuensis reached the maximum under SSP585 scenario, while that of F. taipaiensis reached the maximum under SSP126 scenario. The high niche overlap among three Fritillaria species showed correlation with the chemical composition (P ≤ 0.05), while no correlation was observed between niche overlap and DNA barcodes, indicating that spatial distribution had a major influence on chemical composition in the Fritillaria species. Finally, the acquisition of species-specific habitats would contribute to decrease in habitat competition, and future conservation and cultivation of Fritillaria species.},
}
@article {pmid37910295,
year = {2024},
author = {Aalam, SMM and Nguyen, LV and Ritting, ML and Kannan, N},
title = {Clonal tracking in cancer and metastasis.},
journal = {Cancer metastasis reviews},
volume = {43},
number = {2},
pages = {639-656},
pmid = {37910295},
issn = {1573-7233},
support = {P50 CA116201/CA/NCI NIH HHS/United States ; P50 CA136393/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Animals ; *Neoplasms/pathology/genetics/therapy ; *Neoplastic Stem Cells/pathology/metabolism ; *Neoplasm Metastasis ; Cell Tracking/methods ; CRISPR-Cas Systems ; },
abstract = {The eradication of many cancers has proven challenging due to the presence of functionally and genetically heterogeneous clones maintained by rare cancer stem cells (CSCs), which contribute to disease progression, treatment refractoriness, and late relapse. The characterization of functional CSC activity has necessitated the development of modern clonal tracking strategies. This review describes viral-based and CRISPR-Cas9-based cellular barcoding, lineage tracing, and imaging-based approaches. DNA-based cellular barcoding technology is emerging as a powerful and robust strategy that has been widely applied to in vitro and in vivo model systems, including patient-derived xenograft models. This review also highlights the potential of these methods for use in the clinical and drug discovery contexts and discusses the important insights gained from such approaches.},
}
@article {pmid37909987,
year = {2023},
author = {Ito, S and Tsurumi, K and Shindo, N and Soma, S and Yamaguchi, K and Tamai, K and Mochizuki, M and Fujimori, H and Morita, M and Watanabe, K and Suzuki, A and Fukuhara, T and Yasuda, J},
title = {Multi-gene Liquid Biopsy to Detect Resistance to First-line Osimertinib in Patients With EGFR-mutated Lung Adenocarcinoma.},
journal = {Anticancer research},
volume = {43},
number = {11},
pages = {5031-5040},
doi = {10.21873/anticanres.16702},
pmid = {37909987},
issn = {1791-7530},
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung ; *Lung Neoplasms/drug therapy/genetics ; Neoplasm Recurrence, Local ; *Adenocarcinoma of Lung/drug therapy/genetics ; Liquid Biopsy ; *Cell-Free Nucleic Acids ; Recurrence ; ErbB Receptors/genetics ; },
abstract = {BACKGROUND/AIM: Osimertinib is currently used as a first-line treatment for EGFR-mutated non-small cell lung cancer, and the emergence of drug resistance poses a substantial challenge. Liquid biopsy with a multi-gene panel can examine both the molecular mechanisms and possibility of early resistance diagnosis.<br><br>PATIENTS AND METHODS: We used a molecular barcode library construction kit (Archer[&#xae;] LiquidPlex&#x2122;) that allowed the analysis of multiple cancer-related genes using cell-free DNA from the plasma samples of patients. We collected plasma from 17 consecutive patients with lung adenocarcinoma at our hospital at various time points and cell-free DNA was extracted and subjected to LiquidPlex analysis.<br><br>RESULTS: Plasma DNA concentration was not associated with the presence or absence of resistance to osimertinib. The pathological mutations detected using next-generation sequencing in the resistant specimens were in MAP2K1, PIK3CA, TP53, BRAF, and EGFR. Among the recurrent cases, EGFR mutations identified at the initial diagnosis were detected within 6 months before relapse confirmation in four cases (average 88 days). Many of the recurrent cases without detection of known EGFR mutations in the liquid biopsy showed a longer interval between the detection of relapse and the last blood draw for the liquid biopsy (average 255 days).<br><br>CONCLUSION: Frequent liquid biopsies are useful for identifying known EGFR mutations as markers for early detection of relapse. Several cancer driver mutations were observed, suggesting a variety of mechanisms of resistance in first-line osimertinib-treated lung adenocarcinoma.},
}
@article {pmid37909383,
year = {2024},
author = {Afshan, NU and Fayyaz, I and Iftikhar, F and Habib, K and Iqbal, MS and Wang, XY and Usman, M and Asif, W and Niazi, AR and Khalid, AN},
title = {New species and new records of genus Buellia (lichenized Ascomycota, Caliciaceae) from Pakistan using electron microscopy and DNA barcoding techniques.},
journal = {Microscopy research and technique},
volume = {87},
number = {1},
pages = {31-41},
doi = {10.1002/jemt.24403},
pmid = {37909383},
issn = {1097-0029},
mesh = {Phylogeny ; *DNA Barcoding, Taxonomic/methods ; Sequence Analysis, DNA ; Pakistan ; DNA, Fungal/genetics ; *Ascomycota/genetics ; Microscopy, Electron ; },
abstract = {Three new species Buellia darelensis, B. densitheca, B. kashmirensis and two new records B. elegans and B. taishanensis are added to the lichen biota of Pakistan. Buellia darelensis and B. kashmirensis share the same habitats found on the rock while B. densitheca colonized on bark of Pinus hardwoods in the Himalayan forest, Pakistan. Morphological, chemical, and phylogenetic analyses were carried out to elucidate the placement of these species and to support the delimitation of the new taxa. Detailed descriptions and figures for the species are given, and a key to all known buellioid species from Pakistan is provided. RESEARCH HIGHLIGHTS: During recent explorations of lichens from different regions of Pakistan, we observed specimens that could not be readily assigned to any known species. A phylogenetic analysis of the internal transcribed spacer nrDNA region confirms their position within the genus Buellia, and morphological data showed distinctiveness of three species from other known species of the genus. We therefore describe these specimens as new species to science, and two species are as new records for the country. Pakistan exhibits a large altitudinal variation, with climatic conditions and a diverse vegetation that supports a diverse and conspicuous lichen biota. The nature reserves have abundant biological resources, and it is expected that more new species of lichen may be discovered in the future.},
}
@article {pmid37905675,
year = {2023},
author = {Jiraska, L and Jones, B and Knight, SJ and Lennox, J and Goddard, MR},
title = {Soil and bark biodiversity forms discrete islands between vineyards that are not affected by distance or management regime.},
journal = {Environmental microbiology},
volume = {25},
number = {12},
pages = {3655-3670},
doi = {10.1111/1462-2920.16513},
pmid = {37905675},
issn = {1462-2920},
support = {//Bragato Research Institute/ ; //New Zealand Winegrowers/ ; PROP-38164-PSHIP//New Zealand Ministry of Business, Innovation &amp; Employment/ ; //NeSI's Collaborator Institutions/ ; },
mesh = {Farms ; *Soil ; Plant Bark ; Fungi/genetics ; Soil Microbiology ; Biodiversity ; *Microbiota ; Bacteria/genetics ; },
abstract = {Within geographic regions, the existing data suggest that physical habitat (bark, soil, etc.) is the strongest factor determining agroecosystem microbial community assemblage, followed by geographic location (site), and then management regime (organic, conventional, etc.). The data also suggest community similarities decay with increasing geographic distance. However, integrated hypotheses for these observations have not been developed. We formalized and tested such hypotheses by sequencing 3.8 million bacterial 16S, fungal ITS2 and non-fungal eukaryotic COI barcodes deriving from 108 samples across two habitats (soil and bark) from six vineyards sites under conventional or conservation management. We found both habitat and site significantly affected community assemblage, with habitat the stronger for bacteria only, but there was no effect of management. There was no evidence for community similarity distance-decay within sites within each habitat. While communities significantly differed between vineyard sites, there was no evidence for between site community similarity distance-decay apart from bark bacterial communities, and no correlations with soil and bark pH apart from soil bacterial communities. Thus, within habitats, vineyard sites represent discrete biodiversity islands, and while bacterial, fungal and non-fungal eukaryotic biodiversity mostly differs between sites, the distance by which they are separated does not define how different they are.},
}
@article {pmid37905147,
year = {2024},
author = {Schmidlin, and Apodaca, and Newell, and Sastokas, and Kinsler, and Geiler-Samerotte, },
title = {Distinguishing mutants that resist drugs via different mechanisms by examining fitness tradeoffs.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37905147},
issn = {2692-8205},
support = {R35 GM133674/GM/NIGMS NIH HHS/United States ; },
abstract = {There is growing interest in designing multidrug therapies that leverage tradeoffs to combat resistance. Tradeoffs are common in evolution and occur when, for example, resistance to one drug results in sensitivity to another. Major questions remain about the extent to which tradeoffs are reliable, specifically, whether the mutants that provide resistance to a given drug all suffer similar tradeoffs. This question is difficult because the drug-resistant mutants observed in the clinic, and even those evolved in controlled laboratory settings, are often biased towards those that provide large fitness benefits. Thus, the mutations (and mechanisms) that provide drug resistance may be more diverse than current data suggests. Here, we perform evolution experiments utilizing lineage-tracking to capture a fuller spectrum of mutations that give yeast cells a fitness advantage in fluconazole, a common antifungal drug. We then quantify fitness tradeoffs for each of 774 evolved mutants across 12 environments, finding these mutants group into 6 classes with characteristically different tradeoffs. Their unique tradeoffs may imply that each group of mutants affects fitness through different underlying mechanisms. Some of the groupings we find are surprising. For example, we find some mutants that resist single drugs do not resist their combination, while others do. And some mutants to the same gene have different tradeoffs than others. These findings, on one hand, demonstrate the difficulty in relying on consistent or intuitive tradeoffs when designing multidrug treatments. On the other hand, by demonstrating that hundreds of adaptive mutations can be reduced to a few groups with characteristic tradeoffs, our findings may yet empower multidrug strategies that leverage tradeoffs to combat resistance. More generally speaking, by grouping mutants that likely affect fitness through similar underlying mechanisms, our work guides efforts to map the phenotypic effects of mutation.},
}
@article {pmid37904971,
year = {2023},
author = {Razo-Mejia, M and Mani, M and Petrov, D},
title = {Bayesian inference of relative fitness on high-throughput pooled competition assays.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37904971},
issn = {2692-8205},
support = {R01 CA230025/CA/NCI NIH HHS/United States ; R01 CA263715/CA/NCI NIH HHS/United States ; U01 AG077922/AG/NIA NIH HHS/United States ; },
abstract = {The tracking of lineage frequencies via DNA barcode sequencing enables the quantification of microbial fitness. However, experimental noise coming from biotic and abiotic sources complicates the computation of a reliable inference. We present a Bayesian pipeline to infer relative microbial fitness from high-throughput lineage tracking assays. Our model accounts for multiple sources of noise and propagates uncertainties throughout all parameters in a systematic way. Furthermore, using modern variational inference methods based on automatic differentiation, we are able to scale the inference to a large number of unique barcodes. We extend this core model to analyze multi-environment assays, replicate experiments, and barcodes linked to genotypes. On simulations, our method recovers known parameters within posterior credible intervals. This work provides a generalizable Bayesian framework to analyze lineage tracking experiments. The accompanying open-source software library enables the adoption of principled statistical methods in experimental evolution.},
}
@article {pmid37902171,
year = {2024},
author = {Swenie, RA and Looney, BP and Ke, YH and Alejandro Rojas, J and Cubeta, MA and Langer, GJ and Vilgalys, R and Matheny, PB},
title = {PacBio high-throughput multi-locus sequencing reveals high genetic diversity in mushroom-forming fungi.},
journal = {Molecular ecology resources},
volume = {24},
number = {1},
pages = {e13885},
doi = {10.1111/1755-0998.13885},
pmid = {37902171},
issn = {1755-0998},
support = {//University of Tennessee/ ; DEB-2030779//National Science Foundation/ ; 1452154//National Science Foundation/ ; },
mesh = {Sequence Analysis, DNA ; *Agaricales ; Phylogeny ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Fungi ; },
abstract = {Multi-locus sequence data are widely used in fungal systematic and taxonomic studies to delimit species and infer evolutionary relationships. We developed and assessed the efficacy of a multi-locus pooled sequencing method using PacBio long-read high-throughput sequencing. Samples included fresh and dried voucher specimens, cultures and archival DNA extracts of Agaricomycetes with an emphasis on the order Cantharellales. Of the 283 specimens sequenced, 93.6% successfully amplified at one or more loci with a mean of 3.3 loci amplified. Our method recovered multiple sequence variants representing alleles of rDNA loci and single copy protein-coding genes rpb1, rpb2 and tef1. Within-sample genetic variation differed by locus and taxonomic group, with the greatest genetic divergence observed among sequence variants of rpb2 and tef1 from corticioid Cantharellales. Our method is a cost-effective approach for generating accurate multi-locus sequence data coupled with recovery of alleles from polymorphic samples and multi-organism specimens. These results have important implications for understanding intra-individual genomic variation among genetic loci commonly used in species delimitation of fungi.},
}
@article {pmid37901679,
year = {2023},
author = {Filippova, N and Zvyagina, E and Rudykina, E and Dobrynina, A and Bolshakov, S},
title = {The diversity of macromycetes in peatlands: nine years of plot-based monitoring and barcoding in the raised bog "Mukhrino", West Siberia.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e105111},
pmid = {37901679},
issn = {1314-2828},
abstract = {BACKGROUND: Peatland ecosystems are defined by soils with sufficient under-decomposed organic layer, called peat, formed under anoxic conditions. Peatlands are widespread around the world, with several highly paludified regions, one of which is the Western Siberian Plain. Peatlands store large amounts of carbon and are important in their intact state to counteract climate change, as well as for a variety of other ecosystem functions. From the practical aspect, these ecosystems are used as a source of peat for fuel, peat-based fertilisers and growing media, berries and Sphagnum plantations. Fungi are the key part of the decomposer community of peatlands, playing a critical role in the aerobic decomposition in the upper peat layer. The community of peatland fungi is adapted to decomposition of peat and dead parts of Sphagnum in wet acidic conditions; they form specific mycorrhizal associations with a variety of plants. Thus, the research of fungal diversity of peatlands is important for several reasons: 1) adding knowledge of peatland fungal diversity to local or global biodiversity databases; 2) studying carbon cycling in peatlands; 3) using peat and peatlands for different applications, such as cultivation of Sphagnum with regards to some parasitic species of fungi and 4) peatland restoration and conservation, to mention a few.<br><br>NEW INFORMATION: The community of macromycetes of the raised bog "Mukhrino" in Western Siberia was studied using plot-based monitoring throughout a 9-year observation period. The revealed species diversity is represented by approximately 500 specimens in the Fungarium of Yugra State University collection. Selected specimens were used for barcoding of the ITS region to reveal a total of 95 species from 33 genera and three classes. The barcoding effort confirmed morphological identifications for most specimens and identified a number of cryptic species and several potentially new taxa. Based on regular all-season observations, we describe the phenology of the community sporophore production. The quantitative community structure, based on sporophores, revealed a difference in abundance between species by four orders of magnitude, with rare species representing nearly half of the species list. The inter-annual fruiting abundance varied several times by the total number of sporophores per year. To make the comparisons with global studies, we created an open access database of literature-based observations of fungi in peatlands, based on about 120 published papers (comprising about 1300 species) and compared our species list with this database.As a result, the study created an accurate representation of taxonomic and quantitative structure of the community of macromycetes in raised bogs in the region. The raw data of plot-based counts was published as a sampling-event dataset and the sequenced specimens with the sequence information as an DNA-derived extension dataset in GBIF.},
}
@article {pmid37901204,
year = {2023},
author = {Nedwed, AS and Helbich, SS and Braband, KL and Volkmar, M and Delacher, M and Marini, F},
title = {Using combined single-cell gene expression, TCR sequencing and cell surface protein barcoding to characterize and track CD4+ T cell clones from murine tissues.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1241283},
pmid = {37901204},
issn = {1664-3224},
mesh = {Mice ; Animals ; *Software ; *CD4-Positive T-Lymphocytes ; Membrane Proteins ; Receptors, Antigen, T-Cell/genetics ; Clone Cells ; Gene Expression ; },
abstract = {Single-cell gene expression analysis using sequencing (scRNA-seq) has gained increased attention in the past decades for studying cellular transcriptional programs and their heterogeneity in an unbiased manner, and novel protocols allow the simultaneous measurement of gene expression, T-cell receptor clonality and cell surface protein expression. In this article, we describe the methods to isolate scRNA/TCR-seq-compatible CD4[+] T cells from murine tissues, such as skin, spleen, and lymph nodes. We describe the processing of cells and quality control parameters during library preparation, protocols for multiplexing of samples, and strategies for sequencing. Moreover, we describe a step-by-step bioinformatic analysis pipeline from sequencing data generated using these protocols. This includes quality control, preprocessing of sequencing data and demultiplexing of individual samples. We perform quantification of gene expression and extraction of T-cell receptor alpha and beta chain sequences, followed by quality control and doublet detection, and methods for harmonization and integration of datasets. Next, we describe the identification of highly variable genes and dimensionality reduction, clustering and pseudotemporal ordering of data, and we demonstrate how to visualize the results with interactive and reproducible dashboards. We will combine different analytic R-based frameworks such as Bioconductor and Seurat, illustrating how these can be interoperable to optimally analyze scRNA/TCR-seq data of CD4[+] T cells from murine tissues.},
}
@article {pmid37898957,
year = {2023},
author = {Zuccolo, V and Rego, FM and Hughes, E and Griffiths, AM},
title = {Endangered shark species traded as "cação" in São Paulo during the COVID-19 lockdown: DNA-barcoding a snapshot of products.},
journal = {Molecular biology reports},
volume = {50},
number = {12},
pages = {9985-9992},
pmid = {37898957},
issn = {1573-4978},
mesh = {Animals ; Humans ; Endangered Species ; *Sharks/genetics ; Conservation of Natural Resources/methods ; Brazil/epidemiology ; Pandemics ; Fisheries ; *COVID-19/epidemiology ; Communicable Disease Control ; DNA ; },
abstract = {BACKGROUND: Elasmobranch populations are declining, predominantly driven by overfishing, and over a third of global sharks, rays, and chimeras are estimated to be threatened with extinction. In terms of trade, Brazil is ranked the eleventh-largest shark producer and the top importer of shark meat in the world. Research has shown that elasmobranchs are sold in Brazil under the name "cação" (a generic designation for cartilaginous fish) to overcome consumer resistance.<br><br>METHODOLOGY AND RESULTS: This study used DNA barcoding to investigate the sale of sharks in the State of S&#xe3;o Paulo during the COVID-19 lockdown. A total of 35 samples of "ca&#xe7;&#xe3;o" were analysed, revealing six different shark species on sale, including Carcharhinus falciformis, Carcharhinus signatus, Carcharias taurus, Isurus oxyrinchus, and Isurus paucus, that are threatened with extinction according to the IUCN red list. This study demonstrates that vulnerable elasmobranchs are being commercialised under the label "ca&#xe7;&#xe3;o" in the S&#xe3;o Paulo State and Brazil.<br><br>CONCLUSIONS: Comparison of shark products traded before and during the COVID-19 pandemic showed no significant difference, suggesting lockdown did not affect patterns of species commercialisation. Effective fisheries and sale monitoring, correct product labelling legislation and increased consumer awareness that "ca&#xe7;&#xe3;o" is shark are needed for appropriate conservation and management of shark populations in Brazil.},
}
@article {pmid37897343,
year = {2024},
author = {Hou, D and Lin, H and Feng, Y and Zhou, K and Li, X and Yang, Y and Wang, S and Yang, X and Wang, J and Zhao, H and Zhang, X and Fan, J and Lu, S and Wang, D and Zhu, L and Ju, D and Chen, YZ and Zeng, X},
title = {CMAUP database update 2024: extended functional and association information of useful plants for biomedical research.},
journal = {Nucleic acids research},
volume = {52},
number = {D1},
pages = {D1508-D1518},
pmid = {37897343},
issn = {1362-4962},
support = {32000479//National Natural Science Foundation of China/ ; 21QB1401800//Shanghai Science and Technology Funds/ ; 21YF1401900//Shanghai Sailing Program/ ; 2019YFA0905900//National Key R&amp;D Program of China/ ; 215-432000282//Scientific Research Grant of Ningbo University/ ; 215-432094250//Ningbo Top Talent Project/ ; 32000479//Funding for open access charge/ ; },
mesh = {Humans ; *Databases, Factual ; Phylogeny ; *Plants, Medicinal/chemistry/classification ; *Phytochemicals/chemistry/pharmacology/therapeutic use ; },
abstract = {Knowledge of the collective activities of individual plants together with the derived clinical effects and targeted disease associations is useful for plant-based biomedical research. To provide the information in complement to the established databases, we introduced a major update of CMAUP database, previously featured in NAR. This update includes (i) human transcriptomic changes overlapping with 1152 targets of 5765 individual plants, covering 74 diseases from 20 027 patient samples; (ii) clinical information for 185 individual plants in 691 clinical trials; (iii) drug development information for 4694 drug-producing plants with metabolites developed into approved or clinical trial drugs; (iv) plant and human disease associations (428 737 associations by target, 220 935 reversion of transcriptomic changes, 764 and 154121 associations by clinical trials of individual plants and plant ingredients); (v) the location of individual plants in the phylogenetic tree for navigating taxonomic neighbors, (vi) DNA barcodes of 3949 plants, (vii) predicted human oral bioavailability of plant ingredients by the established SwissADME and HobPre algorithm, (viii) 21-107% increase of CMAUP data over the previous version to cover 60 222 chemical ingredients, 7865 plants, 758 targets, 1399 diseases, 238 KEGG human pathways, 3013 gene ontologies and 1203 disease ontologies. CMAUP update version is freely accessible at https://bidd.group/CMAUP/index.html.},
}
@article {pmid37897171,
year = {2023},
author = {Mintara, R and Pramual, P},
title = {Common but not connected: high genetic structure and cryptic genetic diversity in the ubiquitous biting midge Culicoides peregrinus Kieffer.},
journal = {Tropical biomedicine},
volume = {40},
number = {3},
pages = {363-369},
doi = {10.47665/tb.40.3.014},
pmid = {37897171},
issn = {2521-9855},
mesh = {Animals ; Cattle ; *Ceratopogonidae/genetics/anatomy &amp; histology ; Phylogeny ; Thailand ; Genetic Structures ; Genetic Variation ; },
abstract = {The biting midge Culicoides peregrinus Kieffer is a significant pest and vector species, and knowledge of its genetic diversity and genetic structure is critically important for designing an effective control program. However, such information is limited to only small sample-size DNA barcoding studies. Therefore, in this study, we used mitochondrial cytochrome c oxidase I (COI) to examine genetic structure and diversity of C. peregrinus from northeastern Thailand. In addition, we also inferred genetic relationships between C. peregrinus from Thailand and those reported from other countries across the geographic range of the species. Maximum intraspecific genetic divergence (3.83%) within Thai specimens was relatively high compared to other Culicoides species. Genetic structure analysis revealed that 71% (32 from 45) of population comparisons were highly significantly different. A high level of genetic structure among populations, even between those in close geographic proximity (22 km geographic distance) suggested that there has been little or no movement between local populations. This is possibly due to the ability to exploit diverse types of breeding site and a generalist feeding habit which enables C. peregrinus to complete its life cycle within cattle pens. Genetic relationships between Thai C. peregrinus and those reported from other countries revealed three genetically divergent lineages (A, B and C) associated with geographic origins. Specimens from Thailand + China formed lineage A, those from Australia formed lineage B and India + Bangladesh belonged to lineage C. These genetically divergent lineages also agree with morphological variation of the wing pale marking spots. Further investigation using independent genetic loci from nuclear genes will be very useful to resolve taxonomic status of these divergent lineages.},
}
@article {pmid37894943,
year = {2023},
author = {Tu, XD and Zhao, Z and Zhou, CY and Zeng, MY and Gao, XY and Li, MH and Liu, ZJ and Chen, SP},
title = {Comparative Analysis of Plastomes in Elsholtzieae: Phylogenetic Relationships and Potential Molecular Markers.},
journal = {International journal of molecular sciences},
volume = {24},
number = {20},
pages = {},
pmid = {37894943},
issn = {1422-0067},
support = {32271957//National Natural Science Foundation of China/ ; 72202200205//Forestry Peak Discipline Construction Project of Fujian Agriculture and Forestry University/ ; },
mesh = {Phylogeny ; *Genome, Plastid ; *Lamiaceae/genetics ; },
abstract = {The Elsholtzieae, comprising ca. 7 genera and 70 species, is a small tribe of Lamiaceae (mint family). Members of Elsholtzieae are of high medicinal, aromatic, culinary, and ornamentals value. Despite the rich diversity and value of Elsholtzieae, few molecular markers or plastomes are available for phylogenetics. In the present study, we employed high-throughput sequencing to assemble two Mosla plastomes, M. dianthera and M. scabra, for the first time, and compared with other plastomes of Elsholtzieae. The plastomes of Elsholtzieae exhibited a quadripartite structure, ranging in size from 148,288 bp to 152,602 bp. Excepting the absence of the pseudogene rps19 in Elsholtzia densa, the exhaustive tally revealed the presence of 132 genes (113 unique genes). Among these, 85 protein-coding genes (CDS), 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes (rps19 and ycf1) were annotated. Comparative analyses showed that the plastomes of these species have minor variations at the gene level. Notably, the E. eriostchya plastid genome exhibited increased GC content regions in the LSC and SSC, resulting in an increased overall GC content of the entire plastid genome. The E. densa plastid genome displayed modified boundaries due to inverted repeat (IR) contraction. The sequences of CDS and intergenic regions (IGS) with elevated variability were identified as potential molecular markers for taxonomic inquiries within Elsholtzieae. Phylogenetic analysis indicated that four genera formed monophyletic entities, with Mosla and Perilla forming a sister clade. This clade was, in turn, sister to Collinsonia, collectively forming a sister group to Elsholtzia. Both CDS, and CDS + IGS could construct a phylogenetic tree with stronger support. These findings facilitate species identification and DNA barcoding investigations in Elsholtzieae and provide a foundation for further exploration and resource utilization within this tribe.},
}
@article {pmid37893896,
year = {2023},
author = {Xie, J and Zhang, Y},
title = {Diversity and Distribution of Mites (ACARI) Revealed by Contamination Survey in Public Genomic Databases.},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {20},
pages = {},
pmid = {37893896},
issn = {2076-2615},
support = {31900152//National Natural Science Foundation of China/ ; KJQN202100632//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; },
abstract = {Acari (mites and ticks) are a biodiverse group of microarthropods within the Arachnida. Because of their diminutive size, mites are often overlooked. We hypothesized that mites, like other closely related microorganisms, could also contaminate public genomic database. Here, using a strategy based on DNA barcodes previously reported, we scanned contaminations related to mites (Acari, exclusive of Ixodida) in Genbank WGS/TSA database. In 22,114 assemblies (17,845 animal and 4269 plant projects), 1717 contigs in 681 assemblies (3.1%) were detected as mite contaminations. Additional taxonomic analysis showed the following: (1) most of the contaminants (1445/1717) were from the specimens of Magnoliopsida, Insecta and Pinopsida; (2) the contamination rates were higher in plant or TSA projects; (3) mite distribution among different classes of hosts varied considerably. Additional phylogenetic analysis of these contaminated contigs further revealed complicated mite-host associations. Overall, we conducted a first systemic survey and analysis of mite contaminations in public genomic database, and these DNA barcode related mite contigs will provide a valuable resource of information for understanding the diversity and phylogeny of mites.},
}
@article {pmid37889717,
year = {2023},
author = {Castro, EB and Beard, JJ and Ochoa, R and Bauchan, GR and Otero-Colina, G and Dowling, APG and Lofego, AC and Feres, RJF},
title = {A New Species of Ultratenuipalpus (Acari: Tenuipalpidae) from Brazil and Re-Description of Ultratenuipalpus meekeri (De Leon), the Type Species of the Genus, with DNA Barcodes.},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {11},
pages = {},
pmid = {37889717},
issn = {2076-2615},
support = {2016/01193-5//S&#xe3;o Paulo Research Foundation/ ; 2017/00458-8//S&#xe3;o Paulo Research Foundation/ ; 2004/04820-3//S&#xe3;o Paulo Research Foundation/ ; 2006/55725-6//S&#xe3;o Paulo Research Foundation/ ; 2006/57868-9//S&#xe3;o Paulo Research Foundation/ ; Edital PROPe 13/2022//S&#xe3;o Paulo State University/ ; },
abstract = {Species of the genus Ultratenuipalpus bear a broad subquadrate propodosoma with many large, flattened, lanceolate to ovate dorsal setae. They also bear some plesiomorphic character states, such as the presence of three pairs of ventral ps setae. Here, we describe Ultratenuipalpus parameekeri Castro, Ochoa &amp; Feres sp. nov. based on adult females, males, and immatures, collected on ferns from Brazil. We also re-describe Ultratenuipalpus meekeri (De Leon), the type species of the genus, based on types and newly collected material from Mexico, and include additional novel data (e.g., dorsal and ventral ornamentation, leg chaetotaxy, and setal measurements) in a standardized form. We include highly detailed images obtained using LT-SEM, accompanied by DNA barcodes, for both species. The ontogenetic additions of leg chaetotaxy are presented and discussed.},
}
@article {pmid37889683,
year = {2023},
author = {Mohd Salleh, MH and Esa, Y and Mohamed, R},
title = {Global Terrapin Character-Based DNA Barcodes: Assessment of the Mitochondrial COI Gene and Conservation Status Revealed a Putative Cryptic Species.},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {11},
pages = {},
pmid = {37889683},
issn = {2076-2615},
abstract = {Technological and analytical advances to study evolutionary biology, ecology, and conservation of the Southern River Terrapin (Batagur affinis ssp.) are realised through molecular approaches, including DNA barcoding. We evaluated the use of COI DNA barcodes in Malaysia's Southern River Terrapin population to better understand the species' genetic divergence and other genetic characteristics. We evaluated 26 sequences, including four from field specimens of Southern River Terrapins obtained in Bota Kanan, Perak, Malaysia, and Kuala Berang, Terengganu, Malaysia, as well as 22 sequences from global terrapins previously included in the Barcode of Life Database (BOLD) Systems and GenBank. The species are divided into three families: eight Geoemydidae species (18%), three Emydidae species (6%), and one Pelomedusidae species (2%). The IUCN Red List assigned the 12 species of terrapins sampled for this study to the classifications of critically endangered (CR) for 25% of the samples and endangered (EN) for 8% of the samples. With new haplotypes from the world's terrapins, 16 haplotypes were found. The intraspecific distance values between the COI gene sequences were calculated using the K2P model, which indicated a potential cryptic species between the Northern River Terrapin (Batagur baska) and Southern River Terrapin (Batagur affinis affinis). The Bayesian analysis of the phylogenetic tree also showed both species in the same lineage. The BLASTn search resulted in 100% of the same species of B. affinis as B. baska. The Jalview alignment visualised almost identical sequences between both species. The Southern River Terrapin (B. affinis affinis) from the west coast of Peninsular Malaysia was found to share the same haplotype (Hap_1) as the Northern River Terrapin from India. However, B. affinis edwardmolli from the east coast of Peninsular Malaysia formed Hap_16. The COI analysis found new haplotypes and showed that DNA barcodes are an excellent way to measure the diversity of a population.},
}
@article {pmid37887830,
year = {2023},
author = {Xu, ZB and He, JB and Yang, N and Kitching, IJ and Hu, SJ},
title = {Review of the Narrow-Banded Hawkmoth, Neogurelca montana (Rothschild &amp; Jordan, 1915) (Lepidoptera: Sphingidae) in China, with Morphological and Phylogenetic Analysis.},
journal = {Insects},
volume = {14},
number = {10},
pages = {},
pmid = {37887830},
issn = {2075-4450},
abstract = {Neogurelca montana (Rothschild &amp; Jordan, 1915) is a species of the genus Neogurelca Hogenes &amp; Treadaway, 1993, that was previously known from Sichuan, Yunnan, and Tibet, China. Recently, however, this species was also found in Beijing and Hebei. These populations differ from those in southwest China in body colour and the shape of the yellow patches of the hindwing-a paler body colour and triangular patches in the former and darker body colour and fan-like patches in the latter. Wing morphology, male and female genitalia, and molecular evidence (DNA barcodes) were analysed for the different localities of this species and three other Neogurelca species-N. hyas, N. himachala, and N. masuriensis. Our molecular data support the Beijing population of montana as a valid subspecies, which we describe as N. montana taihangensisssp. nov. Wing and genital morphology confirm the molecular conclusions. We also collected larvae of the new subspecies in the Beijing suburbs and describe its life history and larval hosts and compare them with those of N. himachala.},
}
@article {pmid37886972,
year = {2023},
author = {Vetchinova, AS and Kapkaeva, MR and Ivanov, MV and Kutukova, KA and Mudzhiri, NM and Frumkina, LE and Brydun, AV and Sukhorukov, VS and Illarioshkin, SN},
title = {Mitochondrial Dysfunction in Dopaminergic Neurons Derived from Patients with LRRK2- and SNCA-Associated Genetic Forms of Parkinson's Disease.},
journal = {Current issues in molecular biology},
volume = {45},
number = {10},
pages = {8395-8411},
pmid = {37886972},
issn = {1467-3045},
support = {19-15-00320//Russian Scientific Foundation/ ; },
abstract = {Parkinson's disease (PD) is the second most common neurodegenerative disease. Some cases of PD may be caused by genetic factors, among which mutations in the LRRK2 and SNCA genes play an important role. To develop effective neuroprotective strategies for PD, it is important to diagnose the disease at the earliest stages of the neurodegenerative process. Therefore, the detection of diagnostic and prognostic markers of Parkinson's disease (PD) is an urgent medical need. Advances in induced pluripotent stem cell (iPSC) culture technology provide new opportunities for the search for new biomarkers of PD and its modeling in vitro. In our work, we used a new technology for multiplex profiling of gene expression using barcoding on the Nanostring platform to assess the activity of mitochondrial genes on iPSC-derived cultures of dopaminergic neurons obtained from patients with LRRK2- and SNCA-associated genetic forms PD and a healthy donor. Electron microscopy revealed ultrastructural changes in mitochondria in both LRRK2 and SNCA mutant cells, whereas mitochondria in cells from a healthy donor were normal. In a culture with the SNCA gene mutation, the ratio of the area occupied by mitochondria to the total area of the cytoplasm was significantly lower than in the control and in the line with the LRRK2 gene mutation. Transcriptome analysis of 105 mitochondria proteome genes using the Nanostring platform revealed differences between the diseased and normal cells in the activity of genes involved in respiratory complex function, the tricarboxylic acid cycle, ATP production, mitochondria-endoplasmic reticulum interaction, mitophagy, regulation of calcium concentration, and mitochondrial DNA replication.},
}
@article {pmid37886685,
year = {2023},
author = {Duong, TKC and Tran, VL and Nguyen, TB and Nguyen, TT and Ho, NTK and Nguyen, TQ},
title = {Ensemble learning-based approach for automatic classification of termite mushrooms.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1208695},
pmid = {37886685},
issn = {1664-8021},
abstract = {Termite mushrooms are edible fungi that provide significant economic, nutritional, and medicinal value. However, identifying these mushroom species based on morphology and traditional knowledge is ineffective due to their short development time and seasonal nature. This study proposes a novel method for classifying termite mushroom species. The method utilizes Gradient Boosting machine learning techniques and sequence encoding on the Internal Transcribed Spacer (ITS) gene dataset to construct a machine learning model for identifying termite mushroom species. The model is trained using ITS sequences obtained from the National Center for Biotechnology Information (NCBI) and the Barcode of Life Data Systems (BOLD). Ensemble learning techniques are applied to classify termite mushroom species. The proposed model achieves good results on the test dataset, with an accuracy of 0.91 and an average AUCROC value of 0.99. To validate the model, eight ITS sequences collected from termite mushroom samples in An Linh commune, Phu Giao district, Binh Duong province, Vietnam were used as the test data. The results show consistent species identification with predictions from the NCBI BLAST software. The results of species identification were consistent with the NCBI BLAST prediction software. This machine-learning model shows promise as an automatic solution for classifying termite mushroom species. It can help researchers better understand the local growth of these termite mushrooms and develop conservation plans for this rare and valuable plant resource.},
}
@article {pmid37886513,
year = {2023},
author = {Linsley, P and Nakayama, M and Balmas, E and Chen, J and Pour, F and Bansal, S and Serti, E and Speake, C and Pugliese, A and Cerosaletti, K},
title = {Self-reactive germline-like TCR alpha chains shared between blood and pancreas.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {37886513},
issn = {2693-5015},
support = {U24 DK098085/DK/NIDDK NIH HHS/United States ; UM1 AI109565/AI/NIAID NIH HHS/United States ; },
abstract = {Human islet antigen reactive CD4 + memory T cells (IAR T cells) from peripheral blood have been studied extensively for their role in the pathogenesis of autoimmune type 1 diabetes (T1D). However, IAR T cells are rare, and it remains poorly understood how they affect T1D progression in the pancreas. Using single cell RNA-sequencing coupled with a multiplexed activation induced marker (AIM) enrichment assay, we identified paired TCR alpha/beta (TRA/TRB) T cell receptors (TCRs) in IAR T cells from the blood of healthy, at-risk, new onset, and established T1D donors. Using TCR sequences as barcodes, we measured infiltration of IAR T cells from blood into pancreas of organ donors with and without T1D. We detected extensive TCR sharing between IAR T cells from peripheral blood and pancreatic infiltrating T cells (PIT), with perfectly matched or single mismatched TRA junctions and J gene regions, comprising ~ 34% of unique IAR TCRs. PIT-matching IAR T cells had public TRA chains that showed increased use of germline-encoded residues in epitope engagement and a propensity for cross-reactivity. The link with T cells in the pancreas implicates autoreactive IAR T cells with shared TRA junctions and increased levels in blood with the prediabetic and new onset phases of T1D progression.},
}
@article {pmid37885298,
year = {2023},
author = {Čadež, N and Boundy-Mills, K and Botha, A and Kachalkin, A and Dlauchy, D and Péter, G},
title = {Taxogenomic placement of Rasporella oleae and Rasporella dianae gen. and spp. nov., two insect associated yeast species.},
journal = {Yeast (Chichester, England)},
volume = {40},
number = {12},
pages = {594-607},
doi = {10.1002/yea.3904},
pmid = {37885298},
issn = {1097-0061},
support = {//Slovenian Research and Innovation Agency/ ; //Russian Ministry of Science and Higher Education/ ; },
mesh = {Animals ; Phylogeny ; Sequence Analysis, DNA ; DNA, Fungal/genetics ; *Insecta ; *Lipase/genetics ; Fatty Acids ; },
abstract = {During the course of independent studies in Europe, North America, and Africa, seven yeast strains were isolated from insect frass, decaying wood, tree flux, and olive oil sediment. Phylogenetic analysis of two barcoding DNA regions (internal transcribed spacer and the D1/D2 domain of the LSU rRNA gene) revealed that they belong to two closely related undescribed species distinct from all genera in the family Debaryomycetaceae. For reliable taxonomic placement the genomes of four strains of the two novel species and six type strains of closely related species were sequenced. Orthologous genes from 54 genomes of representatives of the Pichiomycetes and 23 outgroup taxa were concatenated to construct a fully supported phylogenetic tree. Consistent with the assumptions, we found that the two new species belong to a novel genus. In addition, the delimitation of the novel species was supported by genetic distance calculations from average nucleotide identity (ANI) and digital DNA:DNA hybridization (dDDH) values. The physiological characterization of the novel species was generally consistent with their genomic content. All strains had two alleles encoding secretory lipase in either two or three copies depending on the species. However, lipolytic activity was detected only in strains with three copies of the secretory lipase gene. Nevertheless, lipolytic activity might be related to their association with the insect gut. Based on these results, formal descriptions of the new genus Rasporella gen. nov. and of two new species Rasporella dianae sp. nov. (holotype UCDFST 68-643[T] , MycoBank no.: 850238) and Rasporella oleae sp. nov. (holotype ZIM 2471[T] , MycoBank no.: 850126) are provided.},
}
@article {pmid37880749,
year = {2023},
author = {Jia, H and Gao, S and Tang, L and Fu, Y and Xiong, Y and Ente, M and Mubalake, S and Shao, C and Li, K and Hu, D and Zhang, D},
title = {First report of four rare strongylid species infecting endangered Przewalski's horses (Equus ferus przewalskii) in Xinjiang, China.},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {385},
pmid = {37880749},
issn = {1756-3305},
support = {2019JQ0318//the Beijing Forestry University Outstanding Young Talent Cultivation Project/ ; 2022YFC2601601//National Key Research and Development Program of China/ ; },
mesh = {Animals ; Horses ; Genetic Markers ; *Equidae ; *Animals, Wild ; Endangered Species ; DNA ; },
abstract = {BACKGROUND: The Przewalski's horse (Equus ferus przewalskii) is the only surviving wild horse species in the world. A significant population of Przewalski's horses resides in Xinjiang, China. Parasitosis poses a considerable threat to the conservation of this endangered species. Yet, there is limited information on the nematode parasites that infect these species. To deepen our understanding of parasitic fauna affecting wild horses, we identified the intestinal nematodes of Przewalski's horses in Xinjiang and added new barcode sequences to a public database.<br><br>METHODS: Between 2018 and 2021, nematodes were collected from 104 dewormed Przewalski's horses in Xinjiang. Each nematode was morphologically identified to the species level, and selected species underwent DNA extraction. The extracted DNA was used for molecular identification through the internal transcribed spacer 2 (ITS2) genetic marker.<br><br>RESULTS: A total of 3758 strongylids were identified. To the best of our knowledge, this is the first study to identify four specific parasitic nematodes (Oesophagodontus robustus, Bidentostomum ivashkini, Skrjabinodentus caragandicus, Petrovinema skrjabini) and to obtain the ITS2 genetic marker for P. skrjabini.<br><br>CONCLUSIONS: The ITS2 genetic marker for P. skrjabini enriches our understanding of the genetic characteristics of this species and expands the body of knowledge on parasitic nematodes. Our findings extend the known host range of four strongylid species, thereby improving our understanding of the relationship between Przewalski's horses and strongylids. This, in turn, aids in the enhanced conservation of this endangered species. This study introduces new instances of parasitic infections in wild animals and offers the DNA sequence of P. skrjabini as a valuable resource for molecular techniques in nematode diagnosis among wildlife.},
}
@article {pmid37878191,
year = {2023},
author = {Dhivyakumari, S and Chaudhari, A and Brahmane, MP and Das, DK and Sathiyanarayanan, A and Yashwanth, BS and Pinto, N and Goswami, M},
title = {Development and characterization of a new muscle cell culture system from Clarias magur (Hamilton, 1822).},
journal = {Fish physiology and biochemistry},
volume = {49},
number = {6},
pages = {1295-1302},
pmid = {37878191},
issn = {1573-5168},
mesh = {Animals ; *Catfishes/metabolism ; Muscles ; Cell Line ; Cryopreservation/veterinary ; Cell Culture Techniques ; },
abstract = {The cell line has been used as a novel in vitro tool for executing several studies in life sciences. The current study aimed to develop and characterize a muscle cell culture system derived from Clarias magur. The primary muscle cell cultures derived from the caudal peduncle muscle have been successfully sub cultured up to 13 passages to establish a new muscle cell culture system known as CMM. At a temperature of 28 °C, L-15 medium supplemented with 20% FBS produced the maximum growth of muscle cells. However, muscle cells were optimized to grow at 10% FBS. To enhance the proliferation capacity of the CMM cells, a growth-promoting factor bFGF (10 ng/ml) was added, thereby reducing the time interval of passages for the subsequent cultures. DNA barcoding of the CMM cell culture system authenticated the species of origin. The cell culture system was successfully cryopreserved by a slow freezing procedure at - 80 °C with a revival efficiency of 60%.},
}
@article {pmid37877169,
year = {2024},
author = {Luo, W and Wang, Y and Cahill, JF and Luan, F and Zhong, Y and Li, Y and Li, B and Chu, C},
title = {Root-centric β diversity reveals functional homogeneity while phylogenetic heterogeneity in a subtropical forest.},
journal = {Ecology},
volume = {105},
number = {1},
pages = {e4189},
doi = {10.1002/ecy.4189},
pmid = {37877169},
issn = {1939-9170},
support = {31925027//National Natural Science Foundation of China/ ; 32301341//National Natural Science Foundation of China/ ; 2021M703756//Postdoctoral Research Foundation of China/ ; 2021A1515110362//Basic and Applied Basic Research Foundation of Guangdong Province/ ; },
mesh = {*Ecosystem ; Phylogeny ; *Biodiversity ; Forests ; Soil ; Plants ; },
abstract = {Root-centric studies have revealed fast taxonomic turnover across root neighborhoods, but how such turnover is accompanied by changes in species functions and phylogeny (i.e., β diversity) remains largely unknown. As β diversity can reflect the degree of community-wide biotic homogenization, such information is crucial for better inference of below-ground assembly rules, community structuring, and ecosystem processes. We collected 2480 root segments from 625 0-30 cm soil profiles in a subtropical forest in China. Root segments were identified into 138 species with DNA-barcoding with six root morphological and architectural traits measured per species. By using the mean pairwise (Dpw) and mean nearest neighbor distance (Dnn) to quantify species ecological differences, we first tested the non-random functional and phylogenetic turnover of root neighborhoods that would lend more support to deterministic over stochastic community assembly processes. Additionally, we examined the distance-decay pattern of β diversity, and finally partitioned β diversity into geographical and environmental components to infer their potential drivers of environmental filtering, dispersal limitation, and biotic interactions. We found that functional turnover was often lower than expected given the taxonomic turnover, whereas phylogenetic turnover was often higher than expected. Phylogenetic Dpw (e.g., interfamily species) turnover exhibited a distance-decay pattern, likely reflecting limited dispersal or abiotic filtering that leads to the spatial aggregation of specific plant lineages. Conversely, both functional and phylogenetic Dnn (e.g., intrageneric species) exhibited an inverted distance-decay pattern, likely reflecting strong biotic interactions among spatially and phylogenetically close species leading to phylogenetic and functional divergence. While the spatial distance was generally a better predictor of β diversity than environmental distance, the joint effect of environmental and spatial distance usually overrode their respective pure effects. These findings suggest that root neighborhood functional homogeneity may somewhat increase forest resilience after disturbance by exhibiting an insurance effect. Likewise, root neighborhood phylogenetic heterogeneity may enhance plant fitness by hindering the transmission of host-specific pathogens through root networks or by promoting interspecific niche complementarity not captured by species functions. Our study highlights the potential role of root-centric β diversity in mediating community structures and functions largely ignored in previous studies.},
}
@article {pmid37877103,
year = {2023},
author = {Habib, KA and Islam, MJ and Sakib, MN and Brishti, PS and Neogi, AK},
title = {DNA barcoding of reef-associated fishes of Saint Martin's Island, Northern Bay of Bengal, Bangladesh.},
journal = {Ecology and evolution},
volume = {13},
number = {10},
pages = {e10641},
pmid = {37877103},
issn = {2045-7758},
abstract = {This study employs the DNA barcoding approach to make a molecular taxonomic catalog of reef fishes of Saint Martin's Island (SMI), an ecologically critical area (ECA), and Marine Protected Area (MPA) in Bangladesh. DNA barcoding, along with morphological analysis, confirmed 84 reef-associated fish species in SMI belonging to 16 orders, 39 families, and 67 genera. A total of 184 sequences were obtained in this study where 151 sequences (534-604 bp) of 81 species were identified from the COI barcode gene and 33 sequences (609 bp) of 19 species from the 16S rRNA gene region which were submitted to the GenBank and Barcode of Life Data System (BOLD). Among these sequences, 70 sequences of the COI gene and 16 sequences of 16S rRNA gene region from 41 species were submitted for the first time into the GenBank from Bangladesh. For molecular characterization analysis, another 37 sequences of 15 reef fish species of SMI were added from previous studies, making a total of 221 DNA sequences which comprised 179 sequences of 96 species for the COI gene and 42 sequences of 26 species for the 16S rRNA gene region. The COI sequences contain 145 haplotypes with 337 polymorphic sites, and the mean genetic distances within species, genera, and families were calculated as 0.34%, 12.26%, and 19.03%, respectively. On the contrary, 16S rRNA sequences comprised 31 haplotypes with 241 polymorphic sites, and the mean genetic divergences within species, genera, and families were 0.94%, 4.72%, and 12.43%, respectively. This study is a significant contribution to the marine biodiversity of Bangladesh which would facilitate the assessment of species diversity for strategizing management action. It is also an important input to the DNA barcode library of reef fishes of the northern Bay of Bengal.},
}
@article {pmid37873145,
year = {2023},
author = {Li, W and Miller, D and Liu, X and Tosi, L and Chkaiban, L and Mei, H and Hung, PH and Parekkadan, B and Sherlock, G and Levy, SF},
title = {Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37873145},
issn = {2692-8205},
support = {R01 AI164530/AI/NIAID NIH HHS/United States ; R01 HG011676/HG/NHGRI NIH HHS/United States ; },
abstract = {Sequence verification of plasmid DNA is critical for many cloning and molecular biology workflows. To leverage high-throughput sequencing, several methods have been developed that add a unique DNA barcode to individual samples prior to pooling and sequencing. However, these methods require an individual plasmid extraction and/or in vitro barcoding reaction for each sample processed, limiting throughput and adding cost. Here, we develop an arrayed in vivo plasmid barcoding platform that enables pooled plasmid extraction and library preparation for Oxford Nanopore sequencing. This method has a high accuracy and recovery rate, and greatly increases throughput and reduces cost relative to other plasmid barcoding methods or Sanger sequencing. We use in vivo barcoding to sequence verify >45,000 plasmids and show that the method can be used to transform error-containing dispersed plasmid pools into sequence-perfect arrays or well-balanced pools. In vivo barcoding does not require any specialized equipment beyond a low-overhead Oxford Nanopore sequencer, enabling most labs to flexibly process hundreds to thousands of plasmids in parallel.},
}
@article {pmid37872857,
year = {2023},
author = {Mathur, D and Díaz, SA and Hildebrandt, N and Pensack, RD and Yurke, B and Biaggne, A and Li, L and Melinger, JS and Ancona, MG and Knowlton, WB and Medintz, IL},
title = {Pursuing excitonic energy transfer with programmable DNA-based optical breadboards.},
journal = {Chemical Society reviews},
volume = {52},
number = {22},
pages = {7848-7948},
pmid = {37872857},
issn = {1460-4744},
support = {R00 EB030013/EB/NIBIB NIH HHS/United States ; },
mesh = {*Fluorescence Resonance Energy Transfer ; *Quantum Dots/chemistry ; Biotechnology ; Fluorescent Dyes/chemistry ; DNA/chemistry ; },
abstract = {DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.},
}
@article {pmid37872363,
year = {2023},
author = {Couton, M and Studer, A and Hürlemann, S and Locher, N and Knüsel, M and Alther, R and Altermatt, F},
title = {Integrating citizen science and environmental DNA metabarcoding to study biodiversity of groundwater amphipods in Switzerland.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {18097},
pmid = {37872363},
issn = {2045-2322},
mesh = {Animals ; *DNA, Environmental/genetics ; Ecosystem ; *Amphipoda/genetics ; DNA Barcoding, Taxonomic/methods ; Switzerland ; *Citizen Science ; Biodiversity ; *Groundwater ; Environmental Monitoring/methods ; },
abstract = {Groundwater is the physically largest freshwater ecosystem, yet one of the least explored habitats on earth, both because of accessing difficulties and the scarcity of the organisms inhabiting it. Here, we demonstrate how a two-fold approach provides complementary information on the occurrence and diversity of groundwater amphipods. Firstly, we used a citizen science approach in collaboration with municipal water providers who sampled groundwater organisms in their spring catchment boxes over multiple weeks, followed by DNA barcoding. Secondly, we collected four 10 L water samples at each site, in one sampling event, for environmental DNA (eDNA) metabarcoding. We found that citizen science was very effective in describing the distribution and abundance of groundwater amphipods. Although the single time-point of eDNA sampling did not detect as many amphipods, it allowed the assessment of the entire groundwater community, including microorganisms. By combining both methods, we found different amphipod species co-occurring with distinct sequences from the eDNA-metabarcoding dataset, representing mainly micro-eukaryotic species. We also found a distinct correlation between the diversity of amphipods and the overall biodiversity of groundwater organisms detected by eDNA at each site. We thus suggest that these approaches can be used to get a better understanding of subterranean biodiversity.},
}
@article {pmid37872110,
year = {2023},
author = {Yuan, M and Li, H and Wang, SZ},
title = {Massively parallel reporter assay: a novel technique for analyzing the regulation of gene expression.},
journal = {Yi chuan = Hereditas},
volume = {45},
number = {10},
pages = {859-873},
doi = {10.16288/j.yczz.23-180},
pmid = {37872110},
issn = {0253-9772},
mesh = {*Regulatory Sequences, Nucleic Acid ; *DNA/genetics ; Gene Expression Regulation ; Genes, Reporter ; RNA, Messenger ; },
abstract = {Massively parallel reporter assay (MPRA) is a high-throughput analysis method that can simultaneously investigate the activity of thousands of regulatory elements in the genome. MPRA introduces a uniquely identified barcode on a conventional luciferase reporter gene vector, sequences the DNA barcode before transfection and the mRNA barcode after transfection by next-generation sequencing technology, and uses the ratio of mRNA and DNA barcode reads to analyze the activity of cis-regulatory elements. Since MPRA was proposed, it has been widely used in the identification of genomic cis-regulatory elements and functional variants, the effect of post-transcriptional regulation on phenotypes and so on. In this review, we summarize the development history, basic principles, experimental procedures and statistical analysis methods of MPRA, and its applications in post-transcriptional regulation and cis-regulatory elements. It also provides prospects for its development and useful references for researchers in related fields to understand and apply MPRA.},
}
@article {pmid37871198,
year = {2023},
author = {González-Varo, JP and Albrecht, J and Arroyo, JM and Bueno, RS and Burgos, T and Escribano-Ávila, G and Farwig, N and García, D and Illera, JC and Jordano, P and Kurek, P and Rösner, S and Virgós, E and Sutherland, WJ},
title = {Frugivore-mediated seed dispersal in fragmented landscapes: Compositional and functional turnover from forest to matrix.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {44},
pages = {e2302440120},
pmid = {37871198},
issn = {1091-6490},
support = {H2020-MSCA-IF-2014-656572//European Commission (EC)/ ; RYC-2017-22095//MEC | Spanish National Plan for Scientific and Technical Research and Innovation (Plan Estatal de Investigaci&#xf3;n Cient&#xed;fica y T&#xe9;cnica y de Innovaci&#xf3;n)/ ; IDI/2018/000151//Gobierno del Principado de Asturias (GPA)/ ; PID2019-104922GA-I00//MEC | Spanish National Plan for Scientific and Technical Research and Innovation (Plan Estatal de Investigaci&#xf3;n Cient&#xed;fica y T&#xe9;cnica y de Innovaci&#xf3;n)/ ; },
mesh = {*Ecosystem ; *Seed Dispersal ; Forests ; Seeds ; Fruit ; Trees ; },
abstract = {Seed dispersal by frugivores is a fundamental function for plant community dynamics in fragmented landscapes, where forest remnants are typically embedded in a matrix of anthropogenic habitats. Frugivores can mediate both connectivity among forest remnants and plant colonization of the matrix. However, it remains poorly understood how frugivore communities change from forest to matrix due to the loss or replacement of species with traits that are less advantageous in open habitats and whether such changes ultimately influence the composition and traits of dispersed plants via species interactions. Here, we close this gap by using a unique dataset of seed-dispersal networks that were sampled in forest patches and adjacent matrix habitats of seven fragmented landscapes across Europe. We found a similar diversity of frugivores, plants, and interactions contributing to seed dispersal in forest and matrix, but a high turnover (replacement) in all these components. The turnover of dispersed seeds was smaller than that of frugivore communities because different frugivore species provided complementary seed dispersal in forest and matrix. Importantly, the turnover involved functional changes toward larger and more mobile frugivores in the matrix, which dispersed taller, larger-seeded plants with later fruiting periods. Our study provides a trait-based understanding of frugivore-mediated seed dispersal through fragmented landscapes, uncovering nonrandom shifts that can have cascading consequences for the composition of regenerating plant communities. Our findings also highlight the importance of forest remnants and frugivore faunas for ecosystem resilience, demonstrating a high potential for passive forest restoration of unmanaged lands in the matrix.},
}
@article {pmid37870443,
year = {2023},
author = {Mai, L and Wen, Z and Zhang, Y and Gao, Y and Lin, G and Lian, Z and Yang, X and Zhou, J and Lin, X and Luo, C and Peng, W and Chen, C and Peng, J and Liu, D and Marjani, SL and Tao, Q and Cui, Y and Zhang, J and Wu, X and Weissman, SM and Pan, X},
title = {Shortcut barcoding and early pooling for scalable multiplex single-cell reduced-representation CpG methylation sequencing at single nucleotide resolution.},
journal = {Nucleic acids research},
volume = {51},
number = {21},
pages = {e108},
pmid = {37870443},
issn = {1362-4962},
support = {32071452//National Nature Science Foundation of China/ ; SZBL2020090501003//Open Fund Programs of Shenzhen Bar Laboratory/ ; 2018B030308004//Guangdong Major Basic Cultivation Project/ ; 2019B1515120033//Guangdong Natural Science Foundation Major Projects of Basic and Applied Basic Research/ ; 2017BT01S131//Pearl River Talents Program Local Innovative and Research Teams/ ; },
mesh = {Humans ; CpG Islands/genetics ; *DNA ; *DNA Methylation/genetics ; High-Throughput Nucleotide Sequencing/methods ; K562 Cells ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; Cell Line, Tumor ; },
abstract = {DNA methylation is essential for a wide variety of biological processes, yet the development of a highly efficient and robust technology remains a challenge for routine single-cell analysis. We developed a multiplex scalable single-cell reduced representation bisulfite sequencing (msRRBS) technology. It allows cell-specific barcoded DNA fragments of individual cells to be pooled before bisulfite conversion, free of enzymatic modification or physical capture of the DNA ends, and achieves read mapping rates of 62.5 ± 3.9%, covering 60.0 ± 1.4% of CpG islands and 71.6 ± 1.6% of promoters in K562 cells. Its reproducibility is shown in duplicates of bulk cells with close to perfect correlation (R = 0.97-0.99). At a low 1 Mb of clean reads, msRRBS provides highly consistent coverage of CpG islands and promoters, outperforming the conventional methods with orders of magnitude reduction in cost. Here, we use this method to characterize the distinct methylation patterns and cellular heterogeneity of six cell lines, plus leukemia and hepatocellular carcinoma models. Taking 4 h of hands-on time, msRRBS offers a unique, highly efficient approach for dissecting methylation heterogeneity in a variety of multicellular systems.},
}
@article {pmid37869427,
year = {2023},
author = {Sromek, L and Ylinen, E and Kunnasranta, M and Maduna, SN and Sinisalo, T and Michell, CT and Kovacs, KM and Lydersen, C and Ieshko, E and Andrievskaya, E and Alexeev, V and Leidenberger, S and Hagen, SB and Nyman, T},
title = {Loss of species and genetic diversity during colonization: Insights from acanthocephalan parasites in northern European seals.},
journal = {Ecology and evolution},
volume = {13},
number = {10},
pages = {e10608},
pmid = {37869427},
issn = {2045-7758},
abstract = {Studies on host-parasite systems that have experienced distributional shifts, range fragmentation, and population declines in the past can provide information regarding how parasite community richness and genetic diversity will change as a result of anthropogenic environmental changes in the future. Here, we studied how sequential postglacial colonization, shifts in habitat, and reduced host population sizes have influenced species richness and genetic diversity of Corynosoma (Acanthocephala: Polymorphidae) parasites in northern European marine, brackish, and freshwater seal populations. We collected Corynosoma population samples from Arctic, Baltic, Ladoga, and Saimaa ringed seal subspecies and Baltic gray seals, and then applied COI barcoding and triple-enzyme restriction-site associated DNA (3RAD) sequencing to delimit species, clarify their distributions and community structures, and elucidate patterns of intraspecific gene flow and genetic diversity. Our results showed that Corynosoma species diversity reflected host colonization histories and population sizes, with four species being present in the Arctic, three in the Baltic Sea, two in Lake Ladoga, and only one in Lake Saimaa. We found statistically significant population-genetic differentiation within all three Corynosoma species that occur in more than one seal (sub)species. Genetic diversity tended to be high in Corynosoma populations originating from Arctic ringed seals and low in the landlocked populations. Our results indicate that acanthocephalan communities in landlocked seal populations are impoverished with respect to both species and intraspecific genetic diversity. Interestingly, the loss of genetic diversity within Corynosoma species seems to have been less drastic than in their seal hosts, possibly due to their large local effective population sizes resulting from high infection intensities and effective intra-host population mixing. Our study highlights the utility of genomic methods in investigations of community composition and genetic diversity of understudied parasites.},
}
@article {pmid37867259,
year = {2024},
author = {Rodrigues, BL and da Silva Costa, G and Godoy, RE and Pereira Júnior, AM and Cella, W and Ferreira, GEM and de Medeiros, JF and Shimabukuro, PHF},
title = {Molecular and morphometric study of Brazilian populations of Psychodopygus davisi.},
journal = {Medical and veterinary entomology},
volume = {38},
number = {1},
pages = {83-98},
doi = {10.1111/mve.12701},
pmid = {37867259},
issn = {1365-2915},
support = {Financial code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; APQ-02569-15//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; PPM-00676-18//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; 012/2016//Funda&#xe7;&#xe3;o de Amparo ao Desenvolvimento das A&#xe7;&#xf5;es Cient&#xed;ficas e Tecnol&#xf3;gicas e &#xe0; Pesquisa do Estado de Rond&#xf4;nia/ ; },
mesh = {Animals ; Brazil ; *Psychodidae/genetics ; *Phlebotomus ; Biological Evolution ; Algorithms ; DNA Barcoding, Taxonomic/veterinary ; Phylogeny ; },
abstract = {In this study, we analysed the molecular and morphometric differences of several populations of the putative sand fly vector Psychodopygus davisi (Root, 1934) (Diptera, Psychodidae, Phlebotominae) in Brazil. We amplified the 658 base pair fragments of the DNA barcoding region-cytochrome c oxidase subunit 1 (COI) gene-for 57 specimens of P. davisi and three specimens of Psychodopygus claustrei (Abonnenc, Léger &amp; Fauran, 1979). We merged our data with public sequences of the same species available from GenBank. Then, the combined dataset-87 sequences and 20 localities-was analysed using population structure analysis and different species delimitation approaches. Geometric morphometry of wings was performed for 155 specimens of P. davisi populations from the North, Midwest and Southeast Brazilian regions, analysing the differences in centroid sizes and canonical variates. Molecular analysis indicated high intraspecific genetic distance values for P. davisi (maximum p distance = 5.52%). All algorithms identified P. davisi and P. claustrei as distinct molecular taxonomic units, despite the low interspecific distance (p distance to the nearest neighbour = 4.79%). P. davisi sequences were split into four genetic clusters by population structure analysis and at least five genetic lineages using intermediate scenarios of the species delimitation algorithms. The species validation analysis of BPP strongly supported the five-species model in our dataset. We found high genetic diversity in this taxon, which is in agreement with its wide geographic distribution in Brazil. Furthermore, the wing analysis showed that specimens from the Southeast Region of Brazil are different from those in the North and the Midwest. The evolutionary patterns of P. davisi populations in Brazil suggest the presence of candidate species, which need to be validated in future studies using a more comprehensive approach with both genomic data and morphological characters.},
}
@article {pmid37865658,
year = {2023},
author = {Ronca, S and Ford, CS and Allanguillaume, J and Szabo, C and Kipling, R and Wilkinson, MJ},
title = {The value of twinned pollinator-pollen metabarcoding: bumblebee pollination service is weakly partitioned within a UK grassland community.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {18016},
pmid = {37865658},
issn = {2045-2322},
mesh = {Humans ; Bees ; Animals ; *Pollination ; *Grassland ; Pollen ; Plants ; United Kingdom ; Flowers ; },
abstract = {Predicting ecological impact of declining bumblebee (Bombus) populations requires better understanding of interactions between pollinator partitioning of floral resources and plant partitioning of pollinator resources. Here, we combine Cytochrome Oxidase 1 (CO1) barcoding for bumblebee identification and rbcL metabarcoding of pollen carried by bees in three species-rich UK pastures. CO1 barcoding assigned 272 bees to eight species, with 33 individuals belonging to the cryptic Bombus lucorum complex (16 B. lucorum and 17 B. cryptarum). Seasonal bias in capture rates varied by species, with B. pratorum found exclusively in June/July and B. pascuorum more abundant in August. Pollen metabarcoding coupled with PERMANOVA and NMDS analyses revealed all bees carried several local pollen species and evidence of pollen resource partitioning between some species pairings, with Bombus pratorum carrying the most divergent pollen load. There was no evidence of resource partitioning between the two cryptic species present, but significantly divergent capture rates concorded with previous suggestions of separation on the basis of foraging behaviour being shaped by local/temporal differences in climatic conditions. Considering the bee carriage profile of pollen species revealed no significant difference between the nine most widely carried plant species. However, there was a sharp, tipping point change in community pollen carriage across all three sites that occurred during the transition between late July and early August. This transition resulted in a strong divergence in community pollen carriage between the two seasonal periods in both years. We conclude that the combined use of pollen and bee barcoding offers several benefits for further study of plant-pollinator interactions at the landscape scale.},
}
@article {pmid37865560,
year = {2024},
author = {Mole, B},
title = {[Restoration of the labial barcode by simultaneous "one shot" injection of botulinum toxin-hyaluronic acid in the same syringe].},
journal = {Annales de chirurgie plastique et esthetique},
volume = {69},
number = {1},
pages = {2-16},
doi = {10.1016/j.anplas.2023.05.005},
pmid = {37865560},
issn = {1768-319X},
mesh = {Humans ; Aged ; Hyaluronic Acid ; *Botulinum Toxins, Type A ; Syringes ; Injections ; Lip ; *Neuromuscular Agents ; },
abstract = {The purpose of this technique is to offer patients wishing a labial restoration without morphological changes a simple, fast, discreet, comfortable, adaptable and reversible method by combining the two compounds most used in aesthetic medicine, botulinum toxin and hyaluronic acid. The originality of this combination is based on their mixing in the same syringe and their injection with cannula through a paracommissural approach which makes it possible to treat the entire upper lip in a very homogeneous manner. Botulinum toxin diffuses directly into the underlying muscle layer; hyaluronic acid allows to unfold the damaged cutaneous fan. The useful reciprocal dose of the two products remains intuitive; for starting barcodes the dose of botulinum toxin will be 8-10 Speywood units (4 Allergan units), for those already marked at rest 10-20 Speywood units (4-8 Allergan units); the hyaluronic acid will be chosen according to the depth of the wrinkles. We present a series of 63 patients with an average age of 67 years with a result deemed positive in 79% of cases. The incidents reported are generally due to excessive doses of botulinum toxin which can lead to the classic incidents of fluid leaks in this location (6%). The expected efficacy of the treatment depends on that of the components used (four to six months) but prolonged results have been regularly observed (up to 18 months). All complementary resurfacing treatments have been discarded here since the aim pursued is that of a natural labial restoration allowing an immediate return to socio-professional activities.},
}
@article {pmid37864145,
year = {2023},
author = {Sauvage, T and Cormier, A and Delphine, P},
title = {A comparison of Oxford nanopore library strategies for bacterial genomics.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {627},
pmid = {37864145},
issn = {1471-2164},
support = {ANR-20-CE21-0001-01//Agence Nationale de la Recherche/ ; ANR-20-CE21-0001-01//Agence Nationale de la Recherche/ ; ANR-20-CE21-0001-01//Agence Nationale de la Recherche/ ; },
mesh = {*Nanopores ; High-Throughput Nucleotide Sequencing/methods ; Genome, Bacterial ; Gene Library ; Genomics ; },
abstract = {BACKGROUND: Oxford nanopore Technologies (ONT) provides three main library preparation strategies to sequence bacterial genomes. These include tagmentation (TAG), ligation (LIG) and amplification (PCR). Despite ONT's recommendations, making an informed decision for preparation choice remains difficult without a side-by-side comparison. Here, we sequenced 12 bacterial strains to examine the overall output of these strategies, including sequencing noise, barcoding efficiency and assembly quality based on mapping to curated genomes established herein.<br><br>RESULTS: Average read length ranged closely for TAG and LIG (>&#x2009;5,000 bp), while being drastically smaller for PCR (<&#x2009;1,100 bp). LIG produced the largest output with 33.62 Gbp vs. 11.72 Gbp for TAG and 4.79 Gbp for PCR. PCR produced the most sequencing noise with only 22.7% of reads mappable to the curated genomes, vs. 92.9% for LIG and 87.3% for TAG. Output per channel was most homogenous in LIG and most variable in PCR, while intermediate in TAG. Artifactual tandem content was most abundant in PCR (22.5%) and least in LIG and TAG (0.9% and 2.2%). Basecalling and demultiplexing of barcoded libraries resulted in&#x2009;~&#x2009;20% data loss as unclassified reads and 1.5% read leakage.<br><br>CONCLUSION: The output of LIG was best (low noise, high read numbers of long lengths), intermediate in TAG (some noise, moderate read numbers of long lengths) and less desirable in PCR (high noise, high read numbers of short lengths). Overall, users should not accept assembly results at face value without careful replicon verification, including the detection of plasmids assembled from leaked reads.},
}
@article {pmid37859552,
year = {2023},
author = {Bach, TS and La, VH and Khoi, TX and Nguyen, DH and Cuong, CB and Nguyen, TV},
title = {Identification, Phytochemistry and Biological Activities of Paris polyphylla on Hepatocellular Carcinoma.},
journal = {Pakistan journal of biological sciences : PJBS},
volume = {26},
number = {5},
pages = {203-212},
doi = {10.3923/pjbs.2023.203.212},
pmid = {37859552},
issn = {1812-5735},
mesh = {Female ; Animals ; *Carcinoma, Hepatocellular/drug therapy ; *Liver Neoplasms/drug therapy ; *Coleoptera ; *Liliaceae ; Plant Extracts/pharmacology ; },
abstract = {Background and Objective: Liver cancer is the common cause of cancer death. Paris polyphylla is used as a traditional folk medicine in Vietnam to treat pneumonia, mastitis, bruises and fractures but no study was available regarding its ability to treat liver cancer or slow its growth. In this study, Paris polyphylla samples were identified and evaluated cytotoxic activity against the liver cancer cells. Materials and Methods: Paris polyphylla species were collected from various areas in Yen Bai, Vietnam, which were identified by comparative morphological method and DNA barcoding for the 18S, matK genes and ITS region. Paris polyphylla samples were dried until constant weight, ground into a fine powder and extracted in various solvents. The bioactivity of these extracts were done by the MTT assay. Results: The sequences of 18S, matK genes and ITS region were high similarity to sequences of P. polyphylla in the National Center for Biotechnology Information. The N-hexane and ethyl acetate fractions were produced from the methanol extract of P. polyphylla. The TLC results showed that there was a significant difference in the component of n-hexane and ethyl acetate fraction. The N-hexane fraction contains mainly low-polarity and non-polarity substances. While ethyl acetate fraction consists mainly of polar substances. In addition, ethyl acetate fraction was shown the strongest cytotoxic activity on the cancer cell lines HepG2 and Huh7 with the evaluation of IC50 = 115.11±2.77 μg mL[1] and IC50 = 148.11±1.78 μg mL[1]. Conclusion: The extract of Paris polyphylla demonstrated strong potential to inhibit the growth of the liver cancer cell line. The ethyl acetate fraction has the highest ability for cytotoxicity on the liver and cell line at a concentration of 200 μg mL[1] through MTT.},
}
@article {pmid37858169,
year = {2023},
author = {Guillardín, L and MacKay, JJ},
title = {Comparing DNA isolation methods for forest trees: quality, plastic footprint, and time-efficiency.},
journal = {Plant methods},
volume = {19},
number = {1},
pages = {111},
pmid = {37858169},
issn = {1746-4811},
abstract = {BACKGROUND: Genetic and genomic studies are seeing an increase in sample sizes together with a wider range of species investigated in response to environmental change concerns. In turn, these changes may come with challenges including the time and difficulty to isolate nucleic acids (DNA or RNA), the sequencing cost and environmental impacts of the growing amount of plastic waste generated in the process. Pseudotsuga menziesii var. menziesii (Mirbel) Franco (PM), Tsuga heterophylla (Raf.) Sarg. (TH) and Thuja plicata Donn ex D.Don (TP) are conifer species found in diverse woodlands both as natives and naturalized exotics. Our study was carried out whilst investigating their genetics to understand their population structure and potential for adaptation.<br><br>RESULTS: In the present study, we compared two different DNA isolation methods, i.e., spin-column DNeasy plant mini kit (QIAGEN), and temperature-driven enzymatic cocktail Plant DNA Extraction (MicroGEM). The quantity of recovered DNA and the quality of DNA were assessed along with the plastic footprint and time needed for three tree species. Both methods were optimised and proven to provide enough DNA for each studied species. The yield of DNA for each method depended on the species: QIAGEN showed higher yield in P. menziesii and T. heterophylla, while T. plicata recovered similar amount of DNA for both methods. The DNA quality was investigated using DNA barcoding techniques by confirming species identity and species discrimination. No difference was detected in the PCR amplification of the two barcoding loci, (rbcL and trnH-psbA), and the recovered sequences between DNA isolation methods. Measurement of the plastic use and the processing time per sample indicated that MicroGEM had a 52.64% lower plastic footprint and was 51.8% faster than QIAGEN.<br><br>CONCLUSIONS: QIAGEN gave higher yields in two of the species although both methods showed similar quality results across all species. However, MicroGEM was clearly advantageous to decrease the plastic footprint and improve the time efficiency. Overall, MicroGEM recovers sufficient and reliable DNA to perform common downstream analyses such as PCR and sequencing. Our findings illustrate the benefits of research and efforts towards developing more sustainable methods and techniques to reduce the environmental footprint of molecular analyses.},
}
@article {pmid37857147,
year = {2023},
author = {Dabi, Y and Suisse, S and Marie, Y and Delbos, L and Poilblanc, M and Descamps, P and Golfier, F and Jornea, L and Forlani, S and Bouteiller, D and Touboul, C and Puchar, A and Bendifallah, S and Daraï, E},
title = {New class of RNA biomarker for endometriosis diagnosis: The potential of salivary piRNA expression.},
journal = {European journal of obstetrics, gynecology, and reproductive biology},
volume = {291},
number = {},
pages = {88-95},
doi = {10.1016/j.ejogrb.2023.10.015},
pmid = {37857147},
issn = {1872-7654},
mesh = {Female ; Humans ; Adult ; *Piwi-Interacting RNA ; RNA, Small Interfering/genetics ; *Endometriosis/diagnosis/genetics ; Artificial Intelligence ; Prospective Studies ; Biomarkers ; },
abstract = {OBJECTIVES: In contrast to miRNA expression, little attention has been given to piwiRNA (piRNA) expression among endometriosis patients. The aim of the present study was to explore the human piRNAome and to investigate a potential piRNA saliva-based diagnostic signature for endometriosis.<br><br>METHODS: Data from the prospective "ENDOmiRNA" study (ClinicalTrials.gov Identifier: NCT04728152) were used. Saliva samples from 200 patients were analyzed in order to evaluate human piRNA expression using the piRNA bank. Next Generation Sequencing (NGS), barcoding of unique molecular identifiers and both Artificial Intelligence (AI) and machine learning (ML) were used. For each piRNA, sensitivity, specificity, and ROC AUC values were calculated for the diagnosis of endometriosis.<br><br>RESULTS: 201 piRNAs were identified, none had an AUC&#xa0;&#x2265;&#xa0;0.70, and only three piRNAs (piR-004153, piR001918, piR-020401) had an AUC between &#x2265; 0.6 and&#xa0;<&#xa0;0.70. Seven were differentially expressed: piR-004153, piR-001918, piR-020401, piR-012864, piR-017716, piR-020326 and piR-016904. The respective correlation and accuracy to diagnose endometriosis according to the F1-score, sensitivity, specificity, and AUC ranged from 0 to 0.862&#xa0;%, 0-0.961&#xa0;%, 0.085-1, and 0.425-0.618. A correlation was observed between the patients' age (&#x2265;35&#xa0;years) and piR-004153 (p&#xa0;=&#xa0;0.002) and piR-017716 (p&#xa0;=&#xa0;0.030). Among the 201 piRNAs, four were differentially expressed in patients with and without hormonal treatment: piR-004153 (p&#xa0;=&#xa0;0.015), piR-020401 (p&#xa0;=&#xa0;0.001), piR-012864 (p&#xa0;=&#xa0;0.036) and piR-017716 (p&#xa0;=&#xa0;0.009).<br><br>CONCLUSION: Our results support the link between piRNAs and endometriosis physiopathology and establish its utility as a potential diagnostic biomarker using saliva samples. Per se, piRNA expression should be analyzed along with the clinical status of a patient.},
}
@article {pmid37856492,
year = {2023},
author = {Fox, KA and MacGlover, CAW and Blecha, KA and Stenglein, MD},
title = {Assessing shared respiratory pathogens between domestic (Ovis aries) and bighorn (Ovis canadensis) sheep; methods for multiplex PCR, amplicon sequencing, and bioinformatics to characterize respiratory flora.},
journal = {PloS one},
volume = {18},
number = {10},
pages = {e0293062},
pmid = {37856492},
issn = {1932-6203},
mesh = {Animals ; Sheep ; *Sheep, Bighorn/genetics/microbiology ; Sheep, Domestic ; Multiplex Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; *Sheep Diseases/epidemiology ; *Mannheimia haemolytica/genetics ; *Respiratory Tract Diseases ; Computational Biology ; },
abstract = {Respiratory disease is responsible for dramatic population declines in bighorn sheep (Ovis canadensis), and respiratory pathogen diagnostics contribute to the management of bighorn populations. To create a comprehensive and consistent approach to bighorn sheep respiratory diagnostics, we created a culture-independent assay to detect and strain type Mannheimia haemolytica, Bibersteinia trehalosi, Pasteurella multocida, and Mycoplasma ovipneumoniae. The assay also detects and characterizes the Pasteurellaceae leukotoxin A gene, and broadly assesses the bacterial composition of each sample based on 16S rRNA sequences. The assay is based on a three-step approach: 1) Multiplex PCR to amplify targets including eight loci for each bacterial species, the Pasteurellaceae lktA gene, and the 16S rRNA gene 2) Library preparation, barcoding, and short-read Illumina sequencing to determine the genetic sequences of each target, and 3) Bioinformatics in the form of automated software to analyze genetic sequences. The assay was designed to assess shared pathogens between domestic and bighorn sheep, but could be useful for many applications in bighorn sheep respiratory disease research and management.},
}
@article {pmid37852258,
year = {2023},
author = {Li, L and Bowling, S and McGeary, SE and Yu, Q and Lemke, B and Alcedo, K and Jia, Y and Liu, X and Ferreira, M and Klein, AM and Wang, SW and Camargo, FD},
title = {A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells.},
journal = {Cell},
volume = {186},
number = {23},
pages = {5183-5199.e22},
doi = {10.1016/j.cell.2023.09.019},
pmid = {37852258},
issn = {1097-4172},
support = {R01 DK123216/DK/NIDDK NIH HHS/United States ; P50 HD105351/HD/NICHD NIH HHS/United States ; P01 HL131477/HL/NHLBI NIH HHS/United States ; RC2 DK131963/DK/NIDDK NIH HHS/United States ; R01 HL158192/HL/NHLBI NIH HHS/United States ; T32 HL007574/HL/NHLBI NIH HHS/United States ; 215920/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; R01 HL128850/HL/NHLBI NIH HHS/United States ; K99 HL164969/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Mice ; *Transcriptome/genetics ; *Epigenomics ; Cell Lineage/genetics ; Gene Expression Profiling ; Disease Models, Animal ; DNA ; },
abstract = {Cellular lineage histories and their molecular states encode fundamental principles of tissue development and homeostasis. Current lineage-recording mouse models have insufficient barcode diversity and single-cell lineage coverage for profiling tissues composed of millions of cells. Here, we developed DARLIN, an inducible Cas9 barcoding mouse line that utilizes terminal deoxynucleotidyl transferase (TdT) and 30 CRISPR target sites. DARLIN is inducible, generates massive lineage barcodes across tissues, and enables the detection of edited barcodes in ∼70% of profiled single cells. Using DARLIN, we examined fate bias within developing hematopoietic stem cells (HSCs) and revealed unique features of HSC migration. Additionally, we established a protocol for joint transcriptomic and epigenomic single-cell measurements with DARLIN and found that cellular clonal memory is associated with genome-wide DNA methylation rather than gene expression or chromatin accessibility. DARLIN will enable the high-resolution study of lineage relationships and their molecular signatures in diverse tissues and physiological contexts.},
}
@article {pmid37852122,
year = {2023},
author = {Hossain, MY and Uddin, M and Rahman, MA and Haque, MK and Kormoker, T and Samad, MA and Tanjin, S and Rahman, MA and Parvin, MF and Sarmin, MS and Mawa, Z and Habib, KA and Rahman, MS and Tasmin, R and Yeasmin, S and Mahmud, Y and Idris, AM and Al-Qthanin, RN and Tsang, YF},
title = {Species identification, reproductive biology, and nutritional value of marine shellfish (Meretrix lyrata) in the Bay of Bengal.},
journal = {Marine environmental research},
volume = {192},
number = {},
pages = {106222},
doi = {10.1016/j.marenvres.2023.106222},
pmid = {37852122},
issn = {1879-0291},
mesh = {Animals ; *Bays ; *Bivalvia ; Shellfish ; Seafood ; Reproduction ; Nutritive Value ; Seasons ; Biology ; },
abstract = {Meretrix lyrata which is under the family of Veneridae and under the order of Venerida, is a nutritionally and economically important edible mussel in Bangladesh. However, studies on species identification and nutritional value in M. lyrata are scarce. Therefore, a detailed investigation was conducted on (i) species identification of the common edible mussel through DNA-barcoding and morphometrics, (ii) reproductive features, such as size at sexual maturity, spawning, and peak-spawning seasons under different environmental factors, and (iii) nutritional status through proximate analysis of M. lyrata mussel collected from the Bay of Bengal, Bangladesh. The results indicated that the size at sexual maturity for M. lyrata was 4.2 cm and the spawning seasons were significantly affected by the dissolve oxygen and salinity. The study also demonstrated that the spawning of M. lyrata occurred from January to June and December while peak spawning season was May in the Bay of Bengal. The higher protein and moisture contents with lower fat in M. lyrata indicated that are value-added seafood with higher nutritional values for consumers.},
}
@article {pmid37851281,
year = {2023},
author = {Wong, EB and Kamaruddin, N and Mokhtar, M and Yusof, N and Khairuddin, RFR},
title = {Assessing sequence heterogeneity in Chlorellaceae DNA barcode markers for phylogenetic inference.},
journal = {Journal, genetic engineering &amp; biotechnology},
volume = {21},
number = {1},
pages = {104},
pmid = {37851281},
issn = {2090-5920},
support = {FRGS/1/2018/WAB13/UPSI/02/1//Ministry of Higher Education, Malaysia/ ; },
abstract = {Phylogenetic inference is an important approach that allows the recovery of the evolutionary history and the origin of the Chlorellaceae species. Despite the species' potential for biofuel feedstock production, their high phenotypic plasticity and similar morphological structures among the species have muddled the taxonomy and identification of the Chlorellaceae species. This study aimed to decipher Chlorellaceae DNA barcode marker heterogeneity by examining the sequence divergence and genomic properties of 18S rRNA, ITS (ITS1-5.8S rRNA-ITS2-28S rRNA), and rbcL from 655 orthologous sequences of 64 species across 31 genera in the Chlorellaceae family. The study assessed the distinct evolutionary properties of the DNA markers that may have caused the discordance between individual trees in the phylogenetic inference using the Robinson-Foulds distance and the Shimodaira-Hasegawa test. Our findings suggest that using the supermatrix approach improves the congruency between trees by reducing stochastic error and increasing the confidence of the inferred Chlorellaceae phylogenetic tree. This study also found that the phylogenies inferred through the supermatrix approach might not always be well supported by all markers. The study highlights that assessing sequence heterogeneity prior to the phylogenetic inference could allow the approach to accommodate sequence evolutionary properties and support species identification from the most congruent phylogeny, which can better represent the evolution of Chlorellaceae species.},
}
@article {pmid37850372,
year = {2024},
author = {Kelly, S and Dong, Y and Wang, W and Matthee, S and Wentzel, JM and Durden, LA and Shao, R},
title = {Mitochondrial genome sequence comparisons indicate that the elephant louse Haematomyzus elephantis (Piaget, 1869) contains cryptic species.},
journal = {Medical and veterinary entomology},
volume = {38},
number = {1},
pages = {112-117},
doi = {10.1111/mve.12699},
pmid = {37850372},
issn = {1365-2915},
support = {//University of the Sunshine Coast/ ; },
mesh = {Swine ; Animals ; *Elephants/genetics ; *Phthiraptera/genetics ; *Genome, Mitochondrial ; South Africa ; },
abstract = {The parvorder Rhynchopthirina contains three currently recognised species of lice that parasitize elephants (both African savanna elephant Loxodonta africana and Asian elephant Elephas maximus), desert warthogs (Phacochoerus aethiopicus) and Red River hogs (Potamochoerus porcus), respectively. The Asian elephant lice and the African savanna elephant lice are currently treated as the same species, Haematomyzus elephantis (Piaget, 1869), based on morphology despite the fact that their hosts diverged 8.4 million years ago. In the current study, we sequenced 23 mitochondrial (mt) genes of African savanna elephant lice collected in South Africa and analysed the sequence divergence between African savanna elephant lice and previously sequenced Asian elephant lice. Sequence comparisons revealed >23% divergence for the 23 mt genes as a whole and ~17% divergence for cox1 gene between African savanna and Asian elephant lice, which were far higher than the divergence expected within a species. Furthermore, the mt gene sequence divergences between these lice are 3.76-4.6 times higher than that between their hosts, the African savanna and Asian elephants, which are expected for the co-divergence and co-evolution between lice and their elephant hosts. We conclude that (1) H. elephantis (Piaget, 1869) contains cryptic species and (2) African savanna and Asian elephant lice are different species genetically that may have co-diverged and co-evolved with their hosts.},
}
@article {pmid37848137,
year = {2024},
author = {Pozzi, ACM and Petit, S and Marjolet, L and Youenou, B and Lagouy, M and Namour, P and Schmitt, L and Navratil, O and Breil, P and Branger, F and Cournoyer, B},
title = {Ecological assessment of combined sewer overflow management practices through the analysis of benthic and hyporheic sediment bacterial assemblages from an intermittent stream.},
journal = {The Science of the total environment},
volume = {907},
number = {},
pages = {167854},
doi = {10.1016/j.scitotenv.2023.167854},
pmid = {37848137},
issn = {1879-1026},
mesh = {Humans ; Environmental Monitoring ; Wastewater ; Bacteria ; *Water Purification ; Feces/microbiology ; *Environmental Pollutants ; Sewage ; },
abstract = {Combined sewer overflows (CSO) are used to avoid overloading unitary sewers and wastewater treatment plants. Following the European Council Directive on Urban Wastewater Treatment (UWT), CSO discharges are regulated using guidelines that aim to reduce their ecological impact on aquatic systems. A model CSO, which is part of a long-term experimental field observatory, was modified according to these guidelines and used to evaluate the benefits of compliance through analyses of the bacteriological and chemical states of the receiving intermittent stream. The benthic and hyporheic sediments of similar geomorphic units located upstream and downstream of a monitored CSO outlet were compared before and after changes in CSO regimes. Hydrological, pollutants (Metal Trace Elements, MTE; Polycyclic Aromatic Hydrocarbons, PAH; fecal indicator bacteria, FIB), and tpm-based DNA meta-barcoding datasets resolving the occurrences of >700 bacterial species of nearly 200 genera were studied. The frequency of overflow was confirmed to have significantly decreased following the application of the UWT guidelines. Overflows became almost limited to periods of heavy summer thunderstorm events. These changes were not associated with a significant decrease in most of the surveyed MTE, PAH, and FIB among stream sediments, except for chromium. Ecological benefits were highlighted by significant changes in tpm-based meta-barcoding community patterns between the UWT compliant sampling period and the previous one. Bacterial community change point analyses confirmed this segregation in the meta-barcoding dataset according to hydrological indices such as the number of CSO events and discharged volumes. A significant decline in CSO bacterial taxa in the benthic and hyporheic sediments was observed. Thirty-four CSO indicator species were identified, including Aeromonas caviae, Aeromonas media, and Pseudomonas oleovorans. These indicators, often documented as opportunistic pathogens (to humans, animals or plants) and/or pollutant degraders, were proposed as ecological sentinels for the assessment of CSO impacts.},
}
@article {pmid37847718,
year = {2023},
author = {Alperovich, N and Scott, BM and Ross, D},
title = {Automation protocol for high-efficiency and high-quality genomic DNA extraction from Saccharomyces cerevisiae.},
journal = {PloS one},
volume = {18},
number = {10},
pages = {e0292401},
pmid = {37847718},
issn = {1932-6203},
mesh = {*Saccharomyces cerevisiae/genetics ; *DNA ; Genomics ; Genome ; Automation, Laboratory ; Automation ; },
abstract = {Although many protocols have been previously developed for genomic DNA (gDNA) extraction from S. cerevisiae, to take advantage of recent advances in laboratory automation and DNA-barcode sequencing, there is a need for automated methods that can provide high-quality gDNA at high efficiency. Here, we describe and demonstrate a fully automated protocol that includes five basic steps: cell wall and RNA digestion, cell lysis, DNA binding to magnetic beads, washing with ethanol, and elution. Our protocol avoids the use of hazardous reagents (e.g., phenol, chloroform), glass beads for mechanical cell disruption, or incubation of samples at 100°C (i.e., boiling). We show that our protocol can extract gDNA with high efficiency both from cells grown in liquid culture and from colonies grown on agar plates. We also show results from gel electrophoresis that demonstrate that the resulting gDNA is of high quality.},
}
@article {pmid37845185,
year = {2024},
author = {Bustamante, MI and Elfar, K and Kuzmenko, J and Zaninovich, T and Arreguin, M and Carachure, C and Zhuang, G and Michailides, TJ and Eskalen, A},
title = {Reassessing the Etiology of Aspergillus Vine Canker and Summer Bunch Rot of Table Grapes in California.},
journal = {Plant disease},
volume = {108},
number = {4},
pages = {941-950},
doi = {10.1094/PDIS-06-23-1137-RE},
pmid = {37845185},
issn = {0191-2917},
mesh = {*Vitis/microbiology ; *Plant Diseases/microbiology ; California ; *Aspergillus/genetics/isolation &amp; purification/classification ; *Phylogeny ; Calmodulin/genetics ; Fruit/microbiology ; },
abstract = {Fungal taxonomy is in constant flux, and the advent of reliable DNA barcodes has enabled the enhancement of plant pathogen identification accuracy. In California, Aspergillus vine canker (AVC) and summer bunch rot (SBR) are economically important diseases that affect the wood and fruit of grapevines, respectively, and their causal agents are primarily species of black aspergilli (Aspergillus section Nigri). During the last decade, the taxonomy of this fungal group has been rearranged several times using morphological, physiological, and genetic analyses, which resulted in the incorporation of multiple cryptic species that are difficult to distinguish. Therefore, in this study, we aimed to reassess the etiology of AVC and SBR using a combination of morphological observations with phylogenetic reconstructions based on nucleotide sequences of the calmodulin (CaM) gene. Results revealed that the isolates causing AVC from recent isolations corresponded to A. tubingensis, whereas the isolates obtained from initial surveys when the disease was discovered were confirmed as A. niger and A. carbonarius. Similarly, the isolates obtained from table grapes with SBR symptoms and from spore traps placed in those vineyards were identified primarily as A. tubingensis, followed by A. niger and A. carbonarius. Notably, the A. niger isolates formed a subclade with strains previously known as A. welwitschiae, which is a species that was recently synonymized with A. niger. Overall, the most prevalent species was A. tubingensis, which was associated with both AVC and SBR, and representative isolates recovered from AVC-symptomatic wood, berries SBR symptoms, and spore traps were equally pathogenic in healthy wood and berries of 'Red Globe' grapevines. This study also constitutes the first report of A. tubingensis causing AVC and SBR of grapes in California and in the United States.},
}
@article {pmid37843476,
year = {2025},
author = {Phaka, FM and Netherlands, EC and Van Steenberge, M and Verheyen, E and Sonet, G and Hugé, J and du Preez, LH and Vanhove, MPM},
title = {Barcoding and traditional health practitioner perspectives are informative to monitor and conserve frogs and reptiles traded for traditional medicine in urban South Africa.},
journal = {Molecular ecology resources},
volume = {25},
number = {2},
pages = {e13873},
pmid = {37843476},
issn = {1755-0998},
support = {1513419N//Fonds Wetenschappelijk Onderzoek/ ; 114663//National Research Foundation/ ; 130501//National Research Foundation/ ; //South African Institute of Aquatic Biodiversity/ ; BOF20TT06//Universiteit Hasselt/ ; R-9363//Vlaamse Interuniversitaire Raad/ ; //Youth 4 African Wildlife NPC/ ; },
mesh = {Animals ; South Africa ; *DNA Barcoding, Taxonomic/methods ; *Reptiles/classification/genetics ; *Anura/classification/genetics ; Conservation of Natural Resources/methods ; Medicine, Traditional/methods ; Medicine, African Traditional/methods ; Humans ; Traditional Medicine Practitioners ; },
abstract = {Previous literature suggests that Indigenous cultural practices, specifically traditional medicine, are commonplace among urban communities contrary to the general conception that such practices are restricted to rural societies. We reviewed previous literature for records of herptiles (frog and reptile species) sold by traditional health practitioners in urban South Africa, then used visual confirmation surveys, DNA barcoding and folk taxonomy to identify the herptile species that were on sale. Additionally, we interviewed 11 IsiZulu and SePedi speaking traditional health practitioners to document details of the collection and pricing of herptile specimens along with the practitioners' views of current conservation measures for traditional medicine markets. The 34 herptile species recorded in previous literature on traditional medicine markets included endangered and non-native species. Spectrophotometry measurements of the DNA we extracted from the tissue of herptiles used in traditional medicine were an unreliable predictor of whether those extractions would be suitable for further experimental work. From our initial set of 111 tissue samples, 81 sequencing reactions were successful and 55 of those sequences had species-level matches to COI reference sequences on the NCBI GenBank and/or BOLD databases. Molecular identification revealed that traditional health practitioners correctly labelled 77% of the samples that we successfully identified with DNA barcoding in this study. Our mixed methodology approach is useful for conservation planning as it updates knowledge of animal use in Indigenous remedies and can accurately identify species of high conservation priority. Furthermore, this study highlights the possibility of collaborative conservation planning with traditional health practitioners.},
}
@article {pmid37842057,
year = {2023},
author = {Bieler, R and Collins, TM and Golding, R and Granados-Cifuentes, C and Healy, JM and Rawlings, TA and Sierwald, P},
title = {Replacing mechanical protection with colorful faces-twice: parallel evolution of the non-operculate marine worm-snail genera Thylacodes (Guettard, 1770) and Cayo n. gen. (Gastropoda: Vermetidae).},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15854},
pmid = {37842057},
issn = {2167-8359},
mesh = {Animals ; Male ; Female ; Phylogeny ; *Snails/anatomy &amp; histology ; *Coral Reefs ; Eggs ; Seafood ; },
abstract = {Vermetid worm-snails are sessile and irregularly coiled marine mollusks common in warmer nearshore and coral reef environments that are subject to high predation pressures by fish. Often cryptic, some have evolved sturdy shells or long columellar muscles allowing quick withdrawal into better protected parts of the shell tube, and most have variously developed opercula that protect and seal the shell aperture trapdoor-like. Members of Thylacodes (previously: Serpulorbis) lack such opercular protection. Its species often show polychromatic head-foot coloration, and some have aposematic coloration likely directed at fish predators. A new polychromatic species, Thylacodes bermudensis n. sp., is described from Bermuda and compared morphologically and by DNA barcode markers to the likewise polychromatic western Atlantic species T. decussatus (Gmelin, 1791). Operculum loss, previously assumed to be an autapomorphy of Thylacodes, is shown to have occurred convergently in a second clade of the family, for which a new genus Cayo n. gen. and four new western Atlantic species are introduced: C. margarita n. sp. (type species; with type locality in the Florida Keys), C. galbinus n. sp., C. refulgens n. sp., and C. brunneimaculatus n. sp. (the last three with type locality in the Belizean reef) (all new taxa authored by Bieler, Collins, Golding &amp; Rawlings). Cayo n. gen. differs from Thylacodes in morphology (e.g., a protoconch that is wider than tall), behavior (including deep shell entrenchment into the substratum), reproductive biology (fewer egg capsules and eggs per female; an obliquely attached egg capsule stalk), and in some species, a luminous, "neon-like", head-foot coloration. Comparative investigation of the eusperm and parasperm ultrastructure also revealed differences, with a laterally flattened eusperm acrosome observed in two species of Cayo n. gen. and a spiral keel on the eusperm nucleus in one, the latter feature currently unique within the family. A molecular phylogenetic analysis based on mitochondrial and nuclear rRNA gene sequences (12SrRNA, trnV, 16SrRNA, 28SrRNA) strongly supports the independent evolution of the two non-operculate lineages of vermetids. Thylacodes forms a sister grouping to a clade comprising Petaloconchus, Eualetes, and Cupolaconcha, whereas Cayo n. gen is strongly allied with the small-operculate species Vermetus triquetrus and V. bieleri. COI barcode markers provide support for the species-level status of the new taxa. Aspects of predator avoidance/deterrence are discussed for these non-operculate vermetids, which appear to involve warning coloration, aggressive behavior when approached by fish, and deployment of mucous feeding nets that have been shown, for one vermetid in a prior study, to contain bioactive metabolites avoided by fish. As such, non-operculate vermetids show characteristics similar to nudibranch slugs for which the evolution of warning coloration and chemical defenses has been explored previously.},
}
@article {pmid37841227,
year = {2023},
author = {da Silva, FL and Pinho, LC and Stur, E and Nihei, SS and Ekrem, T},
title = {DNA barcodes provide insights into the diversity and biogeography of the non-biting midge Polypedilum (Diptera, Chironomidae) in South America.},
journal = {Ecology and evolution},
volume = {13},
number = {10},
pages = {e10602},
pmid = {37841227},
issn = {2045-7758},
abstract = {South America, particularly within its tropical belt, is renowned for its unparalleled high levels of species richness, surpassing other major biomes. Certain neotropical areas harbor fragmented knowledge of insect diversity and face imminent threats from biodiversity loss and climate change. Hence, there is an urgent need for rapid estimation methods to complement slower traditional taxonomic approaches. A variety of algorithms for delimiting species through single-locus DNA barcodes have been developed and applied for rapid species diversity estimates across diverse taxa. However, tree-based and distance-based methods may yield different group assignments, leading to potential overestimation or underestimation of putative species. Here, we investigate the performance of different DNA-based species delimitation approaches to rapidly estimate the diversity of Polypedilum (Chironomidae, Diptera) in South America. Additionally, we test the hypothesis that significant differences exist in the community structure of Polypedilum fauna between South America and its neighboring regions, particularly the Nearctic. Our analysis encompasses a dataset of 1492 specimens from 598 locations worldwide, with a specific focus on South America. Within this region, we analyzed a subset of 247 specimens reported from 37 locations. Using various methods including the Barcode Index Number (BIN), Bayesian Poisson tree processes (bPTP), multi-rate Poisson tree processes (mPTP), single-rate Poisson tree processes (sPTP), and generalized mixed Yule coalescent (sGMYC), we identify molecular operational taxonomic units (MOTUs) ranging from 267 to 520. Our results indicate that the sGMYC method is the most suitable for estimating putative species in our dataset, resulting in the identification of 75 species in the Neotropical region, particularly in South America. Notably, this region exhibited higher species richness in comparison to the Palearctic and Oriental realms. Additionally, our findings suggest potential differences in species composition of Polypedilum fauna between the Neotropical and the adjacent Nearctic realms, highlighting high levels of endemism and species richness in the first. These results support our hypothesis that there are substantial differences exist in species composition between the Polypedilum fauna in South America and the neighboring regions.},
}
@article {pmid37841031,
year = {2023},
author = {Cherneva, I and Ellison, CI and Zattara, EE and Norenburg, JL and Schwartz, ML and Junoy, J and Maslakova, SA},
title = {Seven new species of Tetranemertes Chernyshev, 1992 (Monostilifera, Hoplonemertea, Nemertea) from the Caribbean Sea, western Pacific, and Arabian Sea, and revision of the genus.},
journal = {ZooKeys},
volume = {1181},
number = {},
pages = {167-200},
pmid = {37841031},
issn = {1313-2989},
abstract = {The marine ribbon worm genus Tetranemertes Chernyshev, 1992 currently includes three species: the type species T.antonina (Quatrefages, 1846) from the Mediterranean Sea, T.rubrolineata (Kirsteuer, 1965) from Madagascar, and T.hermaphroditica (Gibson, 1982) from Australia. Seven new species are described: T.bifrostsp. nov., T.ocelatasp. nov., T.majinbuuisp. nov., and T.pastafariensissp. nov. from the Caribbean Sea (Panamá), and three species, T.unistriatasp. nov., T.paulayisp. nov., and T.arabicasp. nov., from the Indo-West Pacific (Japan and Oman). As a result, an amended morphological diagnosis of the genus is offered. To improve nomenclatural stability, a neotype of Tetranemertesantonina is designated from the Mediterranean. The newly described species, each characterized by features of external appearance and stylet apparatus, as well as by DNA-barcodes, form a well-supported clade with T.antonina on a molecular phylogeny of monostiliferan hoplonemerteans based on partial sequences of COI, 16S rRNA, 18S rRNA, and 28S rRNA. Six of the seven newly described species, as well as T.rubrolineata, possess the unusual character of having a central stylet basis slightly bilobed to deeply forked posteriorly in fully grown individuals, a possible morphological synapomorphy of the genus. In addition, an undescribed species of Tetranemertes is reported from the Eastern Tropical Pacific (Panamá), increasing the total number of known species in the genus to eleven.},
}
@article {pmid37840603,
year = {2023},
author = {Lee, DJ and Lee, JS and Kim, J and Lee, H and Byun, BK and Roh, SJ},
title = {A new species of the genus Proutia Tutt (Lepidoptera, Psychidae) from Korea, based on morphology and DNA barcodes.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e110313},
pmid = {37840603},
issn = {1314-2828},
abstract = {BACKGROUND: The genus Proutia Tutt, 1899 (Lepidoptera, Psychidae) comprises 14 species found throughout the world. In East Asia, three species, Proutiachinensis Hättenschwiler &amp; Chao, 1990, P.maculatella Saigusa &amp; Sugimoto, 2014 and P.nigra Saigusa &amp; Sugimoto, 2014, are known from Korea, Japan and China.<br><br>NEW INFORMATION: Proutiacornucervae Roh &amp; Lee, sp. nov. is newly recognised from Korea. In addition, Bruandellaniphonica (Hori) is transferred to genus Proutia. Male and genitalia of the species are described and DNA barcodes are provided.},
}
@article {pmid37839913,
year = {2023},
author = {May, DA and Taha, F and Child, MA and Ewald, SE},
title = {How colonization bottlenecks, tissue niches, and transmission strategies shape protozoan infections.},
journal = {Trends in parasitology},
volume = {39},
number = {12},
pages = {1074-1086},
doi = {10.1016/j.pt.2023.09.017},
pmid = {37839913},
issn = {1471-5007},
support = {R21 AI156153/AI/NIAID NIH HHS/United States ; NC/S001239/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; R35 GM138381/GM/NIGMS NIH HHS/United States ; T32 AI007046/AI/NIAID NIH HHS/United States ; 202553/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Humans ; Host-Parasite Interactions ; *Protozoan Infections/parasitology ; *Parasites/physiology ; *Toxoplasma ; *Plasmodium/physiology ; },
abstract = {Protozoan pathogens such as Plasmodium spp., Leishmania spp., Toxoplasma gondii, and Trypanosoma spp. are often associated with high-mortality, acute and chronic diseases of global health concern. For transmission and immune evasion, protozoans have evolved diverse strategies to interact with a range of host tissue environments. These interactions are linked to disease pathology, yet our understanding of the association between parasite colonization and host homeostatic disruption is limited. Recently developed techniques for cellular barcoding have the potential to uncover the biology regulating parasite transmission, dissemination, and the stability of infection. Understanding bottlenecks to infection and the in vivo tissue niches that facilitate chronic infection and spread has the potential to reveal new aspects of parasite biology.},
}
@article {pmid37839019,
year = {2024},
author = {Tiedge, TM and Meiklejohn, KA},
title = {Assessing three soil removal methods for environmental DNA analysis of mock forensic geology evidence.},
journal = {Journal of forensic sciences},
volume = {69},
number = {1},
pages = {52-59},
doi = {10.1111/1556-4029.15399},
pmid = {37839019},
issn = {1556-4029},
support = {2020-R2-CX-0035//National Institute of Justice/ ; },
mesh = {*DNA, Environmental ; Soil ; Geology ; Sequence Analysis, DNA ; Plants/genetics ; DNA Barcoding, Taxonomic/methods ; },
abstract = {Soil is useful in criminal investigations as it is highly variable and readily transferred. Forensic geologists use several different techniques to removal soil from evidence prior to the analysis of inorganic components. There has been recent interest from the forensic science community to analyze environmental deoxyribonucleic acid (eDNA) associated with soil to augment existing forensic analyses. Notably however, limited research has been conducted to compare commonly used soil removal methods for downstream eDNA analysis. In this study, three soil removal methods were assessed: picking/scraping, sonication, and swabbing. Three mock evidence types (t-shirts, boot soles, and trowels) were sampled in triplicate with each removal method (n = 27). Soil samples underwent DNA isolation, quantification, and amplification of four genomic barcode regions: 16S for bacteria, ITS1 for fungi, ITS2 for plants, and COI for arthropods. Amplicons were prepared into libraries for DNA sequencing on an Illumina[®] MiniSeq. DNA concentrations were highest in picked/scraped samples and were statistically significant compared with swabbed and sonicated samples. Amplicon sequence variants (ASVs) were identified, and removal methods had no impact on the recovery of the total number of target ASVs. Additionally, when assessing each sample in multidimensional space, picked/scraped samples tended to cluster separately from swabbed and sonicated samples. The soil core used a reference in this study also clustered with the picked/scraped samples, indicating that these samples may be more reflective of the communities collected from soil cores. Based on these data, we identified that picking/scraping is an acceptable soil removal method for eDNA analysis.},
}
@article {pmid37835466,
year = {2023},
author = {Qian, H and Baglamis, S and Redeker, F and Raaijman, J and Hoebe, RA and Sheraton, VM and Vermeulen, L and Krawczyk, PM},
title = {High-Content and High-Throughput Clonogenic Survival Assay Using Fluorescence Barcoding.},
journal = {Cancers},
volume = {15},
number = {19},
pages = {},
pmid = {37835466},
issn = {2072-6694},
support = {ERC-CoG 101045612/ERC_/European Research Council/International ; },
abstract = {The Clonogenic Survival Assay (CSA) is a fundamental tool employed to assess cell survival and proliferative potential in cancer research. Despite its importance, CSA faces limitations, primarily its time- and labor-intensive nature and its binary output. To overcome these limitations and enhance CSA's utility, several approaches have been developed, focusing on increasing the throughput. However, achieving both high-content and high-throughput analyses simultaneously has remained a challenge. In this paper, we introduce LeGO-CSA, an extension of the classical CSA that employs the imaging of cell nuclei barcoded with fluorescent lentiviral gene ontology markers, enabling both high-content and high-throughput analysis. To validate our approach, we contrasted it with results from a classical assay and conducted a proof-of-concept screen of small-molecule inhibitors targeting various pathways relevant to cancer treatment. Notably, our results indicate that the classical CSA may underestimate clonogenicity and unveil intriguing aspects of clonal cell growth. We demonstrate the potential of LeGO-CSA to offer a robust approach for assessing cell survival and proliferation with enhanced precision and throughput, with promising implications for accelerating drug discovery and contributing to a more comprehensive understanding of cellular behavior in cancer.},
}
@article {pmid37834185,
year = {2023},
author = {Yang, T and Wu, Z and Tie, J and Qin, R and Wang, J and Liu, H},
title = {A Comprehensive Analysis of Chloroplast Genome Provides New Insights into the Evolution of the Genus Chrysosplenium.},
journal = {International journal of molecular sciences},
volume = {24},
number = {19},
pages = {},
pmid = {37834185},
issn = {1422-0067},
support = {No. 32170207//Natural Science Foundation of China/ ; },
mesh = {Phylogeny ; *Genome, Chloroplast ; Genomics/methods ; Mutation ; },
abstract = {Chrysosplenium, a perennial herb in the family Saxifragaceae, prefers to grow in low light and moist environments and is divided into two sections of Alternifolia and Oppositifolia based on phyllotaxy. Although there has been some progress in the phylogeny of Chrysosplenium over the years, the phylogenetic position of some species is still controversial. In this study, we assembled chloroplast genomes (cp genomes) of 34 Chrysosplenium species and performed comparative genomic and phylogenetic analyses in combination with other cp genomes of previously known Chrysosplenium species, for a total of 44 Chrysosplenium species. The comparative analyses revealed that cp genomes of Chrysosplenium species were more conserved in terms of genome structure, gene content and arrangement, SSRs, and codon preference, but differ in genome size and SC/IR boundaries. Phylogenetic analysis showed that cp genomes effectively improved the phylogenetic support and resolution of Chrysosplenium species and strongly supported Chrysosplenium species as a monophyletic taxon and divided into three branches. The results also showed that the sections of Alternifolia and Oppositifolia were not monophyletic with each other, and that C. microspermum was not clustered with other Chrysosplenium species with alternate leaves, but with C. sedakowii into separate branches. In addition, we identified 10 mutational hotspot regions that could serve as potential DNA barcodes for Chrysosplenium species identification. In contrast to Peltoboykinia, the clpP and ycf2 genes of Chrysosplenium were subjected to positive selection and had multiple significant positive selection sites. We further detected a significant positive selection site on the petG gene between the two sections of Chrysosplenium. These evolutionary characteristics may be related to the growth environment of Chrysosplenium species. This study enriches the cp genomes of Chrysosplenium species and provides a reference for future studies on its evolution and origin.},
}
@article {pmid37833354,
year = {2023},
author = {Acford-Palmer, H and Campos, M and Bandibabone, J and N'Do, S and Bantuzeko, C and Zawadi, B and Walker, T and Phelan, JE and Messenger, LA and Clark, TG and Campino, S},
title = {Detection of insecticide resistance markers in Anopheles funestus from the Democratic Republic of the Congo using a targeted amplicon sequencing panel.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {17363},
pmid = {37833354},
issn = {2045-2322},
support = {101285/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; BB/X018156/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/R006040/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/X005895/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; Insecticide Resistance/genetics ; *Insecticides/pharmacology ; *Anopheles/genetics ; Democratic Republic of the Congo ; Mosquito Vectors/genetics ; *Malaria/prevention &amp; control ; *Pyrethrins/pharmacology ; },
abstract = {Vector control strategies have been successful in reducing the number of malaria cases and deaths globally, but the spread of insecticide resistance represents a significant threat to disease control. Insecticide resistance has been reported across Anopheles (An.) vector populations, including species within the An. funestus group. These mosquitoes are responsible for intense malaria transmission across sub-Saharan Africa, including in the Democratic Republic of the Congo (DRC), a country contributing > 12% of global malaria infections and mortality events. To support the continuous efficacy of vector control strategies, it is essential to monitor insecticide resistance using molecular surveillance tools. In this study, we developed an amplicon sequencing ("Amp-seq") approach targeting An. funestus, and using multiplex PCR, dual index barcoding, and next-generation sequencing for high throughput and low-cost applications. Using our Amp-seq approach, we screened 80 An. funestus field isolates from the DRC across a panel of nine genes with mutations linked to insecticide resistance (ace-1, CYP6P4, CYP6P9a, GSTe2, vgsc, and rdl) and mosquito speciation (cox-1, mtND5, and ITS2). Amongst the 18 non-synonymous mutations detected, was N485I, in the ace-1 gene associated with carbamate resistance. Overall, our panel represents an extendable and much-needed method for the molecular surveillance of insecticide resistance in An. funestus populations.},
}
@article {pmid37831281,
year = {2023},
author = {Aung, ST and Bawm, S and Chel, HM and Thu, MJ and Wai, SS and Eshita, Y and Nakao, R and Katakura, K and Htun, LL},
title = {Molecular Identification of Aedes, Armigeres, and Culex Mosquitoes (Diptera: Culicidae) Using Mitochondrial Cytochrome Oxidase Subunit I Genes in Myanmar.},
journal = {Acta parasitologica},
volume = {68},
number = {4},
pages = {862-868},
pmid = {37831281},
issn = {1896-1851},
support = {17H04638//Kakenhi, Japanese Ministry of Education, Culture, Sports, Science and Technology/ ; },
mesh = {Animals ; Humans ; *Culex/genetics ; *Aedes/genetics ; Electron Transport Complex IV/genetics ; Myanmar ; Mosquito Vectors/genetics ; },
abstract = {PURPOSE: Mosquitoes are important vectors that carry disease-causing agents that can affect humans and animals. DNA barcoding is a complementary identification which can be used to validate morphological characterization of mosquito species. The objectives of this study were to identify the mitochondrial sequence of the COI gene and to construct a molecular phylogeny based on the genetic divergence of the mosquito species studied.<br><br>METHODS: In this study, DNA extraction and the amplification of the mitochondrial cytochrome oxidase subunit I genes (COI) were performed on pooled mosquito samples collected in Nay Pyi Taw area, Myanmar.<br><br>RESULTS: Fragments of the COI gene showed 99-100% identity with sequences of Aedes aegypti, Armigeres subalbatus, Culex pipiens complex, and Cx. quinquefasciatus, respectively, deposited in GenBank. This study categorized two haplotypes from each Ar. subalbatus and Cx. pipiens complex COI gene sequence, as well as three haplotypes from Cx. quinquefasciatus COI gene sequences. The highest haplotype diversity and nucleotide diversity were observed in the Ar. subalbatus population (Hd&#x2009;=&#x2009;1.0000; &#x3c0;&#x2009;=&#x2009;0.0033), followed by the Cx. pipiens complex and Cx. quinquefasciatus populations.<br><br>CONCLUSION: This study provides useful information on the molecular identification and genetic diversity of mosquito vectors with medical and veterinary significance, which may assist in the improvement of mosquito control programs.},
}
@article {pmid37828520,
year = {2023},
author = {Grailey, K and Hussain, R and Wylleman, E and Ezzat, A and Huf, S and Franklin, BD},
title = {Understanding the facilitators and barriers to barcode medication administration by nursing staff using behavioural science frameworks. A mixed methods study.},
journal = {BMC nursing},
volume = {22},
number = {1},
pages = {378},
pmid = {37828520},
issn = {1472-6955},
abstract = {INTRODUCTION: Barcode medication administration (BCMA) technology helps ensure correct medications are administered by nursing staff through scanning of patient and medication barcodes. In many hospitals scanning rates are low, limiting the potential safety benefits. We aimed to explore the barriers and facilitators to BCMA use in a London hospital.<br><br>METHODS: In this mixed methods study we used local quantitative data on BCMA scanning rates to identify clinically similar wards (in terms of patient acuity and workload) with different scanning rates for qualitative exploration. Interviews designed to elicit barriers to using BCMA technology were conducted with nursing staff, supported by observations of medication administration. Qualitative data were analysed inductively and a thematic framework constructed housing key themes, subsequently categorised into barriers and facilitators. To explore patient perspectives of BCMA scanning, a purposive sample of patients were also interviewed. These patient data were analysed deductively according to the thematic framework. Themes were mapped to behavioural science frameworks to further understand the behaviours involved.<br><br>RESULTS: BCMA was operational on 15 wards, with only six having medication scan rates of more than 10% of scannable doses. Of three wards selected for qualitative investigation, the lowest scan rate was 6.7%. Twenty-seven nurses and 15 patients were interviewed. Eleven key themes were identified, encompassing both barriers and facilitators to BCMA use. Barriers included poor trolley ergonomics and perceived time inefficiency. Facilitators included a streamlined process and thorough training. All nurses described BCMA as positive for patient safety. Patients described BCMA as making them "feel safer". Behavioural science frameworks highlighted the importance of professional role and an individual's belief in their capability.<br><br>CONCLUSION: We present a novel exploration of facilitators and barriers to BCMA use from the viewpoint of both patients and nursing staff, highlighting a strong perception that BCMA enhances safety. Barriers were reported on both high and low usage wards, demonstrating the importance of behaviours and motivations. These findings provide a detailed understanding from which to design interventions to support behaviour change and increase BCMA use.},
}
@article {pmid37828251,
year = {2023},
author = {Ayadi, ZEM and Tazerouti, F},
title = {Microcotyle justinei n. sp. (Monogenea: Microcotylidae) from the Gills of the Cardinal Fish Apogon imberbis (Teleostei: Apogonidae) off the Algerian Coast of the Western Mediterranean.},
journal = {Acta parasitologica},
volume = {68},
number = {4},
pages = {842-852},
pmid = {37828251},
issn = {1896-1851},
mesh = {Animals ; Gills ; *Perciformes ; Fishes ; *Trematoda ; Genitalia ; *Fish Diseases ; },
abstract = {PURPOSE: A new monogenean Microcotyle justinei n. sp. (Monogenea: Microcotylidae) is described based on specimens found on the gill filaments of the cardinal fish Apogon imberbis (Apogonidae) off the Algerian coast of the Western Mediterranean.<br><br>METHODS: Monogeneans were examined, measured and drawn for a comparative morphological study with other species of Microcotyle and characterised molecularly using a partial fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene. The identification of fish was confirmed by molecular barcoding using the cox1 gene.<br><br>RESULTS: The new species is distinguished from all other species of the genus by a combination of features, such as the number and size of the clamps, the shape and size of the genital atrium and the number of testes. The molecular analysis of the cox1 gene sequences showed that interspecific differences between Microcotyle justinei n. sp. and published sequences of Microcotyle spp. was greater than 8.8%, strongly suggesting that the new species is distinct from other congeners with sequences available on GenBank.<br><br>CONCLUSION: The morphological and molecular analyses support the status of M. justinei as a new species. The present finding extends the list of Microcotyle spp. to 72.},
}
@article {pmid37824674,
year = {2023},
author = {Tian, W and Zhou, J and Bartlett, A and Zeng, Q and Liu, H and Castanon, RG and Kenworthy, M and Altshul, J and Valadon, C and Aldridge, A and Nery, JR and Chen, H and Xu, J and Johnson, ND and Lucero, J and Osteen, JK and Emerson, N and Rink, J and Lee, J and Li, YE and Siletti, K and Liem, M and Claffey, N and O'Connor, C and Yanny, AM and Nyhus, J and Dee, N and Casper, T and Shapovalova, N and Hirschstein, D and Ding, SL and Hodge, R and Levi, BP and Keene, CD and Linnarsson, S and Lein, E and Ren, B and Behrens, MM and Ecker, JR},
title = {Single-cell DNA methylation and 3D genome architecture in the human brain.},
journal = {Science (New York, N.Y.)},
volume = {382},
number = {6667},
pages = {eadf5357},
pmid = {37824674},
issn = {1095-9203},
support = {U01 MH114812/MH/NIMH NIH HHS/United States ; S10 OD023689/OD/NIH HHS/United States ; U01 MH121282/MH/NIMH NIH HHS/United States ; UM1 MH130994/MH/NIMH NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; P30 CA014195/CA/NCI NIH HHS/United States ; },
mesh = {Adult ; Humans ; Male ; *Brain/cytology/metabolism ; Chromatin/metabolism ; *DNA Methylation ; Genome, Human ; Single-Cell Analysis ; Imaging, Three-Dimensional ; *Epigenesis, Genetic ; Atlases as Topic ; },
abstract = {Delineating the gene-regulatory programs underlying complex cell types is fundamental for understanding brain function in health and disease. Here, we comprehensively examined human brain cell epigenomes by probing DNA methylation and chromatin conformation at single-cell resolution in 517 thousand cells (399 thousand neurons and 118 thousand non-neurons) from 46 regions of three adult male brains. We identified 188 cell types and characterized their molecular signatures. Integrative analyses revealed concordant changes in DNA methylation, chromatin accessibility, chromatin organization, and gene expression across cell types, cortical areas, and basal ganglia structures. We further developed single-cell methylation barcodes that reliably predict brain cell types using the methylation status of select genomic sites. This multimodal epigenomic brain cell atlas provides new insights into the complexity of cell-type-specific gene regulation in adult human brains.},
}
@article {pmid37824174,
year = {2023},
author = {Charbonnel, E and Chapuis, MP and Taddei, A and Schutze, MK and Starkie, ML and Benoit, L and Mouttet, R and Ouvrard, D},
title = {Evaluation of identification methods for cryptic Bactrocera dorsalis (Diptera: Tephritidae) specimens: combining morphological and molecular techniques.},
journal = {Journal of economic entomology},
volume = {116},
number = {6},
pages = {2193-2200},
pmid = {37824174},
issn = {1938-291X},
mesh = {Animals ; *Tephritidae/genetics ; Sequence Analysis, DNA ; Mitochondria ; },
abstract = {The potential for population genomics to elucidate invasion pathways of a species is limited by taxonomic identification issues. The Oriental fruit fly pest, Bactrocera dorsalis (Hendel) belongs to a complex in which several sympatric species are attracted to the same lure used in trapping and are morphologically cryptic and/or reported to hybridize. In this study, we evaluated the taxonomic ambiguity between B. dorsalis and 2 major cryptic species, based on morphological expertise and 289 target specimens sampled across the whole distribution range. Specimens were then subjected to DNA sequence analyses of the COI mitochondrial barcode and the EIF3L nuclear marker to evaluate the potential for molecular identification, in particular for specimens for which morphological identification was inconclusive. To this aim, we produced reference datasets with DNA sequences from target specimens whose morphological identification was unambiguous, which we complemented with 56 new DNA sequences from closest relatives and 76 published and curated DNA sequences of different species in the complex. After the necessary morphological observation, about 3.5% of the target dataset and 47.6% of the specimens from Southeast Asian islands displayed ambiguous character states shared with B. carambolae and/or B. occipitalis. Critical interpretation of DNA sequence data solved morphological ambiguities only when combining both mitochondrial and nuclear markers. COI discriminated B. dorsalis from 5 species; EIF3L and ITS from another species. We recommend this procedure to ensure correct identification of B. dorsalis specimens in population genetics studies and surveillance programs.},
}
@article {pmid37822334,
year = {2023},
author = {Corvalán, LCJ and Sobreiro, MB and Carvalho, LR and Dias, RO and Braga-Ferreira, RS and Targueta, CP and Silva-Neto, CME and Berton, BW and Pereira, AMS and Diniz-Filho, JAF and Telles, MPC and Nunes, R},
title = {Chloroplast genome assembly of Serjania erecta Raldk: comparative analysis reveals gene number variation and selection in protein-coding plastid genes of Sapindaceae.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1258794},
pmid = {37822334},
issn = {1664-462X},
abstract = {Serjania erecta Raldk is an essential genetic resource due to its anti-inflammatory, gastric protection, and anti-Alzheimer properties. However, the genetic and evolutionary aspects of the species remain poorly known. Here, we sequenced and assembled the complete chloroplast genome of S. erecta and used it in a comparative analysis within the Sapindaceae family. S. erecta has a chloroplast genome (cpDNA) of 159,297 bp, divided into a Large Single Copy region (LSC) of 84,556 bp and a Small Single Copy region (SSC) of 18,057 bp that are surrounded by two Inverted Repeat regions (IRa and IRb) of 28,342 bp. Among the 12 species used in the comparative analysis, S. erecta has the fewest long and microsatellite repeats. The genome structure of Sapindaceae species is relatively conserved; the number of genes varies from 128 to 132 genes, and this variation is associated with three main factors: (1) Expansion and retraction events in the size of the IRs, resulting in variations in the number of rpl22, rps19, and rps3 genes; (2) Pseudogenization of the rps2 gene; and (3) Loss or duplication of genes encoding tRNAs, associated with the duplication of trnH-GUG in X. sorbifolium and the absence of trnT-CGU in the Dodonaeoideae subfamily. We identified 10 and 11 mutational hotspots for Sapindaceae and Sapindoideae, respectively, and identified six highly diverse regions (tRNA-Lys - rps16, ndhC - tRNA-Val, petA - psbJ, ndhF, rpl32 - ccsA, and ycf1) are found in both groups, which show potential for the development of DNA barcode markers for molecular taxonomic identification of Serjania. We identified that the psaI gene evolves under neutrality in Sapindaceae, while all other chloroplast genes are under strong negative selection. However, local positive selection exists in the ndhF, rpoC2, ycf1, and ycf2 genes. The genes ndhF and ycf1 also present high nucleotide diversity and local positive selection, demonstrating significant potential as markers. Our findings include providing the first chloroplast genome of a member of the Paullinieae tribe. Furthermore, we identified patterns in variations in the number of genes and selection in genes possibly associated with the family's evolutionary history.},
}
@article {pmid37821828,
year = {2023},
author = {Kobayashi, Y and Kayamori, A and Aoki, K and Shiwa, Y and Matsutani, M and Fujita, N and Sugita, T and Iwasaki, W and Tanaka, N and Takashima, M},
title = {Chromosome-level genome assemblies of Cutaneotrichosporon spp. (Trichosporonales, Basidiomycota) reveal imbalanced evolution between nucleotide sequences and chromosome synteny.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {609},
pmid = {37821828},
issn = {1471-2164},
support = {20K06801//Ministry of Education, Culture, Sports, Science and Technology/ ; },
mesh = {Synteny ; Base Sequence ; Chromosomes ; *Genome, Mitochondrial ; *Basidiomycota ; Nucleotides ; Evolution, Molecular ; },
abstract = {BACKGROUND: Since DNA information was first used in taxonomy, barcode sequences such as the internal transcribed spacer (ITS) region have greatly aided fungal identification; however, a barcode sequence alone is often insufficient. Thus, multi-gene- or whole-genome-based methods were developed. We previously isolated Basidiomycota yeasts classified in the Trichosporonales. Some strains were described as Cutaneotrichosporon cavernicola and C. spelunceum, whereas strain HIS471 remained unidentified. We analysed the genomes of these strains to elucidate their taxonomic relationship and genetic diversity.<br><br>RESULTS: The long-read-based assembly resulted in chromosome-level draft genomes consisting of seven chromosomes and one mitochondrial genome. The genome of strain HIS471 has more than ten chromosome inversions or translocations compared to the type strain of C. cavernicola despite sharing identical ITS barcode sequences and displaying an average nucleotide identity (ANI) above 93%. Also, the chromosome synteny between C. cavernicola and the related species, C. spelunceum, showed significant rearrangements, whereas the ITS sequence identity exceeds 98.6% and the ANI is approximately 82%. Our results indicate that the relative evolutionary rates of barcode sequences, whole-genome nucleotide sequences, and chromosome synteny in Cutaneotrichosporon significantly differ from those in the model yeast Saccharomyces.<br><br>CONCLUSIONS: Our results revealed that the relative evolutionary rates of nucleotide sequences and chromosome synteny are different among fungal clades, likely because different clades have diverse mutation/repair rates and distinct selection pressures on their genomic sequences and syntenic structures. Because diverse syntenic structures can be a barrier to meiotic recombination and may lead to speciation, the non-linear relationships between nucleotide and synteny diversification indicate that sequence-level distances at the barcode or whole-genome level are not sufficient for delineating species boundaries.},
}
@article {pmid37819912,
year = {2023},
author = {Bleke, CA and Gese, EM and Roberts, SB and Villalba, JJ},
title = {Seasonal shifts in pronghorn antelope (Antilocapra americana) diets under a new lens: Examining diet composition using a molecular technique.},
journal = {PloS one},
volume = {18},
number = {10},
pages = {e0292725},
pmid = {37819912},
issn = {1932-6203},
mesh = {Animals ; Female ; Pregnancy ; *Antelopes/genetics ; Seasons ; Dietary Proteins ; Plant Breeding ; Diet ; Medicago sativa ; },
abstract = {Foraging is one of the most fundamental activities contributing to the maximization of an animal's fitness, and thus herbivores must optimize their diet selection and intake to meet their nutrient demands for survival, growth, and reproduction. Using plant DNA barcoding, we determined diet composition of five subpopulations of adult female pronghorn antelope (Antilocapra americana) grazing rangelands in southern and southeastern Idaho, USA. Fecal samples were collected for two years (2018-2019), and across metabolically-important adult female life history stages (late gestation, early lactation, breeding season). Plant DNA barcoding yielded 137 detected species within pronghorn diets across subpopulations and sampling periods with forbs being the most abundant. Pronghorn dietary functional group composition ranged from 52.2-60.3% from forbs followed by shrubs (22.6-28.2%), graminoids (8.7-15.7%), and legumes (5.5-9.6%). Dietary protein intake was also highest from forbs and ranged from 32.4-62.4% followed by graminoids (1.2-43.1%), shrubs (18.7-21.3%), and legumes (2.6-7.4%). We found significant intra- and interannual differences in the mean number of genera-based plant detections in pronghorn diets. Dietary protein intake of cultivated legumes (e.g., alfalfa [Medicago sativa] and sainfoin [Onobrychis viciifolia]) was lower than expected, ranging from <1.0-30.8%, suggesting that even within an agricultural-dominated landscape, factors other than plant nutritional composition contributed to pronghorn diets. Although the plant DNA barcoding technique exhibits limitations, it demonstrated potential for elucidating pronghorn dietary species richness, particularly for plants consumed in small proportions, as well as for observing temporal fluctuations in functional group composition and dietary protein intake explained through the interplay between environmental factors, plant chemical composition, and the animals' physiological needs.},
}
@article {pmid37819481,
year = {2023},
author = {Savaris, M and Saldanha, AV and Corrêa, AS and Rainho, HL and Scarpare Filho, JA and Silveira Neto, S and Zucchi, RA},
title = {Establishment of Sinoxylon anale Lesne (Coleoptera, Bostrichidae) in Brazil: Identification, Host Plants, Distribution, and Damage.},
journal = {Neotropical entomology},
volume = {52},
number = {6},
pages = {1144-1154},
pmid = {37819481},
issn = {1678-8052},
mesh = {Animals ; *Coleoptera ; Brazil ; Larva ; Trees ; *Fabaceae ; *Myrtaceae ; },
abstract = {Damage from Sinoxylon anale Lesne, a woodboring beetle not previously known to be established in Brazil, was observed in young jabuticaba trees (Plinia cauliflora, Myrtaceae) in a nursery in the municipality of Laranjal Paulista, state of São Paulo. We immediately advised MAPA ("Ministério da Agricultura, Pecuária e Abastecimento") and collected samples from the nursery and from different hosts in nearby areas, to identify the specimens and investigate the dynamics of the infestation in the jabuticaba trees. Sinoxylon anale was also collected in ethanol-baited and ultraviolet-light traps and in dry branches of the native species pau-jacaré (Piptadenia gonoacantha, Fabaceae) and inga (Inga vera, Fabaceae), and the exotic pau-d'água (Dracaena fragrans, Asparagaceae) in the municipality of Piracicaba, state of São Paulo. These collections established that S. anale larvae and adults develop in dead branches of four new host plants. Taxonomic studies using morphological parameters and DNA barcoding confirmed the identification of S. anale. An illustrated key to the three Sinoxylon species now recorded in Brazil is provided, and the COI gene sequences have been made available in a public database. Sinoxylon anale probably attacked the young jabuticaba trees after they were killed by larvae of long-horned beetles (Cerambycidae). So far, S. anale has been found established only in two locations in the same area of the state of São Paulo.},
}
@article {pmid37818700,
year = {2024},
author = {Dang, K and Zhao, Y and Ye, K and Guo, Y and Wang, W and Ge, Q and Zhao, X},
title = {Construction of multiplexed transcriptome NGS libraries of microdissected tissue samples based on combinational DNA barcode microbeads.},
journal = {Biotechnology journal},
volume = {19},
number = {1},
pages = {e2300294},
doi = {10.1002/biot.202300294},
pmid = {37818700},
issn = {1860-7314},
support = {81827901//National Natural Science Foundation of China/ ; },
mesh = {Mice ; Animals ; *Transcriptome/genetics ; Microspheres ; DNA Barcoding, Taxonomic ; Tissue Fixation/methods ; Gene Expression Profiling/methods ; *Anti-Infective Agents ; DNA ; Formaldehyde ; },
abstract = {The combination of single-cell RNA sequencing and microdissection techniques that preserves positional information has become a major tool for spatial transcriptome analyses. However, high costs and time requirements, especially for experiments at the single cell scale, make it challenging for this approach to meet the demand for increased throughput. Therefore, we proposed combinational DNA barcode (CDB)-seq as a medium-throughput, multiplexed approach combining Smart-3SEQ and CDB magnetic microbeads for transcriptome analyses of microdissected tissue samples. We conducted a comprehensive comparison of conditions for CDB microbead preparation and related factors and then applied CDB-seq to RNA extracts, fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) mouse brain tissue samples. CDB-seq transcriptomic profiles of tens of microdissected samples could be obtained in a simple, cost-effective way, providing a promising method for future spatial transcriptomics.},
}
@article {pmid37817095,
year = {2023},
author = {Yu, J and Han, Y and Xu, H and Han, S and Li, X and Niu, Y and Chen, S and Zhang, F},
title = {Structural divergence and phylogenetic relationships of Ajania (Asteraceae) from plastomes and ETS.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {602},
pmid = {37817095},
issn = {1471-2164},
support = {2019QZKK0502//Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; KFJ-BRP-017-101//Biological Resources Programme of Chinese Academy of Sciences/ ; KFJ-BRP-017-101//Biological Resources Programme of Chinese Academy of Sciences/ ; LHZX-2021-04//Chinese Academy of Sciences -People's Government of Qinghai Province on Sanjiangyuan National Park/ ; 2022-ZJ-Y04//Construction Project for Innovation Platform of Qinghai Province/ ; },
mesh = {Phylogeny ; *Asteraceae ; Evolution, Molecular ; *Genome, Plastid ; Base Sequence ; },
abstract = {BACKGROUND: Ajania Poljakov, an Asteraceae family member, grows mostly in Asia's arid and semi-desert areas and is a significant commercial and decorative plant. Nevertheless, the genus' classification has been disputed, and the evolutionary connections within the genus have not been thoroughly defined. Hence, we sequenced and analyzed Ajania's plastid genomes and combined them with ETS data to assess their phylogenetic relationships.<br><br>RESULTS: We obtained a total of six new Ajania plastid genomes and nine ETS sequences. The whole plastome lengths of the six species sampled ranged from 151,002&#xa0;bp to 151,115&#xa0;bp, showing conserved structures. Combined with publicly available data from GenBank, we constructed six datasets to reconstruct the phylogenetic relationships, detecting nucleoplasmic clashes. Our results reveal the affinities of Artemisia, Chrysanthemum and Stilpnolepis to Ajania and validate the early taxonomy reclassification. Some of the plastid genes with low phylogenetic information and gene trees with topological differences may have contributed to the ambiguous phylogenetic results of Ajania. There is extensive evolutionary rate heterogeneity in plastid genes. The psbH and ycf2 genes, which are involved in photosynthesis and ATP transport, are under selective pressure. Plastomes from Ajania species diverged, and structural aspects of plastomes may indicate some of the real evolutionary connections. We suggest the ycf1 gene as a viable plastid DNA barcode because it has significant nucleotide diversity and better reflects evolutionary connections.<br><br>CONCLUSION: Our findings validate the early Ajania taxonomy reclassification and show evolutionary rate heterogeneity, genetic variety, and phylogenetic heterogeneity of plastid genes. This research might provide new insights into the taxonomy and evolution of Ajania, as well as provide useful information for germplasm innovation and genetic enhancement in horticultural species.},
}
@article {pmid37813635,
year = {2023},
author = {Chalermwong, P and Panthum, T and Wattanadilokcahtkun, P and Ariyaraphong, N and Thong, T and Srikampa, P and Singchat, W and Ahmad, SF and Noito, K and Rasoarahona, R and Lisachov, A and Ali, H and Kraichak, E and Muangmai, N and Chatchaiphan, S and Sriphairoj, K and Hatachote, S and Chaiyes, A and Jantasuriyarat, C and Chailertlit, V and Suksavate, W and Sonongbua, J and Srimai, W and Payungporn, S and Han, K and Antunes, A and Srisapoome, P and Koga, A and Duengkae, P and Matsuda, Y and Na-Nakorn, U and Srikulnath, K},
title = {Overcoming taxonomic challenges in DNA barcoding for improvement of identification and preservation of clariid catfish species.},
journal = {Genomics &amp; informatics},
volume = {21},
number = {3},
pages = {e39},
pmid = {37813635},
issn = {1598-866X},
abstract = {DNA barcoding without assessing reliability and validity causes taxonomic errors of species identification, which is responsible for disruptions of their conservation and aquaculture industry. Although DNA barcoding facilitates molecular identification and phylogenetic analysis of species, its availability in clariid catfish lineage remains uncertain. In this study, DNA barcoding was developed and validated for clariid catfish. 2,970 barcode sequences from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes and D-loop sequences were analyzed for 37 clariid catfish species. The highest intraspecific nearest neighbor distances were 85.47%, 98.03%, and 89.10% for COI, Cytb, and D-loop sequences, respectively. This suggests that the Cytb gene is the most appropriate for identifying clariid catfish and can serve as a standard region for DNA barcoding. A positive barcoding gap between interspecific and intraspecific sequence divergence was observed in the Cytb dataset but not in the COI and D-loop datasets. Intraspecific variation was typically less than 4.4%, whereas interspecific variation was generally more than 66.9%. However, a species complex was detected in walking catfish and significant intraspecific sequence divergence was observed in North African catfish. These findings suggest the need to focus on developing a DNA barcoding system for classifying clariid catfish properly and to validate its efficacy for a wider range of clariid catfish. With an enriched database of multiple sequences from a target species and its genus, species identification can be more accurate and biodiversity assessment of the species can be facilitated.},
}
@article {pmid37809956,
year = {2023},
author = {Lam, TTH and Dinh, QM and Truong, VTB and Truong, NT and Tran, NS and Nguyen, THD},
title = {The use of mtCOI gene sequences in identifying Butis species in the Southwest of Vietnam.},
journal = {Heliyon},
volume = {9},
number = {9},
pages = {e20139},
pmid = {37809956},
issn = {2405-8440},
abstract = {Butis genus is characterised by their small body size and morphological variability, allowing them to adapt to different habitats. This paper analyses the mitochondrial cytochrome C oxidase subunit I gene sequences and morphology of Butis for identification purposes and to understand genetic relationships. The morphological characteristics of Butis koilomatodon differed obviously from Butis humeralis and Butis butis. After classification based on morphology, the total deoxyribonucleic acid of fish samples was isolated, and the mitochondrial cytochrome C oxidase subunit I genes were successfully amplified using the polymerase chain reaction method. At approximately 617bp, the obtained mitochondrial cytochrome C oxidase subunit I gene sequences were highly similar to the reference sequences on Genbank (85.90-100%). The phylogenetic graphic was divided into five distinct groups, where B. koilomatodon was grouped in one group; and B. humeralis and B. butis were grouped together. The results suggest that B. humeralis was an entirely different species from B. butis, with a mean genetic divergence of up to 14%. However, further studies using a combination of other types of deoxyribonucleic acid barcoding together with morphological features should be undertaken to confirm these findings.},
}
@article {pmid37808850,
year = {2024},
author = {Foyt, D and Brown, D and Zhou, S and Huang, B},
title = {HybriSeq: Probe-based Device-free Single-cell RNA Profiling.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37808850},
issn = {2692-8205},
support = {U01 DK127421/DK/NIDDK NIH HHS/United States ; },
abstract = {We have developed the HybriSeq method for single-cell RNA profiling, which utilizes in situ hybridization of multiple probes for targeted transcripts, followed by split-pool barcoding and sequencing analysis of the probes. We have shown that HybriSeq can achieve high sensitivity for RNA detection with multiple probes and profile differential splicing. The utility of HybriSeq is demonstrated in characterizing cell-to-cell heterogeneities of a panel of 95 cell-cycle-related genes and the detection of misannotated transcripts.},
}
@article {pmid37808696,
year = {2023},
author = {Matute, DR and Cooper, BS},
title = {Aedes albopictus is present in the lowlands of southern Zambia.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37808696},
issn = {2692-8205},
support = {R35 GM124701/GM/NIGMS NIH HHS/United States ; R35 GM148244/GM/NIGMS NIH HHS/United States ; },
abstract = {Identifying the current geographic range of disease vectors is a critical first step towards determining effective mechanisms for controlling and potentially eradicating them. This is particularly true given that historical vector ranges may expand due to changing climates and human activity. The Aedes subgenus Stegomyia contains over 100 species, and among them, Ae. aegypti and Ae. albopictus mosquitoes represent the largest concern for public health, spreading dengue, chikungunya, and Zika viruses. While Ae. aegypti has been observed in the country of Zambia for decades, Ae. albopictus has not. In 2015 we sampled four urban and two rural areas in Zambia for Aedes species. Using DNA barcoding, we confirmed the presence of immature and adult Ae. albopictus at two rural sites: Siavonga and Livingstone. These genotypes seem most closely related to specimens previously collected in Mozambique based on CO1 sequence from mtDNA. We resampled Siavonga and Livingstone sites in 2019, again observing immature and adult Ae. albopictus at both sites. Relative Ae. albopictus frequencies were similar between sites, with the exception of immature life stages, which were higher in Siavonga than in Livingstone in 2019. While Ae. albopictus frequencies did not vary through time in Livingstone, both immature and adult frequencies increased through time in Siavonga. This report serves to document the presence of Ae. albopictus in Zambia, which will contribute to the process of determining the potential public health implications of this disease vector in Central Africa.},
}
@article {pmid37804107,
year = {2024},
author = {Adachi, E and Nakagawa, R and Tsuji-Hosokawa, A and Gau, M and Kirino, S and Yogi, A and Nakatani, H and Takasawa, K and Yamaguchi, T and Kosho, T and Murakami, M and Tajima, T and Hasegawa, T and Yamada, T and Morio, T and Ohara, O and Kashimada, K},
title = {A MinION-based Long-Read Sequencing Application With One-Step PCR for the Genetic Diagnosis of 21-Hydroxylase Deficiency.},
journal = {The Journal of clinical endocrinology and metabolism},
volume = {109},
number = {3},
pages = {750-760},
doi = {10.1210/clinem/dgad577},
pmid = {37804107},
issn = {1945-7197},
support = {No. 20FC1020//Ministry of Health, Labour and Welfare of Japan/ ; No. 23ek0109630h0001//Japan Agency for Medical Research and Development/ ; },
mesh = {Humans ; *Steroid 21-Hydroxylase/genetics ; *Adrenal Hyperplasia, Congenital/diagnosis/genetics ; Genotype ; Multiplex Polymerase Chain Reaction ; Mutation ; },
abstract = {CONTEXT: Recently developed long-read sequencing (LRS) technology has been considered an option for CYP21A2 analysis. However, the clinical use of LRS for CYP21A2 analysis is limited.<br><br>OBJECTIVE: This study's objective is to develop an efficient and low-cost LRS system for CYP21A2 screening.<br><br>METHODS: A DNA fragment library was prepared in a single polymerase chain reaction (PCR) that covers the entire CYP21A2 gene and all known junctions caused by TNXB gene structural rearrangements, yielding a single 8-kb product of CYP21A2 or CYP21A1P/CYP21A2 chimera. After barcoding, the PCR products were sequenced on a MinION-based platform with Flongle Flow Cell R9.4.1 and R10.4.1.<br><br>RESULTS: The reference genotypes of 55 patients with 21-hydroxylase deficiency (21OHD) were established using the conventional method with multiplex ligation-dependent probe amplification (MLPA) and nested PCR. LRS using Flongle Flow Cell R9.4.1 yielded consistent results. Additionally, the recently updated LRS "duplex" analysis with Flongle flow cell R10.4.1 was tested to reveal an advantage of accurately sequencing a variant located on the homopolymer region. By introducing a barcode system, the cost was reduced to be comparable to that of conventional analysis. A novel single-nucleotide variation was discovered at the acceptor site of intron 7, c.940-1G > C. We also identified a subtype of the classical chimeric junction CH2, "CH2a," in the region from the latter part of intron 5 to exon 6.<br><br>CONCLUSION: We successfully established a novel low-cost and highly accurate LRS system for 21OHD genetic analysis. Our study provides insight into the feasibility of LRS for diagnosing 21OHD and other genetic diseases caused by structural rearrangements.},
}
@article {pmid37801368,
year = {2023},
author = {Esquivel, JF and Joyce, AL},
title = {Population genetics of Leptoglossus clypealis (Hemiptera: Coreidae) in the Western United States.},
journal = {Journal of economic entomology},
volume = {116},
number = {6},
pages = {2201-2206},
doi = {10.1093/jee/toad177},
pmid = {37801368},
issn = {1938-291X},
mesh = {Animals ; United States ; *Hemiptera/genetics ; *Heteroptera ; Genetics, Population ; DNA, Mitochondrial ; Texas ; Seeds ; },
abstract = {The leaffooted bug, Leptoglossus clypealis Heidemann, is a seed-feeding economic pest of crops including almonds and pistachios. The historical distribution of L. clypealis has been considered to be West of the Mississippi in the United States. L. clypealis was recently found in sorghum in the Coastal Bend of Texas, representing a new host record and new collection locality. This study investigated the genetic diversity of L. clypealis museum voucher samples from the Western United States (i.e., Texas, California, and Idaho) collected from 1994 to 2019, including the L. clypealis samples from the Coastal Bend. Eleven new sequences were obtained. Sample sequences were compared with public sequences of L. clypealis from the Western United States. The mitochondrial DNA cytochrome oxidase 1 (mtDNA COI) barcode gene region revealed differences among and within the collection regions. Texas, Idaho, and California all had samples with unique genotypes, and the combined dataset had a haplotype diversity of 1.0. The Texas specimens recently collected in the Coastal Bend did not match genotypes from California or Idaho, and it is unlikely they were recently introduced. Overall, L. clypealis from Texas, Idaho, and California have a high level of genetic diversity, and the 3 regions appear to be within the native range of the species.},
}
@article {pmid37798751,
year = {2023},
author = {Han, R and Qi, J and Xue, Y and Sun, X and Zhang, F and Gao, X and Li, G},
title = {HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {222},
pmid = {37798751},
issn = {1474-760X},
mesh = {Sequence Analysis, DNA/methods ; *Nanopore Sequencing ; Algorithms ; DNA ; High-Throughput Nucleotide Sequencing/methods ; *Nanopores ; },
abstract = {DNA barcodes enable Oxford Nanopore sequencing to sequence multiple barcoded DNA samples on a single flow cell. DNA sequences with the same barcode need to be grouped together through demultiplexing. As the number of samples increases, accurate demultiplexing becomes difficult. We introduce HycDemux, which incorporates a GPU-parallelized hybrid clustering algorithm that uses nanopore signals and DNA sequences for accurate data clustering, alongside a voting-based module to finalize the demultiplexing results. Comprehensive experiments demonstrate that our approach outperforms unsupervised tools in short sequence fragment clustering and performs more robustly than current state-of-the-art demultiplexing tools for complex multi-sample sequencing data.},
}
@article {pmid37794632,
year = {2023},
author = {Wu, B and Zheng, M and Zhuo, MP and Zhao, YD and Su, Y and Fan, JZ and Luo, P and Gu, LF and Che, ZL and Wang, ZS and Wang, XD},
title = {Organic Bilayer Heterostructures with Built-In Exciton Conversion for 2D Photonic Encryption.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {35},
number = {51},
pages = {e2306541},
doi = {10.1002/adma.202306541},
pmid = {37794632},
issn = {1521-4095},
support = {21971185//National Natural Science Foundation of China/ ; 52203234//National Natural Science Foundation of China/ ; 52173177//National Natural Science Foundation of China/ ; BK20221362//Natural Science Foundation of Jiangsu Province/ ; TJ-2022-002//Science and Technology Support Program of Jiangsu Province/ ; J202310//Textile Vision Basic Research Program/ ; },
abstract = {Organic multilayer heterostructures with accurate spatial organization demonstrate strong light-matter interaction from excitonic responses and efficient carrier transfer across heterojunction interfaces, which are considered as promising candidates toward advanced optoelectronics. However, the precise regulation of the heterojunction surface area for finely adjusting exciton conversion and energy transfer is still formidable. Herein, organic bilayer heterostructures (OBHs) with controlled face-to-face heterojunction via a stepwise seeded growth strategy, which is favorable for efficient exciton propagation and conversion of optical interconnects are designed and synthesized. Notably, the relative position and overlap length ratio of component microwires (LDSA /LBPEA = 0.39-1.15) in OBHs are accurately regulated by modulating the crystallization time of seeded crystals, resulting into a tailored heterojunction surface area (R = Loverlap /LBPEA = 37.6%-65.3%). These as-prepared OBHs present the excitation position-dependent waveguide behaviors for optical outcoupling characteristics with tunable emission colors and intensities, which are applied into two-dimensional (2D) photonic barcodes. This strategy opens a versatile avenue to purposely design OBHs with tailored heterojunctions for efficient energy transfer and exciton conversion, facilitating the application possibilities of advanced integrated optoelectronics.},
}
@article {pmid37792944,
year = {2023},
author = {Lei, Y and Fei, X and Ding, Y and Zhang, J and Zhang, G and Dong, L and Song, J and Zhuo, Y and Xue, W and Zhang, P and Yang, C},
title = {Simultaneous subset tracing and miRNA profiling of tumor-derived exosomes via dual-surface-protein orthogonal barcoding.},
journal = {Science advances},
volume = {9},
number = {40},
pages = {eadi1556},
pmid = {37792944},
issn = {2375-2548},
mesh = {Male ; Humans ; *Exosomes/genetics ; Membrane Proteins ; *MicroRNAs/genetics ; *Prostatic Neoplasms/diagnosis/genetics/pathology ; Biomarkers, Tumor/genetics ; },
abstract = {The clinical potential of miRNA-based liquid biopsy has been largely limited by the heterogeneous sources in plasma and tedious assay processes. Here, we develop a precise and robust one-pot assay called dual-surface-protein-guided orthogonal recognition of tumor-derived exosomes and in situ profiling of microRNAs (SORTER) to detect tumor-derived exosomal miRNAs and enhance the diagnostic accuracy of prostate cancer (PCa). The SORTER uses two allosteric aptamers against exosomal marker CD63 and tumor marker EpCAM to create an orthogonal labeling barcode and achieve selective sorting of tumor-specific exosome subtypes. Furthermore, the labeled barcode on tumor-derived exosomes initiated targeted membrane fusion with liposome probes to import miRNA detection reagents, enabling in situ sensitive profiling of tumor-derived exosomal miRNAs. With a signature of six miRNAs, SORTER differentiated PCa and benign prostatic hyperplasia with an accuracy of 100%. Notably, the diagnostic accuracy reached 90.6% in the classification of metastatic and nonmetastatic PCa. We envision that the SORTER will promote the clinical adaptability of miRNA-based liquid biopsy.},
}
@article {pmid37792910,
year = {2023},
author = {Bachoo, T and Bolton, JJ and Macey, BM and Kandjengo, L and Reddy, MM},
title = {Resolving the identity of commercially cultivated Ulva (Ulvaceae, Chlorophyta) in integrated seaweed-abalone aquaculture farms in South Africa.},
journal = {Journal of phycology},
volume = {59},
number = {6},
pages = {1272-1283},
doi = {10.1111/jpy.13391},
pmid = {37792910},
issn = {1529-8817},
mesh = {*Ulva/genetics ; *Seaweed/genetics ; South Africa ; *Chlorophyta ; Aquaculture ; },
abstract = {Species of Ulva have a wide range of commercial applications and are increasingly being recognized as promising candidates for integrated aquaculture. In South Africa, Ulva has been commercially cultivated in integrated seaweed-abalone aquaculture farms since 2002, with more than 2000 tonnes of biomass cultivated per annum in land-based paddle raceways. However, the identity of the species of Ulva grown on these farms remains uncertain. We therefore characterized samples of Ulva cultivated in five integrated multi-trophic aquaculture farms (IMTA) across a wide geographical range and compared them with foliose Ulva specimens from neighboring seashores. The molecular markers employed for this study were the chloroplast-encoded Ribulose-1,5-bisphosphate carboxylase oxygenase (rbcL), the Internal Transcribed Spacer (ITS) of the nuclear, and the chloroplast elongation factor tufA. All currently cultivated specimens of Ulva were molecularly resolved as a single species, U. lacinulata. The same species has been cultivated for over a decade, although a few specimens of two other species were also present in early South African IMTA systems. The name Ulva uncialis is adopted for the Ulva "Species A" by Fort et al. (2021), Molecular Ecology Resources, 22, 86) significantly extending the distribution range for this species. A comparison with wild Ulva on seashores close to the farms resulted in five new distribution records for South Africa (U. lacinulata, U. ohnoi, U. australis, U. stenophylloides, and U. aragoënsis), the first report of a foliose form of U. compressa in the region, and one new distribution record for Namibia (U. australis). This study reiterates the need for DNA confirmation, especially when identifying morphologically simple macroalgae with potential commercial applications.},
}
@article {pmid37789194,
year = {2023},
author = {Galeano Niño, JL and Wu, H and LaCourse, KD and Srinivasan, H and Fitzgibbon, M and Minot, SS and Sather, C and Johnston, CD and Bullman, S},
title = {INVADEseq to identify cell-adherent or invasive bacteria and the associated host transcriptome at single-cell-level resolution.},
journal = {Nature protocols},
volume = {18},
number = {11},
pages = {3355-3389},
pmid = {37789194},
issn = {1750-2799},
support = {R01 DE027850/DE/NIDCR NIH HHS/United States ; P30 CA015704/CA/NCI NIH HHS/United States ; S10 OD028685/OD/NIH HHS/United States ; T32 CA080416/CA/NCI NIH HHS/United States ; R00 CA229984/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Humans ; Transcriptome ; Bacteria/genetics ; Genomics/methods ; *Neoplasms/pathology ; *Microbiota/genetics ; Mammals/genetics ; Tumor Microenvironment ; },
abstract = {Single-cell RNA sequencing (scRNAseq) technologies have been beneficial in revealing and describing cellular heterogeneity within mammalian tissues, including solid tumors. However, many of these techniques apply poly(A) selection of RNA, and thus have primarily focused on determining the gene signatures of eukaryotic cellular components of the tumor microenvironment. Microbiome analysis has revealed the presence of microbial ecosystems, including bacteria and fungi, within human tumor tissues from major cancer types. Imaging data have revealed that intratumoral bacteria may be located within epithelial and immune cell types. However, as bacterial RNA typically lacks a poly(A) tail, standard scRNAseq approaches have limited ability to capture this microbial component of the tumor microenvironment. To overcome this, we describe the invasion-adhesion-directed expression sequencing (INVADEseq) approach, whereby we adapt 10x Genomics 5' scRNAseq protocol by introducing a primer that targets a conserved region of the bacterial 16S ribosomal RNA gene in addition to the standard primer for eukaryotic poly(A) RNA selection. This 'add-on' approach enables the generation of eukaryotic and bacterial DNA libraries at eukaryotic single-cell level resolution, utilizing the 10x barcode to identify single cells with intracellular bacteria. The INVADEseq method takes 30 h to complete, including tissue processing, sequencing and computational analysis. As an output, INVADEseq has shown to be a reliable tool in human cancer cell lines and patient tumor specimens by detecting the proportion of human cells that harbor bacteria and the identities of human cells and intracellular bacteria, along with identifying host transcriptional programs that are modulated on the basis of associated bacteria.},
}
@article {pmid37789061,
year = {2023},
author = {Pardi-Tóth, V and Kuki, &#xc1; and Kordován, M&#xc1; and Róth, G and Nagy, L and Zsuga, M and Nagy, T and Kéki, S},
title = {Molecular data storage using direct analysis in real time (DART) ionization mass spectrometry for decoding.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {16576},
pmid = {37789061},
issn = {2045-2322},
support = {TKP2021-NKTA-34//National Research, Development and Innovation Fund of Hungary/ ; TKP2021-NKTA-34//National Research, Development and Innovation Fund of Hungary/ ; TKP2021-NKTA-34//National Research, Development and Innovation Fund of Hungary/ ; TKP2021-NKTA-34//National Research, Development and Innovation Fund of Hungary/ ; TKP2021-NKTA-34//National Research, Development and Innovation Fund of Hungary/ ; TKP2021-NKTA-34//National Research, Development and Innovation Fund of Hungary/ ; TKP2021-NKTA-34//National Research, Development and Innovation Fund of Hungary/ ; TKP2021-NKTA-34//National Research, Development and Innovation Fund of Hungary/ ; FK-132385//National Research, Development and Innovation Office/ ; FK-132385//National Research, Development and Innovation Office/ ; FK-132385//National Research, Development and Innovation Office/ ; FK-132385//National Research, Development and Innovation Office/ ; FK-132385//National Research, Development and Innovation Office/ ; FK-132385//National Research, Development and Innovation Office/ ; FK-132385//National Research, Development and Innovation Office/ ; FK-132385//National Research, Development and Innovation Office/ ; GINOP-2.3.3-15-2016-00021//European Union and the European Regional Development Fund/ ; GINOP-2.3.3-15-2016-00021//European Union and the European Regional Development Fund/ ; GINOP-2.3.3-15-2016-00021//European Union and the European Regional Development Fund/ ; GINOP-2.3.3-15-2016-00021//European Union and the European Regional Development Fund/ ; GINOP-2.3.3-15-2016-00021//European Union and the European Regional Development Fund/ ; GINOP-2.3.3-15-2016-00021//European Union and the European Regional Development Fund/ ; GINOP-2.3.3-15-2016-00021//European Union and the European Regional Development Fund/ ; GINOP-2.3.3-15-2016-00021//European Union and the European Regional Development Fund/ ; BO/00212/20/7//Hungarian Academy of Sciences/ ; &#xda;NKP-22-05-DE-426//National Research, Development and Innovation Fund/ ; },
abstract = {Molecular data storage is becoming a viable alternative to traditional information storage systems. Here, we propose a method where the presence or absence of a given molecule in a mixture of compounds represents a bit of information. As a novel approach, direct analysis in real time (DART) ionization mass spectrometry is used to recover and decode the information stored at the molecular level. Nicotinic acid derivatives were synthesized and used as the 'bit compounds'. Their volatility and ease of ionization make these molecules especially suitable for DART-MS detection. The application of DART-MS as a method with an ambient ionization technique, enables the re-reading of digital chemical codes embedded in the material of ordinary objects. Our method is designed to store and read back short pieces of digital information, up to several hundred bits. These codes can have the function of barcodes or QR codes, as shown in our proof-of-principle applications. First, modelling a QR code as a link to our university's website, three solutions were prepared, each representing 22 bits. Proceeding further, the bit compounds were incorporated into a polymer matrix that is suitable for 3D printing, and a toy ship was created with a hidden barcode. In addition, decoding software was developed to process the DART-MS spectra. The nicotinic acid components representing the bits dominated the DART-MS spectra and error-free decoding was achieved.},
}
@article {pmid37788253,
year = {2023},
author = {Boehm, JT and Bovee, E and Harris, SE and Eddins, K and Akahoho, I and Foster, M and Pell, SK and Hickerson, MJ and Amato, G and DeSalle, R and Waldman, J},
title = {The United States dried seahorse trade: A comparison of traditional Chinese medicine and ecommerce-curio markets using molecular identification.},
journal = {PloS one},
volume = {18},
number = {10},
pages = {e0291874},
pmid = {37788253},
issn = {1932-6203},
mesh = {Humans ; Animals ; *Smegmamorpha/genetics ; Medicine, Chinese Traditional ; Commerce ; Internationality ; Endangered Species ; },
abstract = {Tens of millions of dried seahorses (genus Hippocampus) are traded annually, and the pressure from this trade along with their life history traits (involved parental care and small migration distances and home ranges) has led to near global population declines. This and other forms of overexploitation have led to all seahorse species being listed in Appendix II under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). The signatory nations of CITES recommended a 10-cm size limit of seahorses to ensure harvested individuals have reached reproductive maturity, and have thus had the chance to produce offspring, to maintain a more sustainable global seahorse fishery. We assessed adherence to CITES recommendations using DNA barcoding and size measurements to compare two prominent U.S. dried seahorse markets: (1) traditional Chinese medicine (TCM), and (2) non-medicinal ecommerce and coastal curio (ECC). We also estimated U.S. import abundance from CITES records. Of the nine species identified among all samples (n = 532), eight were found in the TCM trade (n = 168); composed mostly (75%) of the Indo-Pacific species Hippocampus trimaculatus, and Hippocampus spinosissimus, and the Latin American Hippocampus ingens. In contrast, ECC samples (n = 344) included 5 species, primarily juvenile Indo-Pacific Hippocampus kuda (51.5%) and the western Atlantic Hippocampus zosterae (40.7). The majority of TCM samples (85.7%) met the CITES size recommendation, in contrast to 4.8% of ECC samples. These results suggest non-size discriminatory bycatch is the most likely source of imported ECC specimens. In addition, CITES records indicate that approximately 602,275 dried specimens were imported into the U.S. from 2004-2020, but the exact species composition remains unknown as many U.S. imports records list one species or Hippocampus spp. from confiscated shipments due to difficulties in morphological identification and large numbers of individuals per shipment. Molecular identification was used to identify the species composition of confiscated shipment imports containing undesignated species, and similar to TCM, found H. trimaculatus and H. spinosissimus the most abundant. By combining DNA barcoding, size comparisons, and CITES database records, these results provide an important glimpse into the two primary dried U.S. seahorse end-markets, and may further inform the conservation status of several Hippocampus species.},
}
@article {pmid37781972,
year = {2023},
author = {Lu, X and Zhang, D and Chen, X and Yao, C and Li, Z},
title = {Interfacial Profiling of MicroRNAs at Patterned Nanogaps for an Integrated Microfluidic-SERS Liquid Biopsy.},
journal = {Analytical chemistry},
volume = {95},
number = {44},
pages = {16049-16053},
doi = {10.1021/acs.analchem.3c02945},
pmid = {37781972},
issn = {1520-6882},
mesh = {Humans ; *MicroRNAs ; Microfluidics ; Spectrum Analysis, Raman/methods ; *Nanotubes ; Prognosis ; *Neoplasms ; *Metal Nanoparticles ; },
abstract = {A versatile microfluidic-SERS barcoding system is developed for sensitive and multiplexed imaging of circulating microRNAs through interfacial probing of encoded nanorod aggregates at diverse patterned nanogaps. The use of a single-layer, vertically oriented nanorod array creates a plasmonic coupling-based electromagnetic field with enormously enhanced Raman outputs. The introduction of the herringbone micromixer with circulated microflow sampling accelerates the hybridization and capture of nanorod aggregates on the plasmonic substrate. The method is able to achieve ideal sensitivities at subfemtomolar levels for four miRNAs, with multiplexed assay capability for an integrated liquid biopsy. The on-chip digital profiling of serum miRNAs in mapping and barcoding formats enable both clear discrimination of untreated cancer patients from the healthy cohort and precise classification of tumor stages, metastatic conditions, and subtypes, with an overall accuracy of 94%. The SERS-based microfluidic barcoding system therefore holds great promise in early cancer screening, diagnosis, and prognosis.},
}
@article {pmid37781910,
year = {2023},
author = {Větrovský, T and Kolaříková, Z and Lepinay, C and Awokunle Hollá, S and Davison, J and Fleyberková, A and Gromyko, A and Jelínková, B and Kolařík, M and Krüger, M and Lejsková, R and Michalčíková, L and Michalová, T and Moora, M and Moravcová, A and Moulíková, &#x160; and Odriozola, I and Öpik, M and Pappová, M and Piché-Choquette, S and Skřivánek, J and Vlk, L and Zobel, M and Baldrian, P and Kohout, P},
title = {GlobalAMFungi: a global database of arbuscular mycorrhizal fungal occurrences from high-throughput sequencing metabarcoding studies.},
journal = {The New phytologist},
volume = {240},
number = {5},
pages = {2151-2163},
doi = {10.1111/nph.19283},
pmid = {37781910},
issn = {1469-8137},
support = {LM2023055//ELIXIR CZ Research Infrastructure Project (MEYS Grant)/ ; PRG1065//Estonian Research Council/ ; PRG1789//Estonian Research Council/ ; 21-17749S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; RVO 67985939//Institute of Botany of the Czech Academy of Sciences/ ; //European Regional Development Fund/ ; },
mesh = {*Mycorrhizae/genetics ; Ecosystem ; Symbiosis ; Plants/genetics ; High-Throughput Nucleotide Sequencing ; Soil Microbiology ; },
abstract = {Arbuscular mycorrhizal (AM) fungi are crucial mutualistic symbionts of the majority of plant species, with essential roles in plant nutrient uptake and stress mitigation. The importance of AM fungi in ecosystems contrasts with our limited understanding of the patterns of AM fungal biogeography and the environmental factors that drive those patterns. This article presents a release of a newly developed global AM fungal dataset (GlobalAMFungi database, https://globalamfungi.com) that aims to reduce this knowledge gap. It contains almost 50 million observations of Glomeromycotinian AM fungal amplicon DNA sequences across almost 8500 samples with geographical locations and additional metadata obtained from 100 original studies. The GlobalAMFungi database is built on sequencing data originating from AM fungal taxon barcoding regions in: i) the small subunit rRNA (SSU) gene; ii) the internal transcribed spacer 2 (ITS2) region; and iii) the large subunit rRNA (LSU) gene. The GlobalAMFungi database is an open source and open access initiative that compiles the most comprehensive atlas of AM fungal distribution. It is designed as a permanent effort that will be continuously updated by its creators and through the collaboration of the scientific community. This study also documented applicability of the dataset to better understand ecology of AM fungal taxa.},
}
@article {pmid37780891,
year = {2023},
author = {Yeom, J and Lee, W},
title = {A new species of Rhyncholagena Lang, 1944 (Copepoda, Harpacticoida, Miraciidae) from Palau.},
journal = {ZooKeys},
volume = {1180},
number = {},
pages = {181-199},
pmid = {37780891},
issn = {1313-2989},
abstract = {A new species of Miraciidae Dana, 1846, Rhyncholagenacuspissp. nov., was described from Palau. Morphological descriptions and gene fragment sequence barcoding were performed on the 11[th] species of Rhyncholagena Lang, 1944 collected from sandy sediment samples in the subtidal zone of the Philippine Sea, Palau. Morphological characteristics were compared and an updated identification key was provided. A new species, Rhyncholagenacuspissp. nov., was found to be morphologically similar to Rhyncholagenalittoralis Por, 1967 and R.bermudensis Malt, 1990. This is the first record of the genus Rhyncholagena in Palau. The study provides basic data for future studies and highlights the need for continued exploration of marine biodiversity in Palau and other regions.},
}
@article {pmid37780373,
year = {2023},
author = {Kerschbaumer, M and Schäffer, S and Pfingstl, T},
title = {Claw shape variation in oribatid mites of the genera Carabodes and Caleremaeus: exploring the interplay of habitat, ecology and phylogenetics.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16021},
pmid = {37780373},
issn = {2167-8359},
mesh = {Animals ; Phylogeny ; *Mites/genetics ; Ecosystem ; Environment ; Soil ; },
abstract = {BACKGROUND: Claws are a commonly observed biological adaptation across a wide range of animal groups. They serve different functions and their link to evolution is challenging to analyze. While there are many studies on the comparative anatomy and morphology of claws in reptiles, birds and several arthropods, knowledge about claws of soil-living oribatid mites, is still limited. Recent research on intertidal oribatid mites has shown that claw shape is strongly correlated with microhabitat and is subject to ecological selective pressures. However, the selective constraints shaping claws in terrestrial oribatid mites are still unknown.<br><br>METHODS: In this study, 300 specimens from 12 different species and two genera were examined. Geometric morphometrics were used to quantify claw length and curvature, and to analyze two-dimensional claw shape. In combination with molecular phylogenetic analyses of investigated populations phylogenetic signal was quantified within genera using Blomberg's K and random replicates. Additionally, ecological information on the investigated species was gathered from previous studies and compiled into tables.<br><br>RESULTS: The claw shapes of Carabodes species vary moderately, with the three species C. reticulatus, C. rugosior and C. tenuis deviating the most from the others. These three species are only found in a small number of habitats, which may require a more specialized claw shape. Our results show that there is a phylogenetic influence on claw shape in Carabodes but not in Caleremaeus. Additionally, habitat specificity and lifestyle were found to have ecological impact on claw shape in both genera. The present results demonstrate that characteristics of the claws of terrestrial oribatid mites are correlated with ecology, but this correlation is apparently weaker than in intertidal oribatid mites that are prone to strong external forces.},
}
@article {pmid37779245,
year = {2023},
author = {Jing, K and Xu, Y and Yang, Y and Yin, P and Ning, D and Huang, G and Deng, Y and Chen, G and Li, G and Tian, SZ and Zheng, M},
title = {ScSmOP: a universal computational pipeline for single-cell single-molecule multiomics data analysis.},
journal = {Briefings in bioinformatics},
volume = {24},
number = {6},
pages = {},
doi = {10.1093/bib/bbad343},
pmid = {37779245},
issn = {1477-4054},
mesh = {*Multiomics ; Reproducibility of Results ; *Genomics ; Chromatin/genetics ; Data Analysis ; },
abstract = {Single-cell multiomics techniques have been widely applied to detect the key signature of cells. These methods have achieved a single-molecule resolution and can even reveal spatial localization. These emerging methods provide insights elucidating the features of genomic, epigenomic and transcriptomic heterogeneity in individual cells. However, they have given rise to new computational challenges in data processing. Here, we describe Single-cell Single-molecule multiple Omics Pipeline (ScSmOP), a universal pipeline for barcode-indexed single-cell single-molecule multiomics data analysis. Essentially, the C language is utilized in ScSmOP to set up spaced-seed hash table-based algorithms for barcode identification according to ligation-based barcoding data and synthesis-based barcoding data, followed by data mapping and deconvolution. We demonstrate high reproducibility of data processing between ScSmOP and published pipelines in comprehensive analyses of single-cell omics data (scRNA-seq, scATAC-seq, scARC-seq), single-molecule chromatin interaction data (ChIA-Drop, SPRITE, RD-SPRITE), single-cell single-molecule chromatin interaction data (scSPRITE) and spatial transcriptomic data from various cell types and species. Additionally, ScSmOP shows more rapid performance and is a versatile, efficient, easy-to-use and robust pipeline for single-cell single-molecule multiomics data analysis.},
}
@article {pmid37779129,
year = {2023},
author = {Yan, M and Dong, S and Gong, Q and Xu, Q and Ge, Y},
title = {Comparative chloroplast genome analysis of four Polygonatum species insights into DNA barcoding, evolution, and phylogeny.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {16495},
pmid = {37779129},
issn = {2045-2322},
mesh = {Phylogeny ; *Polygonatum/genetics ; DNA Barcoding, Taxonomic ; *Genome, Chloroplast/genetics ; DNA ; *Liliaceae ; Chloroplasts/genetics ; },
abstract = {The Polygonatum genus represents a perennial herb with the Liliaceae family, boasting substantial economic and medicinal significance. The majority of Polygonatum plants exhibit notable similarity while lacking distinctive identifying characteristics, thus resulting in the proliferation of adulterated medicinal materials within the market. Within this study, we conducted an in-depth analysis of the complete chloroplast (cp) genomes of four Polygonatum plants and compared them with four closely akin species. The primary objectives were to unveil structural variations, species divergence, and the phylogenetic interrelations among taxa. The cp genomes of the four Polygonatum species were typified by a conventional quadripartite structure, incorporating a large single copy region (LSC), a small single copy region (SSC), and a pair of inverted repeat regions. In total, we annotated a range of 131 to 133 genes, encompassing 84 to 86 protein-coding genes, 38 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 0 to 2 pseudogenes (ycf1, infA). Our comparative analyses unequivocally revealed a remarkable consistency in gene order and GC content within the Polygonatum genus. Furthermore, we predicted a potential 59 to 64 RNA editing sites distributed across 22 protein-coding genes, with the ndhB gene exhibiting the most prominent propensity for RNA editing sites, boasting a tally of 15 sites. Notably, six regions of substantial potential variability were ascertained, characterized by elevated Pi values. Noteworthy, molecular markers for species identification, population genetic scrutiny, and phylogenetic investigations within the genus were identified in the form of the psaJ-rpl33 and trnS + trnT-psaD barcodes. The resultant phylogenetic tree unequivocally depicted the formation of a monophyletic clade comprising species within the evolutionary framework of Liliaceae, demonstrating closer evolutionary affinities with Maianthemum, Dracaeneae, and Asparageae. This comprehensive compendium of findings collectively contributes to the advancement of molecular species identification, elucidation of phylogenetic interrelationships, and the establishment of DNA barcodes tailored to the Polygonatum species.},
}
@article {pmid37776855,
year = {2023},
author = {Jayaraman, S and Montagne, JM and Nirschl, TR and Marcisak, E and Johnson, J and Huff, A and Hsiao, MH and Nauroth, J and Heumann, T and Zarif, JC and Jaffee, EM and Azad, N and Fertig, EJ and Zaidi, N and Larman, HB},
title = {Barcoding intracellular reverse transcription enables high-throughput phenotype-coupled T cell receptor analyses.},
journal = {Cell reports methods},
volume = {3},
number = {10},
pages = {100600},
pmid = {37776855},
issn = {2667-2375},
support = {F32 CA271470/CA/NCI NIH HHS/United States ; T32 GM136577/GM/NIGMS NIH HHS/United States ; K08 CA248624/CA/NCI NIH HHS/United States ; P01 CA247886/CA/NCI NIH HHS/United States ; T32 CA009110/CA/NCI NIH HHS/United States ; U24 AI118633/AI/NIAID NIH HHS/United States ; K22 CA237623/CA/NCI NIH HHS/United States ; U01 CA253403/CA/NCI NIH HHS/United States ; F31 CA250135/CA/NCI NIH HHS/United States ; R01 CA197296/CA/NCI NIH HHS/United States ; P50 CA062924/CA/NCI NIH HHS/United States ; P30 CA006973/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Leukocytes, Mononuclear ; *Reverse Transcription ; CD8-Positive T-Lymphocytes ; Receptors, Antigen, T-Cell/genetics ; Receptors, Antigen, T-Cell, alpha-beta/genetics ; },
abstract = {Assays linking cellular phenotypes with T cell or B cell antigen receptor sequences are crucial for characterizing adaptive immune responses. Existing methodologies are limited by low sample throughput and high cost. Here, we present INtraCEllular Reverse Transcription with Sorting and sequencing (INCERTS), an approach that combines molecular indexing of receptor repertoires within intact cells and fluorescence-activated cell sorting (FACS). We demonstrate that INCERTS enables efficient processing of millions of cells from pooled human peripheral blood mononuclear cell (PBMC) samples while retaining robust association between T cell receptor (TCR) sequences and cellular phenotypes. We used INCERTS to discover antigen-specific TCRs from patients with cancer immunized with a novel mutant KRAS peptide vaccine. After ex vivo stimulation, 28 uniquely barcoded samples were pooled prior to FACS into peptide-reactive and non-reactive CD4[+] and CD8[+] populations. Combining complementary patient-matched single-cell RNA sequencing (scRNA-seq) data enabled retrieval of full-length, paired TCR alpha and beta chain sequences for future validation of therapeutic utility.},
}
@article {pmid37776823,
year = {2023},
author = {Wang, G and Bai, X and Ren, Y and Su, Y and Han, J},
title = {Development of nucleotide signatures for common poisonous organisms provides a new strategy for food poisoning diagnosis.},
journal = {Ecotoxicology and environmental safety},
volume = {265},
number = {},
pages = {115529},
doi = {10.1016/j.ecoenv.2023.115529},
pmid = {37776823},
issn = {1090-2414},
mesh = {Animals ; DNA Barcoding, Taxonomic/methods ; *Poisons ; DNA/genetics ; Biomarkers ; *Foodborne Diseases ; Nucleotides/genetics ; },
abstract = {DNA barcoding is widely used in toxic species authentication, but due to serious DNA degradation of forensic materials, the application of full-length barcode sequences in food poisoning diagnosis is greatly limited. Nucleotide signature, a shorter specific molecular marker, derived from traditional DNA barcoding has been proposed as an emerging tool of toxic species detection in deeply processed materials. In this study, to resolve the frequent food poisoning accidents with unknown origin, we envisioned developing a nucleotide signature data set of common poisonous organisms and combining high-throughput sequencing (HTS) to reveal the poisoning cause. Ninety-three individuals and 1093 DNA barcode sequences of twelve common poisonous plants, fish, mushrooms and their related species were collected. Through sequence alignment and screening, the nucleotide signatures were respectively developed and validated as their specific molecular markers. The sequence length varied from 19 bp to 38 bp. These fragments were conserved within the same species or genera, and the specificity between related species has been also demonstrated. To further evaluate the application potential of nucleotide signature in forensic diagnosis, simulated forensic specimens (SFS) containing different poisonous ingredients were sequenced by HTS with PCR-free libraries. As a result, the nucleotide signature was successfully captured from original HTS data without assembly and annotation, accompanied by a high detection sensitivity of 0.1 ng/µl in mixture system. Therefore, this method was suitable for the assay of forensic materials with serious DNA degradation. The present study undoubtedly provides a new perspective and strong support for the detection of toxic ingredients and the diagnosis of food poisoning.},
}
@article {pmid37776039,
year = {2023},
author = {Wildermuth, B and Seifert, CL and Husemann, M and Schuldt, A},
title = {Metabarcoding reveals that mixed forests mitigate negative effects of non-native trees on canopy arthropod diversity.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {33},
number = {8},
pages = {e2921},
doi = {10.1002/eap.2921},
pmid = {37776039},
issn = {1051-0761},
support = {316045089/GRK 2300//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; *Arthropods ; Biodiversity ; Germany ; Herbivory ; *Picea ; *Tracheophyta ; *Fagus ; *Pseudotsuga ; },
abstract = {Averting climate change-induced forest diebacks increasingly relies on tree species planted outside of their natural range and on the addition of non-native tree species to mixed-species forests. However, the consequences of such changes for associated biodiversity remain poorly understood, especially for the forest canopy as a largely understudied forest stratum. Here, we used flight interception traps and a metabarcoding approach to study the taxonomic and functional (trophic guilds) composition and taxon richness of canopy arthropods. We sampled 15 monospecific and mixed stands of native European beech, native Norway spruce-planted outside its natural range-and non-native Douglas fir in northwest Germany. We found that the diversity of arthropods was lower in non-native Douglas fir compared with native beech stands. Taxon richness of herbivores was reduced by both conifer species. Other functional guilds, however, were not affected by stand type. Arthropod composition differed strongly between native broadleaved beech and monospecific coniferous (native spruce or non-native Douglas fir) stands, with less pronounced differences between the native and non-native conifers. Beech-conifer mixtures consistently hosted intermediate arthropod diversity and community composition compared with the respective monospecific stands. Moreover, arthropod diversity had a positive relationship with the number of canopy microhabitats. Our study shows that considering arthropod taxa of multiple functional groups reveals the multifaceted impact of non-native tree species on forest canopy arthropod communities. Contrasting with previous studies that primarily focused on the forest floor, we found that native beech hosts a rich diversity of arthropods, compared with lower diversity and distinct communities in economically attractive, and especially in non-native, conifers with few canopy microhabitats. Broadleaf-conifer mixtures did not perform better than native beech stands, but mitigated the negative effects of conifers, making such mixtures a compromise to foster both forest-associated diversity and economic yield.},
}
@article {pmid37775594,
year = {2024},
author = {Graham, KA and Gomez, J and Primm, TP and Houston, R},
title = {Comparison of nine extraction methods for bacterial identification using the ONT MinION sequencer.},
journal = {International journal of legal medicine},
volume = {138},
number = {2},
pages = {351-360},
pmid = {37775594},
issn = {1437-1596},
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Nanopores ; Bacteria/genetics ; DNA ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; },
abstract = {The Anthrax mailings bioterrorism attack in 2001 revealed the need for universal and rapid microbial forensic analyses on unknown biological evidence. However, the gold standard for bacterial identification includes culturing isolates, which is laborious. Molecular approaches for bacterial identification revolve around 16S ribosomal gene sequencing using Sanger or next generation sequencing (NGS) platforms, but these techniques are laboratory-based and can also be time-consuming. The Oxford Nanopore Technologies (ONT) MinION sequencer can generate long read lengths that span the entire bacterial 16S rRNA gene and accurately identify the species level. This platform can be used in the field, allowing on-site evidence analysis. However, it requires higher quantities of pure DNA compared to other sequencing platforms; thus, the extraction method for bacterial DNA is critical for downstream analysis, which to date are tailored toward a priori knowledge of the species' taxonomic grouping. During an attack, the investigative team may not know what species they are handling; therefore, identifying an extraction method that can handle all bacterial groups and generate clean DNA for the MinION is useful for microbial forensic analysis. The purpose of this study was to identify a "universal" extraction method that can be coupled with ONT MinION sequencing for use in forensic situations for rapid identification. It also evaluated the cloud-based data analysis software provided by ONT, EPI2ME. No "universal" extraction method was identified as optimal for downstream MinION sequencing. However, the DNeasy PowerSoil Kit and Noda et al. Chelex-100 method gave comparable sequencing results and could be used as rapid extraction techniques. This study showed that the ONT 16S Barcoding Kit 1-24 coupled with the 16S FASTQ workflow might not be the best for use in forensic situations where species-level identification needs to be obtained, as most alignments were approximately 89% accurate. In all seven test organisms and nine extraction methods, accurate species identification was only obtained in 63% of the cases.},
}
@article {pmid37773460,
year = {2023},
author = {Rodrigues, BL and Brilhante, AF and de Souza Pinto, I and Galati, EAB},
title = {Trichophoromyia auraensis: evidence for cryptic species and first record in the state of Maranhão, Brazil.},
journal = {Parasitology research},
volume = {122},
number = {12},
pages = {2933-2944},
pmid = {37773460},
issn = {1432-1955},
mesh = {Animals ; Brazil/epidemiology ; Phylogeny ; *Psychodidae/genetics ; *Leishmania/genetics ; *Phlebotomus/genetics ; DNA Barcoding, Taxonomic ; },
abstract = {Trichophoromyia auraensis (Mangabeira, 1942) (Diptera, Psychodidae, Phlebotominae) has a wide geographic distribution in the western region of the Amazon biome, where it is a putative Leishmania vector. Here, we reported for the first time a population of this species in the Brazilian state of Maranhão, in the eastern Amazon, from which we DNA-barcoded and compared with previously processed specimens from Acre State, in the western Amazon. For this, we analyzed the DNA barcoding fragment (658 bp) of the mitochondrial cytochrome c oxidase subunit I (COI) gene and the nuclear internal transcribed spacer 2 (ITS2) of Trichophoromyia species using phylogenetic gene trees, and species delimitation algorithms. The analyses of COI barcodes showed high values of genetic distance (mean K2P = 5.17) and well-supported clades/MOTUs for the eastern and western populations of T. auraensis, which may indicate a possible complex of cryptic species. The western population of this taxon merged with the close-related sand fly Trichophoromyia velezbernali Posada-López, Galvis and Galati, 2018 from Colombia, which may be associated with the recent speciation history and introgression between these populations. These evidences should be evaluated with a more comprehensive sampling in terms of analyzed populations and molecular markers.},
}
@article {pmid37772481,
year = {2024},
author = {Schwarz, E and Nass, O and Giocondo, V and Kozeniecki Schneider, ML},
title = {Identification of enteral nutrition errors in a single-center quality-improvement audit.},
journal = {Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition},
volume = {39},
number = {2},
pages = {470-474},
doi = {10.1002/ncp.11076},
pmid = {37772481},
issn = {1941-2452},
mesh = {Humans ; *Enteral Nutrition ; *Food, Formulated ; Health Facilities ; Prescriptions ; Quality Improvement ; },
abstract = {BACKGROUND: Enteral nutrition (EN) therapy is a multistep process including evaluation, prescription, procurement, dispensing, labeling, administration, and monitoring. EN therapy is prone to human errors, but these are poorly defined in the literature. The purpose of this study was to audit EN administration practices to quantify errors of execution and identify which components of the EN order were labeled, administered, or documented incorrectly.<br><br>METHODS: On 2 nonconsecutive days, we identified all hospitalized patients with active EN orders and prospectively collected the following information: EN formula hanging/documented, formula hang time, infusion rate/documented rate (continuous EN), infused volume and documented schedule (intermittent EN), and EN modular documentation. Mismatches to the EN order were considered errors. We reviewed 1 month of hospital EN-related safety events for comparison.<br><br>RESULTS: Of 1045 data points collected from 160 patients, we identified 275 errors of execution: 135 labeling errors and 140 administration errors. The most common were hang time >48&#x2009;h (85%), wrong number of modulars documented (48%), and wrong infusion rate (19%). We found one reported safety event (wrong formula delivered but not infused).<br><br>CONCLUSION: We identified a 15.9% error rate in EN order execution/documentation and 14% compliance with documentation of 48-h hang time. Errors (safety events) were grossly underreported. This highlighted several areas of opportunity to improve current EN use process, consistent with previous research on EN and oral nutrition supplement administration. Based on our findings, we plan to recommend implementation of EN barcoding at our institution, to model the familiar medication administration record.},
}
@article {pmid37772165,
year = {2023},
author = {Bisquert-Ribes, M and Rueda, J and Palero, F and Savatenalinton, S and Mesquita-Joanes, F},
title = {Integrative Taxonomy of Cyclocyprididae Kaufmann, 1900 (Ostracoda: Podocopa) with Description of a New Genus and Species.},
journal = {Zoological studies},
volume = {62},
number = {},
pages = {e40},
pmid = {37772165},
issn = {1810-522X},
abstract = {The two widespread ostracod genera Cypria Zenker, 1854 and Physocypria Vávra, 1897 are traditionally distinguished based on the presence or absence of tubercles on the right valve margin. However, recent research based on soft body parts has uncovered new cryptic genera within Cypria and Physocypria. Following this line of research, a new Cyclocyprididae genus and species, Vizcainocypria viator gen. nov. sp. nov., is here described from individuals collected in rice fields and wetlands of the Iberian Peninsula. Vizcainocypria is compared with Cypria, Physocypria, Dentocypria Savatenalinton, 2017, Keysercypria Karanovic, 2011, Brasilocypria Almeida et al., 2023, and Claudecypria Almeida et al., 2023 based on morphological evidence. Besides the presence or absence of tubercles on the right valve, these genera can be distinguished according to their mandibular palp, second thoracopod, caudal ramus, and male hemipenis. Molecular analyses using mitochondrial (COX1), and nuclear (28S rDNA) genes provide further support for the differentiation of Cypria, Dentocypria, Physocypria and Vizcainocypria gen. nov. The present study highlights the importance of using an integrative taxonomy approach, combining shell and soft-body parts morphology and molecular data, to characterize the rich diversity of freshwater ostracods.},
}
@article {pmid37770439,
year = {2023},
author = {Kuzdraliński, A and Miśkiewicz, M and Szczerba, H and Mazurczyk, W and Nivala, J and Księżopolski, B},
title = {Unlocking the potential of DNA-based tagging: current market solutions and expanding horizons.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {6052},
pmid = {37770439},
issn = {2041-1723},
abstract = {The commercialization of DNA tagging is a growing trend that demonstrates the increasing practicality of this novel approach. This interdisciplinary technology is based on the distinctive characteristics of DNA as a molecule that can remain stable in varying environmental conditions and store data following appropriate preparation. Moreover, newly developed technologies could simplify DNA synthesis and the encoding of data within DNA. The implementation of DNA tagging presents distinctive benefits in comparison to conventional labelling techniques, including universal product code (UPC) barcoding, radio-frequency identification (RFID), quick response (QR) codes, and Bluetooth technologies, by surmounting the limitations encountered by these systems. The discourse pertains to extant DNA-tagging mechanisms along with prospective implementations in a wide range of domains, including but not limited to art, the metaverse, forensics, wildlife monitoring, and the military. The potential of DNA labelling in various contexts underscores the importance of continued research and development in this rapidly evolving field.},
}
@article {pmid37770135,
year = {2023},
author = {Smith-Roe, SL and Hobbs, CA and Hull, V and Todd Auman, J and Recio, L and Streicker, MA and Rivas, MV and Pratt, GA and Lo, FY and Higgins, JE and Schmidt, EK and Williams, LN and Nachmanson, D and Valentine Iii, CC and Salk, JJ and Witt, KL},
title = {Adopting duplex sequencing technology for genetic toxicity testing: A proof-of-concept mutagenesis experiment with N-ethyl-N-nitrosourea (ENU)-exposed rats.},
journal = {Mutation research. Genetic toxicology and environmental mutagenesis},
volume = {891},
number = {},
pages = {503669},
pmid = {37770135},
issn = {1879-3592},
support = {HHSN273201300009C/ES/NIEHS NIH HHS/United States ; R44 ES030642/ES/NIEHS NIH HHS/United States ; Z99 ES999999/ImNIH/Intramural NIH HHS/United States ; ZIA ES103378/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Rats ; Male ; Animals ; *Ethylnitrosourea/toxicity ; Reproducibility of Results ; Rats, Sprague-Dawley ; Mutagenesis ; Mutation ; *Nitrosourea Compounds ; Mutagens/toxicity ; },
abstract = {Duplex sequencing (DS) is an error-corrected next-generation sequencing method in which molecular barcodes informatically link PCR-copies back to their source DNA strands, enabling computational removal of errors in consensus sequences. The resulting background of less than one artifactual mutation per 10[7] nucleotides allows for direct detection of somatic mutations. TwinStrand Biosciences, Inc. has developed a DS-based mutagenesis assay to sample the rat genome, which can be applied to genetic toxicity testing. To evaluate this assay for early detection of mutagenesis, a time-course study was conducted using male Hsd:Sprague Dawley SD rats (3 per group) administered a single dose of 40 mg/kg N-ethyl-N-nitrosourea (ENU) via gavage, with mutation frequency (MF) and spectrum analyzed in stomach, bone marrow, blood, and liver tissues at 3 h, 24 h, 7 d, and 28 d post-exposure. Significant increases in MF were observed in ENU-exposed rats as early as 24 h for stomach (site of contact) and bone marrow (a highly proliferative tissue) and at 7 d for liver and blood. The canonical, mutational signature of ENU was established by 7 d post-exposure in all four tissues. Interlaboratory analysis of a subset of samples from different tissues and time points demonstrated remarkable reproducibility for both MF and spectrum. These results demonstrate that MF and spectrum can be evaluated successfully by directly sequencing targeted regions of DNA obtained from various tissues⁠, a considerable advancement compared to currently used in vivo gene mutation assays.},
}
@article {pmid37768976,
year = {2023},
author = {Lutz, &#xcd; and Martins, T and Araújo, F and Ferreira, C and Santana, P and Miranda, J and Matos, S and Sousa, J and Pereira, L and Bentes, B and da Silva, R and Veneza, I and Sampaio, I and Vallinoto, M and Gomes, GE},
title = {Molecular characterization of juvenile fish from the Amazon estuary using DNA barcoding approach.},
journal = {PloS one},
volume = {18},
number = {9},
pages = {e0292232},
pmid = {37768976},
issn = {1932-6203},
mesh = {Humans ; Animals ; *DNA Barcoding, Taxonomic/methods ; *Estuaries ; Electron Transport Complex IV/genetics/metabolism ; Phylogeny ; Fishes ; DNA/genetics ; },
abstract = {The efficiency of the DNA barcoding relies on sequencing fragment of the Cytochrome C Subunit I (COI) gene, which has been claimed as a tool to biodiversity identification from distinct groups. Accordingly, the goal of this study was to identify juvenile fish species along an estuary of Caeté River in the Brazilian Blue Amazon based on. For this purpose, we applied the DNA barcoding and discuss this approach as a tool for discrimination of species in early ontogenetic stages. A 500-bp fragment was obtained from 74 individuals, belonging to 23 species, 20 genera, 13 families and seven orders. About 70% of the 46 haplotypes revealed congruence between morphological and molecular species identification, while 8% of them failed in identification of taxa and 22% demonstrated morphological misidentification. These results proved that COI fragments were effective to diagnose fish species at early life stages, allowing identifying all samples to a species-specific status, except for some taxa whose COI sequences remain unavailable in public databases. Therefore, we recommend the incorporation of DNA barcoding to provide additional support to traditional identification, especially in morphologically controversial groups. In addition, periodic updates and comparative analyses in public COI datasets are encouraged.},
}
@article {pmid37767518,
year = {2023},
author = {Riza, LS and Zain, MI and Izzuddin, A and Prasetyo, Y and Hidayat, T and Abu Samah, KAF},
title = {Implementation of machine learning in DNA barcoding for determining the plant family taxonomy.},
journal = {Heliyon},
volume = {9},
number = {10},
pages = {e20161},
pmid = {37767518},
issn = {2405-8440},
abstract = {The DNA barcoding approach has been used extensively in taxonomy and phylogenetics. The differences in certain DNA sequences are able to differentiate and help classify organisms into taxa. It has been used in cases of taxonomic disputes where morphology by itself is insufficient. This research aimed to utilize hierarchical clustering, an unsupervised machine learning method, to determine and resolve disputes in plant family taxonomy. We take a case study of Leguminosae that historically some classify into three families (Fabaceae, Caesalpiniaceae, and Mimosaceae) but others classify into one family (Leguminosae). This study is divided into several phases, which are: (i) data collection, (ii) data preprocessing, (iii) finding the best distance method, and (iv) determining disputed family. The data used are collected from several sources, including National Center for Biotechnology Information (NCBI), journals, and websites. The data for validation of the methods were collected from NCBI. This was used to determine the best distance method for differentiating families or genera. The data for the case study in the Leguminosae group was collected from journals and a website. From the experiment that we have conducted, we found that the Pearson method is the best distance method to do clustering ITS sequence of plants, both in accuracy and computational cost. We use the Pearson method to determine the disputed family between Leguminosae. We found that the case study of Leguminosae should be grouped into one family based on our research.},
}
@article {pmid37767069,
year = {2022},
author = {Paul, B},
title = {Concatenated 16S rRNA sequence analysis improves bacterial taxonomy.},
journal = {F1000Research},
volume = {11},
number = {},
pages = {1530},
pmid = {37767069},
issn = {2046-1402},
abstract = {Background: Microscopic, biochemical, molecular, and computer-based approaches are extensively used to identify and classify bacterial populations. Advances in DNA sequencing and bioinformatics workflows have facilitated sophisticated genome-based methods for microbial taxonomy although sequencing of the 16S rRNA gene is widely employed to identify and classify bacterial communities as a cost-effective and single-gene approach. However, the 16S rRNA sequence-based species identification accuracy is limited because of the occurrence of multiple copies of the 16S rRNA gene and higher sequence identity between closely related species. The availability of the genomes of several bacterial species provided an opportunity to develop comprehensive species-specific 16S rRNA reference libraries. Methods: Sequences of the 16S rRNA genes were retrieved from the whole genomes available in the Genome databases. With defined criteria, four 16S rRNA gene copy variants were concatenated to develop a species-specific reference library. The sequence similarity search was performed with a web-based BLAST program, and MEGA software was used to construct the phylogenetic tree. Results: Using this approach, species-specific 16S rRNA gene libraries were developed for four closely related Streptococcus species (S. gordonii, S. mitis, S. oralis, and S. pneumoniae). Sequence similarity and phylogenetic analysis using concatenated 16S rRNA copies yielded better resolution than single gene copy approaches. Conclusions: The approach is very effective in classifying genetically closely related bacterial species and may reduce misclassification of bacterial species and genome assemblies.},
}
@article {pmid37767004,
year = {2023},
author = {Jaume-Schinkel, S and Kvifte, GM and Njunjić, I and Schilthuizen, M},
title = {New records of moth flies (Diptera, Psychodidae) for the Dutch Fauna.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e108636},
pmid = {37767004},
issn = {1314-2828},
abstract = {BACKGROUND: Prior to this study, the moth flies in The Netherlands were represented by 61 species. Our findings derive from a citizen-science expedition in the Vondelpark in Amsterdam, one of the oldest public parks and best known parks in The Netherlands. The combination of citizen science and the exploration of a well-known urban park has allowed us to contribute to the knowledge of moth fly species present in The Netherlands. The findings from this study provide valuable insights into the distribution, taxonomy and genetic resources of Psychoda and Panimerus species, enhancing our understanding of insect biodiversity and promoting future research in this field.<br><br>NEW INFORMATION: Our study provides two new geographical records of the moth flies in The Netherlands, namely, Psychodauniformata Haseman, 1907 and Panimerusmaynei (Tonnoir, 1920) elevating the total number of species to 63. Furthermore, we provide re-descriptions of the females of Panimerusnotabilis (Eaton, 1893) and P.goetghebueri (Tonnoir, 1919). Additionally, we make available for the first time, the sequence of the 5'-end of the cytochrome c oxidase subunit I (COI) gene or COI Barcodes for Panimerusnotabilis, P.goetghebueri and P.maynei. These COI Barcodes serve as valuable tools for future species identification within the genus.},
}
@article {pmid37762408,
year = {2023},
author = {Pietrzak-Makyła, B and Korzeniewski, K and Gładysz, P and Lass, A},
title = {Detection and Molecular Characterization of Blastocystis Species in Polish Soldiers Stationed in the Republic of Kosovo.},
journal = {International journal of molecular sciences},
volume = {24},
number = {18},
pages = {},
pmid = {37762408},
issn = {1422-0067},
mesh = {*Blastocystis/genetics ; Kosovo ; Poland ; Feces ; Water ; },
abstract = {Blastocystis species (sp.) is one of the less well-understood water- and foodborne protozoa of medical and veterinary importance linked to different gastrointestinal disorders. Soldiers participating in military missions are particularly vulnerable to infection with this protozoa. The present study used molecular methods to detect, identify, and subtype (ST) Blastocystis sp. in Polish soldiers stationed in the Republic of Kosovo. Fecal samples were collected from 192 soldiers on arrival and after four months of stay. After DNA extraction, the barcoding region of the small subunit ribosomal RNA (SSU-rRNA) gene was amplified and sequenced. The DNA of Blastocystis sp. was detected in six (3.13%) and thirty (15.16%) samples in the first and second batch, respectively. Sequencing analysis revealed infections with ST 2, 3, 4, and 7. There was no statistical association between Blastocystis sp. infection and the parasite's ST or the age or rank of soldiers. The results indicate that the visit to a new environment and prolonged stay in the area of military operation in Kosovo resulted in a significant increase in both Blastocystis sp. infections and ST diversity among surveyed soldiers. This shows the need to undertake appropriate countermeasures to reduce Blastocystis infections in the military environment abroad.},
}
@article {pmid37761149,
year = {2023},
author = {Venuti, I and Ceruso, M and Muscariello, T and Ambrosio, RL and Di Pinto, A and Pepe, T},
title = {Mitochondrial Analysis of Sparidae Species to Detect a New DNA Barcoding Marker for Dentex gibbosus to Utilize against Fraud.},
journal = {Foods (Basel, Switzerland)},
volume = {12},
number = {18},
pages = {},
pmid = {37761149},
issn = {2304-8158},
abstract = {Dentex gibbosus (Pink dentex) is a fish species of increasing economic interest in the Mediterranean Sea that is consumed both whole and processed. The growing value of this sparid in European markets is responsible for its substitution with fraudulent species. The distinctive morphologic feature of D. gibbosus is the conspicuous hump on the forehead in the older and larger specimens. However, the head is regularly convex in young individuals, requiring high skills and competencies for correct identification. Authentication becomes even more challenging in the case of prepared and processed products. Therefore, the molecular characterization of Pink dentex plays a crucial role in preventing commercial fraud with species substitution. This paper proposes a comparative mitogenome analysis between 19 sparid species of commercial interest as a tool to accurately design species-specific primers targeting a fragment of the NAD2 gene for the identification of D. gibbosus. We successfully detected Pink dentex DNA both using endpoint and real-time PCR. The findings showed the high specificity of the designed primers, demonstrating this a suitable, fast, and cost-effective method that could be used for the unambiguous identification of Pink dentex. This innovative approach for sparid authentication is expected to contribute to seafood traceability, public health assurance, integrity, and the credibility of the seafood industry.},
}
@article {pmid37760277,
year = {2023},
author = {Jayasundara, SL and Algewatta, HR and Jayawardana, S and Perera, M and Peiris, LDC},
title = {Molecular Identification and Evolutionary Divergence of the Sri Lankan Sambar Deer, Rusa unicolor (Kerr 1792).},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {18},
pages = {},
pmid = {37760277},
issn = {2076-2615},
support = {ASP/01/RE/SCI/2019/66//University of Sri Jayewardenepura/ ; },
abstract = {The Sambar is one of the largest deer species distributed mainly in Asia, and it has been listed as a vulnerable species. Taxonomy based on morphological characterization has been the gold standard method used to identify the Sambar deer species. Yet, morphological identification is challenging and requires expertise. To conduct species identification and taxonomic decisions, we performed the molecular identification of R. unicolor found in Sri Lanka using DNA barcodes, COI, and Cyt b to compare the Sri Lankan R. unicolor with the Indian R. unicolor and other R. unicolor subspecies. We obtained mitochondrial DNA sequences from COI and Cyt b from blood samples collected from the wet zone in Sri Lanka. A phylogenetic tree was constructed based on the Bayesian analyses using MrBayes 3.2.7. Molecular dating was implemented in Bayesian Evolutionary Analysis Sampling Trees (BEAST v1.8.2) on the concatenated sequence using a log-normal relaxed clock and Yule species tree prior, with four categories. The results showed that the Sri Lankan R. unicolor is genetically different from the Indian R. unicolor and other R. unicolor subspecies. The divergence occurred approximately 1.1 MYA (million years ago) in the Pleistocene era. The results are essential for designing new conservation platforms for these Sambar deer species.},
}
@article {pmid37755418,
year = {2023},
author = {Urbina, H and Jones, C and Moore, M and Gazis, R},
title = {Susceptibility of centipede tongavine (Epipremnum pinnatum) commercially grown in nurseries in Florida to aroid leaf rust (Pseudocerradoa paullula).},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-07-23-1360-PDN},
pmid = {37755418},
issn = {0191-2917},
abstract = {Epipremnum pinnatum (L.) Engl., (Araceae, Monocots) known as dragon-tail plant or centipede tongavine, is the most cultivated aroid species worldwide (Boyce 2004). In 2022, symptomatic dragon-tail plants, collected from plant nurseries in south Florida (e-Xtra Fig.1). Symptoms included round leaf spots often with a yellow halo and erupting pustules mainly distributed in the underside of the leaves. Visits to the nurseries revealed a 60% incidence of approximability 50 mature plants, with some leaves showing up to 30% of tissue damage. The putative pathogen was identified morphologically as Pseudocerradoa paullula (Syd. &amp; P. Syd.) M. Ebinghaus &amp; Dianese (Pucciniaceae, Basidiomycota) (Ebinghaus et al. 2022), characterized by the production of pseudosuprastomatal uredinia with globose to subglobose urediniospores, light-brown, echinulate (1 µm height), 24-31 µm diam with thick walls, 1.5-2.5 µm in height (n=30). Identical morphological features reported by Urbina et al. (2023) (e-Xtra Fig. 1). PCR amplification followed by Sanger sequencing of the internal transcribed spacer (ITS) and large subunit (LSU) of the ribosomal RNA genes (Aime 2006) together with LSU internal species specific primer (Urbina et al. 2023) were used to confirm the identification of the pathogen (GenBank ON887194-ON887196). MegaBlast (Chen et al. 2015) searches resulted in a >99% sequence similarity to a P. paullula specimen collected in Florida (2019-101665, GenBank ON887197). Host identification was made by using the Ribulose-1,5-bisphosphate carboxylase-oxygenase (rbcL. GenBank ON887186, ON887187) and Maturase K (matK) loci (GenBank ON887190, ON887191) (Fazekas et al. 2012). Both barcodes resulted in >99.13% sequence similarity to voucher J.R. Abbott 24912 FLAS (GenBank GU135198 and GU135036, respectively). Symptomatic dried specimens were deposited in the Plant Industry Herbarium (PIHG 16229 - 16232). Koch's postulates were fulfilled using urediniospores collected from an infected E. pinnatum sample that was kept in darkness at 4°C for seven days until inoculation. Eight potted dragon-tail plants were inoculated by hand rubbing urediniospores against upper and lower leaf surfaces and three plants were used as controls. All plants were misted with sterile water and covered with plastic bags (23 °C, >90% RH, 12/12 h daylight). Bags were removed 48 h after inoculation, plants were set in a climate-controlled greenhouse (~30 °C, ~65% RH, 12/12 h light cycle) and monitored daily for symptoms. Chlorotic spots appeared after 10 days, and pustules after 25 days while the non-inoculated controls remained symptomless. Aroid leaf rust is known to infect several aroid species, including dragon-tail (Shaw 1995), which some varieties capable to outdoors in USDA 9a hardiness zones (Wunderlin et al. 2023), but the rust fungus has not been observed on any species of Epipremnum in the landscape yet, suggesting that its susceptibility could be driven by plant growth conditions that favor pathogen infection (e.g., excess of humidity and nutrients, dense planting, overhead irrigation, etc.). Here we encourage dragon-tail plant growers to be aware of its susceptibility to P. paullula and to stay vigilant of the culture conditions to avoid plants from getting infected with this airborne pathogen.},
}
@article {pmid37755132,
year = {2023},
author = {Yen, A and Mateusiak, C and Sarafinovska, S and Gachechiladze, MA and Guo, J and Chen, X and Moudgil, A and Cammack, AJ and Hoisington-Lopez, J and Crosby, M and Brent, MR and Mitra, RD and Dougherty, JD},
title = {Calling Cards: A Customizable Platform to Longitudinally Record Protein-DNA Interactions Over Time in Cells and Tissues.},
journal = {Current protocols},
volume = {3},
number = {9},
pages = {e883},
pmid = {37755132},
issn = {2691-1299},
support = {R35 GM141012/GM/NIGMS NIH HHS/United States ; RF1 MH126723/MH/NIMH NIH HHS/United States ; T32 NS121881/NS/NINDS NIH HHS/United States ; RF1 MH117070/MH/NIMH NIH HHS/United States ; T32 HG000045/HG/NHGRI NIH HHS/United States ; P50 HD103525/HD/NICHD NIH HHS/United States ; },
mesh = {*DNA-Binding Proteins/genetics/metabolism ; Plasmids ; *DNA/genetics ; Genome ; Genomics/methods ; },
abstract = {Calling Cards is a platform technology to record a cumulative history of transient protein-DNA interactions in the genome of genetically targeted cell types. The record of these interactions is recovered by next-generation sequencing. Compared with other genomic assays, readouts of which provide a snapshot at the time of harvest, Calling Cards enables correlation of historical molecular states to eventual outcomes or phenotypes. To achieve this, Calling Cards uses the piggyBac transposase to insert self-reporting transposon "Calling Cards" into the genome, leaving permanent marks at interaction sites. Calling Cards can be deployed in a variety of in vitro and in vivo biological systems to study gene regulatory networks involved in development, aging, and disease. Out of the box, it assesses enhancer usage but can be adapted to profile-specific transcription factor (TF) binding with custom TF-piggyBac fusion proteins. The Calling Cards workflow has five main stages: delivery of Calling Cards reagents, sample preparation, library preparation, sequencing, and data analysis. Here, we first present a comprehensive guide for experimental design, reagent selection, and optional customization of the platform to study additional TFs. Then, we provide an updated protocol for the five steps, using reagents that improve throughput and decrease costs, including an overview of a newly deployed computational pipeline. This protocol is designed for users with basic molecular biology experience to process samples into sequencing libraries in 2 days. Familiarity with bioinformatic analysis and command line tools is required to set up the pipeline in a high-performance computing environment and to conduct downstream analyses. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Preparation and delivery of Calling Cards reagents Support Protocol 1: Next-generation sequencing quantification of barcode distribution within self-reporting transposon plasmid pool and adeno-associated virus genome Basic Protocol 2: Sample collection and RNA purification Support Protocol 2: Library density quantitative PCR Basic Protocol 3: Sequencing library preparation Basic Protocol 4: Library pooling and sequencing Basic Protocol 5: Data analysis.},
}
@article {pmid37754737,
year = {2023},
author = {Lukhtanov, VA and Shapoval, NA and Dantchenko, AV and Eckweiler, W},
title = {Phylogenetic Structure Revealed through Combining DNA Barcodes with Multi-Gene Data for Agrodiaetus Blue Butterflies (Lepidoptera, Lycaenidae).},
journal = {Insects},
volume = {14},
number = {9},
pages = {},
pmid = {37754737},
issn = {2075-4450},
support = {19-14-00202//Russian Science Foundation/ ; 122031100272-3//Russian state research project/ ; },
abstract = {The need for multi-gene analysis in evolutionary and taxonomic studies is generally accepted. However, the sequencing of multiple genes is not always possible. For various reasons, short mitochondrial DNA barcodes are the only source of molecular information for some species in many genera, although multi-locus data are available for other species of the same genera. In particular, such situation exists in the species-rich butterfly subgenus Polyommatus (Agrodiaetus). Here, we analyzed the partitioning of this subgenus into species groups by using three data sets. The first data set was represented by short mitochondrial DNA barcodes for all analyzed samples. The second and third data sets were represented by a combination of short mitochondrial DNA barcodes for part of the taxa with longer mitochondrial sequences COI + tRNA-Leu + COII (data set 2) and with longer mitochondrial COI + tRNA-Leu + COII and nuclear 5.8S rDNA + ITS2 + 28S rDNA sequences (data set 3) for the remaining species. We showed that the DNA barcoding approach (data set 1) failed to reveal the phylogenetic structure, resulting in numerous polytomies in the tree obtained. Combined analysis of the mitochondrial and nuclear sequences (data sets 2 and 3) revealed the species groups and the position within these species groups, even for the taxa for which only short DNA barcodes were available.},
}
@article {pmid37751470,
year = {2023},
author = {Wax, N and Pförtner, LS and Holz, N and Sterzl, S and Melnik, M and Kappel, K and Bade, P and Schröder, U and Haase, I and Fritsche, J and Fischer, M},
title = {Fast and User-Friendly Detection of Flatfish Species (Pleuronectes platessa and Solea solea) via Loop-Mediated Isothermal Amplification (LAMP).},
journal = {Journal of agricultural and food chemistry},
volume = {71},
number = {40},
pages = {14795-14805},
doi = {10.1021/acs.jafc.3c03917},
pmid = {37751470},
issn = {1520-5118},
abstract = {The detection of a Cytochrome b gene (cytb) for species differentiation in fish is intensively used. A fast alternative to expensive and time-consuming DNA barcoding is loop-mediated isothermal amplification (LAMP) in combination with efficient readout systems. For this reason, we developed LAMP assays for rapid species detection of Pleuronectes platessa and Solea solea, two economically important flatfish species in Europe that are prone to mislabeling. Species-specific primer sets targeting cytb were designed, and LAMP assays were optimized. With the optimized LAMP assays, we were able to detect up to 0.1 and 0.01 ng of target DNA of P. platessa and S. solea, respectively, and in each case up to 1% (w/w) of target species in mixtures with nontarget species. For future on-site detection, a lateral flow assay and a pocket-sized lab-on-phone assay were used as readout systems. The lab-on-phone assay with the S. solea specific primer set revealed cross-reactivity to Solea senegalensis. The assay targeting P. platessa proved to be highly specific. Both assays could be performed within 45 min and provided rapid and easy detection of fish species.},
}
@article {pmid37751451,
year = {2023},
author = {Yalcin, GD and Yilmaz, KC and Dilber, T and Acar, A},
title = {Investigation of evolutionary dynamics for drug resistance in 3D spheroid model system using cellular barcoding technology.},
journal = {PloS one},
volume = {18},
number = {9},
pages = {e0291942},
pmid = {37751451},
issn = {1932-6203},
mesh = {Humans ; Irinotecan/pharmacology ; *Spheroids, Cellular ; Cell Line, Tumor ; Drug Resistance ; *Technology ; },
abstract = {Complex evolutionary dynamics governing the drug resistance is one of the major challenges in cancer treatment. Understanding these mechanisms requires a sequencing technology with higher resolution to delineate whether pre-existing or de novo drug mechanisms are behind the drug resistance. Combining this technology with clinically very relevant model system, namely 3D spheroids, better mimicking tumorigenesis and drug resistance have so far been lacking. Thus, we sought to establish dabrafenib and irinotecan resistant derivatives of barcoded 3D spheroids with the ultimate aim to quantify the selection-induced clonal dynamics and identify the genomic determinants in this model system. We found that dabrafenib and irinotecan induced drug resistance in 3D-HT-29 and 3D-HCT-116 spheroids are mediated by pre-existing and de novo resistant barcodes, indicating the presence of polyclonal drug resistance in this system. Moreover, whole-exome sequencing analysis found chromosomal gains and mutations associated with dabrafenib and irinotecan resistance in 3D-HT-29 and 3D-HCT-116 spheroids. Last, we show that dabrafenib and irinotecan resistance are also mediated by multiple drug resistance by detection of upregulation of the drug efflux pumps, ABCB1 and ABCG2, in our spheroid model system. Overall, we present the quantification of drug resistance and evolutionary dynamics in spheroids for the first time using cellular barcoding technology and the underlying genomic determinants of the drug resistance in our model system.},
}
@article {pmid37749315,
year = {2023},
author = {Ben Youssef-Dridi, S and Antar, R and Gey, D and Justine, JL and Gargouri, L},
title = {Morphological and molecular studies of the life-cycle stages of the monorchiid Monorchis parvus (Looss, 1902) (Digenea) from the Southern Mediterranean coast (Tunisia).},
journal = {Parasitology research},
volume = {122},
number = {12},
pages = {2819-2833},
pmid = {37749315},
issn = {1432-1955},
mesh = {Animals ; Tunisia ; *Trematoda ; Life Cycle Stages ; Fishes/parasitology ; *Perciformes/parasitology ; Larva ; *Bivalvia ; Phylogeny ; },
abstract = {The elucidation of life-cycles of digeneans, with their successive larval stages, is facilitated by the use of molecular markers. Samples of sporocysts containing cercariae and metacercariae belonging to Monorchis Monticelli, 1893 were collected from naturally infected bivalves, Cerastoderma glaucum (Bruguière, 1789), and adult forms of Monorchis spp. were collected from sparid fishes of the genus Diplodus. All specimens were collected in the Gulf of Gabès, southern Tunisia. The identities of the examined molluscs and fishes were determined via molecular barcoding of their COI gene. Sequences of COI and ITS1 genes were also obtained for both larval and adult stages of collected parasite specimens. Genetic sequence data generated for the collected larval specimens only differed minimally from the sequence data of adults identified as Monorchis parvus; we attribute the difference to intraspecific variation. The morpho-anatomical study showed that the different stages of M. parvus collected from the Tunisian coasts had the same morphology as those reported in European waters with a lag in maturity and lower measurements. The species is recorded and molecularly characterised for the first time off the Tunisian coasts.},
}
@article {pmid37749269,
year = {2024},
author = {Jindal, K and Adil, MT and Yamaguchi, N and Yang, X and Wang, HC and Kamimoto, K and Rivera-Gonzalez, GC and Morris, SA},
title = {Single-cell lineage capture across genomic modalities with CellTag-multi reveals fate-specific gene regulatory changes.},
journal = {Nature biotechnology},
volume = {42},
number = {6},
pages = {946-959},
pmid = {37749269},
issn = {1546-1696},
support = {R01 GM126112/GM/NIGMS NIH HHS/United States ; R21 AR077825/AR/NIAMS NIH HHS/United States ; R01 GM126112/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Single-Cell Analysis/methods ; *Cell Lineage/genetics ; Mice ; *Cell Differentiation/genetics ; Gene Expression Regulation ; Genomics ; Hematopoiesis/genetics ; Cellular Reprogramming/genetics ; Transcription Factors/metabolism/genetics ; Fibroblasts/metabolism/cytology ; },
abstract = {Complex gene regulatory mechanisms underlie differentiation and reprogramming. Contemporary single-cell lineage-tracing (scLT) methods use expressed, heritable DNA barcodes to combine cell lineage readout with single-cell transcriptomics. However, reliance on transcriptional profiling limits adaptation to other single-cell assays. With CellTag-multi, we present an approach that enables direct capture of heritable random barcodes expressed as polyadenylated transcripts, in both single-cell RNA sequencing and single-cell Assay for Transposase Accessible Chromatin using sequencing assays, allowing for independent clonal tracking of transcriptional and epigenomic cell states. We validate CellTag-multi to characterize progenitor cell lineage priming during mouse hematopoiesis. Additionally, in direct reprogramming of fibroblasts to endoderm progenitors, we identify core regulatory programs underlying on-target and off-target fates. Furthermore, we reveal the transcription factor Zfp281 as a regulator of reprogramming outcome, biasing cells toward an off-target mesenchymal fate. Our results establish CellTag-multi as a lineage-tracing method compatible with multiple single-cell modalities and demonstrate its utility in revealing fate-specifying gene regulatory changes across diverse paradigms of differentiation and reprogramming.},
}
@article {pmid37749223,
year = {2023},
author = {Stephenson, A and Nivala, J},
title = {Barcoding biomarkers with nanopore sequencing.},
journal = {Nature nanotechnology},
volume = {18},
number = {12},
pages = {1385-1386},
pmid = {37749223},
issn = {1748-3395},
mesh = {*Nanopore Sequencing ; Sequence Analysis, DNA ; Biodiversity ; *Nanopores ; High-Throughput Nucleotide Sequencing ; },
}
@article {pmid37749192,
year = {2023},
author = {Akter, S and Rahman, MS and Ali, H and Minch, B and Mehzabin, K and Siddique, MM and Galib, SM and Yesmin, F and Azmuda, N and Adnan, N and Hasan, NA and Rahman, SR and Moniruzzaman, M and Ahmed, MF},
title = {Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {15976},
pmid = {37749192},
issn = {2045-2322},
mesh = {Bays ; Phylogeny ; *Microbiota ; *Alteromonas ; *Dinoflagellida ; },
abstract = {The Bay of Bengal, the world's largest bay, is bordered by populous countries and rich in resources like fisheries, oil, gas, and minerals, while also hosting diverse marine ecosystems such as coral reefs, mangroves, and seagrass beds; regrettably, its microbial diversity and ecological significance have received limited research attention. Here, we present amplicon (16S and 18S) profiling and shotgun metagenomics data regarding microbial communities from BoB's eastern coast, viz., Saint Martin and Cox's Bazar, Bangladesh. From the 16S barcoding data, Proteobacteria appeared to be the dominant phylum in both locations, with Alteromonas, Methylophaga, Anaerospora, Marivita, and Vibrio dominating in Cox's Bazar and Pseudoalteromonas, Nautella, Marinomonas, Vibrio, and Alteromonas dominating the Saint Martin site. From the 18S barcoding data, Ochrophyta, Chlorophyta, and Protalveolata appeared among the most abundant eukaryotic divisions in both locations, with significantly higher abundance of Choanoflagellida, Florideophycidae, and Dinoflagellata in Cox's Bazar. The shotgun sequencing data reveals that in both locations, Alteromonas is the most prevalent bacterial genus, closely paralleling the dominance observed in the metabarcoding data, with Methylophaga in Cox's Bazar and Vibrio in Saint Martin. Functional annotations revealed that the microbial communities in these samples harbor genes for biofilm formation, quorum sensing, xenobiotics degradation, antimicrobial resistance, and a variety of other processes. Together, these results provide the first molecular insight into the functional and phylogenetic diversity of microbes along the BoB coast of Bangladesh. This baseline understanding of microbial community structure and functional potential will be critical for assessing impacts of climate change, pollution, and other anthropogenic disturbances on this ecologically and economically vital bay.},
}
@article {pmid37748058,
year = {2023},
author = {Dufresnes, C and Poyarkov, N and Jablonski, D},
title = {Acknowledging more biodiversity without more species.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {40},
pages = {e2302424120},
pmid = {37748058},
issn = {1091-6490},
mesh = {Animals ; Phylogeny ; *Biodiversity ; *Biota ; Animals, Wild ; Genomics ; },
abstract = {Delimiting and naming biodiversity is a vital step toward wildlife conservation and research. However, species delimitation must be consistent across biota so that the limited resources available for nature protection can be spent effectively and objectively. To date, newly discovered lineages typically are either left undescribed and thus remain unprotected or are being erroneously proposed as new species despite mixed evidence for completed speciation, in turn contributing to the emerging problem of taxonomic inflation. Inspired by recent conceptual and methodological progress, we propose a standardized workflow for species delimitation that combines phylogenetic and hybrid zone analyses of genomic datasets ("genomic taxonomy"), in which phylogeographic lineages that do not freely admix are ranked as species, while those that have remained fully genetically compatible are ranked as subspecies. In both cases, we encourage their formal taxonomic naming, diagnosis, and description to promote social awareness toward biodiversity. The use of loci throughout the genome overcomes the unreliability of widely used barcoding genes when phylogeographic patterns are complex, while the evaluation of divergence and reproductive isolation unifies the long-opposed concepts of lineage species and biological species. We suggest that a shift in conservation assessments from a single level (species) toward a two-level hierarchy (species and subspecies) will lead to a more balanced perception of biodiversity in which both intraspecific and interspecific diversity are valued and more adequately protected.},
}
@article {pmid37746211,
year = {2022},
author = {Van Caenegem, W and Ceryngier, P and Romanowski, J and Pfister, DH and Haelewaters, D},
title = {Hesperomyces (Fungi, Ascomycota) associated with Hyperaspis ladybirds (Coleoptera, Coccinellidae): Rethinking host specificity.},
journal = {Frontiers in fungal biology},
volume = {3},
number = {},
pages = {1040102},
pmid = {37746211},
issn = {2673-6128},
abstract = {Laboulbeniales (Ascomycota, Laboulbeniomycetes) are biotrophic microfungi always attached to the exoskeleton of their arthropod hosts. They do not form hyphae or a mycelium; instead, they undergo determinate growth, developing from a two-celled ascospore to form a multicellular thallus. Hesperomyces virescens has been reported on over 30 species of ladybirds (Coleoptera, Coccinellidae); in reality, it represents a complex of species, presumably segregated by host genus association. In this study, we report on Hesperomyces thalli on Hyperaspis vinciguerrae from the Canary Islands and compare them with the Hesperomyces hyperaspidis described on Hyperaspis sp. from Trinidad. We generated the sequences of the internal transcribed spacer (ITS) region, the large subunit (LSU) nuclear ribosomal RNA gene, and the minichromosome maintenance complex component 7 (MCM7) protein-coding gene. Our phylogenetic reconstruction of Hesperomyces based on a concatenated ITS-LSU-MCM7 dataset revealed Hesperomyces sp. ex Hy. vinciguerrae as a member of the He. virescens species complex distinct from He. virescens sensu stricto (s.s.). It also revealed that the Hesperomyces sp. ex Chilocorus bipustulatus from Algeria is different from He. virescens s.s., which is associated with Chilocorus stigma from the USA. This suggests that the species of Hesperomyces are not solely segregated by host association, but that there is also a biogeographical component involved. Based on these data, we refrained from referring our material from Hy. vinciguerrae to He. hyperaspidis. Finally, we discuss the usefulness of MCM7 as a useful marker for species delimitation in Hesperomyces.},
}
@article {pmid37746000,
year = {2023},
author = {Chen, M and Sun, J and Yao, H and Gong, F and Cai, L and Wang, C and Shao, Q and Wang, Z},
title = {Analysis of genetic and chemical variability of five Curcuma species based on DNA barcoding and HPLC fingerprints.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1229041},
pmid = {37746000},
issn = {1664-462X},
abstract = {The rhizomes of Curcuma species have a long medicinal history in Asia. In China, Curcuma species mainly be utilized to make pharmaceutical products, including C. phaecocaulis, C. aromatica, C. wenyujin, C. kwangsiensis and C. longa. In this study, twenty-four samples were selected to study the genetic and chemical variability among five Curcuma species. The ITS2 and trnK intron gene fragment were used to identify the five Curcuma species, the differences in chemical composition were computed using the Euclidean distance based on the data of HPLC characteristic peak areas and the content of six key components, and agronomic characteristics were analyzed including morphological and volatile oil characteristics. The ITS2 and trnK intron gene fragment could distinguish the five Curcuma species clearly. The genetic distance between Curcuma species ranged from 0.0085 to 0.0767 based on the data of ITS2 gene sequences with 32 variation sites, and the genetic distance between Curcuma species ranged from 0.0003 to 0.0194 based on the data of trnK intron gene sequences with 39 variation sites. Five Curcuma species showed otherness chemical composition characteristics, with the Euclidean distance ranging from 3.373 to 6.998. The C. longa showed the biggest variation compared with other species, with the Euclidean distance above 6.239. Among the samples of the original plants of Ezhu, the volatile oil yield of W1 was the highest, reached to 105.75 mL per single plant. Among all the samples, J6 showed the highest yield of volatile oil, reached to 149.42 mL per single plant. The results showed that chemical composition similarity of the medicinal plants was the primary proof for the selection of the original plants of the Curcuma medicinal materials. The genetic distance and chemical variability were important references for discovering new medicinal plant resources.},
}
@article {pmid37745572,
year = {2023},
author = {Booeshaghi, AS and Sullivan, DK and Pachter, L},
title = {Universal preprocessing of single-cell genomics data.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37745572},
issn = {2692-8205},
support = {T32 GM008042/GM/NIGMS NIH HHS/United States ; UM1 HG012077/HG/NHGRI NIH HHS/United States ; },
abstract = {We describe a workflow for preprocessing a wide variety of single-cell genomics data types. The approach is based on parsing of machine-readable seqspec assay specifications to customize inputs for kb-python, which uses kallisto and bustools to catalog reads, error correct barcodes, and count reads. The universal preprocessing method is implemented in the Python package cellatlas that is available for download at: https://github.com/cellatlas/cellatlas/.},
}
@article {pmid37745469,
year = {2023},
author = {Cheng, YL and Banu, MA and Zhao, W and Rosenfeld, SS and Canoll, P and Sims, PA},
title = {Multiplexed single-cell lineage tracing of mitotic kinesin inhibitor resistance in glioblastoma.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37745469},
issn = {2692-8205},
support = {R01 NS103473/NS/NINDS NIH HHS/United States ; R01 NS118513/NS/NINDS NIH HHS/United States ; U01 CA168426/CA/NCI NIH HHS/United States ; },
abstract = {Glioblastoma (GBM) is a deadly brain tumor, and the kinesin motor KIF11 is an attractive therapeutic target because of its dual roles in proliferation and invasion. The clinical utility of KIF11 inhibitors has been limited by drug resistance, which has mainly been studied in animal models. We used multiplexed lineage tracing barcodes and scRNA-seq to analyze drug resistance time courses for patient-derived GBM neurospheres treated with ispinesib, a potent KIF11 inhibitor. Similar to GBM progression in patients, untreated cells lost their neural lineage identity and transitioned to a mesenchymal phenotype, which is associated with poor prognosis. In contrast, cells subjected to long-term ispinesib treatment exhibited a proneural phenotype. We generated patient-derived xenografts to show that ispinesib-resistant cells form less aggressive tumors in vivo, even in the absence of drug. Finally, we used lineage barcodes to nominate drug combination targets by retrospective analysis of ispinesib-resistant clones in the drug-naïve setting and identified drugs that are synergistic with ispinesib.},
}
@article {pmid37741170,
year = {2023},
author = {Son, H and Moon, J and Ha, EJ and Kim, N and Kim, EY and Lee, HS and Koh, EJ and Phi, JH and Park, CK and Kim, JE and Kim, SK and Lee, ST and Jung, KH and Lee, SK and Cho, WS and Chu, K},
title = {Identification of bacterial pathogens in brain abscesses by metagenomic approach using nanopore 16S amplicon sequencing.},
journal = {Diagnostic microbiology and infectious disease},
volume = {107},
number = {4},
pages = {116041},
doi = {10.1016/j.diagmicrobio.2023.116041},
pmid = {37741170},
issn = {1879-0070},
mesh = {Humans ; *Nanopore Sequencing ; RNA, Ribosomal, 16S/genetics ; *Nanopores ; *Coinfection ; DNA, Bacterial/genetics/analysis ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing ; *Brain Abscess/diagnosis/microbiology ; },
abstract = {Brain abscess is medically challenging. In this study, we applied nanopore sequencing for 16S rRNA analysis and investigated its efficacy and diagnostic value for patients with brain abscesses. Genomic DNA was extracted from the pus samples (n = 27) of brain abscess, and 16S rRNA genes were amplified by PCR. Sequencing libraries were generated using a rapid barcoding kit, and the generated reads were analyzed using the EPI2ME16S workflow. A conventional culture study was performed. More sensitive identification of pathogens was made by 16S sequencing, faster than the culture study. The proportion of anaerobic bacteria identified by 16S sequencing was higher (75%) than that obtained by culturing (32%). Polymicrobial infections were identified in 10 cases (40%) by 16S sequencing, while the culture study identified multiple bacteria in only 2 cases (8%). 16S sequencing was useful for identifying the composition of polymicrobial infections, including rare pathogens, and for the initial diagnosis of space-occupying lesions.},
}
@article {pmid37740537,
year = {2024},
author = {Riaz, M and Afshan, NU and Afzal, S and Zafar, I and Saleem, A and Khalid, AN},
title = {DNA barcoding and scanning electron microscopy reveals Erysiphe ahmadii sp. nov. and a new record Erysiphe populicola (Erysiphaceae, Helotiales) on salicaceous hosts from Pakistan.},
journal = {Microscopy research and technique},
volume = {87},
number = {1},
pages = {21-30},
doi = {10.1002/jemt.24402},
pmid = {37740537},
issn = {1097-0029},
mesh = {*Erysiphe ; Microscopy, Electron, Scanning ; Pakistan ; *DNA Barcoding, Taxonomic ; Phylogeny ; DNA ; },
abstract = {A new species of powdery mildew fungus Erysiphe ahmadii and a new record, Erysiphe populicola, on Salicaceae are described from Pakistan. In addition to light microscopy, scanning electron microscopy is also done to clearly demonstrate the surface characters of chasmothecia. E. ahmadii sp. nov. is characterized by large conidia ((-26)29-35(-37) × (-16)17-21(-23) μm), long chasmothecial appendages (198-286 μm) and small conidiophores. The novelty is confirmed by analyzing the genetic variation of internal transcribed spacer region (ITS1-5.8S-ITS2) of the ribosomal DNA gene, a universal fungal marker. E. populicola is characterized for the first time using molecular phylogenetic markers. Detailed descriptions along with scanning electron microscopy (SEM) photographs are provided in this paper. RESEARCH HIGHLIGHTS: Powdery mildews are obligate biotrophic pathogens of plants. Erysiphe ahmadii, a new powdery mildew fungus on willow trees, is described. First reference sequence of Erysiphe populicola is also generated. Both taxa are discussed in detail using macro- and micro-morphological and DNA barcoding techniques.},
}
@article {pmid37738679,
year = {2023},
author = {Dolan, M and St John, N and Zaidi, F and Doyle, F and Fasullo, M},
title = {High-throughput screening of the Saccharomyces cerevisiae genome for 2-amino-3-methylimidazo [4,5-f] quinoline resistance identifies colon cancer-associated genes.},
journal = {G3 (Bethesda, Md.)},
volume = {13},
number = {12},
pages = {},
pmid = {37738679},
issn = {2160-1836},
support = {R15 ES023685/ES/NIEHS NIH HHS/United States ; R21 ES015954/ES/NIEHS NIH HHS/United States ; T32 GM132066/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Cytochrome P-450 CYP1A2/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; High-Throughput Screening Assays ; Early Detection of Cancer ; Mutagens ; *Quinolines/pharmacology/metabolism ; Ribosomal Proteins ; *Colonic Neoplasms ; *Arylamine N-Acetyltransferase/genetics ; DNA-Binding Proteins ; Ubiquitin-Protein Ligases ; DNA-Directed DNA Polymerase ; },
abstract = {Heterocyclic aromatic amines (HAAs) are potent carcinogenic agents found in charred meats and cigarette smoke. However, few eukaryotic resistance genes have been identified. We used Saccharomyces cerevisiae (budding yeast) to identify genes that confer resistance to 2-amino-3-methylimidazo[4,5-f] quinoline (IQ). CYP1A2 and NAT2 activate IQ to become a mutagenic nitrenium compound. Deletion libraries expressing human CYP1A2 and NAT2 or no human genes were exposed to either 400 or 800 µM IQ for 5 or 10 generations. DNA barcodes were sequenced using the Illumina HiSeq 2500 platform and statistical significance was determined for exactly matched barcodes. We identified 424 ORFs, including 337 genes of known function, in duplicate screens of the "humanized" collection for IQ resistance; resistance was further validated for a select group of 51 genes by growth curves, competitive growth, or trypan blue assays. Screens of the library not expressing human genes identified 143 ORFs conferring resistance to IQ per se. Ribosomal protein and protein modification genes were identified as IQ resistance genes in both the original and "humanized" libraries, while nitrogen metabolism, DNA repair, and growth control genes were also prominent in the "humanized" library. Protein complexes identified included the casein kinase 2 (CK2) and histone chaperone (HIR) complex. Among DNA Repair and checkpoint genes, we identified those that function in postreplication repair (RAD18, UBC13, REV7), base excision repair (NTG1), and checkpoint signaling (CHK1, PSY2). These studies underscore the role of ribosomal protein genes in conferring IQ resistance, and illuminate DNA repair pathways for conferring resistance to activated IQ.},
}
@article {pmid37737001,
year = {2023},
author = {Bernadus, JBB and Pelealu, J and Kandou, GD and Pinaria, AG and Mamahit, JME and Tallei, TE},
title = {Metagenomic Insight into the Microbiome and Virome Associated with Aedes aegypti Mosquitoes in Manado (North Sulawesi, Indonesia).},
journal = {Infectious disease reports},
volume = {15},
number = {5},
pages = {549-563},
pmid = {37737001},
issn = {2036-7430},
abstract = {The aim of this study was to investigate the microbial diversity encompassing bacteria, fungi, and viruses within the composite microbial community associated with Aedes aegypti mosquitoes in Manado, Indonesia, using a whole-genome shotgun metagenomics approach. Female mosquitoes were collected and grouped into pools of 50 individuals, from which genomic DNA (gDNA) and RNA were extracted separately. Whole-genome shotgun metagenomics were performed on gDNA samples. The bioinformatics analysis encompassed quality assessment, taxonomic classification, and visualization. The evaluation of the microbial community entailed an assessment of taxa abundance and diversity using Kraken version 2.1.2. The study delineated the prevalence of dominant bacterial phyla, including Proteobacteria, with varying abundance of Firmicutes, Bacteroidota, and Actinobacteria, and notable occurrence of Tenericutes. Furthermore, the presence of the fungal phylum Ascomycota was also detected. Among the identified barcodes, Barcode04 emerged as the most abundant and diverse, while Barcode06 exhibited greater evenness. Barcode03, 05, and 07 displayed moderate richness and diversity. Through an analysis of the relative abundance, a spectrum of viruses within Ae. aegypti populations was unveiled, with Negarnaviricota constituting the most prevalent phylum, followed by Nucleocytoviricota, Uroviricota, Artverviricota, Kitrinoviricota, Peploviricota, Phixviricota, and Cossaviricota. The presence of Negarnaviricota viruses raises pertinent public health concerns. The presence of other viral phyla underscores the intricate nature of virus-mosquito interactions. The analysis of viral diversity provides valuable insights into the range of viruses carried by Ae. aegypti. The community exhibits low biodiversity, with a few dominant species significantly influencing its composition. This has implications for healthcare and ecological management, potentially simplifying control measures but also posing risks if the dominant species are harmful. This study enriches our comprehension of the microbiome and virome associated with Ae. aegypti mosquitoes, emphasizing the importance of further research to fully comprehend their ecological significance and impact on public health. The findings shed light on the microbial ecology of Ae. aegypti, offering potential insights into mosquito biology, disease transmission, and strategies for vector control. Future studies should endeavor to establish specific associations with Ae. aegypti, elucidate the functional roles of the identified microbial and viral species, and investigate their ecological implications.},
}
@article {pmid37736273,
year = {2023},
author = {von Beeren, C and Pohl, S and Fikáček, M and Kleinfelder, S and Tishechkin, AK and Yamamoto, S and Chani-Posse, M and Żyła, D and Tokareva, A and Maruyama, M and Hall, WE and Sandoval, LP and Kronauer, DJC},
title = {Army ant middens - Home and nursery of a diverse beetle fauna.},
journal = {Ecology and evolution},
volume = {13},
number = {9},
pages = {e10451},
pmid = {37736273},
issn = {2045-7758},
abstract = {Army ants provide nourishment to a large variety of animals. This includes birds that feed on animals flushed out by army ant raids, symbiotic arthropods that consume the ants' prey or their brood, and other arthropods that scavenge on army ant refuse deposits. The latter have not received much attention, and the few published studies lack detailed species identifications. Here we provide a first systematic inventory of the beetle fauna associated with refuse deposits of Eciton army ants, with a focus on Eciton burchellii. We collected 8364 adult beetles, 511 larvae, and 24 eggs from 34 deposits at La Selva Biological Station, Costa Rica. We used a combination of DNA barcoding and morphology to identify a subset of 436 specimens to species level. The samples included several new species, and we here formally describe two water scavenger beetles (Hydrophilidae). Refuse deposits harbored a diverse beetle fauna. The identified subset consisted of 91 beetle species from 12 families, with rove beetles being the most abundant and diverse visitors. Of the 85 species found with E. burchellii, 50 species were collected from only one or two refuse deposits. Conversely, seven species were found in 10 or more refuse deposits, indicating a certain level of habitat specialization. We matched adults and immatures for 22 beetle species via DNA barcodes, demonstrating that army ant middens also serve as a beetle nursery. The present survey highlights the significant ecological function of army ants as promoters of biodiversity and their status as keystone species in tropical rainforests.},
}
@article {pmid37731533,
year = {2023},
author = {Liu, L and Zhang, L and Jin, D and Wang, H and Liu, X and Wu, R},
title = {Molecular and morphological evidence reveals a hidden new taxon in the endemic genus Pseudocuneopsis (Bivalvia, Unionidae) from China.},
journal = {ZooKeys},
volume = {1179},
number = {},
pages = {219-229},
pmid = {37731533},
issn = {1313-2989},
abstract = {A new species of freshwater mussel belonging to the genus Pseudocuneopsis, namely Pseudocuneopsiswuanasp. nov., is diagnosed and described from Guangxi Province, China. This paper provides a detailed shell morphological description, soft-body anatomical characteristics, and partial sequences of mitochondrial COI as DNA barcode data for the novel species. The new species can be distinguished from its congeners (Pseudocuneopsissichuanensis, P.yangshuoensis, and P.capitata) by shell shape, beak position, and surface sculpture. Phylogenetic analyses based on the mitochondrial COI gene reveal that Pseudocuneopsiswuanasp. nov. forms a sister group with P.yangshuoensis and exhibits an interspecific genetic distance of 5.1%. Therefore, we provide robust morphological and molecular evidence to support the validity of this new species.},
}
@article {pmid37730192,
year = {2023},
author = {Hu, L and Xiong, G and Zhao, Y and Chai, R and Xie, J and Xiao, Y and Du, Y and Teng, J and Zhang, W and Guan, C},
title = {Classification and identification of mosquitoes in China based on rDNA 28S D5 region.},
journal = {Acta tropica},
volume = {248},
number = {},
pages = {107028},
doi = {10.1016/j.actatropica.2023.107028},
pmid = {37730192},
issn = {1873-6254},
mesh = {Animals ; DNA, Ribosomal/genetics ; *Culex/genetics ; *Anopheles/genetics ; *Aedes/genetics ; China ; Mosquito Vectors/genetics/anatomy &amp; histology ; },
abstract = {Accurate classification and identification of mosquitoes are essential for the prevention and control of mosquito-borne diseases. In this study, adult mosquitoes were collected from 15 cities across 14 provinces in China. They were identified morphologically with the dominant species determined. Furthermore, representative samples were identified at the molecular level based on rDNA 28S D5. In total, 880 adult mosquitoes were collected belonging to Culex (266), Aedes (473), Armigeres (13), and Anopheles (5). Aedes albopictus and "C. pipiens subgroup" were the dominant species. A total of 140 sequences of 28S D5 region (68 for "C. pipiens subgroup", 51 for Ae. albopictus, 18 for Ar. subalbatus, and three for An. sinensis) ranging from 148 to 161 bp were obtained, with 100 % success of amplification and sequencing. Molecular identification were consistent with morphological classification. Sequence analysis showed that "C. pipiens subgroup" was identified into three clades: the traditional C. pipiens subgroup (Clade I), the newly discovered C. cf. perexiguus (Clade II), and C. new sp. (Clade III). Clade I contained the most abundant haplotypes (16) widely distributed without geographical differences. Clade II included six haplotypes that were aggregately distributed south of the Yangtze River. Only three sequences in Clade III showed two haplotypes with no geographical differences. Further morphological comparisons demonstrated differences in body color, beaks, and abdomens among the three clades. In conclusion, the rDNA 28S D5 region could effectively distinguish Culex, Aedes, Armigeres, and Anopheles species at the lower category level, demonstrating its potential as a mini-DNA barcode for mosquito identification.},
}
@article {pmid37729154,
year = {2023},
author = {Bandaranayake, PCG and Naranpanawa, N and Chandrasekara, CHWMRB and Samarakoon, H and Lokuge, S and Jayasundara, S and Bandaranayake, AU and Pushpakumara, DKNG and Wijesundara, DSA},
title = {Chloroplast genome, nuclear ITS regions, mitogenome regions, and Skmer analysis resolved the genetic relationship among Cinnamomum species in Sri Lanka.},
journal = {PloS one},
volume = {18},
number = {9},
pages = {e0291763},
pmid = {37729154},
issn = {1932-6203},
mesh = {*Cinnamomum/genetics ; Sri Lanka ; *Genome, Chloroplast ; Bayes Theorem ; *Genome, Mitochondrial ; Cinnamomum zeylanicum ; },
abstract = {Cinnamomum species have gained worldwide attention because of their economic benefits. Among them, C. verum (synonymous with C. zeylanicum Blume), commonly known as Ceylon Cinnamon or True Cinnamon is mainly produced in Sri Lanka. In addition, Sri Lanka is home to seven endemic wild cinnamon species, C. capparu-coronde, C. citriodorum, C. dubium, C. litseifolium, C. ovalifolium, C. rivulorum and C. sinharajaense. Proper identification and genetic characterization are fundamental for the conservation and commercialization of these species. While some species can be identified based on distinct morphological or chemical traits, others cannot be identified easily morphologically or chemically. The DNA barcoding using rbcL, matK, and trnH-psbA regions could not also resolve the identification of Cinnamomum species in Sri Lanka. Therefore, we generated Illumina Hiseq data of about 20x coverage for each identified species and a C. verum sample (India) and assembled the chloroplast genome, nuclear ITS regions, and several mitochondrial genes, and conducted Skmer analysis. Chloroplast genomes of all eight species were assembled using a seed-based method.According to the Bayesian phylogenomic tree constructed with the complete chloroplast genomes, the C. verum (Sri Lanka) is sister to previously sequenced C. verum (NC_035236.1, KY635878.1), C. dubium and C. rivulorum. The C. verum sample from India is sister to C. litseifolium and C. ovalifolium. According to the ITS regions studied, C. verum (Sri Lanka) is sister to C. verum (NC_035236.1), C. dubium and C. rivulorum. Cinnamomum verum (India) shares an identical ITS region with C. ovalifolium, C. litseifolium, C. citriodorum, and C. capparu-coronde. According to the Skmer analysis C. verum (Sri Lanka) is sister to C. dubium and C. rivulorum, whereas C. verum (India) is sister to C. ovalifolium, and C. litseifolium. The chloroplast gene ycf1 was identified as a chloroplast barcode for the identification of Cinnamomum species. We identified an 18 bp indel region in the ycf1 gene, that could differentiate C. verum (India) and C. verum (Sri Lanka) samples tested.},
}
@article {pmid37727859,
year = {2023},
author = {Zhuo, J and Vasupalli, N and Wang, Y and Zhou, G and Gao, H and Zheng, Y and Li, B and Hou, D and Lin, X},
title = {Molecular identification of Bambusa changningensis is the natural bamboo hybrid of B. rigida × Dendrocalamus farinosus.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1231940},
pmid = {37727859},
issn = {1664-462X},
abstract = {Bamboo is one of the fastest-growing plants commonly used in food, fibre, paper, biofuel, ornamental and medicinal industries. Natural hybridization in bamboo is rare due to its long vegetative period followed by gregarious flowering and death of the entire population. In the current study, a new bamboo species, Bambusa changningensis, shows intermediate characteristics of Dendrocalamus farinosus and B. rigida morphologically, but it is unknown whether B. changningensis is a natural hybrid. Moreover, B. changningensis has been identified as a superior variety of Sichuan Province with high pulping yield, fibre length and width. Therefore, we analyzed the morphological characteristics, DNA markers, DNA barcoding and chloroplast genomes to identify the hybrid origin of B. changningensis and possible maternal parent. We have developed the transcriptomic data for B. changningensis and mined the SSR loci. The putative parental lines and hybrid were screened for 64 SSR makers and identified that SSR14, SSR28, SSR31 and SSR34 markers showed both alleles of the parental species in B. changningensis, proving heterozygosity. Sequencing nuclear gene GBSSI partial regions and phylogenetic analysis also confirm the hybrid nature of B. changningensis. Further, we have generated the complete chloroplast genome sequence (139505 bp) of B. changningensis. By analyzing the cp genomes of both parents and B. changningensis, we identified that B. rigida might be the female parent. In conclusion, our study identified that B. changningensis is a natural hybrid, providing evidence for bamboo's natural hybridization. This is the first report on confirming a natural bamboo hybrid and its parents through SSR and chloroplast genome sequence.},
}
@article {pmid37725654,
year = {2023},
author = {Lin, X and Chen, Y and Lin, L and Yin, K and Cheng, R and Lin, X and Wang, X and Guo, Y and Wu, Z and Zhang, Y and Li, J and Yang, C and Song, J},
title = {mitoSplitter: A mitochondrial variants-based method for efficient demultiplexing of pooled single-cell RNA-seq.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {39},
pages = {e2307722120},
pmid = {37725654},
issn = {1091-6490},
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung ; RNA, Mitochondrial ; Single-Cell Gene Expression Analysis ; *Lung Neoplasms ; Mitochondria/genetics ; },
abstract = {Single-cell RNA-seq (scRNA-seq) analysis of multiple samples separately can be costly and lead to batch effects. Exogenous barcodes or genome-wide RNA mutations can be used to demultiplex pooled scRNA-seq data, but they are experimentally or computationally challenging and limited in scope. Mitochondrial genomes are small but diverse, providing concise genotype information. We developed "mitoSplitter," an algorithm that demultiplexes samples using mitochondrial RNA (mtRNA) variants, and demonstrated that mtRNA variants can be used to demultiplex large-scale scRNA-seq data. Using affordable computational resources, mitoSplitter can accurately analyze 10 samples and 60,000 cells in 6 h. To avoid the batch effects from separated experiments, we applied mitoSplitter to analyze the responses of five non-small cell lung cancer cell lines to BET (Bromodomain and extraterminal) chemical degradation in a multiplexed fashion. We found the synthetic lethality of TOP2A inhibition and BET chemical degradation in BET inhibitor-resistant cells. The result indicates that mitoSplitter can accelerate the application of scRNA-seq assays in biomedical research.},
}
@article {pmid37725510,
year = {2023},
author = {Alonso-Gil, D and Losada, A},
title = {Protocol to analyze chromatin-bound proteins through the cell cycle using Chromoflow flow cytometry.},
journal = {STAR protocols},
volume = {4},
number = {4},
pages = {102568},
pmid = {37725510},
issn = {2666-1667},
mesh = {Flow Cytometry ; Cell Division ; Cell Cycle ; *Chromatin/genetics ; *Antibodies ; },
abstract = {Chromatin-bound proteins have been conventionally measured through subcellular fractionation followed by immunoblotting or by immunofluorescence microscopy. Here, we present Chromoflow, a protocol for the quantitative analyses of protein levels on chromatin in single cells and throughout the cell cycle using flow cytometry. We describe steps for harvesting cells and for nuclear extraction, and a barcoding strategy to multiplex samples from different conditions that reduces antibody staining variability and eliminates the need for normalization.[1][,][2] We then detail procedures for data acquisition and analysis. For complete details on the use and execution of this protocol, please refer to Alonso-Gil et al. (2023).[3].},
}
@article {pmid37724509,
year = {2024},
author = {Neu, TR and Kuhlicke, U and Karwautz, C and Lüders, T},
title = {Unique architecture of microbial snottites from a methane driven biofilm revealed by confocal microscopy.},
journal = {Microscopy research and technique},
volume = {87},
number = {2},
pages = {205-213},
doi = {10.1002/jemt.24422},
pmid = {37724509},
issn = {1097-0029},
support = {//Helmholtz-Gemeinschaft/ ; },
mesh = {Humans ; *Methane ; *Biofilms ; Glycoconjugates/analysis ; Lectins/metabolism ; Bacteria ; Microscopy, Confocal ; },
abstract = {Microbial biofilms occur in many shapes and different dimensions. In natural and semi-artificial caves they are forming pendulous structures of 10 cm and more. In this study a methane driven microbial community of a former medicinal spring was investigated. The habitat was completely covered by massive biofilms and snottites with a wobbly, gelatinous appearance. By using fluorescence techniques in combination with confocal laser scanning microscopy the architecture of these so far unknown snottites was examined. The imaging approaches applied comprised reflection of geogenic and cellular origin, possible autofluorescence, nucleic acid staining for bacterial cells, protein staining for bacteria and extracellular fine structures, calcofluor white for β 1 → 3, β 1 → 4 polysaccharide staining for possible fungi as well as lectin staining for the extracellular biofilm matrix glycoconjugates. The results showed a highly complex, intricate structure with voluminous, globular, and tube-like glycoconjugates of different dimensions and densities. In addition, filamentous bacteria seem to provide additional strength to the snottites. After screening with all commercially available lectins, by means of fluorescence lectin barcoding and subsequent fluorescence lectin binding analysis, the AAL, PNA, LEA, and Ban lectins identified α-Fuc, β-Gal, β-GlcNAc, and α-Man with α-Fuc as a major component. Examination of the outer boundary with fluorescent beads revealed a potential outer layer which could not be stained by any of the fluorescent probes applied. Finally, suggestions are made to further elucidate the characteristics of these unusual microbial biofilms in form of snottites. RESEARCH HIGHLIGHTS: The gelatinous snottites revealed at the microscale a highly complex structure not seen before. The extracellular matrix of the snottite biofilm was identified as clusters of different shape and density. The matrix of snottites was examined by taking advantage of 78 fluorescently-labeled lectins. The extracellular matrix glycoconjugates of snottites identified comprised: α-Fuc, β-Gal, β-GlcNAc, and α-Man. Probing the snottite outer surface indicated an additional unknown stratum.},
}
@article {pmid37723830,
year = {2023},
author = {Kuroki, Y and Agata, K},
title = {Isolation of planarian viable cells using fluorescence-activated cell sorting for advancing single-cell transcriptome analysis.},
journal = {Genes to cells : devoted to molecular &amp; cellular mechanisms},
volume = {28},
number = {11},
pages = {800-810},
pmid = {37723830},
issn = {1365-2443},
support = {22J13743//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; Flow Cytometry/methods ; *Planarians/genetics ; Single-Cell Gene Expression Analysis ; *Pluripotent Stem Cells ; RNA, Messenger ; },
abstract = {Preparing viable single cells is critical for conducting single-cell RNA sequencing (scRNA-seq) because the presence of ambient RNA from dead or damaged cells can interfere with data analysis. Here, we developed a method for isolating viable single cells from adult planarian bodies using fluorescence-activated cell sorting (FACS). This method was then applied to both adult pluripotent stem cells (aPSCs) and differentiating/differentiated cells. Initially, we employed a violet instead of ultraviolet (UV) laser to excite Hoechst 33342 to reduce cellular damage. After optimization of cell staining conditions and FACS compensation, we generated FACS profiles similar to those created using a previous method that employed a UV laser. Despite successfully obtaining high-quality RNA sequencing data for aPSCs, non-aPSCs produced low-quality RNA reads (i.e., <60% of cells possessing barcoding mRNAs). Subsequently, we identified an effective FACS gating condition that excluded low-quality cells and tissue debris without staining. This non-staining isolation strategy not only reduced post-dissociation time but also enabled high-quality scRNA-seq results for all cell types (i.e., >80%). Taken together, these findings imply that the non-staining FACS strategy may be beneficial for isolating viable cells not only from planarians but also from other organisms and tissues for scRNA-seq studies.},
}
@article {pmid37723667,
year = {2023},
author = {Chen, Z and Liu, Z and Liu, J and Xiao, X},
title = {Research progress in the detection of common foodborne hazardous substances based on functional nucleic acids biosensors.},
journal = {Biotechnology and bioengineering},
volume = {120},
number = {12},
pages = {3501-3517},
doi = {10.1002/bit.28555},
pmid = {37723667},
issn = {1097-0290},
support = {22007045//National Natural Science Foundation of China/ ; C202312067687//Scientific Research Project of Hunan Provincial Health Commission/ ; },
mesh = {*Nucleic Acids ; Hazardous Substances ; DNA ; *Biosensing Techniques/methods ; *Environmental Pollutants ; },
abstract = {With the further improvement of food safety requirements, the development of fast, highly sensitive, and portable methods for the determination of foodborne hazardous substances has become a new trend in the food industry. In recent years, biosensors and platforms based on functional nucleic acids, along with a range of signal amplification devices and methods, have been established to enable rapid and sensitive determination of specific substances in samples, opening up a new avenue of analysis and detection. In this paper, functional nucleic acid types including aptamers, deoxyribozymes, and G-quadruplexes which are commonly used in the detection of food source pollutants are introduced. Signal amplification elements include quantum dots, noble metal nanoparticles, magnetic nanoparticles, DNA walkers, and DNA logic gates. Signal amplification technologies including nucleic acid isothermal amplification, hybridization chain reaction, catalytic hairpin assembly, biological barcodes, and microfluidic system are combined with functional nucleic acids sensors and applied to the detection of many foodborne hazardous substances, such as foodborne pathogens, mycotoxins, residual antibiotics, residual pesticides, industrial pollutants, heavy metals, and allergens. Finally, the potential opportunities and broad prospects of functional nucleic acids biosensors in the field of food analysis are discussed.},
}
@article {pmid37721899,
year = {2023},
author = {Rúa-Giraldo, &#xc1;L},
title = {Fungal taxonomy: A puzzle with many missing pieces.},
journal = {Biomedica : revista del Instituto Nacional de Salud},
volume = {43},
number = {Sp. 1},
pages = {288-311},
pmid = {37721899},
issn = {2590-7379},
abstract = {Fungi are multifaceted organisms found in almost all ecosystems on Earth, where they establish various types of symbiosis with other living beings. Despite being recognized by humans since ancient times, and the high number of works delving into their biology and ecology, much is still unknown about these organisms. Some criteria classically used for their study are nowadays limited, generating confusion in categorizing them, and even more, when trying to understand their genealogical relationships. To identify species within Fungi, phenotypic characters to date are not sufficient, and to construct a broad phylogeny or a phylogeny of a particular group, there are still gaps affecting the generated trees, making them unstable and easily debated. For health professionals, fungal identification at lower levels such as genus and species, is enough to select the most appropriate therapy for their control, understand the epidemiology of clinical pictures associated, and recognize outbreaks and antimicrobial resistance. However, the taxonomic location within the kingdom, information with apparently little relevance, can allow phylogenetic relationships to be established between fungal taxa, facilitating the understanding of their biology, distribution in nature, and pathogenic potential evolution. Advances in molecular biology and computer science techniques from the last 30 years have led to crucial changes aiming to establish the criteria to define a fungal species, allowing us to reach a kind of stable phylogenetic construction. However, there is still a long way to go, and it requires the joint work of the scientific community at a global level and support for basic research.},
}
@article {pmid37720058,
year = {2023},
author = {Pollmann, M and Kuhn, D and König, C and Homolka, I and Paschke, S and Reinisch, R and Schmidt, A and Schwabe, N and Weber, J and Gottlieb, Y and Steidle, JLM},
title = {New species based on the biological species concept within the complex of Lariophagus distinguendus (Hymenoptera, Chalcidoidea, Pteromalidae), a parasitoid of household pests.},
journal = {Ecology and evolution},
volume = {13},
number = {9},
pages = {e10524},
pmid = {37720058},
issn = {2045-7758},
abstract = {The pteromalid parasitoid Lariophagus distinguendus (Foerster) belongs to the Hymenoptera, a megadiverse insect order with high cryptic diversity. It attacks stored product pest beetles in human storage facilities. Recently, it has been shown to consist of two separate species. To further study its cryptic diversity, strains were collected to compare their relatedness using barcoding and nuclear genes. Nuclear genes identified two clusters which agree with the known two species, whereas the barcode fragment determined an additional third Clade. Total reproductive isolation (RI) according to the biological species concept (BSC) was investigated in crossing experiments within and between clusters using representative strains. Sexual isolation exists between all studied pairs, increasing from slight to strong with genetic distance. Postzygotic barriers mostly affected hybrid males, pointing to Haldane's rule. Hybrid females were only affected by unidirectional Spiroplasma-induced cytoplasmic incompatibility and behavioural sterility, each in one specific strain combination. RI was virtually absent between strains separated by up to 2.8% COI difference, but strong or complete in three pairs from one Clade each, separated by at least 7.2%. Apparently, each of these clusters represents one separate species according to the BSC, highlighting cryptic diversity in direct vicinity to humans. In addition, these results challenge the recent 'turbo-taxonomy' practice of using 2% COI differences to delimitate species, especially within parasitic Hymenoptera. The gradual increase in number and strength of reproductive barriers between strains with increasing genetic distance also sheds light on the emergence of barriers during the speciation process in L. distinguendus.},
}
@article {pmid37718009,
year = {2023},
author = {Abdollah, S and Reza, ZH and Abbas, AS and Jafar, A},
title = {Investigating DNA barcodes of plants growing in some areas of Iran with high crime rate: Quercus brantii, Curpressus arizonica, Crataegus pentagyna, Ziziphus Spina-chtista, and Buxus hyrcana.},
journal = {Science &amp; justice : journal of the Forensic Science Society},
volume = {63},
number = {5},
pages = {624-634},
doi = {10.1016/j.scijus.2023.07.006},
pmid = {37718009},
issn = {1876-4452},
mesh = {Humans ; *Crataegus ; *Quercus ; *Buxus ; Iran ; Bayes Theorem ; DNA Barcoding, Taxonomic ; Phylogeny ; *Ziziphus ; DNA ; Crime ; },
abstract = {According to criminal botany, the offender unknowingly carries plant samples from the crime scene. Therefore, studying the genetic data of plants native to the crime scene can solve many ambiguities in the criminal files. In this regard, the aim of this study was to investigate the genome of 5 endemic plants in some areas of Iran with high crime rate. Quercus brantii, Curpressus arizonica, Crataegus pentagyna, Ziziphus Spina-chtista, and Buxus hyrcana were assessed using 1 genetic fragment on plastid regions (trnH-psbA) as well as 1 gene on nuclear chromosome called ITS. The alignment of DNA sequences of trnH-psbA and ITS genes was done using BioEdit, Clustal X, and Muscle v4.0 software programs. The phylogenetic analysis was performed on aligned data using Maximum Parsimony (MP) and the Bayesian methods. The Splits Tree v.4.14.4 software program was used for phylogenetic network analysis. Finally, the data combinability test was conducted using the Incongruence Length Difference (ILD) test by PAUP* software program. All data from nrDNA ITS and trnH-psbA sequences were consistent with Information Compatibility Test (ICT) results. Moreover, the nrDNA ITS indicated more resolved relationship than trnH-psbA. The results from MP and Bayesian analyses did not differ significantly between singular and combined forms, except for a slight variance in confidence interval of branches. As the phylogenetic trees provide more thorough and deeper conception of species relations, it is hoped that they would be useful to illuminate some forensic gaps in regions with high crime rates enriched by these plants, not only in Iran, but also in all areas over the world with this vegetation.},
}
@article {pmid37713487,
year = {2023},
author = {Hershey, BJ and Barozzi, S and Orsenigo, F and Pompei, S and Iannelli, F and Kamrad, S and Matafora, V and Pisati, F and Calabrese, L and Fragale, G and Salvadori, G and Martini, E and Totaro, MG and Magni, S and Guan, R and Parazzoli, D and Maiuri, P and Bachi, A and Patil, KR and Cosentino Lagomarsino, M and Havas, KM},
title = {Clonal cooperation through soluble metabolite exchange facilitates metastatic outgrowth by modulating Allee effect.},
journal = {Science advances},
volume = {9},
number = {37},
pages = {eadh4184},
pmid = {37713487},
issn = {2375-2548},
mesh = {Humans ; Animals ; *Coloring Agents ; Disease Models, Animal ; Population Density ; *Triple Negative Breast Neoplasms ; },
abstract = {Cancers feature substantial intratumoral heterogeneity of genetic and phenotypically distinct lineages. Although interactions between coexisting lineages are emerging as a potential contributor to tumor evolution, the extent and nature of these interactions remain largely unknown. We postulated that tumors develop ecological interactions that sustain diversity and facilitate metastasis. Using a combination of fluorescent barcoding, mathematical modeling, metabolic analysis, and in vivo models, we show that the Allee effect, i.e., growth dependency on population size, is a feature of tumor lineages and that cooperative ecological interactions between lineages alleviate the Allee barriers to growth in a model of triple-negative breast cancer. Soluble metabolite exchange formed the basis for these cooperative interactions and catalyzed the establishment of a polyclonal community that displayed enhanced metastatic dissemination and outgrowth in xenograft models. Our results highlight interclonal metabolite exchange as a key modulator of tumor ecology and a contributing factor to overcoming Allee effect-associated growth barriers to metastasis.},
}
@article {pmid37711497,
year = {2023},
author = {Kits, JH},
title = {The genus Errastunus in the Nearctic region (Hemiptera, Cicadellidae, Deltocephalinae).},
journal = {ZooKeys},
volume = {1178},
number = {},
pages = {143-164},
pmid = {37711497},
issn = {1313-2989},
abstract = {The leafhopper genus Errastunus contains grass-feeding leafhoppers in the deltocephaline tribe Paralimnini. The taxonomy of the genus in the Nearctic region has long been confused, with one to three distinct species recognized by different authors. Some populations have also been suggested to be adventive from Europe. Morphological and molecular data show that there are two distinct species in North America. These taxa are readily distinguishable morphologically although there is evidence of mitochondrial introgression between the species. The distribution of the two species based on historical material in collections suggests that Errastunussobrinus (DeLong &amp; Sleesman, 1929) is native to North America, while E.ocellaris (Fallén, 1806) includes both native and adventive populations. A lectotype is designated for E.sobrinus and Cicadaocellata Scopoli, 1763 is established as a nomen oblitum with Cicadaocellaris as a nomen protectum.},
}
@article {pmid37707732,
year = {2023},
author = {Liu, JL and Yao, J and Zhou, DL and Liu, B and Liu, H and Li, M and Zhao, C and Sunahara, G and Duran, R},
title = {Mining-related multi-resistance genes in sulfate-reducing bacteria treatment of typical karst nonferrous metal(loid) mine tailings in China.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {47},
pages = {104753-104766},
pmid = {37707732},
issn = {1614-7499},
mesh = {RNA, Ribosomal, 16S ; *Metals/analysis ; *Bacteria/metabolism ; Anti-Bacterial Agents/pharmacology ; China ; Sulfates/analysis ; Genes, Bacterial ; },
abstract = {Management of tailings at metal mine smelter sites can reduce the potential hazards associated with exposure to toxic metal(loid)s and residual organic flotation reagents. In addition, microbes in the tailings harboring multi-resistance genes (e.g., tolerance to multiple antimicrobial agents) can cause high rates of morbidity and global economic problems. The potential co-selection mechanisms of antibiotic resistance genes (ARGs) and metal(loid) resistance genes (MRGs) during tailings sulfate-reducing bacteria (SRB) treatment have been poorly investigated. Samples were collected from a nonferrous metal mine tailing site treated with an established SRB protocol and were analyzed for selected geochemical properties and high throughput sequencing of 16S rRNA gene barcoding. Based on the shotgun metagenomic analysis, the bacterial domain was dominant in nonferrous metal(loid)-rich tailings treated with SRB for 12 months. KEGGs related to ARGs and MRGs were detected. Thiobacillus and Sphingomonas were the main genera carrying the bacA and mexEF resistance operons, along with Sulfuricella which were also found as the main genera carrying MRGs. The SRB treatment may mediate the distribution of numerous resistance genes. KOs based on the metagenomic database indicated that ARGs (mexNW, merD, sul, and bla) and MRGs (czcABCR and copRS genes) were found on the same contig. The SRB strains (Desulfosporosinus and Desulfotomaculum), and the acidophilic strain Acidiphilium significantly contributed to the distribution of sul genes. The functional metabolic pathways related to siderophores metabolism were largely from anaerobic genera of Streptomyces and Microbacterium. The presence of arsenate reductase, metal efflux pump, and Fe transport genes indicated that SRB treatment plays a key role in the metal(loid)s transformation. Overall, our findings show that bio-treatment is an effective tool for managing ARGs/MRGs and metals in tailings that contain numerous metal(loid) contaminants.},
}
@article {pmid37706164,
year = {2023},
author = {Oldenbeuving, A and Gómez-Zúniga, A and Florez-Buitrago, X and Gutiérrez-Zuluaga, AM and Machado, CA and Van Dooren, TJM and van Alphen, J and Biesmeijer, JC and Herre, EA},
title = {Field sampling of fig pollinator wasps across host species and host developmental phase: Implications for host recognition and specificity.},
journal = {Ecology and evolution},
volume = {13},
number = {9},
pages = {e10501},
pmid = {37706164},
issn = {2045-7758},
abstract = {Previous genetic studies of pollinator wasps associated with a community of strangler figs (Ficus subgenus Urostigma, section Americana) in Central Panama suggest that the wasp species exhibit a range in host specificity across their host figs. To better understand factors that might contribute to this observed range of specificity, we used sticky traps to capture fig-pollinating wasp individuals at 13 Ficus species, sampling at different phases of the reproductive cycle of the host figs (e.g., trees with receptive inflorescences, or vegetative trees, bearing only leaves). We also sampled at other tree species, using them as non-Ficus controls. DNA barcoding allowed us to identify the wasps to species and therefore assign their presence and abundance to host fig species and the developmental phase of that individual tree. We found: (1) wasps were only very rarely captured at non-Ficus trees; (2) nonetheless, pollinators were captured often at vegetative individuals of some host species; (3) overwhelmingly, wasp individuals were captured at receptive host fig trees representing the fig species from which they usually emerge. Our results indicate that wasp occurrence is not random either spatially or temporally within the forest and across these hosts, and that wasp specificity is generally high, both at receptive and vegetative host trees. Therefore, in addition to studies that show chemicals produced by receptive fig inflorescences attract pollinator wasps, we suggest that other cues (e.g., chemicals produced by the leaves) can also play a role in host recognition. We discuss our results in the context of recent findings on the role of host shifts in diversification processes in the Ficus genus.},
}
@article {pmid37705245,
year = {2023},
author = {Rios, X and Pardias, O and Morales, MA and Bhattacharya, P and Chen, Y and Guo, L and Zhang, C and Di Pierro, EJ and Tian, G and Barragan, GA and Sumazin, P and Metelitsa, LS},
title = {Refining chimeric antigen receptors via barcoded protein domain combination pooled screening.},
journal = {Molecular therapy : the journal of the American Society of Gene Therapy},
volume = {31},
number = {11},
pages = {3210-3224},
pmid = {37705245},
issn = {1525-0024},
mesh = {Humans ; *Receptors, Chimeric Antigen/metabolism ; Protein Domains ; Receptors, Antigen, T-Cell/metabolism ; T-Lymphocytes ; *Neoplasms/metabolism ; Immunoglobulin G/metabolism ; Immunotherapy, Adoptive/methods ; Antigens, CD19 ; },
abstract = {Chimeric antigen receptor (CAR)-T cells represent a promising frontier in cancer immunotherapy. However, the current process for developing new CAR constructs is time consuming and inefficient. To address this challenge and expedite the evaluation and comparison of full-length CAR designs, we have devised a novel cloning strategy. This strategy involves the sequential assembly of individual CAR domains using blunt ligation, with each domain being assigned a unique DNA barcode. Applying this method, we successfully generated 360 CAR constructs that specifically target clinically validated tumor antigens CD19 and GD2. By quantifying changes in barcode frequencies through next-generation sequencing, we characterize CARs that best mediate proliferation and expansion of transduced T cells. The screening revealed a crucial role for the hinge domain in CAR functionality, with CD8a and IgG4 hinges having opposite effects in the surface expression, cytokine production, and antitumor activity in CD19- versus GD2-based CARs. Importantly, we discovered two novel CD19-CAR architectures containing the IgG4 hinge domain that mediate superior in vivo antitumor activity compared with the construct used in Kymriah, a U.S. Food and Drug Administration (FDA)-approved therapy. This novel screening approach represents a major advance in CAR engineering, enabling accelerated development of cell-based cancer immunotherapies.},
}
@article {pmid37704979,
year = {2023},
author = {Zaki, ZMM and Kuroda, A and Morimura, N and Hayashi, Y and Hitoshi, S},
title = {Depletion of transit amplifying cells in the adult brain does not affect quiescent neural stem cell pool size.},
journal = {The journal of physiological sciences : JPS},
volume = {73},
number = {1},
pages = {19},
pmid = {37704979},
issn = {1880-6562},
support = {16H04671//Ministry of Education, Culture, Sports, Science and Technology of Japan/ ; 22K19359//Ministry of Education, Culture, Sports, Science and Technology of Japan/ ; },
mesh = {Animals ; *Brain ; *Neural Stem Cells ; Neurons ; Infusions, Intraventricular ; Longevity ; Mammals ; },
abstract = {Neural stem cells (NSCs) are maintained in the adult mammalian brain throughout the animal's lifespan. NSCs in the subependymal zone infrequently divide and generate transit amplifying cells, which are destined to become olfactory bulb neurons. When transit amplifying cells are depleted, they are replenished by the quiescent NSC pool. However, the cellular basis for this recovery process remains largely unknown. In this study, we traced NSCs and their progeny after transit amplifying cells were eliminated by intraventricular infusion of cytosine β-D-arabinofuranoside. We found that although the number of neurosphere-forming NSCs decreased shortly after the treatment, they were restored to normal levels 3 weeks after the cessation of treatment. More importantly, the depletion of transit amplifying cells did not induce a significant expansion of the NSC pool by symmetric divisions. Our data suggest that the size of the NSC pool is hardly affected by brain damage due to antimitotic drug treatment.},
}
@article {pmid37703242,
year = {2023},
author = {Baker, CS and Claridge, D and Dunn, C and Fetherston, T and Baker, DN and Klinck, H and Steel, D},
title = {Quantification by droplet digital PCR and species identification by metabarcoding of environmental (e)DNA from Blainville's beaked whales, with assisted localization from an acoustic array.},
journal = {PloS one},
volume = {18},
number = {9},
pages = {e0291187},
pmid = {37703242},
issn = {1932-6203},
mesh = {Animals ; Whales/genetics ; DNA/genetics ; *DNA, Environmental/genetics ; *Dolphins ; *Porpoises ; Polymerase Chain Reaction ; Acoustics ; },
abstract = {Detection and identification of species, subspecies or stocks of whales, dolphins and porpoises at sea remain challenging, particularly for cryptic or elusive species like beaked whales (Family: Ziphiidae). Here we investigated the potential for using an acoustically assisted sampling design to collect environmental (e)DNA from beaked whales on the U.S. Navy's Atlantic Undersea Test and Evaluation Center (AUTEC) in The Bahamas. During 12 days of August 2019, we conducted 9 small-boat surveys and collected 56 samples of seawater (paired subsamples of 1L each, including controls) using both a spatial collection design in the absence of visual confirmation of whales, and a serial collection design in the proximity of whales at the surface. There were 7 sightings of whales, including 11 Blainville's beaked whales (Mesoplodon densirostris). All whales were located initially with the assistance of information from a bottom-mounted acoustic array available on the AUTEC range. Quantification by droplet digital (dd)PCR from the four spatial design collections showed no samples of eDNA above the threshold of detection and none of these 20 samples yielded amplicons for conventional or next-generation sequencing. Quantification of the 31 samples from four serial collections identified 11 likely positive detections. eDNA barcoding by conventional sequencing and eDNA metabarcoding by next-generation sequencing confirmed species identification for 9 samples from three of the four serial collections. We further resolved five intra-specific variants (i.e., haplotypes), two of which showed an exact match to previously published haplotypes and three that have not been reported previously to the international repository, GenBank. A minimum spanning network of the five eDNA haplotypes, with all other published haplotypes of Blainville's beaked whales, suggested the potential for further resolution of differences between oceanic populations.},
}
@article {pmid37702121,
year = {2023},
author = {Ramirez, JL and Valdivia, P and Rosas-Puchuri, U and Valdivia, NL},
title = {SPdel: A pipeline to compare and visualize species delimitation methods for single-locus datasets.},
journal = {Molecular ecology resources},
volume = {23},
number = {8},
pages = {1959-1965},
doi = {10.1111/1755-0998.13864},
pmid = {37702121},
issn = {1755-0998},
abstract = {An accurate species delimitation is critical for biological studies. In this context, the use of molecular techniques along with species delimitation methods would help to a rapid and accurate biodiversity assessment. The species delimitation methods cluster data sets of orthologous sequences in molecular operational taxonomic units (MOTU). In particular, the methods based on a single gene are easily integrated with the widely used DNA barcoding approach. We developed SPdel a user-friendly pipeline to integrate different single-gene species delimitation methods. SPdel is designed to calculate and compare MOTUs obtained by different species delimitation approaches. SPdel also outputs diverse ready-to-publish quality figures, that facilitate the interpretation of results. SPdel aims to help researchers use species delimitation methods that would improve biodiversity studies.},
}
@article {pmid37695905,
year = {2023},
author = {Yousefi, M and Andrejka, L and Szamecz, M and Winslow, MM and Petrov, DA and Boross, G},
title = {Fully accessible fitness landscape of oncogene-negative lung adenocarcinoma.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {38},
pages = {e2303224120},
pmid = {37695905},
issn = {1091-6490},
support = {F32 CA236311/CA/NCI NIH HHS/United States ; R01 CA230919/CA/NCI NIH HHS/United States ; R01 CA231253/CA/NCI NIH HHS/United States ; R01 CA234349/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Oncogenes/genetics ; *Adenocarcinoma of Lung/genetics ; Mutation ; *Lung Neoplasms/genetics ; Cell Transformation, Neoplastic ; p120 GTPase Activating Protein ; },
abstract = {Cancer genomes are almost invariably complex with genomic alterations cooperating during each step of carcinogenesis. In cancers that lack a single dominant oncogene mutation, cooperation between the inactivation of multiple tumor suppressor genes can drive tumor initiation and growth. Here, we shed light on how the sequential acquisition of genomic alterations generates oncogene-negative lung tumors. We couple tumor barcoding with combinatorial and multiplexed somatic genome editing to characterize the fitness landscapes of three tumor suppressor genes NF1, RASA1, and PTEN, the inactivation of which jointly drives oncogene-negative lung adenocarcinoma initiation and growth. The fitness landscape was surprisingly accessible, with each additional mutation leading to growth advantage. Furthermore, the fitness landscapes remained fully accessible across backgrounds with the inactivation of additional tumor suppressor genes. These results suggest that while predicting cancer evolution will be challenging, acquiring the multiple alterations that drive the growth of oncogene-negative tumors can be facilitated by the lack of constraints on mutational order.},
}
@article {pmid37692426,
year = {2023},
author = {Senizza, B and Araniti, F and Lewin, S and Wende, S and Kolb, S and Lucini, L},
title = {Trichoderma spp.-mediated mitigation of heat, drought, and their combination on the Arabidopsis thaliana holobiont: a metabolomics and metabarcoding approach.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1190304},
pmid = {37692426},
issn = {1664-462X},
abstract = {INTRODUCTION: The use of substances to increase productivity and resource use efficiency is now essential to face the challenge of feeding the rising global population with the less environmental impact on the ecosystems. Trichoderma-based products have been used as biopesticides, to inhibit pathogenic microorganisms, and as biostimulants for crop growth, nutrient uptake promotion, and resistance to abiotic stresses.<br><br>METHODS: In this work, plant metabolomics combined with roots and rhizosphere bacterial metabarcoding were exploited to inspect the performance of Trichoderma spp. biostimulants on Arabidopsis thaliana under drought, heat and their combination and its impact on plant holobiont.<br><br>RESULTS AND DISCUSSION: An overall modulation of N-containing compounds, phenylpropanoids, terpenes and hormones could be pointed out by metabolomics. Moreover, metabarcoding outlined an impact on alpha and beta-diversity with an abundance of Proteobacteria, Pseudomonadales, Burkholderiales, Enterobacteriales and Azospirillales. A holobiont approach was applied as an integrated analytical strategy to resolve the coordinated and complex dynamic interactions between the plant and its rhizosphere bacteria using Arabidopsis thaliana as a model host species.},
}
@article {pmid37691533,
year = {2024},
author = {Kudláčová, J and Kužílková, D and Bárta, F and Brdičková, N and Vávrová, A and Kostka, L and Hovorka, O and Kalina, T and Etrych, T},
title = {Hybrid Macromolecular Constructs as a Platform for Spectral Nanoprobes for Advanced Cellular Barcoding in Flow Cytometry.},
journal = {Macromolecular bioscience},
volume = {24},
number = {2},
pages = {e2300306},
doi = {10.1002/mabi.202300306},
pmid = {37691533},
issn = {1616-5195},
support = {NU21-08-00280//Ministry of Health of the Czech Republic/ ; NU23J-03-00026//Ministry of Health of the Czech Republic/ ; FV10370//Ministry of Industry and Trade of the Czech Republic/ ; //European Union/ ; LX22NPO5102//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; },
mesh = {Flow Cytometry/methods ; *Antibodies ; *Fluorescent Dyes/chemistry ; Immunophenotyping ; Polymers ; },
abstract = {Herein, an advanced bioconjugation technique to synthesize hybrid polymer-antibody nanoprobes tailored for fluorescent cell barcoding in flow cytometry-based immunophenotyping of leukocytes is applied. A novel approach of attachment combining two fluorescent dyes on the copolymer precursor and its conjugation to antibody is employed to synthesize barcoded nanoprobes of antibody polymer dyes allowing up to six nanoprobes to be resolved in two-dimensional cytometry analysis. The major advantage of these nanoprobes is the construct design in which the selected antibody is labeled with an advanced copolymer bearing two types of fluorophores in different molar ratios. The cells after antibody recognition and binding to the target antigen have a characteristic double fluorescence signal for each nanoprobe providing a unique position on the dot plot, thus allowing antibody-based barcoding of cellular samples in flow cytometry assays. This technique is valuable for cellular assays that require low intersample variability and is demonstrated by the live cell barcoding of clinical samples with B cell abnormalities. In total, the samples from six various donors were successfully barcoded using only two detection channels. This barcoding of clinical samples enables sample preparation and measurement in a single tube.},
}
@article {pmid37690679,
year = {2023},
author = {Trzebny, A and Jedut, S and Nahimova, O and Dabert, M},
title = {Differences in the proliferation trend of 'Microsporidium' sp. PL03 in Culex pipiens and C. torrentium larvae.},
journal = {Journal of invertebrate pathology},
volume = {201},
number = {},
pages = {107990},
doi = {10.1016/j.jip.2023.107990},
pmid = {37690679},
issn = {1096-0805},
mesh = {Animals ; Larva/genetics ; *Microsporidia, Unclassified ; *Culex ; *Microsporidia/genetics ; Cell Proliferation ; },
abstract = {Our study aimed to examine whether there are differences in the proliferation trend of microsporidia in mosquito larvae of the same genus (Culex spp.). DNA-barcoding and quantitative analyses were used to determine microsporidian rDNA copies in 'early' (L1 + L2) and 'late' (L3 + L4) Culex larvae in a natural population. In the study area, C. pipiens and C. torrentium larvae were infected by 'Microsporidium' sp. PL03 at similar levels. Infection by this microsporidian species probably elicits a notable immune response in C. pipiens, whereas in C. torrentium, it may evade or suppress the host immune response.},
}
@article {pmid37690315,
year = {2023},
author = {Ribeiro, GM and Useros, F and Dumack, K and González-Miguéns, R and Siemensma, F and Porfírio-Sousa, AL and Soler-Zamora, C and Pedro Barbosa Alcino, J and Lahr, DJG and Lara, E},
title = {Expansion of the cytochrome C oxidase subunit I database and description of four new lobose testate amoebae species (Amoebozoa; Arcellinida).},
journal = {European journal of protistology},
volume = {91},
number = {},
pages = {126013},
doi = {10.1016/j.ejop.2023.126013},
pmid = {37690315},
issn = {1618-0429},
mesh = {*Amoeba ; Electron Transport Complex IV/genetics ; Phylogeny ; *Amoebozoa ; *Lobosea ; },
abstract = {Arcellinida is ascending in importance in protistology, but description of their diversity still presents multiple challenges. Furthermore, applicable tools for surveillance of these organisms are still in developing stages. Importantly, a good database that sets a correspondence between molecular barcodes and species morphology is lacking. Cytochrome oxidase (COI) has been suggested as the most relevant marker for species discrimination in Arcellinida. However, some major groups of Arcellinida are still lacking a COI sequence. Here we expand the database of COI marker sequences for Arcellinids, using single-cell PCR, transcriptomics, and database scavenging. In the present work, we added 24 new Arcellinida COI sequences to the database, covering all unsampled infra- and suborders. Additionally, we added six new SSUrRNA sequences and described four new species using morphological, morphometrical, and molecular evidence: Heleopera steppica, Centropyxis blatta, Arcella uspiensis, and Cylindrifflugia periurbana. This new database will provide a new starting point to address new research questions from shell evolution, biogeography, and systematics of arcellinids.},
}
@article {pmid37687402,
year = {2023},
author = {Nakkaew, A and Masjon, T and Voravuthikunchai, SP},
title = {Genomic and Transcriptional Profiling Analysis and Insights into Rhodomyrtone Yield in Rhodomyrtus tomentosa (Aiton) Hassk.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {17},
pages = {},
pmid = {37687402},
issn = {2223-7747},
support = {SCI6305052M; SCI6505182d,SCI6201014S,SCI6305052a//National Science, Research and Innovation Fund (NSRF) and Prince of Songkla University (Grant No SCI6305052M; SCI6505182d) and Office of National Higher Education Science Research and Innovation Policy Council (NXPO) (SCI6201014S and SCI6305052a)/ ; },
abstract = {Rhodomyrtus tomentosa is a source of a novel antibiotic, rhodomyrtone. Because of the increasing industrial demand for this compound, germplasm with a high rhodomyrtone content is the key to sustainable future cultivation. In this study, rhodomyrtone genotypes were verified using the plastid genomic region marker matK and nuclear ribosomal internal transcribed spacer ITS. These two DNA barcodes proved to be useful tools for identifying different rhodomyrtone contents via the SNP haplotypes C569T and A561G, respectively. The results were correlated with rhodomyrtone content determined via HPLC. Subsequently, R. tomentosa samples with high- and low-rhodomyrtone genotypes were collected for de novo transcriptome and gene expression analyses. A total of 83,402 unigenes were classified into 25 KOG classifications, and 74,102 annotated unigenes were obtained. Analysis of differential gene expression between samples or groups using DESeq2 revealed highly expressed levels related to rhodomyrtone content in two genotypes. semiquantitative RT-PCR further revealed that the high rhodomyrtone content in these two genotypes correlated with expression of zinc transporter protein (RtZnT). In addition, we found that expression of RtZnT resulted in increased sensitivity of R. tomentosa under ZnSO4 stress. The findings provide useful information for selection of cultivation sites to achieve high rhodomyrtone yields in R. tomentosa.},
}
@article {pmid37687285,
year = {2023},
author = {Tsaballa, A and Kelesidis, G and Krigas, N and Sarropoulou, V and Bagatzounis, P and Grigoriadou, K},
title = {Taxonomic Identification and Molecular DNA Barcoding of Collected Wild-Growing Orchids Used Traditionally for Salep Production.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {17},
pages = {},
pmid = {37687285},
issn = {2223-7747},
support = {DMR1-0014355//This work was supported by the European Regional Development Fund of the European Union and Greek national funds through the call "Actions of collaborations and networking between research institutions, educational institutions and businesses in priority/ ; },
abstract = {Molecular DNA barcoding combined with botanical taxonomy can be used for the identification and conservation of collected Greek orchids used for salep production as well as in the regulation of fair salep trade. A modified CTAB protocol was used for DNA extraction, amplification of barcoding regions (ITS, matK, rbcL, trnH-psbA), and sequencing. Sequencing data were assembled using Bioedit software, and the BLAST algorithm was used on the NCBI database for species identification at the genus level. Molecular barcoding data based on genetic similarity identification was in full coherence with taxonomic classification based on morphological data. The combination of ITS and matK exhibited a greater capacity to identify a species among the Greek salep samples. Out of the 53 samples examined, 52.9% were classified as Dactylorhiza spp. and 33.3% as Anacamptis spp., whereas only 6 samples were identified as Orchis spp. (11.8%). Given that a superior-quality salep beverage comes from tubers of the latter, the number of samples classified as such in northwestern Greece is unexpectedly low. A database of 53 original reference sequences from wild-growing samples of Greek origin was generated, providing a valuable resource for the identification of other salep samples from different regions. The DNA barcoding results unveiled that salep samples from northwestern Greece are related to nine members of four different genera of Orchidaceae. All species are nationally protected and covered by the CITES convention, while many of these orchids are included in the EU Directive 92/43/EEC appendix as "Other Important Species". Thus, expedited coordinated management actions are needed to ensure their survival in the future.},
}
@article {pmid37686021,
year = {2023},
author = {Mo, ZQ and Wang, J and Möller, M and Yang, JB and Gao, LM},
title = {Phylogenetic Relationships and Next-Generation Barcodes in the Genus Torreya Reveal a High Proportion of Misidentified Cultivated Plants.},
journal = {International journal of molecular sciences},
volume = {24},
number = {17},
pages = {},
pmid = {37686021},
issn = {1422-0067},
support = {XDB31000000//the Strategic Priority Research Program of Chinese Academy of Sciences/ ; 2017-LSFGBOWS-02//the Large-scale Scientific Facilities of the Chinese Academy of Sciences/ ; 202101BC070003//the Key Basic Research Program of Yunnan Province, China/ ; 151853KYSB20190027//the International Partnership Program of Chinese Academy of Sciences/ ; },
mesh = {Phylogeny ; *Extinction, Psychological ; Gardening ; Genes, Mitochondrial ; *Taxaceae ; },
abstract = {Accurate species identification is key to conservation and phylogenetic inference. Living plant collections from botanical gardens/arboretum are important resources for the purpose of scientific research, but the proportion of cultivated plant misidentification are un-tested using DNA barcodes. Here, we assembled the next-generation barcode (complete plastid genome and complete nrDNA cistron) and mitochondrial genes from genome skimming data of Torreya species with multiple accessions for each species to test the species discrimination and the misidentification proportion of cultivated plants used in Torreya studies. A total of 38 accessions were included for analyses, representing all nine recognized species of genus Torreya. The plastid phylogeny showed that all 21 wild samples formed species-specific clades, except T. jiulongshanensis. Disregarding this putative hybrid, seven recognized species sampled here were successfully discriminated by the plastid genome. Only the T. nucifera accessions grouped into two grades. The species identification rate of the nrDNA cistron was 62.5%. The Skmer analysis based on nuclear reads from genome skims showed promise for species identification with seven species discriminated. The proportion of misidentified cultivated plants from arboreta/botanical gardens was relatively high with four accessions (23.5%) representing three species. Interspecific relationships within Torreya were fully resolved with maximum support by plastomes, where Torreya jackii was on the earliest diverging branch, though sister to T. grandis in the nrDNA cistron tree, suggesting that this is likely a hybrid species between T. grandis and an extinct Torreya ancestor lineage. The findings here provide quantitative insights into the usage of cultivated samples for phylogenetic study.},
}
@article {pmid37684303,
year = {2023},
author = {Huang, WC and Evacitas, FC and Balisco, RA and Nañola, CL and Chou, TK and Jhuang, WC and Chang, CW and Shen, KN and Shao, KT and Liao, TY},
title = {DNA barcoding of marine teleost fishes (Teleostei) in Cebu, the Philippines, a biodiversity hotspot of the coral triangle.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {14867},
pmid = {37684303},
issn = {2045-2322},
mesh = {Animals ; *Anthozoa ; Philippines ; DNA Barcoding, Taxonomic ; Fishes/genetics ; Biodiversity ; Cebus ; DNA ; },
abstract = {A morphology-based barcoding library of market teleost fishes (Teleostei) in Cebu is built based on cytochrome c oxidase subunit I (COI) sequences and voucher specimens which aimed to establish a reliable reference of frequently traded fishes in the province, a biodiversity hotspot at the center of the Philippine archipelago. A total of 1721 specimens were collected from 18 fish markets and landing sites around the province, in which 538 specimens were sequenced belonging to 393 species from 229 genera, 86 families, and 37 orders. Most speciose families are coral reef or reef-related shallow-water species. Twelve species from 11 families are newly recorded in the Philippine waters, among which 7 species are deep-sea inhabitants, while 3 species have expanded their distribution range. Only 20 taxa could not be identified to the species level due to the difficulty in morphological examinations, absence of matched reference sequences in online databases, and/or problematic species awaiting further studies. This first comprehensive DNA barcoding survey of Cebu fishes can facilitate further taxonomic research as well as the conservation and management of fisheries in the Philippines.},
}
@article {pmid37684044,
year = {2023},
author = {Depierre, D and Perrois, C and Schickele, N and Lhoumaud, P and Abdi-Galab, M and Fosseprez, O and Heurteau, A and Margueron, R and Cuvier, O},
title = {Chromatin in 3D distinguishes dMes-4/NSD and Hypb/dSet2 in protecting genes from H3K27me3 silencing.},
journal = {Life science alliance},
volume = {6},
number = {11},
pages = {},
pmid = {37684044},
issn = {2575-1077},
mesh = {*Chromatin/genetics ; *Histones/genetics ; Heterochromatin/genetics ; Chromatin Assembly and Disassembly ; },
abstract = {Cell type-specific barcoding of genomes requires the establishment of hundreds of heterochromatin domains where heterochromatin-associated repressive complexes hinder chromatin accessibility thereby silencing genes. At heterochromatin-euchromatin borders, regulation of accessibility not only depends on the delimitation of heterochromatin but may also involve interplays with nearby genes and their transcriptional activity, or alternatively on histone modifiers, chromatin barrier insulators, and more global demarcation of chromosomes into 3D compartmentalized domains and topological-associating domain (TADs). Here, we show that depletion of H3K36 di- or tri-methyl histone methyltransferases dMes-4/NSD or Hypb/dSet2 induces reproducible increasing levels of H3K27me3 at heterochromatin borders including in nearby promoters, thereby repressing hundreds of genes. Furthermore, dMes-4/NSD influences genes demarcated by insulators and TAD borders, within chromatin hubs, unlike transcription-coupled action of Hypb/dSet2 that protects genes independently of TADs. Insulator mutants recapitulate the increase of H3K27me3 upon dMes-4/NSD depletion unlike Hypb/dSet2. Hi-C data demonstrate how dMes-4/NSD blocks propagation of long-range interactions onto active regions. Our data highlight distinct mechanisms protecting genes from H3K27me3 silencing, highlighting a direct influence of H3K36me on repressive TADs.},
}
@article {pmid37680970,
year = {2023},
author = {Zhang, W and Xia, S and Tang, X and Zhang, X and Liang, D and Wang, Y},
title = {Topological analysis of functional connectivity in Parkinson's disease.},
journal = {Frontiers in neuroscience},
volume = {17},
number = {},
pages = {1236128},
pmid = {37680970},
issn = {1662-4548},
abstract = {Parkinson's disease (PD) is a clinically heterogeneous disorder, which mainly affects patients' motor and non-motor function. Functional connectivity was preliminary explored and studied through resting state functional magnetic resonance imaging (rsfMRI). Through the topological analysis of 54 PD scans and 31 age-matched normal controls (NC) in the Neurocon dataset, leveraging on rsfMRI data, the brain functional connection and the Vietoris-Rips (VR) complex were constructed. The barcodes of the complex were calculated to reflect the changes of functional connectivity neural circuits (FCNC) in brain network. The 0-dimensional Betti number β0 means the number of connected branches in VR complex. The average number of connected branches in PD group was greater than that in NC group when the threshold δ ≤ 0.7. Two-sample Mann-Whitney U test and false discovery rate (FDR) correction were used for statistical analysis to investigate the FCNC changes between PD and NC groups. In PD group, under threshold of 0.7, the number of FCNC involved was significantly differences and these brain regions include the Cuneus_R, Lingual_R, Fusiform_R and Heschl_R. There are also significant differences in brain regions in the Frontal_Inf_Orb_R and Pallidum_R, when the threshold increased to 0.8 and 0.9 (p < 0.05). In addition, when the length of FCNC was medium, there was a significant statistical difference between the PD group and the NC group in the Neurocon dataset and the Parkinson's Progression Markers Initiative (PPMI) dataset. Topological analysis based on rsfMRI data may provide comprehensive information about the changes of FCNC and may provide an alternative for clinical differential diagnosis.},
}
@article {pmid37680531,
year = {2023},
author = {Fathy, WA and Techen, N and Elsayed, KNM and Essawy, EA and Tawfik, E and Alwutayd, KM and Abdelhameed, MS and Hammouda, O and Ross, SA},
title = {Applying an internal transcribed spacer as a single molecular marker to differentiate between Tetraselmis and Chlorella species.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1228869},
pmid = {37680531},
issn = {1664-302X},
abstract = {In the realm of applied phycology, algal physiology, and biochemistry publications, the absence of proper identification and documentation of microalgae is a common concern. This poses a significant challenge for non-specialists who struggle to identify numerous eukaryotic microalgae. However, a promising solution lies in employing an appropriate DNA barcoding technique and establishing comprehensive databases of reference sequences. To address this issue, we conducted a study focusing on the molecular characterization and strain identification of Tetraselmis and Chlorella species, utilizing the internal transcribed spacer (ITS) barcode approach. By analyzing the full nuclear ITS region through the Sanger sequencing approach, we obtained ITS barcodes that were subsequently compared with other ITS sequences of various Tetraselmis and Chlorella species. To ensure the reliability of our identification procedure, we conducted a meticulous comparison of the DNA alignment, constructed a phylogenetic tree, and determined the percentage of identical nucleotides. The findings of our study reveal the significant value of the ITS genomic region as a tool for distinguishing and identifying morphologically similar chlorophyta. Moreover, our results demonstrate that both the ITS1 and ITS2 regions are capable of effectively discriminating isolates from one another; however, ITS2 is preferred due to its greater intraspecific variation. These results underscore the indispensability of employing ITS barcoding in microalgae identification, highlighting the limitations of relying solely on morphological characterization.},
}
@article {pmid37675839,
year = {2023},
author = {Bacsik, DJ and Dadonaite, B and Butler, A and Greaney, AJ and Heaton, NS and Bloom, JD},
title = {Influenza virus transcription and progeny production are poorly correlated in single cells.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {37675839},
issn = {2050-084X},
support = {75N93021C00015/AI/NIAID NIH HHS/United States ; R01 AI127893/AI/NIAID NIH HHS/United States ; R01 AI165821/AI/NIAID NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Humans ; *Influenza, Human ; Viral Transcription ; Genes, Viral ; Genome, Viral ; Mutation ; },
abstract = {The ultimate success of a viral infection at the cellular level is determined by the number of progeny virions produced. However, most single-cell studies of infection quantify the expression of viral transcripts and proteins, rather than the amount of progeny virions released from infected cells. Here, we overcome this limitation by simultaneously measuring transcription and progeny production from single influenza virus-infected cells by embedding nucleotide barcodes in the viral genome. We find that viral transcription and progeny production are poorly correlated in single cells. The cells that transcribe the most viral mRNA do not produce the most viral progeny and often represent aberrant infections that fail to express the influenza NS gene. However, only some of the discrepancy between transcription and progeny production can be explained by viral gene absence or mutations: there is also a wide range of progeny production among cells infected by complete unmutated virions. Overall, our results show that viral transcription is a relatively poor predictor of an infected cell's contribution to the progeny population.},
}
@article {pmid37674653,
year = {2023},
author = {Rüber, L and Gandolfi, A and Foresti, D and Paltrinieri, L and Splendiani, A and Seehausen, O},
title = {Phylogenetic and biogeographic history of brook lampreys (Lampetra: Petromyzontidae) in the river basins of the Adriatic Sea based on DNA barcode data.},
journal = {Ecology and evolution},
volume = {13},
number = {9},
pages = {e10496},
pmid = {37674653},
issn = {2045-7758},
abstract = {The Adriatic brook lamprey, Lampetra zanandreai Vladykov 1955, was described from northeastern Italy. Its distribution is thought to include left tributaries of the River Po and the river basins of the Adriatic Sea from the River Po to the River Isonzo/Soča in Italy, Switzerland and Slovenia. It also shows a geographically isolated distribution in the Potenza River on the Adriatic slope in Central Italy. Lampetra from the Neretva River system in Croatia and Bosnia and Herzegovina and the Morača River system in Montenegro that were previously identified as L. zanandreai were recently described as a new species Lampetra soljani Tutman, Freyhof, Dulčić, Glamuzina &amp; Geiger 2017 based on morphological data and a genetic distance between the two species of roughly 2.5% in the DNA barcoding gene cytochrome oxidase I (COI). Since DNA barcodes for L. zanandreai are only available for one population from the upper Po River in northwestern Italy, we generated additional COI nucleotide sequence data of this species from Switzerland, northeastern and central Italy comprising near topotypic material and obtained GenBank sequences of the species from Slovenia to better assess the evolutionary history of the two brook lamprey species in the river basins of the Adriatic Sea. Our data show a low sequence divergence of <1% between L. zanandreai from Switzerland, northeastern and central Italy and Slovenia and the Balkan species L. soljani. However, members of the population previously identified as 'L. zanandreai' from northwest Italy are genetically highly divergent from those of L. zanandreai and likely belong to an undescribed species, L. sp. 'upper Po'. The presence of a unique and highly divergent brook lamprey lineage in the upper Po River suggests that L. zanandreai and Lampetra sp. 'upper Po' may have evolved in separate paleo drainages during the formation of the modern Po Valley subsequent to marine inundations in the Pliocene.},
}
@article {pmid37674240,
year = {2023},
author = {Langsiri, N and Worasilchai, N and Irinyi, L and Jenjaroenpun, P and Wongsurawat, T and Luangsa-Ard, JJ and Meyer, W and Chindamporn, A},
title = {Targeted sequencing analysis pipeline for species identification of human pathogenic fungi using long-read nanopore sequencing.},
journal = {IMA fungus},
volume = {14},
number = {1},
pages = {18},
pmid = {37674240},
issn = {2210-6340},
support = {N11A650143//National Research Council of Thailand/ ; RA-MF 47/64//Matching fund, Rachadapisek Sompoch/ ; },
abstract = {Among molecular-based techniques for fungal identification, Sanger sequencing of the primary universal fungal DNA barcode, the internal transcribed spacer (ITS) region (ITS1, 5.8S, ITS2), is commonly used in clinical routine laboratories due to its simplicity, universality, efficacy, and affordability for fungal species identification. However, Sanger sequencing fails to identify mixed ITS sequences in the case of mixed infections. To overcome this limitation, different high-throughput sequencing technologies have been explored. The nanopore-based technology is now one of the most promising long-read sequencing technologies on the market as it has the potential to sequence the full-length ITS region in a single read. In this study, we established a workflow for species identification using the sequences of the entire ITS region generated by nanopore sequencing of both pure yeast isolates and mocked mixed species reads generated with different scenarios. The species used in this study included Candida albicans (n = 2), Candida tropicalis (n = 1), Nakaseomyces glabratus (formerly Candida glabrata) (n = 1), Trichosporon asahii (n = 2), Pichia kudriavzevii (formerly Candida krusei) (n = 1), and Cryptococcus neoformans (n = 1). Comparing various methods to generate the consensus sequence for fungal species identification, the results from this study indicate that read clustering using a modified version of the NanoCLUST pipeline is more sensitive than Canu or VSEARCH, as it classified species accurately with a lower abundance cluster of reads (3% abundance compared to 10% with VSEARCH). The modified NanoCLUST also reduced the number of classified clusters compared to VSEARCH, making the subsequent BLAST+ analysis faster. Subsampling of the datasets, which reduces the size of the datasets by approximately tenfold, did not significantly affect the identification results in terms of the identified species name, percent identity, query coverage, percentage of reads in the classified cluster, and the number of clusters. The ability of the method to distinguish mixed species within sub-populations of large datasets has the potential to aid computer analysis by reducing the required processing power. The herein presented new sequence analysis pipeline will facilitate better interpretation of fungal sequence data for species identification.},
}
@article {pmid37672506,
year = {2023},
author = {Gruppi, C and Sanzenbacher, P and Balekjian, K and Hagar, R and Hagen, S and Rayne, C and Schweizer, TM and Bossu, CM and Cooper, D and Dietsch, T and Smith, TB and Ruegg, K and Harrigan, RJ},
title = {Genetic identification of avian samples recovered from solar energy installations.},
journal = {PloS one},
volume = {18},
number = {9},
pages = {e0289949},
pmid = {37672506},
issn = {1932-6203},
mesh = {Animals ; *Solar Energy ; Renewable Energy ; Animals, Wild ; Birds/genetics ; Climate Change ; },
abstract = {Renewable energy production and development will drastically affect how we meet global energy demands, while simultaneously reducing the impact of climate change. Although the possible effects of renewable energy production (mainly from solar- and wind-energy facilities) on wildlife have been explored, knowledge gaps still exist, and collecting data from wildlife remains (when negative interactions occur) at energy installations can act as a first step regarding the study of species and communities interacting with facilities. In the case of avian species, samples can be collected relatively easily (as compared to other sampling methods), but may only be able to be identified when morphological characteristics are diagnostic for a species. Therefore, many samples that appear as partial remains, or "feather spots"-known to be of avian origin but not readily assignable to species via morphology-may remain unidentified, reducing the efficiency of sample collection and the accuracy of patterns observed. To obtain data from these samples and ensure their identification and inclusion in subsequent analyses, we applied, for the first time, a DNA barcoding approach that uses mitochondrial genetic data to identify unknown avian samples collected at solar facilities to species. We also verified and compared identifications obtained by our genetic method to traditional morphological identifications using a blind test, and discuss discrepancies observed. Our results suggest that this genetic tool can be used to verify, correct, and supplement identifications made in the field and can produce data that allow accurate comparisons of avian interactions across facilities, locations, or technology types. We recommend implementing this genetic approach to ensure that unknown samples collected are efficiently identified and contribute to a better understanding of wildlife impacts at renewable energy projects.},
}
@article {pmid37671015,
year = {2023},
author = {Khirallah, J and Xu, Q},
title = {A high-throughput approach of screening nanoparticles for targeted delivery of mRNA.},
journal = {Cell reports methods},
volume = {3},
number = {8},
pages = {100572},
pmid = {37671015},
issn = {2667-2375},
mesh = {RNA, Messenger ; Chromatography, Liquid ; *Nanoparticles ; Tandem Mass Spectrometry ; },
abstract = {The ability to specifically and efficiently deliver mRNA to target locations could unlock therapeutic strategies for a range of diseases. Rhym et al.[1] have developed an advanced approach for high-throughput, in vivo screening of tissue-targeting nanoparticle formulations, utilizing peptide barcoding and liquid chromatography with tandem mass spectrometry.},
}
@article {pmid37668919,
year = {2024},
author = {Bornhorst, D and Gheller, B and Zon, LI},
title = {Colorimetric Barcoding to Track, Isolate, and Analyze Hematopoietic Stem Cell Clones.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2707},
number = {},
pages = {265-277},
pmid = {37668919},
issn = {1940-6029},
support = {T32 HL007574/HL/NHLBI NIH HHS/United States ; R01 HL144780/HL/NHLBI NIH HHS/United States ; U24 DK126127/DK/NIDDK NIH HHS/United States ; P01 HL131477/HL/NHLBI NIH HHS/United States ; RC2 DK120535/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; *Colorimetry ; *Zebrafish ; Aorta ; Clone Cells ; Hematopoietic Stem Cells ; },
abstract = {In zebrafish, hematopoietic stem cells (HSCs) are born in the developing aorta during embryogenesis. From the definitive wave of hematopoiesis onward, blood homeostasis relies on self-renewal and differentiation of progeny of existing HSCs, or clones, rather than de novo generation. Here, we describe an approach to quantify the number and size of HSC clones at various times throughout the lifespan of the animal using a fluorescent, multicolor labeling strategy. The system is based on combining the multicolor Zebrabow system with an inducible, early lateral plate mesoderm and hematopoietic lineage specific cre driver (draculin (drl)). The cre driver can be temporally controlled and activated in early hematopoiesis to introduce a color barcoding unique to each HSC and subsequently inherited by their daughter cells. Clonal diversity and dominance can be investigated in normal development and blood disease progression, such as blood cancers. This adoptable method allows researchers to obtain quantitative insight into clonality-defining events and their contribution to adult hematopoiesis.},
}
@article {pmid37667092,
year = {2023},
author = {Kar, C and Mariyambi, PC and Raghavan, R and Sureshkumar, S},
title = {Mitochondrial phylogeny of fusilier fishes (family Caesionidae) from the Laccadive archipelago reveals a new species and two new records from the Central Indian Ocean.},
journal = {Journal of fish biology},
volume = {103},
number = {6},
pages = {1445-1451},
doi = {10.1111/jfb.15553},
pmid = {37667092},
issn = {1095-8649},
support = {CRG/2020/004498//Department of Science and Technology, Government of India/ ; 200510341520//University Grants Commission/ ; },
mesh = {Animals ; Phylogeny ; Indian Ocean ; *Fishes/genetics ; *Mitochondria/genetics ; Genes, Mitochondrial ; Pacific Ocean ; },
abstract = {Fusiliers of the family Caesionidae comprise a group of Indo-Pacific reef fishes important in the live bait and artisanal fisheries in many parts of its range, particularly in the Indian Ocean region. Using newly generated mitochondrial COI sequences of 10 species of caesionid fishes from the Laccadive archipelago, we carried out a molecular phylogenetic analysis, which has helped improve our understanding of the diversity, distribution, and systematics of this poorly known group of fishes. The two speciose genera within Caesionidae, Caesio and Pterocaesio, were revealed to be paraphyletic, and as a result, four names earlier considered as subgenera within Caesionidae (Flavicaesio, Odontonectes, Pisinnicaesio, and Squamosicaesio) were elevated to the status of distinct genera. We also discovered the presence of a new lineage in the Central Indian Ocean, sister to Caesio caerulaurea and Caesio xanthalytos, but distinct from both in several morphological characters and a genetic distance of between 2% and 3% in the mitochondrial COI gene. We describe this lineage as Caesio idreesi, a new species, with a distribution spanning the Laccadive Sea and the Bay of Bengal. Our genetic data also helped confirm the first confirmed records of two species, Pisinnicaesio digramma and Squamosicaesio randalli, from the Central Indian Ocean, and a new distribution record for C. xanthalytos in the Laccadive Sea. Combined, these results have helped bridge key biodiversity knowledge gaps of the family Caesionidae and form an excellent baseline for further investigations on their taxonomy, systematics, and life history.},
}
@article {pmid37664513,
year = {2023},
author = {Streicher, MB and Johnson, SD and Willows-Munro, S},
title = {Effect of fuchsin fixation of pollen on DNA barcode recovery.},
journal = {Ecology and evolution},
volume = {13},
number = {9},
pages = {e10475},
pmid = {37664513},
issn = {2045-7758},
abstract = {Pollen grains attached to insects are a valuable source of ecological information which can be used to reconstruct visitation networks. Morphological pollen identification relies on light microscopy with pollen usually stained and mounted in fuchsin jelly, which is also used to remove pollen from the bodies of insects. Pollen embedded in fuchsin jelly could potentially be used for DNA barcoding and metabarcoding (large-scale taxonomic identification of complex mixed samples) and thus provide additional information for pollination networks. In this study, we determine whether fuchsin-embedded pollen can be used for downstream molecular applications. We evaluate the quality of plant barcode (ITS) sequences amplified from DNA extracted from both fresh (untreated) pollen, and pollen which had been embedded in fuchsin jelly. We show that the addition of fuchsin to DNA extraction does not impact DNA barcode sequence quality during short-term storage. DNA extractions from both untreated and fuchsin-treated pollen produced reliable barcode sequences of high quality. Our findings suggest that pollen which has been collected, stained, and embedded in fuchsin jelly for preliminary microscopy work can be used within several days for downstream genetic analysis, though the quality of DNA from pollen stored in fuchsin jelly for extended periods is yet to be established.},
}
@article {pmid37663047,
year = {2023},
author = {Pagliusi, S and Madrid, Y and Bramanti, Y and Wilmansyah, T and Yu, H and Acebal, A and Krishnamurthy, KR and Raju Pinnamaraju, V and Jadhav, P and Park, R and Yang, L},
title = {Vaccine traceability: Key learnings from the supply chain initiative by manufacturers from emerging countries.},
journal = {Vaccine: X},
volume = {15},
number = {},
pages = {100366},
pmid = {37663047},
issn = {2590-1362},
abstract = {The use of global standards, and the placement of barcodes and data matrix codes on vaccine labels and other levels of packaging are crucial elements for the traceability of finished vaccine products. Vaccine manufacturers are committed to improving health through their products, as vaccine production offers opportunities that can be leveraged to benefit immunization systems. In 2019 the Developing Countries Vaccine Manufacturers Network (DCVMN) created the Supply Chain Initiative aimed at prioritize and explore traceability opportunities; concomitantly procurement agencies announced traceability requirements for vaccine global supply. Vaccine traceability brings benefits including supply chain reliability and safety through enhanced product movement visibility, and a reduction of falsified and expired vaccines circulating in the supply chain. DCVMN has coordinated the development and implementation of global traceability standards, at both primary and secondary vaccine packaging levels, to encourage and enable sharing these experiences. Six pilot studies in four different countries showed successful implementation, and constituted part of larger vaccine traceability work within the respective organizations. The main findings from these pilot studies indicated that stepwise approaches to the adoption of traceability standards allowed vaccine manufacturers to learn by doing, initially with lower risk, and to spread their investments over time. Because the value of traceability is in its scale of adoption and the use of the data, it remains important for all stakeholders to engage in and prioritize the journey of vaccine traceability, but also to suitably manage the financial risks. The DCVMN Supply Chain Initiative has demonstrated that its members are committed to driving supply system changes that benefit immunization, while recognizing that supply chain traceability is part of a larger healthcare ecosystem and should be adopted by countries and immunization programmes as well.},
}
@article {pmid37662727,
year = {2023},
author = {Arai, T and Taha, H and Alidon, N and Jumat, J and Azmey, S and Zan, ND and Aimi Mat Jaafar, TN and Habib, A},
title = {Mitochondrial cytochrome c oxidase subunit I gene analysis of the yellowfin snapper, Lutjanus xanthopinnis in the Indo-Pacific region and a note on Lutjanus lutjanus population structure.},
journal = {Heliyon},
volume = {9},
number = {9},
pages = {e19348},
pmid = {37662727},
issn = {2405-8440},
abstract = {The yellowfin snapper, Lutjanus xanthopinnis, was recorded as a newly described species in the Indo-Pacific region in 2015. However, the knowledge of its biology, biogeography and ecology is scarcely understood, and, hence, its current conservation status is categorized as Data Deficient. The mitochondrial cytochrome c oxidase subunit I (COI) gene was examined to confirm species identification. We also examined the COI gene haplotypes of L. xanthopinnis in Brunei Darussalam and Malaysia together with other waters, i.e., Bangladesh, Indonesia, Japan, Singapore, Sri Lanka and Taiwan. Our molecular analyses found that Brunei Darussalam and eastern Peninsular Malaysia samples were genetically similar. However, the former showed higher genetic diversity than the latter. The samples from these two sites also showed signatures of population expansion. Furthermore, identical haplotypes could be found in different locations, suggesting the absence of spatial genetic structure. On the other hand, Lutjanus lutjanus showed a population structure associated with geographical locations, i.e., western Pacific Ocean, Indian Ocean and Maluku in Indonesia.},
}
@article {pmid37662370,
year = {2023},
author = {Liu, Y and Li, N and Qi, J and Xu, G and Zhao, J and Wang, N and Huang, X and Jiang, W and Justet, A and Adams, TS and Homer, R and Amei, A and Rosas, IO and Kaminski, N and Wang, Z and Yan, X},
title = {A hybrid machine learning and regression method for cell type deconvolution of spatial barcoding-based transcriptomic data.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.08.24.554722},
pmid = {37662370},
issn = {2692-8205},
support = {R01 LM014087/LM/NLM NIH HHS/United States ; R21 LM012884/LM/NLM NIH HHS/United States ; },
abstract = {Spatial barcoding-based transcriptomic (ST) data require cell type deconvolution for cellular-level downstream analysis. Here we present SDePER, a hybrid machine learning and regression method, to deconvolve ST data using reference single-cell RNA sequencing (scRNA-seq) data. SDePER uses a machine learning approach to remove the systematic difference between ST and scRNA-seq data (platform effects) explicitly and efficiently to ensure the linear relationship between ST data and cell type-specific expression profile. It also considers sparsity of cell types per capture spot and across-spots spatial correlation in cell type compositions. Based on the estimated cell type proportions, SDePER imputes cell type compositions and gene expression at unmeasured locations in a tissue map with enhanced resolution. Applications to coarse-grained simulated data and four real datasets showed that SDePER achieved more accurate and robust results than existing methods, suggesting the importance of considering platform effects, sparsity and spatial correlation in cell type deconvolution.},
}
@article {pmid37661805,
year = {2023},
author = {Ter Steege, H and Fortes, EA and Rozendaal, DMA and Erkens, RHJ and Sabatier, D and Aymard, G and Duijm, E and Eurlings, M and Grewe, F and Pombo, MM and Gomes, VF and de Mansano, VF and de Oliveira, SM},
title = {Molecular phylogeny and evolution of inflorescence types in Eperua.},
journal = {American journal of botany},
volume = {110},
number = {10},
pages = {e16229},
doi = {10.1002/ajb2.16229},
pmid = {37661805},
issn = {1537-2197},
mesh = {Bees/genetics ; Animals ; Phylogeny ; Inflorescence/genetics ; Bayes Theorem ; *Chiroptera ; Sequence Analysis, DNA ; *Fabaceae ; Evolution, Molecular ; },
abstract = {PREMISE: The Amazonian hyperdominant genus Eperua (Fabaceae) currently holds 20 described species and has two strongly different inflorescence and flower types, with corresponding different pollination syndrome. The evolution of these vastly different inflorescence types within this genus was unknown and the main topic in this study.<br><br>METHODS: We constructed a molecular phylogeny, based on the full nuclear ribosomal DNA and partial plastome, using Bayesian inference and maximum likelihood methods, to test whether the genus is monophyletic, whether all species are monophyletic and if the shift from bat to bee pollination (or vice versa) occurred once in this genus.<br><br>RESULTS: All but two species are well supported by the nuclear ribosomal phylogeny. The plastome phylogeny, however, shows a strong geographic signal suggesting strong local hybridization or chloroplast capture, rendering chloroplast barcodes meaningless in this genus.<br><br>CONCLUSIONS: With our data, we cannot fully resolve the backbone of the tree to clarify sister genera relationships and confirm monophyly of the genus Eperua. Within the genus, the shift from bat to bee and bee to bat pollination has occurred several times but, with the bee to bat not always leading to a pendant inflorescence.},
}
@article {pmid37658933,
year = {2023},
author = {Gao, Y and Zhang, X and Wang, W and Xing, Z and Xu, L and Tian, X},
title = {Qualitative identification of lonicerae japonicae flos in traditional chinese medicine using metabarcoding combined with specific mini-barcodes.},
journal = {Molecular biology reports},
volume = {50},
number = {11},
pages = {8817-8825},
pmid = {37658933},
issn = {1573-4978},
support = {22ZYJDSS00040//Tianjin Science and Technology Program/ ; 20ZYJDJC00120//Natural Science Foundation of Tianjin Municipal Science and Technology Commission/ ; },
mesh = {Medicine, Chinese Traditional ; *Drugs, Chinese Herbal ; Quality Control ; *Lonicera/genetics ; Chromatography, High Pressure Liquid ; },
abstract = {BACKGROUND: Lonicerae japonicae flos, also known as Jinyinhua (JYH), is an important component of traditional Chinese patent medicine (TCPM) products. However, the potential for adulteration and substitution with low-quality materials highlights the need for a reliable and sensitive approach to identify the species composition of TCPM products for consumer safety.<br><br>METHODS AND RESULTS: We used universal ITS2 primers to amplify TCPMs containing JYH. However, the results were inconclusive, as only one operational taxonomic unit (OTU) was identified as Lonicera sp., which could not be identified at the species level. To confirm the species identification of Lonicera sp. in TCPM, we developed a short mini-barcode primer based on the psbA-trnH region, which, in combination with DNA metabarcoding technology, allowed for qualitative and quantitative analysis of artificially mixed samples. We applied the mini-barcode to distinguish TCPMs containing JYH and demonstrated its relatively accurate quantitative ability in identifying two Lonicera species.<br><br>CONCLUSIONS: Our study presents a method for qualitative and quantitative identification of JYH, providing a promising application of DNA metabarcoding technology in the quality control of TCPM products.},
}
@article {pmid37660311,
year = {2023},
author = {Stephens, LD and Allen, ES and Bloch, EM and Crowe, EP and Campbell-Lee, SA and Booth, GS and Kopko, P},
title = {How do we ensure a safe ABO recheck process?.},
journal = {Transfusion},
volume = {63},
number = {10},
pages = {1789-1796},
doi = {10.1111/trf.17530},
pmid = {37660311},
issn = {1537-2995},
mesh = {Humans ; United States ; *Medical Errors/prevention &amp; control ; *Blood Transfusion ; Blood Banks ; Blood Grouping and Crossmatching ; Blood Specimen Collection/methods ; ABO Blood-Group System ; },
abstract = {BACKGROUND: Collecting a patient's blood in a correctly labeled pretransfusion specimen tube is essential for accurate ABO typing and safe transfusion. Noncompliance with specimen collection procedures can lead to wrong blood in tube (WBIT) incidents with potentially fatal consequences. Recent WBIT events inspired the investigation of how various institutions currently reduce the risk of these errors and ensure accurate ABO typing of patient samples.<br><br>MATERIALS AND METHODS: This article describes the techniques employed at various institutions across the United States to mitigate the risk of misidentified pretransfusion patient specimens. Details and considerations for each of these measures are provided.<br><br>RESULTS: Several institutions require the order for an ABO confirmation specimen, if indicated, to be generated from the transfusion medicine (TM) laboratory. Others issue a dedicated collection tube that is available exclusively from the TM service. Many institutions employ barcoding for electronic positive patient identification. Some use a combination of these strategies, depending on the locations or service lines from which the specimens are collected.<br><br>CONCLUSION: The description of various WBIT mitigation strategies will inform TM services on practices that may be effective at their respective institutions. Irrespective of the method(s) utilized, institutions should continue to monitor and mitigate specimen misidentification errors to promote sustained safe transfusion practices.},
}
@article {pmid37659761,
year = {2024},
author = {Li, FG and Shi, XY and Yang, L and Lu, X and Qi, Y and Li, P and Yang, H and Gao, W},
title = {Quantitative proteomics based bioactive proteins discovery and quality control of medicinal leeches.},
journal = {Journal of ethnopharmacology},
volume = {319},
number = {Pt 1},
pages = {117117},
doi = {10.1016/j.jep.2023.117117},
pmid = {37659761},
issn = {1872-7573},
mesh = {Animals ; Proteome ; Proteomics ; Phosphatidylinositol 3-Kinases/metabolism ; *Hirudo medicinalis ; *Leeches/chemistry ; Peptides/chemistry ; },
abstract = {Leech, a classical traditional Chinese medicine for promoting blood circulation and removing blood stasis, is mainly used in the clinical treatment of cardiovascular and cerebrovascular diseases. The discovery of activity proteins or peptides in the dead and dried medicinal leech is an important task with great challenges.<br><br>AIM OF THE STUDY: The aim of this study was to provide a basic proteome profile and help further discover active proteins and quality control for medicinal leeches, which would also provide insight into the research of animal medicines.<br><br>MATERIALS AND METHODS: Seventeen batches of dried medicinal leeches covering three species were collected from medicinal markets, which were authenticated by DNA barcoding. Then the proteome of different species leeches was profiled to reveal the signi&#xfb01;cantly different proteins using label-free proteomics. The characteristic peptides were screened out based on biological pathways analysis, which were further absolutely quantified using the developed stable isotope-labeled based parallel reaction monitoring method.<br><br>RESULTS: Seventeen batches of leech materials were Whitmania pigra Whitman (WP), Whitmania laevis Whitman (WL) and Poecilobdella manillensis Lesson (PM), respectively. A total of 1,035 proteins (452 in WP, 425 in WL and 158 in PM) were identified. Among them, 90 overlapping proteins were mainly concentrated in diverse metabolic pathways and primarily localized in the cytoplasm and mitochondrial inner membrane, which mainly related to ATP binding, catalytic activity and structural molecular activity. In total of 51 uniquely expressed proteins (21 in WP, 23 in WL and 7 in PM), associated with multiple key signaling pathways, including Rap1, cGMP-PKG, PI3K-Akt, Wnt and HIF-1, etc., relevant to treating cardiovascular diseases, diabetes, cancer and even a variety of neurodegenerative diseases. Three proteins with potential bioactivities, including Neurohemerythrin, Hirudin and Eglin C, were selected as the quality makers and then quantified based on the characteristic peptides.<br><br>CONCLUSIONS: This work profiled the proteome of three species of leeches, and addressed potential active proteins of the medicinal leech, which would help to provide the potential molecular mechanisms involved in disease treatment. The proteomics-based approach developed in this work is not only useful for the discovery of proteins with potential bioactivities but also helpful for the bioactivity relevant quality control of animal medicines.},
}
@article {pmid37656634,
year = {2023},
author = {Byrd, D and Tran, M and Kenney, JR and Wilson-Rankin, EE and Mauck, KE},
title = {The aphid Myzus persicae (Hemiptera: Aphididae) acquires chloroplast DNA during feeding on host plants.},
journal = {Environmental entomology},
volume = {52},
number = {5},
pages = {900-906},
doi = {10.1093/ee/nvad086},
pmid = {37656634},
issn = {1938-2936},
abstract = {Aphids (Hemiptera: Aphididae) extract nutrients from host plant phloem via stylets that facilitate salivation and sap uptake. When navigating to the phloem, aphids periodically puncture nonvascular cells and sample cell contents, but rarely cause significant cell damage. As a result, aphids are considered "stealthy" feeders. In contrast, insects that do cause damage, such as chewing herbivores, will take up host cell contents-including DNA-into their guts. Researchers can use molecular barcoding methods to identify recent host use patterns of chewing herbivores. This information is valuable for both pest management and basic ecological studies. Because of their stealthy feeding style, it was assumed that host plant DNA could not be recovered from aphids and other Sternorrhyncha. However, several recent studies document host plant DNA uptake by psyllids, which feed in a similar manner to aphids. Therefore, we hypothesized that aphids may also acquire DNA from host plants. Since aphids puncture and sample cytosol contents from cells, we predicted that aphids would be most likely to acquire DNA from chloroplasts. To test this, we performed host feeding and host transfer experiments with Myzus persicae (Sulzer), then used PCR to recover and sequence a region between the trnT and trnF genes from acquired chloroplast DNA. We found that M. persicae readily acquires chloroplast DNA, even prior to phloem contact, and that fragment sizes sufficient for host plant identification can be recovered. Our work suggests that molecular gut content analysis is a viable tool for studying aphid-host interactions.},
}
@article {pmid37654979,
year = {2023},
author = {Zhang, GQ and Zhao, YX and Zhang, F},
title = {Revisiting the type species of the genus Homidia (Collembola, Entomobryidae).},
journal = {ZooKeys},
volume = {1176},
number = {},
pages = {1-11},
pmid = {37654979},
issn = {1313-2989},
abstract = {Homidiacingula Börner, 1906, the type species of the genus Homidia Börner, 1906, is widespread from India to Southeast Asia, but its detailed morphological characteristics have not yet been described. We examined the morphology of specimens of H.cingula from Indonesia and southwestern China and confirmed their conspecific status by comparing their DNA barcoding sequences. We also compared the morphology of H.cingula with other two closely related species, confirming the valid species status of H.subcingula Denis, 1948. Our study provides new taxonomic and molecular data for the genus Homidia.},
}
@article {pmid37653977,
year = {2023},
author = {Jin, DP and Sim, S and Park, JW and Choi, JE and Yoon, J and Lim, CE and Kim, MH},
title = {Identification of the Plant Family Caryophyllaceae in Korea Using DNA Barcoding.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {10},
pages = {},
pmid = {37653977},
issn = {2223-7747},
support = {NIBR202212101, NIBR202313101//National Institute of Biological Resources/ ; },
abstract = {Caryophyllaceae is a large angiosperm family, with many species being utilized as ornamental or medicinal plants in Korea, in addition to several endangered species that are managed by the government. In this study, we used DNA barcoding for the accurate identification of Korean Caryophyllaceae. A total of 78 taxa (n = 215) were sequenced based on three chloroplast regions (rbcL, matK, and psbA-trnH) and nuclear ribosomal internal transcribed spacers (ITS). In the neighbor-joining tree, a higher accuracy of identification was generally observed when using ITS (>73%) rather than chloroplast regions (<62%). The highest resolution was found for rbcL + ITS (77.6%), although resolution varied according to the genus. Among the genera that included two and more species, five genera (Eremogone, Minuartia, Pseudostellaria, Sagina, and Stellaria) were successfully identified. However, the species of five other genera (Cerastium, Gypsophila, Dianthus, Silene, and Spergularia) showed relatively low resolutions (0-61.1%). In the cases of Cerastium, Dianthus, and Silene, ambiguous taxonomic relationships among unidentified species may have been a factor contributing to such low resolutions. However, in contrast to these results, Gypsophila and Spergularia have been identified well in previous studies. Our findings indicate the need of taxonomic reconsideration in Korea.},
}
@article {pmid37652986,
year = {2023},
author = {Lu, X and Lofgren, SM and Zhao, Y and Mazur, PK},
title = {Multiplexed transcriptomic profiling of the fate of human CAR T cells in vivo via genetic barcoding with shielded small nucleotides.},
journal = {Nature biomedical engineering},
volume = {7},
number = {9},
pages = {1170-1187},
pmid = {37652986},
issn = {2157-846X},
support = {S10 OD024977/OD/NIH HHS/United States ; R01 CA272844/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Animals ; Mice ; *Transcriptome ; *CD4-Positive T-Lymphocytes ; Cell- and Tissue-Based Therapy ; Cytokines ; Nucleotides ; },
abstract = {The design of chimeric antigen receptor (CAR) T cells would benefit from knowledge of the fate of the cells in vivo. This requires the permanent labelling of CAR T cell products and their pooling in the same microenvironment. Here, we report a cell-barcoding method for the multiplexed longitudinal profiling of cells in vivo using single-cell RNA sequencing (scRNA-seq). The method, which we named shielded-small-nucleotide-based scRNA-seq (SSN-seq), is compatible with both 3' and 5' single-cell profiling, and enables the recording of cell identity, from cell infusion to isolation, by leveraging the ubiquitous Pol III U6 promoters to robustly express small-RNA barcodes modified with direct-capture sequences. By using SSN-seq to track the dynamics of the states of CAR T cells in a tumour-rechallenge mouse model of leukaemia, we found that a combination of cytokines and small-molecule inhibitors that are used in the ex vivo manufacturing of CAR T cells promotes the in vivo expansion of persistent populations of CD4[+] memory T cells. By facilitating the probing of cell-state dynamics in vivo, SSN-seq may aid the development of adoptive cell therapies.},
}
@article {pmid37650109,
year = {2023},
author = {Li, Z and Huang, Z and Wan, X and Yu, J and Dong, H and Zhang, J and Zhang, C and Wang, S},
title = {Complete chloroplast genome sequence of Rhododendronmariesii and comparative genomics of related species in the family Ericaeae.},
journal = {Comparative cytogenetics},
volume = {17},
number = {},
pages = {163-180},
pmid = {37650109},
issn = {1993-0771},
abstract = {Rhododendronmariesii Hemsley et Wilson, 1907, a typical member of the family Ericaeae, possesses valuable medicinal and horticultural properties. In this research, the complete chloroplast (cp) genome of R.mariesii was sequenced and assembled, which proved to be a typical quadripartite structure with the length of 203,480 bp. In particular, the lengths of the large single copy region (LSC), small single copy region (SSC), and inverted repeat regions (IR) were 113,715 bp, 7,953 bp, and 40,918 bp, respectively. Among the 151 unique genes, 98 were protein-coding genes, 8 were tRNA genes, and 45 were rRNA genes. The structural characteristics of the R.mariesiicp genome was similar to other angiosperms. Leucine was the most representative amino acid, while cysteine was the lowest representative. Totally, 30 codons showed obvious codon usage bias, and most were A/U-ending codons. Six highly variable regions were observed, such as trnK-pafI and atpE-rpoB, which could serve as potential markers for future barcoding and phylogenetic research of R.mariesii species. Coding regions were more conserved than non-coding regions. Expansion and contraction in the IR region might be the main length variation in R.mariesii and related Ericaeae species. Maximum-likelihood (ML) phylogenetic analysis revealed that R.mariesii was relatively closed to the R.simsii Planchon, 1853 and R.pulchrum Sweet,1831. This research will supply rich genetic resource for R.mariesii and related species of the Ericaeae.},
}
@article {pmid37647219,
year = {2023},
author = {Motyka, M and Kusy, D and Biffi, G and Geiser, M and Kazantsev, SV and Bilkova, R and Jahodarova, E and Vogler, AP and Bocak, L},
title = {Untangling the evolution of soldier beetles (Coleoptera: Cantharidae) and the evaluation of the morphological phylogenetic signal in a soft-bodied elateroid lineage.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {39},
number = {6},
pages = {548-570},
doi = {10.1111/cla.12555},
pmid = {37647219},
issn = {1096-0031},
support = {25937027//Funda&#xe7;&#xe3;o Amparo e Desenvolvimento da Pesquisa/ ; 22-35327S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 21-74-20001//Russian Science Foundation/ ; 3587-ITV/MZ//University of S&#xe3;o Paulo Support Foundation/ ; },
mesh = {Animals ; *Coleoptera ; Phylogeny ; DNA, Mitochondrial ; Larva ; Uncertainty ; },
abstract = {This study addresses the long-standing uncertainty about the internal classification of soldier beetles (Elateroidea: Cantharidae). Four datasets were compiled and analysed: 66 genes for 14 terminals, 15 mtDNA genes for 79 terminals, one mtDNA and two rRNA genes for 217 terminals, and barcodes for 576 terminals. Based on congruent topologies, Chauliognathinae is proposed as a sister to the remaining Cantharidae, followed by the redefined Malthininae (including Tytthonyxini), the paraphyletic "dysmorphocerine" lineages (Dysmorphocerinae sensu stricto and Heteromastiginae subfam. nov.), and Silinae + Cantharinae as a terminal clade. The present phylogeny supersedes earlier morphology and short-fragment molecular hypotheses that have not converged on a consensus. Few morphological characters corroborate the DNA-based relationships (see the adults and larval keys). However, morphology-based hypotheses have relied on a few informative characters, and no evidence strongly rejects the preferred molecular topology. The interpretation of morphological characters and uncertain polarity resulting from the high phenotypic disparity of Elateroidea are discussed in detail. The dated phylogeny hypothesizes the earliest split within the Cantharidae in the Berriasian stage (Early Cretaceous, ~141 Myr) and the diversification of most extant subfamilies and tribes already in the Late Cretaceous. The most diverse subfamily, Cantharinae, represents a delayed radiation that started during the Eocene climatic optimum, 55.5 Myr. The late origin of Cantharinae questions the classification of Cretaceous Cantharidae as members of Cantharinae. Instead, the results suggest their deeper rooting after separating from dysmorphocerine lineages and before the node between Cantharinae and Silinae.},
}
@article {pmid37647183,
year = {2023},
author = {Ali, D and Asaad, A and Jimenez, MJ and Nanda, V and Paluzo-Hidalgo, E and Soriano-Trigueros, M},
title = {A Survey of Vectorization Methods in Topological Data Analysis.},
journal = {IEEE transactions on pattern analysis and machine intelligence},
volume = {45},
number = {12},
pages = {14069-14080},
doi = {10.1109/TPAMI.2023.3308391},
pmid = {37647183},
issn = {1939-3539},
abstract = {Attempts to incorporate topological information in supervised learning tasks have resulted in the creation of several techniques for vectorizing persistent homology barcodes. In this paper, we study thirteen such methods. Besides describing an organizational framework for these methods, we comprehensively benchmark them against three well-known classification tasks. Surprisingly, we discover that the best-performing method is a simple vectorization, which consists only of a few elementary summary statistics. Finally, we provide a convenient web application which has been designed to facilitate exploration and experimentation with various vectorization methods.},
}
@article {pmid37646939,
year = {2023},
author = {Henniges, MC and Leitch, AR and Leitch, IJ},
title = {"BIFloraExplorer": A Taxonomic, Genetic, and Ecological Data Resource for the Vascular Plants of Britain and Ireland.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2703},
number = {},
pages = {83-90},
pmid = {37646939},
issn = {1940-6029},
mesh = {Ireland ; United Kingdom ; *Tracheophyta ; Biological Evolution ; Genome Size ; },
abstract = {The vascular flora of Britain and Ireland is a historically well-documented and clearly delimited study system that offers itself to large-scale analyses of ecology and species assemblages. However, such analyses require clean, curated, and taxonomically resolved data, which are often unavailable. In this chapter, we describe how to access and use a key data resource that combines a taxonomically stable species list with genetic data (genome size, chromosome counts, and DNA barcode information), ecological information (such as life-form, realized niche description, and geographic origin) and distribution records. The data resource enables and encourages the study of natural ecological and evolutionary patterns and processes within the vascular flora of Britain and Ireland.},
}
@article {pmid37644058,
year = {2023},
author = {Kim, J and Kim, S and Yeom, H and Song, SW and Shin, K and Bae, S and Ryu, HS and Kim, JY and Choi, A and Lee, S and Ryu, T and Choi, Y and Kim, H and Kim, O and Jung, Y and Kim, N and Han, W and Lee, HB and Lee, AC and Kwon, S},
title = {Barcoded multiple displacement amplification for high coverage sequencing in spatial genomics.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {5261},
pmid = {37644058},
issn = {2041-1723},
mesh = {*Genomics ; *Amines ; Biological Evolution ; Gene Library ; },
abstract = {Determining mutational landscapes in a spatial context is essential for understanding genetically heterogeneous cell microniches. Current approaches, such as Multiple Displacement Amplification (MDA), offer high genome coverage but limited multiplexing, which hinders large-scale spatial genomic studies. Here, we introduce barcoded MDA (bMDA), a technique that achieves high-coverage genomic analysis of low-input DNA while enhancing the multiplexing capabilities. By incorporating cell barcodes during MDA, bMDA streamlines library preparation in one pot, thereby overcoming a key bottleneck in spatial genomics. We apply bMDA to the integrative spatial analysis of triple-negative breast cancer tissues by examining copy number alterations, single nucleotide variations, structural variations, and kataegis signatures for each spatial microniche. This enables the assessment of subclonal evolutionary relationships within a spatial context. Therefore, bMDA has emerged as a scalable technology with the potential to advance the field of spatial genomics significantly.},
}
@article {pmid37644026,
year = {2023},
author = {Kim, UJ and Lee, S and Kim, H and Roh, Y and Han, S and Kim, H and Park, Y and Kim, S and Chung, MJ and Son, H and Choo, H},
title = {Drug classification with a spectral barcode obtained with a smartphone Raman spectrometer.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {5262},
pmid = {37644026},
issn = {2041-1723},
mesh = {Commerce ; Cytoplasm ; Fingers ; Smartphone ; *Spectrum Analysis, Raman/instrumentation ; },
abstract = {Measuring, recording and analyzing spectral information of materials as its unique finger print using a ubiquitous smartphone has been desired by scientists and consumers. We demonstrated it as drug classification by chemical components with smartphone Raman spectrometer. The Raman spectrometer is based on the CMOS image sensor of the smartphone with a periodic array of band pass filters, capturing 2D Raman spectral intensity map, newly defined as spectral barcode in this work. Here we show 11 major components of drugs are classified with high accuracy, 99.0%, with the aid of convolutional neural network (CNN). The beneficial of spectral barcodes is that even brand name of drug is distinguishable and major component of unknown drugs can be identified. Combining spectral barcode with information obtained by red, green and blue (RGB) imaging system or applying image recognition techniques, this inherent property based labeling system will facilitate fundamental research and business opportunities.},
}
@article {pmid37641111,
year = {2023},
author = {Mak, L and Meleshko, D and Danko, DC and Barakzai, WN and Maharjan, S and Belchikov, N and Hajirasouliha, I},
title = {Ariadne: synthetic long read deconvolution using assembly graphs.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {197},
pmid = {37641111},
issn = {1474-760X},
support = {R35 GM138152/GM/NIGMS NIH HHS/United States ; T32 GM083937/GM/NIGMS NIH HHS/United States ; },
mesh = {*Algorithms ; Genomics ; Metagenome ; },
abstract = {Synthetic long read sequencing techniques such as UST's TELL-Seq and Loop Genomics' LoopSeq combine 3[Formula: see text] barcoding with standard short-read sequencing to expand the range of linkage resolution from hundreds to tens of thousands of base-pairs. However, the lack of a 1:1 correspondence between a long fragment and a 3[Formula: see text] unique molecular identifier confounds the assignment of linkage between short reads. We introduce Ariadne, a novel assembly graph-based synthetic long read deconvolution algorithm, that can be used to extract single-species read-clouds from synthetic long read datasets to improve the taxonomic classification and de novo assembly of complex populations, such as metagenomes.},
}
@article {pmid37640128,
year = {2023},
author = {Hadj-Henni, L and Millot, C and Lehrter, V and Augot, D},
title = {Wing morphometrics of biting midges (Diptera: Culicoides) of veterinary importance in Madagascar.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {114},
number = {},
pages = {105494},
doi = {10.1016/j.meegid.2023.105494},
pmid = {37640128},
issn = {1567-7257},
mesh = {Animals ; Cattle ; *Ceratopogonidae/genetics ; Madagascar ; *Arboviruses ; *African Horse Sickness Virus ; *Orthobunyavirus ; },
abstract = {Biting midges are vectors of arboviruses such as bluetongue virus, bovine ephemeral fever virus, Akabane virus, African horse sickness virus, epizootic haemorrhagic disease virus and Schmallenberg virus. Fast and accurate identification of biting midges is crucial in the study of Culicoides-borne diseases. Morphological identification of biting midges has revealed the presence of cryptic species. A total of 20 species are reported in Madagascar. In this study, we assessed wing morphometric analysis for identification of seven species namely C. dubitatus Kremer, Rebholtz-Hirtzel and Delécolle, C. enderleini Cornet and Brunhes, C. kibatiensis Goetghebuer, C. miombo Meiswinkel, C. moreli Clastrier, C. nevilli Cornet and Brunhes, and C. zuluensis de Meillon. Culicoides enderleini, C. miombo, C. moreli, C. nevilli and C. zuluensis are vectors diseases. A molecular approach, based on the cytochrome oxidase I gene (Cox1), was used for species delimitation. The molecular analysis presented seven different clades grouped two-by-two according to morphological characters. A total of 179 wing images were digitised. We found morphometric variation among seven species based on 11 landmarks and two outlines. Wing shape variation plots showed that species overlapped with species belonging to the same group. The cross-validation revealed a relatively high percentage of correct classification in most species, ranging from 91.3% to 100% for landmarks; 60% to 82.6% for outlines-1 and 77.1% to 91.3% for outlines-2. Our study suggests that wing geometric morphometric analysis is a robust tool for reliable "Moka Fohy" identification in Madagascar. This inexpensive and simple method is a precise supplement to morphological identification, with reaches the accuracy of Cox1 barcoding.},
}
@article {pmid37638293,
year = {2023},
author = {Andreatta, M and Gueguen, P and Borcherding, N and Carmona, SJ},
title = {T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps.},
journal = {Bio-protocol},
volume = {13},
number = {16},
pages = {e4735},
pmid = {37638293},
issn = {2331-8325},
abstract = {T cells are endowed with T-cell antigen receptors (TCR) that give them the capacity to recognize specific antigens and mount antigen-specific adaptive immune responses. Because TCR sequences are distinct in each naïve T cell, they serve as molecular barcodes to track T cells with clonal relatedness and shared antigen specificity through proliferation, differentiation, and migration. Single-cell RNA sequencing provides coupled information of TCR sequence and transcriptional state in individual cells, enabling T-cell clonotype-specific analyses. In this protocol, we outline a computational workflow to perform T-cell states and clonal analysis from scRNA-seq data based on the R packages Seurat, ProjecTILs, and scRepertoire. Given a scRNA-seq T-cell dataset with TCR sequence information, cell states are automatically annotated by reference projection using the ProjecTILs method. TCR information is used to track individual clonotypes, assess their clonal expansion, proliferation rates, bias towards specific differentiation states, and the clonal overlap between T-cell subtypes. We provide fully reproducible R code to conduct these analyses and generate useful visualizations that can be adapted for the needs of the protocol user. Key features Computational analysis of paired scRNA-seq and scTCR-seq data Characterizing T-cell functional state by reference-based analysis using ProjecTILs Exploring T-cell clonal structure using scRepertoire Linking T-cell clonality to transcriptomic state to study relationships between clonal expansion and functional phenotype Graphical overview.},
}
@article {pmid37636532,
year = {2023},
author = {Fernandez-Triana, JL and Shimbori, EM and Whitfield, JB and Penteado-Dias, AM and Shaw, SR and Boudreault, C and Sones, J and Perez, K and Brown, A and Manjunath, R and Burns, JM and Hebert, PDN and Smith, MA and Hallwachs, W and Janzen, DH},
title = {A revision of the parasitoid wasp genus Alphomelon Mason with the description of 30 new species (Hymenoptera, Braconidae).},
journal = {ZooKeys},
volume = {1175},
number = {},
pages = {5-162},
pmid = {37636532},
issn = {1313-2989},
abstract = {The parasitoid wasp genus Alphomelon Mason, 1981 is revised, based on a combination of basic morphology (dichotomous key and brief diagnostic descriptions), DNA barcoding, biology (host data and wasp cocoons), and distribution data. A total of 49 species is considered; the genus is almost entirely Neotropical (48 species recorded from that region), but three species reach the Nearctic, with one of them extending as far north as 45° N in Canada. Alphomelon parasitizes exclusively Hesperiinae caterpillars (Lepidoptera: Hesperiidae), mostly feeding on monocots in the families Arecaceae, Bromeliaceae, Cannaceae, Commelinaceae, Heliconiaceae, and Poaceae. Most wasp species parasitize either on one or very few (2-4) host species, usually within one or two hesperiine genera; but some species can parasitize several hosts from up to nine different hesperiine genera. Among species with available data for their cocoons, roughly half weave solitary cocoons (16) and half are gregarious (17); cocoons tend to be surrounded by a rather distinctive, coarse silk (especially in solitary species, but also distinguishable in some gregarious species). Neither morphology nor DNA barcoding alone was sufficient on its own to delimit all species properly; by integrating all available evidence (even if incomplete, as available data for every species is different) a foundation is provided for future studies incorporating more specimens, especially from South America. The following 30 new species are described: cruzi, itatiaiensis, and palomae, authored by Shimbori &amp; Fernandez-Triana; and adrianguadamuzi, amazonas, andydeansi, calixtomoragai, carolinacanoae, christerhanssoni, diniamartinezae, duvalierbricenoi, eldaarayae, eliethcantillanoae, gloriasihezarae, guillermopereirai, hazelcambroneroae, josecortesi, keineraragoni, luciarosae, manuelriosi, mikesharkeyi, osvaldoespinozai, paramelanoscelis, paranigriceps, petronariosae, ricardocaleroi, rigoi, rostermoragai, sergioriosi, and yanayacu, authored by Fernandez-Triana &amp; Shimbori.},
}
@article {pmid37636375,
year = {2023},
author = {Ngai, HL and Lee, HK and Shaw, PC},
title = {DNA from herbs can be obtained from air and authenticated by polymerase chain reaction.},
journal = {Heliyon},
volume = {9},
number = {8},
pages = {e18946},
pmid = {37636375},
issn = {2405-8440},
abstract = {DNA barcoding of herbs allows accurate species authentication. However, the DNA of herbs are often not easily PCR amplified due to co-extraction of inhibitors. Methods have been developed to improve DNA extraction to reduce contaminants. These methods usually require toxic chemical treatments or expensive commercial kits and are labor intensive. In this report, we collected the air passed from the herbs and directly amplified the DNA obtained. Results showed that DNA could be obtained, and it was PCR amplifiable. Sequencing of the amplified DNA allowed species authentication. This DNA collection method is applicable to herbs from different plant tissues. It has the advantages of reducing the use of toxic substances and more economical.},
}
@article {pmid37628645,
year = {2023},
author = {Tripodi, P},
title = {Application of High-Resolution Melting and DNA Barcoding for Discrimination and Taxonomy Definition of Rocket Salad (Diplotaxis spp.) Species.},
journal = {Genes},
volume = {14},
number = {8},
pages = {},
pmid = {37628645},
issn = {2073-4425},
mesh = {Animals ; Phylogeny ; DNA Barcoding, Taxonomic ; *Salads ; Plant Breeding ; DNA, Ribosomal ; *Brassicaceae/genetics ; *Coleoptera ; },
abstract = {Nuclear and cytoplasmic DNA barcoding regions are useful for plant identification, breeding, and phylogenesis. In this study, the genetic diversity of 17 Diplotaxis species, was investigated with 5 barcode markers. The allelic variation was based on the sequences of chloroplast DNA markers including the spacer between trnL and trnF and tRNA-Phe gene (trnL-F), the rubisco (rbcl), the maturase K (matk), as well as the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA. A highly polymorphic marker (HRM500) derived from a comparison of cytoplasmic genome sequences in Brassicaceae, was also included. Subsequently, a real-time PCR method coupled with HRM analysis was implemented to better resolve taxonomic relationships and identify assays suitable for species identification. Integration of the five barcode regions revealed a grouping of the species according to the common chromosomal set number. Clusters including species with n = 11 (D. duveryrieriana or cretacea, D. tenuifolia, D. simplex and D. acris), n = 8 (D. ibicensis, D. brevisiliqua and D. ilorcitana), and n = 9 (D. brachycarpa, D. virgata, D. assurgens, and D. berthautii) chromosomes were identified. Both phylogenetic analysis and the genetic structure of the collection identified D. siifolia as the most distant species. Previous studies emphasized this species' extremely high glucosinolate content, particularly for glucobrassicin. High-resolution melting analysis showed specific curve patterns useful for the discrimination of the species, thus determining ITS1 as the best barcode for fingerprinting. Findings demonstrate that the approach used in this study is effective for taxa investigations and genetic diversity studies.},
}
@article {pmid37627008,
year = {2023},
author = {Vieira, C and Kim, MS and N'Yeurt, AR and Payri, C and D'Hondt, S and De Clerck, O and Zubia, M},
title = {Marine Flora of French Polynesia: An Updated List Using DNA Barcoding and Traditional Approaches.},
journal = {Biology},
volume = {12},
number = {8},
pages = {},
pmid = {37627008},
issn = {2079-7737},
support = {V406219N//Research Foundation - Flanders/ ; },
abstract = {Located in the heart of the South Pacific Ocean, the French Polynesian islands represent a remarkable setting for biological colonization and diversification, because of their isolation. Our knowledge of this region's biodiversity is nevertheless still incomplete for many groups of organisms. In the late 1990s and 2000s, a series of publications provided the first checklists of French Polynesian marine algae, including the Chlorophyta, Rhodophyta, Ochrophyta, and Cyanobacteria, established mostly on traditional morphology-based taxonomy. We initiated a project to systematically DNA barcode the marine flora of French Polynesia. Based on a large collection of ~2452 specimens, made between 2014 and 2023, across the five French Polynesian archipelagos, we re-assessed the marine floral species diversity (Alismatales, Cyanobacteria, Rhodophyta, Ochrophyta, Chlorophyta) using DNA barcoding in concert with morphology-based classification. We provide here a major revision of French Polynesian marine flora, with an updated listing of 702 species including 119 Chlorophyta, 169 Cyanobacteria, 92 Ochrophyta, 320 Rhodophyta, and 2 seagrass species-nearly a two-fold increase from previous estimates. This study significantly improves our knowledge of French Polynesian marine diversity and provides a valuable DNA barcode reference library for identification purposes and future taxonomic and conservation studies. A significant part of the diversity uncovered from French Polynesia corresponds to unidentified lineages, which will require careful future taxonomic investigation.},
}
@article {pmid37624441,
year = {2023},
author = {Pinheiro Alves de Souza, Y and Schloter, M and Weisser, W and Schulz, S},
title = {Deterministic Development of Soil Microbial Communities in Disturbed Soils Depends on Microbial Biomass of the Bioinoculum.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2882-2893},
pmid = {37624441},
issn = {1432-184X},
mesh = {Biomass ; *Soil ; Soil Microbiology ; Bacteria/genetics ; Archaea/genetics ; *Microbiota ; },
abstract = {Despite its enormous importance for ecosystem services, factors driving microbial recolonization of soils after disturbance are still poorly understood. Here, we compared the microbial recolonization patterns of a disturbed, autoclaved soil using different amounts of the original non-disturbed soil as inoculum. By using this approach, we manipulated microbial biomass, but did not change microbial diversity of the inoculum. We followed the development of a new soil microbiome after reinoculation over a period of 4 weeks using a molecular barcoding approach as well as qPCR. Focus was given on the assessment of bacteria and archaea. We could show that 1 week after inoculation in all inoculated treatments bacterial biomass exceeded the values from the original soil as a consequence of high dissolved organic carbon (DOC) concentrations in the disturbed soil resulting from the disturbance. This high biomass was persistent over the complete experimental period. In line with the high DOC concentrations, in the first 2 weeks of incubation, copiotrophic bacteria dominated the community, which derived from the inoculum used. Only in the disturbed control soils which did not receive a microbial inoculum, recolonization pattern differed. In contrast, archaeal biomass did not recover over the experimental period and recolonization was strongly triggered by amount of inoculated original soil added. Interestingly, the variability between replicates of the same inoculation density decreased with increasing biomass in the inoculum, indicating a deterministic development of soil microbiomes if higher numbers of cells are used for reinoculation.},
}
@article {pmid37623559,
year = {2023},
author = {Wilson, AW and Eberhardt, U and Nguyen, N and Noffsinger, CR and Swenie, RA and Loucks, JL and Perry, BA and Herrera, M and Osmundson, TW and DeLong-Duhon, S and Beker, HJ and Mueller, GM},
title = {Does One Size Fit All? Variations in the DNA Barcode Gaps of Macrofungal Genera.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {8},
pages = {},
pmid = {37623559},
issn = {2309-608X},
abstract = {The nuclear ribosomal internal transcribed spacer (nrITS) region has been widely used in fungal diversity studies. Environmental metabarcoding has increased the importance of the fungal DNA barcode in documenting fungal diversity and distribution. The DNA barcode gap is seen as the difference between intra- and inter-specific pairwise distances in a DNA barcode. The current understanding of the barcode gap in macrofungi is limited, inhibiting the development of best practices in applying the nrITS region toward research on fungal diversity. This study examined the barcode gap using 5146 sequences representing 717 species of macrofungi from eleven genera, eight orders and two phyla in datasets assembled by taxonomic experts. Intra- and inter-specific pairwise distances were measured from sequence and phylogenetic data. The results demonstrate that barcode gaps are influenced by differences in intra- and inter-specific variance in pairwise distances. In terms of DNA barcode behavior, variance is greater in the ITS1 than ITS2, and variance is greater in both relative to the combined nrITS region. Due to the difference in variance, the barcode gaps in the ITS2 region are greater than in the ITS1. Additionally, the taxonomic approach of "splitting" taxa into numerous taxonomic units produces greater barcode gaps when compared to "lumping". The results show variability in the barcode gaps between fungal taxa, demonstrating a need to understand the accuracy of DNA barcoding in quantifying species richness. For taxonomic studies, variability in nrITS sequence data supports the application of multiple molecular markers to corroborate the taxonomic and systematic delineation of species.},
}
@article {pmid37623402,
year = {2023},
author = {Kamdem, MM and Ramoejane, M and Voua Otomo, P},
title = {Local-Scale DNA Barcoding of Afrotropical Hoverflies (Diptera: Syrphidae): A Case Study of the Eastern Free State of South Africa.},
journal = {Insects},
volume = {14},
number = {8},
pages = {},
pmid = {37623402},
issn = {2075-4450},
support = {110858//National Research Foundation/ ; },
abstract = {The Afrotropical hoverflies remain an understudied group of hoverflies. One of the reasons for the lack of studies on this group resides in the difficulties to delimit the species using the available identification keys. DNA barcoding has been found useful in such cases of taxonomical uncertainty. Here, we present a molecular study of hoverfly species from the eastern Free State of South Africa using the mitochondrial cytochrome-c oxidase subunit I gene (COI). The identification of 78 specimens was achieved through three analytical approaches: genetic distances analysis, species delimitation models and phylogenetic reconstructions. In this study, 15 nominal species from nine genera were recorded. Of these species, five had not been previously reported to occur in South Africa, namely, Betasyrphus inflaticornis Bezzi, 1915, Mesembrius strigilatus Bezzi, 1912, Eristalinus tabanoides Jaennicke, 1876, Eristalinus vicarians Bezzi, 1915 and Eristalinus fuscicornis Karsch, 1887. Intra- and interspecific variations were found and were congruent between neighbour-joining and maximum likelihood analyses, except for the genus Allograpta Osten Sacken, 1875, where identification seemed problematic, with a relatively high (1.56%) intraspecific LogDet distance observed in Allograpta nasuta Macquart, 1842. Within the 78 specimens analysed, the assembled species by automatic partitioning (ASAP) estimated the presence of 14-17 species, while the Poisson tree processes based on the MPTP and SPTP models estimated 15 and 16 species. The three models showed similar results (10 species) for the Eristalinae subfamily, while for the Syrphinae subfamily, 5 and 6 species were suggested through MPTP and SPTP, respectively. Our results highlight the necessity of using different species delimitation models in DNA barcoding for species diagnoses.},
}
@article {pmid37620638,
year = {2024},
author = {Lan, X and Wang, J and Zhang, M and Zhou, Q and Xiang, H and Jiang, W},
title = {Molecular Identification of Acrossocheilus jishouensis (Teleostei: Cyprinidae) and Its Complete Mitochondrial Genome.},
journal = {Biochemical genetics},
volume = {62},
number = {2},
pages = {1396-1412},
pmid = {37620638},
issn = {1573-4927},
support = {2020RC3057//Innovation Platform and Talent Plan of Hunan Province/ ; 32060128//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Genome, Mitochondrial ; Phylogeny ; Sequence Analysis, DNA/methods ; *Cyprinidae/genetics ; RNA, Transfer/genetics ; },
abstract = {Molecular identification, such as DNA barcoding, is a useful tool that is widely applied in distinguishing species. To identify the cyprinid Acrossocheilus jishouensis, which was previously known to be restricted to only its type locality, we conducted molecular identification of this species based on 23 samples in five localities. Molecular identification based on the mitochondrial COI gene sequence showed that the morphologically similar samples from the five populations were all A. jishouensis, as the mean genetic distances between populations were very small (0.1-1.6%); thus, the distribution of this species was substantially expanded. The whole mitochondrial genome of one sample was also assembled, which was 16,594 bp in length and consisted of 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and one control region. All PCGs began with ATG except the COI gene, which started with GTG; seven PCGs used the complete stop codon TAA, while four terminated in T(AA) and two ended with TAG. The overall base composition reflected a higher proportion of A+T than G+C and a positive AT-skew and negative GC-skew pattern except for the opposite in ND6. Phylogenetic relationships inferred using BI and ML methods revealed that both Acrossocheilus and Onychostoma were nonmonophyletic, which indicated that the traditional diagnoses between these two genera need to be assessed further. The results of this study not only expanded the known distribution ranges of A. jishouensis, but also provided a valuable data resource for future molecular and evolutionary studies of Acrossocheilus and other cyprinids in Barbinae.},
}
@article {pmid37620406,
year = {2023},
author = {Mohanty, S and Mishra, BK and Dasgupta, M and Acharya, GC and Singh, S and Naresh, P and Bhue, S and Dixit, A and Sarkar, A and Sahoo, MR},
title = {Deciphering phenotyping, DNA barcoding, and RNA secondary structure predictions in eggplant wild relatives provide insights for their future breeding strategies.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {13829},
pmid = {37620406},
issn = {2045-2322},
mesh = {*Solanum melongena/genetics ; DNA Barcoding, Taxonomic ; Plant Breeding ; DNA ; },
abstract = {Eggplant or aubergine (Solanum melongena L.) and its wild cousins, comprising 13 clades with 1500 species, have an unprecedented demand across the globe. Cultivated eggplant has a narrow molecular diversity that hinders eggplant breeding advancements. Wild eggplants need resurgent attention to broaden eggplant breeding resources. In this study, we emphasized phenotypic and genotypic discriminations among 13 eggplant species deploying chloroplast-plastid (Kim matK) and nuclear (ITS2) short gene sequences (400-800 bp) at DNA barcode region followed by ITS2 secondary structure predictions. The identification efficiency at the Kim matK region was higher (99-100%) than in the ITS2 region (80-90%). The eggplant species showed 13 unique secondary structures with a central ring with various helical orientations. Principal component analysis (PCoA) provides the descriptor-wise phenotypic clustering, which is essential for trait-specific breeding. Groups I and IV are categorized under scarlet complexes S. aethiopicum, S. trilobatum, and S. melongena (wild and cultivated). Group II represented the gboma clade (S. macrocarpon, S. wrightii, S. sisymbriifolium, and S. aculeatissimum), and group III includes S. mammosum, and S. torvum with unique fruit shape and size. The present study would be helpful in genetic discrimination, biodiversity conservation, and the safe utilization of wild eggplants.},
}
@article {pmid37616491,
year = {2023},
author = {Mahmudah, NA and Shin, HG and Ock, M and Jo, AJ and Min, A and Pyo, J and Im, D and Kim, S},
title = {Barcode and radio frequency identification utilization varied across Korean hospitals.},
journal = {International journal for quality in health care : journal of the International Society for Quality in Health Care},
volume = {35},
number = {3},
pages = {},
doi = {10.1093/intqhc/mzad063},
pmid = {37616491},
issn = {1464-3677},
support = {HI18C2339//Korea Health Industry Development Institute/Republic of Korea ; },
mesh = {Humans ; *Radio Frequency Identification Device ; Health Facilities ; Hospitals, General ; Tertiary Care Centers ; Republic of Korea ; },
abstract = {Barcodes and radio frequency identification (RFID) are increasingly used in health care to improve patient safety. However, studies on their utilization in clinical settings are limited. This study aimed to comprehensively examine the utilization status of barcodes and RFID in Korean hospitals, recognize the effects and obstacles associated with utilization, and explore the measures to expand the applications of barcodes and RFID. A self-reported online survey was conducted in tertiary hospitals, general hospitals, hospitals, and nursing hospitals in the Republic of Korea. The survey questionnaire comprised questions on barcodes and RFID utilization status, the effect of barcodes and RFID utilization, measures to expand the utilization of barcodes and RFID, and information on respondents' demographics and hospitals. A representative from each of 23 tertiary hospitals, 101 general hospitals, 232 hospitals, and 214 nursing hospitals completed the survey (total response rate 17%). The data were analysed using the chi-square test or Fisher's exact test to determine the differences in responses based on the type and characteristics of hospitals. The tertiary hospitals had the highest utilizations of both RFID and barcodes (n = 10, 43.5%), whereas the nursing hospitals had the lowest (n = 96, 55.1%). Barcodes and RFID were most commonly used in the visits and security management domains. However, the use of barcodes and RFID in medication dispensing and administration safety was low, despite its value in improving patient safety. The hospitals recognized the positive effect of utilization of barcodes and RFID, reporting the highest frequency for the prevention of patient safety incidents (n = 79, 85.9%). Nevertheless, the cost of barcodes and RFID facility investments (n = 128, 90.3%) appeared to be the greatest obstacle to the introduction of barcodes and RFID. Hence, barcodes and RFID facility investment support (n = 133, 95.5%) were given the highest priority among the measures to expand barcode and RFID utilization in health care. The utilization of barcodes and RFID varied across the type and domain of hospitals in the Republic of Korea. Hospitals recognized the positive effects of barcode and RFID utilization. Nonetheless, all hospitals were concerned about the cost of investment and maintenance of barcode and RFID facilities as the main obstacles to utilization. Therefore, a support plan must be developed for the cost of barcodes and RFID facility investments to expand barcode and RFID utilization in health care.},
}
@article {pmid37614126,
year = {2023},
author = {Lindner, MF and Gonçalves, LT and Bianchi, FM and Ferrari, A and Cavalleri, A},
title = {Tiny insects, big troubles: a review of BOLD's COI database for Thysanoptera (Insecta).},
journal = {Bulletin of entomological research},
volume = {113},
number = {5},
pages = {703-715},
doi = {10.1017/S0007485323000391},
pmid = {37614126},
issn = {1475-2670},
mesh = {Animals ; *Thysanoptera/genetics ; DNA Barcoding, Taxonomic ; Insecta/genetics ; Phylogeny ; Phylogeography ; },
abstract = {DNA Barcoding is an important tool for disciplines such as taxonomy, phylogenetics and phylogeography, with Barcode of Life Data System (BOLD) being the largest database of partial cytochrome c oxidase subunit I (COI) sequences. We provide the first extensive revision of the information available in this database for the insect order Thysanoptera, to assess: how many COI sequences are available; how representative these sequences are for the order; and the current potential of BOLD as a reference library for specimen identification and species delimitation. The COI database at BOLD currently represents only about 5% of the over 6400 valid thrips species, with a heavy bias towards a few species of economic importance. Clear Barcode gaps were observed for 24 out of 33 genera evaluated, but many outliers were also observed. We suggest that the COI sequences available in BOLD as a reference would not allow for accurate identifications in about 30% of Thysanoptera species in this database, which rises to 40% of taxa within Thripidae, the most sampled family within the order. Thus, we call for caution and a critical evaluation in using BOLD as a reference library for thrips Barcodes, and future efforts should focus on improving the data quality of this database.},
}
@article {pmid37612786,
year = {2023},
author = {Zhang, Z and Yan, B},
title = {Convolution Neural Network-Assisted Smart Fluorescent-Tongue Based on Lanthanide Ion-Induced Forming MOF/HOF Composite for Differentiation of Flavor Compounds and Wine Identification.},
journal = {ACS sensors},
volume = {8},
number = {9},
pages = {3585-3594},
doi = {10.1021/acssensors.3c01273},
pmid = {37612786},
issn = {2379-3694},
mesh = {*Wine/analysis ; *Metal-Organic Frameworks ; Artificial Intelligence ; Neural Networks, Computer ; Ions ; Tongue ; },
abstract = {Wine flavor is a vital quality characteristic in wine, influenced by those flavor components with low sensory thresholds. It is crucial to recognize and classify the wine components related to their flavor contribution. The integration of fluorescent sensors and artificial intelligence shows huge potential in flavor recognition by emulation of the gustatory perception system. Meanwhile, achieving information identification of wine based on multiple information barcodes has hopeful applications in anticounterfeiting. In this study, we present a simple method in which organic linkers are weaved into a hydrogen-bonded organic framework (HOF) for the available transformation of a metal-bonded organic framework (MOF) induced by lanthanide ions (Ln[3+]). The fluorescent Ln-MOF/HOF composite exhibits high sensitivity, rapid response, and good recyclability for detecting seven flavor compounds in wine, including tannic acid, ionone, vanillin, anethole, anisaldehyde, hydroxybenzaldehyde, and 4-hydroxy-2-methylacetophenone. Depending on its satisfactory detectability, a novel strategy is provided in which a fluorescent sensor is able to function as a smart fluorescent-tongue (F-tongue) by the aid of convolutional neural network to differentiate these seven flavor compounds. In addition, the Ln-MOF/HOF composite has been used to prepare multiple information barcodes for wine information identification on the basis of dynamic fluorescence response toward tannic acid. The mimetic gustatory perception system developed in this study may offer a promising strategy for flavor recognition in food and further food anticounterfeiting.},
}
@article {pmid37612289,
year = {2023},
author = {Xu, Z and Wang, Y and Sheng, K and Rosenthal, R and Liu, N and Hua, X and Zhang, T and Chen, J and Song, M and Lv, Y and Zhang, S and Huang, Y and Wang, Z and Cao, T and Shen, Y and Jiang, Y and Yu, Y and Chen, Y and Guo, G and Yin, P and Weitz, DA and Wang, Y},
title = {Droplet-based high-throughput single microbe RNA sequencing by smRandom-seq.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {5130},
pmid = {37612289},
issn = {2041-1723},
mesh = {Humans ; *Escherichia coli/genetics ; *High-Throughput Nucleotide Sequencing ; RNA-Seq ; Anti-Bacterial Agents/pharmacology ; DNA Primers ; RNA, Ribosomal/genetics ; },
abstract = {Bacteria colonize almost all parts of the human body and can differ significantly. However, the population level transcriptomics measurements can only describe the average bacteria population behaviors, ignoring the heterogeneity among bacteria. Here, we report a droplet-based high-throughput single-microbe RNA-seq assay (smRandom-seq), using random primers for in situ cDNA generation, droplets for single-microbe barcoding, and CRISPR-based rRNA depletion for mRNA enrichment. smRandom-seq showed a high species specificity (99%), a minor doublet rate (1.6%), a reduced rRNA percentage (32%), and a sensitive gene detection (a median of ~1000 genes per single E. coli). Furthermore, smRandom-seq successfully captured transcriptome changes of thousands of individual E. coli and discovered a few antibiotic resistant subpopulations displaying distinct gene expression patterns of SOS response and metabolic pathways in E. coli population upon antibiotic stress. smRandom-seq provides a high-throughput single-microbe transcriptome profiling tool that will facilitate future discoveries in microbial resistance, persistence, microbe-host interaction, and microbiome research.},
}
@article {pmid37609440,
year = {2023},
author = {Cock, PJA and Cooke, DEL and Thorpe, P and Pritchard, L},
title = {THAPBI PICT-a fast, cautious, and accurate metabarcoding analysis pipeline.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15648},
pmid = {37609440},
issn = {2167-8359},
support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Anatomy, Regional ; Artifacts ; Culture ; Databases, Factual ; *Phytophthora ; },
abstract = {THAPBI PICT is an open source software pipeline for metabarcoding analysis of Illumina paired-end reads, including cases of multiplexing where more than one amplicon is amplified per DNA sample. Initially a Phytophthora ITS1 Classification Tool (PICT), we demonstrate using worked examples with our own and public data sets how, with appropriate primer settings and a custom database, it can be applied to other amplicons and organisms, and used for reanalysis of existing datasets. The core dataflow of the implementation is (i) data reduction to unique marker sequences, often called amplicon sequence variants (ASVs), (ii) dynamic thresholds for discarding low abundance sequences to remove noise and artifacts (rather than error correction by default), before (iii) classification using a curated reference database. The default classifier assigns a label to each query sequence based on a database match that is either perfect, or a single base pair edit away (substitution, deletion or insertion). Abundance thresholds for inclusion can be set by the user or automatically using per-batch negative or synthetic control samples. Output is designed for practical interpretation by non-specialists and includes a read report (ASVs with classification and counts per sample), sample report (samples with counts per species classification), and a topological graph of ASVs as nodes with short edit distances as edges. Source code available from https://github.com/peterjc/thapbi-pict/ with documentation including installation instructions.},
}
@article {pmid37609130,
year = {2023},
author = {Ramezani, M and Bauman, J and Singh, A and Weisbart, E and Yong, J and Lozada, M and Way, GP and Kavari, SL and Diaz, C and Haghighi, M and Batista, TM and Pérez-Schindler, J and Claussnitzer, M and Singh, S and Cimini, BA and Blainey, PC and Carpenter, AE and Jan, CH and Neal, JT},
title = {A genome-wide atlas of human cell morphology.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37609130},
issn = {2692-8205},
support = {DP2 GM146252/GM/NIGMS NIH HHS/United States ; },
abstract = {A key challenge of the modern genomics era is developing data-driven representations of gene function. Here, we present the first unbiased morphology-based genome-wide perturbation atlas in human cells, containing three genome-scale genotype-phenotype maps comprising >20,000 single-gene CRISPR-Cas9-based knockout experiments in >30 million cells. Our optical pooled cell profiling approach (PERISCOPE) combines a de-stainable high-dimensional phenotyping panel (based on Cell Painting[1,2]) with optical sequencing of molecular barcodes and a scalable open-source analysis pipeline to facilitate massively parallel screening of pooled perturbation libraries. This approach provides high-dimensional phenotypic profiles of individual cells, while simultaneously enabling interrogation of subcellular processes. Our atlas reconstructs known pathways and protein-protein interaction networks, identifies culture media-specific responses to gene knockout, and clusters thousands of human genes by phenotypic similarity. Using this atlas, we identify the poorly-characterized disease-associated transmembrane protein TMEM251/LYSET as a Golgi-resident protein essential for mannose-6-phosphate-dependent trafficking of lysosomal enzymes, showing the power of these representations. In sum, our atlas and screening technology represent a rich and accessible resource for connecting genes to cellular functions at scale.},
}
@article {pmid37608801,
year = {2023},
author = {Prusokiene, A and Prusokas, A and Retkute, R},
title = {Machine learning based lineage tree reconstruction improved with knowledge of higher level relationships between cells and genomic barcodes.},
journal = {NAR genomics and bioinformatics},
volume = {5},
number = {3},
pages = {lqad077},
pmid = {37608801},
issn = {2631-9268},
abstract = {Tracking cells as they divide and progress through differentiation is a fundamental step in understanding many biological processes, such as the development of organisms and progression of diseases. In this study, we investigate a machine learning approach to reconstruct lineage trees in experimental systems based on mutating synthetic genomic barcodes. We refine previously proposed methodology by embedding information of higher level relationships between cells and single-cell barcode values into a feature space. We test performance of the algorithm on shallow trees (up to 100 cells) and deep trees (up to 10 000 cells). Our proposed algorithm can improve tree reconstruction accuracy in comparison to reconstructions based on a maximum parsimony method, but this comes at a higher computational time requirement.},
}
@article {pmid37608099,
year = {2023},
author = {Shah, AP and Travadi, T and Sharma, S and Pandit, R and Joshi, C and Joshi, M},
title = {Digital PCR: A Tool to Authenticate Herbal Products and Spices.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2967},
number = {},
pages = {17-30},
pmid = {37608099},
issn = {1940-6029},
mesh = {*Spices ; Real-Time Polymerase Chain Reaction ; DNA Primers/genetics ; Biological Assay ; *Carica ; },
abstract = {Authentication of herbal products and spices is experiencing a resurgence using DNA-based molecular tools, mainly species-specific assays and DNA barcoding. However, poor DNA quality and quantity are the major demerits of conventional PCR and real-time quantitative PCR (qPCR), as herbal products and spices are highly enriched in secondary metabolites such as polyphenolic compounds. The third-generation digital PCR (dPCR) technology is a highly sensitive, accurate, and reliable method to detect target DNA molecules as it is less affected by PCR inhibiting secondary metabolites due to nanopartitions. Therefore, it can be certainly used for the detection of adulteration in herbal formulations. In dPCR, extracted DNA is subjected to get amplification in nanopartitions using target gene primers, the EvaGreen master mix, or fluorescently labeled targeted gene-specific probes. Here, we describe the detection of Carica papaya (CP) adulteration in Piper nigrum (PN) products using species-specific primers. We observed an increase in fluorescence signal as the concentration of target DNA increased in PN-CP blended formulations (mock controls). Using species-specific primers, we successfully demonstrated the use of dPCR in the authentication of medicinal botanicals.},
}
@article {pmid37606732,
year = {2023},
author = {Xu, Y and Luo, J and Lai, W and Da, J and Yang, B and Luo, X and Zhan, L and Fei, Y and Liu, L and Zha, Y},
title = {Multiplex lateral flow test strip for detection of carbapenemase genes using barcoded tetrahedral DNA capture probe-based biosensing interface.},
journal = {Mikrochimica acta},
volume = {190},
number = {9},
pages = {360},
pmid = {37606732},
issn = {1436-5073},
support = {81860380//National Natural Science Foundation of China/ ; 82160026//National Natural Science Foundation of China/ ; qkhjc-zk(2021)492//Science and Technology Program of Guizhou Province/ ; qkhjc-zk(2021)474//Science and Technology Program of Guizhou Province/ ; qkhptrc(2018)5636-2//Science and Technology Program of Guizhou Province/ ; GZSYQCC(2023)010//Science and Technology Program of Guizhou Province/ ; },
mesh = {Carbapenems/pharmacology ; *Drug Resistance, Bacterial ; Gammaproteobacteria/drug effects/genetics ; *Genetic Techniques ; *Biosensing Techniques ; Polymerase Chain Reaction/methods ; },
abstract = {Carbapenem-resistant Enterobacterales pose significant global health challenges due to their rapid spread and ability to hydrolyse various beta-lactam antibiotics. Rapid tests for these carbapenemase genes are crucial to ensure appropriate prescription administration and infection control. In this study, we developed a rapid visual nanodiagnostic platform for multiplexed detection of carbapenemase genes using a lateral flow strip. The nanodiagnostic strip was designed with separate barcoded DNA tetrahedrons for the blaKPC and blaNDM genes. These tetrahedrons were distributed on a nitrocellulose membrane at two different test lines as capture probes. When tested against a panel of carbapenemase genes, the tetrahedral probes captured single-stranded amplicons of asymmetric PCR via strand hybridisation. The amplicons acted as bridging elements, binding the DNA-modified gold nanoparticles to the test line of the strip, resulting in clear visual readouts specific to the blaKPC and blaNDM genes. By employing barcoded tetrahedrons and asymmetric PCR in conjunction with the lateral flow strip, a single diagnostic test enabled the detection of multiple carbapenemase genes. The test yielded results as low as 0.12 fM for blaKPC and 0.05 fM for blaNDM within 75 min. Furthermore, the strip effectively identified specific carbapenemase genes in clinical isolates using real-time PCR, antibody-based lateral flow systems for carbapenemase detection, and carbapenemase phenotype experiments. Thus, the strip develop has a high potential for testing blaKPC and blaNDM genes in practice.},
}
@article {pmid37604784,
year = {2023},
author = {Feng, X and Lin, R and Yang, S and Xu, Y and Zhang, T and Chen, S and Ji, Y and Wang, Z and Chen, S and Zhu, C and Gao, Z and Zhao, YS},
title = {Spatially Resolved Organic Whispering-Gallery-Mode Hetero-Microrings for High-Security Photonic Barcodes.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {62},
number = {46},
pages = {e202310263},
doi = {10.1002/anie.202310263},
pmid = {37604784},
issn = {1521-3773},
support = {NO.tsqn202306255//Taishan Scholar Program of Shandong Province/ ; 22275104, 21905145//National Natural Science Foundation of China/ ; ZR2021YQ06//Shandong Provincial Natural Science Foundation/ ; 2022PY013//Scientific Research Foundation in Qilu University of Technology (Shandong Academy of Sciences)/ ; },
abstract = {Whispering-gallery-mode (WGM) microcavities featuring distinguishable sharp peaks in a broadband exhibit enormous advantages in the field of miniaturized photonic barcodes. However, such kind of barcodes developed hitherto are primarily based on microcavities wherein multiple gain medias were blended into a single matrix, thus resulting in the limited and indistinguishable coding elements. Here, a surface tension assisted heterogeneous assembly strategy is proposed to construct the spatially resolved WGM hetero-microrings with multiple spatial colors along its circular direction. Through precisely regulating the charge-transfer (CT) strength, full-color microrings covering the entire visible range were effectively acquired, which exhibit a series of sharp and recognizable peaks and allow for the effective construction of high-quality photonic barcodes. Notably, the spatially resolved WGM hetero-microrings with multiple coding elements were finally acquired through heterogeneous nucleation and growth controlled by the directional diffusion between the hetero-emulsion droplets, thus remarkably promoting the security strength and coding capacity of the barcodes. The results would be useful to fabricate new types of organic hierarchical hybrid WGM heterostructures for optical information recording and security labels.},
}
@article {pmid37603596,
year = {2023},
author = {Cotton, JL and Estrada Diez, J and Sagar, V and Chen, J and Piquet, M and Alford, J and Song, Y and Li, X and Riester, M and DiMare, MT and Schumacher, K and Boulay, G and Sprouffske, K and Fan, L and Burks, T and Mansur, L and Wagner, J and Bhang, HC and Iartchouk, O and Reece-Hoyes, J and Morris, EJ and Hammerman, PS and Ruddy, DA and Korn, JM and Engelman, JA and Niederst, MJ},
title = {Expressed Barcoding Enables High-Resolution Tracking of the Evolution of Drug Tolerance.},
journal = {Cancer research},
volume = {83},
number = {21},
pages = {3611-3623},
doi = {10.1158/0008-5472.CAN-23-0144},
pmid = {37603596},
issn = {1538-7445},
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/drug therapy/genetics/pathology ; *Lung Neoplasms/drug therapy/genetics/pathology ; ErbB Receptors/genetics/metabolism ; Neoplasm Recurrence, Local ; Drug Tolerance ; },
abstract = {UNLABELLED: For a majority of patients with non-small cell lung cancer with EGFR mutations, treatment with EGFR inhibitors (EGFRi) induces a clinical response. Despite this initial reduction in tumor size, residual disease persists that leads to disease relapse. Elucidating the preexisting biological differences between sensitive cells and surviving drug-tolerant persister cells and deciphering how drug-tolerant cells evolve in response to treatment could help identify strategies to improve the efficacy of EGFRi. In this study, we tracked the origins and clonal evolution of drug-tolerant cells at a high resolution by using an expressed barcoding system coupled with single-cell RNA sequencing. This platform enabled longitudinal profiling of gene expression and drug sensitivity in response to EGFRi across a large number of clones. Drug-tolerant cells had higher expression of key survival pathways such as YAP and EMT at baseline and could also differentially adapt their gene expression following EGFRi treatment compared with sensitive cells. In addition, drug combinations targeting common downstream components (MAPK) or orthogonal factors (chemotherapy) showed greater efficacy than EGFRi alone, which is attributable to broader targeting of the heterogeneous EGFRi-tolerance mechanisms present in tumors. Overall, this approach facilitates thorough examination of clonal evolution in response to therapy that could inform the development of improved diagnostic approaches and treatment strategies for targeting drug-tolerant cells.<br><br>SIGNIFICANCE: The evolution and heterogeneity of EGFR inhibitor tolerance are identified in a large number of clones at enhanced cellular and temporal resolution using an expressed barcode technology coupled with single-cell RNA sequencing.},
}
@article {pmid37602958,
year = {2023},
author = {Curnick, DJ and Deaville, R and Bortoluzzi, JR and Cameron, L and Carlsson, JEL and Carlsson, J and Dolton, HR and Gordon, CA and Hosegood, P and Nilsson, A and Perkins, MW and Purves, KJ and Spiro, S and Vecchiato, M and Williams, RS and Payne, NL},
title = {Northerly range expansion and first confirmed records of the smalltooth sand tiger shark, Odontaspis ferox, in the United Kingdom and Ireland.},
journal = {Journal of fish biology},
volume = {103},
number = {6},
pages = {1549-1555},
doi = {10.1111/jfb.15529},
pmid = {37602958},
issn = {1095-8649},
support = {18/SIRG/5549/SFI_/Science Foundation Ireland/Ireland ; },
mesh = {Male ; Female ; Animals ; *Sharks/genetics ; Ireland ; DNA, Mitochondrial/genetics ; United Kingdom ; Climate Change ; },
abstract = {Three Odontaspis ferox (confirmed by mtDNA barcoding) were found in the English Channel and Celtic Sea in 2023 at Lepe, UK (50.7846, -1.3508), Kilmore Quay, Ireland (52.1714, -6.5937), and Lyme Bay, UK (50.6448, -2.9302). These are the first records of O. ferox in either country, and extend the species' range by over three degrees of latitude, to >52° N. They were ~275 (female), 433 (female), and 293 cm (male) total length, respectively. These continue a series of new records, possibly indicative of a climate change-induced shift in the species' range.},
}
@article {pmid37602957,
year = {2023},
author = {Takahashi, M and Wakefield, CB and Newman, SJ and Hillcoat, KB and Saunders, BJ and Harvey, ES},
title = {Utility of body and otolith morphometry to discriminate cryptic juveniles of two sympatric red snappers (Perciformes: Lutjanidae).},
journal = {Journal of fish biology},
volume = {103},
number = {6},
pages = {1312-1320},
doi = {10.1111/jfb.15530},
pmid = {37602957},
issn = {1095-8649},
mesh = {Animals ; *Otolithic Membrane/anatomy &amp; histology ; *Perciformes/genetics ; Fishes/genetics ; DNA ; Ecology ; },
abstract = {The sympatric red snappers, Lutjanus erythropterus and Lutjanus malabaricus, are highly valued by commercial and recreational fishers along the tropical northern coasts of Australia and throughout their distribution. Studies on the life history and ecology of these congeners are confounded by difficulties in distinguishing the cryptic juveniles of each species (i.e., < 200 mm total length). This study aimed to validate a robust and cost-effective method to discriminate these juveniles using body and/or otolith morphometric data in a multivariate analysis. Juvenile samples were collected from the northwest (n = 71) and northeast (n = 19) coasts of Australia, and species identification was confirmed using DNA barcoding. The most parsimonious multivariate models achieved accurate species prediction rates of 98.8%, which consisted of just three body variables (dorsal fin length, the distance from the snout to the anterior edge of the eye, and either jaw length or distance from the snout to the preoperculum). The high level of discrimination for these cryptic juveniles highlights the robustness of this morphometric approach. The slightly lower rate of discrimination using otolith morphology (84.9%) was associated with greater regional variation in L. malabaricus between the northwest and northeast coasts. Slight variations in otolith shape are typically used to determine stock structure, which highlights the potential need to collect samples over a broader area of a species geographic range when using an otolith morphometric discrimination model. The method outlined in this study could be applied to distinguish other cryptic congeneric fish species, including from archived otolith collections. Moreover, this method has the potential to be utilized in assessing species compositions using body measurements from in situ stereo-video.},
}
@article {pmid37602732,
year = {2023},
author = {Dziedzic, E and Sidlauskas, B and Cronn, R and Anthony, J and Cornwell, T and Friesen, TA and Konstantinidis, P and Penaluna, BE and Stein, S and Levi, T},
title = {Creating, curating and evaluating a mitogenomic reference database to improve regional species identification using environmental DNA.},
journal = {Molecular ecology resources},
volume = {23},
number = {8},
pages = {1880-1904},
doi = {10.1111/1755-0998.13855},
pmid = {37602732},
issn = {1755-0998},
mesh = {Humans ; Animals ; *DNA, Environmental ; Biodiversity ; Genomics/methods ; Fishes/genetics ; Genome ; DNA Barcoding, Taxonomic ; Environmental Monitoring/methods ; },
abstract = {Species detection using eDNA is revolutionizing global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information-especially sequence information that includes intraspecific variation-creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of mitogenomic sequence information to evaluate the effectiveness of such data to detect and identify taxa. We created the Oregon Biodiversity Genome Project to create a database of complete, nearly error-free mitogenomic sequences for all of Oregon's fishes. We have successfully assembled the complete mitogenomes of 313 specimens of freshwater, anadromous and estuarine fishes representing 24 families, 55 genera and 129 species and lineages. Comparative analyses of these sequences illustrate that many regions of the mitogenome are taxonomically informative, that the short (~150 bp) mitochondrial 'barcode' regions typically used for eDNA assays do not consistently diagnose for species and that complete single or multiple genes of the mitogenome are preferable for identifying Oregon's fishes. This project provides a blueprint for other researchers to follow as they build regional databases, illustrates the taxonomic value and limits of complete mitogenomic sequences and offers clues as to how current eDNA assays and environmental genomics methods of the future can best leverage this information.},
}
@article {pmid37601830,
year = {2023},
author = {Zhang, Y and Zheng, Y and Tomassini, A and Singh, AK and Raymo, FM},
title = {Photoactivatable Fluorophores for Bioimaging Applications.},
journal = {ACS applied optical materials},
volume = {1},
number = {3},
pages = {640-651},
pmid = {37601830},
issn = {2771-9855},
support = {R01 GM143397/GM/NIGMS NIH HHS/United States ; R21 GM141675/GM/NIGMS NIH HHS/United States ; },
abstract = {Photoactivatable fluorophores provide the opportunity to switch fluorescence on exclusively in a selected area within a sample of interest at a precise interval of time. Such a level of spatiotemporal fluorescence control enables the implementation of imaging schemes to monitor dynamic events in real time and visualize structural features with nanometer resolution. These transformative imaging methods are contributing fundamental insights on diverse cellular processes with profound implications in biology and medicine. Current photoactivatable fluorophores, however, become emissive only after the activation event, preventing the acquisition of fluorescence images and, hence, the visualization of the sample prior to activation. We developed a family of photoactivatable fluorophores capable of interconverting between emissive states with spectrally resolved fluorescence, instead of switching from a nonemissive state to an emissive one. We demonstrated that our compounds allow the real-time monitoring of molecules diffusing across the cellular blastoderm of developing embryos as well as of polymer beads translocating along the intestinal tract of live nematodes. Additionally, they also permit the tracking of single molecules in the lysosomal compartments of live cells and the visualization of these organelles with nanometer resolution. Indeed, our photoactivatable fluorophores may evolve into invaluable analytical tools for the investigation of the fundamental factors regulating the functions and structures of cells at the molecular level.},
}
@article {pmid37601316,
year = {2023},
author = {Pezzini, FF and Ferrari, G and Forrest, LL and Hart, ML and Nishii, K and Kidner, CA},
title = {Target capture and genome skimming for plant diversity studies.},
journal = {Applications in plant sciences},
volume = {11},
number = {4},
pages = {e11537},
pmid = {37601316},
issn = {2168-0450},
abstract = {Recent technological advances in long-read high-throughput sequencing and assembly methods have facilitated the generation of annotated chromosome-scale whole-genome sequence data for evolutionary studies; however, generating such data can still be difficult for many plant species. For example, obtaining high-molecular-weight DNA is typically impossible for samples in historical herbarium collections, which often have degraded DNA. The need to fast-freeze newly collected living samples to conserve high-quality DNA can be complicated when plants are only found in remote areas. Therefore, short-read reduced-genome representations, such as target capture and genome skimming, remain important for evolutionary studies. Here, we review the pros and cons of each technique for non-model plant taxa. We provide guidance related to logistics, budget, the genomic resources previously available for the target clade, and the nature of the study. Furthermore, we assess the available bioinformatic analyses, detailing best practices and pitfalls, and suggest pathways to combine newly generated data with legacy data. Finally, we explore the possible downstream analyses allowed by the type of data generated using each technique. We provide a practical guide to help researchers make the best-informed choice regarding reduced genome representation for evolutionary studies of non-model plants in cases where whole-genome sequencing remains impractical.},
}
@article {pmid37599932,
year = {2023},
author = {Patil, S and Imran, M and Jaquline, RSM and Aeri, V},
title = {Standardization of Euphorbia tithymaloides (L.) Poit. (Root) by Conventional and DNA Barcoding Methods.},
journal = {ACS omega},
volume = {8},
number = {32},
pages = {29324-29335},
pmid = {37599932},
issn = {2470-1343},
abstract = {Adulteration and substitution of medicinal plants have become a matter of great concern in recent years. Euphorbia tithymaloides is one such medicinal plant that has gained importance but is often confused with other plants of the same species. In order to address this issue, this study aimed to conduct a conventional and molecular pharmacognostic study for the identification of the root of E. tithymaloides. The root of the plant was studied for the macroscopic observations, and then, the root was ground into coarse powder for microscopic studies and to determine the physiochemical properties. The powder was subjected to extraction with solvents such as ethanol, ethanol/water (1:1), hexane, and ethyl acetate. The extracts were then used for qualitative and quantitative (phenol, alkaloids, and flavonoids) phytochemical analysis. The molecular study was performed with the DNA barcoding technique. The DNA was extracted from the root of the plant, and its purity was examined by gel electrophoresis (1% w/v). The DNA was then amplified using an Applied Biosystems 2720 thermal cycler for the rbcL, matK, and ITS primers. The amplified primers were sequenced with a 3130 Genetic Analyzer, and the generated sequences were searched for similarity in the GenBank Database using the nucleotide BLAST analysis. The micro- and macroscopic studies revealed the morphological and organoleptic characters as well as the presence of medullary rays, fiber, cork, sclereids, parenchymal cells, and scalariform vessels. The physiochemical properties were found within the limit. The phytochemical analysis revealed the presence of terpenoids, flavonoids, saponins, and alkaloids. In addition, the alkaloidal content was high in the ethanol extract (63.04 ± 3.08 mg At E/g), while the phenol content was high in the hexane extract (10.26667 ± 1.77 mg At E/g), and the flavonoid content was high in the ethyl acetate extract (41.458 ± 1.33 mg At E/g). After the BLAST analysis from the GenBank database, the rbcL, ITS, and matK primers showed a similarity percentage of 99.83, 99.84, and 100. The phylogenetic tree for the species closest to each primer was generated using the MEGA 6 software. The matK loci had the highest percentage similar to the rbcL and ITS loci, indicating that the matK loci can be used to identify the root of E. tithymaloides as a standalone. The results from this study can be used to establish a quality standard for E. tithymaloides that will ensure its quality and purity.},
}
@article {pmid37597018,
year = {2023},
author = {Nama, S and Akter, S and Mallik, A and Behera, A and Nayak, BB and Deshmukhe, G and Jaiswar, AK and Bhushan, S and Kumar, AP and Ramteke, K},
title = {Identification of potential breeding ground of flathead grey mullet, Mugil cephalus (Linnaeus, 1758), along the Mumbai coast, India, for ecological monitoring and conservation strategies.},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {9},
pages = {1064},
pmid = {37597018},
issn = {1573-2959},
mesh = {Animals ; *Environmental Monitoring ; *Smegmamorpha/genetics ; India ; Eggs ; Estuaries ; Larva ; },
abstract = {Identifying the breeding grounds of fishes is crucial for the sustainable management of fisheries resources. The present study is aimed at identifying the potential breeding ground of Mugil cephalus along the estuary of the North Mumbai coast. A total of 1197 specimens of M. cephalus, including 546 eggs, 271 larvae, 235 juveniles, and 235 adults, were collected from four sampling stations in the Karanja estuary between January to October 2022. Water quality parameters, plankton dynamics in the estuary, and the reproductive and feeding biology of M. cephalus were also examined. The eggs, larvae, juveniles, and adults were identified using traditional morpho-meristic and DNA barcoding techniques. The results revealed a potential spawning ground of M. cephalus in the Karanja estuary. The results of reproductive biology also confirmed the occurrence of matured fishes during May-July. The abundance of eggs and larvae at the estuary's mouth and the presence of juveniles and mature individuals of M. cephalus dominantly in the Karanja estuary from May to July infer the presence of a spawning site. It is also recorded that M. cephalus spawn in higher salinity (35 ppt) and seawater temperature (33 °C) where the hatching of offspring takes place successfully. This study emphasizes the significance of DNA barcoding in guiding routine monitoring surveys and demonstrates its usefulness when combined with these techniques in identifying fish spawning grounds. The study findings will serve as baseline information to develop effective conservation and management strategies and protect the ideal spawning stock.},
}
@article {pmid37596543,
year = {2023},
author = {Su, Y and Zhang, M and Guo, Q and Wei, M and Shi, H and Wang, T and Han, Z and Liu, H and Liu, C and Huang, J},
title = {Classification of Isatis indigotica Fortune and Isatis tinctoria Linnaeus via comparative analysis of chloroplast genomes.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {465},
pmid = {37596543},
issn = {1471-2164},
support = {JATS|[2022]461,JATS[2022]291//Jiangsu Modern Agricultural Industrial Technology System Construction Project/ ; JATS|[2022]461,JATS[2022]291//Jiangsu Modern Agricultural Industrial Technology System Construction Project/ ; JATS|[2022]461,JATS[2022]291//Jiangsu Modern Agricultural Industrial Technology System Construction Project/ ; JATS|[2022]461,JATS[2022]291//Jiangsu Modern Agricultural Industrial Technology System Construction Project/ ; JATS|[2022]461,JATS[2022]291//Jiangsu Modern Agricultural Industrial Technology System Construction Project/ ; JATS|[2022]461,JATS[2022]291//Jiangsu Modern Agricultural Industrial Technology System Construction Project/ ; JATS|[2022]461,JATS[2022]291//Jiangsu Modern Agricultural Industrial Technology System Construction Project/ ; JATS|[2022]461,JATS[2022]291//Jiangsu Modern Agricultural Industrial Technology System Construction Project/ ; JATS|[2022]461,JATS[2022]291//Jiangsu Modern Agricultural Industrial Technology System Construction Project/ ; JATS|[2022]461,JATS[2022]291//Jiangsu Modern Agricultural Industrial Technology System Construction Project/ ; },
mesh = {*Genome, Chloroplast ; *Isatis/genetics ; Tetraploidy ; Plant Breeding ; China ; },
abstract = {BACKGROUND: Isatis tinctoria Linnaeus and Isatis indigotica Fortune are very inconsistent in their morphological characteristics, but the Flora of China treats them as the same species. In this work, a new technology that differs from conventional barcodes is developed to prove that they are different species and to clarify their classification.<br><br>RESULTS AND METHODS: I. indigotica was indistinguishable from I. tinctoria when using ITS2. CPGAVAS2 was used to construct the chloroplast genomes. MAFFT and DnaSP were used to calculate nucleotide polymorphism, the chloroplast genomes of the two have high diversity in the rpl32&#x2009;~&#x2009;trnL-UAG short region. When using this region as a mini barcode, it was found that there are obvious differences in the base numbers of I. tinctoria and different ploidy I. indigotica were found, but diploid and tetraploid I. indigotica had the same number of bases. Moreover, the reconstruction of the maximum likelihood (ML) tree, utilizing the mini-barcode, demonstrated that I. tinctoria and both diploid and tetraploid I. indigotica are located on distinct branches. The genome size of tetraploid I. indigotica was approximately 643.773&#xa0;MB, the heterozygosity rate was approximately 0.98%, and the repeat sequence content was approximately 90.43%. This species has a highly heterozygous, extremely repetitive genome.<br><br>CONCLUSION: A new method was established to differentiate between I. indigotica and I. tinctoria. Furthermore, this approach provides a reference and basis for the directional breeding of Isatis.},
}
@article {pmid37590329,
year = {2023},
author = {de Becquevort, S and Mckeown, NJ and Blake, M and Shaw, PW},
title = {Time series DNA barcoding provides insight into factors influencing wood-boring and bark-feeding insect communities in Scots pine, Sitka spruce, and Noble fir stands.},
journal = {Environmental entomology},
volume = {52},
number = {5},
pages = {802-813},
pmid = {37590329},
issn = {1938-2936},
mesh = {Animals ; *Wood ; Plant Bark ; DNA Barcoding, Taxonomic ; Commerce ; Time Factors ; Internationality ; *Coleoptera/genetics ; Trees/genetics ; },
abstract = {Bark-feeding and wood-boring insect pests can have significant negative impacts on conifers and wood production. The damage they cause is expected to increase in the future due to climate change and the growth of international trade. This study employed DNA barcoding of beetle juveniles (Coleoptera) sampled from standing trap trees and cut log piles at regular intervals over a 2-yr period to monitor the beetle community dynamics and associated environmental factors. Tree species was found to have a major influence on beetle communities, most strikingly at the start of early decay stages. Lower species diversity was reported from standing trap tree samples compared to log pile samples, likely due to higher residual defences in dying and recently dead trees. While the species identified from standing trap trees are more likely to be a threat to the forestry sector, the species found in the log piles are more likely to be beneficial due to their high abundance and their ability to compete with pests for breeding substrate. The analysis of beetles collected inside trees revealed additional information on ontogenetic niches and host preferences beyond that acquired solely from flight interception trap data. Our results offer insights on community composition and dynamics of bark-feeding and wood-boring insect species in Welsh conifer forests and provide resources for monitoring and management of potential pest species.},
}
@article {pmid37590309,
year = {2023},
author = {Porta, B and Vosman, B and Visser, RGF and Galván, GA and Scholten, OE},
title = {Genetic diversity of thrips populations on Allium species around the world.},
journal = {PloS one},
volume = {18},
number = {8},
pages = {e0289984},
pmid = {37590309},
issn = {1932-6203},
mesh = {Animals ; *Allium ; *Thysanoptera/genetics ; Phylogeny ; Onions ; Heteroplasmy ; },
abstract = {Thrips are a serious pest in many crops. In onion cultivation, Thrips tabaci is the most important, but not the only thrips species causing damage. We investigated which thrips species affects onion and related species worldwide, how much genetic variation there is within T. tabaci populations, and how this evolves. Furthermore, we determined the reproductive mode and the correlation between the genetic and geographic distances. Thrips samples from infested onions or related species were obtained from 14 different locations worldwide. Species and haplotypes were determined through DNA barcoding with the mitochondrial Cytochrome Oxidase subunit I (COI) gene. Thrips tabaci was the most commonly observed species, but Scirtothrips dorsalis, Thrips palmi, Frankliniella intonsa, Frankliniella occidentalis and Frankliniella tenuicornis were also found, especially at the beginning of the growing seasons and depending on the location. The Nei's genetic distance within T. tabaci was less than 5% and the haplotypes were clustered into two phylogenetic groups, each linked to a specific mode of reproduction, thelytokous or arrhenotokous. Thelytokous thrips were more common and more widely distributed than arrhenotokous thrips. A high percentage of heteroplasmy was detected in the arrhenotokous group. Heteroplasmic thrips were only found in populations where thelytokous and arrhenotokous were present in sympatry. Some T. tabaci haplotypes were present in high frequency at several sampled locations. No correlation was found between the genetic and geographic distances, which points to anthropic activities spreading thrips haplotypes throughout the world.},
}
@article {pmid37589492,
year = {2023},
author = {Sawayama, E and Takahashi, M and Kitamura, SI},
title = {Metagenomic profile of caudal fin morphology of farmed red sea bream Pagrus major.},
journal = {Diseases of aquatic organisms},
volume = {155},
number = {},
pages = {79-85},
doi = {10.3354/dao03742},
pmid = {37589492},
issn = {0177-5103},
mesh = {Animals ; *Sea Bream ; RNA, Ribosomal, 16S/genetics ; *Perciformes ; Farms ; *Tenacibaculum ; },
abstract = {The morphology of farm-reared fish often differs from that of their wild counterparts, impacting their market value. Two caudal fin tip shapes, acutely angled and blunted, are recognized in farmed populations of red sea bream Pagrus major. The angled form is preferred by consumers over the blunt since it resembles that of wild fish. Discovering the cause of the blunted tip is crucial to maximizing the commercial value of farmed red sea bream. We hypothesized that the blunt fin tip is the result of opportunistic bacteria and conducted partial 16S rRNA metagenomic barcoding and generated a clone library of the 16S rRNA gene to compare bacterial communities of the 2 fin forms. Metagenomic barcoding revealed an abundance of 5 bacterial genera, Sulfitobacter, Vibrio, Tenacibaculum, Psychrobacter, and an unknown genus of Rhodobacteraceae, on the caudal fin surface. Sulfitobacter was significantly more common on the angled caudal fin than the blunted. Vibrio is the dominant genus on the blunted caudal fin. The clone library identified these genera to species level, and Sulfitobacter sp., Vibrio harveyi, Tenacibaculum maritimum, and Psychrobacter marincola were frequently observed in blunt caudal fins. Our results suggest that opportunistic pathogenic bacteria such as V. harveyi and T. maritimum are not the primary cause of caudal fin malformation, and multiple factors such as combinations of injury, stress, and pathogenic infection may be involved. The reason for the significantly greater occurrence of Sulfitobacter sp. in the angled caudal fin is unknown, and further investigation is needed.},
}
@article {pmid37586415,
year = {2024},
author = {Devan, J and Nosi, V and Spagnuolo, J and Chancellor, A and Beshirova, A and Loureiro, JP and Vacchini, A and Hendrik Niess, J and Calogero, R and Mori, L and De Libero, G and Hruz, P},
title = {Surface protein and functional analyses identify CD4+CD39+ TCR αβ+ and activated TCR Vδ1+ cells with distinct pro-inflammatory functions in Crohn's disease lesions.},
journal = {Clinical and experimental immunology},
volume = {215},
number = {1},
pages = {79-93},
pmid = {37586415},
issn = {1365-2249},
support = {IISR-2016-101920//Uniscientia foundation and an Investigator Initiated Research/ ; 310030-173240//Swiss National Foundation/ ; },
mesh = {Humans ; *Crohn Disease ; Receptors, Antigen, T-Cell, alpha-beta/genetics ; Membrane Proteins ; Inflammation ; T-Lymphocytes ; },
abstract = {Crohn's disease (CD) is a chronic immune-mediated disorder of the gastrointestinal tract. Extensive screening studies have revealed the accumulation of immune cell subsets with unique plasticity and immunoregulatory properties in patients with CD. We performed phenotypic and functional studies on inflamed and non-inflamed bioptic tissue to investigate the presence of distinct T cells in the intestinal mucosa of CD patients. We analysed hundreds of surface molecules expressed on cells isolated from the intestinal tissue of CD patients using anti-CD45 mAbs-based barcoding. A gene ontology enrichment analysis showed that proteins that regulate the activation of T cells were the most enriched group. We, therefore, designed T-cell focused multicolour flow-cytometry panels and performed clustering analysis which revealed an accumulation of activated TEM CD4+CD39+ T cells producing IL-17 and IL-21 and increased frequency of terminally differentiated TCR Vδ1+ cells producing TNF-α and IFN-γ in inflamed tissue of CD patients. The different functional capacities of CD4+ and TCR Vδ1+ cells in CD lesions indicate their non-overlapping contribution to inflammation. The abnormally high number of terminally differentiated TCR Vδ1+ cells suggests that they are continuously activated in inflamed tissue, making them a potential target for novel therapies.},
}
@article {pmid37585425,
year = {2023},
author = {Chimeno, C and Schmidt, S and Cancian de Araujo, B and Perez, K and von Rintelen, T and Schmidt, O and Hamid, H and Pramesa Narakusumo, R and Balke, M},
title = {Abundant, diverse, unknown: Extreme species richness and turnover despite drastic undersampling in two closely placed tropical Malaise traps.},
journal = {PloS one},
volume = {18},
number = {8},
pages = {e0290173},
pmid = {37585425},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/methods ; *Arthropods/genetics ; DNA/genetics ; Biomass ; },
abstract = {Arthropods account for a large proportion of animal biomass and diversity in terrestrial systems, making them crucial organisms in our environments. However, still too little is known about the highly abundant and megadiverse groups that often make up the bulk of collected samples, especially in the tropics. With molecular identification techniques ever more evolving, analysis of arthropod communities has accelerated. In our study, which was conducted within the Global Malaise trap Program (GMP) framework, we operated two closely placed Malaise traps in Padang, Sumatra, for three months. We analyzed the samples by DNA barcoding and sequenced a total of more than 70,000 insect specimens. For sequence clustering, we applied three different delimitation techniques, namely RESL, ASAP, and SpeciesIdentifier, which gave similar results. Despite our (very) limited sampling in time and space, our efforts recovered more than 10,000 BINs, of which the majority are associated with "dark taxa". Further analysis indicates a drastic undersampling of both sampling sites, meaning that the true arthropod diversity at our sampling sites is even higher. Regardless of the close proximity of both Malaise traps (< 360 m), we discovered significantly distinct communities.},
}
@article {pmid37582217,
year = {2023},
author = {Hernandez Hernandez, D and Ding, L and Murao, A and Dahlin, LR and Li, G and Arnolds, KL and Amezola, M and Klein, A and Mitra, A and Mecacci, S and Linger, JG and Guarnieri, MT and Suzuki, Y},
title = {Improved Combinatorial Assembly and Barcode Sequencing for Gene-Sized DNA Constructs.},
journal = {ACS synthetic biology},
volume = {12},
number = {9},
pages = {2778-2782},
pmid = {37582217},
issn = {2161-5063},
mesh = {*High-Throughput Nucleotide Sequencing ; *DNA/genetics ; },
abstract = {Synergistic and supportive interactions among genes can be incorporated in engineering biology to enhance and stabilize the performance of biological systems, but combinatorial numerical explosion challenges the analysis of multigene interactions. The incorporation of DNA barcodes to mark genes coupled with next-generation sequencing offers a solution to this challenge. We describe improvements for a key method in this space, CombiGEM, to broaden its application to assembling typical gene-sized DNA fragments and to reduce the cost of sequencing for prevalent small-scale projects. The expanded reach of the method beyond currently targeted small RNA genes promotes the discovery and incorporation of gene synergy in natural and engineered processes such as biocontainment, the production of desired compounds, and previously uncharacterized fundamental biological mechanisms.},
}
@article {pmid37569853,
year = {2023},
author = {Chen, J and Wang, F and Zhou, C and Ahmad, S and Zhou, Y and Li, M and Liu, Z and Peng, D},
title = {Comparative Phylogenetic Analysis for Aerides (Aeridinae, Orchidaceae) Based on Six Complete Plastid Genomes.},
journal = {International journal of molecular sciences},
volume = {24},
number = {15},
pages = {},
pmid = {37569853},
issn = {1422-0067},
mesh = {Phylogeny ; *Orchidaceae/metabolism ; *Genome, Plastid ; *Genome, Chloroplast ; },
abstract = {Aerides Lour. (Orchidaceae, Aeridinae) is a group of epiphytic orchids with high ornamental value, mainly distributed in tropical and subtropical forests, that comprises approximately 20 species. The species are of great value in floriculture and garden designing because of their beautiful flower shapes and colors. Although the morphological boundaries of Aerides are clearly defined, the relationship between Aerides and other closely related genera is still ambiguous in terms of phylogeny. To better understand their phylogenetic relationships, this study used next-generation sequencing technology to investigate the phylogeny and DNA barcoding of this taxonomic unit using genetic information from six Aerides plastid genomes. The quadripartite-structure plastomes ranged from 147,244 bp to 148,391 bp and included 120 genes. Among them, 74 were protein coding genes, 38 were tRNA genes and 8 were rRNA genes, while the ndh genes were pseudogenized or lost. Four non-coding mutational hotspots (rpl20-rpl33, psbM, petB, rpoB-trnC[GCA], Pi > 0.06) were identified. A total of 71-77 SSRs and 19-46 long repeats (>30 bp) were recognized in Aerides plastomes, which were mostly located in the large single-copy region. Phylogenetic analysis indicated that Aerides was monophylic and sister to Renanthera. Moreover, our results confirmed that six Aerides species can be divided into three major clades. These findings provide assistance for species identification and DNA barcoding investigation in Aerides, as well as contributes to future research on the phylogenomics of Orchidaceae.},
}
@article {pmid37568190,
year = {2023},
author = {Ferreira, CSM and de Mesquita, DC and de Freitas Lutz, &#xcd;A and Veneza, IB and Martins, TS and Santana, PDCP and Miranda, JAB and de Sousa, JM and Matos, SCDN and Holanda, FCAF and da Cunha Sampaio, MI and Evangelista-Gomes, GF},
title = {First record of rainbow shrimp, exotic species Mierspenaeopsis sculptilis (Heller, 1862), in the Brazilian coastal amazon, validated by DNA barcode.},
journal = {BMC zoology},
volume = {8},
number = {1},
pages = {11},
pmid = {37568190},
issn = {2056-3132},
support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior, Brasil/ ; 439113/2018-0 - GEG//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
abstract = {BACKGROUND: This is the first record of the alien shrimp Mierspenaeopsis sculptilis in Brazil. The invasion was detected within Marine Extractive Reserves based on eight specimens accidentally caught by local fishermen using trawlnets focused on fisheries of native species. These specimens were transported to the Laboratory of Applied Genetics and morphologically identified as Mierspenaeopsis sculptilis (rainbow shrimp). The taxonomic status of analyzed samples was confirmed by DNA barcoding using a 627-bp fragment of the Cytochrome C Oxidase Subunit I (COI) gene.<br><br>RESULTS: A single haplotype was recovered from the eight specimens, being identical to a haplotype reported in India, where this species naturally occurs, and in Mozambique, where the rainbow shrimp is considered an invasive species. The present analyses indicated a putative invasive route (i.e., India-Mozambique-Brazil) mediated by shipping trade.<br><br>CONCLUSIONS: This study presents the first record of Mierspenaeopsis sculptilis in Brazil, in areas of extractive reserves on the Amazon coast. Notably exotic species can cause imbalance in the ecosystem, harming native species. In view of this, the registration of new invasions is essential as they contribute to the implementation of control plans.},
}
@article {pmid37564874,
year = {2023},
author = {Waechter, C and Fehse, L and Welzel, M and Heider, D and Babalija, L and Cheko, J and Mueller, J and Pöling, J and Braun, T and Pankuweit, S and Weihe, E and Kinscherf, R and Schieffer, B and Luesebrink, U and Soufi, M and Ruppert, V},
title = {Comparative analysis of full-length 16s ribosomal RNA genome sequencing in human fecal samples using primer sets with different degrees of degeneracy.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1213829},
pmid = {37564874},
issn = {1664-8021},
abstract = {Next-generation sequencing has revolutionized the field of microbiology research and greatly expanded our knowledge of complex bacterial communities. Nanopore sequencing provides distinct advantages, combining cost-effectiveness, ease of use, high throughput, and high taxonomic resolution through its ability to process long amplicons, such as the entire 16s rRNA genome. We examine the performance of the conventional 27F primer (27F-I) included in the 16S Barcoding Kit distributed by Oxford Nanopore Technologies (ONT) and that of a more degenerate 27F primer (27F-II) in the context of highly complex bacterial communities in 73 human fecal samples. The results show striking differences in both taxonomic diversity and relative abundance of a substantial number of taxa between the two primer sets. Primer 27F-I reveals a significantly lower biodiversity and, for example, at the taxonomic level of the phyla, a dominance of Firmicutes and Proteobacteria as determined by relative abundances, as well as an unusually high ratio of Firmicutes/Bacteriodetes when compared to the more degenerate primer set (27F-II). Considering the findings in the context of the gut microbiomes common in Western industrial societies, as reported in the American Gut Project, the more degenerate primer set (27F-II) reflects the composition and diversity of the fecal microbiome significantly better than the 27F-I primer. This study provides a fundamentally relevant comparative analysis of the in situ performance of two primer sets designed for sequencing of the entire 16s rRNA genome and suggests that the more degenerate primer set (27F-II) should be preferred for nanopore sequencing-based analyses of the human fecal microbiome.},
}
@article {pmid37564109,
year = {2023},
author = {Bidzilya, OV and Huemer, P and Karsholt, O},
title = {Thiotrichasumpichi sp. nov. - a new species of Thiotrichinae (Lepidoptera, Gelechiidae) from south-eastern Europe.},
journal = {ZooKeys},
volume = {1173},
number = {},
pages = {85-96},
pmid = {37564109},
issn = {1313-2989},
abstract = {Thiotrichasumpichisp. nov. is described from Greece and Croatia. The systematic position of the new species within Thiotricha is discussed based on external and genitalia characters and from DNA barcodes of the mitochondrial COI gene (cytochrome c oxidase 1). Adults, details of external morphology, and male and female genitalia of the new species are illustrated.},
}
@article {pmid37560177,
year = {2023},
author = {Yang, H and Jiang, M and Sun, S and Liu, S and Chen, H and Du, Q and Wang, B and Li, Y and Wang, L and Liu, C},
title = {Analysis of the complete plastomes of Albizia kalkora (Roxb.) Prain 1897 (Fabaceae).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {8},
number = {8},
pages = {841-846},
pmid = {37560177},
issn = {2380-2359},
abstract = {Albizia kalkora (Roxb.) Prain 1897, belonging to the family Fabaceae, is not only a landscape tree but also a medicinal plant. At present, few plastomes have been reported from Albizia, which delays the in-depth phylogenomic studies and the development of high-resolution discriminating markers for this genus. Herein, we sequenced the first plastome of A. kalkora by NGS technology. The genome is a circular structure (176,158 bp), containing a large single-copy (LSC) region (91,521 bp), a small copy (SSC) region (5237 bp), and two inverted repeat (IR) regions (39,700 bp each). It has 35.45% GC content and encodes 109 unique genes, which are 76 protein-coding, 4 rRNA, and 29 tRNA genes. The genetic distance analysis of the intergenic spacer regions for A. kalkora, A. odoratissima and A. bracteate shows four intergenic regions with very high K2p values, namely, ccsA-ndhD (15.04), matK-rps16 (10.77), rps11-rpl36 (17.63) and rps3-rps19 (20.08), which can discriminate the three Albizia species. In addition, we identified ten pairs of regions that could be utilized to design primers to discriminate the three Albizia species. The phylogenetic analysis showed Albizia was closely related to Samanea. The results in this study will provide valuable information to elucidate the classification, identification and evolutionary history of Albizia.},
}
@article {pmid37552164,
year = {2023},
author = {Reyes, AM and Smith, ZC and Onufrak, AJ and Pietsch, G and Ony, M and Odoi, M and Khodaei, S and Smallwood, C and Ginzel, M and Klingeman, W and Hadziabdic, D},
title = {First report of Bot Canker (Diplodia corticola) in Pin Oak (Quercus palustris) in Tennessee.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-02-23-0308-PDN},
pmid = {37552164},
issn = {0191-2917},
abstract = {Diplodia corticola is a fungal pathogen contributing to oak (Quercus spp.) decline in the Mediterranean and US (Félix et al., 2017; Ferreira et al., 2021). In 2021, this pathogen was detected in Tennessee (TN) causing branch dieback in Q. alba (Onufrak et al., 2022). In September 2021, a matured pin oak (Q. palustris) with wilted leaves and elongated branch cankers was observed in the State Botanical Garden of Tennessee-Knoxville (TN, US). Small sections of the phloem were sampled from canker margins of a symptomatic branch using a sterile scalpel, surface sterilized, and plated onto potato dextrose agar amended with antibiotics (PDA++) (Gazis et al. 2018). Three days later, a fungal isolate resembling D. corticola was cultured on ½ PDA. Diplodia corticola is characterized on half-strength PDA by fast growth, irregular margins, and dense white mycelium that turns dark, grayish as the mycelium matures (Úrbez-Torres et al., 2010; Alves et al., 2004). Total genomic DNA was extracted from this isolate following Gazis et al. (2018), and the internal transcribed spacer (ITS), large ribosomal subunit (LSU), and transcription elongation factor 1-α (ef1-α) were amplified (Ferreira et al. 2021). Resulting PCR products were sequenced and assembled into consensus sequences using Unipro UGENE v. 44.0 (Okonechnikov et al., 2012). Each consensus sequence identity was determined using BLAST on the NCBI nucleotide database, restricted to type material. The ITS (accession OQ189888), ef-1α (accession OQ201608), and LSU (accession OQ189887) sequences had a 99.6% (accession KF766156.1), 98.6% (accession XM_020275852.1), and 100% (accession KF766323.1) identity match with D. corticola type culture CBS112549, respectively. To complete Koch's postulates and assess potential pathogenicity on economically and ecologically relevant oaks, 10 pin (Q. palustris; caliper 15.6 ± 2.0 mm), 10 overcup (Q. lyrata; caliper 15.1 ± 2.4 mm), and 10 sawtooth (Q. acutissima; 16.1 ± 2.1 mm) oaks were acclimated in the greenhouse for 1 week prior to the experiment. Five trees of each species were then randomly inoculated at 30 cm above the soil line with a 3 mm diameter plug of D. corticola (grown for 10 days on PDA; Sitz et al. 2017). To serve as a control, the remaining 5 trees for each species received a 3 mm diameter PDA plug. Fifteen days post-inoculation, seepage was observed in D. corticola-inoculated pin (5/5 trees), overcup (4/5 trees), and sawtooth (4/5 trees) oaks. No seepage from wound sites was noted in control trees. Cankers were exposed, photographed, and then measured using ImageJ (Rasband, 2012). Using a sterile scalpel, four wood chips were excised from canker margins and plated onto PDA++. We recovered D. corticola from symptomatic inoculated pin (5/5 trees), overcup (4/5 trees), and sawtooth (4/5 trees) oaks and confirmed species identity by extracting DNA and amplifying the ITS, ef-1α, and LSU regions as described above (Gazis et al., 2018; Ferreira et al., 2021). The resulting consensus sequences matched the D. corticola type culture (CBS112549) ITS (99.0%-99.8% identity), ef-1α (91.0%-99.1% identity), and LSU (96.9%-100% identity) barcoding regions. Cankers were significantly larger in D. corticola-inoculated pin (4.7 ± 1.5 cm2; P = 0.003), overcup (6.8 ± 2.9 cm2; P = 0.009), and sawtooth (5.1 ± 1.3 cm2; P = 0.001) oaks in comparison to the control trees from these groups. Based on current reports, this is the first record of D. corticola causing dieback in pin oak (Q. palustris) in TN.},
}
@article {pmid37552039,
year = {2023},
author = {Huang, W and Cheng, Y and Zhai, J and Qin, Y and Zhang, W and Xie, X},
title = {Expanded single-color barcoding in microspheres with fluorescence anisotropy for multiplexed biochemical detection.},
journal = {The Analyst},
volume = {148},
number = {18},
pages = {4406-4413},
doi = {10.1039/d3an00938f},
pmid = {37552039},
issn = {1364-5528},
mesh = {Microspheres ; *Fluorescence Resonance Energy Transfer/methods ; *Quantum Dots ; Diagnostic Imaging ; Fluorescent Dyes/chemistry ; },
abstract = {Single-color barcoding strategies could break the limits of spectral crosstalk in conventional intensity-based fluorescence barcodes. Fluorescence anisotropy (FA), a self-referencing quantity able to differentiate spectrally similar fluorophores, is highly attractive in designing fluorescent barcodes within a limited emission window. In this study, FA-based encoding of polystyrene (PS) microspheres was realized for the first time. The FA signals of fluorophores were stabilized inside PS microspheres owing to hampered rotational motion. Fluorescent labels were incorporated with similar emission but different structures, symmetries, and lifetimes. On the one hand, Förster Resonance Energy Transfer (FRET) including homo-FRET and hetero-FRET resulted in a decrease of steady-state FA with increasing dye loading, converting conventional intensity-based codes into FA-based codes. On the other hand, mixing dyes with different intrinsic FA values generated different FA values at the same fluorescence intensity level. Single color 5-plex FA-encoded microspheres were demonstrated and decoded on a homemade microscopic FA imaging platform in real time. The FA-encoded microspheres were successfully applied to detect the oligonucleotide of the foodborne bacterium, Bacillus cereus, without spectral crosstalk between the encoding and reporting dyes. Overall, FA-based encoding with an expanded coding capacity in the FA dimension holds great potential in multiplexed high-throughput chemical and biological analyses.},
}
@article {pmid37551767,
year = {2024},
author = {Yeo, D and Chan, AHJ and Hiong, KC and Ong, J and Ng, JY and Lim, JM and Zhang, W and Lim, SR and Fernandez, CJ and Wong, AM and Lee, BPY and Khoo, MDY and Cheng, TXW and Lim, BTM and Yeo, HHT and Tan, MMQ and Sng, WBG and Adam, SS and Ang, WF and How, CB and Xie, R and Wasser, SK and Finch, KN and Loo, AHB and Yap, HH and Leong, CC and Er, KBH},
title = {Uncovering the magnitude of African pangolin poaching with extensive nanopore DNA genotyping of seized scales.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {38},
number = {2},
pages = {e14162},
doi = {10.1111/cobi.14162},
pmid = {37551767},
issn = {1523-1739},
mesh = {Humans ; Animals ; *Pangolins ; Genotype ; *Nanopores ; Conservation of Natural Resources/methods ; DNA ; Seizures ; },
abstract = {Trade in pangolins is illegal, and yet tons of their scales and products are seized at various ports. These large seizures are challenging to process and comprehensively genotype for upstream provenance tracing and species identification for prosecution. We implemented a scalable DNA barcoding pipeline in which rapid DNA extraction and MinION sequencing were used to genotype a substantial proportion of pangolin scales subsampled from 2 record shipments seized in Singapore in 2019 (37.5 t). We used reference sequences to match the scales to phylogeographical regions of origin. In total, we identified 2346 cytochrome b (cytb) barcodes of white-bellied (Phataginus tricuspis) (from 1091 scales), black-bellied (Phataginus tetradactyla) (227 scales), and giant (Smutsia gigantea) (1028 scales) pangolins. Haplotype diversity was higher for P. tricuspis scales (121 haplotypes, 66 novel) than that for P. tetradactyla (22 haplotypes, 15 novel) and S. gigantea (25 haplotypes, 21 novel) scales. Of the novel haplotypes, 74.2% were likely from western and west-central Africa, suggesting potential resurgence of poaching and newly exploited populations in these regions. Our results illustrate the utility of extensively subsampling large seizures and outline an efficient molecular approach for rapid genetic screening that should be accessible to most forensic laboratories and enforcement agencies.},
}
@article {pmid37551343,
year = {2023},
author = {Kabus, J and Cunze, S and Dombrowski, A and Karaouzas, I and Shumka, S and Jourdan, J},
title = {Uncovering the Grinnellian niche space of the cryptic species complex Gammarus roeselii.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15800},
pmid = {37551343},
issn = {2167-8359},
mesh = {Animals ; *Amphipoda/genetics ; Biodiversity ; Phylogeny ; Geography ; Biological Evolution ; },
abstract = {BACKGROUND: The discovery of cryptic species complexes within morphologically established species comes with challenges in the classification and handling of these species. We hardly know to what extent species within a species complex differ ecologically. Such knowledge is essential to assess the vulnerability of individual genetic lineages in the face of global change. The abiotic conditions, i.e., the Grinnellian niche that a genetic lineage colonizes, provides insights into how diverse the ecological requirements of each evolutionary lineage are within a species complex.<br><br>MATERIAL AND METHODS: We sampled the cryptic species complex of the amphipod Gammarus roeselii from Central Germany to Greece and identified genetic lineages based on cytochrome c oxidase subunit I (COI) barcoding. At the same time, we recorded various abiotic parameters and local pollution parameters using a series of in vitro assays to then characterize the Grinnellian niches of the morphospecies (i.e., Gammarus roeselii sensu lato) as well as each genetic lineage. Local pollution can be a significant factor explaining current and future distributions in times of increasing production and release of chemicals into surface waters.<br><br>RESULTS: We identified five spatially structured genetic lineages in our dataset that differed to varying degrees in their Grinnellian niche. In some cases, the niches were very similar despite the geographical separation of lineages, supporting the hypothesis of niche conservatism while being allopatrically separated. In other cases, we found a small niche that was clearly different from those of other genetic lineages.<br><br>CONCLUSION: The variable niches and overlaps of different dimensions make the G. roeselii species complex a promising model system to further study ecological, phenotypic and functional differentiation within this species complex. In general, our results show that the Grinnellian niches of genetically distinct molecular operational taxonomic units (MOTUs) within a cryptic species complex can differ significantly between each other, calling for closer inspection of cryptic species in a conservational and biodiversity context.},
}
@article {pmid37550887,
year = {2024},
author = {Hernández, M and Hereira-Pacheco, S and Alberdi, A and Díaz DE LA Vega-Pérez, AH and Estrada-Torres, A and Ancona, S and Navarro-Noya, YE},
title = {DNA metabarcoding reveals seasonal changes in diet composition across four arthropod-eating lizard species (Phrynosomatidae: Sceloporus).},
journal = {Integrative zoology},
volume = {19},
number = {3},
pages = {480-495},
doi = {10.1111/1749-4877.12755},
pmid = {37550887},
issn = {1749-4877},
support = {//Consejo Nacional de Ciencia y Tecnolog&#xed;a (CONACyT)/ ; 205945//Infraestructura project/ ; 137748//Ciencia de Frontera project/ ; 883//C&#xe1;tedras CONACyT project/ ; //Universidad Nacional Aut&#xf3;noma de M&#xe9;xico (UNAM)/ ; },
mesh = {Animals ; *Lizards/physiology ; *Seasons ; *Diet/veterinary ; *DNA Barcoding, Taxonomic ; Arthropods/physiology/genetics ; Species Specificity ; Phylogeny ; Feeding Behavior ; },
abstract = {Diet composition and its ecological drivers are rarely investigated in coexisting closely related species. We used a molecular approach to characterize the seasonal variation in diet composition in four spiny lizard species inhabiting a mountainous ecosystem. DNA metabarcoding revealed that the lizards Sceloporus aeneus, S. bicanthalis, S. grammicus, and S. spinosus mostly consumed arthropods of the orders Hemiptera, Araneae, Hymenoptera, and Coleoptera. The terrestrial lizards S. aeneus and S. bicanthalis mostly predated ants and spiders, whereas the arboreal-saxicolous S. grammicus and saxicolous S. spinosus largely consumed grasshoppers and leafhoppers. The taxonomic and phylogenetic diversity of the prey was higher during the dry season than the rainy season, likely because reduced prey availability in the dry season forced lizards to diversify their diets to meet their nutritional demands. Dietary and phylogenetic composition varied seasonally depending on the species, but only dietary composition varied with altitude. Seasonal dietary turnover was greater in S. spinosus than in S. bicanthalis, suggesting site-specific seasonal variability in prey availability; no other differences among species were observed. S. bicanthalis, which lives at the highest altitude in our study site, displayed interseasonal variation in diet breadth. Dietary differences were correlated with the species' feeding strategies and elevational distribution, which likely contributed to the coexistence of these lizard species in the studied geographic area and beyond.},
}
@article {pmid37550692,
year = {2023},
author = {Permana, DH and Hasmiwati, and Suryandari, DA and Rozi, IE and Syahrani, L and Setiadi, W and Irawati, N and Rizaldi, and Wangsamuda, S and Yusuf, Y and Irdayanti, and Aswad, H and Asih, PBS and Syafruddin, D},
title = {The potential for zoonotic malaria transmission in five areas of Indonesia inhabited by non-human primates.},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {267},
pmid = {37550692},
issn = {1756-3305},
mesh = {Animals ; Humans ; Indonesia/epidemiology ; Mosquito Vectors ; *Malaria/epidemiology/veterinary/parasitology ; *Plasmodium knowlesi/genetics ; Primates ; Macaca ; *Anopheles/parasitology ; },
abstract = {BACKGROUND: Indonesia is home to many species of non-human primates (NHPs). Deforestation, which is still ongoing in Indonesia, has substantially reduced the habitat of NHPs in the republic. This has led to an intensification of interactions between NHPs and humans, which opens up the possibility of pathogen spillover. The aim of the present study was to determine the prevalence of malarial parasite infections in NHPs in five provinces of Indonesia in 2022. Species of the genus Anopheles that can potentially transmit malarial pathogens to humans were also investigated.<br><br>METHODS: An epidemiological survey was conducted by capturing NHPs in traps installed in several localities in the five provinces, including in the surroundings of a wildlife sanctuary. Blood samples were drawn aseptically after the NHPs had been anesthetized; the animals were released after examination. Blood smears were prepared on glass slides, and dried blood spot tests on filter paper. Infections with Plasmodium spp. were determined morphologically from the blood smears, which were stained with Giemsa solution, and molecularly through polymerase chain reaction and DNA sequencing using rplU oligonucleotides. The NHPs were identified to species level by using the mitochondrial cytochrome c oxidase subunit I gene and the internal transcribed spacer 2 gene as barcoding DNA markers. Mosquito surveillance included the collection of larvae from breeding sites and that of adults through the human landing catch (HLC) method together with light traps.<br><br>RESULTS: Analysis of the DNA extracted from the dried blood spot tests of the 110 captured NHPs revealed that 50% were positive for Plasmodium, namely Plasmodium cynomolgi, Plasmodium coatneyi, Plasmodium inui, Plasmodium knowlesi and Plasmodium sp. Prevalence determined by microscopic examination of the blood smears was 42%. Species of the primate genus Macaca and family Hylobatidae were identified by molecular analysis. The most common mosquito breeding sites were ditches, puddles and natural ponds. Some of the Anopheles letifer captured through HLC carried sporozoites of malaria parasites that can cause the disease in primates.<br><br>CONCLUSIONS: The prevalence of malaria in the NHPs was high. Anopheles letifer, a potential vector of zoonotic malaria, was identified following its collection in Central Kalimantan by the HLC method. In sum, the potential for the transmission of zoonotic malaria in several regions of Indonesia is immense.},
}
@article {pmid37550477,
year = {2023},
author = {Serrano, A and Weber, T and Berthelet, J and El-Saafin, F and Gadipally, S and Charafe-Jauffret, E and Ginestier, C and Mariadason, JM and Oakes, SR and Britt, K and Naik, SH and Merino, D},
title = {Experimental and spontaneous metastasis assays can result in divergence in clonal architecture.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {821},
pmid = {37550477},
issn = {2399-3642},
mesh = {Humans ; Female ; *Lung Neoplasms/pathology ; *Breast Neoplasms/genetics/pathology ; Lung/pathology ; Liver/pathology ; Clone Cells/pathology ; },
abstract = {Intratumoural heterogeneity is associated with poor outcomes in breast cancer. To understand how malignant clones survive and grow in metastatic niches, in vivo models using cell lines and patient-derived xenografts (PDX) have become the gold standard. Injections of cancer cells in orthotopic sites (spontaneous metastasis assays) or into the vasculature (experimental metastasis assays) have been used interchangeably to study the metastatic cascade from early events or post-intravasation, respectively. However, less is known about how these different routes of injection impact heterogeneity. Herein we directly compared the clonality of spontaneous and experimental metastatic assays using the human cell line MDA-MB-231 and a PDX model. Genetic barcoding was used to study the fitness of the subclones in primary and metastatic sites. Using spontaneous assays, we found that intraductal injections resulted in less diverse tumours compared to other routes of injections. Using experimental metastasis assays via tail vein injection of barcoded MDA-MB-231 cells, we also observed an asymmetry in metastatic heterogeneity between lung and liver that was not observed using spontaneous metastasis assays. These results demonstrate that these assays can result in divergent clonal outputs in terms of metastatic heterogeneity and provide a better understanding of the biases inherent to each technique.},
}
@article {pmid37548590,
year = {2023},
author = {Guirguis, AA and Ofir-Rosenfeld, Y and Knezevic, K and Blackaby, W and Hardick, D and Chan, YC and Motazedian, A and Gillespie, A and Vassiliadis, D and Lam, EYN and Tran, K and Andrews, B and Harbour, ME and Vasiliauskaite, L and Saunders, CJ and Tsagkogeorga, G and Azevedo, A and Obacz, J and Pilka, ES and Carkill, M and MacPherson, L and Wainwright, EN and Liddicoat, B and Blyth, BJ and Albertella, MR and Rausch, O and Dawson, MA},
title = {Inhibition of METTL3 Results in a Cell-Intrinsic Interferon Response That Enhances Antitumor Immunity.},
journal = {Cancer discovery},
volume = {13},
number = {10},
pages = {2228-2247},
doi = {10.1158/2159-8290.CD-23-0007},
pmid = {37548590},
issn = {2159-8290},
support = {55008729/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; Mice ; *Interferons/genetics ; *Methyltransferases/genetics/metabolism ; RNA, Double-Stranded ; },
abstract = {UNLABELLED: Therapies that enhance antitumor immunity have altered the natural history of many cancers. Consequently, leveraging nonoverlapping mechanisms to increase immunogenicity of cancer cells remains a priority. Using a novel enzymatic inhibitor of the RNA methyl-transferase METTL3, we demonstrate a global decrease in N6-methyladenosine (m6A) results in double-stranded RNA (dsRNA) formation and a profound cell-intrinsic interferon response. Through unbiased CRISPR screens, we establish dsRNA-sensing and interferon signaling are primary mediators that potentiate T-cell killing of cancer cells following METTL3 inhibition. We show in a range of immunocompetent mouse models that although METTL3 inhibition is equally efficacious to anti-PD-1 therapy, the combination has far greater preclinical activity. Using SPLINTR barcoding, we demonstrate that anti-PD-1 therapy and METTL3 inhibition target distinct malignant clones, and the combination of these therapies overcomes clones insensitive to the single agents. These data provide the mole-cular and preclinical rationale for employing METTL3 inhibitors to promote antitumor immunity in the clinic.<br><br>SIGNIFICANCE: This work demonstrates that METTL3 inhibition stimulates a cell-intrinsic interferon response through dsRNA formation. This immunomodulatory mechanism is distinct from current immunotherapeutic agents and provides the molecular rationale for combination with anti-PD-1 immune-checkpoint blockade to augment antitumor immunity. This article is featured in Selected Articles from This Issue, p. 2109.},
}
@article {pmid37548515,
year = {2024},
author = {Hakimzadeh, A and Abdala Asbun, A and Albanese, D and Bernard, M and Buchner, D and Callahan, B and Caporaso, JG and Curd, E and Djemiel, C and Brandström Durling, M and Elbrecht, V and Gold, Z and Gweon, HS and Hajibabaei, M and Hildebrand, F and Mikryukov, V and Normandeau, E and Özkurt, E and M Palmer, J and Pascal, G and Porter, TM and Straub, D and Vasar, M and Větrovský, T and Zafeiropoulos, H and Anslan, S},
title = {A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses.},
journal = {Molecular ecology resources},
volume = {24},
number = {5},
pages = {e13847},
pmid = {37548515},
issn = {1755-0998},
support = {P20 GM103449/GM/NIGMS NIH HHS/United States ; EXC2124//Deutsche Forschungsgemeinschaft (DFG)/ ; MOBTP198//European Regional Development Fund and the programme Mobilitas Pluss/ ; //Genome Canada and Ontario Genomics/ ; U24 CA248454/CA/NCI NIH HHS/United States ; P20GM103449/GM/NIGMS NIH HHS/United States ; 21-17749S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Computational Biology/methods ; *Software ; High-Throughput Nucleotide Sequencing/methods ; Archaea/genetics/classification ; DNA, Environmental/genetics ; Metagenomics/methods ; Data Analysis ; Bacteria/genetics/classification ; Eukaryota/genetics/classification ; },
abstract = {Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through metabarcoding require sophisticated processing of high-throughput sequencing data from taxonomically informative DNA barcodes. Various sets of universal and taxon-specific primers have been developed, extending the usability of metabarcoding across archaea, bacteria and eukaryotes. Accordingly, a multitude of metabarcoding data analysis tools and pipelines have also been developed. Often, several developed workflows are designed to process the same amplicon sequencing data, making it somewhat puzzling to choose one among the plethora of existing pipelines. However, each pipeline has its own specific philosophy, strengths and limitations, which should be considered depending on the aims of any specific study, as well as the bioinformatics expertise of the user. In this review, we outline the input data requirements, supported operating systems and particular attributes of thirty-two amplicon processing pipelines with the goal of helping users to select a pipeline for their metabarcoding projects.},
}
@article {pmid37547468,
year = {2023},
author = {Romano, F and Pitta, P and John, U},
title = {Community dynamics and co-occurrence relationships of pelagic ciliates and their potential prey at a coastal and an offshore station in the ultra-oligotrophic Eastern Mediterranean Sea.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1219085},
pmid = {37547468},
issn = {1664-8021},
abstract = {Ciliates have been recognized as one of the major components of the microbial food web, especially in ultra-oligotrophic waters, such as the Eastern Mediterranean Sea, where nutrients are scarce and the microbial community is dominated by pico- and nano-sized organisms. For this reason, ciliates play an important role in these ecosystems since they are the main planktonic grazers. Regardless the importance of these organisms, little is known about the community structure of heterotrophic and mixotrophic ciliates and how they are associated to their potential prey. In this study, we used 18S V4 rRNA gene metabarcoding to analyze ciliate community dynamics and how the relationship with potential prey changes according to different seasons and depths. Samples were collected seasonally at two stations of the Eastern Mediterranean Sea (HCB: coastal, M3A: offshore) from the surface and deep chlorophyll maximum (DCM) layers. The ciliate community structure varied across depths in HCB and across seasons in M3A, and the network analysis showed that in both stations, mixotrophic oligotrichs were positively associated with diatoms and showed few negative associations with ASVs annotated as marine Stramenopiles (MAST). On the other hand, heterotrophic tintinnids showed negative relationships in both HCB and M3A stations, mostly with Ochrophyta and Chlorophyta. These results showed, in first place that, although the two stations are close to each other, the ciliate dynamics differed between them. Moreover, mixotrophic and heterotrophic ciliates may have different ecological niches since mixotrophic ciliates may be more selective compared to heterotrophic species regarding their prey. These findings are the first glimpse into an understanding of the dynamics between heterotrophic and mixotrophic ciliates and their role in microbial assemblages and dynamics of ultra-oligotrophic environments.},
}
@article {pmid37545007,
year = {2023},
author = {Putt, QY and Ya'cob, Z and Adler, PH and Chen, CD and Hew, YX and Izwan-Anas, N and Lau, KW and Sofian-Azirun, M and Pham, XD and Takaoka, H and Low, VL},
title = {From bites to barcodes: uncovering the hidden diversity of black flies (Diptera: Simuliidae) in Vietnam.},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {266},
pmid = {37545007},
issn = {1756-3305},
support = {BIFA6_017//Ministry of the Environment, Government of Japan/ ; BIFA6_017//Ministry of the Environment, Government of Japan/ ; BIFA6_017//Ministry of the Environment, Government of Japan/ ; BIFA6_017//Ministry of the Environment, Government of Japan/ ; MO002-2019//Ministry of Higher Education, Malaysia/ ; },
mesh = {Animals ; Humans ; *Simuliidae/genetics ; Vietnam ; DNA Barcoding, Taxonomic/methods ; *Bites and Stings ; Phylogeny ; Thailand ; Larva ; },
abstract = {BACKGROUND: Prompt and precise identification of black flies (Simuliidae) is crucial, given their biting behaviour and significant impact on human and animal health. To address the challenges presented by morphology and chromosomes in black fly taxonomy, along with the limited availability of molecular data pertaining to the black fly fauna in Vietnam, this study employed DNA-based approaches. Specifically, we used mitochondrial and nuclear-encoded genes to distinguish nominal species of black flies in Vietnam.<br><br>METHODS: In this study, 135 mitochondrial cytochrome c oxidase subunit I (COI) sequences were established for 45 species in the genus Simulium in Vietnam, encompassing three subgenera (Gomphostilbia, Nevermannia, and Simulium), with 64 paratypes of 27 species and 16 topotypes of six species. Of these COI sequences, 71, representing 27 species, are reported for the first time.<br><br>RESULTS: Combined with GenBank sequences of specimens from Malaysia, Myanmar, Thailand, and Vietnam, a total of 234 DNA barcodes of 53 nominal species resulted in a 71% success rate for species identification. Species from the non-monophyletic Simulium asakoae, S. feuerborni, S. multistriatum, S. striatum, S. tuberosum, and S. variegatum species groups were associated with ambiguous or incorrect identifications. Pairwise distances, phylogenetics, and species delimitation analyses revealed a high level of cryptic diversity, with discovery of 15 cryptic taxa. The current study also revealed the limited utility of a fast-evolving nuclear gene, big zinc finger (BZF), in discriminating closely related, morphologically similar nominal species of the S. asakoae species group.<br><br>CONCLUSION: This study represents the first comprehensive molecular genetic analysis of the black fly fauna in Vietnam to our knowledge, providing a foundation for future research. DNA barcoding exhibits varying levels of differentiating efficiency across species groups but is valuable in the discovery of cryptic diversity.},
}
@article {pmid37544594,
year = {2023},
author = {Guo, W and Hu, Y and Qian, J and Zhu, L and Cheng, J and Liao, J and Fan, X},
title = {Laser capture microdissection for biomedical research: towards high-throughput, multi-omics, and single-cell resolution.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {50},
number = {9},
pages = {641-651},
doi = {10.1016/j.jgg.2023.07.011},
pmid = {37544594},
issn = {1673-8527},
mesh = {Laser Capture Microdissection/methods ; *Multiomics ; *Biomedical Research ; },
abstract = {Spatial omics technologies have become powerful methods to provide valuable insights into cells and tissues within a complex context, significantly enhancing our understanding of the intricate and multifaceted biological system. With an increasing focus on spatial heterogeneity, there is a growing need for unbiased, spatially resolved omics technologies. Laser capture microdissection (LCM) is a cutting-edge method for acquiring spatial information that can quickly collect regions of interest (ROIs) from heterogeneous tissues, with resolutions ranging from single cells to cell populations. Thus, LCM has been widely used for studying the cellular and molecular mechanisms of diseases. This review focuses on the differences among four types of commonly used LCM technologies and their applications in omics and disease research. Key attributes of application cases are also highlighted, such as throughput and spatial resolution. In addition, we comprehensively discuss the existing challenges and the great potential of LCM in biomedical research, disease diagnosis, and targeted therapy from the perspective of high-throughput, multi-omics, and single-cell resolution.},
}
@article {pmid37541243,
year = {2023},
author = {Ceresa, D and Alessandrini, F and Lucchini, S and Marubbi, D and Piaggio, F and Mena Vera, JM and Ceccherini, I and Reverberi, D and Appolloni, I and Malatesta, P},
title = {Early clonal extinction in glioblastoma progression revealed by genetic barcoding.},
journal = {Cancer cell},
volume = {41},
number = {8},
pages = {1466-1479.e9},
doi = {10.1016/j.ccell.2023.07.001},
pmid = {37541243},
issn = {1878-3686},
mesh = {Mice ; Animals ; *Glioblastoma/genetics/pathology ; Retrospective Studies ; *Glioma/genetics ; Gene Expression Profiling ; Phenotype ; },
abstract = {Glioblastoma progression in its early stages remains poorly understood. Here, we transfer PDGFB and genetic barcodes in mouse brain to initiate gliomagenesis and enable direct tracing of glioblastoma evolution from its earliest possible stage. Unexpectedly, we observe a high incidence of clonal extinction events and progressive divergence in clonal sizes, even after the acquisition of malignant phenotype. Computational modeling suggests these dynamics result from clonal-based cell-cell competition. Through bulk and single-cell transcriptome analyses, coupled with lineage tracing, we reveal that Myc transcriptional targets have the strongest correlation with clonal size imbalances. Moreover, we show that the downregulation of Myc expression is sufficient to drive competitive dynamics in intracranially transplanted gliomas. Our findings provide insights into glioblastoma evolution that are inaccessible using conventional retrospective approaches, highlighting the potential of combining clonal tracing and transcriptomic analyses in this field.},
}
@article {pmid37539689,
year = {2023},
author = {Yan, J and Zhao, K and Wu, T and Liu, X and Li, Y and Li, B},
title = {Optical Printing of Silicon Nanoparticles as Strain-Driven Nanopixels.},
journal = {ACS applied materials &amp; interfaces},
volume = {15},
number = {32},
pages = {38682-38692},
doi = {10.1021/acsami.3c06391},
pmid = {37539689},
issn = {1944-8252},
abstract = {Silicon nanoparticles (Si NPs) supporting Mie resonances exhibit vivid structural colors on the subwavelength scale. For future wearable devices, next generation Si-based optical units need to be dynamic and stretchable for display, sensing, or signal processing required by human-computer interaction. Here, by utilizing the distance-sensitive electromagnetic coupling of Mie resonances, we maximize the active tuning effect of Si NP-based structures including dimers, oligomers, and NPs on WS2, which we called Si nanopixels. Through the optical tweezers-assisted printing of Si nanopixels, patterns can be formed on arbitrary flexible substrates. The strain-sensitive tuning of scattering spectra indicates their promising application on strain sensing of various stretchable substrates via a simple "spray and test" process. In the case of Si nanopixels on polydimethylsiloxane (PDMS), local strains around 1% can be detected by a scattering measurement. Moreover, we demonstrate that the scattering intensity variation of Si nanopixels printed on wrinkled tungsten disulfide (WS2) is pixel-dependent and wavelength-dependent. This property facilitates the application of information encryption, and we demonstrate that three barcodes can be independently encoded into the R, G, and B scattering channels through ternary logic represented by the strain-tuning effects of scattering.},
}
@article {pmid37538502,
year = {2023},
author = {Garcia, C and Dejean, S and Savy, N and Bordet, JC and Series, J and Cadot, S and Ribes, A and Voisin, S and Rugeri, L and Payrastre, B and Sié, P},
title = {Multicolor flow cytometry in clinical samples for platelet signaling assessment.},
journal = {Research and practice in thrombosis and haemostasis},
volume = {7},
number = {4},
pages = {100180},
pmid = {37538502},
issn = {2475-0379},
abstract = {BACKGROUND: Availability of multichannel cytometers and specific commercial antibodies makes flow cytometry a new option to simultaneously assess multiple intracellular platelet signaling pathways for clinical purposes, in small volume of blood or low platelet count.<br><br>OBJECTIVES: To describe a multicolor flow cytometry with fluorescent barcoding technique for screening signaling pathways downstream membrane receptors of major platelet agonists (adenosine diphosphate, thrombin, thromboxane, and collagen).<br><br>METHODS: By comparison with immunoblotting, we first selected the target phosphoproteins, AKT, P38MAPK, LIMK, and SPL76; the times of stimulation; and phosphoflow barcoding conditions. We then performed a clinical study on whole blood of patients without evidence of blood platelet disorder on standard biological screening, consulting for trivial or occasionally provoked bleeds without familial antecedent (bleeding of unknown origin, n&#xa0;= 23) or type-1 von Willebrand disease (n&#xa0;= 9). In addition, we included a small group of patients with definite platelet disorders (Glanzmann thrombasthenia, &#x3b4;-storage pool deficiency, and immune glycoprotein VI-related disease with granule secretion defect).<br><br>RESULTS: The range, kinetics, and distribution of fluorescence intensity were established for each agonist-target protein combination. Principal component analysis indicates a correlation in response to a target phosphoprotein (AKT and P38MAPK) to different agonists but no correlation in the response of different target phosphoproteins to the same agonist. The heterogeneity of individual responses in the whole population displayed was analyzed using clustering algorithm. Patients with platelet storage pool deficiency were positioned as lowest responders on the heatmap.<br><br>CONCLUSION: In complement of functional tests, this study introduces a new approach for rapid platelet signaling profiling in clinical practice.},
}
@article {pmid37537170,
year = {2023},
author = {Cundy, ME and Santana-Garcon, J and McLennan, AG and Ayad, ME and Bayer, PE and Cooper, M and Corrigan, S and Harrison, E and Wilcox, C},
title = {Seafood label quality and mislabelling rates hamper consumer choices for sustainability in Australia.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {10146},
pmid = {37537170},
issn = {2045-2322},
mesh = {*Food Labeling ; *Seafood ; Commerce ; Consumer Behavior ; Australia ; },
abstract = {Seafood mislabelling and species substitution, compounded by a convoluted seafood supply chain with significant traceability challenges, hinder efforts towards more sustainable, responsible, and ethical fishing and business practices. We conducted the largest evaluation of the quality and accuracy of labels for 672 seafood products sold in Australia, assessing six seafood groups (i.e., hoki, prawns, sharks and rays, snapper, squid and cuttlefish, and tuna) from fishmongers, restaurants, and supermarkets, including domestically caught and imported products. DNA barcoding revealed 11.8% of seafood tested did not match their label with sharks and rays, and snappers, having the highest mislabelling rate. Moreover, only 25.5% of products were labelled at a species-level, while most labels used vague common names or umbrella terms such as 'flake' and 'snapper'. These poor-quality labels had higher rates of mislabelling than species-specific labels and concealed the sale of threatened or overfished taxa, as well as products with lower nutritional quality, reduced economic value, or potential health risks. Our results highlight Australia's weak seafood labelling regulations and ambiguous non-mandatory naming conventions, which impede consumer choice for accurately represented, sustainable, and responsibly sourced seafood. We recommend strengthening labelling regulations to mitigate seafood mislabelling and substitution, ultimately improving consumer confidence when purchasing seafood.},
}
@article {pmid37536235,
year = {2023},
author = {Saravana Bhavan Venkatachalam, AK and Čepička, I and Hrazdilová, K and Svobodová, M},
title = {Host specificity of passerine Lankesterella (Apicomplexa: Coccidia).},
journal = {European journal of protistology},
volume = {90},
number = {},
pages = {126007},
doi = {10.1016/j.ejop.2023.126007},
pmid = {37536235},
issn = {1618-0429},
mesh = {Humans ; Animals ; *Coccidia/genetics ; Phylogeny ; Host Specificity ; *Apicomplexa ; *Eucoccidiida ; *Passeriformes/parasitology ; },
abstract = {Lankesterella parasites are blood coccidians that have recently gained attention as their records in common passerine species emerge. To date, their occurrence has been molecularly confirmed in several passerine genera, mainly among members of the families Paridae and Acrocephalidae. Despite their relatively high prevalence in some host populations, their life cycles remain unclear, mosquitoes or mites being the proposed vectors. The aim of this study was to reveal Lankesterella host specificity, focusing mainly on parasites of tit and warbler species (families Paridae and Acrocephalidae). We have determined the 18S rRNA gene sequences of Lankesterella from 35 individuals belonging to eight different host species. Phylogenetic analysis revealed that passerine Lankesterella are host-specific, with specificity at the host genus or species level. Besides Lankesterella, Isospora sequences were obtained from avian blood as well, pointing out the need for barcoding.},
}
@article {pmid37535317,
year = {2023},
author = {Saranholi, BH and Rodriguez-Castro, KG and Carvalho, CS and Chahad-Ehlers, S and Gestich, CC and Andrade, SCS and Freitas, PD and Galetti, PM},
title = {Comparing iDNA from mosquitoes and flies to survey mammals in a semi-controlled Neotropical area.},
journal = {Molecular ecology resources},
volume = {23},
number = {8},
pages = {1790-1799},
doi = {10.1111/1755-0998.13851},
pmid = {37535317},
issn = {1755-0998},
support = {150808/2019-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 303014/2017-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 303524/2019-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 317345/2021-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 8887.475596/2020-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 88887.466869/2019-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 2015/20139-9//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/23548-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2019/26436-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2022/01741-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
abstract = {Ingested-derived DNA (iDNA) from insects represents a powerful tool for assessing vertebrate diversity because insects are easy to sample, have a diverse diet and are widely distributed. Because of these advantages, the use of iDNA for detecting mammals has gained increasing attention. Here we aimed to compare the effectiveness of mosquitoes and flies to detect mammals with a small sampling effort in a semi-controlled area, a zoo that houses native and non-native species. We compared mosquitoes and flies regarding the number of mammal species detected, the amount of mammal sequence reads recovered, and the flight distance range for detecting mammals. We also verified if the combination of two mini-barcodes (12SrRNA and 16SrRNA) would perform better than either mini-barcode alone to inform local mammal biodiversity from iDNA. To capture mosquitoes and flies, we distributed insect traps in eight sampling points during 5 days. We identified 43 Operational Taxonomic Units from 10 orders, from the iDNA of 17 mosquitoes and 46 flies. There was no difference in the number of species recovered per individual insect between mosquitoes and flies, but the number of flies captured was higher, resulting in more mammal species recovered by flies. Eight species were recorded exclusively by mosquitoes and 20 by flies, suggesting that using both samplers would allow a more comprehensive screening of the biodiversity. The maximum distance recorded was 337 m for flies and 289 m for mosquitoes, but the average range distance did not differ between insect groups. Our assay proved to be efficient for mammal detection, considering the high number of species detected with a reduced sampling effort.},
}
@article {pmid37533934,
year = {2023},
author = {Cheng, Z and Huang, X},
title = {Two new species of Aphis (Toxoptera) Koch (Hemiptera, Aphididae) from China.},
journal = {ZooKeys},
volume = {1172},
number = {},
pages = {31-46},
pmid = {37533934},
issn = {1313-2989},
abstract = {Two new aphid species, Aphis (Toxoptera) fafuensis Cheng &amp; Huang, sp. nov., feeding on Adinandramillettii (Pentaphylacaceae) from Fujian, China, and Aphis (Toxoptera) sennae Cheng &amp; Huang, sp. nov., feeding on Sennabicapsularis (Fabaceae) from Yunnan, China, were described. Morphological characters and molecular data supported the taxonomic position of the new species within the subgenus Aphis (Toxoptera). A key for identifying species of apterous viviparous females in this subgenus is provided.},
}
@article {pmid37533642,
year = {2023},
author = {Asrat, S and Devlin, JC and Vecchione, A and Klotz, B and Setliff, I and Srivastava, D and Limnander, A and Rafique, A and Adler, C and Porter, S and Murphy, AJ and Atwal, GS and Sleeman, MA and Lim, WK and Orengo, JM},
title = {TRAPnSeq allows high-throughput profiling of antigen-specific antibody-secreting cells.},
journal = {Cell reports methods},
volume = {3},
number = {7},
pages = {100522},
pmid = {37533642},
issn = {2667-2375},
mesh = {Humans ; Animals ; Mice ; *Antibody-Producing Cells ; *Antigens ; B-Lymphocytes ; Antibodies/genetics ; Receptors, Antigen, B-Cell/genetics ; },
abstract = {Following activation by cognate antigen, B cells undergo fine-tuning of their antigen receptors and may ultimately differentiate into antibody-secreting cells (ASCs). While antigen-specific B cells that express surface receptors (B cell receptors [BCRs]) can be readily cloned and sequenced following flow sorting, antigen-specific ASCs that lack surface BCRs cannot be easily profiled. Here, we report an approach, TRAPnSeq (antigen specificity mapping through immunoglobulin [Ig] secretion TRAP and Sequencing), that allows capture of secreted antibodies on the surface of ASCs, which in turn enables high-throughput screening of single ASCs against large antigen panels. This approach incorporates flow cytometry, standard microfluidic platforms, and DNA-barcoding technologies to characterize antigen-specific ASCs through single-cell V(D)J, RNA, and antigen barcode sequencing. We show the utility of TRAPnSeq by profiling antigen-specific IgG and IgE ASCs from both mice and humans and highlight its capacity to accelerate therapeutic antibody discovery from ASCs.},
}
@article {pmid37533555,
year = {2023},
author = {Shimizu, S and Maeto, K},
title = {A New Distinctive Darwin Wasp Represents the First Record of the Ophion minutus Species-group (Hymenoptera: Ichneumonidae: Ophioninae) from Japan and the Far East, with an Analysis of DNA Barcode-based Species Delimitation in Ophion.},
journal = {Zoological studies},
volume = {62},
number = {},
pages = {e27},
pmid = {37533555},
issn = {1810-522X},
abstract = {A new Darwin wasp species, Ophion kobensis Shimizu sp. nov. (Hymenoptera: Ichneumonidae: Ophioninae), is described using the integrated morphological and molecular species delimitation approaches. Our results indicate that the new species is closely related to European O. ventricosus Gravenhorst, 1829 of the O. minutus species-group but can be distinguished using morphological characters, such as entirely black body colour with some light-yellow marks and not inclined epicnemial carina in lateral view. This record of the new species represents the first record of O. minutus species-group from Japan and the Far East. Phylogenetic analysis indicate that the O. minutus species-group is weakly recovered as monophyletic and sister to Ophion s. str. The analysis also indicated that two clades within the O. minutus species-group (O. minutus and O. ventricosus) diverged significantly. This suggests that the species-group, as well as the two included clades, could potentially be treated as separate species-groups or genera. The present study supports previous integrative taxonomic and phylogenetic studies of Ophion and represents a first fundamental step for studies focused on the challenging Japanese and Far Eastern Ophion.},
}
@article {pmid37529098,
year = {2023},
author = {Bradshaw, MJ and Aime, MC and Rokas, A and Maust, A and Moparthi, S and Jellings, K and Pane, AM and Hendricks, D and Pandey, B and Li, Y and Pfister, DH},
title = {Extensive intragenomic variation in the internal transcribed spacer region of fungi.},
journal = {iScience},
volume = {26},
number = {8},
pages = {107317},
pmid = {37529098},
issn = {2589-0042},
support = {R01 AI153356/AI/NIAID NIH HHS/United States ; },
abstract = {Fungi are among the most biodiverse organisms in the world. Accurate species identification is imperative for studies on fungal ecology and evolution. The internal transcribed spacer (ITS) rDNA region has been widely accepted as the universal barcode for fungi. However, several recent studies have uncovered intragenomic sequence variation within the ITS in multiple fungal species. Here, we mined the genome of 2414 fungal species to determine the prevalence of intragenomic variation and found that the genomes of 641 species, about one-quarter of the 2414 species examined, contained multiple ITS copies. Of those 641 species, 419 (∼65%) contained variation among copies revealing that intragenomic variation is common in fungi. We proceeded to show how these copies could result in the erroneous description of hundreds of fungal species and skew studies evaluating environmental DNA (eDNA) especially when making diversity estimates. Additionally, many genomes were found to be contaminated, especially those of unculturable fungi.},
}
@article {pmid37528709,
year = {2023},
author = {Miglietta, MP and Pruski, S},
title = {Cryptic species in time and space: an assessment of cryptic diversity within eight nominal species of Hydrozoa (Cnidaria).},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {2004},
pages = {20230851},
pmid = {37528709},
issn = {1471-2954},
mesh = {Animals ; *Hydrozoa ; Phylogeny ; Biodiversity ; Sympatry ; Gulf of Mexico ; },
abstract = {Sampling in multiple localities, coupled with molecular barcoding, has shown that nominal species with wide geographical distribution often harbour local cryptic species in allopatry. Cryptic species in sympatry, however, can be easily missed if they have different seasonality, because they can be identified only through long-term frequent sampling (i.e. sampling through time of the same species in the same location). This is especially true in planktonic invertebrates that exhibit strong seasonality. By integrating mitochondrial 16S sequences of eight species of Hydrozoa (Cnidaria) collected weekly for a year in one Gulf of Mexico region, with sequences gathered globally, we investigate the presence of cryptic species within a temporal gradient (regionally) and on a spatial (worldwide) scale. We find that eight species of Hydrozoa are composed of 28 cryptic species, with 16 of them appearing in sympatry but with non-overlapping seasonality. The high number of sympatric cryptic species could only be discovered through extensive and prolonged regional sampling efforts. The bi-dimensional cryptic diversity (in time and space) highlighted in this study is essential for understanding processes of evolution, biogeography dispersal in the sea, and for more realistic biodiversity assessments.},
}
@article {pmid37528368,
year = {2023},
author = {Lempang, MEP and Permana, DH and Asih, PBS and Wangsamuda, S and Dewayanti, FK and Rozi, IE and Syahrani, L and Setiadi, W and Malaka, R and Muslimin, L and Syafruddin, D},
title = {Diversity of Anopheles species and zoonotic malaria vector of the Buton Utara Wildlife Sanctuary, Southeast Sulawesi, Indonesia.},
journal = {Malaria journal},
volume = {22},
number = {1},
pages = {221},
pmid = {37528368},
issn = {1475-2875},
mesh = {Animals ; Adult ; Humans ; Female ; *Malaria/epidemiology ; Animals, Wild ; *Anopheles/genetics/parasitology ; Indonesia ; Mosquito Vectors ; *Plasmodium knowlesi/genetics ; Haplorhini ; },
abstract = {BACKGROUND: The recent deforestation for agricultural, mining, and human re-settlement has significantly reduced the habitat of many non-human primates (NHPs) in Indonesia and intensifies interaction between the NHPs and humans and thus opening the possibility of pathogen spill-over. The emergence of zoonotic malaria, such as Plasmodium knowlesi, poses an immense threat to the current malaria control and elimination that aims for the global elimination of malaria by 2030. As malaria in humans and NHPs is transmitted by the female Anopheles mosquito, malaria vector control is very important to mitigate the spill-over of the malaria parasite to humans. The present study aims to explore the Anopheles species diversity in human settlements adjacent to the wildlife sanctuary forest in Buton Utara Regency, Southeast Sulawesi, Indonesia, and identify the species that potentially transmit the pathogen from monkey to human in the area.<br><br>METHODS: Mosquito surveillance was conducted using larval and adult collection, and the collected mosquitoes were identified morphologically and molecularly using the barcoding markers, cytochrome oxidase subunit I (COI), and internal transcribed species 2 (ITS2) genes. Plasmodium sporozoite carriage was conducted on mosquitoes collected through human landing catch (HLC) and human-baited double net trap (HDNT).<br><br>RESULTS: The results revealed several Anopheles species, such as Anopheles flavirostris (16.6%), Anopheles sulawesi (3.3%), Anopheles maculatus (3.3%), Anopheles koliensis (1.2%), and Anopheles vagus (0.4%). Molecular analysis of the sporozoite carriage using the primate-specific malaria primers identified An. sulawesi, a member of the Leucosphyrus group, carrying Plasmodium inui sporozoite.<br><br>CONCLUSIONS: This study indicates that the transmission of zoonotic malaria in the area is possible and alerts to the need for mitigation efforts through a locally-tailored vector control intervention and NHPs habitat conservation.},
}
@article {pmid37528214,
year = {2023},
author = {Hoveida, P and Phoulady, A and Choi, H and May, N and Shahbazmohamadi, S and Tavousi, P},
title = {Terahertz-readable laser engraved marks as a novel solution for product traceability.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {12474},
pmid = {37528214},
issn = {2045-2322},
abstract = {Counterfeit products pose significant economic, security, and health risks. One approach to mitigate these risks involves establishing product provenance by tracing them back to their manufacturing origins. However, current identification methods, such as barcodes and RFIDs, have limitations that make them vulnerable to counterfeiting. Similarly, nonvolatile memories, physically unclonable functions, and emerging techniques like Diamond Unclonable Security Tag and DNA fingerprinting also have their own limitations and challenges. For a traceability solution to gain widespread adoption, it must meet certain criteria, including being inexpensive, unique, immutable, easily readable, standardized, and unclonable. In this paper, we propose a solution that utilizes ultrashort pulsed lasers to create unique, unclonable, and immutable physical tags. These tags can then be read nondestructively using far-field Terahertz (THz) spectroscopy. The primary objective of this paper is to investigate the feasibility of our proposed approach. We aim to assess the ability to distinguish laser marks with varying depths, evaluate the sensitivity of THz reading to laser engraving parameters, examine the capacity to capture high-information-density marks, and explore the ability to capture subsurface tags. By addressing these aspects, our method holds the potential to serve as a universal solution for a wide range of traceability applications.},
}
@article {pmid37524958,
year = {2024},
author = {Wang, K and Hou, L and Wang, X and Zhai, X and Lu, Z and Zi, Z and Zhai, W and He, X and Curtis, C and Zhou, D and Hu, Z},
title = {PhyloVelo enhances transcriptomic velocity field mapping using monotonically expressed genes.},
journal = {Nature biotechnology},
volume = {42},
number = {5},
pages = {778-789},
pmid = {37524958},
issn = {1546-1696},
support = {32270693//National Natural Science Foundation of China (National Science Foundation of China)/ ; 11971405//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2021M693303//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Caenorhabditis elegans/genetics ; *Transcriptome/genetics ; *Single-Cell Analysis/methods ; Humans ; Sequence Analysis, RNA/methods ; Gene Expression Profiling/methods ; Cell Lineage/genetics ; Cell Differentiation/genetics ; Computational Biology/methods ; Phylogeny ; },
abstract = {Single-cell RNA sequencing (scRNA-seq) is a powerful approach for studying cellular differentiation, but accurately tracking cell fate transitions can be challenging, especially in disease conditions. Here we introduce PhyloVelo, a computational framework that estimates the velocity of transcriptomic dynamics by using monotonically expressed genes (MEGs) or genes with expression patterns that either increase or decrease, but do not cycle, through phylogenetic time. Through integration of scRNA-seq data with lineage information, PhyloVelo identifies MEGs and reconstructs a transcriptomic velocity field. We validate PhyloVelo using simulated data and Caenorhabditis elegans ground truth data, successfully recovering linear, bifurcated and convergent differentiations. Applying PhyloVelo to seven lineage-traced scRNA-seq datasets, generated using CRISPR-Cas9 editing, lentiviral barcoding or immune repertoire profiling, demonstrates its high accuracy and robustness in inferring complex lineage trajectories while outperforming RNA velocity. Additionally, we discovered that MEGs across tissues and organisms share similar functions in translation and ribosome biogenesis.},
}
@article {pmid37523588,
year = {2023},
author = {Sarkar, D and Cho, S and Yan, H and Martino, N and Dannenberg, PH and Yun, SH},
title = {Ultrasmall InGa(As)P Dielectric and Plasmonic Nanolasers.},
journal = {ACS nano},
volume = {17},
number = {16},
pages = {16048-16055},
pmid = {37523588},
issn = {1936-086X},
support = {DP1 EB024242/EB/NIBIB NIH HHS/United States ; R01 EB033155/EB/NIBIB NIH HHS/United States ; },
abstract = {Nanolasers have great potential for both on-chip light sources and optical barcoding particles. We demonstrate ultrasmall InGaP and InGaAsP disk lasers with diameters down to 360 nm (198 nm in height) in the red spectral range. Optically pumped, room-temperature, single-mode lasing was achieved from both disk-on-pillar and isolated particles. When isolated disks were placed on gold, plasmon polariton lasing was obtained with Purcell-enhanced stimulated emission. UV lithography and plasma ashing enabled wafer-scale fabrication of nanodisks with an intended random size variation. Silica-coated nanodisk particles generated stable subnanometer spectra from within biological cells across an 80 nm bandwidth from 635 to 715 nm.},
}
@article {pmid37522705,
year = {2023},
author = {Dos Santos, QM and Rindoria, NM and Avenant-Oldewage, A},
title = {Genetic characterisation of four Lamproglena spp. (Copepoda, Lernaeidae) from Africa and the first mitochondrial data.},
journal = {Folia parasitologica},
volume = {70},
number = {},
pages = {},
pmid = {37522705},
issn = {1803-6465},
mesh = {Animals ; Female ; *Copepoda ; Africa ; *Cyprinidae/parasitology ; DNA, Mitochondrial/genetics ; Phylogeny ; DNA, Ribosomal ; },
abstract = {Females of species of Lamproglena von Nordmann, 1832 are parasitic on the gills of teleost fishes and the 38 nominal species are based on mainly morphological data. Only four of these species have been genetically characterised and no mitochondrial data are available for the genus. The present study aimed to provide representative ribosomal DNA (rDNA) data for two additional species of Lamproglena from Africa: Lamproglena clariae Fryer, 1956 and Lamproglena hoi Dippenaar, Luus-Powell et Roux, 2001, alongside mitochondrial DNA (mtDNA) for these and two other African species, Lamproglena hemprichii von Nordmann, 1832 and Lamproglena monodi Capart, 1944. The four species were collected from Clariidae, Cyprinidae, Alestidae and Cichlidae, respectively. Representative 18S rDNA and 28S rDNA data were obtained for L. clariae and L. hoi, while cox1 mtDNA was obtained for all four species. The respective haplotypes supported the distinctness of all species using all three gene regions investigated. Interestingly, species appeared to be grouped more by geographical origin than host family, with L. hoi more closely related to other African species than to Asian species also collected from cyprinid hosts. Even though the results presented here greatly add to the molecular data available for Lamproglena, there are still 32 (>80%) species for which no genetic data are available. The interpretation of the results presented here is thus preliminary and much more data are required before the phylogeny of this genus, and other members of the family, such as Lernaea Linnaeus, 1758, can be studied appropriately.},
}
@article {pmid37518801,
year = {2023},
author = {Molinari, J and Gutiérrez, EE and Lim, BK},
title = {Systematics and biogeography of Anoura cultrata (Mammalia, Chiroptera, Phyllostomidae): a morphometric, niche modeling, and genetic perspective, with a taxonomic reappraisal of the genus.},
journal = {Zootaxa},
volume = {5297},
number = {2},
pages = {151-188},
doi = {10.11646/zootaxa.5297.2.1},
pmid = {37518801},
issn = {1175-5334},
mesh = {Animals ; *Chiroptera/genetics ; Phylogeny ; Ecosystem ; DNA ; },
abstract = {The nectar-feeding bats of the genus Anoura are widely distributed in the Neotropics, but are most speciose in the Andes. Anoura cultrata is a rare mid-elevation bat occurring in South and Central America. It is thought to be one of the few bat species exemplifying a latitudinal cline in body size. We address three systematic and biogeographic questions: 1) is the geographic variation in A. cultrata continuous, as argued to justify its current monotypic status? 2) do ecogeographic barriers to dispersal affect such variation? and 3) how do the genetic divergence and biogeography of the species compare to those of other members of the genus? To answer these questions, we used morphometric analyses, ecological niche modeling, and DNA barcoding. We divided the samples of A. cultrata into six geographic groups, delimited by topographic depressions separating mountain systems. We did not find significant correlations between body size and the geographic coordinates within five groups. Therefore, we conclude that ecogeographic barriers to dispersal between the regions occupied by such groups influenced morphometric variation in A. cultrata, and that despite its general north to south reduction in body size, the species does not show continuous clinal variation. A recent phylogenetic study of the genus Anoura concluded that it contains seven valid species. Our DNA barcoding analysis and morphological examination indicated that at least 10 species should be recognized, including A. peruana distinct from A. geoffroyi, and A. aequatoris and A. luismanueli distinct from A. caudifer. Moreover, we show that Central and South American populations of A. cultrata differ from each other at least at the subspecific level, thus we respectively refer to them as A. cultrata cultrata and as A. c. brevirostrum. Similarly, we refer to Central American and Mexican populations of 'A. geoffroyi' as A. peruana lasiopyga, and to their South American counterparts as A. p. peruana. The range of the latter subspecies reaches northeastern Venezuela. The Andes from southern Colombia to northern Peru appear to be the ancestral range of the genus.},
}
@article {pmid37518782,
year = {2023},
author = {Marin, I and Palatov, D and Copilaș-Ciocianu, D},
title = {The remarkable Ponto-Caspian amphipod diversity of the lower Durso River (SW Caucasus) with the description of Litorogammarus dursi gen. et sp. nov.},
journal = {Zootaxa},
volume = {5297},
number = {4},
pages = {483-517},
doi = {10.11646/zootaxa.5297.4.2},
pmid = {37518782},
issn = {1175-5334},
mesh = {Animals ; *Amphipoda/genetics ; Phylogeny ; Rivers ; *Coleoptera ; DNA, Mitochondrial/genetics ; },
abstract = {The first insight into the unexpectedly diverse amphipod assemblage of the Durso River (Novorossiysk area) in the SW mountainous pre-Caucasian area is presented. The presence of six species is revealed, including three new records for the area and one species new to science. The phylogenetic relationships of all studied species and their relatives were examined based on the divergence of the COI mtDNA gene marker (barcoding). The conducted research clearly showed that the coastal part of the Black Sea and the adjacent pre-Caucasian river/land areas harbors a significant undescribed diversity, and that the transitional sea/river brackish biotopes are important reservoirs of the endemicity. A new genus, Litorogammarus gen. nov. is proposed for native pebble-dwelling species, namely Echinogammarus karadagiensis Grintsov, 2009, Echinogammarus mazestiensis Marin &amp; Palatov, 2021 and the newly discovered Litorogammarus dursi sp. nov., from the lower (estuarine) part of the Durso River and adjacent coastal areas. These three species form a strongly supported molecular clade and share a number of characters such as smooth body without carinae and setae, antenna II armed with dense curled setae, lacking calceoli, pereopods III-VII with sparse, short setation, epimeral plates armed with spines only, telson lobes longer than broad, gradually tapering, bearing only spines. Pectenogammarus oliviiformis (Greze, 1985) comb. nov. is also discovered in the area and is re-described herein. Although this is probably one of the most abundant and common coastal pebble-dwelling species along the northeastern coasts of the Black Sea, it was previously poorly described and thus overlooked by researchers.},
}
@article {pmid37518757,
year = {2023},
author = {Awad, J and Krogmann, L and Talamas, E},
title = {Illuminating a Dark Taxon: Revision of European Trichacis Förster (Hymenoptera: Platygastridae) reveals a glut of synonyms.},
journal = {Zootaxa},
volume = {5278},
number = {3},
pages = {563-577},
doi = {10.11646/zootaxa.5278.3.8},
pmid = {37518757},
issn = {1175-5334},
mesh = {Animals ; *Hymenoptera ; *Wasps/genetics ; },
abstract = {The parasitoid wasp genus Trichacis Förster is revised for Europe. Examination of historical and modern collections combined with DNA barcoding revealed the presence of only a single species in Europe, Trichacis tristis (Nees, 1834), redescribed here. Fourteen new synonymies are proposed for T. tristis: T. abdominalis Thomson, 1859 syn.nov.; T. bidentiscutum Szabó, 1981 syn.nov.; T. didas (Walker, 1835) syn.nov.; T. fusciala Szabó, 1981 syn.nov.; T. hajduica Szabó, 1981 syn.nov.; T. illusor Kieffer, 1916 syn.nov.; T. nosferatus Buhl, 1997 syn.nov.; T. pisis (Walker, 1835) syn.nov.; T. persicus Asadi &amp; Buhl, 2021 syn.nov.; T. pulchricornis Szelényi, 1953 syn.nov.; T. quadriclava Szabó, 1981 syn.nov.; T. remulus (Walker, 1835) syn.nov.; T. vitreus Buhl, 1997 syn.nov.; T. weiperti Buhl, 2019 syn.nov.. Four species are transferred to Amblyaspis Förster: A. afurcata (Szabó, 1977) comb. nov., A. hungarica (Szabó, 1977), comb. nov., A. pannonica (Szabó, 1977) comb. nov., and A. tatika (Szabó, 1977) comb. nov. Intraspecific variation, biological associations, and taxonomic history are discussed. DNA barcodes are provided and analyzed in the context of worldwide Trichacis and its sister genus Isocybus Förster.},
}
@article {pmid37518742,
year = {2023},
author = {Cao, Y and Yu, G and Petrov, AV and Li, Y and Li, T and Tarno, H and Cao, G and Xu, YE and Wang, J},
title = {A new species of Scolytus Geoffroy (Coleoptera, Curculionidae, Scolytinae) from Yunnan, China.},
journal = {Zootaxa},
volume = {5284},
number = {1},
pages = {185-191},
doi = {10.11646/zootaxa.5284.1.9},
pmid = {37518742},
issn = {1175-5334},
mesh = {Female ; Animals ; *Coleoptera ; *Weevils/genetics ; China ; },
abstract = {Scolytus unicornis, a new species of Scolytus Geoffroy from Yunnan, China, is described and illustrated. Three DNA barcoding sequences (COI, 28S, CAD) of this species are provided. The new species is distinguished from other Asian Scolytus species by the longitudinal wrinkles on the frons only in the area below the eyes, a large median spine situated in the middle of the ventrite 2 base, and female frons with a slightly raised blunt tubercle above the epistoma.},
}
@article {pmid37518733,
year = {2023},
author = {Grollmann, MM and Jørgensen, A and Møbjerg, N},
title = {Actinarctus doryphorus (Tanarctidae) DNA barcodes and phylogenetic reinvestigation of Arthrotardigrada with new A. doryphorus and Echiniscoididae sequences.},
journal = {Zootaxa},
volume = {5284},
number = {2},
pages = {351-363},
doi = {10.11646/zootaxa.5284.2.7},
pmid = {37518733},
issn = {1175-5334},
abstract = {Little is still known about the diversity and evolution of marine arthrotardigrades, as they are generally difficult to sample, resulting in a limited amount of molecular data for barcoding and phylogenetic studies. With the current study, we provide the first investigation into COI haplotype diversity in a marine tanarctid and at the same time readdress arthrotardigrade phylogeny. Specifically, we provide COI mtDNA, 18S and 28S rDNA sequences from a population of Actinarctus doryphorus (Tanarctidae) sampled off the coast of Roscoff, France and further provide new 18S sequences from two marine echiniscoidids. A. doryphorus COI sequences confirmed the presence of a single species and further revealed five haplotypes shared among nine sequenced individuals. Our 18S and 28S rDNA datasets were individually and combined analysed with Bayesian inference and Maximum Likelihood. Actinarctus doryphorus was placed together with Tanarctus sequences within a maximally supported Tanarctidae, confirming previous interpretations that the clade is distinct from Halechiniscidae. Although several studies in recent decades have concluded that the marine arthrotardigrades are paraphyletic, recent studies have argued that the clade may not be paraphyletic. Our phylogenetic analyses consistently inferred Arthrotardigrada as paraphyletic, as the clade includes the monophyletic Echiniscoidea. Accordingly, we propose that it is time to suppress the order Arthrotardigrada as it clearly does not reflect tardigrade phylogeny.},
}
@article {pmid37518710,
year = {2023},
author = {Russell, PJC and Pateman, JE and Gagarina, AV and Lukhtanov, VA},
title = {Investigations into the Melitaea ornata species complex in the Levant: M. telona and the newly erected species Melitaea klili Benyamini, 2021 (Lepidoptera: Nymphalidae).},
journal = {Zootaxa},
volume = {5285},
number = {1},
pages = {187-195},
doi = {10.11646/zootaxa.5285.1.9},
pmid = {37518710},
issn = {1175-5334},
mesh = {Male ; Animals ; *Butterflies/genetics ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Genes, Mitochondrial ; DNA Barcoding, Taxonomic ; },
abstract = {Melitaea klili Benyamini, 2021 was recently described from Israel as a species closely related to M. telona Fruhstorfer, 1908, but different in phenology, ecological preferences and with an allopatric distribution. Here, based on comparative examinations of mitochondrial DNA-barcodes, male genitalia and larval behaviour under laboratory conditions, we synonymize M. klili with M. telona. The COI barcodes of M. klili were found to be identical to those of M. telona. Analysis of 658 bp fragment of the mitochondrial gene COI demonstrated that the minimum uncorrected p-distance between M. ornata and M. telona was 1.98%. This value is remarkably less than the 3% threshold traditionally accepted as a species boundary in DNA barcoding studies. The morphological differences between these taxa are minimal. In fact, M. ornata and M. telona represent two phylogenetic lineages, the taxonomic status of which (separate species or subspecies of the same species) is intermediate and debatable.},
}
@article {pmid37518666,
year = {2023},
author = {Bahder, BW and Echavarria, MAZ and Barrantes, EAB and Helmick, EE and Bartlett, CR},
title = {A new species of planthopper in the genus Shellenius (Hemiptera: Fulgoroidea: Derbidae) from palms in Costa Rica.},
journal = {Zootaxa},
volume = {5306},
number = {5},
pages = {571-585},
doi = {10.11646/zootaxa.5306.5.5},
pmid = {37518666},
issn = {1175-5334},
mesh = {Animals ; Costa Rica ; *Hemiptera/genetics ; Phylogeny ; *Arecaceae ; },
abstract = {The genus Shellenius is a small taxon of planthoppers in the family Derbidae (Otiocerinae: Otiocerini) found in the eastern United States and Mesoamerica. A new species of Shellenius associated with palms is herein described from Costa Rica. Molecular data for the barcoding region cytochrome c oxidase subunit I (COI) and 18S rRNA gene is provided to produce a preliminary phylogenetic tree for related taxa and support placement of the novel taxon in Shellenius. A review of Fowler type material suggests that Otiocerus interruptus Fowler is a Shellenius species and is here transferred to that genus as Shellenius interruptus new combination.},
}
@article {pmid37518660,
year = {2023},
author = {László, GM and Hausmann, A and Karisch, T},
title = {Integrative taxonomic revision of the African taxa of the Racotis Moore, 1887 generic complex (Lepidoptera, Geometridae, Ennominae, Boarmiini).},
journal = {Zootaxa},
volume = {5308},
number = {1},
pages = {1-109},
doi = {10.11646/zootaxa.5308.1.1},
pmid = {37518660},
issn = {1175-5334},
mesh = {Animals ; *Moths/anatomy &amp; histology/classification/genetics ; Africa ; Genitalia/anatomy &amp; histology ; *Phylogeny ; Species Specificity ; Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; },
abstract = {The Afrotropical taxa of the Racotis s.l. generic complex are revised utilising integrative taxonomical methods. Based on the evaluation of genital morphology and analyses of DNA barcodes, a new genus, Afroracotis gen. n. is established to include the Afrotropical "Racotis" species. The new genus is subdivided into 5 subgenera: Afroracotis subgen. n., Herbuloracotis subgen. n., Rwandaracotis subgen. n., Zebracotis subgen. n. and Sokokeracotis subgen. n.. A new monotypic genus is described to include Boarmia ugandaria Swinhoe, 1904 which was combined earlier with the genus Chorodna and recently with Racotis: Chorocotis gen. n.. Two species formerly assigned to Cleora are moved to Afroracotis: A. albitrigonis (Prout, 1927) comb. n., A. atriclava (Prout, 1926) comb. n.. Two species are transferred from Racotis to Colocleora: C. breijeri (Prout, 1922) comb. n., C. incauta (Prout, 1916) comb. n.. Seventeen new Afroracotis species (A. aliena, A. stadiei, A. violetteae, A. fiebigi, A. turlini, A. dargei, A. longicornuta, A. aristophanousi, A. muscivirens, A. chaineyi, A. lydiae, A. smithi, A. ochsei, A. milesi, A. helicalis, A. takanoi and A. staudei spp. n.) and 5 new subspecies (A. squalida thomensis, A. argillacea morettoi, A. longicornuta congolana, A. longicornuta ugandana and A. lydiae orientalis sspp. n.) are described, totalling 27 species and 8 subspecies contained in the genus Afroracotis. Adults and genitalia of all taxa are illustrated in 210 colour and 129 black and white figures demonstrating the intraspecific variability. The distribution of all taxa is illustrated in 6 dot maps. The results of the genetic analyses are figured in four phylograms.},
}
@article {pmid37518654,
year = {2023},
author = {Yoğurtçuoğlu, B and Kaya, C and Atalay, MA and Ekmekçi, FG and Freyhof, J},
title = {Two new freshwater blennies from the Eastern Mediterranean basin (Teleostei: Blenniidae).},
journal = {Zootaxa},
volume = {5311},
number = {1},
pages = {85-104},
doi = {10.11646/zootaxa.5311.1.4},
pmid = {37518654},
issn = {1175-5334},
mesh = {Animals ; *Perciformes ; Rivers ; },
abstract = {Two new species of Salariopsis are described from the Eastern Mediterranean basin. Salariopsis burcuae, new species, from the Bay of Antalya east to the Jordan, is characterised by having a short cirrus, usually not overlapping the 9th circum-orbital sensory pore, and many tiny black dots on the cheek not organised in rows or bands. The new species shows a 4.1% K2P sequence divergence on the cytochrome-c-oxidase subunit 1 (COI) barcoding region from its closest relative, S. fluviatilis. Salariopsis renatorum, new species, from the upper Ceyhan drainage and a coastal stream in Arsuz, is distinguished by having an unbranched supraocular tentacle, black lateral line pores, a short snout, and no black dots on the upper part of the flank and on the cheek. It is also distinguished from its geographically closest congener, S. burcuae, by a molecular distance of 8.8% K2P in its COI barcode region.},
}
@article {pmid37518635,
year = {2023},
author = {Prozorov, AM and Prozorova, TA and Spitsyn, VM and Spitsyna, EA and Kondakov, AV and Soboleva, AA and Volkova, JS and Yakovlev, RV and Saldaitis, A and Sulak, HE and Revay, EE and Müller, GC},
title = {New records of Lasiocampidae (Lepidoptera) from Zanzibar Island with taxonomic notes and description of one new species of Odontopacha Aurivillius, 1909.},
journal = {Zootaxa},
volume = {5311},
number = {3},
pages = {417-445},
doi = {10.11646/zootaxa.5311.3.6},
pmid = {37518635},
issn = {1175-5334},
mesh = {Female ; Animals ; *Lepidoptera ; Tanzania ; },
abstract = {Seven genera and seven species of Lasiocampidae are newly recorded from the Zanzibar Island (Unguja): Bombycopsis C. &amp; R. Felder, 1874 with Bombycopsis nigrovittata Aurivillius, 1927; Pallastica Zolotuhin &amp; Gurkovich, 2009 with an unidentified species; Dollmania Tams, 1930 with an unidentified species; Mallocampa Aurivillius, 1902 with Mallocampa leighi Aurivillius, 1922; Eucraera Tams, 1930 with Eucraera witti Prozorov, 2016; Philotherma Möschler, 1887 with Philotherma montibia Strand, 1912; and Odontopacha Aurivillius, 1909 with Odontopacha fenestrata Aurivillius, 1909. The species are followed with taxonomic notes updating the status and distribution of the taxa. Bombycopsis nigrovittata is shown to have the maximum p-distance of 0.3% in cytochrome c oxidase I from Bombycopsis pallida Joannou &amp; Krüger, 2009. Two specimens of Pallastica sp. from Zanzibar are different in wing coloration but identical genetically, both are 0.8-1.2% far from sequenced specimens collected in southern Malawi and eastern Zimbabwe and altogether 3.0-3.8% far from the Zambian and Malawian populations considered to be Pallastica pallens (Bethune-Baker, 1908). The barcoding revealed two distinct lineages of Dollmania in Tanzania with a p-distance of 3.5-3.7% between them, neither can be attributed to either Dollmania marwitzi (Strand, 1913) or Dollmania reussi (Strand, 1913) until the primary types or fresh topotypes are sequenced. The species Ph. montibia is taken out from the synonymy to Philotherma rosa (Druce, 1887) and is stated to be a bona species because of the difference in wing pattern and p-distance of 5.7-5.9%. A new species of the genus Odontopacha - Odontopacha dargei sp. n. - is described from southern Kenya and northern Tanzania where it occurs sympatrically with O. fenestrata. It differs from O. fenestrata by the paler coloration with the spotted external fascia on both wings and a p-distance of 3.04-3.65%. Lectotypes for D. marwitzi and Ph. montibia are established. Mallocampa leighi is recorded from Tanzania for the first time. Females of Chrysopsyche lutulenta Tams, 1923 earlier recorded from Zanzibar Island are figured and the species is recorded from DRC for the first time.},
}
@article {pmid37518631,
year = {2023},
author = {Stuke, JH and Levesque-Beaudin, V},
title = {Two new Nearctic carnid flies of the genus Meoneura Rondani (Diptera: Carnidae).},
journal = {Zootaxa},
volume = {5311},
number = {4},
pages = {557-567},
doi = {10.11646/zootaxa.5311.4.3},
pmid = {37518631},
issn = {1175-5334},
mesh = {Animals ; *Diptera ; *Orthoptera ; },
abstract = {Meoneura pacifica spec. nov. (USA: Montana) and Meoneura tyrionlannisteri spec. nov. (Canada: British Columbia, USA: Montana) are described, and their DNA barcode provided.},
}
@article {pmid37518614,
year = {2023},
author = {Gaboardi, LM and Reeves, LE and Morey, GAM and Stanton, DL and Carney, RM},
title = {A new species of the fish louse genus Dipteropeltis Calman, 1912 (Crustacea: Branchiura) from Peru.},
journal = {Zootaxa},
volume = {5315},
number = {2},
pages = {101-121},
doi = {10.11646/zootaxa.5315.2.1},
pmid = {37518614},
issn = {1175-5334},
abstract = {Dipteropeltis is a poorly described genus of fish louse endemic to South America. In a small blackwater region within Loreto, Peru, 13 adult and juvenile specimens of an unidentified species of Dipteropeltis Calman, 1912, as well as one adult specimen of D. hirundo Calman, 1912, were observed and collected. Scanning electron and light micrographs were acquired to examine and measure key features of these specimens. Morphological differences from the two known species of Dipteropeltis, D. hirundo and D. campanaformis Neethling et al., 2014, indicate that the collected specimens represent a new species. Dipteropeltis longicaudatus sp. nov. is diagnosed by elongate abdominal lobes, a chevron-shaped carapace, and uniquely shaped maxillae. One specimen represents the longest branchiuran documented to date at 31.5 mm. Additionally, we provide the first sequence data for this genus using DNA barcoding, which corroborates our designation of a new species. Videos were also captured that document behaviors including host attachment, pulsating abdominal lobes, suction disc "walking", and swimming. Findings have implications for its teleost hosts, Triportheus albus Cope, 1872 and Brycon amazonicus Spix &amp; Agassiz, 1829, the latter being a critical species for aquaculture and commercial fisheries in Amazonia.},
}
@article {pmid37518601,
year = {2023},
author = {Lee, GE and Lee, YD and Liu, T},
title = {A new species and two new records of Argyresthia Hübner, [1825] (Lepidoptera: Argyresthiidae) from Hallasan National Park of Korea.},
journal = {Zootaxa},
volume = {5315},
number = {3},
pages = {282-290},
doi = {10.11646/zootaxa.5315.3.6},
pmid = {37518601},
issn = {1175-5334},
mesh = {Male ; Animals ; *Lepidoptera ; Parks, Recreational ; Animal Distribution ; *Moths ; Genitalia ; },
abstract = {Argyresthia Hübner, [1825] is a genus of small to medium sized glossy moths which comprises more than 200 species worldwide, but the Korean fauna includes only eight previously known species. In this study, we describe one new species, A. (Argyresthia) brevalbella sp. nov., and report A. (A.) angusta Moriuti, 1969 and A. (Blastotere) densa Liu, Wang et Li, 2017 for the first time from the country. The three species were found in Hallasan National Park located in the southernmost province Jeju-do at altitudes between 900-1,300 m. The new species is externally very similar to A. (A.) longalbella Liu, Wang et Li, 2017 in having a fuscous forewing with a white dorsal band, but can be distinguished by the shape of the valva, saccus and phallus of the male genitalia. We provide photographs of adults and genitalia, differential diagnoses and DNA barcodes for the three species.},
}
@article {pmid37518573,
year = {2023},
author = {Semeraro, L and Blacket, MJ and Rako, L and Cunningham, JP},
title = {The pest sap beetle Carpophilus (Myothorax) truncatus Murray, 1864 (Coleoptera: Nitidulidae)-a new synonymy and a related new species of Carpophilus.},
journal = {Zootaxa},
volume = {5301},
number = {1},
pages = {51-74},
doi = {10.11646/zootaxa.5301.1.2},
pmid = {37518573},
issn = {1175-5334},
mesh = {Animals ; *Coleoptera/genetics ; Larva/genetics ; },
abstract = {Carpophilus truncatus Murray 1864, is a species of sap beetle which has been recorded from many countries worldwide, and has become recognised as an important pest of nuts. In this study, we present a re-description of C. truncatus including diagnostic photographic images of the adults and larvae, and demonstrate that Carpophilus jarijari Powell &amp; Hamilton, 2019 is a junior subjective synonym of C. truncatus. Information about the species' distribution in Australia is updated. DNA barcode sequence data for C. truncatus is reviewed and augmented to enable differentiation from other morphologically similar Carpophilus species that are associated with nuts as hosts, including the cosmopolitan Carpophilus dimidiatus (Fabricius, 1792), for which C. truncatus has sometimes been misidentified. This analysis revealed that existing reference DNA sequences of "C. dimidiatus" consist of three highly genetically divergent lineages, representing three species: the cosmopolitan C. dimidiatus, the widespread C. truncatus, and a newly described species, Carpophilus imitatus sp. nov., known from south-eastern Asia and Australia.},
}
@article {pmid37518572,
year = {2023},
author = {Zhang, R and Zhang, F},
title = {Diversity of the genus Tmarus Simon, 1875 from Xiaolong Mountains in western China (Araneae: Thomisidae).},
journal = {Zootaxa},
volume = {5301},
number = {1},
pages = {75-93},
doi = {10.11646/zootaxa.5301.1.3},
pmid = {37518572},
issn = {1175-5334},
abstract = {Spiders of the genus Tmarus Simon, 1875 from the Xiaolong Mountains in Gansu Province, China, were studied. A total of seven species are reported and illustrated, including one new species, T. subqinlingensis sp. nov., and six known species, T. orientalis Schenkel, 1963, T. piger Walckenaer, 1802, T. qinlingensis Song &amp; Wang, 1994, T. rimosus Paik, 1973, T. taibaiensis Song &amp; Wang, 1994 and T. zhui Sherwood &amp; Li, 2021. The female of T. taibaiensis is described for the first time. Detailed morphological characters, photos and illustrations of the habitus and genital organs are given. DNA barcodes (a partial fragment of the mitochondrial cytochrome oxidase subunit I gene, COI) of T. taibaiensis Song &amp; Wang, 1994 were obtained to confirm matching of the sexes and for future use in molecular studies.},
}
@article {pmid37518563,
year = {2023},
author = {Liang, J and Solovyev, AV and Wang, H},
title = {Pluma, a new genus of slug moths (Lepidoptera: Limacodidae) from South China, with descriptions of two new species.},
journal = {Zootaxa},
volume = {5301},
number = {2},
pages = {246-256},
doi = {10.11646/zootaxa.5301.2.5},
pmid = {37518563},
issn = {1175-5334},
mesh = {Animals ; *Moths/genetics ; *Lepidoptera ; Genitalia ; China ; Trees ; Animal Distribution ; },
abstract = {The genus Pluma, gen. nov. is established to accommodate two new species of limacodid moths, P. shuni sp. nov. and P. yuensis sp. nov., from South China. Based on morphological and molecular characters, the species cannot be placed in any existing genus and therefore they placed in the newly erected one. The new taxa are supported by morphological characters and DNA barcode data. Male adults, including wing venation and genitalia, are illustrated, along with a barcode-based tree.},
}
@article {pmid37518562,
year = {2023},
author = {Fazan, L and Dorchin, N and Giriens, S and Pasta, S and Garfì, G and Remoundou, I and Petrakis, PV and Kozlowski, G},
title = {A new species of Contarinia (Diptera: Cecidomyiidae) from flower galls on the relict tree Zelkova abelicea (Ulmaceae) endemic to Crete (Greece).},
journal = {Zootaxa},
volume = {5301},
number = {2},
pages = {257-268},
doi = {10.11646/zootaxa.5301.2.6},
pmid = {37518562},
issn = {1175-5334},
mesh = {Animals ; *Diptera ; Trees ; Greece ; Ulmaceae ; Nematocera ; Flowers ; },
abstract = {Contarinia ampelitsiae n. sp. Dorchin &amp; Fazan is described as a newly discovered gall-midge species (Diptera: Cecidoymiidae) forming galls in flowers of Zelkova abelicea (Ulmaceae), a tree species endemic to the Mediterranean island of Crete (Greece). Larvae develop within modified filaments of male flowers, contrary to many Contarinia species that develop freely in flowers or in simple flower galls. The species has one generation per year, and its galls are sometimes found in great numbers on individual trees, thus affecting both fruit quantity and weight. This is the first report of a gall midge from Zelkova and the first record of Contarinia from Ulmaceae. Based on its host-plant association and on the barcoding section of the mtCOI gene, this species has no obvious relatives within Contarinia.},
}
@article {pmid37518557,
year = {2023},
author = {Sinclair, BJ},
title = {Revision of New World species of Roederiodes Coquillett (Diptera: Empididae: Clinocerinae).},
journal = {Zootaxa},
volume = {5301},
number = {3},
pages = {336-364},
doi = {10.11646/zootaxa.5301.3.2},
pmid = {37518557},
issn = {1175-5334},
mesh = {Animals ; *Diptera/genetics ; Animal Distribution ; Animal Structures ; DNA, Mitochondrial ; },
abstract = {The New World species of Roederiodes Coquillett, 1901 are revised and includes the following 13 species, of which eight are new to science: R. browni sp. nov., R. chillcotti sp. nov., R. costaricensis sp. nov., R. dedota sp. nov., R. distinctus Chillcott, 1961, R. junctus Coquillett, 1901, R. lawrencei sp. nov., R. moultoni sp. nov., R. notialis sp. nov., R. recurvatus Chillcott, 1961, R. wigginsi Wilder, 1981, R. wirthi Chillcott, 1961 and R. woodi sp. nov. The following new synonyms are proposed: Roederiodes petersoni Chillcott, 1966 and R. vockerothi Chillcott, 1961 = R. junctus Coquillett, 1901. A key to all New World species is provided and their distributions mapped. COI mitochondrial DNA barcode sequences were obtained for seven Nearctic species of Roederiodes.},
}
@article {pmid37518531,
year = {2023},
author = {Ponomarenko, MG and Beljaev, EA},
title = {Description of a new species of the genus Xyrosaris Meyrick (Lepidoptera: Yponomeutidae) from the Far East of Russia with notes on congeneric species.},
journal = {Zootaxa},
volume = {5306},
number = {1},
pages = {135-143},
doi = {10.11646/zootaxa.5306.1.7},
pmid = {37518531},
issn = {1175-5334},
abstract = {A new species, Xyrosaris insularis sp. n., was found in the Far East of Russia. Most of the specimens were obtained through the rearing of larvae that fed on Celastrus orbiculatus Thunb. (Celastraceae). The genetic distances between the mtCOI sequences in X. insularis and congeneric species are in the range 1.2-13.9%. Minimal genetic distance (1.2%) was discovered between new species and X. lichneuta Meyrick from Shaanxi (China), which is lower than the standard mtCOI barcoding threshold of 2% for species delineation, but both taxa differ well in the genital morphology. The description of a new species is accompanied by illustrations of variations in the pattern, by the genitalia of both sexes, and by larva on its host plant.},
}
@article {pmid37518527,
year = {2023},
author = {Kuhara, N and Nozaki, T and Zhang, AO and Zhou, X},
title = {DNA barcoding facilitates discovery and description of two new species of the Mystacides azureus Species Group (Trichoptera: Leptoceridae) in Japan.},
journal = {Zootaxa},
volume = {5306},
number = {2},
pages = {215-231},
doi = {10.11646/zootaxa.5306.2.3},
pmid = {37518527},
issn = {1175-5334},
mesh = {Female ; Animals ; Male ; Japan ; *DNA Barcoding, Taxonomic ; Phylogeny ; *Holometabola ; Mitochondria ; },
abstract = {We examined adult specimens of the Mystacides azureus Species Group (Trichoptera: Leptoceridae) collected in Japan and confirm three species including M. azureus Linnaeus 1761 and two new species, M. rivularis and M. moritai. Males and females of the new species are described. Mystacides azureus in Japan is shown to have a considerable variation in morphology of the male tergum X. We analyzed mitochondrial COI barcodes of the genus Mystacides including these three species to confirm their species status. A maximum likelihood phylogeny based on COI barcodes shows monophyly of the new species. It also supports the hypothesis that morphological variation of the male tergum X in Japanese populations is intraspecific in only M. azureus.},
}
@article {pmid37518510,
year = {2023},
author = {Freyhof, J and Yoğurtçuoğlu, B},
title = {Mystus misrai Anuradha, 1986, a valid species from the Orontes drainage (Teleostei: Bagridae).},
journal = {Zootaxa},
volume = {5306},
number = {4},
pages = {445-462},
doi = {10.11646/zootaxa.5306.4.3},
pmid = {37518510},
issn = {1175-5334},
abstract = {Mystus misrai from the northern Orontes drainage (Mediterranean Sea basin) is re-examined and recognised as a valid species. It is distinguished from M. pelusius from the Gulf basin by the lack of stripes on the flank, shorter fins, the eye situated below the dorsal head profile, and a K2P distance of 7.3% in its COI barcoding gene. Mystus misrai is likely Critically Endangered: only a single, spring-fed lake in Türkiye is known as its habitat. The biogeographic connection between the Orontes and the Gulf is discussed based on molecular data of 27 species native to the region.},
}
@article {pmid37518463,
year = {2023},
author = {Makhov, I},
title = {Geometridae (Lepidoptera) of the Baikal region: identification keys and annotated catalogue with notes to DNA barcoding. Part 2. Archiearinae, Geometrinae, Sterrhinae.},
journal = {Zootaxa},
volume = {5294},
number = {1},
pages = {1-120},
doi = {10.11646/zootaxa.5294.1.1},
pmid = {37518463},
issn = {1175-5334},
mesh = {Animals ; *Lepidoptera/genetics ; DNA Barcoding, Taxonomic ; *Moths/genetics ; DNA ; },
abstract = {Dichotomous keys to 19 genera and 67 species of Archiearinae (2 genera, 3 species), Geometrinae (9 genera, 14 species) and Sterrhinae (8 genera, 50 species) of the Baikal region (Irkutskaya Oblast and Buryatia, Siberia) are given. The annotated catalogue including synonyms, the details of examined specimens, data on distribution and foodplants with references is provided. Distribution of Comibaena amoenaria (Oberthür, 1883) and Idaea falckii (Hedemann, 1879) in China is established. Lectotypes are designated for Hemistola zimmermanni and Hemistola intermedia Djakonov, 1926. Hemistola intermedia is synonymized with H. zimmermanni (syn. n.). Some taxonomic aspects of Hemistola zimmermanni (Hedemann, 1879), Idaea dohlmanni (Hedemann, 1881), Rhodostrophia jacularia (Hübner, [1813]) and Timandra griseata W. Petersen, 1902 are discussed. Results of DNA barcoding of ten species (Comibaena amoenaria (Oberthür, 1880), Hemistola zimmermanni, Thalera chlorosaria (Graeser, 1890), Chlorissa obliterata (Walker, 1863), Cleta jacutica Viidalepp, 1976, Idaea dohlmanni (Hedemann, 1881), Scopula agutsaensis Vasilenko, 1997, S. impersonata Walker, 1861, S. immutata (Linnaeus, 1758) and Scopula ornata (Scopoli, 1763)) are considered. Three cases of misidentifications and an erroneous association of species and its genitalia illustration in the public sources are recognized and corrected.},
}
@article {pmid37518455,
year = {2023},
author = {Huemer, P and Mayr, T},
title = {A surprising new species of Exapate Hübner, 1825 (Lepidoptera, Tortricidae) from Armenia.},
journal = {Zootaxa},
volume = {5296},
number = {1},
pages = {75-82},
doi = {10.11646/zootaxa.5296.1.7},
pmid = {37518455},
issn = {1175-5334},
abstract = {A new species of cold-season moths, Exapate aidasi sp. nov., is described from male specimens collected in Armenia. This is also the first record of the genus Exapate in Armenia and south of the Caucasus. The new species differs from the two previously known congeneric taxa both in phenotypic characteristics and in the structure of the male genitalia. In addition, DNA barcodes (cytochrome c-oxidase subunit 1) are clearly divergent from those of other species. Adult and male genitalia of all three species of Exapate are shown for comparison.},
}
@article {pmid37518454,
year = {2023},
author = {Laššová, K and Čiamporová-Zaťovičová, Z and Jr, F&#x10c;},
title = {Description of the larva of Hypsilara (Coleoptera: Elmidae).},
journal = {Zootaxa},
volume = {5296},
number = {1},
pages = {83-88},
doi = {10.11646/zootaxa.5296.1.8},
pmid = {37518454},
issn = {1175-5334},
mesh = {Animals ; *Coleoptera ; Larva/anatomy &amp; histology ; },
abstract = {The mature larva of the Larainae riffle beetle genus Hypsilara Maier &amp; Spangler, 2011 is described here for the first time, based on larvae of Hypsilara autanai Laššová, Čiampor Jr, Čiamporová-Zaťovičová, 2014. The larvae were collected with adults in the stream near the tepui Cerro Autana and Cerro Cuao (southwestern Venezuela) and associated together using DNA barcoding. Larvae of Hypsilara strongly resemble those of Phanoceroides, here we present important morphological diagnostic characters. This description complements the descriptions of the Larainae larvae in the Neotropics, as the larva of Hypsilara was the last one of the group missing so far.},
}
@article {pmid37518451,
year = {2023},
author = {Theischinger, G and Mitchell, A and Richards, SJ and Polhemus, DA},
title = {Systematics of the Nososticta salomonis complex (Odonata: Zygoptera: Platycnemididae).},
journal = {Zootaxa},
volume = {5296},
number = {2},
pages = {101-146},
doi = {10.11646/zootaxa.5296.2.1},
pmid = {37518451},
issn = {1175-5334},
abstract = {We examined the morphology, colour patterns and genetic relationships of Nososticta populations allied to N. salomonis (Selys) from across Melanesia. Seven species-level taxa are recognised in the N. salomonis 'complex': N. africana (Schmidt), N. boonei sp. nov., N. chrismulleri Theischinger &amp; Richards, N. hedigeri sp. nov., N. salomonis (Selys), N. stueberi sp. nov., and N. tagula sp. nov. All of these species are black damselflies with blue markings, and they differ from all other Nososticta by having: 1) a prominent spike on the male superior appendage, 2) a prominent angular base of the male inferior appendage, and 3) a complex posterior lobe on the female pronotum bearing two pairs of processes in the rough shape of a chair when viewed laterally. A molecular phylogeny based on the DNA barcode fragment of the COI gene plus two nuclear genes indicates that these seven species are closely related, but more extensive sampling of Nososticta species is required to confirm that they form a monophyletic group.},
}
@article {pmid37518435,
year = {2023},
author = {Jiang, ZH and Xu, ZB and Cheng, WD and Li, YF and Hu, SJ},
title = {The life history of Hayesiana triopus (Westwood, 1847), with taxonomic notes on both present and former species of the genus Hayesiana Fletcher, 1982 (Lepidoptera: Sphingidae).},
journal = {Zootaxa},
volume = {5296},
number = {3},
pages = {446-456},
doi = {10.11646/zootaxa.5296.3.7},
pmid = {37518435},
issn = {1175-5334},
mesh = {Female ; Animals ; *Lepidoptera ; Animal Distribution ; *Moths/genetics ; Genitalia ; },
abstract = {The two species previously included in the genus Hayesiana Fletcher, 1982 were studied. The life history of the sole currently included species, Hayesiana triopus (Westwood, 1847) is illustrated in colour for the first time. Field records of Hayesiana triopus and Dahira farintaenia (Zhu &amp; Wang, 1997) (previously Hayesiana farintaenia) are given, with the first description of the female genitalia of the latter. The diagnostic features and DNA barcoding data of Hayesiana triopus and Dahira farintaenia are also discussed.},
}
@article {pmid37518374,
year = {2023},
author = {Huemer, P and Aarvik, L and Berggren, K},
title = {A new species of Neurothaumasia Le Marchand (Lepidoptera, Tineidae) from Crete, Greece.},
journal = {Zootaxa},
volume = {5318},
number = {3},
pages = {401-410},
doi = {10.11646/zootaxa.5318.3.5},
pmid = {37518374},
issn = {1175-5334},
mesh = {Male ; Female ; Animals ; *Lepidoptera ; Greece ; Genitalia ; *Moths/genetics ; Animal Distribution ; },
abstract = {A new species of fungus moths (Tineidae), Neurothaumasia cretica sp. nov., is described from specimens collected on Crete isl. (Greece). It differs from congeneric taxa by the characteristic black and white forewing pattern which is only shared with N. fasciata Petersen, 1959 from the Middle East, and the widespread western Palaearctic N. ankerella (Mann, 1867). However, the new species differs strongly from the former by several characters of male and female genitalia, and from the latter species particularly from external appearance and by the highly divergent DNA barcode (cytochrome c-oxidase subunit 1) (unknown for N. fasciata). Adult and genitalia of N. cretica sp. nov. and the only similar European species N. ankerella are shown for comparison. Finally, a complete checklist of the genus is added.},
}
@article {pmid37518286,
year = {2023},
author = {Zhang, G and Gao, JJ and Takano, KT and Yafuso, M and Suwito, A and Meleng, PA and Toda, MJ},
title = {Phylogenetic classification and palm-inflorescence anthophily of the Colocasiomyia zeylanica species group (Diptera: Drosophilidae), with descriptions of five new species.},
journal = {Zootaxa},
volume = {5278},
number = {2},
pages = {201-238},
doi = {10.11646/zootaxa.5278.2.1},
pmid = {37518286},
issn = {1175-5334},
mesh = {Animals ; *Diptera ; *Drosophilidae/genetics ; Phylogeny ; Inflorescence ; Mitochondria ; },
abstract = {The zeylanica group is one of the six species groups of the anthophilic genus Colocasiomyia de Meijere in the family Drosophilidae. In addition to two known species, five morphospecies have been recognized as members of this species group but left undescribed formally. In this study, species delimitation of these putatively new species was determined by barcoding of the mitochondrial COI (cytochrome c oxydase subunit I) gene and morphological comparison. Phylogenetic relationships within the genus Colocasiomyia were inferred by a cladistic analysis of 89 morphological characters. Based on the results of these analyses, we redefined the zeylanica species group and established two subgroups within it: the zeylanica subgroup comprised of C. zeylanica, C. nepalensis, C. pinangae sp. nov., C. besaris sp. nov. and C. luciphila sp. nov., and the oligochaeta subgroup of C. oligochaeta sp. nov. and C. grimaldii sp. nov. In addition, we briefly address the anthophilic habits of drosophilid flies using palm (Arecaceae) inflorescences, especially of the zeylanica group, compiling scattered collection records from the Oriental and Papuan regions.},
}
@article {pmid37518285,
year = {2023},
author = {Mukherjee, B and Hazra, N},
title = {Taxonomic studies on Harnischia complex from India (Diptera: Chironomidae).},
journal = {Zootaxa},
volume = {5278},
number = {2},
pages = {239-263},
doi = {10.11646/zootaxa.5278.2.2},
pmid = {37518285},
issn = {1175-5334},
mesh = {Male ; Animals ; *Diptera ; *Chironomidae ; Fireflies ; India ; *Sasa ; },
abstract = {Beckidia Sæther, 1979, Kloosia Kruseman, 1933, Parachironomus Lenz, 1921 and Saetheria Jackson, 1977 of the Harnischia complex are four newly recorded genera in India. Beckidia inflata sp. n., Kloosia incurva sp.n., Parachironomus salsus sp.n., Saetheria circinata sp.n., and Harnischia bulbosa sp.n. are described and illustrated. Microchironomus ishii Sasa, 1987, as a new record, is re-described and illustrated based on males. Three species, Paracladopelma nigrotibia (Bhattacharya, Dutta &amp; Chaudhuri, 1985), Cryptotendipes acutus (Goetghebuer, 1936), and Saetheria sacculifera (Chaudhuri &amp; Chattopadhyay, 1990) are proposed here as new combinations. Other Indian species of little known genera within the Harnischia complex are also re-examined and synonymisation is made. Molecular barcodes of five new species Beckidia inflata sp.n., Kloosia incurva sp.n., Parachironomus salsus sp.n., Saetheria circinata sp.n., and Harnischia bulbosa sp.n. and three known species of the Harnischia complex are also provided. Separate world keys of adult males of five genera are also designed here.},
}
@article {pmid37518251,
year = {2023},
author = {Velásquez-Rodríguez, K and Lin, XL and Sánchez-Vendizú, P and Loayza-Muro, R and Huamantinco, A and Prat, N},
title = {DNA Barcode of symbiotic chironomids: Findings in the genus Symbiocladius (Diptera: Chironomidae).},
journal = {Zootaxa},
volume = {5319},
number = {1},
pages = {48-56},
doi = {10.11646/zootaxa.5319.1.3},
pmid = {37518251},
issn = {1175-5334},
mesh = {Animals ; *Chironomidae/genetics ; DNA Barcoding, Taxonomic ; Symbiosis ; *Ephemeroptera ; },
abstract = {Chironomidae of symbiotic habits have been recorded in different parts of the world, among commensals and parasites. There are different genera reported at the moment, however questions such as the origin of commensal or parasitic life, which occurred first or what are their benefits remain debatable. In order to contribute with information to elucidate the above mentioned issues, the present study reports the finding of immature stages of Symbiocladius (Acletus) wygodzinskyi Roback, 1965 in the Churup stream located in the Andes Cordillera (Peru), living on nymphs of Leptophlebiidae (Ephemeroptera). We present a morphological description of immature stages of this species and for the first time the sequence of COX1 gene S. (A.) wygodzinskyi. The genetic result also supports differences between the morphospecies of Symbiocladius (Symbiocladius) rhithrogenae Zavřel, 1924 and S. (A.) wygodzinskyi in 23%.},
}
@article {pmid37518203,
year = {2023},
author = {Makarchenko, EA and Semenchenko, AA},
title = {Review of subfamily Prodiamesinae (Diptera: Chironomidae) from the Russian Far East and bordering territory.},
journal = {Zootaxa},
volume = {5323},
number = {1},
pages = {1-26},
doi = {10.11646/zootaxa.5323.1.1},
pmid = {37518203},
issn = {1175-5334},
abstract = {Based on material from the Russian Far East and Eastern Siberia, a revision of the chironomids of the subfamily Prodiamesinae was carried out. A new species Monodiamesa fontinalis sp. nov., is here described, ten species from four genera-Monodiamesa bathyphila Kieffer, M. kamora Makarchenko et Yavorskaya, M. improvisa Makarchenko, M. nitida Kieffer, Odontomesa fulva Kieffer, Prodiamesa levanidovae Makarchenko, Propsilocerus amurensis Makarchenko, P. jacuticus (Zvereva), P. paradoxus Lundström and P. taimyrus Zelentzov are redescribed with varying degrees of completeness. Propsilocerus taimyrus Zelentzov, 2000 is proposed as senior synonym of P. saetheri Wang, Liu et Paasivirta, 2007. DNA barcoding of four species, M. fontinalis sp. nov., M. bathyphila, P. olivacea Meigen and P. akamusi (Tokunaga) was provided. Species delimitation and phylogenetic relationships using COI DNA barcodes confirms the species validity of M. fontinalis sp. nov.},
}
@article {pmid37518166,
year = {2023},
author = {Cock, MJW and Laguerre, M and Buddie, AG and Cafa, G and Alston-Smith, S and Morrall, J and Gosula, VS},
title = {Using DNA barcodes to test the association of sexes and morphs in Calodesma spp. (Lepidoptera, Erebidae, Arctiinae, Arctiini, Pericopina) of Trinidad, West Indies, with an overview of the genus, taxonomic changes and a new species.},
journal = {Zootaxa},
volume = {5270},
number = {2},
pages = {231-261},
doi = {10.11646/zootaxa.5270.2.4},
pmid = {37518166},
issn = {1175-5334},
mesh = {Female ; Male ; Animals ; Trinidad and Tobago ; DNA Barcoding, Taxonomic ; *Moths/genetics ; *Biological Mimicry ; },
abstract = {Phalaena militta Stoll, [1781], currently in the combination Thyrgis militta, is transferred to the new combination Calodesma militta. Phalaena militta is the type species of Thyrgis Walker, 1854, and so Thyrgis is a junior synonym of Calodesma Hübner, [1820]. The reinstated genus Seileria Dognin, 1923 is the next available name for the genus previously known as Thyrgis, and the remaining eight species and their subspecies currently in Thyrgis are transferred to new combinations as species of Seileria: S. angustifascia (Hering, 1925), S. basipunctata (Hering, 1926), S. constrictifascia (Dognin, 1919), S. flavonigra (Dognin, 1910), S. investigatorum (Toulgoët, 1988), S. marginata (Butler, 1875), S. meres (Druce, 1911), S. phlegon (Druce, 1885), S. phlegon ruscia (Druce, 1895), S. tenuifascia (Hering, 1930) and S. tenuifascia daguana (Hering, 1930). Eucyanoides Toulgoët, 1988, currently a synonym of Thyrgis, is made a new subjective synonym of Seileria. Based on DNA barcodes, we recognise three very similar, sexually dimorphic and in two cases polymorphic South American species of Calodesma with some phenotypes in common but very similar male genitalia: C. militta (BOLD:AAK1660), C. sp. cf. collaris (BOLD:ABZ2392) and C. pseudocollaris Cock new species (BOLD:AEI2170). Calodesma militta is widespread in South America, with two male morphs (collaris and dioptis) and two female morphs with variable markings (white and orange morphs). Centronia plorator Kaye, [1923] and Thyrgis lacryma Dognin, 1919 are variants of the white female morph and are new synonyms of Calodesma militta. A third female morph with red markings was not sequenced and could not be allocated to a species. Calodesma sp. cf. collaris (BOLD:ABZ2392) occurs in southern South America with both male morphs but only a white female morph. Calodesma pseudocollaris new species (BOLD:AEI2170) is only known from Trinidad, with one male morph (collaris) and the white female morph. Although more than ten morphs relating to this complex have been described as species, they cannot be synonymised without more data on distribution of the different species or DNA barcodes from the type specimens. Collated life history information indicates species of this group are split between Malpighiaceae feeders and Bromeliaceae feeders, but more work is needed to define these differences. The morphism patterns observed are discussed in terms of Müllerian mimicry and mimicry rings, and we suggest that in Trinidad (and elsewhere) there is a loose mimicry ring of diurnal black species with white spots or transparent patches on the wings which are most conspicuous and frequently observed when feeding on white Asteraceae flowers.},
}
@article {pmid37518155,
year = {2023},
author = {Verdone, CJ and Beaty, SR and Holland, VB and Williams, BW},
title = {Isoperla riverae, a new stonefly species from the southeast Nearctic, with notes on sympatric species including the larval description of Isoperla lenati Szczytko &amp; Kondratieff, 2015 (Plecoptera: Perlodidae).},
journal = {Zootaxa},
volume = {5270},
number = {3},
pages = {437-470},
doi = {10.11646/zootaxa.5270.3.3},
pmid = {37518155},
issn = {1175-5334},
mesh = {Female ; Male ; Animals ; *Insecta ; Larva ; *Sympatry ; Neoptera ; Chorion ; },
abstract = {Isoperla riverae sp. n. is described from the southeastern USA. The new species is proposed based on details of the adult habitus, male aedeagus, vesicle, female subgenital plate, ovum chorion, and larval habitus. Supporting data includes color images, scanning electron micrographs, genetic analysis of DNA barcodes, and comparative morphology of cognate species. The larva of Isoperla lenati Szczytko &amp; Kondratieff, 2015 is also described supported by color images.},
}
@article {pmid37518148,
year = {2023},
author = {Zhang, YL and Wei, F and Fan, X and Wang, M},
title = {A new species of Hamodes Guenée, 1852 (Lepidoptera: Erebidae) from China.},
journal = {Zootaxa},
volume = {5270},
number = {3},
pages = {593-598},
doi = {10.11646/zootaxa.5270.3.10},
pmid = {37518148},
issn = {1175-5334},
mesh = {Male ; Animals ; *Lepidoptera/genetics ; *Moths/genetics ; China ; Universities ; Genitalia ; },
abstract = {A new species of the genus Hamodes Guenée, 1852, Hamodes zhipengi sp. nov. is described and illustrated from China. The species resembles H. pseudobutleri Wei &amp; Wang, 2019 but differs in wings ground colour; and male genitalia with differently shaped valvae, ampullae and armature of vesica. DNA barcode of the new species and relatives are deposited in GenBank. The holotype is deposited in the Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou.},
}
@article {pmid38321687,
year = {2023},
author = {Zhang, G and Kersten, M and Owen, A and Skidmore, A},
title = {Honey bee foraging and pesticide exposure in a desert urban agroecosystem.},
journal = {Ecotoxicology and environmental safety},
volume = {249},
number = {},
pages = {114472},
doi = {10.1016/j.ecoenv.2022.114472},
pmid = {38321687},
issn = {1090-2414},
mesh = {Bees ; Animals ; *Pesticides ; Agriculture/methods ; Beekeeping ; Farms ; *Urticaria ; },
abstract = {The negative impacts of industrial farming on honey bee health have been widely recognized regarding pesticide use and natural foraging habitat loss. An assessment of suitability of urban farms regarding honey bee health is necessary for sustainable development of agriculture and apiculture in urban settings. Urban farms that adopt organic farming practices with restrictions on synthetic pesticide use and conservation of natural habitat can potentially create an environment to mitigate these environmental stressors on honey bees. In this experiment, bee-collected pollen was taken from honey bee colonies that were located on five organically managed urban farms located in Albuquerque, New Mexico, to evaluate pesticide exposure and forage use. We also explored the influence of hive equipment on honey bee health in a high desert climate. We found that honey bees on organic urban farms were not stressed by pesticides with limited pesticide types detected (2 out of 187), low residue levels (< 20 µg/kg) and low toxicity (either no, or low toxicity with LD50 at 1,450,300 µg/kg). Honey bees had access to diverse forage resources based on pollen barcoding data. When comparing hive equipment between 10-frame, 8-frame Langstroth and top bar hives, it was determined that 8-frame hives could significantly enhance honey bee health including colony survival and weight growth, comb construction and brood production. Our results suggest that organic urban farms are appropriate locations for securing honey bee health and food safety in a desert climate; while, the selection of hive equipment should be considered when mitigating environmental stress to colonies.},
}
@article {pmid38455338,
year = {2022},
author = {Tsoungui Obama, HCJ and Schneider, KA},
title = {A maximum-likelihood method to estimate haplotype frequencies and prevalence alongside multiplicity of infection from SNP data.},
journal = {Frontiers in epidemiology},
volume = {2},
number = {},
pages = {943625},
pmid = {38455338},
issn = {2674-1199},
abstract = {The introduction of genomic methods facilitated standardized molecular disease surveillance. For instance, SNP barcodes in Plasmodium vivax and Plasmodium falciparum malaria allows the characterization of haplotypes, their frequencies and prevalence to reveal temporal and spatial transmission patterns. A confounding factor is the presence of multiple genetically distinct pathogen variants within the same infection, known as multiplicity of infection (MOI). Disregarding ambiguous information, as usually done in ad-hoc approaches, leads to less confident and biased estimates. We introduce a statistical framework to obtain maximum-likelihood estimates (MLE) of haplotype frequencies and prevalence alongside MOI from malaria SNP data, i.e., multiple biallelic marker loci. The number of model parameters increases geometrically with the number of genetic markers considered and no closed-form solution exists for the MLE. Therefore, the MLE needs to be derived numerically. We use the Expectation-Maximization (EM) algorithm to derive the maximum-likelihood estimates, an efficient and easy-to-implement algorithm that yields a numerically stable solution. We also derive expressions for haplotype prevalence based on either all or just the unambiguous genetic information and compare both approaches. The latter corresponds to a biased ad-hoc estimate of prevalence. We assess the performance of our estimator by systematic numerical simulations assuming realistic sample sizes and various scenarios of transmission intensity. For reasonable sample sizes, and number of loci, the method has little bias. As an example, we apply the method to a dataset from Cameroon on sulfadoxine-pyrimethamine resistance in P. falciparum malaria. The method is not confined to malaria and can be applied to any infectious disease with similar transmission behavior. An easy-to-use implementation of the method as an R-script is provided.},
}
@article {pmid38234686,
year = {2022},
author = {Crous, PW and Boers, J and Holdom, D and Osieck, ER and Steinrucken, TV and Tan, YP and Vitelli, JS and Shivas, RG and Barrett, M and Boxshall, AG and Broadbridge, J and Larsson, E and Lebel, T and Pinruan, U and Sommai, S and Alvarado, P and Bonito, G and Decock, CA and De la Peña-Lastra, S and Delgado, G and Houbraken, J and Maciá-Vicente, JG and Raja, HA and Rigueiro-Rodríguez, A and Rodríguez, A and Wingfield, MJ and Adams, SJ and Akulov, A and Al-Hidmi, T and Antonín, V and Arauzo, S and Arenas, F and Armada, F and Aylward, J and Bellanger, JM and Berraf-Tebbal, A and Bidaud, A and Boccardo, F and Cabero, J and Calledda, F and Corriol, G and Crane, JL and Dearnaley, JDW and Dima, B and Dovana, F and Eichmeier, A and Esteve-Raventós, F and Fine, M and Ganzert, L and García, D and Torres-Garcia, D and Gené, J and Gutiérrez, A and Iglesias, P and Istel, &#x141; and Jangsantear, P and Jansen, GM and Jeppson, M and Karun, NC and Karich, A and Khamsuntorn, P and Kokkonen, K and Kolařík, M and Kubátová, A and Labuda, R and Lagashetti, AC and Lifshitz, N and Linde, C and Loizides, M and Luangsa-Ard, JJ and Lueangjaroenkit, P and Mahadevakumar, S and Mahamedi, AE and Malloch, DW and Marincowitz, S and Mateos, A and Moreau, PA and Miller, AN and Molia, A and Morte, A and Navarro-Ródenas, A and Nebesářová, J and Nigrone, E and Nuthan, BR and Oberlies, NH and Pepori, AL and Rämä, T and Rapley, D and Reschke, K and Robicheau, BM and Roets, F and Roux, J and Saavedra, M and Sakolrak, B and Santini, A and Ševčíková, H and Singh, PN and Singh, SK and Somrithipol, S and Spetik, M and Sridhar, KR and Starink-Willemse, M and Taylor, VA and van Iperen, AL and Vauras, J and Walker, AK and Wingfield, BD and Yarden, O and Cooke, AW and Manners, AG and Pegg, KG and Groenewald, JZ},
title = {Fungal Planet description sheets: 1383-1435.},
journal = {Persoonia},
volume = {48},
number = {},
pages = {261-371},
pmid = {38234686},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Agaricus albofoetidus, Agaricus aureoelephanti and Agaricus parviumbrus on soil, Fusarium ramsdenii from stem cankers of Araucaria cunninghamii, Keissleriella sporoboli from stem of Sporobolus natalensis, Leptosphaerulina queenslandica and Pestalotiopsis chiaroscuro from leaves of Sporobolus natalensis, Serendipita petricolae as endophyte from roots of Eriochilus petricola, Stagonospora tauntonensis from stem of Sporobolus natalensis, Teratosphaeria carnegiei from leaves of Eucalyptus grandis × E. camaldulensis and Wongia ficherai from roots of Eragrostis curvula. Canada, Lulworthia fundyensis from intertidal wood and Newbrunswickomyces abietophilus (incl. Newbrunswickomyces gen. nov.) on buds of Abies balsamea. Czech Republic, Geosmithia funiculosa from a bark beetle gallery on Ulmus minor and Neoherpotrichiella juglandicola (incl. Neoherpotrichiella gen. nov.) from wood of Juglans regia. France, Aspergillus rouenensis and Neoacrodontium gallica (incl. Neoacrodontium gen. nov.) from bore dust of Xestobium rufovillosum feeding on Quercus wood, Endoradiciella communis (incl. Endoradiciella gen. nov.) endophytic in roots of Microthlaspi perfoliatum and Entoloma simulans on soil. India, Amanita konajensis on soil and Keithomyces indicus from soil. Israel, Microascus rothbergiorum from Stylophora pistillata. Italy, Calonarius ligusticus on soil. Netherlands, Appendopyricularia juncicola (incl. Appendopyricularia gen. nov.), Eriospora juncicola and Tetraploa juncicola on dead culms of Juncus effusus, Gonatophragmium physciae on Physcia caesia and Paracosmospora physciae (incl. Paracosmospora gen. nov.) on Physcia tenella, Myrmecridium phragmitigenum on dead culm of Phragmites australis, Neochalara lolae on stems of Pteridium aquilinum, Niesslia nieuwwulvenica on dead culm of undetermined Poaceae, Nothodevriesia narthecii (incl. Nothodevriesia gen. nov.) on dead leaves of Narthecium ossifragum and Parastenospora pini (incl. Parastenospora gen. nov.) on dead twigs of Pinus sylvestris. Norway, Verticillium bjoernoeyanum from sand grains attached to a piece of driftwood on a sandy beach. Portugal, Collybiopsis cimrmanii on the base of living Quercus ilex and amongst dead leaves of Laurus and herbs. South Africa, Paraproliferophorum hyphaenes (incl. Paraproliferophorum gen. nov.) on living leaves of Hyphaene sp. and Saccothecium widdringtoniae on twigs of Widdringtonia wallichii. Spain, Cortinarius dryosalor on soil, Cyphellophora endoradicis endophytic in roots of Microthlaspi perfoliatum, Geoglossum lauri-silvae on soil, Leptographium gemmatum from fluvial sediments, Physalacria auricularioides from a dead twig of Castanea sativa, Terfezia bertae and Tuber davidlopezii in soil. Sweden, Alpova larskersii, Inocybe alpestris and Inocybe boreogodeyi on soil. Thailand, Russula banwatchanensis, Russula purpureoviridis and Russula lilacina on soil. Ukraine, Nectriella adonidis on overwintered stems of Adonis vernalis. USA, Microcyclus jacquiniae from living leaves of Jacquinia keyensis and Penicillium neoherquei from a minute mushroom sporocarp. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Boers J, Holdom D, et al. 2022. Fungal Planet description sheets: 1383-1435. Persoonia 48: 261-371. https://doi.org/10.3767/persoonia.2022.48.08.},
}
@article {pmid38046362,
year = {2022},
author = {Nakajima, A and Yoshida, K and Gotoh, A and Katoh, T and Ojima, MN and Sakanaka, M and Xiao, JZ and Odamaki, T and Katayama, T},
title = {A simple method that enhances minority species detection in the microbiota: 16S metagenome-DRIP (Deeper Resolution using an Inhibitory Primer).},
journal = {Microbiome research reports},
volume = {1},
number = {3},
pages = {20},
pmid = {38046362},
issn = {2771-5965},
abstract = {Aim: 16S rRNA gene-based microbiota analyses (16S metagenomes) using next-generation sequencing (NGS) technologies are widely used to examine the microbial community composition in environmental samples. However, the sequencing capacity of NGS is sometimes insufficient to cover the whole microbial community, especially when analyzing soil and fecal microbiotas. This limitation may have hampered the detection of minority species that potentially affect microbiota formation and structure. Methods: We developed a simple method, termed 16S metagenome-DRIP (Deeper Resolution using an Inhibitory Primer), that not only enhances minority species detection but also increases the accuracy of their abundance estimation. The method relies on the inhibition of normal amplicon formation of the 16S rRNA gene of a target major (abundant) species during the first PCR step. The addition of a biotinylated primer that is complementary to the variable sequence of the V3-V4 region of the target species inhibits a normal amplification process to form an aberrant short amplicon. The fragment is then captured by streptavidin beads for removal from the reaction mixture, and the resulting mixture is utilized for the second PCR with barcode-tag primers. Thus, this method only requires two additional experimental procedures to the conventional 16S metagenome analysis. A proof-of-concept experiment was first conducted using a mock sample consisting of the genomes of 14 bacterial species. Then, the method was applied to infant fecal samples using a Bifidobacterium-specific inhibitory primer (n = 11). Results: As a result, the reads assigned to the family Bifidobacteriaceae decreased on average from 16,657 to 1718 per sample without affecting the total read counts (36,073 and 34,778 per sample for the conventional and DRIP methods, respectively). Furthermore, the minority species detection rate increased with neither affecting Bray-Curtis dissimilarity calculated by omitting the target Bifidobacterium species (median: 0.049) nor changing the relative abundances of the non-target species. While 115 amplicon sequence variants (ASVs) were unique to the conventional method, 208 ASVs were uniquely detected for the DRIP method. Moreover, the abundance estimation for minority species became more accurate, as revealed thorough comparison with the results of quantitative PCR analysis. Conclusion: The 16S metagenome-DRIP method serves as a useful technique to grasp a deeper and more accurate microbiota composition when combined with conventional 16S metagenome analysis methods.},
}
@article {pmid37693796,
year = {2021},
author = {Zhao, P and Crous, PW and Hou, LW and Duan, WJ and Cai, L and Ma, ZY and Liu, F},
title = {Fungi of quarantine concern for China I: Dothideomycetes.},
journal = {Persoonia},
volume = {47},
number = {},
pages = {45-105},
pmid = {37693796},
issn = {0031-5850},
abstract = {The current list of Chinese quarantine pests includes 130 fungal species. However, recent changes in the taxonomy of fungi following the one fungus = one name initiative and the implementation of DNA phylogeny in taxonomic revisions, resulted in many changes of these species names, necessitating an update of the current list. In addition, many quarantine fungi lack modern morphological descriptions and authentic DNA sequences, posing significant challenges for the development of diagnostic protocols. The aim of the present study was to review the taxonomy and names of the 33 Chinese quarantine fungi in Dothideomycetes, and provide reliable DNA barcodes to facilitate rapid identification. Of these, 23 names were updated according to the single name nomenclature system, including one new combination, namely Cophinforma tumefaciens comb. nov. (syn. Sphaeropsis tumefaciens). On the basis of phylogenetic analyses and morphological comparisons, a new genus Xenosphaeropsis is introduced to accommodate the monotypic species Xenosphaeropsis pyriputrescens comb. nov. (syn. Sphaeropsis pyriputrescens), the causal agent of a post-harvest disease of pears. Furthermore, four lectotypes (Ascochyta petroselini, Mycosphaerella ligulicola, Physalospora laricina, Sphaeria lingam), three epitypes (Ascochyta petroselini, Phoma lycopersici, Sphaeria lingam), and two neotypes (Ascochyta pinodella, Deuterophoma tracheiphila) are designated to stabilise the use of these names. A further four reference strains are introduced for Cophinforma tumefaciens, Helminthosporium solani, Mycocentrospora acerina, and Septoria linicola. In addition, to assist future studies on these important pathogens, we sequenced and assembled whole genomes for 17 species, including Alternaria triticina, Boeremia foveata, B. lycopersici, Cladosporium cucumerinum, Didymella glomerata, Didymella pinodella, Diplodia mutila, Helminthosporium solani, Mycocentrospora acerina, Neofusicoccum laricinum, Parastagonospora pseudonodorum, Plenodomus libanotidis, Plenodomus lingam, Plenodomus tracheiphilus, Septoria petroselini, Stagonosporopsis chrysanthemi, and Xenosphaeropsis pyriputrescens. Citation: Zhao P, Crous PW, Hou LW, et al. 2021. Fungi of quarantine concern for China I: Dothideomycetes. Persoonia 47: 45-105. https://doi.org/10.3767/persoonia.2021.47.02.},
}
@article {pmid37693795,
year = {2021},
author = {Crous, PW and Osieck, ER and Jurjević, &#x17d; and Boers, J and van Iperen, AL and Starink-Willemse, M and Dima, B and Balashov, S and Bulgakov, TS and Johnston, PR and Morozova, OV and Pinruan, U and Sommai, S and Alvarado, P and Decock, CA and Lebel, T and McMullan-Fisher, S and Moreno, G and Shivas, RG and Zhao, L and Abdollahzadeh, J and Abrinbana, M and Ageev, DV and Akhmetova, G and Alexandrova, AV and Altés, A and Amaral, AGG and Angelini, C and Antonín, V and Arenas, F and Asselman, P and Badali, F and Baghela, A and Bañares, A and Barreto, RW and Baseia, IG and Bellanger, JM and Berraf-Tebbal, A and Biketova, AY and Bukharova, NV and Burgess, TI and Cabero, J and Câmara, MPS and Cano-Lira, JF and Ceryngier, P and Chávez, R and Cowan, DA and de Lima, AF and Oliveira, RL and Denman, S and Dang, QN and Dovana, F and Duarte, IG and Eichmeier, A and Erhard, A and Esteve-Raventós, F and Fellin, A and Ferisin, G and Ferreira, RJ and Ferrer, A and Finy, P and Gaya, E and Geering, ADW and Gil-Durán, C and Glässnerová, K and Glushakova, AM and Gramaje, D and Guard, FE and Guarnizo, AL and Haelewaters, D and Halling, RE and Hill, R and Hirooka, Y and Hubka, V and Iliushin, VA and Ivanova, DD and Ivanushkina, NE and Jangsantear, P and Justo, A and Kachalkin, AV and Kato, S and Khamsuntorn, P and Kirtsideli, IY and Knapp, DG and Kochkina, GA and Koukol, O and Kovács, GM and Kruse, J and Kumar, TKA and Kušan, I and Læssøe, T and Larsson, E and Lebeuf, R and Levicán, G and Loizides, M and Marinho, P and Luangsa-Ard, JJ and Lukina, EG and Magaña-Dueñas, V and Maggs-Kölling, G and Malysheva, EF and Malysheva, VF and Martín, B and Martín, MP and Matočec, N and McTaggart, AR and Mehrabi-Koushki, M and Mešić, A and Miller, AN and Mironova, P and Moreau, PA and Morte, A and Müller, K and Nagy, LG and Nanu, S and Navarro-Ródenas, A and Nel, WJ and Nguyen, TH and Nóbrega, TF and Noordeloos, ME and Olariaga, I and Overton, BE and Ozerskaya, SM and Palani, P and Pancorbo, F and Papp, V and Pawłowska, J and Pham, TQ and Phosri, C and Popov, ES and Portugal, A and Pošta, A and Reschke, K and Reul, M and Ricci, GM and Rodríguez, A and Romanowski, J and Ruchikachorn, N and Saar, I and Safi, A and Sakolrak, B and Salzmann, F and Sandoval-Denis, M and Sangwichein, E and Sanhueza, L and Sato, T and Sastoque, A and Senn-Irlet, B and Shibata, A and Siepe, K and Somrithipol, S and Spetik, M and Sridhar, P and Stchigel, AM and Stuskova, K and Suwannasai, N and Tan, YP and Thangavel, R and Tiago, I and Tiwari, S and Tkalčec, Z and Tomashevskaya, MA and Tonegawa, C and Tran, HX and Tran, NT and Trovão, J and Trubitsyn, VE and Van Wyk, J and Vieira, WAS and Vila, J and Visagie, CM and Vizzini, A and Volobuev, SV and Vu, DT and Wangsawat, N and Yaguchi, T and Ercole, E and Ferreira, BW and de Souza, AP and Vieira, BS and Groenewald, JZ},
title = {Fungal Planet description sheets: 1284-1382.},
journal = {Persoonia},
volume = {47},
number = {},
pages = {178-374},
pmid = {37693795},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Antartica, Cladosporium austrolitorale from coastal sea sand. Australia, Austroboletus yourkae on soil, Crepidotus innuopurpureus on dead wood, Curvularia stenotaphri from roots and leaves of Stenotaphrum secundatum and Thecaphora stajsicii from capsules of Oxalis radicosa. Belgium, Paraxerochrysium coryli (incl. Paraxerochrysium gen. nov.) from Corylus avellana. Brazil, Calvatia nordestina on soil, Didymella tabebuiicola from leaf spots on Tabebuia aurea, Fusarium subflagellisporum from hypertrophied floral and vegetative branches of Mangifera indica and Microdochium maculosum from living leaves of Digitaria insularis. Canada, Cuphophyllus bondii from a grassland. Croatia, Mollisia inferiseptata from a rotten Laurus nobilis trunk. Cyprus, Amanita exilis on calcareous soil. Czech Republic, Cytospora hippophaicola from wood of symptomatic Vaccinium corymbosum. Denmark, Lasiosphaeria deviata on pieces of wood and herbaceous debris. Dominican Republic, Calocybella goethei among grass on a lawn. France (Corsica), Inocybe corsica on wet ground. France (French Guiana), Trechispora patawaensis on decayed branch of unknown angiosperm tree and Trechispora subregularis on decayed log of unknown angiosperm tree. Germany, Paramicrothecium sambuci (incl. Paramicrothecium gen. nov.) on dead stems of Sambucus nigra. India, Aureobasidium microtermitis from the gut of a Microtermes sp. termite, Laccaria diospyricola on soil and Phylloporia tamilnadensis on branches of Catunaregam spinosa. Iran, Pythium serotinoosporum from soil under Prunus dulcis. Italy, Pluteus brunneovenosus on twigs of broadleaved trees on the ground. Japan, Heterophoma rehmanniae on leaves of Rehmannia glutinosa f. hueichingensis. Kazakhstan, Murispora kazachstanica from healthy roots of Triticum aestivum. Namibia, Caespitomonium euphorbiae (incl. Caespitomonium gen. nov.) from stems of an Euphorbia sp. Netherlands, Alfaria junci, Myrmecridium junci, Myrmecridium juncicola, Myrmecridium juncigenum, Ophioceras junci, Paradinemasporium junci (incl. Paradinemasporium gen. nov.), Phialoseptomonium junci, Sporidesmiella juncicola, Xenopyricularia junci and Zaanenomyces quadripartis (incl. Zaanenomyces gen. nov.), from dead culms of Juncus effusus, Cylindromonium everniae and Rhodoveronaea everniae from Evernia prunastri, Cyphellophora sambuci and Myrmecridium sambuci from Sambucus nigra, Kiflimonium junci, Sarocladium junci, Zaanenomyces moderatricis-academiae and Zaanenomyces versatilis from dead culms of Juncus inflexus, Microcera physciae from Physcia tenella, Myrmecridium dactylidis from dead culms of Dactylis glomerata, Neochalara spiraeae and Sporidesmium spiraeae from leaves of Spiraea japonica, Neofabraea salicina from Salix sp., Paradissoconium narthecii (incl. Paradissoconium gen. nov.) from dead leaves of Narthecium ossifragum, Polyscytalum vaccinii from Vaccinium myrtillus, Pseudosoloacrosporiella cryptomeriae (incl. Pseudosoloacrosporiella gen. nov.) from leaves of Cryptomeria japonica, Ramularia pararhabdospora from Plantago lanceolata, Sporidesmiella pini from needles of Pinus sylvestris and Xenoacrodontium juglandis (incl. Xenoacrodontium gen. nov. and Xenoacrodontiaceae fam. nov.) from Juglans regia. New Zealand, Cryptometrion metrosideri from twigs of Metrosideros sp., Coccomyces pycnophyllocladi from dead leaves of Phyllocladus alpinus, Hypoderma aliforme from fallen leaves Fuscopora solandri and Hypoderma subiculatum from dead leaves Phormium tenax. Norway, Neodevriesia kalakoutskii from permafrost and Variabilispora viridis from driftwood of Picea abies. Portugal, Entomortierella hereditatis from a biofilm covering a deteriorated limestone wall. Russia, Colpoma junipericola from needles of Juniperus sabina, Entoloma cinnamomeum on soil in grasslands, Entoloma verae on soil in grasslands, Hyphodermella pallidostraminea on a dry dead branch of Actinidia sp., Lepiota sayanensis on litter in a mixed forest, Papiliotrema horticola from Malus communis, Paramacroventuria ribis (incl. Paramacroventuria gen. nov.) from leaves of Ribes aureum and Paramyrothecium lathyri from leaves of Lathyrus tuberosus. South Africa, Harzia combreti from leaf litter of Combretum collinum ssp. sulvense, Penicillium xyleborini from Xyleborinus saxesenii, Phaeoisaria dalbergiae from bark of Dalbergia armata, Protocreopsis euphorbiae from leaf litter of Euphorbia ingens and Roigiella syzygii from twigs of Syzygium chordatum. Spain, Genea zamorana on sandy soil, Gymnopus nigrescens on Scleropodium touretii, Hesperomyces parexochomi on Parexochomus quadriplagiatus, Paraphoma variabilis from dung, Phaeococcomyces kinklidomatophilus from a blackened metal railing of an industrial warehouse and Tuber suaveolens in soil under Quercus faginea. Svalbard and Jan Mayen, Inocybe nivea associated with Salix polaris. Thailand, Biscogniauxia whalleyi on corticated wood. UK, Parasitella quercicola from Quercus robur. USA, Aspergillus arizonicus from indoor air in a hospital, Caeliomyces tampanus (incl. Caeliomyces gen. nov.) from office dust, Cippumomyces mortalis (incl. Cippumomyces gen. nov.) from a tombstone, Cylindrium desperesense from air in a store, Tetracoccosporium pseudoaerium from air sample in house, Toxicocladosporium glendoranum from air in a brick room, Toxicocladosporium losalamitosense from air in a classroom, Valsonectria portsmouthensis from air in men's locker room and Varicosporellopsis americana from sludge in a water reservoir. Vietnam, Entoloma kovalenkoi on rotten wood, Fusarium chuoi inside seed of Musa itinerans, Micropsalliota albofelina on soil in tropical evergreen mixed forests and Phytophthora docyniae from soil and roots of Docynia indica. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Osieck ER, Jurjević Ž, et al. 2021. Fungal Planet description sheets: 1284-1382. Persoonia 47: 178-374. https://doi.org/10.3767/persoonia.2021.47.06.},
}
@article {pmid37645186,
year = {2021},
author = {Zwyer, M and Çavusoglu, C and Ghielmetti, G and Pacciarini, ML and Scaltriti, E and Van Soolingen, D and Dötsch, A and Reinhard, M and Gagneux, S and Brites, D},
title = {A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics.},
journal = {Open research Europe},
volume = {1},
number = {},
pages = {100},
pmid = {37645186},
issn = {2732-5121},
support = {883582/ERC_/European Research Council/International ; },
abstract = {Background: The bacteria that compose the Mycobacterium tuberculosis complex (MTBC) cause tuberculosis (TB) in humans and in different animals, including livestock. Much progress has been made in understanding the population structure of the human-adapted members of the MTBC by combining phylogenetics with genomics. Accompanying the discovery of new genetic diversity, a body of operational nomenclature has evolved to assist comparative and molecular epidemiological studies of human TB. By contrast, for the livestock-associated MTBC members, Mycobacterium bovis, M. caprae and M. orygis, there has been a lack of comprehensive nomenclature to accommodate new genetic diversity uncovered by emerging phylogenomic studies. We propose to fill this gap by putting forward a new nomenclature covering the main phylogenetic groups within M. bovis, M. caprae and M. orygis. Methods: We gathered a total of 8,736 whole-genome sequences (WGS) from public sources and 39 newly sequenced strains, and selected a subset of 829 WGS, representative of the worldwide diversity of M. bovis, M. caprae and M. orygis. We used phylogenetics and genetic diversity patterns inferred from WGS to define groups. Results: We propose to divide M. bovis, M. caprae and M. orygis in three main phylogenetic lineages, which we named La1, La2 and La3, respectively. Within La1, we identified several monophyletic groups, which we propose to classify into eight sublineages (La1.1-La1.8). These sublineages differed in geographic distribution, with some being geographically restricted and others globally widespread, suggesting different expansion abilities. To ease molecular characterization of these MTBC groups by the community, we provide phylogenetically informed, single nucleotide polymorphisms that can be used as barcodes for genotyping. These markers were implemented in KvarQ and TB-Profiler, which are platform-independent, open-source tools. Conclusions: Our results contribute to an improved classification of the genetic diversity within the livestock-associated MTBC, which will benefit future molecular epidemiological and evolutionary studies.},
}
@article {pmid37744148,
year = {2021},
author = {Boeraeve, M and Leroux, O and De Lange, R and Verbeken, A and Jacquemyn, H},
title = {The Effect of Surrounding Vegetation on the Mycorrhizal Fungal Communities of the Temperate Tree Crataegus monogyna Jacq.},
journal = {Frontiers in fungal biology},
volume = {2},
number = {},
pages = {741813},
pmid = {37744148},
issn = {2673-6128},
abstract = {About 90% of all land plants form mycorrhiza to facilitate the acquisition of essential nutrients such as phosphorus, nitrogen, and sometimes carbon. Based on the morphology of the interaction and the identity of the interacting plants and fungi, four major mycorrhizal types have been distinguished: arbuscular mycorrhiza (AM), ectomycorrhizal (EcM), ericoid mycorrhiza, and orchid mycorrhiza. Although most plants are assumed to form only one type of mycorrhiza, some species simultaneously form associations with two mycorrhizal types within a single root system. However, the dual-mycorrhizal status of many species is under discussion and in some plant species the simultaneous association with two mycorrhizal types varies in space or time or depends on the ecological context. Here, we assessed the mycorrhizal communities associating with common hawthorn (Crataegus monogyna), a small tree that commonly associates with AM fungi, and investigated the potential factors that underlie variation in mycorrhizal community composition. Histological staining of C. monogyna roots showed the presence of a Hartig net and hyphal sheaths in and around the roots, demonstrating the capacity of C. monogyna to form EcM. Meta-barcoding of soil and root samples of C. monogyna collected in AM-dominated grassland vegetation and in mixed AM + EcM forest vegetation showed a much higher number of EcM sequences and OTUs in root and soil samples from mixed AM + EcM vegetation than in samples from pure AM vegetation. We conclude that C. monogyna is able to form both AM and EcM, but that the extent to which it does depends on the environmental context, i.e., the mycorrhizal type of the surrounding vegetation.},
}
@article {pmid37938227,
year = {2021},
author = {Reitmeier, S and Hitch, TCA and Treichel, N and Fikas, N and Hausmann, B and Ramer-Tait, AE and Neuhaus, K and Berry, D and Haller, D and Lagkouvardos, I and Clavel, T},
title = {Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling.},
journal = {ISME communications},
volume = {1},
number = {1},
pages = {31},
pmid = {37938227},
issn = {2730-6151},
abstract = {16S rRNA gene amplicon sequencing is a popular approach for studying microbiomes. However, some basic concepts have still not been investigated comprehensively. We studied the occurrence of spurious sequences using defined microbial communities based on data either from the literature or generated in three sequencing facilities and analyzed via both operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) approaches. OTU clustering and singleton removal, a commonly used approach, delivered approximately 50% (mock communities) to 80% (gnotobiotic mice) spurious taxa. The fraction of spurious taxa was generally lower based on ASV analysis, but varied depending on the gene region targeted and the barcoding system used. A relative abundance of 0.25% was found as an effective threshold below which the analysis of spurious taxa can be prevented to a large extent in both OTU- and ASV-based analysis approaches. Using this cutoff improved the reproducibility of analysis, i.e., variation in richness estimates was reduced by 38% compared with singleton filtering using six human fecal samples across seven sequencing runs. Beta-diversity analysis of human fecal communities was markedly affected by both the filtering strategy and the type of phylogenetic distances used for comparison, highlighting the importance of carefully analyzing data before drawing conclusions on microbiome changes. In summary, handling of artifact sequences during bioinformatic processing of 16S rRNA gene amplicon data requires careful attention to avoid the generation of misleading findings. We propose the concept of effective richness to facilitate the comparison of alpha-diversity across studies.},
}
@article {pmid38217171,
year = {2021},
author = {Adair, JE and Enstrom, MR},
title = {A key toolbox for cellular barcoding analysis.},
journal = {Nature computational science},
volume = {1},
number = {4},
pages = {251-252},
pmid = {38217171},
issn = {2662-8457},
}
@article {pmid37518143,
year = {2023},
author = {Zhang, J and Dolibaina, DR and Cong, Q and Shen, J and Song, L and Mielke, CGC and Casagrande, MM and Mielke, OHH and Grishin, NV},
title = {Taxonomic notes on Neotropical Hesperiidae (Lepidoptera).},
journal = {Zootaxa},
volume = {5271},
number = {1},
pages = {91-114},
doi = {10.11646/zootaxa.5271.1.3},
pmid = {37518143},
issn = {1175-5334},
mesh = {Animals ; *Lepidoptera ; Phylogeny ; *Butterflies ; *Rubiaceae ; },
abstract = {Genomic sequencing (or morphology when indicated) and analysis of Hesperiidae that includes a number of primary type specimens reveals inconsistencies between the phylogenetic trees and the current classification that are resolved here. The following taxonomic changes are proposed. Oeonus Godman, 1900, stat. nov. is a subgenus of Oxynthes Godman, 1900. Decinea lydora (Plötz, 1882), stat. rev. is a valid species, not a synonym of Lindra neroides (Herrich-Schäffer, 1869), comb. nov. The following are: species-level taxa, not subspecies: Cabirus junta Evans, 1952, stat. nov. and Cabirus purda Evans, 1952, stat. nov. (not Cabirus procas (Cramer, 1777)), Orthos hyalinus (E. Bell, 1930), stat. rest. and Orthos minka Evans, 1955, stat. nov. (not Orthos orthos (Godman, 1900)), Eprius obrepta (Kivirikko, 1936), stat. rest. (not Eprius veleda (Godman, 1901)), Corra catargyra (C. Felder &amp; R. Felder, 1867), stat. rest. and Corra conka (Evans, 1955), stat. nov. (not Corra coryna (Hewitson, 1866)), Cymaenes macintyrei Hayward, 1939, stat. rest. (not Cymaenes tripunctata (Latreille, [1824])), Duroca lenta (Evans, 1955), stat. rest. (not Duroca duroca Plötz, 1882), Oarisma (Copaeodes) favor (Evans, 1955), stat. nov. (not Oarisma (Copaeodes) jean (Evans, 1955)), Panoquina eugeon (Godman &amp; Salvin, 1896), stat. rest., Panoquina calna Evans, 1955, stat. nov. and Panoquina albistriga O. Mielke, 1980, stat. nov. (not Panoquina panoquinoides (Skinner, 1891)); subspecies-level taxa, not species: Carystus elvira rufoventris Austin &amp; O. Mielke, 2007, stat. nov.; junior subjective synonyms: Bungalotis gagarini O. Mielke, 1967, syn. nov. of Bungalotis corentinus (Plötz, 1882), Salantoia dinka (Evans, 1952), syn. nov. of Adina adrastor (Mabille and Boullet, 1912), Lindra brasus ackeryi O. Mielke, 1978, stat. nov. of Lindra neroides neroides (Herrich-Schäffer, 1869) (but Lindra brasus (O. Mielke, 1968) is still a valid species), Vidius felus O. Mielke, 1968, syn. nov. of Vidius dagon (Evans, 1955), comb. nov., and Cobalopsis dorpa de Jong, 1983, syn. nov. of Vidius catocala (Herrich-Schäffer, 1869), comb. nov.; new genus-species combinations: Oxynthes (Oxynthes) egma (Evans, 1955), comb. nov. (not Oeonus Godman, 1900), Lindra neroides (Herrich-Schäffer, 1869), comb. nov. (not Decinea Evans, 1955), Mucia rusta (Evans, 1955), comb. nov. (not Psoralis Mabille, 1904), Rhomba mirnae (Siewert, Nakamura &amp; O. Mielke, 2014), comb. nov. (not Alychna Grishin, 2019), Eprius planus (Weeks, 1901), comb. nov. and Eprius penna (Evans, 1955), comb. nov. (changed based on morphology) (not Mnasicles Godman, 1901), Lattus minor (O. Mielke, 1967), comb. nov. (not Eutocus Godman, 1901), Panca fiedleri (Carneiro, O. Mielke &amp; Casagrande, 2015), comb. nov., Eutocus rogan (Evans, 1955), comb. nov. (changed based on morphology and cytochrome c oxidase subunit I (COI) DNA barcode) and Eutocus brasilia (Carneiro, O. Mielke &amp; Casagrande, 2015), comb. nov. (not Ginungagapus Carneiro, O. Mielke &amp; Casagrande, 2015), Eutocus fosca (Evans, 1955), comb. nov. (not Artines Godman, 1901), Rectava cascatona (O. Mielke, 1992), comb. nov. (not Papias Godman, 1900), Lurida zama (Hayward, 1939), comb. nov. and Vehilius campestris (O. Mielke, 1980), comb. nov. (not Cymaenes Scudder, 1872), Corra xanthus (O. Mielke, 1989), comb. nov., Cymaenes catarinae (O. Mielke, 1989), comb. nov., Vehilius spitzi (O. Mielke, 1967), comb. nov., Vehilius tinta (Evans, 1955), comb. nov. (not Vidius Evans, 1955), Cymaenes incomptus (Hayward, 1934), comb. nov. and Vehilius tanta (Evans, 1955), comb. nov. (not Nastra Evans, 1955), Vidius catocala (Herrich-Schäffer, 1869), comb. nov. Vidius cocalus (Hayward, 1939), comb. nov., Vidius dagon (Evans, 1955), and Vidius obscurior (Hayward, 1934), comb. nov. (not Cobalopsis Godman, 1900), Duroca caraca (O. Mielke, 1992), comb. nov. (not Lerema Scudder, 1872), and Cantha eteocla (Plötz, 1882), comb. nov. and Cantha buriti (O. Mielke, 1968), comb. nov. (not Phlebodes Hübner, [1819]); and new species-subspecies combinations: Lindra neroides huxleyi O. Mielke, 1978, comb. nov. (not Lindra brasus (O. Mielke, 1968)), Corra conka argentus (H. Freeman, 1969), stat. nov. (not Corra coryna (Hewitson, 1866)), Panoquina eugeon minima de Jong, 1983, comb. nov. (not Panoquina panoquinoides (Skinner, 1891)). The following neotype and lectotypes are designated to ensure nomenclatural identity and stability: neotype of Cobalus neroides Herrich-Schäffer, 1869 and lectotypes of Cobalus catocala Herrich-Schäffer, 1869 and Lerema elgina Schaus, 1902.},
}
@article {pmid37518128,
year = {2023},
author = {Bruno, MC and Cottarelli, V and Grasso, R and Spena, MT and Caccamo, DV and Marrone, F and Vecchioni, L},
title = {Disentangling cryptic species in Parastenocarididae (Copepoda: Harpacticoida) with an integrative approach: the case of Stammericaris similior sp. nov. and Stammericaris destillans Bruno &amp; Cottarelli 2017.},
journal = {Zootaxa},
volume = {5271},
number = {2},
pages = {271-293},
doi = {10.11646/zootaxa.5271.2.4},
pmid = {37518128},
issn = {1175-5334},
mesh = {Male ; Animals ; *Copepoda ; Phylogeny ; Animal Structures/anatomy &amp; histology ; Microscopy, Electron, Scanning ; },
abstract = {Stammericaris similior sp. nov. is described combining light microscopy, scanning electron microscopy, and genetic barcoding. The new species was collected from rimstone pools in Scrivilleri Cave, a cave in Sicily with so far unexplored microcrustacean fauna. The new species is particularly interesting because it is morphologically very similar to Stammericaris destillans, an epikarstic parastenocaridid endemic to a different Sicilian cave; however, the phylogenetic analysis based on the mitochondrial COI gene of sixteen parastenocaridids shows that these two Stammericaris are two distinct species, with an uncorrected p-distance of 22.9, and the sequences of Stammericaris similior sp. nov. cluster together in a well-supported monophyletic clade, with two different haplotypes. To our knowledge, the presence of different species of almost identical morphology had not been recorded before for the genus Stammericaris. The integrated molecular and morphological analysis, the latter conducted with the support of SEM, allows disentangling the affinities of the new species and identifying a few distinctive characters: the males of the new species are characterized by the caudal rami shorter than the anal somite; the morphology of the P3, which is thin and slightly arched, with three proximal spinules on exp-1; the peculiar structure of the P4 enp; the P4 basis ornamented with two spinules of different length, the one closest to the endopod being the shortest one, and a half-moon shaped lamella. The new species differs from S. destillans for its larger size, the presence of: three spinules, instead of two, on the P3 exp-1; the half-moon shaped lamella on the P4 basis; a row of spinules along the inner margin of P4 exp-1. We also provide data on the ecology and distribution of the new species, a list of the other copepod species collected, and a dichotomic key for the males of all species presently assigned to the genus.},
}
@article {pmid37518126,
year = {2023},
author = {Makarchenko, EA and Semenchenko, AA and Palatov, DM},
title = {Fauna and taxonomy of Diamesinae (Diptera, Chironomidae) from the Caucasus, with a morphological description and DNA barcoding of new taxa and a discussion of diagnostic problems for Diamesa Meigen and Pseudodiamesa Goetghebuer.},
journal = {Zootaxa},
volume = {5271},
number = {2},
pages = {313-328},
doi = {10.11646/zootaxa.5271.2.6},
pmid = {37518126},
issn = {1175-5334},
mesh = {Male ; Animals ; *Chironomidae/genetics ; DNA Barcoding, Taxonomic ; Phylogeny ; DNA ; Databases, Nucleic Acid ; },
abstract = {As a result of the revision of adult males as well as available literature data, 26 species of the subfamily Diamesinae are registered for the Caucasus, belonging to 5 genera. Four species are recorded for the first time for this region, one species, D. elbrusica sp. nov., and one subspecies, D. sakartvella gidanica subsp. nov., are new to science and are described. Six species are classified as endemics of the Caucasus. Distribution of other species of Caucasian Diamesinae is discussed. DNA barcodes of 102 specimens and 20 species of four genera, Boreoheptagyia Brundin, Diamesa Meigen, Pseudodiamesa Goetghebuer and Syndiamesa Kieffer were obtained in this study. Of these, 12 species were deposed in the GenBank and BOLD systems for the first time. We have established that D. cinerella group includes D. kasymovi and probably D. lavillei whereas D. zernyi group includes D. vaillanti and D. valentinae. Highly supported phylogeny and results of species delimitation suggest the description of D. elbrusica sp. nov. and D. sakartvella gidanica subsp. nov. Ps. aff. branickii and Ps. aff. nivosa are new species based on DNA barcoding. The results of species delimitation show that genus Pseudodiamesa includes 10 (ASAP, GMYC), 14 (mPTP) or 21 (BOLD) distinct molecular taxonomic units (mOTUs) among which only Ps. stackelbergi have an undoubted species status that requires a large revision using both morphological and molecular approaches.},
}
@article {pmid37517005,
year = {2023},
author = {Velázquez-Urrieta, Y and Velarde-Aguilar, MG and Oceguera-Figueroa, A and León-Règagnon, V},
title = {New species of Foleyellides (Nematoda: Onchocercidae: Waltonellinae), parasite of Lithobates brownorum (Amphibia: Ranidae) from South-eastern Mexico and genetic barcodes of the Mexican species of the genus.},
journal = {Systematic parasitology},
volume = {100},
number = {6},
pages = {591-599},
pmid = {37517005},
issn = {1573-5192},
mesh = {Animals ; Male ; *Parasites ; Mexico ; Species Specificity ; *Nematoda ; Ranidae/parasitology ; },
abstract = {Specimens of Foleyellides were collected from the body cavity of frogs in different regions of Mexico; Lithobates brownorum from Yucatán, Quintana Roo and Campeche; L. megapoda from Jalisco and Rhinella marina, from Guerrero. Foleyellides calakmulesis n. sp. is described based on specimens found parasitizing L. brownorum. The new species is distinguished from the other members of the genus by the combination of the following male characters: four pairs of caudal papillae different in size and the presence of a preanal plaque. Partial DNA sequences of the mitochondrial Cytochrome Oxidase C, subunit I of the four known Mexican species of Foleyellides and two potentially new species collected in this study were generated and compared, validating the erection of the new species.},
}
@article {pmid37513745,
year = {2023},
author = {Duc, M and Himmel, T and Harl, J and Iezhova, T and Nedorost, N and Matt, J and Ilgūnas, M and Weissenböck, H and Valkiūnas, G},
title = {Comparative Analysis of the Exo-Erythrocytic Development of Five Lineages of Haemoproteus majoris, a Common Haemosporidian Parasite of European Passeriform Birds.},
journal = {Pathogens (Basel, Switzerland)},
volume = {12},
number = {7},
pages = {},
pmid = {37513745},
issn = {2076-0817},
support = {P 33480/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Haemoproteus parasites (Apicomplexa, Haemosporida) are widespread pathogens of birds, with a rich genetic (about 1900 lineages) and morphospecies (178 species) diversity. Nonetheless, their life cycles are poorly understood. The exo-erythrocytic stages of three Haemoproteus majoris (widespread generalist parasite) lineages have been previously reported, each in a different bird species. We aimed to further study and compare the development of five H. majoris lineages-hCCF5, hCWT4, hPARUS1, hPHSIB1, and hWW2-in a wider selection of natural avian hosts. A total of 42 individuals belonging to 14 bird species were sampled. Morphospecies and parasitemia were determined by microscopy of blood films, lineages by DNA-barcoding a 478 bp section of the cytochrome b gene, and exo-erythrocytic stages by histology and chromogenic in situ hybridization. The lineage hCWT4 was morphologically characterized as H. majoris for the first time. All lineage infections exclusively featured megalomeronts. The exo-erythrocytic stages found in all examined bird species were similar, particularly for the lineages hCCF5, hPARUS1, and hPHSIB1. Megalomeronts of the lineages hWW2 and hCWT4 were more similar to each other than to the former three lineages. The kidneys and gizzard were most often affected, followed by lungs and intestines; the site of development showed variation depending on the lineage.},
}
@article {pmid37513398,
year = {2023},
author = {Kong, W and Li, C and Sun, Z and Gao, F and Zheng, J and Jiang, Y},
title = {Nickel-Atom Doping as a Potential Means to Enhance the Photoluminescence Performance of Carbon Dots.},
journal = {Molecules (Basel, Switzerland)},
volume = {28},
number = {14},
pages = {},
pmid = {37513398},
issn = {1420-3049},
support = {5210128//National Natural Science Foundation of China/ ; },
abstract = {Heteroatom doping, particularly with nonmetallic atoms such as N, P, and S, has proven to be an effective strategy for modulating the fluorescent properties of carbon dots (CDs). However, there are few reports on the regulation of the photoluminescence of CDs by transition-metal doping. In this work, nickel-doped CDs (Ni-CDs) were fabricated using the hydrothermal approach. Ni atoms were incorporated into the sp[2] domains of the CDs through Ni-N bonds, resulting in an increased degree of graphitization of the Ni-CDs. Additionally, Ni-atom doping served to shorten the electron transition and recombination lifetimes, and suppress the nonradiative recombination process, resulting in an absolute fluorescence quantum yield of 54.7% for the Ni-CDs. Meanwhile, the as-prepared Ni-CDs exhibited excellent biocompatibility and were utilized for fluorescent bioimaging of HeLa cells. Subsequently, the Ni-CDs were employed as fluorescent anticounterfeiting inks for the successful encryption of two-dimensional barcodes. Our work demonstrates a novel heteroatom doping strategy for the synthesis of highly fluorescence-emitting CDs.},
}
@article {pmid37512886,
year = {2023},
author = {Nallan, K and Ayyavu, V and Ayyanar, E and Thirupathi, B and Gupta, B and Devaraju, P and Kumar, A and Rajaiah, P},
title = {Molecular Evidence of Rickettsia conorii subsp. raoultii and Rickettsia felis in Haemaphysalis intermedia Ticks in Sirumalai, Eastern Ghats, Tamil Nadu, South India.},
journal = {Microorganisms},
volume = {11},
number = {7},
pages = {},
pmid = {37512886},
issn = {2076-2607},
support = {IM 2106//ICMR-VCRC Intra-mural funding/ ; },
abstract = {Rickettsia is an important pathogenic entity among tick-borne diseases (TBD), which are considered serious emerging public health problems globally. In India, though the widespread distribution of ticks and TBD has been documented, its real burden remains underreported. In a preliminary attempt, rickettsial surveillance was carried out in ticks collected from Sirumalai, Eastern Ghats in Tamil Nadu, India by using pathogen genome-based phylogenetic inferences generated through multi-locus sequence typing (MLST), targeting the genes 16s rRNA, OmpA, OmpB, and gltA by nested PCR. The laboratory evidence confirms the circulation of Rickettsia in Haemaphysalis intermedia species collected from this area. Analysis of the four gene sequences detected demonstrates their closest identity to the spotted fever group (SFG) available in the GenBank database. Further, multiple sequence alignment with other sequences derived from the GenBank database showed close relatedness to Rickettsia conorii subsp. raoultii (16s rDNA-99.32%, OmpA-93.38%, OmpB-97.39%, and gltA-98.57%) and Rickettsia felis (16s rDNA 99.54%, OmpA-100%, OmpB-100% and gltA-99.41%). With this genomic evidence, the circulation of rickettsial pathogens in the pools of H. intermedia ticks infesting livestock in the Sirumalai foothill area has been demonstrated and to complement the microscopic identification of the tick species, DNA barcodes were generated for H. intermedia using the mitochondrial cytochrome c oxidase subunit I gene (COI). Nevertheless, R. raoultii and R. felis were found to be the aetiological agents of tick-borne lymphadenopathy and flea-borne spotted fever in human cases, respectively, further study on the determination of their diversity, distribution, clinical relevance, and potential risk to the local community in these areas is highly warranted.},
}
@article {pmid37511909,
year = {2023},
author = {Bardakci, F and Al-Subaie, SHM and Badraoui, R and Adnan, M and Siddiqui, AJ},
title = {Molecular Characterization of Hard Ticks Infesting Camels in the Northern Region of Saudi Arabia Using the Barcoding Gene, Mitochondrial Cytochrome oxidase subunit I.},
journal = {Life (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {37511909},
issn = {2075-1729},
support = {GR-22 052//Scientific Research Deanship at the University of Ha'il, Saudi Arabia/ ; },
abstract = {The present study aimed to molecularly identify and characterize the hard ticks infesting camels from the northern region (Ha'il province) of Saudi Arabia using the mitochondrial barcoding gene cytochrome oxidase subunit I (COI). The sequences of tick samples from camels in three regions of Ha'il were aligned with those previously reported from different geographic regions, revealing nine haplotypes, of which six were newly described in this study for the first time. These haplotypes were used to determine their phylogenetic relationships using the maximum likelihood method, displaying two distinct clades corresponding to Hyalomma dromedarii and H. impeltatum. Moreover, the haplotypes showing the highest homology with those deposited in NCBI-GenBank from different geographic regions, including Saudi Arabia, were obtained and combined to determine their phylogenetic relationships among them. The results showed that the haplotypes belonging to two clades were grouped with those previously determined as H. dromedarii and H. impeltatum. Moreover, the presence of H. scupense (syn. H. detritum) together with H. impeltatum suggests possible asymmetrical hybridization and mitochondrial introgression between these species. H. scupense infesting different mammal species apart from camels were also clustered in a different clade, indicating the presence of different lineages of this species that show different host specificities.},
}
@article {pmid37508467,
year = {2023},
author = {Kezlya, E and Tseplik, N and Kulikovskiy, M},
title = {Genetic Markers for Metabarcoding of Freshwater Microalgae: Review.},
journal = {Biology},
volume = {12},
number = {7},
pages = {},
pmid = {37508467},
issn = {2079-7737},
support = {1/CX/CSRD VA/United States ; },
abstract = {The metabarcoding methods for studying the diversity of freshwater microalgae and routine biomonitoring are actively used in modern research. A lot of experience has been accumulated already, and many methodological questions have been solved (such as the influence of the methods and time of sample conservation, DNA extraction and bioinformatical processing). The reproducibility of the method has been tested and confirmed. However, one of the main problems-choosing a genetic marker for the study-still lacks a clear answer. We analyzed 70 publications and found out that studies on eukaryotic freshwater microalgae use 12 markers (different nuclear regions 18S and ITS and plastids rbcL, 23S and 16S). Each marker has its peculiarities; they amplify differently and have various levels of efficiency (variability) in different groups of algae. The V4 and V9 18S and rbcL regions are used most often. We concentrated especially on the studies that compare the results of using different markers and microscopy. We summarize the data on the primers for each region and on how the choice of a marker affects the taxonomic composition of a community.},
}
@article {pmid37508021,
year = {2023},
author = {Xie, J and Tan, B and Zhang, Y},
title = {A Large-Scale Study into Protist-Animal Interactions Based on Public Genomic Data Using DNA Barcodes.},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {14},
pages = {},
pmid = {37508021},
issn = {2076-2615},
support = {31900152//National Natural Science Foundation of China/ ; cstc2020jcyj-msxmX0695//Chongqing Science and Technology Bureau/ ; },
abstract = {With the birth of next-generation sequencing (NGS) technology, genomic data in public databases have increased exponentially. Unfortunately, exogenous contamination or intracellular parasite sequences in assemblies could confuse genomic analysis. Meanwhile, they can provide a valuable resource for studies of host-microbe interactions. Here, we used a strategy based on DNA barcodes to scan protistan contamination in the GenBank WGS/TSA database. The results showed a total of 13,952 metazoan/animal assemblies in GenBank, where 17,036 contigs were found to be protistan contaminants in 1507 assemblies (10.8%), with even higher contamination rates in taxa of Cnidaria (150/281), Crustacea (237/480), and Mollusca (107/410). Taxonomic analysis of the protists derived from these contigs showed variations in abundance and evenness of protistan contamination across different metazoan taxa, reflecting host preferences of Apicomplexa, Ciliophora, Oomycota and Symbiodiniaceae for mammals and birds, Crustacea, insects, and Cnidaria, respectively. Finally, mitochondrial proteins COX1 and CYTB were predicted from these contigs, and the phylogenetic analysis corroborated the protistan origination and heterogeneous distribution of the contaminated contigs. Overall, in this study, we conducted a large-scale scan of protistan contaminant in genomic resources, and the protistan sequences detected will help uncover the protist diversity and relationships of these picoeukaryotes with Metazoa.},
}
@article {pmid37506634,
year = {2023},
author = {Ajani, PA and Savela, H and Kahlke, T and Harrison, D and Jeffries, T and Kohli, GS and Verma, A and Laczka, O and Doblin, MA and Seymour, JR and Larsson, ME and Potts, J and Scanes, P and Gribben, PE and Harrison, L and Murray, SA},
title = {Response of planktonic microbial assemblages to disturbance in an urban sub-tropical estuary.},
journal = {Water research},
volume = {243},
number = {},
pages = {120371},
doi = {10.1016/j.watres.2023.120371},
pmid = {37506634},
issn = {1879-2448},
mesh = {Ecosystem ; Estuaries ; Plankton ; *Diatoms ; Oceans and Seas ; *Dinoflagellida ; Bacteria/genetics ; },
abstract = {Microbes are sensitive indicators of estuarine processes because they respond rapidly to dynamic disturbance events. As most of the world's population lives in urban areas and climate change-related disturbance events are becoming more frequent, estuaries bounded by cities are experiencing increasing stressors, at the same time that their ecosystem services are required more than ever. Here, using a multidisciplinary approach, we determined the response of planktonic microbial assemblages in response to seasonality and a rainfall disturbance in an urban estuary bounded by Australia's largest city, Sydney. We used molecular barcoding (16S, 18S V4 rRNA) and microscopy-based identification to compare microbial assemblages at locations with differing characteristics and urbanisation histories. Across 142 samples, we identified 8,496 unique free-living bacterial zOTUs, 8,175 unique particle associated bacterial zOTUs, and 1,920 unique microbial eukaryotic zOTUs. Using microscopy, we identified only the top <10% abundant, larger eukaryotic taxa (>10 µm), however quantification was possible. The site with the greater history of anthropogenic impact showed a more even community of associated bacteria and eukaryotes, and a significant increase in dissolved inorganic nitrogen following rainfall, when compared to the more buffered site. This coincided with a reduced proportional abundance of Actinomarina and Synechococcus spp., a change in SAR 11 clades, and an increase in the eukaryotic microbial groups Dinophyceae, Mediophyceae and Bathyoccocaceae, including a temporary dominance of the harmful algal bloom dinoflagellate Prorocentrum cordatum (syn. P. minimum). Finally, a validated hydrodynamic model of the estuary supported these results, showing that the more highly urbanised and upstream location consistently experienced a higher magnitude of salinity reduction in response to rainfall events during the study period. The best abiotic variables to explain community dissimilarities between locations were TDP, PN, modelled temperature and salinity (r = 0.73) for the free living bacteria, TP for the associated bacteria (r = 0.43), and modelled temperature (r = 0.28) for the microbial eukaryotic communities. Overall, these results show that a minor disturbance such as a brief rainfall event can significantly shift the microbial assemblage of an anthropogenically impacted area within an urban estuary to a greater degree than a seasonal change, but may result in a lesser response to the same disturbance at a buffered, more oceanic influenced location. Fine scale research into the factors driving the response of microbial communities in urban estuaries to climate related disturbances will be necessary to understand and implement changes to maintain future estuarine ecosystem services.},
}
@article {pmid37504730,
year = {2023},
author = {Kerr, M and Leavitt, SD},
title = {A Custom Regional DNA Barcode Reference Library for Lichen-Forming Fungi of the Intermountain West, USA, Increases Successful Specimen Identification.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {7},
pages = {},
pmid = {37504730},
issn = {2309-608X},
support = {NA//Brigham Young University/ ; },
abstract = {DNA barcoding approaches provide powerful tools for characterizing fungal diversity. However, DNA barcoding is limited by poor representation of species-level diversity in fungal sequence databases. Can the development of custom, regionally focused DNA reference libraries improve species-level identification rates for lichen-forming fungi? To explore this question, we created a regional ITS database for lichen-forming fungi (LFF) in the Intermountain West of the United States. The custom database comprised over 4800 sequences and represented over 600 formally described and provisional species. Lichen communities were sampled at 11 sites throughout the Intermountain West, and LFF diversity was characterized using high-throughput ITS2 amplicon sequencing. We compared the species-level identification success rates from our bulk community samples using our regional ITS database and the widely used UNITE database. The custom regional database resulted in significantly higher species-level assignments (72.3%) of candidate species than the UNITE database (28.3-34.2%). Within each site, identification of candidate species ranged from 72.3-82.1% using the custom database; and 31.5-55.4% using the UNITE database. These results highlight that developing regional databases may accelerate a wide range of LFF research by improving our ability to characterize species-level diversity using DNA barcoding.},
}
@article {pmid37504687,
year = {2023},
author = {Leavitt, SD and DeBolt, A and McQuhae, E and Allen, JL},
title = {Genomic Resources for the First Federally Endangered Lichen: The Florida Perforate Cladonia (Cladonia perforata).},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {7},
pages = {},
pmid = {37504687},
issn = {2309-608X},
support = {NA//Bureau of Land Management/ ; },
abstract = {Thirty years after its designation as a federally endangered species, the Florida Perforate Cladonia (FPC) remains imperiled in isolated populations in the Florida scrub in the southeastern USA. For threatened and endangered species, such as FPC, reference genomes provide critical insight into genomic diversity, local adaptations, landscape-level genetics, and phylogenomics. Using high-throughput sequencing, we assemble the first draft nuclear and mitochondrial genomes for the FPC mycobiont-Cladonia perforata. We also assess genetic diversity within and among populations in southeastern Florida using genome-scale data and investigate diversity across the entire nuclear ribosomal cistron, including the standard DNA barcoding marker for fungi. The draft nuclear genome spanned 33.6 Mb, and the complete, circular mitochondrial genome was 59 Kb. We also generated the first chloroplast genome, to our knowledge, for the photobiont genus associated with FPC, an undescribed Asterochloris species. We inferred the presence of multiple, distinct mycobiont parental genotypes (genets) occurring at local scales in southeastern Florida, and strikingly, no genets were shared among even the closest sample sites. All sampled thalli shared identical mitochondrial genomes, while the nuclear ribosomal cistron showed limited variability-highlighting the genetic resolution provided by nuclear genome-scale datasets. The genomic resources generated here provide critical resources for informed conservation efforts for the FPC.},
}
@article {pmid37504648,
year = {2023},
author = {Kirichenko, NI and Kolyada, NA and Gomboc, S},
title = {First Discovery of the North American Leaf-Mining Moth Chrysaster ostensackenella (Lepidoptera: Gracillariidae) in Russia: The Genetic Diversity of a Novel Pest in Invaded vs. Native Range.},
journal = {Insects},
volume = {14},
number = {7},
pages = {},
pmid = {37504648},
issn = {2075-4450},
support = {121031000120-9//state assignment "Study and Monitoring of Terrestrial Biological Resources in the South of the Russian Far East" (code of the scientific topic 0207-2021-0003)/ ; 22-16-00075//Russian Science Foundation/ ; },
abstract = {Here, we report the first detection of the North American leaf-mining moth Chrysaster ostensackenella (Fitch, 1859) (Lepidoptera: Gracillariidae) on North American black locust Robinia pseudoacacia (Fabaceae) in Primorsky Krai (the Russian Far East) in July 2022. Overall, six moths were reared from the leaf mines and identified based on adult morphology (forewing pattern and male genitalia) and three of them were DNA barcoding. Description of the leaf mines that allowed us to distinguish the damage of Ch. ostensackenella from other gracillariids associated with R. pseudoacacia is provided. The phylogeographic analysis comparing the DNA barcodes from Russia with those from other invaded countries in Europe (Italy) and East Asia (South Korea and Japan) and from the native range (North America) was performed. Intraspecific genetic diversity reached 3.29%. Altogether, 10 haplotypes were revealed among 21 studied specimens in the Holarctic. The detection of one haplotype common for Japan and the USA (North Carolina) suggests that the invasion to East Asia could have happened from the USA directly, rather than through Europe. A shared haplotype defined for Japan and the Russian Far East points at a possible moth species' spread to Primorsky Krai from earlier invaded Hokkaido. Further distribution of Ch. ostensackenella in East Asia and Europe is expected, bearing in mind the wide planting of R. pseudoacacia in these continents. Furthermore, an accidental introduction of the moth to the Southern Hemisphere, where black locust was introduced, is not ruled out.},
}
@article {pmid37504641,
year = {2023},
author = {Giordani, G and Whitmore, D and Vanin, S},
title = {A New, Non-Invasive Methodology for the Molecular Identification of Adult Sarcophagidae from Collections.},
journal = {Insects},
volume = {14},
number = {7},
pages = {},
pmid = {37504641},
issn = {2075-4450},
abstract = {Correct species identification is the cornerstone of all scientific studies that involve insects. Alongside traditional morphological identification techniques, molecular identification based on the characterization and analysis of specific mitochondrial or nuclear gene regions is becoming commonplace. Despite the good results that can be achieved, DNA extraction usually involves invasive techniques that lead to the partial or total destruction of specimens. In this work, a non-invasive DNA extraction technique is described. The technique was tested on the abdomens of dry-preserved Sarcophagidae (Diptera) specimens collected between 1889 and 2015. This allowed for the correct identification of species without impairing diagnostic morphological structures useful for further studies.},
}
@article {pmid37504622,
year = {2023},
author = {Starkevich, P and Young, CW},
title = {Taxonomic Revision of Tipula (Vestiplex Bezzi) Crane Flies (Diptera, Tipulidae) in Taiwan with Descriptions of Six New Species.},
journal = {Insects},
volume = {14},
number = {7},
pages = {},
pmid = {37504622},
issn = {2075-4450},
abstract = {The crane fly subgenus Tipula (Vestiplex) Bezzi, 1924 (Diptera, Tipulidae) of Taiwan is taxonomically reviewed, entailing the recognition of 18 species, with six of these species newly described, including T. (V.) diamondisp. nov., T. (V.) formosaesp. nov., T. (V.) gracilianasp. nov., T. (V.) pseudobiserrasp. nov., T. (V.) survilaisp. nov., and T. (V.) taiwanicasp. nov. Three species, T. biaciculifera Alexander, 1937, T. niitakensis Alexander, 1938, and T. pseudobiaciculifera Men, Xue and Wang, 2016, listed previously as members of the subgenus T. (Pterelachisus) Rondani, 1842, are now formally placed as member taxa within T. (Vestiplex). Tipula subnata Alexander, 1949 and T. (V.) longarmata Yang and Yang, 1999 are designated as junior synonyms of T. (V.) coxitalis Alexander, 1935; T. (V.) nokonis Alexander, 1935 is designated as a junior synonym of T. (V.) terebrata Edwards, 1921; and T. (V.) takahashiana Alexander, 1938 is designated as a junior synonym of T. (V.) bicornigera Alexander, 1938. Included in this taxonomic revision are a key to species, species diagnoses for all species, complete descriptions for newly described species, and illustrations of the male genitalia for all species, and for female terminalia when available. DNA barcode sequences for all Taiwanese species of T. (Vestiplex) are provided. Males are associated with conspecific females based on CO1 results and maximum likelihood trees resulting from the analyses are presented. The Taiwan fauna of Tipula (Vestiplex) is highly endemic with 16 of the 18 species restricted to the island. At the species group level, no groups are endemic to Taiwan and the groups show closest biogeographic relationships to the Qinghai-Tibetan Plateau.},
}
@article {pmid37504581,
year = {2023},
author = {Gomontean, B and Vaisusuk, K and Chatan, W and Wongpakam, K and Sankul, P and Lachanthuek, L and Mintara, R and Thanee, I and Pramual, P},
title = {Diversity, Abundance and Host Blood Meal Analysis of Culicoides Latreille (Diptera: Ceratopogonidae) from Cattle Pens in Different Land Use Types from Thailand.},
journal = {Insects},
volume = {14},
number = {7},
pages = {},
pmid = {37504581},
issn = {2075-4450},
support = {6516001//Mahasarakham University/ ; },
abstract = {Biting midges of the genus Culicoides Latreille are significant pests and vectors that transmit pathogens to humans and other animals. Cattle are among the important livestock that can potentially be severely affected by Culicoides. In this study, we examined the species diversity, abundance, and host blood meal identification of biting midges in cattle pens located in three different land use types: villages, agricultural areas, and the forest edge. A total of 12,916 biting midges were collected, and most of these were from cattle pens located in villages (34%) and agricultural land (52%). Morphological identification revealed 29 Culicoides species. The most common species were C. oxystoma, C. mahasarakhamense, C. peregrinus, and C. shortti; taken together, these species represented >80% of all specimens collected. Despite midges being less numerous (14% of the total collection), cattle pens located near the forest showed greater diversity (23) than those from villages and agricultural areas. More diverse immature habitats and host blood sources from wildlife in nearby forests possibly explain the greater diversity in the cattle pens near the forest edge. Host blood meal analysis revealed that most (65%) biting midges had fed on buffalo despite the fact that this animal was much less numerous than cows or chickens. Relatively larger size and black-colored skin could be factors that make buffalo more attractive to biting midges than other host species. In this study, we also provided 67 DNA barcoding sequences of 13 species, three of which (C. flaviscutatus, C. geminus, and C. suzukii) were first reported from Thai specimens. DNA barcode analysis indicated cryptic diversity within C. hegneri and C. flavescens in Thailand, and thus, further investigation is required to resolve their species status.},
}
@article {pmid37504111,
year = {2023},
author = {Shi, J and Pan, Y and Liu, X and Cao, W and Mu, Y and Zhu, Q},
title = {Spatial Omics Sequencing Based on Microfluidic Array Chips.},
journal = {Biosensors},
volume = {13},
number = {7},
pages = {},
pmid = {37504111},
issn = {2079-6374},
support = {226-2023-00006//Fundamental Research Funds for the Central Universities/ ; 2-2050205-21-688//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Microfluidics ; },
abstract = {Spatial profiling technologies fill the gap left by the loss of spatial information in traditional single-cell sequencing, showing great application prospects. After just a few years of quick development, spatial profiling technologies have made great progress in resolution and simplicity. This review introduces the development of spatial omics sequencing based on microfluidic array chips and describes barcoding strategies using various microfluidic designs with simplicity and efficiency. At the same time, the pros and cons of each strategy are compared. Moreover, commercialized solutions for spatial profiling are also introduced. In the end, the future perspective of spatial omics sequencing and research directions are discussed.},
}
@article {pmid37502860,
year = {2023},
author = {Shrestha, P and Yang, D and Shih, WM and Wong, WP},
title = {Mapping Single-molecule Protein Complexes in 3D with DNA Nanoswitch Calipers.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.07.10.548386},
pmid = {37502860},
issn = {2692-8205},
abstract = {The ability to accurately map the 3D geometry of single-molecule complexes in trace samples would lead to new insights into molecular mechanics and provide an approach for single-molecule structural proteomics. To enable this, we have developed a high-resolution force-spectroscopy method capable of measuring multiple distances between labeled sites in natively folded protein complexes. Our approach combines reconfigurable nanoscale devices we call DNA Nanoswitch Calipers, which we have previously introduced, with a force-based barcoding system to distinguish each measurement location. We demonstrate our approach by reconstructing the tetrahedral geometry of biotin-binding sites in natively folded streptavidin, with 1.5-2.5 Å agreement to previously reported structures.},
}
@article {pmid37502840,
year = {2023},
author = {Chen, Q and Schafer, CT and Mukherjee, S and Gustavsson, M and Agrawal, P and Yao, XQ and Kossiakoff, AA and Handel, TM and Tesmer, JJG},
title = {ACKR3-arrestin2/3 complexes reveal molecular consequences of GRK-dependent barcoding.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37502840},
issn = {2692-8205},
support = {R01 CA221289/CA/NCI NIH HHS/United States ; R01 CA254402/CA/NCI NIH HHS/United States ; R01 GM117372/GM/NIGMS NIH HHS/United States ; F32 GM137505/GM/NIGMS NIH HHS/United States ; P30 CA023168/CA/NCI NIH HHS/United States ; R35 GM151033/GM/NIGMS NIH HHS/United States ; R01 AI161880/AI/NIAID NIH HHS/United States ; R01 HL071818/HL/NHLBI NIH HHS/United States ; },
abstract = {Atypical chemokine receptor 3 (ACKR3, also known as CXCR7) is a scavenger receptor that regulates extracellular levels of the chemokine CXCL12 to maintain responsiveness of its partner, the G protein-coupled receptor (GPCR), CXCR4. ACKR3 is notable because it does not couple to G proteins and instead is completely biased towards arrestins. Our previous studies revealed that GRK2 and GRK5 install distinct distributions of phosphates (or "barcodes") on the ACKR3 carboxy terminal tail, but how these unique barcodes drive different cellular outcomes is not understood. It is also not known if arrestin2 (Arr2) and 3 (Arr3) bind to these barcodes in distinct ways. Here we report cryo-electron microscopy structures of Arr2 and Arr3 in complex with ACKR3 phosphorylated by either GRK2 or GRK5. Unexpectedly, the finger loops of Arr2 and 3 directly insert into the detergent/membrane instead of the transmembrane core of ACKR3, in contrast to previously reported "core" GPCR-arrestin complexes. The distance between the phosphorylation barcode and the receptor transmembrane core regulates the interaction mode of arrestin, alternating between a tighter complex for GRK5 sites and heterogenous primarily "tail only" complexes for GRK2 sites. Arr2 and 3 bind at different angles relative to the core of ACKR3, likely due to differences in membrane/micelle anchoring at their C-edge loops. Our structural investigations were facilitated by Fab7, a novel Fab that binds both Arr2 and 3 in their activated states irrespective of receptor or phosphorylation status, rendering it a potentially useful tool to aid structure determination of any native GPCR-arrestin complex. The structures provide unprecedented insight into how different phosphorylation barcodes and arrestin isoforms can globally affect the configuration of receptor-arrestin complexes. These differences may promote unique downstream intracellular interactions and cellular responses. Our structures also suggest that the 100% bias of ACKR3 for arrestins is driven by the ability of arrestins, but not G proteins, to bind GRK-phosphorylated ACKR3 even when excluded from the receptor cytoplasmic binding pocket.},
}
@article {pmid37502776,
year = {2023},
author = {Xu, Y and Chen, J and Jiang, LY and Qiao, GX},
title = {Cavariella Del Guercio (Hemiptera, Aphidinae, Macrosiphini) in China, with a new species, new synonymies, and first country records.},
journal = {ZooKeys},
volume = {1169},
number = {},
pages = {235-292},
pmid = {37502776},
issn = {1313-2989},
abstract = {The genus Cavariella is distinguished from other Macrosiphini genera (Aphididae, Aphidinae) because it has a supra-caudal process on abdominal tergite VIII which possesses two setae distally. It is Holarctic in distribution, and half of its species are Asian. The Chinese fauna of this genus, 17 species, have been restudied, morphologically and through DNA barcodes. As a result: Cavariellahidaensis Takahashi is transferred to Elatobium; Cavariellasculptura Qiao &amp; Xu, sp. nov. is described from specimens collected on Torilis and Cryptotaenia (Apiaceae); Cavariellacessana Zhang, Chen, Zhong &amp; Li, syn. nov. and Cavariellalargispiracula Zhang, Chen, Zhong &amp; Li, syn. nov. are respectively junior synonyms of Cavariellaaquatica (Gillette &amp; Bragg) and Cavariellasapporoensis Takahashi; Cavariellagilgiana Zhang, Chen, Zhong &amp; Li and Cavariellalhasana Zhang are confirmed as valid species and complete descriptions are provided; Cavariellabhutanensis Chakrabarti &amp; Das, Cavariellanigra Basu, Cavariellapastinacae (Linnaeus), and Cavariellapustula Essig are recorded for the first time from China. Additionally, keys for species of Cavariella known in China are provided and modifications to the key by Blackman and Eastop of aphid species on Angelica (Aphids on World's Plants) are presented.},
}
@article {pmid37498779,
year = {2023},
author = {Ogawa, M and Takada, N and Noda, S and Takahashi, M and Matsutani, M and Kageyama, D and Ebihara, H},
title = {GENETIC VARIATION OF LEPTOTROMBIDIUM (ACARI: TROMBICULIDAE) MITES CARRYING ORIENTIA TSUTSUGAMUSHI, THE BACTERIAL PATHOGEN CAUSING SCRUB TYPHUS.},
journal = {The Journal of parasitology},
volume = {109},
number = {4},
pages = {340-348},
pmid = {37498779},
issn = {1937-2345},
mesh = {Animals ; Humans ; *Scrub Typhus/microbiology ; *Orientia tsutsugamushi/genetics ; *Trombiculidae ; Phylogeny ; *Acari ; Bacteria ; Genetic Variation ; },
abstract = {Leptotrombidium (Acari: Trombiculidae) mites are carriers of Orientia tsutsugamushi, the bacterial pathogen causing scrub typhus in humans. Classification of Leptotrombidium is vital because limited mite species carry O. tsutsugamushi. Generally, Leptotrombidium at the larval stage (approximately 0.2 mm in size) are used for morphological identification. However, morphological identification is often challenging because it requires considerable skills and taxonomic expertise. In this study, we found that the full-length sequences of the mitochondrial cytochrome c oxidase subunit 1 gene varied among the significant Leptotrombidium. On the basis of these, we modified the canonical deoxyribonucleic acid (DNA) barcoding method for animals by redesigning the primer set to be suitable for Leptotrombidium. Polymerase chain reaction with the redesigned primer set drastically increased the detection sensitivity, especially against Leptotrombidium scutellare (approximately 17% increase), one of the significant mites carrying O. tsutsugamushi. Phylogenetic analysis showed that the samples morphologically classified as L. scutellare and Leptotrombidium pallidum were further split into 3 and 2 distinct subclusters respectively. The mean genetic distance (p-distance) between L. scutellare and L. pallidum was 0.2147, whereas the mean distances within each species were 0.052 and 0.044, respectively. Within L. scutellare, the mean genetic distances between the 3 subclusters were 0.1626-0.1732, whereas the distances within each subcluster were 0.003-0.017. Within L. pallidum, the mean genetic distance between the 2 subclusters was 0.1029, whereas the distances within each subcluster were 0.010-0.013. The DNA barcoding uncovered a broad genetic diversity of Leptotrombidium, especially of L. scutellare and L. pallidum, the notable species carrying O. tsutsugamushi. We conclude that the DNA barcoding using our primers enables precise and detailed classification of Leptotrombidium and implies the existence of a subgenotype in Leptotrombidium that had not been found by morphological identification.},
}
@article {pmid37497108,
year = {2023},
author = {Danisik, N and Yilmaz, KC and Acar, A},
title = {Identification of collateral sensitivity and evolutionary landscape of chemotherapy-induced drug resistance using cellular barcoding technology.},
journal = {Frontiers in pharmacology},
volume = {14},
number = {},
pages = {1178489},
pmid = {37497108},
issn = {1663-9812},
abstract = {Background: One of the most significant challenges impeding cancer treatment effectiveness is drug resistance. Combining evolutionary understanding with drug resistance can pave the way for the identification of second-line drug options that can overcome drug resistance. Although capecitabine and irinotecan are commonly used therapeutic agents in the treatment of CRC patients, resistance to these agents is common. The underlying clonal dynamics of resistance to these agents using high-resolution barcode technology and identification of effective second-line drugs in this context remain unclear. Methods and materials: Caco-2 and HT-29 cell lines were barcoded, and then capecitabine and irinotecan resistant derivatives of these cell lines were established. The frequencies of barcodes from resistant cell lines and harvested medium, longitudinally, were determined. Collateral drug sensitivity testing was carried out on resistant Caco-2 and HT-29 cell lines using single agents or drug combinations. The SyngeryFinder tool was used to analyse drug combination testing. Results: In Caco-2 and HT-29 cell lines, barcode frequency measurements revealed clonal dynamics of capecitabine and irinotecan formed by both pre-existing and de novo barcodes, indicating the presence of polyclonal drug resistance. The temporal dynamics of clonal evolution in Caco-2 and HT-29 cell lines were demonstrated by longitudinal analysis of pre-existing and de novo barcodes from harvested medium. In Caco-2 and HT-29 cell lines, collateral drug sensitivity revealed a number of drugs that were effective alone and in combination. Conclusion: The use of barcoding technology reveals the clonal dynamics of chemotherapy-induced drug resistance not only from harvested cell populations, but also from longitudinal sampling throughout the course of clonal evolution. Second-line drugs that sensitize drug-resistant CRC cell lines are identified through collateral drug testing.},
}
@article {pmid37496777,
year = {2023},
author = {Chen, HC},
title = {A systematic review of the barcoding strategy that contributes to COVID-19 diagnostics at a population level.},
journal = {Frontiers in molecular biosciences},
volume = {10},
number = {},
pages = {1141534},
pmid = {37496777},
issn = {2296-889X},
abstract = {The outbreak of SARS-CoV-2 has made us more alert to the importance of viral diagnostics at a population level to rapidly control the spread of the disease. The critical question would be how to scale up testing capacity and perform a diagnostic test in a high-throughput manner with robust results and affordable costs. Here, the latest 26 articles using barcoding technology for COVID-19 diagnostics and biologically-relevant studies are reviewed. Barcodes are molecular tags, that allow proceeding an array of samples at once. To date, barcoding technology followed by high-throughput sequencing has been made for molecular diagnostics for SARS-CoV-2 infections because it can synchronously analyze up to tens of thousands of clinical samples within a short diagnostic time. Essentially, this technology can also be used together with different biotechnologies, allowing for investigation with resolution of single molecules. In this Mini-Review, I first explain the general principle of the barcoding strategy and then put forward recent studies using this technology to accomplish COVID-19 diagnostics and basic research. In the meantime, I provide the viewpoint to improve the current COVID-19 diagnostic strategy with potential solutions. Finally, and importantly, two practical ideas about how barcodes can be further applied in studying SARS-CoV-2 to accelerate our understanding of this virus are proposed.},
}
@article {pmid37490502,
year = {2023},
author = {Pozzi, A and Nazzicari, N and Capoferri, R and Radovic, S and Bongioni, G},
title = {Assessment of residual plant DNA in bulk milk for Grana Padano PDO production by a metabarcoding approach.},
journal = {PloS one},
volume = {18},
number = {7},
pages = {e0289108},
pmid = {37490502},
issn = {1932-6203},
mesh = {Female ; Animals ; Cattle ; *Milk ; DNA, Plant/genetics ; Thylakoids ; Italy ; *Cheese/analysis ; },
abstract = {The aim of this study was to evaluate the ability of DNA metabarcoding, by rbcl as barcode marker, to identify and classify the small traces of plant DNA isolated from raw milk used to produce Grana Padano (GP) cheese. GP is one of the most popular Italian PDO (Protected Designation of Origin) produced in Italy in accordance with the GP PDO specification rules that define which forage can be used for feeding cows. A total of 42 GP bulk tank milk samples were collected from 14 dairies located in the Grana Padano production area. For the taxonomic classification, a local database with the rbcL sequences available in NCBI on September 2020/March 2021 for the Italian flora was generated. A total of 8,399,591 reads were produced with an average of 204,868 per sample (range 37,002-408,724) resulting in 16, 31 and 28 dominant OTUs at family, genus and species level, respectively. The taxonomic analysis of plant species in milk samples identified 7 families, 14 genera and 14 species, the statistical analysis conducted using alpha and beta diversity approaches, did not highlight differences among the investigated samples. However, the milk samples are featured by a high plant variability and the lack of differences at multiple taxonomic levels could be due to the standardisation of the feed rationing, as requested by the GP rules. The results suggest that DNA metabarcoding is a valuable resource to explore plant DNA traces in a complex matrix such as milk.},
}
@article {pmid37488481,
year = {2023},
author = {Chase-Topping, M and Plastow, G and Dekkers, J and Li, Y and Fang, Y and Gerdts, V and Van Kessel, J and Harding, J and Opriessnig, T and Doeschl-Wilson, A},
title = {The WUR0000125 PRRS resilience SNP had no apparent effect on pigs' infectivity and susceptibility in a novel transmission trial.},
journal = {Genetics, selection, evolution : GSE},
volume = {55},
number = {1},
pages = {51},
pmid = {37488481},
issn = {1297-9686},
support = {BBS/E/D/20002172/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /30002275/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Swine ; Animals ; *Porcine Reproductive and Respiratory Syndrome ; Polymorphism, Single Nucleotide ; *Porcine respiratory and reproductive syndrome virus ; Genotype ; Linear Models ; },
abstract = {BACKGROUND: Porcine reproductive and respiratory syndrome (PRRS) remains one of the most important infectious diseases for the pig industry. A novel small-scale transmission experiment was designed to assess whether the WUR0000125 (WUR for Wageningen University and Research) PRRS resilience single nucleotide polymorphism (SNP) confers lower susceptibility and infectivity to pigs under natural porcine reproductive and respiratory syndrome virus (PRRSV-2) transmission.<br><br>METHODS: Commercial full- and half-sib piglets (n&#x2009;=&#x2009;164) were assigned as either Inoculation, Shedder, or Contact pigs. Pigs were grouped according to their relatedness structure and WUR genotype, with R- and R+&#x2009;referring to pigs with zero and one copy of the dominant WUR resilience allele, respectively. Barcoding of the PRRSV-2 strain (SD09-200) was applied to track pig genotype-specific transmission. Blood and nasal swab samples were collected and concentrations of PRRSV-2 were determined by quantitative (q)-PCR and cell culture and expressed in units of median tissue culture infectious dose (TCID50). The Log10TCID50 at each sampling event, derived infection status, and area under the curve (AUC) were response variables in linear and generalized linear mixed models to infer WUR genotype differences in Contact pig susceptibility and Shedder pig infectivity.<br><br>RESULTS: All Shedder and Contact pigs, except one, became infected through natural transmission. There was no significant (p&#x2009;>&#x2009;0.05) effect of Contact pig genotype on any virus measures that would indicate WUR genotype differences in susceptibility. Contact pigs tended to have higher serum AUC (p&#x2009;=&#x2009;0.017) and log10TCID50 (p&#x2009;=&#x2009;0.034) when infected by an R+&#x2009;shedder, potentially due to more infectious R+&#x2009;shedders at the early stages of the transmission trial. However, no significant Shedder genotype effect was found in serum (p&#x2009;=&#x2009;0.274) or nasal secretion (p&#x2009;=&#x2009;0.951) that would indicate genotype differences in infectivity.<br><br>CONCLUSIONS: The novel design demonstrated that it is possible to estimate genotype effects on Shedder pig infectivity and Contact pig susceptibility that are not confounded by family effects. The study, however, provided no supportive evidence that genetic selection on WUR genotype would affect PRRSV-2 transmission. The results of this study need to be independently validated in a larger trial using different PRRSV strains before dismissing the effects of the WUR marker or the previously detected GBP5 gene on PRRSV transmission.},
}
@article {pmid37487915,
year = {2023},
author = {Miyazaki, T and Aoki, W and Koike, N and Sato, T and Ueda, M},
title = {Application of peptide barcoding to obtain high-affinity anti-PD-1 nanobodies.},
journal = {Journal of bioscience and bioengineering},
volume = {136},
number = {3},
pages = {173-181},
doi = {10.1016/j.jbiosc.2023.07.002},
pmid = {37487915},
issn = {1347-4421},
mesh = {*Single-Domain Antibodies/chemistry ; Immune Checkpoint Inhibitors ; Peptides/chemistry ; Peptide Library ; *Antineoplastic Agents ; },
abstract = {Cancer treatment has been revolutionized by immune checkpoint inhibitors, which regulate immune cell function by blocking the interactions between immune checkpoint molecules and their ligands. The interaction between programmed cell death-1 (PD-1) and programmed cell death-ligand 1 (PD-L1) is a target for immune checkpoint inhibitors. Nanobodies, which are recombinant variable domains of heavy-chain-only antibodies, can replace existing immune checkpoint inhibitors, such as anti-PD-1 or anti-PD-L1 conventional antibodies. However, the screening process for high-affinity nanobodies is laborious and time-consuming. Here, we identified high-affinity anti-PD-1 nanobodies using peptide barcoding, which enabled reliable and efficient screening by distinguishing each nanobody with a peptide barcode that was genetically appended to each nanobody. We prepared a peptide-barcoded nanobody (PBNb) library with thousands of variants. Three high-affinity PBNbs were identified from the PBNb library by quantifying the peptide barcodes derived from high-affinity PBNbs. Furthermore, these three PBNbs neutralized the interaction between PD-1 and PD-L1. Our results demonstrate the utility of peptide barcoding and the resulting nanobodies can be used as experimental tools and antitumor agents.},
}
@article {pmid37486265,
year = {2023},
author = {Seto, K and Simmons, DR and Quandt, CA and Frenken, T and Dirks, AC and Clemons, RA and McKindles, KM and McKay, RML and James, TY},
title = {A combined microscopy and single-cell sequencing approach reveals the ecology, morphology, and phylogeny of uncultured lineages of zoosporic fungi.},
journal = {mBio},
volume = {14},
number = {4},
pages = {e0131323},
pmid = {37486265},
issn = {2150-7511},
support = {1P01ES02328939-01//HHS | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; },
mesh = {Phylogeny ; *Microscopy ; Fungi ; *Chytridiomycota/genetics ; DNA, Ribosomal/genetics ; Fresh Water/microbiology ; DNA, Fungal/genetics/chemistry ; },
abstract = {Environmental DNA analyses of fungal communities typically reveal a much larger diversity than can be ascribed to known species. Much of this hidden diversity lies within undescribed fungal lineages, especially the early diverging fungi (EDF). Although these EDF often represent new lineages even at the phylum level, they have never been cultured, making their morphology and ecology uncertain. One of the methods to characterize these uncultured fungi is a single-cell DNA sequencing approach. In this study, we established a large data set of single-cell sequences of EDF by manually isolating and photographing parasitic fungi on various hosts such as algae, protists, and micro-invertebrates, combined with subsequent long-read sequencing of the ribosomal DNA locus (rDNA). We successfully obtained rDNA sequences of 127 parasitic fungal cells, which clustered into 71 phylogenetic lineages belonging to seven phylum-level clades of EDF: Blastocladiomycota, Chytridiomycota, Aphelidiomycota, Rozellomycota, and three unknown phylum-level clades. Most of our single cells yielded novel sequences distinguished from both described taxa and existing metabarcoding data, indicating an expansive and hidden diversity of parasitic taxa of EDF. We also revealed an unexpected diversity of endobiotic Olpidium-like chytrids and hyper-parasitic lineages. Overall, by combining photographs of parasitic fungi with phylogenetic analyses, we were able to better understand the ecological function and morphology of many of the branches on the fungal tree of life known only from DNA sequences. IMPORTANCE Much of the diversity of microbes from natural habitats, such as soil and freshwater, comprise species and lineages that have never been isolated into pure culture. In part, this stems from a bias of culturing in favor of saprotrophic microbes over the myriad symbiotic ones that include parasitic and mutualistic relationships with other taxa. In the present study, we aimed to shed light on the ecological function and morphology of the many undescribed lineages of aquatic fungi by individually isolating and sequencing molecular barcodes from 127 cells of host-associated fungi using single-cell sequencing. By adding these sequences and their photographs into the fungal tree, we were able to understand the morphology of reproductive and vegetative structures of these novel fungi and to provide a hypothesized ecological function for them. These individual host-fungal cells revealed themselves to be complex environments despite their small size; numerous samples were hyper-parasitized with other zoosporic fungal lineages such as Rozellomycota.},
}
@article {pmid37481907,
year = {2023},
author = {Chen, Q and Liu, M and Xu, C and Bai, J and Feng, H and Chen, C and Zhao, L and Liu, Y and Zhou, S and Zhao, D},
title = {Potential of plant DNA information in determining the provenance and identify of unknown victims.},
journal = {Forensic science international},
volume = {350},
number = {},
pages = {111786},
doi = {10.1016/j.forsciint.2023.111786},
pmid = {37481907},
issn = {1872-6283},
mesh = {Humans ; Female ; DNA, Plant/genetics ; Phylogeny ; China ; Sequence Analysis, DNA ; Cadaver ; *Crops, Agricultural/genetics ; *DNA, Environmental ; },
abstract = {Determination of the personal identity of victims is particularly important for the settlement of criminal cases. Unfortunately, useful information for identification is not always available. We here propose that the particles (pollens) of some plants with specific geographical distributions extracted from human lung tissues contribute to further determining the provenance or long-term residence of unknown victims, thereby considerably narrowing the search scope of the victims. We collected lung tissues from 155 victims with diverse causes of death, extracted DNA from lung tissues, sequenced the DNA fragments of plants on the Illumina Hiseq platform, and barcoded the plant species using phylogenetic methods. Finally, 108 unique plant sequences were detected in 55 samples and identified to belong to 36 species in 32 genera of 29 families. These plants were predominantly insect-pollinated crops and ornamental plants. No significant difference was observed between male and female samples, between urban and rural samples, or among samples of different ages and different sample sizes. There were 16 samples with 21 wild plant species. The original sources of 15 samples were overlapped with the distribution regions of detected plants; 2 samples narrowed the original sources to 2 provinces, which were quite coincident with their source places; 1 sample had no overlapping with its victim source region. Although plant information was only found in one-third of the samples, we further demonstrated the great potential of plant eDNA in identifying the source of unnamed corpses in a real-world case. We used plant eDNA from lung tissues to explore the provenance of an unknown female corpse found in Beijing. The source place of this victim was narrowed to Guangdong and Guangxi provinces, and finally, we confirmed her true identity in the list of missing persons in Guangxi Province. In the presence of a well-covered local reference library, the plant species detected in the lungs can be accurately identified. In difficult criminal cases where physical evidence is relatively weak, plant DNA information may provide new clues. In conclusion, the plant particles trapped in the lungs are promising to help forensic experts narrow the search scope for the identity of unknown victims.},
}
@article {pmid37480109,
year = {2023},
author = {Hew, YX and Ya'cob, Z and Adler, PH and Chen, CD and Lau, KW and Sofian-Azirun, M and Muhammad-Rasul, AH and Putt, QY and Izwan-Anas, N and Hadi, UK and Suana, IW and Takaoka, H and Low, VL},
title = {DNA barcoding of black flies (Diptera: Simuliidae) in Indonesia.},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {248},
pmid = {37480109},
issn = {1756-3305},
support = {BIFA6_017//Biodiversity Information Fund for Asia/ ; MO002-2019//Ministry of Higher Education, Malaysia/ ; SC-1700596//NIFA/USDA/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Indonesia ; *Simuliidae/genetics ; },
abstract = {BACKGROUND: DNA barcoding is a valuable taxonomic tool for rapid and accurate species identification and cryptic species discovery in black flies. Indonesia has 143 nominal species of black flies, but information on their biological aspects, including vectorial capacity and biting habits, remains underreported, in part because of identification problems. The current study represents the first comprehensive DNA barcoding of Indonesian black flies using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences.<br><br>METHODS: Genomic DNA of Indonesian black fly samples were extracted and sequenced, producing 86 COI sequences in total. Two hundred four COI sequences, including 118 GenBank sequences, were analysed. Maximum likelihood (ML) and Bayesian inference (BI) trees were constructed and species delimitation analyses, including ASAP, GMYC and single PTP, were performed to determine whether the species of Indonesian black flies could be delineated. Intra- and interspecific genetic distances were also calculated and the efficacy of COI sequences for species identification was tested.<br><br>RESULTS: The DNA barcodes successfully distinguished most morphologically distinct species (>&#x2009;80% of sampled taxa). Nonetheless, high maximum intraspecific distances (3.32-13.94%) in 11 species suggested cryptic diversity. Notably, populations of the common taxa Simulium (Gomphostilbia) cheongi, S. (Gomphostilbia) sheilae, S. (Nevermannia) feuerborni and S. (Simulium) tani in the islands of Indonesia were genetically distinct from those on the Southeast Asian mainland (Malaysia and Thailand). Integrated morphological, cytogenetic and nuclear DNA studies are warranted to clarify the taxonomic status of these more complex taxa.<br><br>CONCLUSIONS: The findings showed that COI barcoding is a promising taxonomic tool for Indonesian black flies. The DNA barcodes will aid in correct identification and genetic study of Indonesian black flies, which will be helpful in the control and management of potential vector species.},
}
@article {pmid37479953,
year = {2024},
author = {Lai, Y and Li, K and Liu, X},
title = {Comprehensive DNA barcode reference library and optimization of genetic divergence threshold facilitate the exploration of species diversity of green lacewings (Neuroptera: Chrysopidae).},
journal = {Insect science},
volume = {31},
number = {2},
pages = {613-632},
doi = {10.1111/1744-7917.13254},
pmid = {37479953},
issn = {1744-7917},
support = {32130012//National Natural Science Foundation of China/ ; 32170448//National Natural Science Foundation of China/ ; //2115 Talent Development Program of China Agricultural University/ ; //National Animal Collection Resource Center, China/ ; No. 5212011//Beijing Natural Science Foundation/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Insecta/genetics ; Larva ; China ; },
abstract = {Chrysopidae are a family of Neuroptera of significant importance in biocontrol against agricultural pests because of their predatory larvae. Currently, the taxonomy of Chrysopidae lacks a comprehensive revision, which impedes the exploration of species diversity as well as the selection and the conservation of green lacewings as biocontrol agents. We have established a DNA barcode reference library of the Chinese green lacewings based on an approximately complete sampling (95.63%) in 25 of the 34 provincial regions in China, comprising 1 119 barcodes of 25 genera and 197 species (representing 85% genera and 43.62% species from China). Combining other 1 049 high quality green lacewing DNA barcodes, we first inferred the optimal threshold of interspecific genetic divergence (1.87%) for successful species identification in multiple simulated scenarios based on present data. We further inferred the threshold of genetic divergence (7.77%) among genera with biocontrol significance. The inference and performance of the threshold appears to be mainly associated with the completeness of sampling, the proportion of closely related species, and the analytical approaches. Six new combinations, Apertochrysa platypa (Yang &amp; Yang, 1991) comb. nov., Apertochrysa shennongana (Yang &amp; Wang, 1990) comb. nov., Apertochrysa pictifacialis (Yang, 1988) comb. nov., Apertochrysa helana (Yang, 1993) comb. nov., Plesiochrysa rosulata (Yang &amp; Yang, 2002) comb. nov., and Signochrysa hainana (Yang &amp; Yang, 1991), are proposed according to integrative species delimitation. Our library and optimal threshold will effectively facilitate the exploration of species diversity of green lacewings. Our study also provides a methodological reference in molecular delimitation of other insects.},
}
@article {pmid37476210,
year = {2023},
author = {Yang, W and Yang, J and Zhang, J and Yu, H},
title = {A survey of Tmarus Simon, 1875 (Araneae, Thomisidae) from Fanjing Mountain Nature Reserve, Guizhou, China.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e105352},
pmid = {37476210},
issn = {1314-2828},
abstract = {BACKGROUND: Tmarus Simon, 1875 is a relatively large spider genus, currently includes 227 species distributed worldwide. Fanjing Mountain Nature Reserve is one of China's most biodiverse regions. However, Tmarus can be regarded as being poorly represented in Fanjing Mountain, with only one species having been recorded so far: T.fanjing Yang &amp; Yu, 2022.<br><br>NEW INFORMATION: Recently, various expeditions to Fanjing Mountain Nature Reserve were carried out by the authors. In this paper, two Tmarus species were brought to light by those expeditions: T.fanjing Yang &amp; Yu, 2022 and T.circinalis Song &amp; Chai, 1990. T.fanjing is redescribed, based on new material and the female is described and illustrated for the first time. The supplementary micrographs of T.circinalis are given for the first time. The DNA barcodes and a distribution map of both species are provided for future use.},
}
@article {pmid37470283,
year = {2023},
author = {Negreira, GH and de Groote, R and Van Giel, D and Monsieurs, P and Maes, I and de Muylder, G and Van den Broeck, F and Dujardin, JC and Domagalska, MA},
title = {The adaptive roles of aneuploidy and polyclonality in Leishmania in response to environmental stress.},
journal = {EMBO reports},
volume = {24},
number = {9},
pages = {e57413},
pmid = {37470283},
issn = {1469-3178},
mesh = {Humans ; *Leishmania/genetics ; Antimony ; Chromosomes ; Aneuploidy ; },
abstract = {Aneuploidy is generally considered harmful, but in some microorganisms, it can act as an adaptive mechanism against environmental stress. Here, we use Leishmania-a protozoan parasite with remarkable genome plasticity-to study the early steps of aneuploidy evolution under high drug pressure (using antimony or miltefosine as stressors). By combining single-cell genomics, lineage tracing with cellular barcodes, and longitudinal genome characterization, we reveal that aneuploidy changes under antimony pressure result from polyclonal selection of pre-existing karyotypes, complemented by further and rapid de novo alterations in chromosome copy number along evolution. In the case of miltefosine, early parasite adaptation is associated with independent point mutations in a miltefosine transporter gene, while aneuploidy changes only emerge later, upon exposure to increased drug levels. Therefore, polyclonality and genome plasticity are hallmarks of parasite adaptation, but the scenario of aneuploidy dynamics depends on the nature and strength of the environmental stress as well as on the existence of other pre-adaptive mechanisms.},
}
@article {pmid37470247,
year = {2023},
author = {Guo, F and Slos, D and Du, H and Li, K and Li, H and Qing, X},
title = {Transcriptomics of Cruznema velatum (Nematoda: Rhabditidae) with a redescription of the species.},
journal = {Journal of helminthology},
volume = {97},
number = {},
pages = {e57},
doi = {10.1017/S0022149X23000342},
pmid = {37470247},
issn = {1475-2697},
mesh = {Animals ; *Transcriptome ; *Nematoda/genetics ; Caenorhabditis elegans/genetics ; Phylogeny ; China ; },
abstract = {Cruznema velatum isolated from soil in a chestnut orchard located at Guangdong province, China, is redescribed with morphology, molecular barcoding sequences, and transcriptome data. The morphological comparison for C. velatum and six other valid species is provided. Phylogeny analysis suggests genus Cruznema is monophyletic. The species is amphimix, can be cultured with Escherichia coli in 7-9 days from egg to egg-laying adult, and has a lifespan of 11 to 14 days at 20°C. The transcription data generated 45,366 unigenes; 29.9%, 31.3%, 24.8%, and 18.6% of unigenes were annotated in KOG, SwissProt, GO, and KEGG, respectively. Further gene function analysis demonstrated that C. velatum share the same riboflavin, lipoic acid, and vitamin B6 metabolic pathways with Caenorhabditis elegans and Pristionchus pacificus.},
}
@article {pmid37469398,
year = {2023},
author = {Kong, L and Xu, F and Yao, Y and Gao, Z and Tian, P and Zhuang, S and Wu, D and Li, T and Cai, Y and Li, J},
title = {Ascites-derived CDCP1+ extracellular vesicles subcluster as a novel biomarker and therapeutic target for ovarian cancer.},
journal = {Frontiers in oncology},
volume = {13},
number = {},
pages = {1142755},
pmid = {37469398},
issn = {2234-943X},
abstract = {INTRODUCTION: Ovarian cancer (OVCA) is one of the most prevalent malignant tumors of the female reproductive system, and its diagnosis is typically accompanied by the production of ascites. Although liquid biopsy has been widely implemented recently, the diagnosis or prognosis of OVCA based on liquid biopsy remains the primary emphasis.<br><br>METHODS: In this study, using proximity barcoding assay, a technique for analyzing the surface proteins on single extracellular vesicles (EVs). For validation, serum and ascites samples from patients with epithelial ovarian cancer (EOC) were collected, and their levels of CDCP1 was determined by enzyme-linked immunosorbent assay. Tissue chips were prepared to analyze the relationship between different expression levels of CDCP1 and the prognosis of ovarian cancer patients.<br><br>RESULTS: We discovered that the CUB domain-containing protein 1+ (CDCP1+) EVs subcluster was higher in the ascites of OVCA patients compared to benign ascites. At the same time, the level of CDCP1 was considerably elevated in the ascites of OVCA patients. The overall survival and disease-free survival of the group with high CDCP1 expression in EOC were significantly lower than those of the group with low expression. In addition, the receiver operating characteristic curve demonstrates that EVs-derived CDCP1 was a biomarker of early response in OVCA ascites.<br><br>DISCUSSION: Our findings identified a CDCP1+ EVs subcluster in the ascites of OVCA patients as a possible biomarker for EOC prevention.},
}
@article {pmid37468935,
year = {2023},
author = {Rodrigues, BL and de Souza Pinto, I and Galati, EAB},
title = {Morphological and DNA-based description of Trichophoromyia peixotoi n. sp. (Diptera: Psychodidae), a new sand fly species from the Brazilian Amazon.},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {240},
pmid = {37468935},
issn = {1756-3305},
support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
mesh = {Animals ; Male ; *Psychodidae ; Brazil ; Semen ; *Phlebotomus ; DNA ; },
abstract = {BACKGROUND: Phlebotomine sand flies of the genus Trichophoromyia Barretto, 1962 are of great relevance to public health as vectors of Leishmania protozoans. A new phlebotomine species named Trichophoromyia peixotoi n. sp. is here described based on both male morphology and COI DNA barcodes.<br><br>METHODS: The sand fly specimens were collected in the Parque Nacional da Amaz&#xf4;nia (PNA), situated in the municipality of Itaituba, state of Par&#xe1;, Brazil. Morphological description was done based on 10 male specimens. Five specimens were DNA barcoded for the COI gene.<br><br>RESULTS: The morphological and molecular analyses allowed the delimitation of this new species from others of Trichophoromyia. Trichophoromyia peixotoi n. sp. is closely related to other species with aedeagal ducts&#x2009;>&#x2009;4 times the length of the sperm pump, from which it may be distinguished by the gonocoxite bristles and paramere shape.<br><br>CONCLUSIONS: The description of T. peixotoi n. sp. brings the number of species of Trichophoromyia to 45, including 24 for Brazil. The integrative taxonomy effort through the analysis of COI barcodes proved to be effective in the species delimitation of some Trichophoromyia spp.},
}
@article {pmid37468627,
year = {2023},
author = {Goyal, Y and Busch, GT and Pillai, M and Li, J and Boe, RH and Grody, EI and Chelvanambi, M and Dardani, IP and Emert, B and Bodkin, N and Braun, J and Fingerman, D and Kaur, A and Jain, N and Ravindran, PT and Mellis, IA and Kiani, K and Alicea, GM and Fane, ME and Ahmed, SS and Li, H and Chen, Y and Chai, C and Kaster, J and Witt, RG and Lazcano, R and Ingram, DR and Johnson, SB and Wani, K and Dunagin, MC and Lazar, AJ and Weeraratna, AT and Wargo, JA and Herlyn, M and Raj, A},
title = {Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells.},
journal = {Nature},
volume = {620},
number = {7974},
pages = {651-659},
pmid = {37468627},
issn = {1476-4687},
support = {P30 AR069619/AR/NIAMS NIH HHS/United States ; R01 CA238237/CA/NCI NIH HHS/United States ; P30 CA010815/CA/NCI NIH HHS/United States ; F30 CA236129/CA/NCI NIH HHS/United States ; T32 GM007170/GM/NIGMS NIH HHS/United States ; F30 HD103378/HD/NICHD NIH HHS/United States ; P50 CA174523/CA/NCI NIH HHS/United States ; P30 CA016520/CA/NCI NIH HHS/United States ; T32 HG000046/HG/NHGRI NIH HHS/United States ; K00 CA212437/CA/NCI NIH HHS/United States ; T32 GM144295/GM/NIGMS NIH HHS/United States ; P01 CA114046/CA/NCI NIH HHS/United States ; P50 CA261608/CA/NCI NIH HHS/United States ; R00 CA263017/CA/NCI NIH HHS/United States ; T32 GM008216/GM/NIGMS NIH HHS/United States ; R01 CA174746/CA/NCI NIH HHS/United States ; R01 CA232256/CA/NCI NIH HHS/United States ; R01 CA207935/CA/NCI NIH HHS/United States ; P50 CA221703/CA/NCI NIH HHS/United States ; U01 CA227550/CA/NCI NIH HHS/United States ; U54 CA224070/CA/NCI NIH HHS/United States ; R01 GM137425/GM/NIGMS NIH HHS/United States ; F30 NS100595/NS/NINDS NIH HHS/United States ; },
mesh = {Humans ; *Clone Cells/drug effects/metabolism/pathology ; DNA Barcoding, Taxonomic ; *Drug Resistance, Neoplasm/drug effects/genetics ; *Neoplasms/drug therapy/genetics/pathology ; RNA-Seq ; Single-Cell Gene Expression Analysis ; Tumor Cells, Cultured ; *Antineoplastic Agents/pharmacology ; },
abstract = {Even among genetically identical cancer cells, resistance to therapy frequently emerges from a small subset of those cells[1-7]. Molecular differences in rare individual cells in the initial population enable certain cells to become resistant to therapy[7-9]; however, comparatively little is known about the variability in the resistance outcomes. Here we develop and apply FateMap, a framework that combines DNA barcoding with single-cell RNA sequencing, to reveal the fates of hundreds of thousands of clones exposed to anti-cancer therapies. We show that resistant clones emerging from single-cell-derived cancer cells adopt molecularly, morphologically and functionally distinct resistant types. These resistant types are largely predetermined by molecular differences between cells before drug addition and not by extrinsic factors. Changes in the dose and type of drug can switch the resistant type of an initial cell, resulting in the generation and elimination of certain resistant types. Samples from patients show evidence for the existence of these resistant types in a clinical context. We observed diversity in resistant types across several single-cell-derived cancer cell lines and cell types treated with a variety of drugs. The diversity of resistant types as a result of the variability in intrinsic cell states may be a generic feature of responses to external cues.},
}
@article {pmid37467349,
year = {2023},
author = {Amat, E and Gómez, GF and López-Rubio, A and Gómez-Piñerez, LM and Albertino Rafael, J},
title = {A short fragment of mitochondrial DNA for the taxonomic identification of blow flies (Diptera: Calliphoridae) in northwestern South America.},
journal = {Journal of medical entomology},
volume = {60},
number = {5},
pages = {931-943},
doi = {10.1093/jme/tjad092},
pmid = {37467349},
issn = {1938-2928},
mesh = {Animals ; *Diptera/genetics ; DNA, Mitochondrial ; Calliphoridae/genetics ; Forensic Sciences ; Electron Transport Complex IV/genetics ; South America ; DNA Barcoding, Taxonomic ; },
abstract = {Blow flies are of medical, sanitary, veterinary, and forensic importance. Their accurate taxonomic identification is essential for their use in applied research. However, neotropical fauna has not been completely studied or described, and taxa identification without the required training is a difficult task. Additionally, the current morphological keys are not fitting to all extant taxa. Molecular-based approaches are widely used to overcome these issues, including the standard 5' COI barcode fragment (~650 base pairs [bp]) for identification at the species level. Here, a shorter sequence of 5' COI fragment (~342 bp) was assessed for the identification of 28 blow fly species inhabiting the northwest of South America. One tree-based (the generalized mixed Yule-coalescent-GMYC) and 3 distance-based approaches (automatic barcode gap discover - ABGD, the best close match - BCM, and the nearest neighbor - NN) analyses were performed. Noticeably, the amplification and sequencing of samples that had been preserved for up to 57 years were successful. The tree topology assigned 113 sequences to a specific taxon (70% effectiveness), while the distance approach assigned to 95 (59% effectiveness). The short fragment allowed the molecular identification of 19 species (60% of neotropical species except for the Lucilia species and Hemilucilia semidiaphana). According to these findings, the taxonomic and faunistic considerations of the blow fly fauna were provided. Overall, the short fragment approach constitutes an optimal species confirmation tool for the most common blow flies in northwestern South America.},
}
@article {pmid37465151,
year = {2023},
author = {Moraes, SS and Söderholm, MS and Aguiar, TMC and Freitas, AVL and Sihvonen, P},
title = {Micro-CT imaging in species description: exploring beyond sclerotized structures in lichen moths (Lepidoptera: Erebidae, Arctiinae, Lithosiini).},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15505},
pmid = {37465151},
issn = {2167-8359},
mesh = {Female ; Male ; Animals ; *Moths ; X-Ray Microtomography ; *Lichens ; Brazil ; Genitalia/diagnostic imaging ; },
abstract = {X-ray micro-computed tomography imaging (micro-CT) is valuable for systematic research since it permits the non-destructive scanning and imaging of internal structures of very rare species and/or type specimens. Additionally, micro-CT allows to view the morphology and the functional anatomy of structures in their natural anatomical position, without deformations that typically occur using classical dissection protocols. In this study we provide the description of two new species of lichen moths (Lepidoptera: Erebidae, Lithosiini) from the Atlantic Forest in eastern Brazil: Nodozana heliae Moraes sp. nov. from Rio de Janeiro state and Epeiromulona pataxo Moraes &amp; Aguiar sp. nov. from Bahia state. The male and female genitalia as well as the wing morphology were examined by means of non-destructive micro-CT, subsequent 3D model reconstruction, 360 degree spinning animations, 2D images from different angles, and those were compared against classical genitalia dissections from the same specimens. We conclude that techniques complement each other, micro-CT being particularly useful to study wing venation, sclerotized internal structures and muscles, while classical dissection is useful to study membranous structures, particularly in the female genitalia, abdominal skin and specialised scales on the male 8th sternite.},
}
@article {pmid37464896,
year = {2023},
author = {Wei, S and Dou, Y and Yu, Y and Yang, J and Yu, F and Sha, W and Li, T},
title = {A novel biosensor based on a bio-barcode for the detection of Mycobacterium tuberculosis.},
journal = {Analytical methods : advancing methods and applications},
volume = {15},
number = {30},
pages = {3683-3691},
doi = {10.1039/d3ay00772c},
pmid = {37464896},
issn = {1759-9679},
mesh = {Humans ; *Mycobacterium tuberculosis/genetics ; Urease ; *COVID-19 ; DNA ; *Biosensing Techniques/methods ; },
abstract = {Tuberculosis (TB), the second (after COVID-19) deadliest infectious killer, is a chronic infectious disease caused by infection with Mycobacterium tuberculosis (M.T.), where early diagnosis and management are the key to containing the condition. Here, we report a novel biosensor for the detection of M.T. DNA based on magnetic separation, urease catalysis and silicon nanowire field effect transistor (SiNW FET) detection. M.T. DNA is sequence-specifically captured by magnetic nanoparticles and urease-labelled silica nanoparticles simultaneously to form a sandwich complex and urea is catalyzed into ammonium carbonate by urease modified on a sandwich complex. By using SiNW FET, the detection of M.T. DNA is realized indirectly by the detection of ammonium carbonate. The limit of detection (LOD) was determined to be 78.541 fM. The specificity of the biosensor was confirmed by detecting a panel of bacterial species. The utility of the biosensor was demonstrated in real-sample analysis and the recovery study of M.T. DNA was done in the genomic DNA extracted from cultured Mycobacterium tuberculosis. The biosensor holds promise to become a rapid, sensitive and accurate method for clinical diagnosis.},
}
@article {pmid37463472,
year = {2023},
author = {McCarthy, ME and Dodd, WB and Lu, X and Pritko, DJ and Patel, ND and Haskell, CV and Sanabria, H and Blenner, MA and Birtwistle, MR},
title = {Theory for High-Throughput Genetic Interaction Screening.},
journal = {ACS synthetic biology},
volume = {12},
number = {8},
pages = {2290-2300},
pmid = {37463472},
issn = {2161-5063},
support = {R21 CA196418/CA/NCI NIH HHS/United States ; R35 GM141891/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Humans ; *High-Throughput Screening Assays ; Cloning, Molecular ; *Mammals ; },
abstract = {Systematic, genome-scale genetic screens have been instrumental for elucidating genotype-phenotype relationships, but approaches for probing genetic interactions have been limited to at most ∼100 pre-selected gene combinations in mammalian cells. Here, we introduce a theory for high-throughput genetic interaction screens. The theory extends our recently developed Multiplexing using Spectral Imaging and Combinatorics (MuSIC) approach to propose ∼10[5] spectrally unique, genetically encoded MuSIC barcodes from 18 currently available fluorescent proteins. Simulation studies based on constraints imposed by spectral flow cytometry equipment suggest that genetic interaction screens at the human genome-scale may be possible if MuSIC barcodes can be paired to guide RNAs. While experimental testing of this theory awaits, it offers transformative potential for genetic perturbation technology and knowledge of genetic function. More broadly, the availability of a genome-scale spectral barcode library for non-destructive identification of single cells could find more widespread applications such as traditional genetic screening and high-dimensional lineage tracing.},
}
@article {pmid37463293,
year = {2023},
author = {Deng, W and Feng, S and Stejskal, V and Opit, G and Li, Z},
title = {An advanced approach for rapid visual identification of Liposcelis bostrychophila (Psocoptera: Liposcelididae) based on CRISPR/Cas12a combined with RPA.},
journal = {Journal of economic entomology},
volume = {116},
number = {5},
pages = {1911-1921},
doi = {10.1093/jee/toad139},
pmid = {37463293},
issn = {1938-291X},
abstract = {Liposcelis bostrychophila Badonnel (Psocoptera: Liposcelididae) is a booklouse pest that is a threat to commodity storage security worldwide. Accurate and sensitive methods of L. bostrychophila on-site identification are essential prerequisites for its effective management. Evidence suggests that L. bostrychophila contains 3 intraspecific biotypes that are morphologically indistinguishable but can be discriminated at the level of mitochondrial genome organization and sequences. The traditional molecular identification methods, such as DNA barcoding and PCR-RFLP, are instrumentally demanding and time-consuming, limiting the application of the identification in the field. Therefore, this study developed a new CRISPR/Cas12a-based visual nucleic acid system based on the mitochondrial gene coding for NADH dehydrogenase subunit 2 (nad2), combined with recombinase polymerase amplification (RPA) to accurately identify L. bostrychophila from 4 other common stored-product booklice, and also differentiate 3 biotypes of this species at the same time. The entire identification process could be completed at 37 °C within 20 min with high sensitivity. The system could stably detect at least 1 ng/μl of DNA template. The green fluorescence signal produced by the trans-cleaving of the single-stranded DNA reporter could be observed by the naked eye under blue light. Additionally, the suggested system combined with the crude DNA extraction method to extract DNA rapidly, enabled identification of all developmental stages of L. bostrychophila. With crude DNA, this novel diagnostic system successfully identified an unknown booklouse by holding the reaction tubes in the hand, thus can be considered as an accurate, rapid, highly sensitive, and instrument-flexible method for on-site visual identification of L. bostrychophila.},
}
@article {pmid37462745,
year = {2023},
author = {Rauff-Adedotun, AA and Lee, IL and Abd Talib, N and Shaari, N and Yahaya, ZS and Meor Termizi, FH},
title = {Prevalence, potential risk factors and genetic diversity of Blastocystis in ruminant livestock animals from Penang, Malaysia.},
journal = {Parasitology research},
volume = {122},
number = {9},
pages = {2193-2205},
pmid = {37462745},
issn = {1432-1955},
mesh = {Animals ; Female ; Cattle ; Humans ; Sheep ; *Blastocystis/genetics ; Livestock ; Malaysia/epidemiology ; Prevalence ; *Blastocystis Infections/epidemiology/veterinary ; Goats ; Feces ; Genetic Variation ; Phylogeny ; },
abstract = {Blastocystis is a unicellular, anaerobic protist inhabiting the intestinal tract of diverse animal hosts, including human. Information regarding Blastocystis in small ruminants, namely goats and sheep, is limited globally; thus, this study was carried out to investigate the distribution and determinants of Blastocystis in ruminant livestock animals from Penang, Malaysia. Fecal samples from 127 cattle, 149 goats, and 100 sheep were examined for Blastocystis by in vitro cultivation using modified Jones' medium, while DNA barcoding was used for subtyping. Overall, 23.1% (87/376) of animals screened were positive for Blastocystis sp. The prevalence of infection was significantly higher in goats than in cattle and sheep, while the female gender, semi-intensive farming system, and the Northeast Penang Island district were identified as potential risk factors for Blastocystis infection. Blastocystis sp. ST5, ST14, and ST25 were identified in cattle; ST5, ST10, ST13, and ST14 in goats; and ST4, ST5, ST14, and ST15 in sheep. ST5 and ST14 were found to be the most abundant and widespread subtypes in the study area. To the best of our knowledge, this is the first report of ST4 from sheep and ST13 from goats, thus serving as an update to the host range of Blastocystis sp. ST4 and ST13. The isolation of ST4 and ST5 in this study suggests that ruminant livestock animals could serve as reservoirs of human infection.},
}
@article {pmid37461442,
year = {2023},
author = {Chettih, SN and Mackevicius, EL and Hale, S and Aronov, D},
title = {Barcoding of episodic memories in the hippocampus of a food-caching bird.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37461442},
issn = {2692-8205},
support = {DP2 AG071918/AG/NIA NIH HHS/United States ; F32 MH123015/MH/NIMH NIH HHS/United States ; K99 NS131256/NS/NINDS NIH HHS/United States ; },
abstract = {Episodic memory, or memory of experienced events, is a critical function of the hippocampus[1-3]. It is therefore important to understand how hippocampal activity represents specific events in an animal's life. We addressed this question in chickadees - specialist food-caching birds that hide food at scattered locations and use memory to find their caches later in time[4,5]. We performed high-density neural recordings in the hippocampus of chickadees as they cached and retrieved seeds in a laboratory arena. We found that each caching event was represented by a burst of firing in a unique set of hippocampal neurons. These 'barcode-like' patterns of activity were sparse (<10% of neurons active), uncorrelated even for immediately adjacent caches, and different even for separate caches at the same location. The barcode representing a specific caching event was transiently reactivated whenever a bird later interacted with the same cache - for example, to retrieve food. Barcodes co-occurred with conventional place cell activity[6,7], as well as location-independent responses to cached seeds. We propose that barcodes are signatures of episodic memories evoked during memory recall. These patterns assign a unique identifier to each event and may be a mechanism for rapid formation and storage of many non-interfering memories.},
}
@article {pmid37460925,
year = {2023},
author = {Torricelli, F and Donati, B and Reggiani, F and Manicardi, V and Piana, S and Valli, R and Lococo, F and Ciarrocchi, A},
title = {Spatially resolved, high-dimensional transcriptomics sorts out the evolution of biphasic malignant pleural mesothelioma: new paradigms for immunotherapy.},
journal = {Molecular cancer},
volume = {22},
number = {1},
pages = {114},
pmid = {37460925},
issn = {1476-4598},
mesh = {Humans ; *Mesothelioma, Malignant ; *Mesothelioma/genetics/therapy ; Transcriptome ; Ecosystem ; *Pleural Neoplasms/genetics/therapy ; *Lung Neoplasms/genetics ; Prognosis ; Biomarkers, Tumor/genetics ; Immunotherapy ; },
abstract = {BACKGROUND: Malignant Pleural Mesothelioma (MPM) is a dreadful disease escaping the classical genetic model of cancer evolution and characterized by wide heterogeneity and transcriptional plasticity. Clinical evolution of MPM is marked by a progressive transdifferentiation that converts well differentiated epithelioid (E) cells into undifferentiated and pleomorphic sarcomatoid (S) phenotypes. Catching the way this transition takes place is necessary to understand how MPM develops and progresses and it is mandatory to improve patients' management and life expectancy. Bulk transcriptomic approaches, while providing a significant overview, failed to resolve the timing of this evolution and to identify the hierarchy of molecular events through which this transition takes place.<br><br>METHODS: We applied a spatially resolved, high-dimensional transcriptomic approach to study MPM morphological evolution. 139 regions across 8 biphasic MPMs (B-MPMs) were profiled using the GeoMx&#x2122;Digital Spatial Profiler to reconstruct the positional context of transcriptional activities and the spatial topology of MPM cells interactions. Validation was conducted on an independent large cohort of 84 MPMs by targeted digital barcoding analysis.<br><br>RESULTS: Our results demonstrated the existence of a complex circular ecosystem in which, within a strong asbestos-driven inflammatory environment, MPM and immune cells affect each other to support S-transdifferentiation. We also showed that TGFB1 polarized M2-Tumor Associated Macrophages foster immune evasion and that TGFB1 expression correlates with reduced survival probability.<br><br>CONCLUSIONS: Besides providing crucial insights into the multidimensional interactions governing MPM clinical evolution, these results open new perspectives to improve the use of immunotherapy in this disease.},
}
@article {pmid37460719,
year = {2023},
author = {},
title = {A method to map single-cell lineages in the mouse brain by CRISPR-based barcoding.},
journal = {Nature methods},
volume = {20},
number = {8},
pages = {1139-1140},
pmid = {37460719},
issn = {1548-7105},
mesh = {Animals ; Mice ; Cell Lineage ; *CRISPR-Cas Systems/genetics ; *Gene Expression Profiling ; Brain ; DNA Barcoding, Taxonomic ; },
}
@article {pmid37460718,
year = {2023},
author = {Xie, L and Liu, H and You, Z and Wang, L and Li, Y and Zhang, X and Ji, X and He, H and Yuan, T and Zheng, W and Wu, Z and Xiong, M and Wei, W and Chen, Y},
title = {Comprehensive spatiotemporal mapping of single-cell lineages in developing mouse brain by CRISPR-based barcoding.},
journal = {Nature methods},
volume = {20},
number = {8},
pages = {1244-1255},
pmid = {37460718},
issn = {1548-7105},
mesh = {Mice ; Animals ; Cell Lineage ; Cell Differentiation/physiology ; *Stem Cells ; *Brain ; Dopaminergic Neurons ; },
abstract = {A fundamental interest in developmental neuroscience lies in the ability to map the complete single-cell lineages within the brain. To this end, we developed a CRISPR editing-based lineage-specific tracing (CREST) method for clonal tracing in Cre mice. We then used two complementary strategies based on CREST to map single-cell lineages in developing mouse ventral midbrain (vMB). By applying snapshotting CREST (snapCREST), we constructed a spatiotemporal lineage landscape of developing vMB and identified six progenitor archetypes that could represent the principal clonal fates of individual vMB progenitors and three distinct clonal lineages in the floor plate that specified glutamatergic, dopaminergic or both neurons. We further created pandaCREST (progenitor and derivative associating CREST) to associate the transcriptomes of progenitor cells in vivo with their differentiation potentials. We identified multiple origins of dopaminergic neurons and demonstrated that a transcriptome-defined progenitor type comprises heterogeneous progenitors, each with distinct clonal fates and molecular signatures. Therefore, the CREST method and strategies allow comprehensive single-cell lineage analysis that could offer new insights into the molecular programs underlying neural specification.},
}
@article {pmid37460151,
year = {2024},
author = {Reeves, LE and Burkett-Cadena, ND},
title = {Amplification and Identification of Vertebrate Host Cytochrome c Oxidase Subunit I (COI) DNA Barcoding Templates from Mosquito Blood Meals.},
journal = {Cold Spring Harbor protocols},
volume = {2024},
number = {10},
pages = {pdb.prot108292},
doi = {10.1101/pdb.prot108292},
pmid = {37460151},
issn = {1559-6095},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Culicidae/genetics ; *Electron Transport Complex IV/genetics ; *Vertebrates/genetics ; Feeding Behavior ; Blood ; DNA Primers/genetics ; },
abstract = {Mosquitoes take blood meals from a diverse range of host animals and their host associations vary by species. Characterizing these associations is an important element of the transmission dynamics of mosquito-vectored pathogens. To characterize mosquito host associations, various molecular techniques have been developed, which are collectively referred to as blood meal analysis. DNA barcoding has diverse biological applications and is well-suited to mosquito blood meal analysis. The standard DNA barcoding marker for animals is a 5' fragment of the cytochrome c oxidase I (COI) gene. A major advantage of this marker is its taxonomic coverage in DNA sequence reference databases, making it feasible to identify a wider range of mosquito host species than with any other gene. However, the COI gene contains high sequence variation at potential priming sites between vertebrate orders. Coupled with the need for primer sequences to be mismatched with mosquito priming sites so that annealing to mosquito DNA is inhibited, it can be difficult to design primers suitable for blood meal analysis applications. Several primers are available that perform well in mosquito blood meal analysis, annealing to priming sites for most vertebrate host taxa, but not to those of mosquitoes. Because priming site sequence variation among vertebrate taxa can cause amplification to fail, a hierarchical approach to DNA barcoding-based blood meal analysis can be applied. In such an approach, no single primer set is expected to be effective for 100% of potential host species. If amplification fails in the initial reaction, a subsequent reaction is attempted with primers that anneal to different priming sites, and so on, until amplification is successful.},
}
@article {pmid37458477,
year = {2023},
author = {Zhi, S and Zhang, X and Zhang, J and Wang, XY and Bi, S},
title = {Functional Nucleic Acids-Engineered Bio-Barcode Nanoplatforms for Targeted Synergistic Therapy of Multidrug-Resistant Cancer.},
journal = {ACS nano},
volume = {17},
number = {14},
pages = {13533-13544},
doi = {10.1021/acsnano.3c02009},
pmid = {37458477},
issn = {1936-086X},
mesh = {Humans ; Drug Resistance, Multiple ; *DNA, Catalytic ; *Zinc Oxide ; Drug Resistance, Neoplasm ; *Prodrugs/pharmacology ; *Nanoparticles ; *Lung Neoplasms ; Cell Line, Tumor ; },
abstract = {Rational design of multifunctional nanomedicines has revolutionized the therapeutic efficacy of cancers. Herein, we have constructed the functional nucleic acids (FNAs)-engineered nanoplatforms based on the concept of a bio-barcode (BBC) for synergistic targeted therapy of multidrug-resistant (MDR) cancer. In this study, the platinum(IV) prodrug is synthesized to covalently link two kinds of FNAs at a rational ratio to fabricate three-dimensional BBC-like DNA nanoscaffolds, accompanied by the one-pot encapsulation of ZnO nanoparticles (NPs) through electrostatic interaction. The multivalent AS1411 aptamers equipped in ZnO@BBCs facilitate specific and efficient endocytosis into MDR human lung adenocarcinoma cells (A549/DDP). In response to the intracellular environment of A549/DDP cells, such as the lysosome-acidic pH and overexpressed GSH, the ZnO NPs are degraded into Zn[2+] ions for generating reactive oxygen species (ROS), while the Pt(IV) prodrugs are reduced into Pt(II) active species by glutathione (GSH), followed by the release of therapeutic DNAzymes for chemotherapy and gene therapy. In particular, the designed system plays an important role in remodeling the intracellular environment to reverse cancer MDR. On the one hand, the depletion of GSH promotes the downregulation of glutathione peroxidase 4 (GPX4) for amplifying oxidative stress and increasing lipid peroxidation (LPO), resulting in the activation of ferroptosis. On the other hand, the silence of early growth response protein 1 (Egr-1) mRNA by Zn[2+]-dependent DNAzymes directly inhibits the proliferation and migration of MDR cells, which further suppresses the P-glycoprotein (P-gp)-mediated drug efflux. Thus, the proposed nanoplatforms show great promise for the development of versatile therapeutic tools and personalized nanomedicines for MDR cancers.},
}
@article {pmid37454710,
year = {2023},
author = {Pramual, P and Jumpato, W and Adler, PH},
title = {Fast-evolving nuclear genes as barcoding markers for black flies (Diptera: Simuliidae) in Thailand.},
journal = {Acta tropica},
volume = {246},
number = {},
pages = {106988},
doi = {10.1016/j.actatropica.2023.106988},
pmid = {37454710},
issn = {1873-6254},
mesh = {Humans ; Animals ; *Simuliidae/genetics ; Thailand ; Phylogeny ; Larva/genetics ; Electron Transport Complex IV/genetics ; },
abstract = {Rapid and accurate identification is a prerequisite for the study of all aspects of species, particularly for pests and vectors. Black flies are economically significant blood-sucking insects, as many species are pests and vectors that transmit parasites to humans and other animals. We examined the efficiency of two fast-evolving nuclear genes, elongator complex protein 1 (ECP1) and big zinc finger (BZF), for identifying 13 nominal species in three species-groups of black flies, the Simulium multistriatum, S. striatum, and S. tuberosum groups, in Thailand where the mitochondrial cytochrome c oxidase I (COI) gene has not been successful for differentiating many nominal species. ECP1 gene sequences were highly effective for identification, with >96% (181 of 188) of the specimens correctly identified. Unsuccessful identifications based on ECP1 were between S. nakhonense and S. chiangmaiense, which are members of the S. striatum species-group, whereas all identifications of nominal species of the S. multistriatum and S. tuberosum species-groups were successful. In contrast, BZF had successful rates for the S. striatum species-group, with >93% (71 of 76) of the specimens correctly identified. This gene also successfully assigned unknown larvae of the S. striatum group to species. Phylogenetic analyses and molecular species delimitations based on the BZF gene uncovered cryptic diversity in two nominal species, S. nakhonense and S. wangkwaiense, which will require resolution through further study.},
}
@article {pmid37453628,
year = {2024},
author = {Hazarika, S and Hemalatha, S},
title = {Quality control assessment, toxicity profiling, and experimental validation of network pharmacology-predicted anti-inflammatory potential of Natsiatum herpeticum Buch.-Ham. Ex Arn.},
journal = {Journal of ethnopharmacology},
volume = {318},
number = {Pt A},
pages = {116902},
doi = {10.1016/j.jep.2023.116902},
pmid = {37453628},
issn = {1872-7573},
mesh = {Rats ; Animals ; *Network Pharmacology ; *Plant Extracts/toxicity/therapeutic use ; Ethnopharmacology ; Water ; Anti-Inflammatory Agents/therapeutic use/toxicity ; },
abstract = {Natsiatum herpticum Buch.-Ham. Ex Arn., a least-explored plant, is being considered a wild edible plant by the Bankariya community of Nepal and the Mishing, Sonowal Kachari, and several ethnic groups in the north-east region of India. It is also used as a traditional remedy for the treatment of pain and inflammation-associated conditions like cuts and wounds, stomach ache, backache, and headache as a practice of a folkloristic system of medicine. In spite of several previous publications suggesting its use by different tribes, no documentation or scientific approaches have been made hitherto to validate its ethnopharmacological claims.<br><br>AIM OF STUDY: The study aimed at the botanical quality control assessment, toxicity profiling, and network pharmacology-assisted experimental validation of the anti-inflammatory potential of the aqueous extract of N. herpeticum to fill the lacunae in the current knowledge.<br><br>MATERIAL AND METHOD: Plant material was authenticated using a classical taxonomical approach and DNA barcoding. The quality control methods, acute toxicity study, and repeated dose 28-day oral toxicity study were performed as per standard guidelines. QToF-MS analysis, drug-likeness properties, network pharmacology-based anti-inflammatory prediction, and in vitro assays were carried out.<br><br>RESULTS: Quality control assessment was done for the plant. Toxicity studies revealed the aqueous extract to be non-toxic when consumed for short periods at low doses. Alterations in food and water intake, biochemical parameters, and alterations in liver histology (n&#xa0;=&#xa0;2 female rats) implicate repeated exposure to high doses (2000&#xa0;mg/kg) that may possess deleterious effects, particularly in hepatic tissues. 21 representative compounds (14 drug-like molecules) were detected by QToF-MS analysis and then subjected to network pharmacology to predict anti-inflammatory effects. It was found that an anti-inflammatory effect may be exerted by modulating inflammatory pathways involving genes such as TNF, PTGS2, EGFR, STAT3, PPARG, PTGER4, PPARA, NOS2, TRPV1, and JAK2. Further, in vitro studies demonstrated plant extract to possess a good anti-inflammatory effect with IC50 values of 98.76, 85.73, and 96.16&#xa0;&#x3bc;g/ml in protein denaturation, proteinase inhibition, and haemolysis inhibition assays, respectively.<br><br>CONCLUSION: The plant extract was found to be safer at acute dose but may cause potential liver toxicity on prolonged use. The anti-inflammatory property predicted by network pharmacology was further supported by the positive results of in vitro experiments. In summary, to further establish the toxicity profile of this edible plant and its anti-inflammatory properties, chronic toxicity study and in vivo experiments are required.},
}
@article {pmid37453551,
year = {2023},
author = {Sergi, CM},
title = {Computer-assisted diagnostics.},
journal = {Contemporary clinical trials},
volume = {132},
number = {},
pages = {107296},
doi = {10.1016/j.cct.2023.107296},
pmid = {37453551},
issn = {1559-2030},
mesh = {Humans ; Computers ; *Diagnosis, Computer-Assisted ; },
abstract = {Healthcare is at the edge of a profound renovation or collapse due to the rapid inflow of machine learning protocols and procedures able to optimize several processes. Clinical trials are key for the progress of science and the correct interpretation of data. Rickard et al., in this journal, report that data on misidentification rates in medical trials are scarce. In five trials involving more than 800 blood or histology specimens examined, data clarification forms (DCFs) were issued for 21% of instances, and 67% were related to sample identification. The authors suggest that a suitable number of de- recognized data points is critical. Moreover, a formalized process involving the specimen accession employed in routine care is key to mitigate recognition errors and their potential profound impact on clinical research and outcome. We fully agree with the authors and their report is highly relevant today that we face transformation in healthcare. We suggest that 3D barcoding may mitigate several issues on misidentification.},
}
@article {pmid37450566,
year = {2023},
author = {Rifai, OM and O'Shaughnessy, J and Dando, OR and Munro, AF and Sewell, MDE and Abrahams, S and Waldron, FM and Sibley, CR and Gregory, JM},
title = {Distinct neuroinflammatory signatures exist across genetic and sporadic amyotrophic lateral sclerosis cohorts.},
journal = {Brain : a journal of neurology},
volume = {146},
number = {12},
pages = {5124-5138},
pmid = {37450566},
issn = {1460-2156},
support = {/WT_/Wellcome Trust/United Kingdom ; R01 NS127186/NS/NINDS NIH HHS/United States ; 5-R01-NS127186-02/GF/NIH HHS/United States ; 108890/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Amyotrophic Lateral Sclerosis/pathology ; Brain-Derived Neurotrophic Factor/genetics ; NF-kappa B ; *Neurodegenerative Diseases/genetics ; Dystonic Disorders ; Humans ; DNA Repeat Expansion ; C9orf72 Protein/genetics ; *Frontotemporal Dementia/genetics ; },
abstract = {Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by progressive loss of upper and lower motor neurons. ALS is on a pathogenetic disease spectrum with frontotemporal dementia, referred to as ALS-frontotemporal spectrum disorder (ALS-FTSD). For mutations associated with ALS-FTSD, such as the C9orf72 hexanucleotide repeat expansion, the molecular factors associated with heterogeneity along this spectrum require further characterization. Here, using a targeted NanoString molecular barcoding approach, we interrogate neuroinflammatory dysregulation and heterogeneity at the level of gene expression in post-mortem motor cortex tissue from a cohort of clinically heterogeneous C9-ALS-FTSD cases. We identified 20 dysregulated genes in C9-ALS-FTSD, with enrichment of microglial and inflammatory response gene sets. Two genes with significant correlations to available clinical metrics were selected for validation: FKBP5, a correlate of cognitive function, and brain-derived neurotrophic factor (BDNF), a correlate of disease duration. FKBP5 and its signalling partner, NF-κB, appeared to have a cell type-specific staining distribution, with activated (i.e. nuclear) NF-κB immunoreactivity in C9-ALS-FTSD. Expression of BDNF, a correlate of disease duration, was confirmed to be higher in individuals with long compared to short disease duration using BaseScope™ in situ hybridization. Our analyses also revealed two distinct neuroinflammatory panel signatures (NPS), NPS1 and NPS2, delineated by the direction of expression of proinflammatory, axonal transport and synaptic signalling pathways. We compared NPS between C9-ALS-FTSD cases and those from sporadic ALS and SOD1-ALS cohorts and identified NPS1 and NPS2 across all cohorts. Moreover, a subset of NPS was also able to separate publicly available RNA sequencing data from independent C9-ALS and sporadic ALS cohorts into two inflammatory subgroups. Importantly, NPS subgroups did not clearly segregate with available demographic, genetic, clinical or pathological features, highlighting the value of molecular stratification in clinical trials for inflammatory subgroup identification. Our findings thus underscore the importance of tailoring therapeutic approaches based on distinct molecular signatures that exist between and within ALS-FTSD cohorts.},
}
@article {pmid37448846,
year = {2023},
author = {Kusmita, L and Nur Prasetyo Edi, A and Dwi Franyoto, Y and Mutmainah, and Haryanti, S and Dwi Retno Nurcahyanti, A},
title = {Sun protection and antibacterial activities of carotenoids from the soft coral Sinularia sp. symbiotic bacteria from Panjang Island, North Java Sea.},
journal = {Saudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society},
volume = {31},
number = {8},
pages = {101680},
pmid = {37448846},
issn = {1319-0164},
abstract = {Carotenoids have shown beneficial applications in cosmetology, pharmacology, and medicine. However, environmental stress in the marine environment can trigger the production of unique secondary metabolites, such as carotenoids. These compounds can also be sustainably produced by symbiotic bacteria. We hypothesized that the soft corals in tropical regions may produce diverse biological secondary metabolites, including carotenoids, both by the host organism and their bacterial symbiont. The unique carotenoids may provide promising biological activity such as antioxidant, UV photoprotector, and antibacterial activities. To this end, we isolated and characterized the carotenoids isolated from the bacterial symbiont of Sinularia sp., a soft coral from Panjang Island, North Java Sea, strain 19. PP.Sc.13. Bacterial identification was performed using DNA barcoding of the 16S rRNA region. Identification of carotenoids was carried out using a spectrophotometer, High-Performance Liquid Chromatography (HPLC), and attenuated total reflection fourier-transformed infrared (ATR-FTIR) spectroscopy. The antioxidant activity was estimated using the diphenylpicrylhydrazyl (DPPH) method, while the Sun Protection Factor (SPF) and % transmission of erythema and pigmentation were determined based on colorimetric methods. The antibacterial activity assay was carried out using the agar diffusion method against two multidrug-resistant bacteria. The bacterial symbiont was identified as Virgibacillus sp. and the carotenoids isolated from this symbiont exhibited significant antioxidant activity and extra sun protection effect, thus categorized as UVA sunblock. Furthermore, the isolated carotenoids exhibited antibacterial activities against Methicillin Resistant-Staphylococcus aureus (MRSA) and Multidrug-resistant (MDR) Escherichia coli. This study provides evidence of the carotenoids produced by the soft coral bacterial symbiont Virgibacillus sp., which may be used as an antioxidant, sun protection, and antibacterial agent. Further investigation of the de novo biological production of carotenoids by Virgibacillus sp. is warranted.},
}
@article {pmid37448693,
year = {2023},
author = {Chimeno, C and Schmidt, S and Hamid, H and Narakusumo, RP and Peggie, D and Balke, M and Cancian de Araujo, B},
title = {DNA barcoding data release for the Phoridae (Insecta, Diptera) of the Halimun-Salak National Park (Java, Indonesia).},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e104942},
pmid = {37448693},
issn = {1314-2828},
abstract = {Launched in 2015, the large-scale initiative Indonesian Biodiversity Discovery and Information System (IndoBioSys) is a multidisciplinary German-Indonesian collaboration with the main goal of establishing a standardised framework for species discovery and all associated steps. One aspect of the project includes the application of DNA barcoding for species identification and biodiversity assessments. In this framework, we conducted a large-scale assessment of the insect fauna of the Mount Halimun-Salak National Park which is one of the largest tropical rain-forest ecosystems left in West Java. In this study, we present the results of processing 5,034 specimens of Phoridae (scuttle flies) via DNA barcoding. Despite limited sequencing success, we obtained more than 500 clusters using different algorithms (RESL, ASAP, SpeciesIdentifier). Moreover, Chao statistics indicated that we drastically undersampled all trap sites, implying that the true diversity of Phoridae is, in fact, much higher. With this data release, we hope to shed some light on the hidden diversity of this megadiverse group of flies.},
}
@article {pmid37447960,
year = {2023},
author = {Gómez-Cárdenes, &#xd3; and Marichal-Hernández, JG and Son, JY and Pérez Jiménez, R and Rodríguez-Ramos, JM},
title = {An Encoder-Decoder Architecture within a Classical Signal-Processing Framework for Real-Time Barcode Segmentation.},
journal = {Sensors (Basel, Switzerland)},
volume = {23},
number = {13},
pages = {},
pmid = {37447960},
issn = {1424-8220},
support = {Catalina Ruiz training aid program for research personnel//Regional Ministry of Economy, Knowledge, and Employment, as well as the European Social Fund/ ; Estrategia de Especializaci&#xf3;n inteligente de Canarias RIS-3, ProID2020010066//Government of the Canary Islands, and European Regional Development Fund/ ; Research agreement on consumer electronics Wooptix-ULL, 2023//Wooptix, S.L./ ; NRF-2018R1A6A1A03025542//Priority Research Centers Program through the National Research Foundation of Korea (NRF), Ministry of Education/ ; },
mesh = {*Algorithms ; *Image Processing, Computer-Assisted/methods ; Neural Networks, Computer ; },
abstract = {In this work, two methods are proposed for solving the problem of one-dimensional barcode segmentation in images, with an emphasis on augmented reality (AR) applications. These methods take the partial discrete Radon transform as a building block. The first proposed method uses overlapping tiles for obtaining good angle precision while maintaining good spatial precision. The second one uses an encoder-decoder structure inspired by state-of-the-art convolutional neural networks for segmentation while maintaining a classical processing framework, thus not requiring training. It is shown that the second method's processing time is lower than the video acquisition time with a 1024 × 1024 input on a CPU, which had not been previously achieved. The accuracy it obtained on datasets widely used by the scientific community was almost on par with that obtained using the most-recent state-of-the-art methods using deep learning. Beyond the challenges of those datasets, the method proposed is particularly well suited to image sequences taken with short exposure and exhibiting motion blur and lens blur, which are expected in a real-world AR scenario. Two implementations of the proposed methods are made available to the scientific community: one for easy prototyping and one optimised for parallel implementation, which can be run on desktop and mobile phone CPUs.},
}
@article {pmid37446706,
year = {2023},
author = {Hu, Q and Pan, Y and Xia, H and Yu, K and Yao, Y and Guan, F},
title = {Species Identification of Caviar Based on Multiple DNA Barcoding.},
journal = {Molecules (Basel, Switzerland)},
volume = {28},
number = {13},
pages = {},
pmid = {37446706},
issn = {1420-3049},
support = {No. CY2022112//Zhejiang Market Supervision Bureau Project/ ; No. LGC22C060001//Zhejiang Public Welfare Technology Application Research Project/ ; No. 2022C31059//Zhoushan Science and Technology Bureau Project/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *DNA, Mitochondrial/genetics ; Fishes/genetics ; Polymerase Chain Reaction/methods ; DNA Primers ; },
abstract = {This study aimed to explore the applicability of DNA barcoding for assessing the authenticity of caviar on the Chinese market. A set of universal COI primers and two sets of designed primers based on COI and D-loop genes were used to identify maternal species of samples from 21 batches of caviar. The results showed that the PCR products from three sets of primers had more than 98% similarity to the sequences in database. The COI gene could not distinguish sturgeons with closed genetic relationships, while D-loop gene could effectively improve the accuracy of DNA barcoding and was more suitable to the identification of interspecific sturgeon than the COI gene. The neighbor-joining dendrogram further confirmed the applicability and accuracy of COI and D-loop genes in identifying maternal relatives of caviar (Acipenser baerii/Acipenser gueldenstaedtii/Acipenser schrenckii/Huso dauricus/Huso huso). Despite the limitations of mitochondrial DNA in identifying hybrid sturgeon species, the presence of counterfeit caviar of non-sturgeon ingredients could be excluded. All the caviar samples were identified successfully as sturgeon species, but the mislabeling rate of species was 33.4%, indicating that there were illegal phenomena such as disorderly labeling, mislabeling, and adulteration on the market.},
}
@article {pmid37443440,
year = {2023},
author = {Pan, K and Yao, Y and Zhang, Y and Gu, Y and Wang, Y and Ma, P and Hou, W and Yang, G and Zhang, S and Xu, H},
title = {Enolate-Azide [3 + 2]-Cycloaddition Reaction Suitable for DNA-Encoded Library Synthesis.},
journal = {Bioconjugate chemistry},
volume = {34},
number = {8},
pages = {1459-1466},
doi = {10.1021/acs.bioconjchem.3c00235},
pmid = {37443440},
issn = {1520-4812},
mesh = {Cycloaddition Reaction ; *Azides ; Catalysis ; *Copper ; Alkynes ; DNA ; },
abstract = {The DNA-encoded chemical library (DEL) is a powerful hit selection technique in either basic science or innovative drug discovery. With the aim to circumvent the issue concerning DNA barcode damage in a conventional on-DNA copper-catalyzed azide-alkyne cycloaddition reaction (CuAAC), we have successfully developed the first DNA-compatible enolate-azide [3 + 2] cycloaddition reaction. The merits of this DEL chemistry include metal-free reaction and high DNA fidelity, high conversions and easy operation, broad substrate scope, and ready access to the highly substituted 1,4,5-trisubstituted triazoles. Thus, it will not only further enrich the DEL chemistry toolbox but also will have great potential in practical DEL synthesis.},
}
@article {pmid37441047,
year = {2023},
author = {Hill, B and Abraham, S and Akhtar, A and Selvaggio, G and Tschulik, K and Kruss, S},
title = {Surfactant assisted exfoliation of near infrared fluorescent silicate nanosheets.},
journal = {RSC advances},
volume = {13},
number = {30},
pages = {20916-20925},
pmid = {37441047},
issn = {2046-2069},
abstract = {Fluorophores that emit light in the near infrared (NIR) are advantageous in photonics and imaging due to minimal light scattering, absorption, phototoxicity and autofluorescence in this spectral region. The layered silicate Egyptian blue (CaCuSi4O10) emits as a bulk material bright and stable fluorescence in the NIR and is a promising NIR fluorescent material for (bio)photonics. Here, we demonstrate a surfactant-based (mild) exfoliation procedure to produce nanosheets (EB-NS) of high monodispersity, heights down to 1 nm and diameters <20 nm in large quantities. The approach combines planetary ball milling, surfactant assisted bath sonication and centrifugation steps. It avoids the impurities that are typical for the harsh conditions of tip-sonication. Several solvents and surfactants were tested and we found the highest yield for sodium dodecyl benzyl sulfate (SDBS) and water. The NIR fluorescence emission (λem ≈ 930-940 nm) is not affected by this procedure, is extremely stable and is not affected by quenchers. This enables the use of EB-NS for macroscopic patterning/barcoding of materials in the NIR. In summary, we present a simple and mild route to NIR fluorescent nanosheets that promise high potential as NIR fluorophores for optical applications.},
}
@article {pmid37439995,
year = {2023},
author = {Foley, MM},
title = {Next-Generation Sequencing: ForenSeq™ DNA Signature Prep Kit with the Illumina MiSeq FGx.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2685},
number = {},
pages = {397-427},
pmid = {37439995},
issn = {1940-6029},
mesh = {*DNA Fingerprinting/methods ; *Microsatellite Repeats/genetics ; Reproducibility of Results ; High-Throughput Nucleotide Sequencing/methods ; Polymorphism, Single Nucleotide ; DNA Primers ; Sequence Analysis, DNA ; },
abstract = {Sequencing forensic DNA samples that are amplified and prepared with the ForenSeq™ DNA Signature Prep Kit allows for the simultaneous targeting of forensically relevant STR and SNP markers. The MiSeq™ FGx system allows massively parallel sequencing of these markers in a single analysis. The library preparation targets autosomal, Y-, and X-STRs, as well as identity SNPs. The kit can also be used to generate investigative information regarding the DNA contributor by analyzing phenotypic SNPs to predict hair color, eye color, and ancestry SNPs.Through two rounds of amplification, all loci are amplified and tagged with individualizing barcodes for sequencing capture and identification. Using bead-based technology, the libraries are purified by the removal of left-over amplification reagents and then normalized to ensure equal representation of all samples during sequencing. The individual libraries are then pooled for insertion into the MiSeq FGx. The pooled libraries are then added to a pre-packaged cartridge that contains all reagents necessary for optimal sequencing. Libraries are captured on a flow cell and undergo bridge amplification for the generation of individual clusters. Sequencing of each cluster is performed using a Sequence-By-Synthesis technology. The following chapter describes the methodology and process of library preparation of samples using the ForenSeq™ DNA Signature Prep Kit Primer Set A and B. Once completed, the chapter then focuses on the setup of a sequencing run on the MiSeq FGx and the sequencing methodology employed by the instrument.},
}
@article {pmid37439785,
year = {2023},
author = {Shao, X and Zhang, H and Zhu, Z and Ji, F and He, Z and Yang, Z and Xia, Y and Cai, Z},
title = {DpCoA tagSeq: Barcoding dpCoA-Capped RNA for Direct Nanopore Sequencing via Maleimide-Thiol Reaction.},
journal = {Analytical chemistry},
volume = {95},
number = {29},
pages = {11124-11131},
pmid = {37439785},
issn = {1520-6882},
mesh = {Animals ; Mice ; *Nanopore Sequencing ; *Nanopores ; RNA Caps/genetics/metabolism ; Coenzyme A ; Maleimides ; },
abstract = {Recent discoveries of noncanonical RNA caps, such as nicotinamide adenine dinucleotide (NAD[+]) and 3'-dephospho-coenzyme A (dpCoA), have expanded our knowledge of RNA caps. Although dpCoA has been known to cap RNAs in various species, the identities of its capped RNAs (dpCoA-RNAs) remained unknown. To fill this gap, we developed a method called dpCoA tagSeq, which utilized a thiol-reactive maleimide group to label dpCoA cap with a tag RNA serving as the 5' barcode. The barcoded RNAs were isolated using a complementary DNA strand of the tag RNA prior to direct sequencing by nanopore technology. Our validation experiments with model RNAs showed that dpCoA-RNA was efficiently tagged and captured using this protocol. To confirm that the tagged RNAs are capped by dpCoA and no other thiol-containing molecules, we used a pyrophosphatase NudC to degrade the dpCoA cap to adenosine monophosphate (AMP) moiety before performing the tagSeq protocol. We identified 44 genes that transcribe dpCoA-RNAs in mouse liver, demonstrating the method's effectiveness in identifying and characterizing the capped RNAs. This strategy provides a viable approach to identifying dpCoA-RNAs that allows for further functional investigations of the cap.},
}
@article {pmid37437570,
year = {2023},
author = {Horns, F and Martinez, JA and Fan, C and Haque, M and Linton, JM and Tobin, V and Santat, L and Maggiolo, AO and Bjorkman, PJ and Lois, C and Elowitz, MB},
title = {Engineering RNA export for measurement and manipulation of living cells.},
journal = {Cell},
volume = {186},
number = {17},
pages = {3642-3658.e32},
pmid = {37437570},
issn = {1097-4172},
support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 EB030015/EB/NIBIB NIH HHS/United States ; R01 MH116508/MH/NIMH NIH HHS/United States ; },
mesh = {Animals ; Biological Transport ; Mammals/metabolism ; *RNA/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Viruses/genetics ; Molecular Typing ; Sequence Analysis, RNA ; *Cytological Techniques ; *Genetic Techniques ; },
abstract = {A system for programmable export of RNA molecules from living cells would enable both non-destructive monitoring of cell dynamics and engineering of cells capable of delivering executable RNA programs to other cells. We developed genetically encoded cellular RNA exporters, inspired by viruses, that efficiently package and secrete cargo RNA molecules from mammalian cells within protective nanoparticles. Exporting and sequencing RNA barcodes enabled non-destructive monitoring of cell population dynamics with clonal resolution. Further, by incorporating fusogens into the nanoparticles, we demonstrated the delivery, expression, and functional activity of exported mRNA in recipient cells. We term these systems COURIER (controlled output and uptake of RNA for interrogation, expression, and regulation). COURIER enables measurement of cell dynamics and establishes a foundation for hybrid cell and gene therapies based on cell-to-cell delivery of RNA.},
}
@article {pmid37437013,
year = {2023},
author = {Chuctaya, J and Shibatta, OA and Encalada, AC and Barragán, KS and Torres, ML and Rojas, E and Ochoa-Herrera, V and Ferrer, J},
title = {Rediscovery of Rhyacoglanis pulcher (Boulenger, 1887) (Siluriformes: Pseudopimelodidae), a rare rheophilic bumblebee catfish from Ecuadorian Amazon.},
journal = {PloS one},
volume = {18},
number = {7},
pages = {e0287120},
pmid = {37437013},
issn = {1932-6203},
mesh = {Animals ; *Catfishes/genetics ; Ecuador ; Rivers ; },
abstract = {Rhyacoglanis pulcher is a rare Neotropical rheophilic bumblebee catfish known only from the type locality in the Cis-Andean Amazon region, Ecuador, and the type-species of the genus. So far, the three syntypes collected in 1880 were the only specimens unambiguously associated to the name R. pulcher available in scientific collections. Recently, a specimen was discovered in a fast-flowing stretch of the Villano river, a tributary of the Curaray river, Napo river basin, Ecuador, representing a new record after nearly 140 years. Here, we present this new record, identified by morphology, provide the DNA barcode sequence of the specimen, and propose why the species of Rhyacoglanis are scarce in zoological collections. Additionally, we discuss the intraspecific variation in the color pattern observed in R. pulcher.},
}
@article {pmid37434442,
year = {2023},
author = {Karahan, A},
title = {Tunicate Eco-Evo-Devo laboratory in IMS-METU.},
journal = {Genesis (New York, N.Y. : 2000)},
volume = {61},
number = {6},
pages = {e23536},
doi = {10.1002/dvg.23536},
pmid = {37434442},
issn = {1526-968X},
support = {//Orta Do&#x11f;u Teknik &#xdc;niversitesi/ ; ADEP-701-2023-11278//METU-BAP/ ; HDESP-701-2021-10817//METU-BAP/ ; TEZ-D-701-2021-10653//METU-BAP/ ; Y&#xd6;P-701-2018-2666//METU-BAP/ ; BAP-08-11-DPT2012K120880//DEKOSIM/ ; CA16203//Maristem Cost Action/ ; CA20102//MAF Cost Action/ ; },
mesh = {Humans ; Animals ; *Urochordata/genetics ; Universities ; Biological Evolution ; Biodiversity ; Middle East ; },
abstract = {I completed my undergraduate education in Atatürk University, Education Faculty, Biology Department. Then pursued my graduate education at the Biology Department of Mersin University. Both my master's and PhD theses were on the biological and population genetics features of various fish species. My initial encounter with tunicates dates back to my Postdoc at Israel Oceanographic and Limnologic Research Institute (IOLR) in 2011, where I was working on a DNA barcoding project. During that time, the entire institute was actively engaged in research on tunicates, and discussions during lunchtime often revolved around this fascinating group of organisms. Prof. Rinkevich usually only spoke seriously about tunicate biology but 1 day he told me "You know Botryllus schlosseri is riding horse in Black Sea coasts of Turkiye." I was totally surprised and was trying to understand the meaning of this comment from a scientific perspective. He then showed me the picture of a B. schlosseri colony attached to a seahorse. Following several more Postdoc experiences, I began working as a Principal Investigator at Institute of Marine Sciences, Middle East Technical University (IMS-METU) in 2017. Since then, my team and I have been working on tunicate biodiversity, evolutionary biology, genomics, DNA barcoding, metabarcoding, metabolomics, whole-body regeneration (WBR) and aging related pathways.},
}
@article {pmid37434121,
year = {2023},
author = {Haqnawaz, M and Niazi, AR and Khalid, AN},
title = {A study on the genus Candolleomyces (Agaricales: Psathyrellaceae) from Punjab, Pakistan.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {181},
pmid = {37434121},
issn = {1471-2180},
mesh = {*Agaricales ; Pakistan ; Phylogeny ; Sand ; Seafood ; },
abstract = {Many basidiomata of the genus Candolleomyces were found on sandy and loamy soil from the Indus Riverbed, Kot Addu District. A phylogenetic study was conducted to examine the occurrence of Candolleomyces sindhudeltae sp. nov. using a combination of ITS and LSU regions. Our morphological, anatomical, and phylogenetic studies indicated the novelty of Candolleomyces sindhudeltae sp. nov. The distinguishing features of C. sindhudeltae are convex to campanulate and areolate pileus with scalloped to cracked cap margins, branched, and pale reddish lamellae, greenish-brown ellipsoid to ovoid basidiospores, polymorphic cheilo, and caulocystidia. The novel taxa formed independent phylogenetic relationships within the genus Candolleomyces. The addition of our new species to the genus Candolleomyces makes us confident that the genus was separated from Psathyrella accurately.},
}
@article {pmid37432462,
year = {2023},
author = {Furusawa, H and Ikezawa, H and Tsujimoto, SG and Ichikawa-Seki, M and Waki, T},
title = {Introducing the land snail Bradybaena pellucida increased infection risk of the avian parasite Postharmostomum commutatum in the Kanto region of Japan.},
journal = {Parasitology research},
volume = {122},
number = {9},
pages = {2207-2216},
pmid = {37432462},
issn = {1432-1955},
mesh = {Animals ; *Parasites ; Japan/epidemiology ; Chickens ; *Trematoda/genetics ; Snails/parasitology ; Metacercariae ; *Trematode Infections/parasitology ; },
abstract = {The trematode Postharmostomum commutatum is a parasite of the chicken Gallus gallus domesticus. Its heavy infection can cause inflammation and hemorrhage in the cecum of host birds. We found a severe infection of metacercariae of P. commutatum, which was identified based on DNA barcodes with morphology, in the introduced land snail Bradybaena pellucida and its related species in the Kanto region of Japan. Our field survey revealed that metacercariae were detected in 14 of 69 sampling locations in this region. B. pellucida was thought to be the major second intermediate host of metacercariae of the trematode because this snail was most frequently found in the study area and the prevalence and infection intensity were higher than those of the other snail species. The observed increase in metacercariae in introduced populations of B. pellucida can enhance the infection risk of chickens and wild host birds, probably owing to the spillback effect. Our seasonal field study showed that the prevalence and infection intensity of metacercaria seemed to be high in populations of B. pellucida during the summer and early autumn. Therefore, chickens should not be bred outdoors during these seasons to prevent severe infection. Our molecular analysis, based on cytochrome c oxidase subunit I sequences, showed a significantly negative value for Tajima's D in P. commutatum, suggesting an increase in its population size. Thus, P. commutatum distributed in the Kanto region may have increased its population size with the introduction of the host snail.},
}
@article {pmid37430057,
year = {2023},
author = {Reynolds, DE and Galanis, G and Wang, Y and Ko, J},
title = {Single Extracellular Vesicle Analysis Using Droplet Microfluidics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2689},
number = {},
pages = {211-220},
pmid = {37430057},
issn = {1940-6029},
mesh = {Microfluidics ; *Extracellular Vesicles ; Antibodies ; Cell Communication ; *Nucleic Acids ; },
abstract = {Extracellular vesicles (EVs) are lipid-bound nanometer-sized vesicles released by all cell types that contain molecular payload such as proteins and/or nucleic acids. EVs are a key facet of cell-to-cell communication and have the potential to be used in the diagnosis of numerous diseases, chief among them being cancer. However, most methods of EV analysis struggle to identify the rare, malformed proteins indicative of tumor cells as tumor EVs represent only a tiny fraction of the bulk EVs present in the bloodstream. Here, we present a method of single EV analysis, utilizing droplet microfluidics to encapsulate EVs, which are labeled with DNA barcodes linked to antibodies, in droplets with the DNA extension used to amplify the signals associated with each EV. The amplified DNA can then be sequenced to assess the protein content of individual EVs, enabling the detection of rare proteins and EV subpopulations within a bulk EV sample.},
}
@article {pmid37424729,
year = {2023},
author = {Anukul, N and Jenjaroenpun, P and Sirikul, C and Wankaew, N and Nimsamer, P and Roothumnong, E and Pithukpakorn, M and Leetrakool, N and Wongsurawat, T},
title = {Ultrarapid and high-resolution HLA class I typing using transposase-based nanopore sequencing applied in pharmacogenetic testing.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1213457},
pmid = {37424729},
issn = {1664-8021},
abstract = {Nanopore sequencing has been examined as a method for rapid and high-resolution human leukocyte antigen (HLA) typing in recent years. We aimed to apply ultrarapid nanopore-based HLA typing for HLA class I alleles associated with drug hypersensitivity, including HLA-A*31:01, HLA-B*15:02, and HLA-C*08:01. Most studies have used the Oxford Nanopore Ligation Sequencing kit for HLA typing, which requires several enzymatic reactions and remains relatively expensive, even when the samples are multiplexed. Here, we used the Oxford Nanopore Rapid Barcoding kit, which is transposase-based, with library preparation taking less than 1 h of hands-on time and requiring minimal reagents. Twenty DNA samples were genotyped for HLA-A, -B, and -C; 11 samples were from individuals of different ethnicity and nine were from Thai individuals. Two primer sets, a commercial set and a published set, were used to amplify the HLA-A, -B, and -C genes. HLA-typing tools that used different algorithms were applied and compared. We found that without using several third-party reagents, the transposase-based method reduced the hands-on time from approximately 9 h to 4 h, making this a viable approach for obtaining same-day results from 2 to 24 samples. However, an imbalance in the PCR amplification of different haplotypes could affect the accuracy of typing results. This work demonstrates the ability of transposase-based sequencing to report 3-field HLA alleles and its potential for race- and population-independent testing at considerably decreased time and cost.},
}
@article {pmid37424544,
year = {2023},
author = {Gilroy, R and Adam, ME and Kumar, B and Pallen, MJ},
title = {An initial genomic blueprint of the healthy human oesophageal microbiome.},
journal = {Access microbiology},
volume = {5},
number = {6},
pages = {},
pmid = {37424544},
issn = {2516-8290},
abstract = {BACKGROUND: The oesophageal microbiome is thought to contribute to the pathogenesis of oesophageal cancer. However, investigations using culture and molecular barcodes have provided only a low-resolution view of this important microbial community. We therefore explored the potential of culturomics and metagenomic binning to generate a catalogue of reference genomes from the healthy human oesophageal microbiome, alongside a comparison set from saliva.<br><br>RESULTS: Twenty-two distinct colonial morphotypes from healthy oesophageal samples were genome-sequenced. These fell into twelve species clusters, eleven of which represented previously defined species. Two isolates belonged to a novel species, which we have named Rothia gullae. We performed metagenomic binning of reads generated from UK samples from this study alongside reads generated from Australian samples in a recent study. Metagenomic binning generated 136 medium or high-quality metagenome-assembled genomes (MAGs). MAGs were assigned to 56 species clusters, eight representing novel Candidatus species, which we have named Ca. Granulicatella gullae, Ca. Streptococcus gullae, Ca. Nanosynbacter quadramensis, Ca. Nanosynbacter gullae, Ca. Nanosynbacter colneyensis, Ca. Nanosynbacter norwichensis, Ca. Nanosynococcus oralis and Ca. Haemophilus gullae. Five of these novel species belong to the recently described phylum Patescibacteria . Although members of the Patescibacteria are known to inhabit the oral cavity, this is the first report of their presence in the oesophagus. Eighteen of the metagenomic species were, until recently, identified only by hard-to-remember alphanumeric placeholder designations. Here we illustrate the utility of a set of recently published arbitrary Latinate species names in providing user-friendly taxonomic labels for microbiome analyses.Our non-redundant species catalogue contained 63 species derived from cultured isolates or MAGs. Mapping revealed that these species account for around half of the sequences in the oesophageal and saliva metagenomes. Although no species was present in all oesophageal samples, 60 species occurred in at least one oesophageal metagenome from either study, with 50 identified in both cohorts.<br><br>CONCLUSIONS: Recovery of genomes and discovery of new species represents an important step forward in our understanding of the oesophageal microbiome. The genes and genomes that we have released into the public domain will provide a base line for future comparative, mechanistic and intervention studies.},
}
@article {pmid37422609,
year = {2023},
author = {Grostieta, E and Miranda-Caballero, CI and Sánchez-Montes, S and Colunga-Salas, P and González, CAL and Valderas-Muñoz, KD and Arciniega-Luna, G and Aguilar-Tipacamú, G},
title = {DNA barcoding and new records of Ornithodoros yumatensis from Central Mexico.},
journal = {Veterinary research communications},
volume = {47},
number = {4},
pages = {2339-2350},
pmid = {37422609},
issn = {1573-7446},
support = {FONDEC: FNB-2021-05.//Universidad Aut&#xf3;noma de Quer&#xe9;taro/ ; },
mesh = {Male ; Animals ; Female ; *Ornithodoros/genetics ; Mexico ; *Chiroptera/genetics ; DNA Barcoding, Taxonomic/veterinary ; Larva ; Phylogeny ; },
abstract = {Bats represent the second order of mammals with the highest number of species worldwide with over 1,616 species, and almost 10% of them are recorded in Mexico. These mammals have a great diversity of ectoparasites, in particular soft ticks of the genus Ornithodoros. Desmodus rotundus is one of the bat species that has scarcely been studied in terms of tick species richness in Mexico, with three tick species reported in five of the 32 Mexican states. For this reason, the aim of the present work was to identify ticks associated with D. rotundus from Central Mexico. Fieldwork was undertaken in the municipality El Marqués, Ejido Atongo A, Querétaro, Mexico. Bats were captured using mist nets and were visually inspected for tick presence. The ectoparasites were identified morphologically and molecularly with the use of mitochondrial markers 16SrDNA and cytochrome oxidase subunit I (COI). A total of 30 D. rotundus (1 female, 29 males) were captured, from which 20 larvae identified as Ornithodoros yumatensis were recovered. Molecular analysis confirmed the presence of this species with identity values of 99-100% with sequences of this species from the southwestern US, and the Yucatán Peninsula, Mexico. This is the first report of ticks associated with bats for the state of Querétaro, providing the first sequences of the COI gene from Mexican populations of O. yumatensis and shows an increase in the distribution of this soft tick across Central Mexico.},
}
@article {pmid37422553,
year = {2023},
author = {Ruvindy, R and Barua, A and Bolch, CJS and Sarowar, C and Savela, H and Murray, SA},
title = {Genomic copy number variability at the genus, species and population levels impacts in situ ecological analyses of dinoflagellates and harmful algal blooms.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {70},
pmid = {37422553},
issn = {2730-6151},
support = {FT12//Department of Education and Training | Australian Research Council (ARC)/ ; HDR Scholarship//University of Technology Sydney (University of Technology, Sydney)/ ; },
abstract = {The application of meta-barcoding, qPCR, and metagenomics to aquatic eukaryotic microbial communities requires knowledge of genomic copy number variability (CNV). CNV may be particularly relevant to functional genes, impacting dosage and expression, yet little is known of the scale and role of CNV in microbial eukaryotes. Here, we quantify CNV of rRNA and a gene involved in Paralytic Shellfish Toxin (PST) synthesis (sxtA4), in 51 strains of 4 Alexandrium (Dinophyceae) species. Genomes varied up to threefold within species and ~7-fold amongst species, with the largest (A. pacificum, 130 ± 1.3 pg cell[-1] /~127 Gbp) in the largest size category of any eukaryote. Genomic copy numbers (GCN) of rRNA varied by 6 orders of magnitude amongst Alexandrium (10[2]- 10[8] copies cell[-1]) and were significantly related to genome size. Within the population CNV of rRNA was 2 orders of magnitude (10[5] - 10[7] cell[-1]) in 15 isolates from one population, demonstrating that quantitative data based on rRNA genes needs considerable caution in interpretation, even if validated against locally isolated strains. Despite up to 30 years in laboratory culture, rRNA CNV and genome size variability were not correlated with time in culture. Cell volume was only weakly associated with rRNA GCN (20-22% variance explained across dinoflagellates, 4% in Gonyaulacales). GCN of sxtA4 varied from 0-10[2] copies cell[-1], was significantly related to PSTs (ng cell[-1]), displaying a gene dosage effect modulating PST production. Our data indicate that in dinoflagellates, a major marine eukaryotic group, low-copy functional genes are more reliable and informative targets for quantification of ecological processes than unstable rRNA genes.},
}
@article {pmid37415718,
year = {2023},
author = {Ceríaco, LMP and Marques, MP and de Sousa, ACA and Veríssimo, J and Beja, P and Ferreira, S},
title = {Illustrated keys and a DNA barcode reference library of the amphibians and terrestrial reptiles (Amphibia, Reptilia) of São Tomé and Príncipe (Gulf of Guinea, West Africa).},
journal = {ZooKeys},
volume = {1168},
number = {},
pages = {41-75},
pmid = {37415718},
issn = {1313-2989},
abstract = {The herpetofauna of São Tomé and Príncipe consists of nine species of amphibians, all endemic, and 21 species of terrestrial reptiles, of which 17 are endemic. Our current knowledge regarding its natural history, ecology, and distribution is limited. Here two important tools are provided to support researchers, conservationists, and local authorities in the identification of the country's herpetofauna: an illustrated key to the herpetofauna of the two islands and surroundings islets and a DNA barcode reference library. The keys allow a rapid and unambiguous morphological identification of all occurring species. The DNA barcodes for the entire herpetofauna of the country were produced from 79 specimens, all of which are deposited in museum collections. The barcodes generated are available in online repositories and can be used to provide unambiguous molecular identification of most of the species. Future applications and use of these tools are briefly discussed.},
}
@article {pmid37415714,
year = {2023},
author = {Seropian, A and Arsenashvili, E and Bulbulashvili, N and Shubashishvili, A and Iankoshvili, G and Todua, M and Ananiashvili, A and Japarashvili, S and Chkhartisvhili, T and Memishishi, A and Balkhamishvili, S and Chitadze, B and Karalashvili, E and Mumladze, L and Hein, N and Rulik, B},
title = {Into the unknown: the first barcode-assisted checklist of Psocoptera (Insecta, Psocodea) of Georgia with a census on country species richness.},
journal = {ZooKeys},
volume = {1168},
number = {},
pages = {77-105},
pmid = {37415714},
issn = {1313-2989},
abstract = {This checklist reports 47 species of Psocoptera from 15 families and three suborders from Georgia, of which 31 species are recorded for the first time, increasing the known fauna of the country by more than 65%. Of these, 37 species have been barcoded, representing 210 Barcode Identification Numbers (BINs). An additional 14 species are expected to occur in Georgia but remain undiscovered, meaning that only ≈ 77% of the fauna is currently documented. Barcodes, comments on distributions, and images of voucher specimens are given followed by a map of the sampling sites.},
}
@article {pmid37415642,
year = {2023},
author = {Shen, F and Bai, X and Li, L and Fan, X and Song, Y and Yu, M and Cui, M and Jiang, S and Li, Z and Zhao, J and Shi, S},
title = {DBALM: A novel method for identifying ornamental flowering plants based on DNA barcodes-leaf morphology.},
journal = {Ecology and evolution},
volume = {13},
number = {7},
pages = {e10250},
pmid = {37415642},
issn = {2045-7758},
abstract = {Whereas the presence of flowers on ornamental flowering plants is essential for their identification via traditional methods, ornamental flowering plants cannot be reliably identified in non-flowering stages likewise. Here, DBALM (DNA Barcodes-Leaf Morphology), a new approach that combines DNA barcoding data with micromorphological features of the leaf epidermis and that is not limited by the flowering stage, was used to identify 16 evergreen rhododendron cultivars. First, the sequences of DNA barcodes, ITS, matK, psbA-trnH, and rbcL, were obtained from the DNA of leaves. Phylogenetic analysis was conducted to clarify the groupings among all the samples based on the four markers. Then, microscopic features of the leaf epidermis were used to further distinguish individuals from the same clade. DNA barcoding permitted the 16 cultivars to be divided into eight groups. The microscopic features of the leaf epidermis permitted cultivars within the same clade to be distinguished. The matK + psbA-trnH combination was the most effective barcode combination in this study. In addition, the new primer matK-Rh_R was designed, and it increased the amplification rate of evergreen rhododendron cultivars to 100%. In sum, DBALM was capable of accurately identifying the 16 evergreen rhododendron cultivars using data collected from a single leaf in the vegetative growth stage. This method can greatly facilitate the identification and breeding of ornamental flowering plants.},
}
@article {pmid37415354,
year = {2023},
author = {Trinh, QP and Le, TML and Nguyen, TD and Nguyen, HT},
title = {Morphologic, Morphometric, and Molecular Characterization of Vietnamese Populations of Meloidogyne incognita.},
journal = {Plant disease},
volume = {107},
number = {12},
pages = {3693-3700},
doi = {10.1094/PDIS-04-23-0818-SR},
pmid = {37415354},
issn = {0191-2917},
mesh = {Animals ; *Tylenchoidea/genetics ; Plant Diseases/genetics ; Vietnam ; RNA, Ribosomal, 28S/genetics ; Phylogeny ; DNA, Mitochondrial ; },
abstract = {Meloidogyne incognita is considered the most damaging and common root-knot nematode to numerous host plants worldwide. During a survey of nematodes in Vietnam, 1,106 samples from 22 different plant species were collected. M. incognita was recorded on 13 of the 22 host plants. Four populations of M. incognita from four host plants were chosen for comparison and confirmation of their morphologic, morphometric, and molecular characteristics. Genetically based phylogenetic trees were constructed to show relationships among root-knot nematodes. Molecular barcodes of four gene regions, ITS, D2-D3 of 28S rRNA, COI, and Nad5 mtDNA, integrated with morphologic and morphometric data were used as reliable references for molecular identification of M. incognita. Our analyses indicated that tropical root-knot nematodes are very similar in characterization of ITS, D2-D3 of 28S rRNA, and COI regions. However, these gene regions can be used to separate the tropical root-knot nematode group from other groups. On the other hand, the analysis of Nad5 mtDNA and multiplex-PCR with specific primers can be used to distinguish tropical species.},
}
@article {pmid37414208,
year = {2023},
author = {Geraerts, M and Huyse, T and Barson, M and Bassirou, H and Bilong Bilong, CF and Bitja Nyom, AR and Manda, AC and Cruz-Laufer, AJ and Kabalika, CK and Kasembele, GK and Bukinga, FM and Njom, S and Van Steenberge, M and Artois, T and Vanhove, MPM},
title = {Sharing is caring? Barcoding suggests co-introduction of dactylogyrid monogeneans with Nile tilapia and transfer towards native tilapias in sub-Saharan Africa.},
journal = {International journal for parasitology},
volume = {53},
number = {13},
pages = {711-730},
doi = {10.1016/j.ijpara.2023.05.007},
pmid = {37414208},
issn = {1879-0135},
mesh = {Animals ; *Tilapia/parasitology ; *Cichlids/parasitology ; Ecosystem ; *Fish Diseases/parasitology ; Gills/parasitology ; *Trematoda/genetics ; Introduced Species ; Africa South of the Sahara ; },
abstract = {Invasive Nile tilapias negatively impact native tilapia species through hybridisation and competition. However, the co-introduction of parasites with Nile tilapia, and subsequent changes in parasite communities, are scarcely documented. Monogeneans are known pathogens of cultured Nile tilapia, although little is known about their fate once Nile tilapias establish in new ecosystems. We investigate the parasitological consequences of Nile tilapia introduction on native tilapias in basins in Cameroon, the Democratic Republic of the Congo (DRC), and Zimbabwe, focusing on ectoparasitic dactylogyrids (Monogenea). Using the mitochondrial cytochrome oxidase c subunit I (COI) and nuclear 18S-internal transcribed spacer 1 (18S-ITS1) rDNA region of 128 and 166 worms, respectively, we evaluated transmission of several dactylogyrid species. Parasite spillover from Nile tilapia was detected for Cichlidogyrus tilapiae to Coptodon guineensis in Cameroon, Cichlidogyrus thurstonae to Oreochromis macrochir in the DRC, and Cichlidogyrus halli and C. tilapiae to Coptodon rendalli in Zimbabwe. Parasite spillback to Nile tilapia was detected for Cichlidogyrus papernastrema and Scutogyrus gravivaginus from Tilapia sparrmanii and Cichlidogyrus dossoui from C. rendalli or T. sparrmanii in the DRC, and Cichlidogyrus chloeae from Oreochromis cf. mortimeri and S. gravivaginus from O. macrochir in Zimbabwe. 'Hidden' transmissions (i.e. transmission of certain parasite lineages of species that are naturally present on both alien and native hosts) were detected for C. tilapiae and Scutogyrus longicornis between Nile tilapia and Oreochromis aureus and C. tilapiae between Nile tilapia and Oreochromis mweruensis in the DRC, and Cichlidogyrus sclerosus and C. tilapiae between Nile tilapia and O. cf. mortimeri in Zimbabwe. A high density of Nile tilapia occurring together with native tilapias, and the broad host range and/or environmental tolerance of the transmitted parasites, are proposed as factors behind parasite transmission through ecological fitting. However, continuous monitoring and the inclusion of environmental variables are necessary to understand the long-term consequences of these transmissions on native tilapias and to elucidate other underlying factors influencing these transmissions.},
}
@article {pmid37408588,
year = {2023},
author = {Maloney, B and Ramos, EA and Bennice, CO and Young, F and Magnasco, MO},
title = {Genetic confirmation of Octopus insularis (Leite and Haimovici, 2008) in South Florida, United States using physical features and de novo genome assembly.},
journal = {Frontiers in physiology},
volume = {14},
number = {},
pages = {1162807},
pmid = {37408588},
issn = {1664-042X},
abstract = {The distribution of octopuses within the Octopus vulgaris species complex remains inadequately understood. Species determination can be complex and involves characterizing a specimen's physical features and comparing its genetic makeup to other populations. In this study, we present the first genetic confirmation of Octopus insularis (Leite and Haimovici, 2008) inhabiting the coastal waters of the Florida Keys, United States. We employed visual observations to identify species-specific body patterns of three wild-caught octopuses and used de novo genome assembly to confirm their species. All three specimens exhibited a red/white reticulated pattern on their ventral arm surface. Two specimens displayed body pattern components of deimatic display (white eye encircled by a light ring, with darkening around the eye). All visual observations were consistent with distinguishing features of O. insularis. We then compared mitochondrial subunits COI, COIII, and 16S in these specimens across all available annotated octopod sequences, including Sepia apama (Hotaling et al., 2021) as a control outgroup taxon. For species exhibiting intraspecific genomic variation, we included multiple sequences from geographically distinct populations. Laboratory specimens consistently clustered into a single taxonomic node with O. insularis. These findings confirm O. insularis presence in South Florida and suggest a more extensive northern distribution than previously assumed. Whole genome Illumina sequencing of multiple specimens enabled taxonomic identification with well-established DNA barcodes while also generating the first de novo full assembly of O. insularis. Furthermore, constructing and comparing phylogenetic trees for multiple conserved genes is essential for confirming the presence and delineation of cryptic species in the Caribbean.},
}
@article {pmid37405277,
year = {2023},
author = {Zhou, M and Zhang, C and Chen, M and Hu, Z and Li, M and Li, Z and Wu, L and Liang, D},
title = {A protospacer adjacent motif-free, multiplexed, and quantitative nucleic acid detection platform with barcode-based Cas12a activity.},
journal = {MedComm},
volume = {4},
number = {4},
pages = {e310},
pmid = {37405277},
issn = {2688-2663},
abstract = {Clustered regularly interspaced short palindromic repeat (CRISPR)-based biosensors have been developed to facilitate the rapid and sensitive detection of nucleic acids. However, most approaches using CRISPR-based detection have disadvantages associated with the limitations of CRISPR RNA (crRNA), protospacer adjacent motif (PAM) or protospacer flanking sequence restriction, single channel detection, and difficulty in quantitative detection resulting in only some target sites being detected qualitatively. Here, we aimed to develop a barcode-based Cas12a-mediated DNA detection (BCDetection) strategy, which overcomes the aforementioned drawbacks and enables (1) detection with a universal PAM and crRNA without PAM or crRNA restriction, (2) simultaneous detection of multiple targets in a single reaction, and (3) quantitative detection, which can significantly distinguish copy number differences up to as low as a two-fold limit. We could efficiently and simultaneously detect three β-thalassemia mutations in a single reaction using BCDetection. Notably, samples from normal individuals, spinal muscular atrophy (SMA) carriers, and SMA patients were significantly and accurately distinguished using the quantitative detection ability of BCDetection, indicating its potential application in β-thalassemia and SMA carrier screening. Therefore, our findings demonstrate that BCDetection provides a new platform for accurate and efficient quantitative detection using CRISPR/Cas12a, highlighting its bioanalytical applications.},
}
@article {pmid37405149,
year = {2023},
author = {Malloggi, C and Tinacci, L and Giusti, A and Galli, F and Dall'Ara, S and Marconi, P and Gasperetti, L and Armani, A},
title = {Accidental discovery of a Tetraodontidae (Sphoeroides marmoratus) within a cuttlefish (Sepia officinalis) bought in a fish shop in Italy: risk assessment associated with the presence of Tetrodotoxin.},
journal = {Italian journal of food safety},
volume = {12},
number = {2},
pages = {11117},
pmid = {37405149},
issn = {2239-7132},
abstract = {The discovery of a pufferfish specimen (Tetraodontidae) inside a frozen cuttlefish, purchased by a fishmonger, and caught in the Eastern Central Atlantic (FAO 34) is reported. The consumer, who reported this case to FishLab (Department of Veterinary Sciences, University of Pisa) for investigation, was a student of Veterinary Medicine at the University of Pisa. He recognized the Tetraodontidae because he attended practical lessons on fish morphological identification during the course of food inspection and was aware of the risks to human health linked to the Tetrodotoxin (TTX). In this study, the pufferfish was identified morphologically, using the FAO morphological keys, and molecularly, analyzing two markers, the cytochrome oxidase I (COI) and the cytochrome b genes, by DNA barcoding. The pufferfish was identified morphologically as Sphoeroides spp., and molecularly as Sphoeroides marmoratus using the COI gene (99-100% identity values). Literature reports that S. marmoratus from the Eastern Atlantic contains high concentrations of TTX in the gonads and the digestive tract. However, the possible passage of TTX from fish to other organisms linked to contact or ingestion has never been reported. This represents the first case of a potentially toxic pufferfish entering the market inside another organism. The fact that a student observed this occurrence highlights the key role of citizen science in the management of emerging risks.},
}
@article {pmid37404204,
year = {2023},
author = {Kawasaki, F and Mori, Y and Mimori, T and Sato, I and Ota, S},
title = {Identification of In-Droplet Multicellular Communities by Light-Induced Combinatorial DNA Barcoding.},
journal = {Chemistry (Weinheim an der Bergstrasse, Germany)},
volume = {29},
number = {53},
pages = {e202301133},
doi = {10.1002/chem.202301133},
pmid = {37404204},
issn = {1521-3765},
support = {JPMJCR19H1//Japan Science and Technology Agency/ ; JP21H04636//Japan Society for the Promotion of Science/ ; JP21H00416//Japan Society for the Promotion of Science/ ; //Tateisi Science and Technology Foundation/ ; //The Noguchi Institute/ ; //The Naito Foundation/ ; //The Uehara Memorial Foundation/ ; //White Rock Foundation/ ; //The Canon Foundation/ ; //Senri Life Science Foundation/ ; //Secom Science and Technology Foundation/ ; //The UTEC-UTokyo FSI Research Grant Program/ ; Incentive Research Project//RIKEN/ ; },
mesh = {*DNA Barcoding, Taxonomic ; *DNA ; },
abstract = {A microdroplet co-culture system is useful for the parallel assessment of numerous possible cell-cell interactions by generating isolated subcommunities from a pool of heterogeneous cells. However, the integration of single-cell sequencing into such analysis has been limited due to the lack of effective molecular identifiers for each in-droplet subcommunity. Herein, we present a strategy for generating in-droplet subcommunity identifiers using DNA-functionalized microparticles encapsulated within microdroplets. These microparticles serve as initial information carriers, where their combinations act as distinct identifiers for in-droplet subcommunity. Upon optical trigger, DNA barcoding molecules encoding the microparticle information are once released in the microdroplets and then tag cell membranes. The tagged DNA molecules then serve as a second information carrier readable by single-cell sequencing to reconstitute the community in silico in the single-cell RNA sequencing data space.},
}
@article {pmid37402171,
year = {2023},
author = {Hameed, M and Rai, P and Makris, M and Weger-Lucarelli, J},
title = {Optimized protocol for mouse footpad immune cell isolation for single-cell RNA sequencing and flow cytometry.},
journal = {STAR protocols},
volume = {4},
number = {3},
pages = {102409},
pmid = {37402171},
issn = {2666-1667},
support = {R21 AI153919/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Mice ; Flow Cytometry/methods ; Cell Separation/methods ; *Leukocytes ; Sequence Analysis, RNA/methods ; },
abstract = {Single-cell RNA sequencing (scRNA-seq) requires the preparation of a highly viable single-cell suspension to get reliable sequencing results. Here, we present a protocol for isolating mouse footpad leukocytes while maintaining high viability. We describe steps for footpad collection, enzymatic tissue dissociation, leukocyte isolation and purification, and cell fixation and preservation. We then detail combinatorial barcoding, library preparation, scRNA-seq, and data analysis. Cells can be used to generate a complete molecular atlas at the single cell level.},
}
@article {pmid37401921,
year = {2023},
author = {Stevenson, ZC and Moerdyk-Schauwecker, MJ and Banse, SA and Patel, DS and Lu, H and Phillips, PC},
title = {High-throughput library transgenesis in Caenorhabditis elegans via Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS).},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {37401921},
issn = {2050-084X},
support = {R01AG056436/NH/NIH HHS/United States ; R35GM131838/NH/NIH HHS/United States ; R35 GM131838/GM/NIGMS NIH HHS/United States ; R01 AG056436/AG/NIA NIH HHS/United States ; T32 GM007413/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Animals, Genetically Modified ; *Caenorhabditis elegans/genetics ; *Gene Library ; *Gene Transfer Techniques ; *Transgenes/genetics ; DNA Barcoding, Taxonomic ; Genetic Variation ; Promoter Regions, Genetic/genetics ; },
abstract = {High-throughput transgenesis using synthetic DNA libraries is a powerful method for systematically exploring genetic function. Diverse synthesized libraries have been used for protein engineering, identification of protein-protein interactions, characterization of promoter libraries, developmental and evolutionary lineage tracking, and various other exploratory assays. However, the need for library transgenesis has effectively restricted these approaches to single-cell models. Here, we present Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS), a simple yet powerful approach to large-scale transgenesis that overcomes typical limitations encountered in multicellular systems. TARDIS splits the transgenesis process into a two-step process: creation of individuals carrying experimentally introduced sequence libraries, followed by inducible extraction and integration of individual sequences/library components from the larger library cassette into engineered genomic sites. Thus, transformation of a single individual, followed by lineage expansion and functional transgenesis, gives rise to thousands of genetically unique transgenic individuals. We demonstrate the power of this system using engineered, split selectable TARDIS sites in Caenorhabditis elegans to generate (1) a large set of individually barcoded lineages and (2) transcriptional reporter lines from predefined promoter libraries. We find that this approach increases transformation yields up to approximately 1000-fold over current single-step methods. While we demonstrate the utility of TARDIS using C. elegans, in principle the process is adaptable to any system where experimentally generated genomic loci landing pads and diverse, heritable DNA elements can be generated.},
}
@article {pmid37401915,
year = {2023},
author = {Ha, NS and Onley, JR and Deng, K and Andeer, P and Bowen, BP and Gupta, K and Kim, PW and Kuch, N and Kutschke, M and Parker, A and Song, F and Fox, B and Adams, PD and de Raad, M and Northen, TR},
title = {A combinatorial droplet microfluidic device integrated with mass spectrometry for enzyme screening.},
journal = {Lab on a chip},
volume = {23},
number = {15},
pages = {3361-3369},
pmid = {37401915},
issn = {1473-0189},
support = {T32 GM008349/GM/NIGMS NIH HHS/United States ; },
mesh = {Mass Spectrometry/methods ; *Glycoside Hydrolases/metabolism ; *Nanostructures/chemistry ; Lab-On-A-Chip Devices ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {Mass spectrometry (MS) enables detection of different chemical species with a very high specificity; however, it can be limited by its throughput. Integrating MS with microfluidics has a tremendous potential to improve throughput and accelerate biochemical research. In this work, we introduce Drop-NIMS, a combination of a passive droplet loading microfluidic device and a matrix-free MS laser desorption ionization technique called nanostructure-initiator mass spectrometry (NIMS). This platform combines different droplets at random to generate a combinatorial library of enzymatic reactions that are deposited directly on the NIMS surface without requiring additional sample handling. The enzyme reaction products are then detected with MS. Drop-NIMS was used to rapidly screen enzymatic reactions containing low (on the order of nL) volumes of glycoside reactants and glycoside hydrolase enzymes per reaction. MS "barcodes" (small compounds with unique masses) were added to the droplets to identify different combinations of substrates and enzymes created by the device. We assigned xylanase activities to several putative glycoside hydrolases, making them relevant to food and biofuel industrial applications. Overall, Drop-NIMS is simple to fabricate, assemble, and operate and it has potential to be used with many other small molecule metabolites.},
}
@article {pmid37401172,
year = {2023},
author = {Hardoim, CCP and Hardoim, PR and Lôbo-Hajdu, G and Custódio, MR and Thomas, T},
title = {The microbiome of the sponge Aplysina caissara in two sites with different levels of anthropogenic impact.},
journal = {FEMS microbiology letters},
volume = {370},
number = {},
pages = {},
doi = {10.1093/femsle/fnad064},
pmid = {37401172},
issn = {1574-6968},
mesh = {Animals ; *Anthropogenic Effects ; Brazil ; *Microbiota/genetics ; Phylogeny ; *Porifera/microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Geologic Sediments/microbiology ; Host Microbial Interactions ; *Biodiversity ; Archaea/classification/genetics ; Bacteria/classification/genetics ; },
abstract = {Despite the important roles that marine sponges play in ecosystem functioning and structuring, little is known about how the sponge holobiont responds to local anthropogenic impacts. Here we assess the influence of an impacted environment (Praia Preta) on the microbial community associated with the endemic sponge Aplysina caissara in comparison to a less-impacted area (Praia do Guaecá) from the coast of São Paulo state (Brazil, southwestern Atlantic coast). We hypothesized that the local anthropogenic impacts will change the microbiome of A. caissara and that the community assembly will be driven by a different process (i.e. deterministic versus stochastic) under distinct levels of impact. The microbiome at the amplicon sequence variants level was found to be statistically distinct between sponges from the different sites, and this was also seen for the microbial communities of the surrounding seawater and sediments. Microbial communities of A. caissara from both sites were found to be assembled by deterministic processes, even though the sites presented distinct anthropogenic impacts, showing a pivotal role of the sponge host in selecting its own microbiome. Overall, this study revealed that local anthropogenic impacts altered the microbiome of A. caissara; however, assembly processes are largely determined by the sponge host.},
}
@article {pmid37400835,
year = {2023},
author = {Tang, Q and Li, W and Huang, J and Wu, Y and Ma, C and Tu, Y and Zhu, Q and Lu, J and Xie, J and Liu, Y and Mao, X and Wu, W},
title = {Single-cell sequencing analysis of peripheral blood in patients with moyamoya disease.},
journal = {Orphanet journal of rare diseases},
volume = {18},
number = {1},
pages = {174},
pmid = {37400835},
issn = {1750-1172},
mesh = {Humans ; *Moyamoya Disease/genetics/diagnosis ; Gene Expression Profiling ; Angiography, Digital Subtraction ; Transcriptome ; Membrane Glycoproteins ; },
abstract = {BACKGROUND: At present, the etiology of moyamoya disease is not clear, and it is necessary to explore the mechanism of its occurrence and development. Although some bulk sequencing data have previously revealed transcriptomic changes in Moyamoya disease, single-cell sequencing data has been lacking.<br><br>METHODS: Two DSA(Digital Subtraction Angiography)-diagnosed patients with moyamoya disease were recruited between January 2021 and December 2021. Their peripheral blood samples were single-cell sequenced. CellRanger(10 x Genomics, version 3.0.1) was used to process the raw data, demultiplex cellular barcodes, map reads to the transcriptome, and dowm-sample reads(as required to generate normalized aggregate data across samples). There were 4 normal control samples, including two normal samples GSM5160432 and GSM5160434 of GSE168732, and two normal samples of GSE155698, namely GSM4710726 and GSM4710727. Weighted co-expression network analysis was used to explore the gene sets associated with moyamoya disease. GO analysis and KEGG analysis were used to explore gene enrichment pathways. Pseudo-time series analysis and cell interaction analysis were used to explore cell differentiation and cell interaction.<br><br>RESULTS: For the first time, we present a peripheral blood single cell sequencing landscape of Moyamoya disease, revealing cellular heterogeneity and gene expression heterogeneity. In addition, by combining with WGCNA analysis in public database and taking intersection, the key genes in moyamoya disease were obtained. namely PTP4A1, SPINT2, CSTB, PLA2G16, GPX1, HN1, LGALS3BP, IFI6, NDRG1, GOLGA2, LGALS3. Moreover, pseudo-time series analysis and cell interaction analysis revealed the differentiation of immune cells and the relationship between immune cells in Moyamoya disease.<br><br>CONCLUSIONS: Our study can provide information for the diagnosis and treatment of moyamoya disease.},
}
@article {pmid37400597,
year = {2023},
author = {Oehler, S and Lucaroni, L and Migliorini, F and Elsayed, A and Prati, L and Puglioli, S and Matasci, M and Schira, K and Scheuermann, J and Yudin, D and Jia, M and Ban, N and Bushnell, D and Kornberg, R and Cazzamalli, S and Neri, D and Favalli, N and Bassi, G},
title = {A DNA-encoded chemical library based on chiral 4-amino-proline enables stereospecific isozyme-selective protein recognition.},
journal = {Nature chemistry},
volume = {15},
number = {10},
pages = {1431-1443},
pmid = {37400597},
issn = {1755-4349},
abstract = {DNA-encoded chemical libraries (DELs) consist of large chemical compound collections individually linked to DNA barcodes, facilitating pooled construction and screening. However, screening campaigns often fail if the molecular arrangement of the building blocks is not conducive to an efficient interaction with a protein target. Here we postulated that the use of rigid, compact and stereo-defined central scaffolds for DEL synthesis may facilitate the discovery of very specific ligands capable of discriminating between closely related protein targets. We synthesized a DEL comprising 3,735,936 members, featuring the four stereoisomers of 4-aminopyrrolidine-2-carboxylic acid as central scaffolds. The library was screened in comparative selections against pharmaceutically relevant targets and their closely related protein isoforms. Hit validation results revealed a strong impact of stereochemistry, with large affinity differences between stereoisomers. We identified potent isozyme-selective ligands against multiple protein targets. Some of these hits, specific to tumour-associated antigens, demonstrated tumour-selective targeting in vitro and in vivo. Collectively, constructing DELs with stereo-defined elements contributed to high library productivity and ligand selectivity.},
}
@article {pmid37400476,
year = {2023},
author = {Lim, CK and Yeoh, JW and Kunartama, AA and Yew, WS and Poh, CL},
title = {A biological camera that captures and stores images directly into DNA.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {3921},
pmid = {37400476},
issn = {2041-1723},
mesh = {*DNA/genetics ; *DNA Replication ; Light ; High-Throughput Nucleotide Sequencing ; },
abstract = {The increasing integration between biological and digital interfaces has led to heightened interest in utilizing biological materials to store digital data, with the most promising one involving the storage of data within defined sequences of DNA that are created by de novo DNA synthesis. However, there is a lack of methods that can obviate the need for de novo DNA synthesis, which tends to be costly and inefficient. Here, in this work, we detail a method of capturing 2-dimensional light patterns into DNA, by utilizing optogenetic circuits to record light exposure into DNA, encoding spatial locations with barcoding, and retrieving stored images via high-throughput next-generation sequencing. We demonstrate the encoding of multiple images into DNA, totaling 1152 bits, selective image retrieval, as well as robustness to drying, heat and UV. We also demonstrate successful multiplexing using multiple wavelengths of light, capturing 2 different images simultaneously using red and blue light. This work thus establishes a 'living digital camera', paving the way towards integrating biological systems with digital devices.},
}
@article {pmid37399397,
year = {2023},
author = {Heyman, O and Yehezkel, D and Ciolli Mattioli, C and Blumberger, N and Rosenberg, G and Solomon, A and Hoffman, D and Bossel Ben-Moshe, N and Avraham, R},
title = {Paired single-cell host profiling with multiplex-tagged bacterial mutants reveals intracellular virulence-immune networks.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {28},
pages = {e2218812120},
pmid = {37399397},
issn = {1091-6490},
mesh = {Virulence/genetics ; *Salmonella typhimurium ; *Macrophages/metabolism ; Virulence Factors/genetics ; Bacterial Proteins/genetics/metabolism ; Host-Pathogen Interactions/genetics ; },
abstract = {Encounters between host cells and intracellular bacterial pathogens lead to complex phenotypes that determine the outcome of infection. Single-cell RNA sequencing (scRNA-seq) is increasingly used to study the host factors underlying diverse cellular phenotypes but has limited capacity to analyze the role of bacterial factors. Here, we developed scPAIR-seq, a single-cell approach to analyze infection with a pooled library of multiplex-tagged, barcoded bacterial mutants. Infected host cells and barcodes of intracellular bacterial mutants are both captured by scRNA-seq to functionally analyze mutant-dependent changes in host transcriptomes. We applied scPAIR-seq to macrophages infected with a library of Salmonella Typhimurium secretion system effector mutants. We analyzed redundancy between effectors and mutant-specific unique fingerprints and mapped the global virulence network of each individual effector by its impact on host immune pathways. ScPAIR-seq is a powerful tool to untangle bacterial virulence strategies and their complex interplay with host defense strategies that drive infection outcome.},
}
@article {pmid37399206,
year = {2023},
author = {Zhang, Z and Mu, W and Kong, W and Liu, J and Zhao, J and Zhao, Q and Shi, M and Zhao, H and Liu, J and Shi, L},
title = {Validation of the shotgun metabarcoding approach for comprehensively identifying herbal products containing plant, fungal, and animal ingredients.},
journal = {PloS one},
volume = {18},
number = {7},
pages = {e0286069},
pmid = {37399206},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; DNA, Plant/genetics ; *Plants/genetics ; Plant Extracts ; },
abstract = {Identifying plant, fungal, and animal ingredients in a specific mixture remains challenging during the limitation of PCR amplification and low specificity of traditional methods. Genomic DNA was extracted from mock and pharmaceutical samples. Four type of DNA barcodes were generated from shotgun sequencing dataset with the help of a local bioinformatic pipeline. Taxa of each barcode was assigned by blast to TCM-BOL, BOLD, and GenBank. Traditional methods including microscopy, thin layer chromatography (TLC), and high-performance liquid chromatography (HPLC) were carried out according to Chinese pharmacopoeia. On average, 6.8 Gb shotgun reads were sequenced from genomic DNA of each sample. Then, 97, 11, 10, 14, and one operational taxonomic unit (OTU) were generated for ITS2, psbA-trnH, rbcL, matK, and COI, respectively. All the labeled ingredients including eight plant, one fungal, and one animal species were successfully detected in both the mock and pharmaceutical samples, in which Chebulae Fructus, Poria, and Fritilariae Thunbergia Bulbus were identified via mapping reads to organelle genomes. In addition, four unlabeled plant species were detected from pharmaceutical samples, while 30 genera of fungi, such as Schwanniomyces, Diaporthe, Fusarium were detected from mock and pharmaceutical samples. Furthermore, the microscopic, TLC, and HPLC analysis were all in accordance with the standards stipulated by Chinese Pharmacopoeia. This study indicated that shotgun metabarcoding could simultaneously identified plant, fungal, and animal ingredients in herbal products, which has the ability to serve as a valuable complement to traditional methods.},
}
@article {pmid37398666,
year = {2023},
author = {van Nieuwland, M and Esen, I and Reitsema, RD and Abdulahad, WH and van Sleen, Y and Jiemy, WF and Sandovici, M and Brouwer, E and van Bon, L},
title = {Evidence for increased interferon type I activity in CD8+ T cells in giant cell arteritis patients.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1197293},
pmid = {37398666},
issn = {1664-3224},
mesh = {Humans ; *Giant Cell Arteritis/pathology ; Temporal Arteries ; *Interferon Type I/metabolism ; CD8-Positive T-Lymphocytes/metabolism ; Biomarkers/metabolism ; },
abstract = {INTRODUCTION: Giant cell arteritis (GCA) is a vasculitis of the medium- and large-sized arteries. Interferon type I (IFN-I) is increasingly recognized as a key player in autoimmune diseases and might be involved in GCA pathogenesis, however evidence is limited. IFN-I activates Janus kinase/signal transducers and activators of transcription (JAK-STAT) pathways, leading to increased expression of interferon stimulated genes. In this study, IFN-I activity in GCA is explored, focusing on CD8+ T cells.<br><br>METHODS: Expression of phospho-STAT (pSTAT) 1, 3 and 5 was investigated in IFN-&#x3b1;-stimulated peripheral mononuclear cells (PBMCs) gated separately for CD8+ T cells of patients with GCA (n=18), healthy controls (HC, n=15) and infection controls (n=11) by Phosphoflow method combined with fluorescent cell barcoding technique. Furthermore, IFN-I induced myxovirus-resistance protein A (MxA) and CD8+ T cell expression was investigated by immunohistochemistry in temporal artery biopsies (TAB) of GCA patients (n=20) and mimics (n=20), and in aorta tissue of GCA (n=8) and atherosclerosis patients (n=14).<br><br>RESULTS: pSTAT1 expression was increased in IFN-&#x3b1; stimulated CD8+ T cells from GCA patients, whereas no difference was observed in pSTAT3 and pSTAT5 expression. MxA was present in TABs of 13/20 GCA patients compared to 2/20 mimics and in 8/8 GCA+ compared to 13/14 GCA- aorta tissues. MxA location partially co-localized with CD8+T cells.<br><br>CONCLUSIONS: Our results provide evidence for increased IFN-I activity in CD8+ T cells of GCA patients, both systemically and locally. These findings warrant further investigation regarding IFN-I induced biomarkers and IFN-I related novel therapeutic options in GCA.},
}
@article {pmid37398418,
year = {2023},
author = {Solis-Leal, A and Boby, N and Mallick, S and Cheng, Y and Wu, F and De La Torre, G and Dufour, J and Alvarez, X and Shivanna, V and Liu, Y and Fennessey, CM and Lifson, JD and Li, Q and Keele, BF and Ling, B},
title = {Lymphoid tissues contribute to viral clonotypes present in plasma at early post-ATI in SIV-infected rhesus macaques.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.05.30.542512},
pmid = {37398418},
issn = {2692-8205},
support = {P51 OD011104/OD/NIH HHS/United States ; U42 OD024282/OD/NIH HHS/United States ; },
abstract = {UNLABELLED: The rebound-competent viral reservoir (RCVR), comprised of virus that is able to persist during antiretroviral therapy (ART) and mediate reactivation of systemic viral replication and rebound viremia after antiretroviral therapy interruption (ATI), remains the biggest obstacle to the eradication of HIV infection. A better understanding of the cellular and tissue origins and the dynamics of viral populations that initiate rebound upon ATI could help develop targeted therapeutic strategies for reducing the RCVR. In this study, barcoded SIVmac239M was used to infect rhesus macaques to enable monitoring of viral barcode clonotypes contributing to virus detectable in plasma after ATI. Blood, lymphoid tissues (LTs, spleen, mesenteric and inguinal lymph nodes), and non-lymphoid tissues (NLTs, colon, ileum, lung, liver, and brain) were analyzed using viral barcode sequencing, intact proviral DNA assay, single-cell RNA sequencing, and combined CODEX/RNAscope/ in situ hybridization. Four of seven animals had viral barcodes detectable by deep sequencing of plasma at necropsy although plasma viral RNA remained < 22 copies/mL. Among the tissues studied, mesenteric and inguinal lymph nodes, and spleen contained viral barcodes detected in plasma, and trended to have higher cell-associated viral loads, higher intact provirus levels, and greater diversity of viral barcodes. CD4+ T cells were the main cell type harboring viral RNA (vRNA) after ATI. Further, T cell zones in LTs showed higher vRNA levels than B cell zones for most animals. These findings are consistent with LTs contributing to virus present in plasma early after ATI.<br><br>ONE SENTENCE SUMMARY: The reemerging of SIV clonotypes at early post-ATI are likely from the secondary lymphoid tissues.},
}
@article {pmid37397980,
year = {2023},
author = {Curd, EE and Gal, L and Gallego, R and Nielsen, S and Gold, Z},
title = {rCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37397980},
issn = {2692-8205},
support = {P20 GM103449/GM/NIGMS NIH HHS/United States ; },
abstract = {Key to making accurate taxonomic assignments are curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given the large and continuously growing volumes of DNA sequence data and novel reference barcode targets. Monitoring and research applications require a greater diversity of specialized gene regions and targeted taxa to meet taxonomic classification goals then are currently curated by professional staff. Thus, there is a growing need for an easy to implement tool that can generate comprehensive metabarcoding reference libraries for any bespoke locus. We address this need by reimagining CRUX from the Anacapa Toolkit and present the rCRUX package in R. The typical workflow involves searching for plausible seed amplicons (get_seeds_local() or get_seeds_remote()) by simulating in silico PCR to acquire seed sequences containing a user-defined primer set. Next these seeds are used to iteratively blast search seed sequences against a local NCBI formatted database using a taxonomic rank based stratified random sampling approach (blast_seeds()) that results in a comprehensive set of sequence matches. This database is dereplicated and cleaned (derep_and_clean_db()) by identifying identical reference sequences and collapsing the taxonomic path to the lowest taxonomic agreement across all matching reads. This results in a curated, comprehensive database of primer specific reference barcode sequences from NCBI. We demonstrate that rCRUX provides more comprehensive reference databases for the MiFish Universal Teleost 12S, Taberlet trnl, and fungal ITS locus than CRABS, METACURATOR, RESCRIPt, and ECOPCR reference databases. We then further demonstrate the utility of rCRUX by generating 16 reference databases for metabarcoding loci that lack dedicated reference database curation efforts. The rCRUX package provides a simple to use tool for the generation of curated, comprehensive reference databases for user-defined loci, facilitating accurate and effective taxonomic classification of metabarcoding and DNA sequence efforts broadly.},
}
@article {pmid37396648,
year = {2023},
author = {Waswa, EN and Mkala, EM and Odago, WO and Amenu, SG and Mutinda, ES and Muthui, SW and Ding, SX and Hu, GW and Wang, QF},
title = {Comparative chloroplast genome analysis of Sambucus L. (Viburnaceae): inference for phylogenetic relationships among the closely related Sambucus adnata Wall. ex DC Sambucus javanica Blume.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1179510},
pmid = {37396648},
issn = {1664-462X},
abstract = {Sambucus L. is found in the family Viburnaceae (syn. Adoxaceae) and encompasses approximately 29 accepted species. The complex morphology of these species has caused continued confusion concerning their nomenclature, classification, and identification. Despite previous attempts to resolve taxonomic complexities in the Sambucus genus, there are still unclear phylogenetic relationships among several species. In this study, the newly obtained plastome of Sambucus williamsii Hance. as well as the populations of Sambucus canadensis L., Sambucus javanica Blume, and Sambucus adnata Wall. ex DC were sequenced, and their sizes, structural similarity, gene order, gene number, and guanine-cytosine (GC) contents were analyzed. The phylogenetic analyses were conducted using the whole chloroplast genomes and protein-coding genes (PCGs). The findings revealed that the chloroplast genomes of Sambucus species exhibited typical quadripartite double-stranded DNA molecules. Their lengths ranged from 158,012 base pairs (bp) (S. javanica) to 158,716 bp (S. canadensis L). Each genome comprised a pair of inverted repeats (IRs), which separated the large single-copy (LSC) and small single-copy (SSC) regions. In addition, the plastomes contained 132 genes, encompassing 87 protein-coding, 37 tRNA, and four rRNA genes. In the simple sequence repeat (SSR) analysis, A/T mononucleotides had the highest proportion, with the most repetitive sequences observed in S. williamsii. The comparative genome analyses showed high similarities in structure, order, and gene contents. The hypervariable regions in the studied chloroplast genomes were trnT-GGU, trnF-GAA, psaJ, trnL-UAG, ndhF, and ndhE, which may be used as candidate barcodes for species discrimination in Sambucus genus. Phylogenetic analyses supported the monophyly of Sambucus and revealed the separation of S. javanica and S. adnata populations. Sambucus chinensis Lindl. was nested within S. javanica in the same clade, collaborating their conspecific treatment. These outcomes indicate that the chloroplast genome of Sambucus plants is a valuable genetic resource for resolving taxonomic discrepancies at the lower taxonomic levels and can be applied in molecular evolutionary studies.},
}
@article {pmid37394070,
year = {2023},
author = {Park, JW and Park, K and Kwak, IS},
title = {Surveillance spilled Chironomidae (Diptera) larvae from drinking water treatment plants in South Korea using morphogenetic species analysis and eDNA metabarcoding.},
journal = {The Science of the total environment},
volume = {896},
number = {},
pages = {165241},
doi = {10.1016/j.scitotenv.2023.165241},
pmid = {37394070},
issn = {1879-1026},
mesh = {Humans ; Animals ; *Chironomidae/genetics ; Larva ; *Drinking Water ; Ecosystem ; *DNA, Environmental ; },
abstract = {Chironomid larvae (Diptera: Chironomidae) are tremendous indicator species that can tolerate a broad range of environmental conditions, from polluted to unimpaired water ecosystems. These species are ubiquitously observed in all bioregions and can even be found in drinking water treatment plants (DWTPs). Detection of chironomid larvae in DWTPs is a critical issue because their presence may be indicative of the water quality in the supply of tap water for human consumption. Therefore, the aim of the present study was to identify the chironomid communities that reflect the water quality of DWTPs and develop a biomonitoring tool to detect biological contamination of the chironomids in DWTPs. To do so, we investigated the identity and distribution of chironomid larvae in seven DWTP areas using morphological identification, DNA barcoding, and sediment environmental DNA (eDNA) analysis. A total of 7924 chironomid individuals encompassing three subfamilies and 25 species of 19 genera were identified in 33 sites within the DWTPs. The Gongchon and Bupyeong DWTPs were dominated by Chironomus spp. larvae, which were correlated with low levels of dissolved oxygen in the water. In the Samgye DWTP and Hwajeong DWTP, Chironomus spp. were almost absent, and instead, Tanytarsus spp. were abundant. Additionally, the Gangjeong DWTP was dominated by a Microtendipes sp., and two species of Orthocladiinae (a Parametriocnemus sp. and a Paratrichocladius sp.) were found only in the Jeju DWTP. We also identified the eight most abundant Chironomidae larvae found in the DWTPs. Furthermore, eDNA metabarcoding of DWTP sediment indicated the presence of different eukaryotic fauna and confirmed the presence of chironomids in DWTPs. These data provide useful morphological and genetic information regarding chironomid larvae that can be used for the water quality biomonitoring of DWTPs to support the supply of clean drinking water.},
}
@article {pmid37393782,
year = {2023},
author = {Tröster, M and Kotrba, M and Heß, M},
title = {Variation of sperm size and evolution of giant spermatozoa in Lonchopteridae (Diptera).},
journal = {Arthropod structure &amp; development},
volume = {75},
number = {},
pages = {101285},
doi = {10.1016/j.asd.2023.101285},
pmid = {37393782},
issn = {1873-5495},
mesh = {Male ; Animals ; Phylogeny ; *Diptera ; Semen ; Spermatozoa ; },
abstract = {Among species of the spear-winged flies (Lonchopteridae) there is remarkable variation in sperm size, with some species producing giant spermatozoa. With a length of 7500 μm and a width of 1.3 μm the spermatozoon of Lonchoptera fallax ranks among the largest known to date. In the present study body size, testis size, sperm size, and spermatid number per bundle and per testis were examined across 11 Lonchoptera species. Results are discussed in terms of how these characters are related with each other and how their evolution affects the resource allocation amongst spermatozoa. Based on some discrete morphological characters and a molecular tree derived from DNA barcodes a phylogenetic hypothesis of the genus Lonchoptera is proposed. The occurrence of giant spermatozoa in Lonchopteridae is compared to convergent occurrences reported in other taxa.},
}
@article {pmid37392314,
year = {2023},
author = {Techen, N and Parveen, I and Khan, IA},
title = {Deoxyribonucleic Acid Barcoding for the Identification of Botanicals.},
journal = {Progress in the chemistry of organic natural products},
volume = {122},
number = {},
pages = {261-288},
pmid = {37392314},
issn = {2191-7043},
mesh = {*Biological Products ; Dietary Supplements ; Drug Contamination ; Genomics ; DNA ; },
abstract = {The Natural Herbal Products industry uses botanicals or herbs as raw materials for production of herbal products or dietary supplements. Recently, the demand for natural herbal products has increased tremendously and this has led to adulteration and to counterfeit herbal products. The present chapter deals with currently used molecular methods from "simple" single genomic regions to high-throughput whole genome or transcriptome sequencing methods used in the identification of botanicals.},
}
@article {pmid37390697,
year = {2023},
author = {Tébar-Martínez, R and Martín-Arana, J and Gimeno-Valiente, F and Tarazona, N and Rentero-Garrido, P and Cervantes, A},
title = {Strategies for improving detection of circulating tumor DNA using next generation sequencing.},
journal = {Cancer treatment reviews},
volume = {119},
number = {},
pages = {102595},
doi = {10.1016/j.ctrv.2023.102595},
pmid = {37390697},
issn = {1532-1967},
mesh = {Humans ; *Circulating Tumor DNA ; High-Throughput Nucleotide Sequencing/methods ; Mutation ; *Cell-Free Nucleic Acids ; *Neoplasms/diagnosis/genetics ; Biomarkers, Tumor/genetics ; },
abstract = {Cancer has become a global health issue and liquid biopsy has emerged as a non-invasive tool for various applications. In cancer, circulating tumor DNA (ctDNA) can be detected from cell-free DNA (cfDNA) obtained from plasma and has potential for early diagnosis, treatment, resistance, minimal residual disease detection, and tumoral heterogeneity identification. However, the low frequency of ctDNA requires techniques for accurate analysis. Multitarget assay such as Next Generation Sequencing (NGS) need improvement to achieve limits of detection that can identify the low frequency variants present in the cfDNA. In this review, we provide a general overview of the use of cfDNA and ctDNA in cancer, and discuss techniques developed to optimize NGS as a tool for ctDNA detection. We also summarize the results obtained using NGS strategies in both investigational and clinical contexts.},
}
@article {pmid37389182,
year = {2023},
author = {Prasetyo, AP and Cusa, M and Murray, JM and Agung, F and Muttaqin, E and Mariani, S and McDevitt, AD},
title = {Universal closed-tube barcoding for monitoring the shark and ray trade in megadiverse conservation hotspots.},
journal = {iScience},
volume = {26},
number = {7},
pages = {107065},
pmid = {37389182},
issn = {2589-0042},
abstract = {Trade restrictions for endangered elasmobranch species exist to disincentivise their exploitation and curb their declines. However, trade monitoring is challenging due to product variety and the complexity of import/export routes. We investigate the use of a portable, universal, DNA-based tool which would greatly facilitate in-situ monitoring. We collected shark and ray samples across the Island of Java, Indonesia, and selected 28 commonly encountered species (including 22 CITES-listed species) to test a recently developed real-time PCR single-assay originally developed for screening bony fish. In the absence of a bespoke elasmobranch identification online platform in the original FASTFISH-ID model, we employed a deep learning algorithm to recognize species based on DNA melt-curve signatures. By combining visual and machine-learning assignment methods, we distinguished 25/28 species, 20 of which were CITES-listed. With further refinement, this method can improve monitoring of the elasmobranch trade worldwide, without a lab or species-specific assays.},
}
@article {pmid37386355,
year = {2023},
author = {Lin, N and Liu, R and Wang, Y and Guo, P and Wang, Y and Liu, Y and Shang, F},
title = {The complete chloroplast genome of Ulmus mianzhuensis with insights into structural variations, adaptive evolution, and phylogenetic relationships of Ulmus (Ulmaceae).},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {366},
pmid = {37386355},
issn = {1471-2164},
support = {2023HYTP021//the Youth Talent Promotion Project in Henan province/ ; 23A180011//the Key Scientific Research Projects of Higher Education Institutions in Henan Province/ ; 232102110237//the Key Specialized Research and Development Breakthrough Program in Henan Province/ ; 201300110900//Henan Province Major Research Fund of Public Welfare/ ; },
mesh = {*Ulmus ; Ulmaceae ; Phylogeny ; *Genome, Chloroplast ; China ; },
abstract = {BACKGROUND: Ulmus mianzhuensis is an endemic tree species in China with high ornamental and economic value. Currently, little is known regarding its genomic architecture, phylogenetic position, or adaptive evolution. Here, we sequenced the complete chloroplast genome (cp genome) of U. mianzhuensis and further compared the variations in gene organization and structure within Ulmus species to define their genomic evolution, then reconstructed the phylogenomic relationship of 31 related Ulmus species to explore the systematic position of U. mianzhuensis and the utility of cp genome for resolving phylogenetics among Ulmus species.<br><br>RESULTS: Our results revealed that all the Ulmus species exhibited a typical quadripartite structure, with a large single copy (LSC) region of 87,170&#x2009;-&#x2009;88,408&#xa0;bp, a small single copy (SSC) region of 18,650&#x2009;-&#x2009;19,038&#xa0;bp and an inverted repeat (IR) region of 26,288&#x2009;-&#x2009;26,546&#xa0;bp. Within Ulmus species, gene structure and content of cp genomes were highly conserved, although slight variations were found in the boundary of SC/IR regions. Moreover, genome-wide sliding window analysis uncovered the variability of ndhC-trnV-UAC, ndhF-rpl32, and psbI-trnS-GCU were higher among 31 Ulmus that may be useful for the population genetics and potential DNA barcodes. Two genes (rps15 and atpF) were further detected under a positive selection of Ulmus species. Comparative phylogenetic analysis based on the cp genome and protein-coding genes revealed consistent topology that U. mianzhuensis is a sister group to U. parvifolia (sect. Microptelea) with a relatively low-level nucleotide variation of the cp genome. Additionally, our analyses also found that the traditional taxonomic system of five sections in Ulmus is not supported by the current phylogenomic topology with a nested evolutionary relationship between sections.<br><br>CONCLUSIONS: Features of the cp genome length, GC content, organization, and gene order were highly conserved within Ulmus. Furthermore, molecular evidence from the low variation of the cp genome suggested that U. mianzhuensis should be merged into U. parvifolia and regarded as a subspecies of U. parvifolia. Overall, we demonstrated that the cp genome provides valuable information for understanding the genetic variation and phylogenetic relationship in Ulmus.},
}
@article {pmid37385223,
year = {2023},
author = {Lu, Y and Zhao, Y and Hu, L and Zhang, W and Xie, Y and Cheng, S and Zheng, B and Xia, Q},
title = {Exploration of Multi-Gene DNA Barcode Markers to Reveal the Broad Genetic Diversity of Field Ticks (Acari: Ixodidae) in a Tropical Environment of Hainan Island, China.},
journal = {Cytogenetic and genome research},
volume = {163},
number = {1-2},
pages = {59-73},
doi = {10.1159/000531734},
pmid = {37385223},
issn = {1424-859X},
mesh = {Animals ; Humans ; *Ixodidae/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 28S ; DNA Barcoding, Taxonomic ; *Rhipicephalus/genetics ; Genetic Markers ; China ; Genetic Variation/genetics ; Phylogeny ; },
abstract = {Ticks are hematophagous arthropods and obligate ectoparasites of humans and other animals. This study focused on the molecular discrimination of ticks in the tropical environment of Hainan according to multi-gene DNA barcode markers with the expectation of accurately distinguishing species. A total of 420 ticks, including 49 adult ticks, 203 nymphal ticks, and 168 larval ticks, were collected in the field, and the 49 adult ticks were identified as Rhipicephalus turanicus, Dermacentor marginatus, and Haemaphysalis longicornis. The mitochondrial 16S rRNA, ribosomal 28S rRNA D2, and ribosomal internal transcribed spacer 2 (ITS2) regions were used as DNA barcode markers to discriminate species. According to basic local alignment search tool analysis against the GenBank database, 16S rRNA positively identified ticks in the Rhipicephalus, Dermacentor, and Haemaphysalis genera; the 28S rRNA D2 region identified ticks in the Rhipicephalus and Dermacentor genera; and ITS2 identified ticks as D. marginatus. Pairwise sequence comparisons based on these three regions were visualized with a Sequence Demarcation Tool matrix. Substitution saturation tests using data analysis and molecular biology and evolution revealed little substitution saturation (Iss < Iss.c, p < 0.05) in the 16S rRNA region for the Haemaphysalis genus; 28S rRNA D2 region for the Rhipicephalus, Dermacentor, and Haemaphysalis genera; and ITS2 region for the Rhipicephalus and Dermacentor genera. Distinctive sequences for which it is difficult to obtain good matches with the sequences available in GenBank exist in the ticks of Hainan. Future studies should obtain complementary sequences to refine and update the database for the molecular characterization of ticks.},
}
@article {pmid37383606,
year = {2023},
author = {Wang, X and Tian, S and Wang, H and Yang, L and Zou, X and Baskaran, XR and Li, Q and Xing, H and Li, HL},
title = {The complete chloroplast genome sequence of Zingiber teres S. Q. Tong &amp; Y. M. Xia (Zingiberaceae).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {8},
number = {6},
pages = {699-703},
pmid = {37383606},
issn = {2380-2359},
abstract = {Here, the complete chloroplast genome sequence of Zingiber teres is described using MGI paired-end sequencing. The genome is 163,428 bp in length and contains a small single-copy region (SSC) of 15,782 bp, a large single-copy region (LSC) of 88,142 bp, and two inverted repeat (IR) regions of 29,752 bp. The overall GC content is 36.1%, and the GC content of the IR regions is 41.1%, which is higher than that of both the LSC region (33.8%) and SSC region (29.5%). The genome of Z. teres contains 133 complete genes, including 88 protein-coding genes (79 protein-coding gene species), 38 tRNA genes (28 tRNA species), and 8 rRNA genes (four rRNA species). Maximum likelihood phylogenetic analysis yielded a well-resolved tree of the genus Zingiber, and Z. teres and Zingiber mioga were sister species in this tree. The development of DNA barcodes could aid the identification of Zingiber species.},
}
@article {pmid37381954,
year = {2023},
author = {Wang, YS and Jin, YX and Liu, KJ and Guo, C and Wang, YH and Xu, C and Zhang, ZX and Dong, WP},
title = {[Species identification of Ligustrum lucidum].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {48},
number = {11},
pages = {2940-2948},
doi = {10.19540/j.cnki.cjcmm.20230315.101},
pmid = {37381954},
issn = {1001-5302},
mesh = {*Ligustrum/genetics ; Seeds ; Fruit ; Polymerase Chain Reaction ; Research Design ; },
abstract = {Ligustrum lucidum is a woody perennial plant of genus Ligustrum in family Oleaceae. Its dried fruit has high medicinal value. In this study, the authors evaluated the variability and species identification efficiency of three specific DAN barcodes(rbcL-accD, ycf1a, ycf1b) and four general DAN barcodes(matK, rbcL, trnH-psbA, ITS2) for a rapid and accurate molecular identification of Ligustrum species. The results revealed that matK, rbcL, trnH-psbA, ITS2 and ycf1a were inefficient for identifying the Ligustrum species, and a large number of insertions and deletions were observed in rbcL-accD sequence, which was thus unsuitable for development as specific barcode. The ycf1b-2 barcode had DNA barcoding gap and high success rate of PCR amplification and DNA sequencing, which was the most suitable DNA barcode for L. lucidum identification and achieved an accurate result. In addition, to optimize the DNA extraction experiment, the authors extracted and analyzed the DNA of the exocarp, mesocarp, endocarp and seed of L. lucidum fruit. It was found that seed was the most effective part for DNA extraction, where DNAs of high concentration and quality were obtained, meeting the needs of species identification. In this study, the experimental method for DNA extraction of L. lucidum was optimized, and the seed was determined as the optimal part for DNA extraction and ycf1b-2 was the specific DNA barcode for L. lucidum identification. This study laid a foundation for the market regulation of L. lucidum.},
}
@article {pmid37379924,
year = {2023},
author = {Conrado, AC and Demetrio, WC and Stanton, DWG and Bartz, MLC and James, SW and Santos, A and da Silva, E and Ferreira, T and Acioli, ANS and Ferreira, AC and Maia, LS and Silva, TAC and Lavelle, P and Velasquez, E and Tapia-Coral, SC and Muniz, AW and Segalla, RF and Decaëns, T and Nadolny, HS and Peña-Venegas, CP and Pasini, A and de Oliveira Júnior, RC and , and Kille, P and Brown, GG and Cunha, L},
title = {Amazonian earthworm biodiversity is heavily impacted by ancient and recent human disturbance.},
journal = {The Science of the total environment},
volume = {895},
number = {},
pages = {165087},
doi = {10.1016/j.scitotenv.2023.165087},
pmid = {37379924},
issn = {1879-1026},
mesh = {Animals ; Humans ; *Oligochaeta ; Biodiversity ; Forests ; Soil ; Agriculture ; },
abstract = {Despite the importance of earthworms for soil formation, more is needed to know about how Pre-Columbian modifications to soils and the landscape. Gaining a deeper understanding is essential for comprehending the historical drivers of earthworm communities and the development of effective conservation strategies in the Amazon rainforest. Human disturbance can significantly impact earthworm diversity, especially in rainforest soils, and in the particular case of the Amazonian rainforest, both recent and ancient anthropic practices may be important. Amazonian Dark Earths (ADEs) are fertile soils found throughout the Amazon Basin, created by sedentary habits and intensification patterns of pre-Colombian societies primarily developed in the second part of the Holocene period. We have sampled earthworm communities in three Brazilian Amazonian (ADEs) and adjacent reference soils (REF) under old and young forests and monocultures. To better assess taxonomic richness, we used morphology and the barcode region of the COI gene to identify juveniles and cocoons and delimit Molecular Operational Taxonomic Units (MOTUs). Here we suggest using Integrated Operational Taxonomical units (IOTUs) which combine both morphological and molecular data and provide a more comprehensive assessment of diversity, while MOTUs only rely on molecular data. A total of 970 individuals were collected, resulting in 51 taxonomic units (IOTUs, MOTUs, and morphospecies combined). From this total, 24 taxonomic units were unique to REF soils, 17 to ADEs, and ten were shared between both soils. The highest richness was found in old forest sites for ADEs (12 taxonomic units) and REFs (21 taxonomic units). The beta-diversity calculations reveal a high species turnover between ADEs and REF soils, providing evidence that ADEs and REFs possess distinct soil biota. Furthermore, results suggest that ADE sites, formed by Pre-Columbian human activities, conserve a high number of native species in the landscape and maintain a high abundance, despite their long-term nature.},
}
@article {pmid37376541,
year = {2023},
author = {Ruiz, S and Galdames, P and Baumberger, C and Gonzalez, MA and Rojas, C and Oyarzun, C and Orozco, K and Mattar, C and Freiden, P and Sharp, B and Schultz-Cherry, S and Hamilton-West, C and Jimenez-Bluhm, P},
title = {Remote Sensing and Ecological Variables Related to Influenza A Prevalence and Subtype Diversity in Wild Birds in the Lluta Wetland of Northern Chile.},
journal = {Viruses},
volume = {15},
number = {6},
pages = {},
pmid = {37376541},
issn = {1999-4915},
support = {75N93021C00016/AI/NIAID NIH HHS/United States ; HHSN272201400006C/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Influenza, Human ; Chile/epidemiology ; Wetlands ; Ecosystem ; Prevalence ; Remote Sensing Technology ; *Influenza in Birds/epidemiology ; Animals, Wild ; Birds ; *Influenza A virus/genetics ; },
abstract = {The Lluta River is the northernmost coastal wetland in Chile, representing a unique ecosystem and an important source of water in the extremely arid Atacama Desert. During peak season, the wetland is home to more than 150 species of wild birds and is the first stopover point for many migratory species that arrive in the country along the Pacific migratory route, thereby representing a priority site for avian influenza virus (AIV) surveillance in Chile. The aim of this study was to determine the prevalence of influenza A virus (IAV) in the Lluta River wetland, identify subtype diversity, and evaluate ecological and environmental factors that drive the prevalence at the study site. The wetland was studied and sampled from September 2015 to October 2020. In each visit, fresh fecal samples of wild birds were collected for IAV detection by real-time RT-PCR. Furthermore, a count of wild birds present at the site was performed and environmental variables, such as temperature, rainfall, vegetation coverage (Normalized Difference Vegetation Index-NDVI), and water body size were determined. A generalized linear mixed model (GLMM) was built to assess the association between AIV prevalence and explanatory variables. Influenza positive samples were sequenced, and the host species was determined by barcoding. Of the 4349 samples screened during the study period, overall prevalence in the wetland was 2.07% (95% CI: 1.68 to 2.55) and monthly prevalence of AIV ranged widely from 0% to 8.6%. Several hemagglutinin (HA) and neuraminidase (NA) subtypes were identified, and 10 viruses were isolated and sequenced, including low pathogenic H5, H7, and H9 strains. In addition, several reservoir species were recognized (both migratory and resident birds), including the newly identified host Chilean flamingo (Phoenicopterus chilensis). Regarding environmental variables, prevalence of AIV was positively associated with NDVI (OR = 3.65, p < 0.05) and with the abundance of migratory birds (OR = 3.57, p < 0.05). These results emphasize the importance of the Lluta wetland as a gateway to Chile for viruses that come from the Northern Hemisphere and contribute to the understanding of AIV ecological drivers.},
}
@article {pmid37376008,
year = {2023},
author = {Belair, M and Pensec, F and Jany, JL and Le Floch, G and Picot, A},
title = {Profiling Walnut Fungal Pathobiome Associated with Walnut Dieback Using Community-Targeted DNA Metabarcoding.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {12},
pages = {},
pmid = {37376008},
issn = {2223-7747},
support = {#1797//Regional Council of Brittany/ ; 2020 CDE EGAAL//Ministry of Higher Education and Research/ ; CASDAR funds - AAP RT 2020 - CARIBOU project//Ministry of Agriculture and Food (France)/ ; },
abstract = {Walnut dieback can be caused by several fungal pathogenic species, which are associated with symptoms ranging from branch dieback to fruit necrosis and blight, challenging the one pathogen-one disease concept. Therefore, an accurate and extensive description of the walnut fungal pathobiome is crucial. To this end, DNA metabarcoding represents a powerful approach provided that bioinformatic pipelines are evaluated to avoid misinterpretation. In this context, this study aimed to determine (i) the performance of five primer pairs targeting the ITS region in amplifying genera of interest and estimating their relative abundance based on mock communities and (ii) the degree of taxonomic resolution using phylogenetic trees. Furthermore, our pipelines were also applied to DNA sequences from symptomatic walnut husks and twigs. Overall, our results showed that the ITS2 region was a better barcode than ITS1 and ITS, resulting in significantly higher sensitivity and/or similarity of composition values. The ITS3/ITS4_KYO1 primer set allowed to cover a wider range of fungal diversity, compared to the other primer sets also targeting the ITS2 region, namely, GTAA and GTAAm. Adding an extraction step to the ITS2 sequence influenced both positively and negatively the taxonomic resolution at the genus and species level, depending on the primer pair considered. Taken together, these results suggested that Kyo set without ITS2 extraction was the best pipeline to assess the broadest fungal diversity, with a more accurate taxonomic assignment, in walnut organs with dieback symptoms.},
}
@article {pmid37375978,
year = {2023},
author = {Krinitsina, AA and Omelchenko, DO and Kasianov, AS and Karaseva, VS and Selezneva, YM and Chesnokova, OV and Shirobokov, VA and Polevova, SV and Severova, EE},
title = {Aerobiological Monitoring and Metabarcoding of Grass Pollen.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {12},
pages = {},
pmid = {37375978},
issn = {2223-7747},
support = {19-05-50035//Russian Foundation for Basic Research/ ; FFNU-2022-0037//Institute for Information Transmission Problems/ ; },
abstract = {Grass pollen is one of the leading causes of pollinosis, affecting 10-30% of the world's population. The allergenicity of pollen from different Poaceae species is not the same and is estimated from moderate to high. Aerobiological monitoring is a standard method that allows one to track and predict the dynamics of allergen concentration in the air. Poaceae is a stenopalynous family, and thus grass pollen can usually be identified only at the family level with optical microscopy. Molecular methods, in particular the DNA barcoding technique, can be used to conduct a more accurate analysis of aerobiological samples containing the DNA of various plant species. This study aimed to test the possibility of using the ITS1 and ITS2 nuclear loci for determining the presence of grass pollen from air samples via metabarcoding and to compare the analysis results with the results of phenological observations. Based on the high-throughput sequencing data, we analyzed the changes in the composition of aerobiological samples taken in the Moscow and Ryazan regions for three years during the period of active flowering of grasses. Ten genera of the Poaceae family were detected in airborne pollen samples. The representation for most of them for ITS1 and ITS2 barcodes was similar. At the same time, in some samples, the presence of specific genera was characterized by only one sequence: either ITS1 or ITS2. Based on the analysis of the abundance of both barcode reads in the samples, the following order could describe the change with time in the dominant species in the air: Poa, Alopecurus, and Arrhenatherum in early mid-June, Lolium, Bromus, Dactylis, and Briza in mid-late June, Phleum, Elymus in late June to early July, and Calamagrostis in early mid-July. In most samples, the number of taxa found via metabarcoding analysis was higher compared to that in the phenological observations. The semi-quantitative analysis of high-throughput sequencing data well reflects the abundance of only major grass species at the flowering stage.},
}
@article {pmid37375457,
year = {2023},
author = {Talmi-Frank, D and Byas, AD and Murrieta, R and Weger-Lucarelli, J and Rückert, C and Gallichotte, EN and Yoshimoto, JA and Allen, C and Bosco-Lauth, AM and Graham, B and Felix, TA and Brault, AC and Ebel, GD},
title = {Intracellular Diversity of WNV within Circulating Avian Peripheral Blood Mononuclear Cells Reveals Host-Dependent Patterns of Polyinfection.},
journal = {Pathogens (Basel, Switzerland)},
volume = {12},
number = {6},
pages = {},
pmid = {37375457},
issn = {2076-0817},
support = {F31 AI134108/AI/NIAID NIH HHS/United States ; R01 AI067380/AI/NIAID NIH HHS/United States ; T32 OD010437/OD/NIH HHS/United States ; od010437/NH/NIH HHS/United States ; },
abstract = {Arthropod-borne virus (arbovirus) populations exist as mutant swarms that are maintained between arthropods and vertebrates. West Nile virus (WNV) population dynamics are host-dependent. In American crows, purifying selection is weak and population diversity is high compared to American robins, which have 100- to 1000-fold lower viremia. WNV passed in robins leads to fitness gains, whereas that passed in crows does not. Therefore, we tested the hypothesis that high crow viremia allows for higher genetic diversity within individual avian peripheral blood mononuclear cells (PBMCs), reasoning that this could have produced the previously observed host-specific differences in genetic diversity and fitness. Specifically, we infected cells and birds with a molecularly barcoded WNV and sequenced viral RNA from single cells to quantify the number of WNV barcodes in each. Our results demonstrate that the richness of WNV populations within crows far exceeds that in robins. Similarly, rare WNV variants were maintained by crows more frequently than by robins. Our results suggest that increased viremia in crows relative to robins leads to the maintenance of defective genomes and less prevalent variants, presumably through complementation. Our findings further suggest that weaker purifying selection in highly susceptible crows is attributable to this higher viremia, polyinfections and complementation.},
}
@article {pmid37374941,
year = {2023},
author = {Monyama, MC and Taioe, OM and Nkhebenyane, JS and van Wyk, D and Ramatla, T and Thekisoe, OMM},
title = {Bacterial Communities Associated with Houseflies (Musca domestica L.) Inhabiting Hospices in South Africa.},
journal = {Microorganisms},
volume = {11},
number = {6},
pages = {},
pmid = {37374941},
issn = {2076-2607},
abstract = {Houseflies are alleged reservoirs as well as vectors of human and animal pathogens, including bacteria, because they frequently have contact with animal excreta and decaying organic substances. The rapid adaptation process of ingested microbes in the insect gut may involve gene transfer, including antibiotic resistance determinants among different bacterial strains. Six hundred and fifty-seven (n = 657) houseflies were collected from hospices and were identified morphologically and genetically using the 16S rRNA, CO1, and ITS2 barcoding genes. This study also characterized the bacterial communities harboured by the captured houseflies using 16S rRNA metabarcoding on the next-generation sequencing (NGS) platform and further sought to detect antibiotic resistance traits by using gene-specific PCR assays. Generated sequences for the targeted gene fragments matched with Musca domestica and all the sequences were deposited to the GenBank database. The 16S rRNA metabarcoding analysis revealed that the most abundant phyla detected with variable abundance observed among all the houseflies were Proteobacteria, followed by Firmicutes, and Bacteroidetes. Furthermore, the NGS data revealed the presence of multiple bacterial genera, including Providencia, Enterobacter, Dysgonomonas, Escherichia-Shigella, Klebsiella, Pseudomonas, and Streptococcus, which are known to harbour potentially pathogenic species of animals and humans. Antibiotic resistance genes detected from the housefly DNA in this study included ermB, tetA, blaSHV, and blaTEM. Moreover, these genes are associated with resistance to erythromycin, tetracycline, and beta-lactams antibiotics, respectively. The presence of bacterial pathogens and the detection of antibiotic resistance genes from the houseflies collected from the hospices indicates the possible health risk to patients in hospices and the surrounding community. Therefore, it is imperative to keep high standards of hygiene, food preparation, safety, and control of houseflies in hospices.},
}
@article {pmid37373434,
year = {2023},
author = {Wang, Y and Liang, Q and Zhang, C and Huang, H and He, H and Wang, M and Li, M and Huang, Z and Tang, Y and Chen, Q and Miao, H and Li, H and Zhang, F and Wang, Q and Sun, B},
title = {Sequencing and Analysis of Complete Chloroplast Genomes Provide Insight into the Evolution and Phylogeny of Chinese Kale (Brassica oleracea var. alboglabra).},
journal = {International journal of molecular sciences},
volume = {24},
number = {12},
pages = {},
pmid = {37373434},
issn = {1422-0067},
support = {32072586//National Natural Science Foundation of China/ ; 31500247//National Natural Science Foundation of China/ ; 32172593//National Natural Science Foundation of China/ ; 2022NSFSC1689//Natural Science Foundation of Sichuan Province/ ; sccxtd-2022-05//Project of New Varieties Breeding of Sichuan Vegetable Innovation Team/ ; LY21C020002//Natural Science Foundation of Zhejiang Province/ ; 2021Z132//Science and Technology Plan Project of Ningbo City/ ; },
mesh = {*Brassica/genetics ; Phylogeny ; *Genome, Chloroplast ; Sequence Analysis, DNA ; Flowers ; },
abstract = {Chinese kale is a widely cultivated plant in the genus Brassica in the family Brassicaceae. The origin of Brassica has been studied extensively, but the origin of Chinese kale remains unclear. In contrast to Brassica oleracea, which originated in the Mediterranean region, Chinese kale originated in southern China. The chloroplast genome is often used for phylogenetic analysis because of its high conservatism. Fifteen pairs of universal primers were used to amplify the chloroplast genomes of white-flower Chinese kale (Brassica oleracea var. alboglabra cv. Sijicutiao (SJCT)) and yellow-flower Chinese kale (Brassica oleracea var. alboglabra cv. Fuzhouhuanghua (FZHH)) via PCR. The lengths of the chloroplast genomes were 153,365 bp (SJCT) and 153,420 bp (FZHH) and both contained 87 protein-coding genes and eight rRNA genes. There were 36 tRNA genes in SJCT and 35 tRNA genes in FZHH. The chloroplast genomes of both Chinese kale varieties, along with eight other Brassicaceae, were analyzed. Simple sequence repeats, long repeats, and variable regions of DNA barcodes were identified. An analysis of inverted repeat boundaries, relative synonymous codon usage, and synteny revealed high similarity among the ten species, albeit the slight differences that were observed. The Ka/Ks ratios and phylogenetic analysis suggest that Chinese kale is a variant of B. oleracea. The phylogenetic tree shows that both Chinese kale varieties and B. oleracea var. oleracea were clustered in a single group. The results of this study suggest that white and yellow flower Chinese kale comprise a monophyletic group and that their differences in flower color arose late in the process of artificial cultivation. Our results also provide data that will aid future research on genetics, evolution, and germplasm resources of Brassicaceae.},
}
@article {pmid37372635,
year = {2023},
author = {Filonzi, L and Ardenghi, A and Rontani, PM and Voccia, A and Ferrari, C and Papa, R and Bellin, N and Nonnis Marzano, F},
title = {Molecular Barcoding: A Tool to Guarantee Correct Seafood Labelling and Quality and Preserve the Conservation of Endangered Species.},
journal = {Foods (Basel, Switzerland)},
volume = {12},
number = {12},
pages = {},
pmid = {37372635},
issn = {2304-8158},
abstract = {The recent increase in international fish trade leads to the need for improving the traceability of fishery products. In relation to this, consistent monitoring of the production chain focusing on technological developments, handling, processing and distribution via global networks is necessary. Molecular barcoding has therefore been suggested as the gold standard in seafood species traceability and labelling. This review describes the DNA barcoding methodology for preventing food fraud and adulteration in fish. In particular, attention has been focused on the application of molecular techniques to determine the identity and authenticity of fish products, to discriminate the presence of different species in processed seafood and to characterize raw materials undergoing food industry processes. In this regard, we herein present a large number of studies performed in different countries, showing the most reliable DNA barcodes for species identification based on both mitochondrial (COI, cytb, 16S rDNA and 12S rDNA) and nuclear genes. Results are discussed considering the advantages and disadvantages of the different techniques in relation to different scientific issues. Special regard has been dedicated to a dual approach referring to both the consumer's health and the conservation of threatened species, with a special focus on the feasibility of the different genetic and genomic approaches in relation to both scientific objectives and permissible costs to obtain reliable traceability.},
}
@article {pmid37372604,
year = {2023},
author = {Gorini, T and Mezzasalma, V and Deligia, M and De Mattia, F and Campone, L and Labra, M and Frigerio, J},
title = {Check Your Shopping Cart: DNA Barcoding and Mini-Barcoding for Food Authentication.},
journal = {Foods (Basel, Switzerland)},
volume = {12},
number = {12},
pages = {},
pmid = {37372604},
issn = {2304-8158},
support = {CN_00000033//National Biodiversity Future Center - NBFC/ ; },
abstract = {The molecular approach of DNA barcoding for the characterization and traceability of food products has come into common use in many European countries. However, it is important to address and solve technical and scientific issues such as the efficiency of the barcode sequences and DNA extraction methods to be able to analyze all the products that the food sector offers. The goal of this study is to collect the most defrauded and common food products and identify better workflows for species identification. A total of 212 specimens were collected in collaboration with 38 companies belonging to 5 different fields: seafood, botanicals, agrifood, spices, and probiotics. For all the typologies of specimens, the most suitable workflow was defined, and three species-specific primer pairs for fish were also designed. Results showed that 21.2% of the analyzed products were defrauded. A total of 88.2% of specimens were correctly identified by DNA barcoding analysis. Botanicals (28.8%) have the highest number of non-conformances, followed by spices (28.5%), agrifood (23.5%), seafood (11.4%), and probiotics (7.7%). DNA barcoding and mini-barcoding are confirmed as fast and reliable methods for ensuring quality and safety in the food field.},
}
@article {pmid37372435,
year = {2023},
author = {Chatzoglou, E and Tsaousi, N and Apostolidis, AP and Exadactylos, A and Sandaltzopoulos, R and Giantsis, IA and Gkafas, GA and Malandrakis, EE and Sarantopoulou, J and Tokamani, M and Triantaphyllidis, G and Miliou, H},
title = {High-Resolution Melting (HRM) Analysis for Rapid Molecular Identification of Sparidae Species in the Greek Fish Market.},
journal = {Genes},
volume = {14},
number = {6},
pages = {},
pmid = {37372435},
issn = {2073-4425},
mesh = {Animals ; Greece ; *Perciformes/genetics ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Polymerase Chain Reaction ; },
abstract = {The red porgy (Pagrus pagrus) and the common dentex (Dentex dentex) are Sparidae species of high commercial value, traded in the Greek market. In some cases, fish species identification from Greek fisheries is difficult for the consumer due to the strong morphological similarities with their imported counterparts or closely related species such as Pagrus major, Pagrus caeroleustictus, Dentex gibbosus and Pagellus erythrinus, especially when specimens are frozen, filleted or cooked. Techniques based on DNA sequencing, such as COI barcoding, accurately identify species substitution incidents; however, they are time consuming and expensive. In this study, regions of mtDNA were analyzed with RFLPs, multiplex PCR and HRM in order to develop a rapid method for species identification within the Sparidae family. HRM analysis of a 113 bp region of cytb and/or a 156 bp region of 16s could discriminate raw or cooked samples of P. pagrus and D. dentex from the aforementioned closely related species and P. pagrus specimens sampled in the Mediterranean Sea when compared to those fished in the eastern Atlantic. HRM analysis exhibited high accuracy and repeatability, revealing incidents of mislabeling. Multiple samples can be analyzed within three hours, rendering this method a useful tool in fish fraud monitoring.},
}
@article {pmid37372428,
year = {2023},
author = {Sandoval, L and Mohammed Ismail, W and Mazzone, A and Dumbrava, M and Fernandez, J and Munankarmy, A and Lasho, T and Binder, M and Simon, V and Kim, KH and Chia, N and Lee, JH and Weroha, SJ and Patnaik, M and Gaspar-Maia, A},
title = {Characterization and Optimization of Multiomic Single-Cell Epigenomic Profiling.},
journal = {Genes},
volume = {14},
number = {6},
pages = {},
pmid = {37372428},
issn = {2073-4425},
support = {P30 CA015083/CA/NCI NIH HHS/United States ; P50 CA136393/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Leukocytes, Mononuclear ; *Epigenomics ; Multiomics ; Reproducibility of Results ; RNA, Small Nuclear/genetics ; },
abstract = {The snATAC + snRNA platform allows epigenomic profiling of open chromatin and gene expression with single-cell resolution. The most critical assay step is to isolate high-quality nuclei to proceed with droplet-base single nuclei isolation and barcoding. With the increasing popularity of multiomic profiling in various fields, there is a need for optimized and reliable nuclei isolation methods, mainly for human tissue samples. Herein we compared different nuclei isolation methods for cell suspensions, such as peripheral blood mononuclear cells (PBMC, n = 18) and a solid tumor type, ovarian cancer (OC, n = 18), derived from debulking surgery. Nuclei morphology and sequencing output parameters were used to evaluate the quality of preparation. Our results show that NP-40 detergent-based nuclei isolation yields better sequencing results than collagenase tissue dissociation for OC, significantly impacting cell type identification and analysis. Given the utility of applying such techniques to frozen samples, we also tested frozen preparation and digestion (n = 6). A paired comparison between frozen and fresh samples validated the quality of both specimens. Finally, we demonstrate the reproducibility of scRNA and snATAC + snRNA platform, by comparing the gene expression profiling of PBMC. Our results highlight how the choice of nuclei isolation methods is critical for obtaining quality data in multiomic assays. It also shows that the measurement of expression between scRNA and snRNA is comparable and effective for cell type identification.},
}
@article {pmid37372329,
year = {2023},
author = {Kim, KR and Park, SY and Kim, H and Hong, JM and Kim, SY and Yu, JN},
title = {Complete Chloroplast Genome Determination of Ranunculus sceleratus from Republic of Korea (Ranunculaceae) and Comparative Chloroplast Genomes of the Members of the Ranunculus Genus.},
journal = {Genes},
volume = {14},
number = {6},
pages = {},
pmid = {37372329},
issn = {2073-4425},
mesh = {*Ranunculaceae/genetics ; *Ranunculus/genetics ; *Genome, Chloroplast/genetics ; Phylogeny ; Republic of Korea ; },
abstract = {Ranunculus sceleratus (family: Ranunculaceae) is a medicinally and economically important plant; however, gaps in taxonomic and species identification limit its practical applicability. This study aimed to sequence the chloroplast genome of R. sceleratus from Republic of Korea. Chloroplast sequences were compared and analyzed among Ranunculus species. The chloroplast genome was assembled from Illumina HiSeq 2500 sequencing raw data. The genome was 156,329 bp and had a typical quadripartite structure comprising a small single-copy region, a large single-copy region, and two inverted repeats. Fifty-three simple sequence repeats were identified in the four quadrant structural regions. The region between the ndhC and trnV-UAC genes could be useful as a genetic marker to distinguish between R. sceleratus populations from Republic of Korea and China. The Ranunculus species formed a single lineage. To differentiate between Ranunculus species, we identified 16 hotspot regions and confirmed their potential using specific barcodes based on phylogenetic tree and BLAST-based analyses. The ndhE, ndhF, rpl23, atpF, rps4, and rpoA genes had a high posterior probability of codon sites in positive selection, while the amino acid site varied between Ranunculus species and other genera. Comparison of the Ranunculus genomes provides useful information regarding species identification and evolution that could guide future phylogenetic analyses.},
}
@article {pmid37372310,
year = {2023},
author = {Amorim, JA and de Oliveira, TMP and de Sá, ILR and da Silva, TP and Sallum, MAM},
title = {DNA Barcodes of Mansonia (Mansonia) Blanchard, 1901 (Diptera, Culicidae).},
journal = {Genes},
volume = {14},
number = {6},
pages = {},
pmid = {37372310},
issn = {2073-4425},
mesh = {DNA Barcoding, Taxonomic ; *Malvaceae/genetics ; Animals ; Phylogeny ; Brazil ; Databases, Genetic ; Cluster Analysis ; },
abstract = {Females of the genus Mansonia feed on the blood of humans, livestock, and other vertebrates to develop their eggs. The females' biting behavior may cause severe disturbance to blood hosts, with a negative impact on public health and economics. Certain species have been identified as potential or effective disease vectors. The accurate species identification of field-collected specimens is of paramount importance for the success of monitoring and control strategies. Mansonia (Mansonia) morphological species boundaries are blurred by patterns of intraspecific heteromorphism and interspecific isomorphism. DNA barcodes can help to solve taxonomic controversies, especially if combined with other molecular tools. We used cytochrome c oxidase subunit I (COI) gene 5' end (DNA barcode) sequences to identify 327 field-collected specimens of Mansonia (Mansonia) spp. The sampling encompassed males and females collected from three Brazilian regions and previously assigned to species based on their morphological characteristics. Eleven GenBank and BOLD sequences were added to the DNA barcode analyses. Initial morphospecies assignments were mostly corroborated by the results of five clustering methods based on Kimura two-parameter distance and maximum likelihood phylogeny. Five to eight molecular operational taxonomic units may represent taxonomically unknown species. The first DNA barcode records for Mansonia fonsecai, Mansonia iguassuensis, and Mansonia pseudotitillans are presented.},
}
@article {pmid37370177,
year = {2023},
author = {Angstmann, H and Pfeiffer, S and Kublik, S and Ehrhardt, B and Uliczka, K and Rabe, KF and Roeder, T and Wagner, C and Schloter, M and Krauss-Etschmann, S},
title = {The microbial composition of larval airways from Drosophila melanogaster differ between specimens from laboratory and natural habitats.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {55},
pmid = {37370177},
issn = {2524-6372},
abstract = {BACKGROUND: The fruit fly Drosophila melanogaster lives in natural habitats and has also long been used as a model organism in biological research. In this study, we used a molecular barcoding approach to analyse the airways microbiome of larvae of D. melanogaster, which were obtained from eggs of flies of the laboratory strain w[1118] and from immune deficient flies (NF-kB-K), and from wild-caught flies. To assess intergenerational transmission of microbes, all eggs were incubated under the same semi-sterile conditions.<br><br>RESULTS: The airway microbiome of larvae from both lab-strains was dominated by the two families Acetobacteraceae and Lactobacillaceae, while larvae from wild-caught flies were dominated by Lactobacillaceae, Anaplasmataceae and Leuconostocaceae. Barcodes linked to Anaplasmataceae could be further assigned to Wolbachia sp., which is a widespread intracellular pathogen in arthropods. For Leuconostoceae, the most abundant reads were assigned to Weissella sp. Both Wolbachia and Weissella affect the development of the insects. Finally, a relative high abundance of Serratia sp. was found in larvae from immune deficient relish[-/-] compared to w[1118] and wild-caught fly airways.<br><br>CONCLUSIONS: Our results show for the first time that larvae from D. melanogaster harbor an airway microbiome, which is of low complexity and strongly influenced by the environmental conditions and to a lesser extent by the immune status. Furthermore, our data indicate an intergenerational transmission of the microbiome as shaped by the environment.},
}
@article {pmid37370129,
year = {2023},
author = {Wojtowicz, EE and Mistry, JJ and Uzun, V and Hellmich, C and Scoones, A and Chin, DW and Kettyle, LM and Grasso, F and Lord, AM and Wright, DJ and Etherington, GJ and Woll, PS and Belderbos, ME and Bowles, KM and Nerlov, C and Haerty, W and Bystrykh, LV and Jacobsen, SEW and Rushworth, SA and Macaulay, IC},
title = {Panhematopoietic RNA barcoding enables kinetic measurements of nucleate and anucleate lineages and the activation of myeloid clones following acute platelet depletion.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {152},
pmid = {37370129},
issn = {1474-760X},
support = {BB/M011216/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BS/E/T/000PR9818/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG1720/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MC_UU_12009/7/MRC_/Medical Research Council/United Kingdom ; BBS/E/T/000PR9816/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MC_UU_00016/7/MRC_/Medical Research Council/United Kingdom ; MR/P026028/1/MRC_/Medical Research Council/United Kingdom ; 220534/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; MR/T02934X/1/MRC_/Medical Research Council/United Kingdom ; BB/R50659X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MC_UU_12009/5/MRC_/Medical Research Council/United Kingdom ; MC_UU_00016/5/MRC_/Medical Research Council/United Kingdom ; G0801073/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 26815/CRUK_/Cancer Research UK/United Kingdom ; 213731/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; MC_UU_00029/9/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Mice ; Animals ; *Blood Platelets ; *Hematopoiesis ; Cell Lineage ; Kinetics ; Hematopoietic Stem Cells ; Clone Cells ; Cell Differentiation ; },
abstract = {BACKGROUND: Platelets and erythrocytes constitute over 95% of all hematopoietic stem cell output. However, the clonal dynamics of HSC contribution to these lineages remains largely unexplored.<br><br>RESULTS: We use lentiviral genetic labeling of mouse hematopoietic stem cells to quantify output from all lineages, nucleate, and anucleate, simultaneously linking these with stem and progenitor cell transcriptomic phenotypes using single-cell RNA-sequencing. We observe dynamic shifts of clonal behaviors through time in same-animal peripheral blood and demonstrate that acute platelet depletion shifts the output of multipotent hematopoietic stem cells to the exclusive production of platelets. Additionally, we observe the emergence of new myeloid-biased clones, which support short- and long-term production of blood cells.<br><br>CONCLUSIONS: Our approach enables kinetic studies of multi-lineage output in the peripheral blood and transcriptional heterogeneity of individual hematopoietic stem cells. Our results give a unique insight into hematopoietic stem cell reactivation upon platelet depletion and of clonal dynamics in both steady state and under stress.},
}
@article {pmid37367358,
year = {2023},
author = {Aguado-Aranda, P and Ricarte, A and Nedeljković, Z and Kelso, S and van Eck, APW and Skevington, JH and Marcos-García, M&#xc1;},
title = {Are Appearances Deceiving? Morpho-Genetic Complexity of the Eumerus tricolor Group (Diptera: Syrphidae) in Europe, with a Focus on the Iberian Peninsula.},
journal = {Insects},
volume = {14},
number = {6},
pages = {},
pmid = {37367358},
issn = {2075-4450},
support = {PGC2018-095851-A-C65//Ministerio de Ciencia e Innovaci&#xf3;n (Espa&#xf1;a)/ ; UATALENTO17-08//Vicerrectorado de Investigaci&#xf3;n y Transferencia del Conocimiento (Universidad de Alicante)/ ; PRE2019-087508//Ministerio de Ciencia e Innovaci&#xf3;n (Espa&#xf1;a)/ ; },
abstract = {Eumerus Meigen, 1822 is one of the largest Syrphidae genera in the Palaearctic Region, with the highest levels of taxonomic diversity found in the Eumerus tricolor species group. Despite its high diversity, the interspecific levels of morphological variability can be low. Additionally, some species may show certain levels of intraspecific variability. Hence, species delimitation may become challenging. In this work, we assessed the diversity of the E. tricolor group in the Iberian Peninsula through an integrative analysis of nomenclature, morphology and the 5' (COI-5') and 3' (COI-3') end regions of the Cytochrome c oxidase subunit I gene. Two new species, Eumerus ancylostylus Aguado-Aranda &amp; Ricarte sp. n. and Eumerus petrarum Aguado-Aranda, Nedeljković &amp; Ricarte sp. n., were described, and their intra- and interspecific variations discussed. In addition, the first barcodes of Iberian members of the E. tricolor group were obtained, and the distribution ranges of all species were mapped within the study area. The systematic position of the new species is discussed based on the resulting COI-based trees. The male genitalia of Eumerus hispanicus van der Goot, 1966 and Eumerus bayardi Séguy, 1961 were studied and illustrated. A lectotype was designated for Eumerus lateralis (Zetterstedt, 1819). An updated dichotomous key for all known European species of the E. tricolor group is provided. The egg of E. petrarum sp. n. is also described.},
}
@article {pmid37366519,
year = {2023},
author = {Cho, S and Yang, I and Khim, JS and Park, J},
title = {First confirmed report of Nassarius sinarum (Mollusca, Gastropoda) in Korea.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e99661},
pmid = {37366519},
issn = {1314-2828},
abstract = {BACKGROUND: The marine gastropod mollusc Nassarius sinarum has attracted attention due to its status as a potential invasive species and the ecological impact it may have on local environments and the fishing industry. It was observed exclusively within China initially, but its distribution now seems to have expanded into Japan and Korea. Accurate identification of N. sinarum, particularly in its juvenile stage, is vital for understanding its ecological influences and distribution patterns.<br><br>NEW INFORMATION: This study represents the first comprehensive analysis of N. sinarum samples from Korea. It includes morphological examination, scanning electron microscopy images and molecular sequencing. Two live specimens were collected from the Yeongsan River estuary in Korea and their morphological features were analysed and compared to those of samples from China and Japan. The samples' species were confirmed by molecular identification, based on cytochrome c oxidase subunit I (COI) and histone H3 (H3) genetic markers.It was observed that juvenile N. sinarum shells lack key species-characteristic morphological traits, such as a thick outer lip and diminishing axial ribs. However, COI marker-based molecular identification affirmed that these Korean specimens were N. sinarum. The H3 region was registered with the National Center for Biotechnology Information (NCBI) for the first time. Phylogenetic analysis of the H3 region did not resolve species distinctions within the Nassarius, suggesting that the H3 marker is not suitable for species identification within this genus. In this context, multiple genetic markers, when used appropriately, can also be applied to genus-level searches, enhancing species identification accuracy and reducing misidentification.The sequences provided in this study can serve as a valuable reference for future DNA barcoding research. Additional samples and surveys should be conducted through collaborative efforts amongst national and institutional organisations to further clarify the ecological status of N. sinarum and to investigate its distribution and potential impact around East Asia. Finally, a new Korean name, (No-lan-jul-job-ssal-mu-nui-go-dung; &#xb178;&#xb780;&#xc904;&#xc881;&#xc300;&#xbb34;&#xb2ac;&#xace0;&#xb465;) has been proposed for N. sinarum.},
}
@article {pmid37365249,
year = {2023},
author = {Kalendar, R and Kairov, U and Karabayev, D and Aitkulova, A and Tynyshtykbayeva, N and Daniyarov, A and Otarbay, Z and Rakhimova, S and Akilzhanova, A and Sarbassov, D},
title = {Universal whole-genome Oxford nanopore sequencing of SARS-CoV-2 using tiled amplicons.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {10334},
pmid = {37365249},
issn = {2045-2322},
mesh = {Humans ; SARS-CoV-2/genetics ; *COVID-19/diagnosis ; *Nanopore Sequencing/methods ; DNA, Complementary/genetics ; RNA ; },
abstract = {We developed a comprehensive multiplexed set of primers adapted for the Oxford Nanopore Rapid Barcoding library kit that allows universal SARS-CoV-2 genome sequencing. This primer set is designed to set up any variants of the primers pool for whole-genome sequencing of SARS-CoV-2 using single- or double-tiled amplicons from 1.2 to 4.8 kb with the Oxford Nanopore. This multiplexed set of primers is also applicable for tasks like targeted SARS-CoV-2 genome sequencing. We proposed here an optimized protocol to synthesize cDNA using Maxima H Minus Reverse Transcriptase with a set of SARS-CoV-2 specific primers, which has high yields of cDNA template for RNA and is capable of long-length cDNA synthesis from a wide range of RNA amounts and quality. The proposed protocol allows whole-genome sequencing of the SARS-CoV-2 virus with tiled amplicons up to 4.8 kb on low-titer virus samples and even where RNA degradation has occurred. This protocol reduces the time and cost from RNA to genome sequence compared to the Midnight multiplex PCR method for SARS-CoV-2 genome sequencing using the Oxford Nanopore.},
}
@article {pmid37363049,
year = {2023},
author = {Klangnurak, W and Arunrugstichai, S and Manopawitr, P and Krajangdara, T},
title = {DNA-based species identification of shark fins traded in thai markets.},
journal = {Conservation genetics (Print)},
volume = {},
number = {},
pages = {1-10},
pmid = {37363049},
issn = {1566-0621},
abstract = {UNLABELLED: Shark fins are among the most highly prized seafood products in the world with massive consumption in Asia over the past several decades. The demand for shark fins is a major driver of the enormous population declines of elasmobranchs that are generally vulnerable to overexploitation. This study aims to better understand the species composition of shark fin products in Thailand and their conservation statuses by using DNA-based species identification. Various types and sizes of shark fins were collected from 4 locations in Thailand. DNA barcoding method based on a fragment of the cytochrome c oxidase subunit I (COI) gene was applied to species identification. Fins from at least 15 shark species were found from Thailand's markets. The spottail shark (Carcharhinus sorrah) and the night shark (Carcharhinus signatus) were the two dominant species presented in this study. 34% of identifiable samples are the species that have not been record in this region. 62% of species detected from the fin samples are categorized under the threatened categories of IUCN Red List. Species composition reported in shark fin products potentially helps indicate the appropriate conservation action and increases awareness from monitoring the trade in elasmobranch products.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10592-023-01519-0.},
}
@article {pmid37360051,
year = {2023},
author = {Jadid, N and Rosidah, NLA and Ramadani, MRN and Prasetyowati, I and Sa'adah, NN and Widodo, AF and Oktafitria, D},
title = {Plastid DNA Barcoding and RtActin cDNA Fragment Isolation of Reutealis Trisperma: A Promising Bioresource for Biodiesel Production.},
journal = {Bioinformatics and biology insights},
volume = {17},
number = {},
pages = {11779322231182768},
pmid = {37360051},
issn = {1177-9322},
abstract = {Reutealis trisperma belonging to the family Euphorbiaceae is currently used for biodiesel production, and rapid development in plant-based biofuel production has led to its increasing demand. However, massive utilization of bio-industrial plants has led to conservation issues. Moreover, genetic information on R trisperma is still limited, which is crucial for developmental, physiological, and molecular studies. Studying gene expression is essential to explain plant physiological processes. Nonetheless, this technique requires sensitive and precise measurement of messenger RNA (mRNA). In addition, the presence of internal control genes is important to avoid bias. Therefore, collecting and preserving genetic data for R trisperma is indispensable. In this study, we aimed to evaluate the application of plastid loci, rbcL, and matK, to the DNA barcode of R trisperma for use in conservation programs. In addition, we isolated and cloned the RtActin (RtACT) gene fragment for use in gene expression studies. Sequence information was analyzed in silico by comparison with other Euphorbiaceae plants. For actin fragment isolation, reverse-transcription polymerase chain reaction was used. Molecular cloning of RtActin was performed using the pTA2 plasmid before sequencing. We successfully isolated and cloned 592 and 840 bp of RtrbcL and RtmatK fragment genes, respectively. The RtrbcL barcoding marker, rather than the RtmatK plastidial marker, provided discriminative molecular phylogenetic data for R Trisperma. We also isolated 986 bp of RtACT gene fragments. Our phylogenetic analysis demonstrated that R trisperma is closely related to the Vernicia fordii Actin gene (97% identity). Our results suggest that RtrbcL could be further developed and used as a barcoding marker for R trisperma. Moreover, the RtACT gene could be further investigated for use in gene expression studies of plant.},
}
@article {pmid37359554,
year = {2023},
author = {Hulen, TM and Friese, C and Kristensen, NP and Granhøj, JS and Borch, TH and Peeters, MJW and Donia, M and Andersen, MH and Hadrup, SR and Svane, IM and Met, &#xd6;},
title = {Ex vivo modulation of intact tumor fragments with anti-PD-1 and anti-CTLA-4 influences the expansion and specificity of tumor-infiltrating lymphocytes.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1180997},
pmid = {37359554},
issn = {1664-3224},
mesh = {Humans ; *Lymphocytes, Tumor-Infiltrating ; *Melanoma ; Immunotherapy ; Tumor Microenvironment ; },
abstract = {Checkpoint inhibition (CPI) therapy and adoptive cell therapy with autologous tumor-infiltrating lymphocytes (TIL-based ACT) are the two most effective immunotherapies for the treatment of metastatic melanoma. While CPI has been the dominating therapy in the past decade, TIL-based ACT is beneficial for individuals even after progression on previous immunotherapies. Given that notable differences in response have been made when used as a subsequent treatment, we investigated how the qualities of TILs changed when the ex vivo microenvironment of intact tumor fragments were modulated with checkpoint inhibitors targeting programmed death receptor 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4). Initially, we show that unmodified TILs from CPI-resistant individuals can be produced, are overwhelmingly terminally differentiated, and are capable of responding to tumor. We then investigate these properties in ex vivo checkpoint modulated TILs finding that that they retain these qualities. Lastly, we confirmed the specificity of the TILs to the highest responding tumor antigens, and identified this reactivity resides largely in CD39[+]CD69[+] terminally differentiated populations. Overall, we found that anti-PD-1 will alter the proliferative capacity while anti-CTLA4 will influence breadth of antigen specificity.},
}
@article {pmid37355644,
year = {2023},
author = {Bemis, KE and Girard, MG and Santos, MD and Carpenter, KE and Deeds, JR and Pitassy, DE and Flores, NAL and Hunter, ES and Driskell, AC and Macdonald, KS and Weigt, LA and Williams, JT},
title = {Biodiversity of Philippine marine fishes: A DNA barcode reference library based on voucher specimens.},
journal = {Scientific data},
volume = {10},
number = {1},
pages = {411},
pmid = {37355644},
issn = {2052-4463},
mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic ; *Fishes/genetics ; Gene Library ; Philippines ; },
abstract = {Accurate identification of fishes is essential for understanding their biology and to ensure food safety for consumers. DNA barcoding is an important tool because it can verify identifications of both whole and processed fishes that have had key morphological characters removed (e.g., filets, fish meal); however, DNA reference libraries are incomplete, and public repositories for sequence data contain incorrectly identified sequences. During a nine-year sampling program in the Philippines, a global biodiversity hotspot for marine fishes, we developed a verified reference library of cytochrome c oxidase subunit I (COI) sequences for 2,525 specimens representing 984 species. Specimens were primarily purchased from markets, with additional diversity collected using rotenone or fishing gear. Species identifications were verified based on taxonomic, phenotypic, and genotypic data, and sequences are associated with voucher specimens, live-color photographs, and genetic samples catalogued at Smithsonian Institution, National Museum of Natural History. The Biodiversity of Philippine Marine Fishes dataset is released herein to increase knowledge of species diversity and distributions and to facilitate accurate identification of market fishes.},
}
@article {pmid37354241,
year = {2023},
author = {Blaschke, M and Siemonsmeier, A and Harjes, J and Okach, DO and Rambold, G},
title = {Comparison of survey methods for fungi using metabarcoding and fruit body inventories in an altitudinal gradient.},
journal = {Archives of microbiology},
volume = {205},
number = {7},
pages = {269},
pmid = {37354241},
issn = {1432-072X},
support = {22WC412201//Waldklimafonds/ ; 22WC412201//Waldklimafonds/ ; 22WC412203//Waldklimafonds/ ; 22WC412203//Waldklimafonds/ ; 22WC412203//Waldklimafonds/ ; },
mesh = {Fungi/genetics ; Fruit ; *Basidiomycota/genetics ; Altitude ; *Ascomycota ; Biodiversity ; Surveys and Questionnaires ; },
abstract = {Metabarcoding of environmental samples is nowadays an established method in biodiversity research. When it comes to studying fungal populations in various ecotypes, fruit body inventories are the traditional method to assess the diversity of fungal communities. In this study, both methods-metabarcoding of soil samples and a traditional fruit body inventory-were conducted on 144 sample plots in an altitudinal gradient in the Bavarian Forest (Germany) and the results were compared. Metabarcoding detected significantly more species than the traditional fruit body inventory. The majority of taxa recorded in the fruit body inventory belonged to the Basidiomycota, whereas in the metabarcoding data, the distribution of species between Basidiomycota and Ascomycota was approximately balanced. Species of several orders forming inconspicuous or hypogeous fruit bodies were detected only by metabarcoding, while several wood decomposers were recorded only in the fruit body inventory. The proportion of detected wood-colonising species with melanized spores was considerably higher with metabarcoding than with the fruit body inventory, where more than 70% of recorded wood-colonisers had hyaline spores. Based on the metabarcoding data, a decline of species richness with increasing altitude was evident, but this was not visible in the fruit body inventory data. Detrended correspondence analyses yielded similar results for relative species community similarities with both survey methods.},
}
@article {pmid37352839,
year = {2023},
author = {Chung, T and Wang, H and Cai, H},
title = {Dielectric metasurfaces for next-generation optical biosensing: a comparison with plasmonic sensing.},
journal = {Nanotechnology},
volume = {34},
number = {40},
pages = {},
pmid = {37352839},
issn = {1361-6528},
support = {P41 EB017183/EB/NIBIB NIH HHS/United States ; },
mesh = {*Heating ; *Lab-On-A-Chip Devices ; Point-of-Care Systems ; Vibration ; },
abstract = {In the past decades, nanophotonic biosensors have been extended from the extensively studied plasmonic platforms to dielectric metasurfaces. Instead of plasmonic resonance, dielectric metasurfaces are based on Mie resonance, and provide comparable sensitivity with superior resonance bandwidth, Q factor, and figure-of-merit. Although the plasmonic photothermal effect is beneficial in many biomedical applications, it is a fundamental limitation for biosensing. Dielectric metasurfaces solve the ohmic loss and heating problems, providing better repeatability, stability, and biocompatibility. We review the high-Q resonances based on various physical phenomena tailored by meta-atom geometric designs, and compare dielectric and plasmonic metasurfaces in refractometric, surface-enhanced, and chiral sensing for various biomedical and diagnostic applications. Departing from conventional spectral shift measurement using spectrometers, imaging-based and spectrometer-less biosensing are highlighted, including single-wavelength refractometric barcoding, surface-enhanced molecular fingerprinting, and integrated visual reporting. These unique modalities enabled by dielectric metasurfaces point to two important research directions. On the one hand, hyperspectral imaging provides massive information for smart data processing, which not only achieve better biomolecular sensing performance than conventional ensemble averaging, but also enable real-time monitoring of cellular or microbial behaviour in physiological conditions. On the other hand, a single metasurface can integrate both functions of sensing and optical output engineering, using single-wavelength or broadband light sources, which provides simple, fast, compact, and cost-effective solutions. Finally, we provide perspectives in future development on metasurface nanofabrication, functionalization, material, configuration, and integration, towards next-generation optical biosensing for ultra-sensitive, portable/wearable, lab-on-a-chip, point-of-care, multiplexed, and scalable applications.},
}
@article {pmid37352685,
year = {2023},
author = {Baricevic, A and Maric Pfannkuchen, D and Smodlaka Tankovic, M and Knjaz, M and Vlasicek, I and Grizancic, L and Kogovsek, T and Pfannkuchen, M},
title = {Identification of the heterotrophic nanoflagellate Bilabrum latius in the southern Adriatic (Mediterranean Sea).},
journal = {European journal of protistology},
volume = {90},
number = {},
pages = {125999},
doi = {10.1016/j.ejop.2023.125999},
pmid = {37352685},
issn = {1618-0429},
mesh = {*Ecosystem ; Mediterranean Sea ; *Stramenopiles ; Plankton ; Microscopy ; },
abstract = {Heterotrophic flagellates (HF) represent an important protist group in marine ecosystem functioning. Characterised by high taxonomic diversity, identification and classification of HF is often difficult using classical methods of light microscopy (LM). Complementing LM with molecular methods, such as barcoding, enables reliable taxonomic identification of even small size nanoflagellates that share similar or unnoticeable morphological features. The order Bicosoecida is a group of heterotrophic nanoflagellates that are important part of protist plankton and benthic communities of the world oceans. Recently, on the basis of high-resolution light microscopy and barcoding, a new bicosoecid genus, Bilabrum, was described with B. latius sp. as a type species. Our study reports on identification of B. latius from co-culture with the diatom species Chaetoceros affinis isolated from fresh plankton samples collected in the southern Adriatic. This detection of the Adriatic B.latius represents first record of this species outside itś up to now known and described habitat (deep-sea sediment of the South - East Atlantic Ocean) and in diatom co-culture.},
}
@article {pmid37350733,
year = {2023},
author = {Lobo, RR and Arce-Cordero, JA and Agustinho, BC and Ravelo, AD and Vinyard, JR and Johnson, ML and Monteiro, HF and Sarmikasoglou, E and Roesch, LFW and Jeong, KCC and Faciola, AP},
title = {Can dietary magnesium sources and buffer change the ruminal microbiota composition and fermentation of lactating dairy cows?.},
journal = {Journal of animal science},
volume = {101},
number = {},
pages = {},
pmid = {37350733},
issn = {1525-3163},
mesh = {Pregnancy ; Female ; Cattle ; Animals ; *Lactation ; Magnesium/analysis/metabolism/pharmacology ; Fermentation ; Magnesium Oxide/analysis/metabolism/pharmacology ; Detergents/analysis/metabolism/pharmacology ; RNA, Ribosomal, 16S/metabolism ; Digestion ; Milk/metabolism ; Diet/veterinary ; Butyrates/analysis ; Zea mays/metabolism ; *Microbiota ; Lactates/analysis/metabolism/pharmacology ; Rumen/metabolism ; },
abstract = {Magnesium oxide (MgO) is one of the most used Mg supplements in livestock. However, to avoid relying upon only one Mg source, it is important to have alternative Mg sources. Therefore, the objective of this study was to evaluate the effects of the interaction of two Mg sources with buffer use on the ruminal microbiota composition, ruminal fermentation, and nutrient digestibility in lactating dairy cows. Twenty lactating Holstein cows were blocked by parity and days in milk into five blocks with four cows each, in a 2 × 2 factorial design. Within blocks, cows were assigned to one of four treatments: 1) MgO; 2) MgO + Na sesquicarbonate (MgO+); 3) calcium-magnesium hydroxide (CaMgOH); 4) CaMgOH + Na sesquicarbonate (CaMgOH+). For 60 d, cows were individually fed a corn silage-based diet, and treatments were top-dressed. Ruminal fluid was collected via an orogastric tube, for analyses of the microbiota composition, volatile fatty acids (VFA), lactate, and ammonia nitrogen (NH3-N). The microbiota composition was analyzed using V4/16S rRNA gene sequencing, and taxonomy was assigned using the Silva database. Statistical analysis was carried out following the procedures of block design analysis, where block and cow were considered random variables. Effects of Mg source, buffer, and the interaction between Mg Source × Buffer were analyzed through orthogonal contrasts. There was no interaction effect of the two factors evaluated. There was a greater concentration of NH3-N, lactate, and butyrate in the ruminal fluid of cows fed with CaMg(OH)2, regardless of the buffer use. The increase in these fermentation intermediates/ end-products can be explained by an increase in abundance of micro-organisms of the genus Prevotella, Lactobacillus, and Butyrivibrio, which are micro-organisms mainly responsible for proteolysis, lactate-production, and butyrate-production in the rumen, respectively. Also, dietary buffer use did not affect the ruminal fermentation metabolites and pH; however, an improvement of the apparent total tract digestibility of dry matter (DM), organic matter (OM), neutral fiber detergent (NDF), and acid fiber detergent (ADF) were found for animals fed with dietary buffer. In summary, there was no interaction effect of buffer use and Mg source, whereas buffer improved total tract apparent digestibility of DM and OM through an increase in NDF and ADF digestibility and CaMg(OH)2 increased ruminal concentration of butyrate and abundance of butyrate-producing bacteria.},
}
@article {pmid37346768,
year = {2023},
author = {Osawa, M and Chan, TY and Yang, CH},
title = {New records of the squat lobster genus Munidopsis Whiteaves, 1874 (Crustacea, Decapoda, Munidopsidae) from the deep sea off Taiwan.},
journal = {ZooKeys},
volume = {1166},
number = {},
pages = {271-286},
pmid = {37346768},
issn = {1313-2989},
abstract = {Two species of the squat lobster family Munidopsidae, Munidopsisalbatrossae Pequegnat &amp; Pequegnat, 1973 and M.pycnopoda Baba, 2005, are reported from Taiwan for the first time based on specimens collected from lower bathyal depths. The Taiwanese material of M.pycnopoda also represents the first record of the species from the Pacific Ocean and greatly extends this species' geographical range from the western Indian Ocean to western Pacific. The giant Munidopsis specimen from Taiwan is identified as M.albatrossae mainly by DNA barcoding even though M.albatrossae and M.aries (A. Milne-Edwards, 1880) are both morphologically and genetically extremely similar.},
}
@article {pmid37346767,
year = {2023},
author = {Wu, R and Liu, L and Zhang, L and Jia, J and Jin, D and Wu, X and Liu, X},
title = {New species of the genus Pseudocuneopsis Huang, Dai, Chen &amp; Wu, 2022 (Bivalvia, Unionidae) from Guangxi Province, China.},
journal = {ZooKeys},
volume = {1166},
number = {},
pages = {261-270},
pmid = {37346767},
issn = {1313-2989},
abstract = {A new species of freshwater mussel belonging to the genus Pseudocuneopsis, namely Pseudocuneopsisyangshuoensissp. nov., is diagnosed and described from Guangxi Province, China. This paper provides a detailed morphological description, photograph of the type specimen, and anatomical characteristics along with partial sequences of mitochondrial COI as DNA barcode data for this novel species. The new species can be distinguished from its congeners (Pseudocuneopsissichuanensis and Pseudocuneopsiscapitata) by shell shape, beak position and surface sculpture. The interspecies genetic distance based on the COI barcode between P.yangshuoensissp. nov. and P.sichuanensis is 8%, while it reaches 9% with P.capitata. Therefore, we provide robust morphological and molecular evidence to support the validity of this new species.},
}
@article {pmid37346129,
year = {2023},
author = {Zhou, SM and Wang, F and Yan, SY and Zhu, ZM and Gao, XF and Zhao, XL},
title = {Phylogenomics and plastome evolution of Indigofera (Fabaceae).},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1186598},
pmid = {37346129},
issn = {1664-462X},
abstract = {INTRODUCTION: Indigofera L. is the third largest genus in Fabaceae and includes economically important species that are used for indigo dye-producing, medicinal, ornamental, and soil and water conservation. The genus is taxonomically difficult due to the high level of overlap in morphological characters of interspecies, fewer reliability states for classification, and extensive adaptive evolution. Previous characteristic-based taxonomy and nuclear ITS-based phylogenies have contributed to our understanding of Indigofera taxonomy and evolution. However, the lack of chloroplast genomic resources limits our comprehensive understanding of the phylogenetic relationships and evolutionary processes of Indigofera.<br><br>METHODS: Here, we newly assembled 18 chloroplast genomes of Indigofera. We performed a series of analyses of genome structure, nucleotide diversity, phylogenetic analysis, species pairwise Ka/Ks ratios, and positive selection analysis by combining with allied species in Papilionoideae.<br><br>RESULTS AND DISCUSSION: The chloroplast genomes of Indigofera exhibited highly conserved structures and ranged in size from 157,918 to 160,040 bp, containing 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Thirteen highly variable regions were identified, of which trnK-rbcL, ndhF-trnL, and ycf1 were considered as candidate DNA barcodes for species identification of Indigofera. Phylogenetic analysis using maximum likelihood (ML) and Bayesian inference (BI) methods based on complete chloroplast genome and protein-coding genes (PCGs) generated a well-resolved phylogeny of Indigofera and allied species. Indigofera monophyly was strongly supported, and four monophyletic lineages (i.e., the Pantropical, East Asian, Tethyan, and Palaeotropical clades) were resolved within the genus. The species pairwise Ka/Ks ratios showed values lower than 1, and 13 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis using the branch-site model, eight of which were associated with photosynthesis. Positive selection of accD suggested that Indigofera species have experienced adaptive evolution to selection pressures imposed by their herbivores and pathogens. Our study provided insight into the structural variation of chloroplast genomes, phylogenetic relationships, and adaptive evolution in Indigofera. These results will facilitate future studies on species identification, interspecific and intraspecific delimitation, adaptive evolution, and the phylogenetic relationships of the genus Indigofera.},
}
@article {pmid37346120,
year = {2023},
author = {Jiang, RH and Liang, SQ and Wu, F and Tang, LM and Qin, B and Chen, YY and Huang, YH and Li, KX and Zhang, XC},
title = {Phylogenomic analysis, cryptic species discovery, and DNA barcoding of the genus Cibotium in China based on plastome data.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1183653},
pmid = {37346120},
issn = {1664-462X},
abstract = {Germplasm resources are the source of herbal medicine production. The cultivation of superior germplasm resources helps to resolve the conflict between long-term population persistence and growing market demand by consistently producing materials with high quality. The fern species Cibotium barometz is the original plant of cibotii rhizoma ("Gouji"), a traditional Chinese medicine used in the therapy of pain, weakness, and numbness in the lower extremities. Long-history medicinal use has caused serious wild population decline in China. Without sufficient understanding of the species and lineage diversity of Cibotium, it is difficult to propose a targeted conservation scheme at present, let alone select high-quality germplasm resources. In order to fill such a knowledge gap, this study sampled C. barometz and relative species throughout their distribution in China, performed genome skimming to obtain plastome data, and conducted phylogenomic analyses. We constructed a well-supported plastome phylogeny of Chinese Cibotium, which showed that three species with significant genetic differences are distributed in China, namely C. barometz, C. cumingii, and C. sino-burmaense sp. nov., a cryptic species endemic to NW Yunnan and adjacent regions of NE Myanmar. Moreover, our results revealed two differentiated lineages of C. barometz distributed on the east and west sides of a classic phylogeographic boundary that was probably shaped by monsoons and landforms. We also evaluated the resolution of nine traditional barcode loci and designed five new DNA barcodes based on the plastome sequence that can distinguish all these species and lineages of Chinese Cibotium accurately. These novel findings on a genetic basis will guide conservation planners and medicinal plant breeders to build systematic conservation plans and exploit the germplasm resources of Cibotium in China.},
}
@article {pmid37342200,
year = {2023},
author = {Mwamula, AO and Lee, SM and Jung, YH and Lee, HW and Kim, YS and Kim, YH and Lee, DW},
title = {Morphological and Molecular Characterization of Diplogasteroides sp., a Cryptic Population of the Haslacheri Group (Diplogastridae), and Parasitorhabditis terebranus (Rhabditidae) from Korea.},
journal = {Journal of nematology},
volume = {55},
number = {1},
pages = {20230017},
pmid = {37342200},
issn = {0022-300X},
abstract = {Diplogasteroides sp., a cryptic population of D. haslacheri, and Parasitorhabditis terebranus were reported from the frass of Monochamus alternatus galleries in dead Pinus thunbergii for the first time in Korea. Females and males are morphologically characterized and their linked DNA barcodes (18S-rRNA, 28S-rRNA, ITS-rRNA and COI) supplied. Females and males of the two species from Korea conform to the original species descriptions from Europe and the USA, with variations in a few details in morphometrics. Specifically, Diplogasteroides sp. is morphologically very similar to D. haslacheri. However, it cannot be designated as D. haslacheri due to the existence of cryptic species complex within the haslacheri group (D. haslacheri, D. asiaticus, D. nix, D. andrassyi, and D. carinthiacus), a condition requiring hybridization studies to test species identity within the group. Based on analysis of COI sequences, differences among these cryptic species are evident. Thus, in addition to hybridization tests, the COI might be a powerful DNA barcoding marker for the precise identification of these cryptic species within the genus. Additionally, this is the first molecular characterization of P. terebranus, and the species is herein recorded for the first time outside its type locality.},
}
@article {pmid37342154,
year = {2022},
author = {Telagathoti, A and Probst, M and Mandolini, E and Peintner, U},
title = {Mortierellaceae from subalpine and alpine habitats: new species of Entomortierella, Linnemannia, Mortierella, Podila and Tyroliella gen. nov.},
journal = {Studies in mycology},
volume = {103},
number = {},
pages = {25-58},
pmid = {37342154},
issn = {0166-0616},
support = {P 31038/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Fungi are incredibly diverse, but they are unexplored, especially in the subalpine and alpine zone. Mortierellaceae are certainly one of the most abundant, species-rich, and widely distributed cultivable soil fungal families in terrestrial habitats, including subalpine and alpine zones. The phylogeny of Mortierellaceae was recently resolved based on current state of the art molecular techniques, and the paraphyletic genus Mortierella sensu lato (s.l.) was divided into 13 monophyletic genera. Our extensive sampling campaigns in the Austrian Alps resulted in 139 different Mortierellaceae pure culture isolates representing 13 new species. For the definition of taxa, we applied both classical morphological criteria, as well as modern DNA-based methods. Phylogenetic relationships were resolved based on the ribosomal DNA internal transcribed spacer (rDNA ITS), the large subunit (LSU), and the DNA-directed RNA polymerase II largest subunit 1 (RPB1). In this study, we proposed a new genus and described 13 new species belonging to the genera Entomortierella, Linnemannia, Mortierella and Podila. In addition, we proposed eight new combinations, re-defined E. jenkinii at species level, defined a neotype for M. alpina and lecto- as well as epitypes for M. fatshederae, M. jenkinii, and M. longigemmata. The rDNA ITS region is generally applied as classical barcoding gene for fungi. However, the obtained phylogenetic resolution is often too low for an accurate identification of closely related species of Mortierellaceae, especially for small sampling sizes. In such cases, unambiguous identification can be obtained based on morphological characters of pure culture isolates. Therefore, we also provide dichotomous keys for species identification within phylogenetic lineages. Taxonomic novelties: new genus: Tyroliella Telagathoti, Probst &amp; Peintner; New species: Entomortierella galaxiae Telagathoti, M. Probst &amp; Peintner, Linnemannia bainierella Telagathoti, M. Probst &amp; Peintner, Linnemannia stellaris Telagathoti, M. Probst &amp; Peintner, Linnemannia nimbosa Telagathoti, M. Probst &amp; Peintner, Linnemannia mannui Telagathoti, M. Probst &amp; Peintner, Linnemannia friederikiana Telagathoti, M. Probst &amp; Peintner, Linnemannia scordiella Telagathoti, M. Probst &amp; Peintner, Linnemannia solitaria Telagathoti, M. Probst &amp; Peintner, Mortierella triangularis Telagathoti, M. Probst &amp; Peintner, Mortierella lapis Telagathoti, M. Probst &amp; Peintner, Podila himami Telagathoti, M. Probst &amp; Peintner, Podila occulta Telagathoti, M. Probst &amp; Peintner, Tyroliella animus-liberi Telagathoti, Probst &amp; Peintner; New combinations: Entomortierella basiparvispora (W. Gams &amp; Grinb.) Telagathoti, M. Probst &amp; Peintner, Entomortierella jenkinii (A.L. Sm.) Telagathoti, M. Probst &amp; Peintner; Entomortierella sugadairana (Y. Takash. et al.) Telagathoti, M. Probst &amp; Peintner, Linnemannia zonata (Linnem. ex W. Gams) Telagathoti, M. Probst &amp; Peintner, Linnemannia fluviae (Hyang B. Lee et al.) Telagathoti, M. Probst &amp; Peintner, Linnemannia biramosa (Tiegh.) Telagathoti, M. Probst &amp; Peintner, Linnemannia cogitans (Degawa) Telagathoti, M. Probst &amp; Peintner, Tyroliella pseudozygospora (W. Gams &amp; Carreiro) Telagathoti, M. Probst &amp; Peintner; Epitypifications (basionyms): Mortierella bainieri var. jenkinii A.L. Sm., Mortierella fatshederae Linnem., Mortierella longigemmata Linnem. Neotypification (basionym): Mortierella alpina Peyronel. Citation: Telagathoti A, Probst M, Mandolini E, Peintner U (2022). Mortierellaceae from subalpine and alpine habitats: new species of Entomortierella, Linnemannia, Mortierella, Podila and Tyroliella gen. nov. Studies in Mycology 103: 25-58. doi: 10.3114/sim.2022.103.02.},
}
@article {pmid37341269,
year = {2023},
author = {Atencio, GWG and Zanini, R and Deprá, M and Romanowski, HP},
title = {Preliminary population studies of the grassland swallowtail butterfly Euryades corethrus (Lepidoptera, Papilionidae).},
journal = {Anais da Academia Brasileira de Ciencias},
volume = {95},
number = {2},
pages = {e20210503},
doi = {10.1590/0001-3765202320210503},
pmid = {37341269},
issn = {1678-2690},
mesh = {Animals ; *Butterflies/genetics ; Grassland ; Larva ; Argentina ; *Aristolochia ; },
abstract = {Euryades corethrus is a Troidini butterfly (Papilionidae, Papilioninae), endemic to grasslands in southern Brazil, Uruguay, Argentina and Paraguay. Formerly abundant, nowadays it is in the Red list of endangered species for those areas. During its larval stage, it feeds on Aristolochia spp, commonly found in southern grasslands. These native grassland areas are diminishing, being converted to crops and pastures, causing habitat loss for Aristolochia and E. corethrus. This study aimed to assess the genetic diversity, population structure and demographic history of E. corethrus. We sampled eight populations from Rio Grande do Sul, Brazil and based on Cytochrome Oxidase subunit I (COI) molecular marker, our results suggest a low genetic variability between populations, presence of gene flow and, consequently, lack of population structure. A single maternally inherited-genetic marker is insufficient for population-level decisions, but barcoding is a useful tool during early stages of population investigation, bringing out genomic diversity patterns within the target species. Those populations likely faced a bottleneck followed by a rapid expansion during the last glaciation and subsequent stabilization in effective population size. Habitat loss is a threat, which might cause isolation, loss of genetic variability and, ultimately, extinction of E. corethrus if no habitat conservation policy is adopted.},
}
@article {pmid37336285,
year = {2023},
author = {Wang, Y and Zhang, X and Wang, Z},
title = {Cellular barcoding: From developmental tracing to anti-tumor drug discovery.},
journal = {Cancer letters},
volume = {567},
number = {},
pages = {216281},
doi = {10.1016/j.canlet.2023.216281},
pmid = {37336285},
issn = {1872-7980},
mesh = {Humans ; Cell Lineage/genetics ; *Neoplasms/drug therapy/genetics ; *Antineoplastic Agents/pharmacology/therapeutic use ; },
abstract = {Clonal evolution has gained immense attention in explaining cancer cell status, history, and fate during cancer progression. Current single-cell or spatial transcriptome technologies have broadened our understanding of various mechanisms underlying cancer initiation, relapse, and drug resistance. However, technical challenges still hinder a better understanding of the dynamics of distinctive phenotypic states and abnormal trajectories from normal physiological transition to malignant stages. Cellular barcoding enabled lineage tracing on parallelly massive cells at single-cell resolution through different mechanisms lately, enabling new insights into exploring developmental trajectories, cancer progression, and targeted therapies. This review summarizes the latest noteworthy and robust strategies for different types of cellular barcodes. To introduce the major characteristics, advantages and limitations of these different strategies, this review will further guide in choosing or improving cellular barcoding technologies and their applications in cancer research.},
}
@article {pmid37335493,
year = {2023},
author = {Beránková, D and Hřibová, E},
title = {Bulked Oligo-FISH for Chromosome Painting and Chromosome Barcoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2672},
number = {},
pages = {445-463},
pmid = {37335493},
issn = {1940-6029},
mesh = {*Chromosome Painting/methods ; In Situ Hybridization, Fluorescence/methods ; *Chromosomes, Plant/genetics ; Karyotype ; Karyotyping ; },
abstract = {Recently developed bulked oligo-FISH is a highly versatile method, which is applicable in any plant species with an assembled genome sequence. This technique allows in situ identification of individual chromosomes, large chromosomal rearrangements, comparative karyotype analysis, or even the reconstruction of the three-dimensional organization of the genome. The method is based on the identification of thousands of short oligonucleotides, unique to specific genome regions, which are synthesized in parallel, fluorescently labeled and used as probes for FISH. In this chapter, we propose a detailed protocol for amplification and labeling of single-stranded oligo-based painting probes from so-called MYtags immortal libraries, the preparation of mitotic metaphase and meiotic pachytene chromosome spreads, and a protocol for the fluorescence in situ hybridization procedure using the synthetic oligo probes. The proposed protocols are demonstrated for banana (Musa spp.).},
}
@article {pmid37333139,
year = {2023},
author = {Wolin, E and Guo, JK and Blanco, MR and Perez, AA and Goronzy, IN and Abdou, AA and Gorhe, D and Guttman, M and Jovanovic, M},
title = {SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a potential mechanism for selective translational suppression upon cellular stress.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37333139},
issn = {2692-8205},
support = {R01 HG012216/HG/NHGRI NIH HHS/United States ; F30 CA278005/CA/NCI NIH HHS/United States ; U01 DK127420/DK/NIDDK NIH HHS/United States ; R35 GM128802/GM/NIGMS NIH HHS/United States ; R01 DA053178/DA/NIDA NIH HHS/United States ; R01 AG071869/AG/NIA NIH HHS/United States ; },
abstract = {RNA binding proteins (RBPs) play crucial roles in regulating every stage of the mRNA life cycle and mediating non-coding RNA functions. Despite their importance, the specific roles of most RBPs remain unexplored because we do not know what specific RNAs most RBPs bind. Current methods, such as crosslinking and immunoprecipitation followed by sequencing (CLIP-seq), have expanded our knowledge of RBP-RNA interactions but are generally limited by their ability to map only one RBP at a time. To address this limitation, we developed SPIDR (Split and Pool Identification of RBP targets), a massively multiplexed method to simultaneously profile global RNA binding sites of dozens to hundreds of RBPs in a single experiment. SPIDR employs split-pool barcoding coupled with antibody-bead barcoding to increase the throughput of current CLIP methods by two orders of magnitude. SPIDR reliably identifies precise, single-nucleotide RNA binding sites for diverse classes of RBPs simultaneously. Using SPIDR, we explored changes in RBP binding upon mTOR inhibition and identified that 4EBP1 acts as a dynamic RBP that selectively binds to 5'-untranslated regions of specific translationally repressed mRNAs only upon mTOR inhibition. This observation provides a potential mechanism to explain the specificity of translational regulation controlled by mTOR signaling. SPIDR has the potential to revolutionize our understanding of RNA biology and both transcriptional and post-transcriptional gene regulation by enabling rapid, de novo discovery of RNA-protein interactions at an unprecedented scale.},
}
@article {pmid37333079,
year = {2023},
author = {Marshall, WF and Fung, JC},
title = {Homologous chromosome recognition via nonspecific interactions.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.06.09.544427},
pmid = {37333079},
issn = {2692-8205},
support = {P30 ES030284/ES/NIEHS NIH HHS/United States ; },
abstract = {In many organisms, most notably Drosophila, homologous chromosomes in somatic cells associate with each other, a phenomenon known as somatic homolog pairing. Unlike in meiosis, where homology is read out at the level of DNA sequence complementarity, somatic homolog pairing takes place without double strand breaks or strand invasion, thus requiring some other mechanism for homologs to recognize each other. Several studies have suggested a "specific button" model, in which a series of distinct regions in the genome, known as buttons, can associate with each other, presumably mediated by different proteins that bind to these different regions. Here we consider an alternative model, which we term the "button barcode" model, in which there is only one type of recognition site or adhesion button, present in many copies in the genome, each of which can associate with any of the others with equal affinity. An important component of this model is that the buttons are non-uniformly distributed, such that alignment of a chromosome with its correct homolog, compared with a non-homolog, is energetically favored; since to achieve nonhomologous alignment, chromosomes would be required to mechanically deform in order to bring their buttons into mutual register. We investigated several types of barcodes and examined their effect on pairing fidelity. We found that high fidelity homolog recognition can be achieved by arranging chromosome pairing buttons according to an actual industrial barcode used for warehouse sorting. By simulating randomly generated non-uniform button distributions, many highly effective button barcodes can be easily found, some of which achieve virtually perfect pairing fidelity. This model is consistent with existing literature on the effect of translocations of different sizes on homolog pairing. We conclude that a button barcode model can attain highly specific homolog recognition, comparable to that seen in actual cells undergoing somatic homolog pairing, without the need for specific interactions. This model may have implications for how meiotic pairing is achieved.},
}
@article {pmid37326709,
year = {2023},
author = {Lamy, R and Ma'ayeh, S and Chlamydas, S and Stewart, JM},
title = {Proximity Extension Assay (PEA) Platform to Detect Vitreous Biomarkers of Diabetic Retinopathy.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2678},
number = {},
pages = {135-145},
pmid = {37326709},
issn = {1940-6029},
mesh = {Humans ; *Diabetic Retinopathy/diagnosis/metabolism ; Pisum sativum/metabolism ; Retina/metabolism ; Vitreous Body/metabolism ; Biomarkers/metabolism ; *Diabetes Mellitus/metabolism ; },
abstract = {Diabetic retinopathy (DR) is one of the leading causes of blindness, affecting more than 100 million people worldwide. Currently, DR prognosis and management are based mainly on biomarkers identified by direct retinal fundus observation or by imaging devices. The use of molecular biology to discover biomarkers of DR has great potential to impact the standard of care, and the vitreous humor can serve as an indirect source for those molecular biomarkers because it is rich in proteins secreted by the retina. Proximity extension assay (PEA) is a technology that combines antibody-based immunoassays with DNA-coupled methodology to obtain information on the abundance of multiple proteins while using minimal sample volume, with high specificity and sensitivity. Matched antibodies labelled with a complementary sequence of oligonucleotides are used to simultaneously bind a target protein in solution, and when in proximity, the complementary sequences on each antibody hybridize, serving as template for DNA polymerase-dependent extension and the generation of a unique double-stranded DNA "barcode." PEA works well with vitreous matrix and has great potential to support the identification of novel predictive and prognostic biomarkers of DR.},
}
@article {pmid37323661,
year = {2023},
author = {Argyropoulos, DC and Tan, MH and Adobor, C and Mensah, B and Labbé, F and Tiedje, KE and Koram, KA and Ghansah, A and Day, KP},
title = {Performance of SNP barcodes to determine genetic diversity and population structure of Plasmodium falciparum in Africa.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1071896},
pmid = {37323661},
issn = {1664-8021},
support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI084156/AI/NIAID NIH HHS/United States ; },
abstract = {Panels of informative biallelic single nucleotide polymorphisms (SNPs) have been proposed to be an economical method to fast-track the population genetic analysis of Plasmodium falciparum in malaria-endemic areas. Whilst used successfully in low-transmission areas where infections are monoclonal and highly related, we present the first study to evaluate the performance of these 24- and 96-SNP molecular barcodes in African countries, characterised by moderate-to-high transmission, where multiclonal infections are prevalent. For SNP barcodes it is generally recommended that the SNPs chosen i) are biallelic, ii) have a minor allele frequency greater than 0.10, and iii) are independently segregating, to minimise bias in the analysis of genetic diversity and population structure. Further, to be standardised and used in many population genetic studies, these barcodes should maintain characteristics i) to iii) across various iv) geographies and v) time points. Using haplotypes generated from the MalariaGEN P. falciparum Community Project version six database, we investigated the ability of these two barcodes to fulfil these criteria in moderate-to-high transmission African populations in 25 sites across 10 countries. Predominantly clinical infections were analysed, with 52.3% found to be multiclonal, generating high proportions of mixed-allele calls (MACs) per isolate thereby impeding haplotype construction. Of the 24- and 96-SNPs, loci were removed if they were not biallelic and had low minor allele frequencies in all study populations, resulting in 20- and 75-SNP barcodes respectively for downstream population genetics analysis. Both SNP barcodes had low expected heterozygosity estimates in these African settings and consequently biased analyses of similarity. Both minor and major allele frequencies were temporally unstable. These SNP barcodes were also shown to identify weak genetic differentiation across large geographic distances based on Mantel Test and DAPC. These results demonstrate that these SNP barcodes are vulnerable to ascertainment bias and as such cannot be used as a standardised approach for malaria surveillance in moderate-to-high transmission areas in Africa, where the greatest genomic diversity of P. falciparum exists at local, regional and country levels.},
}
@article {pmid37323131,
year = {2023},
author = {Woo, C and Bhuiyan, MIU and Eo, KY and Lee, WS and Kimura, J and Yamamoto, N},
title = {Diversity of fecal parasitomes of wild carnivores inhabiting Korea, including zoonotic parasites and parasites of their prey animals, as revealed by 18S rRNA gene sequencing.},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {21},
number = {},
pages = {179-184},
pmid = {37323131},
issn = {2213-2244},
abstract = {Consisting of diverse groups of organisms, parasites are among the least studied pathogens despite their enormous impacts on humans, livestock, and wildlife. In particular, little is known about their host specificity and diversity in wildlife. Here, using multiple primer pairs and sequencing 18S rRNA genes of diverse groups of parasites, we aimed to investigate fecal parasitomes of carnivorous wildlife in Korea, namely, the raccoon dog (Nyctereutes procyonoides), the leopard cat (Prionailurus bengalensis), and the Eurasian otter (Lutra lutra). A total of 5 host-specific parasite species were identified, including 2 from raccoon dogs, 2 from leopard cats, and 1 from Eurasian otters. In addition, numerous parasite species of their prey animals were detected in their feces. It was found that the parasitome composition varied between host animals, and it was thought that the difference was attributed to the difference in prey animals, as numerous small mammal parasites were detected from feces of leopard cats inhabiting inland areas and fish parasites from feces of Eurasian otters and raccoon dogs inhabiting waterside areas. Furthermore, 5 zoonotic parasites known to infect humans were identified at the species level. Wildlife-associated zoonoses are expected to increase as the proximity between humans and wildlife increases due to urbanization. Vigilance may be necessary, such as by monitoring parasites in wildlife feces, as was done in this study.},
}
@article {pmid37317863,
year = {2023},
author = {Bowman, J and Gull, T and Ulmanis, EG and Ogunbadewa, AJ and Shen, Z and Johnson, GJ and Odemuyiwa, SO},
title = {Metagenomic identification of a novel oomycete cultured from a pyogranulomatous mass on the tail of a domestic cat.},
journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc},
volume = {35},
number = {5},
pages = {507-513},
pmid = {37317863},
issn = {1943-4936},
mesh = {Cats ; Animals ; Phylogeny ; *Pythium/genetics ; Genomics ; },
abstract = {We report here a transiently culturable oomycete pathogen isolated from a pyogranulomatous tail mass in a cat. The organism was morphologically and genetically distinct from Lagenidium and Pythium species. Following next-generation sequencing (NGS) and assembly of contigs, initial phylogenetic analysis using fragments of the cox1 mitochondrial gene identified this specimen as Paralagenidium sp. after nucleotide alignments with sequences obtained from the Barcode of Life Data System (BOLD). However, further analysis of a concatenation of 13 different mitochondrial genes showed that this organism is unique and different from all known oomycetes. A negative PCR result using primers targeting known oomycete pathogens may not be enough to rule out oomycosis in a suspected case. Additionally, the use of a single gene to classify oomycetes may produce misleading results. The advent of metagenomic sequencing and NGS provides a unique opportunity to further explore the diversity of oomycetes as plant and animal pathogens beyond the current capabilities of global barcoding projects that are based on partial genomic sequences.},
}
@article {pmid37317281,
year = {2023},
author = {Nam, B and Lee, HJ and Choi, YJ},
title = {Organic Farming Allows Balanced Fungal and Oomycetes Communities.},
journal = {Microorganisms},
volume = {11},
number = {5},
pages = {},
pmid = {37317281},
issn = {2076-2607},
support = {NRF-2021R1I1A1A01060318//National Research Foundation of Korea/ ; },
abstract = {Conventional and organic farming systems affect soils differently, thereby influencing microbial diversity and composition. Organic farming, which relies on natural processes, biodiversity, and cycles adapted to local conditions, is generally known to improve soil texture and alleviate microbial diversity loss compared with that of conventional farming, which uses synthetic inputs such as chemical fertilisers, pesticides, and herbicides. Although they affect the health and productivity of host plants, the community dynamics of fungi and fungi-like oomycetes (under Chromista) in organic farmland are poorly understood. The present study aimed to determine the differences in the diversity and composition of fungi and oomycetes inhabiting organic and conventional farm soils using culture-based DNA barcoding and culture-independent environmental DNA (eDNA) metabarcoding. Four tomato farms with different farming practices were selected and investigated: mature pure organic (MPO) via non-pesticide and organic fertiliser, mature integrated organic (MIO) via non-pesticide and chemical fertiliser, mature conventional chemical (MCC) via both pesticide and chemical fertiliser, and young conventional chemical (YCC). Culture-based analysis revealed that different genera were dominant on the four farms: Linnemannia in MPO, Mucor in MIO, and Globisporangium in MCC and YCC. eDNA metabarcoding demonstrated that the fungal richness and diversity on the MPO farm were higher than that on other farms. Both conventional farms exhibited simpler fungal and oomycete network structures with lower phylogenetic diversity. Interestingly, a high richness of oomycetes was shown in YCC; in which, Globisporangium, a potential pathogenic group on tomato plants, was abundantly observed. Our findings indicate that organic farming enhances fungal and oomycete diversity, which may provide robust support for maintaining healthy and sustainable agricultural practices. This study contributes to our knowledge on the positive effects of organic farming on crop microbiomes and provides essential information for maintaining biological diversity.},
}
@article {pmid37315874,
year = {2023},
author = {Zhang, Z and Chen, X and Zhang, W and Liu, J and Xie, Y and Zhang, S and Stromberg, AJ and Watt, DS and Liu, X and Wang, C and Liu, C},
title = {Genomic screening methodology not requiring barcoding: Single nucleotide polymorphism-based, mixed-cell screening (SMICS).},
journal = {Genomics},
volume = {115},
number = {5},
pages = {110666},
pmid = {37315874},
issn = {1089-8646},
support = {P30 CA177558/CA/NCI NIH HHS/United States ; UL1 TR001998/TR/NCATS NIH HHS/United States ; },
mesh = {*Polymorphism, Single Nucleotide ; Cell Line, Tumor ; Genomics/methods ; *Antineoplastic Agents ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Although high-throughput, cancer cell-line screening is a time-honored, important tool for anti-cancer drug development, this process involves the testing of each, individual drug in each, individual cell-line. Despite the availability of robotic liquid handling systems, this process remains a time-consuming and costly investment. The Broad Institute developed a new method called Profiling Relative Inhibition Simultaneously in Mixtures (PRISM) to screen a mixture of barcoded, tumor cell-lines. Although this methodology significantly improved the efficiency of screening large numbers of cell-lines, the barcoding process itself was tedious that requires gene transfection and subsequent selection of stable cell-lines. In this study, we developed a new, genomic approach for screening multiple cancer cell-lines using endogenous "tags" that did not require prior barcoding: single nucleotide polymorphism-based, mixed-cell screening (SMICS). The code for SMICS is available at https://github.com/MarkeyBBSRF/SMICS.},
}
@article {pmid37314207,
year = {2023},
author = {Shitikov, E and Bespiatykh, D},
title = {A revised SNP-based barcoding scheme for typing Mycobacterium tuberculosis complex isolates.},
journal = {mSphere},
volume = {8},
number = {4},
pages = {e0016923},
pmid = {37314207},
issn = {2379-5042},
mesh = {Animals ; *Mycobacterium tuberculosis ; Polymorphism, Single Nucleotide ; Phylogeny ; *Tuberculosis/microbiology ; Genotype ; },
abstract = {The development of whole-genome sequencing technologies is gradually leading to a more detailed description of the population structure of the Mycobacterium tuberculosis complex (MTBC). In this study, we correlated previously published classifications on a collection of more than 10,000 genomes and proposed a new, comprehensive nomenclature that unifies the existing ones. In total, we identified 169 lineages and sublineages of M. tuberculosis/M. africanum and 9 animal-adapted species. For the purpose of organizing these genotypes in a more streamlined manner, we stratified them into five hierarchical levels. To represent the classification and compare it with the reference, we compiled a confirmatory data set of 670 high-quality isolates, which includes all genotypes and species of MTBC, and this confirmatory data set can serve as a basis for further studies. We proposed a set of 213 robust barcoding single-nucleotide polymorphisms and a suitable workflow for reliable differentiation of genotypes and species within the complex. This work integrates the results of all the major systematized studies to date to provide an understanding of the global diversity of the MTBC population structure. The results of this work may ultimately help to reliably determine the pathogen genotype and associate it with traits that reflect its prevalence, virulence, vaccination, and treatment efficiency, as well as to reliably find natural features revealed during its spread. IMPORTANCE Through years of research into the Mycobacterium tuberculosis complex (MTBC), a number of ambiguous phylogenetic classifications have emerged, which often overlap with one another. In the present study, we have combined all major studies on MTBC classification and inferred a unified, most complete to date classification and accompanying SNP barcodes.},
}
@article {pmid37313594,
year = {2023},
author = {Zhao, X and Xu, Y and Mi, X},
title = {Fluorescence intensity coded DNA frameworks based on the FRET effect enable multiplexed miRNA imaging in living cells.},
journal = {Analytical methods : advancing methods and applications},
volume = {15},
number = {25},
pages = {3051-3056},
doi = {10.1039/d3ay00578j},
pmid = {37313594},
issn = {1759-9679},
mesh = {Humans ; *MicroRNAs/genetics/analysis ; Fluorescence Resonance Energy Transfer ; Carbocyanines ; DNA/genetics ; },
abstract = {miRNA analysis has played an important role in precise diagnosis, treatment and prognosis of cancer, especially multiplexed miRNA imaging. In this work, a novel fluorescence emission intensity (FEI) encoding strategy was developed based on a tetrahedron DNA framework (TDF) carrier and the FRET effect between Cy3 and Cy5. Six FEI-encoded TDF (FEI-TDF) samples were constructed by tuning the labeling number of Cy3 and Cy5 at the vertexes of the TDF. For fluorescence characterization in vitro, distinct FEIs in the spectra and different colors under ultraviolet (UV) irradiation of FEI-TDF samples were observed. By dividing the ranges of FEIs of samples, the stability of FEIs was highly improved. Based on the ranges of FEIs in each sample, five codes with good discrimination were finally developed. Before the application of intracellular imaging, the excellent biocompatibility of the TDF carrier was proved by CCK-8 assay. The barcode probes based on samples 12, 21 and 11 were designed as example models to realize multiplexed imaging of miRNA-16, miRNA-21 and miRNA-10b in MCF-7 cells with obviously different fluorescence merged colors. FEI-TDFs provide a new research perspective for the development of fluorescence multiplexing strategies in the future.},
}
@article {pmid37308979,
year = {2023},
author = {Posada-López, L and Rodrigues, BL and Velez, ID and Uribe, S},
title = {Improving the COI DNA barcoding library for Neotropical phlebotomine sand flies (Diptera: Psychodidae).},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {198},
pmid = {37308979},
issn = {1756-3305},
support = {860//Departamento Administrativo de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n (COLCIENCIAS)/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
mesh = {Female ; Male ; Animals ; *Psychodidae ; DNA Barcoding, Taxonomic ; *Phlebotomus ; Algorithms ; Central America ; },
abstract = {Sand fly species are traditionally identified using morphological traits, though this method is hampered by the presence of cryptic species. DNA barcoding is a widely used tool in the case of insects of medical importance, where it is necessary to know quickly which species are present in a transmission area. Here, we assess the usefulness of mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding as a practical tool for species identification, correct assignment of isomorphic females, and to evaluate the detection of cryptic diversity that occurs in the same species. A fragment of the COI gene was used to generate 156 new barcode sequences for sand flies from different countries of the Neotropical region, mainly Colombia, which had been identified morphologically as 43 species. The sequencing of the COI gene allowed the detection of cryptic diversity within species and correctly associated isomorphic females with males identified by morphology. The maximum intraspecific genetic distances ranged from 0 to 8.32% and 0 to 8.92% using uncorrected p distances and the Kimura 2-parameter (K2P) model, respectively. The minimum interspecific distance (nearest neighbor) for each species ranged from 1.5 to 14.14% and 1.51 to 15.7% using p and K2P distances, respectively. Three species had more than 3% maximum intraspecific distance: Psychodopygus panamensis, Micropygomyia cayennensis cayennensis, and Pintomyia evansi. They also were split into at least two molecular operational taxonomic units (MOTUs) each, using different species delimitation algorithms. Regarding interspecific genetic distances, the species of the genera Nyssomyia and Trichophoromyia generated values lower than 3% (except Nyssomyia ylephiletor and Ny. trapidoi). However, the maximum intraspecific distances did not exceed these values, indicating the presence of a barcode gap despite their proximity. Also, nine sand fly species were DNA barcoded for the first time: Evandromyia georgii, Lutzomyia sherlocki, Ny. ylephiletor, Ny. yuilli pajoti, Psathyromyia punctigeniculata, Sciopemyia preclara, Trichopygomyia triramula, Trichophoromyia howardi, and Th. velezbernali. The COI DNA barcode analysis enabled the correct delimitation of several Neotropical sand fly species from South and Central America and raised questions about the presence of cryptic species for some taxa, which should be further assessed.},
}
@article {pmid37306873,
year = {2023},
author = {Gangwar, H and Gahlaut, V and Chauhan, R and Singh, S and Jaiswal, V},
title = {Development of species-specific ISSR-derived SCAR marker for early discrimination between Cinnamomum verum and Cinnamomum cassia.},
journal = {Molecular biology reports},
volume = {50},
number = {8},
pages = {6311-6321},
pmid = {37306873},
issn = {1573-4978},
mesh = {Cinnamomum zeylanicum/chemistry ; *Cinnamomum aromaticum ; *Oils, Volatile ; *Lauraceae ; DNA Barcoding, Taxonomic/methods ; },
abstract = {BACKGROUND: Cinnamomum verum (true cinnamon) and Cinnamomum cassia (cassia cinnamon) are two important species belonging to family Lauraceae. These species are recognized by morphological, chemical composition and essential oil contents. The appropriate identification of species would be considerably improved by a genetic method. The main objective of the present study was to develop molecular markers distinguishing between C. verum and C. cassia.<br><br>METHODS AND RESULTS: A total 71 ISSR (Inter simple sequence repeat) and four universal barcoding (ITS, rbcL, matK,&#xa0;and&#xa0;psbA-trnH) genes were used to distinguish both the species. No sequence variation was observed between the two species for any DNA barcode gene. However, one ISSR i.e. ISSR-37 showed a clear distinction between the species and produced 570&#xa0;bp and 746&#xa0;bp amplicons in C. verum and C. cassia, respectively. The polymorphic bands were converted into species-specific SCAR markers. The SCAR-CV was specific to C. verum and amplified 190&#xa0;bp band, however there was no amplification seen in the C. cassia samples.<br><br>CONCLUSION: The SCAR marker generated in this study can be employed as efficient, economical, and reliable molecular tool for the identification of C. verum.},
}
@article {pmid37305789,
year = {2023},
author = {Chen, S and Yin, X and Han, J and Sun, W and Yao, H and Song, J and Li, X},
title = {DNA barcoding in herbal medicine: Retrospective and prospective.},
journal = {Journal of pharmaceutical analysis},
volume = {13},
number = {5},
pages = {431-441},
pmid = {37305789},
issn = {2214-0883},
abstract = {DNA barcoding has been widely used for herb identification in recent decades, enabling safety and innovation in the field of herbal medicine. In this article, we summarize recent progress in DNA barcoding for herbal medicine to provide ideas for the further development and application of this technology. Most importantly, the standard DNA barcode has been extended in two ways. First, while conventional DNA barcodes have been widely promoted for their versatility in the identification of fresh or well-preserved samples, super-barcodes based on plastid genomes have rapidly developed and have shown advantages in species identification at low taxonomic levels. Second, mini-barcodes are attractive because they perform better in cases of degraded DNA from herbal materials. In addition, some molecular techniques, such as high-throughput sequencing and isothermal amplification, are combined with DNA barcodes for species identification, which has expanded the applications of herb identification based on DNA barcoding and brought about the post-DNA-barcoding era. Furthermore, standard and high-species coverage DNA barcode reference libraries have been constructed to provide reference sequences for species identification, which increases the accuracy and credibility of species discrimination based on DNA barcodes. In summary, DNA barcoding should play a key role in the quality control of traditional herbal medicine and in the international herb trade.},
}
@article {pmid37305535,
year = {2023},
author = {Lam, W and Cai, W and Li, Y and Xu, Z and Yang, J},
title = {Editorial: Quality control for efficacy and safety of herbal medicinal products.},
journal = {Frontiers in pharmacology},
volume = {14},
number = {},
pages = {1162698},
pmid = {37305535},
issn = {1663-9812},
}
@article {pmid37304150,
year = {2023},
author = {Nazari, V and Lukhtanov, VA and Naderi, A and Fric, ZF and Dincă, V and Vila, R},
title = {More hidden diversity in a cryptic species complex: a new subspecies of Leptideasinapis (Lepidoptera, Pieridae) from Northern Iran.},
journal = {Comparative cytogenetics},
volume = {17},
number = {},
pages = {113-128},
pmid = {37304150},
issn = {1993-0771},
abstract = {A new subspecies of Leptideasinapis from Northern Iran, discovered by means of DNA barcoding, is described as Leptideasinapistabarestanassp. nov. The new subspecies is allopatric with respect to other populations of L.sinapis and is genetically distinct, appearing as a well-supported sister clade to all other populations in COI-based phylogenetic reconstructions. Details on karyotype, genitalia, ecology and behaviour for the new subspecies are given and a biogeographical speciation scenario is proposed.},
}
@article {pmid37300490,
year = {2023},
author = {Li, Y and Qi, J and Liu, Y and Zheng, Y and Zhu, H and Zang, Y and Guan, X and Xie, S and Zhao, H and Fu, Y and Xiang, H and Zhang, W and Chen, H and Liu, H and Zhao, Y and Feng, Y and Bu, F and Liang, Y and Li, Y and Xu, Q and He, Y and Sun, L and Liu, L and Gu, Y and Xu, X and Hou, Y and Dong, X and Liu, Y},
title = {High-Throughput Screening of Functional Neo-Antigens and Their Specific T-Cell Receptors via the Jurkat Reporter System Combined with Droplet Microfluidics.},
journal = {Analytical chemistry},
volume = {95},
number = {25},
pages = {9697-9705},
doi = {10.1021/acs.analchem.3c01754},
pmid = {37300490},
issn = {1520-6882},
mesh = {Humans ; *High-Throughput Screening Assays ; *Microfluidics ; Receptors, Antigen, T-Cell/genetics/metabolism ; Antigens ; Peptides/metabolism ; },
abstract = {T-cell receptor (TCR)-engineered T cells can precisely recognize a broad repertoire of targets derived from both intracellular and surface proteins of tumor cells. TCR-T adoptive cell therapy has shown safety and promising efficacy in solid tumor immunotherapy. However, antigen-specific functional TCR screening is time-consuming and expensive, which limits its application clinically. Here, we developed a novel integrated antigen-TCR screening platform based on droplet microfluidic technology, enabling high-throughput peptide-major histocompatibility complex (pMHC)-to-TCR paired screening with a high sensitivity and low background signal. We introduced DNA barcoding technology to label peptide antigen candidate-loaded antigen-presenting cells and Jurkat reporter cells to check the specificity of pMHC-TCR candidates. Coupled with the next-generation sequencing pipeline, interpretation of the DNA barcodes and the gene expression level of the Jurkat T-cell activation pathway provided a clear peptide-MHC-TCR recognition relationship. Our proof-of-principle study demonstrates that the platform could achieve pMHC-TCR paired high-throughput screening, which is expected to be used in the cross-reactivity and off-target high-throughput paired testing of candidate pMHC-TCRs in clinical applications.},
}
@article {pmid37295967,
year = {2023},
author = {Sterckx, J and Wouters, K and Mateizel, I and Segers, I and De Vos, A and Van Landuyt, L and Van de Velde, H and Tournaye, H and De Munck, N},
title = {Electronic witnessing in the medically assisted reproduction laboratory: insights and considerations after 10 years of use.},
journal = {Human reproduction (Oxford, England)},
volume = {38},
number = {8},
pages = {1529-1537},
doi = {10.1093/humrep/dead115},
pmid = {37295967},
issn = {1460-2350},
mesh = {Pregnancy ; Female ; Male ; Humans ; *Reproductive Techniques, Assisted ; Pregnancy Rate ; *Semen ; Embryo Transfer/methods ; Reproduction ; Retrospective Studies ; Fertilization in Vitro/methods ; },
abstract = {STUDY QUESTION: What have we learnt after 10 years of electronic witnessing?<br><br>SUMMARY ANSWER: When applied correctly, an electronic witnessing system can replace manual witnessing in the medically assisted reproduction lab to prevent sample mix-up.<br><br>WHAT IS KNOWN ALREADY: Electronic witnessing systems have been implemented to improve the correct identification, processing, and traceability of biological materials. When non-matching samples are simultaneously present in a single workstation, a mismatch event is generated to prevent sample mix-up.<br><br>STUDY DESIGN, SIZE, DURATION: This evaluation investigates the mismatch and administrator assign rate over a 10-year period (March 2011-December 2021) with the use of an electronic witnessing system. Radiofrequency identification tags and barcodes were used for patient and sample identification. Since 2011, IVF and ICSI cycles and frozen embryo transfer cycles (FET) were included; IUIs cycles were included since 2013.<br><br>The total number of tags and witnessing points were recorded. Witnessing points in a particular electronic witnessing system represent all the actions that have been performed from gamete collection through embryo production, to cryopreservation and transfer. Mismatches and administrator assigns were collected and stratified per procedure (sperm preparation, oocyte retrieval, IVF/ICSI, cleavage stage embryo or blastocyst embryo biopsy, vitrification and warming, embryo transfer, medium changeover, and IUI). Critical mismatches (such as mislabelling or non-matching samples within one work area) and critical administrator assigns (such as samples not identified by the electronic witnessing system and unconfirmed witnessing points) were selected.<br><br>A total of 109&#x200a;655 cycles were included: 53&#x200a;023 IVF/ICSI, 36&#x200a;347 FET, and 20&#x200a;285 IUI cycles. The 724&#x200a;096 used tags, led to a total of 849&#x200a;650 witnessing points. The overall mismatch rate was 0.251% (2132/849&#x200a;650) per witnessing point and 1.944% per cycle. In total, 144 critical mismatches occurred over the different procedures. The yearly mean critical mismatch rate was 0.017 &#xb1; 0.007% per witnessing point and 0.129 &#xb1; 0.052% per cycle. The overall administrator assign rate was 0.111% (940/849&#x200a;650) per witnessing point and 0.857% per cycle, including 320 critical administrator assigns. The yearly mean critical administrator assign rate was 0.039 &#xb1; 0.010% per witnessing point and 0.301&#x2009;&#xb1;&#x2009;0.069% per cycle. Overall mismatch and administrator assign rates remained fairly stable during the evaluated time period. Sperm preparation and IVF/ICSI were the procedures most prone to critical mismatch and administrator assigns.<br><br>The procedures and methods of integration of an electronic witnessing system may vary from one laboratory to another and result in differences in the potential risks related to sample identification. Individual embryos cannot (yet) be identified by such a system; this makes extra manual witnessing indispensable at certain critical steps where potential errors are not recorded. The electronic witnessing system still needs to be used in combination with manual labelling of both the bottom and lid of dishes and tubes to guarantee correct assignment in case of malfunction or incorrect use of radiofrequency identification tags.<br><br>Electronic witnessing is considered to be the ultimate tool to safeguard correct identification of gametes and embryos. But this is only possible when used correctly, and proper training and attention of the staff is required. It may also induce new risks, i.e. blind witnessing of samples by the operator.<br><br>No funding was either sought or obtained for this study. J.S. presents webinars on RIW for CooperSurgical. The remaining authors have nothing to declare.<br><br>TRIAL REGISTRATION NUMBER: N/A.},
}
@article {pmid37294469,
year = {2023},
author = {Abed, AB and Hürkan, K and Ünal, A and Aydın, B and Korcan, SE},
title = {Phenotypic and molecular genetics study of Geotrichum candidumLink (1809) and Geotrichum silvicola Pimenta (2005) cultivated on mitis salivarius agar.},
journal = {Molecular biology reports},
volume = {50},
number = {7},
pages = {6049-6061},
pmid = {37294469},
issn = {1573-4978},
mesh = {*Geotrichum/genetics ; Agar ; *Pimenta ; Molecular Biology ; },
abstract = {BACKGROUND: Geotrichum is a genus of fungi found in different habitats throughout the world. Although Geotrichum and its related species have been extensively reclassified and taxonomically revised, it is still the target for many researches.<br><br>METHODS AND RESULTS: In this study, phenotypic and molecular genetics comparisons were performed between Geotrichum candidum and Geotrichum silvicola. Mitis Salivarius Agar was used as the growing medium for the phenotypic comparison study, which was carried out at two temperatures (20-25 and 37&#xa0;&#xb0;C). For genotypic comparison, we compared the 18&#xa0;S, ITS, and 28&#xa0;S sequences of universal DNA barcode regions of both species. Important findings on the new culture media for fungal isolation were revealed by the results. The phenotypic variation between the two species' colonies, including their shapes, sizes, textures and growth rates, were strikingly different. DNA sequences of both species showed that pairwise identities of the species were 99.9% for 18&#xa0;S, 100% for ITS and 99.6% for 28&#xa0;S regions.<br><br>CONCLUSIONS: Contrary to what is commonly seen, the results showed that 18&#xa0;S, ITS and 28&#xa0;S failed to discriminate the species. The first investigation into the performance of Mitis Salivarius Agar as a fungus culture medium is reported in this work, and proved its efficiency. Additionally, this is the first study to compare G. candidum with G. silvicola by means of both phenotypic and genotypic analysis.},
}
@article {pmid37293445,
year = {2023},
author = {Razuvaeva, AV and Ulyanova, EG and Skolotneva, ES and Andreeva, IV},
title = {Species identification of spider mites (Tetranychidae: Tetranychinae): a review of methods.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {27},
number = {3},
pages = {240-249},
doi = {10.18699/VJGB-23-30},
pmid = {37293445},
issn = {2500-0462},
abstract = {Spider mites (Acari: Tetranychidae) are dangerous pests of agricultural and ornamental crops, the most economically significant of them belonging to the genera Tetranychus, Eutetranychus, Oligonychus and Panonychus. The expansion of the distribution areas, the increased harmfulness and dangerous status of certain species in the family Tetranychidae and their invasion of new regions pose a serious threat to the phytosanitary status of agro- and biocenoses. Various approaches to acarofauna species diagnosis determine a rather diverse range of currently existing methods generally described in this review. Identification of spider mites by morphological traits, which is currently considered the main method, is complicated due to the complexity of preparing biomaterials for diagnosis and a limited number of diagnostic signs. In this regard, biochemical and molecular genetic methods such as allozyme analysis, DNA barcoding, restriction fragment length polymorphism (PCR-RFLP), selection of species-specific primers and real-time PCR are becoming important. In the review, close attention is paid to the successful use of these methods for species discrimination in the mites of the subfamily Tetranychinae. For some species, e. g., the two-spotted spider mite (Tetranychus urticae), a range of identification methods has been developed - from allozyme analysis to loop isothermal amplification (LAMP), while for many other species a much smaller variety of approaches is available. The greatest accuracy in the identification of spider mites can be achieved using a combination of several methods, e. g., examination of morphological features and one of the molecular approaches (DNA barcoding, PCR-RFLP, etc.). This review may be useful to specialists who are in search of an effective system for spider mite species identification as well as when developing new test systems relevant to specific plant crops or a specific region.},
}
@article {pmid37292889,
year = {2023},
author = {Pan, X and Li, H and Putta, P and Zhang, X},
title = {LinRace: single cell lineage reconstruction using paired lineage barcode and gene expression data.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {37292889},
issn = {2693-5015},
support = {R35 GM143070/GM/NIGMS NIH HHS/United States ; },
abstract = {Understanding how single cells divide and differentiate into different cell types in developed organs is one of the major tasks of developmental and stem cell biology. Recently, lineage tracing technology using CRISPR/Cas9 genome editing have enabled simultaneous readouts of gene expressions and lineage barcodes in single cells, which allows for the reconstruction of the cell division tree, and even the detection of cell types and differentiation trajectories at the whole organism level. While most state-of-the-art methods for lineage reconstruction utilize only the lineage barcode data, methods that incorporate gene expression data are emerging, aiming to improve the accuracy of lineage reconstruction. However, effectively incorporating the gene expression data requires a reasonable model on how gene expression data changes along generations of divisions. Here, we present LinRace (Lineage Reconstruction with asymmetric cell division model), a method that integrates the lineage barcode and gene expression data using the asymmetric cell division model and infers cell lineage under a framework combining Neighbor Joining and maximum-likelihood heuristics. On both simulated and real data, LinRace outputs more accurate cell division trees than existing methods for lineage reconstruction. Moreover, LinRace can output the cell states (cell types) of ancestral cells, which is rarely performed with existing lineage reconstruction methods. The information on ancestral cells can be used to analyze how a progenitor cell generates a large population of cells with various functionalities. LinRace is available at: https://github.com/ZhangLabGT/LinRace.},
}
@article {pmid37292689,
year = {2023},
author = {Shumba, K and Bor, J and Nattey, C and Gareta, D and Lauren, E and Macleod, W and Fox, MP and Puren, A and Mlisana, K and Onoya, D},
title = {Record linkage without patient identifiers: proof of concept using data from South Africa's national HIV program.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {37292689},
issn = {2693-5015},
abstract = {BACKGROUND: Linkage between health databases typically requires identifiers such as patient names and personal identification numbers. We developed and validated a record linkage strategy to combine administrative health databases without the use of patient identifiers, with application to South Africa's public sector HIV treatment program.<br><br>METHODS: We linked CD4 counts and HIV viral loads from South Africa's HIV clinical monitoring database (TIER.Net) and the National Health Laboratory Service (NHLS) for patients receiving care between 2015-2019 in Ekurhuleni District (Gauteng Province). We used a combination of variables related to lab results contained in both databases (result value; specimen collection date; facility of collection; patient year and month of birth; and sex). Exact matching linked on exact linking variable values while caliper matching applied exact matching with linkage on approximate test dates (&#xb1; 5 days). We then developed a sequential linkage approach utilising specimen barcode matching, then exact matching, and lastly caliper matching. Performance measures were sensitivity and positive predictive value (PPV); share of patients linked across databases; and percent increase in data points for each linkage approach.<br><br>RESULTS: We attempted to link 2,017,290 lab results from TIER.Net (representing 523,558 unique patients) and 2,414,059 lab results from the NHLS database. Linkage performance was evaluated using specimen barcodes (available for a minority of records in TIER.net) as a "gold standard". Exact matching achieved a sensitivity of 69.0% and PPV of 95.1%. Caliper-matching achieved a sensitivity of 75.7% and PPV of 94.5%. In sequential linkage, we matched 41.9% of TIER.Net labs by specimen barcodes, 51.3% by exact matching, and 6.8% by caliper matching, for a total of 71.9% of labs matched, with PPV=96.8% and Sensitivity = 85.9%. The sequential approach linked 86.0% of TIER.Net patients with at least one lab result to the NHLS database (N=1,450,087). Linkage to the NHLS Cohort increased the number of laboratory results associated with TIER.Net patients by 62.6%.<br><br>CONCLUSIONS: Linkage of TIER.Net and NHLS without patient identifiers attained high accuracy and yield without compromising patient privacy. The integrated cohort provides a more complete view of patients' lab history and could yield more accurate estimates of HIV program indicators.},
}
@article {pmid37292580,
year = {2023},
author = {Zhao, Z and Li, B and Zhang, X and Ballarin, F and Pham, DS and Li, S},
title = {Baiyuerius gen. nov., a new genus of Coelotinae (Araneae, Agelenidae) spiders from China and Vietnam.},
journal = {ZooKeys},
volume = {1165},
number = {},
pages = {43-60},
pmid = {37292580},
issn = {1313-2989},
abstract = {Baiyueriusgen. nov., a new genus of the subfamily Coelotinae F. O. Pickard-Cambridge, 1893 is described, including five new species: B.daxisp. nov. (♀), B.pindongsp. nov. (♂), B.tamdaosp. nov. (♀), B.zhupingsp. nov. (♂) and B.zuojiangsp. nov. (♂♀), from southern China and northern Vietnam. Our molecular phylogenetic analyses support Baiyuerius gen. nov. as monophyletic and as a sister group of the newly established genus Yunguirius Li, Zhao &amp; Li, 2023.},
}
@article {pmid37292099,
year = {2023},
author = {Epitashvili, G and Japoshvili, B and Mumladze, L},
title = {Ponticolaalasanicus sp. n. (Gobiiformes, Gobiidae) from the Alazani River Basin, Georgia.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e101095},
pmid = {37292099},
issn = {1314-2828},
abstract = {BACKGROUND: The South Caucasus Region and Georgia, in particular, is a biodiversity hotspot and characterised by high diversity of landscapes and ecosystems, as well as high levels of endemism. At the same time, diversity of freshwater organisms in the region remains poorly studied, including fishes. The freshwater fish fauna of the South Caucasus Region consists of 119 fish species, of which 13 species belong to the order Gobiiformes. It should be noted that gobies are amongst the poorly studied taxa in Georgia and probably unknown/undescribed species still living in the Georgian freshwater ecosystems which requires further research.<br><br>NEW INFORMATION: Ponticolaalasanicus, a new species is described from the Alazani River, western Caspian Sea Basin, Georgia. It is distinguished from its congeners in the Caspian and Black Sea Basins by having the following features: dorsal fin with VI-VII spines and 15&#xbd;-16&#xbd; branched rays, anal fin with 10&#xbd;-12&#xbd; branched rays; lateral line with 48-55 scales; laterally compressed body with dark brown and black blotches - scales ctenoid; first and second dorsal fins almost touching with dorsal fins bases; head large, depressed, wider than deep, its length approaches almost 3.4th of standard length; nape scaled completely; cycloid scales cover upper part of opercle, cheeks noticeably swollen; snout longer than eye, eye diameter 4.5 times its head length; lower jaw slightly protruding; upper lip is uniform; pelvic disc short, elongated and flat, not reaching the anus; the pectoral fins extends vertically through first branched dorsal fin; caudal fin rounded. Ponticolaalasanicus sp. n. belongs to P.syrman group and it is separated by a minimum Kimura 2-parameter distance of 3.5, 3.6 and 4.8% from P.syrman, P.iranicus and P.patimari, respectively.},
}
@article {pmid37291358,
year = {2023},
author = {Mondragón-Martínez, A and Dávila-Rios, M and Martínez-Rojas, R and Cruz-Neyra, L and Ramos Gorbeña, JC and Dávila-Robles, M and García-Candela, E and De-Los-Santos, ER and Delgado-Escalante, A and Sanchez-Venegas, JR and Pulido-Murillo, EA},
title = {Using DNA barcoding to link cystacanths and adults of the acanthocephalan Corynosoma australe of the Southeastern Pacific Ocean (off Peru coast).},
journal = {Parasitology research},
volume = {122},
number = {8},
pages = {1883-1892},
pmid = {37291358},
issn = {1432-1955},
mesh = {Animals ; Peru ; *Sea Lions ; DNA Barcoding, Taxonomic ; Phylogeny ; Pacific Ocean ; *Acanthocephala ; Fishes ; Larva/genetics ; },
abstract = {The objective of this study is to use DNA barcoding to link cystacanths and adults belonging to the acanthocephalans Corynosoma australe found in the Southeastern Pacific Ocean off the coast central from Peru. We sampled three species of commercial fish (Paralichthys adspersus (Steindachner), Paralabrax humeralis (Valenciennes), and Cheilodactylus variegatus (Valenciennes)) and two South American sea lions, Otaria byronia, stranded on the beaches of the city of Huacho and Barranca, Lima province. A total of 509 acanthocephalan larvae were found in the body cavity of 95 fish (prevalence 54.28%, total mean intensity 8.64). A total of 127 adult worms were found in the large intestine from two South American sea lions (P= 100%, MI= 63.5). A total of 203 larvae from P. humeralis were isolates (P=65.71%; MI= 8.83; MA=5.8), 235 (P=54.29%; MI= 12.37; MA= 6.71) from C. variegatus, and 71 (P=42.86%; MI= 4.73; MA= 2.03) from P. adspersus. All adult and larval specimens were morphologically identified as C. australe. They were generated cytochrome c oxidase subunit 1 (cox1) gene sequences of specimens and were compared with available data from GenBank. Molecular phylogenetic analysis supported our morphological identification, where the Peruvian isolates formed a clade with other isolates of C. australe from other countries of the American continent. Of the sequences obtained, two haplotypes were detected and were not identical with previous reports. Based on both DNA barcoding and morphological analyses, our finding represents the first molecular data of C. australe from Peru and the report of Cheilodactylus variegatus as a new paratenic host on the central coast, extending the knowledge and distribution range of this acanthocephalan in Southeastern Pacific Ocean.},
}
@article {pmid37289794,
year = {2023},
author = {Hebert, PDN and Bock, DG and Prosser, SWJ},
title = {Interrogating 1000 insect genomes for NUMTs: A risk assessment for estimates of species richness.},
journal = {PloS one},
volume = {18},
number = {6},
pages = {e0286620},
pmid = {37289794},
issn = {1932-6203},
mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Genome, Insect ; Mitochondria/genetics ; Insecta/genetics ; Risk Assessment ; Cell Nucleus/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The nuclear genomes of most animal species include NUMTs, segments of the mitogenome incorporated into their chromosomes. Although NUMT counts are known to vary greatly among species, there has been no comprehensive study of their frequency/attributes in the most diverse group of terrestrial organisms, insects. This study examines NUMTs derived from a 658 bp 5' segment of the cytochrome c oxidase I (COI) gene, the barcode region for the animal kingdom. This assessment is important because unrecognized NUMTs can elevate estimates of species richness obtained through DNA barcoding and derived approaches (eDNA, metabarcoding). This investigation detected nearly 10,000 COI NUMTs ≥ 100 bp in the genomes of 1,002 insect species (range = 0-443). Variation in nuclear genome size explained 56% of the mitogenome-wide variation in NUMT counts. Although insect orders with the largest genome sizes possessed the highest NUMT counts, there was considerable variation among their component lineages. Two thirds of COI NUMTs possessed an IPSC (indel and/or premature stop codon) allowing their recognition and exclusion from downstream analyses. The remainder can elevate species richness as they showed 10.1% mean divergence from their mitochondrial homologue. The extent of exposure to "ghost species" is strongly impacted by the target amplicon's length. NUMTs can raise apparent species richness by up to 22% when a 658 bp COI amplicon is examined versus a doubling of apparent richness when 150 bp amplicons are targeted. Given these impacts, metabarcoding and eDNA studies should target the longest possible amplicons while also avoiding use of 12S/16S rDNA as they triple NUMT exposure because IPSC screens cannot be employed.},
}
@article {pmid37286063,
year = {2023},
author = {Abalde, S and Crocetta, F and Tenorio, MJ and D'Aniello, S and Fassio, G and Rodríguez-Flores, PC and Uribe, JE and Afonso, CML and Oliverio, M and Zardoya, R},
title = {Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosus.},
journal = {Molecular phylogenetics and evolution},
volume = {186},
number = {},
pages = {107838},
doi = {10.1016/j.ympev.2023.107838},
pmid = {37286063},
issn = {1095-9513},
mesh = {Humans ; Animals ; Phylogeny ; *Mitochondria/genetics ; Genetic Speciation ; *Genome, Mitochondrial ; Snails/genetics ; DNA, Mitochondrial/genetics ; },
abstract = {The Mediterranean cone snail, Lautoconus ventricosus, is currently considered a single species inhabiting the whole Mediterranean basin and the adjacent Atlantic coasts. Yet, no population genetic study has assessed its taxonomic status. Here, we collected 245 individuals from 75 localities throughout the Mediterranean Sea and used cox1 barcodes, complete mitochondrial genomes, and genome skims to test whether L. ventricosus represents a complex of cryptic species. The maximum likelihood phylogeny based on complete mitochondrial genomes recovered six main clades (hereby named blue, brown, green, orange, red, and violet) with sufficient sequence divergence to be considered putative species. On the other hand, phylogenomic analyses based on 437 nuclear genes only recovered four out of the six clades: blue and orange clades were thoroughly mixed and the brown one was not recovered. This mito-nuclear discordance revealed instances of incomplete lineage sorting and introgression, and may have caused important differences in the dating of main cladogenetic events. Species delimitation tests proposed the existence of at least three species: green, violet, and red + blue + orange (i.e., cyan). Green plus cyan (with sympatric distributions) and violet, had West and East Mediterranean distributions, respectively, mostly separated by the Siculo-Tunisian biogeographical barrier. Morphometric analyses of the shell using species hypotheses as factor and shell length as covariate showed that the discrimination power of the studied parameters was only 70.2%, reinforcing the cryptic nature of the uncovered species, and the importance of integrative taxonomic approaches considering morphology, ecology, biogeography, and mitochondrial and nuclear population genetic variation.},
}
@article {pmid37285353,
year = {2023},
author = {Rezenman, S and Knafo, M and Tsigalnitski, I and Barad, S and Jona, G and Levi, D and Dym, O and Reich, Z and Kapon, R},
title = {gUMI-BEAR, a modular, unsupervised population barcoding method to track variants and evolution at high resolution.},
journal = {PloS one},
volume = {18},
number = {6},
pages = {e0286696},
pmid = {37285353},
issn = {1932-6203},
mesh = {Humans ; *Neoplasms ; Clone Cells ; Genome ; },
abstract = {Cellular lineage tracking provides a means to observe population makeup at the clonal level, allowing exploration of heterogeneity, evolutionary and developmental processes and individual clones' relative fitness. It has thus contributed significantly to understanding microbial evolution, organ differentiation and cancer heterogeneity, among others. Its use, however, is limited because existing methods are highly specific, expensive, labour-intensive, and, critically, do not allow the repetition of experiments. To address these issues, we developed gUMI-BEAR (genomic Unique Molecular Identifier Barcoded Enriched Associated Regions), a modular, cost-effective method for tracking populations at high resolution. We first demonstrate the system's application and resolution by applying it to track tens of thousands of Saccharomyces cerevisiae lineages growing together under varying environmental conditions applied across multiple generations, revealing fitness differences and lineage-specific adaptations. Then, we demonstrate how gUMI-BEAR can be used to perform parallel screening of a huge number of randomly generated variants of the Hsp82 gene. We further show how our method allows isolation of variants, even if their frequency in the population is low, thus enabling unsupervised identification of modifications that lead to a behaviour of interest.},
}
@article {pmid37280373,
year = {2023},
author = {Vallot, C},
title = {RNA barcoding: the catalyst for the single-cell revolution.},
journal = {Nature reviews. Genetics},
volume = {24},
number = {8},
pages = {491},
pmid = {37280373},
issn = {1471-0064},
}
@article {pmid37278210,
year = {2023},
author = {Xu, X and Hoffmann, AA and Umina, PA and Ward, SE and Coquilleau, MP and Malipatil, MB and Ridland, PM},
title = {Molecular identification of hymenopteran parasitoids and their endosymbionts from agromyzids.},
journal = {Bulletin of entomological research},
volume = {113},
number = {4},
pages = {481-496},
doi = {10.1017/S0007485323000160},
pmid = {37278210},
issn = {1475-2670},
support = {MT20005//Hort Innovation/ ; },
mesh = {Animals ; Phylogeny ; *Wasps/genetics ; *Diptera/genetics ; Australia ; Crops, Agricultural ; DNA ; },
abstract = {Three polyphagous pest Liriomyza spp. (Diptera: Agromyzidae) have recently invaded Australia and are damaging horticultural crops. Parasitic wasps are recognized as effective natural enemies of leafmining species globally and are expected to become important biocontrol agents in Australia. However, the hymenopteran parasitoid complex of agromyzids in Australia is poorly known and its use hindered due to taxonomic challenges when based on morphological characters. Here, we identified 14 parasitoid species of leafminers based on molecular and morphological data. We linked DNA barcodes (5' end cytochrome c oxidase subunit I (COI) sequences) to five adventive eulophid wasp species (Chrysocharis pubicornis (Zetterstedt), Diglyphus isaea (Walker), Hemiptarsenus varicornis (Girault), Neochrysocharis formosa (Westwood), and Neochrysocharis okazakii Kamijo) and two braconid species (Dacnusa areolaris (Nees) and Opius cinerariae Fischer). We also provide the first DNA barcodes (5' end COI sequences) with linked morphological characters for seven wasp species, with three identified to species level (Closterocerus mirabilis Edwards &amp; La Salle, Trigonogastrella parasitica (Girault), and Zagrammosoma latilineatum Ubaidillah) and four identified to genus (Aprostocetus sp., Asecodes sp., Opius sp. 1, and Opius sp. 2). Phylogenetic analyses suggest C. pubicornis, D. isaea, H. varicornis, and O. cinerariae are likely cryptic species complexes. Neochrysocharis formosa and Aprostocetus sp. specimens were infected with Rickettsia. Five other species (Cl. mirabilis, D. isaea, H. varicornis, Opius sp. 1, and Opius sp. 2) were infected with Wolbachia, while two endosymbionts (Rickettsia and Wolbachia) co-infected N. okazakii. These findings provide background information about the parasitoid fauna expected to help control the leafminers.},
}
@article {pmid37277929,
year = {2023},
author = {Bowd, EJ and Egidi, E and Lindenmayer, DB and Wardle, DA and Kardol, P and Foster, C},
title = {Temporal dynamics of soil fungi in a pyrodiverse dry-sclerophyll forest.},
journal = {Molecular ecology},
volume = {32},
number = {15},
pages = {4181-4198},
doi = {10.1111/mec.17036},
pmid = {37277929},
issn = {1365-294X},
mesh = {Soil ; Forests ; *Mycorrhizae/genetics ; Biodiversity ; *Mycobiome ; },
abstract = {Fire is a major evolutionary and ecological driver that shapes biodiversity in forests. While above-ground community responses to fire have been well-documented, those below-ground are much less understood. However, below-ground communities, including fungi, play key roles in forests and facilitate the recovery of other organisms after fire. Here, we used internal transcribed spacer (ITS) meta-barcoding data from forests with three different times since fire [short (3 years), medium (13-19 years) and long (>26 years)] to characterize the temporal responses of soil fungal communities across functional groups, ectomycorrhizal exploration strategies and inter-guild associations. Our findings indicate that fire effects on fungal communities are strongest in the short to medium term, with clear distinctions between communities in forests with a short time (3 years) since fire, a medium time (13-19 years) and a long time (>26 years) since fire. Ectomycorrhizal fungi were disproportionately impacted by fire relative to saprotrophs, but the direction of the response varied depending on morphological structures and exploration strategies. For instance, short-distance ectomycorrhizal fungi increased with recent fire, while medium-distance (fringe) ectomycorrhizal fungi decreased. Further, we detected strong, negative inter-guild associations between ectomycorrhizal and saprotrophic fungi but only at medium and long times since fire. Given the functional significance of fungi, the temporal changes in fungal composition, inter-guild associations and functional groups after fire demonstrated in our study may have functional implications that require adaptive management to curtail.},
}
@article {pmid37277428,
year = {2023},
author = {Filip, E and Strzała, T and Stępień, E and Cembrowska-Lech, D},
title = {Universal mtDNA fragment for Cervidae barcoding species identification using phylogeny and preliminary analysis of machine learning approach.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {9133},
pmid = {37277428},
issn = {2045-2322},
mesh = {Animals ; Phylogeny ; *DNA, Mitochondrial/genetics ; DNA Barcoding, Taxonomic/methods ; Bayes Theorem ; *Deer/genetics ; Machine Learning ; },
abstract = {The aim of the study was to use total DNA obtained from bone material to identify species of free-living animals based on the analysis of mtDNA fragments by molecular methods using accurate bioinformatics tools Bayesian approach and the machine learning approach. In our research, we present a case study of successful species identification based on degraded samples of bone, with the use of short mtDNA fragments. For better barcoding, we used molecular and bioinformatics methods. We obtained a partial sequence of the mitochondrial cytochrome b (Cytb) gene for Capreolus capreolus, Dama dama, and Cervus elaphus, that can be used for species affiliation. The new sequences have been deposited in GenBank, enriching the existing Cervidae mtDNA base. We have also analysed the effect of barcodes on species identification from the perspective of the machine learning approach. Machine learning approaches of BLOG and WEKA were compared with distance-based (TaxonDNA) and tree-based (NJ tree) methods based on the discrimination accuracy of the single barcodes. The results indicated that BLOG and WEKAs SMO classifier and NJ tree performed better than TaxonDNA in discriminating Cervidae species, with BLOG and WEKAs SMO classifier performing the best.},
}
@article {pmid37276352,
year = {2023},
author = {Yu, W and Zhao, X and Jalloh, AS and Li, Y and Zhao, Y and Dinner, B and Yang, Y and Ouyang, S and Tian, T and Zhao, Z and Yang, R and Chen, M and Lauvau, G and Guo, Z and Wu, P and Li, JP},
title = {Chemoenzymatic Measurement of LacNAc in Single-Cell Multiomics Reveals It as a Cell-Surface Indicator of Glycolytic Activity of CD8[+] T Cells.},
journal = {Journal of the American Chemical Society},
volume = {145},
number = {23},
pages = {12701-12716},
pmid = {37276352},
issn = {1520-5126},
support = {R01 AI103338/AI/NIAID NIH HHS/United States ; R01 AI118842/AI/NIAID NIH HHS/United States ; R35 GM139643/GM/NIGMS NIH HHS/United States ; T32 GM007491/GM/NIGMS NIH HHS/United States ; },
mesh = {*CD8-Positive T-Lymphocytes ; *Multiomics ; Polysaccharides/chemistry ; Transcriptome ; Epitopes ; },
abstract = {Despite the rich information about the physiological state of a cell encoded in the dynamic changes of cell-surface glycans, chemical methods to capture specific glycan epitopes at the single-cell level are quite limited. Here, we report a chemoenzymatic method for the single-cell detection of N-acetyllactosamine (LacNAc) by labeling LacNAc with a specific DNA barcode. The chemoenzymatic labeling does not alter the transcriptional status of immune cells and is compatible with multiple scRNA-seq platforms. Integrated analysis of LacNAc and the transcriptome of T cells at the single-cell level reveals that the amount of cell-surface LacNAc is significantly upregulated in activated CD8[+] T cells but maintained at basal levels in resting CD8[+] T cells (i.e., naive and central memory T cells). Further analysis confirms that LacNAc levels are positively correlated with the glycolytic activity of CD8[+] T cells during differentiation. Taken together, our study demonstrates the feasibility of the chemoenzymatic detection of cell-surface glycan in single-cell RNA sequencing-based multiomics with TCR sequence and cell-surface epitope information (i.e., scTCR and CITE-seq), and provides a new way to characterize the biological role of glycan in diverse physiological states.},
}
@article {pmid37273516,
year = {2023},
author = {Likhitrakarn, N and Srisonchai, R and Siriwut, W and Jirapatrasilp, P and Jeratthitikul, E and Panha, S and Sutcharit, C},
title = {Review of the pill millipede genus Hyperglomeris Silvestri, 1917 (Diplopoda, Glomerida, Glomeridae) with description of two new species from Laos.},
journal = {ZooKeys},
volume = {1163},
number = {},
pages = {177-198},
pmid = {37273516},
issn = {1313-2989},
abstract = {The pill millipede genus Hyperglomeris Silvestri, 1917 is reported from Laos for the first time. Two new species, namely H.bicaudata Likhitrakarn, sp. nov. and H.inkhavilayi Likhitrakarn, sp. nov., from Houaphanh and Khammouane provinces, northern Laos, are described and illustrated based on morphological characters and molecular analyses. Sequences of COI gene were used as DNA barcoding markers, and successfully supported the accurate identification of other Glomeridae species. Interspecific divergence of the COI uncorrected p-distance between these new species and other Hyperglomeris species ranged from 7.84-13.07%, while the intraspecific divergence was 0.45% in H.inkhavilayisp. nov. and 5.3% in H.bicaudatasp. nov. The updated status of Hyperglomeris, a map of its distribution, and identification keys for all species are given.},
}
@article {pmid37272836,
year = {2023},
author = {Liu, W and Wang, Z and Tian, Y and Ji, B},
title = {The complete chloroplast genome sequence of Vincetoxicum mongolicum (Apocynaceae), a perennial medicinal herb.},
journal = {Genetics and molecular biology},
volume = {46},
number = {2},
pages = {e20220303},
pmid = {37272836},
issn = {1415-4757},
abstract = {Vincetoxicum mongolicum Maxim. (1876), is a perennial medicinal herb, widely distributed in the Loess Plateau of China. Here, we sequenced, assembled, and annotated the complete chloroplast (cp) genome of V. mongolicum, and compared the highly variable gene regions and phylogenetic positions between V. mongolicum and other related species. Results showed that the complete cp genome of V. mongolicum was 160,157 bp in length, containing a large single copy (LSC) region of 91,263 bp, a pair of inverted repeats (IR) region of 23,892 bp, and a small single copy (SSC) region of 21,110 bp. The GC content accounts for 37.8%, and we annotated 131 single genes, which include 86 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. By comparing and analyzing the variable region of the cp gene of V. mongolicum and other Vincetoxicum, we found that the variable sequences of rpoC1-rpoB, ycf4-cemA, ndhF, ndhF-rpl32, and rpl32-ccsA fragments were highly significant, which could be targeted as the DNA barcodes for evidence of V. mongolicum and its relatives in Apocynaceae. Maximum-likelihood (ML) phylogenetic tree analysis elucidated that V. mongolicum was sister to V. pycnostelma with strong support. Our results provide useful information for future phylogenetic studies and plastid super-barcodes of the family Apocynaceae.},
}
@article {pmid37269980,
year = {2024},
author = {Li, Z and Yang, W and Wu, P and Shan, Y and Zhang, X and Chen, F and Yang, J and Yang, JR},
title = {Reconstructing cell lineage trees with genomic barcoding: approaches and applications.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {51},
number = {1},
pages = {35-47},
doi = {10.1016/j.jgg.2023.05.011},
pmid = {37269980},
issn = {1673-8527},
mesh = {Cell Lineage/genetics ; *DNA Barcoding, Taxonomic ; *Genomics ; Genome ; },
abstract = {In multicellular organisms, developmental history of cell divisions and functional annotation of terminal cells can be organized into a cell lineage tree (CLT). The reconstruction of the CLT has long been a major goal in developmental biology and other related fields. Recent technological advancements, especially those in editable genomic barcodes and single-cell high-throughput sequencing, have sparked a new wave of experimental methods for reconstructing CLTs. Here we review the existing experimental approaches to the reconstruction of CLT, which are broadly categorized as either image-based or DNA barcode-based methods. In addition, we present a summary of the related literature based on the biological insight provided by the obtained CLTs. Moreover, we discuss the challenges that will arise as more and better CLT data become available in the near future. Genomic barcoding-based CLT reconstructions and analyses, due to their wide applicability and high scalability, offer the potential for novel biological discoveries, especially those related to general and systemic properties of the developmental process.},
}
@article {pmid37269234,
year = {2023},
author = {Huang, WC and Balisco, RA and Evacitas, FC and Liao, TY},
title = {Description of a new moray eel (Anguilliformes: Muraenidae) from the Philippines, with a preliminary assessment of genetic and morphological variations of the Uropterygius concolor species complex.},
journal = {Journal of fish biology},
volume = {103},
number = {3},
pages = {593-602},
doi = {10.1111/jfb.15472},
pmid = {37269234},
issn = {1095-8649},
support = {110-2917-I-110-001//National Science and Technology Council, Taiwan/ ; 106-2923-B-110-002-MY3//National Science and Technology Council, Taiwan/ ; },
mesh = {Animals ; *Eels/anatomy &amp; histology ; Philippines ; Indian Ocean ; Phylogeny ; },
abstract = {Uropterygius concolor Rüppell, the type species of the genus Uropterygius, is a small, uniformly brown moray considered to be widely distributed in the Indo-Pacific region. However, a recent study indicated that the real U. concolor is currently known only from the type locality in the Red Sea, and species recorded outside the Red Sea may represent a species complex that comprises several species. In this study, we assess the genetic and morphological variations of this species complex based on available data. Analyses of cytochrome c oxidase subunit I sequences revealed at least six distinct genetic lineages recognized under 'U. concolor'. After carefully comparing the morphologies, one of the lineages is described herein as a new species, Uropterygius mactanensis sp. nov., based on 21 specimens collected from Mactan Island, Cebu, Philippines. Another distinct lineage is considered to be a possibly undescribed species based on diagnostic morphological characters. Although the taxonomic status of junior synonyms of U. concolor and some lineages still remain unresolved, this study provides informative morphological characters (i.e., tail length, trunk length, vertebrae number, and arrangement of teeth) that can be used in future studies on this species complex.},
}
@article {pmid37269050,
year = {2023},
author = {Tao, G and Li, Q and Xu, S and Song, W and Yang, Z and Zhou, Y and Gao, L and Huang, W and Li, X and Ye, Y},
title = {Rapid identification of chemical compositions from three species of Siegesbeckiae Herba by ultra-performance liquid chromatography-electrospray ionization-quadrupole time of flight-mass spectrometry in combination with deoxyribonucleic acid barcoding.},
journal = {Journal of separation science},
volume = {46},
number = {16},
pages = {e2300160},
doi = {10.1002/jssc.202300160},
pmid = {37269050},
issn = {1615-9314},
support = {LGC21H280002//Zhejiang Provincial Science and Technology Council/ ; },
mesh = {Humans ; *Spectrometry, Mass, Electrospray Ionization/methods ; *Drugs, Chinese Herbal/chemistry ; Chromatography, Liquid/methods ; DNA ; Chromatography, High Pressure Liquid/methods ; },
abstract = {Siegesbeckiae Herba, a traditional Chinese medicine, originates from Siegesbeckia orientalis, S. glabrescens, and S. pubescens in the Pharmacopoeia of the People's Republic of China. However, accurate identification of decoction pieces from the three plants remains a challenge. In this study, 26 batches of Siegesbeckiae Herba were identified by deoxyribonucleic acid barcoding, and their chemical compositions were determined using ultra-performance liquid chromatography-electrospray ionization-quadrupole time of flight-mass spectrometry. The results showed that the internal transcribed spacer 2 and internal transcribed spacer 1-5.8 S- internal transcribed spacer 2 sequences could distinguish three species. In total, 48 compounds were identified including 12 marker compounds screened for three species using the partial least square discriminant analysis. Among these, two diterpenoids 16-O-malonylkirenol and 15-O-malonylkirenol, and a novel diterpenoid 15,16-di-O-malonylkirenol were isolated and identified. A convenient method for the identification of Siegesbeckiae Herba was established using kirenol and 16-O-acetlydarutoside as control standards by thin-layer chromatography. Unexpectedly, none of the batches of S. orientalis contained kirenol, which did not meet the quality standards of Siegesbeckiae Herba, suggesting that the rationality of kirenol as a quality marker for S. orientalis should be further investigated. The results of this study will contribute to the quality control of Siegesbeckiae Herba.},
}
@article {pmid37269018,
year = {2023},
author = {Peña-Espinoza, M and Em, D and Shahi-Barogh, B and Berer, D and Duscher, GG and van der Vloedt, L and Glawischnig, W and Rehbein, S and Harl, J and Unterköfler, MS and Fuehrer, HP},
title = {Molecular pathogen screening of louse flies (Diptera: Hippoboscidae) from domestic and wild ruminants in Austria.},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {179},
pmid = {37269018},
issn = {1756-3305},
support = {Austrian Barcode of Life - Hochschulraum-Strukturmittel//Austrian Federal Ministry of Education, Science and Research/ ; },
mesh = {Humans ; Animals ; Sheep ; Cattle ; *Diptera ; *Deer/parasitology ; Austria/epidemiology ; Phylogeny ; Ruminants ; *Bartonella/genetics ; *Anoplura ; *Anaplasmataceae/genetics ; *Piroplasmida ; },
abstract = {BACKGROUND: Hippoboscid flies (Diptera: Hippoboscidae), also known as louse flies or keds, are obligate blood-sucking ectoparasites of animals, and accidentally of humans. The potential role of hippoboscids as vectors of human and veterinary pathogens is being increasingly investigated, but the presence and distribution of infectious agents in louse flies is still unknown in parts of Europe. Here, we report the use of molecular genetics to detect and characterize vector-borne pathogens in hippoboscid flies infesting domestic and wild animals in Austria.<br><br>METHODS: Louse flies were collected from naturally infested cattle (n&#x2009;=&#x2009;25), sheep (n&#x2009;=&#x2009;3), and red deer (n&#x2009;=&#x2009;12) across Austria between 2015 and 2019. Individual insects were morphologically identified to species level and subjected to DNA extraction for molecular pathogen screening and barcoding. Genomic DNA from each louse fly was screened for Borrelia spp., Bartonella spp., Trypanosomatida, Anaplasmataceae, Filarioidea and Piroplasmida. Obtained sequences of Trypanosomatida and Bartonella spp. were further characterized by phylogenetic and haplotype networking analyses.<br><br>RESULTS: A total of 282 hippoboscid flies corresponding to three species were identified: Hippobosca equina (n&#x2009;=&#x2009;62) collected from cattle, Melophagus ovinus (n&#x2009;=&#x2009;100) from sheep and Lipoptena cervi (n&#x2009;=&#x2009;120) from red deer (Cervus elaphus). Molecular screening revealed pathogen DNA in 54.3% of hippoboscids, including infections with single (63.39%), two (30.71%) and up to three (5.90%) distinct pathogens in the same individual. Bartonella DNA was detected in 36.9% of the louse flies. Lipoptena cervi were infected with 10 distinct and previously unreported Bartonella sp. haplotypes, some closely associated with strains of zoonotic potential. DNA of trypanosomatids was identified in 34% of hippoboscids, including the first description of Trypanosoma sp. in H. equina. Anaplasmataceae DNA (Wolbachia spp.) was detected only in M. ovinus (16%), while < 1% of the louse flies were positive for Borrelia spp. and Filarioidea. All hippoboscids were negative for Piroplasmida.<br><br>CONCLUSIONS: Molecular genetic screening confirmed the presence of several pathogens in hippoboscids infesting domestic and wild ruminants in Austria, including novel pathogen haplotypes of zoonotic potential (e.g. Bartonella spp.) and the first report of Trypanosoma sp. in H. equina, suggesting a potential role of this louse fly as vector of animal trypanosomatids. Experimental transmission studies and expanded monitoring of hippoboscid flies and hippoboscid-associated pathogens are warranted to clarify the competence of these ectoparasites as vectors of infectious agents in a One-Health context.},
}
@article {pmid37265760,
year = {2023},
author = {Gao, M and Huo, X and Lu, L and Liu, M and Zhang, G},
title = {Analysis of codon usage patterns in Bupleurum falcatum chloroplast genome.},
journal = {Chinese herbal medicines},
volume = {15},
number = {2},
pages = {284-290},
pmid = {37265760},
issn = {2589-3610},
abstract = {OBJECTIVE: In order to distinguish the traditional Chinese medicine Bupleurum falcatum and its adulterants effectively and develop a better understanding of the factors affecting synonymous codon usage, codon usage patterns of chloroplast genome, we determine the complete chloroplast (cp) genome of B. falcatum and clarify the main factors that influence codon usage patterns of 78 genes in B. falcatum chloroplast genome.<br><br>METHODS: The total genomic DNA of fresh leaves from a single individual of B. falcatum was extracted with EASYspin plus Total DNA Isolation Kit and 2&#xa0;&#x3bc;g genome DNA was sequenced using Illumina Hiseq 2500 Sequencing Platform. The cp genome of B. falcatum was reconstructed with MITObim v1.8 and annotated in the program CPGAVAS2 with default parameters. Python script and Codon W were used to calculate the codon usage bias parameters.<br><br>RESULTS: The full length of B. falcatum cp genome was 155 851&#xa0;bp, 132 different genes were annotated in this cp genome containing 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The codon usage models tended to use A/T-ending codons. The neutrality plot, ENC plot, PR2-Bias plot and correspondence analysis showed that both compositional constraint under selection and mutation could affect the codon usage models in B. falcatum cp genome. Furthermore, three optimal codons were identified and most of these three optimal codons ended with G/U.<br><br>CONCLUSION: The cp genome of B. falcatum has been characterized and the codon usage bias in B. falcatum cp genome is influenced by natural selection, mutation pressure and nucleotide composition. The results will provide much more barcode information for species discrimination and lay a foundation for future research on codon optimization of exogenous genes, genetic engineering and molecular evolution in B. falcatum.},
}
@article {pmid37265018,
year = {2023},
author = {Chesters, D and Ferrari, RR and Lin, X and Orr, MC and Staab, M and Zhu, CD},
title = {Launching insectphylo.org; a new hub facilitating construction and use of synthesis molecular phylogenies of insects.},
journal = {Molecular ecology resources},
volume = {23},
number = {7},
pages = {1556-1573},
doi = {10.1111/1755-0998.13817},
pmid = {37265018},
issn = {1755-0998},
support = {32250610207//National Natural Science Foundation of China/ ; 31625024//National Science Fund for Distinguished Young Scholars/ ; XDB310304//Strategic Priority Research Program of the Chinese Academy of Science/ ; 2020FSB0001//CAS President's International Fellowship Initiative/ ; },
mesh = {Animals ; Phylogeny ; *Insecta/genetics ; *Diptera/genetics ; DNA ; Biodiversity ; },
abstract = {The Holy Grail of an Insect Tree of Life can only be 'discovered' through extensive collaboration among taxon specialists, phylogeneticists and centralized frameworks such as Open Tree of Life, but insufficient effort from stakeholders has so far hampered this promising approach. The resultant unavailability of synthesis phylogenies is an unfortunate situation given the numerous practical usages of phylogenies in the near term and against the backdrop of the ongoing biodiversity crisis. To resolve this issue, we establish a new online hub that centralizes the collation of relevant phylogenetic data and provides the resultant synthesis molecular phylogenies. This is achieved through key developments in a proposed pipeline for the construction of a species-level insect phylogeny. The functionality of the framework is demonstrated through the construction of a highly supported, species-comprehensive phylogeny of Diptera, built from integrated omics data, COI DNA barcodes, and a compiled database of over 100 standardized, published Diptera phylogenies. Machine-readable forms of the phylogeny (and subsets thereof) are publicly available at insectphylo.org, a new public repository for species-comprehensive phylogenies for biological research.},
}
@article {pmid37263337,
year = {2023},
author = {Mongkolphan, C and Chaiphongpachara, T and Laojun, S and Changbunjong, T},
title = {Molecular characterization and genetic diversity of three Stomoxys flies S. bengalensis, S. calcitrans, and S. sitiens (Diptera: Muscidae) in Central Thailand.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {112},
number = {},
pages = {105455},
doi = {10.1016/j.meegid.2023.105455},
pmid = {37263337},
issn = {1567-7257},
mesh = {*Muscidae/genetics ; Animals ; Genetic Variation ; Thailand ; Genetic Drift ; Male ; Female ; Phylogeny ; Likelihood Functions ; },
abstract = {Stomoxys flies (Diptera: Muscidae) are hematophagous ectoparasites of medical and veterinary importance. In this study, three Stomoxys species, i.e. S. bengalensis, S. calcitrans, and S. sitiens, were collected from three provinces in Central Thailand with the aim of estimating the genetic divergence between species, for species identification, as well as within species, for a genetic diversity study based on the cytochrome c oxidase subunit I (COI) gene. Our results showed that the average intraspecific genetic divergences of Stomoxys flies ranged from 0.11% in S. sitiens to 0.98% in S. calcitrans, whereas the average interspecific genetic divergences ranged from 5.24% between S. sitiens and S. bengalensis to 6.69% between S. calcitrans and S. bengalensis. In addition, there was no overlap between the intraspecific and interspecific genetic divergences. The COI sequence analysis revealed a high haplotype diversity and low nucleotide diversity, reflecting a rapid population expansion after past bottlenecks. Moreover, there was no significant difference (P > 0.05) in the pairwise population differentiation (Fst) among Stomoxys flies in Central Thailand, because of the lack of natural barriers, thus allowing genetic exchange between them. The monitoring of the haplotype network revealed that two lineages of S. calcitrans in Central Thailand were distributed in all study areas, including the Nakhon Pathom, Pathum Thani, and Saraburi Provinces. These findings may improve our understanding of the genetic patterns of these three Stomoxys flies, as well as the underlying biological mechanisms, which is knowledge that can be used for further effective control of these flies.},
}
@article {pmid37262084,
year = {2023},
author = {Zhu, C and Jiang, Y and Bai, Y and Dong, S and Zhirong, S},
title = {Comparative study on chloroplast genomes of three Hansenia forbesii varieties (Apiaceae).},
journal = {PloS one},
volume = {18},
number = {6},
pages = {e0286587},
pmid = {37262084},
issn = {1932-6203},
mesh = {Sequence Analysis, DNA ; *Genome, Chloroplast ; Phylogeny ; *Apiaceae ; },
abstract = {To find the gene hypervariable regions of three varieties of Hansenia forbesii H. Boissieu and determine their phylogenetic relationship, the chloroplast (cp) genome of these three varieties were firstly sequencing by the Illumina hiseq platform. In this study, we assembled the complete cp genome sequences of Hansenia forbesii LQ (156,954 bp), H. forbesii QX (157,181 bp), H. forbesii WQ (156,975 bp). They all contained 84 protein-coding genes, 37 tRNAs, and 8 rRNAs. The hypervariable regions between three cp genomes were atpF-atpH, petD, and rps15-ycf1. Phylogenetic analysis showed that H. forbesii LQ and H. forbesii WQ were closely related, followed by H. forbesii QX. This study showed that the three varieties of H. forbesii could be identified by the complete cp genome and specific DNA barcode (trnC-GCA-petN) and provided a new idea for germplasm identification of similar cultivated varieties.},
}
@article {pmid37261318,
year = {2023},
author = {Liu, Q and Yang, N and Dong, W and Zhao, L},
title = {Molecular evolution and phylogenomic analysis of complete chloroplast genomes of Cotinus (Anacardiaceae).},
journal = {Ecology and evolution},
volume = {13},
number = {5},
pages = {e10134},
pmid = {37261318},
issn = {2045-7758},
abstract = {Cotinus is an oligo-specific ornamentally valuable genus with a disjunct distribution in the Northern Hemisphere. Traditionally, the taxonomy of Cotinus was mainly based on leaf morphological characteristics. However, the limited availability of genomic information greatly hindered the study of molecular evolution and phylogeny of this genus. This study sequenced the chloroplast (cp) genomes of all currently recognized taxa of Cotinus, including three species and four varieties. A comparative analysis was performed to investigate their cp genome characteristics and evolution. Furthermore, we inferred the phylogenetic relationships of Cotinus based on whole cp genomes, protein-coding genes, and nuclear ITS data. All cp genomes exhibited a typical quadripartite structure with genome sizes ranging from 158,865 to 160,155 bp. A total of 113-114 genes were identified in the genomes. Seven non-coding and four coding regions were identified as the most divergent hotspots for potential molecular barcodes and phylogenetic markers. Selection pressure analysis showed that there had been positive selection on genes matK and rps8 in the Cotinus cp genomes. Phylogenetic results confirmed that Cotinus is a monophyletic group but the widely distributed species Cotinus coggygria is not monophyletic. The divergence-time analysis suggested that Cotinus underwent an evolutionary divergence from the middle Eocene and rapid adaptive radiation from the middle Miocene. This study revealed new insights into the cp genome evolution and phylogeny of Cotinus and related taxa.},
}
@article {pmid37258665,
year = {2023},
author = {Karlsson, K and Przybilla, MJ and Kotler, E and Khan, A and Xu, H and Karagyozova, K and Sockell, A and Wong, WH and Liu, K and Mah, A and Lo, YH and Lu, B and Houlahan, KE and Ma, Z and Suarez, CJ and Barnes, CP and Kuo, CJ and Curtis, C},
title = {Deterministic evolution and stringent selection during preneoplasia.},
journal = {Nature},
volume = {618},
number = {7964},
pages = {383-393},
pmid = {37258665},
issn = {1476-4687},
support = {DP1 CA238296/CA/NCI NIH HHS/United States ; K00 CA212433/CA/NCI NIH HHS/United States ; U01 DK085527/DK/NIDDK NIH HHS/United States ; K99 CA263014/CA/NCI NIH HHS/United States ; U01 CA217851/CA/NCI NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; R00 CA263014/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Cell Transformation, Neoplastic/genetics/pathology ; *Clonal Evolution/genetics ; Genomic Instability ; Mutation ; *Stomach Neoplasms/genetics/pathology ; *Selection, Genetic ; *Precancerous Conditions/genetics/pathology ; Organoids/metabolism/pathology ; Aneuploidy ; DNA Copy Number Variations ; Single-Cell Analysis ; Tumor Suppressor Protein p53/deficiency/genetics ; Disease Progression ; Cell Lineage ; },
abstract = {The earliest events during human tumour initiation, although poorly characterized, may hold clues to malignancy detection and prevention[1]. Here we model occult preneoplasia by biallelic inactivation of TP53, a common early event in gastric cancer, in human gastric organoids. Causal relationships between this initiating genetic lesion and resulting phenotypes were established using experimental evolution in multiple clonally derived cultures over 2 years. TP53 loss elicited progressive aneuploidy, including copy number alterations and structural variants prevalent in gastric cancers, with evident preferred orders. Longitudinal single-cell sequencing of TP53-deficient gastric organoids similarly indicates progression towards malignant transcriptional programmes. Moreover, high-throughput lineage tracing with expressed cellular barcodes demonstrates reproducible dynamics whereby initially rare subclones with shared transcriptional programmes repeatedly attain clonal dominance. This powerful platform for experimental evolution exposes stringent selection, clonal interference and a marked degree of phenotypic convergence in premalignant epithelial organoids. These data imply predictability in the earliest stages of tumorigenesis and show evolutionary constraints and barriers to malignant transformation, with implications for earlier detection and interception of aggressive, genome-instable tumours.},
}
@article {pmid37257972,
year = {2023},
author = {Hou, Y and Chen, R and Wang, Z and Lu, R and Wang, Y and Ren, S and Li, S and Wang, Y and Han, T and Yang, S and Zhou, H and Gao, Z},
title = {Bio-barcode assay: A useful technology for ultrasensitive and logic-controlled specific detection in food safety: A review.},
journal = {Analytica chimica acta},
volume = {1267},
number = {},
pages = {341351},
doi = {10.1016/j.aca.2023.341351},
pmid = {37257972},
issn = {1873-4324},
mesh = {*Metal Nanoparticles/chemistry ; Gold/chemistry ; Food Safety ; DNA Probes/chemistry ; Technology ; },
abstract = {Food safety is one of the greatest public health challenges. Developing ultrasensitive detection methods for analytes at ultra-trace levels is, therefore, essential. In recent years, the bio-barcode assay (BCA) has emerged as an effective ultrasensitive detection strategy that is based on the indirect amplification of various DNA probes. This review systematically summarizes the progress of fluorescence, PCR, and colorimetry-based BCA methods for the detection of various contaminants, including pathogenic bacteria, toxins, pesticides, antibiotics, and other chemical substances in food in over 120 research papers. Current challenges, including long experimental times and strict storage conditions, and the prospects for the application of BCA in biomedicine and environmental analyses, have also been discussed herein.},
}
@article {pmid37257802,
year = {2023},
author = {Laojun, S and Changbunjong, T and Sumruayphol, S and Chaiphongpachara, T},
title = {Molecular and morphometric differentiation of secondary filariasis vector Coquillettidia mosquitoes (Diptera: Culicidae) in Thailand.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {112},
number = {},
pages = {105452},
doi = {10.1016/j.meegid.2023.105452},
pmid = {37257802},
issn = {1567-7257},
mesh = {Animals ; Thailand ; Mosquito Vectors/genetics ; *Culicidae/genetics ; *Filariasis ; *Nematode Infections ; },
abstract = {Coquillettidia mosquitoes are important nuisance-biting pests and a vector of brugian filariasis in Thailand. However, comprehensive information about these mosquitoes remains unavailable such as molecular and morphometric differences among species. The lack of vector knowledge on Coquillettidia species could affect future disease control. This study aims to investigate differences in molecular variations based on mitochondrial cytochrome oxidase subunit I (COI) gene and wing geometric traits of three Coquillettidia species, namely Cq. crassipes, Cq. nigrosignata, and Cq. ochracea in Thailand. The results of molecular analyses revealed the differences among three Coquillettidia species. The genetic difference measure based on the Kimura two-parameter model among three Coquillettidia species showed low intraspecific distances (0%-3.05%) and large interspecific distances (10.10%-12.41%). The values of intra- and inter-genetic differences of three Coquillettidia species did not overlap which showed the existence of a barcoding gap indicating the efficiency of the identification based on the COI gene. As with molecular analysis, the landmark-based geometric morphometrics approach based on wing shape analysis indicated three distinct species groups which were supported by the high total performance score of cross-validated classification (97.16%). These results provide the first evidence of taxonomic signal based on molecular and wing geometric differences to support species identification and biological variations of Coquillettidia mosquitoes in Thailand for understanding these rare vector mosquitoes in depth and leading to effective further mosquito control.},
}
@article {pmid37256837,
year = {2023},
author = {Toro-Vargas, DM and González, C and Rougerie, R and Amarillo-Suárez, AR},
title = {Characterization of morphological and biological aspects of venomous caterpillars of the genus Lonomia Walker (Lepidoptera: Saturniidae) in Colombia.},
journal = {PloS one},
volume = {18},
number = {5},
pages = {e0285010},
pmid = {37256837},
issn = {1932-6203},
mesh = {Humans ; Male ; Adult ; Animals ; *Lepidoptera/genetics ; Colombia ; *Arthropod Venoms ; *Manduca ; Larva/genetics ; *Moths ; },
abstract = {The genus Lonomia Walker, 1855 (Lepidoptera: Saturniidae) is of particular interest to the medical community, since the scoli of these caterpillars harbor a venom that induces hemorrhaging in humans. In Colombia, deadly encounters with Lonomia achelous (Cramer, 1777), have been reported since 2000. There is little information on the main biological and ecological aspects of this genus to help better understand and develop prevention strategies. This study aimed to describe morphological and biological aspects (especially of immature stages) of four recently reported species of Lonomia in Colombia that pose a risk to humans. We collected caterpillars and adults from five localities and reared them under laboratory conditions. Specimens were identified using DNA barcoding and dissection of adult male genitalia. We provided the first description, to our knowledge, of part of the life cycles of Lonomia casanarensis Brechlin, 2017 and Lonomia orientoandensis Brechlin &amp; Meister, 2011 and the complete life cycles of Lonomia columbiana Lemaire, 1972 and Lonomia orientocordillera Brechlin, Käch &amp; Meister, 2013. We also present the first records of the parasitoids of L. orientocordillera, and L. casanarensis and new host plants. This information will guide not only their morphological recognition and the identification of their parasitoids and hosts, but also will guide rearing methods of these and other Lonomia species in new studies to prevent incidents with humans and create specific antivenoms.},
}
@article {pmid37255553,
year = {2023},
author = {Travadi, T and Shah, AP and Pandit, R and Sharma, S and Joshi, C and Joshi, M},
title = {A combined approach of DNA metabarcoding collectively enhances the detection efficiency of medicinal plants in single and polyherbal formulations.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1169984},
pmid = {37255553},
issn = {1664-462X},
abstract = {INTRODUCTION: Empirical research has refined traditional herbal medicinal systems. The traditional market is expanding globally, but inadequate regulatory guidelines, taxonomic knowledge, and resources are causing herbal product adulteration. With the widespread adoption of barcoding and next-generation sequencing, metabarcoding is emerging as a potential tool for detecting labeled and unlabeled plant species in herbal products.<br><br>METHODS: This study validated newly designed rbcL and ITS2 metabarcode primers for metabarcoding using in-house mock controls of medicinal plant gDNA pools and biomass pools. The applicability of the multi-barcode sequencing approach was evaluated on 17 single drugs and 15 polyherbal formulations procured from the Indian market.<br><br>RESULTS: The rbcL metabarcode demonstrated 86.7% and 71.7% detection efficiencies in gDNA plant pools and biomass mock controls, respectively, while the ITS2 metabarcode demonstrated 82.2% and 69.4%. In the gDNA plant pool and biomass pool mock controls, the cumulative detection efficiency increased by 100% and 90%, respectively. A 79% cumulative detection efficiency of both metabarcodes was observed in single drugs, while 76.3% was observed in polyherbal formulations. An average fidelity of 83.6% was observed for targeted plant species present within mock controls and in herbal formulations.<br><br>DISCUSSION: In the present study, we achieved increasing cumulative detection efficiency by combining the high universality of the rbcL locus with the high-resolution power of the ITS2 locus in medicinal plants, which shows applicability of multilocus strategies in metabarcoding as a potential tool for the Pharmacovigilance of labeled and unlabeled plant species in herbal formulations.},
}
@article {pmid37252058,
year = {2023},
author = {Xu, M and Liu, Y and Möller, E and LaGreca, S and Moya, P and Wang, X and Timdal, E and de Boer, H and Barreno, E and Wang, L and Thüs, H and Andrésson, &#xd3; and Magnússon, KP and Ólafsdóttir, ES and Heiðmarsson, S},
title = {Mycobiont-specific primers facilitate the amplification of mitochondrial small subunit ribosomal DNA: a focus on the lichenized fungal genus Melanelia (Ascomycota, Parmeliaceae) in Iceland.},
journal = {MycoKeys},
volume = {96},
number = {},
pages = {57-75},
pmid = {37252058},
issn = {1314-4049},
abstract = {The fungal mitochondrial small subunit (mtSSU) ribosomal DNA is one of the most commonly used loci for phylogenetic analysis of lichen-forming fungi, but their primer specificity to mycobionts has not been evaluated. The current study aimed to design mycobiont-specific mtSSU primers and highlights their utility with an example from the saxicolous lichen-forming fungal genus Melanelia Essl. in Iceland. The study found a 12.5% success rate (3 out of 24 specimens with good-quality mycobiont mtSSU sequences) using universal primers (i.e. mrSSU1 and mrSSU3R), not including off-target amplification of environmental fungi, e.g. Cladophialophoracarrionii and Lichenotheliaconvexa. New mycobiont-specific primers (mt-SSU-581-5' and mt-SSU-1345-3') were designed by targeting mycobiont-specific nucleotide sites in comparison with environmental fungal sequences, and assessed for mycobiont primer specificity using in silico PCR. The new mycobiont-specific mtSSU primers had a success rate of 91.7% (22 out of 24 specimens with good-quality mycobiont mtSSU sequences) on the studied Melanelia specimens. Additional testing confirmed the specificity and yielded amplicons from 79 specimens of other Parmeliaceae mycobiont lineages. This study highlights the effectiveness of designing mycobiont-specific primers for studies on lichen identification, barcoding and phylogenetics.},
}
@article {pmid37252053,
year = {2023},
author = {Pykälä, J and Kantelinen, A and Myllys, L},
title = {Taxonomy of Thelidiumauruntii and T.incavatum complexes (lichenized Ascomycota, Verrucariales) in Finland.},
journal = {MycoKeys},
volume = {96},
number = {},
pages = {1-23},
pmid = {37252053},
issn = {1314-4049},
abstract = {The taxonomy of lichen species morphologically similar to Thelidiumauruntii and T.incavatum in Finland is being revised. Based on ITS and morphology, ten species occur in Finland. All species are restricted to calcareous rocks. The Thelidiumauruntii morphocomplex includes six species: T.auruntii, T.huuskoneniisp. nov., T.pseudoauruntiisp. nov., T.sallaense sp. nov, T.toskalharjiensesp. nov. and T. sp. 1. In the ITS phylogeny, T.auruntii, T.pseudoauruntii and T.sallaense group together, but the remaining species are placed outside of this clade. All the species have northern distribution in Finland, occurring on fells in NW Finland and/or in gorges in the Oulanka area in NE Finland. The Thelidiumincavatum morphocomplex includes four species: T.declivumsp. nov., T.incavatum, T.mendaxsp. nov. and T. sp. 2. This morphogroup is not resolved as monophyletic in the ITS phylogeny, with only T.declivum and T.mendax forming a strongly supported group. Thelidiumincavatum is rather common in SW Finland, with one separate locality in eastern Finland. Thelidiumdeclivum occurs only in the Oulanka area. Thelidiummendax occurs in the Oulanka area, but one locality is known from eastern central Finland. Thelidium sp. 2 is known from one locality in SW Lapland.},
}
@article {pmid37251766,
year = {2023},
author = {Ragab, OG and Mamdouh, D and Bedair, R and Smetanska, I and Gruda, NS and Yousif, SKM and Omer, RM and Althobaiti, AT and Abd El-Raouf, HS and El-Taher, AM and El-Sayed, AS and Eldemerdash, MM},
title = {Distinguishing features of Lycium L. species (family Solanaceae) distributed in Egypt based on their anatomical, metabolic, molecular, and ecological characteristics.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1162695},
pmid = {37251766},
issn = {1664-462X},
abstract = {Among the 70-80 species of the genus Lycium (family Solanaceae) disjunctly distributed around the world, only three are frequently distributed in different locations in Egypt. Due to the morphological similarities between these three species, there is a need for alternative tools to distinguish them. Thus, the objective of this study was to revise the taxonomic features of Lycium europaeum L., Lycium shawii Roem. &amp; Schult., and Lycium schweinfurthii var. aschersonii (Dammer) Feinbrun in consideration of their anatomical, metabolic, molecular, and ecological characteristics. In addition to analysis of their anatomical and ecological features, DNA barcoding was performed for molecular characterization through internal transcribed spacer (ITS) sequencing and start codon targeted (SCoT) markers. Furthermore, metabolic profiling of the studied species was conducted based on gas chromatography-mass spectrometry (GC-MS). The observed anatomical features of the adaxial and abaxial epidermal layers, type of mesophyll, crystals, number of palisade and spongy layers, and the vascular system showed variations between the studied species. Beyond this, the anatomy of the leaves showed an isobilateral structure in the studied species, without distinct differences. Species were molecularly identified in terms of ITS sequences and SCoT markers. The ITS sequences were deposited in GenBank with accession numbers ON149839.1, OP597546.1, and ON521125.1 for L. europaeum L., L. shawii, and L. schweinfurthii var. aschersonii, respectively. The sequences showed variations in GC content between the studied species; this was 63.6% in L. europaeum, 61.53% in L. shawii, and 63.55% in L. schweinfurthii var. aschersonii. A total of 62 amplified fragments, including 44 polymorphic fragments with a ratio of 70.97%, were obtained in the SCoT analysis, as well as unique amplicons in L. europaeum L., shawii, and L. schweinfurthii var. aschersonii of 5, 11, and 4 fragments, respectively. Through GC-MS profiling, 38 compounds were identified with clear fluctuations in the extracts of each species. Of these, 23 were distinguishing chemicals that could help in chemical identification of the extracts of the studied species. The present study succeeds in identifying alternative clear and diverse characteristics that can be used to distinguish between L. europaeum, L. shawii, and L. schweinfurthii var. aschersonii.},
}
@article {pmid37251733,
year = {2023},
author = {Tyagi, K and Kumar, P and Pandey, A and Ginwal, HS and Barthwal, S and Nautiyal, R and Meena, RK},
title = {First record of Cladosporium oxysporum as a potential novel fungal hyperparasite of Melampsora medusae f. sp. deltoidae and screening of Populus deltoides clones against leaf rust.},
journal = {3 Biotech},
volume = {13},
number = {6},
pages = {213},
pmid = {37251733},
issn = {2190-572X},
abstract = {UNLABELLED: Melampsora medusae f. sp. deltoidae is causing serious foliar rust disease on Populus deltoides clones in India. In the present study, a novel fungal hyperparasite on M. medusae has been reported. The hyperparasitic fungus was isolated from the uredeniospores of the rust fungi and identified as Cladosporium oxysporum by morphological characterization and DNA barcode technique based on the Internal Transcribed Spacer (ITS) region of nrDNA and beta-tubulin (TUB) gene region. Hyperparasitism was further confirmed through leaf assay and cavity slide methods. Leaf assay method showed no adverse effect of C. oxysporum on poplar leaves. However, the mean germination percentage of urediniospores was significantly decreased (p < 0.05) in the cavity slide method when a conidial suspension (1.5 × 10[7] conidia per ml) of C. oxysporum was applied in different deposition sequences. Scanning and light microscopic observations were made to explore the mode of action of the hyperparasitism. The antagonistic fungus vividly showed three different types of antagonism mechanisms, including enzymatic, direct, and contact parasitism. Alternatively, by screening 25 high-yielding clones of P. deltoides, five clones (FRI-FS-83, FRI-FS-92, FRI-FS-140, FRI-AM-111, and D-121) were enlisted under highly resistant category. Present study revealed an antagonistic relationship between C. oxysporum and M. medusae, which could be an effective method of biocontrol in field plantations of poplar. Combining this biocontrol approach with the use of resistant host germplasm could be an environment friendly strategy for preventing foliar rust and increasing poplar productivity in northern India.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-023-03623-x.},
}
@article {pmid37251406,
year = {2023},
author = {Sun, R and Cai, Y and Zhou, Y and Bai, G and Zhu, A and Kong, P and Sun, J and Li, Y and Liu, Y and Liao, W and Liu, J and Cui, N and Xiang, J and Li, B and Zhao, J and Wu, D and Ran, P},
title = {Proteomic profiling of single extracellular vesicles reveals colocalization of SARS-CoV-2 with a CD81/integrin-rich EV subpopulation in sputum from COVID-19 severe patients.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1052141},
pmid = {37251406},
issn = {1664-3224},
mesh = {Humans ; *COVID-19/metabolism ; SARS-CoV-2 ; Integrins/metabolism ; Sputum ; Proteomics/methods ; *Extracellular Vesicles/metabolism ; Tetraspanin 28 ; },
abstract = {BACKGROUND: The global outbreak of COVID-19, and the limited availability of clinical treatments, forced researchers around the world to search for the pathogenesis and potential treatments. Understanding the pathogenesis of SARS-CoV-2 is crucial to respond better to the current coronavirus disease 2019 (COVID-19) pandemic.<br><br>METHODS: We collected sputum samples from 20 COVID-19 patients and healthy controls. Transmission electron microscopy was used to observe the morphology of SARS-CoV-2. Extracellular vesicles (EVs) were isolated from sputum and the supernatant of VeroE6 cells, and were characterized by transmission electron microscopy, nanoparticle tracking analysis and Western-Blotting. Furthermore, a proximity barcoding assay was used to investigate immune-related proteins in single EV, and the relationship between EVs and SARS-CoV-2.<br><br>RESULT: Transmission electron microscopy images of SARS-COV-2 virus reveal EV-like vesicles around the virion, and western blot analysis of EVs extracted from the supernatant of SARS-COV-2-infected VeroE6 cells showed that they expressed SARS-COV-2 protein. These EVs have the infectivity of SARS-COV-2, and the addition can cause the infection and damage of normal VeroE6 cells. In addition, EVs derived from the sputum of patients infected with SARS-COV-2 expressed high levels of IL6 and TGF-&#x3b2;, which correlated strongly with expression of the SARS-CoV-2 N protein. Among 40 EV subpopulations identified, 18 differed significantly between patients and controls. The EV subpopulation regulated by CD81 was the most likely to correlate with changes in the pulmonary microenvironment after SARS-CoV-2 infection. Single extracellular vesicles in the sputum of COVID-19 patients harbor infection-mediated alterations in host and virus-derived proteins.<br><br>CONCLUSIONS: These results demonstrate that EVs derived from the sputum of patients participate in virus infection and immune responses. This study provides evidence of an association between EVs and SARS-CoV-2, providing insight into the possible pathogenesis of SARS-CoV-2 infection and the possibility of developing nanoparticle-based antiviral drugs.},
}
@article {pmid37250957,
year = {2023},
author = {Sheffield, C},
title = {Agapostemonfasciatus Crawford (Hymenoptera, Halictidae), a valid North American bee species ranging into southern Canada.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e103982},
pmid = {37250957},
issn = {1314-2828},
abstract = {BACKGROUND: Sweat bees of the genus Agapostemon Guérin-Méneville, 1844 (Hymenoptera: Halictidae) are common and widespread in the Americas. Despite distinct morphological characters that were recognised in earlier taxonomic treatments, Agapostemonfasciatus Crawford, 1901 has been considered a variety of A.melliventris Cresson, 1874 since the 1930s and later placed into synonymy under A.melliventris in the early 1970s.<br><br>NEW INFORMATION: A more detailed study of morphology (including examination of type materials), distribution and genetic data (i.e. DNA barcodes) of these two taxa suggests they are not conspecific. As such, A.fasciatus is resurrected as a valid North American bee species. Agapostemonfasciatus ranges further north in North America than A.mellivenrtis, reaching the southern Prairies Ecozone of Canada (Alberta, Saskatchewan), while most records of A.melliventris are from the south-western United States and northern Mexico. More accurate distributions for both species can be modelled as specimens in collections are identified using the diagnostic features provided. However, additional work is required on the A.melliventris species complex in the southern United States as genetic data suggest that multiple taxa could be present.},
}
@article {pmid37250713,
year = {2023},
author = {Nascimento, MHS and Aragão, DG and Silva, JLN and Lima, RC and Birindelli, JLO and Fraga, EC and Barros, MC},
title = {The DNA barcode reveals cryptic diversity and a new record for the genus Leporinus (Characiformes, Anostomidae) in the hydrographic basins of central northern Brazil.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15184},
pmid = {37250713},
issn = {2167-8359},
mesh = {Animals ; *Characiformes/genetics ; Brazil ; DNA Barcoding, Taxonomic/methods ; Phylogeny ; DNA ; },
abstract = {Leporinus is one of the most speciose genera of the order Characiformes, with 81 valid species distributed throughout much of Central and South America. The considerable diversity of this genus has generated extensive debate on its classification and internal arrangement. In the present study, we investigated the species diversity of the genus Leporinus in central northern Brazil, and conclude that six valid species-Leporinus maculatus, Leporinus unitaeniatus, Leporinus affinis, Leporinus venerei, Leporinus cf. friderici, and Leporinus piau-are found in the hydrographic basins of the Brazilian states of Maranhão, Piauí, and Tocantins. We analyzed 182 sequences of the Cytochrome Oxidase subunit I gene, of which, 157 were obtained from Leporinus specimens collected from the basins of the Itapecuru, Mearim, Turiaçu, Pericumã, Periá, Preguiças, Parnaíba, and Tocantins rivers. The species delimitation analyses, based on the ABGD, ASAP, mPTP, bPTP, and GMYC methods, revealed the presence of four distinct molecular operational taxonomic units (MOTUs), identified as L. maculatus, L. unitaeniatus, L. affinis, and L. piau (from the Parnaíba River). The bPTP method restricted L. venerei to a single MOTU, and confirmed the occurrence of this species in the rivers of Maranhão for the first time. The separation of L. cf. friderici into two clades and the subsequent formation of different operational taxonomic units was consistent with polyphyly in this species, which indicates the existence of cryptic diversity. The arrangement of L. cf. friderici and L. piau in two different clades supports the conclusion that the L. piau specimens from Maranhão were misidentified, based on their morphological traits, reflecting the taxonomic inconsistencies that exist among morphologically similar species. Overall, then, the species delimitation methods employed in the present study indicated the presence of six MOTUs-L. maculatus, L. unitaenitus, L. affinis, L. cf. friderici, L. venerei, and L. piau. In the case of two other MOTUs identified in the present study, one (L. venerei) is a new record for the state of Maranhão, and we believe that the other represents a population of L. piau from the basin of the Parnaíba River.},
}
@article {pmid37250705,
year = {2023},
author = {Chimeno, C and Rulik, B and Manfrin, A and Kalinkat, G and Hölker, F and Baranov, V},
title = {Facing the infinity: tackling large samples of challenging Chironomidae (Diptera) with an integrative approach.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15336},
pmid = {37250705},
issn = {2167-8359},
mesh = {Animals ; *Chironomidae ; DNA Barcoding, Taxonomic/methods ; Biodiversity ; },
abstract = {BACKGROUND: Integrative taxonomy is becoming ever more significant in biodiversity research as scientists are tackling increasingly taxonomically challenging groups. Implementing a combined approach not only guarantees more accurate species identification, but also helps overcome limitations that each method presents when applied on its own. In this study, we present one application of integrative taxonomy for the highly abundant and particularly diverse fly taxon Chironomidae (Diptera). Although non-biting midges are key organisms in merolimnic systems, they are often cast aside in ecological surveys because they are very challenging to identify and extremely abundant.<br><br>METHODS: Here, we demonstrate one way of applying integrative methods to tackle this highly diverse taxon. We present a three-level subsampling method to drastically reduce the workload of bulk sample processing, then apply morphological and molecular identification methods in parallel to evaluate species diversity and to examine inconsistencies across methods.<br><br>RESULTS: Our results suggest that using our subsampling approach, identifying less than 10% of a sample's contents can reliably detect >90% of its diversity. However, despite reducing the processing workload drastically, the performance of our taxonomist was affected by mistakes, caused by large amounts of material. We conducted misidentifications for 9% of vouchers, which may not have been recovered had we not applied a second identification method. On the other hand, we were able to provide species information in cases where molecular methods could not, which was the case for 14% of vouchers. Therefore, we conclude that when wanting to implement non-biting midges into ecological frameworks, it is imperative to use an integrative approach.},
}
@article {pmid37250442,
year = {2023},
author = {Liu, H and Wang, D and Zhang, C and Pu, T and Xiong, L and Wei, F and Hu, Y},
title = {Development of short-target primers for species identification in biological studies of Carnivora.},
journal = {Ecology and evolution},
volume = {13},
number = {5},
pages = {e10135},
pmid = {37250442},
issn = {2045-7758},
abstract = {Noninvasive genetic sampling greatly facilitates studies on the genetics, ecology, and conservation of threatened species. Species identification is often a prerequisite for noninvasive sampling-based biological studies. Due to the low quantity and quality of genomic DNA from noninvasive samples, high-performance short-target PCR primers are necessary for DNA barcoding applications. The order Carnivora is characterized by an elusive habit and threatened status. In this study, we developed three pairs of short-target primers for identifying Carnivora species. The COI279 primer pair was suitable for samples with better DNA quality. The COI157a and COI157b primer pairs performed well for noninvasive samples and reduced the interference of nuclear mitochondrial pseudogenes (numts). COI157a could effectively identify samples from Felidae, Canidae, Viverridae, and Hyaenidae, while COI157b could be applied to samples from Ursidae, Ailuridae, Mustelidae, Procyonidae, and Herpestidae. These short-target primers will facilitate noninvasive biological studies and efforts to conserve Carnivora species.},
}
@article {pmid37250426,
year = {2023},
author = {Bizzotto, S},
title = {The human brain through the lens of somatic mosaicism.},
journal = {Frontiers in neuroscience},
volume = {17},
number = {},
pages = {1172469},
pmid = {37250426},
issn = {1662-4548},
abstract = {Every cell in the human brain possesses a unique genome that is the product of the accumulation of somatic mutations starting from the first postzygotic cell division and continuing throughout life. Somatic mosaicism in the human brain has been the focus of several recent efforts that took advantage of key technological innovations to start elucidating brain development, aging and disease directly in human tissue. On one side, somatic mutation occurring in progenitor cells has been used as a natural barcoding system to address cell phylogenies of clone formation and cell segregation in the brain lineage. On the other side, analyses of mutation rates and patterns in the genome of brain cells have revealed mechanisms of brain aging and disorder predisposition. In addition to the study of somatic mosaicism in the normal human brain, the contribution of somatic mutation has been investigated in both developmental neuropsychiatric and neurodegenerative disorders. This review starts with a methodological perspective on the study of somatic mosaicism to then cover the most recent findings in brain development and aging, and ends with the role of somatic mutations in brain disease. Thus, this review underlies what we have learned and what is still possible to discover by looking at somatic mosaicism in the brain genome.},
}
@article {pmid37250365,
year = {2023},
author = {Ramamonjisoa, MM and Rasoamanana, N and Fisher, BL},
title = {Description of the male of Erromyrma Bolton &amp; Fisher, 2016 (Hymenoptera, Formicidae).},
journal = {ZooKeys},
volume = {1163},
number = {},
pages = {61-77},
pmid = {37250365},
issn = {1313-2989},
abstract = {The male of the myrmicine genus Erromyrma is described for the first time on the basis of two specimens of Erromyrmalatinodis (Mayr, 1872) collected in northern Madagascar. We used COI barcoding to confirm the identification of the male specimens as conspecific with Erromyrmalatinodis. We provide an illustrated male-based key to the four Myrmicinae tribes (Attini, Crematogastrini, Solenopsidini, Stenammini) and to the Solenopsidini genera (Adelomyrmex, Erromyrma, Solenopsis, Syllophopsis and Monomorium) for the Malagasy region.},
}
@article {pmid37250203,
year = {2023},
author = {Tongkerd, P and Tumpeesuwan, S and Inkhavilay, K and Prasankok, P and Jeratthitikul, E and Panha, S and Sutcharit, C},
title = {Systematic revision of the snorkel snail genus Rhiostoma Benson, 1860 (Gastropoda, Caenogastropoda, Cyclophoridae) with descriptions of new species.},
journal = {ZooKeys},
volume = {1142},
number = {},
pages = {1-144},
pmid = {37250203},
issn = {1313-2989},
abstract = {The snorkel snail genus Rhiostoma Benson, 1860 is comprised of terrestrial cyclophorid snails with wide-ranging species diversity and radiation in Southeast Asia. The typical characters of the genus are a depressed shell, a detached and descending portion of the last whorl with a distinctive peristomal breathing device attached, and a calcareous cup-shaped operculum. Herein, we have revised the systematics of extant species based on shell morphology combined with COI barcoding. From these thirty recognised species, twelve are described as new to science: R. ? amarapuraensesp. nov., R.anceyisp. nov., R.breviocollarsp. nov., R.ebenozosterasp. nov., R.cheliopegmasp. nov., R.furfurosumsp. nov., R.gnomus, sp. nov., R.lannaensesp. nov., R.laoensesp. nov., R.platymorphasp. nov., R.rhothonotaphrosasp. nov., and R.tigrinasp. nov. All conchological characters are provided via illustrations of type specimens and living snails, and descriptions of the shells and radulae. Phylogenetic analysis based on partial COI gene sequences strongly supports the designated morphospecies and a monophyletic Rhiostoma, confirming that all pterocyclinid snails with a calcareous, cup-shaped operculum belong to the same clade. A high intra-specific divergence was observed in R.jalorensis and R.housei populations from locations in close proximity, suggesting a lower dispersal and higher level of isolation. The low inter-specific divergence found in R.hainesi, R.samuiense, R.asiphon, and R.rhothonotaphrosasp. nov. supports their recent diversification and local adaptation, and is congruent with their marked morphological differences. Finally, nine formerly Rhiostoma-placed species were reclassified into either the genus Cyclotus or the genus Opisthoporus.},
}
@article {pmid37249987,
year = {2023},
author = {Selnekovič, D and Goffová, K and Šoltýs, J and Kováčová, E and Kodada, J},
title = {Mordellistenaplatypoda, a new species of tumbling flower beetle from the island of Ischia in Italy (Coleoptera, Mordellidae).},
journal = {ZooKeys},
volume = {1148},
number = {},
pages = {41-63},
pmid = {37249987},
issn = {1313-2989},
abstract = {Mordellistena A. Costa, 1854, the most species-rich genus of tumbling flower beetles comprises more than 800 species worldwide and more than 150 reported from Europe. Here, a new species Mordellistena(s. str.)platypoda is described from the island of Ischia in Italy. The species hypothesis is based primarily on morphological characters which are visualised using scanning electron microscopy images, high-resolution photographs, and drawings. The species hypothesis is supported by analysis of a 658 bp fragment of cytochrome c oxidase subunit I (COI). Divergences in the COI gene are evaluated using maximum likelihood and Bayesian inference analyses. The species delimitation is assessed using Assemble Species by Automatic Partitioning (ASAP) and Poisson Tree Processes (PTP) methods. Genetic distances are visualised using multidimensional scaling. Mordellistenaplatypoda Selnekovič, Goffová &amp; Kodada, sp. nov. is recovered as a well-separated species by both molecular and morphological analyses. Our results show that M.platypoda Selnekovič, Goffová &amp; Kodada, sp. nov. is most closely related to M.tarsata Mulsant, 1856, although the two species differ significantly in vestiture colouration, presence of lateral ctenidia on the third metatarsomere, and presence of sexual dimorphism on the protibia. The results indicate that such morphological differences, which were traditionally used to distinguish between species groups, may in fact be present between closely related species. Interestingly, examination of the numerous museum material did not reveal additional specimens of the new species, and therefore M.platypoda Selnekovič, Goffová &amp; Kodada, sp. nov. is currently known only from the Italian island of Ischia.},
}
@article {pmid37249883,
year = {2023},
author = {Feau, N and Herath, P and Hamelin, RC},
title = {DNA-Barcoding Identification of Plant Pathogens for Disease Diagnostics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2659},
number = {},
pages = {37-49},
pmid = {37249883},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic/methods ; DNA ; *Oomycetes/genetics ; Sequence Analysis, DNA ; Plants/genetics ; DNA, Plant/genetics ; },
abstract = {The accurate identification of plant pathogens is a critical step to prevent their spread and attenuate their impact. Among the wide range of methods available, DNA-barcoding, i.e., the identification of an organism through the PCR amplification and sequencing of a single locus, remains one of the most straightforward and accurate plant-pathogen identification techniques that can be used in a generic molecular biology lab. This chapter provides a detailed protocol for the isolation of genomic DNA of fungal and oomycete pathogens from fresh field samples and the amplification and sequencing of the internal transcribed spacer (ITS) locus for DNA-barcoding purpose. Amendments to the protocol are provided to help in resolving issues related to the analysis of complicated samples and to the lack of species resolution that can be encountered with ITS barcodes.},
}
@article {pmid37243940,
year = {2023},
author = {Shakhova, N and Volobuev, S},
title = {Cultural and enzymatic activity studies of a pathogenic wood-decaying fungus Fomitiporia hippophaeicola (Hymenochaetales, Basidiomycota), recollected in the Eastern Caucasus.},
journal = {Archives of microbiology},
volume = {205},
number = {6},
pages = {249},
pmid = {37243940},
issn = {1432-072X},
mesh = {*Wood ; Fungi ; *Basidiomycota/genetics ; Russia ; },
abstract = {Stenotrophic basidiomycete fungus Fomitiporia hippophaeicola, being a wood-decaying pathogen of sea buckthorn (Hippophaë rhamnoides), has been recollected after 48 years in the Eastern Caucasus during the mycological and phytopathological investigations in the inner-mountainous part of the Republic of Dagestan, Russia. The identity of the species was confirmed by both morphological and ITS1-5.8S-ITS2 nrDNA data. We introduced and characterized the dikaryotic strain of F. hippophaeicola deposited for permanent storage to the Basidiomycete Culture Collection of the Komarov Botanical Institute RAS (LE-BIN). The morphological features and growth parameters of this xylotrophic fungus with phytopathogenic activity under cultivation on different agarized media (BWA, MEA, PDA) are described for the first time. The LE-BIN 4785 strain of F. hippophaeicola showed differences in growth rate and macromorphology, while the microscopic characteristics remained more robust during growth on the media tested. Qualitative analyses of oxidative and cellulolytic enzyme activities and assessment of the degradation potential of the strain examined in vitro were carried out. As a result, the newly obtained strain of F. hippophaeicola was found to exhibit medium enzyme activities and a moderate capacity to degrade the polyphenol dye azur B.},
}
@article {pmid37243408,
year = {2023},
author = {Franco, AODR and Ashworth, MP and Odebrecht, C},
title = {Comparison between p-distance and single-locus species delimitation models for delineating reproductively tested strains of pennate diatoms (Bacillariophyceae) using cox1, rbcL and ITS.},
journal = {The Journal of eukaryotic microbiology},
volume = {70},
number = {5},
pages = {e12986},
doi = {10.1111/jeu.12986},
pmid = {37243408},
issn = {1550-7408},
mesh = {*Diatoms/genetics ; DNA ; DNA Barcoding, Taxonomic ; Phylogeny ; },
abstract = {Several automated molecular methods have emerged for distinguishing eukaryote species based on DNA sequence data. However, there are knowledge gaps around which of these single-locus methods is more accurate for the identification of microalgal species, such as the highly diverse and ecologically relevant diatoms. We applied genetic divergence, Automatic Barcode Gap Discovery for primary species delimitation (ABGD), Assemble Species by Automatic Partitioning (ASAP), Statistical Parsimony Network Analysis (SPNA), Generalized Mixed Yule Coalescent (GMYC) and Poisson Tree Processes (PTP) using partial cox1, rbcL, 5.8S + ITS2, ITS1 + 5.8S + ITS2 markers to delineate species and compare to published polyphasic identification data (morphological features, phylogeny and sexual reproductive isolation) to test the resolution of these methods. ASAP, ABGD, SPNA and PTP models resolved species of Eunotia, Seminavis, Nitzschia, Sellaphora and Pseudo-nitzschia corresponding to previous polyphasic identification, including reproductive isolation studies. In most cases, these models identified diatom species in similar ways, regardless of sequence fragment length. GMYC model presented smallest number of results that agreed with previous published identification. Following the recommendations for proper use of each model presented in the present study, these models can be useful tools to identify cryptic or closely related species of diatoms, even when the datasets have relatively few sequences.},
}
@article {pmid37240713,
year = {2023},
author = {Kundu, S and De Alwis, PS and Binarao, JD and Lee, SR and Kim, AR and Gietbong, FZ and Yi, M and Kim, HW},
title = {Mitochondrial DNA Corroborates the Genetic Variability of Clarias Catfishes (Siluriformes, Clariidae) from Cameroon.},
journal = {Life (Basel, Switzerland)},
volume = {13},
number = {5},
pages = {},
pmid = {37240713},
issn = {2075-1729},
support = {Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2021R1A6A1A03039211)//National Research Foundation of Korea/ ; },
abstract = {The airbreathing walking catfish (Clariidae: Clarias) comprises 32 species that are endemic to African freshwater systems. The species-level identification of this group is challenging due to their complex taxonomy and polymorphism. Prior to this study, the biological and ecological studies were restricted to a single species, Clarias gariepinus, resulting in a biased view of their genetic diversity in African waters. Here, we generated the 63-mitochondrial Cytochrome c oxidase subunit 1 (COI) gene sequences of Clarias camerunensis and Clarias gariepinus from the Nyong River in Cameroon. Both C. camerunensis and C. gariepinus species maintained adequate intra-species (2.7% and 2.31%) and inter-species (6.9% to 16.8% and 11.4% to 15.1%) genetic distances with other Clarias congeners distributed in African and Asian/Southeast Asian drainages. The mtCOI sequences revealed 13 and 20 unique haplotypes of C. camerunensis and C. gariepinus, respectively. The TCS networks revealed distinct haplotypes of C. camerunensis and shared haplotypes of C. gariepinus in African waters. The multiple species delimitation approaches (ABGD and PTP) revealed a total of 20 and 22 molecular operational taxonomic units (MOTUs), respectively. Among the two Clarias species examined, we found more than one MOTU in C. camerunensis, which is consistent with population structure and tree topology results. The phylogeny generated through Bayesian Inference analysis clearly separated C. camerunensis and C. gariepinus from other Clarias species with high posterior probability supports. The present study elucidates the occurrence of possible cryptic diversity and allopatric speciation of C. camerunensis in African drainages. Further, the present study confirms the reduced genetic diversity of C. gariepinus across its native and introduced range, which might have been induced by unscientific aquaculture practices. The study recommends a similar approach to the same and related species from different river basins to illuminate the true diversity of Clarias species in Africa and other countries.},
}
@article {pmid37239629,
year = {2023},
author = {Le Moual, N and Dumas, O and Bonnet, P and Eworo Nchama, A and Le Bot, B and Sévin, E and Pin, I and Siroux, V and Mandin, C and The Crespi Study Group, },
title = {Exposure to Disinfectants and Cleaning Products and Respiratory Health of Workers and Children in Daycares: The CRESPI Cohort Protocol.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {10},
pages = {},
pmid = {37239629},
issn = {1660-4601},
mesh = {Humans ; Child ; *Disinfectants/analysis ; *Occupational Exposure/analysis ; *Volatile Organic Compounds/analysis ; Longitudinal Studies ; Dust ; },
abstract = {Although cleaning tasks are frequently performed in daycare, no study has focused on exposures in daycares in relation to respiratory health. The CRESPI cohort is an epidemiological study among workers (n~320) and children (n~540) attending daycares. The purpose is to examine the impact of daycare exposures to disinfectants and cleaning products (DCP) on the respiratory health of workers and children. A sample of 108 randomly selected daycares in the region of Paris has been visited to collect settled dust to analyze semi-volatile organic compounds and microbiota, as well as sample indoor air to analyze aldehydes and volatile organic compounds. Innovative tools (smartphone applications) are used to scan DCP barcodes in daycare and inform their use; a database then matches the barcodes with the products' compositions. At baseline, workers/parents completed a standardized questionnaire, collecting information on DCP used at home, respiratory health, and potential confounders. Follow-up regarding children's respiratory health (monthly report through a smartphone application and biannual questionnaires) is ongoing until the end of 2023. Associations between DCP exposures and the respiratory health of workers/children will be evaluated. By identifying specific environments or DCP substances associated with the adverse respiratory health of workers and children, this longitudinal study will contribute to the improvement of preventive measures.},
}
@article {pmid37239380,
year = {2023},
author = {Beck, A and Casanova-Katny, A and Gerasimova, J},
title = {Metabarcoding of Antarctic Lichens from Areas with Different Deglaciation Times Reveals a High Diversity of Lichen-Associated Communities.},
journal = {Genes},
volume = {14},
number = {5},
pages = {},
pmid = {37239380},
issn = {2073-4425},
mesh = {Humans ; *Lichens/genetics ; *Basidiomycota ; Antarctic Regions ; },
abstract = {Lichens have developed numerous adaptations to optimise their survival under harsh abiotic stress, colonise different substrates, and reach substantial population sizes and high coverage in ice-free Antarctic areas, benefiting from a symbiotic lifestyle. As lichen thalli represent consortia with an unknown number of participants, it is important to know about the accessory organisms and their relationships with various environmental conditions. To this end, we analysed lichen-associated communities from Himantormia lugubris, Placopsis antarctica, P. contortuplicata, and Ramalina terebrata, collected from soils with differing deglaciation times, using a metabarcoding approach. In general, many more Ascomycete taxa are associated with the investigated lichens compared to Basidiomycota. Given our sampling, a consistently higher number of lichen-associated eukaryotes are estimated to be present in areas with deglaciation times of longer than 5000 years compared to more recently deglaciated areas. Thus far, members of Dothideomycetes, Leotiomycetes, and Arthoniomycetes have been restricted to the Placopsis specimens from areas with deglaciation times longer than 5000 years. Striking differences between the associated organisms of R. terebrata and H. lugubris have also been discovered. Thus, a species-specific basidiomycete, Tremella, was revealed for R. terebrata, as was a member of Capnodiales for H. lugubris. Our study provides further understanding of the complex terricolous lichen-associated mycobiome using the metabarcoding approach. It also illustrates the necessity to extend our knowledge of complex lichen symbiosis and further improve the coverage of microbial eukaryotes in DNA barcode libraries, including more extended sampling.},
}
@article {pmid37238063,
year = {2023},
author = {Hasan, I and Rimoldi, S and Saroglia, G and Terova, G},
title = {Sustainable Fish Feeds with Insects and Probiotics Positively Affect Freshwater and Marine Fish Gut Microbiota.},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {10},
pages = {},
pmid = {37238063},
issn = {2076-2615},
support = {818367//EU Horizon 2020 AquaIMPACT project (Genomic and nutritional innovations for genetically su-perior farmed fish to improve efficiency in European aquaculture)./ ; },
abstract = {Aquaculture is the fastest-growing agricultural industry in the world. Fishmeal is an essential component of commercial fish diets, but its long-term sustainability is a concern. Therefore, it is important to find alternatives to fishmeal that have a similar nutritional value and, at the same time, are affordable and readily available. The search for high-quality alternatives to fishmeal and fish oil has interested researchers worldwide. Over the past 20 years, different insect meals have been studied as a potential alternate source of fishmeal in aquafeeds. On the other hand, probiotics-live microbial strains-are being used as dietary supplements and showing beneficial effects on fish growth and health status. Fish gut microbiota plays a significant role in nutrition metabolism, which affects a number of other physiological functions, including fish growth and development, immune regulation, and pathogen resistance. One of the key reasons for studying fish gut microbiota is the possibility to modify microbial communities that inhabit the intestine to benefit host growth and health. The development of DNA sequencing technologies and advanced bioinformatics tools has made metagenomic analysis a feasible method for researching gut microbes. In this review, we analyze and summarize the current knowledge provided by studies of our research group on using insect meal and probiotic supplements in aquafeed formulations and their effects on different fish gut microbiota. We also highlight future research directions to make insect meals a key source of proteins for sustainable aquaculture and explore the challenges associated with the use of probiotics. Insect meals and probiotics will undoubtedly have a positive effect on the long-term sustainability and profitability of aquaculture.},
}
@article {pmid37237236,
year = {2023},
author = {Kinsler, G and Schmidlin, K and Newell, D and Eder, R and Apodaca, S and Lam, G and Petrov, D and Geiler-Samerotte, K},
title = {Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch.},
journal = {Journal of molecular evolution},
volume = {91},
number = {3},
pages = {293-310},
pmid = {37237236},
issn = {1432-1432},
support = {R35 GM118165/GM/NIGMS NIH HHS/United States ; R35 GM133674/GM/NIGMS NIH HHS/United States ; R35GM118165/GM/NIGMS NIH HHS/United States ; R35GM133674/GM/NIGMS NIH HHS/United States ; },
mesh = {*Genetic Fitness ; *Selection, Genetic ; },
abstract = {The phrase "survival of the fittest" has become an iconic descriptor of how natural selection works. And yet, precisely measuring fitness, even for single-celled microbial populations growing in controlled laboratory conditions, remains a challenge. While numerous methods exist to perform these measurements, including recently developed methods utilizing DNA barcodes, all methods are limited in their precision to differentiate strains with small fitness differences. In this study, we rule out some major sources of imprecision, but still find that fitness measurements vary substantially from replicate to replicate. Our data suggest that very subtle and difficult to avoid environmental differences between replicates create systematic variation across fitness measurements. We conclude by discussing how fitness measurements should be interpreted given their extreme environment dependence. This work was inspired by the scientific community who followed us and gave us tips as we live tweeted a high-replicate fitness measurement experiment at #1BigBatch.},
}
@article {pmid37235955,
year = {2023},
author = {Li, Z and Ma, H and Guo, Y and Fang, H and Zhu, C and Xue, J and Wang, W and Luo, G and Sun, Y},
title = {Synthesis of uniform Pickering microspheres doped with quantum dot by microfluidic technology and its application in tumor marker.},
journal = {Talanta},
volume = {262},
number = {},
pages = {124495},
doi = {10.1016/j.talanta.2023.124495},
pmid = {37235955},
issn = {1873-3573},
mesh = {*Quantum Dots ; Microfluidics ; Microspheres ; Biomarkers, Tumor ; *Nanoparticles ; },
abstract = {Tumor markers play a significant role in early cancer diagnosis, evaluation of the extent of the disease, and monitoring of therapy response. In this study, we described the Pickering emulsion polymerization method to synthesize uniform magnetic/fluorescent microspheres. A Pickering-structure composed of a lot silica nanoparticle closely covered onto the quantum dot-encoded magnetic microbeads is designed and synthesized. The uniform magnetic/fluorescent microspheres were prepared using a microfluidic device and the performance of the microspheres synthesized by the instruments was evaluated by flow cytometry. To avoid fluorescence quenching and intrinsic toxicity, CdSe/ZnS core-shell quantum dot and Fe3O4 nanoparticle were successfully encapsulated into MFM microspheres using the microfluidic technology. Using this structure enables the facile realization of a theoretical 4 × 4 barcoding matrix combining two colors and four fluorescence intensity levels. Then, different optical codes were prepared by simple changing the emission wavelength and the intensity of the quantum dots. The resulting microsphere are combined with flow cytometer using two lasers for decoding of multiplex tumor markers. Moreover, the stability testing of microspheres demonstrated good performance for further application in detection of tumor markers as well. When applied for the high-throughput ultrasensitive detection of three tumor markers (CEA, CA125 and CA199) in a single sample, the detection limits of 0.027 ng/mL for CEA, 1.48 KU/L for CA125 and 1.09 KU/L for CA199 are achieved, which exhibit superior detection performance. Thus, Pickering-structure magnetic/fluorescent microspheres are promising for application in tumor markers.},
}
@article {pmid37234951,
year = {2023},
author = {Kim, J and Bae, YJ},
title = {Description of two new species of Dicranomyia (Erostrata) crane fly (Diptera, Limoniidae) from Korea, with remarks on DNA barcoding and updated taxonomic key.},
journal = {ZooKeys},
volume = {1157},
number = {},
pages = {193-206},
pmid = {37234951},
issn = {1313-2989},
abstract = {Two new crane fly species, Dicranomyia (Erostrata) jejuensissp. nov. and D. (E.) koreanasp. nov., from Korea are described on the basis of morphology and mitochondrial COI sequences. DNA barcode sequences for other four D. (Erostrata) species from Korea are also provided for the first time. The identification key for all known D. (Erostrata) species is presented.},
}
@article {pmid37234561,
year = {2023},
author = {Gong, LJ and Zeng, MY and Zhong, Y and Yu, HL},
title = {A new species of Pseudopoda (Araneae, Sparassidae) from China, with the description of different and distinctive internal ducts of the female vulva.},
journal = {ZooKeys},
volume = {1159},
number = {},
pages = {189-199},
pmid = {37234561},
issn = {1313-2989},
abstract = {One new species of the genus Pseudopoda Jäger, 2000, Pseudopodadeformis Gong &amp; Zhong, sp. nov. (♂, ♀), is described and documented with digital images from Shennongjia Forestry District, Hubei Province, China, based on morphology and DNA barcodes. This new species is separated from other Pseudopoda species by the unique type of internal ducts of the female vulva that are curved longitudinally, forming a narrow triangle or trapezoidal shape. In addition, DNA barcodes for this species are provided.},
}
@article {pmid37234560,
year = {2023},
author = {Ortiz, AS and Rubio, RM and de Freina, JJ and Guerrero, JJ and Garre, M and Yela, JL},
title = {DNA barcoding and morphology reveal European and western Asian Arctiavillica (Linnaeus, 1758) as a complex of species (Lepidoptera, Erebidae, Arctiinae).},
journal = {ZooKeys},
volume = {1159},
number = {},
pages = {69-86},
pmid = {37234560},
issn = {1313-2989},
abstract = {Currently, the genus Arctia Schrank, 1802 includes approximately 16 species in the Palaearctic region, depending on the taxonomic interpretation. Here, populations of the Arctiavillica (Linnaeus, 1758) morphospecies complex were studied from Europe to the Middle East (Turkey, northern Iran) by molecular methods. Morphological treatment has traditionally revealed the presence of five nominal taxa: A.villica (Linnaeus, 1758), A.angelica (Boisduval, 1829), A.konewkaii (Freyer, 1831), A.marchandi de Freina, 1983, and A.confluens Romanoff, 1884. The molecular approach tests whether they represent well-delimited species. Subsequently, this study corroborates the suitability of the mitochondrial cytochrome c oxidase subunit 1 (COI) marker sequence for species delimitation. In total, 55 barcodes of the Arctiavillica complex were compared, and two molecular species delimitation algorithms were applied to reveal the potential Molecular Operational Taxonomic Units (MOTUs), namely the distance-based Barcode Index Number (BIN) System, and the hierarchical clustering algorithm based on a pairwise genetic distances approach using the Assemble Species by Automatic Partitioning (ASAP). The applied ASAP distance-based species delimitation method for the analysed dataset revealed an interspecific threshold of 2.0-3.5% K2P distance as suitable for species identification purposes of the Iberian A.angelica and the Sicilian A.konewkaii and less than 2% for the three taxa of the A.villica clade: A.villica, A.confluens, and A.marchandi. This study contributes to a better understanding of the taxonomy of the genus Arctia and challenges future revision of this genus in Turkey, the Caucasus, Transcaucasia as well as northern Iran using standard molecular markers.},
}
@article {pmid37234559,
year = {2023},
author = {Wei, M and Wang, S and Lin, Y},
title = {Systematic notes on three new Luthela (Mesothelae, Heptathelidae) spiders from China, with their descriptions.},
journal = {ZooKeys},
volume = {1159},
number = {},
pages = {151-168},
pmid = {37234559},
issn = {1313-2989},
abstract = {Three new segmented trapdoor spider species belonging to the family Heptathelidae Kishida, 1923, i.e., Luthelaasukasp. nov. (♂♀, Sichuan), L.beijingsp. nov. (♂♀, Beijing), and L.kagamisp. nov. (♂♀, Sichuan), are described from China. Their phylogenetic position and relationships within Heptathelidae are tested and assessed using a combination available COI data downloaded from GenBank with new DNA sequences obtained in this study. The results show that the new species form a clade with eight known and one undescribed species of Luthela. High-definition illustrations of the male palps and female genitalia, diagnoses, and DNA barcodes are provided for these three new species, and their distributions are mapped.},
}
@article {pmid37234290,
year = {2023},
author = {Landry, B and Bilat, J and Hayden, J and Solis, MA and Lees, DC and Alvarez, N and Léger, T and Gauthier, J},
title = {The identity of Argyrialacteella (Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species revealed by morphology and DNA capture in type specimens.},
journal = {ZooKeys},
volume = {1146},
number = {},
pages = {1-42},
pmid = {37234290},
issn = {1313-2989},
abstract = {In this study the aim was to resolve the taxonomy of several species of Argyria Hübner (Pyraloidea, Crambinae) with previously unrecognised morphological variation. By analysing the DNA barcode (COI-5P) in numerous specimens, the aim was to reconstruct phylogenetic relationships between species, to provide better evidence for synonymies, and to circumscribe their geographical distribution. Using an innovative DNA hybridisation capture protocol, the DNA barcode of the lectotype of Argyrialacteella (Fabricius, 1794) was partially recovered for comparison with the 229 DNA barcode sequences of Argyria specimens available in the Barcode of Life Datasystems, and this firmly establishes the identity of the species. The same protocol was used for the following type specimens: the Argyriaabronalis (Walker, 1859) holotype, thus confirming the synonymy of this name with A.lacteella, the holotype of A.lusella (Zeller, 1863), syn. rev., the holotype of A.multifacta Dyar, 1914, syn. nov. newly synonymised with A.lacteella, and a specimen of Argyriadiplomochalis Dyar, 1913, collected in 1992. In addition, nine specimens of A.lacteella, A.diplomochalis, A.centrifugens Dyar, 1914 and A.gonogramma Dyar, 1915, from North to South America were sampled using classical COI amplification and Sanger sequencing. Argyriagonogramma Dyar, described from Bermuda, is the name to be applied to the more widespread North American species formerly identified as A.lacteella. Following morphological study of its holotype, Argyriavestalis Butler, 1878, syn. nov. is also synonymised with A.lacteella. The name A.pusillalis Hübner, 1818, is considered a nomen dubium associated with A.gonogramma. The adult morphology is diagnosed and illustrated, and distributions are plotted for A.lacteella, A.diplomochalis, A.centrifugens, and A.gonogramma based on slightly more than 800 specimens. For the first time, DNA barcode sequences are provided for the Antillean A.diplomochalis. This work provides a modified, improved protocol for the efficient hybrid capture enrichment of DNA barcodes from 18[th] and 19[th] century type specimens in order to solve taxonomic issues in Lepidoptera.},
}
@article {pmid37234286,
year = {2023},
author = {Luo, XX and Li, QQ and Zamani, A and Che, YL and Wang, ZQ},
title = {Redescription of Periplanetaarabica (Bey-Bienko, 1938) (Blattodea, Blattidae), with a comparative analysis of three species of Periplaneta Burmeister, 1838 (sensu stricto).},
journal = {ZooKeys},
volume = {1146},
number = {},
pages = {165-183},
pmid = {37234286},
issn = {1313-2989},
abstract = {The blattid cockroach Periplanetaarabica (Bey-Bienko, 1938) has been poorly understood since its original description. In this study, male and female (including nymph) of P.arabica are paired using DNA barcoding, and their morphological characters (including both external characteristics and genitalia) are described. A detailed comparative morphological study of this species and the closely related Periplanetaamericana (Linnaeus, 1758) and Periplanetalateralis Walker, 1868 was carried out to explore phylogenetically relevant characters.},
}
@article {pmid37234283,
year = {2023},
author = {van Achterberg, C and Smit, JT and Ljubomirov, T},
title = {Review of the European Eumenes Latreille (Hymenoptera, Vespidae) using morphology and DNA barcodes, with an illustrated key to species.},
journal = {ZooKeys},
volume = {1143},
number = {},
pages = {93-163},
pmid = {37234283},
issn = {1313-2989},
abstract = {The European species of the potter wasp genus Eumenes Latreille, 1802 (Vespidae, Eumeninae) are illustrated and a new illustrated key to the 13 recognised species is presented. Eumenesmediterraneusaemilianus Guiglia, 1951 is synonymised with E.papillarius (Christ, 1791) (syn. nov.), E.obscurus André, 1884 and E.andrei Dalla Torre, 1894 with E.pedunculatus (Panzer, 1799) (syn. nov.) and E.crimensis Blüthgen, 1938 with E.sareptanus André, 1884 (syn. nov.).},
}
@article {pmid37234282,
year = {2023},
author = {Hrivniak, &#x13d; and Sartori, M and Sroka, P and Bojková, J},
title = {Big diversity in a small hotspot: two new species of Leptophlebiidae (Insecta, Ephemeroptera) from New Caledonia.},
journal = {ZooKeys},
volume = {1143},
number = {},
pages = {71-88},
pmid = {37234282},
issn = {1313-2989},
abstract = {Two new species from Grande Terre Island, New Caledonia, namely Fasciamiruspetersorumsp. nov. and Simulacalararasp. nov. are described based on larval morphology and molecular data (COI sequences). Fasciamiruspetersorumsp. nov. is distributed in the southern part of the island and is characterised by a reduced third segment of the labial palps and all abdominal gills divided from the base. The species inhabits slow-flowing aquatic habitats with fine-grained substrate in forest brooks. Simulacalararasp. nov. is known from a single locality in the northern part of the island and is characterised by narrow and distinctly elongated abdominal gills 1-7. It was collected from fine substrates behind stones in riffles with slightly turbulent flow. Both species were recorded only in areas with ultramafic bedrock.},
}
@article {pmid37233815,
year = {2023},
author = {Ilahiane, L and Colominas-Ciurò, R and Bize, P and Boano, G and Cucco, M and Ferri, M and Masoero, G and Meier, CM and Pavia, M and Ramello, G and Voelker, G and Pellegrino, I},
title = {Molecular investigation on infection by haemosporidians in three Western Palearctic species of swift (Apodidae) and their ectoparasitic louse flies.},
journal = {Parasitology research},
volume = {122},
number = {8},
pages = {1787-1794},
pmid = {37233815},
issn = {1432-1955},
mesh = {Animals ; *Diptera/parasitology ; *Bird Diseases/parasitology ; *Ectoparasitic Infestations/parasitology ; Birds/parasitology ; *Haemosporida/genetics ; *Anoplura ; Phylogeny ; },
abstract = {Swifts (Apodidae) are an unusual group of birds that spend most of their lives in flight, landing only when breeding. Although this aerial lifestyle greatly reduces their likelihood of being bitten by vectors and infected by vector-born parasites, swifts can still be heavily infested during breeding by nest-based vectors such as louse flies (Hippoboscidae). Here, we investigated host, vector, and vector-borne parasite relationships in the three most widespread swift species in the Western Palearctic (WP): common swifts (Apus apus), pallid swifts (A. pallidus), and alpine swifts (Tachymarptis melba), their nest-based louse flies (Crataerina pallida and C. melbae) and avian haemosporidians (genera Haemoproteus, Plasmodium, and Leucocytozoon). Studies of haemosporidian infections in Apodidae remain limited, with clear evidence of infection found to date in just four Neotropical and one Australasian species. The possible role of louse flies in transmitting haemosporidian infections has never been tested in swifts. We assessed the occurrence of haemosporidian infection by PCR screenings of DNA from blood samples from 34 common swifts and 44 pallid swifts from Italy, and 45 alpine swifts from Switzerland. We also screened 20 ectoparasitic louse flies present on 20 birds and identified them by both morphological features and cytochrome oxidase subunit 1 (COI) barcodes. Our results provide no evidence of haemosporidian infection in the 123 swifts tested or in the two louse fly species we identified. Our findings are consistent with available knowledge showing no haemosporidian occurrence in WP swift species and that the most likely infection route for these highly aerial species (via louse fly ectoparasites during nesting) is unlikely.},
}
@article {pmid37233263,
year = {2023},
author = {La Torre, RD and Ramos, D and Mejía, MD and Neyra, E and Loarte, E and Orjeda, G},
title = {Survey of Lichenized Fungi DNA Barcodes on King George Island (Antarctica): An Aid to Species Discovery.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {5},
pages = {},
pmid = {37233263},
issn = {2309-608X},
support = {003-2018-FONDECYT-BM-IADT-AV//Fondo Nacional de Desarrollo Cient&#xed;fico, Tecnol&#xf3;gico y de Innovaci&#xf3;n Tecnol&#xf3;gica/ ; },
abstract = {DNA barcoding is a powerful method for the identification of lichenized fungi groups for which the diversity is already well-represented in nucleotide databases, and an accurate, robust taxonomy has been established. However, the effectiveness of DNA barcoding for identification is expected to be limited for understudied taxa or regions. One such region is Antarctica, where, despite the importance of lichens and lichenized fungi identification, their genetic diversity is far from characterized. The aim of this exploratory study was to survey the lichenized fungi diversity of King George Island using a fungal barcode marker as an initial identification tool. Samples were collected unrestricted to specific taxa in coastal areas near Admiralty Bay. Most samples were identified using the barcode marker and verified up to the species or genus level with a high degree of similarity. A posterior morphological evaluation focused on samples with novel barcodes allowed for the identification of unknown Austrolecia, Buellia, and Lecidea s.l. species. These results contribute to better represent the lichenized fungi diversity in understudied regions such as Antarctica by increasing the richness of the nucleotide databases. Furthermore, the approach used in this study is valuable for exploratory surveys in understudied regions to guide taxonomic efforts towards species recognition and discovery.},
}
@article {pmid37233083,
year = {2023},
author = {Stojanović, DV and Galović, V and Terzin, T and Ačanski, J and Vidović, M and Orlović, S},
title = {The Genus Heterogynis Rambur, 1866 (Heterogynidae, Lepidoptera): Congruence of Molecular, Morphological and Morphometric Evidence Reveal New Species in Serbia.},
journal = {Insects},
volume = {14},
number = {5},
pages = {},
pmid = {37233083},
issn = {2075-4450},
support = {Contract No. 451-03-47/2023-01/200197, Contract No. 451-03-47/2023-01/ 200042, and Contract No. 451-03-68/2022-14/200358//The Ministry of Education, Science and Technological Development of the Republic of Serbia/ ; },
abstract = {The Heterogynidae are a small family of moths consisting of a single genus Heterogynis and sixteen described species distributed in the Mediterranean region. A species new to science, Heterogynis serbica sp. nov., is described from the locality of Srebrenac, Mt. Kopaonik, Republic of Serbia, Balkan Peninsula, by applying an integrative taxonomic approach using morpho-anatomical characteristics, wing morphometics and DNA barcoding. Male genitalia, scanning electron micrographs of adult male head anatomy, abdominal tergites/sternites, cocoons and habitats of the closely related species H. serbica sp. nov. and H. zikici are discussed and illustrated. Photographs of adult males and females, cocoons, plants in which the cocoons were found and habitats are shown. Importantly, marked differences in genital structure and other morphological characters were noted. These differences were confirmed with forewing morphometrics and COI-based DNA barcoding results. Additionally, DNA barcodes for H. serbica sp. nov. and H. zikici were compared against previously available data for the genus to evaluate the phylogenetic relationships. We conclude that deep, previously unknown and unexpected intrageneric morphological diversity exists in the genus Heterogynis.},
}
@article {pmid37233066,
year = {2023},
author = {Ador, K and Gobilik, J and Benedick, S},
title = {Phylogenetic and Morphological Characteristics Reveal Cryptic Speciation in Stingless Bee, Tetragonula laeviceps s.l. Smith 1857 (Hymenoptera; Meliponinae).},
journal = {Insects},
volume = {14},
number = {5},
pages = {},
pmid = {37233066},
issn = {2075-4450},
support = {GUG0193-2/2017//Universiti Malaysia Sabah (Internal Grant)/ ; 20180326-05//NAGAO Natural Environment Foundation/ ; },
abstract = {Tetragonula laeviceps sensu lato (s.l.) Smith 1857 has the most complicated nomenclatural history among the Tetragonula genera. The objective of this study was to investigate whether T. laeviceps s.l. individuals with worker bees are grouped in the same or nearly the same morphological characteristics and have similar COI haplotype cluster groups. A total of 147 worker bees of T. laeviceps s.l. were collected from six sampling sites in Sabah (RDC, Tuaran, Kota Marudu, Putatan, Kinarut and Faculty of Sustainable Agriculture (FSA)), but only 36 were selected for further studies. These specimens were first classified according to the most obvious morphological characteristics, i.e., hind tibia color, hind basitarsus color and body size. Group identification was based on morphological characteristics important for distinguishing the four groups within T. laeviceps s.l. The four groups of T. laeviceps s.l. had significantly different body trait measurements for the TL (total length), HW (head width), HL (head length), CEL (compound eye length), CEW (compound eye width), FWLT (forewing length, including tegula), FWW (forewing width), FWL (forewing length), ML (mesoscutum length), MW (mesoscutum width), SW (mesoscutellum width), SL (mesoscutellum length), HTL = (hind tibia length), HTW (hind tibia width), HBL (hind basitarsus length) and HBW (hind basitarsus width) (p < 0.001). Body color included HC (head color), CC (clypeus color), ASC (antennae scape color), CFPP (Clypeus and frons plumose pubescence), HTC (hind tibia color), BSC (basitarsus color), SP (leg setae pubescence), SP (Thorax mesoscutellum pubescence), SPL (thorax mesoscutellum pubescence length) and TC (thorax color) (p < 0.05). The most distinctive features of the morphological and morphometric characteristics measured by PCA and LDA biplot that distinguish Group 1 (TL6-1, TL6-2 and TL6-3) from the other groups were the yellowish-brown ASC and the dark brown TC. Group 2 (haplotypes TL2-1, TL2-2 and TL2-3 and TL4-1, TL4-2 and TL4-3) had a dark brown ASC and a black TC, while Group 3 (haplotypes TL11-1, TL11-2 and TL11-3) had a blackish-brown ASC, a black TC and the largest TL, FWW and FWL. As for phylogenetic relationships, 12 out of 36 haplotypes showed clear separation with good bootstrap values (97-100%). The rest of the haplotypes did not show clear differentiation between subclades that belonged together, regardless of their morphology and morphometric characteristics. This suggests that the combination of DNA barcoding for species identification and phylogenetic analysis, as well as traditional methods based on morphological grouping by body size and body color, can be reliably used to determine intraspecific variations within T. laeviceps s.l.},
}
@article {pmid37233036,
year = {2023},
author = {Fateryga, AV and Mauss, V and Proshchalykin, MY},
title = {Foraging Behavior of Two Pollen Wasp Species of the Genus Celonites Latreille, 1802 (Hymenoptera: Vespidae: Masarinae), from the Altai Mountains.},
journal = {Insects},
volume = {14},
number = {5},
pages = {},
pmid = {37233036},
issn = {2075-4450},
support = {20-54-44014//Russian Foundation for Basic Research/ ; 121032300023-7//Ministry&#xa0;of&#xa0;Science&#xa0;and&#xa0;Higher&#xa0;Education&#xa0;of&#xa0;the&#xa0;Russian&#xa0;Federation/ ; 121031000151-3//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {Celonites kozlovi Kostylev, 1935, and C. sibiricus Gusenleitner, 2007, coexist in semi-deserts of the Altai Mountains. The trophic relationships of these pollen wasp species to flowers are largely unknown. We observed the flower visits and behaviors of wasps on flowers; pollen-collecting structures of females were studied using SEM; the taxonomic position of these two species was ascertained with the barcoding sequence of the mitochondrial COI-5P gene. Celonites kozlovi and C. sibiricus form a clade together with C. hellenicus Gusenleitner, 1997, and C. iranus Gusenleitner, 2018, within the subgenus Eucelonites Richards, 1962. Celonites kozlovi is polylectic in the narrow sense, collecting pollen from flowers of plants belonging to five families (with the predomination of Asteraceae and Lamiaceae) using diverse methods for both pollen and nectar uptake. In addition, this species is a secondary nectar robber, which has not been observed in pollen wasps before. The generalistic foraging strategy of C. kozlovi is correlated with an unspecialized pollen-collecting apparatus on the fore-tarsi. In contrast, C. sibiricus is broadly oligolectic, predominantly collecting pollen from flowers of Lamiaceae. Its specialized foraging strategy is associated with apomorphic behavioral and morphological traits, particularly specialized pollen-collecting setae on the frons, which enable indirect pollen uptake using nototribic anthers. These adaptations in C. sibiricus evolved independently of similar specializations in the Celonites abbreviatus-complex. Celonites kozlovi is re-described, and males are described for the first time.},
}
@article {pmid37230159,
year = {2023},
author = {Singh, US and Amdep, FL and Kshiar, A and Acharya, P and Karumuthil, T and Kale, S and Mishra, S and Khan, N and Kharbisnop, B and Kessler, A and Carlton, JM and Das, A and Walton, C and Albert, S},
title = {Characterisation of Anopheles species composition and genetic diversity in Meghalaya, northeast India, using molecular identification tools.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {112},
number = {},
pages = {105450},
doi = {10.1016/j.meegid.2023.105450},
pmid = {37230159},
issn = {1567-7257},
support = {U19 AI089676/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; *Anopheles/genetics ; *Malaria/epidemiology ; Mosquito Vectors/genetics ; India/epidemiology ; Genetic Variation ; },
abstract = {Malaria in India is declining, in part due to the use of long-lasting insecticide-treated nets (LLINs) and vector control. Historically, the north-eastern region of India has contributed ~10%-12% of the nation's malaria burden. The important mosquito vectors in northeast India have long been considered to be Anopheles baimaii and An. minimus, both associated with forest habitats. Local deforestation and increased rice cultivation, along with widespread LLIN use, may be changing vector species composition. Understanding if and how vector species composition is changing is critical to successful malaria control. In Meghalaya state, malaria is now at a low level of endemicity with occasional seasonal outbreaks. In a biodiverse setting like Meghalaya, where >24 Anopheles mosquito species have been recorded, accurate morphological identification of all species is logistically challenging. To accurately determine Anopheles species richness in the West Khasi Hills (WKH) and West Jaintia Hills (WJH) districts, adult and larval mosquitoes were collected and identified using molecular methods of allele-specific PCR and cytochrome oxidase I DNA barcoding. In 14 villages across both districts, we identified high species richness, 19 species in total. Molecular findings indicated that An. minimus and An. baimaii were rare, while four other species (An. maculatus, An. pseudowillmori, An. jeyporiensis and An. nitidus) were abundant. Anopheles maculatus was highly prevalent in WKH (39% of light trap collections) and An. pseudowillmori in WJH (45%). Larvae of these four species were found in rice fields, suggesting that land cover change is influencing species composition change. Our results suggest that rice fields might be contributing to the observed abundance of An. maculatus and An. pseudowillmori, which could be playing a role in malaria transmission, either independently due to their high abundance, or in combination with An. baimaii and/or An. minimus.},
}
@article {pmid37228135,
year = {2023},
author = {Ally, HM and Hamss, HE and Simiand, C and Maruthi, MN and Colvin, J and Delatte, H},
title = {Genetic diversity, distribution, and structure of Bemisia tabaci whitefly species in potential invasion and hybridization regions of East Africa.},
journal = {PloS one},
volume = {18},
number = {5},
pages = {e0285967},
pmid = {37228135},
issn = {1932-6203},
mesh = {Animals ; *Hemiptera/genetics ; Phylogeny ; Tanzania ; Africa, Central ; Genetic Variation ; },
abstract = {Outbreaks of whitefly, Bemisia tabaci species in East and Central Africa, have become increasingly prevalent during the previous 25 years and are responsible for driving the spread of plant-virus diseases, such as cassava mosaic disease and cassava brown steak disease. Epidemics of these diseases have expanded their ranges over the same period, spreading from Uganda into other sub-Saharan African countries. It was hypothesised that a highly abundant 'invader' population of B. tabaci was responsible for spreading these diseases from Uganda to neighbouring countries and potentially hybridising with the resident cassava B. tabaci populations. Here, we test this hypothesis by investigating the molecular identities of the highly abundant cassava B. tabaci populations from their supposed origin in Uganda, to the northern, central, eastern and coastal regions of Tanzania. Partial mitochondrial cytochrome oxidase I (mtCOI) barcoding sequences and nuclear microsatellite markers were used to analyse the population genetic diversity and structure of 2734 B. tabaci collected from both countries and in different agroecological zones. The results revealed that: (i) the putative SSA1 species is structured according to countries, so differ between them. (ii) Restricted gene flow occurred between SSA1-SG3 and both other SSA1 subgroups (SG1 and SG2), even in sympatry, demonstrating strong barriers to hybridization between those genotypes. (iii) Not only B. tabaci SSA1-(SG1 and SG2) was found in highly abundant (outbreak) numbers, but B. tabaci SSA1-SG3 and the Indian Ocean (IO) species were also recorded in high numbers in several sites in Tanzania. (iv) The SSA1-(SG1 and SG2) species was distributed in both countries, but in Tanzania, the B. tabaci IO and SSA1-SG3 species predominated. These data confirm that multiple, local Tanzanian B. tabaci species produce highly abundant populations, independent of the spread of the putative invasive B. tabaci SSA1-(SG1 and SG2) populations.},
}
@article {pmid37226989,
year = {2023},
author = {Al-Eshaq, DH and Bradley, RT and McBride, ERA and Ford, JC},
title = {Patient and specimen identification in a tertiary care pediatric hospital: Barcodes do not scan themselves.},
journal = {Transfusion},
volume = {63},
number = {7},
pages = {1310-1317},
doi = {10.1111/trf.17399},
pmid = {37226989},
issn = {1537-2995},
mesh = {Pregnancy ; Humans ; Female ; Child ; *Hospitals, Pediatric ; Tertiary Healthcare ; *Blood Transfusion ; Patients ; Specimen Handling ; },
abstract = {BACKGROUND: Despite the safety improvements linked to the use of barcodes for patient and specimen identification, patient misidentification remains a leading cause of transfusion-associated reactions including fatalities. A wealth of evidence supports the use of barcodes in general, but there is less published evidence of real-world barcode compliance. This project investigates barcode scanning compliance for patient and specimen identification at a tertiary care pediatric/maternity hospital.<br><br>STUDY DESIGN AND METHODS: Transfusion laboratory specimen collection noncompliance events between January 1, 2019, and December 31, 2019 were retrieved from the hospital laboratory information system. Data were analyzed including stratification of collections by collector role and collection event. A survey of blood collectors was conducted.<br><br>RESULTS: Collection compliance for 6285 blood typing specimens was evaluated. Full barcode scanning identification of both patient and specimen was utilized in only 33.6% of total collections. The remaining two thirds of collections were overridden by the blood collector: no barcode scanning occurred in 31.3%, while the specimen accession label was scanned but not the patient armband in 32.3% of total collections. There were significant differences between phlebotomists and nurses, with more phlebotomists performing the full scanning and specimen scanning only, while more nurses obtained specimens without patient or specimen scanning (p&#x2009;<&#x2009;.001). Blood collectors identified hardware challenges and training gaps as key contributors to barcode noncompliance.<br><br>DISCUSSION: Our study highlights an instance of poor barcode scanning compliance for patient and specimen identification. We formulated improvement strategies and launched a quality improvement project to address factors influencing noncompliance.},
}
@article {pmid37225882,
year = {2023},
author = {Reinhardt, SCM and Masullo, LA and Baudrexel, I and Steen, PR and Kowalewski, R and Eklund, AS and Strauss, S and Unterauer, EM and Schlichthaerle, T and Strauss, MT and Klein, C and Jungmann, R},
title = {Ångström-resolution fluorescence microscopy.},
journal = {Nature},
volume = {617},
number = {7962},
pages = {711-716},
pmid = {37225882},
issn = {1476-4687},
mesh = {Biological Science Disciplines/instrumentation/methods/standards ; Immunotherapy ; *Microscopy, Fluorescence/instrumentation/methods/standards ; DNA Barcoding, Taxonomic ; *DNA/analysis/chemistry ; *Antigens, CD20/analysis/chemistry ; *Cells/drug effects/metabolism ; },
abstract = {Fluorescence microscopy, with its molecular specificity, is one of the major characterization methods used in the life sciences to understand complex biological systems. Super-resolution approaches[1-6] can achieve resolution in cells in the range of 15 to 20 nm, but interactions between individual biomolecules occur at length scales below 10 nm and characterization of intramolecular structure requires Ångström resolution. State-of-the-art super-resolution implementations[7-14] have demonstrated spatial resolutions down to 5 nm and localization precisions of 1 nm under certain in vitro conditions. However, such resolutions do not directly translate to experiments in cells, and Ångström resolution has not been demonstrated to date. Here we introdue a DNA-barcoding method, resolution enhancement by sequential imaging (RESI), that improves the resolution of fluorescence microscopy down to the Ångström scale using off-the-shelf fluorescence microscopy hardware and reagents. By sequentially imaging sparse target subsets at moderate spatial resolutions of >15 nm, we demonstrate that single-protein resolution can be achieved for biomolecules in whole intact cells. Furthermore, we experimentally resolve the DNA backbone distance of single bases in DNA origami with Ångström resolution. We use our method in a proof-of-principle demonstration to map the molecular arrangement of the immunotherapy target CD20 in situ in untreated and drug-treated cells, which opens possibilities for assessing the molecular mechanisms of targeted immunotherapy. These observations demonstrate that, by enabling intramolecular imaging under ambient conditions in whole intact cells, RESI closes the gap between super-resolution microscopy and structural biology studies and thus delivers information key to understanding complex biological systems.},
}
@article {pmid37224183,
year = {2023},
author = {Leontyev, D and Ishchenko, Y and Schnittler, M},
title = {Fifteen new species from the myxomycete genus Lycogala.},
journal = {Mycologia},
volume = {115},
number = {4},
pages = {524-560},
doi = {10.1080/00275514.2023.2199109},
pmid = {37224183},
issn = {1557-2536},
mesh = {Microscopy, Electron, Scanning ; *Myxomycetes/classification/genetics/ultrastructure ; Spores, Protozoan/cytology ; Species Specificity ; DNA, Protozoan/genetics ; DNA Barcoding, Taxonomic ; },
abstract = {Based on a study of 255 collections from four continents and four floristic kingdoms, we describe 15 new species of the genus Lycogala. The new species, all morphologically close to L. epidendrum, L. exiguum, and L. confusum, differ from each other by the structure of the peridium and, in some cases, also by the color of the fresh spore mass and the ornamentation of the capillitium and spores. Species delimitation is confirmed by two independently inherited molecular markers, as well as previously performed tests of reproductive isolation and genetic distances. We studied authentic material of L. exiguum and L. confusum and found fresh specimens of these species, which allowed us to obtain molecular barcodes and substantiate the separation of new species from these taxa. We propose to retain the name L. epidendrum for the globally most abundant species, for which we provide a more precise description and a neotypification. Two formerly described species, L. leiosporum and L. fuscoviolaceum, we consider to be dubious. We do not recognize the species L. terrestre.},
}
@article {pmid37224035,
year = {2023},
author = {Algarni, A},
title = {Evaluation of plastid and nuclear DNA markers in barcoding of Aloe saudiarabica, KSA.},
journal = {Cellular and molecular biology (Noisy-le-Grand, France)},
volume = {69},
number = {2},
pages = {126-132},
doi = {10.14715/cmb/2023.69.2.21},
pmid = {37224035},
issn = {1165-158X},
mesh = {Genetic Markers ; *Aloe/genetics ; Plastids/genetics ; *Asphodelaceae ; DNA Primers ; },
abstract = {There is great plant diversity in Saudi Arabia. The Asphodelaceae family is within this great diversity, especially the rare species such as the plant, Aloe saudiarabica. Such plants must be preserved in their natural ranges, hence, the need to document them. Genetic markers have become the approved and widely used method for documenting rare plants. The current study deals with the use of three genetic markers to document A. saudiarabica for the first time. The used genetic markers were Maturase-K (matK), Ribulose-bisphosphate-carboxylase (rbcL), and Internal-transcribed-spacer (ITS). The study found that the primers used for the rbcL gene were not effective in achieving identification. Sequencing of the matK and ITS were achieved successfully. The sequences were determined for both markers using two pairs of primers and deposited in the NCBI databases (GenBank). These markers were effective in identifying A. saudiarabica and determining its evolutionary relationship with other Aloe species in various databases. The study showed that A. vera is high similar (>99%) to the other species. In conclusion, the study showed the likelihood of the different genetic markers to document A. saudiarabica, especially the currently investigated matK and ITS.},
}
@article {pmid37222900,
year = {2024},
author = {Kwiatkowski, SC and Sanford, MR and Donley, M and Welch, K and Kahn, R},
title = {Simplified COI barcoding of blow, flesh, and scuttle flies encountered in medicolegal investigations.},
journal = {Forensic science, medicine, and pathology},
volume = {20},
number = {2},
pages = {412-422},
pmid = {37222900},
issn = {1556-2891},
support = {2019-DU-BX-0022//National Institute of Justice/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Electron Transport Complex IV/genetics ; *Forensic Entomology ; *Diptera/genetics ; *Larva/genetics ; *Pupa/genetics ; *Polymerase Chain Reaction ; Postmortem Changes ; Humans ; Sequence Analysis, DNA ; },
abstract = {Accurate insect identification is critical to the estimation of time of colonization (TOC) and post-mortem interval (PMI) in medicolegal death investigations. DNA testing is advantageous because it enables the identification of immature specimens that may not be identified based on morphology alone. We describe here a simplified DNA barcoding method for identifying relevant species that may be implemented by forensic genetics laboratories. A cytochrome oxidase (COI) fragment is analyzed after PCR amplification with a single primer set. The method is effective for many species commonly encountered in death investigations in the USA: members of blowfly genera Calliphora, Chrysomya, Cochliomyia, Lucilia, and Phormia; members of the flesh fly genera Blaesoxipha, Oxysarcodexia, Ravinia, and Sarcophaga; and the scuttle fly Megaselia scalaris. We tested the method on specimens with verified identifications and used it to build a collection of reference sequences from specimens collected in Harris County, Texas. We show here the correct identification of larvae, pupae, and pupal exuviae from the medicolegal casework.},
}
@article {pmid37222600,
year = {2023},
author = {Tchan, BGO and Ngazoa-Kakou, S and Aka, N and Apia, NKB and Hammoudi, N and Drancourt, M and Saad, J},
title = {PPE Barcoding Identifies Biclonal Mycobacterium ulcerans Buruli Ulcer, Côte d'Ivoire.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0034223},
pmid = {37222600},
issn = {2165-0497},
mesh = {Humans ; *Buruli Ulcer/microbiology ; *Mycobacterium ulcerans/genetics ; Cote d'Ivoire ; Real-Time Polymerase Chain Reaction ; Personal Protective Equipment ; },
abstract = {Mycobacterium ulcerans, an environmental opportunistic pathogen, causes necrotic cutaneous and subcutaneous lesions, named Buruli ulcers, in tropical countries. PCR-derived tests used to detect M. ulcerans in environmental and clinical samples do not allow one-shot detection, identification, and typing of M. ulcerans among closely related Mycobacterium marinum complex mycobacteria. We established a 385-member M. marinum/M. ulcerans complex whole-genome sequence database by assembling and annotating 341 M. marinum/M. ulcerans complex genomes and added 44 M. marinum/M. ulcerans complex whole-genome sequences already deposited in the NCBI database. Pangenome, core genome, and single-nucleotide polymorphism (SNP) distance-based comparisons sorted the 385 strains into 10 M. ulcerans taxa and 13 M. marinum taxa, correlating with the geographic origin of strains. Aligning conserved genes identified one PPE (proline-proline-glutamate) gene sequence to be species and intraspecies specific, thereby genotyping the 23 M. marinum/M. ulcerans complex taxa. PCR sequencing of the PPE gene correctly genotyped nine M. marinum/M. ulcerans complex isolates among one M. marinum taxon and three M. ulcerans taxa in the African taxon (T2.4). Further, successful PPE gene PCR sequencing in 15/21 (71.4%) swabs collected from suspected Buruli ulcer lesions in Côte d'Ivoire exhibited positive M. ulcerans IS2404 real-time PCR and identified the M. ulcerans T2.4.1 genotype in eight swabs and M. ulcerans T2.4.1/T2.4.2 mixed genotypes in seven swabs. PPE gene sequencing could be used as a proxy for whole-genome sequencing for the one-shot detection, identification, and typing of clinical M. ulcerans strains, offering an unprecedented tool for identifying M. ulcerans mixed infections. IMPORTANCE We describe a new targeted sequencing approach that characterizes the PPE gene to disclose the simultaneous presence of different variants of a single pathogenic microorganism. This approach has direct implications on the understanding of pathogen diversity and natural history and potential therapeutic implications when dealing with obligate and opportunistic pathogens, such as Mycobacterium ulcerans presented here as a prototype.},
}
@article {pmid37221926,
year = {2023},
author = {Dong, X and Zhang, H and Zhu, X and Wang, K and Xue, H and Ye, Z and Zheng, C and Bu, W},
title = {Mitochondrial introgression and mito-nuclear discordance obscured the closely related species boundaries in Cletus Stål from China (Heteroptera: Coreidae).},
journal = {Molecular phylogenetics and evolution},
volume = {184},
number = {},
pages = {107802},
doi = {10.1016/j.ympev.2023.107802},
pmid = {37221926},
issn = {1095-9513},
mesh = {Animals ; *Heteroptera ; Phylogeny ; China ; *Genome, Mitochondrial ; Mitochondria ; Mitomycin ; },
abstract = {Accurate taxonomy and delimitation are of great importance for pest control strategies and management programs. Here, we focus on Cletus (Insecta: Hemiptera: Coreidae), which includes many crop pests. The species boundaries still conflict and only cytochrome c oxidase subunit I (COI) barcoding has been previously used for molecular studies. We generated new mitochondrial genome and nuclear genome-wide SNPs to explore the species boundaries of 46 Cletus samples from China using multiple species delimitation approaches. All results recovered a monophyly with high support, except for two closely related species in clade I - C. punctiger and C. graminis. Mitochondrial data demonstrated admixture in clade I, while genome-wide SNPs unambiguously identified two separate species, which were confirmed by morphological classification. Inconsistent nuclear and mitochondrial data indicated mito-nuclear discordance. Mitochondrial introgression is the most likely explanation, and more extensive sampling and more comprehensive data are needed to ascertain a pattern. Accurate species delimitation will shed light on species status; thus, an accurate taxonomy is of particular concern, as there is a pressing need to implement precise control of agricultural pests and to perform further research on diversification.},
}
@article {pmid37221844,
year = {2023},
author = {Isla, J and Jácome-Flores, M and Arroyo, JM and Jordano, P},
title = {The turnover of plant-frugivore interactions along plant range expansion: consequences for natural colonization processes.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {1999},
pages = {20222547},
pmid = {37221844},
issn = {1471-2954},
mesh = {Animals ; *Seeds ; *Fertility ; Phenotype ; Research Design ; },
abstract = {Plant-animal mutualisms such as seed dispersal are key interactions for sustaining plant range shifts. It remains elusive whether the organization of interactions with seed dispersers is reconfigured along the expansion landscape template and, if so, whether its effects accelerate or slow colonization. Here we analyse plant-frugivore interactions in a scenario of rapid population expansion of a Mediterranean juniper. We combined network analyses with field surveys, sampling interactions between individual plants and frugivores by DNA-barcoding and phototrapping over two seasons. We assess the role of intrinsic and extrinsic intraspecific variability in shaping interactions and we estimate the individual plant contributions to the seed rain. The whole interaction network was highly structured, with a distinct set of modules including individual plants and frugivore species arranged concordantly along the expansion gradient. The modular configuration was partially shaped by individual neighbourhood context (density and fecundity) and phenotypic traits (cone size). Interaction reconfiguration resulted in a higher and more uneven propagule contribution, with most effective dispersers having a prominent role at the colonization front stand, where a distinct subset of early arriving plants dominated the seed rain. Our study offers new insights into the key role of mutualistic interactions in colonization scenarios by promoting fast plant expansion processes.},
}
@article {pmid37221210,
year = {2023},
author = {Paukszto, &#x141; and Górski, P and Krawczyk, K and Maździarz, M and Szczecińska, M and Ślipiko, M and Sawicki, J},
title = {The organellar genomes of Pellidae (Marchantiophyta): the evidence of cryptic speciation, conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineage.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {8303},
pmid = {37221210},
issn = {2045-2322},
mesh = {*Hepatophyta ; *Genome, Mitochondrial ; Phylogeny ; Mitochondria ; *Genome, Plastid ; *Anemone ; },
abstract = {Organellar genomes of liverworts are considered as one of the most stable among plants, with rare events of gene loss and structural rearrangements. However, not all lineages of liverworts are equally explored in the field of organellar genomics, and subclass Pellidae is one of the less known. Hybrid assembly, using both short- and long-read technologies enabled the assembly of repeat-rich mitogenomes of Pellia and Apopellia revealing extraordinary reduction of length in the latter which impacts only intergenic spacers. The mitogenomes of Apopellia were revealed to be the smallest among all known liverworts-109 k bp, despite retaining all introns. The study also showed the loss of one tRNA gene in Apopellia mitogenome, although it had no impact on the codon usage pattern of mitochondrial protein coding genes. Moreover, it was revealed that Apopellia and Pellia differ in codon usage by plastome CDSs, despite identical tRNA gene content. Molecular identification of species is especially important where traditional taxonomic methods fail, especially within Pellidae where cryptic speciation is well recognized. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. Application of super-barcodes, based on complete mitochondrial or plastid genomes sequences enable identification of all cryptic lineages within Apopellia and Pellia genera, however in some particular cases, mitogenomes were more efficient in species delimitation than plastomes.},
}
@article {pmid37215936,
year = {2023},
author = {Liu, WB and Wang, Y and Zhao, KZ and Wang, CY and Zhang, JY and Yan, CC and Lin, XL},
title = {New species, a new combination, and DNA barcodes of Parachironomus Lenz, 1921 (Diptera, Chironomidae).},
journal = {ZooKeys},
volume = {1153},
number = {},
pages = {121-140},
pmid = {37215936},
issn = {1313-2989},
abstract = {The genus Parachironomus has a cosmopolitan distribution including 85 valid described species worldwide. Species records and studies of the genus in the Tibetan Plateau are scarce. In this study, the genus Parachironomus from China is revised and two new species, Parachironomuswangi Liu &amp; Lin, sp. nov. and Parachironomusnankaiensis Liu &amp; Lin, sp. nov., are described based on adult morphology and molecular data. Paracladopelmademissum Yan, Wang &amp; Bu is placed in the genus Parachironomus as a new combination. A neighbor-joining tree was reconstructed based on all known ParachironomusCOI DNA barcodes. A key to adult males of the genus Parachironomus from China is also provided.},
}
@article {pmid37215324,
year = {2023},
author = {Anwar, AR and Mur, M and Humar, M},
title = {Microcavity- and Microlaser-Based Optical Barcoding: A Review of Encoding Techniques and Applications.},
journal = {ACS photonics},
volume = {10},
number = {5},
pages = {1202-1224},
pmid = {37215324},
issn = {2330-4022},
abstract = {Optical microbarcodes have recently received a great deal of interest because of their suitability for a wide range of applications, such as multiplexed assays, cell tagging and tracking, anticounterfeiting, and product labeling. Spectral barcodes are especially promising because they are robust and have a simple readout. In addition, microcavity- and microlaser-based barcodes have very narrow spectra and therefore have the potential to generate millions of unique barcodes. This review begins with a discussion of the different types of barcodes and then focuses specifically on microcavity-based barcodes. While almost any kind of optical microcavity can be used for barcoding, currently whispering-gallery microcavities (in the form of spheres and disks), nanowire lasers, Fabry-Pérot lasers, random lasers, and distributed feedback lasers are the most frequently employed for this purpose. In microcavity-based barcodes, the information is encoded in various ways in the properties of the emitted light, most frequently in the spectrum. The barcode is dependent on the properties of the microcavity, such as the size, shape, and the gain materials. Various applications of these barcodes, including cell tracking, anticounterfeiting, and product labeling are described. Finally, the future prospects for microcavity- and microlaser-based barcodes are discussed.},
}
@article {pmid37215163,
year = {2023},
author = {Jin, YL and Nunes Godeiro, N and Bu, Y},
title = {Description of the first species of Scutigerella (Symphyla, Scutigerellidae) from China, with mitogenomic and genetic divergence analysis.},
journal = {ZooKeys},
volume = {1157},
number = {},
pages = {145-161},
pmid = {37215163},
issn = {1313-2989},
abstract = {Scutigerellasinensis Jin &amp; Bu, sp. nov. from China is described and illustrated. It is characterized by a deeply emarginated posterior margin of tergite 2, less differentiated marginal setae on all tergites, absence of seta a3 around the antennal base, and 6-8 setae on the first tergite. The complete mitochondrial genome of the new species is also analyzed and compared with the mitogenome of Scutigerellacauseyae. In the reconstructed Neighbor-Joining tree based on COI gene sequences, S.sinensissp. nov. clusters with S.causeyae, however, with big distances. The genetic divergence among S.sinensissp. nov. and congeners, species of Hanseniella and Scutigerella, and both families of Symphyla was analyzed using COI gene sequences.},
}
@article {pmid37214858,
year = {2023},
author = {Bleich, RM and Li, C and Sun, S and Barlogio, CJ and Broberg, CA and Franks, AR and Bulik-Sullivan, E and Dogan, B and Simpson, KW and Carroll, IM and Fodor, AA and Arthur, JC},
title = {A consortia of clinical E. coli strains with distinct in-vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {37214858},
issn = {2693-5015},
support = {K12 GM000678/GM/NIGMS NIH HHS/United States ; P30 CA016086/CA/NCI NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; P40 OD010995/OD/NIH HHS/United States ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) patients experience recurrent episodes of intestinal inflammation and often follow an unpredictable disease course. Mucosal colonization with adherent-invasive Escherichia coli (AIEC) are believed to perpetuate intestinal inflammation. However, it remains unclear if the 24-year-old AIEC in-vitro definition fully predicts mucosal colonization in-vivo. To fill this gap, we have developed a novel molecular barcoding approach to distinguish strain variants in the gut and have integrated this approach to explore mucosal colonization of distinct patient-derived E. coli isolates in gnotobiotic mouse models of colitis.<br><br>RESULTS: Germ-free inflammation-susceptible interleukin-10-deficient (Il10[-/-]) and inflammation-resistant WT mice were colonized with a consortia of AIEC and non-AIEC strains, then given a murine fecal transplant to provide niche competition. E. coli strains isolated from human intestinal tissue were each marked with a unique molecular barcode that permits identification and quantification by barcode-targeted sequencing. 16S rRNA sequencing was used to evaluate the microbiome response to E. coli colonization. Our data reveal that specific AIEC and non-AIEC strains reproducibly colonize the intestinal mucosa of WT and Il10[-/-] mice. These E. coli expand in Il10[-/-] mice during inflammation and induce compositional dysbiosis to the microbiome in an inflammation-dependent manner. In turn, specific microbes co-evolve in inflamed mice, potentially diversifying E. coli colonization patterns. We observed no selectivity in E. coli colonization patterns in the fecal contents, indicating minimal selective pressure in this niche from host-microbe and interbacterial interactions. Because select AIEC and non-AIEC strains colonize the mucosa, this suggests the in vitro AIEC definition may not fully predict in vivo colonization potential. Further comparison of seven E. coli genomes pinpointed unique genomic features contained only in highly colonizing strains (two AIEC and two non-AIEC). Those colonization-associated features may convey metabolic advantages (e.g., iron acquisition and carbohydrate consumption) to promote efficient mucosal colonization.<br><br>CONCLUSIONS: Our findings establish the in-vivo mucosal colonizer, not necessarily AIEC, as a principal dysbiosis driver through crosstalk with host and associated microbes. Furthermore, we highlight the utility of high-throughput screens to decode the in-vivo colonization dynamics of patient-derived bacteria in murine models.},
}
@article {pmid37214853,
year = {2023},
author = {Smith-Roe, SL and Hobbs, CA and Hull, V and Auman, JT and Recio, L and Streicker, MA and Rivas, MV and Pratt, GA and Lo, FY and Higgins, JE and Schmidt, EK and Williams, LN and Nachmanson, D and Valentine, CC and Salk, JJ and Witt, KL},
title = {Adopting Duplex Sequencing™ Technology for Genetic Toxicity Testing: A Proof-of-Concept Mutagenesis Experiment with N-Ethyl-N-Nitrosourea (ENU)-Exposed Rats.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37214853},
issn = {2692-8205},
support = {HHSN273201300009C/ES/NIEHS NIH HHS/United States ; R44 ES030642/ES/NIEHS NIH HHS/United States ; },
abstract = {UNLABELLED: Duplex sequencing (DuplexSeq) is an error-corrected next-generation sequencing (ecNGS) method in which molecular barcodes informatically link PCR-copies back to their source DNA strands, enabling computational removal of errors by comparing grouped strand sequencing reads. The resulting background of less than one artifactual mutation per 10 [7] nucleotides allows for direct detection of somatic mutations. TwinStrand Biosciences, Inc. has developed a DuplexSeq-based mutagenesis assay to sample the rat genome, which can be applied to genetic toxicity testing. To evaluate this assay for early detection of mutagenesis, a time-course study was conducted using male Hsd:Sprague Dawley SD rats (3 per group) administered a single dose of 40 mg/kg N-ethyl-N-nitrosourea (ENU) via gavage, with mutation frequency (MF) and spectrum analyzed in stomach, bone marrow, blood, and liver tissues at 3 h, 24 h, 7 d, and 28 d post-exposure. Significant increases in MF were observed in ENU-exposed rats as early as 24 h for stomach (site of contact) and bone marrow (a highly proliferative tissue) and at 7 d for liver and blood. The canonical, mutational signature of ENU was established by 7 d post-exposure in all four tissues. Interlaboratory analysis of a subset of samples from different tissues and time points demonstrated remarkable reproducibility for both MF and spectrum. These results demonstrate that MF and spectrum can be evaluated successfully by directly sequencing targeted regions of DNA obtained from various tissues, a considerable advancement compared to currently used in vivo gene mutation assays.<br><br>HIGHLIGHTS: DuplexSeq is an ultra-accurate NGS technology that directly quantifies mutationsENU-dependent mutagenesis was detected 24 h post-exposure in proliferative tissuesMultiple tissues exhibited the canonical ENU mutation spectrum 7 d after exposureResults obtained with DuplexSeq were highly concordant between laboratoriesThe Rat-50 Mutagenesis Assay is promising for applications in genetic toxicology.},
}
@article {pmid37214591,
year = {2023},
author = {Kamimura, Y and Lee, CY and Yamasako, J and Nishikawa, M},
title = {Identification and reproductive isolation of Euborellia species (Insecta, Dermaptera, Anisolabididae) from East and Southeast Asia.},
journal = {ZooKeys},
volume = {1146},
number = {},
pages = {115-134},
pmid = {37214591},
issn = {1313-2989},
abstract = {Euborellia (Anisolabididae: Anisolabidinae) is one of the most speciose genera of earwigs (Dermaptera), and its species-level classification is difficult. To settle the classification of brachypterous species with abbreviated tegmina recorded from East and Southeast Asia, we examined the morphology and reproductive isolation of three tentative Euborellia species, and analyzed the DNA barcoding region of the mitochondrial cytochrome oxidase subunit I (COI) gene. The observed complete reproductive isolation among the three Euborellia taxa and considerable differentiation in the COI sequences clearly show that each should be treated as a separate species. Based on morphology, distribution and the DNA sequence, we identify Euborellia sp. 1 of Malaysia as E.annulata (Fabricius), a circumtropical cosmopolitan with no records of a fully winged form. Samples from Ioto Island (= Iwo-jima Island: Ogasawara Islands, southern Japan) were also identified as this species. Euborellia sp. 3, from the main islands of Japan, was generally larger and lacked a Y-shaped pigmented area on the penis lobe, which is characteristic of Euborellia sp. 1. We propose reinstating E.pallipes (Shiraki) as the oldest name for this taxon. Euborellia sp. 2, even the brachypterous form, can be distinguished from these two species by its paler coloration (particularly the femora), ecarinate post-abdomen, and the shape of the male genitalia (parameres). We tentatively identify this species as E.philippinensis Srivastava based on the morphology of the brachypterous form, although the macropterous form cannot be distinguished from E.femoralis (Dohrn).},
}
@article {pmid37214460,
year = {2023},
author = {Raclariu-Manolică, AC and Mauvisseau, Q and de Boer, HJ},
title = {Horizon scan of DNA-based methods for quality control and monitoring of herbal preparations.},
journal = {Frontiers in pharmacology},
volume = {14},
number = {},
pages = {1179099},
pmid = {37214460},
issn = {1663-9812},
abstract = {Herbal medicines and preparations are widely used in healthcare systems globally, but concerns remain about their quality and safety. New herbal products are constantly being introduced to the market under varying regulatory frameworks, with no global consensus on their definition or characterization. These biologically active mixtures are sold through complex globalized value chains, which create concerns around contamination and profit-driven adulteration. Industry, academia, and regulatory bodies must collaborate to develop innovative strategies for the identification and authentication of botanicals and their preparations to ensure quality control. High-throughput sequencing (HTS) has significantly improved our understanding of the total species diversity within DNA mixtures. The standard concept of DNA barcoding has evolved over the last two decades to encompass genomic data more broadly. Recent research in DNA metabarcoding has focused on developing methods for quantifying herbal product ingredients, yielding meaningful results in a regulatory framework. Techniques, such as loop-mediated isothermal amplification (LAMP), DNA barcode-based Recombinase Polymerase Amplification (BAR-RPA), DNA barcoding coupled with High-Resolution Melting (Bar-HRM), and microfluidics-based methods, offer more affordable tests for the detection of target species. While target capture sequencing and genome skimming are considerably increasing the species identification resolution in challenging plant clades, ddPCR enables the quantification of DNA in samples and could be used to detect intended and unwanted ingredients in herbal medicines. Here, we explore the latest advances in emerging DNA-based technologies and the opportunities they provide as taxa detection tools for evaluating the safety and quality of dietary supplements and herbal medicines.},
}
@article {pmid37214269,
year = {2023},
author = {Carrington-Hoekstra, P and Fernandez-Triana, J and Dyer, LA and Whitfield, J},
title = {Larissimusnigricans sp. nov. (Hymenoptera, Braconidae), a new reared species of a rare neotropical genus recovered through biodiversity inventory in Ecuador.},
journal = {ZooKeys},
volume = {1156},
number = {},
pages = {15-24},
pmid = {37214269},
issn = {1313-2989},
abstract = {A new species of the rarely collected neotropical microgastrine braconid wasp genus Larissimus Nixon, represented previously by only a single described species, L.cassander Nixon, was recovered by the Caterpillars and Parasitoids of the Eastern Andes in Ecuador inventory project. Larissimusnigricanssp. nov. was reared from an unidentified species of arctiine Erebidae feeding on the common bamboo species Chusqueascandens Kunth at the Yanayacu Biological Station near Cosanga, Napo Province, Ecuador. The new species is described and diagnosed from L.cassander using both morphological and DNA barcode data.},
}
@article {pmid37214175,
year = {2023},
author = {Pešić, V and Jovanović, M and Espiridião Oliveira, A and Pedro, A and Freira, M and Morais, MM},
title = {New records of water mites (Acari, Hydrachnidia) from Portugal revealed by DNA barcoding, with the description of Atractidesmarizae sp. nov.},
journal = {ZooKeys},
volume = {1151},
number = {},
pages = {205-222},
pmid = {37214175},
issn = {1313-2989},
abstract = {This study presents the first results of DNA barcoding of water mites from Portugal. DNA barcodes were recovered from 19 water mite specimens morphologically assigned to eight species, seven of them newly reported from Portugal. Two species, Torrenticolahispanica (Lundblad, 1941) and A.cultellatus (K. Viets, 1930) were discovered more than 80 years after they were first described, and Atractidesmarizaesp. nov. is described as new for science.},
}
@article {pmid37213527,
year = {2023},
author = {Heckenhauer, J and Razuri-Gonzales, E and Mwangi, FN and Schneider, J and Pauls, SU},
title = {Holotype sequencing of Silvataresholzenthali Rázuri-Gonzales, Ngera &amp; Pauls, 2022 (Trichoptera, Pisuliidae).},
journal = {ZooKeys},
volume = {1159},
number = {},
pages = {1-15},
pmid = {37213527},
issn = {1313-2989},
abstract = {While DNA barcodes are increasingly provided in descriptions of new species, the whole mitochondrial and nuclear genomes are still rarely included. This is unfortunate because whole genome sequencing of holotypes allows perpetual genetic characterization of the most representative specimen for a given species. Thus, de novo genomes are invaluable additional diagnostic characters in species descriptions, provided the structural integrity of the holotype specimens remains intact. Here, we used a minimally invasive method to extract DNA of the type specimen of the recently described caddisfly species Silvataresholzenthali Rázuri-Gonzales, Ngera &amp; Pauls, 2022 (Trichoptera: Pisuliidae) from the Democratic Republic of the Congo. A low-cost next generation sequencing strategy was used to generate the complete mitochondrial and draft nuclear genome of the holotype. The data in its current form is an important extension to the morphological species description and valuable for phylogenomic studies.},
}
@article {pmid37213501,
year = {2023},
author = {Huang, Y and Jiang, P and Liang, Z and Chen, R and Yue, Z and Xie, X and Guan, C and Fang, X},
title = {Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1145315},
pmid = {37213501},
issn = {1664-302X},
abstract = {Human gut microbiota is associated with human health and disease, and is known to have the second-largest genome in the human body. The microbiota genome is important for their functions and metabolites; however, accurate genomic access to the microbiota of the human gut is hindered due to the difficulty of cultivating and the shortcomings of sequencing technology. Therefore, we applied the stLFR library construction method to assemble the microbiota genomes and demonstrated that assembly property outperformed standard metagenome sequencing. Using the assembled genomes as references, SNP, INDEL, and HGT gene analyses were performed. The results demonstrated significant differences in the number of SNPs and INDELs among different individuals. The individual displayed a unique species variation spectrum, and the similarity of strains within individuals decreased over time. In addition, the coverage depth analysis of the stLFR method shows that a sequencing depth of 60X is sufficient for SNP calling. HGT analysis revealed that the genes involved in replication, recombination and repair, mobilome prophages, and transposons were the most transferred genes among different bacterial species in individuals. A preliminary framework for human gut microbiome studies was established using the stLFR library construction method.},
}
@article {pmid37212833,
year = {2023},
author = {Xu, H and Wang, Y and Fang, J and Wang, J and Zhou, Y},
title = {A rapid diagnosis and treatment of Ornithonyssus bacoti infection.},
journal = {Parasitology research},
volume = {122},
number = {7},
pages = {1567-1572},
pmid = {37212833},
issn = {1432-1955},
support = {202102310808, W.L.//Key Science and Technology Program of Henan Province/ ; W.L.//Major Scientific and Technological Innovation Project of Hebi/ ; 182300410316, Y.Z.//Natural Science Foundation of Henan Province/ ; },
mesh = {Humans ; Animals ; Mice ; *Mite Infestations/diagnosis/drug therapy/parasitology ; Ivermectin ; Phylogeny ; *Mites ; Skin ; },
abstract = {Mites serve as pathogens, allergens, or microbial containers, which can seriously damage the health of humans and animals. The substantial amount of mite species and their similar morphology make it complicated to identify and classify. Our mouse breeder incidentally noticed papular-type erythema with itching and peeling of the skin in several places, and an investigation revealed that this symptom was caused by an uncommon parasite that appeared on the skin and around the nest of the mice. By morphological observation, DNA extraction, PCR amplification, and DNA sequencing, we roughly identified the category of the parasite as a mite. Then, we designed a specific primer cox1, amplified and sequenced the mitochondrial cox1 gene fragment of the mite, calculated the intraspecific and interspecific differences, and reconstructed the phylogenetic tree for sequence alignment. Finally, this species was identified and named this Ornithonyssus bacoti-KF. According to the ivermectin gradient test, we found that 0.1 mg/mL concentration of ivermectin solution was the most effective for mite removal in the bath, with no recurrence after 6 months of treatment. Ornithonyssus bacoti, diagnosed by microscopic exam and confirmed by PCR amplification sequencing, was treated with ivermectin to control the rodent-borne parasite effectively.},
}
@article {pmid37212605,
year = {2023},
author = {Miah, M and Hossain, ME and Hasan, R and Alam, MS and Puspo, JA and Hasan, MM and Islam, A and Chowdhury, S and Rahman, MZ},
title = {Culture-Independent Workflow for Nanopore MinION-Based Sequencing of Influenza A Virus.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0494622},
pmid = {37212605},
issn = {2165-0497},
mesh = {Humans ; *Influenza A virus/genetics ; *Influenza, Human/diagnosis ; Workflow ; *Nanopores ; Whole Genome Sequencing/methods ; },
abstract = {Whole-genome sequencing (WGS) of influenza A virus (IAV) is crucial for identifying diverse subtypes and newly evolved variants and for selecting vaccine strains. In developing countries, where facilities are often inadequate, WGS is challenging to perform using conventional next-generation sequencers. In this study, we established a culture-independent, high-throughput native barcode amplicon sequencing workflow that can sequence all influenza subtypes directly from a clinical specimen. All segments of IAV in 19 clinical specimens, irrespective of their subtypes, were amplified simultaneously using a two-step reverse transcriptase PCR (RT-PCR) system. First, the library was prepared using the ligation sequencing kit, barcoded individually using the native barcodes, and sequenced on the MinION MK 1C platform with real-time base-calling. Then, subsequent data analyses were performed with the appropriate tools. WGS of 19 IAV-positive clinical samples was carried out successfully with 100% coverage and 3,975-fold mean coverage for all segments. This easy-to-install and low-cost capacity-building protocol took only 24 h complete from extracting RNA to obtaining finished sequences. Overall, we developed a high-throughput portable sequencing workflow ideal for resource-limited clinical settings, aiding in real-time surveillance, outbreak investigation, and the detection of emerging viruses and genetic reassortment events. However, further evaluation is required to compare its accuracy with other high-throughput sequencing technologies to validate the widespread application of these findings, including WGS from environmental samples. IMPORTANCE The Nanopore MinION-based influenza sequencing approach we are proposing makes it possible to sequence the influenza A virus, irrespective of its diverse serotypes, directly from clinical and environmental swab samples, so that we are not limited to virus culture. This third-generation, portable, multiplexing, and real-time sequencing strategy is highly convenient for local sequencing, particularly in low- and middle-income countries like Bangladesh. Furthermore, the cost-efficient sequencing method could provide new opportunities to respond to the early phase of an influenza pandemic and enable the timely detection of the emerging subtypes in clinical samples. Here, we meticulously described the entire process that might help the researcher who will follow this methodology in the future. Our findings suggest that this proposed method is ideal for clinical and academic settings and will aid in real-time surveillance and in the detection of potential outbreak agents and newly evolved viruses.},
}
@article {pmid37212374,
year = {2023},
author = {Leroy, BML and Rabl, D and Püls, M and Hochrein, S and Bae, S and Müller, J and Hebert, PDN and Kuzmina, ML and Zakharov, EV and Lemme, H and Hahn, WA and Hilmers, T and Jacobs, M and Kienlein, S and Pretzsch, H and Heidrich, L and Seibold, S and Roth, N and Vogel, S and Kriegel, P and Weisser, WW},
title = {Trait-mediated responses of caterpillar communities to spongy moth outbreaks and subsequent tebufenozide treatments.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {33},
number = {6},
pages = {e2890},
doi = {10.1002/eap.2890},
pmid = {37212374},
issn = {1051-0761},
mesh = {Animals ; *Moths ; *Insecticides ; Ecosystem ; *Bacillus thuringiensis ; },
abstract = {Outbreaks of the spongy moth Lymantria dispar can have devastating impacts on forest resources and ecosystems. Lepidoptera-specific insecticides, such as Bacillus thuringiensis var. kurstaki (BTK) and tebufenozide, are often deployed to prevent heavy defoliation of the forest canopy. While it has been suggested that using BTK poses less risk to non-target Lepidoptera than leaving an outbreak untreated, in situ testing of this assumption has been impeded by methodological challenges. The trade-offs between insecticide use and outbreaks have yet to be addressed for tebufenozide, which is believed to have stronger side effects than BTK. We investigated the short-term trade-offs between tebufenozide treatments and no-action strategies for the non-target herbivore community in forest canopies. Over 3 years, Lepidoptera and Symphyta larvae were sampled by canopy fogging in 48 oak stands in southeast Germany during and after a spongy moth outbreak. Half of the sites were treated with tebufenozide and changes in canopy cover were monitored. We contrasted the impacts of tebufenozide and defoliator outbreaks on the abundance, diversity, and functional structure of chewing herbivore communities. Tebufenozide treatments strongly reduced Lepidoptera up to 6 weeks after spraying. Populations gradually converged back to control levels after 2 years. Shelter-building species dominated caterpillar assemblages in treated plots in the post-spray weeks, while flight-dimorphic species were slow to recover and remained underrepresented in treated stands 2 years post-treatment. Spongy moth outbreaks had minor effects on leaf chewer communities. Summer Lepidoptera decreased only when severe defoliation occurred, whereas Symphyta declined 1 year after defoliation. Polyphagous species with only partial host plant overlap with the spongy moth were absent from heavily defoliated sites, suggesting greater sensitivity of generalists to defoliation-induced plant responses. These results demonstrate that both tebufenozide treatments and spongy moth outbreaks alter canopy herbivore communities. Tebufenozide had a stronger and longer lasting impact, but it was restricted to Lepidoptera, whereas the outbreak affected both Lepidoptera and Symphyta. These results are tied to the fact that only half of the outbreak sites experienced severe defoliation. This highlights the limited accuracy of current defoliation forecast methods, which are used as the basis for the decision to spray insecticides.},
}
@article {pmid37209097,
year = {2023},
author = {Binder, V and Li, W and Faisal, M and Oyman, K and Calkins, DL and Shaffer, J and Teets, EM and Sher, S and Magnotte, A and Belardo, A and Deruelle, W and Gregory, TC and Orwick, S and Hagedorn, EJ and Perlin, JR and Avagyan, S and Lichtig, A and Barrett, F and Ammerman, M and Yang, S and Zhou, Y and Carson, WE and Shive, HR and Blachly, JS and Lapalombella, R and Zon, LI and Blaser, BW},
title = {Microenvironmental control of hematopoietic stem cell fate via CXCL8 and protein kinase C.},
journal = {Cell reports},
volume = {42},
number = {5},
pages = {112528},
pmid = {37209097},
issn = {2211-1247},
support = {R01 DK128238/DK/NIDDK NIH HHS/United States ; K08 DK111920/DK/NIDDK NIH HHS/United States ; U01 HL134812/HL/NHLBI NIH HHS/United States ; R01 HL144780/HL/NHLBI NIH HHS/United States ; P01 HL032262/HL/NHLBI NIH HHS/United States ; P01 HL131477/HL/NHLBI NIH HHS/United States ; RC2 DK120535/DK/NIDDK NIH HHS/United States ; K01 DK111790/DK/NIDDK NIH HHS/United States ; UM1 CA186712/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Endothelial Cells/metabolism ; Hematopoiesis/genetics ; Hematopoietic Stem Cells/metabolism ; Phylogeny ; Protein Kinase C-delta/metabolism ; Stem Cell Niche ; *Zebrafish ; Interleukin-8/metabolism ; },
abstract = {Altered hematopoietic stem cell (HSC) fate underlies primary blood disorders but microenvironmental factors controlling this are poorly understood. Genetically barcoded genome editing of synthetic target arrays for lineage tracing (GESTALT) zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta (PKC-δ, encoded by prkcda) increases the number of HSC clones by up to 80% and expands polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augment HSC competition for residency within the niche and expand defined niche populations. CXCL8 induces association of PKC-δ with the focal adhesion complex, activating extracellular signal-regulated kinase (ERK) signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche that is controlled by CXCL8 and PKC and has significant impact on HSC phylogenetic and phenotypic fate.},
}
@article {pmid37209020,
year = {2023},
author = {Cui, X and Ngang, S and Liu, DD and Cheow, LF},
title = {Rapid Single-Round Pool Testing of Infectious Disease Enabled by Multicolor Digital Melting PCR.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {19},
number = {37},
pages = {e2205636},
doi = {10.1002/smll.202205636},
pmid = {37209020},
issn = {1613-6829},
mesh = {Humans ; SARS-CoV-2/genetics ; *COVID-19/diagnosis ; *Communicable Diseases/diagnosis ; Polymerase Chain Reaction ; Nucleic Acid Amplification Techniques ; Sensitivity and Specificity ; RNA, Viral/genetics ; COVID-19 Testing ; },
abstract = {Pooled nucleic acid amplification test is a promising strategy to reduce cost and resources for screening large populations for infectious disease. However, the benefit of pooled testing is reversed when disease prevalence is high, because of the need to retest each sample to identify infected individual when a pool is positive. Split, Amplify, and Melt analysis of Pooled Assay (SAMPA) is presented, a multicolor digital melting PCR assay in nanoliter chambers that simultaneously identify infected individuals and quantify their viral loads in a single round of pooled testing. This is achieved by early sample tagging with unique barcodes and pooling, followed by single molecule barcode identification in a digital PCR platform using a highly multiplexed melt curve analysis strategy. The feasibility is demonstrated of SAMPA for quantitative unmixing and variant identification from pools of eight synthetic DNA and RNA samples corresponding to the N1 gene, as well as from heat-inactivated SARS-CoV-2 virus. Single round pooled testing of barcoded samples with SAMPA can be a valuable tool for rapid and scalable population testing of infectious disease.},
}
@article {pmid37208352,
year = {2023},
author = {Song, F and Deng, YF and Yan, HF and Lin, ZL and Delgado, A and Trinidad, H and Gonzales-Arce, P and Riva, S and Cano-Echevarría, A and Ramos, E and Aroni, YP and Rivera, S and Arakaki, M and Ge, XJ},
title = {Flora diversity survey and establishment of a plant DNA barcode database of Lomas ecosystems in Peru.},
journal = {Scientific data},
volume = {10},
number = {1},
pages = {294},
pmid = {37208352},
issn = {2052-4463},
mesh = {DNA Barcoding, Taxonomic ; *Ecosystem ; *Loma/genetics ; Peru ; Plants/genetics ; },
abstract = {Lomas formations or "fog oases" are islands of vegetation in the desert belt of the west coast of South America, with a unique vegetation composition among the world's deserts. However, plant diversity and conservation studies have long been neglected, and there exists a severe gap in plant DNA sequence information. To address the lack of DNA information, we conducted field collections and laboratory DNA sequencing to establish a DNA barcode reference library of Lomas plants from Peru. This database provides 1,207 plant specimens and 3,129 DNA barcodes data corresponding with collections from 16 Lomas locations in Peru, during 2017 and 2018. This database will facilitate both rapid species identification and basic studies on plant diversity, thereby enhancing our understanding of Lomas flora's composition and temporal variation, and providing valuable resources for conserving plant diversity and maintaining the stability of the fragile Lomas ecosystems.},
}
@article {pmid37206111,
year = {2023},
author = {Jafari, S and Müller, B and Rulik, B and Rduch, V and S Peters, R},
title = {Another crack in the Dark Taxa wall: a custom DNA barcoding protocol for the species-rich and common Eurytomidae (Hymenoptera, Chalcidoidea).},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e101998},
pmid = {37206111},
issn = {1314-2828},
abstract = {DNA barcodes are a great tool for accelerated species identification and for complementing species delimitation. Furthermore, DNA barcode reference libraries are the decisive backbone feature for any metabarcoding study in biodiversity monitoring, conservation or ecology. However, in some taxa, DNA barcodes cannot be generated with published primers at a satisfying success rate and these groups will consequently be largely missing from any barcoding-based species list. Here, we provide a custom DNA barcoding forward primer for the Eurytomidae (Hymenoptera, Chalcidoidea), elevating the success rate of high-quality DNA barcodes from 33% to 88%. Eurytomidae is a severely understudied, taxonomically challenging, species-rich group of primarily parasitoid wasps. High species numbers, diverse ecological roles and widespread and common presence identify Eurytomidae as one of many crucial families in terrestrial ecosystems. It is now possible to include Eurytomidae when studying and monitoring the terrestrial fauna, highlighting that barcoding-based approaches will need to routinely use different primers to avoid biases in their data and inferences. The new DNA barcoding protocol is also a prerequisite for our integrative taxonomy study of the group, aiming at delimiting and characterising Central European species and filling the GBOL (German Barcode Of Life) DNA barcode reference library with species-named and voucher-linked sequences.},
}
@article {pmid37205700,
year = {2023},
author = {Botha, D and du Plessis, M and Siebert, F and Barnard, S},
title = {Introducing an rbcL and a trnL reference library to aid in the metabarcoding analysis of foraged plants from two semi-arid eastern South African savanna bioregions.},
journal = {PloS one},
volume = {18},
number = {5},
pages = {e0286144},
pmid = {37205700},
issn = {1932-6203},
mesh = {*Grassland ; South Africa ; *DNA Barcoding, Taxonomic ; Phylogeny ; Reproducibility of Results ; Plants ; DNA, Plant/genetics ; },
abstract = {Success of a metabarcoding study is determined by the extent of taxonomic coverage and the quality of records available in the DNA barcode reference database used. This study aimed to create an rbcL and a trnL (UAA) DNA barcode sequence reference database of plant species that are potential herbivore foraging targets and commonly found in semi-arid savannas of eastern South Africa. An area-specific species list of 765 species was compiled according to plant collection records available and areas comparable to an eastern semi-arid South African savanna. Thereafter, rbcL and trnL sequences of species from this list were mined from GenBank and BOLD sequence databases according to specific quality criteria to ensure accurate taxonomic coverage and resolution. These were supplemented with sequences of 24 species sequenced for this study. A phylogenetic approach, employing Neighbor-Joining, was used to verify the topology of the reference libraries to known angiosperm phylogeny. The taxonomic reliability of these reference libraries was evaluated by testing for the presence of a barcode gap, identifying a data-appropriate identification threshold, and determining the identification accuracy of reference sequences via primary distance-based criteria. The final rbcL reference dataset consisted of 1238 sequences representing 318 genera and 562 species. The final trnL dataset consisted of 921 sequences representing 270 genera and 461 species. Barcode gaps were found for 76% of the taxa in the rbcL barcode reference dataset and 68% of the taxa in the trnL barcode reference dataset. The identification success rate, calculated with the k-nn criterion was 85.86% for the rbcL dataset and 73.72% for the trnL dataset. The datasets for rbcL and trnL combined during this study are not presented as complete DNA reference libraries, but rather as two datasets that should be used in unison to identify plants present in the semi-arid eastern savannas of South Africa.},
}
@article {pmid37202847,
year = {2023},
author = {Xie, T and Orr, MC and Zhang, D and Ferrari, RR and Li, Y and Liu, X and Niu, Z and Wang, M and Zhou, Q and Hao, J and Zhu, C and Chesters, D},
title = {Phylogeny-based assignment of functional traits to DNA barcodes outperforms distance-based, in a comparison of approaches.},
journal = {Molecular ecology resources},
volume = {23},
number = {7},
pages = {1526-1539},
doi = {10.1111/1755-0998.13813},
pmid = {37202847},
issn = {1755-0998},
support = {32250610207//National Science Foundation of China/ ; 31772495//National Science Foundation of China/ ; 2018FY100400//Program of Ministry of Science and Technology of China/ ; XDB310304//Strategic Priority Research Program of the Chinese Academy of Science/ ; 31625024//National Science Fund for Distinguished Young Scholars/ ; 2020FSB0001//CAS President's International Fellowship Initiative/ ; },
mesh = {Bees/genetics ; Animals ; Phylogeny ; *DNA Barcoding, Taxonomic/methods ; *DNA/genetics ; China ; },
abstract = {The full potential for using DNA barcodes for profiling functional trait diversity has yet to be determined in plants and animals; thus, we outline a general framework for quantifying functional trait diversity of insect community DNA and propose and assess the accuracy of three methods for achieving this. We built a novel dataset of traits and DNA barcodes for wild bees in China. An informatics framework was developed for phylogeny-based integration of these data and prediction of traits for any subject barcodes, which was compared with two distance-based methods. For Phylogenetic Assignment, we additionally conducted a species-level analysis of publically available bee trait data. Under the specimen-level dataset, the rate of trait assignment was negatively correlated with distance between the query and the nearest trait-known reference, for all methods. Phylogenetic Assignment was found to perform best under several criteria; particularly, it had the lowest false-positive rate (rarely returning a state prediction where success was unlikely; where the distance from query to the nearest reference was high). For a wider range of compiled traits, conservative life-history traits showed the highest rates of assignment; for example, sociality was predicted with confidence at 53%, parasitism at 44% and nest location at 33%. As outlined herein, automated trait assignment might be applied at scale to either barcodes or metabarcodes. With further compilation and databasing of DNA barcode and trait data, the rate and accuracy of trait assignment is expected to increase to the point of being a widely viable and informative approach.},
}
@article {pmid37202502,
year = {2023},
author = {Srivathsan, A and Ang, Y and Heraty, JM and Hwang, WS and Jusoh, WFA and Kutty, SN and Puniamoorthy, J and Yeo, D and Roslin, T and Meier, R},
title = {Convergence of dominance and neglect in flying insect diversity.},
journal = {Nature ecology &amp; evolution},
volume = {7},
number = {7},
pages = {1012-1021},
pmid = {37202502},
issn = {2397-334X},
mesh = {Animals ; *Insecta ; Ecosystem ; Biodiversity ; *Diptera ; Body Size ; },
abstract = {Most of arthropod biodiversity is unknown to science. Consequently, it has been unclear whether insect communities around the world are dominated by the same or different taxa. This question can be answered through standardized sampling of biodiversity followed by estimation of species diversity and community composition with DNA barcodes. Here this approach is applied to flying insects sampled by 39 Malaise traps placed in five biogeographic regions, eight countries and numerous habitats (>225,000 specimens belonging to >25,000 species in 458 families). We find that 20 insect families (10 belonging to Diptera) account for >50% of local species diversity regardless of clade age, continent, climatic region and habitat type. Consistent differences in family-level dominance explain two-thirds of variation in community composition despite massive levels of species turnover, with most species (>97%) in the top 20 families encountered at a single site only. Alarmingly, the same families that dominate insect diversity are 'dark taxa' in that they suffer from extreme taxonomic neglect, with little signs of increasing activities in recent years. Taxonomic neglect tends to increase with diversity and decrease with body size. Identifying and tackling the diversity of 'dark taxa' with scalable techniques emerge as urgent priorities in biodiversity science.},
}
@article {pmid37202254,
year = {2023},
author = {Pacheco, MA and Escalante, AA},
title = {Origin and diversity of malaria parasites and other Haemosporida.},
journal = {Trends in parasitology},
volume = {39},
number = {7},
pages = {501-516},
doi = {10.1016/j.pt.2023.04.004},
pmid = {37202254},
issn = {1471-5007},
mesh = {Animals ; Humans ; *Haemosporida/genetics ; *Parasites ; Ecosystem ; Phylogeny ; *Malaria ; *Bird Diseases/parasitology ; },
abstract = {Symbionts, including parasites, are ubiquitous in all world ecosystems. Understanding the diversity of symbiont species addresses diverse questions, from the origin of infectious diseases to inferring processes shaping regional biotas. Here, we review the current approaches to studying Haemosporida's species diversity and evolutionary history. Despite the solid knowledge of species linked to diseases, such as the agents of human malaria, studies on haemosporidian phylogeny, diversity, ecology, and evolution are still limited. The available data, however, indicate that Haemosporida is an extraordinarily diverse and cosmopolitan clade of symbionts. Furthermore, this clade seems to have originated with their vertebrate hosts, particularly birds, as part of complex community level processes that we are still characterizing.},
}
@article {pmid37200071,
year = {2023},
author = {Salazar, C and Ferrés, I and Paz, M and Costábile, A and Moratorio, G and Moreno, P and Iraola, G},
title = {Fast and cost-effective SARS-CoV-2 variant detection using Oxford Nanopore full-length spike gene sequencing.},
journal = {Microbial genomics},
volume = {9},
number = {5},
pages = {},
pmid = {37200071},
issn = {2057-5858},
mesh = {Humans ; SARS-CoV-2/genetics ; Cost-Benefit Analysis ; *Nanopores ; *COVID-19/diagnosis ; },
abstract = {Most biologically relevant and diagnostic mutations in the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genome have been identified in the S gene through global genomic surveillance efforts. However, large-scale whole-genome sequencing (WGS) is still challenging in developing countries due to higher costs, reagent delays and limited infrastructure. Consequently, only a small fraction of SARS-CoV-2 samples are characterized through WGS in these regions. Here, we present a complete workflow consisting of a fast library preparation protocol based on tiled amplification of the S gene, followed by a PCR barcoding step and sequencing using Nanopore platforms. This protocol facilitates fast and cost-effective identification of main variants of concern and mutational surveillance of the S gene. By applying this protocol, report time and overall costs for SARS-CoV-2 variant detection could be reduced, contributing to improved genomic surveillance programmes, particularly in low-income regions.},
}
@article {pmid37193334,
year = {2023},
author = {Dev, SA and Unnikrishnan, R and Prathibha, PS and Sijimol, K and Sreekumar, VB and AzharAli, A and Anoop, EV and Viswanath, S},
title = {Artificial intelligence in timber forensics employing DNA barcode database.},
journal = {3 Biotech},
volume = {13},
number = {6},
pages = {183},
pmid = {37193334},
issn = {2190-572X},
abstract = {UNLABELLED: Extreme difficulties in species identification of illegally sourced wood with conventional tools have accelerated illicit logging activities, leading to the destruction of natural resources in India. In this regard, the study primarily focused on developing a DNA barcode database for 41 commercial timber tree species which are highly vulnerable to adulteration in south India. The developed DNA barcode database was validated using an integrated approach involving wood anatomical features of traded wood samples collected from south India. Traded wood samples were primarily identified using wood anatomical features using IAWA list of microscopic features for hardwood identification. Consortium of Barcode of Life (CBOL) recommended barcode gene regions (rbcL, matK &amp; psbA-trnH) were employed for developing DNA barcode database. Secondly, we employed artificial intelligence (AI) analytical platform, Waikato Environment for Knowledge Analysis (WEKA) for analyzing DNA barcode sequence database which could append precision, speed, and accuracy for the entire identification process. Among the four classification algorithms implemented in the machine learning algorithm (WEKA), best performance was shown by SMO, which could clearly allocate individual samples to their respective sequence database of biological reference materials (BRM) with 100 % accuracy, indicating its efficiency in authenticating the traded timber species. Major advantage of AI is the ability to analyze huge data sets with more precision and also provides a large platform for rapid authentication of species, which subsequently reduces human labor and time.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-023-03604-0.},
}
@article {pmid37186220,
year = {2023},
author = {Theodosiou, L and Farr, AD and Rainey, PB},
title = {Barcoding Populations of Pseudomonas fluorescens SBW25.},
journal = {Journal of molecular evolution},
volume = {91},
number = {3},
pages = {254-262},
pmid = {37186220},
issn = {1432-1432},
mesh = {*Pseudomonas fluorescens/genetics ; Biological Evolution ; },
abstract = {In recent years, evolutionary biologists have developed an increasing interest in the use of barcoding strategies to study eco-evolutionary dynamics of lineages within evolving populations and communities. Although barcoded populations can deliver unprecedented insight into evolutionary change, barcoding microbes presents specific technical challenges. Here, strategies are described for barcoding populations of the model bacterium Pseudomonas fluorescens SBW25, including the design and cloning of barcoded regions, preparation of libraries for amplicon sequencing, and quantification of resulting barcoded lineages. In so doing, we hope to aid the design and implementation of barcoding methodologies in a broad range of model and non-model organisms.},
}
@article {pmid37185709,
year = {2023},
author = {Yang, Q and Li, Y and Cai, L and Gan, G and Wang, P and Li, W and Li, W and Jiang, Y and Li, D and Wang, M and Xiong, C and Chen, R and Wang, Y},
title = {Characteristics, Comparative Analysis, and Phylogenetic Relationships of Chloroplast Genomes of Cultivars and Wild Relatives of Eggplant (Solanum melongena).},
journal = {Current issues in molecular biology},
volume = {45},
number = {4},
pages = {2832-2846},
pmid = {37185709},
issn = {1467-3045},
support = {GuikeAD22035947&#xff0c;GuikeAA22068088-2//Science and Technology Planning Project of Guangxi/ ; 2022GXNSFBA035560//Guangxi Natural Science Foundation/ ; Guinongke 2021YT100//Basic Special Fund of the Guangxi Academy of Agricultural Sciences/ ; 31660573//National Natural Science Foundation of China/ ; CARS-23-B05//China Agriculture Research System/ ; 19B271//Scientific Research Fund of Hunan Provincial Education Department/ ; },
abstract = {The eggplant (Solanum melongena) is a popular vegetable around the world. However, the origin and evolution of eggplant has long been considered complex and unclear, which has become the barrier to improvements in eggplant breeding. Sequencing and comparative analyses of 13 complete chloroplast (cp) genomes of seven Solanum species were performed. Genome sizes were between 154,942 and 156,004 bp, the smallest genome was from S. torvum and the largest from S. macrocapon. Thirteen cp genomes showed highly conserved sequences and GC contents, particularly at the subgenus level. All genes in the 13 genomes were annotated. The cp genomes in this study comprised 130 genes (i.e., 80 protein-coding genes, 8 rRNA genes, and 42 tRNA genes), apart from S. sisymbriifolium, which had 129 (79 protein-coding genes, 8 rRNA genes, and 42 tRNA genes.). The rps16 was absent from the cp genome of S. sisymbriifolium, resulting in a nonsense mutation. Twelve hotspot regions of the cp genome were identified, which showed a series of sequence variations and differed significantly in the inverted repeat/single-copy boundary regions. Furthermore, phylogenetic analysis was conducted using 46 cp genomic sequences to determine interspecific genetic and phylogenetic relationships in Solanum species. All species formed two branches, one of which contained all cultivars of the subgenus Leptostemonum. The cp genome data and phylogenetic analysis provides molecular evidence revealing the origin and evolutionary relationships of S. melongena and its wild relatives. Our findings suggest precise intra- and interspecies relatedness within the subgenus Leptostemonum, which has positive implications for work on improvements in eggplant breeding, particularly in producing heterosis, expanding the source of species variation, and breeding new varieties.},
}
@article {pmid37181486,
year = {2023},
author = {Papetti, DM and Spolaor, S and Nazari, I and Tirelli, A and Leonardi, T and Caprioli, C and Besozzi, D and Vlachou, T and Pelicci, PG and Cazzaniga, P and Nobile, MS},
title = {Barcode demultiplexing of nanopore sequencing raw signals by unsupervised machine learning.},
journal = {Frontiers in bioinformatics},
volume = {3},
number = {},
pages = {1067113},
pmid = {37181486},
issn = {2673-7647},
abstract = {Introduction: Oxford Nanopore Technologies (ONT) is a third generation sequencing approach that allows the analysis of individual, full-length nucleic acids. ONT records the alterations of an ionic current flowing across a nano-scaled pore while a DNA or RNA strand is threading through the pore. Basecalling methods are then leveraged to translate the recorded signal back to the nucleic acid sequence. However, basecall generally introduces errors that hinder the process of barcode demultiplexing, a pivotal task in single-cell RNA sequencing that allows for separating the sequenced transcripts on the basis of their cell of origin. Methods: To solve this issue, we present a novel framework, called UNPLEX, designed to tackle the barcode demultiplexing problem by operating directly on the recorded signals. UNPLEX combines two unsupervised machine learning methods: autoencoders and self-organizing maps (SOM). The autoencoders extract compact, latent representations of the recorded signals that are then clustered by the SOM. Results and Discussion: Our results, obtained on two datasets composed of in silico generated ONT-like signals, show that UNPLEX represents a promising starting point for the development of effective tools to cluster the signals corresponding to the same cell.},
}
@article {pmid37181209,
year = {2023},
author = {Bähr, S and van der Meij, SET and Terraneo, TI and Xu, T and Benzoni, F},
title = {Interspecific coral competition does not affect the symbiosis of gall crabs (Decapoda: Cryptochiridae) and their scleractinian hosts.},
journal = {Ecology and evolution},
volume = {13},
number = {5},
pages = {e10051},
pmid = {37181209},
issn = {2045-7758},
abstract = {Coral reefs accommodate a myriad of species, many of which live in association with a host organism. Decapod crustaceans make up a large part of this associated fauna on coral reefs. Among these, cryptochirid crabs are obligately associated with scleractinian corals, in which they create dwellings where they permanently reside. These gall crabs show various levels of host specificity, with the majority of cryptochirids inhabiting a specific coral genus or species. Here, we report the first records of gall crabs living in association with two different Porites species in the Red Sea. Crescent-shaped dwellings were observed in Porites rus and a Porites sp. in situ, and colonies with crabs were collected for further study in the laboratory. Using a combination of morphology and DNA barcoding, the crabs were identified as belonging to Opecarcinus, a genus only known to inhabit Agariciidae corals. The coral skeleton was bleached and studied under a stereo microscope, which revealed that the Porites corals overgrew adjoining agariciid Pavona colonies. We hypothesize that the gall crab originally settled on Pavona, its primary host of choice. Due to coral interspecific competition the Porites colony overgrew the adjacent Pavona colonies, resulting in a secondary and never before reported association of Opecarcinus with Porites. These findings suggest that cryptochirid crabs can adapt to the new microenvironment provided by a different coral host and survive competition for space on coral reefs.},
}
@article {pmid37181093,
year = {2023},
author = {Fan, H and Huang, M and Chen, Y and Zhou, W and Hu, Y and Wei, F},
title = {Conservation priorities for global marine biodiversity across multiple dimensions.},
journal = {National science review},
volume = {10},
number = {6},
pages = {nwac241},
pmid = {37181093},
issn = {2053-714X},
abstract = {Marine biodiversity plays important roles in ocean ecosystem services and has substantial economic value. Species diversity, genetic diversity and phylogenetic diversity, which reflect the number, evolutionary potential and evolutionary history of species in ecosystem functioning, are three important dimensions of biodiversity. Marine-protected areas have been demonstrated as an effective area-based tool for protecting marine biodiversity, but only 2.8% of the ocean has been fully protected. It is urgent to identify global conservation priority areas and percentage of the ocean across multiple dimensions of biodiversity based on Post-2020 Global Biodiversity Framework. Here, we investigate the spatial distribution of marine genetic and phylogenetic diversity using 80 075 mitochondrial DNA barcode sequences from 4316 species and a newly constructed phylogenetic tree of 8166 species. We identify that the Central Indo-Pacific Ocean, Central Pacific Ocean and Western Indian Ocean harbor high levels of biodiversity across three dimensions of biodiversity, which could be designated as conservation priority areas. We also find that strategically protecting ∼22% of the ocean would allow us to reach the target of conserving ∼95% of currently known taxonomic, genetic and phylogenetic diversity. Our study provides insights into the spatial distribution pattern of multiple marine diversities and the findings would help to design comprehensive conservation schemes for global marine biodiversity.},
}
@article {pmid37179061,
year = {2023},
author = {Zhao, J and He, C and Yang, H and Long, Y and Dong, J and Wen, L and Hu, Z and Yin, X and Hou, C and Huo, D},
title = {Duplex-specific nuclease powered 3D DNA walker and quantum dots barcodes for homogeneous electrochemical detection of microRNAs.},
journal = {Analytica chimica acta},
volume = {1262},
number = {},
pages = {341246},
doi = {10.1016/j.aca.2023.341246},
pmid = {37179061},
issn = {1873-4324},
mesh = {*MicroRNAs/genetics ; *Quantum Dots ; Reproducibility of Results ; *Biosensing Techniques/methods ; DNA ; Endonucleases ; Electrochemical Techniques/methods ; Carbon ; Limit of Detection ; },
abstract = {Multiplex microRNAs (miRNAs) detection is beneficial for early diagnosis and prognosis of cancer. Herein, duplex-specific nuclease (DSN) powered 3D DNA walker and quantum dots (QDs) barcodes were designed for the simultaneous detection of miRNAs in a homogeneous electrochemical sensor. In the proof-of-concept experiment, the effective active area of the as-prepared graphene aerogel-modified carbon paper (CP-GAs) electrode was ∼14.30 times larger than that of the traditional glassy carbon electrode (GCE), endowing the enhanced capability of loading more metal ions for ultrasensitive detection of miRNAs. In addition, DSN-powered target recycling and DNA walking strategy assured the sensitive detection of miRNAs. After the introduction of magnetic beads (MNs) and electrochemical double enrichment strategies, the integration of triple signal amplification methods yielded good detection results. Under optimal conditions, towards simultaneous detection of microRNA-21 (miR-21) and miRNA-155 (miR-155), a linear range of 10[-16]-10[-7] M and a sensitivity of 10 aM (miR-21) and 2.18 aM (miR-155) were achieved, respectively. It was worth mentioning that the prepared sensor can detect miR-155 down to 0.17 aM, which was also extremely advantageous among the sensors reported so far. What's more, through verification, the prepared sensor had good selectivity and reproducibility, and exhibited good detection ability in complex serum environments, showing great potential in early clinical diagnosis and screening.},
}
@article {pmid37173307,
year = {2023},
author = {Yoneya, K and Ushio, M and Miki, T},
title = {Non-destructive collection and metabarcoding of arthropod environmental DNA remained on a terrestrial plant.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {7125},
pmid = {37173307},
issn = {2045-2322},
mesh = {Animals ; *DNA, Environmental/genetics ; *Arthropods/genetics ; DNA Barcoding, Taxonomic/methods ; DNA/genetics ; Plants/genetics ; Water ; Biodiversity ; },
abstract = {Reliable survey of arthropods is a crucial for their conservation, community ecology, and pest control on terrestrial plants. However, efficient and comprehensive surveys are hindered by challenges in collecting arthropods and identifying especially small species. To address this issue, we developed a non-destructive environmental DNA (eDNA) collection method termed "plant flow collection" to apply eDNA metabarcoding to terrestrial arthropods. This involves spraying distilled or tap water, or using rainfall, which eventually flows over the surface of the plant, and is collected in a container that is set at the plant base. DNA is extracted from collected water and a DNA barcode region of cytochrome c oxidase subunit I (COI) gene is amplified and sequenced using a high-throughput Illumina Miseq platform. We identified more than 64 taxonomic groups of arthropods at the family level, of which 7 were visually observed or artificially introduced species, whereas the other 57 groups of arthropods, including 22 species, were not observed in the visual survey. These results show that the developed method is possible to detect the arthropod eDNA remained on plants although our sample size was small and the sequence size was unevenly distributed among the three water types tested.},
}
@article {pmid37171093,
year = {2023},
author = {Schmey, T and Small, C and Einspanier, S and Hoyoz, LM and Ali, T and Gamboa, S and Mamani, B and Sepulveda, GC and Thines, M and Stam, R},
title = {Small-spored Alternaria spp. (section Alternaria) are common pathogens on wild tomato species.},
journal = {Environmental microbiology},
volume = {25},
number = {10},
pages = {1830-1846},
doi = {10.1111/1462-2920.16394},
pmid = {37171093},
issn = {1462-2920},
mesh = {*Solanum lycopersicum ; Alternaria/genetics ; *Solanum ; Crops, Agricultural ; Chile ; },
abstract = {The wild relatives of modern tomato crops are native to South America. These plants occur in habitats as different as the Andes and the Atacama Desert and are, to some degree, all susceptible to fungal pathogens of the genus Alternaria. Alternaria is a large genus. On tomatoes, several species cause early blight, leaf spots and other diseases. We collected Alternaria-like infection lesions from the leaves of eight wild tomato species from Chile and Peru. Using molecular barcoding markers, we characterized the pathogens. The infection lesions were caused predominantly by small-spored species of Alternaria of the section Alternaria, like A. alternata, but also by Stemphylium spp., Alternaria spp. from the section Ulocladioides and other related species. Morphological observations and an infection assay confirmed this. Comparative genetic diversity analyses show a larger diversity in this wild system than in studies of cultivated Solanum species. As A. alternata has been reported to be an increasing problem in cultivated tomatoes, investigating the evolutionary potential of this pathogen is not only interesting to scientists studying wild plant pathosystems. It could also inform crop protection and breeding programs to be aware of potential epidemics caused by species still confined to South America.},
}
@article {pmid37170748,
year = {2023},
author = {Seo, SY and Lee, WK and Lee, JS},
title = {Surface Functionalization and Reversible Disassembly of DNA-Assembly Nanoparticles for Sensitive and Multiplexed Detection of DNA Targets Without Enzymatic and Catalytic Amplification.},
journal = {Bioconjugate chemistry},
volume = {34},
number = {6},
pages = {1096-1104},
doi = {10.1021/acs.bioconjchem.3c00143},
pmid = {37170748},
issn = {1520-4812},
mesh = {*Metal Nanoparticles/chemistry ; *Biosensing Techniques/methods ; Gold/chemistry ; DNA/chemistry ; Ions ; },
abstract = {Recently, DNA-assembly nanoparticles based on DNA-metal ion interactions are emerging as new building blocks for drug delivery and metal nanostructure synthesis. However, the surface modification of DNA-assembly nanoparticles using functional biomolecules that can identify specific targets has rarely been explored. In this study, we developed a new immobilization chemical strategy to efficiently functionalize the barcode DNA-assembly nanoparticles (bcDNA NPs) with thiolated probe DNA (pDNA) for synthesizing pDNA-functionalized bcDNA NPs (pDNA-bcDNA NPs). We used them as nanoprobes to successfully demonstrate the sensitive and selective detection of multiple DNA targets. Importantly, Au ions played an essential role as anchoring sites via their conjugation with both thiolated pDNA and bcDNA NPs. In addition, we could reversibly and rapidly disassemble the pDNA-bcDNA NPs into the initial bcDNA strands with a recovery rate of 91%; this process significantly amplified the signal by releasing a million bcDNA strands, which enabled DNA quantification from a single pDNA-bcDNA NP. The Au[3+] concentration, pH, and surface passivation conditions were carefully investigated to maximize the pDNA loading to 8500 strands/bcDNA NP. The limit of detection was determined to be 221 fM, which is the most sensitive among the absorbance-based methods without polymerase chain reaction, hybridization chain reactions, catalytic hairpin assembly, and other reactions involving enzymes and catalysts. The reversible disassembly of DNA strands and Au ion-mediated conjugation chemistry could be extended for the detection of other types of targets, such as proteins, metal ions, and small molecules, using other organic functionalities that are or can be thiolated, including polypeptides, aptamers, and antibodies.},
}
@article {pmid37170340,
year = {2022},
author = {Truong, NT and Phan, GH and Lam, TTH and Nguyen, THD and Khang, DT and Tran, MT and Tran, NS and Dinh, QM},
title = {The mismatch between morphological and molecular attribution of three Glossogobius species in the Mekong Delta.},
journal = {BMC zoology},
volume = {7},
number = {1},
pages = {34},
pmid = {37170340},
issn = {2056-3132},
support = {B2020-TCT-13//The Ministry of Education and Training of Vietnam/ ; B2020-TCT-13//The Ministry of Education and Training of Vietnam/ ; B2020-TCT-13//The Ministry of Education and Training of Vietnam/ ; B2020-TCT-13//The Ministry of Education and Training of Vietnam/ ; VINIF.2021.TS.146//Vingroup JSC and supported by the Master, PhD Scholarship Programme of Vingroup Innovation Foundation (VINIF), Institute of Big Data/ ; },
abstract = {BACKGROUND: The Vietnamese Mekong Delta (VMD) is the granary for the whole country, providing animal and plant resources, especially fish. Among the fish species, the genus Glossogobius are the majority. Until now, research for this species has been solely relied on fish morphology for identification. Hence, the present study aimed to describe the morphological variations of the morphologically identified gobies and to validate them at the molecular level through the sequencing of the barcode region, the mitochondrial cytochrome C oxidase subunit I (COI) gene to preliminary provide fundamental information for conservation.<br><br>RESULTS: The mitochondrial cytochrome C oxidase subunit I genes were amplified successfully with an approximate size of 650-680&#x2009;bp. Their morphometries were quite different, and the genetic distance (p-value) among groups and within groups ranged from 0.00 to 0.12. The similarity of the COI gene sequences between the analyzed samples and in the NCBI database was from 87.01 to 100%. The specimens of G. aureus, G. giuris and G. sparsipapillus were interspersed in small branches of the phylogenetic tree with a low genetic distance highlighting that the genetic diversity of COI gene was low among species. Therefore, it is recommended that a combination of morphological method and mtCOI DNA barcoding is required for accurate classification.<br><br>CONCLUSION: This study helps determine three distinct lineages of Glossogobius species, so an appropriate strategy can be proposed for exploitation and conservation.},
}
@article {pmid37170157,
year = {2022},
author = {Casades-Martí, L and Frías, M and Delacour, S and Ruiz-Fons, F},
title = {Confirmed presence of aedes (rusticoidus) refiki Medschid, 1928 in a continental dry Mediterranean peri-urban environment in south-central Spain.},
journal = {BMC zoology},
volume = {7},
number = {1},
pages = {21},
pmid = {37170157},
issn = {2056-3132},
support = {E-RTA-2015-00002-C02-02//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; CD18/00091//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; CGL2017-89866-R//European Social Fund/ ; PEJ2018-003155-A//Universidad de Castilla-La Mancha/ ; },
abstract = {BACKGROUND: The 'snow-melt mosquito' aedes (rusticoidus) refiki is a rare species with a wide distribution in Europe that is usually defined as an aggressive mosquito for mammals, including humans. During a mosquito survey in a peri-urban area in south-central mainland Spain, adult Ae. refiki females were captured and identified by morphological traits. The presence of this species of mosquito has never been molecularly confirmed under continental dry Mediterranean climatic influence with scarce number of days with snow on soil. The aim of this study was to confirm by amplification and sequencing of mitochondrial cytochrome c oxidase subunit I (COI) and internal transcribed spacer 2 (ITS2) region.<br><br>RESULTS: We also successfully amplified and typed the species molecularly by COI and ITS2 regions. The peri-urban area where Ae.&#xa0;refiki was found contrasts with the reported cold, humid and snowy environments required by the species to breed.<br><br>CONCLUSIONS: This finding suggests that the species is already adapted to continental dry Mediterranean environments, questioning whether it is a truly stenotopic species of cold snowy environments.},
}
@article {pmid37170149,
year = {2022},
author = {Zhao, L and Xie, X and Chen, D and Ma, G and Sun, Y},
title = {Microscopic Observations on Form and Structure of the Worm Enchytraeus buchholzi (Clitellata: Enchytraeidae).},
journal = {BMC zoology},
volume = {7},
number = {1},
pages = {31},
pmid = {37170149},
issn = {2056-3132},
support = {2009JZ006//Shaanxi Provincial Science and Technology Department (CN)/ ; SLGPT2019KF04-03//Shaanxi University of Technology (CN)/ ; 2020-NY-62//Shaanxi Provincial Science and Technology Department/ ; },
abstract = {The worm Enchytraeus buchholzi is a new record species for Shaanxi, China, and a key pest on American ginseng Panax quinquefolium. To distinguish the species, the authors prepared its whole mounts and paraffin-embedded sections, and microscopically observed, photographed and measured. Besides, we conducted an experimental study on its DNA barcode. RESULTS: Cells, tissues and organs related to nervous, digestive, circulatory, excretory and reproductive systems were found, photomicrographed and described, including: prostomium, peristomium, segments, clitellum, pygidium, lateral and ventral chaetae; brain, cranial nerves, sensory papillae, ventral nerve cord; pharyngeal pad and glands, retractor muscles and muscular bundles, peptonephridia, esophagus, intestine; dorsal, lateral, ventral and intestinal parietal vessels, coelomocytes, coelomic cavity; nephridia, chloragogen cells; ovaries, groups of germ cells with developing oocytes, mature eggs, spermathecae; testes, seminal vesicles, sperm funnels, penial bulbs. Their shapes and sizes were given, and functions discussed briefly. The visual effect of staining specimens with hematoxylin plus eosin ranked the first, and that with acetocarmine the second. CONCLUSIONS: The supplementary and objective descriptions, with the microphotographs as forceful pieces of evidence, have expanded biological knowledge in aspects of the form, structure and function of the worm, which is helpful for professionals to recognize and understand this species and provide a solid basis for its integrated pest management.},
}
@article {pmid37168534,
year = {2023},
author = {Liu, C and Ashfaq, M and Yin, Y and Zhu, Y and Wang, Z and Cheng, H and Hebert, P},
title = {Using DNA metabarcoding to assess insect diversity in citrus orchards.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15338},
pmid = {37168534},
issn = {2167-8359},
mesh = {Animals ; DNA Barcoding, Taxonomic ; *Citrus/genetics ; Insecta/genetics ; *Moths/genetics ; Biodiversity ; DNA/genetics ; },
abstract = {BACKGROUND: DNA metabarcoding is rapidly emerging as a cost-effective approach for large-scale biodiversity assessment and pest monitoring. The current study employed metabarcoding to assess insect diversity in citrus orchards in Ganzhou City, Jiangxi, China in both 2018 and 2019. Insects were sampled using Malaise traps deployed in three citrus orchards producing a total of 43 pooled monthly samples.<br><br>METHODS: The Malaise trap samples were sequenced following DNA metabarcoding workflow. Generated sequences were curated and analyzed using two cloud databases and analytical platforms, the barcode of life data system (BOLD) and multiplex barcode research and visualization environment (mBRAVE).<br><br>RESULTS: These platforms assigned the sequences to 2,141 barcode index numbers (BINs), a species proxy. Most (63%) of the BINs were shared among the three sampling sites while BIN sharing between any two sites did not exceed 71%. Shannon diversity index (H') showed a similar pattern of BIN assortment at the three sampling sites. Beta diversity analysis by Jaccard similarity coefficient (J) and Bray-Curtis distance matrix (BC) revealed a high level of BIN similarity among the three sites (J = 0.67-0.68; BC = 0.19-0.20). Comparison of BIN records against all those on BOLD made it possible to identify 40% of the BINs to a species, 57% to a genus, 97% to a family and 99% to an order. BINs which received a species match on BOLD were placed in one of four categories based on this assignment: pest, parasitoid, predator, or pollinator. As this study provides the first baseline data on insect biodiversity in Chinese citrus plantations, it is a valuable resource for research in a broad range of areas such as pest management and monitoring beneficial insects in citrus gardens.},
}
@article {pmid37168391,
year = {2023},
author = {de Araújo, AD and Carvalho, ODS and Gava, SG and Caldeira, RL},
title = {DNA barcoding as a valuable tool for delimiting mollusk species of the genus Biomphalaria Preston, 1910 (Gastropoda: Planorbidae).},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1167787},
pmid = {37168391},
issn = {2235-2988},
mesh = {Animals ; *Biomphalaria/genetics ; Phylogeny ; DNA Barcoding, Taxonomic/methods ; DNA ; Schistosoma mansoni/genetics ; },
abstract = {INTRODUCTION: The genus Biomphalaria in Brazil includes 11 species and one subspecies, three of which are intermediate hosts of Schistosoma mansoni. Due to the recent evolution of this group, some species are difficult to identify based on morphological characters, making the use of genetic markers necessary for species identification. This study aimed to evaluate the use of partial sequences of the cytochrome c oxidase I (coi) gene for the identification of Biomphalaria species using phylogenetic reconstruction and species delimitation algorithms. The study tested the use of DNA barcoding technique for species delimitation within the genus.<br><br>METHODS: DNA barcoding was performed by sequencing a partial region of the coi gene from specimens, and the sequences were analyzed using phylogenetic reconstruction and algorithms to delimit Operational Taxonomic Units (OTUs).<br><br>RESULTS: The study found that the use of the coi gene in the reconstruction of the phylogeny of the genus might be an alternative for understanding the evolution and dispersion of species. However, this marker alone is not enough to solve complex taxonomic problems within the genus. A total of 223 sequences were analyzed, 102 of which could be separated using the barcode gap, enabling the correct identification of seven taxa.<br><br>DISCUSSION: The study demonstrated that accurate mollusk identification is necessary for effective schistosomiasis control. The DNA barcoding methodology was found to be promising for accurate mollusk identification, which is crucial for concentrating schistosomiasis control efforts in places where it is needed.},
}
@article {pmid37159665,
year = {2023},
author = {Roux, HM and Figueiredo, S and Sareoua, L and Salmona, M and Hamroune, J and Adoux, L and Migraine, J and Hance, A and Clavel, F and Cheynier, R and Dutrieux, J},
title = {DNA ultra-sensitive quantification, a technology for studying HIV unintegrated linear DNA.},
journal = {Cell reports methods},
volume = {3},
number = {4},
pages = {100443},
pmid = {37159665},
issn = {2667-2375},
mesh = {Humans ; DNA, Viral/genetics ; Technology ; Cell Division ; *HIV Seropositivity ; *HIV-1/genetics ; },
abstract = {Unintegrated HIV DNA represents between 20% and 35% of the total viral DNA in infected patients. Only the linear forms (unintegrated linear DNAs [ULDs]) can be substrates for integration and for the completion of a full viral cycle. In quiescent cells, these ULDs may be responsible for pre-integrative latency. However, their detection remains difficult due to the lack of specificity and sensitivity of existing techniques. We developed an ultra-sensitive, specific, and high-throughput technology for ULD quantification called DUSQ (DNA ultra-sensitive quantification) combining linker-mediated PCR and next-generation sequencing (NGS) using molecular barcodes. Studying cells with different activity levels, we determined that the ULD half-life goes up to 11 days in resting CD4[+] T cells. Finally, we were able to quantify ULDs in samples from patients infected with HIV-1, providing a proof of concept for the use of DUSQ in vivo to track pre-integrative latency. DUSQ can be adapted to the detection of other rare DNA molecules.},
}
@article {pmid37157090,
year = {2023},
author = {Dhillon, B and Chakrabarti, S},
title = {Ganoderma zonatum causes butt rot of areca (Dypsis lutescens) and robellini (Phoenix roebelenii) palms in Florida.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-01-23-0083-PDN},
pmid = {37157090},
issn = {0191-2917},
abstract = {Ganoderma butt rot is a lethal disease of palms (Arecaceae) prevalent in palm-growing regions in the US that infects at least 58 species of palms (Elliott and Broschat 2001). Early symptoms appear as wilting of older fronds in the lower part of the canopy, and as disease progresses, wilting advances to younger leaves higher in the canopy towards the unopened spear leaf eventually killing the palm. A characteristic sign of the disease is the appearance of fruiting bodies (basidiomata) at the base of the palm trunk close to soil line. Ganoderma butt rot disease was detected on clustering palm species, areca palms, with 9 (82%) clusters showing Ganoderma basidiocarps and dead stumps, and mortality was observed in 5 (45%) clusters. A sterile scalpel was used to transfer the context tissue from Ganoderma basidiomata to full-strength potato dextrose agar selective media supplemented with streptomycin (100 mg/l), lactic acid (2 ml/l) and benomyl (4 mg/l). The pure culture for isolate GAN-33 was grown at 28°C in complete darkness for 10 days. The fungal colony was ivory white in color that grew radially as a dense mycelial mat without any sporulation. To establish the identity of the fungus, DNA was extracted using the Qiagen DNeasy PowerSoil kit (Cat. #12888). Three barcoding genes, nuclear ribosomal DNA internal transcribed spacer (ITS) region, RNA polymerase II subunit 2 (rpb2) and translation elongation factor 1α (tef1α) were amplified using primers ITS1/ITS4 (White et al 1990), bRPB2-6f/bRPB2-b7.1R (Matheny et al 2007) and EF1-983F/EF1-2212R (Matheny et al 2007), respectively. The sequences were deposited in GenBank, accession numbers KX853442, KX853466 and KX853491 for ITS, rpb2 and tef1α, respectively (Elliott et al 2018). Comparison to the NCBI nucleotide sequence database identified isolate GAN-33 as Ganoderma zonatum based on 100, 99 and 99% similarity to ITS, rpb2 and tef1α sequences, respectively. Pathogenicity of G. zonatum isolate GAN-33 was determined on 1-year old seedlings of areca palm (Dypsis lutescens) and pygmy date palm (Phoenix roebelenii). Ganoderma zonatum inoculum was prepared by transferring two-week old cultures to autoclaved wheat berries and allowed to colonize for two weeks. Seedlings were gently removed from the pot and the roots were trimmed before placing them back in the pot ensuring that the roots were in contact with the G. zonatum colonized wheat berries. The inoculated and control seedlings were maintained in a growth chamber at 28°C 60% RH (daytime) and 24°C 50% RH (night time), 12h:8h light:dark period, and watered twice a week. Initial wilting symptoms started appearing approximately one month after inoculation and mortality was observed for a total of four seedlings at three months after inoculation i.e., 2 out of 3 G. zonatum inoculated seedlings died for both areca and robellini palms, whereas the non-inoculated areca and robellini palm control seedlings remained healthy and alive. The pathogen was re-isolated from inoculated roots, and its identity was confirmed by colony morphology and PCR using G. zonatum specific primers (Chakrabarti et al 2022). To the best of our knowledge this is the first report establishing G. zonatum as the pathogen responsible for Ganoderma butt rot of palms.},
}
@article {pmid37156352,
year = {2023},
author = {Fakunle, AG and Jafta, N and Bossers, A and Wouters, IM and Kersen, WV and Naidoo, RN and Smit, LAM},
title = {Childhood lower respiratory tract infections linked to residential airborne bacterial and fungal microbiota.},
journal = {Environmental research},
volume = {231},
number = {Pt 1},
pages = {116063},
doi = {10.1016/j.envres.2023.116063},
pmid = {37156352},
issn = {1096-0953},
mesh = {Humans ; Child ; Child, Preschool ; Infant ; *Mycobiome ; *Air Pollution, Indoor/adverse effects/analysis ; RNA, Ribosomal, 16S ; *Microbiota/genetics ; Nigeria ; Dust/analysis ; Bacteria/genetics ; *Respiratory Tract Infections ; Fungi/genetics ; },
abstract = {Residential microbial composition likely contributes to the development of lower respiratory tract infections (LRTI) among children, but the association is poorly understood. We aimed to study the relationship between the indoor airborne dust bacterial and fungal microbiota and childhood LRTI in Ibadan, Nigeria. Ninety-eight children under the age of five years hospitalized with LRTI were recruited and matched by age (±3 months), sex, and geographical location to 99 community-based controls without LRTI. Participants' homes were visited and sampled over a 14-day period for airborne house dust using electrostatic dustfall collectors (EDC). In airborne dust samples, the composition of bacterial and fungal communities was characterized by a meta-barcoding approach using amplicons targeting simultaneously the bacterial 16S rRNA gene and the internal-transcribed-spacer (ITS) region-1 of fungi in association with the SILVA and UNITE database respectively. A 100-unit change in house dust bacterial, but not fungal, richness (OR 1.06; 95%CI 1.03-1.10) and a 1-unit change in Shannon diversity (OR 1.92; 95%CI 1.28-3.01) were both independently associated with childhood LRTI after adjusting for other indoor environmental risk factors. Beta-diversity analysis showed that bacterial (PERMANOVA p < 0.001, R[2] = 0.036) and fungal (PERMANOVA p < 0.001, R[2] = 0.028) community composition differed significantly between homes of cases and controls. Pair-wise differential abundance analysis using both DESEq2 and MaAsLin2 consistently identified the bacterial phyla Deinococcota (Benjamini-Hochberg (BH) adjusted p-value <0.001) and Bacteriodota (BH-adjusted p-value = 0.004) to be negatively associated with LRTI. Within the fungal microbiota, phylum Ascomycota abundance (BH adjusted p-value <0.001) was observed to be directly associated with LRTI, while Basidiomycota abundance (BH adjusted p-value <0.001) was negatively associated with LRTI. Our study suggests that early-life exposure to certain airborne bacterial and fungal communities is associated with LRTI among children under the age of five years.},
}
@article {pmid37155652,
year = {2023},
author = {Lee, GYS and Wertman, DL and Carroll, AL and Hamelin, RC},
title = {Filamentous fungal associates of the alder bark beetle, Alniphagus aspericollis, including an undescribed species of Neonectria.},
journal = {PloS one},
volume = {18},
number = {5},
pages = {e0284393},
pmid = {37155652},
issn = {1932-6203},
mesh = {Animals ; *Coleoptera ; *Weevils/microbiology ; *Alnus ; Plant Bark/microbiology ; *Hypocreales ; *Tracheophyta ; British Columbia ; },
abstract = {Bark beetles (Coleoptera: Curculionidae; Scolytinae) are tree-infesting insects that consume subcortical tissues and fungi. Species capable of killing their host trees are most commonly associated with conifers, as very few bark beetle species infest and kill hardwood hosts directly. The alder bark beetle, Alniphagus aspericollis, is a hardwood-killing bark beetle that colonizes and kills red alder, Alnus rubra. Conifer-killing bark beetles have well-known associations with symbiotic ophiostomatoid fungi that facilitate their life histories, but it is unknown whether A. aspericollis has any fungal associates. This study was conducted to identify any consistent filamentous fungal associates of A. aspericollis and characterize the consistency of observed beetle-fungus relationships. Beetles and gallery phloem samples were collected from seven sites throughout the Greater Vancouver region in British Columbia, Canada. Filamentous fungi were isolated from these samples and identified by DNA barcoding using the internal transcribed spacer (ITS) region and other barcode regions for resolution to the species-level for the most dominant isolates. The most common fungal associate was a previously undescribed Neonectria major-like fungus, Neonectria sp. nov., which was isolated from ~67% of adult beetles, ~59% of phloem samples, and ~94% of the beetle-infested trees. Ophiostoma quercus was isolated from ~28% of adult beetles, ~9% of phloem samples, and ~56% of infested trees and deemed a casual associate of A. aspericollis, while a putatively novel species of Ophiostoma was more infrequently isolated from A. aspericollis and its galleries. Cadophora spadicis, a new record for red alder, was rarely isolated and is probably coincidentally carried by A. aspericollis. Overall, A. aspericollis was only loosely associated with ophiostomatoid fungi, suggesting that these fungi have little ecological significance in the beetle-tree interaction, while Neonectria sp. nov. may be a symbiote of A. aspericollis that is vectored by the beetle.},
}
@article {pmid37150487,
year = {2023},
author = {Pivar, RJ and Moulton, JK and Sinclair, BJ},
title = {First phylogenetic analysis of the Nearctic madicolous midges of the genus Androprosopa Mik (Diptera: Thaumaleidae).},
journal = {Molecular phylogenetics and evolution},
volume = {187},
number = {},
pages = {107807},
doi = {10.1016/j.ympev.2023.107807},
pmid = {37150487},
issn = {1095-9513},
mesh = {Animals ; Female ; Phylogeny ; *Diptera/genetics ; Cell Nucleus ; },
abstract = {Molecular phylogenetic analyses were conducted to infer relationships between the eastern and western Nearctic Androprosopa Mik and amongst the considerably more diverse western Nearctic species. Fresh, molecular-grade material was obtained for all Nearctic Androprosopa species except two Mexican species, An. sonorensis (Arnaud &amp; Boussy) and An. zempoala Sinclair &amp; Huerta, that eluded capture. Molecular sequences from two nuclear protein-coding genes, big zinc finger (BZF) and molybdenum cofactor sulfurase (MCS), were sampled from representatives of several outgroup and ingroup taxa and analyzed phylogenetically using maximum likelihood criteria to confirm identifications of females and immatures using a barcoding approach, test species boundaries among morphologically similar species, and infer relationships among more morphologically disparate groups. Resulting phylogenies suggest the following with significant node (bootstrap) support: (1) the eastern Nearctic Androprosopa species form the sister group to the lineage comprised of all sampled Palearctic thaumaleids, i.e., An. larvata (Mik), An. striata (Okada), and Thaumalea testacea Ruthe; (2) the aforementioned lineage is the sister group to the clade comprised of western Nearctic Androprosopa species; (3) the western Nearctic Androprosopa species form three multispecies lineages, two of which can be further divided into three or more well founded species groups. Our results suggest that Androprosopa as currently defined is paraphyletic. Additionally, we propose several new species groups within the western Nearctic Androprosopa based on molecular and morphological data.},
}
@article {pmid37149606,
year = {2023},
author = {Li, F and Mahadevan, A and Sherlock, G},
title = {An improved algorithm for inferring mutational parameters from bar-seq evolution experiments.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {246},
pmid = {37149606},
issn = {1471-2164},
support = {R01 AI136992/AI/NIAID NIH HHS/United States ; R35 GM131824/GM/NIGMS NIH HHS/United States ; },
mesh = {Bayes Theorem ; *Algorithms ; Computer Simulation ; Mutation ; },
abstract = {BACKGROUND: Genetic barcoding provides a high-throughput way to simultaneously track the frequencies of large numbers of competing and evolving microbial lineages. However making inferences about the nature of the evolution that is taking place remains a difficult task.<br><br>RESULTS: Here we describe an algorithm for the inference of fitness effects and establishment times of beneficial mutations&#xa0;from barcode sequencing data, which builds upon a Bayesian inference method by enforcing self-consistency between the population mean fitness and the individual effects of mutations within lineages. By testing our inference method on a simulation of 40,000 barcoded lineages evolving in serial batch culture, we find that this new method outperforms its predecessor, identifying more adaptive mutations and more accurately inferring their mutational parameters.<br><br>CONCLUSION: Our new algorithm is particularly suited to inference of mutational parameters when read depth is low. We have made Python code for our serial dilution evolution simulations, as well as both the old and new inference methods, available on GitHub (https://github.com/FangfeiLi05/FitMut2), in the hope that it can find broader use by the microbial evolution community.},
}
@article {pmid37147717,
year = {2023},
author = {Bieler, J and Kubik, S and Macheret, M and Pozzorini, C and Willig, A and Xu, Z},
title = {Benefits of applying molecular barcoding systems are not uniform across different genomic applications.},
journal = {Journal of translational medicine},
volume = {21},
number = {1},
pages = {305},
pmid = {37147717},
issn = {1479-5876},
mesh = {Reproducibility of Results ; *Genomics/methods ; Sequence Analysis, DNA/methods ; Mutation/genetics ; *DNA ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {BACKGROUND: Despite the wide variety of Next Generation Sequencing (NGS)-based methods, it remains challenging to detect mutations present at very low frequencies. This problem is particularly relevant in oncology, where the limiting amount of input material, and its low quality, often limit the performance of the assays. Unique Molecular Identifiers (UMIs) are a molecular barcoding system often coupled with computational methods of noise suppression to improve the reliability of detection of rare variants. Although widely adopted, UMI inclusion imposes additional technical complexity and sequencing cost. Currently, there are no guidelines on UMI usage nor a comprehensive evaluation of their advantage across different applications.<br><br>METHODS: We used DNA sequencing data generated by molecular barcoding and hybridization-based enrichment, from various types and quantities of input material (fresh frozen, formaldehyde-treated and cell-free DNA), to evaluate the performance of variant calling in different clinically relevant contexts.<br><br>RESULTS: Noise suppression achieved by read grouping based on fragment mapping positions ensures reliable variant calling for many experimental designs even without exogenous UMIs. Exogenous barcodes significantly improve performance only when mapping position collisions occur, which is common in cell-free DNA.<br><br>CONCLUSIONS: We demonstrate that UMI usage is not universally beneficial across experimental designs and that it is worthwhile to critically consider the comparative advantage of UMI usage for a given NGS application prior to experimental design.},
}
@article {pmid37143529,
year = {2023},
author = {Nascimento Brito, V and Lana Alves, J and Sírio Araújo, K and de Souza Leite, T and Borges de Queiroz, C and Liparini Pereira, O and de Queiroz, MV},
title = {Endophytic Trichoderma species from rubber trees native to the Brazilian Amazon, including four new species.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1095199},
pmid = {37143529},
issn = {1664-302X},
abstract = {Fungi belonging to the genus Trichoderma have been widely recognized as efficient controllers of plant diseases. Although the majority of isolates currently deployed, thus far, have been isolated from soil, endophytic Trichoderma spp. is considered to be a promising option for application in biocontrol. In this study, 30 endophytic Trichoderma isolates-obtained from the leaves, stems, and roots of wild Hevea spp. in the Brazilian Amazon-were analyzed using specific DNA barcodes: sequences of internal transcribed spacers 1 and 2 of rDNA (ITS region), genes encoding translation elongation factor 1-α (TEF1-α), and the second largest subunit of RNA polymerase II (RPB2). The genealogical concordance phylogenetic species recognition (GCPSR) concept was used for species delimitation. A phylogenetic analysis showed the occurrence of Trichoderma species, such as T. erinaceum, T. ovalisporum, T. koningiopsis, T. sparsum, T. lentiforme, T. virens, and T. spirale. Molecular and morphological features resulted in the discovery of four new species, such as T. acreanum sp. nov., T. ararianum sp. nov., T. heveae sp. nov., and T. brasiliensis sp. nov. The BI and ML analyses shared a similar topology, providing high support to the final trees. The phylograms show three distinct subclades, namely, T. acreanum and T. ararianum being paraphyletic with T. koningiopsis; T. heveae with T. subviride; and T. brasiliensis with T. brevicompactum. This study adds to our knowledge of the diversity of endophytic Trichoderma species in Neotropical forests and reveals new potential biocontrol agents for the management of plant diseases.},
}
@article {pmid37143483,
year = {2023},
author = {Gattoni, K and Gendron, EMS and Sandoval-Ruiz, R and Borgemeier, A and McQueen, JP and M Shepherd, R and Slos, D and O Powers, T and L Porazinska, D},
title = {18S-NemaBase: Curated 18S rRNA Database of Nematode Sequences.},
journal = {Journal of nematology},
volume = {55},
number = {1},
pages = {20230006},
pmid = {37143483},
issn = {0022-300X},
abstract = {Nematodes are the most abundant and diverse animals on the planet but lack representation in biodiversity research. This presents a problem for studying nematode diversity, particularly when molecular tools (i.e., barcoding and metabarcoding) rely on well-populated and curated reference databases, which are absent for nematodes. To improve molecular identification and the assessment of nematode diversity, we created and curated an 18S rRNA database specific to nematodes (18S-NemaBase) using sequences sourced from the most recent publicly available 18S rRNA SILVA v138 database. As part of the curation process, taxonomic strings were standardized to contain a fixed number of taxonomic ranks relevant to nematology and updated for the most recent accepted nematode classifications. In addition, apparent erroneous sequences were removed. To test the efficacy and accuracy of 18S-NemaBase, we compared it to an older but also curated SILVA v111 and the newest SILVA v138 by assigning taxonomies and analyzing the diversity of a nematode dataset from the Western Nebraska Sandhills. We showed that 18S-NemaBase provided more accurate taxonomic assignments and diversity assessments than either version of SILVA, with a much easier workflow and no need for manual corrections. Additionally, observed diversity further improved when 18S-NemaBase was supplemented with reference sequences from nematodes present in the study site. Although the 18S-NemaBase is a step in the right direction, a concerted effort to increase the number of high-quality, accessible, full-length nematode reference sequences is more important now than ever.},
}
@article {pmid37142918,
year = {2023},
author = {Giudice, V and Fonseca, V and Selleri, C and Gadina, M},
title = {Cell Viability Multiplexing: Quantification of Cellular Viability by Barcode Flow Cytometry and Computational Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2644},
number = {},
pages = {99-121},
pmid = {37142918},
issn = {1940-6029},
mesh = {Flow Cytometry/methods ; Cell Survival ; *Lymphocytes ; *Fluorescent Dyes ; },
abstract = {Fluorescent cell barcoding (FCB) is a useful flow cytometric technique for high-throughput multiplexed analyses and can minimize technical variations after preliminary optimization and validation of protocols. To date, FCB is widely used for measurement of phosphorylation status of certain proteins, while it can be also employed for cellular viability assessment. In this chapter, we describe the protocol to perform FCB combined with viability assessment on lymphocytes and monocytes using manual and computational analysis. We also provide recommendations for FCB protocol optimization and validation for clinical sample analysis.},
}
@article {pmid37142708,
year = {2023},
author = {Bögels, BWA and Nguyen, BH and Ward, D and Gascoigne, L and Schrijver, DP and Makri Pistikou, AM and Joesaar, A and Yang, S and Voets, IK and Mulder, WJM and Phillips, A and Mann, S and Seelig, G and Strauss, K and Chen, YJ and de Greef, TFA},
title = {DNA storage in thermoresponsive microcapsules for repeated random multiplexed data access.},
journal = {Nature nanotechnology},
volume = {18},
number = {8},
pages = {912-921},
pmid = {37142708},
issn = {1748-3395},
mesh = {Capsules ; *DNA/genetics ; *Information Storage and Retrieval ; Oligonucleotides ; High-Throughput Nucleotide Sequencing ; },
abstract = {DNA has emerged as an attractive medium for archival data storage due to its durability and high information density. Scalable parallel random access to information is a desirable property of any storage system. For DNA-based storage systems, however, this still needs to be robustly established. Here we report on a thermoconfined polymerase chain reaction, which enables multiplexed, repeated random access to compartmentalized DNA files. The strategy is based on localizing biotin-functionalized oligonucleotides inside thermoresponsive, semipermeable microcapsules. At low temperatures, microcapsules are permeable to enzymes, primers and amplified products, whereas at high temperatures, membrane collapse prevents molecular crosstalk during amplification. Our data show that the platform outperforms non-compartmentalized DNA storage compared with repeated random access and reduces amplification bias tenfold during multiplex polymerase chain reaction. Using fluorescent sorting, we also demonstrate sample pooling and data retrieval by microcapsule barcoding. Therefore, the thermoresponsive microcapsule technology offers a scalable, sequence-agnostic approach for repeated random access to archival DNA files.},
}
@article {pmid37142659,
year = {2023},
author = {Zhang, D and Ren, J and Jiang, H and Wanga, VO and Dong, X and Hu, G},
title = {Comparative and phylogenetic analysis of the complete chloroplast genomes of six Polygonatum species (Asparagaceae).},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {7237},
pmid = {37142659},
issn = {2045-2322},
mesh = {Phylogeny ; *Genome, Chloroplast/genetics ; *Polygonatum/genetics ; *Asparagaceae/genetics ; *Genome, Plastid ; },
abstract = {Polygonatum Miller belongs to the tribe Polygonateae of Asparagaceae. The horizontal creeping fleshy roots of several species in this genus serve as traditional Chinese medicine. Previous studies have mainly reported the size and gene contents of the plastomes, with little information on the comparative analysis of the plastid genomes of this genus. Additionally, there are still some species whose chloroplast genome information has not been reported. In this study, the complete plastomes of six Polygonatum were sequenced and assembled, among them, the chloroplast genome of P. campanulatum was reported for the first time. Comparative and phylogenetic analyses were then conducted with the published plastomes of three related species. Results indicated that the whole plastome length of the Polygonatum species ranged from 154,564 bp (P. multiflorum) to 156,028 bp (P. stenophyllum) having a quadripartite structure of LSC and SSC separated by two IR regions. A total of 113 unique genes were detected in each of the species. Comparative analysis revealed that gene content and total GC content in these species were highly identical. No significant contraction or expansion was observed in the IR boundaries among all the species except P. sibiricum1, in which the rps19 gene was pseudogenized owing to incomplete duplication. Abundant long dispersed repeats and SSRs were detected in each genome. There were five remarkably variable regions and 14 positively selected genes were identified among Polygonatum and Heteropolygonatum. Phylogenetic results based on chloroplast genome strongly supported the placement of P. campanulatum with alternate leaves in sect. Verticillata, a group characterized by whorled leaves. Moreover, P. verticillatum and P. cyrtonema were displayed as paraphyletic. This study revealed that the characters of plastomes in Polygonatum and Heteropolygonatum maintained a high degree of similarity. Five highly variable regions were found to be potential specific DNA barcodes in Polygonatum. Phylogenetic results suggested that leaf arrangement was not suitable as a basis for delimitation of subgeneric groups in Polygonatum and the definitions of P. cyrtonema and P. verticillatum require further study.},
}
@article {pmid37140779,
year = {2024},
author = {Gahtori, R and Tripathi, AH and Chand, G and Pande, A and Joshi, P and Rai, RC and Upadhyay, SK},
title = {Phytochemical Screening of Nyctanthes arbor-tristis Plant Extracts and Their Antioxidant and Antibacterial Activity Analysis.},
journal = {Applied biochemistry and biotechnology},
volume = {196},
number = {1},
pages = {436-456},
pmid = {37140779},
issn = {1559-0291},
mesh = {*Plant Extracts/pharmacology/chemistry ; Antioxidants/pharmacology/chemistry ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Kanamycin ; *Oleaceae/chemistry ; Phytochemicals/pharmacology ; Plant Leaves ; },
abstract = {Nyctanthes arbor-tristis, alias "Vishnu Parijat," is a medicinal plant used to treat various inflammation-associated ailments and to combat innumerable infections in the traditional system of medicine. In the present study, we collected the samples of N. arbor-tristis from the lower Himalayan region of Uttarakhand, India, and carried out their molecular identification through DNA barcoding. To examine the antioxidant and antibacterial activities, we prepared the ethanolic and aqueous extracts (from flowers and leaves) and performed their phytochemical analysis by using different qualitative and quantitative approaches. The phytoextracts showed marked antioxidant potential, as revealed by a comprehensive set of assays. The ethanolic leaf extract showed marked antioxidant potential towards DPPH, ABTS, and NO scavenging (IC50 = 30.75 ± 0.006, 30.83 ± 0.002, and 51.23 ± 0.009 μg/mL, respectively). We used TLC-bioautography assay to characterize different antioxidant constituents (based on their Rf values) in the chromatograms ran under different mobile phases. For one of the prominent antioxidant spots in TLC bioautography, GC-MS analysis identified cis-9-hexadecenal and n-hexadecanoic acid as the major constituents. Furthermore, in antibacterial study, the ethanolic leaf extract showed marked activity against Aeromonas salmonicida (113.40 mg/mL of extract was equivalent to 100 μg/mL of kanamycin). In contrast, the ethanolic flower extract showed considerable antibacterial activity against Pseudomonas aeruginosa (125.85 mg/mL of extract ≡100 μg/mL of kanamycin). This study presents the phylogenetic account and unravels the antioxidant-related properties and antibacterial potential of N. arbor-tristis.},
}
@article {pmid37139429,
year = {2023},
author = {Xing, Z and Gao, H and Wang, D and Shang, Y and Tuliebieke, T and Jiang, J and Li, C and Wang, H and Li, Z and Jia, L and Wu, Y and Wang, D and Yang, W and Chang, Y and Zhang, X and Xu, L and Jiang, C and Huang, L and Tian, X},
title = {A novel biological sources consistency evaluation method reveals high level of biodiversity within wild natural medicine: A case study of Amynthas earthworms as "Guang Dilong".},
journal = {Acta pharmaceutica Sinica. B},
volume = {13},
number = {4},
pages = {1755-1770},
pmid = {37139429},
issn = {2211-3835},
abstract = {For wild natural medicine, unanticipated biodiversity as species or varieties with similar morphological characteristics and sympatric distribution may co-exist in a single batch of medical materials, which affects the efficacy and safety of clinical medication. DNA barcoding as an effective species identification tool is limited by its low sample throughput nature. In this study, combining DNA mini-barcode, DNA metabarcoding and species delimitation method, a novel biological sources consistency evaluation strategy was proposed, and high level of interspecific and intraspecific variations were observed and validated among 5376 Amynthas samples from 19 sampling points regarded as "Guang Dilong" and 25 batches of proprietary Chinese medicines. Besides Amynthas aspergillum as the authentic source, 8 other Molecular Operational Taxonomic Units (MOTUs) were elucidated. Significantly, even the subgroups within A. aspergillum revealed here differ significantly on chemical compositions and biological activity. Fortunately, this biodiversity could be controlled when the collection was limited to designated areas, as proved by 2796 "decoction pieces" samples. This batch biological identification method should be introduced as a novel concept regarding natural medicine quality control, and to offer guidelines for in-situ conservation and breeding bases construction of wild natural medicine.},
}
@article {pmid37134296,
year = {2023},
author = {Fang, J and Fu, Z and Chen, X and Liu, Y and Chen, F and Wang, Y and Li, H and Yusran, Y and Wang, K and Valtchev, V and Qiu, S and Zou, B and Fang, Q},
title = {Piezochromism in Dynamic Three-Dimensional Covalent Organic Frameworks.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {62},
number = {27},
pages = {e202304234},
doi = {10.1002/anie.202304234},
pmid = {37134296},
issn = {1521-3773},
support = {2022YFB3704900 and 2021YFF0500500//National Key R&amp;D Program of China/ ; 22025504, 21621001, and 22105082//National Natural Science Foundation of China/ ; //the SINOPEC Research Institute of Petroleum Processing/ ; BP0719036 and B17020//Higher Education Discipline Innovation Project/ ; 2020TQ0118 and 2020M681034//China Postdoctoral Science Foundation/ ; },
abstract = {Piezochromic materials with pressure-dependent photoluminescence tuning properties are important in many fields, such as mechanical sensors, security papers, and storage devices. Covalent organic frameworks (COFs), as an emerging class of crystalline porous materials (CPMs) with structural dynamics and tunable photophysical properties, are suitable for designing piezochromic materials, but there are few related studies. Herein, we report two dynamic three-dimensional COFs based on aggregation-induced emission (AIE) or aggregation-caused quenching (ACQ) chromophores, termed JUC-635 and JUC-636 (JUC=Jilin University China), and for the first time, study their piezochromic behavior by diamond anvil cell technique. Due to the various luminescent groups, JUC-635 has completely different solvatochromism and molecular aggregation behavior in the solvents. More importantly, JUC-635 with AIE effect exhibits a sustained fluorescence upon pressure increase (≈3 GPa), and reversible sensitivity with high-contrast emission differences (Δλem =187 nm) up to 12 GPa, superior to other CPMs reported so far. Therefore, this study will open a new gate to expand the potential applications of COFs as exceptional piezochromic materials in pressure sensing, barcoding, and signal switching.},
}
@article {pmid37134155,
year = {2023},
author = {González, MA and Goiri, F and Cevidanes, A and Hernández-Triana, LM and Barandika, JF and García-Pérez, AL},
title = {Mosquito community composition in two major stopover aquatic ecosystems used by migratory birds in northern Spain.},
journal = {Medical and veterinary entomology},
volume = {37},
number = {3},
pages = {616-629},
doi = {10.1111/mve.12661},
pmid = {37134155},
issn = {1365-2915},
mesh = {Male ; Female ; Humans ; Animals ; *Culicidae ; Ecosystem ; Spain ; Feeding Behavior ; Mammals ; Birds ; Mosquito Vectors ; },
abstract = {Mosquitoes (Diptera: Culicidae) are common bloodsucking Diptera frequently found in aquatic environments, which are valuable ecosystems for many animal species, particularly migrating birds. Therefore, interactions between these animal species and mosquitoes may play a critical role in pathogen transmission. During 2018-2019, mosquitoes were collected from two aquatic ecosystems in northern Spain using different methodologies and identified using classical morphology and molecular tools. A total of 1529 males and females of 22 native mosquito species (including eight new records for the region) were trapped using CO2 -baited Centers for Disease Control and Prevention (CDC) traps and sweep netting. Among the blood-fed female mosquitoes, 11 vertebrate host species-six mammals and five birds-were identified using DNA barcoding. The developmental sites of eight mosquito species were determined across nine microhabitats, and 11 mosquito species were caught landing on humans. The flight period varied among mosquito species, with some peaking in the spring and others in the summer. Our study highlights the advantages of mosquito sampling using various techniques to comprehensively characterise species composition and abundance. Information on the trophic preferences, biting behaviour and influence of climatic variables on the ecology of mosquitoes is also provided.},
}
@article {pmid37133965,
year = {2023},
author = {Gratton, EM and McNeil, DJ and Grozinger, CM and Hines, HM},
title = {Local habitat type influences bumble bee pathogen loads and bee species distributions.},
journal = {Environmental entomology},
volume = {52},
number = {3},
pages = {491-501},
doi = {10.1093/ee/nvad027},
pmid = {37133965},
issn = {1938-2936},
support = {FFAR #549032//Foundation for Food and Agricultural Research/ ; #PEN04716//National Institute of Food and Agriculture/ ; //USDA/ ; },
mesh = {Bees ; Animals ; Ecosystem ; *Hymenoptera ; *Moths ; Forests ; Biodiversity ; },
abstract = {Bumble bees (Hymenoptera: Apidae, Bombus Latreille) perform important ecological services in both managed and natural ecosystems. Anthropogenically induced change has altered floral resources, climate, and insecticide exposure, factors that impact health and disease levels in these bees. Habitat management presents a solution for improving bee health and biodiversity, but this requires better understanding of how different pathogens and bee species respond to habitat conditions. We take advantage of the washboard of repeated ridges (forested) and valleys (mostly developed) in central Pennsylvania to examine whether local variation in habitat type and other landscape factors influence bumble bee community composition and levels of 4 leading pathogens in the common eastern bumble bee, Bombus impatiens Cresson. Loads of viruses (DWV and BQCV) were found to be lowest in forest habitats, whereas loads of a gut parasite, Crithidia bombi, were highest in forests. Ridgetop forests hosted the most diverse bumble bee communities, including several habitat specialists. B. impatiens was most abundant in valleys, and showed higher incidence in areas of greater disturbance, including more developed, unforested, and lower floral resource sites, a pattern which mirrors its success in the face of anthropogenic change. Additionally, DNA barcoding revealed that B. sandersoni is much more common than is apparent from databases. Our results provide evidence that habitat type can play a large role in pathogen load dynamics, but in ways that differ by pathogen type, and point to a need for consideration of habitat at both macro-ecological and local spatial scales.},
}
@article {pmid37133448,
year = {2023},
author = {Roda, N and Cossa, A and Hillje, R and Tirelli, A and Ruscitto, F and Cheloni, S and Priami, C and Dalmasso, A and Gambino, V and Blandano, G and Polazzi, A and Falvo, P and Gatti, E and Mazzarella, L and Luzi, L and Migliaccio, E and Pelicci, PG},
title = {A Rare Subset of Primary Tumor Cells with Concomitant Hyperactivation of Extracellular Matrix Remodeling and dsRNA-IFN1 Signaling Metastasizes in Breast Cancer.},
journal = {Cancer research},
volume = {83},
number = {13},
pages = {2155-2170},
doi = {10.1158/0008-5472.CAN-22-2717},
pmid = {37133448},
issn = {1538-7445},
mesh = {Humans ; Cell Line, Tumor ; *Signal Transduction/genetics ; Prognosis ; *Gene Expression Profiling ; Extracellular Matrix/genetics ; Neoplasm Metastasis ; Gene Expression Regulation, Neoplastic ; },
abstract = {UNLABELLED: Metastatic breast cancer has a poor prognosis and is largely considered incurable. A better understanding of the molecular determinants of breast cancer metastasis could facilitate development of improved prevention and treatment strategies. We used lentiviral barcoding coupled to single-cell RNA sequencing to trace clonal and transcriptional evolution during breast cancer metastasis and showed that metastases derive from rare prometastatic clones that are underrepresented in primary tumors. Both low clonal fitness and high metastatic potential were independent of clonal origin. Differential expression and classification analyses revealed that the prometastatic phenotype was acquired by rare cells characterized by the concomitant hyperactivation of extracellular matrix remodeling and dsRNA-IFN signaling pathways. Notably, genetic silencing of key genes in these pathways (KCNQ1OT1 or IFI6, respectively) significantly impaired migration in vitro and metastasis in vivo, with marginal effects on cell proliferation and tumor growth. Gene expression signatures derived from the identified prometastatic genes predict metastatic progression in patients with breast cancer, independently of known prognostic factors. This study elucidates previously unknown mechanisms of breast cancer metastasis and provides prognostic predictors and therapeutic targets for metastasis prevention.<br><br>SIGNIFICANCE: Transcriptional lineage tracing coupled with single-cell transcriptomics defined the transcriptional programs underlying metastatic progression in breast cancer, identifying prognostic signatures and prevention strategies.},
}
@article {pmid37133356,
year = {2023},
author = {Povlsen, HR and Bentzen, AK and Kadivar, M and Jessen, LE and Hadrup, SR and Nielsen, M},
title = {Improved T cell receptor antigen pairing through data-driven filtering of sequencing information from single cells.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {37133356},
issn = {2050-084X},
support = {75N93019C00001/AI/NIAID NIH HHS/United States ; },
mesh = {*Receptors, Antigen, T-Cell/genetics ; *T-Lymphocytes ; Antigens ; Peptides ; },
abstract = {Novel single-cell-based technologies hold the promise of matching T cell receptor (TCR) sequences with their cognate peptide-MHC recognition motif in a high-throughput manner. Parallel capture of TCR transcripts and peptide-MHC is enabled through the use of reagents labeled with DNA barcodes. However, analysis and annotation of such single-cell sequencing (SCseq) data are challenged by dropout, random noise, and other technical artifacts that must be carefully handled in the downstream processing steps. We here propose a rational, data-driven method termed ITRAP (improved T cell Receptor Antigen Paring) to deal with these challenges, filtering away likely artifacts, and enable the generation of large sets of TCR-pMHC sequence data with a high degree of specificity and sensitivity, thus outputting the most likely pMHC target per T cell. We have validated this approach across 10 different virus-specific T cell responses in 16 healthy donors. Across these samples, we have identified up to 1494 high-confident TCR-pMHC pairs derived from 4135 single cells.},
}
@article {pmid37131128,
year = {2023},
author = {Karin, BR and Arellano, S and Wang, L and Walzer, K and Pomerantz, A and Vasquez, JM and Chatla, K and Sudmant, PH and Bach, BH and Smith, LL and McGuire, JA},
title = {Highly-multiplexed and efficient long-amplicon PacBio and Nanopore sequencing of hundreds of full mitochondrial genomes.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {229},
pmid = {37131128},
issn = {1471-2164},
support = {R35 GM142916/GM/NIGMS NIH HHS/United States ; Pacific Biosciences SMRT Grant//Pacific Biosciences SMRT Grant/ ; },
mesh = {Sequence Analysis, DNA/methods ; *Genome, Mitochondrial ; *Nanopore Sequencing ; High-Throughput Nucleotide Sequencing/methods ; Biodiversity ; *Nanopores ; },
abstract = {BACKGROUND: Mitochondrial genome sequences have become critical to the study of biodiversity. Genome skimming and other short-read based methods are the most common approaches, but they are not well-suited to scale up to multiplexing hundreds of samples. Here, we report on a new approach to sequence hundreds to thousands of complete mitochondrial genomes in parallel using long-amplicon sequencing. We amplified the mitochondrial genome of 677 specimens in two partially overlapping amplicons and implemented an asymmetric PCR-based indexing approach to multiplex 1,159 long amplicons together on a single PacBio SMRT Sequel II cell. We also tested this method on Oxford Nanopore Technologies (ONT) MinION R9.4 to assess if this method could be applied to other long-read technologies. We implemented several optimizations that make this method significantly more efficient than alternative mitochondrial genome sequencing methods.<br><br>RESULTS: With the PacBio sequencing data we recovered at least one of the two fragments for 96% of samples (~&#x2009;80-90%) with mean coverage&#x2009;~&#x2009;1,500x. The ONT data recovered less than 50% of input fragments likely due to low throughput and the design of the Barcoded Universal Primers which were optimized for PacBio sequencing. We compared a single mitochondrial gene alignment to half and full mitochondrial genomes and found, as expected, increased tree support with longer alignments, though whole mitochondrial genomes were not significantly better than half mitochondrial genomes.<br><br>CONCLUSIONS: This method can effectively capture thousands of long amplicons in a single run and be used to build more robust phylogenies quickly and effectively. We provide several recommendations for future users depending on the evolutionary scale of their system. A natural extension of this method is to collect multi-locus datasets consisting of mitochondrial genomes and several long nuclear loci at once.},
}
@article {pmid37127709,
year = {2023},
author = {Rhym, LH and Manan, RS and Koller, A and Stephanie, G and Anderson, DG},
title = {Peptide-encoding mRNA barcodes for the high-throughput in vivo screening of libraries of lipid nanoparticles for mRNA delivery.},
journal = {Nature biomedical engineering},
volume = {7},
number = {7},
pages = {901-910},
pmid = {37127709},
issn = {2157-846X},
mesh = {Animals ; Mice ; RNA, Messenger/chemistry ; *Liposomes ; *Nanoparticles/chemistry ; Peptides ; },
abstract = {Developing safe and effective nanoparticles for the delivery of messenger RNA (mRNA) is slow and expensive, partly due to the lack of predictive power of in vitro screening methods and the low-throughput nature of in vivo screening. While DNA barcoding and batch analysis present methods for increasing in vivo screening throughput, they can also result in incomplete or misleading measures of efficacy. Here, we describe a high-throughput and accurate method for the screening of pooled nanoparticle formulations within the same animal. The method uses liquid chromatography with tandem mass spectrometry to detect peptide barcodes translated from mRNAs in nanoparticle-transfected cells. We show the method's applicability by evaluating a library of over 400 nanoparticle formulations with 384 unique ionizable lipids using only nine mice to optimize the formulation of a biodegradable lipid nanoparticle for mRNA delivery to the liver. Barcoding lipid nanoparticles with peptide-encoding mRNAs may facilitate the rapid development of nanoparticles for mRNA delivery to specific cells and tissues.},
}
@article {pmid37124869,
year = {2023},
author = {Pittella, RS and Bassa, PG and Zefa, E and Bianchi, FM},
title = {Using the Integrative Approach to Update a Gap of One Century: Redescription and New Distribution Records of the South American Tarantulas Grammostola pulchra (Araneae: Mygalomorphae: Theraphosidae).},
journal = {Zoological studies},
volume = {62},
number = {},
pages = {e5},
pmid = {37124869},
issn = {1810-522X},
abstract = {Taxonomic researchers have used multiple sources of evidence to support species hypotheses and delimitations. Grammostola Simon (Mygalomorphae: Theraphosidae) comprises 20 valid species endemic to South America, six occurring in Brazil. The classical morphological approach based mainly on genitalia may be misleading in recognizing species in this genus. Thus, we used morphology, geographical distribution, genetic distance, and phylogeny to support the redescription of Grammostola pulchra from southern Brazil, a species described a century ago. We also diagnosed and illustrated the species. Males have a developed apical keel at the apex of the embolus; for the first time, this type of structure has been reported in a species of Grammostola. The molecular analyses using the partial sequence of Cytochrome c oxidase subunit I showed 7% of genetic distance (p-distance) between G. pulchra and Grammostola anthracina. Distance and tree-based methods (ASAP and bPTP, respectively) assigned G. pulchra as a valid species. The gene-tree under Bayesian and Maximum-Likelihood recovered a similar topology, placing G. pulchra as closely related to Grammostola burzaquensis and G. anthracina. Morphological characters which could be important in the taxonomy of the genus are further discussed.},
}
@article {pmid37120793,
year = {2023},
author = {Cetiz, MV and Turumtay, EA and Burnaz, NA and Özhatay, FN and Kaya, E and Memon, A and Turumtay, H},
title = {Phylogenetic analysis based on the ITS, matK and rbcL DNA barcodes and comparison of chemical contents of twelve Paeonia taxa in Türkiye.},
journal = {Molecular biology reports},
volume = {50},
number = {6},
pages = {5195-5208},
pmid = {37120793},
issn = {1573-4978},
support = {120Z502//T&#xfc;rkiye Bilimsel ve Teknolojik Ara&#x15f;t&#x131;rma Kurumu/ ; },
mesh = {*DNA Barcoding, Taxonomic ; Phylogeny ; *Paeonia/genetics ; Antioxidants ; DNA ; DNA, Plant/genetics ; },
abstract = {BACKGROUD: Twelve taxa of herbaceous Paeonia species were recorded in Türkiye. All definitions were performed morphologically and/or anatomically and there is no study based on DNA barcode sequences. Three barcode regions were sequenced to determine the phylogenetic relationships of Turkish Paeonia taxa. The chemical comparison of roots was also investigated.<br><br>METHODS AND RESULTS: The taxons were collected between May and June 2021 from nine cities. Leaf materials were used for DNA isolation and ITS, matK and rbcL regions were amplified and sequenced. There was no difference among taxa in terms of rbcL sequences. But the ITS and matK regions distinguished 12 taxa and structured them in two groups. ITS region distinguished P. peregrina, P. arietina, and P. tenuifolia from other taxa, while matK region distinguished P. arietina and P. witmanniana from other taxa. Both barcode sequences actually showed that the registration of P. mascula subsp. arasicola was actually 100% similar to P. arietina. ITS was the most polymorphic region (n&#x2009;=&#x2009;54) followed by matK (n&#x2009;=&#x2009;9). These sequences could successfully discriminate Paoenia species from each other and diploid P. tenuifolia. The methanolic root (100 gr) extracts were examined for total phenolic and flavonoid content, and antioxidant activities. Significant variation was found for polyphenolic content, and antioxidant properties (TPC from 204.23 to 2343.89&#xa0;mg, TFC from 7.73 to 66.16&#xa0;mg, and FRAP from 523.81 to 4338.62&#xa0;mg). SC50 values of ABTS and DPPH were ranged from 115.08 to 1115.52&#xa0;&#x3bc;g/ml and 73.83 to 963.59&#xa0;&#x3bc;g/ml, respectively.<br><br>CONCLUSION: It was concluded that 11 of 12 taxa had differences in terms of ITS and matK sequences and these region must be used for the correct identification of Turkish Paeonia.},
}
@article {pmid37113330,
year = {2023},
author = {Bay, LTE and Stokke, T and Syljuåsen, RG and Landsverk, HB},
title = {Analysis of RNA Polymerase II Chromatin Binding by Flow Cytometry.},
journal = {Bio-protocol},
volume = {13},
number = {8},
pages = {e4659},
pmid = {37113330},
issn = {2331-8325},
abstract = {RNA polymerase II (RNAPII) transcribes DNA into mRNA and thereby plays a critical role in cellular protein production. In addition, RNAPII plays a central role in DNA damage responses. Measurements of RNAPII on chromatin may thus give insight into several essential processes in eukaryotic cells. During transcription, the C-terminal domain of RNAPII becomes post-translationally modified, and phosphorylation on serine 5 and serine 2 can be used as markers for the promoter proximal and productively elongating forms of RNAPII, respectively. Here, we provide a detailed protocol for the detection of chromatin-bound RNAPII and its serine 5- and serine 2-phosphorylated forms in individual human cells through the cell cycle. We have recently shown that this method can be used to study the effects of ultraviolet DNA damage on RNAPII chromatin binding and that it can even be used to reveal new knowledge about the transcription cycle itself. Other commonly used methods to study RNAPII chromatin binding include chromatin immunoprecipitation followed by sequencing or chromatin fractionation followed by western blotting. However, such methods are frequently based on lysates made from a large number of cells, which may mask population heterogeneity, e.g., due to cell cycle phase. With strengths such as single-cell analysis, speed of use, and accurate quantitative readouts, we envision that our flow cytometry method can be widely used as a complementary approach to sequencing-based methods to study effects of different stimuli and inhibitors on RNAPII-mediated transcription. Graphical overview.},
}
@article {pmid37110486,
year = {2023},
author = {Maričić, M and Danon, G and Faria, JF and Harris, DJ},
title = {Molecular Screening of Haemogregarine Hemoparasites (Apicomplexa: Adeleorina: Haemogregarinidae) in Populations of Native and Introduced Pond Turtles in Eastern Europe.},
journal = {Microorganisms},
volume = {11},
number = {4},
pages = {},
pmid = {37110486},
issn = {2076-2607},
support = {30709-1//Rufford Foundation/ ; },
abstract = {Haemogregarines (Apicomplexa: Adeleorina) are the most common and widespread reptilian blood parasites. Haemogregarina stepanowi was the first haemogregarine described from a reptile, the European pond turtle Emys orbicularis, and initial assessments indicated it was widespread across different pond turtle host species across much of Europe, the Middle East and North Africa. However, recent molecular assessments have indicated the presence of multiple genetically distinct forms in North Africa and the Iberian Peninsula, and extensive mixed infections which may be associated with a negative impact on the hosts. Here, we screened two native species, E. orbicularis and Mauremys rivulata, and the introduced Trachemys scripta from Serbia and North Macedonia for haemogregarines by amplifying and sequencing part of the 18S rRNA gene of these parasites, and used a standard DNA barcoding approach to identify leeches, the final host, attached to pond turtles. Our results again demonstrate the occurrence of considerable diversity of parasites in the analysed pond turtle species, and that T. scripta are likely infected by local haemogregarine parasites, and not those that are found in its native range. Leeches were identified as Placobdella costata, part of a lineage from Northern Europe. Mixed infections within pond turtles were again common. Current haemogregarine taxonomy does not reflect the genetic diversity identified, and a full taxonomic reassessment is needed.},
}
@article {pmid37110439,
year = {2023},
author = {Laidoudi, Y and Rousset, E and Dessimoulie, AS and Prigent, M and Raptopoulo, A and Huteau, Q and Chabbert, E and Navarro, C and Fournier, PE and Davoust, B},
title = {Tracking the Source of Human Q Fever from a Southern French Village: Sentinel Animals and Environmental Reservoir.},
journal = {Microorganisms},
volume = {11},
number = {4},
pages = {},
pmid = {37110439},
issn = {2076-2607},
abstract = {Coxiella burnetii, also known as the causal agent of Q fever, is a zoonotic pathogen infecting humans and several animal species. Here, we investigated the epidemiological context of C. burnetii from an area in the Hérault department in southern France, using the One Health paradigm. In total, 13 human cases of Q fever were diagnosed over the last three years in an area comprising four villages. Serological and molecular investigations conducted on the representative animal population, as well as wind data, indicated that some of the recent cases are likely to have originated from a sheepfold, which revealed bacterial contamination and a seroprevalence of 47.6%. However, the clear-cut origin of human cases cannot be ruled out in the absence of molecular data from the patients. Multi-spacer typing based on dual barcoding nanopore sequencing highlighted the occurrence of a new genotype of C. burnetii. In addition, the environmental contamination appeared to be widespread across a perimeter of 6 km due to local wind activity, according to the seroprevalence detected in dogs (12.6%) and horses (8.49%) in the surrounding populations. These findings were helpful in describing the extent of the exposed area and thus supporting the use of dogs and horses as valuable sentinel indicators for monitoring Q fever. The present data clearly highlighted that the epidemiological surveillance of Q fever should be reinforced and improved.},
}
@article {pmid37108945,
year = {2023},
author = {Han, X and Liu, D and Zhang, M and He, M and Li, J and Zhu, X and Wang, M and Thongklang, N and Zhao, R and Cao, B},
title = {Macrofungal Diversity and Distribution Patterns in the Primary Forests of the Shaluli Mountains.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {4},
pages = {},
pmid = {37108945},
issn = {2309-608X},
support = {31961143010//National Natural Science Foundation of China/ ; 2019HJ2096001006//Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China/ ; XZ202202YD0031C//Science and Technology Programs of Tibet/ ; },
abstract = {The Shaluli Mountains are located in the southeastern part of the Tibetan Plateau at an elevation of 2500-5000 m. They are characterized by a typical vertical distribution of climate and vegetation and are considered a global biodiversity hotspot. We selected ten vegetation types at different elevation gradients representing distinct forests in the Shaluli Mountains to assess the macrofungal diversity, including subalpine shrub, Pinus spp., Populus spp., Pinus spp. and Quercus spp., Quercus spp., Abies spp., Picea spp. and Abies spp., Picea spp., Juniperus spp., and alpine meadow. In total, 1654 macrofungal specimens were collected. All specimens were distinguished by morphology and DNA barcoding, resulting in the identification of 766 species belonging to 177 genera in two phyla, eight classes, 22 orders, and 72 families. Macrofungal species composition varied widely among vegetation types, but ectomycorrhizal fungi were predominant. In this study, the analysis of observed species richness, the Chao1 diversity index, the invsimpson diversity index, and the Shannon diversity index revealed that the vegetation types with higher macrofungal alpha diversity in the Shaluli Mountains were composed of Abies, Picea, and Quercus. The vegetation types with lower macrofungal alpha diversity were subalpine shrub, Pinus spp., Juniperus spp., and alpine meadow. The results of curve-fitting regression analysis showed that macrofungal diversity in the Shaluli Mountains was closely related to elevation, with a trend of increasing and then decreasing with rising elevation. This distribution of diversity is consistent with the hump-shaped pattern. Constrained principal coordinate analysis based on Bray-Curtis distances indicated that macrofungal community composition was similar among vegetation types at similar elevations, while vegetation types with large differences in elevation differed significantly in macrofungal community composition. This suggests that large changes in elevation increase macrofungal community turnover. This study is the first investigation of the distribution pattern of macrofungal diversity under different vegetation types in high-altitude areas, providing a scientific basis for the conservation of macrofungal resources.},
}
@article {pmid37108927,
year = {2023},
author = {Nguyen, NH and Nguyen, PT and Otake, H and Nagata, A and Hirano, N and Imanishi-Shimizu, Y and Shimizu, K},
title = {Biodiversity of Basidiomycetous Yeasts Associated with Cladonia rei Lichen in Japan, with a Description of Microsporomyces cladoniophilus sp. nov.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {4},
pages = {},
pmid = {37108927},
issn = {2309-608X},
support = {G2019-1-081//Institute for Fermentation/ ; 2020//Goho Life Sciences International Fund/ ; },
abstract = {For more than a century, lichens have been used as an example of dual-partner symbiosis. Recently, this has been challenged by the discovery of various basidiomycetous yeasts that coexist in multiple lichen species, among which Cladonia lichens from Europe and the United States were discovered to be highly specifically associated with the basidiomycetous yeast of the family Microsporomycetaceae. To verify this highly specific relationship, we investigated the diversity of basidiomycetous yeasts associated with Cladonia rei, a widely distributed lichen in Japan, by applying two approaches: yeast isolation from the lichen thalli and meta-barcoding analysis. We obtained 42 cultures of Cystobasidiomycetous yeast which were grouped into six lineages within the family Microsporomycetaceae. Unexpectedly, although the cystobasidiomycetes-specific primer was used, not only the cystobasidiomycetous yeasts but species from other classes were also detected via the meta-barcoding dataset; in particular, pucciniomycetous yeasts were found at a high frequency in some samples. Further, Halobasidium xiangyangense, which was detected in every sample with high abundance, is highly likely a generalist epiphytic fungus that has the ability to associate with C. rei. In the pucciniomycetous group, most of the detected species belong to the scale insect-associated yeast Septobasidium genus. In conclusion, even though Microsporomyces species are not the only yeast group associated with Cladonia lichen, our study demonstrated that the thalli of Cladonia rei lichen could be a suitable habit for them.},
}
@article {pmid37108870,
year = {2023},
author = {Santos, LAD and Aptroot, A and Lücking, R and Cáceres, MEDS},
title = {Lecanora s.lat. (Ascomycota, Lecanoraceae) in Brazil: DNA Barcoding Coupled with Phenotype Characters Reveals Numerous Novel Species.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {4},
pages = {},
pmid = {37108870},
issn = {2309-608X},
abstract = {We sequenced over 200 recent specimens of Lecanora s.lat. from Brazil, delimiting 28 species in our material. Many seem to represent undescribed species, some of which being morphologically and chemically similar to each other or to already described species. Here, we present a phylogenetic analysis based on ITS, including our specimens and GenBank data. We describe nine new species. The purpose of the paper is to illustrate the diversity of the genus in Brazil, not to focus on segregate genera. However, we found that all Vainionora species cluster together and these will be treated separately. Other Lecanora species with dark hypothecium clustered in several different clades. Species with the morphology of Lecanora caesiorubella, in which currently several subspecies with different chemistry and distribution are recognized, fall apart in different, distantly related clades, so they cannot be regarded as subspecies but should be recognized at species level. A key is given for the Lecanora species from Brazil.},
}
@article {pmid37108751,
year = {2023},
author = {Jia, H and Wang, T and Li, X and Zhao, S and Guo, J and Liu, D and Liu, Y and Wu, K},
title = {Pollen Molecular Identification from a Long-Distance Migratory Insect, Spodoptera exigua, as Evidenced for Its Regional Pollination in Eastern Asia.},
journal = {International journal of molecular sciences},
volume = {24},
number = {8},
pages = {},
pmid = {37108751},
issn = {1422-0067},
support = {nt2021003//Laboratory of Lingnan Modern Agriculture Project/ ; },
mesh = {Animals ; Spodoptera ; Pollination ; Ecosystem ; Pollen/genetics ; *Moths/genetics ; Plants ; Asia, Eastern ; *Magnoliopsida ; },
abstract = {Understanding plant-insect interactions requires the uncovering of the host plant use of insect herbivores, but such information is scarce for most taxa, including nocturnal moth species, despite their vital role as herbivores and pollinators. In this study, we determined the plant species visited by an important moth species, Spodoptera exigua, by analyzing attached pollen on migratory individuals in Northeast China. Pollen grains were dislodged from 2334 S. exigua long-distance migrants captured between 2019 and 2021 on a small island in the center of the Bohai Strait, which serves as a seasonal migration pathway for this pest species, and 16.1% of the tested moths exhibited pollen contamination, primarily on the proboscis. Subsequently, 33 taxa from at least 23 plant families and 29 genera were identified using a combination of DNA barcoding and pollen morphology, primarily from the Angiosperm, Dicotyledoneae. Moreover, the sex, inter-annual, and seasonal differences in pollen adherence ratio and pollen taxa were revealed. Notably, compared to previously reported pollen types found on several other nocturnal moths, we found that almost all of the above 33 pollen taxa can be found in multiple nocturnal moth species, providing another important example of conspecific attraction. Additionally, we also discussed the indicative significance of the pollen present on the bodies of migratory individuals for determining their migratory route. Overall, by delineating the adult feeding and pollination behavior of S. exigua, we advanced our understanding of the interactions of the moths with their host plants, and its migration pattern, as well as facilitated the design of (area-wide) management strategies to preserve and optimize ecosystem services that they provide.},
}
@article {pmid37107693,
year = {2023},
author = {Martínez, M and Harms, L and Abele, D and Held, C},
title = {Mitochondrial Heteroplasmy and PCR Amplification Bias Lead to Wrong Species Delimitation with High Confidence in the South American and Antarctic Marine Bivalve Aequiyoldia eightsii Species Complex.},
journal = {Genes},
volume = {14},
number = {4},
pages = {},
pmid = {37107693},
issn = {2073-4425},
mesh = {Humans ; Animals ; *DNA, Mitochondrial/genetics ; Antarctic Regions ; Heteroplasmy ; *Bivalvia/genetics ; Polymerase Chain Reaction ; },
abstract = {The species delimitation of the marine bivalve species complex Aequiyoldia eightsii in South America and Antarctica is complicated by mitochondrial heteroplasmy and amplification bias in molecular barcoding. In this study, we compare different data sources (mitochondrial cytochrome c oxidase subunit I (COI) sequences; nuclear and mitochondrial SNPs). Whilst all the data suggest that populations on either side of the Drake Passage belong to different species, the picture is less clear within Antarctic populations, which harbor three distinct mitochondrial lineages (p-dist ≈ 6%) that coexist in populations and in a subset of individuals with heteroplasmy. Standard barcoding procedures lead to amplification bias favoring either haplotype unpredictably and thus overestimate the species richness with high confidence. However, nuclear SNPs show no differentiation akin to the trans-Drake comparison, suggesting that the Antarctic populations represent a single species. Their distinct haplotypes likely evolved during periods of temporary allopatry, whereas recombination eroded similar differentiation patterns in the nuclear genome after secondary contact. Our study highlights the importance of using multiple data sources and careful quality control measures to avoid bias and increase the accuracy of molecular species delimitation. We recommend an active search for mitochondrial heteroplasmy and haplotype-specific primers for amplification in DNA-barcoding studies.},
}
@article {pmid37106480,
year = {2023},
author = {Jiménez-García, E and Andújar, C and López, H and Emerson, BC},
title = {Towards understanding insect species introduction and establishment: A community-level barcoding approach using island beetles.},
journal = {Molecular ecology},
volume = {32},
number = {13},
pages = {3778-3792},
doi = {10.1111/mec.16962},
pmid = {37106480},
issn = {1365-294X},
mesh = {Animals ; Phylogeny ; *Coleoptera/genetics ; Biodiversity ; Forests ; Introduced Species ; *Arthropods ; },
abstract = {Since Darwin put forward his opposing hypotheses to explain the successful establishment of species in areas outside their native ranges, the preadaptation and competition-relatedness hypotheses, known as Darwin's naturalization conundrum, numerous studies have sought to understand the relative importance of each. Here, we take advantage of well-characterized beetle communities across laurel forests of the Canary Islands for a first evaluation of the relative support for Darwin's two hypotheses within arthropods. We generated a mitogenome backbone tree comprising nearly half of the beetle genera recorded within the Canary Islands for the phylogenetic placement of native and introduced species sampled in laurel forests, using cytochrome c oxidase I (COI) sequences. For comparative purposes, we also assembled and phylogenetically placed a data set of COI sequences for introduced beetle species that were not sampled within laurel forests. Our results suggest a stronger effect of species preadaptation over resource competition, while also revealing an underappreciated shortfall in arthropod biodiversity data-knowledge of species as being native or introduced. We name this the Humboldtean shortfall and suggest that similar studies using arthropods should incorporate DNA barcode sequencing to mitigate this problem.},
}
@article {pmid37106151,
year = {2023},
author = {Mukherjee, S and Kim, B and Cheng, LY and Doerfert, MD and Li, J and Hernandez, A and Liang, L and Jarvis, MI and Rios, PD and Ghani, S and Joshi, I and Isa, D and Ray, T and Terlier, T and Fell, C and Song, P and Miranda, RN and Oberholzer, J and Zhang, DY and Veiseh, O},
title = {Screening hydrogels for antifibrotic properties by implanting cellularly barcoded alginates in mice and a non-human primate.},
journal = {Nature biomedical engineering},
volume = {7},
number = {7},
pages = {867-886},
pmid = {37106151},
issn = {2157-846X},
support = {R01 DK120459/DK/NIDDK NIH HHS/United States ; },
mesh = {Mice ; Animals ; *Alginates/chemistry ; *Hydrogels/chemistry ; Endothelial Cells ; Primates ; Biocompatible Materials/chemistry ; },
abstract = {Screening implantable biomaterials for antifibrotic properties is constrained by the need for in vivo testing. Here we show that the throughput of in vivo screening can be increased by cellularly barcoding a chemically modified combinatorial library of hydrogel formulations. The method involves the implantation of a mixture of alginate formulations, each barcoded with human umbilical vein endothelial cells from different donors, and the association of the identity and performance of each formulation by genotyping single nucleotide polymorphisms of the cells via next-generation sequencing. We used the method to screen 20 alginate formulations in a single mouse and 100 alginate formulations in a single non-human primate, and identified three lead hydrogel formulations with antifibrotic properties. Encapsulating human islets with one of the formulations led to long-term glycaemic control in a mouse model of diabetes, and coating medical-grade catheters with the other two formulations prevented fibrotic overgrowth. High-throughput screening of barcoded biomaterials in vivo may help identify formulations that enhance the long-term performance of medical devices and of biomaterial-encapsulated therapeutic cells.},
}
@article {pmid37105856,
year = {2023},
author = {Howland, KK and Brock, A},
title = {Cellular barcoding tracks heterogeneous clones through selective pressures and phenotypic transitions.},
journal = {Trends in cancer},
volume = {9},
number = {7},
pages = {591-601},
pmid = {37105856},
issn = {2405-8025},
support = {R01 CA226258/CA/NCI NIH HHS/United States ; R01 CA255536/CA/NCI NIH HHS/United States ; U01 CA253540/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Neoplasms/genetics/pathology ; Clone Cells/pathology ; Disease Progression ; },
abstract = {Genomic DNA barcoding has emerged as a sensitive and flexible tool to measure the fates of clonal subpopulations within a heterogeneous cancer cell population. Coupling cellular barcoding with single-cell transcriptomics permits the longitudinal analysis of molecular mechanisms with detailed clone-level resolution. Numerous recent studies have employed these tools to track clonal cell states in cancer progression and treatment response. With these new technologies comes the opportunity to examine longstanding questions about the origins and contributions of tumor cell heterogeneity and the roles of selection and phenotypic plasticity in disease progression and treatment.},
}
@article {pmid37103204,
year = {2023},
author = {Liu, JX and Reshchikov, A and Chen, HY},
title = {Descriptions of Three New Species of the Genus Acerataspis Uchida, 1934 (Hymenoptera, Ichneumonidae, Metopiinae), with an Illustrated Identification Key to Extant Species.},
journal = {Insects},
volume = {14},
number = {4},
pages = {},
pmid = {37103204},
issn = {2075-4450},
support = {2021A15150730//Natural Science Foundation of Guangdong Province/ ; 202203AM140015//Yunnan Intelligence Union Program/ ; },
abstract = {The Asian genus Acerataspis Uchida, 1934 is reviewed based on both morphology and DNA barcodes. Ten species are recognized in total, of which three species from Yunnan Province of China are described as new: Acerataspis maliae sp. nov., A. seperata sp. nov. and A. similis sp. nov. The male of A. fukienensis Chao, 1957 is described and illustrated for the first time. The genus is recorded from Thailand and Southeast Asia for the first time. An illustrated key to all known extant species is provided. With the supplement of DNA barcodes, a few diagnostic morphological characters are found useful in species identification.},
}
@article {pmid37103180,
year = {2023},
author = {Zhao, FY and Yang, L and Zou, QX and Ali, A and Li, SQ and Yao, ZY},
title = {Diversity of Pholcus Spiders (Araneae: Pholcidae) in China's Lüliang Mountains: An Integrated Morphological and Molecular Approach.},
journal = {Insects},
volume = {14},
number = {4},
pages = {},
pmid = {37103180},
issn = {2075-4450},
support = {32170461//National Natural Science Foundation of China/ ; 31872193//National Natural Science Foundation of China/ ; },
abstract = {Spiders of the genus Pholcus were collected for the first time during an expedition to the Lüliang Mountains in Shanxi Province, North China. Phylogenetic analyses of DNA sequence data from COI, H3, wnt, and 28S genes allowed us to group them into nine well-supported clades. We used morphology and four methods of molecular species delimitation, namely Automatic Barcode Gap Discovery (ABGD), the Generalized Mixed Yule Coalescent (GMYC), Bayesian Poisson Tree Processes (bPTP), and Bayesian Phylogenetics and Phylogeography (BPP), to investigate species boundaries. These integrative taxonomic analyses identified the nine clades as nine distinct species, comprising Pholcus luya Peng &amp; Zhang, 2013 and eight other species new to science: Pholcus jiaocheng sp. nov., Pholcus linfen sp. nov., Pholcus lishi sp. nov., Pholcus luliang sp. nov., Pholcus wenshui sp. nov., Pholcus xiangfen sp. nov., Pholcus xuanzhong sp. nov., and Pholcus zhongyang sp. nov. The species occur in geographic proximity and show many morphological similarities. All of them belong to the P. phungiformes species group. The records from the Lüliang Mountains represent the westernmost distribution limit of this species group.},
}
@article {pmid37103167,
year = {2023},
author = {Krupitsky, A and Shapoval, N and Shapoval, G},
title = {DNA Barcoding of the Palaearctic Elfin Butterflies (Lepidoptera, Lycaenidae) with a Description of Four New Species from Vietnam.},
journal = {Insects},
volume = {14},
number = {4},
pages = {},
pmid = {37103167},
issn = {2075-4450},
support = {21-74-00021//Russian Science Foundation/ ; },
abstract = {Phylogenetic analysis is provided for the first time for 12 species of Palaearctic elfin butterflies, members of the previously recognized genera Ahlbergia Bryk, 1947, Cissatsuma Johnson, 1992, and Novosatsuma Johnson, 1992, based on the barcoding region of the mitochondrial cytochrome C oxidase subunit I gene (COI). Comparison of the COI barcodes revealed very low levels of genetic divergence between the species of the Palaearctic elfin butterflies and Callophrys Billberg, 1820 sensu stricto. COI-based phylogeny revealed that Palaearctic Callophrys and the Palaearctic elfin butterflies, except Cissatsuma, are polyphyletic. Four new sympatric species, namely, Callophrys (Ahlbergia) hmong sp. n., C. (A.) tay sp. n., Callophrys (Cissatsuma) devyatkini sp. n. and C. (A.) dao sp. n. are described from Ha Giang Province, North Vietnam, based on wing colouration, the morphologies of the male and female genitalia, and differences in COI sequences. Discovery of the new species expands the distribution range of the group towards the southeast, beyond the Palaearctic region.},
}
@article {pmid37095220,
year = {2023},
author = {Hao, L and Zhao, RT and Welch, NL and Tan, EKW and Zhong, Q and Harzallah, NS and Ngambenjawong, C and Ko, H and Fleming, HE and Sabeti, PC and Bhatia, SN},
title = {CRISPR-Cas-amplified urinary biomarkers for multiplexed and portable cancer diagnostics.},
journal = {Nature nanotechnology},
volume = {18},
number = {7},
pages = {798-807},
pmid = {37095220},
issn = {1748-3395},
support = {P30 CA014051/CA/NCI NIH HHS/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; K99 CA237861/CA/NCI NIH HHS/United States ; P30 ES002109/ES/NIEHS NIH HHS/United States ; R00 CA237861/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Animals ; Mice ; CRISPR-Cas Systems/genetics ; *Neoplasms/diagnosis/genetics ; DNA ; *Nucleic Acids ; Biomarkers ; Tumor Microenvironment ; },
abstract = {Synthetic biomarkers, bioengineered sensors that generate molecular reporters in diseased microenvironments, represent an emerging paradigm in precision diagnostics. Despite the utility of DNA barcodes as a multiplexing tool, their susceptibility to nucleases in vivo has limited their utility. Here we exploit chemically stabilized nucleic acids to multiplex synthetic biomarkers and produce diagnostic signals in biofluids that can be 'read out' via CRISPR nucleases. The strategy relies on microenvironmental endopeptidase to trigger the release of nucleic acid barcodes and polymerase-amplification-free, CRISPR-Cas-mediated barcode detection in unprocessed urine. Our data suggest that DNA-encoded nanosensors can non-invasively detect and differentiate disease states in transplanted and autochthonous murine cancer models. We also demonstrate that CRISPR-Cas amplification can be harnessed to convert the readout to a point-of-care paper diagnostic tool. Finally, we employ a microfluidic platform for densely multiplexed, CRISPR-mediated DNA barcode readout that can potentially evaluate complex human diseases rapidly and guide therapeutic decisions.},
}
@article {pmid37094808,
year = {2023},
author = {Atieli, HE and Zhou, G and Zhong, D and Wang, X and Lee, MC and Yaro, AS and Diallo, M and Githure, J and Kazura, J and Lehmann, T and Yan, G},
title = {Wind-assisted high-altitude dispersal of mosquitoes and other insects in East Africa.},
journal = {Journal of medical entomology},
volume = {60},
number = {4},
pages = {698-707},
pmid = {37094808},
issn = {1938-2928},
support = {D43 TW001505/TW/FIC NIH HHS/United States ; U19 AI129326/AI/NIAID NIH HHS/United States ; },
mesh = {Female ; Humans ; Animals ; Wind ; Altitude ; *Anopheles ; Africa, Eastern ; *Malaria ; Mosquito Vectors ; Mosquito Control ; },
abstract = {Knowledge of insect dispersal is relevant to the control of agricultural pests, vector-borne transmission of human and veterinary pathogens, and insect biodiversity. Previous studies in a malaria endemic area of the Sahel region in West Africa revealed high-altitude, long-distance migration of insects and various mosquito species. The objective of the current study was to assess whether similar behavior is exhibited by mosquitoes and other insects around the Lake Victoria basin region of Kenya in East Africa. Insects were sampled monthly from dusk to dawn over 1 year using sticky nets suspended on a tethered helium-filled balloon. A total of 17,883 insects were caught on nets tethered at 90, 120, and 160 m above ground level; 818 insects were caught in control nets. Small insects (<0.5 cm, n = 15,250) were predominant regardless of height compared with large insects (>0.5 cm, n = 2,334) and mosquitoes (n = 299). Seven orders were identified; dipteran was the most common. Barcoding molecular assays of 184 mosquitoes identified 7 genera, with Culex being the most common (65.8%) and Anopheles being the least common (5.4%). The survival rate of mosquitoes, experimentally exposed to high-altitude overnight, was significantly lower than controls maintained in the laboratory (19% vs. 85%). There were no significant differences in mosquito survival and oviposition rate according to capture height. These data suggest that windborne dispersal activity of mosquito vectors of malaria and other diseases occurs on a broad scale in sub-Saharan Africa.},
}
@article {pmid37093820,
year = {2023},
author = {Baena-Bejarano, N and Reina, C and Martínez-Revelo, DE and Medina, CA and Tovar, E and Uribe-Soto, S and Neita-Moreno, JC and Gonzalez, MA},
title = {Taxonomic identification accuracy from BOLD and GenBank databases using over a thousand insect DNA barcodes from Colombia.},
journal = {PloS one},
volume = {18},
number = {4},
pages = {e0277379},
pmid = {37093820},
issn = {1932-6203},
mesh = {Animals ; *Databases, Nucleic Acid ; DNA Barcoding, Taxonomic/methods ; Reproducibility of Results ; Colombia ; Insecta ; DNA/genetics ; *Coleoptera/genetics ; Phylogeny ; },
abstract = {Recent declines of insect populations at high rates have resulted in the need to develop a quick method to determine their diversity and to process massive data for the identification of species of highly diverse groups. A short sequence of DNA from COI is widely used for insect identification by comparing it against sequences of known species. Repositories of sequences are available online with tools that facilitate matching of the sequences of interest to a known individual. However, the performance of these tools can differ. Here we aim to assess the accuracy in identification of insect taxonomic categories from two repositories, BOLD Systems and GenBank. This was done by comparing the sequence matches between the taxonomist identification and the suggested identification from the platforms. We used 1,160 COI sequences representing eight orders of insects from Colombia. After the comparison, we reanalyzed the results from a representative subset of the data from the subfamily Scarabaeinae (Coleoptera). Overall, BOLD systems outperformed GenBank, and the performance of both engines differed by orders and other taxonomic categories (species, genus and family). Higher rates of accurate identification were obtained at family and genus levels. The accuracy was higher in BOLD for the order Coleoptera at family level, for Coleoptera and Lepidoptera at genus and species level. Other orders performed similarly in both repositories. Moreover, the Scarabaeinae subset showed that species were correctly identified only when BOLD match percentage was above 93.4% and a total of 85% of the samples were correctly assigned to a taxonomic category. These results accentuate the great potential of the identification engines to place insects accurately into their respective taxonomic categories based on DNA barcodes and highlight the reliability of BOLD Systems for insect identification in the absence of a large reference database for a highly diverse country.},
}
@article {pmid37092851,
year = {2023},
author = {Rodriguez, S and Sun, B and McAllen, S and Jiang, M and Parra, ER},
title = {Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {194},
pages = {},
doi = {10.3791/64758},
pmid = {37092851},
issn = {1940-087X},
support = {U24 CA224285/CA/NCI NIH HHS/United States ; },
mesh = {*Paraffin ; *Leukocytes, Mononuclear ; Fluorescent Dyes ; Formaldehyde ; Single-Cell Analysis ; Paraffin Embedding/methods ; },
abstract = {Multiplexed imaging technology using antibody barcoding with oligonucleotides, which sequentially detects multiple epitopes in the same tissue section, is an effective methodology for tumor evaluation that improves the understanding of the tumor microenvironment. The visualization of protein expression in formalin-fixed, paraffin-embedded tissues is achieved when a specific fluorophore is annealed to an antibody-bound barcode via complementary oligonucleotides and then sample imaging is performed; indeed, this method allows for the use of customizable panels of more than 40 antibodies in a single tissue staining reaction. This method is compatible with fresh frozen tissue, formalin-fixed, paraffin-embedded tissue, cultured cells, and peripheral blood mononuclear cells, meaning that researchers can use this technology to view a variety of sample types at single-cell resolution. This method starts with a manual staining and fixing protocol, and all the antibody barcodes are applied using an antibody cocktail. The staining fluidics instrument is fully automated and performs iterative cycles of labeling, imaging, and removing spectrally distinct fluorophores until all the biomarkers have been imaged using a standard fluorescence microscope. The images are then collected and compiled across all the imaging cycles to achieve single-cell resolution for all the markers. The single-step staining and gentle fluorophore removal not only allow for highly multiplexed biomarker analysis but also preserve the sample for additional downstream analysis if desired (e.g., hematoxylin and eosin staining). Furthermore, the image analysis software enables image processing-drift compensation, background subtraction, cell segmentation, and clustering-as well as the visualization and analysis of the images and cell phenotypes for the generation of spatial network maps. In summary, this technology employs a computerized microfluidics system and fluorescence microscope to iteratively hybridize, image, and strip fluorescently labeled DNA probes that are complementary to tissue-bound, oligonucleotide-conjugated antibodies.},
}
@article {pmid37091569,
year = {2023},
author = {Du, YY and Zhang, YP and Lou, ZY and Wang, T},
title = {Unrecognized diversity, genetic structuring, and phylogeography of the genus Triplophysa (Cypriniformes: Nemacheilidae) sheds light on two opposite colonization routes during Quaternary glaciation that occurred in the Qilian Mountains.},
journal = {Ecology and evolution},
volume = {13},
number = {4},
pages = {e10003},
pmid = {37091569},
issn = {2045-7758},
abstract = {In recent years, the influence of historical geological and climatic events on the evolution of flora and fauna in the Tibetan Plateau has been a hot research topic. The Qilian Mountain region is one of the most important sources of biodiversity on the Qinghai-Tibet Plateau. Many species existed in the region during the Pleistocene glacial oscillation, and the complex geographical environment provided suitable conditions for the survival of local species. The shrinkage, expansion, and transfer of the distribution range and population size of species have significant effects on genetic diversity and intraspecific differentiation. To reveal the effects of geological uplift and climate oscillation on the evolution of fish populations in the Qilian Mountains, we investigated the genetic structure, phylogenetic relationship, and phylogeographical characteristics of genus Triplophysa species in the Qilian Mountains using the mitochondrial DNA gene (COI), three nuclear genes (RAG1, sRH, and Myh6) and 11 pairs of nuclear microsatellite markers. We collected 11 species of genus Triplophysa living in the Qilian Mountains, among which Triplophysa hsutschouensis and Triplophysa papillosolabiata are widely distributed in the rivers on the northern slope of the Qilian Mountains. There was a high degree of lineage differentiation among species, and the genetic diversity of endemic species was low. The different geographical groups of T. papillosolabiata presented some allogeneic adaptation and differentiation, which was closely related to the changes in the river system. Except for the population expansion event of T. hsutschouensis during the last glacial period of the Qinghai-Tibet Plateau (0.025 MYA), the population sizes of other plateau loach species remained stable without significant population expansion. Starting from the east and west sides of the Qilian Mountains, T. hsutschouensis, and T. papillosolabiata showed two species colonization routes in opposite directions. The geological events of the uplift of the Qinghai-Tibet Plateau and the climatic oscillation of the Quaternary glaciation had a great influence on the genetic structure of the plateau loach in the Qilian Mountains, which promoted the genetic differentiation of the plateau loach and formed some unique new species. The results of this study have important guiding significance for fish habitat protection in the Qilian Mountains.},
}
@article {pmid37090677,
year = {2023},
author = {Stanley, S and Spaulding, CN and Liu, Q and Chase, MR and Ha, DTM and Thai, PVK and Lan, NH and Thu, DDA and Quang, NL and Brown, J and Hicks, ND and Wang, X and Marin, M and Howard, NC and Vickers, AJ and Karpinski, WM and Chao, MC and Farhat, MR and Caws, M and Dunstan, SJ and Thuong, NTT and Fortune, SM},
title = {High-throughput phenogenotyping of Mycobacteria tuberculosis clinical strains reveals bacterial determinants of treatment outcomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.04.09.536166},
pmid = {37090677},
issn = {2692-8205},
support = {P01 AI132130/AI/NIAID NIH HHS/United States ; P01 AI143575/AI/NIAID NIH HHS/United States ; },
abstract = {BACKGROUND: Combatting the tuberculosis (TB) epidemic caused by Mycobacterium tuberculosis (Mtb) necessitates a better understanding of the factors contributing to patient clinical outcomes and transmission. While host and environmental factors have been evaluated, the impact of Mtb genetic background and phenotypic diversity is underexplored. Previous work has made associations between Mtb genetic lineages and some clinical and epidemiological features, but the bacterial traits underlying these connections are largely unknown.<br><br>METHODS: We developed a high-throughput functional genomics platform for defining genotype-phenotype relationships across a panel of Mtb clinical isolates. These phenotypic fitness profiles function as intermediate traits which can be linked to Mtb genetic variants and associated with clinical and epidemiological outcomes. We applied this approach to a collection of 158 Mtb strains from a study of Mtb transmission in Ho Chi Minh City, Vietnam. Mtb strains were genetically tagged in multiplicate, which allowed us to pool the strains and assess in vitro competitive fitness using deep sequencing across a set of 14 host-relevant antibiotic and metabolic conditions. Phylogenetic and monogenic associations with these intermediate traits were identified and then associated with clinical outcomes.<br><br>FINDINGS: Mtb clinical strains have a broad range of growth and drug response dynamics that can be clustered by their phylogenetic relationships. We identified novel monogenic associations with Mtb fitness in various metabolic and antibiotic conditions. Among these, we find that mutations in Rv1339 , a phosphodiesterase, which were identified through their association with slow growth in glycerol, are further associated with treatment failure. We also identify a previously uncharacterized subclade of Lineage 1 strains (L1.1.1.1) that is phenotypically distinguished by slow growth under most antibiotic and metabolic stress conditions in vitro . This clade is associated with cavitary disease, treatment failure, and demonstrates increased transmission potential.<br><br>INTERPRETATION: High-throughput phenogenotyping of Mtb clinical strains enabled bacterial intermediate trait identification that can provide a mechanistic link between Mtb genetic variation and patient clinical outcomes. Mtb strains associated with cavitary disease, treatment failure, and transmission potential display intermediate phenotypes distinguished by slow growth under various antibiotic and metabolic conditions. These data suggest that Mtb growth regulation is an adaptive advantage for host bacterial success in human populations, in at least some circumstances. These data further suggest markers for the underlying bacterial processes that govern these clinical outcomes.<br><br>FUNDING: National Institutes of Allergy and Infectious Diseases: P01 AI132130 (SS, SMF); P01 AI143575 (XW, SMF); U19 AI142793 (QL, SMF); 5T32AI132120-03 (SS); 5T32AI132120-04 (SS); 5T32AI049928-17 (SS) Wellcome Trust Fellowship in Public Health and Tropical Medicine: 097124/Z/11/Z (NTTT) National Health and Medical Research Council (NHMRC)/A*STAR joint call: APP1056689 (SJD) The funding sources had no involvement in study methodology, data collection, analysis, and interpretation nor in the writing or submission of the manuscript.<br><br>RESEARCH IN CONTEXT: Evidence before this study: We used different combinations of the words mycobacterium tuberculosis, tuberculosis, clinical strains, intermediate phenotypes, genetic barcoding, phenogenomics, cavitary disease, treatment failure, and transmission to search the PubMed database for all studies published up until January 20 [th] , 2022. We only considered English language publications, which biases our search. Previous work linking Mtb determinants to clinical or epidemiological data has made associations between bacterial lineage, or less frequently, genetic polymorphisms to in vitro or in vivo models of pathogenesis, transmission, and clinical outcomes such as cavitary disease, treatment failure, delayed culture conversion, and severity. Many of these studies focus on the global pandemic Lineage 2 and Lineage 4 Mtb strains due in part to a deletion in a polyketide synthase implicated in host-pathogen interactions. There are a number of Mtb GWAS studies that have led to novel genetic determinants of in vitro drug resistance and tolerance. Previous Mtb GWAS analyses with clinical outcomes did not experimentally test any predicted phenotypes of the clinical strains. Published laboratory-based studies of Mtb clinical strains involve relatively small numbers of strains, do not identify the genetic basis of relevant phenotypes, or link findings to the corresponding clinical outcomes. There are two recent studies of other pathogens that describe phenogenomic analyses. One study of 331 M. abscessus clinical strains performed one-by-one phenotyping to identify bacterial features associated with clearance of infection and another details a competition experiment utilizing three barcoded Plasmodium falciparum clinical isolates to assay antimalarial fitness and resistance. Added value of this study: We developed a functional genomics platform to perform high-throughput phenotyping of Mtb clinical strains. We then used these phenotypes as intermediate traits to identify novel bacterial genetic features associated with clinical outcomes. We leveraged this platform with a sample of 158 Mtb clinical strains from a cross sectional study of Mtb transmission in Ho Chi Minh City, Vietnam. To enable high-throughput phenotyping of large numbers of Mtb clinical isolates, we applied a DNA barcoding approach that has not been previously utilized for the high-throughput analysis of Mtb clinical strains. This approach allowed us to perform pooled competitive fitness assays, tracking strain fitness using deep sequencing. We measured the replicative fitness of the clinical strains in multiplicate under 14 metabolic and antibiotic stress condition. To our knowledge, this is the largest phenotypic screen of Mtb clinical isolates to date. We performed bacterial GWAS to delineate the Mtb genetic variants associated with each fitness phenotype, identifying monogenic associations with several conditions. We then defined Mtb phenotypic and genetic features associated with clinical outcomes. We find that a subclade of Mtb strains, defined by variants largely involved in fatty acid metabolic pathways, share a universal slow growth phenotype that is associated with cavitary disease, treatment failure and increased transmission potential in Vietnam. We also find that mutations in Rv1339 , a poorly characterized phosphodiesterase, also associate with slow growth in vitro and with treatment failure in patients. Implications of all the available evidence: Phenogenomic profiling demonstrates that Mtb strains exhibit distinct growth characteristics under metabolic and antibiotic stress conditions. These fitness profiles can serve as intermediate traits for GWAS and association with clinical outcomes. Intermediate phenotyping allows us to examine potential processes by which bacterial strain differences contribute to clinical outcomes. Our study identifies clinical strains with slow growth phenotypes under in vitro models of antibiotic and host-like metabolic conditions that are associated with adverse clinical outcomes. It is possible that the bacterial intermediate phenotypes we identified are directly related to the mechanisms of these outcomes, or they may serve as markers for the causal yet unidentified bacterial determinants. Via the intermediate phenotyping, we also discovered a surprising diversity in Mtb responses to the new anti-mycobacterial drugs that target central metabolic processes, which will be important in considering roll-out of these new agents. Our study and others that have identified Mtb determinants of TB clinical and epidemiological phenotypes should inform efforts to improve diagnostics and drug regimen design.},
}
@article {pmid37090549,
year = {2023},
author = {Feng, W and Beer, J and Hao, Q and Ariyapala, IS and Sahajan, A and Komarov, A and Cha, K and Moua, M and Qiu, X and Xu, X and Iyengar, S and Yoshimura, T and Nagaraj, R and Wang, L and Yu, M and Engel, K and Zhen, L and Xue, W and Lee, CJ and Park, CH and Peng, C and Zhang, K and Grzybowski, A and Hahm, J and Schmidt, SV and Odainic, A and Spitzer, J and , and Buddika, K and Kuo, D and Fang, L and Zhang, B and Chen, S and Latz, E and Yin, Y and Luo, Y and Ma, XJ},
title = {NULISA: a novel proteomic liquid biopsy platform with attomolar sensitivity and high multiplexing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.04.09.536130},
pmid = {37090549},
issn = {2692-8205},
abstract = {The blood proteome holds great promise for precision medicine but poses substantial challenges due to the low abundance of most plasma proteins and the vast dynamic range across the proteome. We report a novel proteomic technology - NUcleic acid Linked Immuno-Sandwich Assay (NULISA™) - that incorporates a dual capture and release mechanism to suppress the assay background and improves the sensitivity of the proximity ligation assay by over 10,000-fold to the attomolar level. It utilizes pairs of antibodies conjugated to DNA oligonucleotides that enable immunocomplex purification and generate reporter DNA containing target- and sample-specific barcodes for a next-generation sequencing-based, highly multiplexed readout. A 200-plex NULISA targeting 124 cytokines and chemokines and 80 other immune response-related proteins demonstrated superior sensitivity for detecting low-abundance proteins and high concordance with other immunoassays. The ultrahigh sensitivity allowed the detection of previously difficult-to-detect, but biologically important, low-abundance biomarkers in patients with autoimmune diseases and COVID-19. Fully automated NULISA addresses longstanding challenges in proteomic analysis of liquid biopsies and makes broad and in-depth proteomic analysis accessible to the general research community and future diagnostic applications.},
}
@article {pmid37090498,
year = {2023},
author = {Pan, X and Li, H and Putta, P and Zhang, X},
title = {LinRace: single cell lineage reconstruction using paired lineage barcode and gene expression data.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37090498},
issn = {2692-8205},
support = {R35 GM143070/GM/NIGMS NIH HHS/United States ; },
abstract = {Understanding how single cells divide and differentiate into different cell types in developed organs is one of the major tasks of developmental and stem cell biology. Recently, lineage tracing technology using CRISPR/Cas9 genome editing has enabled simultaneous readouts of gene expressions and lineage barcodes in single cells, which allows for the reconstruction of the cell division tree, and even the detection of cell types and differentiation trajectories at the whole organism level. While most state-of-the-art methods for lineage reconstruction utilize only the lineage barcode data, methods that incorporate gene expression data are emerging, aiming to improve the accuracy of lineage reconstruction. However, effectively incorporating the gene expression data requires a reasonable model on how gene expression data changes along generations of divisions. Here, we present LinRace (Lineage Reconstruction with asymmetric cell division model), a method that integrates the lineage barcode and gene expression data using the asymmetric cell division model and infers cell lineage under a framework combining Neighbor Joining and maximum-likelihood heuristics. On both simulated and real data, LinRace outputs more accurate cell division trees than existing methods. Moreover, LinRace can output the cell states (cell types) of ancestral cells, which is rarely performed with existing lineage reconstruction methods. The information on ancestral cells can be used to analyze how a progenitor cell generates a large population of cells with various functionalities. LinRace is available at: https://github.com/ZhangLabGT/LinRace.},
}
@article {pmid37090470,
year = {2022},
author = {Novozhilov, YK and Prikhodko, IS and Fedorova, NA and Shchepin, ON and Gmoshinskiy, VI and Schnittler, M},
title = {Lamproderma vietnamense: a new species of myxomycetes with reticulate spores from Phia Oắc - Phia Đén National Park (northern Vietnam) supported by molecular phylogeny and morphological analysis.},
journal = {Mycoscience},
volume = {63},
number = {4},
pages = {149-155},
pmid = {37090470},
issn = {1340-3540},
abstract = {A new species of Lamproderma (Myxomycetes), described herein as L. vietnamense, was recovered in the field on ground litter from mountain subtropical forests (Phia Oắc - Phia Đén National Park) of northern Vietnam. Morphological details were examined by light and scanning electron microscopy. The species is characterized by a distinct and unique combination of morphological features, including a bright blue, shiny and very thin membranous peridium, a small dome-shaped columella, rigid, straight, branched, brown capillitial threads which gradually become pale at the periphery and finally colorless at the tips and small-meshed, banded-reticulate spores with 9-12 meshes across the spore diameter and solid walls without perforations 0.3-0.5 µm high. The stability of the taxonomic characters of L. vietnamense is supported by two well-developed collections found in 2018 and 2019. Partial sequences of three molecular markers (SSU, EF1α, COI) for both collections are identical. A two-gene phylogeny of the first two markers displays the two known accessions as a well-separated entity and indicates affinity of the new species with L. columbinum (the type taxon of the genus), L. violaceum, and several nivicolous Lamproderma species.},
}
@article {pmid37089896,
year = {2023},
author = {Hambleton, S and Liu, M},
title = {DNA barcode sequencing discovered the aecial host of Puccinia chunjiei.},
journal = {Mycoscience},
volume = {64},
number = {1},
pages = {35-39},
pmid = {37089896},
issn = {1340-3540},
abstract = {The telial stage of Puccinia chunjiei was described in 2012 from a single specimen collected in China (DAOM 240982). This species is the closest relative of P. graminis but differs in telial morphology on their grass hosts and in DNA sequences. As part of a DNA-barcoding project for rust herbarium specimens, collections of the aecial stage of P. graminis on Berberis were processed. For one specimen, BPI 1103856, the ITS sequence matched that of P. chunjiei and the aecial morphology differed from P. graminis. An expanded description of P. chunjiei is presented with photographs of the aecial stages of both species.},
}
@article {pmid37088731,
year = {2023},
author = {Imani, SM and Osman, E and Bakhshandeh, F and Qian, S and Sakib, S and MacDonald, M and Gaskin, M and Zhitomirsky, I and Yamamura, D and Li, Y and Didar, TF and Soleymani, L},
title = {Liquid NanoBiosensors Enable One-Pot Electrochemical Detection of Bacteria in Complex Matrices.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {10},
number = {19},
pages = {e2207223},
pmid = {37088731},
issn = {2198-3844},
support = {//NSERC/ ; //Ontario Ministry of Research and Innovation/ ; //Canada Research Chairs/ ; },
mesh = {*Escherichia coli/genetics ; *DNA, Catalytic ; Sensitivity and Specificity ; Bacteria ; DNA ; },
abstract = {There is a need for point-of-care bacterial sensing and identification technologies that are rapid and simple to operate. Technologies that do not rely on growth cultures, nucleic acid amplification, step-wise reagent addition, and complex sample processing are the key for meeting this need. Herein, multiple materials technologies are integrated for overcoming the obstacles in creating rapid and one-pot bacterial sensing platforms. Liquid-infused nanoelectrodes are developed for reducing nonspecific binding on the transducer surface; bacterium-specific RNA-cleaving DNAzymes are used for bacterial identification; and redox DNA barcodes embedded into DNAzymes are used for binding-induced electrochemical signal transduction. The resultant single-step and one-pot assay demonstrates a limit-of-detection of 10[2] CFU mL[-1] , with high specificity in identifying Escherichia coli amongst other Gram positive and negative bacteria including Klebsiella pneumoniae, Staphylococcus aureus, and Bacillus subtilis. Additionally, this assay is evaluated for analyzing 31 clinically obtained urine samples, demonstrating a clinical sensitivity of 100% and specify of 100%. When challenging this assay with nine clinical blood cultures, E. coli-positive and E. coli-negative samples can be distinguished with a probability of p < 0.001.},
}
@article {pmid37087254,
year = {2023},
author = {Li, P and Huang, Y and Zhu, H and Chen, J and Ren, G and Jiang, D and Liu, C},
title = {Authentication, chemical profiles analysis, and quality evaluation of corn silk via DNA barcoding and UPLC-LTQ/Orbitrap MS chemical profiling.},
journal = {Food research international (Ottawa, Ont.)},
volume = {167},
number = {},
pages = {112667},
doi = {10.1016/j.foodres.2023.112667},
pmid = {37087254},
issn = {1873-7145},
mesh = {Chromatography, High Pressure Liquid/methods ; *DNA Barcoding, Taxonomic ; Gas Chromatography-Mass Spectrometry ; *Zea mays/genetics ; Plant Structures/chemistry/genetics ; },
abstract = {Corn silk is commonly consumed in teas, food ingredients, and herbal medicines. Several varieties of corn silk are grown in different habitats in China. However, as information regarding their phytochemistry and genetic diversity is limited, their medicinal potential has not been utilized thoroughly. Thus, we aimed to use a combination of DNA barcoding based on specific primer ITSC sequences and ultra-performance liquid chromatography coupled with linear trap quadrupole-Orbitrap mass spectrometry (UPLC-LTQ/Orbitrap MS) approach for identifying and evaluating corn silk. ITSC barcoding helped us to identify that 52 samples could be classified into 7 groups of corn silk varieties, but the widely used nrITS and psbA-trnH barcodes failed to identify these varieties. UPLC-LTQ/Orbitrap MS was used to study the components in alcohol extracts derived from different corn silk varieties, and the detected chemical components were analyzed via bioinformatics techniques. We proposed 199 components using untargeted UPLC-LTQ/Orbitrap MS-based metabolomics analysis and identified 67 components. PCA and OPLS-DA analysis revealed two distinct chemotypes by selecting 27 components that could act as difference indicators. KEGG analysis showed that the 199 components were enriched in 12 metabolic pathways. The results showed that corn silk is rich in many types of chemicals and DNA barcoding is better than UPLC-LTQ/Orbitrap MS in distinguishing the differences between different varieties of corn silk. Our findings provide new insights into the chemical and molecular characteristics of different varieties of corn silk, which play a crucial role in the utilization of corn silk resources.},
}
@article {pmid37079642,
year = {2023},
author = {Mascarello, M and Lachenaud, O and Amalfi, M and Smets, E and Hardy, OJ and Beeckman, H and Janssens, SB},
title = {Genetic characterization of a group of commercial African timber species: From genomics to barcoding.},
journal = {PloS one},
volume = {18},
number = {4},
pages = {e0284732},
pmid = {37079642},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Ecosystem ; Genomics ; Forests ; *Fabaceae ; Africa, Central ; },
abstract = {In the last decades, illegal logging has posed a serious threat for the integrity of forest ecosystems and for biodiversity conservation in tropical Africa. Although international treaties and regulatory plans have been implemented to reduce illegal logging, much of the total timber volume is harvested and traded illegally from tropical African forest regions. As a result, the development and the application of analytical tools to enhance the traceability and the identification of wood and related products is critical to enforce international regulations. Among available techniques, DNA barcoding is a promising approach for the molecular identification of plant species. However, although it has been used successfully for the discrimination of animal species, no set of genetic markers is available for the universal identification of plant species. In this work, we firstly characterized the genetic diversity of 17 highly-valuable African timber species from five genera (Afzelia, Guibourtia, Leplea, Milicia, Tieghemella) across their distribution ranges in West and Central Africa using the genome skimming approach in order to reconstruct their chloroplast genomes and nuclear ribosomal DNA. Next, we identified single-nucleotide polymorphisms (SNPs) for the discrimination of closely-related species. In this way, we successfully developed and tested novel species-specific genetic barcodes for species identification.},
}
@article {pmid37079631,
year = {2023},
author = {van Valkenburg, JLCH and Osborne, BA and Westenberg, M},
title = {The large Gunnera's (G. tinctoria and G. manicata) in Europe in relation to EU regulation 1143/2014.},
journal = {PloS one},
volume = {18},
number = {4},
pages = {e0284665},
pmid = {37079631},
issn = {1932-6203},
mesh = {*Plants ; *Seeds ; Europe ; Dietary Supplements ; },
abstract = {Incorrect labelling of plants in the horticultural trade and misidentification is widespread. For the inspection services of the EU member states, correct identification of G. tinctoria has become important since the species was added to the List of Union concern in accordance with EU regulation 1143/2014 in August 2017. In the horticultural trade Gunnera plants are generally of modest dimensions and rarely flowering, so that the major distinguishing morphological characters for the identification of the two large species, G. tinctoria and G. manicata, are missing. As G. tinctoria is included in the EU regulation, its trade is prohibited, although the closely related species, G. manicata is not included on the list. Given that it is often difficult to distinguish between these two large herbaceous species using morphological attributes we used standard chloroplast DNA barcode markers, supplemented at a later stage by ITS markers. Plant material of putative G. tinctoria or G. manicata was obtained from the native and introduced range, both from "wild" sources, botanical gardens, and the horticultural trade. In western Europe plants circulating in the horticultural trade turned out to be predominantly G. tinctoria, with only one plant in cultivation identified as true G. manicata and the G. manicata found in botanical gardens was a hybrid recently described as G. x cryptica.},
}
@article {pmid37079527,
year = {2023},
author = {Fitzmeyer, EA and Gallichotte, EN and Ebel, GD},
title = {Scanning barcodes: A way to explore viral populations.},
journal = {PLoS pathogens},
volume = {19},
number = {4},
pages = {e1011291},
pmid = {37079527},
issn = {1553-7374},
support = {R01 AI067380/AI/NIAID NIH HHS/United States ; T32 AI162691/AI/NIAID NIH HHS/United States ; },
}
@article {pmid37079427,
year = {2023},
author = {Shmilovich, K and Chen, B and Karaletsos, T and Sultan, MM},
title = {DEL-Dock: Molecular Docking-Enabled Modeling of DNA-Encoded Libraries.},
journal = {Journal of chemical information and modeling},
volume = {63},
number = {9},
pages = {2719-2727},
doi = {10.1021/acs.jcim.2c01608},
pmid = {37079427},
issn = {1549-960X},
mesh = {Molecular Docking Simulation ; Ligands ; Models, Molecular ; *Proteins/chemistry ; *DNA/chemistry ; Protein Binding ; },
abstract = {DNA-encoded library (DEL) technology has enabled significant advances in hit identification by enabling efficient testing of combinatorially generated molecular libraries. DEL screens measure protein binding affinity though sequencing reads of molecules tagged with unique DNA barcodes that survive a series of selection experiments. Computational models have been deployed to learn the latent binding affinities that are correlated to the sequenced count data; however, this correlation is often obfuscated by various sources of noise introduced in its complicated data-generation process. In order to denoise DEL count data and screen for molecules with good binding affinity, computational models require the correct assumptions in their modeling structure to capture the correct signals underlying the data. Recent advances in DEL models have focused on probabilistic formulations of count data, but existing approaches have thus far been limited to only utilizing 2-D molecule-level representations. We introduce a new paradigm, DEL-Dock, that combines ligand-based descriptors with 3-D spatial information from docked protein-ligand complexes. 3-D spatial information allows our model to learn over the actual binding modality rather than using only structure-based information of the ligand. We show that our model is capable of effectively denoising DEL count data to predict molecule enrichment scores that are better correlated with experimental binding affinity measurements compared to prior works. Moreover, by learning over a collection of docked poses we demonstrate that our model, trained only on DEL data, implicitly learns to perform good docking pose selection without requiring external supervision from expensive-to-source protein crystal structures.},
}
@article {pmid37077311,
year = {2023},
author = {Wang, P and Bai, J and Li, X and Liu, T and Yan, Y and Yang, Y and Li, H},
title = {Phylogenetic relationship and comparative analysis of the main Bupleuri Radix species in China.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15157},
pmid = {37077311},
issn = {2167-8359},
mesh = {Humans ; Phylogeny ; *Medicine, Chinese Traditional ; Photosynthesis ; *Bupleurum/genetics ; China ; },
abstract = {BACKGROUND: Bupleuri Radix (Chaihu) is a famous traditional Chinese medicine derived from Bupleurum, Apiaceae. The origin of cultivated Chaihu germplasm in China is unclear, which has led to unstable Chaihu quality. In this study, we reconstructed the phylogeny of the main Chaihu germplasm species in China and identified potential molecular markers to authenticate its origin.<br><br>METHODS: Three Bupleurum species (eight individuals), B. bicaule, B. chinense, and B. scorzonerifolium, were selected for genome skimming. Published genomes from B. falcatum and B. marginatum var. stenophyllum were used for comparative analysis.<br><br>RESULTS: Sequences of the complete plastid genomes were conserved with 113 identical genes ranging from 155,540 to 155,866 bp in length. Phylogenetic reconstruction based on complete plastid genomes resolved intrageneric relationships of the five Bupleurum species with high support. Conflicts between the plastid and nuclear phylogenies were observed, which were mainly ascribed to introgressive hybridization. Comparative analysis showed that noncoding regions of the plastomes had most of the variable sequences. Eight regions (atpF-atpH, petN-psbM, rps16-psbK, petA-psbJ, ndhC-trnV/UAC and ycf1) had high divergence values in Bupleurum species and could be promising DNA barcodes for Chaihu authentication. A total of seven polymorphic cpSSRs and 438 polymorphic nSSRs were detected across the five Chaihu germplasms. Three photosynthesis-related genes were under positive selection, of which accD reflected the adaptation fingerprint of B. chinense to different ecological habitats. Our study provides valuable genetic information for phylogenetic investigation, germplasm authentication, and molecular breeding of Chaihu species.},
}
@article {pmid37074875,
year = {2023},
author = {Stone, D and Meumann, N and Kuhlmann, AS and Peterson, CW and Xie, H and Roychoudhury, P and Loprieno, MA and Vu, XK and Strongin, DE and Kenkel, EJ and Haick, A and Stensland, L and Obenza, WM and Parrott, J and Nelson, V and Murnane, RD and Huang, ML and Aubert, M and Kiem, HP and Büning, H and Jerome, KR},
title = {A multiplexed barcode approach to simultaneously evaluate gene delivery by adeno-associated virus capsid variants in nonhuman primates.},
journal = {Hepatology communications},
volume = {7},
number = {2},
pages = {e0009},
pmid = {37074875},
issn = {2471-254X},
support = {P30 AI027757/AI/NIAID NIH HHS/United States ; P30 CA015704/CA/NCI NIH HHS/United States ; UM1 AI126623/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Mice ; Female ; Male ; Humans ; *Capsid/metabolism ; *Dependovirus/genetics/metabolism ; Tissue Distribution ; Macaca mulatta/genetics/metabolism ; Capsid Proteins/genetics/metabolism ; Genetic Therapy/methods ; },
abstract = {BACKGROUND AND AIMS: Adeno-associated virus (AAV) vectors are widely used to deliver therapeutic transgenes to distinct tissues, including the liver. Vectors based on naturally occurring AAV serotypes as well as vectors using engineered capsids have shown variations in tissue tropism and level of transduction between different mouse models. Moreover, results obtained in rodents frequently lack translatability into large animal studies. In light of the increasing interest in AAV vectors for human gene therapy, an increasing number of studies are being performed in nonhuman primates. To keep animal numbers to a minimum and thus optimize the process of AAV capsid selection, we developed a multiplex barcoding approach to simultaneously evaluate the in vivo vector performance for a set of serotypes and capsid-engineered AAV vectors across multiple organs.<br><br>APPROACH AND RESULTS: Vector biodistribution and transgene expression were assessed by quantitative PCR, quantitative reverse transcription PCR, vector DNA amplicon Illumina sequencing and vRNAseq in male and female rhesus macaques simultaneously dosed with a mixture of barcoded naturally occurring or engineered AAV vectors encoding the same transgene. As expected, our findings show animal-to-animal variation in both the biodistribution and tissue transduction pattern, which was partly influenced by each animal's distinctive serological status.<br><br>CONCLUSIONS: This method offers a robust approach to AAV vector optimization that can be used to identify and validate AAV vectors for gene delivery to potentially any anatomical site or cell type.},
}
@article {pmid37074171,
year = {2023},
author = {Yu, L and Li, T and Li, H and Ma, M and Li, L and Lin, S},
title = {In Situ Molecular Ecological Analyses Illuminate Distinct Factors Regulating Formation and Demise of a Harmful Dinoflagellate Bloom.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0515722},
pmid = {37074171},
issn = {2165-0497},
mesh = {Humans ; *Dinoflagellida/genetics ; Ecosystem ; Harmful Algal Bloom ; Plankton ; *Diatoms/genetics ; *Flavobacteriaceae ; },
abstract = {The development and demise of a harmful algal bloom (HAB) are generally regulated by multiple processes; identifying specific critical drivers for a specific bloom is important yet challenging. Here, we conducted a whole-assemblage molecular ecological study on a dinoflagellate bloom to address the hypothesis that energy and nutrient acquisition, defense against grazing and microbial attacks, and sexual reproduction are critical to the rise and demise of the bloom. Microscopic and molecular analyses identified the bloom-causing species as Karenia longicanalis and showed that the ciliate Strombidinopsis sp. was dominant in a nonbloom plankton community, whereas the diatom Chaetoceros sp. dominated the after-bloom community, along with remarkable shifts in the community structure for both eukaryotes and prokaryotes. Metatranscriptomic analysis indicated that heightened energy and nutrient acquisition in K. longicanalis significantly contributed to bloom development. In contrast, active grazing by the ciliate Strombidinopsis sp. and attacks by algicidal bacteria (Rhodobacteracea, Cryomorphaceae, and Rhodobacteracea) and viruses prevented (at nonbloom stage) or collapsed the bloom (in after-bloom stage). Additionally, nutrition competition by the Chaetoceros diatoms plausibly contributed to bloom demise. The findings suggest the importance of energy and nutrients in promoting this K. longicanalis bloom and the failure of antimicrobial defense and competition of diatoms as the major bloom suppressor and terminator. This study provides novel insights into bloom-regulating mechanisms and the first transcriptomic data set of K. longicanalis, which will be a valuable resource and essential foundation for further elucidation of bloom regulators of this and related species of Kareniaceae in the future. IMPORTANCE HABs have increasingly occurred and impacted human health, aquatic ecosystems, and coastal economies. Despite great efforts, the factors that drive the development and termination of a bloom are poorly understood, largely due to inadequate in situ data about the physiology and metabolism of the causal species and the community. Using an integrative molecular ecological approach, we determined that heightened energy and nutrient acquisition promoted the bloom, while resource allocation in defense and failure to defend against grazing and microbial attacks likely prevented or terminated the bloom. Our findings reveal the differential roles of multiple abiotic and biotic environmental factors in driving the formation or demise of a toxic dinoflagellate bloom, suggesting the importance of a balanced biodiverse ecosystem in preventing a dinoflagellate bloom. The study also demonstrates the power of whole-assemblage metatranscriptomics coupled to DNA barcoding in illuminating plankton ecological processes and the underlying species and functional diversities.},
}
@article {pmid37070089,
year = {2023},
author = {Courtot, &#xc9; and Boisseau, M and Dhorne-Pollet, S and Serreau, D and Gesbert, A and Reigner, F and Basiaga, M and Kuzmina, T and Lluch, J and Annonay, G and Kuchly, C and Diekmann, I and Krücken, J and von Samson-Himmelstjerna, G and Mach, N and Sallé, G},
title = {Comparison of two molecular barcodes for the study of equine strongylid communities with amplicon sequencing.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15124},
pmid = {37070089},
issn = {2167-8359},
mesh = {Animals ; Horses/genetics ; DNA, Ribosomal/genetics ; *DNA Barcoding, Taxonomic/methods ; Polymerase Chain Reaction ; },
abstract = {Basic knowledge on the biology and epidemiology of equine strongylid species still needs to be improved to contribute to the design of better parasite control strategies. Nemabiome metabarcoding is a convenient tool to quantify and identify species in bulk samples that could overcome the hurdle that cyathostomin morphological identification represents. To date, this approach has relied on the internal transcribed spacer 2 (ITS-2) of the ribosomal RNA gene, with a limited investigation of its predictive performance for cyathostomin communities. Using DNA pools of single cyathostomin worms, this study aimed to provide the first elements to compare performances of the ITS-2 and a cytochrome c oxidase subunit I (COI) barcode newly developed in this study. Barcode predictive abilities were compared across various mock community compositions of two, five and 11 individuals from distinct species. The amplification bias of each barcode was estimated. Results were also compared between various types of biological samples, i.e., eggs, infective larvae or adults. Bioinformatic parameters were chosen to yield the closest representation of the cyathostomin community for each barcode, underscoring the need for communities of known composition for metabarcoding purposes. Overall, the proposed COI barcode was suboptimal relative to the ITS-2 rDNA region, because of PCR amplification biases, reduced sensitivity and higher divergence from the expected community composition. Metabarcoding yielded consistent community composition across the three sample types. However, imperfect correlations were found between relative abundances from infective larvae and other life-stages for Cylicostephanus species using the ITS-2 barcode. While the results remain limited by the considered biological material, they suggest that additional improvements are needed for both the ITS-2 and COI barcodes.},
}
@article {pmid37069924,
year = {2023},
author = {Lv, SY and Ye, XY and Li, ZH and Ma, PF and Li, DZ},
title = {Testing complete plastomes and nuclear ribosomal DNA sequences for species identification in a taxonomically difficult bamboo genus Fargesia.},
journal = {Plant diversity},
volume = {45},
number = {2},
pages = {147-155},
pmid = {37069924},
issn = {2468-2659},
abstract = {Fargesia, the largest genus within the temperate bamboo tribe Arundinarieae, has more than 90 species mainly distributed in the mountains of Southwest China. The Fargesia bamboos are important components of the subalpine forest ecosystems that provide food and habitat for many endangered animals, including the giant panda. However, species-level identification of Fargesia is difficult. Moreover, the rapid radiation and slow molecular evolutionary rate of Fargesia pose a significant challenge to using DNA barcoding with standard plant barcodes (rbcL, matK, and ITS) in bamboos. With progress in the sequencing technologies, complete plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) sequences have been proposed as organelle barcodes for species identification; however, these have not been tested in bamboos. We collected 196 individuals representing 62 species of Fargesia to comprehensively evaluate the discriminatory power of plastomes and nrDNA sequences compared to standard barcodes. Our analysis indicates that complete plastomes have substantially higher discriminatory power (28.6%) than standard barcodes (5.7%), whereas nrDNA sequences show a moderate improvement (65.4%) compared to ITS (47.2%). We also found that nuclear markers performed better than plastid markers, and ITS alone had higher discriminatory power than complete plastomes. The study also demonstrated that plastomes and nrDNA sequences can contribute to intrageneric phylogenetic resolution in Fargesia. However, neither of these sequences were able to discriminate all the sampled species, and therefore, more nuclear markers need to be identified.},
}
@article {pmid37071925,
year = {2023},
author = {Poggi, JD and Conery, C and Mathewson, A and Bolton, D and Lovell, R and Harrington, LC and Notarangelo, M},
title = {Jamestown Canyon virus (Bunyavirales: Peribunyaviridae) vector ecology in a focus of human transmission in New Hampshire, USA.},
journal = {Journal of medical entomology},
volume = {60},
number = {4},
pages = {778-788},
doi = {10.1093/jme/tjad046},
pmid = {37071925},
issn = {1938-2928},
support = {U01 CK000509/CK/NCEZID CDC HHS/United States ; },
mesh = {Humans ; Animals ; *Encephalitis Virus, California ; *Deer ; Carbon Dioxide ; New Hampshire ; Mosquito Vectors ; *Culicidae ; *Anopheles ; *Ochlerotatus ; *Bunyaviridae Infections ; *Aedes ; },
abstract = {Jamestown Canyon virus disease (JCVD) is a potentially neuroinvasive condition caused by the arbovirus Jamestown Canyon virus (JCV). Human cases of JCVD have increased in New Hampshire (NH) over the past decade, but vector surveillance is limited by funding and person power. We conducted mosquito surveillance with a focus on human JCVD cases south central NH during 2021. Routine surveillance with CDC miniature traps baited with CO2 (lights removed) was supplemented by a paired trapping design to test the collection efficiency of octenol, and New Jersey light traps. We performed virus testing, blood meal analysis, and compared morphological identification with DNA barcoding. Over 50,000 mosquitoes were collected representing 28 species. Twelve JCV-positive pools were derived from 6 species of more than 1,600 pools tested. Of those, Aedes excrucians/stimulans (MLE 4.95, Diptera: Culicidae, Walker, 1856, 1848), and Aedes sticticus (MLE 2.02, Meigen, 1838) had the highest JCV infection rates, and Aedes canadensis (MLE 0.13, Theobold, 1901) and Coquillettidia perturbans (0.10, Diptera: Culicidae, Walker, 1856) had the lowest infection rates. One hundred and fifty-one blood meals were matched to a vertebrate host. All putative vectors fed on the amplifying host of JCV, white-tailed deer (36-100% of bloodmeals). Putative vectors that fed on human hosts included Aedes excrucians (8%), Anopheles punctipennis (25%, Diptera: Culicidae, Say, 1823), and Coquillettidia perturbans (51%). CDC traps baited with CO2 were effective for collecting putative vectors. DNA barcoding enhanced morphological identifications of damaged specimens. We present the first ecological overview of JCV vectors in NH.},
}
@article {pmid37069313,
year = {2023},
author = {Sigmund, F and Berezin, O and Beliakova, S and Magerl, B and Drawitsch, M and Piovesan, A and Gonçalves, F and Bodea, SV and Winkler, S and Bousraou, Z and Grosshauser, M and Samara, E and Pujol-Martí, J and Schädler, S and So, C and Irsen, S and Walch, A and Kofler, F and Piraud, M and Kornfeld, J and Briggman, K and Westmeyer, GG},
title = {Genetically encoded barcodes for correlative volume electron microscopy.},
journal = {Nature biotechnology},
volume = {41},
number = {12},
pages = {1734-1745},
pmid = {37069313},
issn = {1546-1696},
support = {ERC-COG 865710//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; LF4D//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Animals ; Mice ; *Volume Electron Microscopy ; Microscopy, Electron, Scanning ; *Drosophila/genetics ; Neurons ; Microscopy, Fluorescence/methods ; },
abstract = {While genetically encoded reporters are common for fluorescence microscopy, equivalent multiplexable gene reporters for electron microscopy (EM) are still scarce. Here, by installing a variable number of fixation-stable metal-interacting moieties in the lumen of encapsulin nanocompartments of different sizes, we developed a suite of spherically symmetric and concentric barcodes (EMcapsulins) that are readable by standard EM techniques. Six classes of EMcapsulins could be automatically segmented and differentiated. The coding capacity was further increased by arranging several EMcapsulins into distinct patterns via a set of rigid spacers of variable length. Fluorescent EMcapsulins were expressed to monitor subcellular structures in light and EM. Neuronal expression in Drosophila and mouse brains enabled the automatic identification of genetically defined cells in EM. EMcapsulins are compatible with transmission EM, scanning EM and focused ion beam scanning EM. The expandable palette of genetically controlled EM-readable barcodes can augment anatomical EM images with multiplexed gene expression maps.},
}
@article {pmid37069311,
year = {2023},
author = {Parvez, S and Brandt, ZJ and Peterson, RT},
title = {Large-scale F0 CRISPR screens in vivo using MIC-Drop.},
journal = {Nature protocols},
volume = {18},
number = {6},
pages = {1841-1865},
pmid = {37069311},
issn = {1750-2799},
support = {K99 HG012593/HG/NHGRI NIH HHS/United States ; R01 GM134069/GM/NIGMS NIH HHS/United States ; T32 HG008962/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; *Zebrafish/genetics ; *CRISPR-Cas Systems/genetics ; Retrospective Studies ; Genetic Testing ; Phenotype ; },
abstract = {The zebrafish is a powerful model system for studying animal development, for modeling genetic diseases, and for large-scale in vivo functional genetics. Because of its ease of use and its high efficiency in targeted gene perturbation, CRISPR-Cas9 has recently gained prominence as the tool of choice for genetic manipulation in zebrafish. However, scaling up the technique for high-throughput in vivo functional genetics has been a challenge. We recently developed a method, Multiplexed Intermixed CRISPR Droplets (MIC-Drop), that makes large-scale CRISPR screening in zebrafish possible. Here, we outline the step-by-step protocol for performing functional genetic screens in zebrafish by using MIC-Drop. MIC-Drop uses multiplexed single-guide RNAs to generate biallelic mutations in injected zebrafish embryos, allowing genetic screens to be performed in F0 animals. Combining microfluidics and DNA barcoding enables simultaneous targeting of tens to hundreds of genes from a single injection needle, while also enabling retrospective and rapid identification of the genotype responsible for an observed phenotype. The primary target audiences for MIC-Drop are developmental biologists, zebrafish geneticists, and researchers interested in performing in vivo functional genetic screens in a vertebrate model system. MIC-Drop will also prove useful in the hands of chemical biologists seeking to identify targets of small molecules that cause phenotypic changes in zebrafish. By using MIC-Drop, a typical screen of 100 genes can be conducted within 2-3 weeks by a single user.},
}
@article {pmid37069150,
year = {2023},
author = {Urbanus, J and Cosgrove, J and Beltman, JB and Elhanati, Y and Moral, RA and Conrad, C and van Heijst, JW and Tubeuf, E and Velds, A and Kok, L and Merle, C and Magnusson, JP and Guyonnet, L and Frisén, J and Fre, S and Walczak, AM and Mora, T and Jacobs, H and Schumacher, TN and Perié, L},
title = {DRAG in situ barcoding reveals an increased number of HSPCs contributing to myelopoiesis with age.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {2184},
pmid = {37069150},
issn = {2041-1723},
support = {P30 CA008748/CA/NCI NIH HHS/United States ; },
mesh = {Adult ; Humans ; Aged ; *Myelopoiesis/genetics ; *Hematopoietic Stem Cells ; Bone Marrow ; Bone Marrow Cells ; Myeloid Cells ; },
abstract = {Ageing is associated with changes in the cellular composition of the immune system. During ageing, hematopoietic stem and progenitor cells (HSPCs) that produce immune cells are thought to decline in their regenerative capacity. However, HSPC function has been mostly assessed using transplantation assays, and it remains unclear how HSPCs age in the native bone marrow niche. To address this issue, we present an in situ single cell lineage tracing technology to quantify the clonal composition and cell production of single cells in their native niche. Our results demonstrate that a pool of HSPCs with unequal output maintains myelopoiesis through overlapping waves of cell production throughout adult life. During ageing, the increased frequency of myeloid cells is explained by greater numbers of HSPCs contributing to myelopoiesis rather than the increased myeloid output of individual HSPCs. Strikingly, the myeloid output of HSPCs remains constant over time despite accumulating significant transcriptomic changes throughout adulthood. Together, these results show that, unlike emergency myelopoiesis post-transplantation, aged HSPCs in their native microenvironment do not functionally decline in their regenerative capacity.},
}
@article {pmid37068158,
year = {2023},
author = {Kuo, CW and Smith, AM},
title = {Digital and Absolute Assays for Low Abundance Molecular Biomarkers.},
journal = {Accounts of chemical research},
volume = {56},
number = {9},
pages = {1031-1042},
pmid = {37068158},
issn = {1520-4898},
support = {R01 CA227699/CA/NCI NIH HHS/United States ; R01 EB032249/EB/NIBIB NIH HHS/United States ; R01 EB032725/EB/NIBIB NIH HHS/United States ; R01 GM131272/GM/NIGMS NIH HHS/United States ; },
mesh = {*Nucleic Acids ; Proteins ; Coloring Agents ; Microfluidics ; Biomarkers ; },
abstract = {There has been a recent surge of advances in biomolecular assays based on the measurement of discrete molecular targets as opposed to signals averaged across molecular ensembles. Many of these "digital" assay designs derive from now-mature technologies involving single-molecule imaging and microfluidics and provide an assortment of new modalities to quantify nucleic acids and proteins in biospecimens such as blood and tissue homogenates. A primary new benefit is the robust detection of trace analytes at attomolar to femtomolar concentrations for which many ensemble assays cannot distinguish signals above noise levels. In addition, multiple biomolecules can be differentiated within a mixture using optical barcodes, with much faster and simpler readouts compared with sequencing methods. In ideal digital assays, signals should, in theory, further represent absolute molecular counts, rather than relative levels, eliminating the need for calibration standards that are the mainstay of typical assays. Several digital assay platforms have now been commercialized but challenges hinder the adoption and diversification of these new formats, as there are broad needs to balance sensitivity and dynamic range of detection, increase analyte multiplexing, improve sample throughput, and reduce cost. Our lab and others have developed technologies to address these challenges by redesigning molecular probes and labels, improving molecular transport within detection focal volumes, and applying solution-based readout methods in flow.This Account describes the principles, formats, and design constraints of digital biomolecular assays that apply optical labels toward the goal of simple and routine target counting that may ultimately approach absolute readout standards. The primary challenges can be understood from fundamental concepts in thermodynamics and kinetics of association reactions, mass transport, and discrete statistics. Major advances include (1) new inorganic nanocrystal probes for more robust counting compared with dyes, (2) diverse molecular amplification tools that endow attachment of numerous labels to single targets, (3) specialized surfaces with patterned features for electromagnetic coupling to labels for signal amplification, (4) surface capture enhancement methods to concentrate targets through disruption of diffusion depletion zones, and (5) flow counting in which analytes are rapidly counted in solution without pull-down to a surface. Further progress and integration of these tools for biomolecular counting could improve the precision of laboratory measurements in life sciences research and benefit clinical diagnostic assays for low abundance biomarkers in limiting biospecimen volumes that are out of reach of traditional ensemble-level bioassays.},
}
@article {pmid37066158,
year = {2023},
author = {Russell, AJC and Weir, JA and Nadaf, NM and Shabet, M and Kumar, V and Kambhampati, S and Raichur, R and Marrero, GJ and Liu, S and Balderrama, KS and Vanderburg, CR and Shanmugam, V and Tian, L and Wu, CJ and Yoon, CH and Macosko, EZ and Chen, F},
title = {Slide-tags: scalable, single-nucleus barcoding for multi-modal spatial genomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.04.01.535228},
pmid = {37066158},
issn = {2692-8205},
support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; T32 HG002295/HG/NHGRI NIH HHS/United States ; },
abstract = {Recent technological innovations have enabled the high-throughput quantification of gene expression and epigenetic regulation within individual cells, transforming our understanding of how complex tissues are constructed. Missing from these measurements, however, is the ability to routinely and easily spatially localise these profiled cells. We developed a strategy, Slide-tags, in which single nuclei within an intact tissue section are 'tagged' with spatial barcode oligonucleotides derived from DNA-barcoded beads with known positions. These tagged nuclei can then be used as input into a wide variety of single-nucleus profiling assays. Application of Slide-tags to the mouse hippocampus positioned nuclei at less than 10 micron spatial resolution, and delivered whole-transcriptome data that was indistinguishable in quality from ordinary snRNA-seq. To demonstrate that Slide-tags can be applied to a wide variety of human tissues, we performed the assay on brain, tonsil, and melanoma. We revealed cell-type-specific spatially varying gene expression across cortical layers and spatially contextualised receptor-ligand interactions driving B-cell maturation in lymphoid tissue. A major benefit of Slide-tags is that it is easily adaptable to virtually any single-cell measurement technology. As proof of principle, we performed multiomic measurements of open chromatin, RNA, and T-cell receptor sequences in the same cells from metastatic melanoma. We identified spatially distinct tumour subpopulations to be differentially infiltrated by an expanded T-cell clone and undergoing cell state transition driven by spatially clustered accessible transcription factor motifs. Slide-tags offers a universal platform for importing the compendium of established single-cell measurements into the spatial genomics repertoire.},
}
@article {pmid37066064,
year = {2023},
author = {Chen, W and Miao, K and Liu, Y and Zhang, J and Zhao, Y and Hu, D and Wang, P and Li, P and Chang, Q and Hu, C},
title = {Using DNA barcoding and field surveys to guide wildlife management at Nanjing Lukou International Airport, China.},
journal = {Ecology and evolution},
volume = {13},
number = {4},
pages = {e10005},
pmid = {37066064},
issn = {2045-7758},
abstract = {The conflicts between wildlife and aircraft have increased due to the development of the aviation industry. While many studies have quantified the relative hazards of wildlife to aircraft, few studies have combined DNA barcoding techniques with field surveys of bird communities in different habitats to reveal the exact species involved in bird strikes and how the habitat heterogeneity around airports affects bird communities and even the occurrence of bird strikes. Taking Nanjing Lukou International Airport in China as an example, based on the DNA barcoding technology and detailed field research, we establish the most commonly struck species, which can help managers identify the level of hazard and lead to meaningful reductions in hazards and costs associated with bird strike. The investigation of bird communities showed that there were 149 bird species recorded within an 8 km radius. There were 89, 88, 61, and 88 species in the woodland, wetland, farmland, and urban area, respectively. In total, 303 samples identified 82 species representing 13 orders and 32 family of birds from bird strike cases, of which 24 species were not found in the field survey. Passeriformes were the most common order of birds identified, with 43 species represented in 167 identifications. Skylark, Thrush, Shrike, Lapwing, and Swallow were most likely to cause damage or substantial damage to aircraft when strikes occurred. In addition to birds, we identified 69 bats individuals (accounting for 22.77%) using DNA barcoding. The Bray-Curtis similarity analysis revealed that species involved in bird strike had the highest similarity with urban area. Our findings suggest that policymakers should pay more attention to managing the wetlands and urban areas surrounding the airport. These findings imply that DNA barcoding can add to the environmental monitoring in airports, which can facilitate hazard management and improve air safety.},
}
@article {pmid37065693,
year = {2023},
author = {Beckmann, LM and Soto-Angel, JJ and Hosia, A and Martell, L},
title = {Odd family reunion: DNA barcoding reveals unexpected relationship between three hydrozoan species.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15118},
pmid = {37065693},
issn = {2167-8359},
mesh = {Humans ; Animals ; *Hydrozoa/genetics ; DNA Barcoding, Taxonomic ; Phylogeny ; Biological Evolution ; Life Cycle Stages/genetics ; },
abstract = {Knowledge of life histories is crucial for understanding ecological and evolutionary processes, but for many hydrozoan species only incomplete life cycles have been described due to challenges in linking hydromedusae with their polyp stages. Using a combination of DNA barcoding, morphology, and ecological information, we describe for the first time the polyp stage of Halopsis ocellata Agassiz, 1865 and re-describe that of Mitrocomella polydiademata (Romanes, 1876). Campanulinid hydroids referable to Lafoeina tenuis Sars, 1874 and collected in the same biogeographic region as the type locality of this species are shown to be the polyp stage of these two mitrocomid hydromedusae. The nominal species L. tenuis thus is a species complex that includes the polyp stage of medusae belonging to at least two genera currently placed in a different family. Consistent morphological and ecological differences were found between the polyps linked to each of these two hydromedusae, but molecular results suggest that yet other species may have morphologically similar hydroids. Polyps morphologically identified to L. tenuis are therefore better referred to as Lafoeina tenuis-type until further associations are resolved, particularly when occurring outside of the area of distribution of H. ocellata and M. polydiademata. Molecular identification integrated with traditional taxonomy is confirmed as an effective approach to link inconspicuous stages of marine invertebrates with hitherto unknown life cycles, especially in often-overlooked taxa. Disentangling the relationships between L. tenuis, H. ocellata, and M. polydiademata lays the ground for future research aimed at resolving the taxonomy and systematics of the enigmatic families Mitrocomidae and Campanulinidae.},
}
@article {pmid37065158,
year = {2023},
author = {Kool, J and Tymchenko, L and Shetty, SA and Fuentes, S},
title = {Reducing bias in microbiome research: Comparing methods from sample collection to sequencing.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1094800},
pmid = {37065158},
issn = {1664-302X},
abstract = {BACKGROUND: Microbiota profiles are strongly influenced by many technical aspects that impact the ability of researchers to compare results. To investigate and identify potential biases introduced by technical variations, we compared several approaches throughout the entire workflow of a microbiome study, from sample collection to sequencing, using commercially available mock communities (from bacterial strains as well as from DNA) and multiple human fecal samples, including a large set of positive controls created as a random mix of several participant samples.<br><br>METHODS: Human fecal material was sampled, and aliquots were used to test two commercially available stabilization solutions (OMNIgene&#xb7;GUT and Zymo Research) in comparison to samples frozen immediately upon collection. In addition, the methodology for DNA extraction, input of DNA, or the number of PCR cycles were analyzed. Furthermore, to investigate the potential batch effects in DNA extraction, sequencing, and barcoding, we included 139 positive controls.<br><br>RESULTS: Samples preserved in both the stabilization buffers limited the overgrowth of Enterobacteriaceae when compared to unpreserved samples stored at room temperature (RT). These stabilized samples stored at RT were different from immediately frozen samples, where the relative abundance of Bacteroidota was higher and Actinobacteriota and Firmicutes were lower. As reported previously, the method used for cell disruption was a major contributor to variation in microbiota composition. In addition, a high number of cycles during PCR lead to an increase in contaminants detected in the negative controls. The DNA extraction had a significant impact on the microbial composition, also observed with the use of different Illumina barcodes during library preparation and sequencing, while no batch effect was observed in replicate runs.<br><br>CONCLUSION: Our study reaffirms the importance of the mechanical cell disruption method and immediate frozen storage as critical aspects in fecal microbiota studies. A comparison of storage conditions revealed that the bias was limited in RT samples preserved in stabilization systems, and these may be a suitable compromise when logistics are challenging due to the size or location of a study. Moreover, to reduce the effect of contaminants in fecal microbiota profiling studies, we suggest the use of ~125 pg input DNA and 25 PCR cycles as optimal parameters during library preparation.},
}
@article {pmid37064523,
year = {2023},
author = {Lee, D and Do, TD and Baek, JW and Mun, MH and An, HE and Kim, CB},
title = {A case study on DNA barcoding for pet food mislabeling in South Korea.},
journal = {Italian journal of food safety},
volume = {12},
number = {1},
pages = {11074},
pmid = {37064523},
issn = {2239-7132},
abstract = {Due to the close relationship between pets and humans, pet owners are highly invested in proper diets for their pets. Even though pet food mislabeling is concerning, there are few studies on this topic. This study investigated pet food mislabeling in South Korea's market based on DNA barcoding. In total, 10 pet food products were purchased, and 200 sequences of the partial Cytochrome c oxidase subunit 1 (COI) gene were generated from clones of the samples. The obtained sequences were compared to available public databases to identify species present in the ingredients. The data analyses showed that the labeled species were consistent with species detected by COI sequences in 6 of the products. However, the expected species were not detected in 4 products, revealing possible mislabeling in these samples. Our findings indicated that DNA barcoding might represent a promising tool to detect pet food mislabeling.},
}
@article {pmid37063184,
year = {2023},
author = {Li, CJ and Xie, XT and Liu, HX and Wang, RN and Li, DZ},
title = {Plastome evolution in the East Asian lobelias (Lobelioideae) using phylogenomic and comparative analyses.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1144406},
pmid = {37063184},
issn = {1664-462X},
abstract = {Lobelia species, as rich source of the alkaloid lobeline which has been shown to have important biological activity, have been used in folk medicine throughout East Asia to treat various diseases. However, Lobelia is a complex and varied genus in East Asia and is thus difficult to identify. Genomic resources would aid identification, however the availability of such information is poor, preventing a clear understanding of their evolutionary history from being established. To close this gap in the available genomic data, in this study, 17 plastomes of East Asian lobelias were newly sequenced and assembled. Although the plastomes of Lobelia sect. Hypsela, L. sect. Speirema, and L. sect. Rhynchopetalum shared the gene structure, the inverted repeat (IR)/large single copy (LSC) boundaries, genome size, and the number of repeats were variable, indicating the non-conservative nature of plastome evolution within these sections. However, the genomes of the Lobelia sect. Delostemon and L. sect. Stenotium showed rearrangements, revealing that these two sections might have undergone different evolutionary histories. We assessed nine hotspot genes and 27-51 simple sequence repeat motifs, which will also serve as valuable DNA barcode regions in future population genetics studies and for the delineation of plant species. Our phylogenetic analysis resolved the evolutionary positions of the five sections in agreement with previous evolutionary trees based on morphological features. Although phylogenetic reconstruction of Lobelioideae based on the rpoC2 gene has rarely been performed, our results indicated that it contains a considerable amount of phylogenetic information and offers great promise for further phylogenetic analysis of Lobelioideae. Our site-specific model identified 173 sites under highly positive selections. The branch-site model exhibited 11 positive selection sites involving four genes in the East Asian branches. These four genes may play critical roles in the adaptation of East Asian taxa to diverse environments. Our study is the first to detect plastome organization, phylogenetic utility, and signatures of positive selection in the plastomes of East Asian lobelias, which will help to further advance taxonomic and evolutionary studies and the utilization of medicinal plant resources.},
}
@article {pmid37062951,
year = {2023},
author = {Sant, P and Rippe, K and Mallm, JP},
title = {Approaches for single-cell RNA sequencing across tissues and cell types.},
journal = {Transcription},
volume = {14},
number = {3-5},
pages = {127-145},
pmid = {37062951},
issn = {2154-1272},
mesh = {*Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; *High-Throughput Nucleotide Sequencing/methods ; Single-Cell Analysis/methods ; RNA/genetics ; },
abstract = {Single-cell sequencing of RNA (scRNA-seq) has advanced our understanding of cellular heterogeneity and signaling in developmental biology and disease. A large number of complementary assays have been developed to profile transcriptomes of individual cells, also in combination with other readouts, such as chromatin accessibility or antibody-based analysis of protein surface markers. As scRNA-seq technologies are advancing fast, it is challenging to establish robust workflows and up-to-date protocols that are best suited to address the large range of research questions. Here, we review scRNA-seq techniques from mRNA end-counting to total RNA in relation to their specific features and outline the necessary sample preparation steps and quality control measures. Based on our experience in dealing with the continuously growing portfolio from the perspective of a central single-cell facility, we aim to provide guidance on how workflows can be best automatized and share our experience in coping with the continuous expansion of scRNA-seq techniques.},
}
@article {pmid37062095,
year = {2023},
author = {Pang, G and Li, X and Ding, M and Jiang, S and Chen, P and Zhao, Z and Gao, R and Song, B and Xu, X and Shen, Q and Cai, FM and Druzhinina, IS},
title = {The distinct plastisphere microbiome in the terrestrial-marine ecotone is a reservoir for putative degraders of petroleum-based polymers.},
journal = {Journal of hazardous materials},
volume = {453},
number = {},
pages = {131399},
doi = {10.1016/j.jhazmat.2023.131399},
pmid = {37062095},
issn = {1873-3336},
mesh = {Polymers ; *Petroleum ; Plastics ; *Ascomycota ; *Microbiota ; Bacteria/genetics ; Biodegradation, Environmental ; },
abstract = {Research into plastic-degrading bacteria and fungi is important for understanding how microorganisms can be used to address the problem of plastic pollution and for developing new approaches to sustainable waste management and bioplastic production. In the present study, we isolated 55 bacterial and 184 fungal strains degrading polycaprolactone (PCL) in plastic waste samples from Dafeng coastal salt marshes, Jiangsu, China. Of these, Jonesia and Streptomyces bacteria also showed potential to degrade other types of petroleum-based polymers. The metabarcoding results proved the existence of plastisphere as a distinct ecological niche regardless of the plastic types where 27 bacterial and 29 fungal amplicon sequence variants (ASVs) were found to be significantly (p < 0.05) enriched, including some belonging to Alternaria (Ascomycota, Fungi) and Pseudomonas (Gammaproteobacteria, Bacteria) that were also mined out by the method of cultivation. Further assembly analyses demonstrated the importance of deterministic processes especially the environmental filtering effect of carbon content and pH on bacteria as well as the carbon and cation content on fungi in shaping the plastisphere communities in this ecosystem. Thus, the unique microbiome of the plastisphere in the terrestrial-marine ecotone is enriched with microorganisms that are potentially capable of utilizing petroleum-based polymers, making it a valuable resource for screening plastic biodegraders.},
}
@article {pmid37060070,
year = {2023},
author = {Li, Y and Sun, Y and Zou, J and Zhong, D and Liu, R and Zhu, C and Li, W and Zhou, Y and Cui, L and Zhou, G and Lu, G and Li, T},
title = {Characterizing the Wolbachia infection in field-collected Culicidae mosquitoes from Hainan Province, China.},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {128},
pmid = {37060070},
issn = {1756-3305},
support = {YSPTZX202004//Research project of Hainan academician innovation platform/ ; 82060379//National Natural Science Foundation of China/ ; 2022NHCTDCKFKT31002//Open Foundation of NHC Key Laboratory of Tropical Disease Control, Hainan Medical University/ ; ZDKJ202003//Major Science and Technology Program of Hainan Province/ ; U19 AI089672/AI/NIAID NIH HHS/United States ; XRC220012//Talent Introduction Fund of Hainan Medical University/ ; 820RC653//Hainan Provincial Natural Science Foundation/ ; },
mesh = {Animals ; Humans ; *Culicidae ; *Wolbachia/genetics ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Mosquito Vectors/genetics ; *Aedes/genetics ; *Culex/genetics ; China/epidemiology ; },
abstract = {BACKGROUND: Mosquitoes are vectors of many pathogens, such as malaria, dengue virus, yellow fever virus, filaria and Japanese encephalitis virus. Wolbachia are capable of inducing a wide range of reproductive abnormalities in their hosts, such as cytoplasmic incompatibility. Wolbachia has been proposed as a tool to modify mosquitoes that are resistant to pathogen infection as an alternative vector control strategy. This study aimed to determine natural Wolbachia infections in different mosquito species across Hainan Province, China.<br><br>METHODS: Adult mosquitoes were collected using light traps, human landing catches and aspirators in five areas in Hainan Province from May 2020 to November 2021. Species were identified based on morphological characteristics, species-specific PCR and DNA barcoding of cox1 assays. Molecular classification of species and phylogenetic analyses of Wolbachia infections were conducted based on the sequences from PCR products of cox1, wsp, 16S rRNA and FtsZ gene segments.<br><br>RESULTS: A total of 413 female adult mosquitoes representing 15 species were identified molecularly and analyzed. Four mosquito species (Aedes albopictus, Culex quinquefasciatus, Armigeres subalbatus and Culex gelidus) were positive for Wolbachia infection. The overall Wolbachia infection rate for all mosquitoes tested in this study was 36.1% but varied among species. Wolbachia types A, B and mixed infections of A&#x2009;&#xd7;&#x2009;B were detected in Ae. albopictus mosquitoes. A total of five wsp haplotypes, six FtsZ haplotypes and six 16S rRNA haplotypes were detected from Wolbachia infections. Phylogenetic tree analysis of wsp sequences classified them into three groups (type A, B and C) of Wolbachia strains compared to two groups each for FtsZ and 16S rRNA sequences. A novel type C Wolbachia strain was detected in Cx. gelidus by both single locus wsp gene and the combination of three genes.<br><br>CONCLUSION: Our study revealed the prevalence and distribution of Wolbachia in mosquitoes from Hainan Province, China. Knowledge of the prevalence and diversity of Wolbachia strains in local mosquito populations will provide part of the baseline information required for current and future Wolbachia-based vector control approaches to be conducted in Hainan Province.},
}
@article {pmid37059915,
year = {2023},
author = {Lear, SK and Lopez, SC and González-Delgado, A and Bhattarai-Kline, S and Shipman, SL},
title = {Temporally resolved transcriptional recording in E. coli DNA using a Retro-Cascorder.},
journal = {Nature protocols},
volume = {18},
number = {6},
pages = {1866-1892},
pmid = {37059915},
issn = {1750-2799},
support = {DP2 GM140917/GM/NIGMS NIH HHS/United States ; },
mesh = {*Escherichia coli/genetics ; *DNA/genetics ; Genomics ; Computational Biology ; CRISPR-Cas Systems ; },
abstract = {Biological signals occur over time in living cells. Yet most current approaches to interrogate biology, particularly gene expression, use destructive techniques that quantify signals only at a single point in time. A recent technological advance, termed the Retro-Cascorder, overcomes this limitation by molecularly logging a record of gene expression events in a temporally organized genomic ledger. The Retro-Cascorder works by converting a transcriptional event into a DNA barcode using a retron reverse transcriptase and then storing that event in a unidirectionally expanding clustered regularly interspaced short palindromic repeats (CRISPR) array via acquisition by CRISPR-Cas integrases. This CRISPR array-based ledger of gene expression can be retrieved at a later point in time by sequencing. Here we describe an implementation of the Retro-Cascorder in which the relative timing of transcriptional events from multiple promoters of interest is recorded chronologically in Escherichia coli populations over multiple days. We detail the molecular components required for this technology, provide a step-by-step guide to generate the recording and retrieve the data by Illumina sequencing, and give instructions for how to use custom software to infer the relative transcriptional timing from the sequencing data. The example recording is generated in 2 d, preparation of sequencing libraries and sequencing can be accomplished in 2-3 d, and analysis of data takes up to several hours. This protocol can be implemented by someone familiar with basic bacterial culture, molecular biology and bioinformatics. Analysis can be minimally run on a personal computer.},
}
@article {pmid37056621,
year = {2023},
author = {Ortiz-Perez, A and Izquierdo-Lozano, C and Meijers, R and Grisoni, F and Albertazzi, L},
title = {Identification of fluorescently-barcoded nanoparticles using machine learning.},
journal = {Nanoscale advances},
volume = {5},
number = {8},
pages = {2307-2317},
pmid = {37056621},
issn = {2516-0230},
abstract = {Barcoding of nano- and micro-particles allows distinguishing multiple targets at the same time within a complex mixture and is emerging as a powerful tool to increase the throughput of many assays. Fluorescent barcoding is one of the most used strategies, where microparticles are labeled with dyes and classified based on fluorescence color, intensity, or other features. Microparticles are ideal targets due to their relative ease of detection, manufacturing, and higher homogeneity. Barcoding is considerably more challenging in the case of nanoparticles (NPs), where their small size results in a lower signal and greater heterogeneity. This is a significant limitation since many bioassays require the use of nano-sized carriers. In this study, we introduce a machine-learning-assisted workflow to write, read, and classify barcoded PLGA-PEG NPs at a single-particle level. This procedure is based on the encapsulation of fluorescent markers without modifying their physicochemical properties (writing), the optimization of their confocal imaging (reading), and the implementation of a machine learning-based barcode reader (classification). We found nanoparticle heterogeneity as one of the main factors that challenges barcode separation, and that information extracted from the dyes' nanoscale confinement effects (such as Förster Resonance Energy Transfer, FRET) can aid barcode identification. Moreover, we provide a guide to reaching the optimal trade-off between the number of simultaneous barcodes and classification accuracy supporting the use of this workflow for a variety of bioassays.},
}
@article {pmid37056375,
year = {2023},
author = {Fang, C and Sun, X and Fan, F and Zhang, X and Wang, O and Zheng, H and Peng, Z and Luo, X and Chen, A and Zhang, W and Drmanac, R and Peters, BA and Song, Z and Kristiansen, K},
title = {High-resolution single-molecule long-fragment rRNA gene amplicon sequencing of bacterial and eukaryotic microbial communities.},
journal = {Cell reports methods},
volume = {3},
number = {3},
pages = {100437},
pmid = {37056375},
issn = {2667-2375},
mesh = {Phylogeny ; *Eukaryota/genetics ; Genes, rRNA ; Sequence Analysis, DNA/methods ; RNA, Ribosomal/genetics ; Bacteria/genetics ; *Microbiota/genetics ; DNA, Ribosomal/genetics ; Soil ; },
abstract = {Sequencing of hypervariable regions as well as internal transcribed spacer regions of ribosomal RNA genes (rDNA) is broadly used to identify bacteria and fungi, but taxonomic and phylogenetic resolution is hampered by insufficient sequencing length using high throughput, cost-efficient second-generation sequencing. We developed a method to obtain nearly full-length rDNA by assembling single DNA molecules combining DNA co-barcoding with single-tube long fragment read technology and second-generation sequencing. Benchmarking was performed using mock bacterial and fungal communities as well as two forest soil samples. All mock species rDNA were successfully recovered with identities above 99.5% compared to the reference sequences. From the soil samples we obtained good coverage with identification of more than 20,000 unknown species, as well as high abundance correlation between replicates. This approach provides a cost-effective method for obtaining extensive and accurate information on complex environmental microbial communities.},
}
@article {pmid37051600,
year = {2023},
author = {Munro, R and Holmes, N and Moore, C and Carlile, M and Payne, A and Tyson, JR and Williams, T and Alder, C and Snell, LB and Nebbia, G and Santos, R and Loose, M},
title = {A framework for real-time monitoring, analysis and adaptive sampling of viral amplicon nanopore sequencing.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1138582},
pmid = {37051600},
issn = {1664-8021},
abstract = {The ongoing SARS-CoV-2 pandemic demonstrates the utility of real-time sequence analysis in monitoring and surveillance of pathogens. However, cost-effective sequencing requires that samples be PCR amplified and multiplexed via barcoding onto a single flow cell, resulting in challenges with maximising and balancing coverage for each sample. To address this, we developed a real-time analysis pipeline to maximise flow cell performance and optimise sequencing time and costs for any amplicon based sequencing. We extended our nanopore analysis platform MinoTour to incorporate ARTIC network bioinformatics analysis pipelines. MinoTour predicts which samples will reach sufficient coverage for downstream analysis and runs the ARTIC networks Medaka pipeline once sufficient coverage has been reached. We show that stopping a viral sequencing run earlier, at the point that sufficient data has become available, has no negative effect on subsequent down-stream analysis. A separate tool, SwordFish, is used to automate adaptive sampling on Nanopore sequencers during the sequencing run. This enables normalisation of coverage both within (amplicons) and between samples (barcodes) on barcoded sequencing runs. We show that this process enriches under-represented samples and amplicons in a library as well as reducing the time taken to obtain complete genomes without affecting the consensus sequence.},
}
@article {pmid37048258,
year = {2023},
author = {Monterisi, S and Zuluaga, MYA and Porceddu, A and Cesco, S and Pii, Y},
title = {The Application of High-Resolution Melting Analysis to trnL (UAA) Intron Allowed a Qualitative Identification of Apple Juice Adulterations.},
journal = {Foods (Basel, Switzerland)},
volume = {12},
number = {7},
pages = {},
pmid = {37048258},
issn = {2304-8158},
abstract = {Food authenticity plays a pivotal role in the modern age since an increased consumers awareness has led them to pay more attention to food commodities. For this reason, it is important to have reliable and fast techniques able to detect possible adulterations in food, which affect qualitative and economic value. Therefore, the aim of this study was to detect possible adulterations in apple juice from others fruit species (i.e., pear, peach, and kiwi) combining DNA barcoding approach, using trnL (UAA) intron, with high resolution melting analysis (HRMA). A preliminary phylogenetic analysis, using sequences retrieved by the GenBank, confirmed the discriminatory power of trnL (UAA) intron among the four fruit species examined. Moreover, the sequencing of the trnL (UAA) fragments obtained from apple, pear, peach, and kiwi, demonstrated the suitability of an inner shorter sequence, P6 loop, to differentiate the considered species. The HRMA coupled with trnL (UAA) intron allowed discrimination among the four fruits but provided incomplete results for juices. Whereas the HRMA targeting the P6 loop amplicons confirmed the suitability of the technique to qualitatively distinguish fruit juices composed by the combination of apple/pear and apple/peach. However, the impossibility of discriminating apple/kiwi juices from the pure kiwi sample highlighted limitations, most likely related to the DNA extraction process. This hypothesis was further confirmed by analyzing DNA blends obtained by combining nucleic acids extracted from pure matrixes (i.e., apple and kiwi fruits). In this specific case, the application of HRMA allowed both qualitative and quantitative assessment of the samples.},
}
@article {pmid37045995,
year = {2023},
author = {Hou, L and Zhang, J and Zhao, F},
title = {Full-length circular RNA profiling by nanopore sequencing with CIRI-long.},
journal = {Nature protocols},
volume = {18},
number = {6},
pages = {1795-1813},
pmid = {37045995},
issn = {1750-2799},
support = {32130020, 32025009, 91940306, 32200530//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; },
mesh = {*RNA, Circular/genetics/metabolism ; *Nanopore Sequencing ; RNA Splicing ; RNA, Messenger/genetics ; Protein Isoforms ; Sequence Analysis, RNA/methods ; RNA/genetics/metabolism ; },
abstract = {Circular RNAs (circRNAs) have important roles in regulating developmental processes and disease progression. As most circRNA sequences are highly similar to their cognate linear transcripts, the current short-read sequencing-based methods rely on the back-spliced junction signal for distinguishing circular and linear reads, which does not allow circRNAs' full-length structure to be effectively reconstructed. Here we describe a long-read sequencing-based protocol, CIRI-long, for the detection of full-length circular RNAs. The CIRI-long protocol combines rolling circular reverse transcription and nanopore sequencing to capture full-length circRNA sequences. After poly(A) tailing, RNase R treatment, and size selection of polymerase chain reaction products, CIRI-long achieves an increased percentage (6%) of circular reads in the constructed library, which is 20-fold higher compared with previous Illumina-based strategies. This method can be applied in cell lines or tissue samples, enabling accurate detection of full-length circRNAs in the range of 100-3,000 bp. The entire protocol can be completed in 1 d, and can be scaled up for large-scale analysis using the nanopore barcoding kit and PromethION sequencing device. CIRI-long can serve as an effective and user-friendly protocol for characterizing full-length circRNAs, generating direct and convincing evidence for the existence of detected circRNAs. The analytical pipeline offers convenient functions for identification of full-length circRNA isoforms and integration of multiple datasets. The assembled full-length transcripts and their splicing patterns provide indispensable information to explore the biological function of circRNAs.},
}
@article {pmid37045438,
year = {2022},
author = {Talaga, S and Gendrin, M},
title = {Three new species of Culex (Melanoconion) (Diptera: Culicidae) from French Guiana based on morphological and molecular data.},
journal = {Zootaxa},
volume = {5205},
number = {2},
pages = {177-189},
doi = {10.11646/zootaxa.5205.2.5},
pmid = {37045438},
issn = {1175-5334},
mesh = {Humans ; Male ; Animals ; *Culex/genetics ; *Culicidae ; French Guiana ; Mosquito Vectors ; Genitalia, Male ; },
abstract = {Culex mosquitoes of the subgenus Melanoconion Theobald, 1903 of the genus Culex Linnaeus, 1758 include numerous species recognized as vectors of viruses affecting humans. This subgenus is the most speciose among the entire mosquito fauna of the Americas. Despite decades of taxonomic research, many species remain undiscovered, especially in the Amazonian biome. In this article, we provide the description of three new species of Culex (Melanoconion) recently discovered in a biological reserve in French Guiana. Culex (Mel.) sallumae n. sp., Cx. (Mel.) hutchingsae n. sp. and Cx. (Mel.) lucakermanni n. sp. are described based on both morphological features of the male genitalia and molecular barcodes obtained from type specimens. Diagnostic characters to assist their identification are provided and their placement within the infrasubgeneric classification of the subgenus Melanoconion is discussed.},
}
@article {pmid37045433,
year = {2022},
author = {Ayala, MM and Díaz, F and Spinelli, GR and Micieli, MV and Ronderos, MM},
title = {Redescription of immature stages of Culicoides paraensis (Goeldi) (Diptera: Ceratopogonidae), vector of the Oropouche virus.},
journal = {Zootaxa},
volume = {5205},
number = {3},
pages = {249-264},
doi = {10.11646/zootaxa.5205.3.4},
pmid = {37045433},
issn = {1175-5334},
mesh = {Animals ; *Ceratopogonidae/genetics ; Insect Vectors/genetics ; *Orthobunyavirus ; },
abstract = {Oropouche fever is an emerging zoonotic disease caused by Oropouche virus (OROV). It has two distinct transmission cycles, with the anthropophilic biting midge Culicoides paraensis (Goeldi) (Diptera: Ceratopogonidae) being the primary vector in the urban cycle. Species identification of Culicoides typically has been carried out on the basis of morphological characters, but molecular tools applied to taxonomy can provide rapid and efficient methods to the identification of vector species. The aim of this work was to obtain the first DNA barcode for C. paraensis collected in Argentina and redescribe the larvae and pupae of this species. Nested PCR amplification was applied in this study to increase the DNA amplification, because the material was preserved in alcohol 70% for a long period of time. The immature stages of C. paraensis are fully described from material collected in Misiones province, Argentina. Both stages are compared with their most similar congeners. This COI sequence complements the identification based on morphological characters and the values of genetic distance between the analysed species show that this sequence is useful to discriminate between species of the Culicoides genus.},
}
@article {pmid37045422,
year = {2022},
author = {Schönberger, D and Giordani, G and Vanin, S and Whitmore, D},
title = {A review of morphological characters for the identification of three common European species of Sarcophaga s.&amp;nbsp;str. (Diptera: Sarcophagidae), with an emphasis on female terminalia.},
journal = {Zootaxa},
volume = {5205},
number = {5},
pages = {463-480},
doi = {10.11646/zootaxa.5205.5.4},
pmid = {37045422},
issn = {1175-5334},
mesh = {Animals ; Female ; Male ; *Diptera ; *Sarcophagidae/genetics/anatomy &amp; histology ; },
abstract = {The subgenus Sarcophaga Meigen, 1824 (s. str.) currently comprises over 30 species distributed in the West Palearctic Region, the identification of which is normally based on characters of the male terminalia. Females of the three closely-related species Sarcophaga (Sarcophaga) carnaria (Linnaeus, 1758), S. (S.) subvicina Rohdendorf, 1937 and S. (S.) variegata (Scopoli, 1763), which are especially widespread and abundant in NW Europe, are considered morphologically indistinguishable by most authors. However, a few authors have proposed keys to separate females of these three species based on external and internal characters of the terminalia. Following a preliminary molecular identification using DNA barcode sequences (COI, cytochrome c oxidase subunit I), we herein revise the morphological characters used to differentiate female S. carnaria, S. subvicina and S. variegata in existing identification keys as well as search for additional diagnostic characters. Our results suggest that only one previously-proposed female character, namely the length to width ratio of abdominal sternite 7, can be used to separate S. subvicina from the other two species (Mann-Whitney U test: p < 0.0001), at least in a majority of cases. Other characters, such as the degree of sclerotisation and setation of tergite 8, show a high degree of overlap that does not allow to reliably separate females of these three species. Nevertheless, we propose a combination of characters that should allow the separation of female S. carnaria from female S. variegata in most cases. An additional analysis of males of the same species showed that the distribution of pruinosity and setation on syntergosternite 7+8, a character mentioned in a previously-published key, is also not reliable for identification.},
}
@article {pmid37045355,
year = {2022},
author = {Freyhof, J and Geiger, MF and Ball, S and Zimmerman, B},
title = {DNA barcode data confirm the placement of subterranean Noemacheilus (Troglocobitis) starostini Parin 1983 in the genus Paracobitis (Teleostei, Nemacheilidae).},
journal = {Zootaxa},
volume = {5190},
number = {4},
pages = {565-574},
doi = {10.11646/zootaxa.5190.4.6},
pmid = {37045355},
issn = {1175-5334},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Phylogeny ; *Cypriniformes ; },
abstract = {DNA barcodes (COI) of Troglocobitis starostini, endemic to a single site in Turkmenistan, were analysed and put into the taxonomic context of the large group of nemacheilid loaches known from Western and Central Asia. All applied phylogenetic tree-based analyses place the species into the genus Paracobitis. This finding supports previous morphological studies. While the exact position of Troglocobitis starostini within Paracobitis was not resolved unambiguously, it was constantly recovered within Paracobitis, irrespective of the tree reconstruction method applied. With a minimum interspecific K2P distance of 7.19% P. persa was the closest hit in our dataset, which comprised a total of ten species of Paracobitis, which showed an average interspecific K2P distance of 5.43% (range 2.78-9.44%).},
}
@article {pmid37045317,
year = {2022},
author = {Opler, PA and Stout, TL and Back, W and Zhang, J and Cong, Q and Shen, J and Grishin, NV},
title = {DNA barcodes reveal different speciation scenarios in the four North American Anthocharis Boisduval, Rambur, [Duménil] &amp; Graslin, [1833] (Lepidoptera: Pieridae: Pierinae: Anthocharidini) species groups.},
journal = {Zootaxa},
volume = {5194},
number = {4},
pages = {519-539},
doi = {10.11646/zootaxa.5194.4.3},
pmid = {37045317},
issn = {1175-5334},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Butterflies/genetics ; DNA, Mitochondrial/genetics ; Mitochondria ; Phylogeny ; },
abstract = {The mitochondrial DNA COI barcode segment sequenced from American Anthocharis specimens across their distribution ranges partitions them into four well-separated species groups and reveals different levels of differentiation within these groups. The lanceolata group experienced the deepest divergence. About 2.7% barcode difference separates the two species: A. lanceolata Lucas, 1852 including A. lanceolata australis (F. Grinnell, 1908), from A. desertolimbus J. Emmel, T. Emmel &amp; Mattoon, 1998. The sara group consists of three species distinctly defined by more than 2% sequence divergence: A. sara Lucas, 1852, A. julia W. H. Edwards, 1872, and A. thoosa (Scudder, 1878). Our treatment is fully consistent with morphological evidence largely based on the characters of fifth instar larvae and pupal cone curvature (Stout, 2005, 2018). In barcodes, it is not possible to see evidence of introgression or hybridization between the three species, and identification by morphology of immature stages always agrees with DNA barcode identification. Interestingly, A. thoosa exhibited the largest intraspecific divergence in DNA barcodes, and several of its metapopulations are identifiable by haplotypes. The cethura group is characterized by the smallest divergence and is best considered as a single species variable in expression of yellow coloration: A cethura C. Felder &amp; R. Felder, 1865. Notably, the most sexually dimorphic subspecies A. cethura morrisoni W. H. Edwards, 1881 is the most distinct by the barcodes. Finally, the midea group barcodes do not always separate A. midea (Hübner, [1809]) and A. limonea (A. Butler, 1871) and we observe gradual accumulation of differences from north (northeastern USA) to south (Hidalgo, Mexico). This barcode gradient suggests a recent origin of the two midea group species and provides another example of vicariant sister species well defined by morphology, ecology and geography, but not necessarily by DNA barcodes.},
}
@article {pmid37045309,
year = {2022},
author = {Kolevatov, V and Marin, I},
title = {Mud shrimps of the genus Wolffogebia Sakai, 1982 (Decapoda: Gebiidea: Upogebiidae) with the description of a new species from the Cần Giớ Mangrove Biosphere Reserve, South Vietnam.},
journal = {Zootaxa},
volume = {5195},
number = {1},
pages = {51-72},
doi = {10.11646/zootaxa.5195.1.3},
pmid = {37045309},
issn = {1175-5334},
mesh = {Animals ; Male ; Animal Distribution ; *Crustacea ; *Decapoda ; Vietnam ; },
abstract = {A new species of mud dwelling burrowing shrimp Wolffogebia cangioensis sp. nov. is described from the Soài Rạp River delta in the Cần Giớ Mangrove Biosphere Reserve, South Vietnam. The presence of Wolffogebia inermis Sakai, 1982 in the same area is also confirmed based on the freshly collected male specimen. Thorough morphological descriptions, genetic data (barcoding) and in situ ecological observations are presented for both species. A review of the previous records from Vietnam and Southeastern Asia as well as the taxonomic status of the genus Wolffogebia Sakai, 1982 within the family Upogebiidae are also discussed in the article. The key to all species of the genus is presented.},
}
@article {pmid37045267,
year = {2023},
author = {Marchán, DF and Novo, M and Domínguez, J and Sánchez, N and Decaëns, T},
title = {Contribution to the knowledge of the genus Boucheona (Oligochaeta, Hormogastridae) in France with a newly described species and a redescribed species.},
journal = {Zootaxa},
volume = {5255},
number = {1},
pages = {68-81},
doi = {10.11646/zootaxa.5255.1.11},
pmid = {37045267},
issn = {1175-5334},
mesh = {Animals ; *Oligochaeta/genetics ; Ecosystem ; Bayes Theorem ; Biological Evolution ; Phylogeny ; France ; },
abstract = {Hormogastrid earthworms are found in the diversity hotspot of the Franco-Iberian domain, together with the better-known family Lumbricidae. Integrative systematics (the combination of morphological, molecular and ecological data) have increased our knowledge of the diversity and evolutionary history of these earthworms, highlighting unresolved taxonomic conflicts. One example of a species group in need of integrative taxonomic revision is the genus Boucheona in France. In this work, we analyzed their diversity using previously published data together with additional data obtained from recently sampled localities. Molecular data including DNA barcodes and additional markers enabled us to reconstruct Bayesian and time-calibrated phylogenies to discuss the evolutionary relationships among the different taxa, and to propose hypotheses regarding their biogeographical history. Based on our results, four species of Boucheona are present in Southern France, including two new taxa. Morphological distinctness and molecular phylogenetics results supported the status of four populations as the newly described Boucheona corbierensis sp. nov., as well as the status of "Hormogaster pretiosa var. nigra" as an independent species, redescribed as Boucheona tenebrae sp. nov. These results provide a new perspective of the importance of the genus Boucheona in southern France, as the possible evolutionary origin of a clade of giant anecic earthworms with unknown (but probably remarkable) impact on ecosystem functioning across their range.},
}
@article {pmid37045265,
year = {2023},
author = {Mustafa, RG and Andleeb, S and Domínguez, J and Abbasi, WA and Ali, S and Marchán, DF},
title = {New Earthworm Record from Division Muzaffarabad, Azad Kashmir, Pakistan Supported by Molecular Markers.},
journal = {Zootaxa},
volume = {5255},
number = {1},
pages = {93-100},
doi = {10.11646/zootaxa.5255.1.13},
pmid = {37045265},
issn = {1175-5334},
mesh = {Animals ; Phylogeny ; *Oligochaeta/genetics ; Pakistan ; Bayes Theorem ; },
abstract = {Earthworm diversity and ecology in Pakistan is poorly known, especially in the region of Azad Jammu &amp; Kashmir. An earthworm community survey assisted by genetic barcoding detected an unidentified species which could constitute a new record for Pakistan. Morphological study revealed its identity as Perelia kaznakovi. Additionally, Bayesian phylogenetic inference based on five mitochondrial and nuclear molecular markers was performed. Results provided a phylogenetic placement of the genus Perelia within Lumbricidae for the first time, indicating a close relationship with Eophila. This approach should be implemented to Perelia arnoldiana and further representatives of the genus in order to understand their biogeography, diversity and evolutionary history.},
}
@article {pmid37045235,
year = {2023},
author = {Bogorodsky, SV and Kovačić, M and Mal, AO and Alpermann, TJ},
title = {A new species of Fusigobius (Teleostei: Gobiidae) from the Red Sea and Gulf of Aden.},
journal = {Zootaxa},
volume = {5256},
number = {2},
pages = {101-124},
doi = {10.11646/zootaxa.5256.2.1},
pmid = {37045235},
issn = {1175-5334},
mesh = {Animals ; Indian Ocean ; Phylogeny ; Yemen ; *Fishes ; *Perciformes ; },
abstract = {The gobiid species, Fusigobius humerosus sp. nov., is described based on 12 type and 18 non-type specimens collected from the Red Sea and Gulf of Aden. The new species can be distinguished from congeners by a combination of meristic and morphometric characters. The new species was formerly misidentified with F. humeralis: both are characterised by a semitranslucent body; head and body with numerous small dusky orange-yellow spots; a round black spot in humeral region just above base of pectoral fin; and a black spot subequal to pupil diameter at midbase of the caudal fin. However, Fusigobius humerosus sp. nov. differs from F. humeralis by scales on side of nape not extending forward to above posterior margin of preopercle (vs. scales variably extending forward to between above posterior preopercular margin and orbit); first dorsal-fin spine longest (vs. second and third dorsal-fin spines longest); shorter upper jaw; shorter anal-fin spine; and posterior nostril about halfway between orbit and anterior nostril (vs. posterior nostril closer to orbit). The most complete description of the genus Fusigobius is provided. In phylogenetic analyses of publicly available sequences of the barcoding portion of the mitochondrial cytochrome oxidase subunit I (COI) gene, sequences derived from the new species form a separate and well-divergent monophyletic lineage. The resulting COI gene tree further suggests that the new Fusigobius species is phylogenetically most closely related to F. humeralis which forms its sister species in the maximum likelihood tree. Molecular species delimitation of available Fusigobius COI barcodes shows that 19 or 20 hypothetical divergent evolutionary lineages can be deduced depending on the analytical approach (ABGD = 19 and bPTP = 20), indicating a potentially higher taxonomic richness than the presently acknowledged 11 valid species. However, the assignment of available species names for some lineages remains uncertain, highlighting the need for an additional integrative taxonomic research on this genus.},
}
@article {pmid37045197,
year = {2022},
author = {Chiu, YC and Chen, HM and Shao, KT},
title = {Additional description on morphology of the Misol snake eel from Taiwan, with four verified barcodes of life sequences.},
journal = {Zootaxa},
volume = {5189},
number = {1},
pages = {114-121},
doi = {10.11646/zootaxa.5189.1.13},
pmid = {37045197},
issn = {1175-5334},
mesh = {Animals ; Taiwan ; Animal Distribution ; *Eels/anatomy &amp; histology ; },
abstract = {An additional description of the Misol snake eel Yirrkala misolensis (Günther, 1872) is reported on the basis of 9 specimens collected from Dong-gang and Ke-tzu-liao, southwestern Taiwan. The species was previously reported from Indonesia and Australia and then extends northward to Taiwan and Japan, and was lacking adequate characterization on morphology. A detail description, fine condition of fresh photographs and 4 partial CO1 sequences are provided for the first time.},
}
@article {pmid37045192,
year = {2022},
author = {Su, YO and Lin, HC and Ho, HC},
title = {A new cryptic species of the pineapple fish genus Monocentris (Family Monocentridae) from the western Pacific Ocean, with redescription of M. japonica (Houttuyn, 1782).},
journal = {Zootaxa},
volume = {5189},
number = {1},
pages = {180-203},
doi = {10.11646/zootaxa.5189.1.18},
pmid = {37045192},
issn = {1175-5334},
mesh = {Animals ; *Ananas ; Pacific Ocean ; Fishes/genetics ; *Perciformes ; },
abstract = {A new pineapple fish is described based on 26 type and 80 non-type specimens collected from Taiwan, Vanuatu, the Solomon Islands, and Queensland, Australia. This new species is sympatric with and similar to Monocentris japonica but can be distinguished from the latter in having only 6 or 7 scales on the third scale row below the lateral line; excisura notched and a small pseudo-excisura present on the sagittal otolith; consistently greater head depth, body depth, postorbital length, dorsal-fin-pelvic-fin length, and dorsal-fin-pectoral-fin length in proportion to standard length. A detailed description and designation of neotype are provided for M. japonica. DNA barcoding analysis supports the distinction of the new species with an estimated average COI gene divergence of 3.6 % from M. japonica.},
}
@article {pmid37045164,
year = {2022},
author = {Makarchenko, EA and Semenchenko, AA and Palatov, DM},
title = {Taxonomy of Diamesa steinboecki group (Diptera: Chironomidae: Diamesinae), with description and DNA barcoding of known species. II. Subgroups davisi, leona and loeffleri.},
journal = {Zootaxa},
volume = {5190},
number = {3},
pages = {361-392},
doi = {10.11646/zootaxa.5190.3.3},
pmid = {37045164},
issn = {1175-5334},
mesh = {Male ; Animals ; *Chironomidae/genetics ; DNA Barcoding, Taxonomic ; Phylogeny ; DNA ; },
abstract = {Illustrated redescription of the adult males Diamesa alpina Tokunaga from the Russian Far East and North America, D. amplexivirilia Hansen from Arctic and the Russian Far East, D. saetheri Willassen from Chukotka Region and Kolyma River basin, D. lupus Willassen from Alaska, D. serratosioi Willassen from Norway and Russian Far East, D. leoniella Hansen from Alaska, D. leona Roback from Eurasia, D. japonica Tokunaga from Japan and Russian Far East, D. khumbugelida Saether et Willassen and D. loeffleri Reiss from Himalayas are provided. Morphological data and DNA sequences of the mitochondrial cytochrome c oxidase subunit I gene (COI) were used to delimit of seven species from subgroups davisi (D. alpina, D. amplexivirilia, D. serratosioi), leona (D. japonica, D. leona) and loeffleri (D. khumbugelida, D. loeffleri). Taxonomic remarks with data on geographical distribution of the investigated species are given.},
}
@article {pmid37045139,
year = {2023},
author = {Nakajima, H and Reimer, JD and Naruse, T},
title = {Morphological and phylogenetic study of Acanthosquilla Manning, 1963 (Stomatopoda: Nannosquillidae) mantis shrimps, with description of two new species from the Ryukyu Islands, Japan.},
journal = {Zootaxa},
volume = {5231},
number = {4},
pages = {351-375},
doi = {10.11646/zootaxa.5231.4.1},
pmid = {37045139},
issn = {1175-5334},
mesh = {Animals ; Japan ; Phylogeny ; Islands ; *Crustacea/genetics ; DNA, Ribosomal ; },
abstract = {Three species of nannosquillid mantis shrimps, including two new species, Acanthosquilla ryukyuensis n. sp. and Acanthosquilla shoheii n. sp., are described based on specimens collected from the Ryukyu Islands, Japan. The two new species resemble A. derijardi Manning, 1970, but can be distinguished from A. derijardi by the following features: 1) rostral plate anterolateral corner forms almost a right angle; 2) the distal tip of the antennular somite dorsal process reaches or slightly falls short of proximal half of rostral plate; and 3) eighth thoracic somite (= TS8) posterior margin is black medially. Furthermore, A. ryukyuensis n. sp. and A. shoheii n. sp. are easy to identify by the bifurcated lateral tooth of the telson, and by the posterodorsal pattern of the telson, respectively. In this study, molecular analyses based on partial sequences of mitochondrial 12S and 16S ribosomal DNA, cytochrome oxidase subunit I (COI), and the partial nuclear gene of 28S ribosomal DNA recovers these three species of Acanthosquilla and A. multifasciata (Wood-Mason, 1895) (the type species of the genus) in a single clade. The resulting trees also suggest the polyphyly of Nannosquillidae but with low nodal support. Detailed examinations of the morphological and color features and DNA barcoding results allowed us to delineate intraspecific variations and interspecific differences. The number and shape of setae under the dorsal spine of raptorial claw carpus was found to be useful in distinguishing A. shoheii n. sp. from A. derijardi and A. ryukyuensis n. sp., while combinations of the coloration of the rostral plate, posterior margin of TS8 and posterodorsal surface of telson are useful to distinguish the three species.},
}
@article {pmid37045089,
year = {2023},
author = {Ortiz, AS and Rubio, RM and Ranki, T and Guerrero, JJ and Yela, JL},
title = {First record of Archanara neurica (Hübner, 1808) from the Iberian Peninsula (Lepidoptera: Noctuidae) according to DNA barcoding and internal male genitalia.},
journal = {Zootaxa},
volume = {5239},
number = {3},
pages = {431-441},
doi = {10.11646/zootaxa.5239.3.7},
pmid = {37045089},
issn = {1175-5334},
mesh = {Male ; Animals ; *Lepidoptera ; DNA Barcoding, Taxonomic ; *Moths ; Europe ; DNA ; Genitalia, Male ; Genitalia ; },
abstract = {Archanara neurica (Hübner, 1808) is recorded for the first time from the Iberian Peninsula. The Iberian population represent a link between central European, including French, and Moroccan populations. Male internal genitalia are comparatively described. DNA barcode is presented and compared with those of the other European Archanara, Lenisa and Globia species, formerly considered congeneric. An analysis based on the COI mitochondrial gene provisionally supports the morphologically proposed statement that recognize the three mentioned taxa at the generic level.},
}
@article {pmid37045068,
year = {2022},
author = {Thorn, S and Kazerani, F and Farashiani, ME and Morinière, J},
title = {Triplax sulphuricollis Reitter, 1887 from the Hyrcanian forests of Iran recognized as a valid species by morphology and barcoding (Coleoptera: Erotylidae).},
journal = {Zootaxa},
volume = {5196},
number = {3},
pages = {443-450},
doi = {10.11646/zootaxa.5196.3.8},
pmid = {37045068},
issn = {1175-5334},
mesh = {Animals ; Iran ; *Coleoptera ; Forests ; Trees ; },
abstract = {The status of Triplax collaris sulphuricollis Reitter, 1887 is reevaluated based on recent records from the Hyrcanian forests in northern Iran. Morphological features and barcoding support separate species status as Triplax sulphuricollis Reitter, 1887, new status. Morphological characteristics include an orange-yellow antennal club and elytral punctation arranged in striae. Triplax sulphuricollis is associated with oyster fungi of the genus Pleurotus growing on dead wood of deciduous trees.},
}
@article {pmid37045053,
year = {2022},
author = {Mukherjee, T and Som, DK and Hazra, N},
title = {Two new species of Pseudosmittia Edwards, 1932 from India with a key to Oriental species adult males (Diptera: Chironomidae: Orthocladiinae).},
journal = {Zootaxa},
volume = {5200},
number = {1},
pages = {51-62},
doi = {10.11646/zootaxa.5200.1.4},
pmid = {37045053},
issn = {1175-5334},
mesh = {Male ; Animals ; *Chironomidae/genetics ; *Diptera ; India ; },
abstract = {In this study, we described and illustrated two new species, Pseudosmittia luna and Pseudosmittia valida based on the adult males from the plains of West Bengal, India. A DNA barcode of Pseudosmittia luna sp. n. compared with selected congeneric sequences from NCBI GenBank, indicates that the species is sister to an unknown species with accession number MG301870. Additionally, we provided a key for the adult males of the Oriental species of the genus.},
}
@article {pmid37045017,
year = {2022},
author = {Wesener, T},
title = {Integrative redescription of the enigmatic monotypic alpine pill millipede genus Simplomeris Verhoeff, 1936 (Glomerida, Glomeridae, Haploglomerinae).},
journal = {Zootaxa},
volume = {5200},
number = {6},
pages = {550-564},
doi = {10.11646/zootaxa.5200.6.3},
pmid = {37045017},
issn = {1175-5334},
mesh = {Animals ; Phylogeny ; *Arthropods ; Environment ; },
abstract = {The European pill millipedes (Glomerida) are especially rich in species and genera of enigmatic status, which have been neither reviewed nor revised since more than 70 years. One of these genera is Simplomeris Verhoeff, 1936 with its single species S. montivaga (Faës, 1902), a high-altitude endemic only known from <5 collection events in the Simplon Valley and the Aletsch Glacier, southern Switzerland. Being one of only a handful of genera in the subfamily Haploglomerinae, distributed in Europe and SE Asia, its morphology is of greater interest in a future phylogenetic sorting of the Glomerida. Fresh material, which was encountered by the author 10 years ago from both known localities, allows here a redescription of this rarely encountered genus. Aside from the first photograph of a living specimen, scanning electron microscopy and genetic barcoding of the COI gene have been conducted. Morphologically, the telopods of Simplomeris resemble those of Haploglomeris Verhoeff, 1906 from the eastern Alps and confirm the present position in the Haploglomerinae. Genetically, Simplomeris belongs to the Glomeris klugii Brandt, 1833 species-group and is particularly close to high-altitude endemics from the southwestern and Bergamasque Alps, especially G. primordialis Verhoeff, 1930, G. transalpina Koch, 1836, and G. oropensis Verhoeff, 1934. Genetic barcoding data confirm the three colour varieties of S. montivaga, S. montivaga var. montivaga Verhoeff, 1936 syn. nov., S. montivaga var. simplonensis Verhoeff, 1936: syn. nov., S. montivaga var. berisalensis Verhoeff, 1936 syn. nov. to be just that, and all three are formally synonymized under S. montivaga.},
}
@article {pmid37045016,
year = {2022},
author = {Kodada, J and Bennas, N and Goffová, K and Čiampor, FJ},
title = {Potamophilus acuminatus (Fabricius, 1792): distribution update in North Africa confirmed by COI barcoding sequencing (Coleoptera, Elmidae).},
journal = {Zootaxa},
volume = {5200},
number = {6},
pages = {565-575},
doi = {10.11646/zootaxa.5200.6.4},
pmid = {37045016},
issn = {1175-5334},
mesh = {Animals ; *Coleoptera/genetics ; Phylogeny ; DNA Barcoding, Taxonomic ; Larva/genetics ; },
abstract = {Potamophilus acuminatus (Fabricius, 1792) is here recorded for the first time from Morocco and the recent distribution in Slovakia is updated. The North African distribution was hitherto based only on two larvae from Tunisia. DNA-barcoding confirmed the identification of specimens from Morocco after comparing ten sequences of P. acuminatus from Germany, France and Slovakia. The COI haplotype of the Moroccan samples was quite divergent (0.033-0.035 uncorrected p-distance) compared with European specimens. These high p-distances suggest the existence of a different intraspecific lineage. A brief morphological diagnosis of adults and larvae is given.},
}
@article {pmid37044978,
year = {2023},
author = {Wesener, T and Moritz, L and Akkari, N},
title = {Integrative redescription of the sucking millipede genus Dawydoffia Attems, 1953, with a description of a new species and a transfer to the family Hirudisomatidae (Diplopoda, Polyzoniida).},
journal = {Zootaxa},
volume = {5263},
number = {3},
pages = {411-429},
doi = {10.11646/zootaxa.5263.3.6},
pmid = {37044978},
issn = {1175-5334},
mesh = {Animals ; Male ; X-Ray Microtomography ; *Arthropods ; },
abstract = {The type species of the monotypic Polyzoniida genus Dawydoffia Attems, 1953, D. kalonota Attems, 1953 from Vietnam, is redescribed based on type material. A second species of the genus, D. siphonocryptida n. sp., is described from Laos based on scanning electron microscopy, micro-computed tomography and molecular barcoding. The species of Dawydoffia are among the shortest and widest of the Polyzoniida, and resemble in habitus those of the Siphonocryptida genus Siphonocryptus Pocock, 1894, both having pleurites that are completely fused to the tergites. Dawydoffia was previously placed in the family Siphonotidae Cook, 1895, but can be identified as a member of the Holarctic Hirudisomatidae Silvestri, 1896 based on the following morphological characters: the uplifted posterior margins of the tergites, the collum covering part of the head, the position of the male gonapophysis or pseudopenis, the retracted telson, and the ozopores situated close to the tergal margin. However, both Dawydoffia species have a slender paronychium, a character previously known only from the Siphonotidae, but also documented here for Hirudisoma roseum (Victor, 1839). A slight redefinition of the Polyzoniida families is provided. The two Dawydoffia species differ in their coloration, as well as in their somatic and gonopodal characters.},
}
@article {pmid37044949,
year = {2022},
author = {Loncle, MK and Quicke, DLJ and Deowanish, S and Butcher, BA},
title = {The first record of Charmon Haliday, 1833 (Braconidae: Charmontinae) from Southeast Asia with description of a new species from Thailand.},
journal = {Zootaxa},
volume = {5213},
number = {1},
pages = {93-100},
doi = {10.11646/zootaxa.5213.1.7},
pmid = {37044949},
issn = {1175-5334},
mesh = {Female ; Animals ; Thailand ; *Hymenoptera ; },
abstract = {Charmon thailandensis sp. nov. from Thailand is described and illustrated based on a female specimen from Doi Phu Kha National Park, Nan Province, Thailand. The new species is distinguished from apparently closely-related species of Charmon Haliday, 1833, based on both morphology and DNA sequence (barcode) data. Morphologically it appears to be near to C. extensor (L., 1758) but DNA data suggest it is quite basal with respect to all the other sequenced species. A checklist of the 10 known species of Charmon with their known distributions is provided. The possibility that C. extensor might represent a complex of more than one species is briefly discussed.},
}
@article {pmid37044942,
year = {2022},
author = {Chen, ZT},
title = {Aposthonia guizhouensis sp. nov., a new webspinner of Oligotomidae (Insecta: Embioptera) from China.},
journal = {Zootaxa},
volume = {5213},
number = {2},
pages = {190-198},
doi = {10.11646/zootaxa.5213.2.7},
pmid = {37044942},
issn = {1175-5334},
mesh = {Male ; Animals ; *Insecta/genetics ; *Neoptera ; Base Sequence ; China ; Animal Distribution ; },
abstract = {Aposthonia guizhouensis sp. nov. from Guizhou Province of China is described and illustrated. The new species is characterized by the distinctive terminalia structure in males. Aposthonia guizhouensis sp. nov. represents the second species of Aposthonia known from China. DNA barcode of the new species is sequenced and compared with its related congeners.},
}
@article {pmid37044915,
year = {2022},
author = {Ramírez-Guillén, LD and Falcon-Brindis, A and Gómez, B},
title = {The Scoliidae wasps (Hymenoptera: Scolioidea) of Mexico: taxonomy and biogeography.},
journal = {Zootaxa},
volume = {5214},
number = {1},
pages = {47-88},
doi = {10.11646/zootaxa.5214.1.2},
pmid = {37044915},
issn = {1175-5334},
mesh = {Animals ; *Wasps ; *Hymenoptera ; Mexico ; },
abstract = {The family Scoliidae is represented by approximately 560 species worldwide. Of these, 64 species are known to occur in the New World. The greatest diversity of these wasps is concentrated in the Pantropical region. However, both the biology and the taxonomy of Scoliidae has remained understudied over the last six decades in the Americas. Taxonomic keys for the New World species are limited to certain regions of North and South America, showing ambiguous descriptions and unillustrated specimens. This situation has largely restricted aspects such as the species richness, ecology, and thus conservation status of these wasps, especially in Mexico, where there are no taxonomic revisions. In this work, the Scoliidae species from Mexico were revised from 12 entomological collections to update and homologize the list of species. In total, we examined 747 specimens from 23 morphospecies and 9 genera. The diagnosis of each species is presented, including their distribution, and a species checklist is provided. Moreover, the first taxonomic key for the Mexican species is presented. Stygocampsomeris servillei Guérin is a new record for the country. Also, two new Nearctic and four Neotropical records are added. The occurrence records are now expanded to 30 Mexican states. Most species (41.6%) occur in both Nearctic and Neotropical regions. The species Scolia fuscipennis Bartlett is still known from a single sex. This work is the first attempt towards the taxonomy and biogeography of the Mexican Scoliidae; thus, it could be an important baseline for faunistic, ecological, and conservation purposes. Overall, the family Scoliidae has been overlooked and poorly represented in Mexican collections. The specimens were scarce and frequently in bad condition, and none of them include biological or ecological attributes. Systematic sampling and appropriate curation of specimens would help to conduct future revisions, as well as the possible integration of barcoding information allowing integrative taxonomic approaches.},
}
@article {pmid37044905,
year = {2022},
author = {Steck, M and Winnicki, E and Kobayashi, DR and Whitney, JL and Ahyong, ST and Porter, ML},
title = {Hawaiian larval stomatopods: molecular and morphological diversity.},
journal = {Zootaxa},
volume = {5214},
number = {2},
pages = {235-260},
doi = {10.11646/zootaxa.5214.2.5},
pmid = {37044905},
issn = {1175-5334},
mesh = {Animals ; Phylogeny ; Hawaii ; Larva/genetics/anatomy &amp; histology ; *Crustacea/genetics ; *Ecosystem ; },
abstract = {Estimating stomatopod species diversity using morphology alone has long been difficult; though over 450 species have been described, new species are still being discovered regularly despite the cryptic behaviors of adults. However, the larvae of stomatopods are more easily obtained due to their pelagic habitat, and have been the focus of recent studies of diversity. Studies of morphological diversity describe both conserved and divergent traits in larval stomatopods, but generally cannot be linked to a particular species. Conversely, genetic studies of stomatopod larvae using DNA barcoding can be used to estimate species diversity, but are generally not linked to known species by analyses of morphological characters. Here we combine these two approaches, larval morphology and genetics, to estimate stomatopod species diversity in the Hawaiian Islands. Over 22 operational taxonomic units (OTUs) were identified genetically, corresponding to 20 characterized morphological types. Species from three major superfamilies of stomatopod were identified: Squilloidea (4 OTUs, 3 morphotypes), Gonodactyloidea (9, 8), and Lysiosquilloidea (6, 7). Among these, lysiosquilloids were more diverse based on larval morphotypes and OTUs as compared to previously documented Hawaiian species (3), while squilloids had a lower diversity of species represented by collected larvae as compared to the seven species previously documented. Two OTUs / morphotypes could not be identified to superfamily as their molecular and morphological features did not closely match any available information, suggesting they belong to poorly sampled superfamilies. The pseudosquillid, Pseudosquillana richeri, was discovered for the first time from Hawai'i. This study contributes an updated estimate for Hawaiian stomatopod diversity for a total of 24 documented species, provides references for identification of larval stomatopods across the three major superfamilies, and emphasizes the lack of knowledge of species diversity in more cryptic stomatopod superfamilies, such as Lysiosquilloidea.},
}
@article {pmid37044847,
year = {2023},
author = {Bahder, BW and Myrie, W and Helmick, EE and Bartlett, CR},
title = {A new species of planthopper in the genus Haplaxius (Hemiptera: Fulgoroidea: Cixiidae) from disturbed submontane rainforest in Jamaica.},
journal = {Zootaxa},
volume = {5230},
number = {2},
pages = {225-237},
doi = {10.11646/zootaxa.5230.2.6},
pmid = {37044847},
issn = {1175-5334},
mesh = {Animals ; *Cocos ; Rainforest ; Jamaica ; *Hemiptera/genetics ; Phylogeny ; },
abstract = {Haplaxius is a large genus of cixiid planthopper found in the New World. The genus is of particular interest due to the ability of H. crudus to transmit the phytoplasmas for lethal decline in various palm species, primarily in the Caribbean and Florida, U.S.A. During recent vector survey work in Jamaica, a specimen was collected at Castleton Botanic Garden and determined to be a new species of Haplaxius. The novel taxon is herein described, Haplaxius fornicus sp. n., and corresponding DNA sequence data is provided for the barcoding region of the cytochrome c oxidase subunit I (COI) gene, 18S rRNA gene, and histone 3 (H3) gene. An updated phylogeny of the genus is provided with currently available taxa demonstrating additional support for the placement of H. fornicus sp. n. in Haplaxius.},
}
@article {pmid37044843,
year = {2023},
author = {Hui, P and Mukherjee, B and Hazra, N},
title = {A new species of the genus Tridactylophagus Subramaniam, 1932 from West Bengal, India with a tentative phylogeny and world key to known males (Strepsiptera: Halictophagidae).},
journal = {Zootaxa},
volume = {5230},
number = {3},
pages = {296-304},
doi = {10.11646/zootaxa.5230.3.2},
pmid = {37044843},
issn = {1175-5334},
mesh = {Male ; Animals ; Phylogeny ; India ; *Holometabola ; },
abstract = {A new species of the genus Tridactylophagus Subramaniam is described and illustrated from West Bengal, India. The new species, T. sufflatus differs from other members of Tridactylophagus by having a flattened, fist-shaped first tarsomere in forelegs and a slightly bulged out antennomere IV on the distal end with a sensory spot on one side. Molecular barcoding of the new species is done. Cladistic analysis and a revised world key of the males of the genus Tridactylophagus are also provided.},
}
@article {pmid37044814,
year = {2022},
author = {Pisanty, G and Scheuchl, E and Martin, T and Cardinal, S and Wood, TJ},
title = {Twenty-five new species of mining bees (Hymenoptera: Andrenidae: Andrena) from Israel and the Levant.},
journal = {Zootaxa},
volume = {5185},
number = {1},
pages = {1-109},
doi = {10.11646/zootaxa.5185.1.1},
pmid = {37044814},
issn = {1175-5334},
mesh = {Animals ; *Bees/classification ; Israel ; Species Specificity ; },
abstract = {Andrena is one of the most diverse bee genera, comprising about 1,600 described species of ground-nesting solitary bees. Many Andrena species are plant specialists, and several taxa have been indicated to be important pollinators of wild and/or crop plants. The Eastern Mediterranean Basin and Israel in particular are one of the main world diversity hotspots of Andrena. Based on extensive examination of museum specimens combined with DNA barcoding, we hereby describe twenty-five Levantine species of Andrena new to science: Andrena anathema Pisanty sp. nov., A. ardentia Pisanty sp. nov., A. asluji Pisanty sp. nov., A. curviocciput Pisanty &amp; Wood sp. nov., A. dividicincta Pisanty sp. nov., A. dorchini Pisanty sp. nov., A. euphorbiae Pisanty sp. nov., A. gageae Wood &amp; Pisanty sp. nov., A. herodesi Pisanty &amp; Wood sp. nov., A. hulae Pisanty sp. nov., A. igraeca Pisanty &amp; Wood sp. nov., A. inusitata Pisanty sp. nov., A. janthinoides Pisanty sp. nov., A. longistilus Pisanty &amp; Wood sp. nov., A. lunaris Pisanty &amp; Wood sp. nov., A. macula Pisanty &amp; Wood sp. nov., A. obtusa Pisanty sp. nov., A. ornithogali Pisanty &amp; Wood sp. nov., A. petrae Wood sp. nov., A. protuber Pisanty sp. nov., A. sulfurea Wood sp. nov., A. turmalina Pisanty &amp; Wood sp. nov., A. veronicae Pisanty &amp; Wood sp. nov., A. veterana Pisanty sp. nov., and A. xera Pisanty sp. nov. We synonymise Andrena edentula Wood with A. tadauchii Gusenleitner syn. nov., and recognise four infraspecific names as valid species: Andrena mediterranea Pisanty &amp; Scheuchl stat. nov., A. mizorhina Warncke stat. nov., A. noacki Alfken sp. resurr. and A. ochraceohirta Alfken sp. resurr. We additionally describe the hitherto unknown sexes of four species, provide new records for fifteen species previously unknown from Israel, and list fourteen taxa whose previously reported presence in Israel is considered erroneous or questionable.},
}
@article {pmid37044802,
year = {2022},
author = {Miko, L and Kolesnikov, VB and Ermilov, SG and Klimov, PB},
title = {Taxonomy of European Damaeidae (Acari, Oribatida) XI. European species of the genus Piribelba Miko 2021: redescriptions of P. rossica (Bulanova-Zachvatkina, 1957) and P. piriformis (Mihelčič, 1964) using morphology and DNA sequence data.},
journal = {Zootaxa},
volume = {5187},
number = {1},
pages = {169-210},
doi = {10.11646/zootaxa.5187.1.11},
pmid = {37044802},
issn = {1175-5334},
mesh = {Animals ; Base Sequence ; *Mites/classification/genetics ; },
abstract = {Two closely related species of the genus Piribelba (Oribatida, Damaeidae) are redescribed based on morphology of adults and developmental instars. Redescription of P. rossica (Bulanova-Zachvatkina, 1957) is based on specimens collected in Russia, including specimens identified by Bulanova-Zachvatkina; redescription of P. piriformis (Mihelčič, 1964) is based on specimens collected in Europe, including Mihelčič's types. COX1 sequence barcoding of P. piriformis and P. rossica indicated that they are distinct species, having 12.0% uncorrected p-distances and 13.3% Kimura two-parameter distances (K2P). Based on the morphological and genetical differences, the synonymy of P. rossica and P. piriformis is rejected. A key to known species of Piribelba is provided.},
}
@article {pmid37044741,
year = {2023},
author = {Wang, YL and Li, BX and Cui, MD and Zhang, Y and Wang, LE and Zhang, CH and Tsaur, SC and Chen, HW and Huang, J},
title = {Revision of the subgenus Stegana (Steganina) from China, with assessment of species delimitation using DNA barcodes (Diptera, Drosophilidae).},
journal = {Zootaxa},
volume = {5250},
number = {1},
pages = {1-109},
doi = {10.11646/zootaxa.5250.1.1},
pmid = {37044741},
issn = {1175-5334},
mesh = {Animals ; *Drosophilidae/genetics ; DNA Barcoding, Taxonomic ; Phylogeny ; China ; DNA ; },
abstract = {A total of 58 (eight known and 50 new) species of the subgenus Stegana (Steganina) from China were surveyed and (re)described: S. (S.) bacilla Chen &amp; Aotsuka, 2004, S. (S.) belokobylskiji Sidorenko, 1997, S. (S.) hirticeps Wang, Gao, &amp; Chen, 2013, S. (S.) izu Sidorenko, 1997, S. (S.) kanmiyai Okada &amp; Sidorenko, 1992, S. (S.) masanoritodai Okada &amp; Sidorenko, 1992, S. (S.) maymyo Sidorenko, 1997, stat. rev., S. (S.) nigripes Zhang &amp; Chen, 2015, S. (S.) alafoliacea Zhang &amp; Chen, sp. nov., S. (S.) baoxing Li &amp; Chen, sp. nov., S. (S.) bibarbata Li &amp; Chen, sp. nov., S. (S.) bimai Cui &amp; Chen, sp. nov., S. (S.) cinereipecta Zhang &amp; Chen, sp. nov., S. (S.) cardua Cui &amp; Chen, sp. nov., S. (S.) cordhirsuta Wang &amp; Chen, sp. nov., S. (S.) cornuta Li &amp; Chen, sp. nov., S. (S.) cucullata Li &amp; Chen, sp. nov., S. (S.) cultella Cui &amp; Chen, sp. nov., S. (S.) curvitabulata Cui &amp; Chen, sp. nov., S. (S.) daiya Cui &amp; Chen, sp. nov., S. (S.) dendrophila Zhang &amp; Chen, sp. nov., S. (S.) flabella Li &amp; Chen, sp. nov., S. (S.) flavipes Li &amp; Chen, sp. nov., S. (S.) formosa Zhang &amp; Chen, sp. nov., S. (S.) fusca Li &amp; Chen, sp. nov., S. (S.) fuscipes Li &amp; Chen, sp. nov., S. (S.) glaucopalpula Cui &amp; Chen, sp. nov., S. (S.) haba Zhang &amp; Chen, sp. nov., S. (S.) hirticlavata Cui &amp; Chen, sp. nov., S. (S.) iaspidea Zhang &amp; Chen, sp. nov., S. (S.) idiasta Cui &amp; Chen, sp. nov., S. (S.) kanda Cui &amp; Chen, sp. nov., S. (S.) labao Li &amp; Chen, sp. nov., S. (S.) lancang Li &amp; Chen, sp. nov., S. (S.) latifoliacea Wang &amp; Chen, sp. nov., S. (S.) liusanjieae Li &amp; Chen, sp. nov., S. (S.) magniflava Cui &amp; Chen, sp. nov., S. (S.) mailangang Li &amp; Chen, sp. nov., S. (S.) marenubila Cui &amp; Chen, sp. nov., S. (S.) menghai Zhang &amp; Chen, sp. nov., S. (S.) menglian Li &amp; Chen, sp. nov., S. (S.) minutiflava Li &amp; Chen, sp. nov., S. (S.) multiprocera Li &amp; Chen, sp. nov., S. (S.) nayun Li &amp; Chen, sp. nov., S. (S.) nigridentata Wang &amp; Chen, sp. nov., S. (S.) nigripalpula Cui &amp; Chen, sp. nov., S. (S.) otphylla Cui &amp; Chen, sp. nov., S. (S.) radiciflava Zhang &amp; Chen, sp. nov., S. (S.) rava Cui &amp; Chen, sp. nov., S. (S.) sciophila Li &amp; Chen, sp. nov., S. (S.) septencolorata Li &amp; Chen, sp. nov., S. (S.) serrata Zhang &amp; Chen, sp. nov., S. (S.) silvestrella Zhang &amp; Chen, sp. nov., S. (S.) simola Cui &amp; Chen, sp. nov., S. (S.) yani Li &amp; Chen, sp. nov., S. (S.) yixiang Zhang &amp; Chen, sp. nov., S. (S.) zaduo Cui &amp; Chen, sp. nov., and S. (S.) zhuoma Cui &amp; Chen, sp. nov. We also provided a complete list of Chinese Steganina species together with their geographical distributions. In addition, the majority of currently available DNA barcode (partial sequence of the mitochondrial cytochrome c oxidase subunit I (COI) gene) sequences of this subgenus (435 sequences of 102 spp.) were employed in a molecular analysis for species delimitation. Taken together, morphology- and molecular-based species delimitation results reached a consensus for an overwhelming majority of these Steganina species (98 of 102 spp.).},
}
@article {pmid37044732,
year = {2023},
author = {Chakraborty, RD and Sreelakshmy, S and Aghana, M and Gayathri, AP and Sreesanth, L},
title = {Occurrence of Deep-sea shrimp, Hadropenaeus lucasii (Spence Bate, 1881) from the southwest coast of India.},
journal = {Zootaxa},
volume = {5254},
number = {1},
pages = {127-132},
doi = {10.11646/zootaxa.5254.1.7},
pmid = {37044732},
issn = {1175-5334},
mesh = {Animals ; Phylogeny ; *Decapoda/genetics ; DNA ; Genes, Mitochondrial ; India ; },
abstract = {The present study provides an integrative report combining morphological and molecular analysis of the deep sea shrimp species Hadropenaeus lucasii (Spence Bate, 1881) from the southwest coast of India. The present specimen was obtained from the depths of 200-300m from the commercial bottom trawlers operated off Sakthikulangara fishing harbour off Kollam, Kerala. A phylogenetic analysis was used to explore the relationships of the genus. DNA barcoding and phylogenetic analysis were used to explore the relationship of the genus Hadropenaeus based on mitochondrial gene (16S: OK571387, OK571388; COI: OK569849, OK569850) sequences of the present specimen with the sequences retrieved from NCBI GenBank revealed an interspecies genetic divergence of 0.0% to 0.6%.},
}
@article {pmid37044724,
year = {2023},
author = {Torii, T and Akagi, T and Uchino, T and Kobayashi, T},
title = {A new species of Enchytraeus (Enchytraeidae, Clitellata) from sewage sludge of a plum processing plant in Japan.},
journal = {Zootaxa},
volume = {5254},
number = {2},
pages = {245-256},
doi = {10.11646/zootaxa.5254.2.5},
pmid = {37044724},
issn = {1175-5334},
mesh = {Animals ; Japan ; *Oligochaeta/classification/genetics ; Prunus domestica ; Sewage ; Manufacturing and Industrial Facilities ; },
abstract = {Enchytraeus ohtakai sp. nov. (Enchytraeidae, Clitellata, Oligochaeta) was discovered in the organic matter of a wastewater treatment facility of a plums processing plant in Honshu, Japan. The wastewater is characterized by high organic matter content and low salt concentration. Morphological analysis and DNA-sequencing of a fragment of the COI barcoding gene show that the new species belongs to the E. albidus species group. Within this group it differs in: vasa deferentia restricted to XII, preclitellar bundles with mostly three chaetae, postclitellar bundles with two or three, dorsal blood vessel from XII or XIII, spermathecal ectal duct completely glandular. spermatheca with a large diverticulum, accessory sexual glands present in XII, clitellum ventrally almost absent. The individual gene trees of COI analysis recovered this new species as a monophyletic group within the genus Enchytraeus, closely related to E. albidus species group.},
}
@article {pmid37044688,
year = {2023},
author = {Sanz-Veiga, PA and Savaris, M and Leivas, FWT and DA Silva Medeiros, A and Amorim, FW},
title = {A new seed-feeding species of Hemicolpus Heller, 1895 from south Brazil and redescription of Hemicolpus abdominalis Hustache, 1938 (Coleoptera: Curculionidae: Conoderinae).},
journal = {Zootaxa},
volume = {5227},
number = {3},
pages = {301-327},
doi = {10.11646/zootaxa.5227.3.1},
pmid = {37044688},
issn = {1175-5334},
mesh = {Female ; Animals ; *Coleoptera ; *Weevils ; Brazil ; Seeds ; *Rubiaceae ; },
abstract = {The genus Hemicolpus Heller, 1895 (Curculionidae: Conoderinae) currently includes six species: H. cubicus (Lacordaire) (Brazil); H. heteromorphus Hustache (Brazil); H. abdominalis Hustache (Bolivia, Brazil, and Paraguay); H. costaricensis Hespenheide (Costa Rica); H. randiae Hespenheide (El Salvador and Mexico) and H. prenai Hespenheide (El Salvador and Mexico). The known species are predispersal seed predators whose larvae feed and develop within fruits of Rubiaceae. Species from Central America have been reared from the fruits of Randia L. (Rubiaceae). In contrast, the only host plant known for the South American species, H. abdominalis, is Tocoyena formosa (Cham. &amp; Schltdl.) K. Schum. (Rubiaceae), a plant species widely distributed in the Cerrado biome, occurring from southeast to north and northeast of Brazil. Here, we describe a seventh species of Hemicolpus, H. maragatensis Sanz-Veiga, Savaris &amp; Leivas, sp. nov., morphologically close to H. abdominalis, associated with fruits of Randia ferox (Cham. &amp; Schltdl.) DC. in the south of Brazil. Furthermore, we designate a lectotype and provide a redescription of H. abdominalis, including additional characters to differentiate it from H. maragatensis. For both species, we provide morphological descriptions of external and internal characters, including male and female genitalia illustrations, distribution data, and notes on the biology and host plant. A barcode region of the mitochondrial DNA is also included for both species adding genetic information to the species characterization and differentiation. We also provide an identification key for the species of the genus.},
}
@article {pmid37044613,
year = {2023},
author = {Lv, JX and Wang, X and Huang, GH},
title = {A new record family Neopseustidae (Insecta: Lepidoptera) from Chongqing of China, with the first description of the Neopseustis archiphenax female adult.},
journal = {Zootaxa},
volume = {5257},
number = {1},
pages = {170-177},
doi = {10.11646/zootaxa.5257.1.13},
pmid = {37044613},
issn = {1175-5334},
mesh = {Male ; Female ; Animals ; *Lepidoptera ; *Moths/genetics ; Insecta ; Genitalia ; China ; DNA ; Animal Distribution ; },
abstract = {In 2022, the insect inventories organized by Prof. Zhi-Sheng Zhang of Southwest University were constructed in Yintiaoling Nature Reserve, Chongqing Municipality, China. The neopseustid moth from Chongqing based on three specimens of Neopseustis archiphenax by light trapping were reported in this paper. The photos of the male and female adults, genitalia, and abdominal special structures are presented with the female described firstly. Also, the DNA barcoding sequence data is provided, and the key to the Neopseustis species is given.},
}
@article {pmid37044521,
year = {2022},
author = {Chang, GD and Kim, SS and Park, KH},
title = {One new species and one new record for the genus Mesogastrura (Collembola, Hypogastruridae) from Korean caves, with DNA barcodes.},
journal = {Zootaxa},
volume = {5222},
number = {4},
pages = {325-342},
doi = {10.11646/zootaxa.5222.4.2},
pmid = {37044521},
issn = {1175-5334},
mesh = {Animals ; *Arthropods/anatomy &amp; histology/classification/genetics ; Caves ; Chiroptera ; DNA/genetics ; DNA Barcoding, Taxonomic ; Republic of Korea ; Species Specificity ; },
abstract = {We collected one new species and one new record in the genus Mesogastrura Bonet, 1930 (family Hypogastruridae) from three caves with different origins in the Korean Peninsula; Mesogastrura seotalensis sp. nov. and Mesogastrura ojcoviensis (Stach, 1919). The genus Mesogastrura Bonet, 1930 is newly recorded from the Korean Peninsula. Mesogastrura seotalensis sp. nov. shows various body color (light brown or much less and light purple), 3 + 3 eyes and unguis with three inner teeth. On the other hand, Mesogastrura ojcoviensis (Stach, 1919) is characterized by white body color, 2 + 2 eyes and unguis without inner tooth (rarely with 1). These species were found in piles of bat's guano inside of caves, so they are considered as troglophilous and guanophilous species. Partial DNA sequences of mitochondrial cytochrome c oxidase subunit I (COI) gene were used as DNA barcodes to clarify the species delimitation.},
}
@article {pmid37044509,
year = {2022},
author = {Wang, M and Lai, Y and Liu, X},
title = {New record of Borniochrysa Brooks &amp; Barnard, 1990 (Neuroptera: Chrysopidae) from China, with description of two new species.},
journal = {Zootaxa},
volume = {5222},
number = {5},
pages = {478-488},
doi = {10.11646/zootaxa.5222.5.6},
pmid = {37044509},
issn = {1175-5334},
mesh = {Animals ; Australia ; *Holometabola ; China ; },
abstract = {Borniochrysa Brooks &amp; Barnard, 1990 (Neuroptera: Chrysopidae: Chrysopinae: Chrysopinae) is a green lacewing genus, with five species previously recorded from the Australian, Oriental, and Afrotropical regions. Here we report the first record of Borniochrysa from China, and describe two new species, Borniochrysa kamayaria sp. nov. and Borniochrysa zhenxiana sp. nov. The standard DNA barcoding region of cytochrome c oxidase subunit I (COI) of these two new species was sequenced. An identification key to the Borniochrysa species is also provided.},
}
@article {pmid37044472,
year = {2023},
author = {Prieto, C and Faynel, C and Lorenc-Brudecka, J},
title = {Integrative description of two new species and two new subspecies of Lamprospilus Geyer (Lepidoptera: Lycaenidae).},
journal = {Zootaxa},
volume = {5244},
number = {2},
pages = {145-159},
doi = {10.11646/zootaxa.5244.2.3},
pmid = {37044472},
issn = {1175-5334},
mesh = {Female ; Male ; Animals ; *Butterflies ; },
abstract = {Lamprospilus stegmaier Prieto &amp; Faynel sp. nov. is described from five specimens collected in sympatry with L. nicetus C. Felder &amp; R. Felder on the northern central range of the Colombian Andes. Lamprospilus bicolor Faynel &amp; Prieto sp. nov. is described from specimens collected in Colombia, Peru and Bolivia. Lamprospilus bicolor mirador Faynel &amp; Prieto ssp. nov. is described from specimens collected in Peru and Bolivia. Lamprospilus decorata valluna Prieto &amp; Faynel ssp. nov. is described from specimens collected in Western Colombia. Male and female phenotypes are associated, and we present morphological and molecular diagnostic characters for the new species. We also evaluate the congruence between a priori morphology-based species identifications and Molecular Operational Taxonomic Units (MOTUs) delimitations based on Barcode Index Numbers (BINs) in the genus. DNA barcodes are in perfect agreement with morphology in 64% of the species. Interspecific distances were found to range from 3.22% to 8.42% (average 5.48%), whilst their mean intraspecific variation ranges from 0.0% to 4.30% (average 1.78%). Based on DNA barcodes evidence of topotypic individuals, the study of original descriptions and illustrations of the holotypes, we consider here that Lamprospilus occidentalis Johnson &amp; Salazar 2004 is a new junior subjective synonym of L. draudti Lathy, 1932.},
}
@article {pmid37044436,
year = {2023},
author = {Timossi, G and Ruzzier, E},
title = {Description of Sphaleroptera orientana meridionalis subs. n. (Lepidoptera: Tortricidae: Cnephasiini) from the Pale di San Martino Mountain plateau (Dolomites, NE Italy).},
journal = {Zootaxa},
volume = {5249},
number = {1},
pages = {1-11},
doi = {10.11646/zootaxa.5249.1.1},
pmid = {37044436},
issn = {1175-5334},
mesh = {Animals ; Environment ; Italy ; *Moths/anatomy &amp; histology/classification/genetics ; },
abstract = {On the base of newly collected material, a new subspecies of the alpine endemic moth Sphaleroptera orientana Whitebread, 2006 (Lepidoptera: Tortricidae) from the Pale di San Martino Group (Dolomites, Northern Italy) is described. Morphological characters of the adults and DNA barcode suggests the presence of allopatric populations of S. orientana in the South-eastern Alps, attributable to two distinct subspecies: S. o. suborientana Whitebread, 2006 in the Catinaccio, the Sella, and the Fanes group, and Julian Alps, and S. o. meridionalis subs. nov. known from the Pale of San Martino group. The main biogeographic barrier is constituted by the complex of the Fiemme valleys-Val di Fassa-by the Pordoi Pass and by the Val Cordevole which from west to north to east separate the distribution area of S. o. suorientana from S.o. meridionalis.},
}
@article {pmid37043852,
year = {2023},
author = {Li, H and Yao, J and Min, N and Sunahara, G and Duran, R},
title = {New insights on the effect of non-ferrous metal mining and smelting activities on microbial activity characteristics and bacterial community structure.},
journal = {Journal of hazardous materials},
volume = {453},
number = {},
pages = {131301},
doi = {10.1016/j.jhazmat.2023.131301},
pmid = {37043852},
issn = {1873-3336},
mesh = {Cadmium/analysis ; RNA, Ribosomal, 16S/genetics ; *Soil Pollutants/toxicity/analysis ; *Metals, Heavy/analysis ; Mining ; Biodegradation, Environmental ; Soil/chemistry ; China ; Environmental Monitoring ; },
abstract = {Mining and smelting activities have brought potentially serious heavy metal(loid)s pollution to their surrounding locale. However, studies on microbial metabolic activities, community structure, and adaptation in soils proximal to non-ferrous metal mining and smelting areas are still lacking. Here the effects of biotic and abiotic characteristics of soil taken from sites surrounding inactive and active non-ferrous metal mine smelting facilities on microbial enzyme activity, microcalorimetry, and high-throughput sequencing of 16S rRNA gene barcoding were studied. Data indicated that the soils were heavily polluted by toxic metal(loid)s, of which As and Cd were the main contaminants. Microbial acid phosphatase activity and microcalorimetric total heat value were sensitive metabolic indicators in the studied areas. Actinobacteriota had the highest relative abundance, followed by Proteobacteria, Chloroflexi, and Acidobacteria. Microbial metabolic activity, bacterial community structure and phenotype varied between inactive and active sites (p < 0.05). Such analyses indicated that electrical conductivity, total As, Cu, and Mn contents, and bioavailable As, Cu, Cd, and Mn concentrations were key factors determining microbial activities, bacterial community structure, and phenotypes. Knowledge of microbial adaptation to heavy metal stressors is important for better understanding the aerial transfer of fugitive heavy metal(loid)s (and possibly microbes) and for designing future strategies for improved soil bioremediation.},
}
@article {pmid37042555,
year = {2023},
author = {Labuschagne, K and Meiswinkel, R and Liebenberg, D and Van Zyl, C and Van Schalkwyk, A and Scholtz, C},
title = {Description of Culicoides truuskae sp. n. (Diptera: Ceratopogonidae) from southern Africa.},
journal = {The Onderstepoort journal of veterinary research},
volume = {90},
number = {1},
pages = {e1-e14},
pmid = {37042555},
issn = {2219-0635},
mesh = {Female ; Male ; Animals ; *Ceratopogonidae ; Phylogeny ; Africa, Southern ; South Africa ; Namibia ; },
abstract = {Culicoides truuskae Labuschagne and Meiswinkel sp. n. is described and illustrated in both sexes from material collected in South Africa and Namibia. It is restricted to the xeric western margin of the subcontinent, occurring in Fynbos, Nama-Karoo and Succulent Karoo ecoregions in South Africa and Desert and Savanna ecoregions in Namibia experiencing 600 mm of rainfall annually. Culicoides truuskae sp. n. is part of the Afrotropical 'plain-wing' Culicoides in which the wing lacks a distinguishing pattern of light and dark spots; the diagnostic dark smudge that traverses wing cell r3 may result in C. truuskae sp. n. being misidentified as the sympatric but phyletically unrelated Culicoides herero (Enderlein) - (of the Similis group, subgenus Oecacta Poey). Additionally, this study is the first description of the male of C. herero. C. truuskae sp. n. and Culicoides coarctatus Clastrier and Wirth share similar characters in the male genitalia, although the two species are separable on wing pattern and female flagellum sensilla coeloconica (SCo) distribution. The breeding habitat and adult female blood-feeding preferences of C. truuskae sp. n. are not known. A maximum likelihood phylogenetic tree, using mitochondrial cytochrome c oxidase I (COI) sequence data, is provided to further clarify the relationship between C. truuskae sp. n., C. coarctatus and C. herero. Extensive light trap data, collected over 30 years, are used to map the distribution ranges of C. truuskae sp. n., C. coarctatus and C. herero in Southern Africa.Contribution: The description of this new species and the description of the male of C. herero increases our understanding of the diversity and distribution of Culicoides species in southern Africa.},
}
@article {pmid37041463,
year = {2023},
author = {Abouseada, HH and Mohamed, AH and Teleb, SS and Badr, A and Tantawy, ME and Ibrahim, SD and Ellmouni, FY and Ibrahim, M},
title = {Genetic diversity analysis in wheat cultivars using SCoT and ISSR markers, chloroplast DNA barcoding and grain SEM.},
journal = {BMC plant biology},
volume = {23},
number = {1},
pages = {193},
pmid = {37041463},
issn = {1471-2229},
mesh = {Humans ; *DNA, Chloroplast ; *Triticum ; Edible Grain ; Plant Breeding ; Polymorphism, Genetic ; },
abstract = {BACKGROUND: Wheat is a major cereal that can narrow the gap between the increasing human population and food production. In this connection, assessing genetic diversity and conserving wheat genetic resources for future exploitation is very important for breeding new cultivars that may withstand the expected climate change. The current study evaluates the genetic diversity in selected wheat cultivars using ISSR and SCoT markers, the rbcL and matK chloroplast DNA barcoding, and grain surface sculpture characteristics. We anticipate that these objectives may prioritize using the selected cultivars to improve wheat production. The selected collection of cultivars may lead to the identification of cultivars adapted to a broad spectrum of climatic environments.<br><br>RESULTS: Multivariate clustering analyses of the ISSR and SCoT DNA fingerprinting polymorphism grouped three Egyptian cultivars with cultivar El-Nielain from Sudan, cultivar Aguilal from Morocco, and cultivar Attila from Mexico. In the other group, cultivar Cook from Australia and cultivar Chinese-166 were differentiated from four other cultivars: cultivar Cham-10 from Syria, cultivar Seri-82 from Mexico, cultivar Inqalab-91 from Pakistan, and cultivar Sonalika from India. In the PCA analysis, the Egyptian cultivars were distinct from the other studied cultivars. The rbcL and&#xa0;matK sequence variation analysis indicated similarities between Egyptian cultivars and cultivar Cham-10 from Syria and cultivar Inqalab-91 from Pakistan, whereas cultivar Attila from Mexico was distinguished from all other cultivars. Combining the data of ISSR and SCoT with the&#xa0;rbcL and&#xa0;matK results retained the close resemblance among the two Egyptian cultivars EGY1: Gemmeiza-9 and EGY3: Sakha-93, and the Moroccan cultivar Aguilal, and the Sudanese cultivar El-Nielain and between Seri-82, Inqalab-91, and Sonalika cultivars. The analysis of all data distinguished cultivar Cham-10 from Syria from all other cultivars, and the analysis of grain traits indicated a close resemblance between cv. Cham-10 from and the two Egyptian cultivars Gemmeiza-9 and Sakha-93.<br><br>CONCLUSIONS: The analysis of rbcL and matK chloroplast DNA barcoding agrees with the ISSR and the SCoT markers in supporting the close resemblance between the Egyptian cultivars, particularly Gemmeiza-9 and Sakha-93. The ISSR and SCoT data analyses significantly expressed high differentiation levels among the examined cultivars. Cultivars with closer resemblance may be recommended for breeding new wheat cultivars adapted to various climatic environments.},
}
@article {pmid37040507,
year = {2023},
author = {Guo, W and Cai, Y and Liu, X and Ji, Y and Zhang, C and Wang, L and Liao, W and Liu, Y and Cui, N and Xiang, J and Li, Z and Wu, D and Li, J},
title = {Single-Exosome Profiling Identifies ITGB3+ and ITGAM+ Exosome Subpopulations as Promising Early Diagnostic Biomarkers and Therapeutic Targets for Colorectal Cancer.},
journal = {Research (Washington, D.C.)},
volume = {6},
number = {},
pages = {0041},
pmid = {37040507},
issn = {2639-5274},
abstract = {Tumor metastasis is a hallmark of colorectal cancer (CRC), in which exosome plays a crucial role with its function in intercellular communication. Plasma exosomes were collected from healthy control (HC) donors, localized primary CRC and liver-metastatic CRC patients. We performed proximity barcoding assay (PBA) for single-exosome analysis, which enabled us to identify the alteration in exosome subpopulations associated with CRC progression. By in vitro and in vivo experiments, the biological impact of these subpopulations on cancer proliferation, migration, invasion, and metastasis was investigated. The potential application of exosomes as diagnostic biomarkers was evaluated in 2 independent validation cohorts by PBA. Twelve distinct exosome subpopulations were determined. We found 2 distinctly abundant subpopulations: one ITGB3-positive and the other ITGAM-positive. The ITGB3-positive cluster is rich in liver-metastatic CRC, compared to both HC group and primary CRC group. On the contrary, ITGAM-positive exosomes show a large-scale increase in plasma of HC group, compared to both primary CRC and metastatic CRC groups. Notably, both discovery cohort and validation cohort verified ITGB3+ exosomes as potential diagnostic biomarker. ITGB3+ exosomes promote proliferation, migration, and invasion capability of CRC. In contrast, ITGAM+ exosomes suppress CRC development. Moreover, we also provide evidence that one of the sources of ITGAM+ exosomes is macrophage. ITGB3+ exosomes and ITGAM+ exosomes are proven 2 potential diagnostic, prognostic, and therapeutic biomarkers for management of CRC.},
}
@article {pmid37040419,
year = {2023},
author = {Brown, MR and Hollingsworth, PM and Forrest, LL and Hart, ML and Leitch, IJ and Jones, L and Ford, C and de Vere, N and Twyford, AD},
title = {Genetic factors predict hybrid formation in the British flora.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {16},
pages = {e2220261120},
pmid = {37040419},
issn = {1091-6490},
support = {NE/L011336/1//UKRI | Natural Environment Research Council (NERC)/ ; BB/M010996/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {Phylogeny ; *Biological Evolution ; *Ploidies ; Nucleic Acid Hybridization ; Hybridization, Genetic ; },
abstract = {Natural hybridization can have a profound evolutionary impact, with consequences ranging from the extinction of rare taxa to the origin of new species. Natural hybridization is particularly common in plants; however, our understanding of the general factors that promote or prevent hybridization is hampered by the highly variable outcomes in different lineages. Here, we quantify the influence of different predictors on hybrid formation across species from an entire flora. We combine estimates of hybridization with ecological attributes and a new species-level phylogeny for over 1,100 UK flowering plant species. Our results show that genetic factors, particularly parental genetic distance, as well as phylogenetic position and ploidy, are key determinants of hybrid formation, whereas many other factors such as range overlap and genus size explain much less variation in hybrid formation. Overall, intrinsic genetic factors shape the evolutionary and ecological consequences of natural hybridization across species in a flora.},
}
@article {pmid37039628,
year = {2023},
author = {Elgart, V and Loscalzo, J},
title = {Local generation and efficient evaluation of numerous drug combinations in a single sample.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {37039628},
issn = {2050-084X},
support = {U54 HL119145/HL/NHLBI NIH HHS/United States ; R01 HL155096/HL/NHLBI NIH HHS/United States ; U01 HL108630/HL/NHLBI NIH HHS/United States ; R01 HL155107/HL/NHLBI NIH HHS/United States ; },
mesh = {*Phenotype ; Drug Combinations ; },
abstract = {We develop a method that allows one to test a large number of drug combinations in a single-cell culture sample. We rely on the randomness of drug uptake in individual cells as a tool to create and encode drug treatment regimens. A single sample containing thousands of cells is treated with a combination of fluorescently barcoded drugs. We create independent transient drug gradients across the cell culture sample to produce heterogeneous local drug combinations. After the incubation period, the ensuing phenotype and corresponding drug barcodes for each cell are recorded. We use these data for statistical prediction of the treatment response to the drugs in a macroscopic population of cells. To further application of this technology, we developed a fluorescent barcoding method that does not require any chemical drug(s) modifications. We also developed segmentation-free image analysis capable of handling large optical fields containing thousands of cells in the sample, even in confluent growth condition. The technology necessary to execute our method is readily available in most biological laboratories, does not require robotic or microfluidic devices, and dramatically reduces resource needs and resulting costs of the traditional high-throughput studies.},
}
@article {pmid37039421,
year = {2023},
author = {Sithole, Y and Musschoot, T and Huyghe, CET and Chakona, A and Vreven, EJWMN},
title = {A new species of Parauchenoglanis (Auchenoglanididae: Siluriformes) from the Upper Lualaba River (Upper Congo), with further evidence of hidden species diversity within the genus.},
journal = {Journal of fish biology},
volume = {102},
number = {6},
pages = {1387-1414},
doi = {10.1111/jfb.15309},
pmid = {37039421},
issn = {1095-8649},
support = {UID 114603//DSI/NRF Professional Development Programme/ ; //RMCA, Belgium/ ; },
mesh = {Animals ; *Rivers ; *Catfishes ; Congo ; Biodiversity ; DNA, Mitochondrial/genetics ; },
abstract = {Parauchenoglanis zebratus sp. nov. is a new species endemic to the Upper Lualaba in the Upper Congo Basin. It is distinguished from all its congeners known from the Congo Basin and adjacent basins by the presence of (1) distinctive dark-brown or black vertical bars on the lateral side of the body, at least for specimens about ≥120 mm LS , (2) a broad and triangular humeral process embedded under the skin and (3) a well-serrated pectoral-fin spine. Genetic analysis based on mtDNA COI sequences confirmed the genetic distinctiveness (2.8%-13.6% K2P genetic divergence) of P. zebratus sp. nov. from congeners within the Congo and adjacent river basins. The study also revealed additional undocumented diversity within P. ngamensis, P. pantherinus, P. punctatus and P. balayi, indicating the need for further in-depth alpha-taxonomic attention to provide more accurate species delimitations for this genus. The discovery of yet another new species endemic to the Upper Lualaba, and this well outside the currently established protected areas, highlights the critical need for further assessments to accurately document the species diversity to guide freshwater conservation prioritisation and biodiversity management in this region.},
}
@article {pmid37039376,
year = {2023},
author = {Domínguez-Contreras, JF and Jiménez-Rosenberg, SPA and Reguera-Rouzaud, N and Sánchez-Velasco, L and Díaz-Viloria, N},
title = {Molecular identification and first morphological description of the Colorado snapper Lutjanus colorado (Perciformes: Lutjanidae) larvae.},
journal = {Journal of fish biology},
volume = {102},
number = {6},
pages = {1481-1491},
doi = {10.1111/jfb.15401},
pmid = {37039376},
issn = {1095-8649},
support = {2015-2//CONACYT, Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 257019//CONACYT, Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 20150176//Secretar&#xed;a de Investigaci&#xf3;n y Posgrado, Instituto Polit&#xe9;cnico Nacional/ ; 20160514//Secretar&#xed;a de Investigaci&#xf3;n y Posgrado, Instituto Polit&#xe9;cnico Nacional/ ; 20210196//Secretar&#xed;a de Investigaci&#xf3;n y Posgrado, Instituto Polit&#xe9;cnico Nacional/ ; 20220560//Secretar&#xed;a de Investigaci&#xf3;n y Posgrado, Instituto Polit&#xe9;cnico Nacional/ ; },
mesh = {Animals ; Larva/anatomy &amp; histology ; Colorado ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Phylogeny ; Fishes/genetics ; *Perciformes/genetics/metabolism ; },
abstract = {This research study obtained the first morphological description of the Colorado snapper (Lutjanus colorado) larvae assisted by DNA barcoding as a molecular identification tool. Sixteen Lutjanidae larvae were separated from zooplankton samples and selected for this study. A fragment of the mitochondrial gene cytochrome oxidase subunit I (COI) of 658 bp was used in the analyses of intra- and interspecific genetic divergences; a neighbour-joining tree (NJ) of K2P distances was performed with reference sequences of 15 Lutjanidae species from the Northeastern Tropical Pacific. Genetic divergences and the NJ tree identified 16 larvae as L. colorado. Morphological investigations of larvae at different developmental stages were performed; similarities and differences are discussed in comparison to four species described previously for the Northeastern Pacific. Pigmentation patterns were the best diagnostic features, particularly the caudal melanophores, at least up to 12.4 mm body length.},
}
@article {pmid37038522,
year = {2023},
author = {Teklemariam, DM and Gailing, O and Siregar, IZ and Amandita, FY and Moura, CCM},
title = {Integrative taxonomy using the plant core DNA barcodes in Sumatra's Burseraceae.},
journal = {Ecology and evolution},
volume = {13},
number = {4},
pages = {e9935},
pmid = {37038522},
issn = {2045-7758},
abstract = {The high diversity and limited floral information in tropical forests often pose a challenge for species identification. However, over the past decade, DNA barcoding has been employed in tropical forests, including Sumatran forests, to enhance floristic surveys. This technique facilitates the discrimination of morphologically similar species and addresses the limitations of conventional species identification, which relies on short-lived reproductive structures. This study aimed to evaluate the efficiency of matK, rbcL, and the combination of both chloroplast markers for species identification in Burseraceae by employing genetic distance and species tree inference. In this study, we collected 197 specimens representing 20 species from five genera of Burseraceae. The highest percentage of specimens' identification (36%) at the species level was obtained using matK + rbcL, followed by matK (31%), and rbcL (7%). The matK dataset presented the highest interspecific divergence with a mean of 0.008. In addition, a lack of barcode gap was observed in both markers, suggesting potential limitations of the core barcodes for distinguishing Sumatran species within Burseraceae. The monophyly test confirmed five species as monophyletic using Bayesian species tree inferences for matK. Overall, our results demonstrate that matK outperforms rbcL in species identification of Burseraceae, whereas their combination did not enhance species delimitation. To improve the molecular species assignments of this family, future studies may consider including more DNA markers in conjuction with matK, and broadening the availability of reference sequences for species that have not yet been included in the databases. The outcomes of molecular species identification vary depending on the taxonomic group under investigation. Implementation of phylogenomics for species delimitation and diagnostic marker development is strongly recommended for tropical biodiversity assessments, especially for poorly studied clades.},
}
@article {pmid37036939,
year = {2023},
author = {Kritsky, DC and Martin, SB},
title = {KANNAPHALLUS RAPHIDIUM N. SP. (MONOGENOIDEA: MAZOCRAEIDEA: HETERAXINIDAE) PARASITIC ON THE GILL LAMELLAE OF THE GOLDEN TREVALLY GNATHANODON SPECIOSUS (CARANGIFORMES: CARANGIDAE) OCCURRING IN THE COASTAL WATERS OF QUEENSLAND AND WESTERN AUSTRALIA.},
journal = {The Journal of parasitology},
volume = {109},
number = {2},
pages = {96-106},
doi = {10.1645/22-116},
pmid = {37036939},
issn = {1937-2345},
mesh = {Animals ; Male ; Queensland ; Western Australia ; Gills/parasitology ; *Parasites ; Bayes Theorem ; *Perciformes/parasitology ; *Fish Diseases/epidemiology/parasitology ; Species Specificity ; *Trematoda ; Fishes ; DNA, Ribosomal ; Phylogeny ; },
abstract = {An undescribed species of KannaphallusUnnithan, 1957 (Monogenoidea: Heteraxinidae) was collected from the gills of the golden trevally Gnathanodon speciosus (Forsskål) (Carangidae) from Moreton Bay, Queensland, during January 2016 and from Ningaloo Reef, Western Australia, during December 2021 and June 2022. The diagnosis for Kannaphallus was emended and the new species, Kannaphallus raphidium, was described. Kannaphallus virilis of Young, nec Unnithan was placed in synonymy with K. raphidium. The distal components of the male reproductive system and the arrangement of the clamp rows of the haptor occurred as mirror images among specimens of K. raphidium, suggesting that the respective antipodes of K. raphidium may have reproductive implications and function in the site selection of the parasite on the host's gills. A specimen of K. raphidium from Western Australia was sequenced for the cytochrome c oxidase subunit 1 (COI) mtDNA and ITS2 rDNA barcoding markers, and the phylogenetically informative 28S rDNA marker. Maximum likelihood and Bayesian inference analyses based on a partial 28S rDNA alignment, including all comparable heteraxinid sequence data available, resolved the Heteraxininae and Cemocotylinae as reciprocatively paraphyletic and provided evidence that Kannaphallus may be paraphyletic. No taxonomic changes concerning the subfamilies and genera of the Heteraxinidae were proposed. Finally, Kannaphallus univaginalisRamalingam, 1960 and Cemocotylelloides univaginalis (Ramalingam, 1960) Nitta, Kondo, Ohtsuka, Kamarudin, and Ismail, 2022 are considered nomen nuda sensu the International Code of Zoological Nomenclature.},
}
@article {pmid37035041,
year = {2023},
author = {Gomes, T and Pereira, JA and Moya-Laraño, J and Poveda, J and Lino-Neto, T and Baptista, P},
title = {Deciphering plant health status: The link between secondary metabolites, fungal community and disease incidence in olive tree.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1048762},
pmid = {37035041},
issn = {1664-462X},
abstract = {Plant-associated microorganisms are increasingly recognized to play key roles in host health. Among several strategies, associated microorganisms can promote the production of specific metabolites by their hosts. However, there is still a huge gap in the understanding of such mechanisms in plant-microorganism interaction. Here, we want to determine whether different levels of olive leaf spot (OLS) disease incidence were related to differences in the composition of fungal and secondary metabolites (i.e. phenolic and volatile compounds) in leaves from olive tree cultivars with contrasting OLS susceptibilities (ranging from tolerant to highly susceptible). Accordingly, leaves with three levels of OLS incidence from both cultivars were used to assess epiphytic and endophytic fungal communities, by barcoding of cultivable isolates, as well as to evaluate leaf phenolic and volatile composition. Fungal and metabolite compositions variations were detected according to the level of disease incidence. Changes were particularly noticed for OLS-tolerant cultivars, opposing to OLS-susceptible cultivars, suggesting that disease development is linked, not only to leaf fungal and metabolite composition, but also to host genotype. A set of metabolites/fungi that can act as predictive biomarkers of plant tolerance/susceptibility to OLS disease were identified. The metabolites α-farnesene and p-cymene, and the fungi Fusarium sp. and Alternaria sp. were more related to disease incidence, while Pyronema domesticum was related to the absence of disease symptoms. Cultivar susceptibility to OLS disease is then suggested to be driven by fungi, volatile and phenolic host leaves composition, and above all to plant-fungus interaction. A deeper understanding of these complex interactions may unravel plant defensive responses.},
}
@article {pmid37030291,
year = {2023},
author = {Eiger, DS and Smith, JS and Shi, T and Stepniewski, TM and Tsai, CF and Honeycutt, C and Boldizsar, N and Gardner, J and Nicora, CD and Moghieb, AM and Kawakami, K and Choi, I and Hicks, C and Zheng, K and Warman, A and Alagesan, P and Knape, NM and Huang, O and Silverman, JD and Smith, RD and Inoue, A and Selent, J and Jacobs, JM and Rajagopal, S},
title = {Phosphorylation barcodes direct biased chemokine signaling at CXCR3.},
journal = {Cell chemical biology},
volume = {30},
number = {4},
pages = {362-382.e8},
pmid = {37030291},
issn = {2451-9448},
support = {P41 GM103493/GM/NIGMS NIH HHS/United States ; T32 AR007098/AR/NIAMS NIH HHS/United States ; R01 GM148972/GM/NIGMS NIH HHS/United States ; R01 GM139858/GM/NIGMS NIH HHS/United States ; 20PRE35120592/AHA/American Heart Association-American Stroke Association/United States ; K08 HL114643/HL/NHLBI NIH HHS/United States ; T32 GM145449/GM/NIGMS NIH HHS/United States ; R01 GM122798/GM/NIGMS NIH HHS/United States ; T32 GM007171/GM/NIGMS NIH HHS/United States ; },
mesh = {Phosphorylation ; beta-Arrestins/metabolism ; Ligands ; *Signal Transduction ; *Receptors, G-Protein-Coupled/metabolism ; Chemokines/metabolism ; },
abstract = {G protein-coupled receptor (GPCR)-biased agonism, selective activation of certain signaling pathways relative to others, is thought to be directed by differential GPCR phosphorylation "barcodes." At chemokine receptors, endogenous chemokines can act as "biased agonists", which may contribute to the limited success when pharmacologically targeting these receptors. Here, mass spectrometry-based global phosphoproteomics revealed that CXCR3 chemokines generate different phosphorylation barcodes associated with differential transducer activation. Chemokine stimulation resulted in distinct changes throughout the kinome in global phosphoproteomics studies. Mutation of CXCR3 phosphosites altered β-arrestin 2 conformation in cellular assays and was consistent with conformational changes observed in molecular dynamics simulations. T cells expressing phosphorylation-deficient CXCR3 mutants resulted in agonist- and receptor-specific chemotactic profiles. Our results demonstrate that CXCR3 chemokines are non-redundant and act as biased agonists through differential encoding of phosphorylation barcodes, leading to distinct physiological processes.},
}
@article {pmid37029267,
year = {2023},
author = {Coleman, K and Hu, J and Schroeder, A and Lee, EB and Li, M},
title = {SpaDecon: cell-type deconvolution in spatial transcriptomics with semi-supervised learning.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {378},
pmid = {37029267},
issn = {2399-3642},
support = {P01 AG066597/AG/NIA NIH HHS/United States ; R01 EY030192/EY/NEI NIH HHS/United States ; R01 GM125301/GM/NIGMS NIH HHS/United States ; R01 HL150359/HL/NHLBI NIH HHS/United States ; },
mesh = {*Transcriptome ; *Gene Expression Profiling/methods ; Supervised Machine Learning ; },
abstract = {Spatially resolved transcriptomics (SRT) has advanced our understanding of the spatial patterns of gene expression, but the lack of single-cell resolution in spatial barcoding-based SRT hinders the inference of specific locations of individual cells. To determine the spatial distribution of cell types in SRT, we present SpaDecon, a semi-supervised learning approach that incorporates gene expression, spatial location, and histology information for cell-type deconvolution. SpaDecon was evaluated through analyses of four real SRT datasets using knowledge of the expected distributions of cell types. Quantitative evaluations were performed for four pseudo-SRT datasets constructed according to benchmark proportions. Using mean squared error and Jensen-Shannon divergence with the benchmark proportions as evaluation criteria, we show that SpaDecon performance surpasses that of published cell-type deconvolution methods. Given the accuracy and computational speed of SpaDecon, we anticipate it will be valuable for SRT data analysis and will facilitate the integration of genomics and digital pathology.},
}
@article {pmid37028451,
year = {2023},
author = {Huayamares, SG and Lokugamage, MP and Rab, R and Da Silva Sanchez, AJ and Kim, H and Radmand, A and Loughrey, D and Lian, L and Hou, Y and Achyut, BR and Ehrhardt, A and Hong, JS and Sago, CD and Paunovska, K and Echeverri, ES and Vanover, D and Santangelo, PJ and Sorscher, EJ and Dahlman, JE},
title = {High-throughput screens identify a lipid nanoparticle that preferentially delivers mRNA to human tumors in vivo.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {357},
number = {},
pages = {394-403},
pmid = {37028451},
issn = {1873-4995},
support = {R01 DE026941/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; Squamous Cell Carcinoma of Head and Neck ; RNA, Messenger/genetics ; Lipids ; *Nanoparticles ; *Head and Neck Neoplasms/genetics ; RNA, Small Interfering/genetics ; },
abstract = {Lipid nanoparticles (LNPs) are a clinically relevant way to deliver therapeutic mRNA to hepatocytes in patients. However, LNP-mRNA delivery to end-stage solid tumors such as head and neck squamous cell carcinoma (HNSCC) remains more challenging. While scientists have used in vitro assays to evaluate potential nanoparticles for HNSCC delivery, high-throughput delivery assays performed directly in vivo have not been reported. Here we use a high-throughput LNP assay to evaluate how 94 chemically distinct nanoparticles delivered nucleic acids to HNSCC solid tumors in vivo. DNA barcodes were used to identify LNP[HNSCC], a novel LNP for systemic delivery to HNSCC solid tumors. Importantly, LNP[HNSCC] retains tropism to HNSCC solid tumors while minimizing off-target delivery to the liver.},
}
@article {pmid37026968,
year = {2023},
author = {Vedelago, C and Li, J and Lowry, K and Howard, C and Wuethrich, A and Trau, M},
title = {A Multiplexed SERS Microassay for Accurate Detection of SARS-CoV-2 and Variants of Concern.},
journal = {ACS sensors},
volume = {8},
number = {4},
pages = {1648-1657},
doi = {10.1021/acssensors.2c02782},
pmid = {37026968},
issn = {2379-3694},
mesh = {Animals ; *SARS-CoV-2 ; *COVID-19/diagnosis ; Epitopes ; Gold ; Nucleocapsid Proteins ; },
abstract = {Severe acute respiratory syndrome coronavirus 2 variants play an important role in predicting patient outcome during postinfection, and with growing fears of COVID-19 reservoirs in domestic and wild animals, it is necessary to adapt detection systems for variant detection. However, variant-specific detection remains challenging. Surface-enhanced Raman scattering is a sensitive and multiplexing technique that allows the simultaneous detection of multiple targets for accurate identification. Here we propose the development of a multiplex SERS microassay to detect both the spike and nucleocapsid structural proteins of SARS-CoV-2. The designed SERS microassay integrates gold-silver hollow nanobox barcodes and electrohydrodynamically induced nanomixing which in combination enables highly specific and sensitive detection of SARS-CoV-2 and the S-protein epitopes to delineate between ancestral prevariant strains with the newer variants of concern, Delta and Omicron. The microassay allows detection from as low as 20 virus/μL and 50 pg/mL RBD protein and can clearly identify the virus among infected versus healthy nasopharyngeal swabs, with the potential to identify between variants. The detection of both S- and N-proteins of SARS-CoV-2 and the differentiation of variants on the SERS microassay can aid the early detection of COVID-19 to reduce transmission rates and lead into adequate treatments for those severely affected by the virus.},
}
@article {pmid37026626,
year = {2023},
author = {Jia, M and Ni, Y and Liu, X and Zhao, H and Zhao, X and He, B and Zhang, C and Liu, H},
title = {First Report of Root Rot Caused by Pythium myriotylum on Sesame in China.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-10-22-2503-PDN},
pmid = {37026626},
issn = {0191-2917},
abstract = {Sesame (Sesamum indicum L.) is a very important oilseed crop and cultivated on 11.7 million hectares, producing 6.02 million tons of seeds with an average seed yield of 512 kg ha-1 in the world (Yadav et al. 2022). In June of 2021, diseased roots were observed on sesame in the villages of Mada and Hanba, Xiangcheng city (114.88°N, 33.13°E), Henan province, China. The diseased plants appeared stunted and wilted at the seedling stage. Approximately 7.1% to 17.7% of plants were affected in two fields, 0.6 ha in total, and disease severity in each affected plant ranged from 50% to 80%. Twenty-four disease plants were collected to confirm the pathogen. The diseased roots were cut into small fragments (2 to 5 mm long), surface sterilized with 75% ethanol (for 1 min), and 10% sodium hypochlorite (for 1 min) and then rinsed in sterilized water three times (1 min each rinse). The fragments were blotted dry and transferred to a potato dextrose agar (PDA) medium (potato 200 g/L, glucose 20 g/L, agar 18 g/L) amended with streptomycin (50 μg/mL). After incubation at 28°C for 24 h, white mycelium grew out from plant fragments. Then, a total of seven morphologically similar strains were transferred onto fresh V8 agar by hyphal tip transfer (Rollins 2003). By light microscope observations, the sporangia were filamentous or digitated, and undifferentiated or inflated lobulate. The oospores were mostly aplerotic, globose or subglobose in shape, and 20.4 to 42.6 μm in diameter (n = 90, n: Total number of oospores measured). Furthermore, antheridia were bulbous-like or clavate-like and were observed attached to the surface of the oospores. The zoospores were abundant and ranged from 8.5 to 14.2 μm in diameter. The morphology characteristics of all strains were consistent with those of Pythium myriotylum (Watanabe et al. 2007). Genomic DNA was extracted from the representative strain 20210628 using the CTAB method (Wangsomboondee et al. 2002). The complete internal transcribed spacer (ITS) and cytochrome oxidase subunit I gene (COI, COX1) can be valid and useful barcodes for accurate identification of many oomycetes (Robideau et al. 2011). The ITS and COI were amplified with the primers ITS1/ITS4 (Riit et al. 2016) and primers OomCox-Levup/OomCox-Levlo (Robideau et al. 2011), respectively. The nucleotide sequences obtained were deposited in the GenBank database under the accession numbers OM230138.2 (ITS) and ON500503.1 (COI). GenBank BLAST search identified the sequences as P. myriotylum ITS and COI sequences (e.g., HQ237488.1 and MK510848.1, respectively) with 100% coverage and 100% identity. To evaluate the pathogenicity, sesame seeds (cultivar: Jinzhi No.3) were planted in 12-cm-diameter plastic pots containing a mixture of sterilized soil, vermiculite and peat mossat a ratio of 3:1:1. Oospores were collected following the procedure of Raftoyannis et al. (2006) with minor modifications. Three-leaf stage sesame roots were soaked with 5 mL of oospore suspension at 1 × 106/mL of the 20210628 strain, and the control plants were inoculated with sterilized water. All plants were maintained in a greenhouse (28±2°C, > 80% R. H.). The experiment was repeated twice with three replications. The plants inoculated with P. myriotylum showed the water soak symptom on the stem base 7 days after inoculation, while control plants were symptomless. Three weeks after inoculation, the plants showed root tissue necrosis, root rot, and dwarfing symptoms that were similar to those observed on sesame plants in the field, while control plants remained healthy. P. myriotylum was re-isolated from the inoculated plants and the morphology was the same as the original strain 20210628. These results suggest that P. myriotylum is the causal agent of sesame root rot. Previous studies have revealed that P. myriotylum can cause root rot in peanuts (Yu et al. 2019), chili pepper (Hyder et al. 2018), green bean (Serrano et al. 2008) and aerial blight of tomato (Roberts et al. 1999). To the best of our knowledge, this is the first report of P. myriotylum causing root rot on sesame. This pathogen can infect plant roots and develop rapidly if no effective control measures are implemented. Once the disease breaks out in a large area, the yield of sesame will be seriously threatened. The results provide important implications for the prevention and management of this disease.},
}
@article {pmid37026429,
year = {2023},
author = {Katemo Manda, B and Snoeks, J and Decru, E and Brecko, J and Vreven, EJWMN},
title = {Revision of Nannocharax luapulae Boulenger, 1915 (Characiformes: Distichodontidae) from the Upper Congo basin: Evidence for a species pair.},
journal = {Journal of fish biology},
volume = {103},
number = {3},
pages = {557-573},
doi = {10.1111/jfb.15400},
pmid = {37026429},
issn = {1095-8649},
support = {//MbiSa Congo I (2013-2018) and MbiSa Congo II (2018-2023) projects (projects of the RMCA funded by the DGD)/ ; //Royal Museum for Central Africa (RMCA, Tervuren, Belgium) and the Belgian Development Cooperation (DGD)/ ; },
mesh = {Animals ; *Characiformes ; Congo ; Rivers ; Skin ; },
abstract = {For many decades, Nannocharax luapulae has been considered to be widespread in the southern part of the Upper Congo basin. However, meristic, morphometric and cytochrome c oxidase subunit I (COI) barcoding evidence revealed that its geographical distribution is restricted to the Luapula-Moero basin. The populations of the Upper Lualaba are assigned to a new species, N. chochamandai. This new species, though highly similar to N. luapulae, can readily be distinguished from it by its lower number of lateral line scales, 41-46 (vs. 49-55), its pectoral fin reaching the pelvic-fin insertion (vs. not reaching the pelvic-fin insertion) and its pelvic fin reaching the base of the anal fin (vs. not reaching the base of the anal fin). Specimens of N. chochamandai display thickened pads on the first three pelvic-fin rays that exhibit intraspecific variation in development, which appears to be related to the flow-strength of the river in which these Nannocharax specimens occur. Nannocharax luapulae is redescribed and an updated identification key to the Nannocharax species of the Congo basin sensu lato is provided as well. Some fish conservation issues related to N. luapulae and N. chochamandai are also highlighted.},
}
@article {pmid37026224,
year = {2023},
author = {Thankachan, M and Surya, P and Sebastian, CD},
title = {Molecular Identification and phylogenetic analysis of mosquito vectors from Mananthavady Taluk, Wayanad, Kerala, India.},
journal = {Journal of vector borne diseases},
volume = {60},
number = {1},
pages = {88-93},
doi = {10.4103/0972-9062.361166},
pmid = {37026224},
issn = {0972-9062},
mesh = {Animals ; Humans ; Mosquito Vectors/anatomy &amp; histology ; Phylogeny ; *Culicidae/genetics ; *Anopheles/genetics ; *Aedes/genetics ; *Culex ; India ; },
abstract = {BACKGROUND &amp; OBJECTIVES: Every year more than one billion people are infected and about one million people die from vector-borne diseases; of which mosquito-borne diseases remain as the world's most severe insect-borne diseases with excessive rates of morbidity and mortality. This study aimed to examine the mosquito vectors and the possible diseases transmitted by them in the Mananthavady Taluk of Wayanad, Kerala.<br><br>METHODS: The area selected for the present study was Mananthavady Taluk of Wayanad district, Kerala, during 2019-2021. The collected specimen were subjected for morphological identification using taxonomic keys and were confirmed by DNA barcoding. Molecular phylogeny assessment was done for the collected species of vector mosquitoes.<br><br>RESULTS: A total of 17 mosquito species belonging to 5 genera, Anopheles, Aedes, Culex, Mansonia and Armigereswere identified. The mitochondrial COI gene sequences generated for molecular identification of these species were submitted to NCBI GenBank.<br><br>Overall, this study extends our understanding of the molecular evolution of mosquito vectors of medical and veterinary concern, which could aid in developing biotechnological approaches used in Culicidae control programs.},
}
@article {pmid37024980,
year = {2023},
author = {You, Y and Prawer, YDJ and De Paoli-Iseppi, R and Hunt, CPJ and Parish, CL and Shim, H and Clark, MB},
title = {Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {66},
pmid = {37024980},
issn = {1474-760X},
mesh = {*Single-Cell Gene Expression Analysis ; *RNA Isoforms ; Single-Cell Analysis/methods ; Sequence Analysis, RNA/methods ; Software ; Gene Expression Profiling/methods ; },
abstract = {Long-read single-cell RNA sequencing (scRNA-seq) enables the quantification of RNA isoforms in individual cells. However, long-read scRNA-seq using the Oxford Nanopore platform has largely relied upon matched short-read data to identify cell barcodes. We introduce BLAZE, which accurately and efficiently identifies 10x cell barcodes using only nanopore long-read scRNA-seq data. BLAZE outperforms the existing tools and provides an accurate representation of the cells present in long-read scRNA-seq when compared to matched short reads. BLAZE simplifies long-read scRNA-seq while improving the results, is compatible with downstream tools accepting a cell barcode file, and is available at https://github.com/shimlab/BLAZE .},
}
@article {pmid37024700,
year = {2023},
author = {Robbins, N and Ketela, T and Kim, SH and Cowen, LE},
title = {Chemical-Genetic Approaches for Exploring Mode of Action of Antifungal Compounds in the Fungal Pathogen Candida albicans.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2658},
number = {},
pages = {145-165},
pmid = {37024700},
issn = {1940-6029},
support = {R01 AI127375/AI/NIAID NIH HHS/United States ; R01 AI120958/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Candida albicans ; Antifungal Agents/pharmacology/therapeutic use ; *Mycoses/drug therapy ; Genomics ; Phenotype ; Microbial Sensitivity Tests ; },
abstract = {Candida albicans is a prevalent fungal pathogen of humans that can cause both superficial and life-threatening disease, primarily in immunocompromised populations. Currently, antifungal drug classes available to treat fungal infections remain limited and the emergence of drug-resistant strains threatens antifungal efficacy, necessitating the discovery and development of additional therapeutics. The construction of the C. albicans double-barcoded heterozygous deletion collection (DBC) enables the rapid and systematic assessment of haploinsufficiency phenotypes in a pooled format. Specifically, this functional genomics resource can be used to identify heterozygous deletion mutants that are hypersensitive to compounds in order to define putative cellular targets and/or other modifiers of compound activity. Here, we describe protocols to characterize the mode of action of small molecules using the C. albicans DBC, including how to prepare compound-treated cultures, isolate genomic DNA, amplify strain-specific barcodes, and prepare DNA libraries for high-throughput sequencing. This technique provides a powerful approach to elucidate the compound mechanism of action in order to bolster the antifungal pipeline.},
}
@article {pmid37023002,
year = {2023},
author = {Sondo, M and Wonni, I and Klonowska, A and Koïta, K and Moulin, L},
title = {Quantification of diversity sampling bias resulting from rice root bacterial isolation on popular and nitrogen-free culture media using 16S amplicon barcoding.},
journal = {PloS one},
volume = {18},
number = {4},
pages = {e0279049},
pmid = {37023002},
issn = {1932-6203},
mesh = {*Oryza/genetics ; Selection Bias ; Nitrogen ; Bacteria ; Proteobacteria/genetics ; Plants/genetics ; Culture Media/chemistry ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; },
abstract = {Culturing bacteria from plant material is well known to be conducive to strong bias compared to the actual diversity in the original samples. This bias is related to the bacterial cultivability, chemical composition of the media and culture conditions. Recovery bias is often observed but has never been quantified on different media using an amplicon barcoding approach whereby plant microbiota DNA extractions are compared to DNA extracted from serial dilutions of the same plant tissues grown on bacterial culture media. In this study, we: i) quantified the bacterial culturing diversity bias using 16S amplicon barcode sequencing by comparing a culture-dependent approach (CDA) focused on rice roots on four commonly used bacterial media (10% and 50% TSA, plant-based medium with rice flour, nitrogen free medium NGN and NFb) versus a culture-independent approach (CIA) assessed with DNA extracted directly from root and rhizosphere samples; ii) assessed enriched and missing taxa detected on the different media; iii) used biostatistics functional predictions to highlight metabolic profiles that could potentially be enriched in the CDA and CIA. A comparative analysis of the two approaches revealed that among the 22 phyla present in microbiota of the studied rice root samples, only five were present in the CDA (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Verrucomicrobia). The Proteobacteria phylum was the most abundant in all CDA samples, showing high gamma-Proteobacteria enrichment. The diversity of the combined culture media represented about a third of the total microbiota diversity, and its genus diversity and frequency was documented. The functional prediction tool (PICRUSt2) detected nitrogenase enzyme enrichment in bacterial taxa sampled from nitrogen-free media, thus validating its predictive capacity. Further functional predictions also showed that the CDA mostly missed anaerobic, methylotrophic, methanotrophic and photosynthetic bacteria compared to the CIA, thereby generating valuable insight that could enable the design of ad-hoc culture media and conditions to increase the rice-associated microbiota cultivability.},
}
@article {pmid37021680,
year = {2023},
author = {Song, F and Li, T and Yan, HF and Feng, Y and Jin, L and Burgess, KS and Ge, XJ},
title = {Plant DNA barcode library for native flowering plants in the arid region of northwestern China.},
journal = {Molecular ecology resources},
volume = {23},
number = {6},
pages = {1389-1402},
doi = {10.1111/1755-0998.13797},
pmid = {37021680},
issn = {1755-0998},
support = {2017-LSFGBOWS-02//Large-scale Scientific Facilities of the Chinese Academy of Sciences/ ; 41271069//National Natural Science Foundation of China/ ; 2018FY100704//Science and Technology Basic Resource Survey Special/ ; 2017FY100201//Science and Technology Basic Resource Survey Special/ ; XDB31000000//Strategic Priority Research Program of Chinese Academy of Sciences/ ; },
mesh = {Humans ; *DNA Barcoding, Taxonomic ; *Magnoliopsida/genetics ; DNA, Plant/genetics ; Plants/genetics ; China ; Phylogeny ; },
abstract = {DNA barcoding is a well-established tool for rapid species identification and biodiversity monitoring. A reliable and traceable DNA barcode reference library with extensive coverage is necessary but unavailable for many geographical regions. The arid region in northwestern China, a vast area of about 2.5 million km[2] , is ecologically fragile and often overlooked in biodiversity studies. In particular, DNA barcode data from the arid region in China are lacking. We develop and evaluate the efficacy of an extensive DNA barcode library for native flowering plants in the arid region of northwestern China. Plant specimens were collected, identified and vouchered for this purpose. The database utilized four DNA barcode markers, namely rbcL, matK, ITS and ITS2, for 1816 accessions (representing 890 species from 385 genera and 72 families), and consisted of 5196 barcode sequences. Individual barcodes varied in resolution rates: species- and genus-level rates for rbcL, matK, ITS and ITS2 were 79.9%-51.1%/76.1%, 79.9%-67.2%/88.9%, 85.0%-72.0%/88.2% and 81.0%-67.4%/84.9%, respectively. The three-barcode combination of rbcL + matK + ITS (RMI) revealed a higher species- and genus-level resolution (75.5%/92.1%, respectively). A total of 110 plastomes were newly generated as super-barcodes to increase species resolution for seven species-rich genera, namely Astragalus, Caragana, Lactuca, Lappula, Lepidium, Silene and Zygophyllum. Plastomes revealed higher species resolution compared to standard DNA barcodes and their combination. We suggest future databases include super-barcodes, especially for species-rich and complex genera. The plant DNA barcode library in the current study provides a valuable resource for future biological investigations in the arid regions of China.},
}
@article {pmid37020624,
year = {2023},
author = {Singh, R and Dutt, S and Sharma, P and Sundramoorthy, AK and Dubey, A and Singh, A and Arya, S},
title = {Future of Nanotechnology in Food Industry: Challenges in Processing, Packaging, and Food Safety.},
journal = {Global challenges (Hoboken, NJ)},
volume = {7},
number = {4},
pages = {2200209},
pmid = {37020624},
issn = {2056-6646},
abstract = {Over the course of the last several decades, nanotechnology has garnered a growing amount of attention as a potentially valuable technology that has significantly impacted the food industry. Nanotechnology helps in enhancing the properties of materials and structures that are used in various fields such as agriculture, food, pharmacy, and so on. Applications of nanotechnology in the food market have included the encapsulation and distribution of materials to specific locations, the improvement of flavor, the introduction of antibacterial nanoparticles into food, the betterment of prolonged storage, the detection of pollutants, enhanced storage facilities, locating, identifying, as well as consumer awareness. Labeling food goods with nano barcodes helps ensure their security and may also be used to track their distribution. This review article presents a discussion about current advances in nanotechnology along with its applications in the field of food-tech, food packaging, food security, enhancing life of food products, etc. A detailed description is provided about various synthesis routes of nanomaterials, that is, chemical, physical, and biological methods. Nanotechnology is a rapidly improving the field of food packaging and the future holds great opportunities for more enhancement via the development of new nanomaterials and nanosensors.},
}
@article {pmid37019975,
year = {2023},
author = {Jiang, Y and Zhu, C and Wang, S and Wang, F and Sun, Z},
title = {Identification of three cultivated varieties of Scutellaria baicalensis using the complete chloroplast genome as a super-barcode.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {5602},
pmid = {37019975},
issn = {2045-2322},
mesh = {*Genome, Chloroplast ; Scutellaria baicalensis ; Phylogeny ; DNA, Chloroplast ; *Plants, Medicinal/genetics ; },
abstract = {Scutellaria baicalensis has been one of the most commonly used traditional Chinese medicinal plants in China for more than 2000 years. The three new varieties cultivated could not be distinguished by morphology before flowering. It will hinder the promotion of later varieties. Chloroplast DNA has been widely used in species identification. Moreover, previous studies have shown that complete chloroplast genome sequences have been suggested as super barcodes for identifying plants. Therefore, we sequenced and annotated the complete chloroplast genomes of three cultivated varieties. The chloroplast genomes of SBW, SBR, and SBP were 151,702 bp, 151,799 bp, and 151,876 bp, which contained 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The analysis of the repeat sequences, codon usage, and comparison of chloroplast genomes shared a high degree of conservation. However, the sliding window results show significant differences among the three cultivated varieties in matK-rps16 and petA-psbJ. And we found that the matK-rps16 sequence can be used as a barcode for the identification of three varieties. In addition, the complete chloroplast genome contains more variations and can be used as a super-barcode to identify these three cultivated varieties. Based on the protein-coding genes, the phylogenetic tree demonstrated that SBP was more closely related to SBW, in the three cultivated varieties. Interestingly, we found that S. baicalensis and S. rehderiana are closely related, which provides new ideas for the development of S. baicalensis. The divergence time analysis showed that the three cultivated varieties diverged at about 0.10 Mya. Overall, this study showed that the complete chloroplast genome could be used as a super-barcode to identify three cultivated varieties of S. baicalensis and provide biological information, and it also contributes to bioprospecting.},
}
@article {pmid37019885,
year = {2023},
author = {Zheng, B and Qin, Y and Xiang, Y and Guo, A and Chen, Y and Hu, Y},
title = {Unique Fluorescent Protein-Encoded Microbeads with Supramaximal Encoding Capacity and High Sensitivity for Multiplex Bioassays.},
journal = {Analytical chemistry},
volume = {95},
number = {16},
pages = {6542-6549},
doi = {10.1021/acs.analchem.2c05231},
pmid = {37019885},
issn = {1520-6882},
mesh = {Microspheres ; *Proteins ; *Fluorescent Dyes/chemistry ; Sensitivity and Specificity ; Biological Assay ; },
abstract = {Fluorescence-encoded microbeads (FEBs) have been widely used as a critical component in multiplexed biomolecular assays. Here, we propose a simple, sustainable, low-cost, and safe strategy for preparing FEBs by assembling fluorescent proteins (FPs) onto magnetic microbeads (MBs) via chemical coupling. Combining the type of FP, the concentration of FP, and the size of the magnetic microbeads as encoding elements, an ultralarge encoding capacity with 506 barcodes was obtained. We demonstrate that the FP-based FEBs have good stability during long-term storage and tolerate the use of an organic solution. Multiplex detection of femtomolar ssDNA molecules was achieved via flow cytometry, and the detection procedure is simple and fast because it does not require amplification and washing strategies. The advantages of this advanced method for multiplex detections including high sensitivity, specificity, accuracy, repeatability, rapidity, and cost-effectiveness show a broad application prospect in basic and applied research fields such as disease diagnosis, food safety, environmental protection, proteomics, genomics, and drug screening.},
}
@article {pmid37019825,
year = {2023},
author = {Troiano, E and Larini, I and Binati, RL and Gatto, V and Torriani, S and Buzzini, P and Turchetti, B and Salvetti, E and Felis, GE},
title = {Finding a correct species assignment for a Metschnikowia strain: insights from the genome sequencing of strain DBT012.},
journal = {FEMS yeast research},
volume = {23},
number = {},
pages = {},
doi = {10.1093/femsyr/foad024},
pmid = {37019825},
issn = {1567-1364},
mesh = {*Metschnikowia/genetics ; Phylogeny ; Yeasts/genetics ; Genomics ; Whole Genome Sequencing ; },
abstract = {Metschnikowia pulcherrima is an important yeast species that is attracting increased interest thanks to its biotechnological potential, especially in agri-food applications. Phylogenetically related species of the so-called 'pulcherrima clade' were first described and then reclassified in one single species, which makes the identification an intriguing issue. Starting from the whole-genome sequencing of the protechnological strain Metschnikowia sp. DBT012, this study applied comparative genomics to calculate similarity with the M. pulcherrima clade publicly available genomes with the aim to verify if novel single-copy putative phylogenetic markers could be selected, in comparison with the commonly used primary and secondary barcodes. The genome-based bioinformatic analysis allowed the identification of 85 consensus single-copy orthologs, which were reduced to three after split decomposition analysis. However, wet-lab amplification of these three genes in nonsequenced type strains revealed the presence of multiple copies, which made them unsuitable as phylogenetic markers. Finally, average nucleotide identity (ANI) was calculated between strain DBT012 and available genome sequences of the M. pulcherrima clade, although the genome dataset is still rather limited. Presence of multiple copies of phylogenetic markers as well as ANI values were compatible with the recent reclassification of the clade, allowing the identification of strain DBT012 as M. pulcherrima.},
}
@article {pmid37019420,
year = {2023},
author = {Montgelard, C and Muller, T and Arnal, V and Maree, S and Taylor, PJ and Sands, AF and Robinson, TJ and Matthee, CA},
title = {Diversification and evolutionary history of the African laminated-toothed rats (Rodentia, Otomyini).},
journal = {Molecular phylogenetics and evolution},
volume = {183},
number = {},
pages = {107779},
doi = {10.1016/j.ympev.2023.107779},
pmid = {37019420},
issn = {1095-9513},
mesh = {Rats ; Animals ; Phylogeny ; *Biological Evolution ; *Ecosystem ; Murinae/genetics ; DNA, Mitochondrial/genetics ; },
abstract = {The African continent was subjected to periodic climatic shifts during the Pliocene and Pleistocene. These habitat changes greatly affected the evolutionary processes and tempo of diversification in numerous, widely distributed mammals. The Otomyini (Family Muridae) comprises three African rodent genera, Parotomys, Otomys and Myotomys, characterized by unique laminated-shaped molars. Species within this tribe generally prefer open-habitat and show low dispersal capabilities, with previous studies suggesting that their diversification was closely associated with climatic oscillations over the last four million years. Our phylogenetic reconstructions, based on three mitochondrial (mtDNA) genes (Cytb, COI and 12S) and four nuclear introns (EF, SPTBN, MGF and THY), identified eight major genetic clades that are distributed across southern, eastern and western Africa. Our data permit the re-examination of the taxonomic status of the three genera as well as the previously proposed mesic-arid dichotomy of the 10 South African species. Moreover, multiple mtDNA species delimitation methods incorporating 168 specimens estimated the number of Otomyini species to be substantially higher than the ∼ 30 recognized, suggesting that the current taxonomy will necessitate an integrative approach to delimit extant species diversity within the Otomyini. The data suggests that the origin of the tribe can be dated back to ∼ 5.7 million years ago (Ma) in southern Africa. The distribution and phylogenetic associations among the eight major otomyine evolutionary lineages can best be explained by several waves of northward colonization from southern Africa, complemented by independent reversed dispersals from eastern back to southern Africa at different time periods. There is strong support for the hypothesis that the radiation, dispersion, and diversification of the otomyine rodents is closely linked to recent Plio-Pleistocene climatic oscillations.},
}
@article {pmid37017784,
year = {2023},
author = {Kutako, M and Hiransuchalert, R and Sarayut Watchasit, and Kaewduang, M and Hanchana, O and Setthamongkol, P and Chindudsadeegul, P and Gunbua, V and Jaritkhuan, S},
title = {Morphological and molecular comparison as a useful tool for identification of the three centric marine diatoms (Bacillariophyceae: Chaetoceros).},
journal = {Archives of microbiology},
volume = {205},
number = {5},
pages = {173},
pmid = {37017784},
issn = {1432-072X},
mesh = {Humans ; *Diatoms ; Chlorophyll A ; Random Amplified Polymorphic DNA Technique ; Microscopy, Electron, Scanning ; DNA, Ribosomal/genetics ; },
abstract = {The objective of this study was to identify morphological and molecular comparison of three marine Chaetoceros species using microscopic observations, sequence analysis of 18S rDNA, random amplified polymorphic DNA (RAPD-PCR) barcoding and nuclear magnetic resonance (NMR) spectroscopy. Chaetoceros were obtained from three different algae laboratories: Center of Excellence for Marine Biotechnology (CEMB), Chanthaburi Coastal Fisheries Research and Development (CHAN) and Institute of Marine Science, Burapha University (BIM). Genomic DNA for the RAPD-PCR analysis was extracted using the phenol-chloroform method, followed by 18S rDNA amplification. The blast results of 18S rDNA sequence confirmed the significantly matched to C. gracilis for Chaetoceros BIM and CHAN and C. muelleri for Chaetoceros CEMB(e-value = 0.0, identity = 99%). The RAPD-PCR results revealed differences in the three Chaetoceros isolates with polymorphisms between 30.43% and 60.00%, and Chaetoceros CEMB showed high polymorphic bands. Scanning electron microscopy revealed that Chaetoceros CEMB were larger and had larger setae compared to the other isolates (P < 0.05). The results of the NMR characterization of metabolites were consistent with the results of the sequence and morphological analyses. The concentrations of several metabolites, including chlorophyll c1, chlorophyll a, Myo-inositol, fucoxanthin, astaxanthin, lutein and zeaxanthin, were lower in Chaetoceros CEMB than in Chaetoceros BIM and CHAN. However, high concentrations of fatty acids, such as oleic acid, linoleic acid, α-linolenic acid and arachidic acid, were observed in all isolates. Generally, the results of this study will aid future studies examining the diversity of Chaetoceros in various cultural environments.},
}
@article {pmid37009964,
year = {2023},
author = {Glidden, CK and Karakoç, C and Duan, C and Jiang, Y and Beechler, B and Jabbar, A and Jolles, AE},
title = {Distinct life history strategies underpin clear patterns of succession in microparasite communities infecting a wild mammalian host.},
journal = {Molecular ecology},
volume = {32},
number = {13},
pages = {3733-3746},
pmid = {37009964},
issn = {1365-294X},
support = {R01 GM126549/GM/NIGMS NIH HHS/United States ; R35 GM133439/GM/NIGMS NIH HHS/United States ; BB/L011085/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Biological Evolution ; Biota ; *Host-Parasite Interactions ; *Life History Traits ; Mammals ; *Parasites ; },
abstract = {Individual animals in natural populations tend to host diverse parasite species concurrently over their lifetimes. In free-living ecological communities, organismal life histories shape interactions with their environment, which ultimately forms the basis of ecological succession. However, the structure and dynamics of mammalian parasite communities have not been contextualized in terms of primary ecological succession, in part because few datasets track occupancy and abundance of multiple parasites in wild hosts starting at birth. Here, we studied community dynamics of 12 subtypes of protozoan microparasites (Theileria spp.) in a herd of African buffalo. We show that Theileria communities followed predictable patterns of succession underpinned by four different parasite life history strategies. However, in contrast to many free-living communities, network complexity decreased with host age. Examining parasite communities through the lens of succession may better inform the effect of complex within host eco-evolutionary dynamics on infection outcomes, including parasite co-existence through the lifetime of the host.},
}
@article {pmid37007806,
year = {2022},
author = {Yuan, Z and Wang, Y and Liu, Q and Liu, L and Li, X},
title = {Macrobiotus hupingensis, a New Tardigrade Species in the Macrobiotus pallarii Complex from China.},
journal = {Zoological studies},
volume = {61},
number = {},
pages = {e86},
pmid = {37007806},
issn = {1810-522X},
abstract = {In this paper we describe Macrobiotus hupingensis, a new tardigrade species of the Macrobiotus pallarii complex from southern China. We used the traditional morphology-based taxonomic analysis, supported by detailed morphometrics, light microscopy imaging, scanning electron microscopy, and analysis of four genetic markers (18S rRNA, 28S rRNA, COI and ITS-2). Macrobiotus hupingensis sp. nov. is characterized by eggs with large, conical processes, each surrounded by six (only sometimes five) hexagonal areolae. Based on the morphological characters of the animals (two macroplacoids, one microplacoid, porous curicle, Y-shaped claws) as well as genetic data, we demonstrate the new species to be a member of the M. pallarii complex. However, it differs specifically from M. pallarii, M. pseudopallarii, and M. ripperi mainly by the absence of sparse granulation between legs III and IV. It also differs from M. margoae mostly by the presence of meshes within the entire egg process wall. Finally, the new species can be easily distinguished from M. caymanensis by the presence of granulation visible in light microscopy in all legs.},
}
@article {pmid37007805,
year = {2022},
author = {Hidaka, C and Yang, CH and Wakabayashi, K},
title = {Finding the Missing Puzzle Piece of the Nisto Stage in the Larval Cycle of the Slipper Lobster Scyllarides squammosus: A Molecular and Morphological Approach.},
journal = {Zoological studies},
volume = {61},
number = {},
pages = {e73},
pmid = {37007805},
issn = {1810-522X},
abstract = {Slipper and spiny lobsters are crustaceans that are in high demand and possess great commercial potential as valuable foods. The early life stages are important to understand the distribution and resource ecology of those lobsters. However, much less information is available about slipper lobsters than spiny lobsters. Biological information concerning the transition stage from the planktonic to the benthic phase, the so-called nisto stage, is limited probably due to its short duration. An individual scyllarid nisto was discovered while scuba diving off Chichijima Island. DNA analyses using mitochondrial 16S rRNA and cytochrome c oxidase subunit 1 (COI) genes confirmed this specimen to be Scyllarides squammosus (H. Milne Edwards, 1837). Detailed morphological observations of this specimen and its comparison with previous reports on Scyllarides nistos suggest that the diagnostic character of S. squammosus nisto is the pleura of the second to fifth pleonites possessing prominent teeth entirely on the lateral margin. Other morphological characteristics are the carapace with the widest distance in the middle and the second to fifth pleonites bearing two tubercles on each side. This report describes the identification of the first worldwide record of a Scyllarides nisto, confirmed by molecular barcoding.},
}
@article {pmid37007803,
year = {2022},
author = {Ho, BH and Hu, FS and Fikáček, M},
title = {The Dung Beetle Oxyomus of Taiwan (Coleoptera: Scarabaeidae): Review of the Fauna, a New Species and its Larva Associated by DNA Barcoding.},
journal = {Zoological studies},
volume = {61},
number = {},
pages = {e80},
pmid = {37007803},
issn = {1810-522X},
abstract = {The Taiwanese fauna of the dung beetle genus Oxyomus Dejean, 1833 (Coleoptera: Scarabaeidae: Aphodiinae) is reviewed based on museum specimens and newly collected material. Four species, all endemic to Taiwan, are recognized, one of which is newly described here: O. alligator sp. nov. Remaining species are diagnosed, compared with similar relatives from outside of Taiwan, and their distribution is mapped. We show that Taiwanese Oxyomus species form three distinct morphological groups, similar to species from Japan, SE Asia and Malay Archipelago, respectively, indicating a possible composite origin of Taiwanese fauna. The species occur in submontane and montane forests at altitudes of 700-2550 m including the secondary Cryptomeria ones. Available data confirm their association with dung of various forest mammals (monkeys, muntjacs and serows), although the discovery of larvae in sifted forest leaf litter may indicate they can also develop in nutrient-rich substrate around the dung. The larva of O. alligator sp. nov. is described in detail, based on the larval specimens associated with adults by DNA barcodes. Larvae of Oxyomus alligator sp. nov. are similar to those of the European O. sylvestris (Scopoli, 1763), with important differences only found on maxilla and abdominal apex.},
}
@article {pmid37007802,
year = {2022},
author = {Jiranuntskul, P and Boonporn, A and Kongrit, C and Panha, S and Jeratthitikul, E},
title = {Biodiversity of the Buffalo Leeches Genus Hirudinaria (Arhynchobdellida, Hirudinidae) in Southern Thailand Revealed from DNA Barcoding.},
journal = {Zoological studies},
volume = {61},
number = {},
pages = {e84},
pmid = {37007802},
issn = {1810-522X},
abstract = {Leeches in the genus Hirudinaria Whitman, 1886, also known as buffalo leeches, are blood-sucking ectoparasites of vertebrates. Although they are widely distributed in Asia and had been highly abundant in the past, studies on diversity and taxonomy of this genus are still scarce. There is probably a large amount of cryptic diversity yet to be discovered, particularly from mainland Southeast Asia. In this study, we used morphology and DNA barcoding with a COI gene fragment to explored the diversity of Hirudinaria leeches in the southern region of Thailand, where a unique geographic feature could have led to the diversification of freshwater biota. Molecular phylogenetic analyses and species delimitation approaches (ABGD, bPTP, GMYC, and BOLD) revealed the presence of four putative species of Hirudinaria leeches from southern Thailand, including H. bpling, H. thailandica, and two morphologically cryptic lineages of H. manillensis. Compared to other leech genera, genetic distances of Hirudinaria leeches were relatively low (0.11-0.65% within species; 3.72-14.36% between species) and barcoding gaps were very narrow (1.54-2.88%). The species diversity, distribution pattern, and a phenomenon of low genetic divergence of Hirudinaria leeches in southern Thailand could be explained by an ancient seaway, paleo-drainage, and anthropogenic activities.},
}
@article {pmid37005807,
year = {2023},
author = {Zhang, ZF and Zhao, ZZ and Wang, X and Yin, GY and Chen, Y and Man, JH and Shi, Y and Huang, YY and Liu, SH and Liu, ZQ and Wang, XH and Wei, SL},
title = {[Specific DNA barcodes, germplasm resources, and genetic diversity of Eleutherococcus senticosus].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {48},
number = {5},
pages = {1229-1237},
doi = {10.19540/j.cnki.cjcmm.20221208.101},
pmid = {37005807},
issn = {1001-5302},
mesh = {*DNA Barcoding, Taxonomic ; *Eleutherococcus/genetics ; Base Sequence ; Chloroplasts/genetics ; Genetic Variation ; Phylogeny ; },
abstract = {Eleutherococcus senticosus is one of the Dao-di herbs in northeast China. In this study, the chloroplast genomes of three E. senticosus samples from different genuine producing areas were sequenced and then used for the screening of specific DNA barcodes. The germplasm resources and genetic diversity of E. senticosus were analyzed basing on the specific DNA barcodes. The chloroplast genomes of E. senticosus from different genuine producing areas showed the total length of 156 779-156 781 bp and a typical tetrad structure. Each of the chloroplast genomes carried 132 genes, including 87 protein-coding genes, 37 tRNAs, and 8 rRNAs. The chloroplast genomes were relatively conserved. Sequence analysis of the three chloroplast genomes indicated that atpI, ndhA, ycf1, atpB-rbcL, ndhF-rpl32, petA-psbJ, psbM-psbD, and rps16-psbK can be used as specific DNA barcodes of E. senticosus. In this study, we selected atpI and atpB-rbcL which were 700-800 bp and easy to be amplified for the identification of 184 E. senticosus samples from 13 genuine producing areas. The results demonstrated that 9 and 10 genotypes were identified based on atpI and atpB-rbcL sequences, respectively. Furthermore, the two barcodes identified 23 genotypes which were named H1-H23. The haplotype with the highest proportion and widest distribution was H10, followed by H2. The haplotype diversity and nucleotide diversity were 0.94 and 1.82×10~(-3), respectively, suggesting the high genetic diversity of E. senticosus. The results of the median-joining network analysis showed that the 23 genotypes could be classified into 4 categories. H2 was the oldest haplotype, and it served as the center of the network characterized by starlike radiation, which suggested that population expansion of E. senticosus occurred in the genuine producing areas. This study lays a foundation for the research on the genetic quality and chloroplast genetic engineering of E. senticosus and further research on the genetic mechanism of its population, providing new ideas for studying the genetic evolution of E. senticosus.},
}
@article {pmid37005794,
year = {2023},
author = {Zhuang, X and Zhao, Z and Feng, X and Lui, GCY and Chan, D and Lee, SS and Hsing, IM},
title = {Integrating Magnetic-Bead-Based Sample Extraction and Molecular Barcoding for the One-Step Pooled RT-qPCR Assay of Viral Pathogens without Retesting.},
journal = {Analytical chemistry},
volume = {95},
number = {14},
pages = {6182-6190},
pmid = {37005794},
issn = {1520-6882},
mesh = {Humans ; *COVID-19 ; Pandemics ; Reproducibility of Results ; COVID-19 Testing ; Magnetic Phenomena ; Sensitivity and Specificity ; RNA, Viral/genetics ; },
abstract = {Pooling multiple samples prior to real-time reverse-transcription polymerase chain reaction (RT-PCR) analysis has been proposed as a strategy to minimize expenses and boost test throughput during the COVID-19 pandemic. Nevertheless, the traditional pooling approach cannot be effectively deployed in high-prevalence settings due to the need for secondary tests in the case of a positive pool. In this study, we present a pooling test platform with high adaptability and simplicity that allows sample-specific detection of multiple-tagged samples in a single run without the need for retesting. This was accomplished by labeling distinct samples with predefined ID-Primers and identifying tagged pooled samples using one-step RT-PCR followed by melting curve analysis with rationally designed universal fluorescence- and quencher-tagged oligo probes. Using magnetic beads (MBs), nucleic acid targets from different individuals can be tagged and extracted concurrently and then pooled before RT, eliminating the need for extra RNA extraction and separate RT and enzyme digestion steps in the recently developed barcoding strategies. Pools of six samples (positive and negative) were successfully identified by melting temperature values under two fluorescent channels, with a detection sensitivity of 5 copies/μL. We validated the reproducibility of this assay by running it on 40 clinical samples with a hypothetical infection rate of 15%. In addition, to aid the scenario of large-scale pooling tests, we constructed a melting curve autoreadout system (MCARS) for statistical analysis of melting curve plots to eliminate error-prone manual result readout. Our results suggest that this strategy could be a simple and adaptable tool for alleviating existing bottlenecks in diagnostic pooling testing.},
}
@article {pmid37005503,
year = {2023},
author = {Palomares-Rius, JE and Clavero-Camacho, I and Cantalapiedra-Navarrete, C and Roca-Castillo, LF and Archidona-Yuste, A and Castillo, P},
title = {First Report of Heterodera zeae Koshy, Swarup &amp; Sethi, 1971 (corn cyst Nematode) Infecting Corn (Zea mays) in Spain.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-02-23-0362-PDN},
pmid = {37005503},
issn = {0191-2917},
abstract = {Heterodera zeae Koshy, Swarup &amp; Sethi, 1971 (corn cyst nematode) is an important disease of corn in several areas of the world, including India, Nepal, Pakistan, Egypt, USA, Greece and Portugal (Subbotin et al., 2010). It is a sedentary semi-endoparasite feeding on corn roots and other Poaceae plants and has been associated with significant yield losses in corn (Subbotin et al., 2010). During autumn 2022 a plant-parasitic nematode survey performed in corn at central-western area of Spain (Talavera de la Reina, Toledo), revealed a commercial field with stunted plants. Nematodes were extracted from soil by centrifugal-flotation method (Coolen, 1979). Corn roots inspection detected infections by immature and mature cysts, and soil revealed also mature live cysts and second-stage juveniles (J2s) with a population density of 1010 eggs and J2s/500 cm3 soil (including eggs from cysts). J2s and cysts were processed to pure glycerine using De Grisse's (1969) method. DNA was isolated from single live fresh J2s specimens for amplifying and sequencing of cytochrome c oxidase subunit II (COII) mitochondrial region using the primer pair species-specific H.Gly-COIIF_inFOR/P116F-1R (Riepsamen et al., 2011); D2 and D3 expansion domains of the 28S rRNA were amplified using the D2A/D3B primers (De Ley et al. 1999); internal transcribed spacer (ITS) region using primers TW81/AB28 (Subbotin et al., 2001); and cytochrome c oxidase subunit 1 (COI) gene was amplified using the primers JB3/JB5 (Bowles et al., 1992). Brown cysts were lemon-shaped with a protruding vulval cone with fenestra ambifenestrate, bullae prominent below underbridge and characteristically arranged in finger-like bullae (Fig. 1). J2 with slightly offset lip region (3-5 annuli), stylet strong with rounded stylet knobs, lateral field with four lines, and tail short and tapering conically. Measurements of cysts (n=10) included body length 559 (432-688) µm, body width 450 (340-522) µm, fenestral length 40 (36-43) µm, semifenestral width 19 (17-21) µm, and vulval slit 40 (35-44) µm. J2 measurements (n=10) included body length 477 (420-536) µm, stylet length 21 (20-22) µm, tail length 51 (47-56) µm, and tail hyaline region 23 (20-26) µm. Morphology and morphometrics of cysts and J2, fit with original description and others from several countries (Subbotin et al., 2010). Two J2s individuals were sequenced for COII region (OQ509010-OQ509011) showing 97.1-98.1% similarity with H. zeae from USA (HM462012). Six almost identical 28S rRNA sequences from J2s (OQ449649-OQ449654) were 99.2-99.4% similar to 28S rRNA sequences of H. zeae from Greece, Afghanistan and USA (GU145612, JN583885, DQ328695). Four identical ITS DNA fragments from J2s (OQ449655-OQ449658) were 97.0-97.8% similar to ITS sequences of H. zeae from Greece, and China (GU145616, MW785771, OP692770). Finally, six COI sequences of 400 bp obtained for J2s (OQ449699-OQ449704) were under 87% similarity to several COI sequences of Heterodera spp. in NCBI, being a new molecular barcoding for identifying this species. On the basis of these results, the cyst nematodes isolated from the corn plants from the central-western area of Spain (Talavera de la Reina, Toledo) were confirmed as H. zeae and up to our knowledge it is the first report in Spain. This is a well-known pest of corn, causing important losses in this crop (Subbotin et al., 2010) and it was previously regulated as a quarantine nematode in the Mediterranean region (EPPO).},
}
@article {pmid37004150,
year = {2023},
author = {Kilian, IC and Swenson, SJ and Mengual, X and Gemeinholzer, B and Hamm, A and Wägele, JW and Peters, RS},
title = {More complex than you think: Taxonomic and temporal patterns of plant-pollinator networks of caraway (Carum carvi L.).},
journal = {Molecular ecology},
volume = {32},
number = {13},
pages = {3702-3717},
doi = {10.1111/mec.16943},
pmid = {37004150},
issn = {1365-294X},
mesh = {Bees ; Animals ; *Carum ; Insecta/genetics ; Pollination ; Plants ; *Diptera/genetics ; Flowers ; },
abstract = {Caraway (Carum carvi L.) is a crop species that is gaining in importance in Europe, especially as a condiment and medicinal plant. Here, we present the plant-pollinator network of caraway in a central European agricultural landscape, focusing on two diverse potential pollinator taxa, Diptera: Brachycera (= true flies) and Hymenoptera (sawflies, bees, and wasps). We specifically studied qualitative differences in interactions between the two insect taxa as well as the intraday and intraseasonal variability of the network. Insect and pollen plant species determination was done via morphological identification and DNA (meta)barcoding. In total, 121 species representing 33 families of Hymenoptera and Brachycera were found to carry caraway pollen. These taxa included many nonhoneybee and nonhoverfly species, showing a wide taxonomic breadth of potential pollinators and a higher network complexity than previously anticipated. There are distinct qualitative differences between Brachycera and Hymenoptera networks, suggesting complementary roles of both taxa in the pollination of native and crop plants. Strong intraday differences in potential pollinator diversity make it necessary to collect insects and pollen at different times of the day to compile complete plant-pollinator networks. Intraseasonal analyses of the plant-pollinator network of caraway show the potential of caraway as an important food source for insect species with an activity peak in late summer.},
}
@article {pmid37000232,
year = {2023},
author = {Stupar, M and Savković, &#x17d; and Popović, S and Simić, GS and Grbić, ML},
title = {Speleomycology of Air in Stopića Cave (Serbia).},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2021-2031},
pmid = {37000232},
issn = {1432-184X},
mesh = {Animals ; Humans ; *Fungi ; Caves/microbiology ; Serbia ; Pandemics ; *COVID-19 ; Seasons ; Air Microbiology ; Environmental Monitoring/methods ; },
abstract = {Fungi can colonize organic matter present in subterranean sites and have a significant role as dwellers in different microniches of cave habitats. In order to analyze the content of airborne fungal propagules in different parts of "Stopića Cave," a touristic site in Serbia, air sampling was carried out in three seasons during 2020, prior to and during the onset of COVID-19 pandemic. Culturable mycobiota was identified using both microscopic techniques and ITS region/BenA gene barcoding, while multivariate analyses were employed to establish the link between fungal taxa and different environmental factors. The maximal measured fungal propagule concentrations were recorded during spring sampling which were based on fungal propagule concentration categories; the cave environment matches the category V. A total of 29 fungal isolates were identified, while Aspergillus, Cladosporium, Fusarium, Lecanicillium, Mucor, and Penicillium were the most diverse genera. According to the trophic mode, most of the isolated fungal species were pathotrophs (75.86%), but when regarding ecological guilds, the most dominant were undefined saprobes and animal pathogens (41.38% for each). Show caves are especially vulnerable to human impacts, and the fungal propagules' concentration within the caves could be good indices for the level of ecological disturbance.},
}
@article {pmid37000033,
year = {2023},
author = {Kozlowski, HN and Malekjahani, A and Li, VYC and Lekuti, AA and Perusini, S and Bell, NG and Voisin, V and Pouyabahar, D and Pai, S and Bader, GD and Mubareka, S and Gubbay, JB and Chan, WCW},
title = {Genotyping SARS-CoV-2 Variants Using Ratiometric Nucleic Acid Barcode Panels.},
journal = {Analytical chemistry},
volume = {95},
number = {14},
pages = {5877-5885},
doi = {10.1021/acs.analchem.2c04630},
pmid = {37000033},
issn = {1520-6882},
support = {FDN-159932//CIHR/Canada ; MOP-130143//CIHR/Canada ; },
mesh = {Humans ; *Nucleic Acids ; SARS-CoV-2/genetics ; *COVID-19/diagnosis ; Genotype ; Nucleotides ; Mutation ; },
abstract = {Designing diagnostic assays to genotype rapidly mutating viruses remains a challenge despite the overall improvements in nucleic acid detection technologies. RT-PCR and next-generation sequencing are unsuitable for genotyping during outbreaks or in point-of-care detection due to their infrastructure requirements and longer turnaround times. We developed a quantum dot barcode multiplexing system to genotype mutated viruses. We designed multiple quantum dot barcodes to target conserved, wildtype, and mutated regions of SARS-CoV-2. We calculated ratios of the signal output from different barcodes that enabled SARS-CoV-2 detection and identified SARS-CoV-2 variant strains from a sample. We detected different sequence types, including conserved genes, nucleotide deletions, and single nucleotide substitutions. Our system detected SARS-CoV-2 patient specimens with 98% sensitivity and 94% specificity across 91 patient samples. Further, we leveraged our barcoding and ratio system to track the emergence of the N501Y SARS-CoV-2 mutation from December 2020 to May 2021 and demonstrated that the more transmissible N501Y mutation started to dominate infections by April 2021. Our barcoding and signal ratio approach can genotype viruses and track the emergence of viral mutations in a single diagnostic test. This technology can be extended to tracking other viruses. Combined with smartphone detection technologies, this assay can be adapted for point-of-care tracking of viral mutations in real time.},
}
@article {pmid36993721,
year = {2023},
author = {Schaff, DL and Fasse, AJ and White, PE and Vander Velde, RJ and Shaffer, SM},
title = {Clonal differences underlie variable responses to sequential and prolonged treatment.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.03.24.534152},
pmid = {36993721},
issn = {2692-8205},
abstract = {Cancer cells exhibit dramatic differences in gene expression at the single-cell level which can predict whether they become resistant to treatment. Treatment perpetuates this heterogeneity, resulting in a diversity of cell states among resistant clones. However, it remains unclear whether these differences lead to distinct responses when another treatment is applied or the same treatment is continued. In this study, we combined single-cell RNA-sequencing with barcoding to track resistant clones through prolonged and sequential treatments. We found that cells within the same clone have similar gene expression states after multiple rounds of treatment. Moreover, we demonstrated that individual clones have distinct and differing fates, including growth, survival, or death, when subjected to a second treatment or when the first treatment is continued. By identifying gene expression states that predict clone survival, this work provides a foundation for selecting optimal therapies that target the most aggressive resistant clones within a tumor.},
}
@article {pmid36993716,
year = {2023},
author = {McLaughlin, JF and Aguilar, C and Bernstein, JM and Navia-Gine, WG and Cueto-Aparicio, LE and Alarcon, AC and Alarcon, BD and Collier, R and Takyar, A and Vong, SJ and López-Chong, OG and Driver, R and Loaiza, JR and De León, LF and Saltonstall, K and Lipshutz, SE and Arcila, D and Brock, KM and Miller, MJ},
title = {Comparative phylogeography reveals widespread cryptic diversity driven by ecology in Panamanian birds.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {36993716},
issn = {2692-8205},
support = {R01 TW005869/TW/FIC NIH HHS/United States ; },
abstract = {Widespread species often harbor unrecognized genetic diversity, and investigating the factors associated with such cryptic variation can help us better understand the forces driving diversification. Here, we identify potential cryptic species based on a comprehensive dataset of COI mitochondrial DNA barcodes from 2,333 individual Panamanian birds across 429 species, representing 391 (59%) of the 659 resident landbird species of the country, as well as opportunistically sampled waterbirds. We complement this dataset with additional publicly available mitochondrial loci, such as ND2 and cytochrome b, obtained from whole mitochondrial genomes from 20 taxa. Using barcode identification numbers (BINs), we find putative cryptic species in 19% of landbird species, highlighting hidden diversity in the relatively well-described avifauna of Panama. Whereas some of these mitochondrial divergence events corresponded with recognized geographic features that likely isolated populations, such as the Cordillera Central highlands, the majority (74%) of lowland splits were between eastern and western populations. The timing of these splits are not temporally coincident across taxa, suggesting that historical events, such as the formation of the Isthmus of Panama and Pleistocene climatic cycles, were not the primary drivers of cryptic diversification. Rather, we observed that forest species, understory species, insectivores, and strongly territorial species-all traits associated with lower dispersal ability-were all more likely to have multiple BINs in Panama, suggesting strong ecological associations with cryptic divergence. Additionally, hand-wing index, a proxy for dispersal capability, was significantly lower in species with multiple BINs, indicating that dispersal ability plays an important role in generating diversity in Neotropical birds. Together, these results underscore the need for evolutionary studies of tropical bird communities to consider ecological factors along with geographic explanations, and that even in areas with well-known avifauna, avian diversity may be substantially underestimated.},
}
@article {pmid36993532,
year = {2023},
author = {Sullivan, DK and Pachter, L},
title = {Flexible parsing, interpretation, and editing of technical sequences with splitcode.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {36993532},
issn = {2692-8205},
support = {T32 GM008042/GM/NIGMS NIH HHS/United States ; U19 MH114830/MH/NIMH NIH HHS/United States ; UM1 HG012077/HG/NHGRI NIH HHS/United States ; },
abstract = {Next-generation sequencing libraries are constructed with numerous synthetic constructs such as sequencing adapters, barcodes, and unique molecular identifiers. Such sequences can be essential for interpreting results of sequencing assays, and when they contain information pertinent to an experiment, they must be processed and analyzed. We present a tool called splitcode, that enables flexible and efficient parsing, interpreting, and editing of sequencing reads. This versatile tool facilitates simple, reproducible preprocessing of reads from libraries constructed for a large array of single-cell and bulk sequencing assays.},
}
@article {pmid36993369,
year = {2023},
author = {Eiger, DS and Smith, JS and Shi, T and Stepniewski, TM and Tsai, CF and Honeycutt, C and Boldizsar, N and Gardner, J and Nicora, CD and Moghieb, AM and Kawakami, K and Choi, I and Zheng, K and Warman, A and Alagesan, P and Knape, NM and Huang, O and Silverman, JD and Smith, RD and Inoue, A and Selent, J and Jacobs, JM and Rajagopal, S},
title = {Phosphorylation barcodes direct biased chemokine signaling at CXCR3.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {36993369},
issn = {2692-8205},
support = {P41 GM103493/GM/NIGMS NIH HHS/United States ; R01 GM139858/GM/NIGMS NIH HHS/United States ; 20PRE35120592/AHA/American Heart Association-American Stroke Association/United States ; K08 HL114643/HL/NHLBI NIH HHS/United States ; R01 GM122798/GM/NIGMS NIH HHS/United States ; T32 GM007171/GM/NIGMS NIH HHS/United States ; },
abstract = {G protein-coupled receptor (GPCR) biased agonism, the activation of some signaling pathways over others, is thought to largely be due to differential receptor phosphorylation, or "phosphorylation barcodes." At chemokine receptors, ligands act as "biased agonists" with complex signaling profiles, which contributes to the limited success in pharmacologically targeting these receptors. Here, mass spectrometry-based global phosphoproteomics revealed that CXCR3 chemokines generate different phosphorylation barcodes associated with differential transducer activation. Chemokine stimulation resulted in distinct changes throughout the kinome in global phosphoproteomic studies. Mutation of CXCR3 phosphosites altered β-arrestin conformation in cellular assays and was confirmed by molecular dynamics simulations. T cells expressing phosphorylation-deficient CXCR3 mutants resulted in agonist- and receptor-specific chemotactic profiles. Our results demonstrate that CXCR3 chemokines are non-redundant and act as biased agonists through differential encoding of phosphorylation barcodes and lead to distinct physiological processes.},
}
@article {pmid36993192,
year = {2023},
author = {Siegel, SV and Amato, R and Trimarsanto, H and Sutanto, E and Kleinecke, M and Murie, K and Whitton, G and Taylor, AR and Watson, JA and Imwong, M and Assefa, A and Rahim, AG and Chau, NH and Hien, TT and Green, JA and Koh, G and White, NJ and Day, N and Kwiatkowski, DP and Rayner, JC and Price, RN and Auburn, S},
title = {Lineage-informative microhaplotypes for spatio-temporal surveillance of Plasmodium vivax malaria parasites.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {36993192},
support = {/WT_/Wellcome Trust/United Kingdom ; 204911/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MR/M006212/1/MRC_/Medical Research Council/United Kingdom ; R01 AI137154/AI/NIAID NIH HHS/United States ; },
abstract = {Challenges in understanding the origin of recurrent Plasmodium vivax infections constrains the surveillance of antimalarial efficacy and transmission of this neglected parasite. Recurrent infections within an individual may arise from activation of dormant liver stages (relapse), blood-stage treatment failure (recrudescence) or new inoculations (reinfection). Molecular inference of familial relatedness (identity-by-descent or IBD) based on whole genome sequence data, together with analysis of the intervals between parasitaemic episodes ("time-to-event" analysis), can help resolve the probable origin of recurrences. Whole genome sequencing of predominantly low-density P. vivax infections is challenging, so an accurate and scalable genotyping method to determine the origins of recurrent parasitaemia would be of significant benefit. We have developed a P. vivax genome-wide informatics pipeline to select specific microhaplotype panels that can capture IBD within small, amplifiable segments of the genome. Using a global set of 615 P. vivax genomes, we derived a panel of 100 microhaplotypes, each comprising 3-10 high frequency SNPs within <200 bp sequence windows. This panel exhibits high diversity in regions of the Asia-Pacific, Latin America and the horn of Africa (median HE = 0.70-0.81) and it captured 89% (273/307) of the polyclonal infections detected with genome-wide datasets. Using data simulations, we demonstrate lower error in estimating pairwise IBD using microhaplotypes, relative to traditional biallelic SNP barcodes. Our panel exhibited high accuracy in predicting the country of origin (median Matthew's correlation coefficient >0.9 in 90% countries tested) and it also captured local infection outbreak and bottlenecking events. The informatics pipeline is available open-source and yields microhaplotypes that can be readily transferred to high-throughput amplicon sequencing assays for surveillance in malaria-endemic regions.},
}
@article {pmid36992699,
year = {2023},
author = {AbdAlla, HAM and Wanga, VO and Mkala, EM and Amenu, SG and Amar, MH and Chen, L and Wang, QF},
title = {Comparative genomics analysis of endangered wild Egyptian Moringa peregrina (Forssk.) Fiori plastome, with implications for the evolution of Brassicales order.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1131644},
pmid = {36992699},
issn = {1664-8021},
abstract = {Moringa is a mono-genus belonging to the Moringaceae family, which includes 13 species. Among them, Moringa peregrina is plant species native to the Arabian Peninsula, Southern Sinai in Egypt, and the Horn of Africa, and comprehensive studies on its nutritional, industrial, and medicinal values have been performed. Herein, we sequenced and analyzed the initial complete chloroplast genome of Moringa peregrina. Concurrently, we analyzed the new chloroplast genome along with 25 chloroplast genomes related to species representing eight families in the Brassicales order. The results indicate that the plastome sequence of M. peregrina consists of 131 genes, with an average GC content of 39.23%. There is a disparity in the IR regions of the 26 species ranging from 25,804 to 31,477 bp. Plastome structural variations generated 20 hotspot regions that could be considered prospective DNA barcode locations in the Brassicales order. Tandem repeats and SSR structures are reported as significant evidence of structural variations among the 26 tested specimens. Furthermore, selective pressure analysis was performed to estimate the substitution rate within the Moringaceae family, which revealing that the ndhA and accD genes are under positive selective pressure. The phylogenetic analysis of the Brassicales order produced an accurate monophyletic annotation cluster of the Moringaceae and Capparaceae species, offering unambiguous identification without overlapping groups between M. oleifera and M. peregrina, which are genetically strongly associated. Divergence time estimation suggests that the two Moringa species recently diversified, 0.467 Ma. Our findings highlight the first complete plastome of the Egyptian wild-type of M. peregrina, which can be used for determining plastome phylogenetic relationships and systematic evolution history within studies on the Moringaceae family.},
}
@article {pmid36988496,
year = {2023},
author = {Calvet-Seral, J and Crespo-Yuste, E and Mathys, V and Rodriguez-Villalobos, H and Ceyssens, PJ and Martin, A and Gonzalo-Asensio, J},
title = {Targeted Chromosomal Barcoding Establishes Direct Genotype-Phenotype Associations for Antibiotic Resistance in Mycobacterium abscessus.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0534422},
pmid = {36988496},
issn = {2165-0497},
mesh = {Humans ; *Mycobacterium abscessus ; *Mycobacterium Infections, Nontuberculous/microbiology ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Bacterial/genetics ; Genetic Association Studies ; Microbial Sensitivity Tests ; },
abstract = {A bedaquiline-resistant Mycobacterium abscessus isolate was sequenced, and a candidate mutation in the atpE gene was identified as responsible for the antibiotic resistance phenotype. To establish a direct genotype-phenotype relationship of this mutation which results in a Asp-to-Ala change at position 29 (D29A), we developed a recombineering-based method consisting of the specific replacement of the desired mutation in the bacterial chromosome. As surrogate bacteria, we used two M. abscessus bedaquiline-susceptible strains: ATCC 19977 and the SL541 clinical isolate. The allelic exchange substrates used in recombineering carried either the sole D29A mutation or a genetic barcode of silent mutations in codons flanking the D29A mutation. After selection of bedaquiline-resistant M. abscessus colonies transformed with both substrates, we obtained equivalent numbers of recombinants. These resistant colonies were analyzed by allele-specific PCR and Sanger sequencing, and we demonstrated that the presence of the genetic barcode was linked to the targeted incorporation of the desired mutation in its chromosomal location. All recombinants displayed the same MIC to bedaquiline as the original isolate, from which the D29A mutation was identified. Finally, to demonstrate the broad applicability of this method, we confirmed the association of bedaquiline resistance with the atpE A64P mutation in analysis performed in independent M. abscessus strains and by independent researchers. IMPORTANCE Antimicrobial resistance (AMR) threatens the effective prevention and treatment of an ever-increasing range of infections caused by microorganisms. On the other hand, infections caused by Mycobacterium abscessus affect people with chronic lung diseases, and their incidence has grown alarmingly in recent years. Further, these bacteria are known to easily develop AMR to the few therapeutic options available, making their treatment long-lasting and challenging. The recent introduction of new antibiotics against M. abscessus, such as bedaquiline, makes us anticipate a future when a plethora of antibiotic-resistant strains will be isolated and sequenced. However, in the era of whole-genome sequencing, one of the challenges is to unequivocally assign a biological function to each identified polymorphism. Thus, in this study, we developed a fast, robust, and reliable method to assign genotype-phenotype associations for putative antibiotic-resistant polymorphisms in M. abscessus.},
}
@article {pmid36987647,
year = {2023},
author = {Nishitsuji, K and Nagata, T and Narisoko, H and Kanai, M and Hisata, K and Shinzato, C and Satoh, N},
title = {An environmental DNA metabarcoding survey reveals generic-level occurrence of scleractinian corals at reef slopes of Okinawa Island.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {1995},
pages = {20230026},
pmid = {36987647},
issn = {1471-2954},
mesh = {Animals ; *Anthozoa/genetics ; Ecosystem ; *DNA, Environmental ; DNA Barcoding, Taxonomic ; Coral Reefs ; },
abstract = {Coral reefs have the highest biodiversity of all marine ecosystems in tropical and subtropical oceans. However, scleractinian corals, keystone organisms of reef productivity, are facing a crisis due to climate change and anthropogenic activities. A broad survey of reef-building corals is essential for worldwide reef preservation. To this end, direct observations made by coral-specialist divers might be supported by another robust method. We improved a recently devised environmental DNA (eDNA) metabarcoding method to identify more than 43 scleractinian genera by sampling 2 l of surface seawater above reefs. Together with direct observations by divers, we assessed the utility of eDNA at 63 locations spanning approximately 250 km near Okinawa Island. Slopes of these islands are populated by diverse coral genera, whereas shallow 'moats' sustain fewer and less varied coral taxa. Major genera recorded by divers included Acropora, Pocillopora, Porites and Montipora, the presence of which was confirmed by eDNA analyses. In addition, eDNA identified more genera than direct observations and documented the presence of previously unrecorded species. This scleractinian coral-specific eDNA method promises to be a powerful tool to survey coral reefs broadly, deeply and robustly.},
}
@article {pmid36985324,
year = {2023},
author = {Vásquez, E and Millones, C},
title = {Isolation and Identification of Bacteria of Genus Bacillus from Composting Urban Solid Waste and Palm Forest in Northern Peru.},
journal = {Microorganisms},
volume = {11},
number = {3},
pages = {},
pmid = {36985324},
issn = {2076-2607},
support = {DITT-2023-MC//Vicerrectorado de Investigaci&#xf3;n/ ; },
abstract = {A technical challenge for composting in Peruvian cities with annual temperatures below 20 °C is that the degradation of municipal solid waste (MSW) is slow, so the identification of cold-adapted bacteria would be interesting for use as inoculants in places with these climatic conditions. This study isolated, identified, and evaluated bacterial strains with cellulolytic and amylolytic activities at low temperatures. Bacterial strains were isolated from the Chachapoyas Municipal Composting Plant and soil from the Ocol Palm Forest in northern Peru. The screening was carried out to evaluate the extracellular enzyme activity of the strains at low temperatures, grouping those with cellulolytic and cellulolytic/amylolytic activities. The DNA-barcoding using 16S rRNA and enzyme activity allowed the identification and selection of five species with enzymatic activity at 15 and 20 °C of the genus Bacillus, three with cellulolytic/amylolytic activity (B. wiedmanii, B. subtilis, and B. velezensis), and two with cellulolytic activity (B. safensis subsp. safensis, and B. subtilis). These strains showed tolerance to temperatures below optimum and could be used in further studies as inoculants for composting organic wastes at temperatures below 20 °C.},
}
@article {pmid36984880,
year = {2023},
author = {Raclariu-Manolică, AC and Socaciu, C},
title = {Detecting and Profiling of Milk Thistle Metabolites in Food Supplements: A Safety-Oriented Approach by Advanced Analytics.},
journal = {Metabolites},
volume = {13},
number = {3},
pages = {},
pmid = {36984880},
issn = {2218-1989},
support = {PN-III-P1-1.1-PD-2019-0522//Unitatea Executiva Pentru Finantarea Invatamantului Superior a Cercetarii Dezvoltarii si Inovarii/ ; },
abstract = {Milk thistle (Silybum marianum (L.) Gaertn.) is among the top-selling botanicals used as a supportive treatment for liver diseases. Silymarin, a mixture of unique flavonolignan metabolites, is the main bioactive component of milk thistle. The biological activities of silymarin have been well described in the literature, and its use is considered safe and well-tolerated in appropriate doses. However, commercial preparations do not always contain the recommended concentrations of silymarin, failing to provide the expected therapeutic effect. While the poor quality of raw material may explain the low concentrations of silymarin, its deliberate removal is suspected to be an adulteration. Toxic contaminants and foreign matters were also detected in milk thistle preparations, raising serious health concerns. Standard methods for determination of silymarin components include thin-layer chromatography (TLC), high-performance thin-layer chromatography (HPTLC), and high-performance liquid chromatography (HPLC) with various detectors, but nuclear magnetic resonance (NMR) and ultra-high-performance liquid chromatography (UHPLC) have also been applied. This review surveys the extraction techniques of main milk thistle metabolites and the quality, efficacy, and safety of the derived food supplements. Advanced analytical authentication approaches are discussed with a focus on DNA barcoding and metabarcoding to complement orthogonal chemical characterization and fingerprinting of herbal products.},
}
@article {pmid36983548,
year = {2023},
author = {Nascimbene, J and Nimis, PL and Klüßendorf, J and Thüs, H},
title = {Freshwater Lichens, Including New Species in the Genera Verrucaria, Placopyrenium and Circinaria, Associated with Lobothallia hydrocharis (Poelt &amp; Nimis) Sohrabi &amp; Nimis from Watercourses of Sardinia.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {3},
pages = {},
pmid = {36983548},
issn = {2309-608X},
abstract = {This work summarizes the results of the exploration of freshwater lichen biota on the island of Sardinia associated with the regional flagship species Lobothallia hydrocharis, a large-sized crustose lichen from the splash zone along mountain streams, so far known from Sardinia only. Molecular data were used to confirm its distinctiveness from other taxa and its systematic placement and to identify critical taxa among its associated lichen biota. We found 25 species of lichenized fungi, including three species new to science in the genera Verrucaria, Placopyrenium, and Circinaria, and seven species new to Sardinia (Hydropunctaria rheithrophila, Ionaspis chrysophana, I. odora, Verrucaria aquatilis, V. collematodes, V. pseudovirescens), or new to Southern Europe (V. devensis). Specific traits for the freshwater lichen biota of Sardinia were identified and compared to those reported from freshwater sites in the Alps and Carpathian mountains, e.g., a relative scarcity of subgelatinous lichens. Parasitic or epilichenic interactions were found frequently but only in the splash zone and not in the permanently submerged zone, i.e., two parasitic Placopyrenium species, and clearly lichenicolous thalli of Kuettlingeria atroflava and Lobothallia hydrocharis. Due to its specific trait profile and the great potential for the discovery of new species, we recommend the inclusion of Sardinian and further Mediterranean sites in continental-scale monitoring programs for freshwater lichens.},
}
@article {pmid36980969,
year = {2023},
author = {Saidon, NA and Wagiran, A and Samad, AFA and Mohd Salleh, F and Mohamed, F and Jani, J and Linatoc, AC},
title = {DNA Barcoding, Phylogenetic Analysis and Secondary Structure Predictions of Nepenthes ampullaria, Nepenthes gracilis and Nepenthes rafflesiana.},
journal = {Genes},
volume = {14},
number = {3},
pages = {},
pmid = {36980969},
issn = {2073-4425},
mesh = {*DNA Barcoding, Taxonomic/methods ; DNA, Plant/genetics ; Phylogeny ; *Caryophyllales/genetics ; },
abstract = {Nepentheceae, the most prominent carnivorous family in the Caryophyllales order, comprises the Nepenthes genus, which has modified leaf trap characteristics. Although most Nepenthes species have unique morphologies, their vegetative stages are identical, making identification based on morphology difficult. DNA barcoding is seen as a potential tool for plant identification, with small DNA segments amplified for species identification. In this study, three barcode loci; ribulose-bisphosphate carboxylase (rbcL), intergenic spacer 1 (ITS1) and intergenic spacer 2 (ITS2) and the usefulness of the ITS1 and ITS2 secondary structure for the molecular identification of Nepenthes species were investigated. An analysis of barcodes was conducted using BLASTn, pairwise genetic distance and diversity, followed by secondary structure prediction. The findings reveal that PCR and sequencing were both 100% successful. The present study showed the successful amplification of all targeted DNA barcodes at different sizes. Among the three barcodes, rbcL was the least efficient as a DNA barcode compared to ITS1 and ITS2. The ITS1 nucleotide analysis revealed that the ITS1 barcode had more variations compared to ITS2. The mean genetic distance (K2P) between them was higher for interspecies compared to intraspecies. The results showed that the DNA barcoding gap existed among Nepenthes species, and differences in the secondary structure distinguish the Nepenthes. The secondary structure generated in this study was found to successfully discriminate between the Nepenthes species, leading to enhanced resolutions.},
}
@article {pmid36980877,
year = {2023},
author = {Collins, GE and Young, MR and Convey, P and Chown, SL and Cary, SC and Adams, BJ and Wall, DH and Hogg, ID},
title = {Biogeography and Genetic Diversity of Terrestrial Mites in the Ross Sea Region, Antarctica.},
journal = {Genes},
volume = {14},
number = {3},
pages = {},
pmid = {36980877},
issn = {2073-4425},
mesh = {Animals ; *Genetic Variation/genetics ; *Mites/genetics ; Antarctic Regions ; Phylogeny ; Genetic Drift ; },
abstract = {Free-living terrestrial mites (Acari) have persisted through numerous glacial cycles in Antarctica. Very little is known, however, of their genetic diversity and distribution, particularly within the Ross Sea region. To redress this gap, we sampled mites throughout the Ross Sea region, East Antarctica, including Victoria Land and the Queen Maud Mountains (QMM), covering a latitudinal range of 72-85 °S, as well as Lauft Island near Mt. Siple (73 °S) in West Antarctica and Macquarie Island (54[o]S) in the sub-Antarctic. We assessed genetic diversity using mitochondrial cytochrome c oxidase subunit I gene sequences (COI-5P DNA barcode region), and also morphologically identified voucher specimens. We obtained 130 sequences representing four genera: Nanorchestes (n = 30 sequences), Stereotydeus (n = 46), Coccorhagidia (n = 18) and Eupodes (n = 36). Tree-based analyses (maximum likelihood) revealed 13 genetic clusters, representing as many as 23 putative species indicated by barcode index numbers (BINs) from the Barcode of Life Datasystems (BOLD) database. We found evidence for geographically-isolated cryptic species, e.g., within Stereotydeus belli and S. punctatus, as well as unique genetic groups occurring in sympatry (e.g., Nanorchestes spp. in QMM). Collectively, these data confirm high genetic divergence as a consequence of geographic isolation over evolutionary timescales. From a conservation perspective, additional targeted sampling of understudied areas in the Ross Sea region should be prioritised, as further diversity is likely to be found in these short-range endemic mites.},
}
@article {pmid36979041,
year = {2023},
author = {Bañón, R and Almón, B and Rábade, S and Ríos, MB and de Carlos, A},
title = {DNA Barcoding of the Genus Magnisudis (Aulopiformes: Paralepididae) with a Coastal Record and Biological Features of Magnisudis atlantica.},
journal = {Biology},
volume = {12},
number = {3},
pages = {},
pmid = {36979041},
issn = {2079-7737},
abstract = {One specimen of the duckbill barracudina Magnisudis atlantica of 402 mm TL was caught in a shallow coastal area in Galician waters, northwest of Spain. Morphometric and meristic parameters along with DNA barcoding, based on cytochrome c oxidase subunit I, were used to confirm the specimen identity. Neighbor-joining analysis of nominal sequences of the genus Magnisudis obtained from the Barcode of Life Data System indicates the presence of six representative groupings of potential species, in contrast to the three that are currently recognized as valid. The stomach contents showed remains of digested crustaceans, tentatively identified as Euphausiids. Histological examination of the gonads revealed the specimen to be an immature female with oocytes at the primary growth stage, indicative of a lack of hermaphroditism. The results add new biological and taxonomic data that contribute to improved understanding of these poorly characterized, mainly deep-water species, demonstrating, once again, the effectiveness of DNA barcoding for identifying deep-sea fishes and characterizing their genetic differences.},
}
@article {pmid36978544,
year = {2023},
author = {Loh, KH and Lim, KC and Then, AY and Adam, S and Leung, AJ and Hu, W and Bong, CW and Wang, A and Sade, A and Musel, J and Du, J},
title = {Advancing DNA Barcoding to Elucidate Elasmobranch Biodiversity in Malaysian Waters.},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {6},
pages = {},
pmid = {36978544},
issn = {2076-2615},
support = {PV049-2019 and PV023-2022//WWF- Malaysia/ ; IF004-2022//Third Institute of Oceanography, Ministry of Natural Resources, China/ ; No: 41961144022//Monitoring and Conservation of the coastal ecosystem in the Soutth China Sea; National Natural Science foundation of China/ ; IF030B-2019//China-ASEAN Maritime Cooperation fund project "Marine Protected Areas Network in Chi-na-ASEAN Countries"/ ; BK018-2015, RP018C-16SUSC//Universiti Malaya grants/ ; },
abstract = {The data provided in this article are partial fragments of the Cytochrome c oxidase subunit 1 mitochondrial gene (CO1) sequences of 175 tissues sampled from sharks and batoids collected from Malaysian waters, from June 2015 to June 2022. The barcoding was done randomly for six specimens from each species, so as to authenticate the code. We generated barcodes for 67 different species in 20 families and 11 orders. DNA was extracted from the tissue samples following the Chelex protocols and amplified by polymerase chain reaction (PCR) using the barcoding universal primers FishF2 and FishR2. A total of 654 base pairs (bp) of barcode CO1 gene from 175 samples were sequenced and analysed. The genetic sequences were blasted into the NCBI GenBank and Barcode of Life Data System (BOLD). A review of the blast search confirmed that there were 68 valid species of sharks and batoids that occurred in Malaysian waters. We provided the data of the COI gene mid-point rooting phylogenetic relation trees and analysed the genetic distances among infra-class and order, intra-species, inter-specific, inter-genus, inter-familiar, and inter-order. We confirmed the addition of Squalus edmundsi, Carcharhinus amboinensis, Alopias superciliosus, and Myliobatis hamlyni as new records for Malaysia. The establishment of a comprehensive CO1 database for sharks and batoids will help facilitate the rapid monitoring and assessment of elasmobranch fisheries using environmental DNA methods.},
}
@article {pmid36977214,
year = {2023},
author = {Beikpour, F and Pellegrini, F and Lanave, G and Camero, M and Catella, C and Di Martino, B and Di Profio, F and Masotti, C and Battistini, R and Serracca, L and La Rosa, G and Martella, V and Suffredini, E},
title = {Exploring the Astrovirome of Shellfish Matrices Using Nanopore Sequencing.},
journal = {Veterinary sciences},
volume = {10},
number = {3},
pages = {},
pmid = {36977214},
issn = {2306-7381},
support = {IZS PLV 02/20 RC//Italian Ministry of Health/ ; PE00000007, INF-ACT//MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases/ ; },
abstract = {Astroviruses are important human enteric pathogens transmissible with contaminated food and water. Astroviruses have also been identified in mammals, birds, lower vertebrates and invertebrates. The genetic diversity of human and animal astroviruses poses a challenge for diagnostics and taxonomy. As a proof of concept, we used a panastrovirus consensus primer set, able to amplify in a nested RT-PCR protocol a 400-nt-long fragment of the RNA-dependent RNA polymerase of most members of the Astroviridae family, in conjunction with a nanopore sequencing platform, to generate information on the astrovirome in filter-feeding mollusks. Amplicons generated from bivalve samples were used to generate libraries for deep sequencing. In three samples, only one unique RdRp sequence type was obtained. However, in seven samples and in three barcodes with eleven pooled samples, we identified a variety of known and unknown RdRp sequence types, in most cases distantly related to astrovirus sequences available in the databases. In total, 37 different sequence contigs were generated. Avian-origin astrovirus sequences were predominant, likely due to contamination of shellfish harvesting waters by marine birds. Astroviruses of the aquatic eco-system were also identified, whereas human astroviruses were not detected.},
}
@article {pmid36975912,
year = {2023},
author = {Song, C and Wang, L and Lei, T and Qi, X},
title = {New Color-Patterned Species of Microtendipes Kieffer, 1913 (Diptera: Chironomidae) and a Deep Intraspecific Divergence of Species by DNA Barcodes.},
journal = {Insects},
volume = {14},
number = {3},
pages = {},
pmid = {36975912},
issn = {2075-4450},
support = {32100353, 32070481//National Natural Science Foundation of China/ ; LY22C040003//Zhejiang Provincial Natural Science Foundation of China/ ; 21hb04, 21nya17, 1902gy23//Science &amp; Technology Project of Taizhou/ ; },
abstract = {The genus Microtendipes Kieffer (Diptera: Chironomidae) has a nearly worldwide distribution, comprising more than 60 species, which are further divided into two species groups based on larval stage. However, species delimitation and identification among the adults of this genus are controversial and uncertain. For instance, previous studies have provided many synonymies based on conspecific color pattern variations in Microtendipes species. Here, we used DNA barcode data to address Microtendipes species delimitation as well as to test whether color pattern variations can be diagnostic characters for interspecific identification. The 151 DNA barcodes used, 51 of which were contributed by our laboratory, represent 21 morphospecies. Species with specific color patterns could be accurately separated based on DNA barcodes. Consequently, the color patterns of adult males could be important diagnostic characters. The average intraspecific and interspecific sequence divergences were 2.8% and 12.5%, respectively, and several species exhibited deep intraspecific divergences higher than 5%. Molecular operational taxonomic units (OTUs) ranged from 21 to 73, based on methods including phylogenetic trees, the assemble species by automatic partitioning method, the Poisson tree process (PTP), and the general mixed Yule-coalescent (GMYC) method. As a result of these analyses, five new species were recognized (M. baishanzuensis sp. nov., M. bimaculatus sp. nov., M. nigrithorax sp. nov., M. robustus sp. nov., and M. wuyiensis sp. nov.).},
}
@article {pmid36973586,
year = {2023},
author = {Jossart, Q and Bauman, D and Moreau, CV and Saucède, T and Christiansen, H and Brasier, MJ and Convey, P and Downey, R and Figuerola, B and Martin, P and Norenburg, J and Rosenfeld, S and Verheye, M and Danis, B},
title = {A pioneer morphological and genetic study of the intertidal fauna of the Gerlache Strait (Antarctic Peninsula).},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {4},
pages = {514},
pmid = {36973586},
issn = {1573-2959},
support = {BR/154/A1/RECTO//Belgian Science Policy Office/ ; BR/154/A1/RECTO//Belgian Science Policy Office/ ; BR/154/A1/RECTO//Belgian Science Policy Office/ ; 895799//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; 801370//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; B2/191/P1/COPE//Belgian Federal Science Policy Office/ ; 2019-BP-00183//Secretary of Universities and Research (Government of Catalonia) - Beatriu de Pin&#xf3;s program/ ; },
mesh = {Animals ; *Ecosystem ; Antarctic Regions ; Environmental Monitoring ; Biodiversity ; *Bivalvia ; },
abstract = {The underexplored intertidal ecosystems of Antarctica are facing rapid changes in important environmental factors. Associated with temperature increase, reduction in coastal ice will soon expose new ice-free areas that will be colonized by local or distant biota. To enable detection of future changes in faunal composition, a biodiversity baseline is urgently required. Here, we evaluated intertidal faunal diversity at 13 locations around the Gerlache Strait (western Antarctic Peninsula), using a combination of a quadrat approach, morphological identification and genetic characterization. Our data highlight a community structure comprising four generally distributed and highly abundant species (the flatworm Obrimoposthia wandeli, the bivalve Kidderia subquadrata, and the gastropods Laevilitorina umbilicata and Laevilitorina caliginosa) as well as 79 rarer and less widely encountered species. The most abundant species thrive in the intertidal zone due to their ability to either survive overwinter in situ or to rapidly colonize this zone when conditions allow. In addition, we confirmed the presence of multiple trophic levels at nearly all locations, suggesting that complex inter-specific interactions occur within these communities. Diversity indices contrasted between sampling locations (from 3 to 32 species) and multivariate approaches identified three main groups. This confirms the importance of environmental heterogeneity in shaping diversity patterns within the investigated area. Finally, we provide the first genetic and photographic baseline of the Antarctic intertidal fauna (106 sequences, 137 macrophotographs), as well as preliminary insights on the biogeography of several species. Taken together, these results provide a timely catalyst to assess the diversity and to inform studies of the potential resilience of these intertidal communities.},
}
@article {pmid36972021,
year = {2023},
author = {Brinkmann, I and Schweizer, M and Singer, D and Quinchard, S and Barras, C and Bernhard, JM and Filipsson, HL},
title = {Through the eDNA looking glass: Responses of fjord benthic foraminiferal communities to contrasting environmental conditions.},
journal = {The Journal of eukaryotic microbiology},
volume = {70},
number = {4},
pages = {e12975},
doi = {10.1111/jeu.12975},
pmid = {36972021},
issn = {1550-7408},
mesh = {Ecosystem ; Estuaries ; *DNA, Environmental/genetics ; *Foraminifera/genetics ; Environmental Monitoring/methods ; Biodiversity ; DNA ; DNA Barcoding, Taxonomic ; },
abstract = {The health of coastal marine environments is severely declining with global changes. Proxies, such as those based on microeukaryote communities, can record biodiversity and ecosystem responses. However, conventional studies rely on microscopic observations of limited taxonomic range and size fraction, missing putatively ecologically informative community components. Here, we tested molecular tools to survey foraminiferal biodiversity in a fjord system (Sweden) on spatial and temporal scales: Alpha and beta diversity responses to natural and anthropogenic environmental trends were assessed and variability of foraminiferal environmental DNA (eDNA) compared to morphology-based data. The identification of eDNA-obtained taxonomic units was aided by single-cell barcoding. Our study revealed wide diversity, including typical morphospecies recognized in the fjords, and so-far unrecognized taxa. DNA extraction method impacted community composition outputs significantly. DNA extractions of 10 g sediment more reliably represented present diversity than of 0.5-g samples and, thus, are preferred for environmental assessments in this region. Alpha- and beta diversity of 10-g extracts correlated with bottom-water salinity similar to morpho-assemblage diversity changes. Sub-annual environmental variability resolved only partially, indicating damped sensitivity of foraminiferal communities on short timescales using established metabarcoding techniques. Systematically addressing the current limitations of morphology-based and metabarcoding studies may strongly improve future biodiversity and environmental assessments.},
}
@article {pmid36970845,
year = {2023},
author = {English, MA and Alcantar, MA and Collins, JJ},
title = {A self-propagating, barcoded transposon system for the dynamic rewiring of genomic networks.},
journal = {Molecular systems biology},
volume = {19},
number = {6},
pages = {e11398},
pmid = {36970845},
issn = {1744-4292},
mesh = {Mutagenesis, Insertional/genetics ; *DNA Transposable Elements/genetics ; *Genomics ; Phenotype ; Gene Regulatory Networks ; },
abstract = {In bacteria, natural transposon mobilization can drive adaptive genomic rearrangements. Here, we build on this capability and develop an inducible, self-propagating transposon platform for continuous genome-wide mutagenesis and the dynamic rewiring of gene networks in bacteria. We first use the platform to study the impact of transposon functionalization on the evolution of parallel Escherichia coli populations toward diverse carbon source utilization and antibiotic resistance phenotypes. We then develop a modular, combinatorial assembly pipeline for the functionalization of transposons with synthetic or endogenous gene regulatory elements (e.g., inducible promoters) as well as DNA barcodes. We compare parallel evolutions across alternating carbon sources and demonstrate the emergence of inducible, multigenic phenotypes and the ease with which barcoded transposons can be tracked longitudinally to identify the causative rewiring of gene networks. This work establishes a synthetic transposon platform that can be used to optimize strains for industrial and therapeutic applications, for example, by rewiring gene networks to improve growth on diverse feedstocks, as well as help address fundamental questions about the dynamic processes that have sculpted extant gene networks.},
}
@article {pmid36968243,
year = {2022},
author = {Hurtado, J and Flynn, C and Lee, JH and Salcedo, EC and Cottrell, CA and Skog, PD and Burton, DR and Nemazee, D and Schief, WR and Landais, E and Sok, D and Briney, B},
title = {Efficient isolation of rare B cells using next-generation antigen barcoding.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {962945},
pmid = {36968243},
issn = {2235-2988},
support = {R01 AI175439/AI/NIAID NIH HHS/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; R01 AI102766/AI/NIAID NIH HHS/United States ; P01 AI177683/AI/NIAID NIH HHS/United States ; P30 AI036214/AI/NIAID NIH HHS/United States ; UM1 AI144462/AI/NIAID NIH HHS/United States ; U19 AI135995/AI/NIAID NIH HHS/United States ; T32 AI007244/AI/NIAID NIH HHS/United States ; R35 GM133682/GM/NIGMS NIH HHS/United States ; },
mesh = {*Antibodies, Neutralizing ; B-Lymphocytes ; HIV Antibodies ; Antigens ; Antibodies, Monoclonal ; *HIV-1 ; },
abstract = {The ability to efficiently isolate antigen-specific B cells in high throughput will greatly accelerate the discovery of therapeutic monoclonal antibodies (mAbs) and catalyze rational vaccine development. Traditional mAb discovery is a costly and labor-intensive process, although recent advances in single-cell genomics using emulsion microfluidics allow simultaneous processing of thousands of individual cells. Here we present a streamlined method for isolation and analysis of large numbers of antigen-specific B cells, including next generation antigen barcoding and an integrated computational framework for B cell multi-omics. We demonstrate the power of this approach by recovering thousands of antigen-specific mAbs, including the efficient isolation of extremely rare precursors of VRC01-class and IOMA-class broadly neutralizing HIV mAbs.},
}
@article {pmid36964519,
year = {2023},
author = {Zang, C and Wang, X and Cheng, P and Liu, L and Guo, X and Wang, H and Lou, Z and Lei, J and Wang, W and Wang, Y and Gong, M and Liu, H},
title = {Evaluation of the evolutionary genetics and population structure of Culex pipiens pallens in Shandong province, China based on knockdown resistance (kdr) mutations and the mtDNA-COI gene.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {145},
pmid = {36964519},
issn = {1471-2164},
support = {81871685//the National Natural Science Foundation of China/ ; ZR2020KH001//Shandong Provincial Natural Science Foundation/ ; NHCKFKT2021-02//NHC Key Laboratory of Parasite and Vector Biology/ ; },
mesh = {Animals ; Female ; Humans ; *Culex/genetics ; *Insecticides/pharmacology ; DNA, Mitochondrial/genetics ; Mosquito Vectors/genetics ; Mutation ; *Pyrethrins/pharmacology ; *Culicidae/genetics ; Insecticide Resistance/genetics ; *Voltage-Gated Sodium Channels/genetics ; China ; Vascular Endothelial Growth Factor Receptor-2/genetics ; },
abstract = {BACKGROUND: Mosquitoes are important vectors for a range of diseases, contributing to high rates of morbidity and mortality in the human population. Culex pipiens pallens is dominant species of Culex mosquito in northern China and a major vector for both West Nile virus and Bancroftian filariasis. Insecticide application were largely applied to control the mosquito-mediated spread of these diseases, contributing to increasing rates of resistance in the mosquito population. The voltage-gated sodium channel (Vgsc) gene is the target site of pyrethroids, and mutations in this gene cause knockdown resistance (kdr). While these kdr mutations are known to be critical to pyrethroid resistance, their evolutionary origins remain poorly understood. Clarifying the origins of these mutations is potential to guide further vector control and disease prevention efforts. Accordingly, the present study was designed to study the evolutionary genetics of kdr mutations and their association with the population structure of Cx. p. pallens in Shandong province, China.<br><br>METHODS: Adult Culex females were collected from Shandong province and subjected to morphological identification under a dissection microscope. Genomic DNA were extracted from the collected mosquitoes, the Vgsc gene were amplified via PCR and sequenced to assess kdr allele frequencies, intron polymorphisms, and kdr codon evolution. In addition, population genetic diversity and related population characteristics were assessed by amplifying and sequencing the mitochondrial cytochrome C oxidase I (COI) gene.<br><br>RESULTS: Totally, 263 Cx. p. pallens specimens were used for DNA barcoding and sequencing analyses to assess kdr allele frequencies in nine Culex populations. The kdr codon L1014 in the Vgsc gene identified two non-synonymous mutations (L1014F and L1014S) in the analyzed population. These mutations were present in the eastern hilly area and west plain region of Shandong Province. However, only L1014F mutation was detected in the southern mountainous area and Dongying city of Shandong Province, where the mutation frequency was low. Compared to other cities, population in Qingdao revealed significant genetic differentiation. Spatial kdr mutation patterns are likely attributable to some combination of prolonged insecticide-mediated selection coupled with the genetic isolation of these mosquito populations.<br><br>CONCLUSIONS: These data suggest that multiple kdr alleles associated with insecticide resistance are present within the Cx. p. pallens populations of Shandong Province, China. The geographical distributions of kdr mutations in this province are likely that the result of prolonged and extensive insecticide application in agricultural contexts together with frequent mosquito population migrations. In contrast, the low-frequency kdr mutation detected in central Shandong Province populations may originate from the limited selection pressure in this area and the relative genetic isolation. Overall, the study compares the genetic patterns revealed by a functional gene with a neutral marker and demonstrates the combined impact of demographic and selection factors on population structure.},
}
@article {pmid36964177,
year = {2023},
author = {Komatsu, J and Cico, A and Poncin, R and Le Bohec, M and Morf, J and Lipin, S and Graindorge, A and Eckert, H and Saffarian, A and Cathaly, L and Guérin, F and Majello, S and Ulveling, D and Vayaboury, A and Fernandez, N and Dimitrova, D and Bussell, X and Fourne, Y and Chaumat, P and André, B and Baldivia, E and Godet, U and Guinin, M and Moretto, V and Ismail, J and Caille, O and Roblot, N and Beaupère, C and Liboz, A and Guillemain, G and Blondeau, B and Walrafen, P and Edelstein, S},
title = {RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {4866},
pmid = {36964177},
issn = {2045-2322},
mesh = {*Sequence Analysis, RNA/methods ; Hydrogels/chemistry ; *Single-Cell Analysis/methods ; Humans ; Animals ; Mice ; Gene Expression Profiling ; },
abstract = {Progress in sample preparation for scRNA-seq is reported based on RevGel-seq, a reversible-hydrogel technology optimized for samples of fresh cells. Complexes of one cell paired with one barcoded bead are stabilized by a chemical linker and dispersed in a hydrogel in the liquid state. Upon gelation on ice the complexes are immobilized and physically separated without requiring nanowells or droplets. Cell lysis is triggered by detergent diffusion, and RNA molecules are captured on the adjacent barcoded beads for further processing with reverse transcription and preparation for cDNA sequencing. As a proof of concept, analysis of PBMC using RevGel-seq achieves results similar to microfluidic-based technologies when using the same original sample and the same data analysis software. In addition, a clinically relevant application of RevGel-seq is presented for pancreatic islet cells. Furthermore, characterizations carried out on cardiomyocytes demonstrate that the hydrogel technology readily accommodates very large cells. Standard analyses are in the 10,000-input cell range with the current gelation device, in order to satisfy common requirements for single-cell research. A convenient stopping point after two hours has been established by freezing at the cell lysis step, with full preservation of gene expression profiles. Overall, our results show that RevGel-seq represents an accessible and efficient instrument-free alternative, enabling flexibility in terms of experimental design and timing of sample processing, while providing broad coverage of cell types.},
}
@article {pmid36962412,
year = {2022},
author = {Karat, AS and McCreesh, N and Baisley, K and Govender, I and Kallon, II and Kielmann, K and MacGregor, H and Vassall, A and Yates, TA and Grant, AD},
title = {Estimating waiting times, patient flow, and waiting room occupancy density as part of tuberculosis infection prevention and control research in South African primary health care clinics.},
journal = {PLOS global public health},
volume = {2},
number = {7},
pages = {e0000684},
pmid = {36962412},
issn = {2767-3375},
abstract = {Transmission of respiratory pathogens, such as Mycobacterium tuberculosis and severe acute respiratory syndrome coronavirus 2, is more likely during close, prolonged contact and when sharing a poorly ventilated space. Reducing overcrowding of health facilities is a recognised infection prevention and control (IPC) strategy; reliable estimates of waiting times and 'patient flow' would help guide implementation. As part of the Umoya omuhle study, we aimed to estimate clinic visit duration, time spent indoors versus outdoors, and occupancy density of waiting rooms in clinics in KwaZulu-Natal (KZN) and Western Cape (WC), South Africa. We used unique barcodes to track attendees' movements in 11 clinics, multiple imputation to estimate missing arrival and departure times, and mixed-effects linear regression to examine associations with visit duration. 2,903 attendees were included. Median visit duration was 2 hours 36 minutes (interquartile range [IQR] 01:36-3:43). Longer mean visit times were associated with being female (13.5 minutes longer than males; p<0.001) and attending with a baby (18.8 minutes longer than those without; p<0.01), and shorter mean times with later arrival (14.9 minutes shorter per hour after 0700; p<0.001). Overall, attendees spent more of their time indoors (median 95.6% [IQR 46-100]) than outdoors (2.5% [IQR 0-35]). Attendees at clinics with outdoor waiting areas spent a greater proportion (median 13.7% [IQR 1-75]) of their time outdoors. In two clinics in KZN (no appointment system), occupancy densities of ~2.0 persons/m2 were observed in smaller waiting rooms during busy periods. In one clinic in WC (appointment system, larger waiting areas), occupancy density did not exceed 1.0 persons/m2 despite higher overall attendance. In this study, longer waiting times were associated with early arrival, being female, and attending with a young child. Occupancy of waiting rooms varied substantially between rooms and over the clinic day. Light-touch estimation of occupancy density may help guide interventions to improve patient flow.},
}
@article {pmid36960591,
year = {2023},
author = {Matthews, AE and Wijeratne, AJ and Sweet, AD and Hernandes, FA and Toews, DPL and Boves, TJ},
title = {Dispersal-Limited Symbionts Exhibit Unexpectedly Wide Variation in Host Specificity.},
journal = {Systematic biology},
volume = {72},
number = {4},
pages = {802-819},
doi = {10.1093/sysbio/syad014},
pmid = {36960591},
issn = {1076-836X},
mesh = {Animals ; Phylogeny ; *Host Specificity ; *Mites/genetics ; Biological Evolution ; Symbiosis ; },
abstract = {A fundamental aspect of symbiotic relationships is host specificity, ranging from extreme specialists associated with only a single host species to generalists associated with many different species. Although symbionts with limited dispersal capabilities are expected to be host specialists, some are able to associate with multiple hosts. Understanding the micro- and macro-evolutionary causes of variations in host specificity is often hindered by sampling biases and the limited power of traditional evolutionary markers. Here, we studied feather mites to address the barriers associated with estimates of host specificity for dispersal-limited symbionts. We sampled feather mites (Proctophyllodidae) from a nearly comprehensive set of North American breeding warblers (Parulidae) to study mite phylogenetic relationships and host-symbiont codiversification. We used pooled-sequencing (Pool-Seq) and short-read Illumina technology to interpret results derived from a traditional barcoding gene (cytochrome c oxidase subunit 1) versus 11 protein-coding mitochondrial genes using concatenated and multispecies coalescent approaches. Despite the statistically significant congruence between mite and host phylogenies, mite-host specificity varies widely, and host switching is common regardless of the genetic marker resolution (i.e., barcode vs. multilocus). However, the multilocus approach was more effective than the single barcode in detecting the presence of a heterogeneous Pool-Seq sample. These results suggest that presumed symbiont dispersal capabilities are not always strong indicators of host specificity or of historical host-symbiont coevolutionary events. A comprehensive sampling at fine phylogenetic scales may help to better elucidate the microevolutionary filters that impact macroevolutionary processes regulating symbioses, particularly for dispersal-limited symbionts. [Codiversification; cophylogenetics; feather mites; host switching; pooled sequencing; species delineation; symbiosis, warblers.].},
}
@article {pmid36951368,
year = {2023},
author = {Yang, S and Feng, X and Xu, B and Lin, R and Xu, Y and Chen, S and Wang, Z and Wang, X and Meng, X and Gao, Z},
title = {Directional Self-Assembly of Facet-Aligned Organic Hierarchical Super-Heterostructures for Spatially Resolved Photonic Barcodes.},
journal = {ACS nano},
volume = {17},
number = {7},
pages = {6341-6349},
doi = {10.1021/acsnano.2c10659},
pmid = {36951368},
issn = {1936-086X},
abstract = {Organic multicolor heterostructures with spatially resolved luminescent colors and identifiable patterns have exhibited considerable potential for achieving micro-/nanoscale photonic barcodes. Nevertheless, such types of barcodes reported thus far are exclusively based on a single heterostructure with limited coding elements. Here, a directional self-assembly strategy is proposed to achieve high-coding-capacity spatially resolved photonic barcodes through rationally constructing organic hierarchical super-heterostructures, where numerous subheterostructure blocks with flat hexagonal facets are precisely oriented with their specific facets via a reconfigurable capillary force. The building blocks were prepared through a one-pot sequential heteroepitaxial growth, which enables the effective modulation of the structural and color characteristics in coding structures. Significantly, a directional facet-to-facet attraction between particles via facet registration leads to the formation of well-defined 1D super-heterostructures, which contain multiple coding elements, thus providing a good platform for constructing the high-coding-capacity photonic barcodes. The results may be useful in fabricating organic hierarchical hybrid super-heterostructures for security labels and optical data recording.},
}
@article {pmid36950495,
year = {2023},
author = {Nagral, A and Rudra, OS and Menezes, S and Menon, S and Shailajan, S and Mallakmir, S and Reddy, R},
title = {Herb-induced Liver Injury-A Guide to Approach. Lessons from the Tinospora cordifolia (Giloy) Case Series Story.},
journal = {Journal of clinical and experimental hepatology},
volume = {13},
number = {2},
pages = {360-371},
pmid = {36950495},
issn = {0973-6883},
abstract = {BACKGROUND: Tinospora cordifolia (TC) is being increasingly consumed in India for its health and suggested immune-enhancing benefits in preventing and countering COVID-19. We previously published our experience of hepatotoxicity with self-medication of TC in six individuals. Since herb-induced liver injury (HILI) has been described with Tinospora crispa (TCR) consumption, it was contested that our patients may have mistakenly self-medicated with TCR which is similar in appearance to TC.<br><br>METHODS: We collected the four plant samples and two commercial preparations that were consumed by our patients for further analysis. The six samples underwent high performance thin layer chromatography phytochemical analysis and DNA barcoding studies for the confirmation of the genus and species. The four plant part samples which included stems and leaves were also analysed by a botanist for the characteristic morphological and microscopic features.<br><br>RESULTS: Based on morphological, microscopic, phytochemical&#xa0;and DNA studies, the four plant part samples were identified as TC. The two commercial preparations could not be analysed on phytochemical analysis or DNA barcoding studies due to other ingredients that most likely interfered with the analysis. The herb consumed by our study subjects was confirmed to be Tinospora cordifolia.<br><br>CONCLUSION: We have highlighted the key morphological and phytochemical differences between these two species. We propose an algorithmic approach to accurately identify the implicated herb in cases of HILI. Future studies on causality need to focus on the serological/histopathological identification of active herb/metabolites in human tissues.},
}
@article {pmid36947858,
year = {2023},
author = {Bramlett, C and Eerdeng, J and Jiang, D and Lee, Y and Garcia, I and Vergel-Rodriguez, M and Condie, P and Nogalska, A and Lu, R},
title = {RNA splicing factor Rbm25 underlies heterogeneous preleukemic clonal expansion in mice.},
journal = {Blood},
volume = {141},
number = {24},
pages = {2961-2972},
pmid = {36947858},
issn = {1528-0020},
support = {R00 HL113104/HL/NHLBI NIH HHS/United States ; R35 HL150826/HL/NHLBI NIH HHS/United States ; R01 HL135292/HL/NHLBI NIH HHS/United States ; F31 HL149278/HL/NHLBI NIH HHS/United States ; P30 CA014089/CA/NCI NIH HHS/United States ; R01 HL138225/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Mice ; *Leukemia ; Mice, Knockout ; *Neoplasms ; Proto-Oncogene Proteins/genetics ; RNA ; *RNA Splicing Factors/metabolism ; },
abstract = {Clonal expansion sets the stage for cancer genesis by allowing for the accumulation of molecular alterations. Although genetic mutations such as Tet2 that induce clonal expansion and malignancy have been identified, these mutations are also frequently found in healthy individuals. Here, we tracked preleukemic clonal expansion using genetic barcoding in an inducible Tet2 knockout mouse model and found that only a small fraction of hematopoietic stem cells (HSCs) expanded excessively upon Tet2 knockout. These overexpanded HSCs expressed significantly lower levels of genes associated with leukemia and RNA splicing than nonoverexpanded Tet2 knockout HSCs. Knocking down Rbm25, an identified RNA splicing factor, accelerated the expansion of Tet2-knockout hematopoietic cells in vitro and in vivo. Our data suggest that mutations of an epigenetic factor Tet2 induce variability in the expression of an RNA splicing factor Rbm25, which subsequently drives heterogeneous preleukemic clonal expansion. This heterogeneous clonal expansion could contribute to the variable disease risks across individuals.},
}
@article {pmid36947747,
year = {2023},
author = {Kusch, S and Vaghefi, N and Kiss, L},
title = {The Good, The Bad, and The Misleading: How to Improve the Quality of 'Genome Announcements'?.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {36},
number = {7},
pages = {393-396},
doi = {10.1094/MPMI-01-23-0009-LE},
pmid = {36947747},
issn = {0894-0282},
mesh = {Phylogeny ; *Genome ; *Genomics ; Whole Genome Sequencing ; DNA ; },
abstract = {When comparing the requirements of diverse journals to publish microbial 'Genome Reports,' we noticed that some mostly focus on benchmarking universal single-copy orthologs scores as a quality measure, while the exclusion of possible contaminating sequences from genomic resources and the possible misidentification of the target microbes receive less attention. To deal with these quality issues, we suggest that DNA barcodes that are widely accepted for the identification of the target microbe species should be extracted from newly reported genome resources and included in phylogenetic analyses to confirm the identity of the sequenced microorganisms before Genome Reports are published. This approach, applied, for example, by the journal IMA Fungus, largely prevents the misidentification of the microbes that are targeted for whole-genome sequencing (WGS). In addition, contig similarity values, including GC content, remapping coverage of WGS reads, and BLASTN searches against the National Center for Biotechnology Information nucleotide database, would also reveal contamination issues. The values of these two recommendations to improve the publication criteria for microbial Genome Reports in diverse journals are demonstrated here through analyses of a draft genome published in Molecular Plant-Microbe Interactions and then retracted due to contaminations. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.},
}
@article {pmid36946506,
year = {2023},
author = {Yang, W and Su, Y and Zeng, L and Zhang, Y and Ullah, F and Wang, X and Li, X and Feng, X and Li, Z},
title = {LAMP Assay as a Rapid Identification Technique of Chinese Citrus Fly and Japanese Orange Fly (Diptera: Tephritidae).},
journal = {Journal of economic entomology},
volume = {116},
number = {3},
pages = {956-962},
doi = {10.1093/jee/toad014},
pmid = {36946506},
issn = {1938-291X},
mesh = {*Tephritidae/genetics ; China ; Nucleic Acid Amplification Techniques ; Japan ; Animals ; Molecular Diagnostic Techniques ; },
abstract = {Bactrocera tsuneonis and Bactrocera minax are the most destructive pests that damage citrus in China. These key pests hinder the citrus trade, cause significant financial losses, drastically lower citrus production and quality, and decrease farmer enthusiasm for citrus planting. Bactrocera minax and B. tsuneonis are very similar in all life stages. There are limited morphological characteristics to differentiate the adult species, and it is nearly impossible to differentiate these two species in the egg and larval stages. Loop-mediated isothermal amplification (LAMP) is a rapid and robust diagnostic tool used to identify these two species accurately. We designed two sets of primers to distinguish B. minax and B. tsuneonis using DNA barcoding region of the COI gene. Only 50 min was needed under a constant temperature of 65ºC to determine the species of the two flies. The reaction system has high specificity and sensitivity, in which these two species can be accurately distinguished between different geographical populations and 1.0 ng/μL was the lowest DNA concentration that could be detected. Our primers can quickly identify these key pests without knowing their morphology, which could facilitate plant protection workers at the primary level to solve problems in plant quarantine.},
}
@article {pmid36945366,
year = {2023},
author = {Mikhaylova, V and Rzepka, M and Kawamura, T and Xia, Y and Chang, PL and Zhou, S and Pham, L and Modi, N and Yao, L and Perez-Agustin, A and Pagans, S and Boles, TC and Lei, M and Wang, Y and Garcia-Bassets, I and Chen, Z},
title = {Targeted Phasing of 2-200 Kilobase DNA Fragments with a Short-Read Sequencer and a Single-Tube Linked-Read Library Method.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {36945366},
issn = {2692-8205},
abstract = {In the human genome, heterozygous sites are genomic positions with different alleles inherited from each parent. On average, there is a heterozygous site every 1-2 kilobases (kb). Resolving whether two alleles in neighboring heterozygous positions are physically linked-that is, phased-is possible with a short-read sequencer if the sequencing library captures long-range information. TELL-Seq is a library preparation method based on millions of barcoded micro-sized beads that enables instrument-free phasing of a whole human genome in a single PCR tube. TELL-Seq incorporates a unique molecular identifier (barcode) to the short reads generated from the same high-molecular-weight (HMW) DNA fragment (known as 'linked-reads'). However, genome-scale TELL-Seq is not cost-effective for applications focusing on a single locus or a few loci. Here, we present an optimized TELL-Seq protocol that enables the cost-effective phasing of enriched loci (targets) of varying sizes, purity levels, and heterozygosity. Targeted TELL-Seq maximizes linked-read efficiency and library yield while minimizing input requirements, fragment collisions on microbeads, and sequencing burden. To validate the targeted protocol, we phased seven 180-200 kb loci enriched by CRISPR/Cas9-mediated excision coupled with pulse-field electrophoresis, four 20 kb loci enriched by CRISPR/Cas9-mediated protection from exonuclease digestion, and six 2-13 kb loci amplified by PCR. The selected targets have clinical and research relevance (BRCA1, BRCA2, MLH1, MSH2, MSH6, APC, PMS2, SCN5A-SCN10A, and PKI3CA). These analyses reveal that targeted TELL-Seq provides a reliable way of phasing allelic variants within targets (2-200 kb in length) with the low cost and high accuracy of short-read sequencing.},
}
@article {pmid36944500,
year = {2023},
author = {Reeves, LE and Sloyer, KE and Tyler-Julian, K and Heinig, R and Rosales, A and Domingo, C and Burkett-Cadena, ND},
title = {Culex (Phenacomyia) lactator (Diptera: Culicidae) in southern Florida, USA: a new subgenus and species country record.},
journal = {Journal of medical entomology},
volume = {60},
number = {3},
pages = {478-486},
doi = {10.1093/jme/tjad023},
pmid = {36944500},
issn = {1938-2928},
mesh = {Male ; Female ; Animals ; *Culicidae ; *Culex ; Florida ; Mosquito Vectors ; Larva ; },
abstract = {The Culex subgenus Phenacomyia is a small and poorly studied group of three mosquito species native to the American tropics. Here, we report the first detections of established populations of Culex (Phenacomyia) lactator Dyar &amp; Knab in three counties of southern Florida. Culex lactator was first detected in May 2018 in southern Miami-Dade County, and, at this locality, was collected in subsequent years from 2018 to 2022 as both adults and immatures. Larvae and adults were subsequently collected in 2022, ~175 km northwest of the initial locality at nine sites in Collier and Lee Counties. Identification of specimens collected in these counties as Cx. lactator is supported by molecular analysis and morphological characters of the adult female, male genitalia, and larva. The host associations and vector competence of Cx. lactator have not been extensively studied, and the public health implications, if any, of the addition of this species to Florida's mosquito fauna are unclear. These collections represent the first detections of Cx. lactator, or any Phenacomyia species, in the United States, adding to a trend in which detections of established populations of mosquito species from the American tropics in Florida appear to be increasing.},
}
@article {pmid36943092,
year = {2023},
author = {Zurita-Artaloitia, JM and Rivera, J and Vinuesa, P},
title = {Extensive Cryptic Diversity and Ecological Associations Uncovered among Mexican and Global Collections of Naegleria and Vermamoeba Species by 18S Ribosomal DNA, Internal Transcribed Spacer, and Cytochrome Oxidase Subunit I Sequence Analysis.},
journal = {Microbiology spectrum},
volume = {11},
number = {2},
pages = {e0379522},
pmid = {36943092},
issn = {2165-0497},
abstract = {Free-living amoebae (FLA) are phagocytic protists that play crucial roles in microbial communities as significant microbial grazers. However, our current knowledge of their diversity, ecology, and population genetic structures is marginal due to the shallow and biased sampling of ecosystems and the use of few, poorly resolving molecular markers. Thirty-two FLA were isolated from soil and water samples collected across representative ecosystems of the State of Morelos in Central Mexico, including the drinking water distribution system (DWDS) from the state capital. We classified our isolates as members of Acanthamoeba, Vermamoeba, Naegleria, and Tetramitus by 18S ribosomal DNA (rDNA) sequencing. Vermamoeba isolates were recovered exclusively from the DWDS samples. In contrast, Naegleria strains displayed a broad distribution in soil and water samples across the natural ecosystems. We used a combination of phylogenetic and population genetic analyses of internal transcribed spacer (ITS) and cytochrome oxidase subunit I (COI) sequences from our isolates and a comprehensive set of reference sequences to analyze the currently known diversity of Naegleria spp. Significant associations were uncovered between the most prevalent lineages of Naegleria and Vermamoeba and broad ecological and geographical variables at regional and global levels. The population structure and cryptic diversity within the Naegleria galeacystis-Naegleria americana and Vermamoeba vermiformis species complexes were thoroughly analyzed. Our results prove that the genus Vermamoeba, which was previously thought to consist of only one species, actually encompasses at least seven widely distributed species, as indicated by consistent evidence from Bayesian phylogenetics, two species-delimitation programs, and population genetics analyses. IMPORTANCE Our study sheds new light on the population genetic structure of V. vermiformis and diverse Naegleria species. Using improved molecular markers and advanced analytical approaches, we discovered that N. americana, previously considered a single species, actually contains multiple distinct lineages, as revealed by COI sequencing. These lineages are highly differentiated, with little gene flow between them. Our findings demonstrate that the genus Vermamoeba holds multiple cryptic species, requiring a significant taxonomic revision in light of multilocus sequence analyses. These results advance our understanding of the ecology, molecular systematics, and biogeography of these genera and species complexes at both regional and global scales. This study has significant implications for diagnosing amoebal infections and evaluating health risks associated with FLA in domestic and recreational waters.},
}
@article {pmid36941704,
year = {2023},
author = {Lubis, WMY and Adrian, M and Jadid, N and Widiastuti, A and Ezura, H and Mubarok, S and Hapsari, DP and Poerwanto, R and Matra, DD},
title = {Transcriptome dataset from Solanum lycopersicum L. cv. Micro-Tom; wild type and two mutants of INDOLE-ACETIC-ACID (SlIAA9) using long-reads sequencing oxford nanopore technologies.},
journal = {BMC research notes},
volume = {16},
number = {1},
pages = {40},
pmid = {36941704},
issn = {1756-0500},
support = {3332/IT3.L1/PT.01.03/P/B/2022//Kementerian Pendidikan, Kebudayaan, Riset, dan Teknologi/ ; 3332/IT3.L1/PT.01.03/P/B/2022//Kementerian Pendidikan, Kebudayaan, Riset, dan Teknologi/ ; 3332/IT3.L1/PT.01.03/P/B/2022//Kementerian Pendidikan, Kebudayaan, Riset, dan Teknologi/ ; 3332/IT3.L1/PT.01.03/P/B/2022//Kementerian Pendidikan, Kebudayaan, Riset, dan Teknologi/ ; },
mesh = {*Solanum lycopersicum/genetics ; Transcriptome ; *Nanopores ; DNA, Complementary/genetics ; Sequence Analysis, RNA ; },
abstract = {OBJECTIVE: Tomatoes are the most widely consumed fruit vegetable and are relatively easy to cultivate. However, an increase in temperature causes some plants to respond with a decrease in fruit production. So, it is necessary to develop plants resistant to extreme temperature changes. The tomato cv. Micro-Tom has genetic variations in the gene of INDOLE-ACETIC-ACID, namely SlIAA9-3 and SlIAA9-5. However, the genetic information regarding the full-length transcript of the gene from this type of tomato plant is unknown. Therefore, this study aimed to determine the full-length transcript of the genes of these three types of tomatoes using long-reads sequencing technology from Oxford Nanopore.<br><br>DATA DESCRIPTION: The total RNA from three types of Micro-Tom was isolated with the RNeasy PowerPlant Kit. Then, the RNA sequencing process used PCR-cDNA Barcoding kit - SQK-PCB109 and continued with the processing of raw reads based on the protocol from microbepore protocol (https://github.com/felixgrunberger/microbepore). The resulting raw reads were 578 374, 409 905, and 851 948 for wildtype, iaa9-3, and iaa9-5, respectively. After obtaining cleaned reads, each sample was mapped to the tomato reference genome (S. lycopersicum ITAG4.0) with the Minimap2 program. In particular, 965 genes were expressed only in the iaa9-3 mutant, and 2332 genes were expressed only in the iaa9-5&#xa0;mutant. Whereas in the wild type, 1536 genes are specifically expressed. In cluster analysis using the heatmap analysis, separate groups were obtained between the wild type and the two mutants. This proves an overall difference in transcript levels between the wild type and the mutants.},
}
@article {pmid36941299,
year = {2023},
author = {Hong, S and Park, B and Kim, G and Choi, EH and Hwang, UW},
title = {Possible species discrimination of a blotched nerite Nerita albicilla with their distribution pattern and demographic history in the Indo-Pacific.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {4545},
pmid = {36941299},
issn = {2045-2322},
mesh = {Phylogeny ; *DNA, Mitochondrial/genetics ; Population Density ; Republic of Korea ; *Genetic Variation ; },
abstract = {The blotched nerite Nerita albicilla (Linnaeus 1758) is distributed in intertidal areas of the Indo-Pacific. In South Korea, it has been found only in the southernmost region of Jeju Island so far. Owing to its limited distribution, it can be a promising intertidal species helpful for monitoring global climate change effects in the Korean Peninsula. We performed population genetic analyses based on 393 COI haplotypes from 697 N. albicilla, including 167 from this study and 530 from public databases. The results showed that there are two distinct genetic lineages in N. albicilla: PAIO (Palearctic, Australasia, Indo-Malay, and Oceania) and Afrotropic lineages. DNA barcoding gap analyses indicated that the two lineages could be differentiated into two different species: N. albicilla (PAIO) and N. originalis sp. nov. (Afrotropic) (3.96%). Additionally, it was revealed that their divergence time was ca. 5.96 Ma and dramatic diversification of COI haplotypes occurred during the late Pliocene and Pleistocene. The results of MDA, BSP, and neutrality test implied recent population size expansion, which was estimated to be ca. 250 Ka. Finally, we discussed whether the observation of N. originalis sp. nov. in South Korea is due to the northward migration through ocean currents caused by global warming or due to artificial activity through marine transportation.},
}
@article {pmid36938043,
year = {2023},
author = {Wan, T and Qiao, BX and Zhou, J and Shao, KS and Pan, LY and An, F and He, XS and Liu, T and Li, PK and Cai, YL},
title = {Evolutionary and phylogenetic analyses of 11 Cerasus species based on the complete chloroplast genome.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1070600},
pmid = {36938043},
issn = {1664-462X},
abstract = {The subgenus Cerasus, one of the most important groups in the genus Prunus sensu lato, comprises over 100 species; however, the taxonomic classification and phylogenetic relationships of Cerasus remain controversial. Therefore, it is necessary to reconstruct the phylogenetic tree for known Cerasus species. Here, we report the chloroplast (cp) genome sequences of 11 Cerasus species to provide insight into evolution of the plastome. The cp genomes of the 11 Cerasus species (157,571-158,830 bp) displayed a typical quadripartite circular structure. The plastomes contain 115 unique genes, including 80 protein-coding genes, four ribosomal RNAs, and 31 transfer RNAs. Twenty genes were found to be duplicated in inverted repeats as well as at the boundary. The conserved non-coding sequences showed significant divergence compared with the coding regions. We found 12 genes and 14 intergenic regions with higher nucleotide diversity and more polymorphic sites, including matK, rps16, rbcL, rps16-trnQ, petN-psbM, and trnL-trnF. During cp plastome evolution, the codon profile has been strongly biased toward the use of A/T at the third base, and leucine and isoleucine codons appear the most frequently. We identified strong purifying selection on the rpoA, cemA, atpA, and petB genes; whereas ccsA, rps19, matK, rpoC2, ycf2 and ndhI showed a signature of possible positive selection during the course of Cerasus evolution. In addition, we further analyzed the phylogenetic relationships of these species with 57 other congenic related species.Through reconstructing the Cerasus phylogeny tree, we found that true cherry is similar to the flora of China forming a distinct group, from which P. mahaleb was separated as an independent subclade. Microcerasus was genetically closer to Amygdalus, Armeniaca, and Prunus (sensu stricto) than to members of true cherry, whereas P. japonica and P. tomentosa were most closely related to P. triloba and P. pedunculata. However, P. tianshanica formed a clade with P. cerasus, P. fruticosa, P. cerasus × P. canescens 'Gisela 6', and P. avium as a true cherry group. These results provide new insights into the plastome evolution of Cerasus, along with potential molecular markers and candidate DNA barcodes for further phylogenetic and phylogeographic analyses of Cerasus species.},
}
@article {pmid36937068,
year = {2023},
author = {Scherz, MD and Schmidt, R and Brown, JL and Glos, J and Lattenkamp, EZ and Rakotomalala, Z and Rakotoarison, A and Rakotonindrina, RT and Randriamalala, O and Raselimanana, AP and Rasolonjatovo, SM and Ratsoavina, FM and Razafindraibe, JH and Glaw, F and Vences, M},
title = {Repeated divergence of amphibians and reptiles across an elevational gradient in northern Madagascar.},
journal = {Ecology and evolution},
volume = {13},
number = {3},
pages = {e9914},
pmid = {36937068},
issn = {2045-7758},
abstract = {How environmental factors shape patterns of biotic diversity in tropical ecosystems is an active field of research, but studies examining the possibility of ecological speciation in terrestrial tropical ecosystems are scarce. We use the isolated rainforest herpetofauna on the Montagne d'Ambre (Amber Mountain) massif in northern Madagascar as a model to explore elevational divergence at the level of populations and communities. Based on intensive sampling and DNA barcoding of amphibians and reptiles along a transect ranging from ca. 470-1470 m above sea level (a.s.l.), we assessed a main peak in species richness at an elevation of ca. 1000 m a.s.l. with 41 species. The proportion of local endemics was highest (about 1/3) at elevations >1100 m a.s.l. Two species of chameleons (Brookesia tuberculata, Calumma linotum) and two species of frogs (Mantidactylus bellyi, M. ambony) studied in depth by newly developed microsatellite markers showed genetic divergence up the slope of the mountain, some quite strong, others very weak, but in each case with genetic breaks between 1100 and 1270 m a.s.l. Genetic clusters were found in transect sections significantly differing in bioclimate and herpetological community composition. A decrease in body size was detected in several species with increasing elevation. The studied rainforest amphibians and reptiles show concordant population genetic differentiation across elevation along with morphological and niche differentiation. Whether this parapatric or microallopatric differentiation will suffice for the completion of speciation is, however, unclear, and available phylogeographic evidence rather suggests that a complex interplay between ecological and allopatric divergence processes is involved in generating the extraordinary species diversity of Madagascar's biota. Our study reveals concordant patterns of diversification among main elevational bands, but suggests that these adaptational processes are only part of the complex of processes leading to species formation, among which geographical isolation is probably also important.},
}
@article {pmid36937067,
year = {2023},
author = {Couëdel, M and Dettai, A and Guillaume, MMM and Bruggemann, F and Bureau, S and Frattini, B and Verde Ferreira, A and Azie, JL and Bruggemann, JH},
title = {New insights into the diversity of cryptobenthic Cirripectes blennies in the Mascarene Archipelago sampled using Autonomous Reef Monitoring Structures (ARMS).},
journal = {Ecology and evolution},
volume = {13},
number = {3},
pages = {e9850},
pmid = {36937067},
issn = {2045-7758},
abstract = {Autonomous Reef Monitoring Structures (ARMS) are artificial mini-reefs designed for standardized sampling of sessile and small motile cryptobenthic organisms. ARMS are also effective for collecting small cryptobenthic fishes, such as the combtooth blennies of the genus Cirripectes. Recent studies discovered several Cirripectes species endemic to islands or archipelagos, in spite of the generally broad distributions of tropical and subtropical blennies. Thus, to evaluate the diversity and distribution of Cirripectes species in the Mascarene Archipelago, a little-studied region but an important biodiversity hotspot, complete mitochondrial genomes, and nuclear rhodopsin genes were sequenced for 39 specimens collected with ARMS deployed on outer reef slopes at Reunion and Rodrigues islands. Mitochondrial COI sequences were analyzed to integrate these specimens within the largest dataset of publicly available sequences. Three species were found in the Mascarene Archipelago, Cirripectes castaneus, Cirripectes randalli, and Cirripectes stigmaticus. C. castaneus and C. stigmaticus both have an Indo-Pacific distribution with several haplotypes shared among distant localities. In agreement with the literature, C. randalli shows a small-range endemism restricted to the Mascarenes. We confirmed the presence of C. castaneus, C. randalli, and C. stigmaticus in Rodrigues, and the presence of C. stigmaticus in Reunion. This study contributes to filling the gaps in taxonomic and molecular knowledge of the reef cryptobiome in the South-West Indian Ocean, and provides the first complete mitogenomes for the genus, a crucial step for future molecular-based inventories (e.g., eDNA).},
}
@article {pmid36937058,
year = {2023},
author = {Rakotonirina, TJ and Viljoen, E and Rakotonirina, AH and Leong Pock Tsy, JM and Radanielina, T},
title = {A DNA barcode reference library for CITES listed Malagasy Dalbergia species.},
journal = {Ecology and evolution},
volume = {13},
number = {3},
pages = {e9887},
pmid = {36937058},
issn = {2045-7758},
abstract = {On Madagascar, the illegal and unsustainable exploitation and illegal international trade of Dalbergia (rosewood) precious woods remain a serious conservation problem. Members of this genus are at high risk of extinction as a consequence of logging, mining, and slash and burn agriculture. Morphological identification of these Malagasy species is difficult in the absence of flowers and fruits, especially in the case of cut trees, sawn wood, and finished product. In this study, we use molecular barcoding to identify the Dalbergia species with the intent to contribute to the control of their illegal trade. Thirty-six Dalbergia samples representing 12 Malagasy species of which 11 have high commercial value, were collected to test the efficacy of a region of the plastid genome (rbcL) and a nuclear-transcribed ITS for barcoding. These widely used markers, as well as DNA barcoding gaps, "best match" and "best close match" approaches, and the neighbor-joining method were employed. All samples were amplified and sequenced using the two markers. Using a single locus, the "best match" and "best close match" approaches revealed that ITS has high discriminatory power within the tested Malagasy species. The combination of rbcL + ITS revealed 100% species discrimination. This study confirms that ITS alone and in combination with chloroplast barcode rbcL allow non-ambiguous identification for the 12 species studied. The results contribute to the development of DNA barcoding as a useful tool to identify Malagasy Dalbergia and suggest that the approach developed should be expanded to all 56 potentially exploited species in reference to international CITES requirements and the sustainable management of valuable resources.},
}
@article {pmid36935909,
year = {2023},
author = {Breitbart, M and Kerr, M and Schram, MJ and Williams, I and Koziol, G and Peebles, E and Stallings, CD},
title = {Evaluation of DNA metabarcoding for identifying fish eggs: a case study on the West Florida Shelf.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15016},
pmid = {36935909},
issn = {2167-8359},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Florida ; *Fishes/genetics ; Ecosystem ; DNA, Mitochondrial/genetics ; },
abstract = {A critical factor in fisheries management is the protection of spawning sites for ecologically and economically important fish species. DNA barcoding (i.e., amplification and sequencing of the mitochondrial cytochrome c oxidase I (COI) gene) of fish eggs has emerged as a powerful technique for identifying spawning sites. However, DNA barcoding of individual fish eggs is time-consuming and expensive. In an attempt to reduce costs and effort for long-term fisheries monitoring programs, here we used DNA metabarcoding, in which DNA is extracted and amplified from a composited sample containing all the fish eggs collected at a given site, to identify fish eggs from 49 stations on the West Florida Shelf. A total of 37 taxa were recovered from 4,719 fish eggs. Egg distributions on the West Florida Shelf corresponded with the known habitat types occupied by these taxa, which included burrower, coastal pelagic, epipelagic, mesopelagic, demersal, deep demersal, commensal, and reef-associated taxa. Metabarcoding of fish eggs was faster and far less expensive than barcoding individual eggs; however, this method cannot provide absolute taxon proportions due to variable copy numbers of mitochondrial DNA in different taxa, different numbers of cells within eggs depending on developmental stage, and PCR amplification biases. In addition, some samples yielded sequences from more taxa than the number of eggs present, demonstrating the presence of contaminating DNA and requiring the application of a threshold proportion of sequences required for counting a taxon as present. Finally, we review the advantages and disadvantages of using metabarcoding vs. individual fish egg barcoding for long-term monitoring programs.},
}
@article {pmid36934108,
year = {2023},
author = {Wirth, J and Huber, N and Yin, K and Brood, S and Chang, S and Martinez-Jimenez, CP and Meier, M},
title = {Spatial transcriptomics using multiplexed deterministic barcoding in tissue.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {1523},
pmid = {36934108},
issn = {2041-1723},
mesh = {Animals ; Mice ; *Transcriptome/genetics ; *Gene Expression Profiling/methods ; RNA, Messenger ; },
abstract = {Spatially resolved transcriptomics of tissue sections enables advances in fundamental and applied biomedical research. Here, we present Multiplexed Deterministic Barcoding in Tissue (xDBiT) to acquire spatially resolved transcriptomes of nine tissue sections in parallel. New microfluidic chips were developed to spatially encode mRNAs over a total tissue area of 1.17 cm[2] with a 50 µm resolution. Optimization of the biochemical protocol increased read and gene counts per spot by one order of magnitude compared to previous reports. Furthermore, the introduction of alignment markers allowed seamless registration of images and spatial transcriptomic spots. Together with technological advances, we provide an open-source computational pipeline to prepare raw sequencing data for downstream analysis. The functionality of xDBiT was demonstrated by acquiring 16 spatially resolved transcriptomic datasets from five different murine organs, including the cerebellum, liver, kidney, spleen, and heart. Factor analysis and deconvolution of spatial transcriptomes allowed for in-depth characterization of the murine kidney.},
}
@article {pmid36933556,
year = {2023},
author = {You, Z and Wang, L and He, H and Wu, Z and Zhang, X and Xue, S and Xu, P and Hong, Y and Xiong, M and Wei, W and Chen, Y},
title = {Mapping of clonal lineages across developmental stages in human neural differentiation.},
journal = {Cell stem cell},
volume = {30},
number = {4},
pages = {473-487.e9},
doi = {10.1016/j.stem.2023.02.007},
pmid = {36933556},
issn = {1875-9777},
mesh = {Humans ; Cell Differentiation/physiology ; *Mesencephalon/metabolism ; *Stem Cells ; Neurons/physiology ; Cell Lineage ; },
abstract = {The cell lineages across developmental stages remain to be elucidated. Here, we developed single-cell split barcoding (SISBAR) that allows clonal tracking of single-cell transcriptomes across stages in an in vitro model of human ventral midbrain-hindbrain differentiation. We developed "potential-spective" and "origin-spective" analyses to investigate the cross-stage lineage relationships and mapped a multi-level clonal lineage landscape depicting the whole differentiation process. We uncovered many previously uncharacterized converging and diverging trajectories. Furthermore, we demonstrate that a transcriptome-defined cell type can arise from distinct lineages that leave molecular imprints on their progenies, and the multilineage fates of a progenitor cell-type represent the collective results of distinct rather than similar clonal fates of individual progenitors, each with distinct molecular signatures. Specifically, we uncovered a ventral midbrain progenitor cluster as the common clonal origin of midbrain dopaminergic (mDA) neurons, midbrain glutamatergic neurons, and vascular and leptomeningeal cells and identified a surface marker that can improve graft outcomes.},
}
@article {pmid36932341,
year = {2023},
author = {Kasmi, Y and Eschbach, E and Hanel, R},
title = {Mare-MAGE curated reference database of fish mitochondrial genes.},
journal = {BMC genomic data},
volume = {24},
number = {1},
pages = {18},
pmid = {36932341},
issn = {2730-6844},
mesh = {Animals ; Databases, Nucleic Acid ; DNA Barcoding, Taxonomic ; *Fishes/genetics ; *Genes, Mitochondrial ; },
abstract = {Biodiversity assessment approaches based on molecular biology techniques such as metabarcoding, RAD-seq, or SnaPshot sequencing are increasingly applied in assessing marine and aquatic ecosystems. Here we present a new reference database for fish meta-barcoding based on mitochondrial genes. The Mare-MAGE database contains quality-checked sequences of the mitochondrial 12S ribosomal RNA and Cytochrome c Oxidase I gene. All sequences were obtained from the National Center for Biotechnology Information- GenBank (NBCI-GenBank), the European Nucleotide Archive (ENA), AquaGene Database and BOLD database, and have undergone intensive processing. They were checked for false annotations and non-target anomalies, according to the Integrated Taxonomic Information System (ITIS) and FishBase. The dataset is compiled in ARB-Home, FASTA and Qiime2 formats, and is publicly available from the Mare-MAGE database website (http://mare-mage.weebly.com/). It includes altogether 231,333 COI and 12S rRNA gene sequences of fish, covering 19,506 species of 4,058 genera and 586 families.},
}
@article {pmid36932065,
year = {2023},
author = {Karlikow, M and Amalfitano, E and Yang, X and Doucet, J and Chapman, A and Mousavi, PS and Homme, P and Sutyrina, P and Chan, W and Lemak, S and Yakunin, AF and Dolezal, AG and Kelley, S and Foster, LJ and Harpur, BA and Pardee, K},
title = {CRISPR-induced DNA reorganization for multiplexed nucleic acid detection.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {1505},
pmid = {36932065},
issn = {2041-1723},
mesh = {Animals ; DNA/genetics ; *Nucleic Acids ; Agriculture ; Head ; RNA/genetics ; CRISPR-Cas Systems/genetics ; Nucleic Acid Amplification Techniques ; *Biosensing Techniques ; },
abstract = {Nucleic acid sensing powered by the sequence recognition of CRIPSR technologies has enabled major advancement toward rapid, accurate and deployable diagnostics. While exciting, there are still many challenges facing their practical implementation, such as the widespread need for a PAM sequence in the targeted nucleic acid, labile RNA inputs, and limited multiplexing. Here we report FACT (Functionalized Amplification CRISPR Tracing), a CRISPR-based nucleic acid barcoding technology compatible with Cas12a and Cas13a, enabling diagnostic outputs based on cis- and trans-cleavage from any sequence. Furthermore, we link the activation of CRISPR-Cas12a to the expression of proteins through a Reprogrammable PAIRing system (RePAIR). We then combine FACT and RePAIR to create FACTOR (FACT on RePAIR), a CRISPR-based diagnostic, that we use to detect infectious disease in an agricultural use case: honey bee viral infection. With high specificity and accuracy, we demonstrate the potential of FACTOR to be applied to the sensing of any nucleic acid of interest.},
}
@article {pmid36930749,
year = {2023},
author = {de Araújo, L and Ramos, LI and Vieira, MMR and Oliveira, AV and Portela-Castro, ALB and Borin-Carvalho, LA and Fernandes, CA},
title = {Cytogenetic and Molecular Characterization of Eigenmannia aff. desantanai (Gymnotiformes: Sternopygidae): A First Report of System of Sex Chromosomes ZW1W2/ZZ in Gymnotiformes.},
journal = {Zebrafish},
volume = {20},
number = {2},
pages = {77-85},
doi = {10.1089/zeb.2022.0059},
pmid = {36930749},
issn = {1557-8542},
mesh = {Female ; Male ; Animals ; *Gymnotiformes/genetics ; Zebrafish/genetics ; Sex Chromosomes ; Cytogenetics ; Cytogenetic Analysis ; },
abstract = {Gymnotiformes a monophyletic group of fish endemic to the Neotropics, represent an important component of the freshwater ichthyofauna that presents relevant taxonomic problems. Thus, in view of the morphological complexity involving Eigenmannia (Gymnotiformes) fish species, this study aimed to characterize Eigenmannia aff. desantanai of the upper Paraguay River basin through cytogenetic and molecular analyses, to help in the correct identification and delimitation of species. This study reports a multiple sex system of the type ZW1W2/ZZ, with 2n = 31 for females and 2n = 30 for males. A single pair of chromosomes carrying the nucleolar organizing regions (NORs) was detected. The heterochromatin was colocated in NOR sites and mainly located in the centromeric regions of chromosomes. Besides that, individual sequences COI from the specimens of E. aff. desantanai were obtained, totalizing three haplotypes. The distance p between the haplotypes in E. aff. desantanai, ranged from 0.2% to 7.1%. Species delimitation tests indicated the existence of two possible operational taxonomic units of E. aff. desantanai. Thus, this study reports a new multiple sex system in Gymnotiformes and these specimens previously identified as E. aff. desantanai may belong to two distinct species.},
}
@article {pmid36929134,
year = {2023},
author = {Kobayashi, M and Yoshimoto, M},
title = {Multiple waves of fetal-derived immune cells constitute adult immune system.},
journal = {Immunological reviews},
volume = {315},
number = {1},
pages = {11-30},
pmid = {36929134},
issn = {1600-065X},
support = {R01 AI121197/AI/NIAID NIH HHS/United States ; },
mesh = {*Immune System/cytology/growth &amp; development ; Humans ; Animals ; Hematopoiesis ; Embryo, Mammalian/cytology ; Hematopoietic Stem Cells/cytology ; Lymphocytes/cytology ; Cell Lineage ; },
abstract = {It has been over three decades since Drs. Herzenberg and Herzenberg proposed the layered immune system hypothesis, suggesting that different types of stem cells with distinct hematopoietic potential produce specific immune cells. This layering of immune system development is now supported by recent studies showing the presence of fetal-derived immune cells that function in adults. It has been shown that various immune cells arise at different embryonic ages via multiple waves of hematopoiesis from special endothelial cells (ECs), referred to as hemogenic ECs. However, it remains unknown whether these fetal-derived immune cells are produced by hematopoietic stem cells (HSCs) during the fetal to neonatal period. To address this question, many advanced tools have been used, including lineage-tracing mouse models, cellular barcoding techniques, clonal assays, and transplantation assays at the single-cell level. In this review, we will review the history of the search for the origins of HSCs, B-1a progenitors, and mast cells in the mouse embryo. HSCs can produce both B-1a and mast cells within a very limited time window, and this ability declines after embryonic day (E) 14.5. Furthermore, the latest data have revealed that HSC-independent adaptive immune cells exist in adult mice, which implies more complicated developmental pathways of immune cells. We propose revised road maps of immune cell development.},
}
@article {pmid36928612,
year = {2023},
author = {Zanovello, L and Girardi, M and Marchesini, A and Galla, G and Casari, S and Micheletti, D and Endrizzi, S and Fedrigotti, C and Pedrini, P and Bertorelle, G and Hauffe, HC},
title = {A validated protocol for eDNA-based monitoring of within-species genetic diversity in a pond-breeding amphibian.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {4346},
pmid = {36928612},
issn = {2045-2322},
mesh = {Animals ; *DNA, Environmental ; Ponds ; Biodiversity ; Anura ; DNA, Mitochondrial/genetics ; Genetic Variation ; Environmental Monitoring/methods ; DNA Barcoding, Taxonomic/methods ; },
abstract = {In light of the dramatic decline in amphibian biodiversity, new cost-efficient tools to rapidly monitor species abundance and population genetic diversity in space and time are urgently needed. It has been amply demonstrated that the use of environmental DNA (eDNA) for single-species detection and characterization of community composition can increase the precision of amphibian monitoring compared to traditional (observational) approaches. However, it has been suggested that the efficiency and accuracy of the eDNA approach could be further improved by more timely sampling; in addition, the quality of genetic diversity data derived from the same DNA has been confirmed in other vertebrate taxa, but not amphibians. Given the availability of previous tissue-based genetic data, here we use the common frog Rana temporaria Linnaeus, 1758 as our target species and an improved eDNA protocol to: (i) investigate differences in species detection between three developmental stages in various freshwater environments; and (ii) study the diversity of mitochondrial DNA (mtDNA) haplotypes detected in eDNA (water) samples, by amplifying a specific fragment of the COI gene (331 base pairs, bp) commonly used as a barcode. Our protocol proved to be a reliable tool for monitoring population genetic diversity of this species, and could be a valuable addition to amphibian conservation and wetland management.},
}
@article {pmid36924341,
year = {2023},
author = {Wu, YH and Hou, SB and Yuan, ZY and Jiang, K and Huang, RY and Wang, K and Liu, Q and Yu, ZB and Zhao, HP and Zhang, BL and Chen, JM and Wang, LJ and Stuart, BL and Chambers, EA and Wang, YF and Gao, W and Zou, DH and Yan, F and Zhao, GG and Fu, ZX and Wang, SN and Jiang, M and Zhang, L and Ren, JL and Wu, YY and Zhang, LY and Yang, DC and Jin, JQ and Yin, TT and Li, JT and Zhao, WG and Murphy, RW and Huang, S and Guo, P and Zhang, YP and Che, J},
title = {DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs.},
journal = {Molecular ecology resources},
volume = {23},
number = {5},
pages = {1124-1141},
doi = {10.1111/1755-0998.13784},
pmid = {36924341},
issn = {1755-0998},
support = {//China's Biodiversity Observation Network (Sino-BON)/ ; 752017//Doctoral Research Starting Foundation of Anhui Normal University/ ; 202103AC100003//Key R &amp; D program/ ; 202102AA310055//Major Science and Technique Program/ ; SQ2022YFC2600301//Ministry of Science and Technology of China/ ; NSFC31071891//National Natural Science Foundation of China/ ; 31471968//National Natural Science Foundation of China/ ; NSFC31372152//National Natural Science Foundation of China/ ; //Open Project of State Key Laboratory of Genetic Resources and Evolution/ ; 2022GF258D-10//Program of Yunnan Forestry and Grassland Administration/ ; 202001AW070016//Programs from the Science and Technology Bureau of Yunnan/ ; 202005AC160046//Programs from the Science and Technology Bureau of Yunnan/ ; 2020YFSY0033//Sciences and Technology Department of Sichuan Province/ ; 2019QZKK0501-0104//Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0501-0105//Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0501-0107//Second Tibetan Plateau Scientific Expedition and Research Program/ ; //Spring City Plan: the High-level Talent Promotion and Training Project of Kunming/ ; XDA20050201//Strategic Priority Research Program A of the Chinese Academy of Sciences/ ; XDA19050303//Strategic Priority Research Program A of the Chinese Academy of Sciences/ ; ZL202203601//Survey of Wildlife Resources in Key Areas of Tibet/ ; 202002AA100007//the Digitalization, Development and Application of Biotic Resource/ ; 2021FY100203//the Ministry of Science and Technology of China/ ; 2019-2021QNRC001//Young talent project of China Association for Science and Technology/ ; },
mesh = {Humans ; Animals ; Phylogeny ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Snakes/genetics ; Electron Transport Complex IV/genetics ; },
abstract = {DNA barcoding has greatly facilitated studies of taxonomy, biodiversity, biological conservation, and ecology. Here, we establish a reliable DNA barcoding library for Chinese snakes, unveiling hidden diversity with implications for taxonomy, and provide a standardized tool for conservation management. Our comprehensive study includes 1638 cytochrome c oxidase subunit I (COI) sequences from Chinese snakes that correspond to 17 families, 65 genera, 228 named species (80.6% of named species) and 36 candidate species. A barcode gap analysis reveals gaps, where all nearest neighbour distances exceed maximum intraspecific distances, in 217 named species and all candidate species. Three species-delimitation methods (ABGD, sGMYC, and sPTP) recover 320 operational taxonomic units (OTUs), of which 192 OTUs correspond to named and candidate species. Twenty-eight other named species share OTUs, such as Azemiops feae and A. kharini, Gloydius halys, G. shedaoensis, and G. intermedius, and Bungarus multicinctus and B. candidus, representing inconsistencies most probably caused by imperfect taxonomy, recent and rapid speciation, weak taxonomic signal, introgressive hybridization, and/or inadequate phylogenetic signal. In contrast, 43 species and candidate species assign to two or more OTUs due to having large intraspecific distances. If most OTUs detected in this study reflect valid species, including the 36 candidate species, then 30% more species would exist than are currently recognized. Several OTU divergences associate with known biogeographic barriers, such as the Taiwan Strait. In addition to facilitating future studies, this reliable and relatively comprehensive reference database will play an important role in the future monitoring, conservation, and management of Chinese snakes.},
}
@article {pmid36921697,
year = {2023},
author = {Wong, D and Norman, H and Creedy, TJ and Jordaens, K and Moran, KM and Young, A and Mengual, X and Skevington, JH and Vogler, AP},
title = {The phylogeny and evolutionary ecology of hoverflies (Diptera: Syrphidae) inferred from mitochondrial genomes.},
journal = {Molecular phylogenetics and evolution},
volume = {184},
number = {},
pages = {107759},
doi = {10.1016/j.ympev.2023.107759},
pmid = {36921697},
issn = {1095-9513},
mesh = {Animals ; Phylogeny ; *Genome, Mitochondrial ; *Diptera/genetics ; Bayes Theorem ; Larva ; },
abstract = {Hoverflies (Diptera: Syrphidae) are a diverse group of pollinators and a major research focus in ecology, but their phylogenetic relationships remain incompletely known. Using a genome skimming approach we generated mitochondrial genomes for 91 species, capturing a wide taxonomic diversity of the family. To reduce the required amount of input DNA and overall cost of the library construction, sequencing and assembly was conducted on mixtures of specimens, which raises the problem of chimera formation of mitogenomes. We present a novel chimera detection test based on gene tree incongruence, but identified only a single mitogenome of chimeric origin. Together with existing data for a final set of 127 taxa, phylogenetic analysis on nucleotide and amino acid sequences using Maximum Likelihood and Bayesian Inference revealed a basal split of Microdontinae from all other syrphids. The remainder consists of several deep clades assigned to the subfamily Eristalinae in the current classification, including a clade comprising the subfamily Syrphinae (plus Pipizinae). These findings call for a re-definition of subfamilies, but basal nodes had insufficient support to fully justify such action. Molecular-clock dating placed the origin of the Syrphidae crown group in the mid-Cretaceous while the Eristalinae-Syrphinae clade likely originated near the K/Pg boundary. Transformation of larval life history characters on the tree suggests that Syrphidae initially had sap feeding larvae, which diversified greatly in diet and habitat association during the Eocene and Oligocene, coinciding with the diversification of angiosperms and the evolution of various insect groups used as larval host, prey, or mimicry models. Mitogenomes proved to be a powerful phylogenetic marker for studies of Syrphidae at subfamily and tribe levels, allowing dense taxon sampling that provided insight into the great ecological diversity and rapid evolution of larval life history traits of the hoverflies.},
}
@article {pmid36921012,
year = {2023},
author = {Deng, W and Marmelat, V and Vanderbilt, DL and Gennaro, F and Smith, BA},
title = {Barcoding, linear and nonlinear analysis of full-day leg movements in infants with typical development and infants at risk of developmental disabilities: Cross-sectional study.},
journal = {Infancy : the official journal of the International Society on Infant Studies},
volume = {28},
number = {3},
pages = {650-666},
pmid = {36921012},
issn = {1532-7078},
support = {K12 HD055929/HD/NICHD NIH HHS/United States ; },
mesh = {Child ; Humans ; Infant ; Cross-Sectional Studies ; *Leg ; *Developmental Disabilities/diagnosis ; Movement ; Acceleration ; },
abstract = {Traditional methods do not capture the multidimensional domains and dynamic nature of infant behavioral patterns. We aim to compare full-day, in-home leg movement data between infants with typical development (TD) and infants at risk of developmental disabilities (AR) using barcoding and nonlinear analysis. Eleven infants with TD (2-10 months) and nine infants AR (adjusted age: 2-14 months) wore a sensor on each ankle for 7 days. We calculated the standard deviation for linear variability and sample entropy (SampEn) of leg acceleration and angular velocity for nonlinear variability. Movements were also categorized into 16 barcoding states, and we calculated the SampEn and proportions of the barcoding. All variables were compared between the two groups using independent-samples t-test or Mann-Whitney U test. The AR group had larger linear variability compared to the TD group. SampEn was lower in the AR group compared to TD group for both acceleration and angular velocity. Two barcoding states' proportions were significantly different between the two groups. The results showed that nonlinear analysis and barcoding could be used to identify the difference of dynamic multidimensional movement patterns between infants AR and infants with TD. This information may help early diagnosis of developmental disabilities in the future.},
}
@article {pmid36915859,
year = {2023},
author = {Suganthi, M and Abirami, G and Jayanthi, M and Kumar, KA and Karuppanan, K and Palanisamy, S},
title = {A method for DNA extraction and molecular identification of Aphids.},
journal = {MethodsX},
volume = {10},
number = {},
pages = {102100},
pmid = {36915859},
issn = {2215-0161},
abstract = {Aphid species (Insecta, Hemiptera) are economically important invasive pest throughout the world, though their identification is intricate due to tiny size and inconspicuous nature of morphology. Mitochondrial cytochrome c oxidase I (mtCOI) region has been proven to be a standard barcode to identify the diverse array of insect groups. Isolation of good quality DNA is a fundamental first step in insect DNA barcoding which is obtained by standardizing the DNA isolation method. In this study, we demonstrate a modified CTAB method for the isolation of DNA to maximize the quality and yield from small aphids. This method will help the researchers to efficiently isolate DNA from small aphid and the method can be utilized for other small insects as well. We evaluated the quality of the isolated DNA and the mtCOI gene region were subjected to PCR amplification. Further, the gene segment was sequenced and gene annotation was done by NCBI BLAST program through which the insect was found to be Aphis gossypii. This study provides a set of molecular tools that can be used for identification of insect at species level through DNA barcoding and biodiversity analysis.•Detailed method to maximize quality and quantity of genomic DNA isolated from aphids.•Molecular identification of aphids using mtCOI gene amplification and sequence validation.•First report on Aphis gossypii infecting Solanum trilobatum provides insights of pest identification and management.},
}
@article {pmid36915659,
year = {2023},
author = {Rodríguez Flores, PC and Schnabel, KE},
title = {New records and species of deep-sea squat lobsters (Galatheoidea, Munidopsidae) from the Hawaiian Archipelago: an integrative approach using micro-CT and barcodes.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e14956},
pmid = {36915659},
issn = {2167-8359},
mesh = {Animals ; Hawaii ; Phylogeny ; X-Ray Microtomography ; *Anomura/anatomy &amp; histology ; Pacific Ocean ; },
abstract = {The Hawaiian Archipelago remains extensively under-sampled for many marine invertebrate taxa, including squat lobsters. During the last few years, several deep-sea expeditions carried out in the Pacific Ocean have conducted opportunistic collections of specimens and image data from the vicinity of Hawai'i. Here we describe a new species: Munidopsis hawaii sp. nov. and provide new records for Munidopsidae in the Archipelago and its associations. We illustrate and describe the new species using an integrative approach including micro-CT 3D imaging. Phylogenetic analyses of the species collected from seamounts from Hawai'i indicate that the new species represents a divergent lineage compared to morphologically similar species such as M. dispar and M. papanui. We also study the genetic distances for the species recorded in Hawai'i and other populations of the same species in the adjacent West Pacific. Three species are now known in the Hawaiian region. We also compiled identifications from images captured with ROVs in the area. These observations suggest that munidopsid species are common in the deep sea of Hawaiian waters below 1,000 m.},
}
@article {pmid36915514,
year = {2023},
author = {Intharuksa, A and Denduangboripant, J and Chansakaow, S and Thongkhao, K and Sukrong, S},
title = {HPLC and DNA barcoding profiles for identification of the selected twelve Mucuna species and its application for detecting prohibited aphrodisiac Mucuna products.},
journal = {Heliyon},
volume = {9},
number = {3},
pages = {e14130},
pmid = {36915514},
issn = {2405-8440},
abstract = {Aphrodisiac herbal products originated from various plants including Mucuna species. In Thai folklore, Mucuna macrocarpa Wall. and M. pruriens (L.) DC. have long been consumed and utilized for their aphrodisiac properties. Consumption of these plants can lead to serious adverse effects caused by l-dopa. The plants have been legally banned for use as foods, dietary supplements, or nutraceuticals by the FDA of several countries. To protect consumers, methods for the identification of illicit plants or herbal products are needed. This study aimed to identify the selected twelve Mucuna species and examine the aphrodisiac herbal products containing M. macrocarpa and M. pruriens by using HPLC analysis of l-dopa coupled with DNA barcoding profiles of ITS, matK, rbcL, and trnH-psbA. The results showed that l-dopa could be found not only in the seeds of M. macrocarpa and M. pruriens but also in associated allied Mucuna species. Then, a DNA barcode was introduced to support in HPLC profiling to identify the plants. DNA barcodes of twelve Mucuna species found in Thailand were established and used to reconstruct a phylogenetic tree. In this study, ITS2 sequences showed the highest interspecific variability and could be used to differentiate all Mucuna species. The results of ITS2 sequence coupled with HPLC analysis revealed that all the purchased aphrodisiac products originated from M. pruriens only. Therefore, the integration of HPLC analysis and DNA barcoding profile was an efficient method for the identification of prohibited Mucuna species for safety monitoring of herbal supplements and protecting customer safety. Regulatory agencies should raise awareness and restrain the use of these commercial products.},
}
@article {pmid36914325,
year = {2023},
author = {Liu, T and Tian, Y and Cao, Y and Wang, Z and Zha, G and Liu, W and Wei, L and Xiao, H and Zhang, Q and Cao, C},
title = {Isoelectric point barcode and similarity analysis with the earth mover's distance for identification of species origin of raw meat.},
journal = {Food research international (Ottawa, Ont.)},
volume = {166},
number = {},
pages = {112600},
doi = {10.1016/j.foodres.2023.112600},
pmid = {36914325},
issn = {1873-7145},
mesh = {*Algorithms ; Isoelectric Point ; *Hemoglobins ; Meat/analysis ; },
abstract = {In this work, by combining the microcolumn isoelectric focusing (mIEF) and similarity analysis with the earth mover's distance (EMD) metric, we proposed the concept of isoelectric point (pI) barcode for the identification of species origin of raw meat. At first, we used the mIEF to analyze 14 meat species, including 8 species of livestock and 6 species of poultry, to generate 140 electropherograms of myoglobin/hemoglobin (Mb/Hb) markers. Secondly, we binarized the electropherograms and converted them into the pI barcodes that only showed the major Mb/Hb bands for the EMD analysis. Thirdly, we efficiently developed the barcode database of 14 meat species and successfully used the EMD method to identify 9 meat products thanks to the high throughput of mIEF and the simplified format of the barcode for similarity analysis. The developed method had the merits of facility, rapidity and low cost. The developed concept and method had evident potential to the facile identification of meat species.},
}
@article {pmid36913648,
year = {2023},
author = {Laforest, LC and Kuntz, MA and Kanumuri, SRR and Mukhopadhyay, S and Sharma, A and O'Connor, SE and McCurdy, CR and Nadakuduti, SS},
title = {Metabolite and Molecular Characterization of Mitragyna speciosa Identifies Developmental and Genotypic Effects on Monoterpene Indole and Oxindole Alkaloid Composition.},
journal = {Journal of natural products},
volume = {86},
number = {4},
pages = {1042-1052},
doi = {10.1021/acs.jnatprod.3c00092},
pmid = {36913648},
issn = {1520-6025},
mesh = {Humans ; *Mitragyna/genetics ; Analgesics, Opioid ; Oxindoles ; Phylogeny ; *Secologanin Tryptamine Alkaloids ; Indoles ; },
abstract = {The monoterpene indole alkaloid (MIA) mitragynine has garnered attention as a potential treatment for pain, opioid use disorder, and opioid withdrawal because of its combined pharmacology at opioid and adrenergic receptors in humans. This alkaloid is unique to Mitragyna speciosa (kratom), which accumulates over 50 MIAs and oxindole alkaloids in its leaves. Quantification of 10 targeted alkaloids from several tissue types and cultivars of M. speciosa revealed that mitragynine accumulation was highest in leaves, followed by stipules and stems, but was absent, along with other alkaloids, in roots. While mitragynine is the predominant alkaloid in mature leaves, juvenile leaves accumulate higher amounts of corynantheidine and speciociliatine. Interestingly, corynantheidine has an inverse relationship with mitragynine accumulation throughout leaf development. Characterization of various cultivars of M. speciosa indicated altered alkaloidal profiles ranging from undetectable to high levels of mitragynine. DNA barcoding and phylogenetic analysis using ribosomal ITS sequences revealed polymorphisms leading M. speciosa cultivars having lower mitragynine content to group with other mitragyna species, suggesting interspecific hybridization events. Root transcriptome analysis of low- and high-mitragynine-producing cultivars indicated significant differences in gene expression and revealed allelic variation, further supporting that hybridization events may have impacted the alkaloid profile of M. speciosa.},
}
@article {pmid36913351,
year = {2023},
author = {Das, S and Anand, DV and Chung, MK},
title = {Topological data analysis of human brain networks through order statistics.},
journal = {PloS one},
volume = {18},
number = {3},
pages = {e0276419},
pmid = {36913351},
issn = {1932-6203},
mesh = {Humans ; Male ; Female ; *Brain/diagnostic imaging ; *Connectome/methods ; Magnetic Resonance Imaging/methods ; Nerve Net/diagnostic imaging ; },
abstract = {Understanding the common topological characteristics of the human brain network across a population is central to understanding brain functions. The abstraction of human connectome as a graph has been pivotal in gaining insights on the topological properties of the brain network. The development of group-level statistical inference procedures in brain graphs while accounting for the heterogeneity and randomness still remains a difficult task. In this study, we develop a robust statistical framework based on persistent homology using the order statistics for analyzing brain networks. The use of order statistics greatly simplifies the computation of the persistent barcodes. We validate the proposed methods using comprehensive simulation studies and subsequently apply to the resting-state functional magnetic resonance images. We found a statistically significant topological difference between the male and female brain networks.},
}
@article {pmid36908969,
year = {2023},
author = {Li, L and Matsuo, B and Levitre, G and McClain, EJ and Voight, EA and Crane, EA and Molander, GA},
title = {Dearomative intermolecular [2 + 2] photocycloaddition for construction of C(sp[3])-rich heterospirocycles on-DNA.},
journal = {Chemical science},
volume = {14},
number = {10},
pages = {2713-2720},
pmid = {36908969},
issn = {2041-6520},
abstract = {DNA-encoded library (DEL) screens have significantly impacted new lead compound identification efforts within drug discovery. An advantage of DELs compared to traditional screening methods is that an exponentially broader chemical space can be effectively screened using only nmol quantities of billions of DNA-tagged, drug-like molecules. The synthesis of DELs containing diverse, sp[3]-rich spirocycles, an important class of molecules in drug discovery, has not been previously reported. Herein, we demonstrate the synthesis of complex and novel spirocyclic cores via an on-DNA, visible light-mediated intermolecular [2 + 2] cycloaddition of olefins with heterocycles, including indoles, azaindoles, benzofurans, and coumarins. The DNA-tagged exo-methylenecyclobutane substrates were prepared from easily accessible alkyl iodides and styrene derivatives. Broad reactivity with many other DNA-conjugated alkene substrates was observed, including unactivated and activated alkenes, and the process is tolerant of various heterocycles. The cycloaddition was successfully scaled from 10 to 100 nmol without diminished yield, indicative of this reaction's suitability for DNA-encoded library production. Evaluation of DNA compatibility with the developed reaction in a mock-library format showed that the DNA barcode was maintained with high fidelity, with <1% mutated sequences and >99% amplifiable DNA from quantitative polymerase chain reaction (PCR) and next generation sequencing (NGS).},
}
@article {pmid36908639,
year = {2023},
author = {Kattenberg, JH and Van Dijk, NJ and Fernández-Miñope, CA and Guetens, P and Mutsaers, M and Gamboa, D and Rosanas-Urgell, A},
title = {Molecular Surveillance of Malaria Using the PF AmpliSeq Custom Assay for Plasmodium falciparum Parasites from Dried Blood Spot DNA Isolates from Peru.},
journal = {Bio-protocol},
volume = {13},
number = {5},
pages = {e4621},
pmid = {36908639},
issn = {2331-8325},
abstract = {Malaria molecular surveillance has great potential to support national malaria control programs (NMCPs), informing policy for its control and elimination. Here, we present a new three-day workflow for targeted resequencing of markers in 13 resistance-associated genes, histidine rich protein 2 and 3 (hrp2&amp;3), a country (Peru)-specific 28 SNP-barcode for population genetic analysis, and apical membrane antigen 1 (ama1), using Illumina short-read sequencing technology. The assay applies a multiplex PCR approach to amplify all genomic regions of interest in a rapid and easily standardizable procedure and allows simultaneous amplification of a high number of targets at once, therefore having great potential for implementation into routine surveillance practice by NMCPs. The assay can be performed on routinely collected filter paper blood spots and can be easily adapted to different regions to investigate either regional trends or in-country epidemiological changes.},
}
@article {pmid36907721,
year = {2023},
author = {Chua, PYS and Bourlat, SJ and Ferguson, C and Korlevic, P and Zhao, L and Ekrem, T and Meier, R and Lawniczak, MKN},
title = {Future of DNA-based insect monitoring.},
journal = {Trends in genetics : TIG},
volume = {39},
number = {7},
pages = {531-544},
doi = {10.1016/j.tig.2023.02.012},
pmid = {36907721},
issn = {0168-9525},
support = {206194/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *Ecosystem ; *Biodiversity ; DNA Barcoding, Taxonomic/methods ; DNA/genetics ; Insecta/genetics ; },
abstract = {Insects are crucial for ecosystem health but climate change and pesticide use are driving massive insect decline. To mitigate this loss, we need new and effective monitoring techniques. Over the past decade there has been a shift to DNA-based techniques. We describe key emerging techniques for sample collection. We suggest that the selection of tools should be broadened, and that DNA-based insect monitoring data need to be integrated more rapidly into policymaking. We argue that there are four key areas for advancement, including the generation of more complete DNA barcode databases to interpret molecular data, standardisation of molecular methods, scaling up of monitoring efforts, and integrating molecular tools with other technologies that allow continuous, passive monitoring based on images and/or laser imaging, detection, and ranging (LIDAR).},
}
@article {pmid36906044,
year = {2023},
author = {Küçükköse, E and Laoukili, J and Gorelick, AN and Degner, S and Laclé, MM and van den Bent, L and Peters, NA and Verheem, A and Hung, WT and Frenkel, NC and Wassenaar, ECE and Lansu, N and Lenos, KJ and Vermeulen, L and Koopman, M and Roodhart, JML and Kops, GJPL and Borel Rinkes, IHM and Hagendoorn, J and Naxerova, K and Kranenburg, O},
title = {Lymphatic Invasion of Plakoglobin-Dependent Tumor Cell Clusters Drives Formation of Polyclonal Lung Metastases in Colon Cancer.},
journal = {Gastroenterology},
volume = {165},
number = {2},
pages = {429-444.e15},
doi = {10.1053/j.gastro.2023.02.047},
pmid = {36906044},
issn = {1528-0012},
mesh = {Mice ; Animals ; Humans ; gamma Catenin/metabolism ; *Lung Neoplasms/pathology ; *Colonic Neoplasms/genetics ; *Liver Neoplasms/pathology ; },
abstract = {BACKGROUND &amp; AIMS: Patients with colon cancer with liver metastases may be cured with surgery, but the presence of additional lung metastases often precludes curative treatment. Little is known about the processes driving lung metastasis. This study aimed to elucidate the mechanisms governing lung vs liver metastasis formation.<br><br>METHODS: Patient-derived organoid (PDO) cultures were established from colon tumors with distinct patterns of metastasis. Mouse models recapitulating metastatic organotropism were created by implanting PDOs into the cecum wall. Optical barcoding was applied to trace the origin and clonal composition of liver and lung metastases. RNA sequencing and immunohistochemistry were used to identify candidate determinants of metastatic organotropism. Genetic, pharmacologic, in&#xa0;vitro, and in&#xa0;vivo modeling strategies identified essential steps in lung metastasis formation. Validation was performed by analyzing patient-derived tissues.<br><br>RESULTS: Cecum transplantation of 3 distinct PDOs yielded models with distinct metastatic organotropism: liver only, lung only, and liver and lung. Liver metastases were seeded by single cells derived from select clones. Lung metastases were seeded by polyclonal clusters of tumor cells entering the lymphatic vasculature with very limited clonal selection. Lung-specific metastasis was associated with high expression of desmosome markers, including plakoglobin. Plakoglobin deletion abrogated tumor cell cluster formation, lymphatic invasion, and lung metastasis formation. Pharmacologic inhibition of lymphangiogenesis attenuated lung metastasis formation. Primary human colon, rectum, esophagus, and stomach tumors with lung metastases had a higher N-stage and more plakoglobin-expressing intra-lymphatic tumor cell clusters than those without lung metastases.<br><br>CONCLUSIONS: Lung and liver metastasis formation are fundamentally distinct processes with different evolutionary bottlenecks, seeding entities, and anatomic routing. Polyclonal lung metastases originate from plakoglobin-dependent tumor cell clusters entering the lymphatic vasculature at the primary tumor site.},
}
@article {pmid36904056,
year = {2023},
author = {Aloi, F and Parlascino, R and Conti Taguali, S and Faedda, R and Pane, A and Cacciola, SO},
title = {Phytophthora pseudocryptogea, P. nicotianae and P. multivora Associated to Cycas revoluta: First Report Worldwide.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {5},
pages = {},
pmid = {36904056},
issn = {2223-7747},
support = {5A722192155//"Investigation of phytopathological problems of the main Sicilian productive contexts and eco-sustainable defense strategies (ME-DIT-ECO)" PiaCeRi-PIAno di inCEntivi per la Ricerca di Ateneo 2020-22 linea 2/ ; B64I2000016000500//Miglioramento delle produzioni agroalimentari mediterranee in condizioni di carenza di ri-sorse idriche-WATER4AGRIFOOD/ ; E69C20000130001//Smart and innovative packaging, postharvest rot management, and shipping of organic citrus fruit (BiOrangePack)/ ; CUP 453E25F2100118000//Italie-Tunisie Cooperation Program 2014-2020" project "PROMETEO &#xab;Un village trans-frontalier pour prot&#xe9;ger les cultures arboricoles m&#xe9;diterran&#xe9;ennes en partageant les connaissanc-es&#xbb; cod. C-5-2.1-36/ ; },
abstract = {A dieback was observed on three-year-old pot-grown plants of Cycas revoluta in Sicily (Italy). Symptoms, including stunting, yellowing and blight of the leaf crown, root rot and internal browning and decay of the basal stem, closely resembled the Phytophthora root and crown rot syndrome, common in other ornamentals. Isolations from rotten stem and roots, using a selective medium, and from rhizosphere soil of symptomatic plants, using leaf baiting, yielded three Phytophthora species, P. multivora, P. nicotianae and P. pseudocryptogea, were obtained. Isolates were identified by both morphological characters and DNA barcoding analysis, using three gene regions: ITS, β-tub and COI. Phytophthora pseudocryptogea was the sole species isolated directly from the stem and roots. The pathogenicity of the isolates of the three Phytophthora species was tested on one-year-old potted plants of C. revoluta, using both stem inoculation by wounding, and root inoculation through infested soil. Phytophthora pseudocryptogea was the most virulent and, like P. nicotianae, reproduced all the symptoms of natural infections, while P. multivora was the least virulent and induced solely very mild symptoms. Phytophthora pseudocryptogea was identified as the causal agent of the decline of C. revoluta, as it was re-isolated from both the roots and stems of artificially infected symptomatic plants, thus fulfilling Koch's postulates.},
}
@article {pmid36901798,
year = {2023},
author = {Michaels, V and Chalabi, S and Legrand, A and Renard, J and Tejerina, E and Daouya, M and Fabrega, S and Megret, J and Olaso, R and Boland, A and Deleuze, JF and Battail, C and Tronik-Le Roux, D and Ezine, S},
title = {Co-Transplantation of Barcoded Lymphoid-Primed Multipotent (LMPP) and Common Lymphocyte (CLP) Progenitors Reveals a Major Contribution of LMPP to the Lymphoid Lineage.},
journal = {International journal of molecular sciences},
volume = {24},
number = {5},
pages = {},
pmid = {36901798},
issn = {1422-0067},
support = {DBI20131228570//Fondation de la Recherche M&#xe9;dicale (FRM) Bioinformatics Analysis for Biology Research program/ ; },
mesh = {Animals ; Mice ; Cell Lineage/genetics ; *Lymphocytes/metabolism ; Hematopoietic Stem Cells/metabolism ; T-Lymphocytes ; *Hematopoietic Stem Cell Transplantation ; Cell Differentiation ; },
abstract = {T cells have the potential to maintain immunological memory and self-tolerance by recognizing antigens from pathogens or tumors. In pathological situations, failure to generate de novo T cells causes immunodeficiency resulting in acute infections and complications. Hematopoietic stem cells (HSC) transplantation constitutes a valuable option to restore proper immune function. However, delayed T cell reconstitution is observed compared to other lineages. To overcome this difficulty, we developed a new approach to identify populations with efficient lymphoid reconstitution properties. To this end, we use a DNA barcoding strategy based on the insertion into a cell chromosome of a lentivirus (LV) carrying a non-coding DNA fragment named barcode (BC). These will segregate through cell divisions and be present in cells' progeny. The remarkable characteristic of the method is that different cell types can be tracked simultaneously in the same mouse. Thus, we in vivo barcoded LMPP and CLP progenitors to test their ability to reconstitute the lymphoid lineage. Barcoded progenitors were co-grafted in immuno-compromised mice and their fate analyzed by evaluating the BC composition in transplanted mice. The results highlight the predominant role of LMPP progenitors for lymphoid generation and reveal valuable novel insights to be reconsidered in clinical transplantation assays.},
}
@article {pmid36900583,
year = {2023},
author = {Tinacci, L and Stratev, D and Strateva, M and Zhelyazkov, G and Kyuchukova, R and Armani, A},
title = {An Authentication Survey on Retail Seafood Products Sold on the Bulgarian Market Underlines the Need for Upgrading the Traceability System.},
journal = {Foods (Basel, Switzerland)},
volume = {12},
number = {5},
pages = {},
pmid = {36900583},
issn = {2304-8158},
support = {DCM &#x2116; 577/17.08.2018//Bulgarian Ministry of Education and Sciences/ ; },
abstract = {Economically motivated or accidental species substitutions lead to economic and potential health damage to consumers with a loss of confidence in the fishery supply chain. In the present study, a three-year survey on 199 retail seafood products sold on the Bulgarian market was addressed to assess: (1) product authenticity by molecular identification; (2) trade name compliance to the list of official trade names accepted in the territory; (3) adherence of the list in force to the market supply. DNA barcoding on mitochondrial and nuclear genes was applied for the identification of whitefish (WF), crustaceans (C) and mollusks (cephalopods-MC; gastropods-MG; bivalves-MB) except for Mytilus sp. products for which the analysis was conducted with a previously validated RFLP PCR protocol. Identification at the species level was obtained for 94.5% of the products. Failures in species allocation were reconducted due to low resolution and reliability or the absence of reference sequences. The study highlighted an overall mislabeling rate of 11%. WF showed the highest mislabeling rate (14%), followed by MB (12.5%), MC (10%) and C (7.9%). This evidence emphasized the use of DNA-based methods as tools for seafood authentication. The presence of non-compliant trade names and the ineffectiveness of the list to describe the market species varieties attested to the need to improve seafood labeling and traceability at the national level.},
}
@article {pmid36900485,
year = {2023},
author = {Denay, G and Preckel, L and Petersen, H and Pietsch, K and Wöhlke, A and Brünen-Nieweler, C},
title = {Benchmarking and Validation of a Bioinformatics Workflow for Meat Species Identification Using 16S rDNA Metabarcoding.},
journal = {Foods (Basel, Switzerland)},
volume = {12},
number = {5},
pages = {},
pmid = {36900485},
issn = {2304-8158},
support = {2020; AZ: 8.80.01.02.07//Ministry for Environment, Agriculture, Conservation and Consumer Protection of the State of North Rhine-Westphalia/ ; },
abstract = {DNA-metabarcoding is becoming more widely used for routine authentication of meat-based food and feed products. Several methods validating species identification methods through amplicon sequencing have already been published. These use a variety of barcodes and analysis workflows, however, no methodical comparison of available algorithms and parameter optimization are published hitherto for meat-based products' authenticity. Additionally, many published methods use very small subsets of the available reference sequences, thereby limiting the potential of the analysis and leading to over-optimistic performance estimates. We here predict and compare the ability of published barcodes to distinguish taxa in the BLAST NT database. We then use a dataset of 79 reference samples, spanning 32 taxa, to benchmark and optimize a metabarcoding analysis workflow for 16S rDNA Illumina sequencing. Furthermore, we provide recommendations as to the parameter choices, sequencing depth, and thresholds that should be used to analyze meat metabarcoding sequencing experiments. The analysis workflow is publicly available, and includes ready-to-use tools for validation and benchmarking.},
}
@article {pmid36900028,
year = {2023},
author = {Thakur, R and Bhatia, P and Singh, M and Sreedharanunni, S and Sharma, P and Singh, A and Trehan, A},
title = {Therapy-Acquired Clonal Mutations in Thiopurine Drug-Response Genes Drive Majority of Early Relapses in Pediatric B-Cell Precursor Acute Lymphoblastic Leukemia.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {13},
number = {5},
pages = {},
pmid = {36900028},
issn = {2075-4418},
support = {EMR/2017/000104//Science and Engineering Research Board/ ; No. 5/13/19/PB/ICRC/2022/NCD-III//Indian Council of Medical Research/ ; JRF-2019/HRD-060//Indian Council of Medical Research/ ; },
abstract = {METHODS: Forty pediatric (0-12 years) B-ALL DNA samples (20 paired Diagnosis-Relapse) and an additional six B-ALL DNA samples (without relapse at 3 years post treatment), as the non-relapse arm, were retrieved from the biobank for advanced genomic analysis. Deep sequencing (1050-5000X; mean 1600X) was performed using a custom NGS panel of 74 genes incorporating unique molecular barcodes.<br><br>RESULTS: A total 47 major clones (>25% VAF) and 188 minor clones were noted in 40 cases after bioinformatic data filtering. Of the forty-seven major clones, eight (17%) were diagnosis-specific, seventeen (36%) were relapse-specific and 11 (23%) were shared. In the control arm, no pathogenic major clone was noted in any of the six samples. The most common clonal evolution pattern observed was therapy-acquired (TA), with 9/20 (45%), followed by M-M, with 5/20 (25%), m-M, with 4/20 (20%) and unclassified (UNC) 2/20 (10%). The TA clonal pattern was predominant in early relapses 7/12 (58%), with 71% (5/7) having major clonal mutations in the NT5C2 or PMS2 gene related to thiopurine-dose response. In addition, 60% (3/5) of these cases were preceded by an initial hit in the epigenetic regulator, KMT2D. Mutations in common relapse-enriched genes comprised 33% of the very early relapses, 50% of the early and 40% of the late relapses. Overall, 14/46 (30%) of the samples showed the hypermutation phenotype, of which the majority (50%) had a TA pattern of relapse.<br><br>CONCLUSIONS: Our study highlights the high frequency of early relapses driven by TA clones, demonstrating the need to identify their early rise during chemotherapy by digital PCR.},
}
@article {pmid36894969,
year = {2023},
author = {Anita, VPD and Matra, DD and Siregar, UJ},
title = {Chloroplast genome draft assembly of Falcataria moluccana using hybrid sequencing technology.},
journal = {BMC research notes},
volume = {16},
number = {1},
pages = {31},
pmid = {36894969},
issn = {1756-0500},
support = {082/E5/PG.02.00.PT/2022//Kementerian Pendidikan, Kebudayaan, Riset, dan Teknologi/ ; 082/E5/PG.02.00.PT/2022//Kementerian Pendidikan, Kebudayaan, Riset, dan Teknologi/ ; 082/E5/PG.02.00.PT/2022//Kementerian Pendidikan, Kebudayaan, Riset, dan Teknologi/ ; },
mesh = {Sequence Analysis, DNA/methods ; *Genome, Chloroplast ; Phylogeny ; Genomics ; *Fabaceae/genetics ; },
abstract = {OBJECTIVES: Falcataria moluccana, known locally as Sengon, is a fast-growing legume tree that is commonly planted in community forests of Java Island, Indonesia. However, the plantations face attacks of Boktor stem borer (Xystrocera festiva) and gall-rust disease (Uromycladium falcatariae) as major threats to its productivity. To control those pest and disease, it is necessary to grow resistant sengon clones, which are developed through tree improvement program, of which needs genetic and genomic information. This dataset was created to construct draft of sengon chloroplast genome and to study the evolution of sengon based on matK and rbcL barcode genes.<br><br>DATA DESCRIPTION: Genomic DNA was extracted from leaf samples of one individual healthy tree in a private plantation. The DNA was sequenced using Illumina Novaseq 6000 (Novogen AIT, Singapore) for short-reads data, and MinION of Nanopore following manufacture's protocols SQK-LSK110 for long-reads data. The 66,3 Gb short-reads and 12 Gb long-reads data were hybrid assembled and used to construct a 128.867&#xa0;bp of F. moluccana chloroplast genome with a quadripartite structure, containing a pair of inverted repeats, a large single-copy and a small single-copy region. Phylogenetic tree constructed using matK and rbcL showed monophyletic origin of F. moluccana and other legume trees.},
}
@article {pmid36893650,
year = {2023},
author = {AbouGabal, AA and Mohamed A, AE and Aboul-Ela, HM and Khaled, AA and Aly, HM and Abdullah, MI and Shalaby, OK},
title = {DNA barcoding of marine macroalgae as bioindicators of heavy metal pollution.},
journal = {Marine pollution bulletin},
volume = {189},
number = {},
pages = {114761},
doi = {10.1016/j.marpolbul.2023.114761},
pmid = {36893650},
issn = {1879-3363},
mesh = {*Seaweed/chemistry ; Environmental Biomarkers ; DNA Barcoding, Taxonomic ; Environmental Monitoring/methods ; *Water Pollutants, Chemical/analysis ; *Metals, Heavy/analysis ; *Ulva ; *Rhodophyta/chemistry ; },
abstract = {Metal pollution in the marine coastal environment is an important topical issue. In this study, the water quality in five locations along the Alexandria coast (Eastern Harbor, El-Tabia pumping station, El Mex Bay, Sidi Bishir, and Abu Talat) was assessed by measuring physicochemical parameters from water samples. Depending on the morphological classification of macroalgae, the collected morphotypes were related to Ulva fasciata, Ulva compressa, Corallina officinalis, Corallina elongata, and Petrocladia capillaceae. Corallina officinalis and Corallina elongata demonstrated a high capacity for Cd, Pb, and Ni accumulation, and the highest values of Fe, Cu, and Mn were reported in Ulva fasciata and Ulva compressa. Two standard markers were applied, and results showed that the morphological classification matched the molecular data. Moreover, the analysis of algae can only reflect the accumulation of metals. The conclusion is that Ulva compressa and Corallina officinalis are potentially suitable indicators of localized short-term heavy metal pollution.},
}
@article {pmid36879903,
year = {2023},
author = {Johnson, GE and Parker, DJ and Lalanne, JB and Parker, ML and Li, GW},
title = {BaM-seq and TBaM-seq, highly multiplexed and targeted RNA-seq protocols for rapid, low-cost library generation from bacterial samples.},
journal = {NAR genomics and bioinformatics},
volume = {5},
number = {1},
pages = {lqad017},
pmid = {36879903},
issn = {2631-9268},
support = {R35 GM124732/GM/NIGMS NIH HHS/United States ; T32 GM007287/GM/NIGMS NIH HHS/United States ; },
abstract = {The ability to profile transcriptomes and characterize global gene expression changes has been greatly enabled by the development of RNA sequencing technologies (RNA-seq). However, the process of generating sequencing-compatible cDNA libraries from RNA samples can be time-consuming and expensive, especially for bacterial mRNAs which lack poly(A)-tails that are often used to streamline this process for eukaryotic samples. Compared to the increasing throughput and decreasing cost of sequencing, library preparation has had limited advances. Here, we describe bacterial-multiplexed-seq (BaM-seq), an approach that enables simple barcoding of many bacterial RNA samples that decreases the time and cost of library preparation. We also present targeted-bacterial-multiplexed-seq (TBaM-seq) that allows for differential expression analysis of specific gene panels with over 100-fold enrichment in read coverage. In addition, we introduce the concept of transcriptome redistribution based on TBaM-seq that dramatically reduces the required sequencing depth while still allowing for quantification of both highly and lowly abundant transcripts. These methods accurately measure gene expression changes with high technical reproducibility and agreement with gold standard, lower throughput approaches. Together, use of these library preparation protocols allows for fast, affordable generation of sequencing libraries.},
}
@article {pmid36879006,
year = {2023},
author = {Clark, IC and Fontanez, KM and Meltzer, RH and Xue, Y and Hayford, C and May-Zhang, A and D'Amato, C and Osman, A and Zhang, JQ and Hettige, P and Ishibashi, JSA and Delley, CL and Weisgerber, DW and Replogle, JM and Jost, M and Phong, KT and Kennedy, VE and Peretz, CAC and Kim, EA and Song, S and Karlon, W and Weissman, JS and Smith, CC and Gartner, ZJ and Abate, AR},
title = {Microfluidics-free single-cell genomics with templated emulsification.},
journal = {Nature biotechnology},
volume = {41},
number = {11},
pages = {1557-1566},
pmid = {36879006},
issn = {1546-1696},
support = {K22 AI152644/AI/NIAID NIH HHS/United States ; R44 GM145185/GM/NIGMS NIH HHS/United States ; K99 GM130964/GM/NIGMS NIH HHS/United States ; R43 GM137648/GM/NIGMS NIH HHS/United States ; R43 CA239978/CA/NCI NIH HHS/United States ; F31 NS115380/NS/NINDS NIH HHS/United States ; RM1 HG009490/HG/NHGRI NIH HHS/United States ; DP2 AI154435/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; Animals ; Mice ; *Microfluidics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Single-Cell Analysis/methods ; Genomics/methods ; Transcriptome/genetics ; },
abstract = {Current single-cell RNA-sequencing approaches have limitations that stem from the microfluidic devices or fluid handling steps required for sample processing. We develop a method that does not require specialized microfluidic devices, expertise or hardware. Our approach is based on particle-templated emulsification, which allows single-cell encapsulation and barcoding of cDNA in uniform droplet emulsions with only a vortexer. Particle-templated instant partition sequencing (PIP-seq) accommodates a wide range of emulsification formats, including microwell plates and large-volume conical tubes, enabling thousands of samples or millions of cells to be processed in minutes. We demonstrate that PIP-seq produces high-purity transcriptomes in mouse-human mixing studies, is compatible with multiomics measurements and can accurately characterize cell types in human breast tissue compared to a commercial microfluidic platform. Single-cell transcriptional profiling of mixed phenotype acute leukemia using PIP-seq reveals the emergence of heterogeneity within chemotherapy-resistant cell subsets that were hidden by standard immunophenotyping. PIP-seq is a simple, flexible and scalable next-generation workflow that extends single-cell sequencing to new applications.},
}
@article {pmid36876144,
year = {2023},
author = {Yu, X and Song, YR and Zhao, ZN},
title = {The complete chloroplast genome of Elsholtzia fruticosa (D. Don) Rehd. (Labiatae), an ornamental plant with high medicinal value.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {8},
number = {3},
pages = {336-341},
pmid = {36876144},
issn = {2380-2359},
abstract = {Elsholtzia fruticosa is an ornamental plant with high medicinal value. In this study, we sequenced and analyzed the complete chloroplast (cp) genome of the species. The complete cp sequence is 151,550 bp, including the large single-copy (LSC) region of 82,778 bp, the small single-copy (SSC) region of 17,492 bp, and a pair of invert repeats (IRs) regions of 25,640 bp. It encodes 132 unique genes in total, including 87 protein-coding genes, 37 transfer RNA genes (tRNAs), and eight ribosomal RNA genes (rRNAs). The comparative analysis of complete cp genomes showed that the genomic structure and gene order of E. fruticosa cps were conserved. The sequences of rps15, rps19, ycf1, ycf3, ycf15, psbL, psaI, trnG-UCC, trnS-GCU, trnR-UCU, trnL-UAG, trnP-UG, and trnL-UAA serve as hotspots for developing the DNA barcoding of Elsholtzia species. There are 49 SSR loci in the cp genome of E. fruticosa, among which the repeat numbers of mononucleotide, dinucleotide, trinucleotide, tetranucleotide, and pentanucleotides SSR are 37, 9, 3, 0, and 0, respectively. A total of 50 repeats were detected, including 15 forward repeats, seven reverse repeats, 26 palindromic repeats, and two complementary repeats. Phylogenetic analysis based on the complete cp genome and protein-coding DNA sequences of 26 plants indicates that E. fruticosa has a dose relationship with E. splendens and E. byeonsanensis.},
}
@article {pmid36865234,
year = {2023},
author = {Weile, J and Ferra, G and Boyle, G and Pendyala, S and Amorosi, C and Yeh, CL and Cote, AG and Kishore, N and Tabet, D and van Loggerenberg, W and Rayhan, A and Fowler, DM and Dunham, MJ and Roth, FP},
title = {Pacybara: Accurate long-read sequencing for barcoded mutagenized allelic libraries.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {36865234},
issn = {2692-8205},
support = {UM1 HG011969/HG/NHGRI NIH HHS/United States ; RM1 HG010461/HG/NHGRI NIH HHS/United States ; UM1 HG011989/HG/NHGRI NIH HHS/United States ; R01 HL164675/HL/NHLBI NIH HHS/United States ; R01 GM132162/GM/NIGMS NIH HHS/United States ; },
abstract = {Long read sequencing technologies, an attractive solution for many applications, often suffer from higher error rates. Alignment of multiple reads can improve base-calling accuracy, but some applications, e.g. sequencing mutagenized libraries where multiple distinct clones differ by one or few variants, require the use of barcodes or unique molecular identifiers. Unfortunately, sequencing errors can interfere with correct barcode identification, and a given barcode sequence may be linked to multiple independent clones within a given library. Here we focus on the target application of sequencing mutagenized libraries in the context of multiplexed assays of variant effects (MAVEs). MAVEs are increasingly used to create comprehensive genotype-phenotype maps that can aid clinical variant interpretation. Many MAVE methods use long-read sequencing of barcoded mutant libraries for accurate association of barcode with genotype. Existing long-read sequencing pipelines do not account for inaccurate sequencing or non-unique barcodes. Here, we describe Pacybara, which handles these issues by clustering long reads based on the similarities of (error-prone) barcodes while also detecting barcodes that have been associated with multiple genotypes. Pacybara also detects recombinant (chimeric) clones and reduces false positive indel calls. In three example applications, we show that Pacybara identifies and correctly resolves these issues.},
}
@article {pmid36864851,
year = {2022},
author = {Kouhpanji, MRZ and Zhang, Y and Um, J and Srinivasan, K and Sharma, A and Shore, D and Gao, Z and Chen, Y and Harpel, A and Porshokouh, ZN and Gage, TE and Dragos-Pinzaru, O and Tabakovic, I and Visscher, PB and Bischof, J and Modiano, JF and Franklin, R and Stadler, BJH},
title = {Bioapplications of Magnetic Nanowires: Barcodes, Biocomposites, Heaters.},
journal = {IEEE transactions on magnetics},
volume = {58},
number = {8},
pages = {},
pmid = {36864851},
issn = {0018-9464},
support = {R01 DK117425/DK/NIDDK NIH HHS/United States ; R01 HL135046/HL/NHLBI NIH HHS/United States ; },
abstract = {Magnetic nanowires (MNWs) can have their moments reversed via several mechanisms that are controlled using the composition, length, diameter, and density of nanowires in arrays as-synthesized or as individual nanoparticles in assays or gels. This tailoring of magnetic reversal leads to unique properties that can be used as a signature for reading out the type of MNW for applications as nano-barcodes. When synthesized inside track-etched polycarbonate membranes, the resulting MNW-embedded membranes can be used as biocompatible bandaids for detection without contact or optical sighting. When etched out of the growth template, free-floating MNWs are internalized by cells at 37 °C such that cells and/or exosomes can be collected and detected. In applications of cryopreservation, MNWs can be suspended in cryopreservation agents (CPAs) for injection into the blood vessels of tissues and organs as they are vitrified to -200 °C. Using an alternating magnetic field, the MNWs can then be nanowarmed rapidly to prevent crystallization and uniformly to prevent cracking of specimens, for example, as grafts or transplants. This invited paper is a review of recent progress in the specific bioapplications of MNWs to barcodes, biocomposites, and nanowarmers.},
}
@article {pmid36864559,
year = {2023},
author = {da Conceição Abreu Bandeira, M and Rodrigues, BL and Soares, GHC and Ferreira, AL and Carvalho Costa, LF and Brazil, RP and Rebêlo, JMM},
title = {DNA Barcoding Culicoides Biting Midges (Diptera: Ceratopogonidae) in Northeast Brazil.},
journal = {Journal of medical entomology},
volume = {60},
number = {3},
pages = {608-614},
doi = {10.1093/jme/tjad013},
pmid = {36864559},
issn = {1938-2928},
mesh = {Animals ; *Ceratopogonidae/genetics ; DNA Barcoding, Taxonomic ; Phylogeny ; Brazil ; DNA ; },
abstract = {Biting midges of the genus Culicoides are small insects associated with the transmission of several pathogens, which requires the correct identification of the species, for implementation of effective strategies against these insects. However, many species are difficult to identify only by morphological characters. Therefore, the use of molecular methods can help in the taxonomy and systematics of this group. Here, the DNA barcode approach was evaluated for nine species of Culicoides from the State of Maranhão, Brazil. We generated 39 sequences from a 476 bp (base pairs) fragment of the cytochrome c oxidase subunit I (COI) mitochondrial gene. To assess the usefulness of COI barcodes for the identification of these species, paired genetic distances from intra and interspecific comparisons and phylogenetic trees were generated in MEGA and RAxML/BEAST softwares, respectively. In addition, species delimitation was performed using the PTP, GMYC, and ABGD algorithms. The intra and interspecific genetic distances showed a clear distinction between them, demonstrating that, for the taxa studied, there can hardly be ambiguous identifications with barcodes. In the same sense, the phylogenetic reconstruction resulted in well-supported clades for all morphospecies analyzed.},
}
@article {pmid36863001,
year = {2023},
author = {Jeong, JE and Sutton, JJ and Ryu, HS and Kang, M and Tay, EJ and Nguyen, TL and Gordon, KC and Shim, SH and Woo, HY},
title = {Resonant Raman-Active Polymer Dot Barcodes for Multiplex Cell Mapping.},
journal = {ACS nano},
volume = {17},
number = {5},
pages = {4800-4812},
doi = {10.1021/acsnano.2c11240},
pmid = {36863001},
issn = {1936-086X},
mesh = {*Quantum Dots/chemistry ; Semiconductors ; Polymers/chemistry ; Light ; Fluorescence ; },
abstract = {Resonance Raman spectroscopy is an efficient tool for multiplex imaging because of the narrow bandwidth of the electronically enhanced vibrational signals. However, Raman signals are often overwhelmed by concurrent fluorescence. In this study, we synthesized a series of truxene-based conjugated Raman probes to show structure-specific Raman fingerprint patterns with a common 532 nm light source. The subsequent polymer dot (Pdot) formation of the Raman probes efficiently suppressed fluorescence via aggregation-induced quenching and improved the dispersion stability of particles without leakage of Raman probes or particle agglomeration for more than 1 year. Additionally, the Raman signal amplified by electronic resonance and increased probe concentration exhibited over 10[3] times higher relative Raman intensities versus 5-ethynyl-2'-deoxyuridine, enabling successful Raman imaging. Finally, multiplex Raman mapping was demonstrated with a single 532 nm laser using six Raman-active and biocompatible Pdots as barcodes for live cells. Resonant Raman-active Pdots may suggest a simple, robust, and efficient way for multiplex Raman imaging using a standard Raman spectrometer, suggesting the broad applicability of our strategy.},
}
@article {pmid36862768,
year = {2023},
author = {Haap, W},
title = {Peptide barcodes meet drug discovery.},
journal = {Science (New York, N.Y.)},
volume = {379},
number = {6635},
pages = {883},
doi = {10.1126/science.adg7484},
pmid = {36862768},
issn = {1095-9203},
mesh = {*Drug Discovery ; *Peptides/chemical synthesis/chemistry/therapeutic use ; *Small Molecule Libraries/chemical synthesis/chemistry ; },
abstract = {Small-molecule libraries encoded by peptide tags may accelerate the search for therapeutics.},
}
@article {pmid36861023,
year = {2023},
author = {Han, W and Tang, H and Wei, L and Zhang, E},
title = {The first DNA barcode library of Chironomidae from the Tibetan Plateau with an evaluation of the status of the public databases.},
journal = {Ecology and evolution},
volume = {13},
number = {2},
pages = {e9849},
pmid = {36861023},
issn = {2045-7758},
abstract = {The main aim of this study was to curate a COI barcode library of Chironomidae from the Tibetan Plateau (TP) as an essential supplement to the public database. Another aim is to evaluate the current status of the public database of Chironomidae in aspects of taxonomic coverage, geographic representation, barcode quality, and efficiency for molecular identification, the Tibetan Plateau, China. In this study, 512 individuals of Chironomidae from the TP were identified based on morphological taxonomy and barcode analysis. The metadata of public records of Chironomidae were downloaded from the BOLD, and the quality of the public barcodes was ranked using the BAGS program. The reliability of the public library for molecular identification was evaluated with the newly curated library using the BLAST method. The newly curated library comprised 159 barcode species of 54 genera, of which 58.4% of species were likely new to science. There were great gaps in the taxonomic coverage and geographic representation in the public database, and only 29.18% of barcodes were identified at the species level. The quality of the public database was of concern, with only 20% of species being determined as concordant between BINs and morphological species. The accuracy of molecular identification using the public database was poor, and about 50% of matched barcodes could be correctly identified at the species level at the identity threshold of 97%. Based on these data, some recommendations are included here for improving barcoding studies on Chironomidae. The species richness of Chironomidae from the TP is much higher than ever recorded. Barcodes from more taxonomic groups and geographic regions are urgently needed to fill the great gap in the current public database of Chironomidae. Users should take caution when public databases are adopted as reference libraries for the taxonomic assignment.},
}
@article {pmid36859472,
year = {2023},
author = {Kim, IS},
title = {Single-Cell Molecular Barcoding to Decode Multimodal Information Defining Cell States.},
journal = {Molecules and cells},
volume = {46},
number = {2},
pages = {74-85},
pmid = {36859472},
issn = {0219-1032},
mesh = {*Multiomics ; *RNA ; Transcriptome ; Single-Cell Analysis ; Sequence Analysis, DNA ; },
abstract = {Single-cell research has provided a breakthrough in biology to understand heterogeneous cell groups, such as tissues and organs, in development and disease. Molecular barcoding and subsequent sequencing technology insert a singlecell barcode into isolated single cells, allowing separation cell by cell. Given that multimodal information from a cell defines precise cellular states, recent technical advances in methods focus on simultaneously extracting multimodal data recorded in different biological materials (DNA, RNA, protein, etc.). This review summarizes recently developed singlecell multiomics approaches regarding genome, epigenome, and protein profiles with the transcriptome. In particular, we focus on how to anchor or tag molecules from a cell, improve throughputs with sample multiplexing, and record lineages, and we further discuss the future developments of the technology.},
}
@article {pmid36854980,
year = {2023},
author = {Rizos, I and Debeljak, P and Finet, T and Klein, D and Ayata, SD and Not, F and Bittner, L},
title = {Beyond the limits of the unassigned protist microbiome: inferring large-scale spatio-temporal patterns of Syndiniales marine parasites.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {16},
pmid = {36854980},
issn = {2730-6151},
abstract = {Marine protists are major components of the oceanic microbiome that remain largely unrepresented in culture collections and genomic reference databases. The exploration of this uncharted protist diversity in oceanic communities relies essentially on studying genetic markers from the environment as taxonomic barcodes. Here we report that across 6 large scale spatio-temporal planktonic surveys, half of the genetic barcodes remain taxonomically unassigned at the genus level, preventing a fine ecological understanding for numerous protist lineages. Among them, parasitic Syndiniales (Dinoflagellata) appear as the least described protist group. We have developed a computational workflow, integrating diverse 18S rDNA gene metabarcoding datasets, in order to infer large-scale ecological patterns at 100% similarity of the genetic marker, overcoming the limitation of taxonomic assignment. From a spatial perspective, we identified 2171 unassigned clusters, i.e., Syndiniales sequences with 100% similarity, exclusively shared between the Tropical/Subtropical Ocean and the Mediterranean Sea among all Syndiniales orders and 25 ubiquitous clusters shared within all the studied marine regions. From a temporal perspective, over 3 time-series, we highlighted 39 unassigned clusters that follow rhythmic patterns of recurrence and are the best indicators of parasite community's variation. These clusters withhold potential as ecosystem change indicators, mirroring their associated host community responses. Our results underline the importance of Syndiniales in structuring planktonic communities through space and time, raising questions regarding host-parasite association specificity and the trophic mode of persistent Syndiniales, while providing an innovative framework for prioritizing unassigned protist taxa for further description.},
}
@article {pmid36854763,
year = {2023},
author = {Vondrák, J and Svoboda, S and Zíbarová, L and Štenclová, L and Mareš, J and Pouska, V and Košnar, J and Kubásek, J},
title = {Alcobiosis, an algal-fungal association on the threshold of lichenisation.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {2957},
pmid = {36854763},
issn = {2045-2322},
mesh = {*Eczema ; Alarmins ; Biological Transport ; Carbon ; Hyphae ; *Keratosis ; *Lichens ; },
abstract = {Alcobiosis, the symbiosis of algae and corticioid fungi, frequently occurs on bark and wood. Algae form a layer in or below fungal basidiomata reminiscent of the photobiont layer in lichens. Identities of algal and fungal partners were confirmed by DNA barcoding. Algal activity was examined using gas exchange and chlorophyll fluorescence techniques. Carbon transfer from algae to fungi was detected as [13]C, assimilated by algae, transferred to the fungal polyol. Nine fungal partners scattered across Agaricomycetes are associated with three algae from Trebouxiophycae: Coccomyxa sp. with seven fungal species on damp wood, Desmococcus olivaceus and Tritostichococcus coniocybes, both with a single species on bark and rain-sheltered wood, respectively. The fungal partner does not cause any obvious harm to the algae. Algae enclosed in fungal tissue exhibited a substantial CO2 uptake, but carbon transfer to fungal tissues was only detected in the Lyomyces-Desmococcus alcobiosis where some algal cells are tightly enclosed by hyphae in goniocyst-like structures. Unlike lichen mycobionts, fungi in alcobioses are not nutritionally dependent on the algal partner as all of them can live without algae. We consider alcobioses to be symbioses in various stages of co-evolution, but still quite different from true lichens.},
}
@article {pmid36853782,
year = {2023},
author = {Hsieh, MS and Kao, HL and Huang, WC and Wang, SY and Lin, SY and Chu, PY and Pan, CC and Chou, TY and Ho, HL and Yeh, YC},
title = {Constant p.L424H Mutation in GTF2I in Micronodular Thymomas With Lymphoid Stroma: Evidence Supporting Close Relationship With Type A and AB Thymomas.},
journal = {Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc},
volume = {36},
number = {2},
pages = {100008},
doi = {10.1016/j.modpat.2022.100008},
pmid = {36853782},
issn = {1530-0285},
mesh = {Humans ; *Thymoma/genetics ; Proto-Oncogene Proteins p21(ras) ; *Thymus Neoplasms/genetics ; Mutation ; *Transcription Factors, TFIII ; *Transcription Factors, TFII/genetics ; },
abstract = {Micronodular thymoma with lymphoid stroma is a rare thymic neoplasm characterized by discrete nodules of epithelial tumor cells separated by abundant lymphoid stroma. The genetic features of micronodular thymoma with lymphoid stroma remain largely unexplored. Owing to the interference of abundant intratumoral, nonneoplastic lymphoid cells, a highly sensitive approach is necessary to study genetic changes in these tumors. In this study, we used a highly sensitive next-generation sequencing assay using the molecular barcoding Ion AmpliSeq HD technology to study the most commonly mutated genes in thymomas, including GTF2I, HRAS, NRAS, KRAS, and TP53. A total of 12 cases of micronodular thymomas with lymphoid stroma were tested, and 2 cases also had areas of type A thymoma in their tumor bed. Two micronodular thymic carcinomas with lymphoid stroma, a histological mimic of micronodular thymoma, were also included for comparison. Recurrent p.L424H mutations in GTF2I were found in all the cases of micronodular thymoma with lymphoid stroma but not in the cases of micronodular thymic carcinomas. In addition, 3 cases of micronodular thymoma with lymphoid stroma also had concomitant HRAS and/or KRAS mutations. Our study showed that p.L424H mutations in GTF2I is a constant genetic feature of micronodular thymoma with lymphoid stroma. This finding strongly suggests that micronodular thymoma with lymphoid stroma is closely related to type A and AB thymomas because they all share p.L424H mutations in GTF2I.},
}
@article {pmid36853583,
year = {2023},
author = {Dominique, NL and Jensen, IM and Kaur, G and Kotseos, CQ and Boggess, WC and Jenkins, DM and Camden, JP},
title = {Giving Gold Wings: Ultrabright and Fragmentation Free Mass Spectrometry Reporters for Barcoding, Bioconjugation Monitoring, and Data Storage.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {62},
number = {21},
pages = {e202219182},
doi = {10.1002/anie.202219182},
pmid = {36853583},
issn = {1521-3773},
mesh = {Animals ; *Gold/chemistry ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; *Metal Nanoparticles/chemistry ; Ligands ; Contrast Media ; Information Storage and Retrieval ; },
abstract = {The widespread application of laser desorption/ionization mass spectrometry (LDI-MS) highlights the need for a bright and multiplexable labeling platform. While ligand-capped Au nanoparticles (AuNPs) have emerged as a promising LDI-MS contrast agent, the predominant thiol ligands suffer from low ion yields and extensive fragmentation. In this work, we develop a N-heterocyclic carbene (NHC) ligand platform that enhances AuNP LDI-MS performance. NHC scaffolds are tuned to generate barcoded AuNPs which, when benchmarked against thiol-AuNPs, are bright mass tags and form unfragmented ions in high yield. To illustrate the transformative potential of NHC ligands, the mass tags were employed in three orthogonal applications: monitoring a bioconjugation reaction, performing multiplexed imaging, and storing and reading encoded information. These results demonstrate that NHC-nanoparticle systems are an ideal platform for LDI-MS and greatly broaden the scope of nanoparticle contrast agents.},
}
@article {pmid36851620,
year = {2023},
author = {Hassanin, A and Rambaud, O},
title = {Retracing Phylogenetic, Host and Geographic Origins of Coronaviruses with Coloured Genomic Bootstrap Barcodes: SARS-CoV and SARS-CoV-2 as Case Studies.},
journal = {Viruses},
volume = {15},
number = {2},
pages = {},
pmid = {36851620},
issn = {1999-4915},
mesh = {Humans ; Animals ; SARS-CoV-2/genetics ; *Severe acute respiratory syndrome-related coronavirus ; *Chiroptera ; Phylogeny ; *COVID-19/epidemiology ; China ; Genomics ; },
abstract = {Phylogenetic trees of coronaviruses are difficult to interpret because they undergo frequent genomic recombination. Here, we propose a new method, coloured genomic bootstrap (CGB) barcodes, to highlight the polyphyletic origins of human sarbecoviruses and understand their host and geographic origins. The results indicate that SARS-CoV and SARS-CoV-2 contain genomic regions of mixed ancestry originating from horseshoe bat (Rhinolophus) viruses. First, different regions of SARS-CoV share exclusive ancestry with five Rhinolophus viruses from Southwest China (RfYNLF/31C: 17.9%; RpF46: 3.3%; RspSC2018: 2.0%; Rpe3: 1.3%; RaLYRa11: 1.0%) and 97% of its genome can be related to bat viruses from Yunnan (China), supporting its emergence in the Rhinolophus species of this province. Second, different regions of SARS-CoV-2 share exclusive ancestry with eight Rhinolophus viruses from Yunnan (RpYN06: 5.8%; RaTG13: 4.8%; RmYN02: 3.8%), Laos (RpBANAL103: 3.3%; RmarBANAL236: 1.7%; RmBANAL52: 1.0%; RmBANAL247: 0.7%), and Cambodia (RshSTT200: 2.3%), and 98% of its genome can be related to bat viruses from northern Laos and Yunnan, supporting its emergence in the Rhinolophus species of this region. Although CGB barcodes are very useful in retracing the origins of human sarbecoviruses, further investigations are needed to better take into account the diversity of coronaviruses in bats from Cambodia, Laos, Myanmar, Thailand and Vietnam.},
}
@article {pmid36843401,
year = {2023},
author = {Kim, JJ and Jang, JE and Lee, HA and Park, MR and Kook, HW and Lee, ST and Choi, JR and Min, YH and Shin, S and Cheong, JW},
title = {Development of a Next-generation Sequencing-based Gene Panel Test to Detect Measurable Residual Disease in Acute Myeloid Leukemia.},
journal = {Annals of laboratory medicine},
volume = {43},
number = {4},
pages = {328-336},
pmid = {36843401},
issn = {2234-3814},
mesh = {Humans ; Neoplasm, Residual/diagnosis/genetics ; *Hematopoietic Stem Cell Transplantation ; *Leukemia, Myeloid, Acute/diagnosis/genetics ; Recurrence ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: AML is a heterogeneous disease, and despite intensive therapy, recurrence is still high in AML patients who achieve the criterion for cytomorphologic remission (residual tumor burden [measurable residual disease, MRD]<5%). This study aimed to develop a targeted next-generation sequencing (NGS) panel to detect MRD in AML patients and validate its performance.<br><br>METHODS: We designed an error-corrected, targeted MRD-NGS panel without using physical molecular barcodes, including 24 genes. Fifty-four bone marrow and peripheral blood samples from 23 AML patients were sequenced using the panel. The panel design was validated using reference material, and accuracy was assessed using droplet digital PCR.<br><br>RESULTS: Dilution tests showed excellent linearity and a strong correlation between expected and observed clonal frequencies (R>0.99). The test reproducibly detected MRD in three dilution series samples, with a sensitivity of 0.25% for single-nucleotide variants. More than half of samples from patients with morphologic remission after one month of chemotherapy had detectable mutations. NGS-MRD positivity for samples collected after one month of chemotherapy tended to be associated with poor overall survival and progression-free survival.<br><br>CONCLUSIONS: Our highly sensitive and accurate NGS-MRD panel can be readily used to monitor most AML patients in clinical practice, including patients without gene rearrangement. In addition, this NGS-MRD panel may allow the detection of newly emerging clones during clinical relapse, leading to more reliable prognoses of AML.},
}
@article {pmid36840586,
year = {2023},
author = {Kattenberg, JH and Fernandez-Miñope, C and van Dijk, NJ and Llacsahuanga Allcca, L and Guetens, P and Valdivia, HO and Van Geertruyden, JP and Rovira-Vallbona, E and Monsieurs, P and Delgado-Ratto, C and Gamboa, D and Rosanas-Urgell, A},
title = {Malaria Molecular Surveillance in the Peruvian Amazon with a Novel Highly Multiplexed Plasmodium falciparum AmpliSeq Assay.},
journal = {Microbiology spectrum},
volume = {11},
number = {2},
pages = {e0096022},
pmid = {36840586},
issn = {2165-0497},
abstract = {Molecular surveillance for malaria has great potential to support national malaria control programs (NMCPs). To bridge the gap between research and implementation, several applications (use cases) have been identified to align research, technology development, and public health efforts. For implementation at NMCPs, there is an urgent need for feasible and cost-effective tools. We designed a new highly multiplexed deep sequencing assay (Pf AmpliSeq), which is compatible with benchtop sequencers, that allows high-accuracy sequencing with higher coverage and lower cost than whole-genome sequencing (WGS), targeting genomic regions of interest. The novelty of the assay is its high number of targets multiplexed into one easy workflow, combining population genetic markers with 13 nearly full-length resistance genes, which is applicable for many different use cases. We provide the first proof of principle for hrp2 and hrp3 deletion detection using amplicon sequencing. Initial sequence data processing can be performed automatically, and subsequent variant analysis requires minimal bioinformatic skills using any tabulated data analysis program. The assay was validated using a retrospective sample collection (n = 254) from the Peruvian Amazon between 2003 and 2018. By combining phenotypic markers and a within-country 28-single-nucleotide-polymorphism (SNP) barcode, we were able to distinguish different lineages with multiple resistance haplotypes (in dhfr, dhps, crt and mdr1) and hrp2 and hrp3 deletions, which have been increasing in recent years. We found no evidence to suggest the emergence of artemisinin (ART) resistance in Peru. These findings indicate a parasite population that is under drug pressure but is susceptible to current antimalarials and demonstrate the added value of a highly multiplexed molecular tool to inform malaria strategies and surveillance systems. IMPORTANCE While the power of next-generation sequencing technologies to inform and guide malaria control programs has become broadly recognized, the integration of genomic data for operational incorporation into malaria surveillance remains a challenge in most countries where malaria is endemic. The main obstacles include limited infrastructure, limited access to high-throughput sequencing facilities, and the need for local capacity to run an in-country analysis of genomes at a large-enough scale to be informative for surveillance. In addition, there is a lack of standardized laboratory protocols and automated analysis pipelines to generate reproducible and timely results useful for relevant stakeholders. With our standardized laboratory and bioinformatic workflow, malaria genetic surveillance data can be readily generated by surveillance researchers and malaria control programs in countries of endemicity, increasing ownership and ensuring timely results for informed decision- and policy-making.},
}
@article {pmid36836360,
year = {2023},
author = {Kaasalainen, U and Kirika, PM and Mollel, NP and Hemp, A and Rikkinen, J},
title = {The Lichen Genus Sticta (Lobariaceae, Peltigerales) in East African Montane Ecosystems.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {2},
pages = {},
pmid = {36836360},
issn = {2309-608X},
support = {408295270//Deutsche Forschungsgemeinschaft/ ; 705777//European Union/ ; },
abstract = {The lichen flora of Africa is still poorly known. In many parts of the tropics, recent studies utilizing DNA methods have revealed extraordinary diversity among various groups of lichenized fungi, including the genus Sticta. In this study, East African Sticta species and their ecology are reviewed using the genetic barcoding marker nuITS and morphological characters. The studied regions represent montane areas in Kenya and Tanzania, including the Taita Hills and Mt. Kilimanjaro, which belong to the Eastern Afromontane biodiversity hotspot. Altogether 14 Sticta species are confirmed from the study region, including the previously reported S. fuliginosa, S. sublimbata, S. tomentosa, and S. umbilicariiformis. Sticta andina, S. ciliata, S. duplolimbata, S. fuliginoides, and S. marginalis are reported as new to Kenya and/or Tanzania. Sticta afromontana, S. aspratilis, S. cellulosa, S. cyanocaperata, and S. munda, are described as new to science. The abundance of new diversity detected and the number of taxa represented by only few specimens show that more comprehensive sampling of the region may be needed to reveal the true diversity of Sticta in East Africa. More generally, our results highlight the need for further taxonomic studies of lichenized fungi in the region.},
}
@article {pmid36835761,
year = {2023},
author = {Mushtaq, HMS and Saleh, AA and Kamran, M and Alatawi, FJ},
title = {Molecular-Based Taxonomic Inferences of Some Spider Mite Species of the Genus Oligonychus Berlese (Acari, Prostigmata, Tetranychidae).},
journal = {Insects},
volume = {14},
number = {2},
pages = {},
pmid = {36835761},
issn = {2075-4450},
support = {IFKSURG-2-1157//Deputyship for Research &amp; Innovation, Ministry of Education in Saudi Arabia/ ; },
abstract = {DNA barcoding technology using short DNA sequences has emerged as an efficient and reliable tool for identifying, confirming, and resolving closely related taxa. This study used ITS2-rDNA and mtCOI DNA sequences to confirm the identity of eight Oligonychus species, representing 68 spider mite samples, collected mainly from Saudi Arabia (SA) and some from Mexico, Pakistan, USA, and Yemen. The intraspecific nucleotide divergences of the studied Oligonychus species ranged from 0% to 1.2% for ITS2 and 0% to 2.9% for COI. However, the interspecific nucleotide divergences were distinctly higher than the intraspecific ones and ranged from 3.7% to 51.1% for ITS2 and 3.2% to 18.1% for COI. Furthermore, molecular data correctly confirmed the species identity of 42 Oligonychus samples lacking males, including a previously claimed sample of O. pratensis from SA. High genetic variations were detected in two Oligonychus species: O. afrasiaticus (McGregor) (nine ITS2 and three COI haplotypes) and O. tylus Baker and Pritchard (four ITS2 and two COI haplotypes). In addition, ITS2- and COI-based phylogenetic trees confirmed the subdivision of the genus Oligonychus. In conclusion, integrative taxonomic approaches are vital to resolve the closely related Oligonychus species, identify the samples lacking male specimens, and assess phylogenetic relationships within and among species.},
}
@article {pmid36835727,
year = {2023},
author = {Peng, L and Zang, H and Sun, C and Wang, L and Wang, B},
title = {Four New Species of the Genus Eoneureclipsis (Trichoptera: Psychomyiidae) from China Inferred from Morphology and DNA Barcodes.},
journal = {Insects},
volume = {14},
number = {2},
pages = {},
pmid = {36835727},
issn = {2075-4450},
support = {No. 41771052//National Natural Science Foundation of China/ ; No. 32200364//National Natural Science Foundation of China/ ; //The Project of Biological Resources Survey in Wuyishan National Park/ ; },
abstract = {Four new species of the genus Eoneureclipsis Kimmins, 1955 from China are described, illustrated, and diagnosed based on male genitalia: Eoneureclipsis jianfenglingensis sp. nov. from Hainan, E. foraminulatus sp. nov. from Guangxi, E. spinosus sp. nov. from Guangxi and Guangdong, and E. gei sp. nov. from Fujian. A dichotomous key to Chinese adult males of Eoneureclipsis is provided. A distribution map for all Eoneureclipsis species is also presented. The DNA barcodes (partial mtCOI sequences) of E. jianfenglingensis sp. nov., E. gei sp. nov., and E. hainanensis Mey, 2013 have been generated and compared with all existing sequences of Eoneureclipsis species.},
}
@article {pmid36835700,
year = {2023},
author = {Saiwichai, T and Laojun, S and Chaiphongpachara, T and Sumruayphol, S},
title = {Species Identification of the Major Japanese Encephalitis Vectors within the Culex vishnui Subgroup (Diptera: Culicidae) in Thailand Using Geometric Morphometrics and DNA Barcoding.},
journal = {Insects},
volume = {14},
number = {2},
pages = {},
pmid = {36835700},
issn = {2075-4450},
abstract = {Japanese encephalitis (JE) is a viral infection of the brain caused by the Japanese encephalitis virus, which spreads globally, particularly in 24 countries of Southeast Asia and the Western Pacific region. In Thailand, the primary vectors of JE are Cx. pseudovishnui, Cx. tritaeniorhynchus, and Cx. vishnui of the Cx. vishnui subgroup. The morphologies of three mosquito species are extremely similar, making identification challenging. Thus, geometric morphometrics (GM) and DNA barcoding were applied for species identification. The results of cross-validation reclassification revealed that the GM technique based on wing shape analysis had relatively high potential for distinguishing Cx. pseudovishnui, Cx. tritaeniorhynchus, and Cx. vishnui (total performance = 88.34% of correctly assigned individuals). While the DNA barcoding yielded excellent results in identifying these Culex species based on the DNA barcode gap (average intraspecific genetic distance = 0.78% ± 0.39% and average interspecific genetic distance = 6.14% ± 0.79%). However, in the absence of the required facilities for DNA barcoding, GM techniques can be employed in conjunction with morphological methods to enhance the reliability of species identification. Based on the results of this study, our approach can help guide efforts to identify members of the Cx. vishnui subgroup, which will be useful for the effective vector control of JE in Thailand.},
}
@article {pmid36835691,
year = {2023},
author = {Christophoryová, J and Krajčovičová, K and Šťáhlavský, F and Španiel, S and Opatova, V},
title = {Integrative Taxonomy Approach Reveals Cryptic Diversity within the Phoretic Pseudoscorpion Genus Lamprochernes (Pseudoscorpiones: Chernetidae).},
journal = {Insects},
volume = {14},
number = {2},
pages = {},
pmid = {36835691},
issn = {2075-4450},
support = {APVV-19-0076//Slovak Research and Development Agency/ ; VEGA grant 1/0704/20//The Ministry of Education, Science, Research and Sport&#xa0;of the Slovak Republic/ ; GAUK 36908//Charles University Grant Agency in the Czech Republic/ ; UNCE 204069//Charles University Research Centre program/ ; the FP7 "Capacities" Program (application No. AT-TAF-4126)//the SYNTHESYS Project http://www.synthesys.info// ; },
abstract = {Pseudoscorpions represent an ancient, but homogeneous group of arachnids. The genus Lamprochernes comprises several morphologically similar species with wide and overlapping distributions. We implemented an integrative approach combining molecular barcoding (cox1), with cytogenetic and morphological analyses in order to assess species boundaries in European Lamprochernes populations. The results suggest ancient origins of Lamprochernes species accompanied by morphological stasis within the genus. Our integrative approach delimited three nominal Lamprochernes species and one cryptic lineage Lamprochernes abditus sp. nov. Despite its Oligocene origin, L. abditus sp. nov. can be distinguished from its closest relative only by molecular and cytogenetic differences, or alternatively, by a complex multivariate morphometric analysis involving other Lamprochernes species. The population structure and common haplotype sharing across geographically distant populations in most Lamprochernes species suggest that a phoretic manner of dispersal is efficient in this group.},
}
@article {pmid36835686,
year = {2023},
author = {Kirichenko, NI and Karpun, NN and Zhuravleva, EN and Shoshina, EI and Anikin, VV and Musolin, DL},
title = {Invasion Genetics of the Horse-Chestnut Leaf Miner, Cameraria ohridella (Lepidoptera: Gracillariidae), in European Russia: A Case of Successful Involvement of Citizen Science in Studying an Alien Insect Pest.},
journal = {Insects},
volume = {14},
number = {2},
pages = {},
pmid = {36835686},
issn = {2075-4450},
support = {21-16-00050//Russian Science Foundation/ ; 0287-2021-0011//Sukachev Institute of Forest SB RAS, the basic project/ ; FGRW-2022-0006//The state task of the Federal Research Center of the SSC RAS/ ; },
abstract = {Based on the intensive monitoring conducted by our team and volunteers in 2021, the secondary range of an alien horse-chestnut leaf miner, Cameraria ohridella Deschka &amp; Dimić, 1986 (Lepidoptera: Gracillariidae), was specified in European Russia. This invasive pest was confirmed in 24 out of 58 administrative regions of Russia, which it has occupied for approximately 16 years. Analysis of the COI mtDNA gene sequenced in 201 specimens collected in 21 regions of the European part of Russia indicates the occurrence of two haplotypes (A and B), which are also present in the secondary range of C. ohridella in Eastern and Western Europe. The haplotype A dominated and was present in 87.5% of specimens from European Russia. In 2021, C. ohridella produced spectacular outbreaks in Aesculus hippocastanum in southern Russia, where it damaged more than 50% of the leaves in trees in 24 out of 30 distant localities. In the south of the country, the pest infested Acer pseudoplatanus, whereas other species of Acer of European, East Asian, and North American origin showed no signs of attacks. Taking into account that Ae. hippocastanum is present in most regions of European Russia, we expect a further range expansion of C. ohridella up to the Ural Mountains.},
}
@article {pmid36835678,
year = {2023},
author = {Kirchgatter, K and Guimarães, LO and Monteiro, EF and Helfstein, VC and Telles-de-Deus, J and Menezes, RMT and Reginato, SL and Chagas, CRF and de Camargo-Neves, VLF},
title = {DNA Barcoding of Morphologically Characterized Mosquitoes Belonging to the Genus Mansonia from the Atlantic Forest and Brazilian Savanna.},
journal = {Insects},
volume = {14},
number = {2},
pages = {},
pmid = {36835678},
issn = {2075-4450},
support = {309396/2021-2//National Council for Scientific and Technological Development/ ; 2012/51427-1, 2017/50345-5, 2018/16232-1//S&#xe3;o Paulo Research Foundation/ ; },
abstract = {The identification of mosquito species is necessary for determining the entomological components of disease transmission. However, identification can be difficult in species that are morphologically similar. The cytochrome c oxidase subunit I (COI) DNA barcode region is considered a valuable and reliable diagnostic tool for mosquito species recognition, including those that belong to species complexes. Mansonia mosquitoes are found in forests near swampy areas. They are nocturnal and are highly attracted to light. Hematophagous adult females exhibit aggressive biting behavior and can become infected with and transmit pathogens during their feeding, including some epizootic viruses and avian malaria. In Brazil, twelve Mansonia species have been reported. In a recent study from the São Paulo Zoo in Brazil, three morphologically distinct species were collected and identified, namely: Mansonia (Mansonia) indubitans, Ma. (Man.) pseudotitillans and Ma. (Man.) titillans. However, confirmation of these species by molecular identification was unsuccessful due to a lack of COI sequences in the GenBank database. Thus, this research aimed to describe the COI DNA barcode sequences of some morphologically characterized Mansonia (Man.) species from Brazil and to determine their utility in delimiting species collected from the Atlantic Forest and Brazilian Savanna. Accordingly, we provide tools for the genetic identification of species that play a significant role in pathogen transmission in wildlife and potentially humans. We show that the delimitation of Mansonia species via five different approaches based on COI DNA sequences (BI, NJ, ASAP, bPTP and GMYC) yield basically the same groups identified by traditional taxonomy, and we provide the identification of specimens that were previously identified only up to the subgenus level. We also provide COI sequences from two Mansonia species that were not previously available in sequence databases, Ma. wilsoni and Ma. pseudotitillans, and thus contribute to the ongoing global effort to standardize DNA barcoding as a molecular means of species identification.},
}
@article {pmid36834753,
year = {2023},
author = {Lu, RS and Hu, K and Zhang, FJ and Sun, XQ and Chen, M and Zhang, YM},
title = {Pan-Plastome of Greater Yam (Dioscorea alata) in China: Intraspecific Genetic Variation, Comparative Genomics, and Phylogenetic Analyses.},
journal = {International journal of molecular sciences},
volume = {24},
number = {4},
pages = {},
pmid = {36834753},
issn = {1422-0067},
mesh = {Phylogeny ; *Dioscorea ; Genomics ; Haplotypes ; Genetic Variation ; },
abstract = {Dioscorea alata L. (Dioscoreaceae), commonly known as greater yam, water yam, or winged yam, is a popular tuber vegetable/food crop worldwide, with nutritional, health, and economical importance. China is an important domestication center of D. alata, and hundreds of cultivars (accessions) have been established. However, genetic variations among Chinese accessions remain ambiguous, and genomic resources currently available for the molecular breeding of this species in China are very scarce. In this study, we generated the first pan-plastome of D. alata, based on 44 Chinese accessions and 8 African accessions, and investigated the genetic variations, plastome evolution, and phylogenetic relationships within D. alata and among members of the section Enantiophyllum. The D. alata pan-plastome encoded 113 unique genes and ranged in size from 153,114 to 153,161 bp. A total of four whole-plastome haplotypes (Haps I-IV) were identified in the Chinese accessions, showing no geographical differentiation, while all eight African accessions shared the same whole-plastome haplotype (Hap I). Comparative genomic analyses revealed that all four whole plastome haplotypes harbored identical GC content, gene content, gene order, and IR/SC boundary structures, which were also highly congruent with other species of Enantiophyllum. In addition, four highly divergent regions, i.e., trnC-petN, trnL-rpl32, ndhD-ccsA, and exon 3 of clpP, were identified as potential DNA barcodes. Phylogenetic analyses clearly separated all the D. alata accessions into four distinct clades corresponding to the four haplotypes, and strongly supported that D. alata was more closely related to D. brevipetiolata and D. glabra than D. cirrhosa, D. japonica, and D. polystachya. Overall, these results not only revealed the genetic variations among Chinese D. alata accessions, but also provided the necessary groundwork for molecular-assisted breeding and industrial utilization of this species.},
}
@article {pmid36833407,
year = {2023},
author = {Hladnik, M and Baruca Arbeiter, A and Bandelj, D},
title = {Sequence Characterization of ITS Regions of Immortelle Helichrysum italicum (Roth) G. Don from the East Adriatic Coast.},
journal = {Genes},
volume = {14},
number = {2},
pages = {},
pmid = {36833407},
issn = {2073-4425},
mesh = {*Helichrysum/chemistry ; *Oils, Volatile/chemistry ; *Anti-Infective Agents ; },
abstract = {The immortelle (Helichrysum italicum (Roth) G. Don) is a typical perennial plant of natural vegetation in the Mediterranean region, and due to secondary metabolites with several biological properties (anti-inflammatory, antioxidant, antimicrobial, and anti-proliferative), it has become an important species for essential oil production, especially in the cosmetic industry. To increase the production of highly priced essential oils, it has been moved to cultivated fields. However, due to the lack of highly characterized planting material, there is a great need for genotype identification, and to provide a link with chemical profiles and geographic origin as a basis for the identification of local superior genotypes. The aims of the study were to characterize the ITS (ribosomal internal transcribed spacer) regions, ITS1 and ITS2, in samples from the East Adriatic region to determine the possibility of using these regions for plant genetic resources identification. Genetic variation was observed when comparing the ITS sequence variants of samples from the North-East Adriatic and the South-East Adriatic. Some rare and unique ITS sequence variants can be helpful for identifying specific populations from different geographical regions.},
}
@article {pmid36833396,
year = {2023},
author = {Safhi, FA and Alshamrani, SM and Bogmaza, AFM and El-Moneim, DA},
title = {DNA Barcoding of Wild Plants with Potential Medicinal Properties from Faifa Mountains in Saudi Arabia.},
journal = {Genes},
volume = {14},
number = {2},
pages = {},
pmid = {36833396},
issn = {2073-4425},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Saudi Arabia ; *Plants, Medicinal/genetics ; Base Sequence ; },
abstract = {Wild medicinal plants are the main source of active ingredients and provide a continuous natural source for many folk medicinal products, a role that is important for society's health with an impressive record of utilization. Thus, surveying, conserving, and precisely identifying wild medicinal plants is required. The current study aimed to precisely identify fourteen wild-sourced medicinal plants from southwest Saudi Arabia, within the Fifa mountains area located in Jazan province, using the DNA barcoding technique. Two DNA regions (nuclear ITS and chloroplast rbcL) were sequenced and analyzed for the collected species using BLAST-based and phylogeny-based identification methods. Based on our analysis, ten of the fourteen species were successfully identified by DNA barcoding, five were identified as morphologically inspected, and three were morphologically indifferent. The study was able to distinguish some key medicinal species and highlight the importance of combining morphological observation with DNA barcoding to ensure the precise identification of wild plants, especially if they are medicinally relevant and associated with public health and safety usage.},
}
@article {pmid36833271,
year = {2023},
author = {Bourke, BP and Wilkerson, RC and Ruiz-Lopez, F and Justi, SA and Pecor, DB and Quinones, ML and Navarro, JC and Ormaza, JA and Ormaza, JA and González, R and Flores-Mendoza, C and Castro, F and Escovar, JE and Linton, YM},
title = {High Levels of Diversity in Anopheles Subgenus Kerteszia Revealed by Species Delimitation Analyses.},
journal = {Genes},
volume = {14},
number = {2},
pages = {},
pmid = {36833271},
issn = {2073-4425},
mesh = {Animals ; *Malaria ; *Anopheles/genetics ; Mosquito Vectors ; DNA, Mitochondrial/genetics ; },
abstract = {The Anopheles subgenus Kerteszia is a poorly understood group of mosquitoes that includes several species of medical importance. Although there are currently twelve recognized species in the subgenus, previous studies have shown that this is likely to be an underestimate of species diversity. Here, we undertake a baseline study of species delimitation using the barcode region of the mtDNA COI gene to explore species diversity among a geographically and taxonomically diverse range of Kerteszia specimens. Beginning with 10 of 12 morphologically identified Kerteszia species spanning eight countries, species delimitation analyses indicated a high degree of cryptic diversity. Overall, our analyses found support for at least 28 species clusters within the subgenus Kerteszia. The most diverse taxon was Anopheles neivai, a known malaria vector, with eight species clusters. Five other species taxa showed strong signatures of species complex structure, among them Anopheles bellator, which is also considered a malaria vector. There was some evidence for species structure within An. homunculus, although the results were equivocal across delimitation analyses. The current study, therefore, suggests that species diversity within the subgenus Kerteszia has been grossly underestimated. Further work will be required to build on this molecular characterization of species diversity and will rely on genomic level approaches and additional morphological data to test these species hypotheses.},
}
@article {pmid36830468,
year = {2023},
author = {Sanz, N and Franch, N and Araguas, RM and Viñas, J and Vidal, O},
title = {Environmental DNA Assay for the Detection of the American Bullfrog (Lithobates catesbeianus) in the Early Stages of the Invasion in the Ebre Delta.},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {4},
pages = {},
pmid = {36830468},
issn = {2076-2615},
support = {2020/B537//the &#xc0;rea de Protecci&#xf3; i Recerca Parc Natural del Delta de l'Ebre, Generalitat de Catalunya/ ; 2021/B531//the &#xc0;rea de Protecci&#xf3; i Recerca Parc Natural del Delta de l'Ebre, Generalitat de Catalunya/ ; },
abstract = {The American bullfrog (Lithobates catesbeianus) is considered to be one of the most harmful invasive species. In the Iberian Peninsula, this species had been cited occasionally until the year 2018, when L. catesbeianus appeared in the Ebre Delta, and, for the first time, it started breeding in a territory of the Peninsula. Using environmental DNA (eDNA) analysis and visual surveys, the American bullfrog invasion in the Ebre Delta was monitored across two consecutive years (2019-2020). No specimens were observed in 2019, and results for the eDNA survey also failed to detect this species in the Delta. In 2020, two individuals were captured and, under the most conservative criteria to constrain the number of positive detections, eDNA analyses detected the presence of the American bullfrog in at least five locations. Performing an eDNA assay yielded a higher sensitivity with a lower sampling effort than traditional methods. Although the American bullfrog does not appear to still be well-established in the Ebre Delta, only a few bullfrog individuals could be enough for their establishment in suitable habitats. In this context, eDNA assays are essential tools to facilitate the detection, control, and eradication of this species in the first stage of the invasion process.},
}
@article {pmid36830347,
year = {2023},
author = {Wu, F and Zhu, D and Wen, P and Tang, Z and Bao, L and Guan, Y and Ge, J and Wang, H},
title = {Domestic Cattle in a National Park Restricting the Sika Deer Due to Diet Overlap.},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {4},
pages = {},
pmid = {36830347},
issn = {2076-2615},
support = {2019FY101700//National Science and Technology Basic Resources Survey Program of China/ ; 32071494//National Natural Science Foundation of China/ ; 32171654//National Natural Science Foundation of China/ ; },
abstract = {Managers need to know the extent of the conflict between livestock and wild animals. Although many studies have reported the conflict between livestock and wild animals, few have checked the extent of the conflict. Cattle raising in the Northeast Tiger and Leopard National Park is considered one of the main driving forces behind the restricted distribution of sika deer. To understand whether foraging competition is contributing to avoidance patterns between sika deer and cattle, we investigated their feeding habits using DNA barcoding and high-throughput sequencing. Our study shows that although cattle are grazers in the traditional division of herbivores, their diet shifted to a predominance of dicotyledonous woody plants, and this diet shift resulted in a high degree of dietary overlap between sika deer and cattle. Moreover, compared to sika deer, cattle diets are more diverse at the species level with a wider ecological niche. Our results confirm that overlapping dietary niches and the superior competitive abilities of cattle contribute to the restricted distribution of the sika deer, which has critical implications for the conservation of their predators. Our study suggests that cattle grazing should be prohibited in the Park and effective measures should be taken for the benefit of sika deer.},
}
@article {pmid36828541,
year = {2023},
author = {Alharbi, MH and Condemine, C and Hesketh, J and Kayuni, SA and Arme, TM and Archer, J and Jones, S and LaCourse, EJ and Makaula, P and Musaya, J and Stothard, JR},
title = {Biomphalaria pfeifferi (Gastropoda: Planorbidae) in Lake Malawi and Upper Shire River, Mangochi District, Malawi: Distribution, Genetic Diversity and Pre-Patent Schistosome Infections.},
journal = {Tropical medicine and infectious disease},
volume = {8},
number = {2},
pages = {},
pmid = {36828541},
issn = {2414-6366},
support = {/WT_/Wellcome Trust/United Kingdom ; 220818/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; },
abstract = {In November 2017, Biomphalaria pfeifferi, the key intermediate host for Schistosoma mansoni in Africa, was first reported in Lake Malawi, Mangochi District. Two subsequent malacological surveys in 2018 and 2019 confirmed its lacustrine presence, as well as its presence along the Upper Shire River. These surveys provided sufficient specimens for analyses of the genetic structure and a transmission assessment for intestinal schistosomiasis. A total of 76 collected snails were characterized by a DNA sequence analysis of a 650 bp fragment of the mitochondrial cytochrome oxidase subunit 1 (cox1); by size fractionation of six fluorescently labelled microsatellite loci (Bgμl16, Bgμl, Bpf8, rg6, U-7, and rg9);by denaturing PAGE; and by detection of pre-patent Schistosoma infection by real-time PCR with a TaqMan[®] probe. Five closely related cox1 haplotypes were identified, all present within a single location, with only one haplotype common across all the other locations sampled. No allelic size variation was detected with the microsatellites and all loci were monomorphic. Overall, the pre-patent prevalence of Schistosoma spp. was 31%, with infected snails found at several sampling locations. In this part of Lake Malawi, Bi. pfeifferi exhibits low genetic diversity and is clearly being exposed to the miracidia of S. mansoni, which is likely facilitating the autochthonous transmission of this parasite.},
}
@article {pmid36828490,
year = {2023},
author = {Mohd-Azami, SNI and Loong, SK and Khoo, JJ and Husin, NA and Lim, FS and Mahfodz, NH and Ishak, SN and Mohd-Taib, FS and Makepeace, BL and AbuBakar, S},
title = {Molecular Surveillance for Vector-Borne Bacteria in Rodents and Tree Shrews of Peninsular Malaysia Oil Palm Plantations.},
journal = {Tropical medicine and infectious disease},
volume = {8},
number = {2},
pages = {},
pmid = {36828490},
issn = {2414-6366},
support = {ID 332192305//Newton-Ungku Omar Fund/ ; MO002-2019//Ministry of Higher Education, Malaysia/ ; },
abstract = {Many human clinical cases attributed to vector-borne pathogens are underreported in Malaysia, especially in rural localities where healthcare infrastructures are lacking. Here, 217 small mammals, consisting of rodents and tree shrews, were trapped in oil palm plantations in the Peninsular Malaysia states of Johor and Perak. Species identification was performed using morphological and DNA barcoding analyses, and 203 small mammals were included in the detection of selected vector-borne bacteria. The DNA extracted from the spleens was examined for Orientia tsutsugamushi, Borrelia spp., Bartonella spp. and Rickettsia spp. using established PCR assays. The small mammals collected in this study included Rattus tanezumi R3 mitotype (n = 113), Rattus argentiventer (n = 24), Rattus tiomanicus (n = 22), Rattus exulans (n = 17), Rattus tanezumi sensu stricto (n = 1) and Tupaia glis (n = 40). Orientia tsutsugamushi, Borrelia spp. and Bartonella phoceensis were detected in the small mammals with the respective detection rates of 12.3%, 5.9% and 4.9%. Rickettsia spp., however, was not detected. This study encountered the presence of both Lyme disease and relapsing fever-related borreliae in small mammals collected from the oil palm plantation study sites. All three microorganisms (Orientia tsutsugamushi, Borrelia spp. and Bartonella phoceensis) were detected in the R. tanezumi R3 mitotype, suggesting that the species is a competent host for multiple microorganisms. Further investigations are warranted to elucidate the relationships between the ectoparasites, the small mammals and the respective pathogens.},
}
@article {pmid36827376,
year = {2023},
author = {Reyes, M and Leff, SM and Gentili, M and Hacohen, N and Blainey, PC},
title = {Microscale combinatorial stimulation of human myeloid cells reveals inflammatory priming by viral ligands.},
journal = {Science advances},
volume = {9},
number = {8},
pages = {eade5090},
pmid = {36827376},
issn = {2375-2548},
support = {R01 AI153142/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *COVID-19 ; Myeloid Cells ; Ligands ; Lab-On-A-Chip Devices ; Single-Cell Analysis ; },
abstract = {Cells sense a wide variety of signals and respond by adopting complex transcriptional states. Most single-cell profiling is carried out today at cellular baseline, blind to cells' potential spectrum of functional responses. Exploring the space of cellular responses experimentally requires access to a large combinatorial perturbation space. Single-cell genomics coupled with multiplexing techniques provide a useful tool for characterizing cell states across several experimental conditions. However, current multiplexing strategies require programmatic handling of many samples in macroscale arrayed formats, precluding their application in large-scale combinatorial analysis. Here, we introduce StimDrop, a method that combines antibody-based cell barcoding with parallel droplet processing to automatically formulate cell population × stimulus combinations in a microfluidic device. We applied StimDrop to profile the effects of 512 sequential stimulation conditions on human dendritic cells. Our results demonstrate that priming with viral ligands potentiates hyperinflammatory responses to a second stimulus, and show transcriptional signatures consistent with this phenomenon in myeloid cells of patients with severe COVID-19.},
}
@article {pmid36826588,
year = {2023},
author = {Morris, N and Alldred, M and Zarnoch, C and Alter, SE},
title = {Estuarine Sediment Microbiomes from a Chronosequence of Restored Urban Salt Marshes.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {916-930},
pmid = {36826588},
issn = {1432-184X},
mesh = {*Wetlands ; Ecosystem ; RNA, Ribosomal, 16S/genetics/metabolism ; Geologic Sediments/microbiology ; *Microbiota ; Bacteria ; Nitrogen/metabolism ; Carbon/metabolism ; },
abstract = {Salt marshes play an important role in the global nutrient cycle. The sediments in these systems harbor diverse and complex bacterial communities possessing metabolic capacities that provide ecosystem services such as nutrient cycling and removal. On the East Coast of the USA, salt marshes have been experiencing degradation due to anthropogenic stressors. Salt marsh islands within Jamaica Bay, New York City (USA), are surrounded by a large highly urbanized watershed and have declined in area. Restoration efforts have been enacted to reduce further loss, but little is known about how microbial communities develop following restoration activities, or how processes such as nitrogen cycling are impacted. Sediment samples were collected at two sampling depths from five salt marsh islands to characterize the bacterial communities found in marsh sediment including a post-restoration chronosequence of 3-12 years. We used 16s rRNA amplicon sequencing to define alpha and beta diversity, taxonomic composition, and predicted metabolic profile of each sediment sample. We found significant differences in alpha diversity between sampling depths, and significant differences in beta diversity, taxonomic composition, and predicted metabolic capacity among the five sampling locations. The youngest restored site and the degraded natural sampling site exhibited the most distinct communities among the five sites. Our findings suggest that while the salt marsh islands are located in close proximity to each other, they harbor distinct bacterial communities that can be correlated with post-restoration age, marsh health, and other environmental factors such as availability of organic carbon. IMPORTANCE: Salt marshes play a critical role in the global nutrient cycle due to sediment bacteria and their metabolic capacities. Many East Coast salt marshes have experienced significant degradation over recent decades, thought largely to be due to anthropogenic stressors such as nitrogen loading, urban development, and sea-level rise. Salt marsh islands in Jamaica Bay (Queens/Brooklyn NY) are exposed to high water column nitrogen due to wastewater effluent. Several receding marsh islands have been subjected to restoration efforts to mitigate this loss. Little is known about the effect marsh restoration has on bacterial communities, their metabolic capacity, or how they develop post-restoration. Here, we describe the bacterial communities found in marsh islands including a post-restoration chronosequence of 3-12 years and one degraded marsh island that remains unrestored. We found distinct communities at marsh sites, despite their geographic proximity. Differences in diversity and community composition were consistent with changes in organic carbon availability that occur during marsh development, and may result in differences in ecosystem function among sites.},
}
@article {pmid36826012,
year = {2023},
author = {Vu, TTT and Vu, LTK and Le, LT and Lo, TTM and Chu, MH},
title = {Analysis of the Chloroplast Genome of Ficus simplicissima Lour Collected in Vietnam and Proposed Barcodes for Identifying Ficus Plants.},
journal = {Current issues in molecular biology},
volume = {45},
number = {2},
pages = {1024-1036},
pmid = {36826012},
issn = {1467-3045},
abstract = {Ficus simplicissima Lour. is an Asian species of fig tree in the family Moraceae. The chloroplast (cp) genome of F. simplicissima m3 was sequenced using the Pacbio sequel platform. The F. simplicissima cpDNA has a size of 160,321 bp in length, of which GC content accounts for 36.13%. The cp genome of F. simplicissima consists of a single large copy (LSC) with a size of 91,346 bp, a single small copy (SSC) with a size of 20,131 bp, and a pair of inverted repeats with a size of 24,421 to 24,423 bp. The cp genome of F. simplicissima has 127 genes, including 85 protein-coding genes, eight rRNA genes, and 34 tRNA genes; 92 simple sequence repeats and 39 long repeats were detected in the cpDNA of F. simplicissim. A comparative cp genome analysis among six species in the Ficus genus indicated that the genome structure and gene content were highly conserved. The non-coding regions show more differentiation than the coding regions, and the LSC and SSC regions show more differences than the inverted repeat regions. Phylogenetic analysis supported that F. simplicissima m3 had a close relationship with F. hirta. The complete cp genome of F. simplicissima was proposed as a chloroplast DNA barcoding for genus-level in the Moraceae family and the psbA-trnH gene region for species-level identification.},
}
@article {pmid36824753,
year = {2023},
author = {Yuan, L and Chen, X and Zhan, H and Gilbert, HL and Zador, AM},
title = {Massive Multiplexing of Spatially Resolved Single Neuron Projections with Axonal BARseq.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {36824753},
issn = {2692-8205},
support = {RF1 MH123403/MH/NIMH NIH HHS/United States ; U19 NS123716/NS/NINDS NIH HHS/United States ; },
abstract = {Neurons in the cortex are heterogenous, sending diverse axonal projections to multiple brain regions. Unraveling the logic of these projections requires single-neuron resolution. Although a growing number of techniques have enabled high-throughput reconstruction, these techniques are typically limited to dozens or at most hundreds of neurons per brain, requiring that statistical analyses combine data from different specimens. Here we present axonal BARseq, a high-throughput approach based on reading out nucleic acid barcodes using in situ RNA sequencing, which enables analysis of even densely labeled neurons. As a proof of principle, we have mapped the long-range projections of >8000 mouse primary auditory cortex neurons from a single brain. We identified major cell types based on projection targets and axonal trajectory. The large sample size enabled us to systematically quantify the projections of intratelencephalic (IT) neurons, and revealed that individual IT neurons project to different layers in an area-dependent fashion. Axonal BARseq is a powerful technique for studying the heterogeneity of single neuronal projections at high throughput within individual brains.},
}
@article {pmid36816806,
year = {2022},
author = {Ndobe, S and Nurdin, MS and Hasanah, N and Putra, AE and Mansyur, K and Nasir, M and Rabuna, ML and Moore, AM},
title = {DNA barcoding detects resurrected taxon Giuris laglaizei (Sauvage 1880) in Sulawesi, Indonesia: Bolano Sau Lake payangka phylogeny, phenotypic characters and implications for Giuris spp. conservation.},
journal = {F1000Research},
volume = {11},
number = {},
pages = {295},
pmid = {36816806},
issn = {2046-1402},
mesh = {Animals ; Female ; Male ; Phylogeny ; *Lakes ; Indonesia ; DNA Barcoding, Taxonomic ; *Perciformes/genetics ; Fishes/genetics ; DNA ; },
abstract = {Background: The freshwater ichthyofauna of Wallacea is diverse and understudied. A baseline survey of Bolano Sau Lake in Parigi Moutong District, Central Sulawesi Province, Indonesia in 2019 found an eleotrid goby (local name payangka) with characters conforming to the genus Giuris, long considered monophyletic as G. margaritacea/G. margaritaceus but recently found to comprise at least eight species. This study focused on the molecular (DNA barcoding) identification and phenotypic characters of the payangka. Methods: Payangka samples were collected from August to December 2019 in collaboration with local fishermen, weighed and measured, and preserved in 75% ethanol. Length, weight, sex (n=111) and 17 morphometric characters/six meristic counts (n=42) were recorded. DNA barcoding was performed on a fin clipping preserved in 96% ethanol. Homologous nucleotide sequences were obtained from public (GenBank and BOLD) databases, analysis conducted in MEGA X, and phylogenetic trees edited in the Interactive Tree of Life (iToL). Results: Within the deeply divided Giuris clade, the payangka sequence resolved into a sub-clade identified as Giuris laglaizei (Sauvage 1880), a recently resurrected taxon, based on a sequence provided by Philippe Keith. The length-weight relationship (L = 0.0087∙W3.162) indicated mildly allometric positive growth. Size distribution differed significantly between male and female fish with significantly larger mean size of males (13.56 cm) than females (11.62 cm). The meristic formula was: D VI-I,8 A I,8 P 13 V I,5 C15. Phylogenetic analysis indicated four Giuris species in wetlands around Tomini Bay and five in Sulawesi. Conclusions: This first record of G. laglaizei in Indonesia advances knowledge of Wallacean and Indo-Pacific Gobiiformes biogeography and highlights the need for a revision of the conservation status of the taxa currently grouped under Giuris margaritacea/G. margaritaceus in the IUCN Red List and FishBase databases. The data will inform biodiversity and fisheries management at local and regional levels.},
}
@article {pmid36821543,
year = {2023},
author = {González, C and Ballesteros-Mejia, L and Díaz-Díaz, J and Toro-Vargas, DM and Amarillo-Suarez, AR and Gey, D and León, C and Tovar, E and Arias, M and Rivera, N and Buitrago, LS and Pinto-Moraes, RH and Sano Martins, IS and Decaëns, T and González, MA and Kitching, IJ and Rougerie, R},
title = {Deadly and venomous Lonomia caterpillars are more than the two usual suspects.},
journal = {PLoS neglected tropical diseases},
volume = {17},
number = {2},
pages = {e0011063},
pmid = {36821543},
issn = {1935-2735},
mesh = {Animals ; Humans ; Larva ; *Arthropod Venoms/toxicity ; *Moths ; Hemorrhage ; South America ; },
abstract = {Caterpillars of the Neotropical genus Lonomia (Lepidoptera: Saturniidae) are responsible for some fatal envenomation of humans in South America inducing hemostatic disturbances in patients upon skin contact with the caterpillars' spines. Currently, only two species have been reported to cause hemorrhagic syndromes in humans: Lonomia achelous and Lonomia obliqua. However, species identifications have remained largely unchallenged despite improved knowledge of venom diversity and growing evidence that the taxonomy used over past decades misrepresents and underestimates species diversity. Here, we revisit the taxonomic diversity and distribution of Lonomia species using the most extensive dataset assembled to date, combining DNA barcodes, morphological comparisons, and geographical information. Considering new evidence for seven undescribed species as well as three newly proposed nomenclatural changes, our integrative approach leads to the recognition of 60 species, of which seven are known or strongly suspected to cause severe envenomation in humans. From a newly compiled synthesis of epidemiological data, we also examine the consequences of our results for understanding Lonomia envenomation risks and call for further investigations of other species' venom activities. This is required and necessary to improve alertness in areas at risk, and to define adequate treatment strategies for envenomed patients, including performing species identification and assessing the efficacy of anti-Lonomia serums against a broader diversity of species.},
}
@article {pmid36819854,
year = {2023},
author = {Huang, XD and Hong, BK and Wen, GH and Li, SH and Zheng, LM},
title = {Photo-controllable heterostructured crystals of metal-organic frameworks via reversible photocycloaddition.},
journal = {Chemical science},
volume = {14},
number = {7},
pages = {1852-1860},
pmid = {36819854},
issn = {2041-6520},
abstract = {Metal-organic framework (MOF)-based heterostructures are attractive because they can provide versatile platforms for various applications but are limited by complex liquid epitaxial growth methods. Here, we employ photolithography to fabricate and control MOF-based heterostructured crystals via [4 + 4] photocycloaddition. A layered dysprosium-dianthracene framework, [Dy(NO3)3(depma2)1.5]·(depma2)0.5 (2) [depma2 = pre-photodimerized 9-diethylphosphonomethylanthracene (depma)] underwent a single-crystal-to-single-crystal transition at 140 °C to form [Dy(NO3)3(depma)(depma2)]·(depma2)0.5 (3). The dissociated anthracene moieties are face-to-face π-π interacted allowing a reversible photocycloaddition between 2 and 3. This structural transformation causes a luminescence switch between blue and yellow-green and thus can be used to fabricate erasable 2 + 3 heterostructured crystals for rewritable photonic barcodes. The internal strain at the heterostructure interface leads to photobending and straightening of the crystal, a photomechanical response that is fast, reversible and durable, even operating at 140 °C, making it promising for photoactuation. This work may inspire the development of intelligent MOF-based heterostructures for photonic applications.},
}
@article {pmid36819662,
year = {2023},
author = {Richman, LP and Goyal, Y and Jiang, CL and Raj, A},
title = {ClonoCluster: A method for using clonal origin to inform transcriptome clustering.},
journal = {Cell genomics},
volume = {3},
number = {2},
pages = {100247},
pmid = {36819662},
issn = {2666-979X},
support = {R01 CA238237/CA/NCI NIH HHS/United States ; U01 CA227550/CA/NCI NIH HHS/United States ; },
abstract = {Clustering cells based on their high-dimensional profiles is an important data reduction process by which researchers infer distinct cellular states. The advent of cellular barcoding, however, provides an alternative means by which to group cells: by their clonal origin. We developed ClonoCluster, a computational method that combines both clone and transcriptome information to create hybrid clusters that weight both kinds of data with a tunable parameter. We generated hybrid clusters across six independent datasets and found that ClonoCluster generated qualitatively different clusters in all cases. The markers of these hybrid clusters were different but had equivalent fidelity to transcriptome-only clusters. The genes most strongly associated with the rearrangements in hybrid clusters were ribosomal function and extracellular matrix genes. We also developed the complementary tool Warp Factor that incorporates clone information in popular 2D visualization techniques like UMAP. Integrating ClonoCluster and Warp Factor revealed biologically relevant markers of cell identity.},
}
@article {pmid36818783,
year = {2023},
author = {Olds, CG and Berta-Thompson, JW and Loucks, JJ and Levy, RA and Wilson, AW},
title = {Applying a modified metabarcoding approach for the sequencing of macrofungal specimens from fungarium collections.},
journal = {Applications in plant sciences},
volume = {11},
number = {1},
pages = {e11508},
pmid = {36818783},
issn = {2168-0450},
support = {P30 GM103324/GM/NIGMS NIH HHS/United States ; R01 GM126463/GM/NIGMS NIH HHS/United States ; },
abstract = {PREMISE: Fungaria are an underutilized resource for understanding fungal biodiversity. The effort and cost of producing DNA barcode sequence data for large numbers of fungal specimens can be prohibitive. This study applies a modified metabarcoding approach that provides a labor-efficient and cost-effective solution for sequencing the fungal DNA barcodes of hundreds of specimens at once.<br><br>METHODS: We applied a two-step PCR approach using nested, barcoded primers to sequence the fungal nrITS2 region of 766 macrofungal specimens using the Illumina platform. The specimens represent a broad taxonomic sampling of the Dikarya. Of these, 382 Lactarius specimens were analyzed to identify molecular operational taxonomic units (MOTUs) using a phylogenetic approach. The raw sequences were trimmed, filtered, assessed, and analyzed using the DADA2 amplicon de-noising toolkit and Biopython. The sequences were compared to the NCBI and UNITE databases and Sanger nrITS sequences from the same specimens.<br><br>RESULTS: The taxonomic identities derived from the nrITS2 sequence data were >90% accurate across all specimens sampled. A phylogenetic analysis of the Lactarius sequences identified 20 MOTUs.<br><br>DISCUSSION: The results demonstrate the capacity of these methods to produce nrITS2 sequences from large numbers of fungarium specimens. This provides an opportunity to more effectively use fungarium collections to advance fungal diversity identification and documentation.},
}
@article {pmid36815562,
year = {2023},
author = {Aires, A and Gonçalves, C and Sampaio, JP},
title = {Hannaella floricola sp. nov., a novel basidiomycetous yeast species isolated from a flower of Lantana camara in Portugal.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {73},
number = {2},
pages = {},
doi = {10.1099/ijsem.0.005740},
pmid = {36815562},
issn = {1466-5034},
mesh = {DNA, Fungal/genetics ; *Lantana/genetics ; Phylogeny ; Portugal ; DNA, Ribosomal Spacer/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Mycological Typing Techniques ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Base Composition ; Fatty Acids/chemistry ; *Ascomycota/genetics ; Flowers ; *Basidiomycota ; },
abstract = {During a survey of floricolous yeasts in Portugal, a basidiomycetous yeast representing a novel species in the genus Hannaella was isolated in Portugal from the flower of Lantana camara, an ornamental exotic species native to Central and South America. A combination of phylogenetic analyses of DNA barcode sequences used in yeast molecular systematics, namely the D1/D2 domain and the complete internal transcribed spacer (ITS) region supported the recognition of a new species of Hannaella, that we designate Hannaella floricola sp. nov. (ex-type strain PYCC 9191[T]=CBS 18097[T]). Although the assignment of the new species to the genus Hannaella was evident, the detection of its closest relatives appeared more problematic. Nevertheless, our analyses suggested that H. floricola sp. nov. belongs a clade that also includes H. coprosmae, H. oryzae and H. surugaensis, together four candidate novel species. In addition we provide the molecular identification of several unidentified strains whose D1/D2 and ITS sequences are available from GenBank.},
}
@article {pmid36810591,
year = {2023},
author = {Sathe, LM and Khan, NN and Williams, JM and Saul, R and Jajieh, K and Sartippour, MR and Young, R and Xie, J and Marquette, DM and Duncan, T and Eskin, E and Arboleda, VA},
title = {3D Printing as an Effective Quality Assurance Implementation in Massive-Scale SARS-CoV-2 Testing at a SwabSeq Next-Generation Sequencing Laboratory.},
journal = {Laboratory medicine},
volume = {54},
number = {5},
pages = {512-518},
doi = {10.1093/labmed/lmac161},
pmid = {36810591},
issn = {1943-7730},
mesh = {Humans ; *SARS-CoV-2/genetics ; *COVID-19/diagnosis ; COVID-19 Testing ; High-Throughput Nucleotide Sequencing ; Printing, Three-Dimensional ; Plastics ; },
abstract = {Massive-scale SARS-CoV-2 testing using the SwabSeq diagnostic platform came with quality assurance challenges due to the novelty and scale of sequencing-based testing. The SwabSeq platform relies on accurate mapping between specimen identifiers and molecular barcodes to match a result back to a patient specimen. To identify and mitigate mapping errors, we instituted quality control using placement of negative controls within a rack of patient samples. We designed 2-dimensional paper templates to fit over a 96-position rack of specimens with holes to show the control tube placements. We designed and 3-dimensionally printed plastic templates that fit onto 4 racks of patient specimens and provide accurate indications of the correct control tube placements. The final plastic templates dramatically reduced plate mapping errors from 22.55% in January 2021 to less than 1% after implementation and training in January 2021. We show how 3D printing can be a cost-effective quality assurance tool to mitigate human error in the clinical laboratory.},
}
@article {pmid36807069,
year = {2023},
author = {Zhu, C and Wang, Z and Ren, B},
title = {Single-Cell Joint Profiling of Open Chromatin and Transcriptome by Paired-Seq.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2611},
number = {},
pages = {155-185},
pmid = {36807069},
issn = {1940-6029},
support = {R00 HG011483/HG/NHGRI NIH HHS/United States ; R01 AG066018/AG/NIA NIH HHS/United States ; K99 HG011483/HG/NHGRI NIH HHS/United States ; U19 MH114831/MH/NIMH NIH HHS/United States ; U01 MH121282/MH/NIMH NIH HHS/United States ; },
mesh = {*Chromatin ; *Transcriptome ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Gene Library ; Single-Cell Analysis/methods ; },
abstract = {Simultaneous detection of chromatin accessibility and transcription from the same cells promises to greatly facilitate the dissection of cell-type-specific gene regulatory programs in complex tissues. Paired-seq enables joint analysis of open chromatin and nuclear transcriptome from up to a million cells in parallel. It achieves ultra-high-throughput single-cell multiomics with the use of a combinatorial barcoding strategy involving sequential ligation of multiplexed DNA barcodes to chromatin DNA fragments and reverse transcription products, followed by high-throughput DNA sequencing of the resulting DNA libraries and deconvolution of single-cell multiomic maps based on cell-specific barcodes.},
}
@article {pmid36806111,
year = {2023},
author = {Aykur, M and Calıskan Kurt, C and Dirim Erdogan, D and Biray Avcı, C and Vardar, R and Aydemir, S and Girginkardesler, N and Gunduz, C and Dagci, H},
title = {Distribution and Phylogenetic Analysis of Subtypes and Alleles of Blastocystis sp. in the Stool Samples Collected from Patients with Gastrointestinal Complaints in İzmir, Turkey.},
journal = {Acta parasitologica},
volume = {68},
number = {2},
pages = {304-316},
pmid = {36806111},
issn = {1896-1851},
support = {13-TIP-092//Ege University Research Foundation/ ; },
mesh = {Animals ; Humans ; *Blastocystis ; *Blastocystis Infections/epidemiology/parasitology ; Phylogeny ; Alleles ; Turkey/epidemiology ; Interleukin-1 Receptor-Like 1 Protein/genetics ; Feces/parasitology ; Diarrhea/parasitology ; DNA, Protozoan/genetics ; Genetic Variation ; },
abstract = {PURPOSE: Blastocystis sp. is one of the most prevalent intestinal protozoa found in humans and many other animals. The present study aimed to examine the distribution and genetic diversity of Blastocystis sp. in stool samples from patients with gastrointestinal complaints in İzmir, Turkey.<br><br>METHODS: All stool samples of 439 patients with gastrointestinal complaints were examined by native-Lugol and trichrome staining. To investigate the presence of Blastocystis sp. in stool samples, DNA was isolated, and PCR was performed with the barcode region in the SSU rRNA gene. PCR positive samples were sequenced to identify subtypes and alleles of Blastocystis sp.<br><br>RESULTS: The prevalence of Blastocystis sp. was found to be 16.6% (73/439) in patients with gastrointestinal complaints in &#x130;zmir, Turkey. Three different Blastocystis sp. subtypes were identified. ST3 (28/55; 51.0%) was the most common subtype followed by ST2 (19/55; 34.5%) and ST1 (8/55; 14.5%). Itching and diarrhea were the most prominent clinical symptoms in Blastocystis sp. positive patients. When clinical symptoms and subtypes were compared, diarrhea was found in 62.5%, 47.4%, and 46.4% of patients with ST1, ST2, and ST3 subtypes, respectively. In addition, itching was found in 37.5%, 32.1%, and 21.1% of patients with ST1, ST3, and ST2, respectively. Six distinct alleles were identified by allele analysis of Blastocystis 18S rRNA gene: allele 4 for ST1, alleles 9, 11, and 12 for ST2, and alleles 34 and 36 for ST3. In this study, Blastocystis sp. was detected in 16 of 21 districts, including the central and rural districts of &#x130;zmir. Although ST1 was detected in central districts, it was not found in rural districts.<br><br>CONCLUSION: This study provides comprehensive data on the prevalence and molecular epidemiology of the genetic diversity at the level of subtypes and alleles of Blastocystis sp. in different districts of &#x130;zmir province in Turkey. To the best of our knowledge, this is the first study which evaluates the distribution of subtypes and alleles of Blastocystis sp. according to PCR and SSU rRNA gene sequencing in patients with gastrointestinal complaints in different districts of &#x130;zmir province in Turkey.},
}
@article {pmid36805273,
year = {2023},
author = {Zhang, B and Tang, WS and Ding, SN},
title = {Magnetic quantum dots barcodes using Fe3O4/TiO2 with weak spectral absorption in the visible region for high-sensitivity multiplex detection of tumor markers.},
journal = {Biosensors &amp; bioelectronics},
volume = {227},
number = {},
pages = {115153},
doi = {10.1016/j.bios.2023.115153},
pmid = {36805273},
issn = {1873-4235},
mesh = {*Quantum Dots ; Biomarkers, Tumor ; *Biosensing Techniques ; Magnetic Phenomena ; },
abstract = {Magnetic quantum dot (QD) barcode holds great potential for automatic suspension array and rapid point-of-care detection since it enables simultaneous target encoding, enrichment and separation. However, a serious obstacle to enhancing the encoding capacity of magnetic QD microbeads (MBs) is the fluorescence quenching of magnetic nanoparticles (MNPs) to quantum dots (QDs) in the visible wavelength range due to the broad and strong optical absorption spectrum of MNPs. Here, we report Fe3O4/TiO2 core/shell MNPs and CdSe/ZnS QDs for the construction of dual-function magnetic QD barcodes. Fe3O4/TiO2 MNPs can significantly inhibit fluorescence quenching because the weak absorption of visible light by the TiO2. The two-dimension barcode library of 30 magnetic QD barcodes was constructed based on Fe3O4/TiO2 MNPs and CdSe/ZnS QDs. Moreover, the magnetic QD barcodes showed high sensitivity for the multiplex detection of four tumor markers, cancer antigen 125 (CA125), cancer antigen 199 (CA199), alpha-fetoprotein (AFP), and neuron specific enolase (NSE) with detection limits of 0.89 KU/L, 0.72 KU/L, 0.05 ng/mL, and 0.15 ng/mL, respectively. This bifunctional magnetic QD barcodes are promising for automatic high-sensitivity multiplex bioassay.},
}
@article {pmid36801925,
year = {2023},
author = {Sabin, S and Jones, S and Patel, D and Subramaniam, G and Kelley, J and Aidoo, M and Talundzic, E},
title = {Portable and cost-effective genetic detection and characterization of Plasmodium falciparum hrp2 using the MinION sequencer.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {2893},
pmid = {36801925},
issn = {2045-2322},
mesh = {Humans ; *Plasmodium falciparum/genetics ; Antigens, Protozoan/genetics ; Protozoan Proteins/genetics ; *Malaria, Falciparum/epidemiology ; Cost-Benefit Analysis ; Diagnostic Tests, Routine/methods ; Gene Deletion ; },
abstract = {The prevalence of Plasmodium falciparum hrp2 (pfhrp2)-deleted parasites threatens the efficacy of the most used and sensitive malaria rapid diagnostic tests and highlights the need for continued surveillance for this gene deletion. While PCR methods are adequate for determining pfhrp2 presence or absence, they offer a limited view of its genetic diversity. Here, we present a portable sequencing method using the MinION. Pfhrp2 amplicons were generated from individual samples, barcoded, and pooled for sequencing. To overcome potential crosstalk between barcodes, we implemented a coverage-based threshold for pfhrp2 deletion confirmation. Amino acid repeat types were then counted and visualized with custom Python scripts following de novo assembly. We evaluated this assay using well-characterized reference strains and 152 field isolates with and without pfhrp2 deletions, of which 38 were also sequenced on the PacBio platform to provide a standard for comparison. Of 152 field samples, 93 surpassed the positivity threshold, and of those samples, 62/93 had a dominant pfhrp2 repeat type. PacBio-sequenced samples with a dominant repeat-type profile from the MinION sequencing data matched the PacBio profile. This field-deployable assay can be used alone for surveilling pfhrp2 diversity or as a sequencing-based addition to the World Health Organization's existing deletion surveillance protocol.},
}
@article {pmid36801401,
year = {2023},
author = {Baker, LA and Beauger, A and Kolovi, S and Voldoire, O and Allain, E and Breton, V and Chardon, P and Miallier, D and Bailly, C and Montavon, G and Bouchez, A and Rimet, F and Chardon, C and Vasselon, V and Ector, L and Wetzel, CE and Biron, DG},
title = {Diatom DNA metabarcoding to assess the effect of natural radioactivity in mineral springs on ASV of benthic diatom communities.},
journal = {The Science of the total environment},
volume = {873},
number = {},
pages = {162270},
doi = {10.1016/j.scitotenv.2023.162270},
pmid = {36801401},
issn = {1879-1026},
mesh = {Ecosystem ; *Diatoms/genetics ; DNA Barcoding, Taxonomic ; *Radioactivity ; Minerals ; },
abstract = {Little is still known about the low dose effects of radiation on the microbial communities in the environment. Mineral springs are ecosystems than can be affected by natural radioactivity. These extreme environments are, therefore, observatories for studying the influence of chronic radioactivity on the natural biota. In these ecosystems we find diatoms, unicellular microalgae, playing an essential role in the food chain. The present study aimed to investigate, using DNA metabarcoding, the effect of natural radioactivity in two environmental compartments (i.e. spring sediments and water) on the genetic richness, diversity and structure of diatom communities in 16 mineral springs in the Massif Central, France. Diatom biofilms were collected during October 2019, and a 312 bp region of the chloroplast gene rbcL (coding for the Ribulose Bisphosphate Carboxylase) used as a barcode for taxonomic assignation. A total of 565 amplicon sequence variants (ASV) were found. The dominant ASV were associated with Navicula sanctamargaritae, Gedaniella sp., Planothidium frequentissimum, Navicula veneta, Diploneis vacillans, Amphora copulata, Pinnularia brebissonii, Halamphora coffeaeformis, Gomphonema saprophilum, and Nitzschia vitrea, but some of the ASVs could not be assigned at the species level. Pearson correlation failed to show a correlation between ASV' richness and radioactivity parameters. Non-parametric MANOVA analysis based on ASVs occurrence or abundances revealed that geographical location was the main factor influencing ASVs distribution. Interestingly, [238]U was the second factor that explained diatom ASV structure. Among the ASVs in the mineral springs monitored, ASV associated with one of the genetic variants of Planothidium frequentissimum was well represented in the springs and with higher levels of [238]U, suggesting its high tolerance to this particular radionuclide. This diatom species may therefore represent a bio-indicator of high natural levels of uranium.},
}
@article {pmid36798377,
year = {2023},
author = {Baryshev, A and La Fleur, A and Groves, B and Michel, C and Baker, D and Ljubetič, A and Seelig, G},
title = {Massively parallel protein-protein interaction measurement by sequencing (MP3-seq) enables rapid screening of protein heterodimers.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {36798377},
issn = {2692-8205},
abstract = {Protein-protein interactions (PPIs) regulate many cellular processes, and engineered PPIs have cell and gene therapy applications. Here we introduce massively parallel protein-protein interaction measurement by sequencing (MP3-seq), an easy-to-use and highly scalable yeast-two-hybrid approach for measuring PPIs. In MP3-seq, DNA barcodes are associated with specific protein pairs, and barcode enrichment can be read by sequencing to provide a direct measure of interaction strength. We show that MP3-seq is highly quantitative and scales to over 100,000 interactions. We apply MP3-seq to characterize interactions between families of rationally designed heterodimers and to investigate elements conferring specificity to coiled-coil interactions. Finally, we predict coiled heterodimer structures using AlphaFold-Multimer (AF-M) and train linear models on physics simulation energy terms to predict MP3-seq values. We find that AF-M and AF-M complex prediction-based models could be valuable for pre-screening interactions, but that measuring interactions experimentally remains necessary to rank their strengths quantitatively.},
}
@article {pmid36798358,
year = {2023},
author = {Olsen, TR and Talla, P and Furnari, J and Bruce, JN and Canoll, P and Zha, S and Sims, PA},
title = {Scalable co-sequencing of RNA and DNA from individual nuclei.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {36798358},
issn = {2692-8205},
support = {R01 CA275184/CA/NCI NIH HHS/United States ; R01 NS103473/NS/NINDS NIH HHS/United States ; U54 CA209997/CA/NCI NIH HHS/United States ; },
abstract = {The ideal technology for directly investigating the relationship between genotype and phenotype would analyze both RNA and DNA genome-wide and with single-cell resolution. However, existing tools lack the throughput required for comprehensive analysis of complex tumors and tissues. We introduce a highly scalable method for jointly profiling DNA and expression following nucleosome depletion (DEFND-seq). In DEFND-seq, nuclei are nucleosome-depleted, tagmented, and separated into individual droplets for mRNA and genomic DNA barcoding. Once nuclei have been depleted of nucleosomes, subsequent steps can be performed using the widely available 10x Genomics droplet microfluidic technology and commercial kits without experimental modification. We demonstrate the production of high-complexity mRNA and gDNA sequencing libraries from thousands of individual nuclei from both cell lines and archived surgical specimens for associating gene expression phenotypes with both copy number and single nucleotide variants.},
}
@article {pmid36796537,
year = {2023},
author = {Tang, X and Chen, J and Zhang, X and Liu, X and Xie, Z and Wei, K and Qiu, J and Ma, W and Lin, C and Ke, R},
title = {Improved in situ sequencing for high-resolution targeted spatial transcriptomic analysis in tissue sections.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {50},
number = {9},
pages = {652-660},
doi = {10.1016/j.jgg.2023.02.004},
pmid = {36796537},
issn = {1673-8527},
mesh = {*Transcriptome/genetics ; *Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; },
abstract = {Spatial transcriptomics enables the study of localization-indexed gene expression activity in tissues, providing the transcriptional landscape that in turn indicates the potential regulatory networks of gene expression. In situ sequencing (ISS) is a targeted spatial transcriptomic technique, based on padlock probe and rolling circle amplification combined with next-generation sequencing chemistry, for highly multiplexed in situ gene expression profiling. Here, we present improved in situ sequencing (IISS) that exploits a new probing and barcoding approach, combined with advanced image analysis pipelines for high-resolution targeted spatial gene expression profiling. We develop an improved combinatorial probe anchor ligation chemistry using a 2-base encoding strategy for barcode interrogation. The new encoding strategy results in higher signal intensity as well as improved specificity for in situ sequencing, while maintaining a streamlined analysis pipeline for targeted spatial transcriptomics. We show that IISS can be applied to both fresh frozen tissue and formalin-fixed paraffin-embedded tissue sections for single-cell level spatial gene expression analysis, based on which the developmental trajectory and cell-cell communication networks can also be constructed.},
}
@article {pmid36793230,
year = {2023},
author = {Vogel, S and Taraschewski, H},
title = {Intermediate host patterns of acanthocephalans in the Weser river system: co-invasion vs host capture.},
journal = {Parasitology},
volume = {150},
number = {5},
pages = {426-433},
pmid = {36793230},
issn = {1469-8161},
mesh = {Animals ; Rivers ; Ecosystem ; Phylogeny ; Host-Parasite Interactions ; *Acanthocephala/physiology ; *Amphipoda/parasitology ; *Parasites ; *Anguilla ; },
abstract = {Anthropogenic interference is a major driver of ecological change in freshwater ecosystems. Pollution and the introduction of new species not only alter macrozoobenthic community structures, but can also affect their respective parasite communities. The ecology of the Weser river system experienced a drastic decline in biodiversity over the past century due to salinization caused by the local potash industry. As a response, the amphipod Gammarus tigrinus was released into the Werra in 1957. A few decades after the introduction and subsequent spread of this North American species, its natural acanthocephalan Paratenuisentis ambiguus was recorded in the Weser in 1988, where it had captured the European eel Anguilla anguilla as a novel host. To assess the recent ecological changes in the acanthocephalan parasite community, we investigated gammarids and eel in the Weser river system. In addition to P. ambiguus, 3 Pomphorhynchus species and Polymorphus cf. minutus were discovered. The introduced G. tigrinus serves as a novel intermediate host for the acanthocephalans Pomphorhynchus tereticollis and P. cf. minutus in the tributary Werra. Pomphorhynchus laevis is persistent in the tributary Fulda in its indigenous host Gammarus pulex. Pomphorhynchus bosniacus colonized the Weser with its Ponto-Caspian intermediate host Dikerogammarus villosus. This study highlights the anthropogenically driven changes in ecology and evolution in the Weser river system. Based on morphological and phylogenetic identification, the shifts in distribution and host usage described here for the first time contribute to the puzzling taxonomy of the genus Pomphorhynchus in times of ecological globalization.},
}
@article {pmid36790858,
year = {2023},
author = {Liu, X and Feng, H and Lü, Z and Xia, K},
title = {Persistent Tor-algebra for protein-protein interaction analysis.},
journal = {Briefings in bioinformatics},
volume = {24},
number = {2},
pages = {},
doi = {10.1093/bib/bbad046},
pmid = {36790858},
issn = {1477-4054},
mesh = {*Protein Interaction Mapping ; *Proteins/chemistry ; Protein Interaction Maps ; },
abstract = {Protein-protein interactions (PPIs) play crucial roles in almost all biological processes from cell-signaling and membrane transport to metabolism and immune systems. Efficient characterization of PPIs at the molecular level is key to the fundamental understanding of PPI mechanisms. Even with the gigantic amount of PPI models from graphs, networks, geometry and topology, it remains as a great challenge to design functional models that efficiently characterize the complicated multiphysical information within PPIs. Here we propose persistent Tor-algebra (PTA) model for a unified algebraic representation of the multiphysical interactions. Mathematically, our PTA is inherently algebraic data analysis. In our PTA model, protein structures and interactions are described as a series of face rings and Tor modules, from which PTA model is developed. The multiphysical information within/between biomolecules are implicitly characterized by PTA and further represented as PTA barcodes. To test our PTA models, we consider PTA-based ensemble learning for PPI binding affinity prediction. The two most commonly used datasets, i.e. SKEMPI and AB-Bind, are employed. It has been found that our model outperforms all the existing models as far as we know. Mathematically, our PTA model provides a highly efficient way for the characterization of molecular structures and interactions.},
}
@article {pmid36789335,
year = {2023},
author = {Liu, Q and Gao, Y and Dong, W and Zhao, L},
title = {Plastome evolution and phylogeny of the tribe Ruteae (Rutaceae).},
journal = {Ecology and evolution},
volume = {13},
number = {2},
pages = {e9821},
pmid = {36789335},
issn = {2045-7758},
abstract = {Rutaceae is a large family, and the genus-level classification in the subfamilies or tribes of this family is not unified based on different taxonomic treatments. Until now, phylogenetic relationships of some genera in traditional tribe Ruteae have not been clearly resolved. In this study, seven new complete plastomes of this tribe were sequenced, and a comparative analysis was performed to investigate their plastome characteristics and evolution. In addition, we inferred the phylogenetic relationships of Ruteae based on complete plastome and nuclear ITS data. All plastomes exhibited a typical quadripartite structure and were relatively conserved in their structure and gene arrangement. Their genome sizes ranged from 154,656 bp to 160,677 bp, and the size variation was found to be associated with differences in IR expansion and gene loss. A total of 112 to 114 genes were identified in the genomes, including 78 to 79 protein-coding genes, 30 tRNA genes, 4 rRNA genes, and 2 pseudogenes. Sequence divergence analysis indicated that non-coding regions exhibited a higher percentage of variable characters, and nine non-coding and six coding regions were identified as divergent hotspots. Phylogenetic results based on different datasets showed that this tribe was divided into three reciprocally exclusive groups. The phylogenetic analyses between plastome and nuclear ITS data were partly incongruent with each other. This study provides new insights into plastome evolution of Ruteae as well as Rutaceae. The availability of these plastomes provides useful genomic resources for molecular DNA barcodes and phylogenetically informative markers and deepens our understanding of the phylogeny in Ruteae.},
}
@article {pmid36789279,
year = {2022},
author = {Crous, PW and Begoude, BAD and Boers, J and Braun, U and Declercq, B and Dijksterhuis, J and Elliott, TF and Garay-Rodriguez, GA and Jurjević, &#x17d; and Kruse, J and Linde, CC and Loyd, A and Mound, L and Osieck, ER and Rivera-Vargas, LI and Quimbita, AM and Rodas, CA and Roux, J and Schumacher, RK and Starink-Willemse, M and Thangavel, R and Trappe, JM and van Iperen, AL and Van Steenwinkel, C and Wells, A and Wingfield, MJ and Yilmaz, N and Groenewald, JZ},
title = {New and Interesting Fungi. 5.},
journal = {Fungal systematics and evolution},
volume = {10},
number = {},
pages = {19-90},
pmid = {36789279},
issn = {2589-3831},
abstract = {Nine new genera, 17 new species, nine new combinations, seven epitypes, three lectotypes, one neotype, and 14 interesting new host and / or geographical records are introduced in this study. New genera: Neobarrmaelia (based on Neobarrmaelia hyphaenes), Neobryochiton (based on Neobryochiton narthecii), Neocamarographium (based on Neocamarographium carpini), Nothocladosporium (based on Nothocladosporium syzygii), Nothopseudocercospora (based on Nothopseudocercospora dictamni), Paracamarographium (based on Paracamarographium koreanum), Pseudohormonema (based on Pseudohormonema sordidus), Quasiphoma (based on Quasiphoma hyphaenes), Rapidomyces (based on Rapidomyces narthecii). New species: Ascocorticium sorbicola (on leaves of Sorbus aucuparia, Belgium), Dactylaria retrophylli (on leaves of Retrophyllum rospigliosii, Colombia), Dactylellina miltoniae (on twigs of Miltonia clowesii, Colombia), Exophiala eucalyptigena (on dead leaves of Eucalyptus viminalis subsp. viminalis supporting Idolothrips spectrum, Australia), Idriellomyces syzygii (on leaves of Syzygium chordatum, South Africa), Microcera lichenicola (on Parmelia sulcata, Netherlands), Neobarrmaelia hyphaenes (on leaves of Hyphaene sp., South Africa), Neobryochiton narthecii (on dead leaves of Narthecium ossifragum, Netherlands), Niesslia pseudoexilis (on dead leaf of Quercus petraea, Serbia), Nothocladosporium syzygii (on leaves of Syzygium chordatum, South Africa), Nothotrimmatostroma corymbiae (on leaves of Corymbia henryi, South Africa), Phaeosphaeria hyphaenes (on leaves of Hyphaene sp., South Africa), Pseudohormonema sordidus (on a from human pacemaker, USA), Quasiphoma hyphaenes (on leaves of Hyphaene sp., South Africa), Rapidomyces narthecii (on dead leaves of Narthecium ossifragum, Netherlands), Reticulascus parahennebertii (on dead culm of Juncus inflexus, Netherlands), Scytalidium philadelphianum (from compressed air in a factory, USA). New combinations: Neobarrmaelia serenoae, Nothopseudocercospora dictamni, Dothiora viticola, Floricola sulcata, Neocamarographium carpini, Paracamarographium koreanum, Rhexocercosporidium bellocense, Russula lilacina. Epitypes: Elsinoe corni (on leaves of Cornus florida, USA), Leptopeltis litigiosa (on dead leaf fronds of Pteridium aquilinum, Netherlands), Nothopseudocercospora dictamni (on living leaves of Dictamnus albus, Russia), Ramularia arvensis (on leaves of Potentilla reptans, Netherlands), Rhexocercosporidium bellocense (on leaves of Verbascum sp., Germany), Rhopographus filicinus (on dead leaf fronds of Pteridium aquilinum, Netherlands), Septoria robiniae (on leaves of Robinia pseudoacacia, Belgium). Lectotypes: Leptopeltis litigiosa (on Pteridium aquilinum, France), Rhopographus filicinus (on dead leaf fronds of Pteridium aquilinum, Netherlands), Septoria robiniae (on leaves of Robinia pseudoacacia, Belgium). Neotype: Camarographium stephensii (on dead leaf fronds of Pteridium aquilinum, Netherlands). Citation: Crous PW, Begoude BAD, Boers J, Braun U, Declercq B, Dijksterhuis J, Elliott TF, Garay-Rodriguez GA, Jurjević Ž, Kruse J, Linde CC, Loyd A, Mound L, Osieck ER, Rivera-Vargas LI, Quimbita AM, Rodas CA, Roux J, Schumacher RK, Starink-Willemse M, Thangavel R, Trappe JM, van Iperen AL, Van Steenwinkel C, Wells A, Wingfield MJ, Yilmaz N, Groenewald JZ (2022) New and Interesting Fungi. 5. Fungal Systematics and Evolution 10: 19-90. doi: 10.3114/fuse.2022.10.02.},
}
@article {pmid36788607,
year = {2023},
author = {Kipp, EJ and Lindsey, LL and Milstein, MS and Blanco, CM and Baker, JP and Faulk, C and Oliver, JD and Larsen, PA},
title = {Nanopore adaptive sampling for targeted mitochondrial genome sequencing and bloodmeal identification in hematophagous insects.},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {68},
pmid = {36788607},
issn = {1756-3305},
support = {T35 OD011118/OD/NIH HHS/United States ; },
mesh = {Rabbits ; Phylogeny ; *Aedes/genetics ; *Culex/genetics ; *Deer ; Vertebrates ; Sparrows ; DNA, Mitochondrial/genetics ; *Nanopores ; Animals ; Mosquito Vectors ; *Genome, Mitochondrial ; Humans ; },
abstract = {BACKGROUND: Blood-feeding insects are important vectors for an array of zoonotic pathogens. While previous efforts toward generating molecular resources have largely focused on major vectors of global medical and veterinary importance, molecular data across a large number of hematophagous insect taxa remain limited. Advancements in long-read sequencing technologies and associated bioinformatic pipelines provide new opportunities for targeted sequencing of insect mitochondrial (mt) genomes. For engorged hematophagous insects, such technologies can be leveraged for both insect mitogenome genome assembly and identification of vertebrate blood-meal sources.<br><br>METHODS: We used nanopore adaptive sampling (NAS) to sequence genomic DNA from four species of field-collected, blood-engorged mosquitoes (Aedes and Culex spp.) and one deer fly (Chrysops sp.). NAS was used for bioinformatical enrichment of mtDNA reads of hematophagous insects and potential vertebrate blood-meal hosts using publically available mt genomes as references. We also performed an experimental control to compare results of traditional non-NAS nanopore sequencing to the mt genome enrichment by the NAS method.<br><br>RESULTS: Complete mitogenomes were assembled and annotated for all five species sequenced with NAS: Aedes trivittatus, Aedes vexans, Culex restuans, Culex territans and the deer fly, Chrysops niger. In comparison to data generated during our non-NAS control experiment, NAS yielded a substantially higher proportion of reference-mapped mtDNA reads, greatly streamlining downstream mitogenome assembly and annotation. The NAS-assembled mitogenomes ranged in length from 15,582 to 16,045&#xa0;bp, contained between 78.1% and 79.0% A&#x2009;+&#x2009;T content and shared the anticipated arrangement of 13 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs. Maximum likelihood phylogenies were generated to further characterize each insect species. Additionally, vertebrate blood-meal analysis was successful in three samples sequenced, with mtDNA-based phylogenetic analyses revealing that blood-meal sources for Chrysops niger, Culex restuans and Aedes trivittatus were human, house sparrow (Passer domesticus) and eastern cottontail rabbit (Sylvilagus floridanus), respectively.<br><br>CONCLUSIONS: Our findings show that NAS has dual utility to simultaneously molecularly identify hematophagous insects and their blood-meal hosts. Moreover, our data indicate NAS can facilitate a wide array of mitogenomic systematic studies through novel 'phylogenetic capture' methods. We conclude that the NAS approach has great potential for broadly improving genomic resources used to identify blood-feeding insects, answer phylogenetic questions and elucidate complex pathways for the transmission of vector-borne pathogens.},
}
@article {pmid36787294,
year = {2023},
author = {Yang, H and Chen, T and Dong, W},
title = {Divergence time of mites of the family Laelapidae based on mitochondrial barcoding region.},
journal = {PloS one},
volume = {18},
number = {2},
pages = {e0279598},
pmid = {36787294},
issn = {1932-6203},
mesh = {Animals ; Phylogeny ; Bayes Theorem ; *Mites/genetics ; Genetic Speciation ; Asia ; },
abstract = {Using the mitochondrial barcoding region to correlate research with 58 species in 19 genera of the family Laelapidae with the aim of determining the origin, phylogenetic relationships, and biogeographic historical distribution characteristics of mites in the family Laelapidae. Phylogenetic trees were obtained using Bayesian inference (BI) and Maximum-likelihood (ML) methods, based on three fossil records calibrated as molecular clock nodes, to estimate the divergence time of mites in the family Laelapidae as well as to apply Dispersal-Extinction-Cladogenesis (DEC) analyses to obtain biogeographic history inferences. The result showed species of the genera Hyperlaelaps and Haemolaelaps and some species of the genus Androlaelaps in the family Laelapidae were divided into clades of the genus Laelaps in both the BI and ML trees. Divergence time estimates and biogeographic history analysis revealed that the family Laelapidae likely diverged from other taxa during the Middle Jurassic (ca. 156.73 Mya), with Asia considered the most likely ancestral region for the family Laelapidae. Species of various genera began to undergo massive diversification events during the Cenozoic Tertiary. The results suggest that some genera in the family Laelapidae need to be re-defined or new genera need to be established; the Late Cretaceous to Late Neogene warm period would have promoted the divergence and expansion of species in the family Laelapidae. The divergence and dispersal of the family Laelapidae species is most likely a joint response to the continued northward drift of the Indian plate away from the Gondwana paleo-continent and gradually closer to Asia during the Late Cretaceous and the geological activity of the Tibetan Plateau during the Cenozoic Tertiary. The results strengthen our understanding of the origin and evolution of species in the family Laelapidae.},
}
@article {pmid36787057,
year = {2023},
author = {Alvarado-Sizzo, H and Alcántara-Ayala, O and Espinosa, D and Rivas, G and Oyama, K and Luna-Vega, I},
title = {Genomic-based microsatellite development for Ternstroemia (Pentaphylacaceae) and transferability to other Ericales.},
journal = {Molecular biology reports},
volume = {50},
number = {4},
pages = {3547-3555},
pmid = {36787057},
issn = {1573-4978},
support = {IN220621 2021-2023.//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; },
mesh = {Humans ; *Ericales/genetics ; Genome ; Genomics ; Heterozygote ; Microsatellite Repeats/genetics ; Alleles ; High-Throughput Nucleotide Sequencing ; Genetic Loci/genetics ; },
abstract = {BACKGROUND: The genus Ternstroemia is associated with the vulnerable tropical montane cloud forest in Mexico and with other relevant vegetation types worldwide. It contains threatened and pharmacologically important species and has taxonomic issues regarding its species limits. This study describes 38 microsatellite markers generated using a genomic-based approach.<br><br>METHODS AND RESULTS: We tested 23 of these markers in a natural population of Ternstroemia lineata. These markers are highly polymorphic (all loci polymorphic with 3-14 alleles per locus and expected heterozygosity between 0.202 and 0.908), most of them (19 out of 23) are in Hardy-Weinberg Equilibrium and free of null alleles (18 out of 23). Also we found no evidence of linkage among them. Finally, we tested the transferability to six other American species of Ternstroemia, two other Pentaphylacaceae species, and four species from different families within the order Ericales.<br><br>CONCLUSIONS: These molecular resources are promising tools to investigate genetic diversity loss and as barcodes for ethnopharmacological applications and species delimitation in the family Pentaphylacaceae and some Ericales, among other applications.},
}
@article {pmid36778872,
year = {2023},
author = {Bourhane, Z and Cagnon, C and Castañeda, C and Rodríguez-Ochoa, R and Álvaro-Fuentes, J and Cravo-Laureau, C and Duran, R},
title = {Vertical organization of microbial communities in Salineta hypersaline wetland, Spain.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {869907},
pmid = {36778872},
issn = {1664-302X},
abstract = {Microbial communities inhabiting hypersaline wetlands, well adapted to the environmental fluctuations due to flooding and desiccation events, play a key role in the biogeochemical cycles, ensuring ecosystem service. To better understand the ecosystem functioning, we studied soil microbial communities of Salineta wetland (NE Spain) in dry and wet seasons in three different landscape stations representing situations characteristic of ephemeral saline lakes: S1 soil usually submerged, S2 soil intermittently flooded, and S3 soil with halophytes. Microbial community composition was determined according to different redox layers by 16S rRNA gene barcoding. We observed reversed redox gradient, negative at the surface and positive in depth, which was identified by PERMANOVA as the main factor explaining microbial distribution. The Pseudomonadota, Gemmatimonadota, Bacteroidota, Desulfobacterota, and Halobacteriota phyla were dominant in all stations. Linear discriminant analysis effect size (LEfSe) revealed that the upper soil surface layer was characterized by the predominance of operational taxonomic units (OTUs) affiliated to strictly or facultative anaerobic halophilic bacteria and archaea while the subsurface soil layer was dominated by an OTU affiliated to Roseibaca, an aerobic alkali-tolerant bacterium. In addition, the potential functional capabilities, inferred by PICRUSt2 analysis, involved in carbon, nitrogen, and sulfur cycles were similar in all samples, irrespective of the redox stratification, suggesting functional redundancy. Our findings show microbial community changes according to water flooding conditions, which represent useful information for biomonitoring and management of these wetlands whose extreme aridity and salinity conditions are exposed to irreversible changes due to human activities.},
}
@article {pmid36778661,
year = {2022},
author = {Kester, L and de Barbanson, B and Lyubimova, A and Chen, LT and van der Schrier, V and Alemany, A and Mooijman, D and Peterson-Maduro, J and Drost, J and de Ridder, J and van Oudenaarden, A},
title = {Integration of multiple lineage measurements from the same cell reconstructs parallel tumor evolution.},
journal = {Cell genomics},
volume = {2},
number = {2},
pages = {100096},
pmid = {36778661},
issn = {2666-979X},
abstract = {Organoid evolution models complemented with integrated single-cell sequencing technology provide a powerful platform to characterize intra-tumor heterogeneity (ITH) and tumor evolution. Here, we conduct a parallel evolution experiment to mimic the tumor evolution process by evolving a colon cancer organoid model over 100 generations, spanning 6 months in time. We use single-cell whole-genome sequencing (WGS) in combination with viral lineage tracing at 12 time points to simultaneously monitor clone size, CNV states, SNV states, and viral lineage barcodes for 1,641 single cells. We integrate these measurements to construct clonal evolution trees with high resolution. We characterize the order of events in which chromosomal aberrations occur and identify aberrations that recur multiple times within the same tumor sub-population. We observe recurrent sequential loss of chromosome 4 after loss of chromosome 18 in four unique tumor clones. SNVs and CNVs identified in our organoid experiments are also frequently reported in colorectal carcinoma samples, and out of 334 patients with chromosome 18 loss in a Memorial Sloan Kettering colorectal cancer cohort, 99 (29.6%) also harbor chromosome 4 loss. Our study reconstructs tumor evolution in a colon cancer organoid model at high resolution, demonstrating an approach to identify potentially clinically relevant genomic aberrations in tumor evolution.},
}
@article {pmid36778402,
year = {2023},
author = {Cheng, Y and Hu, M and Yang, B and Jensen, TB and Yang, T and Yu, R and Ma, Z and Radda, JSD and Jin, S and Zang, C and Wang, S},
title = {Perturb-tracing enables high-content screening of multiscale 3D genome regulators.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {36778402},
issn = {2692-8205},
support = {R35 GM133712/GM/NIGMS NIH HHS/United States ; DP2 GM137414/GM/NIGMS NIH HHS/United States ; T32 GM007205/GM/NIGMS NIH HHS/United States ; R33 CA251037/CA/NCI NIH HHS/United States ; R01 HG011245/HG/NHGRI NIH HHS/United States ; UG3 CA268202/CA/NCI NIH HHS/United States ; T32 GM007499/GM/NIGMS NIH HHS/United States ; },
abstract = {Three-dimensional (3D) genome organization becomes altered during development, aging, and disease[1-23], but the factors regulating chromatin topology are incompletely understood and currently no technology can efficiently screen for new regulators of multiscale chromatin organization. Here, we developed an image-based high-content screening platform (Perturb-tracing) that combines pooled CRISPR screen, a new cellular barcode readout method (BARC-FISH), and chromatin tracing. We performed a loss-of-function screen in human cells, and visualized alterations to their genome organization from 13,000 imaging target-perturbation combinations, alongside perturbation-paired barcode readout in the same single cells. Using 1.4 million 3D positions along chromosome traces, we discovered tens of new regulators of chromatin folding at different length scales, ranging from chromatin domains and compartments to chromosome territory. A subset of the regulators exhibited 3D genome effects associated with loop-extrusion and A-B compartmentalization mechanisms, while others were largely unrelated to these known 3D genome mechanisms. We found that the ATP-dependent helicase CHD7, the loss of which causes the congenital neural crest syndrome CHARGE[24] and a chromatin remodeler previously shown to promote local chromatin openness[25-27], counter-intuitively compacts chromatin over long range in different genomic contexts and cell backgrounds including neural crest cells, and globally represses gene expression. The DNA compaction effect of CHD7 is independent of its chromatin remodeling activity and does not require other protein partners. Finally, we identified new regulators of nuclear architectures and found a functional link between chromatin compaction and nuclear shape. Altogether, our method enables scalable, high-content identification of chromatin and nuclear topology regulators that will stimulate new insights into the 3D genome functions, such as global gene and nuclear regulation, in health and disease.},
}
@article {pmid36778226,
year = {2023},
author = {Yousefi, M and Andrejka, L and Winslow, MM and Petrov, DA and Boross, G},
title = {Fully accessible fitness landscape of oncogene-negative lung adenocarcinoma.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.01.30.526178},
pmid = {36778226},
issn = {2692-8205},
abstract = {Cancer genomes are almost invariably complex with genomic alterations cooperating during each step of carcinogenesis. In cancers that lack a single dominant oncogene mutation, cooperation between the inactivation of multiple tumor suppressor genes can drive tumor initiation and growth. Here, we shed light on how the sequential acquisition of genomic alterations generates oncogene-negative lung tumors. We couple tumor barcoding with combinatorial and multiplexed somatic genome editing to characterize the fitness landscapes of three tumor suppressor genes NF1, RASA1, and PTEN, the inactivation of which jointly drives oncogene-negative lung adenocarcinoma initiation and growth. The fitness landscape was surprisingly accessible, with each additional mutation leading to growth advantage. Furthermore, the fitness landscapes remained fully accessible across backgrounds with additional tumor suppressor mutations. These results suggest that while predicting cancer evolution will be challenging, acquiring the multiple alterations required for the growth of oncogene-negative tumors can be facilitated by the lack of constraints on mutational order.},
}
@article {pmid36777606,
year = {2023},
author = {Fenton, K and Simske, S and Luu, J},
title = {Mitigation of Chemical Reporting Liabilities through Systematic Modernization of Chemical Hazard and Safety Data Management Systems.},
journal = {ACS omega},
volume = {8},
number = {5},
pages = {4928-4936},
pmid = {36777606},
issn = {2470-1343},
abstract = {In the United States alone, approximately 2 billion tons of hazardous material products are manufactured each year for both household and industrial applications and contribute to thousands of worker chemical exposures with as many as 50,000 deaths from prolonged exposure each year. The potential hazards and impacts of these chemicals for human health and the environment are primarily communicated to the public through Safety Data Sheets (SDSs) from the chemical vendors or distributors. These documents provide a standardized approach for how and what information is provided to product users to assist them with assessment of precautionary measures, hazard mitigation, emergency response or cleanup procedures, and environmental, health, and safety (EHS) management. Despite the criticality for hazard communication (HAZCOM) precision, legacy SDS management and industry business practices leave the overall ability to effectively manage chemicals vulnerable to significant liability through a lack of full constituent disclosure, injection of data quality errors through various handling of SDS information and manual data entry, and the lack of direct SDS-to-product association. Chemical spills and accidents often require individuals to look for the appropriate SDS on a local computer, online, or in workplace binders; each of which results in information returned that is often found to be outdated or incorrect. Workplace HAZCOM violations remain among the top citations during EHS inspections by regulatory agencies. More important, however, is the lack of precise association of SDS to hazardous products that can occur through chemical management lifecycles. Incorrect SDSs can yield significant liability, as subsequent environmental and occupational health analyses and reporting are based upon incorrect and, in some cases, entirely different chemical formulations. This paper focuses on the need for a paradigm shift in our chemical management systems and how a standardized management system and various recent technological advances can be incorporated into Environmental Management System operations to reduce or eliminate these liabilities. The following advancements can be used to enhance the lifecycle management of workplace chemicals, reduce potential exposure and spill risks, reduce workplace hazards, and increase the efficiency and accuracy of environmental reporting through a more streamlined systems approach. EHS system enhancement applications discussed in this paper include the following: the need for a centralized universal SDS repository with full chemical disclosure of all product constituents and a nationally adopted machine language SDS standard. The use of artificial intelligence/machine learning in environmental systems and how they can be used as a medium to transition toward an automated standard by reverse-engineering and partitioning SDS components into machine-encoded text that can be validated and uploaded to a centralized repository. Algorithmic and meta-algorithmic approaches to SDS requirement and data validation, hazard characteristic code calculations, and determination of potentially less hazardous substitutions. Application of Natural Language Processing methods for real-time updates from scientific journals, regulatory agencies, and other reputable sources to produce "living" SDSs capable of informing users of relevant regulatory updates, news, and research. Embedded SDSs or SDS links in product barcodes with QR code reader technology to retrieve precise SDSs for each product in emergency situations. Use of advanced QR codes embedding authentication layers, authenticity verification, and alerts of potential product or inventory problems or discrepancies. Benefits of radio frequency identification technology in providing accurate SDS associations while also minimizing manual tracking of hazardous material and hazardous waste containers and monitoring for expired shelf life, incompatible storage, temperature sensitivities, and other inventory concerns.},
}
@article {pmid36776528,
year = {2022},
author = {Teng, K and Jackson, HW},
title = {Genetic perturbations go spatial.},
journal = {Cell genomics},
volume = {2},
number = {4},
pages = {100120},
pmid = {36776528},
issn = {2666-979X},
abstract = {Tissue-tumor interactivity is the culmination of cell intrinsic features and their extrinsic interactions with the environment. Recently in Cell, Dhainaut and Rose et al. established a strategy to track pooled CRISPR-modified cells in vivo using protein barcodes (Pro-Codes) and measure their impact on the tumor microenvironment through multiplexed imaging and spatial transcriptomics of intact tissues.[1].},
}
@article {pmid36775118,
year = {2023},
author = {Strayhorn, J},
title = {Editorial: Modeling and Fantasy Rehearsal: From Self-Injury to Self-Efficacy.},
journal = {Journal of the American Academy of Child and Adolescent Psychiatry},
volume = {62},
number = {6},
pages = {624-626},
doi = {10.1016/j.jaac.2023.02.005},
pmid = {36775118},
issn = {1527-5418},
mesh = {Humans ; *Self Efficacy ; Fantasy ; Learning ; Aggression/psychology ; *Self-Injurious Behavior ; },
abstract = {Trendy depictions of nonsuicidal self-injury in the media appear to promote real-life self-injury, according to an analysis by Lee and colleagues1, published in this issue. The researchers studied rates of emergency visits to all hospitals in Korea for self-injury, before and after video broadcasts disseminated a song called "Barcode." The song compared parallel cuts on the forearm to the barcodes used at checkout counters; an appealing protagonist glamorized self-injury. The timing of increases in rates of self-injury supported the hypothesis that the song engendered imitation -- that social contagion can be fostered by the mass media. In response to this finding, editorial comment places this article in the context of vast amounts of other research on the role of modeling (a.k.a. imitation learning) and fantasy rehearsal (a.k.a. imaginal practice) as general principles of human learning and behavior. Numerous scientists have documented the role of imitation learning, both before and after seminal studies by Albert Bandura. Research strongly contradicts the "catharsis hypothesis" and supports social learning theory's predictions that symbolically enacting aggressive actions does not "get anger out" or "release aggression," but provides practice that promotes behaviors in the same response class. A large set of studies supports the conclusion that media violence tends to increase real-life aggression. Fantasy rehearsal has been used to produce results similar to real-life practice for skills in sports, surgery, dance, musical performance, anxiety reduction, anger control, social skills, and cognitive restructuring. Nonetheless, the idea that media models and technology-assisted fantasy rehearsal have real-life effects has been forcefully disputed, and thus research such as the present study on "Barcode" must continue. But this editorial declares that the time has come when the available evidence demands energetically and systematically finding, creating, and harnessing positive models and positive fantasy rehearsal methods in the service of healthy psychological functioning. It declares that such a time arrived long ago.},
}
@article {pmid36771551,
year = {2023},
author = {Samuels, ME and Lapointe, C and Halwas, S and Worley, AC},
title = {Genomic Sequence of Canadian Chenopodium berlandieri: A North American Wild Relative of Quinoa.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {3},
pages = {},
pmid = {36771551},
issn = {2223-7747},
abstract = {Chenopodium berlandieri (pitseed goosefoot) is a widespread native North American plant, which was cultivated and consumed by indigenous peoples prior to the arrival of European colonists. Chenopodium berlandieri is closely related to, and freely hybridizes with the domesticated South American food crop C. quinoa. As such it is a potential source of wild germplasm for breeding with C. quinoa, for improved quinoa production in North America. The C. berlandieri genome sequence could also be a useful source of information for improving quinoa adaptation. To this end, we first optimized barcode markers in two chloroplast genes, rbcL and matK. Together these markers can distinguish C. berlandieri from the morphologically similar Eurasian invasive C. album (lamb's quarters). Second, we performed whole genome sequencing and preliminary assembly of a C. berlandieri accession collected in Manitoba, Canada. Our assembly, while fragmented, is consistent with the expected allotetraploid structure containing diploid Chenopodium sub-genomes A and B. The genome of our accession is highly homozygous, with only one variant site per 3-4000 bases in non-repetitive sequences. This is consistent with predominant self-fertilization. As previously reported for the genome of a partly domesticated Mexican accession of C. berlandieri, our genome assembly is similar to that of C. quinoa. Somewhat unexpectedly, the genome of our accession had almost as many variant sites when compared to the Mexican C. berlandieri, as compared to C. quinoa. Despite the overall similarity of our genome sequence to that of C. quinoa, there are differences in genes known to be involved in the domestication or genetics of other food crops. In one example, our genome assembly appears to lack one functional copy of the SOS1 (salt overly sensitive 1) gene. SOS1 is involved in soil salinity tolerance, and by extension may be relevant to the adaptation of C. berlandieri to the wet climate of the Canadian region where it was collected. Our genome assembly will be a useful tool for the improved cultivation of quinoa in North America.},
}
@article {pmid36768872,
year = {2023},
author = {Stuart, JD and Wickenkamp, NR and Davis, KA and Meyer, C and Kading, RC and Snow, CD},
title = {Scalable Combinatorial Assembly of Synthetic DNA for Tracking Applications.},
journal = {International journal of molecular sciences},
volume = {24},
number = {3},
pages = {},
pmid = {36768872},
issn = {1422-0067},
support = {UL1 TR002535/TR/NCATS NIH HHS/United States ; AI146740/NH/NIH HHS/United States ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Sequence Analysis, DNA/methods ; *DNA/genetics/analysis ; Gene Library ; High-Throughput Nucleotide Sequencing/methods ; Oligonucleotides/genetics ; },
abstract = {Synthetic DNA barcodes are double-stranded DNA molecules designed to carry recoverable information, information that can be used to represent and track objects and organisms. DNA barcodes offer robust, sensitive detection using standard amplification and sequencing techniques. While numerous research groups have promoted DNA as an information storage medium, less attention has been devoted to the design of economical, scalable DNA barcode libraries. Here, we present an alternative modular approach to sequence design. Barcode sequences were constructed from smaller, interchangeable blocks, allowing for the combinatorial assembly of numerous distinct tags. We demonstrated the design and construction of first-generation (N = 256) and second-generation (N = 512) modular barcode libraries, from fewer than 50 total single-stranded oligonucleotides for each library. To avoid contamination during experimental validation, a liquid-handling robot was employed for oligonucleotide mixing. Generating barcode sequences in-house reduces dependency upon external entities for unique tag generation, increasing flexibility in barcode generation and deployment. Next generation sequencing (NGS) detection of 256 different samples in parallel highlights the multiplexing afforded by the modular barcode design coupled with high-throughput sequencing. Deletion variant analysis of the first-generation library informed sequence design for enhancing barcode assembly specificity in the second-generation library.},
}
@article {pmid36767267,
year = {2023},
author = {Hernández-Alomía, F and Bastidas-Caldes, C and Ballesteros, I and Tenea, GN and Jarrín-V, P and Molina, CA and Castillejo, P},
title = {Beta-Lactam Antibiotic Resistance Genes in the Microbiome of the Public Transport System of Quito, Ecuador.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {3},
pages = {},
pmid = {36767267},
issn = {1660-4601},
mesh = {Humans ; Ecuador ; *beta-Lactamases/genetics/metabolism ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/metabolism ; Monobactams ; Drug Resistance, Multiple, Bacterial ; Microbial Sensitivity Tests ; },
abstract = {Multidrug-resistant bacteria present resistance mechanisms against β-lactam antibiotics, such as Extended-Spectrum Beta-lactamases (ESBL) and Metallo-β-lactamases enzymes (MBLs) which are operon encoded in Gram-negative species. Likewise, Gram-positive bacteria have evolved other mechanisms through mec genes, which encode modified penicillin-binding proteins (PBP2). This study aimed to determine the presence and spread of β-lactam antibiotic resistance genes and the microbiome circulating in Quito's Public Transport (QTP). A total of 29 station turnstiles were swabbed to extract the surface environmental DNA. PCRs were performed to detect the presence of 13 antibiotic resistance genes and to identify and to amplify 16S rDNA for barcoding, followed by clone analysis, Sanger sequencing, and BLAST search. ESBL genes blaTEM-1 and blaCTX-M-1 and MBL genes blaOXA-181 and mecA were detected along QPT stations, blaTEM being the most widely spread. Two subvariants were found for blaTEM-1, blaCTX-M-1, and blaOXA-181. Almost half of the circulating bacteria found at QPT stations were common human microbiota species, including those classified by the WHO as pathogens of critical and high-priority surveillance. β-lactam antibiotic resistance genes are prevalent throughout QPT. This is the first report of blaOXA-181 in environmental samples in Ecuador. Moreover, we detected a new putative variant of this gene. Some commensal coagulase-negative bacteria may have a role as mecA resistance reservoirs.},
}
@article {pmid36766310,
year = {2023},
author = {Rząd, I and Okulewicz, A and Sałamatin, R and Szenejko, M and Panicz, R and Nowakowski, JK and Stapf, A},
title = {Helminth Community Structure of Tits Cyanistes caeruleus and Parus major (Paridae) during Their Autumn Migration on the Southern Baltic Coast.},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {3},
pages = {},
pmid = {36766310},
issn = {2076-2615},
abstract = {The research problem undertaken in this study is to determine the scale of infection of Eurasian blue tit Cyanistes caeruleus and Great tit Parus major and the biological diversity of their internal parasites, helminths. The aim of the study is to gain new knowledge about the structure of the helminth communities of the Eurasian blue tit and Great tit on the southern coast of the Baltic Sea during autumn migration to their wintering grounds. Helminths of tits were collected in 2008-2012 on the southern coast of the Baltic Sea in Poland. PAST v. 2.11 software was used for the calculations. Barcoding DNA was used to identify trematodes initially classified based on morphological characters to the genera Leucochloridium and Urogonimus. Cestodes Anonchotaenia globata were recorded for the first time in Poland. The Eurasian blue tit is a new host in Poland for three species of helminths: cestode Monosertum parinum and filarial nematodes, Cardiofilaria pavlovskyi, and Diplotriaena henryi. The Great tit is a new host in Poland for trematode Urogonimus macrostomus, cestode A. globata and M. parinum, and filarial nematode Diplotriaena obtusa. The nematode C. pavlovskyi was the species most frequently recorded in both host species. A high degree of similarity was found between the component communities and infracommunities of helminths in Eurasian blue tit and Great tit. The new information provided in this study has increased our knowledge of the transmission of helminths in Central Europe.},
}
@article {pmid36765785,
year = {2023},
author = {McMahon, NP and Jones, JA and Anderson, AN and Dietz, MS and Wong, MH and Gibbs, SL},
title = {Flexible Cyclic Immunofluorescence (cyCIF) Using Oligonucleotide Barcoded Antibodies.},
journal = {Cancers},
volume = {15},
number = {3},
pages = {},
pmid = {36765785},
issn = {2072-6694},
support = {R01CA260196/CA/NCI NIH HHS/United States ; TL1 TR002371/TR/NCATS NIH HHS/United States ; R01 CA260196/CA/NCI NIH HHS/United States ; R01 CA253860/CA/NCI NIH HHS/United States ; F31CA271676-01/CA/NCI NIH HHS/United States ; F31 CA271676/CA/NCI NIH HHS/United States ; TL1TR002371/TR/NCATS NIH HHS/United States ; },
abstract = {Advances in our understanding of the complex, multifaceted interactions between tumor epithelia, immune infiltrate, and tumor microenvironmental cells have been driven by highly multiplexed imaging technologies. These techniques are capable of labeling many more biomarkers than conventional immunostaining methods. However, multiplexed imaging techniques suffer from low detection sensitivity, cell loss-particularly in fragile samples-, and challenges with antibody labeling. Herein, we developed and optimized an oligonucleotide antibody barcoding strategy for cyclic immunofluorescence (cyCIF) that can be amplified to increase the detection efficiency of low-abundance antigens. Stained fluorescence signals can be readily removed using ultraviolet light treatment, preserving tissue and fragile cell sample integrity. We also extended the oligonucleotide barcoding strategy to secondary antibodies to enable the inclusion of difficult-to-label primary antibodies in a cyCIF panel. Using both the amplification oligonucleotides to label DNA barcoded antibodies and in situ hybridization of multiple fluorescently labeled oligonucleotides resulted in signal amplification and increased signal-to-background ratios. This procedure was optimized through the examination of staining parameters including staining oligonucleotide concentration, staining temperature, and oligonucleotide sequence design, resulting in a robust amplification technique. As a proof-of-concept, we demonstrate the flexibility of our cyCIF strategy by simultaneously imaging with the original oligonucleotide conjugated antibody (Ab-oligo) cyCIF strategy, the novel Ab-oligo cyCIF amplification strategy, as well as direct and indirect immunofluorescence to generate highly multiplexed images.},
}
@article {pmid36763968,
year = {2023},
author = {Xie, ZN and Lao, J and Liu, H and Zhang, WX and He, W and Zhong, C and Xie, J and Zhang, SH and Jin, J},
title = {Characterization of the chloroplast genome of medicinal herb Polygonatum cyrtonema and identification of molecular markers by comparative analysis.},
journal = {Genome},
volume = {66},
number = {4},
pages = {80-90},
doi = {10.1139/gen-2022-0087},
pmid = {36763968},
issn = {1480-3321},
mesh = {Phylogeny ; *Polygonatum/genetics ; *Genome, Chloroplast ; *Plants, Medicinal/genetics ; China ; },
abstract = {Polygonatum cyrtonema Hua is a traditional Chinese herb medicine, and it is widely distributed in China. The intrageneric taxonomy and phylogenetic relationships within Polygonatum have long been controversial due to their morphological similarity and lacking special DNA barcodes. In this paper, the complete chloroplast genome is a relatively conserved quadripartite structure including a large single copy region of 84 711 bp, a small single copy region of 18 210 bp, and a pair of inverted repeats region of 26 142 bp. A total of 342 simple sequence repeats were identified, and most of them were found to be composed of A/T, including 126 mono-nucleotides and 179 di-nucleotides. Nucleotide diversity was analyzed and eight highly variable regions (psbl∼trnT-CGU, atpF∼atpH, trnT-GGU∼psbD, psaJ∼rps20, trnL-UAG∼ndhD, ndhG∼ndhl, ndhA, and rpl32∼ccsA) were identified as potential molecular markers. Phylogenetic analysis based on the whole chloroplast genome showed that P. cyrtonema, within the family Asparagaceae, is closely related to Polygonatum sibiricum and Polygonatum kingianum. The sequence matK, trnT-GGU &amp; ccsA, and ndhG∼ndhA were identified as three DNA barcodes. The assembly and comparative analysis of P. cyrtonema complete chloroplast genome will provide essential molecular information about the evolution and molecular biology for further study.},
}
@article {pmid36763056,
year = {2022},
author = {Leon-De La Luz, JL and Lichter-Marck, IH},
title = {A new species of Encelia (Compositae, Heliantheae, Enceliinae) from the southern Baja California Peninsula.},
journal = {PhytoKeys},
volume = {212},
number = {},
pages = {97-109},
pmid = {36763056},
issn = {1314-2011},
abstract = {Here, we describe and illustrate Enceliabalandra sp. nov., a new species of Compositae from the Baja California Peninsula. It is rare and known only from the rocky hills around Puerto Balandra and Pichilingüe, inside the bay of La Paz, in the State of Baja California Sur, Mexico. We determine that this new species has affinities with Encelia, based on its suffruticose woody habit, neuter ray florets and compressed disc cypselae with a cleft apex. The taxonomic placement within Encelia is supported by nuclear ribosomal sequence data from two regions, ITS and ETS. We also present detailed photographs, a conservation assessment and a dichotomous key to the Encelia of the southern Baja California Peninsula. Finally, we discuss the uniqueness of Enceliabalandra amongst peninsular Encelia and its potential significance for understanding the enigmatic biogeography of this ecologically important genus.},
}
@article {pmid36762363,
year = {2022},
author = {Zhang, J and Zhang, Q and Long, F and Yu, H and Yi, Y},
title = {Two new species of Diphya Nicolet, 1849 (Araneae, Tetragnathidae) from Southwest China.},
journal = {ZooKeys},
volume = {1124},
number = {},
pages = {131-145},
pmid = {36762363},
issn = {1313-2989},
abstract = {Two new species of tetragnathid spiders from Guizhou and Sichuang provinces of China are described: Diphyaguiyang J. Zhang &amp; H. Yu, sp. nov. (♂♀) and Diphyaweimiani J. Zhang &amp; H. Yu, sp. nov. (♀). Detailed descriptions, diagnoses, and photographs are provided for these two species, as well as a key and a distribution map for Chinese Diphya species. DNA barcodes (a partial fragment of the mitochondrial cytochrome oxidase subunit I gene, COI) of both new species were obtained for species delimitation, matching of different sexes, and future use in molecular studies.},
}
@article {pmid36762361,
year = {2022},
author = {Riedel, A},
title = {Nine new species of Trigonopterus Fauvel (Coleoptera, Curculionidae) from Sundaland.},
journal = {ZooKeys},
volume = {1124},
number = {},
pages = {109-130},
pmid = {36762361},
issn = {1313-2989},
abstract = {The DNA of Trigonopterus specimens from the Sundaland region stored between ten and 32 years in museums could be used for next-generation sequencing. The availability of their cox1 sequence allowed the description of the following nine new species: Trigonopterusgrimmi sp. nov., T.johorensis sp. nov., T.lambirensis sp. nov., T.linauensis sp. nov., T.microreticulatus Riedel, Trnka &amp; Wahab sp. nov., T.mulensis sp. nov., T.sarawakensis sp. nov., T.siamensis sp. nov., and T.singaporensis sp. nov. The alternative original spelling of the name T.tounensis Narakusumo &amp; Riedel is chosen to prevail over T.tounaensis Narakusumo &amp; Riedel. The new species represent the first country records of Trigonopterus for Brunei, Singapore, and Thailand. Thus, the genus´ known area of distribution in the Sundaland region is significantly extended. A key and a catalogue are provided to the Trigonopterus species from Borneo, W-Malaysia, Singapore, and Thailand.},
}
@article {pmid36762239,
year = {2022},
author = {Pimvichai, P and Enghoff, H and Backeljau, T},
title = {Two new millipede species of the genus Coxobolellus Pimvichai, Enghoff, Panha &amp; Backeljau, 2020 (Diplopoda, Spirobolida, Pseudospirobolellidae).},
journal = {ZooKeys},
volume = {1128},
number = {},
pages = {171-190},
pmid = {36762239},
issn = {1313-2989},
abstract = {Two new millipede species of the genus Coxobolellus Pimvichai, Enghoff, Panha &amp; Backeljau, 2020 from Thailand are described: Coxobolellussaratani sp. nov. from Loei Province and Coxobolellusserratoligulatus sp. nov. from Uttaradit Province. The descriptions are based on gonopod morphology and two mitochondrial gene fragments (COI and 16S rRNA). The phylogenetic mtDNA analysis assigned the two new species unequivocally to the consistently well-supported Coxobolellus clade, in which they form a fifth subclade that was well supported by maximum likelihood analysis of 16S rRNA, though neither by Bayesian inference nor by COI. The two new Coxobolellus species share four conspicuous gonopodal synapomorphies of the genus: (1) the protruding process on the coxae of the 3[rd] (and sometimes 4[th]) pair of male legs, (2) a large, triangular coxae on the 4[th]-5[th] pair of legs, (3) a short process of the preanal ring protruding as far as, or slightly beyond, the anal valves, and (4) the posterior gonopod telopodite divided into two parts, with a conspicuous pore opening at the mesal margin at the end of the coxal part of the posterior gonopod. Thus, the two new species provide further evidence of the well-defined monophyly of the genus Coxobolellus. Finally, the paper provides an updated morphological identification key to all currently described Coxobolellus species.},
}
@article {pmid36762232,
year = {2022},
author = {Zhu, CQ and Xu, XD and Zhen, Y},
title = {Systematic review of the firefly genus Emeia Fu, Ballantyne &amp; Lambkin, 2012 (Coleoptera, Lampyridae) from China.},
journal = {ZooKeys},
volume = {1113},
number = {},
pages = {153-166},
pmid = {36762232},
issn = {1313-2989},
abstract = {The Luciolinae genus Emeia Fu, Ballantyne &amp; Lambkin, 2012 is reviewed. Phylogenetic relationships based on cox1 DNA barcoding sequences from 42 fireflies and 2 outgroup species are reconstructed. The dataset included three main Lampyridae subfamilies: Luciolinae, Photurinae and Lampyrinae, and Emeia was recovered within Luciolinae. A new species, Emeiapulchra Zhu &amp; Zhen sp. nov., is described from the wetland of Lishui, Zhejiang, China. Emeiapulchra is sister species to E.pseudosauteri from Sichuan, which is supported by morphological characters and a phylogeny based on DNA barcoding sequences. The two species are separated geographically as shown on the distribution map. A key to species of Emeia using males is provided.},
}
@article {pmid36762231,
year = {2022},
author = {Bribiesca-Contreras, G and Dahlgren, TG and Amon, DJ and Cairns, S and Drennan, R and Durden, JM and Eléaume, MP and Hosie, AM and Kremenetskaia, A and McQuaid, K and O'Hara, TD and Rabone, M and Simon-Lledó, E and Smith, CR and Watling, L and Wiklund, H and Glover, AG},
title = {Benthic megafauna of the western Clarion-Clipperton Zone, Pacific Ocean.},
journal = {ZooKeys},
volume = {1113},
number = {},
pages = {1-110},
pmid = {36762231},
issn = {1313-2989},
abstract = {There is a growing interest in the exploitation of deep-sea mineral deposits, particularly on the abyssal seafloor of the central Pacific Clarion-Clipperton Zone (CCZ), which is rich in polymetallic nodules. In order to effectively manage potential exploitation activities, a thorough understanding of the biodiversity, community structure, species ranges, connectivity, and ecosystem functions across a range of scales is needed. The benthic megafauna plays an important role in the functioning of deep-sea ecosystems and represents an important component of the biodiversity. While megafaunal surveys using video and still images have provided insight into CCZ biodiversity, the collection of faunal samples is needed to confirm species identifications to accurately estimate species richness and species ranges, but faunal collections are very rarely carried out. Using a Remotely Operated Vehicle, 55 specimens of benthic megafauna were collected from seamounts and abyssal plains in three Areas of Particular Environmental Interest (APEI 1, APEI 4, and APEI 7) at 3100-5100 m depth in the western CCZ. Using both morphological and molecular evidence, 48 different morphotypes belonging to five phyla were found, only nine referrable to known species, and 39 species potentially new to science. This work highlights the need for detailed taxonomic studies incorporating genetic data, not only within the CCZ, but in other bathyal, abyssal, and hadal regions, as representative genetic reference libraries that could facilitate the generation of species inventories.},
}
@article {pmid36762071,
year = {2022},
author = {Bolshakov, VV and Movergoz, EA},
title = {Karyotype and COI gene sequences of Chironomusmelanotus Keyl, 1961 from the Yaroslavl region, Russia, and the difficulties with its identification using GenBank and BOLD systems.},
journal = {Comparative cytogenetics},
volume = {16},
number = {3},
pages = {161-172},
pmid = {36762071},
issn = {1993-0771},
abstract = {Karyotype and COI gene sequences of Chironomusmelanotus Keyl, 1961 from the Yaroslavl region (Russia) were analyzed. A low level of chromosomal polymorphism has been confirmed, eventually eight banding sequences were found: melA1, melB1, melC1, melD1, melE1, melF1, and melG1; only melD2 was found in two larvae from the Sunoga river. Analysis of phylogenetic tree and estimated genetic distances has shown not all COI gene sequences of Ch.melanotus in GenBank and BOLD to belong to this species. The lower distance of 0.4% was observed between two sequences from the Yaroslavl region and Finland, apparently these are true Ch.melanotus sequences. The distances between true Ch.melanotus and other sequences from Finland were 9.5% and 12.4%, and from Sweden it was 11%. The average genetic distance between studied sequences of 9.1% is out of the range of the 3% threshold previously determined for chironomids. According to our estimates, there are two sequences with a distance of 2.9% that may belong to Ch.annularius Meigen, 1818, and one sequence with a genetic distance of 2.1%, may belonging to Ch.cingulatus Meigen, 1830, which has been confirmed karyologically. Another two sequences form a separate cluster. We suggest that they either belong to a known species, but are not present in the databases, or belong to a distinct, undescribed species.},
}
@article {pmid36762047,
year = {2022},
author = {Cheng, HJ and Janssens, F and Chang, CH},
title = {An updated checklist of Collembola in Taiwan, with DNA barcoding of Papirioidesjacobsoni Folsom, 1924 (Symphypleona, Dicyrtomidae).},
journal = {ZooKeys},
volume = {1123},
number = {},
pages = {123-146},
pmid = {36762047},
issn = {1313-2989},
abstract = {From urban green space to pristine forest, Collembola is one of the most numerous and species-rich members of the soil fauna around the world. However, due to lack of taxonomic expertise and research, its diversity is poorly understood, especially in tropical and subtropical regions. Collembola biodiversity studies in Taiwan have not seen much progress since 1981, when Hsin Chi reviewed 26 species belonging to 20 genera and eight families. Additionally, reports of new records in Taiwan in the last 40 years are scattered amongst several publications and not easily accessible to most end-users. Thus, a concise summary of related research is urgently needed. In this study, we updated the checklist of Collembola in Taiwan, based on published papers as well as images recorded in 2020-2022. We concluded that 58 species of Collembola belonging to 31 genera and 12 families have been reported in Taiwan, including 13 newly-recorded species. This species richness marks a 123% increase from the 1981 review. The results have been made publicly available in the Catalog of Life in Taiwan database and the images recorded have been used to update species information in collembola.org. We also characterised morphological and genetic variations in the globular springtail species Papirioidesjacobsoni Folsom, 1924 using DNA barcodes and highlighted potential research directions.},
}
@article {pmid36762040,
year = {2022},
author = {Zhao, Y and Wang, H and Huang, H and Zhou, Z},
title = {A DNA barcode library for katydids, cave crickets, and leaf-rolling crickets (Tettigoniidae, Rhaphidophoridae and Gryllacrididae) from Zhejiang Province, China.},
journal = {ZooKeys},
volume = {1123},
number = {},
pages = {147-171},
pmid = {36762040},
issn = {1313-2989},
abstract = {Barcode libraries are generally assembled with two main objectives in mind: specimen identification and species discovery/delimitation. In this study, the standard COI barcode region was sequenced from 681 specimens belonging to katydids (Tettigoniidae), cave crickets (Rhaphidophoridae), and leaf-rolling crickets (Gryllacrididae) from Zhejiang Province, China. Of these, four COI-5P sequences were excluded from subsequent analyses because they were likely NUMTs (nuclear mitochondrial pseudogenes). The final dataset consisted of 677 barcode sequences representing 90 putative species-level taxa. Automated cluster delineation using the Barcode of Life Data System (BOLD) revealed 118 BINs (Barcodes Index Numbers). Among these 90 species-level taxa, 68 corresponded with morphospecies, while the remaining 22 were identified based on reverse taxonomy using BIN assignment. Thirteen of these morphospecies were represented by a single barcode (so-called singletons), and each of 19 morphospecies were split into more than one BIN. The consensus delimitation scheme yielded 55 Molecular Operational Taxonomic Units (MOTUs). Only four morphospecies (I max > DNN) failed to be recovered as monophyletic clades (i.e., Elimaeaterminalis, Phyllomimusklapperichi, Sinochloraszechwanensis and Xizicushowardi), so it is speculated that these may be species complexes. Therefore, the diversity of katydids, cave crickets, and leaf-rolling crickets in Zhejiang Province is probably slightly higher than what current taxonomy would suggest.},
}
@article {pmid36762030,
year = {2022},
author = {Qin, Y and Hu, R and Zhao, H and Wei, G and Lu, Z and Huang, Y},
title = {Taxonomic delimitation and molecular identification of clusters within the species Zanthoxylumnitidum (Rutaceae) in China.},
journal = {PhytoKeys},
volume = {196},
number = {},
pages = {1-20},
pmid = {36762030},
issn = {1314-2011},
abstract = {Zanthoxylumnitidum, known as Liang-Mian-Zhen in China, is a traditional Chinese medicinal plant used to treat traumatic injury, rheumatism, paralysis, toothache, stomach ache, and venomous snake bites. Two varieties of the species have been described and three morphological types have been reported within the original variety. However, taxonomic delimitation and molecular markers for distinguishing these varieties and types within this species remain unknown. Since different populations exhibit varying chemical compositions, easy identification of intraspecific taxa is crucial. We collected 420 individuals from 38 natural populations, 3 samples of standard medicinal material, and 17 folk-medicine samples to perform classification and identification within Zanthoxylumnitidum. Four distinct genetic clusters (A, B, C, and D) were highly supported by the nuclear barcode. Two distinct chloroplast clusters (A1 and A2) were further detected within A, and three others had one-to-one correspondence with the remaining nuclear clusters. Molecular identification showed that the 17 folk samples comprised A1, A2, B, and D, while the 3 standard samples belonged to A2. The internal transcribed spacer (ITS) region and rbcL gene are proposed as barcodes for rapid and accurate identification of the different Liang-Mian-Zhen lineages in China. This study highlights the importance of accurate taxonomic delimitation in combination with rapid and accurate molecular identification of medicinal plants.},
}
@article {pmid36761924,
year = {2022},
author = {Song, C and Zhu, BQ and Moubayed-Breil, J and Lei, T and Qi, X},
title = {Taxonomic study on the genus Stenochironomus Kieffer from the Baishanzu Nature Reserve, China (Diptera, Chironomidae).},
journal = {ZooKeys},
volume = {1104},
number = {},
pages = {93-113},
pmid = {36761924},
issn = {1313-2989},
abstract = {During the summer of July to September 2020, a biodiversity survey on Chironomidae of Baishanzu Nature Reserve, China was made. In total, five Stenochironomus taxa/species were discovered, of which two belong to undescribed species and one (S.okialbus Sasa, 1990) is reported for the first time from China. The male adults of two new species are described and illustrated. Stenochironomusannulus Song &amp; Qi sp. nov. is distinguished in having a wing with two dark spots restricted to the fork area of FCu and RM, the mid- and hind-femur each with a brown annulus, and the inferior volsella with two setae and one strong terminal spine. Stenochironomusbaishanzuensis Song &amp; Qi sp. nov. is distinguished by a combination of characters: a single dark spot on the middle part of the wing, fore legs brown to dark brown except for the basal 3/4 of femur, and the inferior volsella with four long setae and one stout terminal spine. The neighbour-joining tree based on public COI barcodes formed distinct clades with clear support for the new species. An updated key to known male adults of Stenochironomus from China is also provided.},
}
@article {pmid36761923,
year = {2022},
author = {Mullin, KE and Rakotomanga, MG and Dawson, J and Glaw, F and Rakotoarison, A and Orozco-terWengel, P and Scherz, MD},
title = {An unexpected new red-bellied Stumpffia (Microhylidae) from forest fragments in central Madagascar highlights remaining cryptic diversity.},
journal = {ZooKeys},
volume = {1104},
number = {},
pages = {1-28},
pmid = {36761923},
issn = {1313-2989},
abstract = {The Madagascan endemic subfamily Cophylinae in the family Microhylidae, is an example of a taxonomic group for which much is still to be discovered. Indeed, the cophyline frogs present a large portion of Madagascar's cryptic and microendemic amphibian diversity, yet they remain understudied. A new red-bellied species of the microhylid frog genus Stumpffia is described from the central plateau of Madagascar. Visual encounter surveys in Ambohitantely and Anjozorobe in 2019 and 2020 identified this previously unknown Stumpffia species, which closely resembles Stumpffiakibomena known from Andasibe in the east. Stumpffialynnae sp. nov. adds another species to the red-bellied species complex, differing from S.kibomena by genetic differentiation in the mitochondrial 16S rRNA gene (3.6-3.9%) and distinct nuclear RAG1 haplotypes, as well as strongly by its advertisement call. The new species is known from across Ambohitantely Special Reserve and Anjozorobe Angavo protected area, but is known only from one complete specimen and eight individual tissue samples. Based on the rarity of the species, the small number of locations in which it has been found, and its disappearing forest habitat, its IUCN Red List classification is suggested as "Endangered". This species is the first Stumpffia described from Madagascar's central plateau, highlighting the importance of conserving the remnant forest fragments in this area and the ongoing need to survey and protect this threatened habitat type.},
}
@article {pmid36761872,
year = {2022},
author = {Fitmawati, F and Juliantari, E and Silvia, M},
title = {Systematic reinstatement of the Sumatra endemic species Mangiferasumatrana Miq. (Anacardiaceae).},
journal = {PhytoKeys},
volume = {199},
number = {},
pages = {129-140},
pmid = {36761872},
issn = {1314-2011},
abstract = {Mangiferasumatrana Miq. is an endemic species from Sumatra. The taxonomic status of M.sumatrana remains unclear and is currently treated as a synonym of M.laurina. The present study employed morphological and palynological characters and molecular analyses to address the delimitation between the two species. Pollen observations were carried out with a Scanning Electron Microscope (SEM). Phylogenetic relationships were investigated using the ITS and the trnl-F intergenic spacer markers. M.sumatrana differs from M.laurina by having pyramidal panicles with a low density of pale yellow flowers pale, sepals 3-3.5 × 1.7-2 mm, fruit roundish to flattened with pale yellow pulp, a rough fibre texture, and pollen with a prolate spheroidal shape. The MP phylogenetic tree showed a divergent boundary between the two species suggesting that M.sumatrana could be an independent species, not a variety of M.laurina. The present study supports the view that these two taxa can be treated as different species.},
}
@article {pmid36761806,
year = {2022},
author = {Ha, NL and Truong, XL and Ishikawa, T and Jaitrong, W and Lee, CF and Chouangthavy, B and Eguchi, K},
title = {Three new species of the genus Biasticus Stål, 1867 (Insecta, Heteroptera, Reduviidae, Harpactorinae) from Central Highlands, Vietnam.},
journal = {ZooKeys},
volume = {1118},
number = {},
pages = {133-180},
pmid = {36761806},
issn = {1313-2989},
abstract = {Three new assassin bug species of the genus Biasticus Stål, 1867 are recognized in Vietnam based on morphological examination, morphometric and molecular phylogenetic analyses, and described as Biasticustaynguyenensis Ha, Truong &amp; Ishikawa, sp. nov., Biasticusgriseocapillus Ha, Truong &amp; Ishikawa, sp. nov., and Biasticusluteicollis Ha, Truong &amp; Ishikawa, sp. nov. The conspecific male and female associations of the new species were confirmed by phylogenetic analyses and DNA barcoding of the mitochondrial 16S rDNA and COI genes. All three new species are presently restricted to the Central Highlands, Vietnam (Kon Chu Rang NR, Gia Lai Province, and Chu Yang Sin NP, Dak Lak Province).},
}
@article {pmid36761795,
year = {2022},
author = {Nolasco, S and Valdez-Mondragón, A},
title = {To be or not to be… Integrative taxonomy and species delimitation in the daddy long-legs spiders of the genus Physocyclus (Araneae, Pholcidae) using DNA barcoding and morphology.},
journal = {ZooKeys},
volume = {1135},
number = {},
pages = {93-118},
pmid = {36761795},
issn = {1313-2989},
abstract = {Integrative taxonomy is crucial for discovery, recognition, and species delimitation, especially in underestimated species complex or cryptic species, by incorporating different sources of evidence to construct rigorous species hypotheses. The spider genus Physocyclus Simon, 1893 (Pholcidae, Arteminae) is composed of 37 species, mainly from North America. In this study, traditional morphology was compared with three DNA barcoding markers regarding their utility in species delimitation within the genus: 1) Cytochrome c Oxidase subunit 1 (CO1), 2) Internal Transcribed Spacer 2 (ITS2), and 3) Ribosomal large subunit (28S). The molecular species delimitation analyses were carried out using four methods under the corrected p-distances Neighbor-Joining (NJ) criteria: 1) Automatic Barcode Gap Discovery (ABGD), 2) Assemble Species by Automatic Partitioning (ASAP), 3) General Mixed Yule Coalescent model (GMYC), and 4) Bayesian Poisson Tree Processes (bPTP). The analyses incorporated 75 terminals from 22 putative species of Physocyclus. The average intraspecific genetic distance (p-distance) was found to be < 2%, whereas the average interspecific genetic distance was 20.6%. The ABGD, ASAP, and GMYC methods were the most congruent, delimiting 26 or 27 species, while the bPTP method delimited 33 species. The use of traditional morphology for species delimitation was congruent with most molecular methods, with the male palp, male chelicerae, and female genitalia shown to be robust characters that support species-level identification. The barcoding with CO1 and 28S had better resolution for species delimitation in comparison with ITS2. The concatenated matrix and traditional morphology were found to be more robust and informative for species delimitation within Physocyclus.},
}
@article {pmid36761794,
year = {2022},
author = {Zeng, XS and Sun, CH and Huang, XY and Lao, YL and Huang, JL and Li, S and Zhang, Q},
title = {DNA barcoding of Scomberomorus (Scombridae, Actinopterygii) reveals cryptic diversity and misidentifications.},
journal = {ZooKeys},
volume = {1135},
number = {},
pages = {157-170},
pmid = {36761794},
issn = {1313-2989},
abstract = {The genus Scomberomorus is economically important; however, the taxonomic status and phylogenetic relationships in this genus are not clearly resolved, making it difficult to effectively protect and exploit fish resources. To clarify the taxonomic status of Scomberomorus species, mitochondrial cytochrome c oxidase I (COI) gene sequences of 150 samples were analyzed. The average genetic distance among 14 species was approximately 11 times greater than the distances within species, in accordance with the '10× rule' of species identification. Five of the 14 species did not form monophyletic clades based on a Bayesian inference gene tree. The application of four DNA-based species delimitation methods (automatic barcode gap discovery, barcode index numbers, Poisson tree process, and the K/θ method) yielded several key results. (1) Cryptic species were detected within Scomberomoruscommerson. (2) A Scomberomorusqueenslandicus sample from Australia was misidentified as S.commerson in the Barcode of Life Data System (BOLD). (3) Specimens originally identified as Scomberomorusguttatus was differentiated into four OTUs or species, two in the Yellow, South China, and Java seas, and two in geographically distant areas, one each in the Arabian Sea and the Bay of Bengal. (4) Six specimens from South Africa originally identified as S.plurilineatus most likely do not belong to the species. (5) Specimens identified as S.maculatus and S.regalis were conspecific; however, introgression cannot be ruled out. Our findings revealed cryptic diversity and difficulties in morphological identification of species in the genus Scomberomorus. This study provides scientifically based support for the conservation of germplasm resources of the genus Scomberomorus.},
}
@article {pmid36761790,
year = {2022},
author = {Huemer, P},
title = {Underestimated cryptic diversity in the Caryocolumtricolorella species complex (Lepidoptera, Gelechiidae).},
journal = {ZooKeys},
volume = {1103},
number = {},
pages = {189-209},
pmid = {36761790},
issn = {1313-2989},
abstract = {The taxonomy of the Caryocolumtricolorella species complex, an informal subsection of the diverse Caryocoluminteralbicella species group, is revised and four species are separated from DNA barcodes of the mitochondrial COI (cytochrome c oxidase subunit 1) gene and adult morphology: C.tricolorella (Haworth, 1812), C.fibigerium Huemer, 1988, C.herwigvanstaai sp. nov., and C.olekarsholti sp. nov. These species show a vicariant distribution pattern, with C.tricolorella widely distributed in Central and Northern Europe, C.fibigerium restricted to the Iberian Peninsula and southern France, C.herwigvanstaai sp. nov. to the Italian Peninsula, and C.olekarsholti sp. nov. to the Balkans. All species are described in detail, and the adults and genitalia of both sexes are illustrated.},
}
@article {pmid36761789,
year = {2022},
author = {Robertson, DR and Estapé, CJ and Estapé, AM and Richter, L and Peña, E and Victor, B},
title = {An updated, illustrated inventory of the marine fishes of the US Virgin Islands.},
journal = {ZooKeys},
volume = {1103},
number = {},
pages = {79-122},
pmid = {36761789},
issn = {1313-2989},
abstract = {The US Virgin Islands (USVI) include St. John and St. Thomas on the Puerto Rican Platform (PRP) and St. Croix, isolated by 2000 m deep water 45 km south of that platform. Previous inventories of the marine fishes of these islands include a comprehensive 2014 checklist of the fishes of St. Croix and a list of the fishes of the PRP produced in 2000. The latter list noted the locations of many records of the plateau's fishes, allowing the construction of a combined inventory for St. John and St. Thomas. Those two islands are treated here as a single faunal unit because they are only 3.5 km apart on a shared shallow shelf with various islets and reefs in between. Here we provide updated information on those two USVI (St. Croix and St. John-Thomas) marine fish faunas. The additions to the St. Croix and St. John-Thomas inventories presented here are based on a combination of information from the two sources indicated above, more recent publications dealing with those faunas, a review of location records on various online sources of biogeographic data, and voucher photographs taken of fishes in the field by authors of this paper and other citizen scientists. This assessment increased the known fauna of St. Croix by 7.5% to 585 species. The inventory for St. John-Thomas increased by 39.9% from 401 species on the 2000 PRP list to 561 with the inclusion of records from other sources. On-site mtDNA (COI) barcodes are available for approximately one-third of the species of the St. John-Thomas fauna, but for only one species collected at St. Croix. A set of underwater photographs of 372 species (34 of them representing the sole record of a species) from St. John-Thomas and of 11 shallow-water species added to the St. Croix fauna is included. These represent occurrence vouchers and also are intended to facilitate future work that builds on the present compendium.},
}
@article {pmid36761700,
year = {2022},
author = {Vargas, HA},
title = {Scrobipalpulopsisaguilaensis sp. nov. (Lepidoptera, Gelechiidae), the first representative of the genus discovered in the Atacama Desert, northern Chile.},
journal = {ZooKeys},
volume = {1114},
number = {},
pages = {105-119},
pmid = {36761700},
issn = {1313-2989},
abstract = {Genitalia morphology of a new gnorimoschemine micromoth (Lepidoptera, Gelechiidae, Gelechiinae, Gnorimoschemini) discovered in the Atacama Desert, northern Chile, fits the original description of Scrobipalpulopsis Povolný, 1987, a genus previously synonymized with Scrobipalpula Povolný, 1964. The generic assignment of the new species was assessed using a Bayesian phylogenetic analysis based on mitochondrial DNA sequences. The new species, the type species of Scrobipalpulopsis and another species recently transferred from this genus to Scrobipalpula were grouped in a monophyletic cluster distantly related to that of Scrobipalpula. Furthermore, an ancestral state reconstruction analysis suggested that the presence of two pairs of processes on the vinculum in the male genitalia represents a synapomorphy for the cluster of three species. Accordingly, the revalidation of Scrobipalpulopsis gen. rev. (type species Phthorimaeastirodes Meyrick, 1931) and the reinstated combination Scrobipalpulopsislutescella (Clarke, 1934) comb. rev. are proposed. The micromoth Scrobipalpulopsisaguilaensis sp. nov., whose larvae feed on inflorescences of the Chilean endemic Glandulariagynobasis (Verbenaceae), is described and illustrated. Genetic divergence with congenerics was found to be 2.5-4.4% (K2P). This discovery represents the first record of Scrobipalpulopsis from the Atacama Desert.},
}
@article {pmid36761684,
year = {2022},
author = {Sohn, JH and van Achterberg, C and Kim, S and Lim, J and Kim, H},
title = {A new species of the genus Separatatus Chen &amp; Wu (Hymenoptera, Braconidae, Alysiinae) from South Korea.},
journal = {ZooKeys},
volume = {1097},
number = {},
pages = {209-216},
pmid = {36761684},
issn = {1313-2989},
abstract = {Separatatusmegagnathus sp. nov. is recorded as new to science from South Korea. Due to this record, the genus Separatatus Chen &amp; Wu, 1994 (Braconidae: Alysiinae) is recognized for the first time from South Korea. The genus and species are described and illustrated herein plus an identification key including the Korean new species is provided. In addition, the DNA barcode region of the mitochondrial cytochrome c oxidase subunit I (COI) has been analyzed for the new species.},
}
@article {pmid36761651,
year = {2022},
author = {Biella, P and Ssymank, A and Galimberti, A and Galli, P and Perlík, M and Ramazzotti, F and Rota, A and Tommasi, N},
title = {Updating the list of flower-visiting bees, hoverflies and wasps in the central atolls of Maldives, with notes on land-use effects.},
journal = {Biodiversity data journal},
volume = {10},
number = {},
pages = {e85107},
pmid = {36761651},
issn = {1314-2828},
abstract = {Maldives islands host a unique biodiversity, but their integrity is threatened by climate change and impacting land-uses (e.g. cemented or agricultural areas). As pollinators provide key services for the ecosystems and for the inhabitants, it is crucial to know which pollinators occur in the islands, to characterise their genetic identity and to understand which plants they visit and the size of the human impact. Given that no significant faunistic surveys of Hymenoptera have been published for the country in more than 100 years and that Syrphidae were only partly investigated, we sampled islands in the central part of the Maldives country (Faafu and Daahlu atolls) and hand-netted flower-visiting bees, wasps and hoverflies (Hymenoptera: Anthophila, Crabronidae, Sphecidae, Vespidae, Scoliidae and Diptera: Syrphidae). Overall, we found 21 species; 76.4% of the collected specimens were Anthophila (bees), 12.7% belonged to several families of wasps and 10.8% of individuals were Syrphidae. It seems that one third of species are new for the Maldives, based on the published literature. Human land-uses seem to shape the local pollinator fauna since the assemblages of bees, wasps and hoverflies from urbanised and agricultural islands differed from those in resort and natural ones. These pollinators visited 30 plant species in total, although some invasive plants hosted the highest number of flower visitor species. Biogeographically, this pollinating fauna is mostly shared with Sri Lanka and India. Genetically, the used marker hinted for a unique fauna in relation to the rest of the distribution ranges in most cases, although generally within the level of intraspecific genetic variation. This study significantly contributes to increasing the knowledge on the pollinator diversity and genetic identity in Maldives islands also considering the important implications for the islands' land-use and the role of invasive plants. This study will be pivotal for future pollination studies and biodiversity conservation efforts in the region.},
}
@article {pmid36761640,
year = {2022},
author = {Chu, C and Lu, Y and Li, S and Yao, Z},
title = {Taxonomic notes on eleven species of the subfamily Cteninae (Araneae, Ctenidae) from Asia.},
journal = {Biodiversity data journal},
volume = {10},
number = {},
pages = {e96003},
pmid = {36761640},
issn = {1314-2828},
abstract = {BACKGROUND: The spider family Ctenidae Keyserling, 1877 has a worldwide distribution with 584 species belonging to 49 genera. Amongst these, 141 species are from Asia, including 130 species assigned to Cteninae Keyserling, 1877.<br><br>NEW INFORMATION: Nine new species belonging to three genera of Cteninae are reported from Asia: Amauropelmakrabi sp. n. (female; Krabi, Thailand), Am.phangnga sp. n. (male; Phang Nga, Thailand), Am.saraburi sp. n. (male and female; Saraburi, Thailand); Anahitamedog sp. n. (male and female; Tibet, China); Bowieninhbinh sp. n. (male; Ninh Binh, Vietnam) and B.vinhphuc sp. n. (male and female; Vinh Phuc, Vietnam) from the robustus-species group; B.borneo sp. n. (male; Sabah, Malaysia) from the chinagirl-species group; B.engkilili sp. n. (female; Engkilili, Malaysia); B.sabah sp. n. (male and female; Sabah, Malaysia) from the scarymonsters-species group. The male of An.popa J&#xe4;ger &amp; Minn, 2015 and the female of B.fascination J&#xe4;ger, 2022 (robustus-species group) are described for the first time. B.fascination J&#xe4;ger, 2022 is reported from China for the first time. In addition, the DNA barcodes of all the species in this study were obtained, except for B.vinhphuc sp. n.},
}
@article {pmid36761625,
year = {2022},
author = {Zhong, Y and Gong, X and Yu, H},
title = {A new species of the Clubionacorticalis-group (Araneae, Clubionidae) from Jiugong Mountains, Hubei Province, central China.},
journal = {Biodiversity data journal},
volume = {10},
number = {},
pages = {e94735},
pmid = {36761625},
issn = {1314-2828},
abstract = {BACKGROUND: The corticalis group is one of most diverse species-group in genus Clubiona Latreille, 1804. Currently, a total of 81 corticalis group species are known worldwide, amongst them 67 were recorded from China. However, the diversity of this group in China is still insufficiently known.<br><br>NEW INFORMATION: Clubionaxianning sp. nov. is described as a new species of the C.corticalis species-group collected from Hubei Province, China.},
}
@article {pmid36761601,
year = {2022},
author = {Zhang, J and Zhang, W and Deng, L and Lu, Q and Yu, H},
title = {Synemaguiyang sp. nov., the fourth endemic species of Synema Simon, 1864 (Araneae, Thomisidae) from China.},
journal = {Biodiversity data journal},
volume = {10},
number = {},
pages = {e85072},
pmid = {36761601},
issn = {1314-2828},
abstract = {BACKGROUND: Synema Simon, 1864 is a relatively large genus of family Thomisidae Sundevall, 1833 and currently includes 124 species distributed worldwide, except for the Polar Regions. However, Synema can be regarded as being poorly represented in China, with only seven species, three of which are endemic.<br><br>NEW INFORMATION: A new spider species of the genus Synema from Guiyang City in China, is described under the name of S.guiyang J. Zhang, Q. Lu &amp; H. Yu, sp. nov. Detailed descriptions and photographs of the new species are provided. DNA barcodes (a partial fragment of the mitochondrial cytochrome oxidase subunit I gene, COI) of the species were obtained to confirm matching of the sexes and for future use in molecular studies.},
}
@article {pmid36761593,
year = {2022},
author = {Lin, Y and Li, S and Zhao, X and Chen, Z and Chen, H},
title = {Two new Eresus species (Araneae, Eresidae) from Xinjiang, China.},
journal = {Biodiversity data journal},
volume = {10},
number = {},
pages = {e94853},
pmid = {36761593},
issn = {1314-2828},
abstract = {BACKGROUND: Eresidae C. L. Koch, 1845 contains nine genera and 102 species, of which 24 species belong to Eresus Walckenaer, 1805. Four species of the family are known from China: E.granosus Simon, 1895 (Beijing), E.kollari Rossi, 1846 (Hebei), E.lishizheni Lin, Marusik &amp; Li, 2021 (Xinjiang) and Stegodyphustibialis (O. Pickard-Cambridge, 1869) (Yunnan).<br><br>NEW INFORMATION: Two new species of Eresus are described from Xinjiang, China: Eresusda Lin &amp; Li sp. n. and E.yukuni Lin &amp; Li sp. n. Photos and morphological descriptions of new species are given.},
}
@article {pmid36761591,
year = {2022},
author = {Bikashvili, A and Kachlishvili, N and Japoshvili, B and Mumladze, L},
title = {Species diversity and DNA barcode library of freshwater Molluscs of South Caucasus.},
journal = {Biodiversity data journal},
volume = {10},
number = {},
pages = {e84887},
pmid = {36761591},
issn = {1314-2828},
abstract = {This study provides the first attempt to investigate the molecular diversity of South Caucasian freshwater molluscs (Mollusca, Gastropoda) and lay down the first bricks to build up a DNA-barcode library. In total, 289 COI barcode sequences were obtained from 33 morpho-species belonging to 24 molluscan genera and 10 families that represent nearly 30% of known freshwater molluscan diversity of the South Caucasus region. DNA barcodes were analysed by means of the Barcode Index Number (BIN) and the other tools available in BOLD Systems. Results showed that the knowledge of freshwater molluscs diversity in the South Caucasus is far from comprehensive. For the studied 33 morpho-species, 289 barcodes were clustered into 40 BINs, from which unique BINs were defined for 12 species and five species were characterised with more than a single BIN. From the studied taxa, 60% were characterised larger than 2.2% sequence divergence indicating high genetic variation or cryptic diversity. Within our limited taxonomic coverage, we found one new species for the Republic of Georgia (Galbaschirazensis) and at least three undescribed species belonging to the genera Stagnicola, Segmentina and Anisus. Uniqueness and high molecular diversity of the studied species emphasise the need for further intensive morphological and molecular investigations of the South Caucasian freshwater molluscan fauna.},
}
@article {pmid36761556,
year = {2022},
author = {So, WL and Ting, KW and Lai, SY and Huang, EYY and Ma, Y and Chong, TK and Yip, HY and Lee, HT and Cheung, BCT and Chan, MK and Consortium, HKSB and Nong, W and Law, MMS and Lai, DYF and Hui, JHL},
title = {Revealing the millipede and other soil-macrofaunal biodiversity in Hong Kong using a citizen science approach.},
journal = {Biodiversity data journal},
volume = {10},
number = {},
pages = {e82518},
pmid = {36761556},
issn = {1314-2828},
abstract = {BACKGROUND: Soil biodiversity plays important roles in nutrient recycling in both the environment and agriculture. However, they are generally understudied worldwide. To reveal the diversity of soil macrofauna in Hong Kong, here we initiated a citizen science project involving university, non-governmental organisations and secondary school students and teachers. It is envisioned that the citizen science approach used in this study could be used as a demonstration to future biodiversity sampling and monitoring studies.<br><br>NEW INFORMATION: Throughout a year of monitoring and species sampling across different localities in Hong Kong, 150 soil macrofaunal morphospecies were collected. Eighty five of them were further identified by morphology and DNA barcoding was assigned to each identified morphospecies, yielding a total of 646 DNA barcodes, with new millipede sequences deposited to the GenBank. The soil macrofauna morphospecies in Hong Kong found in this study are mainly dominated by millipedes (23 out of 150) and oligochaetes (15 out of 150). Amongst the twenty three identified millipedes, two polyxenid millipedes, Monographisqueenslandica Huynh &amp; Veenstra, 2013 and Alloproctoidesremyi Marquet and Cond&#xe9;, 1950 are first recorded in Hong Kong. Information has been curated on an online platform and database (http://biodiversity.sls.cuhk.edu.hk/millipedes). A postcard summarising the findings of millipedes in Hong Kong has also been made as a souvenir and distributed to citizen participants. The identified macrofauna morphospecies and their 646 DNA barcodes in this study established a solid foundation for further research in soil biodiversity.},
}
@article {pmid36761535,
year = {2022},
author = {Salnitska, M and Solodovnikov, A and Orlov, I},
title = {Sampling and curation of rove beetles (Insecta, Coleoptera, Staphylinidae) for comprehensive and DNA-grade collections to enhance biodiversity exploration in Northern Eurasia.},
journal = {Biodiversity data journal},
volume = {10},
number = {},
pages = {e96080},
pmid = {36761535},
issn = {1314-2828},
abstract = {Staphylinidae beetles form a major portion of terrestrial biodiversity globally and, in particular, in Northern Eurasia, a large area with a historically better known north temperate, subarctic and arctic biota. However, even here, rove beetles remain amongst the so-called "dark taxa" with a high fraction of taxonomically unknown lineage diversity. The propagation of DNA-based technologies in systematic entomology in recent decades has brought new opportunities for biodiversity exploration, true also for Staphylinidae. Simultaneously, new methods have revealed limitations of specimens sampled and curated by traditional practices, as existing legacy collections, whether institutional or private, unfortunately do not always qualify as a source of DNA-grade material. In addition, both legacy and newly-collected DNA-grade material of Staphylinidae remain highly biased towards Central Europe, a region with a traditionally well-developed scientific infrastructure and long-established culture for the maintenance of entomological collections. To increase the degree of biodiversity knowledge for our target organismal group across the globe, efficient sampling of DNA-grade material and, in particular, the development of comprehensive local collections in under-studied regions is highly desirable. To facilitate that, here we provide a practical guide for collecting and curation of Staphylinidae with a focus on capacity building for DNA-grade collections in Siberia and elsewhere in Northern Eurasia.},
}
@article {pmid36761532,
year = {2022},
author = {Vasilita, C and Moser, M and Krogmann, L},
title = {Mission possible: an optimised protocol for the unbarcodable Ceraphronoidea (Hymenoptera).},
journal = {Biodiversity data journal},
volume = {10},
number = {},
pages = {e84860},
pmid = {36761532},
issn = {1314-2828},
abstract = {DNA barcodes provide a reliable and efficient solution to resolving cryptic species complexes and accelerate species discoveries. The superfamily Ceraphronoidea (Hymenoptera) is a group of parasitoid wasps for which a barcoding approach could be of great help, if it were not for the very poor results. The inability to obtain barcodes for the majority of treated ceraphronoids halts progress on the taxonomy of this hyperdiverse parasitoid group. We here present a working protocol for the barcoding of ceraphronoid wasps which yields a first-time over 90% success rate.},
}
@article {pmid36761452,
year = {2022},
author = {Sharkey, MJ and Tucker, EM and Baker, A and Smith, MA and Ratnasingham, S and Manjunath, R and Hebert, P and Hallwachs, W and Janzen, D},
title = {More discussion of minimalist species descriptions and clarifying some misconceptions contained in Meier et al. 2021.},
journal = {ZooKeys},
volume = {1110},
number = {},
pages = {135-149},
pmid = {36761452},
issn = {1313-2989},
abstract = {This is a response to a preprint version of "A re-analysis of the data in Sharkey et al.'s (2021) minimalist revision reveals that BINs do not deserve names, but BOLD Systems needs a stronger commitment to open science", https://www.biorxiv.org/content/10.1101/2021.04.28.441626v2. Meier et al. strongly criticized Sharkey et al.'s publication in which 403 new species were deliberately minimally described, based primarily on COI barcode sequence data. Here we respond to these criticisms. The following points are made: 1) Sharkey et al. did not equate BINs with species, as demonstrated in several examples in which multiple species were found to be in single BINs. 2) We reiterate that BINs were used as a preliminary sorting tool, just as preliminary morphological identification commonly sorts specimens based on color and size into unit trays; despite BINs and species concepts matching well over 90% of species, this matching does not equate to equality. 3) Consensus barcodes were used only to provide a diagnosis to conform to the rules of the International Code of Zoological Nomenclature just as consensus morphological diagnoses are. The barcode of a holotype is definitive and simply part of its cellular morphology. 4) Minimalist revisions will facilitate and accelerate future taxonomic research, not hinder it. 5) We refute the claim that the BOLD sequences of Plesiocoelusvanachterbergi are pseudogenes and demonstrate that they simply represent a frameshift mutation. 6) We reassert our observation that morphological evidence alone is insufficient to recognize species within species-rich higher taxa and that its usefulness lies in character states that are congruent with molecular data. 7) We show that in the cases in which COI barcodes code for the same amino acids in different putative species, data from morphology, host specificity, and other ecological traits reaffirm their utility as indicators of genetically distinct lineages.},
}
@article {pmid36761441,
year = {2022},
author = {Nguyen, TT and Lam, DH and Tran, BTT and Nguyen, AD},
title = {Two new Drawida (Oligochaeta, Moniligastridae) earthworms from Vietnam.},
journal = {ZooKeys},
volume = {1099},
number = {},
pages = {41-56},
pmid = {36761441},
issn = {1313-2989},
abstract = {Two new earthworm species are described, namely Drawidaangiang sp. nov. and Drawidacochinchina sp. nov. The former can be recognized by having male pores on spiniform penises in intersegment 10/11, an erect and sac-shaped spermathecal atrium, glandular prostate, the capsule coiled one round, the vas deferens strongly coiled but small, two large, round, genital markings on segments ix-x, and three gizzards in xiii-xv. The latter species is distinguished in having the male pores placed on highly elevated, backwardly directed, conical penises in 10/11, a slender spermathecal atrium, a glandular prostate, a somewhat folded capsule, the vas deferens strongly coiled as a bunch and equal size to the testis sacs, a pair of genital markings located closely anterior to the penises with 1-3 additional ones in xi-xii, and three or four gizzards in xiii-xvi. The DNA barcode fragment of the COI gene was extracted for each species, and the COI genetic distances and phylogenetic analysis also supported two new species..},
}
@article {pmid36761440,
year = {2022},
author = {Sharkey, MJ and Baker, A and Manjunath, R and Hebert, PDN},
title = {Description of Chilearinus Sharkey gen. nov. and status of Nearctic Earinus Wesmael, 1837 (Braconidae, Agathidinae) with the description of new species.},
journal = {ZooKeys},
volume = {1099},
number = {},
pages = {57-86},
pmid = {36761440},
issn = {1313-2989},
abstract = {The Neotropical members formerly included in Earinus Wesmael, 1837 are transferred to a new genus, Chilearinus Sharkey gen. nov. Presently three Nearctic species of Earinus are recognized, i.e., Earinuserythropoda Cameron, 1887, Earinuslimitaris Say,1835, and Earinuszeirapherae Walley, 1935, and these are retained in Earinus. Earinuschubuquensis Berta, 2000 and Earinusscitus Enderlein, 1920 are transferred to Chilearinus, i.e., C.chubuquensis, and C.scitus, comb. nov. One other species is transferred to Chilearinus, i.e., Microgasterrubricollis Spinola, 1851, Chilearinusrubricollis, comb. nov. Two other Neotropical species, Earinushubrechtae Braet, 2002 and Earinusbourguignoni Braet, 2002 were described under the genus Earinus but are here transferred to Lytopylus, L.hubrechtae, and L.bourguignoni comb. nov. Two new species of Chilearinus are described, C.covidchronos and C.janbert spp. nov. The status of Agathislaevithorax Spinola,1851, Agathisrubricata Spinola,1851, and Agathisareolata Spinola, 1851 is discussed. A neotype is designated for Earinuslimitaris (Say, 1835) and diagnosed with a COI barcode. Earinusaustinbakeri and Earinuswalleyi spp. nov. are described. The status of both Earinus and Chilearinus in the Americas is discussed. A revised key to the genera of Agathidinae of the Americas is presented.},
}
@article {pmid36761338,
year = {2023},
author = {Hishamuddin, MS and Lee, SY and Syazwan, SA and Ramlee, SI and Lamasudin, DU and Mohamed, R},
title = {Highly divergent regions in the complete plastome sequences of Aquilaria are suitable for DNA barcoding applications including identifying species origin of agarwood products.},
journal = {3 Biotech},
volume = {13},
number = {3},
pages = {78},
pmid = {36761338},
issn = {2190-572X},
abstract = {UNLABELLED: Members of Aquilaria Lam. (Thymelaeaceae) are evergreen trees that are widely distributed in the Indomalesia region. Aquilaria is highly prized for its unique scented resin, agarwood, which is often the subject of unlawful trade activities. Survival of the tree is heavily threatened by destructive harvesting and agarwood poaching, leading to its protection under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Unfortunately, an efficient species identification method, which is crucial to aid in the conservation efforts of Aquilaria is lacking. Here, we described our search for a suitable specific DNA barcode for Aquilaria species using eight complete plastome sequences. We identified five highly variable regions (HVR) (matK-rps16, ndhF-rpl32, psbJ-petA, trnD, and trnT-trnL) in the plastomes. These regions were further analyzed using the neighbor-joining (NJ) method to assess their ability at discriminating the eight species. Coupled with in silico primer design, two potential barcoding regions, psbJ-petA and trnT-trnL, were identified. Their strengths in species delimitation were evaluated individually and in combination, via DNA barcoding analysis. Our findings showed that the combined dataset, psbJ-petA + trnT-trnL, effectively resolved members of the genus Aquilaria by clustering all species into their respective clades. In addition, we demonstrated that the newly proposed DNA barcode was capable at identifying the species of origin of six commercial agarwood samples that were included as unknown samples. Such achievement offers a new technical advancement, useful in the combat against illicit agarwood trades and in assisting the conservation of these valuable species in natural populations.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-023-03479-1.},
}
@article {pmid36761317,
year = {2022},
author = {Ossowska, EA and Moncada, B and Kukwa, M and Flakus, A and Rodriguez-Flakus, P and Olszewska, S and Lücking, R},
title = {New species of Sticta (lichenised Ascomycota, lobarioid Peltigeraceae) from Bolivia suggest a high level of endemism in the Central Andes.},
journal = {MycoKeys},
volume = {92},
number = {},
pages = {131-160},
pmid = {36761317},
issn = {1314-4049},
abstract = {Six species of Sticta are described as new to science on the basis of material from Bolivia and supported by phylogenetic analysis of the fungal ITS barcoding marker. The species were resolved in all three of the clades (I, II, III) widespread and common in the Neotropics, as defined in an earlier study on the genus. Comparison with material from neighbouring countries (i.e. Colombia, Ecuador, Peru) suggests that these new species may be potentially endemic to the Bolivian Yungas ecoregion. For each species, a detailed morphological and anatomical description is given. Stictaamboroensis Ossowska, Kukwa, B. Moncada &amp; Lücking is a medium-sized green-algal species with laminal to submarginal apothecia with hirsute margins and with light to dark brown lower tomentum. Stictaaymara Ossowska, Kukwa, B. Moncada, Flakus, Rodriguez-Flakus &amp; Lücking is a comparatively small cyanobacterial taxon with Nostoc as photobiont, laminal, richly branched, aggregate isidia and a golden to chocolate-brown lower tomentum. The medium-sized, cyanobacterial S.bicellulata Ossowska, Kukwa, B. Moncada &amp; Lücking has cyanobacterial photobiont, bicellular ascospores, apothecia with white to golden-brown hairs on the margins, K+ violet apothecial margin (ring around disc) and epihymenium and a white to dark brown lower tomentum. In contrast, the green-algal species, S.carrascoensis Ossowska, Kukwa, B. Moncada &amp; Lücking is characterised by its large size, apothecia with dark brown hairs on the margins and a yellow medulla. The cyanobacterial S.catharinae Ossowska, B. Moncada, Kukwa, Flakus, Rodriguez-Flakus &amp; Lücking forms stipitate thalli with Nostoc as photobiont, abundant, laminal to submarginal apothecia and a golden-brown lower tomentum. Finally, the cyanobacterial S.pseudoimpressula Ossowska, Kukwa, B. Moncada &amp; Lücking produces laminal apothecia with an orange-yellow line of pruina along the margins which reacts K+ carmine-red. In addition to the six new Bolivian taxa, the cyanobacterial S.narinioana B. Moncada, Ossowska &amp; Lücking is described as new from Colombia and it represents the closely-related sister species of the Bolivian S.aymara; it differs from the latter largely in the marginal instead of laminal isidia.},
}
@article {pmid36761291,
year = {2022},
author = {Sheraliev, B and Kayumova, Y and Peng, Z},
title = {Triplophysadaryoae, a new nemacheilid loach species (Teleostei, Nemacheilidae) from the Syr Darya River basin, Central Asia.},
journal = {ZooKeys},
volume = {1125},
number = {},
pages = {47-67},
pmid = {36761291},
issn = {1313-2989},
abstract = {Triplophysadaryoae, new species, is described from the Sokh River, a former tributary of Syr Darya that today fails to reach the river, in the Sokh District, an exclave of Uzbekistan, surrounded by Kyrgyzstan. Triplophysadaryoae is distinguished from other species of Triplophysa in Central Asia by a truncate caudal fin with 13 or 14 branched rays, body without obvious mottling, dorsal-fin origin opposite to pelvic-fin insertion, and absence of the posterior chamber of the air bladder. Molecular data suggest that Triplophysadaryoae is closely related to T.ferganaensis from the Shakhimardan stream, a small tributary of Syr Darya in the Yordon village, another exclave of Uzbekistan in Kyrgyzstan. The two species were separated by a Kimura 2-parameter genetic distance of 2.8% in the mitochondrial DNA cytochrome c oxidase subunit I barcode region; they are also distinguished morphologically. A key to the species of Triplophysa in the Syr Darya basin and adjacent regions is provided.},
}
@article {pmid36761084,
year = {2023},
author = {Vargas, HA},
title = {Disclisioproctaedmondsii (Butler, 1882) comb. nov. (Lepidoptera, Geometridae, Larentiinae).},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e98935},
pmid = {36761084},
issn = {1314-2828},
abstract = {BACKGROUND: The generic assignment of the geometrid moth Xanthorhoeedmondsii (Butler, 1882) (Lepidoptera, Geometridae, Larentiinae), originally described under Hypochroma Guenée, [1858], a junior homonym of Hypochroma Herrich-Schäffer, [1855] (Geometridae, Ennominae), is assessed using genitalia morphology and analysis of mitochondrial DNA sequences.<br><br>NEW INFORMATION: Morphological characters revealed closeness to the type species of Disclisioprocta Wallengren, 1861 (Larentiinae). In agreement with morphology, the molecular analysis clustered X.edmondsii with species of Disclisioprocta in a well-supported monophyletic group distantly related to members of Xanthorhoe H&#xfc;bner, [1825]. Accordingly, Disclisioproctaedmondsii (Butler, 1882) comb. nov. is proposed.},
}
@article {pmid36761079,
year = {2023},
author = {Schubert, HC and Duda, M and Eschner, A and Weigand, E and Kruckenhauser, L},
title = {DNA barcoding as a tool to monitor the diversity of endangered spring snails in an Austrian National Park.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e91496},
pmid = {36761079},
issn = {1314-2828},
abstract = {The Kalkalpen National Park is situated in Upper Austria and contains more than 800 springs. The international importance of this Park is, from the perspective of nature conservation directives, highly significant (European Nature Reserve Natura 2000, recognised wetland of the Ramsar convention). In the current study, the hydrobioid fauna ('spring snails') of the Kalkalpen National Park was evaluated. These tiny snails are difficult to determine; however, their investigation is especially desirable, as several species are threatened and as they are important for water quality assessment. Snails collected in 39 selected springs were examined with classical morphological methods (shell and genital anatomy) and, subsequently, by DNA analysis. For this task, the DNA barcode, a partial sequence of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene (length of the sequence 658-682 bp), was PCR amplified and sequenced. From 107 specimens, the DNA barcoding sequence could be obtained and compared with already existing DNA sequences. The (sub)endemic species Bythinellaconica, Hauffeniakerschneri, Hauffeniawienerwaldensis and Belgrandiellaaulaei could be clearly identified. For Bythiospeumnocki, despite the ambitious collecting effort, only empty shells were found in four springs (including the locus typicus spring) in the Park and its surroundings. The genus Bythinella was detected in 36 springs. From 25 of these localities, DNA barcodes could be created, which matches those of Bythinellaconica (comparison data from ABOL). It is, therefore, concluded that the species occurs widely in the Kalkalpen National Park. The genus Hauffenia was sampled from 16 springs. From one, the haplotype of Hauffeniawienerwaldensis could be identified (spring is 5 km outside the Park) and from six, the haplotype of Hauffeniakerschneri. Belgrandiellaaulaei was found in three springs, which all lie outside the boundaries and are, therefore, not included in the protection measures of the National Park. The data and analyses obtained contribute to the assessment of the taxonomic status of the species studied. The present study gives a good baseline for further monitoring of the hydrobioids in the Kalkalpen National Park, which is important to evaluate current as well as to decide on future protection measures for this group.},
}
@article {pmid36761074,
year = {2022},
author = {Tsukamoto, S and Shimano, S and Eguchi, K},
title = {Two new species of the dwarf centipede genus Nannarrup Foddai, Bonato, Pereira &amp; Minelli, 2003 (Chilopoda, Geophilomorpha, Mecistocephalidae) from Japan.},
journal = {ZooKeys},
volume = {1115},
number = {},
pages = {117-150},
pmid = {36761074},
issn = {1313-2989},
abstract = {The genus Nannarrup Foddai, Bonato, Pereira &amp; Minelli, 2003 is a monotypic genus established on the basis of the possibly introduced species N.hoffmani Foddai, Bonato, Pereira &amp; Minelli, 2003, from New York, USA. In the present study, in a field survey conducted throughout Japan, Nannarrup-like specimens were collected from Honshu, Shikoku, and Kyushu. These specimens clearly showed the diagnostic characteristics of the genus but were morphologically distinct from N.hoffmani. Furthermore, morphological analysis and DNA barcoding revealed that these specimens could be assigned to two distinct undescribed species. On the basis of these results, N.innuptus Tsukamoto, sp. nov. and N.oyamensis Tsukamoto, sp. nov. are described. The three Nannarrup species can be distinguished from each other on the basis of the following combination of characteristics: presence or absence of a pair of smooth or weakly areolate areas along the posterior part of the paraclypeal sutures; the width-to-length ratio of the denticle on the trochanteroprefemur; the pigmentation of the denticle on the tarsungulum. Moreover, the field survey resulted in the collection of exclusively female specimens of N.innuptus Tsukamoto, sp. nov., which shows the possibility of parthenogenesis of this species.},
}
@article {pmid36761016,
year = {2022},
author = {Deng, X and Shan, J and Xiao, C and Zhu, J and Wang, Z and Che, Y},
title = {Establishment of two new Anaplecta species (Blattodea, Blattoidea, Anaplectidae) based on morphological and COI data with an additional description of Anaplectafurcata Deng &amp; Che, 2020.},
journal = {ZooKeys},
volume = {1130},
number = {},
pages = {153-166},
pmid = {36761016},
issn = {1313-2989},
abstract = {Based on morphological characteristics, including male and female genitalia, combined with DNA barcodes, two new species, Anaplectacircinalis Deng &amp; Che, sp. nov. and Anaplectabihamata Deng &amp; Che, sp. nov., are described in detail. Additional information on the female genitalia of Anaplectafurcata Deng &amp; Che, 2020 is also provided. Photographs of external morphology and caudal anatomy of these species, as well as a key to the Chinese Anaplecta species, are provided.},
}
@article {pmid36760985,
year = {2022},
author = {Schallenberg, VM and Heim, R and Schneppat, UE and Müller, P and Rüetschi, J and Neubert, E},
title = {Revision of the family Milacidae from Switzerland (Mollusca, Eupulmonata, Parmacelloidea).},
journal = {ZooKeys},
volume = {1116},
number = {},
pages = {149-179},
pmid = {36760985},
issn = {1313-2989},
abstract = {In this work, the presence of species of the slug family Milacidae in Switzerland was investigated by using the barcoding marker cytochrome c oxidase subunit I (COI) as well as traits of the body and the genital organs. Currently, three species of Tandonia living in Switzerland in established populations could be reported, i.e., T.rustica, T.budapestensis, and T.nigra. The three records of Milaxgagates were re-investigated, but only for one of these records could the identification be reconfirmed. This species has currently no established and thriving population in Switzerland. For all species recorded, detailed descriptions of body morphology, genital anatomy, and distribution data are provided based on the investigated Swiss animals. An unknown pale colour morph of a Tandonia sp. from Canton Ticino could be identified as T.nigra, and the barcodes of T.nigra specimens were submitted to GenBank for the first time. The identity of the Italian and Austrian populations of T.nigra from the Bergamasque Alps and north Tirol is evaluated. Observations on details of the morphology of the genital organs in T.rustica vs. T.kusceri are discussed.},
}
@article {pmid36760820,
year = {2022},
author = {Xu, Y and Jiang, LY and Chen, J and Kholmatov, BR and Qiao, GX},
title = {Six new species of Aspidophorodon Verma, 1967 (Hemiptera, Aphididae, Aphidinae) from China.},
journal = {ZooKeys},
volume = {1106},
number = {},
pages = {1-55},
pmid = {36760820},
issn = {1313-2989},
abstract = {The genus Aspidophorodon Verma is presented including six new species from China namely Aspidophorodoncapitatum Qiao &amp; Xu, sp. nov. Aspidophorodonlongicornutum Qiao &amp; Xu, sp. nov. Aspidophorodonreticulatum Qiao &amp; Xu, sp. nov. Aspidophorodonfurcatum Qiao &amp; Xu, sp. nov. Aspidophorodonlongirostre Qiao &amp; Xu, sp. nov. and Aspidophorodonobtusirostre Qiao &amp; Xu, sp. nov. Aspidophorodoncornuatum Qiao 2015, is considered as a junior synonym of Aspidophorodonlongituberculatum (Zhang Zhong &amp; Zhang 1992), syn. nov. Two species Aspidophorodonharvense Verma and Aspidophorodonindicum (David Rajasingh &amp; Narayanan) are recorded for the first time in China. The genus is mainly distributed in East Asia and is represented by 15 species in the world of which 12 are found in China. Keys to the species of Aspidophorodon are given.},
}
@article {pmid36760818,
year = {2022},
author = {Vasquez-Valverde, LF and Marek, PE},
title = {Phylogenetic review of the millipede genus Cherokia Chamberlin, 1949 (Polydesmida, Xystodesmidae).},
journal = {ZooKeys},
volume = {1106},
number = {},
pages = {141-163},
pmid = {36760818},
issn = {1313-2989},
abstract = {The millipede genus Cherokia Chamberlin, 1949 is a monospecific taxon, with the type species Cherokiageorgiana (Bollman, 1889). The last revision of the genus was made by Hoffman (1960) where he established three subspecies. Here we used molecular phylogenetics to assess the genus and evaluate whether it is a monophyletic group, and if the subspecies are each monophyletic. We included material from literature records and three natural history collections. Newly collected samples were obtained through a citizen science project. Morphological characters underlying subspecies groups-the shape of the paranota, body size, and coloration-were evaluated. A molecular phylogeny of the genus was estimated based on DNA sequences for seven gene loci, and a species delimitation analysis was used to evaluate the status of the subspecies. The documented geographical range of Cherokia in the United States was expanded to include a newly reported state record (Virginia) and about 160 new localities compared to the previously known range. Morphological characters, which included the shape of the paranota and body size that had been historically used to establish subspecies, showed clinal variation with a direct relationship with geographical distribution and elevation, but not with phylogeny. Coloration was highly variable and did not accord with geography or phylogeny. The phylogeny recovered Cherokia as a monophyletic lineage, and the species delimitation test supported the existence of a single species. The subspecies Cherokiageorgianaducilla (Chamberlin, 1939) and Cherokiageorgianalatassa Hoffman, 1960 have been synonymized with Cherokiageorgiana. The molecular and morphological evidence showed that Cherokia is a monospecific genus with the sole species, Cherokiageorgiana, being geographically widespread and highly variable in its morphology.},
}
@article {pmid36760703,
year = {2022},
author = {Zhao, Y and Guo, WR and Golovatch, SI and Liu, WX},
title = {Revision of the javanicus species group of the millipede genus Glyphiulus Gervais, 1847, with descriptions of five new species from China (Diplopoda, Spirostreptida, Cambalopsidae).},
journal = {ZooKeys},
volume = {1108},
number = {},
pages = {89-118},
pmid = {36760703},
issn = {1313-2989},
abstract = {The javanicus-group of Glyphiulus is re-assessed and its Chinese component species are presently divided between the following two newly-circumscribed species groups, i.e. the formosus- and the sinensis-group. The two can be differentiated, based on the diagnostic characters of the first pair of legs in the male. In addition, metatergal crests being complete and the carinotaxy formula on the collum being I-III+P+M are only characteristic of the formosus-group. A molecular phylogeny of the genus, based on DNA sequencing of four gene fragments of four genes, allows for Glyphiulus to be recovered as a monophyletic group, the phylogenetic relationship being ((Clade A, Clade B), Clade C). Molecular evidence is fully congruent with the morphological one. In addition, based on barcoding data, interspecific p-distances between Glyphiulus species amount to 11.2-24.9%, vs. 0-8.2% for intraspecific p-distances. Five new species of Glyphiulus, all cavernicolous, are described from China: G.sinuatoprocessus Zhao &amp; Liu, sp. nov., G.conuliformis Zhao &amp; Liu, sp. nov. (both from Guangdong Province), G.xiniudong Zhao &amp; Liu, sp. nov., G.scutatus Zhao &amp; Liu, sp. nov. and G.portaliformis Zhao &amp; Liu, sp. nov. (all three from Guangxi Zhuang Autonomous Region). The known Chinese species of the formosus-group appear to mainly be confined to the South China region.},
}
@article {pmid36760623,
year = {2022},
author = {Ge, XY and Peng, L and Du, J and Sun, CH and Wang, BX},
title = {New species of the genus Molanna Curtis, 1834 (Trichoptera, Molannidae) in China inferred from morphology and DNA barcodes.},
journal = {ZooKeys},
volume = {1112},
number = {},
pages = {161-178},
pmid = {36760623},
issn = {1313-2989},
abstract = {The male adult of Molannatruncata Ge, Peng &amp; Sun sp. nov. is described and illustrated based on material collected in Si-chuan, China. It could be diagnosed by the subtriangular superior appendages when viewed dorsally, and by the mesal appendages each having a slender thorn and inferior appendages with a tiny inner process. Based on morphology of genitalia, we provide a dichotomous key to adult males of Molanna from the Oriental region. The DNA barcodes (partial mtCOI sequences) of M.truncata sp. nov. are generated and compared with existing sequences of Molanna species from Oriental and Palearctic regions. The mean intraspecific divergence of Molanna was 1.58% with a maximum of 8.50% in M.moesta. The Automatic Barcode Gap Discovery (ABGD) analysis of Molanna inferred 9 OTUs and thresholds of interspecific divergence of 10%. Divergence of M.truncata sp. nov. haplotypes from all other Molanna haplotypes ranged from 10.1% to 18%. We discuss distribution and potential groups of species within the Oriental Molanna species based on morphology.},
}
@article {pmid36760620,
year = {2022},
author = {Wu, X and He, Z and Lin, X and Deng, B and Zhai, Q and Li, J},
title = {Three new species of the genus Alluaudomyia Kieffer, 1913 (Diptera, Ceratopogonidae) from the National Park of Hainan Tropical Rainforest, China.},
journal = {ZooKeys},
volume = {1112},
number = {},
pages = {199-218},
pmid = {36760620},
issn = {1313-2989},
abstract = {Three new species of the predaceous midges of genus Alluaudomyia Kieffer, 1913: A.flavinotum Wu &amp; Li, sp. nov. of the maculipennis group, and A.reflexuralis Wu &amp; Li, sp. nov. and A.limu Wu &amp; Li, sp. nov. of the parva group, are described from the National Park of Hainan Tropical Rainforest, Hainan Island, China. Illustrations and COI barcodes (a fragment of the mitochondrial cytochrome c oxidase subunit 1) of the three new species are also provided. Associations of male and female specimens of two species (A.reflexuralis Wu &amp; Li, sp. nov. and A.limu Wu &amp; Li, sp. nov.) are supported by DNA barcodes. The parva group is reported from China for the first time.},
}
@article {pmid36760494,
year = {2022},
author = {Barroso, M and Moreira, J and Capa, M and Nygren, A and Parapar, J},
title = {A further step towards the characterisation of Terebellides (Annelida, Trichobranchidae) diversity in the Northeast Atlantic, with the description of a new species.},
journal = {ZooKeys},
volume = {1132},
number = {},
pages = {85-126},
pmid = {36760494},
issn = {1313-2989},
abstract = {Several new species of genus Terebellides Sars, 1835 (Annelida, Trichobranchidae) have been recently described from the Northeast Atlantic Ocean after the detection of a large complex of species based on DNA sequence data from previous research. Some of those species (belonging to the so-called Group A) have already been described elsewhere. In this paper, we revise several Terebellides clades belonging to Groups B, C and D resulting in the identification of five nominal species: Terebellidesgracilis Malm, 1874, Terebellidesatlantis Williams, 1984, Terebellideswilliamsae Jirkov, 1989, Terebellidesirinae Gagaev, 2009, and Terebellidesshetlandica Parapar, Moreira &amp; O'Reilly, 2016, plus one new species described here as Terebellideslavesquei sp. nov. All these species are characterised by a combination of morphological features complemented with a nucleotide diagnostic approach (specific COI nucleotides in the alignment position). Morphological characters used to discriminate between taxa refer to the branchial shape, presence/absence of ciliated papillae dorsal to thoracic notopodia and the morphology of thoracic and abdominal uncinal teeth. An updated identification key to all described species of this genus in NE Atlantic waters is also included.},
}
@article {pmid36760492,
year = {2022},
author = {Elgetany, AH and Struck, TH and Glasby, CJ},
title = {Three new species of the genus Perinereis (Annelida, Nereididae) from Egyptian coasts.},
journal = {ZooKeys},
volume = {1132},
number = {},
pages = {163-188},
pmid = {36760492},
issn = {1313-2989},
abstract = {Despite being one of the most common groups of polychaetes on intertidal shores, the genus Perinereis (Nereididae) is comparatively poorly known taxonomically, with confusion still existing due to the lack of comprehensive systematic studies. The systematics of Perinereis species from the intertidal Egyptian coasts of the Red Sea, Gulf of Suez and Suez Canal have been investigated using morphology and the mitochondrial barcoding marker cytochrome oxidase subunit I (COI). New sequence data was obtained for 102 Perinereis specimens and analysis included all publicly available COI data from other Perinereis species. The COI data indicate that monophyly of the P.nuntia species group is doubtful, as specimens identified in this species group from south-eastern Asia and Australia form a monophyletic group exclusive of the three new species described in this study from the Red Sea region. A morphometric character set (26 characters) was used to identify and characterize each specimen in the study. Three distinct morphospecies belonging to the P.nuntia species group were found, each differentiated by the number and type of paragnaths on pharyngeal areas V and VI, relative sizes of parapodial lobes, type of notochaetae and neurochaetae, and form of the neurochaetal falciger blades. The three morphospecies were well supported by COI data: two of the three new species, Perinereissuezensis sp. nov. and Perinereisfayedensis sp. nov., are closely similar to P.nuntia sensu stricto, while the other, Perinereisdamietta sp. nov., is similar to P.heterodonta. The new species are described and illustrated, and bring the number of species in Perinereis to 97. The new species are compared and contrasted to the closely similar P.heterodonta, P.nuntia and other congeners from the region.},
}
@article {pmid36760491,
year = {2022},
author = {Kato, D and Watanabe, K and Kolcsár, LP},
title = {Japanese species of Ormosia Rondani (Diptera, Limoniidae): revision of the subgenera Oreophila Lackschewitz and Parormosia Alexander.},
journal = {ZooKeys},
volume = {1132},
number = {},
pages = {127-162},
pmid = {36760491},
issn = {1313-2989},
abstract = {Japanese species of the subgenera Oreophila Lackschewitz and Parormosia Alexander of the genus Ormosia Rondani (Limoniidae) are revised. Two new species Ormosia (Oreophila) komazawai Kato &amp; Kolcsár, sp. nov. and Ormosia (Parormosia) phalara Kato &amp; Kolcsár, sp. nov. are described. The identities of all Japanese species of the two subgenera are clarified and redescribed with images of habitus and wings, and drawings of male and female terminalia. The first DNA barcode sequences of the species Ormosia (Parormosia) diversipes Alexander and Ormosia (Parormosia) phalara Kato &amp; Kolcsár, sp. nov. are also provided. A key to, and distribution maps of, the Japanese species are provided.},
}
@article {pmid36760486,
year = {2022},
author = {Parmentier, L and Vila, R and Lukhtanov, V},
title = {Integrative analysis reveals cryptic speciation linked to habitat differentiation within Albanian populations of the anomalous blues (Lepidoptera, Lycaenidae, Polyommatus Latreille, 1804).},
journal = {Comparative cytogenetics},
volume = {16},
number = {4},
pages = {211-242},
pmid = {36760486},
issn = {1993-0771},
abstract = {The Balkan Peninsula is one of the greatest hotspots for biodiversity in Europe. While the region has been investigated thoroughly, some parts remain understudied and may still harbour undiscovered diversity, even in well-studied organisms such as Lepidoptera. Here we investigated the group of the so-called anomalous blue butterflies, also known as 'brown complex' of the subgenus Agrodiaetus Hübner, 1822 including the taxa of the entire Polyommatusaroaniensis (Brown, 1976) species complex. This species complex is distributed in the southern part of the Balkan Peninsula and known to be represented by three closely related allopatric species, differentiated by their chromosome numbers (n) and mitochondrial (mt) DNA. These are P.aroaniensis sensu stricto (Southern Greece, Peloponnese, n=47-48; mt haplogroup aroa1), P.timfristos Lukhtanov, Vishnevskaya et Shapoval, 2016 (Central Greece, Attika, n=38, aroa2) and P.orphicus Kolev, 2005 (North-Eastern Greece, Southern Bulgaria, n=41-42, orph1). Based on an analysis of chromosomal, molecular and morphological markers, we demonstrate that a fourth taxon of this species complex exists in Albania. This taxon possesses the mt haplogroup aroa3, which is the most differentiated within the entire P.aroaniensis species complex, and the karyotype (n=42-43), which differs by one fixed chromosome fission from P.orphicus. The Albanian taxon seems to be ecologically specialised (habitat on dark-coloured, ophiolitic substrate soils) and differs in colouration (wing reflectance) from the others taxa of the P.aroaniensis species group. Based on the evidence here presented and following the current view of the taxonomy of the group, we propose considering the Albanian taxon as a new species, here described as Polyommatuslurae sp. nov. At the contact zone between the new species and P.orphicus, in addition to typical ones, we detected specimens with haplogroup orph2, karyotype n=43 and intermediate morphology, which seem to represent P.lurae × P.orphicus hybrids.},
}
@article {pmid36760422,
year = {2022},
author = {Eberhardt, U and Kong, A and Montoya, A and Schütz, N and Bartlett, P and Beker, HJ},
title = {Not (only) poison pies - Hebeloma (Agaricales, Hymenogastraceae) in Mexico.},
journal = {MycoKeys},
volume = {90},
number = {},
pages = {163-202},
pmid = {36760422},
issn = {1314-4049},
abstract = {The species of Hebeloma have been little studied in Mexico, but have received attention as edibles and in trials to enhance production of edible fungi and tree growth through inoculation of seedlings with ectomycorrhizal fungi. Here we describe three new species of Hebeloma that are currently known only from Mexico. These species belong to separate sections of the genus: H.ambustiterranum is a member of H.sect.Hebeloma, H.cohaerens belongs to H.sect.Theobromina, while H.magnicystidiatum belongs to H.sect.Denudata. All three species were collected from subtropical pine-oak woodland; all records of H.cohaerens came from altitudes above 2500 m. Hebelomaambustiterranum is commonly sold in the local markets of Tlaxcala as a prized edible mushroom. An additional nine species are reported from Mexico, of which eight are new records for the country: H.aanenii, H.eburneum, H.excedens, H.ingratum, H.neurophyllum, H.sordidulum, H.subaustrale and H.velutipes. First modern descriptions of H.neurophyllum and H.subaustrale, originally described from the USA, are given here.},
}
@article {pmid36760355,
year = {2022},
author = {Rodriguez, EJ and Steck, GJ and Moore, MR and Norrbom, AL and Diaz, J and Somma, LA and Ruiz-Arce, R and Sutton, BD and Nolazco, N and Muller, A and Branham, MA},
title = {Exceptional larval morphology of nine species of the Anastrephamucronota species group (Diptera, Tephritidae).},
journal = {ZooKeys},
volume = {1127},
number = {},
pages = {155-215},
pmid = {36760355},
issn = {1313-2989},
abstract = {Anastrepha is the most diverse and economically important genus of Tephritidae in the American tropics and subtropics. The striking morphology of the third instars of Anastrephacaballeroi Norrbom, Anastrephacrebra Stone, Anastrephahaplacantha Norrbom &amp; Korytkowski, Anastrephakorytkowskii Norrbom, Anastrephanolazcoae Norrbom &amp; Korytkowski, and three newly discovered and as yet formally unnamed species (Anastrepha sp. Peru-82, Anastrephasp.nr.protuberans, and Anastrepha sp. Sur-16), and the more typical morphology of Anastrephaaphelocentema Stone, are described using light and scanning electron microscopy. To contribute to a better understanding of the interspecific and intraspecific variation among species in the mucronota species group and facilitate phylogenetic studies, we integrate molecular and morphological techniques to confirm the identity and describe third instars. Larva-adult associations and the identification of described larvae were confirmed using DNA barcodes. We provide diagnostic characters to distinguish larvae among these nine species of the mucronota group and separate them from those of the 29 other Anastrepha species previously described. We introduce the vertical comb-like processes on the oral margin as a novel character, and the unusual character states, including position and shape of the preoral lobe, and dentate or fringed posterior margins of the oral ridges and accessory plates. Our comparative morphology concurs with most previously inferred phylogenetic relationships within the mucronota group.},
}
@article {pmid36760327,
year = {2022},
author = {Han, W and Qiu, L and Zhu, J and Wang, ZQ and Che, YL},
title = {Exploring the diversity of Eupolyphaga Chopard, 1929 (Blattodea, Corydioidea): species delimitation based on morphology and molecular analysis.},
journal = {ZooKeys},
volume = {1120},
number = {},
pages = {67-94},
pmid = {36760327},
issn = {1313-2989},
abstract = {Eupolyphaga Chopard, 1929 is a cockroach genus mainly endemic to China. In this study, the species diversity of this genus is further explored through morphology and molecular analysis. Four species are described new to science: Eupolyphagamiracidia Qiu, sp. nov., Eupolyphagaudenostyla Qiu, sp. nov., Eupolyphagareducta Qiu, sp. nov., and Eupolyphagasimila Qiu, sp. nov. New knowledge on some known species is added, including new distribution records and characteristics of females. Forty-five COI sequences were newly sequenced and a molecular species delimitation analysis was performed using ABGD method. Eighteen molecular operational taxonomic units were obtained by ABGD analysis, which are nearly consistent with the results of morphological delimitation.},
}
@article {pmid36759652,
year = {2023},
author = {Andresen, E and Islam, F and Prinz, C and Gehrmann, P and Licha, K and Roik, J and Recknagel, S and Resch-Genger, U},
title = {Assessing the reproducibility and up-scaling of the synthesis of Er,Yb-doped NaYF4-based upconverting nanoparticles and control of size, morphology, and optical properties.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {2288},
pmid = {36759652},
issn = {2045-2322},
abstract = {Lanthanide-based, spectrally shifting, and multi-color luminescent upconverting nanoparticles (UCNPs) have received much attention in the last decades because of their applicability as reporter for bioimaging, super-resolution microscopy, and sensing as well as barcoding and anti-counterfeiting tags. A prerequisite for the broad application of UCNPs in areas such as sensing and encoding are simple, robust, and easily upscalable synthesis protocols that yield large quantities of UCNPs with sizes of 20 nm or more with precisely controlled and tunable physicochemical properties from low-cost reagents with a high reproducibility. In this context, we studied the reproducibility, robustness, and upscalability of the synthesis of β-NaYF4:Yb, Er UCNPs via thermal decomposition. Reaction parameters included solvent, precursor chemical compositions, ratio, and concentration. The resulting UCNPs were then examined regarding their application-relevant physicochemical properties such as size, size distribution, morphology, crystal phase, chemical composition, and photoluminescence. Based on these screening studies, we propose a small volume and high-concentration synthesis approach that can provide UCNPs with different, yet controlled size, an excellent phase purity and tunable morphology in batch sizes of up to at least 5 g which are well suited for the fabrication of sensors, printable barcodes or authentication and recycling tags.},
}
@article {pmid36757949,
year = {2023},
author = {Chen, H and Chen, H and Wang, B and Liu, C},
title = {Conserved chloroplast genome sequences of the genus Clerodendrum Linn. (Lamiaceae) as a super-barcode.},
journal = {PloS one},
volume = {18},
number = {2},
pages = {e0277809},
pmid = {36757949},
issn = {1932-6203},
mesh = {*Clerodendrum/genetics ; *Lamiaceae/genetics ; *Genome, Chloroplast ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The plants of the genus Clerodendrum L. have great potential for development as an ornamental and important herbal resource. There is no significant morphological difference among many species of the genus Clerodendrum, which will lead to confusion among the herbs of this genus and ultimately affect the quality of the herbs. The chloroplast genome will contribute to the development of new markers used for the identification and classification of species.<br><br>METHODS AND RESULTS: Here, we obtained the complete chloroplast genome sequences of Clerodendrum chinense (Osbeck) Mabberley and Clerodendrum thomsoniae Balf.f. using the next generation DNA sequencing technology. The chloroplast genomes of the two species all encode a total of 112 unique genes, including 80 protein-coding, 28 tRNA, and four rRNA genes. A total of 44-42 simple sequence repeats, 19-16 tandem repeats and 44-44 scattered repetitive sequences were identified. Phylogenetic analyses showed that the nine Clerodendrum species were classified into two clades and together formed a monophyletic group. Selective pressure analyses of 77 protein-coding genes showed that there was no gene under positive selection in the Clerodendrum branch. Analyses of sequence divergence found two intergenic regions: trnH-GUG-psbA, nhdD-psaC, exhibiting a high degree of variations. Meanwhile, there was no hypervariable region identified in protein coding genes. However, the sequence identities of these two intergenic spacers (IGSs) are greater than 99% among some species, which will result in the two IGSs not being used to distinguish Clerodendrum species. Analysis of the structure at the LSC (Large single copy) /IR (Inverted repeat) and SSC (Small single copy)/IR boundary regions showed dynamic changes. The above results showed that the complete chloroplast genomes can be used as a super-barcode to identify these Clerodendrum species. The study lay the foundation for the understanding of the evolutionary process of the genus Clerodendrum.},
}
@article {pmid36757061,
year = {2023},
author = {Li, X and Cai, L and Wang, Y and Hong, J and Zhang, D},
title = {Hydrogel Encapsulated Core-Shell Photonic Barcodes for Multiplex Biomarker Quantification.},
journal = {Analytical chemistry},
volume = {95},
number = {7},
pages = {3806-3810},
doi = {10.1021/acs.analchem.2c05087},
pmid = {36757061},
issn = {1520-6882},
mesh = {Humans ; *Hydrogels/chemistry ; Biomarkers ; *Myocardial Infarction/diagnosis ; },
abstract = {Acute myocardial infarction (AMI) is one of the most fatal diseases in the world in recent decades. Because rapid and accurate determination of AMI has the potential to save millions of lives globally, the development of new diagnostic method is of great significance. Here, we designed a magnetic responsive structural color core-shell hydrogel microcarrier as a novel platform for a high-throughput detection of a variety of cardiovascular biomarkers. The composite hydrogel shell was formed from methacrylated gelatin, acrylic acid, and poly(ethylene glycol diacrylate), and the core silica photonic crystals acted as a detector. Fe3O4 nanoparticles were infused into the void of the core-shell structure to impart magnetic response properties to the encoded carrier. The findings indicated that our method possessed high sensitivity and reliable specificity in the high-throughput detection of AMI-related biomarkers Myo, cTnI, and BNP. In addition, the developed method not only showed good specificity and high sensitivity in clinical samples but also was comparable to the clinical gold standard method. Therefore, the magnetic response structural color core-shell hydrogel carriers were regarded as a potential approach to detect some AMI disease-related biomarkers.},
}
@article {pmid36755878,
year = {2023},
author = {Liu, WZ and Song, L and Chen, XJ and Liu, HX},
title = {The complete mitochondrial genome of Rhinogobius szechuanensis (Gobiiformes: Ggobiidae: Gobionellinae).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {8},
number = {2},
pages = {192-196},
pmid = {36755878},
issn = {2380-2359},
abstract = {Here, we sequenced the complete mitogenome of Rhinogobius szechuanensis using the Illumina HiSeq platform and submitted the genome to Genbank with accession number OM617727. Assembly circular mitogenome (16,492 bp) consisted of 54.4% AT content, 13 protein-coding genes, 22 tRNA genes, two rRNA genes, an origin of light-strand replication, and a control region. Phylogenetic analysis supported that R. szechuanensis was grouped with R. rubromaculatus and clustered with other Rhinogobius species. The basal molecular data will be essential for further genetics studies such as evolution, taxonomy, DNA barcoding, and population genetics of Rhinogobius.},
}
@article {pmid36755868,
year = {2023},
author = {Pazmiño, MF and Del Hierro, AG and Flores, FJ},
title = {Genetic diversity and organic waste degrading capacity of Hermetia illucens from the evergreen forest of the Equatorial Choco lowland.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e14798},
pmid = {36755868},
issn = {2167-8359},
mesh = {Animals ; *Ecosystem ; Plastics/metabolism ; *Diptera/genetics ; Larva/genetics ; Forests ; Genetic Variation ; },
abstract = {Globally, microplastics (MP) represent a growing burden for ecosystems due to their increasing presence at different trophic levels. In Ecuador, the lack of waste segregation has increased the quantity of waste, primarily organics and plastics, overloading landfills and water sources. Over time, plastics reduce in size and silently enter the food chain of animals, such as insects. The black soldier fly (BSF) larvae, Hermetia illucens (Linnaeus, 1758), is a species with devouring behavior used for waste management because of its beneficial qualities such as fly pest control, biomass production, and rapid organic waste degradation. Studies have uncovered the insect's ability to tolerate MP, and consider the possibility that they may be able to degrade polymers. For the first time in Ecuador, the present study characterized H. illucens using the sequences of different molecular markers. Finally, H. illucens' degrading capacity was evaluated in the presence of MP and decaying food residues, resembling landfill conditions.},
}
@article {pmid36748075,
year = {2023},
author = {Thabiani Aziz, A},
title = {Distribution and mitochondrial CO1-based genetic diversity of Aedes aegypti L (Culicidae: Diptera) in Saudi Arabia.},
journal = {Saudi journal of biological sciences},
volume = {30},
number = {3},
pages = {103566},
pmid = {36748075},
issn = {1319-562X},
abstract = {Mosquitoes (Diptera: Culicidae) act as vectors for various pathogens and parasites that affect millions of people worldwide. Aedes aegypti (Linnaeus, 1762) is one of the devastating pests of humans, acting as a key vector of dengue viruses. Therefore, correct identification of this serious pest to determine its distribution is paramount in its management. Morphological identification is usually based on the maturity and quality of the specimens. This can still yield ambiguous results in distinguishing Ae. aegypti species due to limited taxonomic expertise and the presence of cryptic species. In this research, mitochondrial CO1 gene-based identification was adopted to analyze 7 samples, each containing 7 specimens of Ae. aegypti from various localities of Saudi Arabia: Jeddah (A1), Makkah (A2), Al Madinah Al Munawwarah (A4), Jazan (A5), Qunfudah (A6), Yanbu (A8), and Najran (A10). DNA barcoding and maximum likelihood (ML) tree analysis revealed that all 49 species belong to Ae. aegypti and showed high similarity with specimens of this species worldwide.},
}
@article {pmid36747638,
year = {2023},
author = {Frank, DT and Byas, AD and Murrieta, R and Weger-Lucarelli, J and Rückert, C and Gallichotte, E and Yoshimoto, JA and Allen, C and Bosco-Lauth, AM and Graham, B and Felix, TA and Brault, A and Ebel, GD},
title = {Intracellular diversity of WNV within circulating avian peripheral blood mononuclear cells reveals host-dependent patterns of polyinfection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {36747638},
issn = {2692-8205},
support = {F31 AI134108/AI/NIAID NIH HHS/United States ; R01 AI067380/AI/NIAID NIH HHS/United States ; T32 OD010437/OD/NIH HHS/United States ; },
abstract = {UNLABELLED: Error-prone replication of RNA viruses generates the genetic diversity required for adaptation within rapidly changing environments. Thus, arthropod-borne virus (arbovirus) populations exist in nature as mutant swarms that are maintained between arthropods and vertebrates. Previous studies have demonstrated that West Nile virus (WNV) population dynamics are host dependent: In American crows, which experience extremely high viremia, purifying selection is weak and population diversity is high compared to American robins, which have 100 to 1000-fold lower viremia. WNV passed in robins experiences fitness gains, whereas that passed in crows does not. Therefore, we tested the hypothesis that high crow viremia allows higher genetic diversity within individual avian peripheral-blood mononuclear cells (PBMCs), reasoning that this could have produced the previously observed host-specific differences in genetic diversity and fitness. Specifically, we infected cells and birds with a novel, barcoded version of WNV and sequenced viral RNA from single cells to quantify the number of WNV barcodes that each contained. Our results demonstrate that the richness of WNV populations within crows far exceeds that in robins. Similarly, rare WNV variants were maintained by crows more frequently than by robins. Our results suggest that increased viremia in crows relative to robins leads to maintenance of defective genomes and less prevalent variants, presumably through complementation. Our findings further suggest that weaker purifying selection in highly susceptible crows is attributable to this higher viremia, polyinfections and complementation. These studies further document the role of particular, ecologically relevant hosts in shaping virus population structure.<br><br>AUTHOR SUMMARY: WNV mutational diversity in vertebrates is species-dependent. In crows, low frequency variants are common, and viral populations are more diverse. In robins, fewer mutations become permanent fixtures of the overall viral population. We infected crows, robins and a chicken cell line with a genetically marked (barcoded) WNV. Higher levels of virus led to multiple unique WNV genomes infecting individual cells, even when a genotype was present at low levels in the input viral stock. Our findings suggest that higher levels of circulating virus in natural hosts allow less fit viruses to survive in RNA virus populations through complementation by more fit viruses. This is significant as it allows less represented and less fit viruses to be maintained at low levels until they potentially emerge when virus environments change. Overall our data reveal new insights on the relationships between host susceptibility to high viremia and virus evolution.},
}
@article {pmid36745633,
year = {2023},
author = {Enabulele, EE and Lawton, SP and Walker, AJ and Kirk, RS},
title = {Molecular epidemiological analyses reveal extensive connectivity between Echinostoma revolutum (sensu stricto) populations across Eurasia and species richness of zoonotic echinostomatids in England.},
journal = {PloS one},
volume = {18},
number = {2},
pages = {e0270672},
pmid = {36745633},
issn = {1932-6203},
mesh = {Animals ; *Echinostoma/genetics/anatomy &amp; histology ; Phylogeny ; *Trematoda ; Birds ; Thailand ; },
abstract = {Echinostoma revolutum (sensu stricto) is a widely distributed member of the Echinostomatidae, a cosmopolitan family of digenetic trematodes with complex life cycles involving a wide range of definitive hosts, particularly aquatic birds. Integrative taxonomic studies, notably those utilising nad1 barcoding, have been essential in discrimination of E. revolutum (s.s.) within the 'Echinostoma revolutum' species complex and investigation of its molecular diversity. No studies, however, have focussed on factors affecting population genetic structure and connectivity of E. revolutum (s.s.) in Eurasia. Here, we used morphology combined with nad1 and cox1 barcoding to determine the occurrence of E. revolutum (s.s.) and its lymnaeid hosts in England for the first time, in addition to other echinostomatid species Echinoparyphium aconiatum, Echinoparyphium recurvatum and Hypoderaeum conoideum. Analysis of genetic diversity in E. revolutum (s.s.) populations across Eurasia demonstrated haplotype sharing and gene flow, probably facilitated by migratory bird hosts. Neutrality and mismatch distribution analyses support possible recent demographic expansion of the Asian population of E. revolutum (s.s.) (nad1 sequences from Bangladesh and Thailand) and stability in European (nad1 sequences from this study, Iceland and continental Europe) and Eurasian (combined data sets from Europe and Asia) populations with evidence of sub-population structure and selection processes. This study provides new molecular evidence for a panmictic population of E. revolutum (s.s.) in Eurasia and phylogeographically expands the nad1 database for identification of echinostomatids.},
}
@article {pmid36744708,
year = {2023},
author = {Mabika, N and Barson, M and Marco Dos Santos, Q and van Dyk, C and Avenant-Oldewage, A},
title = {Additional Taxonomic Information for Lamproglena hemprichii (Copepoda: Lernaeidae) Based on Scanning Electron Microscopy and Genetic Characterization, Alongside Some Aspects of Its Ecology.},
journal = {Zoological science},
volume = {40},
number = {1},
pages = {32-43},
doi = {10.2108/zs220033},
pmid = {36744708},
issn = {0289-0003},
mesh = {Animals ; *Copepoda/anatomy &amp; histology ; Microscopy, Electron, Scanning ; Phylogeny ; Fishes/genetics ; Lakes ; *Fish Diseases/genetics/parasitology ; },
abstract = {Additional taxonomic and ecological data for the lernaeid copepod Lamproglena hemprichii Nordmann, 1832 infecting the African tigerfish, Hydrocynus vittatus Castelnau, 1861, are presented with scanning electron micrographs, molecular characterization, and selected ecological parameters. Eighty fish were collected from Lake Kariba between October 2014 and July 2015. Scanning electron microscopy provided additional data for the morphology, including structures on the antennulae, antennae, and legs. The 18S and 28S rDNA fragments of this species were distinct from those of other Lamproglena taxa but placed this species within this genus. Phylogenetically, L. hemprichii appears closest to L. monodi Capart, 1944, the only other African species for which molecular data is available. The anterior part of the second gill filament was the preferred attachment site. There was a positive correlation (Pearson correlation coefficient r[2] = 0.64; P = 0.77) between the length of the parasite and the length of the fish. A positive correlation (Pearson correlation coefficient r[2] = 0.61; P = 0.03) between the length of the parasite and the length of the gill filament was also observed. Although the specimens studied here are morphologically highly similar to previous reports of L. hemprichii, some morphological variation was observed, and a revision (morphometric and genetic) of the taxon is suggested. This study provides the first detailed genetic characterization and phylogenetic information for the species.},
}
@article {pmid36744076,
year = {2023},
author = {Najera-Cortazar, LA and Keen, A and Kitching, T and Stokes, D and Goodman, SJ},
title = {Phylogenetic analyses reveal bat communities in Northwestern Mexico harbor a high diversity of novel cryptic ectoparasite species.},
journal = {Ecology and evolution},
volume = {13},
number = {2},
pages = {e9645},
pmid = {36744076},
issn = {2045-7758},
abstract = {Parasites are integral parts of ecosystem function and important drivers of evolutionary processes. Characterizing ectoparasite diversity is fundamental to studies of host-parasite interactions, evolution, and conservation, and also for understanding emerging disease threats for some vector borne pathogens. With more than 1400 species, bats represent the second most speciose mammalian clade, but their ectoparasite fauna are poorly known for most species. We sequenced mitochondrial Cytochrome Oxidase C subunit I and nuclear 18S ribosomal gene fragments, and used Bayesian phylogenetic analyses to characterize ectoparasite taxon identity and diversity for 17 species of parasitized bats sampled along the Baja California peninsula and in Northwestern Mexico. The sequence data revealed multiple novel lineages of bat bugs (Cimicidae), flies (Nycteribiidae and Streblidae), and ticks (Argasidae). Within families, the new linages showed more than 10% sequence divergence, which is consistent with separation at least at the species level. Both families of bat flies showed host specificity, particularly on Myotis species. We also identified new records for the Baja peninsula of one tick (Carios kelleyi), and of five Streblid bat fly species. One Nycteribiid bat fly haplotype from Pallid bat (Antrozous pallidus) hosts was found throughout the peninsula, suggesting potential long distance co-dispersal with hosts. Different bat bug and tick communities were found in the north and south of the peninsula. This study is the first systematic survey of bat ectoparasites in the Baja California peninsula, revealing novel lineages that are highly genetically differentiated from other parts of North America. For some ectoparasite species, haplotype distributions may reflect patterns of bat migration. This work is a first step in characterizing ectoparasite diversity over the Baja California peninsula, and understanding how ecological and evolutionary interactions shape bat ectoparasite communities among host species in different parts of their ranges.},
}
@article {pmid36743410,
year = {2023},
author = {Luque, GM and Schiavi-Ehrenhaus, LJ and Jabloñski, M and Balestrini, PA and Novero, AG and Torres, NI and Osycka-Salut, CE and Darszon, A and Krapf, D and Buffone, MG},
title = {High-throughput screening method for discovering CatSper inhibitors using membrane depolarization caused by external calcium chelation and fluorescent cell barcoding.},
journal = {Frontiers in cell and developmental biology},
volume = {11},
number = {},
pages = {1010306},
pmid = {36743410},
issn = {2296-634X},
abstract = {The exclusive expression of CatSper in sperm and its critical role in sperm function makes this channel an attractive target for contraception. The strategy of blocking CatSper as a male, non-hormonal contraceptive has not been fully explored due to the lack of robust screening methods to discover novel and specific inhibitors. The reason for this lack of appropriate methodology is the structural and functional complexity of this channel. We have developed a high-throughput method to screen drugs with the capacity to block CatSper in mammalian sperm. The assay is based on removing external free divalent cations by chelation, inducing CatSper to efficiently conduct monovalent cations. Since Na[+] is highly concentrated in the extracellular milieu, a sudden influx depolarizes the cell. Using CatSper1 KO sperm we demonstrated that this depolarization depends on CatSper function. A membrane potential (Em) assay was combined with fluorescent cell barcoding (FCB), enabling higher throughput flow cytometry based on unique fluorescent signatures of different sperm samples. These differentially labeled samples incubated in distinct experimental conditions can be combined into one tube for simultaneous acquisition. In this way, acquisition times are highly reduced, which is essential to perform larger screening experiments for drug discovery using live cells. Altogether, a simple strategy for assessing CatSper was validated, and this assay was used to develop a high-throughput drug screening for new CatSper blockers.},
}
@article {pmid36740746,
year = {2023},
author = {Voidaleski, MF and Costa, FF and de Hoog, GS and Gomes, RR and Vicente, VA},
title = {Metagenomics reveals an abundance of black yeast-like fungi in the skin microbiome.},
journal = {Mycoses},
volume = {66},
number = {6},
pages = {488-496},
doi = {10.1111/myc.13574},
pmid = {36740746},
issn = {1439-0507},
support = {//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
mesh = {Humans ; Saccharomyces cerevisiae ; Metagenomics ; Skin/microbiology ; *Exophiala/genetics ; *Microbiota/genetics ; Fungi/genetics ; },
abstract = {BACKGROUND: The skin is the first line of defence against communities of resident viruses, bacteria and fungi. The composition of the microbiome might change with factors related to the environment and host. The microbiome is dominated by bacteria. Dermatophytes and yeasts are the predominant fungi that are also involved in opportunistic infections of skin, hair and nails. Among environmental fungi, Chaetothyriales (black yeasts and relatives) are enriched by hydrocarbon pollution in domesticated habitats and comprise numerous species that cause mild-to-severe disease.<br><br>METHODS: We investigated the presence of black fungi in the skin microbiome by conducting an analysis in the publicly available metagenomic SRA database (NCBI). We focused on the causative agents of chromoblastomycosis and phaeohyphomycosis and used barcodes and padlock probe sequences as diagnostic tools.<br><br>RESULTS: A total of 132,159,577&#x2009;MB was analysed and yielded 18,360 reads that matched with 24 species of black fungi. Exophiala was the most prevalent genus, and Cyphellophora europaea was the most abundant species.<br><br>CONCLUSION: This study reveals the abundant presence of Chaetothyriales on the skin without necessarily being associated with infection. Most of the detected causal agents are known from mild skin diseases, while also species were revealed that had been reported from CARD9-deficient patients.},
}
@article {pmid36736573,
year = {2023},
author = {Bloom, M and Malouf, C and Rodriguez-Fraticelli, A and Wilkinson, AC and Sankaran, VG and Cvejic, A},
title = {Exploiting somatic mutations to decipher human blood production: a natural lineage-tracing strategy.},
journal = {Experimental hematology},
volume = {121},
number = {},
pages = {2-5},
doi = {10.1016/j.exphem.2023.01.005},
pmid = {36736573},
issn = {1873-2399},
support = {MC_UU_00016/18/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Adult ; Humans ; Mutation ; Retrospective Studies ; *Hematopoietic Stem Cells/metabolism ; *Hematopoiesis/genetics ; },
abstract = {Lineage tracing using fluorescent proteins, genetic barcodes, and various other strategies has provided critical insights into the dynamics of both fetal and adult hematopoiesis in model organisms. However, these technologies cannot be readily used to study hematopoiesis in human beings. Therefore, there is a critical need to develop strategies to assess cellular dynamics within human hematopoietic tissues in vivo. Recently, researchers have used naturally acquired somatic mutations, coupled with other single-cell technologies, to retrospectively analyze clonal cellular dynamics. In summer 2022, the International Society for Experimental Hematology's New Investigator Committee hosted a webinar focused on novel approaches to dissect fetal and adult hematopoiesis, with presentations from Drs. Ana Cvejic and Vijay Sankaran. Here, we provide an overview of these exciting technological advances and some of the novel insights they have already provided in studying human hematopoiesis.},
}
@article {pmid36730314,
year = {2023},
author = {Pinto, IS and Rodrigues, BL and de Araujo-Pereira, T and Shimabukuro, PHF and de Pita-Pereira, D and Britto, C and Brazil, RP},
title = {DNA barcoding of sand flies (Diptera, Psychodidae, Phlebotominae) from the western Brazilian Amazon.},
journal = {PloS one},
volume = {18},
number = {2},
pages = {e0281289},
pmid = {36730314},
issn = {1932-6203},
mesh = {Animals ; *Psychodidae/genetics ; DNA Barcoding, Taxonomic ; Brazil ; *Phlebotomus/genetics ; DNA ; },
abstract = {The subfamily Phlebotominae comprises important insects for public health. The use of complementary tools such as molecular taxonomy is necessary for interspecific delimitation and/or discovery of cryptic species. Here, we evaluated the DNA barcoding tool to identify different species in the southwestern Brazilian Amazon. For this, we collected sand flies in forest fragments along the highway BR-317, in the municipality of Brasiléia, state of Acre, Brazil. The specimens were DNA-barcoded using a fragment of the cytochrome c oxidase subunit I (COI) gene. The sequences were analyzed to generate K2P pairwise genetic distances and a Neighbour-joining tree. The sand fly barcodes were also clustered into Molecular Operation Taxonomic Units (MOTU) using Automatic Barcode Gap Discovery (ABGD) approach. A total of 59 COI sequences comprising 22 nominal species and ten genera were generated. Of these, 11 species had not been sequenced before, thus being new COI sequences to science. Intraspecific genetic distances ranged between 0 and 4.9%, with Pintomyia serrana presenting the highest values of genetic distance, in addition to having been partitioned into three MOTUs. Regarding the distances to the nearest neighbour, all species present higher values in relation to the maximum intraspecific distance, in addition to forming well supported clusters in the neighbour-joining analysis. The DNA barcoding approach is useful for the molecular identification of sand flies from Brasiléia, state of Acre, and was efficient in detecting cryptic diversity of five species which can be confirmed in future studies using an integrative approach. We also generated new COI barcodes for Trichophoromyia auraensis, Nyssomyia shawi, and Psychodopygus paraensis, which may play a role in the transmission of Leishmania spp. in the Brazilian Amazon.},
}
@article {pmid36729338,
year = {2023},
author = {Verhallen, L and Lackman, JJ and Wendt, R and Gustavsson, M and Yang, Z and Narimatsu, Y and Sørensen, DM and Lafferty, KM and Gouwy, M and Marques, PE and Hjortø, GM and Rosenkilde, MM and Proost, P and Goth, CK},
title = {"Glyco-sulfo barcodes" regulate chemokine receptor function.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {80},
number = {2},
pages = {55},
pmid = {36729338},
issn = {1420-9071},
support = {R322-2019-2171//Lundbeckfonden/ ; (C16/17/010)//Onderzoeksraad, KU Leuven/ ; G080818N//Fonds Wetenschappelijk Onderzoek/ ; ESA-D6247-MSCA-IF-2018//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; },
mesh = {Cricetinae ; Animals ; Humans ; Mice ; *Chemokines/metabolism ; *Signal Transduction ; Protein Processing, Post-Translational ; Receptors, CCR5/genetics ; CHO Cells ; Tyrosine/metabolism ; Protein Binding ; },
abstract = {Chemokine ligands and receptors regulate the directional migration of leukocytes. Post-translational modifications of chemokine receptors including O-glycosylation and tyrosine sulfation have been reported to regulate ligand binding and resulting signaling. Through in silico analyses, we determined potential conserved O-glycosylation and sulfation sites on human and murine CC chemokine receptors. Glyco-engineered CHO cell lines were used to measure the impact of O-glycosylation on CC chemokine receptor CCR5, while mutation of tyrosine residues and treatment with sodium chlorate were performed to determine the effect of tyrosine sulfation. Changing the glycosylation or tyrosine sulfation on CCR5 reduced the receptor signaling by the more positively charged CCL5 and CCL8 more profoundly compared to the less charged CCL3. The loss of negatively charged sialic acids resulted only in a minor effect on CCL3-induced signal transduction. The enzymes GalNAc-T1 and GalNAc-T11 were shown to be involved in the process of chemokine receptor O-glycosylation. These results indicate that O-glycosylation and tyrosine sulfation are involved in the fine-tuning and recognition of chemokine interactions with CCR5 and the resulting signaling.},
}
@article {pmid36727264,
year = {2023},
author = {Gendron, EM and Sevigny, JL and Byiringiro, I and Thomas, WK and Powers, TO and Porazinska, DL},
title = {Nematode mitochondrial metagenomics: A new tool for biodiversity analysis.},
journal = {Molecular ecology resources},
volume = {23},
number = {5},
pages = {975-989},
doi = {10.1111/1755-0998.13761},
pmid = {36727264},
issn = {1755-0998},
support = {AWD07689//National Institute of Food and Agriculture/ ; NH00694//National Institute of Food and Agriculture/ ; },
mesh = {Animals ; Phylogeny ; Metagenomics ; *Nematoda/genetics ; Biodiversity ; DNA ; DNA Barcoding, Taxonomic ; *Genome, Mitochondrial/genetics ; },
abstract = {DNA barcoding approaches have greatly increased our understanding of biodiversity on the planet, and metabarcoding is widely used for classifying members of the phylum Nematoda. However, loci typically utilized in metabarcoding studies are often unable to resolve closely related species or are unable to recover all taxa present in a sample due to inadequate PCR primer binding. Mitochondrial metagenomics (mtMG) is an alternative approach utilizing shotgun sequencing of total DNA to recover the mitochondrial genomes of all species present in samples. However, this approach requires a comprehensive reference database for identification and currently available mitochondrial sequences for nematodes are highly dominated by sequences from the order Rhabditida, and excludes many clades entirely. Here, we analysed the efficacy of mtMG for the recovery of nematode taxa and the generation of mitochondrial genomes. We first developed a curated reference database of nematode mitochondrial sequences and expanded it with 40 newly sequenced taxa. We then tested the mito-metagenomics approach using a series of nematode mock communities consisting of morphologically identified nematode species representing various feeding traits, life stages, and phylogenetic relationships. We were able to identify all but two species through the de novo assembly of COX1 genes. We were also able to recover additional mitochondrial protein coding genes (PCGs) for 23 of the 24 detected species including a full array of 12 PCGs from five of the species. We conclude that mtMG offers a potential for the effective recovery of nematode biodiversity but remains limited by the breadth of the reference database.},
}
@article {pmid36723233,
year = {2023},
author = {Stewart, D and Djoumad, A and Holden, D and Kimoto, T and Capron, A and Dubatolov, VV and Akhanaev, YB and Yakimova, ME and Martemyanov, VV and Cusson, M},
title = {A TaqMan Assay for the Detection and Monitoring of Potentially Invasive Lasiocampids, With Particular Attention to the Siberian Silk Moth, Dendrolimus sibiricus (Lepidoptera: Lasiocampidae).},
journal = {Journal of insect science (Online)},
volume = {23},
number = {1},
pages = {},
pmid = {36723233},
issn = {1536-2442},
mesh = {Animals ; *Bombyx ; Canada ; Ovum ; *Moths/genetics ; *Manduca ; Insecta ; },
abstract = {The Siberian silk moth, Dendrolimus sibiricus Tschetverikov, is a very serious pest of conifers in Russia and is an emerging threat in North America where an accidental introduction could have devastating impacts on native forest resources. Other Dendrolimus Germar species and related Eurasian lasiocampids in the genus Malacosoma (Hubner) could also present a risk to North America's forests. Foreign vessels entering Canadian and U.S. ports are regularly inspected for Lymantria dispar (Linnaeus) and for the presence of other potentially invasive insects, including suspicious lasiocampid eggs. However, eggs are difficult to identify based on morphological features alone. Here, we report on the development of two TaqMan (Roche Molecular Systems, Inc., Rotkreuz, Switzerland) assays designed to assist regulatory agencies in their identification of these insects. Developed using the barcode region of the cytochrome c oxidase I (COI) gene and run in triplex format, the first assay can detect Dendrolimus and Malacosoma DNA, and can distinguish North American from Eurasian Malacosoma species. The second assay is based on markers identified within the internal transcribed spacer 2 (ITS2) region and was designed to specifically identify D. sibiricus, while discriminating closely related Dendrolimus taxa. In addition to providing direct species identification in the context of its use in North America, the D. sibiricus assay should prove useful for monitoring the spread of this pest in Eurasia, where its range overlaps with those of the morphologically identical D. superans (Butler) and similar D. pini (Linnaeus). The assays described here can be performed either in the lab on a benchtop instrument, or on-site using a portable machine.},
}
@article {pmid36714845,
year = {2022},
author = {Stuart, JD and Hartman, DA and Gray, LI and Jones, AA and Wickenkamp, NR and Hirt, C and Safira, A and Regas, AR and Kondash, TM and Yates, ML and Driga, S and Snow, CD and Kading, RC},
title = {Mosquito tagging using DNA-barcoded nanoporous protein microcrystals.},
journal = {PNAS nexus},
volume = {1},
number = {4},
pages = {pgac190},
pmid = {36714845},
issn = {2752-6542},
abstract = {Conventional mosquito marking technology for mark-release-recapture (MRR) is quite limited in terms of information capacity and efficacy. To overcome both challenges, we have engineered, lab-tested, and field-evaluated a new class of marker particles, in which synthetic, short DNA oligonucleotides (DNA barcodes) are adsorbed and protected within tough, crosslinked porous protein microcrystals. Mosquitoes self-mark through ingestion of microcrystals in their larval habitat. Barcoded microcrystals persist trans-stadially through mosquito development if ingested by larvae, do not significantly affect adult mosquito survivorship, and individual barcoded mosquitoes are detectable in pools of up to at least 20 mosquitoes. We have also demonstrated crystal persistence following adult mosquito ingestion. Barcode sequences can be recovered by qPCR and next-generation sequencing (NGS) without detectable amplification of native mosquito DNA. These DNA-laden protein microcrystals have the potential to radically increase the amount of information obtained from future MRR studies compared to previous studies employing conventional mosquito marking materials.},
}
@article {pmid36714701,
year = {2022},
author = {Jeon, H and Kim, JE and Yang, JW and Son, H and Min, K},
title = {Application of direct PCR for phylogenetic analysis of Fusarium fujikuroi species complex isolated from rice seeds.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {1093688},
pmid = {36714701},
issn = {1664-462X},
abstract = {Plant pathogenic fungi cause severe yield losses and mycotoxin contamination in crops. The precise and rapid detection of fungal pathogens is essential for effective disease management. Sequencing universal DNA barcodes has become the standard method for the diagnosis of fungal diseases, as well as for identification and phylogenetic analysis. A major bottleneck in obtaining DNA sequence data from many samples was the laborious and time-consuming process of sample preparation for genomic DNA. Here, we describe a direct PCR approach that bypasses the DNA extraction steps to streamline the molecular identification of fungal species. Using a direct PCR approach, we successfully sequenced the nuclear ribosomal internal transcribed spacer (ITS) region for the representatives of major fungal lineages. To demonstrate the usefulness of this approach, we performed a phylogenetic analysis of the Fusarium fujikuroi species complex, which causes bakanae ("foolish seedling") disease of rice and mycotoxin contamination. A total of 28 candidate strains were isolated from rice seeds in the Republic of Korea, and the identity of the isolates was determined using the DNA sequence of both ITS and translation elongation factor 1-α regions. In addition, 17 F. fujikuroi isolates were examined for fumonisin (FB) production in rice medium using an enzyme-linked immunosorbent assay. Phylogenetic and toxigenic analyses showed that the F. fujikuroi strains could be distinguished into two groups: FB producers (B14-type) and non-producers (B20-type). These results will accelerate the molecular identification of fungal pathogens and facilitate the effective management of fungal diseases.},
}
@article {pmid36714512,
year = {2022},
author = {Yuanawati, D and Farizky, HS and Santanumurti, MB and Jamal, MT and Iqbal Sani, LM and Madduppa, H and Sari, PDW},
title = {The newest COI molecular detection of Asian redtail catfish Hemibagrus nemurus (Valenciennes, 1840) in Progo River, Magelang, Central Java, Indonesia.},
journal = {Journal of advanced veterinary and animal research},
volume = {9},
number = {4},
pages = {591-600},
pmid = {36714512},
issn = {2311-7710},
abstract = {OBJECTIVE: This study describes the newest deoxyribonucleic acid (DNA) barcoding Asian redtail catfish (Hemibagrus nemurus) in the Progo River, Magelang, Central Java, Indonesia.<br><br>MATERIALS AND METHODS: Ten fish were caught in the Progo River, Magelang, Central Java, Indonesia. The polymerase chain reaction was the molecular diagnosis to detect the sequences of DNA of Cytochrome Oxidase I compared to National Center for Biotechnology Information data (GenBank).<br><br>RESULTS: The results showed that the percent identity was not 100% with H. nemurus data from other locations (GenBank), including Indonesia. The closest percent identity was H. nemurus from Java Island (Accession ID: MK312566.1) with 97.6% similarity. The genetic mutation that happened might be due to environmental change (pollution) in the Progo River recently.<br><br>CONCLUSIONS: This study showed a genetic mutation in H. nemurus from Progo River may be caused by environmental change. Low pollution exposure levels may not be detrimental (lethal) to fish. However, it can affect fish fertility, which leads to population degradation (gene variation). Attention must be increased for fish survival in the future.},
}
@article {pmid36713789,
year = {2023},
author = {Zhang, J and Cong, Q and Grishin, NV},
title = {Thirteen new species of butterflies (Lepidoptera: Hesperiidae) from Texas.},
journal = {Insecta mundi},
volume = {2023},
number = {},
pages = {},
pmid = {36713789},
issn = {0749-6737},
support = {R35 GM127390/GM/NIGMS NIH HHS/United States ; },
abstract = {Analyses of whole genomic shotgun datasets, COI barcodes, morphology, and historical literature suggest that the following 13 butterfly species from the family Hesperiidae (Lepidoptera: Papilionoidea) in Texas, USA are distinct from their closest named relatives and therefore are described as new (type localities are given in parenthesis): Spicauda atelis Grishin, new species (Hidalgo Co., Mission), Urbanus (Urbanus) rickardi Grishin, new species (Hidalgo Co., nr. Madero), Urbanus (Urbanus) oplerorum Grishin, new species (Hidalgo Co., Mission/Madero), Telegonus tsongae Grishin, new species (Starr Co., Roma), Autochton caballo Grishin, new species (Hidalgo Co., 6 mi W of Hidalgo), Epargyreus fractigutta Grishin, new species (Hidalgo Co., McAllen), Aguna mcguirei Grishin, new species (Cameron Co., Brownsville), Polygonus pardus Grishin, new species (Hidalgo Co., McAllen), Arteurotia artistella Grishin, new species (Hidalgo Co., Mission), Heliopetes elonmuski Grishin, new species (Cameron Co., Boca Chica), Hesperia balcones Grishin, new species (Travis Co., Volente), Troyus fabulosus Grishin, new species (Hidalgo Co., Peñitas), and Lerema ochrius Grishin, new species (Hidalgo Co., nr. Relampago). Most of these species are known in the US almost exclusively from the Lower Rio Grande Valley in Texas. Nine of the holotypes were collected in 1971-1975, a banner period for butterfly species newly recorded from the Rio Grande Valley of Texas; five of them collected by William W. McGuire, and one by Nadine M. McGuire. At the time, these new species have been recorded under the names of their close relatives. A Neotype is designated for Papilio fulminator Sepp, [1841] (Suriname). Lectotypes are designated for Goniurus teleus Hübner, 1821 (unknown, likely in South America), Goniloba azul Reakirt, [1867] (Mexico: Veracruz) and Eudamus misitra Plötz, 1881 (Mexico). Several taxonomic changes are proposed. The following taxa are species (not subspecies): Spicauda zalanthus (Plötz, 1880), reinstated status (not Spicauda teleus (Hübner, 1821)), Telegonus fulminator (Sepp, [1841]), reinstated status (not Telegonus fulgerator (Walch, 1775), Telegonus misitra (Plötz, 1881), reinstated status (not Telegonus azul (Reakirt, [1867])), Autochton reducta (Mabille and Boullet, 1919), new status (not Autochton potrillo (Lucas, 1857)), Epargyreus gaumeri Godman and Salvin, 1893, reinstated status (not Epargyreus clavicornis (Herrich-Schäffer, 1869)), and Polygonus punctus E. Bell and W. Comstock, 1948, new status (not Polygonus savigny (Latreille, [1824])). Urbanus ehakernae Burns, 2014 and Epargyreus socus chota Evans, 1952 are junior subjective synonyms of Urbanus alva Evans, 1952 and Epargyreus clavicornis (Herrich-Schäffer, 1869), respectively, and Epargyreus gaumeri tenda Evans, 1955, new combination is not a subspecies of E. clavicornis.},
}
@article {pmid36712375,
year = {2022},
author = {Press, WH},
title = {Fast trimer statistics facilitate accurate decoding of large random DNA barcode sets even at large sequencing error rates.},
journal = {PNAS nexus},
volume = {1},
number = {5},
pages = {pgac252},
pmid = {36712375},
issn = {2752-6542},
abstract = {Predefined sets of short DNA sequences are commonly used as barcodes to identify individual biomolecules in pooled populations. Such use requires either sufficiently small DNA error rates, or else an error-correction methodology. Most existing DNA error-correcting codes (ECCs) correct only one or two errors per barcode in sets of typically ≲10[4] barcodes. We here consider the use of random barcodes of sufficient length that they remain accurately decodable even with ≳6 errors and even at [Formula: see text] or 20% nucleotide error rates. We show that length ∼34 nt is sufficient even with ≳10[6] barcodes. The obvious objection to this scheme is that it requires comparing every read to every possible barcode by a slow Levenshtein or Needleman-Wunsch comparison. We show that several orders of magnitude speedup can be achieved by (i) a fast triage method that compares only trimer (three consecutive nucleotide) occurence statistics, precomputed in linear time for both reads and barcodes, and (ii) the massive parallelism available on today's even commodity-grade Graphics Processing Units (GPUs). With 10[6] barcodes of length 34 and 10% DNA errors (substitutions and indels), we achieve in simulation 99.9% precision (decode accuracy) with 98.8% recall (read acceptance rate). Similarly high precision with somewhat smaller recall is achievable even with 20% DNA errors. The amortized computation cost on a commodity workstation with two GPUs (2022 capability and price) is estimated as between US$ 0.15 and US$ 0.60 per million decoded reads.},
}
@article {pmid36711792,
year = {2023},
author = {Chen, S and Zhu, B and Huang, S and Hickey, JW and Lin, KZ and Snyder, M and Greenleaf, WJ and Nolan, GP and Zhang, NR and Ma, Z},
title = {Integration of spatial and single-cell data across modalities with weak linkage.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.01.12.523851},
pmid = {36711792},
issn = {2692-8205},
support = {U54 HG012723/HG/NHGRI NIH HHS/United States ; },
abstract = {single-cell sequencing methods have enabled the profiling of multiple types of molecular readouts at cellular resolution, and recent developments in spatial barcoding, in situ hybridization, and in situ sequencing allow such molecular readouts to retain their spatial context. Since no technology can provide complete characterization across all layers of biological modalities within the same cell, there is pervasive need for computational cross-modal integration (also called diagonal integration) of single-cell and spatial omics data. For current methods, the feasibility of cross-modal integration relies on the existence of highly correlated, a priori "linked" features. When such linked features are few or uninformative, a scenario that we call "weak linkage", existing methods fail. We developed MaxFuse, a cross-modal data integration method that, through iterative co-embedding, data smoothing, and cell matching, leverages all information in each modality to obtain high-quality integration. MaxFuse is modality-agnostic and, through comprehensive benchmarks on single-cell and spatial ground-truth multiome datasets, demonstrates high robustness and accuracy in the weak linkage scenario. A prototypical example of weak linkage is the integration of spatial proteomic data with single-cell sequencing data. On two example analyses of this type, we demonstrate how MaxFuse enables the spatial consolidation of proteomic, transcriptomic and epigenomic information at single-cell resolution on the same tissue section.},
}
@article {pmid36711524,
year = {2023},
author = {Koo, D and Mao, Z and Dimatteo, R and Tsubamoto, N and Noguchi, M and McLaughlin, J and Tran, W and Lee, S and Cheng, D and de Rutte, J and Sojo, GB and Witte, ON and Di Carlo, D},
title = {Defining T cell receptor repertoires using nanovial-based affinity and functional screening.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {36711524},
issn = {2692-8205},
support = {P30 CA016042/CA/NCI NIH HHS/United States ; R21 CA256084/CA/NCI NIH HHS/United States ; },
abstract = {The ability to selectively bind to antigenic peptides and secrete cytokines can define populations of cells with therapeutic potential in emerging T cell receptor (TCR) immunotherapies. We leverage cavity-containing hydrogel microparticles, called nanovials, each coated with millions of peptide-major histocompatibility complex (pMHC) monomers to isolate antigen-reactive T cells. T cells are captured and activated by pMHCs and secrete cytokines on nanovials, allowing sorting based on both affinity and function. The TCRs of sorted cells on nanovials are sequenced, recovering paired αβ-chains using microfluidic emulsion-based single-cell sequencing. By labeling nanovials having different pMHCs with unique oligonucleotide-barcodes we could link TCR sequence to targets with 100% accuracy. We identified with high specificity an expanded repertoire of functional TCRs targeting viral antigens compared to standard techniques.},
}
@article {pmid36708705,
year = {2023},
author = {Ma, P and Amemiya, HM and He, LL and Gandhi, SJ and Nicol, R and Bhattacharyya, RP and Smillie, CS and Hung, DT},
title = {Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states.},
journal = {Cell},
volume = {186},
number = {4},
pages = {877-891.e14},
pmid = {36708705},
issn = {1097-4172},
support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AI117043/AI/NIAID NIH HHS/United States ; },
mesh = {*Gene Expression Profiling ; Sequence Analysis, RNA ; *Single-Cell Gene Expression Analysis ; RNA-Seq ; Bacteria/genetics ; Single-Cell Analysis ; },
abstract = {We introduce BacDrop, a highly scalable technology for bacterial single-cell RNA sequencing that has overcome many challenges hindering the development of scRNA-seq in bacteria. BacDrop can be applied to thousands to millions of cells from both gram-negative and gram-positive species. It features universal ribosomal RNA depletion and combinatorial barcodes that enable multiplexing and massively parallel sequencing. We applied BacDrop to study Klebsiella pneumoniae clinical isolates and to elucidate their heterogeneous responses to antibiotic stress. In an unperturbed population presumed to be homogeneous, we found within-population heterogeneity largely driven by the expression of mobile genetic elements that promote the evolution of antibiotic resistance. Under antibiotic perturbation, BacDrop revealed transcriptionally distinct subpopulations associated with different phenotypic outcomes including antibiotic persistence. BacDrop thus can capture cellular states that cannot be detected by bulk RNA-seq, which will unlock new microbiological insights into bacterial responses to perturbations and larger bacterial communities such as the microbiome.},
}
@article {pmid36707856,
year = {2023},
author = {Poon, ESK and Chen, G and Tsang, HY and Shek, CT and Tsui, WC and Zhao, H and Guénard, B and Sin, SYW},
title = {Species richness of bat flies and their associations with host bats in a subtropical East Asian region.},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {37},
pmid = {36707856},
issn = {1756-3305},
support = {Seed Funding for Strategic Interdisciplinary Research Scheme 2021/22//University of Hong Kong/ ; },
mesh = {Animals ; Asia, Eastern ; *Chiroptera ; *Diptera/genetics ; Host Specificity ; Host-Parasite Interactions ; Phylogeny ; },
abstract = {BACKGROUND: Understanding the interactions between bat flies and host bats offer us fundamental insights into the coevolutionary and ecological processes in host-parasite relationships. Here, we investigated the identities, host specificity, and patterns of host association of bat flies in a subtropical region in East Asia, which is an understudied region for bat fly research.<br><br>METHODS: We used both morphological characteristics and DNA barcoding to identify the bat fly species found on 11 cavernicolous bat species from five bat families inhabiting Hong Kong. We first determined the phylogenetic relationships among bat fly species. Then, we elucidated the patterns of bat-bat fly associations and calculated the host specificity of each bat fly species. Furthermore, we assembled the mitogenomes of three bat fly species from two families (Nycteribiidae and Streblidae) to contribute to the limited bat fly genetic resources available.<br><br>RESULTS: We examined 641 individuals of bat flies and found 20 species, of which many appeared to be new to science. Species of Nycteribiidae included five Nycteribia spp., three Penicillidia spp., two Phthiridium spp., one Basilia sp., and one species from a hitherto unknown genus, whereas Streblidae included Brachytarsina amboinensis, three Raymondia spp., and four additional Brachytarsina spp. Our bat-bat fly association network shows that certain closely related bat flies within Nycteribiidae and Streblidae only parasitized host bat species that are phylogenetically more closely related. For example, congenerics of Raymondia only parasitized hosts in Rhinolophus and Hipposideros, which are in two closely related families in Rhinolophoidea, but not other distantly related co-roosting species. A wide spectrum of host specificity of these bat fly species was also revealed, with some bat fly species being strictly monoxenous, e.g. nycteribiid Nycteribia sp. A, Phthiridium sp. A, and streblid Raymondia sp. A, while streblid B. amboinensis is polyxenous.<br><br>CONCLUSIONS: The bat fly diversity and specificity uncovered in this study have shed light on the complex bat-bat fly ecology in the region, but more bat-parasite association studies are still needed in East Asian regions like China as a huge number of unknown species likely exists. We highly recommend the use of DNA barcoding to support morphological identification to reveal accurate host-ectoparasite relationships for future studies.},
}
@article {pmid36707534,
year = {2023},
author = {Gernat, T and Jagla, T and Jones, BM and Middendorf, M and Robinson, GE},
title = {Automated monitoring of honey bees with barcodes and artificial intelligence reveals two distinct social networks from a single affiliative behavior.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {1541},
pmid = {36707534},
issn = {2045-2322},
support = {R01GM117467/GM/NIGMS NIH HHS/United States ; },
mesh = {Bees ; Animals ; *Artificial Intelligence ; *Behavior, Animal ; Social Behavior ; },
abstract = {Barcode-based tracking of individuals is revolutionizing animal behavior studies, but further progress hinges on whether in addition to determining an individual's location, specific behaviors can be identified and monitored. We achieve this goal using information from the barcodes to identify tightly bounded image regions that potentially show the behavior of interest. These image regions are then analyzed with convolutional neural networks to verify that the behavior occurred. When applied to a challenging test case, detecting social liquid transfer (trophallaxis) in the honey bee hive, this approach yielded a 67% higher sensitivity and an 11% lower error rate than the best detector for honey bee trophallaxis so far. We were furthermore able to automatically detect whether a bee donates or receives liquid, which previously required manual observations. By applying our trophallaxis detector to recordings from three honey bee colonies and performing simulations, we discovered that liquid exchanges among bees generate two distinct social networks with different transmission capabilities. Finally, we demonstrate that our approach generalizes to detecting other specific behaviors. We envision that its broad application will enable automatic, high-resolution behavioral studies that address a broad range of previously intractable questions in evolutionary biology, ethology, neuroscience, and molecular biology.},
}
@article {pmid36702823,
year = {2023},
author = {Garone, MG and Salerno, D and Rosa, A},
title = {Digital color-coded molecular barcoding reveals dysregulation of common FUS and FMRP targets in soma and neurites of ALS mutant motoneurons.},
journal = {Cell death discovery},
volume = {9},
number = {1},
pages = {33},
pmid = {36702823},
issn = {2058-7716},
abstract = {Mutations in RNA binding proteins (RBPs) have been linked to the motor neuron disease amyotrophic lateral sclerosis (ALS). Extensive auto-regulation, cross-regulation, cooperation and competition mechanisms among RBPs are in place to ensure proper expression levels of common targets, often including other RBPs and their own transcripts. Moreover, several RBPs play a crucial role in the nervous system by localizing target RNAs in specific neuronal compartments. These include the RBPs FUS, FMRP, and HuD. ALS mutations in a given RBP are predicted to produce a broad impact on such delicate equilibrium. Here we studied the effects of the severe FUS-P525L mutation on common FUS and FMRP targets. Expression profiling by digital color-coded molecular barcoding in cell bodies and neurites of human iPSC-derived motor neurons revealed altered levels of transcripts involved in the cytoskeleton, neural projection and synapses. One of the common targets is HuD, which is upregulated because of the loss of FMRP binding to its 3'UTR due to mutant FUS competition. Notably, many genes are commonly altered upon FUS mutation or HuD overexpression, suggesting that a substantial part of the effects of mutant FUS on the motor neuron transcriptome could be due to HuD gain-of-function. Among altered transcripts, we also identified other common FUS and FMRP targets, namely MAP1B, PTEN, and AP2B1, that are upregulated upon loss of FMRP binding on their 3'UTR in FUS-P525L motor neurons. This work demonstrates that the impairment of FMRP function by mutant FUS might alter the expression of several genes, including new possible biomarkers and therapeutic targets for ALS.},
}
@article {pmid36701517,
year = {2023},
author = {Radmand, A and Lokugamage, MP and Kim, H and Dobrowolski, C and Zenhausern, R and Loughrey, D and Huayamares, SG and Hatit, MZC and Ni, H and Del Cid, A and Da Silva Sanchez, AJ and Paunovska, K and Schrader Echeverri, E and Shajii, A and Peck, H and Santangelo, PJ and Dahlman, JE},
title = {The Transcriptional Response to Lung-Targeting Lipid Nanoparticles in Vivo.},
journal = {Nano letters},
volume = {23},
number = {3},
pages = {993-1002},
pmid = {36701517},
issn = {1530-6992},
support = {UG3 TR002855/TR/NCATS NIH HHS/United States ; UH3 TR002855/TR/NCATS NIH HHS/United States ; R01 GM132985/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Lipids ; Liposomes/metabolism ; Hepatocytes/metabolism ; *Nanoparticles ; RNA, Messenger/genetics ; RNA, Small Interfering ; },
abstract = {Lipid nanoparticles (LNPs) have delivered RNA to hepatocytes in patients, underscoring the potential impact of nonliver delivery. Scientists can shift LNP tropism to the lung by adding cationic helper lipids; however, the biological response to these LNPs remains understudied. To evaluate the hypothesis that charged LNPs lead to differential cellular responses, we quantified how 137 LNPs delivered mRNA to 19 cell types in vivo. Consistent with previous studies, we observed helper lipid-dependent tropism. After identifying and individually characterizing three LNPs that targeted different tissues, we studied the in vivo transcriptomic response to these using single-cell RNA sequencing. Out of 835 potential pathways, 27 were upregulated in the lung, and of these 27, 19 were related to either RNA or protein metabolism. These data suggest that endogenous cellular RNA and protein machinery affects mRNA delivery to the lung in vivo.},
}
@article {pmid36701437,
year = {2023},
author = {Meekel, EG and Schmidt, EM and Cameron, LJ and Dharma, AD and Windsor, HJ and Duyker, SG and Minelli, A and Pope, T and Lepore, GO and Slater, B and Kepert, CJ and Goodwin, AL},
title = {Truchet-tile structure of a topologically aperiodic metal-organic framework.},
journal = {Science (New York, N.Y.)},
volume = {379},
number = {6630},
pages = {357-361},
doi = {10.1126/science.ade5239},
pmid = {36701437},
issn = {1095-9203},
abstract = {When tiles decorated to lower their symmetry are joined together, they can form aperiodic and labyrinthine patterns. Such Truchet tilings offer an efficient mechanism of visual data storage related to that used in barcodes and QR codes. We show that the crystalline metal-organic framework [OZn4][1,3-benzenedicarboxylate]3 (TRUMOF-1) is an atomic-scale realization of a complex three-dimensional Truchet tiling. Its crystal structure consists of a periodically arranged assembly of identical zinc-containing clusters connected uniformly in a well-defined but disordered fashion to give a topologically aperiodic microporous network. We suggest that this unusual structure emerges as a consequence of geometric frustration in the chemical building units from which it is assembled.},
}
@article {pmid36699719,
year = {2022},
author = {Chen, Y and Mao, L and Lai, D and Xu, W and Zhang, Y and Wu, S and Yang, D and Zhao, S and Liu, Z and Xiao, Y and Tang, Y and Meng, X and Wang, M and Shi, J and Chen, Q and Shu, Q},
title = {Improved targeting of the 16S rDNA nanopore sequencing method enables rapid pathogen identification in bacterial pneumonia in children.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {1001607},
pmid = {36699719},
issn = {2235-2988},
mesh = {Humans ; Child ; DNA, Ribosomal/genetics ; *Nanopore Sequencing ; Prospective Studies ; DNA, Bacterial/genetics/analysis ; Bacteria ; *Pneumonia, Bacterial/diagnosis ; RNA, Ribosomal, 16S/genetics ; },
abstract = {OBJECTIVES: To develop a rapid and low-cost method for 16S rDNA nanopore sequencing.<br><br>METHODS: This was a prospective study on a 16S rDNA nanopore sequencing method. We developed this nanopore barcoding 16S sequencing method by adding barcodes to the 16S primer to reduce the reagent cost and simplify the experimental procedure. Twenty-one common pulmonary bacteria (7 reference strains, 14 clinical isolates) and 94 samples of bronchoalveolar lavage fluid from children with severe pneumonia were tested. Results indicating low-abundance pathogenic bacteria were verified with the polymerase chain reaction (PCR). Further, the results were compared with those of culture or PCR.<br><br>RESULTS: The turnaround time was shortened to 6~8 hours and the reagent cost of DNA preparation was reduced by employing a single reaction adding barcodes to the 16S primer in advance. The accuracy rate for the 21 common pulmonary pathogens with an abundance &#x2265; 99% was 100%. Applying the culture or PCR results as the gold standard, 71 (75.5%) of the 94 patients were positive, including 25 positive cultures (26.6%) and 52 positive quantitative PCRs (55.3%). The median abundance in the positive culture and qPCR samples were 29.9% and 6.7%, respectively. With an abundance threshold increase of 1%, 5%, 10%, 15% and 20%, the test sensitivity decreased gradually to 98.6%, 84.9%, 72.6%, 67.1% and 64.4%, respectively, and the test specificity increased gradually to 33.3%, 71.4%, 81.0%, 90.5% and 100.0%, respectively.<br><br>CONCLUSIONS: The nanopore barcoding 16S sequencing method can rapidly identify the pathogens causing bacterial pneumonia in children.},
}
@article {pmid36699389,
year = {2022},
author = {Faure, R and Lavenier, D},
title = {QuickDeconvolution: fast and scalable deconvolution of linked-read sequencing data.},
journal = {Bioinformatics advances},
volume = {2},
number = {1},
pages = {vbac068},
pmid = {36699389},
issn = {2635-0041},
abstract = {MOTIVATION: Recently introduced, linked-read technologies, such as the 10× chromium system, use microfluidics to tag multiple short reads from the same long fragment (50-200 kb) with a small sequence, called a barcode. They are inexpensive and easy to prepare, combining the accuracy of short-read sequencing with the long-range information of barcodes. The same barcode can be used for several different fragments, which complicates the analyses.<br><br>RESULTS: We present QuickDeconvolution (QD), a new software for deconvolving a set of reads sharing a barcode, i.e. separating the reads from the different fragments. QD only takes sequencing data as input, without the need for a reference genome. We show that QD outperforms existing software in terms of accuracy, speed and scalability, making it capable of deconvolving previously inaccessible data sets. In particular, we demonstrate here the first example in the literature of a successfully deconvoluted animal sequencing dataset, a 33-Gb Drosophila melanogaster dataset. We show that the taxonomic assignment of linked reads can be improved by deconvoluting reads with QD before taxonomic classification.<br><br>Code and instructions are available on https://github.com/RolandFaure/QuickDeconvolution.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.},
}
@article {pmid36695892,
year = {2023},
author = {Qiu, H and Zhang, ZH and Wang, MZ and Jin, XJ and Lin, JD and Comes, HP and Chen, JX and Cui, RN and Duan, RQ and Li, P},
title = {Plastome evolution and phylogenomics of Impatiens (Balsaminaceae).},
journal = {Planta},
volume = {257},
number = {2},
pages = {45},
pmid = {36695892},
issn = {1432-2048},
support = {31970225//the National Natural Science Foundation of China/ ; },
mesh = {*Balsaminaceae/genetics ; *Impatiens/genetics ; Phylogeny ; Base Sequence ; Evolution, Molecular ; },
abstract = {This study reported seven new plastomes from Impatiens and observed three highly variable regions for phylogeny and DNA barcoding, which resolved the relationships among sections of subgenus Impatiens. Impatiens L. (Balsaminaceae, Ericales) is one of the largest and most diverse genera of angiosperms, widely known for its taxonomic difficulty. In this study, we reevaluated the infrageneric relationships within the genus Impatiens, using complete plastome sequence data. Seven complete plastomes of Impatiens (representing 6 species) were newly sequenced and characterized along with 20 previously published plastomes of other Impatiens species, plus 2 plastomes of outgroups (Hydrocera triflora, Balsaminaceae; Marcgravia coriacea, Marcgraviaceae). The total size of these 29 plastomes ranged from 151,538 bp to 152,917 bp, except 2 samples of Impatiens morsei, which exhibited a shorter length and lost some genes encoding NADH dehydrogenase subunits. Moreover, the number of simple sequence repeats (SSRs) ranged from 51 to 113, and the number of long repeats from 17 to 26. In addition, three highly variable regions were identified (trnG-GCC (The previous one), ndhF-rpl32-trnL-UGA-ccsA, and ycf1). Our phylogenomic analysis based on 80 plastome-derived protein-coding genes strongly supported the monophyly of Impatiens and its two subgenera (Clavicarpa and Impatiens), and fully resolved relationships among the six (out of seven) sampled sections of subgenus Impatiens. Overall, the plastome DNA markers and phylogenetic results reported in this study will facilitate future identification, taxonomic and DNA barcoding studies in Impatiens as well as evolutionary studies in Balsaminaceae.},
}
@article {pmid36694721,
year = {2022},
author = {Viesná, &#x415; and Fishman, V},
title = {FastContext: A tool for identification of adapters and other sequence patterns in next generation sequencing (NGS) data.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {26},
number = {8},
pages = {806-809},
doi = {10.18699/VJGB-22-97},
pmid = {36694721},
issn = {2500-0462},
abstract = {The development of next generation sequencing (NGS) methods has created the need for detailed analysis and control of each protocol step. NGS library preparation protocols may include steps with incorporation of various service sequences, such as sequencing adapters, primers, sample-, cell-, and molecule-specific barcodes. Despite a fairly high level of current knowledge, during the protocol development process researches often have to deal with various kinds of unexpected experiment outcomes, which result either from lack of information, lack of knowledge, or defects in reagent manufacturing. Detection and analysis of service sequences, their distribution and linkage may provide important information for protocol optimization. Here we introduce FastContext, a tool designed to analyze NGS read structure, based on sequence features found in reads, and their relative position in the read. The algorithm is able to create human readable read structures with user-specified patterns, to calculate counts and percentage of every read structure. Despite the simplicity of the algorithm, FastContext may be useful in read structure analysis and, as a result, can help better understand molecular processes that take place at different stages of NGS library preparation. The project is open-source software, distributed under GNU GPL v3, entirely written in the programming language Python, and based on well-maintained packages and commonly used data formats. Thus, it is cross-platform, may be patched or upgraded by the user if necessary. The FastContext package is available at the Python Package Index (https://pypi.org/project/FastContext), the source code is available at GitHub (https://github.com/regnveig/FastContext).},
}
@article {pmid36694075,
year = {2023},
author = {Setsuko, S and Yoshimura, K and Ueno, S and Worth, JRP and Ujino-Ihara, T and Katsuki, T and Noshiro, S and Fujii, T and Arai, T and Yoshimaru, H},
title = {A DNA barcode reference library for the native woody seed plants of Japan.},
journal = {Molecular ecology resources},
volume = {23},
number = {4},
pages = {855-871},
doi = {10.1111/1755-0998.13748},
pmid = {36694075},
issn = {1755-0998},
support = {20248017//the Japan Society for the Promotion of Science/ ; 25292098//the Japan Society for the Promotion of Science/ ; 95200//the support program of FFPRI for researchers having family responsibilities/ ; },
mesh = {Humans ; *DNA Barcoding, Taxonomic/methods ; Japan ; Sequence Analysis, DNA ; *DNA ; Seeds/genetics ; DNA, Plant/genetics ; Phylogeny ; },
abstract = {DNA barcode databases are increasingly available for a range of organisms, facilitating the wide application of DNA barcode-based studies. Here we announce the development of a comprehensive DNA barcode reference library of Japanese native woody seed plants representing 43 orders, 99 families, 303 genera and 834 species, and comprising 77.3% of the genera and 72.2% of the species of native woody seed plants in Japan. A total of 6216 plant specimens were collected from 223 sites across the subtropical, temperate, boreal and alpine biomes in Japan with most species represented by multiple accessions. This reference library utilized three chloroplast DNA regions (rbcL, trnH-psbA and matK) and consists of 14,403 barcode sequences. Individual regions varied in their identification rates, with species-level and genus-level rates for rbcL, trnH-psbA and matK based on blast being 57.4%/96.2%, 78.5%/99.1% and 67.8%/98.1%, respectively. Identification rates were higher using region combinations, with total species-level rates for two region combinations (rbcL &amp; trnH-psbA, rbcL &amp; matK and trnH-psbA &amp; matK) ranging between 90.6% and 95.8%, and for all three regions being equal to 98.6%. Genus-level identification rates were even higher, ranging between 99.7% and 100% for two region combinations and being 100% for the three regions. These results indicate that this DNA barcode reference library is an effective resource for investigations of native woody seed plants in Japan using DNA barcodes and provides a useful template for the development of libraries for other components of the Japanese flora.},
}
@article {pmid36693990,
year = {2023},
author = {Hu, Q and Qian, R and Zhang, Y and Ma, X and Ye, Y and Zhang, X and Lin, L and Liu, H and Zheng, J},
title = {Complete chloroplast genome molecular structure, comparative and phylogenetic analyses of Sphaeropteris lepifera of Cyatheaceae family: a tree fern from China.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {1356},
pmid = {36693990},
issn = {2045-2322},
mesh = {*Ferns/genetics ; *Genome, Chloroplast ; Phylogeny ; Molecular Structure ; Chloroplasts/genetics ; },
abstract = {Sphaeropteris lepifera is a tree fern in the Cyatheaceae, a family that has played an important role in the evolution of plant systems. This study aimed to analyze the complete chloroplast genome of S. lepifera and compared it with previously published chloroplast genomes Cyatheaceae family. The chloroplast genome of S. lepifera comprised 162,114 bp, consisting of a large single copy (LSC) region of 86,327 bp, a small single copy (SSC) region of 27,731 bp and a pair of inverted repeats (IRa and IRb) of 24,028 bp each. The chloroplast genome encoded 129 genes, comprising 32 transfer RNAs, 8 ribosomal RNAs, and 89 protein-coding genes. Comparison of the genomes of 7 Cyatheaceae plants showed that the chloroplast genome of S. lepifera was missing the gene trnV-UAC. Expansion of the SSC region led to the difference in the chloroplast genome size of S. lepifera. Eight genes, atpI, ccsA, petA, psaB, rpl16, rpoA, rpoC1, and ycf2 have high nucleic acid diversity and can be regarded as potential molecular markers. The genes trnG-trnR and atpB were suitable for DNA barcodes between different communities of S. lepifera. The S. lepifera groups in Zhejiang Province probably diffused from Pingtan and Ningde, Fujian. The results will provide a basis for species identification, biological studies, and endangerment mechanism of S. lepifera.},
}
@article {pmid36692675,
year = {2023},
author = {Ramasetty, BT and Kumar, RM and S, PH},
title = {DNA barcoding and nutritional profiling of underutilized native indigenous plant species of Karnataka, India.},
journal = {Molecular biology reports},
volume = {50},
number = {4},
pages = {3111-3118},
pmid = {36692675},
issn = {1573-4978},
mesh = {*DNA Barcoding, Taxonomic/methods ; DNA, Plant/genetics ; Phylogeny ; India ; *Crops, Agricultural/genetics ; },
abstract = {BACKGROUND: Locally adapted native indigenous plant species (NIPS) could restore the crop diversity in sustainable agriculture.<br><br>METHODS: Here, we report the molecular identification and nutritional profiling of some five NIPS of Karnataka; Musa paradisiaca cv. Nanjangud rasabale, Piper betle L. cv. Mysore betel leaf, Jasminum grandiflorum cv Mysore mallige, Solanum melongena L. cv. Udupi Mattu Gulla and S. melongena L. cv. Erangere badane of which the first four are Geographical Indication (GI) tagged. The samples were procured, authenticated and sequenced using two standard DNA barcodes: nuclear ITS2 and plastid rbcl.<br><br>RESULTS: The phylogenetic analysis using Neighborhood joining method revealed all the ITS2 tree topologies with higher genetic divergence than rbcl. All the rbcl tree topologies were monophyletic indicating sequence conservation. Though the concatenated ITS2&#x2009;+&#x2009;rbcl trees had higher bootstrap support (>&#x2009;98% except Solanum sp.) differences were observed because of the lack of available sequence deposition at species level. The proximate and nutritional profiling of the NIPS displayed superiority in terms of their nutritional profile and their potential application in phytopharmaceutical sector as nutritional supplements.<br><br>CONCLUSION: To our best knowledge this is the first study reporting the screening of five NIPS plant species of Karnataka for phylogeny and nutritional analysis. We also anticipate that if research towards the identification of NIPS species is accelerated, these nutritionally enhanced crops could be used as a safe and sustainable food in changing global climatic conditions.},
}
@article {pmid36691054,
year = {2023},
author = {Pessanha, TS and Herrera, HM and Jansen, AM and Iñiguez, AM},
title = {"Mi Casa, Tu Casa": the coati nest as a hub of Trypanosoma cruzi transmission in the southern Pantanal biome revealed by molecular blood meal source identification in triatomines.},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {26},
pmid = {36691054},
issn = {1756-3305},
support = {88882.332462/2019-01//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 308768/2017-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; PQ1A//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 312934/2017-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 26/202.945/2016//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; },
mesh = {Humans ; Animals ; *Trypanosoma cruzi/genetics ; Vermilingua ; *Procyonidae/parasitology ; Phylogeny ; *Coinfection ; *Chagas Disease ; *Triatoma/parasitology ; Ecosystem ; Mammals/parasitology ; Genotype ; },
abstract = {BACKGROUND: The study of the ecology of Trypanosoma cruzi is challenging due to its extreme adaptive plasticity, resulting in the parasitism of hundreds of mammal species and dozens of triatomine species. The genetic analysis of blood meal sources (BMS) from the triatomine vector is an accurate and practical approach for gathering information on which wild mammal species participate in a local transmission network. South American coatis, Nasua nasua, act as important reservoir host species of T. cruzi in the Pantanal biome because of their high rate of infection and elevated parasitemia, with the main discrete typing unit (DTU) lineages (TcI and TcII). Moreover, the carnivore coati is the only mammal species to build high arboreal nests for breeding and resting that can be shared by various vertebrate and invertebrate species. Herein, we applied the sensitive and specific methodology of DNA barcoding and molecular cloning to study triatomines found in a coati nest to access the diversity of mammal species that explore this structure, and therefore, may be involved in the parasite transmission network.<br><br>METHODS: Twenty-three Triatoma sordida were collected in one coati's nest in the subregion of Nhecol&#xe2;ndia, Pantanal. The DNA isolated from the gut of insects was subjected to BMS detection by PCR using universal primers that flank variable regions of the cytochrome b (cytb) and 12S rDNA mitochondrial genes from vertebrates. The Trypanosoma spp. diagnosis and DTU genotyping were based on an 18S rDNA molecular marker and also using new cytb gene primers designed in this study. Phylogenetic analyses and chord diagrams were constructed to visualize BMS haplotypes, DTU lineages detected on vectors, and their interconnections.<br><br>RESULTS: Twenty of 23 triatomines analyzed were PCR-positive (86.95%) showing lineages T. cruzi DTU TcI (n&#x2009;=&#x2009;2), TcII (n&#x2009;=&#x2009;6), and a predominance of TcI/TcII (n&#x2009;=&#x2009;12) mixed infection. Intra-DTU diversity was observed mainly from different TcI haplotypes. Genetic analyses revealed that the southern anteater, Tamandua tetradactyla, was the unique species detected as the BMS of triatomines collected from the coati's nest. At least three different individuals of T. tetradactyla served as BMS of 21/23 bugs studied, as indicated by the cytb and 12S rDNA haplotypes identified.<br><br>CONCLUSIONS: The identification of multiple BMS, and importantly, different individuals of the same species, was achieved by the methodology applied. The study demonstrated that the southern anteaters can occupy the South American coati's nest, serving as the BMS of T. sordida specimens. Since anteaters have an individualist nonsocial behavior, the three individuals detected as BMS stayed at the coati's nest at different times, which added a temporal character to BMS detection. The TcI and TcII infection, and significantly, a predominance of TcI/TcII mixed infection profile with different TcI and TcII haplotypes was observed, due to the discriminatory capacity of the methodology applied. Tamandua tetradactyla, a host which has been little studied, may have an important role in the T. cruzi transmission in that Pantanal subregion. The data from the present study indicate the sharing of coatis' nests by other mammal species, expanding the possibilities for T. cruzi transmission in the canopy strata. We propose that coatis' nests can act as the true hubs of the T. cruzi transmission web in Pantanal, instead of the coatis themselves, as previously suggested.},
}
@article {pmid36690509,
year = {2023},
author = {Gerrits van den Ende, B and Rodrigues, AM and Hahn, RC and Hagen, F},
title = {A surprising finding: The curious case of a tongue lesion misdiagnosed as paracoccidioidomycosis.},
journal = {Revista iberoamericana de micologia},
volume = {40},
number = {1},
pages = {10-14},
doi = {10.1016/j.riam.2022.11.002},
pmid = {36690509},
issn = {2173-9188},
mesh = {Humans ; *Paracoccidioidomycosis/diagnosis/pathology ; Phylogeny ; *Paracoccidioides/genetics ; Brazil ; Diagnostic Errors ; Tongue/pathology ; },
abstract = {BACKGROUND: Paracoccidioidomycosis is an endemic mycosis caused by members of the Paracoccidioides genus. Brazil remains the focus area and, to a lesser extent, the disease has been reported from Argentina, Colombia and Venezuela.<br><br>AIMS: A Venezuelan Paracoccidioides brasiliensis strain, isolated from a patient diagnosed with chronic multifocal paracoccidioidomycosis, was subjected to whole genome sequencing to provide more insight about Paracoccidioides outside the endemic focus area.<br><br>METHODS: P. brasiliensis strain CBS 118890 was whole genome sequenced using nanopore; library preparation with the 'native barcoding genomic DNA kit' was followed by sequencing on Flongle and MinION flowcells. Batches of strain CBS 118890 were re-identified by sequencing the internal transcribed spacer (ITS) region, and final identification was made based on phylogenetic analysis.<br><br>RESULTS: Surprisingly, the Venezuelan P. brasiliensis strain CBS 118890 turned out to be a Nannizziopsis species. The batches of this strain were ITS sequenced followed by phylogenetic analysis and resulted in the final identification of Nannizziopsis arthrosporioides.<br><br>CONCLUSIONS: Nannizziopsis infections are commonly seen in a wide variety of reptiles, but are particularly rare in human infections. This case underlines the need for molecular characterization of cases that clinically mimic paracoccidioidomycosis but that are serologically negative for Paracoccidioides.},
}
@article {pmid36689844,
year = {2023},
author = {Bae, S and Kim, P and Yi, CH},
title = {Biodiversity and spatial distribution of ascidian using environmental DNA metabarcoding.},
journal = {Marine environmental research},
volume = {185},
number = {},
pages = {105893},
doi = {10.1016/j.marenvres.2023.105893},
pmid = {36689844},
issn = {1879-0291},
mesh = {Animals ; Ecosystem ; *DNA, Environmental ; DNA Barcoding, Taxonomic/methods ; *Urochordata/genetics ; Environmental Monitoring/methods ; Biodiversity ; },
abstract = {Monitoring studies are necessary to understand the biodiversity of marine ecosystems and are useful for identifying and managing rare or invasive species. Because monitoring has traditionally relied only on visual surveys (e.g., trapping, netting, electrofishing, and SCUBA diving) with limited time and physical resources, environmental DNA (eDNA) analysis is being applied as an efficient monitoring method. This study compared whether the eDNA metabarcoding technique can replace the traditional visual survey in an ascidian fauna study. We designed ascidian-specific primers and identified a clear gap (3.75%) by barcoding gap analysis. Then, we collected seawater samples for eDNA analysis during the summer (August-September) of 2021 at three sites (Mokpo, Yeosu, and Uljin) in South Korea. In the survey sites of this study, 25 species were observed through literature and visual survey, among which 9 species were detected by metabarcoding and 16 species were not detected. On the other hand, 10 species were detected only by metabarcoding, and one of them was identified as Pyura mirabilis, an unrecorded species in South Korea. This study succeeded in detecting cryptic or rare species with one seawater collection, which can be used to determine their unexplored habitat. Therefore, we conclude that monitoring using eDNA is more efficient than visual surveys for detecting rare or cryptic ascidian species. We also suggest that, when combined with traditional monitoring methods, it could be a tool to complement ascidian fauna studies.},
}
@article {pmid36689187,
year = {2023},
author = {Wu, Q and Michaels, YS and Fulga, TA},
title = {Interrogation of Functional miRNA-Target Interactions by CRISPR/Cas9 Genome Engineering.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2630},
number = {},
pages = {243-264},
pmid = {36689187},
issn = {1940-6029},
support = {G0902418/MRC_/Medical Research Council/United Kingdom ; BB/L010275/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N006550/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 105605/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *MicroRNAs/genetics ; CRISPR-Cas Systems ; Cell Line ; Genome ; Response Elements ; },
abstract = {Posttranscriptional silencing by microRNAs (miRNAs) is a critical constituent of eukaryotic gene regulation. miRNAs are short (~22 nt) noncoding RNAs capable of specifically targeting the miRNA-induced silencing complex (miRISC) to transcripts bearing a complementary miRNA response element (MRE). Although recent methodological advances have greatly improved our understanding of miRNA biogenesis and the mechanisms by which miRNAs repress their cognate targets, exploring the physiological relevance of direct miRNA-target interactions in vivo has remained an outstanding challenge. Here we describe the experimental protocol underlying a novel approach, which allows direct in situ interrogation of specific miRNA-MRE interactions by CRISPR/Cas9-mediated genome engineering (Bassett G et al., Nat Commun 5, 4640, 2014). In this instance, the CRISPR/Cas9 system is first used to catalyze homology-directed replacement of candidate MREs with molecular barcodes at endogenous loci. Subsequently, the effect of MRE mutation on transcript abundance (i.e., MRE activity) can be rapidly evaluated by routine quantitative PCR. This strategy enables functional investigation of a putative miRNA-target pair in a pool of transiently transfected cells, obviating the need for generation of clonal cell lines or transgenic animals. This protocol can be implemented in any cell line in less than 2 weeks and can readily be scaled up for multiplex studies. To facilitate the conceptual workflow underlying this strategy, we also describe a genome-wide resource for automated design and computational evaluation of CRISPR/Cas9 guide RNAs targeting all predicted MREs in various species (miR-CRISPR).},
}
@article {pmid36685651,
year = {2023},
author = {Carvalho Leonardo, I and Alberti, A and Denoeud, F and Barreto Crespo, MT and Capelo, J and Bustos Gaspar, F},
title = {The complete plastome of Centaurium erythraea subsp. majus (Hoffmanns. &amp; Link) M.Laínz (Gentianaceae), the first chloroplast genome belonging to the Centaurium genus.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {8},
number = {1},
pages = {86-90},
pmid = {36685651},
issn = {2380-2359},
abstract = {Despite having many historically reported ethnomedicinal uses, Centaurium erythraea Rafn (Rafn and Buchs, 1800; common centaury) also produces cytotoxic secondary metabolites, and its presence should be carefully monitored. In this study, the complete chloroplast of Centaurium erythraea subsp. majus (Hoffmanns. &amp; Link) M.Laínz (Laínz, 1971) isolate BPTPS121 is described, being the first available plastome belonging to the Centaurium genus. The chloroplast genome (GenBank accession number: ON641347) is 153,107 bp in length with 37.9% GC content, displaying a quadripartite structure that contains a pair of inverted repeat regions (25,166 bp each), separated by a large single-copy (84,388 bp) and small single-copy (18,387 bp) regions. A total of 129 genes were predicted, including 37 tRNA genes, eight rRNA genes, and 84 protein-coding genes. The phylogenetic analysis showed that isolate BPTPS121 is placed under the Gentianaceae family, belonging to the Gentianales order. The maximum-likelihood tree supports the already described lineage divergence in the Gentianaceae family, with C. erythraea subsp. majus belonging to the Chironieae tribe positioned below the Exaceae tribe and above the Potalieae and the entire Gentianeae tribes. This study will contribute to conservation, phylogenetic, and evolutionary studies, as well as DNA barcoding applications for food, feed, and supplements safety purposes.},
}
@article {pmid36684429,
year = {2022},
author = {Hines, WC and Hines, WC},
title = {Lost in transduction: Critical considerations when using viral vectors.},
journal = {Frontiers in cell and developmental biology},
volume = {10},
number = {},
pages = {1080265},
pmid = {36684429},
issn = {2296-634X},
abstract = {The application of retroviral vectors in the laboratory requires considerations that often go overlooked but are often easy to circumvent. Here, we discuss the relationship between the observed transduction efficiency of a cell population and per-cell viral insertions-and describe how differential cell-type susceptibilities can confound results. We consider the math underlying this problem and review an alternative approach to the commonly used "multiplicity of infection" (MOI) method of titering and using viral vectors in the biomedical research laboratory.},
}
@article {pmid36679081,
year = {2023},
author = {Nurashov, S and Jumakhanova, G and Barinova, S and Romanov, R and Sametova, E and Jiyenbekov, A and Shalgimbayeva, S and Smith, TE},
title = {Charophytes (Charophyceae, Charales) of South Kazakhstan: Diversity, Distribution, and Tentative Red List.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {2},
pages = {},
pmid = {36679081},
issn = {2223-7747},
abstract = {The presented research was conducted during 2019-2022 in south and southeast Kazakhstan to document the species richness, distribution, and ecology of charophytes (Characeae) as a first step towards to estimate the need for species protection. Across the 54 sites, we found ten species and one variety. Chara vulgaris Linnaeus and C. contraria A.Braun ex Kützing were the most common species, followed by C. canescens Loiseleur, C. kirghisorum C. F. Lessing, C. tomentosa Linnaeus, C. dominii J. Vilhelm, C. globata W. Migula, Nitellopsis obtusa (Desvaux) J. Groves, and Nitella hyalina (De Candolle) C. Agardh. The list of localities for each species was compiled. The distribution of each taxon was mapped in relations to the ecoregions studied. The two most frequent species were found in a wide spectrum of ecoregions, whereas all other species occurred in only a few regions in Kazakhstan. The Kaskelen River Valley had the most sampled sites with the highest number of co-occurring species (up to five together). Statistical maps were plotted in attempt to outline key environmental variables explaining the distribution of each species. A comparison of species and environmental variables distribution maps lets us assume that C. vulgaris prefers low altitude habitats with higher water temperatures, organic enrichments, and color, but low oxygen and pH. Other species prefer clear, alkaline, organically unpolluted, and well-oxygenated waters in lowland habitats. The redundancy detrended analysis (RDA) defined pH and altitude as negative factors for Nitellopsis obtusa whereas an increase in water temperature was positive. Altitude and water temperatures affected Chara contraria positively while altitude negatively influenced the rare species: Chara tomentosa, C. kirghisorum, and C. dominii. The matK sequences were obtained for C. contraria and C. vulgaris to confirm their identity according to morphological traits and to compare populations of C. gymnophylla and C. vulgaris from an arid region in Israel. Our data allowed for the preparation of a tentative red list from the study region. One species was recognized as endangered, four species and one variety as vulnerable, and two species as least concern. There was insufficient data to determine the status of two species and one variety.},
}
@article {pmid36675928,
year = {2023},
author = {Liu, J and Hu, Y and Luo, X and Castañeda-Ruíz, RF and Xia, J and Xu, Z and Cui, R and Shi, X and Zhang, L and Ma, J},
title = {Molecular Phylogeny and Morphology Reveal Four Novel Species of Corynespora and Kirschsteiniothelia (Dothideomycetes, Ascomycota) from China: A Checklist for Corynespora Reported Worldwide.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {1},
pages = {},
pmid = {36675928},
issn = {2309-608X},
support = {32160006, 31970018, 31360011//National Natural Science Foundation of China/ ; },
abstract = {Plant debris are habitats favoring survival and multiplication of various microbial species. During continuing mycological surveys of saprobic microfungi from plant debris in Yunnan Province, China, several Corynespora-like and Dendryphiopsis-like isolates were collected from dead branches of unidentified perennial dicotyledonous plants. Four barcodes, i.e., ITS, LSU, SSU and tef1-α, were amplified and sequenced. Morphological studies and multigene phylogenetic analyses by maximum likelihood and Bayesian inference revealed three new Corynespora species (C. mengsongensis sp. nov., C. nabanheensis sp. nov. and C. yunnanensis sp. nov.) and a new Kirschsteiniothelia species (K. nabanheensis sp. nov.) within Dothideomycetes, Ascomycota. A list of identified and accepted species of Corynespora with major morphological features, host information and locality was compiled. This work improves the knowledge of species diversity of Corynespora and Kirschsteiniothelia in Yunnan Province, China.},
}
@article {pmid36675874,
year = {2022},
author = {Jaramillo-Riofrío, A and Decock, C and Suárez, JP and Benítez, &#xc1; and Castillo, G and Cruz, D},
title = {Screening of Antibacterial Activity of Some Resupinate Fungi, Reveal Gloeocystidiellum lojanense sp. nov. (Russulales) against E. coli from Ecuador.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {1},
pages = {},
pmid = {36675874},
issn = {2309-608X},
abstract = {Bacterial resistance to antibiotics is a serious public health problem that needs new antibacterial compounds for control. Fungi, including resupinated fungi, are a potential source to discover new bioactive compounds efficient again to bacteria resistant to antibiotics. The inhibitory capacity against the bacterial species was statistically evaluated. All the species (basidiomata and strains) were molecularly characterized with the ITS1-5.8S-ITS2 barcoding marker. The strains Ceraceomyces sp., Fuscoporia sp., Gloeocystidiellum sp., Oliveonia sp., Phanerochaete sp., and Xenasmatella sp. correspond to resupinate Basidiomycetes, and only the strain Hypocrea sp. is an Ascomycete, suggesting contamination to the basidiome of Tulasnella sp. According to the antagonistic test, only the Gloeocystidiellum sp. strain had antibacterial activity against the bacterial species Escherichia coli of clinical interest. Statistically, Gloeocystidiellum sp. was significantly (<0.001) active against two E. coli pathotypes (O157:H7 and ATCC 25922). Contrarily, the antibacterial activity of fungi against other pathotypes of E. coli and other strains such as Serratia sp. was not significant. The antibacterial activity between 48 and 72 h increased according to the measurement of the inhibition halos. Because of this antibacterial activity, Gloeocystidiellum sp. was taxonomically studied in deep combined morphological and molecular characterization (ITS1-5.8S-ITS2; partial LSU D1/D2 of nrDNA). A new species Gloeocystidiellum lojanense, a resupinate and corticioid fungus from a tropical montane rainforest of southern Ecuador, with antibacterial potential against E. coli, is proposed to the science.},
}
@article {pmid36672917,
year = {2023},
author = {Feng, J and Xiong, Y and Su, X and Liu, T and Xiong, Y and Zhao, J and Lei, X and Yan, L and Gou, W and Ma, X},
title = {Analysis of Complete Chloroplast Genome: Structure, Phylogenetic Relationships of Galega orientalis and Evolutionary Inference of Galegeae.},
journal = {Genes},
volume = {14},
number = {1},
pages = {},
pmid = {36672917},
issn = {2073-4425},
mesh = {Phylogeny ; *Genome, Chloroplast ; *Galega ; *Fabaceae ; Genomics ; },
abstract = {Galega orientalis, a leguminous herb in the Fabaceae family, is an ecologically and economically important species widely cultivated for its strong stress resistance and high protein content. However, genomic information of Galega orientalis has not been reported, which limiting its evolutionary analysis. The small genome size makes chloroplast relatively easy to obtain genomic sequence for phylogenetic studies and molecular marker development. Here, the chloroplast genome of Galega orientalis was sequenced and annotated. The results showed that the chloroplast genome of G. orientalis is 125,280 bp in length with GC content of 34.11%. A total of 107 genes were identified, including 74 protein-coding genes, 29 tRNAs and four rRNAs. One inverted repeat (IR) region was lost in the chloroplast genome of G. orientalis. In addition, five genes (rpl22, ycf2, rps16, trnE-UUC and pbf1) were lost compared with the chloroplast genome of its related species G. officinalis. A total of 84 long repeats and 68 simple sequence repeats were detected, which could be used as potential markers in the genetic studies of G. orientalis and related species. We found that the Ka/Ks values of three genes petL, rpl20, and ycf4 were higher than one in the pairwise comparation of G. officinalis and other three Galegeae species (Calophaca sinica, Caragana jubata, Caragana korshinskii), which indicated those three genes were under positive selection. A comparative genomic analysis of 15 Galegeae species showed that most conserved non-coding sequence regions and two genic regions (ycf1 and clpP) were highly divergent, which could be used as DNA barcodes for rapid and accurate species identification. Phylogenetic trees constructed based on the ycf1 and clpP genes confirmed the evolutionary relationships among Galegeae species. In addition, among the 15 Galegeae species analyzed, Galega orientalis had a unique 30-bp intron in the ycf1 gene and Tibetia liangshanensis lacked two introns in the clpP gene, which is contrary to existing conclusion that only Glycyrrhiza species in the IR lacking clade (IRLC) lack two introns. In conclusion, for the first time, the complete chloroplast genome of G. orientalis was determined and annotated, which could provide insights into the unsolved evolutionary relationships within the genus Galegeae.},
}
@article {pmid36672828,
year = {2022},
author = {López-Barrera, A and Santos-Ordóñez, E and Pacheco-Coello, R and Villao-Uzho, L and Miranda, M and Gutiérrez, Y and Chóez-Guaranda, I and Ruiz-Reyes, SG},
title = {ITS1 Barcode and Phytochemical Analysis by Gas Chromatography-Mass Spectrometry of Corynaea crassa Hook. f (Balanophoraceae) from Ecuador and Peru.},
journal = {Genes},
volume = {14},
number = {1},
pages = {},
pmid = {36672828},
issn = {2073-4425},
mesh = {Ecuador ; Peru ; Phylogeny ; *Balanophoraceae ; Gas Chromatography-Mass Spectrometry ; *Plants, Medicinal/genetics ; Phytochemicals ; },
abstract = {The use of medicinal plants is the basis of traditional healthcare. Recently, the use of herbal medicine has been increasing among consumers due to availability, economy, and less side effect. For instance, the hemiparasite plant Corynaea crassa has medicinal properties and could be found in some regions of America, from Costa Rica to Bolivia. Phytochemical and genetic characterization of medicinal plants is needed for proper identification of metabolites responsible for medicinal properties and for genotyping, respectively. Moreover, characterization of medicinal plants through the use of DNA barcodes is an important tool for phylogenetic analysis and identification of species; furthermore, complemented with phytochemical analysis, both are useful for identification of plant species and quality control of medicinal products. The objective of this study was to analyze the species of C. crassa collected in Ecuador and Peru from the phylogenetic and phytochemical point of view. Polymerase chain reaction (PCR) was performed for amplification of the internal transcribed spacer 1 (ITS1) region after DNA extraction of samples of C. crassa. Blast analysis was performed in the GenBank database with the ITS1 sequences obtained from two accessions of C. crassa from Ecuador (GenBank accession numbers OM471920 and OM471919 for isolates CIBE-17 and CIBE-18, respectively) and three from Peru (GenBank accession numbers OM471921, OM471922, and OM471923 for isolates CIBE-13, CIBE-14, and CIBE-15, respectively). The accessions available in the GenBank were used for phylogenetic analysis. For the phytochemical analysis, hydroalcoholic extracts were obtained by maceration using 80% ethanol as solvent, followed by a derivatization process and analysis by gas chromatography-mass spectrometry. Based on the phylogenetic analysis of the C. crassa samples, the ITS1 sequence could be used to differentiate C. crassa of different locations. The samples of C. crassa from Ecuador and Peru are more similar between them than with other clades including Helosis spp. The phytochemical study revealed differences in the presence and relative abundance of some metabolites; mainly eugenol, 1,4-lactone arabinonic acid, dimethoxyrabelomycin and azelaic acid, which are reported for the first time for the species under study and the genus Corynaea. These results are the first findings on the combined analysis using genetic and phytochemical analysis for C. crassa, which could be used as a useful tool for quality control of the C. crassa species in medicinal products.},
}
@article {pmid36672805,
year = {2022},
author = {Yan, K and Ran, J and Bao, S and Li, Y and Islam, R and Zhang, N and Zhao, W and Ma, Y and Sun, C},
title = {The Complete Chloroplast Genome Sequence of Eupatorium fortunei: Genome Organization and Comparison with Related Species.},
journal = {Genes},
volume = {14},
number = {1},
pages = {},
pmid = {36672805},
issn = {2073-4425},
mesh = {*Eupatorium/genetics ; *Asteraceae/genetics ; Phylogeny ; *Genome, Chloroplast ; Whole Genome Sequencing ; },
abstract = {Eupatorium fortunei Turcz, a perennial herb of the Asteraceae family, is one of the horticultural and medicinal plants used for curing various diseases and is widely distributed in China and other Asian countries. It possesses antibacterial, antimetastatic, antiangiogenic, and antioxidant properties along with anticancer potential. However, the intrageneric classification and phylogenetic relationships within Eupatorium have long been controversial due to the lack of high-resolution molecular markers, and the complete chloroplast (cp) genome sequencing has not been reported with new evolutionary insights. In the present study, E. fortunei was used as an experimental material, and its genome was sequenced using high-throughput sequencing technology. We assembled the complete cp genome, and a systematic analysis was conducted for E. fortunei, acquiring the correspondence of its NCBI accession number (OK545755). The results showed that the cp genome of E. fortunei is a typical tetrad structure with a total length of 152,401 bp, and the genome encodes 133 genes. Analysis of the complete cp genomes of 20 Eupatorieae shows that the number of simple sequence repeats (SSRs) ranged from 19 to 36 while the number of long sequence repeats was 50 in all cases. Eleven highly divergent regions were identified and are potentially useful for the DNA barcoding of Eupatorieae. Phylogenetic analysis among 22 species based on protein-coding genes strongly supported that E. fortunei is more closely related to Praxelis clematidea and belongs to the same branch. The genome assembly and analysis of the cp genome of E. fortunei will facilitate the identification, taxonomy, and utilization of E. fortunei as well as provide more accurate evidence for the taxonomic identification and localization of Asteraceae plants.},
}
@article {pmid36672774,
year = {2022},
author = {El-Esawi, MA and Elashtokhy, MMA and Shamseldin, SAM and El-Ballat, EM and Zayed, EM and Heikal, YM},
title = {Analysis of Genetic Diversity and Phylogenetic Relationships of Wheat (Triticum aestivum L.) Genotypes Using Phenological, Molecular and DNA Barcoding Markers.},
journal = {Genes},
volume = {14},
number = {1},
pages = {},
pmid = {36672774},
issn = {2073-4425},
mesh = {*Triticum ; *Genetic Variation/genetics ; Phylogeny ; DNA Barcoding, Taxonomic ; Genetic Markers/genetics ; Genotype ; },
abstract = {Wheat (Triticum aestivum L.) is a key food crop, accounting for approximately 765 million tons produced worldwide. The present study evaluated 16 wheat genotypes using 19 morphological and phenological traits, 16 molecular markers (Inter Simple Sequence Repeats and Start Codon Targeted; ISSR and SCoT) and rbcL and matK plastid gene barcoding. The 16 wheat genotypes showed significant genetic variation using the markers assayed. Cell plot of phenological parameters revealed significant differences among the 16-day-old seedlings of wheat genotypes at Z1.1 growth stage. Collectively, W2 genotype had the lowest shoot length (SL), length of first internodes (LFI) and leaf area (LA) values, while W8 genotype had the highest diameter of first internode (DFI) and LA values. Furthermore, W7 genotype had the maximum plant biomass (PB) and leaf width (LW) values. Geometric models grouped wheat kernels into "rounded" and "nearly elongated". Estimates of heritability (H[2]) for these morphological characters ranged from 4.93 to 100%. The highest H[2] values were recorded for root number (RN) (100%) followed by SL (88.72%), LFI (88.30%), LA (87.76%) and Feret diameter (86.68%), while the lowest H[2] value was recorded for DFI (4.93%). Furthermore, highly significant genotypic and phenotypic correlations were also observed among those traits. Reproducible fingerprinting profiles and high levels of polymorphism (PPB%) of SCoT (95.46%) and ISSR (82.41%) were recorded, indicating that they are effective tools for detecting genetic variation levels among wheat genotypes. The informativeness of markers were measured through estimation of polymorphic information content (PIC), resolving power (RP) and marker index (MI). The RP and PPB% of SCoT were significantly higher compared to those of ISSR. Comparatively, the two molecular markers were effective for studying genetic diversity among wheat genotypes, but SCoT markers were more informative. Moreover, based on the two chloroplast DNA regions (rbcL and matK), MatK was found to be more reliable for differentiating among T. aestivum genotypes. Taken together, using all the studied attributes, a clear taxonomic relationship can be used to identify T. aestivum species and improve their pragmatic production and development.},
}
@article {pmid36672453,
year = {2023},
author = {Chhouri, H and Alexandre, D and Grumolato, L},
title = {Mechanisms of Acquired Resistance and Tolerance to EGFR Targeted Therapy in Non-Small Cell Lung Cancer.},
journal = {Cancers},
volume = {15},
number = {2},
pages = {},
pmid = {36672453},
issn = {2072-6694},
support = {PLBIO 2017-157//French National Cancer Institute/ ; FDT202001010860//Fondation pour la Recherche M&#xe9;dicale/ ; },
abstract = {Non-small cell lung cancers (NSCLC) harboring activating mutations of the epidermal growth factor receptor (EGFR) are treated with specific tyrosine kinase inhibitors (EGFR-TKIs) of this receptor, resulting in clinically responses that can generally last several months. Unfortunately, EGFR-targeted therapy also favors the emergence of drug tolerant or resistant cells, ultimately resulting in tumor relapse. Recently, cellular barcoding strategies have arisen as a powerful tool to investigate the clonal evolution of these subpopulations in response to anti-cancer drugs. In this review, we provide an overview of the currently available treatment options for NSCLC, focusing on EGFR targeted therapy, and discuss the common mechanisms of resistance to EGFR-TKIs. We also review the characteristics of drug-tolerant persister (DTP) cells and the mechanistic basis of drug tolerance in EGFR-mutant NSCLC. Lastly, we address how cellular barcoding can be applied to investigate the response and the behavior of DTP cells upon EGFR-TKI treatment.},
}
@article {pmid36671828,
year = {2023},
author = {Bateman, RM and Rudall, PJ},
title = {Morphological Continua Make Poor Species: Genus-Wide Morphometric Survey of the European Bee Orchids (Ophrys L.).},
journal = {Biology},
volume = {12},
number = {1},
pages = {},
pmid = {36671828},
issn = {2079-7737},
abstract = {Despite (or perhaps because of) intensive multidisciplinary research, opinions on the optimal number of species recognised within the Eurasian orchid genus Ophrys range from nine to at least 400. The lower figure of nine macrospecies is based primarily on seeking small but reliable discontinuities in DNA 'barcode' regions, an approach subsequently reinforced and finessed via high-throughput sequencing studies. The upper figure of ca. 400 microspecies reflects the morphological authoritarianism of traditional taxonomy combined with belief in extreme pollinator specificity caused by reliance on pollination through pseudo-copulation, enacted by bees and wasps. Groupings of microspecies that are less inclusive than macrospecies are termed mesospecies. Herein, we present multivariate morphometric analyses based on 51 characters scored for 457 individual plants that together span the full morphological and molecular diversity within the genus Ophrys, encompassing 113 named microspecies that collectively represent all 29 mesospecies and all nine macrospecies. We critique our preferred morphometric approach of accumulating heterogeneous data and analysing them primarily using principal coordinates, noting that our conclusions would have been strengthened by even greater sampling and the inclusion of data describing pseudo-pheromone cocktails. Morphological variation within Ophrys proved to be exceptionally multidimensional, lacking strong directional trends. Multivariate clustering of plants according to prior taxonomy was typically weak, irrespective of whether it was assessed at the level of macrospecies, mesospecies or microspecies; considerable morphological overlap was evident even between subsets of the molecularly differentiable macrospecies. Characters supporting genuine taxonomic distinctions were often sufficiently subtle that they were masked by greater and more positively correlated variation that reflected strong contrasts in flower size, tepal colour or, less often, plant size. Individual macrospecies appear to represent morphological continua, within which taxonomic divisions are likely to prove arbitrary if based exclusively on morphological criteria and adequately sampled across their geographic range. It remains unclear how much of the mosaic of subtle character variation among the microspecies reflects genetic versus epigenetic or non-genetic influences and what proportion of any contrasts observed in gene frequencies can be attributed to the adaptive microevolution that is widely considered to dictate speciation in the genus. Moreover, supplementing weak morphological criteria with extrinsic criteria, typically by imposing constraints on geographic location and/or supposed pollinator preference, assumes rather than demonstrates the presence of even the weakest of species boundaries. Overall, it is clear that entities in Ophrys below the level of macrospecies have insufficiently structured variation, either phenotypic or genotypic, to be resolved into discrete, self-circumscribing ("natural") entities that can legitimately be equated with species as delimited within other less specialised plant genera. Our search for a non-arbitrary (meso)species concept competent to circumscribe an intermediate number of species has so far proven unsuccessful.},
}
@article {pmid36671806,
year = {2023},
author = {Unterberger, SH and Berger, C and Schirmer, M and Pallua, AK and Zelger, B and Schäfer, G and Kremser, C and Degenhart, G and Spiegl, H and Erler, S and Putzer, D and Arora, R and Parson, W and Pallua, JD},
title = {Morphological and Tissue Characterization with 3D Reconstruction of a 350-Year-Old Austrian Ardea purpurea Glacier Mummy.},
journal = {Biology},
volume = {12},
number = {1},
pages = {},
pmid = {36671806},
issn = {2079-7737},
abstract = {Glaciers are dwindling archives, releasing animal mummies preserved in the ice for centuries due to climate changes. As preservation varies, residual soft tissues may differently expand the biological information content of such mummies. DNA studies have proven the possibility of extracting and analyzing DNA preserved in skeletal residuals and sediments for hundreds or thousands of years. Paleoradiology is the method of choice as a non-destructive tool for analyzing mummies, including micro-computed tomography (micro-CT) and magnetic resonance imaging (MRI). Together with radiocarbon dating, histo-anatomical analyses, and DNA sequencing, these techniques were employed to identify a 350-year-old Austrian Ardea purpurea glacier mummy from the Ötztal Alps. Combining these techniques proved to be a robust methodological concept for collecting inaccessible information regarding the structural organization of the mummy. The variety of methodological approaches resulted in a distinct picture of the morphological patterns of the glacier animal mummy. The BLAST search in GenBank resulted in a 100% and 98.7% match in the cytb gene sequence with two entries of the species Purple heron (Ardea purpurea; Accession number KJ941160.1 and KJ190948.1) and a 98% match with the same species for the 16 s sequence (KJ190948.1), which was confirmed by the anatomic characteristics deduced from micro-CT and MRI.},
}
@article {pmid36671720,
year = {2022},
author = {Awad, M and Ben Gharsa, H and ElKraly, OA and Leclerque, A and Elnagdy, SM},
title = {COI Haplotyping and Comparative Microbiomics of the Peach Fruit Fly, an Emerging Pest of Egyptian Olive Orchards.},
journal = {Biology},
volume = {12},
number = {1},
pages = {},
pmid = {36671720},
issn = {2079-7737},
support = {57478537//German Academic Exchange Service/ ; 57626230//German Academic Exchange Service/ ; },
abstract = {The peach fruit fly, Bactrocera zonata (Tephritidae), is economically relevant as a highly polyphagous pest infesting over 50 host plants including commercial fruit and horticultural crops. As an invasive species, B. zonata was firmly established in Egypt and holds potential to spread further across the Mediterranean basin. The present study demonstrated that the peach fruit fly was found multiplying in olive orchards at two distant locations in Egypt. This is the first report of B. zonata developing in olives. COI barcoding has revealed evidence for high diversity across these peach fruit fly populations. These data are consistent with multiple rather than a single event leading to both peach fruit fly invasion to Egypt and its adaptation to olive. Comparative microbiomics data for B. zonata developing on different host plants were indicative for microbiome dynamics being involved in the adaptation to olive as a new niche with a potential adaptive role for Erwinia or Providencia bacteria. The possibility of symbiont transfer from the olive fruit fly to the peach fruit fly is discussed. Potentially host switch relevant bacterial symbionts might be preferred targets of symbiosis disruption strategies for integrated pest management or biological control of B. zonata.},
}
@article {pmid36662006,
year = {2023},
author = {Laojun, S and Changbunjong, T and Chaiphongpachara, T},
title = {Evaluation of Modern Techniques for Species Identification of Lutzia Mosquitoes (Diptera: Culicidae) in Thailand: Geometric Morphometrics and DNA Barcoding.},
journal = {Insects},
volume = {14},
number = {1},
pages = {},
pmid = {36662006},
issn = {2075-4450},
abstract = {There are four species of Lutzia mosquitoes in Thailand, including Lutzia chiangmaiensis, Lt. fuscana, Lt. halifaxii, and Lt. vorax. The accurate species identification of adult Lutzia mosquitoes based on morphological features requires many body parts, including the abdominal terga and wing. However, species identification is difficult in the case of damaged specimens when some of their morphological character is missing due to transit or gathering in the field. Thus, we evaluated the efficacy of the landmark-based geometric morphometric (GM) approach for the discrimination of Lutzia species in Thailand. In addition, DNA barcoding was also used in parallel with the GM approach to identify the species. Larvae of Lutzia were collected, raised into adults, and identified based on their morphological characteristics. The validated reclassification test results clearly demonstrated that wing shape resulted in a high level of success in identification (correct identifications ranged from 92.50% to 100%); however, based on the DNA barcoding analyses, our results showed that it was poorly effective in identifying Lt. fuscana and Lt. halifaxii based on an overlap between the intraspecific and interspecific divergence. Moreover, our survey results provide updates on the distribution of Lt. chiangmaiensis and Lt. vorax in Thailand. This research will help medical entomologists more efficiently identify mosquitoes in the genus Lutzia, resulting in more effective mosquito control and surveillance.},
}
@article {pmid36661968,
year = {2022},
author = {Aishan, Z and Cao, HX and Hu, HY and Zhu, CD},
title = {Chinese Species of the Genus Pseudanaphes Noyes &amp; Valentine (Hymenoptera: Mymaridae) with Description of a New Species.},
journal = {Insects},
volume = {14},
number = {1},
pages = {},
pmid = {36661968},
issn = {2075-4450},
support = {2018D01C059//National Natural Science Foundation of Xinjiang Autonomous Region/ ; 2019QZKK05010605//The second Tibetan Plateau scientific expedition and research (STEP) program/ ; 62031224613//PhD research startup foundation of Xinjiang University/ ; },
abstract = {The fairyfly Mymaridae (Hymenoptera: Chalcidoidea) are widely distributed worldwide, but species of this family have rarely been collected and recorded from the Qinghai-Tibet Plateau. In this study, mymarids collected in Tibet, China, are identified based on morphology and molecular data. Two species of the genus Pseudanaphes Noyes &amp; Valentine are treated and illustrated here, including a known species, P. zhaoi Lin, and a new species, P. yadongicus Aishan &amp; Cao sp. nov. In addition, a key to the world species of Pseudanaphes (females) and DNA barcodes for P. yadongicus and P. zhaoi are provided.},
}
@article {pmid36661966,
year = {2022},
author = {Tsubuki, M and Hayashi, F},
title = {Pupal Warning Coloration of Three Species of Cystidia (Lepidoptera: Geometridae: Ennominae) in Relation to Their Pupation Sites.},
journal = {Insects},
volume = {14},
number = {1},
pages = {},
pmid = {36661966},
issn = {2075-4450},
support = {JPMJSP2156//Japan Science and Technology Agency/ ; },
abstract = {Many insects display a cryptic color to avoid detection by predators that search for prey by sight. However, some species with chemicals that predators dislike may display a warning color (aposematism) to predators. The predators can learn easier that the species is unsuitable as prey if the color is more conspicuous. Therefore, it is assumed that the acquisition of the warning color requires not only unpalatability, but also exposure of the color to predators and the ability of predators to recognize and learn it unpalatable. In the moths of the subfamily Ennominae, almost all of genera produce uniformly brown or green pupae, but the pupae of the genus Cystidia have conspicuous coloration of yellow background and black spots. In this study, to clarify whether the color of these pupae is the warning color or not, we compared the coloration, pupation site, and palatability among the three species of this genus: C. couaggaria, C. truncangulata, and C. stratonice. Learning by the predators was also examined using lizards as a potential predator of the moths. The results showed that all three species were repelled (unpalatable) by the lizards, and that repeated providing of the pupae to the lizards decreased their willingness to prey on them (probably due to learning). Pupation sites of C. couaggaria and C. truncangulata were located on the surface of branches and leaves high above the ground, whereas C. stratonice pupated in the space of leaves spun with course silk at lower site above the ground. Thus, the conspicuous coloration of pupal Cystidia is considered to be a warning color, but the pupae of C. stratonice are more blackish than those of the most closely related C. truncangulata. The pupal color of C. stratonice is likely to have a dual meaning as cryptic and warning colors. The dark colored pupa may be inconspicuous when hidden within the leaf space, but once detected by the predators, the yellow color of the pupa may function as a warning color.},
}
@article {pmid36661932,
year = {2022},
author = {Mushtaq, HMS and Kamran, M and Saleh, AA and Alatawi, FJ},
title = {Evidence for Reconsidering the Taxonomic Status of Closely Related Oligonychus Species in punicae Complex (Acari: Prostigmata: Tetranychidae).},
journal = {Insects},
volume = {14},
number = {1},
pages = {},
pmid = {36661932},
issn = {2075-4450},
support = {IFKSURG-2- 000//Deputyship for Research &amp; Innovation, Ministry of Ed- 533ucation in Saudi Arabia/ ; },
abstract = {To elucidate the taxonomic problems in species delineation within the Oligonychus punicae complex (O. punicae, O. mangiferus, and O. vitis) (Acari: Prostigmata: Tetranychidae), we performed morphological and molecular investigations on mite samples, collected from different hosts/countries. Thirty-nine samples of punicae complex, collected from Egypt, Pakistan, and Saudi Arabia (SA), did not show any considerable morphological differences in females and males. All 39 samples of the punicae complex resembled the original description of O. punicae, while the claimed Mexican O. punicae was distinctively different based on male aedeagus. Molecularly, the low nucleotide diversity ranged from 0% to 2.1% (ITS2-rDNA) and 0% to 1% (COI-mtDNA), and was observed among various DNA sequences of the punicae complex from Egypt, India, Israel, Pakistan, and SA, confirming their identity as one species. The high genetic divergence ranged from 17.2% to 18.8% (ITS2) and 9.2% to 10.2% (COI), observed between the claimed Mexican O. punicae and all other sequences of the punicae complex, indicating that the Mexican sample do not belong to O. punicae. Basing our findings on both morphological and molecular data, we can conclude that O. mangiferus and O. vitis are synonymized with O. punicae. Additionally, this study reveals that the claimed Mexican O. punicae needs to be re-identified.},
}
@article {pmid36656960,
year = {2023},
author = {Matsuo, B and Granados, A and Levitre, G and Molander, GA},
title = {Photochemical Methods Applied to DNA Encoded Library (DEL) Synthesis.},
journal = {Accounts of chemical research},
volume = {56},
number = {3},
pages = {385-401},
pmid = {36656960},
issn = {1520-4898},
support = {R35 GM131680/GM/NIGMS NIH HHS/United States ; },
mesh = {*DNA/chemistry ; *Drug Discovery ; Drug Design ; High-Throughput Screening Assays ; Oligonucleotides ; },
abstract = {DNA-encoded library technology (DELT) is a new screening modality that allows efficient, cost-effective, and rapid identification of small molecules with potential biological activity. This emerging technique represents an enormous advancement that, in combination with other technologies such as high-throughput screening (HTS), fragment-based lead generation, and structure-based drug design, has the potential to transform how drug discovery is carried out. DELT is a hybrid technique in which chemically synthesized compounds are linked to unique genetic tags (or "barcodes") that contain readable information. In this way, millions to billions of building blocks (BBs) attached on-DNA via split-and-pool synthesis can be evaluated against a biological target in a single experiment. Polymerase chain reaction (PCR) amplification and next-generation sequencing (NGS) analysis of the unique sequence of oligonucleotides in the DNA tag are used to identify those ligands with high affinity for the target. This innovative fusion of genetic and chemical technologies was conceived in 1992 by Brenner and Lerner (Proc. Natl. Acad. Sci. 1992, 89, 5381-5383) and is under accelerated development with the implementation of new synthetic techniques and protocols that are compatible with DNA. In fact, reaction compatibility is a key parameter to increasing the chances of identification of a drug target ligand, and a central focus has been the development of new transformations and the transition to robust protocols for on-DNA synthesis. Because the sole use of the DNA tag is as an amplifiable identification barcode, its structural integrity during a new chemical process is mandatory. As such, the use of these sensitive, polyfunctional biological molecules as substrates typically requires aqueous solutions within defined pH and temperature ranges, which is considered a notable challenge in DEL synthesis.Using low-energy visible light as the driving force to promote chemical transformations represents an attractive alternative to classical synthetic methods, and it is an important and well-established synthetic tool for forging chemical bonds in a unique way via radical intermediates. Recent advances in the field of photocatalysis are extraordinary, and this powerful research arena is still under continuous development. Several applications taking advantage of the mild reaction conditions of photoinduced transformations have been directed toward DEL synthesis, allowing the expansion of chemical space available for the evaluation of new building blocks on-DNA. There are no doubts that visible-light-driven reactions have become one of the most powerful approaches for DELT, given the easy way they provide to construct new bonds and the challenges to achieve equal success via classical protocols.Key characteristics of photocatalytic synthesis include the short reaction times and efficiency, which translate into retention of DNA integrity. In this Account, we describe recent advances in the photoinduced diversification of building blocks prepared on-DNA, highlighting the amenability of the techniques employed for preserving the genetic structure of the molecules. We demonstrate with recent research from our group the applicability of photocatalysis to the field and include in the summary a table containing all the photoinduced methods reported to date for DELT, demonstrating their key aspects such as scope, applications, and DNA compatibilities. With this information, practitioners are provided with compelling reasons for developing/choosing photocatalytic methods for DELT applications.},
}
@article {pmid36656075,
year = {2023},
author = {Meglécz, E},
title = {COInr and mkCOInr: Building and customizing a nonredundant barcoding reference database from BOLD and NCBI using a semi-automated pipeline.},
journal = {Molecular ecology resources},
volume = {23},
number = {4},
pages = {933-945},
doi = {10.1111/1755-0998.13756},
pmid = {36656075},
issn = {1755-0998},
abstract = {Reference databases with wide taxonomic coverage are greatly needed in many fields of biology, most particularly for the taxonomic assignment of metabarcoding sequences. Therefore, it is fundamental to be able to access and pool data from different primary databases. The COInr database is a freely available, easy-to-access database of COI reference sequences extracted from the BOLD and NCBI nucleotide databases. It is a comprehensive database: not limited to a taxon, a gene region or a taxonomic rank; therefore, it is a good starting point for creating custom databases. Sequences are dereplicated between databases and within taxa. Each taxon has a unique taxonomic identifier (taxID), fundamental to avoid ambiguous associations of homonyms and synonyms in the source database. TaxIDs form a coherent hierarchical system fully compatible with the NCBI taxIDs, allowing their full or ranked lineages to be created. The mkcoinr tool is a series of Perl scripts designed to download sequences from BOLD and NCBI, to build the COInr database and to customize it according to the users' needs. It is possible to select or eliminate sequences for a list of taxa, select a specific gene region, select for minimum taxonomic resolution, add new custom sequences, and format the database for blast, vtam, qiime and rdp classifier. This is a semi-automated pipeline using command lines in a Linux environment. The COInr database can be downloaded from https://doi.org/10.5281/zenodo.6555985 and mkcoinr and its full documentation is available at https://github.com/meglecz/mkCOInr.},
}
@article {pmid36654082,
year = {2022},
author = {Shin, C and Hong, SH and Jeong, H and Yoon, H and Koh, B},
title = {All-in-one encoder/decoder approach for non-destructive identification of 3D-printed objects.},
journal = {Mathematical biosciences and engineering : MBE},
volume = {19},
number = {12},
pages = {14102-14115},
doi = {10.3934/mbe.2022657},
pmid = {36654082},
issn = {1551-0018},
mesh = {*Printing, Three-Dimensional ; },
abstract = {This paper presents an all-in-one encoder/decoder approach for the nondestructive identification of three-dimensional (3D)-printed objects. The proposed method consists of three parts: 3D code insertion, terahertz (THz)-based detection, and code extraction. During code insertion, a relevant one-dimensional (1D) identification code is generated to identify the 3D-printed object. A 3D barcode corresponding to the identification barcode is then generated and inserted into a blank bottom area inside the object's stereolithography (STL) file. For this objective, it is necessary to find an appropriate area of the STL file and to merge the 3D barcode and the model within the STL file. Next the information generated inside the object is extracted by using THz waves that are transmitted and reflected by the output 3D object. Finally, the resulting THz signal from the target object is detected and analyzed to extract the identification information. We implemented and tested the proposed method using a 3D graphic environment and a THz time-domain spectroscopy system. The experimental results indicate that one-dimensional barcodes are useful for identifying 3D-printed objects because they are simple and practical to process. Furthermore, information efficiency can be increased by using an integral fast Fourier transform to identify any code located in areas deeper within the object. As 3D printing is used in various fields, the proposed method is expected to contribute to the acceleration of the distribution of 3D printing empowered by the integration of the internal code insertion and recognition process.},
}
@article {pmid36653313,
year = {2023},
author = {Krishna Sunkari, Y and Kumar Siripuram, V and Flajolet, M},
title = {Diversity-Oriented Synthesis (DOS) of On-DNA Peptidomimetics from Acid-Derived Phosphonium Ylides.},
journal = {Chemistry (Weinheim an der Bergstrasse, Germany)},
volume = {29},
number = {11},
pages = {e202203037},
doi = {10.1002/chem.202203037},
pmid = {36653313},
issn = {1521-3765},
mesh = {*Peptidomimetics ; Aldehydes/chemistry ; Ketones ; },
abstract = {The DNA-encoded library (DEL) technology represents a revolutionary drug-discovery tool with unprecedented screening power originating from the association of combinatorial chemistry and DNA barcoding. The chemical diversity of DELs and its chemical space will be further expanded as new DNA-compatible reactions are introduced. This work introduces the use of DOS in the context of on-DNA peptidomimetics. Wittig olefination of aspartic acid-derived on-DNA Wittig ylide, combined with a broad substrate scope of aldehydes, led to formation of on-DNA α ${\alpha }
$ , β ${\beta }
$ -unsaturated ketones. The synthesis of on-DNA multi-peptidyl-ylides was performed by incorporating sequential amino acids onto a monomeric ylide. Di-, tri- and tetrameric peptidyl-ylides were validated for Wittig olefination and led to on-DNA α ${\alpha }
$ , β ${\beta }
$ -unsaturated-based peptidomimetics, an important class of intermediates. One on-DNA aryl Wittig ylide was also developed and applied to Wittig olefination for synthesis of on-DNA chalcone-based molecules. Furthermore, DOS was used successfully with electron-deficient peptidomimetics and led to the development of different heterocyclic cores containing on-DNA peptidomimetics.},
}
@article {pmid36652865,
year = {2023},
author = {Dias, HQ and Sukumaran, S},
title = {Are genomic indices effective alternatives to morphology based benthic indices in biomonitoring studies? Perspectives from a major harbour and marine protected area.},
journal = {Marine pollution bulletin},
volume = {187},
number = {},
pages = {114586},
doi = {10.1016/j.marpolbul.2023.114586},
pmid = {36652865},
issn = {1879-3363},
mesh = {Animals ; *Ecosystem ; *Biological Monitoring ; Environmental Monitoring/methods ; Genomics ; Invertebrates/genetics ; },
abstract = {Ecological assessments are currently being conducted by traditional morpho-taxonomical identification techniques that are time-consuming and often inaccurate. Biomonitoring programs are increasingly being complemented by the more rapid and efficient DNA barcoding approach. We compared the congruency of morpho-taxonomic (AMBI - AZTI's Marine Biotic Index) and genomic (gAMBI) benthic indices in ecological quality status (EcoQS) assignation in Mumbai harbour and Malvan Marine Protected area (MPA). The study, first of its kind to adopt the gAMBI tool in the selected milieu, contributed substantial number of macrobenthic cytochrome c oxidase subunit I gene (COI) sequences that were previously unavailable in the reference library, adding sufficient genetic resources for establishing ecostatus. AMBI and gAMBI values based on presence/absence data related significantly with those derived from abundance data matrices. Taxonomic and genomic indices derived ecostatus corresponded sufficiently well despite minor discrepancies, underscoring the viability of gAMBI as a superior alternative to AMBI in monitoring studies.},
}
@article {pmid36651964,
year = {2023},
author = {Johnson, MS and Venkataram, S and Kryazhimskiy, S},
title = {Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes.},
journal = {Journal of molecular evolution},
volume = {91},
number = {3},
pages = {263-280},
pmid = {36651964},
issn = {1432-1432},
support = {R01 GM137112/GM/NIGMS NIH HHS/United States ; 1R01GM137112/GM/NIGMS NIH HHS/United States ; 1R01GM137112/GM/NIGMS NIH HHS/United States ; },
mesh = {*DNA Barcoding, Taxonomic ; *DNA/genetics ; Sequence Analysis, DNA/methods ; Computational Biology ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Random DNA barcodes are a versatile tool for tracking cell lineages, with applications ranging from development to cancer to evolution. Here, we review and critically evaluate barcode designs as well as methods of barcode sequencing and initial processing of barcode data. We first demonstrate how various barcode design decisions affect data quality and propose a new design that balances all considerations that we are currently aware of. We then discuss various options for the preparation of barcode sequencing libraries, including inline indices and Unique Molecular Identifiers (UMIs). Finally, we test the performance of several established and new bioinformatic pipelines for the extraction of barcodes from raw sequencing reads and for error correction. We find that both alignment and regular expression-based approaches work well for barcode extraction, and that error-correction pipelines designed specifically for barcode data are superior to generic ones. Overall, this review will help researchers to approach their barcoding experiments in a deliberate and systematic way.},
}
@article {pmid36650921,
year = {2023},
author = {Argiroff, WA and Zak, DR and Upchurch, RA and Pellitier, PT and Belke, JP},
title = {Fungal community composition and genetic potential regulate fine root decay in northern temperate forests.},
journal = {Molecular ecology},
volume = {32},
number = {8},
pages = {2005-2021},
doi = {10.1111/mec.16852},
pmid = {36650921},
issn = {1365-294X},
support = {//Horace H. Rackham School of Graduate Studies, University of Michigan/ ; //National Science Foundation/ ; },
mesh = {Ecosystem ; *Mycobiome ; Forests ; *Mycorrhizae/physiology ; Plants ; Soil Microbiology ; Fungi/genetics ; Soil ; Trees/microbiology ; },
abstract = {Understanding how genetic differences among soil microorganisms regulate spatial patterns in litter decay remains a persistent challenge in ecology. Despite fine root litter accounting for ~50% of total litter production in forest ecosystems, far less is known about the microbial decay of fine roots relative to aboveground litter. Here, we evaluated whether fine root decay occurred more rapidly where fungal communities have a greater genetic potential for litter decay. Additionally, we tested if linkages between decay and fungal genes can be adequately captured by delineating saprotrophic and ectomycorrhizal fungal functional groups based on whether they have genes encoding certain ligninolytic class II peroxidase enzymes, which oxidize lignin and polyphenolic compounds. To address these ideas, we used a litterbag study paired with fungal DNA barcoding to characterize fine root decay rates and fungal community composition at the landscape scale in northern temperate forests, and we estimated the genetic potential of fungal communities for litter decay using publicly available genomes. Fine root decay occurred more rapidly where fungal communities had a greater genetic potential for decay, especially of cellulose and hemicellulose. Fine root decay was positively correlated with ligninolytic saprotrophic fungi and negatively correlated with ECM fungi with ligninolytic peroxidases, likely because these saprotrophic and ectomycorrhizal functional groups had the highest and lowest genetic potentials for plant cell wall degradation, respectively. These fungal variables overwhelmed direct environmental controls, suggesting fungal community composition and genetic variation are primary controls over fine root decay in temperate forests at regional scales.},
}
@article {pmid36649276,
year = {2023},
author = {Wang, Y and Yao, X and Liu, R and Liu, C},
title = {DDQR (dynamic DNA QR coding): An efficient algorithm to represent DNA barcode sequences.},
journal = {PloS one},
volume = {18},
number = {1},
pages = {e0279994},
pmid = {36649276},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Plants/genetics ; Algorithms ; *Data Compression ; Sequence Analysis, DNA ; Phylogeny ; },
abstract = {A DNA barcode is a short piece of standard DNA sequence used for species determination and discrimination. Representation of DNA barcodes is essential for DNA barcodes' applications in the transportation and recognition of biological materials. Previously, we have compared different strategies for representing the DNA barcodes. In the present study, we have developed a compression algorithm based on binary coding or Huffman coding scheme, followed by converting the binary digits into Base64 digits. The combination of this compression algorithm and the QR representation leads to the dynamic DNA QR coding algorithm (DDQR). We tested the DDQR algorithm on simulated data and real DNA barcode sequences from the commonly used plant and animal DNA barcode markers: rbcL, matK, trnH-psbA, ITS2, and COI. We compared the compression efficiency of DDQR and another state-of-the-art DNA compression algorithm GeCo3 for sequences with various base compositions and lengths. We found that DDQR had a higher compression rate than GeCo3 for DNA sequences shorter than 800 bp, which is the typical size range for DNA barcodes. We also upgraded a web server (http://www.1kmpg.cn/ddqr) that provides three functions: retrieval of DNA barcode sequences, encoding DNA barcode sequences to DDQR codes, and decoding DDQR codes to DNA barcode sequences. The DDQR algorithm and the webserver will be invaluable to applying DNA barcode technology in the food and traditional medicine industries.},
}
@article {pmid36646785,
year = {2023},
author = {Sétamou, M and Soto, YL and Tachin, M and Alabi, OJ},
title = {Report on the first detection of Asian citrus psyllid Diaphorina citri Kuwayama (Hemiptera: Liviidae) in the Republic of Benin, West Africa.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {801},
pmid = {36646785},
issn = {2045-2322},
mesh = {Animals ; *Hemiptera/genetics/microbiology ; *Citrus/microbiology ; Benin ; Plant Diseases/microbiology ; Africa, Western ; *Rhizobiaceae/genetics ; Liberibacter ; },
abstract = {The Asian citrus psyllid (ACP), Diaphorina citri, was detected for the first time in the Republic of Benin, West Africa. The ACP is a known vector of Candidatus Liberibacter asiaticus (CLas), the putative causal agent of the devastating Huanglongbing (HLB; citrus greening disease). During visual surveys, ACP was only observed on residential citrus trees in southern Benin, but not in residential areas or commercial groves in the central and northern parts of the country. Its identity was confirmed morphologically and molecularly via DNA barcoding with published primers. Analysis of the obtained sequences showed that the ACP recorded in Benin clustered with the ones previously reported from Nigeria, suggesting a common origin of both populations. The ACP samples from Benin also carried Ca. Carsonella ruddii and Ca. Profftella armatura, two commonly found ACP endosymbionts. However, all the sampled ACP individuals tested negative for Ca. Liberibacter africanus, Ca. Liberibacter americanus, and CLas by quantitative polymerase chain reaction. This is the second report of the ACP in West Africa after Nigeria, the eastern bordering country of the Republic of Benin. Benin has an expanding commercial citrus industry, especially in the southern part of the country. Although the ACP samples tested negative for the HLB associated bacteria, the detection of ACP in the country requires swift actions including area-wide surveys to determine the extent of spread of this pest and the implementation of eradication or control efforts to prevent its establishment and spread of HLB in the country.},
}
@article {pmid36646350,
year = {2023},
author = {Kantak, M and Batra, P and Shende, P},
title = {Integration of DNA barcoding and nanotechnology in drug delivery.},
journal = {International journal of biological macromolecules},
volume = {230},
number = {},
pages = {123262},
doi = {10.1016/j.ijbiomac.2023.123262},
pmid = {36646350},
issn = {1879-0003},
mesh = {Animals ; Humans ; *DNA Barcoding, Taxonomic/methods ; *DNA/genetics ; Plants/genetics ; Polymerase Chain Reaction ; Nanotechnology ; },
abstract = {In recent years' development in nanotechnology utilization of DNA barcodes with potential benefit of nanoparticulate system is a hallmark for novel advancement in healthcare, biomedical and research sector. Interplay of biological barcoding with nanodimensional system encompasses innovative technologies to offer unique advantages of ultra-sensitivity, error-free, accuracy with minimal label reagents, and less time consumption in comparison to conventional techniques like ELISA, PCR, culture media, electrophoresis. DNA barcoding systems used as universal novel tool for identification and multiplex structural detection of proteins, DNAs, toxins, allergens, and nucleic acids of humans, viruses, animals, bacteria, plants as well as personalized treatment in ovarian cancer, AIDS-related Kaposi sarcoma, breast cancer and cardiovascular diseases. Barcoding tools offer substantial attention in drug delivery, in-vivo screening, gene transport for theranostics, bioimaging, and nano-biosensors applications. This review article outlines the recent advances in nano-mediated DNA barcodes to explore various applications in detection of cancer markers, tumor cells, pathogens, allergens, as theranostics, biological sensors, and plant authentication. Furthermore, it summarizes the diverse newer technologies such as bio-barcode amplification (BBA), Profiling Relative Inhibition Simultaneously in Mixtures (PRISM) and CRISPR-Cas9 gene knockout and their applications as sensors for detections of antigens, allergens, and other specimens.},
}
@article {pmid36645055,
year = {2023},
author = {Austin, L and Dos Santos, QM and Avenant-Oldewage, A},
title = {Additional data on Spinitectus petterae (Nematoda: Rhabditida) from Clarias gariepinus (Siluriformes: Clariidae) in the Vaal River system: conserved morphology or high intraspecific genetic variability?.},
journal = {Folia parasitologica},
volume = {70},
number = {},
pages = {},
pmid = {36645055},
issn = {1803-6465},
mesh = {Animals ; Male ; *Catfishes ; Rivers ; *Rhabditida ; Microscopy, Electron, Scanning ; *Spiruroidea ; DNA, Ribosomal ; },
abstract = {Two species of Spinitectus Fourment, 1884 have been recorded from southern Africa, namely Spinitectus polli Campana-Rouget, 1961 and Spinitectus petterae Boomker, 1993, both from the Limpopo River system. Spinitectus petterae was described from North African catfish, Clarias gariepinus (Burchell), whereas S. polli infects squeakers, Synodontis spp. During parasitological surveys in the Vaal River system (Orange River catchment), Spinitectus specimens were collected from C. gariepinus. These systems are adjacent but not connected. Therefore, this study aimed to identify the specimens collected using morphological and molecular techniques. The morphological study included light and scanning electron microscopy of whole specimens and excised spicules. Specimens were genetically characterised using 18S rDNA, 28S rDNA and cox1 mtDNA. Additionally, immature specimens of S. petterae were collected near the type locality. Morphological characteristics were most similar to S. petterae from C. gariepinus, whereas genetic data were dissimilar to all available data for the genus. Additional morphological characteristics noted for S. petterae in the present study were the details of the left and right spicule structure and the porous structures on the pseudolabia. Specimens from the Vaal River system differed from those originally described as S. petterae by additional spines posterior to the third ring, lacking caudal alae and variable total body and male oesophagus length. Based on 18S rDNA, haplotypes from the type locality varied only slightly from the study material, supporting the morphological identification. However, 28S rDNA and, more conspicuously, cox1 mtDNA displayed substantial variation between specimens from these localities, which needs further investigation. Haplotypes generated in the present study were highly dissimilar to those characterised for S. petterae from Tanzania and Egypt. Nevertheless, the nematodes collected from C. gariepinus in the Vaal River system are considered S. petterae. This study expands the geographical distribution and adds additional morphological and genetic information for S. petterae, contributing to the limited knowledge of African species of Spinitectus.},
}
@article {pmid36644629,
year = {2022},
author = {Shih, HT and Wong, KJH and Chan, BKK and Nguyen, TS and Do, VT and Ngo, XQ and Hsu, PY},
title = {Diversity and Distribution of Fiddler Crabs (Crustacea: Brachyura: Ocypodidae) in Vietnam.},
journal = {Zoological studies},
volume = {61},
number = {},
pages = {e66},
pmid = {36644629},
issn = {1810-522X},
abstract = {Based on recently collected material and records in the literature, 14 species of fiddler crabs (Crustacea: Ocypodidae: Gelasiminae) are reported from Vietnam. DNA barcoding analyses using the mitochondrial gene COI (cytochrome c oxidase subunit I) was performed to identify examined materials and their precise distributional range. Thirteen species-level taxa are identified and, with the exception of Galsimus borealis and G. vocans, have minimum interspcific divergences of at least 7.27%. The identified species include seven species of Tubuca Bott, 1973, three of Austruca Bott, 1973 and three of Gelasimus Latreille, 1817, and one Paraleptuca Bott, 1973. Two new records of Vietnam are herein reported: Tubuca rhizophorae and T. dussumieri. The southernmost distribution limits of East Asian G. borealis, T. acuta and T. arcuata are in northern Vietnam, A. lactea in central Vietnam, whereas northernmost limit of Southeast Asian T. rhizophorae and T. forcipata in southern Vietnam. A dichotomous key to identify the 14 Vietnamese species is provided.},
}
@article {pmid36643652,
year = {2023},
author = {Mugnai, F and Costantini, F and Chenuil, A and Leduc, M and Gutiérrez Ortega, JM and Meglécz, E},
title = {Be positive: customized reference databases and new, local barcodes balance false taxonomic assignments in metabarcoding studies.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e14616},
pmid = {36643652},
issn = {2167-8359},
mesh = {Databases, Factual ; *DNA Barcoding, Taxonomic ; Mediterranean Sea ; *Aquatic Organisms/genetics ; },
abstract = {BACKGROUND: In metabarcoding analyses, the taxonomic assignment is crucial to place sequencing data in biological and ecological contexts. This fundamental step depends on a reference database, which should have a good taxonomic coverage to avoid unassigned sequences. However, this goal is rarely achieved in many geographic regions and for several taxonomic groups. On the other hand, more is not necessarily better, as sequences in reference databases belonging to taxonomic groups out of the studied region/environment context might lead to false assignments.<br><br>METHODS: We investigated the effect of using several subsets of a cytochrome c oxidase subunit I (COI) reference database on taxonomic assignment. Published metabarcoding sequences from the Mediterranean Sea were assigned to taxa using COInr, which is a comprehensive, non-redundant and recent database of COI sequences obtained both from BOLD and NCBI, and two of its subsets: (i) all sequences except insects (COInr-WO-Insecta), which represent the overwhelming majority of COInr database, but are irrelevant for marine samples, and (ii) all sequences from taxonomic families present in the Mediterranean Sea (COInr-Med). Four different algorithms for taxonomic assignment were employed in parallel to evaluate differences in their output and data consistency.<br><br>RESULTS: The reduction of the database to more specific custom subsets increased the number of unassigned sequences. Nevertheless, since most of them were incorrectly assigned by the less specific databases, this is a positive outcome. Moreover, the taxonomic resolution (the lowest taxonomic level to which a sequence is attributed) of several sequences tended to increase when using customized databases. These findings clearly indicated the need for customized databases adapted to each study. However, the very high proportion of unassigned sequences points to the need to enrich the local database with new barcodes specifically obtained from the studied region and/or taxonomic group. Including novel local barcodes to the COI database proved to be very profitable: by adding only 116 new barcodes sequenced in our laboratory, thus increasing the reference database by only 0.04%, we were able to improve the resolution for ca. 0.6-1% of the Amplicon Sequence Variants (ASVs).},
}
@article {pmid36643554,
year = {2023},
author = {Mogharbel, AT and Alluhaybi, AA and Almotairy, ARZ and Aljohani, MM and El-Metwaly, NM and Zaky, R},
title = {Preparation of Lighting in the Dark and Photochromic Electrospun Glass Nanofiber-Reinforced Epoxy Nanocomposites Immobilized with Alkaline Earth Aluminates.},
journal = {ACS omega},
volume = {8},
number = {1},
pages = {1683-1692},
pmid = {36643554},
issn = {2470-1343},
abstract = {Alkaline earth aluminates (AEAs) as photoluminescent agents and silicon dioxide-based electrospun glass nanofibers with an average diameter of 150-450 nm as a roughening agent were prepared and applied to reinforce an epoxy resin toward the development of long-persistent photoluminescent and photochromic smart materials, such as smart windows and anticounterfeiting barcodes. With the physical immobilization of lanthanide-doped aluminate nanoparticles (NPs), a light-induced luminescent transparent glass@epoxy film was developed. The glass@epoxy samples were able to alter their color to green beneath ultraviolet rays and greenish-yellow in the dark, as explored by CIE Lab and luminescence spectral analyses. The morphology of the lanthanide-doped aluminate nanoparticles (43-98 nm) was examined by transmission electron microscopy (TEM). The morphologies and chemical composition of the luminescent glass@epoxy substrates were determined by different analytical techniques. The mechanical properties of the developed photoluminescent glass@epoxy substrates were inspected to show improved scratch resistance as compared to the AEA-free substrate. The photoluminescence spectra were measured to indicate the detection of two emission bands at 494 and 525 nm when excited at 365 nm. The photoluminescent glass@epoxy hybrids with lower AEA contents have showed fast reversibility of photochromism. On the other hand, the glass@epoxy substrates with higher phosphor contents underwent persistent luminescence. Results showed that the luminescent colorless glass@epoxy hybrids have enhanced superhydrophobicity and ultraviolet blocking.},
}
@article {pmid36640300,
year = {2023},
author = {Lee, MC and Cai, H and Murray, CW and Li, C and Shue, YT and Andrejka, L and He, AL and Holzem, AME and Drainas, AP and Ko, JH and Coles, GL and Kong, C and Zhu, S and Zhu, C and Wang, J and van de Rijn, M and Petrov, DA and Winslow, MM and Sage, J},
title = {A multiplexed in vivo approach to identify driver genes in small cell lung cancer.},
journal = {Cell reports},
volume = {42},
number = {1},
pages = {111990},
pmid = {36640300},
issn = {2211-1247},
support = {T32 CA009302/CA/NCI NIH HHS/United States ; U54 CA217450/CA/NCI NIH HHS/United States ; R01 CA231253/CA/NCI NIH HHS/United States ; R35 CA231997/CA/NCI NIH HHS/United States ; R01 CA207133/CA/NCI NIH HHS/United States ; R35 GM118165/GM/NIGMS NIH HHS/United States ; S10 RR027431/RR/NCRR NIH HHS/United States ; R01 CA234349/CA/NCI NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; U24 CA213274/CA/NCI NIH HHS/United States ; F31 CA257169/CA/NCI NIH HHS/United States ; },
mesh = {Mice ; Animals ; Humans ; *Small Cell Lung Carcinoma/pathology ; Phosphatidylinositol 3-Kinases/metabolism ; *Lung Neoplasms/pathology ; Genes, Tumor Suppressor ; Genomics ; },
abstract = {Small cell lung cancer (SCLC) is a lethal form of lung cancer. Here, we develop a quantitative multiplexed approach on the basis of lentiviral barcoding with somatic CRISPR-Cas9-mediated genome editing to functionally investigate candidate regulators of tumor initiation and growth in genetically engineered mouse models of SCLC. We found that naphthalene pre-treatment enhances lentiviral vector-mediated SCLC initiation, enabling high multiplicity of tumor clones for analysis through high-throughput sequencing methods. Candidate drivers of SCLC identified from a meta-analysis across multiple human SCLC genomic datasets were tested using this approach, which defines both positive and detrimental impacts of inactivating 40 genes across candidate pathways on SCLC development. This analysis and subsequent validation in human SCLC cells establish TSC1 in the PI3K-AKT-mTOR pathway as a robust tumor suppressor in SCLC. This approach should illuminate drivers of SCLC, facilitate the development of precision therapies for defined SCLC genotypes, and identify therapeutic targets.},
}
@article {pmid36639717,
year = {2023},
author = {Wang, Z and Jiang, D and Vergel-Rodriguez, M and Nogalska, A and Lu, R},
title = {Lineage tracking to reveal the fate of hematopoietic stem cells influenced by Flk2[-] multipotent progenitors after transplantation.},
journal = {Experimental &amp; molecular medicine},
volume = {55},
number = {1},
pages = {205-214},
pmid = {36639717},
issn = {2092-6413},
support = {R35 HL150826/HL/NHLBI NIH HHS/United States ; K99 HL113104/HL/NHLBI NIH HHS/United States ; R01 HL135292/HL/NHLBI NIH HHS/United States ; P30 CA014089/CA/NCI NIH HHS/United States ; R01 HL138225/HL/NHLBI NIH HHS/United States ; R00 HL113104/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Mice ; Cell Differentiation/genetics ; Cell Lineage/genetics ; *Hematopoietic Stem Cells/metabolism ; *Multipotent Stem Cells/metabolism ; T-Lymphocytes ; },
abstract = {After transplantation, hematopoietic stem cells (HSCs) sustain blood cell regeneration throughout the patient's life. Recent studies suggest that several types of mature blood cells provide feedback signals to regulate HSC fate. However, the potential feedback effect of hematopoietic progenitor cells has not been characterized to date. The present investigation demonstrated that multipotent progenitors (MPPs) promoted T cell production of HSCs when both cell types were cotransplanted in mice. Using genetic barcodes to track individual HSCs in mice, we found that the increased T cell production by HSCs was associated with the combined effects of altered lineage bias and clonal expansion during HSC differentiation. We showed that MPP and HSC co-transplantation promoted the multilineage differentiation of HSCs in the short term while preserving lymphoid-specialized HSC differentiation in the long term. Our findings indicate that MPPs derived from HSCs regulate the fate of HSCs after bone marrow transplantation.},
}
@article {pmid36639408,
year = {2023},
author = {Sioutas, G and Petridou, E and Minoudi, S and Papageorgiou, KV and Symeonidou, I and Giantsis, IA and Triantafyllidis, A and Papadopoulos, E},
title = {Isolation of Listeria monocytogenes from poultry red mite (Dermanyssus gallinae) infesting a backyard chicken farm in Greece.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {685},
pmid = {36639408},
issn = {2045-2322},
mesh = {Animals ; Female ; Chickens ; Poultry ; *Mite Infestations/parasitology ; *Listeria monocytogenes/genetics ; Greece ; Farms ; *Poultry Diseases/parasitology ; *Mites/genetics ; *Trombiculidae ; Escherichia coli ; },
abstract = {The poultry red mite (PRM), Dermanyssus gallinae, is arguably the most harmful, ubiquitous haematophagous ectoparasite infesting egg-laying hens. PRM is a vector of various microorganisms, with some being important for food microbiology and public health. The present study aimed to investigate the presence of specific pathogens, including Escherichia coli, Salmonella spp. and Listeria spp., carried by PRM infesting a chicken farm in Greece. Mites were caught using cardboard traps (Avivet), and 100 unwashed PRM were homogenized and used for microbiological cultures. Microbiological cultures were carried out on general and selective substrates to detect the above-mentioned bacteria. Specifically for Listeria spp., DNA was extracted from bacteria grown in Tryptone Soya Yeast Extract Agar using a commercial kit. The hly gene encoding the Listeriolysin O protein was amplified by PCR. Mites were identified as D. gallinae using morphological keys as well as by COI DNA barcoding. Microbiological cultures and PCR assays were positive for Listeria monocytogenes. No other bacteria were detected. The current study constitutes the first molecular isolation of L. monocytogenes from D. gallinae, confirming that PRM can carry this food-borne pathogen. PRM control measures and hygiene practices should be applied to minimize any possible contamination risk of poultry products with L. monocytogenes and safeguard public health.},
}
@article {pmid36635501,
year = {2023},
author = {Tang, R and Shuldiner, EG and Kelly, M and Murray, CW and Hebert, JD and Andrejka, L and Tsai, MK and Hughes, NW and Parker, MI and Cai, H and Li, YC and Wahl, GM and Dunbrack, RL and Jackson, PK and Petrov, DA and Winslow, MM},
title = {Multiplexed screens identify RAS paralogues HRAS and NRAS as suppressors of KRAS-driven lung cancer growth.},
journal = {Nature cell biology},
volume = {25},
number = {1},
pages = {159-169},
pmid = {36635501},
issn = {1476-4679},
support = {R01 CA231253/CA/NCI NIH HHS/United States ; R01 CA230025/CA/NCI NIH HHS/United States ; R35 GM118165/GM/NIGMS NIH HHS/United States ; R01 CA234349/CA/NCI NIH HHS/United States ; R35 CA197687/CA/NCI NIH HHS/United States ; K99 CA256039/CA/NCI NIH HHS/United States ; P30 CA014195/CA/NCI NIH HHS/United States ; F30 GM142263/GM/NIGMS NIH HHS/United States ; R00 CA256039/CA/NCI NIH HHS/United States ; R35 GM122517/GM/NIGMS NIH HHS/United States ; R01 CA250534/CA/NCI NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; P30 CA006927/CA/NCI NIH HHS/United States ; },
mesh = {Mice ; Animals ; Humans ; *Proto-Oncogene Proteins p21(ras)/genetics/metabolism ; Cell Transformation, Neoplastic/metabolism ; Signal Transduction/genetics ; *Lung Neoplasms/genetics ; Genes, ras ; Mutation ; Membrane Proteins/genetics/metabolism ; GTP Phosphohydrolases/genetics/metabolism ; },
abstract = {Oncogenic KRAS mutations occur in approximately 30% of lung adenocarcinoma. Despite several decades of effort, oncogenic KRAS-driven lung cancer remains difficult to treat, and our understanding of the regulators of RAS signalling is incomplete. Here to uncover the impact of diverse KRAS-interacting proteins on lung cancer growth, we combined multiplexed somatic CRISPR/Cas9-based genome editing in genetically engineered mouse models with tumour barcoding and high-throughput barcode sequencing. Through a series of CRISPR/Cas9 screens in autochthonous lung cancer models, we show that HRAS and NRAS are suppressors of KRAS[G12D]-driven tumour growth in vivo and confirm these effects in oncogenic KRAS-driven human lung cancer cell lines. Mechanistically, RAS paralogues interact with oncogenic KRAS, suppress KRAS-KRAS interactions, and reduce downstream ERK signalling. Furthermore, HRAS and NRAS mutations identified in oncogenic KRAS-driven human tumours partially abolished this effect. By comparing the tumour-suppressive effects of HRAS and NRAS in oncogenic KRAS- and oncogenic BRAF-driven lung cancer models, we confirm that RAS paralogues are specific suppressors of KRAS-driven lung cancer in vivo. Our study outlines a technological avenue to uncover positive and negative regulators of oncogenic KRAS-driven cancer in a multiplexed manner in vivo and highlights the role RAS paralogue imbalance in oncogenic KRAS-driven lung cancer.},
}
@article {pmid36633951,
year = {2023},
author = {Safi, F and Dhapola, P and Erlandsson, E and Ulfsson, LG and Calderón, AS and Böiers, C and Karlsson, G},
title = {In vitro clonal multilineage differentiation of distinct murine hematopoietic progenitor populations.},
journal = {STAR protocols},
volume = {4},
number = {1},
pages = {101965},
pmid = {36633951},
issn = {2666-1667},
mesh = {Animals ; Mice ; Cell Differentiation/genetics ; *Hematopoietic Stem Cells ; Coculture Techniques ; },
abstract = {Here we describe an in vitro co-culture system that can differentiate hematopoietic progenitor populations to all major hematopoietic lineages at clonal level. We present both a sensitive single-cell switch-culture system as well as a less laborious alternative barcoding protocol more convenient for larger cell numbers. Importantly, generation of all lineages from single long-term hematopoietic stem cells are described, following 21 days of culture. This protocol represents an efficient tool for validation experiments for single-cell genomics data. For complete details on the use and execution of this protocol, please refer to Safi et al. (2022).[1].},
}
@article {pmid36633756,
year = {2023},
author = {Wang, W and Wang, X and Shi, Y and Yin, Q and Gao, R and Wang, M and Xiang, L and Wu, L},
title = {Identification of Laportea bulbifera using the complete chloroplast genome as a potentially effective super-barcode.},
journal = {Journal of applied genetics},
volume = {64},
number = {2},
pages = {231-245},
pmid = {36633756},
issn = {2190-3883},
mesh = {Humans ; Aged ; *Genome, Chloroplast ; Phylogeny ; },
abstract = {Laportea bulbifera, a Miao medicine grown in karst areas, has exerted a unique curative effect on skin itching in the elderly, with an annual sales of > 100 million Yuan. Owing to the shortage of resources and large morphological variations in L. bulbifera, it is difficult to identify the species correctly using only traditional methods, which seriously affects the safety of drug usage for patients. This study obtained the complete high-quality L. bulbifera chloroplast (cp) genome, using second- and third-generation high-throughput sequencing. The cp genome was 149,911 bp in length, with a typical quadripartite structure. A total of 127 genes were annotated, including 83 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. There was an inverted small single copy (SSC) structure in the L. bulbifera cp genome, one large-scale rearrangement of ~ 39 kb excised in the SSC and IR regions. The complete cp genome sequence is used as a potentially effective super-barcode and the highly variable regions (ycf1, matK, and ndhD) can be used as potentially specific barcodes to accurately distinguish L. bulbifera from counterfeits and closely related species. This study is important for the identification of L. bulbifera and lays a theoretical foundation for elucidating the phylogenetic relationship of the species.},
}
@article {pmid36633416,
year = {2023},
author = {Loh, JT and Struttmann, EL and Favret, N and Harvey, ML and Pakala, SB and Chopra, A and McClain, MS and Cover, TL},
title = {A Positively Selected fur-R88H Mutation Enhances Helicobacter pylori Fitness in a High-Salt Environment and Alters Fur-Dependent Regulation of Gene Expression.},
journal = {Infection and immunity},
volume = {91},
number = {2},
pages = {e0042022},
pmid = {36633416},
issn = {1098-5522},
support = {P01 CA116087/CA/NCI NIH HHS/United States ; R01 AI118932/AI/NIAID NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; R01 AI039657/AI/NIAID NIH HHS/United States ; I01 BX004447/BX/BLRD VA/United States ; },
mesh = {Humans ; *Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Helicobacter Infections ; *Helicobacter pylori/genetics/physiology ; Mutation ; Sodium Chloride/metabolism ; *Repressor Proteins/genetics/metabolism ; },
abstract = {Both Helicobacter pylori infection and a high-salt diet are risk factors for gastric cancer. We previously showed that a mutation in fur (encoding the ferric uptake regulator variant Fur-R88H) was positively selected in H. pylori strains isolated from experimentally infected Mongolian gerbils receiving a high-salt diet. In the present study, we report that continuous H. pylori growth in high-salt conditions in vitro also leads to positive selection of the fur-R88H mutation. Competition experiments with strains containing wild-type fur or fur-R88H, each labeled with unique nucleotide barcodes, showed that the fur-R88H mutation enhances H. pylori fitness under high-salt conditions but reduces H. pylori fitness under routine culture conditions. The fitness advantage of the fur-R88H mutant under high-salt conditions was abrogated by the addition of supplemental iron. To test the hypothesis that the fur-R88H mutation alters the regulatory properties of Fur, we compared the transcriptional profiles of strains containing wild-type fur or fur-R88H. Increased transcript levels of fecA2, which encodes a predicted TonB-dependent outer membrane transporter, were detected in the fur-R88H variant compared to those in the strain containing wild-type fur under both high-salt and routine conditions. Competition experiments showed that fecA2 contributes to H. pylori fitness under both high-salt and routine conditions. These results provide new insights into mechanisms by which the fur-R88H mutation confers a selective advantage to H. pylori in high-salt environments.},
}
@article {pmid36629362,
year = {2022},
author = {Abbasi, I and Akad, F and Studentsky, L and Avi, IB and Orshan, L and Warburg, A},
title = {A next-generation (DNA) sequencing (NGS)-based method for identifying the sources of sugar meals in mosquito vectors of West Nile virus in Israel.},
journal = {Journal of vector ecology : journal of the Society for Vector Ecology},
volume = {47},
number = {1},
pages = {109-116},
doi = {10.52707/1081-1710-47.1.109},
pmid = {36629362},
issn = {1948-7134},
mesh = {Female ; Animals ; *West Nile virus/genetics ; Mosquito Vectors ; Sugars ; Israel ; *Culicidae ; *Culex ; *Arboviruses ; Meals ; DNA ; *West Nile Fever ; },
abstract = {Mosquitoes of the genus Culex comprise important vectors of pathogenic arboviruses in our region, including West Nile and Rift Valley Fever viruses. To improve our understanding of the epidemiology and transmission dynamics of arboviruses, we need to study the behavior and ecology of their vectors. The feeding patterns of the vector mosquitoes can be very useful in determining how and where to focus control efforts. For example, determining the preferred blood hosts of the females can assist in the implementation of potentially efficacious strategies for focused control of mosquito females. Determining the plants from which both sexes derive their sugar meals can comprise the initial step towards the formulation of efficient lures for trapping mosquitoes. In the past, plant meal identification was based mainly on chemical detection of fructose and microscopical observations of cellulose particles in mosquito guts. More recent studies have utilized DNA barcoding capable of identifying plant food sources. In the current study, we identify multiple plant species from which large numbers of mosquitoes obtained their sugar meals in one experimental procedure. We employed next generation DNA sequencing to sequence the chloroplast specific plant genes atpB and rbcL.},
}
@article {pmid36626250,
year = {2023},
author = {Diamond, B and Ziccheddu, B and Maclachlan, K and Taylor, J and Boyle, E and Ossa, JA and Jahn, J and Affer, M and Totiger, TM and Coffey, D and Chandhok, N and Watts, J and Cimmino, L and Lu, SX and Bolli, N and Bolton, K and Landau, H and Park, JH and Ganesh, K and McPherson, A and Sekeres, MA and Lesokhin, A and Chung, DJ and Zhang, Y and Ho, C and Roshal, M and Tyner, J and Nimer, S and Papaemmanuil, E and Usmani, S and Morgan, G and Landgren, O and Maura, F},
title = {Tracking the evolution of therapy-related myeloid neoplasms using chemotherapy signatures.},
journal = {Blood},
volume = {141},
number = {19},
pages = {2359-2371},
pmid = {36626250},
issn = {1528-0020},
support = {K12 CA226330/CA/NCI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; P30 CA240139/CA/NCI NIH HHS/United States ; U54 CA224019/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Melphalan ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Transplantation, Autologous/adverse effects ; *Leukemia, Myeloid, Acute/drug therapy/genetics/pathology ; *Neoplasms, Second Primary/chemically induced/genetics ; *Antineoplastic Agents/pharmacology ; },
abstract = {Patients treated with cytotoxic therapies, including autologous stem cell transplantation, are at risk for developing therapy-related myeloid neoplasms (tMN). Preleukemic clones (ie, clonal hematopoiesis [CH]) are detectable years before the development of these aggressive malignancies, although the genomic events leading to transformation and expansion are not well defined. Here, by leveraging distinctive chemotherapy-associated mutational signatures from whole-genome sequencing data and targeted sequencing of prechemotherapy samples, we reconstructed the evolutionary life-history of 39 therapy-related myeloid malignancies. A dichotomy was revealed, in which neoplasms with evidence of chemotherapy-induced mutagenesis from platinum and melphalan were hypermutated and enriched for complex structural variants (ie, chromothripsis), whereas neoplasms with nonmutagenic chemotherapy exposures were genomically similar to de novo acute myeloid leukemia. Using chemotherapy-associated mutational signatures as temporal barcodes linked to discrete clinical exposure in each patient's life, we estimated that several complex events and genomic drivers were acquired after chemotherapy was administered. For patients with prior multiple myeloma who were treated with high-dose melphalan and autologous stem cell transplantation, we demonstrate that tMN can develop from either a reinfused CH clone that escapes melphalan exposure and is selected after reinfusion, or from TP53-mutant CH that survives direct myeloablative conditioning and acquires melphalan-induced DNA damage. Overall, we revealed a novel mode of tMN progression that is not reliant on direct mutagenesis or even exposure to chemotherapy. Conversely, for tMN that evolve under the influence of chemotherapy-induced mutagenesis, distinct chemotherapies not only select preexisting CH but also promote the acquisition of recurrent genomic drivers.},
}
@article {pmid36624930,
year = {2023},
author = {Khalil, AM and Gainsford, A and van Herwerden, L},
title = {DNA barcoding of fresh seafood in Australian markets reveals misleading labelling and sale of endangered species.},
journal = {Journal of fish biology},
volume = {102},
number = {3},
pages = {727-733},
doi = {10.1111/jfb.15308},
pmid = {36624930},
issn = {1095-8649},
mesh = {Animals ; *Endangered Species ; DNA Barcoding, Taxonomic ; Reproducibility of Results ; Australia ; Seafood ; Electron Transport Complex IV/genetics ; *Sharks/genetics ; },
abstract = {Flake and shark samples were purchased from outlets in several coastal Australian regions and genetically barcoded using the cytochrome oxidase subunit 1 (CO1) gene to investigate labelling reliability and species-specific sources of ambiguously labelled fillets. Of the 41 shark fillet samples obtained, 23 yielded high-quality CO1 sequences, out of which 57% (n = 13) were labelled ambiguously (misleading) and 35% (n = 8) incorrectly. In contrast, barramundi fillets, which are widely available and sought after in Australian markets, were shown to be accurately labelled. Species identified from shark samples, including the shortfin mako (n = 3) and the scalloped hammerhead (n = 1), are assessed by the IUCN as endangered and critically endangered, respectively, with several others classified as vulnerable and near threatened.},
}
@article {pmid36622295,
year = {2023},
author = {Mutum, RS and Wangkheimayum, VD},
title = {DNA barcoding of indigenous fowl of Manipur, Kaunayen (Gallus gallus domesticus).},
journal = {Animal biotechnology},
volume = {34},
number = {9},
pages = {4430-4434},
doi = {10.1080/10495398.2022.2155178},
pmid = {36622295},
issn = {1532-2378},
mesh = {Animals ; *Chickens/genetics ; *DNA Barcoding, Taxonomic ; Phylogeny ; India ; DNA ; Poultry/genetics ; },
abstract = {The jungle fowl (Gallus gallus) is a tropical bird with important hereditary and phenotypical traits like disease resistance and resistance to harsh conditions and can often survive with scanty diet. However, as commercial chicken breeds replace them, their population is dwindling, which poses a significant threat to fowl genetic resources. There is minimal information on the variety of Indian poultry, mainly native chicken from Northeast India. As a result, the record of the fowl's genetic diversity is essential for its preservation and formulation of conservation strategies. The current study sought to identify indigenous chicken, Kaunayen (Gallus gallus domesticus), from Manipur using barcoding based on DNA sequences. A total of 5 CO1 DNA barcodes from several indigenous chickens were sequenced and compared to the previous data of diverse taxa of Phasianidae using the conventional methodology and were recognized as Gallus gallus. The Phasianid birds that were researched were accurately classified into their appropriate species. There is a minuscule genomic difference between G. gallus and G. varius (1.2%) and the highest between Arborophila rufipectus and Tympanuchus pallidicinctus (22.5%). The phylogenetic relationship established on the NJ tree revealed a coherent gathering of indigenous fowl with G. gallus and unique to all other species studied, showing their taxonomic classification. Nonetheless, the investigation offered a genetic identity tag for indigenous chicken for the first time. It will be a potential guide for identifying distinctive and genetically unique poultry sequences for later requirements.},
}
@article {pmid36613233,
year = {2022},
author = {Liu, K and Xing, R and Sun, R and Ge, Y and Chen, Y},
title = {An Accurate and Rapid Way for Identifying Food Geographical Origin and Authenticity: Editable DNA-Traceable Barcode.},
journal = {Foods (Basel, Switzerland)},
volume = {12},
number = {1},
pages = {},
pmid = {36613233},
issn = {2304-8158},
support = {2022YFF0608203//China Rural Technology Development Center/ ; },
abstract = {DNA offers significant advantages in information density, durability, and replication efficiency compared with information labeling solutions using electronic, magnetic, or optical devices. Synthetic DNA containing specific information via gene editing techniques is a promising identifying approach. We developed a new traceability approach to convert traditional digitized information into DNA sequence information. We used encapsulation to make it stable for storage and to enable reading and detection by DNA sequencing and PCR-capillary electrophoresis (PCR-CE). The synthesized fragment consisted of a short fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene from the Holothuria fuscogilva (ID: LC593268.1), inserted geographical origin information (18 bp), and authenticity information from Citrus sinensis (20 bp). The obtained DNA-traceable barcodes were cloned into vector PMD19-T. Sanger sequencing of the DNA-traceable barcode vector was 100% accurate and provided a complete readout of the traceability information. Using selected recognition primers CAI-B, DNA-traceable barcodes were identified rapidly by PCR amplification. We encapsulated the DNA-traceable barcodes into amorphous silica spheres and improved the encapsulation procedure to ensure the durability of the DNA-traceable barcodes. To demonstrate the applicability of DNA-traceable barcodes as product labels, we selected Citrus sinensis as an example. We found that the recovered and purified DNA-traceable barcode can be analyzed by standard techniques (PCR-CE for DNA-traceable barcode identification and DNA sequencing for readout). This study provides an accurate and rapid approach to identifying and certifying products' authenticity and traceability.},
}
@article {pmid36611700,
year = {2022},
author = {Santander-Neto, J and Rincon, G and Jucá-Queiroz, B and Paes da Cruz, V and Lessa, R},
title = {Distribution and New Records of the Bluntnose Sixgill Shark, Hexanchus griseus (Hexanchiformes: Hexanchidae), from the Tropical Southwestern Atlantic.},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {1},
pages = {},
pmid = {36611700},
issn = {2076-2615},
abstract = {The bluntnose sixgill shark, Hexanchus griseus, is a widely distributed demersal species found in tropical and temperate waters of the Pacific, Atlantic, and Indian Oceans, inhabiting continental shelves and slopes, islands, and mid-ocean ridges at depths ranging from 200 to 1100 m. In the Southwestern Atlantic, this species has been recorded from northeastern to southern Brazil, Argentina, and Uruguay. Despite this, the known distribution of this species in the Southwestern Atlantic is very patchy and, in some cases, still mostly ignored in the literature, such as in northeastern Brazil. This study, therefore, aimed to report 23 new records of Hexanchus griseus in the Tropical Southwestern Atlantic and highlight the presence of this species off the northeastern Brazilian coast. So far, Hexanchus griseus was officially reported from the Fernando de Noronha Archipelago, Saint Peter and Saint Paul Archipelago, and the state of Ceará along the northeast coast of Brazil. Herein, the known distribution is extended to the continental shelf breaks and upper slopes of other Brazilian states, reinforcing the previously reported occurrence of the species near the Saint Peter and Saint Paul Archipelago.},
}
@article {pmid36606710,
year = {2023},
author = {Chen, Q and Liu, C and Wang, W and Meng, X and Cheng, X and Li, X and Cai, L and Luo, L and He, X and Qu, H and Luo, J and Wei, H and Gao, S and Liu, G and Wan, J and Israel, DI and Li, J and Dou, D},
title = {Optimization of PROTAC Ternary Complex Using DNA Encoded Library Approach.},
journal = {ACS chemical biology},
volume = {18},
number = {1},
pages = {25-33},
pmid = {36606710},
issn = {1554-8937},
mesh = {*Nuclear Proteins/metabolism ; *Transcription Factors/metabolism ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitination ; Proteolysis ; },
abstract = {The proteolysis targeting chimera (PROTAC) strategy results in the down-regulation of unwanted protein(s) for disease treatment. In the PROTAC process, a heterobifunctional degrader forms a ternary complex with a target protein of interest (POI) and an E3 ligase, which results in ubiquitination and proteasomal degradation of the POI. While ternary complex formation is a key attribute of PROTAC degraders, modification of the PROTAC molecule to optimize ternary complex formation and protein degradation can be a labor-intensive and tedious process. In this study, we take advantage of DNA-encoded library (DEL) technology to efficiently synthesize a vast number of possible PROTAC molecules and describe a parallel screening approach that utilizes DNA barcodes as reporters of ternary complex formation and cooperative binding. We use a designed PROTAC DEL against BRD4 and CRBN to describe a dual protein affinity selection method and the direct discovery of novel, potent BRD4 PROTACs that importantly demonstrate clear SAR. Such an approach evaluates all the potential PROTACs simultaneously, avoids the interference of PROTAC solubility and permeability, and uses POI and E3 ligase proteins in an efficient manner.},
}
@article {pmid36605190,
year = {2022},
author = {Wu, C and Liang, JA and Brenchley, JM and Shin, T and Fan, X and Mortlock, RD and Abraham, DM and Allan, DSJ and Thomas, ML and Hong, SG and Dunbar, CE},
title = {Barcode clonal tracking of tissue-resident immune cells in rhesus macaque highlights distinct clonal distribution pattern of tissue NK cells.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {994498},
pmid = {36605190},
issn = {1664-3224},
mesh = {Animals ; Clone Cells ; *Killer Cells, Natural ; Macaca mulatta ; *Myeloid Cells ; },
abstract = {Tissue resident (TR) immune cells play important roles in facilitating tissue homeostasis, coordinating immune responses against infections and tumors, and maintaining immunological memory. While studies have shown these cells are distinct phenotypically and functionally from cells found in the peripheral blood (PB), the clonal relationship between these populations across tissues has not been comprehensively studied in primates or humans. We utilized autologous transplantation of rhesus macaque hematopoietic stem and progenitor cells containing high diversity barcodes to track the clonal distribution of T, B, myeloid and natural killer (NK) cell populations across tissues, including liver, spleen, lung, and gastrointestinal (GI) tract, in comparison with PB longitudinally post-transplantation, in particular we focused on NK cells which do not contain endogenous clonal markers and have not been previously studied in this context. T cells demonstrated tissue-specific clonal expansions as expected, both overlapping and distinct from blood T cells. In contrast, B and myeloid cells showed a much more homogeneous clonal pattern across various tissues and the blood. The clonal distribution of TR NK was more heterogenous between individual animals. In some animals, as we have previously reported, we observed large PB clonal expansions in mature CD56-CD16+ NK cells. Notably, we found a separate set of highly expanded PB clones in CD16-CD56- (DN) NK subset that were also contributing to TR NK cells in all tissues examined, both in TR CD56-CD16+ and DN populations but absent in CD56[+]16[-] TR NK across all tissues analyzed. Additionally, we observed sets of TR NK clones specific to individual tissues such as lung or GI tract and sets of TR NK clones shared across liver and spleen, distinct from other tissues. Combined with prior functional data that suggests NK memory is restricted to liver or other TR NK cells, these clonally expanded TR NK cells may be of interest for future investigation into NK cell tissue immunological memory, with implications for development of NK based immunotherapies and an understanding of NK memory.},
}
@article {pmid36604614,
year = {2023},
author = {Qin, HH and Cai, J and Liu, CK and Zhou, RX and Price, M and Zhou, SD and He, XJ},
title = {The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution.},
journal = {BMC plant biology},
volume = {23},
number = {1},
pages = {9},
pmid = {36604614},
issn = {1471-2229},
support = {32170209//National Natural Science Foundation of China/ ; 31872647//National Natural Science Foundation of China/ ; },
mesh = {Phylogeny ; *Ferula ; Evolution, Molecular ; *Genome, Plastid ; *Genome, Chloroplast/genetics ; Codon/genetics ; },
abstract = {BACKGROUND: The Ferula genus encompasses 180-185 species and is one of the largest genera in Apiaceae, with many of Ferula species possessing important medical value. The previous studies provided more information for Ferula, but its infrageneric relationships are still confusing. In addition, its genetic basis of its adaptive evolution remains poorly understood. Plastid genomes with more variable sites have the potential to reconstruct robust phylogeny in plants and investigate the adaptive evolution of plants. Although chloroplast genomes have been reported within the Ferula genus, few studies have been conducted using chloroplast genomes, especially for endemic species in China.<br><br>RESULTS: Comprehensively comparative analyses of 22 newly sequenced and assembled plastomes indicated that these plastomes had highly conserved genome structure, gene number, codon usage, and repeats type and distribution, but varied in plastomes size, GC content, and the SC/IR boundaries. Thirteen mutation hotspot regions were detected and they would serve as the promising DNA barcodes candidates for species identification in Ferula and related genera. Phylogenomic analyses with high supports and resolutions showed that Talassia transiliensis and Soranthus meyeri were nested in the Ferula genus, and thus they should be transferred into the Ferula genus. Our phylogenies also indicated the monophyly of subgenera Sinoferula and subgenera Narthex in Ferula genus. Twelve genes with significant posterior probabilities for codon sites were identified in the positively selective analysis, and their function may relate to the photosystem II, ATP subunit, and NADH dehydrogenase. Most of them might play an important role to help Ferula species adapt to high-temperatures, strong-light, and drought habitats.<br><br>CONCLUSION: Plastome data is powerful and efficient to improve the support and resolution of the complicated Ferula phylogeny. Twelve genes with significant posterior probabilities for codon sites were helpful for Ferula to adapt to the harsh environment. Overall, our study supplies a new perspective for comprehending the phylogeny and evolution of Ferula.},
}
@article {pmid36604557,
year = {2023},
author = {Long, L and Li, Y and Wang, S and Liu, Z and Wang, J and Yang, M},
title = {Complete chloroplast genomes and comparative analysis of Ligustrum species.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {212},
pmid = {36604557},
issn = {2045-2322},
mesh = {Phylogeny ; *Ligustrum/genetics ; *Genome, Chloroplast/genetics ; Bayes Theorem ; },
abstract = {In this study, we assembled and annotated the chloroplast (cp) genomes of four Ligustrum species, L. sinense, L. obtusifolium, L. vicaryi, and L. ovalifolium 'Aureum'. Including six other published Ligustrum species, we compared various characteristics such as gene structure, sequence alignment, codon preference, and nucleic acid diversity, and performed positive-selection genes screening and phylogenetic analysis. The results showed that the cp genome of Ligustrum was 162,185-166,800 bp in length, with a circular tetrad structure, including a large single-copy region (86,885-90,106 bp), a small single-copy region (11,446-11,499 bp), and a pair of IRa and IRb sequences with the same coding but in opposite directions (31,608-32,624 bp). This structure is similar to the cp genomes of most angiosperms. We found 132-137 genes in the cp genome of Ligustrum, including 89-90 protein-coding genes, 35-39 tRNAs, and 8 rRNAs. The GC content was 37.93-38.06% and varied among regions, with the IR region having the highest content. The single-nucleotide (A/T)n was dominant in simple-sequence repeats of the Ligustrum cp genome, with an obvious A/T preference. Six hotspot regions were identified from multiple sequence alignment of Ligustrum; the ycf1 gene region and the clpP1 exon region can be used as potential DNA barcodes for the identification and phylogeny of the genus Ligustrum. Branch-site model and Bayes empirical Bayes (BEB) analysis showed that four protein-coding genes (accD, clpP, ycf1, and ycf2) were positively selected, and BEB analysis showed that accD and rpl20 had positively selected sites. A phylogenetic tree of Oleaceae species was constructed based on the whole cp genomes, and the results were consistent with the traditional taxonomic results. The phylogenetic results showed that genus Ligustrum is most closely related to genus Syringa. Our study provides important genetic information to support further investigations of the phylogenetic development and adaptive evolution of Ligustrum species.},
}
@article {pmid36604333,
year = {2023},
author = {Buddhachat, K and Sriuan, S and Nak-On, S and Chontananarth, T},
title = {Differentiating paramphistome species in cattle using DNA barcoding coupled with high-resolution melting analysis (Bar-HRM).},
journal = {Parasitology research},
volume = {122},
number = {3},
pages = {769-779},
pmid = {36604333},
issn = {1432-1955},
mesh = {Cattle ; Animals ; DNA Barcoding, Taxonomic ; *Trematode Infections/parasitology ; Polymerase Chain Reaction ; *Paramphistomatidae/genetics ; *Fasciola/genetics ; *Cattle Diseases/parasitology ; },
abstract = {Paramphistomosis is caused by paramphistome or amphistome parasites, including Fischoederius elongatus, Gastrothylax crumenifer, Orthocoelium parvipapillatum, and Paramphistomum epiclitum. The control and prevention of these parasite outbreaks are difficult because of the wide occurrence of these species. Besides, the clinical manifestations and their egg characteristics are similar to those of other intestinal flukes in the paramphistome group, leading to misdiagnosis. Here, we employed DNA barcoding using NADH dehydrogenase (ubiquinone, alpha 1) (ND1) and cytochrome c oxidase subunit I (COI), coupled with high-resolution melting analysis (Bar-HRM), for species differentiation. As a result, ParND1_3 and ParCOI4 resulted in positive amplification in the paramphistomes and Fasciola gigantica, with significantly different melting curves for each species. The melting temperatures of each species obtained clearly differed. Regarding sensitivity, the limit of detection (LoD) for all species of paramphistomes was 1 pg/µl. Our findings suggest that Bar-HRM using ParND1_3 is highly suitable for the differentiation of paramphistome species. This approach can be used in parasite detection and epidemiological studies in cattle.},
}
@article {pmid36602515,
year = {2023},
author = {Malhotra, K and Hrovat, D and Kumar, B and Qu, G and Houten, JV and Ahmed, R and Piunno, PAE and Gunning, PT and Krull, UJ},
title = {Lanthanide-Doped Upconversion Nanoparticles: Exploring A Treasure Trove of NIR-Mediated Emerging Applications.},
journal = {ACS applied materials &amp; interfaces},
volume = {15},
number = {2},
pages = {2499-2528},
doi = {10.1021/acsami.2c12370},
pmid = {36602515},
issn = {1944-8252},
mesh = {*Lanthanoid Series Elements/chemistry ; *Nanoparticles/chemistry ; *Quantum Dots ; Luminescence ; Diagnostic Imaging ; },
abstract = {Lanthanide-doped upconversion nanoparticles (UCNPs) possess the remarkable ability to convert multiple near-infrared (NIR) photons into higher energy ultraviolet-visible (UV-vis) photons, making them a prime candidate for several advanced applications within the realm of nanotechnology. Compared to traditional organic fluorophores and quantum dots (QDs), UCNPs possess narrower emission bands (fwhm of 10-50 nm), large anti-Stokes shifts, low toxicity, high chemical stability, and resistance to photobleaching and blinking. In addition, unlike UV-vis excitation, NIR excitation is nondestructive at lower power intensities and has high tissue penetration depths (up to 2 mm) with low autofluorescence and scattering. Together, these properties make UCNPs exceedingly favored for advanced bioanalytical and theranostic applications, where these systems have been well-explored. UCNPs are also well-suited for bioimaging, optically modulating chemistries, forensic science, and other state-of-the-art research applications. In this review, an up-to-date account of emerging applications in UCNP research, beyond bioanalytical and theranostics, are presented including optogenetics, super-resolution imaging, encoded barcodes, fingerprinting, NIR vision, UCNP-assisted photochemical manipulations, optical tweezers, 3D printing, lasing, NIR-II imaging, UCNP-molecule nanohybrids, and UCNP-based persistent luminescent nanocrystals.},
}
@article {pmid36602224,
year = {2023},
author = {Shalu, K and Thomas, L and Ramvilas, G and Shabeena, KS and Philip, S and Sureshkumar, S and Raghavan, R and Ranjeet, K},
title = {DNA barcodes for the pipefish genus Corythoichthys (Actinopterygii: Syngnathiformes) from the Indian Ocean provide insights into cryptic diversity.},
journal = {Journal of fish biology},
volume = {102},
number = {3},
pages = {680-688},
doi = {10.1111/jfb.15300},
pmid = {36602224},
issn = {1095-8649},
support = {CRG/2020/004498//Department of Science and Technology, Ministry of Science and Technology, India/ ; 2061630944//UGC-DAE&#xa0;Consortium for Scientific Research, University Grants Commission/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Indian Ocean ; Phylogeny ; *Smegmamorpha/classification/genetics ; *Biodiversity ; Species Specificity ; *Classification/methods ; },
abstract = {The syngnathiform genus Corythoichthys comprises a group of taxonomically complex, tail-brooding (Syngnathinae) pipefishes widely distributed in the Indo-Pacific region. Due to the presence of overlapping interspecific morphological characters, reliable taxonomic information on Corythoichthys is still lacking. Using 52 CO1 sequences, including seven newly generated, a phylogenetic analysis was carried out to understand the genetic diversity, distribution and 'species groups' within the genus Corythoichthys. Species delimitation using Automatic Barcode Gap Discovery (ABGD) analysis confirmed the presence of 13 species which include 'species-complexes' previously considered as a single taxon. Our results revealed the presence of three species groups, 'C. amplexus', 'C. conspicillatus' and 'C. haematopterus' and four unidentified/undescribed species in the wider Indo-Pacific realm. Interestingly, 60 sequences and a mitogenome identified as Corythoichthys in GenBank are misidentified at the genus level. Based on our findings, we suggest that the taxonomy and systematics of Corythoichthys need to be re-examined and validated using integrative methods, and care should be taken while selecting specimens for genetic studies.},
}
@article {pmid36600117,
year = {2024},
author = {Sohrabi, M and Samsampour, D and Bagheri, A},
title = {Molecular Identification of Fungal Endophytes of Medicinal Plant Citrullus colocynthis (L.) Schrad as a Medicinal Plant: Role of Tissue Type and Sampling Location on the Diversity.},
journal = {Molecular biotechnology},
volume = {66},
number = {3},
pages = {424-431},
pmid = {36600117},
issn = {1559-0305},
mesh = {Endophytes/genetics ; Fungi/genetics ; *Plants, Medicinal ; *Citrullus colocynthis ; Biodiversity ; Plant Leaves/microbiology ; Phylogeny ; },
abstract = {Endophytic fungi are an important group of organisms in association with plants which are able to colonize all plant internal tissues and improve their fitness. The present research aims to isolate and identify endophytic fungi of Citrullus colocynthis plant and then investigate the effects of sampling location and tissue type on the fungal endophyte diversity of this plant. To do so, a sampling program was done in 11 geographically isolated C. colocynthis growing areas of Hormozgan province, Iran. For molecular identification of endophytic fungi of C. colocynthis, the internal transcribed spacer region (ITS1-5.8S-ITS4), as a universal DNA barcode marker for fungi, was amplified using primer sets. Totally, 12 taxa (Alternaria solani, Cladosporium halotolerans, Setosphaeria rostrata, Aspergillus niger, A. allahabadii, A. terreus, A. occultus, A. cristatus, Penicillium chrysogenum, Talaromyces purpureogenus, Fusarium sp., and Pseudozyma flocculosa) were isolated. Our findings also showed that the diversity of fungal endophytes isolated from C. colocynthis was affected by the tissue type and sampling site. Accordingly, the leaves and seeds were found to have the highest and lowest rates of endophyte colonization and richness in all sampling seasons, respectively. Simpson's diversity index of 0.8165 in root tissue indicated the high diversity of endophytes in this organ. In addition, Shannon's diversity index in the root (1.846) was higher than that in the other organs. The highest Shannon's and Simpson's indices were observed in Khoon Sorkh and Minab regions. Generally, at least two factors (region and type of tissue) played the most important roles in determining the composition of fungal endophytes in C. colocynthis.},
}
@article {pmid36599919,
year = {2023},
author = {But, GW and Wu, HY and Siu, TY and Chan, KT and Wong, KH and Lau, DT and Shaw, PC},
title = {Comparison of DNA extraction methods on CITES-listed timber species and application in species authentication of commercial products using DNA barcoding.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {151},
pmid = {36599919},
issn = {2045-2322},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Commerce ; Species Specificity ; Internationality ; DNA ; Endangered Species ; Wood/genetics ; },
abstract = {Quality and quantity of DNA extracted from wood is important for molecular identification of wood species, which can serve for conservation of wood species and law enforcement to combat illegal wood trading. Rosewood (Dalbergia and Pterocarpus) and agarwood (Aquilaria) are the most commonly found hardwood in timber seizure incidents. To monitor international trade of timber and commercial wood products and to protect these endangered wood species from further population decline, in this study, we have compared three extraction protocols for DNA extraction from 12 samples of rosewood and agarwood timber logs, and later applied the best DNA extraction protocol on 10 commercial wood products claimed to be rosewood and agarwood. We also demonstrated the applicability of DNA mini-barcoding with multi-loci combination with reference library for identifying the species of timber and commercial wood products. We found that a silica column-based method with guanidine thiocyanate-containing binding buffer served the best in DNA extraction from different parts of wood in all three genera with good quality and quantity. Single barcode region ITS2 or multi-loci combinations including ITS2 barcode region generally provide better discriminatory power for species identification for both rosewood and agarwood. All 10 products were identified to species-level using multi-loci combination. In terms of accuracy in labelling, 80% of them were labelled correctly. Our work has shown the feasibility of extracting good quality of DNA from authentic wood samples and processed wood products and identifying them to species level based on DNA barcoding technology.},
}
@article {pmid36598645,
year = {2023},
author = {Halvarsson, P and Tydén, E},
title = {The complete ITS2 barcoding region for Strongylus vulgaris and Strongylus edentatus.},
journal = {Veterinary research communications},
volume = {47},
number = {3},
pages = {1767-1771},
pmid = {36598645},
issn = {1573-7446},
support = {H-15-47-097//Foundation for Swedish and Norwegian Equine Research/ ; },
mesh = {Animals ; Horses/genetics ; Strongylus ; *Intestinal Diseases, Parasitic/veterinary ; *Horse Diseases ; },
abstract = {Gastrointestinal nematode parasites are of major concern for horses, where Strongylus vulgaris is considered the most pathogenic among the Strongylus species. Diagnosis of S. vulgaris infections can be determined with next generation sequencing techniques, which are inherently dependent on reference sequences. The best marker for parasitic nematodes is internal transcribed spacer 2 (ITS2) and we provide the first complete ITS2 sequences from five morphologically identified S. vulgaris and additional sequences from two S. edentatus. These sequences have high similarity to already published partial sequences and amplicon sequence variants (ASV) based on next generation sequencing (NGS). The ITS2 sequences from S. vulgaris matched available partial ITS2 sequences and the full ASVs, whereas the S. edentatus sequence matched another complete sequence. We also compare Sanger sequencing and NGS methods and conclude that the ITS2 variation is better represented with NGS methods. Based on this, we recommend that further sequencing of morphologically identified specimens of various species should be performed with NGS cover the intraspecific variation in the ITS2.},
}
@article {pmid36598171,
year = {2023},
author = {Giordani, G and Tuccia, F and Martín-Vega, D and Angell, CS and Pradelli, J and Vanin, S},
title = {Morphological and molecular characterization of puparia of Piophilidae species of forensic relevance.},
journal = {Medical and veterinary entomology},
volume = {37},
number = {2},
pages = {339-358},
doi = {10.1111/mve.12635},
pmid = {36598171},
issn = {1365-2915},
mesh = {Humans ; Animals ; *Diptera/genetics/anatomy &amp; histology ; Larva/genetics ; Cadaver ; },
abstract = {Piophilidae are a small family of Diptera with a worldwide distribution and which are historically associated with human activities. In addition to their economic importance, piophilid larvae can also be of medical and legal relevance. Within a medicolegal context, piophilids are frequently associated with cadavers in advanced stages of decomposition, thus being potentially useful forensic indicators and they have been reported also from archaeo-funerary contexts. An accurate species identification is therefore an essential prerequisite to ensure the reliable analysis of insect material in medical, forensic and archaeological investigations. Identification of the adult piophilid flies is possible because of the availability of identification keys, in contrast immature insects, especially puparia, have been poorly investigated and described. In this paper, puparia of 11 species of forensic interest (Piophila casei, Piophila megastigmata, Parapiophila atrifrons, Parapiophila flavipes, Parapiophila vulgaris, Protopiophila litigata, Liopiophila varipes, Prochyliza nigrimana, Prochyliza xanthosoma and Stearibia nigriceps in subtribe Piophilina and Centrophlebomyia furcata in subtribe Thyreophorina) are described and a molecular analysis, based on the COI sequencing, is presented to show the potential of the molecular approach in their identification.},
}
@article {pmid36598082,
year = {2023},
author = {Nguyen, AHL and Nugraheni, YR and Nguyen, TT and Aung, A and Narapakdeesakul, D and Kaewlamun, W and Asada, M and Kaewthamasorn, M},
title = {Molecular characterization of anopheline mosquitoes from the goat malaria-endemic areas of Thailand.},
journal = {Medical and veterinary entomology},
volume = {37},
number = {2},
pages = {381-395},
doi = {10.1111/mve.12638},
pmid = {36598082},
issn = {1365-2915},
mesh = {Female ; Humans ; Animals ; Goats/genetics ; Thailand ; Mosquito Vectors/genetics ; *Malaria/epidemiology/veterinary ; *Anopheles/parasitology ; DNA, Mitochondrial ; *Goat Diseases ; },
abstract = {Despite the fact that over a 100 anopheline mosquito species have been identified as human malaria vectors, little is known about ungulate malaria vectors. Consequently, we focused on investigating the bionomics and genetic characterizations of anopheline mosquitoes in goat malaria-endemic regions. We also attempted to screen for ungulate malaria potential vectors. A total of 1019 female anopheline mosquitoes were collected from six goat farms in four provinces of Thailand from 2020 to 2021. Mosquitoes were morphologically identified and subsequently confirmed using the mitochondrial DNA barcoding region-cytochrome oxidase c subunit I (MtDNA-COI), mitochondrial DNA-cytochrome c oxidase subunit II (MtDNA-COII), and ribosomal DNA internal transcribed spacer 2 (rDNA-ITS2) sequences. The current study reveals the genetic characteristics and distribution of nine mosquito species within the Anopheles and Cellia subgenera. Four dominant species, including Anopheles peditaeniatus, Anopheles subpictus, Anopheles vagus, and Anopheles aconitus exhibited significant intraspecific gene flow within their corresponding species. Although malaria parasites were not found in 126 mosquito pools, meaning more investigation is necessary, the current study adds to the existing DNA barcoding data collection and improves the current understanding of the genetic structure and distribution of anopheline mosquito species, which could be useful for effective control of mosquito-borne diseases.},
}
@article {pmid36597460,
year = {2023},
author = {Samji, A and Eashwarlal, K and Shanmugavel, S and Kumar, S and Warrier, RR},
title = {Chloroplast genome skimming of a potential agroforestry species Melia dubia. Cav and its comparative phylogenetic analysis with major Meliaceae members.},
journal = {3 Biotech},
volume = {13},
number = {1},
pages = {30},
pmid = {36597460},
issn = {2190-572X},
abstract = {UNLABELLED: Melia dubia Cav. is a fast-growing plywood species gaining popularity due to high economic returns. This study aimed to assemble and annotate the chloroplast (cp) genome of M. dubia and compare it with previously published cp genomes within the Meliaceae family. The chloroplast genome was constructed by the de novo and reference-based assembly of paired-end reads generated by long-read sequencing of genomic DNA. The cp genome, sized 171,956 bp, comprised a typical angiosperm quadripartite structure. The large single-copy (LSC) region of 76,055 bp and a small single-copy (SSC) region of 18,693 bp cover 55% of the genome. The pair of inverted repeats (IRA and IRB) were 38,604 bp each (covering 45% of the genome). We identified unique genes (112), including protein-coding genes (79), tRNA (29) and 4 rRNA genes. Phylogenetic analysis using complete cp genomes of 11 species from Meliaceae revealed that M. dubia and M. azedarach shared a sister clade. Comparative analysis using cp genome of M. dubia, M. azedarach and Azadirachta indica revealed a high sequence similarity (> 70%). Five intergenic regions were highly conserved among the three cp genomes. The gene trnG-UCC at LSC region was found to be more divergent in M. dubia and M. azedarach, while it shows complete conservation within M. dubia and A. indica. This is the first report of the chloroplast genome in M. dubia. The available levels of taxonomic expertise and clarity in species delineation within the Melia genus are low. The information generated provides scope for identifying new barcodes which increases the discriminatory power of the species within the genus beyond morphological identification.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-022-03447-1.},
}
@article {pmid36597245,
year = {2023},
author = {Saleem, M},
title = {Barcode Medication Administration Technology to Prevent Medication Errors.},
journal = {Journal of the College of Physicians and Surgeons--Pakistan : JCPSP},
volume = {33},
number = {1},
pages = {111-112},
doi = {10.29271/jcpsp.2023.01.111},
pmid = {36597245},
issn = {1681-7168},
mesh = {Humans ; *Medication Systems, Hospital ; Electronic Data Processing ; Medication Errors/prevention &amp; control ; *Drug-Related Side Effects and Adverse Reactions ; Patient Safety ; },
abstract = {Medication errors cause harm to patients at any point along the medication administration process and can be prevented. Barcoding medication administration (BCMA) is effective as a clinical decision support system (CDSS) to avoid errors. This viewpoint proposes the implementation of BCMA to avoid potential adverse events. The opinion piece gives an overview of BCMA, reviews the current literature on its effectiveness, and sheds light on the associated challenges and how to overcome them. The objective of this article is to increase awareness regarding BCMA and how it can decrease patient morbidity and mortality, enhance safety, and lower overall hospital-associated costs by preventing medication errors. Key Words: Bar-code medication administration, Medication errors, Adverse drug events, Patient safety.},
}
@article {pmid36596857,
year = {2023},
author = {Mao, L and Zou, Q and Sun, Z and Dong, Q and Cao, X},
title = {Insights into chloroplast genome structure, intraspecific variation, and phylogeny of Cyclamen species (Myrsinoideae).},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {87},
pmid = {36596857},
issn = {2045-2322},
mesh = {Phylogeny ; *Genome, Chloroplast ; *Cyclamen/genetics ; Genetic Markers ; Gene Order ; },
abstract = {Species from the flowering plant genus Cyclamen are popular amongst consumers. In particular Cyclamen persicum Mill. has been significantly used commercially, and certain small flowering species such as Cyclamen hederifolium and Cyclamen coum are gradually growing in popularity in the potted flower market. Here, the chloroplast genomes of nine Cyclamen samples including four Cyclamen species and five varieties of C. hederifolium were sequenced for genome structure comparison, White green septal striped leaves related gene screening and DNA molecular markers were developed for phylogenetic analysis. In comparing Cyclamen species' chloroplast genomes, gene content and gene order were found to be highly similar with the length of genomes ranging from 151,626 to 153,058 bp. The chloroplast genome of Cyclamen has 128 genes, including 84 protein-coding genes, 36 transfer RNA genes, and 8 ribosomal RNA genes. Based on intraspecific variation, seven hotspots, including three genes and four intergenic regions, were identified as variable markers for downstream species delimitation and interspecific relationship analyses. Moreover, a phylogenetic tree constructed with complete chloroplast genomes, revealed that Cyclamen are monophyletic with Lysimachia as the closest neighbor. Phylogenetic analyses of the 14 Cyclamen species with the seven variable regions showed five distinct clades within this genus. The highly supported topologies showed these seven regions may be used as candidate DNA barcode sequences to distinguish Cyclamen species. White green septal striped leaves is common in C. hederifolium, however the molecular mechanism of this has not yet been described. Here, we find that the intergenic region rps4-trnT-UGU seems related to white green septal striped leaves.},
}
@article {pmid36596806,
year = {2023},
author = {Biben, C and Weber, TS and Potts, KS and Choi, J and Miles, DC and Carmagnac, A and Sargeant, T and de Graaf, CA and Fennell, KA and Farley, A and Stonehouse, OJ and Dawson, MA and Hilton, DJ and Naik, SH and Taoudi, S},
title = {In vivo clonal tracking reveals evidence of haemangioblast and haematomesoblast contribution to yolk sac haematopoiesis.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {41},
pmid = {36596806},
issn = {2041-1723},
mesh = {*Yolk Sac ; Hematopoiesis/genetics ; *Hemangioblasts ; Clone Cells ; Endothelium ; Cell Differentiation ; },
abstract = {During embryogenesis, haematopoietic and endothelial lineages emerge closely in time and space. It is thought that the first blood and endothelium derive from a common clonal ancestor, the haemangioblast. However, investigation of candidate haemangioblasts in vitro revealed the capacity for mesenchymal differentiation, a feature more compatible with an earlier mesodermal precursor. To date, no evidence for an in vivo haemangioblast has been discovered. Using single cell RNA-Sequencing and in vivo cellular barcoding, we have unravelled the ancestral relationships that give rise to the haematopoietic lineages of the yolk sac, the endothelium, and the mesenchyme. We show that the mesodermal derivatives of the yolk sac are produced by three distinct precursors with dual-lineage outcomes: the haemangioblast, the mesenchymoangioblast, and a previously undescribed cell type: the haematomesoblast. Between E5.5 and E7.5, this trio of precursors seeds haematopoietic, endothelial, and mesenchymal trajectories.},
}
@article {pmid36590028,
year = {2023},
author = {Fujita, H and Kawai, K and Deville, D and Umino, T},
title = {Quatrefoil light traps for free-swimming stages of cymothoid parasitic isopods and seasonal variation in their species compositions in the Seto Inland Sea, Japan.},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {20},
number = {},
pages = {12-19},
pmid = {36590028},
issn = {2213-2244},
abstract = {Cymothoid parasitic isopods infest a wide range of fish of different taxa living in marine, brackish, and freshwater environments. Most research on the reproductive season of Cymothoidae has been done by collecting or monitoring host fish afflicted with cymothoid parasites. However, collecting ecological data on cymothoid species that infest non-commercial or endangered fishes is complex and challenging. We used a quatrefoil light trap to investigate the seasonal change in species composition of cymothoid free-swimming stages in the Seto Inland Sea, Japan. We also collected preliminary data for efficient light-trap sampling and showed its effectiveness in cymothoid-related research. From October 2020 to December 2021, 613 cymothoid free-swimming stages were sampled monthly. All obtained individuals were identified as Mothocya parvostis (596), Ceratothoa verrucosa (12), and Ceratothoa carinata (5) by DNA barcoding using cytochrome c oxidase subunit I and 16S rRNA gene sequences. Based on the number of M. parvostis mancae collected each month, M. parvostis was anticipated to reproduce from June to December, with two reproduction peaks each year, and C. verrucosa and C. carinata were expected to reproduce in June, July, and September, and September and October, respectively. In addition, free-swimming juveniles were captured, presumably after they had left their optional intermediate hosts. Furthermore, the most effective time to harvest cymothoids with light traps may be during high tide on the night of the new moon. This study serves as a methodological framework for future research on cymothoids using light traps.},
}
@article {pmid36584071,
year = {2022},
author = {Yang, T and Zhang, TL and Guo, YH and Liu, X},
title = {Correction: Identification of Hybrids in Potamogeton: Incongruence between Plastid and ITS Regions Solved by a Novel Barcoding Marker PHYB.},
journal = {PloS one},
volume = {17},
number = {12},
pages = {e0280043},
pmid = {36584071},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0166177.].},
}
@article {pmid36583225,
year = {2023},
author = {Siddig, EE and Nyuykonge, B and Mhmoud, NA and Abdallah, OB and Bahar, MEN and Ahmed, ES and Nyaoke, B and Zijlstra, EE and Verbon, A and Bakhiet, SM and Fahal, AH and van de Sande, WWJ},
title = {Comparing the performance of the common used eumycetoma diagnostic tests.},
journal = {Mycoses},
volume = {66},
number = {5},
pages = {420-429},
doi = {10.1111/myc.13561},
pmid = {36583225},
issn = {1439-0507},
support = {//Drugs for Neglected Diseases initiative/ ; },
mesh = {Humans ; *Mycetoma/diagnosis ; Cross-Sectional Studies ; Sudan/epidemiology ; Polymerase Chain Reaction ; *Madurella/genetics ; Diagnostic Tests, Routine ; },
abstract = {OBJECTIVES: Mycetoma is a neglected tropical implantation disease caused by 70 different infectious agents. Identifying the causative organism to the species level is essential for appropriate patient management. Ultrasound, histopathology, culture and two species-specific PCRs are most the commonly used methods for species identification in endemic regions. The aim of this study was to compare the diagnostic performance of these commonly used assays using sequencing of barcoding genes as the gold standard.<br><br>METHODS: This descriptive cross-sectional study was conducted at the Mycetoma Research Centre, University of Khartoum, Sudan. It included 222 patients suspected of fungal mycetoma caused by Madurella mycetomatis.<br><br>RESULTS: 154 (69.3%) were correctly identified by ultrasound, histology, culture and both species-specific PCRs. In 60 patients, at least one of the diagnostic tests failed to identify M. mycetomatis. Five patients had no evidence of eumycetoma, and for three, only the ultrasound was indicative of mycetoma. The two species-specific PCRs were the most sensitive and specific methods, followed by culture and histology. Ultrasound was the least specific as it only allowed differentiation between actinomycetoma and eumycetoma. The time to result was 9.38&#x2009;minutes for ultrasound, 3.76&#x2009;hours for PCR, 8.5&#x2009;days for histopathology and 21&#x2009;days for grain culturing.<br><br>CONCLUSION: Currently, PCR directly on DNA isolated from grains is the most rapid and reliable diagnostic tool to identify M. mycetomatis eumycetoma.},
}
@article {pmid36578516,
year = {2022},
author = {Fewings, A and Vandelanotte, C and Irwin, C and Ting, C and Williams, E and Khalesi, S},
title = {The use and acceptability of diet-related apps and websites in Australia: Cross-sectional study.},
journal = {Digital health},
volume = {8},
number = {},
pages = {20552076221139091},
pmid = {36578516},
issn = {2055-2076},
abstract = {OBJECTIVE: Diet-related apps and websites are developed to help improve dietary intake. The aim of this study is to explore the use and acceptability of diet-related apps and websites in Australia.<br><br>METHODS: In a cross-sectional study, 241 participants (mean age&#x2009;=&#x2009;40.6 years) completed an online survey about demographic characteristics, lifestyle behaviours and health concerns, experience and confidence in technology use, and preferences, attitudes and perception of diet app and website use. Descriptive analysis and unadjusted multiple logistic regression were used to explore data.<br><br>RESULTS: Overall, 63.5% of participants were current or previous app users. App users were more confident in using technology, more concerned about diet and weight, and more trusting of information provided in diet-related apps compared to non-app users (p &#x2264; .05). Features such as food tracking, nutrient check and barcode scanning were preferred by both users and non-users. The likelihood of using diet-related apps was higher for those who trust the app information (OR 5.51, 95%CI: 2.40-12.66), often count calories (OR 2.28, 95%CI: 1.01-5.24) and are often on diet (OR 4.16, 95% CI: 1.21-14.21) compared to their counterparts.<br><br>CONCLUSIONS: More than half of the Australians that participated in this study used diet-related apps and websites. App features that allow the user to accurately record and monitor food intake and scan barcodes may motivate app use. Future public health strategies may take advantage of diet-related apps and websites to improve dietary behaviour at the population level and reduce the burden of obesity and non-communicable diseases.},
}
@article {pmid36576962,
year = {2023},
author = {Hupało, K and Copilaș-Ciocianu, D and Leese, F and Weiss, M},
title = {Morphology, nuclear SNPs and mate selection reveal that COI barcoding overestimates species diversity in a Mediterranean freshwater amphipod by an order of magnitude.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {39},
number = {2},
pages = {129-143},
doi = {10.1111/cla.12520},
pmid = {36576962},
issn = {1096-0031},
mesh = {Animals ; *Amphipoda/genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Fresh Water ; Polymorphism, Single Nucleotide ; *Electron Transport Complex IV/genetics/metabolism ; *Mating Preference, Animal/physiology ; },
abstract = {DNA sequence information has revealed many morphologically cryptic species worldwide. For animals, DNA-based assessments of species diversity usually rely on the mitochondrial cytochrome c oxidase subunit I (COI) gene. However, a growing amount of evidence indicate that mitochondrial markers alone can lead to misleading species diversity estimates due to mito-nuclear discordance. Therefore, reports of putative species based solely on mitochondrial DNA should be verified by other methods, especially in cases where COI sequences are identical for different morphospecies or where divergence within the same morphospecies is high. Freshwater amphipods are particularly interesting in this context because numerous putative cryptic species have been reported. Here, we investigated the species status of the numerous mitochondrial molecular operational taxonomic units (MOTUs) found within Echinogammarus sicilianus. We used an integrative approach combining DNA barcoding with mate selection observations, detailed morphometrics and genome-wide double digest restriction site-associated DNA sequencing (ddRAD-seq). Within a relatively small sampling area, we detected twelve COI MOTUs (divergence = 1.8-20.3%), co-occurring in syntopy at two-thirds of the investigated sites. We found that pair formation was random and there was extensive nuclear gene flow among the ten MOTUs co-occurring within the same river stretch. The four most common MOTUs were also indistinguishable with respect to functional morphology. Therefore, the evidence best fits the hypothesis of a single, yet genetically diverse, species within the main river system. The only two MOTUs sampled outside the focal area were genetically distinct at the nuclear level and may represent distinct species. Our study reveals that COI-based species delimitation can significantly overestimate species diversity, highlighting the importance of integrative taxonomy for species validation, especially in hyperdiverse complexes with syntopically occurring mitochondrial MOTUs.},
}
@article {pmid36574472,
year = {2023},
author = {Van-Anh Le, T and Mai Nga, TP and Nhi Nguyen, P and Kieu-Oanh Nguyen, T},
title = {Genotypic and Phenotypic Diversity of Endemic Golden Camellias Collected from the North of Vietnam.},
journal = {Chemistry &amp; biodiversity},
volume = {20},
number = {1},
pages = {e202200843},
doi = {10.1002/cbdv.202200843},
pmid = {36574472},
issn = {1612-1880},
support = {THTEXS.05/21-24//Vietnam Academy of Science and Technology/ ; },
mesh = {*Camellia/chemistry ; Vietnam ; Flavonoids/analysis ; Flowers/chemistry ; Plant Leaves ; DNA Barcoding, Taxonomic ; Phylogeny ; DNA, Plant/analysis ; },
abstract = {Golden Camellias have recently been used as a food, cosmetic, and traditional medicine in China and Vietnam. Forty-two species have natural distribution in Vietnam, of which thirty-two species were considered endemic species of this country. The morphology of leaves and flowers of these species were similar; therefore, their taxonomic identification usually needed experts and the authentication has often been confused among species. Our study aims to describe the genetic diversity and the relationship of six species Camellia phanii, Camellia tamdaoensis, Camellia tienii, Camellia flava, Camellia petelotii and Camellia euphlebia by using three chloroplast DNA-barcodes: matK, rbcL and trnH-psbA. We also clarified the significant differences in anatomical characteristics of midvein and blade of their leaves, which suggested the possibility to use these criteria in taxonomy. In addition, preliminary chemical profiles of the methanolic extracts of leaves from six Golden Camellias such as total phenolic content (TPC), total flavonoid content (TFC), total anthocyanin content (TAC) and chlorogenic acids content (TCGAs) also showed the diversity among them. Interestingly, the discrimination on the catechins profile among six species followed the same tendency with the genetic distance on the phylogeny tree suggesting that catechins (i. e., discriminative catechins) can be biomarkers for the chemotaxonomy of these six Golden Camellias.},
}
@article {pmid36568864,
year = {2022},
author = {Ottati, S and Eberle, J and Rulik, B and Köhler, F and Ahrens, D},
title = {From DNA barcodes to ecology: Meta-analysis of central European beetles reveal link with species ecology but also to data pattern and gaps.},
journal = {Ecology and evolution},
volume = {12},
number = {12},
pages = {e9650},
pmid = {36568864},
issn = {2045-7758},
abstract = {DNA barcoding has been used worldwide to identify biological specimens and to delimit species. It represents a cost-effective, fast, and efficient way to assess biodiversity with help of the public Barcode of Life Database (BOLD) accounting for more than 236,000 animal species and more than 10 million barcode sequences. Here, we performed a meta-analysis of available barcode data of central European Coleoptera to detect intraspecific genetic patterns among ecological groups in relation to geographic distance with the aim to investigate a possible link between infraspecific variation and species ecology. We collected information regarding feeding style, body size, as well as habitat and biotope preferences. Mantel tests and two variants of Procrustes analysis, both involving the Principal Coordinates Neighborhood Matrices (PCNM) approach, were applied on genetic and geographic distance matrices. However, significance levels were too low to further use the outcome for further trait investigation: these were in mean for all ecological guilds only 7.5, 9.4, or 15.6% for PCNM + PCA, NMDS + PCA, and Mantel test, respectively, or at best 28% for a single guild. Our study confirmed that certain ecological traits were associated with higher species diversity and foster stronger genetic differentiation. Results suggest that increased numbers of species, sampling localities, and specimens for a chosen area of interest may give new insights to explore barcode data and species ecology for the scope of conservation on a larger scale. We performed a meta-analysis of available barcode data of central European beetles to detect intraspecific genetic patterns among ecological groups in relation to geographic distance, regarding feeding style, body size, as well as habitat and biotope preferences. Our study confirmed that certain ecological traits were associated with higher species diversity and foster stronger genetic differentiation. However, significance levels were too low to further use the outcome for further trait investigation.},
}
@article {pmid36568808,
year = {2022},
author = {Shih, HT and Prema, M and Kumar, AAJ and Saher, NU and Ravichandran, S and Odhano, S and Paulay, G},
title = {Diversity and Distribution of Fiddler Crabs (Crustacea: Brachyura: Ocypodidae) around the Arabian Sea.},
journal = {Zoological studies},
volume = {61},
number = {},
pages = {e65},
pmid = {36568808},
issn = {1810-522X},
abstract = {Nine species of fiddler crabs (Crustacea: Ocypodidae: Gelasiminae) are known from the Arabian Sea and adjacent waters (Red Sea, Gulf of Aden, Gulf of Oman and Arabian/Persian Gulf): five species of Austruca, one Cranuca, two Gelasimus and one Tubuca. COI sequence data match morphological species boundaries and shows high connectivity within each. The fauna is highly endemic, with three species of Austruca (A. albimana, A. iranica and A. sindensis) confined to this region, and four others restricted to the Indian Ocean. restricted to the Indian Ocean. Austruca albimana and A. iranica speciated locally and now have narrowly overlapping ranges in Oman. Our results confirm the westernmost distributions of Austruca annulipes and Tubuca alcocki are Pakistan and the Red Sea, respectively. A key for the nine species is also provided to help identification.},
}
@article {pmid36566190,
year = {2022},
author = {Yang, Z and Ma, W and Yang, X and Wang, L and Zhao, T and Liang, L and Wang, G and Ma, Q},
title = {Plastome phylogenomics provide new perspective into the phylogeny and evolution of Betulaceae (Fagales).},
journal = {BMC plant biology},
volume = {22},
number = {1},
pages = {611},
pmid = {36566190},
issn = {1471-2229},
support = {32101541//National Natural Science Foundation of China/ ; 32101541//National Natural Science Foundation of China/ ; 32101541//National Natural Science Foundation of China/ ; 32101541//National Natural Science Foundation of China/ ; 32101541//National Natural Science Foundation of China/ ; 32101541//National Natural Science Foundation of China/ ; 32101541//National Natural Science Foundation of China/ ; 32101541//National Natural Science Foundation of China/ ; 21326804D//Key Research and Development Program of Hebei Province/ ; },
mesh = {Phylogeny ; *Fagales ; Betulaceae ; Betula ; *Corylus ; Evolution, Molecular ; },
abstract = {BACKGROUND: Betulaceae is a relatively small but morphologically diverse family, with many species having important economic and ecological values. Although plastome structure of Betulaceae has been reported sporadically, a comprehensive exploration for plastome evolution is still lacking. Besides, previous phylogenies had been constructed based on limited gene fragments, generating unrobust phylogenetic framework and hindering further studies on divergence ages, biogeography and character evolution. Here, 109 plastomes (sixteen newly assembled and 93 previously published) were subject to comparative genomic and phylogenomic analyses to reconstruct a robust phylogeny and trace the diversification history of Betulaceae.<br><br>RESULTS: All Betulaceae plastomes were highly conserved in genome size, gene order, and structure, although specific variations such as gene loss and IR boundary shifts were revealed. Ten divergent hotspots, including five coding regions (Pi&#x2009;>&#x2009;0.02) and five noncoding regions (Pi&#x2009;>&#x2009;0.035), were identified as candidate DNA barcodes for phylogenetic analysis and species delimitation. Phylogenomic analyses yielded high-resolution topology that supported reciprocal monophyly between Betula and Alnus within Betuloideae, and successive divergence of Corylus, Ostryopsis, and Carpinus-Ostrya within Coryloideae. Incomplete lineage sorting and hybridization may be responsible for the mutual paraphyly between Ostrya and Carpinus. Betulaceae ancestors originated from East Asia during the upper Cretaceous; dispersals and subsequent vicariance accompanied by historical environment changes contributed to its diversification and intercontinental disjunction. Ancestral state reconstruction indicated the acquisition of many taxonomic characters was actually the results of parallel or reversal evolution.<br><br>CONCLUSIONS: Our research represents the most comprehensive taxon-sampled and plastome-level phylogenetic inference for Betulaceae to date. The results clearly document global patterns of plastome structural evolution, and established a well-supported phylogeny of Betulaceae. The robust phylogenetic framework not only provides new insights into the intergeneric relationships, but also contributes to a perspective on the diversification history and evolution of the family.},
}
@article {pmid36564617,
year = {2022},
author = {Trimarsanto, H and Amato, R and Pearson, RD and Sutanto, E and Noviyanti, R and Trianty, L and Marfurt, J and Pava, Z and Echeverry, DF and Lopera-Mesa, TM and Montenegro, LM and Tobón-Castaño, A and Grigg, MJ and Barber, B and William, T and Anstey, NM and Getachew, S and Petros, B and Aseffa, A and Assefa, A and Rahim, AG and Chau, NH and Hien, TT and Alam, MS and Khan, WA and Ley, B and Thriemer, K and Wangchuck, S and Hamedi, Y and Adam, I and Liu, Y and Gao, Q and Sriprawat, K and Ferreira, MU and Laman, M and Barry, A and Mueller, I and Lacerda, MVG and Llanos-Cuentas, A and Krudsood, S and Lon, C and Mohammed, R and Yilma, D and Pereira, DB and Espino, FEJ and Chu, CS and Vélez, ID and Namaik-Larp, C and Villegas, MF and Green, JA and Koh, G and Rayner, JC and Drury, E and Gonçalves, S and Simpson, V and Miotto, O and Miles, A and White, NJ and Nosten, F and Kwiatkowski, DP and Price, RN and Auburn, S},
title = {A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {1411},
pmid = {36564617},
issn = {2399-3642},
support = {200909/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; U19 AI129392/AI/NIAID NIH HHS/United States ; 200909/WT_/Wellcome Trust/United Kingdom ; 204911/WT_/Wellcome Trust/United Kingdom ; 206194/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; M006212/MRC_/Medical Research Council/United Kingdom ; 204911/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MR/M006212/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Malaria, Vivax/diagnosis/genetics ; Likelihood Functions ; Plasmodium vivax/genetics ; *Malaria ; Internet ; },
abstract = {Traditionally, patient travel history has been used to distinguish imported from autochthonous malaria cases, but the dormant liver stages of Plasmodium vivax confound this approach. Molecular tools offer an alternative method to identify, and map imported cases. Using machine learning approaches incorporating hierarchical fixation index and decision tree analyses applied to 799 P. vivax genomes from 21 countries, we identified 33-SNP, 50-SNP and 55-SNP barcodes (GEO33, GEO50 and GEO55), with high capacity to predict the infection's country of origin. The Matthews correlation coefficient (MCC) for an existing, commonly applied 38-SNP barcode (BR38) exceeded 0.80 in 62% countries. The GEO panels outperformed BR38, with median MCCs > 0.80 in 90% countries at GEO33, and 95% at GEO50 and GEO55. An online, open-access, likelihood-based classifier framework was established to support data analysis (vivaxGEN-geo). The SNP selection and classifier methods can be readily amended for other use cases to support malaria control programs.},
}
@article {pmid36564568,
year = {2022},
author = {Umeki, Y and Ogawa, N and Uegaki, Y and Saga, K and Kaneda, Y and Nimura, K},
title = {DNA barcoding and gene expression recording reveal the presence of cancer cells with unique properties during tumor progression.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {80},
number = {1},
pages = {17},
pmid = {36564568},
issn = {1420-9071},
support = {18 cm0106341h0001//AMED/ ; JP21K19408//JSPS/ ; JP21H05158//JSPS/ ; JP21H05160//JSPS/ ; },
mesh = {Male ; Humans ; Animals ; Mice ; *DNA Barcoding, Taxonomic ; Cell Line ; Clone Cells ; *Lung Neoplasms/genetics ; Gene Expression ; Cell Line, Tumor ; Tumor Microenvironment ; },
abstract = {Tumors comprise diverse cancer cell populations with specific capabilities for adaptation to the tumor microenvironment, resistance to anticancer treatments, and metastatic dissemination. However, whether these populations are pre-existing in cancer cells or stochastically appear during tumor growth remains unclear. Here, we show the heterogeneous behaviors of cancer cells regarding response to anticancer drug treatments, formation of lung metastases, and expression of transcription factors related to cancer stem-like cells using a DNA barcoding and gene expression recording system. B16F10 cells maintained clonal diversity after treatment with HVJ-E, a UV-irradiated Sendai virus, and the anticancer drug dacarbazine. PBS treatment of the primary tumor and intravenous injection of B16F10 cells resulted in metastases formed from clones of multiple cell lineages. Conversely, BL6 and 4T1 cells developed spontaneous lung metastases by a small number of clones. Notably, an identical clone of 4T1 cells developed lung metastases in different mice, suggesting the existence of cells with high metastatic potential. Cas9-based transcription recording analysis in a human prostate cancer cell line revealed that specific cells express POU5F1 in response to an anticancer drug and sphere formation. Our findings provide insights into the diversity of cancer cells during tumor progression.},
}
@article {pmid36562153,
year = {2023},
author = {Trnka, A and Samaš, P and Mąkol, J},
title = {Chigger mite (Acariformes: Trombiculidae) infestation in reed passerine birds in Central Europe: a case of the bearded tit Panurus biarmicus.},
journal = {Parasitology},
volume = {150},
number = {2},
pages = {212-220},
pmid = {36562153},
issn = {1469-8161},
mesh = {Animals ; Humans ; *Trombiculidae ; *Mite Infestations/epidemiology/veterinary ; *Trombiculiasis/epidemiology/veterinary/parasitology ; *Passeriformes/parasitology ; Europe/epidemiology ; Larva ; },
abstract = {Larval trombiculid (chigger) mites are common ectoparasites of terrestrial vertebrates including humans, causing itching and skin inflammation known as trombiculiasis. Investigation of their diversity, distribution and seasonal abundance is therefore important from a veterinary and public health point of view. Although researchers have paid increased attention to these parasites in recent years, there is still little ecological data available on chiggers associated with birds inhabiting different types of habitats such as wetlands, for example. In 2021, we investigated the mite fauna in a specialist reedbed passerine, the bearded tit (Panurus biarmicus), and their effects on this host in the south-west Slovakia, Central Europe. A total of 1134 larvae of 1 mite species Blankaartia acuscutellaris were found in 99 out of 267 examined bearded tits. Juveniles were more infested than adult birds, but no differences were found between sexes. The larvae of mites first appeared on the host during the second half of June and peaked in the second half of July. After that, their numbers decreased gradually until October. Despite the relatively high prevalence and intensity of mite infestation in the bearded tit, no differences in body condition between infested and uninfested birds suggest that infestation by B. acuscutellaris may not have serious negative effects on the host health. Bearded tits can therefore be a reliable indicator of the presence of the chigger mites in wetland habitats.},
}
@article {pmid36559654,
year = {2022},
author = {Han, S and Ding, H and Bi, D and Zhang, S and Yi, R and Gao, J and Yang, J and Ye, Y and Wu, L and Kan, X},
title = {Structural Diversities and Phylogenetic Signals in Plastomes of the Early-Divergent Angiosperms: A Case Study in Saxifragales.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {24},
pages = {},
pmid = {36559654},
issn = {2223-7747},
support = {NEL&amp;MARA-003//the Opening Foundation of National Engineering Laboratory of Soil Pollution Control and Remediation Technologies, and Key Laboratory of Heavy Metal Pollution Prevention &amp; Control, Ministry of Agriculture and Rural Affairs/ ; BK20211078//the Basic Research Program (Natural Science Foundation) of Jiangsu Province/ ; },
abstract = {As representative of the early-divergent groups of angiosperms, Saxifragales is extremely divergent in morphology, comprising 15 families. Within this order, our previous case studies observed significant structural diversities among the plastomes of several lineages, suggesting a possible role in elucidating their deep phylogenetic relationships. Here, we collected 208 available plastomes from 11 constituent families to explore the evolutionary patterns among Saxifragales. With thorough comparisons, the losses of two genes and three introns were found in several groups. Notably, 432 indel events have been observed from the introns of all 17 plastomic intron-containing genes, which could well play an important role in family barcoding. Moreover, numerous heterogeneities and strong intrafamilial phylogenetic implications were revealed in pttRNA (plastomic tRNA) structures, and the unique structural patterns were also determined for five families. Most importantly, based on the well-supported phylogenetic trees, evident phylogenetic signals were detected in combinations with the identified pttRNAs features and intron indels, demonstrating abundant lineage-specific characteristics for Saxifragales. Collectively, the results reported here could not only provide a deeper understanding into the evolutionary patterns of Saxifragales, but also provide a case study for exploring the plastome evolution at a high taxonomic level of angiosperms.},
}
@article {pmid36555212,
year = {2022},
author = {Ślipiko, M and Myszczyński, K and Buczkowska, K and Bączkiewicz, A and Sawicki, J},
title = {Super-Mitobarcoding in Plant Species Identification? It Can Work! The Case of Leafy Liverworts Belonging to the Genus Calypogeia.},
journal = {International journal of molecular sciences},
volume = {23},
number = {24},
pages = {},
pmid = {36555212},
issn = {1422-0067},
support = {2015/19/B/NZ8/03970//The National Science Center in Krak&#xf3;w, Poland/ ; },
mesh = {*Hepatophyta/genetics ; DNA, Plant/genetics ; DNA Barcoding, Taxonomic/methods ; Phylogeny ; Sequence Analysis, DNA ; Plants/genetics ; Species Specificity ; },
abstract = {Molecular identification of species is especially important where traditional taxonomic methods fail. The genus Calypogeia belongs to one of the tricky taxons. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. The finding of the universal single-locus DNA barcode in plants seems to be 'the Holy Grail'; therefore, researchers are increasingly looking for multiloci DNA barcodes or super-barcoding. Since the mitochondrial genome has low sequence variation in plants, species delimitation is usually based on the chloroplast genome. Unexpectedly, our research shows that super-mitobarcoding can also work! However, our outcomes showed that a single method of molecular species delimitation should be avoided. Moreover, it is recommended to interpret the results of molecular species delimitation alongside other types of evidence, such as ecology, population genetics or comparative morphology. Here, we also presented genetic data supporting the view that C. suecica is not a homogeneous species.},
}
@article {pmid36555058,
year = {2022},
author = {Sun, H and Ding, L and Pape, T and Zhang, D},
title = {A New Species of Ascodipteron (Diptera: Hippoboscidae) from China Based on Morphology and DNA Barcodes.},
journal = {Insects},
volume = {13},
number = {12},
pages = {},
pmid = {36555058},
issn = {2075-4450},
support = {31872964//National Natural Science Foundation of China/ ; 32170450//National Natural Science Foundation of China/ ; },
abstract = {A new species of the genus Ascodipteron Adensamer, 1896 (Diptera: Hippoboscidae) is described from Fujian, namely A. guoliangi sp. nov. Habitus and diagnostic details, as well as the attachment sites on the host, are documented with photographs. A detailed comparison of the new species with related species is provided and the new species is accommodated in the most recent key to the world species of Ascodipteron.},
}
@article {pmid36555044,
year = {2022},
author = {Fernández-Santos, NA and Trujillo-García, JC and Hamer, SA and Wei, L and Martínez-Montoya, H and Tamez-Guerra, P and Hamer, GL and Rodríguez-Pérez, MA},
title = {Domestic Triatoma spp. Infections with Trypanosoma cruzi, Household Infestations, and Molecular Identification in Oaxaca, México.},
journal = {Insects},
volume = {13},
number = {12},
pages = {},
pmid = {36555044},
issn = {2075-4450},
support = {20220163//Instituto Polit&#xe9;cnico Nacional/ ; 20195706//Instituto Polit&#xe9;cnico Nacional/ ; },
abstract = {In Latin America, Mexico is the country with the second highest annual estimated number of Chagas disease cases, caused by Trypanosoma cruzi, due to vector-borne transmission. The state of Oaxaca is the location of the first documented human cases of Chagas disease in Mexico and contained the highest T. cruzi seropositive rate (3.5%) from blood donors. Here, entomological surveys, from 2017 to 2019, were conducted to collect triatomines in 124 villages of 60 municipalities. Four principal domestic Triatoma spp. (Hemiptera: Triatominae), Triatoma phyllosoma, T. barberi, T. mazzotti, and T. dimidiata, of Oaxaca, Mexico were identified by morphology and molecular analysis of the barcode region of the cytochrome oxidase 1 (cox1 or COI or CO1) gene. A total of 41 out of 83 T. phyllosoma specimens examined by microscopy were positive for T. cruzi (49%), 49 out of 171 for T. barberi (28%), 31 out of 177 for T. mazzotti (17%), and none out of 10 for T. dimidiata (0%). Overall, the infestation index was 3.1% of households containing at least one triatomine; the crowding index was a mean of two Triatoma spp./household; and the colonization index was 0.38 for households based on presence of nymphs. Geographical distribution of triatomines in Oaxaca at the municipality level and endophilic behavior is also reported. Precise identification, endophilic habits, and infection rates of these triatomines are paramount for vector control programs of the Ministry of Health of Oaxaca and beyond.},
}
@article {pmid36555035,
year = {2022},
author = {Chen, A and Li, Z and Zheng, Y and Zhan, J and Yang, B and Yang, Z},
title = {Decreasing Species Richness with Increase in Elevation and Positive Rapoport Effects of Crambidae (Lepidoptera) on Mount Taibai.},
journal = {Insects},
volume = {13},
number = {12},
pages = {},
pmid = {36555035},
issn = {2075-4450},
support = {31772508//National Natural Science Foundation of China/ ; CEPFQS202169-15//China Environmental Protection Foundation/ ; },
abstract = {Rapoport's rule proposes that a species' range size increases with the increase in a gradient (such as latitude, altitude or water depth). However, altitudinal distributions and Rapoport's rule have rarely been tested for Asian Lepidoptera. Pyraustinae and Spilomelinae (Lepidoptera: Crambidae) are extremely diverse in temperate Asia, including on Mount Taibai, which is considered a hotspot area for studying the vertical distribution patterns of insect species. Based on the investigation of altitudinal distribution data with identification by using both DNA barcoding and the morphological classification of Pyraustinae and Spilomelinae, this paper determines the altitudinal gradient pattern for these two subfamilies on the north slope of Mount Taibai, and provides a test of the universality of Rapoport's rule in Lepidoptera by using four methods, including Stevens' method, Pagel's method, Rohde's method, and the cross-species method. Our results show that the alpha diversity of Pyraustinae and Spilomelinae both decrease with rising altitude. By contrast, the species' ranges increase with rising altitude. Three of the four methods used to test Rapoport's rule yielded positive results, while Rohde's results show a unimodal distribution model and do not support Rapoport's rule. Our findings fill the research gap on the elevational diversity of Lepidoptera in temperate Asia.},
}
@article {pmid36555022,
year = {2022},
author = {Bolshakov, V and Prokin, A and Pavlov, D and Akkizov, A and Movergoz, E},
title = {Karyotypes and COI Gene Sequences of Chironomus sp. Le1 (Kiknadze and Salova, 1996), Ch. laetus (Belyanina and Filinkova, 1996) and Their Hybrid from the Yamal Peninsula, Arctic Zone of Russia.},
journal = {Insects},
volume = {13},
number = {12},
pages = {},
pmid = {36555022},
issn = {2075-4450},
support = {121050500046-8 and 121051100099-5, 121051100109-1, 121051100104-6.//Russia state projects/ ; },
abstract = {The study of the biological diversity of the Arctic zone yields intriguing results. Initial research on the lakes of the Yamal Peninsula resulted in the identification of Chironomus laetus and the hybrid Ch. laetus × Ch. sp. Le1. To avoid misidentification, we used morphological, cytogenetic, and molecular genetic approaches. By cytogenetics, in Ch. sp. Le1, seven banding sequences were found: Le1A1, Le1B1, Le1C1, Le1D1, Le1E1, Le1F1, and Le1G1. The karyotype of Ch. laetus was mapped for the first time; it is the first species with the arm combinations AE BC DF G. We propose the name of a new cytocomplex-"laetus". DNA-barcoding of the COI gene was carried out for Ch. laetus and Ch. laetus × Ch. sp. Le1 for the first time. The estimated genetic distance between the sequences of Ch. laetus and Ch. riihimakiensis is 2.3-2.5%. The high similarity in morphology, banding sequences, and the possibility of hybridization indicate a close relationship between Ch. laetus and Ch. sp. Le1, which is assumed to be the northern variant of Ch. riihimakiensis. Molecular genetic data suggests the presence of a subgroup with Ch. laetus.},
}
@article {pmid36555020,
year = {2022},
author = {Lukhtanov, VA and Gagarina, AV},
title = {Molecular Phylogeny and Taxonomy of the Butterfly Subtribe Scolitantidina with Special Focus on the Genera Pseudophilotes, Glaucopsyche and Iolana (Lepidoptera, Lycaenidae).},
journal = {Insects},
volume = {13},
number = {12},
pages = {},
pmid = {36555020},
issn = {2075-4450},
support = {19-14-00202//Russian Science Foundation/ ; },
abstract = {The Palearctic blue butterfly genus Pseudophilotes Beuret, 1958 is not homogenous regarding the morphology of its genital structures. For this reason, some of its species have been considered to be representatives of other genera of the subtribe Scolitantidina (subfamily Polyommatinae). Here, we address these taxonomic problems by analyzing the phylogenetic relationships between the genera, subgenera, and species of this subtribe inferred via the analysis of five nuclear and two mitochondrial DNA sequences. We demonstrate that the enigmatic Asian species P. panope (Eversmann, 1851) belongs to the genus Pseudophilotes but not to Praephilotes Forster, 1938 or Palaeophilotes Forster, 1938 and does not represent the independent genus Inderskia Korshunov, 2000, as hypothesized previously. We synonymize P. svetlana Yakovlev, 2003 (syn. nov.) and P. marina Zhdanko, 2004 (syn. nov.) with P. panope. We demonstrate a deep genetic divergence between lineages that were previously considered as subspecies of the single species Iolana iolas (Ochsenheimer, 1816). As a result, we confirm the multispecies concept of the genus Iolana Bethune-Baker, 1914. We show that the Holarctic genus Glaucopsyche can be divided into four subgenera: Glaucopsyche Scudder, 1872 (=Shijimiaeoides Beuret, 1958), Apelles Hemming, 1931, Bajluana Korshunov and Ivonin, 1990, and Phaedrotes Scudder, 1876.},
}
@article {pmid36553561,
year = {2022},
author = {Devi, MP and Dasgupta, M and Mohanty, S and Sharma, SK and Hegde, V and Roy, SS and Renadevan, R and Kumar, KB and Patel, HK and Sahoo, MR},
title = {DNA Barcoding and ITS2 Secondary Structure Predictions in Taro (Colocasia esculenta L. Schott) from the North Eastern Hill Region of India.},
journal = {Genes},
volume = {13},
number = {12},
pages = {},
pmid = {36553561},
issn = {2073-4425},
mesh = {*DNA Barcoding, Taxonomic ; *Colocasia/genetics ; Plant Breeding ; Phylogeny ; India ; },
abstract = {Taro (Colocasia esculenta L. Schott, Araceae), an ancient root and tuber crop, is highly polygenic, polyphyletic, and polygeographic in nature, which leads to its rapid genetic erosion. To prevent the perceived loss of taro diversity, species discrimination and genetic conservation of promising taro genotypes need special attention. Reports on genetic discrimination of taro at its center of origin are still untapped. We performed DNA barcoding of twenty promising genotypes of taro indigenous to the northeastern hill region of India, deploying two chloroplast-plastid genes, matK and rbcL, and the ribosomal nuclear gene ITS2. The secondary structure of ITS2 was determined and molecular phylogeny was performed to assess genetic discrimination among the taro genotypes. The matK and rbcL genes were highly efficient (>90%) in amplification and sequencing. However, the ITS2 barcode region achieved significant discrimination among the tested taro genotypes. All the taro genotypes displayed most similar sequences at the conserved matK and rbcL loci. However, distinct sequence lengths were observed in the ITS2 barcode region, revealing accurate discriminations among the genotypes. Multiple barcode markers are unrelated to one another and change independently, providing different estimations of heritable traits and genetic lineages; thus, they are advantageous over a single locus in genetic discrimination studies. A dynamic programming algorithm that used base-pairing interactions within a single nucleic acid polymer or between two polymers transformed the secondary structures into the symbol code data to predict seven different minimum free energy secondary structures. Our analysis strengthens the potential of the ITS2 gene as a potent DNA barcode candidate in the prediction of a valuable secondary structure that would help in genetic discrimination between the genotypes while augmenting future breeding strategies in taro.},
}
@article {pmid36553525,
year = {2022},
author = {Yaradua, SS and Yessoufou, K},
title = {The Complete Chloroplast Genome of Hypoestes forskaolii (Vahl) R.Br: Insights into Comparative and Phylogenetic Analyses within the Tribe Justiceae.},
journal = {Genes},
volume = {13},
number = {12},
pages = {},
pmid = {36553525},
issn = {2073-4425},
mesh = {Phylogeny ; *Genome, Chloroplast ; Bayes Theorem ; *Acanthaceae/genetics ; Genomics ; },
abstract = {Hypoestes forskaolii is one of the most important species of the family Acanthaceae, known for its high economic and medicinal importance. It is well distributed in the Arab region as well as on the African continent. Previous studies on ethnomedicine have reported that H. forskaolii has an anti-parasitic effect as well as antimalarial and anthelmintic activities. Previous studies mainly focused on the ethnomedicinal properties, hence, there is no information on the genomic architecture and phylogenetic positions of the species within the tribe Justiceae. The tribe Justicieae is the most taxonomically difficult taxon in Acanthoideae due to its unresolved infratribal classification. Therefore, by sequencing the complete chloroplast genome (cp genome) of H. forskaolii, we explored the evolutionary patterns of the cp genome and reconstructed the phylogeny of Justiceae. The cp genome is quadripartite and circular in structure and has a length of 151,142 bp. There are 130 genes (86 coding for protein, 36 coding for tRNA and 8 coding for rRNA) present in the plastome. Analyses of long repeats showed only three types of repeats: forward, palindromic and reverse were present in the genome. Microsatellites analysis revealed 134 microsatellites in the cp genome with mononucleotides having the highest frequency. Comparative analyses within Justiceae showed that genomes structure and gene contents were highly conserved but there is a slight distinction in the location of the genes in the inverted repeat and single copy junctions. Additionally, it was discovered that the cp genome includes variable hotspots that can be utilized as DNA barcodes and tools for determining evolutionary relationships in the Justiceae. These regions include: atpH-atpI, trnK-rps16, atpB-rbcL, trnT-trnL, psbI-trnS, matK, trnH-psbA, and ndhD. The Bayesian inference phylogenetic tree showed that H. forskaolii is a sister to the Dicliptra clade and belongs to Diclipterinae. The result also confirms the polyphyly of Justicia and inclusion of Diclipterinae within justicioid. This research has revealed the phylogenetic position of H. forskaolii and also reported the resources that can be used for evolutionary and phylogenetic studies of the species and the Justicieae.},
}
@article {pmid36553462,
year = {2022},
author = {Hlaka, V and Biondi, M and Allsopp, E and van Asch, B},
title = {Argopistes sexvittatus and Argopistes capensis (Chrysomelidae: Alticini): Mitogenomics and Phylogeny of Two Flea Beetles Affecting Olive Trees.},
journal = {Genes},
volume = {13},
number = {12},
pages = {},
pmid = {36553462},
issn = {2073-4425},
mesh = {Animals ; Phylogeny ; *Olea/genetics ; *Coleoptera/genetics ; *Siphonaptera ; Biological Evolution ; *Oleaceae/genetics ; },
abstract = {The genus Argopistes (Chrysomelidae: Alticini) is the only group of flea beetles specialized in plant hosts in the family Oleaceae. In southern Africa, Argopistes are often found feeding on African Wild Olive (Olea europaea subsp. cuspidata) and European cultivated olive (O. e. subsp. europaea), and heavy infestations can be devastating to mature trees and compromise the development of young trees. Despite their negative agricultural impact, African Argopistes are an understudied group for which no genetic data were available. We assessed the species diversity of olive flea beetles in the Western Cape province of South Africa, the largest olive-producing region in sub-Saharan Africa, by collecting adult specimens on wild and cultivated olive trees between 2015 and 2017. Argopistes sexvittatus Bryant, 1922 (n = 289) dominated at all sampling sites, and Argopistes capensis Bryant, 1944 (n = 2) was found only once. Argopistes oleae Bryant, 1922, a third species previously reported in the region, was not found. The complete mitogenomes of one A. capensis and two A. sexvittatus (striped and black morphotypes) individuals were sequenced for phylogenetic reconstruction in the context of other 64 species. The two olive flea beetle species form a monophyletic clade with other Argopistes, supporting the hypothesis that the exclusive feeding habit on Oleaceae is an evolutionary adaptation in this genus.},
}
@article {pmid36552809,
year = {2022},
author = {Maetzig, T and Lieske, A and Dörpmund, N and Rothe, M and Kleppa, MJ and Dziadek, V and Hassan, JJ and Dahlke, J and Borchert, D and Schambach, A},
title = {Real-Time Characterization of Clonal Fate Decisions in Complex Leukemia Samples by Fluorescent Genetic Barcoding.},
journal = {Cells},
volume = {11},
number = {24},
pages = {},
pmid = {36552809},
issn = {2073-4409},
mesh = {Animals ; Mice ; *Leukemia, Myeloid, Acute/genetics/pathology ; Clone Cells ; Clonal Evolution/genetics ; Mutation/genetics ; Phenotype ; },
abstract = {Clonal heterogeneity in acute myeloid leukemia (AML) forms the basis for treatment failure and relapse. Attempts to decipher clonal evolution and clonal competition primarily depend on deep sequencing approaches. However, this prevents the experimental confirmation of the identified disease-relevant traits on the same cell material. Here, we describe the development and application of a complex fluorescent genetic barcoding (cFGB) lentiviral vector system for the labeling and subsequent multiplex tracking of up to 48 viable AML clones by flow cytometry. This approach allowed the visualization of longitudinal changes in the in vitro growth behavior of multiplexed color-coded AML clones for up to 137 days. Functional studies of flow cytometry-enriched clones documented their stably inherited increase in competitiveness, despite the absence of growth-promoting mutations in exome sequencing data. Transplantation of aliquots of a color-coded AML cell mix into mice revealed the initial engraftment of similar clones and their subsequent differential distribution in the animals over time. Targeted RNA-sequencing of paired pre-malignant and de novo expanded clones linked gene sets associated with Myc-targets, embryonic stem cells, and RAS signaling to the foundation of clonal expansion. These results demonstrate the potency of cFGB-mediated clonal tracking for the deconvolution of verifiable driver-mechanisms underlying clonal selection in leukemia.},
}
@article {pmid36552287,
year = {2022},
author = {Ding, H and Han, S and Ye, Y and Bi, D and Zhang, S and Yi, R and Gao, J and Yang, J and Wu, L and Kan, X},
title = {Ten Plastomes of Crassula (Crassulaceae) and Phylogenetic Implications.},
journal = {Biology},
volume = {11},
number = {12},
pages = {},
pmid = {36552287},
issn = {2079-7737},
support = {NEL&amp;MARA-003//the Opening Foundation of National Engineering Laboratory of Soil Pollution Control and Remediation Technologies, and Key Laboratory of Heavy Metal Pollution Prevention &amp; Control, Ministry of Agriculture and Rural Affairs/ ; BK20211078//the Basic Research Program (Natural Science Foundation) of Jiangsu Province/ ; YJS20210136//the Scientific Research Project Foundation of Postgraduate of the Anhui Higher Education Institutions of China/ ; },
abstract = {The genus Crassula is the second-largest genus in the family Crassulaceae, with about 200 species. As an acknowledged super-barcode, plastomes have been extensively utilized for plant evolutionary studies. Here, we first report 10 new plastomes of Crassula. We further focused on the structural characterizations, codon usage, aversion patterns, and evolutionary rates of plastomes. The IR junction patterns-IRb had 110 bp expansion to rps19-were conservative among Crassula species. Interestingly, we found the codon usage patterns of matK gene in Crassula species are unique among Crassulaceae species with elevated ENC values. Furthermore, subgenus Crassula species have specific GC-biases in the matK gene. In addition, the codon aversion motifs from matK, pafI, and rpl22 contained phylogenetic implications within Crassula. The evolutionary rates analyses indicated all plastid genes of Crassulaceae were under the purifying selection. Among plastid genes, ycf1 and ycf2 were the most rapidly evolving genes, whereas psaC was the most conserved gene. Additionally, our phylogenetic analyses strongly supported that Crassula is sister to all other Crassulaceae species. Our findings will be useful for further evolutionary studies within the Crassula and Crassulaceae.},
}
@article {pmid36552002,
year = {2022},
author = {Jung, S and Bong, KW and Na, W},
title = {Multiplex Assay for Rapid Detection and Analysis of Nucleic Acid Using Barcode Receptor Encoded Particle (BREP).},
journal = {Biomedicines},
volume = {10},
number = {12},
pages = {},
pmid = {36552002},
issn = {2227-9059},
support = {NRF-2016R1A5A1010148//National Research Foundation of Korea/ ; },
abstract = {Several multiplex nucleic acid assay platforms have been developed in response to the increasing importance of nucleic acid analysis, but these assays should be optimized as per the requirements of point-of-care for clinical diagnosis. To achieve rapid and accurate detection, involving a simple procedure, we propose a new concept in the field of nucleic acid multiplex assay platforms using hydrogel microparticles, called barcode receptor-encoded particles (BREPs). The BREP assay detects multiple targets in a single reaction with a single fluorophore by analyzing graphically encoded hydrogel particles. By introducing sets of artificially synthesized barcode receptor and barcode probes, the BREP assay is easily applicable in multiplexing any genetic target; sets of barcode receptors and barcode probes should be designed delicately for universal application. The performance of the BREP assay was successfully verified in a multiplex assay for the identification of different malaria species with high sensitivity, wide dynamic range, fast detection time, and multiplexibility.},
}
@article {pmid36550273,
year = {2023},
author = {Lorenz, DA and Her, HL and Shen, KA and Rothamel, K and Hutt, KR and Nojadera, AC and Bruns, SC and Manakov, SA and Yee, BA and Chapman, KB and Yeo, GW},
title = {Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP.},
journal = {Nature methods},
volume = {20},
number = {1},
pages = {65-69},
pmid = {36550273},
issn = {1548-7105},
support = {T32 CA067754/CA/NCI NIH HHS/United States ; },
mesh = {*Transcriptome ; *RNA/genetics ; Binding Sites ; Protein Binding ; RNA-Binding Proteins/metabolism ; Antibodies/chemistry ; Immunoprecipitation ; },
abstract = {Ultraviolet crosslinking and immunoprecipitation (CLIP) methodologies enable the identification of RNA binding sites of RNA-binding proteins (RBPs). Despite improvements in the library preparation of RNA fragments, the enhanced CLIP (eCLIP) protocol requires 4 days of hands-on time and lacks the ability to process several RBPs in parallel. We present a new method termed antibody-barcode eCLIP that utilizes DNA-barcoded antibodies and proximity ligation of the DNA oligonucleotides to RBP-protected RNA fragments to interrogate several RBPs simultaneously. We observe performance comparable with that of eCLIP with the advantage of dramatically increased scaling while maintaining the same material requirement of a single eCLIP experiment.},
}
@article {pmid36545803,
year = {2023},
author = {Pais, G and Spinozzi, G and Cesana, D and Benedicenti, F and Albertini, A and Bernardo, ME and Gentner, B and Montini, E and Calabria, A},
title = {ISAnalytics enables longitudinal and high-throughput clonal tracking studies in hematopoietic stem cell gene therapy applications.},
journal = {Briefings in bioinformatics},
volume = {24},
number = {1},
pages = {},
pmid = {36545803},
issn = {1477-4054},
support = {TTEMB0322TT//Telethon Foundation/ ; GR-2016-02363681//Italian Ministry of Health/ ; },
mesh = {Humans ; Clone Cells ; *Genetic Therapy/adverse effects ; *Hematopoietic Stem Cells ; High-Throughput Nucleotide Sequencing ; Reproducibility of Results ; Clinical Trials as Topic ; },
abstract = {Longitudinal clonal tracking studies based on high-throughput sequencing technologies supported safety and long-term efficacy and unraveled hematopoietic reconstitution in many gene therapy applications with unprecedented resolution. However, monitoring patients over a decade-long follow-up entails a constant increase of large data volume with the emergence of critical computational challenges, unfortunately not addressed by currently available tools. Here we present ISAnalytics, a new R package for comprehensive and high-throughput clonal tracking studies using vector integration sites as markers of cellular identity. Once identified the clones externally from ISAnalytics and imported in the package, a wide range of implemented functionalities are available to users for assessing the safety and long-term efficacy of the treatment, here described in a clinical trial use case for Hurler disease, and for supporting hematopoietic stem cell biology in vivo with longitudinal analysis of clones over time, proliferation and differentiation. ISAnalytics is conceived to be metadata-driven, enabling users to focus on biological questions and hypotheses rather than on computational aspects. ISAnalytics can be fully integrated within laboratory workflows and standard procedures. Moreover, ISAnalytics is designed with efficient and scalable data structures, benchmarked with previous methods, and grants reproducibility and full analytical control through interactive web-reports and a module with Shiny interface. The implemented functionalities are flexible for all viral vector-based clonal tracking applications as well as genetic barcoding or cancer immunotherapies.},
}
@article {pmid36544473,
year = {2023},
author = {Zhang, Y and Lin, X and Yao, Z and Sun, D and Lin, X and Wang, X and Yang, C and Song, J},
title = {Deconvolution algorithms for inference of the cell-type composition of the spatial transcriptome.},
journal = {Computational and structural biotechnology journal},
volume = {21},
number = {},
pages = {176-184},
pmid = {36544473},
issn = {2001-0370},
abstract = {The spatial transcriptome has enabled researchers to resolve transcriptome expression profiles while preserving information about cell location to better understand the complex biological processes that occur in organisms. Due to technical limitations, the current high-throughput spatial transcriptome sequencing methods (known as next-generation sequencing with spatial barcoding methods or spot-based methods) cannot achieve single-cell resolution. A single measurement site, called a spot, in these technologies frequently contains multiple cells of various types. Computational tools for determining the cellular composition of a spot have emerged as a way to break through these limitations. These tools are known as deconvolution tools. Recently, a couple of deconvolution tools based on different strategies have been developed and have shown promise in different aspects. The resulting single-cell resolution expression profiles and/or single-cell composition of spots will significantly affect downstream data mining; thus, it is crucial to choose a suitable deconvolution tool. In this review, we present a list of currently available tools for spatial transcriptome deconvolution, categorize them based on the strategies they employ, and explain their advantages and limitations in detail in order to guide the selection of these tools in future studies.},
}
@article {pmid36541960,
year = {2022},
author = {Hassan, S and Naeem, M and Nasir, MF and Riaz, P and Khan, MN and Atiq, I},
title = {Molecular based identification and phylogenetic relationship by using cytochrome b gene of Pangasius pangasius.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {84},
number = {},
pages = {e268001},
doi = {10.1590/1519-6984.268001},
pmid = {36541960},
issn = {1678-4375},
mesh = {Animals ; Phylogeny ; *Cytochromes b/genetics ; *Catfishes/genetics ; DNA Barcoding, Taxonomic/methods ; },
abstract = {Molecular appraoch for identification of unknown species by using Cytochrome b gene is an effective and reliable as compared with morphological based identification. For DNA barcoding universal molecular genes were used to identify the species. Cytochrome b is a specific gene used for identification purpose. DNA barcoding is a reliable and effective method compared to the different traditional morphological methods of specie identification. So,in the present study which was conducted to identify the species, a total of 50 fish samples were collected from five different sites. DNA was extracted by using the Phenol Chloroform method from muscle tissue. Five sequences were sequenced (one from each site), analyzed, and identified specific species as Pangasius pangasius. Identified sequences were variable in length from 369 bp (Site 1), 364 bp (Site 2), 364 bp (Site 3), 352 bp (Site 4), and 334 bp (Site 5). Identity matches on the NCBI database confirmed the specific specie as P. pangasius. A distancing tree was drawn to show maximum likelihood among the same and different species. Yet, in many cases fishes on diverse development stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even an alternative tool for species identification and phylogenetic study. This work intends to provide an updated and extensive overview on the DNA based methods for fish species identification by using Cytochrome b gene as targeted markers for identification purpose.},
}
@article {pmid36541937,
year = {2023},
author = {Long, W and Yang, J and Zhao, Q and Pan, Y and Luan, X and He, B and Han, X and Wang, Y and Song, Y},
title = {Metal-Organic Framework-DNA Bio-Barcodes Amplified CRISPR/Cas12a Assay for Ultrasensitive Detection of Protein Biomarkers.},
journal = {Analytical chemistry},
volume = {95},
number = {2},
pages = {1618-1626},
doi = {10.1021/acs.analchem.2c04737},
pmid = {36541937},
issn = {1520-6882},
mesh = {CRISPR-Cas Systems/genetics ; *Metal-Organic Frameworks ; Biomarkers, Tumor/genetics ; DNA ; Antibodies ; *Biosensing Techniques ; },
abstract = {CRISPR/Cas12a shows excellent potential in disease diagnostics. However, insensitive signal conversion strategies hindered its application in detecting protein biomarkers. Here, we report a metal-organic framework (MOF)-based DNA bio-barcode integrated with the CRISPR/Cas12a system for ultrasensitive detection of protein biomarkers. In this work, zirconium-based MOF nanoparticles were comodified with antibodies and bio-barcode phosphorylated DNA as an efficient signal converter, which not only recognized the protein biomarker to form the sandwich complex but also released the bio-barcode DNA activators after MOF dissociation to activate the trans-cleavage activity of Cas12a. Due to the obvious advantages, including numerous loaded oligonucleotides, a convenient release process, and the nontoxic release reagent, this MOF-DNA bio-barcode strategy could amplify the CRISPR/Cas12a system to achieve simple and highly sensitive detection of tumor protein biomarkers with detection limits of 0.03 pg/mL (PSA) and 0.1 pg/mL (CEA), respectively. Furthermore, this platform could detect PSA directly in clinical serum samples, offering a powerful tool for early disease diagnosis.},
}
@article {pmid36540705,
year = {2022},
author = {Xu, YL and Shen, HH and Du, XY and Lu, L},
title = {Plastome characteristics and species identification of Chinese medicinal wintergreens (Gaultheria, Ericaceae).},
journal = {Plant diversity},
volume = {44},
number = {6},
pages = {519-529},
pmid = {36540705},
issn = {2468-2659},
abstract = {Wintergreen oil is a folk medicine widely used in foods, pesticides, cosmetics and drugs. In China, nine out of 47 species within Gaultheria (Ericaceae) are traditionally used as Chinese medicinal wintergreens; however, phylogenetic approaches currently used to discriminating these species remain unsatisfactory. In this study, we sequenced and characterized plastomes from nine Chinese wintergreen species and identified candidate DNA barcoding regions for Gaultheria. Each Gaultheria plastome contained 110 unique genes (76 protein-coding, 30 tRNA, and four rRNA genes). Duplication of trnfM, rps14, and rpl23 genes were detected, while all plastomes lacked ycf1 and ycf2 genes. Gaultheria plastomes shared substantially contracted SSC regions that contained only the ndhF gene. Moreover, plastomes of Gaultheria leucocarpa var. yunnanensis contained an inversion in the LSC region and an IR expansion to cover the ndhF gene. Multiple rearrangement events apparently occurred between the Gaultheria plastomes and those from several previously reported families in Ericales. Our phylogenetic reconstruction using 42 plastomes revealed well-supported relationships within all nine Gaultheria species. Additionally, seven mutational hotspot regions were identified as potential DNA barcodes for Chinese medicinal wintergreens. Our study is the first to generate complete plastomes and describe the structural variations of the complicated genus Gaultheria. In addition, our findings provide important resources for identification of Chinese medicinal wintergreens.},
}
@article {pmid36539085,
year = {2023},
author = {Csabai, Z and Čiamporová-Zaťovičová, Z and Boda, P and Čiampor, F},
title = {50%, not great, not terrible: Pan-European gap-analysis shows the real status of the DNA barcode reference libraries in two aquatic invertebrate groups and points the way ahead.},
journal = {The Science of the total environment},
volume = {863},
number = {},
pages = {160922},
doi = {10.1016/j.scitotenv.2022.160922},
pmid = {36539085},
issn = {1879-1026},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Invertebrates ; Insecta ; Biodiversity ; *Coleoptera/genetics ; Balkan Peninsula ; },
abstract = {The essential key to routine molecular species identification (DNA barcoding/metabarcoding) is the existence of an error-free DNA barcode reference library providing full coverage of all species. Published studies generally state the need to produce more barcodes, and control their quality, but unfortunately, the number of barcoded species is still low. However, to initiate real progress, we need to know where the gaps lie, how big they are and why they persist. Our aims were to draw and understand the current state of knowledge regarding species diversity, distribution, and barcode coverage, and offer solutions for improvement. In this study, we used two groups of aquatic insects, beetles and true bugs. We have compiled and critically evaluated an essentially complete and up-to-date European list, containing 1527 species. The list served as a basis for the barcode gap analyses in the Barcode-of-Life-Data-System (BOLD) conducted in three subsequent years (2020-2022). The overall barcode coverage of the pan-European fauna was around 50 % in both groups. The lowest coverage was in the Mediterranean, the Balkans and South-eastern Europe. The coverage in each country depended significantly on the local diversity, the number of rare, endemic species and the similarity of its fauna to that of the most active barcoding European countries. Gap analyses showed a very small increase in species coverage (<1 % in European aquatic beetles) despite an ~25 % increase in the number of barcodes. Hence, it is clear that future barcoding campaigns must prioritise quality over quantity. To visibly improve reference libraries, we need to increase the involvement of taxonomic experts and focus on targeted studies and underexplored but biodiversity-rich areas.},
}
@article {pmid36538397,
year = {2023},
author = {Shin, SM and Hernandez, A and Coyne, E and Munjal, K and Gross, NE and Charmsaz, S and Yuan, X and Yang, H and Ho, WJ},
title = {CyTOF protocol for immune monitoring of solid tumors from mouse models.},
journal = {STAR protocols},
volume = {4},
number = {1},
pages = {101949},
pmid = {36538397},
issn = {2666-1667},
support = {P01 CA247886/CA/NCI NIH HHS/United States ; P30 CA006973/CA/NCI NIH HHS/United States ; R21 CA264004/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Mice ; Monitoring, Immunologic ; *Neoplasms/diagnosis ; Disease Models, Animal ; },
abstract = {Techniques for robust immune profiling of mouse tumor and blood are key to understanding immunological responses in mouse models of cancer. Here, we describe mass cytometry (cytometry by time-of-flight) procedures to facilitate high-parameter profiling of low-volume survival blood samples and end-of-study tumor samples. We employ live-cell barcoding systems to mark all cells from each tumor and blood to improve cost-effectiveness and minimize batch effects. For complete details on the use and execution of this protocol, please refer to Charmsaz et al. (2021).[1].},
}
@article {pmid36536920,
year = {2022},
author = {Grover, A and Sharma, P and Sharma, R and Sinha, R},
title = {Ultrastructural and molecular approach as a tool for taxonomic identification of aquatic macroinvertebrates: A review.},
journal = {Heliyon},
volume = {8},
number = {12},
pages = {e12236},
pmid = {36536920},
issn = {2405-8440},
abstract = {Aquatic insects require water at one or other phase for the completion of their life cycle. The insect larvae serve as food for larger invertebrates and vertebrates in aquatic food chain. Their diversity, number, and abundance act as water quality indicators, and thus species are classified accordingly as pollution tolerant or sensitive. So, identifying these aquatic larvae and macroinvertebrates are important for determining the biodiversity, and classification of insect species, followed by assessment of water health, and understanding the influence of climate change and anthropogenetic activities on these. Chances of misidentification have been reported due to loss of expertise, absence of taxonomic keys for larvae or intermediate stages, or damaged structure during collection or preservation. Recent advances in molecular and electron microscopy have revolutionized the identification procedure. Scanning electron microscopy detail the structure and morphology of the insect, while molecular techniques employing PCRs, DNA barcoding, and molecular markers allow the identification of the insects from any tissue (whole/part), and comparing the nucleotide sequences helps in the evaluating the family tree and lineage. The review summarizes the present status of aquatic invertebrates identification and the importance of these two techniques in the taxonomic identification of aquatic insects.},
}
@article {pmid36536265,
year = {2022},
author = {Rizk, SM and Magdy, M and De Leo, F and Werner, O and Rashed, MA and Ros, RM and Urzì, C},
title = {aroF and cm2: potential molecular markers for the detection of stone-inhabiting Actinobacteria on cultural heritage sites.},
journal = {Archives of microbiology},
volume = {205},
number = {1},
pages = {32},
pmid = {36536265},
issn = {1432-072X},
mesh = {*Actinobacteria ; Ecosystem ; Bacteria/genetics ; *Actinomycetales ; },
abstract = {Tangible archeological sites and stone monuments are naturally decayed and deteriorated over time, providing substances that can sustain life, although they provide a complicated ecosystem characterized by low nutrition and desiccation. Stone-inhabiting bacteria (SIB) and especially members of the phylum Actinobacteria dominate such environments, particularly the members of the family Geodermatophilaceae. We used the published data of two confirmed SIB species to mine their genomes for specific molecular markers to rapidly survey the presence of SIB in cultural heritage material prior to further analysis. The search focused on the mycosporine-like amino acids (MAAs) synthesis pathway. MAAs are intracellular compounds biosynthesized by the shikimic acid pathway to synthesize aromatic amino acids and were found related to abiotic resistance features in microorganisms. Based on genome mining, the DAHP II (aroF) and a homolog of the Chorismate mutase gene (cm2) were found mostly in Actinobacteria and few other species. After calibration on five stone-inhabiting Actinobacteria (SIAb) species using conventional PCR, newly designed primers were successfully applied to environmental DNA extracted from two Egyptian pyramidal sites using a qPCR approach. This is the first report of aroF and cm2 as qPCR markers to detect SIAb from cultural heritage material prior to proceeding with further analysis (e.g., metagenomics and meta-barcoding analyses).},
}
@article {pmid36536113,
year = {2022},
author = {D'Agostino, A and Di Marco, G and Marvelli, S and Marchesini, M and Rizzoli, E and Rolfo, MF and Canini, A and Gismondi, A},
title = {Neolithic dental calculi provide evidence for environmental proxies and consumption of wild edible fruits and herbs in central Apennines.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {1384},
pmid = {36536113},
issn = {2399-3642},
mesh = {Humans ; Animals ; *Fruit ; Plants, Edible ; Pollen ; Poaceae ; Forests ; DNA, Ancient ; *Calculi ; },
abstract = {Looking for a biological fingerprint relative to new aspects of the relationship between humans and natural environment during prehistoric times is challenging. Although many issues still need to be addressed in terms of authentication and identification, microparticles hidden in ancient dental calculus can provide interesting information for bridging this gap of knowledge. Here, we show evidence about the role of edible plants for the early Neolithic individuals in the central Apennines of the Italian peninsula and relative cultural landscape. Dental calculi from human and animal specimens exhumed at Grotta Mora Cavorso (Lazio), one of the largest prehistoric burial deposits, have returned an archaeobotanical record made up of several types of palaeoecological proxies. The organic fraction of this matrix was investigated by a multidisciplinary approach, whose novelty consisted in the application of next generation sequencing to ancient plant DNA fragments, specifically codifying for maturase K barcode gene. Panicoideae and Triticeae starches, together with genetic indicators of Rosaceae fruits, figs, and Lamiaceae herbs, suggested subsistence practices most likely still based on wild plant resources. On the other hand, pollen, and non-pollen palynomorphs allowed us to outline a general vegetational framework dominated by woodland patches alternated with meadows, where semi-permanent settlements could have been established.},
}
@article {pmid36532481,
year = {2022},
author = {Leski, TA and Taitt, CR and Colston, SM and Bangura, U and Holtz, A and Yasuda, CY and Reynolds, ND and Lahai, J and Lamin, JM and Baio, V and Ansumana, R and Stenger, DA and Vora, GJ},
title = {Prevalence of malaria resistance-associated mutations in Plasmodium falciparum circulating in 2017-2018, Bo, Sierra Leone.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1059695},
pmid = {36532481},
issn = {1664-302X},
abstract = {INTRODUCTION: In spite of promising medical, sociological, and engineering strategies and interventions to reduce the burden of disease, malaria remains a source of significant morbidity and mortality, especially among children in sub-Saharan Africa. In particular, progress in the development and administration of chemotherapeutic agents is threatened by evolved resistance to most of the antimalarials currently in use, including artemisinins.<br><br>METHODS: This study analyzed the prevalence of mutations associated with antimalarial resistance in Plasmodium falciparum from 95 clinical samples collected from individuals with clinically confirmed malaria at a hospital in Bo, Sierra Leone between May 2017 and December 2018. The combination of polymerase chain reaction amplification and subsequent high throughput DNA sequencing was used to determine the presence of resistance-associated mutations in five P. falciparum genes - pfcrt, pfmdr1, pfdhfr, pfdhps and pfkelch13. The geographic origin of parasites was assigned using mitochondrial sequences.<br><br>RESULTS: Relevant mutations were detected in the pfcrt (22%), pfmdr1 (>58%), pfdhfr (100%) and pfdhps (>80%) genes while no resistance-associated mutations were found in the pfkelch13 gene. The mitochondrial barcodes were consistent with a West African parasite origin with one exception indicating an isolate imported from East Africa.<br><br>DISCUSSION: Detection of the pfmdr1 NFSND haplotype in 50% of the samples indicated the increasing prevalence of strains with elevated tolerance to artemeter + lumefantrine (AL) threatening the combination currently used to treat uncomplicated malaria in Sierra Leone. The frequency of mutations linked to resistance to antifolates suggests widespread resistance to the drug combination used for intermittent preventive treatment during pregnancy.},
}
@article {pmid36530851,
year = {2023},
author = {Frigerio, J and Gorini, T and Palumbo, C and De Mattia, F and Labra, M and Mezzasalma, V},
title = {A Fast and Simple DNA Mini-barcoding and RPA Assay Coupled with Lateral Flow Assay for Fresh and Canned Mackerel Authentication.},
journal = {Food analytical methods},
volume = {16},
number = {2},
pages = {426-435},
pmid = {36530851},
issn = {1936-9751},
abstract = {UNLABELLED: Nowadays, food authentication is more and more required given its relevance in terms of quality and safety. The seafood market is heavily affected by mislabelling and fraudulent substitutions/adulterations, especially for processed food products such as canned food items, due to the loss of morphological features. This study aims to develop new assays based on DNA to identify fresh mackerel (Scomber spp.) and commercial products. A new primer pair was de novo designed on the 5S rRNA gene and non-transcribed spacer (NTS), identifying a DNA mini-barcoding region suitable for species identification of processed commercial products. Moreover, to offer a fast and low-cost analysis, a new assay based on recombinase polymerase amplification (RPA) was developed for the identification of fresh 'Sgombro' (Scomber scombrus) and 'Lanzardo o Occhione' (Scomber japonicus and Scomber colias), coupled with the lateral flow visualisation for the most expensive species (Scomber scombrus) identification. This innovative portable assay has great potential for supply chain traceability in the seafood market.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12161-022-02429-6.},
}
@article {pmid36530410,
year = {2022},
author = {Kilian, IC and Espeland, M and Mey, W and Wowor, D and Hadiaty, RK and von Rintelen, T and Herder, F},
title = {DNA barcoding unveils a high diversity of caddisflies (Trichoptera) in the Mount Halimun Salak National Park (West Java; Indonesia).},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e14182},
pmid = {36530410},
issn = {2167-8359},
mesh = {Animals ; Bayes Theorem ; DNA ; *DNA Barcoding, Taxonomic ; Environmental Biomarkers ; *Holometabola/genetics ; Indonesia ; Insecta/genetics ; Larva/genetics ; Parks, Recreational ; Phylogeny ; },
abstract = {BACKGROUND: Trichoptera are one of the most diverse groups of freshwater insects worldwide and one of the main bioindicators for freshwater quality. However, in many areas, caddisflies remain understudied due to lack of taxonomic expertise. Meanwhile, globally increasing anthropogenic stress on freshwater streams also threatens Trichoptera diversity.<br><br>METHODS: To assess the Trichoptera diversity of the area within and around the Mount Halimun Salak National Park (MHSNP or Taman Nasional Gunung Halimun Salak) in West Java (Indonesia), we conducted a molecular-morphological study on Trichoptera diversity using larvae from a benthic survey and adults from hand-netting. In addition to morphological identification, we applied four different molecular taxon delimitation approaches (Generalized Mixed Yule Coalescent, Bayesian Poisson Tree Processes, Automatic Barcode Gap Discovery and Assemble Species by Automatic Partitioning) based on DNA barcoding of Cytochrome-C-Oxidase I (COI).<br><br>RESULTS: The molecular delimitation detected 72 to 81 Operational Taxonomic Units (OTU). Only five OTUs could be identified to species level by comparing sequences against the BOLD database using BLAST, and four more to the genus level. Adults and larvae could be successfully associated in 18 cases across six families. The high diversity of Trichoptera in this area highlights their potential as bioindicators for water quality assessment.<br><br>CONCLUSIONS: This study provides an example of how molecular approaches can benefit the exploration of hidden diversity in unexplored areas and can be a valuable tool to link life stages. However, our study also highlights the need to improve DNA barcode reference libraries of Trichoptera for the Oriental region.},
}
@article {pmid36529191,
year = {2023},
author = {Chen, H and Dong, H and Yuan, H and Shan, W and Zhou, Q and Li, X and Peng, H and Ma, Y},
title = {Mitochondrial COI and Cytb gene as valid molecular identification marker of sandfly species (Diptera: Psychodidae) in China.},
journal = {Acta tropica},
volume = {238},
number = {},
pages = {106798},
doi = {10.1016/j.actatropica.2022.106798},
pmid = {36529191},
issn = {1873-6254},
mesh = {Animals ; China ; Cytochromes b/genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; *Phlebotomus ; Phylogeny ; *Psychodidae/genetics ; },
abstract = {The accurate identification of sandfly species is crucial because some species transmit medically significant diseases, including leishmaniasis, bartonellosis and sandfly fever. However, due to the high similarity of the external morphology in sandfly species, identification can only be performed using internal morphological characteristics after dissection, which is time consuming and requires highly experienced staff. Thus, the introduction of suitable molecular markers may solve these identification problems. This study screened suitable DNA barcodes to identify common sandfly species in China. The phlebotomine sandflies were collected from Sichuan, Henan and Hainan Provinces from 2014 to 2016. The species were identified by the morphological characteristics of the pharyngeal armature and spermatheca. The genomic DNA of sandfly was extracted individually, and mitochondrial DNA (mtDNA) cytochrome C oxidase subunit I (COI) and cytochrome B (Cytb) as well as the 18S subunit of ribosomal DNA (rDNA) were amplified using polymerase chain reaction (PCR). Additionally, intraspecific and interspecific differences (p-distance) were calculated to evaluate the feasibility of the three gene fragments as a DNA barcode. The phylogeny trees of all sandfly species in this study were constructed using neighbor joining (NJ) method. Six species were identified by the morphological features, belonging to Phlebotomus and Sergentomyia, as Ph. chinensis s. l., Ph. stantoni, Se. bailyi, Se. iyengari, Se. squamirostris, and Se. squamipleuris. Analysis based on three gene fragments revealed some degree of intraspecific polymorphism among these sandfly species in China. The largest intraspecific variation occurred in Ph. chinensis s. l. (mtDNA COI, p-distance = 0.042; mtDNA Cytb, p-distance = 0.071), but the 18S rDNA fragment showed a small variation (p-distance = 0.005). The ranges of interspecific p-distances for mtDNA COI and mtDNA Cytb were 0.138 - 0.231 and 0.128 - 0.274, respectively. However, the interspecific p-distances of 18S rDNA are relatively low ranging from 0.003 to 0.055. Both mitochondrial COI and Cytb gene fragments are valid molecular identification markers in theses sandfly species. The topological structure of phylogeny trees based on mtDNA COI, mtDNA Cytb and 18S rDNA genes were all consistent with morphological classification. And we also found there were significant intraspecies differences within Ph. chinensis s. l. (0.006-0.071) and Se. bailyi (0.002-0.032) based on mtDNA Cytb gene fragment. Sequence alignment data suggested that Ph. chinensis s. l. from Sichuan should be Ph. sichuanensis, and the sandfly specimen collected from Henan was Ph. chinensis s. s.. There could be cryptic species in Se. bailyi from China.},
}
@article {pmid36527715,
year = {2023},
author = {Alvarez-Arevalo, M and Sterndorff, EB and Faurdal, D and Jørgensen, TS and Mourched, AS and Vuksanovic, O and Saha, S and Weber, T},
title = {Extraction and Oxford Nanopore sequencing of genomic DNA from filamentous Actinobacteria.},
journal = {STAR protocols},
volume = {4},
number = {1},
pages = {101955},
pmid = {36527715},
issn = {2666-1667},
mesh = {Sequence Analysis, DNA/methods ; *Actinobacteria/genetics ; *Nanopore Sequencing ; DNA ; Bacteria ; Genomics/methods ; },
abstract = {Actinomycetota (Actinobacteria) is an ecologically and industrially important phylum which is challenging to extract pure high-molecular-weight (HMW) DNA from. This protocol provides a parallelized, cost-effective, and straightforward approach for consistently extracting pure HMW DNA using modified non-toxic commercial kits suitable for higher throughput applications. We further provide a workflow for sequencing and assembly of complete genomes using an optimized Oxford Nanopore rapid barcoding protocol and Illumina data error correction.},
}
@article {pmid36527458,
year = {2023},
author = {Thakral, D and Singh, VK and Gupta, R and Jha, N and Khan, A and Kaur, G and Rai, S and Kumar, V and Supriya, M and Bakhshi, S and Seth, R},
title = {Integrated single-cell transcriptome analysis of CD34 + enriched leukemic stem cells revealed intra- and inter-patient transcriptional heterogeneity in pediatric acute myeloid leukemia.},
journal = {Annals of hematology},
volume = {102},
number = {1},
pages = {73-87},
pmid = {36527458},
issn = {1432-0584},
support = {No. 55/4/10/CARE-AML/2018-NCD-II//Indian Council of Medical Research/ ; },
mesh = {Child ; Humans ; *Leukemia, Myeloid, Acute/genetics/metabolism ; Single-Cell Gene Expression Analysis ; Antigens, CD34/metabolism ; Gene Expression Profiling ; Stem Cells/metabolism ; Neoplastic Stem Cells/metabolism ; Receptors, Lysophosphatidic Acid/genetics/metabolism ; },
abstract = {To gain insights into the idiosyncrasies of CD34 + enriched leukemic stem cells, we investigated the nature and extent of transcriptional heterogeneity by single-cell sequencing in pediatric AML. Whole transcriptome analysis of 28,029 AML single cells was performed using the nanowell cartridge-based barcoding technology. Integrated transcriptional analysis identified unique leukemic stem cell clusters of each patient and intra-patient heterogeneity was revealed by multiple LSC-enriched clusters differing in their cell cycle processes and BCL2 expression. All LSC-enriched clusters exhibited gene expression profile of dormancy and self-renewal. Upregulation of genes involved in non-coding RNA processing and ribonucleoprotein assembly were observed in LSC-enriched clusters relative to HSC. The genes involved in regulation of apoptotic processes, response to cytokine stimulus, and negative regulation of transcription were upregulated in LSC-enriched clusters as compared to the blasts. Validation of top altered genes in LSC-enriched clusters confirmed upregulation of TCF7L2, JUP, ARHGAP25, LPAR6, and PRDX1 genes, and serine/threonine kinases (STK24, STK26). Upregulation of LPAR6 showed trend towards MRD positive status (Odds ratio = 0.126; 95% CI = 0.0144-1.10; p = 0.067) and increased expression of STK26 significantly correlated with higher RFS (HR = 0.231; 95% CI = 0.0506-1.052; p = 0.04). Our findings addressed the inter- and intra-patient diversity within AML LSC and potential signaling and chemoresistance-associated targets that warrant investigation in larger cohort that may guide precision medicine in the near future.},
}
@article {pmid36526120,
year = {2023},
author = {Aslam, M and Naeem, F and Seher, R and Zubair Shabbir, M and Shehzad, W and Imran, M},
title = {Effect of storage temperature and duration on direct PCR amplification of various feather types and DBS matrices.},
journal = {Gene},
volume = {854},
number = {},
pages = {147116},
doi = {10.1016/j.gene.2022.147116},
pmid = {36526120},
issn = {1879-0038},
mesh = {Animals ; Temperature ; *Feathers ; *Specimen Handling/methods ; Reproducibility of Results ; Polymerase Chain Reaction/methods ; DNA/genetics ; },
abstract = {The use of direct PCR has been pioneered over the last decade for DNA analysis of biological specimens of distinct origins. The information on how longer these specimens can be stored and amplified by direct PCR is however scanty. Such a piece of information could expedite research and diagnostic studies without compromising the reliability of results. The current study was therefore designed to analyze the effect of storage temperature and duration on direct PCR amplification of biological specimens having either low quantity or high quantity of DNA. Whole blood, dried blood spots (DBS), and feathers from chicken were stored for five years at three different temperatures, viz. room temperature (∼25 °C), 4 °C, and -20 °C. These samples were subjected to crude DNA extraction by diluting them in PBS buffer and heating at 98 °C after 1 day, 7 days, 15 days, 1 month, 3 months, 6 months, 1 year, 3 years and 5 years of storage. The crude DNA was PCR-amplified with the use of DNA sexing primers as well as DNA barcoding primers. Incubation at 98 °C for 10 min of any type of sample in PBS buffer was sufficient for crude DNA extraction. There was irrelevant impact of feather type, DBS matrix nature and storage temperature on amplification success over the period of analysis. It was possible to successfully accomplish the amplification of 96 samples with the use of routine PCR reagents within 3.5-6.0 hrs. In short, economical and fast genetic analysis of commonly used avian samples is feasible after their storage for longer time at room temperature.},
}
@article {pmid36525348,
year = {2023},
author = {Januszyk, M and Griffin, M and Mascharak, S and Talbott, HE and Chen, K and Henn, D and Spielman, AF and Parker, JBL and Liang, NE and Cotterell, A and Guardino, N and Foster, DS and Wagh, D and Coller, J and Gurtner, GC and Wan, DC and Longaker, MT},
title = {Multiplexed evaluation of mouse wound tissue using oligonucleotide barcoding with single-cell RNA sequencing.},
journal = {STAR protocols},
volume = {4},
number = {1},
pages = {101946},
pmid = {36525348},
issn = {2666-1667},
support = {F32 CA239312/CA/NCI NIH HHS/United States ; U01 DK119094/DK/NIDDK NIH HHS/United States ; R01 GM116892/GM/NIGMS NIH HHS/United States ; R01 DE027346/DE/NIDCR NIH HHS/United States ; K08 DK134871/DK/NIDDK NIH HHS/United States ; R01 GM136659/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Mice ; Rats ; Animals ; Swine ; *Oligonucleotides ; *Skin Neoplasms ; Wound Healing/genetics ; Sequence Analysis, RNA ; },
abstract = {Despite its rapidly increased availability for the study of complex tissue, single-cell RNA sequencing remains prohibitively expensive for large studies. Here, we present a protocol using oligonucleotide barcoding for the tagging and pooling of multiple samples from healing wounds, which are among the most challenging tissue types for this application. We describe steps to generate skin wounds in mice, followed by tissue harvest and oligonucleotide barcoding. This protocol is also applicable to other species including rats, pigs, and humans. For complete details on the use and execution of this protocol, please refer to Stoeckius et al. (2018),[1] Galiano et al. (2004),[2] and Mascharak et al. (2022).[3].},
}
@article {pmid36525288,
year = {2022},
author = {Wild, SA and Cannell, IG and Nicholls, A and Kania, K and Bressan, D and , and Hannon, GJ and Sawicka, K},
title = {Clonal transcriptomics identifies mechanisms of chemoresistance and empowers rational design of combination therapies.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {36525288},
issn = {2050-084X},
support = {C9545/A24042/CRUK_/Cancer Research UK/United Kingdom ; 29567/CRUK_/Cancer Research UK/United Kingdom ; 16942/CRUK_/Cancer Research UK/United Kingdom ; C14303/A21143/CRUK_/Cancer Research UK/United Kingdom ; P30 CA008748/CA/NCI NIH HHS/United States ; 21143/CRUK_/Cancer Research UK/United Kingdom ; C14303/A19926/CRUK_/Cancer Research UK/United Kingdom ; C14303/A19927/CRUK_/Cancer Research UK/United Kingdom ; },
mesh = {Humans ; Mice ; Animals ; *Drug Resistance, Neoplasm/genetics ; Nuclear Proteins ; Transcriptome ; Asparagine ; Transcription Factors ; *Triple Negative Breast Neoplasms/pathology ; Taxoids/pharmacology/therapeutic use ; },
abstract = {Tumour heterogeneity is thought to be a major barrier to successful cancer treatment due to the presence of drug resistant clonal lineages. However, identifying the characteristics of such lineages that underpin resistance to therapy has remained challenging. Here, we utilise clonal transcriptomics with WILD-seq; Wholistic Interrogation of Lineage Dynamics by sequencing, in mouse models of triple-negative breast cancer (TNBC) to understand response and resistance to therapy, including BET bromodomain inhibition and taxane-based chemotherapy. These analyses revealed oxidative stress protection by NRF2 as a major mechanism of taxane resistance and led to the discovery that our tumour models are collaterally sensitive to asparagine deprivation therapy using the clinical stage drug L-asparaginase after frontline treatment with docetaxel. In summary, clonal transcriptomics with WILD-seq identifies mechanisms of resistance to chemotherapy that are also operative in patients and pin points asparagine bioavailability as a druggable vulnerability of taxane-resistant lineages.},
}
@article {pmid36523621,
year = {2022},
author = {Taghipour, E and Bog, M and Frootan, F and Shojaei, S and Rad, N and Arezoumandi, M and Jafari, M and Salmanian, AH},
title = {DNA barcoding and biomass accumulation rates of native Iranian duckweed species for biotechnological applications.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {1034238},
pmid = {36523621},
issn = {1664-462X},
abstract = {The Lemnaceae family (duckweed) consists of at least three recognized genera with six reported species in Iran that are distributed in wetlands. Duckweeds are the simplest and smallest flowering aquatic monocots with free-floating fronds that can reproduce asexually every 2-3 days. Duckweed could be a major source of balanced amino acids and high protein content, which is increasingly promising for biotechnological applications. For molecular classification and species identification of the collected samples, DNA barcoding was performed using two standard chloroplast markers, the spacer region between the ATP synthase subunits F and H (atpF-atpH) and the intron region of the ribosomal protein S16 (rps16). The results confirm the presence of four species belonging to the two genera Lemna and Spirodela. In addition, L. turionifera was detected for the first time in Iran. Due to the high growth rates of duckweed, measurement of biomass accumulation and doubling time are important factors in determining growth potential, especially for native species. The relative growth rates (RGR), doubling times (DT), biomass accumulation, and relative weekly yields (RY) of 40 distinct duckweed clones were determined under standard cultivation conditions. The dry weight-based RGR ranged from 0.149 to more than 0.600 per day, DT from 1.12 to 9 days, and RY from 7 to 108.9 per week. All values are comparable with previous studies. RGR and RY of selected clones are higher than the growth potential for a wide range of wild plants and common crops. These data support that native duckweed has high productivity value and should be further investigated as a potentially rich protein source for alternative human food, livestock feed, and recombinant protein production.},
}
@article {pmid36521071,
year = {2022},
author = {Paunovska, K and Da Silva Sanchez, AJ and Lokugamage, MP and Loughrey, D and Echeverri, ES and Cristian, A and Hatit, MZC and Santangelo, PJ and Zhao, K and Dahlman, JE},
title = {The Extent to Which Lipid Nanoparticles Require Apolipoprotein E and Low-Density Lipoprotein Receptor for Delivery Changes with Ionizable Lipid Structure.},
journal = {Nano letters},
volume = {22},
number = {24},
pages = {10025-10033},
doi = {10.1021/acs.nanolett.2c03741},
pmid = {36521071},
issn = {1530-6992},
support = {R01 GM132985/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Mice ; *Apolipoproteins E/genetics ; *Lipoproteins, LDL/genetics ; Mice, Knockout ; *Nanoparticles/chemistry ; RNA, Messenger/chemistry ; },
abstract = {Lipid nanoparticles (LNPs) have delivered therapeutic RNA to hepatocytes in humans. Adsorption of apolipoprotein E (ApoE) onto these clinical LNP-mRNA drugs has been shown to facilitate hepatocyte entry via the low-density lipoprotein receptor (LDLR). Since ApoE-LDLR trafficking is conserved in mice, non-human primates, and humans, characterizing this mechanism eased clinical transition. Recently, LNPs have delivered mRNA to non-hepatocytes in mice and non-human primates, suggesting they can target new cell types via ApoE- and LDLR-independent pathways. To test this hypothesis, we quantified how 60 LNPs delivered mRNA with cell type resolution in wild-type mice and three knockout mouse strains related to lipid trafficking: ApoE[-/-], LDLR[-/-], and PCSK9[-/-]. These data suggest that the hydrophobic tail length of diketopiperazine-based lipids can be changed to drive ApoE- and LDLR-independent delivery in vivo. More broadly, the results support the hypothesis that endogenous LNP trafficking can be tuned by modifying lipid chemistry.},
}
@article {pmid36520800,
year = {2022},
author = {Halmschlag, CB and Carneiro de Melo Moura, C and Brambach, F and Siregar, IZ and Gailing, O},
title = {Molecular and morphological survey of Lamiaceae species in converted landscapes in Sumatra.},
journal = {PloS one},
volume = {17},
number = {12},
pages = {e0277749},
pmid = {36520800},
issn = {1932-6203},
mesh = {*Ecosystem ; Indonesia ; Rubber ; *Lamiaceae/genetics ; Trees/genetics ; DNA Barcoding, Taxonomic ; },
abstract = {Molecular biodiversity surveys have been increasingly applied in hyperdiverse tropical regions as an efficient tool for rapid species assessment of partially undiscovered fauna and flora. This is done by overcoming shortfalls in knowledge or availability of reproductive structures during the sampling period, which often represents a bottleneck for accurate specimens' identification. DNA sequencing technology is intensifying species discovery, and in combination with morphological identification, has been filling gaps in taxonomic knowledge and facilitating species inventories of tropical ecosystems. This study aimed to apply morphological taxonomy and DNA barcoding to assess the occurrence of Lamiaceae species in converted land-use systems (old-growth forest, jungle rubber, rubber, and oil palm) in Sumatra, Indonesia. In this species inventory, we detected 89 specimens of Lamiaceae from 18 species distributed in seven subfamilies from the Lamiaceae group. One third of the species identified in this study lacked sequences in the reference database for at least one of the markers used (matK, rbcL, and ITS). The three loci species-tree recovered a total of 12 out of the 18 species as monophyletic lineages and can be employed as a suitable approach for molecular species assignment in Lamiaceae. However, for taxa with a low level of interspecific genetic distance in the barcode regions used in this study, such as Vitex gamosepala Griff. and V. vestita Wall. ex Walp., or Callicarpa pentandra Roxb. and C. candidans (Burm.f.) Hochr., the use of traditional taxonomy remains indispensable. A change in species composition and decline in abundance is associated with an increase in land-use intensification at the family level (i.e., Lamiaceae), and this tendency might be constant across other plant families. For this reason, the maintenance of forest genetic resources needs to be considered for sustainable agricultural production, especially in hyperdiverse tropical regions. Additionally, with this change in species composition, accurate species identification throughout molecular assignments will become more important for conservation planning.},
}
@article {pmid36520388,
year = {2023},
author = {Clemmensen, KE and Ihrmark, K and Durling, MB and Lindahl, BD},
title = {Sample Preparation for Fungal Community Analysis by High-Throughput Sequencing of Barcode Amplicons.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2605},
number = {},
pages = {37-64},
pmid = {36520388},
issn = {1940-6029},
mesh = {*Mycobiome/genetics ; DNA, Fungal/genetics ; DNA Primers/genetics ; Fungi/genetics ; High-Throughput Nucleotide Sequencing/methods ; Soil ; },
abstract = {Fungal species participate in vast numbers of processes in the landscape around us. However, their cryptic mycelial growth, inside various substrates and in highly diverse species assemblages, has been a major obstacle to thorough analysis of fungal communities, hampering exhaustive description of the fungal kingdom. Technological developments allowing rapid, high-throughput sequencing of mixed communities from many samples at once are currently having a tremendous impact in fungal community ecology. Universal DNA extraction followed by amplification and sequencing of fungal species-level barcodes such as the nuclear internal transcribed spacer (ITS) region now enables identification and relative quantification of fungal community members across well-replicated experimental settings.Here, we present the sample preparation procedure presently used in our laboratory for fungal community analysis by high-throughput sequencing of amplified ITS2 markers. We focus on the procedure optimized for studies of total fungal communities in humus-rich soils, wood, and litter. However, this procedure can be applied to other sample types and markers. We focus on the laboratory-based part of sample preparation, i.e., the procedure from the point where samples enter the laboratory until amplicons are submitted for sequencing. Our procedure comprises four main parts: (1) universal DNA extraction, (2) optimization of PCR conditions, (3) production of tagged ITS amplicons, and (4) preparation of the multiplexed amplicon pool to be sequenced. The presented procedure is independent of the specific high-throughput sequencing technology used, which makes it highly versatile.},
}
@article {pmid36519933,
year = {2023},
author = {Conti, A and Casagrande Pierantoni, D and Robert, V and Corte, L and Cardinali, G},
title = {MinION Sequencing of Yeast Mock Communities To Assess the Effect of Databases and ITS-LSU Markers on the Reliability of Metabarcoding Analysis.},
journal = {Microbiology spectrum},
volume = {11},
number = {1},
pages = {e0105222},
pmid = {36519933},
issn = {2165-0497},
mesh = {Humans ; *Saccharomyces cerevisiae/genetics ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; DNA, Ribosomal/genetics ; *Microbiota ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Microbial communities play key roles both for humans and the environment. They are involved in ecosystem functions, maintaining their stability, and provide important services, such as carbon cycle and nitrogen cycle. Acting both as symbionts and as pathogens, description of the structure and composition of these communities is important. Metabarcoding uses ribosomal DNA (rDNA) (eukaryotic) or rRNA gene (prokaryotic) sequences for identification of species present in a site and measuring their abundance. This procedure requires several technical steps that could be source of bias producing a distorted view of the real community composition. In this work, we took advantage of an innovative "long-read" next-generation sequencing (NGS) technology (MinION) amplifying the DNA spanning from the internal transcribed spacer (ITS) to large subunit (LSU) that can be read simultaneously in this platform, providing more information than "short-read" systems. The experimental system consisted of six fungal mock communities composed of species present at various relative amounts to mimic natural situations characterized by predominant and low-frequency species. The influence of the sequencing platform (MinION and Illumina MiSeq) and the effect of different reference databases and marker sequences on metagenomic identification of species were evaluated. The results showed that the ITS-based database provided more accurate species identification than LSU. Furthermore, a procedure based on a preliminary identification with standard reference databases followed by the production of custom databases, including only the best outputs of the first step, is proposed. This additional step improved the estimate of species proportion of the mock communities and reduced the number of ghost species not really present in the simulated communities. IMPORTANCE Metagenomic analyses are fundamental in many research areas; therefore, improvement of methods and protocols for the description of microbial communities becomes more and more necessary. Long-read sequencing could be used for reducing biases due to the multicopy nature of rDNA sequences and short-read limitations. However, these novel technologies need to be assessed and standardized with controlled experiments, such as mock communities. The interest behind this work was to evaluate how long reads performed identification and quantification of species mixed in precise proportions and how the choice of database affects such analyses. Development of a pipeline that mitigates the effect of the barcoding sequences and the impact of the reference database on metagenomic analyses can help microbiome studies go one step further.},
}
@article {pmid36519619,
year = {2022},
author = {Wei, X and Cai, L and Chen, H and Shang, L and Zhao, Y and Sun, W},
title = {Noninvasive Multiplexed Analysis of Bladder Cancer-Derived Urine Exosomes via Janus Magnetic Microspheres.},
journal = {Analytical chemistry},
volume = {94},
number = {51},
pages = {18034-18041},
doi = {10.1021/acs.analchem.2c04408},
pmid = {36519619},
issn = {1520-6882},
mesh = {Humans ; *Exosomes/chemistry ; Microspheres ; *Urinary Bladder Neoplasms/urine ; Urinary Bladder ; Magnetic Phenomena ; },
abstract = {Bladder cancer greatly endangers human health, and its early diagnosis is of vital importance. Exosomes, which contain proteins and nucleic acids related to their source cells, are expected to be an emerging biomarker for bladder cancer detection. Here, we propose a novel system for multiplexed analysis of bladder cancer-derived urine exosomes based on Janus magnetic microspheres as barcoded microcarriers. The microcarriers are constructed by droplet-templated coassembly of colloidal silica nanoparticles and magnetic nanoparticles under a magnetic field. The microcarriers possess one hemisphere with structural color and the other hemisphere with magneto-responsiveness. Benefiting from the unique structure, these Janus microcarriers could serve as barcodes and could move controllably in a sample solution, thus realizing the multiplex detection of exosomes with high sensitivity. Notably, the present platform is noninvasive since a urine specimen, as an ideal source of bladder cancer-derived exosomes, is employed as the sample solution. This feature, together with the good sensitivity, specificity, low sample consumption, and easy operation, indicates the great potential of the platform for bladder cancer diagnosis in clinical applications.},
}
@article {pmid36518272,
year = {2022},
author = {MacIvor, JS and de Keyzer, CW and Marshall, MS and Thurston, GS and Onuferko, TM},
title = {Establishment of the non-native horned-face bee Osmia cornifrons and the taurus mason bee Osmia taurus (Hymenoptera: Megachilidae) in Canada.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e14216},
pmid = {36518272},
issn = {2167-8359},
mesh = {Bees ; Animals ; *Hymenoptera ; Pollination ; Ontario ; Quebec ; Agriculture ; },
abstract = {Established populations of the non-native horned-face bee, Osmia cornifrons (Radoszkowski, 1887), and the taurus mason bee, Osmia taurus Smith, 1873 (Hymenoptera: Megachilidae), have been identified from Canada for the first time. In the US, the importation of O. cornifrons, beginning in the 1970s, led to its release for agricultural crop pollination and spread across the country. In this article, we report on O. cornifrons captured while sampling wild bees in Toronto, Ontario using hand nets, bug vacuums, and vane traps, as well as established populations in trap nests, from 2017-2020. The morphologically similar O. taurus, which was accidentally introduced to the US with shipments of imported O. cornifrons, was also recorded in our samples. Recently, a few individual O. taurus specimens have been identified from Ontario and Quebec; however, the extent of our sampling included nests, indicating it is also established in Canada. Others have shown its population growth to have been associated with concordant declines in abundances of native mason bee species in the US, and similar impacts are possible in Canada if action is not taken. We propose three non-mutually exclusive possible pathways for the arrival of O. cornifrons, as well as O. taurus, in Canada: (1) natural migration northward from non-native populations in the US, (2) international importation in the 1980s-2000s to support agricultural research programs, and (3) unintentional release of mason bee cocoons purchased from non-local vendors. We argue that a focus on enhancing populations of locally occurring native bees and stronger policy on the importation and sale of non-native bees are needed.},
}
@article {pmid36517737,
year = {2022},
author = {Koohdar, F and Sheidai, M},
title = {Molecular barcoding of Melissa officinalis L. (badranjboye) in Iran and identification of adulteration in its medicinal services.},
journal = {BMC plant biology},
volume = {22},
number = {1},
pages = {587},
pmid = {36517737},
issn = {1471-2229},
mesh = {DNA, Chloroplast ; DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; *Melissa/genetics ; Phylogeny ; Iran ; *Plants, Medicinal/genetics ; },
abstract = {Medicinal plants are an important source for treatment of diseases in many countries. Today, controlling the quality of the products of medicinal plants is an important task. Customer health may be in danger due to the fraud and misconduct by the sales associates in the sales centers. Melissa officinalis L. (Lamiaceae) is an important medicinal plant used for treatment of several diseases. In Iran, the species of Dracocephalum, Hymencrater, Nepeta and Stachys are mistakenly sold under the name of Badranjboye that have different pharmaceutical properties. For avoiding this mistake, this investigation was performed with the following aims: 1) Checking for the cheating and identifying the Badranjboye in the Iran's market of medicinal plants, 2) Providing the molecular barcode for the medicinal species of Melissa. For this purpose, Market-sold plant samples (leaves) and original reference plant species were compared by morphology, odor as well as Internal transcribed spacer (ITS) and chloroplast DNA ((psbA-trnH) and (trnL-trnF)) sequences. Various molecular analyses, such as sequencing, determination of genetic distance, and construction of phylogenetic tree were performed. These reports have shown that internal transcribed spacer (ITS) and chloroplast DNA (psbA-trnH) sequences are an efficient molecular marker to produce barcode gap and differentiating Melissa officinalis from other species.},
}
@article {pmid36516431,
year = {2023},
author = {Ngai, HL and Kong, BL and Lau, DT and Shaw, PC},
title = {Differentiation of Lingxiaohua and Yangjinhua by chloroplast genome sequencing and DNA barcoding markers.},
journal = {Genome},
volume = {66},
number = {2},
pages = {21-33},
doi = {10.1139/gen-2022-0063},
pmid = {36516431},
issn = {1480-3321},
mesh = {DNA Barcoding, Taxonomic/methods ; DNA, Plant/genetics ; *Genome, Chloroplast ; *Plants, Medicinal/genetics ; Chloroplasts/genetics ; Genetic Markers ; DNA, Chloroplast/genetics ; },
abstract = {Lingxiaohua (Campsis Flos, Campsis grandiflora (Thunb.) K. Schum) is a medicinal herb used for promoting diuresis and treating blood-related disorders by the promotion of blood circulation. It also possesses anti-inflammatory and antioxidative properties. This non-poisonous plant is frequently confused with poisonous Yangjinhua (Daturae Metelis Flos, Datura metel Linnaeus) in the market, resulting in serious anticholinergic poisoning. The confusion of these two herbs is due to the similarity in their appearances. In our study, we compared the complete chloroplast genomes of the two plants and found that they are very different in terms of their gene content and gene arrangement. There were also significant differences in the number and repeating motifs of microsatellites and complex repeats. We used universal primers for the amplification of rbcL, matK, psbA-trnH, and ITS2 regions and successfully differentiated the two plants. Furthermore, we designed two pairs of primers based on the nucleotide differences in chloroplast genomes at the rps14 and rpoC1 regions to provide additional authentication markers. The universal primers and specific primers when used together can accurately discriminate Lingxiaohua and Yangjinhua.},
}
@article {pmid36515500,
year = {2022},
author = {Martel, R and Shen, ML and DeCorwin-Martin, P and de Araujo, LOF and Juncker, D},
title = {Extracellular Vesicle Antibody Microarray for Multiplexed Inner and Outer Protein Analysis.},
journal = {ACS sensors},
volume = {7},
number = {12},
pages = {3817-3828},
pmid = {36515500},
issn = {2379-3694},
mesh = {*Extracellular Vesicles/metabolism ; Antibodies ; },
abstract = {Proteins are found both outside and inside of extracellular vesicles (EVs) and govern the properties and functions of EVs, while also constituting a signature of the cell of origin and of biological function and disease. Outer proteins on EVs can be directly bound by antibodies to either enrich EVs, or probe the expression of a protein on EVs, including in a combinatorial manner. However, co-profiling of inner proteins remains challenging. Here, we present the high-throughput, multiplexed analysis of EV inner and outer proteins (EVPio). We describe the optimization of fixation and heat-induced protein epitope retrieval for EVs, along with oligo-barcoded antibodies and branched DNA signal amplification for sensitive, multiplexed, and high-throughput assays. We captured four subpopulations of EVs from colorectal cancer (CRC) cell lines HT29 and SW403 based on EpCAM, CD9, CD63, and CD81 expression, and quantified the co-expression of eight outer [integrins (ITGs) and tetraspanins] and four inner (heat shock, endosomal, and inner leaflet) proteins. The differences in co-expression patterns were consistent with the literature and known biological function. In conclusion, EVPio analysis can simultaneously detect multiple inner and outer proteins in EVs immobilized on a surface, opening the way to extensive combinatorial protein profiles for both discovery and clinical translation.},
}
@article {pmid36514136,
year = {2022},
author = {Sunil-Chandra, NP and Fahlman, &#xc5; and Waidyarathna, S and Näslund, J and Jayasundara, MVML and Wesula, LO and Bucht, G},
title = {Evidence of orthohantavirus and leptospira infections in small mammals in an endemic area of Gampaha district in Sri Lanka.},
journal = {One health outlook},
volume = {4},
number = {1},
pages = {17},
pmid = {36514136},
issn = {2524-4655},
support = {2017-05479//Swedish Research Council/ ; 2013-6722//Swedish Research Links Program/ ; },
abstract = {BACKGROUND: Orthohantaviruses and leptospira are emerging zoonotic pathogens of high public health significance. The epidemiology of orthohantavirus infections and leptospirosis is similar and presents related clinical pictures in humans. However, a paucity of data on actual reservoir hosts for orthohantaviruses and leptospira exists. Therefore, this study aimed at determining the occurrence of orthohantaviruses and leptospira in small mammals captured in an endemic region of Sri Lanka.<br><br>METHODS: Rodents and shrews were morphologically and/or genetically identified using morphological keys and DNA barcoding techniques targeting the cytochrome oxidase b subunit gene (Cytb). Lung tissues and sera were subsequently analyzed for the presence of orthohantavirus RNA using qRT-PCR. Sera of rats were tested for IgG antibodies against orthohantaviruses and leptospira.<br><br>RESULTS: Forty-three (43) small mammals representing: Rattus (R.) rattus (black rat) or R. tanezumi (Asian rat), Suncus murinus (Asian house shrew), R. norvegicus (brown rat) and Mus musculus (house mouse) were investigated. No orthohantavirus RNA was detected from the lung tissue or serum samples of these animals. Elevated levels of IgG antibodies against Puumala orthohantavirus (PUUV) and/or Seoul orthohantavirus (SEOV) antigens were detected in sera of 28 (72%) out of the 39 rats analysed. Interestingly, 36 (92%) of the 39 rats also showed presence of anti leptospira-IgG antibodies in their serum, representing dual infection or dual exposure in 26/39 (66.7%) of examined rats.<br><br>CONCLUSIONS: This project targets important public health questions concerning the occupational risk of orthohantavirus infections and/or leptospirosis in an endemic region of Sri Lanka. Most rats (72%) in our study displayed antibodies reacting to orthohantavirus NP antigens, related to PUUV and/or SEOV. No correlation between the orthohantavirus and leptospira IgG antibody levels were noticed. Finally, a combination of both morphological and DNA barcoding approaches revealed that several species of rats may play a role in the maintenance and transmission of orthohantavirus and leptospira in Sri Lanka.},
}
@article {pmid36512680,
year = {2022},
author = {Cai, Q and Shi, H and Sun, M and Ma, N and Wang, R and Yang, W and Qiao, Z},
title = {Sensitive Detection of Salmonella Based on CRISPR-Cas12a and the Tetrahedral DNA Nanostructure-Mediated Hyperbranched Hybridization Chain Reaction.},
journal = {Journal of agricultural and food chemistry},
volume = {70},
number = {51},
pages = {16382-16389},
doi = {10.1021/acs.jafc.2c05831},
pmid = {36512680},
issn = {1520-5118},
mesh = {Humans ; Gold ; CRISPR-Cas Systems ; *Metal Nanoparticles ; *Nanostructures ; Salmonella/genetics ; *Biosensing Techniques ; },
abstract = {Salmonella severely threatens global human health and causes financial burden. The ability to sensitively detect Salmonella in food samples is highly valuable but remains a challenge. Herein, a sensitive detection method for Salmonella was developed by coupling immunomagnetic separation with the CRISPR-Cas12a system and the tetrahedral DNA nanostructure-mediated hyperbranched hybridization chain reaction (TDN-hHCR). In the detection system, the target Salmonella was immunomagnetically separated and labeled with bio-barcode DNA-modified gold nanoparticles (AuNPs), which could transfer and magnify the signal of a bacterial cell into numerous bio-barcode DNA molecules. Afterward, the bio-barcode DNA can trigger the trans-cleavage activity of CRISPR-Cas12a to inhibit the process of the TDN-hHCR to generate a fluorescence readout. Due to the high immunomagnetic separation efficiency and the effective signal amplification of CRISPR-Cas12a and the TDN-hHCR, Salmonella as low as 8 CFU/mL could be easily detected. Meanwhile, this has been applied for practical use and showed the capability to detect 17 and 25 CFU/mL in spiked milk and egg white, respectively, indicating its potential application in real samples.},
}
@article {pmid36512510,
year = {2022},
author = {Collins, EL and Phelan, JE and Hubner, M and Spadar, A and Campos, M and Ward, D and Acford-Palmer, H and Gomes, AR and Silva, K and Ferrero Gomez, L and Clark, TG and Campino, S},
title = {A next generation targeted amplicon sequencing method to screen for insecticide resistance mutations in Aedes aegypti populations reveals a rdl mutation in mosquitoes from Cabo Verde.},
journal = {PLoS neglected tropical diseases},
volume = {16},
number = {12},
pages = {e0010935},
pmid = {36512510},
issn = {1935-2735},
support = {MR/M01360X/1/MRC_/Medical Research Council/United Kingdom ; MR/N010469/1/MRC_/Medical Research Council/United Kingdom ; MR/R025576/1/MRC_/Medical Research Council/United Kingdom ; MR/R020973/1/MRC_/Medical Research Council/United Kingdom ; MR/M01360X/1/MRC_/Medical Research Council/United Kingdom ; MR/R025576/1/MRC_/Medical Research Council/United Kingdom ; MR/R020973/1/MRC_/Medical Research Council/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Insecticide Resistance/genetics ; *Aedes/genetics ; DDT ; Cabo Verde ; *Insecticides/pharmacology ; *Pyrethrins/pharmacology ; Mosquito Vectors/genetics ; *Voltage-Gated Sodium Channels/genetics ; Mutation ; *Zika Virus ; *Zika Virus Infection ; },
abstract = {Aedes mosquito vectors transmit many viruses of global health concern, including dengue, chikungunya and Zika. These vector-borne viral diseases have a limited number of treatment options, and vaccines vary in their effectiveness. Consequently, integrated vector management is a primary strategy for disease control. However, the increasing emergence and spread of insecticide resistance is threatening the efficacy of vector control methods. Identifying mutations associated with resistance in vector populations is important to monitor the occurrence and evolution of insecticide resistance and inform control strategies. Rapid and cost-effective genome sequencing approaches are urgently needed. Here we present an adaptable targeted amplicon approach for cost-effective implementation within next generation sequencing platforms. This approach can identify single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels) in genes involved in insecticide resistance in Aedes aegypti mosquitoes. We designed and tested eleven amplicons, which included segments of the ace-1 (carbamate target), the Voltage-Gated Sodium Channel (vgsc; pyrethroids, DDT and organochlorines), and rdl (dieldrin) genes; thereby covering established knockdown resistance (kdr) mutations (e.g., S989P, I1011M/V, V1016G/I and F1534C), with the potential to identify novel ones. The amplicon assays were designed with internal barcodes, to facilitate multiplexing of large numbers of mosquitoes at low cost, and were sequenced using an Illumina platform. Our approach was evaluated on 152 Ae. aegypti mosquitoes collected in Cabo Verde, an archipelago with a history of arbovirus outbreaks. The amplicon sequence data revealed 146 SNPs, including four non-synonymous polymorphisms in the vgsc gene, one in ace-1 and the 296S rdl mutation previously associated with resistance to organochlorines. The 296S rdl mutation was identified in 98% of mosquitoes screened, consistent with the past use of an organochlorine compound (e.g., DDT). Overall, our work shows that targeted amplicon sequencing is a rapid, robust, and cost-effective tool that can be used to perform high throughput monitoring of insecticide resistance.},
}
@article {pmid36512198,
year = {2023},
author = {Panthum, T and Ariyaphong, N and Wattanadilokchatkun, P and Singchat, W and Ahmad, SF and Kraichak, E and Dokkaew, S and Muangmai, N and Han, K and Duengkae, P and Srikulnath, K},
title = {Quality control of fighting fish nucleotide sequences in public repositories reveals a dark matter of systematic taxonomic implication.},
journal = {Genes &amp; genomics},
volume = {45},
number = {2},
pages = {169-181},
pmid = {36512198},
issn = {2092-9293},
support = {6417400247//High-Quality Research Graduate Development Cooperation Project between Kasetsart University and the National Science and Technology Development Agency (NSTDA)/ ; 3/2564//Thailand Science Research and Innovation through The Kasetsart University Reinventing University Program 2021/ ; P1851131//e-ASIA Joint Research Program/ ; P-19-52238//National Science and Technology Development Agency (NSTDA)/ ; JRA-CO-2564-14003-TH//National Science and Technology Development Agency (NSTDA)/ ; //Postdoctoral researcher award at Kasetsart University/ ; 6414400777//Higher Education for Industry Consortium/ ; //Office of the Ministry of Higher Education, Science, Research and Innovation/ ; //International SciKU Branding (ISB), Faculty of Science, Kasetsart University/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Base Sequence ; *DNA ; Quality Control ; Mitochondria/genetics ; Fishes/genetics ; Cytochromes b/genetics ; },
abstract = {BACKGROUND: The number of nucleotide sequences in public repositories has exploded recently. However, the data contain errors, leading to incorrect species identification. Several fighting fish (Betta spp.) are poorly described, with unresolved cryptic species complexes masking undescribed species. Here, DNA barcoding was used to detect erroneous sequences in public repositories.<br><br>OBJECTIVE: This study reflects the current quantitative and qualitative status of DNA barcoding in fighting fish and provides a rapid and reliable identification tool.<br><br>METHODS: A total of 1034 barcode sequences were analyzed from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes from 71 fighting fish species.<br><br>RESULTS: The nearest neighbor test showed the highest percentage of intraspecific nearest neighbors at 93.41% for COI and 91.67% for Cytb, which can be used as reference barcodes for certain taxa. Intraspecific variation was usually less than 13%, while most species differed by more than 54%. The barcoding gap, calculated from the difference between inter- and intraspecific sequence divergences, was negative in the COI data set indicating overlapping intra- and interspecific sequence divergence. Sequence saturation was observed in the Cytb data set but not in the COI data set.<br><br>CONCLUSION: The COI gene should thus be used as the main barcoding marker for fighting fish.},
}
@article {pmid36510360,
year = {2023},
author = {Garrido, PA and Proaño-Cuenca, F and Flor, FJF and Benítez, EAD and Torres, IFS and Kaiser, ARK and Sain, L and Peñaloza, YAM and Marek, SM and Melouk, H and Daughtrey, M and Garzon, CD},
title = {Identification and Characterization of Pythium, Globisporangium, and Phytopythium Species Present in Floricultural Crops from Long Island, New York.},
journal = {Phytopathology},
volume = {113},
number = {7},
pages = {1335-1346},
doi = {10.1094/PHYTO-06-22-0195-R},
pmid = {36510360},
issn = {0031-949X},
mesh = {*Pythium/genetics ; New York ; Plant Diseases ; Crops, Agricultural ; Population Dynamics ; },
abstract = {Several Pythium, Globisporangium, and Phytopythium species cause Pythium diseases in greenhouse floricultural crops, resulting in significant seasonal losses. Four hundred and eighteen Pythium, Globisporangium, and Phytopythium isolates from flowering crops, growing media, or bench and floor debris were collected from Long Island greenhouses or clinic samples between 2002 and 2013. Isolates were identified to species based on morphology and internal transcribed spacer barcoding. Twenty-two species of Pythium, Phytopythium, and Globisporangium were identified, with Globisporangium irregulare sensu lato (s.l.) being the most common. To determine the origin of inoculum during the 2011 cropping season, 11 microsatellite loci were analyzed in 124 G. irregulare s.l. isolates collected in four greenhouses and six previously collected from clinic samples. Cluster analyses grouped G. irregulare s.l. isolates into four groups: G. irregulare sensu stricto, plus three G. cryptoirregulare clusters. The population structure defined by greenhouse and host was found in two clades. Additionally, the population dynamics of G. irregulare s.l. isolates associated with Pelargonium spp. from 2011 to 2013 were examined using 85 isolates and nine informative microsatellite loci to assess inoculum survival over multiple cropping seasons. Although most isolates had unique genotypes, closely related genotypes were found in the same locations over different years. Our results indicate that G. irregulare s.l. inocula have local as well as remote origins. Isolates may be initially brought into ornamental operations from common sources, such as infected plant materials or infested potting mixes. Our results support the hypothesis that established strains can serve as inocula and survive in greenhouse facilities over multiple seasons.},
}
@article {pmid36504444,
year = {2023},
author = {Cheng, J and Lin, G and Wang, T and Wang, Y and Guo, W and Liao, J and Yang, P and Chen, J and Shao, X and Lu, X and Zhu, L and Wang, Y and Fan, X},
title = {Massively Parallel CRISPR-Based Genetic Perturbation Screening at Single-Cell Resolution.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {10},
number = {4},
pages = {e2204484},
pmid = {36504444},
issn = {2198-3844},
support = {81973701//National Natural Science Foundation of China/ ; ZYYCXTD-D-202002//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; },
mesh = {*Genomics/methods ; *Genetic Testing ; },
abstract = {The clustered regularly interspaced short palindromic repeats (CRISPR)-based genetic screening has been demonstrated as a powerful approach for unbiased functional genomics research. Single-cell CRISPR screening (scCRISPR) techniques, which result from the combination of single-cell toolkits and CRISPR screening, allow dissecting regulatory networks in complex biological systems at unprecedented resolution. These methods allow cells to be perturbed en masse using a pooled CRISPR library, followed by high-content phenotyping. This is technically accomplished by annotating cells with sgRNA-specific barcodes or directly detectable sgRNAs. According to the integration of distinct single-cell technologies, these methods principally fall into four categories: scCRISPR with RNA-seq, scCRISPR with ATAC-seq, scCRISPR with proteome probing, and imaging-based scCRISPR. scCRISPR has deciphered genotype-phenotype relationships, genetic regulations, tumor biological issues, and neuropathological mechanisms. This review provides insight into the technical breakthrough of scCRISPR by systematically summarizing the advancements of various scCRISPR methodologies and analyzing their merits and limitations. In addition, an application-oriented approach guide is offered to meet researchers' individualized demands.},
}
@article {pmid36501423,
year = {2022},
author = {Palomares-Rius, JE and Archidona-Yuste, A and Clavero-Camacho, I and de la Fuente, JAC and Rey, A and Viñegla, B and Liébanas, G and Cantalapiedra-Navarrete, C and Castillo, P},
title = {DNA Barcoding and Morphometry Reveal Further Cryptic Bio-Diversity within the Pin Nematode Genus Paratylenchus (Nematoda: Tylenchulidae).},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {23},
pages = {},
pmid = {36501423},
issn = {2223-7747},
support = {RTI2018-095345-B-C21//Spanish Ministry of Science, Innovation and Universities/ ; },
abstract = {Paratylenchus species are obligate ectoparasitic nematodes on cultivated and wild herbaceous and woody plants occupying numerous soil categories. Several species may cause damage to several crops (viz. P. dianthus, P. enigmaticus, P. microdorus, P. hamatus and P. epacris on carnation, lettuce, rose and walnut, respectively). This investigation proves and emphasizes the relevance of applying integrative taxonomy for the accurate detection of Paratylenchus species in mountainous wild environments in the Malaga province, Southern Spain. This research analyzed 45 soil samples of maritimus pine and one of green heather in southern Spain and identified fourteen Paratylenchus species, two of them are described herein as new species (P. paraaonli sp. nov., P. plesiostraeleni sp. nov.), six of them were first reports for Spain (P. canchicus, P. nainianus, P. neonanus, P. salubris, Paratylenchus sp. 2 SAS, and P. wuae), and six species (P. caravaquenus, P. microdorus, P. nanus, P. neoamblycephalus, P. sheri, and P. variabilis) have been already reported in Spain. Accordingly, these data increase the biodiversity of pin nematodes in Spain comprising a total of 47 species (33.1% out of 142 total species of this genus). Phylogenetic analyses based on ribosomal and mitochondrial markers (D2-D3, ITS, and partial COI) resulted in a consistent position for the newly described Paratylenchus species in this study (P. plesiostraeleni sp. nov., P. paraaonli sp. nov.). Paratylenchus plesiostraeleni sp. nov. grouped in a separated subclade as unequivocal species from the P. straeleni-complex species (including P. straeleni and P. parastraeleni), and P. paraaonli sp. nov. clustered with P. vitecus, but clearly separate from this species. This study indicates that Paratylenchus species diversity in natural environments may be higher than expected, and this study may help in accurate identifications.},
}
@article {pmid36501368,
year = {2022},
author = {Friedjung Yosef, A and Ghazaryan, L and Klamann, L and Kaufman, KS and Baubin, C and Poodiack, B and Ran, N and Gabay, T and Didi-Cohen, S and Bog, M and Khozin-Goldberg, I and Gillor, O},
title = {Diversity and Differentiation of Duckweed Species from Israel.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {23},
pages = {},
pmid = {36501368},
issn = {2223-7747},
support = {16-38-0038//Ministry of Agriculture and Rural Development/ ; },
abstract = {Duckweeds (Lemnaceae) are tiny plants that float on aquatic surfaces and are typically isolated from temperate and equatorial regions. Yet, duckweed diversity in Mediterranean and arid regions has been seldom explored. To address this gap in knowledge, we surveyed duckweed diversity in Israel, an ecological junction between Mediterranean and arid climates. We searched for duckweeds in the north and center of Israel on the surface of streams, ponds and waterholes. We collected and isolated 27 duckweeds and characterized their morphology, molecular barcodes (atpF-atpH and psbK-psbI) and biochemical features (protein content and fatty acids composition). Six species were identified-Lemna minor, L. gibba and Wolffia arrhiza dominated the duckweed populations, and together with past sightings, are suggested to be native to Israel. The fatty acid profiles and protein content further suggest that diverged functions have attributed to different haplotypes among the identified species. Spirodela polyrhiza, W. globosa and L. minuta were also identified but were rarer. S. polyrhiza was previously reported in our region, thus, its current low abundance should be revisited. However, L. minuta and W. globosa are native to America and Far East Asia, respectively, and are invasive in Europe. We hypothesize that they may be invasive species to our region as well, carried by migratory birds that disperse them through their migration routes. This study indicates that the duckweed population in Israel's aquatic environments consists of both native and transient species.},
}
@article {pmid36494024,
year = {2023},
author = {Yandle, Z and Gonzalez, G and Carr, M and Matthijnssens, J and De Gascun, C},
title = {A viral metagenomic protocol for nanopore sequencing of group A rotavirus.},
journal = {Journal of virological methods},
volume = {312},
number = {},
pages = {114664},
doi = {10.1016/j.jviromet.2022.114664},
pmid = {36494024},
issn = {1879-0984},
mesh = {Humans ; *Rotavirus/genetics ; *Nanopore Sequencing ; Phylogeny ; *Rotavirus Infections ; Polymerase Chain Reaction ; Genome, Viral ; Genotype ; },
abstract = {AIM: Development of an unbiased methodology using Oxford Nanopore Technology (ONT) sequencing to obtain whole-genome sequences (WGS) of Rotavirus A (RVA) from clinical samples.<br><br>METHODS: 157 RVA qRT-PCR positive faecal samples were enriched by virus-like particle (VLP) purification and host nuclease digestion to enhance the detection of viral nucleic acids and cDNA generated as per the NetoVIR protocol. ONT sequencing was then performed using the ONT Native Barcoding kit (SQK-LSK-109) on the GridION platform. Data was basecalled, demultiplexed and assembled into near complete RVA genomes. The accuracy and quality of the obtained sequences was assessed by comparing to Sanger sequencing and RVA reference genomes.<br><br>RESULTS: The developed protocol generated 146 near-complete RVA WGS out of the 157 RVA-positive clinical samples. The quality of the assembled genomes was assessed by comparison against publicly-available sequences with results showing 98.76 %&#xa0;&#xb1;&#xa0;0.03 % similarity and >&#xa0;90 % genome coverage. A concordance assessment was performed comparing the identity of partial RVA VP7 and VP4 segments obtained by Sanger sequencing (n&#xa0;=&#xa0;51) against corresponding nanopore sequences which demonstrated an overall identity of 100.0 %&#xa0;&#xb1;&#xa0;0.02 %.<br><br>CONCLUSIONS: The nanopore protocol generated both high quality and accurate RVA WGS extracted from faecal samples. This protocol can be extended to other viral agents in other sample types.},
}
@article {pmid36481242,
year = {2023},
author = {Magbanua, ZV and Hsu, CY and Pechanova, O and Arick, M and Grover, CE and Peterson, DG},
title = {Innovations in double digest restriction-site associated DNA sequencing (ddRAD-Seq) method for more efficient SNP identification.},
journal = {Analytical biochemistry},
volume = {662},
number = {},
pages = {115001},
doi = {10.1016/j.ab.2022.115001},
pmid = {36481242},
issn = {1096-0309},
mesh = {*Polymorphism, Single Nucleotide/genetics ; Phylogeny ; *Genome ; Sequence Analysis, DNA/methods ; Base Sequence ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {We present an improved ddRAD-Seq protocol for identifying single nucleotide polymorphisms (SNPs). It utilizes selected restriction enzyme digestion fragments, quick acting ligases that are neutral with the restriction enzyme buffer eliminating buffer exchange steps, and adapters designed to be compatible with Illumina index primers. Library amplification and barcoding are completed in one PCR step, and magnetic beads are used to purify the genomic fragments from the ligation and library generation steps. Our protocol increases the efficiency and decreases the time to complete a ddRAD-Seq experiment. To demonstrate its utility, we compared SNPs from our protocol with those from whole genome resequencing data from Gossypium herbaceum and Gossypium arboreum. Principal component analysis demonstrated that the variability of the combined data was explained by the genotype (PC1) and methodology applied (PC2). Phylogenetic analysis showed that the SNPs from our method clustered with SNPs from the resequencing data of the corresponding genotype. Sequence alignments illustrated that for homozygous loci, more than 90% of the SNPs from the resequencing data were discovered by our method. Our analyses suggest that our ddRAD-Seq method is reliable in identifying SNPs suitable for phylogenetic and association genetic studies while reducing cost and time over known methods.},
}
@article {pmid36480244,
year = {2023},
author = {Viner, I and Spirin, V and Larsson, KH and Miettinen, O},
title = {Systematic placement of Lagarobasidium cymosum and description of two new species.},
journal = {Mycologia},
volume = {115},
number = {1},
pages = {122-134},
doi = {10.1080/00275514.2022.2146978},
pmid = {36480244},
issn = {1557-2536},
mesh = {*Phylogeny ; DNA, Ribosomal Spacer/genetics ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; North America ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; },
abstract = {Lagarobasidium cymosum is a rare corticioid species with characteristic morphology different from other Lagarobasidium species. We used nuc 5.8S rDNA, nuc 28S rDNA, and mt 12S rDNA loci to infer the phylogenetic position of L. cymosum. Our analyses suggest that it belongs to Xylodon but is not closely related to any of the other taxa referred to Lagarobasidium. Molecular and morphological information shows that the traditional concept of L. cymosum covers at least three species: Xylodon acuminatus from the Neotropics, X. cymosus from North America, and X. subtilissimus distributed in both Europe and North America. Lagarobasidium calongei is transferred to Xylodon, and DNA barcodes for Lyomyces incrustatus and Xylodon hjortstamii are published for the first time.},
}
@article {pmid36479848,
year = {2023},
author = {Rodriguez-Martinez, S and Klaminder, J and Morlock, MA and Dalén, L and Huang, DY},
title = {The topological nature of tag jumping in environmental DNA metabarcoding studies.},
journal = {Molecular ecology resources},
volume = {23},
number = {3},
pages = {621-631},
doi = {10.1111/1755-0998.13745},
pmid = {36479848},
issn = {1755-0998},
support = {P2BEP2-188256//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 2017-04548//Swedish research council/ ; },
mesh = {*DNA, Environmental ; DNA Barcoding, Taxonomic/methods ; Sequence Analysis, DNA/methods ; DNA/genetics ; },
abstract = {Metabarcoding of environmental DNA constitutes a state-of-the-art tool for environmental studies. One fundamental principle implicit in most metabarcoding studies is that individual sample amplicons can still be identified after being pooled with others-based on their unique combinations of tags-during the so-called demultiplexing step that follows sequencing. Nevertheless, it has been recognized that tags can sometimes be changed (i.e., tag jumping), which ultimately leads to sample crosstalk. Here, using four DNA metabarcoding data sets derived from the analysis of soils and sediments, we show that tag jumping follows very specific and systematic patterns. Specifically, we find a strong correlation between the number of reads in blank samples and their topological position in the tag matrix (described by vertical and horizontal vectors). This observed spatial pattern of artefactual sequences could be explained by polymerase activity, which leads to the exchange of the 3' tag of single stranded tagged sequences through the formation of heteroduplexes with mixed barcodes. Importantly, tag jumping substantially distorted our data sets-despite our use of methods suggested to minimize this error. We developed a topological model to estimate the noise based on the counts in our blanks, which suggested that 40%-80% of the taxa in our soil and sedimentary samples were likely false positives introduced through tag jumping. We highlight that the amount of false positive detections caused by tag jumping strongly biased our community analyses.},
}
@article {pmid36479823,
year = {2023},
author = {Sun, JJ and Xia, XM and Wei, XX and Wang, XQ},
title = {Tracing the geographic origin of endangered plant species using transcriptome-derived SNPs: An example of Cathaya argyrophylla.},
journal = {Molecular ecology resources},
volume = {23},
number = {4},
pages = {844-854},
doi = {10.1111/1755-0998.13747},
pmid = {36479823},
issn = {1755-0998},
support = {XDA23080000//Strategic Priority Research Program of Chinese Academy of Sciences (CAS)/ ; },
mesh = {Animals ; Humans ; Commerce ; *Endangered Species ; Internationality ; Polymorphism, Single Nucleotide ; *Transcriptome ; },
abstract = {Genetic markers have emerged as one of the most promising tools for species identification and geographic traceability in biodiversity conservation and international trade of biological products. However, traditional molecular markers rarely have sufficient resolution at lower taxonomic levels, especially for discriminating closely related forest tree species and their populations. In this study, we developed a panel of RNA-Seq based single nucleotide polymorphism (SNP) markers for tracing the geographic origin of an endangered conifer, Cathaya argyrophylla, which is a paleoendemic restricted to four mountain regions in subtropical China. A total of 69 individuals from five populations (DLS, SHS, HP, BMS, and DYS) covering the entire range were used for transcriptome sequencing. Based on these transcriptomic data, we evaluated genetic variation and population structure of C. argyrophylla, and found extremely low nucleotide diversity but strong population differentiation. We also screened 113 population-specific SNP loci, including 96 for BMS, eight for DYS, six for SHS, two for HP, and one for one of the three subpopulations from DLS. According to these geographically diagnostic SNPs, we designed four population-specific molecular barcodes for PCR amplification. To test the utility and efficiency of the four markers in geographic discrimination, double-blind experiment was performed using 157 individuals labelled without any locality information. We found that almost all tested individuals could be successfully assigned to their geographic localities. Our study not only sheds some new light on the genetic profile of C. argyrophylla, but also provides a practical and cost-efficient solution for geographic traceability using transcriptome-derived SNPs.},
}
@article {pmid36479703,
year = {2023},
author = {Mattoon, EM and McHargue, WE and Bailey, CE and Zhang, N and Chen, C and Eckhardt, J and Daum, CG and Zane, M and Pennacchio, C and Schmutz, J and O'Malley, RC and Cheng, J and Zhang, R},
title = {High-throughput identification of novel heat tolerance genes via genome-wide pooled mutant screens in the model green alga Chlamydomonas reinhardtii.},
journal = {Plant, cell &amp; environment},
volume = {46},
number = {3},
pages = {865-888},
pmid = {36479703},
issn = {1365-3040},
support = {R01 GM093123/GM/NIGMS NIH HHS/United States ; },
mesh = {*Chlamydomonas reinhardtii/metabolism ; *Thermotolerance/genetics ; *Chlamydomonas ; Photosynthesis/genetics ; Carbon/metabolism ; },
abstract = {Different high temperatures adversely affect crop and algal yields with various responses in photosynthetic cells. The list of genes required for thermotolerance remains elusive. Additionally, it is unclear how carbon source availability affects heat responses in plants and algae. We utilized the insertional, indexed, genome-saturating mutant library of the unicellular, eukaryotic green alga Chlamydomonas reinhardtii to perform genome-wide, quantitative, pooled screens under moderate (35°C) or acute (40°C) high temperatures with or without organic carbon sources. We identified heat-sensitive mutants based on quantitative growth rates and identified putative heat tolerance genes (HTGs). By triangulating HTGs with heat-induced transcripts or proteins in wildtype cultures and MapMan functional annotations, we presented a high/medium-confidence list of 933 Chlamydomonas genes with putative roles in heat tolerance. Triangulated HTGs include those with known thermotolerance roles and novel genes with little or no functional annotation. About 50% of these high-confidence HTGs in Chlamydomonas have orthologs in green lineage organisms, including crop species. Arabidopsis thaliana mutants deficient in the ortholog of a high-confidence Chlamydomonas HTG were also heat sensitive. This work expands our knowledge of heat responses in photosynthetic cells and provides engineering targets to improve thermotolerance in algae and crops.},
}
@article {pmid36478685,
year = {2023},
author = {Benito-Altamirano, I and Martínez-Carpena, D and Casals, O and Fàbrega, C and Waag, A and Prades, JD},
title = {A dataset of color QR codes generated using back-compatible and random colorization algorithms exposed to different illumination-capture channel conditions.},
journal = {Data in brief},
volume = {46},
number = {},
pages = {108780},
pmid = {36478685},
issn = {2352-3409},
abstract = {Color QR Codes are often generated to encode digital information, but one also could use colors or to allocate colors in a QR Code to act as a color calibration chart. In this dataset, we present several thousand QR Codes images generated with two different colorization algorithms (random and back-compatible) and several tuning variables in these color encoding. The QR Codes were also exposed to three different channel conditions (empty, augmentation and real-life). Also, we derive the SNR and BER computations for these QR Code in comparison with their black and white versions. Finally, we also show if ZBar, a commercial QR Code scanner, is able to read them.},
}
@article {pmid36478393,
year = {2023},
author = {Keck, F and Couton, M and Altermatt, F},
title = {Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses.},
journal = {Molecular ecology resources},
volume = {23},
number = {4},
pages = {742-755},
doi = {10.1111/1755-0998.13746},
pmid = {36478393},
issn = {1755-0998},
support = {31003A_173074//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; //Swiss Federal Office for the Environment (FOEN/BAFU)/ ; //University of Zurich Research Priority Programme in Global Change and Biodiversity/ ; },
mesh = {*DNA Barcoding, Taxonomic ; Biodiversity ; Ecology ; Databases, Nucleic Acid ; *DNA, Environmental ; },
abstract = {Assessment of biodiversity using metabarcoding data, such as from bulk or environmental DNA sampling, is becoming increasingly relevant in ecology, biodiversity sciences and monitoring. Thereby, the taxonomic identification of species from their DNA sequences relies strongly on reference databases that link genetic sequences to taxonomic names. These databases vary in completeness and availability, depending on the taxonomic group studied and the genetic region targeted. The incompleteness of reference databases is an important argument to explain the nondetection by metabarcoding of species supposedly present. However, there exist further and generally overlooked problems with reference databases that can lead to false or inaccurate inferences of taxonomic assignment. Here, we synthesize all possible problems inherent to reference databases. In particular, we identify a complete, mutually nonexclusive list of seven classes of challenges when it comes to selecting, developing and using a reference database for taxonomic assignment. These are: (i) mislabelling, (ii) sequencing errors, (iii) sequence conflict, (iv) taxonomic conflict, (v) low taxonomic resolution, (vi) missing taxa and (vii) missing intraspecific variants. For each problem identified, we provide a description of possible consequences on the taxonomic assignment process. We illustrate the respective problem with examples taken from the literature or obtained by quantitative analyses of public databases, such as GenBank or BOLD. Finally, we discuss possible solutions to the identified problems and how to navigate them. Only by raising users' awareness of the limitations of metabarcoding data and DNA reference databases will adequate interpretations of these data be achieved.},
}
@article {pmid36478047,
year = {2023},
author = {Cao, X and Chen, F and Xue, J and Zhao, Y and Bai, M and Zhao, Y},
title = {Hierarchical DNA branch assembly-encoded fluorescent nanoladders for single-cell transcripts imaging.},
journal = {Nucleic acids research},
volume = {51},
number = {3},
pages = {e13},
pmid = {36478047},
issn = {1362-4962},
mesh = {*DNA ; *DNA, Catalytic ; Nucleic Acid Amplification Techniques/methods ; RNA ; Fluorescence ; Single-Cell Analysis ; },
abstract = {Spatial visualization of single-cell transcripts is limited by signal specificity and multiplexing. Here, we report hierarchical DNA branch assembly-encoded fluorescent nanoladders, which achieve denoised and highly multiplexed signal amplification for single-molecule transcript imaging. This method first offers independent RNA-primed rolling circle amplification without nonspecific amplification based on circular DNAzyme. It then executes programmable DNA branch assembly on these amplicons to encode virtual signals for visualizing numbers of targets by FISH. In theory, more virtual signals can be encoded via the increase of detection spectral channels and repeats of the same sequences on barcode. Our method almost eliminates nonspecific amplification in fixed cells (reducing nonspecific spots of single cells from 16 to nearly zero), and achieves simultaneous quantitation of nine transcripts by using only two detection spectral channels. We demonstrate accurate RNA profiling in different cancer cells, and reveal diverse localization patterns for spatial regulation of transcripts.},
}
@article {pmid36477987,
year = {2022},
author = {Koroiva, R and Santana, DJ},
title = {Evaluation of partial 12S rRNA, 16S rRNA, COI and Cytb gene sequence datasets for potential single DNA barcode for hylids (Anura: Hylidae).},
journal = {Anais da Academia Brasileira de Ciencias},
volume = {94},
number = {4},
pages = {e20200825},
doi = {10.1590/0001-3765202220200825},
pmid = {36477987},
issn = {1678-2690},
mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Cytochromes b ; *Anura ; DNA Barcoding, Taxonomic ; },
abstract = {We evaluated the extent of intraspecific and interspecific genetic distances and the effectiveness of predefined threshold values using the main genes for estimates of biodiversity and specimens' identification in anurans. Partial sequences of the mitochondrial genes for small (12S) and large (16S) ribosomal subunits, cytochrome c oxidase subunit I (COI) and Cytochrome b (Cytb) of the family Hylidae were downloaded from GenBank and curated for length, coverage, and potential contaminations. We performed analyses for all sequences of each gene and the same species present in these datasets by distance and tree (monophyly)-based evaluations. We also evaluated the ability to identify specimens using these datasets applying "nearest neighbor" (NN), "best close match" (BCM) and "BOLD ID" tests. Genetic distance thresholds were generated by the function 'threshVal' and "localMinima" from SPIDER package and traditional threshold values (1%, 3%, 6% and 10%) were also evaluated. Coding genes, especially COI, had a better identification capacity than non-coding genes on barcoding gap and monophyly analysis and NN, BCM, BOLD ID tests. Considering the multiple factors involved in global DNA barcoding evaluations, we present a critical assessment of the use of these genes for biodiversity estimation and specimens' identification in anurans (e.g. hylids).},
}
@article {pmid36474163,
year = {2022},
author = {Wu, TH and Yang, CH and Pai, TW and Ho, LP and Wu, JL and Chou, HY},
title = {Identification of fish species through tRNA-based primer design.},
journal = {BMC bioinformatics},
volume = {22},
number = {Suppl 10},
pages = {633},
pmid = {36474163},
issn = {1471-2105},
support = {MOST 110-2321-B-019-001//Ministry of Science and Technology (TW)/ ; 109-2321-B-019-005//Ministry of Science and Technology, Taiwan/ ; },
mesh = {*RNA, Transfer/genetics ; },
abstract = {BACKGROUND: The correct establishment of the barcode classification system for fish can facilitate biotaxonomists to distinguish fish species, and it can help the government to verify the authenticity of the ingredients of fish products or identify unknown fish related samples. The Cytochrome c oxidation I (COI) gene sequence in the mitochondria of each species possesses unique characteristics, which has been widely used as barcodes in identifying species in recent years. Instead of using COI gene sequences for primer design, flanking tRNA segments of COI genes from 2618 complete fish mitochondrial genomes were analyzed to discover suitable primers for fish classification at taxonomic family level. The minimal number of primer sets is designed to effectively distinguish various clustered groups of fish species for identification applications. Sequence alignment analysis and cross tRNA segment comparisons were applied to check and ensure the primers for each cluster group are exclusive.<br><br>RESULTS: Two approaches were applied to improve primer design and re-cluster fish species. The results have shown that exclusive primers for 2618 fish species were successfully discovered through in silico analysis. In addition, we applied sequence alignment analysis to confirm that each pair of primers can successfully identify all collected fish species at the taxonomic family levels.<br><br>CONCLUSIONS: This study provided a practical strategy to discover unique primers for each fishery species and a comprehensive list of exclusive primers for extracting COI barcode sequences of all known fishery species. Various applications of verification of fish products or identification of unknown fish species could be effectively achieved.},
}
@article {pmid36473412,
year = {2023},
author = {Wang, J and Wang, Y and Lai, J and Li, J and Yu, K},
title = {Improvement and application of qPCR assay revealed new insight on early warning of Phaeocystis globosa bloom.},
journal = {Water research},
volume = {229},
number = {},
pages = {119439},
doi = {10.1016/j.watres.2022.119439},
pmid = {36473412},
issn = {1879-2448},
mesh = {*Haptophyta ; *Harmful Algal Bloom ; *Environmental Monitoring/instrumentation/methods ; Real-Time Polymerase Chain Reaction ; },
abstract = {Phaeocystis globosa bloom develops from its early solitary cells, providing clues for early warning of its bloom and timely responding to possible consequences. However, the early prediction requires quantification of the solitary cells for a thorough understanding of bloom formation. Therefore, we developed an accurate, sensitive, and specific qPCR assay for this need. Results show that the accuracy of qPCR was significantly enhanced by ameliorating DNA barcode design, improving genomic DNA extraction, and introducing a strategy of internal amplification control (IAC). This approach reached a quantification limit of 1 cell/reaction, making low-abundance cells (10[1]-10[3] cells/L) detection possible, and we also observed a plunge in the abundance of the solitary cells before the bloom outbreak in two winters in 2019 and 2020 for the first time, which is quite unique from laboratory results showing an increase instead. The plunge in solitary-cell abundance might be associated with the attachment of solitary cells to solid matrices to form non-solitary attached aggregate, the precursor of colonies, which gains supports from other studies and needs more investigations in the future. Therefore, as the plunge in solitary-cell abundance is a sign of colony formation, it can be used as an early warning indicator to P. globosa bloom.},
}
@article {pmid36472572,
year = {2022},
author = {Pilgrim, J},
title = {The opportunities of research parasitism: A case study using the Barcode of Life Data System (BOLD).},
journal = {GigaScience},
volume = {11},
number = {},
pages = {},
pmid = {36472572},
issn = {2047-217X},
mesh = {*Biological Science Disciplines ; },
abstract = {The Barcode of Life Data System (BOLD) is primarily used to identify biological specimens based on a mitochondrial gene sequence and has been an underpinning resource for life science researchers. Importantly, curators of BOLD archive DNA extracts where possible, and also record contaminant sequences that can be made available on request. This collegial offering of samples and data led to our work describing the serendipitous discovery of new interactions between a Torix Rickettsia bacterium and their arthropod hosts and resulted in winning the 2022 Junior Research Parasite Award. A case study of this work is presented, which discusses the opportunities provided by secondary data and how careful maintenance of such large-scale repositories plays a vital role in scientific research that goes beyond obvious lines of enquiry.},
}
@article {pmid36469010,
year = {2023},
author = {Penter, L and Ten Hacken, E and Southard, J and Lareau, CA and Ludwig, LS and Li, S and Neuberg, DS and Livak, KJ and Wu, CJ},
title = {Mitochondrial DNA Mutations as Natural Barcodes for Lineage Tracing of Murine Tumor Models.},
journal = {Cancer research},
volume = {83},
number = {5},
pages = {667-672},
pmid = {36469010},
issn = {1538-7445},
support = {R01 CA216273/CA/NCI NIH HHS/United States ; P01 CA206978/CA/NCI NIH HHS/United States ; R01 CA155010/CA/NCI NIH HHS/United States ; R50 CA251956/CA/NCI NIH HHS/United States ; R21 CA267527/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Mice ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Chromatin ; Mutation ; *Neoplasms/genetics ; },
abstract = {UNLABELLED: Murine models are indispensable tools for functional genomic studies and preclinical testing of novel therapeutic approaches. Mitochondrial single-cell assay for transposase-accessible chromatin using sequencing (mtscATAC-seq) enables the dissection of cellular heterogeneity and clonal dynamics by capturing chromatin accessibility, copy-number variations (CNV), and mitochondrial DNA (mtDNA) mutations, yet its applicability to murine studies remains unexplored. By leveraging mtscATAC-seq in novel chronic lymphocytic leukemia and Richter syndrome mouse models, we report the detection of mtDNA mutations, particularly in highly proliferative murine cells, alongside CNV and chromatin state changes indicative of clonal evolution upon secondary transplant. This study thus demonstrates the feasibility and utility of multi-modal single-cell and natural barcoding approaches to characterize murine cancer models.<br><br>SIGNIFICANCE: mtDNA mutations can serve as natural barcodes to enable lineage tracing in murine cancer models, which can be used to provide new insights into disease biology and to identify therapeutic vulnerabilities.},
}
@article {pmid36462526,
year = {2023},
author = {Wasakul, V and Disratthakit, A and Mayxay, M and Chindavongsa, K and Sengsavath, V and Thuy-Nhien, N and Pearson, RD and Phalivong, S and Xayvanghang, S and Maude, RJ and Gonçalves, S and Day, NP and Newton, PN and Ashley, EA and Kwiatkowski, DP and Dondorp, AM and Miotto, O},
title = {Malaria outbreak in Laos driven by a selective sweep for Plasmodium falciparum kelch13 R539T mutants: a genetic epidemiology analysis.},
journal = {The Lancet. Infectious diseases},
volume = {23},
number = {5},
pages = {568-577},
pmid = {36462526},
issn = {1474-4457},
support = {/WT_/Wellcome Trust/United Kingdom ; 204911/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Plasmodium falciparum/genetics ; Laos/epidemiology ; *Antimalarials/pharmacology/therapeutic use ; *Malaria, Falciparum/drug therapy ; Molecular Epidemiology ; Drug Resistance/genetics ; *Malaria/epidemiology ; Disease Outbreaks ; Protozoan Proteins/genetics/therapeutic use ; },
abstract = {BACKGROUND: Malaria outbreaks are important public health concerns that can cause resurgence in endemic regions approaching elimination. We investigated a Plasmodium falciparum outbreak in Attapeu Province, Laos, during the 2020-21 malaria season, using genomic epidemiology methods to elucidate parasite population dynamics and identify its causes.<br><br>METHODS: In this genetic analysis, 2164 P falciparum dried blood spot samples were collected from southern Laos between Jan 1, 2017, and April 1, 2021, which included 249 collected during the Attapeu outbreak between April 1, 2020, and April 1, 2021, by routine surveillance. Genetic barcodes obtained from these samples were used to investigate epidemiological changes underpinning the outbreak, estimate population diversity, and analyse population structure. Whole-genome sequencing data from additional historical samples were used to reconstruct the ancestry of outbreak strains using identity-by-descent analyses.<br><br>FINDINGS: The outbreak parasite populations were characterised by unprecedented loss of genetic diversity, primarily caused by rapid clonal expansion of a multidrug-resistant strain (LAA1) carrying the kelch13 Arg539Thr (R539T) mutation. LAA1 replaced kelch13 Cys580Tyr (C580Y) mutants resistant to dihydroartemisinin-piperaquine (KEL1/PLA1) as the dominant strain. LAA1 inherited 58&#xb7;8% of its genome from a strain circulating in Cambodia in 2008. A secondary outbreak strain (LAA2) carried the kelch13 C580Y allele, and a genome that is essentially identical to a Cambodian parasite from 2009. A third, low-frequency strain (LAA7) was a recombinant of KEL1/PLA1 with a kelch13 R539T mutant.<br><br>INTERPRETATION: These results strongly suggest that the outbreak was driven by a selective sweep, possibly associated with multidrug-resistant phenotypes of the outbreak strains. Established resistant populations can circulate at low frequencies for years before suddenly overwhelming dominant strains when the conditions for selection become favourable-eg, when front-line therapies change. Genetic surveillance can support elimination by characterising key properties of outbreaks such as population diversity, drug resistance marker prevalence, and the origins of outbreak strains.<br><br>FUNDING: Bill &amp; Melinda Gates Foundation; The Global Fund to Fight AIDS, Tuberculosis and Malaria; Wellcome Trust.<br><br>TRANSLATION: For the Lao translation of the abstract see Supplementary Materials section.},
}
@article {pmid36462297,
year = {2023},
author = {Crysup, B and Mandape, S and King, JL and Muenzler, M and Kapema, KB and Woerner, AE},
title = {Using unique molecular identifiers to improve allele calling in low-template mixtures.},
journal = {Forensic science international. Genetics},
volume = {63},
number = {},
pages = {102807},
doi = {10.1016/j.fsigen.2022.102807},
pmid = {36462297},
issn = {1878-0326},
mesh = {Humans ; Alleles ; *High-Throughput Nucleotide Sequencing ; *DNA/analysis ; DNA Fingerprinting/methods ; Sequence Analysis, DNA ; Microsatellite Repeats ; },
abstract = {PCR artifacts are an ever-present challenge in sequencing applications. These artifacts can seriously limit the analysis and interpretation of low-template samples and mixtures, especially with respect to a minor contributor. In medicine, molecular barcoding techniques have been employed to decrease the impact of PCR error and to allow the examination of low-abundance somatic variation. In principle, it should be possible to apply the same techniques to the forensic analysis of mixtures. To that end, several short tandem repeat loci were selected for targeted sequencing, and a bioinformatic pipeline for analyzing the sequence data was developed. The pipeline notes the relevant unique molecular identifiers (UMIs) attached to each read and, using machine learning, filters the noise products out of the set of potential alleles. To evaluate this pipeline, DNA from pairs of individuals were mixed at different ratios (1-1, 1-9) and sequenced with different starting amounts of DNA (10, 1 and 0.1 ng). Naïvely using the information in the molecular barcodes led to increased performance, with the machine learning resulting in an additional benefit. In concrete terms, using the UMI data results in less noise for a given amount of drop out. For instance, if thresholds are selected that filter out a quarter of the true alleles, using read counts accepts 2381 noise alleles and using raw UMI counts accepts 1726 noise alleles, while the machine learning approach only accepts 307.},
}
@article {pmid36459311,
year = {2022},
author = {Ghallab, EH and Yousery, A and Shaalan, MG},
title = {Descriptive DNA barcoding of Argas (Persicargas) arboreus and Argas (Persicargas) persicus ticks (Ixodida: Argasidae) infesting birds in Egypt.},
journal = {Experimental &amp; applied acarology},
volume = {88},
number = {3-4},
pages = {397-406},
pmid = {36459311},
issn = {1572-9702},
mesh = {Animals ; *Argasidae/genetics ; *Ticks ; *Argas/genetics ; DNA Barcoding, Taxonomic ; Egypt ; },
abstract = {Argas ticks are primary parasites of birds with veterinary importance. Nevertheless, these ticks have received little attention regarding molecular identification studies. DNA barcoding is a powerful technique for identifying tick species besides traditional morphological identification. The present work is a first effort to divulge DNA sequences of Argas (Persicargas) arboreus from Egypt and worldwide. We used cytochrome c oxidase subunit I (COI) from A. arboreus infesting herons, and from the fowl tick Argas (Persicargas) persicus. Our results pointed out another success for the Folmer primers that are widely used in DNA barcoding, permitting the discrimination of morphologically similar A. arboreus and A. persicus.},
}
@article {pmid36458812,
year = {2023},
author = {Dockerill, M and Winssinger, N},
title = {DNA-Encoded Libraries: Towards Harnessing their Full Power with Darwinian Evolution.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {62},
number = {9},
pages = {e202215542},
doi = {10.1002/anie.202215542},
pmid = {36458812},
issn = {1521-3773},
mesh = {*DNA/genetics/chemistry ; *Small Molecule Libraries/chemistry ; Drug Discovery ; Ligands ; Combinatorial Chemistry Techniques ; },
abstract = {DNA-encoded library (DEL) technologies are transforming the drug discovery process, enabling the identification of ligands at unprecedented speed and scale. DEL makes use of libraries that are orders of magnitude larger than traditional high-throughput screens. While a DNA tag alludes to a genotype-phenotype connection that is exploitable for molecular evolution, most of the work in the field is performed with libraries where the tag serves as an amplifiable barcode but does not allow "translation" into the synthetic product it is linked to. In this Review, we cover technologies that enable the "translation" of the genetic tag into synthetic molecules, both biochemically and chemically, and explore how it can be used to harness Darwinian evolutionary pressure.},
}
@article {pmid36457372,
year = {2022},
author = {Borgmeier, A and Gattoni, K and Harris, T and Higgins, R and Mullin, P and Porazinska, D and Powers, K and Wedin, D and Powers, T},
title = {Plectus of the Prairie: A Case Study of Taxonomic Resolution from a Nematode Biodiversity Survey.},
journal = {Journal of nematology},
volume = {54},
number = {1},
pages = {20220039},
pmid = {36457372},
issn = {0022-300X},
abstract = {Taxonomic resolution is a critical component of biodiversity assessments. In this case study, we examined a single taxon within a larger study of nematode diversity to evaluate the taxonomic resolution of different diversity assessment methods. The selected taxon was the microbial-feeding genus Plectus, a group considered to include multiple cosmopolitan species. The methods included a morphological evaluation by light microscopy, Sanger sequencing of PCR amplicons of COI and 18S gene regions, and 18S metabarcoding sequencing. The study sites were 15 remnant tallgrass prairie plots in eastern Nebraska. In the morphological analysis, we observed two basic morphotypes, a short-tailed form with a small amphid and a long-tailed form with a large amphid. Sanger sequencing of COI sorted Plectus diversity into six distinct clades. The largest two of these six clades keyed to P. parietinus and P. rhizophilus based on morphology. BLAST analysis with COI revealed no close matches in GenBank. Sanger sequencing of the 18S region did not differentiate the six clades. These results illustrate that the method of diversity assessment strongly influences estimates of biodiversity. An additional 95 Plectus specimens, from outside the remnant sites, added taxonomic breadth to the COI phylogenetic tree. There were no geographically widespread COI haplotypes and no evidence of cosmopolitan Plectus species.},
}
@article {pmid36452081,
year = {2022},
author = {Samaai, T and Turner, TL and Kara, J and Yemane, D and Ngwakum, BB and Payne, RP and Kerwath, S},
title = {Confirmation of the southern African distribution of the marine sponge Hymeniacidon perlevis (Montagu, 1814) in the context of its global dispersal.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e14388},
pmid = {36452081},
issn = {2167-8359},
mesh = {Animals ; *Ecosystem ; *Porifera/genetics ; Africa, Southern ; South Africa ; DNA, Ribosomal ; },
abstract = {BACKGROUND: Intertidal rocky shore surveys along the South African coastline (∼3,000 km) have demonstrated the presence and abundance of the encrusting orange sponge Hymeniacidon perlevis (Montagu, 1814), a well-known globally distributed species. After analysing the southern African populations, we gained a better understanding of the genetic structure of this now-accepted global species. Apart from confirming the presence of a single population of H. perlevis, we also determined its distribution in the southern African intertidal rocky shore ecosystem, compared its genetic diversity to congeners, predict its global distribution via environmental niche modelling, and discussed possible underlying mechanisms controlling the species' global distribution.<br><br>METHODS: We surveyed the South African coastline and sampled sponges at 53 rocky shore sites spanning over 3,000 km, from Grosse Bucht south of L&#xfc;deritz (Namibia) to Kosi Bay on the east coast of South Africa. DNA sequences of the nuclear rDNA internal transcribed spacer (ITS1) and the COI mitochondrial gene were obtained from 61 samples and compared them to a world-wide sample of other H. perlevis sequences. Using environmental predictor variables from the global dataset BIO-ORACLE, we predicted the probability of global occurrence of the species using an ensemble of eight distribution models.<br><br>RESULTS: South African specimens were found to be 99-100% identical to other populations of H. perlevis (=H. sinapium) from other world-wide regions. The presence of a single population of H. perlevis in southern Africa is supported by genetic data, extending its distribution to a relatively wide geographical range spanning more than 4,000 km along the temperate southern African coast. The predicted global occurrence by ensemble model matched well with the observed distribution. Surface temperature mean and range were the most important predictor variables.<br><br>CONCLUSION: While H. perlevis appears to have been introduced in many parts of the world, its origins in Europe and southern Africa are unclear.},
}
@article {pmid36448703,
year = {2023},
author = {Edwards, N and Dillard, C and Prashant, NM and Hongyu, L and Yang, M and Ulianova, E and Horvath, A},
title = {SCExecute: custom cell barcode-stratified analyses of scRNA-seq data.},
journal = {Bioinformatics (Oxford, England)},
volume = {39},
number = {1},
pages = {},
pmid = {36448703},
issn = {1367-4811},
support = {MGPC2022//McCormick Genomic and Proteomic Center at George Washington University/ ; },
mesh = {*Software ; Sequence Analysis, RNA ; *Single-Cell Gene Expression Analysis ; Single-Cell Analysis ; Genomics ; High-Throughput Nucleotide Sequencing ; },
abstract = {MOTIVATION: In single-cell RNA-sequencing (scRNA-seq) data, stratification of sequencing reads by cellular barcode is necessary to study cell-specific features. However, apart from gene expression, the analyses of cell-specific features are not sufficiently supported by available tools designed for high-throughput sequencing data.<br><br>RESULTS: We introduce SCExecute, which executes a user-provided command on barcode-stratified, extracted on-the-fly, single-cell binary alignment map (scBAM) files. SCExecute extracts the alignments with each cell barcode from aligned, pooled single-cell sequencing data. Simple commands, monolithic programs, multi-command shell scripts or complex shell-based pipelines are then executed on each scBAM file. scBAM files can be restricted to specific barcodes and/or genomic regions of interest. We demonstrate SCExecute with two popular variant callers-GATK and Strelka2-executed in shell-scripts together with commands for BAM file manipulation and variant filtering, to detect single-cell-specific expressed single nucleotide variants from droplet scRNA-seq data (10X Genomics Chromium System).In conclusion, SCExecute facilitates custom cell-level analyses on barcoded scRNA-seq data using currently available tools and provides an effective solution for studying low (cellular) frequency transcriptome features.<br><br>SCExecute is implemented in Python3 using the Pysam package and distributed for Linux, MacOS and Python environments from https://horvathlab.github.io/NGS/SCExecute.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid36445079,
year = {2022},
author = {Bradshaw, AJ and Backman, TA and Ramírez-Cruz, V and Forrister, DL and Winter, JM and Guzmán-Dávalos, L and Furci, G and Stamets, P and Dentinger, BTM},
title = {DNA Authentication and Chemical Analysis of Psilocybe Mushrooms Reveal Widespread Misdeterminations in Fungaria and Inconsistencies in Metabolites.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {24},
pages = {e0149822},
pmid = {36445079},
issn = {1098-5336},
mesh = {Psilocybin/analysis/metabolism ; *Agaricales/genetics/metabolism ; *Psilocybe/genetics ; Tryptamines/metabolism ; DNA/metabolism ; },
abstract = {The mushroom genus Psilocybe is best known as the core group of psychoactive mushrooms, yet basic information on their diversity, taxonomy, chemistry, and general biology is still largely lacking. In this study, we reexamined 94 Psilocybe fungarium specimens, representing 18 species, by DNA barcoding, evaluated the stability of psilocybin, psilocin, and their related tryptamine alkaloids in 25 specimens across the most commonly vouchered species (Psilocybe cubensis, Psilocybe cyanescens, and Psilocybe semilanceata), and explored the metabolome of cultivated P. cubensis. Our data show that, apart from a few well-known species, the taxonomic accuracy of specimen determinations is largely unreliable, even at the genus level. A substantial quantity of poor-quality and mislabeled sequence data in public repositories, as well as a paucity of sequences derived from types, further exacerbates the problem. Our data also support taxon- and time-dependent decay of psilocybin and psilocin, with some specimens having no detectable quantities of them. We also show that the P. cubensis metabolome possibly contains thousands of uncharacterized compounds, at least some of which may be bioactive. Taken together, our study undermines commonly held assumptions about the accuracy of names and presence of controlled substances in fungarium specimens identified as Psilocybe spp. and reveals that our understanding of the chemical diversity of these mushrooms is largely incomplete. These results have broader implications for regulatory policies pertaining to the storage and sharing of fungarium specimens as well as the use of psychoactive mushrooms for recreation and therapy. IMPORTANCE The therapeutic use of psilocybin, the active ingredient in "magic mushrooms," is revolutionizing mental health care for a number of conditions, including depression, posttraumatic stress disorder (PTSD), and end-of-life care. This has spotlighted the current state of knowledge of psilocybin, including the organisms that endogenously produce it. However, because of international regulation of psilocybin as a controlled substance (often included on the same list as cocaine and heroin), basic research has lagged far behind. Our study highlights how the poor state of knowledge of even the most fundamental scientific information can impact the use of psilocybin-containing mushrooms for recreational or therapeutic applications and undermines critical assumptions that underpin their regulation by legal authorities. Our study shows that currently available chemical studies are mainly inaccurate, irreproducible, and inconsistent, that there exists a high rate of misidentification in museum collections and public databases rendering even names unreliable, and that the concentration of psilocybin and its tryptamine derivatives in three of the most commonly collected Psilocybe species (P. cubensis, P. cyanescens, and P. semilanceata) is highly variable and unstable in museum specimens spanning multiple decades, and our study generates the first-ever insight into the highly complex and largely uncharacterized metabolomic profile for the most commonly cultivated magic mushroom, P. cubensis.},
}
@article {pmid36445037,
year = {2023},
author = {Guan, X and Li, Z and Zhou, Y and Shao, W and Zhang, D},
title = {Active learning for efficient analysis of high-throughput nanopore data.},
journal = {Bioinformatics (Oxford, England)},
volume = {39},
number = {1},
pages = {},
pmid = {36445037},
issn = {1367-4811},
support = {62136004//National Natural Science Foundation of China/ ; },
mesh = {Sequence Analysis, DNA ; Software ; *Nanopores ; High-Throughput Nucleotide Sequencing ; *Nanopore Sequencing ; },
abstract = {MOTIVATION: As the third-generation sequencing technology, nanopore sequencing has been used for high-throughput sequencing of DNA, RNA, and even proteins. Recently, many studies have begun to use machine learning technology to analyze the enormous data generated by nanopores. Unfortunately, the success of this technology is due to the extensive labeled data, which often suffer from enormous labor costs. Therefore, there is an urgent need for a novel technology that can not only rapidly analyze nanopore data with high-throughput, but also significantly reduce the cost of labeling. To achieve the above goals, we introduce active learning to alleviate the enormous labor costs by selecting the samples that need to be labeled. This work applies several advanced active learning technologies to the nanopore data, including the RNA classification dataset (RNA-CD) and the Oxford Nanopore Technologies barcode dataset (ONT-BD). Due to the complexity of the nanopore data (with noise sequence), the bias constraint is introduced to improve the sample selection strategy in active learning. Results: The experimental results show that for the same performance metric, 50% labeling amount can achieve the best baseline performance for ONT-BD, while only 15% labeling amount can achieve the best baseline performance for RNA-CD. Crucially, the experiments show that active learning technology can assist experts in labeling samples, and significantly reduce the labeling cost. Active learning can greatly reduce the dilemma of difficult labeling of high-capacity nanopore data. We hope active learning can be applied to other problems in nanopore sequence analysis.<br><br>The main program is available at https://github.com/guanxiaoyu11/AL-for-nanopore.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid36444901,
year = {2023},
author = {Kiwele Mutambala, P and Abwe, E and Schedel, FDB and Chocha Manda, A and Schliewen, UK and Vreven, EJWMN},
title = {A new Parakneria Poll 1965 (Gonorhynchiformes: Kneriidae), 'Mikinkidi' from the Upper Lufira Basin (Upper Congo: DRC): Evidence from a morphologic and DNA barcoding integrative approach.},
journal = {Journal of fish biology},
volume = {102},
number = {1},
pages = {4-26},
doi = {10.1111/jfb.15206},
pmid = {36444901},
issn = {1095-8649},
support = {//VLIR-UOS (KU Leuven)/ ; //Volkswagen Foundation/ ; //Mbisa Congo II project (RMCA/DGD)/ ; //ABIC program (RMCA/DGD)/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Democratic Republic of the Congo ; *Fishes/genetics ; Biodiversity ; },
abstract = {A new species, Parakneria alytogrammus, is described from the main stream of the Upper Lufira River. This species is easily distinguished from its congeners from the Congo Basin by its unique colouration, consisting of a low number of transversal bands on each of the caudal-fin lobes, 2 (vs. 3-5) and the presence of an uninterrupted lateral mid-longitudinal black band in fresh and preserved specimens (vs. absent). In addition, the new species differs from its Upper Lualaba congeners by the narrow width of its pectoral-fin base, 4.8-5.6% LS [vs. wider, 8.2-10.1% for P. lufirae, 8.6% LS for P. damasi (holotype), and 7.6-7.9% LS for P. thysi]. Finally, it differs from the only species currently known from the Luapula-Mweru system, P. malaissei, by having a short post-dorsal distance, 36.4-36.6% LS (vs. longer, 38.6-41.1% LS) and a short post-pelvic distance of 40.0-40.6% LS (vs. longer, 41.4-44.1% LS). Mitochondrial DNA-haplotypes of P. alytogrammus sp. nov. form a clade, which is sister to the P. thysi clade, and from which it diverges by a genetic (Kimura 2-parameter and uncorrected p) distance of 0.7% in the COI-barcoding locus. The Upper Lufira, one of the sub-basins of the Upper Congo Basin, remains poorly explored relative to its fish fauna. In contrast, the region is well explored with regard to its mineral wealth. Unfortunately, mining exploitation is carried out in the region without proper concern for the environment. Thus, the discovery of this new species for science calls for increased protection and aquatic biodiversity exploration in this mining region.},
}
@article {pmid36444778,
year = {2023},
author = {Hu, XS and Peng, JF and Wang, H and Han, SQ and Li, JW and Yan, FY and Zhou, ZF and Zhang, H and Liu, TX},
title = {Early monitoring of parasitism by Aphidiinae parasitoids on the grain aphid Sitobion miscanthi in wheat fields using DNA barcoding.},
journal = {Pest management science},
volume = {79},
number = {4},
pages = {1381-1387},
doi = {10.1002/ps.7307},
pmid = {36444778},
issn = {1526-4998},
support = {32172425//National Natural Science Foundation of China, grant number/ ; 2016YFGD0300705//National Key Research and Development Foundation, Ministry of Science and Technology of China/ ; 2021JM-085//Natural Science Foundation of Shaanxi Province/ ; },
mesh = {Animals ; *Aphids/genetics ; Triticum/genetics ; DNA Barcoding, Taxonomic ; *Hymenoptera ; DNA ; },
abstract = {BACKGROUND: Sitobion miscanthi is a major wheat pest at the grain-filling stage found in China. Identifying parasitoid species and understanding parasitism rates are keys to controlling the aphids via natural enemies in the wheat field.<br><br>RESULTS: In the present study, a method based on DNA barcoding for early determination of the community composition of Aphidiinae parasitoids and parasitism on the aphid was developed. The proposed method detected Aphidius gifuensis as the predominant parasite, with parasitism rates of 40.1&#x2009;&#xb1;&#x2009;2.8% in 2019 and 65.7&#x2009;&#xb1;&#x2009;3.7% in 2022, and found that the rate varied significantly among different wheat varieties. COI primers efficiently amplified the Aphidiinae parasitoids COI fragments and amplified the aphid COI fragments derived from parasitized (mummified) S. miscanthi. Thus, the COI barcode is not sufficiently specific to unambiguously detect immature parasitoids inside their S. miscanthi hosts. However, it can be used to detect the DNA extracted from mummified aphids. In contrast, the 16S and LWRh primers effectively amplified and identified the parasitoids in parasitized aphids. The 16S primer was reliable even in the early stages of parasitism (24&#x2009;h) and for DNA samples stored at -20&#x2009;&#xb0;C for 5&#x2009;days. The three barcodes from COI, 16S, and LWRh genes could not clearly distinguish a few certain Aphidiinae species owing to relatively low intraspecific and interspecific diversity.<br><br>CONCLUSION: The morphological features remain indispensable when identifying Aphidiinae species. Nonetheless, the COI and 16S primers could be used in combination for monitoring the parasitism rates on S. miscanthi in wheat fields. &#xa9; 2022 Society of Chemical Industry.},
}
@article {pmid36441981,
year = {2023},
author = {Visagie, CM and Yilmaz, N},
title = {Along the footpath of Penicillium discovery: Six new species from the Woodville Big Tree Forest Trail.},
journal = {Mycologia},
volume = {115},
number = {1},
pages = {87-106},
doi = {10.1080/00275514.2022.2135915},
pmid = {36441981},
issn = {1557-2536},
mesh = {*Penicillium/genetics ; DNA, Ribosomal Spacer/genetics ; Phylogeny ; Tubulin/genetics ; Forests ; DNA, Fungal/genetics ; Sequence Analysis, DNA ; },
abstract = {In this study, we studied the diversity of Penicillium occurring in soil collected along the Woodville Big Tree Forest Trail situated close to the coastal town of Wilderness in South Africa. Strains were accessioned into a collection and then identified to species based on β-tubulin DNA sequences, which is the recommended DNA barcode for the genus. The 74 strains were found to represent 18 species, including six we consider undescribed. Here, we introduce them as Penicillium claroviride, P. kalander, P. mattheeae, P. outeniquaense, P. subfuscum, and P. umkhoba. Phylogenetic comparisons were made, and genealogical concordance was demonstrated for these new species using DNA sequences from nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode), β-tubulin, calmodulin, and RNA polymerase II second largest subunit. Notes on morphological characters distinguishing the new species from their close relatives are provided.},
}
@article {pmid36440315,
year = {2022},
author = {Okuno, S and Yin, T and Nanami, S and Matsuyama, S and Kamiya, K and Tan, S and Davies, SJ and Mohamad, M and Yamakura, T and Itoh, A},
title = {Community phylogeny and spatial scale affect phylogenetic diversity metrics in a species-rich rainforest in Borneo.},
journal = {Ecology and evolution},
volume = {12},
number = {11},
pages = {e9536},
pmid = {36440315},
issn = {2045-7758},
abstract = {Community phylogenetic analysis is an effective approach to understanding the process of community formation. The phylogenetic tree of the species pool is reconstructed in the first step, and the phylogenetic tree obtained in the second step is used to analyze phylogenetic diversity. Sythetic trees have often been used in the construction of phylogenentic trees; however, in tropical rainforests with many closely related species, synthetic trees contain many unresolved nodes, which may affect the results of phylogenetic structure analysis. Here, we constructed a phylogenetic tree using DNA barcode sequences (rbcL, matK, trnH-psbA) for 737 tree species from the rainforests of Borneo, which have a high-species diversity and many closely related species. The phylogenetic tree had fewer polytomies and more branch length variations than the Phylocom synthetic trees. Comparison of community phylogenetic analyses indicated that values of the standardized effect size of mean pairwise distance (SES-MPD) were highly correlated between Phylocom and DNA barcode trees, but less so for the standardized effect size of mean nearest taxon distance (SES-MNTD), suggesting that caution is needed when using synthetic trees for communities containing many congeneric species, especially when using SES-MNTD. Simulation analysis suggested that spatial dependence on phylogenetic diversity is related to the phylogenetic signal of the species' habitat niche and the spatial structure of habitat, indicating the importance of detailed phylogeny in understanding community assembly processes.},
}
@article {pmid36437280,
year = {2022},
author = {Parihar, TJ and Sofi, MY and Rasool, RS and Khursheed, S and Bhat, ZA and Hussain, K and Dhekale, B and Zargar, SM and Hakak, AS and Shah, MD and Nehvi, FA and Bhat, MA and Khan, MN and Masoodi, KZ},
title = {Fusarium chlamydosporum, causing wilt disease of chili (Capsicum annum L.) and brinjal (Solanum melongena L.) in Northern Himalayas: a first report.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {20392},
pmid = {36437280},
issn = {2045-2322},
support = {EMR/2016/0005598//Science and Engineering Research Board/ ; AU/ACCTTS/Budget/BA/2021-22/7565-7629 Dated 20-12-2021//SKUAST-K ROC/ ; },
mesh = {Crops, Agricultural ; *Capsicum ; *Solanum melongena/microbiology ; Vegetables ; Fusarium ; },
abstract = {Chili (Capsicum annuum L.) and brinjal (Solanum melongena L.) are the most widely grown solanaceous crops in the world. However, their production has reduced over several years due to the attack of various fungal and bacterial pathogens and various abiotic factors. Still, the major constrain in their production are pathogens with fungal etiology, especially the fungal wilt of solanaceous crops. Fusarium oxysporum and Fusarium solani have been previously identified as the pathogens causing wilt disease in chili and brinjal. Recently, a new fungal pathogen F. equiseti has been reported as the causal agent of wilt disease infecting chili. The current study focused on identifying fungal pathogens associated with the wilted plants of chili and brinjal, collected from different parts of the Himalayan region of Kashmir valley, through morpho-cultural and molecular characterization. DNA extraction, PCR amplification, and sequencing were performed on various isolates. DNA barcoding using the internal transcribed spacer region (ITS) was used to identify the pathogen followed by the pathogenicity test. Further confirmation of the pathogen was done by sequencing of transcription elongation factor (TEF) and Calmodulin (CAL2). In current study Fusarium chlamydosporum has been reported as the wilt causing pathogen of chili and brinjal for the first time in Kashmir Himalayas.},
}
@article {pmid36435214,
year = {2023},
author = {Rodrigues, BL and Galati, EAB},
title = {Molecular taxonomy of phlebotomine sand flies (Diptera, Psychodidae) with emphasis on DNA barcoding: A review.},
journal = {Acta tropica},
volume = {238},
number = {},
pages = {106778},
doi = {10.1016/j.actatropica.2022.106778},
pmid = {36435214},
issn = {1873-6254},
mesh = {Animals ; *Psychodidae/genetics ; DNA Barcoding, Taxonomic ; Phylogeny ; *Phlebotomus ; DNA, Mitochondrial ; },
abstract = {The taxonomy and systematics of sand flies (Diptera, Psychodidae, Phlebotominae) are one of the pillars of research aimed to identifying vector populations and the agents transmitted by these insects. Traditionally, the use of morphological traits has been the main line of evidence for the definition of species, but the use of DNA sequences is useful as an integrative approach for their delimitation. Here, we discuss the current status of the molecular taxonomy of sand flies, including their most sequenced molecular markers and the main results. Only about 37% of all sand fly species have been processed for any molecular marker and are publicly available in the NCBI GenBank or BOLD Systems databases. The genera Phlebotomus, Nyssomyia, Psathyromyia and Psychodopygus are well-sampled, accounting for more than 56% of their sequenced species. However, less than 34% of the species of Sergentomyia, Lutzomyia, Trichopygomyia and Trichophoromyia have been sampled, representing a major gap in the knowledge of these groups. The most sequenced molecular markers are those within mtDNA, especially the DNA barcoding fragment of the cytochrome c oxidase subunit I (coi) gene, which has shown promising results in detecting cryptic diversity within species. Few sequences of conserved genes have been generated, which hampers higher-level phylogenetic inferences. We argue that sand fly species should be sequenced for at least the coi DNA barcoding marker, but multiple markers with different mutation rates should be assessed, whenever possible, to generate multilocus analysis.},
}
@article {pmid36432909,
year = {2022},
author = {Chaneva, G and Tomov, A and Paunov, M and Hristova, V and Ganeva, V and Mihaylova, N and Anev, S and Krumov, N and Yordanova, Z and Tsenov, B and Vassileva, V and Bonchev, G and Zhiponova, M},
title = {Jewel Orchid's Biology and Physiological Response to Aquaponic Water as a Potential Fertilizer.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {22},
pages = {},
pmid = {36432909},
issn = {2223-7747},
support = {&#x2116;80-10-69/11.05.2022//Fund for scientific investigations of Sofia University "St. Kliment Ohridski"/ ; No. &#x414;01-271/02.10.2020//Project BULCode, National Program "European Scientific Networks" funded by the Ministry of Education and Science of Bulgaria/ ; },
abstract = {Ludisia discolor is commonly known as a jewel orchid due to its variegated leaves. Easy maintenance of the orchid allows it to be used as a test system for various fertilizers and nutrient sources, including aquaponic water (AW). First, we applied DNA barcoding to assess the taxonomic identity of this terrestrial orchid and to construct phylogenetic trees. Next, the vegetative organs (leaf, stem, and root) were compared in terms of the level of metabolites (reducing sugars, proteins, anthocyanins, plastid pigments, phenolics, and antioxidant activity) and nutrient elements (carbon, nitrogen, sodium, and potassium), which highlighted the leaves as most functionally active organ. Subsequently, AW was used as a natural source of fish-derived nutrients, and the orchid growth was tested in hydroponics, in irrigated soil, and in an aquaponic system. Plant physiological status was evaluated by analyzing leaf anatomy and measuring chlorophyll content and chlorophyll fluorescence parameters. These results provided evidence of the beneficial effects of AW on the jewel orchid, including increased leaf formation, enhanced chlorophyll content and photosystems' productivity, and stimulated and prolonged flowering. The information acquired in the present study could be used in addressing additional aspects of the growth and development of the jewel orchid, which is also known for its medicinal value.},
}
@article {pmid36432888,
year = {2022},
author = {Bhamra, SK and Heinrich, M and Johnson, MRD and Howard, C and Slater, A},
title = {The Cultural and Commercial Value of Tulsi (Ocimum tenuiflorum L.): Multidisciplinary Approaches Focusing on Species Authentication.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {22},
pages = {},
pmid = {36432888},
issn = {2223-7747},
support = {N/A//De Montfort University/ ; },
abstract = {Tulsi (Holy basil, Ocimum tenuiflorum L., Lamiaceae), native to Asia, has become globalised as the cultural, cosmetic, and medicinal uses of the herb have been popularised. DNA barcoding, a molecular technique used to identify species based on short regions of DNA, can discriminate between different species and identify contaminants and adulterants. This study aimed to explore the values associated with Tulsi in the United Kingdom (UK) and authenticate samples using DNA barcoding. A mixed methods approach was used, incorporating social research (i.e., structured interviews) and DNA barcoding of Ocimum samples using the ITS and trnH-psbA barcode regions. Interviews revealed the cultural significance of Tulsi: including origins, knowledge exchange, religious connotations, and medicinal uses. With migration, sharing of plants and seeds has been seen as Tulsi plants are widely grown in South Asian (SA) households across the UK. Vouchered Ocimum specimens (n = 33) were obtained to create reference DNA barcodes which were not available in databases. A potential species substitution of O. gratissimum instead of O. tenuiflorum amongst SA participants was uncovered. Commercial samples (n = 47) were difficult to authenticate, potentially due to DNA degradation during manufacturing processes. This study highlights the cultural significance of Tulsi, despite a potential species substitution, the plant holds a prestigious place amongst SA families in the UK. DNA barcoding was a reliable way to authenticate Ocimum species.},
}
@article {pmid36427455,
year = {2023},
author = {Saengsawang, P and Desquesnes, M and Yangtara, S and Chalermwong, P and Thongtip, N and Jittapalapong, S and Inpankaew, T},
title = {Molecular detection of Loxodontofilaria spp. in Asian elephants (Elephas maximus) from elephant training camps in Thailand.},
journal = {Comparative immunology, microbiology and infectious diseases},
volume = {92},
number = {},
pages = {101910},
doi = {10.1016/j.cimid.2022.101910},
pmid = {36427455},
issn = {1878-1667},
mesh = {Animals ; Humans ; *Elephants/parasitology ; Phylogeny ; Thailand/epidemiology ; Polymerase Chain Reaction/veterinary ; },
abstract = {Filarial infection is an important disease in human and animal medicine. Several filarial worms are of importance, especially nematodes in the Onchocercidae. The Asian elephant (Elephas maximus) is an endangered animal and is very important from several socio-economic and ecological aspects in Thailand. Various parasites can be found in elephants; however, data related to filarial infections in elephants is limited. The objective of this study was to detect filaria in the blood of Asian elephants in Thailand, based on a polymerase chain reaction (PCR) technique. Blood samples were collected from 208 Asian elephants and detected for filaria using PCR, targeting the region of the internal transcribed spacer 2 (ITS2), the cytochrome c oxidase subunit 1 (cox1), and the RNA polymerase II large subunit (rbp1). In total, 4.33% (9 out of 208) of the sampled elephants had Loxodontofilaria spp. DNA with 100% query coverage. In addition, the obtained cox1 and rbp1 sequences matched with Loxodontofilaria sp., Onchocerca sp., and Dirofilaria sp. There were no identified risk factors (sex, age, location, and packed cell volume) related to Loxodontofilaria infection in elephants. The analyses of the phylogeny of ITS2 sequences demonstrated that the Loxodotofilaria-positive sequences were closely related to Onchocerca dewittei japonica and Onchocerca dewittei dewittei with 100% query coverage. Notably, the concatenated phylogenetic trees of ITS2 and the cox1 and rbp1 genes were closely similar to Loxodontofilaria sp. To describe in detail the genomic DNA of Loxodontofilaria spp., other genes should be additionally studied using a more discriminatory technique, such as DNA barcoding or whole genome sequencing.},
}
@article {pmid36424834,
year = {2022},
author = {Feng, Y and Chen, T and Rao, Q and Xie, X and Zhang, L and Lv, Y},
title = {Time-Resolved Persistent Luminescence Encoding for Multiplexed Severe Acute Respiratory Syndrome Coronavirus 2 Detection.},
journal = {Analytical chemistry},
volume = {94},
number = {48},
pages = {16967-16974},
doi = {10.1021/acs.analchem.2c04788},
pmid = {36424834},
issn = {1520-6882},
mesh = {Humans ; *Luminescence ; SARS-CoV-2 ; COVID-19 Testing ; *COVID-19/diagnosis ; Fluorescence Resonance Energy Transfer ; },
abstract = {Capable of precise simultaneous multitarget identifications within a minimized sample, optical multiplexing is vital for accurate diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) while remaining spectral crowding and background interfering. In merits of an autofluorescence-free background and high-capability throughput, a persistent luminescence (PersL) lifetime/color binary encoding strategy was herein proposed for SARS-CoV-2 diagnosis. Based on luminescence resonance energy transfer processes, the intense lifetimes and representative emissions of PersL nanoplatforms were rationally manipulated to create a temporal coding dimension within a wide seconds-to-minutes range through three individual channels. Particularly, at least four populations of barcoding in a certain channel were successfully decoded by a purpose-built time-resolved PersL technology. As a proof-of-concept, functionalized PersL nanoplatforms were further well developed for the simultaneous quantification of five-plex SARS-CoV-2 biomarkers with limits of detection in the subnanomolar range. Remarkably, PersL nanoplatforms enabled a highly differentiable discrimination of multitargets at various concentrations of ultralow background and high-fidelity resolutions, thereby advancing a powerful tool for optical multiplexing in biomedical applications.},
}
@article {pmid36423582,
year = {2022},
author = {Fang, W and Bell, CM and Sapirstein, A and Asami, S and Leeper, K and Zack, DJ and Ji, H and Kalhor, R},
title = {Quantitative fate mapping: A general framework for analyzing progenitor state dynamics via retrospective lineage barcoding.},
journal = {Cell},
volume = {185},
number = {24},
pages = {4604-4620.e32},
pmid = {36423582},
issn = {1097-4172},
support = {R01 HG009518/HG/NHGRI NIH HHS/United States ; U01 HL156056/HL/NHLBI NIH HHS/United States ; P30 EY001765/EY/NEI NIH HHS/United States ; R01 HG012357/HG/NHGRI NIH HHS/United States ; R01 HG010889/HG/NHGRI NIH HHS/United States ; F31 EY030769/EY/NEI NIH HHS/United States ; },
mesh = {Cell Lineage/genetics ; Retrospective Studies ; Phylogeny ; *Embryonic Development ; Mutagenesis ; },
abstract = {Natural and induced somatic mutations that accumulate in the genome during development record the phylogenetic relationships of cells; whether these lineage barcodes capture the complex dynamics of progenitor states remains unclear. We introduce quantitative fate mapping, an approach to reconstruct the hierarchy, commitment times, population sizes, and commitment biases of intermediate progenitor states during development based on a time-scaled phylogeny of their descendants. To reconstruct time-scaled phylogenies from lineage barcodes, we introduce Phylotime, a scalable maximum likelihood clustering approach based on a general barcoding mutagenesis model. We validate these approaches using realistic in silico and in vitro barcoding experiments. We further establish criteria for the number of cells that must be analyzed for robust quantitative fate mapping and a progenitor state coverage statistic to assess the robustness. This work demonstrates how lineage barcodes, natural or synthetic, enable analyzing progenitor fate and dynamics long after embryonic development in any organism.},
}
@article {pmid36421774,
year = {2022},
author = {Safhi, FA and ALshamrani, SM and Jalal, AS and El-Moneim, DA and Alyamani, AA and Ibrahim, AA},
title = {Genetic Characterization of Some Saudi Arabia's Accessions from Commiphora gileadensis Using Physio-Biochemical Parameters, Molecular Markers, DNA Barcoding Analysis and Relative Gene Expression.},
journal = {Genes},
volume = {13},
number = {11},
pages = {},
pmid = {36421774},
issn = {2073-4425},
mesh = {*Commiphora/genetics ; *DNA Barcoding, Taxonomic ; Saudi Arabia ; Phylogeny ; Plant Breeding ; Codon, Initiator ; Genetic Markers ; Gene Expression ; Defensins/genetics ; },
abstract = {Commiphora gileadensis L. is a medicinal plant, known as balsam, with pharmaceutical potential for its phytochemical activities and chemical constituents. Genetic diversity is a genetic tool used in medicinal plant evolution and conservation. Three accessions from C. gileadensis were collected from three localities in Saudi Arabia (Jeddah, Jizan and Riyadh). Genetic characterization was carried out using physio-biochemical parameters, molecular markers (inter-simple sequence repeat (ISSR) and start codon targeted (SCoT)), DNA barcoding (18 S rRNA and ITS rDNA regions), relative gene expressions (phenylalanine ammonia-lyase 1 (PAL1), defensin (PR-12)) and pathogenesis-related protein (AFPRT). The results of this study showed that C. gileadensis accession C3, collected from Riyadh, had the highest content from the physio-biochemical parameters perspective, with values of 92.54 mg/g and 77.13 mg/g for total phenolic content (TPC) and total flavonoid content (TFC), respectively. Furthermore, the highest content of antioxidant enzyme activity was present in accession C3 with values of 16.87, 60.87, 35.76 and 27.98 U mg[-1] for superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) (mol/min/mg FW) and ascorbate peroxidase (APX) (U mg[-1] protein), respectively. The highest total number of bands and number of unique bands were 138 and 59, respectively, for the SCoT marker. The SCoT marker was the most efficient for the genetic diversity of C. gileadensis by producing the highest polymorphism (75.63%). DNA barcoding using 18 S and ITS showed the nearby Commiphora genus and clustered C. gileadensis accessions from Jeddah and Jizan in one clade and the C. gileadensis accession from Ryiadh in a separate cluster. Moreover, relative gene expression of the PAL1, defensin (PR-12) and AFPRT (PR1) genes was upregulated in the C. gileadensis accession from Ryiadh. In conclusion, ecological and environmental conditions in each locality affect the genomic expression and genetic diversity, which can help the evolution of important medicinal plants and improve breeding and conservation systems.},
}
@article {pmid36419198,
year = {2022},
author = {Hoque, MM and Valentine, MJ and Kelly, PJ and Barua, S and Murillo, DFB and Wang, C},
title = {Modification of the Folmer primers for the cytochrome c oxidase gene facilitates identification of mosquitoes.},
journal = {Parasites &amp; vectors},
volume = {15},
number = {1},
pages = {437},
pmid = {36419198},
issn = {1756-3305},
support = {R21 AI128407/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Electron Transport Complex IV/genetics ; DNA Primers/genetics ; *Anopheles ; *Aedes ; *Culex ; },
abstract = {BACKGROUND: Accurate identification of mosquito species is essential for the development and optimization of strategies to control mosquitoes and mosquito-borne diseases. Problems with the morphological identification of mosquito species have led to the use of molecular identification techniques, in particular the Folmer cytochrome c oxidase subunit I (COI) PCR system (FCOS), originally designed to identify a range of other invertebrates.<br><br>METHODS: As there can be difficulties identifying mosquitoes using FCOS, we re-evaluated the FCOS primers and developed a new COI-based SYBR PCR (the Auburn COI system-AUCOS) to improve the molecular identification of mosquitoes. Sequence data in GenBank for 33 species from 10 genera of mosquitoes were used to develop our AUCOS primers. Two molecular assays (AUCOS, FCOS) and morphological identification were carried out on mosquitoes collected from the field in Auburn, Alabama (USA) and on Saint Kitts.<br><br>RESULTS: With a convenience sample of individual mosquitoes comprising 19 species from six genera in Saint Kitts (n&#x2009;=&#x2009;77) and Auburn (n&#x2009;=&#x2009;48), our AUCOS provided higher-quality sequence data than FCOS. It also proved more sensitive than FCOS, successfully amplifying 67.5% (85/126) as opposed to 16.7% (21/126) of the samples. The species determined by morphology, or genus with damaged samples, matched that as determined by AUCOS for 84.9% (62/73) of the samples. Morphological classification was confirmed by FCOS with 81.0% (17/21) of samples producing utilizable sequences. While both FCOS and AUCOS correctly identified all the Aedes, Anopheles, Deinocerites, and Uranotaenia species in the study, identification of Culex species was less successful with both methods: 50.0% (3/6) by FCOS and 35.7% (5/14) by AUCOS.<br><br>CONCLUSIONS: The AUCOS DNA barcoding system for mosquito species described in this study is superior to the existing FCOS for the identification of mosquito species. As AUCOS and FCOS amplify the same variable region of the COI, the large amount of existing data on GenBank can be used to identify mosquito species with sequences produced by either PCR.},
}
@article {pmid36418947,
year = {2022},
author = {Tong, R and Gui, C and Zhang, Y and Su, N and Hou, X and Liu, M and Yang, Z and Kang, B and Chang, Z and Jabbour, F and Zhao, L},
title = {Phylogenomics, plastome structure and species identification in Mahonia (Berberidaceae).},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {766},
pmid = {36418947},
issn = {1471-2164},
mesh = {*Berberidaceae ; *Mahonia ; Phylogeny ; *Genome, Plastid ; Hybridization, Genetic ; },
abstract = {BACKGROUND: Elucidating the phylogenetic relationships within species-rich genera is essential but challenging, especially when lineages are assumed to have been going through radiation events. Mahonia Nutt. (Berberidaceae) is a genus with cosmopolitan distribution, comprising approximately 100 species, two of which are known as Caulis Mahoniae (M. bealei and M. fortunei) with crucial pharmacological significance in Chinese herbal medicine. Mahonia is a taxonomically challenging genus, and intrageneric phylogenetic relationships still need to be explored using genome data. Universal DNA barcodes and floral morphological attributes have limited discriminatory power in Mahonia.<br><br>RESULTS: We sequenced 17 representative plastomes and integrated three published plastome data together to conduct comparative and phylogenetic analyses. We found that Mahonia and Berberis share a large IR expansion (~&#x2009;12&#xa0;kb), which is recognized as a typical character of Berberideae. Repeated sequences are revealed in the species of Mahonia, which are valuable for further population genetic studies. Using a comparative plastome analysis, we determined eight hypervariable regions whose discriminative power is comparable to that of the whole plastid genomes. The incongruence of the ITS and the plastome tree topologies may be ascribed to ancestral hybridization events and/or to incomplete lineage sorting. In addition, we suggest that leaf epidermal characters could help to distinguish closely related species in Mahonia.<br><br>CONCLUSIONS: We propose an integrative approach combining special barcodes and micromorphological traits to circumscribe Mahonia species. The results cast a new light on the development of an integrative method for accurate species circumscription and provide abundant genetic resources for further research on Mahonia.},
}
@article {pmid36418775,
year = {2023},
author = {Lira, NL and Tonello, S and Lui, RL and Traldi, JB and Brandão, H and Oliveira, C and Blanco, DR},
title = {Identifying fish eggs and larvae: from classic methodologies to DNA metabarcoding.},
journal = {Molecular biology reports},
volume = {50},
number = {2},
pages = {1713-1726},
pmid = {36418775},
issn = {1573-4978},
mesh = {Animals ; Larva/genetics ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics ; DNA ; Biodiversity ; },
abstract = {Studies involving fish eggs and larvae date back to the end of the nineteenth century. Since then, studies with ichthyoplankton have proved to be an essential tool, generating information for the knowledge of the ichthyofauna and the environmental inventory. Most of these studies reveal the difficulty of obtaining a precise taxonomic identification of the collected materials, making research with ichthyoplankton extremely challenging. With the advent of molecular biology, the use of markers such as COI enabled greater taxonomic precision, helping to understand events involving ichthyofauna. Now we can observe the evolution of the molecular identification tool for ichthyoplankton via DNA barcoding, which has been increasingly used over the last few decades. From 2000 to 2010, we found six publications; from 2011 to 2021, 75 papers were published, and in 2022 four studies. Our survey also showed the accuracy of molecular identification when compared to the taxonomic identification of these. In this review, we show the state of the art of studies that used barcode and DNA metabarcoding to identify fish eggs and larvae in different environments and discuss their importance as the best practice for working with these organisms.},
}
@article {pmid36418727,
year = {2023},
author = {Babcock, B and Weir, S},
title = {scRNA-seq for Microcephaly Research [I]: Single-Cell Droplet Encapsulation, mRNA Capture, and cDNA Synthesis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2583},
number = {},
pages = {83-97},
pmid = {36418727},
issn = {1940-6029},
mesh = {Humans ; *Microcephaly ; DNA, Complementary/genetics ; RNA, Messenger/genetics ; Single-Cell Analysis ; Exome Sequencing ; },
abstract = {Single-cell RNA sequencing (scRNA-seq) allows for the transcriptomic profiling of a sample tissue with single-cell resolution. The concept of scRNA-seq builds on traditional, "bulk" RNA-seq by recording and preserving the cellular origin of each transcript throughout library preparation. Here we describe an adaptation of the Drop-Seq method (Macosko et al. Cell 161, 1202-1214, 2015), in which nanoliter-scale droplets are used to physically separate dissociated cells, while a cell-specific DNA barcode is simultaneously introduced. Following barcoding, cDNAs can be mixed and pooled while retaining the identity of the cell of origin. The benefit of the Drop-Seq approach is high throughput from relatively small samples of tissue. The method described here is appropriate for processing an input of as few as 150,000 cells, with a final yield of as many as 5000 single-cell transcripts captured.},
}
@article {pmid36418429,
year = {2022},
author = {Cannet, A and Simon-Chane, C and Akhoundi, M and Histace, A and Romain, O and Souchaud, M and Jacob, P and Delaunay, P and Sereno, D and Bousses, P and Grebaut, P and Geiger, A and de Beer, C and Kaba, D and Sereno, D},
title = {Wing Interferential Patterns (WIPs) and machine learning, a step toward automatized tsetse (Glossina spp.) identification.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {20086},
pmid = {36418429},
issn = {2045-2322},
mesh = {Animals ; Humans ; *Tsetse Flies ; *Trypanosomiasis, African ; Machine Learning ; Databases, Factual ; Neglected Diseases ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {A simple method for accurately identifying Glossina spp in the field is a challenge to sustain the future elimination of Human African Trypanosomiasis (HAT) as a public health scourge, as well as for the sustainable management of African Animal Trypanosomiasis (AAT). Current methods for Glossina species identification heavily rely on a few well-trained experts. Methodologies that rely on molecular methodologies like DNA barcoding or mass spectrometry protein profiling (MALDI TOFF) haven't been thoroughly investigated for Glossina sp. Nevertheless, because they are destructive, costly, time-consuming, and expensive in infrastructure and materials, they might not be well adapted for the survey of arthropod vectors involved in the transmission of pathogens responsible for Neglected Tropical Diseases, like HAT. This study demonstrates a new type of methodology to classify Glossina species. In conjunction with a deep learning architecture, a database of Wing Interference Patterns (WIPs) representative of the Glossina species involved in the transmission of HAT and AAT was used. This database has 1766 pictures representing 23 Glossina species. This cost-effective methodology, which requires mounting wings on slides and using a commercially available microscope, demonstrates that WIPs are an excellent medium to automatically recognize Glossina species with very high accuracy.},
}
@article {pmid36415871,
year = {2022},
author = {Nyman, T and Wutke, S and Koivisto, E and Klemola, T and Shaw, MR and Andersson, T and Haraldseide, H and Hagen, SB and Nakadai, R and Ruohomäki, K},
title = {A curated DNA barcode reference library for parasitoids of northern European cyclically outbreaking geometrid moths.},
journal = {Ecology and evolution},
volume = {12},
number = {11},
pages = {e9525},
pmid = {36415871},
issn = {2045-7758},
abstract = {Large areas of forests are annually damaged or destroyed by outbreaking insect pests. Understanding the factors that trigger and terminate such population eruptions has become crucially important, as plants, plant-feeding insects, and their natural enemies may respond differentially to the ongoing changes in the global climate. In northernmost Europe, climate-driven range expansions of the geometrid moths Epirrita autumnata and Operophtera brumata have resulted in overlapping and increasingly severe outbreaks. Delayed density-dependent responses of parasitoids are a plausible explanation for the 10-year population cycles of these moth species, but the impact of parasitoids on geometrid outbreak dynamics is unclear due to a lack of knowledge on the host ranges and prevalences of parasitoids attacking the moths in nature. To overcome these problems, we reviewed the literature on parasitism in the focal geometrid species in their outbreak range and then constructed a DNA barcode reference library for all relevant parasitoid species based on reared specimens and sequences obtained from public databases. The combined recorded parasitoid community of E. autumnata and O. brumata consists of 32 hymenopteran species, all of which can be reliably identified based on their barcode sequences. The curated barcode library presented here opens up new opportunities for estimating the abundance and community composition of parasitoids across populations and ecosystems based on mass barcoding and metabarcoding approaches. Such information can be used for elucidating the role of parasitoids in moth population control, possibly also for devising methods for reducing the extent, intensity, and duration of outbreaks.},
}
@article {pmid36415859,
year = {2022},
author = {Willassen, E and Westgaard, JI and Kongsrud, JA and Hanebrekke, T and Buhl-Mortensen, P and Holte, B},
title = {Benthic invertebrates in Svalbard fjords-when metabarcoding does not outperform traditional biodiversity assessment.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e14321},
pmid = {36415859},
issn = {2167-8359},
mesh = {Animals ; *Ecosystem ; Svalbard ; *Estuaries ; DNA Barcoding, Taxonomic/methods ; Environmental Monitoring/methods ; Invertebrates/genetics ; Biodiversity ; DNA/genetics ; },
abstract = {To protect and restore ecosystems and biodiversity is one of the 10 challenges identified by the United Nations's Decade of the Ocean Science. In this study we used eDNA from sediments collected in two fjords of the Svalbard archipelago and compared the taxonomic composition with traditional methods through metabarcoding, targeting mitochondrial CO1, to survey benthos. Clustering of 21.6 mill sequence reads with a d value of 13 in swarm, returned about 25 K OTU reads. An identification search with the BOLD database returned 12,000 taxonomy annotated sequences spanning a similarity range of 50% to 100%. Using an acceptance filter of minimum 90% similarity to the CO1 reference sequence, we found that 74% of the ca 100 taxon identified sequence reads were Polychaeta and 22% Nematoda. Relatively few other benthic invertebrate species were detected. Many of the identified sequence reads were extra-organismal DNA from terrestrial, planktonic, and photic zone sources. For the species rich Polychaeta, we found that, on average, only 20.6% of the species identified from morphology were also detected with DNA. This discrepancy was not due to missing reference sequences in the search database, because 90-100% (mean 96.7%) of the visually identified species at each station were represented with barcodes in Boldsystems. The volume of DNA samples is small compared with the volume searched in visual sorting, and the replicate DNA-samples in sum covered only about 2% of the surface area of a grab. This may considerably reduce the detection rate of species that are not uniformly distributed in the sediments. Along with PCR amplification bias and primer mismatch, this may be an important reason for the limited congruence of species identified with the two approaches. However, metabarcoding also identified 69 additional species that are usually overlooked in visual sample sorting, demonstrating how metabarcoding can complement traditional methodology by detecting additional, less conspicuous groups of organisms.},
}
@article {pmid36414009,
year = {2022},
author = {Hausmann, FS and Barrett, JM and Martin, ME and Zhan, H and Shepherd, GMG},
title = {Axonal Barcode Analysis of Pyramidal Tract Projections from Mouse Forelimb M1 and M2.},
journal = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
volume = {42},
number = {41},
pages = {7733-7743},
pmid = {36414009},
issn = {1529-2401},
support = {R01 NS061963/NS/NINDS NIH HHS/United States ; R34 NS116713/NS/NINDS NIH HHS/United States ; },
mesh = {Female ; Male ; Mice ; Animals ; *Pyramidal Tracts/physiology ; Axons/physiology ; Forelimb ; *Motor Cortex/physiology ; Upper Extremity ; },
abstract = {Forelimb-related areas of the motor cortex communicate directly to downstream areas in the brainstem and spinal cord via axons that project to and through the pyramidal tract (PT). To better understand the diversity of the brainstem branching patterns of these pyramidal tract projections, we used MAPseq, a molecular barcode technique for population-scale sampling with single-axon resolution. In experiments using mice of both sexes, we first confirmed prior results demonstrating the basic efficacy of axonal barcode identification of primary motor cortex (M1) PT-type axons, including corticobulbar (CBULB) and corticospinal (CSPI) subclasses. We then used multiplexed MAPseq to analyze projections from M1 and M2 (caudal and rostral forelimb areas). The four basic axon subclasses comprising these projections (M1-CSPI, M1-CBULB, M2-CSPI, M2-CBULB) showed a complex mix of differences and similarities in their brainstem projection profiles. This included relatively abundant branching by all classes in the dorsal midbrain, by M2 subclasses in the pons, and by CSPI subclasses in the dorsal medulla. Cluster analysis showed graded distributions of the basic subclasses within the PT class. Clusters were of diversely mixed subclass composition and showed distinct rostrocaudal and/or dorsomedial projection biases. Exemplifying these patterns was a subcluster likely enriched in corticocuneate branches. Overall, the results indicate high yet systematic PT axon diversity at the level of brainstem branching patterns; projections of M1 and M2 appear qualitatively similar, yet with quantitative differences in subclasses and clusters.SIGNIFICANCE STATEMENT Axons of the PT class of cortical projection neurons, which includes corticospinal and corticobulbar neurons, anatomically link motor cortex to brainstem and spinal cord circuits. Both of these subclasses can form branches to brainstem destinations along the way, but the extent and diversity of these branching patterns is incompletely understood. Here, we used MAPseq to tag PT axons with individual molecular barcodes for high-throughput quantification of branching patterns across the brainstem. The results reveal diverse, complex, yet systematic branching patterns of corticospinal and corticobulbar neurons arising from two motor cortex areas, M1 and M2.},
}
@article {pmid36413582,
year = {2022},
author = {Blois, S and Goetz, BM and Bull, JJ and Sullivan, CS},
title = {Interpreting and de-noising genetically engineered barcodes in a DNA virus.},
journal = {PLoS computational biology},
volume = {18},
number = {11},
pages = {e1010131},
pmid = {36413582},
issn = {1553-7358},
support = {R21 AI147178/AI/NIAID NIH HHS/United States ; },
mesh = {Mice ; Animals ; *DNA Viruses/genetics ; *Nucleic Acids ; },
abstract = {The concept of a nucleic acid barcode applied to pathogen genomes is easy to grasp and the many possible uses are straightforward. But implementation may not be easy, especially when growing through multiple generations or assaying the pathogen long-term. The potential problems include: the barcode might alter fitness, the barcode may accumulate mutations, and construction of the marked pathogens may result in unintended barcodes that are not as designed. Here, we generate approximately 5,000 randomized barcodes in the genome of the prototypic small DNA virus murine polyomavirus. We describe the challenges faced with interpreting the barcode sequences obtained from the library. Our Illumina NextSeq sequencing recalled much greater variation in barcode sequencing reads than the expected 5,000 barcodes-necessarily stemming from the Illumina library processing and sequencing error. Using data from defined control virus genomes cloned into plasmid backbones we develop a vetted post-sequencing method to cluster the erroneous reads around the true virus genome barcodes. These findings may foreshadow problems with randomized barcodes in other microbial systems and provide a useful approach for future work utilizing nucleic acid barcoded pathogens.},
}
@article {pmid36413486,
year = {2022},
author = {Khan, MAA and Ghosh, P and Chowdhury, R and Hossain, F and Mahmud, A and Faruque, ASG and Ahmed, T and Abd El Wahed, A and Mondal, D},
title = {Feasibility of MinION Nanopore Rapid Sequencing in the Detection of Common Diarrhea Pathogens in Fecal Specimen.},
journal = {Analytical chemistry},
volume = {94},
number = {48},
pages = {16658-16666},
doi = {10.1021/acs.analchem.2c02771},
pmid = {36413486},
issn = {1520-6882},
mesh = {Humans ; *Nanopores ; *Nanopore Sequencing ; Feasibility Studies ; Diarrhea/etiology/microbiology ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; },
abstract = {The need for fast detection of etiological agents outside the narrow target range of pathogens that may cause an event of an infectious disease epidemic necessitates rapid sequencing technologies to be implemented in routine diagnostic procedures. We tested the performance of a PCR-free rapid nanopore barcoding assay to detect microbial species by analyzing genomic contents extracted from acute diarrheal case specimens. Sequenced reads were processed in an automated analysis module for species identification, whereas pathogenic subspecies detection was aided by a sequence similarity search against a gene-specific database. Evaluation of assay and analysis parameters (e.g., run-time, sequence length, and species hit abundance level) was carried out using a standard bacterial community for assessing detection accuracy. It was observed that longer sequence length (≥500 nucleotides) along with higher species abundance level (≥1%) can be critical for exclusion of false-negative outcomes, while increased sequencing run-time can affect the proportional abundance of true-positive species. Under optimal parameters, the sensitivity of the rapid assay remained 100% for the detection of a target species in a background of nontarget fecal (diarrheal) DNA that weighed up to 64 times the DNA of the target species. The method was applied to acute diarrheal samples. Among these, 62.5% (5/8) were in agreement with target-specific traditional diagnosis methods for the presence/absence of pathogenic agent(s), 12.5% (1/8) were in disagreement, and pathogenic agents that were not targeted by the traditional methods were revealed by sequencing for 25% (2/8) of samples. These observations suggest that further optimization and evaluation of the rapid nanopore sequencing method could potentiate the widening of the range of pathogens that can be detected in acute diarrheal samples in the context of regular diagnostic needs as well as epidemics.},
}
@article {pmid36412588,
year = {2022},
author = {Zhao, Q and Pan, B and Long, W and Pan, Y and Zhou, D and Luan, X and He, B and Wang, Y and Song, Y},
title = {Metal Organic Framework-Based Bio-Barcode CRISPR/Cas12a Assay for Ultrasensitive Detection of MicroRNAs.},
journal = {Nano letters},
volume = {22},
number = {23},
pages = {9714-9722},
doi = {10.1021/acs.nanolett.2c04022},
pmid = {36412588},
issn = {1530-6992},
mesh = {Humans ; Female ; *MicroRNAs/genetics ; *Metal-Organic Frameworks ; CRISPR-Cas Systems/genetics ; *Breast Neoplasms/diagnosis/genetics ; Cell Differentiation ; *Biosensing Techniques ; },
abstract = {CRISPR/Cas12a has shown great potential in molecular diagnostics, but its application in sensing of microRNAs (miRNAs) was limited by sensitivity and complexity. Here, we have sensitively and conveniently detected microRNAs by reasonably integrating metal-organic frameworks (MOFs) based biobarcodes with CRISPR/Cas12a assay (designated as MBCA). In this work, DNA-functionalized Zr-MOFs were designed as the converter to convert and amplify each miRNA target into activators that can initiate the trans-cleavage activity of CRISPR/Cas12a to further amplify the signal. Such integration provides a universal strategy for sensitive detection of miRNAs. By tuning the complementary sequences modified on nanoprobes, this assay achieves subattomolar sensitivity for different miRNAs and was selective to single-based mismatches. With the proposed method, the expression of miR-21 in different cancer cells can be assessed, and breast cancer patients and healthy individuals can be differentiated by analyzing the target miRNAs extracted from serum samples, holding great potential in clinical diagnosis.},
}
@article {pmid36410732,
year = {2022},
author = {Wei, W and Lu, H and Dai, W and Zheng, X and Dong, H},
title = {Multiplexed Organelles Portrait Barcodes for Subcellular MicroRNA Array Detection in Living Cells.},
journal = {ACS nano},
volume = {16},
number = {12},
pages = {20329-20339},
doi = {10.1021/acsnano.2c06252},
pmid = {36410732},
issn = {1936-086X},
mesh = {*MicroRNAs/genetics ; Fluorescent Dyes/metabolism ; *Tranexamic Acid/metabolism ; Organelles ; Endoplasmic Reticulum ; Molecular Probes/metabolism ; },
abstract = {Multiplexed profiling of microRNAs' subcellular expression and distribution is essential to understand their spatiotemporal function information, but it remains a crucial challenge. Herein, we report an encoding approach that leverages combinational fluorescent dye barcodes, organelle targeting elements, and an independent quantification signal, termed Multiplexed Organelles Portrait Barcodes (MOPB), for high-throughput profiling of miRNAs from organelles. The MOPB barcodes consist of heterochromatic fluorescent dye-loaded shell-core mesoporous silica nanoparticles modified with organelle targeting peptides and molecular beacon detection probes. Using mitochondria and endoplasmic reticulum as models, we encoded four Cy3/AMCA ER-MOPB and four Cy5/AMCA Mito-MOPB by varying the Cy3 and Cy5 intensity for distinguishing eight organelles' miRNAs. Significantly, the MOPB strategy successfully and accurately profiled eight subcellular organelle miRNAs' alterations in the drug-induced Ca[2+] homeostasis breakdown. The approach should allow more widespread application of subcellular miRNAs and multiplexed subcellular protein biomarkers' monitoring for drug discovery, cellular metabolism, signaling transduction, and gene expression regulation readout.},
}
@article {pmid36410451,
year = {2023},
author = {Sagitov, S and Ståhlberg, A},
title = {Counting unique molecular identifiers in sequencing using a multi-type branching process with immigration.},
journal = {Journal of theoretical biology},
volume = {558},
number = {},
pages = {111365},
doi = {10.1016/j.jtbi.2022.111365},
pmid = {36410451},
issn = {1095-8541},
mesh = {*Emigration and Immigration ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Polymerase Chain Reaction/methods ; DNA ; },
abstract = {Detection of extremely rare variant alleles, such as tumor DNA, within a complex mixture of DNA molecules is experimentally challenging due to sequencing errors. Barcoding of target DNA molecules in library construction for next-generation sequencing provides a way to identify and bioinformatically remove polymerase induced errors. During the barcoding procedure involving t consecutive PCR cycles, the DNA molecules become barcoded by Unique Molecular Identifiers (UMIs). Different library construction protocols utilize different values of t. The effect of a larger t and imperfect PCR amplifications in relation to UMI cluster sizes is poorly described. This paper proposes a branching process with growing immigration as a model describing the random outcome of t cycles of PCR barcoding. Our model discriminates between five different amplification rates r1, r2, r3, r4, r for different types of molecules associated with the PCR barcoding procedure. We study this model by focussing on Ct, the number of clusters of molecules sharing the same UMI, as well as Ct(m), the number of UMI clusters of size m. Our main finding is a remarkable asymptotic pattern valid for moderately large t. It turns out that E(Ct(m))/E(Ct)≈2[-m] for m=1,2,…, regardless of the underlying parameters (r1,r2,r3,r4,r). The knowledge of the quantities Ct and Ct(m) as functions of the experimental parameters t and (r1,r2,r3,r4,r) will help the users to draw more adequate conclusions from the outcomes of different sequencing protocols.},
}
@article {pmid36409146,
year = {2022},
author = {Monod, V and Hofstetter, V and Zufferey, V and Viret, O and Gindro, K and Croll, D},
title = {Quantifying Trade-Offs in the Choice of Ribosomal Barcoding Markers for Fungal Amplicon Sequencing: a Case Study on the Grapevine Trunk Mycobiome.},
journal = {Microbiology spectrum},
volume = {10},
number = {6},
pages = {e0251322},
pmid = {36409146},
issn = {2165-0497},
mesh = {DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; Ecosystem ; Fungi ; High-Throughput Nucleotide Sequencing/methods ; *Mycobiome/genetics ; Phylogeny ; *Vitis/microbiology ; },
abstract = {The evolution of sequencing technology and multiplexing has rapidly expanded our ability to characterize fungal diversity in the environment. However, obtaining an unbiased assessment of the fungal community using ribosomal markers remains challenging. Longer amplicons were shown to improve taxonomic resolution and resolve ambiguities by reducing the risk of spurious operational taxonomic units. We examined the implications of barcoding strategies by amplifying and sequencing two ribosomal DNA fragments. We analyzed the performance of the full internal transcribed spacer (ITS) and a longer fragment including also a part of the 28S ribosomal subunit replicated on 60 grapevine trunk core samples. Grapevine trunks harbor highly diverse fungal communities with implications for disease development. Using identical handling, amplification, and sequencing procedures, we obtained higher sequencing depths for the shorter ITS amplicon. Despite the more limited access to polymorphism, the overall diversity in amplified sequence variants was higher for the shorter ITS amplicon. We detected no meaningful bias in the phylogenetic composition due to the amplicon choice across analyzed samples. Despite the increased resolution of the longer ITS-28S amplicon, the higher and more consistent yields of the shorter amplicons produced a clearer resolution of the fungal community of grapevine stem samples. Our study highlights that the choice of ribosomal amplicons should be carefully evaluated and adjusted according to specific goals. IMPORTANCE Surveying fungal communities is key to our understanding of ecological functions of diverse habitats. Fungal communities can inform about the resilience of agricultural ecosystems, risks to human health, and impacts of pathogens. Community compositions are typically analyzed using ribosomal DNA sequences. Due to technical limitations, most fungal community surveys were based on amplifying a short but highly variable fragment. Advances in sequencing technology enabled the use of longer fragments that can address some limitations of species identification. In this study, we examined the implications of choosing either a short or long ribosomal sequence fragment by replicating the analyses on 60 grapevine wood core samples. Using highly accurate long-read sequencing, we found that the shorter fragment produced substantially higher yields. The shorter fragment also revealed more sequence and species diversity. Our study highlights that the choice of ribosomal amplicons should be carefully evaluated and adjusted according to specific goals.},
}
@article {pmid36405018,
year = {2022},
author = {Gold, Z and Wall, AR and Schweizer, TM and Pentcheff, ND and Curd, EE and Barber, PH and Meyer, RS and Wayne, R and Stolzenbach, K and Prickett, K and Luedy, J and Wetzer, R},
title = {A manager's guide to using eDNA metabarcoding in marine ecosystems.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e14071},
pmid = {36405018},
issn = {2167-8359},
support = {GT10483/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {*Ecosystem ; *DNA, Environmental/genetics ; DNA Barcoding, Taxonomic/methods ; Environmental Monitoring/methods ; Biodiversity ; },
abstract = {Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA monitoring program: (1) select genes and primers to target taxa; (2) assemble or develop comprehensive barcode reference databases; (3) apply rigorous site occupancy based decontamination pipelines; (4) conduct pilot studies to define spatial and temporal variance of eDNA; and (5) archive samples, extracts, and raw sequence data. We demonstrate the importance of each of these considerations using a case study of eDNA metabarcoding in the Ports of Los Angeles and Long Beach. eDNA metabarcoding approaches detected 94.1% (16/17) of species observed in paired trawl surveys while identifying an additional 55 native fishes, providing more comprehensive biodiversity inventories. Rigorous benchmarking of eDNA metabarcoding results improved ecological interpretation and confidence in species detections while providing archived genetic resources for future analyses. Well designed and validated eDNA metabarcoding approaches are ideally suited for biomonitoring applications that rely on the detection of species, including mapping invasive species fronts and endangered species habitats as well as tracking range shifts in response to climate change. Incorporating these considerations will enhance the utility and efficacy of eDNA metabarcoding for routine biomonitoring applications.},
}
@article {pmid36404727,
year = {2023},
author = {Razaq, A and Ishaq, A and Ilyas, S and Niaz, S and Sadia, S},
title = {Termitomyces pakistanensis, a new mushroom species from Pakistan based on scanning electron microscopy and ITS-rDNA barcoding.},
journal = {Microscopy research and technique},
volume = {86},
number = {1},
pages = {115-121},
doi = {10.1002/jemt.24265},
pmid = {36404727},
issn = {1097-0029},
support = {7064/2017//Higher Education Commission (HEC) of Pakistan/ ; },
mesh = {DNA, Ribosomal/genetics ; *Agaricales/genetics ; Microscopy, Electron, Scanning ; *Termitomyces/genetics ; Pakistan ; Phylogeny ; DNA, Ribosomal Spacer/genetics ; DNA, Fungal/genetics ; *Basidiomycota/genetics ; Spores, Fungal/genetics ; Sequence Analysis, DNA ; },
abstract = {Termitomyces pakistanensis sp. nov. is a member of an edible genus generally distributed in Asia and Europe. This species has been described as new species based on its different morphology, and scanning electron microscopy (SEM) of basidiospores. The novelty and degree of endemism is confirmed by analyzing the genetic variation of the internal transcribed spacer regions (ITS1-5.8 S-ITS2) of the ribosomal DNA gene, a universal fungal marker. The evolutionary affinities of new species is also evaluated with Asian and European species by phylogenetic analysis based on ITS sequences. In our phylogenetic analysis, this genus is found monophyletic comprising of two monophyletic sub clades: Clade I, Microcarpus, with small sized fruiting bodies generally less than 5 cm without pseudorrhiza and Clade II, Macrocarpus, with large sized fruiting bodies generally more than 5 cm having pseudorrhiza. All collections of Pakistani species clustered independently in Microcarpus clade showing their endemic genetic makeup as it is clustering independently. A comprehensive description, photographs of the basidiocarps and Scanning electron microscopy (SEM) micrographs of spores are provided. RESEARCH HIGHLIGHTS: It has a new species from Pakistan to world based on the scanning electron microscopy and further confirmed by DNA barcoding. The exact shape and size of basidiospores of this novel species is first time introduced by using SEM analysis. This genus is rarely described from Pakistan. This paper has introduced a two clade, Microcarpus and macrocarpus, in the world for this genus.},
}
@article {pmid36399690,
year = {2023},
author = {Leontyev, D and Buttgereit, M and Kochergina, A and Shchepin, O and Schnittler, M},
title = {Two independent genetic markers support separation of the myxomycete Lycogala epidendrum into numerous biological species.},
journal = {Mycologia},
volume = {115},
number = {1},
pages = {32-43},
doi = {10.1080/00275514.2022.2133526},
pmid = {36399690},
issn = {1557-2536},
mesh = {Sequence Analysis, DNA ; *Myxomycetes/genetics ; Genetic Markers ; RNA, Ribosomal, 18S/genetics ; DNA, Ribosomal/genetics ; Phylogeny ; },
abstract = {Lycogala epidendrum is one of the most widely known myxomycete species and the first-ever discovered representative of this group. Using 687 original DNA sequences from 330 herbarium specimens from Europe, Asia, North and Central America, and Australia, we constructed the first detailed phylogenies of the genus Lycogala, based on two independently inherited genetic markers, the ribosome small subunit 18S rRNA nuclear gene (18S rDNA) and the mitochondrial cytochrome oxidase subunit I gene (COI). In both phylogenies, L. epidendrum appeared to be a polyphyletic group, represented by numerous clades. The four other recognized species of the genus (L. confusum, L. conicum, L. exiguum, and L. flavofuscum) are scattered between branches corresponding to L. epidendrum. A barcode gap analysis revealed 60 18S rDNA phylogroups of L. epidendrum, which are distant from each other not less than from other species of the genus Lycogala. For 18 of these phylogroups with both 18S rDNA and COI sequences available, recombination patterns were analyzed to test for reproductive isolation. In contrast to the results of a simulation assuming panmixis, no crossing between ribosomal and mitochondrial phylogroups was found, thus allowing the conclusion that all tested phylogroups represent biospecies. More than one third (39.6%) of the studied specimens share a single 18S rDNA phylogroup, which we consider to be L. epidendrum s. str. This group displays the broadest geographic distribution and the highest intraspecific genetic variability. Nearly all (93.3%) of the remaining non-singleton 18S rDNA phylogroups are restricted to certain continents or even regions. At the same time, various reproductively isolated phylogroups occur sympatric at a given location.},
}
@article {pmid36399330,
year = {2022},
author = {Kovach, BC and Reeves, LE and Domingo, C and L'heureux, SN and Burger, GV and Schermerhorn, SD and Riles, MT},
title = {Aedes pertinax, Anopheles perplexens, Culex declarator, and Cx. interrogator: An Update of Mosquito Species Records for Charlotte County, Florida.},
journal = {Journal of the American Mosquito Control Association},
volume = {38},
number = {4},
pages = {241-249},
doi = {10.2987/22-7087},
pmid = {36399330},
issn = {1943-6270},
mesh = {Animals ; *Culex/genetics/anatomy &amp; histology ; *Anopheles/genetics ; *Aedes/anatomy &amp; histology ; Florida ; *Culicidae/anatomy &amp; histology ; *Ochlerotatus ; },
abstract = {Understanding the geographic occurrence of mosquito species is an important element to addressing public health and nuisance mosquito-related issues, particularly as changing climates and increased global connectivity is likely to facilitate changes in the distribution of mosquitoes and other species. In Charlotte County, FL, routine surveillance of mosquito species for public health in 2019-21 identified 4 mosquito species not previously documented in the county. Aedes pertinax, Anopheles perplexens, Culex declarator, and Cx. interrogator adults were collected and verified to species level. Aedes pertinax and Cx. declarator and were collected in 2019, whereas An. perplexens and Cx. interrogator were documented from collections in 2021. All 4 species were initially visually identified by external morphology and confirmed by sequencing the DNA barcoding region of the cytochrome c oxidase subunit I gene. Apart from native An. perplexens, in which only 1 specimen has been confirmed to date, the 3 newly documented nonnative species are now recognized throughout the county.},
}
@article {pmid36398942,
year = {2023},
author = {Abbasi, F and Asghari, Y and Niazkhani, Z},
title = {Information Adequacy in Histopathology Request Forms: A Milestone in Making a Communication Bridge Between Confusion and Clarity in Medical Diagnosis.},
journal = {Turk patoloji dergisi},
volume = {39},
number = {3},
pages = {185-191},
pmid = {36398942},
issn = {1309-5730},
mesh = {Humans ; Cross-Sectional Studies ; Retrospective Studies ; *Communication ; *Laboratories ; },
abstract = {OBJECTIVE: Information contained in request forms for histopathological examinations plays a critical role in the microscopic interpretation of tissue changes. Despite its importance, studies have shown inadequacies in the information communicated by clinicians. This study aimed to determine how well the necessary information is provided on the histopathology request forms and to compare its variability among different departments of a hospital.<br><br>MATERIAL AND METHOD: A retrospective, 3-month, cross-sectional study was conducted to evaluate all consecutive histopathology request forms received from different departments of a tertiary, academic hospital for three months, regarding the documentation of 12 criteria.<br><br>RESULTS: None of the 2040 requests received had all the required items. Four items of specimen description, laboratory and imaging findings, and physician contact number were available only in less than 12.5% (range between 0.05 to 12.45%) of the requests. However, four other items of patient name and contact number, physician name, and anatomical site of the lesion were documented in more than 90%. The median number of the documented items was the highest in the surgery and orthopedics (9 items) and the lowest in the pulmonology department (7 items). Comparison between departments showed that the documentation of items in the surgery department were significantly better than that of the ENT, urology, and internal medicine departments (p < 0.001). Also, the internal medicine department was significantly different from all other departments (p < 0.001) except neurosurgery (p=0.88).<br><br>CONCLUSION: Our results point out a serious gap in the adequacy of pathology request forms, especially clinical items. Given the implication of such information to ensure patient safety, further studies are recommended to evaluate the impact of educational and supportive computerized interventions such as clinician education and barcoding and specimen tracking systems to help fill in the required items completely.},
}
@article {pmid36395758,
year = {2023},
author = {Aggarwal, SD and Lees, JA and Jacobs, NT and Bee, GCW and Abruzzo, AR and Weiser, JN},
title = {BlpC-mediated selfish program leads to rapid loss of Streptococcus pneumoniae clonal diversity during infection.},
journal = {Cell host &amp; microbe},
volume = {31},
number = {1},
pages = {124-134.e5},
pmid = {36395758},
issn = {1934-6069},
support = {R01 AI150893/AI/NIAID NIH HHS/United States ; R01 AI050867/AI/NIAID NIH HHS/United States ; R37 AI038446/AI/NIAID NIH HHS/United States ; T32 AI007180/AI/NIAID NIH HHS/United States ; R01 AI038446/AI/NIAID NIH HHS/United States ; R21 AI150867/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; Animals ; Mice ; *Streptococcus pneumoniae/genetics ; *Bacteriocins/genetics ; Quorum Sensing ; Pheromones/genetics ; },
abstract = {Successful colonization of a host requires bacterial adaptation through genetic and population changes that are incompletely defined. Using chromosomal barcoding and high-throughput sequencing, we investigate the population dynamics of Streptococcus pneumoniae during infant mouse colonization. Within 1 day post inoculation, diversity was reduced >35-fold with expansion of a single clonal lineage. This loss of diversity was not due to immune factors, microbiota, or exclusive genetic drift. Rather, bacteriocins induced by the BlpC-quorum sensing pheromone resulted in predation of kin cells. In this intra-strain competition, the subpopulation reaching a quorum likely eliminates others that have yet to activate the blp locus. Additionally, this reduced diversity restricts the number of unique clones that establish colonization during transmission between hosts. Genetic variation in the blp locus was also associated with altered transmissibility in a human population, further underscoring the importance of BlpC in clonal selection and its role as a selfish element.},
}
@article {pmid36395729,
year = {2023},
author = {Xie, R and Liu, Y and Wang, S and Shi, X and Zhao, Z and Liu, L and Liu, Y and Li, Z},
title = {Combinatorial perturbation sequencing on single cells using microwell-based droplet random pairing.},
journal = {Biosensors &amp; bioelectronics},
volume = {220},
number = {},
pages = {114913},
doi = {10.1016/j.bios.2022.114913},
pmid = {36395729},
issn = {1873-4235},
mesh = {Humans ; *Biosensing Techniques ; Microfluidics ; Oligonucleotides ; RNA ; *Skin Neoplasms ; },
abstract = {Combinatorial drug therapy reduces drug resistance and disease relapse, but informed drug combinations are lacking due to the high scale of possible combinations and the relatively simple phenotyping strategies. Here we report combinatorial perturbation sequencing (CP-seq) on single cells using microwell-base droplet random pairing. CP-seq uses oligonucleotides to barcode drugs, encapsulates drugs and cells in separate droplets, and pairs cell droplets with two drug droplets randomly on a microwell array chip to complete combinatorial drug treatment and barcode-tagging on cells. The subsequent single-cell RNA sequencing simultaneously detects the single-cell transcriptomes and drug barcodes to demultiplex the corresponding drug treatment. The microfluidic droplet operations had robust performance, with the overall utilization rate of the microwells being up to 83%. We then progressively validated the CP-seq by performing single-drug treatments and then combinatorial-drug treatments, confirming the CP-seq's capability in the collection and analysis of drug-perturbed transcriptomes. Leveraging the advantage of droplet microfluidics in massive multiplexing, the CP-seq represents a great technology for combinatorial perturbation screening with high throughput and comprehensive profiling.},
}
@article {pmid36394140,
year = {2022},
author = {Hayashi, M and Sano, Y and Ishikawa, T and Hagiwara, T and Sasaki, M and Nakao, M and Urabe, M and Waki, T},
title = {Invasion of fish parasite Prosorhynchoides ozakii (Trematoda: Bucephalidae) into Lake Kasumigaura and surrounding rivers of eastern Japan.},
journal = {Diseases of aquatic organisms},
volume = {152},
number = {},
pages = {47-60},
doi = {10.3354/dao03698},
pmid = {36394140},
issn = {0177-5103},
mesh = {Animals ; *Parasites ; Rivers ; Lakes ; Japan/epidemiology ; *Trematoda ; Metacercariae ; *Catfishes ; *Bivalvia/parasitology ; },
abstract = {In 2019 to 2021, the golden mussel Limnoperna fortunei and several freshwater fishes were sampled from 22 sites of the Tone River system including Lake Kasumigaura, Honshu, Japan, to examine the invasion of bucephalid trematodes. The parasite species identification was performed by morphological observation and DNA barcoding based on the sequences of nuclear 28S rDNA and mitochondrial cytochrome c oxidase subunit 1 (cox1). A total of 1719 mussels were collected from 10 sites, and trematode-infected mussels were detected from 8 sites with prevalences between 0.3 and 42.9%. The sporocysts and cercariae were identified as Prosorhynchoides ozakii, a newly introduced species in the river system. A total of 700 fish individuals belonging to 24 species were collected from 15 sites. Two species of catfishes (Silurus asotus and Ictalurus punctatus) harbored mature or immature adults of Pr. ozakii in the intestine with prevalences between 8.3 and 20% including both host species. The metacercariae of Pr. ozakii were found from the fins and epidermis of 13 fish species from 10 sites (prevalence 4.8-100%). Fishes were heavily infected with metacercariae in fins, which were surrounded by the infiltration of hemocytes and rodlet cells. A population genetic analysis of Pr. ozakii did not show an obvious bottleneck, suggesting the possibility that the parasite was intentionally and repeatedly introduced into the river system.},
}
@article {pmid36394090,
year = {2022},
author = {Li, J and Sina, AAI and Antaw, F and Fielding, D and Möller, A and Lobb, R and Wuethrich, A and Trau, M},
title = {Digital Decoding of Single Extracellular Vesicle Phenotype Differentiates Early Malignant and Benign Lung Lesions.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {10},
number = {1},
pages = {e2204207},
pmid = {36394090},
issn = {2198-3844},
support = {DP210103151//Australian Research Council/ ; DE200100345//Australian Research Council/ ; CG-12-07//National Breast Cancer Foundation of Australia/ ; AppID_2010799//Cancer Australia/ ; //Commonwealth Scientific and Industrial Research Organization/ ; APP1173669//National Health and Medical Research Council/ ; APP1175047//National Health and Medical Research Council/ ; APP1185907//National Health and Medical Research Council/ ; },
abstract = {Accurate identification of malignant lung lesions is a prerequisite for rational clinical management to reduce morbidity and mortality of lung cancer. However, classification of lung nodules into malignant and benign cases is difficult as they show similar features in computer tomography and sometimes positron emission tomography imaging, making invasive tissue biopsies necessary. To address the challenges in evaluating indeterminate nodules, the authors investigate the molecular profiles of small extracellular vesicles (sEVs) in differentiating malignant and benign lung nodules via a liquid biopsy-based approach. Aiming to characterize phenotypes between malignant and benign groups, they develop a single-molecule-resolution-digital-sEV-counting-detection (DECODE) chip that interrogates three lung-cancer-associated sEV biomarkers and a generic sEV biomarker to create sEV molecular profiles. DECODE capturessEVs on a nanostructured pillar chip, confines individual sEVs, and profiles sEV biomarker expression through surface-enhanced Raman scattering barcodes. The author utilize DECODE to generate a digitally acquired sEV molecular profiles in a cohort of 33 people, including patients with malignant and benign lung nodules, and healthy individuals. Significantly, DECODE reveals sEV-specific molecular profiles that allow the separation of malignant from benign (area under the curve, AUC = 0.85), which is promising for non-invasive characterisation of lung nodules found in lung cancer screening and warrants further clinincal validaiton with larger cohorts.},
}
@article {pmid36386871,
year = {2022},
author = {Gibbons, M and Hong, JM and Foster, M and Chavarha, M and Shao, S and Ching, L and Church, VA and Schiff, L and Ahadi, S and Berndl, M and Jess, P and Pawlosky, A},
title = {Million spot binding array platform for exploring and optimizing multiple simultaneous detection events.},
journal = {STAR protocols},
volume = {3},
number = {4},
pages = {101829},
pmid = {36386871},
issn = {2666-1667},
mesh = {Gene Library ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; *DNA Barcoding, Taxonomic/methods ; Base Sequence ; },
abstract = {Large-scale, high-throughput specificity assays to characterize binding properties within a competitive and complex environment of potential binder-target pairs remain challenging and cost prohibitive. Barcode cycle sequencing (BCS) is a molecular binding assay for proteins, peptides, and other small molecules that is built on a next-generation sequencing (NGS) chip. BCS uses a binder library and targets labeled with unique DNA barcodes. Upon binding, binder barcodes are ligated to target barcodes and sequenced to identify encoded binding events. For complete details on the use and execution of this protocol, please refer to Hong et al. (2022).},
}
@article {pmid36386468,
year = {2022},
author = {Chen, S and Li, Z and Zhang, S and Zhou, Y and Xiao, X and Cui, P and Xu, B and Zhao, Q and Kong, S and Dai, Y},
title = {Emerging biotechnology applications in natural product and synthetic pharmaceutical analyses.},
journal = {Acta pharmaceutica Sinica. B},
volume = {12},
number = {11},
pages = {4075-4097},
pmid = {36386468},
issn = {2211-3835},
abstract = {Pharmaceutical analysis is a discipline based on chemical, physical, biological, and information technologies. At present, biotechnological analysis is a short branch in pharmaceutical analysis; however, bioanalysis is the basis and an important part of medicine. Biotechnological approaches can provide information on biological activity and even clinical efficacy and safety, which are important characteristics of drug quality. Because of their advantages in reflecting the overall biological effects or functions of drugs and providing visual and intuitive results, some biotechnological analysis methods have been gradually applied to pharmaceutical analysis from raw material to manufacturing and final product analysis, including DNA super-barcoding, DNA-based rapid detection, multiplex ligation-dependent probe amplification, hyperspectral imaging combined with artificial intelligence, 3D biologically printed organoids, omics-based artificial intelligence, microfluidic chips, organ-on-a-chip, signal transduction pathway-related reporter gene assays, and the zebrafish thrombosis model. The applications of these emerging biotechniques in pharmaceutical analysis have been discussed in this review.},
}
@article {pmid36383785,
year = {2022},
author = {Souza, TKM and Westphalen, EVN and Westphalen, SDR and Taniguchi, HH and Elias, CR and Motoie, G and Gava, R and Pereira-Chioccola, VL and Novaes, CTG and Carvalho, NB and Bocchi, EA and Cruz, FDDD and Rocha, MC and Shinjo, SK and Shikanai-Yasuda, MA and Ortiz, PA and Teixeira, MMG and Tolezano, JE},
title = {Genetic diversity of Trypanosoma cruzi strains isolated from chronic chagasic patients and non-human hosts in the state of São Paulo, Brazil.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {117},
number = {},
pages = {e220125},
pmid = {36383785},
issn = {1678-8060},
mesh = {Humans ; Animals ; *Trypanosoma cruzi/genetics ; Phylogeny ; Brazil ; *Chagas Disease/parasitology ; Genotype ; Genetic Variation/genetics ; *Marsupialia ; },
abstract = {BACKGROUND: Trypanosoma cruzi shows an exuberant genetic diversity. Currently, seven phylogenetic lineages, called discrete typing units (DTUs), are recognised: TcI-TcVI and Tcbat. Despite advances in studies on T. cruzi and its populations, there is no consensus regarding its heterogeneity.<br><br>OBJECTIVES: This study aimed to perform molecular characterisation of T. cruzi strains, isolated in the state of S&#xe3;o Paulo, to identify the DTUs involved and evaluate their genetic diversity.<br><br>METHODS: T. cruzi strains were isolated from biological samples of chronic chagasic patients, marsupials and triatomines through culture techniques and subjected to molecular characterisation using the fluorescent fragment length barcoding (FFLB) technique. Subsequently, the results were correlated with complementary information to enable better discrimination between the identified DTUs.<br><br>FINDINGS: It was possible to identify TcI in two humans and two triatomines; TcII/VI in 19 humans, two marsupials and one triatomine; and TcIII in one human host, an individual that also presented a result for TcI, which indicated the possibility of a mixed infection. Regarding the strains characterised by the TcII/VI profile, the correlation with complementary information allowed to suggest that, in general, these parasite populations indeed correspond to the TcII genotype.<br><br>MAIN CONCLUSIONS: The TcII/VI profile, associated with domestic cycles and patients with chronic Chagas disease, was the most prevalent among the identified DTUs. Furthermore, the correlation of the study results with complementary information made it possible to suggest that TcII is the predominant lineage of this work.},
}
@article {pmid36382243,
year = {2022},
author = {Zhang, J and Cong, Q and Lamas, G and Grishin, NV},
title = {Neotype designation for Papilio fulgerator Walch, 1775 (Hesperiidae: Eudaminae).},
journal = {The taxonomic report of the International Lepidoptera Survey},
volume = {10},
number = {8},
pages = {1-8},
pmid = {36382243},
issn = {2643-4806},
support = {R35 GM127390/GM/NIGMS NIH HHS/United States ; },
abstract = {The discovery that a skipper butterfly Telegonus fulgerator (Walch, 1775), previously placed in the genus Astraptes Hübner, [1819], is a complex of many similar-looking species-level taxa with different COI barcodes, caterpillar foodplants and body patterns, and subtle differences in adult phenotypes raised a question about which species is the original T. fulgerator. To answer this question, being unable to locate its holotype, we designate the neotype of Papilio fulgerator Walch, 1775, a female specimen from Suriname in the Zoological State Collection, Munich, Germany. This neotype will form the foundation for a comprehensive revision of the T. fulgerator complex based on genomic sequencing and analysis augmented with phenotypic considerations.},
}
@article {pmid36380268,
year = {2022},
author = {Cai, J and Qin, HH and Lei, JQ and Liu, CK and He, XJ and Zhou, SD},
title = {The phylogeny of Seseli (Apiaceae, Apioideae): insights from molecular and morphological data.},
journal = {BMC plant biology},
volume = {22},
number = {1},
pages = {534},
pmid = {36380268},
issn = {1471-2229},
support = {No. 32070221//National Natural Science Foundation of China/ ; No. 32170209//National Natural Science Foundation of China/ ; },
mesh = {Phylogeny ; *Apiaceae/genetics ; Evolution, Molecular ; Reproducibility of Results ; Base Sequence ; },
abstract = {BACKGROUND: The genus Seseli L., which consists of 125-140 species distributed in the Old World from western Europe and northwestern Africa to China and Japan, is one of the largest and most taxonomically difficult genera of Apiaceae Lindl. Although several previous studies have been conducted on Seseli based on limited morphological characteristics and molecular fragments, a robust and comprehensive phylogeny of Seseli remains elusive. Plastomes provide abundant genetic information and have been widely used in studying plant phylogeny and evolution. Consequently, we newly generated the complete plastomes of eleven Seseli taxa. We combined plastome data and morphological characteristics to investigate the phylogeny of Seseli.<br><br>RESULTS: In our study, we observed that the genome length, gene numbers, IR/SC borders, and repeat composition of the eleven Seseli plastomes were variable. Several appropriate mutation hotspot regions may be developed as candidate DNA barcodes for evolution, phylogeny, and species identification of Seseli. The phylogenetic results identified that Seseli was not a monophyletic group. Moreover, the eleven newly sequenced Seseli taxa did not cluster with S. tortuosum (the type species of Seseli, belonging to the tribe Selineae), where S. delavayi clustered with Eriocycla belonging to the tribe Echinophoreae and the other ten belonged to Selineae. The comparative plastome and morphological characteristics analyses confirmed the reliability of the phylogenetic analyses and implied the complex evolution of Seseli.<br><br>CONCLUSION: Combining molecular and morphological data is efficient and useful for studying the phylogeny of Seseli. We suggest that "a narrow sense" of Seseli will be meaningful for further study and the current taxonomic system of Seseli needs to be revised. In summary, our study can provide new insights into the phylogenetic relationships and taxonomic framework of Seseli.},
}
@article {pmid36378478,
year = {2022},
author = {Pyrcz, TW and Willmott, KR and Lamas, G and Boyer, P and Florczyk, K and Fåhraeus, C and Mahecha, O and Cerdeña, J and Mrozek, A and Farfán, J and Zubek, A},
title = {Considerations on the Systematics of Neotropical Pierina, with the Description of Two New Species of Phulia Herrich-Schäffer from the Peruvian Andes (Lepidoptera: Pieridae, Pierinae, Pierini).},
journal = {Neotropical entomology},
volume = {51},
number = {6},
pages = {840-859},
pmid = {36378478},
issn = {1678-8052},
support = {2018/30/M/NZ8/00293//Narodowe Centrum Nauki/ ; },
mesh = {Animals ; *Butterflies ; Ecosystem ; Ecuador ; Forests ; Peru ; },
abstract = {A comparative analysis of high-Andean Pierina was carried out, including a total of 25 species. Based on morphological evidence, with an emphasis on venation and genitalia and molecular data, using three genetic markers, we confirm the recent subjective synonymy of the generic names Tatochila Butler, 1870, Piercolias, Staudinger, 1894, Hypsochila Ureta, 1955, Infraphulia Field, 1958, Pierphulia Field, 1958, and Theochila Field, 1958 with Phulia Herrich-Schäffer, 1867. Two new species are described, namely Phulia stoddardi Pyrcz &amp; Cerdeña n. sp., from the Andes of Central Peru, which occurs at an unusually high altitude of close to 5000 m a.s.l. in dry puna habitat, and Phulia phantasma Lamas, Willmott &amp; Boyer n. sp., from dry montane forests in northern Peru and southern Ecuador. An overview of high-elevation butterflies is presented, with some discussion on adaptations to this environment.},
}
@article {pmid36373905,
year = {2022},
author = {Daniels, JC and Storer, CG and Hill, GM and Markee, A and Couch, C and Rossetti, KA},
title = {Deploying Community Scientists to Conduct Nondestructive Genetic Sampling of Rare Butterfly Populations.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {188},
pages = {},
doi = {10.3791/63416},
pmid = {36373905},
issn = {1940-087X},
mesh = {Humans ; Animals ; *Butterflies/genetics ; Population Dynamics ; },
abstract = {Global insect declines continue to accelerate. Effective genetic sampling is critically needed to advance the understanding of many taxa and address existing knowledge gaps. This protocol represents a demonstrated method for nondestructively sampling rare butterflies for population genetic structure or DNA barcoding analyses. It uses the chorion of hatched butterfly ovae to yield sufficiently high quantity and quality DNA for successful gene sequencing to confirm species identity and quantify genetic variation. It may be particularly useful when other tissue sampling techniques are impractical or unavailable. While developed for a lepidopteran, it nonetheless could easily be adapted for use with other insect species. It was specifically designed with ease of use as a goal to help maximize broad implementation by individuals of varying experience and skill levels, such as community scientists, conservation practitioners, and students, and for use over large geographic areas to facilitate broad population sampling. The data generated can help inform taxonomic and listing decisions, conservation and management actions, and enhance basic ecological research.},
}
@article {pmid36368323,
year = {2022},
author = {Fu, X and Sun, L and Dong, R and Chen, JY and Silakit, R and Condon, LF and Lin, Y and Lin, S and Palmiter, RD and Gu, L},
title = {Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic pain.},
journal = {Cell},
volume = {185},
number = {24},
pages = {4621-4633.e17},
pmid = {36368323},
issn = {1097-4172},
support = {UG3 CA268096/CA/NCI NIH HHS/United States ; R41 MH130299/MH/NIMH NIH HHS/United States ; R35 GM128918/GM/NIGMS NIH HHS/United States ; R01 DA024908/DA/NIDA NIH HHS/United States ; R21 DA051194/DA/NIDA NIH HHS/United States ; R21 DA051555/DA/NIDA NIH HHS/United States ; },
mesh = {Mice ; Animals ; *Transcriptome ; *Chronic Pain ; DNA ; RNA ; Gels ; },
abstract = {Methods for acquiring spatially resolved omics data from complex tissues use barcoded DNA arrays of low- to sub-micrometer features to achieve single-cell resolution. However, fabricating such arrays (randomly assembled beads, DNA nanoballs, or clusters) requires sequencing barcodes in each array, limiting cost-effectiveness and throughput. Here, we describe a vastly scalable stamping method to fabricate polony gels, arrays of ∼1-micrometer clonal DNA clusters bearing unique barcodes. By enabling repeatable enzymatic replication of barcode-patterned gels, this method, compared with the sequencing-dependent array fabrication, reduced cost by at least 35-fold and time to approximately 7 h. The gel stamping was implemented with a simple robotic arm and off-the-shelf reagents. We leveraged the resolution and RNA capture efficiency of polony gels to develop Pixel-seq, a single-cell spatial transcriptomic assay, and applied it to map the mouse parabrachial nucleus and analyze changes in neuropathic pain-regulated transcriptomes and cell-cell communication after nerve ligation.},
}
@article {pmid36367139,
year = {2022},
author = {Zath, GK and Sperling, RA and Hoffman, CW and Bikos, DA and Abbasi, R and Abate, AR and Weitz, DA and Chang, CB},
title = {Rapid parallel generation of a fluorescently barcoded drop library from a microtiter plate using the plate-interfacing parallel encapsulation (PIPE) chip.},
journal = {Lab on a chip},
volume = {22},
number = {23},
pages = {4735-4745},
pmid = {36367139},
issn = {1473-0189},
support = {R21 AI151923/AI/NIAID NIH HHS/United States ; },
mesh = {Gene Library ; Oligonucleotide Array Sequence Analysis ; *Microfluidics ; Lab-On-A-Chip Devices ; High-Throughput Screening Assays ; *Microfluidic Analytical Techniques ; },
abstract = {In drop-based microfluidics, an aqueous sample is partitioned into drops using individual pump sources that drive water and oil into a drop-making device. Parallelization of drop-making devices is necessary to achieve high-throughput screening of multiple experimental conditions, especially in time-sensitive studies. Here, we present the plate-interfacing parallel encapsulation (PIPE) chip, a microfluidic chip designed to generate 50 to 90 μm diameter drops of up to 96 different conditions in parallel by interfacing individual drop makers with a standard 384-well microtiter plate. The PIPE chip is used to generate two types of optically barcoded drop libraries consisting of two-color fluorescent particle combinations: a library of 24 microbead barcodes and a library of 192 quantum dot barcodes. Barcoded combinations in the drop libraries are rapidly measured within a microfluidic device using fluorescence detection and distinct barcoded populations in the fluorescence drop data are identified using DBSCAN data clustering. Signal analysis reveals that particle size defines the source of dominant noise present in the fluorescence intensity distributions of the barcoded drop populations, arising from Poisson loading for microbeads and shot noise for quantum dots. A barcoded population from a drop library is isolated using fluorescence-activated drop sorting, enabling downstream analysis of drop contents. The PIPE chip can improve multiplexed high-throughput assays by enabling simultaneous encapsulation of barcoded samples stored in a microtiter plate and reducing sample preparation time.},
}
@article {pmid36365353,
year = {2022},
author = {Aneva, I and Zhelev, P and Bonchev, G},
title = {Sideritis elica, a New Species of Lamiaceae from Bulgaria, Revealed by Morphology and Molecular Phylogeny.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {21},
pages = {},
pmid = {36365353},
issn = {2223-7747},
abstract = {Sideritis elica, from the Rhodope Mountains, is described as a species new to science. Results of a detailed morphological analysis were combined with the data of molecular analyses using DNA barcoding as an efficient tool for the genetic, taxonomic identification of plants. The combination of morphological features distinguishes the new species well: Its first three uppermost leaf pairs are significantly shorter and wider, the branchiness of the stems is much more frequent, the whole plant is much more lanate, and it looks almost white, as opposed to the other closed species of section Empedoclia, which look grayish green. The molecular analysis, based on the rbcL and trnH-psbA regions, supports the morphological data about the divergence of Sideritis scardica and Sideritis elica. The studied populations of the two taxa were found to be genetically distant (up to 6.8% polymorphism for trnH-psbA) with distinct population-specific nucleotide patterns, while no polymorphism in the DNA barcodes was detected within the Sideritis elica population. The results confirm the existence of a new species called Sideritis elica, which occurs in the nature reserve Chervenata Stena, located in the northern part of the Central Rhodope Mountains. There were only 12 individuals found in the locality, which underlines the necessity of conservation measures.},
}
@article {pmid36365322,
year = {2022},
author = {Kim, WJ and Noh, S and Choi, G and Moon, BC},
title = {Rapid Identification of Paeoniae Radix and Moutan Radicis Cortex Using a SCAR Marker-Based Conventional PCR Assay.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {21},
pages = {},
pmid = {36365322},
issn = {2223-7747},
support = {NSN2112260//Ministry of Science ICT and Future Planning/ ; KSN2021320//Ministry of Science ICT and Future Planning/ ; },
abstract = {Paeoniae Radix is a herbal medicine prepared from the dried roots of Paeonia lactiflora, P. anomala subsp. veitchii, and P. japonica. Although the herbal medicines prepared from these species are morphologically similar, they have different pharmacological effects depending on how they are processed. In addition, P. japonica is more expensive than other Paeonia spp. in the Korean herbal market. Although there is a clear difference between the Korean and Chinese pharmacopeias of Paeoniae Radix, the processed roots of P. lactiflora and P. anomala subsp. veitchii are commonly used indiscriminately in the herbal market. Moreover, Paeonia suffruticosa, an allied genus of P. lactiflora, is prescribed as Moutan Radicis Cortex. Therefore, accurate taxonomic identification of plant species is vital for quality assurance. A genetic assay is a reliable tool for accurately discriminating species in processed herbal medicines. To develop a genetic assay for the identification of four Paeonia species (P. lactiflora, P. anomala subsp. veitchii, P. japonica, and P. suffruticosa), we analyzed the sequences of two DNA barcoding regions, internal transcribed spacer and rbcL. A conventional PCR assay was established in this study for simple and rapid species identification using sequence characterized amplified region (SCAR) markers based on arbitrary nucleotide-containing primers. This assay was verified to be species specific and highly sensitive and could be applied to Paeonia species identification at an affordable rate.},
}
@article {pmid36364159,
year = {2022},
author = {Xavier, JKAM and Baia, TGC and Alegria, OVC and Figueiredo, PLB and Carneiro, AR and Moreira, ECO and Maia, JGS and Setzer, WN and da Silva, JKR},
title = {Essential Oil Chemotypes and Genetic Variability of Cinnamomum verum Leaf Samples Commercialized and Cultivated in the Amazon.},
journal = {Molecules (Basel, Switzerland)},
volume = {27},
number = {21},
pages = {},
pmid = {36364159},
issn = {1420-3049},
mesh = {*Oils, Volatile/chemistry ; Cinnamomum zeylanicum/chemistry ; Phylogeny ; *Cinnamomum/genetics/chemistry ; Plant Leaves/genetics/chemistry ; DNA Barcoding, Taxonomic ; },
abstract = {Cinnamomum verum (Lauraceae), also known as "true cinnamon" or "Ceylon cinnamon" has been widely used in traditional folk medicine and cuisine for a long time. The systematics of C. verum presents some difficulties due to genetic variation and morphological similarity between other Cinnamomum species. The present work aimed to find chemical and molecular markers of C. verum samples from the Amazon region of Brazil. The leaf EOs and the genetic material (DNA) were extracted from samples cultivated and commercial samples. The chemical composition of the essential oils from samples of C. verum cultivated (Cve1-Cve5) and commercial (Cve6-c-Cv9-c) was grouped by multivariate statistical analysis of Principal Component Analysis (PCA). The major compounds were rich in benzenoids and phenylpropanoids, such as eugenol (0.7-91.0%), benzyl benzoate (0.28-76.51%), (E)-cinnamyl acetate (0.36-32.1%), and (E)-cinnamaldehyde (1.0-19.73%). DNA barcodes were developed for phylogenetic analysis using the chloroplastic regions of the matK and rbcL genes, and psbA-trnH intergenic spacer. The psbA-trnH sequences provided greater diversity of nucleotides, and matK confirmed the identity of C. verum. The combination of DNA barcode and volatile profile was found to be an important tool for the discrimination of C. verum varieties and to examine the authenticity of industrial sources.},
}
@article {pmid36363798,
year = {2022},
author = {Zupičić, IG and Oraić, D and Pavlinec, &#x17d; and Novosel, D and Žuvić, L and Šegvić-Bubić, T and Zrnčić, S},
title = {Is the Illegal Trade of Glass Eels (Anguilla anguilla) Increasing the Spread of Disease? A Case of EVEX.},
journal = {Microorganisms},
volume = {10},
number = {11},
pages = {},
pmid = {36363798},
issn = {2076-2607},
abstract = {The European eel (Anguilla anguilla) is a catadromous species that inhabits the rivers of the Adriatic watershed in Croatia. It is a critically endangered fish species, according to the IUCN, due to its declining abundance in European rivers caused by overfishing and trafficking and by diseases caused by nematodes, pathogenic bacteria and viruses. An illegal parcel of glass eels was confiscated at the Zagreb Airport and was intended to re-populate Croatian rivers. Barcoding was employed to determine species affiliation, and a thorough health check was carried out. This study reports the evaluation of gross lesions, histological findings, and EVEX virus isolation and identification. Since the confiscated glass eels were of unknown origin and given the serological and genetic similarities of EVA and EVEX, we designed primers and probes for almost whole genome sequencing to elucidate the origin of glass eels based on viral phylogeny. Bayesian phylogeny showed that the isolated strain had the most common ancestor with a Danish isolate and likely evolved from the French isolate of EVEX. These findings are discussed in light of the divergence of recently isolated strains and their possible contribution to the decrease of the abundance of the European eel in European waters.},
}
@article {pmid36361999,
year = {2022},
author = {Wang, L and Feng, Y and Wang, Y and Zhang, J and Chen, Q and Liu, Z and Liu, C and He, W and Wang, H and Yang, S and Zhang, Y and Luo, Y and Tang, H and Wang, X},
title = {Accurate Chromosome Identification in the Prunus Subgenus Cerasus (Prunus pseudocerasus) and its Relatives by Oligo-FISH.},
journal = {International journal of molecular sciences},
volume = {23},
number = {21},
pages = {},
pmid = {36361999},
issn = {1422-0067},
support = {31672114//National Natural Science Foundation of China/ ; 31801826//National Natural Science Foundation of China/ ; 2019JDTD0010//Sichuan Science and Technology Program/ ; 202010626010//Cherry Resources Sharing and Service Platform of Sichuan Province, National Undergraduate Innovation Training Program/ ; 2021065//Sichuan Science and Technology Innovation Project/ ; P202107//Shuangzhi Project Innovation Team of Sichuan Agricultural University/ ; },
mesh = {In Situ Hybridization, Fluorescence ; *Prunus/genetics ; *Prunus avium/genetics ; Karyotype ; Oligonucleotides ; },
abstract = {A precise, rapid and straightforward approach to chromosome identification is fundamental for cytogenetics studies. However, the identification of individual chromosomes was not previously possible for Chinese cherry or other Prunus species due to the small size and similar morphology of their chromosomes. To address this issue, we designed a pool of oligonucleotides distributed across specific pseudochromosome regions of Chinese cherry. This oligonucleotide pool was amplified through multiplex PCR with specific internal primers to produce probes that could recognize specific chromosomes. External primers modified with red and green fluorescence tags could produce unique signal barcoding patterns to identify each chromosome concomitantly. The same oligonucleotide pool could also discriminate all chromosomes in other Prunus species. Additionally, the 5S/45S rDNA probes and the oligo pool were applied in two sequential rounds of fluorescence in situ hybridization (FISH) localized to chromosomes and showed different distribution patterns among Prunus species. At the same time, comparative karyotype analysis revealed high conservation among P. pseudocerasus, P. avium, and P. persica. Together, these findings establish this oligonucleotide pool as the most effective tool for chromosome identification and the analysis of genome organization and evolution in the genus Prunus.},
}
@article {pmid36360175,
year = {2022},
author = {Pham, T and Nguyen, QT and Tran, DM and Nguyen, H and Le, HT and Hoang, QTH and Van, YT and Tran, TN},
title = {Phylogenetic Analysis Based on DNA Barcoding and Genetic Diversity Assessment of Morinda officinalis How in Vietnam Inferred by Microsatellites.},
journal = {Genes},
volume = {13},
number = {11},
pages = {},
pmid = {36360175},
issn = {2073-4425},
mesh = {Phylogeny ; *DNA Barcoding, Taxonomic/methods ; DNA, Plant/genetics ; *Morinda ; Sequence Analysis, DNA ; Vietnam ; Genetic Markers ; Microsatellite Repeats/genetics ; Genetic Variation/genetics ; },
abstract = {Morinda officinalis How is well-known as a valuable medicinal plant found in some regions of Vietnam. This species is mainly used for treating male impotence, irregular menstruation, and rheumatoid arthritis. This study aimed to identify the species of and genetic diversity in three M. officinalis populations: one each in Quang Binh (QB), Thua Thien Hue (TTH), and Quang Nam (QN). In this study, four DNA barcoding markers (ITS1, ITS2, matK, and rbcL) were used to identify the species and 22 microsatellite markers were applied for population structure and diversity analyses. The results showed that the sequences of gene regions studied in M. officinalis had a high similarity (>95%) to the ITS1, ITS2, matK, and rbcL sequences of M. officinalis on BLAST. Of the four DNA barcoding markers used, ITS1 and ITS2 showed higher efficiency in DNA amplification of M. officinalis. From this study, 27 GenBank codes were published on BLAST. The results also revealed high levels of genetic diversity in populations. The average observed and expected heterozygosity values were HO = 0.513 and HE = 0.612, respectively. The average FST value was 0.206. Analysis of molecular variance (AMOVA) showed 70% variation within populations and 30% among populations. The population structure of M. officinalis inferred in STRUCTURE revealed that the optimum number of genetic groups for the admixture model was K = 2. These findings provided vital background information for future studies in the conservation of M. officinalis in both ex situ and in situ plans.},
}
@article {pmid36358313,
year = {2022},
author = {Rackevei, AS and Borges, A and Engstler, M and Dandekar, T and Wolf, M},
title = {About the Analysis of 18S rDNA Sequence Data from Trypanosomes in Barcoding and Phylogenetics: Tracing a Continuation Error Occurring in the Literature.},
journal = {Biology},
volume = {11},
number = {11},
pages = {},
pmid = {36358313},
issn = {2079-7737},
support = {EN-305//DFG/ ; 88881.199683/2018-01//CAPES/ ; },
abstract = {The variable regions (V1-V9) of the 18S rDNA are routinely used in barcoding and phylogenetics. In handling these data for trypanosomes, we have noticed a misunderstanding that has apparently taken a life of its own in the literature over the years. In particular, in recent years, when studying the phylogenetic relationship of trypanosomes, the use of V7/V8 was systematically established. However, considering the current numbering system for all other organisms (including other Euglenozoa), V7/V8 was never used. In Maia da Silva et al. [Parasitology 2004, 129, 549-561], V7/V8 was promoted for the first time for trypanosome phylogenetics, and since then, more than 70 publications have replicated this nomenclature and even discussed the benefits of the use of this region in comparison to V4. However, the primers used to amplify the variable region of trypanosomes have actually amplified V4 (concerning the current 18S rDNA numbering system).},
}
@article {pmid36357859,
year = {2022},
author = {Yang, Y and Lyu, M and Liu, J and Wu, J and Wang, Q and Xie, T and Li, H and Chen, R and Sun, D and Yang, Y and Yao, X},
title = {Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars.},
journal = {BMC plant biology},
volume = {22},
number = {1},
pages = {522},
pmid = {36357859},
issn = {1471-2229},
mesh = {*Polymorphism, Single Nucleotide/genetics ; *Brassica/genetics ; Phylogeny ; DNA Fingerprinting ; Genetics, Population ; Genetic Variation ; },
abstract = {Cauliflower is one of the most important vegetable crops grown worldwide. However, the lack of genetic diversity information and efficient molecular markers hinders efforts to improve cauliflower. This study aims to construct DNA fingerprints for 329 cauliflower cultivars based on SNP markers and the KASP system. After rigorous filtering, a total of 1662 candidate SNPs were obtained from nearly 17.9 million SNP loci. The mean values of PIC, MAF, heterozygosity and gene diversity of these SNPs were 0.389, 0.419, 0.075, and 0.506, respectively. We developed a program for in silico simulations on 153 core germplasm samples to generate ideal SNP marker sets from the candidates. Finally, 41 highly polymorphic KASP markers were selected and applied to identify 329 cauliflower cultivars, mainly collected from the public market. Furthermore, based on the KASP genotyping data, we performed phylogenetic analysis and population structure analysis of the 329 cultivars. As a result, these cultivars could be classified into three major clusters, and the classification patterns were significantly related to their curd solidity and geographical origin. Finally, fingerprints of the 329 cultivars and 2D barcodes with the genetic information of each sample were generated. The fingerprinting database developed in this study provides a practical tool for identifying the authenticity and purity of cauliflower seeds and valuable genetic information about the current cauliflower cultivars.},
}
@article {pmid36355866,
year = {2022},
author = {Leviatan, S and Kalka, IN and Vogl, T and Klompas, S and Weinberger, A and Segal, E},
title = {BIPS-A code base for designing and coding of a Phage ImmunoPrecipitation Oligo Library.},
journal = {PLoS computational biology},
volume = {18},
number = {11},
pages = {e1010663},
pmid = {36355866},
issn = {1553-7358},
mesh = {*Bacteriophages/genetics/metabolism ; Gene Library ; Immunoprecipitation ; Software ; Oligonucleotides/genetics/metabolism ; High-Throughput Nucleotide Sequencing ; },
abstract = {BIPS (Build Phage ImmunoPrecipitation Sequencing library) is a software that converts a list of proteins into a custom DNA oligonucleotide library for the PhIP-Seq system. The tool creates constant-length oligonucleotides with internal barcodes, while maintaining the original length of the peptide. This allows using large libraries, of hundreds of thousands of oligonucleotides, while saving on the costs of sequencing and maintaining the accuracy of oligonucleotide reads identification. BIPS is available under GNU public license from: https://github.com/kalkairis/BuildPhIPSeqLibrary.},
}
@article {pmid36354890,
year = {2022},
author = {Manova, V and Stoyanova, Z and Rodeva, R and Boycheva, I and Korpelainen, H and Vesterinen, E and Wirta, H and Bonchev, G},
title = {Morphological, Pathological and Genetic Diversity of the Colletotrichum Species, Pathogenic on Solanaceous Vegetable Crops in Bulgaria.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {11},
pages = {},
pmid = {36354890},
issn = {2309-608X},
support = {BULCode, Agreement N&#x43e; &#x414;01-271-271/02.10.2020//Ministry of Education and Science/ ; SEE-ERA.N&#x415;&#x422; PLUS, project 226/01.//Programme for Cooperation with South-East Europe/ ; },
abstract = {Colletotrichum species are among the most devastating plant pathogens in a wide range of hosts. Their accurate identification requires a polyphasic approach, including geographical, ecological, morphological, and genetic data. Solanaceous crops are of significant economic importance for Bulgarian agriculture. Colletotrichum-associated diseases pose a serious threat to the yield and quality of production but are still largely unexplored. The aim of this study was to identify and characterize 26 pathogenic Colletotrichum isolates that threaten solanaceous crops based on morphological, pathogenic, and molecular data. DNA barcodes enabled the discrimination of three main taxonomic groups: C. acutatum, C. gloeosporioides, and C. coccodes. Three different species of acutatum complex (C. nymphaeae, C. godetiae, and C. salicis) and C. cigarro of the gloeosporioides complex were associated with fruit anthracnose in peppers and tomatoes. The C. coccodes group was divided in two clades: C. nigrum, isolated predominantly from fruits, and C. coccodes, isolated mainly from roots. Only C. salicis and C. cigarro produced sexual morphs. The species C. godetiae, C. salicis, and C. cigarro have not previously been reported in Bulgaria. Our results enrich the knowledge of the biodiversity and specific features of Colletotrichum species, which are pathogenic to solanaceous hosts, and may serve as a scientific platform for efficient disease control and resistance breeding.},
}
@article {pmid36354832,
year = {2022},
author = {Massimino Cocuzza, GE and Magoga, G and Montagna, M and Nieto Nafría, JM and Barbagallo, S},
title = {European and Mediterranean Myzocallidini Aphid Species: DNA Barcoding and Remarks on Ecology with Taxonomic Modifications in An Integrated Framework.},
journal = {Insects},
volume = {13},
number = {11},
pages = {},
pmid = {36354832},
issn = {2075-4450},
abstract = {The genus Myzocallis Passerini (Hemiptera, Aphididae, Calaphidinae, Myzocallidini) is a rather primitive group of aphids currently comprising 45 species and 3 subspecies, subdivided into ten subgenera, three of them having a West Palaearctic distribution. The majority of the species inhabit Fagales plants and some of them are considered pests. Despite their ecological interest and the presence of some taxonomic controversies, there are only a few molecular studies on the group. Here, the main aims were to develop a DNA barcodes library for the molecular identification of West Palaearctic Myzocallis species, to evaluate the congruence among their morphological, ecological and DNA-based delimitation, and verify the congruence of the subgeneric subdivision presently adopted by comparing the results with those obtained for other Panaphidini species. These study findings indicate that Myzocallis (Agrioaphis) leclanti, originally described as a subspecies of M. (A.) castanicola and M. (M.) schreiberi, considered as a subspecies of M. (M.) boerneri, should be regarded at a rank of full species, and the subgenera Agrioaphis, Lineomyzocallis, Neomyzocallis, Pasekia were elevated to the rank of genus, while Myzocallis remain as such.},
}
@article {pmid36354826,
year = {2022},
author = {Vargas, HA},
title = {Flightless Females in the Neotropical Moth Genus Cataspilates Warren (Lepidoptera: Geometridae) †.},
journal = {Insects},
volume = {13},
number = {11},
pages = {},
pmid = {36354826},
issn = {2075-4450},
support = {Fondecyt Regular 1221879//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; UTA-MAYOR 9731-22//University of Tarapac&#xe1;/ ; },
abstract = {Although adults are winged and able to fly in most Lepidoptera species, they are apterous or brachypterous and unable to fly in others, such as the flightless females of some geometrid moths. Records of flightless females in the highly diverse and widespread tribe Boarmiini (Geometridae: Ennominae) are mainly restricted to some Nearctic and Palearctic genera. The aim of this study is to provide the first record of flightless females for Cataspilates Warren, 1897, a Boarmiini genus endemic to the Neotropical Region, through the description of Cataspilates marceloi sp. nov. from the arid highlands of the western slopes of the Andes of northern Chile. DNA barcodes confirmed the conspecificity of brachypterous females and winged males reared from larvae collected on the native shrub Adesmia spinosissima (Fabaceae). This contribution represents the first female description for Cataspilates and provides a new opportunity to improve the understanding of the evolution of flightlessness in geometrid moths.},
}
@article {pmid36354794,
year = {2022},
author = {Kaldor, AD and McHugh, JV and Schmidt, JM and Luo, X and Gariepy, TD and Blaauw, BR},
title = {First Documented Wild Population of the "Hunter Fly", Coenosia attenuata Stein (Diptera: Muscidae) in North America.},
journal = {Insects},
volume = {13},
number = {11},
pages = {},
pmid = {36354794},
issn = {2075-4450},
support = {17BLAA3101//Georgia Specialty Crop Block Grant/ ; GEO00886//USDA National Institute of Food and Agriculture Hatch project/ ; },
abstract = {Coenosia attenuata is a member of the tigrina-group of Coenosia (sensu Hennig 1964) and is a capable generalist predator in its larval and adult stages. C. attenuata is common in greenhouses worldwide, however, there are few documented cases of its presence in the wild. Here, we estimated C. attenuata presence in the southeastern USA peach orchards using pan traps. Over two years, a total of 717 specimens were collected from both commercially managed and fungicide-only managed peach orchards. C. attenuata is a known biological control agent in artificial greenhouse settings, but its impact on pest species in the wild is still unknown. For the first time in North America, we document an established wild population of C. attenuata, provide an overview of basic identification, and review potential benefits for biological control.},
}
@article {pmid36353363,
year = {2022},
author = {Rybakowska, P and Van Gassen, S and Martorell Marugán, J and Quintelier, K and Saeys, Y and Alarcón-Riquelme, ME and Marañón, C},
title = {Protocol for large scale whole blood immune monitoring by mass cytometry and Cyto Quality Pipeline.},
journal = {STAR protocols},
volume = {3},
number = {4},
pages = {101697},
pmid = {36353363},
issn = {2666-1667},
mesh = {Monitoring, Immunologic ; Flow Cytometry/methods ; Reproducibility of Results ; Retrospective Studies ; *Leukocytes, Mononuclear ; Multicenter Studies as Topic ; },
abstract = {Mass cytometry (MC) is a powerful large-scale immune monitoring technology. To maximize MC data quality, we present a protocol for whole blood analysis together with an R package, Cyto Quality Pipeline (CytoQP), which minimizes the experimental artifacts and batch effects to ensure data reproducibility. We describe the steps to stimulate, fix, and freeze blood samples before acquisition to make them suitable for retrospective studies. We then detail the use of barcoding and reference samples to facilitate multicenter and multi-batch experiments. For complete details on the use and execution of this protocol, please refer to Rybakowska et al. (2021a) and (2021b).},
}
@article {pmid36350196,
year = {2022},
author = {Kitajima, C and Ichijo, T and Ichikawa-Seki, M},
title = {The first genetic characterization of Setaria marshalli (Nematoda, Spirurida) with reliable DNA barcoding based on a mitochondrial genetic marker.},
journal = {Parasite (Paris, France)},
volume = {29},
number = {},
pages = {54},
pmid = {36350196},
issn = {1776-1042},
support = {//TI-FRIS/ ; },
mesh = {Animals ; Cattle ; *Setaria Nematode/genetics/anatomy &amp; histology ; DNA Barcoding, Taxonomic ; Phylogeny ; Genetic Markers ; *Spirurida ; *Nematoda/genetics ; },
abstract = {Setaria marshalli is a mosquito-borne filarial nematode that causes infection in calves younger than two years old. In the present study, nematodes were obtained from a calf in Japan and morphologically identified as S. marshalli. Additionally, the partial cytochrome oxidase subunit I (COI) region (596 bp) was analyzed for the first time to establish a reliable DNA barcode. Nucleotide sequences of COI were identical among the seven worms obtained. The COI region can be a useful marker for species discrimination in the case of S. marshalli since nucleotide variations observed between the closest congener, Setaria cervi (51/596 bp), were sufficient to allow species discrimination. However, the phylogenetic relationship of S. marshalli with its congeners was unclear in a maximum likelihood tree. We found that the partial COI sequence of S. marshalli analyzed in the present study matched a relevant section of the complete mitochondrial genome of S. labiatopapillosa that was deposited in the International Nucleotide Sequence Database. This finding suggests that S. marshalli was misdiagnosed as S. labiatopapillosa in a previous study. It is crucial to conduct accurate morphological analyses to obtain reliable molecular information regarding Setaria nematodes.},
}
@article {pmid36349251,
year = {2022},
author = {Mendoza-Ramírez, BH and Páiz-Medina, L and Salvatierra-Suárez, T and Hernández, N and Huete-Pérez, JA},
title = {A survey of aquatic macroinvertebrates in a river from the dry corridor of Nicaragua using biological indices and DNA barcoding.},
journal = {Ecology and evolution},
volume = {12},
number = {11},
pages = {e9487},
pmid = {36349251},
issn = {2045-7758},
abstract = {Aquatic macroinvertebrates are widely used as indicators for water quality assessment around the world. Modern strategies for environmental assessment implement molecular analysis to delimitate species of aquatic macroinvertebrates. Delimitation methods have been established to determine boundaries between species units using sequencing data from DNA barcodes and serve as first exploratory tools for taxonomic revisions. This is useful in regions such as the neotropics where aquatic macroinvertebrate habitats are threatened by human interference and DNA databases remain understudied. We asked whether the biodiversity of aquatic macroinvertebrates in a stream in Nicaragua, within the Central American Dry Corridor, could be characterized with biological indices and DNA barcoding. In this study, we combined regional biological indices (BMWP-CR, IBF-SV-2010) along with distance-based (ASAP, BIN) and tree-based (GMYC, bPTP) delimitation methods, as well as nucleotide BLAST in public barcode databases. We collected samples from the upper, middle, and low reaches of the Petaquilla river. The three sites presented excellent water quality with the BMWP-CR index, but evidence of high organic pollution was found in the middle reach with the IBF-SV-2010 index. We report a total of 219 COI sequences successfully generated from 18 families and 8 orders. Operational taxonomic units (OTUs) designation ranged from 69 to 73 using the four methods, with a congruency of 92% for barcode assignation. Nucleotide BLAST identified 14 species (27.4% of barcodes) and 33 genera (39.3% of barcodes) from query sequences in GenBank and BOLD system databases. This small number of identified OTUs may be explained by the paucity of molecular data from the Neotropical region. Our study provides valuable information about the characterization of macroinvertebrate families that are important biological indicators for the assessment of water quality in Nicaragua. The application of molecular approaches will allow the study of local diversity and further improve the application of molecular techniques for biomonitoring.},
}
@article {pmid36348856,
year = {2022},
author = {Alsayed, BA and Omer, AA},
title = {Curriculum Mapping for Curriculum Development: The Notion of "Curriculum Barcoding" in View of the Saudi Medical Education Directives Framework (SaudiMEDs).},
journal = {Cureus},
volume = {14},
number = {10},
pages = {e29886},
pmid = {36348856},
issn = {2168-8184},
abstract = {Objectives This study aims to map the curriculum of the Faculty of Medicine at Tabuk University to assess its comparability with the SaudiMEDs competency framework. Methodology We developed a checklist based on the essential clinical presentations and skills listed in the SaudiMEDs to map our curriculum and determine the comparability. This cross-sectional descriptive study started on 1 September 2015 until 29 February 2016. The coordinators of the 34 modules completed the checklist and identified whether each clinical presentation or skill is taught in their relevant modules. Results Results showed that our curriculum is lacking in 3.9% of the clinical presentations and 23.9% of the skills deemed necessary by the SaudiMEDs, and require attention. Deficient skills were mainly hospital-based ones. The project yielded a content "expertise" map regarding where the main domains of knowledge and skills in the SaudiMEDs framework are addressed in our curriculum. The "SaudiMEDs barcode" is generated that we hypothesize as a novel method for the description of our program in relation to the national competency framework. Conclusion Curriculum mapping is a powerful tool for curriculum improvement. Our study elucidated a minor gap in the knowledge domains but a significant one in the essential skills in relation to the SaudiMEDs. We recommend structured training during the internship period as an essential supplement to undergraduate medical qualifications. During our experimentation with curriculum mapping, we articulated the "SaudiMEDs barcode" that we suggest as a novel method for curriculum alignment to the matrix of national competency and, hopefully, to aid in the accreditation projects.},
}
@article {pmid36347989,
year = {2022},
author = {Despang, A},
title = {Spatial transcriptomics with light barcodes in intact tissues.},
journal = {Nature biotechnology},
volume = {40},
number = {11},
pages = {1575},
doi = {10.1038/s41587-022-01577-8},
pmid = {36347989},
issn = {1546-1696},
mesh = {*Transcriptome/genetics ; *DNA Barcoding, Taxonomic ; },
}
@article {pmid36347512,
year = {2022},
author = {Aalizadeh, R and Nikolopoulou, V and Thomaidis, NS},
title = {Development of Liquid Chromatographic Retention Index Based on Cocamide Diethanolamine Homologous Series (C(n)-DEA).},
journal = {Analytical chemistry},
volume = {94},
number = {46},
pages = {15987-15996},
pmid = {36347512},
issn = {1520-6882},
mesh = {Chromatography, Liquid/methods ; *Ethanolamines ; Mass Spectrometry ; *Neural Networks, Computer ; },
abstract = {There is a growing need for indexing and harmonizing retention time (tR) data in liquid chromatography derived under different conditions to aid in the identification of compounds in high resolution mass spectrometry (HRMS) based suspect and nontarget screening of environmental samples. In this study, a rigorously tested, inexpensive, and simple system-independent retention index (RI) approach is presented for liquid chromatography (LC), based on the cocamide diethanolamine homologous series (C(n = 0-23)-DEA). The validation of the CDEA based RI system was checked rigorously on eight different instrumentation and LC conditions. The RI values were modeled using molecular descriptor free technique based on structural barcoding and convolutional neural network deep learning. The effect of pH on the elution pattern of more than 402 emerging contaminants were studied under diverse LC settings. The uncertainty associated with the CDEA RI model and the pH effect were addressed and the first RI bank based on CDEA calibrants was developed. The proposed RI system was used to enhance identification confidence in suspect and nontarget screening while facilitating successful comparability of retention index data between various LC settings. The CDEA RI app can be accessed at https://github.com/raalizadeh/RIdea.},
}
@article {pmid36347200,
year = {2023},
author = {Qiao, J and Feng, Z and Zhang, Y and Xiao, X and Dong, J and Haubruge, E and Zhang, H},
title = {Phenolamide and flavonoid glycoside profiles of 20 types of monofloral bee pollen.},
journal = {Food chemistry},
volume = {405},
number = {Pt A},
pages = {134800},
doi = {10.1016/j.foodchem.2022.134800},
pmid = {36347200},
issn = {1873-7072},
mesh = {Animals ; Bees ; *Flavonoids ; *Glycosides ; Pollen ; Spermidine ; Tandem Mass Spectrometry ; Amides/chemistry ; },
abstract = {This study aimed at investigating phenolamides and flavonoid glycosides in 20 types of monofloral bee pollen. The plant origins of pollen samples were determined by DNA barcoding, with the purities to over 70 %. The 31 phenolamides and their 33 cis/trans isomers, and 25 flavonoid glycosides were identified; moreover, 19 phenolamides and 14 flavonoid glycosides as new-found compounds in bee pollen. All phenolics and flavonoids are present in the amidation or glycosylation form. The MS/MS cleavage modes of phenolamides and flavonoid glycosides were summarized. Isorhamnetin-3-O-gentiobioside presented the highest levels 23.61 mg/g in apricot pollen. Phenolamides in 11 types of pollen constituted over 1 % of the total weight, especially 3.9 % in rose and 2.8 % in pear pollen. Tri-p-coumaroyl spermidine and di-p-coumaroyl-caffeoyl spermidine respectively accounted for over 2.6 % of the total weight in pear and rose pollen. The richness in phenolamides and flavonoid glycosides can offer bee pollen more bioactivities as functional foods.},
}
@article {pmid36346244,
year = {2022},
author = {Sebastian, J and Thomas, A and Levine, C and Shrestha, R and Levy, S and Safi, H and Pentakota, SR and Kumar, P and Alland, D},
title = {Origin and Dynamics of Mycobacterium tuberculosis Subpopulations That Predictably Generate Drug Tolerance and Resistance.},
journal = {mBio},
volume = {13},
number = {6},
pages = {e0279522},
pmid = {36346244},
issn = {2150-7511},
support = {U19 AI162598/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Mycobacterium tuberculosis/genetics ; Antitubercular Agents/pharmacology ; *Tuberculosis/microbiology ; Rifampin/pharmacology ; Drug Tolerance ; Drug Resistance, Bacterial/genetics ; },
abstract = {Initial responses to tuberculosis treatment are poor predictors of final therapeutic outcomes in drug-susceptible disease, suggesting that treatment success depends on features that are hidden within a small minority of the overall infecting Mycobacterium tuberculosis population. We developed a multitranswell robotic system to perform numerous parallel cultures of genetically barcoded M. tuberculosis exposed to steady-state concentrations of rifampicin to uncover these difficult-to-eliminate minority populations. We found that tolerance emerged repeatedly from at least two subpopulations of barcoded cells, namely, one that could not grow on solid agar media and a second that could form colonies, but whose kill curves diverged from the general bacterial population within 4 and 16 days of drug exposure, respectively. These tolerant subpopulations reproducibly passed through a phase characterized by multiple unfixed resistance mutations followed by emergent drug resistance in some cultures. Barcodes associated with drug resistance identified an especially privileged subpopulation that was rarely eliminated despite 20 days of drug treatment even in cultures that did not contain any drug-resistant mutants. The association of this evolutionary scenario with a defined subset of barcodes across multiple independent cultures suggested a transiently heritable phenotype, and indeed, glpK phase variation mutants were associated with up to 16% of the resistant cultures. Drug tolerance and resistance were eliminated in a ΔruvA mutant, consistent with the importance of bacterial stress responses. This work provides a window into the origin and dynamics of bacterial drug-tolerant subpopulations whose elimination may be critical for developing rapid and resistance-free cures. IMPORTANCE Tuberculosis is unusual among bacterial diseases in that treatments which can rapidly resolve symptoms do not predictably lead to a durable cure unless treatment is continued for months after all clinical and microbiological signs of disease have been eradicated. Using a novel steady-state antibiotic exposure system combined with chromosomal barcoding, we identified small hidden Mycobacterium tuberculosis subpopulations that repeatedly enter a state of drug tolerance with a predisposition to develop fixed drug resistance after first developing a cloud of unfixed resistance mutations. The existence of these difficult-to-eradicate subpopulations may explain the need for extended treatment regimen for tuberculosis. Their identification provides opportunities to test genetic and therapeutic approaches that may result in shorter and more effective TB treatments.},
}
@article {pmid36345645,
year = {2022},
author = {Dopheide, A and Brav-Cubitt, T and Podolyan, A and Leschen, RAB and Ward, D and Buckley, TR and Dhami, MK},
title = {Fast-tracking bespoke DNA reference database generation from museum collections for biomonitoring and conservation.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13733},
pmid = {36345645},
issn = {1755-0998},
support = {D17.22//Ministry of Business, Innovation and Employment/ ; //Better Border Biosecurity Science Collaboration/ ; //Strategic Science Investment Fund/ ; },
abstract = {Despite recent advances in high-throughput DNA sequencing technologies, a lack of locally relevant DNA reference databases limits the potential for DNA-based monitoring of biodiversity for conservation and biosecurity applications. Museums and national collections represent a compelling source of authoritatively identified genetic material for DNA database development, yet obtaining DNA barcodes from long-stored specimens may be difficult due to sample degradation. Here we demonstrate a sensitive and efficient laboratory and bioinformatic process for generating DNA barcodes from hundreds of invertebrate specimens simultaneously via the Illumina MiSeq system. Using this process, we recovered full-length (334) or partial (105) COI barcodes from 439 of 450 (98%) national collection-held invertebrate specimens. This included full-length barcodes from 146 specimens which produced low-yield DNA and no visible PCR bands, and which produced as little as a single sequence per specimen, demonstrating high sensitivity of the process. In many cases, the identity of the most abundant sequences per specimen were not the correct barcodes, necessitating the development of a taxonomy-informed process for identifying correct sequences among the sequencing output. The recovery of only partial barcodes for some taxa indicates a need to refine certain PCR primers. Nonetheless, our approach represents a highly sensitive, accurate and efficient method for targeted reference database generation, providing a foundation for DNA-based assessments and monitoring of biodiversity.},
}
@article {pmid36344500,
year = {2022},
author = {Baldwin, LA and Bartonicek, N and Yang, J and Wu, SZ and Deng, N and Roden, DL and Chan, CL and Al-Eryani, G and Zanker, DJ and Parker, BS and Swarbrick, A and Junankar, S},
title = {DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and immunotherapy response.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {6539},
pmid = {36344500},
issn = {2041-1723},
mesh = {Humans ; Mice ; Animals ; Female ; *DNA Barcoding, Taxonomic ; Immunotherapy ; Immunologic Factors ; *Breast Neoplasms/genetics/therapy ; Longitudinal Studies ; },
abstract = {Cancers evade the immune system through the process of cancer immunoediting. While immune checkpoint inhibitors are effective for reactivating tumour immunity in some cancer types, many other solid cancers, including breast cancer, remain largely non-responsive. Understanding how non-responsive cancers evade immunity and whether this occurs at the clonal level will improve immunotherapeutic design. Here we use DNA barcoding to track murine mammary cancer cell clones during immunoediting and determine clonal transcriptional profiles that allow immune evasion following anti-PD1 plus anti-CTLA4 immunotherapy. Clonal diversity is significantly restricted by immunotherapy treatment in both primary tumours and metastases, demonstrating selection for pre-existing breast cancer cell populations and ongoing immunoediting during metastasis and treatment. Immunotherapy resistant clones express a common gene signature associated with poor survival of basal-like breast cancer patient cohorts. At least one of these genes has an existing small molecule that can potentially be used to improve immunotherapy response.},
}
@article {pmid36344194,
year = {2022},
author = {Klemm, K and Cembella, A and Clarke, D and Cusack, C and Arneborg, L and Karlson, B and Liu, Y and Naustvoll, L and Siano, R and Gran-Stadniczeñko, S and John, U},
title = {Apparent biogeographical trends in Alexandrium blooms for northern Europe: identifying links to climate change and effective adaptive actions.},
journal = {Harmful algae},
volume = {119},
number = {},
pages = {102335},
doi = {10.1016/j.hal.2022.102335},
pmid = {36344194},
issn = {1878-1470},
mesh = {Humans ; *Climate Change ; Ecosystem ; *Dinoflagellida ; Harmful Algal Bloom ; Salinity ; },
abstract = {The marine dinoflagellate Alexandrium Halim represents perhaps the most significant and intensively studied genus with respect to species diversity, life history strategies, toxigenicity, biogeographical distribution, and global magnitude and consequences harmful algal blooms (HABs). The socioeconomic impacts, environmental and human health risks, and mitigation strategies for toxigenic Alexandrium blooms have also been explored in recent years. Human adaptive actions based on future scenarios of bloom dynamics and shifts in biogeographical distribution under climate-change parameters remain under development and not yet implemented on a regional scale. In the CoCliME (Co-development of climate services for adaptation to changing marine ecosystems) project these issues were addressed with respect to past, current and anticipated future status of key HAB genera and expected benefits of enhanced monitoring. Data on the distribution and frequency of Alexandrium blooms related to paralytic shellfish toxin (PST) events from key CoCliME Case Study areas, comprising the North Sea and adjacent Kattegat-Skagerrak, Norwegian Sea, and Baltic Sea, and eastern North Atlantic marginal seas, were evaluated in a contemporary and historical context over the past several decades. The first evidence of possible biogeographical expansion of Alexandrium taxa into eastern Arctic gateways was provided from DNA barcoding signatures. Various key climate change indicators, such as salinity, temperature, and water-column stratification, relevant to Alexandrium bloom initiation and development were identified. The possible influence of changing variables on bloom dynamics, magnitude, frequency and spatial and temporal distribution were interpreted in the context of regional ocean climate models. These climate change impact indicators may play key roles in selecting for the occurrence and diversity of Alexandrium species within the broader microeukaryote communities. For example, shifts to higher temperature and lower salinity regimes predicted for the southern North Sea indicate the potential for increased Alexandrium blooms, currently absent from this area. Ecological and socioeconomic impacts of Alexandrium blooms and effects on fisheries and aquaculture resources and coastal ecosystem function are evaluated, and, where feasible, effective adaptation strategies are proposed herein as emerging climate services.},
}
@article {pmid36342179,
year = {2022},
author = {Rapti, K and Maiakovska, O and Becker, J and Szumska, J and Zayas, M and Bubeck, F and Liu, J and Gerstmann, E and Krämer, C and Wiedtke, E and Grimm, D},
title = {Isolation of Next-Generation Gene Therapy Vectors through Engineering, Barcoding, and Screening of Adeno-Associated Virus (AAV) Capsid Variants.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {188},
pages = {},
doi = {10.3791/64389},
pmid = {36342179},
issn = {1940-087X},
mesh = {Animals ; *Dependovirus/genetics/metabolism ; *Capsid/metabolism ; Genetic Vectors/genetics ; Capsid Proteins/genetics ; Genetic Therapy/methods ; Peptide Library ; },
abstract = {Gene delivery vectors derived from Adeno-associated virus (AAV) are one of the most promising tools for the treatment of genetic diseases, evidenced by encouraging clinical data and the approval of several AAV gene therapies. Two major reasons for the success of AAV vectors are (i) the prior isolation of various naturally occurring viral serotypes with distinct properties, and (ii) the subsequent establishment of powerful technologies for their molecular engineering and repurposing in high throughput. Further boosting the potential of these techniques are recently implemented strategies for barcoding selected AAV capsids on the DNA and RNA level, permitting their comprehensive and parallel in vivo stratification in all major organs and cell types in a single animal. Here, we present a basic pipeline encompassing this set of complementary avenues, using AAV peptide display to represent the diverse arsenal of available capsid engineering technologies. Accordingly, we first describe the pivotal steps for the generation of an AAV peptide display library for the in vivo selection of candidates with desired properties, followed by a demonstration of how to barcode the most interesting capsid variants for secondary in vivo screening. Next, we exemplify the methodology for the creation of libraries for next-generation sequencing (NGS), including barcode amplification and adaptor ligation, before concluding with an overview of the most critical steps during NGS data analysis. As the protocols reported here are versatile and adaptable, researchers can easily harness them to enrich the optimal AAV capsid variants in their favorite disease model and for gene therapy applications.},
}
@article {pmid36340145,
year = {2022},
author = {Zeng, B and Zhou, Q and Ye, Q and Zhou, T and Yuan, M and Liu, Y and Zeng, D and Li, J and Chen, K and Guo, Y and Guo, L},
title = {Identification and Quality Evaluation of Velvet Antler by DNA Barcoding and Stable Isotope Techniques Combined with Chemometrics.},
journal = {ACS omega},
volume = {7},
number = {43},
pages = {39206-39213},
pmid = {36340145},
issn = {2470-1343},
abstract = {This study aimed to identify Velvet antler and its counterfeits and to further evaluate their quality. Mitochondrial cytochrome b (Cytb) was used as a target gene to identify Velvet antler samples, and a DNA barcoding method was established for species origin identification in Velvet antlers. After identification, the stable isotope contents and ratios were adopted to evaluate the quality of different specifications of authentic Velvet antler in combination with chemometrics. Two stable isotope contents (C % and N %) and ratios (δ[13]C and δ[15]N) in three kinds of Velvet antler slices of different specifications, namely, wax slices, powder slices, and bone slices, were determined. Nine Velvet antler samples sold in the market were identified for label conformity. Only two samples were consistent with the labeled species, and the others were counterfeits. The three slices of Velvet antler of different specifications were clearly distinguished by principal component analysis and hierarchical cluster analysis. Then, the discriminant model of partial least squares discriminant analysis was established, and 100% discrimination accuracy was observed in this model. All the Velvet antler slice samples of different specification samples were grouped clearly according to their sources. In summary, it is feasible for the identification and quality grade evaluation of Velvet antler by DNA barcoding based on mitochondrial Cytb and stable isotope techniques combined with chemometric analysis. The establishment of this method also provided a reference for the evaluation of other animal-derived medicinal materials.},
}
@article {pmid36339998,
year = {2022},
author = {Chaiphongpachara, T and Changbunjong, T and Laojun, S and Sumruayphol, S and Suwandittakul, N and Kuntawong, K and Pimsuka, S},
title = {Geometric morphometric and molecular techniques for discriminating among three cryptic species of the Anopheles barbirostris complex (diptera: culicidae) in Thailand.},
journal = {Heliyon},
volume = {8},
number = {10},
pages = {e11261},
pmid = {36339998},
issn = {2405-8440},
abstract = {Anopheles members of the Barbirostris complex are important vectors of malaria in Thailand. However, they are morphologically indistinguishable because they are closely related species. In this study, wing geometric morphometrics (GM) and DNA barcoding based on the cytochrome c oxidase subunit 1 (C O I) gene were applied to differentiate cryptic species of the Barbirostris complex in Thailand. Three cryptic species of the Barbirostris complex, Anopheles dissidens (19.44%), Anopheles saeungae (24.54%), and Anopheles wejchoochotei (56.02%) were initially identified using the multiplex polymerase chain reaction assay. DNA barcoding analyses showed low intraspecific distances (range, 0.27%-0.63%) and high interspecific distances (range, 1.92%-3.68%), consistent with the phylogenetic analyses that showed clear species groups. While wing size and shape analyses based on landmark-based GM indicated differences between three species (p < 0.05). The cross-validated reclassification revealed that the overall efficacy of wing size analysis for species identification of the Barbirostris complex was less than the wing shape analysis (56.43% vs. 74.29% total performance). Therefore, this study's results are guidelines for applying modern techniques to identify members within the Barbirostris complex, which are still difficult to distinguish by morphology-based identification and contribute to further appropriate malaria control.},
}
@article {pmid36339560,
year = {2022},
author = {Bhowmick, S and Beckmann, M and Shen, J and Mur, LAJ},
title = {Identification and metabolomic characterization of potent anti-MRSA phloroglucinol derivatives from Dryopteris crassirhizoma Nakai (Polypodiaceae).},
journal = {Frontiers in pharmacology},
volume = {13},
number = {},
pages = {961087},
pmid = {36339560},
issn = {1663-9812},
abstract = {Traditional Chinese medicine (TCM) has been used to treat infectious diseases and could offer potential drug leads. This study evaluates the in vitro antimicrobial activities from commercially sourced Dryopteris crassirhizoma Nakai (Polypodiaceae) whose authenticity was confirmed by DNA barcoding based on the ribulose bisphosphate carboxylase (rbcL) gene. Powdered rhizomes were sequentially extracted using n-hexane, dichloromethane, ethyl acetate, and methanol at ambient temperature. The dried extracts at different concentrations were tested for antimicrobial activities against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, methicillin-resistant Staphylococcus aureus (MRSA), and Mycobacterium smegmatis. D. crassirhizoma extracts exhibited significant antimicrobial activities only against MRSA (minimum inhibitory concentration: 3.125 μg/ml n-hexane extract). Activity-led fractionations of D. crassirhizoma and characterization by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) targeted a fraction (A3), with two anti-MRSA phloroglucinol derivatives, flavaspidic acid AB and norflavaspidic acid AB-being greatly enriched in the latter. The impact of A3 on MRSA cells was examined using untargeted metabolomic analysis and compared to that of other established antibiotics (all treatments normalized to MIC50 at 6 h). This suggested that norflavaspidic acid AB had distinctive effects, one of which involved targeting bioenergetic transformation, metabolism, and particularly acetyl-CoA, on MRSA cells. No cytotoxicity was observed for the norflavaspidic acid AB-enriched fraction against murine HepG2 cells. This study requires further experimental validation but can have indicated a naturally available compound that could help counter the threat of clinically relevant strains with antibiotic resistance.},
}
@article {pmid36339543,
year = {2022},
author = {Mahima, K and Sunil Kumar, KN and Rakhesh, KV and Rajeswaran, PS and Sharma, A and Sathishkumar, R},
title = {Advancements and future prospective of DNA barcodes in the herbal drug industry.},
journal = {Frontiers in pharmacology},
volume = {13},
number = {},
pages = {947512},
pmid = {36339543},
issn = {1663-9812},
abstract = {Ethnopharmacological relevance: The past couple of decades have witnessed the global resurgence of medicinal plants in the field of herbal-based health care. Increased consumption of medicinal plants and their derivative products is the major cause of the adulteration issues in herbal industries. As a result, the quality of herbal products is affected by spurious and unauthorized raw materials. Recent development in molecular plant identification using DNA barcodes has become a robust methodology to identify and authenticate the adulterants in herbal samples. Hence, rapid and accurate identification of medicinal plants is the key to success for the herbal industry. Aim of the study: This paper provides a comprehensive review of the application of DNA barcoding and advanced technologies that have emerged over the past 10 years related to medicinal plant identification and authentication and the future prospects of this technology. Materials and methods: Information on DNA barcodes was compiled from scientific databases (Google Scholar, Web of Science, SciFinder and PubMed). Additional information was obtained from books, Ph.D. thesis and MSc. Dissertations. Results: Working out an appropriate DNA barcode for plants is challenging; the single locus-based DNA barcodes (rbcL, ITS, ITS2, matK, rpoB, rpoC, trnH-psbA) to multi-locus DNA barcodes have become the successful species-level identification among herbal plants. Additionally, multi-loci have become efficient in the authentication of herbal products. Emerging advances in DNA barcoding and related technologies such as next-generation sequencing, high-resolution melting curve analysis, meta barcodes and mini barcodes have paved the way for successful herbal plant/samples identification. Conclusion: DNA barcoding needs to be employed together with other techniques to check and rationally and effectively quality control the herbal drugs. It is suggested that DNA barcoding techniques combined with metabolomics, transcriptomics, and proteomics could authenticate the herbal products. The invention of simple, cost-effective and improved DNA barcoding techniques to identify herbal drugs and their associated products of medicinal value in a fool-proof manner will be the future thrust of Pharmacopoeial monograph development for herbal drugs.},
}
@article {pmid36338061,
year = {2022},
author = {Guo, J and Jin, Y and Tian, X and Bao, H and Sun, Y and Gray, T and Song, Y and Zhang, M},
title = {Diet-induced microbial adaptation process of red deer (Cervus elaphus) under different introduced periods.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1033050},
pmid = {36338061},
issn = {1664-302X},
abstract = {Insufficient prey density is a major factor hindering the recovery of the Amur tiger (Panthera tigris altaica), and to effectively restore the Amur tiger, red deer (Cervus elaphus) was released into the Huangnihe National Nature Reserve of Northeast China as the main reinforcement. Differences in feeding and synergistic changes caused by the intestinal microbial communities could impact the adaptation of wildlife following reintroductions into field environments. We analyzed the foraging changes in shaping the intestinal microbial community of the red deer after being released to the Huangnihe National Nature Reserve and screened the key microbial flora of the red deer when processing complex food resources. The feeding and intestinal microbial communities of the red deer were analyzed by plant Deoxyribonucleic acid (DNA) barcoding sequencing and 16S rRNA high-throughput sequencing, respectively. The results showed that there were significant differences in food composition between wild and released groups [released in 2019 (R2): n = 5; released in 2021 (R0): n = 6]; the wild group fed mainly on Acer (31.8%) and Abies (25.6%), R2 fed mainly on Betula (44.6%), R0 had not formed a clear preferred feeding pattern but had certain abilities to process and adapt to natural foods. Firmicutes (77.47%) and Bacteroides (14.16%) constituted the main bacterial phylum of red deer, of which, the phylum Firmicutes was the key species of the introduced red deer for processing complex food resources (p < 0.05). The wild release process significantly changed the intestinal microbial structure of the red deer, making it integrate into the wild red deer. The period since release into the wild may be a key factor in reshaping the structure of the microbial community. This study suggested that the intestinal microbial structure of red deer was significantly different depending on how long since captive deer has been translocated. Individuals that have lived in similar environments for a long time will have similar gut microbes. This is the adaption process of the wildlife to natural environment after wild release, taking into account the gut microbes, and the feeding changes in shaping microbial communities can help introduced red deer match complex food resources and novel field environments.},
}
@article {pmid36335499,
year = {2023},
author = {Hu, Y and Yang, C and Zhang, L and Zhou, X},
title = {Haplotyping-Assisted Diploid Assembly and Variant Detection with Linked Reads.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2590},
number = {},
pages = {161-182},
pmid = {36335499},
issn = {1940-6029},
mesh = {Humans ; *Diploidy ; Sequence Analysis, DNA ; *High-Throughput Nucleotide Sequencing ; Genome, Human ; Haplotypes ; },
abstract = {Phasing is essential for determining the origins of each set of alleles in the whole-genome sequencing data of individuals. As such, it provides essential information for the causes of hereditary diseases and the sources of individual variability. Recent technical breakthroughs in linked-read (referred to as co-barcoding in other chapters of the book) and long-read sequencing and downstream analysis have brought the goal of accurate and complete phasing within reach. Here we review recent progress related to the assembly and phasing of personal genomes based on linked-reads and related applications. Motivated by current limitations in generating high-quality diploid assemblies and detecting variants, a new suite of software tools, Aquila, was developed to fully take advantage of linked-read sequencing technology. The overarching goal of Aquila is to exploit the strengths of linked-read technology including long-range connectivity and inherent phasing of variants for reference-assisted local de novo assembly at the whole-genome scale. The diploid nature of the assemblies facilitates detection and phasing of genetic variation, including single nucleotide variations (SNVs), small insertions and deletions (indels), and structural variants (SVs). An extension of Aquila, Aquila_stLFR, focuses on another newly developed linked-reads sequencing technology, single-tube long-fragment read (stLFR). AquilaSV, a region-based diploid assembly approach, is used to characterize structural variants and can achieve diploid assembly in one target region at a time. Lastly, we introduce HAPDeNovo, a program that exploits phasing information from linked-read sequencing to improve detection of de novo mutations. Use of these tools is expected to harness the advantages of linked-reads technology, improve phasing, and advance variant discovery.},
}
@article {pmid36335495,
year = {2023},
author = {Wang, O and Cheng, X and Drmanac, R and Peters, BA},
title = {A Simple Cost-Effective Method for Whole-Genome Sequencing, Haplotyping, and Assembly.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2590},
number = {},
pages = {101-125},
pmid = {36335495},
issn = {1940-6029},
mesh = {Cost-Benefit Analysis ; Haplotypes ; Whole Genome Sequencing ; *High-Throughput Nucleotide Sequencing/methods ; Gene Library ; Sequence Analysis, DNA ; },
abstract = {In this chapter, we describe single-tube long fragment read (stLFR), a simple preparation method for whole-genome sequencing and physical haplotyping based on the DNA co-barcoding strategy. Similar to LFR, stLFR applies the concept of adding the same barcode to subfragments derived from the same long DNA molecule. However, instead of a 384-well plate, stLFR uses the surface of micron-sized magnetic beads to create millions of virtual compartments in a single reaction tube. This is enabled by a split and pool barcoded bead preparation process capable of generating ~500,000 copies of the same unique barcode, from a library of ~3.6 billion unique barcodes, on each bead. The instruments and devices used in the stLFR process are easily accessible in nearly all standard molecular biology laboratories, and the cost of reagents can be as low as 30 dollars per sample. stLFR libraries can be sequenced by standard second-generation sequencing instruments (e.g., MGI or Illumina devices), and the barcode sharing information enables detection and phasing of all variations, including large structural variations. In addition, stLFR data can be used to scaffold contigs and de novo assemble genomes.},
}
@article {pmid36335494,
year = {2023},
author = {Redin, D},
title = {Low-Cost Genome-Scale Phasing with Barcode-Linked Sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2590},
number = {},
pages = {85-99},
pmid = {36335494},
issn = {1940-6029},
mesh = {Humans ; Sequence Analysis, DNA/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Genome, Human ; Haplotypes ; },
abstract = {Complete comprehension of clinically relevant variation among human genomes is likely only to come from sequencing platforms that are cost-efficient, and which feature both accurate base calling and long-range DNA phasing capability. The NGS revolution has struggled to meet the latter of these needs. Here we describe a protocol to address this limitation by preserving the molecular origin of short sequencing reads with an insignificant increase to sequencing costs. Whole haplotype-resolved genomes with megabase-scale phase blocks can be obtained with this method; offering researchers a unique opportunity to tackle the hurdles of de novo sequencing without being limited by a lack of resources.},
}
@article {pmid36335493,
year = {2023},
author = {McElwain, MA and Peters, BA},
title = {Accurate Sequencing and Haplotyping from 10 Cells Using Long Fragment Read (LFR) Technology.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2590},
number = {},
pages = {71-84},
pmid = {36335493},
issn = {1940-6029},
mesh = {Humans ; Haplotypes/genetics ; *Genome, Human ; Sequence Analysis, DNA/methods ; *High-Throughput Nucleotide Sequencing/methods ; DNA ; Technology ; },
abstract = {In this chapter, we describe how Long Fragment Read (LFR) technology can be applied to samples consisting of very few cells (5-20) to enable complete genome sequencing and haplotyping with a very low false positive error rate. LFR is a method for processing DNA or cells prior to sequencing on any second-generation DNA sequencing platform (e.g., MGI's DNBSEQ, Illumina sequencers, etc.). First, the LFR process incorporates a low-bias whole genome amplification step allowing accurate sequencing from very low DNA inputs (as low as 32 picograms, the mass contained within 5 diploid human cells). In addition, LFR enables the haplotyping of nearly all genomic variations with N50 contig lengths up to ~1 Mb. Furthermore, if data from this method are analyzed with parental genotype data, it is possible to generate phased variants in uninterrupted contigs spanning entire chromosomes. Importantly, the barcoding process utilized in this method allows for the detection and correction of most amplification, sequencing, and mapping errors, yielding false positive error rates as low as 10[-9]. Finally, the cost of this method is modest and enables extremely high-quality whole genome sequence and haplotype data from as few as 5 cells. We know of few other methods that can achieve this.},
}
@article {pmid36331979,
year = {2022},
author = {Post, RJ and Laudisoit, A and Mandro, M and Lakwo, T and Laemmer, C and Pfarr, K and Hoerauf, A and Tortosa, P and Gomard, Y and Ukety, T and Mande, C and Farovitch, L and Amazigo, U and Bakajika, D and Oguttu, DW and Awaca, N and Colebunders, R},
title = {Identification of the onchocerciasis vector in the Kakoi-Koda focus of the Democratic Republic of Congo.},
journal = {PLoS neglected tropical diseases},
volume = {16},
number = {11},
pages = {e0010684},
pmid = {36331979},
issn = {1935-2735},
support = {001/WHO_/World Health Organization/International ; },
mesh = {Adult ; Animals ; Female ; Humans ; *Onchocerciasis/epidemiology ; Democratic Republic of the Congo/epidemiology ; Insect Vectors ; Plant Breeding ; *Onchocerca volvulus ; *Simuliidae/genetics ; },
abstract = {BACKGROUND: The objective of this study was to characterise the vector in a small hyper-endemic focus of onchocerciasis (the Kakoi-Koda focus) which has recently been discovered on the western slopes of the rift valley above Lake Albert.<br><br>Aquatic stages of blackflies were collected by hand from streams and rivers, and anthropophilic adult females were collected by human landing catches. Using a combination of morphotaxonomy and DNA barcoding, the blackflies collected biting humans within the focus were identified as Simulium dentulosum and Simulium vorax, which were also found breeding in local streams and rivers. Simulium damnosum s.l., Simulium neavei and Simulium albivirgulatum were not found (except for a single site in 2009 where crabs were carrying S. neavei). Anthropophilic specimens from the focus were screened for Onchocerca DNA using discriminant qualitative real-time triplex PCR. One specimen of S. vorax was positive for Onchocerca volvulus in the body, and out of 155 S. dentulosum, 30% and 11% were infected and infective (respectively).<br><br>CONCLUSIONS/SIGNIFICANCE: Simulium dentulosum currently appears to be the main vector of human onchocerciasis within the Kakoi-Koda focus, and S. vorax may be a secondary vector. It remains possible that S. neavei was the main (or only) vector in the past having now become rare as a result of the removal of tree-cover and land-use changes. Simulium vorax has previously been shown to support the development of O. volvulus in the laboratory, but this is the first time that S. dentulosum has been implicated as a probable vector of onchocerciasis, and this raises the possibility that other blackfly species which are not generally considered to be anthropophilic vectors might become vectors under suitable conditions. Because S. dentulosum is not a vector in endemic areas surrounding the Kakoi-Koda focus, it is probable that the Kakoi-Koda focus is significantly isolated.},
}
@article {pmid36330024,
year = {2022},
author = {Shih, YJ and Chen, YZ and Guo, YQ},
title = {A New Species of Free-living Marine Nematode (Ptycholaimellus: Chromadoridae: Chromadorida: Nematoda) from Mangrove Wetlands in China.},
journal = {Zoological studies},
volume = {61},
number = {},
pages = {e20},
pmid = {36330024},
issn = {1810-522X},
abstract = {This study presents a new species of free-living marine nematode, Ptycholaimellus luoyang sp. nov., from mangrove wetlands in China. The identification was confirmed by analyzing morphological characteristics and three genes: COI, 18S rDNA, and 28S rDNA. This species is distinguished from allied species by its short cephalic setae, cylindrical pharynx with anterior swelling, sclerotized transverse ridges occurring near the dorsal tooth, rod-like gubernaculum and proximal, arch-like, slightly waved, middle curved, and distally pointed spicules. The Bayesian topology was regarded as morphological evidence of P. luoyang sp. nov. being a distinct species. Interspecific and intrageneric thresholds of the K2P distance divergence have been presented here for the first time.},
}
@article {pmid36329610,
year = {2022},
author = {Banijamali, M and Höjer, P and Nagy, A and Hååg, P and Gomero, EP and Stiller, C and Kaminskyy, VO and Ekman, S and Lewensohn, R and Karlström, AE and Viktorsson, K and Ahmadian, A},
title = {Characterizing single extracellular vesicles by droplet barcode sequencing for protein analysis.},
journal = {Journal of extracellular vesicles},
volume = {11},
number = {11},
pages = {e12277},
pmid = {36329610},
issn = {2001-3078},
mesh = {Humans ; *Extracellular Vesicles/genetics ; Biomarkers/metabolism ; Cell Line ; Membrane Proteins/metabolism ; },
abstract = {Small extracellular vesicles (sEVs) have in recent years evolved as a source of biomarkers for disease diagnosis and therapeutic follow up. sEV samples derived from multicellular organisms exhibit a high heterogeneous repertoire of vesicles which current methods based on ensemble measurements cannot capture. In this work we present droplet barcode sequencing for protein analysis (DBS-Pro) to profile surface proteins on individual sEVs, facilitating identification of sEV-subtypes within and between samples. The method allows for analysis of multiple proteins through use of DNA barcoded affinity reagents and sequencing as readout. High throughput single vesicle profiling is enabled through compartmentalization of individual sEVs in emulsion droplets followed by droplet barcoding through PCR. In this proof-of-concept study we demonstrate that DBS-Pro allows for analysis of single sEVs, with a mixing rate below 2%. A total of over 120,000 individual sEVs obtained from a NSCLC cell line and from malignant pleural effusion (MPE) fluid of NSCLC patients have been analyzed based on their surface proteins. We also show that the method enables single vesicle surface protein profiling and by extension characterization of sEV-subtypes, which is essential to identify the cellular origin of vesicles in heterogenous samples.},
}
@article {pmid36329337,
year = {2023},
author = {Jiang, Z and Zhang, M and Kong, L and Bao, Y and Ren, W and Li, H and Liu, X and Wang, Z and Ma, W},
title = {Identification of Apiaceae using ITS, ITS2 and psba-trnH barcodes.},
journal = {Molecular biology reports},
volume = {50},
number = {1},
pages = {245-253},
pmid = {36329337},
issn = {1573-4978},
support = {2060302//The ability establishment of sustainable use for valuable Chinese medicine resources/ ; ZYRCB2021008//Talent training project supported by the central government for the reform and development of local colleges and Universities/ ; [2019] No. 5//Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education and Heilongjiang Touyan Innovation Team Program/ ; },
mesh = {DNA Barcoding, Taxonomic/methods ; *Apiaceae/genetics ; Phylogeny ; Ecosystem ; DNA, Plant/genetics ; *Plants, Medicinal/genetics ; },
abstract = {Apiaceae plants are used as medicinal herbs, pesticides, spices, and vegetables; thus, accurately identifying Apiaceae species is important. The grassland ecosystem of Heilongjiang Province in northern China has huge reserves of wild Apiaceae plants, but few reports have systematically documented their diversity. In this study, 275 Apiaceae plants of 23 species in 18 genera were collected from this area. We identified Apiaceae species by using nuclear internal transcribed spacer (ITS/ITS2) and psbA-trnH (chloroplast non-coding region) sequences based on experimental data. The identification efficiency of ITS, ITS2 and psbA-trnH sequences was determined and evaluated by sequence alignment and analysis, intraspecific and interspecific genetic distance analyses, and phylogenetic tree construction. ITS, ITS2 could distinguish 21 species from 17 genera of Apiaceae with good identification effect. When identifying species in the Apiaceae family, ITS2 can be used as the core barcode and psbA-trnH can be used as the supplementary barcode. These results can enrich the reference Apiaceae DNA barcode database.},
}
@article {pmid36328452,
year = {2022},
author = {Yasunaga, T and Fukuoka, T and Yamaguchi, A and Ogawa, N and Yamamoto, H},
title = {[Microtaggant Technology for Ensuring Traceability of Pharmaceutical Formulations: Potential for Anti-counterfeiting Measures, Distribution and Medication Management].},
journal = {Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan},
volume = {142},
number = {11},
pages = {1255-1265},
doi = {10.1248/yakushi.22-00147},
pmid = {36328452},
issn = {1347-5231},
mesh = {Humans ; Drug Compounding ; *Medication Therapy Management ; *Counterfeit Drugs ; Pharmaceutical Preparations ; Technology ; },
abstract = {The globalization of drug trade has led to the increased production of falsified medicines. In addition, poor medication adherence increases the costs of healthcare. The need to manage medication has given rise to marketing of highly functional networked digital medicine. Therefore, a growing need has emerged to ensure the traceability of pharmaceutical products from shipment to patient distribution. Microtaggant technologies that can encode individual numbers on pharmaceutical products are expected to serve achieving this goal. Taggants are a class of materials that can be applied to an object to make it identifiable, like barcodes and holograms. Since the smaller size of microtaggant make it invisible to naked eyes, it is more difficult to reverse-engineer than conventional taggants. The U.S. Food and Drug Administration (FDA) has established guidelines for the use of microtaggants. Many studies have explored the use of various analytical technologies and materials as the microtaggants. However, the advantages and disadvantages of each method have not been established yet. In this review, recent research on the use of microtaggants for anti-counterfeiting is summarized and compared to current anti-counterfeiting technologies with spectrographic methods, distribution management systems with barcodes, and medication management systems with sensor devices. We also discuss the microtaggants implementation costs and security level.},
}
@article {pmid36325176,
year = {2022},
author = {Goh, KS and Wang, LJ and Ni, JH and Wang, TY},
title = {Luminescent characteristics and mitochondrial COI barcodes of nine cohabitated Taiwanese fireflies.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e14195},
pmid = {36325176},
issn = {2167-8359},
mesh = {Animals ; Male ; Female ; *Fireflies/genetics ; *Luminescence ; Phylogeny ; Light ; Larva/genetics ; },
abstract = {BACKGROUND: Over 50 Taiwanese firefly species have been discovered, but scientists lack information regarding most of their genetics, bioluminescent features, and cohabitating phenomena. In this study, we focus on morphological species identification and phylogeny reconstructed by COI barcoding, as well as luminescent characteristics of cohabited Taiwanese firefly species to determine the key factors that influenced how distinct bioluminescent species evolved to coexist and proliferate within the same habitat.<br><br>METHODS: In this study, 366 specimens from nine species were collected in northern Taiwan from April to August, 2016-2019. First, the species and sex of the specimens were morphologically and genetically identified. Then, their luminescent spectra and intensities were recorded using a spectrometer and a power meter, respectively. The habitat temperature, relative humidity, and environmental light intensity were also measured. The cytochrome oxidase I (COI) gene sequence was used as a DNA barcode to reveal the phylogenetic relationships of cohabitated species.<br><br>RESULTS: Nine species-eight adult species (Abscondita chinensis, Abscondita cerata, Aquatica ficta, Luciola curtithorax, Luciola kagiana, Luciola filiformis, Curtos sauteri, and Curtos costipennis) and one larval Pyrocoelia praetexta-were morphologically identified. The nine species could be found in April-August. Six of the eight adult species shared an overlap occurrence period in May. Luminescent spectra analysis revealed that the &#x3bb; max of studied species ranged from 552-572 nm (yellow-green to orange-yellow). The average luminescent intensity range of these species was about 1.2-14 lux (182.1-2,048 nW/cm[2]) for males and 0.8-5.8 lux (122.8-850 nW/cm[2]) for females, and the maximum luminescent intensity of males was 1.01-7.26-fold higher than that of females. Compared with previous studies, this study demonstrates that different &#x3bb; max, species-specific flash patterns, microhabitat choices, nocturnal activity time, and/or an isolated mating season are key factors that may lead to the species-specific courtship of cohabitated fireflies. Moreover, we estimated that the fireflies start flashing or flying when the environmental light intensity decreased to 6.49-28.1 lux. Thus, based on a rough theoretical calculation, the sensing distance between male and female fireflies might be 1.8-2.7 m apart in the dark. In addition, the mitochondrial COI barcode identified species with high resolution and suggested that most of the studied species have been placed correctly with congeners in previous phylogenies. Several cryptic species were revealed by the COI barcode with 3.27%-12.3% variation. This study renews the idea that fireflies' luminescence color originated from the green color of a Lampyridae ancestor, then red-shifted to yellow-green in Luciolinae, and further changed to orange-yellow color in some derived species.},
}
@article {pmid36324823,
year = {2022},
author = {Nofal, AP and Dos Santos, QM and Jirsa, F and Avenant-Oldewage, A},
title = {Camallanid nematodes from Clarias gariepinus (Burchell, 1822) in the Crocodile River, Gauteng, South Africa: Exploring diversity and divergence in an acid-mine drainage impacted environment.},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {19},
number = {},
pages = {196-210},
pmid = {36324823},
issn = {2213-2244},
abstract = {Clarias gariepinus collected from Lake Heritage, Crocodile River, were found to harbour camallanid nematodes. Previously, Boomker (1982) surveyed the Hartbeespoort Dam, downstream of the current study site, and identified a high prevalence of Procamallanus (Procamallanus) laeviconchus and Paracamallanus cyathopharynx. Since then, Procamallanus (Procamallanus) pseudolaeviconchus was described from C. gariepinus suggesting reconsideration of the identifications of Procamallanus species in historical studies from clariids. The aim of the current study was to definitively identify the nematodes collected from C. gariepinus in Lake Heritage, using morphological and molecular analyses. Morphological study consisted of light and scanning electron microscopy which confirmed the identity P. (P.) pseudolaeviconchus and P. cyathopharynx. This included descriptions of the detailed morphology of isolated buccal capsules for both species using soft tissue digestion, notably for the first time for P. (P.) pseudolaeviconchus. The morphology of isolated spiculae of both species was described for the first time using SEM. Molecular analyses included genetic characterisation of the small ribosomal subunit (18S) rDNA and cytochrome oxidase 1 (CO1) mtDNA. Genetic data supported the morphological identification of both species, however, divergence was detected in CO1 mtDNA data for P. cyathopharynx indicating two distinct lineages. Due to this variation, the morphometry of P. cyathopharynx specimens were revisited including statistical re-evaluation. No robust morphological traits were identified to support CO1 mtDNA lineages and all specimens were considered conspecific. In terms of camallanid biodiversity in the Crocodile River system, it is similar to that in Boomker (1982), despite the altered water quality from past acid mine pollution in the river.},
}
@article {pmid36324537,
year = {2022},
author = {Pejić, B and Budinski, I and van Schaik, J and Blagojević, J},
title = {Sharing roosts but not ectoparasites: high host-specificity in bat flies and wing mites of Miniopterus schreibersii and Rhinolophus ferrumequinum (Mammalia: Chiroptera).},
journal = {Current zoology},
volume = {68},
number = {5},
pages = {507-516},
pmid = {36324537},
issn = {1674-5507},
abstract = {Schreiber's bent-winged bat Miniopterus schreibersii and the greater horseshoe bat Rhinolophus ferrumequinum are widespread and common cavernicolous species across southern Europe that host numerous specialized ectoparasite species. The objective of this study was to characterize the species assemblage, genetic diversity, and host specificity of bat flies (Nycteribiidae, Diptera) and wing mites (Spinturnicidae, Acari) found on these bat hosts in Serbia and Bosnia and Herzegovina. Notably, while bat flies lay puparia on the cave walls and can thus be transmitted indirectly, wing mites require direct body contact for transmission. Morphological identification and sequencing of a 710-bp fragment of cytochrome oxidase I gene of 207 bat flies yielded 4 species, 3 on M. schreibersii and 1 on R. ferrumequinum. Sequencing of a 460-bp small subunit ribosomal RNA fragment, in all 190 collected wing mites revealed 2 species, 1 per host. In no case was a parasite associated with 1 host found on the other host. Species and genetic diversity of flies were higher in M. schreibersii, likely reflecting their host's larger colony sizes and migratory potential. Mite species of both hosts showed similarly low diversity, likely due to their faster life history and lower winter survival. Our findings highlight a remarkably high host-specificity and segregation of ectoparasite species despite direct contact among their hosts in the roost, suggesting a defined host preference in the investigated ectoparasite species. Furthermore, the differences in ectoparasite genetic diversity exemplify the interplay between host and parasite life histories in shaping parasite population genetic structure.},
}
@article {pmid36321434,
year = {2022},
author = {Andrus, PS and Rae, R and Wade, CM},
title = {Nematodes and trematodes associated with terrestrial gastropods in Nottingham, England.},
journal = {Journal of helminthology},
volume = {96},
number = {},
pages = {e81},
doi = {10.1017/S0022149X22000645},
pmid = {36321434},
issn = {1475-2697},
mesh = {Animals ; Dogs ; *Nematoda/classification/genetics/isolation &amp; purification ; Rhabditoidea/genetics/isolation &amp; purification ; Snails/parasitology ; *Trematoda/classification/genetics/isolation &amp; purification ; Trematode Infections/epidemiology/parasitology/veterinary ; England/epidemiology ; DNA Barcoding, Taxonomic ; Nematode Infections/epidemiology/parasitology/veterinary ; Genotype ; Cities/statistics &amp; numerical data ; Walking ; Dog Diseases/parasitology ; *Gastropoda/parasitology ; },
abstract = {A parasitological survey of terrestrial slugs and snails was conducted at popular dog walking locations across the city of Nottingham, with the intensions of finding gastropods infected with parasites of medical (or veterinary) importance such as lungworm (metastrongyloid nematodes) and trematodes. A total of 800 gastropods were collected from 16 sites over a 225 km[2] area. The extracted nematodes and trematodes were identified by molecular barcoding. Of the 800 gastropods collected, 227 were infected (172 had nematode infections, 37 had trematode infections and 18 had both nematode and trematode infections). Of the nematode infected gastropods genotyped, seven species were identified, Agfa flexilis, Angiostoma gandavense, Angiostoma margaretae, Cosmocerca longicauda, Phasmarhabditis hermaphrodita, Phasmarhabditis neopapillosa and an unknown Cosmocercidae species. Of the trematode infected gastropods genotyped, four species were identified, Brachylaima arcuate, Brachylaima fuscata, Brachylaima mesostoma and an unknown Plagiorchioidea species. No lungworm species were found within the city of Nottingham. To our knowledge, this study represents the first survey of gastropod-associated nematodes and trematodes in the East midlands of the United Kingdom.},
}
@article {pmid36320930,
year = {2022},
author = {Liew, YJM and Chua, KO and Yong, HS and Song, SL and Chan, KG},
title = {Complete chloroplast genome of Boesenbergia rotunda and a comparative analysis with members of the family Zingiberaceae.},
journal = {Revista brasileira de botanica : Brazilian journal of botany},
volume = {45},
number = {4},
pages = {1209-1222},
pmid = {36320930},
issn = {0100-8404},
abstract = {UNLABELLED: Boesenbergia rotunda (L.) Mansf. is a medically important ginger species of the family Zingiberaceae but its genomic information on molecular phylogeny and identification is scarce. In this work, the chloroplast genome of B. rotunda was sequenced, characterized and compared to the other Zingiberaceae species to provide chloroplast genetic resources and to determine its phylogenetic position in the family. The chloroplast genome of B. rotunda was 163,817 bp in length and consisted of a large single-copy (LSC) region of 88,302 bp, a small single-copy (SSC) region of 16,023 bp and a pair of inverted repeats (IRA and IRB) of 29,746 bp each. The chloroplast genome contained 113 unique genes, including 79 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. Several genes had atypical start codons, while most amino acids exhibited biased usage of synonymous codons. Comparative analyses with various chloroplast genomes of Zingiberaceae taxa revealed several highly variable regions (psbK-psbI, trnT-GGU-psbD, rbcL-accD, ndhF-rpl32, and ycf1) in the LSC and SSC regions in the chloroplast genome of B. rotunda that could be utilized as molecular markers for DNA barcoding and species delimitation. Phylogenetic analyses based on shared protein-coding genes revealed that B. rotunda formed a distinct lineage with B. kingii Mood &amp; L.M.Prince, in a subclade that also contained the genera Kaempferia and Zingiber. These findings constitute the first chloroplast genome information of B. rotunda that could be a reference for phylogenetic analysis and identification of genus Boesenbergia within the Zingiberaceae family.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s40415-022-00845-w.},
}
@article {pmid36320474,
year = {2022},
author = {Chines, S and Ehrt, C and Potowski, M and Biesenkamp, F and Grützbach, L and Brunner, S and van den Broek, F and Bali, S and Ickstadt, K and Brunschweiger, A},
title = {Navigating chemical reaction space - application to DNA-encoded chemistry.},
journal = {Chemical science},
volume = {13},
number = {37},
pages = {11221-11231},
pmid = {36320474},
issn = {2041-6520},
abstract = {Databases contain millions of reactions for compound synthesis, rendering selection of reactions for forward synthetic design of small molecule screening libraries, such as DNA-encoded libraries (DELs), a big data challenge. To support reaction space navigation, we developed the computational workflow Reaction Navigator. Reaction files from a large chemistry database were processed using the open-source KNIME Analytics Platform. Initial processing steps included a customizable filtering cascade that removed reactions with a high probability to be incompatible with DEL, as they would e.g. damage the genetic barcode, to arrive at a comprehensive list of transformations for DEL design with applicability potential. These reactions were displayed and clustered by user-defined molecular reaction descriptors which are independent of reaction core substitution patterns. Thanks to clustering, these can be searched manually to identify reactions for DEL synthesis according to desired reaction criteria, such as ring formation or sp[3] content. The workflow was initially applied for mapping chemical reaction space for aromatic aldehydes as an exemplary functional group often used in DEL synthesis. Exemplary reactions have been successfully translated to DNA-tagged substrates and can be applied to library synthesis. The versatility of the Reaction Navigator was then shown by mapping reaction space for different reaction conditions, for amines as a second set of starting materials, and for data from a second database.},
}
@article {pmid36316689,
year = {2022},
author = {Manvell, C and Berman, H and Callahan, B and Breitschwerdt, E and Swain, W and Ferris, K and Maggi, R and Lashnits, E},
title = {Identification of microbial taxa present in Ctenocephalides felis (cat flea) reveals widespread co-infection and associations with vector phylogeny.},
journal = {Parasites &amp; vectors},
volume = {15},
number = {1},
pages = {398},
pmid = {36316689},
issn = {1756-3305},
support = {T32 GM133366/GM/NIGMS NIH HHS/United States ; T32 OD011130/OD/NIH HHS/United States ; 1T32GM133366/NH/NIH HHS/United States ; T32OD011130/NH/NIH HHS/United States ; },
mesh = {Chlamydia ; *Bartonella/genetics ; *Rickettsia/genetics ; Cats ; *Ctenocephalides/microbiology ; Animals ; Flea Infestations/epidemiology/veterinary ; Phylogeny ; Cat Diseases/parasitology ; *Coinfection ; },
abstract = {BACKGROUND: Ctenocephalides felis, the cat flea, is the most common ectoparasite of cats and dogs worldwide. As a cause of flea allergy dermatitis and a vector for two genera of zoonotic pathogens (Bartonella and Rickettsia spp.), the effect of the C. felis microbiome on pathogen transmission and vector survival is of substantial medical importance to both human and veterinary medicine. The aim of this study was to assay the pathogenic and commensal eubacterial microbial communities of individual C. felis from multiple geographic locations and analyze these findings by location, qPCR pathogen prevalence, and flea genetic diversity.<br><br>METHODS: 16S Next Generation Sequencing (NGS) was utilized to sequence the microbiome of fleas collected from free-roaming cats, and the cox1 gene was used for flea phylogenetic analysis. NGS data were analyzed for 168 individual fleas from seven locations within the US and UK. Given inconsistency in the genera historically reported to constitute the C. felis microbiome, we utilized the decontam prevalence method followed by literature review to separate contaminants from true microbiome members.<br><br>RESULTS: NGS identified a single dominant and cosmopolitan amplicon sequence variant (ASV) from Rickettsia and Wolbachia while identifying one dominant Bartonella clarridgeiae and one dominant Bartonella henselae/Bartonella koehlerae ASV. Multiple less common ASVs from these genera were detected within restricted geographical ranges. Co-detection of two or more genera (Bartonella, Rickettsia, and/or Wolbachia) or multiple ASVs from a single genus in a single flea was common. Achromobacter, Peptoniphilus, and Rhodococcus were identified as additional candidate members of the C. felis microbiome on the basis of decontam analysis and literature review. Ctenocephalides felis phylogenetic diversity as assessed by the cox1 gene fell within currently characterized clades while identifying seven novel haplotypes. NGS sensitivity and specificity for Bartonella and Rickettsia spp. DNA detection were compared to targeted qPCR.<br><br>CONCLUSIONS: Our findings confirm the widespread coinfection of fleas with multiple bacterial genera and strains, proposing three additional microbiome members. The presence of minor Bartonella, Rickettsia, and Wolbachia ASVs was found to vary by location and flea haplotype. These findings have important implications for flea-borne pathogen transmission and control.},
}
@article {pmid36316484,
year = {2023},
author = {Meers, MP and Llagas, G and Janssens, DH and Codomo, CA and Henikoff, S},
title = {Multifactorial profiling of epigenetic landscapes at single-cell resolution using MulTI-Tag.},
journal = {Nature biotechnology},
volume = {41},
number = {5},
pages = {708-716},
pmid = {36316484},
issn = {1546-1696},
support = {F32 GM129954/GM/NIGMS NIH HHS/United States ; K99 GM140251/GM/NIGMS NIH HHS/United States ; R01 HG010492/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {*Histones/genetics/metabolism ; *Chromatin/genetics ; Gene Expression Regulation ; Protein Processing, Post-Translational ; Epigenesis, Genetic/genetics ; },
abstract = {Chromatin profiling at locus resolution uncovers gene regulatory features that define cell types and developmental trajectories, but it remains challenging to map and compare different chromatin-associated proteins in the same sample. Here we describe Multiple Target Identification by Tagmentation (MulTI-Tag), an antibody barcoding approach for profiling multiple chromatin features simultaneously in single cells. We optimized MulTI-Tag to retain high sensitivity and specificity, and we demonstrate detection of up to three histone modifications in the same cell: H3K27me3, H3K4me1/2 and H3K36me3. We apply MulTI-Tag to resolve distinct cell types and developmental trajectories; to distinguish unique, coordinated patterns of active and repressive element regulatory usage associated with differentiation outcomes; and to uncover associations between histone marks. Multifactorial epigenetic profiling holds promise for comprehensively characterizing cell-specific gene regulatory landscapes in development and disease.},
}
@article {pmid36313802,
year = {2022},
author = {Barber, KW and Shrock, E and Elledge, SJ},
title = {CasPlay provides a gRNA-barcoded CRISPR-based display platform for antibody repertoire profiling.},
journal = {Cell reports methods},
volume = {2},
number = {10},
pages = {100318},
pmid = {36313802},
issn = {2667-2375},
mesh = {Humans ; *COVID-19 ; SARS-CoV-2/genetics ; Peptide Library ; Antibodies ; Epitopes/chemistry ; },
abstract = {Protein display technologies link proteins to distinct nucleic acid sequences (barcodes), enabling multiplexed protein assays via DNA sequencing. Here, we develop Cas9 display (CasPlay) to interrogate customized peptide libraries fused to catalytically inactive Cas9 (dCas9) by sequencing the guide RNA (gRNA) barcodes associated with each peptide. We first confirm the ability of CasPlay to characterize antibody epitopes by recovering a known binding motif for a monoclonal anti-FLAG antibody. We then use a CasPlay library tiling the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteome to evaluate vaccine-induced antibody reactivities. Using a peptide library representing the human virome, we demonstrate the ability of CasPlay to identify epitopes across many viruses from microliters of patient serum. Our results suggest that CasPlay is a viable strategy for customized protein interaction studies from highly complex libraries and could provide an alternative to phage display technologies.},
}
@article {pmid36312748,
year = {2022},
author = {Pratomo, A and Bengen, DG and Zamani, NP and Lane, C and Humphries, AT and Borbee, E and Subhan, B and Madduppa, H},
title = {Diversity and distribution of Symbiodiniaceae detected on coral reefs of Lombok, Indonesia using environmental DNA metabarcoding.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e14006},
pmid = {36312748},
issn = {2167-8359},
mesh = {Animals ; Coral Reefs ; Ecosystem ; *DNA, Environmental ; Phylogeny ; Indonesia ; Bayes Theorem ; DNA Barcoding, Taxonomic ; *Anthozoa/genetics ; *Dinoflagellida ; },
abstract = {BACKGROUND: Dinoflagellates of family Symbiodiniaceae are important to coral reef ecosystems because of their contribution to coral health and growth; however, only a few studies have investigated the function and distribution of Symbiodiniaceae in Indonesia. Understanding the distribution of different kinds of Symbiodiniaceae can improve forecasting of future responses of various coral reef systems to climate change. This study aimed to determine the diversity of Symbiodiniaceae around Lombok using environmental DNA (eDNA).<br><br>METHODS: Seawater and sediment samples were collected from 18 locations and filtered to obtain fractions of 0.4-12 and >12 &#xb5;m. After extraction, molecular barcoding polymerase chain reaction was conducted to amplify the primary V9-SSU 18S rRNA gene, followed by sequencing (Illumina MiSeq). BLAST, Na&#xef;ve-fit-Bayes, and maximum likelihood routines were used for classification and phylogenetic reconstruction. We compared results across sampling sites, sample types (seawater/sediment), and filter pore sizes (fraction).<br><br>RESULTS: Phylogenetic analyses resolved the amplicon sequence variants into 16 subclades comprising six Symbiodiniaceae genera (or genera-equivalent clades) as follows: Symbiodinium, Breviolum, Cladocopium, Durusdinium, Foraminifera Clade G, and Halluxium. Comparative analyses showed that the three distinct lineages within Cladocopium, Durusdinium, and Foraminifera Clade G were the most common. Most of the recovered sequences appeared to be distinctive of different sampling locations, supporting the possibility that eDNA may resolve regional and local differences among Symbiodiniaceae genera and species.<br><br>CONCLUSIONS: eDNA surveys offer a rapid proxy for evaluating Symbiodiniaceae species on coral reefs and are a potentially useful approach to revealing diversity and relative ecological dominance of certain Symbiodiniaceae organisms. Moreover, Symbiodiniaceae eDNA analysis shows potential in monitoring the local and regional stability of coral-algal mutualisms.},
}
@article {pmid36311137,
year = {2022},
author = {Edy, N and Barus, HN and Finkeldey, R and Polle, A},
title = {Host plant richness and environment in tropical forest transformation systems shape arbuscular mycorrhizal fungal richness.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {1004097},
pmid = {36311137},
issn = {1664-462X},
abstract = {Transformation of tropical lowland rain forests into rubber tree and oil palm plantations is the cause of massive loss of vegetation diversity. The consequences for associated mycorrhizal fungi are not fully understood. We hypothesized that generalist arbuscular mycorrhizal fungi are resistant to removal of host species richness and that forest conversion to oil palm and rubber leads to loss of arbuscular mycorrhizal fungal (AMF) species with host preferences. Plant identities and AMF species were determined by molecular barcoding of 112 roots collected in three land-use systems (rain forest, rubber tree and oil palm plantation) in two landscapes on Sumatra (Indonesia), a world hotspot of forest transformation. The collected roots were from 43 forest plant species, in addition to rubber trees and oil palms. We detected 28 AMF species of which about 75% were present in forest trees and 25% shared among the land use systems. Only one AMF species present in plantation roots was not detected in the analyzed forest roots. Host specificity of arbuscular mycorrhizal fungi was not detected. Oil palm and rubber tree roots exhibited a strong reduction in AMF richness compared with roots from rainforests and were differentiated by soil resources. On basis of an individual root, oil palm had a lower AMF species richness than forest or rubber tree roots. Our results demonstrate that tropical AMF communities are shaped by two mechanisms: (i) root habitat diversity as the result of plant diversity and (ii) habitat properties as the result of plant traits or environmental conditions and management. Collectively, deterioration of habitat diversity and properties exacerbates impoverishment of AMF assemblages.},
}
@article {pmid36309106,
year = {2023},
author = {Williams, KA and Snyman, LP},
title = {In support of morphology: Molecular analysis successfully delineates the Afrotropical genus Atylotus (Diptera: Tabanidae) into species.},
journal = {Acta tropica},
volume = {237},
number = {},
pages = {106725},
doi = {10.1016/j.actatropica.2022.106725},
pmid = {36309106},
issn = {1873-6254},
mesh = {Animals ; *Diptera/genetics ; DNA Barcoding, Taxonomic/methods ; Electron Transport Complex IV/genetics ; Phylogeny ; },
abstract = {Previous studies of the horse fly genus Atylotus in the Afrotropics has shown little to no differentiation into species based on the barcoding region of cytochrome oxidase I (COI), largely due to morphological misidentifications. Using field caught specimens and a museum reference collection together with type comparisons, COI and 16S ribosomal RNA sequences were generated from two specimens of Atylotus agrestis, two A. albipalpus, four A fuscipes and one A. nigromaculatus. Phylogenetic analysis of these sequences produced four separate species clades with strong support. The results showed that COI does delineate the species of Afrotropical Atylotus and that misidentifications of specimens is a common problem. Additionally, Atylotus fuscipes is revived from synonymy and given full species status. Finally, a comprehensive review of the COI barcodes, publicly available on GenBank and BOLD is included that highlights some problems with using sequences from public databases.},
}
@article {pmid36308581,
year = {2023},
author = {Antil, S and Abraham, JS and Sripoorna, S and Maurya, S and Dagar, J and Makhija, S and Bhagat, P and Gupta, R and Sood, U and Lal, R and Toteja, R},
title = {DNA barcoding, an effective tool for species identification: a review.},
journal = {Molecular biology reports},
volume = {50},
number = {1},
pages = {761-775},
pmid = {36308581},
issn = {1573-4978},
mesh = {*DNA Barcoding, Taxonomic/methods ; RNA, Ribosomal, 16S/genetics ; *DNA ; Plants/genetics ; Archaea/genetics ; },
abstract = {DNA barcoding is a powerful taxonomic tool to identify and discover species. DNA barcoding utilizes one or more standardized short DNA regions for taxon identification. With the emergence of new sequencing techniques, such as Next-generation sequencing (NGS), ONT MinION nanopore sequencing, and Pac Bio sequencing, DNA barcoding has become more accurate, fast, and reliable. Rapid species identification by DNA barcodes has been used in a variety of fields, including forensic science, control of the food supply chain, and disease understanding. The Consortium for Barcode of Life (CBOL) presents various working groups to identify the universal barcode gene, such as COI in metazoans; rbcL, matK, and ITS in plants; ITS in fungi; 16S rRNA gene in bacteria and archaea, and creating a reference DNA barcode library. In this article, an attempt has been made to analyze the various proposed DNA barcode for different organisms, strengths &amp; limitations, recent advancements in DNA barcoding, and methods to speed up the DNA barcode reference library construction. This study concludes that constructing a reference library with high species coverage would be a major step toward identifying species by DNA barcodes. This can be achieved in a short period of time by using advanced sequencing and data analysis methods.},
}
@article {pmid36307549,
year = {2022},
author = {Jiang, MZ and Zhu, HZ and Zhou, N and Liu, C and Jiang, CY and Wang, Y and Liu, SJ},
title = {Droplet microfluidics-based high-throughput bacterial cultivation for validation of taxon pairs in microbial co-occurrence networks.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {18145},
pmid = {36307549},
issn = {2045-2322},
support = {31861133002//NSFC-EU Environmental Biotechnology joint program/ ; 2019YFA0905500//National Key Research and Development Program of China/ ; },
mesh = {*Microfluidics/methods ; Microbial Consortia/genetics ; Bacteria/genetics ; *Microbiota/genetics ; Microbial Interactions ; },
abstract = {Co-occurrence networks inferred from the abundance data of microbial communities are widely applied to predict microbial interactions. However, the high workloads of bacterial isolation and the complexity of the networks themselves constrained experimental demonstrations of the predicted microbial associations and interactions. Here, we integrate droplet microfluidics and bar-coding logistics for high-throughput bacterial isolation and cultivation from environmental samples, and experimentally investigate the relationships between taxon pairs inferred from microbial co-occurrence networks. We collected Potamogeton perfoliatus plants (including roots) and associated sediments from Beijing Olympic Park wetland. Droplets of series diluted homogenates of wetland samples were inoculated into 126 96-well plates containing R2A and TSB media. After 10 days of cultivation, 65 plates with > 30% wells showed microbial growth were selected for the inference of microbial co-occurrence networks. We cultivated 129 bacterial isolates belonging to 15 species that could represent the zero-level OTUs (Zotus) in the inferred co-occurrence networks. The co-cultivations of bacterial isolates corresponding to the prevalent Zotus pairs in networks were performed on agar plates and in broth. Results suggested that positively associated Zotu pairs in the co-occurrence network implied complicated relations including neutralism, competition, and mutualism, depending on bacterial isolate combination and cultivation time.},
}
@article {pmid36306355,
year = {2022},
author = {Fernandes, LP and Enriquez-Gasca, R and Gould, PA and Holt, JH and Conde, L and Ecco, G and Herrero, J and Gifford, R and Trono, D and Kassiotis, G and Rowe, HM},
title = {A satellite DNA array barcodes chromosome 7 and regulates totipotency via ZFP819.},
journal = {Science advances},
volume = {8},
number = {43},
pages = {eabp8085},
pmid = {36306355},
issn = {2375-2548},
support = {/WT_/Wellcome Trust/United Kingdom ; FC001099/ARC_/Arthritis Research UK/United Kingdom ; MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; Mice ; *DNA, Satellite/genetics ; Mammals/genetics ; Oligonucleotide Array Sequence Analysis ; *Repressor Proteins/metabolism ; Transcription Factors/genetics ; Chromosomes ; },
abstract = {Mammalian genomes are a battleground for genetic conflict between repetitive elements and KRAB-zinc finger proteins (KZFPs). We asked whether KZFPs can regulate cell fate by using ZFP819, which targets a satellite DNA array, ZP3AR. ZP3AR coats megabase regions of chromosome 7 encompassing genes encoding ZSCAN4, a master transcription factor of totipotency. Depleting ZFP819 in mouse embryonic stem cells (mESCs) causes them to transition to a 2-cell (2C)-like state, whereby the ZP3AR array switches from a poised to an active enhancer state. This is accompanied by a global erosion of heterochromatin roadblocks, which we link to decreased SETDB1 stability. These events result in transcription of active LINE-1 elements and impaired differentiation. In summary, ZFP819 and TRIM28 partner up to close chromatin across Zscan4, to promote exit from totipotency. We propose that satellite DNAs may control developmental fate transitions by barcoding and switching off master transcription factor genes.},
}
@article {pmid36306340,
year = {2022},
author = {Lee, KS and Seo, J and Lee, CK and Shin, S and Choi, Z and Min, S and Yang, JH and Kwon, WS and Yun, W and Park, MR and Choi, JR and Chung, HC and Lee, ST and Rha, SY},
title = {Analytical and Clinical Validation of Cell-Free Circulating Tumor DNA Assay for the Estimation of Tumor Mutational Burden.},
journal = {Clinical chemistry},
volume = {68},
number = {12},
pages = {1519-1528},
doi = {10.1093/clinchem/hvac146},
pmid = {36306340},
issn = {1530-8561},
mesh = {Humans ; *Circulating Tumor DNA/genetics ; Biomarkers, Tumor/genetics ; Liquid Biopsy ; Mutation ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Ultra-deep sequencing to detect low-frequency mutations in circulating tumor-derived DNA (ctDNA) increases the diagnostic value of liquid biopsy. The demand for large ctDNA panels for comprehensive genomic profiling and tumor mutational burden (TMB) estimation is increasing; however, few ctDNA panels for TMB have been validated. Here, we designed a ctDNA panel with 531 genes, named TMB500, along with a technical and clinical validation.<br><br>METHODS: Synthetic reference cell-free DNA materials with predefined allele frequencies were sequenced in a total of 92 tests in 6 batches to evaluate the precision, linearity, and limit of detection of the assay. We used clinical samples from 50 patients with various cancers, 11 healthy individuals, and paired tissue samples. Molecular barcoding and data analysis were performed using customized pipelines.<br><br>RESULTS: The assay showed high precision and linearity (coefficient of determination, r2 =0.87) for all single nucleotide variants, with a limit of detection of 0.24%. In clinical samples, the TMB500 ctDNA assay detected most variants present and absent in tissues, showing that ctDNA could assess tumor heterogeneity in different tissues and metastasis sites. The estimated TMBs correlated well between tissue and blood, except in 4 cases with extreme heterogeneity that showed very high blood TMBs compared to tissue TMBs. A pilot evaluation showed that the TMB500 assay could be used for disease monitoring.<br><br>CONCLUSIONS: The TMB500 assay is an accurate and reliable ctDNA assay for many clinical purposes. It may be useful for guiding the treatment of cancers with diverse genomic profiles, estimating TMB in immune therapy, and disease monitoring.},
}
@article {pmid36305615,
year = {2022},
author = {Juhász, A and Barlow, SEJ and Williams, H and Johnson, B and Walsh, ND and Cunningham, LC and Jones, S and LaCourse, EJ and Stothard, JR},
title = {A report of Bilharziella polonica cercariae in Knowsley Safari, Prescot, United Kingdom, with notes on other trematodes implicated in human cercarial dermatitis.},
journal = {Journal of helminthology},
volume = {96},
number = {},
pages = {e79},
doi = {10.1017/S0022149X22000694},
pmid = {36305615},
issn = {1475-2697},
mesh = {Humans ; Animals ; *Schistosomatidae/genetics ; *Skin Diseases, Parasitic/epidemiology ; *Trematode Infections/epidemiology ; Cercaria/genetics ; *Schistosomiasis ; *Dermatitis/epidemiology ; },
abstract = {As part of surveillance of snail-borne trematodiasis in Knowsley Safari (KS), Prescot, United Kingdom, a collection was made in July 2021 of various planorbid (n = 173) and lymnaeid (n = 218) snails. These were taken from 15 purposely selected freshwater habitats. In the laboratory emergent trematode cercariae, often from single snails, were identified by morphology with a sub-set, of those most accessible, later characterized by cytochrome oxidase subunit 1 (cox1) DNA barcoding. Two schistosomatid cercariae were of special note in the context of human cercarial dermatitis (HCD), Bilharziella polonica emergent from Planorbarius corneus and Trichobilharzia spp. emergent from Ampullacaena balthica. The former schistosomatid was last reported in the United Kingdom over 50 years ago. From cox1 analyses, the latter likely consisted of two taxa, Trichobilharzia anseri, a first report in the United Kingdom, and a hitherto unnamed genetic lineage having some affiliation with Trichobilharzia longicauda. The chronobiology of emergent cercariae from P. corneus was assessed, with the vertical swimming rate of B. polonica measured. We provide a brief risk appraisal of HCD for public activities typically undertaken within KS educational and recreational programmes.},
}
@article {pmid36301451,
year = {2022},
author = {Woo, C and Bhuiyan, MIU and Kim, D and Kumari, P and Lee, SK and Park, JY and Dong, K and Lee, K and Yamamoto, N},
title = {DNA metabarcoding-based study on bacteria and fungi associated with house dust mites (Dermatophagoides spp.) in settled house dust.},
journal = {Experimental &amp; applied acarology},
volume = {88},
number = {3-4},
pages = {329-347},
pmid = {36301451},
issn = {1572-9702},
mesh = {Animals ; Humans ; *Pyroglyphidae ; *Dust ; DNA Barcoding, Taxonomic ; Ecosystem ; RNA, Ribosomal, 16S ; Bacteria/genetics ; },
abstract = {House dust mites (HDMs) including Dermatophagoides spp. are an important cause of respiratory allergies. However, their relationship with microorganisms in house dust has not been fully elucidated. Here, we characterized bacteria and fungi associated with HDMs in house dust samples collected in 107 homes in Korea by using DNA barcode sequencing of bacterial 16S rRNA gene, fungal internal transcribed spacer 2 (ITS2) region, and arthropod cytochrome c oxidase I (COI) gene. Our inter-kingdom co-occurrence network analysis and/or indicator species analysis identified that HDMs were positively related with a xerophilic fungus Wallemia, mycoparasitic fungi such as Cystobasidium, and some human skin-related bacterial and fungal genera, and they were negatively related with the hygrophilous fungus Cephalotrichum. Overall, our study has succeeded in adding novel insights into HDM-related bacteria and fungi in the house dust ecosystem, and in confirming the historically recognized fact that HDMs are associated with xerophilic fungi such as Wallemia. Understanding the microbial ecology in house dust is thought to be important for elucidating the etiology of human diseases including allergies, and our study revealed baseline information of house dust ecology in relation to HDMs. The findings could be useful from a perspective of human health.},
}
@article {pmid36299683,
year = {2022},
author = {Qarni, A and Muhammad, K and Wahab, A and Ali, A and Khizar, C and Ullah, I and Kazmi, A and Sultana, T and Hameed, A and Younas, M and Rahimi, M},
title = {Molecular Characterization of Wild and Cultivated Strawberry (Fragaria × ananassa) through DNA Barcode Markers.},
journal = {Genetics research},
volume = {2022},
number = {},
pages = {9249561},
pmid = {36299683},
issn = {1469-5073},
mesh = {*Fragaria/genetics ; Genome, Plant ; Phylogeny ; DNA Barcoding, Taxonomic ; Genetic Markers/genetics ; },
abstract = {BACKGROUND: DNA barcoding is a useful technique for the identification, conservation, and diversity estimation at the species level in plants. The current research work was carried out to characterize selected Fragaria species from northern Pakistan using DNA barcode markers. Methodology. Initially, the efficacy of eight DNA barcode markers was analyzed based on the amplification and sequencing of the genome of selected Fragaria species. The resultant sequences were analyzed using BLAST, MEGA 7.0, and Bio Edit software. The phylogenetic tree was constructed by using Fragaria current species sequences and reference sequences through the neighbor-joining method or maximum likelihood method.<br><br>RESULTS: Among eight DNA barcode markers, only two (ITS2 and rbclC) were amplified, and sequences were obtained. ITS2 sequence was BLAST in NCBI for related reference species which ranged from 89.79% to 90.05% along with Fragaria vesca (AF163517.1) which have 99.05% identity. Similarly, the rbclC sequence of Fragaria species was ranged from 96% to 99.58% along with Fragaria&#x2009;&#xd7;&#x2009;ananassa (KY358226.1) which had 99.58% identity.<br><br>CONCLUSION: It is recommended that DNA barcode markers are a useful tool to identify the genetic diversity of a species. Moreover, this study could be helpful for the identification of the Fragaria species cultivated in other regions of the world.},
}
@article {pmid36297261,
year = {2022},
author = {Bustamante, MI and Osorio-Navarro, C and Fernández, Y and Bourret, TB and Zamorano, A and Henríquez-Sáez, JL},
title = {First Record of Colletotrichum anthrisci Causing Anthracnose on Avocado Fruits in Chile.},
journal = {Pathogens (Basel, Switzerland)},
volume = {11},
number = {10},
pages = {},
pmid = {36297261},
issn = {2076-0817},
support = {Beca Escuela de Postgrado Facultad de Ciencias Agron&#xf3;micas//Universidad de Chile/ ; },
abstract = {Anthracnose caused by Colletotrichum species is one of the most frequent and damaging fungal diseases affecting avocado fruits (Persea americana Mill.) worldwide. In Chile, the disease incidence has increased over the last decades due to the establishment of commercial groves in more humid areas. Since 2018, unusual symptoms of anthracnose have been observed on Hass avocado fruits, with lesions developing a white to gray sporulation. Morphological features and multi-locus phylogenetic analyses using six DNA barcodes (act, chs-1, gapdh, his3, ITS, and tub2) allowed the identification of the causal agent as Colletotrichum anthrisci, a member of the dematium species complex. Pathogenicity was confirmed by inoculating healthy Hass avocado fruits with representative isolates, reproducing the same symptoms initially observed, and successfully reisolating the same isolates from the margin of the necrotic pulp. Previously, several Colletotrichum species belonging to other species complexes have been associated with avocado anthracnose in other countries. To our knowledge, this is the first record of C. anthrisci and of a species of the dematium species complex causing anthracnose on avocado fruits in Chile and worldwide.},
}
@article {pmid36296368,
year = {2022},
author = {McLennan, K and Ruvindy, R and Ostrowski, M and Murray, S},
title = {Correction: McLennan et al. Assessing the Use of Molecular Barcoding and qPCR for Investigating the Ecology of Prorocentrum minimum (Dinophyceae), a Harmful Algal Species. Microorganisms 2021, 9, 510.},
journal = {Microorganisms},
volume = {10},
number = {10},
pages = {},
pmid = {36296368},
issn = {2076-2607},
abstract = {The authors wish to make the following corrections to this paper [...].},
}
@article {pmid36292964,
year = {2022},
author = {Du, Q and Yang, H and Zeng, J and Chen, Z and Zhou, J and Sun, S and Wang, B and Liu, C},
title = {Comparative Genomics and Phylogenetic Analysis of the Chloroplast Genomes in Three Medicinal Salvia Species for Bioexploration.},
journal = {International journal of molecular sciences},
volume = {23},
number = {20},
pages = {},
pmid = {36292964},
issn = {1422-0067},
support = {2021-I2M-1-022//Chinese Academy of Medical Sciences &amp; Peking Union Medical College/ ; 2018FY100705//National Science &amp;Technology Fundamental Resources Investigation Program of China/ ; 81872966//National Science Foundation/ ; 2020-ZJ-Y20//Qinghai Provincial Key Laboratory of Phytochemistry of Qinghai Tibet Plateau/ ; 2018SK52001//Hunan technological innovation guidance project/ ; },
mesh = {*Genome, Chloroplast ; Phylogeny ; *Salvia/genetics ; Genomics/methods ; Microsatellite Repeats ; DNA, Intergenic/genetics ; },
abstract = {To systematically determine their phylogenetic relationships and develop molecular markers for species discrimination of Salvia bowleyana, S. splendens, and S. officinalis, we sequenced their chloroplast genomes using the Illumina Hiseq 2500 platform. The chloroplast genomes length of S. bowleyana, S. splendens, and S. officinalis were 151,387 bp, 150,604 bp, and 151,163 bp, respectively. The six genes ndhB, rpl2, rpl23, rps7, rps12, and ycf2 were present in the IR regions. The chloroplast genomes of S. bowleyana, S. splendens, and S. officinalis contain 29 tandem repeats; 35, 29, 24 simple-sequence repeats, and 47, 49, 40 interspersed repeats, respectively. The three specific intergenic sequences (IGS) of rps16-trnQ-UUG, trnL-UAA-trnF-GAA, and trnM-CAU-atpE were found to discriminate the 23 Salvia species. A total of 91 intergenic spacer sequences were identified through genetic distance analysis. The two specific IGS regions (trnG-GCC-trnM-CAU and ycf3-trnS-GGA) have the highest K2p value identified in the three studied Salvia species. Furthermore, the phylogenetic tree showed that the 23 Salvia species formed a monophyletic group. Two pairs of genus-specific DNA barcode primers were found. The results will provide a solid foundation to understand the phylogenetic classification of the three Salvia species. Moreover, the specific intergenic regions can provide the probability to discriminate the Salvia species between the phenotype and the distinction of gene fragments.},
}
@article {pmid36292851,
year = {2022},
author = {Adler, PH and Huang, S},
title = {Chromosomes as Barcodes: Discovery of a New Species of Black Fly (Diptera: Simuliidae) from California, USA.},
journal = {Insects},
volume = {13},
number = {10},
pages = {},
pmid = {36292851},
issn = {2075-4450},
support = {SC-1700596//National Institute of Food and Agriculture/ ; },
abstract = {One of the most popular tools for species discovery and resolution is the DNA barcode, typically based on the cytochrome c oxidase I (COI) gene. However, other non-genic barcodes are available for Diptera. The banding sequence of polytene chromosomes in some dipteran cells, particularly of the larval silk glands, can provide a unique species barcode. We used the sequence of bands to reveal a new species of black fly in the Simulium (Boreosimulium) annulus species group from California, USA. To further characterize the species and provide more integrated taxonomy, we morphologically described all life stages above the egg, formally named the species Simulium ustulatum n. sp., and provided a conventional COI barcode. The COI barcode confirmed the chromosomal and morphological evidence that the species is a new member of the S. annulus group, and enabled identification of the larva and female, which are structurally similar to those of other species. The chromosomal barcode shows that this species has the most rearranged complement, compared with the eight other North American members of its species group, with up to 12 times the number of fixed rearrangements. Up to six chromosomal rearrangements, including autosomal polymorphisms and sex-linked phenomena, are shared with other members of the group. The most unique and conspicuous chromosomal feature of this new species is a large, pale-staining chromocenter from which the six chromosomal arms radiate. The distribution of this univoltine species in lowland rivers of California's Central Valley could make it vulnerable, given climate change and increasing land development.},
}
@article {pmid36292824,
year = {2022},
author = {Vidović, B and Anđelković, N and Jojić, V and Cvrković, T and Petanović, R and Marini, F and Cristofaro, M and Rector, BG},
title = {A New Aculodes Species (Prostigmata: Eriophyidae) Described from an Invasive Weed by Morphological, Morphometric and DNA Barcode Analyses.},
journal = {Insects},
volume = {13},
number = {10},
pages = {},
pmid = {36292824},
issn = {2075-4450},
support = {451-03-68/2022-14/200116//Ministry of Education, Science and Technological Development of the Republic of Serbia/ ; L16PG00228//United States Department of the Interior/ ; 451-03-68/2022-14/200007//Ministry of Education, Science and Technological Development of the Republic of Serbia/ ; 451-03-68/2022-14/200010//Ministry of Education, Science and Technological Development of the Republic of Serbia/ ; },
abstract = {A new species of eriophyoid mite, Aculodes marcelli sp. nov., was discovered on cheatgrass, Anisantha tectorum (L.) Nevski (syn. Bromus tectorum L.), an annual grass that is native to Eurasia and Northern Africa. This grass was introduced to North America near the end of the 19th century and now is widespread and associated with the observed increases in the size, frequency, and intensity of wildfires in western N. America. In this paper, A. marcelli sp. nov., is morphologically described and illustrated. Compared with other Aculodes spp., it differs based on morphology and the sequence of the mitochondrial cytochrome oxidase gene, subunit I (MT-CO1). Results of morphometric analysis showed clear differentiation between A. marcelli sp. nov., and the most similar congener, A. altamurgiensis from Taeniatherum caput-medusae. Analysis of MT-CO1 sequence divergence revealed significant levels of genetic variation (17.7%) and supported the results from the morphometric analysis; therefore, it is determined that they are two different species. Aculodes marcelli sp. nov., is a new candidate agent for classical biological control of A. tectorum.},
}
@article {pmid36292711,
year = {2022},
author = {Yang, J and Ling, C and Zhang, H and Hussain, Q and Lyu, S and Zheng, G and Liu, Y},
title = {A Comparative Genomics Approach for Analysis of Complete Mitogenomes of Five Actinidiaceae Plants.},
journal = {Genes},
volume = {13},
number = {10},
pages = {},
pmid = {36292711},
issn = {2073-4425},
mesh = {*Actinidiaceae/genetics ; Phylogeny ; *Genome, Mitochondrial/genetics ; Genomics ; *Actinidia/genetics ; Ascorbic Acid ; RNA ; },
abstract = {Actinidiaceae, an economically important plant family, includes the Actinidia, Clematoclethra and Saurauia genus. Kiwifruit, with remarkably high vitamin C content, is an endemic species widely distributed in China with high economic value. Although many Actinidiaceae chloroplast genomes have been reported, few complete mitogenomes of Actinidiaceae have been studied. Here, complete circular mitogenomes of the four kiwifruit species and Saurauia tristyla were assembled. Codon usage, sequence repeats, RNA editing, gene transfers, selective pressure, and phylogenetic relationships in the four kiwifruit species and S. tristyla were comparatively analyzed. This research will contribute to the study of phylogenetic relationships within Actiniaceae and molecular barcoding in kiwifruit.},
}
@article {pmid36292690,
year = {2022},
author = {Sa, W and Qiao, J and Gao, Q and Li, Z and Shang, Q},
title = {DNA Barcoding and Species Classification of Morchella.},
journal = {Genes},
volume = {13},
number = {10},
pages = {},
pmid = {36292690},
issn = {2073-4425},
mesh = {Humans ; Phylogeny ; Genetic Markers/genetics ; DNA, Fungal/genetics ; *DNA Barcoding, Taxonomic ; *Ascomycota/genetics ; },
abstract = {True morels (Morchella) are a well-known edible fungi, with economically and medicinally important values. However, molecular identification and species taxonomy of the genus Morchella have long been controversial, due to numerous intermediate morphologies among species. In this study, we determined the identification efficiency of DNA barcoding and species classification of 260 individuals from 45 Morchella species, on the basis of multiple nuclear DNA markers. DNA barcoding analysis showed that the individual DNA fragment has a lower resolution of species identification than that of combined multiple DNA markers. ITS showed the highest level of species discrimination among the individual genetic markers. Interestingly, the combined DNA markers significantly increased the resolution of species identification. A combination of four DNA genes (EF1-α, RPB1, RPB2 and ITS) showed a higher species delimitation than that any combination of two or three markers. Phylogenetic analysis suggested that the species in genus Morchella could have been divided into two large genetic clades, the Elata Clade and Esculenta Clade lineages. The two lineages divided approximately 133.11 Mya [95% HPD interval: 82.77-197.95] in the early Cretaceous period. However, some phylogenetic species of Morchella showed inconsistent evolutionary relationships with the traditional morphological classifications, which may have resulted from incomplete lineage sorting and/or introgressive hybridization among species. These findings demonstrate that the interspecific gene introgression may have affected the species identification of true morels, and that the combined DNA markers significantly improve the resolution of species discrimination.},
}
@article {pmid36292670,
year = {2022},
author = {Player, R and Verratti, K and Staab, A and Forsyth, E and Ernlund, A and Joshi, MS and Dunning, R and Rozak, D and Grady, S and Goodwin, B and Sozhamannan, S},
title = {Optimization of Oxford Nanopore Technology Sequencing Workflow for Detection of Amplicons in Real Time Using ONT-DART Tool.},
journal = {Genes},
volume = {13},
number = {10},
pages = {},
pmid = {36292670},
issn = {2073-4425},
mesh = {*Nanopores ; Workflow ; High-Throughput Nucleotide Sequencing/methods ; Multiplex Polymerase Chain Reaction ; Technology ; },
abstract = {An optimized, well-tested and validated targeted genomic sequencing-based high-throughput assay is currently not available ready for routine biodefense and biosurveillance applications. Earlier, we addressed this gap by developing and establishing baseline comparisons of a multiplex end-point Polymerase Chain Reaction (PCR) assay followed by Oxford Nanopore Technology (ONT) based amplicon sequencing to real time PCR and customized data processing. Here, we expand upon this effort by identifying the optimal ONT library preparation method for integration into a novel software platform ONT-DART (ONT-Detection of Amplicons in Real-Time). ONT-DART is a dockerized, real-time, amplicon-sequence analysis workflow that is used to reproducibly process and filter read data to support actionable amplicon detection calls based on alignment metrics, within sample statistics, and no-template control data. This analysis pipeline was used to compare four ONT library preparation protocols using R9 and Flongle (FL) flow cells. The two 4-Primer methods tested required the shortest preparation times (5.5 and 6.5 h) for 48 libraries but provided lower fidelity data. The Native Barcoding and Ligation methods required longer preparation times of 8 and 12 h, respectively, and resulted in higher overall data quality. On average, data derived from R9 flow cells produced true positive calls for target organisms more than twice as fast as the lower throughput FL flow cells. These results suggest that utilizing the R9 flowcell with an ONT Native Barcoding amplicon library method in combination with ONT-DART platform analytics provides the best sequencing-based alternative to current PCR-based biodetection methods.},
}
@article {pmid36289449,
year = {2022},
author = {Rückert, T and Lareau, CA and Mashreghi, MF and Ludwig, LS and Romagnani, C},
title = {Clonal expansion and epigenetic inheritance of long-lasting NK cell memory.},
journal = {Nature immunology},
volume = {23},
number = {11},
pages = {1551-1563},
pmid = {36289449},
issn = {1529-2916},
support = {101055157/ERC_/European Research Council/International ; },
mesh = {Humans ; *Cytomegalovirus Infections/genetics ; Killer Cells, Natural ; Cytomegalovirus/genetics ; *Herpesviridae Infections ; Chromatin ; Epigenesis, Genetic ; },
abstract = {Clonal expansion of cells with somatically diversified receptors and their long-term maintenance as memory cells is a hallmark of adaptive immunity. Here, we studied pathogen-specific adaptation within the innate immune system, tracking natural killer (NK) cell memory to human cytomegalovirus (HCMV) infection. Leveraging single-cell multiomic maps of ex vivo NK cells and somatic mitochondrial DNA mutations as endogenous barcodes, we reveal substantial clonal expansion of adaptive NK cells in HCMV[+] individuals. NK cell clonotypes were characterized by a convergent inflammatory memory signature enriched for AP1 motifs superimposed on a private set of clone-specific accessible chromatin regions. NK cell clones were stably maintained in specific epigenetic states over time, revealing that clonal inheritance of chromatin accessibility shapes the epigenetic memory repertoire. Together, we identify clonal expansion and persistence within the human innate immune system, suggesting that these mechanisms have evolved independent of antigen-receptor diversification.},
}
@article {pmid36288285,
year = {2022},
author = {Deng, J and Ji, Y and Zhu, F and Liu, L and Li, L and Bai, X and Li, H and Liu, X and Luo, Y and Lin, B and Lu, Y},
title = {Mapping secretome-mediated interaction between paired neuron-macrophage single cells.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {44},
pages = {e2200944119},
pmid = {36288285},
issn = {1091-6490},
mesh = {Humans ; *Amyloid beta-Peptides/metabolism ; Secretome ; *Alzheimer Disease/metabolism ; Neurons/metabolism ; Microglia/metabolism ; Cytokines/metabolism ; Macrophages/metabolism ; Nerve Growth Factors/metabolism ; },
abstract = {Neuron-immune interaction through secreted factors contributes significantly to the complex microenvironment in the central nervous system that could alter cell functionalities and fates in both physiological and pathological conditions, which remains poorly characterized at the single-cell level. Herein, using a spatially patterned antibody barcode microchip, we realized the mapping of 12 different secretomes, covering cytokines, neurotrophic factors (NFs), and neuron-derived exosomes (NDEs) from high-throughput, paired single cells (≥ 600) simultaneously under normal conditions and an Alzheimer's disease (AD) model induced with amyloid beta protein 1-42 (Aβ1-42). We applied the platform to analyze the secretion profiles from paired neuron-macrophage and neuron-microglia single cells with human cell lines. We found that pairwise neuron-macrophage interaction would trigger immune responses and attenuate neuron cells' secretion, while neuron-microglia interaction generally results in opposite outcomes in secretion. When neuron cells are induced with Aβ1-42 protein into the AD model, both neuron-macrophage and neuron-microglia interactions lead to increased cytokines and NDEs and decreased NFs. Further analysis of AD patients' serum showed that NDEs were significantly higher in patients' samples than in the control group, validating our observation from the interaction assay. Furthermore, we resolved previously undifferentiated heterogeneity underlying the secretions from single-neuron cells. We found that the NDE and NF secretion was less dependent on the paracrine signaling between one another and that secretions from neuron cells would attenuate after differentiation with Aβ1-42. This study demonstrates the mapping of the different secretomes from paired neuron-immune single cells, providing avenues for understanding how neurons and immune cells interact through the complex secretome network.},
}
@article {pmid36287619,
year = {2023},
author = {Inaba, J and Shao, J and Trivellone, V and Zhao, Y and Dietrich, CH and Bottner-Parker, KD and Ivanauskas, A and Wei, W},
title = {Guilt by Association: DNA Barcoding-Based Identification of Potential Plant Hosts of Phytoplasmas from Their Insect Carriers.},
journal = {Phytopathology},
volume = {113},
number = {3},
pages = {413-422},
doi = {10.1094/PHYTO-09-22-0323-R},
pmid = {36287619},
issn = {0031-949X},
mesh = {Animals ; *Phytoplasma/genetics ; DNA Barcoding, Taxonomic ; Ecosystem ; Plant Diseases/microbiology ; Insecta ; *Hemiptera/microbiology ; Crops, Agricultural ; DNA ; },
abstract = {Phytoplasmas are small phloem-restricted and insect-transmissible bacteria that infect many plant species, including important crops and ornamental plants, causing severe economic losses. Our previous studies screened phytoplasmas in hundreds of leafhoppers collected from natural habitats worldwide and identified multiple genetically different phytoplasmas in seven leafhopper species (potential insect vectors). As an initial step toward determining the impact of these phytoplasmas on the ecosystem, ribulose 1,5-biphosphate carboxylase large subunit (rbcL), a commonly used plant DNA barcoding marker, was employed to identify the plant species that the phytoplasma-harboring leafhoppers feed on. The DNA of 17 individual leafhoppers was PCR amplified using universal rbcL primers. PCR products were cloned, and five clones per amplicon were randomly chosen for Sanger sequencing. Moreover, Illumina high-throughput sequencing on selected PCR products was conducted and confirmed no missing targets in Sanger sequencing. The nucleotide BLAST results revealed 14 plant species, including six well-known plant hosts of phytoplasmas such as tomato, alfalfa, and maize. The remaining species have not been documented as phytoplasma hosts, expanding our knowledge of potential plant hosts. Notably, the DNA of tomato and maize (apparently cultivated in well-managed croplands) was detected in some phytoplasma-harboring leafhopper species sampled in non-crop lands, suggesting the spillover/spillback risk of phytoplasma strains between crop and non-crop areas. Furthermore, our results indicate that barcoding (or metabarcoding) is a valuable tool to study the three-way interactions among phytoplasmas, plant hosts, and vectors. The findings contribute to a better understanding of phytoplasma host range, host shift, and disease epidemiology.},
}
@article {pmid36286606,
year = {2022},
author = {Zhang, Q and Kim, SW and Gorham, JM and DeLaughter, DM and Ward, T and Seidman, CE and Seidman, JG},
title = {Multiplexed Single-Nucleus RNA Sequencing Using Lipid-Oligo Barcodes.},
journal = {Current protocols},
volume = {2},
number = {10},
pages = {e579},
pmid = {36286606},
issn = {2691-1299},
support = {R01 HL080494/HL/NHLBI NIH HHS/United States ; R01 HL084553/HL/NHLBI NIH HHS/United States ; R01 HL151257/HL/NHLBI NIH HHS/United States ; },
mesh = {DNA, Complementary ; *Trypan Blue ; Sequence Analysis, RNA/methods ; *Sucrose ; Oligonucleotides ; Lipids/genetics ; },
abstract = {This protocol describes a robust pipeline for simultaneously analyzing multiple samples by single-nucleus (sn)RNA-seq. cDNA obtained from each single sample are labeled with the same lipid-coupled oligonucleotide barcode (10X Genomics). Nuclei from as many as 12 individual samples can be pooled together and simultaneously processed for cDNA library construction and subsequent DNA sequencing. While previous protocols using lipid-coupled oligonucleotide barcodes were optimized for analysis of samples consisting of viable cells, this protocol is optimized for analyses of quick-frozen cell samples. The protocol ensures efficient recovery of nuclei both by incorporating high sucrose buffered solutions and by including a tracking dye (trypan blue) during nuclei isolation. The protocol also describes a procedure for removing single nuclei 'artifacts' by removing cell debris prior to single nuclear fractionation. This protocol informs the use of computational tools for filtering poorly labeled nuclei and assigning sample identity using barcode unique molecular identifier (UMI) read counts percentages. The computational pipeline is applicable to either cultured or primary, fresh or frozen cells, regardless of their cell types and species. Overall, this protocol reduces batch effects and experimental costs while enhancing sample comparison. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Labeling cells with lipid oligo barcodes and generating multiplexed single-nucleus RNA-seq libraries Basic Protocol 2: Bioinformatic deconvolution of the multiplexed snRNAseq libraries.},
}
@article {pmid36283573,
year = {2023},
author = {Kvist, S and Earl, I and Kink, E and Oceguera-Figueroa, A and Trontelj, P},
title = {Phylogenetic relationships and species delimitation in Haemopis (Annelida: Hirudinea: Haemopidae).},
journal = {Molecular phylogenetics and evolution},
volume = {178},
number = {},
pages = {107648},
doi = {10.1016/j.ympev.2022.107648},
pmid = {36283573},
issn = {1095-9513},
mesh = {Animals ; *Leeches/genetics ; Phylogeny ; *Annelida ; DNA, Ribosomal/genetics ; Fresh Water ; },
abstract = {The Holarctic leech genus Haemopis currently includes 11 species, all of which are macrophagous, as opposed to their more infamous bloodfeeding counterparts among hirudiniform leeches. In spite of their ecological importance as fish food and predators of freshwater invertebrates, there is a paucity of data regarding morphology and genetic variation that might guide future identification efforts for members of the genus. The lack of detailed descriptions of distinguishing morphological features, coupled with the absence of a robust phylogenetic hypothesis for the genus, have conspired to prevent meaningful inferences on the natural history of the group. In an attempt to remedy this, we present new genetic (using COI, 12S rDNA, 28S rDNA and 18S rDNA) data for the majority of the known species diversity within the genus in order to both infer a phylogenetic hypothesis and to introduce authoritative DNA barcodes for the newly collected species. The potential of these barcodes is increased through rigorous morphological investigations of the specimens, with comparisons to the original literature. Our resulting phylogenetic hypothesis is agnostic as to the geographic origin of the genus, with equal probability afforded to both a Nearctic and Palearctic origin. Beyond this, we show that there is a strong tendency towards a barcoding gap within the genus, but that a distinct gap is lacking due to the relatively high genetic variation found within H. marmorata. Taken together, our results shed light on species delimitation within, and evolutionary history of, this often-neglected group of leeches.},
}
@article {pmid36281987,
year = {2022},
author = {García-Castro, H and Solana, J},
title = {Single-cell transcriptomics in planaria: new tools allow new insights into cellular and evolutionary features.},
journal = {Biochemical Society transactions},
volume = {50},
number = {5},
pages = {1237-1246},
pmid = {36281987},
issn = {1470-8752},
support = {BB/V014447/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/S007849/1/MRC_/Medical Research Council/United Kingdom ; MR/W017539/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; *Planarians/genetics/metabolism ; Transcriptome ; *Pluripotent Stem Cells ; Cell Differentiation ; RNA, Messenger/metabolism ; Regeneration/genetics ; },
abstract = {Single-cell transcriptomics has revolutionised biology allowing the quantification of gene expression in individual cells. Since each single cell contains cell type specific mRNAs, these techniques enable the classification of cell identities. Therefore, single cell methods have been used to explore the repertoire of cell types (the single cell atlas) of different organisms, including freshwater planarians. Nowadays, planarians are one of the most prominent animal models in single cell biology. They have been studied at the single cell level for over a decade using most of the available single cell methodological approaches. These include plate-based methods, such as qPCR, nanodroplet methods and in situ barcoding methods. Because of these studies, we now have a very good picture of planarian cell types and their differentiation trajectories. Planarian regenerative properties and other characteristics, such as their developmental plasticity and their capacity to reproduce asexually, ensure that another decade of single cell biology in planarians is yet to come. Here, we review these characteristics, the new biological insights that have been obtained by single-cell transcriptomics and outline the perspectives for the future.},
}
@article {pmid36279293,
year = {2022},
author = {Chavan, D and Adolacion, JRT and Crum, M and Nandy, S and Lee, KH and Vu, B and Kourentzi, K and Sabo, A and Willson, RC},
title = {Isolation and Barcoding of Trace Pollen-free DNA for Authentication of Honey.},
journal = {Journal of agricultural and food chemistry},
volume = {70},
number = {43},
pages = {14084-14095},
doi = {10.1021/acs.jafc.2c04309},
pmid = {36279293},
issn = {1520-5118},
mesh = {*Honey/analysis ; Pollen/genetics ; DNA Barcoding, Taxonomic ; DNA ; },
abstract = {Adulteration and mislabeling of honey to mask its true origin have become a global concern. Pollen microscopy, the current gold standard for identifying honey's geographical and plant origins, is laborious, requires extensive training, and fails to identify filtered honey and honey spiked with pollen from a more favorable plant to disguise its origins. We successfully isolated pollen-free DNA from filtered honey using three types of adsorbents: (i) anti-dsDNA antibodies coupled to magnetic microspheres; (ii) anion-exchange adsorbent; and (iii) ceramic hydroxyapatite. The internal transcribed spacer 2 region of the captured pollen-free DNA was polymerase chain reaction-amplified and subjected to next-generation sequencing. Using an in-house bioinformatics pipeline, initial experiments showed that anion exchange had the greatest capacity to capture trace pollen-free DNA, and it was successfully applied to isolate DNA from five honey samples. Enrichment of trace pollen-free DNA from filtered honey samples opens a new approach for identifying the true origins of honey.},
}
@article {pmid36278890,
year = {2022},
author = {Yin, X and Yang, H and Piao, Y and Zhu, Y and Zheng, Q and Khan, MR and Zhang, Y and Busquets, R and Hu, B and Deng, R and Cao, J},
title = {CRISPR-Based Colorimetric Nucleic Acid Tests for Visual Readout of DNA Barcode for Food Authenticity.},
journal = {Journal of agricultural and food chemistry},
volume = {70},
number = {43},
pages = {14052-14060},
doi = {10.1021/acs.jafc.2c05974},
pmid = {36278890},
issn = {1520-5118},
mesh = {Animals ; *Colorimetry/methods ; DNA Barcoding, Taxonomic ; *DNA, Catalytic ; DNA ; Takifugu ; },
abstract = {Food authenticity is a critical issue associated with the economy, religion, and food safety. Herein, we report a label-free and colorimetric nucleic acid assay for detecting DNA barcodes, enabling the determination of food authenticity with the naked eye. This method, termed the CRISPR-based colorimetric DNA barcoding (Cricba) assay, utilizes CRISPR/Cas12a (CRISPR = clustered regularly interspaced short palindromic repeats; Cas = CRISPR associated protein) to specifically recognize the polymerase chain reaction (PCR) products for further trans-cleavaging the peroxidase-mimicking G-quadruplex DNAzyme. Based on this principle, the presence of the cytochrome oxidase subunit I gene could be directly observed with the naked eye via the color change of 3,3',5,5'-tetramethylbenzidine sulfate (TMB). The whole detection process, including PCR amplification and TMB colorimetric analysis, can be completed within 90 min. The proposed assay can detect pufferfish concentrations diluted to 0.1% (w/w) in a raw pufferfish mixture, making it one of the most sensitive methods for food authenticity. The robustness of the assay was verified by testing four common species of pufferfish, including Lagocephalus inermis, Lagocephalus spadiceus, Takifugu bimaculatus, and Takifugu alboplumbeus. The assay is advantageous in easy signal readout, high sensitivity, and general applicability and thus could be a competitive candidate for food authenticity.},
}
@article {pmid36277610,
year = {2022},
author = {Guo, G and Zhao, Y and Liu, C and Fu, Y and Xi, X and Jin, L and Shi, D and Wang, L and Duan, Y and Huang, J and Tan, S and Yin, G},
title = {Method for persistent topological features extraction of schizophrenia patients' electroencephalography signal based on persistent homology.},
journal = {Frontiers in computational neuroscience},
volume = {16},
number = {},
pages = {1024205},
pmid = {36277610},
issn = {1662-5188},
abstract = {With the development of network science and graph theory, brain network research has unique advantages in explaining those mental diseases, the neural mechanism of which is unclear. Additionally, it can provide a new perspective in revealing the pathophysiological mechanism of brain diseases from the system level. The selection of threshold plays an important role in brain networks construction. There are no generally accepted criteria for determining the proper threshold. Therefore, based on the topological data analysis of persistent homology theory, this study developed a multi-scale brain network modeling analysis method, which enables us to quantify various persistent topological features at different scales in a coherent manner. In this method, the Vietoris-Rips filtering algorithm is used to extract dynamic persistent topological features by gradually increasing the threshold in the range of full-scale distances. Subsequently, the persistent topological features are visualized using barcodes and persistence diagrams. Finally, the stability of persistent topological features is analyzed by calculating the Bottleneck distances and Wasserstein distances between the persistence diagrams. Experimental results show that compared with the existing methods, this method can extract the topological features of brain networks more accurately and improves the accuracy of diagnostic and classification. This work not only lays a foundation for exploring the higher-order topology of brain functional networks in schizophrenia patients, but also enhances the modeling ability of complex brain systems to better understand, analyze, and predict their dynamic behaviors.},
}
@article {pmid36275810,
year = {2022},
author = {Hadj Abed, L and Tak, T and Cosgrove, J and Perié, L},
title = {CellDestiny: A RShiny application for the visualization and analysis of single-cell lineage tracing data.},
journal = {Frontiers in medicine},
volume = {9},
number = {},
pages = {919345},
pmid = {36275810},
issn = {2296-858X},
abstract = {Single-cell lineage tracing permits the labeling of individual cells with a heritable marker to follow the fate of each cell's progeny. Over the last twenty years, several single-cell lineage tracing methods have emerged, enabling major discoveries in developmental biology, oncology and gene therapies. Analytical tools are needed to draw meaningful conclusions from lineage tracing measurements, which are characterized by high variability, sparsity and technical noise. However, the single cell lineage tracing field lacks versatile and easy-to-use tools for standardized and reproducible analyses, in particular tools accessible to biologists. Here we present CellDestiny, a RShiny app and associated web application developed for experimentalists without coding skills to perform visualization and analysis of single cell lineage-tracing datasets through a graphical user interface. We demonstrate the functionality of CellDestiny through the analysis of (i) lentiviral barcoding datasets of murine hematopoietic progenitors; (ii) published integration site data from Wiskott-Aldrich Symdrome patients undergoing gene-therapy treatment; and (iii) simultaneous barcoding and transcriptomic analysis of murine hematopoietic progenitor differentiation in vitro. In summary, CellDestiny is an easy-to-use and versatile toolkit that enables biologists to visualize and analyze single-cell lineage tracing data.},
}
@article {pmid36275512,
year = {2022},
author = {Wang, X and Yoo, E and Lee, S and Cho, GT and Lee, GA and Yi, JY and Du, X and Han, S and Hyun, DY and Ro, N and Kim, KM},
title = {Classification of 17 species Aegilops using DNA barcoding and SNPs, reveals gene flow among Aegilops biuncialis, Aegilops juvenalis, and Aegilops columnaris.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {984825},
pmid = {36275512},
issn = {1664-462X},
abstract = {Rapid changes in agricultural environments caused by global warming pose a major challenge to food production and safety. Common wheat (Triticum aestivum) is a hexaploid plant (AABBDD) that shares large numbers of quantitative traits and resistance genes with B and D genomes of Aegilops species, which are responsible for several metabolic functions and biosynthetic processes, particularly in plant adaptation to biotic as well as abiotic stresses. Comparatively, the abundance of the Aegilops gene pool is much higher than that of Triticum. Therefore, we used four universal DNA barcodes for plants (ITS2, matK, rbcL, and psbM-petN) to construct a phylogenetic tree to classify the genus Aegilops. Fourteen species were distinguished among a total of 17 representative species. Aegilops biuncialis, Aegilops juvenalis, and Aegilops umbellulata could not be grouped into any of the clusters in the phylogenetic tree, indicating that these three species could not be distinguished by four DNA barcodes. Therefore, from 2408 SNPs obtained using genotyping by sequencing (GBS), we manually screened 30 SNPs that could be potentially used to classify these three species. The results of gene flow and genetic differentiation index (Fst) showed that the genetic differentiation among the three species was small, and there was bidirectional horizontal gene transfer between the three species, which was consistent with our results that the three species were difficult to classify by DNA barcode.},
}
@article {pmid36271787,
year = {2023},
author = {Li, Z and Linard, B and Vogler, AP and Yu, DW and Wang, Z},
title = {Phylogenetic diversity only weakly mitigates climate-change-driven biodiversity loss in insect communities.},
journal = {Molecular ecology},
volume = {32},
number = {23},
pages = {6147-6160},
doi = {10.1111/mec.16747},
pmid = {36271787},
issn = {1365-294X},
support = {31601849//National Natural Science Foundation of China/ ; //Animal Branch of the Germplasm Bank of Wild Species, Chinese Academy of Sciences/ ; QYZDY-SSW-SMC024//Key Research Program of Frontier Sciences, CAS/ ; GREKF19-01//State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology/ ; GREKF20-01//State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology/ ; GREKF21-01//State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology/ ; XDA20050202//Strategic Priority Research Program of Chinese Academy of Sciences/ ; //Department of Organismic and Evolutionary Biology/ ; //University of East Anglia/ ; },
mesh = {Animals ; Phylogeny ; Biodiversity ; Insecta ; Biological Evolution ; *Arthropods ; *Coleoptera/genetics ; },
abstract = {To help address the underrepresentation of arthropods and Asian biodiversity from climate-change assessments, we carried out year-long, weekly sampling campaigns with Malaise traps at different elevations and latitudes in Gaoligongshan National Park in southwestern China. From these 623 samples, we barcoded 10,524 beetles and compared scenarios of climate-change-induced biodiversity loss, by designating seasonal, elevational, and latitudinal subsets of beetles as communities that plausibly could go extinct as a group, which we call "loss sets". The availability of a published mitochondrial-genome-based phylogeny of the Coleoptera allowed us to compare the loss of species diversity with and without accounting for phylogenetic relatedness. We hypothesised that phylogenetic relatedness would mitigate extinction, since the extinction of any loss set would result in the disappearance of all its species but only part of its evolutionary history, which is still extant in the remaining loss sets. We found different patterns of community clustering by season and latitude, depending on whether phylogenetic information was incorporated. However, accounting for phylogeny only slightly mitigated the amount of biodiversity loss under climate change scenarios, against our expectations: there is no phylogenetic "escape clause" for biodiversity conservation. We achieve the same results whether phylogenetic information was derived from the mitogenome phylogeny or from a de novo barcode-gene tree. We encourage interested researchers to use this data set to study lineage-specific community assembly patterns in conjunction with life-history traits and environmental covariates.},
}
@article {pmid36271325,
year = {2022},
author = {Xu, L and Zhang, X and Guo, H and Yang, X and Xing, Z and Yang, W and Zhang, J and Tian, X},
title = {Species diversity analysis of commercial Mantidis Ootheca samples contaminated by store pests based on DNA metabarcoding.},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {720},
pmid = {36271325},
issn = {1471-2164},
mesh = {Animals ; DNA Barcoding, Taxonomic ; *Mantodea/genetics ; DNA ; *Coleoptera/genetics ; Quality Control ; },
abstract = {Mantidis Ootheca (Sangpiaoxiao, mantis egg case) is a typical multi-origin Chinese medicinal material. The Chinese Pharmacopoeia stipulates that the Mantidis Ootheca originates from three species of Mantis: Tenodera sinensis, Statilia maculate, and Hierodula patellifera. However, Mantidis Ootheca mainly relies on field collection, which leads to confusion of its actual origin in the market. As the clinical use of Mantidis Ootheca with unknown original mantis species will pose potential risks to drug safety, it is necessary to survey the commercially available Mantidis Ootheca origin species. However, as the egg case of Mantis, the morphological characters of Mantidis Ootheca are limited and usually cannot serve as accurate identification tool. DNA barcoding, which is widely used in taxonomic studies of animals, is severely affected by the impact of storage pests and DNA degradation. Thus, this study collected a total of 4580 Mantidis Ootheca and pooled separately Mantidis Ootheca samples according to 18 different sources as DNA samples to analyze the origin diversity of Mantidis Ootheca individuals contaminated by common store pests collected in in the market using DNA metabarcoding, and to provide a basis for quality control of Mantidis Ootheca. 37 Mantis ASVs and 9 Mantis MOTUs were identified through species delimitation, and the high-level intraspecific diversity was depicted as haplotype network plot. Besides Tenodera sinensis and Hierodula patellifera as genuine original mantis species defined in the Chinese Pharmacopoeia, Tenodera angustipennis was also the origin species of these Mantidis Ootheca samples.},
}
@article {pmid36266692,
year = {2022},
author = {Alkhatib, H and Rubinstein, AM and Vasudevan, S and Flashner-Abramson, E and Stefansky, S and Chowdhury, SR and Oguche, S and Peretz-Yablonsky, T and Granit, A and Granot, Z and Ben-Porath, I and Sheva, K and Feldman, J and Cohen, NE and Meirovitz, A and Kravchenko-Balasha, N},
title = {Computational quantification and characterization of independently evolving cellular subpopulations within tumors is critical to inhibit anti-cancer therapy resistance.},
journal = {Genome medicine},
volume = {14},
number = {1},
pages = {120},
pmid = {36266692},
issn = {1756-994X},
support = {U01 CA238720/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Triple Negative Breast Neoplasms/drug therapy/genetics/pathology ; Cell Line, Tumor ; Signal Transduction ; *Antineoplastic Agents/pharmacology/therapeutic use ; },
abstract = {BACKGROUND: Drug resistance continues to be a major limiting factor across diverse anti-cancer therapies. Contributing to the complexity of this challenge is cancer plasticity, in which one cancer subtype switches to another in response to treatment, for example, triple-negative breast cancer (TNBC) to Her2-positive breast cancer. For optimal treatment outcomes, accurate tumor diagnosis and subsequent therapeutic decisions are vital. This study assessed a novel approach to characterize treatment-induced evolutionary changes of distinct tumor cell subpopulations to identify and therapeutically exploit anticancer drug resistance.<br><br>METHODS: In this research, an information-theoretic single-cell quantification strategy was developed to provide a high-resolution and individualized assessment of tumor composition for a customized treatment approach. Briefly, this single-cell quantification strategy computes cell barcodes based on at least 100,000 tumor cells from each experiment and reveals a cell-specific signaling signature (CSSS) composed of a set of ongoing processes in each cell.<br><br>RESULTS: Using these CSSS-based barcodes, distinct subpopulations evolving within the tumor in response to an outside influence, like anticancer treatments, were revealed and mapped. Barcodes were further applied to assign targeted drug combinations to each individual tumor to optimize tumor response to therapy. The strategy was validated using TNBC models and patient-derived tumors known to switch phenotypes in response to radiotherapy (RT).<br><br>CONCLUSIONS: We show that a barcode-guided targeted drug cocktail significantly enhances tumor response to RT and prevents regrowth of once-resistant tumors. The strategy presented herein shows promise in preventing cancer treatment resistance, with significant applicability in clinical use.},
}
@article {pmid36266371,
year = {2022},
author = {Adhikari, L and Shrestha, S and Wu, S and Crain, J and Gao, L and Evers, B and Wilson, D and Ju, Y and Koo, DH and Hucl, P and Pozniak, C and Walkowiak, S and Wang, X and Wu, J and Glaubitz, JC and DeHaan, L and Friebe, B and Poland, J},
title = {A high-throughput skim-sequencing approach for genotyping, dosage estimation and identifying translocations.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {17583},
pmid = {36266371},
issn = {2045-2322},
mesh = {Genotype ; *Genome, Plant/genetics ; Genetic Markers ; Plant Breeding ; Polymorphism, Single Nucleotide ; Triticum/genetics ; *Hordeum/genetics ; High-Throughput Nucleotide Sequencing/methods ; Genotyping Techniques ; },
abstract = {The development of next-generation sequencing (NGS) enabled a shift from array-based genotyping to directly sequencing genomic libraries for high-throughput genotyping. Even though whole-genome sequencing was initially too costly for routine analysis in large populations such as breeding or genetic studies, continued advancements in genome sequencing and bioinformatics have provided the opportunity to capitalize on whole-genome information. As new sequencing platforms can routinely provide high-quality sequencing data for sufficient genome coverage to genotype various breeding populations, a limitation comes in the time and cost of library construction when multiplexing a large number of samples. Here we describe a high-throughput whole-genome skim-sequencing (skim-seq) approach that can be utilized for a broad range of genotyping and genomic characterization. Using optimized low-volume Illumina Nextera chemistry, we developed a skim-seq method and combined up to 960 samples in one multiplex library using dual index barcoding. With the dual-index barcoding, the number of samples for multiplexing can be adjusted depending on the amount of data required, and could be extended to 3,072 samples or more. Panels of doubled haploid wheat lines (Triticum aestivum, CDC Stanley x CDC Landmark), wheat-barley (T. aestivum x Hordeum vulgare) and wheat-wheatgrass (Triticum durum x Thinopyrum intermedium) introgression lines as well as known monosomic wheat stocks were genotyped using the skim-seq approach. Bioinformatics pipelines were developed for various applications where sequencing coverage ranged from 1 × down to 0.01 × per sample. Using reference genomes, we detected chromosome dosage, identified aneuploidy, and karyotyped introgression lines from the skim-seq data. Leveraging the recent advancements in genome sequencing, skim-seq provides an effective and low-cost tool for routine genotyping and genetic analysis, which can track and identify introgressions and genomic regions of interest in genetics research and applied breeding programs.},
}
@article {pmid36262409,
year = {2022},
author = {Tavakoli-Kolour, P and Farhadi, A and Ajdari, A and Bagheri, D and Hazraty-Kari, S and Ghasemi, A and Vazirzadeh, A},
title = {Genetic species identification and population structure of grouper Epinephelus coioides (Hamilton, 1822) collected from fish markets along the Persian Gulf and the Oman Sea.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e14179},
pmid = {36262409},
issn = {2167-8359},
mesh = {Humans ; Animals ; *Bass/genetics ; Indian Ocean ; Oman ; Iran ; Genetic Markers ; },
abstract = {Many ecologically important and valuable fisheries marine species have been misidentified in terms of both the statistical data and market demand. Correct identification at the species level and the population genetic structure of the orange-spotted grouper (Epinephelus coioides), a precious fish in the Persian Gulf and the Oman Sea, was tested using mitochondrial cytochrome oxidase subunit I (DNA barcoding) and D-loop sequencing. The results revealed that the Epinephelus species found in the region, including E. coioides, E. bleekeri, E. polylepis, and E. chlorostigma were all mistakenly grouped together and identified as only E. coioides. Moreover, the analysis of molecular variance (AMOVA) of E. coioides samples using the D-loop showed a significantly unique genetic structure (ΦST = 0.068, p < 0.001) within the E. coioides population throughout the Persian Gulf and the Oman Sea, with the pairwise genetic difference between sampling locations in UAE and the Iranian coast. Moreover, D-loop sequences analysis showed two distinct haplotype groups scattered among the sampling locations, which did not correlate with the geographic distance between the sampling locations. These findings indicate that the issue of misidentification should be highlighted in the management and conservation of E. coioides. As this type of misidentification is likely to happen to other threatened marine species as well, the efficacy of using genetic markers for the correct identification, both at the species and the population level, is vital.},
}
@article {pmid36261789,
year = {2022},
author = {Hubert, J and Navratilova, B and Sopko, B and Nesvorna, M and Phillips, TW},
title = {Pesticide residue exposure provides different responses of the microbiomes of distinct cultures of the stored product pest mite Acarus siro.},
journal = {BMC microbiology},
volume = {22},
number = {1},
pages = {252},
pmid = {36261789},
issn = {1471-2180},
mesh = {Humans ; Animals ; *Acaridae ; *Pesticide Residues ; *Mites ; *Microbiota ; Bacteroidetes ; },
abstract = {BACKGROUND: The contribution of the microbiome to pesticide breakdown in agricultural pests remains unclear. We analyzed the effect of pirimiphos-methyl (PM) on four geographically different cultures of the stored product pest mite Acarus siro (6 L, 6Tu, 6Tk and 6Z) under laboratory experiments. The effect of PM on mite mortality in the impregnated filter paper test was compared.<br><br>RESULTS: The mite sensitivity to PM decreased in the order of 6 L, 6Tu, 6Tk, and 6Z. Then, the mites were cultured on PM residues (0.0125 and 1.25&#xa0;&#xb5;g&#xb7;g[-1]), and population growth was compared to the control after 21&#xa0;days of exposure. The comparison showed two situations: (i) increasing population growth for the most sensitive cultures (6 L and 6Tu), and (ii) no effect on mite population growth for tolerant cultures (6Z and 6Tk). The microbiome of mites was analyzed by quantification of 16S DNA copies based on quantitative polymerase chain reaction (qPCR) and by barcode sequencing of the V4 fragment of 16S DNA on samples of 30 individuals from the control and PM residues. The microbiome comprised primarily Solitalea-like organisms in all cultures, except for 6Z, followed by Bacillus, Staphylococcus, and Lactobacillus. The microbiomes of mite cultures did not change with increasing population density. The microbiome of cultures without any differences in population density showed differences in the microbiome composition. A Sodalis-like symbiont replaced Solitalea in the 1.25&#xa0;&#xb5;g&#xb7;g[-1] PM in the 6Tk culture. Sodalis and Bacillus prevailed in the microbiomes of PM-treated mites of 6Z culture, while Solitalea was almost absent.<br><br>CONCLUSION: The results showed that the microbiome of A. siro differs in composition and in response to PM residues in the diet. The results indicate that Sodalis-like symbionts can help recover mites from pesticide-induced stress.},
}
@article {pmid36260182,
year = {2022},
author = {Li, Y and Zhang, L and Wang, T and Zhang, C and Wang, R and Zhang, D and Xie, Y and Zhou, N and Wang, W and Zhang, H and Hu, B and Li, W and Zhao, Q and Wang, L and Wu, X},
title = {The complete chloroplast genome sequences of three lilies: genome structure, comparative genomic and phylogenetic analyses.},
journal = {Journal of plant research},
volume = {135},
number = {6},
pages = {723-737},
pmid = {36260182},
issn = {1618-0860},
support = {202104BI090014//Yunnan Rural Revitalization science and technology project/ ; 202102AE090001//National Major Science and Technology Projects of China/ ; },
mesh = {*Genome, Chloroplast/genetics ; Phylogeny ; *Lilium/genetics ; Genomics ; Sequence Alignment ; },
abstract = {We sequenced and analyzed the complete chloroplast genomes of Lilium amoenum, Lilium souliei, and Nomocharis forrestii in detail, including the first sequence and structural comparison of Nomocharis forrestii. We found that the lengths and nucleotide composition of the three chloroplast genes showed little variation. The chloroplast genomes of the three Lilium species contain 87 protein coding genes (PCGs), 38 tRNAs, and 8 rRNA genes. The only difference is that Nomocharis forrestii had an additional infA pseudogene. In the sequence analysis of the Lilium chloroplast genomes, 216 SSRs, 143 pairs of long repeats, 571 SNPs, and 202 indels were detected. In addition, we identified seven hypervariable regions that can be used as potential molecular markers and DNA barcodes of Lilium through complete sequence alignment. The phylogenetic tree was constructed from the three chloroplast genome sequences of Lilium obtained here and 40 chloroplast genome sequences from the NCBI database (including 35 Lilium species, 4 Fritillaria species, and one species of Smilax). The analysis showed that the species clustering of the genus Lilium essentially conformed to the classical morphological classification system of Comber, but differences in the classification of individual species remained. In our report, we support the reclassification of Lilium henryi and Lilium rosthorniiy in the genus Lilium. In general, this study not only provides genome data for three Lilium species, but also provides a comparative analysis of the Lilium chloroplast genomes. These advances will help to identify Lilium species, clarify the phylogenetic analysis of the Lilium genus, and help to solve and improve the disputes and deficiencies in the traditional morphological classification.},
}
@article {pmid36254761,
year = {2022},
author = {Shen, X and Zhao, Y and Wang, Z and Shi, Q},
title = {Recent advances in high-throughput single-cell transcriptomics and spatial transcriptomics.},
journal = {Lab on a chip},
volume = {22},
number = {24},
pages = {4774-4791},
doi = {10.1039/d2lc00633b},
pmid = {36254761},
issn = {1473-0189},
mesh = {*Microfluidics ; },
abstract = {Single-cell RNA sequencing (scRNA-seq) has been developed for characterizing the transcriptome of cells that are rare but of biological significance. With cell barcoding and microchip technologies, a suite of high-throughput scRNA-seq protocols enable transcriptome profiling in thousands of individual cells at single-cell resolution for classifying cell types, discovering novel cell populations, investigating cellular heterogeneity and elucidating lineage trajectories. Microchip technologies including microfluidics- and microwell-based platforms play a major role in high-throughput scRNA-seq. As the emerging technology, spatial transcriptomics integrates cellular transcriptomics with their spatial coordinates within tissues for spatially deciphering cellular composition, heterogeneity and cell-cell communications. Spatial transcriptomics has been increasingly recognized as one of the most powerful tools for discovering new biology and advancing precision medicine. Microfluidics as an enabling technology plays an increasingly important role in spatial transcriptomics. We review the technological spectrum and advances in high-throughput scRNA-seq and spatial transcriptomics, discuss their advantages and limitations, and pitch into new biology learned from these new tools.},
}
@article {pmid36251250,
year = {2023},
author = {Guo, EL and Kream, E and Merlo, A and Friedman, PM},
title = {Liberating more than light: Laser removal of branding tattoos is impactful in the recovery of sex trafficking survivors.},
journal = {Lasers in surgery and medicine},
volume = {55},
number = {1},
pages = {61-66},
doi = {10.1002/lsm.23612},
pmid = {36251250},
issn = {1096-9101},
mesh = {Humans ; *Tattooing ; *Human Trafficking ; Sex Work ; Lasers ; Survivors ; *Laser Therapy ; },
abstract = {OBJECTIVES: Sex trafficking involves the use of force, fraud, or coercion to compel another person to engage in commercial sex acts. In 2020, 16,658 individuals were identified as sex trafficking victims in the United States, with thousands more not reported. Many victims are branded by their traffickers with tattoos conveying ownership, including names, symbols, and barcodes. We have partnered with local non-profits in Houston supporting sex trafficking survivors by providing pro bono laser tattoo removal, however we believe there is a greater need at a national level to support these survivors, allowing them to reclaim their bodies.<br><br>METHODS: An online survey aimed at assessing the need and potential impact for pro bono branding tattoo laser removal services was distributed to United States organizations that support sex trafficking survivors.<br><br>RESULTS: Forty organizations based in the Northeast (15%), Midwest (20%), South (45%), and West (20%) responded. Organizations support on average 81 survivors annually, ranging from 3 to 600 survivors, and estimate that 47% of survivors have branding tattoos. Among survivors with branding tattoos, approximately 67% were identified at an appropriate recovery stage to undergo laser removal. On a scale of 1-10 with 10 being the most impactful on recovery, removal of branding tattoos received an average impact score of 9.2. On a scale of 1-10, with 10 being the most need, pro bono services for laser removal received an average need score of 9.1. Qualitative responses provided several insights: laser removal may be associated with enhanced healing compared to tattoo cover-up, and survivors frequently move during their recovery process thus a successful removal campaign would require a nationwide network of partnering laser surgeons.<br><br>CONCLUSIONS: Approximately 1 in 2 sex trafficking survivors are estimated to have branding tattoos and the removal of these tattoos is recognized as highly impactful on recovery. We propose a philanthropic campaign which involves the American Society for Laser Medicine and Surgery (ASLMS) establishing a national directory to connect sex trafficking survivors seeking removal of branding tattoos with interested ASLMS board-certified physician members.},
}
@article {pmid36251214,
year = {2023},
author = {De Prins, J and Taylor, DBJ and Gonzalez, GF and Dobson, J and Hereward, JP and Shi, B and Rahman, MM and Dhileepan, K},
title = {Taxonomic Delineation of the Old World Species Stomphastis thraustica (Lepidoptera: Gracillariidae) Feeding on Jatropha gossypiifolia (Euphorbiaceae) that Was Collected in the New World and Imported as a Biocontrol Agent to Australia.},
journal = {Neotropical entomology},
volume = {52},
number = {3},
pages = {380-406},
pmid = {36251214},
issn = {1678-8052},
support = {ID 08302//Pontificia Universidad Javeriana/ ; },
mesh = {Animals ; *Lepidoptera ; *Jatropha ; *Euphorbiaceae ; *Moths ; Plants ; Australia ; },
abstract = {We provide the identification and species delineation of this biocontrol agent as Stomphastis thraustica (Meyrick in Trans Ent Soc Lond 80(1):107-120, 1908) belonging to the family Gracillariidae. We clarify the distribution pattern of S. thraustica, its host plant preferences, and present taxonomic and molecular diagnoses based on original morphological and genetic data as well as data retrieved from historic literature and genetic databases. Following our own collecting efforts in three continents Africa, South America, and Australia as well as our study of historic museum collection material, we present many new distribution records of S. thraustica for countries and territories in the world including the new discovery of this species in the Neotropical region and we report its introduction in Australia as a biocontrol agent. Using mitogenomic and COI gene data, we clarified that the closest relative of S. thraustica is Stomphastis sp. that occurs in Madagascar and Australia and feeds on the same host plant as S. thraustica - Jatropha gossypiifolia L. (Euphorbiaceae). The molecular sequence divergence in the mitochondrial DNA barcode fragment between these two closely related species S. thraustica and Stomphastis sp. is over 5.7% supporting that they are different species.},
}
@article {pmid36246949,
year = {2021},
author = {Ung, L and Belanger, NL and Chodosh, J and Gilmore, MS and Bispo, PJM},
title = {Novel Molecular Barcoding for Rapid Pathogen Detection in Infectious Keratitis.},
journal = {Ophthalmology science},
volume = {1},
number = {4},
pages = {100066},
pmid = {36246949},
issn = {2666-9145},
support = {R01 EY013124/EY/NEI NIH HHS/United States ; R01 EY021558/EY/NEI NIH HHS/United States ; R01 EY031600/EY/NEI NIH HHS/United States ; R21 EY032231/EY/NEI NIH HHS/United States ; },
}
@article {pmid36246585,
year = {2022},
author = {Li, J and Fan, R and Xu, J and Hu, L and Su, F and Hao, C},
title = {Comparative analysis of the chloroplast genomes of eight Piper species and insights into the utilization of structural variation in phylogenetic analysis.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {925252},
pmid = {36246585},
issn = {1664-8021},
abstract = {With more than 2000 species, Piper is regarded as having high medicinal, cosmetic, and edible value. There also remain some taxonomic and evolutionary uncertainties about the genus. This study performed chloroplast genome sequencing of eight poorly studied Piper species and a comparative analysis with black pepper (Piper nigrum). All examined species were highly similar in gene content, with 79 protein-coding genes, 24 tRNAs, and four rRNAs. They also harbored significant structural differences: The number of SSRs ranged from 63 to 87, over 10,000 SNPs were detected, and over 1,000 indels were found. The spatial distribution of structural differences was uneven, with the IR and LSC being relatively more conserved and the SSC region highly variable. Such structural variations of the chloroplast genome can help in evaluating the phylogenetic relationships between species, deciding some hard-to-distinguish evolutionary relationships, or eliminating improper markers. The SSC region may be evolving at high speed, and some species showed a high degree of sequence variation in the SSC region, which seriously affected marker sequence detection. Conversely, CDS sequences tended to lack variation, and some CDSs can serve as ideal markers for phylogenetic reconstruction. All told, this study provides an effective strategy for selecting chloroplast markers, analyzing difficult-to-distinguish phylogenetic relationships and avoiding the taxonomic errors caused by high degree of sequence variations.},
}
@article {pmid36240778,
year = {2022},
author = {Rovira-Clavé, X and Drainas, AP and Jiang, S and Bai, Y and Baron, M and Zhu, B and Dallas, AE and Lee, MC and Chu, TP and Holzem, A and Ayyagari, R and Bhattacharya, D and McCaffrey, EF and Greenwald, NF and Markovic, M and Coles, GL and Angelo, M and Bassik, MC and Sage, J and Nolan, GP},
title = {Spatial epitope barcoding reveals clonal tumor patch behaviors.},
journal = {Cancer cell},
volume = {40},
number = {11},
pages = {1423-1439.e11},
pmid = {36240778},
issn = {1878-3686},
support = {U54 CA217450/CA/NCI NIH HHS/United States ; DP2 AI171139/AI/NIAID NIH HHS/United States ; U19 AI100627/AI/NIAID NIH HHS/United States ; U54 HG010426/HG/NHGRI NIH HHS/United States ; 27145/CRUK_/Cancer Research UK/United Kingdom ; R35 CA231997/CA/NCI NIH HHS/United States ; U54 CA209971/CA/NCI NIH HHS/United States ; U2C CA233195/CA/NCI NIH HHS/United States ; U19 AI057229/AI/NIAID NIH HHS/United States ; U2C CA233238/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Epitopes ; *Neoplasms/pathology ; Clonal Evolution ; Clone Cells/pathology ; Cell Lineage ; Tumor Microenvironment ; },
abstract = {Intratumoral heterogeneity is a seminal feature of human tumors contributing to tumor progression and response to treatment. Current technologies are still largely unsuitable to accurately track phenotypes and clonal evolution within tumors, especially in response to genetic manipulations. Here, we developed epitopes for imaging using combinatorial tagging (EpicTags), which we coupled to multiplexed ion beam imaging (EpicMIBI) for in situ tracking of barcodes within tissue microenvironments. Using EpicMIBI, we dissected the spatial component of cell lineages and phenotypes in xenograft models of small cell lung cancer. We observed emergent properties from mixed clones leading to the preferential expansion of clonal patches for both neuroendocrine and non-neuroendocrine cancer cell states in these models. In a tumor model harboring a fraction of PTEN-deficient cancer cells, we observed a non-autonomous increase of clonal patch size in PTEN wild-type cancer cells. EpicMIBI facilitates in situ interrogation of cell-intrinsic and cell-extrinsic processes involved in intratumoral heterogeneity.},
}
@article {pmid36239541,
year = {2023},
author = {Keck, F and Altermatt, F},
title = {Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb.},
journal = {Molecular ecology resources},
volume = {23},
number = {2},
pages = {511-518},
doi = {10.1111/1755-0998.13723},
pmid = {36239541},
issn = {1755-0998},
support = {//Bundesamt f&#xfc;r Umwelt/ ; 31003A_173074//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; //University of Zurich Research Priority Program Global Change and Biodiversity/ ; },
mesh = {*DNA Barcoding, Taxonomic ; *DNA/genetics ; Biodiversity ; Gene Library ; Databases, Nucleic Acid ; },
abstract = {DNA barcoding and metabarcoding are revolutionizing the study and survey of biodiversity. In order to assign taxonomic labels to the DNA sequence data retrieved, these methods are strongly dependent on comprehensive and accurate reference databases. Producing reliable databases linking biological sequences and taxonomic data can be-and often has been-done using mainstream tools such as spreadsheet software. However, spreadsheets quickly become insufficient when the amount of data increases to thousands of taxa and sequences to be matched, and validation operations become more complex and are error prone if done in a manual way. Thus, there is a clear need for providing scientists with user-friendly, reliable and powerful tools to manipulate and manage DNA reference databases in tractable, sound and efficient ways. Here, we introduce the R package refdb as an environment for semi-automatic and assisted construction of DNA reference libraries. The refdb package is a reference database manager offering a set of powerful functions to import, organize, clean, filter, audit and export the data. It is broadly applicable in metabarcoding data generally obtained in biodiversity and biomonitoring studies. We present the main features of the package and outline how refdb can speed up reference database generation, management and handling, and thus contribute to standardization and repeatability in barcoding and metabarcoding studies.},
}
@article {pmid36235428,
year = {2022},
author = {Ibi, A and Du, M and Beuerle, T and Melchert, D and Solnier, J and Chang, C},
title = {A Multi-Pronged Technique for Identifying Equisetum palustre and Equisetum arvense-Combining HPTLC, HPLC-ESI-MS/MS and Optimized DNA Barcoding Techniques.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {19},
pages = {},
pmid = {36235428},
issn = {2223-7747},
abstract = {The most prominent horsetail species, Equisetum arvense, has an array of different medicinal properties, thus the proper authentication and differentiation of the plant from the more toxic Equisetum palustre is important. This study sought to identify different samples of E. arvense and E. palustre using three analytical methods. The first method involved the use of HPTLC analysis, as proposed by the European Pharmacopoeia. The second, HPLC-ESI-MS/MS, is capable of both identification and quantification and was used to determine the Equisetum alkaloid content in each sample. A third method was DNA barcoding, which identifies the samples based on their genetic make-up. Both HPTLC and HPLC-ESI-MS/MS proved to be suitable methods of identification, with HPLC-ESI-MS/MS proving the more sophisticated method for the quantification of alkaloids in the Equisetum samples and for determining the adulteration of E. arvense. For DNA barcoding, optimal primer pairs were elucidated to allow for the combined use of the rbcL and ITS markers to accurately identify each species. As new DNA marker sequences were added to GenBank, the reference library has been enriched for future work with these horsetail species.},
}
@article {pmid36233043,
year = {2022},
author = {Pezzotti, G and Kobara, M and Nakaya, T and Imamura, H and Fujii, T and Miyamoto, N and Adachi, T and Yamamoto, T and Kanamura, N and Ohgitani, E and Marin, E and Zhu, W and Kawai, T and Mazda, O and Nakata, T and Makimura, K},
title = {Raman Metabolomics of Candida auris Clades: Profiling and Barcode Identification.},
journal = {International journal of molecular sciences},
volume = {23},
number = {19},
pages = {},
pmid = {36233043},
issn = {1422-0067},
support = {22K10128//MEXT/JSPS KAKENHI/ ; },
mesh = {Antifungal Agents/pharmacology ; Candida auris ; *Candidiasis ; Chitin ; Glucans ; Water ; *beta-Glucans ; },
abstract = {This study targets on-site/real-time taxonomic identification and metabolic profiling of seven different Candida auris clades/subclades by means of Raman spectroscopy and imaging. Representative Raman spectra from different Candida auris samples were systematically deconvoluted by means of a customized machine-learning algorithm linked to a Raman database in order to decode structural differences at the molecular scale. Raman analyses of metabolites revealed clear differences in cell walls and membrane structure among clades/subclades. Such differences are key in maintaining the integrity and physical strength of the cell walls in the dynamic response to external stress and drugs. It was found that Candida cells use the glucan structure of the extracellular matrix, the degree of α-chitin crystallinity, and the concentration of hydrogen bonds between its antiparallel chains to tailor cell walls' flexibility. Besides being an effective ploy in survivorship by providing stiff shields in the α-1,3-glucan polymorph, the α-1,3-glycosidic linkages are also water-insoluble, thus forming a rigid and hydrophobic scaffold surrounded by a matrix of pliable and hydrated β-glucans. Raman analysis revealed a variety of strategies by different clades to balance stiffness, hydrophobicity, and impermeability in their cell walls. The selected strategies lead to differences in resistance toward specific environmental stresses of cationic/osmotic, oxidative, and nitrosative origins. A statistical validation based on principal component analysis was found only partially capable of distinguishing among Raman spectra of clades and subclades. Raman barcoding based on an algorithm converting spectrally deconvoluted Raman sub-bands into barcodes allowed for circumventing any speciation deficiency. Empowered by barcoding bioinformatics, Raman analyses, which are fast and require no sample preparation, allow on-site speciation and real-time selection of appropriate treatments.},
}
@article {pmid36232937,
year = {2022},
author = {Taylor, JB and Malone-Povolny, MJ and Merricks, EP and Wimsey, LE and Soliman, D and Nichols, TC and Wallet, SM and Maile, R and Schoenfisch, MH},
title = {Mechanisms of Foreign Body Response Mitigation by Nitric Oxide Release.},
journal = {International journal of molecular sciences},
volume = {23},
number = {19},
pages = {},
pmid = {36232937},
issn = {1422-0067},
support = {R01 DK108318/DK/NIDDK NIH HHS/United States ; DK108318/NH/NIH HHS/United States ; },
mesh = {Animals ; Blood Glucose/analysis ; Collagen/metabolism ; Cytokines ; *Foreign Bodies ; Foreign-Body Reaction ; *Gasotransmitters ; Glucose ; Interleukin-1 Receptor-Associated Kinases ; Matrix Metalloproteinase 2 ; *Mitogen-Activated Protein Kinase 14 ; Nitric Oxide/metabolism ; RNA, Messenger ; Swine ; },
abstract = {Implantable glucose biosensors provide real-time information about blood glucose fluctuations, but their utility and accuracy are time-limited due to the foreign body response (FBR) following their insertion beneath the skin. The slow release of nitric oxide (NO), a gasotransmitter with inflammation regulatory properties, from a sensor surface has been shown to dramatically improve sensors' analytical biocompatibility by reducing the overall FBR response. Indeed, work in a porcine model suggests that as long as the implants (sensors) continue to release NO, even at low levels, the inflammatory cell infiltration and resulting collagen density are lessened. While these studies strongly support the benefits of NO release in mitigating the FBR, the mechanisms through which exogenous NO acts on the surrounding tissue, especially under the condition of hyperglycemia, remain vague. Such knowledge would inform strategies to refine appropriate NO dosage and release kinetics for optimal therapeutic activity. In this study, we evaluated mediator, immune cell, and mRNA expression profiles in the local tissue microenvironment surrounding implanted sensors as a function of NO release, diabetes, and implantation duration. A custom porcine wound healing-centric multiplex gene array was developed for nanoString barcoding analysis. Tissues adjacent to sensors with sustained NO release abrogated the implant-induced acute and chronic FBR through modulation of the tissue-specific immune chemokine and cytokine microenvironment, resulting in decreased cellular recruitment, proliferation, and activation at both the acute (7-d) and chronic (14-d) phases of the FBR. Further, we found that sustained NO release abrogated the implant-induced acute and chronic foreign body response through modulation of mRNA encoding for key immunological signaling molecules and pathways, including STAT1 and multiple STAT1 targets including MAPK14, IRAK4, MMP2, and CXCL10. The condition of diabetes promoted a more robust FBR to the implants, which was also controlled by sustained NO release.},
}
@article {pmid36231335,
year = {2022},
author = {Kang, HJ and Baek, MJ and Kang, JH and Bae, YJ},
title = {DNA Barcoding of Chironomid Larvae (Diptera: Chironomidae) from Large Rivers in South Korea to Facilitate Freshwater Biomonitoring and Public Health Surveillance.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {19},
pages = {},
pmid = {36231335},
issn = {1660-4601},
mesh = {Animals ; Biological Monitoring ; *Chironomidae/genetics ; DNA Barcoding, Taxonomic ; *Drinking Water ; Electron Transport Complex IV/genetics ; Larva/genetics ; Public Health Surveillance ; Republic of Korea ; Rivers ; },
abstract = {Chironomid larvae are among the dominant benthic macroinvertebrates in all types of water systems in South Korea. They may pass through pipes in rivers (raw water) and occur in drinking water, thus creating public health issues. However, little is known about the larval stages of chironomids in large South Korean rivers. Therefore, we examined larval-adult associations in chironomids inhabiting major rivers used as water sources. The larvae were collected in 2015 and 2016 from nine locations along the four largest rivers in South Korea using a Ponar grab. Cytochrome oxidase subunit I (COI) sequences were generated from the larval specimens, and the species were identified by comparing these sequences to those in a newly constructed DNA barcode library of Chironomidae in South Korea. The samples from the four rivers yielded 61 mitochondrial COI sequences belonging to 18 species, including Hydrobaenus kondoi Saether, 1989, which was reported for the first time in the Korean Peninsula. Further, morphological identification of the larvae was conducted, and a pictorial taxonomic key to Chironomidae species in large rivers in South Korea was developed to facilitate freshwater biomonitoring research. Finally, an action flow chart was created for the rapid identification of chironomid larvae in infested drinking water or water purification facilities.},
}
@article {pmid36230889,
year = {2022},
author = {Zhang, MG and Kuznetsoff, JN and Owens, DA and Gallo, RA and Kalahasty, K and Cruz, AM and Kurtenbach, S and Correa, ZM and Pelaez, D and Harbour, JW},
title = {Early Mechanisms of Chemoresistance in Retinoblastoma.},
journal = {Cancers},
volume = {14},
number = {19},
pages = {},
pmid = {36230889},
issn = {2072-6694},
support = {P30EY014801/NH/NIH HHS/United States ; P30CA240139/CA/NCI NIH HHS/United States ; R01CA248890/CA/NCI NIH HHS/United States ; R01 CA248890/CA/NCI NIH HHS/United States ; F30 EY032345/EY/NEI NIH HHS/United States ; T32GM112601/NH/NIH HHS/United States ; F30EY032345/EY/NEI NIH HHS/United States ; },
abstract = {Retinoblastoma is the most common eye cancer in children and is fatal if left untreated. Over the past three decades, chemotherapy has become the mainstay of eye-sparing treatment. Nevertheless, chemoresistance continues to represent a major challenge leading to ocular and systemic toxicity, vision loss, and treatment failure. Unfortunately, the mechanisms leading to chemoresistance remain incompletely understood. Here, we engineered low-passage human retinoblastoma cells to study the early molecular mechanisms leading to resistance to carboplatin, one of the most widely used agents for treating retinoblastoma. Using single-cell next-generation RNA sequencing (scRNA-seq) and single-cell barcoding technologies, we found that carboplatin induced rapid transcriptomic reprogramming associated with the upregulation of PI3K-AKT pathway targets, including ABC transporters and metabolic regulators. Several of these targets are amenable to pharmacologic inhibition, which may reduce the emergence of chemoresistance. We provide evidence to support this hypothesis using a third-generation inhibitor of the ABCB1 transporter.},
}
@article {pmid36230296,
year = {2022},
author = {Chen, W and Li, C and Li, X and Li, J and Li, Y},
title = {Unraveling the Drifting Larval Fish Community in a Large Spawning Ground in the Middle Pearl River Using DNA Barcoding.},
journal = {Animals : an open access journal from MDPI},
volume = {12},
number = {19},
pages = {},
pmid = {36230296},
issn = {2076-2615},
support = {2018YFD0900903//National Key R&amp;D Program of China/ ; },
abstract = {Resolving the species composition of a larval pool in a spawning ground can provide novel insights into regional fish stocks and can support the development of effective monitoring and conservation policies. However, it is challenging to identify fish larvae to species due to their high diversity and dramatic phenotypic changes over development. In this study, we collected fish larvae in the Dongta spawning ground (Guiping City, Guangxi Province, China) in the middle reaches of the Pearl River between May and August 2018. We used a DNA barcoding approach to determine the species composition of the larval pool. A total of 905 larvae were chosen for molecular identification, of which 750 yielded high-quality barcoding sequences. Of these, 597 (≈79.6%), 151 (≈20.1%)/and 2 (≈0.3%) were assigned to 28 species, 8 genera, and 1 subfamily using the Barcode of Life Data System and GenBank nucleotide databases, respectively. Among the 28 identified species, 21 were cyprinids. Two species (Mugilogobius myxodermus and Pseudolaubuca engraulis) that were present only infrequently in previous adult surveys were abundant in the larval pool. Six invasive species were identified in the larval pool, implying that these species had successfully colonized the studied river section. Several migratory species common in the lower Pearl River were rare or absent in the investigated region, suggesting that dam construction in the Pearl River has had adverse effects on these migratory species. In summary, our study confirmed the applicability of DNA barcoding to studies of fish larval ecology and provided important reference data for fishery management and conservation in the Pearl River.},
}
@article {pmid36227997,
year = {2022},
author = {Sankaran, VG and Weissman, JS and Zon, LI},
title = {Cellular barcoding to decipher clonal dynamics in disease.},
journal = {Science (New York, N.Y.)},
volume = {378},
number = {6616},
pages = {eabm5874},
pmid = {36227997},
issn = {1095-9203},
support = {R01 CA265726/CA/NCI NIH HHS/United States ; U01 HL134812/HL/NHLBI NIH HHS/United States ; R01 HL144780/HL/NHLBI NIH HHS/United States ; RM1 HG009490/HG/NHGRI NIH HHS/United States ; P01 CA163222/CA/NCI NIH HHS/United States ; P01 HL032262/HL/NHLBI NIH HHS/United States ; P01 HL131477/HL/NHLBI NIH HHS/United States ; R01 HL146500/HL/NHLBI NIH HHS/United States ; R01 DK103794/DK/NIDDK NIH HHS/United States ; U01 CA217882/CA/NCI NIH HHS/United States ; R24 OD017870/OD/NIH HHS/United States ; U54 DK110805/DK/NIDDK NIH HHS/United States ; R24 DK092760/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *DNA Barcoding, Taxonomic ; *Clonal Evolution/genetics ; *Disease/genetics ; Single-Cell Analysis ; },
abstract = {Cellular barcodes are distinct DNA sequences that enable one to track specific cells across time or space. Recent advances in our ability to detect natural or synthetic cellular barcodes, paired with single-cell readouts of cell state, have markedly increased our knowledge of clonal dynamics and genealogies of the cells that compose a variety of tissues and organs. These advances hold promise to redefine our view of human disease. Here, we provide an overview of cellular barcoding approaches, discuss applications to gain new insights into disease mechanisms, and provide an outlook on future applications. We discuss unanticipated insights gained through barcoding in studies of cancer and blood cell production and describe how barcoding can be applied to a growing array of medical fields, particularly with the increasing recognition of clonal contributions in human diseases.},
}
@article {pmid36222650,
year = {2022},
author = {Boddé, M and Makunin, A and Ayala, D and Bouafou, L and Diabaté, A and Ekpo, UF and Kientega, M and Le Goff, G and Makanga, BK and Ngangue, MF and Omitola, OO and Rahola, N and Tripet, F and Durbin, R and Lawniczak, MKN},
title = {High-resolution species assignment of Anopheles mosquitoes using k-mer distances on targeted sequences.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {36222650},
issn = {2050-084X},
support = {207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; 206194/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; WT207492/WT_/Wellcome Trust/United Kingdom ; RG92770/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *Anopheles/genetics ; Burkina Faso ; Gabon ; },
abstract = {The ANOSPP amplicon panel is a genus-wide targeted sequencing panel to facilitate large-scale monitoring of Anopheles species diversity. Combining information from the 62 nuclear amplicons present in the ANOSPP panel allows for a more senstive and specific species assignment than single gene (e.g. COI) barcoding, which is desirable in the light of permeable species boundaries. Here, we present NNoVAE, a method using Nearest Neighbours (NN) and Variational Autoencoders (VAE), which we apply to k-mers resulting from the ANOSPP amplicon sequences in order to hierarchically assign species identity. The NN step assigns a sample to a species-group by comparing the k-mers arising from each haplotype's amplicon sequence to a reference database. The VAE step is required to distinguish between closely related species, and also has sufficient resolution to reveal population structure within species. In tests on independent samples with over 80% amplicon coverage, NNoVAE correctly classifies to species level 98% of samples within the An. gambiae complex and 89% of samples outside the complex. We apply NNoVAE to over two thousand new samples from Burkina Faso and Gabon, identifying unexpected species in Gabon. NNoVAE presents an approach that may be of value to other targeted sequencing panels, and is a method that will be used to survey Anopheles species diversity and Plasmodium transmission patterns through space and time on a large scale, with plans to analyse half a million mosquitoes in the next five years.},
}
@article {pmid36219539,
year = {2023},
author = {Zhang, L and Huang, YW and Huang, JL and Ya, JD and Zhe, MQ and Zeng, CX and Zhang, ZR and Zhang, SB and Li, DZ and Li, HT and Yang, JB},
title = {DNA barcoding of Cymbidium by genome skimming: Call for next-generation nuclear barcodes.},
journal = {Molecular ecology resources},
volume = {23},
number = {2},
pages = {424-439},
doi = {10.1111/1755-0998.13719},
pmid = {36219539},
issn = {1755-0998},
support = {XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2017-LSF-GBOWS-2//Large-scale Scientific Facilities of the Chinese Academy of Sciences/ ; 202103AC100003//Key R &amp; D program of Yunnan Province, China/ ; 202105AE160012//Project for Innovation Team of Yunnan Province/ ; },
mesh = {Humans ; *DNA Barcoding, Taxonomic/methods ; Bayes Theorem ; DNA, Plant/genetics ; *Plants/genetics ; Plastids/genetics ; Sequence Analysis, DNA ; Species Specificity ; Phylogeny ; },
abstract = {Cymbidium is an orchid genus that has undergone rapid radiation and has high ornamental, economic, ecological and cultural importance, but its classification based on morphology is controversial. The plastid genome (plastome), as an extension of plant standard DNA barcodes, has been widely used as a potential molecular marker for identifying recently diverged species or complicated plant groups. In this study, we newly generated 237 plastomes of 50 species (at least two individuals per species) by genome skimming, covering 71.4% of members of the genus Cymbidium. Sequence-based analyses (barcoding gaps and automatic barcode gap discovery) and tree-based analyses (maximum likelihood, Bayesian inference and multirate Poisson tree processes model) were conducted for species identification of Cymbidium. Our work provides a comprehensive DNA barcode reference library for Cymbidium species identification. The results show that compared with standard DNA barcodes (rbcL + matK) as well as the plastid trnH-psbA, the species identification rate of the plastome increased moderately from 58% to 68%. At the same time, we propose an optimized identification strategy for Cymbidium species. The plastome cannot completely resolve the species identification of Cymbidium, the main reasons being incomplete lineage sorting, artificial cultivation, natural hybridization and chloroplast capture. To further explore the potential use of nuclear data in identifying species, the Skmer method was adopted and the identification rate increased to 72%. It appears that nuclear genome data have a vital role in species identification and are expected to be used as next-generation nuclear barcodes.},
}
@article {pmid36216958,
year = {2022},
author = {Kishi, JY and Liu, N and West, ER and Sheng, K and Jordanides, JJ and Serrata, M and Cepko, CL and Saka, SK and Yin, P},
title = {Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing.},
journal = {Nature methods},
volume = {19},
number = {11},
pages = {1393-1402},
pmid = {36216958},
issn = {1548-7105},
support = {UH3 CA255133/CA/NCI NIH HHS/United States ; UG3 HL145600/HL/NHLBI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; DP1 GM133052/GM/NIGMS NIH HHS/United States ; RF1 MH124606/MH/NIMH NIH HHS/United States ; RF1 MH128861/MH/NIMH NIH HHS/United States ; R01 GM124401/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Mice ; *High-Throughput Nucleotide Sequencing/methods ; DNA, Complementary ; *DNA/genetics ; },
abstract = {We present Light-Seq, an approach for multiplexed spatial indexing of intact biological samples using light-directed DNA barcoding in fixed cells and tissues followed by ex situ sequencing. Light-Seq combines spatially targeted, rapid photocrosslinking of DNA barcodes onto complementary DNAs in situ with a one-step DNA stitching reaction to create pooled, spatially indexed sequencing libraries. This light-directed barcoding enables in situ selection of multiple cell populations in intact fixed tissue samples for full-transcriptome sequencing based on location, morphology or protein stains, without cellular dissociation. Applying Light-Seq to mouse retinal sections, we recovered thousands of differentially enriched transcripts from three cellular layers and discovered biomarkers for a very rare neuronal subtype, dopaminergic amacrine cells, from only four to eight individual cells per section. Light-Seq provides an accessible workflow to combine in situ imaging and protein staining with next generation sequencing of the same cells, leaving the sample intact for further analysis post-sequencing.},
}
@article {pmid36215236,
year = {2022},
author = {Sonet, G and Smitz, N and Vangestel, C and Samyn, Y},
title = {DNA barcoding echinoderms from the East Coast of South Africa. The challenge to maintain DNA data connected with taxonomy.},
journal = {PloS one},
volume = {17},
number = {10},
pages = {e0270321},
pmid = {36215236},
issn = {1932-6203},
mesh = {Animals ; Aquatic Organisms ; DNA/genetics ; *DNA Barcoding, Taxonomic/methods ; Echinodermata/genetics ; *Electron Transport Complex IV/genetics ; Phylogeny ; South Africa ; Water ; },
abstract = {Echinoderms are marine water invertebrates that are represented by more than 7000 extant species, grouped in five classes and showing diverse morphologies (starfish, sea lilies, feather stars, sea urchins, sea cucumbers, brittle and basket stars). In an effort to further study their diversity, DNA barcodes (DNA fragments of the 5' end of the cytochrome c oxidase subunit I gene, COI) have been used to complement morphological examination in identifying evolutionary lineages. Although divergent clusters of COI sequences were reported to generally match morphological species delineations, they also revealed some discrepancies, suggesting overlooked species, ecophenotypic variation or multiple COI lineages within one species. Here, we sequenced COI fragments of 312 shallow-water echinoderms of the East Coast of South Africa (KwaZulu-Natal Province) and compared morphological identifications with species delimitations obtained with four methods that are exclusively based on COI sequences. We identified a total of 103 morphospecies including 18 that did not exactly match described species. We also report 46 COI sequences that showed large divergences (>5% p-distances) with those available to date and publish the first COI sequences for 30 species. Our analyses also identified discordances between morphological identifications and COI-based species delimitations for a considerable proportion of the morphospecies studied here (49/103). For most of them, further investigation is necessary to keep a sound connection between taxonomy and the growing importance of DNA-based research.},
}
@article {pmid36214670,
year = {2022},
author = {Niazi, AR and Ghafoor, A and Afshan, NU and Moreno, G},
title = {Tulostoma loonbanglaense: A new species from Azad Jammu and Kashmir using light and scanning electron microscopy and DNA barcoding technique.},
journal = {Microscopy research and technique},
volume = {85},
number = {12},
pages = {3720-3725},
doi = {10.1002/jemt.24240},
pmid = {36214670},
issn = {1097-0029},
support = {//University of the Punjab/ ; },
mesh = {Phylogeny ; Microscopy, Electron, Scanning ; *DNA Barcoding, Taxonomic ; DNA ; *Basidiomycota ; },
abstract = {Tulostoma loonbanglaense sp. nov. is described from Azad Jammu and Kashmir, Pakistan. ITS sequences confirm its position within the genus Tulostoma, and suggest that it is separate from other identified species of this genus. The species has globose to subglobose, with wide, solitary and appressed spines basidiospores, the basidiospores are relatively small, 4.39 × 4.23 μm, that make it distinguished from the related species. Sequences of nr ITS region of the newly described species nested as a distinct taxon in both phylogenetic analyses of the current study.},
}
@article {pmid36210380,
year = {2022},
author = {Villalobos, R and Aylagas, E and Pearman, JK and Curdia, J and Lozano-Cortés, D and Coker, DJ and Jones, B and Berumen, ML and Carvalho, S},
title = {Inter-annual variability patterns of reef cryptobiota in the central Red Sea across a shelf gradient.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {16944},
pmid = {36210380},
issn = {2045-2322},
mesh = {Animals ; *Anthozoa ; Coral Reefs ; Indian Ocean ; },
abstract = {The combination of molecular tools, standard surveying techniques, and long-term monitoring programs are relevant to understanding environmental and ecological changes in coral reef communities. Here we studied temporal variability in cryptobenthic coral reef communities across the continental shelf in the central Red Sea spanning 6 years (three sampling periods: 2013-2019) and including the 2015 mass bleaching event. We used a combination of molecular tools (barcoding and metabarcoding) to assess communities on Autonomous Reef Monitoring Structures (ARMS) as a standardized sampling approach. Community composition associated with ARMS for both methodologies (barcoding and metabarcoding) was statistically different across reefs (shelf position) and time periods. The partition of beta diversity showed a higher turnover and lower nestedness between pre-bleaching and post-bleaching samples than between the two post-bleaching periods, revealing a community shift from the bleaching event. However, a slight return to the pre-bleaching community composition was observed in 2019 suggesting a recovery trajectory. Given the predictions of decreasing time between bleaching events, it is concerning that cryptobenthic communities may not fully recover and communities with new characteristics will emerge. We observed a high turnover among reefs for all time periods, implying a homogenization of the cryptobiome did not occur across the cross shelf following the 2015 bleaching event. It is possible that dispersal limitations and the distinct environmental and benthic structures present across the shelf maintained the heterogeneity in communities among reefs. This study has to the best of our knowledge presented for the first time a temporal aspect into the analysis of ARMS cryptobenthic coral reef communities and encompasses a bleaching event. We show that these structures can detect cryptic changes associated with reef degradation and provides support for these being used as long-term monitoring tools.},
}
@article {pmid36209989,
year = {2023},
author = {Nourrisson, C and Moniot, M and Lavergne, RA and Robert, E and Bonnin, V and Hagen, F and Grenouillet, F and Cafarchia, C and Butler, G and Cassaing, S and Sabou, M and Le Pape, P and Poirier, P and Morio, F},
title = {Acquired fluconazole resistance and genetic clustering in Diutina (Candida) catenulata from clinical samples.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {29},
number = {2},
pages = {257.e7-257.e11},
doi = {10.1016/j.cmi.2022.09.021},
pmid = {36209989},
issn = {1469-0691},
mesh = {Animals ; Humans ; *Fluconazole/pharmacology ; *Antifungal Agents/pharmacology ; Candida ; Amphotericin B/pharmacology ; Voriconazole ; Yeasts ; Candida parapsilosis ; Candida tropicalis ; DNA, Intergenic ; Microbial Sensitivity Tests ; Drug Resistance, Fungal/genetics ; },
abstract = {OBJECTIVES: Diutina (Candida) catenulata is an ascomycetous yeast isolated from environmental sources and animals, occasionally infecting humans. The aim of this study is to shed light on the in vitro antifungal susceptibility and genetic diversity of this opportunistic yeast.<br><br>METHODS: Forty-five D. catenulata strains isolated from various sources (including human and environmental sources) and originating from nine countries were included. Species identification was performed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and confirmed via internal transcribed spacer ribosomal DNA barcoding.&#xa0;In&#xa0;vitro antifungal susceptibility was determined for seven systemic antifungals via the gradient strip method after 48&#xa0;hours of incubation at 35&#xb0;C using Etest&#xae; (Biom&#xe9;rieux) or Liofilchem&#xae; strips. Isolates exhibiting fluconazole minimal inhibitory concentrations (MICs) of &#x2265;8 &#x3bc;g/mL were investigated for mutations in the ERG11 gene. A novel microsatellite genotyping scheme consisting of four markers was developed to assess genetic diversity.<br><br>RESULTS: MIC ranges for amphotericin B, caspofungin, micafungin, isavuconazole, and posaconazole were 0.19-1 &#x3bc;g/mL, 0.094-0.5 &#x3bc;g/mL, 0.012-0.064 &#x3bc;g/mL, 0.003-0.047 &#x3bc;g/mL, and 0.006-0.032 &#x3bc;g/mL, respectively. By comparison, a broad range of MICs was noted for fluconazole (0.75 to >256 &#x3bc;g/mL) and voriconazole (0.012-0.38 mg/L), the higher values being observed among clinical strains. The Y132F amino acid substitution, associated with azole resistance in various Candida species (C. albicans, C. tropicalis, C. parapsilosis, and C. orthopsilosis), was the main substitution identified. Although microsatellite typing showed extensive genetic diversity, most strains with high fluconazole MICs clustered together, suggesting human-to-human transmission or a common source of contamination.<br><br>DISCUSSION: The high rate of acquired fluconazole resistance among clinical isolates of D. catenulata is of concern. In this study, we highlight a link between the genetic diversity of D. catenulata and its antifungal resistance patterns, suggesting possible clonal transmission of resistant isolates.},
}
@article {pmid36209044,
year = {2023},
author = {Ye, Q and Belabed, H and Wang, Y and Yu, Z and Palaniappan, M and Li, JY and Kalovidouris, SA and MacKenzie, KR and Teng, M and Young, DW and Fujihara, Y and Matzuk, MM},
title = {Advancing ASMS with LC-MS/MS for the discovery of novel PDCL2 ligands from DNA-encoded chemical library selections.},
journal = {Andrology},
volume = {11},
number = {5},
pages = {808-815},
pmid = {36209044},
issn = {2047-2927},
support = {P01 HD087157/HD/NICHD NIH HHS/United States ; R01 HD088412/HD/NICHD NIH HHS/United States ; R03 CA259664/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Male ; Female ; Animals ; Mice ; *DNA/metabolism ; *Small Molecule Libraries/chemistry/metabolism/pharmacology ; Drug Discovery ; Ligands ; Chromatography, Liquid ; Tandem Mass Spectrometry ; Semen/metabolism ; },
abstract = {BACKGROUND: A safe, effective, and reversible nonhormonal male contraceptive drug is greatly needed for male contraception as well as for circumventing the side effects of female hormonal contraceptives. Phosducin-like 2 (PDCL2) is a testis-specific phosphoprotein in mice and humans. We recently found that male PDCL2 knockout mice are sterile due to globozoospermia caused by impaired sperm head formation, indicating that PDCL2 is a potential target for male contraception. Herein, our study for the first time developed a biophysical assay for PDCL2 allowing us to screen a series of small molecules, to study structure-activity relationships, and to discover two PDCL2 binders with novel chemical structure.<br><br>OBJECTIVE: To identify a PDCL2 ligand for therapeutic male contraception, we performed DNA-encoded chemical library (DECL) screening and off-DNA hit validation using a unique affinity selection mass spectrometry (ASMS) biophysical profiling strategy.<br><br>MATERIALS AND METHODS: We employed the screening process of DECL, which contains billions of chemically unique DNA-barcoded compounds generated through individual sequences of reactions and different combinations of functionalized building blocks. The structures of the PDCL2 binders are proposed based on the sequencing analysis of the DNA barcode attached to each individual DECL compound. The proposed structure is synthesized through multistep reactions. To confirm and determine binding affinity between the DECL identified molecules and PDCL2, we developed an ASMS assay that incorporates liquid chromatography with tandem mass spectrometry (LC-MS/MS).<br><br>RESULTS: After a screening process of PDCL2 with DECLs containing&#xa0;>440 billion compounds, we identified a series of hits. The selected compounds were synthesized as off-DNA small molecules, characterized by spectroscopy data, and subjected to our ASMS/LC-MS/MS binding assay. By this assay, we discovered two novel compounds, which showed good binding affinity for PDCL2 in comparison to other molecules generated in our laboratory and&#xa0;which were further confirmed by a thermal shift assay.<br><br>With the ASMS/LC-MS/MS assay developed in this paper, we successfully discovered a PDCL2 ligand that warrants further development as a male contraceptive.},
}
@article {pmid36205729,
year = {2022},
author = {Cruz, MM and Hoffmann, LS and Freitas, TRO},
title = {Saint Peter and Saint Paul Archipelago barcoded: Fish diversity in the remoteness and DNA barcodes reference library for metabarcoding monitoring.},
journal = {Genetics and molecular biology},
volume = {45},
number = {3},
pages = {e20210349},
pmid = {36205729},
issn = {1415-4757},
abstract = {In order to monitor the effects of anthropogenic pressures in ecosystems, molecular techniques can be used to characterize species composition. Among molecular markers capable of identifying species, the cytochrome c oxidase I (COI) is the most used. However, new possibilities of biodiversity profiling have become possible, in which molecular fragments of medium and short-length can now be analyzed in metabarcoding studies. Here, a survey of fishes from the Saint Peter and Saint Paul Archipelago was barcoded using the COI marker, which allowed the identification of 21 species. This paved the way to further investigate the fish biodiversity of the archipelago, transitioning from barcoding to metabarcoding analysis. As preparatory steps for future metabarcoding studies, the first extensive COI library of fishes listed for these islands was constructed and includes new data generated in this survey as well as previously available data, resulting in a final database with 9,183 sequences from 169 species and 63 families of fish. A new primer specifically designed for those fishes was tested in silico to amplify a region of 262 bp. The new approach should guarantee a reliable surveillance of the archipelago and can be used to generate policies that will enhance the archipelago's protection.},
}
@article {pmid36203011,
year = {2022},
author = {He, S and Bhatt, R and Brown, C and Brown, EA and Buhr, DL and Chantranuvatana, K and Danaher, P and Dunaway, D and Garrison, RG and Geiss, G and Gregory, MT and Hoang, ML and Khafizov, R and Killingbeck, EE and Kim, D and Kim, TK and Kim, Y and Klock, A and Korukonda, M and Kutchma, A and Lewis, ZR and Liang, Y and Nelson, JS and Ong, GT and Perillo, EP and Phan, JC and Phan-Everson, T and Piazza, E and Rane, T and Reitz, Z and Rhodes, M and Rosenbloom, A and Ross, D and Sato, H and Wardhani, AW and Williams-Wietzikoski, CA and Wu, L and Beechem, JM},
title = {High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging.},
journal = {Nature biotechnology},
volume = {40},
number = {12},
pages = {1794-1806},
pmid = {36203011},
issn = {1546-1696},
mesh = {Humans ; Paraffin Embedding ; *RNA/genetics ; *Proteins ; Molecular Imaging ; Formaldehyde ; },
abstract = {Resolving the spatial distribution of RNA and protein in tissues at subcellular resolution is a challenge in the field of spatial biology. We describe spatial molecular imaging, a system that measures RNAs and proteins in intact biological samples at subcellular resolution by performing multiple cycles of nucleic acid hybridization of fluorescent molecular barcodes. We demonstrate that spatial molecular imaging has high sensitivity (one or two copies per cell) and very low error rate (0.0092 false calls per cell) and background (~0.04 counts per cell). The imaging system generates three-dimensional, super-resolution localization of analytes at ~2 million cells per sample. Cell segmentation is morphology based using antibodies, compatible with formalin-fixed, paraffin-embedded samples. We measured multiomic data (980 RNAs and 108 proteins) at subcellular resolution in formalin-fixed, paraffin-embedded tissues (nonsmall cell lung and breast cancer) and identified >18 distinct cell types, ten unique tumor microenvironments and 100 pairwise ligand-receptor interactions. Data on >800,000 single cells and ~260 million transcripts can be accessed at http://nanostring.com/CosMx-dataset .},
}
@article {pmid36202811,
year = {2022},
author = {Keraite, I and Becker, P and Canevazzi, D and Frias-López, C and Dabad, M and Tonda-Hernandez, R and Paramonov, I and Ingham, MJ and Brun-Heath, I and Leno, J and Abulí, A and Garcia-Arumí, E and Heath, SC and Gut, M and Gut, IG},
title = {A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {5902},
pmid = {36202811},
issn = {2041-1723},
mesh = {DNA, Mitochondrial/genetics ; Deoxyribonuclease I/genetics ; Genome, Human/genetics ; *Genome, Mitochondrial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Nucleotides ; RNA ; Sequence Analysis, DNA/methods ; },
abstract = {Methods to reconstruct the mitochondrial DNA (mtDNA) sequence using short-read sequencing come with an inherent bias due to amplification and mapping. They can fail to determine the phase of variants, to capture multiple deletions and to cover the mitochondrial genome evenly. Here we describe a method to target, multiplex and sequence at high coverage full-length human mitochondrial genomes as native single-molecules, utilizing the RNA-guided DNA endonuclease Cas9. Combining Cas9 induced breaks, that define the mtDNA beginning and end of the sequencing reads, as barcodes, we achieve high demultiplexing specificity and delineation of the full-length of the mtDNA, regardless of the structural variant pattern. The long-read sequencing data is analysed with a pipeline where our custom-developed software, baldur, efficiently detects single nucleotide heteroplasmy to below 1%, physically determines phase and can accurately disentangle complex deletions. Our workflow is a tool for studying mtDNA variation and will accelerate mitochondrial research.},
}
@article {pmid36202798,
year = {2022},
author = {Zhang, ZY and Ding, Y and Ezhilarasan, R and Lhakhang, T and Wang, Q and Yang, J and Modrek, AS and Zhang, H and Tsirigos, A and Futreal, A and Draetta, GF and Verhaak, RGW and Sulman, EP},
title = {Lineage-coupled clonal capture identifies clonal evolution mechanisms and vulnerabilities of BRAF[V600E] inhibition resistance in melanoma.},
journal = {Cell discovery},
volume = {8},
number = {1},
pages = {102},
pmid = {36202798},
issn = {2056-5968},
support = {P30 CA016672/CA/NCI NIH HHS/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; R01 CA190121/CA/NCI NIH HHS/United States ; DefeatGBM//National Brain Tumor Society (National Brain Tumor Society, Inc.)/ ; R01 CA190121-01//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Targeted cancer therapies have revolutionized treatment but their efficacies are limited by the development of resistance driven by clonal evolution within tumors. We developed "CAPTURE", a single-cell barcoding approach to comprehensively trace clonal dynamics and capture live lineage-coupled resistant cells for in-depth multi-omics analysis and functional exploration. We demonstrate that heterogeneous clones, either preexisting or emerging from drug-tolerant persister cells, dominated resistance to vemurafenib in BRAF[V600E] melanoma. Further integrative studies uncovered diverse resistance mechanisms. This includes a previously unrecognized and clinically relevant mechanism, chromosome 18q21 gain, which leads to vulnerability of the cells to BCL2 inhibitor. We also identified targetable common dependencies of captured resistant clones, such as oxidative phosphorylation and E2F pathways. Our study provides new therapeutic insights into overcoming therapy resistance in BRAF[V600E] melanoma and presents a platform for exploring clonal evolution dynamics and vulnerabilities that can be applied to study treatment resistance in other cancers.},
}
@article {pmid36197898,
year = {2022},
author = {Park, YS and Kang, JS and Park, JY and Shim, H and Yang, HO and Kang, JH and Yang, TJ},
title = {Analysis of the complete plastomes and nuclear ribosomal DNAs from Euonymus hamiltonianus and its relatives sheds light on their diversity and evolution.},
journal = {PloS one},
volume = {17},
number = {10},
pages = {e0275590},
pmid = {36197898},
issn = {1932-6203},
mesh = {DNA, Ribosomal ; *Euonymus/genetics ; Evolution, Molecular ; *Genome, Plastid ; Nucleotides ; Phylogeny ; },
abstract = {Euonymus hamiltonianus and its relatives (Celastraceae family) are used for ornamental and medicinal purposes. However, species identification in Euonymus is difficult due to their morphological diversity. Using plastid genome (plastome) data, we attempt to reveal phylogenetic relationship among Euonymus species and develop useful markers for molecular identification. We assembled the plastome and nuclear ribosomal DNA (nrDNA) sequences from five Euonymus lines collected from South Korea: three Euonymus hamiltonianus accessions, E. europaeus, and E. japonicus. We conducted an in-depth comparative analysis using ten plastomes, including other publicly available plastome data for this genus. The genome structures, gene contents, and gene orders were similar in all Euonymus plastomes in this study. Analysis of nucleotide diversity revealed six divergence hotspots in their plastomes. We identified 339 single nucleotide polymorphisms and 293 insertion or deletions among the four E. hamiltonianus plastomes, pointing to abundant diversity even within the same species. Among 77 commonly shared genes, 9 and 33 were identified as conserved genes in the genus Euonymus and E. hamiltonianus, respectively. Phylogenetic analysis based on plastome and nrDNA sequences revealed the overall consensus and relationships between plastomes and nrDNAs. Finally, we developed six barcoding markers and successfully applied them to 31 E. hamiltonianus lines collected from South Korea. Our findings provide the molecular basis for the classification and molecular taxonomic criteria for the genus Euonymus (at least in Korea), which should aid in more objective classification within this genus. Moreover, the newly developed markers will be useful for understanding the species delimitation of E. hamiltonianus and closely related species.},
}
@article {pmid36197893,
year = {2022},
author = {Poitrimol, C and Thiébaut, &#xc9; and Daguin-Thiébaut, C and Le Port, AS and Ballenghien, M and Tran Lu Y, A and Jollivet, D and Hourdez, S and Matabos, M},
title = {Contrasted phylogeographic patterns of hydrothermal vent gastropods along South West Pacific: Woodlark Basin, a possible contact zone and/or stepping-stone.},
journal = {PloS one},
volume = {17},
number = {10},
pages = {e0275638},
pmid = {36197893},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; Ecosystem ; *Gastropoda/genetics ; Humans ; *Hydrothermal Vents ; Pacific Ocean ; Phylogeny ; Phylogeography ; },
abstract = {Understanding drivers of biodiversity patterns is essential to evaluate the potential impact of deep-sea mining on ecosystems resilience. While the South West Pacific forms an independent biogeographic province for hydrothermal vent fauna, different degrees of connectivity among basins were previously reported for a variety of species depending on their ability to disperse. In this study, we compared phylogeographic patterns of several vent gastropods across South West Pacific back-arc basins and the newly-discovered La Scala site on the Woodlark Ridge by analysing their genetic divergence using a barcoding approach. We focused on six genera of vent gastropods widely distributed in the region: Lepetodrilus, Symmetromphalus, Lamellomphalus, Shinkailepas, Desbruyeresia and Provanna. A wide-range sampling was conducted at different vent fields across the Futuna Volcanic Arc, the Manus, Woodlark, North Fiji, and Lau Basins, during the CHUBACARC cruise in 2019. The Cox1-based genetic structure of geographic populations was examined for each taxon to delineate putative cryptic species and assess potential barriers or contact zones between basins. Results showed contrasted phylogeographic patterns among species, even between closely related species. While some species are widely distributed across basins (i.e. Shinkailepas tollmanni, Desbruyeresia melanioides and Lamellomphalus) without evidence of strong barriers to gene flow, others are restricted to one (i.e. Shinkailepas tufari complex of cryptic species, Desbruyeresia cancellata and D. costata). Other species showed intermediate patterns of isolation with different lineages separating the Manus Basin from the Lau/North Fiji Basins (i.e. Lepetodrilus schrolli, Provanna and Symmetromphalus spp.). Individuals from the Woodlark Basin were either endemic to this area (though possibly representing intermediate OTUs between the Manus Basin and the other eastern basins populations) or, coming into contact from these basins, highlighting the stepping-stone role of the Woodlark Basin in the dispersal of the South West Pacific vent fauna. Results are discussed according to the dispersal ability of species and the geological history of the South West Pacific.},
}
@article {pmid36197789,
year = {2023},
author = {Arjona, Y and Arribas, P and Salces-Castellano, A and López, H and Emerson, BC and Andújar, C},
title = {Metabarcoding for biodiversity inventory blind spots: A test case using the beetle fauna of an insular cloud forest.},
journal = {Molecular ecology},
volume = {32},
number = {23},
pages = {6130-6146},
doi = {10.1111/mec.16716},
pmid = {36197789},
issn = {1365-294X},
support = {2017RCE03//Fundaci&#xf3;n Caja Canarias / Obra Social "La Caixa"/ ; 705639//H2020 European Research Council/ ; CGL2015-74178-JIN//Spanish Ministry of Science and Innovation (AEI)/ ; CGL2017-85718-P//Spanish Ministry of Science and Innovation (AEI)/ ; PID2020-116788GB-I00//Spanish Ministry of Science and Innovation (AEI)/ ; },
mesh = {Animals ; *Coleoptera/genetics ; Reproducibility of Results ; DNA Barcoding, Taxonomic/methods ; Biodiversity ; Forests ; *Arthropods/genetics ; Soil ; },
abstract = {Soils harbour a rich arthropod fauna, but many species are still not formally described (Linnaean shortfall) and the distribution of those already described is poorly understood (Wallacean shortfall). Metabarcoding holds much promise to fill this gap, however, nuclear copies of mitochondrial genes, and other artefacts lead to taxonomic inflation, which compromise the reliability of biodiversity inventories. Here, we explore the potential of a bioinformatic approach to jointly "denoise" and filter nonauthentic mitochondrial sequences from metabarcode reads to obtain reliable soil beetle inventories and address open questions in soil biodiversity research, such as the scale of dispersal constraints in different soil layers. We sampled cloud forest arthropod communities from 49 sites in the Anaga peninsula of Tenerife (Canary Islands). We performed whole organism community DNA (wocDNA) metabarcoding, and built a local reference database with COI barcode sequences of 310 species of Coleoptera for filtering reads and the identification of metabarcoded species. This resulted in reliable haplotype data after considerably reducing nuclear mitochondrial copies and other artefacts. Comparing our results with previous beetle inventories, we found: (i) new species records, potentially representing undescribed species; (ii) new distribution records, and (iii) validated phylogeographic structure when compared with traditional sequencing approaches. Analyses also revealed evidence for higher dispersal constraint within deeper soil beetle communities, compared to those closer to the surface. The combined power of barcoding and metabarcoding contribute to mitigate the important shortfalls associated with soil arthropod diversity data, and thus address unresolved questions for this vast biodiversity fraction.},
}
@article {pmid36195412,
year = {2022},
author = {Álvarez, EA and Klemm, K and Hoppenrath, M and Cembella, A and John, U and Karlson, B},
title = {Temporal and spatial distribution of epibenthic dinoflagellates in the Kattegat-Skagerrak, NE Atlantic-Focus on Prorocentrum lima and Coolia monotis.},
journal = {Harmful algae},
volume = {118},
number = {},
pages = {102318},
pmid = {36195412},
issn = {1878-1470},
mesh = {Animals ; *Bivalvia ; *Dinoflagellida/genetics ; Ecosystem ; Harmful Algal Bloom ; Humans ; Phylogeny ; },
abstract = {Epibenthic dinoflagellates occur globally and include many toxin-producing species of concern to human health and benthic ecosystem function. Such benthic harmful algal blooms (BHABs) have been well described from tropical and sub-tropical coastal environments, but assessments from north temperate waters, e.g., northern Europe, and polar regions are scarce. The present study addressed the biodiversity and distribution of potentially toxic epibenthic dinoflagellate populations along the west coast of Sweden (Kattegat-Skagerrak) by morphological and molecular criteria. Morphological analysis conducted by light- and electron-microscopy was then linked by DNA barcoding of the V4 region of 18S rRNA gene sequences to interpret taxonomic and phylogenetic relationships. The presence of two potentially toxigenic epibenthic dinoflagellates, Prorocentrum lima (Ehrenberg) F.Stein and Coolia monotis Meunier was confirmed, along with a description of their spatial and temporal distribution. For P. lima, one third of the cell abundance values exceeded official alarm thresholds for potentially toxic BHAB events (>1000 cells gr[-1] of macroalgae fresh weight). The same species were recorded consecutively for two summers, but without significant temporal variation in cell densities. SEM analyses confirmed the presence of other benthic Prorocentrum species: P. fukuyoi complex, P. cf. foraminosum and P. cf. hoffmannianum. Analyses of the V4 region of the 18S rRNA gene also indicated the presence P. compressum, P. hoffmannianum, P. foraminosum, P. fukuyoi, and P. nanum. These findings provide the first biogeographical evidence of toxigenic benthic dinoflagellates along the west coast of Sweden, in the absence of ongoing monitoring to include epibenthic dinoflagellates. Harmful events due to the presence of Coolia at shellfish aquaculture sites along the Kattegat-Skagerrak are likely to be rather marginal because C. monotis is not known to be toxigenic. In any case, as a preliminary assessment, the results highlight the risk of diarrhetic shellfish poisoning (DSP) events caused by P. lima, which may affect the development and sustainability of shellfish aquaculture in the region.},
}
@article {pmid36190581,
year = {2022},
author = {Eminaga, O and Ge, TJ and Shkolyar, E and Laurie, MA and Lee, TJ and Hockman, L and Jia, X and Xing, L and Liao, JC},
title = {An Efficient Framework for Video Documentation of Bladder Lesions for Cystoscopy: A Proof-of-Concept Study.},
journal = {Journal of medical systems},
volume = {46},
number = {11},
pages = {73},
pmid = {36190581},
issn = {1573-689X},
support = {R01 CA260426/CA/NCI NIH HHS/United States ; R01 CA260426/NH/NIH HHS/United States ; },
mesh = {*Cystoscopy/methods ; Diagnostic Imaging ; Documentation ; Humans ; Urinary Bladder/diagnostic imaging/pathology ; *Urinary Bladder Neoplasms/diagnostic imaging/surgery ; },
abstract = {Processing full-length cystoscopy videos is challenging for documentation and research purposes. We therefore designed a surgeon-guided framework to extract short video clips with bladder lesions for more efficient content navigation and extraction. Screenshots of bladder lesions were captured during transurethral resection of bladder tumor, then manually labeled according to case identification, date, lesion location, imaging modality, and pathology. The framework used the screenshot to search for and extract a corresponding 10-seconds video clip. Each video clip included a one-second space holder with a QR barcode informing the video content. The success of the framework was measured by the secondary use of these short clips and the reduction of storage volume required for video materials. From 86 cases, the framework successfully generated 249 video clips from 230 screenshots, with 14 erroneous video clips from 8 screenshots excluded. The HIPPA-compliant barcodes provided information of video contents with a 100% data completeness. A web-based educational gallery was curated with various diagnostic categories and annotated frame sequences. Compared with the unedited videos, the informative short video clips reduced the storage volume by 99.5%. In conclusion, our framework expedites the generation of visual contents with surgeon's instruction for cystoscopy and potential incorporation of video data towards applications including clinical documentation, education, and research.},
}
@article {pmid36189978,
year = {2022},
author = {Gopurenko, D and Bellis, G and Pengsakul, T and Siriyasatien, P and Thepparat, A},
title = {DNA Barcoding of Culicoides Latreille (Diptera: Ceratopogonidae) From Thailand Reveals Taxonomic Inconsistencies and Novel Diversity Among Reported Sequences.},
journal = {Journal of medical entomology},
volume = {59},
number = {6},
pages = {1960-1970},
doi = {10.1093/jme/tjac142},
pmid = {36189978},
issn = {1938-2928},
mesh = {Animals ; *Ceratopogonidae/genetics ; DNA Barcoding, Taxonomic ; Thailand ; DNA ; Phylogeny ; },
abstract = {Recent focus on Culicoides species diversity in Thailand was prompted by a need to identify vectors responsible for the transmission of African Horse Sickness in that country. To assist rapid genetic identification of species, we sampled mitochondrial cytochrome c oxidase subunit I (COI) DNA barcodes (N = 78) from 40 species of Culicoides biting midge from Thailand, including 17 species for which DNA barcodes were previously unavailable. The DNA barcodes were assigned to 39 Barcode Identification Numbers (BINs) representing terminal genetic clusters at the Barcode of Life Data systems (BOLD). BINs assisted with comparisons to published conspecific DNA barcodes and allowed partial barcodes obtained from seven specimens to be associated with BINs by their similarity. Some taxonomic issues were revealed and attributed to the possible misidentification of earlier reported specimens as well as a potential synonymy of C. elbeli Wirth &amp; Hubert and C. menglaensis Chu &amp; Liu. Comparison with published BINs also revealed genetic evidence of divergent population processes and or potentially cryptic species in 16 described taxa, flagged by their high levels of COI sequence difference among conspecifics. We recommend the BOLD BIN system to researchers preparing DNA barcodes of vouchered species for public release. This will alert them to taxonomic incongruencies between their records and publicly released DNA barcodes, and also flag genetically deep and potentially novel diversity in described species.},
}
@article {pmid36182371,
year = {2022},
author = {Güzel, &#x130; and Munch, E and Khasawneh, FA},
title = {Detecting bifurcations in dynamical systems with CROCKER plots.},
journal = {Chaos (Woodbury, N.Y.)},
volume = {32},
number = {9},
pages = {093111},
doi = {10.1063/5.0102421},
pmid = {36182371},
issn = {1089-7682},
abstract = {Existing tools for bifurcation detection from signals of dynamical systems typically are either limited to a special class of systems or they require carefully chosen input parameters and a significant expertise to interpret the results. Therefore, we describe an alternative method based on persistent homology-a tool from topological data analysis-that utilizes Betti numbers and CROCKER plots. Betti numbers are topological invariants of topological spaces, while the CROCKER plot is a coarsened but easy to visualize data representation of a one-parameter varying family of persistence barcodes. The specific bifurcations we investigate are transitions from periodic to chaotic behavior or vice versa in a one-parameter collection of differential equations. We validate our methods using numerical experiments on ten dynamical systems and contrast the results with existing tools that use the maximum Lyapunov exponent. We further prove the relationship between the Wasserstein distance to the empty diagram and the norm of the Betti vector, which shows that an even more simplified version of the information has the potential to provide insight into the bifurcation parameter. The results show that our approach reveals more information about the shape of the periodic attractor than standard tools, and it has more favorable computational time in comparison with the Rösenstein algorithm for computing the maximum Lyapunov exponent.},
}
@article {pmid36180921,
year = {2022},
author = {Jin, T and Husseneder, C and Foil, L},
title = {Assigning Culicoides larvae to species using DNA barcoding of adult females and phylogenetic associations.},
journal = {Parasites &amp; vectors},
volume = {15},
number = {1},
pages = {349},
pmid = {36180921},
issn = {1756-3305},
support = {12214180//U.S. Department of Agriculture/ ; },
mesh = {Animals ; *Ceratopogonidae ; DNA ; DNA Barcoding, Taxonomic ; *Deer ; Electron Transport Complex IV/genetics ; Female ; Insect Vectors ; Larva/genetics ; Phylogeny ; RNA, Ribosomal, 18S ; Water ; },
abstract = {BACKGROUND: Orbivirus-induced hemorrhagic diseases cause high mortality in wild and captive white-tailed deer in North America. The role of different Culicoides species in Orbivirus transmission outside of areas of intensive animal production has not been established. At our study location, bluetongue virus (BTV) RNA-positive female Culicoides debilipalpis pools have been detected annually since 2012 when BTV transmission was noted in a captive deer herd. Identifying specific larval habitats of suspected vectors at active transmission sites is crucial both for identifying the source of the vectors and for subsequently planning intervention actions. Since C. debilipalpis larvae are known to develop in tree holes, this study was designed to use DNA barcoding to identify larvae collected from tree holes.<br><br>METHODS: Adult female Culicoides were collected using light or emergence traps and morphologically identified to 11 species. Culicoides sonorensis were also obtained from a laboratory colony. Substrate was collected from tree holes and flooded with water to harvest floating larvae. Total DNA from three to seven adult females per species and 19 larvae was extracted. Two loci of the nuclear 18S ribosomal RNA (rRNA) gene, one locus each of the mitochondrial cytochrome oxidase subunit I (COI) gene and the nuclear 28S rRNA gene were amplified using loci-specific primers.<br><br>RESULTS: All 61 adults were sequenced at each of the four loci under study. Since no single locus delineated all putative species and the COI locus yielded unreliable pseudogenes for two individuals of C. arboricola, sequences of all four loci were concatenated to maximize species separation and allow for larval association with identified adults. Sixteen larvae were clearly assigned to species based on DNA barcoding and phylogenetic results. Multiple larvae were assigned to each of the C. debilipalpis clade, the C. villosipennis clade, the C. arboricola clade and the C. nanus clade.<br><br>CONCLUSIONS: Of the approximately 62 species described in the southeast USA, 21 have now been barcoded and sequences are publicly available. In this study, we constructed a database composed of species-specific sequences of adult Culicoides and then identified larvae to species by matching their corresponding sequences with adults. Since Culicoides larvae are difficult to identify, using DNA barcoding to facilitate larval habitat surveys can be a valuable tool.},
}
@article {pmid36171596,
year = {2022},
author = {Zhu, S and Liu, Q and Qiu, S and Dai, J and Gao, X},
title = {DNA barcoding: an efficient technology to authenticate plant species of traditional Chinese medicine and recent advances.},
journal = {Chinese medicine},
volume = {17},
number = {1},
pages = {112},
pmid = {36171596},
issn = {1749-8546},
support = {2017A020213014//the Guangdong Province Science and Technology Plan Project/ ; 2019GDASYL-0503002//the Special Project of International Science and Technology Cooperation Guidance of Guangdong Academy of Sciences/ ; SKLAM002-2018//the Open Fund Project of the State Key Laboratory of Applied Microbiology Southern China/ ; },
abstract = {Traditional Chinese medicine (TCM) plays an important role in the global traditional health systems. However, adulterated and counterfeit TCM is on the rise. DNA barcoding is an effective, rapid, and accurate technique for identifying plant species. In this study, we collected manuscripts on DNA barcoding published in the last decade and summarized the use of this technique in identifying 50 common Chinese herbs listed in the Chinese pharmacopoeia. Based on the dataset of the major seven DNA barcodes of plants in the NCBI database, the strengths and limitations of the barcodes and their derivative barcoding technology, including single-locus barcode, multi-locus barcoding, super-barcoding, meta-barcoding, and mini-barcoding, were illustrated. In addition, the advances in DNA barcoding, particularly identifying plant species for TCM using machine learning technology, are also reviewed. Finally, the selection process of an ideal DNA barcoding technique for accurate identification of a given TCM plant species was also outlined.},
}
@article {pmid36170831,
year = {2022},
author = {Qazi, MA and Salim, SK and Brown, KR and Mikolajewicz, N and Savage, N and Han, H and Subapanditha, MK and Bakhshinyan, D and Nixon, A and Vora, P and Desmond, K and Chokshi, C and Singh, M and Khoo, A and Macklin, A and Khan, S and Tatari, N and Winegarden, N and Richards, L and Pugh, T and Bock, N and Mansouri, A and Venugopal, C and Kislinger, T and Goyal, S and Moffat, J and Singh, SK},
title = {Characterization of the minimal residual disease state reveals distinct evolutionary trajectories of human glioblastoma.},
journal = {Cell reports},
volume = {40},
number = {13},
pages = {111420},
doi = {10.1016/j.celrep.2022.111420},
pmid = {36170831},
issn = {2211-1247},
support = {//CIHR/Canada ; },
mesh = {*Brain Neoplasms/pathology ; *Glioblastoma/genetics/pathology ; Humans ; Neoplasm Recurrence, Local/genetics/pathology ; Neoplasm, Residual/genetics ; Neoplastic Stem Cells/pathology ; Proteomics ; },
abstract = {Recurrence of solid tumors renders patients vulnerable to advanced, treatment-refractory disease state with mutational and oncogenic landscape distinctive from initial diagnosis. Improving outcomes for recurrent cancers requires a better understanding of cell populations that expand from the post-therapy, minimal residual disease (MRD) state. We profile barcoded tumor stem cell populations through therapy at tumor initiation, MRD, and recurrence in our therapy-adapted, patient-derived xenograft models of glioblastoma (GBM). Tumors show distinct patterns of recurrence in which clonal populations exhibit either a pre-existing fitness advantage or an equipotency fitness acquired through therapy. Characterization of the MRD state by single-cell and bulk RNA sequencing reveals a tumor-intrinsic immunomodulatory signature with prognostic significance at the transcriptomic level and in proteomic analysis of cerebrospinal fluid (CSF) collected from patients with GBM. Our results provide insight into the innate and therapy-driven dynamics of human GBM and the prognostic value of interrogating the MRD state in solid cancers.},
}
@article {pmid36170783,
year = {2022},
author = {Reynolds, S and Hedberg, M and Herrin, B and Chelladurai, JRJJ},
title = {Analysis of the complete mitochondrial genomes of Dermacentor albipictus suggests a species complex.},
journal = {Ticks and tick-borne diseases},
volume = {13},
number = {6},
pages = {102038},
doi = {10.1016/j.ttbdis.2022.102038},
pmid = {36170783},
issn = {1877-9603},
abstract = {Dermacentor albipictus is a one-host tick broadly distributed across North America. There are two easily recognizable color variants - ornate and inornate/brown - that have been taxonomically synonymized. Based on mt-cox1 and mt-16S data, there is also evidence for two genetic lineages which do not match the color variants. We present for the first time the complete mitochondrial genomes of the two color variants of D. albipictus including representatives of each lineage. The AT-rich genomes are 14,822 bp - 14,865 bp in length and contain 13 protein coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes, arranged in the conserved type 3 metastriate mitochondrial genome order. The overall differences were 10.66% between the mitochondrial genomes of D. albipictus ornate variant lineage 1 and lineage 2, 10.51% between lineage 1 and inornate/brown variant and 5.87% between lineage 2 and inornate/brown variant. The inornate/brown variant did not form a separate lineage and all inornate isolates were found to belong to lineage 2. Ornate variant isolates occurred in both lineage 1 and 2. The high divergence of the mitochondrial genome suggests that D. albipictus may represent a species complex. Other barcoding genes that may help capture the genetic differences between color and lineage variants include nad1, nad2, nad5, cox1 and atp8 loci. The mtDNA data generated in this study are available in GenBank (Accession numbers: OM678457 - OM678459 and ON032564 - ON032573) for future studies on tick taxonomy, phylogenetics and molecular epidemiology.},
}
@article {pmid36167070,
year = {2022},
author = {Shayya, HJ and Kahiapo, JK and Duffié, R and Lehmann, KS and Bashkirova, L and Monahan, K and Dalton, RP and Gao, J and Jiao, S and Schieren, I and Belluscio, L and Lomvardas, S},
title = {ER stress transforms random olfactory receptor choice into axon targeting precision.},
journal = {Cell},
volume = {185},
number = {21},
pages = {3896-3912.e22},
pmid = {36167070},
issn = {1097-4172},
support = {F30 DC019263/DC/NIDCD NIH HHS/United States ; R01 DC015451/DC/NIDCD NIH HHS/United States ; R21 DC017823/DC/NIDCD NIH HHS/United States ; },
mesh = {Animals ; Axons/*metabolism ; *Endoplasmic Reticulum Stress ; Mice ; Olfactory Bulb ; Olfactory Receptor Neurons/metabolism ; *Receptors, Odorant/genetics/metabolism ; Transcription Factors/metabolism ; },
abstract = {Olfactory sensory neurons (OSNs) convert the stochastic choice of one of >1,000 olfactory receptor (OR) genes into precise and stereotyped axon targeting of OR-specific glomeruli in the olfactory bulb. Here, we show that the PERK arm of the unfolded protein response (UPR) regulates both the glomerular coalescence of like axons and the specificity of their projections. Subtle differences in OR protein sequences lead to distinct patterns of endoplasmic reticulum (ER) stress during OSN development, converting OR identity into distinct gene expression signatures. We identify the transcription factor Ddit3 as a key effector of PERK signaling that maps OR-dependent ER stress patterns to the transcriptional regulation of axon guidance and cell-adhesion genes, instructing targeting precision. Our results extend the known functions of the UPR from a quality-control pathway that protects cells from misfolded proteins to a sensor of cellular identity that interprets physiological states to direct axon wiring.},
}
@article {pmid36164865,
year = {2022},
author = {Zhai, EA and Mi, WJ and Cui, Y and Hong, WF and Wang, YS and Guo, XY and Zou, HQ and Yan, YH},
title = {[Comparison between macroscopic identification and DNA barcoding identification of Amomi Fructus].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {47},
number = {17},
pages = {4600-4608},
doi = {10.19540/j.cnki.cjcmm.20220515.101},
pmid = {36164865},
issn = {1001-5302},
mesh = {Camphanes ; Camphor/analysis ; DNA Barcoding, Taxonomic ; *Drugs, Chinese Herbal/chemistry ; *Fruit/chemistry/genetics ; Limonene/analysis ; Reproducibility of Results ; },
abstract = {This study aims to explore the consistency between macroscopic identification and DNA barcoding identification of Amomi Fructus. With the DNA barcoding identification results, we evaluated the reliability of identifying Amomi Fructus quality by combining macroscopic traits with main volatile chemical components. Thirteen batches of Amomi Fructus samples were collected for identification. Firstly, the morphological and sensory characteristics of each sample were observed and recorded according to the standard in Chinese Pharmacopoeia(2020 edition). The 100-fruit weight, longitudinal diameter, transverse diameter, and longitudinal diameter-to-transverse diameter ratio were measured, which correspond to large, solid, and full kernel representing good quality in the sensory evaluation. The odor value detected by electronic nose and major volatile components(borneol, camphor, limonene, and borneol acetate) correspond to the sensory evaluation of strong odor representing good quality. Secondly, DNA barcoding was employed to identify the 13 batches of samples. Finally, clustering analysis was performed for the main volatile components and macroscopic traits, and the identification results were compared with those of DNA barcoding. Except two batches of samples(No.6 and No.10), the macroscopic identification showed the results consistent with those of DNA barcoding, with an identification rate of 84.62%. The clustering results of the content of four volatile chemical components and macroscopic traits were also consistent with the DNA barcoding identification results. DNA barcoding can verify the results of macroscopic identification and provide a scientific basis for the inheritance and development of macroscopic identification. Moreover, the combination of macroscopic traits and chemical components demonstrates higher accuracy in the quality evaluation of Chinese medicinal materials.},
}
@article {pmid36163343,
year = {2022},
author = {Fan, ZF and Ma, CL},
title = {Comparative chloroplast genome and phylogenetic analyses of Chinese Polyspora.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {15984},
pmid = {36163343},
issn = {2045-2322},
mesh = {China ; Evolution, Molecular ; *Genome, Chloroplast ; Phylogeny ; *Theaceae/genetics ; },
abstract = {Polyspora Sweet (Theaceae) are winter ornamental landscape plants native to southern and southeastern Asia, some of which have medicinal value. The chloroplast (cp) genome data of Polyspora are scarce, and the gene evolution and interspecific relationship are still unclear. In this study, we sequenced and annotated Polyspora chrysandra cp genome and combined it with previously published genomes for other Chinese Polyspora species. The results showed that cp genomes of six Chinese Polyspora varied in length between 156,452 bp (P. chrysandra) and 157,066 bp (P. speciosa), but all contained 132 genes, with GC content of 37.3%, and highly similar genes distribution and codon usage. A total of eleven intergenic spacer regions were found having the highest levels of divergence, and eight divergence hotspots were identified as molecular markers for Phylogeography and genetic diversity studies in Polyspora. Gene selection pressure suggested that five genes were subjected to positive selection. Phylogenetic relationships among Polyspora species based on the complete cp genomes were supported strongly, indicating that the cp genomes have the potential to be used as super barcodes for further analysis of the phylogeny of the entire genus. The cp genomes of Chinese Polyspora species will provide valuable information for species identification, molecular breeding and evolutionary analysis of genus Polyspora.},
}
@article {pmid36161270,
year = {2023},
author = {L'Ambert, G and Gendrot, M and Briolant, S and Nguyen, A and Pages, S and Bosio, L and Palomo, V and Gomez, N and Benoit, N and Savini, H and Pradines, B and Durand, GA and Leparc-Goffart, I and Grard, G and Fontaine, A},
title = {Analysis of trapped mosquito excreta as a noninvasive method to reveal biodiversity and arbovirus circulation.},
journal = {Molecular ecology resources},
volume = {23},
number = {2},
pages = {410-423},
pmid = {36161270},
issn = {1755-0998},
support = {//Direction de la Formation de la Recherche et de l'Innovation (DFRI)/ ; PDH-2-NRBC-2-B-2113//Direction G&#xe9;n&#xe9;rale de l'Armement (DGA)/ ; },
mesh = {Animals ; Humans ; *Culicidae ; *Arboviruses/genetics ; *West Nile virus ; *Flavivirus ; Biodiversity ; },
abstract = {Emerging and endemic mosquito-borne viruses can be difficult to detect and monitor because they often cause asymptomatic infections in human or vertebrate animals or cause nonspecific febrile illness with a short recovery waiting period. Some of these pathogens circulate into complex cryptic cycles involving several animal species as reservoir or amplifying hosts. Detection of cases in vertebrate hosts can be complemented by entomological surveillance, but this method is not adapted to low infection rates in mosquito populations that typically occur in low or nonendemic areas. We identified West Nile virus circulation in Camargue, a wetland area in South of France, using a cost-effective xenomonitoring method based on the molecular detection of virus in excreta from trapped mosquitoes. We also succeeded at identifying the mosquito species community on several sampling sites, together with the vertebrate hosts on which they fed prior to being captured using amplicon-based metabarcoding on mosquito excreta without processing any mosquitoes. Mosquito excreta-based virus surveillance can complement standard surveillance methods because it is cost-effective and does not require personnel with a strong background in entomology. This strategy can also be used to noninvasively explore the ecological network underlying arbovirus circulation.},
}
@article {pmid36161013,
year = {2022},
author = {Wang, J and Yan, Z and Zhong, P and Shen, Z and Yang, G and Ma, L},
title = {Screening of universal DNA barcodes for identifying grass species of Gramineae.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {998863},
pmid = {36161013},
issn = {1664-462X},
abstract = {There is currently international interest in applying DNA barcoding as a tool for plant species discrimination and identification. In this study, we evaluated the utility of four candidate plant DNA barcoding regions [rbcL, matK, trnL-F, and internal transcribed spacer (ITS)] in seven genera of Gramineae including Agropyron, Bromus, Elymus, Elytrigia, Festuca, Leymus, and Lolium. Fourteen accessions were analyzed, and matK and ITS showed the highest species, subspecies, and variety discriminatory power, each resolving 11 accessions. Species discrimination using rbcL and trnL-F was lower, resolving 7 and 8 accessions, respectively. Subspecies and variety discrimination using rbcL and trnL-F could not identify 4 accessions of Agropyron. A technical system can be established using the proposed DNA barcode to rapidly and reliably identify the seven genera of Gramineae. This study serves as a "useful reference" for identifying the genetic diversity of grass germplasm resources. DNA barcoding can be utilized to uncover the relatives of different species within the same family or between different families. It can also be used to determine the related groups of important herbage, turfgrass, and crops and provide crucial background information for discovering excellent genes and improving existing crop varieties.},
}
@article {pmid36158041,
year = {2022},
author = {Yoo, S and Cho, Y and Kim, JS and Kim, M and Lim, YW},
title = {Fourteen Unrecorded Species of Agaricales Underw. (Agaricomycetes, Basidiomycota) from the Republic of Korea.},
journal = {Mycobiology},
volume = {50},
number = {4},
pages = {219-230},
pmid = {36158041},
issn = {1229-8093},
abstract = {Agaricales species form pileate-stipitate fruiting bodies and play important roles in maintaining the terrestrial ecosystem as decomposers, symbionts, and pathogens. Approximately 23,000 Agaricales species have been known worldwide, and 937 species have been recorded in the Republic of Korea. However, most of them were identified solely based on morphological characteristics that often led to misidentifications. The specimens collected from 2018 to 2020 in the Republic of Korea were identified based on phylogenetic analysis of the internal transcribed spacer (ITS) sequences. Their identities were confirmed by microscopic characteristics. As a result, 14 Agaricales species were discovered for the first time in the Republic of Korea. They belonged to nine genera: Agaricus, Calocybe, Cortinarius, Hygrocybe, Inocybe, Lepista, Leucoagaricus, Marasmius, and Psathyrella. Detailed macroscopic and microscopic descriptions were provided to help distinguish these species. The morphological and molecular data provided in this study will serve as reliable references for the identification of Agaricales species.},
}
@article {pmid36156326,
year = {2023},
author = {Emerson, BC and Borges, PAV and Cardoso, P and Convey, P and deWaard, JR and Economo, EP and Gillespie, RG and Kennedy, S and Krehenwinkel, H and Meier, R and Roderick, GK and Strasberg, D and Thébaud, C and Traveset, A and Creedy, TJ and Meramveliotakis, E and Noguerales, V and Overcast, I and Morlon, H and Papadopoulou, A and Vogler, AP and Arribas, P and Andújar, C},
title = {Collective and harmonized high throughput barcoding of insular arthropod biodiversity: Toward a Genomic Observatories Network for islands.},
journal = {Molecular ecology},
volume = {32},
number = {23},
pages = {6161-6176},
doi = {10.1111/mec.16683},
pmid = {36156326},
issn = {1365-294X},
support = {810729//European Commission/ ; },
mesh = {Animals ; *Arthropods/genetics ; Biodiversity ; Genomics ; Plants/genetics ; DNA Barcoding, Taxonomic/methods ; Islands ; },
abstract = {Current understanding of ecological and evolutionary processes underlying island biodiversity is heavily shaped by empirical data from plants and birds, although arthropods comprise the overwhelming majority of known animal species, and as such can provide key insights into processes governing biodiversity. Novel high throughput sequencing (HTS) approaches are now emerging as powerful tools to overcome limitations in the availability of arthropod biodiversity data, and hence provide insights into these processes. Here, we explored how these tools might be most effectively exploited for comprehensive and comparable inventory and monitoring of insular arthropod biodiversity. We first reviewed the strengths, limitations and potential synergies among existing approaches of high throughput barcode sequencing. We considered how this could be complemented with deep learning approaches applied to image analysis to study arthropod biodiversity. We then explored how these approaches could be implemented within the framework of an island Genomic Observatories Network (iGON) for the advancement of fundamental and applied understanding of island biodiversity. To this end, we identified seven island biology themes at the interface of ecology, evolution and conservation biology, within which collective and harmonized efforts in HTS arthropod inventory could yield significant advances in island biodiversity research.},
}
@article {pmid36147664,
year = {2022},
author = {Kleino, I and Frolovaitė, P and Suomi, T and Elo, LL},
title = {Computational solutions for spatial transcriptomics.},
journal = {Computational and structural biotechnology journal},
volume = {20},
number = {},
pages = {4870-4884},
pmid = {36147664},
issn = {2001-0370},
abstract = {Transcriptome level expression data connected to the spatial organization of the cells and molecules would allow a comprehensive understanding of how gene expression is connected to the structure and function in the biological systems. The spatial transcriptomics platforms may soon provide such information. However, the current platforms still lack spatial resolution, capture only a fraction of the transcriptome heterogeneity, or lack the throughput for large scale studies. The strengths and weaknesses in current ST platforms and computational solutions need to be taken into account when planning spatial transcriptomics studies. The basis of the computational ST analysis is the solutions developed for single-cell RNA-sequencing data, with advancements taking into account the spatial connectedness of the transcriptomes. The scRNA-seq tools are modified for spatial transcriptomics or new solutions like deep learning-based joint analysis of expression, spatial, and image data are developed to extract biological information in the spatially resolved transcriptomes. The computational ST analysis can reveal remarkable biological insights into spatial patterns of gene expression, cell signaling, and cell type variations in connection with cell type-specific signaling and organization in complex tissues. This review covers the topics that help choosing the platform and computational solutions for spatial transcriptomics research. We focus on the currently available ST methods and platforms and their strengths and limitations. Of the computational solutions, we provide an overview of the analysis steps and tools used in the ST data analysis. The compatibility with the data types and the tools provided by the current ST analysis frameworks are summarized.},
}
@article {pmid36145832,
year = {2022},
author = {Qian, ZH and Munywoki, JM and Wang, QF and Malombe, I and Li, ZZ and Chen, JM},
title = {Molecular Identification of African Nymphaea Species (Water Lily) Based on ITS, trnT-trnF and rpl16.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {18},
pages = {},
pmid = {36145832},
issn = {2223-7747},
support = {32070231//National Natural Science Foundation of China/ ; Y323771W07 and SAJC201322//Sino Africa Joint Research Center/ ; },
abstract = {The genus Nymphaea L. (water lily) is the most diverse genus in the family Nymphaeaceae, with more than 50 species worldwide, including 11 species distributed in Africa. The complex and variable morphology of Nymphaea makes it extremely difficult to accurately identify species based on morphological characteristics alone. DNA barcoding has the potential to identify species accurately. In this study, 158 Nymphaea populations from seven African countries were collected for species identification by ITS, trnT-trnF and rpl16. Additionally, the three candidate DNA barcodes were evaluated for genetic distance and barcoding gap. Based on the comprehensive analysis of sequence similarity, genetic distance method and phylogenetic tree, a total of 137 populations of seven Nymphaea species from African were well-identified, including N. lotus, N. petersiana, N. zenkeri, N. nouchali var. caerulea, N. micrantha and N. guineensis. ITS has more obvious advantages over trnT-trnF, rpl16 and trnT-trnF+rpl16 in the intraspecific and interspecific variation differences and barcoding gap and can identify most species. trnT-trnF and rpl16 can identify some species that cannot be identified by ITS. The results showed that it is more appropriate to apply the combination of ITS and trnT-trnF (or rpl16) as the DNA barcoding of Nymphaea. Additionally, this study further enriches the DNA barcoding database of Nymphaea and provides a reference basis for studying taxonomy, phylogenetics and evolutionary origin of Nymphaea.},
}
@article {pmid36145422,
year = {2022},
author = {Menegon, M and Tomazatos, A and Severini, F and Raele, DA and Lilja, T and Werner, D and Boccolini, D and Toma, L and Vasco, I and Lühken, R and Kampen, H and Cafiero, MA and Di Luca, M},
title = {Molecular Characterization of Anopheles algeriensis Theobald, 1903 (Diptera: Culicidae) Populations from Europe.},
journal = {Pathogens (Basel, Switzerland)},
volume = {11},
number = {9},
pages = {},
pmid = {36145422},
issn = {2076-0817},
abstract = {Anopheles algeriensis Theobald, 1903, considered a competent vector of Plasmodium parasites, is a mosquito species widely distributed in the Mediterranean area but rare in Northern and Central Europe. The disappearance of its suitable breeding sites in Italy is having a detrimental effect on the occurrence of this species once common along the Southern coasts and on the islands. Recently, molecular investigations have renewed interest in this species, highlighting a genetic heterogeneity among European populations. In this study, An. algeriensis populations from Italy, Germany, Romania, and Sweden were analyzed by molecular typing of the intergenic transcribed spacer 2 (ITS2). The mitochondrial cytochrome c oxidase subunit I (COI) was also analyzed from specimens collected in Southern Italy. With the aim of investigating the population structure of this species, the obtained data were compared to all publicly available ITS2 and COI sequences of An. algeriensis, adding specimens from Spain and Portugal. The analyses of both markers indicate a split between Iberian populations (Spain for ITS2 and Spain/Portugal for COI) and those from the rest of Europe, revealing two cryptic species. The analysis of the COI barcode revealed a third clade representing a cryptic species present in Danube Delta (Romania). The high levels of genetic divergence among the clades of An. algeriensis indicate that this taxon represents a species complex, potentially harboring several distinct cryptic species.},
}
@article {pmid36144352,
year = {2022},
author = {Young, D and Joshi, A and Huang, L and Munk, B and Wurzbacher, C and Youssef, NH and Elshahed, MS and Moon, CD and Ochsenreither, K and Griffith, GW and Callaghan, TM and Sczyrba, A and Lebuhn, M and Flad, V},
title = {Simultaneous Metabarcoding and Quantification of Neocallimastigomycetes from Environmental Samples: Insights into Community Composition and Novel Lineages.},
journal = {Microorganisms},
volume = {10},
number = {9},
pages = {},
pmid = {36144352},
issn = {2076-2607},
support = {I 3808/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Anaerobic fungi from the herbivore digestive tract (Neocallimastigomycetes) are primary lignocellulose modifiers and hold promise for biotechnological applications. Their molecular detection is currently difficult due to the non-specificity of published primer pairs, which impairs evolutionary and ecological research with environmental samples. We developed and validated a Neocallimastigomycetes-specific PCR primer pair targeting the D2 region of the ribosomal large subunit suitable for screening, quantifying, and sequencing. We evaluated this primer pair in silico on sequences from all known genera, in vitro with pure cultures covering 16 of the 20 known genera, and on environmental samples with highly diverse microbiomes. The amplified region allowed phylogenetic differentiation of all known genera and most species. The amplicon is about 350 bp long, suitable for short-read high-throughput sequencing as well as qPCR assays. Sequencing of herbivore fecal samples verified the specificity of the primer pair and recovered highly diverse and so far unknown anaerobic gut fungal taxa. As the chosen barcoding region can be easily aligned and is taxonomically informative, the sequences can be used for classification and phylogenetic inferences. Several new Neocallimastigomycetes clades were obtained, some of which represent putative novel lineages such as a clade from feces of the rodent Dolichotis patagonum (mara).},
}
@article {pmid36144015,
year = {2022},
author = {DiSalvo, M and Cortés-Llanos, B and LaBelle, CA and Murdoch, DM and Allbritton, NL},
title = {Scalable Additive Construction of Arrayed Microstructures with Encoded Properties for Bioimaging.},
journal = {Micromachines},
volume = {13},
number = {9},
pages = {},
pmid = {36144015},
issn = {2072-666X},
support = {CA224763/CA/NCI NIH HHS/United States ; R01 GM123542/GM/NIGMS NIH HHS/United States ; GM123542/GM/NIGMS NIH HHS/United States ; R01 AI150465/AI/NIAID NIH HHS/United States ; R01 CA224763/CA/NCI NIH HHS/United States ; R01 CA233811/CA/NCI NIH HHS/United States ; CA233811/CA/NCI NIH HHS/United States ; },
abstract = {Microarrays are essential components of analytical instruments. The elements of microarrays may be imbued with additional functionalities and encodings using composite materials and structures, but traditional microfabrication methods present substantial barriers to fabrication, design, and scalability. In this work, a tool-free technique was reported to additively batch-construct micromolded, composite, and arrayed microstructures. The method required only a compatible carrier fluid to deposit a material onto a substrate with some topography. Permutations of this basic fabrication approach were leveraged to gain control over the volumes and positions of deposited materials within the microstructures. As a proof of concept, cell micro-carrier arrays were constructed to demonstrate a range of designs, compositions, functionalities, and applications for composite microstructures. This approach is envisioned to enable the fabrication of complex composite biological and synthetic microelements for biosensing, cellular analysis, and biochemical screening.},
}
@article {pmid36142769,
year = {2022},
author = {Drozdova, P and Saranchina, A and Madyarova, E and Gurkov, A and Timofeyev, M},
title = {Experimental Crossing Confirms Reproductive Isolation between Cryptic Species within Eulimnogammarus verrucosus (Crustacea: Amphipoda) from Lake Baikal.},
journal = {International journal of molecular sciences},
volume = {23},
number = {18},
pages = {},
pmid = {36142769},
issn = {1422-0067},
support = {22-14-00128//Russian Science Foundation/ ; },
mesh = {*Amphipoda/genetics ; Animals ; Crustacea ; Lakes ; Phylogeny ; Reproductive Isolation ; },
abstract = {Ancient lakes are known speciation hotspots. One of the most speciose groups in the ancient Lake Baikal are gammaroid amphipods (Crustacea: Amphipoda: Gammaroidea). There are over 350 morphological species and subspecies of amphipods in Baikal, but the extent of cryptic variation is still unclear. One of the most common species in the littoral zone of the lake, Eulimnogammarus verrucosus (Gerstfeldt, 1858), was recently found to comprise at least three (pseudo)cryptic species based on molecular data. Here, we further explored these species by analyzing their mitogenome-based phylogeny, genome sizes with flow cytometry, and their reproductive compatibility. We found divergent times of millions of years and different genome sizes in the three species (6.1, 6.9 and 8 pg), further confirming their genetic separation. Experimental crossing of the western and southern species, which are morphologically indistinguishable and have adjacent ranges, showed their separation with a post-zygotic reproductive barrier, as hybrid embryos stopped developing roughly at the onset of gastrulation. Thus, the previously applied barcoding approach effectively indicated the separate biological species within E. verrucosus. These results provide new data for investigating genome evolution and highlight the need for precise tracking of the sample origin in any studies in this morphospecies.},
}
@article {pmid36142138,
year = {2022},
author = {Borroni, D and Paytuví-Gallart, A and Sanseverino, W and Gómez-Huertas, C and Bonci, P and Romano, V and Giannaccare, G and Rechichi, M and Meduri, A and Oliverio, GW and Rocha-de-Lossada, C and On Behalf Of Lucy Consortium, },
title = {Exploring the Healthy Eye Microbiota Niche in a Multicenter Study.},
journal = {International journal of molecular sciences},
volume = {23},
number = {18},
pages = {},
pmid = {36142138},
issn = {1422-0067},
mesh = {Cross-Sectional Studies ; DNA ; *Health Promotion ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {PURPOSE: This study aims to explore and characterize healthy eye microbiota.<br><br>METHODS: Healthy subjects older than 18 years were selected for this descriptive cross-sectional study. Samples were collected with an eSwab with 1 mL of Liquid Amies Medium (Copan Brescia, Italy). Following DNA extraction, libraries preparation, and amplification, PCR products were purified and end-repaired for barcode ligation. Libraries were pooled to a final concentration of 26 pM. Template preparation was performed with Ion Chef according to Ion 510, Ion 520, and Ion 530 Kit-Chef protocol. Sequencing of the amplicon libraries was carried out on a 520 or 530 chip using the Ion Torrent S5 system (Thermo Fisher; Waltham, MA, USA). Raw reads were analyzed with GAIA (v 2.02).<br><br>RESULTS: Healthy eye microbiota is a low-diversity microbiome. The vast majority of the 137 analyzed samples were highly enriched with Staphylococcus, whereas only in a few of them, other genera such as Bacillus, Pseudomonas, and Corynebacterium predominate. We found an average of 88 genera with an average Shannon index of 0.65.<br><br>CONCLUSION: We identified nine different ECSTs. A better understanding of healthy eye microbiota has the potential to improve disease diagnosis and personalized regimens to promote health.},
}
@article {pmid36140845,
year = {2022},
author = {Acharya, GC and Mohanty, S and Dasgupta, M and Sahu, S and Singh, S and Koundinya, AVV and Kumari, M and Naresh, P and Sahoo, MR},
title = {Molecular Phylogeny, DNA Barcoding, and ITS2 Secondary Structure Predictions in the Medicinally Important Eryngium Genotypes of East Coast Region of India.},
journal = {Genes},
volume = {13},
number = {9},
pages = {},
pmid = {36140845},
issn = {2073-4425},
mesh = {DNA Barcoding, Taxonomic/methods ; DNA, Plant/chemistry/genetics ; *Eryngium ; Genetic Markers/genetics ; Genotype ; Pharmaceutical Preparations ; Phylogeny ; *Plants, Medicinal/genetics ; RNA ; },
abstract = {Commercial interest in the culinary herb, Eryngium foetidum L., has increased worldwide due to its typical pungency, similar to coriander or cilantro, with immense pharmaceutical components. The molecular delimitation and taxonomic classification of this lesser-known medicinal plant are restricted to conventional phenotyping and DNA-based marker evaluation, which hinders accurate identification, genetic conservation, and safe utilization. This study focused on species discrimination using DNA sequencing with chloroplast-plastid genes (matK, Kim matK, and rbcL) and the nuclear ITS2 gene in two Eryngium genotypes collected from the east coast region of India. The results revealed that matK discriminated between two genotypes, however, Kim matK, rbcL, and ITS2 identified these genotypes as E. foetidum. The ribosomal nuclear ITS2 region exhibited significant inter- and intra-specific divergence, depicted in the DNA barcodes and the secondary structures derived based on the minimum free energy. Although the efficiency of matK genes is better in species discrimination, ITS2 demonstrated polyphyletic phylogeny, and could be used as a reliable marker for genetic divergence studies understanding the mechanisms of RNA molecules. The results of this study provide insights into the scientific basis of species identification, genetic conservation, and safe utilization of this important medicinal plant species.},
}
@article {pmid36138756,
year = {2022},
author = {Tzafesta, E and Saccomanno, B and Zangaro, F and Vadrucci, MR and Specchia, V and Pinna, M},
title = {DNA Barcode Gap Analysis for Multiple Marker Genes for Phytoplankton Species Biodiversity in Mediterranean Aquatic Ecosystems.},
journal = {Biology},
volume = {11},
number = {9},
pages = {},
pmid = {36138756},
issn = {2079-7737},
support = {ImPrEco project N.450//EU ADRION programme/ ; FFABR 2017//Italian Ministry of the University/ ; },
abstract = {The implementation of DNA metabarcoding and environmental DNA (eDNA) to the biodiversity assessment and biomonitoring of aquatic ecosystems has great potential worldwide. However, DNA metabarcoding and eDNA are highly reliant on the coverage of the DNA barcode reference libraries that are currently hindered by the substantial lack of reference sequences. The main objective of this study was to analyze the current coverage of DNA barcode reference libraries for phytoplankton species of the aquatic Mediterranean ecoregion in the southeast of Italy (Apulia Region) in order to assess the applicability of DNA metabarcoding and eDNA in this area. To do so, we investigated three main DNA barcode reference libraries, BOLD Systems, GenBank and SILVA, for the availability of DNA barcodes of the examined phytoplankton species. The gap analysis was conducted for three molecular gene markers, 18S, 16S and COI. The results showed a considerable lack of barcodes for all three markers. However, among the three markers, 18S had a greater coverage in the reference libraries. For the 18S gene marker, the barcode coverage gap across the three types of ecosystems examined was 32.21-39.68%, 60.12-65.19% for the 16S marker gene, and 72.44-80.61 for the COI marker gene. Afterwards, the interspecific genetic distance examined on the most represented molecular marker, 18S, was able to distinguish 80% of the species mined for lakes and 70% for both marine and transitional waters. Conclusively, this work highlights the importance of filling the gaps in the reference libraries, and constitutes the basis towards the advancement of DNA metabarcoding and eDNA application for biodiversity assessment and biomonitoring.},
}
@article {pmid36137118,
year = {2022},
author = {Chaiphongpachara, T and Changbunjong, T and Laojun, S and Nutepsu, T and Suwandittakul, N and Kuntawong, K and Sumruayphol, S and Ruangsittichai, J},
title = {Mitochondrial DNA barcoding of mosquito species (Diptera: Culicidae) in Thailand.},
journal = {PloS one},
volume = {17},
number = {9},
pages = {e0275090},
pmid = {36137118},
issn = {1932-6203},
mesh = {Animals ; *Anopheles/genetics ; *Culicidae/genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial ; Electron Transport Complex IV/genetics ; Mosquito Vectors/genetics ; Phylogeny ; Thailand ; },
abstract = {The correct identification of mosquito species is important for effective mosquito vector control. However, the standard morphological identification of mosquito species based on the available keys is not easy with specimens in the field due to missing or damaged morphological features during mosquito collections, often leading to the misidentification of morphologically indistinguishable. To resolve this problem, we collected mosquito species across Thailand to gather genetic information, and evaluated the DNA barcoding efficacy for mosquito species identification in Thailand. A total of 310 mosquito samples, representing 73 mosquito species, were amplified using mitochondrial cytochrome c oxidase subunit I (COI) primers. The average maximum intraspecific genetic variation of the 73 mosquito species was 1% ranged from 0-5.7%. While, average minimum interspecific genetic variation (the distance to the nearest neighbour) of the 73 mosquito species was 7% ranged from 0.3-12.9%. The identification of success rates based on the "Best Match," "Best Close Match," and "All Species Barcodes" methods were 97.7%, 91.6%, and 81%, respectively. Phylogenetic analyses of Anopheles COI sequences demonstrated a clear separation between almost all species (except for those between An. baimaii and An. dirus), with high bootstrap support values (97%-99%). Furthermore, phylogenetic analyses revealed potential sibling species of An. annularis, An. tessellatus, and An. subpictus in Thailand. Our results indicated that DNA barcoding is an effective molecular approach for the accurate identification of mosquitoes in Thailand.},
}
@article {pmid36137040,
year = {2022},
author = {Wattrus, SJ and Smith, ML and Rodrigues, CP and Hagedorn, EJ and Kim, JW and Budnik, B and Zon, LI},
title = {Quality assurance of hematopoietic stem cells by macrophages determines stem cell clonality.},
journal = {Science (New York, N.Y.)},
volume = {377},
number = {6613},
pages = {1413-1419},
pmid = {36137040},
issn = {1095-9203},
support = {U01 HL134812/HL/NHLBI NIH HHS/United States ; R01 HL144780/HL/NHLBI NIH HHS/United States ; K01 DK111790/DK/NIDDK NIH HHS/United States ; F31 HL149154/HL/NHLBI NIH HHS/United States ; P01 HL032262/HL/NHLBI NIH HHS/United States ; P01 HL131477/HL/NHLBI NIH HHS/United States ; RC2 DK120535/DK/NIDDK NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; T32 HL007574/HL/NHLBI NIH HHS/United States ; R24 OD017870/OD/NIH HHS/United States ; U54 DK110805/DK/NIDDK NIH HHS/United States ; R24 DK092760/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; *Apoptosis ; Calbindin 2/genetics/physiology ; *Calreticulin/genetics/metabolism ; *Cell Communication ; *Clonal Hematopoiesis/genetics/physiology ; Embryo, Nonmammalian ; *Hematopoietic Stem Cells/physiology ; *Macrophages/physiology ; Zebrafish ; Zebrafish Proteins/genetics/physiology ; },
abstract = {Tissue-specific stem cells persist for a lifetime and can differentiate to maintain homeostasis or transform to initiate cancer. Despite their importance, there are no described quality assurance mechanisms for newly formed stem cells. We observed intimate and specific interactions between macrophages and nascent blood stem cells in zebrafish embryos. Macrophage interactions frequently led to either removal of cytoplasmic material and stem cell division or complete engulfment and stem cell death. Stressed stem cells were marked by surface Calreticulin, which stimulated macrophage interactions. Using cellular barcoding, we found that Calreticulin knock-down or embryonic macrophage depletion reduced the number of stem cell clones that established adult hematopoiesis. Our work supports a model in which embryonic macrophages determine hematopoietic clonality by monitoring stem cell quality.},
}
@article {pmid36136983,
year = {2022},
author = {Zhang, X and Zhang, Y and Mao, J and Lan, Y and Zhang, Z and Lei, H},
title = {The ITS analysis and identification of Actinidia eriantha and its related species.},
journal = {PloS one},
volume = {17},
number = {9},
pages = {e0274358},
pmid = {36136983},
issn = {1932-6203},
mesh = {*Actinidia/genetics ; Phylogeny ; Plant Roots/genetics ; Plants ; Powders ; },
abstract = {The dried plant material of medically important plant Actinidia eriantha especially when it remains in the form of powder often look morphologically similar to its related species. The lack of efficient methods to distinguish the authentic material from other similar species leads to chances of adulteration. The molecular authentication of herbal plant materials such as the internal transcribed spacer (ITS) sequences is considered as more reliable method compared to morphological traits. In this study, we aim to evaluate the potential of identification for roots of A. eriantha and its related species by ITS sequences. The lengths of ITS regions ranged from 624 to 636 bp with GC content ranging from 50.96% to 59.55%. A total of 194 variation sites and 46 haplotypes were formed in 185 samples. Among them, the roots of A. eriantha possessed specific sites at 85bp (C), 205bp (T), 493bp (C), 542bp (G), 574bp (C), 582bp (T) and 610bp (G), while A. hemsleyana, A. callosa, A. valvata and A. polygama have their own specific sites. The inter-specific genetic distance among 8 Actinidia species in the range 2.28% to 11.00%. The phylogenetic tree constructed with ITS, ITS1 and ITS2 region showed that the ITS sequences have higher potential for identification in 8 Actinidia species. However, as to A. eriantha, A. hemsleyana and A. valvata, these three barcodes have the same identification ability. The ITS regions indicated that different samples from same species can be grouped together, except for A. arguta and A. melanandrah. In conclusion, the ITS sequences can be used as an efficient DNA barcode for the identification of A. eriantha and its related species.},
}
@article {pmid36135707,
year = {2022},
author = {Burgess, TI and White, D and Sapsford, SJ},
title = {Comparison of Primers for the Detection of Phytophthora (and Other Oomycetes) from Environmental Samples.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {9},
pages = {},
pmid = {36135707},
issn = {2309-608X},
abstract = {Many oomycetes are important plant pathogens that cause devastating diseases in agricultural fields, orchards, urban areas, and natural ecosystems. Limitations and difficulties associated with isolating these pathogens have led to a strong uptake of DNA metabarcoding and mass parallel sequencing. At least 21 primer combinations have been designed to amplify oomycetes, or more specifically, Phytophthora species, from environmental samples. We used the Illumina sequencing platform to compare 13 primer combinations on mock communities and environmental samples. The primer combinations tested varied significantly in their ability to amplify Phytophthora species in a mock community and from environmental samples; this was due to either low sensitivity (unable to detect species present in low concentrations) or a lack of specificity (an inability to amplify some species even if they were present in high concentrations). Primers designed for oomycetes underestimated the Phytophthora community compared to Phytophthora-specific primers. We recommend using technical replicates, primer combinations, internal controls, and a phylogenetic approach for assigning a species identity to OTUs or ASVs. Particular care must be taken if sampling substrates where hybrid species could be expected. Overall, the choice of primers should depend upon the hypothesis being tested.},
}
@article {pmid36135704,
year = {2022},
author = {Bertini, L and Perazzolli, M and Proietti, S and Capaldi, G and Savatin, DV and Bigini, V and Longa, CMO and Basaglia, M and Favaro, L and Casella, S and Fongaro, B and Polverino de Laureto, P and Caruso, C},
title = {Biodiversity and Bioprospecting of Fungal Endophytes from the Antarctic Plant Colobanthus quitensis.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {9},
pages = {},
pmid = {36135704},
issn = {2309-608X},
support = {PNRA18_00147//Ministero dell'Universit&#xe0; e della Ricerca/ ; },
abstract = {Microorganisms from extreme environments are considered as a new and valuable reservoir of bioactive molecules of biotechnological interest and are also utilized as tools for enhancing tolerance to (a)biotic stresses in crops. In this study, the fungal endophytic community associated with the leaves of the Antarctic angiosperm Colobanthus quitensis was investigated as a new source of bioactive molecules. We isolated 132 fungal strains and taxonomically annotated 26 representative isolates, which mainly belonged to the Basidiomycota division. Selected isolates of Trametes sp., Lenzites sp., Sistotrema sp., and Peniophora sp. displayed broad extracellular enzymatic profiles; fungal extracts from some of them showed dose-dependent antitumor activity and inhibited the formation of amyloid fibrils of α-synuclein and its pathological mutant E46K. Selected fungal isolates were also able to promote secondary root development and fresh weight increase in Arabidopsis and tomato and antagonize the growth of pathogenic fungi harmful to crops. This study emphasizes the ecological and biotechnological relevance of fungi from the Antarctic ecosystem and provides clues to the bioprospecting of Antarctic Basidiomycetes fungi for industrial, agricultural, and medical applications.},
}
@article {pmid36135657,
year = {2022},
author = {Miller, AN and Karakehian, J and Raudabaugh, DB},
title = {Next-Generation Sequencing of Ancient and Recent Fungarium Specimens.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {9},
pages = {},
pmid = {36135657},
issn = {2309-608X},
abstract = {Fungaria are an unmatched resource for providing genetic data from authoritative, taxonomically-correct fungal species, especially type specimens. These specimens serve to anchor species hypotheses by enabling the correct taxonomic placement of taxa in systematic studies. The DNA from ancient specimens older than 30 years is commonly fragmented, and sometimes highly contaminated by exogenous, non-target fungal DNA, making conventional PCR amplification and Sanger sequencing difficult or impossible. Here, we present the results of DNA extraction, PCR amplification of the ITS2 region, and Illumina MiSeq Nano sequencing of nine recent and 11 ancient specimens, including seven type specimens. The taxa sampled included a range of large and fleshy, to small and tough, or small, melanized specimens of Discina, Gyromitra, Propolis, Stictis, and Xerotrema, with a culture of Lasiosphaeria serving as a positive control. DNA was highly fragmented and in very low quantity for most samples, resulting in inconclusive or incorrect results for all but five samples. Taxonomically-correct sequences were generated from the holotype specimens of G. arctica, G. korshinskii, and G. leucoxantha, from the neotype of G. ussuriensis, and from the positive control. Taxonomic assignments were confirmed through morphology, top BLASTn hits, and maximum likelihood phylogenetic analyses. Though this study was not cost-effective due to the small number of samples submitted and few generating correct sequences, it did produce short DNA barcode fragments for four type specimens that are essential for their correct taxonomic placement in our ongoing systematic studies.},
}
@article {pmid36135630,
year = {2022},
author = {Su, W and Xu, R and Bhunjun, CS and Tian, S and Dai, Y and Li, Y and Phukhamsakda, C},
title = {Diversity of Ascomycota in Jilin: Introducing Novel Woody Litter Taxa in Cucurbitariaceae.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {9},
pages = {},
pmid = {36135630},
issn = {2309-608X},
support = {number 32100007//National Natural Science Foundation of China/ ; D17014//Program of Creation and Utilization of Germplasm of Mushroom Crop of "111" Project/ ; },
abstract = {Cucurbitariaceae has a high biodiversity worldwide on various hosts and is distributed in tropical and temperate regions. Woody litters collected in Changchun, Jilin Province, China, revealed a distinct collection of fungi in the family Cucurbitariaceae based on morphological and molecular data. Phylogenetic analyses of the concatenated matrix of the internal transcribed spacer (ITS) region, the large subunit (LSU) of ribosomal DNA, the RNA polymerase II subunit (rpb2), the translation elongation factor 1-alpha (tef1-α) and β-tubulin (β-tub) genes indicated that the isolates represent Allocucurbitaria and Parafenestella species based on maximum likelihood (ML), maximum parsimony (MP) and Bayesian analysis (BPP). We report four novel species: Allocucurbitaria mori, Parafenestella changchunensis, P. ulmi and P. ulmicola. The importance of five DNA markers for species-level identification in Cucurbitariaceae was determined by Assemble Species by Automatic Partitioning (ASAP) analyses. The protein-coding gene β-tub is determined to be the best marker for species level identification in Cucurbitariaceae.},
}
@article {pmid37091220,
year = {2022},
author = {Obase, K},
title = {Morphological characteristics of ectomycorrhizas formed by in vitro synthesis between conifer seedlings and Tuber mycelial strains of the Puberulum clade isolated in Japan.},
journal = {Mycoscience},
volume = {63},
number = {1},
pages = {39-44},
pmid = {37091220},
issn = {1340-3540},
abstract = {Seedlings of Pinus densiflora and Abies sachalinensis were inoculated with Tuber mycelial strains of the Puberulum clade in vitro to examine the morphological characteristics of their ectomycorrhizas. Axenically germinated seedlings were inoculated with the mycelia of five taxa from the Puberulum clade and grown in glass jars for 4 mo in an illuminated incubator. The seedlings were successfully colonized by the inoculated Tuber strains, as confirmed by the nuclear ribosomal internal transcribed spacer barcoding of the synthesized ectomycorrhizas. The ectomycorrhizas were characterized by a pale yellow to brown color, short needle-shaped cystidia, and net-like hyphal arrangement, and epidermoid cells on the mantle surface; notably, these features are similar to the ectomycorrhizas of various Puberulum clade members. As the ectomycorrhizas of different Tuber species are indistinguishable by morphological characters, molecular techniques are necessary to identify ectomycorrhizas formed by Tuber species within the Puberulum clade.},
}
@article {pmid36776149,
year = {2021},
author = {Gracia Villacampa, E and Larsson, L and Mirzazadeh, R and Kvastad, L and Andersson, A and Mollbrink, A and Kokaraki, G and Monteil, V and Schultz, N and Appelberg, KS and Montserrat, N and Zhang, H and Penninger, JM and Miesbach, W and Mirazimi, A and Carlson, J and Lundeberg, J},
title = {Genome-wide spatial expression profiling in formalin-fixed tissues.},
journal = {Cell genomics},
volume = {1},
number = {3},
pages = {100065},
pmid = {36776149},
issn = {2666-979X},
abstract = {Formalin-fixed paraffin embedding (FFPE) is the most widespread long-term tissue preservation approach. Here, we report a procedure to perform genome-wide spatial analysis of mRNA in FFPE-fixed tissue sections, using well-established, commercially available methods for imaging and spatial barcoding using slides spotted with barcoded oligo(dT) probes to capture the 3' end of mRNA molecules in tissue sections. We applied this method for expression profiling and cell type mapping in coronal sections from the mouse brain to demonstrate the method's capability to delineate anatomical regions from a molecular perspective. We also profiled the spatial composition of transcriptomic signatures in two ovarian carcinosarcoma samples, exemplifying the method's potential to elucidate molecular mechanisms in heterogeneous clinical samples. Finally, we demonstrate the applicability of the assay to characterize human lung and kidney organoids and a human lung biopsy specimen infected with SARS-CoV-2. We anticipate that genome-wide spatial gene expression profiling in FFPE biospecimens will be used for retrospective analysis of biobank samples, which will facilitate longitudinal studies of biological processes and biomarker discovery.},
}
@article {pmid36761999,
year = {2021},
author = {Guerrero, JJ and Pozas, M and Ortiz, AS},
title = {First record and DNA barcoding of Donacaulaniloticus (Zeller, 1867) from the Iberian Peninsula (Lepidoptera: Crambidae).},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e70193},
pmid = {36761999},
issn = {1314-2828},
abstract = {BACKGROUND: Donacaulaniloticus (Zeller, 1867) is known from south-eastern Europe, Middle East and Turkey to Central Asia, northern India and China and widely distributed in North Africa (Morocco, Algeria, Libya and Egypt).<br><br>NEW INFORMATION: Donacaulaniloticus (Zeller 1867) is recorded for the first time from the Iberian Peninsula and the first DNA barcode sequence is published and compared with other European and North American Donacaula species.},
}
@article {pmid36452345,
year = {2021},
author = {Ahmed, MZ and Moore, MR and Rohrig, EA and McKenzie, CL and Liu, D and Feng, J and Normark, BB and Miller, DR},
title = {Taxonomic and identification review of adventive Fiorinia Targioni Tozzetti (Hemiptera, Coccomorpha, Diaspididae) of the United States.},
journal = {ZooKeys},
volume = {1065},
number = {},
pages = {141-203},
pmid = {36452345},
issn = {1313-2989},
abstract = {This work provides general descriptions, illustrations, molecular diagnostic data, taxonomic keys, slide mounting recommendations, and Florida distribution records for Fiorinia Targioni Tozzetti species occurring in the USA. Species treated are F.externa Ferris, F.fioriniae (Targioni Tozzetti), F.japonica Kuwana, F.pinicola Maskell, F.phantasma Cockerell &amp; Robinson, F.proboscidaria Green, and F.theae Green. New descriptions of second-instar males and females of all seven species in addition to first-instar nymphs and adult females of F.phantasma and F.proboscidaria are presented. Taxonomic keys to second-instar males and females are developed for the first time and previously available taxonomic keys to first-instar nymphs and adult females are improved. DNA sequences were used to further evaluate the monophyly of Fiorinia and provide additional diagnostic tools for Fiorinia species. Multigene phylogenetic analyses, COI barcoding methods, and examination of type material indicate that F.yongxingensis Liu, Cai &amp; Feng, 2020, syn. nov. is a junior synonym of F.phantasma. A morphological survey of the genus demonstrates, for the first time, the utility of second-instar males for diagnostics. This study will help inform regulatory and pest management decisions by facilitating morphological and molecular identification of adventive Fiorinia species occurring in the USA.},
}
@article {pmid36606145,
year = {2021},
author = {Obok, EE and Aikpokpodion, PO and Ani, OC and Allainguillaume, J and Wetten, A},
title = {Cacao swollen shoot virus detection and DNA barcoding of its vectors and putative vectors in Theobroma cacao L. by using polymerase chain reaction.},
journal = {Biotechnologia},
volume = {102},
number = {3},
pages = {229-244},
pmid = {36606145},
issn = {2353-9461},
abstract = {Cacao swollen shoot virus (CSSV) is an endemic pathogen causing significant economic losses to cacao (Theobroma cacao L.) production in West Africa. There is limited updated report on the occurrence, spread, genetic diversity and species of CSSV and its mealybug vectors, especially in Nigeria. Nigeria is presently lagging behind in the search for resistance to CSSV and its vectors in T. cacao L. The present study aimed to map and screen for the presence of CSSV and its natural vectors - female mealybugs (Pseudococcidae: Hemiptera) in cacao plantations in Nigeria. Symptomatic and asymptomatic cacao leaves and whole female mealybug samples were collected from major cacao-growing areas in Nigeria - Abia, Akwa Ibom, Cross River, Edo, Ondo and Oyo States. A total of 2568 cacao leaves from 1052 cacao trees were screened with polymerase chain reaction (PCR) using an open reading frame 1 (ORF 1) CSSV-specific primer pair. PCR screening of the mealybug species was performed using the cytochrome c oxidase subunit I (COI) gene. A combination of scanning electron microscopy (SEM) and histology for morphological identification and DNA barcoding enabled to characterise the female mealybug species. The results revealed that CSSV and its mealybug vectors are present in the major cacaogrowing areas in Nigeria. Although CSSV and its vectors have been previously reported in Cross River, Ondo and Oyo States, our results present the first documented evidence of CSSV emergence and its mealybug vectors in Abia, Akwa Ibom and Edo States. We also present the first report of Pseudococcus jackbeardsleyi (Gimpel and Miller) mealybug species on cacao in Nigeria. In conclusion, it is pertinent to re-establish coordinated routine survey and monitoring of CSSV and its mealybug vector presence in T. cacao L. in Nigeria.},
}
@article {pmid36700107,
year = {2021},
author = {Morisse, P and Lemaitre, C and Legeai, F},
title = {LRez: a C++ API and toolkit for analyzing and managing Linked-Reads data.},
journal = {Bioinformatics advances},
volume = {1},
number = {1},
pages = {vbab022},
pmid = {36700107},
issn = {2635-0041},
abstract = {MOTIVATION: Linked-Reads technologies combine both the high quality and low cost of short-reads sequencing and long-range information, through the use of barcodes tagging reads which originate from a common long DNA molecule. This technology has been employed in a broad range of applications including genome assembly, phasing and scaffolding, as well as structural variant calling. However, to date, no tool or API dedicated to the manipulation of Linked-Reads data exist.<br><br>RESULTS: We introduce LRez, a C++ API and toolkit that allows easy management of Linked-Reads data. LRez includes various functionalities, for computing numbers of common barcodes between genomic regions, extracting barcodes from BAM files, as well as indexing and querying BAM, FASTQ and gzipped FASTQ files to quickly fetch all reads or alignments containing a given barcode. LRez is compatible with a wide range of Linked-Reads sequencing technologies, and can thus be used in any tool or pipeline requiring barcode processing or indexing, in order to improve their performances.<br><br>LRez is implemented in C++, supported on Unix-based platforms and available under AGPL-3.0 License at https://github.com/morispi/LRez, and as a bioconda module.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.},
}
@article {pmid36620432,
year = {2021},
author = {Hajdari, A and Pulaj, B and Schmiderer, C and Mala, X and Wilson, B and Lluga-Rizani, K and Mustafa, B},
title = {A phylogenetic analysis of the wild Tulipa species (Liliaceae) of Kosovo based on plastid and nuclear DNA sequence.},
journal = {Advanced genetics (Hoboken, N.J.)},
volume = {2},
number = {3},
pages = {e202100016},
pmid = {36620432},
issn = {2641-6573},
abstract = {In Kosovo, the genus Tulipa is represented by eight taxa, most of which form a species complex surrounding Tulipa scardica. To investigate the phylogenetic relationship of these Tulipa species a Bayesian analysis was undertaken using the ITS nuclear marker and trnL-trnF, rbcL and psbA-trnH plastid markers. The resulting phylogenetic trees show that Kosovarian Tulipa species consistently group into two main clades, the subgenera Eriostemones and Tulipa. Furthermore, our analyses provide some evidence that the subspecies of Tulipa sylvestris are genetically distinguishable, however not significantly enough to support their reclassification as species. In contrast, the markers provide some novel information to reassess the species concepts of the T. scardica complex. Our data provide support for the synonymisation of Tulipa luanica and Tulipa kosovarica under the species Tulipa serbica. Resolution and sampling limitations hinder any concrete conclusion about whether Tulipa albanica and T. scardica are true species, yet our data do provide some support that these are unique taxa and therefore should continue to be treated as such until further clarification. Overall, our work shows that genetic data will be important in determining species concepts in this genus, however, even with a molecular perspective pulling apart closely related taxa can be extremely challenging.},
}
@article {pmid36654283,
year = {2021},
author = {Zheng, JS and Liang, J and Shi, WW and Li, Y and Hu, HG and Tian, CL and Liu, L},
title = {A mirror-image protein-based information barcoding and storage technology.},
journal = {Science bulletin},
volume = {66},
number = {15},
pages = {1542-1549},
doi = {10.1016/j.scib.2021.03.010},
pmid = {36654283},
issn = {2095-9281},
mesh = {Chromatography, Liquid ; *Tandem Mass Spectrometry/methods ; *Proteins/chemistry ; Peptides ; Amino Acid Sequence ; },
abstract = {A mirror-image protein-based information barcoding and storage technology wherein D-amino acids are used to encode information into mirror-image proteins that are chemically synthesized is described. These mirror-image proteins were then fused into various materials from which information-encoded objects were produced. Subsequently, the mirror-image proteins were extracted from the objects using biotin-streptavidin resin-mediated specific enrichment and cleaved using an Ni(II)-mediated selective peptide cleavage. Protein sequencing was accomplished using liquid chromatography/tandem mass spectrometry (LC-MS/MS) and then transcoded into the recorded information. We demonstrated the use of this technology to encode Chinese words into mirror-image proteins, which were then fused onto a poly(ethylene terephthalate) (PET) film and retrieved and decoded by LC-MS/MS sequencing. Compared to information barcoding and storage technologies using natural biopolymers, the mirror-image biopolymers used in our technology may be more stable and durable.},
}
@article {pmid37153067,
year = {2021},
author = {Kumar, P and Shruthi, R and Bindu, I and Raghavendra, P},
title = {Pharmacognosy, phytochemistry, and molecular studies of an important medicinal herb Achillea millefolium L.},
journal = {Ayu},
volume = {42},
number = {2},
pages = {93-102},
pmid = {37153067},
issn = {0974-8520},
abstract = {BACKGROUND: Achillea millefolium L. is traditionally important medicinal herb used for the treatment of various ailments from the centuries. Recent studies showed its biological activities on hay fever, hepato-biliary disorders, and as appetite enhancing drug. It is also reported to be used for the treatments of skin inflammations, wounds, cuts, and abrasions.<br><br>AIM: To investigate preliminary pharmacognostical, phytochemical, and molecular parameters of aerial parts of the drug.<br><br>MATERIALS AND METHODS: A. millefolium was identified and collected from the Himalaya region. The material is properly dried, macro-and microscopic evaluation, phytochemical and molecular studies as per the standard quality control and WHO guidelines.<br><br>RESULTS: The leaves are pinnately lobed, inflorescence compound corymbose. Nonglandular trichomes are uni-seriate, multicellular, and smooth walled; glandular trichomes are bicellular, present throughout the aerial parts. The endodermis is evident in the stem and leaf mesophyll is equifacial. The partial genome sequence analysis showed similarity toward studied species, which can clearly distinguish it from other species of the genus Achillea. The best chromatographic separation was observed with ascentis express C18, 2.7 &#x3bc;m, 100 mm &#xd7; 4.6 mm. The flavonoids and phenolic acids have shown maximum absorbance at 330 nm. The system suitability parameters such as theoretical plate, tailing factor, and resolution met the acceptance criteria with United States pharmacopeia (USP).<br><br>CONCLUSION: The findings of this study will be helpful for the precise identification of the raw drug of A. millefolium from its closely allied species.},
}
@article {pmid36777488,
year = {2021},
author = {Ashkar, GL and Patel, KS and de Jesus, J and Vinnakota, N and Helms, N and Jack, W and Chien, W and Taylor, B},
title = {Evaluation of Decentralized Verifiable Credentials to Authenticate Authorized Trading Partners and Verify Drug Provenance.},
journal = {Blockchain in healthcare today},
volume = {4},
number = {},
pages = {},
pmid = {36777488},
issn = {2573-8240},
abstract = {SUMMARY: In 2013, the Drug Supply Chain Security Act (DSCSA) was signed into law to address the growing threat of counterfeit drugs and to ensure prescription drugs remain safe and effective for patients. As part of this law, US pharmaceutical supply chain stakeholders are required to confirm the authorized status of trading partners for transactions and information disclosures, even when there is no prior business relationship. While larger Authorized Trading Partners (ATPs) have connectivity solutions in place, newer and smaller ATPs have not traditionally participated, including tens of thousands of dispensers. To unlock the full potential of the interoperable system mandated by the DSCSA, the authors tested eXtended ATP (XATP), a blockchain-backed framework for ATP authentication and enhanced verification in a real-world pharmacy with genuine drug packages. The objective of this research study was to prove that electronic authentication and enhanced verification can be achieved between ATPs using a mobile-based solution. Moreover, we tested accurate reading of drug and associated electronic med guides, flagging of expired and recalled drugs, and correct generation of documentation to support saleable returns.<br><br>METHODS: This study involved two dispensers and three participating manufacturers. Dispensers were onboarded to a mobile application and used supporting documentation to authenticate their identities, and then scanned 2D drug barcodes to submit drug verification requests to manufacturers (including 11 additional, randomly selected manufacturers). Genuine and synthetic drug package barcodes were used to test workflows against genuine and synthetic manufacturer serialization data records. Manufacturers authenticated the identity of requesting dispensers with verifiable credentials and responded to verification requests.<br><br>RESULTS: Enhanced drug verification was achieved, with 100% of requests successfully delivered to participating manufacturers and 88% of requests being delivered to other manufacturers (based on the pharmacist selection of random packages from the pharmacy). Drug verification matching against synthetic serialization data records resulted in 86% accuracy, with the 14% error rate attributed to human factors. All barcodes were successfully scanned and provided package-accurate data, and 97% of randomly selected packages successfully generated drug package inserts. All synthetic recalls and expired drugs were successfully flagged. Four of the manufacturers contacted were among the top 15 pharmaceutical manufacturers globally; all four responded.<br><br>CONCLUSIONS: The XATP framework provides a secure, reliable, and seamless remote method to conduct enhanced verification as required by law. Interoperability between manufacturers and dispensers with no prior business relationship can be achieved on 'day zero' using mobile devices that enable digital authentication and rapid barcode scanning. As users retain control of their own private keys, the framework also mitigates the single-point-of-attack risks associated with centrally managed systems.},
}
@article {pmid37090017,
year = {2021},
author = {Hosoya, T},
title = {Systematics, ecology, and application of Helotiales: Recent progress and future perspectives for research with special emphasis on activities within JapanHelotiales: Recent progress and future perspectives for research with special emphasis on activities within Japan.},
journal = {Mycoscience},
volume = {62},
number = {1},
pages = {1-9},
pmid = {37090017},
issn = {1340-3540},
abstract = {Helotiales is one of the most diverse groups of apothecial ascomycetes, including 3000-4000 taxa. Recent progress in the systematics, ecology, and their applications through research is herein reviewed based on the experiences of the author with a special emphasis on activities in Japan. In the past 30 y, more than 50 helotialean taxa have been added to the mycobiota of Japan, including new taxa. With the advent of molecular phylogeny, some families have been revisited, such as members with stroma (Sclerotiniaceae and Rutstroemiaceae) or hairs (Hyaloscyphaceae and Lachnaceae). Although the monophyly of Helotiales has not yet been demonstrated, our understanding of its phylogeny has greatly advanced. The unexpected ecological nature represented by endophytism has been revealed through barcoding and other molecular techniques. The research history of ash dieback is also reviewed, and the endophytism/saprophytism of the pathogen on its original host is discussed. Drug discoveries within Helotiales are reviewed, and successful examples are presented. As future perspectives, both the cumulation of occurrence and sequence data of Helotiales is greatly encouraged to elucidate this important group of fungi.},
}
@article {pmid36330198,
year = {2020},
author = {Wang, NB and Beitz, AM and Galloway, KE},
title = {Engineering cell fate: Applying synthetic biology to cellular reprogramming.},
journal = {Current opinion in systems biology},
volume = {24},
number = {},
pages = {18-31},
pmid = {36330198},
issn = {2452-3100},
support = {F32 NS092417/NS/NINDS NIH HHS/United States ; },
abstract = {Cellular reprogramming drives cells from one stable identity to a new cell fate. By generating a diversity of previously inaccessible cell types from diverse genetic backgrounds, cellular reprogramming is rapidly transforming how we study disease. However, low efficiency and limited maturity have limited the adoption of in vitro-derived cellular models. To overcome these limitations and improve mechanistic understanding of cellular reprogramming, a host of synthetic biology tools have been deployed. Recent synthetic biology approaches have advanced reprogramming by tackling three significant challenges to reprogramming: delivery of reprogramming factors, epigenetic roadblocks, and latent donor identity. In addition, emerging insight from the molecular systems biology of reprogramming reveal how systems-level drivers of reprogramming can be harnessed to further advance reprogramming technologies. Furthermore, recently developed synthetic biology tools offer new modes for engineering cell fate.},
}
@article {pmid37128031,
year = {2020},
author = {Lin, K and Chavalarias, D and Panahi, M and Yeh, T and Takimoto, K and Mizoguchi, M},
title = {Mobile-based traceability system for sustainable food supply networks.},
journal = {Nature food},
volume = {1},
number = {11},
pages = {673-679},
pmid = {37128031},
issn = {2662-1355},
abstract = {Traceability is key to ensure food quality and safety from farm to fork, yet high implementation costs and the complexity of the food supply chain pose challenges to its operation. Here we propose a mobile-based bidirectional tracing system for food products that integrates graph data and peer-to-peer architecture. Our system allows data synchronization to happen seamlessly between all connected nodes, as data are gathered through market transactions and all related product information is concatenated by scanning 2D product barcodes. The system's decentralized and flexible structure favours stakeholder involvement and is applicable to various and dynamic food networks. By promoting resource efficiency and transparency of origin, production and distribution, the system ensures mesh surveillance and sheds light on complex food networks, ultimately contributing to the advancement of food research.},
}
@article {pmid36135622,
year = {2022},
author = {Abi Saad, C and Masiello, M and Habib, W and Gerges, E and Sanzani, SM and Logrieco, AF and Moretti, A and Somma, S},
title = {Diversity of Fusarium Species Isolated from Symptomatic Plants Belonging to a Wide Range of Agri-Food and Ornamental Crops in Lebanon.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {9},
pages = {},
pmid = {36135622},
issn = {2309-608X},
abstract = {Lebanon is a small Mediterranean country with different pedoclimatic conditions that allow the growth of both temperate and tropical plants. Currently, few studies are available on the occurrence and diversity of Fusarium species on Lebanese crops. A wide population of Fusarium strains was isolated from different symptomatic plants in the last 10 years. In the present investigation, a set of 134 representative strains were molecularly identified by sequencing the translation elongation factor, used in Fusarium as a barcoding gene. Great variability was observed, since the strains were grouped into nine different Fusarium Species Complexes (SCs). Fusarium oxysporum SC and Fusarium solani SC were the most frequent (53% and 24%, respectively). Members of important mycotoxigenic SCs were also detected: F. fujikuroi SC (7%), F. sambucinum SC (5%), F. incarnatum-equiseti SC (3%), and F. tricinctum SC (4%). Two strains belonging to F. lateritium SC, a single strain belonging to F. burgessii SC, and a single strain belonging to F. redolens SC were also detected. This paper reports, for the first time, the occurrence of several Fusarium species on Lebanese host plants. The clear picture of the Fusarium species distribution provided in this study can pose a basis for both a better understanding of the potential phytopathological and toxicological risks and planning future Fusarium management strategies in Lebanon.},
}
@article {pmid36135556,
year = {2022},
author = {Querner, P and Szucsich, N and Landsberger, B and Erlacher, S and Trebicki, L and Grabowski, M and Brimblecombe, P},
title = {Identification and Spread of the Ghost Silverfish (Ctenolepisma calvum) among Museums and Homes in Europe.},
journal = {Insects},
volume = {13},
number = {9},
pages = {},
pmid = {36135556},
issn = {2075-4450},
support = {Heritage_2020-043_Modelling-Museum//Austrian Academy of Science/ ; },
abstract = {Ctenolepisma calvum was first described in Sri Lanka (Ceylon) in 1910, and this island is probably the origin of this species. Later, it was also found in the Caribbean (Cuba and Trinidad and Tobago). Up until the present, it has only been identified within buildings (a synanthropic species), and its natural habitat is unknown. In 2007, it was discovered in Germany and was considered a neobiotic species of Lepismatidae in Europe. It has rapidly spread throughout Europe and beyond in recent years. This led us to analyze the available data of the first occurrences in Germany, Austria, and other European countries. Furthermore, we compared the spread inside of museums in Vienna (Austria) and Berlin (Germany). These museums have been monitored for a long period with sticky traps, representing the best source of information on the dispersion dynamics of Ctenolepisma calvum. We found a scattered occurrence of this species in 18 countries in Europe (including Russia and Ukraine). The first record for Poland has not previously been published; however, this species has been present there since 2014. Surprisingly, it was found in Hungary in 2003, but a record was only published online in 2021. Additionally, in Germany and Austria, where most data are available, the spread of the species does not follow any clear pattern. In museums in Berlin, the species has only been found in one location. In contrast, the species rapidly spread in museums in Vienna between 2014 and 2021, from four to 30 locations, and it is now a well-established species with occasional high abundance. We examined the spread of the species at three spatial scales: (i) Europe, (ii) national, and (iii) regional. Our observations indicate that it is possibly distributed with materials (packaging material, hygiene articles, paper, cardboard, and collection items). Little is yet known about the biology of this introduced pest. We describe its preferred habitat within buildings, its climate requirements, and its potential to act as a new museum pest in Central Europe. This species seems to thrive at room temperature in buildings. Further impact on the species due to climate change in the future is also discussed. We offer a simple morphological key and a detailed identification table to help correct species identification.},
}
@article {pmid36135495,
year = {2022},
author = {Zhang, X and Yang, D and Kang, Z},
title = {Net-Winged Midge Genus Blepharicera Macquart (Diptera: Blephariceridae) in China: The First DNA Barcode Database with Descriptions of Four New Species and Notes on Distribution.},
journal = {Insects},
volume = {13},
number = {9},
pages = {},
pmid = {36135495},
issn = {2075-4450},
support = {ZR2019BC034//the Shandong Provincial Natural Science Foundation, China/ ; 663-1119008, 663-1118015//the High-level Talents Funds of Qingdao Agricultural University, China/ ; },
abstract = {Mitochondrial (mt) cytochrome c oxidase 1 (COI) gene is more and more widely used for DNA barcoding, which provides a rapid and timely identification as this technique is not limited by polymorphism, sex, and life stages and fundamentally complements traditional evolutionary taxonomy. The present study generated 33 mt COI sequences of seven Chinese Blepharicera Macquart, 1843 species with an average of 594 bp, which represent the first DNA barcode database for Chinese Blepharicera. Genetic distance analysis reveals that intraspecific distances in the genus are generally less than 1.7%, and interspecific distances range from 5.4% to 20.3%. Phylogenetic analysis shows that each species recovered in our analyses is separated from all neighboring species. Based on molecular and morphological data, four Blepharicera species from China, B. beishanica sp. nov., B. dushanzica sp. nov., B. nigra sp. nov. and B. xinjiangica sp. nov., are described and illustrated as new to science. Identification keys for adults and larvae of Chinese Blepharicera are also presented. Geographical analysis shows that Southwest China is the species’ richest region. Our results will be useful in tackling taxonomic problems, understanding species distribution, and resolving nomenclature conflicts associated with Blepharicera species.},
}
@article {pmid36128177,
year = {2022},
author = {Li, N and Bian, F and Wei, X and Cai, L and Gu, H and Zhao, Y and Shang, L},
title = {Pollen-Inspired Photonic Barcodes with Prickly Surface for Multiplex Exosome Capturing and Screening.},
journal = {Research (Washington, D.C.)},
volume = {2022},
number = {},
pages = {9809538},
pmid = {36128177},
issn = {2639-5274},
abstract = {Exosomes, which play an important role in intercellular communication, are closely related to the pathogenesis of disease. However, their effective capture and multiplex screening are still challenging. Here, inspired by the unique structure of pollens, we present novel photonic crystal (PhC) barcodes with prickly surface by hydrothermal synthesis for multiplex exosome capturing and screening. These pollen-inspired PhC barcodes are imparted with extremely high specific surface area and excellent prickly surface nanostructures, which can improve the capture rate and detection sensitivity of exosomes. As the internal periodic structures are kept during the hydrothermal synthesis process, the pollen-inspired PhC barcodes exhibit obvious and stable structural colors for identification, which enables multiplex detection of exosomes. Thus, the pollen-inspired PhC barcodes can not only effectively capture and enrich cancer-related exosomes but also support multiplex screening of exosomes with high sensitivity. These features make the prickly PhC barcodes ideal for the analysis of exosomes in medical diagnosis.},
}
@article {pmid36124863,
year = {2022},
author = {Xie, YL and Mound, LA and Lima, &#xc9;FB and He, SQ and Zhang, HR and Li, YJ},
title = {Molecular Studies of Relationships and Identifications Among Insects of the Subfamily Panchaetothripinae (Thysanoptera, Thripidae).},
journal = {Journal of insect science (Online)},
volume = {22},
number = {5},
pages = {},
pmid = {36124863},
issn = {1536-2442},
support = {31860614//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Bayes Theorem ; China ; Peptide Elongation Factor 1 ; Phylogeny ; *Thysanoptera/genetics ; },
abstract = {The Panchaetothripinae comprises 42 genera and 146 species of leaf-feeding thrips, some of which are horticultural pests. We examined representatives of the 18 genera that include most of these pests. For species delimitation, we used DNA barcoding to produce171 sequences for 40 morphospecies. Most species were found to be monophyletic, although cryptic diversity was evident in 8 presumptive species. A multilocus molecular phylogenetic assessment was based on one mitochondrial (COI) and three nuclear loci (EF-1α, ITS2, and 28S) from 132 specimens (18 genera and 33 species), representing all genera and ~82% of species in China. Maximum likelihood (ML) and Bayesian inference (BI) confirmed monophyly of each genus with strong support. Monophyly of tribes Panchaetothripini and Monilothripini were refuted, but the well supported tribe Tryphactothripini was confirmed. Rhipiphorothrips was recovered as a sister to the remainder of the genera of Panchaetothripinae combined. Both analyses revealed two major clades. Clade A comprised the majority of the genera, including tribe Tryphactothripini. Clade B included only four genera of which two, Helionothrips and Caliothrips, are particularly species rich. The relationships of some genera remain unresolved.},
}
@article {pmid36124730,
year = {2022},
author = {Gadoin, E and Desnues, C and Bouvier, T and Roque D'orbcastel, E and Auguet, JC and Crochemore, S and Adingra, A and Bettarel, Y},
title = {Tracking spoilage bacteria in the tuna microbiome.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {10},
pages = {},
doi = {10.1093/femsec/fiac110},
pmid = {36124730},
issn = {1574-6941},
mesh = {Animals ; Bacteria/genetics ; Food Microbiology ; Histamine/analysis ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Salts ; *Tuna/genetics/microbiology ; },
abstract = {Like other seafood products, tuna is highly perishable and sensitive to microbial spoilage. Its consumption, whether fresh or canned, can lead to severe food poisoning due to the activity of specific microorganisms, including histamine-producing bacteria. Yet, many grey areas persist regarding their ecology, conditions of emergence, and proliferation in fish. In this study, we used 16S rRNA barcoding to investigate postmortem changes in the bacteriome of fresh and brine-frozen yellowfin tuna (Thunnus albacares), until late stages of decomposition (i.e. 120 h). The results revealed that despite standard refrigeration storage conditions (i.e. 4°C), a diverse and complex spoilage bacteriome developed in the gut and liver. The relative abundance of spoilage bacterial taxa increased rapidly in both organs, representing 82% of the bacterial communities in fresh yellowfin tuna, and less than 30% in brine-frozen tuna. Photobacterium was identified as one of the dominant bacterial genera, and its temporal dynamics were positively correlated with histamine concentration in both gut and liver samples, which ultimately exceeded the recommended sanitary threshold of 50 ppm in edible parts of tuna. The results from this study show that the sanitary risks associated with the consumption of this widely eaten fish are strongly influenced by postcapture storage conditions.},
}
@article {pmid36123605,
year = {2022},
author = {Maes, T and De Corte, Z and Vangestel, C and Virgilio, M and Smitz, N and Djuikwo-Teukeng, FF and Papadaki, MI and Huyse, T},
title = {Large-scale and small-scale population genetic structure of the medically important gastropod species Bulinus truncatus (Gastropoda, Heterobranchia).},
journal = {Parasites &amp; vectors},
volume = {15},
number = {1},
pages = {328},
pmid = {36123605},
issn = {1756-3305},
support = {1S86319N//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Animals ; *Bulinus/parasitology ; *Gastropoda/genetics ; Genetics, Population ; Humans ; Phylogeny ; Schistosoma haematobium/genetics ; },
abstract = {BACKGROUND: Gastropod snails remain strongly understudied, despite their important role in transmitting parasitic diseases. Knowledge of their distribution and population dynamics increases our understanding of the processes driving disease transmission. We report the first study to use high-throughput sequencing (HTS) to elucidate the population genetic structure of the hermaphroditic snail Bulinus truncatus (Gastropoda, Heterobranchia) on a regional (17-150 km) and inter-regional (1000-5400 km) scale. This snail species acts as an intermediate host of Schistosoma haematobium and Schistosoma bovis, which cause human and animal schistosomiasis respectively.<br><br>METHODS: Bulinus truncatus snails were collected in Senegal, Cameroon, Egypt and France and identified through DNA barcoding. A single-end genotyping-by-sequencing (GBS) library, comprising 87 snail specimens from the respective countries, was built and sequenced on an Illumina HiSeq 2000 platform. Reads were mapped against S. bovis and S. haematobium reference genomes to identify schistosome infections, and single nucleotide polymorphisms (SNPs) were scored using the Stacks pipeline. These SNPs were used to estimate genetic diversity, assess population structure and construct phylogenetic trees of B. truncatus.<br><br>RESULTS: A total of 10,750 SNPs were scored and used in downstream analyses. The phylogenetic analysis identified five clades, each consisting of snails from a single country but with two distinct clades within Senegal. Genetic diversity was low in all populations, reflecting high selfing rates, but varied between locations due to habitat variability. Significant genetic differentiation and isolation by distance patterns were observed at both spatial scales, indicating that gene flow is not strong enough to counteract the effects of population bottlenecks, high selfing rates and genetic drift. Remarkably, the population genetic differentiation on a regional scale (i.e. within Senegal) was as large as that between populations on an inter-regional scale. The blind GBS technique was able to pick up parasite DNA in snail tissue, demonstrating the potential of HTS techniques to further elucidate the role of snail species in parasite transmission.<br><br>CONCLUSIONS: HTS techniques offer a valuable toolbox to further investigate the population genetic patterns of intermediate schistosome host snails and the role of snail species in parasite transmission.},
}
@article {pmid36122762,
year = {2022},
author = {Soares, IMN and Polonio, JC and Zequi, JAC and Golias, HC},
title = {Molecular techniques for the taxonomy of Aedes Meigen, 1818 (Culicidae: Aedini): A review of studies from 2010 to 2021.},
journal = {Acta tropica},
volume = {236},
number = {},
pages = {106694},
doi = {10.1016/j.actatropica.2022.106694},
pmid = {36122762},
issn = {1873-6254},
mesh = {*Aedes ; Animals ; *Culicidae ; *DNA, Environmental ; Phylogeny ; },
abstract = {The original description of Aedes Meigen in 1818, written in Latin, was very brief and included a single species, Aedes cinereus. In the last two decades the genus Aedes (Meigen, 1818) has undergone several revisions and reclassifications, with the current proposal being described by Wilkerson in 2015. However, the available keys for morphological identification are still not sufficient to differentiate cryptic species, damaged species, or those with confusing taxonomy. The current study aims to identify and describe the main taxonomic proposals and molecular methodologies available for the identification of the genus Aedes published between the years 2010 and 2021. The main molecular techniques used to identify the genus in the last 10 years, are: Multiplex PCR, DNA barcoding, nuclear and mitochondrial markers, environmental DNA, and bacterial microbiome analysis. This review highlights that there are catalogued data for only a few species of the genus Aedes, being restricted to medically important taxa such as Aedes albopictus and Aedes aegypti. The integrative taxonomy approach is a possibility to reconcile morphological and molecular data to improve species delimitation, contributing to future revisions of the genus.},
}
@article {pmid36121097,
year = {2022},
author = {Luo, X and Kang, B and Chi, X and Xiong, H and Chen, D and Fan, Y and Li, L and Chen, L and Li, A and Gao, J and Lin, H},
title = {[19] F Barcoding Enables Multiplex Detection of Biomarkers Associated with Organ Injury and Cancer.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {61},
number = {46},
pages = {e202211189},
doi = {10.1002/anie.202211189},
pmid = {36121097},
issn = {1521-3773},
mesh = {Mice ; Animals ; Biomarkers ; Magnetic Resonance Spectroscopy ; Magnetic Resonance Imaging ; *Neoplasms/diagnostic imaging/genetics ; *Chemical and Drug Induced Liver Injury ; },
abstract = {Simultaneous detection of multiple biomarkers in complex environments is critical for the in-depth exploration of different biological processes, which is challenging for many current analytical methods due to various limitations. Herein, we report a strategy of [19] F barcoding which takes the advantages of [19] F's high magnetic resonance (MR) sensitivity, prompt signal response to environmental changes, negligible biological background, quantitative signal output, and multiplex capacity. A set of [19] F-barcoded sensors responding to different biomarkers involved in organ injury and cancer are designed, synthesized, and characterized. With these sensors, we accomplish concurrent assessment of different biomarkers in the samples collected from the mice with drug-induced liver/kidney injury or tumor, illustrating the feasibility of this approach for multiplexed detection of different biomarkers in complex environments during various biological processes.},
}
@article {pmid36118301,
year = {2022},
author = {Dietrich, V and Melcher, F},
title = {Mineral Raw Material Supply Chain Transparency and Traceability: Does Provenance Matter in the Supply Chain?.},
journal = {Berg- und huttenmannische Monatshefte},
volume = {167},
number = {12},
pages = {594-597},
pmid = {36118301},
issn = {1613-7531},
abstract = {Raw material supply chains are complex systems. They build on the presence of economically mineable mineral commodities that will undergo several steps until they are finally being used as consumer products. Trustworthiness into the transparency of a supply chain is of increasing importance, both to upstream and downstream companies. Any deviation from best-practice and quality standards in mining, processing and production is critically looked at by consumers. Therefore, certification systems and proof of origin concepts have emerged within the past years, aiming at providing transparency to supply chains. The analytical proof of origin for mineral raw materials could be beneficial to certification schemes in several ways. It represents the least corruptible method of provenance analysis as it relates directly to the chemical composition of the raw material. Other methods, such as documents, tracers, or barcodes, can be outmanoeuvred in one way or another.},
}
@article {pmid36117283,
year = {2022},
author = {Grabner, D and Doliwa, A and Sworobowicz, L and Wysocka, A and Weigand, A and Grabowski, M and Mamos, T and Sures, B},
title = {Microsporidian diversity in the aquatic isopod Asellus aquaticus.},
journal = {Parasitology},
volume = {149},
number = {13},
pages = {1729-1736},
pmid = {36117283},
issn = {1469-8161},
mesh = {Humans ; Animals ; *Microsporidia/genetics ; *Isopoda ; DNA Primers ; Ecosystem ; Geography ; Phylogeny ; },
abstract = {We conducted a molecular survey on microsporidian diversity in different lineages (operational taxonomic units = OTUs) of Asellus aquaticus from 30 sites throughout Europe. Host body length was determined, and DNA was extracted from host tissue excluding the intestine and amplified by microsporidian-specific primers. In total, 247 A. aquaticus specimens were analysed from which 26.7% were PCR-positive for microsporidians, with significantly more infections in larger individuals. Prevalence ranged between 10 and 90%. At 9 sites, no microsporidians were detected. A significant relationship was found between the frequency of infected individuals and habitat type, as well as host OTU. The lowest proportion of infected individuals was detected in spring-habitats (8.7%, n = 46) and the highest in ponds (37.7%, n = 53). Proportion of infected individuals among host OTUs A, D and J was 31.7, 21.7 and 32.1%, respectively. No infections were detected in OTU F. Our results are, however, accompanied by a partially low sample size, as only a minimum of 5 individuals was available at a few locations. Overall, 17 different microsporidian molecular taxonomic units (MICMOTUs) were distinguished with 5 abundant isolates (found in 4–17 host individuals) while the remaining 12 MICMOTUs were “rare” and found only in 1–3 host individuals. No obvious spatio-genetic pattern could be observed. The MICMOTUs predominantly belonged to Nosematida and Enterocytozoonida. The present study shows that microsporidians in A. aquaticus are abundant and diverse but do not show obvious patterns related to host genetic lineages or geography.},
}
@article {pmid36113119,
year = {2022},
author = {Fasullo, M and Dolan, M},
title = {The continuing evolution of barcode applications: Functional toxicology to cell lineage.},
journal = {Experimental biology and medicine (Maywood, N.J.)},
volume = {247},
number = {23},
pages = {2119-2127},
pmid = {36113119},
issn = {1535-3699},
support = {R15 ES023685/ES/NIEHS NIH HHS/United States ; },
mesh = {Cell Lineage/genetics ; *DNA Barcoding, Taxonomic/methods ; *DNA ; Mutation ; },
abstract = {DNA barcoding is a method to identify biological entities, including individual cells, tissues, organs, or species, by unique DNA sequences. With the advent of next generation sequencing (NGS), there has been an exponential increase in data acquisition pertaining to medical diagnosis, genetics, toxicology, ecology, cancer, and developmental biology. While barcoding first gained wide access in identifying species, signature tagged mutagenesis has been useful in elucidating gene function, particularly in microbes. With the advent of CRISPR/CAS9, methodology to profile eukaryotic genes has made a broad impact in toxicology and cancer biology. Designed homing guide RNAs (hgRNAs) that self-target DNA sequences facilitate cell lineage barcoding by introducing stochastic mutations within cell identifiers. While each of these applications has their limitations, the potential of sequence barcoding has yet to be realized. This review will focus on signature-tagged mutagenesis and briefly discuss the history of barcoding, experimental problems, novel detection methods, and future directions.},
}
@article {pmid36109541,
year = {2022},
author = {Oh, JH and Kim, S and Lee, S},
title = {DNA barcodes reveal population-dependent cryptic diversity and various cases of sympatry of Korean leptonetid spiders (Araneae: Leptonetidae).},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {15528},
pmid = {36109541},
issn = {2045-2322},
mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic/methods ; Phylogeny ; *Spiders ; Sympatry ; },
abstract = {Leptonetidae are tiny, rarely encountered spiders that mainly inhabit moist environments, such as caves, leaf litter, and rock piles. Because they are microhabitat specialists, most leptonetid species have short-range endemism, and rarely occur in sympatry. Their small size, relatively simple habitus features and reproductive organ structure increase the difficulty of identification. The identification of leptonetids and other spiders may also be time-consuming due to their sexual dimorphism, polymorphism, and lack of diagnostic characteristics in juveniles. DNA barcoding has been used as an effective tool for species identification to overcome these obstacles. Herein, we conducted a test of DNA barcoding based on 424 specimens of Korean Leptonetidae representing 76 morphospecies. A threshold of 4.2% based on maximum intraspecific genetic divergence was estimated to efficiently differentiate the morphospecies. The species assignments tested by five species delimitation methods (ABGD, ASAP, GMYC, PTP, and bPTP) were consistent with the morphological identifications for only 47 morphospecies (61.8%), indicating many cases of cryptic diversity among the remaining morphospecies. Furthermore, sympatry in leptonetids, which are known to be rare, was revealed to be common in South Korea, especially in epigean species. Our results showed that sympatries within families, congeners, and intraclades potentially occur throughout the entire region of Korea.},
}
@article {pmid36107215,
year = {2022},
author = {Nath, S and Ghosh, N and Ansari, TA and Mundhra, A and Patil, MT and Mane, A and Gopalakrishnan, AV and Rahman, MH and Kumar, M and Radha, and Ghorai, M and Paul, S and Dey, A},
title = {Genetic diversity assessment and biotechnological aspects in Aristolochia spp.},
journal = {Applied microbiology and biotechnology},
volume = {106},
number = {19-20},
pages = {6397-6412},
pmid = {36107215},
issn = {1432-0614},
mesh = {*Aristolochia/chemistry/genetics ; Genetic Markers ; Genetic Variation ; Starch ; *Triterpenes ; },
abstract = {Aristolochia, belonging to the family Aristolochiaceae, has immense ecological significance due to its large size and huge geographic distribution. In the context of dealing with a genus with a huge number of species like Aristolochia, these markers come in handy to precisely identify a particular species and enumerate the genetic diversity. Also, certain species of Aristolochia are economically important due to the presence of secondary metabolites and vast use in traditional and modern medicine. But, the presence of profitable biochemical constituents in Aristolochia is very low and the breeding process of the plant is highly dependable on pollinators. Hence, identifying different biotechnological approaches to fasten the reproductive cycle of Aristolochia and increase the secondary metabolites is of great interest to the researchers. In this study, a comprehensive review has been established on different types of morphological/anatomical markers (starch grains with "Maltese cross"), phytochemical markers (aristolochic acid, triterpenoid, aristolactam etc.) and genetic markers (ISSR, SSR, DNA bar-coding) for various Aristolochia spp. We have also discussed the applications of different biotechnological tools in Aristolochia spp. which include discrete approaches to promote in vitro germination, in vitro shooting, root induction, somatic embryogenesis, synthetic seed production, acclimatization and hardening and sustainable production of secondary metabolites. In a nutshell, the present review is a first of kind approach to comprehensively demonstrate the genetic diversity studies and biotechnological aspects in Aristolochia spp. KEY POINTS: • Insights into the in vitro propagation of Aristolochia spp. • In vitro production and optimization of secondary metabolites. • Assessment of genetic diversity by molecular markers.},
}
@article {pmid36105157,
year = {2022},
author = {Xu, L and Zhang, X and Abd El-Aty, AM and Wang, Y and Cao, Z and Jia, H and Salvador, JP and Hacimuftuoglu, A and Cui, X and Zhang, Y and Wang, K and She, Y and Jin, F and Zheng, L and Pujia, B and Wang, J and Jin, M and Hammock, BD},
title = {A highly sensitive bio-barcode immunoassay for multi-residue detection of organophosphate pesticides based on fluorescence anti-quenching.},
journal = {Journal of pharmaceutical analysis},
volume = {12},
number = {4},
pages = {637-644},
pmid = {36105157},
issn = {2214-0883},
support = {R35 ES030443/ES/NIEHS NIH HHS/United States ; },
abstract = {Balancing the risks and benefits of organophosphate pesticides (OPs) on human and environmental health relies partly on their accurate measurement. A highly sensitive fluorescence anti-quenching multi-residue bio-barcode immunoassay was developed to detect OPs (triazophos, parathion, and chlorpyrifos) in apples, turnips, cabbages, and rice. Gold nanoparticles were functionalized with monoclonal antibodies against the tested OPs. DNA oligonucleotides were complementarily hybridized with an RNA fluorescent label for signal amplification. The detection signals were generated by DNA-RNA hybridization and ribonuclease H dissociation of the fluorophore. The resulting fluorescence signal enables multiplexed quantification of triazophos, parathion, and chlorpyrifos residues over the concentration range of 0.01-25, 0.01-50, and 0.1-50 ng/mL with limits of detection of 0.014, 0.011, and 0.126 ng/mL, respectively. The mean recovery ranged between 80.3% and 110.8% with relative standard deviations of 7.3%-17.6%, which correlate well with results obtained by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The proposed bio-barcode immunoassay is stable, reproducible and reliable, and is able to detect low residual levels of multi-residue OPs in agricultural products.},
}
@article {pmid36103708,
year = {2022},
author = {Mullis, MN and Ghione, C and Lough-Stevens, M and Goldstein, I and Matsui, T and Levy, SF and Dean, MD and Ehrenreich, IM},
title = {Complex genetics cause and constrain fungal persistence in different parts of the mammalian body.},
journal = {Genetics},
volume = {222},
number = {3},
pages = {},
pmid = {36103708},
issn = {1943-2631},
support = {R35 GM130381/GM/NIGMS NIH HHS/United States ; R01 GM110255/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Humans ; Mice ; Alleles ; Chromosome Mapping/methods ; Saccharomyces cerevisiae/genetics ; *Mycoses/microbiology ; Brain/microbiology ; Kidney/microbiology ; Liver/microbiology ; Spleen/microbiology ; },
abstract = {Determining how genetic polymorphisms enable certain fungi to persist in mammalian hosts can improve understanding of opportunistic fungal pathogenesis, a source of substantial human morbidity and mortality. We examined the genetic basis of fungal persistence in mice using a cross between a clinical isolate and the lab reference strain of the budding yeast Saccharomyces cerevisiae. Employing chromosomally encoded DNA barcodes, we tracked the relative abundances of 822 genotyped, haploid segregants in multiple organs over time and performed linkage mapping of their persistence in hosts. Detected loci showed a mix of general and antagonistically pleiotropic effects across organs. General loci showed similar effects across all organs, while antagonistically pleiotropic loci showed contrasting effects in the brain vs the kidneys, liver, and spleen. Persistence in an organ required both generally beneficial alleles and organ-appropriate pleiotropic alleles. This genetic architecture resulted in many segregants persisting in the brain or in nonbrain organs, but few segregants persisting in all organs. These results show complex combinations of genetic polymorphisms collectively cause and constrain fungal persistence in different parts of the mammalian body.},
}
@article {pmid36101321,
year = {2022},
author = {Fochezato, J and Brito, R and Gonalves, GL and Specht, A and Becker, VO and Moreira, GRP},
title = {Description of Porphyrosela arachisella sp. nov. (Lepidoptera: Gracillariidae), the first report of Lithocolletinae for Brazil.},
journal = {Zootaxa},
volume = {5165},
number = {3},
pages = {387-404},
doi = {10.11646/zootaxa.5165.3.4},
pmid = {36101321},
issn = {1175-5334},
mesh = {Animals ; Base Sequence ; Brazil ; Ecosystem ; *Moths ; },
abstract = {During a recent survey of leaf-mining microlepidoptera in the Cerrado biome, mines of an undescribed Porphyrosela Braun (Lepidoptera: Gracillariidae: Lithocolletinae) were found associated with the forage peanut, Arachis pintoi Krapov. W.C. Greg. (Fabaceae). Consequently, adults, immature stages and the leaf mine of Porphyrosela arachisella sp. nov. are herein described based on light and scanning electron microscopy. A preliminary analysis of DNA barcode sequences including putative members of other lithocolletine species and all BINs (Barcode Index Numbers) available for Porphyrosela supports P. arachisella as an independent cluster, with 8 to 11% divergence. Its nearest neighbour was the cluster formed by three BINs (BOLD: ADT2137, BOLD: AAG1161 and BOLD: ADU9985) that includes specimens from Australia, Vietnam and Bangladesh. This is the first report of a lithocolletine gracillariid for Brazil, and the third species recognized for the genus in the Neotropical region.},
}
@article {pmid36101316,
year = {2022},
author = {Qi, L and Huang, J and Wu, H and Wang, Q},
title = {Two new species of Setostylus Matile, 1990 (Diptera: Keroplatidae) from China.},
journal = {Zootaxa},
volume = {5165},
number = {3},
pages = {443-450},
doi = {10.11646/zootaxa.5165.3.9},
pmid = {36101316},
issn = {1175-5334},
mesh = {Animals ; China ; *Diptera/genetics ; Nematocera ; Trees ; },
abstract = {In this study, two new species of Setostylus (Diptera: Keroplatidae: Keroplatinae), S. tridigitus sp. n. and S. triumphus sp. n. are described, with a key to all the species of the genus. Male habitus and images of diagnostic morphological characteristics are provided. Status of these two new species is also supported by the genetic distances and neighbor-joining (NJ) tree in the DNA barcode analysis.},
}
@article {pmid36101301,
year = {2022},
author = {Taberer, TR},
title = {An updated review of the genus Strigivenifera Hering, 1937 (Lepidoptera: Zygaenoidea: Chrysopolomidae) with the description of a new species.},
journal = {Zootaxa},
volume = {5168},
number = {1},
pages = {51-62},
doi = {10.11646/zootaxa.5168.1.4},
pmid = {36101301},
issn = {1175-5334},
mesh = {Animals ; *Moths ; },
abstract = {Following on from a recent revision by Kurshakov Zolotuhin (2013), the genus Strigivenifera Hering, 1937 is reviewed based on recently-collected material held at the African Natural History Research Trust. Investigation of genital morphology and newly-generated barcodes suggested that the diagnoses provided for the species in the previous revision were not entirely reliable for all taxa and as a result, a surplus of names exist in respect to valid species. The following taxonomic changes are implemented: S. livingstonei Kurshakov Zolotuhin, 2013 syn. n. and S. cruisa Kurshakov Zolotuhin, 2013 syn. n. are synonymised with S. albidiscalis (Hampson, 1910), S. ocellaris Kurshakov Zolotuhin, 2013 syn. n. is synonymised with S. eborea Kurshakov Zolotuhin, 2013 and S. tatooifera Kurshakov Zolotuhin, 2013 syn. n. is synonymised with S. bartschi Kurshakov Zolotuhin, 2013. A new species previously confused with S. ocellaris is described from the Western Area Peninsula in Sierra Leone: S. smithi sp. n. The intraspecific variability of the species together with appropriate diagnostic characters for identification are discussed and illustrated and an updated list of the valid species of the genus is provided.},
}
@article {pmid36101273,
year = {2022},
author = {Sueyoshi, M and Nakamura, S and Menzel, F},
title = {A new species of Hyperlasion Schmitz (Diptera: Sciaridae), causing periodic outbreaks in Japan.},
journal = {Zootaxa},
volume = {5168},
number = {4},
pages = {451-463},
doi = {10.11646/zootaxa.5168.4.5},
pmid = {36101273},
issn = {1175-5334},
mesh = {Animals ; Australia ; *Diptera/genetics ; Disease Outbreaks ; Japan ; Nematocera ; },
abstract = {A sciarid species, Hyperlasion breviantenna sp. n., is described from Japan. This is the first record of Hyperlasion Schmitz, 1918, from Asia. We compared the molecular sequence data of the mitochondrial cytochrome c oxidase subunit I (COI) region and external morphological characters among congeners and related genera. Morphological features are described and illustrated, and genetic relatedness to selected species with a one-segmented maxillary palpus is shown as a maximum likelihood tree. The DNA barcoding approach revealed that the genetic sequences of Japanese specimens are identical with those of Australian specimens, which have been assigned to the genus Hyperlasion. The new species occurs in outbreaks during the rainy season, June to July, in Japan and is recognized as a nuisance pest. Newly emerged adults appear in the early morning and enter houses, facilities, and public buildings. The biology of the new species is compared with those of H. wasmanni Schmitz, 1918, and Moehnia erema Pritchard, 1960, which have been recorded as occurring in large aggregations with thousands of individuals abroad, based on published biological notes and reports on these species.},
}
@article {pmid36101261,
year = {2022},
author = {Zhang, YL and Wang, M and Ma, FZ},
title = {Neopheosia pseudofasciata sp. nov., a new species of Notodontidae (Lepidoptera) from Wuyishan National Park, southeastern China.},
journal = {Zootaxa},
volume = {5168},
number = {5},
pages = {589-594},
doi = {10.11646/zootaxa.5168.5.7},
pmid = {36101261},
issn = {1175-5334},
mesh = {Animals ; China ; Genitalia ; Humans ; *Lepidoptera ; Parks, Recreational ; Universities ; },
abstract = {A new species of the genus Neopheosia Matsumura, 1920, N. pseudofasciata sp. nov. is described and illustrated from Fujian province. The species resembles N. fasciata (Moore, 1888) but differs in a forewing pattern in M3 cell; diagnostic differences are observed in genitalia characters as well. DNA barcode data of the new species and its relatives are deposited in GenBank. A key to the Neopheosia species based on morphology is presented. The holotype is deposited in the Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou.},
}
@article {pmid36101200,
year = {2022},
author = {Makarchenko, EA and Semenchenko, AA and Palatov, DM},
title = {Taxonomy of Diamesa steinboecki group (Diptera: Chironomidae: Diamesinae), with description and DNA barcoding of new species. I. Subgroups steinboecki and longipes.},
journal = {Zootaxa},
volume = {5125},
number = {5},
pages = {483-512},
doi = {10.11646/zootaxa.5125.5.2},
pmid = {36101200},
issn = {1175-5334},
mesh = {Animals ; *Chironomidae ; DNA ; DNA Barcoding, Taxonomic ; Male ; Phylogeny ; },
abstract = {The results of a revision of the Diamesa steinboecki group, namely soubgroups steinboecki and longipes (Diptera, Chironomidae, Diamesinae) are presented. Illustrated descriptions of the adult male of D. dragani sp. nov. from Sayan Mountains, D. kownackii sp. nov. from Wrangel Island, D. maisaraensis sp. nov. from Pamir, D. marinskiyi sp. nov. from Tian-Shan, D. zagrosica sp. nov. from Iran, D. moubayedi sp. nov. from Lebanon are provided with redescriptions of D. steinboecki Goetghebuer from Pamir, French and Swiss Alps, D. sakartvella Kownacki et Kownacka from Caucasus and D. praecipua Sther et Willassen from Himalayas. Taxonomic remarks with data on the ecology and biogeography of the investigated species are given. In addition to taxonomic information, 658-bp fragments of the mitochondrial cytochrome oxidase subunit I gene from the eight species are presented and the results of DNA barcoding are discussed. Previous investigations focused to integrative taxonomy and molecular analysis of the Diamesa species collected in various mountain regions such as Alps, Tien Shan and Pamir. In the present work, we focused on the principle of considering morphological groups, giving more emphasis respect to the division in geographical areas.},
}
@article {pmid36101184,
year = {2022},
author = {Przystakowska, A},
title = {A new species of Apisa Walker, 1855 (Lepidoptera: Erebidae: Arctiinae) from Uganda with remarks on the apomorphies of the genus.},
journal = {Zootaxa},
volume = {5128},
number = {1},
pages = {91-106},
doi = {10.11646/zootaxa.5128.1.5},
pmid = {36101184},
issn = {1175-5334},
mesh = {Animals ; Male ; *Moths ; Uganda ; },
abstract = {A new species of Apisa Walker, 1855 from Uganda (East Africa) and Gabon (Central Africa) is described according to morphological characters and DNA barcode information. A diagnosis, detailed description, distribution, and illustrations of specimens and the male genitalia are provided. Diagnostic characters are found in wing shape, strongly marked wing venation and details of the male genital apparatus. The DNA barcode sequences of twelve specimens of A. atrovenosa sp. n. are compared with other members of Apisa. Diagnostic characters of the genus are summarised and discussed for the first time with an emphasis on the lack of arolium as the obvious autapomorphy. This character is shown by SEM photographs.},
}
@article {pmid36101179,
year = {2022},
author = {Freyhof, J and Kaya, C and Geiger, MF},
title = {A practical approach to revise the Oxynoemacheilus bergianus species group (Teleostei: Nemacheilidae).},
journal = {Zootaxa},
volume = {5128},
number = {2},
pages = {151-194},
doi = {10.11646/zootaxa.5128.2.1},
pmid = {36101179},
issn = {1175-5334},
mesh = {Animals ; *Cypriniformes ; Rivers ; Trees ; },
abstract = {The Oxynoemacheilus bergianus species group is revised based on tree topology (ML, NJ, MP), distance (K2P and ASAP) and Poisson tree process analyses of DNA barcode data tested against morphometric and morphological characters including colour patterns. The O. bergianus species group is distinguished from other Oxynoemacheilus groups based on morphological characters: its constituent species have a slender caudal peduncle, a suborbital flap in the male, a mottled or blotched colour pattern, and lack bold, black spots on the caudal-fin base. It is also supported as a monophyletic unit in our molecular analysis. The O. bergianus group includes 10 molecular clades following congruently well-supported NJ, MP and ML based entities. Species described as O. bergianus, O. banarescui, O. erdali, O. fatsaensis, O. samanticus, and O. simavicus from Turkey, O. lenkoranensis from Azerbaijan, and O. longipinnis and O. parvinae from Iran belong to this species group. The group includes also four unnamed molecular clades. We were unable to detect external differences between any of the molecular clades in colour pattern or any morphometric or morphological characters examined. In the 10 molecular clades in the O. bergianus species group, the intraclade K2P distance ranges from 0.01.8% while the distances between molecular clades ranges from 0.65.9%. To resolve the species diversity of this group, we also analysed the intraspecific and interspecific variability in the K2P distance of DNA barcode data from 53 other Oxynoemacheilus species. Here, the intraspecific variability ranges from 0.02.4% while the interspecific K2P distance ranges from 1.220.8%. In the O. bergianus species group, only four groups are detected by the mPTP species delimitation approach distinguished by a K2P distance of 2.9% or more. We treat these four groups as valid species, corresponding to O. banarescui, O. bergianus, O. fatsaensis, and O. simavicus. Oxynoemacheilus samanticus from the Kzlrmak and Seyhan drainages, O. lenkoranensis from the Caspian basin, O. erdali from the Euphrates, and O. longipinnis and O. parvinae from the Tigris drainage are treated as synonyms of O. bergianus. Fishes from an unnamed molecular clade from the upper Tigris, and from a second unnamed clade from the upper Euphrates, are both identified as O. bergianus. Oxynoemacheilus bergianus might be a junior synonym of O. bergi from the Kura. The distribution range of O. simavicus, described from the Simav drainage in the Marmara basin, is expanded to the east and two molecularly differentiated population groups occur in the Sakarya drainage, the Byk Melen River and potentially in other adjacent coastal streams. Oxynoemacheilus fatsaensis, described from the coastal stream Eleki in northern Anatolia, is also widespread in the Yeilrmak drainage. Morphological characters proposed to distinguish O. fatsaensis from the other species of the O. bergianus group could not be confirmed by our data on fishes from the Yeilrmak. This study also discusses the theoretical background, our reasons for conducting this revision in the way we did, and what the alternatives would be.},
}
@article {pmid36101168,
year = {2022},
author = {Govi, G and Fiumi, G and Barbut, J and Scalercio, S and Hausmann, A},
title = {An unexpected species complex unveiled in southern European populations of Phragmatiphila nexa (Hbner, [1808]) (Lepidoptera, Noctuidae, Noctuinae, Apameini).},
journal = {Zootaxa},
volume = {5128},
number = {3},
pages = {355-383},
doi = {10.11646/zootaxa.5128.3.3},
pmid = {36101168},
issn = {1175-5334},
mesh = {Animals ; DNA, Mitochondrial ; Female ; Genitalia, Female ; Genitalia, Male ; Insecta ; Male ; *Moths/genetics ; },
abstract = {DNA barcoding analyses of Phragmatiphila nexa (Hbner, 1808) populations unveiled an unexpected divergence in mtDNA of Italian populations, showing the existence of three allopatric cryptic species. The northernmost BIN is shared with specimens from most other European countries, the southernmost one includes specimens from Basilicata and Calabria regions, and the last BIN includes specimens from Apennines, Sardinia and Corsica. Wing pattern as well as male and female genitalia support the existence of three different species along the Italian peninsula: Phragmatiphila nexa north of the Po River for which we designate a neotype, Phragmatiphila insularis (Turati, 1913), stat. rev. in the Apennines as well as in Sardinia (and Corsica), and Phragmatiphila parenzani sp. n. in the south. The Italian distribution of the genus Phragmatiphila is presented in detail.},
}
@article {pmid36101167,
year = {2022},
author = {Jaume-Schinkel, S and Kvifte, GM and VAN DER Weele, R and Mengual, X},
title = {Alepia viatrix sp. nov. (Diptera: Psychodidae), a new species of a Neotropical genus found on the Azores Archipelago (Portugal).},
journal = {Zootaxa},
volume = {5128},
number = {3},
pages = {384-396},
doi = {10.11646/zootaxa.5128.3.4},
pmid = {36101167},
issn = {1175-5334},
mesh = {Animals ; Azores ; Female ; Male ; Portugal ; *Psychodidae ; },
abstract = {A new species of the Neotropical genus Alepia Enderlein, 1937 is described from the Azores Archipelago based on morphological characters and DNA barcodes from male and female specimens. Images of the new species as well as a discussion of the origin of this species are also provided. Moreover, we include an identification key for the adult male Psychodidae species recorded on the Azores Archipelago and comment on each species present on these islands. This is the first record of the genus Alepia from Azores.},
}
@article {pmid36101163,
year = {2022},
author = {Timossi, G and Huemer, P},
title = {Sattleria enrosadira sp. nov., a new cryptic, high alpine species from Northern Italy revealed by DNA barcodes and morphology (Lepidoptera, Gelechiidae).},
journal = {Zootaxa},
volume = {5128},
number = {3},
pages = {435-443},
doi = {10.11646/zootaxa.5128.3.8},
pmid = {36101163},
issn = {1175-5334},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Female ; Genitalia, Male ; Italy ; Male ; *Moths/anatomy &amp; histology ; Museums ; },
abstract = {Sattleria karsholti Huemer Hebert, 2011 is re-examined based on recently collected material, museum vouchers, and DNA barcodes. Adult and male genitalia morphology and molecular data of the COI barcode region support the existence of two allopatric species, S. karsholti, from the type locality of Pizo Arera in the Orobian Alps (Bergamo Province, Italy), and S. enrosadira sp. nov. from Monte Baldo, Adamello and the Brenta group (Trento and Verona Provinces, Italy). Adults and male genitalia of both species are figured; the females of both species are unknown.},
}
@article {pmid36101129,
year = {2022},
author = {Zhang, J and Chen, L and Ding, Y and Zhang, F and Yu, H},
title = {On the Clubiona reclusa species-group in China, with the description of Clubiona qianlei sp. nov. (Araneae, Clubionidae).},
journal = {Zootaxa},
volume = {5129},
number = {3},
pages = {412-421},
doi = {10.11646/zootaxa.5129.3.5},
pmid = {36101129},
issn = {1175-5334},
mesh = {Animals ; China ; Genes, Mitochondrial ; Microscopy ; *Spiders/genetics ; },
abstract = {The representation of the Clubiona reclusa species-group in China is here established in two species: Clubiona qianlei sp. nov. from Central China and C. interjectaL. Koch, 1879, which is mainly distributed in northern China. Detailed description, diagnosis, photographs of the new species are given. DNA barcodes (a partial fragment of the mitochondrial cytochrome oxidase subunit I gene, COI) of the new species were obtained to confirm matching of the sexes and for future use in molecular studies. Supplementary micrographs of C. interjecta are provided for the first time, alongside an emended diagnosis, to demonstrate the validity of C. qianlei sp. nov.. A distribution map of the reclusa group species in China is given.},
}
@article {pmid36101125,
year = {2022},
author = {Surez, D and Pedrianes, JR and Andjar, C},
title = {DNA barcoding reveals new records of invasive terrestrial flatworms (Platyhelminthes, Tricladida, Geoplanidae) in the Macaronesian region.},
journal = {Zootaxa},
volume = {5129},
number = {3},
pages = {447-450},
doi = {10.11646/zootaxa.5129.3.9},
pmid = {36101125},
issn = {1175-5334},
mesh = {Animals ; DNA ; *DNA Barcoding, Taxonomic ; *Planarians ; },
}
@article {pmid36101107,
year = {2022},
author = {Liang, JY and Zhang, CK and Chen, MX and Liu, W and Zheng, SZ and Hsu, YF},
title = {A new species of the genus Synanthedon Hbner [1819] (Lepidoptera Sesiidae) from Taiwan.},
journal = {Zootaxa},
volume = {5133},
number = {1},
pages = {133-142},
doi = {10.11646/zootaxa.5133.1.7},
pmid = {36101107},
issn = {1175-5334},
mesh = {Animals ; Female ; Male ; *Moths ; *Quercus ; Taiwan ; },
abstract = {A new species of clearwing moth, Synanthedon suhua sp. nov., is described from Taiwan in this article. Adults and genitalia of both sexes are illustrated, DNA barcodes provided, and potential damage to Quercus longinux (Fagaceae) discussed.},
}
@article {pmid36101085,
year = {2022},
author = {Han, YY and VAN Achterberg, K and Chen, XX},
title = {Review of the genera Breviterebra Kusigemati, Charops Holmgren and Scenocharops Uchida (Hymenoptera, Ichneumonidae, Campopleginae) from China, with description of three new species.},
journal = {Zootaxa},
volume = {5133},
number = {4},
pages = {527-542},
doi = {10.11646/zootaxa.5133.4.4},
pmid = {36101085},
issn = {1175-5334},
mesh = {Animals ; China ; *Hymenoptera ; Male ; },
abstract = {Species of the genera Breviterebra Kusigemati, 1982, Charops Holmgren, 1859 and Scenocharops Uchida, 1932 (Hymenoptera, Ichneumonidae, Campopleginae) from China are revised. Of the 13 species recognized, three are described as new species: Breviterebra apicocrinis sp. nov., Charops mauroknemus sp. nov. and Scenocharops yunnanensis sp. nov. The genus Breviterebra Kusigemati and the species Scenocharps montanus Gupta Maheshwary, 1971 are recorded in China for the first time. The distribution area of C. brachypterus (Cameron), C. striatus (Uchida), S. flavipetiolus (Sonan) and S. parasae He in China are updated. DNA barcode fragment of the mitochondrial COI gene of B. apicocrinis sp. nov. is presented. Keys to Breviterebra, Charops and Scenocharops are provided.},
}
@article {pmid36101069,
year = {2022},
author = {Cumming, JM and Brooks, SE},
title = {Establishment of the Microphorella breviradia species group, with a key to the Nearctic species groups of Microphorella Becker (Diptera: Dolichopodidae sensu lato: Parathalassiinae).},
journal = {Zootaxa},
volume = {5134},
number = {2},
pages = {197-214},
doi = {10.11646/zootaxa.5134.2.2},
pmid = {36101069},
issn = {1175-5334},
mesh = {Animals ; *Diptera/genetics ; Phylogeny ; },
abstract = {The Microphorella breviradia species group is established for three new species from western North America, namely Microphorella breviradia sp. nov., M. macdonaldi sp. nov. and M. vespera sp. nov., including an identification key to species. COI mitochondrial DNA barcode sequences were obtained for two of the three species and possibly suggest the existence of additional cryptic species. The phylogenetic relationships of the Microphorella breviradia species group to the remainder of the Microphorella species groups are reviewed on a worldwide basis. A key to the four known Nearctic species groups of Microphorella is also provided.},
}
@article {pmid36101068,
year = {2022},
author = {Lszl, GM and Hausmann, A},
title = {Taxonomic review of the genus Morabia Hausmann amp; Tujuba, 2020 with descriptions of two new species and introducing five new generic combinations (Lepidoptera, Geometridae, Ennominae).},
journal = {Zootaxa},
volume = {5134},
number = {2},
pages = {215-237},
doi = {10.11646/zootaxa.5134.2.3},
pmid = {36101068},
issn = {1175-5334},
mesh = {Animals ; Bees ; DNA ; Female ; *Gastropoda ; *Moths ; },
abstract = {The paper contains the description of two new species of the genus Morabia Hausmann Tujuba, 2020: M. cryptica sp. n. and M. smithi sp. n. The descriptions are based on both morphological data and DNA barcoding. Based on integrative taxonomic analyses, five new combinations are proposed: Morabia nigripunctata (Warren, 1897), comb. n. described from Nigeria, Morabia hero (Viette, 1971), comb. n., Morabia pluto (Viette, 1971), comb. n. described from Madagascar, Morabia herbuloti (Orhant, 2003), comb. n. described from Runion and Morabia distinctaria (Joannis, 1915), comb. n. described from Mauritius are transferred from the genus Ectropis Hbner, 1825 to Morabia. The female genitalia of M. nigripunctata, M. brunnea Hausmann Tujuba, 2020, M. hero and M. herbuloti are described and illustrated for the first time. Detailed diagnoses and re-descriptions of all taxa newly transferred to Morabia are given, interspecific pairwise distances of DNA barcodes are calculated and a maximum likelihood tree is compiled. The paper is illustrated with 38 colour and 38 black and white diagnostic images and a distribution map.},
}
@article {pmid36101053,
year = {2022},
author = {Esmaeili, HR and Jufaili, SA and Masoumi, AH and Zarei, F},
title = {Ichthyodiversity in southeastern Arabian Peninsula: Annotated checklist, taxonomy, short description and distribution of Inland fishes of Oman.},
journal = {Zootaxa},
volume = {5134},
number = {4},
pages = {451-503},
doi = {10.11646/zootaxa.5134.4.1},
pmid = {36101053},
issn = {1175-5334},
mesh = {Animals ; Arabia ; Biodiversity ; *Cyprinodontiformes ; *Ecosystem ; Humans ; Oman ; },
abstract = {Oman, a country in Southwest Asia, situated on the southeastern quarter of the Arabian Peninsula presents a high level of biological diversity especially marine elements. Although arid habitats cover most parts of Oman (82%), the region has several freshwater systems that are vital for the survival of people as well as for different groups of animals and plants. Research works on Oman biodiversity including terrestrial and marine, have been steadily increasing over the last few decades, but freshwater ecosystems have not been well investigated. Oman comprises parts of three freshwater ecoregions including the Oman Mountains, Southwestern Arabian Coast, and Arabian Interior having xeric freshwaters and endorheic (closed) basins which support a variety of inland fishes. The current checklist provides for each species of inland waters of Oman all recognized and named taxa, documenting recent changes and controversies in nomenclature, its records, taxonomic status, synonyms, etymology, common English name, short description, range expansion, and detailed distribution map based on several field surveys throughout the country. We also provide native, endemic, and introduced species. The diversity of inland fishes of Oman included in this annotated checklist consists of 23 recognized species in 15 genera, 10 families, seven orders, and a class. Also, for the first time, we report and confirm the presence of four species in the inland waters of Oman. The most diverse order is Cypriniformes (nine species, 39.13%), followed by Gobiiformes (six species, 26.09%), Cyprinodontiformes (three species, 13.04%), Cichliformes (two species, 8.69%), and Centrarchiformes, Gonorynchiformes and Mugiliformes (one species, 4.35% each). 21 native species (91.3%) in nine families and two exotic species (8.7%) in two families are listed here. Out of 21 native species, eight species (16.8%) in two families are endemic elements that are restricted to the Oman territory only. Identification of all recognized species was confirmed by DNA barcoding (mitochondrial COI). Oman Mountains Ecoregion (OME), Southwestern Arabian Coast Ecoregion (SACE), and Arabian Interior Ecoregion (AIE) harbor 15, 12, and one species, respectively. The provided data will be necessary for increasing the fish knowledge, the development of competent and pragmatic management plans and effective conservation policies.},
}
@article {pmid36101036,
year = {2022},
author = {Gariepy, T and Olmi, M and Guglielmino, A and Mita, T},
title = {DNA barcoding of Sclerogibbidae and confirmation of the opposite sexes of Sclerogibba berlandi Benoit (Hymenoptera: Sclerogibbidae).},
journal = {Zootaxa},
volume = {5138},
number = {1},
pages = {75-82},
doi = {10.11646/zootaxa.5138.1.7},
pmid = {36101036},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Female ; Hymenoptera/anatomy &amp; histology/*classification/genetics ; Male ; *Sex Characteristics ; United Arab Emirates ; },
abstract = {The female and male of Sclerogibba berlandi Benoit, 1963 (Hymenoptera: Sclerogibbidae), collected in Abu Dhabi (United Arab Emirates) and characterized by a pronounced sexual dimorphism, were associated for the first time by mitochondrial COI sequences. A comparison with COI sequences of S. crassifemorata Riggio De Stefani-Perez, 1888 and S. talpiformis Benoit, 1950 from Abu Dhabi proved the diversity of S. berlandi. The COI sequence of a female of S. rossi Olmi, 2005 from Japan, Okinawa-jima, was analyzed for the first time and compared with the other sequences.},
}
@article {pmid36098199,
year = {2022},
author = {Suriana, and Nasaruddin, and Jamili, and Walhidayah, T},
title = {Characteristics Evaluation of a Barcode Sequence of Two Limnonectes (Anura) Sympatric Populations from Kendari, Southeast Sulawesi.},
journal = {Pakistan journal of biological sciences : PJBS},
volume = {25},
number = {8},
pages = {732-740},
doi = {10.3923/pjbs.2022.732.740},
pmid = {36098199},
issn = {1812-5735},
mesh = {Adenine ; Animals ; *Anura/genetics ; Guanine ; Indonesia ; Nucleotides ; *Thymine ; },
abstract = {Background and Objective: Cytochrome c oxidase gene subunit-I (COI) has conserved and variable regions and along with the 658 nucleotide base pairs at the '5 of these have been used as animal barcode, species identification and evolutionary studies of several vertebrates, especially Anura. This research was conducted to characterize the nucleotides of the COI sequence gene of (Limnonectes cf. grunniens) that live sympatrically with L. modestus on several headwater streams in Kendari, Southeast Sulawesi. Materials and Methods: This research is explorative, samples of frogs were obtained from the Lahundape and Moramo headwater streams. A total of 16 frogs were sampled and the genomic DNA of frog samples was extracted and, then amplified using the PCR method. The next steps are sequencing and analysis using MEGA 7. Results: The result showed nucleotides along 688 to 705 base pairs. There were two haplotypes of L. cf. grunniens and three L. modestus. L. cf. grunniens consist of 32.6% Thymine (Uracil), 32.3% Cytisine, 17.9% Adenine and 17.9% Guanine. While L. modestus is 37.6% Thymine, 26.0% Cytosine, 20.7% Adenine and 15.8% Guanine. Based on Kimura-2 parameter, the genetic distance between genera ranges from 0.25-0.26 while the genetic distance between species is 0.00-0.01. Conclusion: Phylogeny trees based on partial sequences of COI frog genes showed that L. cf. grunniens and L. modestus are monophyletic with bootstrapped values ranging from 86-100% and differentiated between species. There is a genetic variability of COI sequences of Limnonectes cf. grunniens and L. modestus from Kendari, Southeast Sulawesi.},
}
@article {pmid36097111,
year = {2022},
author = {Chaudhary, M and Sharma, P and Mukherjee, TK},
title = {Applications of CRISPR/Cas technology against drug-resistant lung cancers: an update.},
journal = {Molecular biology reports},
volume = {49},
number = {12},
pages = {11491-11502},
pmid = {36097111},
issn = {1573-4978},
mesh = {Humans ; CRISPR-Cas Systems/genetics ; *Carcinoma, Non-Small-Cell Lung/genetics/therapy ; *Lung Neoplasms/genetics ; Neoplasm Recurrence, Local/genetics ; Technology ; },
abstract = {Out of all the cancer types, the most prevalent one is lung cancer. Multiple genes and signaling pathways play role in the progression of lung cancer. Considering the wider prevalence and fatality of lung cancer it has become the focus of current cancer research. Though currently used approaches have shown positive results against lung cancer but success against non-small cell lung cancer (NSCLC) still looms as an enigma for the entire research fraternity. The development of resistance against inhibitors within a short span is one of the reasons responsible for the failure and relapse of lung cancer. Under these prevailing conditions genome/gene-editing technology using clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR associated proteins (Cas), popularly known as CRISPR/Cas technology offers a convenient and flexible method for inducing precise changes within the lung cancer cell. Additionally, CRISPR-barcoding and CRISPR knockout screens at the genome-wide level can help in the functional investigation of specific mutations and identification of novel cancer drivers respectively. Several variants of the CRISPR/Cas system are being developed to limit off-targeting with enhanced precision. The present review article updates the usefulness of CRISPR/Cas technology against various types of lung cancers.},
}
@article {pmid36096465,
year = {2023},
author = {Nitta, M},
title = {Capsalid monogeneans of fishes from the Seto Inland Sea, Japan: Description of Benedenia kobudai n. sp. parasitic on Semicossyphus reticulatus (Perciformes: Labridae).},
journal = {Parasitology international},
volume = {92},
number = {},
pages = {102677},
doi = {10.1016/j.parint.2022.102677},
pmid = {36096465},
issn = {1873-0329},
mesh = {Animals ; Female ; Male ; Phylogeny ; Japan ; Reproducibility of Results ; *Trematoda ; *Perciformes/parasitology ; Fishes ; *Fish Diseases/epidemiology/parasitology ; },
abstract = {The Seto Inland Sea, the largest inland sea in Japan, is a rich fishery with high biodiversity and productivity. Monogeneans have been studied for more than 120 years, and 58 nominal species have been recorded in the Seto inland Sea. This study provided DNA information on five species of Benedenia sensu lato (Capsalidae) from marine fishes from the sea, and one of them, Benedenia kobudai n. sp., is described from Semicossyphus reticulatus (Perciformes: Labridae). This new species differs from the other congeners by the hooded appearance between the anterior attachment organs, the morphology of the penis, the absence of the lobe near the vaginal pore and the common genital pore, the position of the vaginal pore, the germarium lying near the slightly hexagonal testes, the morphology of the haptor, and the shape and position of the hamuli. Phylogenetic analysis showed B. kobudai n. sp. in a separate clade from the other Benedenia species, B. epinepheli, B. hoshinai, B. sekii, and B. seriolae collected from the sea. Each of the newly provided DNA sequences (28S rDNA, ITS1-5.8S-ITS2, cox1) of the above four species are based on specimens obtained from the type hosts and/or type localities and are considered important for future taxonomic re-examination and confirmation of the reliability of the registered sequences. Furthermore, these four species are important causes of fish diseases in aquaculture, and it is expected that information on the distribution, host range, and occurrence of fish diseases for each capsalid secured by molecular identification will be accumulated. The Life Science Identifier (LSID): urn:lsid:zoobank.org:pub:26C15D17-CFD1-450D-9FCE-EFFF692D2133.},
}
@article {pmid36095800,
year = {2022},
author = {Komai, T and Chang, SC and Chan, TY},
title = {A new species of the deep-sea shrimp genus Glyphocrangon A. Milne-Edwards, 1880 (Decapoda: Caridea: Glyphocrangonidae) from the South China Sea off Pratas Island.},
journal = {Zootaxa},
volume = {5141},
number = {2},
pages = {140-150},
doi = {10.11646/zootaxa.5141.2.2},
pmid = {36095800},
issn = {1175-5334},
mesh = {Animal Structures ; Animals ; China ; *Decapoda ; },
abstract = {A new species of the deep-sea caridean genus Glyphocrangon A. Milne-Edwards, 1880, G. obtusis n.sp., is described and illustrated on the basis of the material collected in the South China Sea off the Pratas Island. It appears close to G. hakuhoae Takeda Hanamura, 1994 and G. robusta Komai, 2004 among the 93 described species in Glyphocrangon. From G. hakuhoae, the new species is distinguished by the rostrum with less developed convexity on the dorsolateral margin and lacking transverse septa, and the less elevated median carinae on the pleomeres 15. From G. robusta, the new species differs in lacking transverse septa at the rostrum, the fourth carina on the carapace with the two anterior parts unaligned and the posterior part divided into four lobes. Molecular genetic analysis using the barcoding segment of the mitochondrial COI gene supports the establishment of the new species.},
}
@article {pmid36095783,
year = {2022},
author = {Jiang, XK and Chen, HM and Xie, ZC},
title = {Description of two new species of the genus Glyphiulus Gervais, 1847 (Diplopoda: Spirostreptida: Cambalopsidae) from southern China.},
journal = {Zootaxa},
volume = {5141},
number = {4},
pages = {358-372},
doi = {10.11646/zootaxa.5141.4.4},
pmid = {36095783},
issn = {1175-5334},
mesh = {Animals ; *Arthropods ; China ; DNA ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Two new species of the millipede genus Glyphiulus Gervais, 1847 are described from southern China: Glyphiulus fortis sp. nov. and Glyphiulus hainanensis sp. nov. Glyphiulus fortis sp. nov. is cavernicolous, vs. G. hainanensis sp. nov. which was collected from an epigean environment. Both of them belong to the G. javanicus-group. Additionally, DNA barcoding and phylogenetic analyses based on nucleotide sequences of COI and 16S of the two new species, as well as their allied species were conducted. The morphological characteristics, the genetic distances and the phylogenetic tree revealed that the two new species are unambiguously distinct from their congeners.},
}
@article {pmid36095782,
year = {2022},
author = {Makarchenko, EA and Semenchenko, AA and Palatov, DM},
title = {Chironomids are commensals of the larvae and pupae of Blephariceridae and Simuliidae from the North Caucasus (Diptera: Chironomidae: Orthocladiinae).},
journal = {Zootaxa},
volume = {5141},
number = {4},
pages = {373-384},
doi = {10.11646/zootaxa.5141.4.5},
pmid = {36095782},
issn = {1175-5334},
mesh = {Animals ; *Chironomidae/anatomy &amp; histology/genetics ; Larva/anatomy &amp; histology ; Pupa/anatomy &amp; histology ; *Simuliidae/anatomy &amp; histology/genetics ; },
abstract = {Illustrated morphological descriptions of chironomid larvae from subfamily Orthocladiinae Cardiocladius sp. 1, which as commensals live between ventral suckers of Blephariceridae larvae, as well as larvae and pupae of Eukiefferiella claripennis group inhabited of Simuliidae pupal cocoons, are given. DNA barcodes of these chironomid species and sequences of their hosts, three species of Liponeura Loew (Blephariceridae) and one species of Simulium aff. variegatum (Simuliidae), are provided.},
}
@article {pmid36095718,
year = {2022},
author = {Oya, Y and Tsuyuki, A and Kajihara, H},
title = {Descriptions of two new species of Armatoplana (Polycladida: Stylochoplanidae) from the coasts of Japan, with their phylogenetic positions in Leptoplanoidea.},
journal = {Zootaxa},
volume = {5178},
number = {5},
pages = {433-452},
doi = {10.11646/zootaxa.5178.5.2},
pmid = {36095718},
issn = {1175-5334},
mesh = {Animals ; DNA, Ribosomal ; Japan ; Male ; Phylogeny ; *Platyhelminths ; },
abstract = {We describe two new species of Armatoplana Faubel, 1983, namely, A. albomaculata sp. nov. and A. kaburakii sp. nov., from Japan. This is the first record of the genus from the West Pacific. Armatoplana albomaculata sp. nov. has the following characteristics: i) no nuchal tentacles; ii) white spots on the dorsal surface of the body; iii) an elongated oval prostatic vesicle directing posteriorly but curving dorsally in the distal part; iv) a long, curved penis stylet; and v) a small, oval Langs vesicle without accessory vesicles. Armatoplana kaburakii sp. nov. is distinguished from other congeners by having i) no nuchal tentacles; ii) a large, elongated Langs vesicle without accessory vesicles; and iii) gonopores opening closely to each other. We propose to re-circumscribe Armatoplana so that it would not become a junior synonym of Candimboides Prudhoe, 1982 and Phylloplana Laidlaw, 1903. We provide partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene as DNA barcodes for the two new species. Our phylogenetic analyses based on concatenated sequences of the 16S, 18S, and 28S ribosomal DNA and COI revealed that A. albomaculata sp. nov. and A. kaburakii sp. nov. were sister taxa; however, they did not form a monophyletic clade with Armatoplana divae (Marcus, 1947) and Armatoplana leptalea (Marcus, 1947).},
}
@article {pmid36095691,
year = {2022},
author = {Connolly, JK and Marshall, CC and Hudson, PL and Watkins, JM and Scofield, AE and Rudstam, LG},
title = {Reevaluation of the genus Cyclops Mller, 1776 (Cyclopoida: Cyclopidae) in the Laurentian Great Lakes basin: first report of the Palearctic species Cyclops divergens Lindberg, 1936 from Lake Erie and documentation of Cyclops sibiricus Lindberg, 1949 in the St. Marys River.},
journal = {Zootaxa},
volume = {5182},
number = {2},
pages = {183-195},
doi = {10.11646/zootaxa.5182.2.5},
pmid = {36095691},
issn = {1175-5334},
mesh = {Animals ; *Copepoda/genetics ; Documentation ; Environmental Monitoring ; *Lakes ; Rivers ; },
abstract = {Large cyclopoid copepods of the genus Cyclops Mller, 1776 are seldom collected in the Laurentian Great Lakes, with only Cyclops scutifer Sars, 1863 and Cyclops strenuus Fischer, 1851 reported from the region. Rare reports of the species C. strenuus date back to 1972 within the Great Lakes basin. The first specimens reported as C. strenuus were collected from the St. Marys River, and additional specimens have been collected from western Lake Erie since 2013. We examined all available archived materials of C. strenuus from the Great Lakes and determined that specimens from the two localities belong to two separate species, neither of which refer to C. strenuus. Archived specimens collected from the St. Marys River in 1972 and 1995 were reidentified as Cyclops sibiricus Lindberg, 1949, a Holarctic species known from Siberia, Russian Federation, Alaska, USA, and northern regions of Canada. The occurrences of C. sibiricus from the St. Marys River extend the known distribution of the species southward some 1,688 km in the Nearctic region. Cyclops specimens collected from the western basin of Lake Erie in 2013, 2014, and 2019 were identified as the Palearctic species Cyclops divergens Lindberg, 1936 using both conventional taxonomy and genetic barcoding. C. divergens is known from localities across much of Europe and eastward into Central Asia. The occurrences of the species from western Lake Erie constitute the first detection of C. divergens in the Great Lakes and the Nearctic region. Therefore, we expect C. strenuus does not occur in the Great Lakes basin and is likely restricted to the Palearctic region.},
}
@article {pmid36095676,
year = {2022},
author = {Anilkumar, PA and Wesener, T and Moritz, L},
title = {First record of the order Polyzoniida from the Indian subcontinent with an integrative description of a new genus (Diplopoda, Colobognatha, Siphonotidae).},
journal = {Zootaxa},
volume = {5182},
number = {5},
pages = {401-428},
doi = {10.11646/zootaxa.5182.5.1},
pmid = {36095676},
issn = {1175-5334},
mesh = {Animals ; *Arthropods ; Forests ; *Lepidoptera ; Microscopy, Electron, Scanning ; Records ; },
abstract = {Considering the large area of the Indian subcontinent, its known millipede diversity is sparse with only ca. 270 described species in 90 genera, 25 families and 11 orders. So far, not a single polyzoniidan millipede has been described from India. The order Polyzoniida Cook, 1895 is one of the most species-poor millipede groups with less than 80 described species, and includes taxonomically problematic groups, especially in the family Siphonotidae Cook, 1895. Here we report the first representatives of the order Polyzoniida from India, and describe the new genus Theratta n. gen., with the three species Theratta mannavan n. sp., Theratta eravikulam n. sp., and Theratta shola n. sp., using scanning electron microscopy and COI genetic barcoding. Based on the morphological characters we place Theratta n. gen., and the three new species in the tribe Rhinotini Hoffman, 1977 of the family Siphonotidae. The gonopods of the new genus are similar to those of the genus Rhinotus Cook, 1896, but differ from all other Rhinotini in the modification of the podomere II of the anterior telopod, carrying a mesal process on the posterior side and a lamellar process on the anterior side. The three newly described species show a high interspecific genetic distance of 20.925.3%. The specimens were collected from the Shola forests (high altitude montane forests) of the southern Western Ghats in Kerala, India. We suggest that more extensive sampling in this area and in the Indian subcontinent in general will yield more new millipede species for science and expand our understanding of the hitherto neglected Indian millipede fauna.},
}
@article {pmid36095620,
year = {2022},
author = {Bass, A and Needham, K and Bennett, AMR},
title = {First record of Vespa crabro Linnaeus (Hymenoptera: Vespidae) in western North America with a review of recorded species of Vespa Linnaeus in Canada.},
journal = {Zootaxa},
volume = {5154},
number = {3},
pages = {305-318},
doi = {10.11646/zootaxa.5154.3.4},
pmid = {36095620},
issn = {1175-5334},
mesh = {Animals ; Bees ; Introduced Species ; North America ; *Wasps/anatomy &amp; histology/genetics ; },
abstract = {Vespa crabro Linnaeus is newly reported as an adventive species in British Columbia, Canada which is the first record of this invasive species in western North America. The specimen of V. crabro was identified using morphological diagnostic keys and by comparison to authoritatively identified specimens. DNA barcoding provided support that the British Columbia specimen is conspecific with sequenced specimens of V. crabro. It is not possible to be certain of the origin of the specimen, but the DNA barcode was identical to sequence from specimens of V. crabro from South Korea. DNA barcoding was also performed on morphologically identified specimens of Vespa simillima and Vespa soror collected previously in British Columbia and the sequences were closest to V. simillima and V. soror Genbank sequences, respectively. There is no evidence that any of these species have established populations in the province. We provide diagnostic morphological characters to distinguish Canadian Vespa species from each other including Vespa mandarinia which has recently established populations in British Columbia and Washington State, USA. The potential detrimental impacts of each species are discussed.},
}
@article {pmid36095615,
year = {2022},
author = {Mondal, D and Mukherjee, T and Hazra, N},
title = {On a new species of the genus Zavrelimyia Fittkau, 1962 (Diptera: Chironomidae) from India with cladistic relationship and a world key to the known males.},
journal = {Zootaxa},
volume = {5154},
number = {3},
pages = {365-379},
doi = {10.11646/zootaxa.5154.3.9},
pmid = {36095615},
issn = {1175-5334},
mesh = {Animals ; *Chironomidae/genetics ; India ; Larva ; Male ; Pupa ; },
abstract = {The adult male of Zavrelimyia (Paramerina) falcata sp.n. is described and illustrated from India. The DNA barcode of this new species is provided. The original description of Zavrelimyia (P.) valida (Paul, Hazra and Mazumdar, 2013) is corrected. The subgenus Schineriella Murray and Fittkau, 1988 of Zavrelimyia Fittkau is recorded in the Oriental region. A cladistic relationship of the species of Zavrelimyia Fittkau and a world key to the adult males of the genus Zavrelimyia Fittkau are provided.},
}
@article {pmid36095612,
year = {2022},
author = {Zarei, F and Esmaeili, HR and Kovai, M and Schliewen, UK and Abbasi, K},
title = {Ponticola hircaniaensis sp. nov., a new and critically endangered gobiid species (Teleostei: Gobiidae) from the southern Caspian Sea basin.},
journal = {Zootaxa},
volume = {5154},
number = {4},
pages = {401-430},
doi = {10.11646/zootaxa.5154.4.1},
pmid = {36095612},
issn = {1175-5334},
mesh = {Animals ; Caspian Sea ; Fishes ; Hybridization, Genetic ; *Perciformes ; Rivers ; },
abstract = {Ponticola hircaniaensis sp. nov. is described as a new gobiid species from the Kaboudval Stream, southern Caspian Sea basin. The new species is diagnosed among Caspian Sea basin Ponticola species by the following combination of characters: second dorsal-fin branched rays 1416, anal-fin branched rays 1012, scales in lateral series 5259; lower jaw slightly, if at all, prognathous; head and body yellowish brown showing a reticulate brown pattern on a yellow background, first dorsal fin with a marginal bright orangish-yellow band and a dark anterior spot, upper part of pectoral-fin base with a distinct dark brown stripe; length of third spine in first dorsal fin 13.418.3 % of standard length (SL), second dorsal-fin spine length 11.113.8 % SL, caudal peduncle length and depth 16.420.1 % and 11.112.8 % SL, respectively, head depth at nape 70.981.0 % of head length (HL), and at eye 52.566.0 % HL; sagittal otolith dorsal rim with a broad concavity in the middle, dorsal depression absent or indistinct, sulcus length/sulcus height and sulcus height/otolith height ratios 1.471.82 and 0.340.40, respectively. It is also characterised by a K2P nearest neighbour distance of 5% to P. kessleri in the mtDNA COI barcode region. Mitochondrial and nuclear DNA analyses suggested extensive hybridization between P. hircaniaensis sp. nov. and P. gorlap at Kaboudval, providing evidence for the first record of hybridization in the Ponto-Caspian gobiids. Based on narrow geographic range isolated above the Zarrin Gol Dam (< 2 km2), extensive hybridization with P. gorlap, and other threats, the new species should be considered Critically Endangered.},
}
@article {pmid36095610,
year = {2022},
author = {Kabalak, M and Karacaolu, A and Blg, HA and Karaguzel, D and Karaaslan, A},
title = {Comparisons of two cryptic Ampedus species (Coleoptera: Elateridae) by using classical systematics, ecological niche modeling, and DNA barcoding.},
journal = {Zootaxa},
volume = {5154},
number = {4},
pages = {454-468},
doi = {10.11646/zootaxa.5154.4.3},
pmid = {36095610},
issn = {1175-5334},
mesh = {Animals ; Biodiversity ; Climate ; *Coleoptera/genetics ; DNA/genetics ; DNA Barcoding, Taxonomic ; Ecosystem ; },
abstract = {The presence of cryptic species is one of the important problems in systematics. To deal with this systematic issue, certain approaches have been utilized. DNA sequencing is one of the common techniques for estimating biodiversity, such as DNA barcoding, which might reveal cryptic species. In this study, we explore how to identify two cryptic saproxylic species using a combination of general and aedeagus morphologies, distributional patterns (in provinces and altitude), specimen abundance, ecological niche modeling (ENM), and mtDNA sequencing data (for the endemic species Ampedus platiai and A. samedovi). The close relationship and validity of these species based on classical systematics was confirmed by the available literature and by Neighbor-Joining (NJ) analysis in Mega Software. Additionally, the DNA barcoding data acquired in this study also confirmed the species status of these species within the genus Ampedus. This also provides insights into classical systematics. ENMs for possible current and future distributional scenarios of endemic A. platiai and A. samedovi are created by Maxent Software. Possible suitable habitats in 2050 and 2070 for the species are calculated according to IPCC5 Climate scenarios. Precipitation seasonality (coefficient of variation) has the highest percentage contribution to the resulting prediction pattern for A. platiai (52.3), the mean temperature of the wettest quarter has the highest percentage contribution to the resulting prediction pattern for A. samedovi (42.7) respectively among used bioclimatic variables in ENM. Depending on the temperature increase in 2050 and 2070, the distributions of A. platiai and A. samedovi could decrease gradually.},
}
@article {pmid36095607,
year = {2022},
author = {Janion-Scheepers, C and Deharveng, L},
title = {A shocking-red new species of Setanodosa Salmon, 1942 (Collembola: Brachystomellidae) from South Africa.},
journal = {Zootaxa},
volume = {5154},
number = {4},
pages = {483-495},
doi = {10.11646/zootaxa.5154.4.6},
pmid = {36095607},
issn = {1175-5334},
mesh = {Animals ; *Arthropods/genetics ; *Hydrozoa ; Salmon ; South Africa ; },
abstract = {A new species of Setanodosa, S. jacquesi sp. nov. is described from the Western Cape (South Africa). It differs from other species of the genus by its unique shocking red pigmentation, the number of vesicles in the post antennal organ, and the number of clavate tenent hairs on the tibiotarsi. A comparative table of the world Setanodosa and a key of Brachystomellidae species known from South Africa are provided. DNA barcoding results are provided for several Brachystomellidae species from South Africa, Australia and the sub-Antarctic to support our findings. It shows that a species provisionally identified as Brachystomella cf. platensis is unambiguously present in both South Africa and Australia.},
}
@article {pmid36095591,
year = {2022},
author = {Teslenko, VA and Semenchenko, AA},
title = {Morphological description of a new species of Capnia (Plecoptera: Capniidae) with DNA barcoding of genus members from the Russian Far East.},
journal = {Zootaxa},
volume = {5155},
number = {1},
pages = {133-141},
doi = {10.11646/zootaxa.5155.1.7},
pmid = {36095591},
issn = {1175-5334},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Asia, Eastern ; Female ; *Insecta ; Neoptera/genetics ; Russia ; },
abstract = {Capnia yavorskayae, a new species of the stonefly family Capniidae, is described from the Low Amur River Basin, Khabarovskiy Kray of the Russian Far East, on the basis of female morphological features. Confirmation of the uniqueness of the new species was also molecularly compared to other Capnia, including a few Far Eastern species, C. aligera Zapekina-Dulkeit, C. bargusinica Zapekina-Dulkeit, C. khingana Teslenko, C. kurnakovi Zhiltzova, C. nearctica Banks, C. nigra (Pictet), and C. rara Zapekina-Dulkeit for which DNA barcodes were obtained. We support the distinctiveness of the new species with mitochondrial DNA sequences, comparing it to Capnia from the eastern Palaearctic and Nearctic realms and one Zwicknia species. The new species forms a common clade with C. khingana, C. kurnakovi from the Russian Far East, and an undetermined Capnia species from Honshu, Japan. Each species from the Russian Far East has high interspecific distances from other Capnia species except C. nearctica which was close to C. atra Morton.},
}
@article {pmid36095557,
year = {2022},
author = {Degaard, F and Abenius, J and Paukkunen, J},
title = {Ceropales pallida sp. nov. (Hymenoptera, Pompilidae, Ceropalinae) described from northern Europe.},
journal = {Zootaxa},
volume = {5159},
number = {1},
pages = {103-116},
doi = {10.11646/zootaxa.5159.1.4},
pmid = {36095557},
issn = {1175-5334},
mesh = {Animals ; Europe ; *Wasps/genetics ; },
abstract = {A new pompilid wasp, Ceropales pallida sp. nov., is described, illustrated and distinguished from its close relative Ceropales maculata. The new species is supported by evidence from morphological characters as well as DNA barcoding. The type specimens were collected at several localities in southern Norway, Sweden and Finland.},
}
@article {pmid36095538,
year = {2022},
author = {Patidar, A and Singha, D and Kumar, V and Tyagi, K},
title = {A new species of Psephenothrips (Thysanoptera:Phlaeothripidae) with one new record from India.},
journal = {Zootaxa},
volume = {5159},
number = {3},
pages = {440-444},
doi = {10.11646/zootaxa.5159.3.8},
pmid = {36095538},
issn = {1175-5334},
mesh = {Animals ; India ; Mitochondria ; *Thysanoptera/genetics ; },
abstract = {Psephenothrips uttarakhandensis sp. n. is described and illustrated from India. Also, Neohydatothrips xestosternitus (Han Cui) is newly recorded from India. The DNA barcode data using partial mitochondrial cytochrome c oxidase subunit I (mtCOI) from the holotype of the new species and one sequence of Neohydatothrips xestosternitus were generated and submitted to The Barcode of Life Data Systems (BOLD).},
}
@article {pmid36095534,
year = {2022},
author = {Shin, B and Choi, SW and Kim, SS},
title = {Fourteen new records of Crambidae (Lepidoptera) from South Korea.},
journal = {Zootaxa},
volume = {5159},
number = {4},
pages = {513-534},
doi = {10.11646/zootaxa.5159.4.3},
pmid = {36095534},
issn = {1175-5334},
mesh = {Animals ; DNA ; Female ; Male ; *Moths/genetics ; Republic of Korea ; },
abstract = {This article reports 14 species of Crambidae for the first time in South Korea: Paracymoriza distinctalis (Leech, 1889) (Acentropinae), Pseudocatharylla duplicellus (Hampson, 1896) (Crambinae), Psammotis orientalis Munroe Mutuura, 1968, Anania albeoverbascalis Yamanaka, 1966, Anania stachydalis (Germar, 1821), and Ecpyrrhorrhoe rubiginalis (Hbner, 1796)(Pyraustinae), Scoparia iwasakii Sasaki, 1991 (Scoparinae), and Haritalodes basipunctalis (Bremer, 1864), Nagiella inferior (Hampson, 1899), Notarcha aurolinealis (Walker, 1859), Herpetogramma okamotoi Yamanaka, 1976, Glyphodes formosanus Shibuya, 1928, Mecyna fusei (Inoue, 1982), and Udea tritalis (Christoph, 1881)(Spilomelinae). Additionally, the diagnosis, distribution, pictures, and DNA barcode information of adults and male and female genitalia of these 14 crambid moth species are provided.},
}
@article {pmid36095523,
year = {2022},
author = {Rodrguez-Snchez, E and Giraldo-Kalil, LJ and Quicke, DLJ and Zaldvar-Rivern, A},
title = {Two new species of the braconid wasp genus Bracon (Braconinae) from Los Tuxtlas region in Veracruz, Mexico, reared from fruits of three species of Lauraceae.},
journal = {Zootaxa},
volume = {5162},
number = {1},
pages = {67-77},
doi = {10.11646/zootaxa.5162.1.4},
pmid = {36095523},
issn = {1175-5334},
mesh = {Animals ; *Coleoptera ; Fruit ; *Lauraceae ; Mexico ; *Wasps ; },
abstract = {Two new species belonging to the braconid genus Bracon (Braconinae) are described from the tropical rainforest of Los Tuxtlas in the state of Veracruz, Mexico, B. laurae sp. nov. and B. rosamondae sp. nov. These species are morphologically similar and were reared from fruits of three Lauraceae species, Damburneya ambigens, D. salicifolia and Nectandra turbacensis. However, comparison of their DNA barcoding locus and a fragment of the nuclear ribosomal 28S gene confirmed their allospecificity. These two species share a number of morphological features with the two described Neotropical Bracon species that are known to be phytophagous (seed predators), B. phytophagus Quicke and B. zuleideae Perioto Lara. We therefore propose a new species-group for the above four species, the B. phytophagus Quicke species-group, and suggest that the two newly described species also have a phytophagous feeding strategy.},
}
@article {pmid36095513,
year = {2022},
author = {Zhu, C and Xu, X and Zhen, Y},
title = {Two new species of Pyrocoelia Gorham (Coleoptera: Lampyridae) from Southwest China.},
journal = {Zootaxa},
volume = {5162},
number = {2},
pages = {173-182},
doi = {10.11646/zootaxa.5162.2.6},
pmid = {36095513},
issn = {1175-5334},
mesh = {Animals ; China ; *Coleoptera ; *Fireflies ; Male ; Phylogeny ; },
abstract = {Two new species of the genus Pyrocoelia Gorham, 1880, Pyrocoelia cenwanglaoensis sp. nov. and P. rubrothorax sp. nov. were described from Mt. Cenwanglaoshan of Guangxi, Southwest China. Pyrocoelia cenwanglaoensis is morphologically similar to P. pectoralis Olivier, 1883 and P. amplissima Olivier, 1886, while Pyrocoelia rubrothorax resembles P. praetexta Olivier, 1911 and P. sanguiniventer Olivier, 1911 respectively, but these species can be distinguished based on external morphological characters and male genitalia. The diagnostic features of the two new species are described and illustrated based on morphological features. Phylogenetic reconstruction using cox1 barcoding sequences confirms the two new species belong to genus Pyrocoelia. We further summarized the distribution of accepted Pyrocoelia species currently known in China.},
}
@article {pmid36095477,
year = {2022},
author = {Ashrafi, H and Anker, A and Uri, Z},
title = {Salmoneus shojaei, a new species of mangrove-dwelling alpheid shrimp (Decapoda: Caridea) from Iran.},
journal = {Zootaxa},
volume = {5165},
number = {1},
pages = {121-132},
doi = {10.11646/zootaxa.5165.1.7},
pmid = {36095477},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology ; Animals ; *Decapoda ; Iran ; RNA, Ribosomal, 16S/genetics ; },
abstract = {During a survey of the mangrove infauna on the Iranian side of the Persian Gulf and the Gulf of Oman several specimens of a new alpheid shrimp, Salmoneus shojaei sp. nov., were collected around pneumatophores of mangrove trees, mostly in association with the larger burrowing snapping shrimps of the genus Alpheus Fabricius, 1798. The new species appears to be a member of the S. gracilipes species group and is morphologically closest to S. colinorum De Grave, 2004 and S. alpheophilus Anker Marin, 2006. However, a unique combination of morphological characters, such as the carapace without rostral carina, the unarmed ischium of the major cheliped, the armed ischia of the minor cheliped and second pereiopod, the very slender dactyli of the fourth and third pereiopods, and the posterior margin of the telson with a deep U-shaped notch, distinguishes the new species from all other members of the S. gracilipes group. In addition, S. shojaei sp. nov. presents a diagnostic, albeit very faint, banding of the pleon, which separates it from most other species of the S. gracilipes group with known colour patterns. A DNA barcode (a partial fragment of the mitochondrial gene, CO1), as well as partial fragments of the mitochondrial 16S rRNA and the nuclear H3 genes, are provided to genetically characterise the new taxon.},
}
@article {pmid36095451,
year = {2022},
author = {Barbagallo, S and Cocuzza, GEM},
title = {Description of a new Myzocallis (Hemiptera Aphididae) living on Valonia oak in Southern Italy with DNA barcoding accounts on allied species-group.},
journal = {Zootaxa},
volume = {5183},
number = {1},
pages = {187-202},
doi = {10.11646/zootaxa.5183.1.15},
pmid = {36095451},
issn = {1175-5334},
mesh = {Animals ; *Aphids/anatomy &amp; histology/genetics ; DNA Barcoding, Taxonomic ; Female ; Italy ; Nymph ; *Quercus/genetics ; },
abstract = {The aphid Myzocallis macrolepidis sp. n. is described from the Apulia region, Italy, where it was collected on Quercus macrolepis. The new taxon has a pale-yellow colour in life as alate viviparous females and paler nymphs. Its life cycle remains unknown at present, as sexual morphs were not yet collected; nevertheless, being the aphid host plant a deciduous oak species, very probably the insect performs a monoecious holocycle. Morphologically most similar aphids are M. occidentalis and M. schreiberi from which the new species can be mainly distinguished by the different ratio of last rostral joint to second hind tarsomer and a few other morphological and ecological features. The molecular analysis also confirms the genetic difference of the new taxon from the other allied congeneric species, and molecular differences are briefly discussed.},
}
@article {pmid36095450,
year = {2022},
author = {Dederich, AE and Halbert, SE and VON Dohlen, CD},
title = {Description of a new species of Hamamelistes forming galls on Fothergilla spp. (Hamamelidaceae) and the generic limits of Hormaphidini (Sternorrhyncha: Aphididae: Hormaphidinae).},
journal = {Zootaxa},
volume = {5183},
number = {1},
pages = {203-219},
doi = {10.11646/zootaxa.5183.1.16},
pmid = {36095450},
issn = {1175-5334},
mesh = {Animals ; *Aphids ; *Hamamelidaceae ; },
abstract = {Hamamelistes and Hormaphis aphids of the tribe Hormaphidini are distributed disjunctly in eastern North America and Eurasia. Host-alternating species have life cycles encompassing generations in a gall on witch-hazel (Hamamelis spp.) and generations on leaves of birch (Betula spp.). In Hamamelistes, generations on witch-hazel induce globular pouch galls on flower or leaf buds. Herbarium specimens of a related Hamamelidaceae genus, Fothergilla, contain large galls in place of the seed head. We obtained a fresh sample of these elongate pouch galls collected from F. milleri in Alabama, USA. The galls were formed in place of fruiting structures and contained numerous aphids. Examination of morphology and the cytochrome oxidase subunit I barcode DNA sequence confirmed that the aphids are an undescribed species of Hamamelistes. Here, we describe the new species, Hamamelistes blackmani Dederich von Dohlen sp. n., from the morphology of foundresses, immatures, and winged forms in the gall. The life cycle is presumed monoecious. In addition, we review the evidence for including other genera in Hormaphidini and recommend that this tribe be restricted to Hamamelistes and Hormaphis.},
}
@article {pmid36095437,
year = {2022},
author = {Barjadze, S and Halbert, SE and Moore, MR and Kanturski, M},
title = {Morphology, molecular phylogenetics, and DNA barcoding revealed a new unusual species of the aphid genus Pleotrichophorus from the USA (Insecta, Hemiptera: Aphididae).},
journal = {Zootaxa},
volume = {5183},
number = {1},
pages = {390-422},
doi = {10.11646/zootaxa.5183.1.29},
pmid = {36095437},
issn = {1175-5334},
mesh = {Animals ; *Aphids ; *Asteraceae ; DNA Barcoding, Taxonomic ; Female ; Microscopy, Electron, Scanning ; Phylogeny ; United States ; },
abstract = {Here, we present the descriptions of a new aphid species in the genus Pleotrichophorus Brner, 1930 (Hemiptera: Aphididae: Macrosiphini), found by Kenneth L. Hibbard, inspection supervisor for the Florida Department of Agriculture and Consumer Services, Division of Plant Industry. It is associated with Euthamia graminifolia (L.) Nutt. (Asteraceae) a native plant species in Florida, USA. Apterous and alate viviparous and oviparous females of Pleotrichophorus blackmani sp. n. are described and illustrated using light and scanning electron microscopy (SEM). SEM images of apterous viviparous female of Pleotrichophorus glandulosus (Kaltenbach, 1846), type species of the genus Pleotrichophorus, are given for the first time. Taxonomic notes are given, and an updated key to the apterae of the Euthamia-feeding aphids is provided. A multigene phylogenetic analyses of two New World Pleotrichophorus species places the genus in the tribe Macrosiphini sensu stricto. Pleotrichophorus glandulosus, the type species of the genus, was described from Germany. European specimens of P. glandulosus from France had similar molecular sequences to both Florida species, strongly suggesting that the new species belongs in Pleotrichophorus. COI and gnd sequence data indicate that P. blackmani sp. n. can be identified reliably by DNA barcodes.},
}
@article {pmid36095398,
year = {2022},
author = {Nefediev, PS},
title = {Review of the genus Schizoturanius Verhoeff, 1931, with the description of a new species from the Altais, Asian Russia (Diplopoda: Polydesmida: Polydesmidae).},
journal = {Zootaxa},
volume = {5174},
number = {3},
pages = {262-276},
doi = {10.11646/zootaxa.5174.3.4},
pmid = {36095398},
issn = {1175-5334},
mesh = {Animals ; *Arthropods ; Microscopy, Electron, Scanning ; Phylogeny ; Russia ; },
abstract = {Schizoturanius krugovae sp. nov. is described from the Tigirek State Nature Reserve and its immediate adjacent areas in the Altai Krai, southwestern Siberia, Russia. The new species is diagnosed and described using scanning electron microscopy, compound microscopy, and genetic data. The list of all accepted species of the genus Schizoturanius, notes on their distribution and other short remarks are given. A brief phylogenetic analysis for three Schizoturanius species is provided, and barcoding information (a fragment of the mitochondrial COI nucleotide sequence) of the new species has been deposited in GenBank. A key is presented to all nine species of the genus, and their distribution is mapped.},
}
@article {pmid36095375,
year = {2022},
author = {Mukherjee, B and Hazra, N},
title = {Two new species of Demicryptochironomus Lenz, 1941 from India with tentative phylogenetic relationship and a revised world key to known males (Diptera: Chironomidae).},
journal = {Zootaxa},
volume = {5175},
number = {1},
pages = {88-100},
doi = {10.11646/zootaxa.5175.1.4},
pmid = {36095375},
issn = {1175-5334},
mesh = {Animals ; *Chironomidae ; India ; Male ; Phylogeny ; },
abstract = {Demicryptochironomus (s. str.) praeacutus sp. n. and D. (Irmakia) dividuus sp. n. are described based on adult males from India. A revised world key to the known males of the genus and molecular barcodes of both species are provided. A tentative phylogenetic relationship based on morphological characters of adult males of the genus Demicryptochironomus Lenz is also proposed.},
}
@article {pmid36095358,
year = {2022},
author = {Pal, S and Kumar, V and Panjaliya, RK and Tyagi, K},
title = {A new genus and species of subfamily Dendrothripinae (Thysanoptera: Thripidae) from India.},
journal = {Zootaxa},
volume = {5175},
number = {3},
pages = {383-388},
doi = {10.11646/zootaxa.5175.3.5},
pmid = {36095358},
issn = {1175-5334},
mesh = {Animals ; India ; *Thysanoptera ; },
abstract = {Jammuthrips paikulensis gen. et sp. n. is described from Jammu Kashmir, Union territory of India and the morphological relationships among the closely related genera of subfamily Dendrothripinae are discussed. Key to Indian genera of subfamily Dendrothripinae is provided. Two DNA barcodes of new species were generated and submitted to The Barcode of Life Data Systems (BOLD).},
}
@article {pmid36095338,
year = {2022},
author = {Kabalak, M and Karacaolu, A and Blg, HA and Karaguzel, D and Karaaslan, A},
title = {Erratum: MAHMUT KABALAK, AAAN KARACAOLU, HAYRYE AKEL BLG, DILARA KARAGUZEL amp; AATAY KARAASLAN (2022) Comparisons of two cryptic Ampedus species (Coleoptera: Elateridae) by using classical systematics, ecological niche modeling, and DNA barcoding. Zootaxa, 5154 (4): 454468.},
journal = {Zootaxa},
volume = {5175},
number = {5},
pages = {600},
doi = {10.11646/zootaxa.5175.5.9},
pmid = {36095338},
issn = {1175-5334},
}
@article {pmid36093941,
year = {2023},
author = {Petterson, SA and Sørensen, MD and Burton, M and Thomassen, M and Kruse, TA and Michaelsen, SR and Kristensen, BW},
title = {Differential expression of checkpoint markers in the normoxic and hypoxic microenvironment of glioblastomas.},
journal = {Brain pathology (Zurich, Switzerland)},
volume = {33},
number = {1},
pages = {e13111},
pmid = {36093941},
issn = {1750-3639},
support = {4183-00183//Danish Medical Research Council/ ; },
mesh = {Adult ; Humans ; *Glioblastoma ; Biomarkers, Tumor/genetics ; T-Lymphocytes ; Macrophages/metabolism ; Hypoxia ; Tumor Microenvironment ; },
abstract = {Glioblastoma is the most common primary malignant brain tumor in adults with an overall survival of only 14.6 months. Hypoxia is known to play a role in tumor aggressiveness but the influence of hypoxia on the immune microenvironment is not fully understood. The aim of this study was to investigate the expression of immune-related proteins in normoxic and hypoxic tumor areas by digital spatial profiling. Tissue samples from 10 glioblastomas were stained with a panel of 40 antibodies conjugated to photo-cleavable oligonucleotides. The free oligo-tags from normoxic and hypoxic areas were hybridized to barcodes for digital counting. Differential expression patterns were validated by Ivy Glioblastoma Atlas Project (GAP) data and an independent patient cohort. We found that CD44, Beta-catenin and B7-H3 were upregulated in hypoxia, whereas VISTA, CD56, KI-67, CD68 and CD11c were downregulated. PD-L1 and PD-1 were not affected by hypoxia. Focusing on the checkpoint-related markers CD44, B7-H3 and VISTA, our findings for CD44 and VISTA could be confirmed with Ivy GAP RNA sequencing data. Immunohistochemical staining and digital quantification of CD44, B7-H3 and VISTA in an independent cohort confirmed our findings for all three markers. Additional stainings revealed fewer T cells and high but equal amounts of tumor-associated microglia and macrophages in both hypoxic and normoxic regions. In conclusion, we found that CD44 and B7-H3 were upregulated in areas with hypoxia whereas VISTA was downregulated together with the presence of fewer T cells. This heterogeneous expression should be taken into consideration when developing novel therapeutic strategies.},
}
@article {pmid36087263,
year = {2022},
author = {Sigal, N and Maecker, HT},
title = {Mass Cytometry Assessment of Cell Phenotypes and Signaling States in Human Whole Blood.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2543},
number = {},
pages = {113-128},
pmid = {36087263},
issn = {1940-6029},
support = {U19 AI057229/AI/NIAID NIH HHS/United States ; U24 CA224309/CA/NCI NIH HHS/United States ; },
mesh = {Cytokines ; Flow Cytometry/methods ; Humans ; *Immunologic Tests ; Phenotype ; *Signal Transduction ; },
abstract = {Phosphoflow is a powerful tool that allows researchers to measure distinct signaling responses to various stimuli in multiple subpopulations of cells. Extension of this technique to mass cytometry (cytometry by time-of-flight or CyTOF) allows many more cell phenotypes and signaling nodes to be interrogated in parallel. The use of fresh whole blood is ideal for capturing the in vivo signaling state of all leukocytes, including granulocytes. In this chapter, we provide a detailed protocol for performing CyTOF phosphoflow in human whole blood, using cytokines and other stimuli. Barcoding and combining of multiple samples and other techniques to reduce batch effects and provide optimal comparability between samples/stimulations are also described.},
}
@article {pmid36087262,
year = {2022},
author = {Drápela, S and Fedr, R and Vacek, O and Remšík, J and Souček, K},
title = {High-Throughput, Parallel Flow Cytometry Screening of Hundreds of Cell Surface Antigens Using Fluorescent Barcoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2543},
number = {},
pages = {99-111},
pmid = {36087262},
issn = {1940-6029},
mesh = {*Antigens, Surface ; Biomarkers/analysis ; Flow Cytometry ; Fluorescent Dyes ; *Research ; },
abstract = {Multicolor flow cytometry allows for analysis of tens of cellular parameters in millions of cells at a single-cell resolution within minutes. The lack of technologies that would facilitate feasible and relatively cheap profiling of such a number of cells with an antibody-based approach led us to the development of a high-throughput cytometry-based platform for surface profiling. We coupled the fluorescent cell barcoding with preexisting, commercially available screening tools to analyze cell surface fingerprint at a large scale. This powerful approach will help to identify novel biomarkers and druggable targets and facilitate the discovery of new concepts in immunology, oncology, and developmental biology.},
}
@article {pmid36087202,
year = {2022},
author = {Malone, M and Ma, KY and Zhang, SQ and Jiang, N},
title = {Tetramer-Associated T Cell Receptor Sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2574},
number = {},
pages = {183-208},
pmid = {36087202},
issn = {1940-6029},
mesh = {High-Throughput Nucleotide Sequencing ; *Receptors, Antigen, T-Cell/genetics ; *T-Lymphocytes ; },
abstract = {Linking antigen specificity to T cell receptor (TCR) sequences is critical, albeit challenging, to both understanding T cell biology and developing T cell-based therapeutics. Here, we describe in detail tetramer-associated TCR sequencing (TetTCR-Seq), a novel approach to tackling this challenge. TetTCR-Seq is accomplished by multiplexing DNA-barcoded peptide-MHC (pMHC) tetramers, allowing for simultaneous recall of antigen specificity and TCR sequences after single cell sequencing. Additionally, TetTCR-Seq simplifies labor and cuts cost by taking advantage of in vitro transcription and translation (IVTT) to generate peptide libraries and DNA barcodes, in parallel, from the same template. Thus, TetTCR-Seq is a powerful technology capable of quickly and affordably surveying the T cell repertoire for hundreds of antigen specificities in a single experiment.},
}
@article {pmid36087201,
year = {2022},
author = {Jivanjee, T and Ibrahim, S and Nyquist, SK and Gatter, GJ and Bromley, JD and Jaiswal, S and Berger, B and Behar, SM and Love, JC and Shalek, AK},
title = {Enriching and Characterizing T Cell Repertoires from 3' Barcoded Single-Cell Whole Transcriptome Amplification Products.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2574},
number = {},
pages = {159-182},
pmid = {36087201},
issn = {1940-6029},
support = {R35 GM141861/GM/NIGMS NIH HHS/United States ; T32 GM087237/GM/NIGMS NIH HHS/United States ; },
mesh = {Receptors, Antigen, T-Cell/genetics ; Sequence Analysis, RNA/methods ; Single-Cell Analysis/methods ; *T-Lymphocytes ; *Transcriptome ; },
abstract = {Antigen-specific T cells play an essential role in immunoregulation and many diseases such as cancer. Characterizing the T cell receptor (TCR) sequences that encode T cell specificity is critical for elucidating the antigenic determinants of immunological diseases and designing therapeutic remedies. However, methods of obtaining single-cell TCR sequencing data are labor and cost intensive, typically requiring both cell sorting and full-length single-cell RNA-sequencing (scRNA-seq). New high-throughput 3' cell-barcoding scRNA-seq methods can simplify and scale this process; however, they do not routinely capture TCR sequences during library preparation and sequencing. While 5' cell-barcoding scRNA-seq methods can be used to examine TCR repertoire at single-cell resolution, doing so requires specialized reagents which cannot be applied to samples previously processed using 3' cell-barcoding methods.Here, we outline a method for sequencing TCRα and TCRβ transcripts from samples already processed using 3' cell-barcoding scRNA-seq platforms, ensuring TCR recovery at a single-cell resolution. In short, a fraction of the 3' barcoded whole transcriptome amplification (WTA) product typically used to generate a massively parallel 3' scRNA-seq library is enriched for TCR transcripts using biotinylated probes and further amplified using the same universal primer sequence from WTA. Primer extension using TCR V-region primers and targeted PCR amplification using a second universal primer result in a 3' barcoded single-cell CDR3-enriched library that can be sequenced with custom sequencing primers. Coupled with 3' scRNA-seq of the same WTA, this method enables simultaneous analysis of single-cell transcriptomes and TCR sequences which can help interpret inherent heterogeneity among antigen-specific T cells and salient disease biology. The method presented here can also be adapted readily to enrich and sequence other transcripts of interest from both 3' and 5' barcoded scRNA-seq WTA libraries.},
}
@article {pmid36083558,
year = {2022},
author = {Satz, AL and Cui, W},
title = {Analysis of DNA-Encoded Library Screening Data: Selection of Molecules for Synthesis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2541},
number = {},
pages = {195-205},
pmid = {36083558},
issn = {1940-6029},
mesh = {Base Sequence ; *DNA/chemistry/genetics ; Gene Library ; *Small Molecule Libraries/chemistry ; },
abstract = {DNA-encoded library (DEL) screens are used to discover novel chemical matter capable of modulating the activity of pharmaceutically interesting protein targets. DEL selections are accomplished by immobilizing a target protein on a resin and capturing library molecules that bind to the target. The barcodes of the captured library molecules are then amplified and sequenced. This chapter outlines simple methods for visualizing the resulting screening data (using free open-source software), such that enriched molecules can be selected for synthesis and follow-up activity confirmation. Measures of enrichment and the concept of sub-libraries are also illustrated.},
}
@article {pmid36083548,
year = {2022},
author = {Xu, H and Ma, P},
title = {DNA Encoding of Natural Products.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2541},
number = {},
pages = {81-87},
pmid = {36083548},
issn = {1940-6029},
mesh = {*Biological Products ; *Combinatorial Chemistry Techniques/methods ; DNA/chemistry/genetics ; Gene Library ; Humans ; Small Molecule Libraries/chemistry ; },
abstract = {DNA-encoded library (DEL) links the powers of genetics and chemicals via high-efficient enzymatic ligation of DNA barcodes and the "split and pool" combinatorial synthesis. Natural products (NPs) are evolutionary optimized compounds that have played a key role in the history of human drug discovery. Herein, we describe a method for functionality-independent annotation of complex natural products with amplifiable DNA barcodes to generate a DNA-encoded natural product library (nDEL). This method provides a simple and practical solution to leverage natural products by DNA barcoding.},
}
@article {pmid36083348,
year = {2022},
author = {Du, Q and Li, J and Wang, L and Chen, H and Jiang, M and Chen, Z and Jiang, C and Gao, H and Wang, B and Liu, C},
title = {Complete chloroplast genomes of two medicinal Swertia species: the comparative evolutionary analysis of Swertia genus in the Gentianaceae family.},
journal = {Planta},
volume = {256},
number = {4},
pages = {73},
pmid = {36083348},
issn = {1432-2048},
support = {2018FY100705//National Science &amp;Technology Fundamental Resources Investigation Program of China/ ; 2021-I2M-1-022//Chinese Academy of Medical Sciences, Innovation Funds for Medical Sciences/ ; 81872966//National Science Foundation/ ; 2020-ZJ-Y20//Qinghai Provincial Key Laboratory of Phytochemistry of Qinghai Tibet Plateau/ ; 2018SK52001//Hunan technological innovation guidance project/ ; },
mesh = {Codon ; *Genome, Chloroplast/genetics ; *Gentianaceae/genetics ; Microsatellite Repeats/genetics ; Phylogeny ; RNA, Transfer/genetics ; *Swertia/genetics ; },
abstract = {The complete chloroplast genome of Swertia kouitchensis has been sequenced and assembled, compared with that of S. bimaculata to determine the evolutionary relationships among species of the Swertia in the Gentianaceae family. Swertia kouitchensis and S. bimaculata are from the Gentianaceae family. The complete chloroplast genome of S. kouitchensis was newly assembled, annotated, and analyzed by Illumina Hiseq 2500 platform. The chloroplast genomes of the two species encoded a total of 133, 134 genes, which included 88-89 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA genes. One intron was contained in each of the eight protein-coding genes and eight tRNA-coding genes, whereas two introns were found in two genes (ycf3 and clpP). The most abundant codon of the two species was for isoleucine, and the least abundant codon was for cysteine. The number of microsatellite repeat sequences was twenty-eight and thirty-two identified in the chloroplast genomes of S. kouitchensis and S. bimaculata, respectively. A total of 1127 repeat sequences were identified in all the 23 Swertia chloroplast genomes, and they fell into four categories. Furthermore, five divergence hotspot regions can be applied to discriminate these 23 Swertia species through genomes comparison. One pair of genus-specific DNA barcodes primer has been accurately identified. Therefore, the diverse regions cloned by a specific primer may become an effective and powerful molecular marker for the identification of Swertia genus. Moreover, four genes (ccsA, ndhK, rpoC1, and rps12) were positive selective pressure. The phylogenetic tree showed that the 23 Swertia species were clustered into a large clade including four evident subbranches, whereas the two species of S. kouitchensis and S. bimaculata were separately clustered into the diverse but correlated species group.},
}
@article {pmid36080967,
year = {2022},
author = {Khan, G and Hegge, A and Gemeinholzer, B},
title = {Development and Testing of the A1 Volumetric Air Sampler, an Automatic Pollen Trap Suitable for Long-Term Monitoring of eDNA Pollen Diversity.},
journal = {Sensors (Basel, Switzerland)},
volume = {22},
number = {17},
pages = {},
pmid = {36080967},
issn = {1424-8220},
support = {01LC19031//Federal Ministry of Education and Research/ ; },
mesh = {*Air Pollutants/analysis ; Biodiversity ; *Environmental Monitoring/methods ; Humans ; Pollen/chemistry ; },
abstract = {Airborne pollen surveys provide information on various aspects of biodiversity and human health monitoring. Such surveys are typically conducted using the Burkard Multi-Vial Cyclone Sampler, but have to be technically optimized for eDNA barcoding. We here developed and tested a new airborne pollen trap, especially suitable for autonomous eDNA-metabarcoding analyses, called the A1 volumetric air sampler. The trap can sample pollen in 24 different tubes with flexible intervals, allowing it to operate independently in the field for a certain amount of time. We compared the efficiency of the new A1 volumetric air sampler with another automated volumetric spore trap, the Burkard Multi-Vial Cyclone Sampler, which features shorter and fewer sampling intervals to evaluate the comparability of ambient pollen concentrations. In a sterile laboratory environment, we compared trap performances between the automated volumetric air samplers by using pure dry pollen of three species-Fagus sylvatica, Helianthus annuus and Zea mays-which differ both by exine ornamentation and pollen size. The traps had a standard suction flow rate of 16.5 L/min, and we counted the inhaled pollen microscopically after a predefined time interval. Our results showed that though we put three different pollen types in the same container, both the traps inhaled all the pollens in a statistically significant manner irrespective of their size. We found that, on average, both traps inhaled equal an number of pollens for each species. We did not detect any cross-contamination between tubes. We concluded that the A1 volumetric air sampler has the potential to be used for longer and more flexible sampling intervals in the wild, suitable for autonomous monitoring of eDNA pollen diversity.},
}
@article {pmid36077793,
year = {2022},
author = {Vaquero-Siguero, N and Schleussner, N and Volk, J and Mastel, M and Meier, J and Jackstadt, R},
title = {Modeling Colorectal Cancer Progression Reveals Niche-Dependent Clonal Selection.},
journal = {Cancers},
volume = {14},
number = {17},
pages = {},
pmid = {36077793},
issn = {2072-6694},
support = {NA//Dietmar Hopp Stiftung/ ; },
abstract = {Colorectal cancer (CRC) is among the deadliest cancers worldwide, with metastasis being the main cause of patient mortality. During CRC progression the complex tumor ecosystem changes in its composition at virtually every stage. However, clonal dynamics and associated niche-dependencies at these stages are unknown. Hence, it is of importance to utilize models that faithfully recapitulate human CRC to define its clonal dynamics. We used an optical barcoding approach in mouse-derived organoids (MDOs) that revealed niche-dependent clonal selection. Our findings highlight that clonal selection is controlled by a site-specific niche, which critically contributes to cancer heterogeneity and has implications for therapeutic intervention.},
}
@article {pmid36076185,
year = {2022},
author = {Xiao, TW and Ge, XJ},
title = {Plastome structure, phylogenomics, and divergence times of tribe Cinnamomeae (Lauraceae).},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {642},
pmid = {36076185},
issn = {1471-2164},
support = {XDB31000000//Chinese Academy of Sciences/ ; XDB31000000//Chinese Academy of Sciences/ ; },
mesh = {Evolution, Molecular ; *Lauraceae/genetics ; Phylogeny ; Plastids/genetics ; },
abstract = {BACKGROUND: Tribe Cinnamomeae is a species-rich and ecologically important group in tropical and subtropical forests. Previous studies explored its phylogenetic relationships and historical biogeography using limited loci, which might result in biased molecular dating due to insufficient parsimony-informative sites. Thus, 15 plastomes were newly sequenced and combined with published plastomes to study plastome structural variations, gene evolution, phylogenetic relationships, and divergence times of this tribe.<br><br>RESULTS: Among the 15 newly generated plastomes, 14 ranged from 152,551&#x2009;bp to 152,847&#x2009;bp, and the remaining one (Cinnamomum chartophyllum XTBGLQM0164) was 158,657&#x2009;bp. The inverted repeat (IR) regions of XTBGLQM0164 contained complete ycf2, trnI[CAU], rpl32, and rpl2. Four hypervariable plastid loci (ycf1, ycf2, ndhF-rpl32-trnL[UAG], and petA-psbJ) were identified as candidate DNA barcodes. Divergence times based on a few loci were primarily determined by prior age constraints rather than by DNA data. In contrast, molecular dating using complete plastid protein-coding genes (PCGs) was determined by DNA data rather than by prior age constraints. Dating analyses using PCGs showed that Cinnamomum sect. Camphora diverged from C. sect. Cinnamomum in the late Oligocene (27.47&#x2009;Ma).<br><br>CONCLUSIONS: This study reports the first case of drastic IR expansion in tribe Cinnamomeae, and indicates that plastomes have sufficient parsimony-informative sites for molecular dating. Besides, the dating analyses provide preliminary insights into the divergence time within tribe Cinnamomeae and can facilitate future studies on its historical biogeography.},
}
@article {pmid36076168,
year = {2022},
author = {Peng, JY and Zhang, XS and Zhang, DG and Wang, Y and Deng, T and Huang, XH and Kuang, TH and Zhou, Q},
title = {Newly reported chloroplast genome of Sinosenecio albonervius Y. Liu &amp; Q. E. Yang and comparative analyses with other Sinosenecio species.},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {639},
pmid = {36076168},
issn = {1471-2164},
support = {31860117//National Natural Science Foundation of China/ ; 31860117//National Natural Science Foundation of China/ ; 31860117//National Natural Science Foundation of China/ ; 31860117//National Natural Science Foundation of China/ ; 31860117//National Natural Science Foundation of China/ ; 31860117//National Natural Science Foundation of China/ ; 31860117//National Natural Science Foundation of China/ ; 31860117//National Natural Science Foundation of China/ ; },
mesh = {*Asteraceae/genetics ; Chloroplasts/genetics ; *Genome, Chloroplast ; Microsatellite Repeats/genetics ; Phylogeny ; },
abstract = {BACKGROUND: Sinosenecio B. Nordenstam (Asteraceae) currently comprises 44 species. To investigate the interspecific relationship, several chloroplast markers, including ndhC-trnV, rpl32-trnL, matK, and rbcL, are used to analyze the phylogeny of Sinosenecio. However, the chloroplast genomes of this genus have not been thoroughly investigated. We sequenced and assembled the Sinosenecio albonervius chloroplast genome for the first time. A detailed comparative analysis was performed in this study using the previously reported chloroplast genomes of three Sinosenecio species.<br><br>RESULTS: The results showed that the chloroplast genomes of four Sinosenecio species exhibit a typical quadripartite structure. There are equal numbers of total genes, protein-coding genes and RNA genes among the annotated genomes. Per genome, 49-56 simple sequence repeats and 99 repeat sequences were identified. Thirty codons were identified as RSCU values greater than 1 in the chloroplast genome of S. albonervius based on 54 protein-coding genes, indicating that they showed biased usage. Among 18 protein-coding genes, 46 potential RNA editing sites were discovered. By comparing these chloroplast genomes' structures, inverted repeat regions and coding regions were more conserved than single-copy and non-coding regions. The junctions among inverted repeat and single-copy regions showed slight difference. Several hot spots of genomic divergence were detected, which can be used as new DNA barcodes for species identification. Phylogenetic analysis of the whole chloroplast genome showed that the four Sinosenecio species have close interspecific relationships.<br><br>CONCLUSIONS: The complete chloroplast genome of Sinosenecio albonervius was revealed in this study, which included a comparison of Sinosenecio chloroplast genome structure, variation, and phylogenetic analysis for related species. These will help future research on Sinosenecio taxonomy, identification, origin, and evolution to some extent.},
}
@article {pmid36076164,
year = {2022},
author = {Yang, L and Abduraimov, O and Tojibaev, K and Shomurodov, K and Zhang, YM and Li, WJ},
title = {Analysis of complete chloroplast genome sequences and insight into the phylogenetic relationships of Ferula L.},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {643},
pmid = {36076164},
issn = {1471-2164},
support = {FZ-20200929321//Taxonomic revision of polymorphic plant families of the flora of Uzbekistan/ ; Grant No.2021xjkk0600//The work was supported by the Third Xinjiang Scientific Expedition Program/ ; 2019FY100204//the National Science and Technology Basic Program of China/ ; 2021E01020//the Shanghai cooperation organization partnership and international technology cooperation plan of science and technology projects/ ; No. 2019429//Youth Innovation Promotion Association Foundation of the Chinese Academy of Sciences, China/ ; },
mesh = {*Ferula/genetics ; *Genome, Chloroplast ; Microsatellite Repeats ; Phylogeny ; },
abstract = {BACKGROUND: Ferula L. is one of the largest and most taxonomically complicated genera as well as being an important medicinal plant resource in the family Apiaceae. To investigate the plastome features and phylogenetic relationships of Ferula and its neighboring genera Soranthus Ledeb., Schumannia Kuntze., and Talassia Korovin, we sequenced 14 complete plastomes of 12 species. RESULTS: The size of the 14 complete chloroplast genomes ranged from 165,607 to 167,013 base pairs (bp) encoding 132 distinct genes (87 protein-coding, 37 tRNA, and 8 rRNA genes), and showed a typical quadripartite structure with a pair of inverted repeats (IR) regions. Based on comparative analysis, we found that the 14 plastomes were similar in codon usage, repeat sequence, simple sequence repeats (SSRs), and IR borders, and had significant collinearity. Based on our phylogenetic analyses, Soranthus, Schumannia, and Talassia should be considered synonymous with Ferula. Six highly divergent regions (rps16/trnQ-UUG, trnS-UGA/psbZ, psbH/petB, ycf1/ndhF, rpl32, and ycf1) were also detected, which may represent potential molecular markers, and combined with selective pressure analysis, the weak positive selection gene ccsA may be a discriminating DNA barcode for Ferula species.<br><br>CONCLUSION: Plastids contain abundant informative sites for resolving phylogenetic relationships. Combined with previous studies, we suggest that there is still much room for improvement in the classification of Ferula. Overall, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of this genus.},
}
@article {pmid36075938,
year = {2022},
author = {Godunko, RJ and Alba-Tercedor, J and Grabowski, M and Rewicz, T and Staniczek, AH},
title = {Cenozoic origins of the genus Calliarcys (Insecta, Ephemeroptera) revealed by Micro-CT, with DNA barcode gap analysis of Leptophlebiinae and Habrophlebiinae.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {15228},
pmid = {36075938},
issn = {2045-2322},
mesh = {*Amber ; Animals ; DNA Barcoding, Taxonomic ; *Ephemeroptera ; Fossils ; Insecta ; X-Ray Microtomography ; },
abstract = {Mayflies (Ephemeroptera) are among the oldest pterygote insects, with the earliest fossils dating back to the Late Carboniferous. Within mayflies, Leptophlebiidae are a highly diverse and widespread group, with approximately 140 genera and 640 species. Whereas taxonomy, systematics, and phylogeny of extant Leptophlebiidae are in the focus of extensive studies, little is known about leptophlebiid fossil taxa. Because fossil remains of Ephemeroptera in sedimentary rocks are relatively rare, inclusions of mayflies in amber are a unique source of information on their evolution and diversity in the past. Leptophlebiidae found in Cenozoic resins mostly belong to the subfamilies Leptophlebiinae (in Eocene Baltic amber) and Atalophlebiinae (in Miocene Dominican and Mexican ambers). In the present contribution, we confirm the first finding of the genus Calliarcys from Eocene Baltic amber by using Micro-CT, which allowed confirming its generic placement by visualizing diagnostic key characters otherwise hidden by a cloud of turbidity. Additionally, we present first molecular data on the extant species Calliarcys humilis Eaton, 1881 from the Iberian Peninsula and the barcode gap analysis for Leptophlebiinae and Habrophlebiinae.},
}
@article {pmid36073103,
year = {2022},
author = {Geldenhuys, S and Boltman, C and Steinberg, WJ and Botes, J and Van Rooyen, C},
title = {Clinical review of the clinical necessity of lumbar punctures performed on adults at National District Hospital Emergency Department.},
journal = {South African family practice : official journal of the South African Academy of Family Practice/Primary Care},
volume = {64},
number = {1},
pages = {e1-e8},
pmid = {36073103},
issn = {2078-6204},
mesh = {Adult ; Emergency Service, Hospital ; *Hospitals, District ; Humans ; Lipopolysaccharides ; Retrospective Studies ; *Spinal Puncture/methods ; },
abstract = {BACKGROUND: Previous studies have found that indications for lumbar punctures (LPs) are managed differently, which raises the question of whether all LPs performed are clinically necessary. This study aimed to determine whether unnecessary (clinically not indicated) LPs were being performed at a district hospital in the Free State, South Africa.<br><br>METHOD: This was a retrospective descriptive study. A list from the National Health Laboratory Service (NHLS) was used to identify all patients on whom an LP was performed in the adult emergency department of National District Hospital (NDH) in Bloemfontein, from 1 January 2018 to 30 June 2018. Data were captured on a data sheet and included demographic information, clinical signs and symptoms the patients presented with and the cerebrospinal fluid results.<br><br>RESULTS: A total of 364 patients fit the inclusion criteria. Of these patients, 97 files (26.6%) could not be found, patient gender and LP results could be retrieved from the NHLS barcodes. After reviewing the presenting symptoms and signs captured on the 267 files, the primary researcher considered 150 (56.4%) of the LPs performed to have been carried out unnecessarily. From the total population of 364 patients, 246 (67.6%) of the LP results were normal. Only 118 (32.4%) of the LPs performed showed some form of central nervous system pathology. Of the 150 LPs assessed to have been unnecessarily performed, 124 (84.0%) were normal.<br><br>CONCLUSION: This retrospective review indicates that a high percentage of LPs that were clinically not indicated were performed at NDH during the study period.},
}
@article {pmid36070299,
year = {2022},
author = {Fuchs, S and Babin, L and Andraos, E and Bessiere, C and Willier, S and Schulte, JH and Gaspin, C and Meggetto, F},
title = {Generation of full-length circular RNA libraries for Oxford Nanopore long-read sequencing.},
journal = {PloS one},
volume = {17},
number = {9},
pages = {e0273253},
pmid = {36070299},
issn = {1932-6203},
mesh = {High-Throughput Nucleotide Sequencing/methods ; Humans ; *Nanopores ; RNA/genetics ; *RNA, Circular ; Sequence Analysis, RNA/methods ; },
abstract = {Circular RNA (circRNA) is a noncoding RNA class with important implications for gene expression regulation, mostly by interaction with other RNA species or RNA-binding proteins. While the commonly applied short-read Illumina RNA-sequencing techniques can be used to detect circRNAs, their full sequence is not revealed. However, the complete sequence information is needed to analyze potential interactions and thus the mechanism of action of circRNAs. Here, we present an improved protocol to enrich and sequence full-length circRNAs by using the Oxford Nanopore long-read sequencing platform. The protocol involves an enrichment of lowly abundant circRNAs by exonuclease treatment and negative selection of linear RNAs. Then, a cDNA library is created and amplified by PCR. This protocol provides enough material for several sequencing runs. The library is used as input for ligation-based sequencing together with native barcoding. Stringent quality control of the libraries is ensured by a combination of Qubit, Fragment Analyzer and qRT-PCR. Multiplexing of up to 4 libraries yields in total more than 1-2 Million reads per library, of which 1-2% are circRNA-specific reads with >99% of them full-length. The protocol works well with human cancer cell lines. We further provide suggestions for the bioinformatic analysis of the created data, as well as the limitations of our approach together with recommendations for troubleshooting and interpretation. Taken together, this protocol enables reliable full-length analysis of circRNAs, a noncoding RNA type involved in a growing number of physiologic and pathologic conditions. Metadata Associated content. https://dx.doi.org/10.17504/protocols.io.rm7vzy8r4lx1/v2.},
}
@article {pmid36068087,
year = {2022},
author = {Xavier, JKAM and da Trindade, RCS and Cibelle Moreira, E and Figueiredo, PLB and Maia, JGS and Setzer, WN and da Silva, JKR},
title = {The Volatile Profiles and DNA Barcodes of Lauraceae Species from the Ocotea Complex with Occurrence in the Brazilian Amazon.},
journal = {Chemistry &amp; biodiversity},
volume = {19},
number = {10},
pages = {e202200337},
doi = {10.1002/cbdv.202200337},
pmid = {36068087},
issn = {1612-1880},
support = {//National Council for Scientific and Technological Development (CNPq, Brazilian Government)/ ; },
mesh = {*Ocotea/chemistry ; *Lauraceae/genetics/chemistry ; Brazil ; DNA Barcoding, Taxonomic ; Phylogeny ; Bayes Theorem ; *Oils, Volatile/chemistry ; Terpenes ; *Sesquiterpenes ; Plant Extracts ; },
abstract = {The Ocotea complex accommodates most of the taxonomic diversity of Neotropical Lauraceae with economic importance and biological potential attributed to their essential oils (EOs) and extracts. However, the botanical taxonomy has had limitations due to the difficulty of identifying and delimiting species and genera. The chemical and molecular markers of Ocotea complex species in Pará state, Brazil, were assessed according to their EO compositions and DNA sequences of matK, trnL-trnF, and ITS regions. The multivariate analysis of EOs constituents has classified them into two main clusters characterized by oils rich in (I) terpenoids and phenylpropanoids and (II) sesquiterpenes. We conducted a phylogenetic analysis of species based on DNA barcode sequences on the Bayesian Inference (PP: 0.70-1,0) and Maximum Likelihood (BS: 72-100 %). The comparison between the volatile profiles and phylogenetic data indicates two main groups for these species collected from the Ocotea complex.},
}
@article {pmid36065846,
year = {2022},
author = {Martin, PCN and Kim, H and Lövkvist, C and Hong, BW and Won, KJ},
title = {Vesalius: high-resolution in silico anatomization of spatial transcriptomic data using image analysis.},
journal = {Molecular systems biology},
volume = {18},
number = {9},
pages = {e11080},
pmid = {36065846},
issn = {1744-4292},
mesh = {Animals ; Mice ; *Transcriptome/genetics ; },
abstract = {Characterization of tissue architecture promises to deliver insights into development, cell communication, and disease. In silico spatial domain retrieval methods have been developed for spatial transcriptomics (ST) data assuming transcriptional similarity of neighboring barcodes. However, domain retrieval approaches with this assumption cannot work in complex tissues composed of multiple cell types. This task becomes especially challenging in cellular resolution ST methods. We developed Vesalius to decipher tissue anatomy from ST data by applying image processing technology. Vesalius uniquely detected territories composed of multiple cell types and successfully recovered tissue structures in high-resolution ST data including in mouse brain, embryo, liver, and colon. Utilizing this tissue architecture, Vesalius identified tissue morphology-specific gene expression and regional specific gene expression changes for astrocytes, interneuron, oligodendrocytes, and entorhinal cells in the mouse brain.},
}
@article {pmid36064961,
year = {2022},
author = {Iwanami, N and Petersen, M and Diekhoff, D and Boehm, T},
title = {Clonal dynamics underlying the skewed CD4/CD8 ratio of mouse thymocytes revealed by TCR-independent barcoding.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {911},
pmid = {36064961},
issn = {2399-3642},
mesh = {Animals ; CD4-Positive T-Lymphocytes ; CD8-Positive T-Lymphocytes ; Cells, Cultured ; Mice ; *Receptors, Antigen, T-Cell, alpha-beta/genetics ; *Thymocytes ; },
abstract = {T cell differentiation in the thymus generates CD4[+] helper and cytotoxic CD8[+] cells as the two principal T cell lineages. Curiously, at the end of this complex selection process, CD4[+] cells invariably outnumber CD8[+] cells. Here, we examine the dynamics of repertoire formation and the emergence of the skewed CD4/CD8 ratio using high-resolution endogenous CRISPR/Cas9 barcoding that indelibly marks immature T cells at the DN2/DN3 pre-TCR stage. In wild-type mice, greater clone size of CD4[+] cells and an intrinsically greater probability of Tcr β clonotypes for pMHCII interactions are major contributors to the skewed CD4/CD8 ratio. Clonal perturbations of thymocyte differentiation following the precocious expression of a rearranged iNKT invariant TCR α chain are due to loss of Tcr β clonotypes from the CD4 lineage-committed pre-selection repertoire. The present barcoding scheme offers a novel means to examine the clonal dynamics of lymphocyte differentiation orthogonal to that using TCR clonotypes.},
}
@article {pmid36062164,
year = {2022},
author = {Lalli, M and Yen, A and Thopte, U and Dong, F and Moudgil, A and Chen, X and Milbrandt, J and Dougherty, JD and Mitra, RD},
title = {Measuring transcription factor binding and gene expression using barcoded self-reporting transposon calling cards and transcriptomes.},
journal = {NAR genomics and bioinformatics},
volume = {4},
number = {3},
pages = {lqac061},
pmid = {36062164},
issn = {2631-9268},
support = {P50 HD103525/HD/NICHD NIH HHS/United States ; RF1 MH117070/MH/NIMH NIH HHS/United States ; RF1 MH126723/MH/NIMH NIH HHS/United States ; T32 HG000045/HG/NHGRI NIH HHS/United States ; },
abstract = {Calling cards technology using self-reporting transposons enables the identification of DNA-protein interactions through RNA sequencing. Although immensely powerful, current implementations of calling cards in bulk experiments on populations of cells are technically cumbersome and require many replicates to identify independent insertions into the same genomic locus. Here, we have drastically reduced the cost and labor requirements of calling card experiments in bulk populations of cells by introducing a DNA barcode into the calling card itself. An additional barcode incorporated during reverse transcription enables simultaneous transcriptome measurement in a facile and affordable protocol. We demonstrate that barcoded self-reporting transposons recover in vitro binding sites for four basic helix-loop-helix transcription factors with important roles in cell fate specification: ASCL1, MYOD1, NEUROD2 and NGN1. Further, simultaneous calling cards and transcriptional profiling during transcription factor overexpression identified both binding sites and gene expression changes for two of these factors. Lastly, we demonstrated barcoded calling cards can record binding in vivo in the mouse brain. In sum, RNA-based identification of transcription factor binding sites and gene expression through barcoded self-reporting transposon calling cards and transcriptomes is an efficient and powerful method to infer gene regulatory networks in a population of cells.},
}
@article {pmid36061787,
year = {2022},
author = {Shen, J and Li, P and Wang, Y and Yang, K and Li, Y and Yao, H and Wang, Q and Xiao, P and He, C},
title = {Pharmacophylogenetic study of Scutellaria baicalensis and its substitute medicinal species based on the chloroplast genomics, metabolomics, and active ingredient.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {951824},
pmid = {36061787},
issn = {1664-462X},
abstract = {The genetic relationships among the species in Scutellaria genus remain unclear because of the variation in the number of species and complex trait. The usage of S. baicalensis and its four substitute medicinal species (S. amoena, S. hypericifolia, S. likiangensis, and S. viscidula) in traditional medicines make their specialized metabolism important in China, but interspecific genetic and chemical differences have rarely been reported for these species. In this study, the chloroplast genomes of four substitute species for S. baicalensis were assembled, and comparative and phylogenetic analyses were performed with these species and other Scutellaria relatives. In addition, metabolomics analyses were performed and the contents of the main active compounds were determined to reveal the interspecific chemical diversity of S. baicalensis and its four substitute species. The full lengths of their chloroplast genomes ranged from 151,574 to 151,816 bp with an average GC content of 38.34%, and a total of 113 genes were annotated. In the chloroplast genomes of S. baicalensis and its four substitutes, one hypervariable region (petA-psbL) is proposed as a potential DNA barcode. Phylogenetic analysis showed that the subdivision of the genus Scutellaria should be reconsidered. The metabolomics and content determination analyses showed that the four species exhibit a metabolism similar to that of S. baicalensis in different parts. Except for the roots of S. likiangensis, all parts of the substitute species showed high contents of baicalin. Genetic and chemical analyses of four substitute medicinal species for S. baicalensis were performed here for the first time, and their pharmacophylogenetic relationships were further explored, providing a scientific basis for the subsequent development of the medicinal value and resource utilization of Scutellaria.},
}
@article {pmid36060568,
year = {2022},
author = {Dawan, J and Ahn, J},
title = {Application of DNA barcoding for ensuring food safety and quality.},
journal = {Food science and biotechnology},
volume = {31},
number = {11},
pages = {1355-1364},
pmid = {36060568},
issn = {2092-6456},
abstract = {With increasing international food trade, food quality and safety are high priority worldwide. The consumption of contaminated and adulterated food can cause serious health problems such as infectious diseases and allergies. Therefore, the authentication and traceability systems are needed to improve food safety. The mitochondrial DNA can be used for species authentication of food and food products. Effective DNA barcode markers have been developed to correctly identify species. The US FDA approved to the use of DNA barcoding for various food products. The DNA barcoding technology can be used as a regulatory tool for identification and authenticity. The application of DNA barcoding can reduce the microbiological and toxicological risks associated with the consumption of food and food products. DNA barcoding can be a gold-standard method in food authenticity and fraud detection. This review describes the DNA barcoding method for preventing food fraud and adulteration in meat, fish, and medicinal plants.},
}
@article {pmid36059898,
year = {2022},
author = {Chen, Q and Bakhshi, M and Balci, Y and Broders, KD and Cheewangkoon, R and Chen, SF and Fan, XL and Gramaje, D and Halleen, F and Jung, MH and Jiang, N and Jung, T and Májek, T and Marincowitz, S and Milenković, I and Mostert, L and Nakashima, C and Nurul Faziha, I and Pan, M and Raza, M and Scanu, B and Spies, CFJ and Suhaizan, L and Suzuki, H and Tian, CM and Tomšovský, M and Úrbez-Torres, JR and Wang, W and Wingfield, BD and Wingfield, MJ and Yang, Q and Yang, X and Zare, R and Zhao, P and Groenewald, JZ and Cai, L and Crous, PW},
title = {Genera of phytopathogenic fungi: GOPHY 4.},
journal = {Studies in mycology},
volume = {101},
number = {},
pages = {417-564},
pmid = {36059898},
issn = {0166-0616},
abstract = {This paper is the fourth contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions and information about the pathology, distribution, hosts and disease symptoms, as well as DNA barcodes for the taxa covered. Moreover, 12 whole-genome sequences for the type or new species in the treated genera are provided. The fourth paper in the GOPHY series covers 19 genera of phytopathogenic fungi and their relatives, including Ascochyta, Cadophora, Celoporthe, Cercospora, Coleophoma, Cytospora, Dendrostoma, Didymella, Endothia, Heterophaeomoniella, Leptosphaerulina, Melampsora, Nigrospora, Pezicula, Phaeomoniella, Pseudocercospora, Pteridopassalora, Zymoseptoria, and one genus of oomycetes, Phytophthora. This study includes two new genera, 30 new species, five new combinations, and 43 typifications of older names. Taxonomic novelties: New genera: Heterophaeomoniella L. Mostert, C.F.J. Spies, Halleen &amp; Gramaje, Pteridopassalora C. Nakash. &amp; Crous; New species: Ascochyta flava Qian Chen &amp; L. Cai, Cadophora domestica L. Mostert, R. van der Merwe, Halleen &amp; Gramaje, Cadophora rotunda L. Mostert, R. van der Merwe, Halleen &amp; Gramaje, Cadophora vinacea J.R. Úrbez-Torres, D.T. O'Gorman &amp; Gramaje, Cadophora vivarii L. Mostert, Havenga, Halleen &amp; Gramaje, Celoporthe foliorum H. Suzuki, Marinc. &amp; M.J. Wingf., Cercospora alyssopsidis M. Bakhshi, Zare &amp; Crous, Dendrostoma elaeocarpi C.M. Tian &amp; Q. Yang, Didymella chlamydospora Qian Chen &amp; L. Cai, Didymella gei Qian Chen &amp; L. Cai, Didymella ligulariae Qian Chen &amp; L. Cai, Didymella qilianensis Qian Chen &amp; L. Cai, Didymella uniseptata Qian Chen &amp; L. Cai, Endothia cerciana W. Wang. &amp; S.F. Chen, Leptosphaerulina miscanthi Qian Chen &amp; L. Cai, Nigrospora covidalis M. Raza, Qian Chen &amp; L. Cai, Nigrospora globospora M. Raza, Qian Chen &amp; L. Cai, Nigrospora philosophiae-doctoris M. Raza, Qian Chen &amp; L. Cai, Phytophthora transitoria I. Milenković, T. Májek &amp; T. Jung, Phytophthora panamensis T. Jung, Y. Balci, K. Broders &amp; I. Milenković, Phytophthora variabilis T. Jung, M. Horta Jung &amp; I. Milenković, Pseudocercospora delonicicola C. Nakash., L. Suhaizan &amp; I. Nurul Faziha, Pseudocercospora farfugii C. Nakash., I. Araki, &amp; Ai Ito, Pseudocercospora hardenbergiae Crous &amp; C. Nakash., Pseudocercospora kenyirana C. Nakash., L. Suhaizan &amp; I. Nurul Faziha, Pseudocercospora perrottetiae Crous, C. Nakash. &amp; C.Y. Chen, Pseudocercospora platyceriicola C. Nakash., Y. Hatt, L. Suhaizan &amp; I. Nurul Faziha, Pseudocercospora stemonicola C. Nakash., Y. Hatt., L. Suhaizan &amp; I. Nurul Faziha, Pseudocercospora terengganuensis C. Nakash., Y. Hatt., L. Suhaizan &amp; I. Nurul Faziha, Pseudocercospora xenopunicae Crous &amp; C. Nakash.; New combinations: Heterophaeomoniella pinifoliorum (Hyang B. Lee et al.) L. Mostert, C.F.J. Spies, Halleen &amp; Gramaje, Pseudocercospora pruni-grayanae (Sawada) C. Nakash. &amp; Motohashi., Pseudocercospora togashiana (K. Ito &amp; Tak. Kobay.) C. Nakash. &amp; Tak. Kobay., Pteridopassalora nephrolepidicola (Crous &amp; R.G. Shivas) C. Nakash. &amp; Crous, Pteridopassalora lygodii (Goh &amp; W.H. Hsieh) C. Nakash. &amp; Crous; Typification: Epitypification: Botrytis infestans Mont., Cercospora abeliae Katsuki, Cercospora ceratoniae Pat. &amp; Trab., Cercospora cladrastidis Jacz., Cercospora cryptomeriicola Sawada, Cercospora dalbergiae S.H. Sun, Cercospora ebulicola W. Yamam., Cercospora formosana W. Yamam., Cercospora fukuii W. Yamam., Cercospora glochidionis Sawada, Cercospora ixorana J.M. Yen &amp; Lim, Cercospora liquidambaricola J.M. Yen, Cercospora pancratii Ellis &amp; Everh., Cercospora pini-densiflorae Hori &amp; Nambu, Cercospora profusa Syd. &amp; P. Syd., Cercospora pyracanthae Katsuki, Cercospora horiana Togashi &amp; Katsuki, Cercospora tabernaemontanae Syd. &amp; P. Syd., Cercospora trinidadensis F. Stevens &amp; Solheim, Melampsora laricis-urbanianae Tak. Matsumoto, Melampsora salicis-cupularis Wang, Phaeoisariopsis pruni-grayanae Sawada, Pseudocercospora angiopteridis Goh &amp; W.H. Hsieh, Pseudocercospora basitruncata Crous, Pseudocercospora boehmeriigena U. Braun, Pseudocercospora coprosmae U. Braun &amp; C.F. Hill, Pseudocercospora cratevicola C. Nakash. &amp; U. Braun, Pseudocercospora cymbidiicola U. Braun &amp; C.F. Hill, Pseudocercospora dodonaeae Boesew., Pseudocercospora euphorbiacearum U. Braun, Pseudocercospora lygodii Goh &amp; W.H. Hsieh, Pseudocercospora metrosideri U. Braun, Pseudocercospora paraexosporioides C. Nakash. &amp; U. Braun, Pseudocercospora symploci Katsuki &amp; Tak. Kobay. ex U. Braun &amp; Crous, Septogloeum punctatum Wakef.; Neotypification: Cercospora aleuritis I. Miyake; Lectotypification: Cercospora dalbergiae S.H. Sun, Cercospora formosana W. Yamam., Cercospora fukuii W. Yamam., Cercospora glochidionis Sawada, Cercospora profusa Syd. &amp; P. Syd., Melampsora laricis-urbanianae Tak. Matsumoto, Phaeoisariopsis pruni-grayanae Sawada, Pseudocercospora symploci Katsuki &amp; Tak. Kobay. ex U. Braun &amp; Crous. Citation: Chen Q, Bakhshi M, Balci Y, Broders KD, Cheewangkoon R, Chen SF, Fan XL, Gramaje D, Halleen F, Horta Jung M, Jiang N, Jung T, Májek T, Marincowitz S, Milenković T, Mostert L, Nakashima C, Nurul Faziha I, Pan M, Raza M, Scanu B, Spies CFJ, Suhaizan L, Suzuki H, Tian CM, Tomšovský M, Úrbez-Torres JR, Wang W, Wingfield BD, Wingfield MJ, Yang Q, Yang X, Zare R, Zhao P, Groenewald JZ, Cai L, Crous PW (2022). Genera of phytopathogenic fungi: GOPHY 4. Studies in Mycology 101: 417-564. doi: 10.3114/sim.2022.101.06.},
}
@article {pmid36056960,
year = {2022},
author = {da Silva, BR and Vanstreels, RET and Serafini, PP and Fontana, CS and da Silva, TW and Chiarani, E and Carvalho, AM and Ferreira Junior, FC and Braga, &#xc9;M and Locatelli-Dittrich, R},
title = {Blood parasites of passerines in the Brazilian Pampas and their implications for a potential population supplementation program for the endangered Yellow Cardinal (Gubernatrix cristata).},
journal = {Parasitology research},
volume = {121},
number = {11},
pages = {3203-3215},
pmid = {36056960},
issn = {1432-1955},
support = {422053/2016-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 309438/2016-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 304334/2019-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 1717498//National Science Foundation/ ; APQ-00645-18//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; },
mesh = {Animals ; *Bird Diseases/parasitology ; Brazil ; Dietary Supplements ; Ecosystem ; *Haemosporida/genetics ; *Lepidoptera ; *Parasites/genetics ; Phylogeny ; *Protozoan Infections, Animal/epidemiology/parasitology ; *Sparrows ; },
abstract = {Espinilho savanna ("seasonal steppe savanna") is a unique vegetation formation of the Pampas biome that is found near the tri-border of Brazil, Uruguay, and Argentina. The Yellow Cardinal (Gubernatrix cristata) is a flagship species of this ecosystem, but it is classified as "critically endangered" in Brazil due to habitat loss and poaching for the illegal trade. Population supplementation through the release of individuals that were captive-bred or apprehended by authorities from the illegal trade has been considered as a conservation strategy for this species; however, the risk of pathogen introduction is a critical concern. We used microscopy and molecular methods to investigate the occurrence of blood parasites in wild passerines (n = 64, including three Yellow Cardinals) at Espinilho State Park, Rio Grande do Sul, Brazil, and in captive Yellow Cardinals (n = 30) at three facilities in Brazil. Haemosporidian parasites were detected in the blood smears of 10.9% of the wild passerines, comprising the morphospecies Haemoproteus erythrogravidus in Rufous-collared Sparrow (Zonotrichia capensis), H. quiscalus in Grayish Baywing (Agelaioides badius), and H. tyranni in Great Kiskadee (Pitangus sulphuratus); these are the southernmost records for these morphospecies and their first record for the Pampas biome. No haemosporidian parasites were detected in the blood smears of the Yellow Cardinals, wild or captive. Microfilariae were detected in the blood smears of 14.1% of the wild passerines, including all wild Yellow Cardinals, and in 43.3% of captive Yellow Cardinals. Trypanosoma sp. was detected in the blood smear of one captive Yellow Cardinal. Nested PCR and gene sequencing of the cyt-b gene of Haemoproteus/Plasmodium was used to test a subset of wild passerines and captive Yellow Cardinals, allowing for the molecular barcoding of H. quiscalus lineage AGEBAD04 and H. tyranni lineage PITSUL01; additionally, DNA identical to that of lineage PITSUL01 was detected in the blood of one captive Yellow Cardinal. This study provides valuable data to support the conservation management of the Yellow Cardinal and other threatened passerines from the Pampas and highlights the need for further studies on the epidemiology and pathology of filarioid worms and trypanosomes in passerines from this biome.},
}
@article {pmid36052346,
year = {2022},
author = {Gadalla, R and Boukhaled, GM and Brooks, DG and Wang, BX},
title = {Mass cytometry immunostaining protocol for multiplexing clinical samples.},
journal = {STAR protocols},
volume = {3},
number = {3},
pages = {101643},
pmid = {36052346},
issn = {2666-1667},
support = {FDN148386//CIHR/Canada ; },
mesh = {*Antibodies ; Flow Cytometry/methods ; *Isotopes ; Palladium ; Staining and Labeling ; },
abstract = {This is a cytometry by time-of-flight (CyTOF) staining protocol for hematopoietic-derived cells, that leverages live-cell barcoding using receptor-type tyrosine-protein phosphatase C (CD45) antibodies conjugated to metal isotopes in combination with DNA-based palladium barcoding to multiplex up to 40 samples. In this protocol, DNA-based barcoding is performed before surface and intracellular immunostaining, which reduces the batch effects that result from day-to-day variations in staining and instrument sensitivity. This protocol also reduces antibody consumption and eliminates the need for repeated instrument adjustment.},
}
@article {pmid36051302,
year = {2022},
author = {Palumbo, F and Draga, S and Scariolo, F and Gabelli, G and Sacilotto, GB and Gazzola, M and Barcaccia, G},
title = {First genomic insights into the Mandevilla genus.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {983879},
pmid = {36051302},
issn = {1664-462X},
abstract = {Mandevilla (Apocynaceae) is a greatly appreciated genus in the world ornamental market. In this study, we attempted to address the poor genetic knowledge and the huge taxonomic gaps existing in this genus by analyzing a collection of 55 accessions. After cytometrically determining the triploid genome size (1,512.64 Mb) of a reference sample (variety "Mandevilla 2001"), the plastidial genome (cpDNA, 0.18 Mb) and a draft of the nuclear genome (nuDNA, 207 Mb) were assembled. While cpDNA was effective in reconstructing the phylogenesis of the Apocynaceae family based on a DNA superbarcoding approach, the nuDNA assembly length was found to be only 41% of the haploid genome size (506 Mb, predicted based on the K-mer frequency distribution). Its annotation enabled the prediction of 37,811 amino acid sequences, of which 10,562 resulted full length proteins. Among them, we identified nine proteins whose orthologs (in Catharanthus roseus) are involved in the biosynthesis of monoterpene indole alkaloids (MIAs), including catharanthine, tabersonine, and vincadifformine. The nuclear genome draft was also useful to develop a highly informative (average polymorphism information content, PIC = 0.62) set of 23 simple sequence repeat (SSR) markers that was validated on the Mandevilla collection. These results were integrated with cytometric measurements, nuclear ITS1 haplotyping and chloroplast DNA barcoding analyses to assess the origin, divergence and relationships existing among the 55 accessions object of the study. As expected, based on the scarce information available in the literature, the scenario was extremely intricate. A reasonable hypothesis is that most of the accessions represent interspecific hybrids sharing the same species as maternal parent (i.e., Mandevilla sanderi).},
}
@article {pmid36047242,
year = {2022},
author = {Khan, MU and Andleeb, S and Khan, MF and Mustafa, RG},
title = {Molecular Characterization and Phylogenetic Analysis of Earthworm Species Collected from Different Soil Habitats of Poonch Division Azad Jammu and Kashmir Pakistan.},
journal = {Journal of oleo science},
volume = {71},
number = {9},
pages = {1349-1361},
doi = {10.5650/jos.ess21450},
pmid = {36047242},
issn = {1347-3352},
mesh = {Animals ; Ecosystem ; *Oligochaeta/genetics ; Pakistan ; Phylogeny ; Soil ; },
abstract = {This study aims to analyze molecular characterization and phylogenetic analysis of earthworm species collected from different soil habitats of Poonch division Azad Kashmir Pakistan by using CO1 gene partial sequencing methodology. Samples gathered randomly from 18 study sites (127 localities) by digging and hand sorting methods were preserved in pure ethanol at -20°C. The modified CTAB (Cetyltrimethyl ammonium bromide) method extracted high quality DNA from region of representative earthworm's caudal region. This extracted DNA was used to amplify the 700 bp partial region of the cytochrome oxidase I (COI) gene with LCO1490 and HCO2198 universal primers. All of the obtained amplified gene sequences were aligned, edited and analyzed using MEGA X software to characterize different species of earthworms. Thirty-eight (38) Barcoding sequences belonging to 11 different strains of earthworms were successfully generated. Their phylogenetic analysis revealed that 7 Barcoding sequences gave maximum similarity with the available online database, while the rest of the 4 sequences gave lower similarity than the maximum threshold level. The collected DNA barcode sequences were also clustered together by the maximum likelihood method and the resultant phylogenetic tree revealed they belong to different family lineages. Moreover the identified earthworm species have a close evolutionary link with the earthworm fauna of south and central Asia instead of Europe, which might be due to similar climate of both regions.},
}
@article {pmid36046624,
year = {2022},
author = {Wincott, CJ and Sritharan, G and Benns, HJ and May, D and Gilabert-Carbajo, C and Bunyan, M and Fairweather, AR and Alves, E and Andrew, I and Game, L and Frickel, EM and Tiengwe, C and Ewald, SE and Child, MA},
title = {Cellular barcoding of protozoan pathogens reveals the within-host population dynamics of Toxoplasma gondii host colonization.},
journal = {Cell reports methods},
volume = {2},
number = {8},
pages = {100274},
pmid = {36046624},
issn = {2667-2375},
support = {217202/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; 208780/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; /DH_/Department of Health/United Kingdom ; 202553/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; T32 AI007046/AI/NIAID NIH HHS/United States ; NC/S001239/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; FC001076/ARC_/Arthritis Research UK/United Kingdom ; R35 GM138381/GM/NIGMS NIH HHS/United States ; T32 AI055432/AI/NIAID NIH HHS/United States ; /CRUK_/Cancer Research UK/United Kingdom ; },
mesh = {Mice ; Animals ; *Toxoplasma/genetics ; Protozoan Proteins/genetics ; Mice, Inbred CBA ; Virulence ; Brain/metabolism ; },
abstract = {Cellular barcoding techniques are powerful tools to understand microbial pathogenesis. However, barcoding strategies have not been broadly applied to protozoan parasites, which have unique genomic structures and virulence strategies compared with viral and bacterial pathogens. Here, we present a CRISPR-based method to barcode protozoa, which we successfully apply to Toxoplasma gondii and Trypanosoma brucei. Using libraries of barcoded T. gondii, we evaluate shifts in the population structure from acute to chronic infection of mice. Contrary to expectation, most barcodes were present in the brain one month post-intraperitoneal infection in both inbred CBA/J and outbred Swiss mice. Although parasite cyst number and barcode diversity declined over time, barcodes representing a minor fraction of the inoculum could become a dominant population in the brain by three months post-infection. These data establish a cellular barcoding approach for protozoa and evidence that the blood-brain barrier is not a major bottleneck to colonization by T. gondii.},
}
@article {pmid36046153,
year = {2022},
author = {McDonald, ND and Rhea, KA and Davies, JP and Zacharko, JL and Berk, KL and Buckley, PE},
title = {Evaluating the persistence and stability of a DNA-barcoded microbial system in a mock home environment.},
journal = {Synthetic biology (Oxford, England)},
volume = {7},
number = {1},
pages = {ysac016},
pmid = {36046153},
issn = {2397-7000},
abstract = {Recent advancements in engineered microbial systems capable of deployment in complex environments have enabled the creation of unique signatures for environmental forensics operations. These microbial systems must be robust, able to thrive in specific environments of interest and contain molecular signatures, enabling the detection of the community across conditions. Furthermore, these systems must balance biocontainment concerns with the stability and persistence required for environmental forensics. Here we evaluate the stability and persistence of a recently described microbial system composed of germination-deficient Bacillus subtilis and Saccharomyces cerevisiae spores containing nonredundant DNA barcodes in a controlled simulated home environment. These spore-based microbial communities were found to be persistent in the simulated environment across 30-day periods and across multiple surface types. To improve the repeatability and reproducibility in detecting the DNA barcodes, we evaluated several spore lysis and sampling processes paired with Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) -CRISPR-associated proteins (Cas) detection (Sherlock). Finally, having optimized the detectability of the spores, we demonstrate that we can detect the spores transferring across multiple material types. Together, we further demonstrate the utility of a recently described microbial forensics system and highlight the importance of independent validation and verification of synthetic biology tools and applications. Graphical Abstract.},
}
@article {pmid36043652,
year = {2022},
author = {Alzahrani, DA and Abba, A and Yaradua, SS and Albokhari, EJ},
title = {An insight on the complete chloroplast genome of Gomphocarpus siniacus and Duvalia velutina, Asclepiadoideae (Apocynaceae).},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {84},
number = {},
pages = {e257145},
doi = {10.1590/1519-6984.257145},
pmid = {36043652},
issn = {1678-4375},
mesh = {*Apocynaceae/genetics ; Chloroplasts ; *Genome, Chloroplast/genetics ; Phylogeny ; },
abstract = {We studied the complete chloroplast genome of Gomphocarpus siniacus and Duvalia velutina from Asclepiadoideae subfamily; due to their medicinal importance and distribution worldwide their interest became high. In this study we analyzed the complete chloroplast genomes of G. siniacus and D. velutina using Illumina sequencing technology. The sequences were compared with the other species from Apocynaceae family. The complete genome of G. siniacus is 162,570 bp while D. velutina has154, 478 bp in length. Both genomes consist of 119 genes; encode 31 tRNA genes, and eight rRNA genes. Comparative studies of the two genomes showed variations in SSR markers in which G. siniacus possesses 223 while D. velutina has 186. This could be used for barcoding in order to aid in easy identification of the species. Phylogenetic analysis on the other hand reaffirms the tribal position of G. siniacus in Asclepiadeae and D. velutina in Ceropegieae. These findings could be used in subsequent research studies of angiosperms identification, genetic engineering, herb genomics and phylogenomic studies of Apocynaceae family.},
}
@article {pmid36043152,
year = {2022},
author = {Ikeuchi, A and Kondoh, D and Halajian, A and Ichikawa-Seki, M},
title = {Morphological and molecular characterization of Calicophoron raja (Näsmark, 1937) collected from wild Bovidae in South Africa.},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {19},
number = {},
pages = {38-43},
pmid = {36043152},
issn = {2213-2244},
abstract = {Paramphistomes, commonly known as rumen flukes, are digenean parasites that infect ruminants. Accurate morphological identification of paramphistome species is challenging and often neglected. For instance, it requires sagittal midline sections of adult flukes, which are difficult to prepare. Therefore, the majority of the genetic information on paramphistomes found in the International Nucleotide Sequence Database is not supported by morphological descriptions, and the DNA barcodes of paramphistome species remain unreliable. In the present study, both morphological and molecular characterizations were simultaneously performed to ensure the reliability of the DNA information for the paramphistome species Calichophoron raja (Näsmark, 1937). The morphological characteristics of the sagittal and horizontal sections of adult flukes from a black wildebeest (Connochaetes gnou) and a waterbuck (Kobus ellipsiprymnus) in South Africa were identical to those previously described for Ca. raja. Additionally, this study represents a new host record of the species from Co. gnou. All sequences of the internal transcribed spacer 2 region of ribosomal DNA were 100% identical among the 18 flukes analyzed in the present study. A single nucleotide mutation was observed between Ca. raja in this study and Ca. raja detected in domestic ruminants in Kenya.},
}
@article {pmid36042884,
year = {2022},
author = {Chi, WY and Au, G and Liang, J and Chen, CC and Huang, CH and Yang, JM},
title = {Imaging and analysis for simultaneous tracking of fluorescent biosensors in barcoded cells.},
journal = {STAR protocols},
volume = {3},
number = {3},
pages = {101611},
pmid = {36042884},
issn = {2666-1667},
support = {P50 CA098252/CA/NCI NIH HHS/United States ; R01 GM136711/GM/NIGMS NIH HHS/United States ; S10 OD016374/OD/NIH HHS/United States ; K22 CA212060/CA/NCI NIH HHS/United States ; },
mesh = {*Biosensing Techniques/methods ; Proteins ; },
abstract = {We recently developed a biosensor barcoding approach for highly multiplexed tracking of molecular activities in live cells. In this protocol, we detail the labeling of cells expressing different genetically encoded fluorescent biosensors with a pair of barcoding proteins and parallel imaging. Signals from cells with the same barcodes are then pooled together to obtain the dynamics of the corresponding biosensor activity. We describe the steps involved in cell barcoding, image acquisition, and analysis by deep learning models. For complete details on the use and execution of this protocol, please refer to Yang et al. (2021).},
}
@article {pmid36042168,
year = {2022},
author = {Deng, G and Gao, RR and Wang, WT and Wu, TZ and Zhang, YP and Wang, B and Xiang, L and Liu, X},
title = {Comparative Genomic and Phylogenetic Analysis of Forty Gentiana Chloroplast Genomes.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {27},
number = {8},
pages = {236},
doi = {10.31083/j.fbl2708236},
pmid = {36042168},
issn = {2768-6698},
mesh = {Base Sequence ; *Genome, Chloroplast/genetics ; Genomics ; *Gentiana/genetics ; Phylogeny ; },
abstract = {BACKGROUND: Gentiana plants, which have great medicinal and ornamental value, are widely distributed in diverse habitats and have complex taxonomy. Here 40 Gentiana chloroplast genomes were used for comparative genomic analysis and divergence time estimation.<br><br>METHODS: The complete chloroplast genome of G. rhodantha was sequenced, assembled, and annotated. Comparative genomic and phylogenetic analysis were provided for variation analysis of Gentiana.<br><br>RESULTS: Gentiana species satisfy the characteristics of intra-Sect conservation and inter-Sect variation in chloroplast genome structure and IR boundaries. All Gentiana Sects can be clustered into a single one and separated from each other; however, Ser. Apteroideae and Ser. Confertifoliae in Sect. Monopodiae are more closely related to Sect. Frigida and Sect. Cruciata, respectively. Gentiana has experienced two large gene loss events; the first, the collective loss of the rps16 gene at genus formation and the second, the collective loss of the ndh gene when Ser. Ornatae and Ser. Verticillatae completed their differentiation. Comparative genomic analysis support that Sect. Stenogyne and Sect. Otophora became the independent genera Metagentiana and Kuepferia. Seven divergence hotspot regions were screened based on Pi values, and could serve as DNA-specific barcodes for Gentiana.<br><br>CONCLUSIONS: This study provides a further theoretical basis for taxonomic analysis, genetic diversity, evolutionary mechanism and molecular identification in Gentiana.},
}
@article {pmid36035788,
year = {2022},
author = {Cheung, V and Chung, P and Feinberg, EH},
title = {Transcriptional profiling of mouse projection neurons with VECTORseq.},
journal = {STAR protocols},
volume = {3},
number = {3},
pages = {101625},
pmid = {36035788},
issn = {2666-1667},
support = {DP2 MH119426/MH/NIMH NIH HHS/United States ; P30 AI027763/AI/NIAID NIH HHS/United States ; R01 NS109060/NS/NINDS NIH HHS/United States ; S10 RR028962/RR/NCRR NIH HHS/United States ; },
mesh = {Animals ; *High-Throughput Nucleotide Sequencing ; Interneurons ; Mice ; Neurons ; *RNA ; Sequence Analysis, RNA ; },
abstract = {Existing techniques for transcriptional profiling of projection neurons could be applied to only one neuronal population per experiment. To increase throughput, we developed VECTORseq, which repurposes retrogradely infecting viruses to deliver multiplexable RNA barcodes, enabling projection anatomy to be read out in single-cell datasets. In this protocol, we describe the delivery of viral barcodes to mouse brain to label different projection neurons. We then detail single-cell or nuclei isolation for sequencing, followed by the analysis of single-cell sequencing data. For complete details on the use and execution of this protocol, please refer to Cheung et al. (2021).},
}
@article {pmid36032746,
year = {2022},
author = {Mohammad Rahimi, H and Karamati, SA and Nemati, S and Mirjalali, H and Zali, MR},
title = {Molecular Identification, Subtypes Distribution, and Alleles Discrimination of Blastocystis sp., Isolated from Immunocompromised Subjects in Iran.},
journal = {Iranian journal of parasitology},
volume = {17},
number = {2},
pages = {184-193},
pmid = {36032746},
issn = {1735-7020},
abstract = {BACKGROUND: Blastocystis sp., is a prevalent protist isolated from humans and animals, which its opportunistic role in immunocompromised patients is still controversial. The current study aimed to evaluate the subtype and alleles distribution of Blastocystis sp., among immunocompromised patients.<br><br>METHODS: Totally, 33 microscopically Blastocystis-positive stool samples, isolated from Guilan province during April 2018 to May 2019 were investigated. Total DNA extraction was performed and the barcoding region of the small subunit ribosomal RNA (SSU rRNA) gene was amplified. Targeted fragments were sequenced to characterize subtypes and relevant alleles. Phylogenetic tree was constructed using Maximum-likelihood and Tamura 3-parameter to illustrate the correlation between subtypes and certain immunodeficiency.<br><br>RESULTS: Subtype analysis revealed the presence of ST1, ST2, ST3, and ST7 among 13/33 (39.4%), 5 (15.2%), 14/33 (42.4%), and 1/33 (3%), of samples, respectively. ST1 was the major subtype among cancer patients 5/7 (71.42%), while ST3 was the predominant subtype among rheumatoid arthritis (RA) patients 3/6 (50%), internal ward patients 5/10 (50%), and asthma and allergy patients 2/3 (66.66%). ST7 was isolated from a patient hospitalized in internal ward. No significant correlation was seen between the type of immunodeficiency and subtypes (P-value = 0.771). The phylogenetic tree showed no separation regarding the type of immunodeficiency.<br><br>CONCLUSION: Among studied immunocompromised patients, ST3 was the most prevalent subtype followed by ST1. There was no specific correlation between subtypes and alleles with type of immunodeficiency. Putative zoonotic alleles were highlighted the probability of zoonotic transmission for Blastocystis sp.},
}
@article {pmid36028901,
year = {2022},
author = {Stow, EC and Baddoo, M and LaRosa, AJ and LaCoste, D and Deininger, P and Belancio, V},
title = {SCIFER: approach for analysis of LINE-1 mRNA expression in single cells at a single locus resolution.},
journal = {Mobile DNA},
volume = {13},
number = {1},
pages = {21},
pmid = {36028901},
issn = {1759-8753},
support = {R01 AG057597/AG/NIA NIH HHS/United States ; },
abstract = {BACKGROUND: Endogenous expression of L1 mRNA is the first step in an L1-initiated mutagenesis event. However, the contribution of individual cell types to patterns of organ-specific L1 mRNA expression remains poorly understood, especially at single-locus resolution. We introduce a method to quantify expression of mobile elements at the single-locus resolution in scRNA-Seq datasets called Single Cell Implementation to Find Expressed Retrotransposons (SCIFER). SCIFER aligns scRNA-Seq reads uniquely to the genome and extracts alignments from single cells by cell-specific barcodes. In contrast to the alignment performed using default parameters, this alignment strategy increases accuracy of L1 locus identification by retaining only reads that are uniquely mapped to individual L1 loci. L1 loci expressed in single cells are unambiguously identified using a list of L1 loci manually validated to be expressed in bulk RNA-Seq datasets generated from the same cell line or organ.<br><br>RESULTS: Validation of SCIFER using MCF7 cells determined technical parameters needed for optimal detection of L1 expression in single cells. We show that unsupervised analysis of L1 expression in single cells exponentially inflates both the levels of L1 expression and the number of expressed L1 loci. Application of SCIFER to analysis of scRNA-Seq datasets generated from mouse and human testes identified that mouse Round Spermatids and human Spermatogonia, Spermatocytes, and Round Spermatids express the highest levels of L1 mRNA. Our analysis also determined that similar to mice, human testes from unrelated individuals share as much as 80% of expressed L1 loci. Additionally, SCIFER determined that individual mouse cells co-express different L1 sub-families and different families of transposable elements, experimentally validating their co-existence in the same cell.<br><br>CONCLUSIONS: SCIFER detects mRNA expression of individual L1 loci in single cells. It is compatible with scRNA-Seq datasets prepared using traditional sequencing methods. Validated using a human cancer cell line, SCIFER analysis of mouse and human testes identified key cell types supporting L1 expression in these species. This will further our understanding of differences and similarities in endogenous L1 mRNA expression patterns in mice and humans.},
}
@article {pmid36028808,
year = {2022},
author = {Dong, S and Zhou, M and Zhu, J and Wang, Q and Ge, Y and Cheng, R},
title = {The complete chloroplast genomes of Tetrastigma hemsleyanum (Vitaceae) from different regions of China: molecular structure, comparative analysis and development of DNA barcodes for its geographical origin discrimination.},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {620},
pmid = {36028808},
issn = {1471-2164},
support = {LGF22H280005//the Basic Public Welfare Research Project of Zhejiang Province/ ; 2021JKZKTS020B//the Research Project of Zhejiang Chinese Medical University/ ; },
mesh = {DNA Barcoding, Taxonomic ; *Genome, Chloroplast ; Molecular Structure ; Phylogeny ; *Vitaceae ; },
abstract = {BACKGROUND: Tetrastigma hemsleyanum is a valuable traditional Chinese medicinal plant widely distributed in the subtropical areas of China. It belongs to the Cayratieae tribe, family Vitaceae, and exhibited significant anti-tumor and anti-inflammatory activities. However, obvious differences were observed on the quality of T. hemsleyanum root from different regions, requiring the discrimination strategy for the geographical origins.<br><br>RESULT: This study characterized five complete chloroplast (cp) genomes of T. hemsleynum samples from different regions, and conducted a comparative analysis with other representing species from family Vitaceae to reveal the structural variations, informative markers and phylogenetic relationships. The sequenced cp genomes of T. hemsleyanum exhibited a conserved quadripartite structure with full length ranging from 160,124&#x2009;bp of Jiangxi Province to 160,618&#x2009;bp of Zhejiang Province. We identified 112 unique genes (80 protein-coding, 28 tRNA and 4 rRNA genes) in the cp genomes of T. hemsleyanum with highly similar gene order, content and structure. The IR contraction/expansion events occurred on the junctions of ycf1, rps19 and rpl2 genes with different degrees, causing the differences of genome sizes in T. hemsleyanum and Vitaceae plants. The number of SSR markers discovered in T. hemsleyanum was 56-57, exhibiting multiple differences among the five geographic groups. Phylogenetic analysis based on conserved cp genome proteins strongly grouped the five T. hemsleyanum species into one clade, showing a sister relationship with T. planicaule. Comparative analysis of the cp genomes from T. hemsleyanum and Vitaceae revealed five highly variable spacers, including 4 intergenic regions and one protein-coding gene (ycf1). Furthermore, five mutational hotspots were observed among T. hemsleyanum cp genomes from different regions, providing data for designing DNA barcodes trnL and trnN. The combination of molecular markers of trnL and trnN clustered the T. hemsleyanum samples from different regions into four groups, thus successfully separating specimens of Sichuan and Zhejiang from other areas.<br><br>CONCLUSION: Our study obtained the chloroplast genomes of T. hemsleyanum from different regions, and provided a potential molecular tracing tool for determining the geographical origins of T. hemsleyanum, as well as important insights into the molecular identification approach and and phylogeny in Tetrastigma genus and Vitaceae family.},
}
@article {pmid36015403,
year = {2022},
author = {Bosi, G and De Felice, S and Wilkinson, MJ and Allainguillaume, J and Arru, L and Nascimbene, J and Buldrini, F},
title = {Brassica and Sinapis Seeds in Medieval Archaeological Sites: An Example of Multiproxy Analysis for Their Identification and Ethnobotanical Interpretation.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {16},
pages = {},
pmid = {36015403},
issn = {2223-7747},
abstract = {The genus Brassica includes some of the most important vegetable and oil crops worldwide. Many Brassica seeds (which can show diagnostic characters useful for species identification) were recovered from two archaeological sites in northern Italy, dated from between the Middle Ages and the Renaissance. We tested the combined use of archaeobotanical keys, ancient DNA barcoding, and references to ancient herbarium specimens to address the issue of diagnostic uncertainty. An unequivocal conventional diagnosis was possible for much of the material recovered, with the samples dominated by five Brassica species and Sinapis. The analysis using ancient DNA was restricted to the seeds with a Brassica-type structure and deployed a variant of multiplexed tandem PCR. The quality of diagnosis strongly depended on the molecular locus used. Nevertheless, many seeds were diagnosed down to species level, in concordance with their morphological identification, using one primer set from the core barcode site (matK). The number of specimens found in the Renaissance herbaria was not high; Brassica nigra, which is of great ethnobotanical importance, was the most common taxon. Thus, the combined use of independent means of species identification is particularly important when studying the early use of closely related crops, such as Brassicaceae.},
}
@article {pmid36015028,
year = {2022},
author = {Silva-Campos, M and Nadiminti, P and Cahill, D},
title = {Rapid and Accurate Detection of Gnomoniopsis smithogilvyi the Causal Agent of Chestnut Rot, through an Internally Controlled Multiplex PCR Assay.},
journal = {Pathogens (Basel, Switzerland)},
volume = {11},
number = {8},
pages = {},
pmid = {36015028},
issn = {2076-0817},
support = {n/a//Premium Chestnuts Australia/ ; },
abstract = {The fungus Gnomoniopsis smithogilvyi is a significant threat to the production of sweet chestnut (Castanea sativa) nuts in Australia and worldwide. The pathogen causes nut rot, which leads to substantial production losses. Early and accurate diagnosis of the disease is essential to delineate and implement control strategies. A specific and sensitive multiplex PCR was developed based on the amplification of three barcode sequences of G. smithogilvyi. The assay reliability was enhanced by including the amplification of a host gene as an internal control. Primers were thoroughly evaluated in silico before assessing them in vitro. Primer annealing temperature and concentration were optimised to enhance the assay sensitivity and specificity. The assay detection limit ranged between 0.1 and 1.0 pg (5 and 50 fg/μL) of genomic DNA per reaction. No cross-reactivity was observed with genomic DNA from closely and distantly related fungal species. We also characterised Australian G. smithogilvyi isolates phenotypically and genotypically and found significant differences in morphologic and virulence traits of the isolates. An understanding of the virulence of G. smithogilvyi and the availability of a reliable and accurate diagnostic technique will enable earlier detection of the pathogen, which will contribute to effective control strategies for the disease.},
}
@article {pmid36013986,
year = {2022},
author = {Franco-Duarte, R and Fernandes, I and Gulis, V and Cássio, F and Pascoal, C},
title = {ITS rDNA Barcodes Clarify Molecular Diversity of Aquatic Hyphomycetes.},
journal = {Microorganisms},
volume = {10},
number = {8},
pages = {},
pmid = {36013986},
issn = {2076-2607},
support = {PTDC / CTA-AMB / 31245/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; UIDB/04050/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; NSF DEB-1655797//National Science Foundation/ ; },
abstract = {Aquatic hyphomycetes are key microbial decomposers of allochthonous organic matter in freshwater ecosystems. Although their importance in carbon flow and food webs in streams is widely recognized, there are still gaps in our understanding of their molecular diversity and distribution patterns. Our study utilized the growing database of ITS rDNA barcodes of aquatic hyphomycetes (1252 sequences) and aimed to (i) produce new barcodes for some lesser-known taxa; (ii) clarify the taxonomic placement of some taxa at the class or order level, based on molecular data; and (iii) provide insights into the biogeographical origins of some taxa. This study increased the number of aquatic hyphomycete species with available ITS barcodes from 119 (out of ~300 species described) to 136. Phylogenetically, the 136 species were distributed between 2 phyla, 6 classes, and 10 orders of fungi. Future studies should strive to increase the database of ITS sequences, especially focusing on species with unclear phylogenetic relationships (incertae sedis) and with few sequences available. The geographical distribution of species with available ITS sequences included 50 countries from five continents, but 6 countries had more than 20 species associated, showing a bias toward the northern hemisphere, likely due to sampling bias.},
}
@article {pmid36013950,
year = {2022},
author = {Portier, P and Taghouti, G and Bertrand, PE and Briand, M and Dutrieux, C and Lathus, A and Fischer-Le Saux, M},
title = {Analysis of the Diversity of Xylophilus ampelinus Strains Held in CIRM-CFBP Reveals a Strongly Homogenous Species.},
journal = {Microorganisms},
volume = {10},
number = {8},
pages = {},
pmid = {36013950},
issn = {2076-2607},
support = {Lycovitis//National Research Institute for Agriculture, Food and Environment/ ; Taxomic//National Research Institute for Agriculture, Food and Environment/ ; },
abstract = {Xylophilus ampelinus is the causal agent of blight and canker on grapevine. Only a few data are available on this species implying that the occurrence of this pathogen may be underestimated, and its actual ecological niche may not be understood. Moreover, its genetic diversity is not well known. To improve our knowledge of this species, an analysis of the complete genome sequences available in NCBI was performed. It appeared that several sequences are misidentified. The complete genome sequence of the type strain was obtained and primers designed in order to sequence gyrB and rpoD genes for the strains held in CIRM-CFBP. The genetic barcoding data were obtained for 93 strains, isolated over 35 years and from several geographical origins. The species revealed to be strongly homogenous, displaying nearly identical sequences for all strains. However, the oldest strains of this collection were isolated in 2001 therefore, a new isolation campaign and epidemiological surveys are necessary, along with the obtention of new complete genome sequences for this species.},
}
@article {pmid36012792,
year = {2022},
author = {Oliveira, M and Azevedo, L},
title = {Molecular Markers: An Overview of Data Published for Fungi over the Last Ten Years.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {8},
pages = {},
pmid = {36012792},
issn = {2309-608X},
support = {POCI-01-0145-FEDER-007274//COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI)/ ; },
abstract = {Fungi are amongst the most abundant and diverse organisms. Despite being widely known for their adverse role in food spoilage or as pathogens for humans, animals, or plants, they also present several beneficial effects. Fungi contribute to human well-being due to their role as decomposers, degrading decay matter into smaller molecules which can be easily used by other ecosystem members. These organisms can produce medicinal compounds or modulate protective immune responses in human intestine. Fungi intervene in diverse food processes or act as a food supply. Due to fungal diversity, the unequivocal identification of these organisms is crucial to increasing their practical applications and decreasing their adverse effects. The process of identification could be achieved through the integral sequencing of fungi genomes. However, this procedure would be time-consuming and rather cost-inefficient. Therefore, several molecular markers have been developed to overcome these limitations. The chronology of DNA-based molecular markers development can be divided into three main steps: (1) prior to the development of the PCR technique (RFLP); (2) after the development of the PCR technique (RAPD, AFLP, ISSR, VNTR, SNP, InDels, and DNA barcoding); (3) after the development of the massive parallel sequencing technique (Metabarcoding and WGS). Therefore, the present review covers an overview of the most recently developed molecular markers used for fungal detection and identification.},
}
@article {pmid36011659,
year = {2022},
author = {Wang, Y and Wang, J and Chen, Y and Liu, S and Zhao, Y and Chen, N},
title = {Comparative Analysis of Bacillariophyceae Chloroplast Genomes Uncovers Extensive Genome Rearrangements Associated with Speciation.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {16},
pages = {},
pmid = {36011659},
issn = {1660-4601},
mesh = {DNA, Chloroplast/genetics ; *Diatoms/genetics ; Ecosystem ; Evolution, Molecular ; *Genome, Chloroplast ; Phylogeny ; },
abstract = {The Bacillariophyceae is a species-rich, ecologically significant class of Bacillariophyta. Despite their critical importance in marine ecosystems as primary producers and in the development of harmful algal blooms (HABs), taxonomic research on Bacillariophyceae species has been hindered because of their limited morphological features, plasticity of morphologies, and the low resolution of common molecular markers. Hence molecular markers with improved resolution are urgently needed. Organelle genomes, which can be constructed efficiently with the recent development of high throughput DNA sequencing technologies and the advancement of bioinformatics tools, have been proposed as super barcodes for their higher resolution for distinguishing different species and intra-species genomic variations. In this study, we tested the value of full-length chloroplast genomes (cpDNAs) as super barcodes for distinguishing diatom species, by constructing cpDNAs of 11 strains of the class Bacillariophyceae, including Nitzschia ovalis, Nitzschia traheaformis, Cylindrotheca spp., Psammodictyon constrictum, Bacillaria paxillifer, two strains of Haslea tsukamotoi, Haslea avium, Navicula arenaria, and Pleurosigma sp. Comparative analysis of cpDNAs revealed that cpDNAs were not only adequate for resolving different species, but also for enabling recognition of high levels of genome rearrangements between cpDNAs of different species, especially for species of the genera Nitzschia, Cylindrotheca, Navicula and Haslea. Additionally, comparative analysis suggested that the positioning of species in the genus Haslea should be transferred to the genus Navicula. Chloroplast genome-based evolutionary analysis suggested that the Bacillariophyceae species first appeared during the Cretaceous period and the diversity of species rose after the mass extinction about 65 Mya. This study highlighted the value of cpDNAs in research on the biodiversity and evolution of Bacillariophyceae species, and, with the construction of more cpDNAs representing additional genera, deeper insight into the biodiversity and evolutionary relationships of Bacillariophyceae species will be gained.},
}
@article {pmid36008757,
year = {2022},
author = {Miao, Y and Chen, H and Xu, W and Yang, Q and Liu, C and Huang, L},
title = {Structural mutations of small single copy (SSC) region in the plastid genomes of five Cistanche species and inter-species identification.},
journal = {BMC plant biology},
volume = {22},
number = {1},
pages = {412},
pmid = {36008757},
issn = {1471-2229},
mesh = {*Cistanche/genetics ; DNA, Intergenic ; *Genome, Plastid/genetics ; Mutation ; *Orobanchaceae/genetics ; Phylogeny ; },
abstract = {BACKGROUND: Cistanche is an important genus of Orobanchaceae, with critical medicinal, economic, and desertification control values. However, the phylogenetic relationships of Cistanche genus remained obscure. To date, no effective molecular markers have been reported to discriminate effectively the Cistanche closely related species reported here. In this study, we obtained and characterized the plastomes of four Cistanche species from China, to clarify the phylogenetic relationship within the genus, and to develop molecular markers for species discrimination. RESULTS: Four Cistanche species (Cistanche deserticola, Cistanche salsa, Cistanche tubulosa and Cistanche sinensis), were deep-sequenced with Illumina. Their plastomes were assembled using SPAdes and annotated using CPGAVAS2. The plastic genomes were analyzed in detail, finding that all showed the conserved quadripartite structure (LSC-IR-SSC-IR) and with full sizes ranging from 75 to 111 Kbp. We observed a significant contraction of small single copy region (SSC, ranging from 0.4-29 Kbp) and expansion of inverted repeat region (IR, ranging from 6-30 Kbp), with C. deserticola and C. salsa showing the smallest SSCs with only one gene (rpl32). Compared with other Orobanchaceae species, Cistanche species showed extremely high rates of gene loss and pseudogenization, as reported for other parasitic Orobanchaceae species. Furthermore, analysis of sequence divergence on protein-coding genes showed the three genes (rpl22, clpP and ycf2) had undergone positive selection in the Cistanche species under study. In addition, by comparison of all available Cistanche plastomes we found 25 highly divergent intergenic spacer (IGS) regions that were used to predict two DNA barcode markers (Cis-mk01 and Cis-mk02 based on IGS region trnR-ACG-trnN-GUU) and eleven specific DNA barcode markers using Ecoprimer software. Experimental validation showed 100% species discrimination success rate with both type of markers.<br><br>CONCLUSION: Our findings have shown that Cistanche species are an ideal model to investigate the structure variation, gene loss and pseudogenization during the process of plastome evolution in parasitic species, providing new insights into the evolutionary relationships among the Cistanche species. In addition, the developed DNA barcodes markers allow the proper species identification, ensuring the effective and safe use of Cistanche species as medicinal products.},
}
@article {pmid36007103,
year = {2023},
author = {Ashley, CW and Selenica, P and Patel, J and Wu, M and Nincevic, J and Lakhman, Y and Zhou, Q and Shah, RH and Berger, MF and Da Cruz Paula, A and Brown, DN and Marra, A and Iasonos, A and Momeni-Boroujeni, A and Alektiar, KM and Long Roche, K and Zivanovic, O and Mueller, JJ and Zamarin, D and Broach, VA and Sonoda, Y and Leitao, MM and Friedman, CF and Jewell, E and Reis-Filho, JS and Ellenson, LH and Aghajanian, C and Abu-Rustum, NR and Cadoo, K and Weigelt, B},
title = {High-Sensitivity Mutation Analysis of Cell-Free DNA for Disease Monitoring in Endometrial Cancer.},
journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},
volume = {29},
number = {2},
pages = {410-421},
pmid = {36007103},
issn = {1557-3265},
support = {P30 CA008748/CA/NCI NIH HHS/United States ; P50 CA247749/CA/NCI NIH HHS/United States ; },
mesh = {Female ; Humans ; *Cell-Free Nucleic Acids/genetics ; *Circulating Tumor DNA/genetics ; *Endometrial Neoplasms/diagnosis/genetics ; Prognosis ; Mutation ; High-Throughput Nucleotide Sequencing/methods ; Biomarkers, Tumor/genetics ; },
abstract = {PURPOSE: We sought to determine whether sequencing analysis of circulating cell-free DNA (cfDNA) in patients with prospectively accrued endometrial cancer captures the mutational repertoire of the primary lesion and allows for disease monitoring.<br><br>EXPERIMENTAL DESIGN: Peripheral blood was prospectively collected from 44 newly diagnosed patients with endometrial cancer over a 24-month period (i.e., baseline, postsurgery, every 6 months after). DNA from the primary endometrial cancers was subjected to targeted next-generation sequencing (NGS) of 468 cancer-related genes, and cfDNA to a high-depth NGS assay of 129 genes with molecular barcoding. Sequencing data were analyzed using validated bioinformatics methods.<br><br>RESULTS: cfDNA levels correlated with surgical stage in endometrial cancers, with higher levels of cfDNA being present in advanced-stage disease. Mutations in cfDNA at baseline were detected preoperatively in 8 of 36 (22%) patients with sequencing data, all of whom were diagnosed with advanced-stage disease, high tumor volume, and/or aggressive histologic type. Of the 38 somatic mutations identified in the primary tumors also present in the cfDNA assay, 35 (92%) and 38 (100%) were detected at baseline and follow-up, respectively. In 6 patients with recurrent disease, changes in circulating tumor DNA (ctDNA) fraction/variant allele fractions in cfDNA during follow-up closely mirrored disease progression and therapy response, with a lead time over clinically detected recurrence in two cases. The presence of ctDNA at baseline (P < 0.001) or postsurgery (P = 0.014) was significantly associated with reduced progression-free survival.<br><br>CONCLUSIONS: cfDNA sequencing analysis in patients with endometrial cancer at diagnosis has prognostic value, and serial postsurgery cfDNA analysis enables disease and treatment response monitoring. See related commentary by Grant et al., p. 305.},
}
@article {pmid36006287,
year = {2022},
author = {Alharbi, MH and Iravoga, C and Kayuni, SA and Cunningham, L and LaCourse, EJ and Makaula, P and Stothard, JR},
title = {First Molecular Identification of Bulinus africanus in Lake Malawi Implicated in Transmitting Schistosoma Parasites.},
journal = {Tropical medicine and infectious disease},
volume = {7},
number = {8},
pages = {},
pmid = {36006287},
issn = {2414-6366},
abstract = {The freshwater snail genus Bulinus plays a vital role in transmitting parasites of the Schistosoma haematobium group. A hybrid schistosome between S. haematobium and S. mattheei has been recently detected using DNA-based identification methods in school children along the Lake Malawi shoreline in Mangochi District. This finding raised the need for contemporary revaluation of local interactions between schistosomes and snails, with a particular focus on snail species within the Bulinus africanus group. In 2017 and 2018, malacological surveys sampled several freshwater sites in Mangochi District. Collected snails (n = 250) were characterised using cytochrome oxidase subunit 1 gene (cox1), with DNA barcoding of the 'Folmer' region and a rapid PCR-RFLP typing assay with double digestion with HaeIII and SacI restriction enzymes. DNA cox1 sequence analysis, with phylogenetic tree construction, suggested the presence of at least three B. africanus group taxa in Lake Malawi, B. globosus, alongside first reports of B. africanus and B. angolensis, which can be differentiated by PCR-RFLP methods. In addition, a total of 30 of the 106 B. africanus group snails (28.30%) were positive to the Schistosoma-specific screen using real-time PCR methods. This study provides new insight into the recent changes in the epidemiology of urogenital schistosomiasis as likely driven by a new diversity of B. africanus group snails within the Lake.},
}
@article {pmid36005305,
year = {2022},
author = {Stein, F and Wagner, S and Bräsicke, N and Gailing, O and Moura, CCM and Götz, M},
title = {A Non-Destructive High-Speed Procedure to Obtain DNA Barcodes from Soft-Bodied Insect Samples with a Focus on the Dipteran Section of Schizophora.},
journal = {Insects},
volume = {13},
number = {8},
pages = {},
pmid = {36005305},
issn = {2075-4450},
support = {FKZ 22019814//Fachagentur f&#xfc;r Nachwachsende Rohstoffe/ ; },
abstract = {While the need for biodiversity research is growing, paradoxically, global taxonomical expertise is decreasing as a result of the neglected funding for young academics in taxonomy. Non-destructive approaches for DNA barcoding are necessary for a more efficient use of this dwindling expertise to fill gaps, and identify incorrect entries in sequence databases like BOLD or GenBank. They are efficient because morphological re-examination of species vouchers is still possible post-DNA barcoding. Non-destructive approaches for Diptera with a comprehensive species representation or the consideration of diagnostic fragile morphological characters are missing. Additionally, most non-destructive approaches combine a time intensive and non-destructive digestion step with common DNA extraction methods, such as commercial kits or CTAB DNA isolation. We circumvented those approaches and combined a modified non-destructive TE buffer high-speed DNA extraction, with a PCR inhibitor-resistant PCR reaction system, to a non-destructive DNA barcoding procedure for fresh and frozen samples of the Schizophora (Diptera). This method avoids morphological impairment and the application of harmful chemicals, is cost and time effective, restricts the need for laboratory equipment to a minimum, and prevents cross-contamination risk during DNA isolation. Moreover, the study indicates that the presented non-destructive DNA barcoding procedure is transferable to other soft-bodied insects. We suggest that PCR inhibitor-resistant master mixes enable the development of new-and the modification of existing-non-destructive approaches with the avoidance of further DNA template cleaning.},
}
@article {pmid36003926,
year = {2022},
author = {Neu, TR and Kuhlicke, U},
title = {Matrix glycoconjugate characterization in multispecies biofilms and bioaggregates from the environment by means of fluorescently-labeled lectins.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {940280},
pmid = {36003926},
issn = {1664-302X},
abstract = {Environmental biofilms represent a complex mixture of different microorganisms. Their identity is usually analyzed by means of nucleic acid-based techniques. However, these biofilms are also composed of a highly complex extracellular matrix produced by the microbes within a particular biofilm system. The biochemical identity of this extracellular matrix remains in many cases an intractable part of biofilms and bioaggregates. Consequently, there is a need for an approach that will give access to the fully hydrated structure of the extracellular matrix or at least a major part of it. A crucial compound of the matrix identified as carbohydrate-based polymers represents major structural and functional constituents. These glycoconjugates can be characterized by using fluorescently-labeled lectins in combination with confocal laser scanning microscopy. The lectin approach is defined previously, as fluorescence lectin barcoding (FLBC) and fluorescence lectin-binding analysis (FLBA), where FLBC is equal to the screening of a particular sample with all the commercially available lectins and FLBA is the actual analysis of the matrix throughout an experiment with a selected panel of lectins. As the application of immune-based techniques in environmental biofilm systems is impossible, the lectin approach is currently the only option for probing lectin-specific glycoconjugates in complex biofilms and bioaggregates. From all the commercially available lectins tested, the lectins such as AAL, HAA, WGA, ConA, IAA, HPA, and LEA showed the highest binding efficiency. Furthermore, 20 of the overall lectins tested showed an intermediate signal intensity, nevertheless very useful for the assessment of matrix glycoconjugates. With the data compiled, we shall virtually shed more light on the dark matter of the extracellular matrix and their 3-dimensional distribution in environmental biofilm systems. The results will be helpful in future studies with a focus on the extracellular matrix glycoconjugates present in environmental microbial communities.},
}
@article {pmid36000184,
year = {2022},
author = {Perera, TWNK and Weerasinghe, WRH and Attanayake, RN and Paranagama, PA},
title = {Biodeterioration of low-density polyethylene by mangrove-associated endolichenic fungi and their enzymatic regimes.},
journal = {Letters in applied microbiology},
volume = {75},
number = {6},
pages = {1526-1537},
doi = {10.1111/lam.13819},
pmid = {36000184},
issn = {1472-765X},
support = {MSTR/TRD/AGR/03/02/07//Ministry of Science Technology and Research/ ; },
mesh = {*Polyethylene ; Ecosystem ; *Phanerochaete ; Laccase ; Microscopy, Electron, Scanning ; Fungi/genetics ; },
abstract = {Fungal involvement in the biodeterioration of low-density polyethylene (LDPE) has received great attention in recent years. Among diverse groups of fungi, endolichenic fungi (ELF) are adapted to thrive in resource-limited conditions. The present study was designed to investigate the potential of mangrove-associated ELF, in the biodeterioration of LDPE and to quantify key-depolymerizing enzymes. A total of 31 ELF species, isolated from 22 lichens of mangrove ecosystems in Negombo lagoon, Sri Lanka were identified using DNA barcoding techniques. ELF were inoculated into a mineral salt medium, containing LDPE strips and incubated at 28 ± 2°C, for 21 days, under laboratory conditions. After incubation, biodeterioration was monitored based on percent reductions in weights and tensile properties, increments in the degree of water absorption, changes in peaks of infrared spectra and surface erosions using scanning electron microscopy. Out of 31 species, Chaetomium globosum, Daldinia eschscholtzii, Neofusicoccum occulatum, Phanerochaete chrysosporium, Schizophyllum commune and Xylaria feejeensis showed significant changes. Production of depolymerizing enzymes by these species was assayed qualitatively using plate-based methods and quantitatively by mass-level enzyme production. Among them, Phanerochaete chrysosporium showed the highest enzyme activities as (9·69 ± 0·04) × 10[-3] , (1·96 ± 0·01) × 10[-3] , (5·73 ± 0·03) × 10[-3] , (0·88 ± 0·01), (0·64 ± 0·06), (1·43 ± 0·01) U ml[-1] for laccase, lignin peroxidase, manganese peroxidase, amylase, lipase and esterase, respectively.},
}
@article {pmid35999132,
year = {2023},
author = {Szumska, J and Grimm, D},
title = {Boosters for adeno-associated virus (AAV) vector (r)evolution.},
journal = {Cytotherapy},
volume = {25},
number = {3},
pages = {254-260},
doi = {10.1016/j.jcyt.2022.07.005},
pmid = {35999132},
issn = {1477-2566},
mesh = {Humans ; *Dependovirus/genetics ; *Genetic Therapy/methods ; Gene Transfer Techniques ; Capsid Proteins/chemistry/genetics ; Capsid ; Genetic Vectors/genetics ; },
abstract = {Adeno-associated virus (AAV) is one of the most exciting and most versatile templates for engineering of gene-delivery vectors for use in human gene therapy, owing to the existence of numerous naturally occurring capsid variants and their amenability to directed molecular evolution. As a result, the field has witnessed an explosion of novel "designer" AAV capsids and ensuing vectors over the last two decades, which have been isolated from comprehensive capsid libraries generated through technologies such as DNA shuffling or peptide display, and stratified under stringent positive and/or negative selection pressures. Here, we briefly highlight a panel of recent, innovative and transformative methodologies that we consider to have exceptional potential to advance directed AAV capsid evolution and to thereby accelerate AAV vector revolution. These avenues comprise original technologies for (i) barcoding and high-throughput screening of individual AAV variants or entire capsid libraries, (ii) selection of transduction-competent AAV vectors on the DNA level, (iii) enrichment of expression-competent AAV variants on the RNA level, as well as (iv) high-resolution stratification of focused AAV capsid libraries on the single-cell level. Together with other emerging AAV engineering stratagems, such as rational design or machine learning, these pioneering techniques promise to provide an urgently needed booster for AAV (r)evolution.},
}
@article {pmid35996183,
year = {2022},
author = {Cowan, DA and Lebre, PH and Amon, C and Becker, RW and Boga, HI and Boulangé, A and Chiyaka, TL and Coetzee, T and de Jager, PC and Dikinya, O and Eckardt, F and Greve, M and Harris, MA and Hopkins, DW and Houngnandan, HB and Houngnandan, P and Jordaan, K and Kaimoyo, E and Kambura, AK and Kamgan-Nkuekam, G and Makhalanyane, TP and Maggs-Kölling, G and Marais, E and Mondlane, H and Nghalipo, E and Olivier, BW and Ortiz, M and Pertierra, LR and Ramond, JB and Seely, M and Sithole-Niang, I and Valverde, A and Varliero, G and Vikram, S and Wall, DH and Zeze, A},
title = {Biogeographical survey of soil microbiomes across sub-Saharan Africa: structure, drivers, and predicted climate-driven changes.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {131},
pmid = {35996183},
issn = {2049-2618},
mesh = {Biodiversity ; Desert Climate ; Ecosystem ; *Microbiota/genetics ; *Soil/chemistry ; Soil Microbiology ; },
abstract = {BACKGROUND: Top-soil microbiomes make a vital contribution to the Earth's ecology and harbor an extraordinarily high biodiversity. They are also key players in many ecosystem services, particularly in arid regions of the globe such as the African continent. While several recent studies have documented patterns in global soil microbial ecology, these are largely biased towards widely studied regions and rely on models to interpolate the microbial diversity of other regions where there is low data coverage. This is the case for sub-Saharan Africa, where the number of regional microbial studies is very low in comparison to other continents.<br><br>RESULTS: The aim of this study was to conduct an extensive biogeographical survey of sub-Saharan Africa's top-soil microbiomes, with a specific focus on investigating the environmental drivers of microbial ecology across the region. In this study, we sampled 810 sample sites across 9 sub-Saharan African countries and used taxonomic barcoding to profile the microbial ecology of these regions. Our results showed that the sub-Saharan nations included in the study harbor qualitatively distinguishable soil microbiomes. In addition, using soil chemistry and climatic data extracted from the same sites, we demonstrated that the top-soil microbiome is shaped by a broad range of environmental factors, most notably pH, precipitation, and temperature. Through the use of structural equation modeling, we also developed a model to predict how soil microbial biodiversity in sub-Saharan Africa might be affected by future climate change scenarios. This model predicted that the soil microbial biodiversity of countries such as Kenya will be negatively affected by increased temperatures and decreased precipitation, while the fungal biodiversity of Benin will benefit from the increase in annual precipitation.<br><br>CONCLUSION: This study represents the most extensive biogeographical survey of sub-Saharan top-soil microbiomes to date. Importantly, this study has allowed us to identify countries in sub-Saharan Africa that might be particularly vulnerable to losses in soil microbial ecology and productivity due to climate change. Considering the reliance of many economies in the region on rain-fed agriculture, this study provides crucial information to support conservation efforts in the countries that will be most heavily impacted by climate change. Video Abstract.},
}
@article {pmid35993907,
year = {2022},
author = {Shi, Q and Liu, S and Kristiansen, K and Liu, L},
title = {The FASTQ+ format and PISA.},
journal = {Bioinformatics (Oxford, England)},
volume = {38},
number = {19},
pages = {4639-4642},
doi = {10.1093/bioinformatics/btac562},
pmid = {35993907},
issn = {1367-4811},
mesh = {Sequence Analysis, DNA ; *Software ; Polymerase Chain Reaction ; *Language ; },
abstract = {SUMMARY: The FASTQ+ format is designed for single-cell experiments. It extends various optional tags, including cell barcodes and unique molecular identifiers, to the sequence identifier and is fully compatible with the FASTQ format. In addition, PISA implements various utilities for processing sequences in the FASTQ format and alignments in the SAM/BAM/CRAM format from single-cell experiments, such as converting FASTQ format to FASTQ+, annotating alignments, PCR deduplication, feature counting and barcodes correction. The software is open-source and written in C language.<br><br>https://doi.org/10.5281/zenodo.7007056 or https://github.com/shiquan/PISA.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid35991367,
year = {2022},
author = {Guo, M and Yuan, C and Tao, L and Cai, Y and Zhang, W},
title = {Life barcoded by DNA barcodes.},
journal = {Conservation genetics resources},
volume = {14},
number = {4},
pages = {351-365},
pmid = {35991367},
issn = {1877-7252},
abstract = {The modern concept of DNA-based barcoding for cataloguing biodiversity was proposed in 2003 by first adopting an approximately 600 bp fragment of the mitochondrial COI gene to compare via nucleotide alignments with known sequences from specimens previously identified by taxonomists. Other standardized regions meeting barcoding criteria then are also evolving as DNA barcodes for fast, reliable and inexpensive assessment of species composition across all forms of life, including animals, plants, fungi, bacteria and other microorganisms. Consequently, global DNA barcoding campaigns have resulted in the formation of many online workbenches and databases, such as BOLD system, as barcode references, and facilitated the development of mini-barcodes and metabarcoding strategies as important extensions of barcode techniques. Here we intend to give an overview of the characteristics and features of these barcode markers and major reference libraries existing for barcoding the planet's life, as well as to address the limitations and opportunities of DNA barcodes to an increasingly broader community of science and society.},
}
@article {pmid35990900,
year = {2022},
author = {Trujillo-Argueta, S and Del Castillo, RF and Velasco-Murguía, A},
title = {Testing the effectiveness of rbcLa DNA-barcoding for species discrimination in tropical montane cloud forest vascular plants (Oaxaca, Mexico) using BLAST, genetic distance, and tree-based methods.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13771},
pmid = {35990900},
issn = {2167-8359},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Phylogeny ; Mexico ; Bayes Theorem ; *Plants ; DNA ; },
abstract = {DNA-barcoding is a species identification tool that uses a short section of the genome that provides a genetic signature of the species. The main advantage of this novel technique is that it requires a small sample of tissue from the tested organism. In most animal groups, this technique is very effective. However, in plants, the recommended standard markers, such as rbcLa, may not always work, and their efficacy remains to be tested in many plant groups, particularly from the Neotropical region. We examined the discriminating power of rbcLa in 55 tropical cloud forest vascular plant species from 38 families (Oaxaca, Mexico). We followed the CBOL criteria using BLASTn, genetic distance, and monophyly tree-based analyses (neighbor-joining, NJ, maximum likelihood, ML, and Bayesian inference, BI). rbcLa universal primers amplified 69.0% of the samples and yielded 91.3% bi-directional sequences. Sixty-three new rbcLa sequences were established. BLAST discriminates 80.8% of the genus but only 15.4% of the species. There was nil minimum interspecific genetic distances in Quercus, Oreopanax, and Daphnopsis. Contrastingly, Ericaceae (5.6%), Euphorbiaceae (4.6%), and Asteraceae (3.3%) species displayed the highest within-family genetic distances. According to the most recent angiosperm classification, NJ and ML trees successfully resolved (100%) monophyletic species. ML trees showed the highest mean branch support value (87.3%). Only NJ and ML trees could successfully discriminate Quercus species belonging to different subsections: Quercus martinezii (white oaks) from Q. callophylla and Q. laurina (red oaks). The ML topology could distinguish species in the Solanaceae clade with similar BLAST matches. Also, the BI topology showed a polytomy in this clade, and the NJ tree displayed low-support values. We do not recommend genetic-distance approaches for species discrimination. Severe shortages of rbcLa sequences in public databases of neotropical species hindered effective BLAST comparisons. Instead, ML tree-based analysis displays the highest species discrimination among the tree-based analyses. With the ML topology in selected genera, rbcLa helped distinguish infra-generic taxonomic categories, such as subsections, grouping affine species within the same genus, and discriminating species. Since the ML phylogenetic tree could discriminate 48 species out of our 55 studied species, we recommend this approach to resolve tropical montane cloud forest species using rbcLa, as an initial step and improve DNA amplification methods.},
}
@article {pmid35990814,
year = {2022},
author = {Habibi, N and Al Salameen, F and Rahman, M and Shajan, A and Zakir, F and Abdulrazzack, N},
title = {Comparison and optimization of DNA Isolation protocols for high throughput genomic studies of Acacia pachyceras Schwartz.},
journal = {MethodsX},
volume = {9},
number = {},
pages = {101799},
pmid = {35990814},
issn = {2215-0161},
abstract = {We describe the optimization and validation of six DNA isolation protocols from fresh leaves of the rare tree Acacia pachyceras. The first four protocols employed three commercial kits (Sigma, Nucleospin1, Nucleospin 2, Promega) whereas the remaining two were based on the traditional sodium dodecyl sulfate (SDS) and cetyltrimethylammonium bromide CTAB methods. Each protocol provided significantly different results concerning DNA concentration (p < 0.032), yield (p < 0.000), contaminant carry over, protocol duration, cost per sample, and comprehensive cost. We demonstrated the applicability of all the tested protocols in DNA barcoding. The protocol yielded maximum amounts (92.85 µg) of DNA in a rapid turnaround time (8 h). The quantity and purity surpassed all the other tested methods. DNA extracted by the CTAB method was the best for NGS (Phred score >Q30). These protocols will be useful tools for molecular research of Acacia pachyceras and other closely related tree species.},
}
@article {pmid35990516,
year = {2022},
author = {Banerjee, P and Stewart, KA and Dey, G and Antognazza, CM and Sharma, RK and Maity, JP and Saha, S and Doi, H and de Vere, N and Chan, MWY and Lin, PY and Chao, HC and Chen, CY},
title = {Environmental DNA analysis as an emerging non-destructive method for plant biodiversity monitoring: a review.},
journal = {AoB PLANTS},
volume = {14},
number = {4},
pages = {plac031},
pmid = {35990516},
issn = {2041-2851},
abstract = {Environmental DNA (eDNA) analysis has recently transformed and modernized biodiversity monitoring. The accurate detection, and to some extent quantification, of organisms (individuals/populations/communities) in environmental samples is galvanizing eDNA as a successful cost and time-efficient biomonitoring technique. Currently, eDNA's application to plants remains more limited in implementation and scope compared to animals and microorganisms. This review evaluates the development of eDNA-based methods for (vascular) plants, comparing its performance and power of detection with that of traditional methods, to critically evaluate and advise best-practices needed to innovate plant biomonitoring. Recent advancements, standardization and field applications of eDNA-based methods have provided enough scope to utilize it in conservation biology for numerous organisms. Despite our review demonstrating only 13% of all eDNA studies focus on plant taxa to date, eDNA has considerable environmental DNA has considerable potential for plants, where successful detection of invasive, endangered and rare species, and community-level interpretations have provided proof-of-concept. Monitoring methods using eDNA were found to be equal or more effective than traditional methods; however, species detection increased when both methods were coupled. Additionally, eDNA methods were found to be effective in studying species interactions, community dynamics and even effects of anthropogenic pressure. Currently, elimination of potential obstacles (e.g. lack of relevant DNA reference libraries for plants) and the development of user-friendly protocols would greatly contribute to comprehensive eDNA-based plant monitoring programs. This is particularly needed in the data-depauperate tropics and for some plant groups (e.g., Bryophytes and Pteridophytes). We further advocate to coupling traditional methods with eDNA approaches, as the former is often cheaper and methodologically more straightforward, while the latter offers non-destructive approaches with increased discrimination ability. Furthermore, to make a global platform for eDNA, governmental and academic-industrial collaborations are essential to make eDNA surveys a broadly adopted and implemented, rapid, cost-effective and non-invasive plant monitoring approach.},
}
@article {pmid35986714,
year = {2023},
author = {Luo, M and Ji, Y and Warton, D and Yu, DW},
title = {Extracting abundance information from DNA-based data.},
journal = {Molecular ecology resources},
volume = {23},
number = {1},
pages = {174-189},
pmid = {35986714},
issn = {1755-0998},
support = {QYZDY-SSW-SMC024//Key Research Program of Frontier Sciences, CAS/ ; //University of Chinese Academy of Sciences/ ; //Kunming Institute of Zoology/ ; GREKF19-01//State Key Laboratory of Genetic Resources and Evolution/ ; GREKF20-01//State Key Laboratory of Genetic Resources and Evolution/ ; GREKF21-01//State Key Laboratory of Genetic Resources and Evolution/ ; //University of East Anglia/ ; SMC024//Chinese Academy of Sciences/ ; sCom//idiv.de/ ; XDA20050202//Strategic Priority Research Program, Chinese Academy of Sciences/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Metagenomics/methods ; DNA/genetics ; Biodiversity ; },
abstract = {The accurate extraction of species-abundance information from DNA-based data (metabarcoding, metagenomics) could contribute usefully to diet analysis and food-web reconstruction, the inference of species interactions, the modelling of population dynamics and species distributions, the biomonitoring of environmental state and change, and the inference of false positives and negatives. However, multiple sources of bias and noise in sampling and processing combine to inject error into DNA-based data sets. To understand how to extract abundance information, it is useful to distinguish two concepts. (i) Within-sample across-species quantification describes relative species abundances in one sample. (ii) Across-sample within-species quantification describes how the abundance of each individual species varies from sample to sample, such as over a time series, an environmental gradient or different experimental treatments. First, we review the literature on methods to recover across-species abundance information (by removing what we call "species pipeline biases") and within-species abundance information (by removing what we call "pipeline noise"). We argue that many ecological questions can be answered with just within-species quantification, and we therefore demonstrate how to use a "DNA spike-in" to correct for pipeline noise and recover within-species abundance information. We also introduce a model-based estimator that can be used on data sets without a physical spike-in to approximate and correct for pipeline noise.},
}
@article {pmid35986181,
year = {2022},
author = {Credle, JJ and Gunn, J and Sangkhapreecha, P and Monaco, DR and Zheng, XA and Tsai, HJ and Wilbon, A and Morgenlander, WR and Rastegar, A and Dong, Y and Jayaraman, S and Tosi, L and Parekkadan, B and Baer, AN and Roederer, M and Bloch, EM and Tobian, AAR and Zyskind, I and Silverberg, JI and Rosenberg, AZ and Cox, AL and Lloyd, T and Mammen, AL and Benjamin Larman, H},
title = {Unbiased discovery of autoantibodies associated with severe COVID-19 via genome-scale self-assembled DNA-barcoded protein libraries.},
journal = {Nature biomedical engineering},
volume = {6},
number = {8},
pages = {992-1003},
pmid = {35986181},
issn = {2157-846X},
support = {K23 HL151826/HL/NHLBI NIH HHS/United States ; R01 GM127353/GM/NIGMS NIH HHS/United States ; T32 GM136577/GM/NIGMS NIH HHS/United States ; },
mesh = {*Autoantibodies ; *COVID-19/therapy ; Gene Library ; Humans ; Immunization, Passive ; Interferon-alpha ; COVID-19 Serotherapy ; },
abstract = {Pathogenic autoreactive antibodies that may be associated with life-threatening coronavirus disease 2019 (COVID-19) remain to be identified. Here, we show that self-assembled genome-scale libraries of full-length proteins covalently coupled to unique DNA barcodes for analysis by sequencing can be used for the unbiased identification of autoreactive antibodies in plasma samples. By screening 11,076 DNA-barcoded proteins expressed from a sequence-verified human ORFeome library, the method, which we named MIPSA (for Molecular Indexing of Proteins by Self-Assembly), allowed us to detect circulating neutralizing type-I and type-III interferon (IFN) autoantibodies in five plasma samples from 55 patients with life-threatening COVID-19. In addition to identifying neutralizing type-I IFN-α and IFN-ω autoantibodies and other previously known autoreactive antibodies in patient plasma, MIPSA enabled the detection of as yet unidentified neutralizing type-III anti-IFN-λ3 autoantibodies that were not seen in healthy plasma samples or in convalescent plasma from ten non-hospitalized individuals with COVID-19. The low cost and simple workflow of MIPSA will facilitate unbiased high-throughput analyses of protein-antibody, protein-protein and protein-small-molecule interactions.},
}
@article {pmid35985139,
year = {2022},
author = {Chang, M and Kim, JY and Lee, H and Lee, EJ and Lee, WH and Moon, S and Choe, S and Choung, CM},
title = {Development of diagnostic SNP markers and a novel SNP genotyping assay for distinguishing opium poppies.},
journal = {Forensic science international},
volume = {339},
number = {},
pages = {111416},
doi = {10.1016/j.forsciint.2022.111416},
pmid = {35985139},
issn = {1872-6283},
mesh = {Genotype ; Nucleotides ; *Papaver/genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; },
abstract = {The opium poppy acts as an important natural pain reliever but is also responsible for increased rates of severe drug abuse and addiction owing to its characteristic psychoactive effect. Non-medical illicit use of the poppy plant is markedly increasing worldwide, thereby highlighting the need for a robust species identification strategy. In this study, we identified SNPs within the region of two universal DNA barcodes, matK (maturase K) and the trnL-trnF (tRNA-Leu [3'exon]-tRNA-Phe [exon] intergenic spacer, that are forensically applicable for distinguishing opium poppy species based on a genetic analysis of 164 samples of family Papaveraceae obtained from locations spanning Jeolla-do and Jeju Island, Republic of Korea. A comparative analysis of the DNA barcode sequences for two narcotic types of the Papaver species (Papaver somniferum, Papaver somniferum subs. setigerum) to eight non-narcotic species revealed three unique nucleotide substitution events. Newly identified SNPs were located at position 255 of matK and at positions 305 and 306 of trnL-trnF; the narcotic species contained C, A, and T, whereas non-narcotic species contained T, G, and C at these positions. Phylogenetic analysis demonstrated that newly identified SNPs, which we named PsMAT255 and PsLF305/306, could be used to clearly differentiate between the narcotic and non-narcotic types of Papaver species based on the patterns of nucleotide variation. These results indicate that the nucleotide differences between the narcotic and non-narcotic species may influence genetic markers. We, therefore, developed a novel SNP-based allelic genotyping assay using the RT-PCR system that can reliably differentiate the narcotic type of the Papaver species. In summary, our findings suggest that the newly identified species-specific SNPs of both matK and trnL-trnF can be used as identification markers of narcotic Papaver species. Furthermore, a newly developed TaqMan allelic discrimination assay may be used as a practically applicable diagnostic method to survey several illicit narcotic specimens carrying the type-specific SNP.},
}
@article {pmid35983894,
year = {2022},
author = {Xue, J and Fu, Y and Fan, S and Cao, X and Huang, W and Zhang, J and Zhao, Y and Chen, F},
title = {Branched immunochip-integrated pairwise barcoding amplification exploring the spatial proximity of two post-translational modifications in distinct cell subpopulations.},
journal = {Chemical communications (Cambridge, England)},
volume = {58},
number = {72},
pages = {10020-10023},
doi = {10.1039/d2cc03833a},
pmid = {35983894},
issn = {1364-548X},
mesh = {*Epigenesis, Genetic ; *Protein Processing, Post-Translational ; },
abstract = {Investigating the spatial information of post-translational modifications (PTMs) in distinct cell subpopulations represents a new direction toward single-cell analysis. The specific capture of cell populations combined with PTM spatial proximity visualization making it practically challenging. Here, we develop branched immunochip-integrated pairwise barcoding amplification, termed biChip-PBA, which can perform the respective capture of cell subpopulations expressing different membrane proteins and successive PBA-based fluorescence imaging of PTM proximities. Our work may provide multilevel information for new insights into epigenetic regulation and cell function.},
}
@article {pmid35982229,
year = {2022},
author = {Serrano, A and Berthelet, J and Naik, SH and Merino, D},
title = {Mastering the use of cellular barcoding to explore cancer heterogeneity.},
journal = {Nature reviews. Cancer},
volume = {22},
number = {11},
pages = {609-624},
pmid = {35982229},
issn = {1474-1768},
mesh = {Humans ; Clone Cells ; *Neoplasms/genetics ; Tumor Microenvironment/genetics ; },
abstract = {Tumours are often composed of a multitude of malignant clones that are genomically unique, and only a few of them may have the ability to escape cancer therapy and grow as symptomatic lesions. As a result, tumours with a large degree of genomic diversity have a higher chance of leading to patient death. However, clonal fate can be driven by non-genomic features. In this context, new technologies are emerging not only to track the spatiotemporal fate of individual cells and their progeny but also to study their molecular features using various omics analysis. In particular, the recent development of cellular barcoding facilitates the labelling of tens to millions of cancer clones and enables the identification of the complex mechanisms associated with clonal fate in different microenvironments and in response to therapy. In this Review, we highlight the recent discoveries made using lentiviral-based cellular barcoding techniques, namely genetic and optical barcoding. We also emphasize the strengths and limitations of each of these technologies and discuss some of the key concepts that must be taken into consideration when one is designing barcoding experiments. Finally, we suggest new directions to further improve the use of these technologies in cancer research.},
}
@article {pmid35982179,
year = {2022},
author = {Wei, Y and Qin, Q and Yan, C and Hayes, MN and Garcia, SP and Xi, H and Do, D and Jin, AH and Eng, TC and McCarthy, KM and Adhikari, A and Onozato, ML and Spentzos, D and Neilsen, GP and Iafrate, AJ and Wexler, LH and Pyle, AD and Suvà, ML and Dela Cruz, F and Pinello, L and Langenau, DM},
title = {Single-cell analysis and functional characterization uncover the stem cell hierarchies and developmental origins of rhabdomyosarcoma.},
journal = {Nature cancer},
volume = {3},
number = {8},
pages = {961-975},
pmid = {35982179},
issn = {2662-1347},
support = {R35 HG010717/HG/NHGRI NIH HHS/United States ; R01 CA154923/CA/NCI NIH HHS/United States ; R01 CA215118/CA/NCI NIH HHS/United States ; S10 RR023440/RR/NCRR NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; S10 RR020936/RR/NCRR NIH HHS/United States ; R00 HG008399/HG/NHGRI NIH HHS/United States ; R01 AR064327/AR/NIAMS NIH HHS/United States ; S10 OD016372/OD/NIH HHS/United States ; R01 CA211734/CA/NCI NIH HHS/United States ; K99 CA278696/CA/NCI NIH HHS/United States ; U54 CA231630/CA/NCI NIH HHS/United States ; S10 OD012027/OD/NIH HHS/United States ; },
mesh = {Child ; Humans ; Muscle, Skeletal/pathology ; *Rhabdomyosarcoma/genetics ; *Rhabdomyosarcoma, Embryonal ; Single-Cell Analysis ; Stem Cells/pathology ; },
abstract = {Rhabdomyosarcoma (RMS) is a common childhood cancer that shares features with developing skeletal muscle. Yet, the conservation of cellular hierarchy with human muscle development and the identification of molecularly defined tumor-propagating cells has not been reported. Using single-cell RNA-sequencing, DNA-barcode cell fate mapping and functional stem cell assays, we uncovered shared tumor cell hierarchies in RMS and human muscle development. We also identified common developmental stages at which tumor cells become arrested. Fusion-negative RMS cells resemble early myogenic cells found in embryonic and fetal development, while fusion-positive RMS cells express a highly specific gene program found in muscle cells transiting from embryonic to fetal development at 7-7.75 weeks of age. Fusion-positive RMS cells also have neural pathway-enriched states, suggesting less-rigid adherence to muscle-lineage hierarchies. Finally, we identified a molecularly defined tumor-propagating subpopulation in fusion-negative RMS that shares remarkable similarity to bi-potent, muscle mesenchyme progenitors that can make both muscle and osteogenic cells.},
}
@article {pmid35978191,
year = {2022},
author = {Deng, Y and Bartosovic, M and Ma, S and Zhang, D and Kukanja, P and Xiao, Y and Su, G and Liu, Y and Qin, X and Rosoklija, GB and Dwork, AJ and Mann, JJ and Xu, ML and Halene, S and Craft, JE and Leong, KW and Boldrini, M and Castelo-Branco, G and Fan, R},
title = {Spatial profiling of chromatin accessibility in mouse and human tissues.},
journal = {Nature},
volume = {609},
number = {7926},
pages = {375-383},
pmid = {35978191},
issn = {1476-4687},
support = {R37 AR040072/AR/NIAMS NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; RF1 MH128876/MH/NIMH NIH HHS/United States ; UG3 CA257393/CA/NCI NIH HHS/United States ; UH3 CA257393/CA/NCI NIH HHS/United States ; U54 DK106857/DK/NIDDK NIH HHS/United States ; U54 AG076043/AG/NIA NIH HHS/United States ; U01 CA260507/CA/NCI NIH HHS/United States ; R01 CA245313/CA/NCI NIH HHS/United States ; UH3 TR002151/TR/NCATS NIH HHS/United States ; 681893/ERC_/European Research Council/International ; },
mesh = {Animals ; Brain/metabolism ; Cell Differentiation ; Cell Lineage ; *Chromatin/genetics/metabolism ; *Chromatin Assembly and Disassembly/genetics ; *Chromatin Immunoprecipitation Sequencing/methods ; Epigenomics ; Gene Expression Profiling ; Genome ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Mice ; Palatine Tonsil/cytology/immunology ; },
abstract = {Cellular function in tissue is dependent on the local environment, requiring new methods for spatial mapping of biomolecules and cells in the tissue context[1]. The emergence of spatial transcriptomics has enabled genome-scale gene expression mapping[2-5], but the ability to capture spatial epigenetic information of tissue at the cellular level and genome scale is lacking. Here we describe a method for spatially resolved chromatin accessibility profiling of tissue sections using next-generation sequencing (spatial-ATAC-seq) by combining in situ Tn5 transposition chemistry[6] and microfluidic deterministic barcoding[5]. Profiling mouse embryos using spatial-ATAC-seq delineated tissue-region-specific epigenetic landscapes and identified gene regulators involved in the development of the central nervous system. Mapping the accessible genome in the mouse and human brain revealed the intricate arealization of brain regions. Applying spatial-ATAC-seq to tonsil tissue resolved the spatially distinct organization of immune cell types and states in lymphoid follicles and extrafollicular zones. This technology progresses spatial biology by enabling spatially resolved chromatin accessibility profiling to improve our understanding of cell identity, cell state and cell fate decision in relation to epigenetic underpinnings in development and disease.},
}
@article {pmid35977843,
year = {2022},
author = {Perry, I and Hernadi, SB and Cunha, L and Short, S and Marchbank, A and Spurgeon, DJ and Orozco-terWengel, P and Kille, P},
title = {Molecular insights into high-altitude adaption and acclimatisation of Aporrectodea caliginosa.},
journal = {Life science alliance},
volume = {5},
number = {11},
pages = {},
pmid = {35977843},
issn = {2575-1077},
mesh = {Adaptation, Physiological/genetics ; *Altitude ; Animals ; Genome ; *Oligochaeta ; },
abstract = {Here, we explore the high-altitude adaptions and acclimatisation of Aporrectodea caliginosa Population diversity is assessed through mitochondrial barcoding, identifying closely related populations across the island of Pico (Azores). We present the first megabase N50 assembly size (1.2 Mbp) genome for A. caliginosa High- and low-altitude populations were exposed experimentally to a range of oxygen and temperature conditions, simulating altitudinal conditions, and the transcriptomic responses explored. SNP densities are assessed to identify signatures of selective pressure and their link to differentially expressed genes. The high-altitude A. caliginosa population had lower differential expression and fewer co-expressed genes between conditions, indicating a more condition-refined epigenetic response. Genes identified as under adaptive pressure through Fst and nucleotide diversity in the high-altitude population clustered around the differentially expressed an upstream environmental response control gene, HMGB1. The high-altitude population of A. caliginosa indicated adaption and acclimatisation to high-altitude conditions and suggested resilience to extreme weather events. This mechanistic understanding could help offer a strategy in further identifying other species capable of maintaining soil fertility in extreme environments.},
}
@article {pmid35975224,
year = {2022},
author = {Huston, DC and Khudhir, M and Hodda, M},
title = {Reliability and Utility of Standard Gene Sequence Barcodes for the Identification and Differentiation of Cyst Nematodes of the Genus Heterodera.},
journal = {Journal of nematology},
volume = {54},
number = {1},
pages = {20220024},
pmid = {35975224},
issn = {0022-300X},
abstract = {Difficulties inherent in the morphological identification of cyst nematodes of the genus Heterodera Schmidt, 1871, an important lineage of plant parasites, has led to broad adoption of molecular methods for diagnosing and differentiating species. The pool of publicly available sequence data has grown significantly over the past few decades, and over half of all known species of Heterodera have been characterized using one or more molecular markers commonly employed in DNA barcoding (18S, internal transcribed spacer [ITS], 28S, coxI). But how reliable are these data and how useful are these four markers for differentiating species? We downloaded all 18S, ITS, 28S, and coxI gene sequences available on the National Center for Biotechnology Information (NCBI) database, GenBank, for all species of Heterodera for which data were available. Using a combination of sequence comparison and tree-based phylogenetic methods, we evaluated this dataset for erroneous or otherwise problematic sequences and examined the utility of each molecular marker for the delineation of species. Although we find the rate of obviously erroneous sequences to be low, all four molecular markers failed to differentiate between at least one species pair. Our results suggest that while a combination of multiple markers is best for species identification, the coxI marker shows the most utility for species differentiation and should be favored over 18S, ITS, and 28S, where resources are limited. Presently, less than half the valid species of Heterodera have a sequence of coxI available, and only a third have more than one sequence of this marker.},
}
@article {pmid35975006,
year = {2022},
author = {Zhao, X and Sun, S and Yu, W and Zhu, W and Zhao, Z and Zhou, Y and Ding, X and Fang, N and Yang, R and Li, JP},
title = {Improved ClickTags enable live-cell barcoding for highly multiplexed single cell sequencing.},
journal = {RSC chemical biology},
volume = {3},
number = {8},
pages = {1052-1060},
pmid = {35975006},
issn = {2633-0679},
abstract = {Click chemistry-enabled DNA barcoding of cells provides a universal strategy for sample multiplexing in single-cell RNA-seq (scRNA-seq). However, current ClickTags are limited to fixed samples as they only label cells efficiently in methanol. Herein, we report the development of a new protocol for barcoding live cells with improved ClickTags. The optimized reactions barcoded live cells without perturbing their physiological states, which allowed sample multiplexing of live cells in scRNA-seq. The general applicability of this protocol is demonstrated in diversified types of samples, including murine and human primary samples. Up to 16 samples across these two species are successfully multiplexed and demultiplexed with high consistency. The wide applications of this method could help to increase throughput, reduce cost and remove the batch effect in scRNA-seq, which is especially valuable for studying clinical samples from a large cohort.},
}
@article {pmid35974073,
year = {2022},
author = {Campos, M and Phelan, J and Spadar, A and Collins, E and Gonçalves, A and Pelloquin, B and Vaselli, NM and Meiwald, A and Clark, E and Stica, C and Orsborne, J and Sylla, M and Edi, C and Camara, D and Mohammed, AR and Afrane, YA and Kristan, M and Walker, T and Gomez, LF and Messenger, LA and Clark, TG and Campino, S},
title = {High-throughput barcoding method for the genetic surveillance of insecticide resistance and species identification in Anopheles gambiae complex malaria vectors.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {13893},
pmid = {35974073},
issn = {2045-2322},
support = {101285/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; R01AI123074/AI/NIAID NIH HHS/United States ; MR/M01360X/1/MRC_/Medical Research Council/United Kingdom ; MR/R020973/1/MRC_/Medical Research Council/United Kingdom ; MR/R006040/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/N010469/1/MRC_/Medical Research Council/United Kingdom ; R01 AI123074/AI/NIAID NIH HHS/United States ; MR/R025576/1/MRC_/Medical Research Council/United Kingdom ; BB/R013063/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *Anopheles/genetics ; Insecticide Resistance/genetics ; *Insecticides/pharmacology ; *Malaria ; Mosquito Vectors/genetics ; },
abstract = {Surveillance of malaria vector species and the monitoring of insecticide resistance are essential to inform malaria control strategies and support the reduction of infections and disease. Genetic barcoding of mosquitoes is a useful tool to assist the high-throughput surveillance of insecticide resistance, discriminate between sibling species and to detect the presence of Plasmodium infections. In this study, we combined multiplex PCR, custom designed dual indexing, and Illumina next generation sequencing for high throughput single nucleotide polymorphism (SNP)-profiling of four species from the Anopheles (An.) gambiae complex (An. gambiae sensu stricto, An. coluzzii, An. arabiensis and An. melas). By amplifying and sequencing only 14 genetic fragments (500 bp each), we were able to simultaneously detect Plasmodium infection; insecticide resistance-conferring SNPs in ace1, gste2, vgsc and rdl genes; the partial sequences of nuclear ribosomal internal transcribed spacers (ITS1 and ITS2) and intergenic spacers (IGS), Short INterspersed Elements (SINE), as well as mitochondrial genes (cox1 and nd4) for species identification and genetic diversity. Using this amplicon sequencing approach with the four selected An. gambiae complex species, we identified a total of 15 non-synonymous mutations in the insecticide target genes, including previously described mutations associated with resistance and two new mutations (F1525L in vgsc and D148E in gste2). Overall, we present a reliable and cost-effective high-throughput panel for surveillance of An. gambiae complex mosquitoes in malaria endemic regions.},
}
@article {pmid35972336,
year = {2022},
author = {Chen, Z and Jin, C and Wang, X and Deng, Y and Tian, X and Li, X and Zhang, Q and Zeng, Y and Liao, J and Zhang, L},
title = {Characterization of the Complete Chloroplast Genome of Four Species in Callerya.},
journal = {Journal of AOAC International},
volume = {106},
number = {1},
pages = {146-155},
doi = {10.1093/jaoacint/qsac097},
pmid = {35972336},
issn = {1944-7922},
support = {81960697//National Natural Science Foundation of China (The fundamental relationship of spatholobus suberectus Dunn/ ; //Jiangxi University of Chinese Medicine Science, and Technology Innovation Team Development Program/ ; },
mesh = {*Fabaceae/genetics ; *Genome, Chloroplast ; Phylogeny ; China ; },
abstract = {BACKGROUND: Callerya reticulata (Bentham) Schot, Callerya dielsiana (Harms) P.K. Loc ex Z. Wei &amp; Pedley, Callerya nitida var. hirsutissima (Z. Wei) X.Y. Zhu, and Callerya nitida (Bentham) R. Geesink, which belongs to the Leguminosae family, are important medicinal plants in China. The genus Callerya includes 26 species, 18 species are distributed in China, and the vine stems of some species are used as traditional medicinal herbs because they have important pharmacological activity. Due to the high similarity of appearance, it is difficult to identify them in the market by appearance alone. Therefore, circulating of Callerya-related materia medica on the market is confusing, sometimes even leading to drug safety problems. It is urgent to develop molecular methods for their identification.<br><br>OBJECTIVE: To sequence and analyze the complete chloroplast (cp) genomes of C. reticulata, C. dielsiana, C. nitida var. hirsutissima, and C. nitida and to analyze their cp genome differences as a basis for seeking easier DNA barcoding for their identification.<br><br>METHOD: After using Illumina high-throughput sequencing and nanopore sequencing to obtain the genome data, some bioinformatics software was used to assembly and analyze the molecular structure of cp genomes.<br><br>RESULTS: The complete cp genomes of the four species were circular molecules, which ranged from 130&#x200a;435 to 132&#x200a;546&#x2009;bp, and GC contents ranged from 33.89% to 34.89%. Each of them includes a large single-copy region, a small single-copy region, and without large inverted repeat regions.<br><br>CONCLUSIONS: These results suggested that highly variable regions of the four cp genomes would provide useful plastid markers, which could be used as a potential genomic resource to resolve phylogenetic questions and provide a reference for mining specific DNA barcodes of these species.<br><br>HIGHLIGHTS: Our study provided highly effective molecular markers for subsequent phylogenetic analysis, species identification, and biogeographic analysis of Callerya.},
}
@article {pmid35972144,
year = {2022},
author = {Carrasquilla, M and Drammeh, NF and Rawat, M and Sanderson, T and Zenonos, Z and Rayner, JC and Lee, MCS},
title = {Barcoding Genetically Distinct Plasmodium falciparum Strains for Comparative Assessment of Fitness and Antimalarial Drug Resistance.},
journal = {mBio},
volume = {13},
number = {5},
pages = {e0093722},
pmid = {35972144},
issn = {2150-7511},
support = {210918/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; 206194/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Antimalarials/pharmacology ; *Artemisinins/pharmacology ; Complex Mixtures ; Drug Resistance/genetics ; *Plasmodium falciparum/drug effects/physiology ; Protozoan Proteins/genetics ; Genetic Fitness ; },
abstract = {The repeated emergence of antimalarial drug resistance in Plasmodium falciparum, including to the current frontline antimalarial artemisinin, is a perennial problem for malaria control. Next-generation sequencing has greatly accelerated the identification of polymorphisms in resistance-associated genes but has also highlighted the need for more sensitive and accurate laboratory tools to profile current and future antimalarials and to quantify the impact of drug resistance acquisition on parasite fitness. The interplay of fitness and drug response is of fundamental importance in understanding why particular genetic backgrounds are better at driving the evolution of drug resistance in natural populations, but the impact of parasite fitness landscapes on the epidemiology of drug resistance has typically been laborious to accurately quantify in the lab, with assays being limited in accuracy and throughput. Here we present a scalable method to profile fitness and drug response of genetically distinct P. falciparum strains with well-described sensitivities to several antimalarials. We leverage CRISPR/Cas9 genome-editing and barcode sequencing to track unique barcodes integrated into a nonessential gene (pfrh3). We validate this approach in multiplex competitive growth assays of three strains with distinct geographical origins. Furthermore, we demonstrate that this method can be a powerful approach for tracking artemisinin response as it can identify an artemisinin resistant strain within a mix of multiple parasite lines, suggesting an approach for scaling the laborious ring-stage survival assay across libraries of barcoded parasite lines. Overall, we present a novel high-throughput method for multiplexed competitive growth assays to evaluate parasite fitness and drug response. IMPORTANCE The complex interplay between antimalarial resistance and parasite fitness has important implications for understanding the development and spread of drug resistance alleles and the impact of genetic background on transmission. One limitation with current methodologies to measure parasite fitness is the ability to scale this beyond simple head-to-head competition experiments between a wildtype control line and test line, with a need for a scalable approach that allows tracking of parasite growth in complex mixtures. In our study, we have used CRISPR editing to insert unique DNA barcodes into a safe-harbor genomic locus to tag multiple parasite strains and use next-generation sequencing to read out strain dynamics. We observe inherent fitness differences between the strains, as well as sensitive modulation of responses to challenge with clinically relevant antimalarials, including artemisinin.},
}
@article {pmid35970837,
year = {2022},
author = {Ni, H and Hatit, MZC and Zhao, K and Loughrey, D and Lokugamage, MP and Peck, HE and Cid, AD and Muralidharan, A and Kim, Y and Santangelo, PJ and Dahlman, JE},
title = {Piperazine-derived lipid nanoparticles deliver mRNA to immune cells in vivo.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {4766},
pmid = {35970837},
issn = {2041-1723},
support = {UG3 TR002855/TR/NCATS NIH HHS/United States ; UH3 TR002855/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; *Lipids/chemistry ; Liposomes ; *Nanoparticles/chemistry ; Piperazine ; RNA, Messenger/metabolism ; RNA, Small Interfering/metabolism ; },
abstract = {In humans, lipid nanoparticles (LNPs) have safely delivered therapeutic RNA to hepatocytes after systemic administration and to antigen-presenting cells after intramuscular injection. However, systemic RNA delivery to non-hepatocytes remains challenging, especially without targeting ligands such as antibodies, peptides, or aptamers. Here we report that piperazine-containing ionizable lipids (Pi-Lipids) preferentially deliver mRNA to immune cells in vivo without targeting ligands. After synthesizing and characterizing Pi-Lipids, we use high-throughput DNA barcoding to quantify how 65 chemically distinct LNPs functionally delivered mRNA (i.e., mRNA translated into functional, gene-editing protein) in 14 cell types directly in vivo. By analyzing the relationships between lipid structure and cellular targeting, we identify lipid traits that increase delivery in vivo. In addition, we characterize Pi-A10, an LNP that preferentially delivers mRNA to the liver and splenic immune cells at the clinically relevant dose of 0.3 mg/kg. These data demonstrate that high-throughput in vivo studies can identify nanoparticles with natural non-hepatocyte tropism and support the hypothesis that lipids with bioactive small-molecule motifs can deliver mRNA in vivo.},
}
@article {pmid35969901,
year = {2022},
author = {Yuan, C and Tao, R and Xia, R and Chen, L and Li, C and Zhang, S},
title = {Species identification on shark fin fragments based on DNA barcoding technique.},
journal = {Forensic science international. Genetics},
volume = {61},
number = {},
pages = {102754},
doi = {10.1016/j.fsigen.2022.102754},
pmid = {35969901},
issn = {1878-0326},
mesh = {Animals ; *Sharks/genetics ; DNA Barcoding, Taxonomic/methods ; Conservation of Natural Resources ; Species Specificity ; DNA/genetics ; },
}
@article {pmid35969779,
year = {2022},
author = {Boni, N and Shapiro, L and Honig, B and Wu, Y and Rubinstein, R},
title = {On the formation of ordered protein assemblies in cell-cell interfaces.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {34},
pages = {e2206175119},
pmid = {35969779},
issn = {1091-6490},
support = {R01 GM120238/GM/NIGMS NIH HHS/United States ; R01 GM122804/GM/NIGMS NIH HHS/United States ; R01 MH114817/MH/NIMH NIH HHS/United States ; },
mesh = {Animals ; Electron Microscope Tomography ; Monte Carlo Method ; *Neurons/metabolism ; Protein Binding ; *Protein Conformation ; *Protocadherins/chemistry ; Vertebrates ; },
abstract = {Crystal structures of many cell-cell adhesion receptors reveal the formation of linear "molecular zippers" comprising an ordered one-dimensional array of proteins that form both intercellular (trans) and intracellular (cis) interactions. The clustered protocadherins (cPcdhs) provide an exemplar of this phenomenon and use it as a basis of barcoding of vertebrate neurons. Here, we report both Metropolis and kinetic Monte Carlo simulations of cPcdh zipper formation using simplified models of cPcdhs that nevertheless capture essential features of their three-dimensional structure. The simulations reveal that the formation of long zippers is an implicit feature of cPcdh structure and is driven by their cis and trans interactions that have been quantitatively characterized in previous work. Moreover, in agreement with cryo-electron tomography studies, the zippers are found to organize into two-dimensional arrays even in the absence of attractive interactions between individual zippers. Our results suggest that the formation of ordered two-dimensional arrays of linear zippers of adhesion proteins is a common feature of cell-cell interfaces. From the perspective of simulations, they demonstrate the importance of a realistic depiction of adhesion protein structure and interactions if important biological phenomena are to be properly captured.},
}
@article {pmid35962931,
year = {2023},
author = {Sayed, HA and Mostafa, S and Haggag, IM and Hassan, NA},
title = {DNA Barcoding of Prunus Species Collection Conserved in the National Gene Bank of Egypt.},
journal = {Molecular biotechnology},
volume = {65},
number = {3},
pages = {410-418},
pmid = {35962931},
issn = {1559-0305},
support = {US-joint (grant No 1119)//Science and Technology Development Fund/ ; },
mesh = {*DNA Barcoding, Taxonomic ; Phylogeny ; *Prunus/genetics ; Genetic Variation ; Egypt ; DNA, Chloroplast/genetics ; DNA, Intergenic/genetics ; Nucleotides ; DNA, Plant/genetics ; Sequence Analysis, DNA ; },
abstract = {Two intergenic spacers cpDNA barcoding regions were used to assess the genetic diversity and phylogenetic structure of a collection of 25 Prunus accessions. The trnH-psbA and trnL-trnF intergenic spacers were able to distinguish and identify only four Prunus species. The average aligned length was 316-352 bp and 701-756 bp for trnH-psbA and trnL-trnF, respectively. The overall evolutionary divergence was higher in trnH-psbA than trnL-trnF. The transition/transversion bias (R) recorded as 0.59 in trnL-trnF and 0.89 in trnH-psbA. The number of invariable sites, nucleotide diversity (Pi), and the average number of nucleotide differences (k) was higher in the trnH-psbA region. The trnL-trnF records was above the other region in the number of variable sites, number of singleton variable sites, and the parsimony informative sites. Phylogenetic relationships among the 25 accessions of Prunus species were investigated. Most of the different Prunus species clustered in a homogenized distribution in both regions, except for the plum (P. domestica) accession (African Rose) was assigned with the peach (P. persica) accessions. The two intergenic cpDNA trnH-psbA and trnL-trnF were able to distinguish and identify the four Prunus species accessions.},
}
@article {pmid35962326,
year = {2022},
author = {Milián-García, Y and Hempel, CA and Janke, LAA and Young, RG and Furukawa-Stoffer, T and Ambagala, A and Steinke, D and Hanner, RH},
title = {Mitochondrial genome sequencing, mapping, and assembly benchmarking for Culicoides species (Diptera: Ceratopogonidae).},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {584},
pmid = {35962326},
issn = {1471-2164},
support = {project ID FAP # 2122-002//Canadian Food Inspection Agency/ ; project ID FAP # 2122-002//Canadian Food Inspection Agency/ ; project ID FAP # 2122-002//Canadian Food Inspection Agency/ ; project ID FAP # 2122-002//Canadian Food Inspection Agency/ ; project ID FAP # 2122-002//Canadian Food Inspection Agency/ ; project ID FAP # 2122-002//Canadian Food Inspection Agency/ ; },
mesh = {Animals ; Benchmarking ; Cattle ; *Ceratopogonidae/genetics ; Genes, Mitochondrial ; *Genome, Mitochondrial/genetics ; Humans ; Insect Vectors/genetics ; },
abstract = {BACKGROUND: Mitochondrial genomes are the most sequenced genomes after bacterial and fungal genomic DNA. However, little information on mitogenomes is available for multiple metazoan taxa, such as Culicoides, a globally distributed, megadiverse genus containing 1,347 species.<br><br>AIM: &#xa0;Generating novel mitogenomic information from single Culicoides sonorensis and C. biguttatus specimens, comparing available mitogenome mapping and de novo assembly tools, and identifying the best performing strategy and tools for Culicoides species.<br><br>RESULTS: We present two novel and fully annotated mitochondrial haplotypes for two Culicoides species, C. sonorensis and C. biguttatus. We also annotated or re-annotated the only available reference mitogenome for C. sonorensis and C. arakawae. All species present a high similarity in mitogenome organization. The general gene arrangement for all Culicoides species was identical to the ancestral insect mitochondrial genome. Only short spacers were found in C. sonorensis (up to 30&#xa0;bp), contrary to C. biguttatus (up to 114&#xa0;bp). The mitochondrial genes ATP8, NAD2, NAD6, and LSU rRNA exhibited the highest nucleotide diversity and pairwise interspecific p genetic distance, suggesting that these genes might be suitable and complementary molecular barcodes for Culicoides identification in addition to the commonly utilized COI gene. We observed performance differences between the compared mitogenome generation strategies. The mapping strategy outperformed the de novo assembly strategy, but mapping results were partially biased in the absence of species-specific reference mitogenome. Among the utilized tools, BWA performed best for C. sonorensis while SPAdes, MEGAHIT, and MitoZ were among the best for C. biguttatus. The best-performing mitogenome annotator was MITOS2. Additionally, we were able to recover exogenous mitochondrial DNA from Bos taurus (biting midges host) from a C. biguttatus blood meal sample.<br><br>CONCLUSIONS: Two novel annotated mitogenome haplotypes for C. sonorensis and C. biguttatus using High-Throughput Sequencing are presented. Current results are useful as the baseline for mitogenome reconstruction of the remaining Culicoides species from single specimens to HTS and genome annotation. Mapping to a species-specific reference mitogenome generated better results for Culicoides mitochondrial genome reconstruction than de novo assembly, while de novo assembly resulted better in the absence of a closely related reference mitogenome. These results have direct implications for molecular-based identification of these vectors of human and zoonotic diseases, setting the basis for using the whole mitochondrial genome as a marker in Culicoides identification.},
}
@article {pmid35959477,
year = {2022},
author = {Hoban, ML and Whitney, J and Collins, AG and Meyer, C and Murphy, KR and Reft, AJ and Bemis, KE},
title = {Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13790},
pmid = {35959477},
issn = {2167-8359},
mesh = {Animals ; *Genome, Mitochondrial/genetics ; DNA Barcoding, Taxonomic/methods ; Fishes ; Biodiversity ; DNA ; },
abstract = {DNA barcoding is critical to conservation and biodiversity research, yet public reference databases are incomplete. Existing barcode databases are biased toward cytochrome oxidase subunit I (COI) and frequently lack associated voucher specimens or geospatial metadata, which can hinder reliable species assignments. The emergence of metabarcoding approaches such as environmental DNA (eDNA) has necessitated multiple marker techniques combined with barcode reference databases backed by voucher specimens. Reference barcodes have traditionally been generated by Sanger sequencing, however sequencing multiple markers is costly for large numbers of specimens, requires multiple separate PCR reactions, and limits resulting sequences to targeted regions. High-throughput sequencing techniques such as genome skimming enable assembly of complete mitogenomes, which contain the most commonly used barcoding loci (e.g., COI, 12S, 16S), as well as nuclear ribosomal repeat regions (e.g., ITS1&amp;2, 18S). We evaluated the feasibility of genome skimming to generate barcode references databases for marine fishes by assembling complete mitogenomes and nuclear ribosomal repeats. We tested genome skimming across a taxonomically diverse selection of 12 marine fish species from the collections of the National Museum of Natural History, Smithsonian Institution. We generated two sequencing libraries per species to test the impact of shearing method (enzymatic or mechanical), extraction method (kit-based or automated), and input DNA concentration. We produced complete mitogenomes for all non-chondrichthyans (11/12 species) and assembled nuclear ribosomal repeats (18S-ITS1-5.8S-ITS2-28S) for all taxa. The quality and completeness of mitogenome assemblies was not impacted by shearing method, extraction method or input DNA concentration. Our results reaffirm that genome skimming is an efficient and (at scale) cost-effective method to generate all mitochondrial and common nuclear DNA barcoding loci for multiple species simultaneously, which has great potential to scale for future projects and facilitate completing barcode reference databases for marine fishes.},
}
@article {pmid35958061,
year = {2022},
author = {Homchan, S and Gupta, YM},
title = {The complete mitochondrial genome of giant cricket, Tarbinskiellus portentosus (Orthoptera: Gryllidae) and its curation.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {7},
number = {8},
pages = {1427-1431},
pmid = {35958061},
issn = {2380-2359},
abstract = {Tarbinskiellus portentosus, commonly known as giant cricket one of the important edible cricket species. However, the genetic information of these species is still limited. Therefore, we have assembled and annotated the first mitochondrial genome of T. portentosus. The mitogenome is 15710 bp long and has GC content of 27.19%. The nucleotide composition is similar with other insect mitogenomes (A 40.6%; T 32.2%; C 17.3%; G 9.9%). The gene organization in the mitogenome of T. portentosus is identical to the mitogenome of other cricket species. The complete mitogenome of T. portentosus consisted 37 genes including 13 protein coding genes, 22 tRNA genes, and two rRNA genes. The newly assembled mitogenome will help molecular biology research on edible crickets. Since mitogenome genes are traditionally used for DNA barcoding and phylogenetic analysis, comparative analysis of T. portentosus mitogenome with other related cricket species will also aid researchers in developing universal primers for species identification toward food security. Apart from the main goal of providing full mitogenome of T. portentosus, paper also provides conceptual workflow based on de novo assembly and its correction for final mitogenome construction.},
}
@article {pmid35958059,
year = {2022},
author = {Wang, A and Wu, H and Gopurenko, D},
title = {Complete chloroplast genome of Serrated Tussock, Nassella trichotoma (Poaceae: Stipeae).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {7},
number = {8},
pages = {1432-1434},
pmid = {35958059},
issn = {2380-2359},
abstract = {Nassella trichotoma is one of the most serious weed species in Australia. It is often confused with other Nassella and stipoid species, especially at the young seedling stage, adding another layer of complexity in effective weed management. We report here the complete chloroplast genome of N. trichotoma (137,568 bp, GenBank accession number KX792500.2) sequenced using Next Generation Sequencing technology (Illumina). The N. trichotoma was grouped closely with other Nassella species and separated from other Stipeae species in the phylogenetic tree constructed based on the complete chloroplast genome sequences. The sequence information could be used for further identification of novel DNA barcodes for correct weed identification and subsequently improve management of this invasive grass.},
}
@article {pmid35956828,
year = {2022},
author = {Wirawan, IGP and Dewi, NKES and Sasadara, MMV and Sunyamurthi, IGNA and Jawi, IM and Wijaya, IN and Darmawati, IAP and Suada, IK and Krisnandika, AAK},
title = {Phytochemical Analysis and Molecular Identification of Green Macroalgae Caulerpa spp. from Bali, Indonesia.},
journal = {Molecules (Basel, Switzerland)},
volume = {27},
number = {15},
pages = {},
pmid = {35956828},
issn = {1420-3049},
support = {B/78.331/UN14.4.A/PT.01.03/2022//Udayana University/ ; },
mesh = {*Caulerpa/chemistry ; Indonesia ; Phylogeny ; Phytochemicals/metabolism ; *Seaweed ; },
abstract = {The studies of the Bulung Boni and Bulung Anggur (Caulerpa spp.) species and secondary metabolites are still very limited. Proper identification will support various aspects, such as cultivation, utilization, and economic interests. Moreover, understanding the secondary metabolites will assist in developing algae-based products. This study aimed to identify these indigenous Caulerpa algae and analyze their bioactive components. The tufA sequence was employed as a molecular marker in DNA barcoding, and its bioactive components were identified using the GC-MS method. The phylogenetic tree was generated in MEGA 11 using the maximum likelihood method, and the robustness of the tree was evaluated using bootstrapping with 1000 replicates. This study revealed that Bulung Boni is strongly connected to Caulerpa cylindracea. However, Bulung Anggur shows no close relationship to other Caulerpa species. GC-MS analysis of ethanolic extracts of Bulung Boni and Bulung Anggur showed the presence of 11 and 13 compounds, respectively. The majority of the compounds found in these algae have been shown to possess biological properties, such as antioxidant, antibacterial, anticancer, anti-inflammation, and antidiabetic. Further study is necessary to compare the data obtained using different molecular markers in DNA barcoding, and to elucidate other undisclosed compounds in these Caulerpa algae.},
}
@article {pmid35953050,
year = {2022},
author = {Shin, S and Kim, JE and Son, H},
title = {Identification and Characterization of Fungal Pathogens Associated with Boxwood Diseases in the Republic of Korea.},
journal = {The plant pathology journal},
volume = {38},
number = {4},
pages = {304-312},
pmid = {35953050},
issn = {1598-2254},
support = {321101-03//Ministry of Agriculture, Food and Rural Affairs/ ; 321107-03//Ministry of Agriculture, Food and Rural Affairs/ ; 2021R1A2C1004673//National Research Foundation of Korea/ ; },
abstract = {Boxwood is a representative ornamental shrub that is widely used in landscaping horticulture. After pruning, damaged leaves or stems of boxwoods are unavoidably vulnerable to infection by various plant pathogens. Several boxwood diseases caused by fungi, such as Volutella blight and Macrophoma leaf spot, have been reported worldwide including Republic of Korea. In this study, we isolated and identified fungal pathogens of boxwood diseases that occurred in Korea and characterized their morphological and taxonomic characteristics. Boxwood samples showing blight symptoms were collected in Seoul, Republic of Korea, and the putative fungal pathogens Pseudonectria buxi, P. foliicola, and Neofusicoccum buxi were successfully identified. Investigation of the morphological features of the field isolates, including mycelial growth and conidial morphology, and phylogenetic analysis of multiple DNA barcode loci revealed that there were some morphological and genetic variations among isolates, but all of the analyzed isolates were closely related to the corresponding reference strains. We also found that P. foliicola strains were more virulent than P. buxi, and the N. buxi strains isolated in this study were weak pathogens or saprophytes. The results of our study will contribute to the development of control strategies for boxwood diseases caused by fungi and accelerate research on the complex ecology of boxwood diseases.},
}
@article {pmid35952789,
year = {2022},
author = {Pérez-Burillo, J and Mann, DG and Trobajo, R},
title = {Evaluation of two short overlapping rbcL markers for diatom metabarcoding of environmental samples: Effects on biomonitoring assessment and species resolution.},
journal = {Chemosphere},
volume = {307},
number = {Pt 3},
pages = {135933},
doi = {10.1016/j.chemosphere.2022.135933},
pmid = {35952789},
issn = {1879-1298},
mesh = {Bayes Theorem ; Biological Monitoring ; DNA Barcoding, Taxonomic ; *Diatoms/genetics ; Environmental Monitoring ; Rivers ; United Kingdom ; },
abstract = {Two short diatom rbcL barcodes, 331 bp and 263 bp in length, have frequently been used in diatom metabarcoding studies. They overlap in a common 263-bp region but differ in the presence or absence of a 68-bp tail at the 5' end. Though the effectiveness of both has been demonstrated in separate biomonitoring and diversity studies, the impact of the 68-bp non-shared region has not been evaluated. Here we compare the two barcodes in terms of the values of a biotic index (IPS) and the ecological status classes derived from their application to an extensive metabarcoding dataset from United Kingdom rivers; this comprised 1703 samples and was produced using the 331-bp primers. In addition, we assess the effectiveness of each barcode for discrimination of genetic variants around and below the species level. The strong correlation found in IPS values between barcodes (Pearson's R = 0.98) indicates that the choice of the barcode does not have major implications for current WFD ecological assessments, although a very few sites (55: 3.23% of those analysed) were downgraded from an acceptable WFD class ("Good") to an unacceptable one ("Moderate"). Analyses of the taxonomic resolution of the two barcodes indicate that for many ASVs, the use of either marker - 263-bp and 331-bp - gives unambiguous assignations at species level though with differences in bootstrap confidence values. Such differences are caused by the stochasticity involved in the naïve Bayesian classifier used and by the fact that genetic distance, regarding closely related species, is increased when using the 331-bp barcode. However, in three cases, species differentiation fails with the shorter marker, leading to underestimates of species diversity. Finally, two ASVs from Nitzschia species evidenced that the use of the shorter marker can sometimes lead to false positives when the extent and nature of infraspecific variation are poorly known.},
}
@article {pmid35952576,
year = {2022},
author = {Xin, T and Li, R and Lou, Q and Lin, Y and Liao, H and Sun, W and Guan, M and Zhou, J and Song, J},
title = {Application of DNA barcoding to the entire traditional Chinese medicine industrial chain: A case study of Rhei Radix et Rhizoma.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {105},
number = {},
pages = {154375},
doi = {10.1016/j.phymed.2022.154375},
pmid = {35952576},
issn = {1618-095X},
mesh = {DNA Barcoding, Taxonomic ; *Drugs, Chinese Herbal ; Medicine, Chinese Traditional ; *Rheum ; Rhizome ; },
abstract = {BACKGROUND: Safety concerns, caused by complex and unpredictable adulterants, run through the entire industrial chain of traditional Chinese medicines (TCMs). However, the conventional circulation traceability system only focuses on a certain end or link at the back end of the TCM industrial chain, ignoring the integrity of the links cross the entire industrial chain and lacking traceability. In consequence, a strict and rational supervision system is urgently required for the entire industrial chain.<br><br>HYPOTHESIS/PURPOSE: We hypothesize that DNA barcoding would be a suitable measure for the traceability of adulterants in the entire TCM industrial chain.<br><br>METHODS: In this study, Rhei Radix et Rhizoma was selected as a model to establish a traceability system for the entire TCM industrial chain. A total of 110 samples, including leaves, seeds, roots, decoction pieces, and traditional Chinese patent medicines (TCPMs), were collected upstream, midstream, and downstream of the entire industrial chain of Rhei Radix et Rhizoma. The ndhF-rpl32 fragment rather than the universal DNA barcodes, which could not distinguish the three original species of Rhei Radix et Rhizoma, was selected as a specific DNA barcode to evaluate the practical application of DNA barcoding in the chain.<br><br>RESULTS: The results showed that the ndhF-rpl32 fragment in all samples could be amplified and bi-directionally sequenced. Based on the standard operating procedures of DNA barcoding, the ndhF-rpl32 fragment clearly distinguished the seven Rheum species collected upstream of the entire industrial chain. For the samples collected midstream and downstream of the entire industrial chain, 25% of the 36 commercial decoction pieces samples were identified as adulterants, whereas the eight TCPM samples were all derived from genuine Rhei Radix et Rhizoma.<br><br>CONCLUSIONS: This study shows that DNA barcoding is a powerful and suitable technology that can be applied to trace TCMs in the entire industrial chain, thereby assuring clinical medication safety.},
}
@article {pmid35951642,
year = {2022},
author = {Vences, M and Stützer, D and Rasoamampionona Raminosoa, N and Ziegler, T},
title = {Towards a DNA barcode library for Madagascar's threatened ichthyofauna.},
journal = {PloS one},
volume = {17},
number = {8},
pages = {e0271400},
pmid = {35951642},
issn = {1932-6203},
mesh = {Animals ; *Cichlids/genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Fishes/genetics ; Madagascar ; Phylogeny ; },
abstract = {In order to improve the molecular resources available for conservation management of Madagascar's threatened ichthyofauna, we elaborated a curated database of 2860 mitochondrial sequences of the mitochondrial COI, 16S and ND2 genes of Malagasy fishes, of which 1141 sequences of freshwater fishes were newly sequenced for this data set. The data set is mostly composed of COI (2015 sequences) while 16S and ND2 sequences from partly the same samples were used to match the COI sequences to reliably identified reference sequences of these genes. We observed COI uncorrected pairwise genetic distances of 5.2‒31.0% (mean 20.6%) among species belonging to different genera, and 0.0‒22.4% (mean 6.4%) for species belonging to the same genus. Deeply divergent mitochondrial lineages of uncertain attribution were found among Malagasy freshwater eleotrids and gobiids, confirming these groups are in need of taxonomic revision. DNA barcodes assigned to introduced cichlids (tilapias) included Coptodon rendallii, C. zillii, Oreochromis aureus (apparently a new country record), O. cf. mossambicus, O. niloticus, and one undetermined species of Oreochromis, with sequences of up to three species found per location. In aplocheiloid killifishes of the genus Pachypanchax, most species from northern Madagascar had only low mitochondrial divergences, three of these species (P. omalonotus, P. patriciae, and P. varatraza) were not reciprocally monophyletic, and one genetically deviant lineage was discovered in a northern locality, suggesting a need for partial taxonomic revision of this genus. While the lack of voucher specimens for most of the samples sequenced herein precludes final conclusions, our first step towards a DNA barcoding reference library of Madagascar's fishes already demonstrates the value of such a data set for improved taxonomic inventory and conservation management. We strongly suggest further exploration of Madagascar's aquatic environments, which should include detailed photographic documentation and tissue sampling of large numbers of specimens, and collection of preserved voucher specimens as well as of living fish for the buildup of ex situ assurance populations of threatened species complying with the One Plan Approach proposed by the IUCN SSC Conservation Breeding Specialist Group (CBSG).},
}
@article {pmid35951477,
year = {2023},
author = {Hua, Z and Jiang, C and Song, S and Tian, D and Chen, Z and Jin, Y and Zhao, Y and Zhou, J and Zhang, Z and Huang, L and Yuan, Y},
title = {Accurate identification of taxon-specific molecular markers in plants based on DNA signature sequence.},
journal = {Molecular ecology resources},
volume = {23},
number = {1},
pages = {106-117},
doi = {10.1111/1755-0998.13697},
pmid = {35951477},
issn = {1755-0998},
support = {2060302//Key project at central government level for the ability establishment of sustainable use for valuable Chinese medicine resources/ ; CI2021B014/CI2021A041//Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; 2018FY10080002//Special Funds for Basic Resources Investigation Research of the Ministry of Science and Technology/ ; 2019YFC1711000//The National Key Research and Development Program of China/ ; },
mesh = {*Plants/genetics ; High-Throughput Nucleotide Sequencing ; Genetic Markers ; *Magnoliopsida/genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA/methods ; DNA Barcoding, Taxonomic/methods ; DNA, Plant/genetics ; Phylogeny ; },
abstract = {Accurate identification of plants remains a significant challenge for taxonomists and is the basis for plant diversity conservation. Although DNA barcoding methods are commonly used for plant identification, these are limited by the low amplification success and low discriminative power of selected genomic regions. In this study, we developed a k-mer-based approach, the DNA signature sequence (DSS), to accurately identify plant taxon-specific markers, especially at the species level. DSS is a constant-length nucleotide sequence capable of identifying a taxon and distinguishing it from other taxa. In this study, we performed the first large-scale study of DSS markers in plants. DSS candidates of 3899 angiosperm plant species were calculated based on a chloroplast data set with 4356 assemblies. Using Sanger sequencing of PCR amplicons and high-throughput sequencing, DSSs were validated in four and 165 species, respectively. Based on this, the universality of the DSSs was over 79.38%. Several indicators influencing DSS marker identification and detection have also been evaluated, and common criteria for DSS application in plant identification have been proposed.},
}
@article {pmid35937994,
year = {2022},
author = {Boileau, E and Li, X and Naarmann-de Vries, IS and Becker, C and Casper, R and Altmüller, J and Leuschner, F and Dieterich, C},
title = {Full-Length Spatial Transcriptomics Reveals the Unexplored Isoform Diversity of the Myocardium Post-MI.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {912572},
pmid = {35937994},
issn = {1664-8021},
abstract = {We introduce Single-cell Nanopore Spatial Transcriptomics (scNaST), a software suite to facilitate the analysis of spatial gene expression from second- and third-generation sequencing, allowing to generate a full-length near-single-cell transcriptional landscape of the tissue microenvironment. Taking advantage of the Visium Spatial platform, we adapted a strategy recently developed to assign barcodes to long-read single-cell sequencing data for spatial capture technology. Here, we demonstrate our workflow using four short axis sections of the mouse heart following myocardial infarction. We constructed a de novo transcriptome using long-read data, and successfully assigned 19,794 transcript isoforms in total, including clinically-relevant, but yet uncharacterized modes of transcription, such as intron retention or antisense overlapping transcription. We showed a higher transcriptome complexity in the healthy regions, and identified intron retention as a mode of transcription associated with the infarct area. Our data revealed a clear regional isoform switching among differentially used transcripts for genes involved in cardiac muscle contraction and tissue morphogenesis. Molecular signatures involved in cardiac remodeling integrated with morphological context may support the development of new therapeutics towards the treatment of heart failure and the reduction of cardiac complications.},
}
@article {pmid35931117,
year = {2022},
author = {Balsamo, JA and Penton, KE and Zhao, Z and Hayes, MJ and Lima, SM and Irish, JM and Bachmann, BO},
title = {An immunogenic cell injury module for the single-cell multiplexed activity metabolomics platform to identify promising anti-cancer natural products.},
journal = {The Journal of biological chemistry},
volume = {298},
number = {9},
pages = {102300},
pmid = {35931117},
issn = {1083-351X},
support = {T32 GM007628/GM/NIGMS NIH HHS/United States ; R01 CA226833/CA/NCI NIH HHS/United States ; P30 DK058404/DK/NIDDK NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; R01 GM092218/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenosine Triphosphate ; Animals ; *Antineoplastic Agents/isolation &amp; purification/pharmacology ; *Biological Products/isolation &amp; purification/pharmacology ; Biomarkers ; Calreticulin/metabolism ; Cell Death/immunology ; *HMGB1 Protein/metabolism ; Histones/metabolism ; Humans ; *Metabolomics/methods ; *Neoplasms/immunology ; *Single-Cell Analysis ; },
abstract = {Natural products constitute and significantly impact many current anti-cancer medical interventions. A subset of natural products induces injury processes in malignant cells that recruit and activate host immune cells to produce an adaptive anti-cancer immune response, a process known as immunogenic cell death. However, a challenge in the field is to delineate forms of cell death and injury that best promote durable antitumor immunity. Addressing this with a single-cell chemical biology natural product discovery platform, like multiplex activity metabolomics, would be especially valuable in human leukemia, where cancer cells are heterogeneous and may react differently to the same compounds. Herein, a new ten-color, fluorescent cell barcoding-compatible module measuring six immunogenic cell injury signaling readouts are as follows: DNA damage response (γH2AX), apoptosis (cCAS3), necroptosis (p-MLKL), mitosis (p-Histone H3), autophagy (LC3), and the unfolded protein response (p-EIF2α). A proof-of-concept screen was performed to validate functional changes in single cells induced by secondary metabolites with known mechanisms within bacterial extracts. This assay was then applied in multiplexed activity metabolomics to reveal an unexpected mammalian cell injury profile induced by the natural product narbomycin. Finally, the functional consequences of injury pathways on immunogenicity were compared with three canonical assays for immunogenic hallmarks, ATP, HMGB1, and calreticulin, to correlate secondary metabolite-induced cell injury profiles with canonical markers of immunogenic cell death. In total, this work demonstrated a new phenotypic screen for discovery of natural products that modulate injury response pathways that can contribute to cancer immunogenicity.},
}
@article {pmid35930571,
year = {2022},
author = {Shi, X and Xu, W and Wan, M and Sun, Q and Chen, Q and Zhao, C and Sun, K and Shu, Y},
title = {Comparative analysis of chloroplast genomes of three medicinal Carpesium species: Genome structures and phylogenetic relationships.},
journal = {PloS one},
volume = {17},
number = {8},
pages = {e0272563},
pmid = {35930571},
issn = {1932-6203},
mesh = {*Asteraceae/genetics ; Chloroplasts/genetics ; Evolution, Molecular ; *Genome, Chloroplast ; Phylogeny ; },
abstract = {Carpesium (Asteraceae) is a genus that contains many plant species with important medicinal values. However, the lack of chloroplast genome research of this genus has greatly hindered the study of its molecular evolution and phylogenetic relationship. This study used the Illumina sequencing platform to sequence three medicinal plants of the Carpesium genus: Carpesium abrotanoides, Carpesium cernuum, and Carpesium faberi, obtaining three complete chloroplast genome sequences after assembly and annotation. It was revealed that the three chloroplast genomes were typical quadripartite structures with lengths of 151,389 bp (C. abrotanoides), 151,278 bp (C. cernuum), and 151,250 bp (C. faberi), respectively. A total of 114 different genes were annotated, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Abundant SSR loci were detected in all three chloroplast genomes, with most composed of A/T. The expansion and contraction of the IR region indicate that the boundary regions of IR/SC are relatively conserved for the three species. Using C. abrotanoides as a reference, most of the non-coding regions of the chloroplast genomes were significantly different among the three species. Five different mutation hot spots (trnC-GCA-petN, psaI, petA-psbJ, ndhF, ycf1) with high nucleotide variability (Pi) can serve as potential DNA barcodes of Carpesium species. Additionally, phylogenetic evolution analysis of the three species suggests that C. cernuum has a closer genetic relationship to C. faberi than C. abrotanoides. Simultaneously, Carpesium is a monophyletic group closely related to the genus Inula. Complete chloroplast genomes of Carpesium species can help study the evolutionary and phylogenetic relationships and are expected to provide genetic marker assistance to identify Carpesium species.},
}
@article {pmid35926067,
year = {2022},
author = {Fang, Y and Sun, P and Xie, X and Du, M and Du, F and Ye, J and Kalveram, BK and Plante, JA and Plante, KS and Li, B and Bai, XC and Shi, PY and Chen, ZJ},
title = {An antibody that neutralizes SARS-CoV-1 and SARS-CoV-2 by binding to a conserved spike epitope outside the receptor binding motif.},
journal = {Science immunology},
volume = {7},
number = {76},
pages = {eabp9962},
pmid = {35926067},
issn = {2470-9468},
support = {R01 AI134907/AI/NIAID NIH HHS/United States ; U19 AI171413/AI/NIAID NIH HHS/United States ; HHSN272201600013C/AI/NIAID NIH HHS/United States ; R24 AI120942/AI/NIAID NIH HHS/United States ; R43 AI145617/AI/NIAID NIH HHS/United States ; UL1 TR001439/TR/NCATS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Mice ; Animals ; *SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Epitopes ; Angiotensin-Converting Enzyme 2 ; Antibodies, Viral ; Peptidyl-Dipeptidase A/metabolism ; Receptors, Virus/metabolism ; *COVID-19 ; },
abstract = {The rapid evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), such as the Omicron variants that are highly transmissible and immune evasive, underscores the need to develop therapeutic antibodies with broad neutralizing activities. Here, we used the LIBRA-seq technology, which identified SARS-CoV-2-specific B cells via DNA barcoding and subsequently single-cell sequenced BCRs, to identify an antibody, SW186, which could neutralize major SARS-CoV-2 variants of concern, including Beta, Delta, and Omicron, as well as SARS-CoV-1. The cryo-EM structure of SW186 bound to the receptor binding domain (RBD) of the viral spike protein showed that SW186 interacted with an epitope of the RBD that is not at the interface of its binding to the ACE2 receptor but is highly conserved among SARS coronaviruses. This epitope encompasses a glycosylation site (N343) of the viral spike protein. Administration of SW186 in mice after they were infected with SARS-CoV-2 Alpha, Beta, or Delta variants reduced the viral loads in the lung. These results demonstrated that SW186 neutralizes diverse SARS coronaviruses by binding to a conserved RBD epitope, which could serve as a target for further antibody development.},
}
@article {pmid35924796,
year = {2022},
author = {Schneider, R and Prati, S and Grabner, D and Sures, B},
title = {First report of microsporidians in the non-native shrimp Neocaridina davidi from a temperate European stream.},
journal = {Diseases of aquatic organisms},
volume = {150},
number = {},
pages = {125-130},
doi = {10.3354/dao03681},
pmid = {35924796},
issn = {0177-5103},
mesh = {Animals ; *Decapoda ; *Enterocytozoon/genetics ; *Microsporidia ; *Penaeidae/parasitology ; Polymerase Chain Reaction/veterinary ; Rivers ; },
abstract = {The release of ornamental pets outside their native range can directly or indirectly impact the recipient community, e.g. via the co-introduction of associated pathogens. However, studies on parasites associated with non-native species, in particular freshwater decapods, have focused mainly on a limited set of pathogens. Here we provide data for the first time on microsporidian parasites of the non-native ornamental shrimp Neocaridina davidi, collected in a stream in Germany. Furthermore, we confirm an ongoing range expansion of the warm-adapted N. davidi from thermally polluted colder water. In the investigated shrimps, the microsporidian parasite Enterocytozoon hepatopenaei and an unknown microsporidian isolate were detected, raising concerns about their transmission potential and pathogenicity on native crustacean species.},
}
@article {pmid35924489,
year = {2022},
author = {Meleshko, D and Yang, R and Marks, P and Williams, S and Hajirasouliha, I},
title = {Efficient detection and assembly of non-reference DNA sequences with synthetic long reads.},
journal = {Nucleic acids research},
volume = {50},
number = {18},
pages = {e108},
pmid = {35924489},
issn = {1362-4962},
support = {R35 GM138152/GM/NIGMS NIH HHS/United States ; },
mesh = {Algorithms ; Base Sequence ; *Genome, Human ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Sequence Analysis, DNA/methods ; },
abstract = {Recent pan-genome studies have revealed an abundance of DNA sequences in human genomes that are not present in the reference genome. A lion's share of these non-reference sequences (NRSs) cannot be reliably assembled or placed on the reference genome. Improvements in long-read and synthetic long-read (aka linked-read) technologies have great potential for the characterization of NRSs. While synthetic long reads require less input DNA than long-read datasets, they are algorithmically more challenging to use. Except for computationally expensive whole-genome assembly methods, there is no synthetic long-read method for NRS detection. We propose a novel integrated alignment-based and local assembly-based algorithm, Novel-X, that uses the barcode information encoded in synthetic long reads to improve the detection of such events without a whole-genome de novo assembly. Our evaluations demonstrate that Novel-X finds many non-reference sequences that cannot be found by state-of-the-art short-read methods. We applied Novel-X to a diverse set of 68 samples from the Polaris HiSeq 4000 PGx cohort. Novel-X discovered 16 691 NRS insertions of size > 300 bp (total length 18.2 Mb). Many of them are population specific or may have a functional impact.},
}
@article {pmid35918646,
year = {2022},
author = {Nanjala, C and Wanga, VO and Odago, W and Mutinda, ES and Waswa, EN and Oulo, MA and Mkala, EM and Kuja, J and Yang, JX and Dong, X and Hu, GW and Wang, QF},
title = {Plastome structure of 8 Calanthe s.l. species (Orchidaceae): comparative genomics, phylogenetic analysis.},
journal = {BMC plant biology},
volume = {22},
number = {1},
pages = {387},
pmid = {35918646},
issn = {1471-2229},
mesh = {Gene Order ; Genome ; *Genome, Chloroplast ; Genomics ; *Orchidaceae/genetics ; Phylogeny ; },
abstract = {BACKGROUND: Calanthe (Epidendroideae, Orchidaceae) is a pantropical genus distributed in Asia and Africa. Its species are of great importance in terms of economic, ornamental and medicinal values. However, due to limited and confusing delimitation characters, the taxonomy of the Calanthe alliance (Calanthe, Cephalantheropsis, and Phaius) has not been sufficiently resolved. Additionally, the limited genomic information has shown incongruences in its systematics and phylogeny. In this study, we used illumina platform sequencing, performed a de novo assembly, and did a comparative analysis of 8 Calanthe group species' plastomes: 6 Calanthe and 2 Phaius species. Phylogenetic analyses were used to reconstruct the relationships of the species as well as with other species of the family Orchidaceae.<br><br>RESULTS: The complete plastomes of the Calanthe group species have a quadripartite structure with varied sizes ranging between 150,105bp-158,714bp, including a large single-copy region (LSC; 83,364bp- 87,450bp), a small single-copy region (SSC; 16,297bp -18,586bp), and a pair of inverted repeat regions (IRs; 25,222bp - 26,430bp). The overall GC content of these plastomes ranged between 36.6-36.9%. These plastomes encoded 131-134 differential genes, which included 85-88 protein-coding genes, 37-38 tRNA genes, and 8 rRNA genes. Comparative analysis showed no significant variations in terms of their sequences, gene content, gene order, sequence repeats and the GC content hence highly conserved. However, some genes were lost in C. delavayi (P. delavayi), including ndhC, ndhF, and ndhK genes. Compared to the coding regions, the non-coding regions had more sequence repeats hence important for species DNA barcoding. Phylogenetic analysis revealed a paraphyletic relationship in the Calanthe group, and confirmed the position of Phaius delavayi in the genus Calanthe as opposed to its previous placement in Phaius.<br><br>CONCLUSION: This study provides a report on the complete plastomes of 6 Calanthe and 2 Phaius species and elucidates the structural characteristics of the plastomes. It also highlights the power of plastome data to resolve phylogenetic relationships and clarifies taxonomic disputes among closely related species to improve our understanding of their systematics and evolution. Furthermore, it also provides valuable genetic resources and a basis for studying evolutionary relationships and population genetics among orchid species.},
}
@article {pmid35918453,
year = {2022},
author = {Chaiphongpachara, T and Changbunjong, T and Sumruayphol, S and Laojun, S and Suwandittakul, N and Kuntawong, K},
title = {Geometric morphometrics versus DNA barcoding for the identification of malaria vectors Anopheles dirus and An. baimaii in the Thai-Cambodia border.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {13236},
pmid = {35918453},
issn = {2045-2322},
mesh = {Animals ; *Anopheles/genetics ; Cambodia ; DNA ; DNA Barcoding, Taxonomic ; *Malaria ; Mosquito Vectors/genetics ; Thailand/epidemiology ; },
abstract = {Anopheles (Cellia) dirus Peyton &amp; Harrison and Anopheles baimaii Sallum &amp; Peyton are sibling species within the Dirus complex belonging to the Leucosphyrus group, and have been incriminated as primary vectors of malaria in Thailand. In the present study, DNA barcoding and geometric morphometrics were used to distinguish between An. dirus and An. baimaii in the international border areas, Trat Province, eastern Thailand. Our results revealed that DNA barcoding based on the cytochrome c oxidase subunit I gene could not be used to distinguish An. dirus from An. baimaii. The overlapping values between intra- and interspecific genetic divergence indicated no barcoding gap present for An. dirus and An. baimaii (ranging from 0 to 0.99%). However, the results of the geometric morphometric analysis based on the wing shape clearly distinguished An. dirus and An. baimaii, with 92.42% of specimens assigned to the correct species. We concluded that geometric morphometrics is an effective tool for the correct species identification of these two malaria vectors. Our findings could be used to make entomological surveillance information more accurate, leading to further effective mosquito control planning in Thailand and other countries in Southeast Asia.},
}
@article {pmid35915209,
year = {2022},
author = {Costine, B and Zhang, M and Chhajed, S and Pearson, B and Chen, S and Nadakuduti, SS},
title = {Exploring native Scutellaria species provides insight into differential accumulation of flavones with medicinal properties.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {13201},
pmid = {35915209},
issn = {2045-2322},
mesh = {Chromatography, Liquid ; *Flavanones/metabolism ; *Flavones/metabolism ; Flavonoids/metabolism ; Phylogeny ; Plant Roots/metabolism ; *Scutellaria ; Scutellaria baicalensis/metabolism ; Tandem Mass Spectrometry ; },
abstract = {Scutellaria baicalensis is a well-studied medicinal plant belonging to the Lamiaceae family, prized for the unique 4'-deoxyflavones produced in its roots. In this study, three native species to the Americas, S. lateriflora, S. arenicola, and S. integrifolia were identified by DNA barcoding, and phylogenetic relationships were established with other economically important Lamiaceae members. Furthermore, flavone profiles of native species were explored. 4'-deoxyflavones including baicalein, baicalin, wogonin, wogonoside, chrysin and 4'-hydroxyflavones, scutellarein, scutellarin, and apigenin, were quantified from leaves, stems, and roots. Qualitative, and quantitative differences were identified in their flavone profiles along with characteristic tissue-specific accumulation. 4'-deoxyflavones accumulated in relatively high concentrations in root tissues compared to aerial tissues in all species except S. lateriflora. Baicalin, the most abundant 4'-deoxyflavone detected, was localized in the roots of S. baicalensis and leaves of S. lateriflora, indicating differential accumulation patterns between the species. S. arenicola and S. integrifolia are phylogenetically closely related with similar flavone profiles and distribution patterns. Additionally, the S. arenicola leaf flavone profile was dominated by two major unknown peaks, identified using LC-MS/MS to most likely be luteolin-7-O-glucuronide and 5,7,2'-trihydroxy-6-methoxyflavone 7-O-glucuronide. Collectively, results presented in this study suggest an evolutionary divergence of flavonoid metabolic pathway in the Scutellaria genus of Lamiaceae.},
}
@article {pmid35915108,
year = {2022},
author = {Mathur, L and Szalai, B and Du, NH and Utharala, R and Ballinger, M and Landry, JJM and Ryckelynck, M and Benes, V and Saez-Rodriguez, J and Merten, CA},
title = {Combi-seq for multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in single-cell droplets.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {4450},
pmid = {35915108},
issn = {2041-1723},
mesh = {Drug Combinations ; *Gene Expression Profiling ; Humans ; K562 Cells ; Microfluidics ; *Transcriptome ; },
abstract = {Anti-cancer therapies often exhibit only short-term effects. Tumors typically develop drug resistance causing relapses that might be tackled with drug combinations. Identification of the right combination is challenging and would benefit from high-content, high-throughput combinatorial screens directly on patient biopsies. However, such screens require a large amount of material, normally not available from patients. To address these challenges, we present a scalable microfluidic workflow, called Combi-Seq, to screen hundreds of drug combinations in picoliter-size droplets using transcriptome changes as a readout for drug effects. We devise a deterministic combinatorial DNA barcoding approach to encode treatment conditions, enabling the gene expression-based readout of drug effects in a highly multiplexed fashion. We apply Combi-Seq to screen the effect of 420 drug combinations on the transcriptome of K562 cells using only ~250 single cell droplets per condition, to successfully predict synergistic and antagonistic drug pairs, as well as their pathway activities.},
}
@article {pmid35915106,
year = {2022},
author = {Velo-Antón, G and Henrique, M and Liz, AV and Martínez-Freiría, F and Pleguezuelos, JM and Geniez, P and Crochet, PA and Brito, JC},
title = {DNA barcode reference library for the West Sahara-Sahel reptiles.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {459},
pmid = {35915106},
issn = {2052-4463},
support = {CRE-7629-04, CRE-8412-08, GEFNE-53-12//National Geographic Society/ ; 11052709, 11052707, 13257467//Mohamed bin Zayed Species Conservation Fund/ ; SG-15399-1, SG-17893-1//Rufford Foundation (Rufford Small Grants Foundation)/ ; },
mesh = {Africa, Northern ; Animals ; Biodiversity ; *DNA Barcoding, Taxonomic ; Gene Library ; Phylogeny ; *Reptiles/genetics ; },
abstract = {DNA barcode reference libraries are now continuously produced for the tree of life, which are essential pillars for the study of biological diversity. Yet, our knowledge about global diversity is largely limited in undersampled regions such as the largest warm desert, the Sahara-Sahel. This dataset provides a DNA barcode reference library for the reptiles of the Western Sahara-Sahel (WSS) and neighbouring countries across this region. It includes 760 barcodes from 133 reptile taxa, distributed in 23 families, and covering the intraspecific diversity of some species. A total of 84 species were collected in the WSS (83% of the total reptile species richness) over 18 overland field expeditions conducted since 2003. DNA barcodes resulted in a high success rate (95%) of species identification and barcoding gap analysis highlighted the effectiveness of the COI fragment as a barcode marker for the WSS reptiles. This dataset represents a comprehensive and reliable DNA reference library for the WSS, filling an important biodiversity gap across a remote and hard-to-sample region.},
}
@article {pmid35907388,
year = {2022},
author = {Holzmann, M and Gooday, AJ and Majewski, W and Pawlowski, J},
title = {Molecular and morphological diversity of monothalamous foraminifera from South Georgia and the Falkland Islands: Description of four new species.},
journal = {European journal of protistology},
volume = {85},
number = {},
pages = {125909},
doi = {10.1016/j.ejop.2022.125909},
pmid = {35907388},
issn = {1618-0429},
mesh = {Antarctic Regions ; Falkland Islands ; *Foraminifera/genetics ; Phylogeny ; },
abstract = {Based on molecular and morphological data, we describe three new genera and four new species of monothalamids from the sublittoral zone (21-250 m) in South Georgia fjords that belong to different monothalamid clades. Limaxia alba gen. nov. sp. nov. (Clade A) has an elongate, subcylindrical test, 359-688 µm long, with some detritus attached to the organic wall. Hilla argentea gen. nov. sp. nov. (Clade Y) has a cylindrical, finely agglutinated test, 535-755 µm long. Pseudoconqueria lenticularis gen. nov. sp. nov. branches separately. It has a spindle-shaped, finely agglutinated test, 280-574 µm long. Bathyallogromia olivacea sp. nov. (Clade C) has an ovate organic-walled test, 369-433 µm long. We present the first genetic data on two monothalamid species originally described from South Georgia, Hippocrepinella alba (Clade C) and Hippocrepinella hirudinea (Clade D), as well as a single sequence for C. delacai (Clade J) originally described from McMurdo Sound, Antarctica. In addition, we report nine undescribed species branching in six different monothalamid clades (A, B, BM, C, J, Y), eight of them sampled around South Georgia and one collected from the Falkland Islands near Stanley.},
}
@article {pmid35906365,
year = {2022},
author = {Balaur, E and Sadatnajafi, C and Abbey, B},
title = {Optical barcoding using polarisation sensitive plasmonic biosensors for the detection of self-assembled monolayers.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {13081},
pmid = {35906365},
issn = {2045-2322},
mesh = {*Biosensing Techniques/methods ; Nanotechnology/methods ; Refractometry ; *Surface Plasmon Resonance/methods ; },
abstract = {Periodic subwavelength apertures have the ability to passively detect variations in the dielectric properties of the local sample environment through modification of the plasmon resonances associated with these structures. The resulting resonance peak can effectively provide a 'fingerprint' indicative of the dielectric properties of the medium within the near-surface region. Here we report on the use of bimodal silver-based plasmonic colour filters for molecular sensing. Firstly, by exploring the optical output of these devices as a function of the incident polarisation for a range of different analytes of known refractive index, we were able to both maximise and quantify their sensitivity. We then apply this concept to the real-time monitoring of the formation of self-assembled monolayers based on detection of the optical output using a spectrometer. This highlights the potential for bimodal plasmonic devices to be able to dynamically monitor variations in the local environment down to the level of single molecules without the need for specific functionalisation or labelling. Advantages of using this technique include the ability for these devices to be miniaturised and to dynamically tailor their optical output permitting the analysis of very small sample volumes and maximise their dynamic range for a specific analyte.},
}
@article {pmid35905777,
year = {2022},
author = {Carvalho, LPC and Costa, GDS and Pereira Júnior, AM and de Paulo, PFM and Silva, GS and Carioca, ALPM and Rodrigues, BL and Pessoa, FAC and Medeiros, JF},
title = {DNA Barcoding of genus Culicoides biting midges (Diptera: Ceratopogonidae) in the Brazilian Amazon.},
journal = {Acta tropica},
volume = {235},
number = {},
pages = {106619},
doi = {10.1016/j.actatropica.2022.106619},
pmid = {35905777},
issn = {1873-6254},
mesh = {Animals ; Brazil ; *Ceratopogonidae/genetics ; DNA ; DNA Barcoding, Taxonomic ; Phylogeny ; },
abstract = {Culicoides biting midges are capable to transmit Oropouche virus, Bluetongue virus and Mansonella spp. This study aimed to assess the utility of DNA barcode as an alternative method in the Culicoides species identification. The study was conducted in Jamari National Forest. Biting midges were collected using HP light traps during four months, February, April, August and October 2018. Insects were morphologically identified to the species level, and rest of the body were subjected to DNA extraction and PCR targeting a fragment of the cytochrome c oxidase subunit I (COI) gene, which were analyzed and deposited in GenBank. A phylogenetic gene tree was reconstructed using RAxML software, and the sequences were assigned at Molecular Operational Taxonomic Unit (MOTU) level by species delimitation algorithms. According to morphological approach, 18 species of 2 subgenera and 7 species groups were identified. A total of 191 new COI barcodes from 18 species were generated. Of these, fifteen species have been deposited for the first time in all datasets in the world. These sequences allowed the correct identification of 188 and 187 specimens according to the BM and BCM criteria, respectively. The intraspecific genetic distances ranged from 0 to 16.5%, while the interspecific ones ranged from 2.1 to 27.1%. The nominal species Culicoides glabellus and C. tetrathyris splitted into three and two MOTUs, respectively, except for mPTP, indicating a cryptic diversity in these species. Also, sequences of C. pseudodiabolicus formed two MOTUs using all algorithms, except for PTP and ABGD, suggesting the existence of two potential species. In contrast, some barcodes of C. quasiparaensis and C. paraensis merged into a single MOTU, which can be explained by the complex characteristics of the paraensis group, since these species have similar morphological characters. Here, we provided the first COI barcodes for biting midges in Rondônia and Brazil, and demonstrates that these are sufficient to discriminate between some species.},
}
@article {pmid35904776,
year = {2022},
author = {Ramos De Dios, SM and Tiwari, VK and McCune, CD and Dhokale, RA and Berkowitz, DB},
title = {Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization.},
journal = {Chemical reviews},
volume = {122},
number = {16},
pages = {13800-13880},
doi = {10.1021/acs.chemrev.2c00213},
pmid = {35904776},
issn = {1520-6890},
support = {C06 RR016544/RR/NCRR NIH HHS/United States ; },
mesh = {*Alkynes/chemistry ; Amination ; *Artificial Intelligence ; Catalysis ; DNA ; },
abstract = {Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.},
}
@article {pmid35904108,
year = {2022},
author = {Polsomboon Nelson, S and Bourke, BP and Badr, R and Tarpey, J and Caicedo-Quiroga, L and Leiva, D and Pott, M and Cruz, A and Chao, CC and Achee, NL and Grieco, JP and Jiang, L and Jiang, J and Farris, CM and Linton, YM},
title = {Ticks (Acari: Ixodidae) and Associated Pathoge Collected From Domestic Animals and Vegetation in Stann Creek District, Southeastern Belize, Central America.},
journal = {Journal of medical entomology},
volume = {59},
number = {5},
pages = {1749-1755},
pmid = {35904108},
issn = {1938-2928},
mesh = {Amblyomma ; Animals ; Animals, Domestic ; Belize ; *Dog Diseases/epidemiology/microbiology ; Dogs ; Ehrlichia/genetics ; *Horse Diseases/epidemiology ; Horses ; Humans ; *Ixodidae/microbiology ; *Rhipicephalus sanguineus ; *Rickettsia/genetics ; *Tick Infestations/epidemiology/veterinary ; },
abstract = {Data on the prevalence and distribution of ticks and tick-borne diseases in Belize are lacking. Ticks (n = 564) collected from dogs, horses, and vegetation in two villages in Stann Creek District in southeastern Belize in 2018, were molecularly identified and screened for tick-borne nonviral human pathogens. The identity of 417 ticks was molecularly confirmed by DNA barcoding as Rhipicephalus sanguineus (Latreille) (66.43%), Amblyomma ovale Koch (15.59%), Dermacentor nitens Neumann (11.51%), Amblyomma sp. ADB0528 (3.6%), and the remainder being small records (2.87%) of Amblyomma coelebs Neumann, Amblyomma imitator Kohls, Amblyomma tapirellum Dunn, Amblyomma auricularium Conil, and Amblyomma maculatum Koch. Individual tick extracts were screened for the presence of Rickettsia spp., Babesia spp., Babesia microti, Borrelia spp., Ehrlichia spp., and Anaplasma spp. using available conventional polymerase chain reaction (PCR) assays. Rickettsia parkeri strain Atlantic Rainforest was identified in five specimens of A. ovale, and one other unidentified tick, all collected from dogs. Another unidentified tick-also collected from a dog-tested positive for an undefined but previously detected Ehrlichia sp. With the exception of D. nitens, all eight other tick species identified in this study were collected on dogs, suggesting that dogs could be usefully employed as sentinel animals for tick surveillance in Belize.},
}
@article {pmid35903316,
year = {2022},
author = {den Hollander, NHM and Roep, BO},
title = {From Disease and Patient Heterogeneity to Precision Medicine in Type 1 Diabetes.},
journal = {Frontiers in medicine},
volume = {9},
number = {},
pages = {932086},
pmid = {35903316},
issn = {2296-858X},
abstract = {Type 1 diabetes (T1D) remains a devastating disease that requires much effort to control. Life-long daily insulin injections or an insulin pump are required to avoid severe complications. With many factors contributing to disease onset, T1D is a complex disease to cure. In this review, the risk factors, pathophysiology and defect pathways are discussed. Results from (pre)clinical studies are highlighted that explore restoration of insulin production and reduction of autoimmunity. It has become clear that treatment responsiveness depends on certain pathophysiological or genetic characteristics that differ between patients. For instance, age at disease manifestation associated with efficacy of immune intervention therapies, such as depleting islet-specific effector T cells or memory B cells and increasing immune regulation. The new challenge is to determine in whom to apply which intervention strategy. Within patients with high rates of insulitis in early T1D onset, therapy depleting T cells or targeting B lymphocytes may have a benefit, whereas slow progressing T1D in adults may be better served with more sophisticated, precise and specific disease modifying therapies. Genetic barcoding and immune profiling may help determining from which new T1D endotypes patients suffer. Furthermore, progressed T1D needs replenishment of insulin production besides autoimmunity reversal, as too many beta cells are already lost or defect. Recurrent islet autoimmunity and allograft rejection or necrosis seem to be the most challenging obstacles. Since beta cells are highly immunogenic under stress, treatment might be more effective with stress reducing agents such as glucagon-like peptide 1 (GLP-1) analogs. Moreover, genetic editing by CRISPR-Cas9 allows to create hypoimmunogenic beta cells with modified human leukocyte antigen (HLA) expression that secrete immune regulating molecules. Given the differences in T1D between patients, stratification of endotypes in clinical trials seems essential for precision medicines and clinical decision making.},
}
@article {pmid35903040,
year = {2022},
author = {Anthoons, B and Lagiotis, G and Drouzas, AD and de Boer, H and Madesis, P},
title = {Barcoding High Resolution Melting (Bar-HRM) enables the discrimination between toxic plants and edible vegetables prior to consumption and after digestion.},
journal = {Journal of food science},
volume = {87},
number = {9},
pages = {4221-4232},
doi = {10.1111/1750-3841.16253},
pmid = {35903040},
issn = {1750-3841},
support = {765000//H2020-MSCA-ITN-ETN Plant.ID/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; DNA Primers ; DNA, Plant/genetics ; Digestion ; Humans ; *Plants, Toxic ; Vegetables ; },
abstract = {The consumption of poisonous plants can lead to serious health problems or even casualties due to various factors, including easy access to poisonous plants due to their common distribution, co-occurrence and resemblance with edible plants, and the lack of regulation in the food product supply chain. Clinical diagnosis of intoxications usually relies on the availability of the plant consumed by the patient and on the morphology of the plant parts found in the patient's stomach. Therefore, given the fragmented nature of ingested plant material, species identification may face serious difficulties, can be inaccurate, and time-consuming. This highlights the need for rapid and reliable tools to identify toxic species. In the present study, we developed an ITS2-high-resolution melting (HRM) assay for: (1) the discrimination of common toxic plants and their edible lookalikes, and (2) the detection of toxic plants in digested samples. More specifically, we designed species-specific ITS2 primers for the authentication of poisonous species in simulated mixtures and verified them with Bar-HRM. Moreover, the developed HRM-based molecular tool was capable of quantifying the toxic species Datura stramonium in simulated mixtures with the edible Amaranthus retroflexus down to at least 0.5% v/v. This study shows that species-specific ITS2 primers can amplify the DNA from fragmented and/or artificially digested samples and that Bar-HRM is capable of detecting poisonous plant species in digested samples even after 4 h. The developed Bar-HRM protocol has important implications for application in medicine, forensics, and the agricultural industry, either to accurately detect the cause of plant intoxications or as a tool for quality control in the supply chain. PRACTICAL APPLICATION: In this work, we established a high-resolution melting DNA-based protocol capable of discriminating between phenotypically similar common toxic and edible plant species in mixtures, even at very low quantities. This technology also proved efficient in detecting the toxic species in mixtures digested in artificial gastric acid, as it would be the case after accidental ingestion. This work is expected to have important implications for application in medicine, forensics, and the agricultural industry, either for identifying the cause of plant intoxications or as a tool for quality control in different steps of the supply chain.},
}
@article {pmid35901781,
year = {2022},
author = {Wong, WH and Curtis, C},
title = {"Fateful" encounter: Lineage tracing meets phylogeny to unravel mysteries of cancer progression.},
journal = {Developmental cell},
volume = {57},
number = {14},
pages = {1680-1682},
doi = {10.1016/j.devcel.2022.07.002},
pmid = {35901781},
issn = {1878-1551},
mesh = {Animals ; Biological Evolution ; Cell Lineage/genetics ; Humans ; Mice ; *Neoplasms/genetics ; Phylogeny ; },
abstract = {In a recent issue of Cell, Yang et al. utilize evolvable cellular barcodes to investigate the evolutionary trajectories of murine lung adenocarcinoma. Reconstructing the life histories of these tumors based on cellular barcodes reveals stringent selection and phenotypic differences across subclonal lineages.},
}
@article {pmid35900362,
year = {2022},
author = {Fang, W and Wang, J and Lu, S and Gu, Q and He, X and Wang, F and Wang, L and Tian, Y and Liu, H and Fan, C},
title = {Encoding Morphogenesis of Quasi-Triangular Gold Nanoprisms with DNA.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {61},
number = {39},
pages = {e202208688},
doi = {10.1002/anie.202208688},
pmid = {35900362},
issn = {1521-3773},
mesh = {DNA ; *Gold/chemistry ; *Metal Nanoparticles/chemistry ; Morphogenesis ; Sulfhydryl Compounds ; },
abstract = {Properties of gold nanoparticles vary with their morphologies. Typically, the research on the properties and applications of the nonequilibrium intermediates generated by the morphological evolution of triangular gold nanoprisms is still incomplete. Herein, we employ thiol-DNA (HS-DNA) to protect the low-stability quasi-nanoprisms with different truncation degrees (R values). The presence of HS-DNA not only increases the stability of the quasi-nanoprisms in different microenvironments, but also facilitates us to investigate their intrinsic plasmonic properties related to morphology. Additionally, we serve quasi-nanoprisms loaded with HS-DNA as assembly modules and nanoplatforms for programmable self-assembly higher-order hybrid structures, as well as carriers for encoding and decoding of orthogonal barcode-like information, which opens new opportunities for developing novel building blocks for light manipulation at nanoscale.},
}
@article {pmid35900347,
year = {2023},
author = {Abad, ZG and Burgess, TI and Redford, AJ and Bienapfl, JC and Srivastava, S and Mathew, R and Jennings, K},
title = {IDphy: An International Online Resource for Molecular and Morphological Identification of Phytophthora.},
journal = {Plant disease},
volume = {107},
number = {4},
pages = {987-998},
doi = {10.1094/PDIS-02-22-0448-FE},
pmid = {35900347},
issn = {0191-2917},
mesh = {*Phytophthora/genetics ; Phylogeny ; DNA, Ribosomal Spacer/genetics ; DNA, Ribosomal/genetics ; DNA, Intergenic ; },
abstract = {Phytophthora, with 203 species, is a genus of high importance in agriculture worldwide. Here, we present the online resource "IDphy", developed to facilitate the correct identification of species of Phytophthora using the type specimens from the original descriptions wherever possible. IDphy emphasizes species of high economic impact and regulatory concern for the United States. IDphy presents an interactive Lucid key and a tabular key for 161 culturable species described as of May 2018, including 141 ex-types and 20 well-authenticated specimens. IDphy contains standard operating procedures for morphological and molecular characterization, as well as a glossary, image gallery, and numerous links. Each of the 161 factsheets includes access to nomenclature and morphological and molecular features, including sequences of the internal transcribed spacer ribosomal DNA, cytochrome C oxidase subunit I (barcoding genes), YPT1, β-tubulin, elongation factor 1a, L10, heat shock protein 90, and other genes. IDphy contains an innovative in silico BLAST and phylogenetic sequence analysis using NCBI. The IDphy mobile app, released in August 2021 (free for Android or iOS), allows users to take the Lucid key into the laboratory. IDphy is the first online identification tool based on the ex-types implemented for plant pathogens. In this article, we also include information for 21 new species and one hybrid described after the publication of IDphy, the status of the specimens of the types and ex-types at international herbaria and culture collections, and the status of genomes at the GenBank (currently 153 genome assemblies which correspond to 42 described species, including 16 ex-types). The effectiveness of the IDphy online resource and the content of this article could inspire other researchers to develop additional identification tools for other important groups of plant pathogens.},
}
@article {pmid35899806,
year = {2022},
author = {Li, C and Song, Y and Li, L and Tessnow, AE and Zhu, J and Guan, X and Guo, W and Cui, H and Lu, Z and Lv, S and Yu, Y and Men, X},
title = {Two Microsatellite Types Within NAD6 Gene Help to Distinguish Populations and Infer the Migratory Route of the Invasive Fall Armyworm, Spodoptera frugiperda, (Lepidoptera, Noctuidae) in China.},
journal = {Journal of economic entomology},
volume = {115},
number = {5},
pages = {1409-1416},
doi = {10.1093/jee/toac114},
pmid = {35899806},
issn = {1938-291X},
support = {2019YFD0300105//National Key R&amp;D Program of China/ ; 2020CXGC010802//Key R&amp;D Program of Shandong Province/ ; CXGC2021A42//Agricultural Science and Technology Innovation Project of Shandong Academy of Agricultural Sciences/ ; },
mesh = {Animals ; China ; DNA, Mitochondrial/genetics ; *Microsatellite Repeats ; *Oryza/genetics ; Spodoptera/genetics ; Zea mays/genetics ; },
abstract = {Spodoptera frugiperda is a major agricultural pest that has invaded China since January 2019. Given that most of the individuals present in China carried the diagnostic rice-strain mtDNA (COI-RS), there was no efficient method to distinguish populations of S. frugiperda. In this study, we identified and characterized two variant microsatellite alleles in the mitochondrial NAD6 gene of S. frugiperda retrieved from the National Center for Biotechnology Center GenBank. We then sequenced partial NAD6 genes containing the microsatellite region and the diagnostic COI barcoding gene (used to distinguish the corn-strain and the rice-strain) of 429 invasive S. frugiperda individuals that were collected from the main infested regions in China during 2019-2020. Our data indicates that two kinds of interrupted repeat sequences, (ATA)4T(ATA)3 and (ATA)5T(ATA)3, exist in the microsatellite region which we defined as the deletion type (NAD6-D), and the insertion type (NAD6-I) based on the repeat units' differentiation, respectively. The presence of these two microsatellite types in the mtDNA genome of S. frugiperda was further confirmed with the sequencing results in 429 samples. Moreover, NAD6-I and NAD6-D types were both present in individuals with COI-RS, while only NAD6-D type was detected in the COI-CS individuals. Interestingly, the two microsatellite types suggested a possible geographic distribution: the western migratory route (Yunan and Chongqing) was comprised exclusively of NAD6-I type, while both NAD6-I and NAD6-D types were identified in the predicted eastern migration trajectories (Hainan, Guangxi, Shandong, etc.). These results suggested that NAD6-D and NAD6-I types may be useful in distinguishing between populations, analyzing the evolutionary mechanism of mtDNA microsatellite polymorphism, inferring the migratory route of S. frugiperda in China, and developing precise and integrated control strategies for S. frugiperda.},
}
@article {pmid35899252,
year = {2022},
author = {Lance, RF and Guan, X and Swift, JF and Edwards, CE and Lindsay, DL and Britzke, ER},
title = {Multifaceted DNA metabarcoding of guano to uncover multiple classes of ecological data in two different bat communities.},
journal = {Evolutionary applications},
volume = {15},
number = {7},
pages = {1189-1200},
pmid = {35899252},
issn = {1752-4571},
abstract = {DNA contained in animal scat provides a wealth of information about the animal, and DNA metabarcoding of scat collections can provide key information about animal populations and communities. Next-generation DNA sequencing technologies and DNA metabarcoding provide an efficient means for obtaining information available in scat samples. We used multifaceted DNA metabarcoding (MDM) of noninvasively collected bat guano pellets from a Myotis lucifugus colony on Fort Drum Military Installation, New York, USA, and from two mixed-species bat roosts on Fort Huachuca Military Installation, Arizona, USA, to identify attributes such as bat species composition, sex ratios, diet, and the presence of pathogens and parasites. We successfully identified bat species for nearly 98% of samples from Fort Drum and 90% of samples from Fort Huachuca, and identified the sex for 84% and 67% of samples from these same locations, respectively. Species and sex identification matched expectations based on prior censuses of bat populations utilizing those roosts, though samples from some species were more or less common than anticipated within Fort Huachuca roosts. Nearly 62% of guano samples from Fort Drum contained DNA from Pseudogymnoascus destructans, where bats with wing damage from White-nose Syndrome were commonly observed. Putative dietary items were detected in a majority of samples from insectivorous bats on Fort Drum (81%) and Fort Huachuca (63%). A minority of guano samples identified as the nectarivorous Leptonycteris yerbabuenae (28%) provided DNA sequences from putative forage plant species. Finally, DNA sequences from both putative ecto- and endoparasite taxa were detected in 35% and 56% of samples from Fort Drum and Fort Huachuca, respectively. This study demonstrates that the combination of noninvasive sampling, DNA metabarcoding, and sample and locus multiplexing provide a wide array of data that are otherwise difficult to obtain.},
}
@article {pmid35896746,
year = {2022},
author = {Bhattarai-Kline, S and Lear, SK and Fishman, CB and Lopez, SC and Lockshin, ER and Schubert, MG and Nivala, J and Church, GM and Shipman, SL},
title = {Recording gene expression order in DNA by CRISPR addition of retron barcodes.},
journal = {Nature},
volume = {608},
number = {7921},
pages = {217-225},
pmid = {35896746},
issn = {1476-4687},
support = {DP2 GM140917/GM/NIGMS NIH HHS/United States ; },
mesh = {*CRISPR-Cas Systems/genetics ; *DNA/biosynthesis/genetics ; *Gene Editing/methods ; *Gene Expression ; Genome/genetics ; *Information Storage and Retrieval/methods ; Integrases/metabolism ; Prokaryotic Cells/metabolism ; *RNA/genetics ; *Reverse Transcription ; Time Factors ; },
abstract = {Biological processes depend on the differential expression of genes over time, but methods to make physical recordings of these processes are limited. Here we report a molecular system for making time-ordered recordings of transcriptional events into living genomes. We do this through engineered RNA barcodes, based on prokaryotic retrons[1], that are reverse transcribed into DNA and integrated into the genome using the CRISPR-Cas system[2]. The unidirectional integration of barcodes by CRISPR integrases enables reconstruction of transcriptional event timing based on a physical record through simple, logical rules rather than relying on pretrained classifiers or post hoc inferential methods. For disambiguation in the field, we will refer to this system as a Retro-Cascorder.},
}
@article {pmid35895732,
year = {2022},
author = {Jamdade, R and Al-Shaer, K and Al-Sallani, M and Al-Harthi, E and Mahmoud, T and Gairola, S and Shabana, HA},
title = {Multilocus marker-based delimitation of Salicornia persica and its population discrimination assisted by supervised machine learning approach.},
journal = {PloS one},
volume = {17},
number = {7},
pages = {e0270463},
pmid = {35895732},
issn = {1932-6203},
mesh = {*Chenopodiaceae/genetics ; *DNA Barcoding, Taxonomic/methods ; DNA, Chloroplast/genetics ; DNA, Plant/genetics ; Genetic Markers ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Supervised Machine Learning ; },
abstract = {The Salicornia L. has been considered one of the most taxonomically challenging genera due to high morphological plasticity, intergradation between related species, and lack of diagnostic features in preserved herbarium specimens. In the United Arab Emirates (UAE), only one species of this genus, Salicornia europaea, has been reported, though investigating its identity at the molecular level has not yet been undertaken. Moreover, based on growth form and morphology variation between the Ras-Al-Khaimah (RAK) population and the Umm-Al-Quwain (UAQ) population, we suspect the presence of different species or morphotypes. The present study aimed to initially perform species identification using multilocus DNA barcode markers from chloroplast DNA (cpDNA) and nuclear ribosomal DNA (nrDNA), followed by the genetic divergence between two populations (RAK and UAQ) belonging to two different coastal localities in the UAE. The analysis resulted in high-quality multilocus barcode sequences subjected to species discrimination through the unsupervised OTU picking and supervised learning methods. The ETS sequence data from our study sites had high identity with the previously reported sequences of Salicornia persica using NCBI blast and was further confirmed using OTU picking methods viz., TaxonDNAs Species identifier and Assemble Species by Automatic Partitioning (ASAP). Moreover, matK sequence data showed a non-monophyletic relationship, and significant discrimination between the two populations through alignment-based unsupervised OTU picking, alignment-free Co-Phylog, and alignment &amp; alignment-free supervised learning approaches. Other markers viz., rbcL, trnH-psbA, ITS2, and ETS could not distinguish the two populations individually, though their combination with matK (cpDNA &amp; cpDNA+nrDNA) showed enough population discrimination. However, the ITS2+ETS (nrDNA) exhibited much higher genetic divergence, further splitting both the populations into four haplotypes. Based on the observed morphology, genetic divergence, and the number of haplotypes predicted using the matK marker, it can be suggested that two distinct populations (RAK and UAQ) do exist. Further extensive morpho-taxonomic studies are required to determine the inter-population variability of Salicornia in the UAE. Altogether, our results suggest that S. persica is the species that grow in the present study area in UAE, and do not support previous treatments as S. europaea.},
}
@article {pmid35894651,
year = {2022},
author = {Ji, C and Zhang, Q and Shi, R and Li, J and Wang, X and Wu, Z and Ma, Y and Guo, J and He, X and Zheng, W},
title = {Determination of the Authenticity and Origin of Panax Notoginseng: A Review.},
journal = {Journal of AOAC International},
volume = {105},
number = {6},
pages = {1708-1718},
doi = {10.1093/jaoacint/qsac081},
pmid = {35894651},
issn = {1944-7922},
support = {202102AE090042//Major Science and Technology Project of Yunnan and Kunming/ ; 2019ZG00901//Special Programme of Yunnan Green Food International Cooperative Research Center Project Subproject/ ; 046180201//Tianjin Normal University/ ; //Open Fund of Key Laboratory of Biotechnology and Bioresources Utilization/ ; KF2021006//Ministry of Education/ ; //China Agriculture Research System/ ; 2021JH002//Major Science and Technology Project of Kunming/ ; },
mesh = {*Panax notoginseng/genetics/chemistry ; *Drugs, Chinese Herbal ; Drug Contamination ; *Panax ; },
abstract = {Panax notoginseng, a traditional medicinal and edible plant, is widely used in medicine, health care, cosmetics, and other industries. Affected by the discrepancy between market supply and demand and price, the adulteration of P. notoginseng products with other plant-derived ingredients occurs at times. With the continuous development of technologies such as spectroscopy, chromatography, and DNA barcoding, the detection techniques for rapid and sensitive determination of the authenticity identification and origin of P. notoginseng have become more diversified to meet the needs of different regulatory goals and could effectively control practices that mislead consumers and promote false labeling. This review analyzes and summarizes the existing technologies for determining the authenticity and origin of P. notoginseng from these three aspects: morphological, chemical, and molecular biology methods from the literature since 2001; on this basis, the current problems and future research directions are discussed to provide a reference for the establishment of rapid and accurate methods to verify authenticity and origin to promote the further development and improvement of quality control technology systems for P. notoginseng.},
}
@article {pmid35889959,
year = {2022},
author = {González, MA and Bravo-Barriga, D and Rodríguez-Sosa, MA and Rueda, J and Frontera, E and Alarcón-Elbal, PM},
title = {Species Diversity, Habitat Distribution, and Blood Meal Analysis of Haematophagous Dipterans Collected by CDC-UV Light Traps in the Dominican Republic.},
journal = {Pathogens (Basel, Switzerland)},
volume = {11},
number = {7},
pages = {},
pmid = {35889959},
issn = {2076-0817},
support = {2018-19-2B2-043//Ministerio de Educaci&#xf3;n Superior, Ciencia y Tecnolog&#xed;a/ ; },
abstract = {Haematophagous insects cause major economic losses by both direct damage and the transmission of pathogens. However, the biting Diptera species in the Caribbean region have been poorly documented. During 2021, CDC downdraft suction traps with UV light were employed to assess both the species occurrence and blood meal sources across three different habitats in the Dominican Republic. Eighteen species of mosquitoes (n = 274), six species of Culicoides (n = 803), two black fly species (n = 2), and one species of muscid fly (n = 25) were identified at species-level by morphology and/or molecular phylogenetic approaches based on the mitochondrial cytochrome c oxidase subunit 1 (COI). Engorged mosquito (n = 5) and Culicoides (n = 28) females showed host preferences derived exclusively from mammals (cows and pigs), except Culex species containing the blood of chickens. Our study provides new records of the Diptera Dominican catalogue (Culex salinarius for the Greater Antilles, Culicoides jamaicensis for Hispaniola, and Culicoides haitiensis and Culicoides borinqueni for the Dominican Republic), the first available COI DNA sequences of different Diptera in the GenBank, some pictures of diagnostic features of closely related specimens, spatial distribution across the habitats studied, and new insights on their feeding preferences in the Caribbean region.},
}
@article {pmid35887467,
year = {2022},
author = {Chen, Y and Tian, W and Guo, Y and Madrid, H and Maharachchikumbura, SSN},
title = {Synhelminthosporium gen. et sp. nov. and Two New Species of Helminthosporium (Massarinaceae, Pleosporales) from Sichuan Province, China.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {7},
pages = {},
pmid = {35887467},
issn = {2309-608X},
support = {A1098531023601245//University of Electronic Science and Technology of China/ ; },
abstract = {Helminthosporium is a polyphyletic genus in Massarinaceae (Pleosporales). Species of Helminthosporium are characterized by having septate and erect conidiophores, acro-pleurogenous and distoseptate conidia with a ring-shaped scar at the base. During a survey of fungal diversity in Sichuan Province, China, six Helminthosporium-like isolates were collected from dead branches of unknown trees. Five barcodes, including ITS (ITS1-5.8S-ITS2), SSU, LSU, TEF1, and RPB2 were amplified and sequenced. Morphological examination and multi-locus phylogenetic analyses revealed two new Helminthosporium species (H. chengduense sp. nov., and H. chinense sp. nov.), a new genus (Synhelminthosporium gen. nov.) with a type species Synhelminthosporium synnematoferum sp. nov., and two known species (Helminthosporium submersum and H. velutinum) within Massarinaceae. The new genus Synhelminthosporium differs from the phylogenetically closest genus Helminthosporium by producing synnematous conidiophores. This work expands our understanding of the diversity of Helminthosporium-like taxa in Sichuan Province, China.},
}
@article {pmid35887409,
year = {2022},
author = {Wang, XC and Zhuang, WY},
title = {New Species of Talaromyces (Trichocomaceae, Eurotiales) from Southwestern China.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {7},
pages = {},
pmid = {35887409},
issn = {2309-608X},
support = {31750001//National Natural Science Foundation of China/ ; QYZDY-SSW-SMC029//Key Research Program of Frontier Science, Chinese Academy of Sciences/ ; },
abstract = {Species of Talaromyces are cosmopolitan and ubiquitous, and some are of industrial and medicinal importance. Species of Talaromyces have been successively reported in China. During our examinations of samples collected from southwestern China, two new species belonging to Talaromyces sect. Talaromyces were further discovered based on phylogenetic analyses and morphological comparisons. Talaromyces ginkgonis sp. nov., isolated from a partially colonized fruit of Ginkgo biloba, differs from closely-related fungi in the combination of conidia ellipsoidal, smooth and 3.5-4 × 2-3 μm, no growth on CYA at 37 °C and sequence divergences; T. shilinensis sp. nov. is distinguished from its related allies in the combination of smooth conidia, colonies 10-11 mm diameter on CYA at 25 °C and sequence differences. Detailed descriptions and illustrations of the new taxa are given.},
}
@article {pmid35886824,
year = {2022},
author = {Ricarte, A and Nedeljković, Z and Aguado-Aranda, P and Marcos-García, M&#xc1;},
title = {Assessing the Diversity and Systematics of Brachyopini Hoverflies (Diptera: Syrphidae) in the Iberian Peninsula, Including the Descriptions of Two New Species.},
journal = {Insects},
volume = {13},
number = {7},
pages = {},
pmid = {35886824},
issn = {2075-4450},
support = {PGC2018-095851-A-C65//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; PRE2019-087508//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; UATALENTO17-08//Vicerrectorado de Investigaci&#xf3;n y Transferencia del Conocimiento/ ; },
abstract = {Five genera of Brachyopini, Chrysogaster Meigen, 1800, Melanogaster Rondani, 1857, Lejogaster Rondani, 1857, Orthonevra Macquart, 1829 and Riponnensia Maibach et al. 1994a are here revised from the Iberian region. Two new species, Melanogaster baetica Ricarte and Nedeljković, sp. n. and Orthonevra arcana Ricarte and Nedeljković sp. n., are described from Spain, and a third species, Chrysogaster coerulea Strobl in Czerny and Strobl, 1909 stat. n., is reinstated as valid and redescribed. A lectotype is designated for Orthonevra plumbago (Loew, 1840). The holotype of Orthonevra incisa (Loew, 1843) and the lectotype of O. plumbago are described in detail and illustrated. Melanogaster baetica sp. n. is similar to Melanogaster parumplicata (Loew, 1840) in male genitalia morphology, while O. arcana sp. n. is similar to O. incisa in the entirely-pollinose sternum I and the conspicuous incision on the posterior margin of tergum V in female. The first Iberian record of Chrysogaster rondanii Maibach and Goeldlin de Tiefenau, 1995 is provided, whilst Melanogaster aerosa is removed from the Iberian checklist of Syrphidae. Identification keys are presented to the five Brachyopini genera and 18 species now reported from the Iberian Peninsula (Chrysogaster, 6 spp.; Lejogaster, 2 spp.; Melanogaster, 3 spp.; Orthonevra, 5 spp.; Riponnensia, 2 spp.). COI (Cytochrome c oxidase subunit I) barcodes of the two new species plus C. coerulea, Chrysogaster solstitialis (Fallén, 1817), Orthonevra nobilis (Fallén, 1817) and Orthonevra frontalis (Loew, 1843) were successfully obtained from Spanish specimens. A COI-based tree was produced to locate these taxa in a wider systematic framework within the tribe.},
}
@article {pmid35886783,
year = {2022},
author = {Smit, SJ and Allsopp, E and Nethavhani, Z and Caleca, V and Oberprieler, RG and van Asch, B},
title = {Mitogenomics of the Olive Seed Weevil, Anchonocranus oleae Marshall and Implications for Its Phylogenetic Position in Curculionidae.},
journal = {Insects},
volume = {13},
number = {7},
pages = {},
pmid = {35886783},
issn = {2075-4450},
support = {WCACF-2020//SA Olive/ ; },
abstract = {Anchonocranus oleae Marshall (Coleoptera: Curculionidae) is a seed-feeding weevil native to southern Africa; its larvae are known to develop in the fruits of the African Wild Olive and, more rarely, cultivated olives. The species has been mainly found in the Western Cape province of South Africa, but it has remained in relative obscurity because it does not seem to represent a current threat to commercial olive production. As part of an ongoing effort to produce baseline genetic data for olive-associated entomofauna in South Africa, we generated reference DNA barcodes for A. oleae collected from wild and cultivated olives and sequenced its mitogenome for assessment of the phylogenetic position of the species in the family Curculionidae. The mitochondrial phylogeny estimate indicated that A. oleae shares a common ancestor with Elaidobius (tribe Derelomini), but a definite and close relationship to this tribe and the precise tribal placement of A. oleae in the subfamily Curculioninae could not be inferred due to the lack of representative mitogenomes of other relevant curculionine tribes and genera. This study will assist future work on the DNA-based species identification, genetic diversity, and phylogenetic position of the genus Anchonocranus and related taxa.},
}
@article {pmid35886777,
year = {2022},
author = {Sonnekus, B and Slippers, B and Hurley, BP and Joubert, E and Stiller, M and Fourie, G},
title = {Diversity and Molecular Barcoding of Stink Bugs (Hemiptera: Pentatomidae) Associated with Macadamia in South Africa.},
journal = {Insects},
volume = {13},
number = {7},
pages = {},
pmid = {35886777},
issn = {2075-4450},
support = {n/a//University of Pretoria/ ; n/a//Forestry and Agricultural Biotechnology Institute/ ; n/a//DSI-NRF Centre of Excellence in Plant Health Biotechnology/ ; TTK180409318747//DSI-NRF Centre of Excellence in Plant Health Biotechnology/ ; n/a//Macadamias South Africa NPC/ ; },
abstract = {Stink bugs are major pests of macadamia in South Africa. Accurate identification and knowledge of species composition are important to inform management practices. The overall aims of this study were to identify stink bug species from macadamia orchards in South Africa using morphology, and to establish a DNA database based on the cytochrome c oxidase subunit 1 gene region. A total of 21 stink bug species were found in macadamia orchards in KwaZulu-Natal, Limpopo and Mpumalanga provinces. Bathycoelia distincta Distant, 1878, was the dominant species throughout all three growing regions. Two unidentified species of Boerias Kirkaldy, 1909, here designated as Boerias sp. 1 and Boerias sp. 2, were the second and third most abundant species found in KwaZulu-Natal. No species of Boerias has previously been reported in association with macadamia. Evidence of a cryptic third species of Boerias was also found. Species composition fluctuated over three growing seasons in Limpopo and differed between the three growing regions during the 2019-2020 season, highlighting the need for ongoing monitoring of these important pest species. The DNA barcode database developed in this study will be valuable for future monitoring and identifications, including cryptic or polymorphic stink bug species and different life stages.},
}
@article {pmid35886769,
year = {2022},
author = {Zheng, X and Chen, Z and Mu, P and Ma, Z and Zhou, C},
title = {Descriptions and Barcoding of Five New Chinese Deuterophlebia Species Revealing This Genus in Both Holarctic and Oriental Realms (Diptera: Deuterophlebiidae).},
journal = {Insects},
volume = {13},
number = {7},
pages = {},
pmid = {35886769},
issn = {2075-4450},
support = {31750002//National Natural Science Foundation of China/ ; 32070475//National Natural Science Foundation of China/ ; },
abstract = {The monotypic family Deuterophlebiidae of China was recorded twice previously from far northwest upon adults, the most parts of this country have not been investigated, leaving a huge blank of knowledge on their morphology, diversity, biology, or distribution. After deliberated collecting and rearing in recent years, we obtained more than one thousand specimens of Deuterophlebiidae, they are classified into five new species herein: Deuterophlebia sinensis sp. nov., D. yunnanensis sp. nov., D. wuyiensis sp. nov., D. acutirhina sp. nov. and D. alata sp. nov. Detailed descriptions and photographs of gathered life stages are given for these new species. Adults of them can be identified by chaetotaxy and length ratio of flagellomeres and legs, microtrichia on postgena and shape of their clypeus, pupae can be recognized by thoracic spines and abdominal chitin bands, and larvae can be separated by setae on thorax and abdomen. Genetic distances between species are 0.086-0.175 based on their COI genes. This contribution represents the first database of the enigmatic Deuterophlebiidae from China and shows a new distribution pattern of Deuterophlebia. In addition, the discovery throws some light on the origin and biogeography of the genus and family.},
}
@article {pmid35886741,
year = {2022},
author = {Johnson, A and Forschler, BT},
title = {Biodiversity and Distribution of Reticulitermes in the Southeastern USA.},
journal = {Insects},
volume = {13},
number = {7},
pages = {},
pmid = {35886741},
issn = {2075-4450},
support = {620-3- 384 .01(2)//Georgia Department of Agriculture/ ; },
abstract = {Reticulitermes subterranean termites are widely distributed ecosystem engineers and structural pests, yet describing their species distribution worldwide or regionally has been hindered by taxonomic uncertainties. Morphological plasticity confounds the use of taxonomic keys, while recent species descriptions and molecular techniques lacking taxonomic support have caused a muddle in interpreting the literature on Reticulitermes species distributions. We employed an integrative taxonomic approach combining behavioral, morphological, and molecular techniques to identify 4371 Reticulitermes samples to species. Five Reticulitermes species were collected from wood-on-ground at 1570 sites covering 153,900 km[2] in the state of Georgia, USA. Three species were collected throughout Georgia, with R. flavipes identified from every one of the 159 counties. R. nelsonae was the second most frequently collected species, found in 128 counties, with R. virginicus third with 122. Two species had distributions confined to the northern part of the state. R. malletei was collected from 73 counties, while the least collected species, R. hageni, was found in 16. Results show that the most recently described species (R. nelsonae, 2012) is widely distributed and the second-most frequently encountered termite, representing 23% of all samples. The invasive species R. flavipes represented half of all the samples collected, while R. hageni, the least at less than 1%. A search of GenBank identified a number of accessions mismatched to a species designation resulting in the literature under-reporting the biodiversity of the genus. We, therefore, outline a path to standardize methods for species identification using an integrated taxonomic approach with appropriate barcodes for consistent identification across research teams worldwide. The data also illuminate new opportunities to examine questions related to the ecology, evolution, dispersal, and resource partitioning behaviors of these sympatric species across distinct geographical regions.},
}
@article {pmid35885975,
year = {2022},
author = {Xu, T and Kong, L and Li, Q},
title = {Testing Efficacy of Assembly-Free and Alignment-Free Methods for Species Identification Using Genome Skims, with Patellogastropoda as a Test Case.},
journal = {Genes},
volume = {13},
number = {7},
pages = {},
pmid = {35885975},
issn = {2073-4425},
mesh = {Animals ; *Gastropoda/genetics ; *Genome/genetics ; Genomics/methods ; Phylogeny ; Software ; },
abstract = {Most recently, species identification has leaped from DNA barcoding into shotgun sequencing-based "genome skimming" alternatives. Genome skims have mainly been used to assemble organelle genomes, which discards much of the nuclear genome. Recently, an alternative approach was proposed for sample identification, using unassembled genome skims, which can effectively improve phylogenetic signal and identification resolution. Studies have shown that the software Skmer and APPLES work well at estimating genomic distance and performing phylogenetic placement in birds and insects using low-coverage genome skims. In this study, we use Skmer and APPLES based on genome skims of 11 patellogastropods to perform assembly-free and alignment-free species identification and phylogenetic placement. Whether or not data corresponding to query species are present in the reference database, Skmer selects the best matching or closest species with COI barcodes under different sizes of genome skims except lacking species belonging to the same family as a query. APPLES cannot place patellogastropods in the correct phylogenetic position when the reference database is sparse. Our study represents the first attempt at assembly-free and alignment-free species identification of marine mollusks using genome skims, demonstrating its feasibility for patellogastropod species identification and flanking the necessity of establishing a database to share genome skims.},
}
@article {pmid35883033,
year = {2022},
author = {Gao, M and Guo, P and Liu, X and Zhang, P and He, Z and Wen, L and Liu, S and Zhou, Z and Zhu, W},
title = {Systematic study of single-cell isolation from musculoskeletal tissues for single-sell sequencing.},
journal = {BMC molecular and cell biology},
volume = {23},
number = {1},
pages = {32},
pmid = {35883033},
issn = {2661-8850},
support = {31900583//National Natural Science Foundation of China/ ; 81772400//National Natural Science Foundation of China/ ; 19ykzd05//Fundamental Research Funds for the Central Universities/ ; 201704030082//Natural Science Foundation of Guangzhou City/ ; 201807010031//Natural Science Foundation of Guangzhou City/ ; JCYJ20190809142211354//Foundation of Shenzhen Committee for Science and Technology Innovation/ ; GJHZ20180929160004704//Foundation of Shenzhen Committee for Science and Technology Innovation/ ; SZSM201911002//Sanming Project of Medicine in Shenzhen/ ; BMHC-2019-9//Beijing Municipal Health Commission/ ; BMHC-2018-4//Beijing Municipal Health Commission/ ; PXM2020_026275_000002//Beijing Municipal Health Commission/ ; },
mesh = {*Cartilage, Articular ; Cell Separation/methods ; Cell Survival ; Humans ; Sequence Analysis, RNA/methods ; Suspensions ; },
abstract = {BACKGROUND: The single-cell platform provided revolutionary way to study cellular biology. Technologically, a sophistic protocol of isolating qualified single cells would be key to deliver to single-cell platform, which requires high cell viability, high cell yield and low content of cell aggregates or doublets. For musculoskeletal tissues, like bone, cartilage, nucleus pulposus and tendons, as well as their pathological state, which are tense and dense, it's full of challenge to efficiently and rapidly prepare qualified single-cell suspension. Conventionally, enzymatic dissociation methods were wildly used but lack of quality control. In the present study, we designed the rapid cycling enzymatic processing method using tissue-specific enzyme cocktail to treat different human pathological musculoskeletal tissues, including degenerated nucleus pulposus (NP), ossifying posterior longitudinal ligament (OPLL) and knee articular cartilage (AC) with osteoarthritis aiming to rapidly and efficiently harvest qualified single-cell suspensions for single-cell RNA-sequencing (scRNA-seq).<br><br>RESULTS: We harvested&#xa0;highly qualified&#xa0;single-cell suspensions from NP and OPLL with sufficient cell numbers and high cell viability&#xa0;using the rapid cycling enzymatic processing method,&#xa0;which significantly increased the cell viability compared with the conventional long-time continuous digestion group&#xa0;(P < 0.05). Bioanalyzer trace showed expected cDNA size distribution of the scRNA-seq library and a clear separation of cellular barcodes from background partitions were verified by the barcode-rank plot after sequencing. T-SNE visualization revealed highly heterogeneous cell subsets in NP&#xa0;and OPLL. Unfortunately, we failed to obtain eligible samples from articular cartilage due to low cell viability and excessive cell aggregates and doublets.<br><br>CONCLUSIONS: In conclusion, using the rapid cycling enzymatic processing method,&#xa0;we provided thorough protocols for preparing single-cell suspensions from human musculoskeletal tissues, which was timesaving, efficient and protective to cell viability. The strategy would greatly guarantee the cell heterogeneity, which is critical for&#xa0;scRNA-seq data analysis.&#xa0;The protocol to treat human OA articular cartilage should be further improved.},
}
@article {pmid35880121,
year = {2022},
author = {Simmons, AJ and Lau, KS},
title = {Dissociation and inDrops microfluidic encapsulation of human gut tissues for single-cell atlasing studies.},
journal = {STAR protocols},
volume = {3},
number = {3},
pages = {101570},
pmid = {35880121},
issn = {2666-1667},
support = {P50 CA236733/CA/NCI NIH HHS/United States ; R01 DK103831/DK/NIDDK NIH HHS/United States ; U2C CA233291/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Microfluidics ; *Neoplasms ; RNA, Messenger ; Sequence Analysis, RNA/methods ; *Single-Cell Analysis/methods ; },
abstract = {In droplet-based single-cell RNA-sequencing (scRNA-seq) experiments, cells, along with some of their surrounding buffer and ambient material, are encapsulated into droplets for mRNA capture and barcoding. This protocol details the steps for human gut tissue dissociation using cold active protease, and subsequent isolation of single epithelial cells, with enrichment of viability through washes. Next, the steps for encapsulation on the inDrops scRNA-seq platform are described. This procedure has been demonstrated to be applicable to polyps, cancers, and inflamed tissues. For complete details on the use and execution of this protocol, please refer to Chen et al. (2021).},
}
@article {pmid35879270,
year = {2022},
author = {Bak, SK and Seong, W and Rha, E and Lee, H and Kim, SK and Kwon, KK and Kim, H and Lee, SG},
title = {Novel High-Throughput DNA Part Characterization Technique for Synthetic Biology.},
journal = {Journal of microbiology and biotechnology},
volume = {32},
number = {8},
pages = {1026-1033},
pmid = {35879270},
issn = {1738-8872},
mesh = {*DNA ; Gene Regulatory Networks ; High-Throughput Nucleotide Sequencing ; Metabolic Networks and Pathways ; *Synthetic Biology ; },
abstract = {This study presents a novel DNA part characterization technique that increases throughput by combinatorial DNA part assembly, solid plate-based quantitative fluorescence assay for phenotyping, and barcode tagging-based long-read sequencing for genotyping. We confirmed that the fluorescence intensities of colonies on plates were comparable to fluorescence at the single-cell level from a high-end, flow-cytometry device and developed a high-throughput image analysis pipeline. The barcode tagging-based long-read sequencing technique enabled rapid identification of all DNA parts and their combinations with a single sequencing experiment. Using our techniques, forty-four DNA parts (21 promoters and 23 RBSs) were successfully characterized in 72 h without any automated equipment. We anticipate that this high-throughput and easy-to-use part characterization technique will contribute to increasing part diversity and be useful for building genetic circuits and metabolic pathways in synthetic biology.},
}
@article {pmid35875860,
year = {2022},
author = {Hegde, R and Hegde, S and Gataraddi, S and Kulkarni, SS and Gai, PB},
title = {Novel and PCR ready rapid DNA isolation from Drosophila.},
journal = {Nucleosides, nucleotides &amp; nucleic acids},
volume = {41},
number = {11},
pages = {1162-1173},
doi = {10.1080/15257770.2022.2104313},
pmid = {35875860},
issn = {1532-2335},
mesh = {Animals ; *Drosophila/genetics ; Random Amplified Polymorphic DNA Technique ; *Drosophila melanogaster/genetics ; Polymerase Chain Reaction/methods ; DNA/chemistry ; },
abstract = {INTRODUCTION: Isolation of genomic DNA is an initial step in molecular biology techniques. The quality of isolated DNA depends on procedures and chemicals, as well as source and types of the sample used. Several existing procedures are expensive and time consuming. In this study, we isolated high quality genomic DNA with an inexpensive and least time consuming procedure using Drosophila melanogaster flies, larvae, and pupae.<br><br>METHODS: Drosophila melanogaster samples were collected from pre-cultured bottles, and genomic DNA was extracted using a proposed novel and PCR-ready method from three different pools of flies [PF1, PF2, and PF3], similarly from larvae and pupae [PL1, PL2, PL3, PP1, PP2, and PP3, respectively]. Isolated genomic DNA was subjected to PCR amplification with different dilutions using the COI gene and further amplicons were used for RAPD and DNA sequencing.<br><br>RESULTS: The high quality of isolated genomic DNA was confirmed by 0.8% agarose gel electrophoresis and the purity and quantity of the DNA isolated from single fly, larva and pupa was similar to the purity and quantity of the DNA isolated using the NucleoSpin[R] Tissue kit method. Isolated genomic DNA was successfully amplified when the template was diluted in the ratio of 1:10. Further successful RAPD amplification and sequencing analysis of the COI gene confirms the efficiency of the downstream application of the proposed novel method.<br><br>CONCLUSION: The present Novel and PCR ready rapid DNA isolation method will be potentially beneficial, and it can be successfully used for quick isolation of high molecular weight DNA from Drosophila flies larvae and pupae for DNA barcoding, identification of new species, genotyping, RAPD analysis, etc. Moreover, it can also be easily scaled up for bulk preparations.},
}
@article {pmid35875052,
year = {2022},
author = {Aalam, SMM and Tang, X and Song, J and Ray, U and Russell, SJ and Weroha, SJ and Bakkum-Gamez, J and Shridhar, V and Sherman, ME and Eaves, CJ and Knapp, DJHF and Kalari, KR and Kannan, N},
title = {DNA barcoded competitive clone-initiating cell analysis reveals novel features of metastatic growth in a cancer xenograft model.},
journal = {NAR cancer},
volume = {4},
number = {3},
pages = {zcac022},
pmid = {35875052},
issn = {2632-8674},
support = {P30 CA015083/CA/NCI NIH HHS/United States ; },
abstract = {A problematic feature of many human cancers is a lack of understanding of mechanisms controlling organ-specific patterns of metastasis, despite recent progress in identifying many mutations and transcriptional programs shown to confer this potential. To address this gap, we developed a methodology that enables different aspects of the metastatic process to be comprehensively characterized at a clonal resolution. Our approach exploits the application of a computational pipeline to analyze and visualize clonal data obtained from transplant experiments in which a cellular DNA barcoding strategy is used to distinguish the separate clonal contributions of two or more competing cell populations. To illustrate the power of this methodology, we demonstrate its ability to discriminate the metastatic behavior in immunodeficient mice of a well-established human metastatic cancer cell line and its co-transplanted LRRC15 knockdown derivative. We also show how the use of machine learning to quantify clone-initiating cell (CIC) numbers and their subsequent metastatic progeny generated in different sites can reveal previously unknown relationships between different cellular genotypes and their initial sites of implantation with their subsequent respective dissemination patterns. These findings underscore the potential of such combined genomic and computational methodologies to identify new clonally-relevant drivers of site-specific patterns of metastasis.},
}
@article {pmid35874278,
year = {2022},
author = {Carvalho Leonardo, I and Barreto Crespo, MT and Capelo, J and Bustos Gaspar, F},
title = {The complete plastome of Nonea vesicaria (L.) Rchb. (Boraginaceae), the first chloroplast genome belonging to the Nonea genus.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {7},
number = {7},
pages = {1302-1304},
pmid = {35874278},
issn = {2380-2359},
abstract = {The predominantly Western Mediterranean weed Nonea vesicaria (L.) Rchb. can be found in agricultural or other man-made environments. Despite containing some beneficial compounds, extracts from this plant have also been described as detrimental and should be carefully monitored. In this study, the complete chloroplast of N. vesicaria isolate BPTPS250 is described, being the first available plastome from an isolate belonging to the Nonea genus. The chloroplast genome is 151,099 bp in length with a 37.3% GC content. It displays a quadripartite structure that contains a pair of inverted repeat regions (27,012 bp) that separate a large single-copy region (80,041 bp) and a small single-copy region (17,034 bp). A total of 134 genes were predicted, including 89 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis confirmed the placement of N. vesicaria under the Boraginaceae family, belonging to the Boraginales order, with a close relationship with Borago officinalis L. This study will contribute to conservation, phylogenetic, and evolutionary studies, as well as DNA barcoding applications for food and feed safety and quality.},
}
@article {pmid35873997,
year = {2022},
author = {Song, S and Zubov, D and Comes, HP and Li, H and Liu, X and Zhong, X and Lee, J and Yang, Z and Li, P},
title = {Plastid Phylogenomics and Plastome Evolution of Nandinoideae (Berberidaceae).},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {913011},
pmid = {35873997},
issn = {1664-462X},
abstract = {Subfamily Nandinoideae Heintze (Berberidaceae), comprising four genera and ca. 19 species, is disjunctively distributed in eastern North America vs. Eurasia (eastern Asia, Central Asia, Middle East, and southeastern Europe), and represents an ideal taxon to explore plastid phylogenomics and plastome evolution in Berberidaceae. Many species of this subfamily have been listed as national or international rare and endangered plants. In this study, we sequenced and assembled 20 complete plastomes, representing three genera and 13 species of Nandinoideae. Together with six plastomes from GenBank, a total of 26 plastomes, representing all four genera and 16 species of Nandinoideae, were used for comparative genomic and phylogenomic analyses. These plastomes showed significant differences in overall size (156,626-161,406 bp), which is mainly due to the expansion in inverted repeat (IR) regions and/or insertion/deletion (indel) events in intergenic spacer (IGS) regions. A 75-bp deletion in the ndhF gene occurred in Leontice and Gymnospermium when compared with Nandina and Caulophyllum. We found a severe truncation at the 5' end of ycf1 in three G. altaicum plastomes, and a premature termination of ropC1 in G. microrrhynchum. Our phylogenomic results support the topology of {Nandina, [Caulophyllum, (Leontice, Gymnospermium)]}
. Within the core genus Gymnospermium, we identified G. microrrhynchum from northeastern Asia (Clade A) as the earliest diverging species, followed by G. kiangnanense from eastern China (Clade B), while the rest species clustered into the two sister clades (C and D). Clade C included three species from West Tianshan (G. albertii, G. darwasicum, G. vitellinum). Clade D consisted of G. altaicum from northern Central Asia, plus one species from the Caucasus Mountains (G. smirnovii) and three from southeastern Europe (G. odessanum, G. peloponnesiacum, G. scipetarum). Overall, we identified 21 highly variable plastome regions, including two coding genes (rpl22, ycf1) and 19 intergenic spacer (IGS) regions, all with nucleotide diversity (Pi) values > 0.02. These molecular markers should serve as powerful tools (including DNA barcodes) for future phylogenetic, phylogeographic and conservation genetic studies.},
}
@article {pmid35873908,
year = {2022},
author = {Mizukami, I and Fourreau, CJL and Matsuo, S and Reimer, JD},
title = {Diversity and distribution of air-breathing sea slug genus Peronia Fleming, 1822 (Gastropoda: Onchidiidae) in southern Japanese waters.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13720},
pmid = {35873908},
issn = {2167-8359},
mesh = {Animals ; Humans ; Aplysia ; *Gastropoda/genetics ; Japan ; Phylogeny ; },
abstract = {Species of the genus Peronia Fleming, 1822, are air-breathing onchidiid sea slugs that inhabit intertidal reef flats of temperate to tropical zones. In the Ryukyu Islands of southern subtropical Japan, Peronia species are a traditional food source for local people. To date, there have been three species recorded around Okinawajima Island; P. verruculata and P. peronii, along with recently described P. okinawensis, which was described as possibly endemic to Okinawajima Island. This study aimed to map the distribution ranges of these three Peronia species within the Ryukyu Islands using molecular analyses in order to understand the specific distribution of each species. Since Peronia species are generally indistinguishable by gross external morphology, a DNA barcoding approach was employed to identify specimens. The molecular data showed that there are four species present in the Ryukyu Islands. P. verruculata (unit #1 sensu Dayrat et al., 2020) was dominant at almost all locations, while P. peronii was present in much lower numbers than P. verruculata, but found across a relatively wide range in the Ryukyu Islands. We newly record P. okinawensis and P. setoensis from Amami Oshima Island and from several places around Okinawajima Island, and also identified high levels of genetic variation within P. setoensis. Peronia okinawensis and P. setoensis have been thought to be endemic to Okinawajima Island and to Honshu, mainland Japan, respectively. However, as both species were observed around Okinawajima and Amami Oshima islands, other islands of the Ryukyus are also likely to harbor these species, and their distribution ranges are wider than previously thought. Based on the results from molecular analyses, we provide general descriptions of each species. Sizes of specimens were consistently smaller for P. setoensis and relatively larger for P. peronii specimens. On the other hand, P. verruculata and P. okinawensis had similar size ranges, but P. okinawensis had comparatively much more distinct papillae. This study revealed that the Ryukyu Islands are the only region currently known with four sympatric Peronia species, and this work provides a basis for future research on these Peronia species throughout the northwest Pacific Ocean, representing the first step in more effective management of the local Peronia fisheries in the Ryukyu Islands.},
}
@article {pmid35871253,
year = {2022},
author = {Starkie, ML and Fowler, EV and Zhu, X and Agarwal, A and Rako, L and Schneider, IC and Schutze, MK and Royer, JE and Gopurenko, D and Gillespie, P and Blacket, MJ},
title = {Loop-mediated isothermal amplification (LAMP) assays for detection of the New Guinea fruit fly Bactrocera trivialis (Drew) (Diptera: Tephritidae).},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {12602},
pmid = {35871253},
issn = {2045-2322},
mesh = {Animals ; Australia ; Drosophila ; Molecular Diagnostic Techniques ; New Guinea ; Nucleic Acid Amplification Techniques ; *Tephritidae/genetics ; },
abstract = {The cue-lure-responding New Guinea fruit fly, Bactrocera trivialis, poses a biosecurity risk to neighbouring countries, e.g., Australia. In trapping programs, lure caught flies are usually morphologically discriminated from non-target species; however, DNA barcoding can be used to confirm similar species where morphology is inconclusive, e.g., Bactrocera breviaculeus and B. rufofuscula. This can take days-and a laboratory-to resolve. A quicker, simpler, molecular diagnostic assay would facilitate a more rapid detection and potential incursion response. We developed LAMP assays targeting cytochrome c oxidase subunit I (COI) and Eukaryotic Translation Initiation Factor 3 Subunit L (EIF3L); both assays detected B. trivialis within 25 min. The BtrivCOI and BtrivEIF3L assay anneal derivatives were 82.7 ± 0.8 °C and 83.3 ± 1.3 °C, respectively, detecting down to 1 × 10[1] copies/µL and 1 × 10[3] copies/µL, respectively. Each assay amplified some non-targets from our test panel; however notably, BtrivCOI eliminated all morphologically similar non-targets, and combined, the assays eliminated all non-targets. Double-stranded DNA gBlocks were developed as positive controls; anneal derivatives for the COI and EIF3L gBlocks were 84.1 ± 0.7 °C and 85.8 ± 0.2 °C, respectively. We recommend the BtrivCOI assay for confirmation of suspect cue-lure-trapped B. trivialis, with BtrivEIF3L used for secondary confirmation when required.},
}
@article {pmid35868331,
year = {2023},
author = {Kretschmer, N and Durchschein, C and Heubl, G and Pferschy-Wenzig, EM and Kunert, O and Bauer, R},
title = {Discrimination of Zicao Samples Based on DNA Barcoding and HPTLC Fingerprints, and Identification of (22E)-Ergosta-4,6,8(14),22-tetraen-3-one As a Marker Compound.},
journal = {Planta medica},
volume = {89},
number = {8},
pages = {824-832},
doi = {10.1055/a-1855-1778},
pmid = {35868331},
issn = {1439-0221},
support = {P27505//Austrian Science Fund/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; DNA, Chloroplast ; *Lithospermum/genetics ; DNA, Plant/genetics ; },
abstract = {The unambiguous identification of plant material is a prerequisite of rational phytotherapy. Misidentification can even cause serious health problems, as in the case of the Chinese medicinal herb Zicao. Commercial material labelled "Zicao" may be derived from the roots of Arnebia euchroma (ruan zicao), Lithospermum erythrorhizon (ying zicao), or Onosma paniculata (dian zicao). All of these roots contain shikonin derivatives as main bioactive constituents, but ying zicao and dian zicao contain also hepatotoxic pyrrolizidine alkaloids in high amounts. Therefore, the use of A. euchroma with a very low pyrrolizidine alkaloid content is desirable. Confusions of the species occur quite often, indicating an urgent need for an unambiguous identification method. Discrimination of 23 zicao samples has been achieved by analyses of the nuclear internal transcribed spacer ITS2 and trnL-F intergenic spacer of the chloroplast DNA. Data were analyzed using Bioedit, ClustalX, Mega 11 and BLAST. Results indicate that ITS2 barcoding can accurately distinguish Arnebia euchroma from their adulterants. Subsequently, an HPTLC method has been developed allowing a chemical discrimination of the most widely used species. (22E)-Ergosta-4,6,8(14),22-tetraen-3-one has been identified as characteristic marker compound, allowing an unambiguous discrimination of A. euchroma and L. erythrorhizon.},
}
@article {pmid35868237,
year = {2022},
author = {Rizzo, L and Minichino, R and Virgili, R and Tanduo, V and Osca, D and Manfredonia, A and Consoli, P and Colloca, F and Crocetta, F},
title = {Benthic litter in the continental slope of the Gulf of Naples (central-western Mediterranean Sea) hosts limited fouling communities but facilitates molluscan spawning.},
journal = {Marine pollution bulletin},
volume = {181},
number = {},
pages = {113915},
doi = {10.1016/j.marpolbul.2022.113915},
pmid = {35868237},
issn = {1879-3363},
mesh = {Animals ; *Ecosystem ; *Environmental Monitoring ; Mediterranean Sea ; Mollusca ; Plastics ; Waste Products/analysis ; },
abstract = {Seafloor pollution by benthic litter is an emerging phenomenon, although debris colonization by biota remains largely unexplored. We characterized the litter of the continental slope (~400-600 m) of the Gulf of Naples (Mediterranean) and investigated its fouling biota through integrative taxonomic approaches. Plastic pieces (82 %) with land-based origin (96 %) and limited sizes (10-20 cm) were the items most commonly encountered, suggesting a transfer to deep waters through floating and sinking. The majority of the items were not fouled, and the debris hosted an impoverished biota, leading to hypothesize that benthic litter supports wide communities only in shallow waters. Higher colonization rates were observed for gastropod and cephalopod eggs with no preference for materials and sizes, suggesting that even small pieces of soft plastic provide a spawning habitat for molluscs and affect species' connectivity in the deep-sea ecosystem. Holistic approaches are necessary to evaluate interactions between litter and biota.},
}
@article {pmid35867665,
year = {2022},
author = {Deinhart, M and Mills, MS and Schils, T},
title = {Community assessment of crustose calcifying red algae as coral recruitment substrates.},
journal = {PloS one},
volume = {17},
number = {7},
pages = {e0271438},
pmid = {35867665},
issn = {1932-6203},
mesh = {Animals ; *Anthozoa ; Coral Reefs ; Ecosystem ; Larva ; *Rhodophyta ; },
abstract = {Successful recruitment of invertebrate larvae to reef substrates is essential to the health of tropical coral reef ecosystems and to their capacity to recover from disturbances. Crustose calcifying red algae (CCRA) are a species rich group of seaweeds that have been identified as important recruitment substrates for scleractinian corals. Most studies on the settlement preference of coral larvae on CCRA use morphological species identifications that can lead to unreliable species identification and do not allow for examining species-specific interactions between coral larvae and CCRA. Accurate identifications of CCRA species is important for coral reef restoration and management to assess CCRA community composition and to detect CCRA species that are favored as coral recruitment substrates. In this study, DNA sequence analysis, was used to identify CCRA species to (1) investigate the species richness and community composition of CCRA on experimental coral recruitment tiles and (2) assess if the coral Acropora surculosa preferred any of these CCRA species as recruitment substrates. The CCRA community assemblages on the coral recruitment tiles was species-rich, comprising 27 distinct CCRA species of the orders Corallinales and Peyssonneliales which constitute new species records for Guam. Lithophylloideae sp. 1 (Corallinales) was the CCRA species that was significantly favored by coral larvae as a recruitment substrate. Lithophylloideae sp. 1 showed to hold a valuable ecological role for coral larval recruitment preference. Lithophylloideae sp. 1 had the highest benthic cover on the recruitment tiles and contained most A. surculosa recruits. DNA barcoding revealed a high taxonomic diversity of CCRA species on a microhabitat scale and provided detailed insight into the species-specific ecological interactions between CCRA and corals. With a steady decline in coral cover, detailed information on species interactions that drive reef recovery is valuable for the planning of marine management actions and restoration efforts.},
}
@article {pmid35866879,
year = {2022},
author = {Delgado-Gonzalez, A and Laz-Ruiz, JA and Cano-Cortes, MV and Huang, YW and Gonzalez, VD and Diaz-Mochon, JJ and Fantl, WJ and Sanchez-Martin, RM},
title = {Hybrid Fluorescent Mass-Tag Nanotrackers as Universal Reagents for Long-Term Live-Cell Barcoding.},
journal = {Analytical chemistry},
volume = {94},
number = {30},
pages = {10626-10635},
pmid = {35866879},
issn = {1520-6882},
support = {R01 CA234553/CA/NCI NIH HHS/United States ; R21 CA231280/CA/NCI NIH HHS/United States ; U19 AI057229/AI/NIAID NIH HHS/United States ; },
mesh = {Cell Line ; *Electronic Data Processing ; Flow Cytometry/methods ; *Fluorescent Dyes/chemistry ; Proteomics ; },
abstract = {Barcoding and pooling cells for processing as a composite sample are critical to minimize technical variability in multiplex technologies. Fluorescent cell barcoding has been established as a standard method for multiplexing in flow cytometry analysis. In parallel, mass-tag barcoding is routinely used to label cells for mass cytometry. Barcode reagents currently used label intracellular proteins in fixed and permeabilized cells and, therefore, are not suitable for studies with live cells in long-term culture prior to analysis. In this study, we report the development of fluorescent palladium-based hybrid-tag nanotrackers to barcode live cells for flow and mass cytometry dual-modal readout. We describe the preparation, physicochemical characterization, efficiency of cell internalization, and durability of these nanotrackers in live cells cultured over time. In addition, we demonstrate their compatibility with standardized cytometry reagents and protocols. Finally, we validated these nanotrackers for drug response assays during a long-term coculture experiment with two barcoded cell lines. This method represents a new and widely applicable advance for fluorescent and mass-tag barcoding that is independent of protein expression levels and can be used to label cells before long-term drug studies.},
}
@article {pmid35866013,
year = {2022},
author = {Cowart, DA and Schiaparelli, S and Alvaro, MC and Cecchetto, M and Le Port, AS and Jollivet, D and Hourdez, S},
title = {Origin, diversity, and biogeography of Antarctic scale worms (Polychaeta: Polynoidae): a wide-scale barcoding approach.},
journal = {Ecology and evolution},
volume = {12},
number = {7},
pages = {e9093},
pmid = {35866013},
issn = {2045-7758},
abstract = {The Antarctic marine environment hosts diversified and highly endemic benthos owing to its unique geologic and climatic history. Current warming trends have increased the urgency of understanding Antarctic species history to predict how environmental changes will impact ecosystem functioning. Antarctic benthic lineages have traditionally been examined under three hypotheses: (1) high endemism and local radiation, (2) emergence of deep-sea taxa through thermohaline circulation, and (3) species migrations across the Polar Front. In this study, we investigated which hypotheses best describe benthic invertebrate origins by examining Antarctic scale worms (Polynoidae). We amassed 691 polynoid sequences from the Southern Ocean and neighboring areas: the Kerguelen and Tierra del Fuego (South America) archipelagos, the Indian Ocean, and waters around New Zealand. We performed phylogenetic reconstructions to identify lineages across geographic regions, aided by mitochondrial markers cytochrome c oxidase subunit I (Cox1) and 16S ribosomal RNA (16S). Additionally, we produced haplotype networks at the species scale to examine genetic diversity, biogeographic separations, and past demography. The Cox1 dataset provided the most illuminating insights into the evolution of polynoids, with a total of 36 lineages identified. Eunoe sp. was present at Tierra del Fuego and Kerguelen, in favor of the latter acting as a migration crossroads. Harmothoe fuligineum, widespread around the Antarctic continent, was also present but isolated at Kerguelen, possibly resulting from historical freeze-thaw cycles. The genus Polyeunoa appears to have diversified prior to colonizing the continent, leading to the co-occurrence of at least three cryptic species around the Southern and Indian Oceans. Analyses identified that nearly all populations are presently expanding following a bottleneck event, possibly caused by habitat reduction from the last glacial episodes. Findings support multiple origins for contemporary Antarctic polynoids, and some species investigated here provide information on ancestral scenarios of (re)colonization. First, it is apparent that species collected from the Antarctic continent are endemic, as the absence of closely related species in the Kerguelen and Tierra del Fuego datasets for most lineages argues in favor of Hypothesis 1 of local origin. Next, Eunoe sp. and H. fuligineum, however, support the possibility of Kerguelen and other sub-Antarctic islands acting as a crossroads for larvae of some species, in support of Hypothesis 3. Finally, the genus Polyeunoa, conversely, is found at depths greater than 150 m and may have a deep origin, in line with Hypothesis 2. These "non endemic" groups, nevertheless, have a distribution that is either north or south of the Antarctic Polar Front, indicating that there is still a barrier to dispersal, even in the deep sea.},
}
@article {pmid35863432,
year = {2022},
author = {Chen, Q and Tesmer, JJG},
title = {G protein-coupled receptor interactions with arrestins and GPCR kinases: The unresolved issue of signal bias.},
journal = {The Journal of biological chemistry},
volume = {298},
number = {9},
pages = {102279},
pmid = {35863432},
issn = {1083-351X},
support = {R01 CA221289/CA/NCI NIH HHS/United States ; R01 CA254402/CA/NCI NIH HHS/United States ; R01 HL071818/HL/NHLBI NIH HHS/United States ; },
mesh = {*Arrestins/metabolism ; *G-Protein-Coupled Receptor Kinases/metabolism ; Humans ; Phosphorylation ; *Receptors, G-Protein-Coupled/metabolism ; Signal Transduction/physiology ; },
abstract = {G protein-coupled receptor (GPCR) kinases (GRKs) and arrestins interact with agonist-bound GPCRs to promote receptor desensitization and downregulation. They also trigger signaling cascades distinct from those of heterotrimeric G proteins. Biased agonists for GPCRs that favor either heterotrimeric G protein or GRK/arrestin signaling are of profound pharmacological interest because they could usher in a new generation of drugs with greatly reduced side effects. One mechanism by which biased agonism might occur is by stabilizing receptor conformations that preferentially bind to GRKs and/or arrestins. In this review, we explore this idea by comparing structures of GPCRs bound to heterotrimeric G proteins with those of the same GPCRs in complex with arrestins and GRKs. The arrestin and GRK complexes all exhibit high conformational heterogeneity, which is likely a consequence of their unusual ability to adapt and bind to hundreds of different GPCRs. This dynamic behavior, along with the experimental tactics required to stabilize GPCR complexes for biophysical analysis, confounds these comparisons, but some possible molecular mechanisms of bias are beginning to emerge. We also examine if and how the recent structures advance our understanding of how arrestins parse the "phosphorylation barcodes" installed in the intracellular loops and tails of GPCRs by GRKs. In the future, structural analyses of arrestins in complex with intact receptors that have well-defined native phosphorylation barcodes, such as those installed by the two nonvisual subfamilies of GRKs, will be particularly illuminating.},
}
@article {pmid35860518,
year = {2022},
author = {Matczyszyn, JN and Harris, T and Powers, K and Everhart, SE and Powers, TO},
title = {Ecological and Morphological Differentiation Among COI Haplotype Groups in the Plant Parasitic Nematode Species Mesocriconema Xenoplax.},
journal = {Journal of nematology},
volume = {54},
number = {1},
pages = {20220009},
pmid = {35860518},
issn = {0022-300X},
abstract = {DNA barcoding with the mitochondrial COI gene reveals distinct haplotype subgroups within the monophyletic and parthenogenetic nematode species, Mesocriconema xenoplax. Biological attributes of these haplotype groups (HG) have not been explored. An analysis of M. xenoplax from 40 North American sites representing both native plant communities and agroecosystems was conducted to identify possible subgroup associations with ecological, physiological, or geographic factors. A dataset of 132 M. xenoplax specimens was used to generate sequences of a 712 bp region of the cytochrome oxidase subunit I gene. Maximum-likelihood and Bayesian phylogenies recognized seven COI HG (≥99/0.99 posterior probability/bootstrap value). Species delimitation metrics largely supported the genetic integrity of the HG. Discriminant function analysis of HG morphological traits identified stylet length, total body length, and stylet knob width as the strongest distinguishing features among the seven groups, with stylet length as the strongest single distinguishing morphological feature. Multivariate analysis identified land cover, ecoregion, and maximum temperature as predictors of 53.6% of the total variation (P = 0.001). Within land cover, HG categorized under "herbaceous," "woody wetlands," and "deciduous forest" were distinct in DAPC and RDA analyses and were significantly different (analysis of molecular variance P = 0.001). These results provide empirical evidence for molecular, morphological, and ecological differentiation associated with HG within the monophyletic clade that represents the species Mesocriconema xenoplax.},
}
@article {pmid35858570,
year = {2022},
author = {Todd, NK and Huang, Y and Lee, JY and Doruker, P and Krieger, JM and Salisbury, R and MacDonald, M and Bahar, I and Thathiah, A},
title = {GPCR kinases generate an APH1A phosphorylation barcode to regulate amyloid-β generation.},
journal = {Cell reports},
volume = {40},
number = {3},
pages = {111110},
pmid = {35858570},
issn = {2211-1247},
support = {R01 GM139297/GM/NIGMS NIH HHS/United States ; R01 AG058851/AG/NIA NIH HHS/United States ; R01 MH118497/MH/NIMH NIH HHS/United States ; P41 GM103712/GM/NIGMS NIH HHS/United States ; R01 MH125235/MH/NIMH NIH HHS/United States ; },
mesh = {*Alzheimer Disease ; Amyloid Precursor Protein Secretases/metabolism ; Amyloid beta-Peptides/metabolism ; Endopeptidases/*metabolism ; *G-Protein-Coupled Receptor Kinases/metabolism ; Humans ; Membrane Proteins/*metabolism ; Phosphorylation/physiology ; beta-Arrestin 2/metabolism ; beta-Arrestins/metabolism ; },
abstract = {Emerging evidence suggests that G protein-coupled receptor (GPCR) kinases (GRKs) are associated with the pathophysiology of Alzheimer's disease (AD). However, GRKs have not been directly implicated in regulation of the amyloid-β (Aβ) pathogenic cascade in AD. Here, we determine that GRKs phosphorylate a non-canonical substrate, anterior pharynx-defective 1A (APH1A), an integral component of the γ-secretase complex. Significantly, we show that GRKs generate distinct phosphorylation barcodes in intracellular loop 2 (ICL2) and the C terminus of APH1A, which differentially regulate recruitment of the scaffolding protein β-arrestin 2 (βarr2) to APH1A and γ-secretase-mediated Aβ generation. Further molecular dynamics simulation studies reveal an interaction between the βarr2 finger loop domain and ICL2 and ICL3 of APH1A, similar to a GPCR-β-arrestin complex, which regulates γ-secretase activity. Collectively, these studies provide insight into the molecular and structural determinants of the APH1A-βarr2 interaction that critically regulate Aβ generation.},
}
@article {pmid35857747,
year = {2022},
author = {Bhardwaj, V and Dela Cruz, M and Subramanyam, D and Kumar, R and Markan, S and Parker, B and Roy, HK},
title = {Exercise-induced myokines downregulates the ACE2 level in bronchial epithelial cells: Implications for SARS-CoV-2 prevention.},
journal = {PloS one},
volume = {17},
number = {7},
pages = {e0271303},
pmid = {35857747},
issn = {1932-6203},
support = {R01 CA224911/CA/NCI NIH HHS/United States ; R21 MD013631/MD/NIMHD NIH HHS/United States ; R33 CA225323/CA/NCI NIH HHS/United States ; },
mesh = {Angiotensin-Converting Enzyme 2/*metabolism ; Animals ; *COVID-19 ; Epithelial Cells/metabolism ; Humans ; Pandemics ; Peptidyl-Dipeptidase A/genetics/metabolism ; Proteomics ; RNA, Messenger ; SARS-CoV-2 ; },
abstract = {BACKGROUND: The Covid-19 pandemic has emerged as the leading public health challenge of our time (20th century). While vaccinations have finally blunted the death rate, concern has remained about more virulent forms highlighting the need for alternative approaches. Epidemiological studies indicate that physical activity has been shown to decrease the risk of infection of some respiratory viruses. Part of the salutary effects of exercise is believed to be through the elaboration of cytokines by contracting skeletal muscles (termed myokines). The objective of this study was to investigate whether exercise-induced myokines would mitigate the SARS-CoV-2 infectivity of the bronchial epithelium through modulating the SARS-CoV-2 Covid-19 receptor (angiotensin-converting enzyme 2 -ACE2) its priming enzyme, transmembrane serine protease 2 (TMPRSS2).<br><br>METHODS: We utilized a cell culture model of exercise to generate myokines by differentiating C2C12 cells into myotubules and inducing them to contract via low-frequency electric pulse stimulation. Condition media was concentrated via centrifugation and applied to human immortalized human bronchial epithelium cell line (6HBE14o) along with conditioned media from unstimulated myotubules as controls. Following exposure to myokines, the 16HBE14o cells were harvested and subjected to quantitative RT-PCR and Enzyme-Linked Immunosorbent Assay (ELISA) for assessment of mRNA and protein levels of ACE2 and TMPRSS2, respectively. Pilot proteomic data was performed with isotope barcoding and mass spectroscopy.<br><br>RESULTS: Quantitative Real-Time PCR of 16HBE14o with 48 h treated unstimulated vs. stimulated myokine treatment revealed a reduction of ACE2 and TMPRSS2 mRNA by 32% (p<2.69x10-5) and 41% (p<4.57x10-5), respectively. The high sensitivity of ELISAs showed downregulation of ACE2 and TMPRSS2 protein expression in 16HBE14o cells by 53% (p<0.01) and 32% (p<0.03) respectively with 48 h treated. For rigor, this work was replicated in the human lung cancer cell line A549, which mirrored the downregulation. Proteomic analysis showed dramatic alteration in myokine profile between contracted and uncontracted C2C12 tubules.<br><br>CONCLUSIONS: The current study explores a novel approach of a modified exercise cell culture system and uses ACE2 and TMPRSS2 as a surrogate marker of SARS-CoV-2 infectivity. In conclusion, we demonstrated biological data supporting exercise's protective effect against Covid-19. These further strengthen myokines' beneficial role as potential therapeutic targets against SARS-CoV-2 and similar viruses albeit these preliminary cell culture studies will require future validation in animal models.},
}
@article {pmid35853031,
year = {2022},
author = {Yao, R and Guo, R and Liu, Y and Kou, Z and Shi, B},
title = {Identification and phylogenetic analysis of the genus Syringa based on chloroplast genomic DNA barcoding.},
journal = {PloS one},
volume = {17},
number = {7},
pages = {e0271633},
pmid = {35853031},
issn = {1932-6203},
mesh = {Chloroplasts/genetics ; DNA Barcoding, Taxonomic/methods ; *DNA, Chloroplast/genetics ; DNA, Plant/genetics ; Genomics ; Phylogeny ; Sequence Analysis, DNA ; *Syringa/genetics ; },
abstract = {DNA barcoding is a supplementary tool in plant systematics that is extensively used to resolve species-level controversies. This study assesses the significance of using two DNA barcoding loci (e.g., psbA-trnH and trnC-petN) in distinguishing 33 plant samples of the genus Syringa. Results showed that the average genetic distance K2P of psbA-trnH DNA marker was 0.0521, which is much higher than that of trnC-petN, which is 0.0171. A neighbor-joining phylogenetic tree based on psbA-trnH and trnC-petN indicated that the identification rate of psbA-trnH and trnC-petN alone were 75% and 62.5%, respectively. The barcode combination of psbA-trnH+trnC-petN could identify 33 samples of the genus Syringa accurately and effectively with an identification rate of 87.5%. The 33 Syringa samples were divided into four groups: Group I is series Syringa represented by Syringa oblata; Group II is series Villosae represented by Syringa villosa; Group III is series Pubescentes represented by Syringa meyeri; and Group IV is section Ligustrina represented by Syringa reticulata subsp. pekinensis. These research results provided strong evidence that the combinatorial barcode of psbA-trnH+trnC-petN had high-efficiency identification ability and application prospects in species of the genus Syringa.},
}
@article {pmid35851378,
year = {2022},
author = {Ludwig, KU and Schmithausen, RM and Li, D and Jacobs, ML and Hollstein, R and Blumenstock, K and Liebing, J and Słabicki, M and Ben-Shmuel, A and Israeli, O and Weiss, S and Ebert, TS and Paran, N and Rüdiger, W and Wilbring, G and Feldman, D and Lippke, B and Ishorst, N and Hochfeld, LM and Beins, EC and Kaltheuner, IH and Schmitz, M and Wöhler, A and Döhla, M and Sib, E and Jentzsch, M and Moench, EC and Borrajo, JD and Strecker, J and Reinhardt, J and Cleary, B and Geyer, M and Hölzel, M and Macrae, R and Nöthen, MM and Hoffmann, P and Exner, M and Regev, A and Zhang, F and Schmid-Burgk, JL},
title = {Author Correction: LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding.},
journal = {Nature biotechnology},
volume = {40},
number = {8},
pages = {1295},
doi = {10.1038/s41587-022-01428-6},
pmid = {35851378},
issn = {1546-1696},
}
@article {pmid35850203,
year = {2022},
author = {Guo, H and Wang, L and Xu, W and Huo, Z and Yang, P and Zhang, Q and Wang, H and Li, P and Lu, X},
title = {The complete chloroplast genome sequence of Cyathula officinalis and comparative analysis with four related species.},
journal = {Gene},
volume = {839},
number = {},
pages = {146728},
doi = {10.1016/j.gene.2022.146728},
pmid = {35850203},
issn = {1879-0038},
mesh = {Codon Usage ; *Genome, Chloroplast ; Microsatellite Repeats ; Phylogeny ; Sequence Alignment ; },
abstract = {Cyathula officinalis is a medicinal and edible herb, which can remove blood stasis, stimulate menstrual flow, and ease joint movement. In this study, the complete chloroplast genome of Cyathula officinalis was sequenced, assembled, and analyzed. Compared with the chloroplast genomes of Cyathula capitata, Achyranthes bidentata, Achyranthes longifolianine and Achyranthes aspera, the basic characteristics, codon usage bias, repeat sequences, simple sequence repeats, and phylogenetic tree were analyzed. In addition, according to nucleotide diversity analysis and sequence alignment, DNA barcoding and allele-specific PCR primers were designed to identify and distinguish Cyathula officinalis from its fake drugs, which has effectively practical significance for the authentication of "Chuan Niuxi" crude drug in the market.},
}
@article {pmid35845488,
year = {2022},
author = {Song, Y and Yang, Z and Wang, P and Song, K and Zhang, S and Fan, T},
title = {Next-generation sequencing and targeted quantitative real-time polymerase chain reaction for detection of Akebiae Caulis in the traditional Chinese medical formula Longdan Xiegan Wan.},
journal = {Annals of translational medicine},
volume = {10},
number = {12},
pages = {706},
pmid = {35845488},
issn = {2305-5839},
abstract = {BACKGROUND: Akebiae Caulis (Mu Tong) is commonly misused by Aristolochiae Manshuriensis Caulis (Guan Mutong) and Clematidis Armandii Caulis (Chuan Mutong), which are nephrotoxic and carcinogenic. However, in the Pharmacopoeia of the People's Republic of China (2015 Edition), the method for determining Akebiae Caulis remains undefined.<br><br>METHODS: We used DNA barcode-based next-generation sequencing (NGS) combined with quantitative real-time polymerase chain reaction (qPCR) to detect Akebiae Caulis in Longdan Xiegan Wan (LDXGW) for the first time. Compared with chromatographic studies, NGS enables better evaluation of the ingredient components of traditional Chinese medicine (TCM) preparations. The feasibility of qPCR using species-specific primers to determine the authenticity of species has been validated. In this study, the constituents of Akebiae Caulis in LDXGW from three different manufacturers were scanned by NGS. The independently developed qPCR detection primers of Akebiae Caulis, Aristolochiae Manshuriensis Caulis, and Clematidis Armandii Caulis were specifically used to analyze the LDXGW mentioned above.<br><br>RESULTS: The results showed that qPCR detected Clematidis Armandii Caulis in all commercial samples. Meanwhile, NGS detected the counterfeit species Clematis peterae (Tie-Xian Lian) in all samples. We found that qPCR shows a difference in detecting Akebiae Caulis, but it was not able to identify the unknown additives and adulterants for the primer pairs of Clematidis Armandii Caulis.<br><br>CONCLUSIONS: Hence, it is sensitive and rapid, qPCR is not suitable for detection alone. The NGS approaches offer important novel insights that complement the qPCR method. The combination of NGS and qPCR will be a powerful complement to traditional identification methods of TCM substances.},
}
@article {pmid35845369,
year = {2022},
author = {Wu, R and Liu, X and Guo, L and Zhou, C and Ouyang, S and Wu, X},
title = {DNA barcoding, multilocus phylogeny, and morphometry reveal phenotypic plasticity in the Chinese freshwater mussel Lamprotula caveata (Bivalvia: Unionidae).},
journal = {Ecology and evolution},
volume = {12},
number = {7},
pages = {e9035},
pmid = {35845369},
issn = {2045-7758},
abstract = {Accurate species identification is crucial for developing conservation strategies for freshwater mussels, one of the most imperiled faunas in the world. Traditionally, mussel species description primarily relied on conchological characters. However, shell morphology has great variability, which leads to the complexity of species delimitation. As endemic species to China, Lamprotula caveata was originally described by Heude (1877). Lamprotula quadrangulosus and Lamprotula contritus were considered for synonymization of L. caveata based on shell variants in the early 20th century, which has been long debated due to lack of rigorous molecular analysis. Moreover, great morphological variation caused doubt whether there are cryptic species. In this study, we used a combined phylogenetic and morphometric approach to verify the validity of the synonymization of L. caveata. The results of molecular species delimitation showed that two molecular operational taxonomic units (MOTUs) were identified in Lamprotula spp., including the L. leaii lineage and the complex lineage (L. quadrangulosa, L. cornuumlunae, L. contritus, and L. caveata). Phylogenetic analyses revealed that L. cornuumlunae formed a basal monophyletic clade, whose divergence time was relatively recent (4.26 Ma [95% HPD = 1.91-7.22 Ma]), and L. contritus, L. caveata, and L. quadrangulosa formed a large polytomy group with very shallow branches. In the previous study, we have demonstrated the validity of L. cornuumlunae. The molecular evidences supported that the complex (L. quadrangulosa + L. contritus + L. caveata) was a valid species; L. quadrangulosa and L. contritus were synonyms of L. caveata. In addition, three morphospecies (L. quadrangulosa, L. contritus, and L. caveata) were aggregated without clear differentiation based on shell morphometric analysis. We confirmed multiple phenotypes in L. caveata for species identification and presumed that the phenotypic plasticity was a response to specific habitats. This study clarified the diversity and phylogeny of the Lamprotula group, which is a crucial step for developing new conservation and management strategies for this imperiled group.},
}
@article {pmid35844052,
year = {2023},
author = {Wang, Q and Song, R and Fan, S and Coleman, JJ and Xu, X and Hu, X},
title = {Diversity of Fusarium community assembly shapes mycotoxin accumulation of diseased wheat heads.},
journal = {Molecular ecology},
volume = {32},
number = {10},
pages = {2504-2518},
doi = {10.1111/mec.16618},
pmid = {35844052},
issn = {1365-294X},
mesh = {*Mycotoxins/analysis ; *Fusarium/genetics ; Triticum ; Plant Diseases ; Edible Grain/chemistry ; },
abstract = {Fusarium head blight (FHB) is a major disease worldwide on cultivated cereals, caused by several Fusarium species. FHB can cause not only yield reduction but also accumulation of mycotoxins in the grain contaminating the food supply. Much of the earlier research has focused on Fusarium pathogenesis, conditions required for disease development and toxin accumulation, and FHB management. However, the Fusarium community composition within the micro-habitat of a single diseased wheat head in the field has had limited investigation. Similarly, the relationship between the Fusarium community structure and mycotoxin accumulation within diseased heads remains unclear. In the present study, we investigated the Fusarium community in diseased heads sampled from different geographical sites in China. Several sites in Shandong province formed a transitional region which contained highly variable profiles of Fusarium OTUs, where a single diseased head could contain more than 10 Fusarium OTUs. Mycotoxin accumulation was independent of geographical properties, however, deoxynivalenol, 15-acetyldeoxynivalenol and zearalenone concentrations showed a significant negative correlation with Fusarium diversity on diseased heads while a significant positive correlation between nivalenol concentration and Fusarium diversity was observed. Taken together, the Fusarium OTU diversity within diseased heads in the field significantly influences mycotoxin accumulation, providing an important point to consider in FHB disease management and mycotoxin research.},
}
@article {pmid35843280,
year = {2022},
author = {Zou, G and Niu, L and Li, Y and Zhang, W and Wang, L and Li, Y and Zhang, H and Wang, L and Gao, Y},
title = {Depth induced assembly discrepancy of multitrophic microbial communities affect microbial nitrogen transformation processes in river cross-sections.},
journal = {Environmental research},
volume = {214},
number = {Pt 2},
pages = {113913},
doi = {10.1016/j.envres.2022.113913},
pmid = {35843280},
issn = {1096-0953},
mesh = {Bacteria/genetics/metabolism ; Cross-Sectional Studies ; Geologic Sediments ; *Microbiota ; Nitrogen/metabolism ; *Rivers ; },
abstract = {Understanding how the structures and functions of bacterial and microeukaryotic communities vary within cross-sections will improve managements aimed at restoring river ecological functions. However, no comprehensive investigation has examined how microbial community characteristics vary within cross-sections, which makes the accurate calculation and prediction of microbial metabolic processing of substances in rivers difficult. Here, the distributions, co-occurrence networks, and assemblies of bacterial and microeukaryotic communities and their feedback to nitrogen transformation in cross-sections of the Yangtze River were studied by coupling ecological theory, biogeochemistry, and DNA meta-barcoding methods. The study found that depth in cross-sections was the primary driving factor regulating the composition of sediment bacterial and microeukaryotic communities. Co-occurrence network analysis indicated that the effect of bacteria on the co-occurrence network decreased and the network become more simplified and instability with depth in river cross-sections. Quantified using the β-nearest taxon index, the H2 layer sediment (depth 10-20 m) displayed the largest variation in selection processes for microbial assemblies, while homogeneous selection and homogenizing dispersal contributed most to the bacterial and microeukaryotic assemblies in the H3 layer (depth >20 m). Cross-sectional depth and denitrification genes had a significant quadratic correlation, with the highest microbial nitrogen-removal potential occurring in the H2 layer sediment. Structural equation models showed that the sediment nitrogen distributions were regulated by distinct environmental pathways at different depths, and that the H2 layer sediment was primary driven by bacterial community. In this layer, river cross-sectional depth influenced nitrogen transformation by regulating the distribution of sediment particle sizes, which then influenced the assembly of the multitrophic microbial communities. This study will improve river management by clarifying the importance of cross-sectional depth to the ecological function of rivers.},
}
@article {pmid35843130,
year = {2022},
author = {Li, H and Liu, X and Zhu, F and Ma, D and Miao, C and Su, H and Deng, J and Ye, H and Dong, H and Bai, X and Luo, Y and Lin, B and Liu, T and Lu, Y},
title = {Spatial barcoding-enabled highly multiplexed immunoassay with digital microfluidics.},
journal = {Biosensors &amp; bioelectronics},
volume = {215},
number = {},
pages = {114557},
doi = {10.1016/j.bios.2022.114557},
pmid = {35843130},
issn = {1873-4235},
mesh = {Antibodies ; *Biosensing Techniques ; Immunoassay ; *Microfluidics ; Polytetrafluoroethylene ; Reproducibility of Results ; },
abstract = {Digital microfluidics (DMF), facilitating independent manipulation of microliter samples, provides an ideal platform for immunoassay detection; however, suffering limited multiplexity. To address the need, herein we described a digital microfluidics (DMF) platform that realizes spatial barcoding on the Teflon-coated indium tin oxide (ITO) glass side to fulfill highly multiplexed immunoassay (10+) with low-volume samples (∼4 μL) in parallel, representing the highest multiplexing recorded to date for DMF-actuated immunoassay. Planar-based spatial immobilization of multiple capture antibodies was realized on a Teflon-coated ITO glass side, which was then used as the top plate of the DMF device. Droplets containing analytes, secondary antibodies, and fluorescent signaling reporters with low volume, which were electrically manipulated by our DMF control system, were shuttled sequentially along the working electrodes to complete the immuno-reaction. Evaluation of platform performance with recombinant proteins showed excellent sensitivity and reproducibility. To test the feasibility of our platform in analyzing multiplex biomarkers of the immune response, we used lipopolysaccharide-stimulated macrophages as a model system for protein secretion dynamics studies. As a result, temporal profiling of pro-inflammatory cytokine secretion dynamics was obtained. The spatial barcoding strategy presented here is easy-to-operate to enable a more comprehensive evaluation of protein abundance from biological samples, paving the way for new opportunities to realize multiplexity-associated applications with the DMF platform.},
}
@article {pmid35838796,
year = {2022},
author = {Ramos, P and Varandas, R and Conceição, IL and Grade, A and Oliveira, MM and Alexandre-Pires, G and Rosa, F},
title = {Diclidophora luscae (Monogenea: Diclidophoridae) in pouting, Trisopterus luscus (Linnaeus, 1758) from the northeast Atlantic; epidemiology, morphology, molecular and phylogenetic analysis.},
journal = {Parasitology research},
volume = {121},
number = {9},
pages = {2517-2535},
pmid = {35838796},
issn = {1432-1955},
support = {FCT PTDC/ASP-PES/29576/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; CESAM (UIDP/50017/2020+UIDB/50017/2020+LA/P/0094/2020)//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BD/130172/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; MAR-02.05.01-FEAMP-0004//SAN&#xc1;QUA/ ; Centro2020//ReNature/ ; Centro-01-0145-FEDER-000007//ReNature/ ; },
mesh = {Animals ; *Fish Diseases/epidemiology/parasitology ; Fishes/parasitology ; *Gadiformes/parasitology ; Gills ; Phylogeny ; *Trematoda ; },
abstract = {Diclidophora (Monogenea) species are gill parasites with a stenoxenic specificity occurring only in Gadiformes. Epidemiological, morphological, molecular and phylogenetic studies were performed on 594 Diclidophora specimens collected from 213 Trisopterus luscus captured in the northeast Atlantic off the Portuguese coast during 2012, 2013 and 2020. Prevalence, parasite abundance and infection intensity were determined. Positive correlation between fish weight and length and infection intensity was observed. The effects of preservation on the parasite morphological features were studied, highlighting that specimen's identification should be reinforced by molecular studies. A sequence of D. luscae capelanii from T. capelanus captured in the Mediterranean Sea included in the 28S rDNA molecular analysis was nested within a robust D. luscae clade. Data analysis suggested that this species is in fact D. luscae, which is compatible with T. luscus and T. capelanus. The identity of fish hosts was confirmed by barcoding. For the first time, data on the infection parameters is shown, highlighting the importance of including this parasite in the monitoring plans for a holistic approach with possible effects for the management of pouting resources aiming of attaining sustainable development and biodiversity conservation measures, according to the 14th objective of the 2030 agenda.},
}
@article {pmid35838095,
year = {2022},
author = {Ghazali, SNA and Emelia, O and Hidayatulfathi, O and Syamsa, RA},
title = {Potential application of Gustatory Receptor 1 (CmegGr1) gene as a molecular marker for identification of Chrysomya megacephala (Diptera: Calliphoridae).},
journal = {Tropical biomedicine},
volume = {39},
number = {2},
pages = {226-230},
doi = {10.47665/tb.39.2.008},
pmid = {35838095},
issn = {2521-9855},
mesh = {Animals ; Calliphoridae ; *Diptera/genetics ; *Forensic Entomology ; Larva ; Phylogeny ; Rabbits ; },
abstract = {Chrysomya megacephala larvae can easily be identified using cheap traditional microscopy techniques. Nevertheless, identification using taxonomy keys may be hampered, if the morphological characteristics of the larvae are incomplete, or immature for microscopic identification. To overcome the difficulty of species determination, molecular identification has gained relevance and is applied in forensic investigations. This study aimed to identify a novel target gene, known as the gustatory receptor 1 gene (CmegGr1), which has never been used for identification. The third instar larvae of Ch. megacephala (n = 30) and eight other forensically important fly species were obtained from two sources; rabbit carcasses and the Forensic Entomology Unit collection. Their DNAs were extracted and the CmegGr1 gene was amplified using polymerase chain reaction (PCR). The resulting sequences were subjected to phylogenetic analysis. A 209 bp fragment of the CmegGr1 gene was successfully amplified in 80% (24/30) of Ch. megacephala samples, while all of the non-Ch. megacephala species were not amplified. The phylogenetic analysis revealed that the evolutionary tree of CmegGr1 shares many traits with the 21a gustatory receptors of Calliphora stygia and Lucilia cuprina (Gr21a), which are also classified as necrophagous fly species. The high specificity of species identification was demonstrated in the present study using DNA barcoding, which led to the conclusion that the CmegGr1 gene could serve as an alternative marker for identifying Ch. megacephala.},
}
@article {pmid35836685,
year = {2022},
author = {Falcón-Brindis, A and León-Cortés, JL and Mancilla-Brindis, RF and Estrada-Virgen, MO and Cambero-Campos, OJ},
title = {A new species of Pseudophanerotoma (Hymenoptera, Braconidae) from Nayarit, Mexico.},
journal = {ZooKeys},
volume = {1095},
number = {},
pages = {165-177},
pmid = {35836685},
issn = {1313-2989},
abstract = {Parasitoid wasps are known to be among the most abundant and species-rich on Earth and thus considered an ecologically important group of arthropods. Braconid wasps play a key role in regulating the populations of Lepidoptera, Coleoptera, and Diptera. However, the biology and taxonomy of numerous parasitoid species remain poorly known. In Mexico, only 17 species of the subfamily Cheloninae have been described. A new species of Pseudophanerotoma Zettel, 1990 (Hymenoptera, Braconidae), P.huichol sp. nov., is described from Nayarit, Mexico. The tortricid moth Cryptaspasmaperseana Gilligan &amp; Brown, 2011 is reported as the host of this parasitoid wasp. Detailed taxonomic and barcoding information are provided.},
}
@article {pmid35835808,
year = {2022},
author = {Scholtz, L and Eckert, JG and Elahi, T and Lübkemann, F and Hübner, O and Bigall, NC and Resch-Genger, U},
title = {Luminescence encoding of polymer microbeads with organic dyes and semiconductor quantum dots during polymerization.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {12061},
pmid = {35835808},
issn = {2045-2322},
mesh = {Coloring Agents ; Luminescence ; Microspheres ; Polymerization ; Polystyrenes/chemistry ; *Quantum Dots/chemistry ; Semiconductors ; },
abstract = {Luminescence-encoded microbeads are important tools for many applications in the life and material sciences that utilize luminescence detection as well as multiplexing and barcoding strategies. The preparation of such beads often involves the staining of premanufactured beads with molecular luminophores using simple swelling procedures or surface functionalization with layer-by-layer (LbL) techniques. Alternatively, these luminophores are sterically incorporated during the polymerization reaction yielding the polymer beads. The favorable optical properties of semiconductor quantum dots (QDs), which present broadly excitable, size-tunable, narrow emission bands and low photobleaching sensitivity, triggered the preparation of beads stained with QDs. However, the colloidal nature and the surface chemistry of these QDs, which largely controls their luminescence properties, introduce new challenges to bead encoding that have been barely systematically assessed. To establish a straightforward approach for the bead encoding with QDs with minimized loss in luminescence, we systematically assessed the incorporation of oleic acid/oleylamine-stabilized CdSe/CdS-core/shell-QDs into 0.5-2.5 µm-sized polystyrene (PS) microspheres by a simple dispersion polymerization synthesis that was first optimized with the organic dye Nile Red. Parameters addressed for the preparation of luminophore-encoded beads include the use of a polymer-compatible ligand such as benzyldimethyloctadecylammonium chloride (OBDAC) for the QDs, and crosslinking to prevent luminophore leakage. The physico-chemical and optical properties of the resulting beads were investigated with electron microscopy, dynamic light scattering, optical spectroscopy, and fluorescence microscopy. Particle size distribution, fluorescence quantum yield of the encapsulated QDs, and QD leaking stability were used as measures for bead quality. The derived optimized bead encoding procedure enables the reproducible preparation of bright PS microbeads encoded with organic dyes as well as with CdSe/CdS-QDs. Although these beads show a reduced photoluminescence quantum yield compared to the initially very strongly luminescent QDs, with values of about 35%, their photoluminescence quantum yield is nevertheless still moderate.},
}
@article {pmid35822862,
year = {2021},
author = {Borch Jensen, M and Marblestone, A},
title = {Corrigendum: In Vivo Pooled Screening: A Scalable Tool to Study the Complexity of Aging and Age-Related Disease.},
journal = {Frontiers in aging},
volume = {2},
number = {},
pages = {804856},
doi = {10.3389/fragi.2021.804856},
pmid = {35822862},
issn = {2673-6217},
abstract = {[This corrects the article DOI: 10.3389/fragi.2021.714926.].},
}
@article {pmid35822810,
year = {2022},
author = {Senn, S and Pangell, K and Bowerman, AL},
title = {Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxia.},
journal = {Biotech (Basel (Switzerland))},
volume = {11},
number = {1},
pages = {},
pmid = {35822810},
issn = {2673-6284},
abstract = {The purpose of this paper is to elucidate the roles that microbes may be playing in the rootzone of the medicinal plant Daturainoxia. We hypothesized that the microbes associated with the Datura rootzone would be significantly different than the similar surrounding fields in composition and function. We also hypothesized that rhizospheric and endophytic microbes would be associated with similar metabolic functions to the plant rootzone they inhabited. The methods employed were microbial barcoding, tests of essential oils against antibiotic resistant bacteria and other soil bacterial isolates, 16S Next Generation Sequencing (NGS) metabarcoding, and Whole Genome Shotgun (WGS) taxonomic and functional analyses. A few of the main bacterial genera of interest that were differentially abundant in the Datura root microbiome were Flavobacterium (p = 0.007), Chitinophaga (p = 0.0007), Pedobacter (p = 6 × 10[-5]), Bradyhizobium (p = 1 × 10[-8]), and Paenibacillus (p = 1.46 × 10[-6]). There was significant evidence that the microbes associated with the Datura rootzone had elevated function related to bacterial chalcone synthase (p = 1.49 × 10[-3]) and permease genes (p < 0.003). There was some evidence that microbial functions in the Datura rootzone provided precursors to important plant bioactive molecules or were beneficial to plant growth. This is important because these compounds are phyto-protective antioxidants and are precursors to many aromatic bioactive compounds that are relevant to human health. In the context of known interactions, and current results, plants and microbes influence the flavonoid biosynthetic pathways of one other, in terms of the regulation of the phenylpropanoid pathway. This is the first study to focus on the microbial ecology of the Datura rootzone. There are possible biopharmaceutical and agricultural applications of the natural interplay that was discovered during this study of the Datura inoxia rhizosphere.},
}
@article {pmid35822038,
year = {2021},
author = {Borch Jensen, M and Marblestone, A},
title = {In vivo Pooled Screening: A Scalable Tool to Study the Complexity of Aging and Age-Related Disease.},
journal = {Frontiers in aging},
volume = {2},
number = {},
pages = {714926},
pmid = {35822038},
issn = {2673-6217},
abstract = {Biological aging, and the diseases of aging, occur in a complex in vivo environment, driven by multiple interacting processes. A convergence of recently developed technologies has enabled in vivo pooled screening: direct administration of a library of different perturbations to a living animal, with a subsequent readout that distinguishes the identity of each perturbation and its effect on individual cells within the animal. Such screens hold promise for efficiently applying functional genomics to aging processes in the full richness of the in vivo setting. In this review, we describe the technologies behind in vivo pooled screening, including a range of options for delivery, perturbation and readout methods, and outline their potential application to aging and age-related disease. We then suggest how in vivo pooled screening, together with emerging innovations in each of its technological underpinnings, could be extended to shed light on key open questions in aging biology, including the mechanisms and limits of epigenetic reprogramming and identifying cellular mediators of systemic signals in aging.},
}
@article {pmid35819606,
year = {2022},
author = {Pusz-Bochenska, K and Pérez-López, E and Dumonceaux, TJ and Olivier, C and Wist, TJ},
title = {Rapid Molecular Diagnostics in the Field and Laboratory to Detect Plant Pathogen DNA in Potential Insect Vectors.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2536},
number = {},
pages = {179-199},
pmid = {35819606},
issn = {1940-6029},
mesh = {Animals ; DNA Primers/genetics ; *DNA, B-Form/analysis ; *Insect Vectors/microbiology ; *Plant Diseases/microbiology ; Recombinases ; },
abstract = {A variety of sensitive and specific molecular diagnostic assays has been described for detecting nucleic acids in biological samples that may harbor pathogens of interest. These methods include very rapid, isothermal nucleic acid amplification methods that can be deployed outside of the laboratory environment, such as loop-mediated isothermal DNA amplification (LAMP) and recombinase-polymerase amplification (RPA). However, all molecular diagnostic assays must be preceded by nucleic acid extraction from the biological samples of interest, which provides suitable template molecules for the assays. To exploit the features of the amplification assays and be utilized outside of the lab, these methods must be rapid and avoid the need for typical laboratory chemicals and equipment. We describe a protocol for the extraction of DNA from field-collected insects that can be implemented at the point of collection and used to detect the presence of DNA sequences from potential plant pathogens that may be vectored by the insects. This protocol provides template DNA that is suitable for PCR, LAMP, and RPA. The FTA PlantSaver card-based DNA extraction product was also confirmed to amplify the mitochondrial cytochrome oxidase 1 (CO1) universal barcode that could later be sequenced to identify any insect. Lastly, we provide an example using field-collected insects, Neokolla (Graphocephala) heiroglyphica, and demonstrate the detection of the plant pathogen Xylella fastidiosa in carrier insects using PCR, RPA, and LAMP.},
}
@article {pmid35816611,
year = {2022},
author = {Emerson, NT and Yang, H},
title = {Sorting Nanoparticles by Valency with DNA Barcoding.},
journal = {Journal of the American Chemical Society},
volume = {144},
number = {28},
pages = {12915-12923},
doi = {10.1021/jacs.2c04744},
pmid = {35816611},
issn = {1520-5126},
mesh = {DNA/chemistry ; DNA Barcoding, Taxonomic ; Gold/chemistry ; *Metal Nanoparticles/chemistry ; *Nanoparticles ; *Nanostructures/chemistry ; },
abstract = {Self-assembly of DNA-labeled nanoparticles is an effective strategy to fabricate new nanocomposite materials and nanoscale devices from the bottom-up. To tailor the properties of the resulting material or device, one requires access to a wide range of nanoparticle sizes and shapes, as well as control over the number (valency) of DNA molecules on the nanoparticle surface. Currently, nanoparticles with a defined DNA valency can only be obtained in a narrow range of sizes, and in small quantities, limiting the properties of the resulting composite structures and their applications. Here, we leverage the digital information encoded in the number and sequence of short DNA barcodes to generate preparatory amounts of nanoparticles bearing a specific number of DNA molecules, irrespective of the identity of the nanocomponent. We show that this DNA valency sorting chromatography, which is driven by the selective affinity of Watson-Crick base pairs, is applicable to arbitrary DNA sequences and a broad range of nanoparticle sizes, shapes, and material compositions. To further demonstrate this fact, we use valency-sorted large gold nanospheres directly in self-assembly schemes to create, in one synthesis step, large amounts of several previously inaccessible molecule-like dimer and trimer nanostructures with unique optical properties. We anticipate that the expanded scope of DNA valency-defined nanoparticle reagents, and the increased scale at which they can be produced, will open new avenues for the molecularly precise manipulation of nanoscale matter.},
}
@article {pmid35811172,
year = {2022},
author = {van Klink, R and August, T and Bas, Y and Bodesheim, P and Bonn, A and Fossøy, F and Høye, TT and Jongejans, E and Menz, MHM and Miraldo, A and Roslin, T and Roy, HE and Ruczyński, I and Schigel, D and Schäffler, L and Sheard, JK and Svenningsen, C and Tschan, GF and Wäldchen, J and Zizka, VMA and Åström, J and Bowler, DE},
title = {Emerging technologies revolutionise insect ecology and monitoring.},
journal = {Trends in ecology &amp; evolution},
volume = {37},
number = {10},
pages = {872-885},
doi = {10.1016/j.tree.2022.06.001},
pmid = {35811172},
issn = {1872-8383},
mesh = {Animals ; *Ecology/methods ; *Insecta ; },
abstract = {Insects are the most diverse group of animals on Earth, but their small size and high diversity have always made them challenging to study. Recent technological advances have the potential to revolutionise insect ecology and monitoring. We describe the state of the art of four technologies (computer vision, acoustic monitoring, radar, and molecular methods), and assess their advantages, current limitations, and future potential. We discuss how these technologies can adhere to modern standards of data curation and transparency, their implications for citizen science, and their potential for integration among different monitoring programmes and technologies. We argue that they provide unprecedented possibilities for insect ecology and monitoring, but it will be important to foster international standards via collaboration.},
}
@article {pmid35810417,
year = {2022},
author = {Kazim, AR and Low, VL and Tappe, D and Houssaini, J and Heo, CC},
title = {Rhipicephalus annulatus, R. australis or R. microplus? Discordance between morphological and genetic data among three cattle tick species.},
journal = {Experimental &amp; applied acarology},
volume = {87},
number = {1},
pages = {119-131},
pmid = {35810417},
issn = {1572-9702},
support = {Higher Institution Centre of Excellence (HICoE) program (MO002-2019)//Ministry of Higher Education/ ; },
mesh = {Animals ; Cattle ; *Cattle Diseases/genetics ; *Coleoptera ; Female ; Malaysia ; Male ; Phylogeny ; *Rhipicephalus/anatomy &amp; histology ; *Tick Infestations/veterinary ; },
abstract = {The taxonomy of ticks of the subgenus Boophilus has been extensively debated and is often complicated by the high intraspecific variation of morphological features between species. Notably, the cattle tick Rhipicephalus microplus is a species complex consisting of Rhipicephalus annulatus, Rhipicephalus australis and the three mitochondrial clades (A-C) of R. microplus. To gain insight into the taxonomic status of this species complex, we performed morphological and molecular analyses on these cattle ticks across four states in peninsular Malaysia. We morphologically identified 60 males and 104 females of R. microplus, 298 males and 374 females of R. australis, and one R. annulatus male in our field collection, of which the latter two species have never been recorded in Malaysia. However, all three morphologically identified species were molecularly assigned as R. microplus clade A based on the barcoding cytochrome oxidase subunit I (COI) analysis. The discrepancy between morphological and genetic data highlights an urgent need for further exploration and in-depth research into the taxonomic status of these sympatric tick species.},
}
@article {pmid35809200,
year = {2022},
author = {Han, S and Bi, D and Yi, R and Ding, H and Wu, L and Kan, X},
title = {Plastome evolution of Aeonium and Monanthes (Crassulaceae): insights into the variation of plastomic tRNAs, and the patterns of codon usage and aversion.},
journal = {Planta},
volume = {256},
number = {2},
pages = {35},
pmid = {35809200},
issn = {1432-2048},
support = {NEL&amp;MARA-003//the Opening Foundation of National Engineering Laboratory of Soil Pollution Control and Remediation Technologies, and Key Laboratory of Heavy Metal Pollution Prevention &amp; Control, Ministry of Agriculture and Rural Affairs/ ; BK20211078//the Natural Science Foundation of Jiangsu Province/ ; YJS20210136//the Scientific Research Project Foundation of Postgraduate of the Anhui Higher Education Institutions of China/ ; },
mesh = {*Codon Usage ; *Crassulaceae ; Evolution, Molecular ; Phylogeny ; RNA, Transfer ; },
abstract = {This study reported 13 new plastomes from Aeonium and Monanthes, and observed new markers for phylogeny and DNA barcoding, such as novel tRNA structures and codon usage bias and aversion. The Macaronesian clade of Crassulaceae consists of three genera: Aichryson, with about 15 species; Monanthes, with about 10 species; Aeonium, with about 40 species. Within this clade, Aeonium, known as "the botanical equivalent of Darwin's finches", is regarded as an excellent model plant for researching adaptive evolution. Differing from the well-resolved relationships among three genera of the Macaronesian clade, the internal branching patterns within the genus Aeonium are largely unclear. In this study, we first reported 13 new plastomes from genus Aeonium and the closely related genus Monanthes. We further performed comprehensive analyses of the plastomes, with focuses on the secondary structures of pttRNAs and the patterns of codon usage and aversion. With a typical circular and quadripartite structure, the 13 plastomes ranged from 149,900 to 151,030 bp in size, and the unique pattern in IR junctions might become a family-specific marker for Crassulaceae species. Surprisingly, the π values of plastomes from Monanthes were almost twice those from Aeonium. Most importantly, we strongly recommend that highly polymorphic regions, novel putative pttRNA structures, patterns of codon usage bias and aversion derived from plastomes might have phylogenetic implications, and could act as new markers for DNA barcoding of plants. The results of phylogenetic analyses strongly supported a clear internal branching pattern in Macaronesian clade (represented by Aeonium and Monanthes), with higher nodal support values. The findings reported here will provide new insights into the variation of pttRNAs, and the patterns of codon usage and aversion of the family Crassulaceae.},
}
@article {pmid35808858,
year = {2023},
author = {Cassidy-Hanley, DM and Doerder, FP and Hossain, M and Devine, C and Clark, T},
title = {Molecular identification of Tetrahymena species.},
journal = {The Journal of eukaryotic microbiology},
volume = {70},
number = {1},
pages = {e12936},
pmid = {35808858},
issn = {1550-7408},
support = {P40 OD010964/OD/NIH HHS/United States ; P40 RR019688/RR/NCRR NIH HHS/United States ; },
mesh = {*Tetrahymena/genetics ; Mitochondria/genetics ; DNA, Intergenic/genetics ; Phylogeny ; },
abstract = {Mitochondrial cox1 689 bp barcodes are routinely used for identification of Tetrahymena species. Here, we examine whether two shorter nuclear sequences, the 5.8S rRNA gene region and the intergenic region between H3 and H4 histone genes, might also be useful either singly or in combination with each other or cox1. We obtained sequences from ~300 wild isolates deposited at the Tetrahymena Stock Center and analyzed additional sequences obtained from GenBank. The 5.8S rRNA gene and portions of its transcribed flanks identify isolates as to their major clade and uniquely identify some, but not all, species. The ~330 bp H3/H4 intergenic region possesses low intraspecific variability and is unique for most species. However, it fails to distinguish between two pairs of common species and their rarer counterparts, and its use is complicated by the presence of duplicate genes in some species. The results show that while the cox1 sequence is the best single marker for Tetrahymena species identification, 5.8S rRNA, and the H3/H4 intergenic regions sequences are useful, singly or in combination, to confirm cox1 species assignments or as part of a preliminary survey of newly collected Tetrahymena. From our newly collected isolates, the results extend the biogeographical range of T. shanghaiensis and T. malaccensis and identify a new species, Tetrahymena arleneae n. sp. herein described.},
}
@article {pmid35804326,
year = {2022},
author = {Dubois, B and Debode, F and Hautier, L and Hulin, J and Martin, GS and Delvaux, A and Janssen, E and Mingeot, D},
title = {A detailed workflow to develop QIIME2-formatted reference databases for taxonomic analysis of DNA metabarcoding data.},
journal = {BMC genomic data},
volume = {23},
number = {1},
pages = {53},
pmid = {35804326},
issn = {2730-6844},
mesh = {Computational Biology/methods ; *DNA ; *DNA Barcoding, Taxonomic/methods ; Plants ; Workflow ; },
abstract = {BACKGROUND: The DNA metabarcoding approach has become one of the most used techniques to study the taxa composition of various sample types. To deal with the high amount of data generated by the high-throughput sequencing process, a bioinformatics workflow is required and the QIIME2 platform has emerged as one of the most reliable and commonly used. However, only some pre-formatted reference databases dedicated to a few barcode sequences are available to assign taxonomy. If users want to develop a new custom reference database, several bottlenecks still need to be addressed and a detailed procedure explaining how to develop and format such a database is currently missing. In consequence, this work is aimed at presenting a detailed workflow explaining from start to finish how to develop such a curated reference database for any barcode sequence.<br><br>RESULTS: We developed DB4Q2, a detailed workflow that allowed development of plant reference databases dedicated to ITS2 and rbcL, two commonly used barcode sequences in plant metabarcoding studies. This workflow addresses several of the main bottlenecks connected with the development of a curated reference database. The detailed and commented structure of DB4Q2 offers the possibility of developing reference databases even without extensive bioinformatics skills, and avoids 'black box' systems that are sometimes encountered. Some filtering steps have been included to discard presumably fungal and misidentified sequences. The flexible character of DB4Q2 allows several key sequence processing steps to be included or not, and downloading issues can be avoided. Benchmarking the databases developed using DB4Q2 revealed that they performed well compared to previously published reference datasets.<br><br>CONCLUSION: This study presents DB4Q2, a detailed procedure to develop custom reference databases in order to carry out taxonomic analyses with QIIME2, but also with other bioinformatics platforms if desired. This work also provides ready-to-use plant ITS2 and rbcL databases for which the prediction accuracy has been assessed and compared to that of other published databases.},
}
@article {pmid35796594,
year = {2022},
author = {Magoga, G and Forni, G and Brunetti, M and Meral, A and Spada, A and De Biase, A and Montagna, M},
title = {Curation of a reference database of COI sequences for insect identification through DNA metabarcoding: COins.},
journal = {Database : the journal of biological databases and curation},
volume = {2022},
number = {},
pages = {},
pmid = {35796594},
issn = {1758-0463},
mesh = {Animals ; DNA/genetics ; *DNA Barcoding, Taxonomic/methods ; Databases, Nucleic Acid ; Insecta/genetics ; *Numismatics ; },
abstract = {DNA metabarcoding is a widespread approach for the molecular identification of organisms. While the associated wet-lab and data processing procedures are well established and highly efficient, the reference databases for taxonomic assignment can be implemented to improve the accuracy of identifications. Insects are among the organisms for which DNA-based identification is most commonly used; yet, a DNA-metabarcoding reference database specifically curated for their species identification using software requiring local databases is lacking. Here, we present COins, a database of 5' region cytochrome c oxidase subunit I sequences (COI-5P) of insects that includes over 532 000 representative sequences of >106 000 species specifically formatted for the QIIME2 software platform. Through a combination of automated and manually curated steps, we developed this database starting from all COI sequences available in the Barcode of Life Data System for insects, focusing on sequences that comply with several standards, including a species-level identification. COins was validated on previously published DNA-metabarcoding sequences data (bulk samples from Malaise traps) and its efficiency compared with other publicly available reference databases (not specific for insects). COins can allow an increase of up to 30% of species-level identifications and thus can represent a valuable resource for the taxonomic assignment of insects' DNA-metabarcoding data, especially when species-level identification is needed https://doi.org/10.6084/m9.figshare.19130465.v1.},
}
@article {pmid35795895,
year = {2023},
author = {Ebmer, D and Balfanz, F and Voracek, T and Hering-Hagenbeck, S and Pichler-Scheder, C and Walochnik, J and Kniha, E},
title = {The Palearctic blackfly Simulium equinum (Diptera: Simuliidae) as a biting pest of captive nyala antelopes (Tragelaphus angasii).},
journal = {Zoo biology},
volume = {42},
number = {1},
pages = {150-156},
pmid = {35795895},
issn = {1098-2361},
support = {//&#xd6;sterreichischen Akademie der Wissenschaften/ ; },
mesh = {Animals ; *Simuliidae ; *Antelopes ; Animals, Zoo ; Phylogeny ; },
abstract = {Blackflies (Diptera: Simuliidae) are cosmopolitan nuisance pests of great economic importance as well as vectors of many pathogens. After reports of massive blackfly biting of captive nyala antelopes in the Vienna Zoo, Austria, this study aimed to identify the species causing multiple skin lesions on the antelope hosts. The Palearctic species Simulium equinum, belonging to the medically and veterinary important Wilhelmia subgenus, was identified as the most likely causative agent. Barcoding and maximum likelihood analysis supported morphological species identification and highlighted the complex phylogeny of the subgenus Wilhelmia. Our study gives first evidence of the multi-host feeding blackfly S. equinum in the Vienna Zoo, thereby raising the question whether other hosts could also be bitten on a regular basis. The preliminary results urge for further analysis of blackfly breeding sites as well as the clarification of the host spectrum to assess the medical and veterinary importance of blackflies in the Zoo.},
}
@article {pmid35795775,
year = {2022},
author = {Inderbitzin, A and Loosli, T and Kouyos, RD and Metzner, KJ},
title = {Quantification of transgene expression in GSH AAVS1 with a novel CRISPR/Cas9-based approach reveals high transcriptional variation.},
journal = {Molecular therapy. Methods &amp; clinical development},
volume = {26},
number = {},
pages = {107-118},
pmid = {35795775},
issn = {2329-0501},
abstract = {Genomic safe harbors (GSH) are defined as sites in the host genome that allow stable expression of inserted transgenes while having no adverse effects on the host cell, making them ideal for use in basic research and therapeutic applications. Silencing and fluctuations in transgene expression would be highly undesirable effects. We have previously shown that transgene expression in Jurkat T cells is not silenced for up to 160 days after CRISPR-Cas9-mediated insertion of reporter genes into the adeno-associated virus site 1 (AAVS1), a commonly used GSH. Here, we studied fluctuations in transgene expression upon targeted insertion into the GSH AAVS1. We have developed an efficient method to generate and validate highly complex barcoded plasmid libraries to study transgene expression on the single-cell level. Its applicability is demonstrated by inserting the barcoded transgene Cerulean into the AAVS1 locus in Jurkat T cells via the CRISPR-Cas9 technology followed by next-generation sequencing of the transcribed barcodes. We observed large transcriptional variations over two logs for transgene expression in the GSH AAVS1. This barcoded transgene insertion model is a powerful tool to investigate fluctuations in transgene expression at any GSH site.},
}
@article {pmid35790799,
year = {2022},
author = {Copilaş-Ciocianu, D and Rewicz, T and Sands, AF and Palatov, D and Marin, I and Arbačiauskas, K and Hebert, PDN and Grabowski, M and Audzijonyte, A},
title = {A DNA barcode reference library for endemic Ponto-Caspian amphipods.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {11332},
pmid = {35790799},
issn = {2045-2322},
mesh = {*Amphipoda/genetics ; Animals ; *Butterflies ; DNA ; DNA Barcoding, Taxonomic/methods ; Gene Library ; },
abstract = {The Ponto-Caspian region is an endemicity hotspot that harbours several crustacean radiations, among which amphipods are the most diverse. These poorly known species are severely threatened in their native range, while at the same time they are invading European inland waters with significant ecological consequences. A proper taxonomic knowledge of this fauna is paramount for its conservation within the native region and monitoring outside of it. Here, we assemble a DNA barcode reference library for nearly 60% of all known Ponto-Caspian amphipod species. We use several methods to define molecular operational taxonomic units (MOTUs), based on two mitochondrial markers (COI and 16S), and assess their congruence with current species-level taxonomy based on morphology. Depending on the method, we find that 54-69% of species had congruent morpho-molecular boundaries. The cases of incongruence resulted from lumping distinct morphospecies into a single MOTU (7-27%), splitting a morphospecies into several MOTUs (4-28%), or both (4-11%). MOTUs defined by distance-based methods without a priori divergence thresholds showed the highest congruence with morphological taxonomy. These results indicate that DNA barcoding is valuable for clarifying the diversity of Ponto-Caspian amphipods, but reveals that extensive work is needed to resolve taxonomic uncertainties. Our study advances the DNA barcode reference library for the European aquatic biota, paving the way towards improved taxonomic knowledge needed to enhance monitoring and conservation efforts.},
}
@article {pmid35789203,
year = {2022},
author = {Yu, XQ and Jiang, YZ and Folk, RA and Zhao, JL and Fu, CN and Fang, L and Peng, H and Yang, JB and Yang, SX},
title = {Species discrimination in Schima (Theaceae): Next-generation super-barcodes meet evolutionary complexity.},
journal = {Molecular ecology resources},
volume = {22},
number = {8},
pages = {3161-3175},
doi = {10.1111/1755-0998.13683},
pmid = {35789203},
issn = {1755-0998},
support = {32070369//National Natural Science Foundation of China/ ; XDB31000000//the Strategic Priority Research Program of Chinese Academy of Sciences/ ; 2017-LSFGBOWS-02//the Large-scale Scientific Facilities of the Chinese Academy of Sciences/ ; 2021393//the Youth Innovation Promotion Association CAS/ ; },
mesh = {DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; DNA, Ribosomal ; *Genome, Plastid ; Humans ; Phylogeny ; Plants/genetics ; Sequence Analysis, DNA ; Species Specificity ; *Theaceae/genetics ; },
abstract = {Plastid genome and nuclear ribosomal DNA (nrDNA) arrays, proposed recently as "super-barcodes," might provide additional discriminatory power and overcome the limitations of traditional barcoding loci, yet super-barcodes need to be tested for their effectiveness in more plant groups. Morphological homoplasy among Schima species makes the genus a model for testing the efficacy of super-barcodes. In this study, we generated multiple data sets comprising standard DNA barcodes (matK, rbcL, trnH-psbA, nrITS) and super-barcodes (plastid genome, nrDNA arrays) across 58 individuals from 12 out of 13 species of Schima from China. No samples were correctly assigned to species using standard DNA barcodes and nrDNA arrays, while only 27.27% of species with multiple accessions were distinguished using the plastid genome and its partitioned data sets-the lowest estimated rate of super-barcode success in the literature so far. For Schima and other taxa with similarly recently divergence and low levels of genetic variation, incomplete lineage sorting, hybridization or taxonomic oversplitting are all possible causes of the failure. Taken together, our study suggests that by no means are super-barcodes immune to the challenges imposed by evolutionary complexity. We therefore call for developing multilocus nuclear markers for species discrimination in plant groups.},
}
@article {pmid35788906,
year = {2024},
author = {Graham, K and Houston, R},
title = {Evaluation of chloroplast DNA barcoding markers to individualize Papaver somniferum for forensic intelligence purposes.},
journal = {International journal of legal medicine},
volume = {138},
number = {1},
pages = {267-275},
pmid = {35788906},
issn = {1437-1596},
mesh = {Humans ; *Papaver/genetics ; DNA, Chloroplast/genetics ; Latex ; Acrylates ; },
abstract = {The opium poppy, Papaver somniferum L., is a forensically important plant due to the medicinal and illegal uses for the milky latex stored in the pods. This latex contains the alkaloids morphine, codeine, and thebaine that are used for their analgesic properties and/or for synthesizing other opioids. However, these compounds are highly addictive and have caused a national opioid epidemic. Two other Papaver species, P. setigerum DC. and P. bracteatum Lindl., are also of forensic interest because they pose both forensic and legal issues. They are largely uncontrolled under the Controlled Substances Act, making these species a common defense strategy. Current morphological and chemical identification methods have been moderately successful but have drawbacks. There is also a lack of sequencing data available. Therefore, exploiting the genome using chloroplast DNA barcoding markers could help to accurately identify these species of interest when plant material is taken. This study screened and assessed the genetic variation both between species and within populations of P. somniferum in nine cpDNA barcode regions (ndhF-rpl32, petA-psbJ, rpl32-trnL, rps16-trnQ, trnE-trnT, trnH-psbA, trnL-trnF, rpl16 intron, and psbE-petL). Published reference genomes from the NCBI GenBank database were aligned and compared for an initial in silico screening. Additionally, ten P. somniferum seed samples from various vendors were sequenced and compared across samples and to published reference data at the various barcode regions of interest. This study showed that the regions trnH-psbA and petA-psbJ have promise for utility in individualization for both inter- and intra-species individualization of P. somniferum.},
}
@article {pmid35788590,
year = {2022},
author = {Guo, Q and Spasic, M and Maynard, AG and Goreczny, GJ and Bizuayehu, A and Olive, JF and van Galen, P and McAllister, SS},
title = {Clonal barcoding with qPCR detection enables live cell functional analyses for cancer research.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {3837},
pmid = {35788590},
issn = {2041-1723},
support = {R01 CA166284/CA/NCI NIH HHS/United States ; },
mesh = {Cell Line ; Clonal Evolution/genetics ; Clone Cells ; *High-Throughput Nucleotide Sequencing/methods ; *Neoplasms ; Real-Time Polymerase Chain Reaction ; },
abstract = {Single-cell analysis methods are valuable tools; however, current approaches do not easily enable live cell retrieval. That is a particular issue when further study of cells that were eliminated during experimentation could provide critical information. We report a clonal molecular barcoding method, called SunCatcher, that enables longitudinal tracking and live cell functional analysis. From complex cell populations, we generate single cell-derived clonal populations, infect each with a unique molecular barcode, and retain stocks of individual barcoded clones (BCs). We develop quantitative PCR-based and next-generation sequencing methods that we employ to identify and quantify BCs in vitro and in vivo. We apply SunCatcher to various breast cancer cell lines and combine respective BCs to create versions of the original cell lines. While the heterogeneous BC pools reproduce their original parental cell line proliferation and tumor progression rates, individual BCs are phenotypically and functionally diverse. Early spontaneous metastases can also be identified and quantified. SunCatcher thus provides a rapid and sensitive approach for studying live single-cell clones and clonal evolution, and performing functional analyses.},
}
@article {pmid35783061,
year = {2022},
author = {Carvalho Leonardo, I and Barreto Crespo, MT and Capelo, J and Bustos Gaspar, F},
title = {The complete plastome of Echium plantagineum L. (Boraginaceae), the first chloroplast genome belonging to the Echium genus.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {7},
number = {6},
pages = {1154-1156},
pmid = {35783061},
issn = {2380-2359},
abstract = {Besides being a common weed, the presence of Echium plantagineum L. in food and feed commodities can represent a safety hazard due to their content in pyrrolizidine alkaloids. In this study, the complete chloroplast of E. plantagineum isolate BPTPS251 is described, being the first available plastome from an isolate belonging to the Echium genus. The chloroplast genome is 149,776 bp in length with 37.5% GC content, displaying a quadripartite structure that contains a pair of inverted repeats regions (25,754 bp each), separated by a large single-copy (80,978 bp) and a small single-copy (17,290 bp) regions. A total of 131 genes were predicted, including 37 tRNA genes, 8 rRNA genes, and 86 protein-coding genes. The phylogenetic analysis confirmed the placement of E. plantagineum under the Boraginaceae family, belonging to the Boraginales order. This study will contribute to conservation, phylogenetic, and evolutionary studies, as well as DNA barcoding applications for food and feed safety purposes.},
}
@article {pmid35782097,
year = {2022},
author = {Vaupel, A and Hommel, B and Beule, L},
title = {High-resolution melting (HRM) curve analysis as a potential tool for the identification of earthworm species and haplotypes.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13661},
pmid = {35782097},
issn = {2167-8359},
mesh = {Animals ; DNA/genetics ; Ecosystem ; Haplotypes/genetics ; *Oligochaeta/genetics ; Polymerase Chain Reaction ; Soil ; },
abstract = {BACKGROUND: Earthworm communities are an important component of soil biodiversity and contribute to a number of ecosystem functions such as soil-nutrient cycling. Taxonomic identification is an essential requirement to assess earthworm biodiversity and functionality. Although morphological identification of species is labour-intensive, it is the most commonly used method due to a lack of cost-efficient alternatives. Molecular approaches to identify earthworms at species and haplotype level such as DNA barcoding are gaining popularity in science but are rarely applied in practice. In contrast to barcoding, the differentiation of PCR products based on their thermal denaturation properties using high-resolution melting (HRM) curve analysis is a fast and cost-efficient molecular closed-tube, post-PCR tool that allows identification of taxa.<br><br>METHODS: We developed a HRM curve assay to identify eight earthworm species common to agricultural soils in Central Europe (Allolobophora chlorotica, Aporrectodea caliginosa, Apo. limicola, Apo. longa, Apo. rosea, Lumbricus castaneus, L. rubellus, and L. terrestris). For this, a new primer pair targeting a 158-bp long subregion of the cytochrome c oxidase I (COI) gene was designed. Our HRM assay was further tested for the differentiation of COI haplotypes using 28 individuals of the earthworm species Allo. chlorotica. Furthermore, we developed a novel extraction method for DNA from earthworm tissue that is fast and requires minimal consumables and laboratory equipment.<br><br>RESULTS: The developed HRM curve assay allowed identifying all eight earthworm species. Performing the assay on 28 individuals of the earthworm species Allo. chlorotica enabled the distinction among different COI haplotypes. Furthermore, we successfully developed a rapid, robust, scalable, and inexpensive method for the extraction of earthworm DNA from fresh or frozen tissue.<br><br>CONCLUSIONS: HRM curve analysis of COI genes has the potential to identify earthworm species and haplotypes and could complement morphological identification, especially for juvenile or damaged individuals. Our rapid and inexpensive DNA extraction method from earthworm tissue helps to reduce the costs of molecular analyses and thereby promote their application in practice.},
}
@article {pmid35778106,
year = {2022},
author = {Seth, S and Bhattacharya, A},
title = {How capture affects polymer translocation in a solitary nanopore.},
journal = {The Journal of chemical physics},
volume = {156},
number = {24},
pages = {244902},
pmid = {35778106},
issn = {1089-7690},
support = {R21 HG011236/HG/NHGRI NIH HHS/United States ; },
mesh = {DNA ; Electricity ; Molecular Dynamics Simulation ; *Nanopores ; Polymers ; },
abstract = {DNA capture with high fidelity is an essential part of nanopore translocation. We report several important aspects of the capture process and subsequent translocation of a model DNA polymer through a solid-state nanopore in the presence of an extended electric field using the Brownian dynamics simulation that enables us to record statistics of the conformations at every stage of the translocation process. By releasing the equilibrated DNAs from different equipotentials, we observe that the capture time distribution depends on the initial starting point and follows a Poisson process. The field gradient elongates the DNA on its way toward the nanopore and favors a successful translocation even after multiple failed threading attempts. Even in the limit of an extremely narrow pore, a fully flexible chain has a finite probability of hairpin-loop capture, while this probability decreases for a stiffer chain and promotes single file translocation. Our in silico studies identify and differentiate characteristic distributions of the mean first passage time due to single file translocation from those due to translocation of different types of folds and provide direct evidence of the interpretation of the experimentally observed folds [M. Gershow and J. A. Golovchenko, Nat. Nanotechnol. 2, 775 (2007) and Mihovilovic et al., Phys. Rev. Lett. 110, 028102 (2013)] in a solitary nanopore. Finally, we show a new finding-that a charged tag attached at the 5' end of the DNA enhances both the multi-scan rate and the uni-directional translocation (5' → 3') probability that would benefit the genomic barcoding and sequencing experiments.},
}
@article {pmid35777281,
year = {2022},
author = {Snyman, LP and Penning, KE and Williams, KA},
title = {The first reported case of accidental intestinal myiasis in a domestic dog by the flesh fly, Sarcophaga africa (Wiedeman, 1824).},
journal = {Research in veterinary science},
volume = {149},
number = {},
pages = {71-73},
doi = {10.1016/j.rvsc.2022.06.010},
pmid = {35777281},
issn = {1532-2661},
mesh = {Africa ; Animals ; *Diptera ; *Dog Diseases/diagnosis ; Dogs ; Larva ; *Myiasis/diagnosis/veterinary ; *Sarcophagidae ; },
abstract = {Myiasis occurs when fly larvae, or maggots, feed on the tissue, secretions or digestive content of a live vertebrate. Here, a rare case of accidental intestinal or enteric myiasis is reported in a domestic dog. The species of fly is molecularly identified as Sarcophaga africa (Wiedeman, 1824) using the barcoding region of cytochrome oxidase I (COI). A brief critique on the usage of the term "pseudomyiasis" is provided and the complex taxonomy of S. africa is briefly summarised in order to shed light on the erroneous use of S. cruenata and S. haemorrhoidalis with obvious downstream effects. Finally, a comparative assessment to the limited cases in the literature is provided. These few cases are however highly fragmented and our understanding of accidental intestinal myiasis and the clinical manifestations thereof remain incomplete.},
}
@article {pmid35776657,
year = {2022},
author = {Lee, HW and Kim, E and Cho, KJ and Park, HJ and Seo, J and Lee, H and Baek, E and Choi, JR and Han, KH and Lee, ST and Park, JY},
title = {Applications of molecular barcode sequencing for the detection of low-frequency variants in circulating tumour DNA from hepatocellular carcinoma.},
journal = {Liver international : official journal of the International Association for the Study of the Liver},
volume = {42},
number = {10},
pages = {2317-2326},
doi = {10.1111/liv.15356},
pmid = {35776657},
issn = {1478-3231},
mesh = {Biomarkers, Tumor/genetics ; *Carcinoma, Hepatocellular/diagnosis/genetics ; *Circulating Tumor DNA/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Liver Neoplasms/diagnosis/genetics ; Mutation ; },
abstract = {PURPOSE: Liquid biopsy has emerged as a promising tool for minimally invasive and accurate detection of various malignancies. We aimed to apply molecular barcode sequencing to circulating tumour DNA (ctDNA) from liquid biopsies of hepatocellular carcinoma (HCC).<br><br>STUDY DESIGN: Patients with HCC or benign liver disease were enrolled between 2017 and 2018. Matched tissue and serum samples were obtained from these patients. Plasma cell-free DNA was extracted and subjected to targeted sequencing with ultra-high coverage and molecular barcoding.<br><br>RESULTS: The study included 143 patients: 102 with HCC, 7 with benign liver tumours and 34 with chronic liver disease. No tier 1/2 or oncogenic mutations were detected in patients with benign liver disease. Among the HCC patients, 49 (48%) had tier 1/2 mutations in at least one gene; detection rates were higher in advanced stages (75%) than in early stages (26%-33%). TERT was the most frequently mutated gene (30%), followed by TP53 (16%), CTNNB1 (14%), ARID2 (5%), ARID1A (4%), NFE2L2 (4%), AXIN1 (3%) and KRAS (1%). Survival among patients with TP53 mutations was significantly worse (p&#xa0;=&#xa0;0.007) than among patients without these mutations, whereas CTNNB1 and TERT mutations did not affect survival. ctDNA testing combined with &#x3b1;-fetoprotein and prothrombin induced by vitamin K absence-II analyses improved HCC detection, even in early stages.<br><br>CONCLUSIONS: ctDNA detection using molecular barcoding technology offers dynamic and personalized information concerning tumour biology, such information can guide clinical diagnosis and management. This detection also has the potential as a minimally invasive approach for prognostic stratification and post-therapeutic monitoring.},
}
@article {pmid35774270,
year = {2021},
author = {Ueda, K and Yanagimoto, T and Chow, S and Kuroki, M and Yamakawa, T},
title = {Molecular Identification of Mid to Final Stage Slipper Lobster Phyllosoma Larvae of the Genus Chelarctus (Crustacea: Decapoda: Scyllaridae) Collected in the Pacific with Descriptions of Their Larval Morphology.},
journal = {Zoological studies},
volume = {60},
number = {},
pages = {e75},
pmid = {35774270},
issn = {1810-522X},
abstract = {Morphological descriptions of phyllosoma larvae are essential for correct species identification and investigating the spatiotemporal distribution and recruitment process of spiny and slipper lobsters. Species identification of the phyllosoma larvae in the Scyllarinae subfamily is particularly difficult because of the morphological similarities among species and the scarcity of morphological information describing correct species identity. We extracted mid-to final-stage (V to VIII) phyllosoma larvae (n = 12) belonging to the subfamily Scyllarinae from several plankton samples collected in the Pacific and then performed molecular species identification using mitochondrial DNA COI and 16S rDNA sequence analyses. Three larvae collected around the Ryukyu Archipelago were identified as Chelarctus aureus (stage VI to VIII), and four collected around the Ryukyu Archipelago and Ogasawara Islands were identified as C. virgosus (V to VIII). One larva (V) collected in the central South Pacific was determined to be a subspecies of C. crosnieri. DNA barcodes could not be made for the remaining four larvae (V to VIII) collected around the Ryukyu Archipelago (designated by ?Chelarctus sp-1). Based on the morphological characteristics of the C. virgosus phyllosoma described in this study and the adult distributions reported to date, C. cultrifer phyllosomas previously reported in Japanese and Taiwanese waters are likely to be C. virgosus. This paper also presents a set of diagnostic morphological characteristics that can be used to discriminate among these four species of Chelarctus and from other genera in the subfamily Scyllarinae.},
}
@article {pmid35774269,
year = {2021},
author = {Huang, YH and Shih, HT},
title = {Diversity in the Taiwanese Swimming Crabs (Crustacea: Brachyura: Portunidae) Estimated through DNA Barcodes, with Descriptions of 14 New Records.},
journal = {Zoological studies},
volume = {60},
number = {},
pages = {e60},
pmid = {35774269},
issn = {1810-522X},
abstract = {The swimming crabs (family Portunidae) are distributed worldwide and commonly inhabit estuaries, mangroves, reefs, shallow and the deep sea. Previously, 75 species and 19 genera in this family were known to Taiwan. Our study examined specimens in Taiwanese waters, including the islands, collected between 2016 and 2020 or deposited in museums. Through the cytochrome oxidase subunit I DNA barcode marker and morphological examination, 71 species were identified. The minimum interspecific distances were greater than 4.09%, except in two unresolved groups: Charybdis miles (De Haan, 1835) and Ch. sagamiensis Parisi, 1916, as well as Thranita pelsarti (Montgomery, 1931) and Thr. prymna (Herbst, 1803). In addition, 14 species belonging to nine genera were confirmed as new records to Taiwan, viz. Carupa ohashii Takeda, 1993, Lupocyclus inaequalis (Walker, 1887), Luu. tugelae Barnard, 1950, Lupocycloporus minutus (Shen, 1937), Monomia gladiator (Fabricius, 1798), M. lucida Koch &amp; Ďuriš, 2018, Podophthalmus minabensis Sakai, 1961, Thalamita gatavakensis Nobili, 1906, Tha. spinifera Borradaile, 1902, Thalamitoides quadridens A. Milne-Edwards, 1869, Tho. tridens A. Milne-Edwards, 1869, Thr. cerasma (Wee &amp; Ng, 1995), Thr. coeruleipes (Hombron &amp; Jacquinot, 1846) and Xiphonectes tuberculosus (A. Milne-Edwards, 1861). This study thus raises the total number of Portunidae species in Taiwan to 89.},
}
@article {pmid35774266,
year = {2022},
author = {Chou, TK and Liao, TY},
title = {A New Species of Parascorpaena Bleeker, 1876 (Teleostei: Scorpaenidae) from Taiwan.},
journal = {Zoological studies},
volume = {60},
number = {},
pages = {e9},
pmid = {35774266},
issn = {1810-522X},
abstract = {A new species of scorpionfish, Poseidon's scorpionfish Parascorpaena poseidon, is described on the basis of ten specimens collected from southwestern Taiwanese waters ranging from Penghu to Chufongbi, Pingtung. The morphological and molecular analyses reveal the new species is clearly separated from the two similar species, P. aurita and P. mossambica. Parascorpaena poseidon is distinguished from congeners by the following combination of characters: three equal-sized suborbital spines without ridge; supraocular tentacle absent or very short; pectoral-fin rays 15-16 (usually 16); pored lateral-line scales 22-26 (usually 22-23); longitudinal scale rows 43-47; pre-dorsal-fin scale rows 2-3 (usually 3); 10-12 scale rows between 6th dorsal-fin spine base and lateral line; 10-12 scale rows between the last dorsal-fin spine base and lateral line; total gill rakers 15-16, gill rakers on hypobranchial 2-3; ratio of 11th and 12th dorsal-fin spine 60%-81% (mean 73%); blackish spots randomly distributed on all fins; absence of a distinct black blotch on spinous dorsal fin in male; body size relatively large.},
}
@article {pmid35774258,
year = {2021},
author = {Alshari, NFMAH and Ahmad, SZ and Azlan, A and Lee, YH and Azzam, G and Nor, SAM},
title = {Metabarcoding of Fish Larvae in the Merbok River Reveals Species Diversity and Distribution Along its Mangrove Environment.},
journal = {Zoological studies},
volume = {60},
number = {},
pages = {e76},
pmid = {35774258},
issn = {1810-522X},
abstract = {The Merbok River (north-west of Peninsular Malaysia) is a mangrove estuary that provides habitat for over 100 species of fish, which are economically and ecologically important. Threats such as habitat loss and overfishing are becoming a great concern for fisheries conservation and management. The identification of larval fish in this estuarine system is important to complement information on the adults. This is because the data could inform the spawning behaviour, reproductive biology, selection of nursery grounds and migration route of fish. Such information is invaluable for fisheries and aquatic environmental monitoring, and thus for their conservation and management. However, identifying fish larvae is a challenging task based only on morphology and even traditional DNA barcoding. To address this, DNA metabarcoding was utilised to detect the diversity of fish in the Merbok River. To complete the study, the fish larvae were collected at six sampling sites of the river. The extracted larval DNA was amplified for the Cytochrome Oxidase subunit 1 (COI) and 12S ribosomal RNA (12S rRNA) genes based on the metabarcoding approach using shotgun sequencing on the next-generation sequencing (NGS) Illumina MiSeq platform. Eighty-nine species from 65 genera and 41 families were detected, with Oryzias javanicus, Oryzias dancena, Lutjanus argentimaculatus and Lutjanus malabaricus among the most common species. The lower diversity observed from previous morphological studies is suggested to be mainly due to seasonal variation over the sampling period between the two methods and limited 12S rRNA sequences in current databases. The metabarcode data and a validation Sanger sequencing step using 15 species-specific primer pairs detected three species in common: Oryzias javanicus, Decapterus maruadsi and Pennahia macrocephalus. Several discrepancies observed between the two molecular approaches could be attributed to contaminants during sampling and DNA extraction, which could mask the presence of target species, especially when DNA from the contaminants is more abundant than the target organisms. In conclusion, this rapid and cost-effective identification method using DNA metabarcoding allowed the detection of numerous fish species from bulk larval samples in the Merbok River. This method can be applied to other sites and other organisms of interest.},
}
@article {pmid35774256,
year = {2022},
author = {Amorim, PF and Katz, AM and Ottoni, FP and de Bragança, PHN},
title = {Genetic Structure of the Mangrove Killifish Kryptolebias hermaphroditus Costa, 2011 (Cyprinodontiformes: Aplocheiloidei) Supports A Wide Connection among its Populations.},
journal = {Zoological studies},
volume = {60},
number = {},
pages = {e4},
pmid = {35774256},
issn = {1810-522X},
abstract = {The Kryptolebias marmoratus species group is composed of the only three vertebrate species that lack females. These species present only males and simultaneously hermaphroditic individuals; that are able to reproduce by allogamy, with males, or by autogamy, performing self-fertilization and generating clones of themselves. The proportion of males is variable among those species and even among their populations. Kryptolebias hermaphroditus has the smallest proportion of males. Indeed, no males have been recorded in most known populations. This is a mainly autogamous species, with small populations having a disjunct distribution along the eastern and northern coast of Brazil. Species presenting such adaptations would be expected to have an elevated rate of genetic population structure, reflecting any barriers that obstruct gene flow between populations. Partial sequences of the mitochondrial cytochrome c oxidase I (COI) gene from 335 individuals were sampled to perform a population analysis. Only a single haplotype of COI, widely distributed throughout all the sampled populations, was recovered for K. hermaphroditus. Here we hypothesize that the high degree of communication within populations is probably the main biological feature leading to this pattern.},
}
@article {pmid35771889,
year = {2022},
author = {Arai, S and Kuwata, R and Higa, Y and Maekawa, Y and Tsuda, Y and Roychoudhury, S and Bertuso, AG and Phong, TV and Yen, NT and Etoh, T and Otuka, A and Matsumura, M and Nabeshima, T and Taya, KT and Okabe, N and Kobayashi, M and Sawabe, K},
title = {Two hidden taxa in the Japanese encephalitis vector mosquito, Culex tritaeniorhynchus, and the potential for long-distance migration from overseas to Japan.},
journal = {PLoS neglected tropical diseases},
volume = {16},
number = {6},
pages = {e0010543},
pmid = {35771889},
issn = {1935-2735},
mesh = {Animals ; *Culex ; *Culicidae ; *Encephalitis Virus, Japanese/genetics ; *Encephalitis, Japanese/epidemiology ; Japan ; Mosquito Vectors ; Phylogeny ; },
abstract = {The Culex vishnui subgroups, particularly Culex tritaeniorhynchus, are considered the primary vectors of the Japanese encephalitis virus (JEV) in Asia. Recent molecular phylogenetic analyses of JEV isolates from Asian countries have shown that JEVs with diverse genetic variants are present in Asia. Furthermore, some JEV strains have been found to have crossed the East China Sea and been introduced into Japan. In this study, the possibility of overseas migration of the JE vector mosquito, Cx. tritaeniorhynchus was examined from the genetic, physical, and meteorological perspectives. Molecular phylogenetic analysis was performed based on both whole coding sequences and on the barcoding region of the mitochondrial cytochrome c oxidase subunit I (COI) gene of Cx. vishnui subgroups collected from Asian countries. Culex tritaeniorhymchus was classified into two genetically independent taxa by COI sequences: the Japanese type (Ct-J), which inhabits Japan except for the Amami Islands of southern Japan, and the continental type (Ct-C), which inhabits the Asian region except for Japan. It was confirmed that approximately 10% of Cx. tritaeniorhynchus trapped during the summer in western Kyushu were Ct-C, and that they could fly for up to 38 h continuously. The meteorological analysis also confirmed that the atmospheric flow occurring over the continent coincided with the date of Ct-C capture. This is the first report showing the existence of two taxa in Cx. tritaeniorhynchus. Their physical and physiological characteristics suggest the possibility of long-distance migration from overseas regions to Japan across the East China Sea. Future efforts are expected to provide evidence to support the occurrence of long-distance migration of Cx. tritaeniorhynchus with JEV.},
}
@article {pmid35770795,
year = {2022},
author = {Grabski, IN and Irizarry, RA},
title = {A probabilistic gene expression barcode for annotation of cell types from single-cell RNA-seq data.},
journal = {Biostatistics (Oxford, England)},
volume = {23},
number = {4},
pages = {1150-1164},
pmid = {35770795},
issn = {1468-4357},
support = {R01 HG005220/HG/NHGRI NIH HHS/United States ; R35 GM131802/GM/NIGMS NIH HHS/United States ; },
mesh = {Gene Expression ; *Gene Expression Profiling/methods ; Humans ; RNA-Seq ; Sequence Analysis, RNA/methods ; *Single-Cell Analysis ; Software ; },
abstract = {Single-cell RNA sequencing (scRNA-seq) quantifies gene expression for individual cells in a sample, which allows distinct cell-type populations to be identified and characterized. An important step in many scRNA-seq analysis pipelines is the annotation of cells into known cell types. While this can be achieved using experimental techniques, such as fluorescence-activated cell sorting, these approaches are impractical for large numbers of cells. This motivates the development of data-driven cell-type annotation methods. We find limitations with current approaches due to the reliance on known marker genes or from overfitting because of systematic differences, or batch effects, between studies. Here, we present a statistical approach that leverages public data sets to combine information across thousands of genes, uses a latent variable model to define cell-type-specific barcodes and account for batch effect variation, and probabilistically annotates cell-type identity from a reference of known cell types. The barcoding approach also provides a new way to discover marker genes. Using a range of data sets, including those generated to represent imperfect real-world reference data, we demonstrate that our approach substantially outperforms current reference-based methods, particularly when predicting across studies.},
}
@article {pmid35768613,
year = {2022},
author = {Dobrowolski, C and Paunovska, K and Schrader Echeverri, E and Loughrey, D and Da Silva Sanchez, AJ and Ni, H and Hatit, MZC and Lokugamage, MP and Kuzminich, Y and Peck, HE and Santangelo, PJ and Dahlman, JE},
title = {Nanoparticle single-cell multiomic readouts reveal that cell heterogeneity influences lipid nanoparticle-mediated messenger RNA delivery.},
journal = {Nature nanotechnology},
volume = {17},
number = {8},
pages = {871-879},
pmid = {35768613},
issn = {1748-3395},
support = {R01 DE026941/DE/NIDCR NIH HHS/United States ; UG3 TR002855/TR/NCATS NIH HHS/United States ; UH3 TR002855/TR/NCATS NIH HHS/United States ; },
mesh = {*Lipids ; Liposomes ; *Nanoparticles ; RNA, Messenger/genetics/metabolism ; RNA, Small Interfering/genetics ; },
abstract = {Cells that were previously described as homogeneous are composed of subsets with distinct transcriptional states. However, it remains unclear whether this cell heterogeneity influences the efficiency with which lipid nanoparticles (LNPs) deliver messenger RNA therapies in vivo. To test the hypothesis that cell heterogeneity influences LNP-mediated mRNA delivery, we report here a new multiomic nanoparticle delivery system called single-cell nanoparticle targeting-sequencing (SENT-seq). SENT-seq quantifies how dozens of LNPs deliver DNA barcodes and mRNA into cells, the subsequent protein production and the transcriptome, with single-cell resolution. Using SENT-seq, we have identified cell subtypes that exhibit particularly high or low LNP uptake as well as genes associated with those subtypes. The data suggest that cell subsets have distinct responses to LNPs that may affect mRNA therapies.},
}
@article {pmid35768041,
year = {2022},
author = {Scarpassa, VM and Batista, ET and Ferreira, VDC and Santos Neto, VAD and Roque, RA and Tadei, WP and Ferreira, FADS and Costa, FMD},
title = {DNA barcoding suggests new species for the Mansonia subgenus (Mansonia, Mansoniini, Culicidae, Diptera) in the area surrounding the Jirau hydroelectric dam, Porto Velho municipality, Rondônia state, Brazil.},
journal = {Acta tropica},
volume = {233},
number = {},
pages = {106574},
doi = {10.1016/j.actatropica.2022.106574},
pmid = {35768041},
issn = {1873-6254},
mesh = {Animals ; Bayes Theorem ; Brazil ; *Culicidae ; DNA ; DNA Barcoding, Taxonomic ; *Malvaceae ; },
abstract = {Previous studies have linked the construction of hydroelectric dams with increases in the density of mosquitoes, especially Mansonia. In Brazil, Mansonia mosquitoes are still poorly studied at the taxonomic, biological, ecological and epidemiological levels, and nothing is known about the genetic diversity and the cryptic speciation of the group. The current study analyzed the molecular taxonomy of Mansonia species captured in the area surrounding the Jirau hydroelectric dam, Rondônia state, Brazil. Samples were collected from fifteen locations between 2018 and 2019. Genomic DNA of the specimens was extracted, and the DNA barcode region of the Cytochrome Oxidase, subunit I gene was amplified with PCR and both DNA strands were sequenced. The dataset was analyzed using MEGA, Mr. Bayes and DnaSP software. The results provided COI sequences for 100 specimens collected in the area surrounding from Jirau hydroelectric dam. These belonged to five species of the Mansonia subgenus, identified morphologically as Mansonia humeralis, Mansonia amazonensis, Mansonia titillans, Mansonia dyari and Mansonia indubitans. Findings showed that the COI gene is an effective and accessible DNA barcode that provides a high-resolution tool for delimiting species within the subgenus Mansonia, with the tree construction (Bayesian Inference) well supported and non-overlapping intraspecific and interspecific (K2-P) genetic distance values. These findings also indicate the occurrence of cryptic speciation within M. dyari and near of M. titillans. This is the first study to apply molecular tools to the taxonomy of Mansonia species from Brazil.},
}
@article {pmid35766443,
year = {2022},
author = {Li, Y and Molyneaux, N and Zhang, H and Zhou, G and Kerr, C and Adams, MD and Berkner, KL and Runge, KW},
title = {A multiplexed, three-dimensional pooling and next-generation sequencing strategy for creating barcoded mutant arrays: construction of a Schizosaccharomyces pombe transposon insertion library.},
journal = {Nucleic acids research},
volume = {50},
number = {17},
pages = {e102},
pmid = {35766443},
issn = {1362-4962},
support = {R01 AG019960/AG/NIA NIH HHS/United States ; R01 AG051601/AG/NIA NIH HHS/United States ; P30 CA043703/CA/NCI NIH HHS/United States ; R01 HL081093/HL/NHLBI NIH HHS/United States ; R01 HL055666/HL/NHLBI NIH HHS/United States ; R01 HL152678/HL/NHLBI NIH HHS/United States ; },
mesh = {DNA ; DNA Transposable Elements/genetics ; Gene Library ; Genes, Essential ; High-Throughput Nucleotide Sequencing/methods ; Mutagenesis, Insertional ; RNA, Untranslated ; Saccharomyces cerevisiae/genetics ; *Schizosaccharomyces/genetics ; Untranslated Regions ; },
abstract = {Arrayed libraries of defined mutants have been used to elucidate gene function in the post-genomic era. Yeast haploid gene deletion libraries have pioneered this effort, but are costly to construct, do not reveal phenotypes that may occur with partial gene function and lack essential genes required for growth. We therefore devised an efficient method to construct a library of barcoded insertion mutants with a wider range of phenotypes that can be generalized to other organisms or collections of DNA samples. We developed a novel but simple three-dimensional pooling and multiplexed sequencing approach that leveraged sequence information to reduce the number of required sequencing reactions by orders of magnitude, and were able to identify the barcode sequences and DNA insertion sites of 4391 Schizosaccharomyces pombe insertion mutations with only 40 sequencing preparations. The insertion mutations are in the genes and untranslated regions of nonessential, essential and noncoding RNA genes, and produced a wider range of phenotypes compared to the cognate deletion mutants, including novel phenotypes. This mutant library represents both a proof of principle for an efficient method to produce novel mutant libraries and a valuable resource for the S. pombe research community.},
}
@article {pmid35765158,
year = {2022},
author = {Suzuki, IK},
title = {Evolutionary innovations of human cerebral cortex viewed through the lens of high-throughput sequencing.},
journal = {Developmental neurobiology},
volume = {82},
number = {6},
pages = {476-494},
doi = {10.1002/dneu.22893},
pmid = {35765158},
issn = {1932-846X},
mesh = {Animals ; Brain ; *Cerebral Cortex ; *High-Throughput Nucleotide Sequencing ; Humans ; },
abstract = {Humans had acquired a tremendously enlarged cerebral cortex containing a huge quantity and variety of cells during evolution. Such evolutionary uniqueness offers a neural basis of our cognitive innovation and human-specific features of neurodevelopmental and psychiatric disorders. Since human brain is hardly examined in vivo with experimental approaches commonly applied on animal models, the recent advancement of sequencing technologies offers an indispensable viewpoint of human brain anatomy and development. This review introduces the recent findings on the unique features in the adult and the characteristic developmental processes of the human cerebral cortex, based on high-throughput DNA sequencing technologies.},
}
@article {pmid35763198,
year = {2022},
author = {Devi, ML and Thorat, SS and Devi, KK and Sharma, KC and Singh, YD and Mishra, A and Das, S},
title = {Internal Transcribed Spacer (ITS) Region of Nuclear Ribosomal DNA as a Suitable DNA Barcode for Identification of Zanthoxylum armatum DC. from Manipur.},
journal = {Molecular biotechnology},
volume = {64},
number = {12},
pages = {1454-1467},
pmid = {35763198},
issn = {1559-0305},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; DNA, Ribosomal ; DNA, Ribosomal Spacer/genetics ; India ; Phylogeny ; *Zanthoxylum/genetics ; },
abstract = {Zanthoxylum armatum DC. is a plant with many medicinal values which is extensively used in traditional system of medicine for curing various diseases and ailments, including cancer. The aim of the present study is to identify Zanthoxylum armatum collected from different parts of Manipur, India, at molecular level. Molecular markers like internal transcribed spacer (ITS) region and other DNA barcoding genes such as matK, rbcL, psbA-trnH and trnL-trnF were targeted to find out the most suitable DNA barcode for identifying this species. Sequences obtained using the five primer pairs-ITS An5 and ITS An4, matK-413f-1 and matK-1227r-1, rbcL-1F and rbcL-724R, psbA-F and trnH-R and trnL-F and trnF-R were submitted to GenBank, NCBI. Amongst the five DNA barcoding targets, one nuclear and four chloroplast genes were successfully amplified by PCR (100%) and sequencing (100%) in all the eight plant samples. Sequence similarity of total ITS region (620 bp) when compared to the reference sequence were found to be between 98.55 and 99.68%. In our study, ITS sequence in combination with DNA barcoding sequences of rbcL, trnH-psbA and trnL-trnF was very successful in identification of Z. armatum and differentiate other species clearly in the phylogeny analysis. Our work shows ITS region to be the most suitable DNA barcode which formed a monophyletic group of the species in the phylogenetic tree analysis. The sequences of the barcoding genes of Z. armatum DC. obtained from this study adds to the already available resources which will be helpful in the future research endeavours.},
}
@article {pmid35762844,
year = {2022},
author = {Zhang, YM and Sheikh, SI and Ward, AKG and Forbes, AA and Prior, KM and Stone, GN and Gates, MW and Egan, SP and Zhang, L and Davis, C and Weinersmith, KL and Melika, G and Lucky, A},
title = {Delimiting the cryptic diversity and host preferences of Sycophila parasitoid wasps associated with oak galls using phylogenomic data.},
journal = {Molecular ecology},
volume = {31},
number = {16},
pages = {4417-4433},
doi = {10.1111/mec.16582},
pmid = {35762844},
issn = {1365-294X},
mesh = {Animals ; Phenotype ; Phylogeny ; Plants ; *Quercus/genetics ; *Wasps/genetics ; },
abstract = {Cryptic species diversity is a major challenge regarding the species-rich community of parasitoids attacking oak gall wasps due to a high degree of sexual dimorphism, morphological plasticity, small size and poorly known biology. As such, we know very little about the number of species present, nor the evolutionary forces responsible for generating this diversity. One hypothesis is that trait diversity in the gall wasps, including the morphology of the galls they induce, has evolved in response to selection imposed by the parasitoid community, with reciprocal selection driving diversification of the parasitoids. Using a rare, continental-scale data set of Sycophila parasitoid wasps reared from 44 species of cynipid galls from 18 species of oak across the USA, we combined mitochondrial DNA barcodes, ultraconserved elements (UCEs), morphological and natural history data to delimit putative species. Using these results, we generate the first large-scale assessment of ecological specialization and host association in this species-rich group, with implications for evolutionary ecology and biocontrol. We find most Sycophila target specific subsets of available cynipid host galls with similar morphologies, and generally attack larger galls. Our results suggest that parasitoid wasps such as Sycophila have adaptations allowing them to exploit particular host trait combinations, while hosts with contrasting traits are resistant to attack. These findings support the tritrophic niche concept for the structuring of plant-herbivore-parasitoid communities.},
}
@article {pmid35762356,
year = {2022},
author = {Zhu, H and Galdos, FX and Lee, D and Waliany, S and Huang, YV and Ryan, J and Dang, K and Neal, JW and Wakelee, HA and Reddy, SA and Srinivas, S and Lin, LL and Witteles, RM and Maecker, HT and Davis, MM and Nguyen, PK and Wu, SM},
title = {Identification of Pathogenic Immune Cell Subsets Associated With Checkpoint Inhibitor-Induced Myocarditis.},
journal = {Circulation},
volume = {146},
number = {4},
pages = {316-335},
pmid = {35762356},
issn = {1524-4539},
support = {DP1 LM012179/LM/NLM NIH HHS/United States ; F32 HL149188/HL/NHLBI NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; K08 HL161405/HL/NHLBI NIH HHS/United States ; RM1 GM131981/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Antineoplastic Agents/adverse effects ; *Antineoplastic Agents, Immunological/adverse effects ; Epitopes/adverse effects ; Humans ; Leukocytes, Mononuclear/metabolism ; Longitudinal Studies ; Mice ; *Myocarditis/metabolism ; },
abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) are monoclonal antibodies used to activate the immune system against tumor cells. Despite therapeutic benefits, ICIs have the potential to cause immune-related adverse events such as myocarditis, a rare but serious side effect with up to 50% mortality in affected patients. Histologically, patients with ICI myocarditis have lymphocytic infiltrates in the heart, implicating T cell-mediated mechanisms. However, the precise pathological immune subsets and molecular changes in ICI myocarditis are unknown.<br><br>METHODS: To identify immune subset(s) associated with ICI myocarditis, we performed time-of-flight mass cytometry on peripheral blood mononuclear cells from 52 individuals: 29 patients with autoimmune adverse events (immune-related adverse events) on ICI, including 8 patients with ICI myocarditis, and 23 healthy control subjects. We also used multiomics single-cell technology to immunophenotype 30 patients/control subjects using single-cell RNA sequencing, single-cell T-cell receptor sequencing, and cellular indexing of transcriptomes and epitopes by sequencing with feature barcoding for surface marker expression confirmation. To correlate between the blood and the heart, we performed single-cell RNA sequencing/T-cell receptor sequencing/cellular indexing of transcriptomes and epitopes by sequencing on MRL/Pdcd1[-/-] (Murphy Roths large/programmed death-1-deficient) mice with spontaneous myocarditis.<br><br>RESULTS: Using these complementary approaches, we found an expansion of cytotoxic CD8[+] T effector cells re-expressing CD45RA (Temra CD8[+] cells) in patients with ICI myocarditis compared with control subjects. T-cell receptor sequencing demonstrated that these CD8[+] Temra cells were clonally expanded in patients with myocarditis compared with control subjects. Transcriptomic analysis of these Temra CD8[+] clones confirmed a highly activated and cytotoxic phenotype. Longitudinal study demonstrated progression of these Temra CD8[+] cells into an exhausted phenotype 2 months after treatment with glucocorticoids. Differential expression analysis demonstrated elevated expression levels of proinflammatory chemokines (CCL5/CCL4/CCL4L2) in the clonally expanded Temra CD8[+] cells, and ligand receptor analysis demonstrated their interactions with innate immune cells, including monocytes/macrophages, dendritic cells, and neutrophils, as well as the absence of key anti-inflammatory signals. To complement the human study, we performed single-cell RNA sequencing/T-cell receptor sequencing/cellular indexing of transcriptomes and epitopes by sequencing in Pdcd1[-/-] mice with spontaneous myocarditis and found analogous expansions of cytotoxic clonal effector CD8[+] cells in both blood and hearts of such mice compared with controls.<br><br>CONCLUSIONS: Clonal cytotoxic Temra CD8[+] cells are significantly increased in the blood of patients with ICI myocarditis, corresponding to an analogous increase in effector cytotoxic CD8[+] cells in the blood/hearts of Pdcd1[-/-] mice with myocarditis. These expanded effector CD8[+] cells have unique transcriptional changes, including upregulation of chemokines CCL5/CCL4/CCL4L2, which may serve as attractive diagnostic/therapeutic targets for reducing life-threatening cardiac immune-related adverse events in ICI-treated patients with cancer.},
}
@article {pmid35757869,
year = {2022},
author = {Li, TC and Miao, YH and Wang, T and Zu, GH and Huang, DW and Xiao, JH},
title = {Impact of mitotype diversity on metabarcoding biodiversity estimations in Insecta and Arachnida using different sample preparation strategies.},
journal = {Molecular ecology resources},
volume = {22},
number = {8},
pages = {2967-2980},
doi = {10.1111/1755-0998.13678},
pmid = {35757869},
issn = {1755-0998},
support = {91822294//"the Fundamental Research Funds for the Central Universities", Nankai University/ ; 96172158//"the Fundamental Research Funds for the Central Universities", Nankai University/ ; 96173250//"the Fundamental Research Funds for the Central Universities", Nankai University/ ; 31830084//National Natural Science Foundation of China/ ; 31970440//National Natural Science Foundation of China/ ; 32070466//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Arachnida ; Biodiversity ; *DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/genetics ; Insecta/genetics ; },
abstract = {DNA barcoding and metabarcoding have been increasingly used in species delimitation and species diversity assessment, respectively, and the molecular markers used in animals are mainly derived from mitochondrial DNA. It is well known that the phenomenon of multiple mitochondrial haplotypes within the same specimen (hereafter referred to as "mitotype diversity") may have a negative impact on the proper assessment of biodiversity by metabarcoding. However, few studies have focused on the incidence of this phenomenon and its effects on metabarcoding results using different sample preparation strategies, such as mock community construction using pooled high-throughput sequencing (HTS) data, DNA-pooling and Tissue-pooling. In this study, we investigated mitotype diversity and its influence on metabarcoding based on 398 specimens from 66 species of Insecta and 82 specimens from 16 species of Arachnida by HTS of the mitochondrial cox1 gene fragment. The results revealed that mitotype diversity was common in the studied taxa and significantly increased the number of operational taxonomic units (OTUs) using the three sample preparation strategies. The results also showed that the bioinformatics pipeline based on authentic amplicon sequence variants was more reliable than the pipeline based on OTUs. Regarding the sample preparation strategies of DNA-pooling and Tissue-pooling commonly used in metabarcoding, our results revealed that their results of metabarcoding were quite similar, and the Tissue-pooling strategy was therefore preferred because of its simplicity. Our study calls for additional attention to the interference of mitotype diversity on the results of DNA metabarcoding in biodiversity assessment.},
}
@article {pmid35755251,
year = {2022},
author = {Potowski, M and Kunig, VBK and Eberlein, L and Škopić, MK and Vakalopoulos, A and Kast, SM and Brunschweiger, A},
title = {Investigations Into Chemically Stabilized Four-Letter DNA for DNA-Encoded Chemistry.},
journal = {Frontiers in chemistry},
volume = {10},
number = {},
pages = {894563},
pmid = {35755251},
issn = {2296-2646},
abstract = {DNA-encoded libraries are a prime technology for target-based small molecule screening. Native DNA used as genetic compound barcode is chemically vulnerable under many reaction conditions. DNA barcodes that are composed of pyrimidine nucleobases, 7-deazaadenine, and 7-deaza-8-azaguanine have been investigated for their suitability for encoded chemistry both experimentally and computationally. These four-letter barcodes were readily ligated by T4 ligation, amplifiable by Taq polymerase, and the resultant amplicons were correctly sequenced. Chemical stability profiling showed a superior chemical stability compared to native DNA, though higher susceptibility to depurination than a three-letter code based on pyrimidine DNA and 7-deazaadenine.},
}
@article {pmid35754509,
year = {2022},
author = {Ibrahim, IS and Mohd Said, M and Mohammad Zainoor, N and Jamal, JA},
title = {Authentication of Marantodes pumilum (Blume) Kuntze: A Systematic Review.},
journal = {Frontiers in pharmacology},
volume = {13},
number = {},
pages = {855384},
pmid = {35754509},
issn = {1663-9812},
abstract = {Botanical drug products consist of complex phytochemical constituents that vary based on various factors that substantially produce different pharmacological activities and possible side effects. Marantodes pumilum (Blume) Kuntze (Primulaceae) is one of the most popular Malay traditional botanical drugs and widely recognized for its medicinal use. Many studies have been conducted focusing on the identification of bioactive substances, pharmacological and toxicological activities in its specific varieties but less comprehensive study on M. pumilum authentication. Lack of quality control (QC) measurement assessment may cause different quality issues on M. pumilum containing products like adulteration by pharmaceutical substances, substitution, contamination, misidentification with toxic plant species, which may be detrimental to consumers' health and safety. This systematic literature review aims to provide an overview of the current scenario on the quality control of botanical drug products as determined by pharmacopoeia requirements specifically for M. pumilum authentication or identification. A systematic search for peer-reviewed publications to document literature search for M. pumilum authentication was performed using four electronic databases: Web of Science, PubMed, Scopus and ScienceDirect for related studies from January 2010 to December 2021. The research studies published in English and related articles for identification or authentication of M. pumilum were the main inclusion criteria in this review. A total 122 articles were identified, whereby 33 articles met the inclusion criteria. Macroscopy, microscopy, chemical fingerprinting techniques using chromatography, spectroscopy and hyphenated techniques, and genetic-based fingerprinting using DNA barcoding method have been used to identify M. pumilum and to distinguish between different varieties and plant parts. The study concluded that a combination of approaches is necessary for authenticating botanical drug substances and products containing M. pumilum to assure the quality, safety, and efficacy of marketed botanical drug products, particularly those with therapeutic claims.},
}
@article {pmid35754060,
year = {2022},
author = {Simonson, PD and Valencia, I and Patel, SS},
title = {Tyramide-conjugated DNA barcodes enable signal amplification for multiparametric CODEX imaging.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {627},
pmid = {35754060},
issn = {2399-3642},
mesh = {*Antibodies/metabolism ; Antigens ; DNA ; *DNA Barcoding, Taxonomic ; Staining and Labeling ; },
abstract = {Multiparametric imaging allows researchers to measure the expression of many biomarkers simultaneously, allowing detailed characterization of cell microenvironments. One such technique, CODEX, allows fluorescence imaging of >30 proteins in a single tissue section. In the commercial CODEX system, primary antibodies are conjugated to DNA barcodes. This modification can result in antibody dysfunction, and development of a custom antibody panel can be very costly and time consuming as trial and error of modified antibodies proceeds. To address these challenges, we developed novel tyramide-conjugated DNA barcodes that can be used with primary antibodies via peroxidase-conjugated secondary antibodies. This approach results in signal amplification and imaging without the need to conjugate primary antibodies. When combined with commercially available barcode-conjugated primary antibodies, we can very quickly develop working antibody panels. We also present methods to perform antibody staining using a commercially available automated tissue stainer and in situ hybridization imaging on a CODEX platform. Future work will include application of the combined tyramide-based and regular CODEX approach to image specific tumors with their immune cell infiltrates, including biomarkers that are currently difficult to image by regular CODEX.},
}
@article {pmid35753209,
year = {2022},
author = {Shang, F and Rodewald, HR},
title = {Toward the dissection of hematopoietic stem cell fates and their determinants.},
journal = {Current opinion in genetics &amp; development},
volume = {75},
number = {},
pages = {101945},
doi = {10.1016/j.gde.2022.101945},
pmid = {35753209},
issn = {1879-0380},
mesh = {Cell Differentiation/genetics ; Cell Lineage/genetics ; *Hematopoiesis/genetics ; *Hematopoietic Stem Cells ; },
abstract = {Hematopoietic stem cell (HSC) functions have long been difficult to study under physiological conditions. Recently, genetic in vivo approaches have been developed for lineage tracing of differentiating progeny emerging from HSC over time (output), and for high-resolution, endogenous barcoding to uncover the lineages that HSC contribute to (fate). Such fate measurements have in principle led to the recognition of three major fate groups of HSC: multilineage, myelo-erythroid-restricted, and inactive, that is, no or no known progeny, in addition to a minor group of megakaryocyte-restricted HSC. The most recent RNA-barcoding experiments have begun to directly link fate measurements with transcriptome reading in HSC clones and single HSC, which yielded insights into transcriptional signatures associated with fate patterns. Here, we discuss these findings in light of the structure of the hematopoietic differentiation hierarchy, and we provide an outlook on strategies to dissect molecular determinants of HSC fates.},
}
@article {pmid35752172,
year = {2022},
author = {Hughes, NW and Qu, Y and Zhang, J and Tang, W and Pierce, J and Wang, C and Agrawal, A and Morri, M and Neff, N and Winslow, MM and Wang, M and Cong, L},
title = {Machine-learning-optimized Cas12a barcoding enables the recovery of single-cell lineages and transcriptional profiles.},
journal = {Molecular cell},
volume = {82},
number = {16},
pages = {3103-3118.e8},
pmid = {35752172},
issn = {1097-4164},
support = {R01 CA231253/CA/NCI NIH HHS/United States ; R01 GM141627/GM/NIGMS NIH HHS/United States ; R35 HG011316/HG/NHGRI NIH HHS/United States ; S10 OD023452/OD/NIH HHS/United States ; },
mesh = {*CRISPR-Cas Systems ; Cell Lineage/genetics ; *DNA Barcoding, Taxonomic/methods ; Humans ; Machine Learning ; Phylogeny ; },
abstract = {The development of CRISPR-based barcoding methods creates an exciting opportunity to understand cellular phylogenies. We present a compact, tunable, high-capacity Cas12a barcoding system called dual acting inverted site array (DAISY). We combined high-throughput screening and machine learning to predict and optimize the 60-bp DAISY barcode sequences. After optimization, top-performing barcodes had ∼10-fold increased capacity relative to the best random-screened designs and performed reliably across diverse cell types. DAISY barcode arrays generated ∼12 bits of entropy and ∼66,000 unique barcodes. Thus, DAISY barcodes-at a fraction of the size of Cas9 barcodes-achieved high-capacity barcoding. We coupled DAISY barcoding with single-cell RNA-seq to recover lineages and gene expression profiles from ∼47,000 human melanoma cells. A single DAISY barcode recovered up to ∼700 lineages from one parental cell. This analysis revealed heritable single-cell gene expression and potential epigenetic modulation of memory gene transcription. Overall, Cas12a DAISY barcoding is an efficient tool for investigating cell-state dynamics.},
}
@article {pmid35751818,
year = {2022},
author = {Sater, V and Viailly, PJ and Lecroq, T and Prieur-Gaston, &#xc9; and Bohers, &#xc9; and Viennot, M and Ruminy, P and Dauchel, H and Vera, P and Jardin, F},
title = {UMI-Varcal: A Low-Frequency Variant Caller for UMI-Tagged Paired-End Sequencing Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2493},
number = {},
pages = {235-245},
pmid = {35751818},
issn = {1940-6029},
mesh = {Artifacts ; Computational Biology ; DNA/genetics ; *DNA Copy Number Variations ; *High-Throughput Nucleotide Sequencing/methods ; },
abstract = {The rapid transition from traditional sequencing methods to Next-Generation Sequencing (NGS) has allowed for a faster and more accurate detection of somatic variants (Single-Nucleotide Variant (SNV) and Copy Number Variation (CNV)) in tumor cells. NGS technologies require a succession of steps during which false variants can be silently added at low frequencies. Filtering these artifacts can be a rather difficult task especially when the experiments are designed to look for very low frequency variants. Recently, adding unique molecular barcodes called UMI (Unique Molecular Identifier) to the DNA fragments appears to be a very effective strategy to specifically filter out false variants from the variant calling results (Kukita et al. DNA Res 22(4):269-277, 2015; Newman et al. Nat Biotechnol 34(5):547-555, 2016; Schmitt et al. Proc Natl Acad Sci U S A 109(36):14508-14513). Here, we describe UMI-VarCal (Sater et al. Bioinformatics 36:2718-2724, 2020), which can use the UMI information from UMI-tagged reads to offer a faster and more accurate variant calling analysis.},
}
@article {pmid35751212,
year = {2022},
author = {Zhang, W and Sheng, W and Zhang, H and Jin, Z and Zhang, B and Huang, N and Wang, S},
title = {Freeze-synthesized bio-barcode immunoprobe based multiplex fluorescence immunosensor for simultaneous determination of four nitrofuran metabolites.},
journal = {Food chemistry},
volume = {393},
number = {},
pages = {133424},
doi = {10.1016/j.foodchem.2022.133424},
pmid = {35751212},
issn = {1873-7072},
mesh = {*Biosensing Techniques ; Chromatography, Liquid ; Gold ; Immunoassay ; *Metal Nanoparticles ; *Nitrofurans/metabolism ; Tandem Mass Spectrometry ; },
abstract = {Here we have reported a simple and sensitive bio-barcode immunosensor for simultaneous detection of 3-amino-2-oxazolidinone (AOZ), 3-amino-5-morpholinomethyl-2-oxazolidinone (AMOZ), 1-aminohydantoin (AHD), and semicarbazide (SEM) in aquatic products. According to freeze-thaw strategy, four fluorophores (FAM, HEX, ROX, Cy5) labeled single-stranded DNA (ssDNA) were conjugated onto the surface of gold nanoparticles (AuNPs) with corresponding four nitrofuran metabolites monoclonal antibodies (mAbs) for forming four bio-barcode fluorescence immunoprobes. The fluorescence of immunoprobes was quenched by AuNPs. In test progress, the ssDNA with fluorophores were released by adding the dithiothreitol (DTT) and the fluorescence recovered. The immunosensor exhibited sensitive and specific detection of nitrofuran metabolites from 0.05 to 28 μg/L. The limit of detection (LOD) was 0.01, 0.02, 0.02, and 0.05 μg/L for AOZ, AMOZ, AHD, and SEM, respectively. The recoveries of four nitrofuran metabolites in spiked aquatic products have been confirmed by UPLC-MS/MS. The bio-barcode based multiplex immunosensor provides a promising strategy for simultaneous detection of multiple targets.},
}
@article {pmid35750774,
year = {2022},
author = {Basset, Y and Hajibabaei, M and Wright, MTG and Castillo, AM and Donoso, DA and Segar, ST and Souto-Vilarós, D and Soliman, DY and Roslin, T and Smith, MA and Lamarre, GPA and De León, LF and Decaëns, T and Palacios-Vargas, JG and Castaño-Meneses, G and Scheffrahn, RH and Rivera, M and Perez, F and Bobadilla, R and Lopez, Y and Ramirez Silva, JA and Cruz, MM and Galván, AA and Barrios, H},
title = {Comparison of traditional and DNA metabarcoding samples for monitoring tropical soil arthropods (Formicidae, Collembola and Isoptera).},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {10762},
pmid = {35750774},
issn = {2045-2322},
support = {669609/ERC_/European Research Council/International ; },
mesh = {Animals ; *Ants/genetics ; *Arthropods/genetics ; Biodiversity ; DNA/genetics ; DNA Barcoding, Taxonomic/methods ; *Isoptera/genetics ; Soil ; },
abstract = {The soil fauna of the tropics remains one of the least known components of the biosphere. Long-term monitoring of this fauna is hampered by the lack of taxonomic expertise and funding. These obstacles may potentially be lifted with DNA metabarcoding. To validate this approach, we studied the ants, springtails and termites of 100 paired soil samples from Barro Colorado Island, Panama. The fauna was extracted with Berlese-Tullgren funnels and then either sorted with traditional taxonomy and known, individual DNA barcodes ("traditional samples") or processed with metabarcoding ("metabarcoding samples"). We detected 49 ant, 37 springtail and 34 termite species with 3.46 million reads of the COI gene, at a mean sequence length of 233 bp. Traditional identification yielded 80, 111 and 15 species of ants, springtails and termites, respectively; 98%, 37% and 100% of these species had a Barcode Index Number (BIN) allowing for direct comparison with metabarcoding. Ants were best surveyed through traditional methods, termites were better detected by metabarcoding, and springtails were equally well detected by both techniques. Species richness was underestimated, and faunal composition was different in metabarcoding samples, mostly because 37% of ant species were not detected. The prevalence of species in metabarcoding samples increased with their abundance in traditional samples, and seasonal shifts in species prevalence and faunal composition were similar between traditional and metabarcoding samples. Probable false positive and negative species records were reasonably low (13-18% of common species). We conclude that metabarcoding of samples extracted with Berlese-Tullgren funnels appear suitable for the long-term monitoring of termites and springtails in tropical rainforests. For ants, metabarcoding schemes should be complemented by additional samples of alates from Malaise or light traps.},
}
@article {pmid35747387,
year = {2022},
author = {Ebrahimi, G and Orabi, B and Robinson, M and Chauve, C and Flannigan, R and Hach, F},
title = {Fast and accurate matching of cellular barcodes across short-reads and long-reads of single-cell RNA-seq experiments.},
journal = {iScience},
volume = {25},
number = {7},
pages = {104530},
pmid = {35747387},
issn = {2589-0042},
abstract = {Single-cell RNA sequencing allows for characterizing the gene expression landscape at the cell type level. However, because of its use of short-reads, it is severely limited at detecting full-length features of transcripts such as alternative splicing. New library preparation techniques attempt to extend single-cell sequencing by utilizing both long-reads and short-reads. These techniques split the library material, after it is tagged with cellular barcodes, into two pools: one for short-read sequencing and one for long-read sequencing. However, the challenge of utilizing these techniques is that they require matching the cellular barcodes sequenced by the erroneous long-reads to the cellular barcodes detected by the short-reads. To overcome this challenge, we introduce scTagger, a computational method to match cellular barcodes data from long-reads and short-reads. We tested scTagger against another state-of-the-art tool on both real and simulated datasets, and we demonstrate that scTagger has both significantly better accuracy and time efficiency.},
}
@article {pmid35741703,
year = {2022},
author = {Orlova, VF and Solovyeva, EN and Dunayev, EA and Ananjeva, NB},
title = {Integrative Taxonomy within Eremias multiocellata Complex (Sauria, Lacertidae) from the Western Part of Range: Evidence from Historical DNA.},
journal = {Genes},
volume = {13},
number = {6},
pages = {},
pmid = {35741703},
issn = {2073-4425},
mesh = {Animals ; DNA, Mitochondrial/genetics ; *Lizards/genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The Kokshaal racerunner, Eremias kokshaaliensis Eremchenko et Panfilov, 1999, together with other central Asian racerunner species, is included in the Eremias multiocellata complex. In the present work, for the first time, the results of the analysis of historical mitochondrial DNA (barcode) are presented and the taxonomic status and preliminary phylogenetic relationships within the complex are specified. We present, for the first time, the results of the molecular analysis using historical DNA recovered from specimens of several species of this complex (paratypes of the Kokshaal racerunner and historical collections of the Kashgar racerunner E. buechneri from Kashgaria) using DNA barcoding.},
}
@article {pmid35741404,
year = {2022},
author = {Zohir, WF and Kapase, VU and Kumar, S},
title = {Identification and Characterization of a New Microalga Dysmorphococcus globosus-HI from the Himalayan Region as a Potential Source of Natural Astaxanthin.},
journal = {Biology},
volume = {11},
number = {6},
pages = {},
pmid = {35741404},
issn = {2079-7737},
support = {DBT/12/17//Department of Biotechnology/ ; BT/PB/Centre/03/ICGEB/2011-II//Department of Biotechnology/ ; },
abstract = {Synthesized astaxanthin (ASX), stereoisomers of 3S,3'R, 3R,3'R, and 3S,3'S, have over 95% market share and have relatively poor antioxidant and bioactivity properties, with persistent issues in terms of biological functions, health benefits, and biosafety if compared to natural ASX. Bioprospecting of new microalgal strains could be vital for a new source of powerful antioxidant (ASX). In this study, a new algal strain was isolated from the Indian foothills of the Himalayas. Its identity was discerned by morphological and DNA barcode studies. It is a unicellular spheroidal cell-shaped alga with 100-200 μm diameter. The isolate has 93.4% similarity to Dysmorphococcus globosus species based on 18S-rDNA phylogenetic analysis and named as D. globosus-HI (HI stands for Himalayan India). Its growth and major cellular components (carotenoids, carbohydrates, protein, lipids, fatty acid profile, and ASX) were optimized using the seven different culture media. The highest biomass (1.14 g L[-1]) was observed in the MBBM medium, with a specific growth rate (0.087 day[-1]), division/day (0.125), and cellular yield (6.16 x 10[6] cells/mL). The highest carotenoids (1.56 mg g[-1]), lipids (32.5 mg L[-1]), and carbohydrates (135.62 mg L[-1]) were recorded in the 3N-BBM medium. The maximum ω3-FAs (17.78%), ω6-FAs (23.11%), and ω9-FAs (7.06%) were observed in MBBM, JW, and BG-11 medium respectively. The highest amount of antioxidant ASX was accumulated in the 3N-BBM medium (391 mg L[-1]). It is more than any other known algal species used in the production of natural ASX. The optimized biochemical studies on the D. globosus-HI strain should fulfill the increasing demand for natural ASX for commercial application.},
}
@article {pmid35739482,
year = {2022},
author = {Costa, D and Tavares, RM and Baptista, P and Lino-Neto, T},
title = {The influence of bioclimate on soil microbial communities of cork oak.},
journal = {BMC microbiology},
volume = {22},
number = {1},
pages = {163},
pmid = {35739482},
issn = {1471-2180},
mesh = {Bacteria/genetics ; Forests ; Fungi/genetics ; *Microbiota ; *Quercus/microbiology ; Soil ; Soil Microbiology ; },
abstract = {BACKGROUND: Soil microbiomes are important to maintain soil processes in forests and confer protection to plants against abiotic and biotic stresses. These microbiomes can be affected by environmental changes. In this work, soil microbial communities from different cork oak Portuguese forests under different edaphoclimatic conditions were described by using a metabarcoding strategy targeting ITS2 and 16S barcodes.<br><br>RESULTS: A total of 11,974 fungal and 12,010 bacterial amplicon sequence variants (ASVs) were obtained, revealing rich and diverse microbial communities associated with different cork oak forests. Bioclimate was described as the major factor influencing variability in these communities (or bioclimates/cork oak forest for fungal community), followed by boron and granulometry. Also, pH explained variation of fungal communities, while C:N ratio contributed to bacterial variation. Fungal and bacterial biomarker genera for specific bioclimates were described. Their co-occurrence network revealed the existence of a complex and delicate balance among microbial communities.<br><br>CONCLUSIONS: The findings revealed that bacterial communities are more likely to be affected by different edaphoclimatic conditions than fungal communities, also predicting a higher impact of climate change on bacterial communities. The integration of cork oak fungal and bacterial microbiota under different bioclimates could be further explored to provide information about useful interactions for increasing cork oak forest sustainability in a world subject to climate changes.},
}
@article {pmid35738448,
year = {2022},
author = {Chen, C and Xia, X and Peng, J and Wang, D},
title = {Comparative analyses of six complete chloroplast genomes from the genus Cupressus and Juniperus (Cupressaceae).},
journal = {Gene},
volume = {837},
number = {},
pages = {146696},
doi = {10.1016/j.gene.2022.146696},
pmid = {35738448},
issn = {1879-0038},
mesh = {*Cupressaceae/genetics ; *Cupressus/genetics ; *Genome, Chloroplast ; *Juniperus/genetics ; Phylogeny ; },
abstract = {Cupressaceae is a conifer family distributed around the world. Cupressus and Juniperus are the main genera of the Cupressaceae family and have important medicinal value. This leads to confusion between Cupressus and Juniperus due to similar morphologies. Here, the complete cp genomes of two Cupressus (C. duclouxiana and C. funebri) and four Juniperus (J. chinensis, J. gaussenii J. pingii and J. procumbens) were sequenced. The results revealed that the length of the cp genomes ranged from 126,996 bp to 129,959 bp, with 119 genes comprising 82 protein-coding genes, 33 transfer RNAs and 4 ribosomal RNAs. All chloroplast genomes of Cupressus and Juniperus lost whole IR regions, which is consistent with gymnosperm cp genome studies. In addition, the number of SSRs per species ranged from 54 to 73 and was dominated by mononucleotide repeats. In the six cp genomes of Cupressus and Juniperus, five highly divergent regions, including accD, accD-rpl2, ycf1, ycf2 and rrn23-rrn4.5, can be used as DNA barcodes of interspecific relationships and potential genetic markers. We compared the gene selection pressures (C. chengiana as reference species), and 6 genes underwent positive selection, the majority of which were related to photosynthesis. Phylogenetic results showed that the monophyly of Cupressus and Juniperus supported most bootstrap support. Cupressus funebris and J. chinensis were resolved to be early diverging species within Cupressus and Juniperus, and the two genera were sister groups to each other. This research revealed a new understanding of the structural pluralism and phylogenetic relationships of Cupressaceae cp genomes. These results will facilitate comprehension of the complexity and diversity of conifer cp genomes.},
}
@article {pmid35736427,
year = {2022},
author = {Lv, B and Xu, R and Xing, X and Liao, C and Zhang, Z and Zhang, P and Xu, F},
title = {Discovery of Synergistic Drug Combinations for Colorectal Cancer Driven by Tumor Barcode Derived from Metabolomics "Big Data".},
journal = {Metabolites},
volume = {12},
number = {6},
pages = {},
pmid = {35736427},
issn = {2218-1989},
support = {82073812//National Natural Science Foundation of China/ ; 82104117//National Natural Science Foundation of China/ ; BK20210427//Natural Science Foundation of Jiangsu Province/ ; 2017ZX09101001//National Science and Technology Major Project/ ; 2632021PY03//Fundamental Research Funds for the Central Universities/ ; DQCP20/21PQ08//Open Project Program of MOE Key Laboratory of Drug Quality Control and Pharmacovigilance/ ; },
abstract = {The accumulation of cancer metabolomics data in the past decade provides exceptional opportunities for deeper investigations into cancer metabolism. However, integrating a large amount of heterogeneous metabolomics data to draw a full picture of the metabolic reprogramming and to discover oncometabolites of certain cancers remains challenging. In this study, a tumor barcode constructed based upon existing metabolomics "big data" using the Bayesian vote-counting method is proposed to identify oncometabolites in colorectal cancer (CRC). Specifically, a panel of oncometabolites of CRC was generated from 39 clinical studies with 3202 blood samples (1332 CRC vs. 1870 controls) and 990 tissue samples (495 CRC vs. 495 controls). Next, an oncometabolite-protein network was constructed by combining the tumor barcode and its involved proteins/enzymes. The effect of anti-cancer drugs or drug combinations was then mapped into this network by the random walk with restart process. Utilizing this network, potential Irinotecan (CPT-11)-sensitizing agents for CRC treatment were discovered by random forest and Xgboost. Finally, a compound named MK-2206 was highlighted and its synergy with CPT-11 was validated on two CRC cell lines. To summarize, we demonstrate in the present study that the metabolomics "big data"-based tumor barcodes and the subsequent network analyses are potentially useful for drug combination discovery or drug repositioning.},
}
@article {pmid35735898,
year = {2022},
author = {Polaszek, A and Fusu, L and Viggiani, G and Hall, A and Hanson, P and Polilov, AA},
title = {Revision of the World Species of Megaphragma Timberlake (Hymenoptera: Trichogrammatidae).},
journal = {Insects},
volume = {13},
number = {6},
pages = {},
pmid = {35735898},
issn = {2075-4450},
support = {JP100330/2010//Royal Society/ ; },
abstract = {Megaphragma species are important models for basic organismal research, and many are potential biological control agents. We present the first extensive revision of species of the genus Megaphragma based on morphological and molecular data. Our revision includes all previously described species, 6 of which are synonymized, and 22 of which are described here as new. We also provide the first key to all species of the genus and reconstruct their phylogeny based on 28S and CO1 molecular markers. The following species are synonymized with M. longiciliatum Subba Rao: M. aligarhensis Yousuf and Shafee syn. nov.; M. amalphitanum Viggiani syn. nov.; M. decochaetum Lin syn. nov.; M. magniclava Yousuf and Shafee syn. nov.; M. shimalianum Hayat syn. nov.M. anomalifuniculi Yuan and Lou syn. nov. is synonymized with M. polychaetum Lin. The following species are described as new: M. antecessor Polaszek and Fusu sp. nov.; M. breviclavum Polaszek and Fusu sp. nov.; M. chienleei Polaszek and Fusu sp. nov.; M. cockerilli Polaszek and Fusu sp. nov.; M. digitatum Polaszek and Fusu sp. nov.; M. fanenitrakely Polaszek and Fusu sp. nov.; M. funiculatum Fusu, Polaszek, and Viggiani sp. nov.; M. giraulti Viggiani, Fusu, and Polaszek sp. nov.; M. hansoni Polaszek, Fusu, and Viggiani sp. nov.; M. kinuthiae Polaszek, Fusu, and Viggiani sp. nov.; M. liui Polaszek and Fusu sp. nov.; M. momookherjeeae Polaszek and Fusu sp. nov.; M. nowickii Polaszek, Fusu, and Viggiani sp. nov.; M. noyesi Polaszek and Fusu sp. nov.; M. pintoi Viggiani sp. nov.; M. polilovi Polaszek, Fusu, and Viggiani sp. nov.; M. rivelloi Viggiani sp. nov.; M. tamoi Polaszek, Fusu, and Viggiani sp. nov.; M. tridens Fusu, and Polaszek sp. nov.; M. uniclavum Polaszek and Fusu sp. nov.; M. vanlentereni Polaszek and Fusu sp. nov.; M. viggianii Fusu, Polaszek, and Polilov sp. nov.},
}
@article {pmid35734262,
year = {2022},
author = {Wei, XP and Zhang, XY and Dong, YQ and Cheng, JL and Bai, YJ and Liu, JS and Qi, YD and Zhang, BG and Liu, HT},
title = {Molecular Structure and Phylogenetic Analyses of the Complete Chloroplast Genomes of Three Medicinal Plants Conioselinum vaginatum, Ligusticum sinense, and Ligusticum jeholense.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {878263},
pmid = {35734262},
issn = {1664-462X},
abstract = {Most plants of Ligusticum have an important medicinal and economic value with a long history, Ligusticum sinense and L. jeholense ("Gaoben") has long been used in traditional Chinese medicine for the treatment of carminative, dispelling cold, dehumidification, and analgesia. While in the market Conioselinum vaginatum (Xinjiang Gaoben) is substitution for Gaoben, and occupies a higher market share. These three Gaoben-related medicinal materials are similar in morphology, and are difficult to distinguish from each other by the commonly used DNA barcodes. The chloroplast genome has been widely used for molecular markers, evolutionary biology, and barcoding identification. In this study, the complete chloroplast genome sequences of C. vaginatum, L. sinense, and L. jeholense were reported. The results showed that the complete chloroplast genomes of these three species have typical quadripartite structures, which were comprised of 148,664, 148,539, and 148,497 bp. A total of 114 genes were identified, including 81 protein-coding genes (PCGs), 29 tRNA genes, and four rRNA genes. Our study indicated that highly variable region ycf2-trnL and accD-ycf4 that can be used as specific DNA barcodes to distinguish and identify C. vaginatum, L. sinense, and L. jeholense. In addition, phylogenetic study showed that C. vaginatum nested in Ligusticum and as a sister group of L. sinense and L. jeholense, which suggested these two genera are both in need of revision. This study offer valuable information for future research in the identification of Gaoben-related medicinal materials and will benefit for further phylogenetic study of Apiaceae.},
}
@article {pmid35733091,
year = {2022},
author = {Rakesh, M and Aris-Brosou, S and Xia, X},
title = {Testing alternative hypotheses on the origin and speciation of Hawaiian katydids.},
journal = {BMC ecology and evolution},
volume = {22},
number = {1},
pages = {83},
pmid = {35733091},
issn = {2730-7182},
mesh = {Animals ; *Evolution, Molecular ; Hawaii ; *Orthoptera ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Hawaiian Islands offer a unique and dynamic evolutionary theatre for studying origin and speciation as the islands themselves sequentially formed by erupting undersea volcanos, which would subsequently become dormant and extinct. Such dynamics have not been used to resolve the controversy surrounding the origin and speciation of Hawaiian katydids in the genus Banza, whose ancestor could be from either the Old-World genera Ruspolia and Euconocephalus, or the New World Neoconocephalus. To address this question, we performed a chronophylogeographic analysis of Banza species together with close relatives from the Old and New Worlds.<br><br>RESULTS: Based on extensive dated phylogeographic analyses of two mitochondrial genes (COX1 and CYTB), we show that our data are consistent with the interpretation that extant Banza species resulted from two colonization events, both by katydids from the Old World rather than from the New World. The first event was by an ancestral lineage of Euconocephalus about 6 million years ago (mya) after the formation of Nihoa about 7.3&#xa0;mya, giving rise to B. nihoa. The second colonization event was by a sister lineage of Ruspolia dubia. The dating result suggests that this ancestral lineage first colonized an older island in the Hawaiian-Emperor seamount chain before the emergence of Hawaii Islands, but colonized Kauai after its emergence in 5.8&#xa0;mya. This second colonization gave rise to the rest of the Banza species in two major lineages, one on the older northwestern islands, and the other on the newer southwestern islands.<br><br>CONCLUSION: Chronophylogeographic analyses with well-sampled taxa proved crucial for resolving phylogeographic controversies on the origin and evolution of species colonizing a new environment.},
}
@article {pmid35729905,
year = {2022},
author = {Sun, N and Zhao, X and Yau, SS},
title = {An efficient numerical representation of genome sequence: natural vector with covariance component.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13544},
pmid = {35729905},
issn = {2167-8359},
mesh = {Humans ; Phylogeny ; Genome ; Biological Evolution ; Nucleotides/genetics ; Genomics ; *Viruses ; Bacteria/genetics ; Archaea/genetics ; *Mimiviridae/genetics ; },
abstract = {BACKGROUND: The characterization and comparison of microbial sequences, including archaea, bacteria, viruses and fungi, are very important to understand their evolutionary origin and the population relationship. Most methods are limited by the sequence length and lack of generality. The purpose of this study is to propose a general characterization method, and to study the classification and phylogeny of the existing datasets.<br><br>METHODS: We present a new alignment-free method to represent and compare biological sequences. By adding the covariance between each two nucleotides, the new 18-dimensional natural vector successfully describes 24,250 genomic sequences and 95,542 DNA barcode sequences. The new numerical representation is used to study the classification and phylogenetic relationship of microbial sequences.<br><br>RESULTS: First, the classification results validate that the six-dimensional covariance vector is necessary to characterize sequences. Then, the 18-dimensional natural vector is further used to conduct the similarity relationship between giant virus and archaea, bacteria, other viruses. The nearest distance calculation results reflect that the giant viruses are closer to bacteria in distribution of four nucleotides. The phylogenetic relationships of the three representative families, Mimiviridae, Pandoraviridae and Marsellieviridae from giant viruses are analyzed. The trees show that ten sequences of Mimiviridae are clustered with Pandoraviridae, and Mimiviridae is closer to the root of the tree than Marsellieviridae. The new developed alignment-free method can be computed very fast, which provides an effective numerical representation for the sequence of microorganisms.},
}
@article {pmid35729477,
year = {2022},
author = {Fayaz, S and Mahajan, R and Hami, A and Husaini, AM and Bhat, SA and Murtaza, I and Dhekale, B and Bhat, BA and Zargar, SM},
title = {Polyphenolics, antioxidant characterization and DNA barcoding of Kala zeera [Bunium persicum (Boiss.) Fedtsch] through multiple barcode analysis to unravel best barcode combination.},
journal = {Molecular biology reports},
volume = {49},
number = {7},
pages = {7205-7217},
pmid = {35729477},
issn = {1573-4978},
support = {DST/WOS-B/2018/832//Department of Science and Technology, Ministry of Science and Technology/ ; },
mesh = {Antioxidants ; *Apiaceae/genetics ; *DNA Barcoding, Taxonomic/methods ; DNA, Plant/genetics ; Plant Breeding ; Seeds/genetics ; },
abstract = {BACKGROUND: Kala zeera [Bunium persicum (Boiss.) Fedtsch] is one of the important spice crops of North Western Himalayas with lot of medicinal and culinary values. In spite of having great importance, this crop is under the threat of extinction due to loss of habitat and lack of awareness. The limited availability of the seeds has ultimately increased the economic value of this spice. The upmarket of Kala zeera leads to its adulteration with other black seeds and cumin seeds. The present investigation was undertaken to evaluate polyphenolics and antioxidant properties of Kala zeera genotypes collected from North Western Himalayas and to develop DNA barcodes that can ensure their purity and can also guide in conservation of selected Kala zeera germplasm lines.<br><br>METHODS AND RESULTS: Various locations of North Western Himalayas were explored for collecting 31 diverse germplasm lines of Kala zeera. The collected germplasm was maintained at our experimental stations during 2019-2020 and 2020-2021. These genotypes were evaluated for different seed traits and the methanolic extract from Kala zeera seeds was examined for total phenolic content, total flavonoid content, antioxidant activities by DPPH and FRAP. The results revealed significant variation in seed traits, polyphenolic content and antioxidant properties. 100 seed weight ranged from 0.05 to 0.35&#xa0;g, TPC ranged from 7.5 to 22.56&#xa0;mg/g, TFC ranged from 0.58 to 4.15&#xa0;mg/g, antioxidant properties DPPH ranged from 168 to 624.4&#xa0;&#x3bc;g/ml and FRAP ranged from 0.72 to 6.91&#xa0;mg/g. Further, three different barcodes (ITS, rbcL and psbA-trnH) were used to reveal the authenticity of selected Kala zeera. MEGA 5 software was used for clustering and the barcodes did clustering based on geographical distribution of Kala zeera germplasm.<br><br>CONCLUSION: Based on molecular barcoding, best barcode combination was identified that may discriminate the Kala zeera germplasm vis-a-vis can authenticate their purity. Moreover, the identified DNA barcodes will have significant role in studying the evolutionary biology of Bunium species and will be important for designing a strategy to conserve the selected Kala zeera germplasm lines. The identified genotypes with high phenolic content and antioxidant activity can further be utilized in Kala zeera breeding programmes.},
}
@article {pmid35727806,
year = {2022},
author = {Cohen-Aharonov, LA and Rebibo-Sabbah, A and Yaacov, A and Granit, RZ and Strauss, M and Colodner, R and Cheshin, O and Rosenberg, S and Eavri, R},
title = {High throughput SARS-CoV-2 variant analysis using molecular barcodes coupled with next generation sequencing.},
journal = {PloS one},
volume = {17},
number = {6},
pages = {e0253404},
pmid = {35727806},
issn = {1932-6203},
mesh = {*COVID-19/diagnosis ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Pandemics ; *SARS-CoV-2/genetics ; },
abstract = {The identification of SARS-CoV-2 variants across the globe and their implications on the outspread of the pandemic, infection potential and resistance to vaccination, requires modification of the current diagnostic methods to map out viral mutations rapidly and reliably. Here, we demonstrate that integrating DNA barcoding technology, sample pooling and Next Generation Sequencing (NGS) provide an applicable solution for large-population viral screening combined with specific variant analysis. Our solution allows high throughput testing by barcoding each sample, followed by pooling of test samples using a multi-step procedure. First, patient-specific barcodes are added to the primers used in a one-step RT-PCR reaction, amplifying three different viral genes and one human housekeeping gene (as internal control). Then, samples are pooled, purified and finally, the generated sequences are read using an Illumina NGS system to identify the positive samples with a sensitivity of 82.5% and a specificity of 97.3%. Using this solution, we were able to identify six known and one unknown SARS-CoV-2 variants in a screen of 960 samples out of which 258 (27%) were positive for the virus. Thus, our diagnostic solution integrates the benefits of large population and epidemiological screening together with sensitive and specific identification of positive samples including variant analysis at a single nucleotide resolution.},
}
@article {pmid35727546,
year = {2022},
author = {Núñez-Pons, L and Mazzella, V and Rispo, F and Efremova, J and Calcinai, B},
title = {DNA Barcoding Procedures for Taxonomical and Phylogenetic Studies in Marine Animals: Porifera as a Case Study.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2498},
number = {},
pages = {195-223},
pmid = {35727546},
issn = {1940-6029},
mesh = {Animals ; DNA Barcoding, Taxonomic/methods ; Phylogeny ; *Porifera/genetics ; },
abstract = {DNA barcoding is a versatile approach that has revolutionized taxonomy and other akin topics in biology and ecology, due to its simplicity and relatively costless procedures. The method consists in the production of one or a few amplicons from informative genetic regions via Sanger sequencing. These markers are selected because they tend to evolve at a similar pace as speciation, allowing to discriminate organismal species. The applicability of this technique is here portrayed for the taxonomical identification of marine sponges (phylum: Porifera) as an exemplification.},
}
@article {pmid35727545,
year = {2022},
author = {Schiaparelli, S and Alvaro, MC and Cecchetto, M and Guzzi, A},
title = {Barcoding of Antarctic Marine Invertebrates: From Field Sampling to Lab Procedures.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2498},
number = {},
pages = {177-194},
pmid = {35727545},
issn = {1940-6029},
mesh = {Animals ; Antarctic Regions ; *Aquatic Organisms/genetics ; DNA/genetics ; *DNA Barcoding, Taxonomic/methods ; Invertebrates/genetics ; },
abstract = {DNA barcoding is a powerful and widespread method used to identify large numbers of species collected in the framework of sampling activities in the field. With the exception of research projects that may count on large teams characterized by tasks' delegation and where many activities may run in parallel, in the majority of cases the barcoding effort is handled by a limited number of persons. The guidelines here reported focus on this second case, with a special attention paid to field procedures, whose efficiency and smoothness are often overlooked.},
}
@article {pmid35727443,
year = {2022},
author = {Handal-Marquez, P and Koch, M and Kestemont, D and Arangundy-Franklin, S and Pinheiro, VB},
title = {Antha-Guided Automation of Darwin Assembly for the Construction of Bespoke Gene Libraries.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2461},
number = {},
pages = {43-66},
pmid = {35727443},
issn = {1940-6029},
support = {BB/N01023X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Automation/methods ; Gene Library ; *High-Throughput Nucleotide Sequencing/methods ; Protein Engineering/methods ; *Software ; },
abstract = {Protein engineering through directed evolutison is facilitated by the screening and characterization of protein libraries. Efficient and effective methods for multiple site-saturation mutagenesis, such as Darwin Assembly, can accelerate the sampling of relevant sequence space and the identification of variants with desired functionalities. Here, we present the automation of the Darwin Assembly method, using a Gilson PIPETMAX™ liquid handling platform under the control of the Antha software platform, which resulted in the accelerated construction of complex, multiplexed gene libraries error-free and with minimal hands-on time, while maintaining flexibility over experimental parameters through a graphical user interface rather than requiring user-driven library-dependent programming of the liquid handling platform. We also present an approach for barcoding libraries that overcomes amplicon length limitations in next generation sequencing and enables fast reconstruction of library reads.},
}
@article {pmid35725712,
year = {2022},
author = {Yu, HX and Zhang, J and Zhu, YZ and Cheng, Q and Yu, XT and Huang, P and Dang, YH and Shi, GF},
title = {Bibliometrics Analysis in English and Chinese Literature on Drowning in Forensic Medicine from 1991 to 2020.},
journal = {Fa yi xue za zhi},
volume = {38},
number = {1},
pages = {98-109},
doi = {10.12116/j.issn.1004-5619.2021.411209},
pmid = {35725712},
issn = {1004-5619},
mesh = {Bibliometrics ; China/epidemiology ; *Drowning/diagnosis ; Forensic Medicine ; Humans ; Publications ; },
abstract = {OBJECTIVES: To explore the research hotspots and development trends of the field of forensic drowning from 1991 to 2020 by bibliometrics methods.<br><br>METHODS: Based on Web of Science, CNKI database, Wanfang Data knowledge service platform, python 3.9.2, CiteSpace 5.8.R3, Gephi 0.9.2, etc. were used to analyze the publishing trends, countries/regions, institutions, authors and topics of the study on drowning.<br><br>RESULTS: A total of 631 English literature were obtained, including 59 articles from Chinese authors, and 386 Chinese literature were obtained. The Chinese and English journals with the largest number of related literatures were Chinese Journal of Forensic Science (80 articles) and Forensic Science International (106 articles), respectively. Japan published the most articles in English, and China ranked third. Osaka City Univ (Japan, 28 articles) published the most English articles, and Guangzhou Forens Sci Inst (China, 22 articles) ranked second. Among Chinese literature, Guangzhou Forens Sci Inst (32 articles) published the most. The topic analysis of Chinese and English literature showed that diatom examination, virtual autopsy, postmortem biochemical examination, the nature of death, and postmortem submersion interval were the hot spots of current research, but English literature had more studies on new technologies and methods, while Chinese literature was more inclined to practice, application and experience summary.<br><br>CONCLUSIONS: The number of literature in forensic medicine on drowning is relatively stable. The scope of international and domestic collaborations in this field is still limited. The automated examination of diatoms, the establishment of diatom DNA barcodes and virtual autopsy will be the most important research hotspots in the coming period and are expected to achieve breakthroughs in drowning diagnosis, drowning location inference, postmortem submersion interval estimation, etc.},
}
@article {pmid35724315,
year = {2023},
author = {Bourret, TB and Fajardo, SN and Frankel, SJ and Rizzo, DM},
title = {Cataloging Phytophthora Species of Agriculture, Forests, Horticulture, and Restoration Outplantings in California, U.S.A.: A Sequence-Based Meta-Analysis.},
journal = {Plant disease},
volume = {107},
number = {1},
pages = {67-75},
doi = {10.1094/PDIS-01-22-0187-RE},
pmid = {35724315},
issn = {0191-2917},
mesh = {*Ecosystem ; *Phytophthora/genetics ; Forests ; Plants ; Agriculture ; Horticulture ; DNA, Intergenic ; California ; },
abstract = {California contains a diverse flora, and knowledge of the pathogens that threaten those plants is essential to managing their long-term health. To better understand threats to California plant health, a meta-analysis of Phytophthora detections within the state was conducted using publicly available sequences as a primary source of data rather than published records. Accessions of internal transcribed spacer (ITS) ribosomal DNA were cataloged from 800 Californian Phytophthora isolates, analyzed, and determined to correspond to 80 taxa, including several phylogenetically distinct provisional species. A number of Phytophthora taxa not previously reported from California were identified, including 20 described species. Pathways of introduction and spread were analyzed by categorizing isolates' origins, grouped by land-use: (i) agriculture, (ii) forests and other natural ecosystems, (iii) horticulture and nurseries, or (iv) restoration outplantings. The pooled Phytophthora metacommunities of the restoration outplantings and horticulture land-use categories were the most similar, whereas the communities pooled from forests and agriculture were least similar. Phytophthora cactorum, P. pini, P. pseudocryptogea, and P. syringae were identified in all four land-use categories, while 13 species were found in three. P. gonapodyides was the most common species by number of ITS accessions and exhibited the greatest diversity of ITS haplotypes. P. cactorum, P. ramorum, and P. nicotianae were associated with the greatest number of host genera. In this analysis, the Phytophthora spp. most prevalent in California differ from those compiled from the scientific literature.},
}
@article {pmid35723752,
year = {2022},
author = {Bakran-Lebl, K and Harmankaya, K and Fuehrer, HP and Heidenreich, E and Marton, L and Zechmeister, T and Allerberger, F and Preusser, M},
title = {Dermatitis linearis outbreak associated with Paederus balcanicus in Austria.},
journal = {Wiener klinische Wochenschrift},
volume = {134},
number = {13-14},
pages = {511-515},
pmid = {35723752},
issn = {1613-7671},
mesh = {Adult ; Animals ; Austria/epidemiology ; Child ; *Coleoptera ; *Dermatitis/epidemiology ; Disease Outbreaks ; Europe ; Humans ; },
abstract = {BACKGROUND: Dermatitis linearis is a toxic skin lesion caused by contact with certain beetles of the genus Paederus (Coleoptera: Staphylinidae). Dermatitis linearis outbreaks have been described mainly in tropical and subtropical regions, but so far not in Central Europe, and are considered an emerging public health concern potentially associated with climate change.<br><br>MATERIAL AND METHODS: Following diagnosis of dermatitis linearis in a&#xa0;cluster of six adults and one child with reported exposure to beetles with morphological characteristics of Paederus species at a&#xa0;recreational public open-air bath at Lake Neusiedl (Illmitz, Burgenland, Austria), we performed on-site inspection and installed light and pitfall traps. Collected beetle specimens of the genus Paederus were classified using morphological characteristics and DNA barcoding.<br><br>RESULTS: A&#xa0;total of 32&#xa0;Paederus beetles were collected using an aspirator (n&#x202f;=&#x2009;2) and light traps (n&#x202f;=&#x2009;30). No individuals of the genus Paederus were captured with the pitfall traps. Morphological analyses identified them as members of the Paederus balcanicus species, which was confirmed by genetic specification of four arbitrarily chosen individuals. Dermatitis linearis lesions were treated with topical steroids and healed but partly leaving scars and hyperpigmentation, over the course of a&#xa0;few weeks in all affected persons.<br><br>CONCLUSION: We report for the first time (a)&#xa0;an outbreak of dermatitis linearis associated with exposure to autochthonous Paederus species in Austria, and (b)&#xa0;that contact to the species Paederus balcanicus may cause dermatitis linearis in humans. Adequate measures should be taken to prevent dermatitis linearis outbreaks in areas with resident Paederus occurrence.},
}
@article {pmid35716352,
year = {2023},
author = {Ip, YCA and Chang, JJM and Oh, RM and Quek, ZBR and Chan, YKS and Bauman, AG and Huang, D},
title = {Seq' and ARMS shall find: DNA (meta)barcoding of Autonomous Reef Monitoring Structures across the tree of life uncovers hidden cryptobiome of tropical urban coral reefs.},
journal = {Molecular ecology},
volume = {32},
number = {23},
pages = {6223-6242},
doi = {10.1111/mec.16568},
pmid = {35716352},
issn = {1365-294X},
support = {R-154-000-649-507//AXA Postdoctoral Fellowship/ ; MSRDP-P03//National Research Foundation Singapore/ ; R-154-000-A63-114//Singapore Ministry of Education Academic Research Fund Tier 1/ ; },
mesh = {Animals ; Coral Reefs ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; *Anthozoa/genetics ; *Microbiota ; DNA ; Biodiversity ; },
abstract = {Coral reefs are among the richest marine ecosystems on Earth, but there remains much diversity hidden within cavities of complex reef structures awaiting discovery. While the abundance of corals and other macroinvertebrates are known to influence the diversity of other reef-associated organisms, much remains unknown on the drivers of cryptobenthic diversity. A combination of standardized sampling with 12 units of the Autonomous Reef Monitoring Structure (ARMS) and high-throughput sequencing was utilized to uncover reef cryptobiome diversity across the equatorial reefs in Singapore. DNA barcoding and metabarcoding of mitochondrial cytochrome c oxidase subunit I, nuclear 18S and bacterial 16S rRNA genes revealed the taxonomic composition of the reef cryptobiome, comprising 15,356 microbial ASVs from over 50 bacterial phyla, and 971 MOTUs across 15 metazoan and 19 non-metazoan eukaryote phyla. Environmental factors across different sites were tested for relationships with ARMS diversity. Differences among reefs in diversity patterns of metazoans and other eukaryotes, but not microbial communities, were associated with biotic (coral cover) and abiotic (distance, temperature and sediment) environmental variables. In particular, ARMS deployed at reefs with higher coral cover had greater metazoan diversity and encrusting plate cover, with larger-sized non-coral invertebrates influencing spatial patterns among sites. Our study showed that DNA barcoding and metabarcoding of ARMS constitute a valuable tool for quantifying cryptobenthic diversity patterns and can provide critical information for the effective management of coral reef ecosystems.},
}
@article {pmid35716293,
year = {2022},
author = {Shashank, PR and Naveena, NL and Rajgopal, NN and Elliott, TA and Sreedevi, K and Sunil, S and Meshram, NM},
title = {DNA barcoding of insects from India: Current status and future perspectives.},
journal = {Molecular biology reports},
volume = {49},
number = {11},
pages = {10617-10626},
pmid = {35716293},
issn = {1573-4978},
support = {CRG/2018/000753//Science and Engineering Research Board/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Ecosystem ; Insecta/genetics ; Biodiversity ; *Coleoptera/genetics ; DNA/genetics ; },
abstract = {Insect fauna occupy the largest proportion of animal biodiversity on earth, but the assessment or quantification in terms of species diversity is far from complete. Several recent studies have demonstrated the rapid pace at which insect population decline is occurring. There is an urgent need to document and quantify the diversity of insect fauna for a proper understanding of terrestrial ecosystems. This can be achieved by using modern technology to identify species much faster than relying on traditional methods alone. In line with this, the molecular approach through DNA barcoding coupled with morphological identification needs to be focused and accelerated. The present paper describes the current status of barcoding of insect species in India along with the gaps that need to be remedied. This analysis shows that barcoded specimens cover a very meagre proportion of less than 3.73% of the known taxa/described species and the most represented orders are Lepidoptera and Hemiptera followed by Diptera and Coleoptera. There is a need to expedite insect species discovery and documentation in a collaborative mode between traditional taxonomists and molecular biologists, to accomplish the DNA barcoding of all known insect taxa from India.},
}
@article {pmid35714082,
year = {2022},
author = {Kumar, G and Reaume, AM and Farrell, E and Gaither, MR},
title = {Comparing eDNA metabarcoding primers for assessing fish communities in a biodiverse estuary.},
journal = {PloS one},
volume = {17},
number = {6},
pages = {e0266720},
pmid = {35714082},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/methods ; *DNA, Environmental ; Estuaries ; Fishes/genetics ; },
abstract = {Metabarcoding of environmental DNA is increasingly used for biodiversity assessments in aquatic communities. The efficiency and outcome of these efforts are dependent upon either de novo primer design or selecting an appropriate primer set from the dozens that have already been published. Unfortunately, there is a lack of studies that have directly compared the efficacy of different metabarcoding primers in marine and estuarine systems. Here we evaluate five commonly used primer sets designed to amplify rRNA barcoding genes in fishes and compare their performance using water samples collected from estuarine sites in the highly biodiverse Indian River Lagoon in Florida. Three of the five primer sets amplify a portion of the mitochondrial 12S gene (MiFish_12S, 171bp; Riaz_12S, 106 bp; Valentini_12S, 63 bp), one amplifies 219 bp of the mitochondrial 16S gene (Berry_16S), and the other amplifies 271 bp of the nuclear 18S gene (MacDonald_18S). The vast majority of the metabarcoding reads (> 99%) generated using the 18S primer set assigned to non-target (non-fish) taxa and therefore this primer set was omitted from most analyses. Using a conservative 99% similarity threshold for species level assignments, we detected a comparable number of species (55 and 49, respectively) and similarly high Shannon's diversity values for the Riaz_12S and Berry_16S primer sets. Meanwhile, just 34 and 32 species were detected using the MiFish_12S and Valentini_12S primer sets, respectively. We were able to amplify both bony and cartilaginous fishes using the four primer sets with the vast majority of reads (>99%) assigned to the former. We detected the greatest number of elasmobranchs (six species) with the Riaz_12S primer set suggesting that it may be a suitable candidate set for the detection of sharks and rays. Of the total 76 fish species that were identified across all datasets, the combined three 12S primer sets detected 85.5% (65 species) while the combination of the Riaz_12S and Berry_16S primers detected 93.4% (71 species). These results highlight the importance of employing multiple primer sets as well as using primers that target different genomic regions. Moreover, our results suggest that the widely adopted MiFish_12S primers may not be the best choice, rather we found that the Riaz_12S primer set was the most effective for eDNA-based fish surveys in our system.},
}
@article {pmid35712991,
year = {2023},
author = {Govender, A and Singh, S and Groeneveld, J and Pillay, S and Willows-Munro, S},
title = {Metabarcoding analysis of marine zooplankton confirms the ecological role of a sheltered bight along an exposed continental shelf.},
journal = {Molecular ecology},
volume = {32},
number = {23},
pages = {6210-6222},
doi = {10.1111/mec.16567},
pmid = {35712991},
issn = {1365-294X},
support = {//National Research Foundation (NRF)/ ; 110763//DSI/NRF/ACEP Captor Project/ ; },
mesh = {Animals ; *Zooplankton/genetics ; *Ecosystem ; South Africa ; Food Chain ; Phytoplankton ; Fishes ; },
abstract = {Zooplankton plays an essential role in marine ecosystems as the link between primary producers (phytoplankton) and higher trophic levels in food webs, and as a dynamic pool of recruits for invertebrates and fish. Zooplankton communities are diverse with a patchy distribution at different spatial scales, influenced by oceanographic processes. The continental shelf of eastern South Africa is narrow and exposed to the western-boundary Agulhas Current, with some shelter against strong directional flow provided by the broader KwaZulu-Natal Bight, a coastal offset adjacent to an estuary. We compared zooplankton species richness, diversity and relative abundance of key taxa among sheltered and exposed shelf areas using metabarcoding and community analysis, to explore the ecological role of the bight in a highly dynamic ocean region. Metabarcoding recovered higher richness and diversity at a finer resolution than could previously be achieved with traditional microscopy. Of 271 operational taxonomic units (OTUs) recovered through metabarcoding, 63% could be matched with >95% sequence similarity to reference barcodes. OTUs were dominated by malacostracan crustaceans (161 spp.), ray-finned fishes (45 spp.) and copepods (28 spp.). Species richness, diversity and the relative abundance of key taxa differed between sheltered and exposed shelf areas. Lower species richness in the bight was partly attributed to structurally homogeneous benthic habitats, and an associated reduction of meroplanktonic species originating from local benthic-pelagic exchange. High relative abundance of a ray-finned fish in the bight, as observed based on fish eggs and read counts, confirmed that the bight is an important fish spawning area. Overall, zooplankton metabarcoding outputs were congruent with findings of previous ecological research using more traditional methods of observation.},
}
@article {pmid35712658,
year = {2022},
author = {Oinam, L and Tateno, H},
title = {Glycan Profiling by Sequencing to Uncover Multicellular Communication: Launching Glycobiology in Single Cells and Microbiomes.},
journal = {Frontiers in cell and developmental biology},
volume = {10},
number = {},
pages = {919168},
pmid = {35712658},
issn = {2296-634X},
abstract = {Glycans are essential building blocks of life that are located at the outermost surface of all cells from mammals to bacteria and even viruses. Cell surface glycans mediate multicellular communication in diverse biological processes and are useful as "surface markers" to identify cells. Various single-cell sequencing technologies have already emerged that enable the high-throughput analysis of omics information, such as transcriptome and genome profiling on a cell-by-cell basis, which has advanced our understanding of complex multicellular interactions. However, there has been no robust technology to analyze the glycome in single cells, mainly because glycans with branched and heterogeneous structures cannot be readily amplified by polymerase chain reactions like nucleic acids. We hypothesized that the generation of lectins conjugated with DNA barcodes (DNA-barcoded lectins) would enable the conversion of glycan information to gene information, which may be amplified and measured using DNA sequencers. This technology will enable the simultaneous analysis of glycan and RNA in single cells. Based on this concept, we developed a technology to analyze glycans and RNA in single cells, which was referred to as scGR-seq. Using scGR-seq, we acquired glycan and gene expression profiles of individual cells constituting heterogeneous cell populations, such as tissues. We further extended Glycan-seq to the profiling of the surface glycans of bacteria and even gut microbiota. Glycan-seq and scGR-seq are new technologies that enable us to elucidate the function of glycans in cell-cell and cell-microorganism communication, which extends glycobiology to the level of single cells and microbiomes.},
}
@article {pmid35709340,
year = {2022},
author = {Ellestad, P and Farrera, MAP and Forest, F and Buerki, S},
title = {Uncovering haplotype diversity in cultivated Mexican vanilla species.},
journal = {American journal of botany},
volume = {109},
number = {7},
pages = {1120-1138},
doi = {10.1002/ajb2.16024},
pmid = {35709340},
issn = {1537-2197},
mesh = {Genetic Variation ; Genomics ; Haplotypes/genetics ; Mexico ; Phylogeny ; *Vanilla/genetics ; },
abstract = {PREMISE: Although vanilla is one of the best-known spices, there is only a limited understanding of its biology and genetics within Mexico, where its cultivation originated and where phenotypic variability is high. This study aims to augment our understanding of vanilla's genetic resources by assessing species delimitation and genetic, geographic, and climatic variability within Mexican cultivated vanilla.<br><br>METHODS: Using nuclear and plastid DNA sequence data from 58 Mexican samples collected from three regions and 133 ex situ accessions, we assessed species monophyly using phylogenetic analyses and genetic distances. Intraspecific genetic variation was summarized through the identification of haplotypes. Within the primarily cultivated species, Vanilla planifolia, haplotype relationships were further verified using plastome and rRNA gene sequences. Climatic niche and haplotype composition were assessed across the landscape.<br><br>RESULTS: Three species (Vanilla planifolia, V. pompona, and V. insignis) and 13 haplotypes were identified among Mexican vanilla. Within V. planifolia haplotypes, hard phylogenetic incongruences between plastid and nuclear sequences suggest past hybridization events. Eight haplotypes consisted exclusively of Mexican samples. The dominant V. planifolia haplotype occurred throughout all three regions as well as outside of its country of origin. Haplotype richness was found to be highest in regions around Papantla and Chinantla.<br><br>CONCLUSIONS: Long histories of regional cultivation support the consideration of endemic haplotypes as landraces shaped by adaptation to local conditions and/or hybridization. Results may aid further genomic investigations of vanilla's genetic resources and ultimately support the preservation of genetic diversity within the economically important crop.},
}
@article {pmid35709217,
year = {2022},
author = {Kang, Y and Liu, P and Lv, F and Zhang, Y and Yang, Y and Wei, J},
title = {Genetic relationship and source species identification of 58 Qi-Nan germplasms of Aquilaria species in China that easily form agarwood.},
journal = {PloS one},
volume = {17},
number = {6},
pages = {e0270167},
pmid = {35709217},
issn = {1932-6203},
mesh = {Bayes Theorem ; China ; DNA Barcoding, Taxonomic/methods ; DNA, Plant/genetics ; Phylogeny ; *Plant Breeding ; *Thymelaeaceae/genetics ; },
abstract = {Recently, Qi-Nan germplasm, the germplasm of Aquilaria species that easily forms agarwood, has been widely cultivated in Guangdong and Hainan Provinces in China. Since the morphological characteristics of Qi-Nan germplasm are similar to those of Aquilaria species and germplasm is bred by grafting, it is difficult to determine the source species of this germplasm by traditional taxonomic characteristics. In this study, we performed a DNA barcoding analysis of 58 major Qi-Nan germplasms as well as Aquilaria sinensis, A. yunnanensis, A. crassna, A. malaccensis and A. hirta with 5 primers (nuclear gene internal transcribed spacer 2 (ITS2) and the chloroplast genes matK, trnH-psbA, rbcL and trnL-trnF). This field survey in the Qi-Nan germplasm plantations in Guangdong and Hainan Provinces aimed to accurately identify the source species of Qi-Nan germplasm. According to the results, ITS2 and matK showed the most variability and the highest divergence at all genetic distances. This ITS2+matK combination, screened for with TaxonDNA analysis, showed the highest success rate in species identification of the Qi-Nan germplasm. Clustering in the phylogenetic trees constructed with Bayesian inference and maximum likelihood indicated that the Qi-Nan germplasm was most closely related to A. sinensis and more distantly related to A. yunnanensis, A. crassna, A. malaccensis and A. hirta. Therefore, this study determined that the source species of the Qi-Nan germplasm is A. sinensis.},
}
@article {pmid35708611,
year = {2022},
author = {Tavakolian, N and Frazão, JG and Bendixsen, D and Stelkens, R and Li, CB},
title = {Shepherd: accurate clustering for correcting DNA barcode errors.},
journal = {Bioinformatics (Oxford, England)},
volume = {38},
number = {15},
pages = {3710-3716},
pmid = {35708611},
issn = {1367-4811},
support = {2017-04963//Swedish Research Council/ ; 2017.0163//Knut and Alice Wallenberg Foundation/ ; UPD2018-0196//Wenner-Gren Foundations/ ; SU FV-1.2.1-0124-17//Faculty of Science, Stockholm University/ ; },
mesh = {Humans ; Sequence Analysis, DNA/methods ; *DNA Barcoding, Taxonomic ; Bayes Theorem ; *High-Throughput Nucleotide Sequencing/methods ; Cluster Analysis ; DNA/genetics ; Algorithms ; },
abstract = {MOTIVATION: DNA barcodes are short, random nucleotide sequences introduced into cell populations to track the relative counts of hundreds of thousands of individual lineages over time. Lineage tracking is widely applied, e.g. to understand evolutionary dynamics in microbial populations and the progression of breast cancer in humans. Barcode sequences are unknown upon insertion and must be identified using next-generation sequencing technology, which is error prone. In this study, we frame the barcode error correction task as a clustering problem with the aim to identify true barcode sequences from noisy sequencing data. We present Shepherd, a novel clustering method that is based on an indexing system of barcode sequences using k-mers, and a Bayesian statistical test incorporating a substitution error rate to distinguish true from error sequences.<br><br>RESULTS: When benchmarking with synthetic data, Shepherd provides barcode count estimates that are significantly more accurate than state-of-the-art methods, producing 10-150 times fewer spurious lineages. For empirical data, Shepherd produces results that are consistent with the improvements seen on synthetic data. These improvements enable higher resolution lineage tracking and more accurate estimates of biologically relevant quantities, e.g. the detection of small effect mutations.<br><br>A Python implementation of Shepherd is freely available at: https://www.github.com/Nik-Tavakolian/Shepherd.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid35705990,
year = {2022},
author = {Cypris, O and Franzen, J and Frobel, J and Glück, P and Kuo, CC and Schmitz, S and Nüchtern, S and Zenke, M and Wagner, W},
title = {Hematopoietic differentiation persists in human iPSCs defective in de novo DNA methylation.},
journal = {BMC biology},
volume = {20},
number = {1},
pages = {141},
pmid = {35705990},
issn = {1741-7007},
mesh = {Animals ; Cell Differentiation/genetics ; DNA (Cytosine-5-)-Methyltransferases/genetics/metabolism ; DNA Methylation ; DNA Methyltransferase 3A ; Epigenesis, Genetic ; Humans ; *Induced Pluripotent Stem Cells/metabolism/pathology ; *Leukemia, Myeloid, Acute ; Mice ; },
abstract = {BACKGROUND: DNA methylation is involved in the epigenetic regulation of gene expression during developmental processes and is primarily established by the DNA methyltransferase 3A (DNMT3A) and 3B (DNMT3B). DNMT3A is one of the most frequently mutated genes in clonal hematopoiesis and leukemia, indicating that it plays a crucial role for hematopoietic differentiation. However, the functional relevance of Dnmt3a for hematopoietic differentiation and hematological malignancies has mostly been analyzed in mice, with the specific role for human hematopoiesis remaining elusive. In this study, we therefore investigated if DNMT3A is essential for hematopoietic differentiation of human induced pluripotent stem cells (iPSCs).<br><br>RESULTS: We generated iPSC lines with knockout of either exon 2, 19, or 23 and analyzed the impact of different DNMT3A exon knockouts on directed differentiation toward mesenchymal and hematopoietic lineages. Exon 19[-/-] and 23[-/-] lines displayed an almost entire absence of de novo DNA methylation during mesenchymal and hematopoietic differentiation. Yet, differentiation efficiency was only slightly reduced in exon 19[-/-] and rather increased in exon 23[-/-] lines, while there was no significant impact on gene expression in hematopoietic progenitors (iHPCs). Notably, DNMT3A[-/-] iHPCs recapitulate some DNA methylation patterns of acute myeloid leukemia (AML) with DNMT3A mutations. Furthermore, multicolor genetic barcoding revealed growth advantage of exon 23[-/-] iHPCs in a syngeneic competitive differentiation assay.<br><br>CONCLUSIONS: Our results demonstrate that iPSCs with homozygous knockout of different exons of DNMT3A remain capable of mesenchymal and hematopoietic differentiation-and exon 23[-/-] iHPCs even gained growth advantage-despite loss of almost the entire de novo DNA methylation. Partial recapitulation of DNA methylation patterns of AML with DNMT3A mutations by our DNMT3A knockout iHPCs indicates that our model system can help to elucidate mechanisms of clonal hematopoiesis.},
}
@article {pmid35705805,
year = {2022},
author = {Patel, SH and Christodoulou, C and Weinreb, C and Yu, Q and da Rocha, EL and Pepe-Mooney, BJ and Bowling, S and Li, L and Osorio, FG and Daley, GQ and Camargo, FD},
title = {Lifelong multilineage contribution by embryonic-born blood progenitors.},
journal = {Nature},
volume = {606},
number = {7915},
pages = {747-753},
pmid = {35705805},
issn = {1476-4687},
support = {P01 HL131471/HL/NHLBI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {*Aging ; Animals ; *Cell Lineage ; *Embryo, Mammalian/cytology ; *Hematopoiesis ; *Hematopoietic Stem Cells/cytology ; Mice ; Multipotent Stem Cells/cytology ; },
abstract = {Haematopoietic stem cells (HSCs) arise in the embryo from the arterial endothelium through a process known as the endothelial-to-haematopoietic transition (EHT)[1-4]. This process generates hundreds of blood progenitors, of which a fraction go on to become definitive HSCs. It is generally thought that most adult blood is derived from those HSCs, but to what extent other progenitors contribute to adult haematopoiesis is not known. Here we use in situ barcoding and classical fate mapping to assess the developmental and clonal origins of adult blood in mice. Our analysis uncovers an early wave of progenitor specification-independent of traditional HSCs-that begins soon after EHT. These embryonic multipotent progenitors (eMPPs) predominantly drive haematopoiesis in the young adult, have a decreasing yet lifelong contribution over time and are the predominant source of lymphoid output. Putative eMPPs are specified within intra-arterial haematopoietic clusters and represent one fate of the earliest haematopoietic progenitors. Altogether, our results reveal functional heterogeneity during the definitive wave that leads to distinct sources of adult blood.},
}
@article {pmid35701424,
year = {2022},
author = {Amato, KA and Haddock, LA and Braun, KM and Meliopoulos, V and Livingston, B and Honce, R and Schaack, GA and Boehm, E and Higgins, CA and Barry, GL and Koelle, K and Schultz-Cherry, S and Friedrich, TC and Mehle, A},
title = {Influenza A virus undergoes compartmentalized replication in vivo dominated by stochastic bottlenecks.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {3416},
pmid = {35701424},
issn = {2041-1723},
support = {F30 AI145182/AI/NIAID NIH HHS/United States ; R01 AI140766/AI/NIAID NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; R01 AI125392/AI/NIAID NIH HHS/United States ; T32 AI007414/AI/NIAID NIH HHS/United States ; T32 GM140935/GM/NIGMS NIH HHS/United States ; T32 GM007215/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Ferrets ; Genotype ; Humans ; *Influenza A virus/genetics ; *Influenza, Human ; *Orthomyxoviridae Infections ; Virus Replication/genetics ; },
abstract = {Transmission of influenza A viruses (IAV) between hosts is subject to numerous physical and biological barriers that impose genetic bottlenecks, constraining viral diversity and adaptation. The bottlenecks within hosts and their potential impacts on evolutionary pathways taken during infection are poorly understood. To address this, we created highly diverse IAV libraries bearing molecular barcodes on two gene segments, enabling high-resolution tracking and quantification of unique virus lineages within hosts. Here we show that IAV infection in lungs is characterized by multiple within-host bottlenecks that result in "islands" of infection in lung lobes, each with genetically distinct populations. We perform site-specific inoculation of barcoded IAV in the upper respiratory tract of ferrets and track viral diversity as infection spreads to the trachea and lungs. We detect extensive compartmentalization of discrete populations within lung lobes. Bottleneck events and localized replication stochastically sample individual viruses from the upper respiratory tract or the trachea that become the dominant genotype in a particular lobe. These populations are shaped strongly by founder effects, with limited evidence for positive selection. The segregated sites of replication highlight the jackpot-style events that contribute to within-host influenza virus evolution and may account for low rates of intrahost adaptation.},
}
@article {pmid35700925,
year = {2022},
author = {Fan, M and Yang, D and Ng, B and Jackson, J and Bouris, K and Eng, S and Rolko, E and Trbovich, P},
title = {Impact of technology-assisted versus manual sterile compounding on safety and efficiency in a Canadian community hospital.},
journal = {American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists},
volume = {79},
number = {19},
pages = {1685-1696},
pmid = {35700925},
issn = {1535-2900},
mesh = {Canada ; Drug Compounding/methods ; Hospitals, Community ; Humans ; *Pharmacy Service, Hospital ; Technology ; },
abstract = {PURPOSE: Interventions to improve the safety and efficiency of manual sterile compounding are needed. This study evaluated the impact of a technology-assisted workflow system (TAWS) on sterile compounding safety (checks, traceability, and error detection), and efficiency (task time).<br><br>METHODS: Observations were conducted in an oncology pharmacy transitioning from a manual to a TAWS process for sterile compounding. Process maps were generated to compare manual and TAWS checks and traceability. The numbers and types of errors detected were collected, and task times were observed directly or via TAWS data logs.<br><br>RESULTS: Analysis of safety outcomes showed that, depending on preparation type, 3 to 4 product checks occurred in the manual process, compared to 6 to 10 checks with TAWS use. TAWS checks (barcoding and gravimetric verification) produced better traceability (documentation). The rate of incorrect-drug errors decreased with technology-assisted compounding (from 0.4% [5 of 1,350 preparations] with the manual process to 0% [0 of 1,565 preparations] with TAWS use; P < 0.02). The TAWS increased detection of (1) errors in the amount of drug withdrawn from vials (manual vs TAWS, 0.4% [5/1,350] vs 1.2% [18/1565]; P < 0.02), and (2) errors in the amount of drug injected into the final container (manual vs TAWS, 0% [0/1,236] vs 0.9% [11/1,272]; P < 0.002). With regard to efficiency outcomes, TAWS use increased the mean mixing time (manual vs TAWS, 275 seconds vs 355 seconds; P < 0.001), had no significant impact on average visual checking time (manual vs TAWS, 21.4 seconds vs 21.6 seconds), and decreased average physical checking time (manual vs TAWS, 58.6 seconds vs 50.9 seconds; P < 0.001).<br><br>CONCLUSION: In comparison to manual sterile compounding, use of the TAWS improved safety through more frequent and rigorous checks, improved traceability (via superior documentation), and enhanced error detection. Results related to efficiency were mixed.},
}
@article {pmid35700230,
year = {2022},
author = {Hennart, M and Guglielmini, J and Bridel, S and Maiden, MCJ and Jolley, KA and Criscuolo, A and Brisse, S},
title = {A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains.},
journal = {Molecular biology and evolution},
volume = {39},
number = {7},
pages = {},
pmid = {35700230},
issn = {1537-1719},
support = {/WT_/Wellcome Trust/United Kingdom ; 218205/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Genome, Bacterial ; Genomics ; Genotype ; *Klebsiella pneumoniae/genetics ; Multilocus Sequence Typing ; Phylogeny ; },
abstract = {Sublineages (SLs) within microbial species can differ widely in their ecology and pathogenicity, and their precise definition is important in basic research and for industrial or public health applications. Widely accepted strategies to define SLs are currently missing, which confuses communication in population biology and epidemiological surveillance. Here, we propose a broadly applicable genomic classification and nomenclature approach for bacterial strains, using the prominent public health threat Klebsiella pneumoniae as a model. Based on a 629-gene core genome multilocus sequence typing (cgMLST) scheme, we devised a dual barcoding system that combines multilevel single linkage (MLSL) clustering and life identification numbers (LINs). Phylogenetic and clustering analyses of >7,000 genome sequences captured population structure discontinuities, which were used to guide the definition of 10 infraspecific genetic dissimilarity thresholds. The widely used 7-gene multilocus sequence typing (MLST) nomenclature was mapped onto MLSL SLs (threshold: 190 allelic mismatches) and clonal group (threshold: 43) identifiers for backwards nomenclature compatibility. The taxonomy is publicly accessible through a community-curated platform (https://bigsdb.pasteur.fr/klebsiella), which also enables external users' genomic sequences identification. The proposed strain taxonomy combines two phylogenetically informative barcode systems that provide full stability (LIN codes) and nomenclatural continuity with previous nomenclature (MLSL). This species-specific dual barcoding strategy for the genomic taxonomy of microbial strains is broadly applicable and should contribute to unify global and cross-sector collaborative knowledge on the emergence and microevolution of bacterial pathogens.},
}
@article {pmid35700118,
year = {2022},
author = {Schultz, JA and Hebert, PDN},
title = {Do pseudogenes pose a problem for metabarcoding marine animal communities?.},
journal = {Molecular ecology resources},
volume = {22},
number = {8},
pages = {2897-2914},
doi = {10.1111/1755-0998.13667},
pmid = {35700118},
issn = {1755-0998},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; NFRFT-2020-00073//New Frontiers in Research Fund/ ; //Ontario Genomics/ ; //Genome Canada/ ; //Government of Canada/ ; },
mesh = {Animals ; Codon, Terminator ; *DNA, Environmental ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Phylogeny ; *Pseudogenes/genetics ; },
abstract = {Because DNA metabarcoding typically employs sequence diversity among mitochondrial amplicons to estimate species composition, nuclear mitochondrial pseudogenes (NUMTs) can inflate diversity. This study quantifies the incidence and attributes of NUMTs derived from the 658-bp barcode region of cytochrome c oxidase I (COI) in 156 marine animal genomes. NUMTs were examined to ascertain if they could be recognized by their possession of indels or stop codons. In total, 309 NUMTs ≥150 bp were detected, with an average of 1.98 per species (range = 0-33) and a mean length of 391 ± 200 bp. Among this total, 75 (24.3%) lacked indels or stop codons. NUMTs appear to pose the greatest interpretational risk when short (<313 bp) amplicons are used, such as in environmental DNA studies, dietary analyses or processed fish identification. Employing the standard amplicon length (313 bp) for marine metabarcoding, NUMTs could potentially inflate the operational taxonomic unit (OTU) count by 21% above the true species count while also raising intraspecific variation at COI by 15%. However, when both amplicon length and position are considered, inflation in OTU counts and in barcode variation were just 9% and 10%, respectively, suggesting NUMTs will not seriously distort biodiversity assessments. There was a weak positive correlation between genome size and NUMT count but no variation among phyla or trophic groups. Until bioinformatic advances improve NUMT detection, the best defence involves targeting long amplicons and developing reference databases that include both mitochondrial sequences and their NUMT derivatives.},
}
@article {pmid35695889,
year = {2022},
author = {Saar, I and Thorn, RG and Nagasawa, E and Henkel, TW and Cooper, JA},
title = {A phylogenetic overview of Squamanita, with descriptions of nine new species and four new combinations.},
journal = {Mycologia},
volume = {114},
number = {4},
pages = {769-797},
doi = {10.1080/00275514.2022.2059639},
pmid = {35695889},
issn = {1557-2536},
mesh = {*Agaricales/classification/genetics ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; Phylogeny ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; },
abstract = {Nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode) sequence data from eight type specimens of previously described Squamanita species were obtained. Phylogenetic analysis of ITS and partial nuc 28S rDNA data revealed Squamanita as paraphyletic splitting into two monophyletic groups, which we recognize as the genera Squamanita and Dissoderma. We accept 14 Squamanita and nine Dissoderma species, provide the first sequences of 13 of these, and describe six new species of Squamanita and three new species of Dissoderma. We transfer three species of Squamanita into Dissoderma, one into Cystoderma, and treat S. basii and S. umbilicata as synonyms of D. paradoxum. Squamanita can be distinguished from Dissoderma by the generally larger fleshier basidiomata with a tricholomatoid or amanitoid stature and yellowish to tawny brown pileus and often similarly colored stipe. Most species have cheilo- and pleurocystidia. Species of Dissoderma are small, collybioid or mycenoid, lack cystidia, and the pileus and often upper stipe are purplish gray. Both genera parasitize basidiomata of other agarics.},
}
@article {pmid35693929,
year = {2022},
author = {Rabé, M and Fonteneau, L and Oliver, L and Morales-Molina, A and Jubelin, C and Garcia-Castro, J and Heymann, D and Gratas, C and Vallette, FM},
title = {Cellular Heterogeneity and Cooperativity in Glioma Persister Cells Under Temozolomide Treatment.},
journal = {Frontiers in cell and developmental biology},
volume = {10},
number = {},
pages = {835273},
pmid = {35693929},
issn = {2296-634X},
abstract = {We have observed a drug-tolerant/persister state in a human glioblastoma (GBM) cell line after exposure to temozolomide, the standard-of-care chemotherapeutic agent for GBM. We used a multicolor lentiviral genetic barcode labeling to follow cell population evolution during temozolomide treatment. We observed no change in the distribution of the different colored populations of cells in persister or resistant cells suggesting that pre-existing minor subpopulations, which would be expected to be restricted to a single color, were not amplified/selected during the response to the drug. We have previously identified four genes (CHI3L1, FAT2, KLK5, and HB-EGF) that were over-expressed during the persister stage. Single-cell analysis of these four genes indicated that they were expressed in different individual cells ruling out the existence of a single persister-specific clone but suggesting rather a global answer. Even so, the transitory silencing of CHI3L1, FAT2, or KLK5 influenced the expression of the other three genes and the survival of U251 cells in absence of temozolomide. Since proteins encoded by the four genes are all localized in the extracellular matrix or interact within the extracellular compartment, we propose that cellular interactions and communications are important during the persister stage before the acquisition of chemo-resistance. Thus, persisters might be a new therapeutically relevant target in GBM.},
}
@article {pmid35690834,
year = {2022},
author = {González, MA and Goiri, F and Prosser, SWJ and Cevidanes, A and Hernández-Triana, LM and Barandika, JF and Hebert, PDN and García-Pérez, AL},
title = {Culicoides species community composition and feeding preferences in two aquatic ecosystems in northern Spain.},
journal = {Parasites &amp; vectors},
volume = {15},
number = {1},
pages = {199},
pmid = {35690834},
issn = {1756-3305},
support = {FPI-2019//Department of Economic Development and Infrastructures of the Basque Government/ ; FJC2019-041737-I//'Juan de la Cierva-Formaci&#xf3;n' post-doctoral grant - MCIN/AEI/ 10.13039/501100011033/ ; SV3045//The Scottish Government and Welsh Government/ ; },
mesh = {Animals ; Birds ; *Ceratopogonidae/genetics ; *Deer ; Ecosystem ; Feeding Behavior ; Female ; Spain ; },
abstract = {BACKGROUND: Aquatic ecosystems provide breeding sites for blood-sucking insects such as Culicoides biting midges (Diptera: Ceratopogonidae), but factors affecting their distribution and host choice are poorly understood. A study was undertaken at two nature reserves in northern Spain to examine the abundance, species composition, population dynamics and feeding patterns of biting midges between 2018 and 2019.<br><br>METHODS: Culicoides were captured by light suction traps baited with CO2 and by sweep netting vegetation. Blood meals and species identification of blood-fed specimens were determined using cytochrome c oxidase I subunit (COI) DNA barcoding. Multivariate generalized linear models were used to evaluate the associations between the abundance of Culicoides, the species richness and other parameters.<br><br>RESULTS: The 4973 identified specimens comprised 28 species of Culicoides. These included two species reported for the first time in northern Spain, thus raising to 54 the number of Culicoides species described in the region. Specimens of all 28 species and 99.6% of the total specimens collected were caught in suction traps, while sweep netting vegetation revealed just 11 species and 0.4% of the total specimens. Midge abundance peaked in June/early July, with five species comprising > 80% of the captures: Culicoides alazanicus (24.9%), Culicoides griseidorsum (20.3%), Culicoides poperinghensis (16.2%), Culicoides kibunensis (10.7%) and Culicoides clastrieri (9.6%). DNA barcode analysis of blood meals from eight Culicoides species revealed that they fed on 17 vertebrate species (3 mammals and 14 birds). Species in the subgenus Avaritia were primarily ornithophilic, except for C. griseidorsum and C. poperinghensis. Host DNA from blood meals was successfully amplified from 75% of blood-fed females. A pictorial blood meal digestion scale is provided to accurately assess the blood-fed status of female Culicoides.<br><br>CONCLUSIONS: The large number of different blood meal sources identified in the midges captured in this study signals the likely importance of wild birds and mammals (e.g. red deer and wild boar) as reservoir/amplifying hosts for pathogens. Available hosts are more exposed to being bitten by biting midge populations in aquatic ecosystems in late spring and early summer.},
}
@article {pmid35689254,
year = {2022},
author = {Dong, L and Wei, C and Xiong, S and Yu, P and Zhou, R and Cheng, L},
title = {Spliceosome inhibitor induces human hematopoietic progenitor cell reprogramming toward stemness.},
journal = {Experimental hematology &amp; oncology},
volume = {11},
number = {1},
pages = {37},
pmid = {35689254},
issn = {2162-3619},
support = {92068101//National Natural Science Foundation of China/ ; 828313//Shanghai Municipal Education Commission-Gaofeng Clinical Medicine Grant Support/ ; TMSK-2021-106//Project from National Research Center for Translational Medicine at Shanghai/ ; 2019CXJQ01//Shanghai Collaborative Innovation Program on Regenerative Medicine and Stem Cell Research/ ; },
abstract = {The application of hematopoietic stem cells (HSCs) has been restricted due to limited cell sources and conventional methods for generating these cells by cell expansion and pluripotent stem cell differentiation have not been clinically achieved. Cell reprogramming technique provides a new hope for generating desirable cells. We previously reported that mouse differentiated hematopoietic cell reprogramming could be induced by small molecule compounds to generate hematopoietic stem/progenitor-like cells, whether the human hematopoietic cells could also be reprogrammed into HSCs by chemical compounds remains elusive. Here, we demonstrated for the first time that human committed hematopoietic progenitors could be reprogrammed into multipotent progenitors by spliceosome inhibitor. Combination of single cell RNA-sequencing and genetic lineage tracing including exogenous barcodes and endogenous mitochondrial DNA mutations confirmed the reprogramming procession. Although the small chemical compound inhibiting spliceosome function only induces the differentiated hematopoietic progenitors to acquire plasticity and reprograms them into multipotent progenitors but not stem cells so far, this study still provides a proof-of-concept strategy for generating HSCs based on combining two independent steps together in future, first differentiating rare HSCs into large number of progenitors then reprogramming these progenitors into huge number of HSCs. Further dissecting the mechanism underlying spliceosome inhibitor-induced human hematopoietic cell reprogramming in future will help us comprehensively understanding not only the chemical reprogramming to generate desirable human cells for clinical translation but also hematopoiesis under physiological and pathological conditions.},
}
@article {pmid35688884,
year = {2022},
author = {Urumarudappa, SKJ and Tungphatthong, C and Jaipaew, J and Pornputtapong, N and Pakdeesattayapong, D and Vimolmangkang, S and Sukrong, S},
title = {Development of a DNA barcode library of plants in the Thai Herbal Pharmacopoeia and Monographs for authentication of herbal products.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {9624},
pmid = {35688884},
issn = {2045-2322},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Intergenic ; DNA, Plant/genetics ; Gene Library ; Phytotherapy ; *Plants, Medicinal/genetics ; Thailand ; },
abstract = {Traditional herbal medicine has long been practiced as a method of health care in many countries worldwide. The usage of herbal products has been increasing and is expected to continue to do so in the future. However, admixture and adulteration are concerns regarding the quality of herbal medicine, including its safety and efficacy. We aimed to develop a reference DNA barcode library of plants listed in the Thai Herbal Pharmacopoeia (THP) and Monographs of Selected Thai Materia Medica (TMM) (n = 101 plant species) using four core barcode regions, namely, the ITS2, matK, rbcL and trnH-psbA intergenic spacer regions, for authentication of the plant origin of raw materials and herbal products. Checking sequences from samples obtained from local markets and the Thai Food and Drug Administration (Thai FDA) against our digital reference DNA barcode system revealed the authenticity of eighteen out of twenty tested samples as claimed on their labels. Two samples, no. 3 and 13, were not Cyanthillium cinereum (L.) H.Rob. and Pueraria candollei Wall. ex Benth. as claimed, respectively. They were recognized as Emilia sonchifolia (L.) DC. and Butea superba (Roxb.), respectively. Hence, it is important for the Thai FDA or regulatory agencies to immediately initiate strict enforcement for the development of pharmacopoeial standards as well as revisions or modifications of available regulatory guidelines and to implement close monitoring for the quality control of herbal products in terms of authentication before they enter the herbal market. The centralized digital reference DNA barcode database developed here could play a very important role in monitoring or checking the authenticity of medicinal plants.},
}
@article {pmid35685220,
year = {2022},
author = {Senel, E and Rajewsky, N and Karaiskos, N},
title = {Optocoder: computational decoding of spatially indexed bead arrays.},
journal = {NAR genomics and bioinformatics},
volume = {4},
number = {2},
pages = {lqac042},
pmid = {35685220},
issn = {2631-9268},
abstract = {Advancing technologies that quantify gene expression in space are transforming contemporary biology research. A class of spatial transcriptomics methods uses barcoded bead arrays that are optically decoded via microscopy and are later matched to sequenced data from the respective libraries. To obtain a detailed representation of the tissue in space, robust and efficient computational pipelines are required to process microscopy images and accurately basecall the bead barcodes. Optocoder is a computational framework that processes microscopy images to decode bead barcodes in space. It efficiently aligns images, detects beads, and corrects for confounding factors of the fluorescence signal, such as crosstalk and phasing. Furthermore, Optocoder employs supervised machine learning to strongly increase the number of matches between optically decoded and sequenced barcodes. We benchmark Optocoder using data from an in-house spatial transcriptomics platform, as well as from Slide-Seq(V2), and we show that it efficiently processes all datasets without modification. Optocoder is publicly available, open-source and provided as a stand-alone Python package on GitHub: https://github.com/rajewsky-lab/optocoder.},
}
@article {pmid35684242,
year = {2022},
author = {Chen, G and Stepanenko, A and Lakhneko, O and Zhou, Y and Kishchenko, O and Peterson, A and Cui, D and Zhu, H and Xu, J and Morgun, B and Gudkov, D and Friesen, N and Borysyuk, M},
title = {Biodiversity of Duckweed (Lemnaceae) in Water Reservoirs of Ukraine and China Assessed by Chloroplast DNA Barcoding.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
pmid = {35684242},
issn = {2223-7747},
abstract = {Monitoring and characterizing species biodiversity is essential for germplasm preservation, academic studies, and various practical applications. Duckweeds represent a group of tiny aquatic plants that include 36 species divided into 5 genera within the Lemnaceae family. They are an important part of aquatic ecosystems worldwide, often covering large portions of the water reservoirs they inhabit, and have many potential applications, including in bioremediation, biofuels, and biomanufacturing. Here, we evaluated the biodiversity of duckweeds in Ukraine and Eastern China by characterizing specimens using the two-barcode protocol with the chloroplast atpH-atpF and psbK-psbI spacer sequences. In total, 69 Chinese and Ukrainian duckweed specimens were sequenced. The sequences were compared against sequences in the NCBI database using BLAST. We identified six species from China (Spirodela polyrhiza, Landoltia punctata, Lemna aequinoctialis, Lemna minor, Lemna turionifera, and Wolffia globosa) and six from Ukraine (S. polyrhiza, Lemna gibba, Lemna minor, Lemna trisulca, Lemna turionifera, and Wolffia arrhiza). The most common duckweed species in the samples from Ukraine were Le. minor and S. polyrhiza, accounting for 17 and 15 out of 40 specimens, respectively. The most common duckweed species in the samples from China was S. polyrhiza, accounting for 15 out of 29 specimens. La. punctata and Le. aequinoctialis were also common in China, accounting for five and four specimens, respectively. According to both atpH-atpF and psbK-psbI barcode analyses, the species identified as Le. aequinoctialis does not form a uniform taxon similar to other duckweed species, and therefore the phylogenetic status of this species requires further clarification. By monitoring duckweeds using chloroplast DNA sequencing, we not only precisely identified local species and ecotypes, but also provided background for further exploration of native varieties with diverse genetic backgrounds. These data could be useful for future conservation, breeding, and biotechnological applications.},
}
@article {pmid35681319,
year = {2022},
author = {Pappalardo, AM and Giuga, M and Raffa, A and Nania, M and Rossitto, L and Calogero, GS and Ferrito, V},
title = {COIBar-RFLP Molecular Strategy Discriminates Species and Unveils Commercial Frauds in Fishery Products.},
journal = {Foods (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
pmid = {35681319},
issn = {2304-8158},
support = {PIACERI linea 2 2021//University of Catania/ ; },
abstract = {The DNA analysis is the best approach to authenticate species in seafood products and to unveil frauds based on species substitution. In this study, a molecular strategy coupling Cytochrome Oxidase I (COI) DNA barcoding with the consolidated methodology of Restriction Fragment Length Polymorphisms (RFLPs), named COIBar-RFLP, was applied for searching pattern of restriction enzyme digestion, useful to discriminate seven different fish species (juveniles of Engraulis encrasicolus and Sardina pilchardus sold in Italy as "bianchetto" and Aphia minuta sold as "rossetto"; icefish Neosalanx tangkahkeii; European perch, Perca fluviatilis and the Nile Perch, Lates niloticus; striped catfish, Pangasianodon hypophthalmus). A total of 30 fresh and frozen samples were processed for DNA barcoding, analyzed against a barcode library of COI sequences retrieved from GenBank, and validated for COIBar-RFLP analysis. Cases of misdescription were detected: 3 samples labeled as "bianchetto" were substituted by N. tangkahkeii (2 samples) and A. minuta (1 sample); 3 samples labeled as "persico reale" (P. fluviatilis) were substituted by L. niloticus and P. hypophthalmus. All species were simultaneously discriminated through the restriction pattern obtained with MspI enzyme. The results highlighted that the COIBar-RFLP could be an effective tool to authenticate fish in seafood products by responding to the emerging interest in molecular identification technologies.},
}
@article {pmid35679267,
year = {2022},
author = {Thongkhao, K and Tungphatthong, C and Pichetkun, V and Gaewtongliam, S and Wiwatcharakornkul, W and Sukrong, S},
title = {Combining DNA and HPTLC profiles to differentiate a pain relief herb, Mallotus repandus, from plants sharing the same common name, "Kho-Khlan".},
journal = {PloS one},
volume = {17},
number = {6},
pages = {e0268680},
pmid = {35679267},
issn = {1932-6203},
mesh = {Chromatography, Thin Layer ; *DNA Barcoding, Taxonomic/methods ; DNA, Plant/genetics ; *Mallotus Plant ; Pain ; Plants/genetics ; },
abstract = {The pain relief formula "Ya Pa Som Kho-Khlan (YPSKK)" or "ยาผสมโคคลาน" in Thai is officially recorded in the Natural List of Essential Medicines (NLEM) of Thailand. The main component is Mallotus repandus (Willd.) Müll. Arg.; however, Anamirta cocculus (L.) Wight &amp; Arn and Croton caudatus Gleiseler share the same common name: "Kho-Khlan". Confused usage of A. cocculus or C. caudatus can have effects via toxicity or unsuccessful treatment. This study aimed to combine a high-performance thin-layer chromatography (HPTLC) technique and DNA barcoding coupled with high-resolution melting (Bar-HRM) to differentiate M. repandus from the other two species. The M. repandus extract exhibited a distinct HPTLC profile that could be used to differentiate it from the others. DNA barcodes of the rbcL, matK, ITS and psbA-trnH intergenic spacer regions of all the plants were established to assist HPTLC analysis. The rbcL region was selected for Bar-HRM analysis. PCR amplification was performed to obtain 102 bp amplicons encompassing nine polymorphic nucleotides. The amplicons were subjected to HRM analysis to obtain melting curve profiles. The melting temperatures (Tm) of authentic A. cocculus (A), C. caudatus (C) and M. repandus (M) were separated at 82.03±0.09°C, 80.93±0.04°C and 80.05±0.07°C, respectively. The protocol was applied to test crude drugs (CD1-6). The HPTLC profiles of CD2-6 showed distinct bands of M. repandus, while CD1 showed unclear band results. The Bar-HRM method was applied to assist the HPTLC and indicated that CD1 was C. caudatus. While ambiguous melting curves from the laboratory-made formulae were obtained, HPTLC analysis helped reveal distinct patterns for the identification of the plant species. The combination of HPTLC and Bar-HRM analysis could be a tool for confirming the identities of plant species sharing the same name, especially for those whose sources are multiple and difficult to identify by either chemical or DNA techniques.},
}
@article {pmid35679240,
year = {2022},
author = {Zangl, L and Schäffer, S and Daill, D and Friedrich, T and Gessl, W and Mladinić, M and Sturmbauer, C and Wanzenböck, J and Weiss, SJ and Koblmüller, S},
title = {A comprehensive DNA barcode inventory of Austria's fish species.},
journal = {PloS one},
volume = {17},
number = {6},
pages = {e0268694},
pmid = {35679240},
issn = {1932-6203},
mesh = {Animals ; Austria ; DNA/genetics ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics ; Fresh Water ; Phylogeny ; },
abstract = {Austria is inhabited by more than 80 species of native and non-native freshwater fishes. Despite considerable knowledge about Austrian fish species, the latest Red List of threatened species dates back 15 years and a systematic genetic inventory of Austria's fish species does not exist. To fulfill this deficit, we employed DNA barcoding to generate an up-to-date and comprehensive genetic reference database for Austrian fish species. In total, 639 newly generated cytochrome c oxidase subunit 1 (COI) sequences were added to the 377 existing records from the BOLD data base, to compile a near complete reference dataset. Standard sequence similarity analyses resulted in 83 distinct clusters almost perfectly reflecting the expected number of species in Austria. Mean intraspecific distances of 0.22% were significantly lower than distances to closest relatives, resulting in a pronounced barcoding gap and unique Barcode Index Numbers (BINs) for most of the species. Four cases of BIN sharing were detected, pointing to hybridization and/or recent divergence, whereas in Phoxinus spp., Gobio spp. and Barbatula barbatula intraspecific splits, multiple BINs and consequently cryptic diversity were observed. The overall high identification success and clear genetic separation of most of the species confirms the applicability and accuracy of genetic methods for bio-surveillance. Furthermore, the new DNA barcoding data pinpoints cases of taxonomic uncertainty, which need to be addressed in further detail, to more precisely assort genetic lineages and their local distribution ranges in a new National Red-List.},
}
@article {pmid35679087,
year = {2022},
author = {Hoenig, BD and Trevelline, BK and Latta, SC and Porter, BA},
title = {Integrating DNA-Based Prey Occurrence Probability into Stable Isotope Mixing Models.},
journal = {Integrative and comparative biology},
volume = {62},
number = {2},
pages = {211-222},
doi = {10.1093/icb/icac086},
pmid = {35679087},
issn = {1557-7023},
support = {//Duquesne University/ ; //American Ornithological Society/ ; },
mesh = {Animals ; Bayes Theorem ; DNA ; *Diet ; Food Chain ; *Isotopes ; },
abstract = {The introduction of laboratory methods to animal dietary studies has allowed researchers to obtain results with accuracy and precision, not possible with observational techniques. For example, DNA barcoding, or the identification of prey with taxon-specific DNA sequences, allows researchers to classify digested prey tissues to the species-level, while stable isotope analysis paired with Bayesian mixing models can quantify dietary contributions by comparing a consumer's isotopic values to those derived from their prey. However, DNA-based methods are currently only able to classify, but not quantify, the taxa present in a diet sample, while stable isotope analysis can only quantify dietary taxa that are identified a priori as prey isotopic values are a result of life history traits, not phylogenetic relatedness. Recently, researchers have begun to couple these techniques in dietary studies to capitalize on the reciprocal benefits and drawbacks offered by each approach, with some even integrating DNA-based results directly into Bayesian mixing models as informative priors. As the informative priors used in these models must represent known dietary compositions (e.g., percentages of prey biomasses), researchers have scaled the DNA-based frequency of occurrence of major prey groups so that their normalized frequency of occurrence sums to 100%. Unfortunately, such an approach is problematic as priors stemming from binomial, DNA-based data do not truly reflect quantitative information about the consumer's diet and may skew the posterior distribution of prey quantities as a result. Therefore, we present a novel approach to incorporate DNA-based dietary information into Bayesian stable isotope mixing models that preserves the binomial nature of DNA-based results. This approach uses community-wide frequency of occurrence or logistic regression-based estimates of prey occurrence to dictate the probability that each prey group is included in each mixing model iteration, and, in turn, the probability that each iteration's results are included in the posterior distribution of prey composition possibilities. Here, we demonstrate the utility of this method by using it to quantify the prey composition of nestling Louisiana waterthrush (Parkesia motacilla).},
}
@article {pmid35678355,
year = {2022},
author = {Woodyard, ET and Bierman, AE and Edwards, JJ and Finney, JC and Rosser, TG and Griffin, MJ and Marancik, DP},
title = {Kudoa hypoepicardialis and associated cardiac lesions in invasive red lionfish Pterois volitans in Grenada, West Indies.},
journal = {Diseases of aquatic organisms},
volume = {149},
number = {},
pages = {97-108},
doi = {10.3354/dao03663},
pmid = {35678355},
issn = {0177-5103},
mesh = {Animals ; Capsules ; DNA, Ribosomal ; Grenada ; Introduced Species ; *Myxozoa/genetics ; *Perciformes/parasitology ; },
abstract = {Invasive red lionfish Pterois volitans (Linnaeus, 1758) represent an ongoing ecological threat within temperate and tropical waters. Relatively little is known regarding the overall health of P. volitans and their potential for spreading pathogens in non-native regions. Lionfish collected from inshore reefs of Grenada, West Indies, in 2019 and 2021 were identified as P. volitans based on cytochrome c oxidase subunit 1 barcoding. Gross and microscopic examination of tissues revealed myxozoan plasmodia in the hearts of 24/76 (31.6%) lionfish by histopathology or wet mount cytology. Further histopathologic examination revealed severe granulomatous inflammation and myofiber necrosis associated with developing plasmodia and presporogonic life stages. Fresh myxospores were morphologically and molecularly consistent with Kudoa hypoepicardialis, being quadrate in apical view with 4 valves and 4 equal polar capsules. The spore body was 5.1-7.9 (mean: 6.0) µm long, 8.1-9.8 (8.7) µm wide, and 6.9-8.5 (7.7) µm thick. Polar capsules were 2.3-2.7 (2.5) µm long and 0.9-1.6 (1.3) µm wide. 18S small subunit rDNA sequences were 99.81-99.87% similar to sequence data from the original description of the species. Novel 28S large subunit rDNA and elongation factor 2 data, which did not match any previously reported species, were provided. This is the first account of a myxozoan parasite of P. volitans, a new host record and locality for K. hypoepicardialis, and one of few reports describing pathogen-associated lesions in invasive lionfish.},
}
@article {pmid35675678,
year = {2022},
author = {Feng, L and Wu, H and Yue, H and Chu, Y and Zhang, J and Huang, X and Pang, S and Zhang, L and Li, Y and Wang, W and Zou, B and Zhou, G},
title = {Multiplexed and Rapid AST for Escherichia coli Infection by Simultaneously Pyrosequencing Multiple Barcodes Each Specific to an Antibiotic Exposed to a Sample.},
journal = {Analytical chemistry},
volume = {94},
number = {24},
pages = {8633-8641},
doi = {10.1021/acs.analchem.2c00312},
pmid = {35675678},
issn = {1520-6882},
mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria ; Escherichia coli/genetics ; *Escherichia coli Infections/drug therapy/microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Microbial Sensitivity Tests ; },
abstract = {Antimicrobial susceptibility testing (AST) is an effective way to guide antibiotic selection. However, conventional culture-based phenotypic AST is time-consuming. The key point to shorten the test is to quantify the small change in the bacterial number after the antibiotic exposure. To achieve rapid AST, we proposed a combination of multiplexed PCR with barcoded pyrosequencing to significantly shorten the time for antibiotic exposure. First, bacteria exposed to each antibiotic were labeled with a unique barcode. Then, the pool of the barcoded products was amplified by PCR with a universal primer pair. Finally, barcodes in the amplicons were individually and quantitatively decoded by pyrosequencing. As pyrosequencing is able to discriminate as low as 5% variation in target concentrations, as short as 7.5 min was enough for cultivation to detect the susceptibility of Escherichia coli to an antibiotic. The barcodes enable more than six kinds of drugs or six kinds of concentrations of a drug to be tested at a time. The susceptibility of 6 antibiotics to 43 E. coli-positive samples from 482 clinical urine samples showed a consistency of 99.3% for drug-resistant samples and of 95.7% for drug-sensitive samples in comparison with the conventional method. In addition, the minimum inhibitory concentration (MIC) of 29 E. coli samples was successfully measured. The proposed AST is dye free (pyrosequencing), multiplexed (six antibiotics), fast (a half-working day for reporting the results), and able to detect the MIC, thus having a great potential for clinical use in quick antibiotic selection.},
}
@article {pmid35675173,
year = {2022},
author = {Smith, SA and Santoferrara, LF and Katz, LA and McManus, GB},
title = {Genome architecture used to supplement species delineation in two cryptic marine ciliates.},
journal = {Molecular ecology resources},
volume = {22},
number = {8},
pages = {2880-2896},
doi = {10.1111/1755-0998.13664},
pmid = {35675173},
issn = {1755-0998},
support = {DEB-1541511//National Science Foundation/ ; OCE-1924527//National Science Foundation/ ; OCE-1924570//National Science Foundation/ ; },
mesh = {*Ciliophora/genetics ; Genomics ; Phylogeny ; RNA, Ribosomal ; Species Specificity ; },
abstract = {The purpose of this study is to determine which taxonomic methods can elucidate clear and quantifiable differences between two cryptic ciliate species, and to test the utility of genome architecture as a new diagnostic character in the discrimination of otherwise indistinguishable taxa. Two cryptic tintinnid ciliates, Schmidingerella arcuata and Schmidingerella meunieri, are compared via traditional taxonomic characters including lorica morphometrics, ribosomal RNA (rRNA) gene barcodes and ecophysiological traits. In addition, single-cell 'omics analyses (single-cell transcriptomics and genomics) are used to elucidate and compare patterns of micronuclear genome architecture between the congeners. The results include a highly similar lorica that is larger in S. meunieri, a 0%-0.5% difference in rRNA gene barcodes, two different and nine indistinguishable growth responses among 11 prey treatments, and distinct patterns of micronuclear genomic architecture for genes detected in both ciliates. Together, these results indicate that while minor differences exist between S. arcuata and S. meunieri in common indices of taxonomic identification (i.e., lorica morphology, DNA barcode sequences and ecophysiology), differences exist in their genomic architecture, which suggests potential genetic incompatibility. Different patterns of micronuclear architecture in genes shared by both isolates also enable the design of species-specific primers, which are used in this study as unique "architectural barcodes" to demonstrate the co-occurrence of both ciliates in samples collected from a NW Atlantic estuary. These results support the utility of genomic architecture as a tool in species delineation, especially in ciliates that are cryptic or otherwise difficult to differentiate using traditional methods of identification.},
}
@article {pmid35674381,
year = {2022},
author = {Ainciburu, M and Morgan, DM and DePasquale, EAK and Love, JC and Prósper, F and van Galen, P},
title = {WAT3R: recovery of T-cell receptor variable regions from 3' single-cell RNA-sequencing.},
journal = {Bioinformatics (Oxford, England)},
volume = {38},
number = {14},
pages = {3645-3647},
pmid = {35674381},
issn = {1367-4811},
support = {R00 CA218832/CA/NCI NIH HHS/United States ; //Ludwig Center at Harvard/ ; //Gilead Sciences, the Bertarelli Rare Cancers Fund/ ; //William Guy Forbeck Research Foundation/ ; FPU18/05488//Glenn Foundation for Medical Research and American Federation for Aging Research/ ; //Government of Spain/ ; },
mesh = {*Leukocytes, Mononuclear/metabolism ; *Receptors, Antigen, T-Cell/chemistry ; Software ; Clone Cells/metabolism ; RNA ; Single-Cell Analysis ; Receptors, Antigen, T-Cell, alpha-beta/genetics ; },
abstract = {SUMMARY: Diversity of the T-cell receptor (TCR) repertoire is central to adaptive immunity. The TCR is composed of α and β chains, encoded by the TRA and TRB genes, of which the variable regions determine antigen specificity. To generate novel biological insights into the complex functioning of immune cells, combined capture of variable regions and single-cell transcriptomes provides a compelling approach. Recent developments enable the enrichment of TRA and TRB variable regions from widely used technologies for 3'-based single-cell RNA-sequencing (scRNA-seq). However, a comprehensive computational pipeline to process TCR-enriched data from 3' scRNA-seq is not available. Here, we present an analysis pipeline to process TCR variable regions enriched from 3' scRNA-seq cDNA. The tool reports TRA and TRB nucleotide and amino acid sequences linked to cell barcodes, enabling the reconstruction of T-cell clonotypes with associated transcriptomes. We demonstrate the software using peripheral blood mononuclear cells from a healthy donor and detect TCR sequences in a high proportion of single T cells. Detection of TCR sequences is low in non-T-cell populations, demonstrating specificity. Finally, we show that TCR clones are larger in CD8 Memory T cells than in other T-cell types, indicating an association between T-cell clonotypes and differentiation states.<br><br>The Workflow for Association of T-cell receptors from 3' single-cell RNA-seq (WAT3R), including test data, is available on GitHub (https://github.com/mainciburu/WAT3R), Docker Hub (https://hub.docker.com/r/mainciburu/wat3r) and a workflow on the Terra platform (https://app.terra.bio). The test dataset is available on GEO (accession number GSE195956).<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid35672336,
year = {2022},
author = {Chiu, R and Rajan-Babu, IS and Birol, I and Friedman, JM},
title = {Linked-read sequencing for detecting short tandem repeat expansions.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {9352},
pmid = {35672336},
issn = {2045-2322},
support = {153452//CIHR/Canada ; },
mesh = {Algorithms ; *High-Throughput Nucleotide Sequencing/methods ; *Microsatellite Repeats/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {Detection of short tandem repeat (STR) expansions with standard short-read sequencing is challenging due to the difficulty in mapping multicopy repeat sequences. In this study, we explored how the long-range sequence information of barcode linked-read sequencing (BLRS) can be leveraged to improve repeat-read detection. We also devised a novel algorithm using BLRS barcodes for distance estimation and evaluated its application for STR genotyping. Both approaches were designed for genotyping large expansions (> 1 kb) that cannot be sized accurately by existing methods. Using simulated and experimental data of genomes with STR expansions from multiple BLRS platforms, we validated the utility of barcode and phasing information in attaining better STR genotypes compared to standard short-read sequencing. Although the coverage bias of extremely GC-rich STRs is an important limitation of BLRS, BLRS is an effective strategy for genotyping many other STR loci.},
}
@article {pmid35671473,
year = {2022},
author = {Da Silva Sanchez, AJ and Dobrowolski, C and Cristian, A and Echeverri, ES and Zhao, K and Hatit, MZC and Loughrey, D and Paunovska, K and Dahlman, JE},
title = {Universal Barcoding Predicts In Vivo ApoE-Independent Lipid Nanoparticle Delivery.},
journal = {Nano letters},
volume = {22},
number = {12},
pages = {4822-4830},
doi = {10.1021/acs.nanolett.2c01133},
pmid = {35671473},
issn = {1530-6992},
mesh = {Animals ; Apolipoproteins E/genetics/metabolism ; Endothelial Cells/metabolism ; *Lipids ; Lipoproteins, LDL ; Liposomes ; Mice ; *Nanoparticles/metabolism ; RNA, Small Interfering/genetics ; },
abstract = {To predict whether preclinical lipid nanoparticle (LNP) delivery will translate in humans, it is necessary to understand whether the mechanism used by LNPs to enter cells is conserved across species. In mice, non-human primates, and humans, LNPs deliver RNA to hepatocytes by adsorbing apolipoprotein E (ApoE), which binds low-density lipoprotein receptor (LDLR). A growing number of LNPs can deliver RNA to nonhepatocytes, suggesting that ApoE- and LDLR-independent interactions could affect LNP tropism. To evaluate this hypothesis, we developed a universal DNA barcoding system that quantifies how chemically distinct LNPs deliver small interfering RNA in any mouse model, including genetic knockouts. We quantified how 98 different LNPs targeted 11 cell types in wildtype, LDLR[-/-], very low-density lipoprotein receptor, and ApoE[-/-] mice, studying how these genes, which traffic endogenous lipids, affected LNP delivery. These data identified a novel, stereopure LNP that targets Kupffer cells, endothelial cells, and hepatocytes in an ApoE-independent manner. These results suggest that non-ApoE interactions can affect the tropism of LNP-RNA drugs.},
}
@article {pmid35668693,
year = {2022},
author = {Martin Cerezo, ML and Raval, R and de Haro Reyes, B and Kucka, M and Chan, FY and Bryk, J},
title = {Identification and quantification of chimeric sequencing reads in a highly multiplexed RAD-seq protocol.},
journal = {Molecular ecology resources},
volume = {22},
number = {8},
pages = {2860-2870},
pmid = {35668693},
issn = {1755-0998},
support = {0518338//Microsoft Research/ ; },
mesh = {Chimera ; *DNA ; Gene Library ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Sequence Analysis, DNA/methods ; },
abstract = {Highly multiplexed approaches have become common in genomic studies. They have improved the cost-effectiveness of genotyping hundreds of individuals using combinatorially barcoded adapters. These strategies, however, can potentially misassigned reads to incorrect samples. Here, we used a modified quaddRAD protocol to analyse the occurrence of index hopping and PCR chimeras in a series of experiments with up to 100 multiplexed samples per sequencing lane (639 samples in total). We created two types of sequencing libraries: four libraries of type A, where PCRs were run on individual samples before multiplexing, and three libraries of type B, where PCRs were run on pooled samples. We used fixed pairs of inner barcodes to identify chimeric reads. Type B libraries show a higher percentage of misassigned reads (1.15%) than type A libraries (0.65%). We also quantify the commonly undetectable chimeric sequences that occur whenever multiplexed groups of samples with different outer barcodes are sequenced together on a single flow cell. Our results suggest that these types of chimeric sequences represent up to 1.56% and 1.29% of reads in type A and B libraries, respectively. We also show that increasing the number of mismatches allowed for barcode rescue to above 2 dramatically increases the number of recovered chimeric reads. We provide recommendations for developing highly multiplexed RAD-seq protocols and analysing the resulting data to minimize the generation of chimeric sequences, allowing their quantification and a finer control on the number of PCR cycles necessary to generate enough input DNA for library preparation.},
}
@article {pmid35668357,
year = {2022},
author = {Raubach, S and Schreiber, M and Shaw, PD},
title = {GridScore: a tool for accurate, cross-platform phenotypic data collection and visualization.},
journal = {BMC bioinformatics},
volume = {23},
number = {1},
pages = {214},
pmid = {35668357},
issn = {1471-2105},
support = {BB/S004610/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Crops, Agricultural ; Data Collection ; Phenotype ; *Plant Breeding ; },
abstract = {BACKGROUND: Plant breeding and crop research rely on experimental phenotyping trials. These trials generate data for large numbers of traits and plant varieties that needs to be captured efficiently and accurately to support further research and downstream analysis. Traditionally scored by hand, phenotypic data is nowadays collected using spreadsheets or specialized apps. While many solutions exist, which increase efficiency and reduce errors, none offer the same familiarity as printed field plans which have been used for decades and offer an intuitive overview over the trial setup, previously recorded data and plots still requiring scoring.<br><br>RESULTS: We introduce GridScore which utilizes cutting-edge web technologies to reproduce the familiarity of printed field plans while enhancing the phenotypic data collection process by adding advanced features like georeferencing, image tagging and speech recognition. GridScore is a cross-platform open-source plant phenotyping app that combines barcode-based systems with a guided data collection approach while offering a top-down view onto the data collected in a field layout. GridScore is compared to existing tools across a wide spectrum of criteria including support for barcodes, multiple platforms, and visualizations.<br><br>CONCLUSION: Compared to its competition, GridScore shows strong performance across the board offering a complete manual phenotyping experience.},
}
@article {pmid35666173,
year = {2022},
author = {Runnel, K and Abarenkov, K and Copoț, O and Mikryukov, V and Kõljalg, U and Saar, I and Tedersoo, L},
title = {DNA barcoding of fungal specimens using PacBio long-read high-throughput sequencing.},
journal = {Molecular ecology resources},
volume = {22},
number = {8},
pages = {2871-2879},
doi = {10.1111/1755-0998.13663},
pmid = {35666173},
issn = {1755-0998},
support = {PRG1170//Eesti Teadusfond/ ; PRG632//Eesti Teadusfond/ ; Centre of Excellence EcolChange//European Regional Development Fund/ ; Enhancing the conservation performance of protected forest fragments//Estonian State Forest Management Centre/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; DNA, Fungal/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; RNA, Ribosomal, 28S ; Sequence Analysis, DNA ; },
abstract = {Molecular methods are increasingly used to identify species that lack conspicuous macro- or micromorphological characters. Taxonomic and ecological research teams barcode large numbers of collected voucher specimens annually. In this study we assessed the efficiency of long-read high throughput sequencing (HTS) as opposed to the traditionally used Sanger method for taxonomic identification of multiple vouchered fungal specimens. We also evaluated whether this method can provide reference information about intraindividual gene polymorphism. We developed a workflow based on a test set of 423 basidiomycete specimens (representing 195 species), the PacBio HTS method, and ribosomal rRNA operon internal transcribed spacer (ITS) and 28S rRNA gene (LSU) markers. The PacBio HTS had a higher success rate than Sanger sequencing at a comparable cost. Species identification based on PacBio reads was usually straightforward, because the dominant operational taxonomic unit (OTU) typically represented the targeted organism. The PacBio HTS also enabled us to detect widespread polymorphism within the ITS marker. We conclude that multiplex DNA barcoding of the fungal ITS and LSU markers using PacBio HTS is a useful tool for taxonomic identification of large amounts of collected voucher specimens at a competitive price. Furthermore, PacBio HTS accurately recovers various alleles and paralogues, which can provide crucial information for species delimitation and population-level studies.},
}
@article {pmid35665087,
year = {2021},
author = {Okanishi, M and Matsuo, T and Fujita, T},
title = {A New Species of the Genus Ophiomonas Djakonov (Echinodermata: Ophiuroidea: Amphilepididae) from the Deep-Sea of Japan.},
journal = {Zoological studies},
volume = {60},
number = {},
pages = {e59},
pmid = {35665087},
issn = {1810-522X},
abstract = {A new species, Ophiomonas shinseimaruae, is described based on five specimens collected from deep water settings, southeast of Cape Erimo, Hokkaido, Japan. Ophiomonas shinseimaruae sp. n. is distinguished from other congeners based on the following characters: elongate semi-circular and separated radial shields; triangular oral shields; flat and broad tentacle scales on the second tentacle pore; octagonal dorsal arm plates, approximately three times wider than long on proximal portion of the arm; and three arm spines present proximally on the arm. This is the first record of the genus Ophiomonas from Japanese waters. The COI nucleotide sequence for Ophiomonas shinseimaruae sp. n. is provided.},
}
@article {pmid35655992,
year = {2022},
author = {Zhang, L and Huang, W and Zhang, S and Li, Q and Wang, Y and Chen, T and Jiang, H and Kong, D and Lv, Q and Zheng, Y and Ren, Y and Liu, P and Jiang, Y and Chen, Y},
title = {Rapid Detection of Bacterial Pathogens and Antimicrobial Resistance Genes in Clinical Urine Samples With Urinary Tract Infection by Metagenomic Nanopore Sequencing.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {858777},
pmid = {35655992},
issn = {1664-302X},
abstract = {Urinary tract infections (UTIs) are among the most common acquired bacterial infections in humans. The current gold standard method for identification of uropathogens in clinical laboratories is cultivation. However, culture-based assays have substantial drawbacks, including long turnaround time and limited culturability of many potential pathogens. Nanopore sequencing technology can overcome these limitations and detect pathogens while also providing reliable predictions of drug susceptibility in clinical samples. Here, we optimized a metagenomic nanopore sequencing (mNPS) test for pathogen detection and identification in urine samples of 76 patients with acute uncomplicated UTIs. We first used twenty of these samples to show that library preparation by the PCR Barcoding Kit (PBK) led to the highest agreement of positive results with gold standard clinical culture tests, and enabled antibiotic resistance detection in downstream analyses. We then compared the detection results of mNPS with those of culture-based diagnostics and found that mNPS sensitivity and specificity of detection were 86.7% [95% confidence interval (CI), 73.5-94.1%] and 96.8% (95% CI, 82.4-99.9%), respectively, indicating that the mNPS method is a valid approach for rapid and specific detection of UTI pathogens. The mNPS results also performed well at predicting antibiotic susceptibility phenotypes. These results demonstrate that our workflow can accurately diagnose UTI-causative pathogens and enable successful prediction of drug-resistant phenotypes within 6 h of sample receipt. Rapid mNPS testing is thus a promising clinical diagnostic tool for infectious diseases, based on clinical urine samples from UTI patients, and shows considerable potential for application in other clinical infections.},
}
@article {pmid35655052,
year = {2022},
author = {Abdelsalam, NR and Hasan, ME and Javed, T and Rabie, SMA and El-Wakeel, HEMF and Zaitoun, AF and Abdelsalam, AZ and Aly, HM and Ghareeb, RY and Hemeida, AA and Shah, AN},
title = {Endorsement and phylogenetic analysis of some Fabaceae plants based on DNA barcoding.},
journal = {Molecular biology reports},
volume = {49},
number = {6},
pages = {5645-5657},
pmid = {35655052},
issn = {1573-4978},
mesh = {Chloroplasts/genetics ; *DNA Barcoding, Taxonomic/methods ; DNA, Plant/genetics ; *Fabaceae/genetics ; Phylogeny ; },
abstract = {BACKGROUND: DNA barcoding have been considered as a tool to facilitate species identification based on its simplicity and high-level accuracy in compression to the complexity and subjective biases linked to morphological identification of taxa. MaturaseK gene (MatK gene) of the chloroplast is very vital in the plant system which is involved in the group II intron splicing. The main objective of this study is to determine the relative utility of the "MatK" chloroplast gene for barcoding in 15 legume as a tool to facilitate species identification based on their simplicity and high-level accuracy linked to morphological identification of taxa.<br><br>METHODS AND RESULTS: MatK gene sequences were submitted to GenBank and the accession numbers were obtained with sequence length ranging from 730 to 1545 nucleotides. These DNA sequences were aligned with database sequence using PROMALS server, Clustal Omega server and Bioedit program. Maximum likelihood and neighbor-joining algorithms were employed for constructing phylogeny. Overall, these results indicated that the phylogenetic tree analysis and the evolutionary distances of an individual dataset of each species were agreed with a phylogenetic tree of all each other consisting of two clades, the first clade comprising (Enterolobium contortisiliquum, Albizia lebbek), Acacia saligna, Leucaena leucocephala, Dichrostachys Cinerea, (Delonix regia, Parkinsonia aculeata), (Senna surattensis, Cassia fistula, Cassia javanica) and Schotia brachypetala were more closely to each other, respectively. The remaining four species of Erythrina humeana, (Sophora secundiflora, Dalbergia Sissoo, Tipuana Tipu) constituted the second clade.<br><br>CONCLUSION: Moreover, their sequences could be successfully utilized in single nucleotide polymorphism or as part of the sequence as DNA fragment analysis utilizing polymerase chain reaction in plant systematic. Therefore, MatK gene is considered promising a candidate for DNA barcoding in the plant family Fabaceae and provides a clear relationship between the families.},
}
@article {pmid35653470,
year = {2022},
author = {Zheng, W and Zhao, S and Yin, Y and Zhang, H and Needham, DM and Evans, ED and Dai, CL and Lu, PJ and Alm, EJ and Weitz, DA},
title = {High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome.},
journal = {Science (New York, N.Y.)},
volume = {376},
number = {6597},
pages = {eabm1483},
doi = {10.1126/science.abm1483},
pmid = {35653470},
issn = {1095-9203},
support = {P01 HL120839/HL/NHLBI NIH HHS/United States ; R21 AI125990/AI/NIAID NIH HHS/United States ; R21 AI128623/AI/NIAID NIH HHS/United States ; R01 AI153156/AI/NIAID NIH HHS/United States ; },
mesh = {*Bacteria/genetics ; Bacteriophages/genetics ; Bacteroides/genetics/virology ; DNA, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbial Interactions ; Single-Cell Analysis/methods ; },
abstract = {Characterizing complex microbial communities with single-cell resolution has been a long-standing goal of microbiology. We present Microbe-seq, a high-throughput method that yields the genomes of individual microbes from complex microbial communities. We encapsulate individual microbes in droplets with microfluidics and liberate their DNA, which we then amplify, tag with droplet-specific barcodes, and sequence. We explore the human gut microbiome, sequencing more than 20,000 microbial single-amplified genomes (SAGs) from a single human donor and coassembling genomes of almost 100 bacterial species, including several with multiple subspecies strains. We use these genomes to probe microbial interactions, reconstructing the horizontal gene transfer (HGT) network and observing HGT between 92 species pairs; we also identify a significant in vivo host-phage association between crAssphage and one strain of Bacteroides vulgatus. Microbe-seq contributes high-throughput culture-free capabilities to investigate genomic blueprints of complex microbial communities with single-microbe resolution.},
}
@article {pmid35653374,
year = {2022},
author = {Kapustina, &#x17d; and Medžiūnė, J and Dubovskaja, V and Matjošaitis, K and Žeimytė, S and Lubys, A},
title = {Sensitive and accurate analysis of gene expression signatures enabled by oligonucleotide-labelled cDNA.},
journal = {RNA biology},
volume = {19},
number = {1},
pages = {774-780},
pmid = {35653374},
issn = {1555-8584},
mesh = {DNA, Complementary/genetics ; *Oligonucleotides/genetics ; RNA, Messenger/genetics/metabolism ; Sequence Analysis, RNA/methods ; *Transcriptome ; },
abstract = {High-throughput RNA sequencing offers a comprehensive analysis of transcriptome complexity originated from regulatory events, such as differential gene expression, alternative polyadenylation and others, and allows the increase in diagnostic capacity and precision. For gene expression profiling applications that do not specifically require information on alternative splicing events, the mRNA 3' termini counting approach is a cost-effective alternative to whole transcriptome sequencing. Here, we report MTAS-seq (mRNA sequencing via terminator-assisted synthesis) - a novel RNA-seq library preparation method directed towards mRNA 3' termini. We demonstrate the specific enrichment for 3'-terminal regions by simple and quick single-tube protocol with built-in molecular barcoding to enable accurate estimation of transcript abundance. To achieve that, we synthesized oligonucleotide-modified dideoxynucleotides which enable the generation of cDNA libraries at the reverse transcription step. We validated the performance of MTAS-seq on well-characterized reference bulk RNA and further tested it with eukaryotic cell lysates.},
}
@article {pmid35652724,
year = {2022},
author = {Minamoto, T},
title = {Environmental DNA analysis for macro-organisms: species distribution and more.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {29},
number = {3},
pages = {},
pmid = {35652724},
issn = {1756-1663},
mesh = {Biodiversity ; DNA Barcoding, Taxonomic/methods ; *DNA, Environmental ; Ecosystem ; Environmental Monitoring/methods ; },
abstract = {In an era of severe biodiversity loss, biological monitoring is becoming increasingly essential. The analysis of environmental DNA (eDNA) has emerged as a new approach that could revolutionize the biological monitoring of aquatic ecosystems. Over the past decade, macro-organismal eDNA analysis has undergone significant developments and is rapidly becoming established as the golden standard for non-destructive and non-invasive biological monitoring. In this review, I summarize the development of macro-organismal eDNA analysis to date and the techniques used in this field. I also discuss the future perspective of these analytical methods in combination with sophisticated analytical techniques for DNA research developed in the fields of molecular biology and molecular genetics, including genomics, epigenomics, and single-cell technologies. eDNA analysis, which to date has been used primarily for determining the distribution of organisms, is expected to develop into a tool for elucidating the physiological state and behaviour of organisms. The fusion of microbiology and macrobiology through an amalgamation of these technologies is anticipated to lead to the future development of an integrated biology.},
}
@article {pmid35652461,
year = {2022},
author = {Tounsi, WA and Lenis, VP and Tammi, SM and Sainio, S and Haimila, K and Avent, ND and Madgett, TE},
title = {Rh Blood Group D Antigen Genotyping Using a Portable Nanopore-based Sequencing Device: Proof of Principle.},
journal = {Clinical chemistry},
volume = {68},
number = {9},
pages = {1196-1201},
doi = {10.1093/clinchem/hvac075},
pmid = {35652461},
issn = {1530-8561},
mesh = {Alleles ; Genotype ; Humans ; *Nanopore Sequencing ; *Nanopores ; Rh-Hr Blood-Group System/genetics ; },
abstract = {BACKGROUND: Nanopore sequencing is direct sequencing of a single-stranded DNA molecule using biological pores. A portable nanopore-based sequencing device from Oxford Nanopore Technologies (MinION) depends on driving a DNA molecule through nanopores embedded in a membrane using a voltage. Changes in current are then measured by a sensor, thousands of times per second and translated to nucleobases.<br><br>METHODS: Genomic DNA (gDNA) samples (n&#x2009;=&#x2009;13) were tested for Rh blood group D antigen (RHD) gene zygosity using droplet digital PCR. The RHD gene was amplified in 6 overlapping amplicons using long-range PCR. Amplicons were purified, and the sequencing library was prepared following the 1D Native barcoding gDNA protocol. Sequencing was carried out with 1D flow cells R9 version. Data analysis included basecalling, aligning to the RHD reference sequence, and calling variants. Variants detected were compared to the results acquired previously by the Ion Personal Genome Machine (Ion PGM).<br><br>RESULTS: Up to 500&#xd7; sequence coverage across the RHD gene allowed accurate variant calling. Exonic changes in the RHD gene allowed RHD allele determination for all samples sequenced except 1 RHD homozygous sample, where 2 heterozygous RHD variant alleles are suspected. There were 3 known variant RHD alleles (RHD*01W.02, RHD*11, and RHD*15) and 6 novel RHD variant alleles, as previously seen in Ion PGM sequencing data for these samples.<br><br>CONCLUSIONS: MinION was effective in blood group genotyping, provided enough sequencing data to achieve high coverage of the RHD gene, and enabled confident calling of variants and RHD allele determination.},
}
@article {pmid35651766,
year = {2022},
author = {Petrova, D and Gašić, U and Yocheva, L and Hinkov, A and Yordanova, Z and Chaneva, G and Mantovska, D and Paunov, M and Ivanova, L and Rogova, M and Shishkova, K and Todorov, D and Tosheva, A and Kapchina-Toteva, V and Vassileva, V and Atanassov, A and Mišić, D and Bonchev, G and Zhiponova, M},
title = {Catmint (Nepeta nuda L.) Phylogenetics and Metabolic Responses in Variable Growth Conditions.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {866777},
pmid = {35651766},
issn = {1664-462X},
abstract = {Nepeta nuda (catmint; Lamiaceae) is a perennial medicinal plant with a wide geographic distribution in Europe and Asia. This study first characterized the taxonomic position of N. nuda using DNA barcoding technology. Since medicinal plants are rich in secondary metabolites contributing to their adaptive immune response, we explored the N. nuda metabolic adjustment operating under variable environments. Through comparative analysis of wild-grown and in vitro cultivated plants, we assessed the change in phenolic and iridoid compounds, and the associated immune activities. The wild-grown plants from different Bulgarian locations contained variable amounts of phenolic compounds manifested by a general increase in flowers, as compared to leaves, while a strong reduction was observed in the in vitro plants. A similar trend was noted for the antioxidant and anti-herpesvirus activity of the extracts. The antimicrobial potential, however, was very similar, regardless the growth conditions. Analysis of the N. nuda extracts led to identification of 63 compounds including phenolic acids and derivatives, flavonoids, and iridoids. Quantification of the content of 21 target compounds indicated their general reduction in the extracts from in vitro plants, and only the ferulic acid (FA) was specifically increased. Cultivation of in vitro plants under different light quality and intensity indicated that these variable light conditions altered the content of bioactive compounds, such as aesculin, FA, rosmarinic acid, cirsimaritin, naringenin, rutin, isoquercetin, epideoxyloganic acid, chlorogenic acid. Thus, this study generated novel information on the regulation of N. nuda productivity using light and other cultivation conditions, which could be exploited for biotechnological purposes.},
}
@article {pmid35651283,
year = {2023},
author = {Tommasi, N and Biella, P and Maggioni, D and Fallati, L and Agostinetto, G and Labra, M and Galli, P and Galimberti, A},
title = {DNA metabarcoding unveils the effects of habitat fragmentation on pollinator diversity, plant-pollinator interactions, and pollination efficiency in Maldive islands.},
journal = {Molecular ecology},
volume = {32},
number = {23},
pages = {6394-6404},
doi = {10.1111/mec.16537},
pmid = {35651283},
issn = {1365-294X},
support = {PONRI FSE REACT-EU 2014-2020 - "Azione IV.4 -//Ministero dell'Universit&#xe0; e della Ricerca/ ; //"Azione IV.4-: Dottorati e contratti di ricerca su tematiche dell'innovazione, Azione IV.6 Contratti di ricerca su tematiche Green"/ ; },
mesh = {Bees ; Animals ; *Ecosystem ; *Pollination ; DNA Barcoding, Taxonomic ; Maldives ; Insecta ; Plants ; Flowers ; },
abstract = {Habitat fragmentation affects biodiversity, but with unclear effects on pollinators and their interactions with plants in anthropized landscapes. Islands could serve as open air laboratories, suitable to disentangle how land-use alteration impacts pollination ecology. In Maldive islands we investigated how pollinator richness, plant-pollinator interactions and pollination efficiency are influenced by the green area fragmentation (i.e., gardens and semi-natural patches). Moreover, we considered the mediating role of pollinator body size and the plant trait of being invasive in shaping interactions. To do this, we surveyed pollinator insects from 11 islands representing a gradient of green area fragmentation. A DNA metabarcoding approach was adopted to identify the pollen transported by pollinators and characterize the plant-pollinator interactions. We found that intermediate levels of green area fragmentation characterized pollinator communities and increased their species richness, while decreasing interaction network complexity. Invasive plants were more frequently found on pollinator bodies than native or exotic noninvasive ones, indicating a concerningly higher potential for pollen dispersal and reproduction of the former ones. Intriguingly, pollinator body size mediated the effect of landscape alteration on interactions, as only the largest bees expanded the foraging diet in terms of plant richness in the transported pollen at increasing fragmentation. In parallel, the pollination efficiency increased with pollinator species richness in two sentinel plants. This study shows that moderate landscape fragmentation of green areas shapes many aspects of the pollination ecosystem service, where despite interactions being less complex and mediated by pollinator body size, pollinator insect biodiversity and potential plant reproduction are supported.},
}
@article {pmid35648650,
year = {2022},
author = {Stachowski, TR and Vanarotti, M and Seetharaman, J and Lopez, K and Fischer, M},
title = {Water Networks Repopulate Protein-Ligand Interfaces with Temperature.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {61},
number = {31},
pages = {e202112919},
pmid = {35648650},
issn = {1521-3773},
support = {P30 GM133893/GM/NIGMS NIH HHS/United States ; R35 GM142772/GM/NIGMS NIH HHS/United States ; },
mesh = {Binding Sites ; Crystallography, X-Ray ; Ligands ; Protein Binding ; Protein Conformation ; *Proteins/chemistry ; Temperature ; *Water ; },
abstract = {High-resolution crystal structures highlight the importance of water networks in protein-ligand interactions. However, as these are typically determined at cryogenic temperature, resulting insights may be structurally precise but not biologically accurate. By collecting 10 matched room-temperature and cryogenic datasets of the biomedical target Hsp90α, we identified changes in water networks that impact protein conformations at the ligand binding interface. Water repositioning with temperature repopulates protein ensembles and ligand interactions. We introduce Flipper conformational barcodes to identify temperature-sensitive regions in electron density maps. This revealed that temperature-responsive states coincide with ligand-responsive regions and capture unique binding signatures that disappear upon cryo-cooling. Our results have implications for discovering Hsp90 selective ligands, and, more generally, for the utility of hidden protein and water conformations in drug discovery.},
}
@article {pmid35643322,
year = {2022},
author = {Nakao, M and Ishikawa, T and Hibino, Y and Ohari, Y and Taniguchi, R and Takeyama, T and Nakamura, S and Kakino, W and Ikadai, H and Sasaki, M},
title = {Resolution of cryptic species complexes within the genus Metagonimus (Trematoda: Heterophyidae) in Japan, with descriptions of four new species.},
journal = {Parasitology international},
volume = {90},
number = {},
pages = {102605},
doi = {10.1016/j.parint.2022.102605},
pmid = {35643322},
issn = {1873-0329},
mesh = {Animals ; Fishes/parasitology ; *Heterophyidae/anatomy &amp; histology ; Japan/epidemiology ; Metacercariae/genetics ; Mice ; *Trematoda ; *Trematode Infections/epidemiology/parasitology/veterinary ; },
abstract = {A nationwide fish survey was conducted in Japan to detect metacercariae of the genus Metagonimus (Trematoda: Heterophyidae). The metacercariae were subjected to DNA barcoding for molecular species identification. A phylogeny inferred from the sequences of mitochondrial cytochrome c oxidase subunit 1 (cox1) prompted us to recognize three cryptic species complexes (i.e., the M. miyatai complex, the M. takahashii complex, and the M. katsuradai complex). Each complex included one or two undescribed species. For morphological description, adult flukes of each species were raised through the experimental infections of immunosuppressed mice. We propose M. saitoi n. sp., M. kogai n. sp., M. shimazui n. sp., and M. kinoi n. sp., based on their phylogeny, morphology, biogeography, and ecology (host-parasite relationships). The originally described species, M. miyatai, was split into M. miyatai sensu stricto and M. saitoi n. sp. The former is distributed mainly in eastern Japan and uses the sweetfish (Plecoglossus altivelis) and daces (Pseudaspius hakonensis and Ps. sachalinensis) as principal second intermediate hosts, while the latter is in western Japan and its principal fish hosts are the dark chub (Nipponocypris temminckii) and the pale chub (Opsariichthys platypus). The present survey resolves a long-standing controversy on the microtaxonomy of Metagonimus in Japan since the first discovery of Metagonimus yokogawai in 1912, and shows that 10 species of Metagonimus are still distributed in Japan, although human metagonimiasis is almost eradicated.},
}
@article {pmid35642794,
year = {2022},
author = {Kumar, R},
title = {Materiomically Designed Polymeric Vehicles for Nucleic Acids: Quo Vadis?.},
journal = {ACS applied bio materials},
volume = {5},
number = {6},
pages = {2507-2535},
doi = {10.1021/acsabm.2c00346},
pmid = {35642794},
issn = {2576-6422},
mesh = {Excipients ; Gene Editing ; Gene Transfer Techniques ; Genetic Therapy ; *Nucleic Acids/genetics ; Polymers/chemistry ; },
abstract = {Despite rapid advances in molecular biology, particularly in site-specific genome editing technologies, such as CRISPR/Cas9 and base editing, financial and logistical challenges hinder a broad population from accessing and benefiting from gene therapy. To improve the affordability and scalability of gene therapy, we need to deploy chemically defined, economical, and scalable materials, such as synthetic polymers. For polymers to deliver nucleic acids efficaciously to targeted cells, they must optimally combine design attributes, such as architecture, length, composition, spatial distribution of monomers, basicity, hydrophilic-hydrophobic phase balance, or protonation degree. Designing polymeric vectors for specific nucleic acid payloads is a multivariate optimization problem wherein even minuscule deviations from the optimum are poorly tolerated. To explore the multivariate polymer design space rapidly, efficiently, and fruitfully, we must integrate parallelized polymer synthesis, high-throughput biological screening, and statistical modeling. Although materiomics approaches promise to streamline polymeric vector development, several methodological ambiguities must be resolved. For instance, establishing a flexible polymer ontology that accommodates recent synthetic advances, enforcing uniform polymer characterization and data reporting standards, and implementing multiplexed in vitro and in vivo screening studies require considerable planning, coordination, and effort. This contribution will acquaint readers with the challenges associated with materiomics approaches to polymeric gene delivery and offers guidelines for overcoming these challenges. Here, we summarize recent developments in combinatorial polymer synthesis, high-throughput screening of polymeric vectors, omics-based approaches to polymer design, barcoding schemes for pooled in vitro and in vivo screening, and identify materiomics-inspired research directions that will realize the long-unfulfilled clinical potential of polymeric carriers in gene therapy.},
}
@article {pmid35640913,
year = {2022},
author = {Longo, AV},
title = {Metabarcoding Approaches in Amphibian Disease Ecology: Disentangling the Functional Contributions of Skin Bacteria on Disease Outcome.},
journal = {Integrative and comparative biology},
volume = {62},
number = {2},
pages = {252-261},
doi = {10.1093/icb/icac062},
pmid = {35640913},
issn = {1557-7023},
support = {DEB-1310036//National Science Foundation/ ; //University of Florida College of Liberal Arts and Sciences/ ; //Department of Biology/ ; },
mesh = {Animals ; Anura/genetics ; Bacteria/genetics ; *Chytridiomycota/genetics ; RNA, Ribosomal, 16S/genetics ; Skin/microbiology ; },
abstract = {Molecular technologies have revolutionized the field of wildlife disease ecology, allowing the detection of outbreaks, novel pathogens, and invasive strains. In particular, metabarcoding approaches, defined here as tools used to amplify and sequence universal barcodes from a single sample (e.g., 16S rRNA for bacteria, ITS for fungi, 18S rRNA for eukaryotes), are expanding our traditional view of host-pathogen dynamics by integrating microbial interactions that modulate disease outcome. Here, I provide an analysis from the perspective of the field of amphibian disease ecology, where the emergence of multi-host pathogens has caused global declines and species extinctions. I reanalyzed an experimental mesocosm dataset to infer the functional profiles of the skin microbiomes of coqui frogs (Eleutherodactylus coqui), an amphibian species that is consistently found infected with the fungal pathogen Batrachochytrium dendrobatidis and has high turnover of skin bacteria driven by seasonal shifts. I found that the metabolic activities of microbiomes operate at different capacities depending on the season. Global enrichment of predicted functions was more prominent during the warm-wet season, indicating that microbiomes during the cool-dry season were either depauperate, resistant to new bacterial colonization, or that their functional space was more saturated. These findings suggest important avenues to investigate how microbes regulate population growth and contribute to host physiological processes. Overall, this study highlights the current challenges and future opportunities in the application of metabarcoding to investigate the causes and consequences of disease in wild systems.},
}
@article {pmid35638512,
year = {2022},
author = {O Attia, A and A Ismail, I and S Dessoky, ED and S Aljuaid, B},
title = {Using of DNA-Barcoding, SCoT and SDS-PAGE Protein to Assess Soma-Clonal Variation in Micro-Propagated Fig (Ficus carica L.) Plant.},
journal = {Pakistan journal of biological sciences : PJBS},
volume = {25},
number = {5},
pages = {415-425},
doi = {10.3923/pjbs.2022.415.425},
pmid = {35638512},
issn = {1812-5735},
mesh = {Codon, Initiator ; DNA, Plant/genetics ; Electrophoresis, Polyacrylamide Gel ; *Ficus/genetics ; Genetic Markers ; Phylogeny ; },
abstract = {Background and Objective: In vitro propagation of fig (Ficus carica L.) is one of the possible approaches that may be used to maximize the diversity of plant species. The current work was carried out to evaluate genetic stability of micropropagated fig plantlets and to determine the effect of in vitro propagation on genomic content of Saudi fig. Materials and Methods: The start codon-targeted (SCoT), DNA-barcoding chloroplast gene RNA polymerase1 (rpoC1 sequencing) and total protein profiling assays (SDS-PAGE) techniques were used to detect genetic stability in micropropagated fig plantlets. Results: The Scorable PCR bands were produced with 10 SCoT primers used, where the total number of bands was 135 bands. Twenty polymorphic bands were generated with 18.4% of a polymorphism percentage. According to the result, no visual unique bands were generated which confirmed the genetic homogeneity of micropropagated plantlets samples compared to the control sample (mother plant). Sequence analysis and phylogenetic tree generated using fig rpoC1 sequence showed high similarity between control and plantlets samples of fig plant. The protein profiling results revealed no remarkable changes between micropropagated plantlets and the mother plant. Conclusion: The results indicate that using SCoT, DNA barcoding and protein profiling have demonstrated their utility to detect genetic homogeneity in micropropagated fig plantlets, which suggests using of micropropagation protocol of plants applied on the plantlets in the current study as a reliable protocol for in vitro culture and conservation of fig plant.},
}
@article {pmid35637791,
year = {2022},
author = {Li, Z and Núñez, R and Light, ME and Ruiz, E and Teixidor, F and Viñas, C and Ruiz-Molina, D and Roscini, C and Planas, JG},
title = {Water-Stable Carborane-Based Eu[3+]/Tb[3+] Metal-Organic Frameworks for Tunable Time-Dependent Emission Color and Their Application in Anticounterfeiting Bar-Coding.},
journal = {Chemistry of materials : a publication of the American Chemical Society},
volume = {34},
number = {10},
pages = {4795-4808},
pmid = {35637791},
issn = {0897-4756},
abstract = {Luminescent lanthanide metal-organic frameworks (Ln-MOFs) have been shown to exhibit relevant optical properties of interest for practical applications, though their implementation still remains a challenge. To be suitable for practical applications, Ln-MOFs must be not only water stable but also printable, easy to prepare, and produced in high yields. Herein, we design and synthesize a series of m CB-Eu y Tb 1-y (y = 0-1) MOFs using a highly hydrophobic ligand mCBL1: 1,7-di(4-carboxyphenyl)-1,7-dicarba-closo-dodecaborane. The new materials are stable in water and at high temperature. Tunable emission from green to red, energy transfer (ET) from Tb[3+] to Eu[3+], and time-dependent emission of the series of mixed-metal m CB-Eu y Tb 1-y MOFs are reported. An outstanding increase in the quantum yield (QY) of 239% of mCB-Eu (20.5%) in the mixed mCB-Eu0.1Tb0.9 (69.2%) is achieved, along with an increased and tunable lifetime luminescence (from about 0.5 to 10 000 μs), all of these promoted by a highly effective ET process. The observed time-dependent emission (and color), in addition to the high QY, provides a simple method for designing high-security anticounterfeiting materials. We report a convenient method to prepare mixed-metal Eu/Tb coordination polymers (CPs) that are printable from water inks for potential applications, among which anticounterfeiting and bar-coding have been selected as a proof-of-concept.},
}
@article {pmid35631799,
year = {2022},
author = {Cahyaningsih, R and Compton, LJ and Rahayu, S and Magos Brehm, J and Maxted, N},
title = {DNA Barcoding Medicinal Plant Species from Indonesia.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {10},
pages = {},
pmid = {35631799},
issn = {2223-7747},
support = {20160722038259//Ministry of Finance of the Republic of Indonesia (Indonesia Endowment Fund for Education (LPDP))/ ; },
abstract = {Over the past decade, plant DNA barcoding has emerged as a scientific breakthrough and is often used to help with species identification or as a taxonomical tool. DNA barcoding is very important in medicinal plant use, not only for identification purposes but also for the authentication of medicinal products. Here, a total of 61 Indonesian medicinal plant species from 30 families and a pair of ITS2, matK, rbcL, and trnL primers were used for a DNA barcoding study consisting of molecular and sequence analyses. This study aimed to analyze how the four identified DNA barcoding regions (ITS2, matK, rbcL, and trnL) aid identification and conservation and to investigate their effectiveness for DNA barcoding for the studied species. This study resulted in 212 DNA barcoding sequences and identified new ones for the studied medicinal plant species. Though there is no ideal or perfect region for DNA barcoding of the target species, we recommend matK as the main region for Indonesian medicinal plant identification, with ITS2 and rbcL as alternative or complementary regions. These findings will be useful for forensic studies that support the conservation of medicinal plants and their national and global use.},
}
@article {pmid35631772,
year = {2022},
author = {Karapatzak, E and Krigas, N and Ganopoulos, I and Papanastasi, K and Kyrkas, D and Yfanti, P and Nikisianis, N and Karydas, A and Manthos, I and Kosma, IS and Badeka, AV and Fotakis, D and Maloupa, E and Patakioutas, G},
title = {Documenting Greek Indigenous Germplasm of Cornelian Cherry (Cornus mas L.) for Sustainable Utilization: Molecular Authentication, Asexual Propagation, and Phytochemical Evaluation.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {10},
pages = {},
pmid = {35631772},
issn = {2223-7747},
support = {T1EDK-05434//RESEARCH-CREATE-INNOVATE/ ; },
abstract = {Wild-growing Cornelian cherries (Cornus mas L., Cornaceae) are well-known native fruits in Greece since ancient times that are still consumed locally nowadays. Modern research has highlighted the value of Cornelian cherries as functional food with exceptional health benefits on account of the fruits’ biochemical profile. However, apart from local consumption directly from wild growing individuals, Greek native C. mas populations have not yet been investigated or sustainably utilized. A multifaceted evaluation was conducted herein including authorized collection-documentation, taxonomic identification, and molecular authentication (DNA barcoding), asexual propagation via cuttings and phytochemical evaluation (multiple antioxidant profiling) of neglected and underutilized Greek native C. mas germplasm sources. Successive botanical expeditions resulted in the collection of 18 samples of genotypes from distant C. mas populations across different natural habitats in Greece, most of which were DNA fingerprinted for the first time. Asexual propagation trials revealed high variability in rooting frequencies among Greek genotypes with low (<25%), average (25−50%), and adequate propagation potential (>50%) using external indole-3-butyric acid (IBA) hormone application on soft- or hard-wood cuttings. The comparative phytochemical evaluation of the studied Greek genotypes showed significant potential in terms of antioxidant activity (>80% radical scavenging activity in 13 genotypes), but with variable phenolic content (47.58−355.46 mg GAE/100 g), flavonoid content (0.15−0.86 mg CE/100 g), and vitamin C content (1−59 mg AAE/100 g). The collected material is currently maintained under ex situ conservation for long-term monitoring coupled with ongoing pilot cultivation trials. The pivotal data create for the first time a framework for the sustainable utilization of Greek native C. mas germplasm as a superfood with significant agronomic potential.},
}
@article {pmid35631742,
year = {2022},
author = {Ha, WY and Wong, KL and Ma, WY and Lau, YY and Chan, WH},
title = {Enhancing Testing Laboratory Engagement in Plant DNA Barcoding through a Routine Workflow-A Case Study on Chinese Materia Medica (CMM).},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {10},
pages = {},
pmid = {35631742},
issn = {2223-7747},
abstract = {Introduction of DNA standards into Pharmacopoeia in different parts of the world enables identification of herbal materials in a complementary manner. However, little has been discussed about the quality requirements for a testing laboratory to implement DNA barcoding methods for herbal materials, which has limited the test method to be developed as a routine service. To encourage the engagement of testing laboratory in application of DNA barcode, a practical workflow including the components of analytical run and the corresponding quality control plan was suggested and employed to address a real-life challenge faced by the differentiation of plant-derived Chinese Materia Medica (CMM), Herba Potentillae Chinensis (Wei ling Cai), Herba Potentillae Discoloris (Fan Bai Cai), Radix Pulsatillae (Bai Tou Weng), and Radix Arnebiae (Zi Cao), which share similar morphological characteristics and multiple species involved. The ITS2 barcode results indicated that there are significant differences among the four CMM, together with quality control plan data to ensure the measurement traceability and validity of test results.},
}
@article {pmid35631007,
year = {2022},
author = {Noureldin, E and Tan, D and Daffalla, O and Almutairi, H and Ghzwani, J and Torno, M and Mashi, O and Hobani, Y and Ding, H and Alamri, A and Shrwani, K and Albarrag, A and Eisa, Z},
title = {DNA Barcoding of Potential Mosquito Disease Vectors (Diptera, Culicidae) in Jazan Region, Saudi Arabia.},
journal = {Pathogens (Basel, Switzerland)},
volume = {11},
number = {5},
pages = {},
pmid = {35631007},
issn = {2076-0817},
abstract = {The conventional morphological characterization of mosquito species remains heavily used for species identification in Jazan, Saudi Arabia. It requires substantial expertise and time, as well as having difficulty in confirming identity of morphologically similar species. Therefore, to establish a reliable and accurate identification system that can be applied to understanding spatial distribution of local mosquito species from the Jazan region, DNA barcoding was explored as an integrated tool for mosquito species identification. In this study, 44 adult mosquito specimens were analyzed, which contain 16 species belong to three genera of potential mosquito disease vectors (Aedes, Anopheles, and Culex). The specimens were collected from the Jazan region located in southwest Saudi Arabia. These included old and preserved mosquito voucher specimens. In addition, we assessed the genetic distance based on the generated mitochondrial partial COI DNA barcodes to detect cryptic diversity across these taxa. Nine mosquito species belonging to three genera were successfully barcoded and submitted to GenBank, namely: Aedes aegypti, Aedes caspius, Aedes vexans, Aedes vittatus, Anopheles arabiensis, Culex pipiens, Culex quinquefasciatus, Culex sitiens, and Culex tritaeniorhynchus. Of these nine species, Aedes vexans, Aedes vittatus, Culex sitiens, and Culex tritaeniorhynchus were registered in GenBank for the first time from Saudi Arabia. The DNA barcodes generated a 100% match to known barcodes of these mosquito species, that also matched with the morphological identification. Ae. vexans was found to be either a case of cryptic species (subspecies) or a new species from the region. However, more research has to be conducted to prove the latter. This study directly contributes to the development of a molecular reference library of mosquito species from the Jazan region and Saudi Arabia. The library is essential for confirmation of species in support of existing mosquito surveillance and control programmes.},
}
@article {pmid35630455,
year = {2022},
author = {Weslati, M and Ghrab, J and Benabid, M and Souissi, O and Aoun, K and Bouratbine, A},
title = {Diversity, Abundance and Leishmania infantum Infection Rate of Phlebotomine Sandflies in an Area with Low Incidence of Visceral Leishmaniasis in Northern Tunisia.},
journal = {Microorganisms},
volume = {10},
number = {5},
pages = {},
pmid = {35630455},
issn = {2076-2607},
support = {LR16IPT06//Ministry of Higher Education and Scientific Research/ ; },
abstract = {We report the study of sandfly Leishmania infection in an area of low incidence of visceral leishmaniasis in Tunisia. Sandflies were collected monthly using CDC light-traps set in houses and animal shelters during May-November 2016 and 2017. All males were identified at the species level. A sample of 878 females including all gravid specimens was subjected to kDNA qPCR for Leishmania detection and parasite load estimation. Leishmania species were determined by ITS1 PCR sequencing, and species identification of infected sandflies was performed by DNA barcoding. Phlebotomus perfiliewi and P. perniciosus were the dominant species during the two-year period. However, comparison of their relative abundances showed that P. perniciosus was more abundant during peaks of 2017 with longer activity duration. Real-time kDNA PCR did not detect Leishmania infection in 2016, although it identified four positive specimens (0.7%) in 2017. All four infected specimens were identified as P. perniciosus. ITS1 PCR sequencing allowed L. infantum identification in one kDNA qPCR-positive specimen. This was a P. perniciosus gravid female with a high parasite load caught during the long-lasting peak of 2017. This work highlights the usefulness of multi-seasonal studies of sandfly dynamics and kDNA qPCR in screening Leishmania infection and determining L. infantum vectors in hypo-endemic foci of human leishmaniasis.},
}
@article {pmid35628459,
year = {2022},
author = {Ishino, T and Takeno, S and Takemoto, K and Yamato, K and Oda, T and Nishida, M and Horibe, Y and Chikuie, N and Kono, T and Taruya, T and Hamamoto, T and Ueda, T},
title = {Distinct Gene Set Enrichment Profiles in Eosinophilic and Non-Eosinophilic Chronic Rhinosinusitis with Nasal Polyps by Bulk RNA Barcoding and Sequencing.},
journal = {International journal of molecular sciences},
volume = {23},
number = {10},
pages = {},
pmid = {35628459},
issn = {1422-0067},
support = {22K09668//the Japan Society for the Promotion of Science KAKENHI grant/ ; 21FC1013//the Health Labor Sciences Research grant/ ; 0G20KA7383//Research Collaboration Fund with Universal Sound Design Inc/ ; },
mesh = {Chronic Disease ; Humans ; *Nasal Polyps/complications/genetics/metabolism ; RNA ; *Rhinitis/complications/genetics ; *Sinusitis/complications/genetics ; },
abstract = {Chronic rhinosinusitis with nasal polyps (CRSwNP) is a chronic inflammatory disease with a high symptom burden, including nasal congestion and smell disorders. This study performed a detailed transcriptomic analysis in CRSwNP classified as eosinophilic CRS (ECRS), nonECRS according to the Japanese Epidemiological Survey of Refractory Eosinophilic Chronic Rhinosinusitis (JESREC) criteria, and a group of ECRS with comorbid aspirin intolerant asthma (Asp). Gene expression profiles of nasal polyps and the uncinate process in CRSwNP patients and normal subjects (controls) were generated by bulk RNA barcoding and sequencing (BRB-seq). A differentially expressed genes (DEGs) analysis was performed using DESeq2 software in iDEP to clarify any relationship between gene expression and disease backgrounds. A total of 3004 genes were identified by DEGs analysis to be associated with ECRS vs control, nonECRS vs control, and Asp vs control. A pathway analysis showed distinct profiles between the groups. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) showed distinct phenotype-specific pathways of expressed genes. In the specific pathway of "cytokine-cytokine receptor interaction", the differentially expressed genes were widely distributed. This study indicates that transcriptome analysis using BRB-seq may be a valuable tool to explore the pathogenesis of type 2 inflammation in CRSwNP.},
}
@article {pmid35628169,
year = {2022},
author = {Pezzotti, G and Kobara, M and Nakaya, T and Imamura, H and Miyamoto, N and Adachi, T and Yamamoto, T and Kanamura, N and Ohgitani, E and Marin, E and Zhu, W and Nishimura, I and Mazda, O and Nakata, T and Makimura, K},
title = {Raman Spectroscopy of Oral Candida Species: Molecular-Scale Analyses, Chemometrics, and Barcode Identification.},
journal = {International journal of molecular sciences},
volume = {23},
number = {10},
pages = {},
pmid = {35628169},
issn = {1422-0067},
support = {N/A//The Strategic Foundational Technology Improvement Support Operation 2019 of the Japanese Government/ ; N/A//Tokuyama Science Foundation/ ; N/A//Young Scientists at Kyoto Prefectural Public University Corporation/ ; },
mesh = {*Candida/chemistry/genetics ; Candida albicans ; *Candidiasis, Oral/diagnosis ; Chemometrics ; Spectrum Analysis, Raman/methods ; },
abstract = {Oral candidiasis, a common opportunistic infection of the oral cavity, is mainly caused by the following four Candida species (in decreasing incidence rate): Candida albicans, Candida glabrata, Candida tropicalis, and Candida krusei. This study offers in-depth Raman spectroscopy analyses of these species and proposes procedures for an accurate and rapid identification of oral yeast species. We first obtained average spectra for different Candida species and systematically analyzed them in order to decode structural differences among species at the molecular scale. Then, we searched for a statistical validation through a chemometric method based on principal component analysis (PCA). This method was found only partially capable to mechanistically distinguish among Candida species. We thus proposed a new Raman barcoding approach based on an algorithm that converts spectrally deconvoluted Raman sub-bands into barcodes. Barcode-assisted Raman analyses could enable on-site identification in nearly real-time, thus implementing preventive oral control, enabling prompt selection of the most effective drug, and increasing the probability to interrupt disease transmission.},
}
@article {pmid35627046,
year = {2022},
author = {Karppinen, K and Avetisyan, A and Hykkerud, AL and Jaakola, L},
title = {A dPCR Method for Quantitative Authentication of Wild Lingonberry (Vaccinium vitis-idaea) versus Cultivated American Cranberry (V. macrocarpon).},
journal = {Foods (Basel, Switzerland)},
volume = {11},
number = {10},
pages = {},
pmid = {35627046},
issn = {2304-8158},
support = {//European Regional Developmental Fund, Interreg Baltic Sea Region Programme/ ; },
abstract = {Berries of the genus Vaccinium are highly valued health-beneficial superfoods, which are commonly subjected to adulteration and mixed with each other, or with other common berry species. A quantitative DNA-based method utilizing a chip-based digital polymerase chain reaction (dPCR) technique was developed for identifying and quantifying wild lingonberry (V. vitis-idaea) and cultivated American cranberry (V. macrocarpon). The dPCR method with species-specific primers for mini-barcoding was designed based on the indel regions found in the trnI-CAU-trnL-CAA locus in the chloroplast genome. The designed primers were able to amplify only target species, enabling to distinguish the two closely related species with good sensitivity. Our results illustrated the ability of the method to identify lingonberry and American cranberry DNA using PCR without the need for probes or further sequencing. The dPCR method could also quantify the DNA copy number in mixed samples. Based on this study, the method provides a basis for a simple, fast, and sensitive quantitative authentication analysis of lingonberry and American cranberry by dPCR. Moreover, it can also provide a platform for authentication analyses of other plant species as well by utilizing the indel regions of chloroplast genomes.},
}
@article {pmid35625400,
year = {2022},
author = {Tittarelli, R and Gismondi, A and Di Marco, G and Mineo, F and Vernich, F and Russo, C and Marsella, LT and Canini, A},
title = {Forensic Application of Genetic and Toxicological Analyses for the Identification and Characterization of the Opium Poppy (Papaver somniferum L.).},
journal = {Biology},
volume = {11},
number = {5},
pages = {},
pmid = {35625400},
issn = {2079-7737},
abstract = {BACKGROUND: A reliable and science-based taxonomic determination of Papaver somniferum L. (opium poppy), the illegal species of the genus Papaver, may have practical and legal implications for law enforcement. P. somniferum is a controlled plant because of its narcotic substances, such as morphine and codeine. As poppy plants have rather similar morphological features, both chemical and genetic analysis are required in order to achieve an accurate characterization of such species. The chemical structures of alkaloids are extremely variable even within the same species, which is why the genetic approach may lead to a more scientific Papaver sp. differentiation. The aim of our study was the taxonomic identification of poppy capsules seized by the Italian Police Forces being considered as potential P. somniferum derivatives.<br><br>METHODS: The alkaloids detected using gas chromatography/mass-spectrometry (GC/MS) were morphine, codeine, thebaine, noscapine, meconin, hydrocotarnine, and traces of papaverine. Further genetic analysis was carried out simultaneously using three plastid DNA barcoding regions (matK, trnH-psbA, and rbcL) for the samples' identification.<br><br>RESULTS: The Random Amplification of Polymorphic DNA (RAPD) method showed that the analysed samples were genetically identical.<br><br>CONCLUSIONS: The morphological, toxicological, and genetic profile of the samples revealed that they belonged to P. somniferum species. Furthermore, the alkaloid content of dried poppy capsules might be used to investigate and track their origin.},
}
@article {pmid35624112,
year = {2022},
author = {Ni, Z and Prasad, A and Chen, S and Halberg, RB and Arkin, LM and Drolet, BA and Newton, MA and Kendziorski, C},
title = {SpotClean adjusts for spot swapping in spatial transcriptomics data.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {2971},
pmid = {35624112},
issn = {2041-1723},
support = {R01 GM102756/GM/NIGMS NIH HHS/United States ; P30 CA014520/CA/NCI NIH HHS/United States ; P50 HD105353/HD/NICHD NIH HHS/United States ; UL1 TR002373/TR/NCATS NIH HHS/United States ; P50 CA278595/CA/NCI NIH HHS/United States ; },
mesh = {Cluster Analysis ; *Electronic Data Processing ; Models, Statistical ; *Transcriptome ; },
abstract = {Spatial transcriptomics is a powerful and widely used approach for profiling the gene expression landscape across a tissue with emerging applications in molecular medicine and tumor diagnostics. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind RNA. Ideally, unique molecular identifiers (UMIs) at a spot measure spot-specific expression, but this is often not the case in practice due to bleed from nearby spots, an artifact we refer to as spot swapping. To improve the power and precision of downstream analyses in spatial transcriptomics experiments, we propose SpotClean, a probabilistic model that adjusts for spot swapping to provide more accurate estimates of gene-specific UMI counts. SpotClean provides substantial improvements in marker gene analyses and in clustering, especially when tissue regions are not easily separated. As demonstrated in multiple studies of cancer, SpotClean improves tumor versus normal tissue delineation and improves tumor burden estimation thus increasing the potential for clinical and diagnostic applications of spatial transcriptomics technologies.},
}
@article {pmid35622319,
year = {2022},
author = {Villarese, P and Abdo, C and Bertrand, M and Thonier, F and Giraud, M and Salson, M and Macintyre, E},
title = {One-Step Next-Generation Sequencing of Immunoglobulin and T-Cell Receptor Gene Recombinations for MRD Marker Identification in Acute Lymphoblastic Leukemia.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2453},
number = {},
pages = {43-59},
pmid = {35622319},
issn = {1940-6029},
mesh = {*Genes, T-Cell Receptor/genetics/immunology ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; *Immunoglobulins/genetics/immunology ; Neoplasm, Residual/diagnosis/genetics ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/diagnosis/genetics/immunology ; *Recombination, Genetic/genetics/immunology ; },
abstract = {Within the EuroClonality-NGS group, immune repertoire analysis for target identification in lymphoid malignancies was initially developed using two-stage amplicon approaches, essentially as a progressive modification of preceding methods developed for Sanger sequencing. This approach has, however, limitations with respect to sample handling, adaptation to automation, and risk of contamination by amplicon products. We therefore developed one-step PCR amplicon methods with individual barcoding for batched analysis for IGH, IGK, TRD, TRG, and TRB rearrangements, followed by Vidjil-based data analysis.},
}
@article {pmid35621785,
year = {2022},
author = {Huangfu, N and Cao, HX and Zhu, CD},
title = {Notes on the Genus Aceratoneuromyia Girault (Hymenoptera: Eulophidae).},
journal = {Insects},
volume = {13},
number = {5},
pages = {},
pmid = {35621785},
issn = {2075-4450},
support = {31625024//National Natural Science Foundation of China/ ; },
abstract = {Fruit flies in the family Tephritidae are well known as economically important pests of edible fruits and can often cause serious damage and losses to both agriculture and the economy. One of the common parasitoids of fruit flies, Aceratoneuromyia indica (Silvestri), has been used in biological programs. However, the biocontrol utilities of parasitoids are impeded by the difficulties of proper identification. Species of the genus Aceratoneuromyia Girault (Hymenoptera: Eulophidae), usually developed as parasitoids of fruit flies, are studied here. Trjapitzinichus Kostjukov and Kosheleva is proposed as a new synonym under Aceratoneuromyia. Three new species of Aceratoneuromyia, A. bilinis Huangfu and Cao sp. nov., A. carinata Cao and Zhu sp. nov., and A. trilinus Cao and Zhu sp. nov., are described and illustrated from China. Aceratoneuromyia indica is also treated here with diagnosis and illustrations. DNA barcodes of A. bilinis and A. indica and a key to the world species of Aceratoneuromyia are provided. This study provided important identification information of parasitoids with morphology and molecular evidence, which is useful for imperative needs regarding the identity of parasitoids attacking fruit flies.},
}
@article {pmid35621776,
year = {2022},
author = {Liu, T and Geng, X and Tang, Y and Li, B and Zhang, H and Teng, K},
title = {First Report of the Immature Stages of the Leaf-Mining Genus Subclemensia Kozlov, 1987 (Lepidoptera: Incurvariidae), with a Re-Illustration of the Type Species and a Generic Concept Discussion Based on Immature Characters.},
journal = {Insects},
volume = {13},
number = {5},
pages = {},
pmid = {35621776},
issn = {2075-4450},
support = {ZR2017BC051//Shandong Provincial Natural Science Foundation, China/ ; 2005DKA21400//National Specimen Information Infrastructure/ ; No. 32000320//The National Natural Science Foundation of China/ ; },
abstract = {The immature stages of primitive Lepidoptera can provide quite different but often useful morphological evidence and synapomorphies from those of adults. Incurvariidae is one of the most primitive lineages of extant Lepidoptera, which is species-poor but highly diverse, but half of the genera lack any information on immature stages. New knowledge on the immature stages of the family is expected to provide useful morphological evidence and synapomorphies to stabilize the generic nomenclature. Subclemensia Kozlov, 1987 is one of the monotypic genera in Incurvariidae. In this study, the immature stages of the type species of Subclemensia are reported for the first time. The leaf mine, host plant and its biological characteristics are also provided. DNA barcodes were generated to aid the species delimitation. The adult male and female genitalia are re-illustrated by color photography to supplement the original line drawings. The generic concepts of Subclemensia and other related genera are discussed based on immature characters.},
}
@article {pmid35621761,
year = {2022},
author = {Zhang, H and Bu, W},
title = {Exploring Large-Scale Patterns of Genetic Variation in the COI Gene among Insecta: Implications for DNA Barcoding and Threshold-Based Species Delimitation Studies.},
journal = {Insects},
volume = {13},
number = {5},
pages = {},
pmid = {35621761},
issn = {2075-4450},
support = {31820103013//National Natural Science Foundation of China/ ; ZR2020QC053//Natural Science Foundation of Shandong Province/ ; },
abstract = {The genetic variation in the COI gene has had a great effect on the final results of species delimitation studies. However, little research has comprehensively investigated the genetic divergence in COI among Insecta. The fast-growing COI data in BOLD provide an opportunity for the comprehensive appraisal of the genetic variation in COI among Insecta. We calculated the K2P distance of 64,414 insect species downloaded from BOLD. The match ratios of the clustering analysis, based on different thresholds, were also compared among 4288 genera (35,068 species). The results indicate that approximately one-quarter of the species of Insecta showed high intraspecific genetic variation (>3%), and a conservative estimate of this proportion ranges from 12.05% to 22.58%. The application of empirical thresholds (e.g., 2% and 3%) in the clustering analysis may result in the overestimation of the species diversity. If the minimum interspecific genetic distance of the congeneric species is greater than or equal to 2%, it is possible to avoid overestimating the species diversity on the basis of the empirical thresholds. In comparison to the fixed thresholds, the “threshOpt” and “localMinima” algorithms are recommended for the provision of a reference threshold for threshold-based species delimitation studies.},
}
@article {pmid35621381,
year = {2022},
author = {Dannenberg, PH and Kang, J and Martino, N and Kashiparekh, A and Forward, S and Wu, J and Liapis, AC and Wang, J and Yun, SH},
title = {Laser particle activated cell sorting in microfluidics.},
journal = {Lab on a chip},
volume = {22},
number = {12},
pages = {2343-2351},
pmid = {35621381},
issn = {1473-0189},
support = {DP1 EB024242/EB/NIBIB NIH HHS/United States ; R01 EB033155/EB/NIBIB NIH HHS/United States ; },
mesh = {Cell Separation/methods ; *Lasers ; Light ; *Microfluidics ; Single-Cell Analysis ; },
abstract = {Laser particles providing bright, spectrally narrowband emission renders them suitable for use as cellular barcodes. Here, we demonstrate a microfluidic platform integrated with a high-speed spectrometer, capable of reading the emission from laser particles in fluidic channels and routing cells based on their optical barcodes. The sub-nanometer spectral emission of each laser particle enables us to distinguish individual cells labeled with hundreds of different laser colors in the near infrared. Furthermore, cells tagged with laser particles are sorted based on their spectral barcodes at a kilohertz rate by using a real-time field programmable gate array and 2-way electric field switch. We demonstrate several different flavors of sorting, including isolation of barcoded cells, and cells tagged with a specific laser color. We term this novel sorting technique laser particle activated cell sorting (LACS). This flow reading and sorting technology adds to the arsenal of single-cell analysis tools using laser particles.},
}
@article {pmid35621380,
year = {2022},
author = {Vu, D and Nilsson, RH and Verkley, GJM},
title = {Dnabarcoder: An open-source software package for analysing and predicting DNA sequence similarity cutoffs for fungal sequence identification.},
journal = {Molecular ecology resources},
volume = {22},
number = {7},
pages = {2793-2809},
pmid = {35621380},
issn = {1755-0998},
mesh = {Base Sequence ; Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; Genetic Markers ; *Software ; },
abstract = {The accuracy and precision of fungal molecular identification and classification are challenging, particularly in environmental metabarcoding approaches as these often trade accuracy for efficiency given the large data volumes at hand. In most ecological studies, only a single similarity cutoff value is used for sequence identification. This is not sufficient since the most commonly used DNA markers are known to vary widely in terms of inter- and intraspecific variability. We address this problem by presenting a new tool, dnabarcoder, to predict local similarity cutoffs and measure the resolving powers of a biomarker for sequence identification for different clades of fungi. It was shown that the predicted similarity cutoffs varied significantly between the clades of a recently released ITS DNA barcode data set from the CBS culture collection of the Westerdijk Fungal Biodiversity Institute. When classifying a large public fungal ITS data set-the UNITE database-against the barcode data set, the local similarity cutoffs assigned fewer sequences than the traditional cutoffs used in metabarcoding studies. However, the obtained accuracy and precision were significantly improved. Our study showed that it might be better to extract the ITS region from the ITS barcodes to optimize taxonomic assignment accuracy. Furthermore, 15.3, 25.6, and 26.3% of the fungal species of the barcode data set were indistinguishable by full-length ITS, ITS1, and ITS2, respectively. Except for these indistinguishable species, the resolving powers of full-length ITS, ITS1, and ITS2 sequences were similar at the species level. Nevertheless, the complete ITS region had a better resolving power at higher taxonomic levels.},
}
@article {pmid35621046,
year = {2022},
author = {Sandin, MM and Romac, S and Not, F},
title = {Intra-genomic rRNA gene variability of Nassellaria and Spumellaria (Rhizaria, Radiolaria) assessed by Sanger, MinION and Illumina sequencing.},
journal = {Environmental microbiology},
volume = {24},
number = {7},
pages = {2979-2993},
pmid = {35621046},
issn = {1462-2920},
mesh = {Genes, rRNA ; Genomics ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; *Rhizaria/genetics ; Sequence Analysis, DNA ; },
abstract = {Ribosomal RNA (rRNA) genes are known to be valuable markers for the barcoding of eukaryotic life and its phylogenetic classification at various taxonomic levels. The large-scale exploration of environmental microbial diversity through metabarcoding approaches has been focused mainly on the V4 and V9 regions of the 18S rRNA gene. The accurate interpretation of such environmental surveys is hampered by technical (e.g. PCR and sequencing errors) and biological biases (e.g. intra-genomic variability). Here we explored the intra-genomic diversity of Nassellaria and Spumellaria specimens (Radiolaria) by comparing Sanger sequencing with Illumina and Oxford Nanopore Technologies (MinION). Our analysis determined that intra-genomic variability of Nassellaria and Spumellaria is generally low, yet some Spumellaria specimens showed two different copies of the V4 with <97% similarity. Of the different sequencing methods, Illumina showed the highest number of contaminations (i.e. environmental DNA, cross-contamination, tag-jumping), revealed by its high sequencing depth; and MinION showed the highest sequencing rate error (~14%). Yet the long reads produced by MinION (~2900 bp) allowed accurate phylogenetic reconstruction studies. These results highlight the requirement for a careful interpretation of Illumina-based metabarcoding studies, in particular regarding low abundant amplicons, and open future perspectives towards full-length rDNA environmental metabarcoding surveys.},
}
@article {pmid35617151,
year = {2022},
author = {Weber, TA and Metzler, L and Fosso Tene, PL and Brandstetter, T and Rühe, J},
title = {Single-Color Barcoding for Multiplexed Hydrogel Bead-Based Immunoassays.},
journal = {ACS applied materials &amp; interfaces},
volume = {14},
number = {22},
pages = {25147-25154},
pmid = {35617151},
issn = {1944-8252},
mesh = {Antibodies ; Biomarkers ; Humans ; *Hydrogels/chemistry ; Immunoassay/methods ; *Microfluidics/methods ; },
abstract = {Current developments in precision medicine require the simultaneous detection of an increasing number of biomarkers in heterogeneous, complex solutions, such as blood samples. To meet this need, immunoassays on barcoded hydrogel beads have been proposed, although the encoding and decoding of these barcodes is usually complex and/or resource-intensive. Herein, an efficient method for the fabrication of barcoded, functionalized hydrogel beads is presented. The hydrogel beads are generated using droplet-based microfluidics in combination with photochemically induced C-H insertion reactions, allowing photo-crosslinking, (bio-) functionalization, and barcode integration to be performed in a single step. The generated functionalized beads carry single-color barcodes consisting of green-fluorescent particles of different sizes and concentrations, allowing simple and simultaneous readout with a standard plate reader. As a test example, the performance of barcoded hydrogel beads (3 × 3 matrix) functionalized with capture molecules of interest (e.g., antigens) is investigated for the detection of Lyme-disease-specific antibodies in patient sera. The described barcoding strategy for hydrogel beads does not interfere with the bioanalytical process and captivates by its simplicity and versatility, making it an attractive candidate for multiplex bioanalytical processes.},
}
@article {pmid35614354,
year = {2022},
author = {Álvarez-Barragán, J and Cravo-Laureau, C and Duran, R},
title = {Fungal-bacterial network in PAH-contaminated coastal marine sediment.},
journal = {Environmental science and pollution research international},
volume = {29},
number = {48},
pages = {72718-72728},
pmid = {35614354},
issn = {1614-7499},
mesh = {Bacteria/metabolism ; Biodegradation, Environmental ; *Geologic Sediments/microbiology ; Humans ; *Polycyclic Aromatic Hydrocarbons/analysis ; Soil ; },
abstract = {Fungal microbiome interacts with the other biotic components in coastal sediment playing a key role in the overall coordination of the whole microbial community. These interactions are affected by human activities, such as the constant affluence of polycyclic aromatic hydrocarbons (PAHs). Although fungi and bacteria interactions have been found to play a key role in PAH bioremediation in soil, the effect of PAHs on fungal diversity and their specific interactions with bacteria in coastal sediments are yet to be investigated. The understanding of fungal bacterial interactions under PAH contamination is critical for further bioremediation regarding the important fungal diversity observed in coastal sediment. Here, we investigated the fungal bacterial co-occurrence in PAH-contaminated sediments. The co-occurrence network, constructed with sequencing data (bacterial 16S and fungal 18S rRNA genes barcoding) from 51 PAH-contaminated samples, revealed modules dominated by either fungi or bacteria, reflecting probably the different types of interaction possible between fungi and bacteria. Then, a network constructed from non-contaminated sample data was compared with a network built from the corresponding PAH-contaminated samples issued from a mesocosm experiment. The comparison revealed the effect of PAHs in fungi and bacteria interactions, characterized by a PAH-contaminated network exhibiting less abundant and diverse fungal and bacterial ASVs than the non-contaminated network. However, the links between the remaining ASVs in the PAH-contaminated network showed stronger correlations. Noteworthy, an ASV affiliated to Chrytridiomycota phylum was identified as a keystone fungal ASV forming a module in association with facultative anaerobic and anaerobic bacteria affiliated to the families Prolixibacteraceae, Fusobacteriaceae, and Desulfobulbaceae. These results suggest that fungi promote bacterial anaerobic metabolisms, which are important to cope with the presence of PAHs in sediments. Our study reveals the importance of fungal bacterial interactions in coastal sediments paving the way for future studies to fully understand fungal role in coastal sediment.},
}
@article {pmid35614226,
year = {2022},
author = {Nusser, A and Sagar, and Swann, JB and Krauth, B and Diekhoff, D and Calderon, L and Happe, C and Grün, D and Boehm, T},
title = {Developmental dynamics of two bipotent thymic epithelial progenitor types.},
journal = {Nature},
volume = {606},
number = {7912},
pages = {165-171},
pmid = {35614226},
issn = {1476-4687},
support = {/ERC_/European Research Council/International ; },
mesh = {Aging ; Animals ; Autocrine Communication ; CRISPR-Cas Systems ; Cellular Microenvironment ; *Epithelial Cells/cytology/metabolism ; Epithelium ; Fibroblast Growth Factor 7 ; Mice ; RNA-Seq ; Single-Cell Analysis ; *Stem Cells/cytology ; *T-Lymphocytes/cytology/metabolism ; *Thymus Gland/cytology ; },
abstract = {T cell development in the thymus is essential for cellular immunity and depends on the organotypic thymic epithelial microenvironment. In comparison with other organs, the size and cellular composition of the thymus are unusually dynamic, as exemplified by rapid growth and high T cell output during early stages of development, followed by a gradual loss of functional thymic epithelial cells and diminished naive T cell production with age[1-10]. Single-cell RNA sequencing (scRNA-seq) has uncovered an unexpected heterogeneity of cell types in the thymic epithelium of young and aged adult mice[11-18]; however, the identities and developmental dynamics of putative pre- and postnatal epithelial progenitors have remained unresolved[1,12,16,17,19-27]. Here we combine scRNA-seq and a new CRISPR-Cas9-based cellular barcoding system in mice to determine qualitative and quantitative changes in the thymic epithelium over time. This dual approach enabled us to identify two principal progenitor populations: an early bipotent progenitor type biased towards cortical epithelium and a postnatal bipotent progenitor population biased towards medullary epithelium. We further demonstrate that continuous autocrine provision of Fgf7 leads to sustained expansion of thymic microenvironments without exhausting the epithelial progenitor pools, suggesting a strategy to modulate the extent of thymopoietic activity.},
}
@article {pmid35613123,
year = {2022},
author = {Machado, S and Hartwig Bessa, M and Nornberg, B and Silva Gottschalk, M and Robe, LJ},
title = {Unveiling the Mycodrosophila projectans (Diptera, Drosophilidae) species complex: Insights into the evolution of three Neotropical cryptic and syntopic species.},
journal = {PloS one},
volume = {17},
number = {5},
pages = {e0268657},
pmid = {35613123},
issn = {1932-6203},
mesh = {Animals ; Brazil ; *Drosophilidae ; Genetic Speciation ; Phylogeny ; Sympatry ; },
abstract = {The Zygothrica genus group has been shown to be speciose, with a high number of cryptic species. DNA barcoding approaches have been a valuable tool to uncover cryptic diversity in this lineage, as recently suggested for the Neotropical Mycodrosophila projectans complex, which seems to comprise at least three different species. The aim of this study was to confirm the subdivision of the M. projectans complex while shedding some light on the patterns and processes related to its diversification. In this sense, the use of single and multi-locus datasets under phylogenetic, distance, coalescence, and diagnostic nucleotide approaches confirmed the presence of at least three species under the general morphotype previously described as M. projectans. Only a few subtle morphological differences were found for the three species in terms of aedeagus morphology and abdominal color patterns. Ecologically, sympatry and syntopy seem to be recurrent for these three cryptic species, which present widely overlapping niches, implying niche conservatism. This morphological and ecological similarity has persisted though cladogenesis within the complex, which dates back to the Miocene, providing an interesting example of morphological conservation despite ancient divergence. These results, in addition to contrasting patterns of past demographic fluctuations, allowed us to hypothesize patterns of allopatric or parapatric diversification with secondary contact in Southern Brazil. Nevertheless, genetic diversity was generally high within species, suggesting that migration may encompass an adaptive response to the restrictions imposed by the ephemerality of resources.},
}
@article {pmid35612214,
year = {2022},
author = {Descalzo, JM and Cassarino, M and Grande Ratti, MF and Smith, M and Luna, D},
title = {Semi-Structured Interviews to Evaluate a BCMA Implementation Trouble Areas.},
journal = {Studies in health technology and informatics},
volume = {294},
number = {},
pages = {815-816},
doi = {10.3233/SHTI220594},
pmid = {35612214},
issn = {1879-8365},
mesh = {Electronic Data Processing ; Humans ; *Medication Errors/prevention &amp; control ; Medication Systems, Hospital ; Patient Safety ; Pharmaceutical Preparations ; },
abstract = {Errors in medication administration involve risks to patient safety. "Bar-Coding Medication Administration" is implemented to prevent these errors. Adoption by nurses is one of the main determinants of their effectiveness. The Hospital Italiano de Buenos Aires implemented BCMA 6 years ago, but its adoption rate still finds resistance in certain sectors. We conducted semi-structured interviews with nursing staff to explore the barriers to the use in low-usage wards and explore the current perceptions of nurses. While nurses recognised the safety and usefulness of the BCMA system, they reported many difficulties. The feedback obtained through this process was useful for the implementation team to plan future interventions, priorities and improvements on the system. The semi-structured interview methodology proved useful as a continuous monitoring strategy.},
}
@article {pmid35612195,
year = {2022},
author = {Lichtner, V and Dowding, D},
title = {Mindful Workarounds in Bar Code Medication Administration.},
journal = {Studies in health technology and informatics},
volume = {294},
number = {},
pages = {740-744},
doi = {10.3233/SHTI220575},
pmid = {35612195},
issn = {1879-8365},
mesh = {Electronic Data Processing/methods ; Humans ; *Medication Errors/prevention &amp; control ; *Medication Systems, Hospital ; Pharmaceutical Preparations ; },
abstract = {Bar-Coded Medication Administration systems (BCMA) are often used with workarounds. These workarounds are usually judged against standard operating procedures or the use of the technology as 'designers' intended'. However, some workarounds may be reasonable and justified to prevent safety errors. In this conceptual paper, we clarify BCMA safety mechanisms and provide a framework to identify workarounds with BCMA that nullify the error prevention mechanisms inherent in the technology design and process. We also highlight the importance of understanding the purpose behind a nurse's workaround in BCMA, focusing on the notion of mindful (thoughtful) workarounds that have the potential to improve patient safety.},
}
@article {pmid35610940,
year = {2022},
author = {Bacelar, PAA and Jaeger, LH and Calegar, DA and Santos, JP and Coronato-Nunes, B and Reis, ERC and Bóia, MN and Monteiro, KJL and Carvalho-Costa, FA},
title = {Molecular detection of Metastrongylus salmi eggs from pigs in low-resource communities in the state of Piauí, northeastern Brazil.},
journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc},
volume = {34},
number = {4},
pages = {689-692},
pmid = {35610940},
issn = {1943-4936},
mesh = {Animals ; Brazil/epidemiology ; *Metastrongyloidea/genetics ; Species Specificity ; *Strongylida Infections/epidemiology/parasitology/veterinary ; Swine ; *Swine Diseases/diagnosis/epidemiology/parasitology ; },
abstract = {Metastrongylosis is an infection of the respiratory tract of pigs caused by parasites of the genus Metastrongylus, whose eggs are similar to other Strongylida through light microscopy; species-specific identification can be performed with molecular tools. We explored the species composition and the genetic diversity of Metastrongylus infecting pigs in close contact with humans in impoverished rural communities in the state of Piauí, in northeastern Brazil. Fecal samples (n = 78) were collected for parasitologic tests. Egg morphometry and molecular characterization, using the cytochrome c oxidase subunit 1 (cox1) gene, were performed. For strongyliform eggs, 62 of 78 (80%) pigs were positive and 6 of 99 (6%) eggs had dimensions compatible with Metastrongylus. Of the 37 samples submitted to PCR, 10 were identified as M. salmi. We found 3 M. salmi haplotypes, including 2 new and 1 described previously in Europe. Overall, M. salmi demonstrated lower intraspecific genetic diversity: diversity index (H) ± SD = 0.318 ± 0.164, n = 12, compared with published M. pudendotectus sequences (1.000 ± 0.272, n = 3). To our knowledge, M. salmi DNA sequences have not been published previously from pigs in South America.},
}
@article {pmid35607971,
year = {2022},
author = {Bektas, Y and Aksu, &#x130; and Kaya, C and Bayçelebi, E and Turan, D},
title = {DNA barcoding and species delimitation of the genus Oxynoemacheilus (Teleostei: Nemacheilidae) in Anatolia.},
journal = {Journal of fish biology},
volume = {101},
number = {3},
pages = {505-514},
doi = {10.1111/jfb.15114},
pmid = {35607971},
issn = {1095-8649},
support = {2015.53008.103.01.01//Recep Tayyip Erdogan University (RTEU-BAP)/ ; },
mesh = {Animals ; Bayes Theorem ; *Cypriniformes ; DNA ; *DNA Barcoding, Taxonomic/methods ; Phylogeny ; Turkey ; },
abstract = {The DNA barcoding approach was used for the determination of evolutionary relationships and species delimitation of the genus Oxynoemacheilus (Teleostei: Nemacheilidae). The COI barcode region (615 bp amplicon) was used to barcode 444 individuals from 64 morphologically identified species in the genus Oxynoemacheilus and 189 haplotypes were identified. The average of the interspecific p distance (9.59%) was about 21-fold higher than the average intraspecific distance (0.44%). A general genetic threshold of 1.46% sequence divergence was defined for species delimitation. The multiple species delimitation methods (BCM, GMYC, bPTP and TCS) revealed a total of 62 molecular operational taxonomic units for 64 morphospecies with a new loach species from the BuyukMelen River. Neighbour-joining, maximum likelihood and Bayesian inference analyses indicated that all haplotypes were clustered into 62 clades, which corresponded to Oxynoemacheilus species, with strong bootstrap support (≥95%). Furthermore, all samples grouped in concurrence with the taxonomic status of the species except for species groups (O. germencicus-O. cinicus-O. mesudae and O. leontinae-O. namiri) that were showed intraspecific overlap in genetic diversity for COI-based barcodes. In conclusion, our analyses indicate that COI-based barcodes provide reliable species discrimination. Therefore, we currently recommend COI barcodes as the suitable barcode for genus Oxynoemacheilus.},
}
@article {pmid35605810,
year = {2022},
author = {Sartori, AGO and Cesar, ASM and Woitowicz, FCG and Saliba, ASMC and Ikegaki, M and Rosalen, PL and Coutinho, LL and Alencar, SM},
title = {Plant genetic diversity by DNA barcoding to investigate propolis origin.},
journal = {Phytochemistry},
volume = {200},
number = {},
pages = {113226},
doi = {10.1016/j.phytochem.2022.113226},
pmid = {35605810},
issn = {1873-3700},
mesh = {*Ascomycota ; Chromatography, High Pressure Liquid ; DNA ; DNA Barcoding, Taxonomic ; Gas Chromatography-Mass Spectrometry ; Genetic Variation ; Plants/chemistry ; *Populus/chemistry/genetics ; *Propolis/chemistry ; Resins, Plant/analysis ; },
abstract = {Identify the botanical origins of a certain type of propolis may be challenging and time demanding, since it involves bee's behavior observation, plant resins collection and chemical analysis. Thus, this study aimed to determine the plant genetic materials in propolis from southern Brazil using the DNA barcoding to investigate their botanical origins, as well as to compare it with the phytochemical composition determined by ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry (UHPLC-HRMS) and with the pollinic profile. As principal results, non-native Populus carolinensis Moench (Salicaceae) was almost the only DNA source in some propolis samples, which coincided with the presence of flavonoids typical from poplar exudates. Conversely, other propolis samples had DNA material coming mainly from native plant species, most of them characterized to the species level, although no specific chemical markers from those plants could be identified by UHPLC-HRMS. However, pollen from several plants identified by the DNA barcoding were extracted from some propolis samples. Despite the identification of typical diterpenes, DNA material from Araucaria angustifolia (Bertol.) Kuntze (Araucariaceae), which have been indicated as a major resin source for propolis from preservation areas in southern Brazil, was found in very small abundancies, likely because bees do not drag tissue material containing DNA when collecting resin from this native species. In conclusion, DNA barcoding analysis successfully provided information about the provenance of propolis, although, depending on the plant resin sources, this information is likely to come from pollen.},
}
@article {pmid35603167,
year = {2022},
author = {Gutierrez, C and Vilas, CK and Wu, CJ and Al'Khafaji, AM},
title = {Functionalized Lineage Tracing Can Enable the Development of Homogenization-Based Therapeutic Strategies in Cancer.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {859032},
pmid = {35603167},
issn = {1664-3224},
mesh = {*Antineoplastic Agents/therapeutic use ; Clone Cells ; Humans ; *Neoplasms/pathology ; },
abstract = {The therapeutic landscape across many cancers has dramatically improved since the introduction of potent targeted agents and immunotherapy. Nonetheless, success of these approaches is too often challenged by the emergence of therapeutic resistance, fueled by intratumoral heterogeneity and the immense evolutionary capacity inherent to cancers. To date, therapeutic strategies have attempted to outpace the evolutionary tempo of cancer but frequently fail, resulting in lack of tumor response and/or relapse. This realization motivates the development of novel therapeutic approaches which constrain evolutionary capacity by reducing the degree of intratumoral heterogeneity prior to treatment. Systematic development of such approaches first requires the ability to comprehensively characterize heterogeneous populations over the course of a perturbation, such as cancer treatment. Within this context, recent advances in functionalized lineage tracing approaches now afford the opportunity to efficiently measure multimodal features of clones within a tumor at single cell resolution, enabling the linkage of these features to clonal fitness over the course of tumor progression and treatment. Collectively, these measurements provide insights into the dynamic and heterogeneous nature of tumors and can thus guide the design of homogenization strategies which aim to funnel heterogeneous cancer cells into known, targetable phenotypic states. We anticipate the development of homogenization therapeutic strategies to better allow for cancer eradication and improved clinical outcomes.},
}
@article {pmid35600695,
year = {2022},
author = {Ranasinghe, UGSL and Eberle, J and Thormann, J and Bohacz, C and Benjamin, SP and Ahrens, D},
title = {Multiple species delimitation approaches with COI barcodes poorly fit each other and morphospecies - An integrative taxonomy case of Sri Lankan Sericini chafers (Coleoptera: Scarabaeidae).},
journal = {Ecology and evolution},
volume = {12},
number = {5},
pages = {e8942},
pmid = {35600695},
issn = {2045-7758},
abstract = {DNA taxonomy including barcoding and metabarcoding is widely used to explore the diversity in biodiversity hotspots. In most of these hotspot areas, chafers are represented by a multitude of species, which are well defined by the complex shape of male genitalia. Here, we explore how well COI barcode data reflect morphological species entities and thus their usability for accelerated species inventorization. We conducted dedicated field surveys in Sri Lanka to collect the species-rich and highly endemic Sericini chafers (Coleoptera: Scarabaeidae). Congruence among results of a series of protocols for de novo species delimitation and with morphology-based species identifications was investigated. Different delimitation methods, such as the Poisson tree processes (PTP) model, Statistical Parsimony Analysis (TCS), Automatic Barcode Gap Discovery (ABGD), Assemble Species by Automatic Partitioning (ASAP), and Barcode Index Number (BIN) assignments, resulted in different numbers of molecular operational taxonomic units (MOTUs). All methods showed both over-splitting and lumping of morphologically identified species. Only 18 of the observed 45 morphospecies perfectly matched MOTUs from all methods. The congruence of delimitation between MOTUs and morphospecies expressed by the match ratio was low, ranging from 0.57 to 0.67. TCS and multirate PTP (mPTP) showed the highest match ratio, while (BIN) assignment resulted in the lowest match ratio and most splitting events. mPTP lumped more species than any other method. Principal coordinate analysis (PCoA) on a match ratio-based distance matrix revealed incongruent outcomes of multiple DNA delimitation methods, although applied to the same data. Our results confirm that COI barcode data alone are unlikely to correctly delimit all species, in particular, when using only a single delimitation approach. We encourage the integration of various approaches and data, particularly morphology, to validate species boundaries.},
}
@article {pmid35599857,
year = {2022},
author = {Wang, J and Fu, CN and Mo, ZQ and Möller, M and Yang, JB and Zhang, ZR and Li, DZ and Gao, LM},
title = {Testing the Complete Plastome for Species Discrimination, Cryptic Species Discovery and Phylogenetic Resolution in Cephalotaxus (Cephalotaxaceae).},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {768810},
pmid = {35599857},
issn = {1664-462X},
abstract = {Species of Cephalotaxus have great economic and ecological values. However, the taxonomy and interspecific phylogenetic relationships within the genus have been controversial and remained not fully resolved until now. To date, no study examined the efficiency of the complete plastome as super-barcode across Cephalotaxus species with multiple samples per taxon. In this study, we have evaluated the complete plastome in species discrimination and phylogenetic resolution in Cephalotaxus by including 32 individuals of all eight recognized species and five varieties following Farjon's classification (2010) with multiple samples per taxon. Our results indicated that not all species recognized in recent taxonomic revisions of Cephalotaxus could be distinguished and not all were monophyletic. Based on the plastome phylogeny, a new taxonomic classification for the genus comprising nine species and two varieties, including a cryptic species, was proposed. The phylogeny also resolved all interspecific relationships. Compared to the plastome based classification, standard DNA barcodes, alone or in combination, only recognized a maximum of seven out of the nine species. Moreover, two highly variable single loci, ycf1 and rps16, each alone achieved full species discrimination. With the moderate length of 1079 bp, rps16 is proposed as a specific barcode to discriminate Cephalotaxus species. The super-barcodes and specific barcode candidates will aid in the identification of endangered Cephalotaxus species, and to help focus conservation measures.},
}
@article {pmid35597236,
year = {2022},
author = {Liedmann, S and Liu, X and Guy, CS and Crawford, JC and Rodriguez, DA and Kuzuoğlu-Öztürk, D and Guo, A and Verbist, KC and Temirov, J and Chen, MJ and Ruggero, D and Zhang, H and Thomas, PG and Green, DR},
title = {Localization of a TORC1-eIF4F translation complex during CD8[+] T cell activation drives divergent cell fate.},
journal = {Molecular cell},
volume = {82},
number = {13},
pages = {2401-2414.e9},
pmid = {35597236},
issn = {1097-4164},
support = {P30 CA021765/CA/NCI NIH HHS/United States ; R01 AI123322/AI/NIAID NIH HHS/United States ; R01 AI136514/AI/NIAID NIH HHS/United States ; R01 AI154470/AI/NIAID NIH HHS/United States ; },
mesh = {*CD8-Positive T-Lymphocytes ; Cell Differentiation ; *Eukaryotic Initiation Factor-4F ; Lymphocyte Activation ; Mechanistic Target of Rapamycin Complex 1/genetics ; },
abstract = {Activated CD8[+] T lymphocytes differentiate into heterogeneous subsets. Using super-resolution imaging, we found that prior to the first division, dynein-dependent vesicular transport polarized active TORC1 toward the microtubule-organizing center (MTOC) at the proximal pole. This active TORC1 was physically associated with active eIF4F, required for the translation of c-myc mRNA. As a consequence, c-myc-translating polysomes polarized toward the cellular pole proximal to the immune synapse, resulting in localized c-myc translation. Upon division, the TORC1-eIF4A complex preferentially sorted to the proximal daughter cell, facilitating asymmetric c-Myc synthesis. Transient disruption of eIF4A activity at first division skewed long-term cell fate trajectories to memory-like function. Using a genetic barcoding approach, we found that first-division sister cells often displayed differences in transcriptional profiles that largely correlated with c-Myc and TORC1 target genes. Our findings provide mechanistic insights as to how distinct T cell fate trajectories can be established during the first division.},
}
@article {pmid35596135,
year = {2022},
author = {Dey, TK and Mandal, S and Mukherjee, S},
title = {Gene expression data classification using topology and machine learning models.},
journal = {BMC bioinformatics},
volume = {22},
number = {Suppl 10},
pages = {627},
pmid = {35596135},
issn = {1471-2105},
support = {ccf-2049010//National Science Foundation/ ; ccf-1839252//National Science Foundation/ ; },
mesh = {*Data Analysis ; Gene Expression ; *Machine Learning ; },
abstract = {BACKGROUND: Interpretation of high-throughput gene expression data continues to require mathematical tools in data analysis that recognizes the shape of the data in high dimensions. Topological data analysis (TDA) has recently been successful in extracting robust features in several applications dealing with high dimensional constructs. In this work, we utilize some recent developments in TDA to curate gene expression data. Our work differs from the predecessors in two aspects: (1) Traditional TDA pipelines use topological signatures called barcodes to enhance feature vectors which are used for classification. In contrast, this work involves curating relevant features to obtain somewhat better representatives with the help of TDA. This representatives of the entire data facilitates better comprehension of the phenotype labels. (2) Most of the earlier works employ barcodes obtained using topological summaries as fingerprints for the data. Even though they are stable signatures, there exists no direct mapping between the data and said barcodes.<br><br>RESULTS: The topology relevant curated data that we obtain provides an improvement in shallow learning as well as deep learning based supervised classifications. We further show that the representative cycles we compute have an unsupervised inclination towards phenotype labels. This work thus shows that topological signatures are able to comprehend gene expression levels and classify cohorts accordingly.<br><br>CONCLUSIONS: In this work, we engender representative persistent cycles to discern the gene expression data. These cycles allow us to directly procure genes entailed in similar processes.},
}
@article {pmid35595858,
year = {2022},
author = {Whitford, W and Hawkins, V and Moodley, KS and Grant, MJ and Lehnert, K and Snell, RG and Jacobsen, JC},
title = {Proof of concept for multiplex amplicon sequencing for mutation identification using the MinION nanopore sequencer.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {8572},
pmid = {35595858},
issn = {2045-2322},
mesh = {Genomics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Mutation ; *Nanopore Sequencing/methods ; *Sequence Analysis, DNA/methods ; },
abstract = {Rapid, cost-effective identification of genetic variants in small candidate genomic regions remains a challenge, particularly for less well equipped or lower throughput laboratories. The application of Oxford Nanopore Technologies' MinION sequencer has the potential to fulfil this requirement. We demonstrate a proof of concept for a multiplexing assay that pools PCR amplicons for MinION sequencing to enable sequencing of multiple templates from multiple individuals, which could be applied to gene-targeted diagnostics. A combined strategy of barcoding and sample pooling was developed for simultaneous multiplex MinION sequencing of 100 PCR amplicons. The amplicons are family-specific, spanning a total of 30 loci in DNA isolated from 82 human neurodevelopmental cases and family members. The target regions were chosen for further interrogation because a potentially disease-causative variant had been identified in affected individuals following Illumina exome sequencing. The pooled MinION sequences were deconvoluted by aligning to custom references using the minimap2 aligner software. Our multiplexing approach produced an interpretable and expected sequence from 29 of the 30 targeted genetic loci. The sequence variant which was not correctly resolved in the MinION sequence was adjacent to a five nucleotide homopolymer. It is already known that homopolymers present a resolution problem with the MinION approach. Interestingly despite equimolar quantities of PCR amplicon pooled for sequencing, significant variation in the depth of coverage (127×-19,626×; mean = 8321×, std err = 452.99) was observed. We observed independent relationships between depth of coverage and target length, and depth of coverage and GC content. These relationships demonstrate biases of the MinION sequencer for longer templates and those with lower GC content. We demonstrate an efficient approach for variant discovery or confirmation from short DNA templates using the MinION sequencing device. With less than 130 × depth of coverage required for accurate genotyping, the methodology described here allows for rapid highly multiplexed targeted sequencing of large numbers of samples in a minimally equipped laboratory with a potential cost as much 200 × less than that from Sanger sequencing.},
}
@article {pmid35594271,
year = {2022},
author = {Damian-Serrano, A and Hetherington, ED and Choy, CA and Haddock, SHD and Lapides, A and Dunn, CW},
title = {Characterizing the secret diets of siphonophores (Cnidaria: Hydrozoa) using DNA metabarcoding.},
journal = {PloS one},
volume = {17},
number = {5},
pages = {e0267761},
pmid = {35594271},
issn = {1932-6203},
support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; },
mesh = {Animals ; Conservation of Natural Resources ; DNA Barcoding, Taxonomic ; Diet ; Ecosystem ; Fisheries ; Food Chain ; *Hydrozoa/anatomy &amp; histology ; Predatory Behavior ; },
abstract = {Siphonophores (Cnidaria: Hydrozoa) are abundant and diverse gelatinous predators in open-ocean ecosystems. Due to limited access to the midwater, little is known about the diets of most deep-dwelling gelatinous species, which constrains our understanding of food-web structure and nutrient flow in these vast ecosystems. Visual gut-content methods can rarely identify soft-bodied rapidly-digested prey, while observations from submersibles often overlook small prey items. These methods have been differentially applied to shallow and deep siphonophore taxa, confounding habitat and methodological biases. DNA metabarcoding can be used to assess both shallow and deep species' diets under a common methodological framework, since it can detect both small and gelatinous prey. We (1) further characterized the diets of open-ocean siphonophores using DNA metabarcoding, (2) compared the prey detected by visual and molecular methods to evaluate their technical biases, and (3) evaluated tentacle-based predictions of diet. To do this, we performed DNA metabarcoding analyses on the gut contents of 39 siphonophore species across depths to describe their diets, using six barcode regions along the 18S gene. Taxonomic identifications were assigned using public databases combined with local zooplankton sequences. We identified 55 unique prey items, including crustaceans, gelatinous animals, and fish across 47 siphonophore specimens in 24 species. We reported 29 novel predator-prey interactions, among them the first insights into the diets of nine siphonophore species, many of which were congruent with the dietary predictions based on tentilla morphology. Our analyses detected both small and gelatinous prey taxa underrepresented by visual methods in species from both shallow and deep habitats, indicating that siphonophores play similar trophic roles across depth habitats. We also reveal hidden links between siphonophores and filter-feeders near the base of the food web. This study expands our understanding of the ecological roles of siphonophores in the open ocean, their trophic roles within the 'jelly-web', and the importance of their diversity for nutrient flow and ecosystem functioning. Understanding these inconspicuous yet ubiquitous predator-prey interactions is critical to predict the impacts of climate change, overfishing, and conservation policies on oceanic ecosystems.},
}
@article {pmid35593525,
year = {2022},
author = {Chen, W and Hubert, N and Li, Y and Xiang, D and Cai, X and Zhu, S and Yang, J and Zhou, C and Li, X and Li, J},
title = {Large-scale DNA barcoding of the subfamily Culterinae (Cypriniformes: Xenocyprididae) in East Asia unveils a geographical scale effect, taxonomic warnings and cryptic diversity.},
journal = {Molecular ecology},
volume = {31},
number = {14},
pages = {3871-3887},
pmid = {35593525},
issn = {1365-294X},
mesh = {Animals ; *Cypriniformes ; DNA ; *DNA Barcoding, Taxonomic ; Phylogeny ; Phylogeography ; },
abstract = {Geographical scale might be expected to impact significantly the efficiency of DNA barcoding as spatially comprehensive sampling provides opportunities to uncover intricate relationships among closely related species and to detect cryptic diversity for widespread taxa. Here, we present a DNA barcoding study on a Xencyprididae subfamily (Culterinae) involving the production of 998 newly generated DNA barcodes from East Asian drainages (80 localities). Together with 513 barcodes mined from BOLD and GenBank, a reference library consisting of 1511 DNA barcodes (116 localities) for 42 species was assembled, accounting for 66% of known Culterinae species. Intraspecific genetic distances are positively correlated to geographical scale, while a negative correlation is detected between interspecific genetic distances and geographical scale. The present study demonstrates that geographical scale influences the efficiency of DNA barcoding by narrowing the width of the barcoding gap. DNA-based species delimitation analyses delimited 44 molecular operational taxonomic units (MOTUs). Rampant cryptic diversity is detected within eight species with multiple MOTUs, whereas 25 species present mismatch between morphological and molecular delimitations. A total of 18 species are lumped into nine MOTUs due to low interspecific divergence and/or mixed lineages. Several MOTU divergences are hypothesized to relate to known biogeographical barriers and geological events during the Pliocene and Pleistocene. This study provides new insights into the taxonomy and phylogeography of the subfamily Culterinae.},
}
@article {pmid35592487,
year = {2022},
author = {Jiang, S and Chen, F and Qin, P and Xie, H and Peng, G and Li, Y and Guo, X},
title = {The specific DNA barcodes based on chloroplast genes for species identification of Theaceae plants.},
journal = {Physiology and molecular biology of plants : an international journal of functional plant biology},
volume = {28},
number = {4},
pages = {837-848},
pmid = {35592487},
issn = {0971-5894},
abstract = {UNLABELLED: More than 600 species in over 40 genera have been identified in family Theaceae worldwide. The accurate identification of Theaceae plants can ensure the market economic order, and it plays a vital role in achieving the sustainable utilization of germplasm resources. DNA barcoding, one of the most potential species identification technologies at present, has advanced in the rapid, accurate and repetitive discrimination of species. In this study, matK + ndhF + ycf1 was observed as the optimal combined candidate gene sequence of DNA barcodes by analyzing genetic information of four single chloroplast DNA sequences, including matK, rbcL, ndhF and ycf1, as well as six combined gene sequences. Subsequently, the experiments were performed on phylogenetic analysis based on genetic distance to study the phylogenetic relationship of Theaceae plants and evaluate the species identification accuracy of matK + ndhF + ycf1. Lastly, the species-specific DNA barcodes were designed by searching the variable sites (one type of single nucleotide polymorphism sites) for the accurate identification of Camellia amplexicaulis, Franklinia alatamaha, Gordonia brandegeei and Stewartia micrantha. The previous methods of screening and testing candidate gene sequences were optimized, and innovation was made in the above methods. The process of making visual DNA barcodes was standardized. Besides, DNA barcoding technology increased the accuracy of species identification and DNA barcoding was analyzed in accordance with the theories of population genetics (e.g., neutral theory of molecular evolution). The results of the study will lay a basis for the identification and protection of Theaceae species and germplasm resources.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-022-01175-7.},
}
@article {pmid35590622,
year = {2022},
author = {Le, MQ and Taylor, D},
title = {Persistent homology of convection cycles in network flows.},
journal = {Physical review. E},
volume = {105},
number = {4-1},
pages = {044311},
doi = {10.1103/PhysRevE.105.044311},
pmid = {35590622},
issn = {2470-0053},
abstract = {Convection is a well-studied topic in fluid dynamics, yet it is less understood in the context of network flows. Here, we incorporate techniques from topological data analysis (namely, persistent homology) to automate the detection and characterization of convective flows (also called cyclic or chiral flows) over networks, particularly those that arise for irreversible Markov chains. As two applications, we study convection cycles arising under the PageRank algorithm and we investigate chiral edge flows for a stochastic model of a bimonomer's configuration dynamics. Our experiments highlight how system parameters-e.g., the teleportation rate for PageRank and the transition rates of external and internal state changes for a monomer-can act as homology regularizers of convection, which we summarize with persistence barcodes and homological bifurcation diagrams. Our approach establishes a connection between the study of convection cycles and homology, the branch of mathematics that formally studies cycles, which has diverse potential applications throughout the sciences and engineering.},
}
@article {pmid35589054,
year = {2022},
author = {Rodriguez, AK and Krug, PJ},
title = {Ecological speciation by sympatric host shifts in a clade of herbivorous sea slugs, with introgression and localized mitochondrial capture between species.},
journal = {Molecular phylogenetics and evolution},
volume = {174},
number = {},
pages = {107523},
doi = {10.1016/j.ympev.2022.107523},
pmid = {35589054},
issn = {1095-9513},
mesh = {Animals ; DNA, Mitochondrial/genetics ; *Gastropoda/genetics ; Genetic Speciation ; *Herbivory ; Phylogeny ; Species Specificity ; },
abstract = {Host shifting in insect-plant systems was historically important to the development of ecological speciation theory, yet surprisingly few studies have examined whether host shifting drives diversification of marine herbivores. When small-bodied consumers feed and also mate on a preferred host, disruptive selection can split a population into host races despite gene flow. Support for host shifts is notably lacking for invertebrates associated with macroalgae, where the scale of dispersal by planktonic larvae often far exceeds the grain of host patchiness, and adults are typically less specialized than terrestrial herbivores. Here, we present a candidate example of ecological speciation in a clade of sea slugs that primarily consume green algae in the genus Caulerpa, including highly invasive species. Ancestral character state reconstructions supported 'sea grapes' (C. racemosa, C. lentillifera) as the ancestral host for a tropical radiation of 12 Elysia spp., with one shift onto alternative Caulerpa spp. in the Indo-Pacific. A Caribbean radiation of three species included symaptric host shifts to Rhipocephalus brevicaulis in the ancestor of E. pratensis Ortea &amp; Espinosa, 1996, and to C. prolifera in E. hamanni Krug, Vendetti &amp; Valdes 2016, plus a niche expansion to a range of Caulerpa spp. in E. subornata Verrill, 1901. All three species are broadly sympatric across the Caribbean but are host-partitioned at a fine grain, and distinct by morphology and at nuclear loci. However, non-recombining mtDNA revealed a history of gene flow between E. pratensis and E. subornata: COI haplotypes from E. subornata were 10.4% divergent from E. pratensis haplotypes from four sites, but closely related to all E. pratensis haplotypes sampled from six Bahamian islands, indicating historical introgression and localized "mitochondrial capture." Disruptive selective likely fueled divergence and adaptation to distinct host environments, indicating ecological speciation may be an under-appreciated driver of diversification for marine herbivores as well as epibionts and other resource specialists.},
}
@article {pmid35587493,
year = {2022},
author = {Tadmor-Levi, R and Borovski, T and Marcos-Hadad, E and Shapiro, J and Hulata, G and Golani, D and David, L},
title = {Establishing and using a genetic database for resolving identification of fish species in the Sea of Galilee, Israel.},
journal = {PloS one},
volume = {17},
number = {5},
pages = {e0267021},
pmid = {35587493},
issn = {1932-6203},
mesh = {Animals ; DNA ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Fishes/genetics ; *Fresh Water ; Israel ; Phylogeny ; },
abstract = {Freshwaters are a very valuable resource in arid areas, such as Mediterranean countries. Freshwater systems are vulnerable ecological habitats, significantly disturbed globally and especially in arid areas. The Sea of Galilee is the largest surface freshwater body in the Middle East. It is an isolated habitat supporting unique fish populations, including endemic species and populations on the edge of their distribution range. Using the Sea of Galilee for water supply, fishing and recreation has been placing pressure on these fish populations. Therefore, efficient monitoring and effective actions can make a difference in the conservation of these unique fish populations. To set a baseline and develop molecular tools to do so, in this study, DNA barcoding was used to establish a database of molecular species identification based on sequences of Cytochrome C Oxidase subunit I gene. DNA barcodes for 22 species were obtained and deposited in Barcode of Life Database. Among these, 12 barcodes for 10 species were new to the database and different from those already there. Barcode sequences were queried against the database and similar barcodes from the same and closely related species were obtained. Disagreements between morphological and molecular species identification were identified for five species, which were further studied by phylogenetic and genetic distances analyses. These analyses suggested the Sea of Galilee contained hybrid fish of some species and other species for which the species definition should be reconsidered. Notably, the cyprinid fish defined as Garra rufa, should be considered as Garra jordanica. Taken together, along with data supporting reconsideration of species definition, this study sets the basis for further using molecular tools for monitoring fish populations, understanding their ecology, and effectively managing their conservation in this unique and important habitat and in the region.},
}
@article {pmid35586290,
year = {2022},
author = {Kodada, J and Jäch, MA and Selnekovič, D and Goffová, K},
title = {Okalianecopinata sp. nov. (Insecta, Coleoptera, Elmidae) from Gunung Mulu National Park in Sarawak (Malaysia).},
journal = {ZooKeys},
volume = {1092},
number = {},
pages = {79-92},
pmid = {35586290},
issn = {1313-2989},
abstract = {Okalianecopinata sp. nov., from Sarawak, northwest Borneo, Malaysia, is described and illustrated along with an identification key. The standard barcoding fragment of the mitochondrial gene coding for cytochrome c oxidase subunit I (COI) was used together with morphological characters to delimit the taxonomic boundaries of the two known species, which live in shallow streams flowing through dense primary forests in limestone areas in Pahang (West Malaysia) and Sarawak (East Malaysia). The majority of all examined Okalia are flightless. Morphological distinguishing characters are the length of the granulated fifth elytral interval, the elytral and pronotal punctation, the aedeagal morphology, and the distal portion of the ovipositor.},
}
@article {pmid35586287,
year = {2022},
author = {David, KJ and Hancock, DL and Sachin, K and Gracy, RG and Salini, S},
title = {Two new species of Platensina Enderlein (Diptera, Tephritidae, Tephritinae, Dithrycini) from India.},
journal = {ZooKeys},
volume = {1092},
number = {},
pages = {123-146},
pmid = {35586287},
issn = {1313-2989},
abstract = {Two new species of Platensina Enderlein, P.rabbanii David &amp; Hancock, sp. nov., and P.flavistigma David &amp; Hancock, sp. nov., are described from Meghalaya and southern India, respectively. Platensinarabbanii can be differentiated from P.alboapicalis Hering by the presence of a single hyaline indentation in cell r1 and the apical hyaline band in cell r2+3 restricted to the apex; P.flavistigma differs from P.quadrula Hardy by the presence of a yellow/fulvous pterostigma and shape of the epandrium. DNA barcode sequences of P.acrostacta (Wiedemann), P.flavistigma and P.platyptera Hendel were obtained and reported. Postabdominal descriptions and illustrations of P.acrostacta, P.platyptera and P.zodiacalis (Bezzi) are also provided along with keys to all 23 species and the 7 known from India.},
}
@article {pmid35586019,
year = {2022},
author = {Guo, XJ and Cheng, R and Jiang, S and Xue, DY and Han, HX},
title = {Four new species of Ditrigona Moore (Lepidoptera, Drepanidae) in China and an annotated catalogue.},
journal = {ZooKeys},
volume = {1091},
number = {},
pages = {57-98},
pmid = {35586019},
issn = {1313-2989},
abstract = {The Chinese species of the genus Ditrigona Moore, 1888 are reviewed and an annotated catalogue is provided. Four new species are described from China: Ditrigonasinespina Jiang &amp; Han, sp. nov., Ditrigonaparva Jiang &amp; Han, sp. nov., Ditrigonaconcava Guo &amp; Han, sp. nov., and Ditrigonafusca Guo &amp; Han, sp. nov. Derocacrystalla Chu &amp; Wang, 1987 and Auzatellapentesticha Chu &amp; Wang, 1987 are newly combined into, respectively, the derocina and quinaria species groups of Ditrigona. Ditrigonadiana Wilkinson is newly recorded in China. This results in 43 species of Ditrigona for the fauna of China. Illustrations of habitus and genitalia of the new species and most known species are presented.},
}
@article {pmid35585126,
year = {2022},
author = {Rezaei Tavabe, K and Tavana, M and Mirvaghefi, AR and Jouladeh-Roudbar, A and Rahimi, P and Doadrio, I and Ghanavi, HR},
title = {Barcoding and species delimitation of Iranian freshwater crabs of the Potamidae family (Decapoda: Brachyura).},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {8288},
pmid = {35585126},
issn = {2045-2322},
mesh = {Animals ; *Brachyura/genetics ; Ecosystem ; Fresh Water ; Iran ; *Lice Infestations ; Water ; },
abstract = {Freshwater ecosystems are under multiple threats in modern times such as water extraction for human consumption, industries and agricultural activities, water contamination and habitat destruction for example. At the same time the biodiversity of these ecosystems are often poorly studied, especially in arid countries such as Iran. In this work, we study one of the ecologically important members of Iranian freshwater fauna, freshwater crab species of the genus Potamon. Here, we barcoded the different populations occurring in the country and delimited the species to allow for a better understanding of their distribution and taxonomy. In this study, we evaluated the taxonomical statues of Potamon species in Iran using genetic data. In addition, we created the first barcoding reference for Iranian freshwater crabs, which is an important resource for future environmental and conservation studies.},
}
@article {pmid35585085,
year = {2022},
author = {Stenvers, VI and Sherlock, RE and Reisenbichler, KR and Robison, BH},
title = {ROV observations reveal infection dynamics of gill parasites in midwater cephalopods.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {8282},
pmid = {35585085},
issn = {2045-2322},
mesh = {Animals ; Decapodiformes ; *Dinoflagellida ; Gills ; Humans ; *Octopodiformes ; *Parasites ; },
abstract = {Gill parasites of coleoid cephalopods are frequently observed during remotely operated vehicle (ROV) dives in the Monterey Submarine Canyon. However, little knowledge exists on the identity of the parasite species or their effects on the cephalopod community. With the help of ROV-collected specimens and in situ footage from the past 27 years, we report on their identity, prevalence and potential infection strategy. Gill parasites were genetically and morphologically identified from collected specimens of Chiroteuthis calyx, Vampyroteuthis infernalis and Gonatus spp. In situ prevalence was estimated from video footage for C. calyx, Galiteuthis spp., Taonius spp. and Japetella diaphana, enabled by their transparent mantle tissue. The most common parasite was identified as Hochbergia cf. moroteuthensis, a protist of unresolved taxonomic ranking. We provide the first molecular data for this parasite and show a sister group relationship to the dinoflagellate genus Oodinium. Hochbergia cf. moroteuthensis was most commonly observed in adult individuals of all species and was sighted year round over the analyzed time period. In situ prevalence was highest in C. calyx (75%), followed by Galiteuthis spp. (29%), Taonius spp. (27%) and J. diaphana (7%). A second parasite, not seen on the in situ footage, but occurring within the gills of Gonatus berryi and Vampyroteuthis infernalis, could not be found in the literature or be identified through DNA barcoding. The need for further investigation is highlighted, making this study a starting point for unravelling ecological implications of the cephalopod-gill-parasite system in deep pelagic waters.},
}
@article {pmid35585055,
year = {2022},
author = {Kaufman, T and Nitzan, E and Firestein, N and Ginzberg, MB and Iyengar, S and Patel, N and Ben-Hamo, R and Porat, Z and Hunter, J and Hilfinger, A and Rotter, V and Kafri, R and Straussman, R},
title = {Visual barcodes for clonal-multiplexing of live microscopy-based assays.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {2725},
pmid = {35585055},
issn = {2041-1723},
mesh = {Clone Cells ; *DNA ; DNA Barcoding, Taxonomic/methods ; *Microscopy ; },
abstract = {While multiplexing samples using DNA barcoding revolutionized the pace of biomedical discovery, multiplexing of live imaging-based applications has been limited by the number of fluorescent proteins that can be deconvoluted using common microscopy equipment. To address this limitation, we develop visual barcodes that discriminate the clonal identity of single cells by different fluorescent proteins that are targeted to specific subcellular locations. We demonstrate that deconvolution of these barcodes is highly accurate and robust to many cellular perturbations. We then use visual barcodes to generate 'Signalome' cell-lines by mixing 12 clones of different live reporters into a single population, allowing simultaneous monitoring of the activity in 12 branches of signaling, at clonal resolution, over time. Using the 'Signalome' we identify two distinct clusters of signaling pathways that balance growth and proliferation, emphasizing the importance of growth homeostasis as a central organizing principle in cancer signaling. The ability to multiplex samples in live imaging applications, both in vitro and in vivo may allow better high-content characterization of complex biological systems.},
}
@article {pmid35584942,
year = {2022},
author = {Mohd-Azami, SNI and Loong, SK and Khoo, JJ and Sahimin, N and Lim, FS and Husin, NA and Mahfodz, NH and Mohd-Taib, FS and Ishak, SN and Makepeace, BL and Abubakar, S},
title = {Molecular evidence of rat bocavirus among rodents in Peninsular Malaysia.},
journal = {The Journal of veterinary medical science},
volume = {84},
number = {7},
pages = {938-941},
pmid = {35584942},
issn = {1347-7439},
mesh = {Animals ; *Bocavirus/genetics ; Malaysia/epidemiology ; Phylogeny ; Rats ; Rodentia ; },
abstract = {Rat bocavirus (RBoV) and rodent bocavirus (RoBoV) have previously been detected in Rattus norvegicus; however, these viruses have not been reported in rodent populations in Malaysia. We investigated the presence of RBoV and RoBoV in archived rodent specimens. DNA barcoding of the rodent cytochrome c oxidase gene identified five different species: Rattus tanezumi R3 mitotype, Rattus tiomanicus, Rattus exulans, Rattus argentiventer, and Rattus tanezumi sensu stricto. Three spleens were positive for RBoV (1.84%; 3/163), but no RoBoV was detected. Phylogenetic analyzes of the partial non-structural protein 1 gene grouped Malaysian RBoV strains with RBoV strains from China. Further studies among rats from different geographical locations are warranted for this relatively new virus.},
}
@article {pmid35577840,
year = {2022},
author = {Wang, AK and Lu, QF and Zhu, ZX and Liu, SH and Zhong, H and Xiao, ZZ and Zou, YG and Gu, LJ and Du, XH and Cai, HJ and Bi, YF},
title = {Exploring phylogenetic relationships within the subgenera of Bambusa based on DNA barcodes and morphological characteristics.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {8018},
pmid = {35577840},
issn = {2045-2322},
mesh = {*Bambusa/genetics ; Chloroplasts/genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Chloroplast/genetics ; DNA, Plant/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The genus Bambusa belongs to the subtribe Bambusinae and the subfamily Bambusoideae. The subgenera of Bambusa has not been satisfactorily circumscribed, and this remains a major taxonomic issue. Simultaneously, genera such as Dendrocalamus and Gigantochloa have not been confidently assigned to Bambusa. Here, the phylogenetic relationships among subgenera were investigated using five chloroplast DNA markers (rpl32-trnL, rpl16, matK, rbcL, and trnH-psbA) for a sample of 50 ingroup and 16 outgroup species. A total of 186 key morphological descriptors were studied for the 50 ingroup species. The results indicated that five chloroplast DNA markers were possible to distinguish Bambusa species from other species and divide them into several clusters. Phylogenetic analyses conducted using morphological descriptors and a combined marker (rpl32-trnL+rpl16) revealed three and five distinct lineages, respectively, among the currently recognized Bambusa species. The branching pattern of the dendrogram was not completely consistent with the classical taxonomic classification of Bambusa. In addition, not all varieties and cultivars were clustered with McClure classifications. As the maximum parsimony topology and morphological analyses were inconsistent, some clustering results overlapped. Overall, the results obtained here do not support the current classification of the Bambusa subgenera.},
}
@article {pmid35577294,
year = {2022},
author = {Xu, X and Yu, L and Li, F and Wang, B and Liu, F and Li, D},
title = {Phylogenetic placement and species delimitation of the crab spider genus Phrynarachne (Araneae: Thomisidae) from China.},
journal = {Molecular phylogenetics and evolution},
volume = {173},
number = {},
pages = {107521},
doi = {10.1016/j.ympev.2022.107521},
pmid = {35577294},
issn = {1095-9513},
mesh = {Animals ; China ; Mitochondria/genetics ; Phylogeny ; *Spiders/genetics ; },
abstract = {Evolutionary biologists have long been fascinated by the striking resemblance to bird droppings of the sit-and-wait crab spiders of the genus Phrynarachne. In doing so, species of Phrynarachne have evolved not to avoid detection, but rather, to cause predators to misidentify them as inedible and/or inanimate bird droppings. However, the lack of a phylogeny for Phrynarachne impedes our understanding of the evolution of this trait in the genus. Here we explore species boundaries in species of Phrynarachne from China using single- and multi-locus species delimitation approaches based on 30 Phrynarachne samples. All species delimitation approaches supported six species of Phrynarachne in China. We further present the first phylogenetic analysis of the genus Phrynarachne and estimate divergence times using two mitochondrial and three nuclear genes. All of our phylogenetic analyses supported the monophyly of Phrynarachne in China, with the genus still included within the higher 'Thomisus group' based on our results. Our dating analyses place the crown age of Phrynarachne in China to the middle Miocene. Taken together, our study provides a time-calibrated phylogeny of the genus Phrynarachne in China for testing hypotheses regarding the evolution of the lineage and bird dropping masquerade.},
}
@article {pmid35573680,
year = {2022},
author = {Konturek-Ciesla, A and Bryder, D},
title = {Stem Cells, Hematopoiesis and Lineage Tracing: Transplantation-Centric Views and Beyond.},
journal = {Frontiers in cell and developmental biology},
volume = {10},
number = {},
pages = {903528},
pmid = {35573680},
issn = {2296-634X},
abstract = {An appropriate production of mature blood cells, or hematopoiesis, is essential for organismal health and homeostasis. In this developmental cascade, hematopoietic stem cells (HSCs) differentiate into intermediate progenitor types, that subsequently give rise to the many distinct blood cell lineages. Here, we describe tools and methods that permit for temporal and native clonal-level HSC lineage tracing in the mouse, and that can now be combined with emerging single-cell molecular analyses. We integrate new insights derived from such experimental paradigms with past knowledge, which has predominantly been derived from transplantation-based approaches. Finally, we outline current knowledge and novel strategies derived from studies aimed to trace human HSC-derived hematopoiesis.},
}
@article {pmid35573480,
year = {2022},
author = {Abrecht, C and Hallisey, M and Dennis, J and Nazzaro, M and Brainard, M and Hathaway, E and Schork, AN and Hodi, FS and Severgnini, M and Baginska, J},
title = {Simplified mass cytometry protocol for in-plate staining, barcoding, and cryopreservation of human PBMC samples in clinical trials.},
journal = {STAR protocols},
volume = {3},
number = {2},
pages = {101362},
pmid = {35573480},
issn = {2666-1667},
support = {U24 CA224331/CA/NCI NIH HHS/United States ; },
mesh = {*Cryopreservation/methods ; Flow Cytometry/methods ; Humans ; Immunophenotyping ; *Leukocytes, Mononuclear ; Staining and Labeling ; },
abstract = {With the increasing use of mass cytometry in clinical research, a simplified and standardized protocol for immunophenotyping human peripheral blood mononuclear cells (PBMCs) in clinical trials is needed. We present a simplified in-plate staining protocol for up to 80 samples, for laboratories of all mass cytometry expertise levels, aimed to generate reproducible datasets for large clinical cohorts. In this protocol, we provide details on the requirements to obtain meaningful results, spanning from sample quality, barcoding, and batch-freezing of stained samples.},
}
@article {pmid35571761,
year = {2022},
author = {Verkuil, YI and Nicolaus, M and Ubels, R and Dietz, MW and Samplonius, JM and Galema, A and Kiekebos, K and de Knijff, P and Both, C},
title = {DNA metabarcoding quantifies the relative biomass of arthropod taxa in songbird diets: Validation with camera-recorded diets.},
journal = {Ecology and evolution},
volume = {12},
number = {5},
pages = {e8881},
pmid = {35571761},
issn = {2045-7758},
abstract = {Ecological research is often hampered by the inability to quantify animal diets. Diet composition can be tracked through DNA metabarcoding of fecal samples, but whether (complex) diets can be quantitatively determined with metabarcoding is still debated and needs validation using free-living animals. This study validates that DNA metabarcoding of feces can retrieve actual ingested taxa, and most importantly, that read numbers retrieved from sequencing can also be used to quantify the relative biomass of dietary taxa. Validation was done with the hole-nesting insectivorous Pied Flycatcher whose diet was quantified using camera footage. Size-adjusted counts of food items delivered to nestlings were used as a proxy for provided biomass of prey orders and families, and subsequently, nestling feces were assessed through DNA metabarcoding. To explore potential effects of digestion, gizzard and lower intestine samples of freshly collected birds were subjected to DNA metabarcoding. For metabarcoding with Cytochrome Oxidase subunit I (COI), we modified published invertebrate COI primers LCO1490 and HCO1777, which reduced host reads to 0.03%, and amplified Arachnida DNA without significant changing the recovery of other arthropod taxa. DNA metabarcoding retrieved all commonly camera-recorded taxa. Overall, and in each replicate year (N = 3), the relative scaled biomass of prey taxa and COI read numbers correlated at R = .85 (95CI:0.68-0.94) at order level and at R = .75 (CI:0.67-0.82) at family level. Similarity in arthropod community composition between gizzard and intestines suggested limited digestive bias. This DNA metabarcoding validation demonstrates that quantitative analyses of arthropod diet is possible. We discuss the ecological applications for insectivorous birds.},
}
@article {pmid35570323,
year = {2022},
author = {Bessey, C and Gao, Y and Truong, YB and Miller, H and Jarman, SN and Berry, O},
title = {Comparison of materials for rapid passive collection of environmental DNA.},
journal = {Molecular ecology resources},
volume = {22},
number = {7},
pages = {2559-2572},
pmid = {35570323},
issn = {1755-0998},
support = {Environomics Future Science Platform//Commonwealth Scientific and Industrial Research Organisation/ ; },
mesh = {Animals ; Biodiversity ; Cellulose ; *Chitosan ; DNA Barcoding, Taxonomic/methods ; *DNA, Environmental ; Environmental Monitoring/methods ; Fishes/genetics ; },
abstract = {Passive collection is an emerging sampling method for environmental DNA (eDNA) in aquatic systems. Passive eDNA collection is inexpensive and efficient, and requires minimal equipment, making it suited to high-density sampling and remote deployment. Here, we compare the effectiveness of nine membrane materials for passively collecting fish eDNA from a 3-million-litre marine mesocosm. We submerged materials (cellulose, cellulose with 1% and 3% chitosan, cellulose overlayed with electrospun nanofibres and 1% chitosan, cotton fibres, hemp fibres, and sponge with either zeolite or active carbon) for intervals between 5 and 1080 min. We show that for most materials, with as little as 5 min of submersion, mitochondrial fish eDNA measured with qPCR, and fish species richness measured with metabarcoding, was comparable to that collected by conventional filtering. Furthermore, PCR template DNA concentrations and species richness were generally not improved significantly by longer submersion. Species richness detected for all materials ranged between 11 and 37 species, with a median of 27, which was comparable to the range for filtered eDNA (19-32). Using scanning electron microscopy, we visualized biological matter adhering to the surface of materials, rather than entrapped, with images also revealing a diversity in size and structure of putative eDNA particles. eDNA can be collected rapidly from seawater with a passive approach and using a variety of materials. This will suit cost- and time-sensitive biological surveys, and where access to equipment is limited.},
}
@article {pmid35570274,
year = {2022},
author = {Pendl, H and Hernández-Lara, C and Kubacki, J and Borel, N and Albini, S and Valkiūnas, G},
title = {Exo-erythrocytic development of Plasmodium matutinum (lineage pLINN1) in a naturally infected roadkill fieldfare Turdus pilaris.},
journal = {Malaria journal},
volume = {21},
number = {1},
pages = {148},
pmid = {35570274},
issn = {1475-2875},
support = {09.3.3-LMT-K-712-19-0005//Lietuvos Mokslo Taryba/ ; },
mesh = {Animals ; Endothelial Cells ; *Haemosporida/physiology ; *Malaria, Avian/parasitology ; Mammals ; Phylogeny ; *Plasmodium/physiology ; *Songbirds/parasitology ; },
abstract = {BACKGROUND: Species of Plasmodium (Haemosporida, Plasmodiidae) are remarkably diverse haemoparasites. Information on genetic diversity of avian malaria pathogens has been accumulating rapidly, however exo-erythrocytic development of these organisms remains insufficiently addressed. This is unfortunate because, contrary to Plasmodium species parasitizing mammals, the avian malaria parasites undergo several cycles of exo-erythrocytic development, often resulting in damage of various organs. Insufficient knowledge on the exo-erythrocytic development in most described Plasmodium species precludes the understanding of mechanisms of virulence during avian malaria. This study extends information on the exo-erythrocytic development of bird malaria parasites.<br><br>METHODS: A roadkill fieldfare (Turdus pilaris) was sampled in Switzerland and examined using pathologic, cytologic, histologic, molecular and microbiologic methods. Avian malaria was diagnosed, and erythrocytic and exo-erythrocytic stages of the parasite were identified using morphologic characteristics and barcode DNA sequences of the cytochrome b gene. The species-specific characteristics were described, illustrated, and pathologic changes were reported.<br><br>RESULTS: An infection with Plasmodium matutinum lineage pLINN1 was detected. Parasitaemia was relatively low (0.3%), with all erythrocytic stages (trophozoites, meronts and gametocytes) present in blood films. Most growing erythrocytic meronts were markedly vacuolated, which is a species-specific feature of this parasite's development. Phanerozoites at different stages of maturation were seen in leukocytes, macrophages, and capillary endothelial cells in most organs examined; they were particularly numerous in the brain. Like the erythrocytic meronts, growing phanerozoites were markedly vacuolated. Conspicuous exo-erythrocytic development and maturation in leucocytes suggests that this fieldfare was not adapted to the infection and the parasite was capable to escape from cellular immunity.<br><br>CONCLUSIONS: This is the first report of exo-erythrocytic development of the malaria parasite lineage pLINN1 during single infection and the first report of this lineage in the fieldfare. The findings of multiple phanerozoites in brain, skeletal muscle, and eye tissue in combination with signs of vascular blockage and thrombus formation strongly suggest an impaired vision and neuromuscular responsiveness as cause of the unexpected collision with a slowly moving car. Further studies on exo-erythrocytic stages of haemosporidian parasites are pivotal to understand the true level of populational damage of avian malaria in wild birds.},
}
@article {pmid35567324,
year = {2022},
author = {Victorious, A and Zhang, Z and Chang, D and Maclachlan, R and Pandey, R and Xia, J and Gu, J and Hoare, T and Soleymani, L and Li, Y},
title = {A DNA Barcode-Based Aptasensor Enables Rapid Testing of Porcine Epidemic Diarrhea Viruses in Swine Saliva Using Electrochemical Readout.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {61},
number = {31},
pages = {e202204252},
doi = {10.1002/anie.202204252},
pmid = {35567324},
issn = {1521-3773},
mesh = {Animals ; *Coronavirus Infections/diagnosis/veterinary ; DNA Barcoding, Taxonomic ; Diarrhea/diagnosis/veterinary ; *Porcine epidemic diarrhea virus/genetics ; Saliva ; Sensitivity and Specificity ; Swine ; *Swine Diseases/diagnosis ; },
abstract = {Pen-side testing of farm animals for infectious diseases is critical for preventing transmission in herds and providing timely intervention. However, most existing pathogen tests have to be conducted in centralized labs with sample-to-result times of 2-4 days. Herein we introduce a test that uses a dual-electrode electrochemical chip (DEE-Chip) and a barcode-releasing electroactive aptamer for rapid on-farm detection of porcine epidemic diarrhea viruses (PEDv). The sensor exploits inter-electrode spacing reduction and active field mediated transport to accelerate barcode movement from electroactive aptamers to the detection electrode, thus expediting assay operation. The test yielded a clinically relevant limit-of-detection of 6 nM (0.37 μg mL[-1]) in saliva-spiked PEDv samples. Clinical evaluation of this biosensor with 12 porcine saliva samples demonstrated a diagnostic sensitivity of 83 % and specificity of 100 % with a concordance value of 92 % at an analysis time of one hour.},
}
@article {pmid35565532,
year = {2022},
author = {Ma, H and Zhang, H and Deng, J and Zhao, H and Kong, F and Jiang, W and Zhang, H and Dong, X and Wang, Q},
title = {Detection the eDNA of Batrachuperus taibaiensis from the Zhouzhi Heihe River Using a Nested PCR Method and DNA Barcoding.},
journal = {Animals : an open access journal from MDPI},
volume = {12},
number = {9},
pages = {},
pmid = {35565532},
issn = {2076-2615},
support = {2020k-19//Shaanxi Academy of Science of China/ ; 2021k-19//Shaanxi Academy of Sciences of China/ ; 2017k-10//Shaanxi Academy of Science of China/ ; 2020JQ-972//Natural Science Foundation of Shaanxi Province of China/ ; 2021SF-437//Shaanxi Science and Technology Department of China/ ; },
abstract = {The Taibai stream salamander (Batrachuperus taibaiensis) is a recently described species of the genus Batrachuperus that occurs in the Zhouzhi Heihe River and is endangered in its native range. Here, we have established a method for water environmental DNA (eDNA) analysis of Batrachuperus using a series of optimizations. We have designed a specific set of primers for the genus Batrachuperus to amplify a 160 bp fragment of Cytb. The sequences were obtained from nested PCR on eDNA extracted from water samples, after which DNA barcoding was performed according to sequence analysis to determine the presence of the target species in the water. The method was validated using water from the Zhouzhi Heihe River with known B. taibaiensis populations and found that B. taibaiensis eDNA can move at least 150 m downstream from its point of origin. This study is the first to establish an optimal method for obtaining the eDNA of Batrachuperus from water samples, which provides a theoretical basis for resource investigation and the protection of B. taibaiensis in future research. It is also an example of the eDNA extraction of other species that live in similar waters and are less genetically diverse between species.},
}
@article {pmid35561209,
year = {2022},
author = {Yeh, CC and Amorosi, CJ and Showman, S and Dunham, MJ},
title = {PacRAT: a program to improve barcode-variant mapping from PacBio long reads using multiple sequence alignment.},
journal = {Bioinformatics (Oxford, England)},
volume = {38},
number = {10},
pages = {2927-2929},
pmid = {35561209},
issn = {1367-4811},
support = {R01 GM101091/GM/NIGMS NIH HHS/United States ; R01 GM132162/GM/NIGMS NIH HHS/United States ; T32 HG00035//National Human Genome Research Institute of the NIH/ ; },
mesh = {Algorithms ; *High-Throughput Nucleotide Sequencing ; Sequence Alignment ; Sequence Analysis, DNA ; *Software ; },
abstract = {SUMMARY: Use of PacBio sequencing for characterizing barcoded libraries of genetic variants is on the rise. However, current approaches in resolving PacBio sequencing artifacts can result in a high number of incorrectly identified or unusable reads. Here, we developed a PacBio Read Alignment Tool (PacRAT) that improves the accuracy of barcode-variant mapping through several steps of read alignment and consensus calling. To quantify the performance of our approach, we simulated PacBio reads from eight variant libraries of various lengths and showed that PacRAT improves the accuracy in pairing barcodes and variants across these libraries. Analysis of real (non-simulated) libraries also showed an increase in the number of reads that can be used for downstream analyses when using PacRAT.<br><br>PacRAT is written in Python and is freely available (https://github.com/dunhamlab/PacRAT).<br><br>SUPPLEMENTARY INFORMATION: Supplemental data are available at Bioinformatics online.},
}
@article {pmid35561197,
year = {2022},
author = {Putri, GH and Anders, S and Pyl, PT and Pimanda, JE and Zanini, F},
title = {Analysing high-throughput sequencing data in Python with HTSeq 2.0.},
journal = {Bioinformatics (Oxford, England)},
volume = {38},
number = {10},
pages = {2943-2945},
pmid = {35561197},
issn = {1367-4811},
mesh = {Documentation ; Genomics ; *High-Throughput Nucleotide Sequencing ; Licensure ; *Software ; },
abstract = {SUMMARY: HTSeq 2.0 provides a more extensive application programming interface including a new representation for sparse genomic data, enhancements for htseq-count to suit single-cell omics, a new script for data using cell and molecular barcodes, improved documentation, testing and deployment, bug fixes and Python 3 support.<br><br>HTSeq 2.0 is released as an open-source software under the GNU General Public License and is available from the Python Package Index at https://pypi.python.org/pypi/HTSeq. The source code is available on Github at https://github.com/htseq/htseq.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid35560328,
year = {2022},
author = {Bois, A and Tervil, B and Moreau, A and Vienne-Jumeau, A and Ricard, D and Oudre, L},
title = {A topological data analysis-based method for gait signals with an application to the study of multiple sclerosis.},
journal = {PloS one},
volume = {17},
number = {5},
pages = {e0268475},
pmid = {35560328},
issn = {1932-6203},
mesh = {Biomechanical Phenomena ; Data Analysis ; Gait/physiology ; Humans ; Lower Extremity ; *Multiple Sclerosis ; },
abstract = {In the past few years, light, affordable wearable inertial measurement units have been providing to clinicians and researchers the possibility to quantitatively study motor degeneracy by comparing gait trials from patients and/or healthy subjects. To do so, standard gait features can be used but they fail to detect subtle changes in several pathologies including multiple sclerosis. Multiple sclerosis is a demyelinating disease of the central nervous system whose symptoms include lower limb impairment, which is why gait trials are commonly used by clinicians for their patients' follow-up. This article describes a method to compare pairs of gait signals, visualize the results and interpret them, based on topological data analysis techniques. Our method is non-parametric and requires no data other than gait signals acquired with inertial measurement units. We introduce tools from topological data analysis (sublevel sets, persistence barcodes) in a practical way to make it as accessible as possible in order to encourage its use by clinicians. We apply our method to study a cohort of patients suffering from progressive multiple sclerosis and healthy subjects. We show that it can help estimate the severity of the disease and also be used for longitudinal follow-up to detect an evolution of the disease or other phenomena such as asymmetry or outliers.},
}
@article {pmid35560223,
year = {2022},
author = {Su, Y and Lin, HC and Ho, HC},
title = {Hoplostethus roseus, a new roughy fish from the western Pacific based on morphology and DNA barcoding (family Trachichthyidae).},
journal = {Journal of fish biology},
volume = {101},
number = {3},
pages = {441-452},
doi = {10.1111/jfb.15086},
pmid = {35560223},
issn = {1095-8649},
support = {//National Museum of Marine Biology and Aquarium/ ; //National Sun Yat-sen University/ ; },
mesh = {Animals ; DNA Barcoding, Taxonomic ; Fishes/genetics ; Gills ; *Perciformes/anatomy &amp; histology ; },
abstract = {A new species of the roughy fish genus Hoplostethus is described from 11 types and a non-type specimen collected from Taiwanese waters. It can be distinguished from its congeners by a combination of characters: pectoral-fin rays 14-17 (modally 15-16); pyloric caeca 65-84; total gill rakers 19-20; predorsal scales 18-22; oral cavity, branchial chamber, top and underside of tongue, and peritoneum uniformly black; distal margin of membrane between dorsal-fin spines black; caudal fin without a black margin; caudal-fin base brownish. Comparisons of the new species with similar species are provided. DNA barcoding supports the monophyly of the new species, which appears to be closely related to Hoplostethus japonicus [average cytochrome c oxidase subunit I Kimura-2-parameter (COI K2P) distance of 4.1%].},
}
@article {pmid35556139,
year = {2022},
author = {Hartop, E and Srivathsan, A and Ronquist, F and Meier, R},
title = {Towards Large-Scale Integrative Taxonomy (LIT): Resolving the Data Conundrum for Dark Taxa.},
journal = {Systematic biology},
volume = {71},
number = {6},
pages = {1404-1422},
pmid = {35556139},
issn = {1076-836X},
mesh = {*Biodiversity ; Cluster Analysis ; *DNA Barcoding, Taxonomic/methods ; High-Throughput Nucleotide Sequencing ; Phylogeny ; },
abstract = {New, rapid, accurate, scalable, and cost-effective species discovery and delimitation methods are needed for tackling "dark taxa," here defined as groups for which $<$10$\%$ of all species are described and the estimated diversity exceeds 1,000 species. Species delimitation for these taxa should be based on multiple data sources ("integrative taxonomy") but collecting multiple types of data risks impeding a discovery process that is already too slow. We here develop large-scale integrative taxonomy (LIT), an explicit method where preliminary species hypotheses are generated based on inexpensive data that can be obtained quickly and cost-effectively. These hypotheses are then evaluated based on a more expensive type of "validation data" that is only obtained for specimens selected based on objective criteria applied to the preliminary species hypotheses. We here use this approach to sort 18,000 scuttle flies (Diptera: Phoridae) into 315 preliminary species hypotheses based on next-generation sequencing barcode (313 bp) clusters (using objective clustering [OC] with a 3$\%$ threshold). These clusters are then evaluated with morphology as the validation data. We develop quantitative indicators for predicting which barcode clusters are likely to be incongruent with morphospecies by randomly selecting 100 clusters for in-depth validation with morphology. A linear model demonstrates that the best predictors for incongruence between barcode clusters and morphology are maximum p-distance within the cluster and a newly proposed index that measures cluster stability across different clustering thresholds. A test of these indicators using the 215 remaining clusters reveals that these predictors correctly identify all clusters that are incongruent with morphology. In our study, all morphospecies are true or disjoint subsets of the initial barcode clusters so that all incongruence can be eliminated by varying clustering thresholds. This leads to a discussion of when a third data source is needed to resolve incongruent grouping statements. The morphological validation step in our study involved 1,039 specimens (5.8$\%$ of the total). The formal LIT protocol we propose would only have required the study of 915 (5.1$\%$: 2.5 specimens per species), as we show that clusters without signatures of incongruence can be validated by only studying two specimens representing the most divergent haplotypes. To test the generality of our results across different barcode clustering techniques, we establish that the levels of incongruence are similar across OC, Automatic Barcode Gap Discovery (ABGD), Poisson Tree Processes (PTP), and Refined Single Linkage (RESL) (used by Barcode of Life Data System to assign Barcode Index Numbers [BINs]). OC and ABGD achieved a maximum congruence score with the morphology of 89$\%$ while PTP was slightly less effective (84$\%$). RESL could only be tested for a subset of the specimens because the algorithm is not public. BINs based on 277 of the original 1,714 haplotypes were 86$\%$ congruent with morphology while the values were 89$\%$ for OC, 74$\%$ for PTP, and 72$\%$ for ABGD. [Biodiversity discovery; dark taxa; DNA barcodes; integrative taxonomy.].},
}
@article {pmid35553302,
year = {2022},
author = {Martin, SB and Cutmore, SC},
title = {Siphoderina hustoni n. sp. (Platyhelminthes: Trematoda: Cryptogonimidae) from the Maori snapper Lutjanus rivulatus (Cuvier) on the Great Barrier Reef.},
journal = {Systematic parasitology},
volume = {99},
number = {4},
pages = {403-417},
pmid = {35553302},
issn = {1573-5192},
mesh = {Animals ; Australia ; DNA, Ribosomal/genetics ; Female ; *Fish Diseases/parasitology ; Fishes/parasitology ; Humans ; Male ; Phylogeny ; Species Specificity ; *Trematoda/genetics ; *Trematode Infections/parasitology ; },
abstract = {A new cryptogonimid trematode, Siphoderina hustoni n. sp., is reported, collected off Lizard Island, Queensland, Australia, from the Maori snapper Lutjanus rivulatus (Cuvier). The new species is moderately distinctive within the genus. It is larger and more elongate than most other species of Siphoderina Manter, 1934, has the shortest forebody of any, a relatively large ventral sucker, a long post-testicular zone, and is perhaps most recognisable for the substantial space in the midbody between the ventral sucker and ovary devoid of uterine coils and vitelline follicles, the former being restricted to largely posterior to the ovary and the latter distributed from the level of the anterior testis to the level of the ovary. In phylogenetic analyses of 28S ribosomal DNA, the new species resolved with the other nine species of Siphoderina for which sequence data are available, all of which are from Queensland waters and from lutjanid and haemulid fishes. Molecular barcode data were also generated, for the ITS2 ribosomal DNA and cox1 mitochondrial DNA markers. The new species is the first cryptogonimid known from L. rivulatus and the first metazoan parasite reported from that fish in Australian waters.},
}
@article {pmid35551774,
year = {2022},
author = {Xiong, C and Huang, CH and Wu, L and Xu, R and Xue, JP and Liu, ZG and Sun, W},
title = {Identification of Andrographis Herba and its common products using mini-barcode.},
journal = {Chinese journal of natural medicines},
volume = {20},
number = {5},
pages = {393-400},
doi = {10.1016/S1875-5364(22)60157-2},
pmid = {35551774},
issn = {1875-5364},
mesh = {*Andrographis ; Andrographis paniculata ; DNA Primers ; *Drugs, Chinese Herbal ; },
abstract = {Andrographis Herba, the aerial part of Andrographis paniculata (Burm. f.) Wall. ex Nees (Acanthaceae), has a wide geographic distribution and has been used for the treatment of fever, cold, inflammation, and other infectious diseases. In markets, sellers and buyers commonly inadvertently confuse with related species. In addition, most Chinese medicinal herbs are subjected to traditional processing procedures, such as steaming and boiling, before they are sold at dispensaries; therefore, it is very difficult to identify Andrographis Herba when it is processed into Chinese medicines. The identification of species and processed medicinal materials is a growing issue in the marketplace. However, conventional methods of identification have limitations, while DNA barcoding has received considerable attention as a new potential means to identify species and processed medicinal materials. In this study, 17 standard reference materials of A. paniculata, 2 standard decoctions, 27 commercial products and two adulterants were collected. Based on the ITS2 sequence, it could successfully identify A. paniculata and adulterants. Moreover, a nucleotide signature consisting of 71 bp was designed, this sequence is highly conserved and specific within A. paniculata while divergent among other species. Then, we used these new primers to amplify the nucleotide signature region from processed materials. In conclusion, the DNA barcoding method developed in the present study for authenticating A. paniculata is rapid and cost-effective. It can be used in the future to guarantee the quality of Andrographis Herba of each regulatory link for clinical use.},
}
@article {pmid35538602,
year = {2022},
author = {Kennedy, AH and Schoch, CL and Marrero, G and Brover, V and Robbertse, B},
title = {Publicly Available and Validated DNA Reference Sequences Are Critical to Fungal Identification and Global Plant Protection Efforts: A Use-Case in Colletotrichum.},
journal = {Plant disease},
volume = {106},
number = {6},
pages = {1573-1596},
pmid = {35538602},
issn = {0191-2917},
support = {Z99 LM999999/ImNIH/Intramural NIH HHS/United States ; },
mesh = {*Colletotrichum/genetics ; Commerce ; DNA ; Internationality ; Phylogeny ; },
abstract = {Publicly available and validated DNA reference sequences useful for phylogeny estimation and identification of fungal pathogens are an increasingly important resource in the efforts of plant protection organizations to facilitate safe international trade of agricultural commodities. Colletotrichum species are among the most frequently encountered and regulated plant pathogens at U.S. ports-of-entry. The RefSeq Targeted Loci (RTL) project at NCBI (BioProject no. PRJNA177353) contains a database of curated fungal internal transcribed spacer (ITS) sequences that interact extensively with NCBI Taxonomy, resulting in verified name-strain-sequence type associations for >12,000 species. We present a publicly available dataset of verified and curated name-type strain-sequence associations for all available Colletotrichum species. This includes an updated GenBank Taxonomy for 238 species associated with up to 11 protein coding loci and an updated RTL ITS dataset for 226 species. We demonstrate that several marker loci are well suited for phylogenetic inference and identification. We improve understanding of phylogenetic relationships among verified species, verify or improve phylogenetic circumscriptions of 14 species complexes, and reveal that determining relationships among these major clades will require additional data. We present detailed comparisons between phylogenetic and similarity-based approaches to species identification, revealing complex patterns among single marker loci that often lead to misidentification when based on single-locus similarity approaches. We also demonstrate that species-level identification is elusive for a subset of samples regardless of analytical approach, which may be explained by novel species diversity in our dataset and incomplete lineage sorting and lack of accumulated synapomorphies at these loci.},
}
@article {pmid35538127,
year = {2022},
author = {Ezpeleta, J and Garcia Labari, I and Villanova, GV and Bulacio, P and Lavista-Llanos, S and Posner, V and Krsticevic, F and Arranz, S and Tapia, E},
title = {Robust and scalable barcoding for massively parallel long-read sequencing.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {7619},
pmid = {35538127},
issn = {2045-2322},
mesh = {*DNA Barcoding, Taxonomic/methods ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Nucleic-acid barcoding is an enabling technique for many applications, but its use remains limited in emerging long-read sequencing technologies with intrinsically low raw accuracy. Here, we apply so-called NS-watermark barcodes, whose error correction capability was previously validated in silico, in a proof of concept where we synthesize 3840 NS-watermark barcodes and use them to asymmetrically tag and simultaneously sequence amplicons from two evolutionarily distant species (namely Bordetella pertussis and Drosophila mojavensis) on the ONT MinION platform. To our knowledge, this is the largest number of distinct, non-random tags ever sequenced in parallel and the first report of microarray-based synthesis as a source for large oligonucleotide pools for barcoding. We recovered the identity of more than 86% of the barcodes, with a crosstalk rate of 0.17% (i.e., one misassignment every 584 reads). This falls in the range of the index hopping rate of established, high-accuracy Illumina sequencing, despite the increased number of tags and the relatively low accuracy of both microarray-based synthesis and long-read sequencing. The robustness of NS-watermark barcodes, together with their scalable design and compatibility with low-cost massive synthesis, makes them promising for present and future sequencing applications requiring massive labeling, such as long-read single-cell RNA-Seq.},
}
@article {pmid35535318,
year = {2022},
author = {Zhang, J and Cong, Q and Shen, J and Song, L and Grishin, NV},
title = {Genomic DNA sequencing reveals two new North American species of Staphylus (Hesperiidae: Pyrginae: Carcharodini).},
journal = {The taxonomic report of the International Lepidoptera Survey},
volume = {10},
number = {},
pages = {},
pmid = {35535318},
issn = {2643-4806},
support = {R35 GM127390/GM/NIGMS NIH HHS/United States ; },
abstract = {Two new skipper butterfly (Hesperiidae) species are described from the United States: Staphylus floridus Grishin, sp. n. (type locality in Florida, Volusia Co.) and Staphylus ecos Grishin, sp. n. (type locality in Texas, Brewster Co.). They are cryptic and hence escaped recognition. They differ from their sister species by the relative size and morphology of genitalia and by genotype-including and beyond the COI barcode-thus suggesting genetic isolation that argues for their species-level status. A lectotype is designated for Helias ascalaphus Staudinger, 1876. Staphylus opites (Godman &amp; Salvin, 1896), stat. rest. is a species-level taxon and not a synonym of Staphylus vincula (Plötz, 1886), while Pholisora iguala Williams &amp; Bell, 1940, syn. n. is a junior subjective synonym of S. vincula.},
}
@article {pmid35534254,
year = {2022},
author = {Jin, YX and Wang, YS and Gao, YW and Zhou, LW and Wang, YH and Yuan, QJ and Dong, WP},
title = {[Complete chloroplast genome of Ligustrum lucidum and highly variable marker identification for Ligustrum].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {47},
number = {7},
pages = {1847-1856},
doi = {10.19540/j.cnki.cjcmm.20220116.103},
pmid = {35534254},
issn = {1001-5302},
mesh = {Fruit ; *Genome, Chloroplast ; *Ligustrum/chemistry/genetics ; Phylogeny ; Plant Breeding ; },
abstract = {Ligustri Lucidi Fructus, the sun-dried mature fruit of Ligustrum lucidum, is cool, plain, sweet, and bitter, which can be used as both food and medicine, with the effects of improving vision, blacking hair, and tonifying liver and kidney. It takes effect slowly. However, little is known about the genetic information of the medicinal plant and it is still a challenge to distinguish Ligustrum species. In this study, the complete chloroplast genome of L. lucidum was obtained by genome skimming and then compared with that of five other Ligustrum species, which had been reported. This study aims to evaluate the interspecific variation of chloroplast genome within the genus and develop molecular markers for species identification of the genus. The result showed that the chloroplast genome of L. lucidum was 162 162 bp with a circular quadripartite structure of two single-copy regions separated by a pair of inverted repeats. The Ligustrum chloroplast genomes were conserved with small interspecific difference. Comparative analysis of six Ligustrum chloroplast genomes revealed three variable regions(rbcL-accD, ycf1a, and ycf1b), and ycf1a and ycf1b can be used as the species-specific DNA barcode for Ligustrum. Phylogeny analysis provided the best resolution of Ligustrum and supported that L. lucidum was sister to L. gracile. This study clarified the genetic diversity of L. lucidum from provenance, which can serve as a reference for further analysis of pharmacological differences and breeding of excellent varieties with stable drug effects.},
}
@article {pmid35534251,
year = {2022},
author = {Zhang, JH and Liu, SH and Zhang, ZF and Shi, Y and Man, JH and Yin, GY and Wang, X and Liu, FB and Wang, XH and Wei, SL},
title = {[Identification and quality evaluation of germplasm resources of commercial Scutellaria baicalensis based on DNA barcode and HPLC].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {47},
number = {7},
pages = {1814-1823},
doi = {10.19540/j.cnki.cjcmm.20220117.101},
pmid = {35534251},
issn = {1001-5302},
mesh = {Chromatography, High Pressure Liquid ; *DNA Barcoding, Taxonomic/methods ; DNA, Plant/genetics ; Phylogeny ; *Scutellaria baicalensis/genetics ; },
abstract = {Scutellaria baicalensis is a commonly used Chinese medicinal herb. In this study, we identified the germplasm resources of commercial S. baicalensis samples based on trnH-psbA, petA-psbJ, and ycf4-cemA sequences according to the available chloroplast genome sequencing results, and measured the content of baicalin by HPLC. Through the above means we determined the best DNA barcode that can be used to detect the germplasm resources and evaluate the quality of commercial S. baicalensis samples. A total of 104 samples were collected from 24 provinces, from which DNA was extracted for PCR amplification. The amplification efficiencies of trnH-psbA, petA-psbJ, and ycf4-cemA sequences were 100%, 59.62%, and 25.96%, respectively. The results of sequence analysis showed that 5, 4, and 2 haplotypes were identified based on trnH-psbA, petA-psbJ, and ycf4-cemA sequences, respectively. However, the sequences of haplotypes in commercial samples were different from that of the wild type, and the joint analysis of three fragments of S. baicalensis only identified 6 haplotypes. Furthermore, the phylogenetic analysis and genetic distance analysis indicated that trnH-psbA could be used to identify S. baicalensis from adulterants. The above analysis showed that trnH-psbA was the best fragment for identifying the germplasm resources of commercial S. baicalensis samples. We then analyzed the haplotypes(THap1-THap5) of commercial S. baicalensis samples based on trnH-psbA and found that THap2 was the main circulating haplotype of the commercial samples, accounting for 86.55% of the total samples, which indicated the scarce germplasm resources of commercial S. baicalensis samples. The content of baicalin in all the collected commercial S. baicalensis samples exceeded the standard in Chinese Pharmacopoeia and had significant differences(maximum of 12.21%) among samples, suggesting that the quality of commercial S. baicalensis samples varied considerably. However, there was no significant difference in baicalin content between different provinces or between different haplotypes. This study facilitates the establishment of the standard identification system for S. baicalensis, and can guide the commercial circulation and reasonable medication of S. baicalensis.},
}
@article {pmid35532013,
year = {2022},
author = {Warneford-Thomson, R and Shah, PP and Lundgren, P and Lerner, J and Morgan, J and Davila, A and Abella, BS and Zaret, K and Schug, J and Jain, R and Thaiss, CA and Bonasio, R},
title = {A LAMP sequencing approach for high-throughput co-detection of SARS-CoV-2 and influenza virus in human saliva.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {35532013},
issn = {2050-084X},
support = {DP2 HL147123/HL/NHLBI NIH HHS/United States ; },
mesh = {*COVID-19/diagnosis ; Humans ; *Orthomyxoviridae ; Pandemics ; RNA, Viral/analysis ; SARS-CoV-2/genetics ; Saliva ; Sensitivity and Specificity ; },
abstract = {The COVID-19 pandemic has created an urgent need for rapid, effective, and low-cost SARS-CoV-2 diagnostic testing. Here, we describe COV-ID, an approach that combines RT-LAMP with deep sequencing to detect SARS-CoV-2 in unprocessed human saliva with a low limit of detection (5-10 virions). Based on a multi-dimensional barcoding strategy, COV-ID can be used to test thousands of samples overnight in a single sequencing run with limited labor and laboratory equipment. The sequencing-based readout allows COV-ID to detect multiple amplicons simultaneously, including key controls such as host transcripts and artificial spike-ins, as well as multiple pathogens. Here, we demonstrate this flexibility by simultaneous detection of 4 amplicons in contrived saliva samples: SARS-CoV-2, influenza A, human STATHERIN, and an artificial SARS calibration standard. The approach was validated on clinical saliva samples, where it showed excellent agreement with RT-qPCR. COV-ID can also be performed directly on saliva absorbed on filter paper, simplifying collection logistics and sample handling.},
}
@article {pmid35531600,
year = {2023},
author = {Dokhov, O and Bogdanovich, V},
title = {Barcodes as Optical Marks for an Objective Assessment of Laparoscopic Skills in a Box Trainer.},
journal = {Surgical innovation},
volume = {30},
number = {1},
pages = {123-125},
doi = {10.1177/15533506221100297},
pmid = {35531600},
issn = {1553-3514},
mesh = {*Laparoscopy ; Curriculum ; Clinical Competence ; Computer Simulation ; },
abstract = {Background/Need. The sensor-equipped box trainers can objectively evaluate psychomotor skills similar to virtual simulators. However, such box models are least of all involved in curricula in minimally invasive surgery, probably because of their complexity or high cost. This discrepancy prompted us to find a simple solution that provides an objective assessment of laparoscopic skills on any box trainer. Methodology and Device Description. We used QR code, Code 128, and Circular Code 128 as optical marks in tasks on box trainers. These were marks of errors and positive actions. Polyvinylchloride and a nontransparent silicone sheet served as materials for the tasks. All barcode images were printed with black ink on office paper. In addition, we have developed an app that allows dealing with selected types of barcodes. Preliminary results. We designed 6 tasks based on our approach. Every task provides a precision registration of time, errors, and correct actions, comparable with virtual simulators. However, only 4 tasks showed satisfactory results during face validity's obtaining. We found that primitive barcode scanning technology can provide an objective assessment of trainees on box trainers. The proposed approach is well suited for both commercial and custom box trainers. Current status. The research is currently underway to establish construct validity for the developed tasks. Besides, we intend to study features of other types of barcodes, such as Aztec Code, EAN-8, DataMatrix, and annular barcodes.},
}
@article {pmid35530514,
year = {2022},
author = {Muller, RY and Meacham, ZA and Ingolia, NT},
title = {Plasmid and Sequencing Library Preparation for CRISPRi Barcoded Expression Reporter Sequencing (CiBER-seq) in Saccharomyces cerevisiae.},
journal = {Bio-protocol},
volume = {12},
number = {7},
pages = {e4376},
pmid = {35530514},
issn = {2331-8325},
support = {DP2 CA195768/CA/NCI NIH HHS/United States ; R01 GM130996/GM/NIGMS NIH HHS/United States ; R01 GM135233/GM/NIGMS NIH HHS/United States ; S10 OD018174/OD/NIH HHS/United States ; },
abstract = {Genetic networks regulate nearly all biological processes, including cellular differentiation, homeostasis, and immune responses. Determining the precise role of each gene within a regulatory network can explain its overall, integrated function, and pinpoint mechanisms underlying misregulation in disease states. Transcriptional reporter assays are a useful tool for dissecting these genetic networks, because they link a molecular process to a measurable readout, such as the expression of a fluorescent protein. Here, we introduce a new technique that uses expressed RNA barcodes as reporters, to measure transcriptional changes induced by CRISPRi-mediated genetic perturbation across a diverse, genome-wide library of guide RNAs. We describe an exemplary reporter based on the promoter that drives His4 expression in these guidelines, which can be used as a framework to interrogate other expression phenotypes. In this workflow, a library of plasmids is assembled, encoding a CRISPRi guide RNA (gRNA) along with one or more transcriptional reporters that drive expression of guide-specific nucleotide barcode sequences. For example, when interrogating regulation of the budding yeast HIS4 promoter normalized against a control housekeeping promoter that drives Pgk1 expression, this plasmid library contains a gRNA expression cassette, a HIS4 reporter driving expression of one gRNA-specific nucleotide barcode, and a PGK1 reporter driving expression of a second, gRNA-specific barcode. Long-read sequencing is used to determine which gRNA is associated with these nucleotide barcodes. The plasmid library is then transformed into yeast cells, where each cell receives one plasmid, and experiences a genetic perturbation driven by the guide on that plasmid. The expressed RNA barcodes are extracted in bulk and quantified using high-throughput sequencing, thereby measuring the effect of their corresponding gRNA on barcoded reporter expression. In the case of the HIS4 reporter described above, guides disrupting translation elongation will increase expression of the associated HIS4 barcode specifically, without changing expression of the PGK1 control barcode. It is further possible to quantify plasmid abundance by DNA sequencing, as an additional approach to normalize for differences in plasmid abundance within the population of cells. This protocol outlines the steps to prepare barcode reporter CRISPRi plasmid libraries, link guides to barcodes with long-read sequencing, and measure expression changes through barcode RNA and DNA sequencing. This method is ideal for probing transcriptional or post-transcriptional regulation, as it measures the effects of a genetic perturbation by directly quantifying reporter RNA abundance, rather than relying on indirect growth or fluorescence readouts. Graphic abstract.},
}
@article {pmid35524129,
year = {2022},
author = {Chochinov, CA and Nguyen Ba, AN},
title = {Bulk-Fitness Measurements Using Barcode Sequencing Analysis in Yeast.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2477},
number = {},
pages = {399-415},
pmid = {35524129},
issn = {1940-6029},
mesh = {DNA ; *High-Throughput Nucleotide Sequencing ; *Saccharomyces cerevisiae/genetics ; Sequence Analysis, DNA ; },
abstract = {The use of DNA barcodes for determining changes in genotype frequencies has been instrumental to increase the scale at which we can phenotype strain libraries by using next-generation sequencing technologies. Here, we describe the determination of strain fitness for thousands of yeast strains simultaneously in a single assay using recent innovations that increase the precision of these measurements, such as the inclusion of unique-molecular identifiers (UMIs) and purification by solid-phase reverse immobilization (SPRI) beads.},
}
@article {pmid35524126,
year = {2022},
author = {Després, PC and Dubé, AK and Yachie, N and Landry, CR},
title = {High-Throughput Gene Mutagenesis Screening Using Base Editing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2477},
number = {},
pages = {331-348},
pmid = {35524126},
issn = {1940-6029},
support = {387697//CIHR/Canada ; },
mesh = {Base Sequence ; *CRISPR-Cas Systems/genetics ; *Gene Editing ; Mutagenesis/genetics ; RNA, Guide, CRISPR-Cas Systems/genetics ; },
abstract = {Base editing is a CRISPR-Cas9 genome engineering tool that allows programmable mutagenesis without the creation of double-stranded breaks. Here, we describe the design and execution of large-scale base editing screens using the Target-AID base editor in yeast. Using this approach, thousands of sites can be mutated simultaneously. The effects of these mutations on fitness can be measured using a pooled growth competition assay followed by DNA sequencing of gRNAs as barcodes.},
}
@article {pmid35510791,
year = {2022},
author = {Gregorič, M and Kutnjak, D and Bačnik, K and Gostinčar, C and Pecman, A and Ravnikar, M and Kuntner, M},
title = {Spider webs as eDNA samplers: Biodiversity assessment across the tree of life.},
journal = {Molecular ecology resources},
volume = {22},
number = {7},
pages = {2534-2545},
doi = {10.1111/1755-0998.13629},
pmid = {35510791},
issn = {1755-0998},
support = {Z1-8143//Slovenian Research Agency/ ; P1-0236//Slovenian Research Agency/ ; P4-0407//Slovenian Research Agency/ ; P1-0198//Slovenian Research Agency/ ; P1-0255//Slovenian Research Agency/ ; J1-9163//Slovenian Research Agency/ ; J1-1703//Slovenian Research Agency/ ; },
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/methods ; *DNA, Environmental ; Environmental Monitoring/methods ; *Spiders/genetics ; },
abstract = {The concept of environmental DNA (eDNA) utilizes nucleic acids of organisms directly from the environment. Recent breakthrough studies have successfully detected a wide spectrum of prokaryotic and eukaryotic eDNA from a variety of environments, ranging from ancient to modern, and from terrestrial to aquatic. With their diversity and ubiquity in nature, spider webs might act as powerful biofilters and could thus represent a promising new source of eDNA, but their utility under natural field conditions is severely understudied. Here, we bridge this knowledge gap to establish spider webs as a source of eDNA with far reaching implications. First, we conducted a field study to track specific arthropod targets from different spider webs. We then used high-throughput amplicon sequencing of taxonomic barcodes to investigate the utility of spider web eDNA for biodiversity monitoring of animals, fungi and bacteria. Our results show that genetic remains on spider webs allow the detection of even the smallest target organisms. We also demonstrate that eDNA from spider webs is useful in research of community compositions across the different domains of life, with potentially highly detailed temporal and spatial information.},
}
@article {pmid35505067,
year = {2022},
author = {Salifu, D and Ibrahim, EA and Tonnang, HEZ},
title = {Leveraging machine learning tools and algorithms for analysis of fruit fly morphometrics.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {7208},
pmid = {35505067},
issn = {2045-2322},
mesh = {*Algorithms ; *Machine Learning ; Neural Networks, Computer ; ROC Curve ; Support Vector Machine ; },
abstract = {Analysis of landmark-based morphometric measurements taken on body parts of insects have been a useful taxonomic approach alongside DNA barcoding in insect identification. Statistical analysis of morphometrics have largely been dominated by traditional methods and approaches such as principal component analysis (PCA), canonical variate analysis (CVA) and discriminant analysis (DA). However, advancement in computing power creates a paradigm shift to apply modern tools such as machine learning. Herein, we assess the predictive performance of four machine learning classifiers; K-nearest neighbor (KNN), random forest (RF), support vector machine (the linear, polynomial and radial kernel SVMs) and artificial neural network (ANNs) on fruit fly morphometrics that were previously analysed using PCA and CVA. KNN and RF performed poorly with overall model accuracy lower than "no-information rate" (NIR) (p value > 0.1). The SVM models had a predictive accuracy of > 95%, significantly higher than NIR (p < 0.001), Kappa > 0.78 and area under curve (AUC) of the receiver operating characteristics was > 0.91; while ANN model had a predictive accuracy of 96%, significantly higher than NIR, Kappa of 0.83 and AUC was 0.98. Wing veins 2, 3, 8, 10, 14 and tibia length were of higher importance than other variables based on both SVM and ANN models. We conclude that SVM and ANN models could be used to discriminate fruit fly species based on wing vein and tibia length measurements or any other morphologically similar pest taxa. These algorithms could be used as candidates for developing an integrated and smart application software for insect discrimination and identification. Variable importance analysis results in this study would be useful for future studies for deciding what must be measured.},
}
@article {pmid35502700,
year = {2022},
author = {Cowell, TW and Dobria, A and Han, HS},
title = {Simplified, Shear Induced Generation of Double Emulsions for Robust Compartmentalization during Single Genome Analysis.},
journal = {ACS applied materials &amp; interfaces},
volume = {14},
number = {18},
pages = {20528-20537},
doi = {10.1021/acsami.1c22692},
pmid = {35502700},
issn = {1944-8252},
mesh = {Emulsions ; *Microfluidics/methods ; },
abstract = {Drop microfluidics has driven innovations for high throughput, low input analysis techniques such as single-cell RNA-seq. However, the instability of single emulsion (SE) drops occasionally causes significant merging during drop processing, limiting most applications to single-step reactions in drops. Here, we show that double emulsion (DE) drops address this critical limitation and completely prevent drop contents from mixing. DEs show excellent stability during thermal cycling. More importantly, DEs undergo rupture into the continuous phase instead of merging, preventing content mixing and eliminating unstable drops from the downstream analysis. Due to the lack of drop merging, the monodispersity of drops is maintained throughout a workflow, enabling the deterministic manipulation of drops downstream. We also developed a simple, one-layer DE drop maker compatible with simple surface treatment using a plasma cleaner. The device allows for the robust production of single-core DEs at a wide range of flow rates and better control over the shell thickness, both of which have been significant limitations of conventional two-layer devices. This approach makes the fabrication of DE devices much more accessible, facilitating its broader adoption. Finally, we show that DE droplets eliminate content mixing and maintain compartmentalization of single virus genomes during PCR-based amplification and barcoding, while SEs mixed contents due to merging. With their resistance to content mixing, DE drops have key advantages for multistep reactions in drops, which is limited in SEs due to merging and content mixing.},
}
@article {pmid35500552,
year = {2022},
author = {Takagui, FH and Baumgärtner, L and Viana, P and Lima, MCC and Bitencourt, JA and Venere, PC and Lui, RL and Moreira-Filho, O and Feldberg, E and Almeida Simões, F and Birindelli, JL and Giuliano-Caetano, L},
title = {Karyotype Evolution of Talking Thorny Catfishes Anadoras (Doradidae, Astrodoradinae): A Process Mediated by Structural Rearrangements and Intense Reorganization of Repetitive DNAs.},
journal = {Cytogenetic and genome research},
volume = {162},
number = {1-2},
pages = {64-75},
doi = {10.1159/000523747},
pmid = {35500552},
issn = {1424-859X},
mesh = {Animals ; *Catfishes/genetics ; Chromosome Inversion ; DNA, Ribosomal/genetics ; Evolution, Molecular ; Heterochromatin/genetics ; Karyotype ; Phylogeny ; },
abstract = {Anadoras is a thorny catfish genus widespread through the Amazon and Paraguay river basins. It includes 2 nominal species, A. grypus and A. weddellii, plus Anadoras sp. "araguaia," an undescribed species only recognized morphologically. Since Anadoras occupies a basal position within the Astrodoradinae phylogeny, it is crucial to identify its cytogenetic features to comprehend the mechanisms involved in the chromosomal diversification of this subfamily. Therefore, we performed a comparative cytogenetic analysis including all species of Anadoras. Furthermore, we applied a species delimitation analysis based on 600 bp of the mitochondrial cytochrome oxidase subunit 1 (CO1) gene to investigate the taxonomic status of the species. Cytogenetic markers revealed a high degree of similarity among Anadoras weddellii and Anadoras sp. "araguaia," both have 2n = 56 chromosomes (24m + 10sm + 22st/a), single NOR sites on acrocentric pair 28, and 5S rDNA sites on submetacentric pair 15. A. grypus has the most divergent chromosomal characteristics because, even though it also has 2n = 56 chromosomes, it exhibits several differences in the chromosome formula, heterochromatin distribution, and number/position of the rDNA sites. In sum, we believe that the chromosome diversification of Anadoras is due to 4 mechanisms: centric fusion, pericentric/paracentric inversions, nonreciprocal translocations, and activity of transposable elements. Additionally, our phylogenetic tree revealed well-supported clades and, by barcode species delimitation analysis, confirmed the existence of 3 molecular operational taxonomic units, including the putative new species Anadoras sp. "araguaia."},
}
@article {pmid35497186,
year = {2022},
author = {Ashfaq, M and Khan, AM and Rasool, A and Akhtar, S and Nazir, N and Ahmed, N and Manzoor, F and Sones, J and Perez, K and Sarwar, G and Khan, AA and Akhter, M and Saeed, S and Sultana, R and Tahir, HM and Rafi, MA and Iftikhar, R and Naseem, MT and Masood, M and Tufail, M and Kumar, S and Afzal, S and McKeown, J and Samejo, AA and Khaliq, I and D'Souza, ML and Mansoor, S and Hebert, PDN},
title = {A DNA barcode survey of insect biodiversity in Pakistan.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13267},
pmid = {35497186},
issn = {2167-8359},
mesh = {Animals ; *Biodiversity ; DNA ; *DNA Barcoding, Taxonomic/methods ; *Insecta/genetics ; Pakistan ; },
abstract = {Although Pakistan has rich biodiversity, many groups are poorly known, particularly insects. To address this gap, we employed DNA barcoding to survey its insect diversity. Specimens obtained through diverse collecting methods at 1,858 sites across Pakistan from 2010-2019 were examined for sequence variation in the 658 bp barcode region of the cytochrome c oxidase 1 (COI) gene. Sequences from nearly 49,000 specimens were assigned to 6,590 Barcode Index Numbers (BINs), a proxy for species, and most (88%) also possessed a representative image on the Barcode of Life Data System (BOLD). By coupling morphological inspections with barcode matches on BOLD, every BIN was assigned to an order (19) and most (99.8%) were placed to a family (362). However, just 40% of the BINs were assigned to a genus (1,375) and 21% to a species (1,364). Five orders (Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera) accounted for 92% of the specimens and BINs. More than half of the BINs (59%) are so far only known from Pakistan, but others have also been reported from Bangladesh (13%), India (12%), and China (8%). Representing the first DNA barcode survey of the insect fauna in any South Asian country, this study provides the foundation for a complete inventory of the insect fauna in Pakistan while also contributing to the global DNA barcode reference library.},
}
@article {pmid35496467,
year = {2022},
author = {Han, J},
title = {Barcoding drug information to recycle unwanted household pharmaceuticals: a review.},
journal = {Environmental chemistry letters},
volume = {20},
number = {5},
pages = {2989-3003},
pmid = {35496467},
issn = {1610-3653},
abstract = {Huge quantities of unwanted pharmaceuticals are left in households, notably as a consequence of the rising drug demand caused by improved healthcare and the aging population. Unwanted pharmaceuticals may thus easily end up polluting ecosystems upon disposal. This pharmaceutical waste issue has been aggravated during the coronavirus disease pandemic (COVID-19) by excess prescription and panic buying. Unwanted household pharmaceuticals are normally collected by owners and volunteers, then incinerated in centralized facilities, yet with low efficiency during the COVID-19 lockdowns. Most pharmaceuticals could be recycled because they are rather stable, however there is actually no sustainable strategy to manage unwanted pharmaceuticals in a pandemic. Here I review the management of unwanted pharmaceuticals in households during the pandemic, with emphasis on drug take-back programs, waste minimization and recycling efforts. Reducing pharamaceutical waste could be done by informing people on what to do with unwanted pharmaceutical products; using machine-readable codes for automatic sorting; and applying existing techniques for recovery of active pharmaceutical ingredients for reuse. I propose a new strategy where owners sort their unwanted pharmaceuticals and submit information online. This will generate coded mailing labels that allow the owner to separate pharmaceuticals into categories such as opened, unused, expired, and non-expired. Once collected by recycling facilities and manufacturers, active ingredients will be extracted to create new pharmaceuticals which will be recycled to other patients.},
}
@article {pmid35495680,
year = {2022},
author = {Marsay, KS and Koucherov, Y and Davidov, K and Iankelevich-Kounio, E and Itzahri, S and Salmon-Divon, M and Oren, M},
title = {High-Resolution Screening for Marine Prokaryotes and Eukaryotes With Selective Preference for Polyethylene and Polyethylene Terephthalate Surfaces.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {845144},
pmid = {35495680},
issn = {1664-302X},
abstract = {Marine plastic debris serve as substrates for the colonization of a variety of prokaryote and eukaryote organisms. Of particular interest are the microorganisms that have adapted to thrive on plastic as they may contain genes, enzymes or pathways involved in the adhesion or metabolism of plastics. We implemented DNA metabarcoding with nanopore MinION sequencing to compare the 1-month-old biomes of hydrolyzable (polyethylene terephthalate) and non-hydrolyzable (polyethylene) plastics surfaces vs. those of glass and the surrounding water in a Mediterranean Sea marina. We sequenced longer 16S rRNA, 18S rRNA, and ITS barcode loci for a more comprehensive taxonomic profiling of the bacterial, protist, and fungal communities, respectively. Long read sequencing enabled high-resolution mapping to genera and species. Using previously established methods we performed differential abundance screening and identified 30 bacteria and five eukaryotic species, that were differentially abundant on plastic compared to glass. This approach will allow future studies to characterize the plastisphere communities and to screen for microorganisms with a plastic-metabolism potential.},
}
@article {pmid35495195,
year = {2022},
author = {Nitta, JH and Chambers, SM},
title = {Identifying cryptic fern gametophytes using DNA barcoding: A review.},
journal = {Applications in plant sciences},
volume = {10},
number = {2},
pages = {e11465},
pmid = {35495195},
issn = {2168-0450},
abstract = {Ferns and lycophytes are unique among land plants in having sporophyte (diploid) and gametophyte (haploid) generations that can grow independently of each other. While most studies of fern ecology focus on the more visible sporophytic stage, the gametophyte is critically important, as it is the sexual phase of the life cycle. Yet, fern gametophytes have long been neglected in field studies due to their small size and cryptic morphology. DNA barcoding is a powerful method that can be used to identify field-collected gametophytes to species and allow for detailed study of their ecology. Here, we review the state of DNA barcoding as applied to fern gametophytes. First, we trace the history of DNA barcoding and how it has come to be applied to fern gametophytes. Next, we summarize case studies that show how DNA barcoding has been used to better understand fern species distributions, gametophyte ecology, and community ecology. Finally, we propose avenues for future research using this powerful tool, including next-generation DNA sequencing for in-field identification of cryptic gametophytes.},
}
@article {pmid35493491,
year = {2022},
author = {Iyer, A and Hamers, AAJ and Pillai, AB},
title = {CyTOF[®] for the Masses.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {815828},
pmid = {35493491},
issn = {1664-3224},
support = {P30 CA240139/CA/NCI NIH HHS/United States ; },
mesh = {*Antibodies ; Flow Cytometry/methods ; Immunophenotyping ; *Single-Cell Analysis/methods ; Staining and Labeling ; },
abstract = {Mass cytometry has revolutionized immunophenotyping, particularly in exploratory settings where simultaneous breadth and depth of characterization of immune populations is needed with limited samples such as in preclinical and clinical tumor immunotherapy. Mass cytometry is also a powerful tool for single-cell immunological assays, especially for complex and simultaneous characterization of diverse intratumoral immune subsets or immunotherapeutic cell populations. Through the elimination of spectral overlap seen in optical flow cytometry by replacement of fluorescent labels with metal isotopes, mass cytometry allows, on average, robust analysis of 60 individual parameters simultaneously. This is, however, associated with significantly increased complexity in the design, execution, and interpretation of mass cytometry experiments. To address the key pitfalls associated with the fragmentation, complexity, and analysis of data in mass cytometry for immunologists who are novices to these techniques, we have developed a comprehensive resource guide. Included in this review are experiment and panel design, antibody conjugations, sample staining, sample acquisition, and data pre-processing and analysis. Where feasible multiple resources for the same process are compared, allowing researchers experienced in flow cytometry but with minimal mass cytometry expertise to develop a data-driven and streamlined project workflow. It is our hope that this manuscript will prove a useful resource for both beginning and advanced users of mass cytometry.},
}
@article {pmid35491231,
year = {2022},
author = {Irinyi, L and Roper, M and Malik, R and Meyer, W},
title = {Finding a Needle in a Haystack - In Silico Search for Environmental Traces of Candida auris.},
journal = {Japanese journal of infectious diseases},
volume = {75},
number = {5},
pages = {490-495},
doi = {10.7883/yoken.JJID.2022.068},
pmid = {35491231},
issn = {1884-2836},
mesh = {Antifungal Agents ; *Candida/genetics ; Candida auris ; *Candidiasis/drug therapy ; DNA, Fungal/genetics ; Humans ; },
abstract = {Candida auris, first described from an ear infection in Japan, is an important emerging multidrug-resistant pathogenic fungal species. Its environmental niche remained a mystery until its isolation from the wetlands of the Andaman Islands, India, in 2020. We screened a subset of the world's largest sequence repository, the Sequence Read Archive at National Center for Biotechnology Information, using a DNA metabarcoding approach based on either the internal transcribed spacer (ITS)1 or ITS2 region of the official primary fungal DNA barcode, to identify potential environmental sources of C. auris. Our search identified 34 matches with partial C. auris ITS sequences from seven metabarcoding studies, providing wider evidence for the presence of C. auris outside human-maintained facilities.},
}
@article {pmid35489252,
year = {2022},
author = {Gao, Z and Jousset, A and Kowalchuk, GA and Geisen, S},
title = {Five Groups in the Genus Allovahlkampfia and the Description of the New Species Vahlkampfia bulbosis n.sp.},
journal = {Protist},
volume = {173},
number = {3},
pages = {125870},
doi = {10.1016/j.protis.2022.125870},
pmid = {35489252},
issn = {1618-0941},
mesh = {*Amoeba ; DNA, Bacterial/genetics ; *Naegleria/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil ; },
abstract = {Heterolobosea is one of the major protist groups in soils. While an increasing number of soil heterolobosean species has been described, we have likely only scratched the surface of heterolobosean diversity in soils. Here, we expand this knowledge by morphologically and molecularly classifying four novel strains. One was identified as Naegleria clarki, while the remaining three strains had no identical Blast hit against GenBank and could only be reliably identified to the genus level: two strains as Allovahlkampfia spp. and one strain as Vahlkampfia sp. One Allovahlkampfia strain was most closely affiliated with Allovahlkampfia sp. Nl64 and the other strain was affiliated with 'Solumitrus' palustris, which is now named Allovahlkampfia palustris comb.nov. As there are only two valid species described within Allovahlkampfia, we combined all published sequences related to Allovahlkampfia and propose five new groups within this genus. The last strain was most closely related, but clearly distinct from, Vahlkampfia orchilla, based on DNA barcoding. As such, we propose this amoeba as a new species named Vahlkampfia bulbosis n.sp. Together, our study extends the described diversity of soil heteroloboseans through the description of a new Vahlkampfia species and by revising the morphologically and phylogenetically diverse genus Allovahlkampfia.},
}
@article {pmid35489139,
year = {2022},
author = {Wang, G and Liu, Y and Bai, X and Cao, P and Pang, X and Han, J},
title = {Identification and poisoning diagnosis of Aconitum materials using a genus-specific nucleotide signature.},
journal = {Ecotoxicology and environmental safety},
volume = {237},
number = {},
pages = {113539},
doi = {10.1016/j.ecoenv.2022.113539},
pmid = {35489139},
issn = {1090-2414},
mesh = {*Aconitum/genetics ; *Alkaloids ; *Genome, Chloroplast ; High-Throughput Nucleotide Sequencing ; Nucleotides ; },
abstract = {Aconitum genus generally contains hypertoxic alkaloids. Poisoning incidents due to the improper ingestion of Aconitum materials frequently occur around the world. DNA barcoding is considered as a powerful tool for species identification, but complete sequences of conventional DNA barcodes are sometimes unattainable from food and highly processed products due to severe DNA degradation. Therefore, a shorter molecular marker will be more profitable for the authentication and poisoning diagnosis of Aconitum materials. In this study, 1246 psbA-trnH sequences and chloroplast genomes representing 183 taxa of Aconitum were collected, and a 23-bp nucleotide signature unique to Aconitum genus (5'-TATATGAGTCATTGAAGTTGCAG-3') was developed. The nucleotide signature was conserved and universal within Aconitum while divergent among other genera. The specific molecular signature was then successfully applied to the detection of processed Aconitum ingredients. To further evaluate the application potential of nucleotide signature in completely unknown mixture samples, boiled food mixtures, containing different ratios of Aconitum materials, were sequenced by high-throughput sequencing technology. The results showed that the nucleotide signature sequence could be directly extracted from raw sequencing data, even at a low DNA concentration of 0.2 ng/µl. Consequently, the 23-bp genus-specific nucleotide signature represents a significant step forward in the use of DNA barcoding to identify processed samples and food mixtures with degraded DNA. This study undoubtedly provides a new perspective and strong support for the identification and detection of Aconitum-containing products, which can be further introduced to the diagnosis of food poisoning.},
}
@article {pmid35485747,
year = {2022},
author = {Prati, S and Grabner, DS and Pfeifer, SM and Lorenz, AW and Sures, B},
title = {Generalist parasites persist in degraded environments: a lesson learned from microsporidian diversity in amphipods.},
journal = {Parasitology},
volume = {149},
number = {7},
pages = {1-10},
pmid = {35485747},
issn = {1469-8161},
support = {//Deutsche Forschungsgemeinschaft/ ; //Deutsche Forschungsgemeinschaft/ ; },
abstract = {The present study provides new insight into suitable microsporidian–host associations. It relates regional and continental-wide host specialization in microsporidians infecting amphipods to degraded and recovering habitats across 2 German river catchments. It provides a unique opportunity to infer the persistence of parasites following anthropogenic disturbance and their establishment in restored rivers. Amphipods were collected in 31 sampling sites with differing degradation and restoration gradients. Specimens were morphologically (hosts) and molecularly identified (host and parasites). Amphipod diversity and abundance, microsporidian diversity, host phylogenetic specificity and continental-wide β-specificity were investigated and related to each other and/or environmental variables. Fourteen microsporidian molecular operational taxonomic units (MOTUs), mainly generalist parasites, infecting 6 amphipod MOTUs were detected, expanding the current knowledge on the host range by 17 interactions. There was no difference in microsporidian diversity and host specificity among restored and near-natural streams (Boye) or between those located in urban and rural areas (Kinzig). Similarly, microsporidian diversity was generally not influenced by water parameters. In the Boye catchment, host densities did not influence microsporidian MOTU richness across restored and near-natural sites. High host turnover across the geographical range suggests that neither environmental conditions nor host diversity plays a significant role in the establishment into restored areas. Host diversity and environmental parameters do not indicate the persistence and dispersal of phylogenetic host generalist microsporidians in environments that experienced anthropogenic disturbance. Instead, these might depend on more complex mechanisms such as the production of resistant spores, host switching and host dispersal acting individually or conjointly.},
}
@article {pmid35485289,
year = {2022},
author = {Pekmezci, GZ and Yildirim, A and Duzlu, O and Simsek, E and Balta, F and Yardimci, B and Onuk, EE and Onder, Z and Ciloglu, A and Yetismis, G and Yilmaz, E and Inci, A},
title = {Genetic diversity of Ichthyophthirius multifiliis (Fouquet, 1876) infecting farmed rainbow trout (Oncorhynchus mykiss Walbaum, 1792) in Turkey.},
journal = {Journal of fish diseases},
volume = {45},
number = {8},
pages = {1109-1115},
doi = {10.1111/jfd.13633},
pmid = {35485289},
issn = {1365-2761},
support = {TOA-2017-7742.//Erciyes University Scientific Research Projects Coordination Unit, Kayseri, Turkey. Grant number/ ; },
mesh = {Animals ; *Ciliophora Infections/epidemiology/veterinary ; *Fish Diseases/epidemiology ; Genetic Variation ; *Hymenostomatida/genetics ; *Oncorhynchus mykiss ; Phylogeny ; Turkey/epidemiology ; },
abstract = {We assessed genetic diversities among Ichthyophthirius multifiliis (Ich) field isolates collected from farmed rainbow trout (Oncorhynchus mykiss) in Turkey. The overall prevalence of Ich was 35.3% (634/1798). Five novel Ich genotypes (ImulTR1 and ImulTR3-ImulTR6) were described based on mitochondrial cox-1 and nad1_b genes. The remaining genotype ImulTR2 was identical to the previously reported NY3 (or Ark9 and TW7) genotype from the United States and South Asia. Phylogenetic analysis indicated Turkish Ich isolates separated genetically into at least four distinct groups. Our study presents the first data on the genotypes of Ich in Turkey. We also provide evidence for the wide distribution of the NY3 genotype (or Ark9 and TW7) from the United States and South Asia to Turkey. Genetic diversities within the mitochondrial genes provided adequate resolution for describing novel genotypes and identifying the known genotype within Turkish Ich isolates. Description of the Ich genotypes allows for tracking of pathogen genotypes worldwide. Thus, we can better understand the connections between Ich outbreaks in the fisheries aquaculture.},
}
@article {pmid35482734,
year = {2022},
author = {Bukowski, B and Ratnasingham, S and Hanisch, PE and Hebert, PDN and Perez, K and deWaard, J and Tubaro, PL and Lijtmaer, DA},
title = {DNA barcodes reveal striking arthropod diversity and unveil seasonal patterns of variation in the southern Atlantic Forest.},
journal = {PloS one},
volume = {17},
number = {4},
pages = {e0267390},
pmid = {35482734},
issn = {1932-6203},
mesh = {Animals ; DNA ; *DNA Barcoding, Taxonomic ; *Diptera/genetics ; Forests ; Insecta ; Seasons ; },
abstract = {The Atlantic Forest harbors 7% of global biodiversity and possesses high levels of endemism, but many of its component taxa remain unstudied. Due to the importance of tropical forests and the urgency to protect them, there is a compelling need to address this knowledge gap. To provide more information on its arthropod fauna, a Malaise trap was deployed for 12 months in a semi-degraded area of the southern Upper Paraná ecoregion of the Atlantic Forest. All specimens were DNA barcoded and the Barcode Index Number (BIN) system was employed to assign each specimen to a species proxy. DNA barcodes were obtained from 75,500 arthropods that included representatives of 8,651 BINs. Nearly 81% of these BINs were first records, highlighting the high rates of endemism and lack of study of arthropods from the Atlantic Forest. Diptera was the most abundant order, followed by Hemiptera, Lepidoptera and Hymenoptera. Diptera was also the most species-rich order, followed by Hymenoptera, Lepidoptera, and Coleoptera, a result consistent with studies in other biogeographic regions. Insects were most abundant in winter and most diverse in autumn and winter. This pattern, however, was caused mainly by the dynamics of dipteran diversity as other orders differed in their seasonal variation. The BIN composition of the insect community varied sharply through the year and also differed between the two consecutive summers included in the sampling period. The study of the 38 commonest BINs showed that seasonal patterns of abundance were not order-specific. Temperature had the strongest impact on seasonal abundance variation. Our results highlight the striking and understudied arthropod diversity of the highly fragmented Atlantic Forest, the predominance of dipterans, and the fact that abundance and richness in this insect community peak in the coolest months. Standardized studies like this generate fast and reliable biodiversity inventories and unveil ecological patterns, thus providing valuable information for conservation programs.},
}
@article {pmid35480566,
year = {2022},
author = {Hirano, T and Kagawa, O and Fujimoto, M and Saito, T and Uchida, S and Yamazaki, D and Ito, S and Mohammad Shariar, S and Sawahata, T and Chiba, S},
title = {Species identification of introduced veronicellid slugs in Japan.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13197},
pmid = {35480566},
issn = {2167-8359},
mesh = {Animals ; Humans ; Male ; Japan ; *Gastropoda/genetics ; Ecosystem ; Phylogeny ; DNA ; },
abstract = {Reliable identification of species is important for protecting native ecosystems against the invasion of non-native species. DNA barcoding using molecular markers, such as the mitochondrial cytochrome oxidase subunit 1 (COI) gene, helps researchers distinguish species. In this study, we focused on introduced veronicellid slugs in the Ryukyu Islands and some greenhouses on mainland Japan. Some veronicellids are medium-to-high risk pest species for humans. Identifying veronicellid species by their external morphology is difficult and unreliable because there is substantial overlap between intraspecific variation and interspecific differentiation. Therefore, internal morphologies such as male genitalia have been the primary traits used to distinguish veronicellids. To identify introduced veronicellid slugs in Japan to the species level, we used morphological assessment of male genitalia and DNA barcoding of the standard COI gene fragment. We also conducted species-delimitation analyses based on the genetic data. The results showed that five evolutionarily significant units, corresponding to four nominal species inhabit the Ryukyu Islands, of which two species were also found in the greenhouses of mainland Japan, including the first record of Sarasinula plebeia in Japan. The presence of non-native slug species could increase the transmission of parasites in Japan.},
}
@article {pmid35480563,
year = {2022},
author = {Di-Nizo, CB and Suárez-Villota, EY and Silva, MJJ},
title = {Species limits and recent diversification of Cerradomys (Sigmodontinae: Oryzomyini) during the Pleistocene.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13011},
pmid = {35480563},
issn = {2167-8359},
mesh = {Animals ; *Sigmodontinae ; Phylogeny ; *Biological Evolution ; Mitochondria ; South America ; },
abstract = {Cerradomys is a genus of the tribe Oryzomyini with eight species currently recognized, and a controversial taxonomy. These species are mainly distributed in the South America dry diagonal, but some species extend into Atlantic Forest, reaching the coastal sandy plains known as Restingas. This study aimed to address species limits and patterns of diversification of Cerradomys species. For this purpose, we performed cytogenetic and molecular analyses (phylogeny, coalescent species delimitation, barcoding, and divergence times estimation) using multiple mitochondrial and nuclear markers on a comprehensive sampling, representing all nominal taxa reported so far. Chromosomal information was a robust marker recognizing eight Cerradomys species. Reciprocal monophyly was recovered for all the species, except for C. subflavus. These results together with coalescent analyses recovered eight species as the most congruent species delimitation scenario for the genus (mean C tax : 0.72). Divergence time estimates revealed that Cerradomys' diversification occurred about 1.32 million years ago (Mya) during the Pleistocene. Although our results conservatively support the eight Cerradomys species described so far, different lines of evidence suggest that C. langguthi and C. subflavus could potentially be species-complexes. We discussed this scenario in the light of multiple evolutionary processes within and between species and populations, since Cerradomys comprises a species group with recent diversification affected by Pleistocene climatic changes and by the complex biogeographic history of South America dry diagonal. This work supports that the diversity of Cerradomys is underestimated and reiterates that interdisciplinary approaches are mandatory to identify small rodent species properly, and to unhide cryptic species.},
}
@article {pmid35475919,
year = {2022},
author = {Jeong, HW and Lee, S},
title = {Nurses' Perceptions of Using Personal Digital Assistants in Tertiary Hospitals.},
journal = {Computers, informatics, nursing : CIN},
volume = {40},
number = {10},
pages = {682-690},
pmid = {35475919},
issn = {1538-9774},
mesh = {Attitude of Health Personnel ; Computers, Handheld ; Humans ; *Nurses ; *Nursing Care ; Tertiary Care Centers ; },
abstract = {Personal digital assistants can perform multiple functions such as Internet search, documentation, calculating, and barcode scanning. This study examined nurses' perceptions of personal digital assistants used as a barcode scanner for medication administration, blood transfusions, and blood collection. A total of 236 nurses participated in the survey using the instrument developed by the researchers. The data collected were analyzed using descriptive statistics, one-way analysis of variance, and the Scheffe test. Written responses to the advantages and drawbacks of using personal digital assistants were categorized by meaning. The results showed that the nurses perceived more drawbacks than advantages in using personal digital assistants because of nonworking barcodes, prescription practice requiring additional scanning, poor interfacing between personal digital assistants and the EMR, and frequent Wi-Fi disconnection. The drawbacks resulted in delays in nursing workflow for patient care. Therefore, increasing the availability of barcode scanning for all medications applicable to personal digital assistant use, redesigning the practice of current prescriptions to eliminate additional scanning, and seamless interfacing between personal digital assistants and EMRs should be considered. This enables the nurses to use personal digital assistants more efficiently and effectively for patient care.},
}
@article {pmid35469200,
year = {2022},
author = {Hlebec, D and Sivec, I and Podnar, M and Kučinić, M},
title = {DNA barcoding for biodiversity assessment: Croatian stoneflies (Insecta: Plecoptera).},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13213},
pmid = {35469200},
issn = {2167-8359},
mesh = {Humans ; Male ; Animals ; Female ; *Insecta/genetics ; *DNA Barcoding, Taxonomic/methods ; Croatia ; Ecosystem ; DNA ; Biodiversity ; },
abstract = {BACKGROUND: The hemi-metabolous aquatic order Plecoptera (stoneflies) constitutes an indispensable part of terrestrial and aquatic food webs due to their specific life cycle and habitat requirements. Stoneflies are considered one of the most sensitive groups to environmental changes in freshwater ecosystems and anthropogenic changes have caused range contraction of many species. Given the critical threat to stoneflies, the study of their distribution, morphological variability and genetic diversity should be one of the priorities in conservation biology. However, some aspects about stoneflies, especially a fully resolved phylogeny and their patterns of distribution are not well known. A study that includes comprehensive field research and combines morphological and molecular identification of stoneflies has not been conducted in Croatia so far. Thus, the major aim of this study was to regenerate a comprehensive and taxonomically well-curated DNA barcode database for Croatian stoneflies, to highlight the morphological variability obtained for several species and to elucidate results in light of recent taxonomy.<br><br>METHODS: A morphological examination of adult specimens was made using basic characteristics for distinguishing species: terminalia in males and females, head and pronotum patterns, penial morphology, and egg structures. DNA barcoding was applied to many specimens to help circumscribe known species, identify cryptic or yet undescribed species, and to construct a preliminary phylogeny for Croatian stoneflies.<br><br>RESULTS: Sequences (658 bp in length) of 74 morphospecies from all families present in Croatia were recovered from 87% of the analysed specimens (355 of 410), with one partial sequence of 605 bp in length for Capnopsis schilleri balcanica Zwick, 1984. A total of 84% morphological species could be unambiguously identified using COI sequences. Species delineation methods confirmed the existence of five deeply divergent genetic lineages, with monophyletic origin, which also differ morphologically from their congeners and represent distinct entities. BIN (Barcode Index Number) assignment and species delineation methods clustered COI sequences into different numbers of operational taxonomic units (OTUs). ASAP delimited 76 putative species and achieved a maximum match score with morphology (97%). ABGD resulted in 62 and mPTP in 61 OTUs, indicating a more conservative approach. Most BINs were congruent with traditionally recognized species. Deep intraspecific genetic divergences in some clades highlighted the need for taxonomic revision in several species-complexes and species-groups. Research has yielded the first molecular characterization of nine species, with most having restricted distributions and confirmed the existence of several species which had been declared extinct regionally.},
}
@article {pmid35467372,
year = {2022},
author = {Moriarty, RV and Rodgers, MA and Ellis, AL and Balgeman, AJ and Larson, EC and Hopkins, F and Chase, MR and Maiello, P and Fortune, SM and Scanga, CA and O'Connor, SL},
title = {Spontaneous Control of SIV Replication Does Not Prevent T Cell Dysregulation and Bacterial Dissemination in Animals Co-Infected with M. tuberculosis.},
journal = {Microbiology spectrum},
volume = {10},
number = {3},
pages = {e0172421},
pmid = {35467372},
issn = {2165-0497},
support = {P51 OD011106/OD/NIH HHS/United States ; R01 AI111815/AI/NIAID NIH HHS/United States ; R01 AI114674/AI/NIAID NIH HHS/United States ; R21 AI127127/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; CD4-Positive T-Lymphocytes ; *Coinfection/microbiology ; Granuloma ; *HIV Infections/complications ; Macaca fascicularis ; *Mycobacterium tuberculosis ; *Simian Acquired Immunodeficiency Syndrome/complications ; *Simian Immunodeficiency Virus ; T-Lymphocytes ; *Tuberculosis ; },
abstract = {Individuals co-infected with HIV and Mycobacterium tuberculosis (Mtb) are more likely to develop severe tuberculosis (TB) disease than HIV-naive individuals. To understand how a chronic pre-existing Simian immunodeficiency virus (SIV) infection impairs the early immune response to Mtb, we used the Mauritian cynomolgus macaque (MCM) model of SIV/Mtb co-infection. We examined the relationship between peripheral viral control and Mtb burden, Mtb dissemination, and T cell function between SIV+ spontaneous controllers, SIV+ non-controllers, and SIV-naive MCM who were challenged with a barcoded Mtb Erdman strain 6 months post-SIV infection and necropsied 6 weeks post-Mtb infection. Mycobacterial burden was highest in the SIV+ non-controllers in all assessed tissues. In lung granulomas, the frequency of TNF-α-producing CD4[+] T cells was reduced in all SIV+ MCM, but IFNγ-producing CD4[+] T cells were only lower in the SIV+ non-controllers. Further, while all SIV+ MCM had more PD1+ and TIGIT+ T cells in the lung granulomas relative to SIV-naive MCM, SIV+ controllers exhibited the highest frequency of cells expressing these markers. To measure the effect of SIV infection on within-host bacterial dissemination, we sequenced the molecular barcodes of Mtb present in each tissue and characterized the Mtb population complexity. While Mtb population complexity was not associated with SIV infection group, lymph nodes had increased complexity when compared with lung granulomas across all groups. These results provide evidence that SIV+ animals, independent of viral control, exhibit a dysregulated T cell immune response and enhanced dissemination of Mtb, likely contributing to the poor TB disease course across all SIV/Mtb co-infected animals. IMPORTANCE HIV and TB remain significant global health issues, despite the availability of treatments. Individuals with HIV, including those who are virally suppressed, are at an increased risk to develop and succumb to severe TB disease when compared with HIV-naive individuals. Our study aims to understand the relationship between the extent of SIV replication, mycobacterial growth, and T cell function in the tissues of co-infected Mauritian cynomolgus macaques during the first 6 weeks of Mtb infection. Here we demonstrate that increased viral replication is associated with increased bacterial burden in the tissues and impaired T cell responses, and that the immunological damage attributed to virus infection is not fully eliminated when animals spontaneously control virus replication.},
}
@article {pmid35466594,
year = {2022},
author = {Chen, H and Bian, F and Guo, J and Zhao, Y},
title = {Aptamer-Functionalized Barcodes in Herringbone Microfluidics for Multiple Detection of Exosomes.},
journal = {Small methods},
volume = {6},
number = {6},
pages = {e2200236},
doi = {10.1002/smtd.202200236},
pmid = {35466594},
issn = {2366-9608},
support = {2020YFA0908200//National Key Research and Development Program of China/ ; 52073060//National Natural Science Foundation of China/ ; 61927805//National Natural Science Foundation of China/ ; JCYJ20190813152616459//Shenzhen Fundamental Research Program/ ; JCYJ20210324133214038//Shenzhen Fundamental Research Program/ ; },
mesh = {*Aptamers, Nucleotide/analysis ; *Exosomes/chemistry ; Humans ; Microfluidics ; *Neoplasms ; },
abstract = {Tumor-derived exosomes are vital for clinical dynamic and accurate tumor diagnosis, thus developing sensitive and multiple exosomes detection technology has attracted remarkable attention of scientists. Here, a novel herringbone microfluidic device with aptamer-functionalized barcodes integration for specific capture and multiple detection of tumor-derived exosomes is presented. The barcodes with core-shell constructions are obtained by partially replicating the periodically ordered hexagonal close-packaged colloidal crystal beads. As their inverse opal hydrogel shell possesses rich interconnected pores, the barcodes could provide abundant surface area for functionalization of DNA aptamers to realize specific recognition of target exosomes. Besides, the encoded structure colors of the barcodes can be maintained stably during the detection events as their hardish cores are with sufficient mechanical strength. It is demonstrated that by embedding these barcodes in herringbone groove microfluidic device with designed patterns, the specific capture efficiency and synergetic detection of multiple tumor-derived exosomes in peripheral blood can be significantly improved due to enhanced resistance of turbulent flow. These features make the aptamer-functionalized barcodes and herringbone microfluidics integrated platform promising for exosomes extraction and dynamic tumor diagnosis.},
}
@article {pmid35466537,
year = {2022},
author = {Domènech, M and Wangensteen, OS and Enguídanos, A and Malumbres-Olarte, J and Arnedo, MA},
title = {For all audiences: Incorporating immature stages into standardised spider inventories has a major impact on the assessment of biodiversity patterns.},
journal = {Molecular ecology resources},
volume = {22},
number = {6},
pages = {2319-2332},
doi = {10.1111/1755-0998.13625},
pmid = {35466537},
issn = {1755-0998},
support = {2017SGR73//Generalitat de Catalunya/ ; 485/2012//Organismo Aut&#xf3;nomo de Parques Nacionales/ ; //Universitat de Barcelona/ ; },
mesh = {Animals ; *Arthropods ; Biodiversity ; DNA Barcoding, Taxonomic/methods ; Forests ; *Spiders/genetics ; },
abstract = {Although arthropods are the largest component of animal diversity, they are traditionally underrepresented in biological inventories and monitoring programmes. However, no biodiversity assessment can be considered informative without including them. Arthropod immature stages are often discarded during sorting, despite frequently representing more than half of the collected individuals. To date, little effort has been devoted to characterising the impact of discarding nonadult specimens on our diversity estimates. Here, we used a metabarcoding approach to analyse spiders from oak forests in the Iberian Peninsula, to assess (1) the contribution of juvenile stages to local diversity estimates, and (2) their effect on the diversity patterns (compositional differences) across assemblages. We further investigated the ability of metabarcoding to inform on abundance. We obtained 363 and 331 species as adults and juveniles, respectively. Including the species represented only by juveniles increased the species richness of the whole sampling in 35% with respect to those identified from adults. Differences in composition between assemblages were greatly reduced when immature stages were considered, especially across latitudes, possibly due to phenological differences. Moreover, our results revealed that metabarcoding data are to a certain extent quantitative, but some sort of taxonomic conversion factor may be necessary to provide accurate informative estimates. Although our findings do not question the relevance of the information provided by adult-based inventories, they also reveal that juveniles provide a novel and relevant layer of knowledge that, especially in areas with marked seasonality, may influence our interpretations, providing more accurate information from standardised biological inventories.},
}
@article {pmid35463454,
year = {2022},
author = {Xiong, C and Sun, W and Wu, L and Xu, R and Zhang, Y and Zhu, W and J, HE and Panjwani, and Liu, Z and Zhao, B},
title = {Evaluation of Four Commonly Used DNA Barcoding Loci for Ardisia Species Identification.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {860778},
pmid = {35463454},
issn = {1664-462X},
abstract = {Ardisia plants have been used as medicinal plants for a long time in China. Traditional techniques such as morphological, microscopic, and chemical identification methods all have limitations in the species identification of Ardisia. For the sake of drug safety, four DNA barcodes (psbA-trnH, ITS, rbcL, and matK) were assessed for Chinese Ardisia plants using a total of 121 individuals from 33 species. Four criteria (The success rates of PCR amplification, DNA barcoding gap, DNA sequence similarity analysis and NJ tree clustering analysis) were used to evaluate the species identification ability of these four DNA barcodes. The results show that ITS had the highest efficiency in terms of PCR and sequencing and exhibited the most apparent inter- and intra-specific divergences and the highest species identification efficiency. There was no significant increase in species identification after combining the three cpDNA fragments with the ITS fragment. Considering the cost and experimental effectiveness, we recommend ITS as the core barcode for identifying Chinese Ardisia plants.},
}
@article {pmid35462756,
year = {2022},
author = {Yeh, WB and Tsai, CL and Pham, TH and Wu, S and Chang, CW and Bui, HM},
title = {Differentiation patterns of emperor moths (Lepidoptera: Saturniidae: Saturniinae) of a continental island: divergent evolutionary history driven by Pleistocene glaciations.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13240},
pmid = {35462756},
issn = {2167-8359},
mesh = {Animals ; Phylogeny ; *Moths/genetics ; DNA, Mitochondrial/genetics ; Biological Evolution ; Asia, Eastern ; *Manduca/genetics ; },
abstract = {BACKGROUND: On the basis of molecular dating, Pleistocene glaciations have been proposed as the major driving force of biota speciation in the Palearctic and the pre-Quaternary origin of Amazonian taxa. However, the major driving factors in East Asia remain unclear. All 16 saturniine species inhabiting Taiwan with congeners of populations, subspecies, or species in East Asia constitute research objects for addressing the mode of speciation because of the repeated formation and disappearance of a landbridge from the Asian mainland to Taiwan during glacial cycles.<br><br>METHODS: The genetic divergences of mitochondrial cytochrome c oxidase subunit I (COI) and 16S rDNA and the nuclear 28S rDNA of the saturniine species from Taiwan and the Asian mainland were assessed to determine the monophyly of each genus and species of Saturniinae. Moreover, 519 saturniine COI sequences of 114 taxa from adjacent East and Southeast Asian populations and closely related species were retrieved from GenBank and analyzed. The differentiation timing and possible origination of the insular saturniines were elucidated based on phylogenetic relationships, haplotype networks, and lineage calibrations.<br><br>RESULTS: Approximately 90% of intraspecific COI divergence was <2%; all divergences exceeding 2% originated from comparisons between allopatric populations or subspecies. Relationship analyses revealed that multiple introductions likely occurred in insular saturniines and that some East Asian saturniines were paraphyletic as deduced by analyzing endemic insular species. Calibration dating revealed that Taiwanese endemic saturniines split from sibling Asian species 0.2-2.7 million years ago (Mya), whereas subspecific-level and population-level splitting events occurred 0.1-1.7 Mya and 0.2-1.2 Mya, respectively. Moreover, phylogenetic patterns combined with geographical distributions revealed that hill-distributed Taiwanese saturniines are closely related to those from southern China and Southeast Asia, whereas saturniines inhabiting altitudes higher than 1,500 m in Taiwan have siblings distributed in temperate Northeast Asia.<br><br>DISCUSSION: The Global DNA Barcoding Initiative was successfully applied to study the population genetic structure in species. Most Formosan saturniines are distinct and monophyletic, reflecting the vicariant barrier of the Taiwan Strait; Pleistocene glacial cycles provided opportunities for insular saturniines to experience repeated isolation from and secondary contact with the continental mainland. Each insular saturniine may have evolved with a unique differentiation timing pattern that possibly emerged in the Early, Middle, or Late Pleistocene with these patterns differing from the consistent pattern that occurred in the temperate Palearctic and tropical Amazonian regions. Moreover, multiple migrations or artificial genetic admixtures may have also occurred, as suggested by the coexistence of two divergent lineages in a few Taiwanese saturniines.},
}
@article {pmid35462560,
year = {2022},
author = {Laidoudi, Y and Bedjaoui, S and Latrofa, MS and Fanelli, A and Dantas-Torres, F and Otranto, D},
title = {Genetic and geographical delineation of zoonotic vector-borne helminths of canids.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {6699},
pmid = {35462560},
issn = {2045-2322},
mesh = {Animals ; *Canidae ; *Dirofilaria immitis ; *Dirofilaria repens ; Disease Vectors ; Genetic Variation ; Onchocerca ; Phylogeny ; },
abstract = {Several zoonotic vector-borne helminths (VBHs) infesting canids cause serious veterinary and medical diseases worldwide. Increasing the knowledge about their genetic structures is pivotal to identify them and therefore to settle effective surveillance and control measures. To overcome the limitation due to the heterogeneity of large DNA sequence-datasets used for their genetic characterization, available cytochrome c oxidase subunit 1 (cox1) (n = 546) and the 12S rRNA (n = 280) sequences were examined using combined bioinformatic approach (i.e., distance-clustering, maximum likelihood phylogeny and phylogenetic evolutionary placement). Out of the 826 DNA available sequences from GenBank, 94.7% were characterized at the haplotype level regardless sequence size, completeness and/or their position. A total of 89 different haplotypes were delineated either by cox1 (n = 35), 12S rRNA (n = 21) or by both genes (n = 33), for 14 VBHs (e.g., Acanthocheilonema reconditum, Brugia spp., Dirofilaria immitis, Dirofilaria repens, Onchocerca lupi and Thelazia spp.). Overall, the present approach could be useful for studying global genetic diversity and phylogeography of VBHs. However, as barcoding sequences were restricted to two mitochondrial loci (cox1 and 12S rRNA), the haplotype delineation proposed herein should be confirmed by the characterization of other nuclear loci also to overcome potential limitations caused by the heteroplasmy phenomenon within the mitogenome of VBHs.},
}
@article {pmid35462529,
year = {2022},
author = {Hartke, J and Reuss, F and Kramer, IM and Magdeburg, A and Deblauwe, I and Tuladhar, R and Gautam, I and Dhimal, M and Müller, R},
title = {A barcoding pipeline for mosquito surveillance in Nepal, a biodiverse dengue-endemic country.},
journal = {Parasites &amp; vectors},
volume = {15},
number = {1},
pages = {145},
pmid = {35462529},
issn = {1756-3305},
support = {OPP1210801//Bill and Melinda Gates Foundation/ ; },
mesh = {Adult ; *Aedes ; Animals ; *Dengue/epidemiology/prevention &amp; control ; Entomology ; Humans ; Mosquito Vectors ; Nepal/epidemiology ; },
abstract = {BACKGROUND: Vector-borne diseases are on the rise on a global scale, which is anticipated to further accelerate because of anthropogenic climate change. Resource-limited regions are especially hard hit by this increment with the currently implemented surveillance programs being inadequate for the observed expansion of potential vector species. Cost-effective methods that can be easily implemented in resource-limited settings, e.g. under field conditions, are thus urgently needed to function as an early warning system for vector-borne disease epidemics. Our aim was to enhance entomological capacity in Nepal, a country with endemicity of numerous vector-borne diseases and with frequent outbreaks of dengue fever.<br><br>METHODS: We used a field barcoding pipeline based on DNA nanopore sequencing (Oxford Nanopore Technologies) and verified its use for different mosquito life stages and storage methods. We furthermore hosted an online workshop to facilitate knowledge transfer to Nepalese scientific experts from different disciplines.<br><br>RESULTS: The use of the barcoding pipeline could be verified for adult mosquitos and eggs, as well as for homogenized samples, dried specimens, samples that were stored in ethanol and frozen tissue. The transfer of knowledge was successful, as reflected by feedback from the participants and their wish to implement the method.<br><br>CONCLUSIONS: Cost effective strategies are urgently needed to assess the likelihood of disease outbreaks. We were able to show that field sequencing provides a solution that is cost-effective, undemanding in its implementation and easy to learn. The knowledge transfer to Nepalese scientific experts from different disciplines provides an opportunity for sustainable implementation of low-cost portable sequencing solutions in Nepal.},
}
@article {pmid35462292,
year = {2022},
author = {Marica, I and Aluaș, M and Cîntă Pînzaru, S},
title = {Raman technology application for plastic waste management aligned with FAIR principle to support the forthcoming plastic and environment initiatives.},
journal = {Waste management (New York, N.Y.)},
volume = {144},
number = {},
pages = {479-489},
doi = {10.1016/j.wasman.2022.04.021},
pmid = {35462292},
issn = {1879-2456},
mesh = {Environmental Pollution ; *Plastics ; Recycling ; Solid Waste ; Technology ; *Waste Management ; },
abstract = {Plastic production and worldwide use of plastic materials have continued to rise due to their convenience and excellent marketing advantages. This is generating an environmental crisis and global scale pollution which is one of the greatest threats to our planet. One of the best responses could be accomplished by improving recycling and waste management strategies. In this paper we conducted Raman analyses of representative stock of plastics aged in terrestrial or aquatic environments spanning in age up to 15 years. We aimed to establish any potential influence of the aging conditions on the Raman signature of specific plastics. This information is further used to build up a Raman logic gate for automatic sorting of plastic waste recovered from environment. Pigments and aging introduced indeed small changes in the Raman signature of the respective plastics. However, we were able to identify unique spectral ranges characteristic for the main plastic types and intensity threshold of fingerprint bands sufficiently strong for building robust Raman barcodes for sorting. Waste plastics Raman data handling and the proposed methodology for sorting complies with the FAIR (Findability, Accessibility, Interoperability and Reusability) principles of scientific data, being useful for researchers, policymakers and stakeholders. Our spectral characterization of solid plastic waste comes in support of improved waste plastic management and could have economic and environmental positive impact.},
}
@article {pmid35459089,
year = {2022},
author = {Baeza, JA and García-De León, FJ},
title = {Are we there yet? Benchmarking low-coverage nanopore long-read sequencing for the assembling of mitochondrial genomes using the vulnerable silky shark Carcharhinus falciformis.},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {320},
pmid = {35459089},
issn = {1471-2164},
support = {IN210711//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; 2005-12058//CONACYT/ ; },
mesh = {Animals ; *Genome, Mitochondrial/genetics ; Gold ; High-Throughput Nucleotide Sequencing/methods ; *Nanopore Sequencing ; *Nanopores ; Phylogeny ; Sequence Analysis, DNA/methods ; *Sharks/genetics ; },
abstract = {BACKGROUND: Whole mitochondrial genomes are quickly becoming markers of choice for the exploration of within-species genealogical and among-species phylogenetic relationships. Most often, 'primer walking' or 'long PCR' strategies plus Sanger sequencing or low-pass whole genome sequencing using Illumina short reads are used for the assembling of mitochondrial chromosomes. In this study, we first confirmed that mitochondrial genomes can be sequenced from long reads using nanopore sequencing data exclusively. Next, we examined the accuracy of the long-reads assembled mitochondrial chromosomes when comparing them to a 'gold' standard reference mitochondrial chromosome assembled using Illumina short-reads sequencing.<br><br>RESULTS: Using a specialized bioinformatics tool, we first produced a short-reads mitochondrial genome&#xa0;assembly for the silky shark C. falciformis with an average base coverage of 9.8x. The complete mitochondrial genome of C. falciformis was 16,705&#x2009;bp in length and 934&#x2009;bp shorter than a previously assembled genome (17,639&#x2009;bp in length) that used bioinformatics tools not specialized for the assembly of mitochondrial chromosomes. Next, low-pass whole genome sequencing using a MinION ONT pocket-sized platform plus customized de-novo and reference-based workflows assembled and circularized a highly accurate mitochondrial genome in the silky shark Carcharhinus falciformis. Indels at the flanks of homopolymer regions explained most of the dissimilarities observed between the 'gold' standard reference mitochondrial genome (assembled using Illumina short reads) and each of the long-reads mitochondrial genome assemblies. Although not completely accurate, mitophylogenomics and barcoding analyses (using entire mitogenomes and the D-Loop/Control Region, respectively) suggest that long-reads assembled mitochondrial genomes are reliable for identifying a sequenced individual, such as C. falciformis, and separating the same individual from others belonging to closely related congeneric species.<br><br>CONCLUSIONS: This study confirms that mitochondrial genomes can be sequenced from long-reads nanopore sequencing data exclusively. With further development, nanopore technology can be used to quickly test in situ mislabeling in the shark fin fishing industry and thus, improve surveillance protocols, law enforcement, and the regulation of this fishery. This study will also assist with the transferring of high-throughput sequencing technology to middle- and low-income countries so that international scientists can explore population genomics in sharks using inclusive research strategies. Lastly, we recommend assembling mitochondrial genomes using specialized assemblers instead of other assemblers developed for bacterial and/or nuclear genomes.},
}
@article {pmid35457959,
year = {2022},
author = {Dong, L and Hang, H and Park, JG and Mio, W and Liang, R},
title = {Detecting Carbon Nanotube Orientation with Topological Analysis of Scanning Electron Micrographs.},
journal = {Nanomaterials (Basel, Switzerland)},
volume = {12},
number = {8},
pages = {},
pmid = {35457959},
issn = {2079-4991},
support = {FA9550-17-1-0005//United States Air Force Office of Scientific Research/ ; DMS-1722995//National Science Foundation/ ; },
abstract = {As the aerospace industry is increasingly demanding stronger, lightweight materials, ultra-strong carbon nanotube (CNT) composites with highly aligned CNT network structures could be the answer. In this work, a novel methodology applying topological data analysis (TDA) to scanning electron microscope (SEM) images was developed to detect CNT orientation. The CNT bundle extensions in certain directions were summarized algebraically and expressed as visible barcodes. The barcodes were then calculated and converted into the total spread function, V(X, θ), from which the alignment fraction and the preferred direction could be determined. For validation purposes, the random CNT sheets were mechanically stretched at various strain ratios ranging from 0 to 40%, and quantitative TDA was conducted based on the SEM images taken at random positions. The results showed high consistency (R[2] = 0.972) compared to Herman's orientation factors derived from polarized Raman spectroscopy and wide-angle X-ray scattering analysis. Additionally, the TDA method presented great robustness with varying SEM acceleration voltages and magnifications, which might alter the scope of alignment detection. With potential applications in nanofiber systems, this study offers a rapid and simple way to quantify CNT alignment, which plays a crucial role in transferring the CNT properties into engineering products.},
}
@article {pmid35454695,
year = {2022},
author = {Dobrovolny, S and Uhlig, S and Frost, K and Schlierf, A and Nichani, K and Simon, K and Cichna-Markl, M and Hochegger, R},
title = {Interlaboratory Validation of a DNA Metabarcoding Assay for Mammalian and Poultry Species to Detect Food Adulteration.},
journal = {Foods (Basel, Switzerland)},
volume = {11},
number = {8},
pages = {},
pmid = {35454695},
issn = {2304-8158},
abstract = {Meat species authentication in food is most commonly based on the detection of genetic variations. Official food control laboratories frequently apply single and multiplex real-time polymerase chain reaction (PCR) assays and/or DNA arrays. However, in the near future, DNA metabarcoding, the generation of PCR products for DNA barcodes, followed by massively parallel sequencing by next generation sequencing (NGS) technologies, could be an attractive alternative. DNA metabarcoding is superior to well-established methodologies since it allows simultaneous identification of a wide variety of species not only in individual foodstuffs but even in complex mixtures. We have recently published a DNA metabarcoding assay for the identification and differentiation of 15 mammalian species and six poultry species. With the aim to harmonize analytical methods for food authentication across EU Member States, the DNA metabarcoding assay has been tested in an interlaboratory ring trial including 15 laboratories. Each laboratory analyzed 16 anonymously labelled samples (eight samples, two subsamples each), comprising six DNA extract mixtures, one DNA extract from a model sausage, and one DNA extract from maize (negative control). Evaluation of data on repeatability, reproducibility, robustness, and measurement uncertainty indicated that the DNA metabarcoding method is applicable for meat species authentication in routine analysis.},
}
@article {pmid35451659,
year = {2022},
author = {Srivastava, RP and Saxena, G and Singh, L and Singh, A and Verma, PC and Kaur, G},
title = {Interspecific and intraspecific analysis of Selinum spp. collected from Indian Himalayas using DNA barcoding.},
journal = {Journal, genetic engineering &amp; biotechnology},
volume = {20},
number = {1},
pages = {63},
pmid = {35451659},
issn = {2090-5920},
support = {2121430322//UGC-DAE&#xa0;Consortium for Scientific Research, University Grants Commission/ ; },
abstract = {BACKGROUND: DNA barcoding is a powerful method for phylogenetic mapping and species identification. However, recent research has come to a consistent conclusion about the universality of DNA barcoding. We used matK and rbcL markers to test the universality of twelve accessions from different locations belonging to two Selinum species, Selinum tenuifolium Wall. C. B. Clarke and Selinum vaginatum C. B. Clarke, keeping in mind their ability to identify species and establish phylogenetic relationships within and between the accessions.<br><br>RESULTS: The success rates of PCR amplification using matK and rbcL were 75.26% &#xb1; 3.65% and 57.24% &#xb1; 4.42%, and the rate of DNA sequencing was 63.84% &#xb1; 4.32% and 50.82% &#xb1; 4.36%, respectively, suggesting that success rates of species identification of the two fragments were higher than 41.00% (matK, 41.50% &#xb1; 2.81%; rbcL, 42.88% &#xb1; 2.59%), proving that these fragments might be used to identify species. The best evolutionary tree with good supporting values was produced utilizing combinations of matK + rbcL markers when phylogenetic relationships were built with random fragment combinations. The twelve accessions of Selinum collected from different locations and their molecular sequences of matK and rbcL markers were blasted with other genera of Apiaceae family, and it was found that Selinum is most closely related to Angelica species of Apiaceae family.<br><br>CONCLUSION: The present study has grouped twelve accessions of Selinum species using molecular markers into phylogenies, which is first-of-its-kind report that established interrelationships within different species of Apiaceae with respect to Selinum.},
}
@article {pmid35451535,
year = {2022},
author = {Perez-Lamarque, B and Öpik, M and Maliet, O and Afonso Silva, AC and Selosse, MA and Martos, F and Morlon, H},
title = {Analysing diversification dynamics using barcoding data: The case of an obligate mycorrhizal symbiont.},
journal = {Molecular ecology},
volume = {31},
number = {12},
pages = {3496-3512},
pmid = {35451535},
issn = {1365-294X},
mesh = {Biodiversity ; Biological Evolution ; *Glomeromycota/genetics ; *Mycorrhizae/genetics ; Symbiosis/genetics ; },
abstract = {Analysing diversification dynamics is key to understanding the past evolutionary history of clades that led to present-day biodiversity patterns. While such analyses are widespread in well-characterized groups of species, they are much more challenging in groups for which diversity is mostly known through molecular techniques. Here, we use the largest global database on the small subunit (SSU) rRNA gene of Glomeromycotina, a subphylum of microscopic arbuscular mycorrhizal fungi that provide mineral nutrients to most land plants by forming one of the oldest terrestrial symbioses, to analyse the diversification dynamics of this clade in the past 500 million years. We perform a range of sensitivity analyses and simulations to control for potential biases linked to the nature of the data. We find that Glomeromycotina tend to have low speciation rates compared to other eukaryotes. After a peak of speciations between 200 and 100 million years ago, they experienced an important decline in speciation rates toward the present. Such a decline could be at least partially related to a shrinking of their mycorrhizal niches and to their limited ability to colonize new niches. Our analyses identify patterns of diversification in a group of obligate symbionts of major ecological and evolutionary importance and illustrate that short molecular markers combined with intensive sensitivity analyses can be useful for studying diversification dynamics in microbial groups.},
}
@article {pmid35448806,
year = {2022},
author = {Sokołowska, J and Fuchs, H and Celiński, K},
title = {Assessment of ITS2 Region Relevance for Taxa Discrimination and Phylogenetic Inference among Pinaceae.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {8},
pages = {},
pmid = {35448806},
issn = {2223-7747},
support = {Research paper financed from the budget for science in 2018-2020, as a research project under the &quot;Diamond Grant&quot; program No. DI2017003147.//Research paper financed from the budget for science in 2018-2020, as a research project under the &quot;Diamond Grant&quot; program No. DI2017003147./ ; },
abstract = {The internal transcribed spacer 2 (ITS2) is one of the best-known universal DNA barcode regions. This short nuclear region is commonly used not only to discriminate taxa, but also to reconstruct phylogenetic relationships. However, the efficiency of using ITS2 in these applications depends on many factors, including the family under study. Pinaceae represents the largest family of extant gymnosperms, with many species of great ecological, economic, and medical importance. Moreover, many members of this family are representatives of rare, protected, or endangered species. A simple method for the identification of Pinaceae species based on DNA is necessary for their effective protection, authentication of products containing Pinaceae representatives, or phylogenetic inference. In this study, for the first time, we conducted a comprehensive study summarizing the legitimacy of using the ITS2 region for these purposes. A total of 368 sequences representing 71 closely and distantly related taxa of the seven genera and three subfamilies of Pinaceae were characterized for genetic variability and divergence. Intra- and interspecies distances of ITS2 sequences as well as rates of sequence identification and taxa discrimination among Pinaceae at various taxonomic levels, i.e., the species complex, genus, subfamily, and family, were also determined. Our study provides a critical assessment of the suitability of the ITS2 nuclear DNA region for taxa discrimination among Pinaceae. The obtained results clearly show that its usefulness for this purpose is limited.},
}
@article {pmid35448577,
year = {2022},
author = {Pánek, M and Maňasová, M and Wenzlová, J and Zouhar, M and Mazáková, J},
title = {Peronosporales Species Associated with Strawberry Crown Rot in the Czech Republic.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {4},
pages = {},
pmid = {35448577},
issn = {2309-608X},
support = {QK1710377//Ministry of Agriculture/ ; MZE-RO0418//Ministry of Agriculture/ ; },
abstract = {The symptoms of crown rot on strawberry plants are considered typical for the pathogen Phytophthora cactorum, which causes high losses of this crop. However, an unknown number of related species of pathogens of Peronosporales cause symptoms quite similar to those caused by P. cactorum. To determine their spectrum and importance, strawberry plants were sampled from 41 farms in the Czech Republic. The cultures were isolated from the symptomatic plants using the baiting method, with subsequent cultivation on a semiselective medium. Isolates were identified to the species level using nuclear ribosomal internal transcribed spacer (ITS) barcoding after preliminary morphological determination. In total, 175 isolates of 24 species of Phytophthora, Phytopythium, Pythium, and Globisporangium were detected. The most represented was Phytophthora cactorum, with 113 (65%) isolates, which was recorded in 61% of farms, and the Pythium dissotocum complex with 20 (11%) isolates, which was recorded in 27% of farms. Other species were represented in units of percent. Large differences between farms in the species spectra were ascertained. The differences between species in cardinal growth temperatures and different management of the farms are discussed as a main reason for such a diversification. Regarding the dissimilar sensitivity of various species of Peronosporales against fungicides, the proper determination of the cause of disease is of crucial significance in plant protection.},
}
@article {pmid35447788,
year = {2022},
author = {Kang, HJ and Baek, MJ and Kang, JH and Bae, YJ},
title = {Diversity and DNA Barcode Analysis of Chironomids (Diptera: Chironomidae) from Large Rivers in South Korea.},
journal = {Insects},
volume = {13},
number = {4},
pages = {},
pmid = {35447788},
issn = {2075-4450},
abstract = {Most large rivers in South Korea run through major cities, which often experience many environmental problems, including outbreaks of non-biting midges (Diptera: Chironomidae). However, chironomid species inhabiting large rivers have not been thoroughly investigated. We aimed to identify chironomid species collected from the four main large rivers in South Korea, construct a corresponding DNA barcode library, and examine the distribution and community structure of the identified riverine species. Adult chironomids were collected from nine sites along the rivers by using sweep nets and light traps during June and August 2015. Adults were morphologically identified, and COI nucleotide sequences were generated to verify the species identification and construct a DNA barcode library. The distribution and community structure of the identified species were also analyzed. A total of 124 COI sequences were established from 37 species belonging to 19 genera, and the resulting DNA barcode library effectively discriminated >90% of riverine Chironomidae in South Korea. Ten species, which are considered indicator species for large rivers, were collected from all four rivers. In addition, members of the subfamily Chironominae were collected more frequently than members of other subfamilies, with Tanytarsus tamagotoi being the most common and widespread chironomid species in South Korea. The DNA barcode library developed in this study will facilitate environmental studies of large rivers, such as biomonitoring chironomid larvae.},
}
@article {pmid35443606,
year = {2022},
author = {Eldemerdash, MM and El-Sayed, ASA and Hussein, HA and Teleb, SS and Shehata, RS},
title = {Molecular and metabolic traits of some Egyptian species of Cassia L. and Senna Mill (Fabaceae-Caesalpinioideae).},
journal = {BMC plant biology},
volume = {22},
number = {1},
pages = {205},
pmid = {35443606},
issn = {1471-2229},
mesh = {*Cassia/genetics ; Egypt ; Esters ; *Fabaceae ; Phylogeny ; Random Amplified Polymorphic DNA Technique ; *Senna Plant/genetics ; },
abstract = {The genus Cassia and Senna have been classified under subfamily Caesalpinioideae of family Fabaceae (Leguminosae) of order Fabales. There is a scarce taxonomical studies of the genus Cassia and Senna inhabiting Egyptian environments, thus, the main objective of the current was to revise and authenticate the phylogenetic relationship between studied taxa of the species of the genera Cassia and Senna in Egypt using the recent tools of ITS barcoding, RAPD analysis and metabolic profiling, in comparing to the traditional taxonomical features. From the cluster analysis of the traditional 27 morphological characters, the studied taxa were categorized into two major clades with an average taxonomic distance of 4.3. The clade I include Cassia fistula, C. renigera, C. javanica L subsp. nodosa and C. roughiia that belongs to series Obolospermae, and C. grandis that belongs to series Grandes. The clade (II) includes Senna surattensis and S. alata at taxonomic level 3.6. The taxonomical description of the studied taxa was confirmed from the molecular analysis of ITS sequences and RAPD analysis. The ITS sequences of the tested plants species C. fistula L, C. grandis MD4, C. javanica subsp. nodosa MD7, C. roxburghii MD5, C. renigera MD5 were deposited at genbank with accession numbers MW367973, MZ960447, MW386305, MW326753 and MW32685, respectively. While, the ITS sequences of the S. surrattensis and S. alata were deposited into genbank accession # MD14 MW367670 and MD20 MW412635, respectively. Thus, from the molecular analysis, two clades were clearly separated into Clade I of Cassia and Clade II of Senna. The cluster I represented by C. fistula, C. renigera, C. roxburghii, and C. javanica sub nodosa, and the cluster II represented by S. alata and S. surattensis. From the PCA of RAPD, a clearly discrimination between the two Taxa was observed revealing the characteristic grouping of Cassia and Senna. The species Senna alata and Senna surattensis were grouped together, but the species of C. renigera, C. javanica, C. roxburghii and C. grandis was grouped on a distinct group. The separation of Cassia and Senna species into two clusters verify the segregation of the genus Cassia L. senso lato into two distinct genera namely Senna P. and Cassia L. The morphological, molecular traits of the studied plants were authenticated from the metabolic profiling by GC-MS analysis. Among the 23 identified metabolites, four compounds namely hexadecanoic acid, methyl ester, 9-Octadecenoic acid (Z)-ethyl ester and Vitamin E were detected with fluctuated concentrations, among C. fistula, C. grandis, C. javanica subsp. nodosa and C. roxburghii. Conclusively, the traditional morphological features, molecular barcoding using ITS sequences, RAPD analysis and metabolic traits by GC-MS analysis, authenticates the taxonomical diversity of the genus Cassia and Senna.},
}
@article {pmid35441356,
year = {2022},
author = {Chen, C and Liao, Y and Peng, G},
title = {Connecting past and present: single-cell lineage tracing.},
journal = {Protein &amp; cell},
volume = {13},
number = {11},
pages = {790-807},
pmid = {35441356},
issn = {1674-8018},
mesh = {Animals ; Cell Lineage/genetics ; *Clustered Regularly Interspaced Short Palindromic Repeats ; },
abstract = {Central to the core principle of cell theory, depicting cells' history, state and fate is a fundamental goal in modern biology. By leveraging clonal analysis and single-cell RNA-seq technologies, single-cell lineage tracing provides new opportunities to interrogate both cell states and lineage histories. During the past few years, many strategies to achieve lineage tracing at single-cell resolution have been developed, and three of them (integration barcodes, polylox barcodes, and CRISPR barcodes) are noteworthy as they are amenable in experimentally tractable systems. Although the above strategies have been demonstrated in animal development and stem cell research, much care and effort are still required to implement these methods. Here we review the development of single-cell lineage tracing, major characteristics of the cell barcoding strategies, applications, as well as technical considerations and limitations, providing a guide to choose or improve the single-cell barcoding lineage tracing.},
}
@article {pmid35438192,
year = {2022},
author = {Liu, B and Yang, JW and Liu, BS and Zhang, N and Guo, L and Guo, HY and Zhang, DC},
title = {Detection and identification of marine fish mislabeling in Guangzhou's supermarkets and sushi restaurants using DNA barcoding.},
journal = {Journal of food science},
volume = {87},
number = {6},
pages = {2440-2449},
doi = {10.1111/1750-3841.16150},
pmid = {35438192},
issn = {1750-3841},
mesh = {Animals ; DNA ; *DNA Barcoding, Taxonomic/methods ; Fish Products/analysis ; Fishes/genetics ; *Restaurants ; Supermarkets ; },
abstract = {In this study, DNA barcoding was applied to identify the distinct species of fish products in Guangzhou supermarkets and sushi restaurants in order to confirm whether products were correctly labeled. Samples were analyzed using mitochondrial cytochrome C oxidase subunit I (CO I) gene as the target. Our results showed that the CO I gene of all 139 samples examined was successfully amplified by PCR. When sequenced, 30 samples (21.58%) were mislabeled as the wrong species, 11 samples had insufficient information provided on the label to determine if the labeling was correct (7.91%), and four samples failed sequencing (2.88%). We also found that the use of proper labels for fish products in sushi restaurants was higher than that in supermarkets. As a simple, rapid, and efficient technology, DNA barcoding can be widely used for species identification of fish products. Our work shows that regulation of the labeling of fish products, as we evaluated in Guangzhou and other markets in China, is needed on a global scale.},
}
@article {pmid35437472,
year = {2022},
author = {Popoola, MO and Schedel, FDB and Hebert, PD and Schliewen, UK},
title = {First DNA barcode library for the ichthyofauna of the Jos Plateau (Nigeria) with comments on potential undescribed fish species.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13049},
pmid = {35437472},
issn = {2167-8359},
mesh = {Animals ; Nigeria/epidemiology ; DNA Barcoding, Taxonomic ; *Cichlids ; *Cyprinidae/genetics ; Lakes ; *Catfishes ; Water ; },
abstract = {Located in the central region of northern Nigeria, the Jos Plateau covers approximately 9,400 km[2] with an average altitude of 1,280 m and constitutes a unique terrestrial ecoregion known as the Jos Plateau forest-grassland mosaic. The biota of the Jos Plateau include endemic elements, but very limited information is available on its ichthyofauna. This is despite the fact that the ancient plateau contributes to several large rivers spanning multiple major drainage systems including the Niger and Benue Rivers, and Lake Chad. This study provides the first species list for the fishes of the Jos Plateau based mainly on 175 DNA barcoded museum voucher specimens representing 20 species, and another three species without a DNA barcode. In total, 23 species from eight families and 17 genera were collected from the Jos Plateau including five putatively new species, four in the family Cyprinidae and one in the Clariidae. With ten species, the Cyprinidae is the most diverse fish family on the Jos Plateau, followed by Clariidae and Cichlidae, each with three species. The study also provides data on species distribution and habitat parameters including information on water chemistry that strongly suggests that selected water bodies are heavily impacted by anthropogenic activities. Urgent management steps are required to preserve the unique and diverse fish communities of the Jos Plateau and their habitats.},
}
@article {pmid35437403,
year = {2022},
author = {Kuralt, &#x17d; and Ratajc, U and Pajek Arambašić, N and Ferle, M and Gabor, M and Kos, I},
title = {Inventory and DNA-barcode library of ground-dwelling predatory arthropods from Krokar virgin forest, Slovenia.},
journal = {Biodiversity data journal},
volume = {10},
number = {},
pages = {e77661},
pmid = {35437403},
issn = {1314-2828},
abstract = {BACKGROUND: At a time of immense human pressure on nature and the resulting global environmental changes, the inventory of biota - especially of undisturbed natural areas - is of unprecedented value as it provides a baseline for future research. Krokar, an example of such an undisturbed area, is the largest virgin forest remnant in Slovenia. It is located in the Dinaric Alps, which are believed to harbour the most diverse fauna of soil invertebrates in Europe. Nevertheless, the soil fauna of the Krokar virgin forest has not been thoroughly studied. Moreover, modern taxonomic approaches often rely on genetic information (e.g. DNA-barcodes), while extensive reference libraries from the Dinaric area are lacking. Our work, therefore, focused on addressing this lack of faunistic and genetic data from the Dinaric area.<br><br>NEW INFORMATION: A total of 2336 specimens belonging to 100 taxa (45 spiders, 30 centipedes, 25 ground-dwelling beetles) were collected and deposited to GBIF. DNA-barcodes of 124 specimens belonging to 73 species were successfully obtained and deposited in GenBank and BOLD databases.},
}
@article {pmid35437365,
year = {2022},
author = {Nupponen, K and Sihvonen, P},
title = {Revision of Neotropical Scythrididae moths and descriptions of 22 new species from Argentina, Chile, and Peru (Lepidoptera, Gelechioidea).},
journal = {ZooKeys},
volume = {1087},
number = {},
pages = {19-104},
pmid = {35437365},
issn = {1313-2989},
abstract = {The taxonomy of South American Scythrididae (Lepidoptera: Gelechioidea) is revised, based on external morphology, genitalia, male abdominal segment VIII, and DNA barcodes using genetic distances, BINs, and a tentative molecular phylogeny. Data include both historical and fresh specimens from Argentina, Brazil, Colombia, Chile, Ecuador, Paraguay, and Peru. Thirty-four species are recognised as valid, and the fauna classified in three genera. Type specimens and morphology of all species are described and figured in detail. DNA barcode sequences of the COI gene were successful for 22 species, the average genetic divergence between species being 5.1%. A key to Neotropical Scythrididae species is provided, based on the male genitalia and abdominal segment VIII, which show most and easily accessible interspecific differences. Our study revealed that the Scythridae fauna of South America is more or less completely unknown. As a result, 22 new species are described, increasing the number of South American Scythrididae species from 13 to 34. All new species are authored by Kari Nupponen (incertae sedis means the genus combination is uncertain and needs further research, country of the type locality is given in parentheses): Rhamphurasubdimota sp. nov. (Argentina), R.pozohondaensis sp. nov. (Argentina), R.spiniuncus sp. nov. (Argentina), R.angulisociella sp. nov. incertae sedis (Argentina), R.curvisociella sp. nov. incertae sedis (Argentina), R.tetrafasciella sp. nov. incertae sedis (Argentina), Landryiaankylosauroides sp. nov. incertae sedis (Argentina), L.chilensis sp. nov. incertae sedis (Chile), Scythrisdirectiphallella sp. nov. (Argentina), S.furciphallella sp. nov. (Argentina), S.manchaoensis sp. nov. (Argentina), S.salinasgrandensis sp. nov. (Argentina), S.angustivalvella sp. nov. (Argentina), S.caimancitoensis sp. nov. (Argentina), S.lequetepequensis sp. nov. (Peru), S.sanfriscoensis sp. nov. (Argentina), S.tigrensis sp. nov. (Argentina), S.bicoloristrigella sp. nov. incertae sedis (Argentina), S.saldaitisi sp. nov. incertae sedis (Argentina), S.wikstromi sp. nov. incertae sedis (Argentina), S.andensis sp. nov. incertae sedis (Argentina), S.mendozaensis sp. nov. incertae sedis (Argentina). The following new combinations are proposed: Scythrisdepressa Meyrick, 1931 and Scythrisdimota Meyrick, 1931 are transferred from Scythris Hübner, 1825 to Rhamphura Landry, 1991 comb. nov. Three species classified in Scythris earlier are now classified as Scythris (incertae sedis): Scythrisdividua Meyrick, 1916, S.medullata Meyrick, 1916 and S.notorrhoa Meyrick, 1921. The taxon Syntetrernisneocompsa Meyrick, 1933, recently classified in Scythrididae: Scythris, is excluded from Scythrididae and it is now classified in Cosmopterigidae incertae sedis.},
}
@article {pmid35437364,
year = {2022},
author = {Krčmar, S and Kučinić, M and Pezzi, M and Mađarić, BB},
title = {DNA barcoding of the horsefly fauna (Diptera, Tabanidae) of Croatia with notes on the morphology and taxonomy of selected species from Chrysopsinae and Tabaninae.},
journal = {ZooKeys},
volume = {1087},
number = {},
pages = {141-161},
pmid = {35437364},
issn = {1313-2989},
abstract = {In the Croatian fauna, horseflies (Tabanidae) are represented by 78 species belonging to two subfamilies, five tribes, and 10 genera. Identification of these species is based on morphological characteristics. In this study, 43 species of horseflies were analyzed. The highest number of species (19) belongs to the genus Tabanus, followed by the genera Hybomitra with seven species, Haematopota with six species, Chrysops with four species, Atylotus and Philipomyia with two species each, and the genera Silvius, Dasyrhamphis, and Heptatoma with one species each. The standard DNA barcoding region of the mitochondrial cytochrome c oxidase gene, subunit I (COI), was sequenced and compared to the Barcode of Life Database (BOLD). Our analyses confirmed our morphological identifications and added 16 new Barcode Index Numbers (BINs) for Tabanidae to BOLD. Potential problems in the systematics and taxonomy of this family are highlighted.},
}
@article {pmid35437363,
year = {2022},
author = {Khalaji-Pirbalouty, V and Oraie, H and Santamaria, CA and Wägele, JW},
title = {Redescription of Tylosmaindroni Giordani Soika, 1954 (Crustacea, Isopoda, Oniscidea) based on SEM and molecular data.},
journal = {ZooKeys},
volume = {1087},
number = {},
pages = {123-139},
pmid = {35437363},
issn = {1313-2989},
abstract = {The woodlouse species Tylosmaindroni Giordani Soika, 1954 (Crustacea, Isopoda, Oniscidea) is redescribed from the Persian Gulf based on light and scanning electron microscopy. This species differs from the closely related T.exiguus Stebbing, 1910, from the Red Sea (coasts of Sudan and Eritrea), and Socotra Island, by pereopod 1 superior margin without a prominent projection and pleopod 2 endopod 2.3 times as long as exopod, vs. 3.6 in T.exiguus. A distribution map for T.maindroni is provided. In addition, we studied the molecular differentiation of five populations of T.maindroni from the Persian Gulf, based on partial cytochrome c oxidase subunit I (COI) gene sequences. The results revealed low levels of population structuring between the analyzed populations.},
}
@article {pmid35434364,
year = {2022},
author = {Yen, LT and Park, J},
title = {The complete nucleotide sequence of Viburnum odoratissimum chloroplast genome.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {7},
number = {4},
pages = {635-636},
pmid = {35434364},
issn = {2380-2359},
abstract = {The complete chloroplast genome (cpDNA) Viburnum odoratissimumis sequenced and assembled from the whole genome data. The cpDNA of V. odoratissimum is 158,744bp in lengthwith the overall GC content of 38.1%. It consists of a pair of inverted repeats (IRa and IRb, 26,494bp) which separate a large single copy (LCS, 87,348 bp) and small single copy (SSC,18,408 bp). The complete chloroplast genome contains 129 genes, including 84 protein-coding genes, 8 rRNA genes and 37 tRNA genes. A phylogenetic tree of DNA sequences of barcoding regions, including rbcL, matK, psbA-trnHfrom 8 species of the Genus Viburnum shows that V. odoratissimum is closely related to V. furcatum and V. burejaeticum.},
}
@article {pmid35433122,
year = {2022},
author = {Zhang, G and Wang, H and Shi, L and Liu, Y and Yao, R and Sui, C and Yang, C and Ji, H and Wang, Q and Wei, J},
title = {Identification of the original plants of cultivated Bupleuri Radix based on DNA barcoding and chloroplast genome analysis.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13208},
pmid = {35433122},
issn = {2167-8359},
mesh = {Humans ; DNA Barcoding, Taxonomic ; *Genome, Chloroplast ; Plant Roots/genetics ; *Plants, Medicinal/genetics ; Medicine, Chinese Traditional ; *Bupleurum/genetics ; },
abstract = {Bupleuri Radix is the dry root of certain species of the genus Bupleurum and is commonly used in traditional Chinese medicine. The increasing global demand for Bupleuri Radix cannot be fulfilled with wild populations only. Therefore, cultivated Bupleurum is now the main commercial source of this medicinal product. Different species of Bupleurum show different medicinal properties and clinical effects, making reliable authentication and assignment of correct botanical origin for medicinal species critical. However, accurate identification of the cultivated Bupleurum species is difficult due to dramatic morphological variations resulting from cultivation. In this study, we sampled 56 cultivated Bupleurum populations of six different morphotypes (Types A-F) from the main production areas of China, and 10 wild populations of four species were used as reference materials. Conventional DNA barcoding was conducted to identify cultivated Bupleurum species. Additionally, verification based on complete chloroplast genomes was performed and new chloroplast markers were developed and evaluated. The combination of these methods resulted in the successful identification of all cultivated Bupleurum individuals. Three chloroplast regions are recommended as additional barcodes for the genus: ycf4_cemA, psaJ_rpl33, and ndhE_ndhG. This is a reliable and promising strategy that can be applied to the authentication of natural products and the identification of other medicinal plant species with similar taxonomic problems.},
}
@article {pmid35432922,
year = {2022},
author = {Foster, NR and van Dijk, KJ and Biffin, E and Young, JM and Thomson, VA and Gillanders, BM and Jones, AR and Waycott, M},
title = {A targeted capture approach to generating reference sequence databases for chloroplast gene regions.},
journal = {Ecology and evolution},
volume = {12},
number = {4},
pages = {e8816},
pmid = {35432922},
issn = {2045-7758},
abstract = {Metabarcoding has improved the way we understand plants within our environment, from their ecology and conservation to invasive species management. The notion of identifying plant taxa within environmental samples relies on the ability to match unknown sequences to known reference libraries. Without comprehensive reference databases, species can go undetected or be incorrectly assigned, leading to false-positive and false-negative detections. To improve our ability to generate reference sequence databases, we developed a targeted capture approach using the OZBaits_CP V1.0 set, designed to capture chloroplast gene regions across the entirety of flowering plant diversity. We focused on generating a reference database for coastal temperate plant species given the lack of reference sequences for these taxa. Our approach was successful across all specimens with a target gene recovery rate of 92%, which was achieved in a single assay (i.e., samples were pooled), thus making this approach much faster and more efficient than standard barcoding. Further testing of this database highlighted 80% of all samples could be discriminated to family level across all gene regions with some genes achieving greater resolution than others-which was also dependent on the taxon of interest. Thus, we demonstrate the importance of generating reference sequences across multiple chloroplast gene regions as no single loci are sufficient to discriminate across all plant groups. The targeted capture approach outlined in this study provides a way forward to achieve this.},
}
@article {pmid35432422,
year = {2022},
author = {Yang, X and Yu, X and Zhang, X and Guo, H and Xing, Z and Xu, L and Wang, J and Shen, Y and Yu, J and Lv, P and Wang, Y and Liu, M and Tian, X},
title = {Development of Mini-Barcode Based on Chloroplast Genome and Its Application in Metabarcoding Molecular Identification of Chinese Medicinal Material Radix Paeoniae Rubra (Chishao).},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {819822},
pmid = {35432422},
issn = {1664-462X},
abstract = {Radix Paeoniae Rubra (Chishao), a typical multi-origin Chinese medicinal material, originates from the dried roots of Paeonia lactiflora or P. veitchii. The previous study suggested that these two commonly used Chishao showed variation in their chemical compositions and clinical efficacies. Therefore, accurate identification of different Chishao species was of great significance for the guide of clinical medication, and timely treatment of patients. In this study, the chloroplast genome sequences of P. lactiflora and P. veitchii were obtained by next-generation sequencing (NGS) technology, and then the hypervariable regions were selected to design two mini-barcode candidates for species identification. Combined with DNA metabarcoding technology, we performed qualitative and quantitative analysis on the artificially mixed samples of P. lactiflora and P. veitchii and evaluated the identification ability of these mini-barcode candidates. Furtherly, the mini-barcode with good performance was applied to distinguish the Chinese patent medicine "cerebral thrombosis tablets" containing Chishao. The results indicated that the chloroplast genomes of P. lactiflora and P. veitchii were 152,750 and 152,527 bp, respectively. As published previously, they exhibited a typical quadripartite structure including a large single-copy region (LSC), a small single-copy region (SSC) and a pair of inverted repeat regions (IRs). The nucleotide polymorphism analysis revealed seven variable protein-coding regions as petL, psaI, psbJ, rpl16, ycf1b, psaC, and ndhF, and two mini-barcodes were developed from ycf1b and ndhF respectively. The result suggested that both two mini-barcodes performed well distinguishing P. lactiflora from P. veitchii. Besides, P. lactiflora was the only raw material of Chishao in all collected "cerebral thrombosis tablets" samples. In general, this study has established a method to realize the qualitative and quantitative identification of Chishao as multi-origin Chinese medicinal materials, which can be applied to Chinese patent medicines containing Chishao.},
}
@article {pmid35430871,
year = {2022},
author = {Carey, AF and Wang, X and Cicchetti, N and Spaulding, CN and Liu, Q and Hopkins, F and Brown, J and Sixsmith, J and Sutiwisesak, R and Behar, SM and Ioerger, TR and Fortune, SM},
title = {Multiplexed Strain Phenotyping Defines Consequences of Genetic Diversity in Mycobacterium tuberculosis for Infection and Vaccination Outcomes.},
journal = {mSystems},
volume = {7},
number = {3},
pages = {e0011022},
pmid = {35430871},
issn = {2379-5077},
support = {T32 AI007061/AI/NIAID NIH HHS/United States ; T32 CA009216/CA/NCI NIH HHS/United States ; R01 AI106725/AI/NIAID NIH HHS/United States ; P01 AI132130/AI/NIAID NIH HHS/United States ; K08 AI139339/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Mice ; Humans ; *Mycobacterium tuberculosis/genetics ; *Tuberculosis/epidemiology ; BCG Vaccine ; Vaccination ; Genetic Variation/genetics ; },
abstract = {There is growing evidence that genetic diversity in Mycobacterium tuberculosis, the causative agent of tuberculosis, contributes to the outcomes of infection and public health interventions, such as vaccination. Epidemiological studies suggest that among the phylogeographic lineages of M. tuberculosis, strains belonging to a sublineage of Lineage 2 (mL2) are associated with concerning clinical features, including hypervirulence, treatment failure, and vaccine escape. The global expansion and increasing prevalence of this sublineage has been attributed to the selective advantage conferred by these characteristics, yet confounding host and environmental factors make it difficult to identify the bacterial determinants driving these associations in human studies. Here, we developed a molecular barcoding strategy to facilitate high-throughput, experimental phenotyping of M. tuberculosis clinical isolates. This approach allowed us to characterize growth dynamics for a panel of genetically diverse M. tuberculosis strains during infection and after vaccination in the mouse model. We found that mL2 strains exhibit distinct growth dynamics in vivo and are resistant to the immune protection conferred by Bacillus Calmette-Guerin (BCG) vaccination. The latter finding corroborates epidemiological observations and demonstrates that mycobacterial features contribute to vaccine efficacy. To investigate the genetic and biological basis of mL2 strains' distinctive phenotypes, we performed variant analysis, transcriptional studies, and genome-wide transposon sequencing. We identified functional genetic changes across multiple stress and host response pathways in a representative mL2 strain that are associated with variants in regulatory genes. These adaptive changes may underlie the distinct clinical characteristics and epidemiological success of this lineage. IMPORTANCE Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, is a remarkably heterogeneous disease, a feature that complicates clinical care and public health interventions. The contributions of pathogen genetic diversity to this heterogeneity are uncertain, in part due to the challenges of experimentally manipulating M. tuberculosis, a slow-growing, biosafety level 3 organism. To overcome these challenges, we applied a molecular barcoding strategy to a panel of M. tuberculosis clinical isolates. This novel application of barcoding permitted the high-throughput characterization of M. tuberculosis strain growth dynamics and vaccine resistance in the mouse model of infection. Integrating these results with genomic analyses, we uncover bacterial pathways that contribute to infection outcomes, suggesting targets for improved therapeutics and vaccines.},
}
@article {pmid35426262,
year = {2022},
author = {Lin, X and Sun, T and Tang, M and Yang, A and Yan-Do, R and Chen, D and Gao, Y and Duan, X and Kai, JJ and Wang, F and Shi, P},
title = {3D Upconversion Barcodes for Combinatory Wireless Neuromodulation in Behaving Animals.},
journal = {Advanced healthcare materials},
volume = {11},
number = {13},
pages = {e2200304},
doi = {10.1002/adhm.202200304},
pmid = {35426262},
issn = {2192-2659},
mesh = {Animals ; Brain/physiology ; *Deep Brain Stimulation ; Neurons/physiology ; *Optogenetics/methods ; Wireless Technology ; },
abstract = {Upconversion techniques offer all-optical wireless alternatives to modulate targeted neurons in behaving animals, but most existing upconversion-based optogenetic devices show prefixed emission that is used to excite just one channelrhodopsin at a restricted brain region. Here, a hierarchical upconversion device is reported to enable spatially selective and combinatory optogenetics in behaving rodent animals. The device assumes a multiarrayed optrode format containing engineered upconversion nanoparticles (UCNPs) to deliver dynamic light palettes as a function of excitation wavelength. Three primary emissions at 477, 540, and 654 nm are selected to match the absorption of different channelrhodopsins. The UCNPs are barcode assembled to multiple nanomachined optical pinholes in a microscale pipette device to allow remotely addressable, spectrum programmable, and spatially selective optical interrogation of complex brain circuits. Using the unique device, the basolateral amygdala and caudoputamen circuits are selectively modulated and the associated fear or anxiety behavior in freely behaving rodents is successfully differentiated. It is believed that the 3D barcode upconversion device would be a great supplement to current optogenetic toolsets and opens up new possibilities for sophisticated neural control.},
}
@article {pmid35422786,
year = {2022},
author = {Liao, YC and Wu, HC and Liou, CH and Lauderdale, TY and Huang, IW and Lai, JF and Chen, FJ},
title = {Rapid and Routine Molecular Typing Using Multiplex Polymerase Chain Reaction and MinION Sequencer.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {875347},
pmid = {35422786},
issn = {1664-302X},
abstract = {Molecular typing is an essential tool that has been extensively applied in laboratories as well as in clinical settings. Next-generation sequencing technologies promise high-throughput and cost-effective molecular applications; however, the accessibility of these technologies is limited due to the high capital cost. Oxford Nanopore Technologies (ONT) offers a MinION device with the advantages of real-time data analysis, rapid library preparation, and low cost per test. However, the advantages of the MinION device are often overshadowed by its lower raw accuracy. Herein, we present a concise multilocus sequence typing protocol of Staphylococcus aureus using multiplex polymerase chain reaction and Rapid Barcoding Kit for barcoding and MinION device for sequencing. Moreover, to clarify the effects of carryover DNA on tasks that require high sequence accuracy, we used the MinION flow cell in successive runs of washing and reusing. Our results revealed that the MinION flow cell could achieve accurate typing of a total of 467 samples with 3,269 kilobase-long genes within a total of 5 runs. This thus demonstrates the effectiveness of a portable nanopore MinION sequencer in providing accurate, rapid, and routine molecular typing.},
}
@article {pmid35421189,
year = {2022},
author = {Ngai, HL and Yang, X and Chu, AJ and Harper, R and Jacobsen, ABJE and Lau, DT and Yu, HY and Lee, HK and Shaw, PC},
title = {Multi-methodological approach for the Quality assessment of Senecionis scandentis Herba (Qianliguang) in the herbal market.},
journal = {PloS one},
volume = {17},
number = {4},
pages = {e0267143},
pmid = {35421189},
issn = {1932-6203},
mesh = {Anti-Bacterial Agents/pharmacology ; Chromatography, Liquid ; DNA Barcoding, Taxonomic ; *Plants, Medicinal/genetics ; *Senecio/genetics ; Staphylococcus aureus/genetics ; Tandem Mass Spectrometry ; },
abstract = {We set forth to assess the quality of an herbal medicine sold in Hong Kong called Qianliguang by employing a multi-methodological approach. The quality is set by its identity, chemical composition, and bioactivities, among others. Qianliguang (Senecionis scandentis Herba, Senecio scandens Buch.-Ham. ex D.Don) has known antibacterial properties. However, it is poisonous and overconsumption can result in liver damage. Eighteen Qianliguang samples were purchased from herbal shops at various districts in Hong Kong. Samples were first authenticated organoleptically. DNA barcoding at the psbA-trnH, ITS2, and rbcL loci was then conducted to confirm the species. HPLC-UV was performed to screen for the presence of the chemical compounds and to quantify the flavonoid hyperoside. UPLC-MS was used to quantify the amount of the toxic pyrrolizidine alkaloid (PA) adonifoline. Microdilution assay was performed to show the antibacterial effect on Streptococcus aureus and S. pneumoniae. Results showed that five samples were found to be substituted by species belonging to the genus Lespedeza; four samples were mixtures containing not only Qianliguang but also Achyranthes aspera L., Lonicera confusa DC., or Solanum nigrum L. HPLC-UV showed that only ten contained enough hyperoside to meet the standard requirement. In addition, nine samples had adonifoline that exceeded the toxicity standard requirement. In the microdilution assay, samples containing Qianliguang showed inhibition on S. aureus and S. pneumoniae, while among the five Lespedeza sp. samples the antibacterial effects on S. aureus were not detectable; only one sample showed inhibition to S. pneumoniae. Our study illustrated the necessity of using a multi-methodological approach for herbal medicine quality assessment. We also showed that Qianliguang samples in the Hong Kong market were either toxic or adulterated. It is therefore essential to improve the quality control of Qianliguang and probably other herbs in the herbal market.},
}
@article {pmid35421106,
year = {2022},
author = {Munguia-Vega, A and Terrazas-Tapia, R and Dominguez-Contreras, JF and Reyna-Fabian, M and Zapata-Morales, P},
title = {DNA barcoding reveals global and local influences on patterns of mislabeling and substitution in the trade of fish in Mexico.},
journal = {PloS one},
volume = {17},
number = {4},
pages = {e0265960},
pmid = {35421106},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Fishes/genetics ; Mexico ; *Perciformes ; Restaurants ; Seafood/analysis ; },
abstract = {Mislabeling of seafood is a global phenomenon that can misrepresent the status and level of consumption of wild fish stocks while concealing the use of many other wild species or those originating from aquaculture and sold as substitutes. We conducted a DNA barcoding study in three cities within Mexico (Mazatlan, Mexico City and Cancun) and sequenced the COI gene in 376 fish samples sold as 48 distinct commercial names at fish markets, grocery stores, and restaurants. Our goal was to identify the main species sold, their mislabeling rates and the species most used as substitutes. Overall, the study-wide mislabeling rate was 30.8% (95% CI 26.4-35.6). Half of the samples collected belonged to five species traded globally (yellowfin tuna, Atlantic salmon, mahi, swai, and tilapia), most of them with important aquaculture or ranching production levels. These species were commonly used as substitutes for other species and showed low mislabeling rates themselves (≤ 11%, except mahi mahi with 39% mislabeling). The other half of the samples revealed nearly 100 species targeted by small-scale fishers in Mexico and sold under 42 distinct commercial names. Popular local commercial names (dorado, marlin, mero, robalo, mojarra, huachinango, pargo, sierra) showed the highest mislabeling rates (36.3% to 94.4%) and served to sell many of the 53 species identified as substitutes in our study. We discuss the observed patterns in relation to landing and import data showing differences in availability of commercial species and the links to explain observed mislabeling rates and the use of a species as a substitute for other species. We also outline some of the implications of establishing a labeling and traceability standard as an alternative to improve transparency in the trade of seafood products in Mexico.},
}
@article {pmid35418016,
year = {2022},
author = {Yuan, F and Lan, X},
title = {Sequencing the organelle genomes of Bougainvillea spectabilis and Mirabilis jalapa (Nyctaginaceae).},
journal = {BMC genomic data},
volume = {23},
number = {1},
pages = {28},
pmid = {35418016},
issn = {2730-6844},
mesh = {*Genome, Chloroplast/genetics ; *Genome, Mitochondrial/genetics ; *Mirabilis/genetics ; Mitochondria/genetics ; *Nyctaginaceae/genetics ; },
abstract = {OBJECTIVES: Mirabilis jalapa L. and Bougainvillea spectabilis are two Mirabilis species known for their ornamental and pharmaceutical values. The organelle genomes are highly conserved with a rapid evolution rate making them suitable for evolutionary studies. Therefore, mitochondrial and chloroplast genomes of B. spectabilis and M. jalapa were sequenced to understand their evolutionary relationship with other angiosperms.<br><br>DATA DESCRIPTION: Here, we report the complete mitochondrial genomes of B. spectabilis and M. jalapa (343,746&#xa0;bp and 267,334&#xa0;bp, respectively) and chloroplast genomes of B. spectabilis (154,520&#xa0;bp) and M. jalapa (154,532&#xa0;bp) obtained from Illumina NovaSeq. The mitochondrial genomes of B. spectabilis and M. jalapa consisted of 70 and 72 genes, respectively. Likewise, the chloroplast genomes of B. spectabilis and M. jalapa contained 131 and 132 genes, respectively. The generated genomic data will be useful for molecular characterization and evolutionary studies.},
}
@article {pmid35415703,
year = {2022},
author = {Willocx, M and Van der Beeten, I and Asselman, P and Delgat, L and Baert, W and Janssens, SB and Leliaert, F and Picron, JF and Vanhee, C},
title = {Sorting out the plants responsible for a contamination with pyrrolizidine alkaloids in spice seeds by means of LC-MS/MS and DNA barcoding: Proof of principle with cumin and anise spice seeds.},
journal = {Food chemistry. Molecular sciences},
volume = {4},
number = {},
pages = {100070},
pmid = {35415703},
issn = {2666-5662},
abstract = {High value commodities such as spices suffer from occasional contaminations of both chemical and biological origin. Consequently, quality control and safety monitoring has become a pressing issue for the spice industry. Two recent independent studies showed that at least one third of the analyzed cumin and green anise spice seeds samples surpassed the by the European Union recently established threshold value for toxic pyrrolizidine alkaloids (PAs) and their corresponding N-oxides (PANOs). These heterocyclic secondary plant metabolites are produced by a large number of different plant families. In those spice seeds, it was found by means of DNA metabarcoding, that predominant contamination was due to the presence of herbal material from the Heliotropium genus (Boraginaceae). Unfortunately, the use of this specific type of DNA-based identification remains controversial for the majority of the official instances and preference is still given to the use of more tangible classical approaches, including microscopy and chemical analysis. However, these methodologies often suffer from inherent drawbacks. Here we demonstrate that at least for spice seeds, a combinatory approach of microscopy, chemical analysis and classical DNA barcoding of the isolated contaminants using the matK and trnH-psbA loci, provides qualitative and quantitative information on the amount of plant material responsible for the contaminations and the extent of the contamination. The generated data also demonstrates that the presence of a very limited number of Heliotropium sp. seeds in a standard commercially available canister is sufficient to surpass the allowed threshold value, illustrating once more the importance of weed control.},
}
@article {pmid35415645,
year = {2021},
author = {Delgado-Tejedor, A and Leekitcharoenphon, P and Aarestrup, FM and Otani, S},
title = {Evaluating the usefulness of next-generation sequencing for herb authentication.},
journal = {Food chemistry. Molecular sciences},
volume = {3},
number = {},
pages = {100044},
pmid = {35415645},
issn = {2666-5662},
abstract = {Food authentication is a rapidly growing field driven by increasing public awareness of food quality and safety. Foods containing herbs are particularly prone to industrial fraud and adulteration. Several methodologies are currently used to evaluate food authenticity. DNA-based technologies have increased focus, with DNA barcoding the most widely used. DNA barcoding is based on the sequencing and comparison of orthologous DNA regions from all species in a sample, but the approach is limited by its low resolution to distinguish closely-related species. Here we developed a customised database and bioinformatics pipeline (Herbs Authenticity - GitHub) to identify herbal ingredients implemented as a metagenomics approach for plant-derived product authenticity testing. We evaluated the accuracy of the method by using publicly available plant genomes and databases to allow the construction of our customised database barcodes, which were also complemented with entries from publicly available resources (iBOL and ENA). The pipeline performance was then tested with new 47 de novo partly sequenced whole plant genomes or barcodes as query sequences. Our results show that using our mapping algorithm with the customised barcode database correctly identifies the main components of a wide range of plant-derived samples, albeit with variable additional noise across samples depending on the tested samples and barcodes. Our result also show that at the current stage the usefulness of metagenomics is limited by the availability of reference sequences and the needed sequencing depth. However, this method shows promise for evaluating the authenticity of different herbal products provided that the method is further refined to increase the qualitative and quantitative accuracy.},
}
@article {pmid35414391,
year = {2022},
author = {Kim, S and Kim, JH and Kim, S and Park, JS and Cha, BS and Lee, ES and Han, J and Shin, J and Jang, Y and Park, KS},
title = {Loop-mediated isothermal amplification-based nucleic acid lateral flow assay for the specific and multiplex detection of genetic markers.},
journal = {Analytica chimica acta},
volume = {1205},
number = {},
pages = {339781},
doi = {10.1016/j.aca.2022.339781},
pmid = {35414391},
issn = {1873-4324},
mesh = {Genetic Markers ; Molecular Diagnostic Techniques/methods ; *Nucleic Acid Amplification Techniques/methods ; *Nucleic Acids ; Salmonella/genetics ; Sensitivity and Specificity ; },
abstract = {In this study, a loop-mediated isothermal amplification-based nucleic acid lateral flow assay (LAMP-NALFA) system was developed for the specific and multiplex detection of genetic markers at a low cost. In principle, the LAMP reaction was optimized to generate a single-stranded sequence in the LAMP product, which was designed to serve as a barcode sequence and to specifically bind to the DNA capture on a NALFA strip. As a target genetic marker, the Salmonella enterotoxin (stn) gene was chosen and determined down to 9 aM (∼5.44 copies/μL). Importantly, the proposed system clearly discriminated the specific target amplification products from non-specific amplification products resulting from primers or non-target nucleic acids, proving the high selectivity of the LAMP-NALFA system. Furthermore, the practical applicability of the system was demonstrated by detecting Salmonella bacteria in Luria-Bertani medium, drinking water, and eggshells, with a limit of detection of 1.6 CFU. Finally, two different bacteria (Salmonella and Staphylococcus) were simultaneously determined by the multiplex LAMP-NALFA system. It is expected that the LAMP-NALFA system could be used in a point-of-care setting for the detection of bacteria or viruses, consequently improving both individual and public health.},
}
@article {pmid35414224,
year = {2022},
author = {Maslakova, S and Ellison, CI and Hiebert, TC and Conable, F and Heaphy, MC and Venera-Pontón, DE and Norenburg, JL and Schwartz, ML and Moss, ND and Boyle, MJ and Driskell, AC and Macdonald, KS and Zattara, EE and Collin, R},
title = {Sampling multiple life stages significantly increases estimates of marine biodiversity.},
journal = {Biology letters},
volume = {18},
number = {4},
pages = {20210596},
pmid = {35414224},
issn = {1744-957X},
mesh = {Animals ; *Biodiversity ; Caribbean Region ; DNA ; DNA Barcoding, Taxonomic ; *Ecosystem ; Larva/genetics ; },
abstract = {Biodiversity assessments are critical for setting conservation priorities, understanding ecosystem function and establishing a baseline to monitor change. Surveys of marine biodiversity that rely almost entirely on sampling adult organisms underestimate diversity because they tend to be limited to habitat types and individuals that can be easily surveyed. Many marine animals have planktonic larvae that can be sampled from the water column at shallow depths. This life stage often is overlooked in surveys but can be used to relatively rapidly document diversity, especially for the many species that are rare or live cryptically as adults. Using DNA barcode data from samples of nemertean worms collected in three biogeographical regions-Northeastern Pacific, the Caribbean Sea and Eastern Tropical Pacific-we found that most species were collected as either benthic adults or planktonic larvae but seldom in both stages. Randomization tests show that this deficit of operational taxonomic units collected as both adults and larvae is extremely unlikely if larvae and adults were drawn from the same pool of species. This effect persists even in well-studied faunas. These results suggest that sampling planktonic larvae offers access to a different subset of species and thus significantly increases estimates of biodiversity compared to sampling adults alone. Spanish abstract is available in the electronic supplementary material.},
}
@article {pmid35413246,
year = {2022},
author = {Aykur, M and Camyar, A and Türk, BG and Sin, AZ and Dagci, H},
title = {Evaluation of association with subtypes and alleles of Blastocystis with chronic spontaneous urticaria.},
journal = {Acta tropica},
volume = {231},
number = {},
pages = {106455},
doi = {10.1016/j.actatropica.2022.106455},
pmid = {35413246},
issn = {1873-6254},
mesh = {Alleles ; *Blastocystis/genetics ; *Blastocystis Infections/parasitology ; Case-Control Studies ; *Chronic Urticaria ; DNA, Protozoan/genetics ; Feces/parasitology ; Genetic Variation ; Humans ; Interleukin-1 Receptor-Like 1 Protein/genetics ; Phylogeny ; },
abstract = {Blastocystis is a single-celled parasite commonly found in humans and its pathogenic role is still controversial. In recent years, some studies have suggested that Blastocystis may be a possible agent of gastrointestinal and dermatological symptoms such as acute or chronic urticaria, angioedema, rash, itch, palmoplantar, and diffuse pruritus. We aimed to investigate whether there is a relationship between Blastocystis subtypes and alleles in patients with chronic spontaneous urticaria (CSU) as a case-control study. In this study, stool samples were collected from patients with CSU (n=135) and healthy individuals (n=54). The presence of Blastocystis was investigated using the direct saline smear, Lugol's iodine staining, trichrome staining, Jones' medium culture and PCR assays in stool samples and subtypes (STs) were determined by sequencing according to DNA barcoding. The presence of Blastocystis was identified in 30.4% (64/210) the stool samples, including 31.9% (43/135) of the patients with CSU and 14.8% (8/54) of the control group. Moreover, it was found statistically significant the presence of Blastocystis in terms of both groups (p<0.018). ST3 was detected in 45.9% and 62.5 % as the most prevalent subtype the patients with CSU and the control group, respectively. ST1 (18.9%), ST2 (27%) and ST7 (8.1%) was identified in the patients with CSU group. There was no statistically significant correlation between Blastocystis subtypes and both the groups (p<0.240, p<0.323). Allele 4 for ST1; alleles 9, 10, 11 and 12 for ST2; alleles 34, 36 and 38 for ST3; alleles 41 and 101 for ST7 were detected. Allele 34 (ST3) was found significant in the patients with CSU as compared with control group (p<0.020). Moreover, statistically significant association was found between total IgE value and the certain subtypes (ST2 and ST3) (p<0.0001). As a result of this study, the presence of Blastocystis ST3 allele 34 significantly associated with chronic spontaneous urticaria was revealed.},
}
@article {pmid35412632,
year = {2022},
author = {Pan, X and Li, H and Zhang, X},
title = {TedSim: temporal dynamics simulation of single-cell RNA sequencing data and cell division history.},
journal = {Nucleic acids research},
volume = {50},
number = {8},
pages = {4272-4288},
pmid = {35412632},
issn = {1362-4962},
support = {R35 GM143070/GM/NIGMS NIH HHS/United States ; },
mesh = {*CRISPR-Cas Systems ; Cell Division/genetics ; Cell Lineage/genetics ; Sequence Analysis, RNA/methods ; *Single-Cell Analysis/methods ; },
abstract = {Recently, lineage tracing technology using CRISPR/Cas9 genome editing has enabled simultaneous readouts of gene expressions and lineage barcodes, which allows for the reconstruction of the cell division tree and makes it possible to reconstruct ancestral cell types and trace the origin of each cell type. Meanwhile, trajectory inference methods are widely used to infer cell trajectories and pseudotime in a dynamic process using gene expression data of present-day cells. Here, we present TedSim (single-cell temporal dynamics simulator), which simulates the cell division events from the root cell to present-day cells, simultaneously generating two data modalities for each single cell: the lineage barcode and gene expression data. TedSim is a framework that connects the two problems: lineage tracing and trajectory inference. Using TedSim, we conducted analysis to show that (i) TedSim generates realistic gene expression and barcode data, as well as realistic relationships between these two data modalities; (ii) trajectory inference methods can recover the underlying cell state transition mechanism with balanced cell type compositions; and (iii) integrating gene expression and barcode data can provide more insights into the temporal dynamics in cell differentiation compared to using only one type of data, but better integration methods need to be developed.},
}
@article {pmid35411044,
year = {2022},
author = {Pomerantz, A and Sahlin, K and Vasiljevic, N and Seah, A and Lim, M and Humble, E and Kennedy, S and Krehenwinkel, H and Winter, S and Ogden, R and Prost, S},
title = {Rapid in situ identification of biological specimens via DNA amplicon sequencing using miniaturized laboratory equipment.},
journal = {Nature protocols},
volume = {17},
number = {6},
pages = {1415-1443},
pmid = {35411044},
issn = {1750-2799},
mesh = {Biodiversity ; DNA/genetics ; *DNA Barcoding, Taxonomic/methods ; Humans ; *Nanopores ; Sequence Analysis, DNA/methods ; },
abstract = {In many parts of the world, human-mediated environmental change is depleting biodiversity faster than it can be characterized, while invasive species cause agricultural damage, threaten human health and disrupt native habitats. Consequently, the application of effective approaches for rapid surveillance and identification of biological specimens is increasingly important to inform conservation and biosurveillance efforts. Taxonomic assignments have been greatly advanced using sequence-based applications, such as DNA barcoding, a diagnostic technique that utilizes PCR and DNA sequence analysis of standardized genetic regions. However, in many biodiversity hotspots, endeavors are often hindered by a lack of laboratory infrastructure, funding for biodiversity research and restrictions on the transport of biological samples. A promising development is the advent of low-cost, miniaturized scientific equipment. Such tools can be assembled into functional laboratories to carry out genetic analyses in situ, at local institutions, field stations or classrooms. Here, we outline the steps required to perform amplicon sequencing applications, from DNA isolation to nanopore sequencing and downstream data analysis, all of which can be conducted outside of a conventional laboratory environment using miniaturized scientific equipment, without reliance on Internet connectivity. Depending on sample type, the protocol (from DNA extraction to full bioinformatic analyses) can be completed within 10 h, and with appropriate quality controls can be used for diagnostic identification of samples independent of core genomic facilities that are required for alternative methods.},
}
@article {pmid35410325,
year = {2022},
author = {Holm, JS and Funt, SA and Borch, A and Munk, KK and Bjerregaard, AM and Reading, JL and Maher, C and Regazzi, A and Wong, P and Al-Ahmadie, H and Iyer, G and Tamhane, T and Bentzen, AK and Herschend, NO and De Wolf, S and Snyder, A and Merghoub, T and Wolchok, JD and Nielsen, M and Rosenberg, JE and Bajorin, DF and Hadrup, SR},
title = {Neoantigen-specific CD8 T cell responses in the peripheral blood following PD-L1 blockade might predict therapy outcome in metastatic urothelial carcinoma.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {1935},
pmid = {35410325},
issn = {2041-1723},
support = {K12 CA184746/CA/NCI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; P50 CA221745/CA/NCI NIH HHS/United States ; },
mesh = {B7-H1 Antigen/genetics ; CD8-Positive T-Lymphocytes ; *Carcinoma, Transitional Cell/drug therapy/genetics ; Humans ; Immune Checkpoint Inhibitors ; *Urinary Bladder Neoplasms/drug therapy/genetics ; },
abstract = {CD8[+] T cell reactivity towards tumor mutation-derived neoantigens is widely believed to facilitate the antitumor immunity induced by immune checkpoint blockade (ICB). Here we show that broadening in the number of neoantigen-reactive CD8[+] T cell (NART) populations between pre-treatment to 3-weeks post-treatment distinguishes patients with controlled disease compared to patients with progressive disease in metastatic urothelial carcinoma (mUC) treated with PD-L1-blockade. The longitudinal analysis of peripheral CD8[+] T cell recognition of patient-specific neopeptide libraries consisting of DNA barcode-labelled pMHC multimers in a cohort of 24 patients from the clinical trial NCT02108652 also shows that peripheral NARTs derived from patients with disease control are characterised by a PD1[+] Ki67[+] effector phenotype and increased CD39 levels compared to bystander bulk- and virus-antigen reactive CD8[+] T cells. The study provides insights into NART characteristics following ICB and suggests that early-stage NART expansion and activation are associated with response to ICB in patients with mUC.},
}
@article {pmid35410128,
year = {2022},
author = {Yermanos, A and Hong, KL and Agrafiotis, A and Han, J and Nadeau, S and Valenzuela, C and Azizoglu, A and Ehling, R and Gao, B and Spahr, M and Neumeier, D and Chang, CH and Dounas, A and Petrillo, E and Nissen, I and Burcklen, E and Feldkamp, M and Beisel, C and Oxenius, A and Savic, M and Stadler, T and Rudolf, F and Reddy, ST},
title = {DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2.},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {289},
pmid = {35410128},
issn = {1471-2164},
mesh = {*COVID-19/diagnosis ; Genomics ; Humans ; Mutation ; *SARS-CoV-2/genetics ; Whole Genome Sequencing ; },
abstract = {BACKGROUND: The continued spread of SARS-CoV-2 and emergence of new variants with higher transmission rates and/or partial resistance to vaccines has further highlighted the need for large-scale testing and genomic surveillance. However, current diagnostic testing (e.g., PCR) and genomic surveillance methods (e.g., whole genome sequencing) are performed separately, thus limiting the detection and tracing of SARS-CoV-2 and emerging variants.<br><br>RESULTS: Here, we developed DeepSARS, a high-throughput platform for simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2 by the integration of molecular barcoding, targeted deep sequencing, and computational phylogenetics. DeepSARS enables highly sensitive viral detection, while also capturing genomic diversity and viral evolution. We show that DeepSARS can be rapidly adapted for identification of emerging variants, such as alpha, beta, gamma, and delta strains, and profile mutational changes at the population level.<br><br>CONCLUSIONS: DeepSARS sets the foundation for quantitative diagnostics that capture viral evolution and diversity. DeepSARS uses molecular barcodes (BCs) and multiplexed targeted deep sequencing (NGS) to enable simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2. Image was created using Biorender.com .},
}
@article {pmid35408741,
year = {2022},
author = {Wang, G and Bai, X and Chen, X and Ren, Y and Han, J},
title = {Development of a Genus-Universal Nucleotide Signature for the Identification and Supervision of Ephedra-Containing Products.},
journal = {Molecules (Basel, Switzerland)},
volume = {27},
number = {7},
pages = {},
pmid = {35408741},
issn = {1420-3049},
support = {2019YFC1604701//National Key Research and Development Program of China/ ; },
mesh = {*Alkaloids/metabolism ; *Ephedra/genetics/metabolism ; Ephedrine/metabolism ; Humans ; *Methamphetamine ; Nucleotides ; Plant Extracts ; },
abstract = {Ephedra plants generally contain ephedrine alkaloids, which are the critical precursor compounds of methamphetamine (METH). METH could cause serious physical and mental damage, and therefore Ephedra materials are strictly in supervision internationally. However, unlawful utilization of Ephedra herbs and its products still exist. Thus, it is imperative to establish a universal method for monitoring Ephedra ingredients in complex mixtures and processed products. In this study, 224 ITS2 sequences representing 59 taxa within Ephedra were collected, and a 23-bp genus-level nucleotide signature (GTCCGGTCCGCCTCGGCGGTGCG) was developed for the identification of the whole genus. The specific primers MH-1F/1R were designed, and 125 individuals of twelve Ephedra species/varieties were gathered for applicability verification of the nucleotide signature. Additionally, seven batches of Chinese patent medicines containing Ephedra herbs were used to test the application of the nucleotide signature in complex and highly processed materials. The results demonstrated that the 23-bp molecular marker was unique to Ephedra and conserved within the genus. It can be successfully utilized for the detection of Ephedra components in complex preparations and processed products with severe DNA degradation. The method developed in this study could undoubtedly serve as a strong support for the supervision of illegal circulation of Ephedra-containing products.},
}
@article {pmid35407094,
year = {2022},
author = {Dudu, A and Samu, M and Maereanu, M and Georgescu, SE},
title = {A Multistep DNA-Based Methodology for Accurate Authentication of Sturgeon Species.},
journal = {Foods (Basel, Switzerland)},
volume = {11},
number = {7},
pages = {},
pmid = {35407094},
issn = {2304-8158},
abstract = {The sturgeons (order Acipenseriformes) are caviar producers and some of the most valuable fish species worldwide. Due to different reasons, wild populations are now at the brink of extinction. The high demand for caviar has led to the development of aquaculture for restocking and caviar production. Since the caviar from different species has different prices depending on the quality and attempts of commercial fraud based on species substitution have been found, correct species identification is more than necessary. We report a new multistep methodology for an accurate species identification based on both nuclear and mitochondrial markers. Our test integrates data from the analysis of microsatellites (Afu19, Afu34, Afu39, Afu54, Aox27, AoxD234, AnacC11 and AnacE4), nuclear gene markers (RPS7, vimentin and rhodopsin) and mtDNA barcoding to give a reliable molecular diagnostic for five sturgeon species (Huso huso, Acipenser stellatus, Acipenser ruthenus, Acipenser gueldenstaedtii and Acipenser baerii). In addition to species identification, our methodology allows the identification of bester, sterbe and best beluga hybrids, but also the identification of hybrids of unknown origin. This methodology has a good potential to contribute to the conservation of highly threatened sturgeon populations and also to the traceability of their products.},
}
@article {pmid35406927,
year = {2022},
author = {Bosmali, I and Lagiotis, G and Haider, N and Osathanunkul, M and Biliaderis, C and Madesis, P},
title = {DNA-Based Identification of Eurasian Vicia Species Using Chloroplast and Nuclear DNA Barcodes.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {7},
pages = {},
pmid = {35406927},
issn = {2223-7747},
support = {T1EDK- 04448//European Regional Development Fund of the European Union and Greek national funds through the Operational Program &quot;Competitiveness, Entrepreneurship and Innovation&quot;/ ; },
abstract = {Many legume species of the Vicia L. genus (Fabaceae Lindl.) are key components of the Mediterranean diet and have an integral role in sustainable agriculture. Given the importance of the Vicia species for Eurasian culture, it is necessary to implement methodologies, such as DNA barcoding, that can enable the effective authentication and identification of species in the genus. In this study, we analysed the chloroplast trnL and rpoC1, as well as the nuclear ITS2 DNA barcoding regions, to identify 71 Vicia specimens of Eurasian descent. Both the trnL and ITS2 regions were highly effective in discriminating the analysed taxa, while the more conserved rpoC1 region could not identify all of the selected species due to high sequence conservation or non-annotated or absent rpoC1 species sequences in GenBank. A dendrographic representation of the generated trnL data showed sufficient clustering for most of the analysed taxa, although some topological discrepancies were observed. ITS2 and rpoC1 reconstructions were also used for resolving the topological discrepancies observed in the trnL tree. Our analysis suggests that a combination of DNA barcoding regions is essential for accurate species discrimination within the Vicia genus, while single-locus analyses do not provide the necessary resolution.},
}
@article {pmid35405792,
year = {2022},
author = {Choy, CPP and Wainwright, BJ},
title = {What Is in Your Shark Fin Soup? Probably an Endangered Shark Species and a Bit of Mercury.},
journal = {Animals : an open access journal from MDPI},
volume = {12},
number = {7},
pages = {},
pmid = {35405792},
issn = {2076-2615},
support = {none//Yale-NUS/ ; none//Shark Conservation Fund/ ; },
abstract = {Shark fin soup, consumed by Asian communities throughout the world, is one of the principal drivers of the demand of shark fins. This near USD 1 billion global industry has contributed to a shark population declines of up to 70%. In an effort to arrest these declines, the trade in several species of sharks is regulated under the auspices of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Despite this legal framework, the dried fins of trade-regulated sharks are frequently sold in markets and consumed in shark fin soup. Shark fins found in soups break down into a fibrous mass of ceratotrichia, meaning that identifying the species of sharks in the soup becomes impossible by visual methods. In this paper, we use DNA barcoding to identify the species of sharks found in bowls of shark fin soup collected in Singapore. The most common species identified in our samples was the blue shark (Prionace glauca), a species listed as Near Threatened on the International Union for Conservation of Nature (IUCN) Red List with a decreasing population, on which scientific data suggests catch limits should be imposed. We identified four other shark species that are listed on CITES Appendix II, and in total ten species that are assessed as Critically Endangered, Endangered or Vulnerable under the IUCN Red List of Threatened Species. Globally, the blue shark has been shown to contain levels of mercury that frequently exceed safe dose limits. Given the prevalence of this species in the examined soups and the global nature of the fin trade, it is extremely likely that consumers of shark fin soup will be exposed to unsafe levels of this neurotoxin.},
}
@article {pmid35404341,
year = {2022},
author = {Ge, Y and van Roon, L and Chen, HS and Methorst, R and Paton, M and DeRuiter, MC and Kielbasa, SM and Jongbloed, MRM},
title = {Low-input Nucleus Isolation and Multiplexing with Barcoded Antibodies of Mouse Sympathetic Ganglia for Single-nucleus RNA Sequencing.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {181},
pages = {},
doi = {10.3791/63397},
pmid = {35404341},
issn = {1940-087X},
mesh = {Animals ; Autonomic Nervous System ; *Endothelial Cells ; *Ganglia, Sympathetic ; Mice ; RNA, Small Nuclear ; Sequence Analysis, RNA/methods ; },
abstract = {The cardiac autonomic nervous system is crucial in controlling cardiac function, such as heart rate and cardiac contractility, and is divided into sympathetic and parasympathetic branches. Normally, there is a balance between these two branches to maintain homeostasis. However, cardiac disease states such as myocardial infarction, heart failure, and hypertension can induce the remodeling of cells involved in cardiac innervation, which is associated with an adverse clinical outcome. Although there are vast amounts of data for the histological structure and function of the cardiac autonomic nervous system, its molecular biological architecture in health and disease is still enigmatic in many aspects. Novel technologies such as single-cell RNA sequencing (scRNA-seq) hold promise for the genetic characterization of tissues at single-cell resolution. However, the relatively large size of neurons may impede the standardized use of these techniques. Here, this protocol exploits droplet-based single-nucleus RNA sequencing (snRNA-seq), a method to characterize the biological architecture of cardiac sympathetic neurons in health and disease. A stepwise approach is demonstrated to perform snRNA-seq of the bilateral superior cervical (SCG) and stellate ganglia (StG) dissected from adult mice. This method enables long-term sample preservation, maintaining an adequate RNA quality when samples from multiple individuals/experiments cannot be collected all at once within a short period of time. Barcoding the nuclei with hashtag oligos (HTOs) enables demultiplexing and the trace-back of distinct ganglionic samples post sequencing. Subsequent analyses revealed successful nuclei capture of neuronal, satellite glial, and endothelial cells of the sympathetic ganglia, as validated by snRNA-seq. In summary, this protocol provides a stepwise approach for snRNA-seq of sympathetic extrinsic cardiac ganglia, a method that has the potential for broader application in studies of the innervation of other organs and tissues.},
}
@article {pmid35401648,
year = {2022},
author = {Wang, Y and Liu, S and Wang, J and Yao, Y and Chen, Y and Xu, Q and Zhao, Z and Chen, N},
title = {Diatom Biodiversity and Speciation Revealed by Comparative Analysis of Mitochondrial Genomes.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {749982},
pmid = {35401648},
issn = {1664-462X},
abstract = {Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically significant groups of phytoplankton, comprising 100,000-200,000 species in three classes Bacillariophyceae, Mediophyceae, and Coscinodiscophyceae. However, due to the limited resolution of common molecular markers including 18S rDNA, 28S rDNA, ITS, rbcL, and cox1, diatom biodiversity has not been adequately ascertained. Organelle genomes including mitochondrial genomes (mtDNAs) have been proposed to be "super barcodes" for distinguishing diatom species because of their rich genomic content, and the rapid progress of DNA sequencing technologies that has made it possible to construct mtDNAs with increasing throughout and decreasing cost. Here, we constructed complete mtDNAs of 15 diatom species including five Coscinodiscophyceae species (Guinardia delicatula, Guinardia striata, Stephanopyxis turris, Paralia sulcata, and Actinocyclus sp.), four Mediophyceae species (Hemiaulus sinensis, Odontella aurita var. minima, Lithodesmioides sp., and Helicotheca tamesis), and six Bacillariophyceae species (Nitzschia ovalis, Nitzschia sp., Nitzschia traheaformis, Cylindrotheca closterium, Haslea tsukamotoi, and Pleurosigma sp.) to test the practicality of using mtDNAs as super barcodes. We found that mtDNAs have much higher resolution compared to common molecular markers as expected. Comparative analysis of mtDNAs also suggested that mtDNAs are valuable in evolutionary studies by revealing extensive genome rearrangement events with gene duplications, gene losses, and gains and losses of introns. Synteny analyses of mtDNAs uncovered high conservation among species within an order, but extensive rearrangements including translocations and/or inversions between species of different orders within a class. Duplication of cox1 was discovered for the first time in diatoms in Nitzschia traheaformis and Haslea tsukamotoi. Molecular dating analysis revealed that the three diatom classes split 100 Mya and many diatom species appeared since 50 Mya. In conclusion, more diatom mtDNAs representing different orders will play great dividends to explore biodiversity and speciation of diatoms in different ecological regions.},
}
@article {pmid35401446,
year = {2022},
author = {Mahnkopp-Dirks, F and Radl, V and Kublik, S and Gschwendtner, S and Schloter, M and Winkelmann, T},
title = {Dynamics of Bacterial Root Endophytes of Malus domestica Plants Grown in Field Soils Affected by Apple Replant Disease.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {841558},
pmid = {35401446},
issn = {1664-302X},
abstract = {Apple replant disease (ARD) is a worldwide problem for tree nurseries and orchards leading to reduced plant growth and fruit quality. The etiology of this complex phenomenon is poorly understood, but shifts of the bulk soil and rhizosphere microbiome seem to play an important role. Since roots are colonized by microbes from the rhizosphere, studies of the endophytic microbiome in relation to ARD are meaningful. In this study, culture-independent and culture-dependent approaches were used in order to unravel the endophytic root microbiome of apple plants 3, 7, and 12 months after planting in ARD-affected soil and ARD-unaffected control soil at two different field sites. Next to a high diversity of Pseudomonas in roots from all soils, molecular barcoding approaches revealed an increase in relative abundance of endophytic Actinobacteria over time in plants grown in ARD and control plots. Furthermore, several amplicon sequence variants (ASVs) linked to Streptomyces, which had been shown in a previous greenhouse ARD biotest to be negatively correlated to shoot length and fresh mass, were also detected in roots from both field sites. Especially in roots of apple plants from control soil, these Streptomyces ASVs increased in their relative abundance over time. The isolation of 150 bacterial strains in the culture-dependent approach revealed a high diversity of members of the genus Pseudomonas, confirming the data of the molecular barcoding approach. However, only partial overlaps were found between the two approaches, underlining the importance of combining these methods in order to better understand this complex disease and develop possible countermeasures. Overall, this study suggests a key role of Streptomyces in the etiology of ARD in the field.},
}
@article {pmid35399522,
year = {2022},
author = {Mann, Z and Sengar, M and Verma, YK and Rajalingam, R and Raghav, PK},
title = {Hematopoietic Stem Cell Factors: Their Functional Role in Self-Renewal and Clinical Aspects.},
journal = {Frontiers in cell and developmental biology},
volume = {10},
number = {},
pages = {664261},
pmid = {35399522},
issn = {2296-634X},
abstract = {Hematopoietic stem cells (HSCs) possess two important properties such as self-renewal and differentiation. These properties of HSCs are maintained through hematopoiesis. This process gives rise to two subpopulations, long-term and short-term HSCs, which have become a popular convention for treating various hematological disorders. The clinical application of HSCs is bone marrow transplant in patients with aplastic anemia, congenital neutropenia, sickle cell anemia, thalassemia, or replacement of damaged bone marrow in case of chemotherapy. The self-renewal attribute of HSCs ensures long-term hematopoiesis post-transplantation. However, HSCs need to be infused in large numbers to reach their target site and meet the demands since they lose their self-renewal capacity after a few passages. Therefore, a more in-depth understanding of ex vivo HSCs expansion needs to be developed to delineate ways to enhance the self-renewability of isolated HSCs. The multifaceted self-renewal process is regulated by factors, including transcription factors, miRNAs, and the bone marrow niche. A developed classical hierarchical model that outlines the hematopoiesis in a lineage-specific manner through in vivo fate mapping, barcoding, and determination of self-renewal regulatory factors are still to be explored in more detail. Thus, an in-depth study of the self-renewal property of HSCs is essentially required to be utilized for ex vivo expansion. This review primarily focuses on the Hematopoietic stem cell self-renewal pathway and evaluates the regulatory molecular factors involved in considering a targeted clinical approach in numerous malignancies and outlining gaps in the current knowledge.},
}
@article {pmid35397643,
year = {2022},
author = {Yao, Q and Zhu, X and Han, M and Chen, C and Li, W and Bai, H and Ning, K},
title = {Decoding herbal materials of TCM preparations with the multi-barcode sequencing approach.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {5988},
pmid = {35397643},
issn = {2045-2322},
mesh = {*Drugs, Chinese Herbal/analysis ; High-Throughput Nucleotide Sequencing ; *Medicine, Chinese Traditional ; Quality Control ; Reproducibility of Results ; },
abstract = {With the rapid development of high-throughput sequencing technology, approaches for assessing biological ingredients in Traditional Chinese Medicine (TCM) preparations have also advanced. Using a multi-barcode sequencing approach, all biological ingredients could be identified from TCM preparations in theory, as long as their DNA is present. The biological ingredients of several classical TCM preparations were analyzed successfully based on this approach in previous studies. However, the universality, sensitivity and reliability of this approach on a diverse set of TCM preparations remain unclear. In this study, we selected four representative TCM preparations, namely Bazhen Yimu Wan, Da Huoluo Wan, Niuhuang Jiangya Wan, and You Gui Wan, for concrete assessment of the multi-barcode sequencing approach. Based on ITS2 and trnL biomarkers, we have successfully detected the prescribed herbal materials (PHMs) in these representative TCM preparations (minimum sensitivity: 77.8%, maximum sensitivity: 100%). The results based on ITS2 have also shown higher reliability than trnL at species level, while their combination could provide higher sensitivity and reliability. The multi-barcode sequencing approach has shown good universality, sensitivity and reliability in decoding these four representative TCM preparations. In the omics big-data era, this work has undoubtedly made one step forward for applying multi-barcode sequencing approach in PHMs analysis of TCM preparation, towards better digitization and modernization of drug quality control.},
}
@article {pmid35396822,
year = {2022},
author = {Umina, PA and Weeks, AR and Maino, JL and Hoffmann, AA and Song, SV and Thia, J and Severtson, D and Cheng, X and van Rooyen, A and Arthur, AA},
title = {Australian Bryobia mites (Trombidiformes: Tetranychidae) form a complex of cryptic taxa with unique climatic niches and insecticide responses.},
journal = {Pest management science},
volume = {78},
number = {7},
pages = {2860-2871},
pmid = {35396822},
issn = {1526-4998},
support = {//Grains Research and Development Corporation/ ; },
mesh = {Animals ; Australia ; Crops, Agricultural ; *Insecticides ; Pest Control ; *Tetranychidae/genetics ; },
abstract = {BACKGROUND: Bryobia (Koch) mites belong to the economically important spider mite family, the Tetranychidae, with >130 species described worldwide. Due to taxonomic difficulties and most species being asexual, species identification relies heavily on genetic markers. Multiple putative Bryobia mite species have been identified attacking pastures and grain crops in Australia. In this study, we collected 79 field populations of Bryobia mites and combined these with 134 populations that were collected previously. We characterised taxonomic variation of mites using 28S rDNA amplicon-based DNA metabarcoding using next-generation sequencing approaches and direct Sanger sequencing. We then undertook species distribution modelling of the main genetic lineages and examined the chemical responses of multiple field populations.<br><br>RESULTS: We identified 47 unique haplotypes across all mites sampled that grouped into four distinct genetic lineages. These lineages have different distributions, with three of the four putative lineages showing different climatic envelopes, as inferred from species distribution modelling. Bryobia mite populations also showed different responses to a widely used insecticide (the organophosphate, omethoate), but not to another chemical (the pyrethroid, bifenthrin) when examined using laboratory bioassays.<br><br>CONCLUSION: Our findings indicate that cryptic diversity is likely to complicate the formulation of management strategies for Bryobia mites. Although focussed on Australia, this study demonstrates the challenges of studying Bryobia and highlights the importance of further research into this complex group of mites across the world. &#xa9; 2022 The Authors. Pest Management Science published by John Wiley &amp; Sons Ltd on behalf of Society of Chemical Industry.},
}
@article {pmid35396496,
year = {2022},
author = {Schär, S and Talavera, G and Rana, JD and Espadaler, X and Cover, SP and Shattuck, SO and Vila, R},
title = {Integrative taxonomy reveals cryptic diversity in North American Lasius ants, and an overlooked introduced species.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {5970},
pmid = {35396496},
issn = {2045-2322},
support = {P2SKP3_161677/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Animals ; *Ants/genetics ; DNA, Mitochondrial/genetics ; Ecosystem ; Introduced Species ; Phylogeny ; },
abstract = {Biological invasions are a grave threat to ecosystems. The black garden ant (Lasius niger) is a pest species in Europe. Current literature states that L. niger occupies a disjunct native distribution in the Holarctic, however, based on recent work, we re-evaluate this distribution. The native range of L. niger is reconsidered based on phylogenetic relationships (nine mitochondrial and nuclear markers, 5670 bp), DNA-barcoding (98 Holarctic specimens), morphometry (88 Holarctic specimens, 19 different measurements) and subjective assessment of phenotype. The potential spread of this species is estimated using ecological niche modeling. Lasius niger is more closely related to other Palearctic species than to the Nearctic ants known under this name. The latter are described as a distinct species, L. ponderosae sp. nov. However, DNA-barcoding discovered established populations of L. niger in metropolitan areas in Canada (Vancouver and Halifax). We describe a morphometrical method to delineate L. ponderosae sp. nov. and L. niger. MtDNA diversity and divergence is high within L. ponderosae sp. nov., but low within L. niger. More than 1,000,000 km[2] are suitable as a habitat for L. niger in North America. This case emphasizes the critical role of integrative taxonomy to detect cryptic species and identify potential biological invasions in their nascent stages.},
}
@article {pmid35395127,
year = {2022},
author = {Tedersoo, L and Bahram, M and Zinger, L and Nilsson, RH and Kennedy, PG and Yang, T and Anslan, S and Mikryukov, V},
title = {Best practices in metabarcoding of fungi: From experimental design to results.},
journal = {Molecular ecology},
volume = {31},
number = {10},
pages = {2769-2795},
doi = {10.1111/mec.16460},
pmid = {35395127},
issn = {1365-294X},
mesh = {Biodiversity ; DNA Barcoding, Taxonomic/methods ; Fungi/genetics ; *Microbiota/genetics ; *Mycobiome/genetics ; Research Design ; },
abstract = {The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview of current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational analyses. By reanalysing published data sets, we demonstrate that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity, a finding that is particularly evident for long markers. Additionally, analysis of the full-length ITS region allows more accurate taxonomic placement of fungi and other eukaryotes compared to the ITS2 subregion. Finally, we show that specific methods for compositional data analyses provide more reliable estimates of shifts in community structure. We conclude that metabarcoding analyses of fungi are especially promising for integrating fungi into the full microbiome and broader ecosystem functioning context, recovery of novel fungal lineages and ancient organisms as well as barcoding of old specimens including type material.},
}
@article {pmid35395020,
year = {2022},
author = {Chen, S and Loper, J and Zhou, P and Paninski, L},
title = {Blind demixing methods for recovering dense neuronal morphology from barcode imaging data.},
journal = {PLoS computational biology},
volume = {18},
number = {4},
pages = {e1009991},
pmid = {35395020},
issn = {1553-7358},
support = {U19 NS104649/NS/NINDS NIH HHS/United States ; U19 NS107613/NS/NINDS NIH HHS/United States ; U19 NS123716/NS/NINDS NIH HHS/United States ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Neurons ; *Optical Imaging ; },
abstract = {Cellular barcoding methods offer the exciting possibility of 'infinite-pseudocolor' anatomical reconstruction-i.e., assigning each neuron its own random unique barcoded 'pseudocolor,' and then using these pseudocolors to trace the microanatomy of each neuron. Here we use simulations, based on densely-reconstructed electron microscopy microanatomy, with signal structure matched to real barcoding data, to quantify the feasibility of this procedure. We develop a new blind demixing approach to recover the barcodes that label each neuron, and validate this method on real data with known barcodes. We also develop a neural network which uses the recovered barcodes to reconstruct the neuronal morphology from the observed fluorescence imaging data, 'connecting the dots' between discontiguous barcode amplicon signals. We find that accurate recovery should be feasible, provided that the barcode signal density is sufficiently high. This study suggests the possibility of mapping the morphology and projection pattern of many individual neurons simultaneously, at high resolution and at large scale, via conventional light microscopy.},
}
@article {pmid35394373,
year = {2022},
author = {Mari-Ribeiro, IP and Scorsim, B and Oliveira, AV and Portela-Castro, ALB},
title = {Cytogenetic and Molecular Characterization of Oligosarcus pintoi (Characidae): A New Record of Supernumerary Chromosome in this Species.},
journal = {Zebrafish},
volume = {19},
number = {2},
pages = {71-80},
doi = {10.1089/zeb.2021.0065},
pmid = {35394373},
issn = {1557-8542},
mesh = {Animals ; *Characidae/genetics ; DNA, Ribosomal/genetics ; In Situ Hybridization, Fluorescence ; Karyotype ; Karyotyping ; Zebrafish/genetics ; },
abstract = {The genus Oligosarcus currently comprises 24 valid species distributed in the major river basins of South America. In this group, nine species were cytogenetically investigated, and found to share a diploid number of 50 chromosomes. Despite the conservation of the diploid number, variations in the karyotypic formula, number and position of the nucleolar organizer regions, and longitudinal bands have been described between both species and populations. In this study, we present cytogenetic and molecular data from Oligosarcus pintoi specimens from the Keller River, a tributary of the Ivaí River (Upper Paraná basin), using DNA barcoding and cytogenetic markers (C-band, silver-stained nucleolar organizer regions, and fluorescence in situ hybridization of 18S and 5S rDNA). The genetic inferences reached after analyzing the cytochrome c oxidade subunit 1 gene allowed us to confirm the identity of the individuals with 2n = 50 chromosomes. However, one specimen contained a medium subtelocentric supernumerary chromosome (2n = 51). This is the second record of additional chromosomes in O. pintoi, thereby confirming the existence of a supernumerary chromosome in allopatric populations of this species, a fact that demonstrates an evolutionary path that is divergent from other populations and/or species of Oligosarcus analyzed so far, contributing to the karyotypic diversification of the group.},
}
@article {pmid35391452,
year = {2022},
author = {Kirik, H and Tummeleht, L and Kurina, O},
title = {Rediscovering the mosquito fauna (Diptera: Culicidae) of Estonia: an annotated checklist with distribution maps and DNA evidence.},
journal = {Zootaxa},
volume = {5094},
number = {2},
pages = {261-287},
doi = {10.11646/zootaxa.5094.2.3},
pmid = {35391452},
issn = {1175-5334},
mesh = {*Aedes ; Animals ; *Culicidae/anatomy &amp; histology/genetics ; DNA ; Estonia ; Female ; Male ; Mosquito Vectors/genetics ; *Ochlerotatus/genetics ; },
abstract = {Female mosquitoes (Diptera: Culicidae) affect their hosts in numerous negative ways and are crucial to the spread of vector-borne pathogens. It is, therefore, important to have a detailed overview of regional mosquitoes, to be able to detect changes in species diversity and identify possible health threats. The aim of this study was to update the checklist of the mosquito fauna of Estonia for the first time since 1957. For this purpose, 24,344 adult mosquitoes (94% females) were collected in Estonia from 2008 to 2020 using various trapping methods. Specimens were primarily identified by morphological characteristics, but DNA barcoding based on the partial cytochrome c oxidase subunit 1 gene (COI) was also used. Species were included in the checklist based on historical records as well as new collections, while also considering reports from neighboring countries. Species records are supplemented with voucher specimens, distribution maps and DNA evidence. The updated checklist includes 34 species, 27 of which were confirmed with recently collected material. All in all, Aedes communis (de Geer, 1776) proved to be the most common mosquito in Estonia, accounting for 30.1% of the specimens collected. This is noteworthy, as this species has been implicated in the transmission of multiple disease agents present in the area. New evidence revealed the presence of Ae. hexodontus Dyar, 1916, Ae. sticticus (Meigen, 1838), Anopheles messeae Falleroni, 1926 and Culiseta bergrothi (Edwards, 1921) in Estonia.},
}
@article {pmid35391436,
year = {2022},
author = {Grebennikov, VV},
title = {The first molecular phylogeny of Blosyrini weevils (Coleoptera: Curculionidae: Entiminae) rejects monophyly of the tribe and documents a new Asian clade with the highest diversity in the Hengduan Mountains.},
journal = {Zootaxa},
volume = {5094},
number = {4},
pages = {553-572},
doi = {10.11646/zootaxa.5094.4.2},
pmid = {35391436},
issn = {1175-5334},
mesh = {Animals ; China ; *Coleoptera/genetics ; DNA ; Phylogeny ; *Weevils ; },
abstract = {This paper targets diversity and phylogeny of the Old World weevil tribe Blosyrini and, specifically, its Asian members. Phylogenetic analysis of one mitochondrial and two nuclear DNA fragments from 78 terminals reveals that Blosyrini weevils, although monophyletic in Asia, in Madagascar, and in continental Africa, do not share a unique common ancestor. Instead, they form a strongly supported clade together with representatives of two other tribes of broad-nosed weevils: Cneorhinini and Dermatodini. The Asian members of the tribe form a moderately supported clade, of which the monophyletic genus Trachyphloeoides is a sister to the strongly supported rest, Blosyrini Clade X (BCX). Owing to the convoluted and non-phylogenetic taxonomy, BCX cannot be at present reliably referred to by any existing genus-group name. All 112 DNA barcodes of BCX (including one larva) from China, Kazakhstan, Kyrgyzstan, and Nepal form 34 Barcode Index Numbers (BINs). Each of seven comprehensively sampled mountainous localities in Sichuan (Gongga Shan, Emei Shan, Songpan) and Yunnan (Cang Shan, Gaoligong Shan, Haba Shan, Jizu Shan) supports between one and six BINs of BCX. With two exceptions, all BINs of BCX in Sichuan (8) and Yunnan (10) display strong biological preferences for either mid-altitude primary deciduous forests or the high elevation alpine zone. Seven strongly supported clades are recognized within BCX, some of them morphologically diagnosable. Temporal analysis corroborates the results of BIN clustering and interrelationships within BCX. The most recent common ancestor of BCX lived in the mid-Miocene (14.15 Ma, 95% confidence interval 17.511.2 Ma), with much of the subsequent diversification preceding or coinciding with the Pliocene-Pleistocene climatic fluctuations.},
}
@article {pmid35391434,
year = {2022},
author = {Li, H and He, Y and Zhang, J and Yu, H},
title = {A new species of Utivarachna Kishida, 1940 from Fanjing Mountain Nature Reserve, Guizhou, China (Araneae: Trachelidae).},
journal = {Zootaxa},
volume = {5094},
number = {4},
pages = {587-594},
doi = {10.11646/zootaxa.5094.4.4},
pmid = {35391434},
issn = {1175-5334},
mesh = {Animals ; Body Size ; China ; Genes, Mitochondrial ; Organ Size ; *Spiders/genetics ; },
abstract = {A new species belonging to the kinabaluensis group of the trachelid genus Utivarachna Kishida, 1940, U. fanjing sp. nov., is described from southwestern China. Detailed description, diagnosis, photographs and distribution map of the new species are given. DNA barcodes (a partial fragment of the mitochondrial cytochrome oxidase subunit I gene, COI) of the species were obtained to confirm matching of the sexes and for future use in molecular studies.},
}
@article {pmid35391428,
year = {2022},
author = {Liu, J and Lu, X and Zhang, Q and Wu, X and Yang, D and Bian, X},
title = {Contribution to the knowledge of Chinese Gryllacrididae (Orthoptera) V: Further study on the Chinese Capnogryllacris and comment on the phylogenetic relationships of the Gryllacrididae.},
journal = {Zootaxa},
volume = {5099},
number = {1},
pages = {1-45},
doi = {10.11646/zootaxa.5099.1.1},
pmid = {35391428},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology ; Animals ; Bayes Theorem ; Body Size ; China ; Humans ; Male ; Organ Size ; *Orthoptera ; Phylogeny ; },
abstract = {Based on the specimens deposited in Guangxi Normal University, the paper mainly deals with Capnogryllacris and reports one new species and four new subspecies, viz. Capnogryllacris sequestris Liu, Lu Bian sp. nov. (Chinese name:), Capnogryllacris erythrocephala maculates Liu, Lu Bian ssp. nov. (Chinese name:), Capnogryllacris nigromarginata hainanensis Liu, Lu Bian ssp. nov. (Chinese name:), Capnogryllacris nigromarginata rectispina Liu, Lu Bian ssp. nov. (Chinese name:) and Capnogryllacris xichou flavifrons Liu, Lu Bian ssp. nov. (Chinese name:). The next-generation sequencing technology was used to sequence the mitochondrial genomes of 13 specimens of Gryllacrididae, and the characteristics of newly obtained mitogenomes were introduced. The gene arrangements are completely consistent with other known orthopteran insects, and there is a long IGS of 166 bp217 bp between trnK and cox2 genes in three individuals of C. erythrocephala maculatis ssp. nov.. Meanwhile, fourteen specimens of Capnogryllacris were delimited using COI barcode by constructing NJ tree and two distance-based barcoding methods (ABGD and jMOTU). Among the three methods, C. erythrocephala maculatis, C. rufonotata and C. spinosa can be correctly identified, but C. nigromarginata shows some differences in morphological and genetic distance, and Capnogryllacris melanocrania is divided into two clades. The Bayesian inference (BI) and Maximum likelihood (ML) trees based on the 13 protein-coding genes data supported the division of Gryllacrididae into two groups according to whether the male ninth abdominal tergite with median furrow or split along the midline or not.},
}
@article {pmid35391362,
year = {2022},
author = {Xie, L and Wang, M and Chen, Y and Wang, H},
title = {Review of the genus Leucoma Hbner, 1822 (Lepidoptera: Erebidae: Lymantriinae) from China, with description of two new species.},
journal = {Zootaxa},
volume = {5115},
number = {3},
pages = {361-380},
doi = {10.11646/zootaxa.5115.3.3},
pmid = {35391362},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; *Bivalvia ; China ; Genitalia ; *Lepidoptera ; *Moths/genetics ; },
abstract = {The genus Leucoma Hbner from China is reviewed. Based on morphological characters and DNA barcode data, fourteen species belonging to this genus are recognized, with descriptions of two new species: L. nyingchiensis sp. nov. and L. sichuana sp. nov.. Illustrations of adults and their genitalia are provided along with a key to all currently known species of Leucoma in China.},
}
@article {pmid35391334,
year = {2022},
author = {Krasheninnikov, AB and Tanadbaeva, DA and Vshivkova, KA},
title = {Description of Chaetocladius (Chaetocladius) spiridonovi sp. nov. from the Russian Arctic Region (Diptera, Chironomidae).},
journal = {Zootaxa},
volume = {5116},
number = {2},
pages = {292-298},
doi = {10.11646/zootaxa.5116.2.6},
pmid = {35391334},
issn = {1175-5334},
mesh = {Animals ; *Chironomidae/genetics ; *Diptera ; *Lepidoptera ; Male ; Phylogeny ; Russia ; },
abstract = {The male adult of Chaetocladius (Chaetocladius) spiridonovi sp. nov. is described and diagnosed based on morphological and phylogenetic data. The new species is characterized by the following features: anal point very long, almost reaching apex of gonocoxite, presence of a dorsal hump at base; inferior volsella sub-rectangular to large lobe shaped, inner and caudal margin with undulation; virga composed of 2 long spines; gonostylus massively globular with rounded posterior margin. Comparison of COI with that of other known Chaetocladius species shows a K2P genetic distances of 8.9220.31%, values well associated with interspecific variation. The barcodes of the new species were identical to that of Chaetocladius sp. 7ES in BOLD systems. Molecular data were also used for the reconstruction of the phylogenetic relationships within the subgenus Chaetocladius.},
}
@article {pmid35391320,
year = {2022},
author = {Piovesan, M and Orlandin, E and Mielke, OHH and Casagrande, MM},
title = {Revalidation of Yphthimoides inornata (Hayward, 1962 (Lepidoptera: Nymphalidae: Satyrinae: Satyrini: Euptychiina) based on morphological and molecular data with description of the immature stages.},
journal = {Zootaxa},
volume = {5116},
number = {4},
pages = {550-562},
doi = {10.11646/zootaxa.5116.4.4},
pmid = {35391320},
issn = {1175-5334},
mesh = {Animals ; *Butterflies/anatomy &amp; histology/genetics ; Ecosystem ; Female ; Genitalia ; *Lepidoptera ; Male ; },
abstract = {Yphthimoides inornata (Hayward, 1962) stat. rev., currently regarded as a nomen dubium and synonym of Yphthimoides yphthima (C. Felder R. Felder, 1867) has its status revalidated based on morphological characters and the DNA barcode. Images of the male and female, including their genitalia, information on the distribution, habitat, and immature stages are provided.},
}
@article {pmid35391314,
year = {2022},
author = {Xu, ZB and Melichar, T and He, JB and Zhang, C and Zhang, XY and Feng, DU and Hu, SJ},
title = {A new species of Rhodambulyx Mell, 1939 (Lepidoptera: Sphingidae) from Southwest Chongqing, China.},
journal = {Zootaxa},
volume = {5105},
number = {1},
pages = {48-62},
doi = {10.11646/zootaxa.5105.1.2},
pmid = {35391314},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; China ; Genitalia ; Genitalia, Male ; *Lepidoptera ; Male ; *Moths/genetics ; },
abstract = {A new species of the genus Rhodambulyx Mell, 1939, Rhodambulyx xinyuae sp. nov., is described from Simianshan Nature Reserve in Southwest Chongqing, China. This species is similar to R. davidi Mell, 1939 and R. kitchingi Brechlin, 2015 in habitus, but can be distinguished by a different wing pattern, male genitalia structure and DNA barcode sequence. In addition, Rhodambulyx namvui Eitschberger Nguyen, 2017 is removed from synonymy with R. kitchingi and synonymized instead with R. davidi, although whether it would be better treated as a subspecies of R. davidi requires further investigation.},
}
@article {pmid35391297,
year = {2022},
author = {Bhansali, S and Wesener, T},
title = {New Thai giant pill-millipede species, with new genetic barcoding data (Diplopoda, Sphaerotheriida, Zephroniidae).},
journal = {Zootaxa},
volume = {5105},
number = {3},
pages = {357-380},
doi = {10.11646/zootaxa.5105.3.2},
pmid = {35391297},
issn = {1175-5334},
mesh = {Animals ; *Arthropods ; Microscopy ; Thailand ; },
abstract = {Three new species of giant pill-millipedes, Sphaerobelum meridionalis Bhansali Wesener sp. nov., Zephronia chrysomallos Bhansali Wesener sp. nov. and Zephronia erawani Bhansali Wesener sp. nov. are described based on museum samples from Thailand. All three species are described in an integrative manner, combining light microscopy, scanning electron microscopy, CT scans and genetic barcoding. Genetic barcoding was successfully conducted for all holotypes of the new species. In addition, genetic barcoding data of four recently described Thai Zephronia species, Zephronia lannaensis Likhitrakarn Golovatch, 2021 in Likhitrakarn et al. 2021, Z. phrain Likhitrakarn Golovatch, 2021, Z. panhai Srisonchai et al. 2021 and Z. golovatchi Srisonchai et al. 2021, together with new locality records, were added to the dataset. Our dataset includes all published sequences of the family Zephroniidae, including all but one (Z. enghoffi Srisonchai et al., 2021) of the described species from Thailand, Laos and Cambodia. All new species are genetically distant from other Zephroniidae from Thailand and surrounding countries showing uncorrected p-distances of >10 %. S. meridionalis sp. nov. is genetically and morphologically close to a recently described aberrant Sphaerobelum, S. aesculus Rosenmejer Wesener, 2021, as well as an unspecified specimen from Malaysia, and might represent a genus different from Sphaerobelum Verhoeff, 1924. Both new Zephronia species are geographically, morphologically and genetically close to Z. panhai, but differ from the latter by >10% p-distance in the COI gene and numerous morphological characters. Virtual cybertypes of the holotype of Zephronia erawani sp. nov. and of a paratype of Z. chrysomallos sp. nov. were created and made publicly accessible.},
}
@article {pmid35391289,
year = {2022},
author = {Russell, BC and Bogorodsky, SV and Mal, AO and Bineesh, KK and Alpermann, TJ},
title = {The taxonomic identity of the monocle bream Scolopsis vosmeri species complex (Perciformes: Nemipteridae), with comments on molecular phylogenetic relationships within the genus Scolopsis.},
journal = {Zootaxa},
volume = {5105},
number = {4},
pages = {501-538},
doi = {10.11646/zootaxa.5105.4.3},
pmid = {35391289},
issn = {1175-5334},
mesh = {Animals ; Fishes ; *Perciformes ; Phylogeny ; },
abstract = {The monocle bream Scolopsis vosmeri species complex is revised. Three species in the complex are recognized: Scolopsis vosmeri (Bloch, 1792), widespread in the Indo-West Pacific, from the northern Indian Ocean (Pakistan, western India, Sri Lanka, Bay of Bengal, and the Andaman Sea, but not recorded from the Red Sea or Arabian Gulf, east African coast or Madagascar) to western Indonesia and Borneo; S. japonica (Bloch, 1793), restricted to the western Pacific Ocean from western Indonesia and north-western Australia east to the Philippines and north to southern Japan; and S. curite Cuvier, 1815, widespread from the western to the eastern Indian Ocean, including the Red Sea and Arabian Gulf. All three species are similar morphologically, and have been confused taxonomically, but phylogenetic analysis of the COI barcoding region shows they are evolutionarily divergent. The three species are redescribed in detail and characters found to distinguish them. Scolopsis vosmeri is easily distinguished from S. japonica and S. curite in having a white band along the side of the body; having a black spot on most body scales (versus greenish yellow spot in S. japonica and S. curite); in lacking a distinct black spot (sometimes a small and faint spot present) on the upper pectoral-fin base (versus small black wedge-shaped spot present in S. japonica and S. curite); caudal peduncle whitish in live individuals (versus caudal peduncle usually yellowish in S. japonica and S. curite); and pelvic and anal fins crimson to orange-red (versus yellow in S. japonica and S. curite). Scolopsis japonica and S. curite are indistinguishable by color pattern but differ in the degree of spination on the preopercular margin. Neotypes are designated for Scolopsis japonica and S. curite. Nomenclatural problems, including validity of the genus Scolopsis, are discussed. We regard Scolopsis curite Cuvier, 1815 as a valid binomial name and thus the type species of Scolopsis Cuvier, 1814 by subsequent monotypy.},
}
@article {pmid35391247,
year = {2022},
author = {Mukherjee, B and Hazra, N},
title = {First records of three genera, Cyphomella Sther, 1977, Olecryptotendipes Zorina, 2007 and Robackia Sther, 1977 of the Harnischia complex from India with description of O. extentus sp. n., O. obtunsus sp. n. and R. aequilongia sp. n. (Diptera: Chironomidae).},
journal = {Zootaxa},
volume = {5091},
number = {2},
pages = {330-340},
doi = {10.11646/zootaxa.5091.2.5},
pmid = {35391247},
issn = {1175-5334},
mesh = {Animals ; Camelus ; *Chironomidae ; India ; Male ; },
abstract = {Three genera, Cyphomella Sther, 1977, Olecryptotendipes Zorina, 2007 and Robackia Sther, 1977, of the Harnischia complex are recorded for the first time from India. Two new species of Olecryptotendipes and one new species of Robackia are described on the basis of adult males. Cyphomella camelus (Kieffer, 1955), described from Afrotropical and Palaearctic regions, is recorded for the first time from India and its description is supplemented. The molecular barcodes of three species, O. obtunsus sp. n., C. camelus and R. aequilongia sp. n., are also provided. Revised world keys to the adult males of the Olecryptotendipes and Robackia are also provided.},
}
@article {pmid35391231,
year = {2022},
author = {Chen, Z and Liu, F and Li, D and Xu, X},
title = {Four new species of the primitively segmented spider genus Songthela (Mesothelae, Liphistiidae) from Chongqing Municipality, China.},
journal = {Zootaxa},
volume = {5091},
number = {4},
pages = {546-558},
doi = {10.11646/zootaxa.5091.4.2},
pmid = {35391231},
issn = {1175-5334},
mesh = {Animals ; China ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Female ; Male ; Mitochondria/genetics ; *Spiders/genetics ; },
abstract = {This paper reports four new species of the primitively segmented spider genus Songthela from Chongqing Municipality, China, based on morphological characters of both males and females: S. jinyun sp. nov., S. longbao sp. nov., S. serriformis sp. nov. and S. wangerbao sp. nov. We also provide the GenBank accession codes of mitochondrial DNA barcode gene, cytochrome c oxidase subunit I (COI), for the holotype of four new species for future identification.},
}
@article {pmid35391220,
year = {2022},
author = {Tatarnic, NJ and Cassis, G},
title = {Turrana ejuncida, a new species of Acanthocorini (Hemiptera: Heteroptera: Coreidae) from Cape Range, Western Australia, with discussion of its systematic position and host plant associations.},
journal = {Zootaxa},
volume = {5092},
number = {1},
pages = {85-96},
doi = {10.11646/zootaxa.5092.1.4},
pmid = {35391220},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Female ; *Hemiptera ; *Heteroptera ; Male ; Microscopy, Electron, Scanning ; Western Australia ; },
abstract = {The coreid genus Turrana Distant 1911 is redescribed, and a new species Turrana ejuncida sp. nov. is described from specimens collected from Cape Range National Park, Western Australia in 2019 and 2021. Habitus photographs and scanning electron microscopy images are presented of key characters, with X-Ray microtomography deployed to document the male and female genitalia. In addition, DNA barcodes for mitochondrial gene regions COI and 16S were obtained and are made available on Genbank. Finally, the evidence provided in this work is discussed in relation to the systematic position of Turrana.},
}
@article {pmid35391203,
year = {2022},
author = {Irfan, M and Wang, LY and Zhao, J and Zhang, ZS},
title = {Three new species of the spider genus Pimoa Chamberlin amp; Ivie, 1943 (Araneae, Pimoidae) from Qinghai-Tibet Plateau of China.},
journal = {Zootaxa},
volume = {5092},
number = {3},
pages = {318-330},
doi = {10.11646/zootaxa.5092.3.4},
pmid = {35391203},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; China ; DNA ; Phylogeny ; *Spiders/genetics ; Tibet ; },
abstract = {Three new species of the spider genus Pimoa Chamberlin Ivie, 1943 are described: P. pingwuensis n. sp. () and P. yajiangensis n. sp. () from Sichuan and P. zekogensis n. sp. () from Qinghai. These new species are distinguished from other known Pimoa species by genital characters as well as by DNA barcodes. Detailed descriptions, photographs of genital characters and somatic features, a distribution map, comparisons to closely related species and DNA barcodes of the new species are presented. Illustrations of new species are provided and their phylogenetic relationships within the genus Pimoa are also discussed.},
}
@article {pmid35391199,
year = {2022},
author = {Ashrafi, H and Uri, Z and Anker, A},
title = {The first complete specimen of the deep-water shrimp Batella praecipua De Grave, 2004 (Crustacea: Decapoda: Alpheidae).},
journal = {Zootaxa},
volume = {5092},
number = {3},
pages = {378-386},
doi = {10.11646/zootaxa.5092.3.8},
pmid = {35391199},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures ; Animals ; *Anthozoa ; *Decapoda ; Water ; },
abstract = {The deep-water alpheid shrimp Batella praecipua De Grave, 2004 was originally described based on two incomplete specimens, both with their first chelipeds missing, collected at 400440 m off New Caledonia. During the recent KANADEEP 1 expedition in the Coral Sea in 2017, the first complete specimen of B. praecipua was collected at a depth of 370380 m. The morphology of this specimen is presented in detail, with emphasis on the highly diagnostic chelipeds, which are described and illustrated for the first time. A slight intraspecific variation of B. praecipua is reported and a DNA barcode (CO1) is provided for this species. The main differences between the three presently known species of Batella Holthuis, 1955 are discussed.},
}
@article {pmid35391186,
year = {2022},
author = {Rajaei, H and Hausmann, A and Trusch, R},
title = {Taxonomic review of the genus Rhodostrophia Hbner, 1823 (Geometridae: Sterrhinae) in Iran.},
journal = {Zootaxa},
volume = {5118},
number = {1},
pages = {1-64},
doi = {10.11646/zootaxa.5118.1.1},
pmid = {35391186},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Iran ; *Moths ; Surveys and Questionnaires ; },
abstract = {So far, the species of the genus Rhodostrophia Hbner, 1823 (Geometridae), their diagnostic characters and their distribution in Iran have not been investigated in detail. Moreover, some species were misunderstood by earlier authors. To solve these problems, a survey of the Iranian Rhodostrophia species based on over 1700 specimens has been executed. The type series of all species known from Iran were examined. Additionally extensive material from different museums and private collections was morphologically studied and compared with the type material. DNA-barcoding was used as an independent line of information and the results were compared with the morphological data. Examination of the type material revealed that R.cuprinaria (Christoph, 1876) was misinterpreted for a long time. The taxon R.nubifera Brandt, 1941 syn. nov. is a younger synonym of Hugo Christophs R.cuprinaria, which was misidentified by himself in his later publications. An available name for R.cuprinaria in the old, erroneous sense is R.phaenicearia (Hampson, 1907). Three subspecies were recognized for R. terrestraria, including R. terrestraria farsi ssp. nov. Additionally, R. terrestraria furialis Brandt, 1941 syn. nov. is hereregarded as junior synonym ofR. terrestraria(Lederer, 1869); Rhodostrophia nubifera nubifera Brandt, 1941 syn. nov. and R. nubifera klapperichi Wiltshire, 1966 syn. nov. are here regarded as junior synonyms of R. cuprinaria (Christoph, 1876). R. abscisaria chlorotica Wiltshire, 1967 syn. nov. is downgraded to synonymy of R. abscisaria Brandt, 1941 and R. peripheres debilis Wiltshire, 1949 syn. nov. to synonymy of R. peripheres Prout, 1938. Rhodostrophia vahabzadehi sp. nov. is described as a new species. In total, 15 species are regarded as valid for the fauna of Iran. External and internal morphological characters for all examined species are illustrated. Distribution data are shown on maps for of all species. An updated checklist is presented for the Iranian representatives of the genus Rhodostrophia.},
}
@article {pmid35391162,
year = {2022},
author = {Brown, BV},
title = {Some remarkably common, but undescribed, Megaselia Rondani (Diptera: Phoridae) from northwestern Costa Rica.},
journal = {Zootaxa},
volume = {5120},
number = {3},
pages = {373-390},
doi = {10.11646/zootaxa.5120.3.4},
pmid = {35391162},
issn = {1175-5334},
mesh = {Animals ; Costa Rica ; *Diptera ; },
abstract = {A collection of 16,521 barcoded phorid flies from rea de Conservacin Guanacaste (ACG) in northwestern Costa Rica contains 1,498 recognized BINs (Barcode Index Numbers) in the BOLD database. These BINs were identified to genus, based on photographs, and the collection was found to be composed largely (893/1,498=60%) of specimens of the enormous genus Megaselia Rondani. The nine most common ACG Megaselia, represented by 100 or more specimens each, are briefly described, and diagnosed largely based on DNA barcodes. This study is a prelude and pilot to naming the many less-common species in a similar format.},
}
@article {pmid35391083,
year = {2022},
author = {Liu, H and Liu, T},
title = {Two new species of Bucculatrix Zeller from southeast China (Lepidoptera: Bucculatricidae).},
journal = {Zootaxa},
volume = {5100},
number = {1},
pages = {137-144},
doi = {10.11646/zootaxa.5100.1.8},
pmid = {35391083},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; China ; Genitalia ; Genitalia, Male ; *Lepidoptera ; Male ; *Moths ; },
abstract = {Two new species of the genus Bucculatrix Zeller, 1839, B. coadnata sp. n. and B. nigerivalva sp. n., from southeast China are described herein. Male adult and genitalia are described and illustrated. Both species share remarkably reduced and/or fused valva in the male genitalia. DNA barcodes of the holotypes are also provided for aiding species identification.},
}
@article {pmid35390955,
year = {2021},
author = {Unap, E and Choi, SW and Matov, A and Tammaru, T},
title = {Description of Nola estonica sp. nov., with comparison to N. aerugula and N. atomosa stat. rev. (Lepidoptera, Nolidae, Nolinae).},
journal = {Zootaxa},
volume = {5082},
number = {5},
pages = {401-424},
doi = {10.11646/zootaxa.5082.5.1},
pmid = {35390955},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Genitalia ; *Lepidoptera ; *Moths ; Phylogeny ; },
abstract = {Nola estonica unap sp. nov. (Lepidoptera, Nolidae, Nolinae) is described based on type material from Estonia. The lectotype is designated for Glaphyra atomosa Bremer, 1861, which is reinstated from a subspecies of Nola aerugula (Hbner, [1793]) to a full species: Nola atomosa (Bremer, 1861) stat. rev. The status of these three taxa as separate species is supported by the results of phylogenetic analysis of DNA barcodes, as well as external and genital morphology of adult specimens. Two new synonyms are established as follows: Nola atomosa (Bremer, 1861) = Nola candidalis Staudinger, 1892 syn. nov. and Nola shin Inoue, 1982 syn. nov. N. estonica occurs sympatrically with N. aerugula in Estonia, and with N. atomosa in South Korea and easternmost Russia. While the available data suggest a disjunct distribution of N. estonica (eastern Europe and the temperate Far East), it appears highly possible that the species has a wide transpalaearctic distribution.},
}
@article {pmid35390954,
year = {2021},
author = {Pei, V and Zawal, A and Saboori, A and Smit, H},
title = {New records of water mites (Acari, Hydrachnidia) from Iran with the description of one new species based on morphology and DNA barcodes.},
journal = {Zootaxa},
volume = {5082},
number = {5},
pages = {425-440},
doi = {10.11646/zootaxa.5082.5.2},
pmid = {35390954},
issn = {1175-5334},
mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic ; Iran ; *Mites/anatomy &amp; histology/genetics ; Water ; },
abstract = {In this study, based on morphology and DNA barcodes, new records of water mites (Acari, Hydrachnidia) collected in August 2017 in North Iran are presented. Hydrodroma golestanica n. sp. (Hydrodromidae) is described as new for science. We also resurrect three previously synonymized species: Sperchon amuzgari Bader Sepasgosarian, 1979 (Sperchontidae), Monatractides persicus Pei Saboori, 2004 and Torrenticola baueri Bader Sepasgozarian, 1987 (Torrenticolidae).},
}
@article {pmid35390953,
year = {2021},
author = {Budashkin, Y and Richter, I},
title = {New records of Cochylini moths (Lepidoptera: Tortricidae) from the Balkans.},
journal = {Zootaxa},
volume = {5082},
number = {5},
pages = {441-456},
doi = {10.11646/zootaxa.5082.5.3},
pmid = {35390953},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Balkan Peninsula ; Genitalia ; *Lepidoptera ; Male ; *Moths/genetics ; },
abstract = {In the course of expeditions conducted on the Balkan Peninsula by Ignc Richter in 20042019, altogether 45 species of Cochylini moths were collected. The examination of the collected specimens revealed one new species of the genus Aethes: Aethes larissae sp. nov., from the North Macedonia. Additionally, a new subspecies, Aethes kindermanniana macedonica ssp. nov. is described from the North Macedonia too. Phtheochroa amasiana (Ragonot, 1894) and Cochylimorpha erlebachi Huemer Trematerra, 1997 are recorded from the Balkans for the first time. A male of Aethes eichleri Razowski, 1983 is collected for the first time, and DNA barcoding data of this species was obtained. We established a new synonymy: Aethes eichleri Razowski, 1983 syn. nov. of Aethes francillana (Fabricius, 1794). Illustrations of specimens and photographs of the genitalia of all described taxa are provided.},
}
@article {pmid35390872,
year = {2021},
author = {Chen, J and Zhang, R},
title = {Two new species of subgenus Tripodura Towns (Diptera, Chironomidae, Polypedilum) from Oriental China.},
journal = {Zootaxa},
volume = {5072},
number = {2},
pages = {191-199},
doi = {10.11646/zootaxa.5072.2.8},
pmid = {35390872},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; China ; *Chironomidae/genetics ; Cities ; *Diptera ; Male ; },
abstract = {P. (T.) anningense sp. n. and P. (T.) biloborum sp. n. are described and illustrated as male imagines from Oriental China. DNA barcodes of two new species are also presented. A key to known male imagines of the subgenus Tripodura from China is given.},
}
@article {pmid35390870,
year = {2021},
author = {Mahecha-J, O and Florczyk, K and Willmott, K and Cerdea, J and Zubek, A and Boyer, P and Farfn, J and Lachowska-Cierlik, D and Pyrcz, TW},
title = {Solving the cryptic diversity of the genus Manerebia Staudinger in northern Peru: description of new species and considerations on the biogeographical role of the Huancabamba Deflection (Nymphalidae: Satyrinae: Pronophilina).},
journal = {Zootaxa},
volume = {5072},
number = {3},
pages = {201-237},
doi = {10.11646/zootaxa.5072.3.1},
pmid = {35390870},
issn = {1175-5334},
mesh = {Animals ; Biodiversity ; *Butterflies ; Peru ; Phylogeny ; Wings, Animal ; },
abstract = {The Huancabamba Deflection in the Andes of northern Peru and southern Ecuador is a pivotal area for Neotropical biogeography, where exceptional biodiversity coincides with high rates of endemism. These characteristics are well illustrated within the montane butterfly genus Manerebia Staudinger (Nymphalidae, Satyrinae). Here, six new, apparently endemic species, and two new subspecies, are described from this region: M. inducta Pyrcz Willmott n. sp., M. ronda Pyrcz Boyer, n. sp., M. ronda amplia Pyrcz Boyer, n. ssp., M. punku Pyrcz Farfn n. sp., M. huamanii Cerdea Pyrcz n. sp., M. placida Pyrcz Willmott n. sp., M. granatus Willmott, Radford Pyrcz n. sp. and M. prattorum udima Pyrcz Boyer, n. ssp. A total of 22 species of Manerebia is reported from the study region, as much as half the total number of species in this genus distributed throughout the tropical Andes. The alpha-taxonomy of Manerebia is particularly demanding, as colour patterns have apparently converged among different species making identification virtually impossible in some cases without comparison of their genitalia, which prove taxonomically and phylogenetically highly valuable. On the other hand, several species differ markedly in wing colour patterns and occur at different elevations but have identical genitalia. Furthermore, our data show that DNA barcoding is only partly viable as an alpha-taxonomic tool, as some markedly different species of Manerebia, in terms of external morphology and ecological preferences, are genetically not separable using only COI markers. On the other hand, several species barely differing morphologically are identified based on barcode. Barcodes of 26 species, including 18 from the northern Andes, are studied here, showing strong differences within some taxa previously considered conspecific based on morphological characters, suggesting that their taxonomic status needs to be re-evaluated. In particular, M. trimaculata and the widely distributed polytypic M. inderena may be highly variable species or complexes of several species. A total of 16 species are found north of the Chamaya valley in southern Ecuador and extreme northern Peru, compared to 14 species south of it in northern Peru. The faunal (Jaccard) similarity coefficient of the two adjacent regions is low (0.3), reflecting the role of the Huancabamba Deflection as a biogeographical barrier.},
}
@article {pmid35390846,
year = {2021},
author = {Han, WU and Liu, J and Luo, Y and Tang, H},
title = {No longer endemic to Africa: Kribiodosis Kieffer, 1921 (Diptera, Chironomidae) new to Oriental China with a phylogeny and expanded adult generic diagnoses.},
journal = {Zootaxa},
volume = {5072},
number = {6},
pages = {560-574},
doi = {10.11646/zootaxa.5072.6.4},
pmid = {35390846},
issn = {1175-5334},
mesh = {Africa ; Animals ; Bayes Theorem ; China ; *Chironomidae/genetics ; *Diptera ; Female ; Male ; Phylogeny ; Pupa ; },
abstract = {Kribiodosis Kieffer, 1921, an African genus of Chironomini (Diptera: Chironomidae), is newly recorded from the Oriental region through a new species K. cantonensis sp. n. Detailed descriptions of the male, female and a DNA barcode are provided. With the inclusion of the new species bearing scutal tubercle and fused tibial comb, the generic diagnosis needs revision and expansion. The phylogenetic position of Kribiodosis within the tribe Chironomini is explored based on five concatenated genetic makers (18S, 28S, CAD1, CAD4 and COI-3P) using both mixed-model Bayesian inference and maximum likelihood methods. Kribiodosis is placed as a core member of the Microtendipes group but its precise sister group remains unclear. Inclusion of the analysis of Nilodosis Kieffer, another Chironomini genus with an African-Oriental distribution, reveals an unexpected robust position as sister to a large and diverse inclusive group of many Chironomini.},
}
@article {pmid35390828,
year = {2022},
author = {Stadie, D and Fiebig, R and Rajaei, H},
title = {Taxonomic review of the genus Hydria Hbner, 1822 (Lepidoptera, Geometridae, Larentiinae) in the Middle East, with description of three new species and one new subspecies.},
journal = {Zootaxa},
volume = {5092},
number = {5},
pages = {501-530},
doi = {10.11646/zootaxa.5092.5.1},
pmid = {35390828},
issn = {1175-5334},
mesh = {Animals ; Ecosystem ; Genitalia ; *Lepidoptera ; Middle East ; *Moths ; Wings, Animal ; },
abstract = {The species of the genus Hydria in the Middle East are revised. The revision is based on morphological examination and genetic data (DNA-barcode). Additionally, information on the habitat preference, pre-imaginal stages and biology of the species are given as much as available. Three species (H. gernoti sp. n., H. schachti sp. n., H. loebeli sp. n.) and one subspecies (Hydria cervinalis taurica ssp. n.) are described as new to science. The taxonomic status of Hydria hyrcana (Staudinger, 1871) as bona species could be confirmed. The East African species, Hydria relicta (Herbulot. 1953) comb. n., is transferred from genus Rheumaptera to Hydria. Wing pattern and genitalia structures of all discussed species are illustrated.},
}
@article {pmid35390811,
year = {2022},
author = {Peng, H and Lin, Y and Chen, H},
title = {Morphological and molecular evidence of eight new species of the genus Scaptodrosophila Duda (Diptera, Drosophilidae) from China.},
journal = {Zootaxa},
volume = {5093},
number = {2},
pages = {169-194},
doi = {10.11646/zootaxa.5093.2.3},
pmid = {35390811},
issn = {1175-5334},
mesh = {Animals ; China ; DNA ; DNA Barcoding, Taxonomic ; *Drosophilidae ; Phylogeny ; },
abstract = {By integrating morphological and molecular evidences, seven new species of the Scaptodrosophila coracina species group and one new species of uncertain affinity to this genus from China are recognized and described: S. angustifolia sp. nov., S. apunctata sp. nov., S. latifoliacea sp. nov., S. longiciliata sp. nov., S. melanovittata sp. nov., S. polytricapillum sp. nov., S. undulata sp. nov. and S. curvata sp. nov. A key to the examined species is provided. Intra- and interspecific, pairwise p-distances with DNA barcodes (partial sequences of the mitochondrial COI, i.e., cytochrome c oxidase subunit I gene) are calculated and summarized. In addition, S. zebrina Liu Chen, 2018 from Yunnan, China is recognized as junior homonym of S. zebrina (Bezzi, 1928) and renamed as S. zebromyia nom. nov.},
}
@article {pmid35386194,
year = {2022},
author = {Dimitriu, MA and Lazar-Contes, I and Roszkowski, M and Mansuy, IM},
title = {Single-Cell Multiomics Techniques: From Conception to Applications.},
journal = {Frontiers in cell and developmental biology},
volume = {10},
number = {},
pages = {854317},
pmid = {35386194},
issn = {2296-634X},
abstract = {Recent advances in methods for single-cell analyses and barcoding strategies have led to considerable progress in research. The development of multiplexed assays offers the possibility to conduct parallel analyses of multiple factors and processes for comprehensive characterization of cellular and molecular states in health and disease. These technologies have expanded extremely rapidly in the past years and constantly evolve and provide better specificity, precision and resolution. This review summarizes recent progress in single-cell multiomics approaches, and focuses, in particular, on the most innovative techniques that integrate genome, epigenome and transcriptome profiling. It describes the methodologies, discusses their advantages and limitations, and explains how they have been applied to studies on cell heterogeneity and differentiation, and epigenetic reprogramming.},
}
@article {pmid35382009,
year = {2022},
author = {Moura, CJ and Ropa, N and Magalhães, BI and Gonçalves, JM},
title = {Insight into the cryptic diversity and phylogeography of the peculiar fried egg jellyfish Phacellophora (Cnidaria, Scyphozoa, Ulmaridae).},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13125},
pmid = {35382009},
issn = {2167-8359},
mesh = {Animals ; *Cnidaria/genetics ; *Scyphozoa/genetics ; Phylogeography ; Phylogeny ; DNA, Mitochondrial/genetics ; },
abstract = {The fried egg jellyfish Phacellophora camtschatica (senso lato) is a morphologically peculiar and conspicuous species occurring mostly in the cold waters of the North Pacific. It is less common in the cold waters of the NW Atlantic, and occasionally has been reported in the Mediterranean, Arctic, East and South Pacific, and E, SW and NE Atlantic. However, sightings of this scyphozoan jellyfish have intensified during the past two to three decades in Macaronesia, the Iberian Peninsula and the Mediterranean. These jellyfish are known to be voracious predators of other jellies, but also of other taxa, including fish of commercial interest. Therefore, Phacellophora aggregations may threaten local fisheries, aquaculture, and local biodiversity structuring. We report the first known occurrences of Phacellophora in the Azores Islands, which apparently become more frequent in recent years of the past decade. We confirm, through DNA barcoding of COI and 16S mitochondrial markers, the genetic identity of Phacellophora occurring in the Azores (NE Atlantic). We reveal, with COI sequence data, three (potentially four) cryptic species within the Phacellophora camtschatica complex. Two Phacellophora species co-occur in the North Pacific. In the North Atlantic (and possibly in the Mediterranean) one or two distinct species exist. Three nominal species of the genus that are currently synonymized, with type localities in the N Pacific, NW Atlantic, and the Mediterranean, need reassessment. The morphotypes previously defined for the four putative species names given for Phacellophora might be eventually differentiated by the number and disposition of the marginal lappets of umbrellae. This morphologic character has to be further inspected in vouchers of the four genetic lineages of Phacellophora, to decide between the description of new species, and the resurrection of junior synonyms through the designation of neotypes with DNA Barcodes, to validate the identity of the cryptic taxa detected. More haplotype sampling is necessary across the distribution of the genus to further investigate the genetic diversity and phylogeographic history of Phacellophora. The high genetic relatedness of Phacellophora from the cold NW Atlantic and the sub-tropical shores of the Azores, revealed by 16S and COI sequence data, suggests a recent invasion, in terms of geologic time, of the temperate waters of the NE Atlantic (and possibly of the Mediterranean). The medusivorous habits of Phacellophora, and especially its predation on the mauve stinger (Pelagia spp.) which frequently blooms in Macaronesia and Mediterranean waters, could relate to the recent reports of Phacellophora in the Azores, Madeira, Canary Islands, and the Mediterranean. More investment, including on scientific staff, is necessary to catalog, DNA barcode and monitor jellyfish dynamics more accurately worldwide.},
}
@article {pmid35381574,
year = {2022},
author = {Mukai, H and Ogawa, K and Kato, N and Kawakami, S},
title = {Recent advances in lipid nanoparticles for delivery of nucleic acid, mRNA, and gene editing-based therapeutics.},
journal = {Drug metabolism and pharmacokinetics},
volume = {44},
number = {},
pages = {100450},
pmid = {35381574},
issn = {1880-0920},
mesh = {*COVID-19/therapy ; *Gene Editing ; Humans ; Lipids ; Liposomes ; Nanoparticles ; RNA, Messenger/genetics ; },
abstract = {Lipid nanoparticles (LNPs) are becoming popular as a means of delivering therapeutics, including those based on nucleic acids and mRNA. The mRNA-based coronavirus disease 2019 vaccines are perfect examples to highlight the role played by drug delivery systems in advancing human health. The fundamentals of LNPs for the delivery of nucleic acid- and mRNA-based therapeutics, are well established. Thus, future research on LNPs will focus on addressing the following: expanding the scope of drug delivery to different constituents of the human body, expanding the number of diseases that can be targeted, and studying the change in the pharmacokinetics of LNPs under physiological and pathological conditions. This review article provides an overview of recent advances aimed at expanding the application of LNPs, focusing on the pharmacokinetics and advantages of LNPs. In addition, analytical techniques, library construction and screening, rational design, active targeting, and applicability to gene editing therapy have also been discussed.},
}
@article {pmid35380614,
year = {2022},
author = {Liu, Y and Wang, T and Duggan, B and Sharpnack, M and Huang, K and Zhang, J and Ye, X and Johnson, TS},
title = {SPCS: a spatial and pattern combined smoothing method for spatial transcriptomic expression.},
journal = {Briefings in bioinformatics},
volume = {23},
number = {3},
pages = {},
pmid = {35380614},
issn = {1477-4054},
support = {P20 GM121176/GM/NIGMS NIH HHS/United States ; },
mesh = {Gene Expression Profiling/methods ; RNA ; Sequence Analysis, RNA/methods ; *Single-Cell Analysis/methods ; Software ; *Transcriptome ; },
abstract = {High-dimensional, localized ribonucleic acid (RNA) sequencing is now possible owing to recent developments in spatial transcriptomics (ST). ST is based on highly multiplexed sequence analysis and uses barcodes to match the sequenced reads to their respective tissue locations. ST expression data suffer from high noise and dropout events; however, smoothing techniques have the promise to improve the data interpretability prior to performing downstream analyses. Single-cell RNA sequencing (scRNA-seq) data similarly suffer from these limitations, and smoothing methods developed for scRNA-seq can only utilize associations in transcriptome space (also known as one-factor smoothing methods). Since they do not account for spatial relationships, these one-factor smoothing methods cannot take full advantage of ST data. In this study, we present a novel two-factor smoothing technique, spatial and pattern combined smoothing (SPCS), that employs the k-nearest neighbor (kNN) technique to utilize information from transcriptome and spatial relationships. By performing SPCS on multiple ST slides from pancreatic ductal adenocarcinoma (PDAC), dorsolateral prefrontal cortex (DLPFC) and simulated high-grade serous ovarian cancer (HGSOC) datasets, smoothed ST slides have better separability, partition accuracy and biological interpretability than the ones smoothed by preexisting one-factor methods. Source code of SPCS is provided in Github (https://github.com/Usos/SPCS).},
}
@article {pmid35379811,
year = {2022},
author = {Wu, LR and Dai, P and Wang, MX and Chen, SX and Cohen, EN and Jayachandran, G and Zhang, JX and Serrano, AV and Xie, NG and Ueno, NT and Reuben, JM and Barcenas, CH and Zhang, DY},
title = {Ensemble of nucleic acid absolute quantitation modules for copy number variation detection and RNA profiling.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {1791},
pmid = {35379811},
issn = {2041-1723},
support = {U01 CA233364/CA/NCI NIH HHS/United States ; R01 CA203964/CA/NCI NIH HHS/United States ; },
mesh = {*Breast Neoplasms/diagnosis/genetics ; *Cell-Free Nucleic Acids ; DNA Copy Number Variations ; Female ; Humans ; Polymerase Chain Reaction ; RNA/analysis ; },
abstract = {Current gold standard for absolute quantitation of a specific DNA sequence is droplet digital PCR (ddPCR), which has been applied to copy number variation (CNV) detection. However, the number of quantitation modules in ddPCR is limited by fluorescence channels, which thus limits the CNV sensitivity due to sampling error following Poisson distribution. Here we develop a PCR-based molecular barcoding NGS approach, quantitative amplicon sequencing (QASeq), for accurate absolute quantitation scalable to over 200 quantitation modules. By attaching barcodes to individual target molecules with high efficiency, 2-plex QASeq exhibits higher and more consistent conversion yield than ddPCR in absolute molecule count quantitation. Multiplexed QASeq improves CNV sensitivity allowing confident distinguishment of 2.05 ploidy from normal 2.00 ploidy. We apply multiplexed QASeq to serial longitudinal plasma cfDNA samples from patients with metastatic ERBB2+ (HER2+) breast cancer seeking association with tumor progression. We further show an RNA QASeq panel for targeted expression profiling.},
}
@article {pmid35377521,
year = {2022},
author = {Zhan, SH and Chen, L and Liao, CP and Chang, WR and Li, CC and Tang, GY and Liou, CY and Wang, WL and Wang, SW and Liu, SL},
title = {Geographic distance, sedimentation, and substrate shape cryptic crustose coralline algal assemblages in the world's largest subtropical intertidal algal reef.},
journal = {Molecular ecology},
volume = {31},
number = {11},
pages = {3056-3071},
doi = {10.1111/mec.16455},
pmid = {35377521},
issn = {1365-294X},
mesh = {Animals ; *Anthozoa/genetics ; Biodiversity ; *Coral Reefs ; Humans ; Taiwan ; },
abstract = {Algal reefs, concreted by crustose coralline algae (CCA), are the main biotic reefs in temperate waters but rare in the subtropics and tropics. The world's largest known intertidal algal reef in the subtropics is the Taoyuan Algal Reef (TAR) located in the northwestern coast of Taiwan. The biodiversity and ecology of the TAR are scarcely explored, and now the reef is imperiled by industrialization. Here, we document cryptic species of CCA in Taiwan, particularly the TAR, by sequencing the psbA genes of over 1800 specimens collected across Taiwan. We also examine the ecological background of the TAR by surveying its benthic composition and measuring its environmental parameters. Our data reveal that the TAR harbours a high diversity of cryptic CCA species (27 molecular operational taxonomic units, or mOTUs), many of which are potentially new to science (18 mOTUs) and/or endemic to the TAR (9 mOTUs). Comparing the CCA species inventory of the TAR with the rest of Taiwan shows that the TAR represents a unique hotspot of CCA taxa in the waters of Taiwan. Our analyses show that variation in the CCA assemblages in the TAR is associated with geographic distance, sedimentation, and substrate type (for example, reef vs. hermit crab shell), suggesting that dispersal limitation and contemporary environmental selection shape the CCA assemblages in the TAR. The data from this study can inform the monitoring of human impacts on the health of the TAR and contribute to our understanding of the ecological processes underlying algal reef development.},
}
@article {pmid35369669,
year = {2022},
author = {Palmer, CM and Wershoven, NL and Martinson, SJ and Ter Hofstede, HM and Kress, WJ and Symes, LB},
title = {Patterns of Herbivory in Neotropical Forest Katydids as Revealed by DNA Barcoding of Digestive Tract Contents.},
journal = {Diversity},
volume = {14},
number = {2},
pages = {},
pmid = {35369669},
issn = {1424-2818},
support = {P20 GM103449/GM/NIGMS NIH HHS/United States ; },
abstract = {Many well-studied animal species use conspicuous, repetitive signals that attract both mates and predators. Orthopterans (crickets, katydids, and grasshoppers) are renowned for their acoustic signals. In Neotropical forests, however, many katydid species produce extremely short signals, totaling only a few seconds of sound per night, likely in response to predation by acoustically orienting predators. The rare signals of these katydid species raises the question of how they find conspecific mates in a structurally complex rainforest. While acoustic mechanisms, such as duetting, likely facilitate mate finding, we test the hypothesis that mate finding is further facilitated by colocalization on particular host plant species. DNA barcoding allows us to identify recently consumed plants from katydid stomach contents. We use DNA barcoding to test the prediction that katydids of the same species will have closely related plant species in their stomach. We do not find evidence for dietary specialization. Instead, katydids consumed a wide mix of plants within and across the flowering plants (27 species in 22 genera, 16 families, and 12 orders) with particular representation in the orders Fabales and Laurales. Some evidence indicates that katydids may gather on plants during a narrow window of rapid leaf out, but additional investigations are required to determine whether katydid mate finding is facilitated by gathering at transient food resources.},
}
@article {pmid35369100,
year = {2022},
author = {Wang, G and Bai, X and Chen, X and Ren, Y and Pang, X and Han, J},
title = {Detection of Adulteration and Pesticide Residues in Chinese Patent Medicine Qipi Pill Using KASP Technology and GC-MS/MS.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {837268},
pmid = {35369100},
issn = {2296-861X},
abstract = {Chinese patent medicines (CPMs) are of great value for the prevention and treatment of diseases. However, adulterants and pesticide residues in CPMs have become the "bottleneck" impeding the globalization of traditional Chinese medicine. In this study, 12 batches of commercially available Qipi pill (a famous CPM recorded in Chinese Pharmacopeia) from different manufacturers were investigated to evaluate their authenticity and quality safety. Considering the severely degraded DNA in CPMs, kompetitive allele specific PCR (KASP) technology combined with DNA mini-barcodes was proposed for the quality regulation of a large number of products in CPM market. The residues of four kinds of pesticides including pentachloronitrobenzene (PCNB), hexachlorocyclohexane (HCH), aldrin, and dichlorodiphenyltrichloroethane (DDT) were quantified using gas chromatography and tandem mass spectrometry (GC-MS/MS). The results indicated that in two of the 12 batches of Qipi pill, the main herbal ingredient Panax ginseng was completely substituted by P. quinquefolius, and one sample was partially adulterated with P. quinquefolius. The PCNB residue was detected in 11 batches of Qipi pill, ranging from 0.11 to 0.46 mg/kg, and the prohibited pesticide HCH was present in four samples. Both adulteration and banned pesticides were found in two CPMs. This study suggests that KASP technology combined with DNA mini-barcodes can be used for the quality supervision of large sample size CPMs with higher efficiency but lower cost. Our findings also provide the insight that pesticide residues in CPMs should be paid more attention in the future.},
}
@article {pmid35368674,
year = {2022},
author = {Li, F and Liu, Y and Wang, J and Xin, P and Zhang, J and Zhao, K and Zhang, M and Yun, H and Ma, W},
title = {Comparative Analysis of Chloroplast Genome Structure and Phylogenetic Relationships Among Six Taxa Within the Genus Catalpa (Bignoniaceae).},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {845619},
pmid = {35368674},
issn = {1664-8021},
abstract = {Species within the Genus Catalpa are mostly semievergreen or deciduous trees with opposite or whorled leaves. C. bungei, C. fargesii f. duclouxii and C. fargesii are sources of traditional precious wood in China, known as the "kings of wood". Due to a lack of phenotypic and molecular studies and insufficient sequence information, intraspecific morphological differences, common DNA barcodes and partial sequence fragments cannot clearly reveal the phylogenetic or intraspecific relationships within Catalpa. Therefore, we sequenced the complete chloroplast genomes of six taxa of the genus Catalpa and analyzed their basic structure and evolutionary relationships. The chloroplast genome of Catalpa shows a typical tetrad structure with a total length ranging from 157,765 bp (C. fargesii) to 158,355 bp (C. ovata). The length of the large single-copy (LSC) region ranges from 84,599 bp (C. fargesii) to 85,004 bp (C. ovata), that of the small single-copy (SSC) region ranges from 12,662 bp (C. fargesii) to 12,675 bp (C. ovata), and that of the inverted repeat (IR) regions ranges from 30,252 bp (C. fargesii) to 30,338 bp (C. ovata). The GC content of the six chloroplast genomes were 38.1%. In total, 113 unique genes were detected, and there were 19 genes in IR regions. The 113 genes included 79 protein-coding genes, 30 tRNA genes and four rRNA genes. Five hypervariable regions (trnH-psbA, rps2-rpoC2, rpl22, ycf15-trnl-CAA and rps15) were identified by analyzing chloroplast nucleotide polymorphisms, which might be serve as potential DNA barcodes for the species. Comparative analysis showed that single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) were highly diverse in the six species. Codon usage patterns were highly similar among the taxa included in the present study. In addition to the stop codons, all codons showed a preference for ending in A or T. Phylogenetic analysis of the entire chloroplast genome showed that all taxa within the genus Catalpa formed a monophyletic group, clearly reflecting the relationships within the genus. This study provides information on the chloroplast genome sequence, structural variation, codon bias and phylogeny of Catalpa, which will facilitate future research efforts.},
}
@article {pmid35368141,
year = {2022},
author = {Shittu, OB and Iwaloye, OF and Oloyede, AR and Oni, EO and Ajibola, AT and Arowosegbe, AO and Oluwasanya, GO},
title = {Water safety, antifungal-resistant aflatoxigenic aspergillus flavus and other pathogenic fungi in a community hand-dug wells.},
journal = {Journal of applied microbiology},
volume = {133},
number = {2},
pages = {673-682},
doi = {10.1111/jam.15559},
pmid = {35368141},
issn = {1365-2672},
mesh = {*Aflatoxins/analysis ; Antifungal Agents/analysis/pharmacology ; Aspergillus ; Aspergillus flavus/genetics ; Fungi ; *Penicillium/genetics ; Water ; },
abstract = {AIM: To investigate hand-dug well water used for drinking and domestic purposes in a rural community in Southwest Nigeria for water safety and fungal presence as well as to determine the antifungal resistance and aflatoxigenic potentials of isolated fungi.<br><br>METHODS AND RESULTS: Water samples were analysed for risk of contamination, bacteriological and mycological parameters using a standard sanitary survey checklist and microbiological culturing. Isolates were identified and subjected to antifungal resistance profiling using the diffusion method for susceptibility testing of filamentous fungi. Multidrug-resistant strains were confirmed with DNA barcoding identification. Fungal isolates were screened for aflatoxigenic potentials by culture methods and confirmed by densitometric analysis. From the 23 hand-dug wells assessed, 56.52% had a high risk of contamination (ROC) score, nitrate >50&#x2009;mg/L (73.9%), and the presence of total coliforms (100%), Escherichia coli (43.48%) and fungi (91.3%). Spearman rank correlation coefficient gave a positive and strong correlation between Total Fungi and Faecal Coliform (r&#xa0;=&#xa0;0.701; p&#xa0;=&#xa0;0.016; n&#xa0;=&#xa0;23) at 0.05 significance level (2-tailed). Aspergillus sp. (34%), Penicillium sp. (18%) and Rhizopus sp. (17%) were the most dominant fungal genera. Isolates were resistant to fluconazole (76.19%), ketoconazole (73.80%), clotrimazole (92.86%), griseofulvin (88.09%) and nystatin (100%). Penicillium and Aspergillus (50%) were positive for cultural mycotoxin screening. A strain of antifungal-resistant A. flavus produced aflatoxin B1 (752&#x2009;ppb) and B2 (15&#x2009;ppb).<br><br>SIGNIFICANCE OF THE STUDY: The existence of antifungal-resistant and aflatoxigenic fungi in water used for drinking and domestic purposes shows that filamentous fungi constitute greater threats than previously recognized and this call for a paradigm shift from the perceived safety of untreated hand-dug well-water.},
}
@article {pmid35367996,
year = {2021},
author = {Victoriano-Belvis, AFB and Lao, RG and Morato, MKT and Repotente, ECT and Saclauso, SA and Inovejas, SAB and Matias, RR},
title = {A Preliminary Investigation on the Antiviral Activities of the Philippine Marshmint (Mentha arvensis) Leaf Extracts against Dengue Virus Serotype 2 In Vitro.},
journal = {The Kobe journal of medical sciences},
volume = {67},
number = {3},
pages = {E98-E111},
pmid = {35367996},
issn = {1883-0498},
mesh = {Animals ; Antiviral Agents/pharmacology ; Chlorocebus aethiops ; *Dengue Virus ; *Mentha ; Philippines ; Plant Extracts/pharmacology ; Serogroup ; Vero Cells ; },
abstract = {In this study, we investigated the antiviral activity of lyophilized crude leaf extracts of the Philippine marshmint (Mentha arvensis L., commonly called yerba buena) against DENV-2 in vitro. The plant specimen was authenticated by DNA barcoding analysis using standard primers for amplification of rbcL, matK, ITS1, ITS2 and trnH-psbA. Aqueous, methanol and ethanol leaf extracts were prepared, and lyophilized prior to testing for its cytotoxicity and antiviral activities. All extracts presented cytotoxic activities against Vero cells in a dose-dependent manner. Half maximal cytotoxicity concentration (CC50) was calculated at 2,889.60 µg/mL for the aqueous extract, 1,928.62 µg/mL for the methanol extract, and 3,380.30 µg/mL for the ethanol extract. Antiviral activities assessed by plaque reduction assay revealed reduced DENV-2 viral infectivity, with the ethanol extract observed to have the strongest activity decreasing plaque numbers by 62% relative to the control. The methanol extract was observed to be most effective when added before infection causing 72% reduction in plaque numbers, whereas none of the extracts inhibited plaque formation by more than 40% when added after infection. DENV-2 NS1 antigen production was significantly reduced by the methanol extract, while viral RNA levels were also decreased as determined by real time RT-PCR. Phytochemical analysis revealed the presence of flavonoids, phenolics, tannins, proteins, reducing sugars and saponins. Our preliminary results are promising, however, it should be interpreted with caution as further studies are needed to establish its potential therapeutic application against dengue infection.},
}
@article {pmid35365192,
year = {2022},
author = {Papaiakovou, M and Littlewood, DTJ and Doyle, SR and Gasser, RB and Cantacessi, C},
title = {Worms and bugs of the gut: the search for diagnostic signatures using barcoding, and metagenomics-metabolomics.},
journal = {Parasites &amp; vectors},
volume = {15},
number = {1},
pages = {118},
pmid = {35365192},
issn = {1756-3305},
support = {/WT_/Wellcome Trust/United Kingdom ; MR/T020733/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract ; Metabolomics ; Metagenomics ; *Microbiota ; },
abstract = {Gastrointestinal (GI) helminth infections cause significant morbidity in both humans and animals worldwide. Specific and sensitive diagnosis is central to the surveillance of such infections and to determine the effectiveness of treatment strategies used to control them. In this article, we: (i) assess the strengths and limitations of existing methods applied to the diagnosis of GI helminth infections of humans and livestock; (ii) examine high-throughput sequencing approaches, such as targeted molecular barcoding and shotgun sequencing, as tools to define the taxonomic composition of helminth infections; and (iii) discuss the current understanding of the interactions between helminths and microbiota in the host gut. Stool-based diagnostics are likely to serve as an important tool well into the future; improved diagnostics of helminths and their environment in the gut may assist the identification of biomarkers with the potential to define the health/disease status of individuals and populations, and to identify existing or emerging anthelmintic resistance.},
}
@article {pmid35363869,
year = {2021},
author = {Hilton, LK and Scott, DW},
title = {Harnessing Mitochondrial Mutations to ATAC Clonal Evolution in CLL.},
journal = {Cancer discovery},
volume = {11},
number = {12},
pages = {2965-2967},
doi = {10.1158/2159-8290.CD-21-1225},
pmid = {35363869},
issn = {2159-8290},
mesh = {Clonal Evolution/genetics ; Humans ; *Leukemia, Lymphocytic, Chronic, B-Cell/genetics ; Mutation ; Sequence Analysis, DNA/methods ; Transposases/genetics ; },
abstract = {In this issue of Cancer Discovery, Penter and colleagues describe the results of applying the recently described technology of combined assay for transposase-accessible chromatin using sequencing and mitochondrial DNA sequencing in single cells from serial samples from nine patients with chronic lymphocytic leukemia. The naturally occurring barcodes, provided by mitochondrial DNA mutations, allowed tracking of subclones with distinct chromatin accessibility profiles and copy-number alterations demonstrating distinct patterns of tumor evolution under a range of selection pressures. See related article by Penter et al., p. 3048.},
}
@article {pmid35361256,
year = {2022},
author = {Janjic, A and Wange, LE and Bagnoli, JW and Geuder, J and Nguyen, P and Richter, D and Vieth, B and Vick, B and Jeremias, I and Ziegenhain, C and Hellmann, I and Enard, W},
title = {Prime-seq, efficient and powerful bulk RNA sequencing.},
journal = {Genome biology},
volume = {23},
number = {1},
pages = {88},
pmid = {35361256},
issn = {1474-760X},
mesh = {Base Sequence ; Gene Library ; *RNA/genetics ; Sequence Analysis, RNA/methods ; Exome Sequencing ; },
abstract = {Cost-efficient library generation by early barcoding has been central in propelling single-cell RNA sequencing. Here, we optimize and validate prime-seq, an early barcoding bulk RNA-seq method. We show that it performs equivalently to TruSeq, a standard bulk RNA-seq method, but is fourfold more cost-efficient due to almost 50-fold cheaper library costs. We also validate a direct RNA isolation step, show that intronic reads are derived from RNA, and compare cost-efficiencies of available protocols. We conclude that prime-seq is currently one of the best options to set up an early barcoding bulk RNA-seq protocol from which many labs would profit.},
}
@article {pmid35360706,
year = {2022},
author = {Wang, EY and Dai, Y and Rosen, CE and Schmitt, MM and Dong, MX and Ferré, EMN and Liu, F and Yang, Y and González-Hernández, JA and Meffre, E and Hinchcliff, M and Koumpouras, F and Lionakis, MS and Ring, AM},
title = {High-throughput identification of autoantibodies that target the human exoproteome.},
journal = {Cell reports methods},
volume = {2},
number = {2},
pages = {},
pmid = {35360706},
issn = {2667-2375},
support = {DP5 OD023088/OD/NIH HHS/United States ; P30 CA016359/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Autoantibodies ; Saccharomyces cerevisiae ; *Lupus Erythematosus, Systemic/genetics ; Autoantigens ; Patient Acuity ; *Polyendocrinopathies, Autoimmune/complications ; },
abstract = {Autoantibodies that recognize extracellular proteins (the exoproteome) exert potent biological effects but are challenging to detect. Here, we developed rapid extracellular antigen profiling (REAP), a high-throughput technique for the comprehensive discovery of exoproteome-targeting autoantibodies. Patient samples are applied to a genetically barcoded yeast surface display library containing 2,688 human extracellular proteins. Antibody-coated yeast are isolated, and sequencing of barcodes is used to identify displayed antigens. To benchmark REAP's performance, we screened 77 patients with autoimmune polyglandular syndrome type 1 (APS-1). REAP sensitively and specifically detected both known and previously unidentified autoantibodies in APS-1. We further screened 106 patients with systemic lupus erythematosus (SLE) and identified numerous autoantibodies, several of which were associated with disease severity or specific clinical manifestations and exerted functional effects on cell signaling ex vivo. These findings demonstrate the utility of REAP to atlas the expansive landscape of exoproteome-targeting autoantibodies and their impacts on patient health outcomes.},
}
@article {pmid35359938,
year = {2022},
author = {DePasquale, EAK and Ssozi, D and Ainciburu, M and Good, J and Noel, J and Villanueva, MA and Couturier, CP and Shalek, AK and Aranki, SF and Mallidi, HR and Griffin, GK and Lane, AA and van Galen, P},
title = {Single-Cell Multiomics Reveals Clonal T-Cell Expansions and Exhaustion in Blastic Plasmacytoid Dendritic Cell Neoplasm.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {809414},
pmid = {35359938},
issn = {1664-3224},
support = {R00 CA218832/CA/NCI NIH HHS/United States ; R37 CA225191/CA/NCI NIH HHS/United States ; },
mesh = {Dendritic Cells ; Humans ; Interferon-alpha/metabolism ; *Myeloproliferative Disorders/metabolism ; *Skin Neoplasms/pathology ; T-Lymphocytes ; },
abstract = {The immune system represents a major barrier to cancer progression, driving the evolution of immunoregulatory interactions between malignant cells and T-cells in the tumor environment. Blastic plasmacytoid dendritic cell neoplasm (BPDCN), a rare acute leukemia with plasmacytoid dendritic cell (pDC) differentiation, provides a unique opportunity to study these interactions. pDCs are key producers of interferon alpha (IFNA) that play an important role in T-cell activation at the interface between the innate and adaptive immune system. To assess how uncontrolled proliferation of malignant BPDCN cells affects the tumor environment, we catalog immune cell heterogeneity in the bone marrow (BM) of five healthy controls and five BPDCN patients by analyzing 52,803 single-cell transcriptomes, including 18,779 T-cells. We test computational techniques for robust cell type classification and find that T-cells in BPDCN patients consistently upregulate interferon alpha (IFNA) response and downregulate tumor necrosis factor alpha (TNFA) pathways. Integrating transcriptional data with T-cell receptor sequencing via shared barcodes reveals significant T-cell exhaustion in BPDCN that is positively correlated with T-cell clonotype expansion. By highlighting new mechanisms of T-cell exhaustion and immune evasion in BPDCN, our results demonstrate the value of single-cell multiomics to understand immune cell interactions in the tumor environment.},
}
@article {pmid35359315,
year = {2022},
author = {Karahan, A and Öztürk, E and Temiz, B and Blanchoud, S},
title = {Studying Tunicata WBR Using Botrylloides anceps.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2450},
number = {},
pages = {311-332},
pmid = {35359315},
issn = {1940-6029},
mesh = {Animals ; Phylogeny ; Research ; *Urochordata ; },
abstract = {Tunicates are marine filter-feeding invertebrates that can be found worldwide and which are the closest phylogenetic group to the vertebrates (Craniata). Of particular interest, colonial tunicates are the only known chordates that can undergo Whole-Body Regeneration (WBR) via vascular budding. In Botrylloides anceps, a fully functional adult regenerates from a fragment of the vascular system in around 2 weeks after amputation. In this chapter, we present protocols to collect B. anceps colonies, confirm their species, breed them in the lab, monitor WBR and perform histological staining on cryosections.},
}
@article {pmid35358691,
year = {2022},
author = {Goto, R and Takano, T and Seike, K and Yamashita, M and Paulay, G and Rodgers, KS and Hunter, CL and Tongkerd, P and Sato, S and Hong, JS and Endo, K},
title = {Stasis and diversity in living fossils: Species delimitation and evolution of lingulid brachiopods.},
journal = {Molecular phylogenetics and evolution},
volume = {175},
number = {},
pages = {107460},
doi = {10.1016/j.ympev.2022.107460},
pmid = {35358691},
issn = {1095-9513},
mesh = {Animals ; Asia, Eastern ; *Fossils ; *Hydrozoa ; Invertebrates/genetics ; Phylogeny ; },
abstract = {The Lingulidae are often considered living fossils, because they have shown little morphological change since the Paleozoic. Limited morphological variation has also made the taxonomic study of living lingulids challenging. We investigated species diversity and phylogenetic relationships of extant lingulids and show that they are substantially more diverse than realized, demonstrating that morphological stasis was commonly accompanied by speciation. Species delimitation based on cytochrome c oxidase subunit I (COI) gene sequences from 194 specimens sampled from East Asia, Australia, Oceania, and the Americas suggested 14-22 species in the lingulids (9-17 species in Lingula and 4-5 species in Glottidia), in contrast to the 11-12 species currently recognized globally in the family. Four-gene phylogenetic analyses supported the sister relationship between Lingula and Glottidia. Within Lingula, L. adamsi, which possesses large, brownish shells, was recovered as sister to all remaining Lingula species, which have more or less greenish shells. Within the greenish Lingula clade, the 'L. anatina' complex was sister to the clade that includes the 'L. reevei' complex. The 'L. anatina' complex was further separated into two major clades with partly separate ranges centered on (i) temperate East Asia, and (ii) the tropical west-central Pacific. Within Glottidia, Pacific species were nested within Atlantic species. Time-calibrated phylogenetic analyses suggested that Lingula likely originated in the early Cretaceous contrary to a previously proposed hypothesis advocating a Cenozoic origin. The separation of Lingula and Glottidia appears to date from the Mesozoic, not from the Carboniferous, contrary to a previous hypothesis. Overall, our results uncovered substantial cryptic diversity in lingulids, which will form the basis for conservation and further taxonomic revision.},
}
@article {pmid35356558,
year = {2022},
author = {Orfinger, AB and Morse, JC and Hix, RL},
title = {Associating life stages and sexes of Nearctic Polycentropus Curtis, 1835 (Trichoptera: Polycentropodidae) using mitochondrial DNA barcoding.},
journal = {Ecology and evolution},
volume = {12},
number = {3},
pages = {e8741},
pmid = {35356558},
issn = {2045-7758},
abstract = {Alpha taxonomy of caddisflies (order Trichoptera) is based primarily on male genital morphology. As such, associations of adult females and other life stages typically require conclusive association with the species' identifiable male. The aim of this study was to use molecular methods to associate females and larvae of Polycentropus species represented in the Nearctic. Analysis of mtCOI sequences using distance- and tree-based methods resulted in the association of larvae for 14 species of Polycentropus (P. alabamensis Hamilton, Harris &amp; Lago, 1990, P. blicklei Ross &amp; Yamamoto 1965, P. carlsoni Morse 1971, P. carolinensis Banks 1905, P. colei Ross 1941, P. confusus Hagen 1861, P. denningi Smith 1962, P. elarus Ross 1944, P. gertschi Denning 1950, Polycentropus halidus Milne 1936, P. maculatus Banks 1908, P. pentus Ross 1941, P. rickeri Yamamoto 1966, and P. variegatus Banks 1900) and females for 2 species (P. carolinensis and P. chelatus Ross &amp; Yamamoto 1965). Searches for, and descriptions of, diagnostic morphological characters for these previously unidentifiable life forms are now possible. The identity of the larva of P. centralis Banks, 1914 is confirmed and some interesting phylogenetic relationships and a possible cryptic species and potential synonyms are implied in the results. Targets for future immature- and female-male associations are discussed along with a preliminary assessment of morphological differences among larvae.},
}
@article {pmid35347184,
year = {2022},
author = {Guimarães, KLA and Lima, MP and Santana, DJ and de Souza, MFB and Barbosa, RS and Rodrigues, LRR},
title = {DNA barcoding and phylogeography of the Hoplias malabaricus species complex.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {5288},
pmid = {35347184},
issn = {2045-2322},
mesh = {Animals ; *Characiformes/genetics ; *DNA Barcoding, Taxonomic ; Fresh Water ; Phylogeography ; Rivers ; },
abstract = {Hoplias malabaricus (Bloch, 1794) is a carnivorous fish species widely distributed from northern to southern South America. This taxon is believed to be a good model for the investigation of biogeographic events that shape the ichthyofauna evolution in the Neotropical freshwater systems. However, many studies have revealed that H. malabaricus hides a species complex that hampers its taxonomic identity and limit its practical value for evolutionary and biogeographic studies. In this paper, we used the mitochondrial gene cytochrome c oxidase subunit I (COI) to delimit cryptic species and explore the phylogeography of H. malabaricus sensu stricto. We found genetic evidence for putative new species in the genus Hoplias and showed that H. malabaricus (Bloch, 1794) is a major clade assigned to barcode index number (BIN) BOLD:ABZ3047. This species is structured in six subpopulations differentiated by high Fst values and restricts gene flow. The subpopulations of the São Francisco/East Atlantic/Eastern Northeast Atlantic/Parnaíba/Itapecuru River basins and Tapajós River Basin were the most differentiated and showed demographic fluctuations. The present distributional pattern is most likely explained through a scenario from the Pleistocene.},
}
@article {pmid35344171,
year = {2022},
author = {Grassmann, S and Sun, JC and Buchholz, VR},
title = {Retrogenic Color-Barcoding for Fate Mapping of Single Innate Lymphocytes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2463},
number = {},
pages = {117-127},
pmid = {35344171},
issn = {1940-6029},
support = {P30 CA008748/CA/NCI NIH HHS/United States ; },
mesh = {*Hematopoiesis ; *Hematopoietic Stem Cells ; Killer Cells, Natural ; },
abstract = {Lymphocyte fate mapping using single-cell transfers has been used to study T and B cell differentiation. Recently, retrogenic color-barcoding has allowed the extension of this approach to single innate lymphocytes such as NK cells. This new and versatile technology is based on the transduction of hematopoietic stem cells (HSCs) with a collection of retroviruses encoding distinct fluorescent proteins. Through combinatorial transduction, fluorescent protein barcodes are generated, which are inherited by the progeny of HSCs after transfer. By sorting individual cells expressing unique color-barcodes from the mature lymphocyte populations derived from these HSCs, it is now possible to track the fate of innate lymphocytes in vivo.},
}
@article {pmid35343423,
year = {2022},
author = {Yeo, H and Harjoko, DN and Rheindt, FE},
title = {Double trouble: untangling mixed sequence signals in bird samples with avian haemosporidian co-infections.},
journal = {Parasitology},
volume = {},
number = {},
pages = {1-12},
doi = {10.1017/S0031182022000245},
pmid = {35343423},
issn = {1469-8161},
abstract = {Blood parasites comprise some of the most prevalent pathogens in nature, and their detection and identification are major objectives in varied fields such as ecology and biomedicine. Two approaches were compared, one based on Sanger sequencing and the other next-generation sequencing (NGS) based, in terms of their performance in detecting avian blood parasites across tropical Southeast Asian birds. Across a panel of 528 bird individuals, 43 birds were ascertained to be infected with avian haemosporidians using a polymerase chain reaction-based detection method. Among these samples, NGS-based barcoding confirmed co-infections by multiple blood parasites in all eight cases where Sanger sequencing produced double peaks. Importantly however, the NGS-based method produced another five diagnoses of co-infections (62.5%) in which Sanger-based barcoding remained equivocal. In contrast to Sanger sequencing, the NGS-based method was able to identify co-infecting haemosporidian lineages via their barcodes. The accuracy of avian haemosporidian lineage identification was not compromised by the shorter length of NGS sequences, with ~94% of NGS barcodes producing matches identical to those of the Sanger barcodes. The application of NGS-based barcoding methods promises to enhance parasite identification and reduce erroneous inferences based on artefacts.},
}
@article {pmid35341040,
year = {2022},
author = {Berba, CMP and Matias, AMA},
title = {State of biodiversity documentation in the Philippines: Metadata gaps, taxonomic biases, and spatial biases in the DNA barcode data of animal and plant taxa in the context of species occurrence data.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13146},
pmid = {35341040},
issn = {2167-8359},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Philippines ; *Metadata ; Biodiversity ; Documentation ; Bias ; },
abstract = {Anthropogenic changes in the natural environment have led to alarming rates of biodiversity loss, resulting in a more urgent need for conservation. Although there is an increasing cognizance of the importance of incorporating biodiversity data into conservation, the accuracy of the inferences generated from these records can be highly impacted by gaps and biases in the data. Because of the Philippines' status as a biodiversity hotspot, the assessment of potential gaps and biases in biodiversity documentation in the country can be a critical step in the identification of priority research areas for conservation applications. In this study, we systematically assessed biodiversity data on animal and plant taxa found in the Philippines by examining the extent of metadata gaps, taxonomic biases, and spatial biases in DNA barcode data while using species occurrence data as a backdrop of the 'Philippines' biodiversity. These barcode and species occurrence datasets were obtained from public databases, namely: GenBank, Barcode of Life Data System and Global Biodiversity Information Facility. We found that much of the barcode data had missing information on either records and publishing, geolocation, or taxonomic metadata, which consequently, can limit the usability of barcode data for further analyses. We also observed that the amount of barcode data can be directly associated with the amount of species occurrence data available for a particular taxonomic group and location-highlighting the potential sampling biases in the barcode data. While the majority of barcode data came from foreign institutions, there has been an increase in local efforts in recent decades. However, much of the contribution to biodiversity documentation only come from institutions based in Luzon.},
}
@article {pmid35336835,
year = {2022},
author = {Kostas, S and Hatzilazarou, S and Pipinis, E and Bourgou, S and Ben Haj Jilani, I and Ben Othman, W and Megdiche-Ksouri, W and Ghrabi-Gammar, Z and Libiad, M and Khabbach, A and El Haissoufi, M and Lamchouri, F and Koundourakis, E and Greveniotis, V and Papaioannou, E and Sakellariou, MA and Anestis, I and Tsoktouridis, G and Krigas, N},
title = {DNA Barcoding, GIS-Facilitated Seed Germination and Pilot Cultivation of Teucrium luteum subsp. gabesianum (Lamiaceae), a Tunisian Local Endemic with Potential Medicinal and Ornamental Value.},
journal = {Biology},
volume = {11},
number = {3},
pages = {},
pmid = {35336835},
issn = {2079-7737},
support = {no. 618127.//ARIMNet2 (ERA-NET) from the European Union's Seventh Framework Programme for research, technological development, and demonstration/ ; },
abstract = {In the context of plant conservation and sustainable use of unique neglected and underutilized phytogenetic resources, this study focused on the Tunisian local endemic Teucrium luteum subsp. gabesianum (Lamiaceae). Using Geographical Information Systems and online databases, detailed taxon-specific ecological profiling was produced for the first time, which illustrated the temperature and climate conditions in its wild habitats and facilitated the investigation of how temperature affects its seed germination, thus making its cultivation in anthropogenic environments possible. Following the seed propagation first reported herein (77.5−81.25% at temperatures between 15 and 25 °C), species-specific in situ and ex situ conservation efforts or sustainable exploitation strategies can be enabled. This study also reported for the first time how chemical and integrated nutrient management (INM) fertilizers affect the growth and pilot cultivation of its seedlings (INM more advantageous). The firstly-reported herein DNA barcoding may enable its traceability, allowing future product design. The multidisciplinary approach followed has paved the way to bridge important research gaps hindering conservation efforts and/or the sustainable exploitation of this local Tunisian endemic plant to date. Based on the aforementioned results, the feasibility and readiness timescale for its sustainable exploitation was overviewed and re-evaluated herein, upgrading (>two-fold) its potential value for the medicinal-cosmetic, agro-alimentary, and ornamental-horticultural sectors.},
}
@article {pmid35333964,
year = {2022},
author = {Ferri, G and Corradini, B and Gianfreda, D and Ferrari, F and Silingardi, E},
title = {Two caseworks for one gene: successful species identification from compromised bone materials with the 12S rRNA.},
journal = {International journal of legal medicine},
volume = {136},
number = {5},
pages = {1255-1260},
pmid = {35333964},
issn = {1437-1596},
mesh = {DNA Primers/genetics ; *DNA, Mitochondrial/genetics ; Humans ; Phylogeny ; Polymerase Chain Reaction ; *RNA, Ribosomal/genetics ; },
abstract = {The availability of a reliable molecular assay in species recognition in forensic cases is of paramount importance when visual inspection or morphological methods are not exhaustive, especially from challenging samples. Here, two different caseworks involving bone samples founded during medico-legal outdoor investigations are presented. In order to exclude the human nature of the specimens and to determine the exact species they belong to, we proceeded with the molecular approach trying to generate sequences from the classical mtDNA markers cyt b and COI. However, they both gave critical results. For this reason, a short amplicon of ~ 150 bp of the 12S rRNA gene was used as an alternative.This short fragment was sufficient to identify the biological origin of the bone specimens with a high degree of certainty leading to the exclusion of their human nature. This work highlights the utility of the 12S rRNA and underlines the importance of deepen the choice of alternative shorter markers with respect to the classical ones, in order to achieve species identification even from challenging and degraded material in forensic criminal and wildlife caseworks.},
}
@article {pmid35332171,
year = {2022},
author = {Kirichenko, NI and Zakharov, EV and Lopez-Vaamonde, C},
title = {Tracing the invasion of a leaf-mining moth in the Palearctic through DNA barcoding of historical herbaria.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {5065},
pmid = {35332171},
issn = {2045-2322},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Asia, Eastern ; Genetic Variation ; Haplotypes ; *Moths/genetics ; Phylogeny ; Trees ; },
abstract = {The lime leaf-miner, Phyllonorycter issikii is an invasive micromoth with an unusually higher number of haplotypes in the invaded area (Europe, Western Siberia) compared to its putative native region (East Asia). The origin of the genetic diversity in the neocolonized region remains unclear. We surveyed over 15 thousand herbarium specimens of lime trees (Tilia spp.) collected across the Palearctic over a period of 252 years (1764-2016) looking for preserved larvae within the archival leaf mines. We found 203 herbarium specimens with leaf mines of Ph. issikii collected in East Asia, one of them dating back to 1830, i.e. 133 years before the description of the species. In contrast, only 22 herbarium specimens collected in the West Palearctic in the last three decades (1987-2015) carried leaf mines. DNA barcoding of archival specimens revealed 32 haplotypes out of which 23 were novel (not known from modern populations) and found exclusively in East Asia. Six haplotypes are shared between both native and invaded areas and only two were responsible for the recent invasion of the Western Palearctic. The remarkable number of newly discovered haplotypes in archival populations supports East Asia as the native region and the source area of invasion.},
}
@article {pmid35331133,
year = {2022},
author = {Gong, W and Kim, HJ and Garry, DJ and Kwak, IY},
title = {Single cell lineage reconstruction using distance-based algorithms and the R package, DCLEAR.},
journal = {BMC bioinformatics},
volume = {23},
number = {1},
pages = {103},
pmid = {35331133},
issn = {1471-2105},
support = {2020R1C1C1A01013020//National Research Foundation of Korea/ ; },
mesh = {*Algorithms ; Cell Lineage ; *Software ; },
abstract = {BACKGROUND: DCLEAR is an R package used for single cell lineage reconstruction. The advances of CRISPR-based gene editing technologies have enabled the prediction of cell lineage trees based on observed edited barcodes from each cell. However, the performance of existing reconstruction methods of cell lineage trees was not accessed until recently. In response to this problem, the Allen Institute hosted the Cell Lineage Reconstruction Dream Challenge in 2020 to crowdsource relevant knowledge from across the world. Our team won sub-challenges 2 and 3 in the challenge competition.<br><br>RESULTS: The DCLEAR package contained the R codes, which was submitted in response to sub-challenges 2 and 3. Our method consists of two steps: (1) distance matrix estimation and (2) the tree reconstruction from the distance matrix. We proposed two novel methods for distance matrix estimation as outlined in the DCLEAR package. Using our method, we find that two of the more sophisticated distance methods display a substantially improved level of performance compared to the traditional Hamming distance method. DCLEAR is open source and freely available from R CRAN and from under the GNU General Public License, version 3.<br><br>CONCLUSIONS: DCLEAR is a powerful resource for single cell lineage reconstruction.},
}
@article {pmid35330305,
year = {2022},
author = {Bourret, TB and Fajardo, SN and Engert, CP and Rizzo, DM},
title = {A Barcode-Based Phylogenetic Characterization of Phytophthora cactorum Identifies Two Cosmopolitan Lineages with Distinct Host Affinities and the First Report of Phytophthora pseudotsugae in California.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {3},
pages = {},
pmid = {35330305},
issn = {2309-608X},
support = {N/A//USDA Forest Service, Forest Health Protection/ ; N/A//USDA Forest Service, Pacific Southwest Research Station/ ; N/A//National Fish and Wildlife Association/ ; N/A//Santa Clara Valley Water District/ ; N/A//San Francisco Public Utilities Commission/ ; DEB-1115664//National Science Foundation/ ; ES-1753965//National Science Foundation/ ; N/A//UC Davis Jastro Shields/ ; },
abstract = {A collection of 30 Phytophthora cactorum and 12 P. pseudotsugae (subclade 1a) strains isolated from several recent surveys across California was phylogenetically compared to a worldwide collection of 112 conspecific strains using sequences from three barcoding loci. The surveys baited P. cactorum from soil and water across a wide variety of forested ecosystems with a geographic range of more than 1000 km. Two cosmopolitan lineages were identified within the widespread P. cactorum, one being mainly associated with strawberry production and the other more closely associated with apple orchards, oaks and ornamental trees. Two other well-sampled P. cactorum lineages, including one that dominated Californian restoration outplantings, were only found in the western United States, while a third was only found in Japan. Coastal California forest isolates of both Phytophthora species exhibited considerable diversity, suggesting both may be indigenous to the state. Many isolates with sequence accessions deposited as P. cactorum were determined to be P. hedraiandra and P. ×serendipita, with one hybrid lineage appearing relatively common across Europe and Asia. This study contains the first report of P. pseudotsugae from the state of California and one of the only reports of that species since its original description.},
}
@article {pmid35330277,
year = {2022},
author = {Steinová, J and Holien, H and Košuthová, A and Škaloud, P},
title = {An Exception to the Rule? Could Photobiont Identity Be a Better Predictor of Lichen Phenotype than Mycobiont Identity?.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {3},
pages = {},
pmid = {35330277},
issn = {2309-608X},
support = {204069//Charles University Research Centre/ ; EEA and Norway grants 2014-2021//EEA and Norway grants 2014-2021/ ; },
abstract = {With rare exceptions, the shape and appearance of lichen thalli are determined by the fungal partner; thus, mycobiont identity is normally used for lichen identification. However, it has repeatedly been shown in recent decades that phenotypic data often does not correspond with fungal gene evolution. Here, we report such a case in a three-species complex of red-fruited Cladonia lichens, two of which clearly differ morphologically, chemically, ecologically and in distribution range. We analysed 64 specimens of C. bellidiflora, C. polydactyla and C. umbricola, mainly collected in Europe, using five variable mycobiont-specific and two photobiont-specific molecular markers. All mycobiont markers exhibited very low variability and failed to separate the species. In comparison, photobiont identity corresponded better with lichen phenotype and separated esorediate C. bellidiflora from the two sorediate taxa. These results can be interpreted either as an unusual case of lichen photomorphs or as an example of recent speciation, in which phenotypic differentiation precedes the separation of the molecular markers. We hypothesise that association with different photobionts, which is probably related to habitat differentiation, may have triggered speciation in the mycobiont species.},
}
@article {pmid35328579,
year = {2022},
author = {Gotzhein, F and Aranyossy, T and Thielecke, L and Sonntag, T and Thaden, V and Fehse, B and Müller, I and Glauche, I and Cornils, K},
title = {The Reconstitution Dynamics of Cultivated Hematopoietic Stem Cells and Progenitors Is Independent of Age.},
journal = {International journal of molecular sciences},
volume = {23},
number = {6},
pages = {},
pmid = {35328579},
issn = {1422-0067},
support = {CO 1692/1-1//Deutsche Forschungsgemeinschaft/ ; GL 721/1-1//Deutsche Forschungsgemeinschaft/ ; //Dr. Werner Jackst&#xe4;dt-Stiftung/ ; //Burkhard Meyer Stiftung/ ; },
mesh = {Animals ; Genetic Therapy ; *Hematologic Neoplasms/therapy ; *Hematopoietic Stem Cell Transplantation ; Hematopoietic Stem Cells ; Mice ; },
abstract = {Hematopoietic stem cell transplantation (HSCT) represents the only curative treatment option for numerous hematologic malignancies. While the influence of donor age and the composition of the graft have already been examined in clinical and preclinical studies, little information is available on the extent to which different hematological subpopulations contribute to the dynamics of the reconstitution process and on whether and how these contributions are altered with age. In a murine model of HSCT, we therefore simultaneously tracked different cultivated and transduced hematopoietic stem and progenitor cell (HSPC) populations using a multicolor-coded barcode system (BC32). We studied a series of age-matched and age-mismatched transplantations and compared the influence of age on the reconstitution dynamics. We show that reconstitution from these cultured and assembled grafts was substantially driven by hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs) independent of age. The reconstitution patterns were polyclonal and stable in all age groups independently of the variability between individual animals, with higher output rates from MPPs than from HSCs. Our experiments suggest that the dynamics of reconstitution and the contribution of cultured and individually transduced HSPC subpopulations are largely independent of age. Our findings support ongoing efforts to expand the application of HSCT in older individuals as a promising strategy to combat hematological diseases, including gene therapy applications.},
}
@article {pmid35327998,
year = {2022},
author = {Liu, Y and Chen, Z and Li, J and Zhu, Z and Pang, S and Xu, J and Wu, J},
title = {Extensive Diversity and Prevalent Fluconazole Resistance among Environmental Yeasts from Tropical China.},
journal = {Genes},
volume = {13},
number = {3},
pages = {},
pmid = {35327998},
issn = {2073-4425},
mesh = {Antifungal Agents/pharmacology ; *Drug Resistance, Fungal/genetics ; *Fluconazole/pharmacology ; Humans ; Multilocus Sequence Typing ; Yeasts/genetics ; },
abstract = {Yeasts play important roles in both the environment and in human welfare. While some environmental yeasts positively contribute to nutrient cycling and food production, a significant number of yeast species are opportunistic human pathogens, including several that are tolerant/resistant to commonly used antifungal drugs. At present, most of our understanding of environmental yeasts has come from a few terrestrial environments in selected geographic regions. Relatively little is known about yeast diversity in tropical environments and their potential impacts on human health. Here, we characterize culturable yeasts in 968 environmental samples from eight regions in tropical China. Among the 516 soil, 273 freshwater, and 179 seawater samples, 71.5%, 85.7%, and 43.6% contained yeasts, respectively. A total of 984 yeast isolates were analyzed for their DNA barcode sequences and their susceptibilities to fluconazole. DNA sequence comparisons revealed that the 984 yeast isolates likely belonged to 144 species, including 106 known species and 38 putative novel species. About 38% of the 984 isolates belonged to known human pathogens and the most common species was Candida tropicalis, accounting for 21% (207/984) of all isolates. Further analyses based on multi-locus sequence typing revealed that some of these environmental C. tropicalis shared identical genotypes with clinical isolates previously reported from tropical China and elsewhere. Importantly, 374 of the 984 (38%) yeast isolates showed intermediate susceptibility or resistance to fluconazole. Our results suggest that these environmental yeasts could have significant negative impacts on human health.},
}
@article {pmid35326533,
year = {2022},
author = {Hesin, A and Kumar, S and Gahramanov, V and Becker, M and Vilenchik, M and Alexandrov, I and Yaglom, J and Sherman, MY},
title = {A Cell Double-Barcoding System for Quantitative Evaluation of Primary Tumors and Metastasis in Animals That Uncovers Clonal-Specific Anti-Cancer Drug Effects.},
journal = {Cancers},
volume = {14},
number = {6},
pages = {},
pmid = {35326533},
issn = {2072-6694},
support = {ISF-1444/18, ISF-2465/18//Israel Science Foundation/ ; },
abstract = {Imaging in monitoring metastasis in mouse models has low sensitivity and is not quantitative. Cell DNA barcoding, demonstrating high sensitivity and resolution, allows monitoring effects of drugs on the number of tumor and metastatic clones. However, this technology is not suitable for comparison of sizes of metastatic clones in different animals, for example, drug treated and untreated, due to high biological and technical variability upon tumor and metastatic growth and isolation of barcodes from tissue DNA. However, both numbers of clones and their sizes are critical parameters for analysis of drug effects. Here we developed a modification of the barcoding approach for monitoring drug effects on tumors and metastasis that is quantitative, highly sensitive and highly reproducible. This novel cell double-barcoding system allows simultaneously following the fate of two or more cell variants or cell lines in xenograft models in vivo, and also following the fates of individual clones within each of these populations. This system allows comparing effects of drugs on different cell populations and thus normalizing drug effects by drug-resistant lines, which corrects for both biological and technical variabilities and significantly increases the reproducibility of results. Using this barcoding system, we uncovered that effects of a novel DYRK1B kinase inhibitor FX9847 on primary tumors and metastasis is clone-dependent, while a distinct drug osimertinib demonstrated clone-independent effects on cancer cell populations. Overall, a cell double-barcoding approach can significantly enrich our understanding of drug effects in basic research and preclinical studies.},
}
@article {pmid35324380,
year = {2022},
author = {Bizzarri, L and Baer, CS and García-Robledo, C},
title = {DNA Barcoding Reveals Generalization and Host Overlap in Hummingbird Flower Mites: Implications for the Mating Rendezvous Hypothesis.},
journal = {The American naturalist},
volume = {199},
number = {4},
pages = {576-583},
doi = {10.1086/718474},
pmid = {35324380},
issn = {1537-5323},
mesh = {Animals ; Birds ; DNA ; DNA Barcoding, Taxonomic ; Flowers ; *Mites/genetics ; },
abstract = {AbstractHummingbird flower mites are assumed to monopolize single host plant species owing to sexual selection for unique mating rendezvous sites. We tested the main assumption of the mating rendezvous hypothesis-extreme host specialization-by reconstructing interactions among tropical hummingbird flower mites and their host plants using DNA barcoding and taxonomic identifications. We collected 10,654 mites from 489 flowers. We extracted DNA from 1,928 mite specimens and amplified the cytochrome c oxidase I (CO1) DNA barcode. We analyzed the network structure to assess the degree of generalization or specialization of mites to their host plants. We recorded 18 species of hummingbird flower mites from three genera (Proctolaelaps, Rhinoseius, and Tropicoseius) interacting with 14 species of plants. We found that generalist mites are common, and congeneric mite species often share host plants. Our results challenge the assumption of strict specialization that supports this system as an example of mating rendezvous evolution.},
}
@article {pmid35324087,
year = {2022},
author = {Huang, YF and Huang, YC and Lo, YC and Latkin, C and Huang, HY and Lee, CC and Pan, LC and Kuo, HS},
title = {Towards the first 90: impact of the national HIV self-test program on case finding and factors associated with linkage to confirmatory diagnosis in Taiwan.},
journal = {Journal of the International AIDS Society},
volume = {25},
number = {3},
pages = {e25897},
pmid = {35324087},
issn = {1758-2652},
mesh = {Adult ; Female ; *HIV Infections/diagnosis/epidemiology/prevention &amp; control ; Homosexuality, Male ; Humans ; Male ; Retrospective Studies ; Self-Testing ; *Sexual and Gender Minorities ; Taiwan/epidemiology ; },
abstract = {INTRODUCTION: Being aware of one's HIV-positive status can help reduce unprotected sex and promote early treatment seeking. Therefore, HIV self-test (HIVST) programs may help control the HIV epidemic by case finding. The aims of this study were to determine the effect of HIVST programs on HIV case finding, time to confirmatory diagnosis and factors associated with linkage to confirmatory diagnosis in Taiwan.<br><br>METHODS: The Centers for Disease Control in Taiwan initiated HIVST programs and imported 78,000 self-test kits in 2017 and 2019. Clients paid 7 US dollars for a self-test kit at facilities, vending machines or online. The programs set up an HIVST logistics management system; each kit had a unique barcode for monitoring the programs because purchases were anonymous. When clients provided their test results with photo barcodes online or at HIV/AIDS-designated hospitals, they received full monetary reimbursement. We conducted a quasi-experimental interrupted time-series (ITS) analysis that covered a period of 60 months from 2015 to 2019. We enrolled a retrospective cohort of reported HIV cases with initial positive results from HIVST programs between March 2017 and July 2020.<br><br>RESULTS: The ITS analysis included data from 10,976 reported HIV cases from 2015 to 2019. The HIVST-positive cohort included 386 reported HIV cases, of whom 99.7% were males and 97% were men who have sex with men (MSM); the median age was 28 years. The ITS analysis showed a positive slope change in the number of reported HIV cases immediately in the beginning implementation month (coefficient: 51.09 in 2017 and 3.62 in 2019), but there was a significant decrease over time. It was a negative slope change by 9.52 cases per month in 2017 and 5.56 cases per month in 2019. In the HIVST-positive cohort, three of five individuals linked to HIV confirmatory diagnosis within 1 month after a positive self-test result, and an early linkage to confirmatory diagnosis was associated with HIVST disclosure (adjusted OR = 6.5; 95% CI: 3.9-10.6).<br><br>CONCLUSIONS: HIVST programs were associated with an increase in HIV case finding. Our findings suggest that countries with a high incidence of HIV among MSM populations should offer multichannel HIVST services.},
}
@article {pmid35323559,
year = {2022},
author = {Ma, Z and Ren, J and Zhang, R},
title = {Identifying the Genetic Distance Threshold for Entiminae (Coleoptera: Curculionidae) Species Delimitation via COI Barcodes.},
journal = {Insects},
volume = {13},
number = {3},
pages = {},
pmid = {35323559},
issn = {2075-4450},
abstract = {The subfamily Entiminae is the largest group in the family Curculionidae, and it has long represented a challenge in traditional and molecular classification. Here, we analyzed intra- and interspecific genetic distances of 621 public COI barcode sequences (658bp) from 39 genera and 110 species of Entiminae, to determine parameters most congruent in retaining established species. We found that the mean intraspecific genetic distance (3.07%) was much smaller than the mean interspecific one (21.96%), but there is a wide range of overlap between intra- and interspecific genetic distances (0.77−18.01%), indicating that there is no consistent, universal barcoding gap. Specifically, DNA barcoding gap analysis for morphospecies revealed that 102 of 110 morphospecies had barcoding gaps, and 9.18% was the optimum threshold of genetic distances for 97 species delimitation. We further confirmed this threshold with barcodes from 27 morphologically identified specimens (including 21 newly reported barcodes) sequenced from five genera and seven species. We also identified thresholds to delimit congeneric species within 14 selected genera (species > 2), which varied from 7.42% (Trichalophus) to 13.48% (Barypeithes). We herein present optimal parameters for species identification in the Entiminae. Our study suggests that despite no universal genetic distance threshold value in subfamily Entiminae, 9.18% is optimal for most species. We recommend a wider sampling of geographic populations to better account for intraspecific distance variation, and that genetic distance thresholds for species delimitation should be refined at the genus level.},
}
@article {pmid35322263,
year = {2022},
author = {Bizzotto, S and Walsh, CA},
title = {Genetic mosaicism in the human brain: from lineage tracing to neuropsychiatric disorders.},
journal = {Nature reviews. Neuroscience},
volume = {23},
number = {5},
pages = {275-286},
pmid = {35322263},
issn = {1471-0048},
support = {/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Adult ; *Autism Spectrum Disorder/genetics ; Brain ; Humans ; *Mosaicism ; Mutation/genetics ; Retrospective Studies ; },
abstract = {Genetic mosaicism is the result of the accumulation of somatic mutations in the human genome starting from the first postzygotic cell generation and continuing throughout the whole life of an individual. The rapid development of next-generation and single-cell sequencing technologies is now allowing the study of genetic mosaicism in normal tissues, revealing unprecedented insights into their clonal architecture and physiology. The somatic variant repertoire of an adult human neuron is the result of somatic mutations that accumulate in the brain by different mechanisms and at different rates during development and ageing. Non-pathogenic developmental mutations function as natural barcodes that once identified in deep bulk or single-cell sequencing can be used to retrospectively reconstruct human lineages. This approach has revealed novel insights into the clonal structure of the human brain, which is a mosaic of clones traceable to the early embryo that contribute differentially to the brain and distinct areas of the cortex. Some of the mutations happening during development, however, have a pathogenic effect and can contribute to some epileptic malformations of cortical development and autism spectrum disorder. In this Review, we discuss recent findings in the context of genetic mosaicism and their implications for brain development and disease.},
}
@article {pmid35320571,
year = {2022},
author = {Gimond, C and Poullet, N and Braendle, C},
title = {Isolating Caenorhabditis elegans from the Natural Habitat.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2468},
number = {},
pages = {283-292},
pmid = {35320571},
issn = {1940-6029},
mesh = {Animals ; *Caenorhabditis elegans/genetics ; *Ecosystem ; Reproduction/genetics ; },
abstract = {Wild populations of the model organism C. elegans represent a valuable resource, allowing for genetic characterization underlying natural phenotypic variation. Here we provide a simple protocol on how to sample and rapidly identify C. elegans wild isolates. We outline how to find suitable habitats and organic substrates, followed by describing isolation and identification of C. elegans live cultures based on easily recognizable morphological characteristics, molecular barcodes, and mating tests. This protocol uses standard laboratory equipment and requires little prior knowledge of C. elegans biology.},
}
@article {pmid35318559,
year = {2022},
author = {Tang, D and Lin, Y and Wei, F and Quan, C and Wei, K and Wei, Y and Cai, Z and Kashif, MH and Miao, J},
title = {Characteristics and comparative analysis of Mesona chinensis Benth chloroplast genome reveals DNA barcode regions for species identification.},
journal = {Functional &amp; integrative genomics},
volume = {22},
number = {4},
pages = {467-479},
pmid = {35318559},
issn = {1438-7948},
support = {2018JJB130096//Natural Science Foundation of Guangxi/ ; 2018GXNSFBA294016//Natural Science Foundation of Guangxi/ ; GuiKe AA18242040//Guangxi Innovation-Driven Development Project/ ; CARS-21//China Agriculture Research System/ ; GuiYaoJi202011//Scientific Research Funding Project of Guangxi Botanical Garden of Medicinal Plants/ ; GuiYaoChuang2019005//"Guangxi Bagui Scholars" and Research Innovation Team Project/ ; },
mesh = {DNA Barcoding, Taxonomic ; *Genome, Chloroplast ; *Lamiaceae/genetics ; Phylogeny ; Plant Breeding ; },
abstract = {Mesona chinensis Benth (MCB) is an important medicinal and edible plant in Southern China and Southeast Asian countries. Chloroplast (cp) genome is usually used for plant phylogeny, species identification, and chloroplast genetic engineering. To characterize the cp genome and determine the evolutionary position and perform the genetic diversity analysis of MCB, we sequence and characterize the MCB cp genome. The results show that the cp genome of MCB is a single circular molecule with a length of 152,635 bp. It is a typical quadripartite structure, comprising a large single-copy region (LSC, 83,514 bp) and a small single-copy region (SSC, 17,751 bp) separated by two inverted repeat regions (IRs, 51,370 bp). It encodes 129 unique genes, including 84 protein-coding genes (PCGs), 37 transfer RNAs (tRNAs), and 8 ribosomal RNAs (rRNAs). Altogether 127 simple sequence repeats (SSRs) are identified in the MCB cp genome with 86.61% of mononucleotide repeats. Phylogenetic analysis reveals that MCB is most closely related to Ocimum basilicum based on the whole cp genomes. Several highly divergent regions are found, such as trnH_psbA, rps16_trnQ, trnS_trnG, trnE_trnT, psaA_ycf3, rpl32_trnL, ccsA_ndhD, ndhG_ndhI, and rps15_ycf1, which can be proposed for use as DNA barcode regions. Genetic diversity analysis unveils a relatively narrow genetic basis of MCB germplasm resources. Therefore, the innovative breeding of MCB is very urgent and necessary in future research.},
}
@article {pmid35317843,
year = {2022},
author = {Wu, HY and Shaw, PC},
title = {Strategies for molecular authentication of herbal products: from experimental design to data analysis.},
journal = {Chinese medicine},
volume = {17},
number = {1},
pages = {38},
pmid = {35317843},
issn = {1749-8546},
abstract = {Molecular herbal authentication has gained worldwide popularity in the past decade. DNA-based methods, including DNA barcoding and species-specific amplification, have been adopted for herbal identification by various pharmacopoeias. Development of next-generating sequencing (NGS) drastically increased the throughput of sequencing process and has sped up sequence collection and assembly of organelle genomes, making more and more reference sequences/genomes available. NGS allows simultaneous sequencing of multiple reads, opening up the opportunity of identifying multiple species from one sample in one go. Two major experimental approaches have been applied in recent publications of identification of herbal products by NGS, the PCR-dependent DNA metabarcoding and PCR-free genome skimming/shotgun metagenomics. This review provides a brief introduction of the use of DNA metabarcoding and genome skimming/shotgun metagenomics in authentication of herbal products and discusses some important considerations in experimental design for botanical identification by NGS, with a specific focus on quality control, reference sequence database and different taxon assignment programs. The potential of quantification or abundance estimation by NGS is discussed and new scientific findings that could potentially interfere with accurate taxon assignment and/or quantification is presented.},
}
@article {pmid35316656,
year = {2022},
author = {Kudo, T and Lane, K and Covert, MW},
title = {A multiplexed epitope barcoding strategy that enables dynamic cellular phenotypic screens.},
journal = {Cell systems},
volume = {13},
number = {5},
pages = {376-387.e8},
doi = {10.1016/j.cels.2022.02.006},
pmid = {35316656},
issn = {2405-4720},
mesh = {Epitopes ; Gene Library ; *High-Throughput Screening Assays/methods ; *Microscopy ; },
abstract = {Pooled genetic libraries have improved screening throughput for mapping genotypes to phenotypes. However, selectable phenotypes are limited, restricting screening to outcomes with a low spatiotemporal resolution. Here, we integrated live-cell imaging with pooled library-based screening. To enable intracellular multiplexing, we developed a method called EPICode that uses a combination of short epitopes, which can also appear in various subcellular locations. EPICode thus enables the use of live-cell microscopy to characterize a phenotype of interest over time, including after sequential stimulatory/inhibitory manipulations, and directly connects behavior to the cellular genotype. To test EPICode's capacity against an important milestone-engineering and optimizing dynamic, live-cell reporters-we developed a live-cell PKA kinase translocation reporter with improved sensitivity and specificity. The use of epitopes as fluorescent barcodes introduces a scalable strategy for high-throughput screening broadly applicable to protein engineering and drug discovery settings where image-based phenotyping is desired.},
}
@article {pmid35314836,
year = {2022},
author = {Madhusoodanan, J},
title = {Molecular barcodes reveal tumour lineages.},
journal = {Nature},
volume = {603},
number = {7902},
pages = {752-754},
pmid = {35314836},
issn = {1476-4687},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; Humans ; *Neoplasms/genetics ; },
}
@article {pmid35313810,
year = {2022},
author = {Fu, N and Ji, M and Rouard, M and Yan, HF and Ge, XJ},
title = {Comparative plastome analysis of Musaceae and new insights into phylogenetic relationships.},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {223},
pmid = {35313810},
issn = {1471-2164},
support = {No. 32070237, 31261140366//National Natural Science Foundation of China/ ; No. 32070237, 31261140366//National Natural Science Foundation of China/ ; No. 32070237, 31261140366//National Natural Science Foundation of China/ ; },
mesh = {Bayes Theorem ; *Magnoliopsida ; *Musa/genetics ; *Musaceae/genetics ; Phylogeny ; },
abstract = {BACKGROUND: Musaceae is an economically important family consisting of 70-80 species. Elucidation of the interspecific relationships of this family is essential for a more efficient conservation and utilization of genetic resources for banana improvement. However, the scarcity of herbarium specimens and quality molecular markers have limited our understanding of the phylogenetic relationships in wild species of Musaceae. Aiming at improving the phylogenetic resolution of Musaceae, we analyzed a comprehensive set of 49 plastomes for 48 species/subspecies representing all three genera of this family.<br><br>RESULTS: Musaceae plastomes have a relatively well-conserved genomic size and gene content, with a full length ranging from 166,782&#xa0;bp to 172,514&#xa0;bp. Variations in the IR borders were found to show phylogenetic signals to a certain extent in Musa. Codon usage bias analysis showed different preferences for the same codon between species and three genera and a common preference for A/T-ending codons. Among the two genes detected under positive selection (dN/dS > 1), ycf2 was indicated under an intensive positive selection. The divergent hotspot analysis allowed the identification of four regions (ndhF-trnL, ndhF, matK-rps16, and accD) as specific DNA barcodes for Musaceae species. Bayesian and maximum likelihood phylogenetic analyses using full plastome resulted in nearly identical tree topologies with highly supported relationships between species. The monospecies genus Musella is sister to Ensete, and the genus Musa was divided into two large clades, which corresponded well to the basic number of n = x = 11 and n = x =10/9/7, respectively. Four subclades were divided within the genus Musa. A dating analysis covering the whole Zingiberales indicated that the divergence of Musaceae family originated in the Palaeocene (59.19&#xa0;Ma), and the genus Musa diverged into two clades in the Eocene (50.70&#xa0;Ma) and then started to diversify from the late Oligocene (29.92&#xa0;Ma) to the late Miocene. Two lineages (Rhodochlamys and Australimusa) radiated recently in the Pliocene /Pleistocene periods.<br><br>CONCLUSIONS: The plastome sequences performed well in resolving the phylogenetic relationships of Musaceae and generated new insights into its evolution. Plastome sequences provided valuable resources for population genetics and phylogenetics at lower taxon.},
}
@article {pmid35312761,
year = {2022},
author = {Suetsugu, K and Matsubayashi, J},
title = {Foliar chlorophyll concentration modulates the degree of fungal exploitation in a rhizoctonia-associated orchid.},
journal = {Journal of experimental botany},
volume = {73},
number = {12},
pages = {4204-4213},
doi = {10.1093/jxb/erac124},
pmid = {35312761},
issn = {1460-2431},
support = {17H05016//Japan Society for the Promotion of Science/ ; },
mesh = {Carbon ; Carbon Isotopes/analysis ; Chlorophyll ; *Mycorrhizae/physiology ; *Orchidaceae/genetics ; Rhizoctonia/physiology ; Symbiosis ; },
abstract = {Some green orchids obtain carbon from both mycobionts and photosynthesis at the adult stage. Intriguingly, these orchids can produce albino and, in rare cases, variegated phenotypes. Here, we studied a Platanthera hondoensis population with green, variegated, and albino individuals. Although its closely related Platanthera species are usually associated with non-ectomycorrhizal rhizoctonias, and several studies have failed to find evidence of trophic plasticity in rhizoctonia-associated orchids, variegated and albino P. hondoensis must possess a higher fungal dependency than green P. hondoensis. Therefore, we investigated whether (i) P. hondoensis is associated with non-ectomycorrhizal rhizoctonias and (ii) the degree of mycoheterotrophy (using 13C abundance as a proxy) correlates with the foliar chlorophyll concentration. High-throughput DNA sequencing revealed that all P. hondoensis phenotypes were dominantly associated with a rhizoctonia from Ceratobasidiaceae belonging to a clade distinct from recognized ectomycorrhizal clades. Regression analysis revealed a positive linear relationship between foliar chlorophyll concentration and the degree of mycoheterotrophy. This study strongly suggests that rhizoctonia-associated P. hondoensis can dynamically adjust fungal exploitation in response to photosynthetic carbon levels. Since rhizoctonia is the most common orchid mycorrhizal partner, trophic plasticity may be a widespread adaptive trait in green orchids.},
}
@article {pmid35311808,
year = {2022},
author = {Crombie, TA and Tanny, RE and Buchanan, CM and Roberto, NM and Andersen, EC},
title = {A Highly Scalable Approach to Perform Ecological Surveys of Selfing Caenorhabditis Nematodes.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {181},
pages = {},
doi = {10.3791/63486},
pmid = {35311808},
issn = {1940-087X},
mesh = {Animals ; *Caenorhabditis/genetics ; Caenorhabditis elegans/genetics ; Male ; Plants ; Reproduction ; },
abstract = {Caenorhabditis elegans is one of the major model organisms in biology, but only recently have researchers focused on its natural ecology. The relative sparsity of information about C. elegans in its natural context comes from the challenges involved in the identification of the small nematode in nature. Despite these challenges, an increasing focus on the ecology of C. elegans has caused a wealth of new information regarding its life outside of the laboratory. The intensified search for C. elegans in nature has contributed to the discovery of many new Caenorhabditis species and revealed that congeneric nematodes frequently cohabitate in the wild, where they feed on microbial blooms associated with rotting plant material. The identification of new species has also revealed that the androdioecious mating system of males and self-fertilizing hermaphrodites has evolved three times independently within Caenorhabditis. The other two selfing species, C. briggsae and C. tropicalis, share the experimental advantages of C. elegans and have enabled comparative studies into the mechanistic basis of important traits, including self-fertilization. Despite these advances, much remains to be learned about the ecology and natural diversity of these important species. For example, we still lack functional information for many of their genes, which might only be attained through an understanding of their natural ecology. To facilitate ecological research of selfing Caenorhabditis nematodes, we developed a highly scalable method to collect nematodes from the wild. Our method makes use of mobile data collection platforms, cloud-based databases, and the R software environment to enhance researchers' ability to collect nematodes from the wild, record associated ecological data, and identify wild nematodes using molecular barcodes.},
}
@article {pmid35309745,
year = {2022},
author = {Zhan, J and Zheng, Y and Xia, Q and Wang, J and Liu, S and Yang, Z},
title = {Diversity investigation by application of DNA barcoding: A case study of lepidopteran insects in Xinjiang wild fruit forests, China.},
journal = {Ecology and evolution},
volume = {12},
number = {3},
pages = {e8678},
pmid = {35309745},
issn = {2045-7758},
abstract = {To investigate the species diversity of lepidopteran insects in Xinjiang wild fruit forests, establish insect community monitoring systems, and determine the local species pool, we test the applicability of DNA barcoding based on cytochrome c oxidase subunit I (COI) gene for accurate and rapid identification of insect species. From 2017 to 2019, a total of 212 samples with ambiguous morphological identification were selected for DNA barcoding analysis. Five sequence-based methods for species delimitation (ABGD, BINs, GMYC, jMOTU, and bPTP) were conducted for comparison to traditional morphology-based identification. In total, 2,422 samples were recorded, representing 143 species of 110 genera in 17 families in Lepidoptera. The diversity analysis showed that the richness indices for Noctuidae was the highest (54 species), and for Pterophoridae, Cossidae, Limacodidae, Lasiocampidae, Pieridae, and Lycaenidae were the lowest (all with 1 species). The Shannon-Wiener species diversity index (H') and Pielou's evenness (J') of lepidopteran insects first increased and then decreased across these 3 years, while the Simpson diversity index showed a trend of subtracted then added. For molecular-based identification, 67 lepidopteran species within 61 genera in 14 families were identified through DNA barcoding. Neighbor-joining (NJ) analysis showed that conspecific individuals were clustered together and formed monophyletic groups with a high support value, except for Lacanobia contigua (Denis &amp; Schiffermüller, 1775) (Noctuidae: Hadeninae). Sixty-seven morphospecies were classified into various numbers of MOTUs based on ABGD, BINs, GMYC, jMOTU, and bPTP (70, 96, 2, 71, and 71, respectively). In Xinjiang wild fruit forests, the family with the largest number of species is Noctuidae, followed by Geometridae, Crambidae, and the remaining families. The highest Shannon diversity index is observed for the family Noctuidae. Our results indicate that the distance-based methods (ABGD and jMOTU) and character-based method (bPTP) outperform GMYC. BINs is inclined to overestimate species diversity compared to other methods.},
}
@article {pmid35309039,
year = {2022},
author = {Occhibove, F and McKeown, NJ and Risley, C and Ironside, JE},
title = {Eco-epidemiological screening of multi-host wild rodent communities in the UK reveals pathogen strains of zoonotic interest.},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {17},
number = {},
pages = {278-287},
pmid = {35309039},
issn = {2213-2244},
abstract = {Wild rodent communities represent ideal systems to study pathogens and parasites shared among sympatric species. Such studies are useful in the investigation of eco-epidemiological dynamics, improving disease management strategies and reducing zoonotic risk. The aim of this study was to investigate pathogen and parasites shared among rodent species (multi-host community) in West Wales in an area where human/wildlife disease risk was not previously assessed. West Wales is predominantly rural, with human settlements located alongside to grazing areas and semi-natural landscapes, creating a critical human-livestock-wildlife interface. Ground-dwelling wild rodent communities in Wales were live-trapped and biological samples - faeces and ectoparasites - collected and screened for a suite of pathogens and parasites that differ in types of transmission and ecology. Faecal samples were examined to detect Herpesvirus, Escherichia coli, and Mycobacterium microti. Ticks and fleas were collected, identified to species based on morphology and genetic barcodes, and then screened for Anaplasma phagocytophilum, Babesia microti, Borrelia burgdorferi sensu lato, and Bartonella sp. All the pathogens and parasites screened pose a characteristic epidemiological challenge, such as variable level of generalism, unknown zoonotic potential, and lack of data. The results showed that the bank vole Myodes glareolus had the highest prevalence of all pathogens and parasites. Higher flea species diversity was detected than in previous studies, and at least two Bartonella species were found circulating, one of which has not previously been detected in the UK. These key findings offer new insights into the distribution of selected pathogen and parasites and subsequent zoonotic risk, and provide new baselines and perspectives for further eco-epidemiological research.},
}
@article {pmid35305558,
year = {2022},
author = {Li, B and Liu, T and Ali, A and Xiao, Y and Shan, N and Sun, J and Huang, Y and Zhou, Q and Zhu, Q},
title = {Complete chloroplast genome sequences of three aroideae species (Araceae): lights into selective pressure, marker development and phylogenetic relationships.},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {218},
pmid = {35305558},
issn = {1471-2164},
mesh = {*Araceae/genetics ; Chloroplasts/genetics ; Evolution, Molecular ; *Genome, Chloroplast ; Phylogeny ; },
abstract = {BACKGROUND: Colocasia gigantea, Caladium bicolor and Xanthosoma sagittifolium are three worldwide famous ornamental and/or vegetable plants in the Araceae family, these species in the subfamily Aroideae are phylogenetically perplexing due to shared interspecific morphological traits and variation.<br><br>RESULT: This study, for the first time ever, assembled and analyzed complete chloroplast genomes of C. gigantea, C. bicolor and X. sagittifolium with genome sizes of 165,906&#x2009;bp, 153,149&#x2009;bp and 165,169&#x2009;bp in length, respectively. The genomes were composed of conserved quadripartite circular structures with a total of 131 annotated genes, including 8 rRNA, 37 tRNA and 86 protein-coding genes. A comparison within Aroideae showed seven protein-coding genes (accD, ndhF, ndhK, rbcL, rpoC1, rpoC2 and matK) linked to environmental adaptation. Phylogenetic analysis confirmed a close relationship of C. gigantea with C. esculenta and S. colocasiifolia, and the C. bicolor with X. sagittifolium. Furthermore, three DNA barcodes (atpH-atpI&#x2009;+&#x2009;psaC-ndhE, atpH-atpI&#x2009;+&#x2009;trnS-trnG, atpH-atpI&#x2009;+&#x2009;psaC-ndhE&#x2009;+&#x2009;trnS-trnG) harbored highly variable regions to distinguish species in Aroideae subfamily.<br><br>CONCLUSION: These results would be beneficial for species identification, phylogenetic relationship, genetic diversity, and potential of germplasm resources in Aroideae.},
}
@article {pmid35304450,
year = {2022},
author = {Matsui, T and Mullis, MN and Roy, KR and Hale, JJ and Schell, R and Levy, SF and Ehrenreich, IM},
title = {The interplay of additivity, dominance, and epistasis on fitness in a diploid yeast cross.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {1463},
pmid = {35304450},
issn = {2041-1723},
support = {R35 GM130381/GM/NIGMS NIH HHS/United States ; R01 HG010378/HG/NHGRI NIH HHS/United States ; R01 AI164530/AI/NIAID NIH HHS/United States ; R01 HG011676/HG/NHGRI NIH HHS/United States ; T32 GM118289/GM/NIGMS NIH HHS/United States ; R01 GM110255/GM/NIGMS NIH HHS/United States ; },
mesh = {*Diploidy ; Epistasis, Genetic ; Exercise ; Humans ; Models, Genetic ; Phenotype ; *Saccharomyces cerevisiae/genetics ; },
abstract = {In diploid species, genetic loci can show additive, dominance, and epistatic effects. To characterize the contributions of these different types of genetic effects to heritable traits, we use a double barcoding system to generate and phenotype a panel of ~200,000 diploid yeast strains that can be partitioned into hundreds of interrelated families. This experiment enables the detection of thousands of epistatic loci, many whose effects vary across families. Here, we show traits are largely specified by a small number of hub loci with major additive and dominance effects, and pervasive epistasis. Genetic background commonly influences both the additive and dominance effects of loci, with multiple modifiers typically involved. The most prominent dominance modifier in our data is the mating locus, which has no effect on its own. Our findings show that the interplay between additivity, dominance, and epistasis underlies a complex genotype-to-phenotype map in diploids.},
}
@article {pmid35303948,
year = {2022},
author = {Zhang, C and Luo, C and Yang, R and Yang, Y and Guo, X and Deng, Y and Zhou, H and Zhang, Y},
title = {Morphological and molecular identification reveals a high diversity of Anopheles species in the forest region of the Cambodia-Laos border.},
journal = {Parasites &amp; vectors},
volume = {15},
number = {1},
pages = {94},
pmid = {35303948},
issn = {1756-3305},
support = {31601002//National Natural Science Foundation of China/ ; 81160357//National Natural Science Foundation of China/ ; 30960327//National Natural Science Foundation of China/ ; 30660160//National Natural Science Foundation of China/ ; U1902211//National Natural Science Foundation of China/ ; 2014YNPHXT03//Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control/ ; },
mesh = {Animals ; *Anopheles ; Cambodia ; Forests ; Laos ; *Malaria ; Mosquito Vectors/genetics ; Phylogeny ; },
abstract = {BACKGROUND: To develop an effective malaria vector intervention method in forested international border regions within the Greater Mekong Subregion (GMS), more in-depth studies should be conducted on local Anopheles species composition and bionomic features. There is a paucity of comprehensive surveys of biodiversity integrating morphological and molecular species identification conducted within the border of Laos and Cambodia.<br><br>METHODS: A total of 2394 adult mosquitoes were trapped in the Cambodia-Laos border region. We first performed morphological identification of Anopheles mosquitoes and subsequently performed molecular identification using 412 recombinant DNA-internal transcribed spacer 2 (rDNA-ITS2) and 391 mitochondrial DNA-cytochrome c oxidase subunit 2 (mtDNA-COII) sequences. The molecular and morphological identification results were compared, and phylogenetic analysis of rDNA-ITS2 and mtDNA-COII was conducted for the sequence divergence among species.<br><br>RESULTS: Thirteen distinct species of Anopheles were molecularly identified in a 26,415 km[2] border region in Siem Pang (Cambodia) and Pathoomphone (Laos). According to the comparisons of morphological and molecular identity, the interpretation of local species composition for dominant species in the Cambodia-Laos border (An. dirus, An. maculatus, An. philippinensis, An. kochi and An. sinensis) achieved the highest accuracy of morphological identification, from 98.37 to 100%. In contrast, the other species which were molecularly identified were less frequently identified correctly (0-58.3%) by morphological methods. The average rDNA-ITS2 and mtDNA-COII interspecific divergence was respectively 318 times and 15 times higher than their average intraspecific divergence. The barcoding gap ranged from 0.042 to 0.193 for rDNA-ITS2, and from 0.033 to 0.047 for mtDNA-COII.<br><br>CONCLUSIONS: The Cambodia-Laos border hosts a high diversity of Anopheles species. The morphological identification of Anopheles species provides higher accuracy for dominant species than for other species. Molecular methods combined with morphological analysis to determine species composition, population dynamics and bionomic characteristics can facilitate a better understanding of the factors driving malaria transmission and the effects of interventions, and can aid in achieving the goal of eliminating malaria.},
}
@article {pmid35302746,
year = {2022},
author = {Rand, A and Zimny, P and Nagel, R and Telang, C and Mollison, J and Bruns, A and Leff, E and Reisner, WW and Dunbar, WB},
title = {Electronic Mapping of a Bacterial Genome with Dual Solid-State Nanopores and Active Single-Molecule Control.},
journal = {ACS nano},
volume = {16},
number = {4},
pages = {5258-5273},
pmid = {35302746},
issn = {1936-086X},
support = {R21 HG011236/HG/NHGRI NIH HHS/United States ; },
mesh = {Humans ; *Nanopores ; Escherichia coli/genetics ; Nanotechnology/methods ; DNA/genetics ; Genome, Bacterial ; Electronics ; },
abstract = {We present an electronic mapping of a bacterial genome using solid-state nanopore technology. A dual-nanopore architecture and active control logic are used to produce single-molecule data that enables estimation of distances between physical tags installed at sequence motifs within double-stranded DNA. Previously developed "DNA flossing" control logic generates multiple scans of each captured DNA. We extended this logic in two ways: first, to automate "zooming out" on each molecule to progressively increase the number of tags scanned during flossing, and second, to automate recapture of a molecule that exited flossing to enable interrogation of the same and/or different regions of the molecule. Custom analysis methods were developed to produce consensus alignments from each multiscan event. The combined multiscanning and multicapture method was applied to the challenge of mapping from a heterogeneous mixture of single-molecule fragments that make up the Escherichia coli (E. coli) chromosome. Coverage of 3.1× across 2355 resolvable sites of the E. coli genome was achieved after 5.6 h of recording time. The recapture method showed a 38% increase in the merged-event alignment length compared to single-scan alignments. The observed intertag resolution was 150 bp in engineered DNA molecules and 166 bp natively within fragments of E. coli DNA, with detection of 133 intersite intervals shorter than 200 bp in the E. coli reference map. We present results on estimating distances in repetitive regions of the E. coli genome. With an appropriately designed array, higher throughput implementations could enable human-sized genome and epigenome mapping applications.},
}
@article {pmid35301264,
year = {2022},
author = {Mikheenko, A and Prjibelski, AD and Joglekar, A and Tilgner, HU},
title = {Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns.},
journal = {Genome research},
volume = {32},
number = {4},
pages = {726-737},
pmid = {35301264},
issn = {1549-5469},
support = {R01 GM135247/GM/NIGMS NIH HHS/United States ; RF1 MH121267/MH/NIMH NIH HHS/United States ; },
mesh = {DNA, Complementary ; High-Throughput Nucleotide Sequencing/methods ; *Nanopores ; RNA ; Sequence Analysis, DNA/methods ; Technology ; },
abstract = {Long-read transcriptomics require understanding error sources inherent to technologies. Current approaches cannot compare methods for an individual RNA molecule. Here, we present a novel platform-comparison method that combines barcoding strategies and long-read sequencing to sequence cDNA copies representing an individual RNA molecule on both Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT). We compare these long-read pairs in terms of sequence content and isoform patterns. Although individual read pairs show high similarity, we find differences in (1) aligned length, (2) transcription start site (TSS), (3) polyadenylation site (poly(A)-site) assignment, and (4) exon-intron structures. Overall, 25% of read pairs disagree on either TSS, poly(A)-site, or splice site. Intron-chain disagreement typically arises from alignment errors of microexons and complicated splice sites. Our single-molecule technology comparison reveals that inconsistencies are often caused by sequencing error-induced inaccurate ONT alignments, especially to downstream GUNNGU donor motifs. However, annotation-disagreeing upstream shifts in NAGNAG acceptors in ONT are often confirmed by PacBio and are thus likely real. In both barcoded and nonbarcoded ONT reads, we find that intron number and proximity of GU/AGs better predict inconsistencies with the annotation than read quality alone. We summarize these findings in an annotation-based algorithm for spliced alignment correction that improves subsequent transcript construction with ONT reads.},
}
@article {pmid35300721,
year = {2022},
author = {Roman, MG and Gutierrez, R and Houston, R},
title = {Massively parallel sequencing of Cannabis sativa chloroplast hotspots for forensic typing.},
journal = {Journal of cannabis research},
volume = {4},
number = {1},
pages = {13},
pmid = {35300721},
issn = {2522-5782},
abstract = {BACKGROUND: Marijuana (Cannabis sativa) is the most commonly used illicit drug in the USA, and the use of DNA barcodes could assist drug trafficking investigations by indicating the biogeographical origin and crop type of a sample and providing a means for linking cases. Additionally, the legality of marijuana in the USA remains complicated with some states fully legalizing marijuana for recreational use while federally marijuana remains completely illegal. Massively parallel sequencing (MPS) offers distinct advantages over capillary electrophoresis (CE), including more comprehensive coverage of target loci, analysis of hundreds of markers simultaneously, and high throughput capabilities.<br><br>METHODS: This study reports on the development of a MiSeq FGx&#xae; assay targeting seven "hotspot" regions in the Cannabis sativa chloroplast genome that are highly polymorphic and informative in attempts to determine biogeographical origin and distinguishing between marijuana and hemp. Sequencing results were compared to previous studies that used CE-based genotyping methods.<br><br>RESULTS: A total of 49 polymorphisms were observed, 16 of which have not been previously reported. Additionally, sequence data revealed isoalleles at one locus, which were able to differentiate two samples that had the same haplotype using CE-based methods. This study reports preliminary results from sequencing 14 hemp and marijuana samples from different countries using the developed MPS assay.<br><br>CONCLUSION: Future studies should genotype a more comprehensive sample set from around the world to build a haplotype database, which could be used to provide investigative leads for law enforcement agencies investigating marijuana trafficking.},
}
@article {pmid35298775,
year = {2022},
author = {González, MA and Delacour-Estrella, S and Bengoa, M and Barceló, C and Bueno-Marí, R and Eritja, R and Ruiz-Arrondo, I},
title = {A Survey on Native and Invasive Mosquitoes and Other Biting Dipterans in Northern Spain.},
journal = {Acta parasitologica},
volume = {67},
number = {2},
pages = {867-877},
pmid = {35298775},
issn = {1896-1851},
mesh = {Animals ; *Ceratopogonidae ; *Culicidae ; Ecosystem ; Humans ; Larva ; Spain ; },
abstract = {PURPOSE: Haematophagous Diptera, such as mosquitoes (Culicidae), biting midges (Ceratopogonidae), and black flies (Simuliidae), are important insects for public and animal health due to their capacity to bite and transmit pathogens. Outdoor recreation areas are usually affected by biting species and provide suitable habitats to both adult and immature stages. This study aimed to determine the species diversity and larval sites of these Diptera groups in two golf courses.<br><br>METHODS: A multi-method collection approach using ultraviolet-CDC traps, human landing catches, collection in breeding sites, and ovitraps was implemented during summer 2020 in northern Spain. Insects were determined by morphological features accompanied by DNA barcoding.<br><br>RESULTS: A total of ten native mosquito species were recorded either as adults or as larval stages. The invasive species Aedes japonicus was collected only at egg or pupa stage in ovitraps. Culex pipiens s.l. and Culex torrentium were both common mosquito species accounting for 47.9% of the total larval site collections and their larvae might be found in a wide range of natural and artificial sites. Culiseta longiareolata specimens were also prominent (30.1% of the total) and occurred exclusively in man-made water-filled containers. A total of 13 Culicoides species were identified, 10 of which were captured by ultraviolet-CDC traps, particularly members of the Obsoletus complex (Culicoides obsoletus/Culicoides scoticus, 74.9%) and seven species by emergence traps, being the two most abundant C. kibunensis (44.8%) and C. festivipennis (34.9%). Simulium cryophilum was also collected hovering around the operator under field sampling.<br><br>CONCLUSION: A comprehensive representation of the blood-sucking Diptera fauna and their larval sites was obtained by the multi-method approach in two Spanish golf courses.},
}
@article {pmid35296859,
year = {2022},
author = {Zhao, Q and Yu, CD and Wang, R and Xu, QJ and Dai Pra, R and Zhang, L and Chang, RB},
title = {A multidimensional coding architecture of the vagal interoceptive system.},
journal = {Nature},
volume = {603},
number = {7903},
pages = {878-884},
pmid = {35296859},
issn = {1476-4687},
support = {K01 DK113047/DK/NIDDK NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; DP2 HL151354/HL/NHLBI NIH HHS/United States ; R01 HL150449/HL/NHLBI NIH HHS/United States ; R01 AT012041/AT/NCCIH NIH HHS/United States ; },
mesh = {Animals ; Brain/metabolism ; Calcium/metabolism ; Mammals/metabolism ; Mice ; *Perception ; *Psychophysiology ; Sensory Receptor Cells/metabolism ; *Vagus Nerve ; *Vomeronasal Organ ; },
abstract = {Interoception, the ability to timely and precisely sense changes inside the body, is critical for survival[1-4]. Vagal sensory neurons (VSNs) form an important body-to-brain connection, navigating visceral organs along the rostral-caudal axis of the body and crossing the surface-lumen axis of organs into appropriate tissue layers[5,6]. The brain can discriminate numerous body signals through VSNs, but the underlying coding strategy remains poorly understood. Here we show that VSNs code visceral organ, tissue layer and stimulus modality-three key features of an interoceptive signal-in different dimensions. Large-scale single-cell profiling of VSNs from seven major organs in mice using multiplexed projection barcodes reveals a 'visceral organ' dimension composed of differentially expressed gene modules that code organs along the body's rostral-caudal axis. We discover another 'tissue layer' dimension with gene modules that code the locations of VSN endings along the surface-lumen axis of organs. Using calcium-imaging-guided spatial transcriptomics, we show that VSNs are organized into functional units to sense similar stimuli across organs and tissue layers; this constitutes a third 'stimulus modality' dimension. The three independent feature-coding dimensions together specify many parallel VSN pathways in a combinatorial manner and facilitate the complex projection of VSNs in the brainstem. Our study highlights a multidimensional coding architecture of the mammalian vagal interoceptive system for effective signal communication.},
}
@article {pmid35290693,
year = {2022},
author = {Su, Y and Wu, B and Chen, S and Sun, JH and Yu, YJ and Zhuo, MP and Wang, ZS and Wang, XD},
title = {Organic Branched Heterostructures with Optical Interconnects for Photonic Barcodes.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {61},
number = {22},
pages = {e202117857},
doi = {10.1002/anie.202117857},
pmid = {35290693},
issn = {1521-3773},
support = {52173177, 21971185//National Natural Science Foundation of China/ ; BX20190228//National Postdoctoral Program for Innovative Talents/ ; },
abstract = {Optical interconnects exhibit superior potential in the precise regulation of photon transmission for organic photonic circuits. However, the rational design of well-defined organic heterostructures toward active optoelectronics remains challenging. Herein, we designed organic branched heterostructures (OBHs) with accurate spatial organization for optical interconnection. Notably, the precise regulation of OBHs has been controllably achieved including the trunk morphologies and the branched microwire number. Significantly, these as-prepared OBHs inherently exhibit the multichannel coupling outputs and the excitation position-dependent waveguide characteristics, leading to various outcoupling signals with tunable intensity and emission colors. The optical interconnects are realized due to the occurrence of exciton conversion and photon propagation between branch and trunk at the heterojunction, benefiting the application possibilities of two-dimensional (2D) optical barcodes.},
}
@article {pmid35290433,
year = {2022},
author = {Zhang, D and Zhang, J and Du, J and Zhou, Y and Wu, P and Liu, Z and Sun, Z and Wang, J and Ding, W and Chen, J and Wang, J and Xu, Y and Ouyang, C and Yang, Q},
title = {Optimized Sequencing Adaptors Enable Rapid and Real-Time Metagenomic Identification of Pathogens during Runtime of Sequencing.},
journal = {Clinical chemistry},
volume = {68},
number = {6},
pages = {826-836},
doi = {10.1093/clinchem/hvac024},
pmid = {35290433},
issn = {1530-8561},
mesh = {Fungi/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenome ; *Metagenomics/methods ; Sensitivity and Specificity ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) offers the promise of unbiased detection of emerging pathogens. However, in indexed sequencing, the sequential paradigm of data acquisition, demultiplexing, and analysis restrain read assignment in advance and real-time analysis, resulting in lengthy turnaround time for clinical metagenomic detection.<br><br>METHODS: We described the utility of internal-index adaptors with different lengths of barcode in multiplex sequencing. The base composition for each position within these adaptors was well-balanced to ensure nucleotide diversity and optimal sequencing performance and to achieve the early assignment of reads by first sequencing the barcodes. Combined with an automated library preparation device, we delivered a rapid and real-time bioinformatics pathogen identification solution for the Illumina NextSeq platform. The diagnostic performance was evaluated by testing 153 lower respiratory tract specimens using mNGS in comparison to culture, 16S/internal transcribed spacer amplicon sequencing, and additional PCR-based tests.<br><br>RESULTS: By calculating the average F1 scores of all read lengths under different threshold values, we established the optimal threshold for pathogens identification, and found that 36 bp was the optimal shortest read length for rapid mNGS analysis. Rapid detection had a negative percentage agreement and positive percentage agreement of 100% and 85.1% for bacteria and 97.4% and 80.3% for fungi, when compared to a composite standard. The rapid mNGS solution enabled accurate pathogen identification in about 9.1 to 10.1 h sample-to-answer turnaround time.<br><br>CONCLUSIONS: Optimized internal index adaptors combined with a real-time analysis pipeline provide a potential tool for a first-line test in critically ill patients.},
}
@article {pmid35287585,
year = {2022},
author = {Xu, K and Lin, C and Lee, SY and Mao, L and Meng, K},
title = {Comparative analysis of complete Ilex (Aquifoliaceae) chloroplast genomes: insights into evolutionary dynamics and phylogenetic relationships.},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {203},
pmid = {35287585},
issn = {1471-2164},
mesh = {Aquifoliaceae/genetics ; Chloroplasts/genetics ; *Genome, Chloroplast ; *Ilex/genetics ; Phylogeny ; },
abstract = {BACKGROUND: Ilex (Aquifoliaceae) are of great horticultural importance throughout the world for their foliage and decorative berries, yet a dearth of genetic information has hampered our understanding of phylogenetic relationships and evolutionary history. Here, we compare chloroplast genomes from across Ilex and estimate phylogenetic relationships.<br><br>RESULTS: We sequenced the chloroplast genomes of seven Ilex species and compared them with 34 previously published Ilex plastomes. The length of the seven newly sequenced Ilex chloroplast genomes ranged from 157,182&#x2009;bp to 158,009&#x2009;bp, and contained a total of 118 genes, including 83 protein-coding, 31 rRNA, and four tRNA genes. GC content ranged from 37.6 to 37.69%. Comparative analysis showed shared genomic structures and gene rearrangements. Expansion and contraction of the inverted repeat regions at the LSC/IRa and IRa/SSC junctions were observed in 22 and 26 taxa, respectively; in contrast, the IRb boundary was largely invariant. A total of 2146 simple sequence repeats and 2843 large repeats were detected in the 41 Ilex plastomes. Additionally, six genes (psaC, rbcL, trnQ, trnR, trnT, and ycf1) and two intergenic spacer regions (ndhC-trnV and petN-psbM) were identified as hypervariable, and thus potentially useful for future phylogenetic studies and DNA barcoding. We recovered consistent phylogenetic relationships regardless of inference methodology or choice of loci. We recovered five distinct, major clades, which were inconsistent with traditional taxonomic systems.<br><br>CONCLUSION: Our findings challenge traditional circumscriptions of the genus Ilex and provide new insights into the evolutionary history of this important clade. Furthermore, we detail hypervariable and repetitive regions that will be useful for future phylogenetic and population genetic studies.},
}
@article {pmid35283910,
year = {2022},
author = {Chen, Q and Hu, H and Zhang, D},
title = {DNA Barcoding and Phylogenomic Analysis of the Genus Fritillaria in China Based on Complete Chloroplast Genomes.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {764255},
pmid = {35283910},
issn = {1664-462X},
abstract = {The Fritillaria is an extremely complicated genus in taxonomy and phylogeny, which contains numerous medicinal species in China. Both traditional characteristic-based taxonomy and universal DNA barcodes (ITS, trnH-psbA, and rbcL) are difficult to effectively identify the species. Here, we generated a large dataset of chloroplast genomes from multiple accessions per species of Fritillaria to evaluate their effectiveness in species discrimination. Moreover, phylogeny of species in China was explored based on the complete chloroplast genomes, and then divergence times of each node were estimated. The results showed that all 21 species in Fritillaria here (including two suspicious species) could be correctly discriminated using cpDNA genomes except F. cirrhosa, which suggested that DNA super-barcode could greatly enhance species discriminatory resolution for complicated genera. Furthermore, four regions (ycf1, matK-trnG-GCC, rpoC1, and matK) gained remarkably higher resolution than that of other plastid regions, but only matK might be suitable to identify Fritillaria species in consideration of its lengths. Phylogenomic analysis showed that the subgenus Fritillaria in China was divided into four major clades with obvious geographic structure. Among them, Clade I, mainly distributed in southwest China, was a young and complicated group. Moreover, according to the analysis, taxonomic treatments of the two suspicious species, namely "F. omeiensis" and "F. hupehensis" in Flora of China (2000) are questionable and might need further revision. Molecular dating revealed that both origin and divergence of subgenus Fritillaria, as well as its four major clades, were significantly associated with geological and climatic fluctuations during the Middle to Late Miocene. This study would enrich case studies of DNA super-barcode and provide new insights on speciation, lineage diversification, and biogeography of the Fritillaria in China.},
}
@article {pmid35283127,
year = {2022},
author = {Hanson, MC and Petch, GM and Ottosen, TB and Skjøth, CA},
title = {Climate change impact on fungi in the atmospheric microbiome.},
journal = {The Science of the total environment},
volume = {830},
number = {},
pages = {154491},
doi = {10.1016/j.scitotenv.2022.154491},
pmid = {35283127},
issn = {1879-1026},
mesh = {Agriculture ; *Climate Change ; Fungi ; Humans ; *Microbiota ; Spores, Fungal ; },
abstract = {The atmospheric microbiome is one of the least studied microbiomes of our planet. One of the most abundant, diverse and impactful parts of this microbiome is arguably fungal spores. They can be very potent outdoor aeroallergens and pathogens, causing an enormous socio-economic burden on health services and annual damages to crops costing billions of Euros. We find through hypothesis testing that an expected warmer and drier climate has a dramatic impact on the atmospheric microbiome, conceivably through alteration of the hydrological cycle impacting agricultural systems, with significant differences in leaf wetness between years (p-value <0.05). The data were measured via high-throughput sequencing analysis using the DNA barcode marker, ITS2. This was complemented by remote sensing analysis of land cover and dry matter productivity based on the Sentinel satellites, on-site detection of atmospheric and vegetation variables, GIS analysis, harvesting analysis and footprint modelling on trajectory clusters using the atmospheric transport model HYSPLIT. We find the seasonal spore composition varies between rural and urban zones reflecting both human activities (e.g. harvest), type and status of the vegetation and the prevailing climate rather than mesoscale atmospheric transport. We find that crop harvesting governs the composition of the atmospheric microbiome through a clear distinction between harvest and post-harvest beta-diversity by PERMANOVA on Bray-Curtis dissimilarity (p-value <0.05). Land cover impacted significantly by two-way ANOVA (p-value <0.05), while there was minimal impact from air mass transport over the 3 years. The hypothesis suggests that the fungal spore composition will change dramatically due to climate change, an until now unforeseen effect affecting both food security, human health and the atmospheric hydrological cycle. Consequently the management of crop diseases and impact on human health through aeroallergen exposure need to consider the timing of crop treatments and land management, including post harvest, to minimize exposure of aeroallergens and pathogens.},
}
@article {pmid35281123,
year = {2022},
author = {Zhang, YM and Han, LJ and Yang, CW and Yin, ZL and Tian, X and Qian, ZG and Li, GD},
title = {Comparative chloroplast genome analysis of medicinally important Veratrum (Melanthiaceae) in China: Insights into genomic characterization and phylogenetic relationships.},
journal = {Plant diversity},
volume = {44},
number = {1},
pages = {70-82},
pmid = {35281123},
issn = {2468-2659},
abstract = {Members of Veratrum are perennial herbs widely used in traditional Chinese medicine to induce vomiting, resolve blood stasis and relieve pain. However, the intrageneric classification and phylogenetic relationships within Veratrum have long been controversial due to the complexity of morphological variations and lack of high-resolution molecular markers. In this study, we reevaluated the infrageneric relationships with the genus Veratrum using complete chloroplast genome sequence data. Herein, the complete cp genomes of ten species of Veratrum were newly sequenced and characterized. The complete cp genomes of ten species of Veratrum had the typical quadripartite structure, ranging from 151,597 bp to 153,711 bp in size and comprising a total of 135 genes. The structure of Veratrum cp genomes (i.e., gene order, content, and genome components) was highly similar across species. The number of simple sequence repeats (SSRs) ranged from 63 to 78, and of long repeats ranged from 31 to 35. Eight highly divergent regions (ndhF, psbC-psbZ, psbK-psbI, rpoB-trnC_GCA, trnK_UUU-trnQ_UUG, trnS_GCU-trnG_UCC, trnT_UGU-trnL_UAA and ycf1) were identified and are potentially useful for the DNA barcoding of Veratrum. Phylogenetic analysis among 29 taxa based on cp genomes, total genes, protein-coding genes and intergenic regions strongly supported the monophyly of Veratrum. The circumscription and relationships of the infrageneric taxa of Veratrum were well-presented with great resolution. These results will facilitate the identification, taxonomy, and utilization of Veratrum plants as well as the evolutionary studies of Melanthiaceae.},
}
@article {pmid35279202,
year = {2022},
author = {Zeller, C and Richter, D and Jurinovic, V and Valtierra-Gutiérrez, IA and Jayavelu, AK and Mann, M and Bagnoli, JW and Hellmann, I and Herold, T and Enard, W and Vick, B and Jeremias, I},
title = {Adverse stem cell clones within a single patient's tumor predict clinical outcome in AML patients.},
journal = {Journal of hematology &amp; oncology},
volume = {15},
number = {1},
pages = {25},
pmid = {35279202},
issn = {1756-8722},
mesh = {Clone Cells ; Cytarabine/therapeutic use ; Drug Resistance, Neoplasm/genetics ; Humans ; *Leukemia, Myeloid, Acute/drug therapy/genetics/pathology ; *Proteomics ; Recurrence ; Stem Cells/pathology ; },
abstract = {Acute myeloid leukemia (AML) patients suffer dismal prognosis upon treatment resistance. To study functional heterogeneity of resistance, we generated serially transplantable patient-derived xenograft (PDX) models from one patient with AML and twelve clones thereof, each derived from a single stem cell, as proven by genetic barcoding. Transcriptome and exome sequencing segregated clones according to their origin from relapse one or two. Undetectable for sequencing, multiplex fluorochrome-guided competitive in vivo treatment trials identified a subset of relapse two clones as uniquely resistant to cytarabine treatment. Transcriptional and proteomic profiles obtained from resistant PDX clones and refractory AML patients defined a 16-gene score that was predictive of clinical outcome in a large independent patient cohort. Thus, we identified novel genes related to cytarabine resistance and provide proof of concept that intra-tumor heterogeneity reflects inter-tumor heterogeneity in AML.},
}
@article {pmid35271248,
year = {2022},
author = {Bernhards, CB and Liem, AT and Berk, KL and Roth, PA and Gibbons, HS and Lux, MW},
title = {Putative Phenotypically Neutral Genomic Insertion Points in Prokaryotes.},
journal = {ACS synthetic biology},
volume = {11},
number = {4},
pages = {1681-1685},
pmid = {35271248},
issn = {2161-5063},
mesh = {*CRISPR-Cas Systems/genetics ; *Gene Editing ; Genome ; Genomics ; Software ; },
abstract = {The barriers to effective genome editing in diverse prokaryotic organisms have been falling at an accelerated rate. As editing becomes easier in more organisms, quickly identifying genomic locations to insert new genetic functions without disrupting organism fitness becomes increasingly useful. When the insertion is noncoding DNA for applications such as information storage or barcoding, a neutral insertion point can be especially important. Here we describe an approach to identify putatively neutral insertion sites in prokaryotes. An algorithm (targetFinder) finds convergently transcribed genes with gap sizes within a specified range, and looks for annotations within the gaps. We report putative editing targets for 10 common synthetic biology chassis organisms, including coverage of available RNA-seq data, and provide software to apply to others. We further experimentally evaluate the neutrality of six identified targets in Escherichia coli through insertion of a DNA barcode. We anticipate this information and the accompanying tool will prove useful for synthetic biologists seeking neutral insertion points for genome editing.},
}
@article {pmid35268776,
year = {2022},
author = {Kim, JH and Doh, EJ and Lee, G},
title = {Chemotaxonomic Classification of Peucedanum japonicum and Its Chemical Correlation with Peucedanum praeruptorum, Angelica decursiva, and Saposhnikovia divaricata by Liquid Chromatography Combined with Chemometrics.},
journal = {Molecules (Basel, Switzerland)},
volume = {27},
number = {5},
pages = {},
pmid = {35268776},
issn = {1420-3049},
support = {//Wonkwang University/ ; },
mesh = {*Angelica/genetics ; *Apiaceae/chemistry ; Chemometrics ; Chromatography, Liquid ; Coumarins/analysis ; Plant Roots/chemistry ; },
abstract = {The roots of Peucedanum japonicum (Apiaceae) have been used as an alternative to the roots of Saposhnikovia divaricata (Apiaceae) to treat common cold-related symptoms in Korea. However, a variety of Peucedanum species, including the roots of P. praeruptorum or Angelica decursiva (=P. decursivum), have been used to treat phlegm-heat-induced symptoms in China. Hence, as there are differences in the medicinal application of P. japonicum roots between Korea and China, chemotaxonomic classification of P. japonicum was evaluated. Sixty samples derived from P. japonicum, P. praeruptorum, A. decursiva, and S. divaricata were phylogenetically identified using DNA barcoding tools, and chemotaxonomic correlations among the samples were evaluated using chromatographic profiling with chemometric analyses. P. japonicum samples were phylogenetically grouped into the same cluster as P. praeruptorum samples, followed by S. divaricata samples at the next cluster level, whereas A. decursiva samples were widely separated from the other species. Moreover, P. japonicum samples showed higher chemical correlations with P. praeruptorum samples or A. decursiva samples, but lower or negative chemical correlations with S. divaricata samples. These results demonstrate that P. japonicum is more genetically and chemically relevant to P. praeruptorum or A. decursiva and, accordingly, the medicinal application of P. japonicum might be closer to the therapeutic category of these two species than that of S. divaricata.},
}
@article {pmid35267025,
year = {2022},
author = {Sasaki, M and Iwaki, T and Nakao, M},
title = {REDISCOVERY OF MICHAJLOVIA TURDI (DIGENEA: BRACHYLAIMOIDEA) FROM JAPAN.},
journal = {The Journal of parasitology},
volume = {108},
number = {2},
pages = {122-126},
doi = {10.1645/21-93},
pmid = {35267025},
issn = {1937-2345},
mesh = {Animals ; Japan ; Phylogeny ; RNA, Ribosomal, 28S/genetics ; *Songbirds ; *Trematoda ; },
abstract = {Michajlovia turdi (Yamaguti, 1939) (Digenea: Brachylaimoidea) has been found from the Japanese thrush, Turdus cardis Temminck, 1831, in Hokkaido, the northernmost island of Japan. This is a rediscovery of M. turdi in Japan after approximately 80 years from the original description of the species as Leucochloridium turdiYamaguti, 1939. Here we redescribe the morphology of M. turdi and generate DNA barcodes for the species by sequencing nuclear ribosomal RNA (18S and 28S) and mitochondrial cytochrome c oxidase subunit I (COI) genes. Our molecular phylogenetic analysis was not effective at determining the taxonomic rank of Michajlovia in Brachylaimoidea, and consequently the genus remains as incertae sedis.},
}
@article {pmid35263562,
year = {2022},
author = {Reynolds, G and Tirard, A and Villani, AC},
title = {Plasmacytoid dendritic cells: Welcome back to the DC fold.},
journal = {Immunity},
volume = {55},
number = {3},
pages = {380-382},
doi = {10.1016/j.immuni.2022.02.011},
pmid = {35263562},
issn = {1097-4180},
mesh = {Cells, Cultured ; *Dendritic Cells/immunology ; },
abstract = {The presumed common origin of plasmacytoid and conventional dendritic cells has been the contentious subject of recent debate. In this issue of Immunity, Feng et al. employed an inducible cell barcoding system to track clonal relationships and uncovered a surprising close developmental relationship between cDC1s and pDCs.},
}
@article {pmid35263170,
year = {2022},
author = {Coto-Llerena, M and Benjak, A and Gallon, J and Meier, MA and Boldanova, T and Terracciano, LM and Ng, CKY and Piscuoglio, S},
title = {Circulating Cell-Free DNA Captures the Intratumor Heterogeneity in Multinodular Hepatocellular Carcinoma.},
journal = {JCO precision oncology},
volume = {6},
number = {},
pages = {e2100335},
pmid = {35263170},
issn = {2473-4284},
mesh = {Biomarkers, Tumor/genetics ; *Carcinoma, Hepatocellular/genetics ; *Cell-Free Nucleic Acids/genetics ; Humans ; *Liver Neoplasms/genetics ; Exome Sequencing ; },
abstract = {PURPOSE: Hepatocellular carcinoma (HCC) is a highly heterogeneous disease, with more than 40% of patients initially diagnosed with multinodular HCCs. Although circulating cell-free DNA (cfDNA) has been shown to effectively detect somatic mutations, little is known about its utility to capture intratumor heterogeneity in patients with multinodular HCC undergoing systemic treatment.<br><br>MATERIALS AND METHODS: Tumor biopsies and plasma were synchronously collected from seven prospectively recruited patients with HCC before and during systemic therapy. Plasma-derived cfDNA and matched germline were subjected to high-depth targeted sequencing with molecular barcoding. The mutational profile of the cfDNA was compared with whole-exome sequencing from matched tumor biopsies.<br><br>RESULTS: Genomic data revealed that out of the seven patients, five were considered intrahepatic metastasis and two multicentric HCCs. cfDNA captured the majority of mutations in the tumors and detected significantly more mutations than tumor biopsies. Driver mutations such as CTNNB1 S33C, NRAS Q61R, ARID1A R727fs, and NF1 E2368fs as well as standard-of-care biomarkers of response to targeted therapy were detected only in cfDNA. In the two patients with multicentric HCC, cfDNA detected mutations derived from the genetically independent and spatially distinct nodules. Moreover, cfDNA was not only able to capture clonal mutations but also the subclonal mutations detected in only one of the multiple biopsied nodules. Furthermore, serial cfDNA detected variants of tumor origin emerging during treatment.<br><br>CONCLUSION: This study revealed that the genetic analysis of cfDNA captures the intratumor heterogeneity in multinodular HCC highlighting the potential for cfDNA as a sensitive and noninvasive tool for precision medicine.},
}
@article {pmid35262169,
year = {2022},
author = {Nogueira, L and Rodrigues Filho, LFDS and Solé, M and Affonso, PRAM and Siqueira, S and Sampaio, I},
title = {DNA barcode reveals candidate species of Scinax and Ololygon (Anura: Hylidae) in Atlantic Forest.},
journal = {Genetics and molecular biology},
volume = {45},
number = {1},
pages = {e20210177},
pmid = {35262169},
issn = {1415-4757},
abstract = {Molecular species delimitation methods are efficient tools to identify species, including the discovery of new taxa and cryptic organisms, thus being useful to biodiversity studies. In the present work, 16S mitochondrial sequences and cytochrome oxidase I (COI) were used to evaluate the richness of species in the genus Scinax and Ololygon from a biodiversity hotspot in Atlantic Forest. A total of 109 specimens formally belonging to eight species of Scinax and three species of Ololygon were collected in 13 localities along the state of Bahia (northeastern Brazil) and one site in Espírito Santo (southeastern Brazil). Of the Scinax species collected in this study, three were morphologically differentiated from other described species and identified as putative new species (Scinax sp.1, Scinax sp.2 and Scinax sp.3). The species delimitations were inferred using three different methods: ABGD, PTP and mPTP which allowed recognizing 11 Scinax species and five Ololygon species. Scinax sp. 1, Scinax sp. 2 and Scinax sp. 3, have been confirmed as new putative species and Ololygon argyreornata possibly contains cryptic species. We suggest additional studies, including morphological and bioacoustic data to validate these new putative species.},
}
@article {pmid35261737,
year = {2022},
author = {Vierstraete, AR and Braeckman, BP},
title = {Amplicon_sorter: A tool for reference-free amplicon sorting based on sequence similarity and for building consensus sequences.},
journal = {Ecology and evolution},
volume = {12},
number = {3},
pages = {e8603},
pmid = {35261737},
issn = {2045-7758},
abstract = {Oxford Nanopore Technologies (ONT) is a third-generation sequencing technology that is gaining popularity in ecological research for its portable and low-cost sequencing possibilities. Although the technology excels at long-read sequencing, it can also be applied to sequence amplicons. The downside of ONT is the low quality of the raw reads. Hence, generating a high-quality consensus sequence is still a challenge. We present Amplicon_sorter, a tool for reference-free sorting of ONT sequenced amplicons based on their similarity in sequence and length and for building solid consensus sequences.},
}
@article {pmid35261129,
year = {2022},
author = {Yan, S and Wang, L and Wang, Y and Cao, Z and Zhang, S and Du, X and Fan, P and Zhang, P and Chen, HY and Huang, S},
title = {Non-binary Encoded Nucleic Acid Barcodes Directly Readable by a Nanopore.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {61},
number = {20},
pages = {e202116482},
doi = {10.1002/anie.202116482},
pmid = {35261129},
issn = {1521-3773},
mesh = {DNA/metabolism ; Mycobacterium smegmatis ; *Nanopores ; *Nucleic Acids/metabolism ; Porins/metabolism ; },
abstract = {A large collection of unique molecular barcodes is useful in the simultaneous sensing or screening of molecular analytes. Though the sequence of DNA has been widely applied to encode for molecular barcodes, decoding of these barcodes is normally assisted by sequencing. We here demonstrate a barcode system based solely on self-assembly of synthetic nucleic acids and direct nanopore decoding. Each molecular barcode is composed of "n" distinct information nodes in a non-binary manner and can be sequentially scanned and decoded by a Mycobacterium smegmatis porin A (MspA) nanopore. Nanopore events containing step-shaped features were consistently reported. 14 unique information nodes were developed which in principle could encode for 14[n] unique molecular barcodes in a barcode containing "n" information nodes. These barcode probes were adapted to detect different antibody proteins or cancer-related microRNAs, suggesting their immediate application in a wide variety of sensing applications.},
}
@article {pmid35260723,
year = {2022},
author = {Palmieri, D and Javorina, A and Siddiqui, J and Gardner, A and Fries, A and Chapleau, RR and Starr, C and Fishel, R and Miles, WO},
title = {Mass COVID-19 patient screening using UvsX and UvsY mediated DNA recombination and high throughput parallel sequencing.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {4082},
pmid = {35260723},
issn = {2045-2322},
support = {R01 CA067007/CA/NCI NIH HHS/United States ; R01 CA251753/CA/NCI NIH HHS/United States ; R01 GM129764/GM/NIGMS NIH HHS/United States ; },
mesh = {COVID-19/*diagnosis/virology ; DNA-Binding Proteins/*metabolism ; High-Throughput Nucleotide Sequencing ; Humans ; Mass Screening ; Membrane Proteins/*metabolism ; Nucleic Acid Amplification Techniques/*methods ; RNA, Viral/analysis/metabolism ; SARS-CoV-2/*genetics/isolation &amp; purification ; Viral Proteins/*metabolism ; },
abstract = {The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), also known as 2019 novel coronavirus (2019-nCoV), is a highly infectious RNA virus. A percentage of patients develop coronavirus disease 2019 (COVID-19) after infection, whose symptoms include fever, cough, shortness of breath and fatigue. Acute and life-threatening respiratory symptoms are experienced by 10-20% of symptomatic patients, particularly those with underlying medical conditions. One of the main challenges in the containment of COVID-19 is the identification and isolation of asymptomatic/pre-symptomatic individuals. A number of molecular assays are currently used to detect SARS-CoV-2. Many of them can accurately test hundreds or even thousands of patients every day. However, there are presently no testing platforms that enable more than 10,000 tests per day. Here, we describe the foundation for the REcombinase Mediated BaRcoding and AmplificatioN Diagnostic Tool (REMBRANDT), a high-throughput Next Generation Sequencing-based approach for the simultaneous screening of over 100,000 samples per day. The REMBRANDT protocol includes direct two-barcoded amplification of SARS-CoV-2 and control amplicons using an isothermal reaction, and the downstream library preparation for Illumina sequencing and bioinformatics analysis. This protocol represents a potentially powerful approach for community screening of COVID-19 that may be modified for application to any infectious or non-infectious genome.},
}
@article {pmid35260714,
year = {2022},
author = {Shomroni, O and Sitte, M and Schmidt, J and Parbin, S and Ludewig, F and Yigit, G and Zelarayan, LC and Streckfuss-Bömeke, K and Wollnik, B and Salinas, G},
title = {A novel single-cell RNA-sequencing approach and its applicability connecting genotype to phenotype in ageing disease.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {4091},
pmid = {35260714},
issn = {2045-2322},
mesh = {Aging ; Genotype ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Phenotype ; RNA ; *Single-Cell Analysis/methods ; },
abstract = {Single cell multi-omics analysis has the potential to yield a comprehensive understanding of the cellular events that underlie the basis of human diseases. The cardinal feature to access this information is the technology used for single-cell isolation, barcoding, and sequencing. Most currently used single-cell RNA-sequencing platforms have limitations in several areas including cell selection, documentation and library chemistry. In this study, we describe a novel high-throughput, full-length, single-cell RNA-sequencing approach that combines the CellenONE isolation and sorting system with the ICELL8 processing instrument. This method offers substantial improvements in single cell selection, documentation and capturing rate. Moreover, it allows the use of flexible chemistry for library preparations and the analysis of living or fixed cells, whole cells independent of sizing and morphology, as well as of nuclei. We applied this method to dermal fibroblasts derived from six patients with different segmental progeria syndromes and defined phenotype associated pathway signatures with variant associated expression modifiers. These results validate the applicability of our method to highlight genotype-expression relationships for molecular phenotyping of individual cells derived from human patients.},
}
@article {pmid35259071,
year = {2023},
author = {Suresh, E and Rathipriya, A and Shanmugam, SA and Hamsavalli, R and Kathirvelpandian, A},
title = {Character-based diagnostic keys, molecular identification and phylogenetic relationships of threadfin breams (family: Nemipteridae) based on mitochondrial genes from the Southern coromandel Coast, India.},
journal = {Animal biotechnology},
volume = {34},
number = {4},
pages = {1553-1565},
doi = {10.1080/10495398.2022.2040522},
pmid = {35259071},
issn = {1532-2378},
mesh = {Animals ; *Genes, Mitochondrial/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Fishes/genetics ; DNA, Mitochondrial/genetics ; India ; Nucleotides ; },
abstract = {DNA barcoding, primarily focusing on cytochrome c oxidase subunit I (COI) gene has been appraised as an effective tool for species identification. In this study, we focused on the marine fishes of Family Nemipteridae, one of the commercially important group distributed within the Coromandel Coast. The Partial sequences of COI and 16S rRNA of mitochondrial genes were analyzed for species identification and phylogenetic relationship of Nemipterus species (Nemipterus japonicus, Nemipterus peronii, Nemipterus bipunctatus, Nemipterus bathybius). Character-based identification approaches that categorize specimens to species using classification rules that compactly identify species in terms of key diagnostic nucleotides in selected gene sequences. Using the BLOG 2.0 software, species-specific diagnostic nucleotides were identified for the selected group of species. A data set of 198 mtCOI sequences was obtained from published resources and used to screen character-based molecular diagnostic keys for species in silico. Partial sequences of both the genes provided sufficient phylogenetic information to distinguish the four Nemipterus species indicating the usefulness of mtDNA-based approach in species identification. This study proves the use of mtDNA genes sequence-based approach is a support tool along with traditional taxonomy for identifying fish species at a faster pace.},
}
@article {pmid35257114,
year = {2022},
author = {Rezaei, S and Uffenorde, J and Gimm, O and Hosseinpour Feizi, MA and Miemczyk, S and Coutinho, LL and Jensen, P and Guerrero-Bosagna, C and Pértille, F},
title = {GBS-MeDIP: A protocol for parallel identification of genetic and epigenetic variation in the same reduced fraction of genomes across individuals.},
journal = {STAR protocols},
volume = {3},
number = {1},
pages = {101202},
pmid = {35257114},
issn = {2666-1667},
mesh = {*DNA/genetics ; *DNA Methylation/genetics ; Epigenesis, Genetic ; Genotype ; Humans ; Immunoprecipitation ; },
abstract = {The GBS-MeDIP protocol combines two previously described techniques, Genotype-by-Sequencing (GBS) and Methylated-DNA-Immunoprecipitation (MeDIP). Our method allows for parallel and cost-efficient interrogation of genetic and methylomic variants in the DNA of many reduced genomes, taking advantage of the barcoding of DNA samples performed in the GBS and the subsequent creation of DNA pools, then used as an input for the MeDIP. The GBS-MeDIP is particularly suitable to identify genetic and methylomic biomarkers when resources for whole genome interrogation are lacking.},
}
@article {pmid35256815,
year = {2022},
author = {Hardwick, SA and Hu, W and Joglekar, A and Fan, L and Collier, PG and Foord, C and Balacco, J and Lanjewar, S and Sampson, MM and Koopmans, F and Prjibelski, AD and Mikheenko, A and Belchikov, N and Jarroux, J and Lucas, AB and Palkovits, M and Luo, W and Milner, TA and Ndhlovu, LC and Smit, AB and Trojanowski, JQ and Lee, VMY and Fedrigo, O and Sloan, SA and Tombácz, D and Ross, ME and Jarvis, E and Boldogkői, Z and Gan, L and Tilgner, HU},
title = {Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue.},
journal = {Nature biotechnology},
volume = {40},
number = {7},
pages = {1082-1092},
pmid = {35256815},
issn = {1546-1696},
support = {R01 HL136520/HL/NHLBI NIH HHS/United States ; R01 GM135247/GM/NIGMS NIH HHS/United States ; U01 DA053625/DA/NIDA NIH HHS/United States ; R01 NS105477/NS/NINDS NIH HHS/United States ; R01 DA008259/DA/NIDA NIH HHS/United States ; R56 AI164599/AI/NIAID NIH HHS/United States ; T32 DA039080/DA/NIDA NIH HHS/United States ; RF1 MH121267/MH/NIMH NIH HHS/United States ; R01 MH125956/MH/NIMH NIH HHS/United States ; R01 AG072758/AG/NIA NIH HHS/United States ; R01 AG051390/AG/NIA NIH HHS/United States ; U54 NS100717/NS/NINDS NIH HHS/United States ; UM1 AI164559/AI/NIAID NIH HHS/United States ; U54 NS117170/NS/NINDS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; P01 HD067244/HD/NICHD NIH HHS/United States ; R01 NS123562/NS/NINDS NIH HHS/United States ; R01 AG054214/AG/NIA NIH HHS/United States ; U19 AG062418/AG/NIA NIH HHS/United States ; },
mesh = {Alternative Splicing/genetics ; *Brain/metabolism ; Exons/genetics ; Humans ; Protein Isoforms/genetics ; *RNA/genetics ; Sequence Analysis, RNA ; },
abstract = {Single-nuclei RNA sequencing characterizes cell types at the gene level. However, compared to single-cell approaches, many single-nuclei cDNAs are purely intronic, lack barcodes and hinder the study of isoforms. Here we present single-nuclei isoform RNA sequencing (SnISOr-Seq). Using microfluidics, PCR-based artifact removal, target enrichment and long-read sequencing, SnISOr-Seq increased barcoded, exon-spanning long reads 7.5-fold compared to naive long-read single-nuclei sequencing. We applied SnISOr-Seq to adult human frontal cortex and found that exons associated with autism exhibit coordinated and highly cell-type-specific inclusion. We found two distinct combination patterns: those distinguishing neural cell types, enriched in TSS-exon, exon-polyadenylation-site and non-adjacent exon pairs, and those with multiple configurations within one cell type, enriched in adjacent exon pairs. Finally, we observed that human-specific exons are almost as tightly coordinated as conserved exons, implying that coordination can be rapidly established during evolution. SnISOr-Seq enables cell-type-specific long-read isoform analysis in human brain and in any frozen or hard-to-dissociate sample.},
}
@article {pmid35255817,
year = {2022},
author = {Liu, CK and Lei, JQ and Jiang, QP and Zhou, SD and He, XJ},
title = {The complete plastomes of seven Peucedanum plants: comparative and phylogenetic analyses for the Peucedanum genus.},
journal = {BMC plant biology},
volume = {22},
number = {1},
pages = {101},
pmid = {35255817},
issn = {1471-2229},
mesh = {Apiaceae/*classification/*genetics ; China ; *Classification ; *Evolution, Molecular ; Genetic Variation ; Genome Size ; *Genome, Plastid ; Genotype ; *Phylogeny ; },
abstract = {BACKGROUND: The Peucedanum genus is the backbone member of Apiaceae, with many economically and medically important plants. Although the previous studies on Peucedanum provide us with a good research basis, there are still unclear phylogenetic relationships and many taxonomic problems in Peucedanum, and a robust phylogenetic framework of this genus still has not been obtained, which severely hampers the improvement and revision of taxonomic system for this genus. The plastid genomes possessing more variable characters have potential for reconstructing a robust phylogeny in plants.<br><br>RESULTS: In the current study, we newly sequenced and assembled seven Peucedanum plastid genomes. Together with five previously published plastid genomes of Peucedanum, we performed a comprehensively comparative analyses for this genus. Twelve Peucedanum plastomes were similar in terms of genome structure, codon bias, RNA editing sites, and SSRs, but varied in genome size, gene content and arrangement, and border of SC/IR. Fifteen mutation hotspot regions were identified among plastid genomes that can serve as candidate DNA barcodes for species identification in Peucedanum. Our phylogenetic analyses based on plastid genomes generated a phylogeny with high supports and resolutions for Peucedanum that robustly supported the non-monophyly of genus Peucedanum.<br><br>CONCLUSION: The plastid genomes of Peucedanum showed both conservation and diversity. The plastid genome data were efficient and powerful for improving the supports and resolutions of phylogeny for the complex Peucedanum genus. In summary, our study provides new sights into the plastid genome evolution, taxonomy, and phylogeny for Peucedanum species.},
}
@article {pmid35253492,
year = {2022},
author = {Ma, W and Yang, J and Gao, X and Han, T and Liu, J and Ding, J and Zhao, W and Peng, YL and Bhadauria, V},
title = {First Report of Didymella glomerata Causing Didymella Leaf Blight on Maize in China.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-02-22-0282-PDN},
pmid = {35253492},
issn = {0191-2917},
abstract = {Maize (Zea mays L.) is a staple food crop worldwide. In July 2021, gray leaf blight was observed on maize leaves in a field located in Panjin (41°7'11.98" N, 122°4'14.57" E), Liaoning Province, China. Nearly 5% of the maize plants were affected in the field. The leaves of the affected plants showed oval to oblong, gray, sunken lesions with yellow or tan margins. The lesions were scattered all over the leaf surface; however, they were absent on the stalks and other parts of the affected plants. To isolate the pathogen, leaf discs (1.25 mm2) excised from the blight lesions were surface-sterilized with 70% ethanol for 30 seconds, followed by 20% NaOCl for 2 minutes and finally rinsed three times with sterilized water. The discs were cultured on potato dextrose agar (PDA) plates supplemented with streptomycin (100 mg/L) and incubated at 25oC under a 12-h photoperiod for 7 days. Six single spore isolates (two per sampled infected leaf) were purified from the PDA culture plates. The fungal colonies of three selected isolates (one per sampled infected leaf; Pj-1, Pj-2, and Pj-3) were dark brown on the PDA plates and devoid of aerial hyphae; all three isolates grew 11 mm/day on the PDA plates. The number of conidia produced by the isolates on the 6-cm PDA plates 7 days after incubation was ranged from 160 x 108 to 208 x 108 (n = 36). Conidia were hyaline, single-celled and ellipsoidal (3.35-3.56 µm [width] x 6.47-6.70 [length] µm; n = 36). To identify the pathogen, four loci, i.e., 28S subunit (large subunit [LSU]) of the nuclear ribosomal (nr) DNA, internal transcribed spacer (ITS) region (ITS1, 5.8S subunit of nrDNA, and ITS2), the second-largest subunit of RNA polymerase II (rpb2) and β-tubulin (tub2) were amplified using the primer sets described in the study by Chen el al. 2015. BLASTn search against GenBank revealed that the four amplicon sequences originating from Pj-1, Pj-2, and Pj-3 showed 99-100% homology to the type strain CBS 528.66 of D. glomerata. A phylogenetic tree deduced from a maximum likelihood analysis of a concatenated MUSCLE-based alignment of LSU, ITS region, rpb2, and tub2 sequences of 12 isolates/strains showed that the Pj isolates clustered together with CBS 528.66, along with other D. glomerata isolates/strains, with a high bootstrap support value (i.e., 99). Based on both morphological characteristics and molecular phylogeny, Pj-1, Pj-2, and Pj-3 were identified as the D. glomerata isolates. Since the amplicon sequences of the three isolates were identical, only Pj-2 sequences were deposited in GenBank with accession numbers OM372474 (LSU), OK485138 (ITS), OM406188 (rpb2), and OK485135 (tub2). To confirm pathogenicity, 14-day-old plants (V3 growth stage) of a maize cultivar P178 were spray-inoculated with the Pj-2 conidia (1 x 107 conidia/mL) in a growth chamber. The inoculated leaves exhibited typical gray leaf blight lesions (similar to those detected in the maize field) 7 days post-inoculation at 25oC and 95-100% humidity under a 12-h photoperiod, whereas the leaves spray-inoculated with sterilized water remained healthy. The pathogenicity assay was repeated three times; the pathogen was re-isolated from the inoculated leaves each time and confirmed by the morphological characteristics and the molecular phylogeny based on the four loci to be D. glomerata, fulfilling Koch's postulates. This first report of D. glomerata causing Didymella leaf blight on maize will help develop robust disease management strategies against this emerging fungal pathogen.},
}
@article {pmid35252450,
year = {2022},
author = {Song, Y and Zhao, W and Xu, J and Li, M and Zhang, Y},
title = {Chloroplast Genome Evolution and Species Identification of Styrax (Styracaceae).},
journal = {BioMed research international},
volume = {2022},
number = {},
pages = {5364094},
pmid = {35252450},
issn = {2314-6141},
mesh = {Chloroplasts/genetics ; *Genome, Chloroplast/genetics ; Phylogeny ; *Styracaceae/genetics ; Styrax ; },
abstract = {The genus Styrax L. consists of approximately 130 species distributed in the Americas, eastern Asia, and the Mediterranean region. The phylogeny and evolutionary history of this genus are not clear. Knowledge of the phylogenetic relationships and the method for species identification will be critical for the evolution of this genus. In this study, we sequenced the chloroplast genome of 17 Styrax samples and added 17 additional chloroplast genome sequences from GenBank. The data were used to investigate chloroplast genome evolution, infer phylogenetic relationships, and access the species identification rate within Styrax. The Styrax chloroplast genome contains typical quadripartite structures, ranging from 157,641 bp to 159,333 bp. The chloroplast genome contains 114 unique genes. The P distance among the Styrax species ranged from 0.0003 to 0.00611. Seventeen small inversions and SSR sites were discovered in the Styrax chloroplast genome. By comparing with the chloroplast genome sequences, six mutation hotspots were identified, and the markers ycf1b and trnT-trnL were identified as the best Styrax-specific DNA barcodes. The specific barcodes and superbarcode exhibited higher discriminatory power than universal barcodes. Chloroplast phylogenomic results improved the resolution of the phylogenetic relationships of Styrax compared to previous analyses.},
}
@article {pmid35250948,
year = {2022},
author = {Mahata, PK and Dass, RS and Pan, A and Muthusamy, B},
title = {Substantive Morphological Descriptions, Phylogenetic Analysis and Single Nucleotide Polymorphisms of Aspergillus Species From Foeniculum vulgare.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {832320},
pmid = {35250948},
issn = {1664-302X},
abstract = {Ascomycetous fungi are found associated with a wide variety of substrates which range from fresh water to marine ecosystems, tropical to temperate forest soils and deserts, throughout the world over. These demystifying fungi exist as endophytes, pathogens and saprobes. They have been studied due to their ability to contaminate foods and feedstuffs, causing an elaboration of mycotoxins. The objectives of the study included extensive analyses of the morphological features of fungi, especially Aspergilli, which have been presented while studying them on specific mycological media. It is also an elaborate compilation of substantive macro- and micro-morphological characterization of different Aspergilli isolated from the spice Foeniculum vulgare used in India and other countries in the world. Further, a first of its kind attempt has been made to study their relative abundance and frequency of occurrence, molecular phylogeny and genetic relatedness to characterize the Aspergilli into specific sections, groups and clades. Single nucleotide polymorphism (SNP) analysis was carried out to evaluate the functional consequences of nucleotide variations, synonymous and non-synonymous mutations in the protein structure. The study resulted in a total of 3,506 Aspergillus isolates, which were obtained from seventy (70) fennel samples, representing 14 Aspergillus species. The two most frequently found species were A. niger and A. flavus with a relative abundance of 32.24 and 11.63%, respectively. The taxonomy and current placements have been reappraised with suggestions and prospects for future research from six sections namely Terrei, Flavi, Fumigati, Nidulantes, Nigri, and Versicolores. In addition, a total number of 27 isolates were studied and deposited at the National Centre for Biotechnology Information (NCBI) and five Aspergillus species have been identified and are being reported for the first time from the fennel seeds, based on partial sequence analysis of the official fungal barcode namely, Internal Transcribed Spacer (ITS) and a functional gene, beta tubulin gene locus, coupled with phenotypic characterization. SNPs for specific DNA regions have been used to identify variants in Aspergilli obtained from Indian fennel seeds for the first time. The need for a polyphasic approach of morphological identification and genetic characterization of Aspergilli from Foeniculum vulgare is addressed and presented here in adequate detail. Our current work makes extensive use of partial beta-tubulin gene sequences analyses to evaluate the association between SNPs in five Aspergillus species sections.},
}
@article {pmid35247587,
year = {2022},
author = {Hookabe, N and Motobayashi, H and Jimi, N and Kajihara, H and Ueshima, R},
title = {First record of the decapod-egg predator Ovicides paralithodis (Nemertea, Carcinonemertidae) from the snow crab Chionoecetes opilio (Decapoda, Brachyura).},
journal = {Parasitology international},
volume = {89},
number = {},
pages = {102567},
doi = {10.1016/j.parint.2022.102567},
pmid = {35247587},
issn = {1873-0329},
mesh = {*Acanthocephala ; Animals ; *Brachyura ; Genes, Mitochondrial ; Japan ; },
abstract = {The carcinonemertid monostiliferan Ovicides paralithodis Kajihara and Kuris, 2013 was originally described as an egg predator of the red-king crab Paralithodes camtschaticus (Tilesius, 1815) in the Sea of Okhotsk, the Bering Sea, and the Gulf of Alaska. In the present study, several carcinonemertid specimens were obtained from the egg mass of the snow crab Chionoecetes opilio (O. Fabricius, 1788) in the Sea of Japan. Partial sequences of the mitochondrial cytochrome c oxidase subunit I gene (COI) determined from two specimens of the carcinonemertid were identical with a barcode sequence from the holotype of O. paralithodis, indicating that the host range of the species covers at least the two decapod species, P. camtschaticus and C. opilio.},
}
@article {pmid35246772,
year = {2022},
author = {Singh, M and Lalronunga, S and Ramliana, L},
title = {Integrative taxonomy peeps a new torrent catfish species of genus Amblyceps (Siluriformes: Amblycipitidae) in Kaladan River of Mizoram, India.},
journal = {Molecular biology reports},
volume = {49},
number = {6},
pages = {4565-4572},
pmid = {35246772},
issn = {1573-4978},
support = {BT/388/NE/TBP/2012//Department of Biotechnology , Ministry of Science and Technology/ ; },
mesh = {Animals ; *Catfishes/genetics ; DNA ; Genes, Mitochondrial ; India ; Phylogeny ; Rivers ; },
abstract = {BACKGROUND: Explorations of the Kaladan River of Mizoram, India during the last decade have given a large number of new species. Integrative taxonomy, when used at the time of discovery of new species, can correlate the morphological characters with the species-specific DNA signatures and ameliorate the process of species identification. Based on this approach, Amblyceps hmolaii sp. nov., a new torrent catfish species is described from the Kaladan River drainage.<br><br>METHODS AND RESULTS: The new species is distinguished from all twenty-two congeners by morphometric measurements and meristic counts. Sequence analysis of mitochondrial gene cytochrome c oxidase subunit I (COI), generated in this study and those available in NCBI, separated A. hmolaii sp. nov. from seven species of Amblyceps. Analysis of COI sequences, with ABGD software to delimit the species, also provided eight stable groups corresponding to the eight species of Amblyceps. The new species was separated from its congeners with an average genetic distance of 11.77%. Maximum-likelihood (ML) phylogenetic tree was constructed using the best fit nucleotide substitution model HKY&#x2009;+&#x2009;G&#x2009;+&#x2009;I.<br><br>CONCLUSION: This study used all the twenty-two congeners in morphomeristic analysis and seven congeners in molecular analysis, for comparison with the new species. This approach unambiguously resolved the new species from other species of Amblyceps and created its species-specific DNA signatures. The discovery of new species even marked the first record of genus Amblyceps from the Kaladan drainage.},
}
@article {pmid35246040,
year = {2022},
author = {Draper, J and Rodgers, T and Young, JK},
title = {Beating the heat: ecology of desert bobcats.},
journal = {BMC ecology and evolution},
volume = {22},
number = {1},
pages = {25},
pmid = {35246040},
issn = {2730-7182},
mesh = {Animals ; Animals, Wild ; Ecology ; Ecosystem ; Hot Temperature ; *Lynx/genetics ; },
abstract = {BACKGROUND: Relative to temperate regions, little is known about bobcats (Lynx rufus) in the Sonoran Desert portion of their range, in part due to the difficulty of sampling an elusive carnivore in harsh desert environments. Here, we quantify habitat selection and evaluate diet of bobcats at Kofa National Wildlife Refuge, Arizona, USA, using multiple sampling techniques including GPS telemetry, camera traps, and DNA metabarcoding.<br><br>RESULTS: Home ranges during the hot season were smaller than during the cool season. Camera trapping failed to yield a high enough detection rate to identify habitat occupancy trends but third-order resource selection from GPS-collar data showed a preference for higher elevations and rugged terrain at lower elevations. Diet composition consisted of a diverse range of available small prey items, including a higher frequency of avian prey than previously observed in bobcats.<br><br>CONCLUSIONS: Desert bobcats in our study maintained smaller home ranges and primarily consumed smaller prey than their more northern relatives. This study illustrates the benefit of employing multiple, complementary sampling methods to understand the ecology of elusive species.},
}
@article {pmid35245325,
year = {2022},
author = {Mulcahy, DG and Ibáñez, R and Jaramillo, CA and Crawford, AJ and Ray, JM and Gotte, SW and Jacobs, JF and Wynn, AH and Gonzalez-Porter, GP and McDiarmid, RW and Crombie, RI and Zug, GR and de Queiroz, K},
title = {DNA barcoding of the National Museum of Natural History reptile tissue holdings raises concerns about the use of natural history collections and the responsibilities of scientists in the molecular age.},
journal = {PloS one},
volume = {17},
number = {3},
pages = {e0264930},
pmid = {35245325},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; DNA ; *DNA Barcoding, Taxonomic ; *Museums ; Natural History ; Reptiles/genetics ; },
abstract = {Natural history collections are essential to a wide variety of studies in biology because they maintain large collections of specimens and associated data, including genetic material (e.g., tissues) for DNA sequence data, yet they are currently under-funded and collection staff have high workloads. With the advent of aggregate databases and advances in sequencing technologies, there is an increased demand on collection staff for access to tissue samples and associated data. Scientists are rapidly developing large DNA barcode libraries, DNA sequences of specific genes for species across the tree of life, in order to document and conserve biodiversity. In doing so, mistakes are made. For instance, inconsistent taxonomic information is commonly taken from different lending institutions and deposited in data repositories, such as the Barcode of Life Database (BOLD) and GenBank, despite explicit disclaimers regarding the need for taxonomic verification by the lending institutions. Such errors can have profound effects on subsequent research based on these mis-labelled sequences in data repositories. Here, we present the production of a large DNA barcode library of reptiles from the National Museum of Natural History tissue holdings. The library contains 2,758 sequences (2,205 COI and 553 16S) from 2260 specimens (four crocodilians, 37 turtles, and 2,219 lizards, including snakes), representing 583 named species, from 52 countries. In generating this library, we noticed several common mistakes made by scientists depositing DNA barcode data in public repositories (e.g., BOLD and GenBank). Our goal is to raise awareness of these concerns and offer advice to avoid such mistakes in the future to maintain accurate DNA barcode libraries to properly document Earth's biodiversity.},
}
@article {pmid35242361,
year = {2022},
author = {Gallego-García, P and Varela, N and Estévez-Gómez, N and De Chiara, L and Fernández-Silva, I and Valverde, D and Sapoval, N and Treangen, TJ and Regueiro, B and Cabrera-Alvargonzález, JJ and Del Campo, V and Pérez, S and Posada, D},
title = {Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters.},
journal = {Virus evolution},
volume = {8},
number = {1},
pages = {veac008},
pmid = {35242361},
issn = {2057-1577},
abstract = {A detailed understanding of how and when severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission occurs is crucial for designing effective prevention measures. Other than contact tracing, genome sequencing provides information to help infer who infected whom. However, the effectiveness of the genomic approach in this context depends on both (high enough) mutation and (low enough) transmission rates. Today, the level of resolution that we can obtain when describing SARS-CoV-2 outbreaks using just genomic information alone remains unclear. In order to answer this question, we sequenced forty-nine SARS-CoV-2 patient samples from ten local clusters in NW Spain for which partial epidemiological information was available and inferred transmission history using genomic variants. Importantly, we obtained high-quality genomic data, sequencing each sample twice and using unique barcodes to exclude cross-sample contamination. Phylogenetic and cluster analyses showed that consensus genomes were generally sufficient to discriminate among independent transmission clusters. However, levels of intrahost variation were low, which prevented in most cases the unambiguous identification of direct transmission events. After filtering out recurrent variants across clusters, the genomic data were generally compatible with the epidemiological information but did not support specific transmission events over possible alternatives. We estimated the effective transmission bottleneck size to be one to two viral particles for sample pairs whose donor-recipient relationship was likely. Our analyses suggest that intrahost genomic variation in SARS-CoV-2 might be generally limited and that homoplasy and recurrent errors complicate identifying shared intrahost variants. Reliable reconstruction of direct SARS-CoV-2 transmission based solely on genomic data seems hindered by a slow mutation rate, potential convergent events, and technical artifacts. Detailed contact tracing seems essential in most cases to study SARS-CoV-2 transmission at high resolution.},
}
@article {pmid35242042,
year = {2022},
author = {Wu, L and Nie, L and Guo, S and Wang, Q and Wu, Z and Lin, Y and Wang, Y and Li, B and Gao, T and Yao, H},
title = {Identification of Medicinal Bidens Plants for Quality Control Based on Organelle Genomes.},
journal = {Frontiers in pharmacology},
volume = {13},
number = {},
pages = {842131},
pmid = {35242042},
issn = {1663-9812},
abstract = {Bidens plants are annuals or perennials of Asteraceae and usually used as medicinal materials in China. They are difficult to identify by using traditional identification methods because they have similar morphologies and chemical components. Universal DNA barcodes also cannot identify Bidens species effectively. This situation seriously hinders the development of medicinal Bidens plants. Therefore, developing an accurate and effective method for identifying medicinal Bidens plants is urgently needed. The present study aims to use phylogenomic approaches based on organelle genomes to address the confusing relationships of medicinal Bidens plants. Illumina sequencing was used to sequence 12 chloroplast and eight mitochondrial genomes of five species and one variety of Bidens. The complete organelle genomes were assembled, annotated and analysed. Phylogenetic trees were constructed on the basis of the organelle genomes and highly variable regions. The organelle genomes of these Bidens species had a conserved gene content and codon usage. The 12 chloroplast genomes of the Bidens species were 150,489 bp to 151,635 bp in length. The lengths of the eight mitochondrial genomes varied from each other. Bioinformatics analysis revealed the presence of 50-71 simple sequence repeats and 46-181 long repeats in the organelle genomes. By combining the results of mVISTA and nucleotide diversity analyses, seven candidate highly variable regions in the chloroplast genomes were screened for species identification and relationship studies. Comparison with the complete mitochondrial genomes and common protein-coding genes shared by each organelle genome revealed that the complete chloroplast genomes had the highest discriminatory power for Bidens species and thus could be used as a super barcode to authenticate Bidens species accurately. In addition, the screened highly variable region trnS-GGA-rps4 could be also used as a potential specific barcode to identify Bidens species.},
}
@article {pmid35241112,
year = {2022},
author = {Lu, G and Qiao, J and Wang, L and Liu, H and Wu, G and Zhu, Y and Zhao, Y and Xie, G and Qin, M},
title = {An integrated study of Violae Herba (Viola philippica) and five adulterants by morphology, chemical compositions and chloroplast genomes: insights into its certified plant origin.},
journal = {Chinese medicine},
volume = {17},
number = {1},
pages = {32},
pmid = {35241112},
issn = {1749-8546},
support = {(2019) 39//Department of Social Security, Ministry of Finance (CN)/ ; },
abstract = {BACKGROUND: Viola philippica Cav. is the only original plant for Violae Herba, as described in the Chinese Pharmacopoeia. The quality of this crude drug is affected by several adulterants from congeneric Viola species, and the authentic plant origin of Violae Herba is still controversial. Genome-based identification offers abundant genetic information and potential molecular markers that can be used for the authentication of closely related species. This study aims to investigate the certified origin of Violae Herba and to develop more effective markers for these easily confused species at the genetic level.<br><br>METHODS: We compared the morphology and chemical composition of 18 batches of commercial samples and six widespread medicinal Viola plants used as Violae Herba or its substitutes by TLC and HPLC-Triple-TOF-MS/MS analyses. The complete chloroplast genomes of these species were sequenced and analyzed, including the general features, repeat sequences, mutational hotspots and phylogeny. The complete chloroplast genomes used as superbarcodes and some specific barcodes screened from mutational hotspots were tested for their ability to distinguish Viola species.<br><br>RESULTS: A comparative study showed that Violae Herba is a multi-origin traditional Chinese medicine. Commercial decoction pieces and the standard reference drug were mainly derived from V. prionantha, clashing with the record in the Chinese Pharmacopoeia. Chloroplast genome analyses of V. philippica and five adulterants indicated that sequence divergence was relatively low within Viola species. By tree-based approaches, the complete chloroplast genomes showed a better discrimination ability and phylogenetic resolution for each Viola species. These results indicate that the whole chloroplast genomes can be used as superbarcodes to differentiate Viola medicinal plants. More specific DNA barcodes could be further developed from the Viola chloroplast genomes for more efficient and rapid identification of commercial Violae Herba and its adulterants.<br><br>CONCLUSIONS: This study has implications for chloroplast genome-based phylogenetic analysis and the authentication of multiple Viola species used as Violae Herba. The legal origin recorded in the Chinese Pharmacopoeia should be further revised to V. prionantha, in line with the commercial Violae Herba in the TCM markets.},
}
@article {pmid35238211,
year = {2022},
author = {Nelson, BC and Borgos, SE},
title = {High-throughput synthesis and characterization of next-generation lipid nanoparticles for enhanced in vivo performance.},
journal = {Nanomedicine (London, England)},
volume = {17},
number = {9},
pages = {573-576},
doi = {10.2217/nnm-2022-0024},
pmid = {35238211},
issn = {1748-6963},
mesh = {Liposomes ; *Nanoparticles ; },
}
@article {pmid35238000,
year = {2022},
author = {Saigusa, R and Durant, CP and Suryawanshi, V and Ley, K},
title = {Single-Cell Antibody Sequencing in Atherosclerosis Research.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2419},
number = {},
pages = {765-778},
pmid = {35238000},
issn = {1940-6029},
support = {P01 HL136275/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; *Atherosclerosis/genetics ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Mice ; Sequence Analysis, RNA ; *Single-Cell Analysis ; Transcriptome ; },
abstract = {The transcriptomic information obtained by single cell RNA sequencing (scRNA-seq) can be supplemented by information on the cell surface phenotype by using oligonucleotide-tagged monoclonal antibodies (scAb-Seq). This is of particular importance in immune cells, where the correlation between mRNA and cell surface expression is very weak. scAb-Seq is facilitated by the availability of commercial antibodies and antibody mixes. Now panels of up to 200 antibodies are available for human and mouse cells. Proteins are detected by antibodies conjugated to a tripartite DNA sequence that contains a primer for amplification and sequencing, a unique oligonucleotide that acts as an antibody barcode and a poly(dA) sequence, simultaneously detecting extension of antibody-specific DNA sequences and cDNAs in the same poly(dT)-primed reaction. For each cell, surface protein expression is captured and sequenced along with the cell's transcriptome. Here, we list the steps needed to produce antibody sequencing data from tissue or blood cells.},
}
@article {pmid35234597,
year = {2022},
author = {Pereira, RIDS and Maciel, CR and Iketani, G},
title = {Molecular features of Probopyrus sp. (Isopoda: Bopyridae) from Brazilian Amazonia and the parasitism of inland populations of Macrobrachium amazonicum (Decapoda: Palaemonidae).},
journal = {Parasitology},
volume = {149},
number = {2},
pages = {203-208},
pmid = {35234597},
issn = {1469-8161},
mesh = {Animals ; Brazil ; Electron Transport Complex IV/genetics ; Fresh Water ; *Isopoda/genetics ; *Palaemonidae/parasitology ; },
abstract = {Bopyrid isopods of the genus Probopyrus are well-known parasites of freshwater prawns of the genus Macrobrachium. The parasitism of coastal populations of Macrobrachium amazonicum by Probopyrus bithynis, for example, has been documented since the late 1980s. Despite this, molecular data on different populations are not available for any Probopyrus species. The present study is the first to describe Probopyrus populations from distinct regions of the Amazon basin based on sequences of two genes, the mitochondrial cytochrome oxidase C subunit I (COI) and the nuclear 18S ribosomal DNA (18S rDNA) gene. The analyses indicated the presence of two Probopyrus species, each parasitizing either the coastal or the inland populations of M. amazonicum. The results indicated the potential use of the COI barcode for the identification of Probopyrus species. We discuss the potential implications of the findings for the taxonomy of Probopyrus bithynis and other species of the genus Probopyrus.},
}
@article {pmid35234373,
year = {2022},
author = {Gan, Y and Lu, M and Lai, Q and Zhu, B},
title = {[Application and progress in high-throughput sequencing technology for meat adulteration detection].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {38},
number = {2},
pages = {411-426},
doi = {10.13345/j.cjb.210113},
pmid = {35234373},
issn = {1872-2075},
mesh = {DNA ; Food Contamination/analysis ; High-Throughput Nucleotide Sequencing/methods ; *Meat/analysis ; *Meat Products ; Technology ; },
abstract = {Adulteration in meat products is a widespread issue that could lead to serious threats to public health and religious violations. Technology that offers rapid, sensitive, accurate and reliable detection of meat species is the key to an effectual monitoring and control against meat adulteration. In recent years, high-throughput sequencing-based DNA metabarcoding technology has developed rapidly. With the characteristics of being high-throughput, highly precise and high-speed, this technology can simultaneously identify multiple species in complex samples, thus offering pronounced advantages in the surveillance of adulteration in meat and meat products. Starting with an introduction of the major developments in the high-throughput sequencing technology in the past two decades, this review provides an overview of the technical characteristics and research methods of DNA metabarcoding, summarizes the application of DNA metabarcoding technology in meat adulteration detection over the last few years, discusses the challenges of using DNA metabarcoding technology in the detection of meat adulteration, and provides future prospects on the development of this technology.},
}
@article {pmid35233115,
year = {2021},
author = {Obodai, E and Kyei, GB and Aboagye, J and Bonney, EY and Asante, IA and Bonney, JKH and Adusei-Poku, M and Lamptey, H and Adu, B and Kenu, E and Koram, KA and Ampofo, WK and Odoom, JK},
title = {Data management during COVID-19 outbreak response in Ghana: a reference laboratory perspective on key issues and measures.},
journal = {Ghana medical journal},
volume = {55},
number = {2 Suppl},
pages = {51-55},
pmid = {35233115},
issn = {2616-163X},
mesh = {*COVID-19/epidemiology ; Data Management ; Disease Outbreaks ; Ghana/epidemiology ; Humans ; Laboratories ; Pandemics ; SARS-CoV-2 ; },
abstract = {UNLABELLED: The COVID-19 pandemic caused by SARS-CoV-2 is an important subject for global health. Ghana experienced low-moderate transmission of the disease when the first case was detected in March 12, 2020 until the middle of July when the number of cases begun to drop. By August 24, 2020, the country's total number of confirmed cases stood at 43,622, with 263 deaths. By the same time, the Noguchi Memorial Institute for Medical Research (NMIMR) of the University of Ghana, the primary testing centre for COVID-19, had tested 285,501 with 28,878 confirmed cases. Due to database gaps, there were initial challenges with timely reporting and feedback to stakeholders during the peak surveillance period. The gaps resulted from mismatches between samples and their accompanying case investigation forms, samples without case investigation forms and vice versa, huge data entry requirements, and delayed test results. However, a revamp in data management procedures, and systems helped to improve the turnaround time for reporting results to all interested parties and partners. Additionally, inconsistencies such as multiple entries and discrepant patient-sample information were resolved by introducing a barcoding electronic capture system. Here, we describe the main challenges with COVID-19 data management and analysis in the laboratory and recommend measures for improvement.<br><br>FUNDING: The work was supported by the Government of Ghana.},
}
@article {pmid35230911,
year = {2022},
author = {Shukla, I and Hill, JE},
title = {cpn60 barcode sequences accurately identify newly defined genera within the Lactobacillaceae.},
journal = {Canadian journal of microbiology},
volume = {68},
number = {6},
pages = {457-464},
doi = {10.1139/cjm-2021-0296},
pmid = {35230911},
issn = {1480-3275},
mesh = {*Chaperonin 60/genetics ; DNA Primers ; *Lactobacillaceae ; Lactobacillus ; Phylogeny ; Polymerase Chain Reaction/methods ; },
abstract = {The cpn60 barcode sequence has been established as an informative target for microbial species identification. Applications of cpn60 barcode sequencing are supported by the availability of "universal" PCR primers for amplification and a curated reference database of cpn60 sequences, cpnDB. A recent reclassification of lactobacilli involving the definition of 23 new genera provided an opportunity to update cpnDB and to determine if the cpn60 barcode could be used for accurate identification of species consistent with the new framework. Analysis of 275 cpn60 sequences representing 258/269 of the validly named species in Lactobacillus, Paralactobacillus, and the 23 newer genera showed that cpn60-based sequence relationships were generally consistent with whole-genome-based phylogeny. Aligning or mapping full-length barcode sequences or a 150 bp subsequence resulted in accurate and unambiguous species identification in almost all cases. Taken together, our results show that the combination of available reference sequence data, "universal" barcode amplification primers, and the inherent sequence diversity within the cpn60 barcode makes it a useful target for the detection and identification of lactobacilli, as defined by the latest taxonomic framework.},
}
@article {pmid35230532,
year = {2022},
author = {Mursyidin, DH and Makruf, MI and Badruzsaufari, and Noor, A},
title = {Molecular diversity of exotic durian (Durio spp.) germplasm: a case study of Kalimantan, Indonesia.},
journal = {Journal, genetic engineering &amp; biotechnology},
volume = {20},
number = {1},
pages = {39},
pmid = {35230532},
issn = {2090-5920},
abstract = {BACKGROUND: Durian of Indonesia, specifically Durio zibethinus, is a potential agricultural commodity for domestic and international markets. However, its quality is still less competitive or significantly lower to fulfill the export market, compared to a similar one from other countries. This study aimed to determine and analyze the genetic diversity and relationship of the exotic durian (Durio spp.) germplasm originally from Kalimantan, Indonesia, using the rbcL marker.<br><br>RESULTS: Based on this marker, the durian germplasm has a low genetic diversity (&#x3c0;%=0.24). It may strongly correspond with the variability sites or mutation present in the region. In this case, the rbcL region of the durian germplasm has generated 23 variable sites with a transition/transversion (Ti/Tv) bias value of 1.00. However, following the phylogenetic and principal component analyses, this germplasm is separated into four main clades and six groups, respectively. In this case, D. zibethinus was very closely related to D. exleyanus. Meanwhile, D. lowianus and D. excelsus were the farthest. In further analysis, 29 durians were very closely related, and the farthest was shown by Durian Burung (D. acutifolius) and Kalih Haliyang (D. kutejensis) as well as Pampaken Burung Kecil (D. kutejensis) and Durian Burung (D. acutifolius) with a divergence coefficient of 0.011. The Pearson correlation analysis confirms that 20 pairs of individual durians have a strong relation, shown by, e.g., Maharawin Hamak and Durian Burung as well as Mantuala Batu Hayam and Durian Burung Besar.<br><br>CONCLUSION: While the durian has a low genetic diversity, the phylogenetic analyses revealed that this germplasm originally from Kalimantan, Indonesia, shows unique relationships. These findings may provide a beneficial task in supporting the durian genetic conservation and breeding practices in the future, locally and globally.},
}
@article {pmid35229583,
year = {2021},
author = {Bušić, N and Kučinić, M and Merdić, E and Bruvo-Mađarić, B},
title = {Diversity of mosquito fauna (Diptera, Culicidae) in higher-altitude regions of Croatia.},
journal = {Journal of vector ecology : journal of the Society for Vector Ecology},
volume = {46},
number = {1},
pages = {65-75},
doi = {10.52707/1081-1710-46.1.65},
pmid = {35229583},
issn = {1948-7134},
mesh = {*Aedes/genetics ; Altitude ; Animals ; Croatia ; *Culex ; *Culicidae/genetics ; Mosquito Vectors/genetics ; },
abstract = {Global climate change and the accompanying rise in temperature could affect the biology and ecology of a number of vectors, including mosquitoes. High altitude areas that were previously unsuitable for the spread of mosquito vector populations could become suitable. The aim of this research was to study the distribution of mosquito species in higher altitude regions of Croatia. Samples were collected in three areas: Slavonian Mountains, Gorski Kotar, and Middle Velebit. Specimens were morphologically determined and confirmed by DNA barcoding and other genetic markers and showed the presence of 16 species belonging to six genera. The most abundant species were the Culex pipiens complex with 50% of the collected specimens. Both pipiens (Linnaeus, 1758) and molestus (Forskal, 1775) biotypes and their hybrids were identified within the complex, followed by Culex torrentium (Martini, 1925) (20.2%), Culiseta longiareolata (Macquart, 1838) (8.5%), and the invasive species Aedes japonicus (Theobald, 1901) (7.8% of the total number of collected specimens). The remaining 12 species made up 14.7% of the collected specimens. Intraspecific COI p-distances were within the standard barcoding threshold for OTUs, while interspecific genetic distances were much higher, confirming the existence of barcoding gaps. Mosquito fauna of Croatian mountains showed a moderate variety and made 30.8% of the total number of recorded mosquito species in Croatia thus far.},
}
@article {pmid35228909,
year = {2022},
author = {Martoni, F and Piper, AM and Rodoni, BC and Blacket, MJ},
title = {Disentangling bias for non-destructive insect metabarcoding.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e12981},
pmid = {35228909},
issn = {2167-8359},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Insecta/genetics ; DNA/genetics ; Biodiversity ; Plants/genetics ; },
abstract = {A fast and reliable method for obtaining a species-level identification is a fundamental requirement for a wide range of activities, from plant protection and invasive species management to biodiversity assessments and ecological studies. For insects, novel molecular techniques such as DNA metabarcoding have emerged as a rapid alternative to traditional morphological identification, reducing the dependence on limited taxonomic experts. Until recently, molecular techniques have required a destructive DNA extraction, precluding the possibility of preserving voucher specimens for future studies, or species descriptions. Here we paired insect metabarcoding with two recent non-destructive DNA extraction protocols, to obtain a rapid and high-throughput taxonomic identification of diverse insect taxa while retaining a physical voucher specimen. The aim of this work was to explore how non-destructive extraction protocols impact the semi-quantitative nature of metabarcoding, which alongside species presence/absence also provides a quantitative, but biased, representation of their relative abundances. By using a series of mock communities representing each stage of a typical metabarcoding workflow we were able to determine how different morphological (i.e., insect biomass and exoskeleton hardness) and molecular traits (i.e., primer mismatch and amplicon GC%), interact with different protocol steps to introduce quantitative bias into non-destructive metabarcoding results. We discuss the relevance of taxonomic bias to metabarcoding identification of insects and potential approaches to account for it.},
}
@article {pmid35228905,
year = {2022},
author = {Cortés-Carrasco, F and Elías-Gutiérrez, M and García-Madrigal, MDS},
title = {Holothuriophilus trapeziformis Nauck, 1880 (Decapoda: Pinnotheridae) from the Pacific coast of Mexico: taxonomic revision based on integrative taxonomy.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e12774},
pmid = {35228905},
issn = {2167-8359},
mesh = {Animals ; Male ; Mexico ; *Holothuria ; Chile ; Seafood ; *Cypriniformes ; *Decapoda ; },
abstract = {BACKGROUND: Holothuriophilus trapeziformis Nauck, 1880 is a holothurian-dweller pinnotherid crab representing one of the two species of the genus distributed along the Pacific coast of Mexico and Chile, respectively. While the parasitic ecological interaction with its host is well established, the morphology of the male remains unknown, and DNA information for the species is not available. Furthermore, the only morphological trait separating both species of the genus is subjective and corresponds to the presence or absence of a gap between the fingers of the chelae. Our goal is to complete and clarify the taxonomic status of H. trapeziformis and describe the male morphology with the use of the integrative taxonomy, providing additional characters to differentiate this species.<br><br>METHODS: We collected new biological material in the Pacific coast of Mexico including the topotypes. We also reviewed material from national collections to integrate morphology (based on a complete and detailed description and illustration of the species using light microscopy), ecological data (based on the identification of the host and the place where it was located within the host), and the mtCOI gene information (commonly known as DNA barcode) to differentiate Holothuriophilus trapeziformis from other related crabs.<br><br>RESULTS: This species presents marked sexual dimorphism only in the primary sexual characters. For the first time we describe morphological variability of traditionally stable characters. In addition to the gap between the fingers of the chelae, Holothuriophilus trapeziformis differs from H. pacificus (Poeppig, 1836) by their ornamentation, the shape of the male abdomen, and the gonopod. Cytocrome Oxidase 1 gene (COI) distance divergence was >3% between both Holothuriophilus species forming a clear clade. DNA barcoding indicates only one taxon, with a maximum divergence of 2.2%. All the specimens have the same Barcode Index Number (BIN; BOLD: ADE9974). All the hosts for H. trapeziformis were identified as Holothuria (Halodeima) inornata Semper, 1868; the presence of the crab in the host's coelomic cavity was confirmed, and for the first time we found it within the intestine. The geographical distribution is the Pacific coast of Mexico. Based on the data presented here, the taxonomic status of Holothuriophilus trapeziformis is now complete.},
}
@article {pmid35222946,
year = {2022},
author = {Majoros, SE and Adamowicz, SJ},
title = {Phylogenetic signal of sub-arctic beetle communities.},
journal = {Ecology and evolution},
volume = {12},
number = {2},
pages = {e8520},
pmid = {35222946},
issn = {2045-7758},
abstract = {Postglacial dispersal and colonization processes have shaped community patterns in sub-Arctic regions such as Churchill, Manitoba, and Canada. This study investigates evolutionary community structure within the beetle (Coleoptera) families of Churchill and tests whether biological traits have played a role in governing colonization patterns from refugial and southerly geographic regions. This study quantifies sub-Arctic beetle phylogenetic community structure for each family using the net relatedness index (NRI) and nearest taxon index (NTI), calculated using publicly available data from the Barcode of Life Data Systems (BOLD); compares patterns across families with different traits (habitat, diet) using standard statistical analysis (ANOVA) as well as phylogenetic generalized least squares (PGLS) using a family-level beetle phylogeny obtained from the literature; and compares community structure in Churchill with a region in southern Canada (Guelph, Ontario). These analyses were also repeated at a genus level. The dominant pattern detected in our study was that aquatic families were much better represented in Churchill compared to terrestrial families, when compared against richness sampled from across Canada and Alaska. Individually, most families showed significant phylogenetic clustering in Churchill, likely due to the strong environmental filtering present in Arctic environments. There was no significant difference in phylogenetic structure between Churchill and Guelph but with a trend toward stronger clustering in the North. Fungivores were significantly more overdispersed than other feeding modes, predators were significantly more clustered, and aquatic families showed significantly stronger clustering compared to terrestrial. This study contributes to our understanding of the traits and processes structuring insect biodiversity and macroecological trends in the sub-Arctic.},
}
@article {pmid35221575,
year = {2022},
author = {Qin, Q and Li, J and Zeng, S and Xu, Y and Han, F and Yu, J},
title = {The complete plastomes of red fleshed pitaya (Selenicereus monacanthus) and three related Selenicereus species: insights into gene losses, inverted repeat expansions and phylogenomic implications.},
journal = {Physiology and molecular biology of plants : an international journal of functional plant biology},
volume = {28},
number = {1},
pages = {123-137},
pmid = {35221575},
issn = {0971-5894},
abstract = {UNLABELLED: Selenicereus is a genus of perennial shrub from the family Cactaceae, and some of them play an important role in the food industry, pharmaceuticals, cosmetics and medicine. To date, there are few reports on Selenicereus plastomes, which limits our understanding of this genus. Here, we have reported the complete plastomes of four Selenicereus species (S. monacanthus, S. annthonyanus, S. grandifloras, and S. validus) and carried out a comprehensive comparative analysis. All four Selenicereus plastomes have a typical quartile structure. The plastome size ranged from 133,146 to 134,450 bp, and contained 104 unique genes, including 30 tRNA genes, 4 rRNA genes and 70 protein-coding genes. Comparative analysis showed that there were massive losses of ndh genes in Selenicereus. Besides, we observed the inverted repeat regions had undergone a dramatic expansion and formed a previously unreported small single copy/inverted repeat border in the intron region of the atpF gene. Furthermore, we identified 6 hypervariable regions (trnF-GAA-rbcL, ycf1, accD, clpP-trnS-GCU, clpP-trnT-CGU and rpl22-rps19) that could be used as potential DNA barcodes for the identification of Selenicereus species. Our study enriches the plastome in the family Cactaceae, and provides the basis for the reconstruction of phylogenetic relationships.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01121-z.},
}
@article {pmid35220423,
year = {2022},
author = {Fernández, DC and VanLaerhoven, SL and Rodríguez-Leyva, E and Zhang, YM and Labbé, R},
title = {Population Structure and Genetic Diversity of the Pepper Weevil (Coleoptera: Curculionidae) Using the COI Barcoding Region.},
journal = {Journal of insect science (Online)},
volume = {22},
number = {1},
pages = {},
pmid = {35220423},
issn = {1536-2442},
mesh = {Animals ; *Capsicum ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; Genetic Variation ; *Genetics, Population ; Haplotypes ; *Weevils/genetics ; },
abstract = {The pepper weevil Anthonomus eugenii Cano (Coleoptera: Curculionidae) is a pest of economic importance for Capsicum species pepper in North America that attacks the reproductive structures of the plant. The insect is distributed across Mexico, the United States, and the Caribbean, and is occasionally found during the pepper growing season in southern Ontario, Canada. Continuous spread of the insect to new areas is partially the result of global pepper trade. Here, we describe the genetic diversity of the pepper weevil using the mitochondrial COI barcoding region across most of its geographic range. In this study, 44 (H1-H44) highly similar haplotypes were identified, the greatest number of haplotypes and haplotype diversity were observed among specimens from its native Mexico, followed by specimens from the United States. Unlike Mexico, a low haplotype diversity was found among specimens from Canada, the Dominican Republic, Italy, and the Netherlands. Out of these 44 haplotypes, 29 are reported for the first time. Haplotype diversity in the Canadian population suggests either multiple and continuous introductions of the pepper weevil into this area or a single introduction of genetically diverse individuals. We discuss the importance of such population genetic data in tailoring pepper weevil management programs, using Canada as an example.},
}
@article {pmid35216033,
year = {2022},
author = {Hassanin, A and Rambaud, O and Klein, D},
title = {Genomic Bootstrap Barcodes and Their Application to Study the Evolution of Sarbecoviruses.},
journal = {Viruses},
volume = {14},
number = {2},
pages = {},
pmid = {35216033},
issn = {1999-4915},
support = {ANR-21-CO12-0002//Agence Nationale de la Recherche/ ; },
mesh = {Animals ; China ; Chiroptera/virology ; DNA Barcoding, Taxonomic/*methods ; Disease Reservoirs/*veterinary/virology ; *Evolution, Molecular ; Genome, Viral ; Genomics/*methods ; Phylogeography ; *Recombination, Genetic ; Severe acute respiratory syndrome-related coronavirus/*genetics ; SARS-CoV-2/*genetics ; },
abstract = {Recombination creates mosaic genomes containing regions with mixed ancestry, and the accumulation of such events over time can complicate greatly many aspects of evolutionary inference. Here, we developed a sliding window bootstrap (SWB) method to generate genomic bootstrap (GB) barcodes to highlight the regions supporting phylogenetic relationships. The method was applied to an alignment of 56 sarbecoviruses, including SARS-CoV and SARS-CoV-2, responsible for the SARS epidemic and COVID-19 pandemic, respectively. The SWB analyses were also used to construct a consensus tree showing the most reliable relationships and better interpret hidden phylogenetic signals. Our results revealed that most relationships were supported by just a few genomic regions and confirmed that three divergent lineages could be found in bats from Yunnan: SCoVrC, which groups SARS-CoV related coronaviruses from China; SCoV2rC, which includes SARS-CoV-2 related coronaviruses from Southeast Asia and Yunnan; and YunSar, which contains a few highly divergent viruses recently described in Yunnan. The GB barcodes showed evidence for ancient recombination between SCoV2rC and YunSar genomes, as well as more recent recombination events between SCoVrC and SCoV2rC genomes. The recombination and phylogeographic patterns suggest a strong host-dependent selection of the viral RNA-dependent RNA polymerase. In addition, SARS-CoV-2 appears as a mosaic genome composed of regions sharing recent ancestry with three bat SCoV2rCs from Yunnan (RmYN02, RpYN06, and RaTG13) or related to more ancient ancestors in bats from Yunnan and Southeast Asia. Finally, our results suggest that viral circular RNAs may be key molecules for the mechanism of recombination.},
}
@article {pmid35211136,
year = {2021},
author = {Odago, WO and Waswa, EN and Nanjala, C and Mutinda, ES and Wanga, VO and Mkala, EM and Oulo, MA and Wang, Y and Zhang, CF and Hu, GW and Wang, QF},
title = {Analysis of the Complete Plastomes of 31 Species of Hoya Group: Insights Into Their Comparative Genomics and Phylogenetic Relationships.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {814833},
pmid = {35211136},
issn = {1664-462X},
abstract = {Hoya is a genus in Apocynaceae-Asclepiadoideae, known for its showy wax flowers, making it a popular ornamental plant. However, phylogenetic relationships among most Hoya species are not yet fully resolved. In this study, we sequenced 31 plastomes of Hoya group species using genome skimming data and carried out multiple analyses to understand genome variation to resolve the phylogenetic positions of some newly sequenced Chinese endemic species. We also screened possible hotspots, trnT-trnL-trnF, psba-trnH, and trnG-UCC, ndhF, ycf1, matK, rps16, and accD genes that could be used as molecular markers for DNA barcoding and species identification. Using maximum likelihood (ML) and Bayesian Inference (BI), a species phylogeny was constructed. The newly assembled plastomes genomes showed the quasi-tripartite structure characteristic for Hoya and Dischidia with a reduced small single copy (SSC) and extremely enlarged inverted repeats (IR). The lengths ranged from 175,404 bp in Hoya lacunosa to 179,069 bp in H. ariadna. The large single copy (LSC) regions ranged from 80,795 bp (Hoya liangii) to 92,072 bp (Hoya_sp2_ZCF6006). The massively expanded IR regions were relatively conserved in length, with the small single-copy region reduced to a single gene, ndhF. We identified 235 long dispersed repeats (LDRs) and ten highly divergent hotspots in the 31 Hoya plastomes, which can be used as DNA barcodes for species identification. The phylogeny supports Clemensiella as a distinct genus. Hoya ignorata is resolved as a relative to Clade VI species. This study discloses the advantages of using Plastome genome data to study phylogenetic relationships.},
}
@article {pmid35210921,
year = {2022},
author = {Tochihara, Y and Hosoya, T},
title = {Examination of the generic concept and species boundaries of the genus Erioscyphella (Lachnaceae, Helotiales, Ascomycota) with the proposal of new species and new combinations based on the Japanese materials.},
journal = {MycoKeys},
volume = {87},
number = {},
pages = {1-52},
pmid = {35210921},
issn = {1314-4049},
abstract = {The genus Erioscyphella Kirschst., which was morphologically confused with Lachnum, was herein examined. Based on molecular phylogenetic analyses using a combined dataset of ITS, LSU, mtSSU, and RPB2 and morphological examinations, Erioscyphella was distinguished from Lachnum and redefined by longer ascospores and the presence of apical amorphous materials and/or resinous materials equipped on hairs. Species boundaries recognized by morphology/ecology and phylogenetic analyses were cross-checked using species delimitation analyses based on DNA barcode sequences downloaded from UNITE, resulting in that species' taxonomic problems being uncovered. Six new species (E.boninensis, E.insulae, E.otanii, E.papillaris, E.paralushanensis, and E.sasibrevispora) and two new combinations (E.hainanensis and E.sinensis) were proposed.},
}
@article {pmid35210917,
year = {2022},
author = {Zhang, Y and Huang, S and Wang, M},
title = {First record of the genus Olepa Watson, 1980 from China (Lepidoptera, Erebidae, Arctiinae, Arctiini).},
journal = {Biodiversity data journal},
volume = {10},
number = {},
pages = {e78167},
pmid = {35210917},
issn = {1314-2828},
abstract = {BACKGROUND: The tribe Arctiini is a species-rich tribe of the subfamily Arctiinae of the family Erebidae. The genus Olepa Watson, 1980 is distributed in the Oriental and Palearctic Regions and the diversity reaches its peak in south Asia.<br><br>NEW INFORMATION: We herein describe the first record of the genus Olepa from China and re-describe Oleparicini (Fabricius, 1775), together with illustrations of its adult and male genitalia. Furthermore, based on an analysis of 658-bp COI barcoding sequences, together with morphological studies, we consider that Olepaschleini Witt et al., 2005 syn. n. is a new synonym of O.ricini.},
}
@article {pmid35210909,
year = {2022},
author = {Berggren, K and Aarvik, L and Huemer, P and Lee, KM and Mutanen, M},
title = {Integrative taxonomy reveals overlooked cryptic diversity in the conifer feeding Batrachedrapinicolella (Zeller, 1839) (Lepidoptera, Batrachedridae).},
journal = {ZooKeys},
volume = {1085},
number = {},
pages = {165-182},
pmid = {35210909},
issn = {1313-2989},
abstract = {During efforts to generate DNA barcodes for all European Lepidoptera, Batrachedrapinicolella (Zeller, 1839) was found to comprise two genetically distinct clusters. Morphological investigation and results from two nuclear markers and ddRAD sequencing furthermore support the existence of two distinct taxa which we treat as two separate species, B.pinicolella and B.confusella sp. nov. A lectotype for B.pinicolella is designated. Available data indicate that the biology of both species also differs, with Piceaabies (L.) Karsten as a proved host-plant for B.pinicolella and Pinussylvestris L. for B.confusella sp. nov. Both species are mainly distributed on the European continent with B.pinicolella occurring in boreal parts of North and Central Europe and introduced to Canada, reflecting a boreo-montane distribution pattern. Batrachedraconfusella sp. nov. is more widely distributed in temperate Northern and Central Europe.},
}
@article {pmid35210908,
year = {2022},
author = {Li, Y and Luo, X and Zhang, J and Wang, Z and Che, Y},
title = {A new species of Bundoksia Lucañas, 2021 with comments on its subfamilial placement, based on morphological and molecular data.},
journal = {ZooKeys},
volume = {1085},
number = {},
pages = {145-163},
pmid = {35210908},
issn = {1313-2989},
abstract = {One new species of Bundoksia Lucañas, 2021 from China is described. We construct a haplotype network from 21 COI sequences to display the relationships amongst populations of Bundoksialongissima sp. nov., mainly from Hainan Island, Yunnan Province and Guangxi Province, China. For the first time, we provide the details of female genitalia in addition to the known external morphology and male genitalia of the genus. Six molecular markers (12S, 16S, 18S, 28S, COI and COII) from a total of 38 samples, including three samples of Bundoksialongissima sp. nov., are used to reconstruct phylogenetic trees using Maximum Likelihood (ML) and Bayesian Inference (BI) to assess the phylogenetic affinities of Bundoksia. Photographs of the morphology and a key to the three Bundoksia species are also provided.},
}
@article {pmid35210907,
year = {2022},
author = {Vargas, HA and Solis, MA and Vargas-Ortiz, M},
title = {The South American moth Rheumapteramochica (Dognin, 1904) (Lepidoptera, Geometridae, Larentiinae) rediscovered after more than a century of anonymity.},
journal = {ZooKeys},
volume = {1085},
number = {},
pages = {129-143},
pmid = {35210907},
issn = {1313-2989},
abstract = {Rheumapteramochica (Dognin, 1904) (Lepidoptera, Geometridae, Larentiinae) is reported from Chile for the first time. It was described from the western slopes of the Andes of southern Peru more than 100 years ago, and was recently rediscovered in Chile after larvae were collected and reared on the shrub Sennabirostrisvar.arequipensis (Meyen ex Vogel) H.S. Irwin &amp; Barneby (Fabaceae). This discovery expands the known distribution of this moth and provides its first host plant record. The genitalia of R.mochica are described and illustrated for the first time and compared to those of R.affirmata (Guenée, [1858]). A maximum likelihood analysis based on mitochondrial DNA sequences clustered R.mochica as sister to R.affirmata with 3.6-3.8% divergence (K2P). A lectotype is designated for Calocalpemochica Dognin, 1904.},
}
@article {pmid35210901,
year = {2022},
author = {Gittenberger, E and Gyeltshen, C and Stelbrink, B},
title = {The genus Erhaia (Gastropoda, Truncatelloidea, Amnicolidae), with a new species from Bhutan.},
journal = {ZooKeys},
volume = {1085},
number = {},
pages = {1-9},
pmid = {35210901},
issn = {1313-2989},
abstract = {The distribution of the five Erhaia (Gastropoda, Truncatelloidea, Amnicolidae) species that are diagnosed by both morphological and molecular data is combined with several records of less completely diagnosed nominal Erhaia species. The resulting distribution pattern is summarized in a map and is discussed herein. Erhaianorbui sp. nov. is described from Bhutan on the basis of shell morphology and two mitochondrial DNA barcoding markers. A molecular phylogeny is presented for the five Erhaia species for which molecular data are available, three of which form a separate clade and are from Bhutan.},
}
@article {pmid35210624,
year = {2022},
author = {Ratz, M and von Berlin, L and Larsson, L and Martin, M and Westholm, JO and La Manno, G and Lundeberg, J and Frisén, J},
title = {Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics.},
journal = {Nature neuroscience},
volume = {25},
number = {3},
pages = {285-294},
pmid = {35210624},
issn = {1546-1726},
mesh = {Animals ; Brain ; Cell Differentiation ; Clone Cells ; Mammals ; Mice ; Neuroepithelial Cells ; *Stem Cells ; *Transcriptome ; },
abstract = {The mammalian brain contains many specialized cells that develop from a thin sheet of neuroepithelial progenitor cells. Single-cell transcriptomics revealed hundreds of molecularly diverse cell types in the nervous system, but the lineage relationships between mature cell types and progenitor cells are not well understood. Here we show in vivo barcoding of early progenitors to simultaneously profile cell phenotypes and clonal relations in the mouse brain using single-cell and spatial transcriptomics. By reconstructing thousands of clones, we discovered fate-restricted progenitor cells in the mouse hippocampal neuroepithelium and show that microglia are derived from few primitive myeloid precursors that massively expand to generate widely dispersed progeny. We combined spatial transcriptomics with clonal barcoding and disentangled migration patterns of clonally related cells in densely labeled tissue sections. Our approach enables high-throughput dense reconstruction of cell phenotypes and clonal relations at the single-cell and tissue level in individual animals and provides an integrated approach for understanding tissue architecture.},
}
@article {pmid35207443,
year = {2022},
author = {Cabezas, MP and Guerra-García, JM and Santos, AM},
title = {Disentangling the Taxonomic Status of Caprella penantis sensu stricto (Amphipoda: Caprellidae) Using an Integrative Approach.},
journal = {Life (Basel, Switzerland)},
volume = {12},
number = {2},
pages = {},
pmid = {35207443},
issn = {2075-1729},
support = {NORTE-01-0145-FEDER-000031//Norte Portugal Regional Operational Programme (NORTE 2020)/ ; },
abstract = {Despite its importance in intertidal and shallow-water marine ecosystems, Caprella penantis continues to be one of the most taxonomically challenging amphipods in the world. A recent molecular study focusing on C. penantis sensu stricto pointed out the existence of three highly divergent lineages, indicating the possible existence of a process of ongoing speciation and, thus, casting doubt on the taxonomic status of this species. In the present study, we used an integrative approach to continue to shed light on the taxonomy and distribution of this caprellid. To this end, we combined morphological and genetic data (COI and 18S) and included, for the first time, populations from its type locality. Our analyses provide strong evidence of the existence of potentially three distinct species, genetically and geographically restricted, within C. penantis sensu stricto, with the distribution of the true C. penantis sensu stricto restricted to the UK (type locality), the northern coast of the Iberian Peninsula, and the Azores. Results show the co-occurrence of two of these species in a locality of northern Portugal and indicate the existence of distinct evolutionary and diversification patterns along the eastern Atlantic region. Overall, our study highlights the use of an integrative approach to properly assess species boundaries and unravel hidden biodiversity in amphipods.},
}
@article {pmid35206777,
year = {2022},
author = {Zubrii, NA and Filippov, BY and Kondakov, AV and Khruleva, OA and Rybalov, LB and Vikhreva, DV},
title = {DNA Barcoding versus Morphological Variability of Pterostichus brevicornis brevicornis (Kirby, 1837) (Coleoptera, Carabidae) in the Arctic and Subarctic.},
journal = {Insects},
volume = {13},
number = {2},
pages = {},
pmid = {35206777},
issn = {2075-4450},
support = {19-34-60042//Russian Foundation for Basic Research/ ; AAAA-A17-117033010132-2//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {The geographic patterns of genetic and morphological variability in ground beetles were examined throughout Northern Eurasia and North America using the most abundant circumpolar tundra subspecies, Pterostichus (Cryobius) brevicornis brevicornis (Kirby, 1837), as a model. Phylogenetic structure was assessed on the basis of a Bayesian approach using two DNA markers (partial sequences of the COI and 28S rRNA genes), while phylogeographic patterns and population genetic diversity were estimated using the COI gene only. Morphological patterns were analysed using elliptical Fourier coefficients that were calculated based on the pronotum and male genitalia shape outlines. The subspecies shares 23 COI haplotypes throughout its entire circumpolar range, while eight haplotypes of 28S rRNA were detected in Northern Eurasia. Phylogenetic analysis did not reveal subdivided species lineages with strict geographical imprint. The network, FST and uncorrected pairwise divergence analyses showed that the genetic distances between populations increase by longitude from Northeastern Asia to Europe. The genetic variability among the five studied geographical population groups of P. b. brevicornis was relatively high. The MANOVA showed significant regional divergence between local populations in Northern Eurasia based on both morphological markers, but only male genitalia variability was geographically structured. Neither the pronotum shape nor the male genitalia shape aligned with the phylogeographic patterns discovered on the basis of COI sequences. The genetic (COI) marker had more variation within, rather than among, population groups in addition to morphology of pronotum but not male genitalia.},
}
@article {pmid35206732,
year = {2022},
author = {Fröhlich, D and Zangl, L and Raspotnig, G and Koblmüller, S},
title = {Inter- and Intrasexual Variation in Cuticular Hydrocarbons in Trichrysis cyanea (Linnaeus, 1758) (Hymenoptera: Chrysididae).},
journal = {Insects},
volume = {13},
number = {2},
pages = {},
pmid = {35206732},
issn = {2075-4450},
support = {"Hochschulraum-Strukturmittel" Funds//Federal Ministry of Science, Research and Economics/ ; },
abstract = {Cuckoo wasps (Chrysididae, Hymenoptera) are known for their parasitoid or cleptoparasitic life histories. Indeed, the biology of only a few species has been studied in detail and often only little more is known than the host species. By mimicking their hosts' cuticular hydrocarbon (CHC) profiles, species that parasitize single (or a few closely related) host species manage to deceive their hosts. However, the variability of the CHC profile in generalist cuckoo-wasp species is still unknown. Here, we used gas chromatography-mass spectrometry (GC-MS) and DNA barcoding to study intraspecific variation in cuticular hydrocarbons of one less host-specific species of cuckoo wasps, Trichrysis cyanea. Cuticular hydrocarbon (CHC) patterns were found to differ between males and females. Additionally, we found chemical polymorphism among females, which formed three distinct chemical subgroups characterized by different alkene patterns. A lack of divergence in the DNA barcoding region suggests that these different chemotypes do not represent cryptic species. Whether this intrasexual CHC-profile variation is an adaptation (mimicry) to different host species, or simply signaling the reproductive status, remains unclear.},
}
@article {pmid35206721,
year = {2022},
author = {Kjærandsen, J},
title = {Current State of DNA Barcoding of Sciaroidea (Diptera)-Highlighting the Need to Build the Reference Library.},
journal = {Insects},
volume = {13},
number = {2},
pages = {},
pmid = {35206721},
issn = {2075-4450},
abstract = {DNA barcoding has tremendous potential for advancing species knowledge for many diverse groups of insects, potentially paving way for machine identification and semi-automated monitoring of whole insect faunas. Here, I review the current state of DNA barcoding of the superfamily Sciaroidea (Diptera), a diverse group consisting of eight understudied fly families where the described species in the world makes up some 10% (≈16,000 species) of all Diptera. World data of Sciaroidea were extracted from the Barcode of Life online database BoldSystems (BOLD) and contrasted with results and experiences from a Nordic project to build the reference library. Well over 1.2 million (1,224,877) Sciaroidea specimens have been submitted for barcoding, giving barcode-compliant sequences resulting in 56,648 so-called barcode index numbers (BINs, machine-generated proxies for species). Although the BINs on BOLD already represent 3.5 times the number of described species, merely some 2850 named species (described or interim names, 5% of the BINs) currently have been assigned a BIN. The other 95% remain as dark taxa figuring in many frontier publications as statistics representing proxies for species diversity within a family. In the Nordic region, however, substantial progress has been made towards building a complete reference library, currently making up 55% of all named Sciaroidea BINs on BOLD. Another major source (31%) of named Sciaroidea BINs on BOLD comes from COI sequences mined from GenBank, generated through phylogenetic and integrative studies outside of BOLD. Building a quality reference library for understudied insects such as Sciaroidea requires heavy investment, both pre sequence and post sequence, by trained taxonomists to build and curate voucher collections, to continually improve the quality of the data and describe new species. Only when the BINs are properly calibrated by a rigorously quality-checked reference library can the great potential of both classical taxonomic barcoding, metabarcoding, and eDNA ecology be realized.},
}
@article {pmid35206694,
year = {2022},
author = {Lima, &#xc9;FB and Alencar, &#xc1;RS and Nanini, F and Michelotto, MD and Corrêa, AS},
title = {"Unmasking the Villain": Integrative Taxonomy Reveals the Real Identity of the Key Pest (Thysanoptera: Thripidae) of Peanuts (Arachis hypogaea L.) in South America.},
journal = {Insects},
volume = {13},
number = {2},
pages = {},
pmid = {35206694},
issn = {2075-4450},
support = {2020/12581-1//S&#xe3;o Paulo Research Foundation/ ; PI 2855-2017//Federal University of Piau&#xed;/ ; },
abstract = {The peanut thrips, Enneothrips enigmaticus sp. n., is the key pest of Arachis hypogaea L. in South America, where it can cause yield losses of up to 85%. This species has historically been identified as Enneothrips flavens, but access to the holotype of this species and freshly collected material from southeastern and northern Brazil revealed that specimens commonly collected on peanut crops are not conspecific with E. flavens. Biological, molecular, and morphological assessments were carried out and led to the conclusion that the key pest of A. hypogaea belongs to a previously undescribed species: Enneothrips enigmaticus sp. n.},
}
@article {pmid35205381,
year = {2022},
author = {Marchán, DF and Domínguez, J},
title = {Evaluating the Conservation Status of a North-Western Iberian Earthworm (Compostelandrilus cyaneus) with Insight into Its Genetic Diversity and Ecological Preferences.},
journal = {Genes},
volume = {13},
number = {2},
pages = {},
pmid = {35205381},
issn = {2073-4425},
mesh = {Animals ; Conservation of Natural Resources ; *Ecosystem ; Genetic Variation/genetics ; *Oligochaeta/genetics ; Soil ; },
abstract = {In spite of the high conservation value of soil fauna, the evaluation of their conservation status has usually been neglected. This is more evident for earthworms, one of the most important ecosystem service providers in temperate habitats but rarely the subject of conservation research. These studies have not been developed in Western Europe, which comprises high diversity and several early-branching, relic genera. One potentially menaced representative of this fauna is Compostelandrilus cyaneus; this risk can be assessed by implementing potential distribution modeling and genetic diversity monitoring to their known populations. Genetic barcoding was performed in representatives of four populations (three of them newly sampled) in order to estimate genetic diversity and population genetics parameters. Ensemble species distribution models were built by combining several algorithms and using the five more relevant bioclimatic and soil variables as predictors. A large amount of genetic diversity was found in a small area of less than 20 km[2], with populations located in less managed, better-preserved habitats showing higher genetic variability than populations isolated from natural habitats and surrounded by anthropic habitats. Potential distribution appears to be strongly restricted at a regional scale, and suitable habitats within the extent of occurrence appear fragmented and relatively limited. In addition, the main variables determining the ecological niche of C. cyaneus suggests a vulnerability to climate change and increasing soil compaction. Based on this knowledge, this species was assessed as Critically Endangered following the IUCN Red List of Threatened Species criteria, and some potential conservation actions are suggested.},
}
@article {pmid35205308,
year = {2022},
author = {Mudliar, SKR and Kulsum, U and Rufai, SB and Umpo, M and Nyori, M and Singh, S},
title = {Snapshot of Mycobacterium tuberculosis Phylogenetics from an Indian State of Arunachal Pradesh Bordering China.},
journal = {Genes},
volume = {13},
number = {2},
pages = {},
pmid = {35205308},
issn = {2073-4425},
mesh = {Antitubercular Agents/pharmacology/therapeutic use ; Drug Resistance, Multiple, Bacterial/genetics ; Humans ; *Mycobacterium tuberculosis/genetics ; Phylogeny ; *Tuberculosis, Multidrug-Resistant/drug therapy/microbiology ; },
abstract = {Uncontrolled transmission of Mycobacterium tuberculosis (M. tuberculosis, MTB) drug resistant strains is a challenge to control efforts of the global tuberculosis program. Due to increasing multi-drug resistant (MDR) cases in Arunachal Pradesh, a northeastern state of India, the tracking and tracing of these resistant MTB strains is crucial for infection control and spread of drug resistance. This study aims to correlate the phenotypic DST, genomic DST (gDST) and phylogenetic analysis of MDR-MTB strains in the region. Of the total 200 samples 22 (11%) patients suspected of MDR-TB and 160 (80%) previously treated MDR-TB cases, 125 (62.5%) were identified as MTB. MGIT-960 SIRE DST detected 71/125 (56.8%) isolates as MDR/RR-MTB of which 22 (30.9%) were detected resistant to second-line drugs. Whole-genome sequencing of 65 isolates and their gDST found Ser315Thr mutation in katG (35/45; 77.8%) and Ser531Leu mutation in rpoB (21/41; 51.2%) associated with drug resistance. SNP barcoding categorized the dataset with Lineage2 (41; 63.1%) being predominant followed by Lineage3 (10; 15.4%), Lineage1 (8; 12.3%) and Lineage4 (6; 9.2%) respectively. Phylogenetic assignment by cgMLST gave insights of two Beijing sub-lineages viz; 2.2.1 (SNP difference < 19) and 2.2.1.2 (SNP difference < 9) associated with recent ongoing transmission in Arunachal Pradesh. This study provides insights in identifying two virulent Beijing sub-lineages (sub-lineage 2.2.1 and 2.2.1.2) with ongoing transmission of TB drug resistance in Arunachal Pradesh.},
}
@article {pmid35201669,
year = {2022},
author = {Ojeda, AA and Novillo, A and Lanzone, C and Rodríguez, MD and Cuevas, MF and Jayat, JP and Teta, P and Ojeda, RA and Borisenko, A},
title = {DNA barcodes highlight genetic diversity patterns in rodents from lowland desert and Andean areas in Argentina.},
journal = {Molecular ecology resources},
volume = {22},
number = {6},
pages = {2349-2362},
doi = {10.1111/1755-0998.13603},
pmid = {35201669},
issn = {1755-0998},
mesh = {Animals ; Argentina ; Bayes Theorem ; DNA ; *DNA Barcoding, Taxonomic/methods ; Genetic Variation ; Phylogeny ; *Rodentia/genetics ; },
abstract = {Rodents are an important component of South America fauna. Their high diversity has motivated researchers to continually review their taxonomy, genetic diversity, species limits, and phylogenetic relationships. Here, we applied DNA-barcodes for assessing the taxonomic and genetic diversity in the two major lineages of South American rodents: caviomorphs and sigmodontines. We analysed 335 COI barcodes in 34 morphologically determined species from 39 localities along central Andes and arid lands of Argentina. Neighbour-joining and maximum likelihood reconstruction provided clear separation between species. The Barcode Index number and Bayesian Poisson tree processes were used to confirm concordance between sequence clusters and species designations by taxonomy. We found deep divergence within the Phyllotis xanthopygus species complex, with distances up to 13.0% between geographically separated lineages. Minor divergences (3.30% and 2.52%) were found within Abrothrix hirta, and Tympanoctomys barrerae, respectively, with differentiation in their genetic lineages. Also, we documented geographically separated clusters for Akodon spegazzinii and A. oenos with up to 2.3% divergence, but clustering methods failed to distinguish them as different species. Sequence results show a clear barcode gap with a mean intraspecific divergence (0.56%) versus a minimum nearest-neighbour distance averaging (10.1%). Distances between congeneric species varied from 4.1 to 14%, with the exception of two related forms within Euneomys and the sister species Akodon spegazzinii and A. oenos. This study constitutes a substantial contribution to the global barcode reference library. It provides insights into the complex phylogeographic patterns and speciation scenarios in rodents, while highlighting areas that require in-depth taxonomic and integrative research.},
}
@article {pmid35201516,
year = {2022},
author = {Pinya, T and Intharuksa, A and Yanaso, S and Kamnuan, S and Phrutivorapongkul, A},
title = {Conventional and molecular pharmacognostic characters integrated with chemical profiles of five Piper plants in the Thai herbal pharmacopoeia and their admixture/adulteration/substitution situations in Thailand.},
journal = {Journal of natural medicines},
volume = {76},
number = {3},
pages = {605-620},
pmid = {35201516},
issn = {1861-0293},
mesh = {DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; *Piper/genetics ; *Plants, Medicinal/genetics ; Thailand ; },
abstract = {The morphological and microscopy were combined with DNA-barcoding, together with rapid TLC for the characterization of Piper betle (PB), P. nigrum (PN), P. retrofractum (PR), P. sarmentosum (PS), and P. wallichii (PW), five medicinal Piper plants announced in the Thai Herbal Pharmacopoeia (THP). The authentic plants collected from various locations and voucher Piper products bought from commercial sites in Thailand were studied. The reproductive parts of authentic plants were subjected to ensure their morphological characters. Using sequencing analysis and genetic divergence for analyzing discriminatory performance, ITS2 was selected from eight candidate DNA markers to authenticate the origin of Piper crude drugs together with microscopic and TLC profiles for examining their characters, admixtures, adulterants, and substituents. PB and PR exhibited unique characters of the species, with no admixture, adulteration, and substitution. PN showed no variable characters of morphology and genetics. However, the microscopy could illustrate some commercial products of PN sold in Thailand have been adulterated with rice starch and roasted rice. In the herbal trade, PS has been sold in the form of mixed leaf, root, and stem more than the isolated part, but there is no variable character of the species. PW has shown more than one character of species explained by microscopic, chemical components, and genetic data. In conclusion, the conventional and molecular pharmacognostic data combined with chemical profile of authentic five Piper plants could be applied to indicate the plant origin and clarify the situations of admixture, adulteration, and substitution of the commercial Piper products launched in Thailand.},
}
@article {pmid35197990,
year = {2021},
author = {Chen, J and Guo, Y and Hu, X and Zhou, K},
title = {Comparison of the Chloroplast Genome Sequences of 13 Oil-Tea Camellia Samples and Identification of an Undetermined Oil-Tea Camellia Species From Hainan Province.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {798581},
pmid = {35197990},
issn = {1664-462X},
abstract = {The comparison of chloroplast genome (cpDNA) sequences among different plant species is an important source of plant molecular phylogenetic data. In this paper, the cpDNA sequences of 13 different oil-tea camellia samples were compared to identify an undetermined oil-tea camellia species from Hainan Province. The cpDNA of the samples was sequenced and resequenced, and divergence hotspots and simple sequence repeat (SSR) variations were analyzed. Bayesian inference (BI) and maximum-likelihood (ML) phylogenetic trees were constructed based on the full cpDNA sequences. The cpDNA sequences were 156512∼157089 bp in length and had the circular tetrad structure typical of angiosperms. The inverted repeats (IRs) of different species included varying contractions and expansions. The cpDNA sequences of the samples of the undetermined species of oil-tea camellia from Hainan Province and Camellia gauchowensis from Xuwen County were identical. In total, 136 genes were annotated, including 91 protein-coding genes (PCGs), 37 tRNA genes and 8 rRNA genes. The GC content of the cpDNA was 37.3%. The small single-copy (SSC)/IR boundary was rich in variation. Divergence hotspots were mainly located in the intergenic space (IGS) and coding sequences (CDSs), and there were obvious differences in divergence hotspots among species. The same divergence hotspots were found in Camellia vietnamensis, Camellia gauchowensis and the undetermined species of oil-tea camellia from Hainan Province. A total of 191∼198 SSR loci were detected. Most of the SSRs included A or T, and the distribution of SSRs in the cpDNA was uneven. Different species shared common SSRs and exhibited unique SSRs. Based on the full cpDNA sequences, the evolutionary relationships of different species of Camellia were well identified. The thirteen samples were classified into 2 clades and 6 subclades, and the different sections of Camellia clustered on the same branch in 2 clades and 2 subclades. Camellia vietnamensis was more closely related to the undetermined species of oil-tea camellia from Hainan Province and the sample of Camellia gauchowensis from Xuwen County than to the sample of Camellia gauchowensis from Luchuan County. Camellia osmantha was closely related to Camellia gauchowensis and Camellia vietnamensis. In conclusion, the cpDNA of different oil-tea camellia species has a conserved tetrad structure with certain length polymorphisms. SSRs are expected to be developed as "barcodes" or "identity cards" for species identification. SSR variations and other factors result in abundant divergence hotspots in the CDSs and IGS (one non-CDS region), indicating that full cpDNA sequences can be used for the species identification and phylogenetic analysis of Camellia. Accordingly, the undetermined species of oil-tea camellia from Hainan Province is likely Camellia vietnamensis, Camellia vietnamensis and Camellia gauchowensis may be the same species, and additional genetic evidence is needed to determine whether Camellia osmantha is a new independent species. The previous division of related sections of Camellia may need readjustment based on full cpDNA sequences.},
}
@article {pmid35197782,
year = {2022},
author = {Algarni, AA},
title = {Molecular identification and phylogenetic analysis of Aloe shadensis from Saudi Arabia based on matK, rbcL and ITS DNA barcode sequence.},
journal = {Saudi journal of biological sciences},
volume = {29},
number = {2},
pages = {1125-1133},
pmid = {35197782},
issn = {1319-562X},
abstract = {The Kingdom of Saudi Arabia thrives with great plant diversity, including rare plants of the family Asphodelaceae that have multiple benefits and are still being studied. Aloe shadensis is one of these plants that must be preserved and documented in its natural environment. The most appropriate molecular approach currently approved for documentation is the sequencing of some genomic markers. The current study is the first to use genomic markers to record this rare plant. In this study, the plastid genes matK (Maturase K), rbcL (Ribulose-bisphosphate carboxylase/oxygenase large subunit), and the nuclear region ITS (Internal transcribed spacer) were used to reveal their efficiency in identifying the plant under study. This study is the first to deal with this plant and document it using these genetic markers. The study showed a promising result concerning identifying the sequence of the matK gene and ITS region, while the rbcL gene did not give a good indicator through the used primers. The obtained sequences of the matK gene and the ITS region were determined through two different sets of primers in each case then deposited in GenBank. The evolutionary relatedness of Aloe shadensis was established with the different species of Aloe. The study showed that the closest species is Aloe vera with a similarity of more than 99 %. The study concludes with the possibility of using these genes to correctly identify, distinguish and document the species of Aloe shadensis.},
}
@article {pmid35197533,
year = {2022},
author = {Oskay, F and Vettraino, AM and Doğmuş, HT and Lehtijärvi, A and Woodward, S and Cleary, M},
title = {Seed quantity affects the fungal community composition detected using metabarcoding.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {3060},
pmid = {35197533},
issn = {2045-2322},
mesh = {DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing ; Mycobiome/*genetics ; Plants/microbiology ; Sample Size ; Seeds/*genetics ; Trees/microbiology ; },
abstract = {Pest introductions via trade in tree seed may result from a lack of adequate survey and validation protocols. Developing better diagnostic protocols to identify potentially harmful pests and pathogens in forest tree seed is of critical importance. High-throughput sequencing-based barcoding and metabarcoding provide effective tools for screening potentially harmful organisms in various plant materials, including seeds. However, the sample size needed to detect the total microorganism diversity of a community is a major challenge in microbiome studies. In this work, we examined how increasing sample size (ranging between 100 and 1000 seeds) influences diversity of fungal communities detected by high throughput sequencing in Pinus sylvestris seeds. Our results showed that as sample size increased, fungal alpha diversity also increased. Beta-diversity estimators detected significant differences between the mycobiota from different samples. However, taxonomic and functional diversity were not correlated with sample size. In addition, we found that increasing the number of PCR replicates resulted in a higher abundance of plant pathogens. We concluded that for the purpose of screening for potentially harmful pathogens using HTS, greater efforts should be made to increase the sample size and replicates when testing tree seed.},
}
@article {pmid35195064,
year = {2022},
author = {De Rop, FV and Ismail, JN and Bravo González-Blas, C and Hulselmans, GJ and Flerin, CC and Janssens, J and Theunis, K and Christiaens, VM and Wouters, J and Marcassa, G and de Wit, J and Poovathingal, S and Aerts, S},
title = {Hydrop enables droplet-based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {35195064},
issn = {2050-084X},
mesh = {Animals ; Chromatin ; *Chromatin Immunoprecipitation Sequencing ; *High-Throughput Nucleotide Sequencing/methods ; Hydrogels ; Mice ; RNA ; RNA-Seq ; Single-Cell Analysis ; },
abstract = {Single-cell RNA-seq and single-cell assay for transposase-accessible chromatin (ATAC-seq) technologies are used extensively to create cell type atlases for a wide range of organisms, tissues, and disease processes. To increase the scale of these atlases, lower the cost and pave the way for more specialized multiome assays, custom droplet microfluidics may provide solutions complementary to commercial setups. We developed HyDrop, a flexible and open-source droplet microfluidic platform encompassing three protocols. The first protocol involves creating dissolvable hydrogel beads with custom oligos that can be released in the droplets. In the second protocol, we demonstrate the use of these beads for HyDrop-ATAC, a low-cost noncommercial scATAC-seq protocol in droplets. After validating HyDrop-ATAC, we applied it to flash-frozen mouse cortex and generated 7996 high-quality single-cell chromatin accessibility profiles in a single run. In the third protocol, we adapt both the reaction chemistry and the capture sequence of the barcoded hydrogel bead to capture mRNA, and demonstrate a significant improvement in throughput and sensitivity compared to previous open-source droplet-based scRNA-seq assays (Drop-seq and inDrop). Similarly, we applied HyDrop-RNA to flash-frozen mouse cortex and generated 9508 single-cell transcriptomes closely matching reference single-cell gene expression data. Finally, we leveraged HyDrop-RNA's high capture rate to analyze a small population of fluorescence-activated cell sorted neurons from the Drosophila brain, confirming the protocol's applicability to low input samples and small cells. HyDrop is currently capable of generating single-cell data in high throughput and at a reduced cost compared to commercial methods, and we envision that HyDrop can be further developed to be compatible with novel (multi) omics protocols.},
}
@article {pmid35194029,
year = {2022},
author = {Jin, J and Yamamoto, R and Takeuchi, T and Cui, G and Miyauchi, E and Hojo, N and Ikuta, K and Ohno, H and Shiroguchi, K},
title = {High-throughput identification and quantification of single bacterial cells in the microbiota.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {863},
pmid = {35194029},
issn = {2041-1723},
mesh = {Animals ; Bacteria/genetics ; DNA, Bacterial/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Mice ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {The bacterial microbiota works as a community that consists of many individual organisms, i.e., cells. To fully understand the function of bacterial microbiota, individual cells must be identified; however, it is difficult with current techniques. Here, we develop a method, Barcoding Bacteria for Identification and Quantification (BarBIQ), which classifies single bacterial cells into taxa-named herein cell-based operational taxonomy units (cOTUs)-based on cellularly barcoded 16S rRNA sequences with single-base accuracy, and quantifies the cell number for each cOTU in the microbiota in a high-throughput manner. We apply BarBIQ to murine cecal microbiotas and quantify in total 3.4 × 10[5] bacterial cells containing 810 cOTUs. Interestingly, we find location-dependent global differences in the cecal microbiota depending on the dietary vitamin A deficiency, and more differentially abundant cOTUs at the proximal location than the distal location. Importantly, these location differences are not clearly shown by conventional 16S rRNA gene-amplicon sequencing methods, which quantify the 16S rRNA genes, not the cells. Thus, BarBIQ enables microbiota characterization with the identification and quantification of individual constituent bacteria, which is a cornerstone for microbiota studies.},
}
@article {pmid35189412,
year = {2022},
author = {Kim, S and Han, J and Park, JS and Kim, JH and Lee, ES and Cha, BS and Park, KS},
title = {DNA barcode-based detection of exosomal microRNAs using nucleic acid lateral flow assays for the diagnosis of colorectal cancer.},
journal = {Talanta},
volume = {242},
number = {},
pages = {123306},
doi = {10.1016/j.talanta.2022.123306},
pmid = {35189412},
issn = {1873-3573},
mesh = {Biomarkers, Tumor/genetics ; *Colorectal Neoplasms/diagnosis/genetics ; DNA Barcoding, Taxonomic ; *Exosomes/chemistry/genetics ; Humans ; *MicroRNAs/analysis ; },
abstract = {Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer-related deaths worldwide. The standard methods for diagnosing CRC, endoscopy and tissue biopsy, are invasive and time-consuming. Herein, we propose a novel method for the accurate and non-invasive diagnosis of CRC based on the analysis of exosomes that are circulating in biological fluids using a DNA barcode-based nucleic acid lateral flow assay (NALFA). Our technology combines reverse transcription using a stem-loop primer with DNA barcode-based NALFA. A colorimetric signal is generated only in the presence of the target exosomal miRNA, which can be determined even with the naked eye. The proposed system successfully detected miR-92a and miR-141, which are overexpressed in CRC exosomes. Moreover, when applied to plasma samples from CRC patients, our system simultaneously detected multiple markers in one strip. By combining these markers, we achieved high analytical performance with a sensitivity and a specificity of 95.24% and 100.0%, respectively, demonstrating that the proposed assay can be a simple diagnostic platform for the detection of exosomal miRNA.},
}
@article {pmid35186004,
year = {2021},
author = {Sun, Y and Zou, P and Jiang, N and Fang, Y and Liu, G},
title = {Comparative Analysis of the Complete Chloroplast Genomes of Nine Paphiopedilum Species.},
journal = {Frontiers in genetics},
volume = {12},
number = {},
pages = {772415},
pmid = {35186004},
issn = {1664-8021},
abstract = {Paphiopedilum is known as "lady's or Venus" slipper orchids due to its prominent shoe-shaped labellum, with high ornamental value. Phylogenetic relationships among some species in Paphiopedilum genus cannot be effectively determined by morphological features alone or through the analysis of nuclear or chloroplast DNA fragments. In order to provide aid in understanding the evolutionary and phylogenetic relationship in Paphiopedilum at chloroplast (cp) genome-scale level, the complete cp genomes of six Paphiopedilum species were newly sequenced in this study, and three other published cp genome sequences of Paphiopedilum were included in the comparative analyses. The cp genomes of the six Paphiopedilum species ranged from 154,908 bp (P. hirsutissimum) to 161,300 bp (P. victoria-mariae) in size, all constituting four-part annular structures. Analyses of the nucleotide substitutions, insertions/deletions, and simple sequence repeats in the cp genomes were conducted. Ten highly variable regions that could serve as potential DNA barcodes or phylogenetic markers for this diverse genus were identified. Sequence variations in the non-coding regions were greater than that in the conserved protein-coding regions, as well as in the large single copy (LSC) and small single copy (SSC) regions than in the inverted repeat (IR) regions. Phylogenetic analysis revealed that all Paphiopedilum species clustered in one monophyletic clade in the Cypripedioideae subfamily and then subdivided into seven smaller branches corresponding to different subgenus or sections of the genus, with high bootstrap supports, indicate that cp genome sequencing can be an effective means in resolving the complex relationship in Paphiopedilum.},
}
@article {pmid35185949,
year = {2021},
author = {Matiz-Ceron, L and Reyes, A and Anzola, J},
title = {Taxonomical Evaluation of Plant Chloroplastic Markers by Bayesian Classifier.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {782663},
pmid = {35185949},
issn = {1664-462X},
abstract = {DNA barcodes are standardized sequences that range between 400 and 800 bp, vary at different taxonomic levels, and make it possible to assign sequences to species that have been previously taxonomically characterized. Several DNA barcodes have been postulated for plants, nonetheless, their classification potential has not been evaluated for metabarcoding, and as a result, it would appear as none of them excels above the others in this area. One tool that has been widely used and served as a baseline when evaluating new approaches is Naïve Bayesian Classifiers (NBC). The present study aims at evaluating the classification power of several plant chloroplast genetic markers that have been proposed as barcodes (trnL, rpoB, rbcL, matK, psbA-trnH, and psbK) using an NBC. We performed the classification at different taxonomic levels, and identified problematic genera when resolution was desired. We propose matK and trnL as potential candidate markers with resolution up to genus level. Some problematic genera within certain families could lead to the misclassification no matter which marker is used (i.e., Aegilops, Gueldenstaedtia, Helianthus, Oryza, Shorea, Thysananthus, and Triticum). Finally, we suggest recommendations for the taxonomic identification of plants in samples with potential mixtures.},
}
@article {pmid35185817,
year = {2021},
author = {Frantal, D and Agatha, S and Beisser, D and Boenigk, J and Darienko, T and Dirren-Pitsch, G and Filker, S and Gruber, M and Kammerlander, B and Nachbaur, L and Scheffel, U and Stoeck, T and Qian, K and Weißenbacher, B and Pröschold, T and Sonntag, B},
title = {Molecular Data Reveal a Cryptic Diversity in the Genus Urotricha (Alveolata, Ciliophora, Prostomatida), a Key Player in Freshwater Lakes, With Remarks on Morphology, Food Preferences, and Distribution.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {787290},
pmid = {35185817},
issn = {1664-302X},
support = {I 2238/FWF_/Austrian Science Fund FWF/Austria ; I 3268/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Species of the ciliate genus Urotricha are key players in freshwater plankton communities. In the pelagial of lakes, about 20 urotrich species occur throughout an annual cycle, some of which play a pivotal role in aquatic food webs. For example, during the phytoplankton spring bloom, they consume a remarkable proportion of the algal production. In ecological studies, urotrich ciliates are usually merely identified to genus rank and grouped into size classes. This is unsatisfying considering the distinct autecological properties of individual species and their specific spatial and temporal distribution patterns. As a basis for future research, we characterized in detail four common urotrich morphotypes, i.e., specimens identified as U. furcata and tentatively as U. agilis, U. pseudofurcata, and U. castalia, using state-of-the-art methods. We used an integrative polyphasic approach, in which morphological studies (in vivo observation, silver staining methods, scanning electron microscopy) were linked with a molecular approach exploiting four different gene fragments as taxonomic DNA barcodes with different resolution potential (SSU rDNA, ITS-1, ITS-2, hypervariable V4 and V9 regions of the SSU rDNA). We shed light on the diversity of urotrich ciliates as well as on their global distribution patterns, and annual cycles. Additionally, we coupled individual species occurrences and environmental parameters, and subsequently modeled the distribution and occurrence, using logistic regressions. Furthermore, for one strain putatively identified as U. castalia, we ascertained the optimal cultivation media and food preferences. Thereby, our comprehensive view on these important freshwater ciliates that frequently occur in environmental high throughput sequencing datasets worldwide will allow future studies to better exploit protistan plankton data from lakes.},
}
@article {pmid35183127,
year = {2022},
author = {Moghaddam, M and Ohta, A and Shimizu, M and Terauchi, R and Kazempour-Osaloo, S},
title = {The complete chloroplast genome of Onobrychis gaubae (Fabaceae-Papilionoideae): comparative analysis with related IR-lacking clade species.},
journal = {BMC plant biology},
volume = {22},
number = {1},
pages = {75},
pmid = {35183127},
issn = {1471-2229},
mesh = {Codon Usage ; Fabaceae/*genetics ; *Genome, Chloroplast ; Genome, Plant ; High-Throughput Nucleotide Sequencing ; Iran ; *Phylogeny ; Repetitive Sequences, Nucleic Acid ; Selection, Genetic ; },
abstract = {BACKGROUND: Plastome (Plastid genome) sequences provide valuable markers for surveying evolutionary relationships and population genetics of plant species. Papilionoideae (papilionoids) has different nucleotide and structural variations in plastomes, which makes it an ideal model for genome evolution studies. Therefore, by sequencing the complete chloroplast genome of Onobrychis gaubae in this study, the characteristics and evolutionary patterns of plastome variations in IR-loss clade were compared.<br><br>RESULTS: In the present study, the complete plastid genome of O. gaubae, endemic to Iran, was sequenced using Illumina paired-end sequencing and was compared with previously known genomes of the IRLC species of legumes. The O. gaubae plastid genome was 122,688&#xa0;bp in length and included a large single-copy (LSC) region of 81,486&#xa0;bp, a small single-copy (SSC) region of 13,805&#xa0;bp and one copy of the inverted repeat (IRb) of 29,100&#xa0;bp. The genome encoded 110 genes, including 76 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosome RNA (rRNA) genes and possessed 83 simple sequence repeats (SSRs) and 50 repeated structures with the highest proportion in the LSC. Comparative analysis of the chloroplast genomes across IRLC revealed three hotspot genes (ycf1, ycf2, clpP) which could be used as DNA barcode regions. Moreover, seven hypervariable regions [trnL(UAA)-trnT(UGU), trnT(GGU)-trnE(UUC), ycf1, ycf2, ycf4, accD and clpP] were identified within Onobrychis, which could be used to distinguish the Onobrychis species. Phylogenetic analyses revealed that O. gaubae is closely related to Hedysarum. The complete O. gaubae genome is a valuable resource for investigating evolution of Onobrychis species and can be used to identify related species.<br><br>CONCLUSIONS: Our results reveal that the plastomes of the IRLC are dynamic molecules and show multiple gene losses and inversions. The identified hypervariable regions could be used as molecular markers for resolving phylogenetic relationships and species identification and also provide new insights into plastome evolution across IRLC.},
}
@article {pmid35180378,
year = {2022},
author = {Feng, J and Pucella, JN and Jang, G and Alcántara-Hernández, M and Upadhaya, S and Adams, NM and Khodadadi-Jamayran, A and Lau, CM and Stoeckius, M and Hao, S and Smibert, P and Tsirigos, A and Idoyaga, J and Reizis, B},
title = {Clonal lineage tracing reveals shared origin of conventional and plasmacytoid dendritic cells.},
journal = {Immunity},
volume = {55},
number = {3},
pages = {405-422.e11},
pmid = {35180378},
issn = {1097-4180},
support = {R37 AI072571/AI/NIAID NIH HHS/United States ; F32 HL145997/HL/NHLBI NIH HHS/United States ; T32 AI100853/AI/NIAID NIH HHS/United States ; R21 AI115382/AI/NIAID NIH HHS/United States ; R21 AI128730/AI/NIAID NIH HHS/United States ; T32 CA009161/CA/NCI NIH HHS/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; R01 AI158808/AI/NIAID NIH HHS/United States ; R01 AI072571/AI/NIAID NIH HHS/United States ; R01 AG049074/AG/NIA NIH HHS/United States ; },
mesh = {Animals ; *B-Lymphocytes ; Cell Count ; Chorea ; *Dendritic Cells ; Hematopoietic Stem Cells ; Mice ; },
abstract = {Developmental origins of dendritic cells (DCs) including conventional DCs (cDCs, comprising cDC1 and cDC2 subsets) and plasmacytoid DCs (pDCs) remain unclear. We studied DC development in unmanipulated adult mice using inducible lineage tracing combined with clonal DNA "barcoding" and single-cell transcriptome and phenotype analysis (CITE-seq). Inducible tracing of Cx3cr1[+] hematopoietic progenitors in the bone marrow showed that they simultaneously produce all DC subsets including pDCs, cDC1s, and cDC2s. Clonal tracing of hematopoietic stem cells (HSCs) and of Cx3cr1[+] progenitors revealed clone sharing between cDC1s and pDCs, but not between the two cDC subsets or between pDCs and B cells. Accordingly, CITE-seq analyses of differentiating HSCs and Cx3cr1[+] progenitors identified progressive stages of pDC development including Cx3cr1[+] Ly-6D[+] pro-pDCs that were distinct from lymphoid progenitors. These results reveal the shared origin of pDCs and cDCs and suggest a revised scheme of DC development whereby pDCs share clonal relationship with cDC1s.},
}
@article {pmid35179820,
year = {2023},
author = {Cabodevilla, X and Gómez-Moliner, BJ and Abad, N and Madeira, MJ},
title = {Simultaneous analysis of the intestinal parasites and diet through eDNA metabarcoding.},
journal = {Integrative zoology},
volume = {18},
number = {3},
pages = {399-413},
doi = {10.1111/1749-4877.12634},
pmid = {35179820},
issn = {1749-4877},
support = {PRE_2018_2_0273//Basque Country Government/ ; IT1163-19//Sistem&#xe1;tica, Biogeograf&#xed;a, Ecolog&#xed;a del comportamiento y Evoluci&#xf3;n/ ; //Additional funds for this study were provided by the project 201630E096 funded by CSIC/ ; },
mesh = {Animals ; *Parasites/genetics ; DNA Barcoding, Taxonomic/methods ; *DNA, Environmental ; DNA/genetics ; Biodiversity ; Diet/veterinary ; Environmental Monitoring ; },
abstract = {Agricultural expansion and intensification are having a huge impact on plant and arthropod diversity and abundance, affecting food availability for farmland birds. Difficult food access, in turn, can lead to immunosuppression and a higher incidence of parasites. In the studies designed to examine changes in the diet of birds and their parasites, metabarcoding is proving particularly useful. This technique requires mini-barcodes capable of amplifying the DNA of target organisms from fecal environmental DNA. To help to understand the impact of agricultural expansion on biodiversity, this study sought to design and identify mini-barcodes that might simultaneously assess diet and intestinal parasites from the feces of farmland birds. The capacity to identify diet and parasites of 2 existing and 3 newly developed mini-barcodes was tested "in silico" in relation to the behavior of a reference eukaryotic barcode. Among the newly designed mini-barcodes, MiniB18S_81 showed the higher taxonomic coverage of eukaryotic taxa and a greater amplification and identification capacity for diet and parasite taxa. Moreover, when it was tested on fecal samples from 5 different steppe bird species, MiniB18S_81 showed high taxonomic resolution of the most relevant diet and parasite phyla, Arthropoda, Nematoda, Platyhelminthes, and Apicomplexa at the order level. Thus, the mini-barcode developed emerges as an excellent tool to simultaneously provide detailed information regarding the diet and parasites of birds, essential for conservation and management.},
}
@article {pmid35178894,
year = {2022},
author = {Yin, Y and Yao, LF and Hu, Y and Shao, ZK and Hong, XY and Hebert, PDN and Xue, XF},
title = {DNA barcoding uncovers cryptic diversity in minute herbivorous mites (Acari, Eriophyoidea).},
journal = {Molecular ecology resources},
volume = {22},
number = {5},
pages = {1986-1998},
doi = {10.1111/1755-0998.13599},
pmid = {35178894},
issn = {1755-0998},
support = {31970437//National Natural Science Foundation of China/ ; },
mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic ; Host Specificity/genetics ; Humans ; *Mites/anatomy &amp; histology/genetics ; Plants/genetics ; },
abstract = {Eriophyoid mites (Acari: Eriophyoidea) are among the smallest of terrestrial arthropods and the most species-rich group of herbivorous mites with a high host specificity. However, knowledge of their species diversity has been impeded by the difficulty of their morphological differentiation. This study assembles a DNA barcode reference library that includes 1850 mitochondrial COI sequences which provides coverage for 45% of the 930 species of eriophyoid mites known from China, and for 37 North American species. Sequence analysis showed a clear barcode gap in nearly all species, reflecting the fact that intraspecific divergences averaged 0.97% versus a mean of 18.51% for interspecific divergences (minimum nearest-neighbour distances) in taxa belonging to three families. Based on these results, we used DNA barcoding to explore the species diversity of eriophyoid mites as well as their host interactions. The 1850 sequences were assigned to 531 barcode index numbers (BINs). Analyses examining the correspondence between these BINs and species identifications based on morphology revealed that members of 45 species were assigned to two or more BINs, resulting in 1.16 times more BINs than morphospecies. Richness projections suggest that over 2345 BINs occurred at the sampled locations. Host plant analysis showed that 89% of these mites (BINs) attack only one or two congeneric host species, but the others have several hosts. Furthermore, host-mite network analyses demonstrate that eriophyoid mites are high host-specific, and modularity is high in plant-mite networks. By creating a highly effective identification system for eriophyoid mites in the Barcode of Life Data Systems database (BOLD), DNA barcoding will advance our understanding of the diversity of eriophyoid mites and their host interactions.},
}
@article {pmid35178303,
year = {2022},
author = {Ayadi, ZEM and Tazerouti, F and Gey, D and Justine, JL},
title = {A revision of Plectanocotyle (Monogenea, Plectanocotylidae), with molecular barcoding of three species and the description of a new species from the streaked gurnard Chelidonichthys lastoviza off Algeria.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e12873},
pmid = {35178303},
issn = {2167-8359},
mesh = {Animals ; Algeria ; *Trematoda/genetics ; *Perciformes/parasitology ; *Bass ; Gills/parasitology ; },
abstract = {BACKGROUND: The family Plectanocotylidae includes parasites of the gills of marine fish; although nine genera and about 20 species have been described, almost no molecular information is available. Putting aside Plectanocotyle elliptica Diesing, 1850, supposedly a parasite of the white perch Morone americana, never found again since its original description, two species were valid within Plectanocotyle Diesing, 1850 before this work: Plectanocotyle gurnardi (Van Beneden &amp; Hesse, 1863) Llewellyn, 1941 and Plectanocotyle major Boudaya, Neifar &amp; Euzet, 2006.<br><br>METHODS: In this paper, we describe the third species of the genus Plectanocotyle and perform a comparative morphological and molecular analysis of the three species and of Triglicola obscura (Euzet &amp; Suriano, 1974) Mamaev, 1976. Host fishes were also barcoded (COI) for confirmation of host identifications.<br><br>RESULTS: Plectanocotyle lastovizae n. sp. is described from the gills of the streaked gurnard Chelidonichthys lastoviza collected off Algeria. The species is compared with specimens of Plectanocotyle cf. gurnardi (from C. lastoviza) from the same locality and P. major and T. obscura (both from the longfin gurnard C. obscurus). Molecules from Plectanocotyle cf. gurnardi could not be compared with P. gurnardi from the type-host and type-locality and we kept the status of the Mediterranean specimens as pending. Algeria is a new geographic record for P. major and T. obscura. Plectanocotyle lastovizae n. sp. is distinguished from the other species found in the Mediterranean by the measurements of clamps, number of testes, and COI sequences, with notable divergence (7.8-11.8%) from the other two species of the genus.<br><br>DISCUSSION: We briefly present a list of currently known members of the family Plectanocotylidae, their biology and their hosts.},
}
@article {pmid35178296,
year = {2022},
author = {Young, MR and Hebert, PDN},
title = {Unearthing soil arthropod diversity through DNA metabarcoding.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e12845},
pmid = {35178296},
issn = {2167-8359},
mesh = {Humans ; Animals ; *Arthropods/genetics ; DNA Barcoding, Taxonomic ; Soil ; DNA/genetics ; Biodiversity ; },
abstract = {DNA metabarcoding has the potential to greatly advance understanding of soil biodiversity, but this approach has seen limited application for the most abundant and species-rich group of soil fauna-the arthropods. This study begins to address this gap by comparing information on species composition recovered from metabarcoding two types of bulk samples (specimens, soil) from a temperate zone site and from bulk soil samples collected at eight sites in the Arctic. Analysis of 22 samples (3 specimen, 19 soil) revealed 410 arthropod OTUs belonging to 112 families, 25 orders, and nine classes. Studies at the temperate zone site revealed little overlap in species composition between soil and specimen samples, but more overlap at higher taxonomic levels (families, orders) and congruent patterns of α- and β-diversity. Expansion of soil analyses to the Arctic revealed locally rich, highly dissimilar, and spatially structured assemblages compatible with dispersal limited and environmentally driven assembly. The current study demonstrates that DNA metabarcoding of bulk soil enables rapid, large-scale assessments of soil arthropod diversity. However, deep sequence coverage is required to adequately capture the species present in these samples, and expansion of the DNA barcode reference library is necessary to improve taxonomic resolution of the sequences recovered through this approach.},
}
@article {pmid35178290,
year = {2022},
author = {Justine, JL and Gastineau, R and Gros, P and Gey, D and Ruzzier, E and Charles, L and Winsor, L},
title = {Hammerhead flatworms (Platyhelminthes, Geoplanidae, Bipaliinae): mitochondrial genomes and description of two new species from France, Italy, and Mayotte.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e12725},
pmid = {35178290},
issn = {2167-8359},
mesh = {Animals ; *Genome, Mitochondrial/genetics ; Phylogeny ; Comoros ; *Planarians ; Italy ; France ; },
abstract = {BACKGROUND: New records of alien land planarians are regularly reported worldwide, and some correspond to undescribed species of unknown geographic origin. The description of new species of land planarians (Geoplanidae) should classically be based on both external morphology and histology of anatomical structures, especially the copulatory organs, ideally with the addition of molecular data.<br><br>METHODS: Here, we describe the morphology and reproductive anatomy of a species previously reported as Diversibipalium "black", and the morphology of a species previously reported as Diversibipalium "blue". Based on next generation sequencing, we obtained the complete mitogenome of five species of Bipaliinae, including these two species.<br><br>RESULTS: The new species Humbertium covidum n. sp. (syn: Diversibipalium "black" of Justine et al., 2018) is formally described on the basis of morphology, histology and mitogenome, and is assigned to Humbertium on the basis of its reproductive anatomy. The type-locality is Casier, Italy, and other localities are in the Department of Pyr&#xe9;n&#xe9;es-Atlantiques, France; some published or unpublished records suggest that this species might also be present in Russia, China, and Japan. The mitogenomic polymorphism of two geographically distinct specimens (Italy vs France) is described; the cox1 gene displayed 2.25% difference. The new species Diversibipalium mayottensis n. sp. (syn: Diversibipalium "blue" of Justine et al., 2018) is formally described on the basis of external morphology and complete mitogenome and is assigned to Diversibipalium on the basis of an absence of information on its reproductive anatomy. The type- and only known locality is the island of Mayotte in the Mozambique Channel off Africa. Phylogenies of bipaliine geoplanids were constructed on the basis of SSU, LSU, mitochondrial proteins and concatenated sequences of cox1, SSU and LSU. In all four phylogenies, D. mayottensis was the sister-group to all the other bipaliines. With the exception of D. multilineatum which could not be circularised, the complete mitogenomes of B. kewense, B. vagum, B. adventitium, H. covidum and D. mayottensis were colinear. The 16S gene in all bipaliine species was problematic because usual tools were unable to locate its exact position.<br><br>CONCLUSION: Next generation sequencing, which can provide complete mitochondrial genomes as well as traditionally used genes such as SSU, LSU and cox1, is a powerful tool for delineating and describing species of Bipaliinae when the reproductive structure cannot be studied, which is sometimes the case of asexually reproducing invasive species. The unexpected position of the new species D. mayottensis as sister-group to all other Bipaliinae in all phylogenetic analyses suggests that the species could belong to a new genus, yet to be described.},
}
@article {pmid35175140,
year = {2022},
author = {Viveros-Santos, V and Hernández-Triana, LM and Ibáñez-Bernal, S and Ortega-Morales, AI and Nikolova, NI and Pairot, P and Fooks, AR and Casas-Martínez, M},
title = {Integrated Approaches for the Identification of Mosquitoes (Diptera: Culicidae) from the Volcanoes of Central America Physiographic Subprovince of the State of Chiapas, Mexico.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {22},
number = {2},
pages = {120-137},
doi = {10.1089/vbz.2021.0034},
pmid = {35175140},
issn = {1557-7759},
mesh = {*Aedes ; Animals ; *Anopheles ; *Culex ; *Culicidae ; Ecosystem ; Mexico ; },
abstract = {Nowadays, there is a lack of information on the mosquito's fauna and DNA barcoding sequence reference library from many areas in Mexico, including the Volcanoes of Central America physiographic subprovince in the state of Chiapas. Consequently, a survey was undertaken to delineate the mosquito (Diptera: Culicidae) fauna in this region across different seasons using different collecting techniques. All species were identified by morphology and DNA barcoding, and their ecological features were also defined. In total, 62 taxa were morphologically examined, 60 of these were successfully identified based on morphological characteristics, but two were unable to be identified at the species level. The genera Aedes, Anopheles, Culex, and Wyeomyia are the most diverse among mosquito genera collected and include several species of medical and veterinary importance. Ecological characteristics of the immature habitats indicated that they were grouped into four categories namely, (1) large water bodies at ground level, (2) small and shady phytotelmata (e.g., tree holes and bamboo internodes), (3) large phytotelmata (e.g., plant leaves and axis bromeliad), and (4) artificial containers. The cytochrome c oxidase subunit I (COI) DNA barcoding sequences successfully separated the majority of these species, although specific species showed >2% intraspecific genetic divergences.},
}
@article {pmid35174283,
year = {2021},
author = {Xie, GL and Ma, XR and Liu, QY and Meng, FX and Li, C and Wang, J and Guo, YH},
title = {Genetic structure of Culex tritaeniorhynchus (Diptera: Culicidae) based on COI DNA barcodes.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {6},
number = {4},
pages = {1411-1415},
pmid = {35174283},
issn = {2380-2359},
abstract = {Culex tritaeniorhynchus Gile is a major vector of Japanese encephalitis in China. The population genetics study is crucial as it helps understanding the epidemiological aspects of mosquito-brone diseases and improving vector control measures. Here, the genetic population structure of C. tritaeniorhynchus in the mainland China were estimated using the cytochrome c oxidase subunit 1 (COI) DNA barcodes region. 485 individuals of C. tritaeniorhynchus were collected from 38 sampling sites in 21 geographic populations in the mainland China. In total, 485 sequences were used to explore the population structure and genetic diversity. The results showed that the populations of C. tritaeniorhynchus had high haplotype diversity (Hd = 0.98, with 303 haplotypes), low nucleotide diversity (p = 0.02245) and high gene flow (Nm = 47.11) with two maternal lineages and four groups. An AMOVA indicated that 98.8% of the total variation originated from variation within populations. In addition, the population genetic structure exhibited by C. tritaeniorhynchus filling the vacant of the genetic structure in the mainland China. Human activities may also assist mosquito movement and migration. Gene flow among the populations of C. tritaeniorhynchus can facilitate the spread of insecticide resistance genes over geographical areas, and it will be a challenging for controlling the populations.},
}
@article {pmid35173265,
year = {2022},
author = {Vázquez, M and Muñoz, D and Medina, R and Paxton, RJ and de Oliveira, FF and Quezada-Euán, JJG},
title = {Sympatric cleptobiotic stingless bees have species-specific cuticular profiles that resemble their hosts.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {2621},
pmid = {35173265},
issn = {2045-2322},
mesh = {Adaptation, Biological ; Animals ; Bees/classification/*genetics/*physiology ; Biological Evolution ; Biota ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Ecology ; *Species Specificity ; *Sympatry ; },
abstract = {Stingless bees are the largest group of eusocial pollinators with diverse natural histories, including obligate cleptobionts (genus Lestrimelitta) that completely abandoned flower visitation to rely on other stingless bees for food and nest materials. Species of Lestrimeliita are thought to specialize upon different host species, and deception through chemical similarity has been proposed as a mechanism to explain this phenomenon. In the Yucatan Peninsula of Mexico, Scaptotrigona pectoralis is a species chemically distinct from, and not preferred as a host by, locally widespread Lestrimeliita niitkib; witnessing attacks on S. pectoralis colonies offered the opportunity to test the sensory deception hypothesis to cletoparasitism. Analysis of cuticular profiles revealed that the Lestrimelitta attacking S. pectoralis differed significantly in odour bouquet to L. niitkib and, in contrast, it resembled that of S. pectoralis. Further analyses, including morphometrics, mtDNA barcoding, and the examination of taxonomic features, confirmed the existence of two sympatric Lestrimelitta species. The results give support to the hypothesis of chemical deception as a cleptobiotic strategy in Lestrimelitta sp. This is the first evidence that sympatric cleptobionts of the same genus select hosts in accordance with species-specific cuticular profiles, with possible consequences for ecological adaptation and the evolution of these remarkable organisms and the community of stingless bee hosts.},
}
@article {pmid35172874,
year = {2022},
author = {Mylka, V and Matetovici, I and Poovathingal, S and Aerts, J and Vandamme, N and Seurinck, R and Verstaen, K and Hulselmans, G and Van den Hoecke, S and Scheyltjens, I and Movahedi, K and Wils, H and Reumers, J and Van Houdt, J and Aerts, S and Saeys, Y},
title = {Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq.},
journal = {Genome biology},
volume = {23},
number = {1},
pages = {55},
pmid = {35172874},
issn = {1474-760X},
mesh = {Animals ; Antibodies/chemistry ; COVID-19/*blood ; Case-Control Studies ; Cell Line, Tumor ; Cell Nucleus/chemistry ; Humans ; Lipids/chemistry ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Neutrophils/chemistry/immunology/virology ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis/*methods ; Mice ; },
abstract = {BACKGROUND: Multiplexing of samples in single-cell RNA-seq studies allows a significant reduction of the experimental costs, straightforward identification of doublets, increased cell throughput, and reduction of sample-specific batch effects. Recently published multiplexing techniques using oligo-conjugated antibodies or -lipids allow barcoding sample-specific cells, a process called "hashing."<br><br>RESULTS: Here, we compare the hashing performance of TotalSeq-A and -C antibodies, custom synthesized lipids and MULTI-seq lipid hashes in four cell lines, both for single-cell RNA-seq and single-nucleus RNA-seq. We also compare TotalSeq-B antibodies with CellPlex reagents (10x Genomics) on human PBMCs and TotalSeq-B with different lipids on primary mouse tissues. Hashing efficiency was evaluated using the intrinsic genetic variation of the cell lines and mouse strains. Antibody hashing was further evaluated on clinical samples using PBMCs from healthy and SARS-CoV-2 infected patients, where we demonstrate a more affordable approach for large single-cell sequencing clinical studies, while simultaneously reducing batch effects.<br><br>CONCLUSIONS: Benchmarking of different hashing strategies and computational pipelines indicates that correct demultiplexing can be achieved with both lipid- and antibody-hashed human cells and nuclei, with MULTISeqDemux as the preferred demultiplexing function and antibody-based hashing as the most efficient protocol on cells. On nuclei datasets, lipid hashing delivers the best results. Lipid hashing also outperforms antibodies on cells isolated from mouse brain. However, antibodies demonstrate better results on tissues like spleen or lung.},
}
@article {pmid35169641,
year = {2022},
author = {Tineo, D and Bustamante, DE and Calderon, MS and Huaman, E},
title = {Exploring the diversity of andean berries from northern Peru based on molecular analyses.},
journal = {Heliyon},
volume = {8},
number = {2},
pages = {e08839},
pmid = {35169641},
issn = {2405-8440},
abstract = {More than 12,000 species have been listed under the category of berries, and most of them belong to the orders Ericales and Rosales. Recent phylogenetic studies using molecular data have revealed disagreements with morphological approaches mainly due to diverse floral arrangements, which has proven to be a problem when recognizing species. Therefore, the use of multilocus sequence data is essential to establish robust species boundaries. Although berries are common in Andean cloud forests, diversity of these taxa has not been extensively evaluated in the current context of DNA-based techniques. In this regard, this study characterized morphologically and constructed multilocus phylogenies using four molecular markers, two chloroplast markers (matK and rbcL) and two nuclear markers (ITS and GBSSI-2). Specimens did not show diagnostic features to delimit species of berries. A total of 125 DNA-barcodes of andean berries were newly generated for the four molecular markers. The multilocus phylogenies constructed from these markers allowed the identification of 24 species grouped into the order Ericales (Cavendishia = 1, Clethra = 2, Disterigma = 2, Gaultheria = 4, Thibaudia = 4, Vaccinium = 3) and Rosales (Rubus = 8), incorporating into the Peruvian flora four new records (Disterigma ecuadorense, Disterigma synanthum, Vaccinium meridionale and Rubus glabratus) and revealing the genus Rubus as the most diverse group of berries in the Amazonas region. The results of this study showed congruence in all the multilocus phylogenies, with internal transcribed spacer (ITS) showing the best resolution to distinguish the species. These species were found in coniferous forests, dry and humid forests, rocky slopes, and grasslands at 2,506-3,019 masl from Amazonas region. The integration of morphological and DNA-based methods is recommended to understand the diversity of berries along the Peruvian Andean cloud forest. Abstract in Quechua language Qhawarqan astawan chunka iskayniyuq waranqa especiekuna bayasmanta huch'uy mit'a maypichus hatun rak'i chayaqi ordenkunata Ericaleswan Rosaleswan. Chayraqpi Khuski filogeneticamanta rurachiy allincharqan chanikuna molecularkuna willarqan ayñi rikunawanta morfologicokunamanta, qaylla llapan rantichay t'ika tiktutaywan ñawray, ima kay kaqta qhawacgirqan kay huk champay pachaman riqsiypa especiekunamanta. Hina kaqtintaq, chanikuna qatikipaykunamanta multilocus hat'alliy tiksipmi takyachiypaq saywakuna sinchikuna especiekunamanta. Pana bayaskuna kanku allatinkuna sach'a-sach'api phuyusqa anti runap, ñawran manan karqan achka kamaykuy kunan pacha allwiyaraykupi takyasqakuna ADN. Chayrayku, Noqanchispa taqwi allincharqan huk filogenia multilocus, rarachikupúnmi tawa molecular marcadorkuna, caspa iskay markadorkunawan cloroplastomanta (matK, rbcL) iskay markadorkunawan nuclearkunamanta (ITS, GBSSI-2). Kaykunawan filogeniamanta huniqamuran kikinchay iskay chunka tawayoq especies ima tantaqamuran q'anchis generospi (Cavendishia=1, Clethra=2, Disterigma=2, Gaultheria=4, Thibaudia=4, Vaccinium=3, Rubus=8), kaykunata huñuyqamuranta piruwanu llacha kamay tawa musuq quillqakamachikuta (Disterigma ecuadorense, Disterigma synanthum, Vaccinium meridionale, Rubus glabratus). Nocaykuq lluqsisqan kuwirinti rikuchirurqan llapankuna filogeniaspi multilocusmanta, kaspa espaciador transcrito interno (ITS) pi rikuchina kutuwi mihur rantichay riqsiypaq especiekunata. Abstract in Awajun language Dekanauwai juú weantug 12000 sag nagkaikiut, júna nejég tente ainawai nuintushkam kuashtai Ericales nuigtu Rosales weantui. Molecularesjai takasmaug juki filogeneticos augtus yamá dekai antugnaiñasmauwa nuna Morfologicosjai disa umikmaug, juka waignawai kuashag yagkunum, juwai dekaata tamanum kuashat utugchata ama nunuka. Nunui asamtai multilocus takasmauwa nujai dekanui wajukut ainawa pipish tumaig aidaush. Tujashkam kuashtai tentee nejég ainaug ikam naig yujagkim amuamua nunuig, wajupá kuashtakit tusajig ashi dekapasjig ADNjain dischamui. Nuni tamaugmak, ii augtusag duka takasé filogenia multilocus dekamua nujai, takasji ipák usumat marcadores molecularesjai, jimag marcadores cloroplastosjai (matK nuigtu rbcL) nuigtu jimag marcadores nuclearesjai (ITS nuigtu GBSSI-2). Juu filogenias dekaji 24 sag nagkaikiut tuwaka 7 generosnug tuwaka awa nunu (Cavendishia=1, Clethra=2, Disterigma=2, Gaultheria=4, Thibaudia=4, Vaccinium=3, Rubus=8), juui dekanai yamajam ipák usumat ajag perunum awanunu (Disterigma ecuadorense, Disterigma synanthum, Vaccinium meridionale nuigtu Rubus glabratus).},
}
@article {pmid35168568,
year = {2022},
author = {Wang, Y and Xie, S and Armendariz, D and Hon, GC},
title = {Computational identification of clonal cells in single-cell CRISPR screens.},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {135},
pmid = {35168568},
issn = {1471-2164},
support = {DP2GM128203/GM/NIGMS NIH HHS/United States ; RP190451//Cancer Prevention and Research Institute of Texas/ ; UM1 HG011996/HG/NHGRI NIH HHS/United States ; DP2 GM128203/GM/NIGMS NIH HHS/United States ; 1019804//Burroughs Wellcome Fund/ ; UM1HG011996/HG/NHGRI NIH HHS/United States ; },
mesh = {CRISPR-Cas Systems/genetics ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Genome ; *RNA, Guide, CRISPR-Cas Systems ; Reproducibility of Results ; },
abstract = {BACKGROUND: Single-cell CRISPR screens are powerful tools to understand genome function by linking genetic perturbations to transcriptome-wide phenotypes. However, since few cells can be affordably sequenced in these screens, biased sampling of cells could affect data interpretation. One potential source of biased sampling is clonal cell expansion.<br><br>RESULTS: Here, we identify clonal cells in single cell screens using multiplexed sgRNAs as barcodes. We find that the cells in each clone share transcriptional similarities and bear segmental copy number changes. These analyses suggest that clones are genetically distinct. Finally, we show that the transcriptional similarities of clonally expanded cells contribute to false positives in single-cell CRISPR screens.<br><br>CONCLUSIONS: Experimental conditions that reduce clonal expansion or computational filtering of clonal cells will improve the reliability of single-cell CRISPR screens.},
}
@article {pmid35166672,
year = {2022},
author = {Eisele, AS and Cosgrove, J and Magniez, A and Tubeuf, E and Tenreira Bento, S and Conrad, C and Cayrac, F and Tak, T and Lyne, AM and Urbanus, J and Perié, L},
title = {Erythropoietin directly remodels the clonal composition of murine hematopoietic multipotent progenitor cells.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {35166672},
issn = {2050-084X},
mesh = {Animals ; Cell Differentiation ; Erythropoiesis/physiology ; *Erythropoietin/genetics/pharmacology ; *Hematopoietic Stem Cells ; Mice ; Multipotent Stem Cells ; },
abstract = {The cytokine erythropoietin (EPO) is a potent inducer of erythrocyte development and one of the most prescribed biopharmaceuticals. The action of EPO on erythroid progenitor cells is well established, but its direct action on hematopoietic stem and progenitor cells (HSPCs) is still debated. Here, using cellular barcoding, we traced the differentiation of hundreds of single murine HSPCs, after ex vivo EPO exposure and transplantation, in five different hematopoietic cell lineages, and observed the transient occurrence of high-output myeloid-erythroid-megakaryocyte-biased and myeloid-B-cell-dendritic cell-biased clones. Single-cell RNA sequencing analysis of ex vivo EPO-exposed HSPCs revealed that EPO induced the upregulation of erythroid associated genes in a subset of HSPCs, overlapping with multipotent progenitor (MPP) 1 and MPP2. Transplantation of barcoded EPO-exposed MPP2 confirmed their enrichment in myeloid-erythroid-biased clones. Collectively, our data show that EPO does act directly on MPP independent of the niche and modulates fate by remodeling the clonal composition of the MPP pool.},
}
@article {pmid35161250,
year = {2022},
author = {Aneva, I and Zhelev, P and Bonchev, G and Boycheva, I and Simeonova, S and Kancheva, D},
title = {DNA Barcoding Study of Representative Thymus Species in Bulgaria.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {3},
pages = {},
pmid = {35161250},
issn = {2223-7747},
support = {DN 16/3//Bulgarian Science Fund/ ; },
abstract = {We present a study on the taxonomy of eleven Thymus species, belonging to two sections and occurring naturally in Bulgaria. Four DNA barcoding markers-matK, rbcL, trnH-psbA and ITS-were applied to discriminate the species and to reveal their phylogenetic relationships. The results showed that rbcL has the lowest discriminating power regarding the studied species, while the other markers yielded results fitting better to the existing taxonomic schemes based on morphological traits. However, even in the case of better performing markers, the results were not straightforward-morphologically distinct species belonging to different sections were grouped together, and closely related species appeared genetically distinct. The results are typical for taxonomically complex groups, such as the genus Thymus, characterized in Bulgaria with great diversity, high percentage of endemism and still requiring a full and comprehensive taxonomic study. The results are discussed in the light of unresolved taxonomic problems and application of DNA barcoding methods.},
}
@article {pmid35161227,
year = {2022},
author = {Ahmad, A and Ahmad, N and Anis, M and Faisal, M and Alatar, AA and Abdel-Salam, EM and Meena, RP and Sivanesan, I},
title = {Biotechnological Advances in Pharmacognosy and In Vitro Manipulation of Pterocarpus marsupium Roxb.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {3},
pages = {},
pmid = {35161227},
issn = {2223-7747},
support = {RGP-175//King Saud University/ ; },
abstract = {Trees are vital resources for economic, environmental, and industrial growth, supporting human life directly or indirectly through a wide variety of therapeutic compounds, commodities, and ecological services. Pterocarpus marsupium Roxb. (Fabaceae) is one of the most valuable multipurpose forest trees in India and Sri Lanka, as it is cultivated for quality wood as well as pharmaceutically bioactive compounds, especially from the stem bark and heartwood. However, propagation of the tree in natural conditions is difficult due to the low percentage of seed germination coupled with overexploitation of this species for its excellent multipurpose properties. This overexploitation has ultimately led to the inclusion of P. marsupium on the list of endangered plant species. However, recent developments in plant biotechnology may offer a solution to the overuse of such valuable species if such advances are accompanied by technology transfer in the developing world. Specifically, techniques in micropropagation, genetic manipulation, DNA barcoding, drug extraction, delivery, and targeting as well as standardization, are of substantial concern. To date, there are no comprehensive and detailed reviews of P. marsupium in terms of biotechnological research developments, specifically pharmacognosy, pharmacology, tissue culture, authentication of genuine species, and basic gene transfer studies. Thus, the present review attempts to present a comprehensive overview of the biotechnological studies centered on this species and some of the recent novel approaches for its genetic improvement.},
}
@article {pmid35159744,
year = {2022},
author = {Murar, M and Albertazzi, L and Pujals, S},
title = {Advanced Optical Imaging-Guided Nanotheranostics towards Personalized Cancer Drug Delivery.},
journal = {Nanomaterials (Basel, Switzerland)},
volume = {12},
number = {3},
pages = {},
pmid = {35159744},
issn = {2079-4991},
abstract = {Nanomedicine involves the use of nanotechnology for clinical applications and holds promise to improve treatments. Recent developments offer new hope for cancer detection, prevention and treatment; however, being a heterogenous disorder, cancer calls for a more targeted treatment approach. Personalized Medicine (PM) aims to revolutionize cancer therapy by matching the most effective treatment to individual patients. Nanotheranostics comprise a combination of therapy and diagnostic imaging incorporated in a nanosystem and are developed to fulfill the promise of PM by helping in the selection of treatments, the objective monitoring of response and the planning of follow-up therapy. Although well-established imaging techniques, such as Magnetic Resonance Imaging (MRI), Computed Tomography (CT), Positron Emission Tomography (PET) and Single-Photon Emission Computed Tomography (SPECT), are primarily used in the development of theranostics, Optical Imaging (OI) offers some advantages, such as high sensitivity, spatial and temporal resolution and less invasiveness. Additionally, it allows for multiplexing, using multi-color imaging and DNA barcoding, which further aids in the development of personalized treatments. Recent advances have also given rise to techniques permitting better penetration, opening new doors for OI-guided nanotheranostics. In this review, we describe in detail these recent advances that may be used to design and develop efficient and specific nanotheranostics for personalized cancer drug delivery.},
}
@article {pmid35159410,
year = {2022},
author = {Vieira, MB and Faustino, MV and Lourenço, TF and Oliveira, MM},
title = {DNA-Based Tools to Certify Authenticity of Rice Varieties-An Overview.},
journal = {Foods (Basel, Switzerland)},
volume = {11},
number = {3},
pages = {},
pmid = {35159410},
issn = {2304-8158},
support = {UIDB/04551/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; PD/BD/148694/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; CEECIND/03641/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; 1934//PRIMA Programme Horizon 2020,European Union's Framework Programme for Research and Innovatio/ ; },
abstract = {Rice (Oryza sativa L.) is one of the most cultivated and consumed crops worldwide. It is mainly produced in Asia but, due to its large genetic pool, it has expanded to several ecosystems, latitudes and climatic conditions. Europe is a rice producing region, especially in the Mediterranean countries, that grow mostly typical japonica varieties. The European consumer interest in rice has increased over the last decades towards more exotic types, often more expensive (e.g., aromatic rice) and Europe is a net importer of this commodity. This has increased food fraud opportunities in the rice supply chain, which may deliver mixtures with lower quality rice, a problem that is now global. The development of tools to clearly identify undesirable mixtures thus became urgent. Among the various tools available, DNA-based markers are considered particularly reliable and stable for discrimination of rice varieties. This review covers aspects ranging from rice diversity and fraud issues to the DNA-based methods used to distinguish varieties and detect unwanted mixtures. Although not exhaustive, the review covers the diversity of strategies and ongoing improvements already tested, highlighting important advantages and disadvantages in terms of costs, reliability, labor-effort and potential scalability for routine fraud detection.},
}
@article {pmid35158849,
year = {2022},
author = {Shembrey, C and Smith, J and Grandin, M and Williams, N and Cho, HJ and Mølck, C and Behrenbruch, C and Thomson, BN and Heriot, AG and Merino, D and Hollande, F},
title = {Longitudinal Monitoring of Intra-Tumoural Heterogeneity Using Optical Barcoding of Patient-Derived Colorectal Tumour Models.},
journal = {Cancers},
volume = {14},
number = {3},
pages = {},
pmid = {35158849},
issn = {2072-6694},
support = {GNT1164081//National Health and Medical Research Council/ ; Senior Research Grant//Tour de Cure Foundation, Australia/ ; },
abstract = {Geno- and phenotypic heterogeneity amongst cancer cell subpopulations are established drivers of treatment resistance and tumour recurrence. However, due to the technical difficulty associated with studying such intra-tumoural heterogeneity, this phenomenon is seldom interrogated in conventional cell culture models. Here, we employ a fluorescent lineage technique termed "optical barcoding" (OBC) to perform simultaneous longitudinal tracking of spatio-temporal fate in 64 patient-derived colorectal cancer subclones. To do so, patient-derived cancer cell lines and organoids were labelled with discrete combinations of reporter constructs, stably integrated into the genome and thus passed on from the founder cell to all its clonal descendants. This strategy enables the longitudinal monitoring of individual cell lineages based upon their unique optical barcodes. By designing a novel panel of six fluorescent proteins, the maximum theoretical subpopulation resolution of 64 discriminable subpopulations was achieved, greatly improving throughput compared with previous studies. We demonstrate that all subpopulations can be purified from complex clonal mixtures via flow cytometry, permitting the downstream isolation and analysis of any lineages of interest. Moreover, we outline an optimized imaging protocol that can be used to image optical barcodes in real-time, allowing for clonal dynamics to be resolved in live cells. In contrast with the limited intra-tumour heterogeneity observed in conventional 2D cell lines, the OBC technique was successfully used to quantify dynamic clonal expansions and contractions in 3D patient-derived organoids, which were previously demonstrated to better recapitulate the heterogeneity of their parental tumour material. In summary, we present OBC as a user-friendly, inexpensive, and high-throughput technique for monitoring intra-tumoural heterogeneity in in vitro cell culture models.},
}
@article {pmid35158170,
year = {2022},
author = {Krčmar, S and Klobučar, A and Vucelja, M and Boljfetić, M and Kučinić, M and Madić, J and Cvek, M and Bruvo Mađarić, B},
title = {DNA barcoding of hard ticks (Ixodidae), notes on distribution of vector species and new faunal record for Croatia.},
journal = {Ticks and tick-borne diseases},
volume = {13},
number = {3},
pages = {101920},
doi = {10.1016/j.ttbdis.2022.101920},
pmid = {35158170},
issn = {1877-9603},
mesh = {Animals ; Croatia ; DNA Barcoding, Taxonomic ; *Ixodes ; *Ixodidae/genetics ; *Rhipicephalus sanguineus ; },
abstract = {Molecular methods are increasingly being utilized for accurate identification of ticks (Acari: Ixodidae), especially in cases of morphologically highly similar species. In this study, we performed molecular research of the tick fauna in Croatia using DNA barcoding method. Ticks were sampled in three biogeographical regions and thirteen species were recorded: Dermacentor marginatus, Dermacentor reticulatus, Haemaphysalis concinna, Haemaphysalis inermis, Haemaphysalis punctata, Hyalomma marginatum, Ixodes frontalis, Ixodes hexagonus, Ixodes kaiseri, Ixodes ricinus, Rhipicephalus bursa, Rhipicephalus sanguineus s.l. and Rhipicephalus turanicus. Ixodes kaiseri is for the first time recorded in the fauna of Croatia. Of the thirteen hard tick species analyzed in this study, pathogens from different groups (bacteria, protozoa and viruses) have been detected in eight species in Croatia so far. For the important vector species R. sanguineus s.s., new distributional data for Croatia are given. The standard COI barcoding region was amplified, and the sequences were analyzed by species delimitation methods together with the sequences of conspecific and congeneric species from the public BOLD database. Our specimens of H. punctata represent a new, genetically distinct MOTU. A brief overview of the available public DNA barcoding data for Ixodidae is presented, highlighting the need for an integrative approach for the clarification of the taxonomic status of problematic Ixodid taxa. The results provide a basis for the establishment of a molecular data platform for the Ixodidae of the Croatian fauna.},
}
@article {pmid35157186,
year = {2022},
author = {Ito, H and Ito, M},
title = {Comparison of phenolic compounds contained in Aquilaria leaves of different species.},
journal = {Journal of natural medicines},
volume = {76},
number = {3},
pages = {693-702},
pmid = {35157186},
issn = {1861-0293},
mesh = {Glycosides/pharmacology ; Phenols/pharmacology ; Plant Extracts/chemistry/pharmacology ; Plant Leaves ; *Thymelaeaceae/chemistry ; alpha-Glucosidases ; },
abstract = {Leaves of Aquilaria plants contain a variety of phenolic compounds such as iriflophenone glycosides, mangiferin, and genkwanin. Previous studies showed that Aquilaria leaf extracts exhibit many pharmacological activities, including antidiabetic and laxative effects. However, a few studies have reported differences in the chemical content and compositions of Aquilaria species. Here, three Aquilaria species were identified using matK and trnL-trnF sequences and their leaves were analyzed by HPLC and LC/MS. Comparison of the chemical components and α-glucosidase inhibition activity of the three species showed that the level of iriflophenone glycosides in A. rugosa was higher than in A. sinensis and A. crassna. There was no difference in the α-glucosidase inhibition activity of leaf extracts of the three species, but the strength of the inhibition activity can possibly be explained by the total sum of active compounds in the leaf extracts.},
}
@article {pmid35154244,
year = {2021},
author = {Liu, B and Li, Y and Zhang, L},
title = {Analysis and Visualization of Spatial Transcriptomic Data.},
journal = {Frontiers in genetics},
volume = {12},
number = {},
pages = {785290},
pmid = {35154244},
issn = {1664-8021},
abstract = {Human and animal tissues consist of heterogeneous cell types that organize and interact in highly structured manners. Bulk and single-cell sequencing technologies remove cells from their original microenvironments, resulting in a loss of spatial information. Spatial transcriptomics is a recent technological innovation that measures transcriptomic information while preserving spatial information. Spatial transcriptomic data can be generated in several ways. RNA molecules are measured by in situ sequencing, in situ hybridization, or spatial barcoding to recover original spatial coordinates. The inclusion of spatial information expands the range of possibilities for analysis and visualization, and spurred the development of numerous novel methods. In this review, we summarize the core concepts of spatial genomics technology and provide a comprehensive review of current analysis and visualization methods for spatial transcriptomics.},
}
@article {pmid35153530,
year = {2022},
author = {Gueidan, C and Li, L},
title = {A long-read amplicon approach to scaling up the metabarcoding of lichen herbarium specimens.},
journal = {MycoKeys},
volume = {86},
number = {},
pages = {195-212},
pmid = {35153530},
issn = {1314-4049},
abstract = {Reference sequence databases are critical to the accurate detection and identification of fungi in the environment. As repositories of large numbers of well-curated specimens, herbaria and fungal culture collections have the material resources to generate sequence data for large number of taxa, and could therefore allow filling taxonomic gaps often present in reference sequence databases. Financial resources to do that are however often lacking, so that recent efforts have focused on decreasing sequencing cost by increasing the number of multiplexed samples per sequencing run while maintaining high sequence quality. Following a previous study that aimed at decreasing sequencing cost for lichen specimens by generating fungal ITS barcodes for 96 specimens using PacBio amplicon sequencing, we present a method that further decreases lichen specimen metabarcoding costs. A total of 384 mixed DNA extracts obtained from lichen herbarium specimens, mostly from the four genera Buellia, Catillaria, Endocarpon and Parmotrema, were used to generate new fungal ITS sequences using a Sequel I sequencing platform and the PacBio M13 barcoded primers. The average success rate across all taxa was high (86.5%), with particularly high rates for the crustose saxicolous taxa (Buellia, Catillaria and others; 93.3%) and the terricolous squamulose taxa (Endocarpon and others; 96.5%). On the other hand, the success rate for the foliose genus Parmotrema was lower (60.4%). With this taxon sampling, greater specimen age did not appear to impact sequencing success. In fact, the 1966-1980 collection date category showed the highest success rate (97.3%). Compared to the previous study, the abundance-based sequence denoising method showed some limitations, but the cost of generating ITS barcodes was further decreased thanks to the higher multiplexing level. In addition to contributing new ITS barcodes for specimens of four interesting lichen genera, this study further highlights the potential and challenges of using new sequencing technologies on collection specimens to generate DNA sequences for reference databases.},
}
@article {pmid35153529,
year = {2022},
author = {Abarenkov, K and Kristiansson, E and Ryberg, M and Nogal-Prata, S and Gómez-Martínez, D and Stüer-Patowsky, K and Jansson, T and Põlme, S and Ghobad-Nejhad, M and Corcoll, N and Scharn, R and Sánchez-García, M and Khomich, M and Wurzbacher, C and Nilsson, RH},
title = {The curse of the uncultured fungus.},
journal = {MycoKeys},
volume = {86},
number = {},
pages = {177-194},
pmid = {35153529},
issn = {1314-4049},
abstract = {The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as "uncultured fungus". These sequences beget low-resolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length fungal ITS sequences to estimate what proportion of the 95,055 "uncultured fungus" sequences that represent truly unidentifiable fungal taxa - and what proportion of them that would have been straightforward to annotate to some more meaningful taxonomic level at the time of sequence deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers' perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked.},
}
@article {pmid35150047,
year = {2022},
author = {Junker, F and Camillo Teixeira, P},
title = {Barcoding of live peripheral blood mononuclear cells to assess immune cell phenotypes using full spectrum flow cytometry.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {101},
number = {11},
pages = {909-921},
doi = {10.1002/cyto.a.24543},
pmid = {35150047},
issn = {1552-4930},
mesh = {Immunophenotyping ; Flow Cytometry/methods ; *Leukocytes, Mononuclear ; *Single-Cell Analysis/methods ; Phenotype ; },
abstract = {Barcoded flow cytometry is a multiplexing technique allowing for the simultaneous acquisition of cells from different donors or experimental conditions in a high-throughput manner. This approach allows to synchronize acquisition of samples and reduce variance introduced through the operator or technical platform. However, to date, only very few flow cytometry barcoding protocols have been developed, which often suffer from technical limitations. Here, we developed a novel barcoding protocol for a full-spectrum flow cytometry platform. We developed a 21-color immunophenotyping assay for up to 20 different samples analyzed simultaneously with comparable variance between repeated single-tube acquisition and postde-multiplexing. Barcoding offers great potential in parallelizing the analysis of complex cell populations such as peripheral blood mononuclear cells (PBMCs). Consequently, we assessed the performance of our method in situations where PBMCs were challenged with phytohaemagglutinin (PHA), a strong mitogen and broad activator of B cells and T cells, and superantigen Staphylococcus enterotoxin B (SEB) that has been reported to induce polyclonal T cell activation. PBMCs were either barcoded before pooled challenge or challenged individually pre-barcoding. Our final workflow included pooled immunophenotyping followed by machine learning aided single-cell data analysis and enabled us to identify robust PHA and SEB mode of action related phenotypic changes in PBMC immune cell lineages. Conclusively, we present a novel technique allowing the barcoded acquisition and analysis of PBMCs from up to 20 different donors and present a valid basis for the future development of complex immunophenotyping protocols.},
}
@article {pmid35149753,
year = {2022},
author = {Vickovic, S and Schapiro, D and Carlberg, K and Lötstedt, B and Larsson, L and Hildebrandt, F and Korotkova, M and Hensvold, AH and Catrina, AI and Sorger, PK and Malmström, V and Regev, A and Ståhl, PL},
title = {Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {129},
pmid = {35149753},
issn = {2399-3642},
support = {U54 CA225088/CA/NCI NIH HHS/United States ; BS2019-0040//Royal Swedish Academy of Sciences (Kungl. Vetenskapsakademien)/ ; P19-0052//Svenska S&#xe4;llskapet f&#xf6;r Medicinsk Forskning (Swedish Society for Medical Research)/ ; 2017.0454//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {*Arthritis, Rheumatoid/genetics/metabolism ; Humans ; Synovial Membrane/metabolism ; *Transcriptome ; },
abstract = {The inflamed rheumatic joint is a highly heterogeneous and complex tissue with dynamic recruitment and expansion of multiple cell types that interact in multifaceted ways within a localized area. Rheumatoid arthritis synovium has primarily been studied either by immunostaining or by molecular profiling after tissue homogenization. Here, we use Spatial Transcriptomics, where tissue-resident RNA is spatially labeled in situ with barcodes in a transcriptome-wide fashion, to study local tissue interactions at the site of chronic synovial inflammation. We report comprehensive spatial RNA-Seq data coupled to cell type-specific localization patterns at and around organized structures of infiltrating leukocyte cells in the synovium. Combining morphological features and high-throughput spatially resolved transcriptomics may be able to provide higher statistical power and more insights into monitoring disease severity and treatment-specific responses in seropositive and seronegative rheumatoid arthritis.},
}
@article {pmid35145533,
year = {2021},
author = {Doležalová, A and Sládeková, L and Šimoníková, D and Holušová, K and Karafiátová, M and Varshney, RK and Doležel, J and Hřibová, E},
title = {Karyotype Differentiation in Cultivated Chickpea Revealed by Oligopainting Fluorescence in situ Hybridization.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {791303},
pmid = {35145533},
issn = {1664-462X},
abstract = {Chickpea (Cicer arietinum L.) is one of the main sources of plant proteins in the Indian subcontinent and West Asia, where two different morphotypes, desi and kabuli, are grown. Despite the progress in genome mapping and sequencing, the knowledge of the chickpea genome at the chromosomal level, including the long-range molecular chromosome organization, is limited. Earlier cytogenetic studies in chickpea suffered from a limited number of cytogenetic landmarks and did not permit to identify individual chromosomes in the metaphase spreads or to anchor pseudomolecules to chromosomes in situ. In this study, we developed a system for fast molecular karyotyping for both morphotypes of cultivated chickpea. We demonstrate that even draft genome sequences are adequate to develop oligo-fluorescence in situ hybridization (FISH) barcodes for the identification of chromosomes and comparative analysis among closely related chickpea genotypes. Our results show the potential of oligo-FISH barcoding for the identification of structural changes in chromosomes, which accompanied genome diversification among chickpea cultivars. Moreover, oligo-FISH barcoding in chickpea pointed out some problematic, most probably wrongly assembled regions of the pseudomolecules of both kabuli and desi reference genomes. Thus, oligo-FISH appears as a powerful tool not only for comparative karyotyping but also for the validation of genome assemblies.},
}
@article {pmid35145503,
year = {2022},
author = {Helmann, TC and Filiatrault, MJ and Stodghill, PV},
title = {Genome-Wide Identification of Genes Important for Growth of Dickeya dadantii and Dickeya dianthicola in Potato (Solanum tuberosum) Tubers.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {778927},
pmid = {35145503},
issn = {1664-302X},
abstract = {Dickeya species are causal agents of soft rot diseases in many economically important crops, including soft rot disease of potato (Solanum tuberosum). Using random barcode transposon-site sequencing (RB-TnSeq), we generated genome-wide mutant fitness profiles of Dickeya dadantii 3937, Dickeya dianthicola ME23, and Dickeya dianthicola 67-19 isolates collected after passage through several in vitro and in vivo conditions. Though all three strains are pathogenic on potato, D. dadantii 3937 is a well-characterized model while D. dianthicola strains ME23 and 67-19 are recent isolates. Strain ME23 specifically was identified as a representative strain from a 2014 outbreak on potato. This study generated comparable gene fitness measurements across ecologically relevant conditions for both model and non-model strains. Tubers from the potato cultivars "Atlantic," "Dark Red Norland," and "Upstate Abundance" provided highly similar conditions for bacterial growth. Using the homolog detection software PyParanoid, we matched fitness values for orthologous genes in the three bacterial strains. Direct comparison of fitness among the strains highlighted shared and variable traits important for growth. Bacterial growth in minimal medium required many metabolic traits that were also essential for competitive growth in planta, such as amino acid, carbohydrate, and nucleotide biosynthesis. Growth in tubers specifically required the pectin degradation gene kduD. Disruption in three putative DNA-binding proteins had strain-specific effects on competitive fitness in tubers. Though the Soft Rot Pectobacteriaceae can cause disease with little host specificity, it remains to be seen the extent to which strain-level variation impacts virulence.},
}
@article {pmid35145339,
year = {2022},
author = {Torres-Garcia, D and Gené, J and García, D},
title = {New and interesting species of Penicillium (Eurotiomycetes, Aspergillaceae) in freshwater sediments from Spain.},
journal = {MycoKeys},
volume = {86},
number = {},
pages = {103-145},
pmid = {35145339},
issn = {1314-4049},
abstract = {Penicillium species are common fungi found worldwide from diverse substrates, including soil, plant debris, food products and air. Their diversity in aquatic environments is still underexplored. With the aim to explore the fungal diversity in Spanish freshwater sediments, numerous Penicillium strains were isolated using various culture-dependent techniques. A preliminary sequence analysis of the β-tubulin (tub2) gene marker allowed us to identify several interesting species of Penicillium, which were later characterized phylogenetically with the barcodes recommended for species delimitation in the genus. Based on the multi-locus phylogeny of the internal transcribed spacer region (ITS) of the ribosomal DNA, and partial fragments of tub2, calmodulin (cmdA), and the RNA polymerase II largest subunit (rpb2) genes, in combination with phenotypic analyses, five novel species are described. These are P.ausonanum in sectionLanata-Divaricata, P.guarroi in sect.Gracilenta, P.irregulare in sect.Canescentia, P.sicoris in sect.Paradoxa and P.submersum in sect.Robsamsonia. The study of several isolates from samples collected in different locations resulted in the reinstatement of P.vaccaeorum into sectionCitrina. Finally, P.heteromorphum (sect.Exilicaulis) and P.tardochrysogenum (sect.Chrysogena) are reported, previously only known from Antarctica and China, respectively.},
}
@article {pmid35145087,
year = {2022},
author = {Vickovic, S and Lötstedt, B and Klughammer, J and Mages, S and Segerstolpe, &#xc5; and Rozenblatt-Rosen, O and Regev, A},
title = {SM-Omics is an automated platform for high-throughput spatial multi-omics.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {795},
pmid = {35145087},
issn = {2041-1723},
support = {/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; Brain ; Brain Neoplasms ; Colorectal Neoplasms ; Fluorescent Antibody Technique ; Mice ; Mice, Inbred C57BL ; Proteomics/methods ; *RNA ; RNA-Seq ; Spleen ; Splenic Neoplasms ; Staining and Labeling/methods ; *Transcriptome ; },
abstract = {The spatial organization of cells and molecules plays a key role in tissue function in homeostasis and disease. Spatial transcriptomics has recently emerged as a key technique to capture and positionally barcode RNAs directly in tissues. Here, we advance the application of spatial transcriptomics at scale, by presenting Spatial Multi-Omics (SM-Omics) as a fully automated, high-throughput all-sequencing based platform for combined and spatially resolved transcriptomics and antibody-based protein measurements. SM-Omics uses DNA-barcoded antibodies, immunofluorescence or a combination thereof, to scale and combine spatial transcriptomics and spatial antibody-based multiplex protein detection. SM-Omics allows processing of up to 64 in situ spatial reactions or up to 96 sequencing-ready libraries, of high complexity, in a ~2 days process. We demonstrate SM-Omics in the mouse brain, spleen and colorectal cancer model, showing its broad utility as a high-throughput platform for spatial multi-omics.},
}
@article {pmid35143615,
year = {2022},
author = {David, BM and Wyllie, RM and Harouaka, R and Jensen, PA},
title = {A reinforcement learning framework for pooled oligonucleotide design.},
journal = {Bioinformatics (Oxford, England)},
volume = {38},
number = {8},
pages = {2219-2225},
pmid = {35143615},
issn = {1367-4811},
support = {R35 GM138210/GM/NIGMS NIH HHS/United States ; 2093481//Laboratory Directed Research and Development (LDRD) Program of Sandia National Laboratories/ ; //Sandia National Laboratories is a multi-mission laboratory managed and operated by the National Technology &amp; Engineering Solutions of Sandia/ ; //Honeywell International Inc./ ; DE-NA0003525//U.S. Department of Energy's National Nuclear Security Administration/ ; },
mesh = {*Software ; *DNA ; Gene Library ; Oligonucleotides ; },
abstract = {MOTIVATION: The goal of oligonucleotide (oligo) design is to select oligos that optimize a set of design criteria. Oligo design problems are combinatorial in nature and require computationally intensive models to evaluate design criteria. Even relatively small problems can be intractable for brute-force approaches that test every possible combination of oligos, so heuristic approaches must be used to find near-optimal solutions.<br><br>RESULTS: We present a general reinforcement learning (RL) framework, called OligoRL, to solve oligo design problems with complex constraints. OligoRL allows 'black-box' design criteria and can be adapted to solve many oligo design problems. We highlight the flexibility of OligoRL by building tools to solve three distinct design problems: (i) finding pools of random DNA barcodes that lack restriction enzyme recognition sequences (CutFreeRL); (ii) compressing large, non-degenerate oligo pools into smaller degenerate ones (OligoCompressor) and (iii) finding Not-So-Random hexamer primer pools that avoid rRNA and other unwanted transcripts during RNA-seq library preparation (NSR-RL). OligoRL demonstrates how RL offers a general solution for complex oligo design problems.<br><br>OligoRL and all simulation codes are available as a Julia package at http://jensenlab.net/tools and archived at https://archive.softwareheritage.org/browse/origin/directory/?origin_url=https://github.com/bmdavid2/OligoRL.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid35143307,
year = {2022},
author = {Deng, Y and Bartosovic, M and Kukanja, P and Zhang, D and Liu, Y and Su, G and Enninful, A and Bai, Z and Castelo-Branco, G and Fan, R},
title = {Spatial-CUT&amp;Tag: Spatially resolved chromatin modification profiling at the cellular level.},
journal = {Science (New York, N.Y.)},
volume = {375},
number = {6581},
pages = {681-686},
pmid = {35143307},
issn = {1095-9203},
support = {U54 CA209992/CA/NCI NIH HHS/United States ; RF1 MH128876/MH/NIMH NIH HHS/United States ; UG3 CA257393/CA/NCI NIH HHS/United States ; UH3 CA257393/CA/NCI NIH HHS/United States ; U54 DK106857/DK/NIDDK NIH HHS/United States ; R01 CA245313/CA/NCI NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; 681893/ERC_/European Research Council/International ; },
mesh = {Animals ; Brain/*cytology/embryology/growth &amp; development/*metabolism ; Cell Nucleus/metabolism ; Chromatin/*metabolism ; *Epigenesis, Genetic ; Epigenome ; High-Throughput Nucleotide Sequencing ; *Histone Code ; Histones/*metabolism ; Mice ; Microfluidics ; Neurons/cytology ; Single-Cell Analysis ; },
abstract = {Spatial omics emerged as a new frontier of biological and biomedical research. Here, we present spatial-CUT&amp;Tag for spatially resolved genome-wide profiling of histone modifications by combining in situ CUT&amp;Tag chemistry, microfluidic deterministic barcoding, and next-generation sequencing. Spatially resolved chromatin states in mouse embryos revealed tissue-type-specific epigenetic regulations in concordance with ENCODE references and provide spatial information at tissue scale. Spatial-CUT&amp;Tag revealed epigenetic control of the cortical layer development and spatial patterning of cell types determined by histone modification in mouse brain. Single-cell epigenomes can be derived in situ by identifying 20-micrometer pixels containing only one nucleus using immunofluorescence imaging. Spatial chromatin modification profiling in tissue may offer new opportunities to study epigenetic regulation, cell function, and fate decision in normal physiology and pathogenesis.},
}
@article {pmid35141439,
year = {2022},
author = {Ahmed, MS and Barua, A and Datta, SK and Saha, T and Antu, DR and Ahmed, S},
title = {Characterization of spiny lobsters from Bangladesh waters using morphology, COI and 16S rRNA sequences.},
journal = {Heliyon},
volume = {8},
number = {2},
pages = {e08846},
pmid = {35141439},
issn = {2405-8440},
abstract = {This study aims to taxonomically identify and characterise the phylogenetic relationships of spiny lobsters based on mitochondrial cytochrome c oxidase I (COI) and 16S rRNA genes from Bangladesh waters. A total of 19 barcode sequences (10 partial COI sequences and 9 partial 16S rRNA) were successfully generated from 12 collected spiny lobster samples representing four species belonging to the family Palinuridae. The average genetic distances within and between species were 0.834 ± 0.427 and 17.810 ± 0.830, respectively, in COI and 0.107 ± 0.255 and 8.401 ± 2.547, respectively, in 16S rRNA genes. The successful amplification rate of 16S rRNA was higher than that of the COI marker. In the maximum likelihood (ML) tree, the sequences of the same species were clustered together under a single clade for both COI and 16S rRNA, which supports the efficacy of both marker genes in differentiating lobster species.},
}
@article {pmid35141133,
year = {2022},
author = {Ingelbrecht, J and Morgan, DL and Lear, KO and Fazeldean, T and Lymbery, AJ and Norman, BM and Martin, SB},
title = {A new microbothriid monogenean Dermopristis pterophilus n. sp. from the skin of the Critically Endangered green sawfish Pristis zijsron Bleeker, 1851 (Batoidea: Pristidae) in Western Australia.},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {17},
number = {},
pages = {185-193},
pmid = {35141133},
issn = {2213-2244},
abstract = {A new microbothriid monogenean Dermopristis pterophilus n. sp. is described from the skin of the Critically Endangered green sawfish Pristis zijsron Bleeker, 1851 in the Ashburton River delta, northern Western Australia. Analyses of the 28S ribosomal DNA marker and the molecular barcoding markers Histone 3 and Elongation Factor 1 α confirmed position among the Microbothriidae, with close affinity to the only other sequenced representative of Dermopristis Kearn, Whittington and Evans-Groing, 2010. The new species is morphologically consistent with the concept of Dermopristis; it has two testes, lacks a male copulatory organ and has a simple haptor. It is smaller than its two congeners D. paradoxus Kearn, Whittington and Evans-Gowing, 2010 and D. cairae Whittington and Kearn, 2011 and is most similar to the former, distinguished only in that it lacks the strong, transverse, parallel ridges on the ventral body surface that characterise that species. It is more easily distinguished from D. cairae, differing in body shape, possession of a seminal receptacle, and relative position and size of the haptor. It may further differ from both species by fine details of the gut diverticula, although these details are difficult to ascertain. Spermatophores were observed in the new species, similar to those previously reported for D. cairae. The new species exhibits site attachment preference: infections were greatest on and immediately adjacent to the host pelvic fins (including male reproductive organs, i.e. claspers), moderate in proximity to the dorsal and pectoral fins, few on the caudal fin and peduncle, and infrequently, isolated worms occurred elsewhere on the dorsal and ventral surfaces of the body. There was no incidence of infection on the head (including rostrum). We presume D. pterophilus is restricted to P. zijsron and thus likely faces the same threat of extinction.},
}
@article {pmid35140226,
year = {2022},
author = {Tellechea-Luzardo, J and Hobbs, L and Velázquez, E and Pelechova, L and Woods, S and de Lorenzo, V and Krasnogor, N},
title = {Versioning biological cells for trustworthy cell engineering.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {765},
pmid = {35140226},
issn = {2041-1723},
mesh = {Animals ; Automation ; Bacteria/genetics/metabolism ; *Biological Products ; Biotechnology ; Cell Engineering/*methods ; Cell Line ; Genetic Engineering/methods ; Humans ; Metabolic Engineering ; Synthetic Biology/methods ; },
abstract = {"Full-stack" biotechnology platforms for cell line (re)programming are on the horizon, thanks mostly to (a) advances in gene synthesis and editing techniques as well as (b) the growing integration of life science research with informatics, the internet of things and automation. These emerging platforms will accelerate the production and consumption of biological products. Hence, traceability, transparency, and-ultimately-trustworthiness is required from cradle to grave for engineered cell lines and their engineering processes. Here we report a cloud-based version control system for biotechnology that (a) keeps track and organizes the digital data produced during cell engineering and (b) molecularly links that data to the associated living samples. Barcoding protocols, based on standard genetic engineering methods, to molecularly link to the cloud-based version control system six species, including gram-negative and gram-positive bacteria as well as eukaryote cells, are shown. We argue that version control for cell engineering marks a significant step toward more open, reproducible, easier to trace and share, and more trustworthy engineering biology.},
}
@article {pmid35138659,
year = {2022},
author = {Bickford, WA and Goldberg, DE and Zak, DR and Snow, DS and Kowalski, KP},
title = {Plant effects on and response to soil microbes in native and non-native Phragmites australis.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {32},
number = {4},
pages = {e2565},
doi = {10.1002/eap.2565},
pmid = {35138659},
issn = {1051-0761},
mesh = {Bacteria ; Plants ; *Poaceae/microbiology ; *Soil ; Soil Microbiology ; Wetlands ; },
abstract = {Plant-soil feedbacks (PSFs) mediate plant community dynamics and may plausibly facilitate plant invasions. Microbially mediated PSFs are defined by plant effects on soil microbes and subsequent changes in plant performance (responses), both positive and negative. For microbial interactions to benefit invasive plants disproportionately, native and invasive plants must either (1) have different effects on and responses to soil microbial communities or (2) only respond differently to similar microbial communities. In other words, invasive plants do not need to cultivate different microbial communities than natives if they respond differently to them. However, effects and responses are not often explored separately, making it difficult to determine the underlying causes of performance differences. We performed a reciprocal-transplant PSF experiment with multiple microbial inhibition treatments to determine how native and non-native lineages of Phragmites australis affect and respond to soil bacteria, fungi, and oomycetes. Non-native Phragmites is a large, fast-growing, cosmopolitan invasive plant, whereas the North American native variety is comparatively smaller, slower growing, and typically considered a desirable wetland plant. We identified the effects of each plant lineage on soil microbes using DNA meta-barcoding and linked plant responses to microbial communities. Both Phragmites lineages displayed equally weak, insignificant PSFs. We found evidence of slight differential effects on microbial community composition, but no significant differential plant responses. Soils conditioned by each lineage differed only slightly in bacterial community composition, but not in fungal composition. Additionally, native and non-native Phragmites lineages did not significantly differ in their response to similar soil microbial communities. Neither lineage appreciably differed when plant biomass was compared between those grown in sterile and live soils. Targeted microbial inhibitor treatments revealed both lineages were negatively impacted by soil bacteria, but the negative response was stronger in non-native Phragmites. These observations were opposite of expectations from invasion theory and imply that the success of non-native Phragmites, relative to the native lineage, does not result from its interaction with soil microorganisms. More broadly, quantifying plant effects on, and responses to soil microbes separately provides detailed and nuanced insight into plant-microbial interactions and their role in invasions, which could inform management outcomes for invasive plants.},
}
@article {pmid35135350,
year = {2022},
author = {Li, X and Hamilton, CA and St Laurent, R and Ballesteros-Mejia, L and Markee, A and Haxaire, J and Rougerie, R and Kitching, IJ and Kawahara, AY},
title = {A diversification relay race from Caribbean-Mesoamerica to the Andes: historical biogeography of Xylophanes hawkmoths.},
journal = {Proceedings. Biological sciences},
volume = {289},
number = {1968},
pages = {20212435},
pmid = {35135350},
issn = {1471-2954},
mesh = {Animals ; Bayes Theorem ; Caribbean Region ; Genetic Speciation ; *Moths ; Phylogeny ; Phylogeography ; },
abstract = {The regions of the Andes and Caribbean-Mesoamerica are both hypothesized to be the cradle for many Neotropical lineages, but few studies have fully investigated the dynamics and interactions between Neotropical bioregions. The New World hawkmoth genus Xylophanes is the most taxonomically diverse genus in the Sphingidae, with the highest endemism and richness in the Andes and Caribbean-Mesoamerica. We integrated phylogenomic and DNA barcode data and generated the first time-calibrated tree for this genus, covering 93.8% of the species diversity. We used event-based likelihood ancestral area estimation and biogeographic stochastic mapping to examine the speciation and dispersal dynamics of Xylophanes across bioregions. We also used trait-dependent diversification models to compare speciation and extinction rates of lineages associated with different bioregions. Our results indicate that Xylophanes originated in Caribbean-Mesoamerica in the Late Miocene, and immediately diverged into five major clades. The current species diversity and distribution of Xylophanes can be explained by two consecutive phases. In the first phase, the highest Xylophanes speciation and emigration rates occurred in the Caribbean-Mesoamerica, and the highest immigration rates occurred in the Andes, whereas in the second phase the highest immigration rates were found in Amazonia, and the Andes had the highest speciation and emigration rates.},
}
@article {pmid35134858,
year = {2022},
author = {Balech, B and Sandioniggi, A and Marzano, M and Pesole, G and Santamaria, M},
title = {MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences.},
journal = {Database : the journal of biological databases and curation},
volume = {2022},
number = {},
pages = {},
pmid = {35134858},
issn = {1758-0463},
mesh = {Animals ; Base Sequence ; *DNA Barcoding, Taxonomic ; *DNA, Mitochondrial ; Databases, Genetic ; Electron Transport Complex IV/genetics ; },
abstract = {Nucleotide sequences reference collections or databases are fundamental components in DNA barcoding and metabarcoding data analyses pipelines. In such analyses, the accurate taxonomic assignment is a crucial aspect, relying directly on the availability of comprehensive and curated reference sequence collection and its taxonomy information. The currently wide use of the mitochondrial cytochrome oxidase subunit-I (COXI) as a standard DNA barcode marker in metazoan biodiversity studies highlights the need to shed light on the availability of the related relevant information from different data sources and their eventual integration. To adequately address data integration process, many aspects should be markedly considered starting from DNA sequence curation followed by taxonomy alignment with solid reference backbone and metadata harmonization according to universal standards. Here, we present MetaCOXI, an integrated collection of curated metazoan COXI DNA sequences with their associated harmonized taxonomy and metadata. This collection was built on the two most extensive available data resources, namely the European Nucleotide Archive (ENA) and the Barcode of Life Data System (BOLD). The current release contains more than 5.6 million entries (39.1% unique to BOLD, 3.6% unique to ENA, and 57.2% shared between both), their related taxonomic classification based on NCBI reference taxonomy, and their available main metadata relevant to environmental DNA studies, such as geographical coordinates, sampling country and host species. MetaCOXI is available in standard universal formats ('fasta' for sequences &amp; 'tsv' for taxonomy and metadata), which can be easily incorporated in standard or specific DNA barcoding and/or metabarcoding data analysis pipelines. Database URL: https://github.com/bachob5/MetaCOXI.},
}
@article {pmid35132167,
year = {2022},
author = {Hatit, MZC and Lokugamage, MP and Dobrowolski, CN and Paunovska, K and Ni, H and Zhao, K and Vanover, D and Beyersdorf, J and Peck, HE and Loughrey, D and Sato, M and Cristian, A and Santangelo, PJ and Dahlman, JE},
title = {Species-dependent in vivo mRNA delivery and cellular responses to nanoparticles.},
journal = {Nature nanotechnology},
volume = {17},
number = {3},
pages = {310-318},
pmid = {35132167},
issn = {1748-3395},
support = {R01 GM132985/GM/NIGMS NIH HHS/United States ; T32 GM008169/GM/NIGMS NIH HHS/United States ; UG3 TR002855/TR/NCATS NIH HHS/United States ; UH3 TR002855/TR/NCATS NIH HHS/United States ; },
mesh = {Animals ; *Lipids ; Liposomes ; Mice ; *Nanoparticles ; RNA, Messenger/genetics ; },
abstract = {Nanoparticles are tested in mice and non-human primates before being selected for clinical trials. Yet the extent to which mRNA delivery, as well as the cellular response to mRNA drug delivery vehicles, is conserved across species in vivo is unknown. Using a species-independent DNA barcoding system, we have compared how 89 lipid nanoparticles deliver mRNA in mice with humanized livers, primatized livers and four controls: mice with 'murinized' livers as well as wild-type BL/6, Balb/C and NZB/BlNJ mice. We assessed whether functional delivery results in murine, non-human primate and human hepatocytes can be used to predict delivery in the other species in vivo. By analysing in vivo hepatocytes by RNA sequencing, we identified species-dependent responses to lipid nanoparticles, including mRNA translation and endocytosis. These data support an evidence-based approach to making small-animal preclinical nanoparticle studies more predictive, thereby accelerating the development of RNA therapies.},
}
@article {pmid35130837,
year = {2022},
author = {Chan, AHE and Saralamba, N and Saralamba, S and Ruangsittichai, J and Thaenkham, U},
title = {The potential use of mitochondrial ribosomal genes (12S and 16S) in DNA barcoding and phylogenetic analysis of trematodes.},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {104},
pmid = {35130837},
issn = {1471-2164},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; DNA, Ribosomal ; Genes, Mitochondrial ; Phylogeny ; RNA, Ribosomal ; RNA, Ribosomal, 16S/genetics ; *Trematoda/genetics ; },
abstract = {BACKGROUND: Genetic markers like the nuclear ribosomal RNA (rRNA) genes, internal transcribed spacer regions, mitochondrial protein-coding genes, and genomes have been utilized for molecular identification of parasitic trematodes. However, challenges such as the design of broadly applicable primers for the vast number of species within Digenea and the genetic markers' ability to provide sufficient species-level resolution limited their utility. This study presented novel and broadly applicable primers using the mitochondrial 12S and 16S rRNA genes for Digenea and aimed to show their suitability as alternative genetic markers for molecular identification of orders Plagiorchiida, Echinostomida, and Strigeida.<br><br>RESULTS: Our results revealed that the mitochondrial 12S and 16S rRNA genes are suitable for trematode molecular identification, with sufficient resolution to discriminate closely related species and achieve accurate species identification through phylogenetic placements. Moreover, the robustness of our newly designed primers to amplify medically important parasitic trematodes encompassing three orders was demonstrated through successful amplification. The convenience and applicability of the newly designed primers and adequate genetic variation of the mitochondrial rRNA genes can be useful as complementary markers for trematode molecular-based studies.<br><br>CONCLUSIONS: We demonstrated that the mitochondrial rRNA genes could be alternative genetic markers robust for trematode molecular identification and potentially helpful for DNA barcoding where our primers can be widely applied across the major Digenea orders. Furthermore, the potential of the mitochondrial rRNA genes for molecular systematics can be explored, enhancing their appeal for trematode molecular-based studies. The novelty of utilizing the mitochondrial rRNA genes and the designed primers in this study can potentially open avenues for species identification, discovery, and systematics in the future.},
}
@article {pmid35129698,
year = {2022},
author = {Bhattacharya, P and Tiwari, P and Talukdar, G and Rawat, GS},
title = {Shifts in Bacterial Community Composition and Functional Traits at Different Time Periods Post-deglaciation of Gangotri Glacier, Himalaya.},
journal = {Current microbiology},
volume = {79},
number = {3},
pages = {91},
pmid = {35129698},
issn = {1432-0991},
support = {Grant no. DST/SPLICE/CCP/NMSHE/TF-2/WII/2014[G]//Department of Science and Technology, Government of India/ ; Grant no. 7/2/2015-CC//United Nations Development Programme, and the Ministry of Environment, Forest and Climate Change Government of India/ ; 7/2/2015-CC//United Nations Development Programme, and the Ministry of Environment, Forest and Climate Change Government of India/ ; 09/668(0012)/2019- EMR-I//Council of Scientific and Industrial Research, Government of India/ ; },
mesh = {Carbon ; Ecosystem ; *Ice Cover ; Soil ; *Soil Microbiology ; },
abstract = {Climate change causes an unprecedented increase in glacial retreats. The melting ice exposes land for colonization and diversification of bacterial communities leading to soil development, changes in plant community composition, and ecosystem functioning. Although a few studies have focused on macro-level deglaciation impacts, little is known about such effects on the bacterial community succession. Here, we provide meta-barcoding-based insight into the ecological attributes of bacterial community across different retreating periods of the Gangotri glacier, western Himalaya. We selected three sites along a terminal moraine representing recent (~ 20 yrs), intermediate (~ 100 yrs), and late (~ 300 yrs) deglaciation periods. Results showed that the genus Mycobacterium belonging to phylum Actinobacteria dominated recently deglaciated land. Relative abundance of these pioneer bacterial taxa decreased by 20-50% in the later stages with the emergence of new and rising of the less abundant members of the phyla Proteobacteria, Firmicutes, Planctomycetes, Acidobacteria, Verrucomicrobia, Candidatus TM6, and Chloroflexi. The community in the recent stage was less rich and harbored competitive interactions, while the later stages experienced a surge in bacterial diversity with cooperative interactions. The shift in α-diversity and composition was strongly influenced by soil organic carbon, carbon to nitrogen ratio, and soil moisture content. The functional analyses revealed a progression from a metabolism focused to a functionally progressive community required for bacterial co-existence and succession in plant communities. Overall, the findings indicate that the bacterial communities inhabit, diversify, and develop specialized functions post-deglaciation leading to nutrient inputs to soil and vegetation development, which may provide feedback to climate change.},
}
@article {pmid35123385,
year = {2022},
author = {Carvalho, DC},
title = {Ichthyoplankton DNA metabarcoding: Challenges and perspectives.},
journal = {Molecular ecology},
volume = {31},
number = {6},
pages = {1612-1614},
doi = {10.1111/mec.16387},
pmid = {35123385},
issn = {1365-294X},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Ecology ; Fisheries ; *Fishes/classification/genetics ; Rivers ; },
abstract = {DNA metabarcoding has been widely used to access and monitor species. However, several challenges remain open for its mainstream application in ecological studies, particularly when dealing with a quantitative approach. In a From the Cover article in this issue of Molecular Ecology, Mariac et al. (2021) report species-level ichthyoplankton dynamics for 97 fish species from two Amazon river basins using a clever quantitative metabarcoding approach employing a probe capture method. They clearly show that most species spawned during the floods, although ~20% also spawned mainly during the receding period and some other year-round, but interestingly, species from the same genus reproduced in distinct periods (i.e., inverse phenology). Opportunistically, Mariac et al. (2021) reported that during an intense hydrological anomaly, several species had a sharp reduction in spawning activity, demonstrating a quick response to environmental cues. This is an interesting result since the speed at which fish species can react to environmental changes, during the spawning period, is largely unknown. Thus, this study brings remarkable insights into basic life history information that is imperative for proposing strategies that could lead to a realistic framework for sustainable fisheries management practices and conservation, fundamental for an understudied and threatened realm, such as the Amazon River basin.},
}
@article {pmid35116199,
year = {2022},
author = {Hu, J and Pentinsaari, M and Hebert, PDN},
title = {Measuring mass: variation among 3,161 species of Canadian Coleoptera and the prospects of a mass registry for all insects.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e12799},
pmid = {35116199},
issn = {2167-8359},
mesh = {Animals ; *Coleoptera/genetics ; Canada ; DNA Barcoding, Taxonomic/methods ; Reproducibility of Results ; Insecta ; Registries ; },
abstract = {Although biomass values are critical for diverse ecological and evolutionary analyses, they are unavailable for most insect species. Museum specimens have the potential to address this gap, but the variation introduced by sampling and preservation methods is uncertain. This study quantifies species-level variation in the body mass of Canadian Coleoptera based on the analysis of 3,744 specimens representing 3,161 Barcode Index Number (BIN) clusters. Employing the BIN system as a proxy for species allows the inclusion of groups where the taxonomic impediment prevents the assignment of specimens to a Linnaean species. By validating the reproducibility of measurements and evaluating the error introduced by operational complexities such as curatorial practice and the loss of body parts, this study demonstrates that museum specimens can speed the assembly of a mass registry. The results further indicate that congeneric species of Coleoptera generally have limited variation in mass, so a genus-level identification allows prediction of the body mass of species that have not been weighed or measured. Building on the present results, the construction of a mass registry for all insects is feasible.},
}
@article {pmid35116196,
year = {2022},
author = {Jarquín-González, J and Carrera-Parra, LF},
title = {Chondrochelia Guţu, 2016 (Crustacea, Peracarida, Tanaidacea, Leptocheliidae) from North America: new species, redescription and distribution using morphological and molecular data.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e12773},
pmid = {35116196},
issn = {2167-8359},
mesh = {Animals ; *Crustacea/anatomy &amp; histology ; North America ; Gulf of Mexico ; Brazil ; Caribbean Region ; },
abstract = {Until now, four species of the genus Chondrochelia Guţu, 2016 have been recorded from America. Using morphological and molecular data, we were able to recognize and describe two new species, Chondrochelia caribensis sp. nov. from the Mexican Caribbean and Chondrochelia winfieldi sp. nov. from the Gulf of Mexico. We found significant genetic divergence values between species based on the nucleotide sequences of cytochrome oxidase subunit I to support the morphological data. Also, the range of distribution of two species: Chondrochelia mexicana (Jarquín-González, García-Madrigal &amp; Carrera-Parra, 2015) and Chondrochelia ortizi (Jarquín-González, 2016), were expanded within their described geographic regions. In contrast, the supposed distribution of the Brazilian C. dubia in the Mexican Caribbean and the Gulf of Mexico was rejected. Additionally, Chondrochelia algicola (Harger, 1878) was redescribed based upon type material. Minute details and ornamentation of some structures of three species were examined using SEM.},
}
@article {pmid35115876,
year = {2022},
author = {Boucher, S and Savage, J},
title = {DNA barcoding of the leaf-miner flies (Diptera, Agromyzidae) of Mitaraka, French Guiana.},
journal = {ZooKeys},
volume = {1083},
number = {},
pages = {147-168},
pmid = {35115876},
issn = {1313-2989},
abstract = {Species level identification of Agromyzidae based on morphology is often challenging due to their small size and morphological homogeneity. DNA barcoding has been used regularly to assist with the identification of economically important species of Agromyzidae, but rarely as a tool for species delineation or identification in biodiversity surveys. The main objective of this study was to investigate whether DNA barcoding and the BIN (Barcoding Index) system could assist with species identification, species delineation, male/ female association, and diversity assessment of Agromyzidae material previously determined to morphospecies from Mitaraka, French Guiana. Amplification success was low, with sequences over 400 bp recovered for only 24 (48%) of the selected specimens. Sequences assigned to 17 morphospecies formed 16 distinct branches or clusters separated by very high (minimum of 10%) sequence divergence. Following the reassessment and subsequent reassignment of one specimen, congruence between morphology and DNA barcodes was high with a single instance of two morphospecies sharing identical sequences. While DNA barcoding did not assist with identification (none of our sequences matched those of named taxa in BOLD or GenBank), it did provide support for most of our morphospecies concepts, including male/female associations. The BIN system also provided access to information about the distribution and habitat preferences of several taxa. We conclude that DNA barcoding was a useful approach to study the species diversity of our samples but that much work remains to be done before it can be used as an identification tool for the Agromyzidae fauna of Mitaraka and the rest of the Neotropical region.},
}
@article {pmid35115867,
year = {2022},
author = {Raupach, MJ and Rulik, B and Spelda, J},
title = {Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea).},
journal = {ZooKeys},
volume = {1082},
number = {},
pages = {103-125},
pmid = {35115867},
issn = {1313-2989},
abstract = {DNA barcoding has become the most popular approach for species identification in recent years. As part of the German Barcode of Life project, the first DNA barcode library for terrestrial and freshwater isopods from Germany is presented. The analyzed barcode library included 38 terrestrial (78% of the documented species of Germany) and five freshwater (63%) species. A total of 513 new barcodes was generated and 518 DNA barcodes were analyzed. This analysis revealed surprisingly high intraspecific genetic distances for numerous species, with a maximum of 29.4% for Platyarthrushoffmannseggii Brandt, 1833. The number of BINs per species ranged from one (32 species, 68%) to a maximum of six for Trachelipusrathkii (Brandt, 1833). In spite of such high intraspecific variability, interspecific distances with values between 12.6% and 29.8% allowed a valid species assignment of all analyzed isopods. The observed high intraspecific distances presumably result from phylogeographic events, Wolbachia infections, atypical mitochondrial DNAs, heteroplasmy, or various combinations of these factors. Our study represents the first step in generating an extensive reference library of DNA barcodes for terrestrial and freshwater isopods for future molecular biodiversity assessment studies.},
}
@article {pmid35113572,
year = {2022},
author = {Škopić, MK and Losch, F and McMillan, AE and Willeke, N and Malenica, M and Bering, L and Bode, J and Brunschweiger, A},
title = {Reagent-Based Scaffold Diversity for DNA-Encoded Library Design: Solid Phase Synthesis of DNA-Tagged sp[3]-Rich Heterocycles by SnAP Chemistry.},
journal = {Organic letters},
volume = {24},
number = {6},
pages = {1383-1387},
doi = {10.1021/acs.orglett.2c00228},
pmid = {35113572},
issn = {1523-7052},
mesh = {DNA/*chemical synthesis/chemistry ; Gene Library ; Heterocyclic Compounds/*chemistry ; Molecular Structure ; *Solid-Phase Synthesis Techniques ; },
abstract = {Reactions that require strictly dry conditions are challenging to translate to a DNA-encoded library format. Controlled pore glass solid support-connected DNA oligonucleotide-aldehyde conjugates could be condensed with SnAP reagents and cyclized to various sp[3]-rich heterocycles. The Boc-group of products provided a handle for product purification, and its facile removal under acidic conditions was tolerated by a chemically stabilized barcode. The reaction provides reagent-based scaffold diversity with functionalities for further library synthesis.},
}
@article {pmid35111399,
year = {2022},
author = {Antich, A and Palacín, C and Turon, X and Wangensteen, OS},
title = {DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e12758},
pmid = {35111399},
issn = {2167-8359},
mesh = {Entropy ; *Software ; *Algorithms ; DNA, Ribosomal ; Codon ; },
abstract = {DNA metabarcoding is broadly used in biodiversity studies encompassing a wide range of organisms. Erroneous amplicons, generated during amplification and sequencing procedures, constitute one of the major sources of concern for the interpretation of metabarcoding results. Several denoising programs have been implemented to detect and eliminate these errors. However, almost all denoising software currently available has been designed to process non-coding ribosomal sequences, most notably prokaryotic 16S rDNA. The growing number of metabarcoding studies using coding markers such as COI or RuBisCO demands a re-assessment and calibration of denoising algorithms. Here we present DnoisE, the first denoising program designed to detect erroneous reads and merge them with the correct ones using information from the natural variability (entropy) associated to each codon position in coding barcodes. We have developed an open-source software using a modified version of the UNOISE algorithm. DnoisE implements different merging procedures as options, and can incorporate codon entropy information either retrieved from the data or supplied by the user. In addition, the algorithm of DnoisE is parallelizable, greatly reducing runtimes on computer clusters. Our program also allows different input file formats, so it can be readily incorporated into existing metabarcoding pipelines.},
}
@article {pmid35107001,
year = {2022},
author = {Kakui, K and Hiruta, C},
title = {Description of a New Hamatipeda Species, with an 18S Molecular Phylogeny (Crustacea: Tanaidacea: Typhlotanaidae).},
journal = {Zoological science},
volume = {39},
number = {1},
pages = {140-146},
doi = {10.2108/zs210065},
pmid = {35107001},
issn = {0289-0003},
mesh = {Animals ; *Crustacea/genetics ; Japan ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; },
abstract = {We describe a new typhlotanaid species, Hamatipeda kohtsukai sp. nov., collected from between 167 and 488 m depth in the Sagami Sea, Japan. This is the first record of Hamatipeda from the northern hemisphere. Hamatipeda kohtsukai resembles Hamatipeda trapezoida from the Subantarctic region in having pereonites 1-3 widest anteriorly (not rectangular), but differs from it in the length ratio of antennal articles 4/5; the number of setae on the dactyli of pereopods 1-3, ischia of pereopods 4-6, and carpi of pereopods 4-6; the shape of the unguis of pereopods 4-6; and the shape of the uropodal endopod. We determined partial sequences for the cytochrome c oxidase subunit I (COI; cox1) and 18S rRNA (18S) genes in H. kohtsukai. A phylogenetic reconstruction based on the 18S sequences recovered a highly supported Typhlotanaidae clade containing H. kohtsukai and Typhlotanais mixtus, with Paranarthrura sp. (Agathotanaidae) as the sister taxon. A key to species of Hamatipeda is presented.},
}
@article {pmid35106483,
year = {2022},
author = {Nijman, V and Stein, FM},
title = {Meta-analyses of molecular seafood studies identify the global distribution of legal and illegal trade in CITES-regulated European eels.},
journal = {Current research in food science},
volume = {5},
number = {},
pages = {191-195},
pmid = {35106483},
issn = {2665-9271},
abstract = {Authentication of seafood products by means of molecular techniques has relevance for food sustainability and security, as well as international trade regulation, linked to transparency in food manufacturing. We focus on the molecular detection of the depleted European eel Anguilla anguilla, a species for which strict international trade regulations are in place since 2010, in studies conducted outside Europe. We found thirteen studies from nine countries (Canada, China, Japan, Malaysia, Peru, Singapore, South Korea, Taiwan, and USA) for which, on average, 59 ± 28% of the 330 sequenced eel samples comprised European eel. Only China, Japan, South Korea, and USA reported the import of European eel in the years prior to sampling. The authentication of eel products demonstrates a global, in part illegal, trade in European eel, covered up by incomplete or fraudulent labelling. This calls into question the compliance with existing national and international trade regulations and its implications for food safety and sustainability.},
}
@article {pmid35103987,
year = {2022},
author = {Maduenyane, M and Dos Santos, QM and Avenant-Oldewage, A},
title = {Light and scanning electron microscopy of the effects of Macrogyrodactylus congolensis (Prudhoe, 1957) on the skin of the African sharptooth catfish Clarias gariepinus (Burchell, 1822).},
journal = {Journal of fish diseases},
volume = {45},
number = {4},
pages = {595-602},
doi = {10.1111/jfd.13584},
pmid = {35103987},
issn = {1365-2761},
support = {//The Foundational Biodiversity Information Programme of South Africa/ ; //National Research Foundation of South Africa/ ; //University of Johannesburg Global Excellence and Stature 4.0/ ; },
mesh = {Animals ; *Catfishes/parasitology ; *Fish Diseases/parasitology ; Microscopy, Electron, Scanning ; Skin/parasitology ; *Trematoda ; },
abstract = {Clarias gariepinus (Burchell, 1822) is one of the two most actively cultured freshwater fish in Africa and therefore, economically important. Specimens of this species were purchased from a fish farm near Hartbeespoort Dam (North West, South Africa) and introduced into the tanks of the research aquarium in the Department of Zoology at the University of Johannesburg. However, the skin of these fish was infected with Macrogyrodactylus congolensis (Prudhoe, 1957), which proliferated profusely in the favourable conditions of the aquarium, posing a potential threat to its host. The current study was aimed at examining the pathology caused by M. congolensis on the skin of C. gariepinus. Species identification of the parasite was confirmed using light microscopy (LM), scanning electron microscopy (SEM) and DNA barcoding of the internal transcribed spacer region. Examination of the pathology was studied using LM of haematoxylin and eosin-stained sections (epoxy embedded) and SEM of parasites attached to the hosts' skin. Infected skin exhibited excessive mucus production, corroborated by an increased number of mucus cells alongside proliferated and abnormally enlarged club cells, resulting in varying thickness of the epidermal layer. At the site of attachment, the basement membrane detached from the dermis. Hamulus points and marginal hooks of the parasite pierce through the hosts' skin resulting in tearing. Epidermal cells and melanin granules were observed in the intestinal lumen of the parasite. Melanin granules were absorbed by the parasite's intestinal epithelium confirming that the parasite feeds on host skin tissue.},
}
@article {pmid35103966,
year = {2022},
author = {van Breugel, ME and van Leeuwen, F},
title = {Epi-Decoder: Decoding the Local Proteome of a Genomic Locus by Massive Parallel Chromatin Immunoprecipitation Combined with DNA-Barcode Sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2458},
number = {},
pages = {123-150},
pmid = {35103966},
issn = {1940-6029},
mesh = {*Chromatin/genetics ; Chromatin Immunoprecipitation/methods ; DNA/chemistry ; Genomics/methods ; *Proteome/metabolism ; Sequence Analysis, DNA ; },
abstract = {The genome in a eukaryotic cell is packaged into chromatin and regulated by chromatin-binding and chromatin-modifying factors. Many of these factors and their complexes have been identified before, but how each genomic locus interacts with its surrounding proteins in the nucleus over time and in changing conditions remains poorly described. Measuring protein-DNA interactions at a specific locus in the genome is challenging and current techniques such as capture of a locus followed by mass spectrometry require high levels of enrichment. Epi-Decoder, a method developed in budding yeast, enables systematic decoding of the proteome of a single genomic locus of interest without the need for locus enrichment. Instead, Epi-Decoder uses massive parallel chromatin immunoprecipitation of tagged proteins combined with barcoding a genomic locus and counting of coimmunoprecipitated barcodes by DNA sequencing (TAG-ChIP-Barcode-Seq). In this scenario, DNA barcode counts serve as a quantitative readout for protein binding of each tagged protein to the barcoded locus. Epi-Decoder can be applied to determine the protein-DNA interactions at a wide range of genomic loci, such as coding genes, noncoding genes, and intergenic regions. Furthermore, Epi-Decoder provides the option to study protein-DNA interactions upon changing cellular and/or genetic conditions. In this protocol, we describe in detail how to construct Epi-Decoder libraries and how to perform an Epi-Decoder analysis.},
}
@article {pmid35102279,
year = {2022},
author = {Song, P and Wu, LR and Yan, YH and Zhang, JX and Chu, T and Kwong, LN and Patel, AA and Zhang, DY},
title = {Limitations and opportunities of technologies for the analysis of cell-free DNA in cancer diagnostics.},
journal = {Nature biomedical engineering},
volume = {6},
number = {3},
pages = {232-245},
pmid = {35102279},
issn = {2157-846X},
support = {P01 CA163222/CA/NCI NIH HHS/United States ; R01 CA197486/CA/NCI NIH HHS/United States ; R01 CA203964/CA/NCI NIH HHS/United States ; U01 CA233364/CA/NCI NIH HHS/United States ; },
mesh = {Biomarkers/analysis ; *Cell-Free Nucleic Acids/analysis/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Liquid Biopsy/methods ; *Neoplasms/diagnosis/genetics ; },
abstract = {Cell-free DNA (cfDNA) in the circulating blood plasma of patients with cancer contains tumour-derived DNA sequences that can serve as biomarkers for guiding therapy, for the monitoring of drug resistance, and for the early detection of cancers. However, the analysis of cfDNA for clinical diagnostic applications remains challenging because of the low concentrations of cfDNA, and because cfDNA is fragmented into short lengths and is susceptible to chemical damage. Barcodes of unique molecular identifiers have been implemented to overcome the intrinsic errors of next-generation sequencing, which is the prevailing method for highly multiplexed cfDNA analysis. However, a number of methodological and pre-analytical factors limit the clinical sensitivity of the cfDNA-based detection of cancers from liquid biopsies. In this Review, we describe the state-of-the-art technologies for cfDNA analysis, with emphasis on multiplexing strategies, and discuss outstanding biological and technical challenges that, if addressed, would substantially improve cancer diagnostics and patient care.},
}
@article {pmid35099361,
year = {2023},
author = {Zhang, Z and Wang, J and Hu, G and Huang, J and Chen, L and Yin, Y and Cai, Y and Shen, X and Ji, N},
title = {Isolation and characterization of an algicidal bacterium against the bloom-forming algae raphidophyte Heterosigma akashiwo.},
journal = {Environmental technology},
volume = {44},
number = {17},
pages = {2607-2616},
doi = {10.1080/09593330.2022.2036250},
pmid = {35099361},
issn = {1479-487X},
mesh = {*Ecosystem ; Bacteria ; Harmful Algal Bloom ; Phytoplankton ; China ; *Dinoflagellida ; },
abstract = {Harmful algae blooms (HABs) have increased in intensity and frequency worldwide, causing negative effects on public health and marine ecosystems. This study isolated and identified the bloom causing species and its associated algicidal bacterium during a phytoplankton bloom in coastal waters of Lianyungang, China. Morphological observations and DNA barcoding analysis indicate that the studied phytoplankton bloom was caused by the raphidophyte Heterosigma akashiwo, and the algicidal bacterium, strain LD-B1, was identified as a species belonging to the genus Pseudoalteromonas. Furthermore, the algicidal effects of strain LD-B1 against H. akashiwo were characterized; revealing strain LD-B1 show strong algicidal activity against H. akashiwo. After 48 h of bacterium culture addition, the algicidal rate reached up to 98.8% with a 1% final volume rate. Moreover, our findings indicate strain LD-B1's extracellular compounds involved in algicidal activity are likely not proteinaceous. These findings indicate that the isolated strain, LD-B1, is a promising algicidal bacterium to control H. akashiwo blooms.},
}
@article {pmid35095292,
year = {2022},
author = {Hirota, SK and Yahara, T and Fuse, K and Sato, H and Tagane, S and Fujii, S and Minamitani, T and Suyama, Y},
title = {Molecular phylogeny and taxonomy of the Hydrangeaserrata complex (Hydrangeaceae) in western Japan, including a new subspecies of H.acuminata from Yakushima.},
journal = {PhytoKeys},
volume = {188},
number = {},
pages = {49-71},
pmid = {35095292},
issn = {1314-2011},
abstract = {According to the contemporary classification of Hydrangea native to Japan, H.serrata is a polymorphic species including six varieties. We discovered a plant identified as H.serrata, but morphologically distinct from previously known varieties, in Yakushima island where approximately 50 endemic species are known. To determine the relationship of this plant with previously known varieties, we examined morphology and constructed a highly resolved phylogeny of H.serrata and its relatives using three chloroplast genomic regions, rbcL, trnL intron, psbA-trnH, and two nuclear genomic regions, ITS1 and ITS2, and Multiplex ISSR genotyping by sequencing (MIG-seq). Based on these morphological and phylogenetic observations, we describe Hydrangeaacuminatasubsp.yakushimensissubsp. nov. as a newly discovered lineage in Yakushima, Japan and propose Hydrangeaminamitanii stat. nov. and Hydrangeaacuminatasubsp.australisstat. nov. which were previously treated as varieties of H.serrata.},
}
@article {pmid35095289,
year = {2022},
author = {Linh, NN and Hang, PLB and Hue, HTT and Ha, NH and Hanh, HH and Ton, ND and Hien, LTT},
title = {Species discrimination of novel chloroplast DNA barcodes and their application for identification of Panax (Aralioideae, Araliaceae).},
journal = {PhytoKeys},
volume = {188},
number = {},
pages = {1-18},
pmid = {35095289},
issn = {1314-2011},
abstract = {Certain species within the genus Panax L. (Araliaceae) contain pharmacological precious ginsenosides, also known as ginseng saponins. Species containing these compounds are of high commercial value and are thus of particular urgency for conservation. However, within this genus, identifying the particular species that contain these compounds by morphological means is challenging. DNA barcoding is one method that is considered promising for species level identification. However, in an evolutionarily complex genus such as Panax, commonly used DNA barcodes such as nrITS, matK, psbA-trnH, rbcL do not provide species-level resolution. A recent in silico study proposed a set of novel chloroplast markers, trnQ-rps16, trnS-trnG, petB, and trnE-trnT for species level identification within Panax. In the current study, the discriminatory efficiency of these molecular markers is assessed and validated using 91 reference barcoding sequences and 38 complete chloroplast genomes for seven species, one unidentified species and one sub-species of Panax, and two outgroup species of Aralia L. along with empirical data of Panax taxa present in Vietnam via both distance-based and tree-based methods. The obtained results show that trnQ-rps16 can classify with species level resolution every clade tested here, including the highly valuable Panaxvietnamensis Ha et Grushv. We thus propose that this molecular marker to be used for identification of the species within Panax to support both its conservation and commercial trade.},
}
@article {pmid35094504,
year = {2022},
author = {Fedosov, A and Achaz, G and Gontchar, A and Puillandre, N},
title = {mold, a novel software to compile accurate and reliable DNA diagnoses for taxonomic descriptions.},
journal = {Molecular ecology resources},
volume = {22},
number = {5},
pages = {2038-2053},
doi = {10.1111/1755-0998.13590},
pmid = {35094504},
issn = {1755-0998},
support = {19-74-10020//Russian Science Foundation/ ; 865101//European Research Council (ERC)/ ; },
mesh = {*DNA ; DNA Barcoding, Taxonomic ; Phylogeny ; Reproducibility of Results ; Sequence Alignment ; *Software ; },
abstract = {DNA data are increasingly being used for phylogenetic inference, and taxon delimitation and identification, but scarcely for the formal description of taxa, despite their undisputable merits in taxonomy. The uncertainty regarding the robustness of DNA diagnoses, however, remains a major impediment to their use. We have developed a new program, mold, that identifies diagnostic nucleotide combinations (DNCs) in DNA sequence alignments for selected taxa, which can be used to provide formal diagnoses of these taxa. To test the robustness of DNA diagnoses, we carry out iterated haplotype subsampling for selected query species in published DNA data sets of varying complexity. We quantify the reliability of diagnosis by diagnosing each query subsample and then checking if this diagnosis remains valid against the entire data set. We demonstrate that widely used types of diagnostic DNA characters are often absent for a query taxon or are not sufficiently reliable. We thus propose a new type of DNA diagnosis, termed "redundant DNC" (or rDNC), which takes into account unsampled genetic diversity, and constitutes a much more reliable descriptor of a taxon. mold successfully retrieves rDNCs for all but two species in the analysed data sets, even in those comprising hundreds of species. mold shows unparalleled efficiency in large DNA data sets and is the only available software capable of compiling DNA diagnoses that suit predefined criteria of reliability.},
}
@article {pmid35094502,
year = {2022},
author = {van Steenderen, CJM and Sutton, GF},
title = {SPEDE-sampler: An R Shiny application to assess how methodological choices and taxon sampling can affect Generalized Mixed Yule Coalescent output and interpretation.},
journal = {Molecular ecology resources},
volume = {22},
number = {5},
pages = {2054-2069},
pmid = {35094502},
issn = {1755-0998},
support = {//South African Working for Water (WfW) programme of the Department of Forestry, Fisheries and the Environment: Natural Resource Management Programmes (DFFE: NRMP)/ ; //South African Research Chairs Initiative of the Department of Science and Technology and the National Research Foundation (NRF)/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Phylogeny ; Sample Size ; },
abstract = {Species delimitation tools are vital to taxonomy and the discovery of new species. These tools can make use of genetic data to estimate species boundaries, where one of the most widely used methods is the Generalized Mixed Yule Coalescent (GMYC) model. Despite its popularity, a number of factors are known to influence the performance and resulting inferences of the GMYC. Moreover, the few studies that have assessed model performance to date have been predominantly based on simulated data sets, where model assumptions are not violated. Here, we present a user-friendly R Shiny application, 'SPEDE-sampler' (SPEcies DElimitation sampler), that assesses the effect of computational and methodological choices, in combination with sampling effects, on the GMYC model. Output phylogenies are used to test the effect that (1) sample size, (2) BEAST and GMYC parameters (e.g. prior settings, single vs multiple threshold, clock model), and (3) singletons have on GMYC output. Optional predefined grouping information (e.g. morphospecies/ecotypes) can be uploaded in order to compare it with GMYC species and estimate percentage match scores. Additionally, predefined groups that contribute to inflated species richness estimates are identified by SPEDE-sampler, allowing for the further investigation of potential cryptic species or geographical substructuring in those groups. Merging by the GMYC is also recorded to identify where traditional taxonomy has overestimated species numbers. Four worked examples are provided to illustrate the functionality of the program's workflow, and the variation that can arise when applying the GMYC model to empirical data sets. The R Shiny program is available for download at https://github.com/clarkevansteenderen/spede_sampler_R.},
}
@article {pmid35094339,
year = {2022},
author = {Yu, F and Leong, KW and Makrigiorgos, GM},
title = {Nuclease-Assisted, Multiplexed Minor-Allele Enrichment: Application in Liquid Biopsy of Cancer.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2394},
number = {},
pages = {433-451},
pmid = {35094339},
issn = {1940-6029},
support = {R33 CA217652/CA/NCI NIH HHS/United States ; R01 CA221874/CA/NCI NIH HHS/United States ; },
mesh = {Alleles ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Liquid Biopsy/methods ; Mutation ; *Neoplasms/diagnosis/genetics ; },
abstract = {The use of next-generation sequencing (NGS) to profile genomic variation of individual cancer species is revolutionizing the practice of clinical oncology. In liquid biopsy of cancer, sequencing of circulating-free DNA (cfDNA) is gradually applied to all stages of cancer diagnosis and treatment, serving as complement or replacement of tissue biopsies. However, analysis of cfDNA obtained from blood draws still faces technical obstacles due in part to an excess of wild-type DNA originating from normal tissues and hematopoietic cells. The resulting low-level mutation abundance often falls below routine NGS detection sensitivity and limits reliable mutation identification that meets clinical sensitivity and specificity standards. Despite sample preparation advances that reduce sequencing error rates via use of unique molecular identifiers (molecular barcodes) and error-suppression algorithms, excessive amounts of sequencing are still required to detect mutations at allelic frequency levels below 1%. This requirement reduces throughput and increases cost.In this chapter, we describe a sensitive multiplex mutation detection method that enriches mutation-containing DNA during sample preparation, prior to sequencing, thereby increasing signal-to-noise ratios and providing low-level mutation detection without excessive sequencing depth. We couple targeted next-generation sequencing with wild-type DNA removal using Nuclease-assisted Minor-allele Enrichment using Probe Overlap, NaME-PrO, a recently developed method to eliminate wild-type sequences from multiple targets simultaneously. A step by step guide to library preparation and data analysis are provided as well as some precautions during the sample handling.},
}
@article {pmid35094325,
year = {2022},
author = {Gardner, A and Morgan, D and Al'Khafaji, A and Brock, A},
title = {Functionalized Lineage Tracing for the Study and Manipulation of Heterogeneous Cell Populations.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2394},
number = {},
pages = {109-131},
pmid = {35094325},
issn = {1940-6029},
support = {R21 CA212928/CA/NCI NIH HHS/United States ; },
mesh = {*CRISPR-Cas Systems/genetics ; Cell Lineage/genetics ; Genes, Reporter ; *RNA, Guide, CRISPR-Cas Systems/genetics ; },
abstract = {The ability to track and isolate unique cell lineages from large heterogeneous populations increases the resolution at which cellular processes can be understood under normal and pathogenic states beyond snapshots obtained from single-cell RNA sequencing (scRNA-seq). Here, we describe the Control of Lineages by Barcode Enabled Recombinant Transcription (COLBERT) method in which unique single guide RNA (sgRNA) barcodes are used as functional tags to identify and recall specific lineages of interest. An sgRNA barcode is stably integrated and actively transcribed, such that all cellular progeny will contain the parental barcode and produce a functional sgRNA. The sgRNA barcode has all the benefits of a DNA barcode and added functionalities. Once a barcode pertaining to a lineage of interest is identified, the lineage of interest can be isolated using an activator variant of Cas9 (such as dCas9-VPR) and a barcode-matched sequence upstream of a fluorescent reporter gene. CRISPR activation of the fluorescent reporter will only occur in cells producing the matched sgRNA barcode, allowing precise identification and isolation of lineages of interest from heterogeneous populations.},
}
@article {pmid35090787,
year = {2022},
author = {Pauken, KE and Lagattuta, KA and Lu, BY and Lucca, LE and Daud, AI and Hafler, DA and Kluger, HM and Raychaudhuri, S and Sharpe, AH},
title = {TCR-sequencing in cancer and autoimmunity: barcodes and beyond.},
journal = {Trends in immunology},
volume = {43},
number = {3},
pages = {180-194},
pmid = {35090787},
issn = {1471-4981},
support = {P01 AI148102/AI/NIAID NIH HHS/United States ; P01 CA236749/CA/NCI NIH HHS/United States ; R01 CA227473/CA/NCI NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; U01 HG012009/HG/NHGRI NIH HHS/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; P01 AI039671/AI/NIAID NIH HHS/United States ; R01 CA216846/CA/NCI NIH HHS/United States ; T32 GM144273/GM/NIGMS NIH HHS/United States ; P01 AI108545/AI/NIAID NIH HHS/United States ; P01 AI073748/AI/NIAID NIH HHS/United States ; P01 AI056299/AI/NIAID NIH HHS/United States ; T32 CA233414/CA/NCI NIH HHS/United States ; R01 AR063759/AR/NIAMS NIH HHS/United States ; P50 CA121974/CA/NCI NIH HHS/United States ; U01 HG009379/HG/NHGRI NIH HHS/United States ; UH2 AR067677/AR/NIAMS NIH HHS/United States ; },
mesh = {*Autoimmunity/genetics ; Humans ; *Neoplasms/genetics ; Receptors, Antigen, T-Cell/genetics ; T-Lymphocytes ; },
abstract = {The T cell receptor (TCR) endows T cells with antigen specificity and is central to nearly all aspects of T cell function. Each naïve T cell has a unique TCR sequence that is stably maintained during cell division. In this way, the TCR serves as a molecular barcode that tracks processes such as migration, differentiation, and proliferation of T cells. Recent technological advances have enabled sequencing of the TCR from single cells alongside deep molecular phenotypes on an unprecedented scale. In this review, we discuss strengths and limitations of TCR sequences as molecular barcodes and their application to study immune responses following Programmed Death-1 (PD-1) blockade in cancer. Additionally, we consider applications of TCR data beyond use as a barcode.},
}
@article {pmid35089702,
year = {2022},
author = {Zhou, Y and Yuan, Y and Wu, Y and Li, L and Jameel, A and Xing, XH and Zhang, C},
title = {Encoding Genetic Circuits with DNA Barcodes Paves the Way for Machine Learning-Assisted Metabolite Biosensor Response Curve Profiling in Yeast.},
journal = {ACS synthetic biology},
volume = {11},
number = {2},
pages = {977-989},
doi = {10.1021/acssynbio.1c00595},
pmid = {35089702},
issn = {2161-5063},
mesh = {*Biosensing Techniques/methods ; DNA/genetics/metabolism ; DNA Barcoding, Taxonomic ; Machine Learning ; *Saccharomyces cerevisiae/genetics/metabolism ; },
abstract = {Genetically encoded biosensors are valuable tools used in the precise engineering of metabolism. Although a large number of biosensors have been developed, the fine-tuning of their dose-response curves, which promotes the applications of biosensors in various scenarios, still remains challenging. To address this issue, we leverage a DNA trackable assembly method and fluorescence-activated cell sorting coupled with next-generation sequencing (FACS-seq) technology to set up a novel workflow for construction and comprehensive characterization of thousands of biosensors in a massively parallel manner. An FapR-fapO-based malonyl-CoA biosensor was used as proof of concept to construct a trackable combinatorial library, containing 5184 combinations with 6 levels of transcription factor dosage, 4 different operator positions, and 216 possible upstream enhancer sequence (UAS) designs. By applying the FACS-seq technique, the response curves of 2632 biosensors out of 5184 combinations were successfully characterized to provide large-scale genotype-phenotype association data of the designed biosensors. Finally, machine-learning algorithms were applied to predict the genotype-phenotype relationships of the uncharacterized combinations to generate a panoramic scanning map of the combinatorial space. With the assistance of our novel workflow, a malonyl-CoA biosensor with the largest dynamic response range was successfully obtained. Moreover, feature importance analysis revealed that the recognition sequence insertion scheme and the choice of UAS have a significant impact on the dynamic range. Taken together, our pipeline provides a platform for the design, tuning, and profiling of biosensor response curves and shows great potential to facilitate the rational design of genetic circuits.},
}
@article {pmid35084678,
year = {2022},
author = {Yan, H and Li, Q and Chen, B and Shi, M and Zhang, T},
title = {Identification and feeding characteristics of the mixotrophic flagellate Poterioochromonas malhamensis, a microalgal predator isolated from planting water of Pontederia cordata.},
journal = {Environmental science and pollution research international},
volume = {29},
number = {27},
pages = {40599-40611},
pmid = {35084678},
issn = {1614-7499},
support = {31170443//Innovative Research Group Project of the National Natural Science Foundation of China/ ; },
mesh = {*Microalgae ; *Microcystis ; Pheromones ; *Pontederiaceae/chemistry ; *Stramenopiles ; Water ; },
abstract = {The microorganisms and allelochemicals in Pontederia cordata planting water may have a synergistic inhibitory effect on algae. To study this synergy, an algae-inhibiting organism was isolated and identified, and its growth and feeding characteristics were studied. The organism was identified as Poterioochromonas malhamensis yzs924 based on both its morphology and molecular barcoding employing 18S rDNA gene sequences.The growth and feeding of P. malhamensis were affected by environmental factors and the state of its prey. (1) P. malhamensis is a mixotrophic flagellate. Its heterotrophic growth was the fastest in a wheat grain medium, and its growth rate in this study reached 2.5 day[-1]. (2) Within a short period of time (2 days), P. malhamensis growth was slower under continuous dark conditions than under alternating light and dark conditions, but it fed on Microcystis aeruginosa more rapidly under dark conditions. (3) High pH was disadvantageous to the growth and grazing of P. malhamensis. When the pH was kept stable at 9, P. malhamensis could not grow continuously. (4) When the initial density of M. aeruginosa was 5 × 10[7] cells/mL or is in a period of decline, P. malhamensis could not remove all M. aeruginosa. The combined use of P. malhamensis and allelochemicals may represent a method of M. aeruginosa control, but this approach requires further research.},
}
@article {pmid35084033,
year = {2022},
author = {Brüning, RS and Tombor, L and Schulz, MH and Dimmeler, S and John, D},
title = {Comparative analysis of common alignment tools for single-cell RNA sequencing.},
journal = {GigaScience},
volume = {11},
number = {},
pages = {},
pmid = {35084033},
issn = {2047-217X},
mesh = {Animals ; Cluster Analysis ; *Computational Biology/methods ; *Genomics ; Mice ; RNA ; Sequence Analysis, RNA/methods ; Single-Cell Analysis ; Software ; },
abstract = {BACKGROUND: With the rise of single-cell RNA sequencing new bioinformatic tools have been developed to handle specific demands, such as quantifying unique molecular identifiers and correcting cell barcodes. Here, we benchmarked several datasets with the most common alignment tools for single-cell RNA sequencing data. We evaluated differences in the whitelisting, gene quantification, overall performance, and potential variations in clustering or detection of differentially expressed genes. We compared the tools Cell Ranger version 6, STARsolo, Kallisto, Alevin, and Alevin-fry on 3 published datasets for human and mouse, sequenced with different versions of the 10X sequencing protocol.<br><br>RESULTS: Striking differences were observed in the overall runtime of the mappers. Besides that, Kallisto and Alevin showed variances in the number of valid cells and detected genes per cell. Kallisto reported the highest number of cells; however, we observed an overrepresentation of cells with low gene content and unknown cell type. Conversely, Alevin rarely reported such low-content cells. Further variations were detected in the set of expressed genes. While STARsolo, Cell Ranger 6, Alevin-fry, and Alevin produced similar gene sets, Kallisto detected additional genes from the Vmn and Olfr gene family, which are likely mapping artefacts. We also observed differences in the mitochondrial content of the resulting cells when comparing a prefiltered annotation set to the full annotation set that includes pseudogenes and other biotypes.<br><br>CONCLUSION: Overall, this study provides a detailed comparison of common single-cell RNA sequencing mappers and shows their specific properties on 10X Genomics data.},
}
@article {pmid35081163,
year = {2022},
author = {Tsoupas, A and Papavasileiou, S and Minoudi, S and Gkagkavouzis, K and Petriki, O and Bobori, D and Sapounidis, A and Koutrakis, E and Leonardos, I and Karaiskou, N and Triantafyllidis, A},
title = {DNA barcoding identification of Greek freshwater fishes.},
journal = {PloS one},
volume = {17},
number = {1},
pages = {e0263118},
pmid = {35081163},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; *Fishes/classification/genetics ; Greece ; *Rivers ; },
abstract = {Biodiversity is a key factor for the functioning and efficiency of an ecosystem. Greece, though covering a relatively small surface area, hosts a great deal of species diversity. This is especially true for freshwater fishes. In recent years, the traditional methods of species identification have been supplemented by the use of molecular markers. The present study therefore aims to extensively produce DNA barcodes for Greek freshwater fish species and investigate thoroughly if the presently accepted species classification is in agreement with molecular data. A 624-bases long fragment of the COI gene was sequenced, from 406 freshwater fish specimens belonging to 24 genera and originating from 18 lake and river sites. These sequences were used along with 596 sequences from the same genera, recovered from BOLD, for the construction of phylogenetic trees and the estimation of genetic distances between individuals. In total, 1002 sequences belonging to 72 species were analyzed. The method was found to be effective for 55 of 72 studied species. 17 closely related species with low interspecific genetic distances were observed, for which further study is proposed. It should also be noted that, in four cases, cryptic diversity was observed, where groups originally identified as one species exhibited genetic distance great enough to be separated into discrete species. Region specific haplotypes were also detected within populations of 14 species, giving the possibility to identify even the geographic origin of a species. Our findings are discussed in the light of the rich history of the Balkan peninsula and provide a significant steppingstone for the further study of Greek and European freshwater fish biodiversity.},
}
@article {pmid35078997,
year = {2022},
author = {Kawakami, K and Yanagawa, M and Hiratsuka, S and Yoshida, M and Ono, Y and Hiroshima, M and Ueda, M and Aoki, J and Sako, Y and Inoue, A},
title = {Heterotrimeric Gq proteins act as a switch for GRK5/6 selectivity underlying β-arrestin transducer bias.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {487},
pmid = {35078997},
issn = {2041-1723},
mesh = {Angiotensin II/*pharmacology ; Cell Line ; G-Protein-Coupled Receptor Kinase 2/*metabolism ; G-Protein-Coupled Receptor Kinase 5/*metabolism ; GTP-Binding Protein alpha Subunits, Gq-G11/*metabolism ; Humans ; Oligopeptides/*pharmacology ; Phosphorylation ; Receptor, Angiotensin, Type 1/*metabolism ; Signal Transduction ; Vasoconstrictor Agents/pharmacology ; beta-Arrestins/*metabolism ; },
abstract = {Signaling-biased ligands acting on G-protein-coupled receptors (GPCRs) differentially activate heterotrimeric G proteins and β-arrestins. Although a wealth of structural knowledge about signaling bias at the GPCR level exists (preferential engagement of a specific transducer), little is known about the bias at the transducer level (different functions mediated by a single transducer), partly due to a poor understanding of GPCR kinase (GRK)-mediated GPCR phosphorylation. Here, we reveal a unique role of the Gq heterotrimer as a determinant for GRK-subtype selectivity that regulates subsequent β-arrestin conformation and function. Using the angiotensin II (Ang II) type-1 receptor (AT1R), we show that β-arrestin recruitment depends on both GRK2/3 and GRK5/6 upon binding of Ang II, but solely on GRK5/6 upon binding of the β-arrestin-biased ligand TRV027. With pharmacological inhibition or genetic loss of Gq, GRK-subtype selectivity and β-arrestin functionality by Ang II is shifted to those of TRV027. Single-molecule imaging identifies relocation of AT1R and GRK5, but not GRK2, to an immobile phase under the Gq-inactive, AT1R-stimulated conditions. These findings uncover a previously unappreciated Gq-regulated mechanism that encodes GRK-subtype selectivity and imparts distinct phosphorylation-barcodes directing downstream β-arrestin functions.},
}
@article {pmid35077667,
year = {2022},
author = {Mascharak, S and Talbott, HE and Januszyk, M and Griffin, M and Chen, K and Davitt, MF and Demeter, J and Henn, D and Bonham, CA and Foster, DS and Mooney, N and Cheng, R and Jackson, PK and Wan, DC and Gurtner, GC and Longaker, MT},
title = {Multi-omic analysis reveals divergent molecular events in scarring and regenerative wound healing.},
journal = {Cell stem cell},
volume = {29},
number = {2},
pages = {315-327.e6},
pmid = {35077667},
issn = {1875-9777},
support = {R01 DE027346/DE/NIDCR NIH HHS/United States ; R01 GM116892/GM/NIGMS NIH HHS/United States ; R01 GM136659/GM/NIGMS NIH HHS/United States ; U24 DE029463/DE/NIDCR NIH HHS/United States ; },
mesh = {Animals ; *Cicatrix/pathology ; Fibroblasts/metabolism ; Fibrosis ; Mechanotransduction, Cellular ; Mice ; Repressor Proteins/genetics/metabolism ; Skin/pathology ; *Wound Healing/genetics ; },
abstract = {Regeneration is the holy grail of tissue repair, but skin injury typically yields fibrotic, non-functional scars. Developing pro-regenerative therapies requires rigorous understanding of the molecular progression from injury to fibrosis or regeneration. Here, we report the divergent molecular events driving skin wound cells toward scarring or regenerative fates. We profile scarring versus YAP-inhibition-induced wound regeneration at the transcriptional (single-cell RNA sequencing), protein (timsTOF proteomics), and tissue (extracellular matrix ultrastructural analysis) levels. Using cell-surface barcoding, we integrate these data to reveal fibrotic and regenerative "molecular trajectories" of healing. We show that disrupting YAP mechanotransduction yields regenerative repair by fibroblasts with activated Trps1 and Wnt signaling. Finally, via in vivo gene knockdown and overexpression in wounds, we identify Trps1 as a key regulatory gene that is necessary and partially sufficient for wound regeneration. Our findings serve as a multi-omic map of wound regeneration and could have therapeutic implications for pathologic fibroses.},
}
@article {pmid35076854,
year = {2022},
author = {Kumar, S and Kaushik, RA and Jain, D and Saini, VP and Babu, SR and Choudhary, R and Ercisli, S},
title = {Genetic diversity among local mango (Mangifera indica L.) germplasm using morphological, biochemical and chloroplast DNA barcodes analyses.},
journal = {Molecular biology reports},
volume = {49},
number = {5},
pages = {3491-3501},
pmid = {35076854},
issn = {1573-4978},
mesh = {Chloroplasts/genetics ; DNA, Chloroplast ; Fruit/genetics ; Genetic Variation ; *Mangifera/genetics ; Phylogeny ; },
abstract = {BACKGROUND: In this study, the genetic diversity of local mango (Mangifera indica L.) germplasm including 14 genotypes were evaluated by using morphological, biochemical markers and DNA barcoding technique. Morphological characterization is the first step towards utilizing these germplasm in crop improvement studies. The advanced chloroplast based DNA barcode method can be utilized to assess the genetic diversity and phylogenetic structure in such populations.<br><br>METHODS: The study was carried out during 2018-2019&#xa0;years to evaluate local mango germplasm including 14 diverse genotypes based on a number of morphological and biochemical traits and chloroplast DNA barcoding as well. The experiment was laid out in one way ANOVA design with fourteen germplasm indicated with indigenous collection number.<br><br>RESULTS: Among local mango germplasm, IC 589756 was found to be the most promising with respect to high magnitudes of fruit length, fruit width, fruit weight, pulp weight, soluble solid content (SSC)/Acidity ratio, pH and low acidity followed by IC 589746 exhibiting the highest pulp percentage and SSC accompanied with lowest stone weight and stone percent as compared to the other genotypes. Further, the dendrogram and cluster analyses based on sequencing of chloroplast marker i.e., trnH- psbA and trnCD depicted the relationship among mango genotypes and clearly clustered them into two main clusters at a similarity coefficient 0.035 and 0.150, respectively. The first cluster includes only one genotype and cluster-II contains 13 genotypes.<br><br>CONCLUSIONS: Particularly results revealed that DNA barcoding of local mango germplasm can assist not only in molecular identification but also help in elucidation of their phylogenetic relationship and thus important in maintaining biodiversity inventories.},
}
@article {pmid35073752,
year = {2022},
author = {Leducq, JB and Seyer-Lamontagne, &#xc9; and Condrain-Morel, D and Bourret, G and Sneddon, D and Foster, JA and Marx, CJ and Sullivan, JM and Shapiro, BJ and Kembel, SW},
title = {Fine-Scale Adaptations to Environmental Variation and Growth Strategies Drive Phyllosphere Methylobacterium Diversity.},
journal = {mBio},
volume = {13},
number = {1},
pages = {e0317521},
pmid = {35073752},
issn = {2150-7511},
mesh = {*Methylobacterium ; Phylogeny ; Forests ; Plants/microbiology ; Host Specificity ; Plant Leaves/microbiology ; },
abstract = {Methylobacterium is a prevalent bacterial genus of the phyllosphere. Despite its ubiquity, little is known about the extent to which its diversity reflects neutral processes like migration and drift, versus environmental filtering of life history strategies and adaptations. In two temperate forests, we investigated how phylogenetic diversity within Methylobacterium is structured by biogeography, seasonality, and growth strategies. Using deep, culture-independent barcoded marker gene sequencing coupled with culture-based approaches, we uncovered a considerable diversity of Methylobacterium in the phyllosphere. We cultured different subsets of Methylobacterium lineages depending upon the temperature of isolation and growth (20°C or 30°C), suggesting long-term adaptation to temperature. To a lesser extent than temperature adaptation, Methylobacterium diversity was also structured across large (>100 km; between forests) and small (<1.2 km; within forests) geographical scales, among host tree species, and was dynamic over seasons. By measuring the growth of 79 isolates during different temperature treatments, we observed contrasting growth performances, with strong lineage- and season-dependent variations in growth strategies. Finally, we documented a progressive replacement of lineages with a high-yield growth strategy typical of cooperative, structured communities in favor of those characterized by rapid growth, resulting in convergence and homogenization of community structure at the end of the growing season. Together, our results show how Methylobacterium is phylogenetically structured into lineages with distinct growth strategies, which helps explain their differential abundance across regions, host tree species, and time. This work paves the way for further investigation of adaptive strategies and traits within a ubiquitous phyllosphere genus. IMPORTANCE Methylobacterium is a bacterial group tied to plants. Despite the ubiquity of methylobacteria and the importance to their hosts, little is known about the processes driving Methylobacterium community dynamics. By combining traditional culture-dependent and -independent (metabarcoding) approaches, we monitored Methylobacterium diversity in two temperate forests over a growing season. On the surface of tree leaves, we discovered remarkably diverse and dynamic Methylobacterium communities over short temporal (from June to October) and spatial (within 1.2 km) scales. Because we cultured different subsets of Methylobacterium diversity depending on the temperature of incubation, we suspected that these dynamics partly reflected climatic adaptation. By culturing strains under laboratory conditions mimicking seasonal variations, we found that diversity and environmental variations were indeed good predictors of Methylobacterium growth performances. Our findings suggest that Methylobacterium community dynamics at the surface of tree leaves results from the succession of strains with contrasting growth strategies in response to environmental variations.},
}
@article {pmid35073261,
year = {2022},
author = {Hakoda, C and Pantea, C and Chillara, VK},
title = {Multilevel Frequency-Specific Information Storage Using Engineered Electromechanical Resonances in Piezoelectric Wafer Arrays.},
journal = {IEEE transactions on ultrasonics, ferroelectrics, and frequency control},
volume = {69},
number = {4},
pages = {1392-1398},
doi = {10.1109/TUFFC.2022.3145859},
pmid = {35073261},
issn = {1525-8955},
mesh = {*Information Storage and Retrieval ; },
abstract = {Multilevel information storage methods have the potential for increasing storage density and improving information security through obfuscation. Taking inspiration from the color quick response codes, we have developed a method for encoding layers of information in an array of thin piezoelectric wafers. Information storage is accomplished by altering the size of the circular polarization domain of individual wafers to engineer the response of the electromechanical resonances. By using this approach, we can store one layer of information per electromechanical resonance. In this study, we experimentally demonstrate this approach on a 20-element piezoelectric wafer array with up to two layers of information storage using binary encoding. We first discuss the relevant theory behind the proposed approach and the method for designing the polarization profiles for these wafer arrays to enable multilevel information storage. The effect of the size of the polarization domain on the strength of the electromechanical resonances and optimal size to enhance/suppress these resonances is discussed. Last, we describe how the proposed approach could be used to encode four or more layers of frequency-specific information. The proposed technology finds application in embedded barcodes, product tags, tamper-evident seals, and other secure applications such as shipping sensitive materials/containers.},
}
@article {pmid35071947,
year = {2021},
author = {Hossain, TJ and Das, M and Ali, F and Chowdhury, SI and Zedny, SA},
title = {Substrate preferences, phylogenetic and biochemical properties of proteolytic bacteria present in the digestive tract of Nile tilapia (Oreochromis niloticus).},
journal = {AIMS microbiology},
volume = {7},
number = {4},
pages = {528-545},
pmid = {35071947},
issn = {2471-1888},
abstract = {Vertebrate intestine appears to be an excellent source of proteolytic bacteria for industrial and probiotic use. We therefore aimed at obtaining the gut-associated proteolytic species of Nile tilapia (Oreochromis niloticus). We have isolated twenty six bacterial strains from its intestinal tract, seven of which showed exoprotease activity with the formation of clear halos on skim milk. Their depolymerization ability was further assessed on three distinct proteins including casein, gelatin, and albumin. All the isolates could successfully hydrolyze the three substrates indicating relatively broad specificity of their secreted proteases. Molecular taxonomy and phylogeny of the proteolytic isolates were determined based on their 16S rRNA gene barcoding, which suggested that the seven strains belong to three phyla viz. Firmicutes, Proteobacteria, and Actinobacteria, distributed across the genera Priestia, Citrobacter, Pseudomonas, Stenotrophomonas, Burkholderia, Providencia, and Micrococcus. The isolates were further characterized by a comprehensive study of their morphological, cultural, cellular and biochemical properties which were consistent with the phylogenetic annotations. To reveal their proteolytic capacity alongside substrate preferences, enzyme-production was determined by the diffusion assay. The Pseudomonas, Stenotrophomonas and Micrococcus isolates appeared to be most promising with maximum protease production on casein, gelatin, and albumin media respectively. Our findings present valuable insights into the phylogenetic and biochemical properties of gut-associated proteolytic strains of Nile tilapia.},
}
@article {pmid35071922,
year = {2022},
author = {Feng, Z and Guo, Q and Wang, Y and Ge, Y and Zhang, Z and Wu, Y and Li, Q and Masoomi, H and Gu, H and Xu, H},
title = {Evolution of "On-Barcode" Luminescence Oxygen Channeling Immunoassay by Exploring the Barcode Structure and the Assay System.},
journal = {ACS omega},
volume = {7},
number = {2},
pages = {2344-2355},
pmid = {35071922},
issn = {2470-1343},
abstract = {The multiplexed luminescence oxygen channeling immunoassay (multi-LOCI) platform we developed recently that combines conventional LOCI and suspension array technology is capable of realizing facile "mix-and-measure" multiplexed assays without tedious washing steps. However, previous work lacks comprehensive studies of the structure-performance relationship of the host-guest-structured barcode, which may obstruct the evolution and further translation of this exciting new technology to practical applications. Accordingly, this work revealed that polyelectrolyte interlayers played a crucial role in tuning the packing density of guest acceptor beads (ABs). More interestingly, we noticed that "sparse" barcodes (barcodes with low ABs packing density) exhibited comparable assay performance with "compact" ones (barcodes with high ABs packing density). The high robustness of barcodes allows for multi-LOCI to be a more universal and flexible assay platform. Furthermore, through optimization of the assay system including the laser power, as well as the concentrations of donor beads and biotinylated detection antibodies, the multi-LOCI platform showed a significant improvement in sensitivity compared with our previous work, with the limit of detection decreasing to as low as ca. 1 pg/mL. Impressively, multi-LOCI that enabled simultaneous detection of multiple analytes exhibited comparable sensitivity with the classical single-plexed LOCI, due to the ingenious structural design of the multi-LOCI barcode and the unique "on-barcode" assay format.},
}
@article {pmid35068977,
year = {2022},
author = {Mejía-Estrada, M and Jiménez-Segura, LF and Hernández-Zapata, M and Soto Calderón, ID},
title = {Contribution to a reference library of DNA barcodes of Colombian freshwater fishes.},
journal = {Biodiversity data journal},
volume = {10},
number = {},
pages = {e65981},
pmid = {35068977},
issn = {1314-2828},
abstract = {BACKGROUND: The Barcode of Life initiative was originally motivated by the large number of species, taxonomic difficulties and the limited number of expert taxonomists. Colombia has 1,610 freshwater fish species and comprises the second largest diversity of this group in the world. As genetic information continues to be limited, we constructed a reference collection of DNA sequences of Colombian freshwater fishes deposited in the Ichthyology Collection of the University of Antioquia (CIUA), thus joining the multiple efforts that have been made in the country to contribute to the knowledge of genetic diversity in order to strengthen the inventories of biological collections and facilitate the solution of taxonomic issues in the future.<br><br>NEW INFORMATION: This study contributes to the knowledge on the DNA barcodes and occurrence records of 96 species of Colombian freshwater fishes. Fifty-seven of the species represented in this dataset were already available in the Barcode Of Life Data System (BOLD System), while 39 correspond to new species to the BOLD System. Forty-nine specimens were collected in the Atrato River Basin and 708 in the Magdalena-Cauca asin during the period 2010-2020. Two species (Loricariichthysbrunneus (Hancock, 1828) and Poeciliasphenops Valenciennes, 1846) are considered exotic to the Atrato, Cauca and Magdalena Basins and four species (Oncorhynchusmykiss (Walbaum, 1792), Oreochromisniloticus (Linnaeus, 1758), Parachromisfriedrichsthalii (Heckel, 1840) and Xiphophorushelleri Heckel, 1848) are exotic to the Colombian hydrogeographic regions. All specimens are deposited in CIUA and have their DNA barcodes made publicly available in the BOLD online database. The geographical distribution dataset can be freely accessed through the Global Biodiversity Information Facility (GBIF).},
}
@article {pmid35068974,
year = {2021},
author = {Yahara, T and Hirota, SK and Fuse, K and Sato, H and Tagane, S and Suyama, Y},
title = {A new subspecies of Stellariaalsine (Caryophyllaceae) from Yakushima, Japan.},
journal = {PhytoKeys},
volume = {187},
number = {},
pages = {177-188},
pmid = {35068974},
issn = {1314-2011},
abstract = {An unknown taxon of Stellaria was discovered in Yakushima, a Japanese island known to harbor several endemic species. To determine the identity of this taxon, this study employed MIG-seq for the reconstruction of a finely resolved phylogenetic tree of the newly discovered taxon, along with some related species of Stellaria. The results showed that the newly discovered taxon is a relative of S.alsine. Based on this result, Stellariaalsinesubsp.nanasubsp. nov. was published.},
}
@article {pmid35068964,
year = {2022},
author = {Zhu, J and Zhang, J and Luo, X and Wang, Z and Che, Y},
title = {Three cryptic Anaplecta (Blattodea, Blattoidea, Anaplectidae) species revealed by female genitalia, plus seven new species from China.},
journal = {ZooKeys},
volume = {1080},
number = {},
pages = {53-97},
pmid = {35068964},
issn = {1313-2989},
abstract = {Morphological characteristics, including male and female genitalia, combined with DNA barcodes were used to identify 470 Anaplecta specimens sampled from China. Ten Anaplecta species are new to science, including three cryptic species: A.paraomei Zhu &amp; Che, sp. nov., A.condensa Zhu &amp; Che, sp. nov., and A.longihamata Zhu &amp; Che, sp. nov., which are distinguished mainly by their female genitalia. The other seven new species are as follows: A.bicruris Zhu &amp; Che, sp. nov., A.spinosa Zhu &amp; Che, sp. nov., A.ungulata Zhu &amp; Che, sp. nov., A.anomala Zhu &amp; Che, sp. nov., A.serrata Zhu &amp; Che, sp. nov., A.bombycina Zhu &amp; Che, sp. nov., and A.truncatula Zhu &amp; Che, sp. nov. This study illustrates that differences in female genitalia can be used to distinguish among species of Anaplecta. The female genitalia of 19 Chinese Anaplecta species are described and illustrated in this paper.},
}
@article {pmid35068955,
year = {2021},
author = {Urfer, K and Spasojevic, T and Klopfstein, S and Baur, H and Lasut, L and Kropf, C},
title = {Incongruent molecular and morphological variation in the crab spider Synemaglobosum (Araneae, Thomisidae) in Europe.},
journal = {ZooKeys},
volume = {1078},
number = {},
pages = {107-134},
pmid = {35068955},
issn = {1313-2989},
abstract = {Establishing species boundaries is one of the challenges taxonomists around the world have been tackling for centuries. The relation between intraspecific and interspecific variability is still under discussion and in many taxa it remains understudied. Here the hypothesis of single versus multiple species of the crab spider Synemaglobosum (Fabricius) is tested. The wide distribution range as well as its high morphological variability makes this species an interesting candidate for re-evaluation using an integrative approach. This study combines information from barcoding, phylogenetic reconstruction based on mitochondrial CO1 and ITS2 of more than 60 specimens collected over a wide range of European localities, and morphology. The findings show deep clades with up to 6% mean pairwise distance in the CO1 barcode without any biogeographical pattern. The nuclear ITS2 gene did not support the CO1 clades. Morphological assessment of somatic and genital characters in males and females and a morphometric analysis of the male palp uncovered high intraspecific variation that does not match the CO1 or ITS2 phylogenies or biogeography either. Screening for endosymbiotic Wolbachia bacteria was conducted and only a single infected specimen was found. Several scenarios might explain these inconsistent patterns. While the deep divergences in the barcoding marker might suggest cryptic or ongoing speciation or geographical isolation in the past, the lack of congruent variation in the nuclear ITS2 gene or the studied morphological character systems, especially the male palp, indicates that S.globosum might simply be highly polymorphic both in terms of its mtDNA and morphology. Therefore, more data on ecology and behaviour and full genome sequences are necessary to ultimately resolve this taxonomically intriguing case.},
}
@article {pmid35068954,
year = {2021},
author = {Hlebec, D and Sivec, I and Podnar, M and Skejo, J and Kučinić, M},
title = {Morphological and molecular characterisation of the Popijač's Yellow Sally, Isoperlapopijaci sp. nov., a new stenoendemic stonefly species from Croatia (Plecoptera, Perlodidae).},
journal = {ZooKeys},
volume = {1078},
number = {},
pages = {85-106},
pmid = {35068954},
issn = {1313-2989},
abstract = {A new species of the Yellow Sally genus (Isoperla Banks, 1906) is described, based on morphological (males and females adults, larval and egg) and molecular (the barcode region of the cytochrome c oxidase subunit I gene (COI)) features. Popijač's Yellow Sally, I.popijaci Hlebec &amp; Sivec, sp. nov. inhabits two karstic sources of the Krasulja rivulet in Croatia. Male and female of the new species are characterised by colouration patterns of the head and pronotum; the dimensions of the female subgenital plate; the medial penial armature and oval-shaped egg without collar and anchor. The larvae differ from their congeners by the uniquely coloured head and pronotum. Based on morphological characteristics I.popijaci sp. nov. belongs to the I.tripartita species group. Phylogenetic and taxonomic relationships were reconstructed using three methods of phylogenetic inference and three species delimitation methods. As I.popijaci sp. nov. occurs at a narrow area of the Krasulja rivulet in Krbava field, the study puts emphasis on the conservation and hotspot importance of the temporary rivers in the Dinaric karst. Furthermore, the study accentuates the necessity for further research on the genetic diversity of Plecoptera in Croatia.},
}
@article {pmid35068695,
year = {2022},
author = {Nunes, VV and Silva-Mann, R and Souza, JL and Calazans, CC},
title = {Pharmaceutical, food potential, and molecular data of Hancornia speciosa Gomes: a systematic review.},
journal = {Genetic resources and crop evolution},
volume = {69},
number = {2},
pages = {525-543},
pmid = {35068695},
issn = {0925-9864},
abstract = {UNLABELLED: Hancornia speciosa Gomes is a fruit and medicinal tree species native to South America, which in Brazil is considered of potential economic value and priority for research and development. We present a map of the state-of-art, including articles, patents, and molecular data of the species to identify perspectives for future research. The annual scientific production, intellectual, social, and conceptual structure were evaluated, along with the number of patent deposits, components of the plant used, countries of deposit, international classification and assignees, and the accessibility of available molecular data. Brazil has the most significant publications (306) between 1992 and 2020. Technological products (29) have been developed from different tissues of the plant. Most of the articles and patents were developed by researchers from public universities from different regions of Brazil. The molecular data are sequences of nucleotides (164) and proteins (236) of the chloroplast genome and are described to identify the species as DNA barcodes and proteins involved in photosynthesis. The compilation and report of scientific, technological, and molecular information in the present review allowed the identification of new perspectives of research to be developed based on the gaps in knowledge regarding the species and perspectives for the definition of future research.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10722-021-01319-w.},
}
@article {pmid35065179,
year = {2022},
author = {Todorov, TI and Wolle, MM and Conklin, SD},
title = {Distribution of 26 major and trace elements in edible seaweeds from the US market.},
journal = {Chemosphere},
volume = {294},
number = {},
pages = {133651},
doi = {10.1016/j.chemosphere.2022.133651},
pmid = {35065179},
issn = {1879-1298},
mesh = {*Mercury ; Microwaves ; *Seaweed ; Spectrum Analysis ; *Trace Elements/analysis ; },
abstract = {In this study we present an elemental profile of 46 edible seaweed samples purchased in the United States. The seaweeds were grouped in 13 subgroups/species based on DNA barcoding analysis. The seaweeds were decomposed by microwave accelerated acid digestion followed by quantification of 26 elements by ICP-MS. Elements were grouped into macronutrient (Na, K, Ca, S, Mg and P), essential (Fe, Zn, Mn, V, Cu, Cr, Ni, Mo and Se), non-essential including toxic elements (Sr, Ba, Th, Sn and Sb As, Cd, Pb, U, W and Hg). The highest levels were found for Na and the lowest were for Hg. The elemental profiles depended on the taxonomy of the species and several elements (Fe, Ba, Cr, Pb, W and Th) also exhibited high intraspecies variations, likely due to geographic origin or food processing conditions. Higher Cd and Pb accumulation was observed in wakame, hijiki and nori, with Cd as high 4.05 mg/kg and Pb as high as 2.85 mg/kg in kombu. A study of correlation between the elements using Pearson's coefficients revealed multiple pairs of highly correlated elements in seaweed, as well as triple and quintuple correlations of certain elements.},
}
@article {pmid35064726,
year = {2022},
author = {Oliveira, HFM and Pinheiro, RBP and Varassin, IG and Rodríguez-Herrera, B and Kuzmina, M and Rossiter, SJ and Clare, EL},
title = {The structure of tropical bat-plant interaction networks during an extreme El Niño-Southern Oscillation event.},
journal = {Molecular ecology},
volume = {31},
number = {6},
pages = {1892-1906},
pmid = {35064726},
issn = {1365-294X},
mesh = {Animals ; *Chiroptera/genetics ; Ecosystem ; *El Nino-Southern Oscillation ; Forests ; Seasons ; Tropical Climate ; },
abstract = {Interaction network structure reflects the ecological mechanisms acting within biological communities, which are affected by environmental conditions. In tropical forests, higher precipitation usually increases fruit production, which may lead frugivores to increase specialization, resulting in more modular and less nested animal-plant networks. In these ecosystems, El Niño is a major driver of precipitation, but we still lack knowledge of how species interactions change under this influence. To understand bat-plant network structure during an extreme El Niño-Southern Oscillation event, we determined the links between plantivorous bat species and the plants they consume by DNA barcoding seeds and pulp in bat faeces. These interactions were recorded in the dry forest and rainforest of Costa Rica, during the dry and the wet seasons of an extreme El Niño year. From these we constructed seasonal and whole-year bat-plant networks and analysed their structures and dissimilarities. In general, networks had low nestedness, had high modularity, and were dominated by one large compartment which included most species and interactions. Contrary to our expectations, networks were less nested and more modular in drier conditions, both in the comparison between forest types and between seasons. We suggest that increased competition, when resources are scarce during drier seasons and habitats, lead to higher resource partitioning among bats and thus higher modularity. Moreover, we have found similar network structures between dry and rainforests during El Niño and non-El Niño years. Finally, most interaction dissimilarity among networks occurred due to interaction rewiring among species, potentially driven by seasonal changes in resource availability.},
}
@article {pmid35063093,
year = {2022},
author = {Terai, T and Campbell, RE},
title = {Barcodes, co-cultures, and deep learning take genetically encoded biosensor multiplexing to the nth degree.},
journal = {Molecular cell},
volume = {82},
number = {2},
pages = {239-240},
doi = {10.1016/j.molcel.2021.12.017},
pmid = {35063093},
issn = {1097-4164},
mesh = {*Biosensing Techniques ; Coculture Techniques ; *Deep Learning ; },
abstract = {Yang et al. (2021) describe a co-culture multiplexed imaging method that can provide an order of magnitude increase in the number of barcoded biosensors that can be imaged in a single experiment.},
}
@article {pmid35060340,
year = {2022},
author = {Sipiczki, M},
title = {When barcoding fails: Genome chimerization (admixing) and reticulation obscure phylogenetic and taxonomic relationships.},
journal = {Molecular ecology resources},
volume = {22},
number = {5},
pages = {1762-1785},
pmid = {35060340},
issn = {1755-0998},
support = {2019-2.1.11-T&#xc9;T-2019-00001//National Research, Development and Innovation Office of Hungary/ ; K-124417//National Research, Development and Innovation Office of Hungary/ ; },
mesh = {*DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; Humans ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {DNA barcoding is based on the premise that the barcode sequences can distinguish individuals (strains) of different species because their sequence variation between species exceeds that within species. The primary barcodes used in fungal and yeast taxonomy are the ITS segments and the LSU (large subunit) D1/D2 domain of the homogenized multicopy rDNA repeats. The secondary barcodes are conserved segments of protein-encoding genes, which usually have single copies in haploid genomes. This study shows that the analysis of barcode sequences fails to reconstruct accurate species trees and differentiate species when the organisms have chimeric genomes composed of admixed mosaics of different origins. It is shown that the type strains of 10 species of the pulcherrima clade of the ascomycetous yeast genus Metschnikowia cannot be differentiated with standard barcodes because their intragenomic diversity is comparable to or even higher than the interstrain diversity. The analysis of a large group of genes of the sequenced genomes of the clade and the viability and segregation of the hybrids of ex-type strains indicate that the high intragenomic barcode differences can be attributed to admixed genome structures. Because of the mosaic structures of the genomes, the rDNA repeats do not form continuous arrays and thus cannot be homogenized. Since the highly diverse ITS and D1/D2 sequences of the type strains form a continuous pool including pseudogenes, the evolution of their rDNA appears to involve reticulation. The secondary barcode sequences and the nonbarcode genes included in the analysis show incongruent phylogenetic relationships among the type strains, which can also be attributed to differences in the phylogenetic histories of the genes.},
}
@article {pmid35059459,
year = {2022},
author = {Ahmed, S and Ibrahim, M and Nantasenamat, C and Nisar, MF and Malik, AA and Waheed, R and Ahmed, MZ and Ojha, SC and Alam, MK},
title = {Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward.},
journal = {BioMed research international},
volume = {2022},
number = {},
pages = {1846485},
pmid = {35059459},
issn = {2314-6141},
mesh = {Arabidopsis/*genetics ; *Bacteria/classification/genetics ; *DNA Barcoding, Taxonomic ; DNA, Bacterial/*genetics ; DNA, Fungal/*genetics ; DNA, Plant/*genetics ; *Fungi/classification/genetics ; },
abstract = {DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.},
}
@article {pmid35057947,
year = {2022},
author = {He, S and Yu, S and Feng, Y and He, L and Liu, L and Effah, CY and Wu, Y},
title = {A digital immuno-PCR assay for simultaneous determination of 5-methylcytosine and 5-hydroxymethylcytosine in human serum.},
journal = {Analytica chimica acta},
volume = {1192},
number = {},
pages = {339321},
doi = {10.1016/j.aca.2021.339321},
pmid = {35057947},
issn = {1873-4324},
mesh = {*5-Methylcytosine/analogs &amp; derivatives ; *Cytosine ; DNA Methylation ; Humans ; Polymerase Chain Reaction ; },
abstract = {This work aimed to develop an ultrasensitive and specific immunosorbent assay for simultaneous detection of double DNA methylation marks. Being considered the most important indicators in disease diagnosis, clinical treatment, and prognosis, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) were chosen as the proof-of-concept targets. The described strategy consisted of Phos-tag Biotin anchoring at streptavidin-magnetic nanoparticles, specific immune recognition of anti-5mC antibody and anti-5hmC antibody and labeling of Barcode-antibody, signal amplification of immune PCR and digital PCR machine. Under optimal conditions, the digital immuno-PCR assay showed a board dynamic range from 2.7 × 10[-13] mol/L to 2.7 × 10[-9] mol/L and the detection limits were 61.7 fmol/L for 5mC, and of 0.111 pmol/L for 5hmC. A 16-fold and 186-fold improvement of LOD were obtained by the proposed approach for 5mC and 5hmC detection compared with real-time immune PCR. The approach also showed ideal specificity, repeatability and stability. The recovery test demonstrated that the digital immuno-PCR assay is a promising platform for the simultaneous determination of the two DNA methylation marks in human serum sample.},
}
@article {pmid35055925,
year = {2022},
author = {Chimeno, C and Hausmann, A and Schmidt, S and Raupach, MJ and Doczkal, D and Baranov, V and Hübner, J and Höcherl, A and Albrecht, R and Jaschhof, M and Haszprunar, G and Hebert, PDN},
title = {Peering into the Darkness: DNA Barcoding Reveals Surprisingly High Diversity of Unknown Species of Diptera (Insecta) in Germany.},
journal = {Insects},
volume = {13},
number = {1},
pages = {},
pmid = {35055925},
issn = {2075-4450},
support = {16LI1901B//Federal Ministry of Education and Research/ ; },
abstract = {Determining the size of the German insect fauna requires better knowledge of several megadiverse families of Diptera and Hymenoptera that are taxonomically challenging. This study takes the first step in assessing these "dark taxa" families and provides species estimates for four challenging groups of Diptera (Cecidomyiidae, Chironomidae, Phoridae, and Sciaridae). These estimates are based on more than 48,000 DNA barcodes (COI) from Diptera collected by Malaise traps that were deployed in southern Germany. We assessed the fraction of German species belonging to 11 fly families with well-studied taxonomy in these samples. The resultant ratios were then used to estimate the species richness of the four "dark taxa" families (DT families hereafter). Our results suggest a surprisingly high proportion of undetected biodiversity in a supposedly well-investigated country: at least 1800-2200 species await discovery in Germany in these four families. As this estimate is based on collections from one region of Germany, the species count will likely increase with expanded geographic sampling.},
}
@article {pmid35055909,
year = {2022},
author = {Thube, SH and Pandian, TP and Bhavishya, A and Babu, M and Josephrajkumar, A and Chaithra, M and Hegde, V and Ruzzier, E},
title = {Xylosandrus crassiusculus (Motschulsky) (Coleoptera: Curculionidae) and Its Fungal Symbiont Ambrosiella roeperi Associated with Arecanut Kernel Decay in Karnataka, India.},
journal = {Insects},
volume = {13},
number = {1},
pages = {},
pmid = {35055909},
issn = {2075-4450},
support = {1000765041//Indian Council of Agricultural Research/ ; },
abstract = {Xylosandrus crassiusculus (Coleoptera: Curculionidae: Scolytinae) is reported causing damage to areca palm plantations (Areca catechu L.-Arecaceae) in Karnataka (India). In particular, X. crassiusculus has been observed attacking and successfully reproducing on areca nuts; besides the new host plant record, the data provided here represent the first documented case of spermatophagy for this xyleborine beetle. All infestation symptoms of this polyphagous pest were documented and illustrated. The identity of the scolytid, besides morphologically, was confirmed by its DNA barcoding. Eggs, larvae and pupae were found within the galleries of infested kernels. All galleries of the infested kernels were characterized by the presence of whitish to greyish fungal growth. The fungus was identified as Ambrosiella roeperi, a known symbiont of Xylosandrus crassiusculus. Incidence of this symbiotic insect-fungus complex in the economic part of arecanut, i.e., the kernel, is of serious concern. In a climate change scenario, this beetle with fungal symbionts may pose a serious threat to arecanut production in India and elsewhere.},
}
@article {pmid35055894,
year = {2022},
author = {Rossaro, B and Marziali, L and Magoga, G and Montagna, M and Boggero, A},
title = {Corrections and Additions to Descriptions of Some Species of the Subgenus Orthocladius s. str. (Diptera, Chironomidae, Orthocladiinae).},
journal = {Insects},
volume = {13},
number = {1},
pages = {},
pmid = {35055894},
issn = {2075-4450},
abstract = {The larvae of some species of the subgenus Orthocladius s. str. (Diptera, Chironomidae) are here described for the first time with corrections and additions to the descriptions of adult males and pupal exuviae. The identification of larvae is generally not possible without association with pupal exuviae and/or adult males, so the descriptions here are based only on reared material or on pupae with the associated larval exuviae. Usually, Chironomidae larvae can be separated on the basis of morphometric characters, the most discriminant ones are: (1) the ratio between the width of median tooth of mentum (Dm) and the width of the first lateral tooth (Dl) = mental ratio (DmDl), (2) the ratio between the length of the first antennal segment (A1) and the combined length of segments 2-5 (A2-5) = antennal ratio (AR). The shape of mandible, maxilla, and other body parts are almost identical in all the species considered in this study. The larva of Orthocladius (Symposiocladius) lignicola is very characteristic and can be separated by the shape of mentum and the larvae of all the known species of Symposiocladius are characterized by the presence of large Lauterborn organs on antennae and of tufts of setae on abdominal segments. The larvae of Orthocladius (Orthocladius) oblidens and Orthocladius (Orthocladius) rhyacobius can be distinguished from other species basing on their large Dm and to each other by AR. A principal component analysis was carried out using 5 characters: (1) Dm, (2) Dl, (3) length of A1, (4) width of A1 (A1W), (5) combined length of segments 2-5 (A2-5). The most discriminant characters were Dm and A1, confirming that DmDl and AR can be used to separate species at larval stage, but the large superposition of morphometric characters in different species confirms that association with pupal exuviae is in any case needed to identify larvae. In future perspective, the development of reference DNA barcodes from specimens identified by specialists is recommended since possibly the best tool for larvae identification, but association of barcodes with morphotypes is in any case fundamental.},
}
@article {pmid35055862,
year = {2021},
author = {Ševčík, J and Hippa, H and Burdíková, N},
title = {Just a Fragment of Undescribed Diversity: Twenty New Oriental and Palearctic Species of Sciaroidea (Diptera), including DNA Sequence Data and Two New Fossil Genera.},
journal = {Insects},
volume = {13},
number = {1},
pages = {},
pmid = {35055862},
issn = {2075-4450},
abstract = {The following 17 extant new species of Sciaroidea (Diptera: Bibionomorpha) are described: Bolitophila nikolae Ševčík sp. nov. (Bolitophilidae, Taiwan), Catocha jingfui sp. nov. (Cecidomyiidae, Taiwan), Catocha manmiaoe sp. nov. (Cecidomyiidae, Taiwan), Catocha shengfengi sp. nov. (Cecidomyiidae, Taiwan), Planetella taiwanensis sp. nov. (Cecidomyiidae, Taiwan), Diadocidia pseudospinusola sp. nov. (Diadocidiidae, Taiwan), Asioditomyia bruneicola sp. nov. (Ditomyiidae, Brunei), Asioditomyia lacii sp. nov. (Ditomyiidae, Taiwan), Ditomyia asiatica sp. nov. (Ditomyiidae, Thailand), Chetoneura davidi sp. nov. (Keroplatidae, Brunei), Euceroplatus mantici sp. nov. (Keroplatidae, Thailand), Setostylus fangshuoi sp. nov. (Keroplatidae, Taiwan), Platyceridion yunfui sp. nov. (Keroplatidae, Hainan), Terocelion adami sp. nov. (Keroplatidae, Taiwan), Hadroneura martini sp. nov. (Mycetophilidae, Taiwan), Paratinia furcata sp. nov. (Mycetophilidae, Czech Republic, Slovakia), and Nepaletricha sikorai sp. nov. (Sciaroidea incertae sedis, Thailand). Two new genera are described from the mid-Cretaceous Burmese amber, Burmasymmerus gen. nov. (Ditomyiidae, type species Burmasymmerus korneliae sp. nov., including also B. wieslawi sp. nov.), representing the first record of the family Ditomyiidae from the Mesozoic, and Burmatricha gen. nov. (Sciaroidea incertae sedis, type species Burmatricha mesozoica sp. nov.). Molecular phylogeny of Ditomyiidae, based on two DNA markers (28S, COI), as well as that of Catocha Haliday, 1833, based on the mitochondrial COI and 16S fragments, are also presented.},
}
@article {pmid35055849,
year = {2021},
author = {Soldi, E and Fuller, E and Tiley, AMM and Murchie, AK and Hodkinson, TR},
title = {First Report of the Ash Sawfly, Tomostethus nigritus, Established on Fraxinus excelsior in the Republic of Ireland.},
journal = {Insects},
volume = {13},
number = {1},
pages = {},
pmid = {35055849},
issn = {2075-4450},
support = {2019R578//Department of Agriculture, Food &amp; the Marine (DAFM)/ ; 2019R578//Department of Agriculture, Environment and Rural Affairs (DAERA)/ ; },
abstract = {This is the first report of the ash sawfly, Tomostethus nigritus, in the Republic of Ireland. We observed defoliated leaves of Fraxinus excelsior L. and T. nigritus larvae at a forestry plantation in Co. Kildare. Morphological observation of the larvae and DNA analysis using mitochondrial COI barcoding confirmed the identification of this pest of ash.},
}
@article {pmid35048980,
year = {2022},
author = {Smith, JJ and Brzezinski, P and Dziedziula, J and Rosenthal, E and Klaus, M},
title = {Partial Ribosomal Nontranscribed Spacer Sequences Distinguish Rhagoletis zephyria (Diptera: Tephritidae) From the Apple Maggot, R. pomonella.},
journal = {Journal of economic entomology},
volume = {115},
number = {2},
pages = {647-661},
pmid = {35048980},
issn = {1938-291X},
mesh = {Animals ; *Diptera ; Larva ; *Malus ; *Tephritidae/genetics ; Washington ; },
abstract = {The apple maggot, Rhagoletis pomonella (Walsh), was introduced into the apple-growing regions of the Pacific Northwest in the U.S.A. during the past 60-100 yr. Apple maggot (larvae, puparia, and adults) is difficult to distinguish from its morphologically similar sister species, Rhagoletis zephyria Snow, which is native and abundant in the Pacific Northwest. While morphological identifications are common practice, a simple, inexpensive assay based on genetic differences would be very useful when morphological traits are unclear. Here we report nucleotide substitution and insertion-deletion mutations in the nontranscribed spacer (NTS) of the ribosomal RNA gene cistron of R. pomonella and R. zephyria that appear to be diagnostic for these two fly species. Insertion-deletion variation is substantial and results in a 49 base-pair difference in PCR amplicon size between R. zephyria and R. pomonella that can be scored using agarose gel electrophoresis. PCR amplification and DNA sequencing of 766 bp of the NTS region from 38 R. pomonella individuals and 35 R. zephyria individuals from across their geographic ranges led to the expected PCR fragments of approx. 840 bp and 790 bp, respectively, as did amplification and sequencing of a smaller set of 26 R. pomonella and 16 R. zephyria flies from a sympatric site in Washington State. Conversely, 633 bp mitochondrial COI barcode sequences from this set of flies were polyphyletic with respect to R. pomonella and R. zephyria. Thus, differences in NTS PCR products on agarose gels potentially provide a simple way to distinguish between R. pomonella and R. zephyria.},
}
@article {pmid35048690,
year = {2022},
author = {Makino, K and Susaki, EA and Endo, M and Asanuma, H and Kashida, H},
title = {Color-Changing Fluorescent Barcode Based on Strand Displacement Reaction Enables Simple Multiplexed Labeling.},
journal = {Journal of the American Chemical Society},
volume = {144},
number = {4},
pages = {1572-1579},
doi = {10.1021/jacs.1c09844},
pmid = {35048690},
issn = {1520-5126},
abstract = {Fluorescence imaging techniques have contributed to our understanding of various biological phenomenon; however, fluorescence spectral overlap significantly restricts multiplexing capability. Several strategies have been reported to overcome this limitation by utilizing the superior programmability of DNA technologies and nanostructures, but in practice, it remains challenging to achieve broad adoption of these multiplexed detection methods due to the complexities of these DNA designs. Here we report a color-changing fluorescent barcode (CCFB) approach that enables multiple labeling with simple and small nucleic acid structure design based on sequential toehold-mediated strand displacement reaction. The emission color of CCFB can vary in the predetermined sequence so that multiple targets can be detected simultaneously. The CCFB complex is composed of several oligonucleotides, and its color sequence can be easily expanded further. The CCFB approach is easy and time-saving to operate since the irreversible color-changing reaction occurs by simply adding complementary oligonucleotide. We herein developed 27 different CCFB labels, which required only 14 oligonucleotides. We demonstrated that the CCFB system can be used to label multiple targets by attaching CCFB label to polystyrene beads. Moreover, the CCFB can be used to detect intracellular proteins simultaneously when it is attached to antibodies. We expect that this practical platform will be adopted for comprehensive biomolecular imaging in cells.},
}
@article {pmid35047236,
year = {2022},
author = {Hettiarachchi, SA and Hyeon, JY and Mahardini, A and Kim, HS and Byun, JH and Kim, HJ and Jeong, JG and Yeo, JK and Kim, SK and Kim, SJ and Heo, YS and Sathyadith, J and Kang, DH and Hur, SP},
title = {DNA barcoding and morphological identification of spiny lobsters in South Korean waters: a new record of Panulirus longipes and Panulirus homarus homarus.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e12744},
pmid = {35047236},
issn = {2167-8359},
mesh = {Animals ; *Palinuridae/genetics ; Phylogeny ; Nephropidae/genetics ; Bayes Theorem ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; },
abstract = {To date, 19 species of spiny lobsters from the genus Panulirus have been discovered, of which only P. japonicus, P. penicilatus, P. stimpsoni, and P. versicolor have been documented in South Korean waters. In this study, we aimed to identify and update the current list of spiny lobster species that inhabit South Korean waters based on the morphological features and the phylogenetic profile of cytochrome oxidase I (COI) of mitochondrial DNA (mtDNA). Spiny lobsters were collected from the southern and eastern coasts of Jeju Island, South Korea. Phylogenetic analyses were performed using neighbor-joining (NJ), maximum likelihood (ML), and Bayesian inference (BI) methods. The ML tree was used to determine the spiny lobster lineages, thereby clustering the 17 specimens collected in this study into clades A, B, C, and D, which were reciprocally monophyletic with P. japonicus, P. homarus homarus, P. longipes, and P. stimpsoni, respectively. These clades were also supported by morphological examinations. Interestingly, morphological variations, including the connected pleural and transverse groove at the third abdominal somite, were observed in four specimens that were genetically confirmed as P. japonicus. This finding is novel within the P. japonicus taxonomical reports. Additionally, this study updates the documentation of spiny lobsters inhabiting South Korean waters as P. longipes and P. homarus homarus were recorded for the first time in this region.},
}
@article {pmid35046946,
year = {2021},
author = {Penter, L and Gohil, SH and Wu, CJ},
title = {Natural Barcodes for Longitudinal Single Cell Tracking of Leukemic and Immune Cell Dynamics.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {788891},
pmid = {35046946},
issn = {1664-3224},
support = {P01 CA229092/CA/NCI NIH HHS/United States ; R01 CA216273/CA/NCI NIH HHS/United States ; U24 CA224331/CA/NCI NIH HHS/United States ; R01 CA155010/CA/NCI NIH HHS/United States ; UG1 CA233338/CA/NCI NIH HHS/United States ; },
mesh = {Cell Lineage ; Cell Tracking/methods/trends ; DNA Barcoding, Taxonomic/*methods/*trends ; Humans ; Immunophenotyping/methods/trends ; *Leukemia ; Single-Cell Analysis/*methods/*trends ; },
abstract = {Blood malignancies provide unique opportunities for longitudinal tracking of disease evolution following therapeutic bottlenecks and for the monitoring of changes in anti-tumor immunity. The expanding development of multi-modal single-cell sequencing technologies affords newer platforms to elucidate the mechanisms underlying these processes at unprecedented resolution. Furthermore, the identification of molecular events that can serve as in-vivo barcodes now facilitate the tracking of the trajectories of malignant and of immune cell populations over time within primary human samples, as these permit unambiguous identification of the clonal lineage of cell populations within heterogeneous phenotypes. Here, we provide an overview of the potential for chromosomal copy number changes, somatic nuclear and mitochondrial DNA mutations, single nucleotide polymorphisms, and T and B cell receptor sequences to serve as personal natural barcodes and review technical implementations in single-cell analysis workflows. Applications of these methodologies include the study of acquired therapeutic resistance and the dissection of donor- and host cellular interactions in the context of allogeneic hematopoietic stem cell transplantation.},
}
@article {pmid35046752,
year = {2021},
author = {Sharkey, MJ and Baker, A and McCluskey, K and Smith, A and Naik, S and Ratnasingham, S and Manjunath, R and Perez, K and Sones, J and D'Souza, M and Jacques, BS and Hebert, P and Hallwachs, W and Janzen, D},
title = {?Addendum to a minimalist revision of Costa Rican Braconidae: 28 new species and 23 host records.},
journal = {ZooKeys},
volume = {1075},
number = {},
pages = {77-136},
pmid = {35046752},
issn = {1313-2989},
abstract = {Twenty-nine species are treated, most of which have host caterpillar and food plant records, and all but one are new to science. The first host record for the agathidine genus Amputoearinus is given. Gnathopleurajosequesadai Sharkey, sp. nov. is reported as a hyperparasitoid of fly larvae, the first such record for the genus. The following new species are diagnosed primarily using COI barcode data; Sharkey is the authority for all: Agathidinae: Aerophilusdavidwagneri, Aerophilusfundacionbandorum, Aerophilusnicklaphami, Lytopylusdavidstopaki, Lytopylusdavidschindeli; Alysiinae: Gnathopleurajosequesadai; Braconinae: Braconandreamezae, Braconfranklinpaniaguai, Braconrafagutierrezi, Braconguillermoblancoi, Braconoscarmasisi, Braconpauldimaurai, Braconshebadimaurae, Saciremakarendimaurae; Cheloninae: Chelonusminorzunigai; Homolobinae: Homolobusstevestroudi; Macrocentrinae: Macrocentrusmichaelstroudi; Orgilinae: Stantoniagilbertfuentesi; Rhysipolinae: Rhysipolisstevearonsoni; Rogadinae: Aleiodeskaydodgeae, Aleiodeskerrydresslerae, Aleiodesjosesolanoi, Aleiodesjuniorporrasi, Aleiodesrocioecheverri, Aleiodesronaldzunigai, Choreborogasjesseausubeli, Triraphisdoncombi, and Yeliconesmayrabonillae.},
}
@article {pmid35046750,
year = {2021},
author = {Moran, KM and Skevington, JH},
title = {Taxonomic revision of Romaleosyrphus Bigot (Diptera, Syrphidae), including descriptions of seven new species.},
journal = {ZooKeys},
volume = {1075},
number = {},
pages = {1-32},
pmid = {35046750},
issn = {1313-2989},
abstract = {The genus Romaleosyrphus Bigot is reviewed, including the description of seven new species (R.argosi Moran, sp. nov., R.bigoti Moran, sp. nov., R.drysus Moran, sp. nov., R.nephelaeus Moran &amp; Thompson, sp. nov., R.soletluna Moran &amp; Thompson, sp. nov., R.vockerothi Moran &amp; Thompson, sp. nov. and R.woodi Moran, sp. nov.). Romaleosyrphusarctophiloides (Giglio-Tos), comb. nov. is transferred to Romaleosyrphus. Romaleosyrphus stat. rev. is redefined to represent the monophyletic unit of species within Criorhinina which possess holoptic males, a proximal ventral half of vein C with setae, a broad intersection of vein R1 with vein C, the distal part of R4+5 beyond M1 longer than cross-vein h and appressed pile on the abdomen. Descriptions, habitus and genitalia photographs, distributions, and an illustrated key for all nine Romaleosyrphus are presented. DNA barcode data are provided for eight of the species with a cytochrome c oxidase subunit I gene tree presented and discussed.},
}
@article {pmid35043260,
year = {2022},
author = {Tu, J and Qiao, Y and Xu, Z and Lu, N and Long, N and Lu, Z},
title = {dCITI-Seq: droplet combinational indexed transposon insertion sequencing.},
journal = {Analytical and bioanalytical chemistry},
volume = {414},
number = {8},
pages = {2661-2670},
pmid = {35043260},
issn = {1618-2650},
support = {2019-SWYY-004//Six Talent Peaks Project of Jiangsu Province/ ; BK20211513//Natural Science Foundation of Jiangsu Province/ ; 61971125//National Natural Science Foundation of China/ ; },
mesh = {*Computational Biology ; Gene Library ; *High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; },
abstract = {The rapid development of high-throughput parallel sequencing poses new challenges for large-scale barcoding and sequencing library construction. Here, we present droplet combinational indexed transposon insertion sequencing (dCITI-Seq), in which samples are indexed by the direct insertion of index-containing adaptors through transposition. The random combination of two sets of adaptors with known barcodes and massively parallel transposition was realized via a robust droplet pairing and merging platform. This strategy potentially enlarges the indexing capacity and decreases index crosstalk. Also, dCITI-Seq exhibited a lower GC base preference than conventional in-tube transposition library preparation. With a custom bioinformatic processing, it could be further applied to large-scale single-cell sequencing.},
}
@article {pmid35038324,
year = {2022},
author = {Sasaki, M and Miura, O and Nakao, M},
title = {PHILOPHTHALMUS HECHINGERI N. SP. (DIGENEA: PHILOPHTHALMIDAE), A HUMAN-INFECTING EYE FLUKE FROM THE ASIAN MUD SNAIL, BATILLARIA ATTRAMENTARIA.},
journal = {The Journal of parasitology},
volume = {108},
number = {1},
pages = {44-52},
doi = {10.1645/21-69},
pmid = {35038324},
issn = {1937-2345},
mesh = {Animals ; Bird Diseases/parasitology ; DNA Barcoding, Taxonomic ; DNA, Ribosomal/chemistry ; Electron Transport Complex IV/genetics ; Eye Infections, Parasitic/*parasitology ; Gastropoda/*parasitology ; Genetic Variation ; Humans ; Japan ; Likelihood Functions ; Phylogeny ; Quail ; RNA, Ribosomal, 28S/genetics ; Sequence Alignment ; Trematoda/*classification/genetics/growth &amp; development/isolation &amp; purification ; Trematode Infections/*parasitology ; },
abstract = {Two cases of human philophthalmosis have been reported in Japan. Gravid flukes removed from the eyes of the patients were broken, but their morphological characteristics suggest that an unknown species of the genus Philophthalmus is involved as a pathogen for humans. The mitochondrial DNA barcode of the human eye fluke enabled us to discover its larval stage from the Japanese mud snail, Batillaria attramentaria. The discovered cercaria had previously been temporarily described as "Philophthalmid sp. I." In this study, we examined the infection status of B. attramentaria with Philophthalmid sp. I found on a muddy seashore of the Seto Inland Sea, Japan, and the resulting metacercariae were experimentally administered to Japanese quails to develop them into the gravid adult stage. The complete specimens of the adult and larval stages allowed us to describe a new species. Based on morphological and molecular analyses, Philophthalmus hechingeri n. sp. is proposed for the human-infecting eye fluke in Japan. The natural definitive hosts of the new species are unknown. However, the habitat of B. attramentaria suggests that shorebirds (seagulls, sandpipers, and plovers) might be the possible candidates.},
}
@article {pmid35036110,
year = {2021},
author = {Dartois, M and Pante, E and Viricel, A and Becquet, V and Sauriau, PG},
title = {Molecular genetic diversity of seaweeds morphologically related to Ulva rigida at three sites along the French Atlantic coast.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e11966},
pmid = {35036110},
issn = {2167-8359},
abstract = {Foliose species of the genus Ulva are notoriously difficult to identify due to their variable morphological characteristics and high phenotypic plasticity. We reassessed the taxonomic status of several distromatic foliose Ulva spp., morphologically related to Ulva rigida, using DNA barcoding with the chloroplastic tufA and rbcL (for a subset of taxa) genes for 339 selected attached Ulva specimens collected from three intertidal rocky sites. Two of the collection sites were in Brittany and one site was in Vendée, along the Atlantic coast of France. Molecular analyses included several museum specimens and the holotype of Ulva armoricana Dion, Reviers &amp; Coat. We identified five different tufA haplotypes using a combination of phylogenetic analysis, with the support of several recently sequenced holotypes and lectotypes, and a species delimitation method based on hierarchical clustering. Four haplotypes were supported by validly named species: Ulva australis Areschoug, Ulva fenestrata Postels &amp; Ruprecht, Ulva lacinulata (Kützing) Wittrock and U. rigida C. Agardh. The later was additionally investigated using rbcL. The fifth haplotype represented exact sequence matches to an unnamed species from European Atlantic coasts. Our results support: (1) the synonymy of both U. rigida sensu Bliding non C. Agardh and U. armoricana with U. lacinulata. This finding is based on current genetic analysis of tufA from the U. armoricana holotype and recent molecular characterization of the lectotype of U. laetevirens, which is synonymous to U. australis, (2) the presence of U. australis as a misidentified introduced species in Brittany, and (3) the presence of U. fenestrata and U. rigida in southern Brittany. The taxonomic history of each species is discussed, highlighting issues within distromatic foliose taxa of the genus Ulva and the need to genetically characterize all its available type specimens.},
}
@article {pmid35035629,
year = {2022},
author = {Colin, L and Abed-Navandi, D and Conde, DA and Craggs, J and da Silva, R and Janse, M and Källström, B and Pearce-Kelly, A and Yesson, C},
title = {What's left in the tank? Identification of non-ascribed aquarium's coral collections with DNA barcodes as part of an integrated diagnostic approach.},
journal = {Conservation genetics resources},
volume = {14},
number = {2},
pages = {167-182},
pmid = {35035629},
issn = {1877-7252},
abstract = {UNLABELLED: The unprecedented threats to coral reef ecosystems from global climate change require an urgent response from the aquarium community, which is becoming an increasingly vital coral conservation resource. Unfortunately, many hermatypic corals in aquaria are not identified to species level, which hinders assessment of their conservation significance. Traditional methods of species identification using morphology can be challenging, especially to non-taxonomists. DNA barcoding is an option for species identification of Scleractinian corals, especially when used in concert with morphology-based assessment. This study uses DNA barcodes to try to identify aquarium specimens of the diverse reef-forming genus Acropora from 127 samples. We identified to our best current knowledge, to species name 44% of the analysed samples and provided provisional identification for 80% of them (101/127, in the form of a list of species names with associate confidence values). We highlighted a sampling bias in public nucleotide sequences repertories (e.g. GenBank) towards more charismatic and more studied species, even inside a well-studied genus like Acropora. In addition, we showed a potential "single observer" effect with over a quarter of the reference sequences used for these identifications coming from the same study. We propose the use of barcoding and query matching as an additional tool for taxonomic experts and general aquarists, as an additional tool to increase their chances of making high confidence species-level identifications. We produce a standardised and easily repeatable methodology to increase the capacity of aquariums and other facilities to assess non-ascribed species, emphasising the value of integrating this approach with morphological identification optimising usage of authoritative identification guides and expert opinion.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12686-021-01250-3.},
}
@article {pmid35035254,
year = {2021},
author = {Huang, S and Hou, Y and Zhu, L and Xu, Y and Wang, M and Fan, X and Long, Y and Da, W and Chen, L},
title = {?Description of a new species of the genus Neopseustis Meyrick, 1909 from China, with a new classification of the genus (Lepidoptera, Neopseustoidea, Neopseustidae).},
journal = {ZooKeys},
volume = {1078},
number = {},
pages = {35-48},
pmid = {35035254},
issn = {1313-2989},
abstract = {A new species of the genus Neopseustis Meyrick, 1909, Neopseustischentangensis S.Y. Huang &amp; Chen sp. nov., which was confirmed by both morphological and molecular methods, is described from Xizang, China. This is currently the westernmost species in Asia of the primitive lepidopteran family Neopseustidae. The new species is externally reminiscent of N.moxiensis Chen &amp; Owada, 2009; however, it can be easily distinguished from the latter by comparison of the male genitalia and is further distinguished by the large genetic distance in DNA barcodes (COI). The adult and genitalia of the new and similar species have been illustrated. Utilizing our new data, a new classification of the genus is provided, with its members subdivided into four species groups: the meyricki-group, the moxiensis-group, the bicornuta-group, and the chentangensis-group, which are supported by both molecular and morphological evidence. A checklist of the genus and a key to the species groups are also provided.},
}
@article {pmid35033286,
year = {2022},
author = {Waghchoure, AP and Reddy, JP and Bhosale, RS},
title = {Fluorescence based miniaturized microfluidic and nanofluidic systems for biomedical applications.},
journal = {Progress in molecular biology and translational science},
volume = {186},
number = {1},
pages = {217-243},
doi = {10.1016/bs.pmbts.2021.07.029},
pmid = {35033286},
issn = {1878-0814},
mesh = {*Microfluidic Analytical Techniques ; Microfluidics ; *Nanostructures ; Nanotechnology ; Protein Binding ; },
abstract = {Over the last two decades miniaturized microfluidic and nanofluidic systems with fluorescence setup emerged as a powerful technological platform for diverse biomedical applications. Bio-macromolecules such as nucleic acids and proteins are the core cellular components, their single molecule analysis allow us to understand biological processes, disease creation and progression, and development of novel treatment policies. Design and development of foolproof treatment methods requires rigorously analysis of nucleic acids and proteins such as length quantifications, sequence profiling, sequence mapping, analysis of conformational changes, analysis and recognition of epigenetic changes, and their interactions with other biomolecules. Miniaturized microfluidic and nanofluidic systems with fluorescence spectroscopy enable worldwide researchers to perform nucleic acids and proteins extractions and single molecule analysis from the trace amount of biological samples. In the present chapter we mostly highlighted over one decade applications of microfluidic and nanofluidic systems for single cell micro ribonucleic acid (miRNA) isolation and detection, deoxyribonucleic acid (DNA) mapping, DNA barcoding, identification of epigenetic mark on single DNA molecule, DNA-protein interactions study, protein sensing, protein sequencing, protein binding kinetics and many other applications. We also presented the recently reported microfluidic platform for the preparation of reproducible unisize aggregation induced emission (AIE) active nanomaterials and their biological applications.},
}
@article {pmid35033159,
year = {2022},
author = {Trzebny, A and Liberska, J and Slodkowicz-Kowalska, A and Dabert, M},
title = {Metabarcoding reveals low prevalence of microsporidian infections in castor bean tick (Ixodes ricinus).},
journal = {Parasites &amp; vectors},
volume = {15},
number = {1},
pages = {26},
pmid = {35033159},
issn = {1756-3305},
support = {05/IDUB/2019/94//Initiative of Excellence-Research University at Adam Mickiewicz University, Poznan, Poland/ ; POWR.03.02.00-00-I006/17//Passport to the Future-Interdisciplinary doctoral studies at the Faculty of Biology/ ; POWR.03.02.00-00-I006/17//Passport to the Future-Interdisciplinary doctoral studies at the Faculty of Biology/ ; 2020/37/N/NZ8/01735//Narodowe Centrum Nauki/ ; },
mesh = {Animals ; Arachnid Vectors/*microbiology ; Base Sequence ; Cat Diseases/parasitology ; Cats ; DNA Barcoding, Taxonomic ; DNA, Fungal/chemistry/isolation &amp; purification ; DNA, Ribosomal/chemistry ; Dog Diseases/parasitology ; Dogs ; Electron Transport Complex IV/chemistry ; Female ; Ixodes/*microbiology ; Male ; Microsporidia/classification/*physiology ; Parks, Recreational ; Phylogeny ; Poland ; Prevalence ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Tick Infestations/parasitology/veterinary ; },
abstract = {BACKGROUND: Microsporidia is a large group of eukaryotic obligate intracellular spore-forming parasites, of which 17 species can cause microsporidiosis in humans. Most human-infecting microsporidians belong to the genera Enterocytozoon and Encephalitozoon. To date, only five microsporidian species, including Encephalitozoon-like, have been found in hard ticks (Ixodidae) using microscopic methods, but no sequence data are available for them. Furthermore, no widespread screening for microsporidian-infected ticks based on DNA analysis has been carried out to date. Thus, in this study, we applied a recently developed DNA metabarcoding method for efficient microsporidian DNA identification to assess the role of ticks as potential vectors of microsporidian species causing diseases in humans.<br><br>METHODS: In total, 1070 (493 juvenile and 577 adult) unfed host-seeking Ixodes ricinus ticks collected at urban parks in the city of Poznan, Poland, and 94 engorged tick females fed on dogs and cats were screened for microsporidian DNA. Microsporidians were detected by PCR amplification and sequencing of the hypervariable V5 region of 18S rRNA gene (18S profiling) using the microsporidian-specific primer set. Tick species were identified morphologically and confirmed by amplification and sequencing of the shortened fragment of cytochrome c oxidase subunit I gene (mini-COI).<br><br>RESULTS: All collected ticks were unambiguously assigned to I. ricinus. Potentially zoonotic Encephalitozoon intestinalis was identified in three fed ticks (3.2%) collected from three different dogs. In eight unfed host-seeking ticks (0.8%), including three males (1.1%), two females (0.7%) and three nymphs (0.7%), the new microsporidian sequence representing a species belonging to the genus Endoreticulatus was identified.<br><br>CONCLUSIONS: The lack of zoonotic microsporidians in host-seeking ticks suggests that I. ricinus is not involved in transmission of human-infecting microsporidians. Moreover, a very low occurrence of the other microsporidian species in both fed and host-seeking ticks implies that mechanisms exist to defend ticks against infection with these parasites.},
}
@article {pmid35029611,
year = {2022},
author = {Du, X and Wang, Y and Zhai, J and Guo, C and Zhang, Y and Huang, W and Ma, X and Xie, X},
title = {One-pot synthesized organosilica nanospheres for multiplexed fluorescent nanobarcoding and subcellular tracking.},
journal = {Nanoscale},
volume = {14},
number = {5},
pages = {1787-1795},
doi = {10.1039/d1nr06540h},
pmid = {35029611},
issn = {2040-3372},
mesh = {Flow Cytometry ; Fluorescein ; Fluorescent Dyes ; *Nanospheres ; *Nanostructures ; },
abstract = {Multicolor microbeads are widely used in flow cytometry for various cellular and immunoassays. However, they are limited by their large size of around one to tens of micrometers. Nanomaterials for multiplexed analysis are emerging as valuable tools in high-throughput assays and fluorescence cell barcoding. We present barcoding and related cellular studies based on mass-produced organosilane-derived multifunctional nanospheres with a uniform size. Functional groups including thiols, amines, and azides were integrated in one step from various organosilanes without additional orthosilicates. Fluorescent nanobarcodes (NBs) were achieved through flexible physical adsorption and chemical ligation of spectrally separated fluorescent dyes. Live cells labeled with the NBs were readily distinguished by flow cytometry. The NBs have a small and uniform size (ca. 27 nm in diameter), excellent biocompatibility, rapid cellular uptake, and low dye leakage. The fluorescent nanospheres were applied for long-term cell tracking during multiple rounds of cell division and monitored over 48 hours. While most nanospheres were endolysosome-targeting, modification with fluorescein isothiocyanate (FITC) surprisingly lighted up the cell nucleus. This work lays the foundation of a unique family of functional nanomaterials promising for multiplex detection and other chemical and biological applications.},
}
@article {pmid35026989,
year = {2022},
author = {Ma, Q and Wang, Y and Li, S and Wen, J and Zhu, L and Yan, K and Du, Y and Ren, J and Li, S and Chen, Z and Bi, C and Li, Q},
title = {Assembly and comparative analysis of the first complete mitochondrial genome of Acer truncatum Bunge: a woody oil-tree species producing nervonic acid.},
journal = {BMC plant biology},
volume = {22},
number = {1},
pages = {29},
pmid = {35026989},
issn = {1471-2229},
mesh = {Acer/*genetics/*metabolism ; Fatty Acids, Monounsaturated/*metabolism ; Genetic Variation ; *Genome, Mitochondrial ; Phylogeny ; Plant Oils/*metabolism ; Trees/*genetics ; },
abstract = {BACKGROUND: Acer truncatum (purpleblow maple) is a woody tree species that produces seeds with high levels of valuable fatty acids (especially nervonic acid). The species is admired as a landscape plant with high developmental prospects and scientific research value. The A. truncatum chloroplast genome has recently been reported; however, the mitochondrial genome (mitogenome) is still unexplored.<br><br>RESULTS: We characterized the A. truncatum mitogenome, which was assembled using reads from PacBio and Illumina sequencing platforms, performed a comparative analysis against different species of Acer. The circular mitogenome of A. truncatum has a length of 791,052&#x2009;bp, with a base composition of 27.11% A, 27.21% T, 22.79% G, and 22.89% C. The A. truncatum mitogenome contains 62 genes, including 35 protein-coding genes, 23 tRNA genes and 4 rRNA genes. We also examined codon usage, sequence repeats, RNA editing and selective pressure in the A. truncatum mitogenome. To determine the evolutionary and taxonomic status of A. truncatum, we conducted a phylogenetic analysis based on the mitogenomes of A. truncatum and 25 other taxa. In addition, the gene migration from chloroplast and nuclear genomes to the mitogenome were analyzed. Finally, we developed a novel NAD1 intron indel marker for distinguishing several Acer species.<br><br>CONCLUSIONS: In this study, we assembled and annotated the mitogenome of A. truncatum, a woody oil-tree species producing nervonic acid. The results of our analyses provide comprehensive information on the A. truncatum mitogenome, which would facilitate evolutionary research and molecular barcoding in Acer.},
}
@article {pmid35026052,
year = {2022},
author = {Deng, J and Liu, W and Sun, M and Walther, A},
title = {Dissipative Organization of DNA Oligomers for Transient Catalytic Function.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {61},
number = {10},
pages = {e202113477},
pmid = {35026052},
issn = {1521-3773},
abstract = {The development of synthetic non-equilibrium systems opens doors for man-made life-like materials. Yet, creating distinct transient functions from artificial fuel-driven structures remains a challenge. Building on our ATP-driven dynamic covalent DNA assembly in an enzymatic reaction network of concurrent ATP-powered ligation and restriction, we introduce ATP-fueled transient organization of functional subunits for various functions. The programmability of the ligation/restriction site allows to precisely organize multiple sticky-end-encoded oligo segments into double-stranded (ds) DNA complexes. We demonstrate principles of ATP-driven organization into sequence-defined oligomers by sensing barcode-embedded targets with different defects. Furthermore, ATP-fueled DNAzymes for substrate cleavage are achieved by transiently ligating two DNAzyme subunits into a dsDNA complex, rendering ATP-fueled transient catalytic function.},
}
@article {pmid35025214,
year = {2022},
author = {Guo, C and Zhai, J and Wang, Y and Du, X and Wang, Z and Xie, X},
title = {Photoswitch-Based Fluorescence Encoding of Microspheres in a Limited Spectral Window for Multiplexed Detection.},
journal = {Analytical chemistry},
volume = {94},
number = {3},
pages = {1531-1536},
doi = {10.1021/acs.analchem.1c04856},
pmid = {35025214},
issn = {1520-6882},
mesh = {*COVID-19 ; Fluorescent Dyes ; Humans ; Microspheres ; SARS-CoV-2 ; Staining and Labeling ; },
abstract = {Fluorescence barcoding with multicolor fluorophores is limited by spectral crowding. Herein, we propose a fluorescence encoding method in a single-color channel with photoswitches. The photochromic naphthopyran was used to mediate the fluorescence of polystyrene microspheres through resonance energy transfer. The initial fluorescence intensity (F0) and the fluorescence after UV light activation (F/F0) were combined to generate hundreds of 2-dimensional barcodes. The coding capacity was further expanded with the different chemical kinetics of the photoswitches. The photoswitch-based fluorescence barcodes were applied to simultaneously and selectively detect the DNA sequences of COVID-19 (with related mutations) as a proof-of-concept for real applications. The compatibility with the state-of-the-art fluorescence microscopes and simple encoding and decoding make the method very attractive for multiplexed and high-throughput analyses.},
}
@article {pmid35018745,
year = {2022},
author = {Liu, Y and Zhao, K and Ren, Y and Wan, S and Yang, C and Li, J and Wang, F and Chen, C and Su, J and Chen, D and Zhao, Y and Liu, K and Zhang, H},
title = {Highly Plasticized Lanthanide Luminescence for Information Storage and Encryption Applications.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {9},
number = {7},
pages = {e2105108},
pmid = {35018745},
issn = {2198-3844},
support = {2018YFA0902600//National Key R&amp;D Program of China/ ; 2020YFA0712102//National Key R&amp;D Program of China/ ; 21877104//National Natural Science Foundation of China/ ; 21834007//National Natural Science Foundation of China/ ; 21878258//National Natural Science Foundation of China/ ; 22020102003//National Natural Science Foundation of China/ ; 22125701//National Natural Science Foundation of China/ ; GJTD-2018-09//K. C. Wong Education Foundation/ ; 2020M681055//China Postdoctoral Science Foundation/ ; },
abstract = {The development of new storage media to meet the demands for diverse information storage scenarios is a great challenge. Here, a series of lanthanide-based luminescent organogels with ultrastrong mechanical performance and outstanding plasticity are developed for patterned information storage and encryption applications. The organogels possessing outstanding mechanical properties and tunable luminescent colors are prepared by electrostatic and coordinative interactions between natural DNA, synthetic ligands, and rare earth (RE) ions. The organogel-REs can be stretched by 180 times and show an ultrastrong breaking strength of 80 MPa. A series of applications with both information storage and encryption, such as self-information pattern, quick response (QR) code, and barcode, are successfully demonstrated by the organogel-REs. The developed information storage systems have various advantages of good processability, high stretchability, excellent stability, and versatile design of information patterns. Therefore, the organogel-RE-based information storage systems are suitable for applications under different scenarios, such as flexible devices under repeating rude operations. The advancements will enable the design and development of luminescent organogel-REs as information storage and encryption media for various scenarios.},
}
@article {pmid35016204,
year = {2022},
author = {Stalmann, USA and Ticconi, F and Snoeren, IAM and Li, R and Gleitz, HFE and Cowley, GS and McConkey, ME and Wong, AB and Schmitz, S and Fuchs, SNR and Sood, S and Leimkühler, NB and Martinez-Høyer, S and Banjanin, B and Root, D and Brümmendorf, TH and Pearce, JE and Schuppert, A and Bindels, EMJ and Essers, MA and Heckl, D and Stiehl, T and Costa, IG and Ebert, BL and Schneider, RK},
title = {Genetic barcoding systematically compares genes in del(5q) MDS and reveals a central role for CSNK1A1 in clonal expansion.},
journal = {Blood advances},
volume = {6},
number = {6},
pages = {1780-1796},
pmid = {35016204},
issn = {2473-9537},
support = {R01 HL082945/HL/NHLBI NIH HHS/United States ; },
mesh = {*Chromosome Deletion ; Haploinsufficiency ; Hematopoietic Stem Cells/pathology ; Humans ; *Myelodysplastic Syndromes/pathology ; },
abstract = {How genetic haploinsufficiency contributes to the clonal dominance of hematopoietic stem cells (HSCs) in del(5q) myelodysplastic syndrome (MDS) remains unresolved. Using a genetic barcoding strategy, we performed a systematic comparison on genes implicated in the pathogenesis of del(5q) MDS in direct competition with each other and wild-type (WT) cells with single-clone resolution. Csnk1a1 haploinsufficient HSCs expanded (oligo)clonally and outcompeted all other tested genes and combinations. Csnk1a1-/+ multipotent progenitors showed a proproliferative gene signature and HSCs showed a downregulation of inflammatory signaling/immune response. In validation experiments, Csnk1a1-/+ HSCs outperformed their WT counterparts under a chronic inflammation stimulus, also known to be caused by neighboring genes on chromosome 5. We therefore propose a crucial role for Csnk1a1 haploinsufficiency in the selective advantage of 5q-HSCs, implemented by creation of a unique competitive advantage through increased HSC self-renewal and proliferation capacity, as well as increased fitness under inflammatory stress.},
}
@article {pmid35015377,
year = {2022},
author = {Pouchon, C and Boyer, F and Roquet, C and Denoeud, F and Chave, J and Coissac, E and Alsos, IG and , and , and Lavergne, S},
title = {ORTHOSKIM: In silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications.},
journal = {Molecular ecology resources},
volume = {22},
number = {5},
pages = {2018-2037},
doi = {10.1111/1755-0998.13584},
pmid = {35015377},
issn = {1755-0998},
support = {ANR-10-INBS-09-08//Agence Nationale de la Recherche/ ; ANR-16-CE93-0004//Agence Nationale de la Recherche/ ; SNF-310030L_170059//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 14-14//Norwegian Biodiversity Information Centre/ ; 70184209//Norwegian Biodiversity Information Centre/ ; 226134/F50//Norges Forskningsr&#xe5;d/ ; 250963/F20//Norges Forskningsr&#xe5;d/ ; },
mesh = {DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; *Genome, Chloroplast ; Genomics/methods ; Phylogeny ; Sequence Analysis, DNA/methods ; *Transcriptome ; },
abstract = {Low-coverage whole genome shotgun sequencing (or genome skimming) has emerged as a cost-effective method for acquiring genomic data in nonmodel organisms. This method provides sequence information on chloroplast genome (cpDNA), mitochondrial genome (mtDNA) and nuclear ribosomal regions (rDNA), which are over-represented within cells. However, numerous bioinformatic challenges remain to accurately and rapidly obtain such data in organisms with complex genomic structures and rearrangements, in particular for mtDNA in plants or for cpDNA in some plant families. Here we introduce the pipeline ORTHOSKIM, which performs in silico capture of targeted sequences from genomic and transcriptomic libraries without assembling whole organelle genomes. ORTHOSKIM proceeds in three steps: (i) global sequence assembly, (ii) mapping against reference sequences and (iii) target sequence extraction; importantly it also includes a range of quality control tests. Different modes are implemented to capture both coding and noncoding regions of cpDNA, mtDNA and rDNA sequences, along with predefined nuclear sequences (e.g., ultraconserved elements) or collections of single-copy orthologue genes. Moreover, aligned DNA matrices are produced for phylogenetic reconstructions, by performing multiple alignments of the captured sequences. While ORTHOSKIM is suitable for any eukaryote, a case study is presented here, using 114 genome-skimming libraries and four RNA sequencing libraries obtained for two plant families, Primulaceae and Ericaceae, the latter being a well-known problematic family for cpDNA assemblies. ORTHOSKIM recovered with high success rates cpDNA, mtDNA and rDNA sequences, well suited to accurately infer evolutionary relationships within these families. ORTHOSKIM is released under a GPL-3 licence and is available at: https://github.com/cpouchon/ORTHOSKIM.},
}
@article {pmid35014949,
year = {2022},
author = {Gaio, D and Anantanawat, K and To, J and Liu, M and Monahan, L and Darling, AE},
title = {Hackflex: low-cost, high-throughput, Illumina Nextera Flex library construction.},
journal = {Microbial genomics},
volume = {8},
number = {1},
pages = {},
pmid = {35014949},
issn = {2057-5858},
mesh = {Australia ; Bacteria/classification/*genetics ; Base Composition ; DNA, Bacterial/genetics ; Escherichia coli/classification/genetics ; *Gene Library ; High-Throughput Nucleotide Sequencing ; Pseudomonas aeruginosa/classification/genetics ; Sequence Analysis, DNA/*economics/*methods ; Staphylococcus aureus/classification/genetics ; },
abstract = {We developed a low-cost method for the production of Illumina-compatible sequencing libraries that allows up to 14 times more libraries for high-throughput Illumina sequencing to be generated for the same cost. We call this new method Hackflex. The quality of library preparation was tested by constructing libraries from Escherichia coli MG1655 genomic DNA using either Hackflex, standard Nextera Flex (recently renamed as Illumina DNA Prep) or a variation of standard Nextera Flex in which the bead-linked transposase is diluted prior to use. In order to test the library quality for genomes with a higher and a lower G+C content, library construction methods were also tested on Pseudomonas aeruginosa PAO1 and Staphylococcus aureus ATCC 25923, respectively. We demonstrated that Hackflex can produce high-quality libraries and yields a highly uniform coverage, equivalent to the standard Nextera Flex kit. We show that strongly size-selected libraries produce sufficient yield and complexity to support de novo microbial genome assembly, and that assemblies of the large-insert libraries can be much more contiguous than standard libraries without strong size selection. We introduce a new set of sample barcodes that are distinct from standard Illumina barcodes, enabling Hackflex samples to be multiplexed with samples barcoded using standard Illumina kits. Using Hackflex, we were able to achieve a per-sample reagent cost for library prep of A$7.22 (Australian dollars) (US $5.60; UK £3.87, £1=A$1.87), which is 9.87 times lower than the standard Nextera Flex protocol at advertised retail price. An additional simple modification and further simplification of the protocol by omitting the wash step enables a further price reduction to reach an overall 14-fold cost saving. This method will allow researchers to construct more libraries within a given budget, thereby yielding more data and facilitating research programmes where sequencing large numbers of libraries is beneficial.},
}
@article {pmid35013617,
year = {2022},
author = {Quinodoz, SA and Bhat, P and Chovanec, P and Jachowicz, JW and Ollikainen, N and Detmar, E and Soehalim, E and Guttman, M},
title = {SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding.},
journal = {Nature protocols},
volume = {17},
number = {1},
pages = {36-75},
pmid = {35013617},
issn = {1750-2799},
support = {F30 CA247447/CA/NCI NIH HHS/United States ; T32 GM008042/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; U01 HL130007/HL/NHLBI NIH HHS/United States ; DP5 OD012190/OD/NIH HHS/United States ; U01 DA040612/DA/NIDA NIH HHS/United States ; },
mesh = {Animals ; Cell Line ; *Cell Nucleus/genetics/physiology ; *DNA/genetics/metabolism ; DNA Barcoding, Taxonomic/*methods ; Female ; Genetic Techniques ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; Mice ; *Software ; },
abstract = {A fundamental question in gene regulation is how cell-type-specific gene expression is influenced by the packaging of DNA within the nucleus of each cell. We recently developed Split-Pool Recognition of Interactions by Tag Extension (SPRITE), which enables mapping of higher-order interactions within the nucleus. SPRITE works by cross-linking interacting DNA, RNA and protein molecules and then mapping DNA-DNA spatial arrangements through an iterative split-and-pool barcoding method. All DNA molecules within a cross-linked complex are barcoded by repeatedly splitting complexes across a 96-well plate, ligating molecules with a unique tag sequence, and pooling all complexes into a single well before repeating the tagging. Because all molecules in a cross-linked complex are covalently attached, they will sort together throughout each round of split-and-pool and will obtain the same series of SPRITE tags, which we refer to as a barcode. The DNA fragments and their associated barcodes are sequenced, and all reads sharing identical barcodes are matched to reconstruct interactions. SPRITE accurately maps pairwise DNA interactions within the nucleus and measures higher-order spatial contacts occurring among up to thousands of simultaneously interacting molecules. Here, we provide a detailed protocol for the experimental steps of SPRITE, including a video (https://youtu.be/6SdWkBxQGlg). Furthermore, we provide an automated computational pipeline available on GitHub that allows experimenters to seamlessly generate SPRITE interaction matrices starting with raw fastq files. The protocol takes ~5 d from cell cross-linking to high-throughput sequencing for the experimental steps and 1 d for data processing.},
}
@article {pmid35013360,
year = {2022},
author = {Henniges, MC and Powell, RF and Mian, S and Stace, CA and Walker, KJ and Gornall, RJ and Christenhusz, MJM and Brown, MR and Twyford, AD and Hollingsworth, PM and Jones, L and de Vere, N and Antonelli, A and Leitch, AR and Leitch, IJ},
title = {A taxonomic, genetic and ecological data resource for the vascular plants of Britain and Ireland.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {1},
pmid = {35013360},
issn = {2052-4463},
support = {NE/L002485/1//RCUK | Natural Environment Research Council (NERC)/ ; },
mesh = {*Biodiversity ; Databases as Topic ; Ecosystem ; Introduced Species ; Ireland ; Tracheophyta/*classification ; United Kingdom ; },
abstract = {The vascular flora of Britain and Ireland is among the most extensively studied in the world, but the current knowledge base is fragmentary, with taxonomic, ecological and genetic information scattered across different resources. Here we present the first comprehensive data repository of native and alien species optimized for fast and easy online access for ecological, evolutionary and conservation analyses. The inventory is based on the most recent reference flora of Britain and Ireland, with taxon names linked to unique Kew taxon identifiers and DNA barcode data. Our data resource for 3,227 species and 26 traits includes existing and unpublished genome sizes, chromosome numbers and life strategy and life-form assessments, along with existing data on functional traits, species distribution metrics, hybrid propensity, associated biomes, realized niche description, native status and geographic origin of alien species. This resource will facilitate both fundamental and applied research and enhance our understanding of the flora's composition and temporal changes to inform conservation efforts in the face of ongoing climate change and biodiversity loss.},
}
@article {pmid35009140,
year = {2022},
author = {Nazar, N and Howard, C and Slater, A and Sgamma, T},
title = {Challenges in Medicinal and Aromatic Plants DNA Barcoding-Lessons from the Lamiaceae.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {1},
pages = {},
pmid = {35009140},
issn = {2223-7747},
support = {n.a.//Daphne Jackson Trust/ ; },
abstract = {The potential value of DNA barcoding for the identification of medicinal plants and authentication of traded plant materials has been widely recognized; however, a number of challenges remain before DNA methods are fully accepted as an essential quality control method by industry and regulatory authorities. The successes and limitations of conventional DNA barcoding are considered in relation to important members of the Lamiaceae. The mint family (Lamiaceae) contains over one thousand species recorded as having a medicinal use, with many more exploited in food and cosmetics for their aromatic properties. The family is characterized by a diversity of secondary products, most notably the essential oils (EOs) produced in external glandular structures on the aerial parts of the plant that typify well-known plants of the basil (Ocimum), lavender (Lavandula), mint (Mentha), thyme (Thymus), sage (Salvia) and related genera. This complex, species-rich family includes widely cultivated commercial hybrids and endangered wild-harvested traditional medicines, and examples of potential toxic adulterants within the family are explored in detail. The opportunities provided by next generation sequencing technologies to whole plastome barcoding and nuclear genome sequencing are also discussed with relevant examples.},
}
@article {pmid35006470,
year = {2021},
author = {Jiao, Y and Zhou, L and Tao, R and Wang, Y and Hu, Y and Jiang, L and Li, L and Yao, S},
title = {Random-PE: an efficient integration of random sequences into mammalian genome by prime editing.},
journal = {Molecular biomedicine},
volume = {2},
number = {1},
pages = {36},
pmid = {35006470},
issn = {2662-8651},
support = {No. 81771220//National Natural Science Foundation of China/ ; No. 81974238//National Natural Science Foundation of China/ ; ZYJC21018//West China Hospital, Sichuan University/ ; },
abstract = {Prime editing (PE) enables efficiently targeted introduction of multiple types of small-sized genetic change without requiring double-strand breaks or donor templates. Here we designed a simple strategy to introduce random DNA sequences into targeted genomic loci by prime editing, which we named random prime editing (Random-PE). In our strategy, the prime editing guide RNA (pegRNA) was engineered to harbor random sequences between the primer binding sequence (PBS) and homologous arm (HA) of the reverse transcriptase templates. With these pegRNAs, we achieved efficient targeted insertion or substitution of random sequences with different lengths, ranging from 5 to 10, in mammalian cells. Importantly, the diversity of inserted sequences is well preserved. By fine-tuning the design of random sequences, we were able to make simultaneously insertions or substitutions of random sequences in multiple sites, allowing in situ evolution of multiple positions in a given protein. Therefore, these results provide a framework for targeted integration of random sequences into genomes, which can be redirected for manifold applications, such as in situ protospacer adjacent motif (PAM) library construction, enhancer screening, and DNA barcoding.},
}
@article {pmid35005580,
year = {2021},
author = {Viner, I and Bortnikov, F and Ryvarden, L and Miettinen, O},
title = {On six African species of Lyomyces and Xylodon.},
journal = {Fungal systematics and evolution},
volume = {8},
number = {},
pages = {163-178},
pmid = {35005580},
issn = {2589-3831},
abstract = {We studied a number of sub-Saharan collections of corticioid Xylodon and Lyomyces species, including several types. Morphological descriptions and molecular analyses based on the ribosomal DNA loci nuc rDNA ITS1-5.8S-ITS2 and when possible nuc 28S rDNA, allow us to introduce four new species: L. densiusculus, X. angustisporus, X. dissiliens, and X. laxiusculus. DNA barcodes for X. submucronatus and X. pruniaceus are published for the first time and X. pruniaceus is re-described.},
}
@article {pmid35005536,
year = {2022},
author = {Hong, JM and Gibbons, M and Bashir, A and Wu, D and Shao, S and Cutts, Z and Chavarha, M and Chen, Y and Schiff, L and Foster, M and Church, VA and Ching, L and Ahadi, S and Hieu-Thao Le, A and Tran, A and Dimon, M and Coram, M and Williams, B and Jess, P and Berndl, M and Pawlosky, A},
title = {ProtSeq: Toward high-throughput, single-molecule protein sequencing via amino acid conversion into DNA barcodes.},
journal = {iScience},
volume = {25},
number = {1},
pages = {103586},
pmid = {35005536},
issn = {2589-0042},
abstract = {We demonstrate early progress toward constructing a high-throughput, single-molecule protein sequencing technology utilizing barcoded DNA aptamers (binders) to recognize terminal amino acids of peptides (targets) tethered on a next-generation sequencing chip. DNA binders deposit unique, amino acid-identifying barcodes on the chip. The end goal is that, over multiple binding cycles, a sequential chain of DNA barcodes will identify the amino acid sequence of a peptide. Toward this, we demonstrate successful target identification with two sets of target-binder pairs: DNA-DNA and Peptide-Protein. For DNA-DNA binding, we show assembly and sequencing of DNA barcodes over six consecutive binding cycles. Intriguingly, our computational simulation predicts that a small set of semi-selective DNA binders offers significant coverage of the human proteome. Toward this end, we introduce a binder discovery pipeline that ultimately could merge with the chip assay into a technology called ProtSeq, for future high-throughput, single-molecule protein sequencing.},
}
@article {pmid35005084,
year = {2021},
author = {Xu, H and Nottingham, RM and Lambowitz, AM},
title = {TGIRT-seq Protocol for the Comprehensive Profiling of Coding and Non-coding RNA Biotypes in Cellular, Extracellular Vesicle, and Plasma RNAs.},
journal = {Bio-protocol},
volume = {11},
number = {23},
pages = {e4239},
pmid = {35005084},
issn = {2331-8325},
support = {R35 GM136216/GM/NIGMS NIH HHS/United States ; },
abstract = {High-throughput RNA sequencing (RNA-seq) has extraordinarily advanced our understanding of gene expression and disease etiology, and is a powerful tool for the identification of biomarkers in a wide range of organisms. However, most RNA-seq methods rely on retroviral reverse transcriptases (RTs), enzymes that have inherently low fidelity and processivity, to convert RNAs into cDNAs for sequencing. Here, we describe an RNA-seq protocol using Thermostable Group II Intron Reverse Transcriptases (TGIRTs), which have high fidelity, processivity, and strand-displacement activity, as well as a proficient template-switching activity that enables efficient and seamless RNA-seq adapter addition. By combining these activities, TGIRT-seq enables the simultaneous profiling of all RNA biotypes from small amounts of starting material, with superior RNA-seq metrics, and unprecedented ability to sequence structured RNAs. The TGIRT-seq protocol for Illumina sequencing consists of three steps: (i) addition of a 3' RNA-seq adapter, coupled to the initiation of cDNA synthesis at the 3' end of a target RNA, via template switching from a synthetic adapter RNA/DNA starter duplex; (ii) addition of a 5' RNA-seq adapter, by using thermostable 5' App DNA/RNA ligase to ligate an adapter oligonucleotide to the 3' end of the completed cDNA; (iii) minimal PCR amplification, to add capture sites and indices for Illumina sequencing. TGIRT-seq for the Illumina sequencing platform has been used for comprehensive profiling of coding and non-coding RNAs in ribodepleted, chemically fragmented cellular RNAs, and for the analysis of intact (non-chemically fragmented) cellular, extracellular vesicle (EV), and plasma RNAs, where it yields continuous full-length end-to-end sequences of structured small non-coding RNAs (sncRNAs), including tRNAs, snoRNAs, snRNAs, pre-miRNAs, and full-length excised linear intron (FLEXI) RNAs. Graphic abstract: Figure 1.Overview of the TGIRT-seq protocol for Illumina sequencing.Major steps are: (1) Template switching from a synthetic R2 RNA/R2R DNA starter duplex with a 1-nt 3' DNA overhang (a mixture of A, C, G, and T residues, denoted N) that base pairs to the 3' nucleotide of a target RNA, and upon initiating reverse transcription by adding dNTPs, seamlessly links an R2R adapter to the 5' end of the resulting cDNA; (2) Ligation of an R1R adapter to the 3' end of the completed cDNA; and (3) Minimal PCR amplification with primers that add Illumina capture sites (P5 and P7) and barcode sequences (indices 5 and 7). The index 7 barcode is required, while the index 5 barcode is optional, to provide unique dual indices (UDIs).},
}
@article {pmid35003093,
year = {2021},
author = {Wang, Q and Zeng, H and Zhu, Y and Wang, M and Zhang, Y and Yang, X and Tang, H and Li, H and Chen, Y and Ma, C and Lan, C and Liu, B and Yang, W and Yu, X and Zhang, Z},
title = {Dual UMIs and Dual Barcodes With Minimal PCR Amplification Removes Artifacts and Acquires Accurate Antibody Repertoire.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {778298},
pmid = {35003093},
issn = {1664-3224},
mesh = {Antibodies/*analysis/genetics ; Artifacts ; Cells, Cultured ; Gene Library ; Healthy Volunteers ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Leukocytes, Mononuclear ; *Polymerase Chain Reaction ; Primary Cell Culture ; Vaccine Development/methods ; },
abstract = {Antibody repertoire sequencing (Rep-seq) has been widely used to reveal repertoire dynamics and to interrogate antibodies of interest at single nucleotide-level resolution. However, polymerase chain reaction (PCR) amplification introduces extensive artifacts including chimeras and nucleotide errors, leading to false discovery of antibodies and incorrect assessment of somatic hypermutations (SHMs) which subsequently mislead downstream investigations. Here, a novel approach named DUMPArts, which improves the accuracy of antibody repertoires by labeling each sample with dual barcodes and each molecule with dual unique molecular identifiers (UMIs) via minimal PCR amplification to remove artifacts, is developed. Tested by ultra-deep Rep-seq data, DUMPArts removed inter-sample chimeras, which cause artifactual shared clones and constitute approximately 15% of reads in the library, as well as intra-sample chimeras with erroneous SHMs and constituting approximately 20% of the reads, and corrected base errors and amplification biases by consensus building. The removal of these artifacts will provide an accurate assessment of antibody repertoires and benefit related studies, especially mAb discovery and antibody-guided vaccine design.},
}
@article {pmid35002360,
year = {2021},
author = {Mahima, K and Umapathy, S and Sudhakar, JV and Sathishkumar, R},
title = {Systematic reinstatement of highly sacred Ficuskrishnae based on differences in morphology and DNA barcoding from Ficusbenghalensis (Moraceae).},
journal = {PhytoKeys},
volume = {186},
number = {},
pages = {121-138},
pmid = {35002360},
issn = {1314-2011},
abstract = {Ficuskrishnae is considered as native to India and is well-known for the peculiarity in nature of its cup-shaped leaves where both the vernacular name (Krishna Fig) and specific epithet were derived. The taxonomic status of Ficuskrishnae is still unclear and currently treated as a subspecies or variety under Ficusbenghalensis. In the present study, morphological characters and molecular analysis were employed to address their species delimitation. The spacer markers ITS2 and trnH-psbA were used for constructing phylogenetic trees along with morphometric analysis. Ficuskrishnae distinctly differs from Ficusbenghalensis by having cup-forming leaves and the nature of the aerial roots, stipules, petioles, ostiolar bracts of the receptacle, DNA content, chromosome differences and nodal anatomy. The results showed that the highest divergence is observed in trnH-psbA (20.8 ± 12.2), followed by ITS2 (5.7 ± 3.2). The phylogenetic tree construction using Bayesian analysis showed a divergent boundary between the two species suggesting that F.krishnae could be an independent species, not a variety of F.benghalensis. The present study's findings support the view that these two floras can be treated as different species.},
}
@article {pmid35001925,
year = {2021},
author = {Mokhtar, AS and Sahimin, N and Hanapi, IRM and Lau, YL and Zain, SNM and AbuBakar, S and Ya'çob, Z},
title = {Molecular survey of head lice (Pediculus humanus capitis) infestation among disadvantaged children in Klang Valley, Malaysia.},
journal = {Tropical biomedicine},
volume = {38},
number = {4},
pages = {590-593},
doi = {10.47665/tb.38.4.102},
pmid = {35001925},
issn = {2521-9855},
mesh = {Adolescent ; Animals ; Child ; Child, Preschool ; Humans ; *Lice Infestations/epidemiology ; Malaysia/epidemiology ; *Pediculus/genetics ; Surveys and Questionnaires ; Vulnerable Populations ; },
abstract = {Ectoparasitic infestations including pediculosis capitis are common in people of disadvantaged communities as they live in overcrowded institutions, a condition that often favourable for disease transmission. In this study, we evaluated the prevalence of head lice infestation among disadvantaged children aged between five to 14 years-old living in five poor conditions located across the Klang Valley, Malaysia. Of total 335 children examined, 14% were positively infected with head lice. Molecular analysis using the universal cytochrome c oxidase subunit I (COI) barcoding gene on total of 167 head lice collected in this study indicated they are belonging to the A and C clades; confirming the global distribution of clade A and expansion of clade C in Southeast Asia, which is reported for the first time in Malaysia.},
}
@article {pmid35001923,
year = {2021},
author = {Mokhtar, AS and Muslimin, M and Mat-Saat, AY and Ghazali, AM and Ismail, AK and Abdul-Aziz, NM},
title = {Bite envenomation by Latrodectus geometricus (Araneae: Theridiidae) spiders in Malaysia.},
journal = {Tropical biomedicine},
volume = {38},
number = {4},
pages = {568-577},
doi = {10.47665/tb.38.4.100},
pmid = {35001923},
issn = {2521-9855},
mesh = {Animals ; Bites and Stings/*epidemiology ; Humans ; Malaysia/epidemiology ; Male ; *Spiders ; },
abstract = {We report two confirmed human bite cases by Lactrodectus geometricus , also known as the brown widow spider. These are the first reported bite envenomation incidents by L. geometricus in Malaysia. The incidents occurred in Tawau, Sabah and Paka, Terengganu. Both men were bitten on their ear while putting on motorcycle helmets. The spiders appeared to have nested in the helmets. The dead specimens were collected and sent to the Invertebrate and Vertebrate Neurobiology Laboratory, Department of Parasitology, Universiti Malaya for identification. The species identity was confirmed by DNA barcoding.},
}
@article {pmid35001392,
year = {2022},
author = {Chen, Y and Li, S and Wu, W and Geng, S and Mao, M},
title = {Distinct mutations and lineages of SARS-CoV-2 virus in the early phase of COVID-19 pandemic and subsequent 1-year global expansion.},
journal = {Journal of medical virology},
volume = {94},
number = {5},
pages = {2035-2049},
pmid = {35001392},
issn = {1096-9071},
mesh = {*COVID-19/epidemiology/virology ; Cross-Sectional Studies ; *Genome, Viral ; Humans ; Mutation ; Pandemics ; Phylogeny ; *SARS-CoV-2/genetics ; },
abstract = {A novel coronavirus, SARS-CoV-2, has caused over 274 million cases and over 5.3 million deaths worldwide since it occurred in December 2019 in Wuhan, China. Here we conceptualized the temporospatial evolutionary and expansion dynamics of SARS-CoV-2 by taking a series of the cross-sectional view of viral genomes from early outbreak in January 2020 in Wuhan to the early phase of global ignition in early April, and finally to the subsequent global expansion by late December 2020. Based on the phylogenetic analysis of the early patients in Wuhan, Wuhan/WH04/2020 is supposed to be a more appropriate reference genome of SARS-CoV-2, instead of the first sequenced genome Wuhan-Hu-1. By scrutinizing the cases from the very early outbreak, we found a viral genotype from the Seafood Market in Wuhan featured with two concurrent mutations (i.e., M type) had become the overwhelmingly dominant genotype (95.3%) of the pandemic 1 year later. By analyzing 4013 SARS-CoV-2 genomes from different continents by early April, we were able to interrogate the viral genomic composition dynamics of the initial phase of global ignition over a time span of 14 weeks. Eleven major viral genotypes with unique geographic distributions were also identified. WE1 type, a descendant of M and predominantly witnessed in western Europe, consisted of half of all the cases (50.2%) at the time. The mutations of major genotypes at the same hierarchical level were mutually exclusive, which implies that various genotypes bearing the specific mutations were propagated during human-to-human transmission, not by accumulating hot-spot mutations during the replication of individual viral genomes. As the pandemic was unfolding, we also used the same approach to analyze 261 323 SARS-CoV-2 genomes from the world since the outbreak in Wuhan (i.e., including all the publicly available viral genomes) to recapitulate our findings over 1-year time span. By December 25, 2020, 95.3% of global cases were M type and 93.0% of M-type cases were WE1. In fact, at present all the five variants of concern (VOC) are the descendants of WE1 type. This study demonstrates that viral genotypes can be utilized as molecular barcodes in combination with epidemiologic data to monitor the spreading routes of the pandemic and evaluate the effectiveness of control measures. Moreover, the dynamics of viral mutational spectrum in the study may help the early identification of new strains in patients to reduce further spread of infection, guide the development of molecular diagnosis and vaccines against COVID-19, and help assess their accuracy and efficacy in real world at real time.},
}
@article {pmid34998185,
year = {2022},
author = {Lee, SL and Zakaria, NF and Tnah, LH and Ng, CH and Ng, KKS and Lee, CT and Lau, KH and Chua, LSL},
title = {DNA databases of a CITES listed species Aquilaria malaccensis (Thymelaeaceae) as the tracking tools for forensic identification and chain of custody certification.},
journal = {Forensic science international. Genetics},
volume = {57},
number = {},
pages = {102658},
doi = {10.1016/j.fsigen.2021.102658},
pmid = {34998185},
issn = {1878-0326},
mesh = {Bayes Theorem ; Certification ; DNA, Chloroplast/genetics ; Databases, Nucleic Acid ; Humans ; *Thymelaeaceae/genetics ; },
abstract = {Aquilaria malaccensis (Thymelaeaceae) is the main source of high-grade agarwood in Southeast Asia. Aggressive collections and trade activities over the past decades have put great pressure on the natural stands and raised concerns over the long-term survival potential of A. malaccensis. Tracking and authentication of agarwood require method with a high degree of accuracy. Therefore, this study aimed to develop DNA databases of A. malaccensis as the tracking tools at species, population and individual levels for forensic identification and chain of custody certification. Using two cpDNA (rbcL and matK) and an rDNA (ITS2) markers, species identification database of Aquilaria was developed to distinguish A. malaccensis from A. hirta, A. microcarpa, A. beccariana, A. crassna, A. sinensis and A. rostrata. In addition, based on 35 populations of A. malaccensis throughout Peninsular Malaysia, cpDNA haplotype and STR allele frequency databases were developed for population and individual identification. A haplotype distribution map based on 29 haplotypes derived from seven cpDNA showed that the A. malaccensis in Peninsular Malaysia can be associated to Kedah-Perak and Kelantan-Johor regions. Similarly, genetic relatedness and Bayesian clustering analyses based on 10 STR markers also divided the 35 populations into two main genetic clusters, corresponding to Kedah-Perak and Kelantan-Johor regions. The STR allele frequency databases were established and characterized according to these two regions. To determine the performance of the STR allele frequency databases for population identification, independent self-assignment tests showed that the percentage of individuals correctly assigned into the origin population was 93.88% in Kedah-Perak and 90.29% in Kelantan-Johor. For the STR allele frequency databases to be used for individual identification, conservativeness tests showed that the θ should be adjusted to 0.250 and 0.200 in the Kedah-Perak and Kelantan-Johor databases, respectively. To ensure consistency in allele calling for the dinucleotide repeat loci across different electrophoretic platforms or laboratories, allelic ladders have been developed for the 10 STR loci. Two case studies are presented of how these databases were used to track A. malaccensis to the origin population and stump. These databases are ready to be used to provide admissible forensic evidence for legal proceedings against the illegal harvesters of agarwood and for agarwood certification to meet the consumer country regulations.},
}
@article {pmid34997305,
year = {2022},
author = {Ragot, R and Villemur, R},
title = {eDNA profiling of mammals, birds, and fish of surface waters by mitochondrial metagenomics: application for source tracking of fecal contamination in surface waters.},
journal = {Environmental monitoring and assessment},
volume = {194},
number = {2},
pages = {72},
pmid = {34997305},
issn = {1573-2959},
support = {RGPIN-2016-06061//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; Birds ; Cattle ; *DNA, Environmental ; DNA, Mitochondrial ; Ecosystem ; Environmental Monitoring ; Feces ; Fishes/genetics ; Humans ; Mammals/genetics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Knowing the composition of animals present in aquatic ecosystems can tell us about the anthropic pressures on these environments. One of these pressures is the occurrence of fecal contamination. However, this contamination can originate from more than one animal species in areas where urban and agricultural activities overlap. Mitochondrial DNA (mtDNA) has become the standard barcoding tool to identify the presence of animal species in environment. Amplicon-sequencing metagenomics is a powerful approach to derive the animal profile in an environment. However, PCR primers targeting mtDNA of a broad range of animals are highly degenerate or generate short DNA fragments that could cause ambiguous affiliation. Here we report the development of a new set of primers targeting the mitochondrial 16S ribosomal RNA genes of a broad range of terrestrial and aquatic animals, which include mammals, birds, and fishes. These primers successfully amplified mtDNA from environmental DNA (eDNA) extracted from surface waters. Sequencing the resulting amplicons revealed the presence of mammals and birds that may contribute in fecal contamination of surface water. In one of the river samples high in fecal indicator bacteria, human and bovine mtDNA accounted for 40.5% and 4.1% of the sequences, respectively, suggesting fecal contamination by these two animals. These findings indicate that our PCR primers coupled with amplicon-sequencing metagenomics contribute in profiling the animal diversity in the surface waters and its surrounding. This approach could be a valuable tool to identify simultaneously the potential contribution of various animals as sources of fecal contamination in surface waters.},
}
@article {pmid34997149,
year = {2022},
author = {Cross, DE and Healey, AJE and McKeown, NJ and Thomas, CJ and Macarie, NA and Siaziyu, V and Singini, D and Liywalii, F and Sakala, J and Silumesii, A and Shaw, PW},
title = {Temporally consistent predominance and distribution of secondary malaria vectors in the Anopheles community of the upper Zambezi floodplain.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {240},
pmid = {34997149},
issn = {2045-2322},
support = {NE/P013481/1//Natural Environment Research Council/ ; NE/P013481/1//Natural Environment Research Council/ ; },
mesh = {Animal Distribution ; Animals ; Anopheles/classification/*genetics/growth &amp; development/physiology ; Female ; Floods ; Larva/genetics/growth &amp; development/physiology ; Malaria ; Male ; Mosquito Control ; Mosquito Vectors/classification/*genetics/growth &amp; development/physiology ; Phylogeny ; Seasons ; Zambia ; },
abstract = {Regional optimisation of malaria vector control approaches requires detailed understanding both of the species composition of Anopheles mosquito communities, and how they vary over spatial and temporal scales. Knowledge of vector community dynamics is particularly important in settings where ecohydrological conditions fluctuate seasonally and inter-annually, such as the Barotse floodplain of the upper Zambezi river. DNA barcoding of anopheline larvae sampled in the 2019 wet season revealed the predominance of secondary vector species, with An. coustani comprising > 80% of sampled larvae and distributed ubiquitously across all ecological zones. Extensive larval sampling, plus a smaller survey of adult mosquitoes, identified geographic clusters of primary vectors, but represented only 2% of anopheline larvae. Comparisons with larval surveys in 2017/2018 and a contemporaneous independent 5-year dataset from adult trapping corroborated this paucity of primary vectors across years, and the consistent numerical dominance of An. coustani and other secondary vectors in both dry and wet seasons, despite substantial inter-annual variation in hydrological conditions. This marked temporal consistency of spatial distribution and anopheline community composition presents an opportunity to target predominant secondary vectors outdoors. Larval source management should be considered, alongside prevalent indoor-based approaches, amongst a diversification of vector control approaches to more effectively combat residual malaria transmission.},
}
@article {pmid34995484,
year = {2022},
author = {Feng, J and Qian, Y and Zhou, Z and Ertmer, S and Vivas, EI and Lan, F and Hamilton, JJ and Rey, FE and Anantharaman, K and Venturelli, OS},
title = {Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions.},
journal = {Cell host &amp; microbe},
volume = {30},
number = {2},
pages = {200-215.e12},
pmid = {34995484},
issn = {1934-6069},
support = {R01 EB030340/EB/NIBIB NIH HHS/United States ; R35 GM124774/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Bacterial Proteins/metabolism ; Bacteroides/genetics/metabolism ; *Gastrointestinal Microbiome/genetics ; Genes, Bacterial ; *Genetic Fitness ; Humans ; Mice ; Polysaccharides/metabolism ; },
abstract = {Polysaccharide utilization loci (PULs) are co-regulated bacterial genes that sense nutrients and enable glycan digestion. Human gut microbiome members, notably Bacteroides, contain numerous PULs that enable glycan utilization and shape ecological dynamics. To investigate the role of PULs on fitness and inter-species interactions, we develop a CRISPR-based genome editing tool to study 23 PULs in Bacteroides uniformis (BU). BU PULs show distinct glycan-degrading functions and transcriptional coordination that enables the population to adapt upon loss of other PULs. Exploiting a BU mutant barcoding strategy, we demonstrate that in vitro fitness and BU colonization in the murine gut are enhanced by deletion of specific PULs and modulated by glycan availability. PULs mediate glycan-dependent interactions with butyrate producers that depend on the degradation mechanism and glycan utilization ability of the butyrate producer. Thus, PULs determine community dynamics and butyrate production and provide a selective advantage or disadvantage depending on the nutritional landscape.},
}
@article {pmid34995403,
year = {2022},
author = {Abouabdallah, MA and Peyrard, N and Franc, A},
title = {Does clustering of DNA barcodes agree with botanical classification directly at high taxonomic levels? Trees in French Guiana as a case study.},
journal = {Molecular ecology resources},
volume = {22},
number = {5},
pages = {1746-1761},
doi = {10.1111/1755-0998.13579},
pmid = {34995403},
issn = {1755-0998},
support = {//INRAE/ ; ANR-10-LABX-25-01//Agence Nationale de la Recherche/ ; //Institut national de recherche en informatique et en automatique (INRIA)/ ; },
mesh = {Biodiversity ; Cluster Analysis ; *DNA Barcoding, Taxonomic/methods ; French Guiana ; Humans ; Phylogeny ; *Trees/genetics ; },
abstract = {Characterizing biodiversity is one of the main challenges for the coming decades. Most diversity has not been morphologically described, and barcoding is now complementing morphological-based taxonomy to further develop inventories. Both approaches have been cross-validated at the level of species and OTUs. However, many known species are not listed in reference databases. One path to speed up inventories using barcoding is to directly identify individuals at coarser taxonomic levels. We therefore studied in barcoding of plants whether morphological-based and molecular-based approaches are in agreement at genus, family and order levels. We used Agglomerative Hierarchical Clustering (with Ward, Complete and Single Linkage) and Stochastic Block Models (SBM), with two dissimilarity measures (Smith-Waterman scores, kmers). The agreement between morphological-based and molecular-based classifications ranges in most of the cases from good to very good at taxonomic levels above species, even though it decreases when taxonomic levels increase, or when using the tetramer-based distance. Agreement is correlated with the entropy of morphological-based classification and with the ratio of the mean within- and mean between-groups dissimilarities. The Ward method globally leads to the best agreement, whereas Single Linkage can show poor behaviours. SBM provides a useful tool to test whether or not the dissimilarities are structured by the botanical groups. These results suggest that automatic clustering and group identification at taxonomic levels above species are possible in barcoding.},
}
@article {pmid34995351,
year = {2022},
author = {Tang, Q and Luo, QI and Duan, Q and Deng, L and Zhang, R},
title = {DNA Barcode Identification of Fish Products from Guiyang Markets in Southwestern People's Republic of China.},
journal = {Journal of food protection},
volume = {85},
number = {4},
pages = {583-590},
doi = {10.4315/JFP-21-258},
pmid = {34995351},
issn = {1944-9097},
mesh = {Animals ; China ; *Conservation of Natural Resources ; DNA ; *DNA Barcoding, Taxonomic/methods ; Fish Products/analysis ; Fisheries ; Fishes ; Humans ; Phylogeny ; },
abstract = {ABSTRACT: Global fish consumption is increasing in tandem with population growth, resulting in the dilemma of overfishing. Overfished high-value fish are often replaced with other fish in markets. Therefore, the accurate identification of fish products in the market is important. In this study, full-DNA and mini-DNA barcoding were used to detect fish product fraud in Guiyang, Guizhou Province, People's Republic of China. The molecular results revealed that 39 (20.42%) of the 191 samples were inconsistent with the labels. The percentages of mislabeling of fresh, frozen, cooked, and canned fish products were 11.70, 20.00, 34.09, and 50.00%, respectively. The average Kimura two-parameter distances of mini-DNA barcoding within species and within genera were 0.56 and 6.42%, respectively, and those of full-DNA barcoding were 0.53 and 7.25%, respectively. Commercial fraud was evident in this study; most high-priced fish were replaced with low-priced fish with similar features. Our findings indicate that DNA barcoding is an effective tool for identifying fish products and could be used to enhance transparency and fair trade in domestic fisheries.},
}
@article {pmid34994123,
year = {2021},
author = {Wei, XP and Dong, YQ and Qiang, TY and Li, WJ and Song, YC and Zhang, BG and Zhang, Z and Huot, T and Liu, HT and Qi, YD},
title = {[Molecular identification and efficacy analysis of herbs at Orussey Herbal Market, Phnom Penh, Cambodia].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {46},
number = {24},
pages = {6312-6322},
doi = {10.19540/j.cnki.cjcmm.20211014.101},
pmid = {34994123},
issn = {1001-5302},
mesh = {Cambodia ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Humans ; Plant Leaves ; *Plants, Medicinal/genetics ; },
abstract = {Cambodia is rich in medicinal plant resources. One hundred and thirty-three medicinal material samples, including the hole herb, root, stem/branch, leaf, flower, fruit, seed, and resin, were collected from the Orussey Herbal Market in Phnom Penh, Cambodia, and then authenticated by ITS and psbA-trnH. A total of 46 samples were identified based on ITS sequences, belonging to 24 families, 40 genera, and 42 species. A total of 100 samples were identified by psbA-trnH sequences to belong to 42 families, 77 genera, and 84 species. A total of 103 samples were identified by two DNA barcodes. According to the morphological characteristics of the medicinal materials, 120 samples classified into 50 species, 86 genera, and 86 families were identified, and the majority of them were from Zingiberaceae, Fabaceae, and Acanthaceae. Such samples have been commonly used in traditional Cambodian medicine, Ayurvedic medicine, Unani medicine, traditional Chinese medicine, and ethnomedicine, but different medical systems focus on different functional aspects of the same medicinal material. The results of this study have demonstrated that DNA barcoding has a significant advantage in identifying herbal products, and this study has provided basic data for understanding the traditional medicinal materials used in Cambodia.},
}
@article {pmid34993702,
year = {2022},
author = {Minasiewicz, J and Krawczyk, E and Znaniecka, J and Vincenot, L and Zheleznaya, E and Korybut-Orlowska, J and Kull, T and Selosse, MA},
title = {Weak population spatial genetic structure and low infraspecific specificity for fungal partners in the rare mycoheterotrophic orchid Epipogium aphyllum.},
journal = {Journal of plant research},
volume = {135},
number = {2},
pages = {275-293},
pmid = {34993702},
issn = {1618-0860},
support = {2011/03/N/NZ8/02847//Narodowym Centrum Nauki/ ; WFO&#x15a;/D/210/131/2011//Wojew&#xf3;dzki Fundusz Ochrony &#x15a;rodowiska i Gospodarki Wodnej w Gda&#x144;sku/ ; },
mesh = {Bayes Theorem ; Genetic Structures ; *Mycorrhizae/genetics ; *Orchidaceae/genetics/microbiology ; Phylogeny ; Plants/genetics ; Symbiosis/genetics ; },
abstract = {Some plants abandoned photosynthesis and developed full dependency on fungi for nutrition. Most of the so-called mycoheterotrophic plants exhibit high specificity towards their fungal partners. We tested whether natural rarity of mycoheterotrophic plants and usual small and fluctuating population size make their populations more prone to genetic differentiation caused by restricted gene flow and/or genetic drift. We also tested whether these genetic characteristics might in turn shape divergent fungal preferences. We studied the mycoheterotrophic orchid Epipogium aphyllum, addressing the joint issues of genetic structure of its populations over Europe and possible consequences for mycorrhizal specificity within the associated fungal taxa. Out of 27 sampled E. aphyllum populations, nine were included for genetic diversity assessment using nine nuclear microsatellites and plastid DNA. Population genetic structure was inferred based on the total number of populations. Individuals from 17 locations were included into analysis of genetic identity of mycorrhizal fungi of E. aphyllum based on barcoding by nuclear ribosomal DNA. Epipogium aphyllum populations revealed high genetic diversity (uHe = 0.562) and low genetic differentiation over vast distances (FST = 0.106 for nuclear microsatellites and FST = 0.156 for plastid DNA). Bayesian clustering analyses identified only two genetic clusters, with a high degree of admixture. Epipogium aphyllum genets arise from panmixia and display locally variable, but relatively high production of ramets, as shown by a low value of rarefied genotypic richness (Rr = 0.265). Epipogium aphyllum genotype control over partner selection was negligible as (1) we found ramets from a single genetic individual associated with up to 68% of the known Inocybe spp. associating with the plant species, (2) and partner identity did not show any geographic structure. The absence of mosaicism in the mycorrhizal specificity over Europe may be linked to preferential allogamous habit of E. aphyllum and significant gene flow, which tend to promote host generalism.},
}
@article {pmid34991482,
year = {2022},
author = {Yang, J and Hu, G and Hu, G},
title = {Comparative genomics and phylogenetic relationships of two endemic and endangered species (Handeliodendron bodinieri and Eurycorymbus cavaleriei) of two monotypic genera within Sapindales.},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {27},
pmid = {34991482},
issn = {1471-2164},
mesh = {Animals ; Endangered Species ; *Genome, Chloroplast ; Genomics ; Phylogeny ; *Sapindaceae/genetics ; },
abstract = {BACKGROUND: Handeliodendron Rehder and Eurycorymbus Hand.-Mazz. are the monotypic genera in the Sapindaceae family. The phylogenetic relationship of these endangered species Handeliodendron bodinieri (Lévl.) Rehd. and Eurycorymbus cavaleriei (Lévl.) Rehd. et Hand.-Mazz. with other members of Sapindaceae s.l. is not well resolved. A previous study concluded that the genus Aesculus might be paraphyletic because Handeliodendron was nested within it based on small DNA fragments. Thus, their chloroplast genomic information and comparative genomic analysis with other Sapindaceae species are necessary and crucial to understand the circumscription and plastome evolution of this family.<br><br>RESULTS: The chloroplast genome sizes of Handeliodendron bodinieri and Eurycorymbus cavaleriei are 151,271 and 158,690&#x2009;bp, respectively. Results showed that a total of 114 unique genes were annotated in H. bodinieri and E. cavaleriei, and the ycf1 gene contained abundant SSRs in both genomes. Comparative analysis revealed that gene content, PCGs, and total GC content were remarkably similar or identical within 13 genera from Sapindaceae, and the chloroplast genome size of four genera was generally smaller within the family, including Acer, Dipteronia, Aesculus, and Handeliodendron. IR boundaries of the H. bodinieri showed a significant contraction, whereas it presented a notable expansion in E. cavaleriei cp genome. Ycf1, ndhC-trnV-UAC, and rpl32-trnL-UAG-ccsA were remarkably divergent regions in the Sapindaceae species. Analysis of selection pressure showed that there are a few positively selected genes. Phylogenetic analysis based on different datasets, including whole chloroplast genome sequences, coding sequences, large single-copy, small single-copy, and inverted repeat regions, consistently demonstrated that H. bodinieri was sister to the clade consisting of Aesculus chinensis and A. wangii and strongly support Eurycorymbus cavaleriei as sister to Dodonaea viscosa.<br><br>CONCLUSION: This study revealed that the cp genome size of the Hippocastanoideae was generally smaller compared to the other subfamilies within Sapindaceae, and three highly divergent regions could be used as the specific DNA barcodes within Sapindaceae. Phylogenetic results strongly support that the subdivision of four subfamilies within Sapindaceae, and Handeliodendron is not nested within the genus Aesculus.},
}
@article {pmid34985054,
year = {2022},
author = {Ji, DD and Wu, MX and Ding, SN},
title = {Photonic crystal barcodes assembled from dendritic silica nanoparticles for the multiplex immunoassays of ovarian cancer biomarkers.},
journal = {Analytical methods : advancing methods and applications},
volume = {14},
number = {3},
pages = {298-305},
doi = {10.1039/d1ay01658j},
pmid = {34985054},
issn = {1759-9679},
mesh = {Biomarkers, Tumor ; *Cadmium Compounds ; Humans ; Immunoassay/methods ; *Nanoparticles ; *Ovarian Neoplasms/diagnosis ; *Quantum Dots ; Reproducibility of Results ; Silicon Dioxide/chemistry ; Tellurium ; },
abstract = {The combined detection of CA125, CEA and AFP is of great significance in the diagnosis of ovarian cancer. Photonic crystal (PhC) barcodes have apparent advantages in multiplex immunoassays of ovarian cancer markers. In this paper, a novel PhC barcode was assembled from dendritic silica nanoparticles (dSiO2) for multiplex detection of ovarian cancer biomarkers. The interconnected macroporous structure of the dSiO2 PhC beads and the open porous topography of dendritic silica particles could increase the surface area to volume ratio for antibody immobilization. We simultaneously detected multiple ovarian cancer markers in one test tube using the sandwich immunization method by utilizing dSiO2 PhC beads as a barcode and CdTe QDs as a detection signal. The detection limits of the three ovarian cancer markers, AFP, CEA and CA125, were 0.52 ng mL[-1], 0.64 ng mL[-1] and 0.79 U mL[-1], respectively (the signal-to-noise ratio was 3). Compared with the classic silica colloidal crystal bead (SCCB) suspension array, the sensitivity of the dSiO2 PhC bead suspension array was increased. In addition, the results showed that this barcode suspension array had acceptable accuracy and good reproducibility.},
}
@article {pmid34983744,
year = {2022},
author = {Oehm, AW and Jaeger, L and Stoll, A and Knubben-Schweizer, G and Jaeger-Scheuerle, MC},
title = {Setaria tundra in a roe deer (Capreolus capreolus) in the Donau-Ries district of Bavaria, Germany.},
journal = {Schweizer Archiv fur Tierheilkunde},
volume = {164},
number = {1},
pages = {107-111},
doi = {10.17236/sat00341},
pmid = {34983744},
issn = {1664-2848},
mesh = {Animals ; *Deer ; Germany/epidemiology ; Male ; *Reindeer ; *Setaria Nematode ; Tundra ; },
abstract = {Setaria tundra is known as a common parasite of sylvatic ungulates in Northern latitudes. Although mostly considered of low pathogenicity, severe disease outbreaks and remarkable economic losses have been observed in reindeer (Rangifer tarandus tarandus). Host density and climatic factors are major drivers of the expansion of Setaria spp. facilitating their development and spread. Five adult specimens of S. tundra were retrieved from a male roe deer in Bavaria, Germany. Deoxyribonucleic acid (DNA) barcoding confirmed morphological identification. Cyclooxygenase 1 gene sequences showed 98,73-99,68 % similarity to sequences of other S. tundra specimens found in deer (Cervidae) and mosquitoes (Culicidae). The results raise awareness for the presence of S. tundra in a hitherto unkown endemic region and represent a starting point for broader investigations to understand the biology and distribution of this parasite in roe deer as well as other potential definitive hosts.},
}
@article {pmid34982802,
year = {2022},
author = {Mariac, C and Duponchelle, F and Miranda, G and Ramallo, C and Wallace, R and Tarifa, G and Garcia-Davila, C and Ortega, H and Pinto, J and Renno, JF},
title = {Unveiling biogeographical patterns of the ichthyofauna in the Tuichi basin, a biodiversity hotspot in the Bolivian Amazon, using environmental DNA.},
journal = {PloS one},
volume = {17},
number = {1},
pages = {e0262357},
pmid = {34982802},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; Brazil ; *Conservation of Natural Resources ; DNA Barcoding, Taxonomic/*methods ; DNA, Environmental/*analysis/genetics ; *Ecosystem ; Environmental Monitoring/*methods ; Fishes/*genetics/growth &amp; development ; Seasons ; },
abstract = {To date, more than 2400 valid fish species have been recorded in the Amazon basin. However, some regions remain poorly documented. This is the case in the Beni basin and in particular in one of its main sub-basins, the Tuichi, an Andean foothills rivers flowing through the Madidi National Park in the Bolivian Amazonia. The knowledge of its ichthyological diversity is, however, essential for the management and protection of aquatic ecosystems, which are threatened by the development of infrastructures (dams, factories and cities), mining and deforestation. Environmental DNA (eDNA) has been relatively little used so far in the Amazon basin. We sampled eDNA from water in 34 sites in lakes and rivers in the Beni basin including 22 sites in the Tuichi sub-basin, during the dry season. To assess the biogeographical patterns of the amazonian ichthyofauna, we implemented a metabarcoding approach using two pairs of specific primers designed and developed in our laboratory to amplify two partially overlapping CO1 fragments, one of 185bp and another of 285bp. We detected 252 fish taxa (207 at species level) among which 57 are newly identified for the Beni watershed. Species compositions are significantly different between lakes and rivers but also between rivers according to their hydrographic rank and altitude. Furthermore, the diversity patterns are related to the different hydro-ecoregions through which the Tuichi flows. The eDNA approach makes it possible to identify and complete the inventory of the ichthyofauna in this still poorly documented Amazon basin. However, taxonomic identification remains constrained by the lack of reference barcodes in public databases and does not allow the assignment of all OTUs. Our results can be taken into account in conservation and management strategies and could serve as a baseline for future studies, including on other Andean tributaries.},
}
@article {pmid34981337,
year = {2022},
author = {Idnan, M and Mansoor, S and Khawar, MB and Javid, A and Hussain, A and Imran, M and Ullah, A},
title = {Range extension and species confirmation of Rhyneptesicus nasutus (Sind Serotine Bat) (Mammalia:Chiroptera) from Bajaur Agency, FATA, Pakistan.},
journal = {Molecular biology reports},
volume = {49},
number = {3},
pages = {1791-1797},
pmid = {34981337},
issn = {1573-4978},
mesh = {Animals ; *Chiroptera/genetics ; Cytochromes b/genetics ; Iran ; Pakistan ; Phylogeny ; },
abstract = {BACKGROUND: The lack of morphological differentiation among chiropteran species and cryptic speciation impedes species identification. DNA-based approaches help species identification and contribute to the discovery of additional species. Rhyneptesicus nasutus (Sind Serotine Bat) is a rare and poorly studied species in Pakistan.<br><br>METHODS: This study explores the range extension of Sind Bat within the territorial limits of Pakistan from Sind and Baluchistan to Federally Administered Areas of Pakistan. No molecular record exists for the species in Pakistan. In the present study, we for the first time confirm species identification of Rhyneptesicus nasutus from Pakistan using a genetic marker (cytochrome b) along with morphometric analysis. A neighbor-joining tree based on Kimura-2 parameters was created to infer phylogenetic relationships. We sequenced the cytochrome b gene segment and conducted a phylogenetic analysis with previously published data from other countries.<br><br>RESULTS: Sequences from Pakistan formed a clade with Iranian Rhyneptesicus nasutus specimens suggesting a common ancestry. Various morphometric parameters (mean values) were measured, including Head and Body length (44.3&#xa0;mm), Tail length (43.4&#xa0;mm), Hindfoot length (8.3&#xa0;mm), Forearm length (35.7&#xa0;mm), and Ear length 36&#xa0;mm while 5th Metacarpal Length, 4th Metacarpal Length, and 3rd Metacarpal Lengths were 33.2&#xa0;mm, 34.7&#xa0;mm, and 35.3&#xa0;mm. Approaches based on DNA barcoding reveal a high diversity of bat species in the study area.<br><br>CONCLUSION: The data will enable researchers to build an improved evolutionary framework of the Serotine Bats from this region and subsequently reconstruct a detailed evolutionary history of the genus. Further research is required to test other molecular markers to support the findings of the current study in Pakistan.},
}
@article {pmid34981190,
year = {2022},
author = {Thanni, B and Merckx, R and De Bauw, P and Boeraeve, M and Peeters, G and Hauser, S and Honnay, O},
title = {Spatial variability and environmental drivers of cassava-arbuscular mycorrhiza fungi (AMF) associations across Southern Nigeria.},
journal = {Mycorrhiza},
volume = {32},
number = {1},
pages = {1-13},
pmid = {34981190},
issn = {1432-1890},
mesh = {Biodiversity ; Fungi ; *Manihot ; *Mycorrhizae ; Nigeria ; Plant Roots ; Soil ; Soil Microbiology ; },
abstract = {Cassava, forming starch-rich, tuberous roots, is an important staple crop in smallholder farming systems in sub-Saharan Africa. Its relatively good tolerance to drought and nutrient-poor soils may be partly attributed to the crop's association with arbuscular mycorrhiza fungi (AMF). Yet insights into AMF-community composition and richness of cassava, and knowledge of its environmental drivers are still limited. Here, we sampled 60 cassava fields across three major cassava-growing agro-ecological zones in Nigeria and used a DNA meta-barcoding approach to quantify large-scale spatial variation and evaluate the effects of soil characteristics and common agricultural practices on AMF community composition, richness and Shannon diversity. We identified 515 AMF operational taxonomic units (OTUs), dominated by Glomus, with large variation across agro-ecological zones, and with soil pH explaining most of the variation in AMF community composition. High levels of soil available phosphorus reduced OTU richness without affecting Shannon diversity. Long fallow periods (> 5 years) reduced AMF richness compared with short fallows, whereas both zero tillage and tractor tillage reduced AMF diversity compared with hoe tillage. This study reveals that the symbiotic relationship between cassava and AMF is strongly influenced by soil characteristics and agricultural management and that it is possible to adjust cassava cultivation practices to modify AMF diversity and community structure.},
}
@article {pmid34979934,
year = {2022},
author = {Adolfo, LM and Rao, X and Dixon, RA},
title = {Identification of Pueraria spp. through DNA barcoding and comparative transcriptomics.},
journal = {BMC plant biology},
volume = {22},
number = {1},
pages = {10},
pmid = {34979934},
issn = {1471-2229},
mesh = {*DNA Barcoding, Taxonomic ; Gene Expression Profiling ; Isoflavones/*analysis ; Plant Roots/chemistry ; Plant Weeds/*classification/genetics ; Pueraria/*classification/genetics ; *Transcriptome ; },
abstract = {BACKGROUND: Kudzu is a term used generically to describe members of the genus Pueraria. Kudzu roots have been used for centuries in traditional Chinese medicine in view of their high levels of beneficial isoflavones including the unique 8-C-glycoside of daidzein, puerarin. In the US, kudzu is seen as a noxious weed causing ecological and economic damage. However, not all kudzu species make puerarin or are equally invasive. Kudzu remains difficult to identify due to its diverse morphology and inconsistent nomenclature.<br><br>RESULTS: We have generated sequences for the internal transcribed spacer 2 (ITS2) and maturase K (matK) regions of Pueraria montana lobata, P. montana montana, and P. phaseoloides, and identified two accessions previously used for differential analysis of puerarin biosynthesis as P. lobata and P. phaseoloides. Additionally, we have generated root transcriptomes for the puerarin-producing P. m. lobata and the non-puerarin producing P. phaseoloides. Within the transcriptomes, microsatellites were identified to aid in species identification as well as population diversity.<br><br>CONCLUSIONS: The barcode sequences generated will aid in fast and efficient identification of the three kudzu species. Additionally, the microsatellites identified from the transcriptomes will aid in genetic analysis. The root transcriptomes also provide a molecular toolkit for comparative gene expression analysis towards elucidation of the biosynthesis of kudzu phytochemicals.},
}
@article {pmid34975990,
year = {2021},
author = {Fan, Y and Jin, Y and Ding, M and Tang, Y and Cheng, J and Zhang, K and Zhou, M},
title = {The Complete Chloroplast Genome Sequences of Eight Fagopyrum Species: Insights Into Genome Evolution and Phylogenetic Relationships.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {799904},
pmid = {34975990},
issn = {1664-462X},
abstract = {Buckwheat (Fagopyrum genus, Polygonaceae), is an annual or perennial, herbaceous or semi-shrub dicotyledonous plant. There are mainly three cultivated buckwheat species, common buckwheat (Fagopyrum esculentum) is widely cultivated in Asia, Europe, and America, while Tartary buckwheat (F. tataricum) and F. cymosum (also known as F. dibotrys) are mainly cultivated in China. The genus Fagopyrum is taxonomically confusing due to the complex phenotypes of different Fagopyrum species. In this study, the chloroplast (cp) genomes of three Fagopyrum species, F. longistylum, F. leptopodum, F. urophyllum, were sequenced, and five published cp genomes of Fagopyrum were retrieved for comparative analyses. We determined the sequence differentiation, repeated sequences of the cp genomes, and the phylogeny of Fagopyrum species. The eight cp genomes ranged, gene number, gene order, and GC content were presented. Most of variations of Fagopyrum species cp genomes existed in the LSC and SSC regions. Among eight Fagopyrum chloroplast genomes, six variable regions (ndhF-rpl32, trnS-trnG, trnC, trnE-trnT, psbD, and trnV) were detected as promising DNA barcodes. In addition, a total of 66 different SSR (simple sequence repeats) types were found in the eight Fagopyrum species, ranging from 8 to 16 bp. Interestingly, many SSRs showed significant differences especially in some photosystem genes, which provided valuable information for understanding the differences in light adaptation among different Fagopyrum species. Genus Fagopyrum has shown a typical branch that is distinguished from the Rumex, Rheum, and Reynoutria, which supports the unique taxonomic status in Fagopyrum among the Polygonaceae. In addition, phylogenetic analysis based on the cp genomes strongly supported the division of eight Fagopyrum species into two independent evolutionary directions, suggesting that the separation of cymosum group and urophyllum group may be earlier than the flower type differentiation in Fagopyrum plants. The results of the chloroplast-based phylogenetic tree were further supported by the matK and Internal Transcribed Spacer (ITS) sequences of 17 Fagopyrum species, which may help to further anchor the taxonomic status of other members in the urophyllum group in Fagopyrum. This study provides valuable information and high-quality cp genomes for identifying species and evolutionary analysis for future Fagopyrum research.},
}
@article {pmid34975932,
year = {2021},
author = {Zhang, Y and Song, MF and Li, Y and Sun, HF and Tang, DY and Xu, AS and Yin, CY and Zhang, ZL and Zhang, LX},
title = {Complete Chloroplast Genome Analysis of Two Important Medicinal Alpinia Species: Alpinia galanga and Alpinia kwangsiensis.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {705892},
pmid = {34975932},
issn = {1664-462X},
abstract = {Most Alpinia species are valued as foods, ornamental plants, or plants with medicinal properties. However, morphological characteristics and commonly used DNA barcode fragments are not sufficient for accurately identifying Alpinia species. Difficulties in species identification have led to confusion in the sale and use of Alpinia for medicinal use. To mine resources and improve the molecular methods for distinguishing among Alpinia species, we report the complete chloroplast (CP) genomes of Alpinia galanga and Alpinia kwangsiensis species, obtained via high-throughput Illumina sequencing. The CP genomes of A. galanga and A. kwangsiensis exhibited a typical circular tetramerous structure, including a large single-copy region (87,565 and 87,732 bp, respectively), a small single-copy region (17,909 and 15,181 bp, respectively), and a pair of inverted repeats (27,313 and 29,705 bp, respectively). The guanine-cytosine content of the CP genomes is 36.26 and 36.15%, respectively. Furthermore, each CP genome contained 133 genes, including 87 protein-coding genes, 38 distinct tRNA genes, and 8 distinct rRNA genes. We identified 110 and 125 simple sequence repeats in the CP genomes of A. galanga and A. kwangsiensis, respectively. We then combined these data with publicly available CP genome data from four other Alpinia species (A. hainanensis, A. oxyphylla, A. pumila, and A. zerumbet) and analyzed their sequence characteristics. Nucleotide diversity was analyzed based on the alignment of the complete CP genome sequences, and five candidate highly variable site markers (trnS-trnG, trnC-petN, rpl32-trnL, psaC-ndhE, and ndhC-trnV) were found. Twenty-eight complete CP genome sequences belonging to Alpinieae species were used to construct phylogenetic trees. The results fully demonstrated the phylogenetic relationship among the genera of the Alpinieae, and further proved that Alpinia is a non-monophyletic group. The complete CP genomes of the two medicinal Alpinia species provides lays the foundation for the use of CP genomes in species identification and phylogenetic analyses of Alpinia species.},
}
@article {pmid34969984,
year = {2022},
author = {He, Z and Maynard, A and Jain, A and Gerber, T and Petri, R and Lin, HC and Santel, M and Ly, K and Dupré, JS and Sidow, L and Sanchis Calleja, F and Jansen, SMJ and Riesenberg, S and Camp, JG and Treutlein, B},
title = {Lineage recording in human cerebral organoids.},
journal = {Nature methods},
volume = {19},
number = {1},
pages = {90-99},
pmid = {34969984},
issn = {1548-7105},
mesh = {CRISPR-Cas Systems ; Cell Lineage ; Cerebral Cortex/*cytology ; *Genes, Reporter ; Humans ; Induced Pluripotent Stem Cells/*cytology ; Microscopy/methods ; Mutation ; Neurons/cytology/physiology ; Organoids/*cytology ; Recombinant Proteins/genetics/metabolism ; Sequence Analysis, RNA ; Single-Cell Analysis/*methods ; Tuberous Sclerosis Complex 2 Protein/genetics ; },
abstract = {Induced pluripotent stem cell (iPSC)-derived organoids provide models to study human organ development. Single-cell transcriptomics enable highly resolved descriptions of cell states within these systems; however, approaches are needed to directly measure lineage relationships. Here we establish iTracer, a lineage recorder that combines reporter barcodes with inducible CRISPR-Cas9 scarring and is compatible with single-cell and spatial transcriptomics. We apply iTracer to explore clonality and lineage dynamics during cerebral organoid development and identify a time window of fate restriction as well as variation in neurogenic dynamics between progenitor neuron families. We also establish long-term four-dimensional light-sheet microscopy for spatial lineage recording in cerebral organoids and confirm regional clonality in the developing neuroepithelium. We incorporate gene perturbation (iTracer-perturb) and assess the effect of mosaic TSC2 mutations on cerebral organoid development. Our data shed light on how lineages and fates are established during cerebral organoid formation. More broadly, our techniques can be adapted in any iPSC-derived culture system to dissect lineage alterations during normal or perturbed development.},
}
@article {pmid34966517,
year = {2021},
author = {Bolshakov, VV and Prokin, AA and Artemenko, SV},
title = {Karyotype and COI gene sequence of Chironomusheteropilicornis Wülker, 1996 (Diptera, Chironomidae) from the Gydan Peninsula, Russia.},
journal = {Comparative cytogenetics},
volume = {15},
number = {4},
pages = {447-458},
pmid = {34966517},
issn = {1993-0771},
abstract = {The karyotype features and gene COI sequence of Chironomusheteropilicornis Wülker, 1996 from the Gydan Peninsula are presented for the first time. Nine banding sequences were determined, eight of them hpiA2, hpiB1, hpiC1, hpiC2, hpiD1, hpiE1, hpiF3 and hpiG1 were previously known from European, Georgian (South Caucasus) and Siberian populations. One new banding sequence for Ch.heteropilicornis, hpiB2, was found. The hpiA2 banding sequence was found in all individuals, and this is its second finding after the Georgian population (Karmokov 2019). The hpiF3 banding sequence was found only in the homozygous state. Additional B-chromosomes are absent. The genetic distances (K2P) between Ch.heteropilicornis COI gene sequence from Gydan Peninsula and Norway are 1.1--1.3%, and Georgia - 1.8%, much lower than the commonly accepted threshold of 3% for species of genus Chironomus Meigen, 1803. The phylogenetic tree for COI gene sequences estimated by Bayesian inference showed geographically determined clusters of Norway and Gydan and a separate lineage of the Georgian population of Ch.heteropilicornis. The analysis of karyotype and COI gene sequences shows that the population of Ch.heteropilicornis from the Gydan Peninsula has an intermediate position within the Ch.pilicornis group between Georgian, Yakutian and Norwegian populations. The position of Ch.pilicornis Fabricius, 1787 from Canada and Greenland on the phylogenetic tree is discussed.},
}
@article {pmid34966245,
year = {2021},
author = {Pešić, V and Zawal, A and Manović, A and Bańkowska, A and Jovanović, M},
title = {A DNA barcode library for the water mites of Montenegro.},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e78311},
pmid = {34966245},
issn = {1314-2828},
abstract = {Water mites (Acari, Hydrachnidia) are a significant component of freshwater ecosystems inhabiting a wide range of aquatic habitats. This study provides a first comprehensive DNA barcode library for the water mites of Montenegro. DNA barcodes were analysed from 233 specimens of water mites morphologically assigned to 86 species from 28 genera and 15 families. In the course of the study, four species, i.e. Lebertiareticulata (Koenike, 1919), Atractidesinflatipalpis K.Viets, 1950, A.latipes (Szalay, 1935) and Parabrachypodamontii (Maglio, 1924) were molecularly confirmed as new for Montenegro and three species, i.e. Protziaoctopora Lundblad, 1954, Pionalaminata (Thor, 1901) and Unionicolaypsilophora (Bonz, 1783) are new for the Balkan Peninsula. Results are analysed using the Barcode Index Number system (BIN) and the Refined Single Linkage (RESL) of BOLD. The BIN assigned sequences to 98 clusters, while the RESL reveal 103 operational taxonomic units (OTUs). Unique BINs were revealed for 72 species (83.7%), whereas twelve species (14%) were characterised by two BINs and two species (2.3%) with three BINs. Amongst the studied taxa, 14 species were found with a high intraspecific sequence divergences (˃ 2.2%), emphasising the need for additional comprehensive morphological and molecu-lar analysis of these species.},
}
@article {pmid34963753,
year = {2021},
author = {Yang, LL and Li, HH},
title = {The genus Dryadaula Meyrick (Lepidoptera, Tineoidea, Dryadaulidae) in China, with descriptions of four new species and a world checklist.},
journal = {ZooKeys},
volume = {1074},
number = {},
pages = {61-81},
pmid = {34963753},
issn = {1313-2989},
abstract = {Four new species of the genus Dryadaula Meyrick, 1893 from China are described: Dryadaulaauriformis sp. nov., D.flavostriata sp. nov., D.hirtiglobosa sp. nov. and D.securiformis sp. nov. Photographs of adults and genitalia of the new species are provided. DNA barcodes of D.auriformis sp. nov., D.hirtiglobosa sp. nov. and D.securiformis sp. nov. are given. A key to the species in China and a detailed checklist for the genus with all 49 known species in the world are presented.},
}
@article {pmid34963611,
year = {2022},
author = {Bouchali, R and Mandon, C and Marti, R and Michalon, J and Aigle, A and Marjolet, L and Vareilles, S and Kouyi, GL and Polomé, P and Toussaint, JY and Cournoyer, B},
title = {Bacterial assemblages of urban microbiomes mobilized by runoff waters match land use typologies and harbor core species involved in pollutant degradation and opportunistic human infections.},
journal = {The Science of the total environment},
volume = {815},
number = {},
pages = {152662},
doi = {10.1016/j.scitotenv.2021.152662},
pmid = {34963611},
issn = {1879-1026},
mesh = {Bacteria/genetics ; *Environmental Pollutants ; Humans ; *Microbiota ; RNA, Ribosomal, 16S ; *Water Pollutants, Chemical/analysis ; },
abstract = {Cities are patchworks of urban catchments divided into functional units according to their commercial, residential and industrial activities, and socio-urbanistic patterns. The hypothesis of city surface microbiomes being structured by socio-urbanistic variables leading to an emergence of synurbic taxa was tested. According to the r/K microbial ecology theory, a gradient of well-adapted synurbic K-strategists and of opportunistic -r-strategists should occur over city surfaces. K-strategists would be core components while r-ones would be transiently detected. To resolve these patterns, sub-catchments (n = 21) of an area of high commercial and industrial activities were investigated over three time periods covering one year. The sub-catchments' land use patterns and associated human behaviors were converted into socio-urbanistic variables and groupings. Bacterial cells mobilized by runoffs per sub-catchment were recovered, and analyzed by classical approaches, microbial source tracking DNA assays and DNA meta-barcoding approaches. Relationships between these datasets, the runoff physico-chemical properties, and descriptors of the socio-urbanistic groupings were investigated. 16S rRNA meta-barcoding analyses showed evidence of the occurrence of K- and r-like strategists. Twenty-eight core genera were identified, and correlation networks revealed large bacterial modules organized around actinobacterial taxa involved in hydrocarbon degradation processes. Other bacterial networks were related to the occurrences of hygienic wastes, and involved bacteria originating from fecal contaminations. Several r-strategists like Sulfurospirillum were recorded and found associated to point source pollutions. The tpm-metabarcoding approach deciphered these r / K strategists at the species level among more than ten genera. Nine core K-like Pseudomomas species were identified. The P. aeruginosa human opportunistic pathogen and P. syringae phytopathogens were part of these K-strategists. Other tpm-harboring bacterial pathogens showed r-like opportunistic distribution patterns. Correlation network analyses indicated a strong incidence of hygienic wastes and hydrocarbon-pollutions on tpm-harboring bacteria. These analyses demonstrated the occurrence of core synurbic bacterial K-strategists over city surfaces.},
}
@article {pmid34961238,
year = {2021},
author = {Braglia, L and Breviario, D and Gianì, S and Gavazzi, F and De Gregori, J and Morello, L},
title = {New Insights into Interspecific Hybridization in Lemna L. Sect. Lemna (Lemnaceae Martinov).},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {12},
pages = {},
pmid = {34961238},
issn = {2223-7747},
abstract = {Duckweeds have been increasingly studied in recent years, both as model plants and in view of their potential applications as a new crop in a circular bioeconomy perspective. In order to select species and clones with the desired attributes, the correct identification of the species is fundamental. Molecular methods have recently provided a more solid base for taxonomy and yielded a consensus phylogenetic tree, although some points remain to be elucidated. The duckweed genus Lemna L. comprises twelve species, grouped in four sections, which include very similar sister species. The least taxonomically resolved is sect. Lemna, presenting difficulties in species delimitation using morphological and even barcoding molecular markers. Ambiguous species boundaries between Lemna minor L. and Lemna japonica Landolt have been clarified by Tubulin Based Polymorphism (TBP), with the discovery of interspecific hybrids. In the present work, we extended TBP profiling to a larger number of clones in sect. Lemna, previously classified using only morphological features, in order to test that classification, and to investigate the possible existence of other hybrids in this section. The analysis revealed several misidentifications of clones, in particular among the species L. minor, L. japonica and Lemna gibba L., and identified six putative 'L. gibba' clones as interspecific hybrids between L. minor and L. gibba.},
}
@article {pmid34961211,
year = {2021},
author = {Jamdade, R and Upadhyay, M and Al Shaer, K and Al Harthi, E and Al Sallani, M and Al Jasmi, M and Al Ketbi, A},
title = {Evaluation of Arabian Vascular Plant Barcodes (rbcL and matK): Precision of Unsupervised and Supervised Learning Methods towards Accurate Identification.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {12},
pages = {},
pmid = {34961211},
issn = {2223-7747},
abstract = {Arabia is the largest peninsula in the world, with >3000 species of vascular plants. Not much effort has been made to generate a multi-locus marker barcode library to identify and discriminate the recorded plant species. This study aimed to determine the reliability of the available Arabian plant barcodes (>1500; rbcL and matK) at the public repository (NCBI GenBank) using the unsupervised and supervised methods. Comparative analysis was carried out with the standard dataset (FINBOL) to assess the methods and markers' reliability. Our analysis suggests that from the unsupervised method, TaxonDNA's All Species Barcode criterion (ASB) exhibits the highest accuracy for rbcL barcodes, followed by the matK barcodes using the aligned dataset (FINBOL). However, for the Arabian plant barcode dataset (GBMA), the supervised method performed better than the unsupervised method, where the Random Forest and K-Nearest Neighbor (gappy kernel) classifiers were robust enough. These classifiers successfully recognized true species from both barcode markers belonging to the aligned and alignment-free datasets, respectively. The multi-class classifier showed high species resolution following the two classifiers, though its performance declined when employed to recognize true species. Similar results were observed for the FINBOL dataset through the supervised learning approach; overall, matK marker showed higher accuracy than rbcL. However, the lower rate of species identification in matK in GBMA data could be due to the higher evolutionary rate or gaps and missing data, as observed for the ASB criterion in the FINBOL dataset. Further, a lower number of sequences and singletons could also affect the rate of species resolution, as observed in the GBMA dataset. The GBMA dataset lacks sufficient species membership. We would encourage the taxonomists from the Arabian Peninsula to join our campaign on the Arabian Barcode of Life at the Barcode of Life Data (BOLD) systems. Our efforts together could help improve the rate of species identification for the Arabian Vascular plants.},
}
@article {pmid34961105,
year = {2021},
author = {Maloupa, E and Karapatzak, E and Ganopoulos, I and Karydas, A and Papanastasi, K and Kyrkas, D and Yfanti, P and Nikisianis, N and Zahariadis, A and Kosma, IS and Badeka, AV and Patakioutas, G and Fotakis, D and Krigas, N},
title = {Molecular Authentication, Phytochemical Evaluation and Asexual Propagation of Wild-Growing Rosa canina L. (Rosaceae) Genotypes of Northern Greece for Sustainable Exploitation.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {12},
pages = {},
pmid = {34961105},
issn = {2223-7747},
support = {T1EDK-05434//Operational Program Competitiveness, Entrepreneurship and Innovation, under the call RE-SEARCH-CREATE-INNOVATE/ ; },
abstract = {Dogroses belong to a taxonomically difficult genus and family and represent important phytogenetic resources associated with high ornamental, pharmaceutical-cosmetic and nutritional values, thus suggesting a potentially high exploitation merit. Triggered by these prospects, wild-growing Rosa canina populations of Greece were selected for investigation and evaluation of their potential for integrated domestication. We collected ripe rosehips from Greek native wild-growing populations (samples from seven genotypes) for phytochemical analysis (total phenolics, total flavonoids, antioxidant activity and vitamin C content), leaf samples for DNA analysis using the ITS2 sequence (nine genotypes) and fresh soft-wood stem cuttings for propagation trials (seven genotypes). After evaluation of these materials, this study reports for the first-time distinct DNA-fingerprinted genotypes from Greece with interesting phytochemical profiles mainly in terms of Vitamic C content (up to 500.22 ± 0.15 mg of ascorbic acid equivalents/100 g of sample) as well as effective asexual propagation protocols for prioritized R. canina genotypes via cuttings. The latter highlights the importance of the levels of external hormone application (2000 ppm of indole-3-butyric acid), the effect of season (highly-effective spring trials) and genotype-specific differences in rooting capacities of the studied genotypes. All inclusive, this study offers new artificially selected material of Greek native R. canina with a consolidated identity and interesting phytochemical profile. These materials are currently under ex-situ conservation for further evaluation and characterization in pilot field studies, thus facilitating its sustainable exploitation for applications in the agro-alimentary, medicinal-cosmetic, and ornamental sectors.},
}
@article {pmid34955026,
year = {2022},
author = {Zhukov, M and Hasan, MS and Nesterov, P and Sabbouh, M and Burdulenko, O and Skorb, EV and Nosonovsky, M},
title = {Topological Data Analysis of Nanoscale Roughness in Brass Samples.},
journal = {ACS applied materials &amp; interfaces},
volume = {14},
number = {1},
pages = {2351-2359},
doi = {10.1021/acsami.1c20694},
pmid = {34955026},
issn = {1944-8252},
abstract = {Rough surfaces possess complex topographies, which cannot be characterized by a single parameter. The selection of appropriate roughness parameters depends on a particular application. Large datasets representing surface topography possess orderliness, which can be expressed in terms of topological features in high-dimensional dataspaces reflecting properties such as anisotropy and the number of lay directions. The features are scale-dependent because both sampling length and resolution affect them. We study nanoscale surface roughness using 3 × 3, 4 × 4, and 5 × 5 pixel patches obtained from atomic force microscopy (AFM) images of brass (Cu Zn alloy) samples roughened by a sonochemical treatment. We calculate roughness parameters, correlation length, extremum point distribution, persistence diagrams, and barcodes. These parameters of interest are discussed and compared.},
}
@article {pmid34952969,
year = {2022},
author = {Nemr, WA and Radwan, NK},
title = {Typing of alpha and beta coronaviruses by DNA barcoding of NSP12 gene.},
journal = {Journal of medical virology},
volume = {94},
number = {5},
pages = {1926-1934},
pmid = {34952969},
issn = {1096-9071},
mesh = {Animals ; *COVID-19 ; DNA Barcoding, Taxonomic ; Humans ; Mammals ; *Pandemics ; Phylogeny ; SARS-CoV-2/genetics ; },
abstract = {Since the spread of the COVID-19 pandemic, the world paid attention to coronaviruses (CoVs) evolution and their diverged lineages because many researches studies supposed that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is evolutionarily developed from a lineage of bats CoVs. This is due to the ability of some mutant CoVs to transmit from a host to different hosts. For this reason, there are many fears about the pathogenicity of the upcoming variants of CoVs. Thus, it is important to get a rapid and economic technique for typing a wide range of human and animal CoVs species for following up their mutant transmission. Therefore, the present study aims at approaching a simple design of DNA barcoding of a wide range of mammals' CoVs (including alpha and beta CoVs), by universal amplification of a species-specific sequence inside a conserved gene (NSP12) followed by amplicon sequencing. The in silico evaluation involved 96 nucleotide sequences of different CoVs (18 alpha CoVs and 78 beta CoVs), and was applied experimentally into the lab on 5 human CoVs isolates; 3 of them belong to beta CoVs (OC43, MERS, and SARS-CoV-2) and 2 are alpha CoVs (229E and NL63). The results indicated that the designed universal primers are able to amplify 332 bp of a taxonomic region inside the NSP12 coding sequence that facilitates the identification and classification of mammals' CoVs upon the resulting phylogenetic tree.},
}
@article {pmid34951634,
year = {2022},
author = {MacLeod, N and Canty, RJ and Polaszek, A},
title = {Morphology-Based Identification of Bemisia tabaci Cryptic Species Puparia via Embedded Group-Contrast Convolution Neural Network Analysis.},
journal = {Systematic biology},
volume = {71},
number = {5},
pages = {1095-1109},
pmid = {34951634},
issn = {1076-836X},
support = {OPP1058938/GATES/Bill &amp; Melinda Gates Foundation/United States ; },
mesh = {Animals ; *Hemiptera ; Neural Networks, Computer ; Phylogeny ; },
abstract = {The Bemisia tabaci species complex is a group of tropical-subtropical hemipterans, some species of which have achieved global distribution over the past 150 years. Several species are regarded currently as among the world's most pernicious agricultural pests, causing a variety of damage types via direct feeding and plant-disease transmission. Long considered a single variable species, genetic, molecular and reproductive compatibility analyses have revealed that this "species" is actually a complex of between 24 and 48 morphologically cryptic species. However, determinations of which populations represent distinct species have been hampered by a failure to integrate genetic/molecular and morphological species-diagnoses. This, in turn, has limited the success of outbreak-control and eradication programs. Previous morphological investigations, based on traditional and geometric morphometric procedures, have had limited success in identifying genetic/molecular species from patterns of morphological variation in puparia. As an alternative, our investigation focused on exploring the use of a deep-learning convolution neural network (CNN) trained on puparial images and based on an embedded, group-contrast training protocol as a means of searching for consistent differences in puparial morphology. Fifteen molecular species were selected for analysis, all of which had been identified via DNA barcoding and confirmed using more extensive molecular characterizations and crossing experiments. Results demonstrate that all 15 species can be discriminated successfully based on differences in puparium morphology alone. This level of discrimination was achieved for laboratory populations reared on both hairy-leaved and glabrous-leaved host plants. Moreover, cross-tabulation tests confirmed the generality and stability of the CNN discriminant system trained on both ecophenotypic variants. The ability to identify B. tabaci species quickly and accurately from puparial images has the potential to address many long-standing problems in B. tabaci taxonomy and systematics as well as playing a vital role in ongoing pest-management efforts. [Aleyrodidae; entomology; Hemiptera; machine learning; morphometrics; pest control; systematics; taxonomy; whiteflies.].},
}
@article {pmid34951515,
year = {2022},
author = {Sancho, R and Inda, LA and Díaz-Pérez, A and Des Marais, DL and Gordon, S and Vogel, JP and Lusinska, J and Hasterok, R and Contreras-Moreira, B and Catalán, P},
title = {Tracking the ancestry of known and 'ghost' homeologous subgenomes in model grass Brachypodium polyploids.},
journal = {The Plant journal : for cell and molecular biology},
volume = {109},
number = {6},
pages = {1535-1558},
doi = {10.1111/tpj.15650},
pmid = {34951515},
issn = {1365-313X},
mesh = {*Brachypodium/genetics ; Genome, Plant/genetics ; Humans ; Polyploidy ; },
}
@article {pmid34950159,
year = {2021},
author = {Herklotz, V and Kovařík, A and Wissemann, V and Lunerová, J and Vozárová, R and Buschmann, S and Olbricht, K and Groth, M and Ritz, CM},
title = {Power and Weakness of Repetition - Evaluating the Phylogenetic Signal From Repeatomes in the Family Rosaceae With Two Case Studies From Genera Prone to Polyploidy and Hybridization (Rosa and Fragaria).},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {738119},
pmid = {34950159},
issn = {1664-462X},
abstract = {Plant genomes consist, to a considerable extent, of non-coding repetitive DNA. Several studies showed that phylogenetic signals can be extracted from such repeatome data by using among-species dissimilarities from the RepeatExplorer2 pipeline as distance measures. Here, we advanced this approach by adjusting the read input for comparative clustering indirectly proportional to genome size and by summarizing all clusters into a main distance matrix subjected to Neighbor Joining algorithms and Principal Coordinate Analyses. Thus, our multivariate statistical method works as a "repeatomic fingerprint," and we proved its power and limitations by exemplarily applying it to the family Rosaceae at intrafamilial and, in the genera Fragaria and Rosa, at the intrageneric level. Since both taxa are prone to hybridization events, we wanted to show whether repeatome data are suitable to unravel the origin of natural and synthetic hybrids. In addition, we compared the results based on complete repeatomes with those from ribosomal DNA clusters only, because they represent one of the most widely used barcoding markers. Our results demonstrated that repeatome data contained a clear phylogenetic signal supporting the current subfamilial classification within Rosaceae. Accordingly, the well-accepted major evolutionary lineages within Fragaria were distinguished, and hybrids showed intermediate positions between parental species in data sets retrieved from both complete repeatomes and rDNA clusters. Within the taxonomically more complicated and particularly frequently hybridizing genus Rosa, we detected rather weak phylogenetic signals but surprisingly found a geographic pattern at a population scale. In sum, our method revealed promising results at larger taxonomic scales as well as within taxa with manageable levels of reticulation, but success remained rather taxon specific. Since repeatomes can be technically easy and comparably inexpensively retrieved even from samples of rather poor DNA quality, our phylogenomic method serves as a valuable alternative when high-quality genomes are unavailable, for example, in the case of old museum specimens.},
}
@article {pmid34949956,
year = {2021},
author = {Zhou, T and Jiang, W and Wang, H and Cui, Y},
title = {DNA barcoding of Naididae (Annelida, Oligochaeta), based on cytochrome C oxidase gene and ITS2 region in China.},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e73556},
pmid = {34949956},
issn = {1314-2828},
abstract = {Exploring the effectiveness of DNA barcoding in species identification is a prerequisite for biodiversity conservation and environmental monitoring. Aquatic oligochaetes could serve as excellent indicators in aquatic monitoring programmes. However, few studies have examined the effectiveness of DNA barcoding in these specific organisms. The mitochondrial cytochrome C oxidase (COI) gene of 83 specimens belonging to 40 species of 18 genera were sequenced in this study. The results showed that there was a barcode gap between species of Naididae and the intraspecific genetic distances of each species were smaller than interspecific genetic distances. The classification results of ABGD (Automatic Barcode Gap Discovery) were consistent with those of morphological identification, except for Tubifextubifex and Lumbriculusvariegatus. All species were successfully distinguished in the phylogenetic tree, based on the ITS2 region, which was coincident with the morphological result. Our results provided evidence that DNA barcoding can be used as an effective and convenient tool for species identification of the family Naididae and even for other aquatic oligochaetes.},
}
@article {pmid34947079,
year = {2021},
author = {Réblová, M and Kolařík, M and Nekvindová, J and Réblová, K and Sklenář, F and Miller, AN and Hernández-Restrepo, M},
title = {Phylogenetic Reassessment, Taxonomy, and Biogeography of Codinaea and Similar Fungi.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {7},
number = {12},
pages = {},
pmid = {34947079},
issn = {2309-608X},
support = {20-14840S//Czech Science Foundation/ ; },
abstract = {The genus Codinaea is a phialidic, dematiaceous hyphomycete known for its intriguing morphology and turbulent taxonomic history. This polyphasic study represents a new, comprehensive view on the taxonomy, systematics, and biogeography of Codinaea and its relatives. Phylogenetic analyses of three nuclear loci confirmed that Codinaea is polyphyletic. The generic concept was emended; it includes four morphotypes that contribute to its morphological complexity. Ancestral inference showed that the evolution of some traits is correlated and that these traits previously used to delimit taxa at the generic level occur in species that were shown to be congeneric. Five lineages of Codinaea-like fungi were recognized and introduced as new genera: Codinaeella, Nimesporella, Stilbochaeta, Tainosphaeriella, and Xyladelphia. Dual DNA barcoding facilitated identification at the species level. Codinaea and its segregates thrive on decaying plants, rarely occurring as endophytes or plant pathogens. Environmental ITS sequences indicate that they are common in bulk soil. The geographic distribution found using GlobalFungi database was consistent with known data. Most species are distributed in either the Holarctic realm or tropical geographic regions. The ancestral climatic zone was temperate, followed by transitions to the tropics; these fungi evolved primarily in Eurasia and Americas, with subsequent transitions to Africa and Australasia.},
}
@article {pmid34946199,
year = {2021},
author = {Pembaur, A and Sallard, E and Weil, PP and Ortelt, J and Ahmad-Nejad, P and Postberg, J},
title = {Simplified Point-of-Care Full SARS-CoV-2 Genome Sequencing Using Nanopore Technology.},
journal = {Microorganisms},
volume = {9},
number = {12},
pages = {},
pmid = {34946199},
issn = {2076-2607},
abstract = {The scale of the ongoing SARS-CoV-2 pandemic warrants the urgent establishment of a global decentralized surveillance system to recognize local outbreaks and the emergence of novel variants of concern. Among available deep-sequencing technologies, nanopore-sequencing could be an important cornerstone, as it is mobile, scalable, and cost-effective. Therefore, streamlined nanopore-sequencing protocols need to be developed and optimized for SARS-CoV-2 variants identification. We adapted and simplified existing workflows using the 'midnight' 1200 bp amplicon split primer sets for PCR, which produce tiled overlapping amplicons covering almost the entire SARS-CoV-2 genome. Subsequently, we applied Oxford Nanopore Rapid Barcoding and the portable MinION Mk1C sequencer combined with the interARTIC bioinformatics pipeline. We tested a simplified and less time-consuming workflow using SARS-CoV-2-positive specimens from clinical routine and identified the CT value as a useful pre-analytical parameter, which may help to decrease sequencing failures rates. Complete pipeline duration was approx. 7 h for one specimen and approx. 11 h for 12 multiplexed barcoded specimens. The adapted protocol contains fewer processing steps and can be completely conducted within one working day. Diagnostic CT values deduced from qPCR standardization experiments can act as principal criteria for specimen selection. As a guideline, SARS-CoV-2 genome copy numbers lower than 4 × 10[6] were associated with a coverage threshold below 20-fold and incompletely assembled SARS-CoV-2 genomes. Thus, based on the described thermocycler/chemistry combination, we recommend CT values of ~26 or lower to achieve full and high-quality SARS-CoV-2 (+)RNA genome coverage.},
}
@article {pmid34940175,
year = {2021},
author = {Iacob, GM and Craioveanu, C and Hula, V and Aurelian, VM and Beldean, M and Sitar, C},
title = {Improving the Knowledge on Distribution, Food Preferences and DNA Barcoding of Natura 2000 Protected Species Paracossulus thrips (Lepidoptera, Cossidae) in Romania.},
journal = {Insects},
volume = {12},
number = {12},
pages = {},
pmid = {34940175},
issn = {2075-4450},
support = {PN-III-P4-ID-PCCF-2016-0016//Ministerul Cercet&#x103;rii &#x219;i Inov&#x103;rii/ ; Special research scholarship//Babe&#x219;-Bolyai University/ ; Scholarship Grant//Milvus Group Association/ ; },
abstract = {Paracossulus thrips (Lepidoptera, Cossidae) is one of the locally distributed and endangered species. In Europe, it is also one of the few protected moth species, through Annexes II and IV of the Council Directive 92/43/EEC, Annex II of the Bern Convention. To date, little is known about the biology and ecology of this species. Our study was conducted in Transylvania, Romania. Romania hosts some of the strongest populations of the species in the European region. As part of the study, we conducted field observations, vegetation analyses, and genetic analyses. In our paper, we show the habitat types where we encounter P. thrips in Transylvania and confirm Phlomis tuberosa as a host plant. Furthermore, a piece of important information for habitat conservation is given. In this paper, we present the eggs and larvae of P. thrips, the first DNA barcoding sequences, and four new populations of P. thrips in Romania. Our study provides baseline knowledge about the biology and ecology of P. thrips, which is important for conservation and establishing management measures.},
}
@article {pmid34940126,
year = {2021},
author = {Choi, H and Kang, WS and Kim, JS and Na, CS and Kim, S},
title = {De Novo Assembly and Species-Specific Marker Development as a Useful Tool for the Identification of Scutellaria L. Species.},
journal = {Current issues in molecular biology},
volume = {43},
number = {3},
pages = {2177-2188},
pmid = {34940126},
issn = {1467-3045},
support = {2021-DD-UP-0380//Korea Innovation Foundation (INNIPOLIS) grant funded by the Korean government (Ministry of Science and ICT)/ ; },
mesh = {*Biomarkers ; Computational Biology/methods ; DNA Barcoding, Taxonomic ; Genes, Plant ; Genomics/methods ; Molecular Sequence Annotation ; Phenotype ; RNA-Seq ; Scutellaria/*classification/*genetics ; *Species Specificity ; },
abstract = {Scutellaria L. (family Lamiaceae) includes approximately 470 species found in most parts of the world and is commonly known as skullcaps. Scutellaria L. is a medicinal herb used as a folk remedy in Korea and East Asia, but it is difficult to identify and classify various subspecies by morphological methods. Since Scutellaria L. has not been studied genetically, to expand the knowledge of species in the genus Scutellaria L., de novo whole-genome assembly was performed in Scutellaria indica var. tsusimensis (H. Hara) Ohwi using the Illumina sequencing platform. We aimed to develop a molecular method that could be used to classify S.indica var. tsusimensis (H. Hara) Ohwi, S. indica L. and three other Scutellaria L. species. The assembly results for S.indica var. tsusimensis (H. Hara) Ohwi revealed a genome size of 318,741,328 bp and a scaffold N50 of 78,430. The assembly contained 92.08% of the conserved BUSCO core gene set and was estimated to cover 94.65% of the genome. The obtained genes were compared with previously registered Scutellaria nucleotide sequences and similar regions using the NCBI BLAST service, and a total of 279 similar nucleotide sequences were detected. By selecting the 279 similar nucleotide sequences and nine chloroplast DNA barcode genes, primers were prepared so that the size of the PCR product was 100 to 1000 bp. As a result, a species-specific primer set capable of distinguishing five species of Scutellaria L. was developed.},
}
@article {pmid34939038,
year = {2021},
author = {Gutierrez, C and Al'Khafaji, AM and Brenner, E and Johnson, KE and Gohil, SH and Lin, Z and Knisbacher, BA and Durrett, RE and Li, S and Parvin, S and Biran, A and Zhang, W and Rassenti, L and Kipps, TJ and Livak, KJ and Neuberg, D and Letai, A and Getz, G and Wu, CJ and Brock, A},
title = {Multifunctional barcoding with ClonMapper enables high-resolution study of clonal dynamics during tumor evolution and treatment.},
journal = {Nature cancer},
volume = {2},
number = {7},
pages = {758-772},
pmid = {34939038},
issn = {2662-1347},
support = {U10 CA180861/CA/NCI NIH HHS/United States ; R01 CA226258/CA/NCI NIH HHS/United States ; P01 CA206978/CA/NCI NIH HHS/United States ; R21 CA212928/CA/NCI NIH HHS/United States ; T32 EB007507/EB/NIBIB NIH HHS/United States ; R50 CA251956/CA/NCI NIH HHS/United States ; },
mesh = {Cell Line ; Clone Cells ; Genomics ; Humans ; *Leukemia, Lymphocytic, Chronic, B-Cell/genetics ; Transcriptome ; },
abstract = {Lineage-tracing methods have enabled characterization of clonal dynamics in complex populations, but generally lack the ability to integrate genomic, epigenomic and transcriptomic measurements with live-cell manipulation of specific clones of interest. We developed a functionalized lineage-tracing system, ClonMapper, which integrates DNA barcoding with single-cell RNA sequencing and clonal isolation to comprehensively characterize thousands of clones within heterogeneous populations. Using ClonMapper, we identified subpopulations of a chronic lymphocytic leukemia cell line with distinct clonal compositions, transcriptional signatures and chemotherapy survivorship trajectories; patterns that were also observed in primary human chronic lymphocytic leukemia. The ability to retrieve specific clones before, during and after treatment enabled direct measurements of clonal diversification and durable subpopulation transcriptional signatures. ClonMapper is a powerful multifunctional approach to dissect the complex clonal dynamics of tumor progression and therapeutic response.},
}
@article {pmid34936877,
year = {2021},
author = {Cheung, V and Chung, P and Bjorni, M and Shvareva, VA and Lopez, YC and Feinberg, EH},
title = {Virally encoded connectivity transgenic overlay RNA sequencing (VECTORseq) defines projection neurons involved in sensorimotor integration.},
journal = {Cell reports},
volume = {37},
number = {12},
pages = {110131},
pmid = {34936877},
issn = {2211-1247},
support = {DP2 MH119426/MH/NIMH NIH HHS/United States ; P30 AI027763/AI/NIAID NIH HHS/United States ; R01 NS109060/NS/NINDS NIH HHS/United States ; S10 RR028962/RR/NCRR NIH HHS/United States ; },
mesh = {Animals ; Gene Expression Profiling/methods ; Genetic Techniques ; High-Throughput Screening Assays/*methods ; Male ; Mice ; Mice, Inbred C57BL ; Neural Pathways/physiology ; Neurons/*classification/*physiology ; Optogenetics ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis/*methods ; Transgenes ; },
abstract = {Behavior arises from concerted activity throughout the brain. Consequently, a major focus of modern neuroscience is defining the physiology and behavioral roles of projection neurons linking different brain areas. Single-cell RNA sequencing has facilitated these efforts by revealing molecular determinants of cellular physiology and markers that enable genetically targeted perturbations such as optogenetics, but existing methods for sequencing defined projection populations are low throughput, painstaking, and costly. We developed a straightforward, multiplexed approach, virally encoded connectivity transgenic overlay RNA sequencing (VECTORseq). VECTORseq repurposes commercial retrogradely infecting viruses typically used to express functional transgenes (e.g., recombinases and fluorescent proteins) by treating viral transgene mRNA as barcodes within single-cell datasets. VECTORseq is compatible with different viral families, resolves multiple populations with different projection targets in one sequencing run, and identifies cortical and subcortical excitatory and inhibitory projection populations. Our study provides a roadmap for high-throughput identification of neuronal subtypes based on connectivity.},
}
@article {pmid34936345,
year = {2022},
author = {Herrera, V and Hsu, SJ and Naveen, VY and Liu, WF and Haun, JB},
title = {Multiplexed Detection of Secreted Cytokines at near-Molecular Resolution Elucidates Macrophage Polarization Heterogeneity.},
journal = {Analytical chemistry},
volume = {94},
number = {2},
pages = {658-668},
doi = {10.1021/acs.analchem.1c02222},
pmid = {34936345},
issn = {1520-6882},
support = {DP2 DE023319/DE/NIDCR NIH HHS/United States ; R21 CA206953/CA/NCI NIH HHS/United States ; },
mesh = {*Cytokines/analysis ; Immunoassay/methods ; Lipopolysaccharides/pharmacology ; Macrophages/chemistry ; *Tumor Necrosis Factor-alpha/analysis ; },
abstract = {Monitoring the secretion of proteins from single cells can provide important insights into how cells respond to their microenvironment. This is particularly true for immune cells, which can exhibit a large degree of response heterogeneity. Microfabricated well arrays provide a powerful and versatile method to assess the secretion of cytokines, chemokines, and growth factors from single cells, but detection sensitivity has been limited to high levels on the order of 10,000 per cell. Recently, we reported a quantum dot-based immunoassay that lowered the detection limit for the cytokine TNF-α to concentrations to nearly the single-cell level. Here, we adapted this detection method to three additional targets while maintaining high detection sensitivity. Specifically, we detected MCP-1, TGF-β, IL-10, and TNF-α using quantum dots with different emission spectra, each of which displayed a detection threshold in the range of 1-10 fM or ∼1-2 molecules per well. We then quantified secretion of all four proteins from single macrophage cells that were stimulated toward a pro-inflammatory state with lipopolysaccharide (LPS) or toward a pro-healing state with both LPS and interleukin 4 (IL-4). We found that MCP-1 and TGF-β were predominantly secreted at high levels only (>10,000 molecules/cell), while a substantial number of cells secreted IL-10 and TNF-α at lower levels that could only be detected using our method. Subsequent principal component and cluster analysis revealed that secretion profiles could be classified as either exclusively pro-inflammatory, including MCP-1 and/or TNF-α, or more subtle responses displaying both pro-healing and pro-inflammatory characters. Our results highlight the heterogeneous and nondiscrete nature of macrophage phenotypes following in vitro stimulation of a cell line. Future work will focus on expanding the multiplexing capacity by extending emission spectra bandwidth and/or spatially barcoding capture antibodies, as well as evaluating the enhanced detection sensitivity capabilities with normal and diseased immune cell populations in vitro and in vivo.},
}
@article {pmid34934048,
year = {2021},
author = {Mavrommati, I and Johnson, F and Echeverria, GV and Natrajan, R},
title = {Subclonal heterogeneity and evolution in breast cancer.},
journal = {NPJ breast cancer},
volume = {7},
number = {1},
pages = {155},
pmid = {34934048},
issn = {2374-4677},
support = {Programme Funding to the Breast Cancer Now Toby Robins Research Centre to R.N//Breast Cancer Now (BCN)/ ; 1K22CA241113-01//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; K22 CA241113/CA/NCI NIH HHS/United States ; Programmatic funding to RN//Breast Cancer Now (BCN)/ ; RR200009//Cancer Prevention and Research Institute of Texas (Cancer Prevention Research Institute of Texas)/ ; },
abstract = {Subclonal heterogeneity and evolution are characteristics of breast cancer that play a fundamental role in tumour development, progression and resistance to current therapies. In this review, we focus on the recent advances in understanding the epigenetic and transcriptomic changes that occur within breast cancer and their importance in terms of cancer development, progression and therapy resistance with a particular focus on alterations at the single-cell level. Furthermore, we highlight the utility of using single-cell tracing and molecular barcoding methodologies in preclinical models to assess disease evolution and response to therapy. We discuss how the integration of single-cell profiling from patient samples can be used in conjunction with results from preclinical models to untangle the complexities of this disease and identify biomarkers of disease progression, including measures of intra-tumour heterogeneity themselves, and how enhancing this understanding has the potential to uncover new targetable vulnerabilities in breast cancer.},
}
@article {pmid34930559,
year = {2022},
author = {Hilário, S and Santos, L and Phillips, AJL and Alves, A},
title = {Caveats of the internal transcribed spacer region as a barcode to resolve species boundaries in Diaporthe.},
journal = {Fungal biology},
volume = {126},
number = {1},
pages = {54-74},
doi = {10.1016/j.funbio.2021.10.005},
pmid = {34930559},
issn = {1878-6146},
mesh = {DNA, Ribosomal ; Phylogeny ; Plants ; *Saccharomycetales ; },
abstract = {Species in Diaporthe are largely reported as important plant pathogens. Identification of species in this genus has been complemented by morphological and molecular features. However, one important factor delaying this process is the struggle to formulate robust species concepts to create adequate international phytosanitary measures. Regardless of the wide use of the internal transcribed spacer (ITS) rDNA region, established as the primary DNA barcode for fungi, the tendency for intraspecific variation has been reported, misleading interpretation of phylogenetic analyses. Therefore, the present study aimed to illustrate, using specific examples, how the ITS region may be problematic for species delimitation. We showed that the ITS region is highly variable, with strains of Diaporthe malorum and Diaporthe novem falling into more than one clade, which if analyzed on their own, would be likely recognized as distinct taxa. Divergent ITS paralogs were also proven to coexist within the genome of D. novem. We also suggest that ITS may have escaped from concerted evolution or has undergone a duplication event. Furthermore, this study reports for the first time the existence of a putative hybrid in the genus Diaporthe. Our findings offer new clues towards the intraspecific and intragenomic variation in the ITS region, raising questions about its value for barcoding, i.e., identifying species in the genus Diaporthe. Therefore, we recommend that the ITS region be analyzed cautiously and always compared for congruence prior to description of novel taxa.},
}
@article {pmid34929415,
year = {2022},
author = {Liu, Y and Deng, G},
title = {Automating inventorying of blood stations: A system based on ultrahigh-frequency radio-frequency identification (UHF RFID) technology.},
journal = {Transfusion clinique et biologique : journal de la Societe francaise de transfusion sanguine},
volume = {29},
number = {2},
pages = {134-137},
doi = {10.1016/j.tracli.2021.12.003},
pmid = {34929415},
issn = {1953-8022},
mesh = {Humans ; *Radio Frequency Identification Device/methods ; Technology ; },
abstract = {Inventorying blood products is an essential process in blood station management. Traditional methods need to integrate barcodes with refrigerators, which suffer from low time efficiency, high error rate and high labour cost. Several methods have been proposed to automate this process in blood stations. However, none of them is ideal enough. In this paper, we analyse the difficulties of automation in blood inventory, and propose an automated blood inventory system based on UHF RFID technology. Comparisons over our method with manual inventory and handheld RFID inventory are conducted. The result shows that our method is nearly 10 times higher than manual inventory in time efficiency while increases the accuracy to 100%.},
}
@article {pmid34928952,
year = {2021},
author = {Sturm, A and Vos, MW and Henderson, R and Eldering, M and Koolen, KMJ and Sheshachalam, A and Favia, G and Samby, K and Herreros, E and Dechering, KJ},
title = {Barcoded Asaia bacteria enable mosquito in vivo screens and identify novel systemic insecticides and inhibitors of malaria transmission.},
journal = {PLoS biology},
volume = {19},
number = {12},
pages = {e3001426},
pmid = {34928952},
issn = {1545-7885},
mesh = {Acetobacteraceae/genetics ; Animals ; Anopheles/genetics/microbiology ; Antimalarials/pharmacology ; DNA Barcoding, Taxonomic/*methods ; Drug Evaluation, Preclinical/*methods ; Insecticides ; Malaria/parasitology/*prevention &amp; control/transmission ; Mosquito Vectors/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {This work addresses the need for new chemical matter in product development for control of pest insects and vector-borne diseases. We present a barcoding strategy that enables phenotypic screens of blood-feeding insects against small molecules in microtiter plate-based arrays and apply this to discovery of novel systemic insecticides and compounds that block malaria parasite development in the mosquito vector. Encoding of the blood meals was achieved through recombinant DNA-tagged Asaia bacteria that successfully colonised Aedes and Anopheles mosquitoes. An arrayed screen of a collection of pesticides showed that chemical classes of avermectins, phenylpyrazoles, and neonicotinoids were enriched for compounds with systemic adulticide activity against Anopheles. Using a luminescent Plasmodium falciparum reporter strain, barcoded screens identified 48 drug-like transmission-blocking compounds from a 400-compound antimicrobial library. The approach significantly increases the throughput in phenotypic screening campaigns using adult insects and identifies novel candidate small molecules for disease control.},
}
@article {pmid34928124,
year = {2022},
author = {Lima, GM and Atrazhev, A and Sarkar, S and Sojitra, M and Reddy, R and Torres-Obreque, K and de Oliveira Rangel-Yagui, C and Macauley, MS and Monteiro, G and Derda, R},
title = {DNA-Encoded Multivalent Display of Chemically Modified Protein Tetramers on Phage: Synthesis and in Vivo Applications.},
journal = {ACS chemical biology},
volume = {17},
number = {11},
pages = {3024-3035},
doi = {10.1021/acschembio.1c00835},
pmid = {34928124},
issn = {1554-8937},
mesh = {Mice ; Animals ; *Bacteriophages/genetics ; Asparaginase/genetics ; Proteins/metabolism ; Cell Surface Display Techniques ; DNA/metabolism ; Peptide Library ; Bacteriophage M13/genetics/metabolism ; },
abstract = {Phage display links the phenotype of displayed polypeptides with the DNA sequence in the phage genome and offers a universal method for the discovery of proteins with novel properties. However, the display of large multisubunit proteins on phages remains a challenge. A majority of protein display systems are based on monovalent phagemid constructs, but methods for the robust display of multiple copies of large proteins are scarce. Here, we describe a DNA-encoded display of a ∼ 200 kDa tetrameric l-asparaginase protein on M13 and fd phages produced by ligation of SpyCatcher-Asparaginase fusion (ScA) and PEGylated-ScA (PEG-ScA) to barcoded phage clones displaying SpyTag peptide. Starting from the SpyTag display on p3 or p8 coat proteins yielded constructs with five copies of ScA displayed on p3 (ScA-p3), ∼100 copies of ScA on p8 protein (ScA-p8) and ∼300 copies of PEG-ScA on p8 protein (PEG-ScA-p8). Display constructs of different valencies and chemical modifications on protein (e.g., PEGylation) can be injected into mice and analyzed by deep sequencing of the DNA barcodes associated with phage clones. In these multiplexed studies, we observed a density and protein-dependent clearance rate in vivo. Our observations link the absence of PEGylation and increase in density of the displayed protein with the increased rate of the endocytosis by cells in vivo. In conclusion, we demonstrate that a multivalent display of l-asparaginase on phages could be used to study the circulation life of this protein in vivo, and such an approach opens the possibility to use DNA sequencing to investigate multiplexed libraries of other multisubunit proteins in vivo.},
}
@article {pmid34925527,
year = {2021},
author = {Liu, M and Wang, K and Chen, B and Cai, Y and Li, C and Yang, W and Wei, M and Zheng, G},
title = {Intraspecific DNA Barcoding and Variation Analysis for Citri Reticulatae Pericarpium of Citrus reticulata "Chachi".},
journal = {Evidence-based complementary and alternative medicine : eCAM},
volume = {2021},
number = {},
pages = {2609935},
pmid = {34925527},
issn = {1741-427X},
abstract = {Citri Reticulatae Pericarpium, the desiccative mature peel of Citrus reticulata Blanco or its cultivated varieties, is a national geographical indicated product that has the concomitant function of both medicine and foodstuff. The primary source of Citri Reticulatae Pericarpium is Citrus reticulata "Chachi," called "Guang chenpi," while it differs in variety, propagation, grafting rootstock, and tree age, and the hereditary stability of its biological information between intraspecific plants is worthy of our attention. Homologous analysis result of 4 DNA barcodings in the ribosome or the chloroplast showed that the homology of them (ITS2, rbcl, matK, and psbA-trnH) of 22 samples was 100.00%, 99.97%, 99.99%, and 99.81%, respectively, which indicated that 4 DNA barcodes maintained a high degree of genetic stability in Citrus reticulata "Chachi." Also, ITS2 was considered to identify Citrus reticulata "Chachi" from other varieties because it presented not only low variability within a certain taxon but also a high level of interspecies variability. Simultaneously, variant site detection of Citrus reticulata "Chachi" was analyzed by comparing with the reference Citrus reticulata genome, and 2652697 SNP sites and 533906 InDel sites were detected from whole-genome resequencing data of 22 samples, providing the data resources and theoretical foundation for the future study about the relevant molecular makers of "Guang chenpi."},
}
@article {pmid34922013,
year = {2022},
author = {Liu, Q and Bi, Q and Zhang, J and Qin, W and Yi, S and Hu, Q and Sun, J and Ji, S and Tan, N},
title = {A rapid and simple signature peptides-based method for species authentication of three main commercial Pheretima.},
journal = {Journal of proteomics},
volume = {255},
number = {},
pages = {104456},
doi = {10.1016/j.jprot.2021.104456},
pmid = {34922013},
issn = {1876-7737},
mesh = {Animals ; Chromatography, Liquid ; *Oligochaeta/chemistry/genetics/metabolism ; Peptides/genetics/metabolism ; Proteomics/methods ; *Tandem Mass Spectrometry/methods ; },
abstract = {Pheretima with various activities is a commonly used animal-derived traditional medicine in Asia countries. However, almost half of them are non-pharmacopoeia species in the market due to the similar morphological characteristics between medicinal and non-medicinal species. This study aims to establish an effective method based on signature peptides for species authentication of three main commercial Pheretima, including two major Pheretima species (Amynthas aspergillum, Metaphire vulgaris) and one main adulteration (Metaphire magna). Firstly, the species of 52 batches of commercial Pheretima were authenticated based on DNA barcodes. Secondly, proteomic analysis was performed for protein characterization of three main commercial Pheretima. Furthermore, their signature peptides were screened and validated using ultra-high performance liquid chromatography coupled with mass spectrometry (UPLC-MS/MS) in multiple reaction monitoring (MRM) mode. Moreover, a simplified sample processing method was developed. Finally, large quantities of commercial Pheretima samples were analyzed for further verifying the feasibility of the signature peptides-based method. The result showed that the established method had a great application potential for authenticity identification of commercial Pheretima. SIGNIFICANCE: The authenticity assessment of medicinal materials is a main issue in the quality control process as deceptive practices could imply severe health risks. In this study, a rapid and simple method based on signature peptides was established for species authentication of three main commercial Pheretima, which can be an effective alternative to complex DNA barcoding and difficult morphological identification, and provided a reference for improvement of Pheretima quality standards.},
}
@article {pmid34919116,
year = {2021},
author = {Xu, X and Li, J and Chu, R and Luan, M and Wang, H and Song, K and Wei, S and Shi, Y and Zhu, S and Wei, Z},
title = {Comparative and phylogenetic analyses of Swertia L. (Gentianaceae) medicinal plants (from Qinghai, China) based on complete chloroplast genomes.},
journal = {Genetics and molecular biology},
volume = {45},
number = {1},
pages = {e20210092},
pmid = {34919116},
issn = {1415-4757},
abstract = {Swertia L. is a large genus in Swertiinae (Gentianaceae). In China, many Swertia species are used as traditional Tibetan medicines, known as "Zangyinchen" or "Dida". However, the phylogenetic relationships among Swertia medicinal plants and their wild relatives have remained unclear. In this study, we sequenced and assembled 16 complete chloroplast (cp) genomes of 10 Swertia species, mainly distributed in Qinghai Province, China. The results showed that these species have typical structures and characteristics of plant cp genomes. The sizes of Swertia cp genomes are ranging from 149,488 bp to 154,097 bp. Most Swertia cp genomes presented 134 genes, including 85 protein coding genes, eight rRNA genes, 37 tRNA genes, and four pseudogenes. Furthermore, the GC contents and boundaries of cp genomes are similar among Swertia species. The phylogenetic analyses indicated that Swertia is a complex polyphyletic group. In addition, positive selection was found in psaI and petL genes, indicating the possible adaptation of Qinghai Swertia species to the light environment of the Qinghai-Tibet plateau. These new cp genome data could be further investigated to develop DNA barcodes for Swertia medicinal plants and for additional systematic studies of Swertia and Swertiinae species.},
}
@article {pmid34918844,
year = {2022},
author = {Kortmann, M and Roth, N and Buse, J and Hilszczański, J and Jaworski, T and Morinière, J and Seidl, R and Thorn, S and Müller, JC},
title = {Arthropod dark taxa provide new insights into diversity responses to bark beetle infestations.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {32},
number = {2},
pages = {e2516},
doi = {10.1002/eap.2516},
pmid = {34918844},
issn = {1051-0761},
mesh = {Animals ; *Arthropods ; Biodiversity ; *Coleoptera ; Forests ; Plant Bark ; },
abstract = {Natural disturbances are increasing around the globe, also impacting protected areas. Although previous studies have indicated that natural disturbances result in mainly positive effects on biodiversity, these analyses mostly focused on a few well established taxonomic groups, and thus uncertainty remains regarding the comprehensive impact of natural disturbances on biodiversity. Using Malaise traps and meta-barcoding, we studied a broad range of arthropod taxa, including dark and cryptic taxa, along a gradient of bark beetle disturbance severities in five European national parks. We identified order-level community thresholds of disturbance severity and classified barcode index numbers (BINs; a cluster system for DNA sequences, where each cluster corresponds to a species) as negative or positive disturbance indicators. Negative indicator BINs decreased above thresholds of low to medium disturbance severity (20%-30% of trees killed), whereas positive indicator BINs benefited from high disturbance severity (76%-98%). BINs allocated to a species name contained nearly as many positive as negative disturbance indicators, but dark and cryptic taxa, particularly Diptera and Hymenoptera in our data, contained higher numbers of negative disturbance indicator BINs. Analyses of changes in the richness of BINs showed variable responses of arthropods to disturbance severity at lower taxonomic levels, whereas no significant signal was detected at the order level due to the compensatory responses of the underlying taxa. We conclude that the analyses of dark taxa can offer new insights into biodiversity responses to disturbances. Our results suggest considerable potential for forest management to foster arthropod diversity, for example by maintaining both closed-canopy forests (>70% cover) and open forests (<30% cover) on the landscape.},
}
@article {pmid34918473,
year = {2022},
author = {Tay, WT and Court, LN and Macfadyen, S and Jacomb, F and Vyskočilová, S and Colvin, J and De Barro, PJ},
title = {A high-throughput amplicon sequencing approach for population-wide species diversity and composition survey.},
journal = {Molecular ecology resources},
volume = {22},
number = {5},
pages = {1706-1724},
pmid = {34918473},
issn = {1755-0998},
support = {OPP1058938/GATES/Bill &amp; Melinda Gates Foundation/United States ; OPP1058938/GATES/Bill &amp; Melinda Gates Foundation/United States ; },
mesh = {Animals ; *Hemiptera/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Insecta ; *Manihot ; *Plant Viruses ; },
abstract = {Management of agricultural pests requires an understanding of pest species diversity, their interactions with beneficial insects and spatial-temporal patterns of pest abundance. Invasive and agriculturally important insect pests can build up very high populations, especially in cropping landscapes. Traditionally, sampling effort for species identification involves small sample sizes and is labour intensive. Here, we describe a multiprimer high throughput sequencing (HTS) metabarcoding method and associated analytical workflow for a rapid, intensive, high-volume survey of pest species compositions. We demonstrate our method using the taxonomically challenging Bemisia pest cryptic species complex as examples. The whiteflies Bemisia including the"tabaci" species are agriculturally important capable of vectoring diverse plant viruses that cause diseases and crop losses. Our multiprimer metabarcoding HTS amplicon approach simultaneously process high volumes of whitefly individuals, with efficiency to detect rare (i.e., 1%) test-species, while our improved whitefly primers for metabarcoding also detected beneficial hymenopteran parasitoid species from whitefly nymphs. Field-testing our redesigned Bemisia metabarcoding primer sets across the Tanzania, Uganda and Malawi cassava cultivation landscapes, we identified the sub-Saharan Africa 1 Bemisia putative species as the dominant pest species, with other cryptic Bemisia species being detected at various abundances. We also provide evidence that Bemisia species compositions can be affected by host crops and sampling techniques that target either nymphs or adults. Our multiprimer HTS metabarcoding method incorporated two overlapping amplicons of 472 bp and 518 bp that spanned the entire 657 bp 3' barcoding region for Bemisia, and is particularly suitable to molecular diagnostic surveys of this highly cryptic insect pest species complex that also typically exhibited high population densities in heavy crop infestation episodes. Our approach can be adopted to understand species biodiversity across landscapes, with broad implications for improving transboundary biosecurity preparedness, thus contributing to molecular ecological knowledge and the development of control strategies for high-density, cryptic, pest-species complexes.},
}
@article {pmid34918287,
year = {2022},
author = {Gonzalez, VD and Huang, YW and Fantl, WJ},
title = {Mass Cytometry for the Characterization of Individual Cell Types in Ovarian Solid Tumors.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2424},
number = {},
pages = {59-94},
pmid = {34918287},
issn = {1940-6029},
support = {P01 HL108797/HL/NHLBI NIH HHS/United States ; R01 CA234553/CA/NCI NIH HHS/United States ; R21 CA231280/CA/NCI NIH HHS/United States ; },
mesh = {Antibodies ; Female ; Flow Cytometry ; Humans ; Isotopes ; Mass Spectrometry ; *Ovarian Neoplasms ; Single-Cell Analysis ; },
abstract = {Mass cytometry aka Cytometry by Time-Of-Flight (CyTOF) is one of several recently developed multiparametric single-cell technologies designed to address cellular heterogeneity within healthy and diseased tissue. Mass cytometry is an adaptation of flow cytometry in which antibodies are labeled with stable heavy metal isotopes and the readout is by time-of-flight mass spectrometry. With minimal spillover between channels, mass cytometry enables readouts of up to 60 parameters per single cell. Critically, mass cytometry can identify minority cell populations that are lost in bulk tissue analysis. Mass cytometry has been used to great effect for the study of immune cells. We have extended its use to examine single cells within disaggregated solid tissues, specifically freshly resected tubo-ovarian high-grade serous tumors. Here we detail our protocols designed to ensure the production of high-quality single-cell datasets. The methodology can be modified to accommodate the study of other solid tissues.},
}
@article {pmid34916873,
year = {2021},
author = {Haas, M and Baur, H and Schweizer, T and Monje, JC and Moser, M and Bigalk, S and Krogmann, L},
title = {Tiny wasps, huge diversity - A review of German Pteromalidae with new generic and species records (Hymenoptera: Chalcidoidea).},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e77092},
pmid = {34916873},
issn = {1314-2828},
abstract = {BACKGROUND: Despite their ecological and economic importance, hymenopteran parasitoids are severely understudied. Even in countries with a long taxonomic history such as Germany, dating back to the 18th century and including prolific figures like Christian Gottfired Nees von Esenbeck and Otto Schmiedeknecht, those species-rich groups are seldom the subject of comprehensive research efforts, leaving their true diversity unknown. This is often due to their small size of a few millimetres on average, leading to difficulties in their identification and examination. The chalcidoid family Pteromalidae is no exception to this neglect. So far, 735 species have been reported from Germany. Estimating the diversity of this group is not possible, but it has to be assumed that many more species are still to be discovered in Germany.<br><br>NEW INFORMATION: With this study, we improve the knowledge on pteromalid diversity and present new records of 17 genera and 41 species, previously unknown to occur in Germany. We also match and describe previously unknown sexes of two species, based on DNA barcode data. The results of this study were generated as part of the German Barcode of Life Project. The newly-recorded species are illustrated and notes on the biology and distribution are given. The ecological significance of Pteromalidae and potential value as indicators for nature conservation efforts are briefly discussed.},
}
@article {pmid34912114,
year = {2022},
author = {Delgado, RN and Allen, DE and Keefe, MG and Mancia Leon, WR and Ziffra, RS and Crouch, EE and Alvarez-Buylla, A and Nowakowski, TJ},
title = {Individual human cortical progenitors can produce excitatory and inhibitory neurons.},
journal = {Nature},
volume = {601},
number = {7893},
pages = {397-403},
pmid = {34912114},
issn = {1476-4687},
support = {RF1 MH121268/MH/NIMH NIH HHS/United States ; R01 NS028478/NS/NINDS NIH HHS/United States ; U01 MH115747/MH/NIMH NIH HHS/United States ; K08 NS116161/NS/NINDS NIH HHS/United States ; R01 MH125516/MH/NIMH NIH HHS/United States ; R01 EY025174/EY/NEI NIH HHS/United States ; T32 HD007470/HD/NICHD NIH HHS/United States ; },
mesh = {*Cell Lineage ; *Cerebral Cortex/cytology ; GABAergic Neurons/cytology ; Humans ; *Interneurons/cytology ; *Neural Inhibition ; *Neurons/cytology ; },
abstract = {The cerebral cortex is a cellularly complex structure comprising a rich diversity of neuronal and glial cell types. Cortical neurons can be broadly categorized into two classes-excitatory neurons that use the neurotransmitter glutamate, and inhibitory interneurons that use γ-aminobutyric acid (GABA). Previous developmental studies in rodents have led to a prevailing model in which excitatory neurons are born from progenitors located in the cortex, whereas cortical interneurons are born from a separate population of progenitors located outside the developing cortex in the ganglionic eminences[1-5]. However, the developmental potential of human cortical progenitors has not been thoroughly explored. Here we show that, in addition to excitatory neurons and glia, human cortical progenitors are also capable of producing GABAergic neurons with the transcriptional characteristics and morphologies of cortical interneurons. By developing a cellular barcoding tool called 'single-cell-RNA-sequencing-compatible tracer for identifying clonal relationships' (STICR), we were able to carry out clonal lineage tracing of 1,912 primary human cortical progenitors from six specimens, and to capture both the transcriptional identities and the clonal relationships of their progeny. A subpopulation of cortically born GABAergic neurons was transcriptionally similar to cortical interneurons born from the caudal ganglionic eminence, and these cells were frequently related to excitatory neurons and glia. Our results show that individual human cortical progenitors can generate both excitatory neurons and cortical interneurons, providing a new framework for understanding the origins of neuronal diversity in the human cortex.},
}
@article {pmid34912013,
year = {2021},
author = {Bozáňová, J and Čiampor, F and Mamos, T and Grabowski, M and Čiamporová-Zat'ovičová, Z},
title = {DNA barcodes evidence the contact zone of eastern and western caddisfly lineages in the Western Carpathians.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {24020},
pmid = {34912013},
issn = {2045-2322},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; *Ecosystem ; Europe ; Fresh Water ; Genetic Variation ; Genetics, Population ; Insecta/*classification/*genetics ; Phylogeny ; Phylogeography ; },
abstract = {The region of the Western Carpathians is, among other aspects, very important for survival and diversity of European freshwater fauna due to the presence of a large number of (sub)mountain springs and streams. However, these ecologically and faunistically diversified habitats are still understudied in the context of genetic diversity and population structure of their inhabitants. This study focuses on genetic diversity and distribution patterns of the caddisfly Rhyacophila tristis, common and widespread representative of mountain freshwater fauna. Analysis of the COI mitochondrial marker revealed presence of the western and eastern lineages, with samples from both lineages being grouped in BOLD (Barcode of Life Data System) into separate BINs (Barcode Index Numbers). Our data indicates that eastern lineage (BIN_E) is more closely related to the Balkan populations than to co-occurring western lineage (BIN_W), and that the contact zone of the lineages passes through the W Carpathians. The study revealed phylogeographic and demographic differences between lineages, supporting hypothesis of their evolutionary independence and specific ecological preferences. The obtained genetic data of the R. tristis population from W Carpathians improved our knowledge about population genetics of this aquatic species and can contribute to understanding the state and evolution of biodiversity of freshwater ecosystems in Europe.},
}
@article {pmid34911733,
year = {2022},
author = {Chang, CA and Jen, J and Jiang, S and Sayad, A and Mer, AS and Brown, KR and Nixon, AML and Dhabaria, A and Tang, KH and Venet, D and Sotiriou, C and Deng, J and Wong, KK and Adams, S and Meyn, P and Heguy, A and Skok, JA and Tsirigos, A and Ueberheide, B and Moffat, J and Singh, A and Haibe-Kains, B and Khodadadi-Jamayran, A and Neel, BG},
title = {Ontogeny and Vulnerabilities of Drug-Tolerant Persisters in HER2+ Breast Cancer.},
journal = {Cancer discovery},
volume = {12},
number = {4},
pages = {1022-1045},
pmid = {34911733},
issn = {2159-8290},
support = {P01 CA229086/CA/NCI NIH HHS/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; R01 CA148761/CA/NCI NIH HHS/United States ; R01 CA049152/CA/NCI NIH HHS/United States ; R01 CA264933/CA/NCI NIH HHS/United States ; MOP-142375//CIHR/Canada ; R01 GM124446/GM/NIGMS NIH HHS/United States ; },
mesh = {*Breast Neoplasms/drug therapy/genetics/pathology ; Cell Line, Tumor ; Drug Resistance, Neoplasm ; Female ; Humans ; Phosphatidylinositol 3-Kinases/metabolism ; Receptor, ErbB-2/genetics/metabolism ; Signal Transduction ; },
abstract = {UNLABELLED: Resistance to targeted therapies is an important clinical problem in HER2-positive (HER2+) breast cancer. "Drug-tolerant persisters" (DTP), a subpopulation of cancer cells that survive via reversible, nongenetic mechanisms, are implicated in resistance to tyrosine kinase inhibitors (TKI) in other malignancies, but DTPs following HER2 TKI exposure have not been well characterized. We found that HER2 TKIs evoke DTPs with a luminal-like or a mesenchymal-like transcriptome. Lentiviral barcoding/single-cell RNA sequencing reveals that HER2+ breast cancer cells cycle stochastically through a "pre-DTP" state, characterized by a G0-like expression signature and enriched for diapause and/or senescence genes. Trajectory analysis/cell sorting shows that pre-DTPs preferentially yield DTPs upon HER2 TKI exposure. Cells with similar transcriptomes are present in HER2+ breast tumors and are associated with poor TKI response. Finally, biochemical experiments indicate that luminal-like DTPs survive via estrogen receptor-dependent induction of SGK3, leading to rewiring of the PI3K/AKT/mTORC1 pathway to enable AKT-independent mTORC1 activation.<br><br>SIGNIFICANCE: DTPs are implicated in resistance to anticancer therapies, but their ontogeny and vulnerabilities remain unclear. We find that HER2 TKI-DTPs emerge from stochastically arising primed cells ("pre-DTPs") that engage either of two distinct transcriptional programs upon TKI exposure. Our results provide new insights into DTP ontogeny and potential therapeutic vulnerabilities. This article is highlighted in the In This Issue feature, p. 873.},
}
@article {pmid34910721,
year = {2021},
author = {Plaisance, L and Matterson, K and Fabricius, K and Drovetski, S and Meyer, C and Knowlton, N},
title = {Effects of low pH on the coral reef cryptic invertebrate communities near CO2 vents in Papua New Guinea.},
journal = {PloS one},
volume = {16},
number = {12},
pages = {e0258725},
pmid = {34910721},
issn = {1932-6203},
mesh = {Animals ; *Anthozoa/classification/genetics/growth &amp; development ; *Biodiversity ; Carbon Dioxide/*analysis ; Coral Reefs ; *Crustacea/classification/genetics/growth &amp; development ; DNA Barcoding, Taxonomic ; *Gastropoda/classification/genetics/growth &amp; development ; Hydrogen-Ion Concentration ; Papua New Guinea ; Seawater/*analysis ; },
abstract = {Small cryptic invertebrates (the cryptofauna) are extremely abundant, ecologically important, and species rich on coral reefs. Ongoing ocean acidification is likely to have both direct effects on the biology of these organisms, as well as indirect effects through cascading impacts on their habitats and trophic relationships. Naturally acidified habitats have been important model systems for studying these complex interactions because entire communities that are adapted to these environmental conditions can be analyzed. However, few studies have examined the cryptofauna because they are difficult to census quantitatively in topographically complex habitats and are challenging to identify. We addressed these challenges by using Autonomous Reef Monitoring Structures (ARMS) for sampling reef-dwelling invertebrates >2 mm in size and by using DNA barcoding for taxonomic identifications. The study took place in Papua New Guinea at two reef localities, each with three sites at varying distances from carbon dioxide seeps, thereby sampling across a natural gradient in acidification. We observed sharp overall declines in both the abundance (34-56%) and diversity (42-45%) of organisms in ARMS under the lowest pH conditions sampled (7.64-7.75). However, the overall abundance of gastropods increased slightly in lower pH conditions, and crustacean and gastropod families exhibited varying patterns. There was also variability in response between the two localities, despite their close proximity, as one control pH site displayed unusually low diversity and abundances for all invertebrate groups. The data illustrate the complexity of responses of the reef fauna to pH conditions, and the role of additional factors that influence the diversity and abundance of cryptic reef invertebrates.},
}
@article {pmid34904939,
year = {2021},
author = {Wang, R and Belew, AT and Achuthan, V and El Sayed, N and DeStefano, JJ},
title = {Physiological magnesium concentrations increase fidelity of diverse reverse transcriptases from HIV-1, HIV-2, and foamy virus, but not MuLV or AMV.},
journal = {The Journal of general virology},
volume = {102},
number = {12},
pages = {},
pmid = {34904939},
issn = {1465-2099},
support = {R01 AI150480/AI/NIAID NIH HHS/United States ; },
mesh = {DNA, Viral/biosynthesis/genetics ; Drug Resistance, Viral/genetics ; Magnesium/analysis/*metabolism ; Mutation ; Mutation Rate ; RNA-Directed DNA Polymerase/*genetics/metabolism ; Retroviridae/classification/enzymology/*genetics ; },
abstract = {Reverse transcriptases (RTs) are typically assayed using optimized Mg[2+] concentrations (~5-10 mM) several-fold higher than physiological cellular free Mg[2+] (~0.5 mM). Recent analyses demonstrated that HIV-1, but not Moloney murine leukaemia (MuLV) or avain myeloblastosis (AMV) virus RTs has higher fidelity in low Mg[2+]. In the current report, lacZα-based α-complementation assays were used to measure the fidelity of several RTs including HIV-1 (subtype B and A/E), several drug-resistant HIV-1 derivatives, HIV-2, and prototype foamy virus (PFV), all which showed higher fidelity using physiological Mg[2+], while MuLV and AMV RTs demonstrated equivalent fidelity in low and high Mg[2+]. In 0.5 mM Mg[2+], all RTs demonstrated approximately equal fidelity, except for PFV which showed higher fidelity. A Next Generation Sequencing (NGS) approach that used barcoding to determine mutation profiles was used to examine the types of mutations made by HIV-1 RT (type B) in low (0.5 mM) and high (6 mM) Mg[2+] on a lacZα template. Unlike α-complementation assays which are dependent on LacZα activity, the NGS assay scores mutations at all positions and of every type. Consistent with α-complementation assays, a ~four-fold increase in mutations was observed in high Mg[2+]. These findings help explain why HIV-1 RT displays lower fidelity in vitro (with high Mg[2+] concentrations) than other RTs (e.g. MuLV and AMV), yet cellular fidelity for these viruses is comparable. Establishing in vitro conditions that accurately represent RT's activity in cells is pivotal to determining the contribution of RT and other factors to the mutation profile observed with HIV-1.},
}
@article {pmid34903916,
year = {2021},
author = {Sarker, BR and Mitpasa, T and Macotpet, A and Bupata, PA and Sangmaneedet, S and Taweenan, W},
title = {First report on molecular prevalence and identification of Anaplasma platys in dogs in Khon Kaen, Thailand.},
journal = {Veterinary world},
volume = {14},
number = {10},
pages = {2613-2619},
pmid = {34903916},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: Anaplasma platys is a blood parasite that infects platelets, causing thrombocytopenia. Rhipicephalus sanguineus ticks are believed to transmit A. platys. To identify A. platys, nested polymerase chain reaction (PCR) has proven to be an effective diagnostic tool. In this study, the molecular prevalence of A. platys infection in dogs was investigated for the 1[st] time in the Khon Kaen region of Thailand. The association between risk factors and A. platys infection was also evaluated.<br><br>MATERIALS AND METHODS: A total of 130 blood samples were collected from dogs in Khon Kaen, Thailand. DNA from the samples was extracted and nested PCR was applied for molecular analysis. Platelet count and packed cell volume (PCV) levels were measured. Platelet counts were categorized into four grades: Non-thrombocytopenia (platelets >200,000 cells/&#x3bc;L), mild thrombocytopenia (platelets 150,000-200,000 cells/&#x3bc;L), moderate thrombocytopenia (platelets 100,000-150,000 cells/&#x3bc;L), and severe thrombocytopenia (platelets <100,000 cells/&#x3bc;L). Four categories for PCV levels of >37%, 30-37%, 20-29%, and <20% were defined as no anemia, mild anemia, moderate anemia, and severe anemia, respectively. DNA sequencing was analyzed using BTSeq&#x2122; (Barcode-Tagged Sequencing; CELEMICS, Seoul, South Korea) for similarity index.<br><br>RESULTS: Among the 130 samples, 9 (6.9%) were positive for A. platys infection. There was an association between low platelet count and infection (p<0.05). PCV level was also associated with A. platys infection (p<0.05). DNA sequencing results of the nine positive samples showed similarity to known sequences of A. platys with 99.36-100% nucleotide identity. These results suggested low genetic diversity in A. platys infecting dogs in the Khon Kaen area.<br><br>CONCLUSION: By amplifying 16S rRNA, A. platys infection was detected in the blood of Thai dogs. Further work should be performed to identify risk factors potentially associated with A. platys infection in dogs in Khon Kaen. Other related factors should also be considered, such as location and breeding, as well as the environmental characteristics of each locality. In addition, sampling a larger number of animals may reveal predictors for the positivity of A. platys in dogs in this region.},
}
@article {pmid34901584,
year = {2021},
author = {Morgan, D and Jost, TA and De Santiago, C and Brock, A},
title = {Applications of high-resolution clone tracking technologies in cancer.},
journal = {Current opinion in biomedical engineering},
volume = {19},
number = {},
pages = {},
pmid = {34901584},
issn = {2468-4511},
support = {R21 CA212928/CA/NCI NIH HHS/United States ; U01 CA253540/CA/NCI NIH HHS/United States ; },
abstract = {Tumors are comprised of dynamic, heterogenous cell populations characterized by numerous genetic and non-genetic alterations that accumulate and change with disease progression and treatment. Retrospective analyses of tumor evolution have relied on the measurement of genetic markers (such as copy number variants) to infer clonal dynamics. However, these approaches neglect the critical contributions of non-genetic drivers of disease. Techniques that harness the power of prospective clone tracking via heritable barcode tags provide an alternative strategy. In this review, we discuss methods for high-resolution, quantitative clone tracking, including recent advancements to pair barcode-specific functionality with scRNA-seq, clonal cell isolation, and in situ hybridization and imaging. We discuss these approaches in the context of cancer cell heterogeneity and treatment resistance.},
}
@article {pmid34899006,
year = {2021},
author = {Li, Y and Li, S and Lin, Y},
title = {Taxonomic study on fourteen symphytognathid species from Asia (Araneae, Symphytognathidae).},
journal = {ZooKeys},
volume = {1072},
number = {},
pages = {1-47},
pmid = {34899006},
issn = {1313-2989},
abstract = {Fourteen symphytognathid species belonging to three genera are examined, including the descriptions of eight new species and two new genera from China, Vietnam, Thailand and Myanmar: Patu Marples, 1951: P.catba S. Li &amp; Lin, sp. nov. (♂, Vietnam), P.dakou S. Li &amp; Lin, sp. nov. (♂♀, China), P.damtao S. Li &amp; Lin, sp. nov. (♂, Vietnam), P.jiangzhou S. Li &amp; Lin, sp. nov. (♀, China), P.jidanweishi Miller, Griswold &amp; Yin, 2009 (♂♀, China), P.nagarat S. Li &amp; Lin, sp. nov. (♂♀, Thailand), P.nigeri Lin &amp; S. Li, 2009 (♀, China), P.putao S. Li &amp; Lin, sp. nov. (♀, Myanmar), P.qiqi Miller, Griswold &amp; Yin, 2009 (♀, China) and P.xiaoxiao Miller, Griswold &amp; Yin, 2009 (♂♀, China); Kirinua S. Li &amp; Lin, gen. nov.: K.maguai S. Li &amp; Lin, sp. nov. (♂♀, China) and K.yangshuo S. Li &amp; Lin, sp. nov. (♂♀, China); Swilda S. Li &amp; Lin, gen. nov.: S.longtou (Miller, Griswold &amp; Yin, 2009), comb. nov. (♂♀, China) is transferred from Crassignatha Wunderlich, 1995 and S.spinathoraxi (Lin &amp; S. Li, 2009), comb. nov. (♂♀, China) is transferred from Patu. Diagnoses, descriptions and illustrations are provided for new taxa, as well as a distribution map. The males of P.xiaoxiao and S.longtou are described for the first time. Type specimens of P.jidanweishi, P.nigeri, P.qiqi, P.xiaoxiao, S.longtou and S.spinathoraxi are re-examined and photographed. All Asian Patu species are revised and two species, P.kishidai Shinkai, 2009 and P.bispina Lin, Pham &amp; S. Li, 2009, are transferred to Crassignatha and proposed as new combinations: Crassignathakishidai comb. nov. and C.bispina comb. nov. In addition, DNA barcodes and genetic distances of ten species treated in this paper were obtained to confirm identification.},
}
@article {pmid34895334,
year = {2021},
author = {Wang, T and Redman, EM and Morosetti, A and Chen, R and Kulle, S and Morden, N and McFarland, C and Vineer, HR and Colwell, DD and Morgan, ER and Gilleard, JS},
title = {Seasonal epidemiology of gastrointestinal nematodes of cattle in the northern continental climate zone of western Canada as revealed by internal transcribed spacer-2 ribosomal DNA nemabiome barcoding.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {604},
pmid = {34895334},
issn = {1756-3305},
support = {ANH.04.17//Beef Cattle Research Council/ ; BB/R010250/1//UK Research and Innovation/ ; },
mesh = {Alberta/epidemiology ; Animals ; Cattle ; Cattle Diseases/*epidemiology/parasitology ; DNA Barcoding, Taxonomic/veterinary ; DNA, Protozoan/genetics ; DNA, Ribosomal Spacer/genetics ; Farms ; Feces/parasitology ; Gastrointestinal Tract/parasitology ; Larva ; Nematoda/genetics/*isolation &amp; purification ; Nematode Infections/epidemiology/parasitology/*veterinary ; Ostertagia/genetics/isolation &amp; purification ; Poaceae ; Seasons ; },
abstract = {BACKGROUND: Gastrointestinal nematode (GIN) epidemiology is changing in many regions of the world due to factors such as global warming and emerging anthelmintic resistance. However, the dynamics of these changes in northern continental climate zones are poorly understood due to a lack of empirical data.<br><br>METHODS: We studied the accumulation on pasture of free-living infective third-stage larvae (L3) of different GIN species from fecal pats deposited by naturally infected grazing cattle. The field study was conducted on three organic farms in Alberta, western Canada. Grass samples adjacent to 24 fecal pats were collected from each of three different pastures on each farm. Internal transcribed spacer-2 nemabiome metabarcoding was used to determine the GIN species composition of the harvested larvae. The rotational grazing patterns of the cattle ensured that each pasture was contaminated only once by fecal pat deposition. This design allowed us to monitor the accumulation of L3 of specific GIN species on pastures under natural climatic conditions without the confounding effects of pasture recontamination or anthelmintic treatments.<br><br>RESULTS: In seven out of the nine pastures, grass L3 counts peaked approximately 9&#xa0;weeks after fecal deposition and then gradually declined. However, a relatively large number of L3 remained in the fecal pats at the end of the grazing season. Nemabiome metabarcoding revealed that Cooperia oncophora and Ostertagia ostertagi were the two most abundant species on all of the pastures and that the dynamics of larval accumulation on grass were similar for both species. Daily precipitation and temperature across the whole sampling period were similar for most of the pastures, and multiple linear regression showed that accumulated rainfall 1&#xa0;week prior to sample collection had a significant impact on the pasture L3 population, but accumulated rainfall 3&#xa0;weeks prior to sample collection did not.<br><br>CONCLUSIONS: The results suggest that the pasture L3 population was altered by short-term microclimatic conditions conducive for horizontal migration onto grass. Overall, the results show the importance of the fecal pat as a refuge and reservoir for L3 of cattle GIN on western Canadian pastures, and provide an evidence base for the risk assessment of rotational grazing management in the region.},
}
@article {pmid34894203,
year = {2022},
author = {Ren, N and Li, B and Liu, Q and Yang, L and Liu, X and Huang, Q},
title = {Dinucleotide tag-based parallel reporter gene assay method enables efficient identification of regulatory mutations.},
journal = {Biotechnology journal},
volume = {17},
number = {4},
pages = {e2100341},
doi = {10.1002/biot.202100341},
pmid = {34894203},
issn = {1860-7314},
support = {ZR2016CM50//Shandong Provincial Natural Science Foundation, China/ ; 31872809//National Natural Science Foundation of China/ ; },
mesh = {Genes, Reporter/genetics ; *Genetic Predisposition to Disease ; Humans ; Male ; Mutation ; *Polymorphism, Single Nucleotide/genetics ; Regulatory Sequences, Nucleic Acid ; },
abstract = {BACKGROUND: The causal single nucleotide polymorphisms (SNPs) leading to increased cancer predisposition mainly function as gene regulatory elements, the evaluation of which largely relies on the parallel reporter gene assay system. However, the common DNA barcodes used in parallel reporter gene assay systems typically because nucleotide composition bias, and many barcodes must be allocated for each sequence to reduce the bias effect.<br><br>Here, a versatile dinucleotide-tag reporter system (DiR) that enables parallel analysis of regulatory elements with minimized bias based on next-generation sequencing is described. The DiR system is more robust than the classical luciferase assay method, particularly for the investigation of moderate-level regulatory elements. The authors applied the DiR-seq assay in the functional evaluation of SNPs with prostate cancer risk and nominated two and six regulatory SNPs in PC-3 and LNCaP cells, respectively.<br><br>CONCLUSIONS AND IMPLICATIONS: The DiR system has great potential to advance the functional study of SNPs associated with polygenic disease risks.},
}
@article {pmid34891160,
year = {2021},
author = {Arredondo-Alonso, S and Pöntinen, AK and Cléon, F and Gladstone, RA and Schürch, AC and Johnsen, PJ and Samuelsen, &#xd8; and Corander, J},
title = {A high-throughput multiplexing and selection strategy to complete bacterial genomes.},
journal = {GigaScience},
volume = {10},
number = {12},
pages = {},
pmid = {34891160},
issn = {2047-217X},
mesh = {Gene Library ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing/methods ; *Nanopores ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: Bacterial whole-genome sequencing based on short-read technologies often results in a draft assembly formed by contiguous sequences. The introduction of long-read sequencing technologies permits those contiguous sequences to be unambiguously bridged into complete genomes. However, the elevated costs associated with long-read sequencing frequently limit the number of bacterial isolates that can be long-read sequenced. Here we evaluated the recently released 96 barcoding kit from Oxford Nanopore Technologies (ONT) to generate complete genomes on a high-throughput basis. In addition, we propose an isolate selection strategy that optimizes a representative selection of isolates for long-read sequencing considering as input large-scale bacterial collections.<br><br>RESULTS: Despite an uneven distribution of long reads per barcode, near-complete chromosomal sequences (assembly contiguity = 0.89) were generated for 96 Escherichia coli isolates with associated short-read sequencing data. The assembly contiguity of the plasmid replicons was even higher (0.98), which indicated the suitability of the multiplexing strategy for studies focused on resolving plasmid sequences. We benchmarked hybrid and ONT-only assemblies and showed that the combination of ONT sequencing data with short-read sequencing data is still highly desirable (i) to perform an unbiased selection of isolates for long-read sequencing, (ii) to achieve an optimal genome accuracy and completeness, and (iii) to include small plasmids underrepresented in the ONT library.<br><br>CONCLUSIONS: The proposed long-read isolate selection ensures the completion of bacterial genomes that span the genome diversity inherent in large collections of bacterial isolates. We show the potential of using this multiplexing approach to close bacterial genomes on a high-throughput basis.},
}
@article {pmid34883532,
year = {2022},
author = {Banerjee, P and Elliott, E and Rifai, OM and O'Shaughnessy, J and McDade, K and Abrahams, S and Chandran, S and Smith, C and Gregory, JM},
title = {NLRP3 inflammasome as a key molecular target underlying cognitive resilience in amyotrophic lateral sclerosis.},
journal = {The Journal of pathology},
volume = {256},
number = {3},
pages = {262-268},
doi = {10.1002/path.5846},
pmid = {34883532},
issn = {1096-9896},
support = {/WT_/Wellcome Trust/United Kingdom ; NC/N001419/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; MR/L016400/1/MRC_/Medical Research Council/United Kingdom ; MC_EX_MR/N50192X/1/MRC_/Medical Research Council/United Kingdom ; MR/N013255/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Amyotrophic Lateral Sclerosis/*genetics/immunology/physiopathology/radiotherapy ; Brain/*immunology/physiopathology ; *Cognition ; Cognitive Dysfunction/*genetics/immunology/physiopathology/psychology ; Gene Expression Profiling ; Humans ; Inflammasomes/*genetics/immunology ; NLR Family, Pyrin Domain-Containing 3 Protein/*genetics/immunology ; *Resilience, Psychological ; Transcriptome ; },
abstract = {Up to 50% of amyotrophic lateral sclerosis patients present with cognitive deficits in addition to motor dysfunction, but the molecular mechanisms underlying diverse clinical and pathological presentations remain poorly understood. There is therefore an unmet need to identify molecular drivers of cognitive dysfunction to enable better therapeutic targeting and prognostication. To address this, we employed a non-biased approach to identify molecular targets using a deeply phenotyped, clinically stratified cohort of cognitively affected and unaffected brain regions from three brain regions of 13 amyotrophic lateral sclerosis patients with the same cognitive screening test performed during life. Using NanoString molecular barcoding as a sensitive mRNA sequencing technique on post-mortem tissue, we profiled a data-driven panel of 770 genes using the Neuropathology Panel, followed by region and cell type-specific validation using BaseScope in situ hybridisation and immunohistochemistry. We identified 50 significantly dysregulated genes that are distinct between cognitively affected and unaffected brain regions. Using BaseScope in situ hybridisation, we also demonstrate that macromolecular complex regulation, notably NLRP3 inflammasome modulation, is a potential, therapeutically targetable, pathological correlate of cognitive resilience in ALS. © 2021 The Authors. The Journal of Pathology published by John Wiley &amp; Sons, Ltd on behalf of The Pathological Society of Great Britain and Ireland.},
}
@article {pmid34880881,
year = {2021},
author = {Wang, C and Zhang, Y and Ding, H and Song, M and Yin, J and Yu, H and Li, Z and Han, L and Zhang, Z},
title = {Authentication of Zingiber Species Based on Analysis of Metabolite Profiles.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {705446},
pmid = {34880881},
issn = {1664-462X},
abstract = {Zingiber corallinum and Zingiber montanum, which belong to the Zingiberaceae family, are traditional Chinese folk medicinal herbs in Guizhou and Yunnan Province of China. They share great similarities in morphology, chemical constituent, and DNA barcoding sequence. The taxonomy of the two Zingiber species is controversial and discrimination of traditional Chinese medicines directly affects the pharmacological and clinical effects. In the present study, we performed a systemic analysis of "super-barcode" and untargeted metabolomics between Z. corallinum and Z. montanum using chloroplast (cp) genome sequencing and gas chromatography-mass spectrometry (GC-MS) analysis. Comparison and phylogenetic analysis of cp genomes of the two Zingiber species showed that the cp genome could not guarantee the accuracy of identification. An untargeted metabolomics strategy combining GC-MS with chemometric methods was proposed to distinguish the Zingiber samples of known variety. A total of 51 volatile compounds extracted from Z. corallinum and Z. montanum were identified, and nine compounds were selected as candidate metabolic markers to reveal the significant difference between Z. corallinum and Z. montanum. The performance of the untargeted metabolomic approach was verified with unknown Zingiber samples. Although the cp genomes could not be used to identify Zingiber species in this study, it will still provide a valuable genomics resource for population studies in the Zingiberaceae family, and the GC-MS based metabolic fingerprint is more promising for species identification and safe application of Z. corallinum and Z. montanum.},
}
@article {pmid34880496,
year = {2022},
author = {Fennell, KA and Vassiliadis, D and Lam, EYN and Martelotto, LG and Balic, JJ and Hollizeck, S and Weber, TS and Semple, T and Wang, Q and Miles, DC and MacPherson, L and Chan, YC and Guirguis, AA and Kats, LM and Wong, ES and Dawson, SJ and Naik, SH and Dawson, MA},
title = {Non-genetic determinants of malignant clonal fitness at single-cell resolution.},
journal = {Nature},
volume = {601},
number = {7891},
pages = {125-131},
pmid = {34880496},
issn = {1476-4687},
support = {/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; *Cell Competition/drug effects ; Cell Line ; Cell Lineage/drug effects ; Clone Cells/drug effects/metabolism/*pathology ; Female ; Humans ; Leukemia, Myeloid, Acute/drug therapy/genetics/*pathology ; Mice ; Mice, Inbred C57BL ; Secretory Leukocyte Peptidase Inhibitor/metabolism ; *Single-Cell Analysis ; },
abstract = {All cancers emerge after a period of clonal selection and subsequent clonal expansion. Although the evolutionary principles imparted by genetic intratumour heterogeneity are becoming increasingly clear[1], little is known about the non-genetic mechanisms that contribute to intratumour heterogeneity and malignant clonal fitness[2]. Here, using single-cell profiling and lineage tracing (SPLINTR)-an expressed barcoding strategy-we trace isogenic clones in three clinically relevant mouse models of acute myeloid leukaemia. We find that malignant clonal dominance is a cell-intrinsic and heritable property that is facilitated by the repression of antigen presentation and increased expression of the secretory leukocyte peptidase inhibitor gene (Slpi), which we genetically validate as a regulator of acute myeloid leukaemia. Increased transcriptional heterogeneity is a feature that enables clonal fitness in diverse tissues and immune microenvironments and in the context of clonal competition between genetically distinct clones. Similar to haematopoietic stem cells[3], leukaemia stem cells (LSCs) display heritable clone-intrinsic properties of high, and low clonal output that contribute to the overall tumour mass. We demonstrate that LSC clonal output dictates sensitivity to chemotherapy and, although high- and low-output clones adapt differently to therapeutic pressure, they coordinately emerge from minimal residual disease with increased expression of the LSC program. Together, these data provide fundamental insights into the non-genetic transcriptional processes that underpin malignant clonal fitness and may inform future therapeutic strategies.},
}
@article {pmid34880330,
year = {2021},
author = {Raskoti, BB and Ale, R},
title = {DNA barcoding of medicinal orchids in Asia.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {23651},
pmid = {34880330},
issn = {2045-2322},
mesh = {Asia ; *DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; Orchidaceae/*genetics ; Plants, Medicinal/*genetics ; Sequence Analysis, DNA/methods ; },
abstract = {Growing popularity of herbal medicine has increased the demand of medicinal orchids in the global markets leading to their overharvesting from natural habitats for illegal trade. To stop such illegal trade, the correct identification of orchid species from their traded products is a foremost requirement. Different species of medicinal orchids are traded as their dried or fresh parts (tubers, pseudobulbs, stems), which look similar to each other making it almost impossible to identify them merely based on morphological observation. To overcome this problem, DNA barcoding could be an important method for accurate identification of medicinal orchids. Therefore, this research evaluated DNA barcoding of medicinal orchids in Asia where illegal trade of medicinal orchids has long existed. Based on genetic distance, similarity-based and tree-based methods with sampling nearly 7,000 sequences from five single barcodes (ITS, ITS2, matK, rbcL, trnH-psbA and their seven combinations), this study revealed that DNA barcoding is effective for identifying medicinal orchids. Among single locus, ITS performed the best barcode, whereas ITS + matK exhibited the most efficient barcode among multi-loci. A barcode library as a resource for identifying medicinal orchids has been established which contains about 7,000 sequences of 380 species (i.e. 90%) of medicinal orchids in Asia.},
}
@article {pmid34880150,
year = {2022},
author = {Hussain, M and Liaqat, I and Mubin, M and Nisar, B and Shahzad, K and Durrani, AI and Zafar, U and Afzaal, M and Ehsan, A and Rubab, S},
title = {DNA Barcoding: Molecular Identification and Phylogenetic Analysis of Pheretimoid Earthworm (Metaphire sp. and Amynthas sp.) Based on Mitochondrial Partial COI Gene from Sialkot, Pakistan.},
journal = {Journal of oleo science},
volume = {71},
number = {1},
pages = {83-93},
doi = {10.5650/jos.ess21246},
pmid = {34880150},
issn = {1347-3352},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Mitochondria/*enzymology/*genetics ; Oligochaeta/anatomy &amp; histology/classification/*genetics ; Pakistan ; *Phylogeny ; Species Specificity ; },
abstract = {The extremely difficult and challenging process is identifying pheretimoid species, genus Metaphire and Amynthas involving increased homoplasy in various morphological characteristics. The molecular identification, phylogenetic relationships, and evolutionary divergence time of earthworms belonging to the pheretimoid complex were investigated in this study using partial mitochondrial COI (cytochrome C oxidase subunit I) gene sequences ranging from 550-680 bp. Results revealed that 86 pheretimoid earthworms were morphologically different from a total of 342 mature worms. Moreover, 11 pheretimoid species were molecularly identified, including Metaphire posthuma (02), M. anomala (01), M. houlleti (02), M. californica (01), M. birmanica (02), Amynthas minimus (01), A. morrisi (01), and M. bununa (01). A phylogenetic tree was constructed with bootstrap values of 95%, which supported a monophyletic lineage of two well-supported clades formed by 12 partial COI sequences and 48 GenBank sequences using Hirudo medicinalis as an outgroup. The monophyly of these obtained genera indicated overall similarity at species level. Today, species like Amynthas, Metaphire and Pheretima have worm diversity in the form of pheretimoid earthworms, which dates to the Late Miocene (11.2-5.3 Mya) and the Pliocene (5.3-2.4 Mya). Compared to all relevant pheretimoid species, genetic p-distance values ranged from 0.0% to 0.57% (less than 1%). These low range values demonstrated that both genera Metaphire and Amynthas, supported the theory, which states that there are shared similarities among the species, despite different morphology. The current study is the first attempt in Pakistan to identify earthworms through DNA barcoding thus providing a genomic stamp. The work explored the significance of COI gene sequences to construct molecular tools that will be useful to overcome the different obstacles in morphologically similar earthworm identification and their phylogenetic study.},
}
@article {pmid34879732,
year = {2022},
author = {Torres-Cruz, TJ and Whitaker, BK and Proctor, RH and Broders, K and Laraba, I and Kim, HS and Brown, DW and O'Donnell, K and Estrada-Rodríguez, TL and Lee, YH and Cheong, K and Wallace, EC and McGee, CT and Kang, S and Geiser, DM},
title = {FUSARIUM-ID v.3.0: An Updated, Downloadable Resource for Fusarium Species Identification.},
journal = {Plant disease},
volume = {106},
number = {6},
pages = {1610-1616},
doi = {10.1094/PDIS-09-21-2105-SR},
pmid = {34879732},
issn = {0191-2917},
mesh = {DNA, Fungal/genetics ; *Fusarium/genetics ; Phylogeny ; },
abstract = {Species within Fusarium are of global agricultural, medical, and food/feed safety concern and have been extensively characterized. However, accurate identification of species is challenging and usually requires DNA sequence data. FUSARIUM-ID (http://isolate.fusariumdb.org/blast.php) is a publicly available database designed to support the identification of Fusarium species using sequences of multiple phylogenetically informative loci, especially the highly informative ∼680-bp 5' portion of the translation elongation factor 1-alpha (TEF1) gene that has been adopted as the primary barcoding locus in the genus. However, FUSARIUM-ID v.1.0 and 2.0 had several limitations, including inconsistent metadata annotation for the archived sequences and poor representation of some species complexes and marker loci. Here, we present FUSARIUM-ID v.3.0, which provides the following improvements: (i) additional and updated annotation of metadata for isolates associated with each sequence, (ii) expanded taxon representation in the TEF1 sequence database, (iii) availability of the sequence database as a downloadable file to enable local BLAST queries, and (iv) a tutorial file for users to perform local BLAST searches using either freely available software, such as SequenceServer, BLAST+ executable in the command line, and Galaxy, or the proprietary Geneious software. FUSARIUM-ID will be updated on a regular basis by archiving sequences of TEF1 and other loci from newly identified species and greater in-depth sampling of currently recognized species.},
}
@article {pmid34878132,
year = {2022},
author = {Abrams, MB and Chuong, JN and AlZaben, F and Dubin, CA and Skerker, JM and Brem, RB},
title = {Barcoded reciprocal hemizygosity analysis via sequencing illuminates the complex genetic basis of yeast thermotolerance.},
journal = {G3 (Bethesda, Md.)},
volume = {12},
number = {2},
pages = {},
pmid = {34878132},
issn = {2160-1836},
support = {R01 GM120430/GM/NIGMS NIH HHS/United States ; R01 GM120430/NH/NIH HHS/United States ; },
mesh = {Chromosome Mapping/methods ; Genome-Wide Association Study/methods ; Humans ; Phenotype ; Saccharomyces cerevisiae/genetics ; *Thermotolerance/genetics ; },
abstract = {Decades of successes in statistical genetics have revealed the molecular underpinnings of traits as they vary across individuals of a given species. But standard methods in the field cannot be applied to divergences between reproductively isolated taxa. Genome-wide reciprocal hemizygosity mapping (RH-seq), a mutagenesis screen in an interspecies hybrid background, holds promise as a method to accelerate the progress of interspecies genetics research. Here, we describe an improvement to RH-seq in which mutants harbor barcodes for cheap and straightforward sequencing after selection in a condition of interest. As a proof of concept for the new tool, we carried out genetic dissection of the difference in thermotolerance between two reproductively isolated budding yeast species. Experimental screening identified dozens of candidate loci at which variation between the species contributed to the thermotolerance trait. Hits were enriched for mitosis genes and other housekeeping factors, and among them were multiple loci with robust sequence signatures of positive selection. Together, these results shed new light on the mechanisms by which evolution solved the problems of cell survival and division at high temperature in the yeast clade, and they illustrate the power of the barcoded RH-seq approach.},
}
@article {pmid34877379,
year = {2021},
author = {Monfared, M and Koochari, A and Monshianmotlagh, R},
title = {QR-DN1.0: A new distorted and noisy QRs dataset.},
journal = {Data in brief},
volume = {39},
number = {},
pages = {107605},
doi = {10.1016/j.dib.2021.107605},
pmid = {34877379},
issn = {2352-3409},
abstract = {Barcodes are playing a significant role in different industries in the recent years and among the two most popular 2D barcodes, the QR code has grown exponentially. The QR-DN1.0 dataset includes 5 categories of QR codes that will cover low to high density levels. Each group has 15 QR codes: 5 images for testing and 10 images for training. After embedding the QRs into 30 color images using blind watermarking techniques and then extracting the QRs from the images taken with the mobile phone camera with three different methods, we will have three groups of 2250 extracted QR images, which provides a total of 6750 distorted and noisy QR images. In each of the mentioned three categories, the data is divided into two parts: testing, with 750 images, and training, with 2250 images. For every distorted QR in the dataset, a non-distorted instance of it is placed as a ground truth. One of the advantages of this data set is that it is real. Because no simulated noise has been added to the images and this dataset is completely derived from the real word challenge of extracting embedded QRs in color images captured from the watermarked image on the screen. It also includes various types of QRs such as single character, short sentence, long sentence, URL and location.},
}
@article {pmid34872502,
year = {2021},
author = {Dong, S and Ying, Z and Yu, S and Wang, Q and Liao, G and Ge, Y and Cheng, R},
title = {Complete chloroplast genome of Stephania tetrandra (Menispermaceae) from Zhejiang Province: insights into molecular structures, comparative genome analysis, mutational hotspots and phylogenetic relationships.},
journal = {BMC genomics},
volume = {22},
number = {1},
pages = {880},
pmid = {34872502},
issn = {1471-2164},
mesh = {*Genome, Chloroplast ; *Menispermaceae ; Molecular Structure ; Phylogeny ; *Stephania tetrandra ; },
abstract = {BACKGROUND: The Stephania tetrandra S. Moore (S. tetrandra) is a medicinal plant belonging to the family Menispermaceae that has high medicinal value and is well worth doing further exploration. The wild resources of S. tetrandra were widely distributed in tropical and subtropical regions of China, generating potential genetic diversity and unique population structures. The geographical origin of S. tetrandra is an important factor influencing its quality and price in the market. In addition, the species relationship within Stephania genus still remains uncertain due to high morphological similarity and low support values of molecular analysis approach. The complete chloroplast (cp) genome data has become a promising strategy to determine geographical origin and understand species evolution for closely related plant species. Herein, we sequenced the complete cp genome of S. tetrandra from Zhejiang Province and conducted a comparative analysis within Stephania plants to reveal the structural variations, informative markers and phylogenetic relationship of Stephania species.<br><br>RESULTS: The cp genome of S. tetrandra voucher ZJ was 157,725&#x2009;bp, consisting of a large single copy region (89,468&#x2009;bp), a small single copy region (19,685&#x2009;bp) and a pair of inverted repeat regions (24,286&#x2009;bp each). A total of 134 genes were identified in the cp genome of S. tetrandra, including 87 protein-coding genes, 8 rRNA genes, 37 tRNA genes and 2 pseudogene copies (ycf1 and rps19). The gene order and GC content were highly consistent in the Stephania species according to the comparative analysis results, with the highest RSCU value in arginine (1.79) and lowest RSCU value in serine of S. tetrandra, respectively. A total of 90 SSRs have been identified in the cp genome of S. tetrandra, where repeats that consisting of A or T bases were much higher than that of G or C bases. In addition, 92 potential RNA editing sites were identified in 25 protein-coding genes, with the most predicted RNA editing sites in ndhB gene. The variations on length and expansion extent to the junction of ycf1 gene were observed between S. tetrandra vouchers from different regions, indicating potential markers for further geographical origin discrimination. Moreover, the values of transition to transversion ratio (Ts/Tv) in the Stephania species were significantly higher than 1 using Pericampylus glaucus as reference. Comparative analysis of the Stephania cp genomes revealed 5 highly variable regions, including 3 intergenic regions (trnH-psbA, trnD-trnY, trnP) and two protein coding genes (rps16 and ndhA). The identified mutational hotspots of Stephania plants exhibited multiple SNP sites and Gaps, as well as different Ka/Ks ratio values. In addition, five pairs of specific primers targeting the divergence regions were accordingly designed, which could be utilized as potential molecular markers for species identification, population genetic and phylogenetic analysis in Stephania species. Phylogenetic tree analysis based on the conserved chloroplast protein coding genes indicated a sister relationship between S. tetrandra and the monophyletic group of S. japonica and S. kwangsiensis with high support values, suggesting a close genetic relationship within Stephania plants. However, two S. tetrandra vouches from different regions failed to cluster into one clade, confirming the occurrences of genetic diversities and requiring further investigation for geographical tracing strategy.<br><br>CONCLUSIONS: Overall, we provided comprehensive and detailed information on the complete chloroplast genome and identified nucleotide diversity hotspots of Stephania species. The obtained genetic resource of S. tetrandra from Zhejiang Province would facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of Stephania plants.},
}
@article {pmid34866964,
year = {2021},
author = {Vargas, HA},
title = {New distribution records, first host plant record and DNA barcoding of the Neotropical plume moth Oidaematophoruspseudotrachyphloeus Gielis (Lepidoptera, Pterophoridae).},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e77167},
pmid = {34866964},
issn = {1314-2828},
abstract = {BACKGROUND: Oidaematophoruspseudotrachyphloeus Gielis, 2011 (Lepidoptera, Pterophoridae) is a little-known Neotropical plume moth previously recorded in Ecuador, Peru and Argentina. Its host plants and DNA barcodes are unknown.<br><br>NEW INFORMATION: Oidaematophoruspseudotrachyphloeus is recorded for the first time from Chile, based on six specimens from the Azapa Valley (Arica Province) and two from Guayac&#xe1;n (Coquimbo Province). Those from the Azapa Valley were reared from folivorous larvae collected on Ambrosiacumanensis Kunth (Asteraceae), representing the first host plant record for this plume moth. The first DNA barcode sequences of O.pseudotrachyphloeus are provided and used to explore relationships with congenerics.},
}
@article {pmid34865465,
year = {2021},
author = {Lee, I and Kwon, SJ and Sorci, M and Heeger, PS and Dordick, JS},
title = {Highly Sensitive Immuno-CRISPR Assay for CXCL9 Detection.},
journal = {Analytical chemistry},
volume = {93},
number = {49},
pages = {16528-16534},
pmid = {34865465},
issn = {1520-6882},
support = {U01 AI063594/AI/NIAID NIH HHS/United States ; },
mesh = {Chemokine CXCL9/*urine ; *Clustered Regularly Interspaced Short Palindromic Repeats ; *DNA, Single-Stranded ; Graft Rejection/*diagnosis ; Humans ; *Immunoassay ; Kidney Transplantation ; Limit of Detection ; RNA ; Streptavidin ; Transplant Recipients ; },
abstract = {CRISPR-based detection of target DNA or RNA exploits a dual function, including target sequence-specific recognition followed by trans-cleavage activity of a collateral ssDNA linker between a fluorophore (F) and a quencher (Q), which amplifies a fluorescent signal upon cleavage. In this work, we have extended such dual functionality in a modified immunoassay format to detect a target protein, CXCL9, which is markedly elevated in the urine of kidney transplant recipients undergoing acute rejection episodes. To establish the "immuno-CRISPR" assay, we used anti-CXCL9 antibody-DNA barcode conjugates to target CXCL9 and amplify fluorescent signals via Cas12a-based trans-cleavage activity of FQ reporter substrates, respectively, and in the absence of an isothermal amplification step. To enhance detection sensitivity, the DNA barcode system was engineered by introducing multiple Cas12a recognition sites. Use of biotinylated DNA barcodes enabled self-assembly onto streptavidin (SA) to generate SA-DNA barcode complexes to increase the number and density of Cas12a recognition sites attached to biotinylated anti-CXCL9 antibody. As a result, we improved the rate of CXCL9 detection approximately 8-fold when compared to the use of a monomeric DNA barcode. The limit of detection (LOD) for CXCL9 using the immuno-CRISPR assay was 14 pg/mL, which represented an ∼7-fold improvement when compared to traditional HRP-based ELISA. Selectivity was shown with a lack of crossover reactivity with the related chemokine CXCL1. Finally, we successfully evaluated the presence of CXCL9 in urine samples from 11 kidney transplant recipients using the immuno-CRISPR assay, resulting in 100% accuracy to clinical CXCL9 determination and paving the way for use as a point-of-care noninvasive biomarker for the detection of kidney transplant rejection.},
}
@article {pmid34863107,
year = {2021},
author = {Mao, X and Xie, W and Li, X and Shi, S and Guo, Z},
title = {Establishing community-wide DNA barcode references for conserving mangrove forests in China.},
journal = {BMC plant biology},
volume = {21},
number = {1},
pages = {571},
pmid = {34863107},
issn = {1471-2229},
mesh = {China ; Conservation of Natural Resources/*methods ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Magnoliopsida/*genetics ; Plants/*genetics ; *Wetlands ; },
abstract = {BACKGROUND: Mangrove ecosystems have been the focus of global attention for their crucial role in sheltering coastal communities and retarding global climate change by sequestering 'blue carbon'. China is relatively rich in mangrove diversity, with one-third of the ca. 70 true mangrove species and a number of mangrove associate species occurring naturally along the country's coasts. Mangrove ecosystems, however, are widely threatened by intensifying human disturbances and rising sea levels. DNA barcoding technology may help protect mangrove ecosystems by providing rapid species identification.<br><br>RESULTS: To investigate this potential, 898 plant specimens were collected from 33 major mangrove sites in China. Based on the morphologic diagnosis, the specimens were assigned to 72 species, including all 28 true mangrove species and all 12 mangrove associate species recorded in China. Three chloroplast DNA markers rbcL, trnH-psbA, matK, and one nuclear marker ITS2 were chosen to investigate the utility of using barcoding to identify these species. According to the criteria of barcoding gaps in genetic distance, sequence similarity, and phylogenetic monophyly, we propose that a single marker, ITS2, is sufficient to barcode the species of mangroves and their associates in China. Furthermore, rbcL or trnH-psbA can also be used to gather supplement confirming data. In using these barcodes, we revealed a very low level of genetic variation among geographic locations in the mangrove species, which is an alert to their vulnerability to climate and anthropogenic disturbances.<br><br>CONCLUSION: We suggest using ITS2 to barcode mangrove species and terrestrial coastal plants in South China. The DNA barcode sequences we obtained would be valuable in monitoring biodiversity and the restoration of ecosystems, which are essential for mangrove conservation.},
}
@article {pmid34863029,
year = {2022},
author = {Wührl, L and Pylatiuk, C and Giersch, M and Lapp, F and von Rintelen, T and Balke, M and Schmidt, S and Cerretti, P and Meier, R},
title = {DiversityScanner: Robotic handling of small invertebrates with machine learning methods.},
journal = {Molecular ecology resources},
volume = {22},
number = {4},
pages = {1626-1638},
doi = {10.1111/1755-0998.13567},
pmid = {34863029},
issn = {1755-0998},
support = {//Center for Integrative Biodiversity Discovery at the Museum f&#xfc;r Naturkunde Berlin/ ; },
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/methods ; Ecosystem ; Humans ; Invertebrates/genetics ; Machine Learning ; *Robotic Surgical Procedures ; *Robotics ; },
abstract = {Invertebrate biodiversity remains poorly understood although it comprises much of the terrestrial animal biomass, most species and supplies many ecosystem services. The main obstacle is specimen-rich samples obtained with quantitative sampling techniques (e.g., Malaise trapping). Traditional sorting requires manual handling, while molecular techniques based on metabarcoding lose the association between individual specimens and sequences and thus struggle with obtaining precise abundance information. Here we present a sorting robot that prepares specimens from bulk samples for barcoding. It detects, images and measures individual specimens from a sample and then moves them into the wells of a 96-well microplate. We show that the images can be used to train convolutional neural networks (CNNs) that are capable of assigning the specimens to 14 insect taxa (usually families) that are particularly common in Malaise trap samples. The average assignment precision for all taxa is 91.4% (75%-100%). This ability of the robot to identify common taxa then allows for taxon-specific subsampling, because the robot can be instructed to only pick a prespecified number of specimens for abundant taxa. To obtain biomass information, the images are also used to measure specimen length and estimate body volume. We outline how the DiversityScanner can be a key component for tackling and monitoring invertebrate diversity by combining molecular and morphological tools: the images generated by the robot become training images for machine learning once they are labelled with taxonomic information from DNA barcodes. We suggest that a combination of automation, machine learning and DNA barcoding has the potential to tackle invertebrate diversity at an unprecedented scale.},
}
@article {pmid34861482,
year = {2022},
author = {Hassdenteufel, S and Schuldiner, M},
title = {Show your true color: Mammalian cell surface staining for tracking cellular identity in multiplexing and beyond.},
journal = {Current opinion in chemical biology},
volume = {66},
number = {},
pages = {102102},
doi = {10.1016/j.cbpa.2021.102102},
pmid = {34861482},
issn = {1879-0402},
mesh = {Animals ; Cell Membrane/metabolism ; *Fluorescent Dyes/chemistry ; *Mammals ; Microscopy, Fluorescence/methods ; Staining and Labeling ; },
abstract = {Fluorescence microscopy revolutionized cell biology and changed requirements for dyes towards higher brightness, novel capacities, and specific targets. With the need for multiplexing assays in high-throughput methodologies, surface staining gained particular interest because it allows rapid application of exogenous stains to track cellular identity in mixed populations. Indeed, the last decade has enriched the toolbox of general lipid stains, fluorescent lipid analogues, sugar-binding lectins, and protein-specific antibodies enabling the first rationally designed plasma membrane-specific dyes. Still, multiple challenges exist, and the unique properties of each dye must be considered when selecting a staining approach for a specific application. Recent advances are also promising that future dyes will provide ultimate brightness and photostability in diverse colors and reduced sizes for high-resolution imaging.},
}
@article {pmid34860432,
year = {2022},
author = {Philippe, F and Dubrulle, N and Marteaux, B and Bonnet, B and Choisy, P and Berthon, JY and Garnier, L and Leconte, N and Milesi, S and Morvan, PY and Saunois, A and Sun, JS and Weber, S and Giraud, N},
title = {Combining DNA Barcoding and Chemical fingerprints to authenticate Lavender raw material.},
journal = {International journal of cosmetic science},
volume = {44},
number = {1},
pages = {91-102},
pmid = {34860432},
issn = {1468-2494},
mesh = {*DNA Barcoding, Taxonomic/methods ; DNA, Plant/genetics ; Genetic Markers ; *Lavandula/genetics ; Reproducibility of Results ; },
abstract = {OBJECTIVE: This study was initiated and conducted by several laboratories, 3 of the main cosmetic ingredient suppliers and 4 brands of cosmetics in France. Its objective is to show the interest and robustness of coupling chemical and genetic analyses in the identification of plant species. In this study, the Lavandula genus was used.<br><br>METHODS: In this study, we used two analytical methods. Chemical analysis from UHPLC (ultra-high-performance liquid chromatography) and genetic analysis from barcoding with genetic markers.<br><br>RESULTS: Eleven lavender species were selected (botanically authenticated) and analysed. The results show that three chemical compounds (coumaric acid hexoside, ferulic acid hexoside and rosmarinic acid) and three genetic markers (RbcL, trnH-psbA and ITS) are of interest for the differentiation of species of the genus lavandula.<br><br>CONCLUSION: The results show that the combination of complementary analytical methods is a relevant system to prove the botanical identification of lavender species. This first study, carried out on a plant of interest for cosmetics, demonstrates the need for authentication using a tool combining genetic and chemical analysis as an advance over traditional investigation methods used alone, in terms of identification and authentication reliability.},
}
@article {pmid34860238,
year = {2022},
author = {Vicente, E and Lesniewski, M and Newman, D and Vujaskovic, Z and Jackson, IL},
title = {Best Practices for Authentication of Cell Lines to Ensure Data Reproducibility and Integrity.},
journal = {Radiation research},
volume = {197},
number = {3},
pages = {209-217},
doi = {10.1667/RADE-21-00148.1},
pmid = {34860238},
issn = {1938-5404},
support = {HHSO100201500009I/HH/HHS/United States ; HHSO10033001T/HH/HHS/United States ; },
mesh = {Animals ; Cattle ; Cell Line ; *DNA ; *Endothelial Cells ; Mice ; Polymerase Chain Reaction ; Rabbits ; Reproducibility of Results ; },
abstract = {Cell line misidentification and contamination are major contributors to the reproducibility crisis in academic research. Authentication of cell lines provides assurances of the data generated; however, commercially available cells are often not subjected to rigorous identification testing. In this study, commercially available cell lines underwent testing to confirm cell identity and purity. The methods reported here outline the best practices for cell line authentication. Briefly, a commercially available primary rabbit aortic endothelial cell line was purchased for the intent of producing target proteins necessary for generating species-specific recombinant antibodies. These rabbit-specific antibodies would then be utilized for the development of in-house enzyme-linked immunosorbent assays (ELISA) to evaluate blood-based biomarkers of vascular injury after total-body irradiation. To authenticate the cell line, cell identity and purity were determined by single tandem repeat (STR) testing, flow cytometry, polymerase chain reaction (PCR), and cytochrome c oxidase subunit 1 (CO1) DNA Barcoding in-house and/or through commercial vendors. Fresh cells obtained from a New Zealand White rabbit (Charles River, Wilmington, DE) were used as a positive control. The results of STR and flow cytometry analyses indicated the cells were not contaminated with human or mouse cells, and that the cells were not of endothelial origin. PCR demonstrated that cells were also not of rabbit origin, which was further confirmed by a third-party vendor. An unopened vial of cells was submitted to another vendor for CO1 DNA Barcoding analysis, which identified the cells as being purely of bovine origin. Results revealed that despite purchase through a commercial vendor, the cell line marketed as primary rabbit aortic endothelial cells were of bovine origin. Purity analysis found cells were misidentified rather than contaminated. Further investigation to determine the cell type was not performed. The most cost-effective and efficient methodology for confirming cell line identity was found to be CO1 DNA Barcoding performed by a commercial vendor.},
}
@article {pmid34858079,
year = {2021},
author = {Pichler, A and Walters, TL and Frischer, ME and Nejstgaard, JC and Ptáčníková, R},
title = {Application of species-specific primers to estimate the in situ diet of Bythotrephes [Cladocera, Onychopoda] in its native European range via molecular gut content analysis.},
journal = {Journal of plankton research},
volume = {43},
number = {6},
pages = {945-956},
pmid = {34858079},
issn = {0142-7873},
abstract = {The study of invasive species often focuses on regions of recent introduction rather than native habitats. Understanding an invasive species in its natural environment, however, can provide important insights regarding the long-term outcome of invasions. In this study we investigated the diet of the invasive spiny water flea, Bythotrephes longimanus, in two Austrian perialpine lakes, where it is native. The gut contents of wild-caught Bythotrephes individuals were estimated by quantitative polymerase chain reaction, targeting species-specific fragments of the barcoding region of the cytochrome c oxidase I gene of potential prey. The observed prey spectrum of Bythotrephes in the study lakes consisted primarily of Eudiaptomus gracilis and Diaphanosoma brachyurum. The Daphnia longispina complex, Leptodora kindtii and Mesocyclops leuckarti also contributed to the diet. Results indicate that Bythotrephes is a generalist feeder with a preference for epilimnetic prey.},
}
@article {pmid34857936,
year = {2021},
author = {Liu, K and Deng, S and Ye, C and Yao, Z and Wang, J and Gong, H and Liu, L and He, X},
title = {Mapping single-cell-resolution cell phylogeny reveals cell population dynamics during organ development.},
journal = {Nature methods},
volume = {18},
number = {12},
pages = {1506-1514},
pmid = {34857936},
issn = {1548-7105},
mesh = {Alleles ; Animals ; Animals, Genetically Modified ; Cell Division ; Cell Lineage ; Computational Biology/*methods ; DNA Replication ; Drosophila melanogaster/embryology/*metabolism ; Endonucleases/metabolism ; Likelihood Functions ; Male ; Microscopy/*methods ; Mutagenesis ; *Mutation ; Phenotype ; Phylogeny ; Saccharomyces cerevisiae/genetics ; Single-Cell Analysis ; },
abstract = {Mapping the cell phylogeny of a complex multicellular organism relies on somatic mutations accumulated from zygote to adult. Available cell barcoding methods can record about three mutations per barcode, enabling only low-resolution mapping of the cell phylogeny of complex organisms. Here we developed SMALT, a substitution mutation-aided lineage-tracing system that outperforms the available cell barcoding methods in mapping cell phylogeny. We applied SMALT to Drosophila melanogaster and obtained on average more than 20 mutations on a three-kilobase-pair barcoding sequence in early-adult cells. Using the barcoding mutations, we obtained high-quality cell phylogenetic trees, each comprising several thousand internal nodes with 84-93% median bootstrap support. The obtained cell phylogenies enabled a population genetic analysis that estimates the longitudinal dynamics of the number of actively dividing parental cells (Np) in each organ through development. The Np dynamics revealed the trajectory of cell births and provided insight into the balance of symmetric and asymmetric cell division.},
}
@article {pmid34854729,
year = {2021},
author = {Yin, G and Jurick, WM and Zhao, G and Bennett, JW},
title = {New Names for Three Penicillium Strains Based on Updated Barcoding and Phylogenetic Analyses.},
journal = {Microbiology resource announcements},
volume = {10},
number = {48},
pages = {e0046621},
pmid = {34854729},
issn = {2576-098X},
}
@article {pmid34849489,
year = {2021},
author = {Yan, R and Cheng, X and Guo, F},
title = {Protocol for scChaRM-seq: Simultaneous profiling of gene expression, DNA methylation, and chromatin accessibility in single cells.},
journal = {STAR protocols},
volume = {2},
number = {4},
pages = {100972},
pmid = {34849489},
issn = {2666-1667},
mesh = {Cells, Cultured ; *Chromatin/chemistry/genetics ; DNA Methylation/*genetics ; *Genetic Techniques ; Humans ; Oocytes/chemistry/metabolism ; Single-Cell Analysis/*methods ; Transcriptome/*genetics ; },
abstract = {Single-cell multi-omics sequencing technology can infer cell heterogeneity and reveal relationships across molecular layers. Combining single-cell RNA sequencing, DNA methylation, and chromatin accessibility allows a multimodal understanding of cell function and epigenetic regulation within individual cells. Here, we offer a protocol to perform scChaRM-seq (single-cell chromatin accessibility, RNA barcoding, and DNA methylation sequencing), which has been applied to study de novo DNA methylation and its relationship with transcription and chromatin accessibility in single human oocytes. For complete details on the use and execution of this protocol, please refer to Yan et al. (2021).},
}
@article {pmid34847786,
year = {2022},
author = {Avarave, S and Thomas, J},
title = {Biodiversity of South Indian tea clones with detection of plant-based adulterants in tea dust using DNA barcoding.},
journal = {Natural product research},
volume = {36},
number = {18},
pages = {4614-4619},
doi = {10.1080/14786419.2021.2002325},
pmid = {34847786},
issn = {1478-6427},
mesh = {Biodiversity ; *Camellia sinensis/genetics ; Clone Cells ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Dust ; Phylogeny ; Plants ; Sequence Analysis, DNA ; Tea/genetics ; },
abstract = {Tea is by and large a highly penetrated product in south India. Hence the adulteration risk in tea dust gets hiked in the markets. We constructed a standard database using plant plastid markers (rbcL, matK, trnH-psbA, rpoC, rpoB, ycf 1) and nuclear (ITS2) locus from prominent south Indian tea clones representing Assam, China, and Cambod varieties. These barcodes were used as reference algorithm to investigate the authenticity of 10 sampled commercial tea dust by recovering its DNA barcodes using rbcL, matK, and ITS2 loci. PCR amplification success, sequencing efficiency, genetic polymorphisms, BLAST search, and phylogenetic analysis were performed to enhance genotypic information on south tea cultivars and in authenticating the commercial samples of Camellia sinensis. Findings suggest that the chloroplast and nuclear loci can identify tea plant at the genus and varietal level respectively and rbcL as the potential marker for detecting plant-based admixtures coupled with TA cloning after DNA barcoding.},
}
@article {pmid34847223,
year = {2021},
author = {Whipps, CM and McAllister, CT and Lindsay, KA},
title = {GENETIC DIVERSITY OF CYSTODISCUS SPECIES IN AMPHIBIANS IN THE SOUTHERN UNITED STATES.},
journal = {The Journal of parasitology},
volume = {107},
number = {6},
pages = {912-922},
doi = {10.1645/21-73},
pmid = {34847223},
issn = {1937-2345},
mesh = {Amphibians/*parasitology ; Animals ; Anura/parasitology ; Arkansas/epidemiology ; Gallbladder/parasitology ; *Genetic Variation ; Myxozoa/classification/*genetics ; Oklahoma/epidemiology ; Parasitic Diseases, Animal/epidemiology/*parasitology ; Phylogeny ; Prevalence ; Sequence Analysis, DNA/veterinary ; Caudata/parasitology ; },
abstract = {Myxosporean species in the genus Cystodiscus are parasites of amphibians and have been reported from several continents. Typically used for the identification of myxozoans, the spores produced by these species are similar to one another, possessing 2 polar capsules and being ovoid. The number of transverse depressions on the spore can be useful for delineating species, but these can sometimes be difficult to distinguish. In North America, Cystodiscus serotinus and Cystodiscus melleni have been described, and for C. serotinus in particular, numerous reports and a wide range of hosts have been associated with this species. Given the challenges of identifying some of these species, we questioned whether all encounters of Cystodiscus species can be attributed to these 2 described species, or if there may be additional undescribed species or cryptic species. Over 7 yr, 383 amphibians representing 13 species of toads, frogs, and salamanders were collected from sites in Oklahoma and Arkansas. Cystodiscus infections were found in 56 individuals (14.6%). Tissues from these infected individuals were preserved in alcohol for genetic analysis. The small subunit (SSU) and large subunit (LSU) ribosomal RNA genes were partially sequenced and analyzed phylogenetically. Nine distinct SSU sequence types and 7 distinct LSU sequence types were identified. Phylogenetically, sequence types were attributable to C. serotinus, C. melleni, Cystodiscus axonis, and an undescribed species. For the previously described species, there were multiple SSU sequence types: 4 for C. serotinus and 2 for both C. melleni and C. axonis. Phylogenetic patterns were similar for the LSU sequence analysis using a shorter sequence than the SSU, and we propose that the LSU is useful for initial barcoding of Cystodiscus species in any future surveys. In our qualitative assessment of sequence types compared to geography and host species, SSU types C1 and C2 (C. axonis) were only found in Union County, Arkansas, and McCurtain County, Oklahoma, respectively. Also, salamanders were only infected with SSU types B or D (C. melleni), and type B was only found in salamanders. Our finding of C. axonis in North America is notable because this species was described in Australia and is associated with host pathology. Our work reveals that there are cryptic species of Cystodiscus in the United States, one of which may be a pathogen, highlighting the importance of genetic analysis for future surveys of these species.},
}
@article {pmid34846701,
year = {2022},
author = {Senapati, A and Basak, S and Rangan, L},
title = {A Review on Application of DNA Barcoding Technology for Rapid Molecular Diagnostics of Adulterants in Herbal Medicine.},
journal = {Drug safety},
volume = {45},
number = {3},
pages = {193-213},
pmid = {34846701},
issn = {1179-1942},
mesh = {DNA ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Herbal Medicine ; Humans ; Pathology, Molecular ; *Plants, Medicinal/genetics ; Technology ; },
abstract = {The rapid molecular diagnostics of adulterants in herbal medicine using DNA barcoding forms the core of this meticulously detailed review, based on two decades of data. With 80% of the world's population using some form of herbal medicine, authentication, quality control, and detection of adulterants warrant DNA barcoding. A combined group of keywords were used for literature review using the PubMed, the ISI Web of Knowledge, Web of Science (WoS), and Google Scholar databases. All the papers (N = 210) returned by the search engines were downloaded and systematically analyzed. Detailed analysis of conventional DNA barcodes were based on retrieved sequences for internal transcribed spacer (ITS) (412,189), rbcL (251,598), matK (210,835), and trnH-psbA (141,846). The utility of databases such as The Barcode of Life Data System (BOLD), NCBI, GenBank, and Medicinal Materials DNA Barcode Database (MMDBD) has been critically examined for the identification of unknown species from known databases. The current review gives an overview of the ratio of adulterated to authentic drugs for some countries along with the state of the art technology currently being used in the identification of adulterated medicines. In this review, efforts were made to systematically analyze and arrange the research and reviews on the basis of technical progress. The review concludes with the future of DNA-based herbal medicine adulteration detection, forecasting the reliance on the metabarcoding technology. DNA barcoding technology for differentiating adulterated herbal medicine.},
}
@article {pmid34843574,
year = {2021},
author = {Torstensson, E and Goyal, G and Johnning, A and Westerlund, F and Ambjörnsson, T},
title = {Combining dense and sparse labeling in optical DNA mapping.},
journal = {PloS one},
volume = {16},
number = {11},
pages = {e0260489},
pmid = {34843574},
issn = {1932-6203},
mesh = {DNA/*analysis ; DNA Barcoding, Taxonomic/*methods ; Databases, Nucleic Acid ; Fluorescent Dyes/analysis ; Optical Imaging/*methods ; Plasmids/analysis ; },
abstract = {Optical DNA mapping (ODM) is based on fluorescent labeling, stretching and imaging of single DNA molecules to obtain sequence-specific fluorescence profiles, DNA barcodes. These barcodes can be mapped to theoretical counterparts obtained from DNA reference sequences, which in turn allow for DNA identification in complex samples and for detecting structural changes in individual DNA molecules. There are several types of DNA labeling schemes for ODM and for each labeling type one or several types of match scoring methods are used. By combining the information from multiple labeling schemes one can potentially improve mapping confidence; however, combining match scores from different labeling assays has not been implemented yet. In this study, we introduce two theoretical methods for dealing with analysis of DNA molecules with multiple label types. In our first method, we convert the alignment scores, given as output from the different assays, into p-values using carefully crafted null models. We then combine the p-values for different label types using standard methods to obtain a combined match score and an associated combined p-value. In the second method, we use a block bootstrap approach to check for the uniqueness of a match to a database for all barcodes matching with a combined p-value below a predefined threshold. For obtaining experimental dual-labeled DNA barcodes, we introduce a novel assay where we cut plasmid DNA molecules from bacteria with restriction enzymes and the cut sites serve as sequence-specific markers, which together with barcodes obtained using the established competitive binding labeling method, form a dual-labeled barcode. All experimental data in this study originates from this assay, but we point out that our theoretical framework can be used to combine data from all kinds of available optical DNA mapping assays. We test our multiple labeling frameworks on barcodes from two different plasmids and synthetically generated barcodes (combined competitive-binding- and nick-labeling). It is demonstrated that by simultaneously using the information from all label types, we can substantially increase the significance when we match experimental barcodes to a database consisting of theoretical barcodes for all sequenced plasmids.},
}
@article {pmid34842356,
year = {2021},
author = {Guo, LW and Li, XG and Yang, YS and Lu, XX and Han, XC and Lang, GT and Chen, L and Shao, ZM and Hu, X},
title = {Large-scale genomic sequencing reveals adaptive opportunity of targeting mutated-PI3Kα in early and advanced HER2-positive breast cancer.},
journal = {Clinical and translational medicine},
volume = {11},
number = {11},
pages = {e589},
pmid = {34842356},
issn = {2001-1326},
support = {81672601//National Natural Science Foundation of China/ ; 81872137//National Natural Science Foundation of China/ ; 81803555//National Natural Science Foundation of China/ ; 82072917//National Natural Science Foundation of China/ ; 2018YFE020160//Ministry of Science and Technology of China/ ; },
mesh = {Adaptation, Physiological/drug effects/genetics ; Breast Neoplasms/*drug therapy/genetics/physiopathology ; China ; Cohort Studies ; Female ; Humans ; Prospective Studies ; Receptor, ErbB-2/*genetics ; Sequence Analysis/methods/*statistics &amp; numerical data ; },
abstract = {BACKGROUND: Few studies have discussed the contradictory roles of mutated-PI3Kα in HER2-positive (HER2+) breast cancer. Thus, we characterised the adaptive roles of PI3Kα mutations among HER2+ tumour progression.<br><br>METHODS: We conducted prospective clinical sequencing of 1923 Chinese breast cancer patients and illustrated the clinical significance of PIK3CA mutations in locally advanced and advanced HER2+ cohort. A high-throughput PIK3CA mutations-barcoding screen was performed to reveal impactful mutation sites in tumour growth and drug responses.<br><br>RESULTS: PIK3CA mutations acted as a protective factor in treatment-na&#xef;ve patients; however, advanced/locally advanced patients harbouring mutated-PI3K&#x3b1; exhibited a higher progressive disease rate (100% vs. 15%, p&#xa0;=&#xa0;.000053) and a lower objective response rate (81.7%&#xa0;vs. 95.4%, p&#xa0;=&#xa0;.0008) in response to trastuzumab-based therapy. Meanwhile, patients exhibiting anti-HER2 resistance had a relatively high variant allele fraction (VAF) of PIK3CA mutations; we defined the VAF&#xa0;>&#xa0;12.23% as a predictor of poor anti-HER2 neoadjuvant treatment efficacy. Pooled mutations screen revealed that specific PI3K&#x3b1; mutation alleles mediated own biological effects. PIK3CA functional mutations suppressed the growth of HER2+ cells, but conferred anti-HER2 resistance, which can be reversed by the PI3K&#x3b1;-specific inhibitor BYL719.<br><br>CONCLUSIONS: We proposed adaptive treatment strategies that the mutated PIK3CA and amplified ERBB2 should be concomitantly inhibited when exposing to continuous anti-HER2 therapy, while the combination of anti-HER2 and anti-PI3K&#x3b1; treatment was not essential for anti-HER2 treatment-na&#xef;ve patients. These findings improve the understanding of genomics-guided treatment in the different progressions of HER2+ breast cancer.},
}
@article {pmid34838160,
year = {2021},
author = {Yang, JM and Chi, WY and Liang, J and Takayanagi, S and Iglesias, PA and Huang, CH},
title = {Deciphering cell signaling networks with massively multiplexed biosensor barcoding.},
journal = {Cell},
volume = {184},
number = {25},
pages = {6193-6206.e14},
pmid = {34838160},
issn = {1097-4172},
support = {P50 CA098252/CA/NCI NIH HHS/United States ; K22 CA212060/CA/NCI NIH HHS/United States ; S10 OD023548/OD/NIH HHS/United States ; R01 GM136711/GM/NIGMS NIH HHS/United States ; S10 OD016374/OD/NIH HHS/United States ; },
mesh = {Biosensing Techniques/*methods ; Cell Line, Tumor ; Cells/*ultrastructure ; Humans ; Microscopy, Fluorescence/*methods ; Single-Cell Analysis/*methods ; },
abstract = {Genetically encoded fluorescent biosensors are powerful tools for monitoring biochemical activities in live cells, but their multiplexing capacity is limited by the available spectral space. We overcome this problem by developing a set of barcoding proteins that can generate over 100 barcodes and are spectrally separable from commonly used biosensors. Mixtures of barcoded cells expressing different biosensors are simultaneously imaged and analyzed by deep learning models to achieve massively multiplexed tracking of signaling events. Importantly, different biosensors in cell mixtures show highly coordinated activities, thus facilitating the delineation of their temporal relationship. Simultaneous tracking of multiple biosensors in the receptor tyrosine kinase signaling network reveals distinct mechanisms of effector adaptation, cell autonomous and non-autonomous effects of KRAS mutations, as well as complex interactions in the network. Biosensor barcoding presents a scalable method to expand multiplexing capabilities for deciphering the complexity of signaling networks and their interactions between cells.},
}
@article {pmid34834891,
year = {2021},
author = {Mohamed, AH and Omar, AA and Attya, AM and Elashtokhy, MMA and Zayed, EM and Rizk, RM},
title = {Morphological and Molecular Characterization of Some Egyptian Six-Rowed Barley (Hordeum vulgare L.).},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {11},
pages = {},
pmid = {34834891},
issn = {2223-7747},
abstract = {Barley production is essential in Egypt. In the present study, 15 different six-rowed Egyptian barley cultivars were studied. To differentiate between the different cultivars under study in terms of morphological characteristics and ISSR, molecular characterization reactions were carried out. Moreover, four cultivars (Giza 123, Giza 126, Giza 136, and Giza 138) were selected for further studies using scanning electron microscopy (SEM). Computational analysis of the DNA barcoding sequences of the two plastid markers rbcL and matK was executed, and the results were deposited in the NCBI database. The morphological traits showed low statistical significance among the different cultivars under study via the data collected from two seasons, suggesting that the mean field performance of these Egyptian cultivars may be equal under these conditions. The results showed that the phylogenetic tree was divided into four groups, one of which contained the most closely related genotypes in the genetic distance, including Giza 124, Giza 130, Giza 138, Giza 136, and Giza 137, which converge in the indicative uses of farmers. The seed coat of the studied cultivars was "rugose". The elevation folding of the rugose pattern ranged from 11 ± 1.73 µm (Giza 126) to 14.67 ± 2.43 µm (Giza 123), suggesting variation in seed quality and its uses in feed and the food industry. According to the similarity matrix of ISSR analysis, the highest similarity value (93%) was recorded between Giza 133 and Giza 132, as well as between Giza 2000 and Giza 126. On the other hand, the lowest similarity value (80%) was recorded between Giza 130 and (Giza 133 and Giza 132), indicating that these cultivars were distantly related. Polymorphism information content (PIC) ranged from 0.26 for the primer ISSR UBC 835 to 0.37 for the primers ISSR UBC 814 and ISSR UBC 840. The current study showed that the matK gene is more mutable than the rbcL gene among the tested cultivars.},
}
@article {pmid34834801,
year = {2021},
author = {Al-Dakhil, M and Alghamdi, S and Migdadi, H and Afzal, M and Ali, AA},
title = {Morphological Characterization and DNA Barcoding of Duckweed Species in Saudi Arabia.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {11},
pages = {},
pmid = {34834801},
issn = {2223-7747},
support = {The initiative of the DSR Graduate Students Research Support (GSR).//Deanship of Scientific Research in King Saud University/ ; },
abstract = {Duckweeds, or Lemnaceae, are widespread aquatic plants. Morphology-based identification of duckweed species is difficult because of their structural complexity. Hence, molecular tools provide significant advantages for characterizing and selecting species or clones for sustainable commercial use. In this study, we collected and characterized ten duckweed isolates from nine different regions in Saudi Arabia (SA). Based on the morphological characterization and phylogenetic analysis of intergenic spacer sequences of chloroplast DNA using six barcoding markers, the clones were classified into three genera, represented by seven species: Lemna gibba L., Lemna minor L., Lemna japonica Landolt, Lemna aequinoctialis Welw., Lemna perpusilla Torr., Spirodela polyryiza (L.) Schleid., and Landoltia punctate G. Mey. Lemna gibba was revealed to be a distinct dominant duckweed species in many regions of SA. Five barcoding markers showed that L. gibba, L. minor, and L. punctata were the most widely distributed species in the country. However, L. punctata, L. perpusilla, and S. polyryiza were the dominant species in the Al-Qassim, Madinah-1, and Madinah-2 regions, respectively. Moreover, the morphological traits revealed variations for these clones, relative to other studied duckweed clones. According to the results obtained in this study, three out of six plastid markers (trnH-psbA, matK, and atpF-atpH) helped to identify the dominant duckweed species in Saudi Arabia. Further evaluation based on adaptability, molecular genetic studies, and functional genomics is needed for these species to be used at the commercial level in Saudi Arabia.},
}
@article {pmid34834799,
year = {2021},
author = {Pellegrini, M and Ercole, C and Gianchino, C and Bernardi, M and Pace, L and Del Gallo, M},
title = {Fusarium Oxysporum f. sp. Cannabis Isolated from Cannabis Sativa L.: In Vitro and In Planta Biocontrol by a Plant Growth Promoting-Bacteria Consortium.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {11},
pages = {},
pmid = {34834799},
issn = {2223-7747},
abstract = {Industrial hemp (Cannabis sativa L.) is a multipurpose plant used in several fields. Several phytopathogens attack hemp crops. Fusarium oxysporum is a common fungal pathogen that causes wilt disease in nurseries and in field cultivation and causes high losses. In the present study, a pathogenic strain belonging to F. oxysporum f. sp. cannabis was isolated from a plant showing Fusarium wilt. After isolation, identification was conducted based on morphological and molecular characterizations and pathogenicity tests. Selected plant growth-promoting bacteria with interesting biocontrol properties-Azospirillum brasilense, Gluconacetobacter diazotrophicus, Herbaspirillum seropedicae and Burkholderia ambifaria-were tested against this pathogen. In vitro antagonistic activity was determined by the dual culture method. Effective strains (in vitro inhibition > of 50%) G. diazotrophicus, H. seropedicae and B. ambifaria were combined in a consortium and screened for in planta antagonistic activity in pre-emergence (before germination) and post-emergence (after germination). The consortium counteracted Fusarium infection both in pre-emergence and post-emergence. Our preliminary results show that the selected consortium could be further investigated as an effective biocontrol agent for the management of this pathogen.},
}
@article {pmid34833122,
year = {2021},
author = {Frolova, M and Yudin, S and Makarov, V and Glazunova, O and Alikina, O and Markelova, N and Kolzhetsov, N and Dzhelyadin, T and Shcherbakova, V and Trubitsyn, V and Panyukov, V and Zaitsev, A and Kiselev, S and Shavkunov, K and Ozoline, O},
title = {Lacticaseibacillus paracasei: Occurrence in the Human Gut Microbiota and K-Mer-Based Assessment of Intraspecies Diversity.},
journal = {Life (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
pmid = {34833122},
issn = {2075-1729},
support = {State Contract No. 0373100122121000059//Federal Medical and Biological Agency of Russia/ ; },
abstract = {Alignment-free approaches employing short k-mers as barcodes for individual genomes have created a new strategy for taxonomic analysis and paved a way for high-resolution phylogeny. Here, we introduce this strategy for the Lacticaseibacillus paracasei species as a taxon requiring barcoding support for precise systematics. Using this approach for phylotyping of L. paracasei VKM B-1144 at the genus level, we identified four L. paracasei phylogroups and found that L. casei 12A belongs to one of them, rather than to the L. casei clade. Therefore, we propose to change the specification of this strain. At the genus level we found only one relative of L. paracasei VKM B-1144 among 221 genomes, complete or available in contigs, and showed that the coding potential of the genome of this "rare" strain allows its consideration as a potential probiotic component. Four sets of published metagenomes were used to assess the dependence of L. paracasei presence in the human gut microbiome on chronic diseases, dietary changes and antibiotic treatment. Only antibiotics significantly affected their presence, and strain-specific barcoding allowed the identification of the main scenarios of the adaptive response. Thus, suggesting bacteria of this species for compensatory therapy, we also propose strain-specific barcoding for selecting optimal strains for target microbiomes.},
}
@article {pmid34833043,
year = {2021},
author = {Zheng, HD and Zhuang, WY},
title = {The Genus Chlorosplenium (Helotiales, Leotiomycetes) from China with Notes on C. chlora Complex.},
journal = {Life (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
pmid = {34833043},
issn = {2075-1729},
support = {31770019, 31750001//National Natural Science Foundation of China/ ; },
abstract = {The small fruitbodies of Chlorosplenium are greenish yellow and mainly grow on woody substrates. The species diversity of the genus in China was investigated based on specimens formerly deposited in the Herbarium Mycologicum Academiae Sinicae as well as new collections gained in recent years. Our phylogenetic results revealed the species diversity of the genus is underestimated and the commonly known Chlorosplenium chlora is a species complex. Based on morphology studies and sequence analyses of three regions (ITS, LSU and RPB1), the Chinese collections represent two new species which are described and illustrated here as C. sinicum and C. sinochlora. Chlorosplenium fusisporum is quite possibly a species of the genus Chlorociboria, and C. hyperici-maculati should be excluded from the genus.},
}
@article {pmid34832628,
year = {2021},
author = {Helmer, N and Blatterer, H and Hörweg, C and Reier, S and Sattmann, H and Schindelar, J and Szucsich, NU and Haring, E},
title = {First Record of Trichobilharzia physellae (Talbot, 1936) in Europe, a Possible Causative Agent of Cercarial Dermatitis.},
journal = {Pathogens (Basel, Switzerland)},
volume = {10},
number = {11},
pages = {},
pmid = {34832628},
issn = {2076-0817},
abstract = {Several species of avian schistosomes are known to cause dermatitis in humans worldwide. In Europe, this applies above all to species of the genus Trichobilharzia. For Austria, a lot of data are available on cercarial dermatitis and on the occurrence of Trichobilharzia, yet species identification of trematodes in most cases is doubtful due to the challenging morphological determination of cercariae. During a survey of trematodes in freshwater snails, we were able to detect a species in the snail Physella acuta (Draparnaud, 1805) hitherto unknown for Austria, Trichobilharzia physellae; this is also the first time this species has been reported in Europe. Species identification was performed by integrative taxonomy combining morphological investigations with molecular genetic analyses. The results show a very close relationship between the parasite found in Austria and North American specimens (similarity found in CO1 ≥99.57%). Therefore, a recent introduction of T. physellae into Europe can be assumed.},
}
@article {pmid34831099,
year = {2021},
author = {Xiang, Y and Sugimura, R},
title = {Single-Cell Approaches to Deconvolute the Development of HSCs.},
journal = {Cells},
volume = {10},
number = {11},
pages = {},
pmid = {34831099},
issn = {2073-4409},
mesh = {Hematopoietic Stem Cells/*cytology ; Humans ; Models, Biological ; RNA-Seq ; Single-Cell Analysis/*methods ; Time Factors ; },
abstract = {Hematopoietic stem cells (HSCs) play a core role in blood development. The ability to efficiently produce HSCs from various pluripotent stem cell sources is the Holy Grail in the hematology field. However, in vitro or in vivo HSC production remains low, which may be attributable to the lack of understanding of hematopoiesis. Here, we review the recent progress in this area and introduce advanced technologies, such as single-cell RNA-seq, spatial transcriptomics, and molecular barcoding, which may help to acquire missing information about HSC generation. We finally discuss unresolved questions, the answers to which may be conducive to HSC production, providing a promising path toward HSC-based immunotherapies.},
}
@article {pmid34829156,
year = {2021},
author = {Preckel, L and Brünen-Nieweler, C and Denay, G and Petersen, H and Cichna-Markl, M and Dobrovolny, S and Hochegger, R},
title = {Identification of Mammalian and Poultry Species in Food and Pet Food Samples Using 16S rDNA Metabarcoding.},
journal = {Foods (Basel, Switzerland)},
volume = {10},
number = {11},
pages = {},
pmid = {34829156},
issn = {2304-8158},
support = {VI-2 - 0.0215 / 2.2125.11.4 VI-3 - 0007.12//Ministry for Environment, Agriculture, Conservation and Consumer Protection of the State of North Rhine-Westphalia/ ; },
abstract = {The substitution of more appreciated animal species by animal species of lower commercial value is a common type of meat product adulteration. DNA metabarcoding, the combination of DNA barcoding with next-generation sequencing (NGS), plays an increasing role in food authentication. In the present study, we investigated the applicability of a DNA metabarcoding method for routine analysis of mammalian and poultry species in food and pet food products. We analyzed a total of 104 samples (25 reference samples, 56 food products and 23 pet food products) by DNA metabarcoding and by using a commercial DNA array and/or by real-time PCR. The qualitative and quantitative results obtained by the DNA metabarcoding method were in line with those obtained by PCR. Results from the independent analysis of a subset of seven reference samples in two laboratories demonstrate the robustness and reproducibility of the DNA metabarcoding method. DNA metabarcoding is particularly suitable for detecting unexpected species ignored by targeted methods such as real-time PCR and can also be an attractive alternative with respect to the expenses as indicated by current data from the cost accounting of the AGES laboratory. Our results for the commercial samples show that in addition to food products, DNA metabarcoding is particularly applicable to pet food products, which frequently contain multiple animal species and are also highly prone to adulteration as indicated by the high portion of analyzed pet food products containing undeclared species.},
}
@article {pmid34828447,
year = {2021},
author = {Panozzo, S and Mascanzoni, E and Scarabel, L and Milani, A and Dalazen, G and Merotto, AJ and Tranel, PJ and Sattin, M},
title = {Target-Site Mutations and Expression of ALS Gene Copies Vary According to Echinochloa Species.},
journal = {Genes},
volume = {12},
number = {11},
pages = {},
pmid = {34828447},
issn = {2073-4425},
mesh = {Acetolactate Synthase/antagonists &amp; inhibitors/chemistry/*genetics/metabolism ; Binding Sites ; Drug Resistance ; Echinochloa/classification/drug effects/*genetics ; Enzyme Inhibitors/pharmacology ; Gene Dosage ; *Mutation ; Plant Proteins/*genetics/metabolism ; Protein Binding ; },
abstract = {The sustainability of rice cropping systems is jeopardized by the large number and variety of populations of polyploid Echinochloa spp. resistant to ALS inhibitors. Better knowledge of the Echinochloa species present in Italian rice fields and the study of ALS genes involved in target-site resistance could significantly contribute to a better understanding of resistance evolution and management. Using a CAPS-rbcL molecular marker, two species, E. crus-galli (L.) P. Beauv. and E. oryzicola (Vasinger) Vasing., were identified as the most common species in rice in Italy. Mutations involved in ALS inhibitor resistance in the different species were identified and associated with the ALS homoeologs. The relative expression of the ALS gene copies was evaluated. Molecular characterization led to the identification of three ALS genes in E. crus-galli and two in E. oryzicola. The two species also carried different point mutations conferring resistance: Ala122Asn in E. crus-galli and Trp574Leu in E. oryzicola. Mutations were carried in the same gene copy (ALS1), which was significantly more expressed than the other copies (ALS2 and ALS3) in both species. These results explain the high resistance level of these populations and why mutations in the other ALS copies are not involved in herbicide resistance.},
}
@article {pmid34828370,
year = {2021},
author = {Park, I and Song, J and Yang, S and Choi, G and Moon, B},
title = {A Comprehensive Study of the Genus Sanguisorba (Rosaceae) Based on the Floral Micromorphology, Palynology, and Plastome Analysis.},
journal = {Genes},
volume = {12},
number = {11},
pages = {},
pmid = {34828370},
issn = {2073-4425},
mesh = {Chloroplasts/*genetics ; DNA Barcoding, Taxonomic/*methods ; Flowers/*anatomy &amp; histology/classification/genetics ; Genetic Markers ; Genome Size ; Genome, Chloroplast ; Phylogeny ; Pollen/anatomy &amp; histology/classification/genetics ; Sanguisorba/anatomy &amp; histology/*classification/genetics ; Selection, Genetic ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Sanguisorba, commonly known as burnet, is a genus in the family Rosaceae native to the temperate regions of the Northern hemisphere. Five of its thirty species are distributed in Korea: Sanguisorba officinalis, S. stipulata, S. hakusanensis, S. longifolia, and S. tenuifolia. S. officinalis has been designated as a medicinal remedy in the Chinese and Korean Herbal Pharmacopeias. Despite being a valuable medicinal resource, the morphological and genomic information, as well as the genetic characteristics of Sanguisorba, are still elusive. Therefore, we carried out the first comprehensive study on the floral micromorphology, palynology, and complete chloroplast (cp) genome of the Sanguisorba species. The outer sepal waxes and hypanthium characters showed diagnostic value, despite a similar floral micromorphology across different species. All the studied Sanguisorba pollen were small to medium, oblate to prolate-spheroidal, and their exine ornamentation was microechinate. The orbicules, which are possibly synapomorphic, were consistently absent in this genus. Additionally, the cp genomes of S. officinalis, S. stipulata, and S. hakusanensis have been completely sequenced. The comparative analysis of the reported Sanguisorba cp genomes revealed local divergence regions. The nucleotide diversity of trnH-psbA and rps2-rpoC2, referred to as hotspot regions, revealed the highest pi values in six Sanguisorba. The ndhG indicated positive selection pressures as a species-specific variation in S. filiformis. The S. stipulata and S. tenuifolia species had psbK genes at the selected pressures. We developed new DNA barcodes that distinguish the typical S. officinalis and S. officinalis var. longifolia, important herbal medicinal plants, from other similar Sanguisorba species with species-specific distinctive markers. The phylogenetic trees showed the positions of the reported Sanguisorba species; S. officinalis, S. tenuifolia, and S. stipulata showed the nearest genetic distance. The results of our comprehensive study on micromorphology, pollen chemistry, cp genome analysis, and the development of species identification markers can provide valuable information for future studies on S. officinalis, including those highlighting it as an important medicinal resource.},
}
@article {pmid34828262,
year = {2021},
author = {Scariolo, F and Palumbo, F and Vannozzi, A and Sacilotto, GB and Gazzola, M and Barcaccia, G},
title = {Genotyping Analysis by RAD-Seq Reads Is Useful to Assess the Genetic Identity and Relationships of Breeding Lines in Lavender Species Aimed at Managing Plant Variety Protection.},
journal = {Genes},
volume = {12},
number = {11},
pages = {},
pmid = {34828262},
issn = {2073-4425},
mesh = {Base Sequence ; Chloroplasts/genetics ; Conservation of Natural Resources/methods ; Crosses, Genetic ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/analysis/genetics ; Genetic Techniques ; Genotype ; Genotyping Techniques/methods ; High-Throughput Nucleotide Sequencing ; Hybridization, Genetic ; Lavandula/*classification/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {Lavender species are widely distributed in their wild forms around the Mediterranean Basin and they are also cultivated worldwide as improved and registered clonal varieties. The economic interest of the species belonging to the Lavandula genus is determined by their use as ornamental plants and important source of essential oils that are destinated to the production of cosmetics, pharmaceuticals and foodstuffs. Because of the increasing number of cases of illegal commercialization of selected varieties, the protection of plant breeders' rights has become of main relevance for the recognition of breeding companies' royalties. With this aim, genomic tools based on molecular markers have been demonstrated to be very reliable and transferable among laboratories, and also much more informative than morphological descriptors. With the rising of the next-generation sequencing (NGS) technologies, several genotyping-by-sequencing approaches are now available. This study deals with a deep characterization of 15 varietal clones, belonging to two distinct Lavandula species, by means of restriction-site associated DNA sequencing (RAD-Seq). We demonstrated that this technology screens single nucleotide variants that enable to assess the genetic identity of individual accessions, to reconstruct genetic relationships among related breeding lines, to group them into genetically distinguishable main subclusters, and to assign their molecular lineages to distinct ancestors. Moreover, a number of polymorphic sites were identified within genes putatively involved in biosynthetic pathways related to both tissue pigmentation and terpene production, useful for breeding and/or protecting newly registered varieties. Overall, the results highlighted the presence of pure ancestries and interspecific hybrids for the analyzed Lavandula species, and demonstrated that RAD-Seq analysis is very informative and highly reliable for characterizing Lavandula clones and managing plant variety protection.},
}
@article {pmid34827127,
year = {2021},
author = {Lee, HT and Liao, CH and Hsu, TH},
title = {Environmental DNA (eDNA) Metabarcoding in the Fish Market and Nearby Seafood Restaurants in Taiwan Reveals the Underestimation of Fish Species Diversity in Seafood.},
journal = {Biology},
volume = {10},
number = {11},
pages = {},
pmid = {34827127},
issn = {2079-7737},
support = {NTOU2019, NTOU2020, NTOU2021//National Taiwan Ocean University/ ; LPP2019, LPP2020, LPP2021//Longchen Paper &amp; Packaging Co., Ltd/ ; 109toffrest001, 110toffrest001//Taiwan Ocean Conservation and Fisheries Sustainability Foundation/ ; },
abstract = {Seafood, especially the traditional one in Taiwan, is rarely sourced from a fixed species and routinely from similar species depending on their availability. Hence, the species composition of seafood can be complicated. While a DNA-based approach has been routinely utilized for species identification, a large scale of seafood identification in fish markets and restaurants could be challenging (e.g., elevated cost and time-consuming only for a limited number of species identification). In the present study, we aimed to identify the majority of fish species potentially consumed in fish markets and nearby seafood restaurants using environmental DNA (eDNA) metabarcoding. Four eDNA samplings from a local fish market and nearby seafood restaurants were conducted using Sterivex cartridges. Nineteen universal primers previously validated for fish species identification were utilized to amplify the fragments of mitochondrial DNA (12S, COI, ND5) of species in eDNA samples and sequenced with NovaSeq 6000 sequencing. A total of 153 fish species have been identified based on 417 fish related operational taxonomic units (OTUs) generated from 50,534,995 reads. Principal Coordinate Analysis (PCoA) further showed the differences in fish species between the sampling times and sampling sites. Of these fish species, 22 chondrichthyan fish, 14 Anguilliformes species, and 15 Serranidae species were respectively associated with smoked sharks, braised moray eels, and grouper fish soups. To our best knowledge, this work represents the first study to demonstrate the feasibility of a large scale of seafood identification using eDNA metabarcoding approach. Our findings also imply the species diversity in traditional seafood might be seriously underestimated and crucial for the conservation and management of marine resources.},
}
@article {pmid34827084,
year = {2021},
author = {Pinna, M and Saccomanno, B and Marini, G and Zangaro, F and Kabayeva, A and Khalaj, M and Shaimardan, L and D'Attis, S and Tzafesta, E and Specchia, V},
title = {Testing the Influence of Incomplete DNA Barcode Libraries on Ecological Status Assessment of Mediterranean Transitional Waters.},
journal = {Biology},
volume = {10},
number = {11},
pages = {},
pmid = {34827084},
issn = {2079-7737},
support = {ImPrEco project N.450//EU Interreg Adrion programme 2014/2020/ ; FFABR 2017//MIUR/ ; },
abstract = {The ecological assessment of European aquatic ecosystems is regulated under the framework directives on strategy for water and marine environments. Benthic macroinvertebrates are the most used biological quality element for ecological assessment of rivers, coastal-marines, and transitional waters. The morphological identification of benthic macroinvertebrates is the current tool for their assessment. Recently, DNA-based tools have been proposed as effective alternatives. The main current limits of DNA-based applications include the incompleteness of species recorded in the DNA barcode reference libraries and the primers bias. Here, we analysed the influence of the incompleteness of DNA barcode databases on species diversity indices, ecological indicators, and ecological assessment in transitional waters of the southeast Mediterranean, taking into account the availability of commonly sequenced and deposited genomic regions for listed species. The ecological quality status assigned through the potential application of both approaches to the analysed transitional water ecosystems was different in 27% of sites. We also analysed the inter-specific genetic distances to evaluate the potential application of the DNA metabarcoding method. Overall, this work highlights the importance to expand the barcode databases and to analyse, at the regional level, the gaps in the DNA barcodes.},
}
@article {pmid34824910,
year = {2021},
author = {Uhlir, C and Schwentner, M and Meland, K and Kongsrud, JA and Glenner, H and Brandt, A and Thiel, R and Svavarsson, J and Lörz, AN and Brix, S},
title = {Adding pieces to the puzzle: insights into diversity and distribution patterns of Cumacea (Crustacea: Peracarida) from the deep North Atlantic to the Arctic Ocean.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e12379},
pmid = {34824910},
issn = {2167-8359},
abstract = {The Nordic Seas have one of the highest water-mass diversities in the world, yet large knowledge gaps exist in biodiversity structure and biogeographical distribution patterns of the deep macrobenthic fauna. This study focuses on the marine bottom-dwelling peracarid crustacean taxon Cumacea from northern waters, using a combined approach of morphological and molecular techniques to present one of the first insights into genetic variability of this taxon. In total, 947 specimens were assigned to 77 morphologically differing species, representing all seven known families from the North Atlantic. A total of 131 specimens were studied genetically (16S rRNA) and divided into 53 putative species by species delimitation methods (GMYC and ABGD). In most cases, morphological and molecular-genetic delimitation was fully congruent, highlighting the overall success and high quality of both approaches. Differences were due to eight instances resulting in either ecologically driven morphological diversification of species or morphologically cryptic species, uncovering hidden diversity. An interspecific genetic distance of at least 8% was observed with a clear barcoding gap for molecular delimitation of cumacean species. Combining these findings with data from public databases and specimens collected during different international expeditions revealed a change in the composition of taxa from a Northern Atlantic-boreal to an Arctic community. The Greenland-Iceland-Scotland-Ridge (GIS-Ridge) acts as a geographical barrier and/or predominate water masses correspond well with cumacean taxa dominance. A closer investigation on species level revealed occurrences across multiple ecoregions or patchy distributions within defined ecoregions.},
}
@article {pmid34824813,
year = {2021},
author = {Bell, KL and Petit, RA and Cutler, A and Dobbs, EK and Macpherson, JM and Read, TD and Burgess, KS and Brosi, BJ},
title = {Comparing whole-genome shotgun sequencing and DNA metabarcoding approaches for species identification and quantification of pollen species mixtures.},
journal = {Ecology and evolution},
volume = {11},
number = {22},
pages = {16082-16098},
pmid = {34824813},
issn = {2045-7758},
abstract = {Molecular identification of mixed-species pollen samples has a range of applications in various fields of research. To date, such molecular identification has primarily been carried out via amplicon sequencing, but whole-genome shotgun (WGS) sequencing of pollen DNA has potential advantages, including (1) more genetic information per sample and (2) the potential for better quantitative matching. In this study, we tested the performance of WGS sequencing methodology and publicly available reference sequences in identifying species and quantifying their relative abundance in pollen mock communities. Using mock communities previously analyzed with DNA metabarcoding, we sequenced approximately 200Mbp for each sample using Illumina HiSeq and MiSeq. Taxonomic identifications were based on the Kraken k-mer identification method with reference libraries constructed from full-genome and short read archive data from the NCBI database. We found WGS to be a reliable method for taxonomic identification of pollen with near 100% identification of species in mixtures but generating higher rates of false positives (reads not identified to the correct taxon at the required taxonomic level) relative to rbcL and ITS2 amplicon sequencing. For quantification of relative species abundance, WGS data provided a stronger correlation between pollen grain proportion and sequence read proportion, but diverged more from a 1:1 relationship, likely due to the higher rate of false positives. Currently, a limitation of WGS-based pollen identification is the lack of representation of plant diversity in publicly available genome databases. As databases improve and costs drop, we expect that eventually genomics methods will become the methods of choice for species identification and quantification of mixed-species pollen samples.},
}
@article {pmid34824781,
year = {2021},
author = {Fenwick, GD and Greenwood, MJ and Hogg, ID and Meyer, SJ},
title = {High diversity and local endemism in Aotearoa New Zealand's groundwater crustacean fauna.},
journal = {Ecology and evolution},
volume = {11},
number = {22},
pages = {15664-15682},
pmid = {34824781},
issn = {2045-7758},
abstract = {We used DNA barcoding to assess the diversity and distribution of New Zealand's groundwater amphipods and isopods (Crustacea) and to determine whether biodiversity and endemism within tectonically active New Zealand are similar to those of more tectonically stable continents. Sixty-five wells were sampled in seven aquifers across four regions within the North and South islands of New Zealand, and resident invertebrates were morphologically identified and then assessed using sequencing of the mitochondrial DNA cytochrome c oxidase subunit one (COI) gene. Invertebrates were found in 54 wells. Of the 228 individual amphipods and isopods found in 36 of the wells, 154 individuals were successfully sequenced for COI (68% success rate) from 25 wells, with at least one well in each aquifer containing sequenced individuals. Of the 45 putative species identified using Barcode Index Numbers (BINs), 30 BINs (78% of all taxa and 83% of amphipods) were previously unrecorded. Substantial morphologically cryptic, species-level diversity was revealed, particularly within the amphipod Family Paraleptamphopidae. Similarly, one isopod taxon morphologically identified as Cruregens fontanus was assigned to five well-separated BINs based on COI sequences. Endemism appeared high, with all taxa regionally endemic; 87% of species were restricted to one aquifer and more than 50% restricted to one well. Non-saturated species accumulation curves indicated that, while additional sampling may increase the range of some currently identified taxa, additional range-restricted taxa are also likely to be discovered. Patterns of diversity and short-range endemism were similar to those found elsewhere, including locations which are more tectonically stable. The predominance of local endemism within New Zealand's groundwater fauna suggests that land-use activities and groundwater extraction require careful evaluation to minimize threats to groundwater biodiversity.},
}
@article {pmid34824350,
year = {2021},
author = {Song, S and Manook, M and Kwun, J and Jackson, AM and Knechtle, SJ and Kelsoe, G},
title = {A cell-based multiplex immunoassay platform using fluorescent protein-barcoded reporter cell lines.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {1338},
pmid = {34824350},
issn = {2399-3642},
support = {P01 AI089618/AI/NIAID NIH HHS/United States ; R01 AI128832/AI/NIAID NIH HHS/United States ; },
mesh = {Antibodies/*isolation &amp; purification ; Cell Line ; Epitopes/chemistry ; *Flow Cytometry ; Fluorescent Dyes/chemistry ; Hemagglutinins/chemistry ; Immunoassay/instrumentation/*methods ; Influenza A virus/chemistry ; Membrane Proteins/*chemistry ; Mutation ; Protein Multimerization ; Receptors, CCR2/chemistry ; Receptors, CCR5/chemistry ; },
abstract = {Multiplex immunoassays with acellular antigens are well-established based on solid-phase platforms such as the Luminex[®] technology. Cell barcoding by amine-reactive fluorescent dyes enables analogous cell-based multiplex assays, but requires multiple labeling reactions and quality checks prior to every assay. Here we describe generation of stable, fluorescent protein-barcoded reporter cell lines suitable for multiplex screening of antibody to membrane proteins. The utility of this cell-based system, with the potential of a 256-plex cell panel, is demonstrated by flow cytometry deconvolution of barcoded cell panels expressing influenza A hemagglutinin trimers, or native human CCR2 or CCR5 multi-span proteins and their epitope-defining mutants. This platform will prove useful for characterizing immunity and discovering antibodies to membrane-associated proteins.},
}
@article {pmid34823581,
year = {2021},
author = {Bleidorn, C and Henze, K},
title = {A new primer pair for barcoding of bees (Hymenoptera: Anthophila) without amplifying the orthologous coxA gene of Wolbachia bacteria.},
journal = {BMC research notes},
volume = {14},
number = {1},
pages = {427},
pmid = {34823581},
issn = {1756-0500},
mesh = {Animals ; Bacteria ; Bees/genetics ; DNA Barcoding, Taxonomic ; Hip ; *Hymenoptera ; *Wolbachia/genetics ; },
abstract = {OBJECTIVES: DNA barcoding became an effective method for the identification and monitoring of bees. However, standard primer pairs used for barcoding often result in (co-) amplification of bacterial endosymbionts of the genus Wolbachia, which are widespread among bee species. Here we designed a new primer pair and compared it with the performance of the standard Folmer-primers for a small sample set of bees representing the main taxonomic groups of bees.<br><br>RESULTS: The newly designed primer pair (BeeCox1F1/BeeCox1R2) outperformed the standard barcoding primer (LCO1490/HCO2198). By generating barcodes for a small test set of bees we found that the new primer pair produced high-quality sequences in all cases for unambiguous species identification using BOLD. Conversely, the standard barcoding primers often co-amplified the homologous Wolbachia gene and resulted in mixed chromatogram signals. These sequences showed high similarity with the bacterial endosymbiont instead of the host.},
}
@article {pmid34823565,
year = {2021},
author = {Yu, Y and Han, Y and Peng, Y and Tian, Z and Zeng, P and Zong, H and Zhou, T and Cai, J},
title = {Comparative and phylogenetic analyses of eleven complete chloroplast genomes of Dipterocarpoideae.},
journal = {Chinese medicine},
volume = {16},
number = {1},
pages = {125},
pmid = {34823565},
issn = {1749-8546},
support = {5113190037//the Thousand Talents Plan/ ; 20GH020169//the Talents Team Construction Fund of Northwestern Polytechnical University/ ; 3102019JC007//the Fundamental Research Funds for the Central Universities/ ; },
abstract = {BACKGROUND: In South-east Asia, Dipterocarpoideae is predominant in most mature forest communities, comprising around 20% of all trees. As large quantity and high quality wood are produced in many species, Dipterocarpoideae plants are the most important and valuable source in the timber market. The d-borneol is one of the essential oil components from Dipterocarpoideae (for example, Dryobalanops aromatica or Dipterocarpus turbinatus) and it is also an important traditional Chinese medicine (TCM) formulation known as "Bingpian" in Chinese, with antibacterial, analgesic and anti-inflammatory effects and can enhance anticancer efficiency.<br><br>METHODS: In this study, we analyzed 20 chloroplast&#xa0;(cp) genomes characteristics of Dipterocarpoideae, including eleven newly reported genomes and nine cp genomes previously published elsewhere, then we explored the chloroplast genomic features, inverted repeats contraction and expansion, codon usage, amino acid frequency, the repeat sequences and selective pressure analyses. At last, we constructed phylogenetic relationships of Dipterocarpoideae and found the potential barcoding loci.<br><br>RESULTS: The cp genome of this subfamily has a typical quadripartite structure and maintains a high degree of consistency among species. There were slightly more tandem repeats in cp genomes of Dipterocarpus and Vatica, and the psbH gene was subjected to positive selection in the common ancestor of all the 20 species of Dipterocarpoideae compared with three outgroups. Phylogenetic tree showed that genus Shorea was not a monophyletic group, some Shorea species and genus Parashorea are placed in one clade. In addition, the rpoC2 gene can be used as a potential marker to achieve accurate and rapid species identification in subfamily Dipterocarpoideae.<br><br>CONCLUSIONS: Dipterocarpoideae had similar cp genomic features and psbM, rbcL, psbH may function in the growth of Dipterocarpoideae. Phylogenetic analysis suggested new taxon treatment is needed for this subfamily indentification. In addition, rpoC2 is potential to be a barcoding gene to TCM distinguish.},
}
@article {pmid34822165,
year = {2021},
author = {Ciapponi, A and Fernandez Nievas, SE and Seijo, M and Rodríguez, MB and Vietto, V and García-Perdomo, HA and Virgilio, S and Fajreldines, AV and Tost, J and Rose, CJ and Garcia-Elorrio, E},
title = {Reducing medication errors for adults in hospital settings.},
journal = {The Cochrane database of systematic reviews},
volume = {11},
number = {11},
pages = {CD009985},
pmid = {34822165},
issn = {1469-493X},
mesh = {Adult ; Hospitalization ; Hospitals ; Humans ; *Medication Errors/prevention &amp; control ; *Medication Reconciliation ; Pharmacists ; },
abstract = {BACKGROUND: Medication errors are preventable events that may cause or lead to inappropriate medication use or patient harm while the medication is in the control of the healthcare professional or patient. Medication errors in hospitalised adults may cause harm, additional costs, and even death.<br><br>OBJECTIVES: To determine the effectiveness of interventions to reduce medication errors in adults in hospital settings.<br><br>SEARCH METHODS: We searched CENTRAL, MEDLINE, Embase, five other databases and two trials registers on 16 January 2020.&#xa0; SELECTION CRITERIA: We included randomised controlled trials (RCTs) and interrupted time series (ITS) studies investigating interventions aimed at reducing medication errors in hospitalised adults, compared with usual care or other interventions. Outcome measures included adverse drug events (ADEs), potential ADEs, preventable ADEs, medication errors, mortality, morbidity, length of stay, quality of life and identified/solved discrepancies. We included any hospital setting, such as inpatient care units, outpatient care settings, and accident and emergency departments.<br><br>DATA COLLECTION AND ANALYSIS: We followed the standard methodological procedures expected by Cochrane and the Effective Practice and Organisation of Care (EPOC) Group. Where necessary, we extracted and reanalysed ITS study data using piecewise linear regression, corrected for autocorrelation and seasonality, where possible.&#xa0; MAIN RESULTS: We included 65 studies: 51 RCTs and 14 ITS studies, involving 110,875 participants. About half of trials gave rise to 'some concerns' for risk of bias during the randomisation process and one-third lacked blinding of outcome assessment. Most ITS studies presented low risk of bias. Most studies came from high-income countries or high-resource settings. Medication reconciliation -the process of comparing a patient's medication orders to the medications that the patient has been taking- was the most common type of intervention studied. Electronic prescribing systems, barcoding for correct administering of medications, organisational changes, feedback on medication errors, education of professionals and improved medication dispensing systems were other interventions studied. Medication reconciliation Low-certainty evidence suggests that medication reconciliation (MR) versus no-MR may reduce medication errors (odds ratio [OR] 0.55, 95% confidence interval (CI) 0.17 to 1.74; 3 studies; n=379). Compared to no-MR, MR probably reduces ADEs (OR 0.38, 95%CI 0.18 to 0.80; 3 studies, n=1336 ; moderate-certainty evidence), but has little to no effect on length of stay (mean difference (MD) -0.30 days, 95%CI -1.93 to 1.33 days; 3 studies, n=527) and quality of life (MD -1.51, 95%CI -10.04 to 7.02; 1 study, n=131).&#xa0; Low-certainty evidence suggests that, compared to MR by other professionals, MR by pharmacists may reduce medication errors (OR 0.21, 95%CI 0.09 to 0.48; 8 studies, n=2648) and may increase ADEs (OR 1.34, 95%CI 0.73 to 2.44; 3 studies, n=2873). Compared to MR by other professionals, MR by pharmacists may have little to no effect on length of stay (MD -0.25, 95%CI -1.05 to 0.56; 6 studies, 3983). Moderate-certainty evidence shows that this intervention probably has little to no effect on mortality during hospitalisation (risk ratio (RR) 0.99, 95%CI 0.57 to 1.7; 2 studies, n=1000), and on readmissions at one month (RR 0.93, 95%CI 0.76 to 1.14; 2 studies, n=997); and low-certainty evidence suggests that the intervention may have little to no effect on quality of life (MD 0.00, 95%CI -14.09 to 14.09; 1 study, n=724).&#xa0; Low-certainty evidence suggests that database-assisted MR conducted by pharmacists, versus unassisted MR conducted by pharmacists, may reduce potential ADEs (OR 0.26, 95%CI 0.10 to 0.64; 2 studies, n=3326), and may have no effect on length of stay (MD 1.00, 95%CI -0.17 to 2.17; 1 study, n=311).&#xa0; Low-certainty evidence suggests that MR&#xa0;performed by trained pharmacist technicians, versus pharmacists, may have little to no difference on length of stay (MD -0.30, 95%CI -2.12 to 1.52; 1 study, n=183). However, the CI is compatible with important beneficial and detrimental effects. Low-certainty evidence suggests that MR before admission may increase the identification of discrepancies compared with MR after admission (MD 1.27, 95%CI 0.46 to 2.08; 1 study, n=307). However, the CI is compatible with important beneficial and detrimental effects. Moderate-certainty evidence shows that multimodal interventions probably increase discrepancy resolutions compared to usual care (RR 2.14, 95%CI 1.81 to 2.53; 1 study, n=487). Computerised physician order entry (CPOE)/clinical decision support systems (CDSS) Moderate-certainty evidence shows that CPOE/CDSS probably reduce medication errors compared to paper-based systems (OR 0.74, 95%CI 0.31 to 1.79; 2 studies, n=88).&#xa0; Moderate-certainty evidence shows that, compared with standard CPOE/CDSS, improved CPOE/CDSS probably reduce medication errors (OR 0.85, 95%CI 0.74 to 0.97; 2 studies, n=630). Low-certainty evidence suggests that prioritised alerts provided by CPOE/CDSS may prevent ADEs compared to non-prioritised (inconsequential) alerts (MD 1.98, 95%CI 1.65 to 2.31; 1 study; participant numbers unavailable). Barcode identification of participants/medications Low-certainty evidence suggests that barcoding may reduce medication errors (OR 0.69, 95%CI 0.59 to 0.79; 2 studies, n=50,545). Reduced working hours Low-certainty evidence suggests that reduced working hours may reduce serious medication errors (RR 0.83, 95%CI 0.63 to 1.09; 1 study, n=634). However, the CI is compatible with important beneficial and detrimental effects. Feedback on prescribing errors Low-certainty evidence suggests that feedback on prescribing errors may reduce medication errors (OR 0.47, 95%CI 0.33 to 0.67; 4 studies, n=384). Dispensing system Low-certainty evidence suggests that dispensing systems in surgical wards may reduce medication errors (OR 0.61, 95%CI 0.47 to 0.79; 2 studies, n=1775).<br><br>AUTHORS' CONCLUSIONS: Low- to moderate-certainty evidence suggests that, compared to usual care, medication reconciliation, CPOE/CDSS, barcoding, feedback and dispensing systems in surgical wards may reduce medication errors and ADEs. However, the results are imprecise for some outcomes related to medication reconciliation and CPOE/CDSS. The evidence for other interventions is very uncertain. Powered and methodologically sound studies are needed to address the identified evidence gaps. Innovative, synergistic strategies -including those that involve patients- should also be evaluated.},
}
@article {pmid34821794,
year = {2021},
author = {Puig, AS and Wurzel, S and Suarez, S and Marelli, JP and Niogret, J},
title = {Mealybug (Hemiptera: Pseudococcidae) Species Associated with Cacao Mild Mosaic Virus and Evidence of Virus Acquisition.},
journal = {Insects},
volume = {12},
number = {11},
pages = {},
pmid = {34821794},
issn = {2075-4450},
abstract = {Theobroma cacao is affected by viruses on every continent where the crop is cultivated, with the most well-known ones belonging to the Badnavirus genus. One of these, cacao mild mosaic virus (CaMMV), is present in the Americas, and is transmitted by several species of Pseudococcidae (mealybugs). To determine which species are associated with virus-affected cacao plants in North America, and to assess their potential as vectors, mealybugs (n = 166) were collected from infected trees in Florida, and identified using COI, ITS2, and 28S markers. The species present were Pseudococcus jackbeardsleyi (38%; n = 63), Maconellicoccus hirsutus (34.3%; n = 57), Pseudococcus comstocki (15.7%; n = 26), and Ferrisia virgata (12%; n = 20). Virus acquisition was assessed by testing mealybug DNA (0.8 ng) using a nested PCR that amplified a 500 bp fragment of the movement protein-coat protein region of CaMMV. Virus sequences were obtained from 34.6 to 43.1% of the insects tested; however, acquisition did not differ among species, X[2] (3, N = 166) = 0.56, p < 0.91. This study identified two new mealybug species, P. jackbeardsleyi and M. hirsutus, as potential vectors of CaMMV. This information is essential for understanding the infection cycle of CaMMV and developing effective management strategies.},
}
@article {pmid34821775,
year = {2021},
author = {Changbunjong, T and Prakaikowit, N and Maneephan, P and Kaewwiset, T and Weluwanarak, T and Chaiphongpachara, T and Dujardin, JP},
title = {Landmark Data to Distinguish and Identify Morphologically Close Tabanus spp. (Diptera: Tabanidae).},
journal = {Insects},
volume = {12},
number = {11},
pages = {},
pmid = {34821775},
issn = {2075-4450},
support = {78.131/00069//Faculty of Veterinary Science, Mahidol University/ ; },
abstract = {Tabanus spp., also known as horse flies (Diptera: Tabanidae), are important vectors of several animal pathogens. Adult females of Tabanus&amp;nbsp;megalops and Tabanus striatus, which are members of the T. striatus complex, are morphologically similar and hence difficult to distinguish using morphological characteristics. In addition, molecular identification by DNA barcoding is also unable to distinguish these species. These two species can occur sympatrically with Tabanus rubidus, which is morphologically similar to T. megalops and T. striatus. Wing geometric morphometrics has been widely used in various insects to distinguish morphologically similar species. This study explored the effectiveness of landmark-based geometrics at distinguishing and identifying T. megalops, T. rubidus, and T. striatus in Thailand. Specimens were collected from different geographical regions of Thailand, and only unambiguously identified specimens were used for geometric morphometric analyses. Left wings of females of T. megalops (n = 160), T. rubidus (n = 165), and T. striatus (n = 85) were photographed, and 22 wing landmarks were used for the analysis. Wing shape was able to distinguish among species with high accuracy scores, ranging from 94.38% to 99.39%. We showed that morphologically very close species of Tabanus can be reliably distinguished by the geometry of their wing venation, and we showed how our experimental material could be used as a reference to tentatively identify new field collected specimens.},
}
@article {pmid34821765,
year = {2021},
author = {Cao, Y and Dietrich, CH},
title = {Identification of Potential Host Plants of Sap-Sucking Insects (Hemiptera: Cicadellidae) Using Anchored Hybrid By-Catch Data.},
journal = {Insects},
volume = {12},
number = {11},
pages = {},
pmid = {34821765},
issn = {2075-4450},
support = {DEB-1639601//National Science Foundation/ ; },
abstract = {Reliable host plant records are available for only a small fraction of herbivorous insect species, despite their potential agricultural importance. Most available data on insect-plant associations have been obtained through field observations of occurrences of insects on particular plants. Molecular methods have more recently been used to identify potential host plants using DNA extracted from insects, but most prior studies using these methods have focused on chewing insects that ingest tissues expected to contain large quantities of plant DNA. Screening of Illumina data obtained from sap feeders of the hemipteran family Cicadellidae (leafhoppers) using anchored hybrid enrichment indicates that, despite feeding on plant fluids, these insects often contain detectable quantities of plant DNA. Although inclusion of probes for bacterial 16S in the original anchored hybrid probe kit yielded relatively high detection rates for chloroplast 16S, the Illumina short reads also, in some cases, included DNA for various plant barcode genes as "by-catch". Detection rates were generally only slightly higher for Typhlocybinae, which feed preferentially on parenchyma cell contents, compared to other groups of leafhoppers that feed preferentially on phloem or xylem. These results indicate that next-generation sequencing provides a powerful tool to investigate the specific association between individual insect and plant species.},
}
@article {pmid34819769,
year = {2021},
author = {Sohn, JH and van Achterberg, C and Han, Y and Kim, H},
title = {A new species of the genus Hylcalosia Fischer (Hymenoptera: Braconidae: Alysiinae) from South Korea, with a key to the Korean species.},
journal = {ZooKeys},
volume = {1070},
number = {},
pages = {31-40},
pmid = {34819769},
issn = {1313-2989},
abstract = {The species of the genus Hylcalosia Fischer, 1967 (Braconidae: Alysiinae) from South Korea are revised. One species, Hylcalosiabicolor sp. nov., is new to science. They are described and illustrated herein and an identification key to the Korean species is added. In addition, the DNA barcode region of the mitochondrial cytochrome c oxidase subunit I (COI) has been analysed for the new species and H.sutchanica is used for genetic comparison.},
}
@article {pmid34819549,
year = {2021},
author = {Trujillo-Argueta, S and Del Castillo, RF and Tejero-Diez, D and Matias-Cervantes, CA and Velasco-Murguía, A},
title = {DNA barcoding ferns in an unexplored tropical montane cloud forest area of southeast Oaxaca, Mexico.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {22837},
pmid = {34819549},
issn = {2045-2322},
support = {20211341//Instituto Polit&#xe9;cnico Nacional/ ; },
mesh = {*DNA Barcoding, Taxonomic ; Ferns/classification/*genetics/growth &amp; development ; *Forests ; Gene Expression Regulation, Plant ; *Genes, Plant ; Mexico ; Phylogeny ; Species Specificity ; *Tropical Climate ; },
abstract = {DNA barcoding can be useful for species identification and phylogenetic analysis, but its effectivity has not been verified in most neotropical cloud forest plants. We tested three plastid barcodes, rbcLa, matK, and trnH-psbA, in selected pteridophytes, a well-represented group in these forests, from a little-explored area in Oaxaca, Mexico, applying the CBOL criteria for barcoding. We used BLASTn, genetic distance, and monophyly tree-based analyses employing neighbor-joining (NJ), maximum likelihood (ML), and Bayesian inference methods. Universal primers for rbcLa and trnH-psbA were successfully amplified and bi-directionally sequenced, but matK could not be amplified for most species. rbcLa showed the highest species discrimination in BLASTn (66.67%). trnH-psbA exhibited higher significant interspecific divergence values than rbcL and rbcLa + trnH-psbA (two-sample sign test, P value < 2.2e-16). Using NJ and ML phylogenetic trees, monophyletic species were successfully resolved (100%), differing only in support values and displaying full agreement with the most recent fern classification. ML trees showed the highest mean support value (80.95%). trnH-psbA was the only barcode that could detect the Elaphoglossoideae subfamily. Species discrimination did not increase using rbcLa + trnH-psbA. rbcLa is useful for fern barcoding, trnH-psbA is most helpful for phylogenetic analyses, and matK may not work as a universal barcoding marker.},
}
@article {pmid34817614,
year = {2021},
author = {Ortega-Morales, AI and Hernández-Triana, LM and Chan-Chable, RJ and Garza-Hernández, JA and González-Álvarez, VH and Ruiz-Arrondo, I and Nikolova, NI and MartÍnez-Arce, A and Fooks, AR and Rodríguez-Pérez, MA},
title = {DNA Barcoding of Mosquitoes from the Pantanos de Centla Biosphere Reserve, Southeastern Mexico.},
journal = {Journal of the American Mosquito Control Association},
volume = {37},
number = {4},
pages = {198-207},
doi = {10.2987/21-6967},
pmid = {34817614},
issn = {1943-6270},
mesh = {Animals ; Bayes Theorem ; *Culex/genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Mexico ; Phylogeny ; },
abstract = {Accurate identification of mosquito species is essential to support programs that involve the study of distribution and mosquito control. Numerous mosquito species are difficult to identify based only on morphological characteristics, due to the morphological similarities in different life stages and large numbers of some species that are members of morphologically similar species complexes. In the present study, the mosquitoes collected in the Pantanos de Centla Biosphere Reserve, southeastern Mexico, were evaluated using a combination of morphological and molecular approaches (mitochondrial cytochrome c oxidase subunit I [COI] DNA barcode). A total of 1,576 specimens of 10 genera and 35 species, mostly adult stages, were collected. A total of 225 COI DNA barcode sequences were analyzed; most species formed well-supported groups in the neighbor joining, maximum likelihood, and Bayesian inference trees. The intraspecific Kimura 2-parameter (K2P) genetic distance averaged 1.52%. An intraspecific K2P distance of 6.20% was observed in Anopheles crucians s.l., while a deep split was identified in Culex erraticus and Cx. conspirator. This study showed that COI DNA barcodes offer a reliable approach to support mosquito species identification in Mexico.},
}
@article {pmid34815452,
year = {2021},
author = {Warchałowska-Śliwa, E and Grzywacz, B and Kociński, M and Maryańska-Nadachowska, A and Heller, KG and Hemp, C},
title = {Highly divergent karyotypes and barcoding of the East African genus Gonatoxia Karsch (Orthoptera: Phaneropterinae).},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {22781},
pmid = {34815452},
issn = {2045-2322},
mesh = {Africa, Eastern ; Animals ; *Chromosome Aberrations ; DNA Barcoding, Taxonomic/*methods ; *Genetic Variation ; Karyotyping/*methods ; Orthoptera/classification/*genetics ; *Phylogeny ; Species Specificity ; },
abstract = {East Africa is a hotspot of biodiversity of many orthopteran taxa, including bushcrickets. Gonatoxia Karsch, 1889 species are fully alate Phaneropterinae, which are perfectly adapted to the foliage of forests. We examined five species using combined cytogenetic and molecular data to determine the inter- and intraspecific genetic diversity. The variation in the diploid number of chromosomes in males ranged from 2n = 28 + X0 and 26 + X0 to 2n = 6 + X0. Fluorescence in situ hybridization showed from one to many 18S rDNA loci as well as interstitial sequences, especially in G. helleri. 18S rDNA loci coincided with active NOR and C-banding patterns. The isolation of populations of the species explains differences in the number of chromosomes (G. maculata), chromosomal polymorphism and chromosomal heterozygosity (G. helleri). Our molecular phylogeny based on the COI locus supported the monophyly of the genus Gonatoxia and separateness of the five examined species in accordance with their morphological features and chromosome numbers as well as the species' distribution.},
}
@article {pmid34813293,
year = {2021},
author = {Ma, Y and Chen, K and Xia, F and Atwal, R and Wang, H and Ahmed, SU and Cardarelli, L and Lui, I and Duong, B and Wang, Z and Wells, JA and Sidhu, SS and Kelley, SO},
title = {Phage-Based Profiling of Rare Single Cells Using Nanoparticle-Directed Capture.},
journal = {ACS nano},
volume = {15},
number = {12},
pages = {19202-19210},
doi = {10.1021/acsnano.1c03935},
pmid = {34813293},
issn = {1936-086X},
support = {//CIHR/Canada ; },
mesh = {*Bacteriophages ; Cell Line, Tumor ; Cell Separation ; Humans ; Microfluidics ; *Nanoparticles ; *Neoplastic Cells, Circulating ; Tumor Microenvironment ; },
abstract = {Advances in single-cell level profiling of the proteome require quantitative and versatile platforms, especially for rare cell analyses such as circulating tumor cell (CTC) profiling. Here we demonstrate an integrated microfluidic chip that uses magnetic nanoparticles to capture single tumor cells with high efficiency, permits on-chip incubation, and facilitates in situ cell-surface protein expression analysis. Combined with phage-based barcoding and next-generation sequencing technology, we were able to monitor changes in the expression of multiple surface markers stimulated in response to CTC adherence. Interestingly, we found fluctuations in the expression of Frizzled2 (FZD2) that reflected the microenvironment of the single cells. This platform has a high potential for in-depth screening of multiple surface antigens simultaneously in rare cells with single-cell resolution, which will provide further insights regarding biological heterogeneity and human disease.},
}
@article {pmid34811339,
year = {2021},
author = {Motamedinia, B and Skevington, JH and Kelso, S},
title = {Revision of Tomosvaryella Aczl (Diptera: Pipunculidae) in the Middle East, with description of 19 new species.},
journal = {Zootaxa},
volume = {5002},
number = {1},
pages = {1-103},
doi = {10.11646/zootaxa.5002.1.1},
pmid = {34811339},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; *Diptera ; Genes, Mitochondrial ; Middle East ; },
abstract = {The genus Tomosvaryella Aczl, 1939 is revised from the Middle East. Fifty-nine species are recorded and 19 of these are new to science: T. acantha Motamedinia Skevington sp. nov., T. ampliasa Motamedinia Skevington sp. nov., T. anahitae Motamedinia Skevington sp. nov., T. bistounensis Motamedinia Skevington sp. nov., T. cyprusensis Motamedinia Skevington sp. nov., T. ellipiensis Motamedinia Skevington sp. nov., T. emaratensis Motamedinia Skevington sp. nov., T. hamounensis Motamedinia Skevington sp. nov., T. kiansiae Motamedinia Skevington sp. nov., T. nimroozensis Motamedinia Skevington sp. nov., T. oshidae Motamedinia Skevington sp. nov., T. osteodes Motamedinia Skevington sp. nov., T. saudiensis Motamedinia Skevington sp. nov., T. soziana Motamedinia Skevington sp. nov., T. spinula Motamedinia Skevington sp. nov., T. subtransvaalensis Motamedinia Skevington sp. nov., T. susa Motamedinia Skevington sp. nov., T. unicorna Motamedinia Skevington sp. nov. and T. yemenensis Motamedinia Skevington sp. nov. are described and illustrated based on sequence information from the mitochondrial COI barcoding gene and morphological parameters. DNA barcodes are provided for 37 of the 59 species. Descriptions of new species, diagnoses, distribution maps and an illustrated key for all species are provided.},
}
@article {pmid34811237,
year = {2021},
author = {Ahrens, D and Ahyong, ST and Ballerio, A and Barclay, MVL and Eberle, J and Espeland, M and Huber, BA and Mengual, X and Pacheco, TL and Peters, RS and Rulik, B and Vaz-DE-Mello, F and Wesener, T and Krell, FT},
title = {Is it time to describe new species without diagnoses?A comment on Sharkey et al. (2021).},
journal = {Zootaxa},
volume = {5027},
number = {2},
pages = {151-159},
doi = {10.11646/zootaxa.5027.2.1},
pmid = {34811237},
issn = {1175-5334},
mesh = {Animals ; *Biodiversity ; DNA ; *DNA Barcoding, Taxonomic ; Phylogeny ; },
abstract = {New methods in taxonomy and systematics can influence the overall practice of formally naming and describing biodiversity. DNA barcoding has been controversial since its emergence, but now, large scale species descriptions exclusively based on barcodes have created what can be called a 'new quality of performance. Its limitations are discussed from different perspectives: nomenclature, general pragmatism, and problems of DNA-based species delimitation in the light of the central aim of achieving a robust and stable nomenclature of organisms, essential for all applications of biodiversity research. This issue needs to be addressed to prevent restraining the progress of taxonomy and its ability to contribute to modern science.},
}
@article {pmid34811226,
year = {2021},
author = {Muoz, I and Garca-Isarch, E and Cuesta, JA},
title = {Annotated and updated checklist of marine crabs (Decapoda: Brachyura) of Mozambique supported by morphological and molecular data from shelf and slope species of the MOZAMBIQUE surveys.},
journal = {Zootaxa},
volume = {5056},
number = {1},
pages = {1-67},
doi = {10.11646/zootaxa.5056.1.1},
pmid = {34811226},
issn = {1175-5334},
mesh = {Animals ; *Brachyura/genetics ; Female ; *Lice Infestations ; Mozambique ; RNA, Ribosomal, 16S ; },
abstract = {An updated checklist of Mozambican marine brachyuran crabs is generated based on an exhaustive revision of the existing literature, together with the additional records provided by the specimens collected throughout the three MOZAMBIQUE surveys carried out in Mozambican waters during three consecutive years (20072009) by the Instituto Espaol de Oceanografa, (Spanish Institute of Oceanography, IEO). A total of 269 species, grouped in 15 superfamilies, 26 families and 172 genera are reported in the checklist, and a detailed inventory is produced with the list and remarks about the brachyuran species collected. Thirty-nine crab species belonging to 19 families were identified based on morphological characteristics and/or genetic tools. DNA barcode sequences (16S rRNA and/or COI) were obtained for 37 species, including 16S and COI sequences that are new for 26 and 14 species, respectively. Colour photographs of fresh specimens illustrate the comments about most species, being the first time that the original colour pattern is described for some of them. New records in Mozambican waters are reported for the species Paromolopsis boasi, Mursia aspera, Carcinoplax ischurodous, Tanaoa pustulosus, Euclosiana exquisita, Oxypleurodon difficilis, Naxioides robillardi, Samadinia galathea, Cyrtomaia gaillardi, Paramaja gibba, Pleistacantha ori, Parathranites granosus, Parathranites orientalis, Ovalipes iridescens and Charybdis smithii, and second records for Moloha alcocki, Samadinia pulchra and Charybdis africana. In addition, Raninoides crosnieri, S. galathea and P. ori were collected for the first time after their descriptions. The female of Samadinia galathea is described for the first time, and a potential new species of Mursia is reported. Some records expand the known bathymetric range of certain species and/or their general distribution. New molecular and morphological data suggest the necessity of the revision of P. boasi, R. crosnieri, C. africana and the genera Platymaia and Carcinoplax. The variability and taxonomic validity of some morphological characters in brachyuran systematic is discussed.},
}
@article {pmid34811220,
year = {2021},
author = {Sithole, Y and Heemstra, E and Mwale, M},
title = {Revalidation and redescription of Serranus knysnaensis Gilchrist, 1904, (Perciformes: Serranidae) with a new distribution record.},
journal = {Zootaxa},
volume = {5057},
number = {1},
pages = {99-113},
doi = {10.11646/zootaxa.5057.1.6},
pmid = {34811220},
issn = {1175-5334},
mesh = {Animals ; *Bass ; DNA, Mitochondrial ; *Perciformes/genetics ; Phylogeny ; },
abstract = {A southwestern Indian Ocean (SWIO) percoid fish Serranus knysnaensis Gilchrist, 1904, was long synonymised with the comber, Serranus cabrilla (Linnaeus, 1758), from the eastern Atlantic Ocean, Mediterranean and Black Sea. However, when the species was brought out of synonymy by Heemstra Heemstra (2004), reasons for this decision were not given. This study aims to revalidate the present taxonomic status of S. knysnaensis using morphological and molecular assessments. The two species are distinguished by the number of circumpeduncular scales (2634 in S. knysnaensis versus 3438 in S. cabrilla) and total gill rakers (1822 versus 2224). Serranus knysnaensis is also distinct from S. novemcinctus Kner, 1864, the other SWIO species of Serranus, based on total gill raker counts (1822 versus 3135). Genetic analysis of mitochondrial DNA barcode (COI) sequences for 17 Serranus species revealed three closely-related monophyletic clusters corresponding to S. cabrilla, S. novemcinctus and S. knysnaensis that were supported (P 0.001) by species delimitation methods. Even though the genetic distances among the three species were the lowest in the genus (1.60-1.99%), these species may be ecomorphs or lineages that have only recently diverged from each other. These three species also have allopatric distributions and our morphological and molecular data thus confirm that S. knysnaensis is a valid species.},
}
@article {pmid34811207,
year = {2021},
author = {Zhang, L and Li, Y and Smith, SM and Wang, J},
title = {Scolytus jiulianshanensis, a new species of bark beetle (Coleoptera: Curculionidae: Scolytinae) from elm in China.},
journal = {Zootaxa},
volume = {5057},
number = {2},
pages = {295-300},
doi = {10.11646/zootaxa.5057.2.9},
pmid = {34811207},
issn = {1175-5334},
mesh = {Animals ; China ; *Coleoptera/genetics ; Plant Bark ; *Ulmus ; *Weevils/genetics ; },
abstract = {A new species of bark beetle, Scolytus jiulianshanensis Zhang, Li Smith sp. nov., from Jiangxi, China is described and illustrated. This new species was collected from dead elm (Ulmus sp.) trees. A DNA barcoding sequence of this species is provided. The new species is distinguished from other Asian Scolytus species by the apical margins of ventrites 3 and 4 of the male each armed with a broad median tubercle and lacking ventral spines.},
}
@article {pmid34811137,
year = {2021},
author = {Liu, YJ and He, ZQ},
title = {A new species of the genus Parapentacentrus Shiraki, 1930 from Yunnan, China (Orthoptera: Gryllidae: Itarinae).},
journal = {Zootaxa},
volume = {5032},
number = {1},
pages = {143-146},
doi = {10.11646/zootaxa.5032.1.9},
pmid = {34811137},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures ; Animals ; Body Size ; China ; *Gryllidae/genetics ; Male ; Organ Size ; },
abstract = {The genus Parapentacentrus Shiraki, 1930 includes two species with long wings. In this paper, we report one new species, P. brevipennis He sp. nov., from Jinping, Yunnan, China. The new species have short forewings and hindwings, and have differences in the shape of supra-anal plate and male genitalia. DNA Barcode (COI gene) of this new species are provided. The type specimens are deposited in Museum of Biology, East China Normal University (ECNU).},
}
@article {pmid34811124,
year = {2021},
author = {Praz, C and Al-Shahat, AM and Gadallah, NS},
title = {Taxonomic revision of the subgenus Eutricharaea Thomson in Egypt, with a key to the species and the description of two new species (Hymenoptera, Anthophila, Megachilidae, genus Megachile Latreille).},
journal = {Zootaxa},
volume = {5032},
number = {3},
pages = {301-330},
doi = {10.11646/zootaxa.5032.3.1},
pmid = {34811124},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Bees ; Egypt ; Female ; *Hymenoptera ; Male ; *Moths ; },
abstract = {The subgenus Eutricharaea Thomson of the genus Megachile Latreille (Hymenoptera: Megachilidae) in Egypt is revised. Fifteen species are recognized, of which two are new: Megachile laniventris Praz sp. nov. and M. rufomandibularis Praz sp. nov. In addition, three unclear taxa known from few specimens in one sex are documented to facilitate future work. The following new synonymies are proposed: M. microxantha Cockerell 1937, M. privigna Rebmann 1968, and M. submucida Alfken 1926 are synonymized with M. leucostoma Prez 1907 (syn. nov.); M. blanda Rebmann 1968 with M. walkeri Dalla Torre 1896 (syn. nov.); M. uniformis Alfken 1934 (not M. uniformis Mitchell 1929) and the replacement name M. minutuloides Alfken 1936 with M. minutissima Radoszkowski 1876 (syn. nov.); and M. tkalcui Zanden 1996 with M. rugipuncta Alfken 1934 (syn. nov.). Lectotypes are designated for M. soikai Benoist 1961, M. rugipuncta, M. tenuistriga Alfken 1938, M. niveascopa Ferton 1908, and M. naevia Kohl 1906. The previously unknown males of M. impressipuncta Alfken 1934 and M. rugipuncta, as well as the undescribed female of M. soikai are described. Illustrated keys for both males and females are provided and DNA barcodes are published for most species.},
}
@article {pmid34811107,
year = {2021},
author = {Merlin, BL and Castilho, RC and DE Moraes, GJ},
title = {A new species of Lasioseius (Acari: Blattisociidae) from Brazil with morphological and DNA barcode data.},
journal = {Zootaxa},
volume = {5032},
number = {4},
pages = {583-599},
doi = {10.11646/zootaxa.5032.4.8},
pmid = {34811107},
issn = {1175-5334},
mesh = {Animals ; Brazil ; DNA Barcoding, Taxonomic ; Ecosystem ; Female ; *Mites/genetics ; Phylogeny ; },
abstract = {Lasioseius foliatisetus n. sp. is described based on the morphology and molecular markers of adult females collected in litter/soil samples of the Caatinga and Pantanal, extensive Brazilian biomes. This new species can be distinguished from other Lasioseius species mainly by having fixed cheliceral digit with three teeth in addition to apical tooth, most dorsal shield setae leaf-shaped, and ventrianal shield with seven pairs of setae (including Jv5) in addition to the circumanal setae. The determined nucleotide sequences of the CytB gene and of ITSS of Lasioseius foliatisetus n. sp. are the first data of these types deposited in a published database (GenBank) for a species of this genus. The phylogenetic tree generated in the analysis of ITSS sequences showed a clade constituted only by species of the superfamily Phytoseoidea, including L. foliatisetus n. sp.. The phylogenetic tree generated in the ML analysis based on CytB showed a separation of the blattisociid species (including L. foliatisetus n. sp.) in one clade and the phytoseiid species in another clade. The analysis of the 28S 13 domain by itself did not allow the separation of the new species here described from species of other blattisociid genera.},
}
@article {pmid34811088,
year = {2021},
author = {Wiberg-Larsen, P and Hansen, SB and Rinne, A and Viitanen, E and Krogh, PH},
title = {Key to Ptychopteridae (Diptera) larvae of Northern Europe, with notes on distribution and biology.},
journal = {Zootaxa},
volume = {5039},
number = {2},
pages = {179-200},
doi = {10.11646/zootaxa.5039.2.2},
pmid = {34811088},
issn = {1175-5334},
mesh = {Animals ; Biology ; *Diptera/genetics ; Europe ; Larva/genetics ; Nematocera ; },
abstract = {A key to larvae of Ptychopteridae (phantom crane flies) is provided for species inhabiting Northern Europe. The key encompasses seven species, including the previously undescribed larvae of Ptychoptera longicauda (Tonnoir 1919). Larval specimens examined were primarily sampled from sites in Denmark. Larvae were associated with correctly identified adults based on DNA barcode (COI) sequence. In the development of the key, a wide suite of morphological characteristics were examined and evaluated for their utility to separate species. Current distribution maps are provided for all species occurring within Northern Europe. Based on records of larvae from Denmark and Finland, notes on larval habitats are given. We also present flight periods for all species examined during this study. Finally, the status of the enigmatic species Ptychoptera obscura (Peus 1958) is briefly discussed.},
}
@article {pmid34811083,
year = {2021},
author = {Wang, Y and Teng, K and Liu, T},
title = {New record of Epermenia (Calotripis) sinjovi Gaedike (Lepidoptera: Epermeniidae) in China: DNA barcode, adult, immature stages, host plant and biology.},
journal = {Zootaxa},
volume = {5039},
number = {2},
pages = {263-276},
doi = {10.11646/zootaxa.5039.2.7},
pmid = {34811083},
issn = {1175-5334},
mesh = {Animals ; Biology ; China ; *DNA Barcoding, Taxonomic ; *Moths/genetics ; Pupa ; },
abstract = {Epermenia (Calotripis) sinjovi Gaedike, 1993, feeding on Angelica pubescens Maxim. and A. ursina Maxim., was previously recorded in Russia (Far East, Southern Siberia and Transbaikalia), Kunashir Island and Japan. This species is for the first time reported in China by rearing from a new host plant A. polymorpha Maxim. The larva and pupa are illustrated and described for the first time. Available biological information associated with the new host plant is also reported. Reference DNA barcodes are provided for E. (C.) sinjovi, which confirms that forewing distinct colors and morphological differences found in venation and genitalia among individuals are intraspecific variations. The adult morphological variations within population are analyzed and discussed.},
}
@article {pmid34811077,
year = {2021},
author = {Fraser, TH and Bogorodsky, SV and Mal, AO and Alpermann, TJ},
title = {Review of the cardinalfishes of the genus Cercamia (Percomorpha: Apogonidae) of the Red Sea and Indian Ocean with descriptions of three new species.},
journal = {Zootaxa},
volume = {5039},
number = {3},
pages = {363-394},
doi = {10.11646/zootaxa.5039.3.3},
pmid = {34811077},
issn = {1175-5334},
mesh = {Animals ; Indian Ocean ; *Perciformes ; Phylogeny ; },
abstract = {The representatives of Cercamia from the Indian Ocean including Red Sea are reviewed and three new species are described: Cercamia spio n. sp., formerly known as C. eremia (Allen, 1987), is described from 14 specimens, 1733 mm SL, collected in 1015 meters from northern (Duba) to central (Jeddah) Saudi Arabia and from Jezirat Faraun, Egypt. It also has been photographed from the Gulf of Aqaba (Dahab, Egypt) and El Quseir (Mangrove Bay, Egypt). The new species is distinguished from other Indian Ocean Cercamia in having fewer developed gill rakers on lower limb (usually 11 versus usually 1213) and fewer anal-fin rays (11 versus usually 1213). Another new species, Cercamia laamu, n. sp., is described only from the Maldives and Chagos Archipelago based on five specimens 16.030.5 mm SL. It differs from all Indian Ocean Cercamia in having more greater number of the second dorsal-fin rays (10 versus usually 9), and a translucent body devoid of reddish marks versus small reddish dots and crisscross lines. The third new species, Cercamia mascarene, n. sp., is described from 40 specimens 1936 mm SL, from Rodrigues Island, Mauritius. It differs from Cercamia eremia in having a greater number of developed gill rakers on the lower limb of the first gill arch (usually 13 versus usually 12). Free neuromasts and cephalic pores are illustrated for Cercamia mascarene and free neuromasts on the body and caudal fin are illustrated for Japanese specimens of C. cf. eremia. New diagnoses are provided for Cercamia cladara, the type species of the genus, and C. eremia. A map of collection locations for species of Cercamia is presented to show the breath of known occurrences in the Red Sea and Indian Ocean. A new morphologic diagnosis is provided for Cercamia. A phylogenetic analysis of the barcoding portion of the mitochondrial COI gene, including all available sequences from members of the genus Cercamia, displays a much higher species diversity than expected, with high levels of divergence among recognized and undescribed species. A key to the described Indian Ocean species is provided.},
}
@article {pmid34810979,
year = {2021},
author = {Yamana, Y and Nakaguchi, K and Yamaguchi, S and Katoh, M and Ogawa, A and Ohtsuka, S},
title = {Four new dendrochirotid holothurians collected from the Seto Inland Sea and the western part of the Sea of Japan, western Japan.},
journal = {Zootaxa},
volume = {5023},
number = {1},
pages = {1-43},
doi = {10.11646/zootaxa.5023.1.1},
pmid = {34810979},
issn = {1175-5334},
mesh = {Animals ; Japan ; *Sea Cucumbers ; },
abstract = {Fifteen dendrochirotid holothurians, including four new species, were collected from the Seto Inland Sea and the western part of the Sea of Japan, western Japan by the training and research vessel (TR/V) TOYOSHIO MARU of Hiroshima University, during the 201415 surveys. Massinium toyoshiomaruae sp. nov., Thyone kyushuensis sp. nov., T. liaoi sp. nov., and T. toyoshiomaruae sp. nov. are described as new species. Massinium toyoshiomaruae sp. nov. is readily distinguishable from all congeners by the absence of bodywall ossicles and the presence of table ossicles in the tentacle base. Thyone kyushuensis sp. nov. possesses large polyporous-tables in the introvert and tentacles, bodywall ossicles of a peculiar shape, and tentacle ossicles comprised mostly of unbranching rods and/or rod-like rosettes, which differ from those of all congeners. Thyone liaoi sp. nov. resembles T. pedata Semper, 1867 in its bodywall ossicles, however, it is distinguishable by the absences of huge ossicles in the body wall and the needle-shaped ossicles in the gonadal tubules. Thyone toyoshiomaruae sp. nov. is distinguishable from all other Thyone by the presence of the peculiar shape of the bodywall ossicles. Partial sequences of the mitochondrial cytochrome c oxidase subunit I gene are provided from the type specimens of the new species as DNA barcoding data.},
}
@article {pmid34810918,
year = {2021},
author = {Zhang, AO and Zhou, X},
title = {The larvae of Chinese Hydropsychidae (Insecta: Trichoptera), Part III: Hydromanicus melli Complex, H. canaliculatus, and H. umbonatus.},
journal = {Zootaxa},
volume = {5026},
number = {4},
pages = {527-540},
doi = {10.11646/zootaxa.5026.4.4},
pmid = {34810918},
issn = {1175-5334},
mesh = {Animals ; China ; Genes, Mitochondrial ; *Holometabola ; Insecta ; Larva ; },
abstract = {A total of 45 adult and larval specimens of 6 Chinese Hydromanicus species are included in this molecular association analysis. Of these, the larvae of Hydromanicus melli Complex, H. canaliculatus, and H. umbonatus were associated with their adults using independent DNA sequences (the nuclear 28S-D2 fragment and the mitochondrial COI barcode gene) and were compared to metamorphotypes where available. Phylograms based on both genes revealed deep intraspecific divergences in several species, suggesting that cryptic diversity is likely common within the genus. Illustrated larval descriptions are provided for the three associated species. However, the larvae of species in the H. melli Complex cannot be morphologically differentiated from each other.},
}
@article {pmid34810885,
year = {2021},
author = {Tang, CN},
title = {Description of a new codling species of Physiculus from Taiwan (Gadiformes: Moridae).},
journal = {Zootaxa},
volume = {5052},
number = {1},
pages = {105-116},
doi = {10.11646/zootaxa.5052.1.6},
pmid = {34810885},
issn = {1175-5334},
mesh = {Animals ; *Gadiformes ; Gills ; Taiwan ; },
abstract = {A new species of codling Physiculus megastomus sp. nov. is described based on the holotype and a subadult paratype collected from northern and eastern Taiwan. The new species is classified in Physiculus by the presence of a ventral light organ on the abdomen and a chin barbel, and the absence of vomerine teeth. It is distinguished from congeners in having a large mouth with the posterior end of the maxilla extending well behind the level of the posterior margin of the orbit, its length 57.8‒60.7% in head length (HL) and the combination of the following characters: both jaws bearing caniniform teeth; snout, suborbital area, and gular region fully scaled; ventral light organ small, its length 5.5‒6.7% of distance from the interventral line to the origin of the anal fin (InV-af), located approximately at the mid-point of InV-af; five gill rakers on the upper limb of the first gill arch. DNA barcoding supported the establishment of the new species.},
}
@article {pmid34810814,
year = {2021},
author = {Forrester, GE and McCaffrey, MT and Terpis, KX and Lane, CE},
title = {Using DNA barcoding to identify host-parasite interactions between cryptic species of goby (Coryphopterus: Gobiidae, Perciformes) and parasitic copepods (Pharodes tortugensis: Chondracanthidae, Cyclopoida).},
journal = {Zootaxa},
volume = {5048},
number = {1},
pages = {99-117},
doi = {10.11646/zootaxa.5048.1.5},
pmid = {34810814},
issn = {1175-5334},
mesh = {Animals ; *Copepoda/genetics ; DNA Barcoding, Taxonomic ; Host-Parasite Interactions ; *Parasites ; *Perciformes/genetics ; Phylogeny ; },
abstract = {Previous work, using morphological characters, identified a generalist copepod parasite (Pharodes tortugensis) at high prevalence on two common gobies (Coryphopterus glaucofraenum and C. dicrus) in the British Virgin Islands (BVI). DNA barcoding subsequently revealed C. glaucofraenum to be three morphologically similar species (C. glaucofraenum, C. venezuelae and C. tortugae), casting doubt on host identities in the BVI and the classification of the parasite as a single species. Mitochondrial cytochrome c oxidase subunit I (COI) data from 67 gobies in the BVI showed that, in addition to C. dicrus, host gobies were a mix of C. glaucofraenum and C. venezuelae, while C. tortugae was unexpectedly absent from the study area. COI data (n = 70) indicated that the copepod infecting all three hosts was a single species, almost certainly P. tortugensis. The pharodes-coryphopterus interaction has a strong impact on host dynamics in the BVI, and a revised understanding of these dynamics must account for any differences among the three newly confirmed hosts in transmission of, and susceptibility to, the shared parasite. No other infected hosts were discovered at our sites, but P. tortugensis is reportedly widespread and infects 12 additional host species elsewhere. Further DNA barcoding is thus needed to test whether P. tortugensis is truly a widespread generalist, or instead represents a group of more specialized cryptic species.},
}
@article {pmid34810811,
year = {2021},
author = {Singha, D and Patidar, A and Kumar, V and Tyagi, K},
title = {A new species of Mycterothrips Trybom (Thysanoptera: Thripidae) from India with new record of the genus Paithrips Nonaka amp; Jangvitaya.},
journal = {Zootaxa},
volume = {5048},
number = {1},
pages = {135-140},
doi = {10.11646/zootaxa.5048.1.8},
pmid = {34810811},
issn = {1175-5334},
mesh = {Animals ; India ; Mitochondria ; *Thysanoptera ; },
abstract = {Mycterothrips nainiae sp. n. (Thripinae) is described and illustrated from India, and one genus and species, Paithrips circularis Nonaka and Jangvitaya, is newly recorded from India. A key to species of Mycterothrips from India is also provided. The DNA barcode data using partial mitochondrial cytochrome c oxidase subunit I (mtCOI) from the holotype also five sequences of Paithrips circularis were generated.},
}
@article {pmid34810774,
year = {2021},
author = {Frolov, AV and Vishnevskaya, MS and Akhmetova, LA},
title = {Identification of larvae of two Aphodius Helwig, 1798 (Coleoptera: Scarabaeidae: Aphodiinae) species using morphology and DNA barcode.},
journal = {Zootaxa},
volume = {5047},
number = {2},
pages = {153-164},
doi = {10.11646/zootaxa.5047.2.4},
pmid = {34810774},
issn = {1175-5334},
mesh = {Animals ; *Coleoptera/genetics ; DNA Barcoding, Taxonomic ; Larva/genetics ; Microscopy, Electron, Scanning ; },
abstract = {The third instar larvae of Aphodius (Alocoderus) hydrochaeris (Fabricius, 1798) and A. (Bodilus) ictericus (Laicharting, 1781) are described based on scanning electron microscopy and COI sequences. COI barcode sequence for A. (A.) hydrohaeris is provided for the first time. Two haplotypes are discovered in A. (B.) ictericus.},
}
@article {pmid34810731,
year = {2021},
author = {Mousavi-Sabet, H and Eagderi, S and Vatandoust, S and Freyhof, J},
title = {Five new species of the sisorid catfish genus Glyptothorax from Iran (Teleostei: Sisoridae).},
journal = {Zootaxa},
volume = {5067},
number = {4},
pages = {451-484},
doi = {10.11646/zootaxa.5067.4.1},
pmid = {34810731},
issn = {1175-5334},
mesh = {Animals ; *Catfishes/genetics ; DNA, Mitochondrial ; Iran ; Mitochondria ; Rivers ; },
abstract = {Five new species of Glyptothorax are described from Iran. Glyptothorax alidaeii, new species, from the Seimare in the Karkheh drainage, G. galaxias, new species, from the upper Karun drainage, G. hosseinpanahii, new species, from the Zohreh drainage, G. pallens, new species, from the Sirvan drainage, and G. shapuri, new species, from Shapur in the Helleh drainage. Glyptothorax silviae from the Jarrahi drainage is re-diagnosed. All six species are morphologically distinguishable by the structure of the thoracic adhesive apparatus, as well as morphometric characters and details in the colour pattern. They form distinct mitochondrial clades between 1.2% and 4.1% minimum K2P distance based on the mitochondrial DNA barcode region.},
}
@article {pmid34810636,
year = {2021},
author = {Amor, MD and Hart, AM},
title = {Octopus djinda (Cephalopoda: Octopodidae): a new member of the Octopus vulgaris group from southwest Australia.},
journal = {Zootaxa},
volume = {5061},
number = {1},
pages = {145-156},
doi = {10.11646/zootaxa.5061.1.7},
pmid = {34810636},
issn = {1175-5334},
mesh = {Animals ; Australia ; Male ; *Octopodiformes/genetics ; Western Australia ; },
abstract = {A new Octopus Cuvier, 1797 species, Octopus djinda Amor, 2021 (previously treated as O. cf. tetricus and O. aff. tetricus), is described from the shallow waters off southwest Australia. This species was classified as conspecific with O. tetricus Gould, 1852 from Australias east coast and New Zealand but is shown here to be morphologically and genetically distinct. This description is based on 25 individuals across three localities in southwest Australia, encompassing most of its distribution. Greater and non-overlapping sucker counts on the males hectocotylised arm delimit east and west coast forms. DNA barcoding using cytochrome c oxidase subunit I also successfully differentiates between these taxa; 13 polymorphisms along a 349 bp partial fragment (3.7% sequence divergence). A close relative of the O. vulgaris Cuvier, 1797 species-group, O. djinda, sp. nov. supports a highly productive fishery and is currently one of two octopod fisheries worldwide to have received sustainable certification from the Marine Stewardship Council. The taxonomic description presented here provides formal recognition of the taxonomic status of southwest Australias common octopus, O. djinda, sp. nov. and facilitates appropriate fisheries catch reporting and management.},
}
@article {pmid34810579,
year = {2021},
author = {Marin, IN and Palatov, DM},
title = {The hidden diversity of the genus Lyurella Derzhavin, 1939 (Crustacea: Amphipoda: Crangonyctidae): four new species from the subterranean habitats of the northwestern Caucasus, Russia.},
journal = {Zootaxa},
volume = {5006},
number = {1},
pages = {127-168},
doi = {10.11646/zootaxa.5006.1.17},
pmid = {34810579},
issn = {1175-5334},
mesh = {*Amphipoda/genetics ; Animals ; Ecosystem ; Phylogeny ; Russia ; Species Specificity ; },
abstract = {Four new species of the Palaearctic crangonyctid amphipod genus Lyurella Derzhavin, 1939 (Crustacea: Amphipoda: Crangonyctidae), L. mikhailovi sp. n., L. fanagorica sp. n., L. fontinalis sp. n. and L. asheensis sp. n., are described based on an integrative approach from the subterranean habitats of the southwestern foothills of the Greater Caucasian Ridge (the north-eastern Black Sea coast). Despite the relative proximity of the habitats, the interspecific genetic divergence (by COI mtDNA gene marker) between the newly outlined Caucasian species of the genus varied from 11 to 21%, demonstrating a long-term isolation and lack of gene flow for at least 37Mya, starting from the Pliocene. The lowest genetic divergence between L. shepsiensis Sidorov, 2015 and L. asheensis sp. n., estimated as 4%, is also considered species-specific due to the presence of distinct morphological differences. We discuss the phylogeny, morphology, and distribution and provide a key for all known species of Lyurella. DNA barcoding data for all species, including the type species of the genus, Lyurella hyrcana Derzhavin, 1939, are presented for the first time.},
}
@article {pmid34810541,
year = {2021},
author = {Japaridze, LG and Malkiewicz, A and Sanakoeva, A and Tsulaia, M and Bulbulashvili, N and Unap, E},
title = {Description of the female Apocolotois smirnovi (Romanoff, 1885) (Lepidoptera: Geometridae, Ennominae), with comments on the biology and distribution of the species.},
journal = {Zootaxa},
volume = {4996},
number = {1},
pages = {153-162},
doi = {10.11646/zootaxa.4996.1.6},
pmid = {34810541},
issn = {1175-5334},
mesh = {Animals ; Biology ; DNA ; Female ; Larva ; *Lepidoptera ; Male ; *Moths/genetics ; Pupa ; },
abstract = {The hitherto unknown female of Apocolotois smirnovi (Romanoff, 1885) is described based on two specimens from Tbilisi, Georgia. To date, only males of this rare Transcaucasian species were known. The results of DNA barcoding are presented, larva and pupa of A. smirnovi are figured, and the biology and distribution of the species are commented on.},
}
@article {pmid34810516,
year = {2021},
author = {Ruiz-Garca, A and Garzn, A and Zamora-Muoz, C},
title = {Redescription of the last instar larva of Stenophylax fissus (McLachlan 1875) and the DNA barcode of Stenophylax crossotus McLachlan 1884 (Trichoptera: Limnephilidae) with an updated diagnostic matrix of the known larvae of Stenophylax species of the Iberian Peninsula.},
journal = {Zootaxa},
volume = {4996},
number = {3},
pages = {513-524},
doi = {10.11646/zootaxa.4996.3.6},
pmid = {34810516},
issn = {1175-5334},
mesh = {Animals ; *Coleoptera ; DNA Barcoding, Taxonomic ; Female ; *Holometabola ; Insecta ; Larva/genetics ; },
abstract = {The larva of Stenophylax fissus (McLachlan 1875) is redescribed, illustrated, and compared with morphologically similar Limnephilidae larvae from the Iberian Peninsula. In addition, the sequence of the mtCOI gene in the barcode region of one individual is reported. Likewise, the barcode and the conspecificity between two larvae and one female of the non-sequenced species S. crossotus are given. In addition, the high genetic diversity among S. sequax populations is highlighted, suggesting a complex of cryptic species. Finally, a diagnostic matrix of the known larvae of Stenophylax species from the Iberian Peninsula is provided.},
}
@article {pmid34810432,
year = {2021},
author = {Wang, LY and Zhao, JX and Irfan, M and Zhang, ZS},
title = {Review of the spider genus Ectatosticta Simon, 1892 (Araneae: Hypochilidae) with description of four new species from China.},
journal = {Zootaxa},
volume = {5016},
number = {4},
pages = {523-542},
doi = {10.11646/zootaxa.5016.4.4},
pmid = {34810432},
issn = {1175-5334},
mesh = {Animals ; China ; DNA ; *Spiders/genetics ; },
abstract = {Species of the genus Ectatosticta Simon, 1892 are studied from China, including seven known species E. bajie Lin Li, 2021 from Sichuan Prov., E. davidi (Simon, 1889) from Shaanxi, E. deltshevi Platnick Jger, 2009 from Qinghai, E. rulai Lin Li, 2021 from Sichuan, E. wukong Lin Li, 2020 from Sichuan, E. xuanzang Lin Li, 2020 from Tibet, E. yukuni Lin Li, 2021 from Shaanxi, and four new species: E. nyingchiensis sp. nov. from Tibet, E. pingwuensis sp. nov. from Sichuan, E. shennongjiaensis sp. nov. from Hubei and E. songpanensis sp. nov. from Sichuan. We provide detailed descriptions, including DNA barcode information, and images of all the species.},
}
@article {pmid34808870,
year = {2021},
author = {Dannenberg, PH and Wang, J and Zhuo, Y and Cho, S and Kim, KH and Yun, SH},
title = {Droplet microfluidic generation of a million optical microparticle barcodes.},
journal = {Optics express},
volume = {29},
number = {23},
pages = {38109-38118},
pmid = {34808870},
issn = {1094-4087},
support = {DP1 EB024242/EB/NIBIB NIH HHS/United States ; P41 EB015903/EB/NIBIB NIH HHS/United States ; },
abstract = {Micron-scale barcode particles enable labelling of small objects. Here, we demonstrate high-throughput barcode fabrication inside a microfluidic chip that can embed multiple, dye-doped high quality-factor whispering gallery mode cavities inside aqueous droplets at kilohertz rates. These droplets are then cured to form polyacrylamide hydrogel beads as small as 30 μm in diameter. Optical resonance spectra of the embedded cavities provide the hydrogels with unique barcodes with their diversity combinatorically scaled with the number of embedded cavities. Using 3 cavities per hydrogel, we obtain approximately one million uniquely identifiable, optically readable barcode microparticles.},
}
@article {pmid34806023,
year = {2021},
author = {Cong, Q and Barbosa, EP and Marín, MA and Freitas, AVL and Lamas, G and Grishin, NV},
title = {Two new species of Hermeuptychia from North America and three neotype designations (Nymphalidae: Satyrinae).},
journal = {The taxonomic report of the International Lepidoptera Survey},
volume = {9},
number = {},
pages = {},
pmid = {34806023},
issn = {2643-4806},
support = {R35 GM127390/GM/NIGMS NIH HHS/United States ; },
abstract = {Two new species of Hermeuptychia Forster, 1964 are described. Hermeuptychia sinuosa Grishin, sp. n. (type locality Guatemala: El Progreso, Morazán) is an isolated member of the genus that does not readily fit into known species groups, as suggested by its distinct male and female genitalia and COI DNA barcode sequences. It is distinguished from its congeners by prominently wavy submarginal lines, rounder wings and distinctive genitalia, and can typically be identified by a white dot, instead of an eyespot, near the ventral hindwing apex. Hermeuptychia occidentalis Grishin, sp. n. (type locality Mexico: Guerrero, Acapulco) belongs to the Hermeuptychia sosybius group as indicated by the presence of androconia on the dorsal surface of the wings, genitalia and COI DNA barcodes, and in addition to DNA characters, differs from its relatives in the shape of the uncus and female genitalia. Neotypes of Oreas strigata canthe Hübner, [1811] (type locality Suriname: Gelderland, Suriname River), Megisto acmenis Hübner, 1823 (type locality Argentina: Buenos Aires), and Satyrus cantheus Godart, [1824] (type locality USA: Florida, Pinellas Co., St. Petersburg) and lectotype of Euptychia celmis var. bonaërensis [sic] Burmeister, 1878 (type locality Argentina: Buenos Aires) are designated. These designations establish Hermeuptychia canthe as a valid species widely distributed in South America from Colombia to Bolivia and Southeast Brazil, Euptychia celmis var. bonaërensis [sic] Burmeister, 1878 as a junior objective synonym of Yphthimoides acmenis, and S. cantheus as a junior subjective synonym of Hermeuptychia sosybius (Fabricius, 1793). Papilio camerta Cramer, 1780 is treated as nomen dubium requiring further studies to determine an identity that is consistent with the original description, as it may be conspecific with Paryphthimoides poltys (Prittwitz, 1865) instead of being a Hermeuptychia species as currently assumed.},
}
@article {pmid34805524,
year = {2021},
author = {Yu, J and Liu, J and Li, C and Wu, W and Feng, F and Wang, Q and Ying, X and Qi, D and Qi, G},
title = {Characterization of the complete mitochondrial genome of Otus lettia: exploring the mitochondrial evolution and phylogeny of owls (Strigiformes).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {6},
number = {12},
pages = {3443-3451},
pmid = {34805524},
issn = {2380-2359},
abstract = {Large-scale molecular phylogenetic studies of the avian order Strigiformes have been performed, and numerous mitochondrial genomes have been determined. However, their intergeneric relationships are still controversial, and few comprehensive comparative analyses of mitochondrial genomes have been conducted on Strigiformes. In this study, the mitochondrial genome of Otus lettia was determined and compared with other Strigiformes. The O. lettia mitochondrial genome was 16,951 bp in size. For Strigiformes, atp8 can be used as a suitable molecular marker for population genetic diversity, while cox1 is a candidate barcoding marker for species identification. All protein-coding genes may be under strong purifying selection pressure, and one extra cytosine insertion located in nad3 is common to all owls except Tyto longimembris, T. alba, and Athene noctua. Four different mitochondrial gene arrangement types were found among the Strigiformes mitogenomes, and their evolutionary relationship between each other can be perfectly explained by the tandem duplication and random loss model. The phylogenetic topologies using the mitochondrial genomes showed that target species O. lettia had a closer relationship with O. scops + O. sunia than O. bakkamoena, the genus Glaucidium was paraphyletic, and the Ninox clade was located at the basal position of Strigidae lineage. Our phylogenetic trees also supported the previous recommendations that Sceloglaux albifacies, Ciccaba nigrolineata, and Ketupa flavipes should be transferred to Ninox, Strix, and Bubo, respectively. These findings will be helpful in further unraveling the mitochondrial evolution and phylogeny of Strigiformes.},
}
@article {pmid34803949,
year = {2021},
author = {Koch, RA and Herr, JR},
title = {Global Distribution and Richness of Armillaria and Related Species Inferred From Public Databases and Amplicon Sequencing Datasets.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {733159},
pmid = {34803949},
issn = {1664-302X},
abstract = {Armillaria is a globally distributed fungal genus most notably composed of economically important plant pathogens that are found predominantly in forest and agronomic systems. The genus sensu lato has more recently received attention for its role in woody plant decomposition and in mycorrhizal symbiosis with specific plants. Previous phylogenetic analyses suggest that around 50 species are recognized globally. Despite this previous work, no studies have analyzed the global species richness and distribution of the genus using data derived from fungal community sequencing datasets or barcoding initiatives. To assess the global diversity and species richness of Armillaria, we mined publicly available sequencing datasets derived from numerous primer regions for the ribosomal operon, as well as ITS sequences deposited on Genbank, and clustered them akin to metabarcoding studies. Our estimates reveal that species richness ranges from 50 to 60 species, depending on whether the ITS1 or ITS2 marker is used. Eastern Asia represents the biogeographic region with the highest species richness. We also assess the overlap of species across geographic regions and propose some hypotheses regarding the drivers of variability in species diversity and richness between different biogeographic regions.},
}
@article {pmid34803722,
year = {2021},
author = {Jiang, L and Zhou, B and Wang, X and Bi, Y and Guo, W and Wang, J and Yao, R and Li, M},
title = {The Quality Monitoring of Cistanches Herba (Cistanche deserticola Ma): A Value Chain Perspective.},
journal = {Frontiers in pharmacology},
volume = {12},
number = {},
pages = {782962},
pmid = {34803722},
issn = {1663-9812},
abstract = {Cistanche deserticola Ma was used as a medicine food homology, which was mainly produced in the Alxa region of northwest China. In recent years, it has been widely used in various food items. The increasing demand for Cistanches Herba has led to problems such as overexploitation and quality deterioration. The quality and safety of herbal medicines are critical and have been shown to be affected by the value chain (VC). Using the VC framework, the study is embedded in a larger study aiming to investigate the effects of different VCs types on the quality and stakeholders of Cistanches Herba. In this study, 90 Cistanches Herba samples were collected during fieldwork. An additional 40 samples were obtained from the herbal markets and medicine purchasing stations. Semi-structured interviews and key informant interviews were performed to collect data on stakeholders in major production areas. These samples were analyzed using high performance liquid chromatography (HPLC) coupled with the k-means clustering method; a targeted quality assessment strategy based on chemical analysis was adopted to understand the quality of Cistanches Herba. Based on market research, the collected samples were divided into different grades through k-means clustering analysis. Moreover, quality differences of Cistanches Herba in Alxa region were explored through DNA barcoding and chemical analysis. Accordingly, 10 different types of VCs were determined in the production of Cistanches Herba. The results show that there is a close relationship between the quality of Cistanches Herba and stakeholder benefits. Vertical integration at different levels was found for independent farmer-based VCs, horizontal collaboration was found in the cooperative-based VCs. The vertical coordination has led to a more consistent traceability system and strict regulation of supply chains. At the same time, the Cistanches Herba were divided into three grades. Through DNA barcoding and chemical analysis, we found that the quality differences between Cistanches Herba in the Alxa area were not significant. It was found that geographical suitability and vertical integration could impact the quality and sustainable production of Cistanches Herba. At the same time, the well-developed VCs can provide products with reliable quality, and ensure adequate financial revenue for relevant stakeholders.},
}
@article {pmid34803462,
year = {2021},
author = {Xu, X and Peng, X and Li, D},
title = {Four new species of the jumping spider genus Portia (Araneae, Salticidae) from China.},
journal = {ZooKeys},
volume = {1068},
number = {},
pages = {27-40},
pmid = {34803462},
issn = {1313-2989},
abstract = {We diagnose and describe four new species of Portia Karsch, 1878 and describe for the first time the male of P.zhaoi Peng, Li &amp; Chen, 2003 from China based on morphological characters. The females of Portiabawang sp. nov. have the narrowest epigyne orifice. The males of Portiaerlangping sp. nov. have the shortest embolus among all the species. The females of Portiafajing sp. nov. can be distinguished from other species by the anterior orifice margin, which is nearly parallel to the posterior orifice margin. The males of Portiaxishan sp. nov. can be identified by the tegular furrow which extends to form a membrane and by the tegular apophysis which is obscured; the females of Portiaxishan sp. nov. can be diagnosed by the slit-like epigynal orifice. The males of P.zhaoi have the longest embolus among all the species, and females can be diagnosed by the circular epigyne orifice and the longest copulatory ducts. To facilitate future identification, we also provide the GenBank accession codes of the DNA barcode gene, Cytochrome c oxidase subunit I (COI), for all the type specimens.},
}
@article {pmid34802424,
year = {2021},
author = {Zhao, G and Wang, X and Liu, L and Dai, P and Kong, X},
title = {Noninvasive prenatal diagnosis of duchenne muscular dystrophy in five Chinese families based on relative mutation dosage approach.},
journal = {BMC medical genomics},
volume = {14},
number = {1},
pages = {275},
pmid = {34802424},
issn = {1755-8794},
mesh = {China ; Dystrophin/genetics ; Female ; Humans ; Male ; *Muscular Dystrophy, Duchenne/diagnosis/genetics ; Mutation ; *Noninvasive Prenatal Testing ; Pregnancy ; },
abstract = {BACKGROUND: Relative haplotype dosage (RHDO) approach has been applied in noninvasive prenatal diagnosis (NIPD) of Duchenne muscular dystrophy (DMD). However, the RHDO procedure is relatively complicated and the parental haplotypes need to be constructed. Furthermore, it is not suitable for the diagnosis of de novo mutations or mosaicism in germ cells. Here, we investigated NIPD of DMD using a relative mutation dosage (RMD)-based approach-cell-free DNA Barcode-Enabled Single-Molecule Test (cfBEST), which has not previously been applied in the diagnosis of exon deletion.<br><br>METHODS: Five DMD families caused by DMD gene point mutations or exon deletion were recruited for this study. After the breakpoints of exon deletion were precisely mapped with multiple PCR, the genotypes of the fetuses from the five DMD families were inferred using cfBEST, and were further validated by invasive prenatal diagnosis.<br><br>RESULTS: The cfBEST results of the five families indicated that one fetus was female and did not carry the familial molecular alteration, three fetuses were carriers and one was male without the familial mutation. The invasive prenatal diagnosis results were consistent with those of the cfBEST procedure.<br><br>CONCLUSION: This is the first report of NIPD of DMD using the RMD-based approach. We extended the application of cfBEST from point mutation to exon deletion mutation. The results showed that cfBEST would be suitable for NIPD of DMD caused by different kinds of mutation types.},
}
@article {pmid34801757,
year = {2021},
author = {Nemati, S and Falahati Anbaran, M and Mohammad Rahimi, H and Hosseini, MS and Aghaei, S and Khalili, N and Mirjalali, H and Zali, MR},
title = {Evolutionary and phylogenetic analyses of the barcoding region suggest geographical relationships among Blastocystis sp., ST3 in humans.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {96},
number = {},
pages = {105151},
doi = {10.1016/j.meegid.2021.105151},
pmid = {34801757},
issn = {1567-7257},
mesh = {Bayes Theorem ; Biological Evolution ; Blastocystis/*genetics ; DNA Barcoding, Taxonomic ; *Evolution, Molecular ; *Genes, Protozoan ; Geography ; *Haplotypes ; *Phylogeny ; },
abstract = {Blastocystis sp., has 21 distinct subtypes of which ST3 thought to be the most prevalent subtype. This study aims to analyze the global variations of ST3. In total, 496 sequences with more than 400 nucleotides from Asia, Europe, Africa, and America were included in this study. Results show that allele 34 was the most prevalent allele in all continents. The lowest and highest allele diversity were observed in Europe and Africa, respectively. The nucleotide diversity ranged from 0.0077 in Europe to 0.02 in Africa, and haplotype diversity ranged from 0.461 in America to 0.6 in Africa. The haplotype network and Bayesian structure showed at least two major clusters including Asia and Europe-Africa-America. Tajima's D values for all continents were negative and statistically significant, indicating an excess of rare nucleotide variants. Similarly, the Fu's FS test showed negative values for all regions, indicating an excess of rare haplotypes. Pairwise FST exhibited a high genetic differentiation between Asia and other continents. Mismatch analysis for all populations showed a unimodal distribution. Our findings indicate that there are two probable major clusters of Blastocystis sp. ST3, a cluster which is shared between Europe, Africa, and America, and a cluster which is restricted to Asia.},
}
@article {pmid34801080,
year = {2021},
author = {Gąsiorek, P and Vončina, K and Nelson, DR and Michalczyk, &#x141;},
title = {The importance of being integrative: a remarkable case of synonymy in the genus Viridiscus (Heterotardigrada: Echiniscidae).},
journal = {Zoological letters},
volume = {7},
number = {1},
pages = {13},
pmid = {34801080},
issn = {2056-306X},
support = {2019/33/N/NZ8/02777//narodowe centrum nauki/ ; 2016/22/E/NZ8/00417//narodowe centrum nauki/ ; 2020/36/T/NZ8/00360//narodowe centrum nauki/ ; START 28.2020//fundacja na rzecz nauki polskiej/ ; },
abstract = {There are two predominant sources of taxonomically useful morphological variability in the diverse tardigrade family Echiniscidae: the internal structure and surface sculpture of the cuticular plates covering the dorsum (sculpturing) and the arrangement and morphology of the trunk appendages (chaetotaxy). However, since the appendages often exhibit intraspecific variation (they can be reduced or can develop asymmetrically), sculpturing has been considered more stable at the species level and descriptions of new echiniscid species based solely on morphology are still being published. Here, we present a case study in which a detailed analysis of the morphology and multiple genetic markers of several species of the genus Viridiscus shows that cuticular sculpture may also exhibit considerable intraspecific variation and lead to false taxonomic conclusions. In a population collected from the eastern Nearctic, in the type locality of the recently described species V. miraviridis, individuals with transitional morphotypes between those reported for V. viridissimus and V. miraviridis were found. Importantly, all morphotypes within the viridissimus-miraviridis spectrum were grouped in a single monospecific clade according to rapidly evolving markers (ITS-1, ITS-2 and COI). Given the morphological and genetic evidence, we establish V. miraviridis as a junior synonym of V. viridissimus. This study explicitly demonstrates that a lack of DNA data associated with morphological descriptions of new taxa jeopardizes the efforts to unclutter tardigrade systematics. Additionally, V. perviridis and V. viridissimus are reported from Lâm Đồng Province in southern Vietnam, which considerably broadens their known geographic ranges.},
}
@article {pmid34797017,
year = {2022},
author = {Woolley, VC and Tembo, YL and Ndakidemi, B and Obanyi, JN and Arnold, SE and Belmain, SR and Ndakidemi, PA and Ogendo, JO and Stevenson, PC},
title = {The diversity of aphid parasitoids in East Africa and implications for biological control.},
journal = {Pest management science},
volume = {78},
number = {3},
pages = {1109-1116},
doi = {10.1002/ps.6723},
pmid = {34797017},
issn = {1526-4998},
support = {BB/R020361/1//NaPROCLA/ ; },
mesh = {Animals ; *Aphids/genetics ; Biological Control Agents ; Ecosystem ; Pest Control, Biological ; *Wasps ; },
abstract = {BACKGROUND: Hymenopteran parasitoids provide key natural pest regulation services and are reared commercially as biological control agents. Therefore, understanding parasitoid community composition in natural populations is important to enable better management for optimized natural pest regulation. We carried out a field study to understand the parasitoid community associated with Aphis fabae on East African smallholder farms. Either common bean (Phaseolus vulgaris) or lablab (Lablab purpureus) sentinel plants were infested with Aphis fabae and deployed in 96 fields across Kenya, Tanzania, and Malawi.<br><br>RESULTS: A total of 463 parasitoids emerged from sentinel plants of which 424 were identified by mitochondrial cytochrome oxidase I (COI) barcoding. Aphidius colemani was abundant in Kenya, Tanzania and Malawi, while Lysiphlebus testaceipes was only present in Malawi. The identity of Aphidius colemani specimens were confirmed by sequencing LWRh and 16S genes and was selected for further genetic and population analyses. A total of 12 Aphidius colemani haplotypes were identified. Of these, nine were from our East African specimens and three from the Barcode of Life Database (BOLD).<br><br>CONCLUSION: Aphidius colemani and Lysiphlebus testaceipes are potential targets for conservation biological control in tropical smallholder agro-ecosystems. We hypothesize that high genetic diversity in East African populations of Aphidius colemani suggests that this species originated in East Africa and has spread globally due to its use as a biological control agent. These East African populations could have potential for use as strains in commercial biological control or to improve existing Aphidius colemani strains by selective breeding.},
}
@article {pmid34792799,
year = {2022},
author = {Guimarães, KLA and Rosso, JJ and González-Castro, M and Souza, MFB and Díaz de Astarloa, JM and Rodrigues, LRR},
title = {A new species of Hoplias malabaricus species complex (Characiformes: Erythrinidae) from the Crepori River, Amazon basin, Brazil.},
journal = {Journal of fish biology},
volume = {100},
number = {2},
pages = {425-443},
doi = {10.1111/jfb.14953},
pmid = {34792799},
issn = {1095-8649},
mesh = {Animals ; Brazil ; *Characiformes/genetics ; Rivers ; Spine ; },
abstract = {A new species belonging to the Hoplias malabaricus complex from the Amazon basin, Brazil, is described. The new species is characterized by 15-16 predorsal scales, 37-39 lateral-line scales, 5 scales from dorsal fin to lateral line, 38-39 vertebrae, iii-iv, 7-8 anal-fin rays, ii-iv, 12-15 caudal-fin rays, last vertical series of scales on the base of caudal-fin rays forming a straight line, 6-7 dark bands in anal fin and no distinctive dark bands or blotches on flanks. The new species is also distinguished from other congeners of the H. malabaricus species-group by means of landmark-based morphometrics and DNA Barcoding (Cytochrome c Oxidase I gene). An identification key to species of the H. malabaricus species complex is provided.},
}
@article {pmid34792068,
year = {2021},
author = {Khajvand, T and Huang, P and Li, L and Zhang, M and Zhu, F and Xu, X and Huang, M and Yang, C and Lu, Y and Zhu, Z},
title = {Interfacing droplet microfluidics with antibody barcodes for multiplexed single-cell protein secretion profiling.},
journal = {Lab on a chip},
volume = {21},
number = {24},
pages = {4823-4830},
doi = {10.1039/d1lc00567g},
pmid = {34792068},
issn = {1473-0189},
mesh = {Antibodies ; Cell Line, Tumor ; Humans ; *Microfluidic Analytical Techniques ; *Microfluidics ; Secretome ; Single-Cell Analysis ; },
abstract = {Multiplexed protein secretion analysis of single cells is important to understand the heterogeneity of cellular functions and processes in healthy and disease states. However, current single-cell platforms, such as microwell-, microchamber-, or droplet-based assays, suffer from low single-cell occupancy, waste of reagents, limited sensitivity, or inability to perform necessary operations, etc. To overcome these drawbacks, we present an integrated droplet microfluidic device that interfaces with spatially patterned antibody barcodes for multiplexed single-cell secretome analysis. The trapping array of 100 picoliter-sized isolation chambers could achieve >80% single-cell capture efficiency with >90% viability. The single-cell analysis microchip was validated by the detection of four-plexed cytokines, including IL-8, MCP-1, MIP-1b, and TNF-a/IL-10, from unstimulated and lipopolysaccharide (LPS)-stimulated individual human macrophages. We also successfully applied the platform to profile protein secretions of human tumor cell lines and primary/metastatic cancer cells dissociated from cancer patients to observe the secretion heterogeneity among cells. This unique microfluidic platform enables multiplexed secretion assays for static droplet microfluidics, provides a reliable and straightforward workflow for protein secretion assays based on a low number of single cells in a short incubation time (∼4 h), and could have widespread applications for studying secretion-mediated cellular heterogeneity.},
}
@article {pmid34790868,
year = {2021},
author = {Bhaskar, R and Das, MK and Sharon, EA and Kumar, RR and R G, C},
title = {Genetic identification of marine eels (Anguilliformes: Congroidei) through DNA barcoding from Kasimedu fishing harbour.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {6},
number = {12},
pages = {3354-3361},
pmid = {34790868},
issn = {2380-2359},
abstract = {Along with the mysteries of their body's shape like snakes, marine eels have fascinated biologists for centuries. Information on the molecular taxonomy of marine eels is scarce from the Southeast Indian region and hence, the present study aimed to barcode marine eels collected from Kasimedu fishing harbor, Chennai, Tamil Nadu. A total of 44 specimens were collected and DNA barcoding was done with a COI marker. The evolutionary history was inferred using the BA method. We observed 17 species, 10 genera, 4 families from the suborder Congroidei of which the genus Ariosoma and Conger were found to be predominant. The species of the family Muraenesocidae and Congridae are highly variable. The average Kimura two-parameter (K2P) distances within species, genera, and families were 3.08%, 6.80%, 13.80%, respectively. Maximum genetic distance (0.307) was observed between the species Muraenesox cinereus and Ariosoma sp.1. BA tree topology revealed distinct clusters in concurrence with the taxonomic status of the species. A deeper split was observed in Uroconger lepturus. We sequenced for the first-time barcode of Sauromuraenesox vorax and a new species Ophichthus chennaiensis is the gap-filling in identifying this taxon in the Indian context. We found a correct match between morphological and genetic identification of the species analyzed, depending on the cluster analysis performed (BINs and ASAP). This demonstrates that the COI gene sequence is suitable for phylogenetic analysis and species identification.},
}
@article {pmid34782652,
year = {2021},
author = {Xie, C and An, W and Liu, S and Huang, Y and Yang, Z and Lin, J and Zheng, X},
title = {Comparative genomic study on the complete plastomes of four officinal Ardisia species in China.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {22239},
pmid = {34782652},
issn = {2045-2322},
support = {81903741//National Natural Science Foundation of China/ ; },
mesh = {Ardisia/*classification/*genetics ; China ; Computational Biology/methods ; *Genome, Chloroplast ; *Genomics/methods ; Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Exome Sequencing ; },
abstract = {Ardisia Sw. (Primulaceae) is naturally distributed in tropical and subtropical areas. Most of them possess edible and medicinal values and are popular in clinical and daily use in China. However, ambiguous species delineation and genetic information limit the development and utilization of this genus. In this study, the chloroplast genomes of four Ardisia species, namely A. gigantifolia Stapf, A. crenata Sims, A. villosa Roxb. and A. mamillata Hance, were sequenced, annotated, and analyzed comparatively. All the four chloroplast genomes possess a typical quadripartite structure, and each of the genomes is about 156 Kb in size. The structure and gene content of the Ardisia plastomes were conservative and showed low sequence divergence. Furthermore, we identified five mutation hotspots as candidate DNA barcodes for Ardisia, namely, trnT-psbD, ndhF-rpl32, rpl32-ccsA, ccsA-ndhD and ycf1. Phylogenetic analysis based on the whole-chloroplast genomes data showed that Ardisia was sister to Tapeinosperma Hook. f. In addition, the results revealed a great topological profile of Ardisia's with strong support values, which matches their geographical distribution patterns. Summarily, our results provide useful information for investigations on taxonomic differences, molecular identification, and phylogenetic relationships of Ardisia plants.},
}
@article {pmid34774617,
year = {2022},
author = {Ahmad, A and Lee, JR and Metz, JM and Tang, X and Lin, SC and Bagarozzi, DA and Petway, D and Herzegh, O},
title = {Development and Evaluation of a TaqMan Real-Time PCR Assay for the Rapid Detection of Cross-Contamination of RD (Human) and L20B (Mouse) Cell Lines Used in Poliovirus Surveillance.},
journal = {Journal of virological methods},
volume = {300},
number = {},
pages = {114354},
pmid = {34774617},
issn = {1879-0984},
support = {CC999999/ImCDC/Intramural CDC HHS/United States ; },
mesh = {Animals ; Cell Line ; Haplorhini/genetics ; Humans ; Mice ; Nucleic Acid Amplification Techniques ; *Poliovirus/genetics ; Rats ; Real-Time Polymerase Chain Reaction ; Sensitivity and Specificity ; },
abstract = {BACKGROUND: The cross-contamination of cell lines in culture is a persistent problem. Genetically modified L20B (Mouse) and RD (Human Rhabdomyosarcoma) cell lines are commonly used in poliovirus research, surveillance, and diagnostics. Cross-contamination between these cell lines leads to unreproducible results and unreliable surveillance data, negatively affecting public health. The gold standard method for cell authentication is Short Tandem Repeats analysis, which is time-consuming and expensive. The disadvantage of STR is limited detection of interspecies contamination.<br><br>METHODS: This assay targets the mitochondrial cytochrome c oxidase subunit I (MTCO1) gene, a highly conserved and emergent DNA barcode region for detection of cross-contamination in RD and L20B cell lines. The MagNA Pure Compact instrument and ABI 7500 Fast Dx Real-time PCR systems were used for DNA extraction and to perform real-time PCR respectively.<br><br>RESULTS: The newly developed assay is very sensitive with a limit of detection of 100 RD cells/1 million L20B/mL. The amplification efficiency and R[2]-value were 102.26% and 0.9969 respectively. We evaluated specificity of the assay with five human and four mouse cell lines, as well as monkey and rat cell lines. The assay showed no cross-reactivity with genomic DNA from human, mouse, rat, or monkey cell lines. The analytical sensitivity was also evaluated by spiking varying amounts of RD cells (0.001% - 10%) into L20B cells. There was no difference in CT values when running single-plex or duplex PCR reactions with similar experimental conditions.<br><br>CONCLUSIONS: We have developed and validated a TaqMan real-time PCR assay, a sensitive method for the detection of cross-contamination of RD and L20B cell lines.},
}
@article {pmid34772985,
year = {2021},
author = {Macher, JN and Wideman, JG and Girard, EB and Langerak, A and Duijm, E and Jompa, J and Sadekov, A and Vos, R and Wissels, R and Renema, W},
title = {First report of mitochondrial COI in foraminifera and implications for DNA barcoding.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {22165},
pmid = {34772985},
issn = {2045-2322},
support = {DBI-2119963//National Science Foundation/ ; },
mesh = {Computational Biology/methods ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Foraminifera/*classification/*genetics ; Gene Library ; *Genes, Mitochondrial ; Genes, rRNA ; High-Throughput Nucleotide Sequencing ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; },
abstract = {Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in many marine environments and play a major role in global carbon cycling. Species recognition in Foraminifera is mainly based on morphological characters and nuclear 18S ribosomal RNA barcoding. The 18S rRNA contains variable sequence regions that allow for the identification of most foraminiferal species. Still, some species show limited variability, while others contain high levels of intragenomic polymorphisms, thereby complicating species identification. The use of additional, easily obtainable molecular markers other than 18S rRNA will enable more detailed investigation of evolutionary history, population genetics and speciation in Foraminifera. Here we present the first mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences ("barcodes") of Foraminifera. We applied shotgun sequencing to single foraminiferal specimens, assembled COI, and developed primers that allow amplification of COI in a wide range of foraminiferal species. We obtained COI sequences of 49 specimens from 17 species from the orders Rotaliida and Miliolida. Phylogenetic analysis showed that the COI tree is largely congruent with previously published 18S rRNA phylogenies. Furthermore, species delimitation with ASAP and ABGD algorithms showed that foraminiferal species can be identified based on COI barcodes.},
}
@article {pmid34772448,
year = {2021},
author = {Hohmeister, N and Werner, D and Kampen, H},
title = {The invasive Korean bush mosquito Aedes koreicus (Diptera: Culicidae) in Germany as of 2020.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {575},
pmid = {34772448},
issn = {1756-3305},
mesh = {Aedes/classification/genetics/growth &amp; development/*physiology ; Animal Distribution ; Animals ; Female ; Germany ; Introduced Species/*statistics &amp; numerical data ; Male ; Mosquito Vectors/classification/genetics/growth &amp; development/physiology ; Phylogeny ; Republic of Korea ; },
abstract = {BACKGROUND: The Korean bush mosquito Aedes koreicus was recently reported to have established a population in western Germany (Wiesbaden) in 2016. The species is difficult to distinguish morphologically from its close relative, the invasive Japanese bush mosquito Ae. japonicus, which is already widely distributed in many parts of Germany, including the area colonised by Ae. koreicus. Genetic confirmation of morphologically identified "Ae. japonicus" collection material, however, had only been done exceptionally before the German Ae. koreicus population became known.<br><br>METHODS: Dried archived "Ae. japonicus" specimens both from the municipality of Wiesbaden and from deliberately and randomly selected distribution sites all over Germany were re-examined morphologically and genetically for admixture by Ae. koreicus. Moreover, cemeteries in the greater Wiesbaden area were sampled in 2019 and 2020 to check for Ae. koreicus spread. Korean and Japanese bush mosquitoes submitted to the German citizen science mosquito monitoring scheme "Mueckenatlas" in 2019 and 2020 were also subjected to particularly thorough species identification. The ND4 DNA sequences generated in this study in the context of species identification were phylogenetically compared to respective GenBank entries of Ae. koreicus. As a by-product, several genetic markers were evaluated for their suitability to identify Ae. koreicus.<br><br>RESULTS: Aedes koreicus specimens could be identified in mosquito collection material and submissions from Wiesbaden from 2015 onwards, suggesting establishment to have happened in the same year as Ae. japonicus establishment. Detections of Ae. koreicus from 2019 and 2020 in Wiesbaden indicate a negligible enlargement of the populated area as described for 2018. Two Ae. koreicus specimens were also submitted from the city of Munich, southern Germany, in 2019 but further specimens could not be identified during immediate local inspections. Comparison of ND4 sequences generated in this and other studies demonstrate a high degree of homology, suggesting that this DNA region is not informative enough for clarification of origins and relationships of Ae. koreicus populations. For genetic identification of Ae. koreicus, PCR primers used for classical CO1 barcoding were found to lead to mismatches and produce no or incorrect amplicons. Alternative CO1 primers or a validated ND4 marker should be used instead.<br><br>CONCLUSIONS: Aedes koreicus is probably introduced into Germany every now and then but rarely succeeds in becoming established. As with most European populations, the German population is characterised by a limited expansion tendency. Since Ae. koreicus is a potential vector, however, Asian bush mosquitoes found at new places should be examined quite carefully and known distribution areas of Ae. japonicus regularly checked for the presence of Ae. koreicus.},
}
@article {pmid34766275,
year = {2022},
author = {Wong, M and Kosman, C and Takahashi, L and Ramalingam, N},
title = {Simultaneous Quantification of Single-Cell Proteomes and Transcriptomes in Integrated Fluidic Circuits.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2386},
number = {},
pages = {219-261},
pmid = {34766275},
issn = {1940-6029},
mesh = {Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; *Proteome/genetics ; RNA ; Sequence Analysis, RNA ; Single-Cell Analysis ; *Transcriptome ; },
abstract = {Understanding the principles of gene regulation at single-cell resolution would require measurement and integration of multiple methods such as DNA mutation profiling, open chromatin profiling, RNA expression, protein quantification, and DNA methylation. Recent developments in single-cell multi-omic technologies have enabled integration of these modes in various combinations.With the advent of RNA expression and protein sequencing assay (REAP-seq), researchers can simultaneously analyze protein and gene expression within the same cell. In REAP-seq , cells are labeled with antibodies conjugated to unique DNA sequences. A barcode of 8 nucleotides can allow up to 65,536 unique barcodes for multiplex analysis of proteins, circumventing the limitations of fluorescence (~17 targets). Here, we describe the implementation of REAP-seq assay in the Fluidigm[®] C1™ mRNA Seq HT (high-throughput) v2 system.},
}
@article {pmid34766267,
year = {2022},
author = {Kim, SC and Haliburton, JR and Gartner, ZJ and Abate, AR},
title = {Single-Cell Protein Profiling by Microdroplet Barcoding and Next-Generation Sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2386},
number = {},
pages = {101-111},
pmid = {34766267},
issn = {1940-6029},
support = {DP2 AR068129/AR/NIAMS NIH HHS/United States ; R01 EB019453/EB/NIBIB NIH HHS/United States ; R21 HG007233/HG/NHGRI NIH HHS/United States ; },
mesh = {DNA ; DNA Barcoding, Taxonomic ; *High-Throughput Nucleotide Sequencing ; Microfluidics ; Proteins/genetics ; *Single-Cell Analysis ; },
abstract = {DNA barcoding of individual cells combined with next-generation sequencing enables high-throughput parallel analysis of biomolecules at the single-cell level. Encoding protein identity with DNA barcoding of specific antibody binders achieves sequencing-based protein quantitation by converting protein signals into DNA signals. Here, we describe how to prepare DNA-barcoded antibodies and connect protein identities to cellular identities using droplet microfluidics. This approach allows for multiplex single-cell protein analysis compatible with single-cell transcriptomic and mutational profiling methods.},
}
@article {pmid34765126,
year = {2021},
author = {Soto, D and De Palmas, S and Ho, MJ and Denis, V and Allen Chen, C},
title = {A molecular census of early-life stage scleractinian corals in shallow and mesophotic zones.},
journal = {Ecology and evolution},
volume = {11},
number = {21},
pages = {14573-14584},
pmid = {34765126},
issn = {2045-7758},
abstract = {The decline of coral reefs has fueled interest in determining whether mesophotic reefs can shield against disturbances and help replenish deteriorated shallower reefs. In this study, we characterized spatial (horizontal and vertical) and seasonal patterns of diversity in coral recruits from Dabaisha and Guiwan reefs at Ludao, Taiwan. Concrete blocks supporting terra-cotta tiles were placed at shallow (15m) and mesophotic (40m) depths, during 2016-2018. Half of the tiles were retrieved and replaced biannually over three 6-month surveys (short-term); the remainder retrieved at the end of the 18-month (long-term) survey. 451 recruits were located using fluorescent censusing and identified by DNA barcoding. Barcoding the mitochondrial cytochrome oxidase I (COI) gene resulted in 17 molecular operational taxonomic units (MOTUs). To obtain taxonomic resolution to the generic level, Pocillopora were phylotyped using the mitochondrial open reading frame (ORF), resolving eight MOTUs. Acropora, Isopora, and Montipora recruits were identified by the nuclear PaxC intron, yielding ten MOTUs. Overall, 35 MOTUs were generated and were comprised primarily of Pocillopora and, in fewer numbers, Acropora, Isopora, Pavona, Montipora, Stylophora, among others. 40% of MOTUs recruited solely within mesophotic reefs while 20% were shared by both depth zones. MOTUs recruiting across a broad depth distribution appear consistent with the hypothesis of mesophotic reefs acting as a refuge for shallow-water coral reefs. In contrast, Acropora and Isopora MOTUs were structured across depth zones representing an exception to this hypothesis. This research provides an imperative assessment of coral recruitment in understudied mesophotic reefs and imparts insight into the refuge hypothesis.},
}
@article {pmid34765121,
year = {2021},
author = {Gupta, M and Kaur, R and Gupta, A and Raychoudhury, R},
title = {Are ecological communities the seat of endosymbiont horizontal transfer and diversification? A case study with soil arthropod community.},
journal = {Ecology and evolution},
volume = {11},
number = {21},
pages = {14490-14508},
pmid = {34765121},
issn = {2045-7758},
abstract = {Maternally inherited endosymbionts of arthropods are one of the most abundant and diverse group of bacteria. These bacterial endosymbionts also show extensive horizontal transfer to taxonomically unrelated hosts and widespread recombination in their genomes. Such horizontal transfers can be enhanced when different arthropod hosts come in contact like in an ecological community. Higher rates of horizontal transfer can also increase the probability of recombination between endosymbionts, as they now share the same host cytoplasm. However, reports of community-wide endosymbiont data are rare as most studies choose few host taxa and specific ecological interactions among the hosts. To better understand endosymbiont spread within host populations, we investigated the incidence, diversity, extent of horizontal transfer, and recombination of three endosymbionts (Wolbachia, Cardinium, and Arsenophonus) in a specific soil arthropod community. Wolbachia strains were characterized with MLST genes whereas 16S rRNA gene was used for Cardinium and Arsenophonus. Among 3,509 individual host arthropods, belonging to 390 morphospecies, 12.05% were infected with Wolbachia, 2.82% with Cardinium and 2.05% with Arsenophonus. Phylogenetic incongruence between host and endosymbiont indicated extensive horizontal transfer of endosymbionts within this community. Three cases of recombination between Wolbachia supergroups and eight incidences of within-supergroup recombination were also found. Statistical tests of similarity indicated supergroup A Wolbachia and Cardinium show a pattern consistent with extensive horizontal transfer within the community but not for supergroup B Wolbachia and Arsenophonus. We highlight the importance of extensive community-wide studies for a better understanding of the spread of endosymbionts across global arthropod communities.},
}
@article {pmid34764253,
year = {2021},
author = {Contreras-Trujillo, H and Eerdeng, J and Akre, S and Jiang, D and Contreras, J and Gala, B and Vergel-Rodriguez, MC and Lee, Y and Jorapur, A and Andreasian, A and Harton, L and Bramlett, CS and Nogalska, A and Xiao, G and Lee, JW and Chan, LN and Müschen, M and Merchant, AA and Lu, R},
title = {Deciphering intratumoral heterogeneity using integrated clonal tracking and single-cell transcriptome analyses.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {6522},
pmid = {34764253},
issn = {2041-1723},
support = {R00 HL113104/HL/NHLBI NIH HHS/United States ; R35 HL150826/HL/NHLBI NIH HHS/United States ; P30 CA014089/CA/NCI NIH HHS/United States ; R01 HL138414/HL/NHLBI NIH HHS/United States ; R35 CA197628/CA/NCI NIH HHS/United States ; P01 CA233412/CA/NCI NIH HHS/United States ; R01 CA213138/CA/NCI NIH HHS/United States ; R01 CA157644/CA/NCI NIH HHS/United States ; F31 CA206463/CA/NCI NIH HHS/United States ; R01 HL138225/HL/NHLBI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 HL135292/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Cell Adhesion/genetics/physiology ; Cells, Cultured ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; DNA Barcoding, Taxonomic ; Humans ; Mice ; Sequence Analysis, RNA ; Single-Cell Analysis/*methods ; Transcriptome/*genetics ; },
abstract = {Cellular heterogeneity is a major cause of treatment resistance in cancer. Despite recent advances in single-cell genomic and transcriptomic sequencing, it remains difficult to relate measured molecular profiles to the cellular activities underlying cancer. Here, we present an integrated experimental system that connects single cell gene expression to heterogeneous cancer cell growth, metastasis, and treatment response. Our system integrates single cell transcriptome profiling with DNA barcode based clonal tracking in patient-derived xenograft models. We show that leukemia cells exhibiting unique gene expression respond to different chemotherapies in distinct but consistent manners across multiple mice. In addition, we uncover a form of leukemia expansion that is spatially confined to the bone marrow of single anatomical sites and driven by cells with distinct gene expression. Our integrated experimental system can interrogate the molecular and cellular basis of the intratumoral heterogeneity underlying disease progression and treatment resistance.},
}
@article {pmid34760373,
year = {2021},
author = {Jażdżewska, AM and Tandberg, AHS and Horton, T and Brix, S},
title = {Global gap-analysis of amphipod barcode library.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e12352},
pmid = {34760373},
issn = {2167-8359},
abstract = {In the age of global climate change and biodiversity loss there is an urgent need to provide effective and robust tools for diversity monitoring. One of the promising techniques for species identification is the use of DNA barcoding, that in Metazoa utilizes the so called 'gold-standard' gene of cytochrome c oxidase (COI). However, the success of this method relies on the existence of trustworthy barcode libraries of the species. The Barcode of Life Data System (BOLD) aims to provide barcodes for all existing organisms, and is complemented by the Barcode Index Number (BIN) system serving as a tool for potential species recognition. Here we provide an analysis of all public COI sequences available in BOLD of the diverse and ubiquitous crustacean order Amphipoda, to identify the barcode library gaps and provide recommendations for future barcoding studies. Our gap analysis of 25,702 records has shown that although 3,835 BINs (indicating putative species) were recognised by BOLD, only 10% of known amphipod species are represented by barcodes. We have identified almost equal contribution of both records (sequences) and BINs associated with freshwater and with marine realms. Three quarters of records have a complete species-level identification provided, while BINs have just 50%. Large disproportions between identification levels of BINs coming from freshwaters and the marine environment were observed, with three quarters of the former possessing a species name, and less than 40% for the latter. Moreover, the majority of BINs are represented by a very low number of sequences rendering them unreliable according to the quality control system. The geographical coverage is poor with vast areas of Africa, South America and the open ocean acting as "white gaps". Several, of the most species rich and highly abundant families of Amphipoda (e.g., Phoxocephalidae, Ampeliscidae, Caprellidae), have very poor representation in the BOLD barcode library. As a result of our study we recommend stronger effort in identification of already recognised BINs, prioritising the studies of families that are known to be important and abundant components of particular communities, and targeted sampling programs for taxa coming from geographical regions with the least knowledge.},
}
@article {pmid34760329,
year = {2021},
author = {L'Imperio, V and Gibilisco, F and Fraggetta, F},
title = {What is Essential is (No More) Invisible to the Eyes: The Introduction of BlocDoc in the Digital Pathology Workflow.},
journal = {Journal of pathology informatics},
volume = {12},
number = {},
pages = {32},
pmid = {34760329},
issn = {2229-5089},
abstract = {BACKGROUND: The implementation of a fully digital workflow in any anatomic pathology department requires a complete conversion to a tracked system. Ensuring the strict correspondence of the material submitted for the analysis, from the accessioning to the reporting phase, is mandatory in the anatomic pathology laboratory, especially when implementing the digital pathology for primary histological diagnosis. The proposed solutions, up to now, rely on the verification that all the materials present in the glass slide are also present in the whole slide images (WSIs). Although different methods have already been implemented for this purpose (e.g., the "macroimage" of the digital slide, representing the overview of the glass slide), the recent introduction of a device to capture the cut surface of paraffin blocks put the quality control of the digital workflow a step forward, allowing to match the digitized slide with the corresponding block. This system may represent a reliable, easy-to-use alternative to further reduce tissue inconsistencies between material sent to the lab and the final glass slides or WSIs.<br><br>METHODS: The Anatomic Pathology of the Gravina Hospital in Caltagirone, Sicily, Italy, has implemented the application of the BlocDoc devices (SPOT Imaging, Sterling Heights, USA) in its digital workflow. The instruments were positioned next to every microtome/sectioning station, with the possibility to capture the "normal" and the polarized image of the cut surface of the blocks directly by the technician. The presence of a monitor in the BlocDoc device allowed the technician to check the concordance between the cut surface of the block and the material on the corresponding slide. The link between BlocDoc and the laboratory information system, through the presence of the 2D barcode, allowed the pathologists to access the captured image of the cut surface of the block at the pathologist workstation, thus enabling the direct comparison between this image and the WSI (thumbnail and "macroimage").<br><br>RESULTS: During the implementation period, more than 10.000 (11.248) blocks were routinely captured using the BlocDoc. The employment of this approach allowed a drastic reduction of the discordances and tissue inconsistencies. The implementation of the BlocDoc in the routine allowed the detection of two different types of "errors," the so-called "systematic" and "occasional" ones. The first type was intrinsic of some specific specimens (e.g., transurethral resection of the prostate, nasal polypectomies, and piecemeal uterine myomectomies) characterized by the three-dimensional nature of the fragments and affected almost 100% of these samples. On the other hand, the "occasional" errors, mainly due to inexperience or extreme caution of the technicians in handling tiny specimens, affected 98 blocks (0.9%) of these samples and progressively reduced with the rising confidence with the BlocDoc. One of these cases was clinically relevant. No problems in the recognition of the 2D barcodes were encountered using a laser cassette printer. Finally, rare failures have been recorded during the period, accounting for <0.1% of all the cases, mainly due to network connection issues.<br><br>CONCLUSIONS: The implementation of BlocDoc can further improve the effectiveness of the digital workflow, demonstrating its safety and robustness as a valid alternative to the traditional, nontracked analogic workflow.},
}
@article {pmid34758388,
year = {2022},
author = {Jaimes-Dueñez, J and Leal-Rueda, DA and Jaimes-Dueñez, JD and Cáceres-Rivera, DI and Castillo-Castañeda, A and Ramírez, JD},
title = {Human urogenital myiasis caused by the 'rat-tailed' larvae of Palpada scutellaris (Fabricius, 1805) in Santander, eastern Colombia: A case report.},
journal = {Parasitology international},
volume = {87},
number = {},
pages = {102496},
doi = {10.1016/j.parint.2021.102496},
pmid = {34758388},
issn = {1873-0329},
mesh = {Abdominal Pain ; Animals ; Child ; Colombia ; DNA Barcoding, Taxonomic ; *Diptera/classification/genetics ; Female ; Humans ; Larva ; Myiasis/diagnosis/*parasitology ; Oliguria/parasitology ; Rural Population ; Urogenital Diseases/diagnosis/*parasitology ; },
abstract = {The Palpada genus, which belongs to the Diptera order (family, Syrphidae), has been rarely reported to cause accidental myiasis in humans. Herein, we report the first case of genitourinary myiasis caused by a larva of the Palpada genus in a 9-year-old girl from Colombia. The girl, who resided in a rural area in the municipality of Floridablanca, Santander, near Bucaramanga city, in eastern Colombia, presented with lower abdominal pain accompanied by oliguria, followed by the subsequent elimination of a larva through the urine. The next day, the patient visited a primary healthcare centre, and no signs or symptoms were observed on clinical examination. Haematological analysis showed high plateletcrit levels and platelet large cell counts. The results of the urine test revealed a decrease in specific gravity and a slight increase in bacterial content and mucus. DNA barcoding analyses showed that the etiological agent corresponded to a third instar larva of the Palpada scutellaris species. This is the first case to report genitourinary myiasis caused by larvae of the genus Palpada in humans. However, we believe that additional cases might be accurately detected if adequate tests are performed to confirm the clinical and molecular features associated with this infection.},
}
@article {pmid34758183,
year = {2022},
author = {Cai, B and Krusemark, CJ},
title = {Multiplexed Small-Molecule-Ligand Binding Assays by Affinity Labeling and DNA Sequence Analysis.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {61},
number = {3},
pages = {e202113515},
pmid = {34758183},
issn = {1521-3773},
support = {P30 CA023168/CA/NCI NIH HHS/United States ; R35 GM128894/GM/NIGMS NIH HHS/United States ; 1R35GM128894-01/GM/NIGMS NIH HHS/United States ; },
mesh = {Affinity Labels/*chemistry ; DNA/chemistry/metabolism ; Fluorescent Dyes/chemistry ; High-Throughput Screening Assays/methods ; Ligands ; Protein Binding ; Proteins/chemistry/metabolism ; Sequence Analysis, DNA/*methods ; Small Molecule Libraries/*chemistry/metabolism ; },
abstract = {Small-molecule binding assays to target proteins are a core component of drug discovery and development. While a number of assay formats are available, significant drawbacks still remain in cost, sensitivity, and throughput. To improve assays by capitalizing on the power of DNA sequence analysis, we have developed an assay method that combines DNA encoding with split-and-pool sample handling. The approach involves affinity labeling of DNA-linked ligands to a protein target. Critically, the labeling event assesses ligand binding and enables subsequent pooling of several samples. Application of a purifying selection on the pool for protein-labeled DNAs allows detection of ligand binding by quantification of DNA barcodes. We demonstrate the approach in both ligand displacement and direct binding formats and demonstrate its utility in determination of relative ligand affinity, profiling ligand specificity, and high-throughput small-molecule screening.},
}
@article {pmid34755261,
year = {2021},
author = {Quaresma, A and Brodschneider, R and Gratzer, K and Gray, A and Keller, A and Kilpinen, O and Rufino, J and van der Steen, J and Vejsnæs, F and Pinto, MA},
title = {Preservation methods of honey bee-collected pollen are not a source of bias in ITS2 metabarcoding.},
journal = {Environmental monitoring and assessment},
volume = {193},
number = {12},
pages = {785},
pmid = {34755261},
issn = {1573-2959},
support = {SANTE/E4/SI2.788418-SI2.788452-INSIGINIA-PP-1-1-2018//directorate-general for health and food safety/ ; },
mesh = {Animals ; Bees ; Bias ; *DNA Barcoding, Taxonomic ; Environmental Monitoring ; *Honey ; Pollen ; },
abstract = {Pollen metabarcoding is emerging as a powerful tool for ecological research and offers unprecedented scale in citizen science projects for environmental monitoring via honey bees. Biases in metabarcoding can be introduced at any stage of sample processing and preservation is at the forefront of the pipeline. While in metabarcoding studies pollen has been preserved at - 20 °C (FRZ), this is not the best method for citizen scientists. Herein, we compared this method with ethanol (EtOH), silica gel (SG) and room temperature (RT) for preservation of pollen collected from hives in Austria and Denmark. After ~ 4 months of storage, DNAs were extracted with a food kit, and their quality and concentration measured. Most DNA extracts exhibited 260/280 absorbance ratios close to the optimal 1.8, with RT samples from Austria performing slightly worse than FRZ and SG samples (P < 0.027). Statistical differences were also detected for DNA concentration, with EtOH samples producing lower yields than RT and FRZ samples in both countries and SG in Austria (P < 0.042). Yet, qualitative and quantitative assessments of floral composition obtained using high-throughput sequencing with the ITS2 barcode gave non-significant effects of preservation methods on richness, relative abundance and Shannon diversity, in both countries. While freezing and ethanol are commonly employed for archiving tissue for molecular applications, desiccation is cheaper and easier to use regarding both storage and transportation. Since SG is less dependent on ambient humidity and less prone to contamination than RT, we recommend SG for preserving pollen for metabarcoding. SG is straightforward for laymen to use and hence robust for widespread application in citizen science studies.},
}
@article {pmid34754263,
year = {2021},
author = {Narakusumo, RP and Riedel, A},
title = {Twenty-eight new species of Trigonopterus Fauvel (Coleoptera, Curculionidae) from Central Sulawesi.},
journal = {ZooKeys},
volume = {1065},
number = {},
pages = {29-79},
pmid = {34754263},
issn = {1313-2989},
abstract = {Here we present 28 new species of Trigonopterus from Central Sulawesi, mostly from Mt Dako and Mt Pompangeo: Trigonopterusacutus sp. nov., T.ancora sp. nov., T.arcanus sp. nov., T.corona sp. nov., T.dakoensis sp. nov., T.daun sp. nov., T.ewok sp. nov., T.gundala sp. nov., T.hoppla sp. nov., T.kakimerah sp. nov., T.katopasensis sp. nov., T.matakensis sp. nov., T.moduai sp. nov., T.mons sp. nov., T.paramoduai sp. nov. T.pomberimbensis sp. nov., T.pompangeensis sp. nov., T.puspoi sp. nov., T.rosichoni sp. nov., T.rubidus sp. nov., T.sarinoi sp. nov., T.sutrisnoi sp. nov., T.tanah sp. nov., T.tejokusumoi sp. nov., T.toboliensis sp. nov., T.tolitoliensis sp. nov., T.tounaensis sp. nov., T.unyil sp. nov. This fills important areas of distribution and brings the number of Trigonopterus species recorded from Sulawesi to 132.},
}
@article {pmid34754261,
year = {2021},
author = {Song, C and Zhu, B and Liu, W and Qi, X},
title = {On the genus Polypedilum, subgenus Collartomyia, with description of P. (Col.) baishanzuensis sp. nov. from Baishanzu Nature Reserve, China (Diptera, Chironomidae).},
journal = {ZooKeys},
volume = {1065},
number = {},
pages = {1-12},
pmid = {34754261},
issn = {1313-2989},
abstract = {A new species of the genus Polypedilum Kieffer, 1912 is described from Baishanzu Nature Reserve, China, based on molecular and morphological data. Molecular phylogenetic analysis based on standard barcode sequences confirmed a new clade of Polypedilum (Collartomyia) species. The new species is easily distinguished from its congeners by a combination of the following morphological characters: membrane of wing with a large spot occupying 70% of the proximal area; tergite without dark brown band pigmentation; tarsi I-V dark brown; superior volsella with three outer lateral setae and six long setae along inner base; inferior volsella with setose tubercules. An updated key to adult males of the subgenus Collartomyia is also provided.},
}
@article {pmid34752673,
year = {2022},
author = {Hu, JL and Ci, XQ and Liu, ZF and Dormontt, EE and Conran, JG and Lowe, AJ and Li, J},
title = {Assessing candidate DNA barcodes for Chinese and internationally traded timber species.},
journal = {Molecular ecology resources},
volume = {22},
number = {4},
pages = {1478-1492},
doi = {10.1111/1755-0998.13546},
pmid = {34752673},
issn = {1755-0998},
support = {ZSSD-013//Biodiversity Conservation Program of Chinese Academy of Sciences/ ; 2017FY100100//Science and Technology Basic Resources Investigation Program of China: Survey and Germplasm Conservation of Plant Species with Extremely Small Populations in South-west China/ ; 2017XTBG-T03//135 Programme of the Chinese Academy of Sciences/ ; 31770569//National Natural Science Foundation of China/ ; },
mesh = {China ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Forests ; Humans ; Sequence Analysis, DNA ; Species Specificity ; *Trees/genetics ; },
abstract = {Accurate identification of species from timber is an essential step to help control illegal logging and forest loss. However, current approaches to timber identification based on morphological and anatomical characteristics have limited species resolution. DNA barcoding is a proven tool for plant species identification, but there is a need to build reliable reference data across broad taxonomic and spatial scales. Here, we construct a species barcoding library consisting of 1550 taxonomically diverse timber species from 656 genera and 124 families, representing a comprehensive genetic reference data set for Chinese timber species and international commercial traded timber species, using four barcodes (rbcL, matK, trnH-psbA, and ITS2). The ITS2 fragment was found to be the most efficient locus for Chinese timber species identification among the four barcodes tested, both at the species and genus level, despite its low recovery rate. Nevertheless, the barcode combination matK+trnH-psbA+ITS2 was required as a complementary barcode to distinguish closely related species in complex data sets involving internationally traded timber species. Comparative analyses of family-level discrimination and species/genus ratios indicated that the inclusion of closely related species is an important factor affecting the resolution ability of barcodes for timber species verification. Our study indicates that although nuclear ITS2 is the most efficient single barcode for timber species authentication in China, complementary combinations like matK+trnH-psbA+ITS2 are required to provide broader discrimination power. These newly-generated sequences enrich the existing publicly available databases, especially for tropical and subtropical evergreen timber trees and this current timber species barcode reference library can serve as an important genetic resource for forestry monitoring, illegal logging prosecution and biodiversity projects.},
}
@article {pmid34748543,
year = {2021},
author = {Naufal, F and Brady, CJ and Wolle, MA and Saheb Kashaf, M and Mkocha, H and Bradley, C and Kabona, G and Ngondi, J and Massof, RW and West, SK},
title = {Evaluation of photography using head-mounted display technology (ICAPS) for district Trachoma surveys.},
journal = {PLoS neglected tropical diseases},
volume = {15},
number = {11},
pages = {e0009928},
pmid = {34748543},
issn = {1935-2735},
support = {P20 GM103644/GM/NIGMS NIH HHS/United States ; },
mesh = {Child ; Child, Preschool ; Diagnostic Techniques and Procedures/instrumentation ; Female ; Humans ; Infant ; Male ; Photography/instrumentation/*methods ; Prevalence ; Rural Population/statistics &amp; numerical data ; Surveys and Questionnaires ; Tanzania/epidemiology ; Trachoma/*diagnosis/epidemiology ; },
abstract = {BACKGROUND: As the prevalence of trachoma declines worldwide, it is becoming increasingly expensive and challenging to standardize graders in the field for surveys to document elimination. Photography of the tarsal conjunctiva and remote interpretation may help alleviate these challenges. The purpose of this study was to develop, and field test an Image Capture and Processing System (ICAPS) to acquire hands-free images of the tarsal conjunctiva for upload to a virtual reading center for remote grading.<br><br>This observational study was conducted during a district-level prevalence survey for trachomatous inflammation-follicular (TF) in Chamwino, Tanzania. The ICAPS was developed using a Samsung Galaxy S8 smartphone, a Samsung Gear VR headset, a foot pedal trigger and customized software allowing for hands-free photography. After a one-day training course, three trachoma graders used the ICAPS to collect images from 1305 children ages 1-9 years, which were expert-graded remotely for comparison with field grades. In our experience, the ICAPS was successful at scanning and assigning barcodes to images, focusing on the everted eyelid with adequate examiner hand visualization, and capturing images with sufficient detail to grade TF. The percentage of children with TF by photos and by field grade was 5%. Agreement between grading of the images compared to the field grades at the child level was kappa = 0.53 (95%CI = 0.40-0.66). There were ungradable images for at least one eye in 199 children (9.1%), with more occurring in children ages 1-3 (18.5%) than older children ages 4-9 (4.2%) (&#x3c7;2 = 145.3, p<0.001).<br><br>CONCLUSIONS/SIGNIFICANCE: The prototype ICAPS device was robust, able to image 1305 children in a district level survey and transmit images from rural Tanzania to an online grading platform. More work is needed to improve the percentage of ungradable images and to better understand the causes of disagreement between field and photo grading.},
}
@article {pmid34746461,
year = {2021},
author = {Nugraha, A and Daniel, DR and Utama, AAGS},
title = {Improving multi-sport event ticketing accounting information system design through implementing RFID and blockchain technologies within COVID-19 health protocols.},
journal = {Heliyon},
volume = {7},
number = {10},
pages = {e08167},
pmid = {34746461},
issn = {2405-8440},
abstract = {To run a multi-sport event, it is necessary to have a design of accounting information system for ticket sales that can run efficiently and can reduce opportunities of fraudulent acts. A case study during the 18[th] Asian Games 2018 shows that there were problems of inadequate ticket sales facilities for prospective spectators due to vendor diversion to the frictional problems such as venues located in various regions and protection of spectator rights in accordance with the purchased tickets. Some cases found in the multi-sport event were false seats and fictitious spectators allowed entrance to some arenas they did not have the right to enter, although they have gone through verification measures using line-of-sight barcoding technology. Some cases were also found during the 18[th] Asian Games 2018, in which there was a problem of inadequate ticket sales facilities for prospective spectators due to a change of vendor. There were also frictional problems on venues which are spread in various regions and regarding protection of spectators' rights per their purchased tickets. Moreover, it is fundamental that we take concern in the current pandemic situation, all event organizers are obliged to consider implementing health protocols issued by the World Health Organization (WHO) for safety to break the chain of COVID-19 infection. This study is conducted to identify the core of those problems and offer a solution by implementing radio-frequency identification (RFID) and blockchain technology to optimize the services applied in the multi-sport event, especially during and post-pandemic. Ticketing effectiveness for spectators are also challenged by budgetary and eco-friendliness issues.},
}
@article {pmid34745814,
year = {2021},
author = {Dev, SA and Unnikrishnan, R and Jayaraj, R and Sujanapal, P and Anitha, V},
title = {Quantification of adulteration in traded ayurvedic raw drugs employing machine learning approaches with DNA barcode database.},
journal = {3 Biotech},
volume = {11},
number = {11},
pages = {463},
pmid = {34745814},
issn = {2190-572X},
abstract = {UNLABELLED: Adulteration of expensive raw drugs with inferior taxa has become a routine practice, conceding the quality and safety of derived herbal products. In this regard, the study addresses the development of an integrated approach encompassing DNA barcode and HPTLC fingerprinting to authenticate chiefly traded ayurvedic raw drugs in south India [viz. Saraca asoca (Roxb.) Willd., Terminalia arjuna (Roxb. ex DC.) Wight and Arn., Sida alnifolia L. and Desmodium gangeticum (L.) DC.] from its adulterants. Consortium of Barcode of Life (CBOL) recommended DNA barcode gene regions viz. nuclear ribosomal-Internal Transcribed Spacer (nrDNA-ITS), maturase K (matK), ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) and psbA-trnH spacer regions along with HPTLC profiling were experimented and a reference database was created. Further, an integrated analytical approach employing genetic distance-based Maximum Likelihood phylogenetic tree and Artificial Intelligence (AI)based Machine Learning Algorithms (MLA)-Waikato Environment for Knowledge Analysis (WEKA) and Barcoding with Logic (BLOG) were employed to prove efficacy of DNA barcode tool. Even though, among the four barcodes, psbA-trnH (S. alnifolia and its adulterants, T. arjuna and its adulterants) or ITS region (S. asoca and its adulterants, D. gangeticum and its adulterants) showed highest inter specific divergences in the selected Biological Reference Materials (BRMs), rbcL or matK barcode regions alone were successful for authentication of traded samples. The automated species identification techniques, WEKA and BLOG, experimented for the first time in India for raw drug validation, could achieve rapid and precise identification. A national certification agency for raw drug authentication employing an integrated approach involving a DNA barcoding tool along with standard organoleptic and analytical methods can strengthen and ensure safety and quality of herbal medicines in India.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-03001-5.},
}
@article {pmid34744472,
year = {2021},
author = {Bidzilya, O and Huemer, P and Landry, JF and Šumpich, J},
title = {Gelechiaomelkoi sp. nov. - a new species from the Russian Altai Mountains related to the Nearctic Gelechiamandella Busck, 1904 (Lepidoptera, Gelechiidae), with a synopsis of Gelechia from the Altai Republic of Russia.},
journal = {ZooKeys},
volume = {1063},
number = {},
pages = {105-120},
pmid = {34744472},
issn = {1313-2989},
abstract = {Gelechiaomelkoi sp. nov. is described from the Ukok plateau and South Chuisky ridge in the Altai Mountains of Russia. The adult of the new species, including its male genitalia, is illustrated and compared with species most similar in morphology and DNA barcodes-G.sororculella (Hübner, 1817) and G.jakovlevi Krulikovsky, 1905 from the Palaearctic region, as well as G.mandella Busck, 1904 from Canada. This last species is redescribed based on adult specimens, including the genitalia of both sexes, and a lectotype is designated. Gelechiasirotina Omelko, 1986 is recorded from the Altai Republic for the first time. An updated list of six species of Gelechia from the Altai Mountains of Russia is given. Dorsal habitus photographs of all species are provided. The male genitalia of the lectotype of G.jakovlevi is illustrated for the first time.},
}
@article {pmid34742253,
year = {2021},
author = {Graper, AL and Noyszewski, AK and Anderson, NO and Smith, AG},
title = {Variability in ITS1 and ITS2 sequences of historic herbaria and extant (fresh) Phalaris species (Poaceae).},
journal = {BMC plant biology},
volume = {21},
number = {1},
pages = {515},
pmid = {34742253},
issn = {1471-2229},
mesh = {Phalaris/*genetics ; Poaceae/*genetics ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide/*genetics ; },
abstract = {BACKGROUND: Phalaris species (Poaceae) occupy diverse environments throughout all continents except Antarctica. Phalaris arundinacea is an important forage, ornamental, wetland restoration and biofuel crop grown globally as well as being a wetland invasive. The nuclear ribosomal internal transcribed spacer (ITS) region has been used for Phalaris barcoding as a DNA region with high nucleotide diversity for Phalaris species identification. Recent findings that P. arundinacea populations in Minnesota USA are most likely native and not European prompted this analysis to determine whether Eurasian vs. native North American P. arundinacea differed in ITS regions. Our objectives were to amplify and compare ITS regions (ITS1 and ITS2) of historic herbaria (1882-2001) and extant (fresh) Phalaris specimens; analyze ITS regions for species-specific polymorphisms (diagnostic SNPs) and compare ITS regions of historic Phalaris specimens with known, extant Phalaris species.<br><br>RESULTS: We obtained complete ITS1 and ITS2 sequences from 31 Phalaris historic (herbaria samples, 1908 to 2001) and five extant (fresh) specimens. Herbaria Phalaris specimens did not produce new SNPs (single nucleotide polymorphisms) not present in extant specimens. Diagnostic SNPs were identified in 8/12 (66.6%) Phalaris species. This study demonstrates the use of herbaria tissue for barcoding as a means for improved species identification of Phalaris herbaria specimens. No significant correlation between specimen age and genomic DNA concentration was found. Phalaris arundinacea showed high SNP variation within its clade, with the North American being distinctly different than other USA and most Eurasian types, potentially allowing for future identification of specific SNPs to geographic origin.<br><br>CONCLUSIONS: While not as efficient as extant specimens to obtain DNA, Phalaris herbaria specimens can produce high quality ITS sequences to evaluate historic genetic resources and facilitate identification of new species-specific barcodes. No correlation between DNA concentration and age of historic samples (119&#x2009;year range) occurred. Considerable polymorphism was exhibited in the P. arundinacea clade with several N. American accessions being distinct from Eurasian types. Further development of within species- and genus-specific barcodes could contribute to designing PCR primers for efficient and accurate identification of N. American P. arundinacea. Our finding of misidentified Phalaris species indicates the need to exercise stringent quality control measures on newly generated sequence data and to approach public sequence databases in a critical way.},
}
@article {pmid34740777,
year = {2021},
author = {Mohsin, M and Li, Y and Zhang, X and Wang, Y and Huang, Z and Yin, G and Zhang, Z},
title = {Development of CRISPR-CAS9 based RNA drugs against Eimeria tenella infection.},
journal = {Genomics},
volume = {113},
number = {6},
pages = {4126-4135},
doi = {10.1016/j.ygeno.2021.10.019},
pmid = {34740777},
issn = {1089-8646},
mesh = {Animals ; CRISPR-Cas Systems ; Chickens/genetics ; *Eimeria tenella/genetics ; RNA ; RNA, Messenger/genetics ; },
abstract = {Parasitic diseases are major trouble in many parts of the world. We consider that if a chemical can break a DNA barcode sequence, it might be used to develop a species-specific anti-parasitic agent. To examine this hypothesis, we constructed sgRNAs that target both the control (5.8S rDNA) and a DNA barcode (ITS) sequence in Eimeria tenella. In vitro experiment showed that Cas9 mRNA combined with sgRNAs could reduce the sporulation percentage of oocysts and the survival rate of sporulated oocysts and sporozoites. Quantitative real-time PCR showed that the DNAs of parasites exposed to Cas9 mRNA and sgRNAs were significantly affected, regardless of whether they were exposed to a combination of two sgRNAs or just a single sgRNA. The DNA sequencing also indicated that the experimental group exposed to two sgRNAs mixed with Cas9-induced deletion of large parts and a single sgRNA mixed with Cas9-induced mutation at sgRNA targeted fragments. In vivo trial, the effect of sgRNA and Cas9 RNA on the pathogenicity of E. tenella in chicken showed less lesion score and oocysts score (P < 0.05) in experimental groups than control groups. The results and concepts presented in this research can lead to discovering novel nucleic acid therapeutic drugs for Eimeriasis and other parasitic infections, which provide insights into the development of species-specific anti-parasitic agents.},
}
@article {pmid34739528,
year = {2021},
author = {Dvirnas, A and Stewart, C and Müller, V and Bikkarolla, SK and Frykholm, K and Sandegren, L and Kristiansson, E and Westerlund, F and Ambjörnsson, T},
title = {Detection of structural variations in densely-labelled optical DNA barcodes: A hidden Markov model approach.},
journal = {PloS one},
volume = {16},
number = {11},
pages = {e0259670},
pmid = {34739528},
issn = {1932-6203},
mesh = {*Markov Chains ; *DNA Barcoding, Taxonomic/methods ; *Algorithms ; DNA/genetics/analysis ; },
abstract = {Large-scale genomic alterations play an important role in disease, gene expression, and chromosome evolution. Optical DNA mapping (ODM), commonly categorized into sparsely-labelled ODM and densely-labelled ODM, provides sequence-specific continuous intensity profiles (DNA barcodes) along single DNA molecules and is a technique well-suited for detecting such alterations. For sparsely-labelled barcodes, the possibility to detect large genomic alterations has been investigated extensively, while densely-labelled barcodes have not received as much attention. In this work, we introduce HMMSV, a hidden Markov model (HMM) based algorithm for detecting structural variations (SVs) directly in densely-labelled barcodes without access to sequence information. We evaluate our approach using simulated data-sets with 5 different types of SVs, and combinations thereof, and demonstrate that the method reaches a true positive rate greater than 80% for randomly generated barcodes with single variations of size 25 kilobases (kb). Increasing the length of the SV further leads to larger true positive rates. For a real data-set with experimental barcodes on bacterial plasmids, we successfully detect matching barcode pairs and SVs without any particular assumption of the types of SVs present. Instead, our method effectively goes through all possible combinations of SVs. Since ODM works on length scales typically not reachable with other techniques, our methodology is a promising tool for identifying arbitrary combinations of genomic alterations.},
}
@article {pmid34738428,
year = {2021},
author = {Hu, HS and Zhang, DQ},
title = {[DNA super-barcoding of several medicinal species in Gentiana from Yunnan province].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {46},
number = {20},
pages = {5260-5269},
doi = {10.19540/j.cnki.cjcmm.20210720.103},
pmid = {34738428},
issn = {1001-5302},
mesh = {China ; DNA ; *Genome, Chloroplast/genetics ; *Gentiana/genetics ; Phylogeny ; },
abstract = {Gentiana is an important but complicated group in Gentianaceae. The genus covers numerous medicinal plants which are difficult to be identified. In the present study, several medicinal species in Gentiana from Yunnan province, including G. rigescens, G.rhodantha, and G. delavayi, were sequenced using the Illumina HiSeq 2500 system. Three complete chloroplast genome sequences were obtained after assembly and annotation. According to several published genome sequences of G. crassicaulis, the DNA super-barcoding of species in Gentiana was preliminarily carried out. The results revealed that chloroplast genomes of the three species were conservative with short lengths(146 944, 148 992, and 148 796 bp, respectively). The genomes encoded 114 genes, including 78 protein-coding genes, 30 tRNA genes, 4 rRNA genes, and 2 pseudogenes. Furthermore, these medicinal species in Yunnan province were identified using DNA super-barcoding based on chloroplast genomes. The results showed that the Gentiana species could be gathered into monophyletic branches with a high support value(100%). It indicated that DNA super-barcoding possessed obvious advantages in discriminating species in complicated genera. This study is expected to provide a scientific basis for the identification, utilization, and conservation of Gentiana species.},
}
@article {pmid34733866,
year = {2021},
author = {Yoon, HY and Moon, SJ and Song, JW},
title = {Lung Tissue Microbiome Is Associated With Clinical Outcomes of Idiopathic Pulmonary Fibrosis.},
journal = {Frontiers in medicine},
volume = {8},
number = {},
pages = {744523},
pmid = {34733866},
issn = {2296-858X},
abstract = {Background: Several studies using bronchoalveolar lavage fluid (BALF) reported that lung microbial communities were associated with the development and clinical outcome of idiopathic pulmonary fibrosis (IPF). However, the microbial communities in IPF lung tissues are not well known. This study is aimed to investigate bacterial microbial communities in lung tissues and determine their impact on the clinical outcomes of patients with IPF. Methods: Genomic DNA extracted from lung tissues of patients with IPF (n = 20; 10 non-survivors) and age- and sex-matched controls (n = 20) was amplified using fusion primers targeting the V3 and V4 regions of the 16S RNA genes with indexing barcodes. Results: Mean age of IPF subjects was 63.3 yr, and 65% were male. Alpha diversity indices did not significantly differ between IPF patients and controls, or between IPF non-survivors and survivors. The relative abundance of Lactobacillus, Paracoccus, and Akkermansia was increased, whereas that of Caulobacter, Azonexus, and Undibacterium decreased in patients with IPF compared with that in the controls. A decreased relative abundance of Pelomonas (odds ratio [OR], 0.352, p = 0.027) and Azonexus (OR, 0.013, p = 0.046) was associated with a diagnosis of IPF in the multivariable logistic analysis adjusted by age and gender. Multivariable Cox analysis adjusted for age and forced vital capacity (FVC) revealed that higher relative abundance of Streptococcus (hazard ratio [HR], 1.993, p = 0.044), Sphingomonas (HR, 57.590, p = 0.024), and Clostridium (HR, 37.189, p = 0.038) was independently associated with IPF mortality. The relative abundance of Curvibacter (r = 0.590) and Thioprofundum (r = 0.373) was correlated positively, whereas that of Anoxybacillus (r = -0.509) and Enterococcus (r = -0.593) was correlated inversely with FVC. In addition, the relative abundance of the Aquabacterium (r = 0.616) and Peptoniphilus (r = 0.606) genera was positively correlated, whereas that of the Fusobacterium (r = -0.464) and Phycicoccus (r = -0.495) genera was inversely correlated with distance during the 6-min walking test. Conclusions: The composition of the microbiome in lung tissues differed between patients with IPF and controls and was associated with the diagnosis, mortality, and disease severity of IPF.},
}
@article {pmid34733801,
year = {2021},
author = {Venuti, I and Ceruso, M and Palma, G and Smaldone, G and Pepe, T},
title = {DNA barcoding and nutritional analysis as a tool for promoting the market of inland fish species.},
journal = {Italian journal of food safety},
volume = {10},
number = {3},
pages = {9565},
pmid = {34733801},
issn = {2239-7132},
abstract = {The increasing world market demand for seafood requires an expansion of product categories available to consumers. Inland fish are usually considered having unmarked taste and are less appreciated by consumers; thus, they have low commercial value. Therefore, the marketing of the lake's fresh and processed fish is limited to the local market and consumers are currently uninformed and mistrustful about these species. In this study, six different fish species were caught in the Fondi lake (Lazio, central Italy): Anguilla anguilla, Tinca tinca, Carassius gibelio, Cyprinus carpio, Micropterus salmoides, Chelon ramada. All the samples were subjected to nutritional and DNA barcoding analysis. Moisture, protein, fat, carbohydrates, ash, and sodium content were measured. As regards the fatty acids profile, the most abundant were MUFAs with the highest value in Anguilla anguilla (45.97%). Oleic acid (C18: 1 n9 cis) was particularly high in Cyprinus carpio (55.46%). The fraction of polyunsaturated fatty acids (PUFA) revealed a higher DHA content (C22: 6 n3) in Anguilla anguilla than the other species (>12 %) while Chelon ramada presented both higher EPA content (C 20: 5 n3) and total fraction of omega 3 PUFAs. Concerning molecular analysis, a 655 bp fragment of cytochrome C oxidase subunit I (COI) gene was successfully used for the identification at the species level using both BOLD and BLAST public databases. The present study gives the basis for improving the knowledge and promoting inland fish' market and traceability along the supply chain.},
}
@article {pmid34733399,
year = {2021},
author = {Gallardo, RJ and Grishin, NV},
title = {Orange fringes, crenulate hindwings and genomic DNA identify a new species of Jonaspyge from Honduras (Hesperiidae: Pyrrhopyginae).},
journal = {Tropical lepidoptera research},
volume = {31},
number = {1},
pages = {48-52},
pmid = {34733399},
issn = {1941-7659},
support = {R35 GM127390/GM/NIGMS NIH HHS/United States ; },
abstract = {Jonaspyge elizabethae n. sp. is described from southwestern Honduras. It is similar to the other two Jonaspyge O. Mielke, 2002 species in having metallic dark-blue wings with purple sheen, crenulate hindwing outer margin, and black body with orange palpi and an orange abdomen tip. It is diagnosed by bright-orange (instead of white) fringes and dark (instead of orange) cheeks. Genomic sequence analysis of Jonaspyge reveals that it is a close relative of Jonaspyge jonas (C. Felder &amp; R. Felder, 1859) and Jonaspyge tzotzili (H. Freeman, 1969), differing from them by 5.3% in the COI DNA barcode. This new, third species of Jonaspyge is the most divergent member of the genus.},
}
@article {pmid34732241,
year = {2021},
author = {Șuleșco, T and Bușmachiu, G and Lange, U and Schmidt-Chanasit, J and Lühken, R},
title = {The first record of the invasive mosquito species Aedes albopictus in Chişinӑu, Republic of Moldova, 2020.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {565},
pmid = {34732241},
issn = {1756-3305},
mesh = {Aedes/*classification/genetics/growth &amp; development/physiology ; Animals ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Insect Proteins/genetics ; Introduced Species ; Male ; Moldova ; Mosquito Vectors/*classification/genetics/growth &amp; development/physiology ; },
abstract = {BACKGROUND: In Europe, Aedes albopictus is an important vector of chikungunya virus and Dirofilaria nematodes and has been involved in local autochthonous circulation of dengue and Zika viruses. Due to the ongoing spread, targeted field surveillance at potential points of entry of invasive Aedes mosquitoes was initiated by the Republic of Moldova in 2020 as part of the transboundary "Invasive Aedes Mosquitoes COST-Action project."<br><br>METHODS: In 2020, ovitraps were positioned at each of three locations: the border crossing to Romania in Leu&#x15f;eni (Hancesti region), Chi&#x15f;in&#x4d1;u International Airport and Chi&#x15f;in&#x4d1;u Botanical Garden.<br><br>RESULTS: A total of 188 Aedes spp. eggs were collected at the Chi&#x15f;in&#x4d1;u International Airport between August and September 2020. Twenty-three adults reared in the laboratory were identified morphologically as Ae. albopictus (Skuse, 1895), and 12 selected specimens were confirmed by molecular barcoding of the cytochrome oxidase subunit I gene region. In addition, one adult Ae. albopictus female at the same site was caught with a manual aspirator.<br><br>CONCLUSIONS: This is the first documented report of Ae. albopictus in the Republic of Moldova. The presence of immature and adult stages indicates the local reproduction of the species in the country. Therefore, it is crucial to extend and strengthen surveillance of the invasive Aedes mosquitoes to prevent Ae. albopictus and other exotic mosquito species from becoming established in the Republic of Moldova.},
}
@article {pmid34730487,
year = {2021},
author = {Cornet, L and D'hooge, E and Magain, N and Stubbe, D and Packeu, A and Baurain, D and Becker, P},
title = {The taxonomy of the Trichophyton rubrum complex: a phylogenomic approach.},
journal = {Microbial genomics},
volume = {7},
number = {11},
pages = {},
pmid = {34730487},
issn = {2057-5858},
mesh = {*Arthrodermataceae/genetics ; Phylogeny ; *Trichophyton/genetics ; },
abstract = {The medically relevant Trichophyton rubrum species complex has a variety of phenotypic presentations but shows relatively little genetic differences. Conventional barcodes, such as the internal transcribed spacer (ITS) region or the beta-tubulin gene, are not able to completely resolve the relationships between these closely related taxa. T. rubrum, T. soudanense and T. violaceum are currently accepted as separate species. However, the status of certain variants, including the T. rubrum morphotypes megninii and kuryangei and the T. violaceum morphotype yaoundei, remains to be deciphered. We conducted the first phylogenomic analysis of the T. rubrum species complex by studying 3105 core genes of 18 new strains from the BCCM/IHEM culture collection and nine publicly available genomes. Our analyses revealed a highly resolved phylogenomic tree with six separate clades. Trichophyton rubrum, T. violaceum and T. soudanense were confirmed in their status of species. The morphotypes T. megninii, T. kuryangei and T. yaoundei all grouped in their own respective clade with high support, suggesting that these morphotypes should be reinstituted to the species-level. Robinson-Foulds distance analyses showed that a combination of two markers (a ubiquitin-protein transferase and a MYB DNA-binding domain-containing protein) can mirror the phylogeny obtained using genomic data, and thus represent potential new markers to accurately distinguish the species belonging to the T. rubrum complex.},
}
@article {pmid34728738,
year = {2021},
author = {Matsuzaki, Y and Aoki, W and Miyazaki, T and Aburaya, S and Ohtani, Y and Kajiwara, K and Koike, N and Minakuchi, H and Miura, N and Kadonosono, T and Ueda, M},
title = {Peptide barcoding for one-pot evaluation of sequence-function relationships of nanobodies.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {21516},
pmid = {34728738},
issn = {2045-2322},
support = {JPMJFR204K//JST FOREST/ ; JPMJCR16G2//Core Research for Evolutional Science and Technology/ ; JPMJPF2008//JST COI-NEXT/ ; },
mesh = {Green Fluorescent Proteins/genetics/*metabolism ; Humans ; Peptide Fragments/chemistry/genetics/immunology/*metabolism ; Peptide Library ; Protein Binding ; Protein Engineering/*methods ; Proteomics ; Single-Domain Antibodies/chemistry/genetics/immunology/*metabolism ; },
abstract = {Optimisation of protein binders relies on laborious screening processes. Investigation of sequence-function relationships of protein binders is particularly slow, since mutants are purified and evaluated individually. Here we developed peptide barcoding, a high-throughput approach for accurate investigation of sequence-function relationships of hundreds of protein binders at once. Our approach is based on combining the generation of a mutagenised nanobody library fused with unique peptide barcodes, the formation of nanobody-antigen complexes at different ratios, their fine fractionation by size-exclusion chromatography and quantification of peptide barcodes by targeted proteomics. Applying peptide barcoding to an anti-GFP nanobody as a model, we successfully identified residues important for the binding affinity of anti-GFP nanobody at once. Peptide barcoding discriminated subtle changes in KD at the order of nM to sub-nM. Therefore, peptide barcoding is a powerful tool for engineering protein binders, enabling reliable one-pot evaluation of sequence-function relationships.},
}
@article {pmid34728378,
year = {2022},
author = {Sasaki, M and Iwaki, T and Waki, T and Nakao, M},
title = {An unknown species of Leucochloridium (Trematoda: Leucochloridiidae) from northern Honshu, Japan.},
journal = {Parasitology international},
volume = {87},
number = {},
pages = {102491},
doi = {10.1016/j.parint.2021.102491},
pmid = {34728378},
issn = {1873-0329},
mesh = {Animals ; Base Sequence ; Birds ; DNA, Helminth/chemistry ; DNA, Ribosomal/chemistry ; Japan ; Phylogeny ; RNA, Helminth/genetics ; RNA, Ribosomal, 28S/genetics ; Snails/*parasitology ; Trematoda/anatomy &amp; histology/*classification/genetics/isolation &amp; purification ; },
abstract = {Pulsating broodsacs of Leucochloridium sp. (Trematoda: Leucochloridiidae) were found from amber snails (Succinea lauta) in Iwate, the northern part of Honshu, Japan. A pattern with red-brown vertical stripes was characteristic of the broodsac. Very similar broodsacs were already detected from Okinawa Islands, the southern archipelago of Japan, and tentatively identified as Leucochloridium cf. passeri. A phylogenetic analysis based on DNA sequences of mitochondrial cytochrome c oxidase subunit 1 (cox1) showed that Leucochloridium sp. is different at species level from L. cf. passeri and that both species are related to Leucochloridium vogtianum from Europe. In this study the definitive identification of larval Leucochloridium sp. was impossible, but the resulting phylogeny confirmed that at least 4 species of Leucochloridium are distributed in Japan, depending on locality and climate. The DNA barcode generated in this study will be useful in detecting the adult stage of Leucochloridium sp. from birds.},
}
@article {pmid34724600,
year = {2022},
author = {Cheng, L and Lin, Z and Xin, C and Sun, H and Li, X},
title = {Molecular identification and phylogenetic analysis of Papaver based on ITS2 barcoding.},
journal = {Journal of forensic sciences},
volume = {67},
number = {2},
pages = {712-719},
doi = {10.1111/1556-4029.14925},
pmid = {34724600},
issn = {1556-4029},
support = {2020YCYB49//Graduate innovation ability improvement project for the Criminal Investigation Police University of China/ ; },
mesh = {DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; *Papaver/genetics ; Phylogeny ; },
abstract = {In forensic cases suspected to involve Papaver somniferum, species identification is key to the investigation. To accurately detect and identify P. somniferum as well as common adulterants of the same genus, 19 internal transcribed spacer 2 (ITS2) sequences of P. somniferum (256 bp), Papaver canescens (254 bp), Papaver nudicaule (254 bp), Papaver pavoninum (250 bp), Papaver radicatum (254 bp), and Papaver rhoeas (256 bp) were obtained. Based on the ITS2 sequence, similarity analysis via BLAST, the nearest Kimura-2-parameter (K2P) genetic distances were calculated, and a phylogenetic tree was constructed using MEGA X software for the identification of six species of Papaver. Finally, differences in the ITS2 secondary structure between species were analyzed. The best matches of the P. somniferum ITS2 sequence were of other P. somniferum from different sources. The nearest K2P genetic distances between P. somniferum and its counterparts from other sources were zero, which was the smallest pairwise genetic distance among distances from the other five Papaver species. Various sources of P. somniferum clustered into an independent branch in the phylogenetic tree. The secondary structures of P. somniferum and P. rhoeas were significantly different from those of the other four species of Papaver. In summary, P. somniferum can be effectively distinguished from five closely related plants of the same genus by using ITS2 as a DNA barcode.},
}
@article {pmid34721994,
year = {2021},
author = {Gong, L and Zhang, D and Ding, X and Huang, J and Guan, W and Qiu, X and Huang, Z},
title = {DNA barcode reference library construction and genetic diversity and structure analysis of Amomum villosum Lour. (Zingiberaceae) populations in Guangdong Province.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e12325},
pmid = {34721994},
issn = {2167-8359},
abstract = {BACKGROUND: Amomum villosum Lour. is the plant that produces the famous traditional Chinese medicine Amomi Fructus. Frequent habitat destruction seriously threatens A. villosum germplasm resources. Genetic diversity is very important to the optimization of germplasm resources and population protection, but the range of inherited traits within A. villosum is unclear. In this study, we analyzed the genetic diversity and genetic structures of A. villosum populations in Guangdong and constructed a local reference DNA barcode library as a resource for conservation efforts.<br><br>METHODS: DNA barcoding and Inter-Simple Sequence Repeat (ISSR) markers were used to investigate the population genetics of A. villosum. Five universal DNA barcodes were amplified and used in the construction of a DNA barcode reference library. Parameters including percentage of polymorphic sites (PPB), number of alleles (Na), effective number of alleles (Ne), Nei's gene diversity index (H), and Shannon's polymorphism information index (I) were calculated for the assessment of genetic diversity. Genetic structure was revealed by measuring Nei's gene differentiation coefficient (Gst), total population genetic diversity (Ht), intra-group genetic diversity (Hs), and gene flow (Nm). Analysis of molecular variance (AMOVA), Mantel tests, unweighted pair-group method with arithmetic mean (UPGMA) dendrogram, and principal co-ordinates (PCoA) analysis were used to elucidate the genetic differentiation and relationship among populations.<br><br>RESULTS: A total of 531 sequences were obtained from the five DNA barcodes with no variable sites from any of the barcode sequences. A total of 66 ISSR bands were generated from A. villosum populations using the selected six ISSR primers; 56 bands, 84.85% for all the seven A. villosum populations were polymorphic. The A. villosum populations showed high genetic diversity (H&#xa0;=&#xa0;0.3281, I&#xa0;=&#xa0;0.4895), whereas the gene flow was weak (Nm = 0.6143). Gst (0.4487) and AMOVA analysis indicated that there is obvious genetic differentiation amongA. villosum populations and more genetic variations existed within each population. The genetic relationship of each population was relatively close as the genetic distances were between 0.0844 and 0.3347.},
}
@article {pmid34721483,
year = {2021},
author = {Li, C and Cai, C and Tao, Y and Sun, Z and Jiang, M and Chen, L and Li, J},
title = {Variation and Evolution of the Whole Chloroplast Genomes of Fragaria spp. (Rosaceae).},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {754209},
pmid = {34721483},
issn = {1664-462X},
abstract = {Species identification is vital for protecting species diversity and selecting high-quality germplasm resources. Wild Fragaria spp. comprise rich and excellent germplasm resources; however, the variation and evolution of the whole chloroplast (cp) genomes in the genus Fragaria have been ignored. In the present study, 27 complete chloroplast genomes of 11 wild Fragaria species were sequenced using the Illumina platform. Then, the variation among complete cp genomes of Fragaria was analyzed, and phylogenetic relationships were reconstructed from those genome sequences. There was an overall high similarity of sequences, with some divergence. According to analysis with mVISTA, non-coding regions were more variable than coding regions. Inverted repeats (IRs) were observed to contract or expand to different degrees, which resulted in different sizes of cp genomes. Additionally, five variable loci, trnS-trnG, trnR-atpA, trnC-petN, rbcL-accD, and psbE-petL, were identified that could be used to develop DNA barcoding for identification of Fragaria species. Phylogenetic analyses based on the whole cp genomes supported clustering all species into two groups (A and B). Group A species were mainly distributed in western China, while group B contained several species from Europe and Americas. These results support allopolyploid origins of the octoploid species F. chiloensis and F. virginiana and the tetraploid species F. moupinensis and F. tibetica. The complete cp genomes of these Fragaria spp. provide valuable information for selecting high-quality Fragaria germplasm resources in the future.},
}
@article {pmid34720617,
year = {2021},
author = {Schmid-Egger, C and Schmidt, S},
title = {Unexpected diversity in Central European Vespoidea (Hymenoptera, Mutillidae, Myrmosidae, Sapygidae, Scoliidae, Tiphiidae, Thynnidae, Vespidae), with description of two species of Smicromyrme Thomson, 1870.},
journal = {ZooKeys},
volume = {1062},
number = {},
pages = {49-72},
pmid = {34720617},
issn = {1313-2989},
abstract = {The present study presents DNA barcoding results for 134 species of Central European Vespoidea, families Mutillidae, Myrmosidae, Sapygidae, Scoliidae, Tiphiidae, Thynnidae, and Vespidae, including DNA barcodes for 100 of the 114 German species. DNA barcoding resulted in unexpected diversity in several families, each with two or more genetic clusters identified by Barcode Index Numbers (BINs). Smicromyrmeburgeri Schmid-Egger, sp. nov. and S.langobardensis Schmid-Egger, sp. nov. are described as new from Germany and Italy, respectively. A neotype is designated for Smicromyrmerufipes (Fabricius, 1878). The results of DNA barcoding are discussed in respect to detecting cryptic species and refining species limits.},
}
@article {pmid34720612,
year = {2021},
author = {Kirichenko, NI and Akulov, EN and Triberti, P and Belokobylskij, SA},
title = {A new species of Micrurapteryx (Lepidoptera, Gracillariidae) feeding on Thermopsislanceolata (Fabaceae) in southern Siberia and its hymenopterous parasitoids.},
journal = {ZooKeys},
volume = {1061},
number = {},
pages = {131-163},
pmid = {34720612},
issn = {1313-2989},
abstract = {A new species of leaf-mining moth described here as Micrurapteryxbaranchikovi Kirichenko, Akulov &amp; Triberti, sp. nov. was detected in large numbers feeding on Thermopsislanceolata (Fabaceae) in the Republic of Khakassia (Russia) in 2020. A morphological diagnosis of adults, bionomics and DNA barcoding data of the new species are provided. The developmental stages (larva, pupa, adult), male and female genitalia, as well as the leaf mines and the infestation plot in Khakassia are illustrated; the pest status of the new species in the studied region is discussed. Additionally, parasitism rate was estimated, the parasitoid wasps reared from pupae of the new species were identified (morphologically and genetically) and illustrated . Among them, one ichneumonid, Campoplexsp. aff.borealis (Zetterstedt) and two braconids, Agathisfuscipennis (Zetterstedt) and Illidopssubversor (Tobias et Kotenko), are novel records for the Republic of Khakassia. Furthermore, they are all documented as parasitoids of Gracillariidae for the first time. The DNA barcode of A.fuscipennis is newly obtained and can be used as a reference sequence for species identification.},
}
@article {pmid34720610,
year = {2021},
author = {Salgado-Neto, G and Vásquez, CAN and Max, DS and Whitfield, JB},
title = {Cotesiacassina sp. nov. from southwestern Colombia: a new gregarious microgastrine wasp (Hymenoptera, Braconidae) reared from the pest species Opsiphanescassina Felder &amp; Felder (Lepidoptera, Nymphalidae) feeding on Elaeis oil palm trees (Arecaceae).},
journal = {ZooKeys},
volume = {1061},
number = {},
pages = {11-22},
pmid = {34720610},
issn = {1313-2989},
abstract = {A new species of microgastrine wasp, Cotesiacassina Salgado-Neto, Vásquez &amp; Whitfield, sp. nov., is described from southwestern Colombia in Tumaco, Nariño. This species is a koinobiont gregarious larval endoparasitoid, and spins a common mass of cocoons underneath the host caterpillars of Opsiphanescassina (Felder &amp; Felder) (Lepidoptera, Nymphalidae), feeding on oil palm trees (interspecific hybrid Elaeisoleifera × E.guineensis) (Arecaceae). While superficially similar, both morphologically and biologically, to C.invirae Salgado-Neto &amp; Whitfield from southern Brazil, the two species are distinct based on DNA barcodes, host species, geographical range and morphological characters.},
}
@article {pmid34718994,
year = {2022},
author = {Tiirola, M and Mäki, A},
title = {Construction of Metatranscriptomic Libraries for 5' End Sequencing of rRNAs for Microbiome Research.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2349},
number = {},
pages = {137-146},
pmid = {34718994},
issn = {1940-6029},
mesh = {Archaea/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Metatranscriptomic sequencing enables studying community-wide gene expression profiles of microbial samples and getting functional insight on their up- or downregulated pathways. However, shotgun sequencing is not the most efficient way to study expression of ribosomal RNA genes or to compare lot of samples in experimental setups. Here we describe an efficient primer-independent method for processing and barcoding libraries for directional sequencing of the 5' end region of the RNA. When applying size selection of the original RNA, the method forms an optimal solution for the simultaneous analysis of bacterial, archaeal, and eukaryotic rRNA diversity.},
}
@article {pmid34711319,
year = {2021},
author = {Buchan, E and Kelleher, L and Clancy, M and Stanley Rickard, JJ and Oppenheimer, PG},
title = {Spectroscopic molecular-fingerprint profiling of saliva.},
journal = {Analytica chimica acta},
volume = {1185},
number = {},
pages = {339074},
doi = {10.1016/j.aca.2021.339074},
pmid = {34711319},
issn = {1873-4324},
mesh = {Algorithms ; Humans ; Machine Learning ; Neural Networks, Computer ; *Saliva ; *Spectrum Analysis, Raman ; },
abstract = {Saliva analysis has been gaining interest as a potential non-invasive source of disease indicative biomarkers due to being a complex biofluid correlating with blood-based constituents on a molecular level. For saliva to cement its usage for analytical applications, it is paramount to gain underpinning molecular knowledge and establish a 'baseline' of the salivary composition in healthy individuals as well as characterize how these factors are impacting its performance as potential analytical biofluid. Here, we have systematically studied the molecular spectral fingerprint of saliva, including the changes associated with gender, age, and time. Via hybrid artificial neural network algorithms and Raman spectroscopy, we have developed a non-destructive molecular profiling approach enabling the assessment of salivary spectral changes yielding the determination of gender and age of the biofluid source. Our classification algorithm successfully identified the gender and age from saliva with high classification accuracy. Discernible spectral molecular 'barcodes' were subsequently constructed for each class and found to primarily stem from amino acid, protein, and lipid changes in saliva. This unique combination of Raman spectroscopy and advanced machine learning techniques lays the platform for a variety of applications in forensics and biosensing.},
}
@article {pmid34709609,
year = {2022},
author = {Huggler, KS and Rossiter, NJ and Flickinger, KM and Cantor, JR},
title = {CRISPR/Cas9 Screening to Identify Conditionally Essential Genes in Human Cell Lines.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2377},
number = {},
pages = {29-42},
pmid = {34709609},
issn = {1940-6029},
support = {K22 CA225864/CA/NCI NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; },
mesh = {*CRISPR-Cas Systems/genetics ; Cell Line ; DNA ; *Genes, Essential ; High-Throughput Nucleotide Sequencing ; Humans ; RNA, Guide, CRISPR-Cas Systems/genetics ; },
abstract = {Forward genetic screens across hundreds of cancer cell lines have started to define the genetic dependencies of proliferating human cells. However, most such screens have been performed in vitro with little consideration into how medium composition might affect gene essentiality. This protocol describes a method to use CRISPR/Cas9-based loss-of-function screens to ask how gene essentiality in human cell lines varies with medium composition. First, a single-guide RNA (sgRNA) library is packaged into lentivirus, and an optimal infection titer is determined for the target cells. Following selection, genomic DNA (gDNA) is extracted from an aliquot of the transduced cells. The remaining transduced cells are then screened in at least two distinct cell culture media. At the conclusion of the screening period, gDNA is collected from each cell population. Next, high-throughput sequencing is used to determine sgRNA barcode abundances from the initial and each of the final populations. Finally, an analytical pipeline is used to identify medium-essential candidate genes from these screen results.},
}
@article {pmid34707820,
year = {2021},
author = {Muster, C and Spelda, J and Rulik, B and Thormann, J and von der Mark, L and Astrin, JJ},
title = {The dark side of pseudoscorpion diversity: The German Barcode of Life campaign reveals high levels of undocumented diversity in European false scorpions.},
journal = {Ecology and evolution},
volume = {11},
number = {20},
pages = {13815-13829},
pmid = {34707820},
issn = {2045-7758},
abstract = {DNA barcoding is particularly useful for identification and species delimitation in taxa with conserved morphology. Pseudoscorpions are arachnids with high prevalence of morphological crypsis. Here, we present the first comprehensive DNA barcode library for Central European Pseudoscorpiones, covering 70% of the German pseudoscorpion fauna (35 out of 50 species). For 21 species, we provide the first publicly available COI barcodes, including the rare Anthrenochernes stellae Lohmander, a species protected by the FFH Habitats Directive. The pattern of intraspecific COI variation and interspecific COI variation (i.e., presence of a barcode gap) generally allows application of the DNA barcoding approach, but revision of current taxonomic designations is indicated in several taxa. Sequences of 36 morphospecies were assigned to 74 BINs (barcode index numbers). This unusually high number of intraspecific BINs can be explained by the presence of overlooked cryptic species and by the accelerated substitution rate in the mitochondrial genome of pseudoscorpions, as known from previous studies. Therefore, BINs may not be an appropriate proxy for species numbers in pseudoscorpions, while partitions built with the ASAP algorithm (Assemble Species by Automatic Partitioning) correspond well with putative species. ASAP delineated 51 taxonomic units from our data, an increase of 42% compared with the present taxonomy. The Neobisium carcionoides complex, currently considered a polymorphic species, represents an outstanding example of cryptic diversity: 154 sequences from our dataset were allocated to 23 BINs and 12 ASAP units.},
}
@article {pmid34707629,
year = {2021},
author = {Su, N and Liu, BB and Wang, JR and Tong, RC and Ren, C and Chang, ZY and Zhao, L and Potter, D and Wen, J},
title = {On the Species Delimitation of the Maddenia Group of Prunus (Rosaceae): Evidence From Plastome and Nuclear Sequences and Morphology.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {743643},
pmid = {34707629},
issn = {1664-462X},
abstract = {The recognition, identification, and differentiation of closely related plant species present significant and notorious challenges to taxonomists. The Maddenia group of Prunus, which comprises four to seven species, is an example of a group in which species delimitation and phylogenetic reconstruction have been difficult, due to the lack of clear morphological distinctions, limited sampling, and low informativeness of molecular evidence. Thus, the precise number of species in the group and the relationships among them remain unclear. Here, we used genome skimming to generate the DNA sequence data for 22 samples, including 17 Maddenia individuals and five outgroups in Amygdaloideae of Rosaceae, from which we assembled the plastome and 446 single-copy nuclear (SCN) genes for each sample. The phylogenetic relationships of the Maddenia group were then reconstructed using both concatenated and coalescent-based methods. We also identified eight highly variable regions and detected simple sequence repeats (SSRs) and repeat sequences in the Maddenia species plastomes. The phylogenetic analysis based on the complete plastomes strongly supported three main subclades in the Maddenia group of Prunus, while five subclades were recognized based on the nuclear tree. The phylogenetic network analysis detected six hybridization events. Integrating the nuclear and morphological evidence, we proposed to recognize five species within the Maddenia group, i.e., Prunus fujianensis, P. himalayana, P. gongshanensis, P. hypoleuca, and P. hypoxantha. Within this group, the first three species are well-supported, while the gene flow occurring throughout the Maddenia group seems to be especially frequent between P. hypoleuca and P. hypoxantha, eroding the barrier between them. The phylogenetic trees based on eight concatenated hypervariable regions had a similar topology with the complete plastomes, showing their potential as molecular markers and effective barcodes for further phylogeographic studies on Maddenia.},
}
@article {pmid34707582,
year = {2021},
author = {Sirag, B and Khidir, ES and Dumyati, M and Sindi, B and Alsinnari, M and Faidah, H and Ahmed, A},
title = {Cryptococcus neoformans and Other Opportunistic Cryptococcus Species in Pigeon Dropping in Saudi Arabia: Identification and Characterization by DNA Sequencing.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {726203},
pmid = {34707582},
issn = {1664-302X},
abstract = {The prevalent variants of Cryptococcus neoformans, and other Cryptococcus species in pigeon excreta in Western Region of Saudi Arabia were studied. Ninety pigeon dropping samples were plated directly on Niger seed agar, and suspected colonies were sequenced using Illumina MiSeq. Species identification was determined using sequence read mapping to reference genomes of the two C. neoformans variants. In addition, sequence reads were identified using the KmerFinder tool. internal transcribed spacer 2 in the rDNA was also used for fungal barcoding of none of the C. neoformans species using two fungal identification databases. Phylogeny was studied using CSI Phylogeny (Center for Genomic Epidemiology, Denmark). The C. neoformans var. grubii mitochondrion and chromosome 1 reference sequences (accession numbers NC_004336.1 and CP022321.1, respectively) were used for sequence comparison and variant calling. Fifteen Cryptococcus isolates were isolated, 11 were identified as C. neoformans var. grubii, and 4 were found to be other opportunistic Cryptococcus species. Phylogeny analysis of C. neoformans var. grubii isolates showed a high degree of similarity between the C. neoformans isolates especially at the mitochondrial genome level. This study supports the fact that pathogenic and opportunistic Cryptococcus species are prevalent in domestic bird excreta which is an easy source of infection in the susceptible population.},
}
@article {pmid34707455,
year = {2021},
author = {Han, YD and Mironov, SV and Kim, JH and Min, GS},
title = {Feather mites (Acariformes, Astigmata) from marine birds of the Barton Peninsula (King George Island, Antarctica), with descriptions of two new species.},
journal = {ZooKeys},
volume = {1061},
number = {},
pages = {109-130},
pmid = {34707455},
issn = {1313-2989},
abstract = {We report on the first investigation of feather mites associated with birds living on the Barton Peninsula (King George Island, Antarctica). We found seven feather mite species of the superfamily Analgoidea from four host species. Two new species are described from two charadriiform hosts: Alloptes (Sternalloptes) antarcticussp. nov. (Alloptidae) from Stercorariusmaccormicki Saunders (Stercorariidae), and Ingrassiachionis sp. nov. (Xolalgidae) from Chionisalbus (Gmelin) (Chionidae). Additionally, we provide partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI), which was utilized as a DNA barcode, for all seven feather mite species.},
}
@article {pmid34706209,
year = {2021},
author = {Barber, K and Middlebrooks, M and Bell, S and Pierce, S},
title = {The Specialist Marine Herbivore Elysia papillosa Grows Faster on a Less Utilized Algal Diet.},
journal = {The Biological bulletin},
volume = {241},
number = {2},
pages = {158-167},
doi = {10.1086/716508},
pmid = {34706209},
issn = {1939-8697},
mesh = {Animals ; *Chlorophyta ; Chloroplasts ; Diet ; *Gastropoda ; Herbivory ; },
abstract = {AbstractMany small specialist herbivores utilize their food resources both for nutrition and as a structural refuge or resource. Trophic linkage cannot solely be inferred from physical association of herbivores with a potential food item, because herbivores may temporarily inhabit algae or plants on which they do not feed. Elysia papillosa, a small sacoglossan sea slug, consumes and sequesters chloroplasts from the siphonaceous, chlorophytic alga Penicillus capitatus; it also maintains moderate densities on this alga. Recently, E. papillosa was also infrequently found in association with the alga Penicillus lamourouxii, which displays density similar to that of P. capitatus. After collecting E. papillosa from each of the two algal species from a shallow-water site along the west central coast of Florida, we used DNA barcoding of the rbcL gene sequences in order to determine whether the slug was consuming both algal species. The molecular data indicated that E. papillosa consumed and sequestered chloroplasts from the same algal species from which they were collected. A laboratory feeding experiment tested whether algal diet (P. capitatus or P. lamourouxii) had an impact on slug growth rate as measured by change in body size (mm). After 3 weeks E. papillosa fed P. lamourouxii achieved a mean body length that was 1.5-2 times that recorded for slugs fed P. capitatus, but maximum growth depended on the original field host. Thus, while the highest densities of E. papillosa in the field occurred on P. capitatus, slugs grew much faster on P. lamourouxii in the laboratory. The observed association of E. papillosa with P. capitatus must be related to other factors, such as foraging efficiency, algal morphology, algal biochemistry, or algal suitability as a refuge.},
}
@article {pmid34706068,
year = {2022},
author = {Wursthorn, A and Schwager, C and Kurth, I and Peitzsch, C and Herold-Mende, C and Debus, J and Abdollahi, A and Nowrouzi, A},
title = {High-Complexity cellular barcoding and clonal tracing reveals stochastic and deterministic parameters of radiation resistance.},
journal = {International journal of cancer},
volume = {150},
number = {4},
pages = {663-677},
doi = {10.1002/ijc.33855},
pmid = {34706068},
issn = {1097-0215},
mesh = {Biomarkers, Tumor ; Cell Line, Tumor ; Clonal Selection, Antigen-Mediated ; Head and Neck Neoplasms/pathology/*radiotherapy ; Humans ; *Radiation Tolerance ; Squamous Cell Carcinoma of Head and Neck/pathology/*radiotherapy ; Stochastic Processes ; },
abstract = {It is elusive whether clonal selection of tumor cells in response to ionizing radiation (IR) is a deterministic or stochastic process. With high resolution clonal barcoding and tracking of over 400 000 HNSCC patient-derived tumor cells the clonal dynamics of tumor cells in response to IR was analyzed. Fractionated IR induced a strong selective pressure for clonal reduction which significantly exceeded uniform clonal survival probabilities indicative for a strong clone-to-clone difference within tumor cell lines. IR induced clonal reduction affected the majority of tumor cells ranging between 96% and 75% and correlated to the degree of radiation sensitivity. Survival to IR is driven by a deterministic clonal selection of a smaller population which commonly survives radiation, while increased clonogenic capacity is a result of clonal competition of cells which have been selected stochastically. A 2-fold increase in radiation resistance results in a 4-fold (P < .05) higher deterministic clonal selection showing that the ratio of these parameters is amenable to radiation sensitivity which correlates to prognostic biomarkers of HNSCC. Evidence for the existence of a rare subpopulation with an intrinsically radiation resistant phenotype commonly surviving IR was found at a frequency of 0.6% to 3.3% (P < .001, FDR 3%). With cellular barcoding we introduce a novel functional heterogeneity associated qualitative readout for tracking dynamics of clonogenic survival in response to radiation. This enables the quantification of intrinsically radiation resistant tumor cells from patient samples and reveals the contribution of stochastic and deterministic clonal selection processes in response to IR.},
}
@article {pmid34703030,
year = {2022},
author = {Kuiken, HJ and Dhakal, S and Selfors, LM and Friend, CM and Zhang, T and Callari, M and Schackmann, RCJ and Gray, GK and Crowdis, J and Bhang, HC and Baslan, T and Stegmeier, F and Gygi, SP and Caldas, C and Brugge, JS},
title = {Clonal populations of a human TNBC model display significant functional heterogeneity and divergent growth dynamics in distinct contexts.},
journal = {Oncogene},
volume = {41},
number = {1},
pages = {112-124},
pmid = {34703030},
issn = {1476-5594},
support = {16942/CRUK_/Cancer Research UK/United Kingdom ; 29567/CRUK_/Cancer Research UK/United Kingdom ; P01 CA080111/CA/NCI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; *Genetic Heterogeneity ; Humans ; Mice ; Mutation ; Triple Negative Breast Neoplasms/*genetics/pathology ; Tumor Microenvironment/*genetics ; },
abstract = {Intratumoral heterogeneity has been described for various tumor types and models of human cancer, and can have profound effects on tumor progression and drug resistance. This study describes an in-depth analysis of molecular and functional heterogeneity among subclonal populations (SCPs) derived from a single triple-negative breast cancer cell line, including copy number analysis, whole-exome and RNA sequencing, proteome analysis, and barcode analysis of clonal dynamics, as well as functional assays. The SCPs were found to have multiple unique genetic alterations and displayed significant variation in anchorage independent growth and tumor forming ability. Analyses of clonal dynamics in SCP mixtures using DNA barcode technology revealed selection for distinct clonal populations in different in vitro and in vivo environmental contexts, demonstrating that in vitro propagation of cancer cell lines using different culture conditions can contribute to the establishment of unique strains. These analyses also revealed strong enrichment of a single SCP during the development of xenograft tumors in immune-compromised mice. This SCP displayed attenuated interferon signaling in vivo and reduced sensitivity to the antiproliferative effects of type I interferons. Reduction in interferon signaling was found to provide a selective advantage within the xenograft microenvironment specifically. In concordance with the previously described role of interferon signaling as tumor suppressor, these findings suggest that similar selective pressures may be operative in human cancer and patient-derived xenograft models.},
}
@article {pmid34698546,
year = {2021},
author = {Anderson, VM and Wendt, KL and Najar, FZ and McCall, LI and Cichewicz, RH},
title = {Building Natural Product Libraries Using Quantitative Clade-Based and Chemical Clustering Strategies.},
journal = {mSystems},
volume = {6},
number = {5},
pages = {e0064421},
pmid = {34698546},
issn = {2379-5077},
support = {R25 AI147376/AI/NIAID NIH HHS/United States ; },
abstract = {The success of natural product-based drug discovery is predicated on having chemical collections that offer broad coverage of metabolite diversity. We propose a simple set of tools combining genetic barcoding and metabolomics to help investigators build natural product libraries aimed at achieving predetermined levels of chemical coverage. It was found that such tools aided in identifying overlooked pockets of chemical diversity within taxa, which could be useful for refocusing collection strategies. We have used fungal isolates identified as Alternaria from a citizen-science-based soil collection to demonstrate the application of these tools for assessing and carrying out predictive measurements of chemical diversity in a natural product collection. Within Alternaria, different subclades were found to contain nonequivalent levels of chemical diversity. It was also determined that a surprisingly modest number of isolates (195 isolates) was sufficient to afford nearly 99% of Alternaria chemical features in the data set. However, this result must be considered in the context that 17.9% of chemical features appeared in single isolates, suggesting that fungi like Alternaria might be engaged in an ongoing process of actively exploring nature's metabolic landscape. Our results demonstrate that combining modest investments in securing internal transcribed spacer (ITS)-based sequence information (i.e., establishing gene-based clades) with data from liquid chromatography-mass spectrometry (i.e., generating feature accumulation curves) offers a useful route to obtaining actionable insights into chemical diversity coverage trends in a natural product library. It is anticipated that these outcomes could be used to improve opportunities for accessing bioactive molecules that serve as the cornerstone of natural product-based drug discovery. IMPORTANCE Natural product drug discovery efforts rely on libraries of organisms to provide access to diverse pools of compounds. Actionable strategies to rationally maximize chemical diversity, rather than relying on serendipity, can add value to such efforts. Readily implementable biological (i.e., ITS sequence analysis) and chemical (i.e., mass spectrometry-based feature and scaffold measurements) diversity assessment tools can be employed to monitor and adjust library development tactics in real time. In summary, metabolomics-driven technologies and simple gene-based specimen barcoding approaches have broad applicability to building chemically diverse natural product libraries.},
}
@article {pmid34698117,
year = {2021},
author = {Kim, MJ and Lee, KH and Park, JS and Jeong, JS and Jeong, NR and Lee, W and Kim, I},
title = {Complete Mitochondrial Genomes of Metcalfa pruinosa and Salurnis marginella (Hemiptera: Flatidae): Genomic Comparison and Phylogenetic Inference in Fulgoroidea.},
journal = {Current issues in molecular biology},
volume = {43},
number = {3},
pages = {1391-1418},
pmid = {34698117},
issn = {1467-3045},
support = {PJ01338901//Cooperative Research Program for Agriculture Science and Technology Development, Rural Development Administration, Republic of Korea/ ; },
mesh = {Animals ; Base Sequence ; Computational Biology/methods ; Conserved Sequence ; DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer ; Gene Rearrangement ; Genes, Insect ; Genes, Mitochondrial ; Genetic Variation ; *Genome, Mitochondrial ; *Genomics ; Hemiptera/*classification/*genetics ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Nucleotide Motifs ; *Phylogeny ; },
abstract = {The complete mitochondrial genomes (mitogenomes) of two DNA barcode-defined haplotypes of Metcalfa pruinosa and one of Salurnis marginella (Hemiptera: Flatidae) were sequenced and compared to those of other Fulgoroidea species. Furthermore, the mitogenome sequences were used to reconstruct phylogenetic relationships among fulgoroid families. The three mitogenomes, including that of the available species of Flatidae, commonly possessed distinctive structures in the 1702-1836 bp A+T-rich region, such as two repeat regions at each end and a large centered nonrepeat region. All members of the superfamily Fulgoroidea, including the Flatidae, consistently possessed a motiflike sequence (TAGTA) at the ND1 and trnS2 junction. The phylogenetic analyses consistently recovered the familial relationships of (((((Ricaniidae + Issidae) + Flatidae) + Fulgoridae) + Achilidae) + Derbidae) in the amino acid-based analysis, with the placement of Cixiidae and Delphacidae as the earliest-derived lineages of fulgoroid families, whereas the monophyly of Delphacidae was not congruent between tree-constructing algorithms.},
}
@article {pmid34695878,
year = {2022},
author = {Reynolds, NK and Jusino, MA and Stajich, JE and Smith, ME},
title = {Understudied, underrepresented, and unknown: Methodological biases that limit detection of early diverging fungi from environmental samples.},
journal = {Molecular ecology resources},
volume = {22},
number = {3},
pages = {1065-1085},
doi = {10.1111/1755-0998.13540},
pmid = {34695878},
issn = {1755-0998},
support = {FLA-PLP-005289//National Institute of Food and Agriculture/ ; DEB 1441677//The National Science Foundation/ ; DEB 1441715//The National Science Foundation/ ; },
mesh = {Bias ; DNA Primers/genetics ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; *Fungi/genetics ; Phylogeny ; },
abstract = {Metabarcoding is an important tool for understanding fungal communities. The internal transcribed spacer (ITS) rDNA is the accepted fungal barcode but has known problems. The large subunit (LSU) rDNA has also been used to investigate fungal communities but available LSU metabarcoding primers were mostly designed to target Dikarya (Ascomycota + Basidiomycota) with little attention to early diverging fungi (EDF). However, evidence from multiple studies suggests that EDF comprise a large portion of unknown diversity in community sampling. Here, we investigate how DNA marker choice and methodological biases impact recovery of EDF from environmental samples. We focused on one EDF lineage, Zoopagomycota, as an example. We evaluated three primer sets (ITS1F/ITS2, LROR/LR3, and LR3 paired with new primer LR22F) to amplify and sequence a Zoopagomycota mock community and a set of 146 environmental samples with Illumina MiSeq. We compared two taxonomy assignment methods and created an LSU reference database compatible with AMPtk software. The two taxonomy assignment methods recovered strikingly different communities of fungi and EDF. Target fragment length variation exacerbated PCR amplification biases and influenced downstream taxonomic assignments, but this effect was greater for EDF than Dikarya. To improve identification of LSU amplicons we performed phylogenetic reconstruction and illustrate the advantages of this critical tool for investigating identified and unidentified sequences. Our results suggest much of the EDF community may be missed or misidentified with "standard" metabarcoding approaches and modified techniques are needed to understand the role of these taxa in a broader ecological context.},
}
@article {pmid34692854,
year = {2021},
author = {Mohan, PK and Adarsh Krishna, TP and Senthil Kumar, T and Ranjitha Kumari, BD},
title = {Pharmaco-chemical profiling of Desmodium gangeticum (L.) DC. with special reference to soil chemistry.},
journal = {Future journal of pharmaceutical sciences},
volume = {7},
number = {1},
pages = {210},
pmid = {34692854},
issn = {2314-7253},
abstract = {BACKGROUND: Desmodium gangeticum (L.) DC. (Fabaceae) (DG) is a perennial non-climbing herb or shrub and folklore medicine, widely shows a large number of medicinal properties, as well as contains divergent bioactive compounds. Many of the herbal formulations contain this medicinal plant, which is considered as master of medicinal plant in Ayurveda. This study is an attempt to establish this plant material based on its pharmaco-chemical profiles with special reference to soil chemistry. The pharmaco-chemical features such as organoleptic, DNA sequence, physicochemical, proximate, phytochemical, UV, and FTIR profiling were carried out using standard techniques. Moreover, the ADME-PK properties of the selected molecules were established.<br><br>RESULTS: The pharmaco-chemical features like organoleptic, DNA sequence, physicochemical, proximate, phytochemical, UV, and FTIR profiling, ADME-PK properties, and soil chemistry of&#xa0;D. gangeticum revealed its unique and diagnostic peculiarities. DNA barcoding showed that the sequence was 99.77% similar to D. gangeticum (KP094638) having 100% query coverage. The soil analysis revealed the presence of moderately high content of NPK and sufficient amount of all essential macro- and micronutrients (S, Fe, Mn, Cu, Zn, and B). The phytochemical profiling showed that the ethanolic extract of the aerial part contained glycoside, amino acid, phenols, alkaloids, flavonoids, and coumarins, while the ethanolic root extract of the plant revealed the presence of glycoside, amino acid, phenols, alkaloids, flavonoids, coumarins, and triterpenoids. FTIR results indicated that the plant extracts are mainly rich in phenolic derivatives. ADME-PK properties of pterocarpan such as gangetin (1a), gangetinin (1b), desmocarpin (1c), and desmodin (1d) were found to pass the Lipinski, Ghose, Veber, and Egan rules, supporting the drug-likeliness.<br><br>CONCLUSION: This is the first record of pharmaco-chemical profiling of D. gangeticum along with soil chemistry, and this information helps in the proper identification and future studies on this species.},
}
@article {pmid34692246,
year = {2021},
author = {Goren, M and Stern, N},
title = {Cryptocentrus steinhardti (Actinopterygii; Gobiidae): a new species of shrimp-goby, and a new invasive to the Mediterranean Sea.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e12136},
pmid = {34692246},
issn = {2167-8359},
abstract = {A new species of shrimp-goby was collected at depths of 60-80 m off the southern Israeli Mediterranean coast. A unique 'DNA barcoding' signature (mtDNA COI and Cytb) revealed that it differs from any other previously bar-coded goby species clustered phylogenetically with the shrimp-gobies group, in which Cryptocentrus is the most speciose genus. A morphological study supported the assignment of the fish to Cryptocentrus and differentiated the new species from its congeners. The species is described here as Cryptocentrus steinhardti n. sp. However, the present phylogenetic analysis demonstrates a paraphyly of Cryptocentrus and emphasizes the need for revision of the genus based on integrating morphological and genetic characteristics. This finding constitutes the third record of an invasive shrimp goby in the Mediterranean Sea. An intriguing ecological issue arises regarding the possible formation of a fish-shrimp symbiosis in a newly invaded territory. Describing an alien tropical species in the Mediterranean prior to its discovery in native distribution is an unusual event, although not the first such case. Several similar examples are provided in the present article.},
}
@article {pmid34690518,
year = {2021},
author = {Nguyen, DT and Ho, LT and Nguyen, SG},
title = {Description of a new species of the Charaeacoomani group (Coleoptera: Chrysomelidae: Galerucinae) from Vietnam with a key to species.},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e72158},
pmid = {34690518},
issn = {1314-2828},
abstract = {BACKGROUND: The genus Charaea Baly is distributed in the eastern Palaearctic, Himalayas, China and adjacent countries of the Oriental Region. Currently, 59 species of the genus Charaea have been recorded. The species of Charaea is characterised with a robust tubular aedeagus that terminates with a more or less distinct apical process with the Charaeacoomani group having an internal sac with long sharp lateral sclerites. Up to now, 13 species of this group have been described in the Oriental Region, four of which are found in Vietnam.<br><br>NEW INFORMATION: Charaeadinhcuongi sp. nov. is described as a new species, based on specimens collected from Phu Quoc Island in southern Vietnam. Colour photographs of habitus and body details and DNA barcode sequences are presented. An identification key is provided for all Vietnamese species from the Charaeacoomani group.},
}
@article {pmid34690515,
year = {2021},
author = {Ferreira, S and Oosterbroek, P and Starý, J and Sousa, P and Mata, VA and da Silva, LP and Paupério, J and Beja, P},
title = {The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Diptera 02 - Limoniidae, Pediciidae and Tipulidae.},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e69841},
pmid = {34690515},
issn = {1314-2828},
abstract = {BACKGROUND: The InBIO Barcoding Initiative (IBI) Diptera 02 dataset contains records of 412 crane fly specimens belonging to the Diptera families: Limoniidae, Pediciidae and Tipulidae. This dataset is the second release by IBI on Diptera and it greatly increases the knowledge on the DNA barcodes and distribution of crane flies from Portugal. All specimens were collected in Portugal, including six specimens from the Azores and Madeira archipelagos. Sampling took place from 2003 to 2019. Specimens have been morphologically identified to species level by taxonomists and belong to 83 species in total. The species, represented in this dataset, correspond to about 55% of all the crane fly species known from Portugal and 22% of crane fly species known from the Iberian Peninsula. All DNA extractions and most specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources.<br><br>NEW INFORMATION: Fifty-three species were new additions to the Barcode of Life Data System (BOLD), with another 18 species' barcodes added from under-represented species in BOLD. Furthermore, the submitted sequences were found to cluster in 88 BINs, 54 of which were new to BOLD. All specimens have their DNA barcodes publicly accessible through BOLD online database and its collection data can be accessed through the Global Biodiversity Information Facility (GBIF). One species, Gonomyiatenella (Limoniidae), is recorded for the first time from Portugal, raising the number of crane flies recorded in the country to 145 species.},
}
@article {pmid34690511,
year = {2021},
author = {Lindemann, JP and Søli, G and Kjærandsen, J},
title = {Revision of the Exechiaparva group (Diptera: Mycetophilidae).},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e67134},
pmid = {34690511},
issn = {1314-2828},
abstract = {BACKGROUND: Exechia is a diverse genus of small fungus gnats, widespread in the Holarctic Region, while the fauna is largely unknown elsewhere, such as in the Afrotropical and Oriental Region. Members of Exechia can be arranged into several species groups, based on homologies in the male and female terminalia. The Exechiaparva group is delimited, based on male terminalia possessing a pair of gonocoxal lobes on the apicoventral gonocoxal margin. Eight previously-described species can be placed in this group, of which six are from the Holarctic Region, while one is recorded each from the Oriental and the Afrotropical Regions.<br><br>NEW INFORMATION: The Exechiaparva group was reviewed and found to include 33 species, of which 24 were described as new to science and six were re-described. Identification keys to 32 species for males and nine species for females are provided together with illustrations and photos of male and female terminalia. Species delimitations were based on morphological examination of 94 male and female specimens, as well as DNA barcodes obtained from 124 specimens. Molecular and morphological species delimitations were mostly congruent, except in two cases where two species were delimited within a single Barcode Index Number (BIN). We found that each species is only known from a single zoogeographical region and that several species complexes are largely congruent with zoogeographical divisions, indicating that intercontinental barriers may have a strong impact on the species diversity of the group.},
}
@article {pmid34687704,
year = {2022},
author = {Millar, EN and Surette, MG and Kidd, KA},
title = {Altered microbiomes of aquatic macroinvertebrates and riparian spiders downstream of municipal wastewater effluents.},
journal = {The Science of the total environment},
volume = {809},
number = {},
pages = {151156},
doi = {10.1016/j.scitotenv.2021.151156},
pmid = {34687704},
issn = {1879-1026},
mesh = {Animals ; Insecta ; *Microbiota ; Ontario ; RNA, Ribosomal, 16S/genetics ; *Spiders ; Wastewater ; },
abstract = {Municipal wastewater treatment plants (WWTPs) contain numerous contaminants, including antimicrobials, that could affect the composition of the beneficial bacterial communities associated with host aquatic organisms. There is also potential for these effects to transfer to terrestrial predators. Riparian spiders and five families of aquatic macroinvertebrates were collected from sites upstream and downstream of two WWTPs, Waterloo and Kitchener, discharging to the Grand River, Ontario, Canada. Whole-body microbiota were analyzed following the extraction, PCR amplification, and sequencing of bacterial DNA using the V3-V4 hypervariable regions of the 16S rRNA genetic barcode. Changes in the relative abundance of major microbiome phyla were observed in all downstream aquatic insects except Hydropsychidae caddisflies, which exhibited little site variation. Shannon alpha diversity differed among sites for Tetragnathidae spiders, Perlidae, Hydropsychidae, and Heptageniidae. Downstream of the Waterloo WWTP alpha diversity decreased in spiders, while downstream of the Kitchener WWTP this measure decreased in Perlidae and increased in spiders. Bray-Curtis beta diversity was dissimilar among sites in all invertebrate taxa; upstream sites differed from those downstream of Waterloo in spiders, Perlidae, and Hydropsychidae, and from those downstream of Kitchener in spiders, Perlidae, and Hydropsychidae. Finally, effluent-derived bacteria were found in the microbiomes of downstream spiders and aquatic insects and not upstream. Overall, results indicated that the microbiomes of invertebrates collected downstream differed from those collected upstream of WWTPs, which has implications for altered host health and transport of WWTP-derived bacteria through aquatic ecosystems.},
}
@article {pmid34687591,
year = {2022},
author = {Klunder, L and van Bleijswijk, JDL and Kleine Schaars, L and van der Veer, HW and Luttikhuizen, PC and Bijleveld, AI},
title = {Quantification of marine benthic communities with metabarcoding.},
journal = {Molecular ecology resources},
volume = {22},
number = {3},
pages = {1043-1054},
pmid = {34687591},
issn = {1755-0998},
mesh = {Biodiversity ; *DNA Barcoding, Taxonomic/methods ; *DNA, Environmental ; Ecology ; Environmental Monitoring/methods ; },
abstract = {DNA metabarcoding methods have been implemented in studies aimed at detecting and quantifying marine benthic biodiversity. In such surveys, universal barcodes are amplified and sequenced from environmental DNA. To quantify biodiversity with DNA metabarcoding, a relation between the number of DNA sequences of a species and its biomass and/or the abundance is required. However, this relationship is complicated by many factors, and it is often unknown. In this study, we validate estimates of biomass and abundance from molecular approaches with those from the traditional morphological approach. Abundance and biomass were quantified from 126 samples of benthic intertidal mudflat using traditional morphological approaches and compared with frequency of occurrence and relative read abundance estimates from a molecular approach. A relationship between biomass and relative read abundance was found for two widely dispersed annelid taxa (Pygospio and Scoloplos). None of the other taxons, however, showed such a relationship. We discuss how quantification of abundance and biomass using molecular approaches are hampered by the ecology of DNA i.e. all the processes that determine the amount of DNA in the environment, including the ecology of the benthic species as well as the compositional nature of sequencing data.},
}
@article {pmid34686990,
year = {2022},
author = {Fonseca, BM and Câmara, PEAS and Ogaki, MB and Pinto, OHB and Lirio, JM and Coria, SH and Vieira, R and Carvalho-Silva, M and Amorim, ET and Convey, P and Rosa, LH},
title = {Green algae (Viridiplantae) in sediments from three lakes on Vega Island, Antarctica, assessed using DNA metabarcoding.},
journal = {Molecular biology reports},
volume = {49},
number = {1},
pages = {179-188},
pmid = {34686990},
issn = {1573-4978},
mesh = {Antarctic Regions ; Chlorophyta/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Algal/genetics ; DNA, Intergenic/*genetics ; DNA, Ribosomal/*genetics ; High-Throughput Nucleotide Sequencing ; Lakes ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Vega Island is located off the eastern tip of the Antarctic Peninsula (Maritime Antarctica), in the Weddell Sea. In this study, we used metabarcoding to investigate green algal DNA sequence diversity present in sediments from three lakes on Vega Island (Esmeralda, Copépodo, and Pan Negro Lakes).<br><br>METHODS AND RESULTS: Total DNA was extracted and the internal transcribed spacer 2 region of the nuclear ribosomal DNA was used as a DNA barcode for molecular identification. Green algae were represented by sequences representing 78 taxa belonging to Phylum Chlorophyta, of which 32% have not previously been recorded from Antarctica. Sediment from Pan Negro Lake generated the highest number of DNA reads (11,205), followed by Esmeralda (9085) and Cop&#xe9;podo (1595) Lakes. Esmeralda Lake was the richest in terms of number of taxa (59), with Cop&#xe9;podo and Pan Negro Lakes having 30 taxa each. Bray-Curtis dissimilarity among lakes was high (~&#x2009;0.80). The Order Chlamydomonadales (Chlorophyceae) gave the highest contribution in terms of numbers of taxa and DNA reads in all lakes. The most abundant taxon was Chlorococcum microstigmatum.<br><br>CONCLUSIONS: The study confirms the utility of DNA metabarcoding in assessing potential green algal diversity in Antarctic lakes, generating new Antarctic records.},
}
@article {pmid34686666,
year = {2021},
author = {Buddhachat, K and Paenkaew, S and Sripairoj, N and Gupta, YM and Pradit, W and Chomdej, S},
title = {Bar-cas12a, a novel and rapid method for plant species authentication in case of Phyllanthus amarus Schumach. &amp; Thonn.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {20888},
pmid = {34686666},
issn = {2045-2322},
mesh = {CRISPR-Cas Systems/*genetics ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; Phyllanthus/*genetics ; RNA, Guide, CRISPR-Cas Systems/genetics ; },
abstract = {Rapid and accurate species diagnosis accelerates performance in numerous biological fields and associated areas. However, morphology-based species taxonomy/identification might hinder study and lead to ambiguous results. DNA barcodes (Bar) has been employed extensively for plant species identification. Recently, CRISPR-cas system can be applied for diagnostic tool to detect pathogen's DNA based on the collateral activity of cas12a or cas13. Here, we developed barcode-coupled with cas12a assay, "Bar-cas12a" for species authentication using Phyllanthus amarus as a model. The gRNAs were designed from trnL region, namely gRNA-A and gRNA-B. As a result, gRNA-A was highly specific to P. amarus amplified by RPA in contrast to gRNA-B even in contaminated condition. Apart from the large variation of gRNA-A binding in DNA target, cas12a- specific PAM's gRNA-A as TTTN can be found only in P. amarus. PAM site may be recognized one of the potential regions for increasing specificity to authenticate species. In addition, the sensitivity of Bar-cas12a using both gRNAs gave the same detection limit at 0.8 fg and it was 1,000 times more sensitive compared to agarose gel electrophoresis. This approach displayed the accuracy degree of 90% for species authentication. Overall, Bar-cas12a using trnL-designed gRNA offer a highly specific, sensitive, speed, and simple approach for plant species authentication. Therefore, the current method serves as a promising tool for species determination which is likely to be implemented for onsite testing.},
}
@article {pmid34686316,
year = {2021},
author = {Wang, K and Xiao, Z and Yan, Y and Ye, R and Hu, M and Bai, S and Sei, E and Qiao, Y and Chen, H and Lim, B and Lin, SH and Navin, NE},
title = {Simple oligonucleotide-based multiplexing of single-cell chromatin accessibility.},
journal = {Molecular cell},
volume = {81},
number = {20},
pages = {4319-4332.e10},
pmid = {34686316},
issn = {1097-4164},
support = {P30 CA016672/CA/NCI NIH HHS/United States ; R01 CA236864/CA/NCI NIH HHS/United States ; R01 CA240526/CA/NCI NIH HHS/United States ; U01 CA216468/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Antineoplastic Agents/pharmacology ; Chemoradiotherapy ; Chromatin/genetics/*metabolism ; *Chromatin Assembly and Disassembly ; Chromatin Immunoprecipitation Sequencing ; *Epigenesis, Genetic ; Female ; *Gene Expression Regulation, Neoplastic ; *Genetic Heterogeneity ; Humans ; K562 Cells ; Kinetics ; Lung Neoplasms/genetics/*metabolism/pathology/therapy ; Male ; Mice, 129 Strain ; RNA-Seq ; Radiotherapy Dosage ; *Single-Cell Analysis ; Transcription Factors/genetics/*metabolism ; Mice ; },
abstract = {Microdroplet single-cell ATAC-seq is widely used to measure chromatin accessibility, however, highly scalable and simple sample multiplexing procedures are not available. Here, we present a transposome-assisted single nucleus barcoding approach for ATAC-seq (SNuBar-ATAC) that utilizes a single oligonucleotide adaptor for multiplexing samples during the existing tagmentation step and does not require a pre-labeling procedure. The accuracy and scalability of SNuBar-ATAC was evaluated using cell line mixture experiments. We applied SNuBar-ATAC to investigate treatment-induced chromatin accessibility dynamics by multiplexing 28 mice with lung tumors that received different combinations of chemo, radiation, and targeted immunotherapy. We also applied SNuBar-ATAC to study spatial epigenetic heterogeneity by multiplexing 32 regions from a human breast tissue. Additionally, we show that SNuBar can multiplex single cell ATAC and RNA multiomic assays in cell lines and human breast tissue samples. Our data show that SNuBar is a highly accurate, easy-to-use, and scalable system for multiplexing scATAC-seq and scATAC and RNA co-assay experiments.},
}
@article {pmid34686008,
year = {2021},
author = {Alkaraki, AK and Aldmoor, MA and Lahham, JN and Awad, M},
title = {DNA Barcoding of Two Thymelaeaceae Species: Daphne mucronata Royle and Thymelaea hirsuta (L.) Endl.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {10},
pages = {},
pmid = {34686008},
issn = {2223-7747},
support = {17/2020//Yarmouk University/ ; },
abstract = {Daphne mucronata Royle and Thymelaea hirsuta (L.) Endl both belong to the Thymelaeaceae family. Both species are used traditionally to treat several diseases along with various daily applications by Jordanian Bedouins. Traditionally, those species are identified through personal proficiency, which could be misleading due to human errors or lack of expertise. This study aims to investigate an effective DNA barcoding method to identify and characterize Daphne mucronata Royle and Thymelaea hirsuta plant species at the molecular level. Daphne mucronata Royle and Thymelaea hirsuta were collected from the ancient city of Petra in the Southern part of Jordan. Sequences of candidate DNA barcodes were amplified (rbcL, matK, and rpoC1), sequenced, and aligned to the blastn database. Moreover, the obtained sequences were compared with available sequences of related species at the GenBank database. Our results showed that DNA barcoding successfully identifies the two plant species using any of chloroplast genes (rbcL, matK, or rpoC1). The results emphasize the ability of DNA barcoding for identifying and characterizing different plant species through the recruitment of different barcode loci in molecular identification.},
}
@article {pmid34685929,
year = {2021},
author = {Frigerio, J and Agostinetto, G and Mezzasalma, V and De Mattia, F and Labra, M and Bruno, A},
title = {DNA-Based Herbal Teas' Authentication: An ITS2 and psbA-trnH Multi-Marker DNA Metabarcoding Approach.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {10},
pages = {},
pmid = {34685929},
issn = {2223-7747},
support = {Dipartimenti di Eccellenza-2017//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; },
abstract = {Medicinal plants have been widely used in traditional medicine due to their therapeutic properties. Although they are mostly used as herbal infusion and tincture, employment as ingredients of food supplements is increasing. However, fraud and adulteration are widespread issues. In our study, we aimed at evaluating DNA metabarcoding as a tool to identify product composition. In order to accomplish this, we analyzed fifteen commercial products with DNA metabarcoding, using two barcode regions: psbA-trnH and ITS2. Results showed that on average, 70% (44-100) of the declared ingredients have been identified. The ITS2 marker appears to identify more species (n = 60) than psbA-trnH (n = 35), with an ingredients' identification rate of 52% versus 45%, respectively. Some species are identified only by one marker rather than the other. Additionally, in order to evaluate the quantitative ability of high-throughput sequencing (HTS) to compare the plant component to the corresponding assigned sequences, in the laboratory, we created six mock mixtures of plants starting both from biomass and gDNA. Our analysis also supports the application of DNA metabarcoding for a relative quantitative analysis. These results move towards the application of HTS analysis for studying the composition of herbal teas for medicinal plants' traceability and quality control.},
}
@article {pmid34685901,
year = {2021},
author = {Purahong, W and Tanunchai, B and Wahdan, SFM and Buscot, F and Schulze, ED},
title = {Molecular Screening of Microorganisms Associated with Discolored Wood in Dead European Beech Trees Suffered from Extreme Drought Event Using Next Generation Sequencing.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {10},
pages = {},
pmid = {34685901},
issn = {2223-7747},
abstract = {Drought events weaken trees and make them vulnerable to attacks by diverse plant pathogens. Here, we propose a molecular method for fast screening of microorganisms associated with European beech decline after an extreme drought period (2018) in a forest of Thuringia, Germany. We used Illumina sequencing with a recent bioinformatics approach based on DADA2 to identify archaeal, bacterial, and fungal ASVs (amplicon sequence variants) based on bacterial and archaeal 16S and fungal ITS genes. We show that symptomatic beech trees are associated with both bacterial and fungal plant pathogens. Although the plant pathogen sequences were detected in both discolored and non-discolored wood areas, they were highly enriched in the discolored wood areas. We show that almost each individual tree was associated with a different combination of pathogens. Cytospora spp. and Neonectria coccinea were among the most frequently detected fungal pathogens, whereas Erwinia spp. and Pseudomonas spp. were the dominant bacterial plant pathogens. We demonstrate that bacterial plant pathogens may be of major importance in beech decline.},
}
@article {pmid34685843,
year = {2021},
author = {Liu, Q and Guo, S and Zheng, X and Shen, X and Zhang, T and Liao, B and He, W and Hu, H and Cheng, R and Xu, J},
title = {Licorice Germplasm Resources Identification Using DNA Barcodes Inner-Variants.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {10},
pages = {},
pmid = {34685843},
issn = {2223-7747},
abstract = {Based on the gradual transformation from wild growth to artificial cultivation, the accurate authentication of licorice seeds contributes to the first committed step of its quality control and is pivotal to ensure the clinical efficacy of licorice. However, it is still challenging to obtain genetically stable licorice germplasm resources due to the multi-source, multi-heterozygous, polyploid, and hybrid characteristics of licorice seeds. Here, a new method for determining the heterozygosity of licorice seed mixture, based on the various sites, and finding the composition characteristics of licorice seed is preliminarily designed and proposed. Namely, high-throughput full-length multiple DNA barcodes(HFMD), based on ITS multi-copy variation exist, the full-length amplicons of ITS2, psbA-trnH and ITS are directly sequenced by rDNA through the next-generation sequence(NGS) and single-molecule real-time (SMRT) technologies. By comparing the three sequencing methods, our results proved that SMRT sequencing successfully identified the complete gradients of complex mixed samples with the best performance. Meanwhile, HFMD is a brilliant and feasible method for evaluating the heterozygosity of licorice seeds. It shows a perfect interpretation of DNA barcoding and can be applied in multi-base multi-heterozygous and polyploid species.},
}
@article {pmid34685831,
year = {2021},
author = {Thariwong, S and Intharuksa, A and Sirisa-Ard, P and Charoensup, W and Chansakaow, S},
title = {Specification and DNA Barcoding of Thai Traditional Remedy for Chronic Kidney Disease: Pikad Tri-phol-sa-mut-than.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {10},
pages = {},
pmid = {34685831},
issn = {2223-7747},
support = {R000026714//Department of Thai Traditional and Alternative Medicine/ ; },
abstract = {The Pikad Tri-phol-sa-mut-than (TS) remedy, a Thai traditional medicine, is officially recorded in Tamra Paetsart Sonkrau Chabub Anurak for its capabilities in treating kidney deficiency. TS remedy is composed of three fruit species-Aegle marmelos (L.) Corrêa., Coriandrum sativum L., and Morinda citrifolia L.-in an equal part by weight. The quality of the raw material is one of the essential factors that can affect the effectiveness and safety of treatment by herbal remedy. The pharmacognostic evaluation and DNA barcode of the three fruit species and TS remedy were performed in this study to authenticate them from contamination, and to provide the scientific database for further uses. Macroscopic and microscopic examination, chemical profile by TLC, and DNA barcoding were employed to positively identify the raw materials bought from the herbal market, especially the powder form. Consequently, the outcomes of this investigation can be used to develop an essential and effective tool for the authentication of crude drugs and herbal remedies.},
}
@article {pmid34685813,
year = {2021},
author = {Diaz-Silveira, GL and Deutsch, J and Little, DP},
title = {DNA Barcode Authentication of Devil's Claw Herbal Dietary Supplements.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {10},
pages = {},
pmid = {34685813},
issn = {2223-7747},
abstract = {Devil's claw is the vernacular name for a genus of medicinal plants that occur in the Kalahari Desert and Namibia Steppes. The genus comprises two distinct species: Harpagophytum procumbens and H. zeyheri. Although the European pharmacopeia considers the species interchangeable, recent studies have demonstrated that H. procumbens and H. zeyheri are chemically distinct and should not be treated as the same species. Further, the sale of H. zeyheri as an herbal supplement is not legal in the United States. Four markers were tested for their ability to distinguish H. procumbens from H. zeyheri: rbcL, matK, nrITS2, and psbA-trnH. Of these, only psbA-trnH was successful. A novel DNA mini-barcode assay that produces a 178-base amplicon in Harpagophytum (specificity = 1.00 [95% confidence interval = 0.80-1.00]; sensitivity = 1.00 [95% confidence interval = 0.75-1.00]) was used to estimate mislabeling frequency in a sample of 23 devil's claw supplements purchased in the United States. PCR amplification failed in 13% of cases. Among the 20 fully-analyzable supplements: H. procumbens was not detected in 75%; 25% contained both H. procumbens and H. zeyheri; none contained only H. procumbens. We recommend this novel mini-barcode region as a standard method of quality control in the manufacture of devil's claw supplements.},
}
@article {pmid34685791,
year = {2021},
author = {Yang, J and Choi, MJ and Kim, SH and Choi, HJ and Kim, SC},
title = {Plastome Characterization and Phylogenomic Analysis Yield New Insights into the Evolutionary Relationships among the Species of the Subgenus Bryocles (Hosta; Asparagaceae) in East Asia.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {10},
pages = {},
pmid = {34685791},
issn = {2223-7747},
support = {NIBR202107101//National Institute of Biological Resources/ ; },
abstract = {The genus Hosta, which has a native distribution in temperate East Asia and a number of species ranging from 23 to 40, represents a taxonomically important and ornamentally popular plant. Despite its taxonomic and horticultural importance, the genus Hosta has remained taxonomically challenging owing to insufficient diagnostic features, continuous morphological variation, and the process of hybridization and introgression, making species circumscription and phylogenetic inference difficult. In this study, we sequenced 11 accessions of Hosta plastomes, including members of three geographically defined subgenera, Hosta, Bryocles, and Giboshi, determined the characteristics of plastomes, and inferred their phylogenetic relationships. We found highly conserved plastomes among the three subgenera, identified several mutation hotspots that can be used as barcodes, and revealed the patterns of codon usage bias and RNA editing sites. Five positively selected plastome genes (rbcL, rpoB, rpoC2, rpl16, and rpl20) were identified. Phylogenetic analysis suggested (1) the earliest divergence of subg. Hosta, (2) non-monophyly of subg. Bryocles and its two sections (Lamellatae and Stoloniferae), (3) a sister relationship between H. sieboldiana (subg. Giboshi) and H. ventricosa (subg. Bryocles), and (4) reciprocally monophyletic and divergent lineages of H. capitata in Korea and Japan, requiring further studies of their taxonomic distinction.},
}
@article {pmid34681071,
year = {2021},
author = {Kondratov, IG and Sitnikova, TY and Kaygorodova, IA and Denikina, NN and Annenkov, VV and Khanaev, IV and Kirilchik, SV and Nebesnykh, IA and Dzyuba, EV},
title = {Amazing Discoveries of Benthic Fauna from the Abyssal Zone of Lake Baikal.},
journal = {Biology},
volume = {10},
number = {10},
pages = {},
pmid = {34681071},
issn = {2079-7737},
abstract = {Lake Baikal is a natural laboratory for the study of species diversity and evolution, as a unique freshwater ecosystem meeting the all of the main criteria of the World Heritage Convention. However, despite many years of research, the true biodiversity of the lake is clearly insufficiently studied, especially that of deep-water benthic sessile organisms. For the first time, plastic waste was raised from depths of 110 to 190 m of Lake Baikal. The aim of this study was to examine the biological community inhabiting the plastic substrate using morphological and molecular genetic analysis. Fragments of plastic packaging materials were densely populated: bryozoans, leeches and their cocoons, capsules of gastropod eggs, and turbellaria cocoons were found. All the data obtained as a result of an analysis of the nucleotide sequences of the standard bar-coding fragment of the mitochondrial genome turned out to be unique. Our results demonstrate the prospects for conducting comprehensive studies of artificial substrates to determine the true biodiversity of benthos in the abyssal zone of Lake Baikal.},
}
@article {pmid34680699,
year = {2021},
author = {Rodriguez-Soto, MM and Richmond, DS and Ramirez, RA and Xiong, X and Enders, LS},
title = {Characterizing Billbug (Sphenophorus spp.) Seasonal Biology Using DNA Barcodes and a Simple Morphometric Analysis.},
journal = {Insects},
volume = {12},
number = {10},
pages = {},
pmid = {34680699},
issn = {2075-4450},
support = {2017-70006-27274.//National Institute of Food and Agriculture/ ; },
abstract = {Billbugs (Sphenophorus spp.) are a complex of grass-feeding weevil species that reduce the aesthetic and functional qualities of turfgrass. Effective billbug monitoring and management programs rely on a clear understanding of their seasonal biology. However, our limited understanding of regional variation in the species compositions and seasonal biology of billbugs, stemming primarily from our inability to identify the damaging larval stage to species level, has hindered efforts to articulate efficient IPM strategies to growers. We used a combination of DNA barcoding methods and morphometric measures to begin filling critical gaps in our understanding of the seasonal biology of the billbug species complex across a broad geographic range. First, we developed a DNA barcoding reference library using cytochrome oxidase subunit 1 (COI) sequences from morphologically identified adult billbugs collected across Indiana, Missouri, Utah and Arizona. Next, we used our reference library for comparison and identification of unknown larval specimens collected across the growing season in Utah and Indiana. Finally, we combined our DNA barcoding approach with larval head capsule diameter, a proxy for developmental instar, to develop larval phenology charts. Adult COI sequences varied among billbug species, but variation was not influenced by geography, indicating that this locus alone was useful for resolving larval species identity. Overlaid with head capsule diameter data from specimens collected across the growing season, a better visualization of billbug species composition and seasonal biology emerged. This approach will provide researchers with the tools necessary to fill critical gaps in our understanding of billbug biology and facilitate the development of turfgrass pest management programs.},
}
@article {pmid34680660,
year = {2021},
author = {Liu, Z and Yang, SJ and Wang, YY and Peng, YQ and Chen, HY and Luo, SX},
title = {Tackling the Taxonomic Challenges in the Family Scoliidae (Insecta, Hymenoptera) Using an Integrative Approach: A Case Study from Southern China.},
journal = {Insects},
volume = {12},
number = {10},
pages = {},
pmid = {34680660},
issn = {2075-4450},
support = {2018FY100406//Program of Ministry of Science and Technology of China/ ; 2019HJ2096001006//Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China/ ; 20K089//Scientific Research Fund of Hunan Provincial Education Department/ ; 2020JJ5392//Hunan Provincial Natural Science Foundation of China/ ; },
abstract = {Species of the family Scoliidae are larval parasitoids of scarabaeoid beetles and pollinators of various plants. Despite their great importance in pest biological control and plant pollination, the taxonomy and systematics of these parasitoids are far from clear. Some species of the family are extremely morphologically similar and difficult to identify, especially in males. In this study, an integrative taxonomic approach, combining morphology and molecular data, was used to discriminate the species of Scoliidae from southern China. In total, 52 COI sequences belonging to 22 morphospecies of 9 genera in two tribes were obtained. The COI sequences worked well for the identification of all the studied species, with intraspecific genetic distances generally less than 2%, while interspecific distances ranged between 5.3% and 20.8%. The delimitations of the problematic species and subspecies of Scolia and Megacampsomeris are well solved by COI sequences, suggesting that DNA barcoding could be a useful identification tool for Scoliidae. Based on both morphological and molecular evidence, we discovered one undescribed cryptic species of the polytypic species Solia (Discolia) superciliaris Saussure, 1864, five newly recorded species, i.e., Scolia (Discolia) sikkimensis Bingham, 1896, Sericocampsomeris flavomaculata Gupta and Jonathan, 1989, Megacampsomeris asiatica (Saussure, 1858), Megacampsomeris pulchrivestita (Cameron, 1902) and Megacampsomeris shillongensis (Betrem, 1928) and one pending subspecies of Scolia (Discolia) watanabei (Matsumura, 1912) from China. Our study indicates that such an integrative approach, combing both molecular and morphological evidence, is a potent tool to tackle the taxonomic challenges in the family Scoliidae, or even, in other diverse groups of Aculeata, of which sexual dimorphism and cryptic species are common.},
}
@article {pmid34676941,
year = {2022},
author = {Shchepin, O and Novozhilov, Y and Woyzichovski, J and Bog, M and Prikhodko, I and Fedorova, N and Gmoshinskiy, V and Borg Dahl, M and Dagamac, NHA and Yajima, Y and Schnittler, M},
title = {Genetic structure of the protist Physarum albescens (Amoebozoa) revealed by multiple markers and genotyping by sequencing.},
journal = {Molecular ecology},
volume = {31},
number = {1},
pages = {372-390},
doi = {10.1111/mec.16239},
pmid = {34676941},
issn = {1365-294X},
support = {075-15-2021-1056//Ministry of Science and Higher Education of the Russian Federation/ ; DFG//Deutsche Forschungsgemeinschaft/ ; RTG 2010 RESPONSE//Deutsche Forschungsgemeinschaft/ ; SCHN1080/2-1//Deutsche Forschungsgemeinschaft/ ; AAAA-A19-119020890079-6//Komarov Botanical Institute, Russian Academy of Sciences/ ; },
mesh = {*Amoebozoa ; Base Sequence ; Genetic Variation ; Genotype ; Phylogeny ; *Physarum ; },
abstract = {Myxomycetes are terrestrial protists with many presumably cosmopolitan species dispersing via airborne spores. A truly cosmopolitan species would suffer from outbreeding depression hampering local adaptation, while locally adapted species with limited distribution would be at a higher risk of extinction in changing environments. Here, we investigate intraspecific genetic diversity and phylogeography of Physarum albescens over the entire Northern Hemisphere. We sequenced 324 field collections of fruit bodies for 1-3 genetic markers (SSU, EF1A, COI) and analysed 98 specimens with genotyping by sequencing. The structure of the three-gene phylogeny, SNP-based phylogeny, phylogenetic networks, and the observed recombination pattern of three independently inherited gene markers can be best explained by the presence of at least 18 reproductively isolated groups, which can be seen as cryptic species. In all intensively sampled regions and in many localities, members of several phylogroups coexisted. Some phylogroups were found to be abundant in only one region and completely absent in other well-studied regions, and thus may represent regional endemics. Our results demonstrate that the widely distributed myxomycete species Ph. albescens represents a complex of at least 18 cryptic species, and some of these seem to have a limited geographical distribution. In addition, the presence of groups of presumably clonal specimens suggests that sexual and asexual reproduction coexist in natural populations of myxomycetes.},
}
@article {pmid34676606,
year = {2022},
author = {Paulus, E and Brix, S and Siebert, A and Martínez Arbizu, P and Rossel, S and Peters, J and Svavarsson, J and Schwentner, M},
title = {Recent speciation and hybridization in Icelandic deep-sea isopods: An integrative approach using genomics and proteomics.},
journal = {Molecular ecology},
volume = {31},
number = {1},
pages = {313-330},
doi = {10.1111/mec.16234},
pmid = {34676606},
issn = {1365-294X},
support = {BR3843/4-1//Deutsche Forschungsgemeinschaft/ ; BR3843/5-1//Deutsche Forschungsgemeinschaft/ ; RE2808/3-1//Deutsche Forschungsgemeinschaft/ ; RE2808/3-2//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; DNA, Mitochondrial/genetics ; Genetic Speciation ; Genetic Variation ; Genomics ; Iceland ; *Isopoda/genetics ; Male ; Phylogeny ; Phylogeography ; Proteomics ; },
abstract = {The crustacean marine isopod species Haploniscus bicuspis (Sars, 1877) shows circum-Icelandic distribution in a wide range of environmental conditions and along well-known geographic barriers, such as the Greenland-Iceland-Faroe (GIF) Ridge. We wanted to explore population genetics, phylogeography and cryptic speciation as well as investigate whether previously described, but unaccepted subspecies have any merit. Using the same set of specimens, we combined mitochondrial COI sequences, thousands of nuclear loci (ddRAD), and proteomic profiles, plus selected morphological characters using confocal laser scanning microscopy (CLSM). Five divergent genetic lineages were identified by COI and ddRAD, two south and three north of the GIF Ridge. Assignment of populations to the three northern lineages varied and detailed analyses revealed hybridization and gene flow between them, suggesting a single northern species with a complex phylogeographic history. No apparent hybridization was observed among lineages south of the GIF Ridge, inferring the existence of two more species. Differences in proteomic profiles between the three putative species were minimal, implying an ongoing or recent speciation process. Population differentiation was high, even among closely associated populations, and higher in mitochondrial COI than nuclear ddRAD loci. Gene flow is apparently male-biased, leading to hybrid zones and instances of complete exchange of the local nuclear genome through immigrating males. This study did not confirm the existence of subspecies defined by male characters, which probably instead refer to different male developmental stages.},
}
@article {pmid34675260,
year = {2021},
author = {Pérez-Lachaud, G and Rocha, FH and Pozo, C and Kaminski, LA and Seraphim, N and Lachaud, JP},
title = {A new ant-butterfly symbiosis in the forest canopy fills an evolutionary gap.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {20770},
pmid = {34675260},
issn = {2045-2322},
mesh = {Animals ; Ants/anatomy &amp; histology/*physiology ; Behavior, Animal ; Biological Evolution ; Butterflies/anatomy &amp; histology/*physiology ; Forests ; Oviposition ; *Symbiosis ; },
abstract = {Myrmecophilous butterflies can establish complex symbiotic relationships with ants. A caterpillar wandering among the brood of the aggressive ponerine ant Neoponera villosa was found inside the core of a nest built in the myrmecophytic bromeliad Aechmea bracteata. This is the first caterpillar found living inside a ponerine ant nest. Its DNA barcode was sequenced, and an integrative approach was used to identify it as Pseudonymphidia agave, a poorly known member of the subtribe Pachythonina in the riodinid tribe Nymphidiini. The cuticle of the tank-like caterpillar lacks projections or tubercles and is covered dorsally by specialized flat setae that form an armor of small plates. Ant-organs potentially related to caterpillar-ant signaling, such as perforated cupola organs and tentacle nectary organs, are present. These morphological traits, together with evidence of social integration (direct contact with host brood, protective morphology, slow movement, no host aggressiveness), suggest that P. agave is a symbiotic, social parasite of N. villosa, preying on its host brood. However, several knowledge gaps remain, including oviposition site, dependence on bromeliad association, steps to colony integration, and larval diet through development. Carnivory has been reported in all known members of the subtribe Pachythonina (caterpillars prey on honeydew-producing hemipterans) suggesting a shift to myrmecophagy inside the ant nests as a possible evolutionary transition.},
}
@article {pmid34667143,
year = {2021},
author = {Notaras, M and Lodhi, A and Fang, H and Greening, D and Colak, D},
title = {The proteomic architecture of schizophrenia iPSC-derived cerebral organoids reveals alterations in GWAS and neuronal development factors.},
journal = {Translational psychiatry},
volume = {11},
number = {1},
pages = {541},
pmid = {34667143},
issn = {2158-3188},
mesh = {Adult ; Genome-Wide Association Study ; Humans ; *Induced Pluripotent Stem Cells ; Organoids ; Proteomics ; *Schizophrenia/genetics ; },
abstract = {Schizophrenia (Scz) is a brain disorder that has a typical onset in early adulthood but otherwise maintains unknown disease origins. Unfortunately, little progress has been made in understanding the molecular mechanisms underlying neurodevelopment of Scz due to ethical and technical limitations in accessing developing human brain tissue. To overcome this challenge, we have previously utilized patient-derived Induced Pluripotent Stem Cells (iPSCs) to generate self-developing, self-maturating, and self-organizing 3D brain-like tissue known as cerebral organoids. As a continuation of this prior work, here we provide an architectural map of the developing Scz organoid proteome. Utilizing iPSCs from n = 25 human donors (n = 8 healthy Ctrl donors, and n = 17 Scz patients), we generated 3D cerebral organoids, employed 16-plex isobaric sample-barcoding chemistry, and simultaneously subjected samples to comprehensive high-throughput liquid-chromatography/mass-spectrometry (LC/MS) quantitative proteomics. Of 3,705 proteins identified by high-throughput proteomic profiling, we identified that just ~2.62% of the organoid global proteomic landscape was differentially regulated in Scz organoids. In sum, just 43 proteins were up-regulated and 54 were down-regulated in Scz patient-derived organoids. Notably, a range of neuronal factors were depleted in Scz organoids (e.g., MAP2, TUBB3, SV2A, GAP43, CRABP1, NCAM1 etc.). Based on global enrichment analysis, alterations in key pathways that regulate nervous system development (e.g., axonogenesis, axon development, axon guidance, morphogenesis pathways regulating neuronal differentiation, as well as substantia nigra development) were perturbed in Scz patient-derived organoids. We also identified prominent alterations in two novel GWAS factors, Pleiotrophin (PTN) and Podocalyxin (PODXL), in Scz organoids. In sum, this work serves as both a report and a resource that researchers can leverage to compare, contrast, or orthogonally validate Scz factors and pathways identified in observational clinical studies and other model systems.},
}
@article {pmid34666829,
year = {2021},
author = {Alghamdi, SQ and Low, VL and Alkathiry, HA and Alagaili, AN and McGarry, JW and Makepeace, BL},
title = {Automatic barcode gap discovery reveals diverse clades of Rhipicephalus spp. and Haemaphysalis spp. ticks from small mammals in 'Asir, Saudi Arabia.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {541},
pmid = {34666829},
issn = {1756-3305},
mesh = {Animals ; Cyclooxygenase 1/genetics ; DNA Barcoding, Taxonomic/*standards ; Genetic Variation ; Ixodidae/*classification/*genetics ; Male ; Mammals/parasitology ; Nymph ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Rhipicephalus/classification/*genetics ; Saudi Arabia ; Tick Infestations/*veterinary ; },
abstract = {BACKGROUND: The ixodid tick genera Rhipicephalus and Haemaphysalis contain several species of medical and/or veterinary importance, but their diversity in some regions of the world remains under-explored. For instance, very few modern studies have been performed on the taxonomy of these genera on the Arabian Peninsula.<br><br>METHODS: In this study, we trapped small mammals in the 'Asir Mountains of south-western Saudi Arabia and collected tick specimens for morphological examination and molecular barcoding, targeting three mitochondrial loci: cox1, 16S rRNA and 12S rRNA.<br><br>RESULTS: We obtained a total of 733 ticks (608 Haemaphysalis spp. and 125 Rhipicephalus spp.) from 75 small mammal hosts belonging to six species. All tick specimens were immature except for nine adults recovered from a hedgehog (Paraechinus aethiopicus). Morphologically, the Rhipicephalus ticks resembled R. camicasi, but the Haemaphysalis ticks showed differences in palp morphology compared with species previously described from Saudi Arabia. Phylogenetic analysis and automatic barcode gap discovery identified a novel clade of Rhipicephalus sp. representing most of the nymphs. This was most closely related to R. leporis, R. guilhoni and R. linnaei. The adult ticks and a small proportion of nymphs clustered with R. camicasi sequences from a previous study. Finally, the Haemaphysalis nymphs formed two distinct clades that were clearly separated from all reference sequences but closest to some African species.<br><br>CONCLUSIONS: This apparent high level of tick diversity observed in a single study site of only&#x2009;~&#x2009;170 km[2], on a relatively small number of hosts, highlights the potential for the discovery of new tick species on the Arabian Peninsula.},
}
@article {pmid34666483,
year = {2021},
author = {Capocefalo, A and Quintiero, E and Conti, C and Ghofraniha, N and Viola, I},
title = {Droplet Lasers for Smart Photonic Labels.},
journal = {ACS applied materials &amp; interfaces},
volume = {13},
number = {43},
pages = {51485-51494},
pmid = {34666483},
issn = {1944-8252},
abstract = {Microscopic lasers represent a promising tool for the development of cutting-edge photonic devices thanks to their ability to enhance light-matter interaction at the microscale. In this work, we realize liquid microlasers with tunable emission by exploiting the self-formation of three-dimensional liquid droplets into a polymeric matrix driven by viscoelastic dewetting. We design a flexible device to be used as a smart photonic label which is detachable and reusable on various types of substrates such as paper or fabric. The innovative lasing emission mechanism proposed here is based on whispering gallery mode emission coupled to random lasing, the latter prompted by the inclusion of dielectric compounds into the active gain medium. The wide possibility of modulating the emission wavelength of the microlasers by acting on different parameters, such as the cavity size, type and volume fraction of the dielectrics, and gain medium, offers a multitude of spectroscopic encoding schemes for the realization of photonic barcodes and labels to be employed in anticounterfeiting applications and multiplexed bioassays.},
}
@article {pmid34665841,
year = {2021},
author = {Ellepola, G and Herath, J and Manamendra-Arachchi, K and Wijayathilaka, N and Senevirathne, G and Pethiyagoda, R and Meegaskumbura, M},
title = {Molecular species delimitation of shrub frogs of the genus Pseudophilautus (Anura, Rhacophoridae).},
journal = {PloS one},
volume = {16},
number = {10},
pages = {e0258594},
pmid = {34665841},
issn = {1932-6203},
mesh = {Amphibian Proteins/genetics ; Animals ; Anura/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; Databases, Genetic ; Homeodomain Proteins/*genetics ; India ; Phylogeny ; Phylogeography ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; },
abstract = {Sri Lanka is an amphibian hotspot of global significance. Its anuran fauna is dominated by the shrub frogs of the genus Pseudophilautus. Except for one small clade of four species in Peninsular India, these cool-wet adapted frogs, numbering some 59 extant species, are distributed mainly across the montane and lowland rain forests of the island. With species described primarily by morphological means, the diversification has never yet been subjected to a molecular species delimitation analysis, a procedure now routinely applied in taxonomy. Here we test the species boundaries of Pseudophilautus in the context of the phylogenetic species concept (PSC). We use all the putative species for which credible molecular data are available (nDNA-Rag-1; mt-DNA- 12S rRNA, 16S rRNA) to build a well resolved phylogeny, which is subjected to species delimitation analyses. The ABGD, bPTP, mPTP and bGMYC species delimitation methods applied to the 16S rRNA frog barcoding gene (for all species), 12S rRNA and Rag-1 nDNA grouped P. procax and P. abundus; P. hallidayi and P. fergusonianus; P. reticulatus and P. pappilosus; P. pleurotaenia and P. hoipolloi; P. hoffmani and P. asankai; P. silvaticus and P. limbus; P. dilmah and P. hankeni; P. fulvus and P. silus.. Surprisingly, all analyses recovered 14 unidentified potential new species as well. The geophylogeny affirms a distribution across the island's aseasonal 'wet zone' and its three principal hill ranges, suggestive of allopatric speciation playing a dominant role, especially between mountain masses. Among the species that are merged by the delimitation analyses, a pattern leading towards a model of parapatric speciation emerges-ongoing speciation in the presence of gene flow. This delimitation analysis reinforces the species hypotheses, paving the way to a reasonable understanding of Sri Lankan Pseudophilautus, enabling both deeper analyses and conservation efforts of this remarkable diversification. http://zoobank.org/urn:lsid:zoobank.org:pub:DA869B6B-870A-4ED3-BF5D-5AA3F69DDD27.},
}
@article {pmid34665731,
year = {2022},
author = {Elhami, G and Scholefield, A and Vetterli, M},
title = {Three-Dimensional Cubic Barcodes.},
journal = {IEEE transactions on image processing : a publication of the IEEE Signal Processing Society},
volume = {31},
number = {},
pages = {3166-3181},
doi = {10.1109/TIP.2021.3120049},
pmid = {34665731},
issn = {1941-0042},
abstract = {We consider three-dimensional cubic barcodes, consisting of smaller cubes, each built from one of two possible materials and carry one bit of information. To retrieve the information stored in the barcode, we measure a 2D projection of the barcode using a penetrating wave such as X-rays, either using parallel-beam or cone-beam scanners from an unknown direction. We derive a theoretical representation of this scanning process and show that for a known barcode pose with respect to the scanner, the projection operator is linear and can be easily inverted. Moreover, we provide a method to estimate the unknown pose of the barcode from a single 2D scan. We also propose coding schemes to correct errors and ambiguities in the reconstruction process. Finally, we test our designed barcode and reconstruction algorithms with several simulations, as well as a real-world barcode acquired with an X-ray cone-beam scanner, as a proof of concept.},
}
@article {pmid34665332,
year = {2021},
author = {Zeng, S and Li, J and Yang, Q and Wu, Y and Yu, J and Pei, X and Yu, J},
title = {Comparative plastid genomics of Mazaceae: focusing on a new recognized genus, Puchiumazus.},
journal = {Planta},
volume = {254},
number = {5},
pages = {99},
pmid = {34665332},
issn = {1432-2048},
support = {31772260//national natural science foundation of china/ ; cx2019052//chongqing municipal education commission foundation/ ; },
mesh = {*Evolution, Molecular ; Genomics ; *Lamiales ; Phylogeny ; Plastids/genetics ; },
abstract = {Six Mazaceae plastomes were assembled in this study, including the newly recognized genus, Puchiumazus. Comparative plastid genomic analysis provided new insights into Mazaceae. The phylogenetic categorization of Mazus lanceifolius (Mazaceae) has long been uncertain. In 2021, the scholars Bo Li, D. G. Zhang, and C. L. Xiang republished M. lanceifolius as a new species Puchiumazus lanceifolius, within a new genus Puchiumazus. However, there is little plastome information on Mazaceae. Following the publishing of the new genus Puchiumazus, it is now necessary to study the Mazaceae plastome features to comprehensively understand this young family. The Mazaceae plastomes all have a typical quartile structure. The plastomes have a size ranging from 152,388 to 154,252 bp, and each plastome contains 112 unique genes, including 78 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. A comparative analysis showed that these plastome sequences are highly conserved. Furthermore, we identified four relatively hypervariable regions (trnQ-UUC-psbK, trnS-GCU- trnS-CGA, trnT-UGU-trnL-UAA and ycf1) that can be used as potential DNA barcodes for the identification of this clade. Phylogenetic relationships based on the whole plastome sequences of 25 samples of 14 genera of Lamiales placed M. lanceifolius in the basal clade of the family Mazaceae, with 100% bootstrap support. In summary, the M. lanceifolius results indicate that a new monotype genus (Puchiumazus) should be established at the whole-plastome level. This study provides plastid genomic resources for exploring the phylogeny of Mazaceae.},
}
@article {pmid35935896,
year = {2021},
author = {Visagie, CM and Frisvad, JC and Houbraken, J and Visagie, A and Samson, RA and Jacobs, K},
title = {A re-evaluation of Penicillium section Canescentia, including the description of five new species.},
journal = {Persoonia},
volume = {46},
number = {},
pages = {163-187},
pmid = {35935896},
issn = {0031-5850},
abstract = {A survey of Penicillium in the fynbos biome from South Africa resulted in the isolation of 61 species of which 29 were found to be new. In this study we focus on Penicillium section Canescentia, providing a phylogenetic re-evaluation based on the analysis of partial beta-tubulin (BenA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) sequence data. Based on phylogenies we show that five fynbos species are new and several previously assigned synonyms of P. canescens and P. janczewskii should be considered as distinct species. As such, we provide descriptions for the five new species and introduce the new name P. elizabethiae for the illegitimate P. echinatum. We also update the accepted species list and synonymies of section Canescentia species and provide a review of extrolites produced by these species. Citation: Visagie CM, Frisvad JC, Houbraken J, et al. 2021. A re-evaluation of Penicillium section Canescentia, including the description of five new species. Persoonia 46: 163-187. https://doi.org/10.3767/persoonia.2021.46.06.},
}
@article {pmid35935893,
year = {2021},
author = {Crous, PW and Cowan, DA and Maggs-Kölling, G and Yilmaz, N and Thangavel, R and Wingfield, MJ and Noordeloos, ME and Dima, B and Brandrud, TE and Jansen, GM and Morozova, OV and Vila, J and Shivas, RG and Tan, YP and Bishop-Hurley, S and Lacey, E and Marney, TS and Larsson, E and Le Floch, G and Lombard, L and Nodet, P and Hubka, V and Alvarado, P and Berraf-Tebbal, A and Reyes, JD and Delgado, G and Eichmeier, A and Jordal, JB and Kachalkin, AV and Kubátová, A and Maciá-Vicente, JG and Malysheva, EF and Papp, V and Rajeshkumar, KC and Sharma, A and Spetik, M and Szabóová, D and Tomashevskaya, MA and Abad, JA and Abad, ZG and Alexandrova, AV and Anand, G and Arenas, F and Ashtekar, N and Balashov, S and Bañares, &#xc1; and Baroncelli, R and Bera, I and Biketova, AY and Blomquist, CL and Boekhout, T and Boertmann, D and Bulyonkova, TM and Burgess, TI and Carnegie, AJ and Cobo-Diaz, JF and Corriol, G and Cunnington, JH and da Cruz, MO and Damm, U and Davoodian, N and de A Santiago, ALCM and Dearnaley, J and de Freitas, LWS and Dhileepan, K and Dimitrov, R and Di Piazza, S and Fatima, S and Fuljer, F and Galera, H and Ghosh, A and Giraldo, A and Glushakova, AM and Gorczak, M and Gouliamova, DE and Gramaje, D and Groenewald, M and Gunsch, CK and Gutiérrez, A and Holdom, D and Houbraken, J and Ismailov, AB and Istel, &#x141; and Iturriaga, T and Jeppson, M and Jurjević, &#x17d; and Kalinina, LB and Kapitonov, VI and Kautmanová, I and Khalid, AN and Kiran, M and Kiss, L and Kovács, &#xc1; and Kurose, D and Kušan, I and Lad, S and Læssøe, T and Lee, HB and Luangsa-Ard, JJ and Lynch, M and Mahamedi, AE and Malysheva, VF and Mateos, A and Matočec, N and Mešić, A and Miller, AN and Mongkolsamrit, S and Moreno, G and Morte, A and Mostowfizadeh-Ghalamfarsa, R and Naseer, A and Navarro-Ródenas, A and Nguyen, TTT and Noisripoom, W and Ntandu, JE and Nuytinck, J and Ostrý, V and Pankratov, TA and Pawłowska, J and Pecenka, J and Pham, THG and Polhorský, A and Pošta, A and Raudabaugh, DB and Reschke, K and Rodríguez, A and Romero, M and Rooney-Latham, S and Roux, J and Sandoval-Denis, M and Smith, MT and Steinrucken, TV and Svetasheva, TY and Tkalčec, Z and van der Linde, EJ and V D Vegte, M and Vauras, J and Verbeken, A and Visagie, CM and Vitelli, JS and Volobuev, SV and Weill, A and Wrzosek, M and Zmitrovich, IV and Zvyagina, EA and Groenewald, JZ},
title = {Fungal Planet description sheets: 1182-1283.},
journal = {Persoonia},
volume = {46},
number = {},
pages = {313-528},
pmid = {35935893},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Algeria, Phaeoacremonium adelophialidum from Vitis vinifera. Antarctica, Comoclathris antarctica from soil. Australia, Coniochaeta salicifolia as endophyte from healthy leaves of Geijera salicifolia, Eremothecium peggii in fruit of Citrus australis, Microdochium ratticaudae from stem of Sporobolus natalensis, Neocelosporium corymbiae on stems of Corymbia variegata, Phytophthora kelmanii from rhizosphere soil of Ptilotus pyramidatus, Pseudosydowia backhousiae on living leaves of Backhousia citriodora, Pseudosydowia indooroopillyensis, Pseudosydowia louisecottisiae and Pseudosydowia queenslandica on living leaves of Eucalyptus sp. Brazil, Absidia montepascoalis from soil. Chile, Ilyonectria zarorii from soil under Maytenus boaria. Costa Rica, Colletotrichum filicis from an unidentified fern. Croatia, Mollisia endogranulata on deteriorated hardwood. Czech Republic, Arcopilus navicularis from tea bag with fruit tea, Neosetophoma buxi as endophyte from Buxus sempervirens, Xerochrysium bohemicum on surface of biscuits with chocolate glaze and filled with jam. France, Entoloma cyaneobasale on basic to calcareous soil, Fusarium aconidiale from Triticum aestivum, Fusarium juglandicola from buds of Juglans regia. Germany, Tetraploa endophytica as endophyte from Microthlaspi perfoliatum roots. India, Castanediella ambae on leaves of Mangifera indica, Lactifluus kanadii on soil under Castanopsis sp., Penicillium uttarakhandense from soil. Italy, Penicillium ferraniaense from compost. Namibia, Bezerromyces gobabebensis on leaves of unidentified succulent, Cladosporium stipagrostidicola on leaves of Stipagrostis sp., Cymostachys euphorbiae on leaves of Euphorbia sp., Deniquelata hypolithi from hypolith under a rock, Hysterobrevium walvisbayicola on leaves of unidentified tree, Knufia hypolithi and Knufia walvisbayicola from hypolith under a rock, Lapidomyces stipagrostidicola on leaves of Stipagrostis sp., Nothophaeotheca mirabibensis (incl. Nothophaeotheca gen. nov.) on persistent inflorescence remains of Blepharis obmitrata, Paramyrothecium salvadorae on twigs of Salvadora persica, Preussia procaviicola on dung of Procavia sp., Sordaria equicola on zebra dung, Volutella salvadorae on stems of Salvadora persica. Netherlands, Entoloma ammophilum on sandy soil, Entoloma pseudocruentatum on nutrient poor (acid) soil, Entoloma pudens on plant debris, amongst grasses. New Zealand, Amorocoelophoma neoregeliae from leaf spots of Neoregelia sp., Aquilomyces metrosideri and Septoriella callistemonis from stem discolouration and leaf spots of Metrosideros sp., Cadophora neoregeliae from leaf spots of Neoregelia sp., Flexuomyces asteliae (incl. Flexuomyces gen. nov.) and Mollisia asteliae from leaf spots of Astelia chathamica, Ophioceras freycinetiae from leaf spots of Freycinetia banksii, Phaeosphaeria caricis-sectae from leaf spots of Carex secta. Norway, Cuphophyllus flavipesoides on soil in semi-natural grassland, Entoloma coracis on soil in calcareous Pinus and Tilia forests, Entoloma cyaneolilacinum on soil semi-natural grasslands, Inocybe norvegica on gravelly soil. Pakistan, Butyriboletus parachinarensis on soil in association with Quercus baloot. Poland, Hyalodendriella bialowiezensis on debris beneath fallen bark of Norway spruce Picea abies. Russia, Bolbitius sibiricus on à moss covered rotting trunk of Populus tremula, Crepidotus wasseri on debris of Populus tremula, Entoloma isborscanum on soil on calcareous grasslands, Entoloma subcoracis on soil in subalpine grasslands, Hydropus lecythiocystis on rotted wood of Betula pendula, Meruliopsis faginea on fallen dead branches of Fagus orientalis, Metschnikowia taurica from fruits of Ziziphus jujube, Suillus praetermissus on soil, Teunia lichenophila as endophyte from Cladonia rangiferina. Slovakia, Hygrocybe fulgens on mowed grassland, Pleuroflammula pannonica from corticated branches of Quercus sp. South Africa, Acrodontium burrowsianum on leaves of unidentified Poaceae, Castanediella senegaliae on dead pods of Senegalia ataxacantha, Cladophialophora behniae on leaves of Behnia sp., Colletotrichum cliviigenum on leaves of Clivia sp., Diatrype dalbergiae on bark of Dalbergia armata, Falcocladium heteropyxidicola on leaves of Heteropyxis canescens, Lapidomyces aloidendricola as epiphyte on brown stem of Aloidendron dichotomum, Lasionectria sansevieriae and Phaeosphaeriopsis sansevieriae on leaves of Sansevieria hyacinthoides, Lylea dalbergiae on Diatrype dalbergiae on bark of Dalbergia armata, Neochaetothyrina syzygii (incl. Neochaetothyrina gen. nov.) on leaves of Syzygium chordatum, Nothophaeomoniella ekebergiae (incl. Nothophaeomoniella gen. nov.) on leaves of Ekebergia pterophylla, Paracymostachys euphorbiae (incl. Paracymostachys gen. nov.) on leaf litter of Euphorbia ingens, Paramycosphaerella pterocarpi on leaves of Pterocarpus angolensis, Paramycosphaerella syzygii on leaf litter of Syzygium chordatum, Parateichospora phoenicicola (incl. Parateichospora gen. nov.) on leaves of Phoenix reclinata, Seiridium syzygii on twigs of Syzygium chordatum, Setophoma syzygii on leaves of Syzygium sp., Starmerella xylocopis from larval feed of an Afrotropical bee Xylocopa caffra, Teratosphaeria combreti on leaf litter of Combretum kraussii, Teratosphaericola leucadendri on leaves of Leucadendron sp., Toxicocladosporium pterocarpi on pods of Pterocarpus angolensis. Spain, Cortinarius bonachei with Quercus ilex in calcareus soils, Cortinarius brunneovolvatus under Quercus ilex subsp. ballota in calcareous soil, Extremopsis radicicola (incl. Extremopsis gen. nov.) from root-associated soil in a wet heathland, Russula quintanensis on acidic soils, Tubaria vulcanica on volcanic lapilii material, Tuber zambonelliae in calcareus soil. Sweden, Elaphomyces borealis on soil under Pinus sylvestris and Betula pubescens. Tanzania, Curvularia tanzanica on inflorescence of Cyperus aromaticus. Thailand, Simplicillium niveum on Ophiocordyceps camponoti-leonardi on underside of unidentified dicotyledonous leaf. USA, Calonectria californiensis on leaves of Umbellularia californica, Exophiala spartinae from surface sterilised roots of Spartina alterniflora, Neophaeococcomyces oklahomaensis from outside wall of alcohol distillery. Vietnam, Fistulinella aurantioflava on soil. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Cowan DA, Maggs-Kölling, et al. 2021. Fungal Planet description sheets: 1182-1283. Persoonia 46: 313-528. https://doi.org/10.3767/persoonia.2021.46.11.},
}
@article {pmid35935888,
year = {2021},
author = {Ammirati, J and Liimatainen, K and Bojantchev, D and Peintner, U and Kuhnert-Finkernagel, R and Cripps, C and Dentinger, B and Niskanen, T},
title = {Cortinarius subgenus Leprocybe, unexpected diversity and significant differences in species compositions between western and eastern North America.},
journal = {Persoonia},
volume = {46},
number = {},
pages = {216-239},
pmid = {35935888},
issn = {0031-5850},
abstract = {The focus of this paper is the North American species of Cortinarius in subg. Leprocybe. Eighteen species, including twelve new ones, and two tentative (aff.) species, are delimited based on morphological and molecular data (DNA ITS-LSU sequences). Existing type specimens of species in subg. Leprocybe were also studied, and neo- or epitypes designated for C. cotoneus, C. melanotus, C. phrygianus and C. venetus to stabilize the nomenclature. In addition, to improve the infrasubgeneric classification of Leprocybe three new sections are proposed: sect. Fuscotomentosi, sect. Melanoti and sect. Squamiveneti. This study adds substantial information to the knowledge of subg. Leprocybe in North America against a background of European species. To date only two species, C. phrygianus and C. squamivenetus have been reported from both continents. Citation: Ammirati J, Liimatainen K, Bojantchev D, et al. 2021. Cortinarius subgenus Leprocybe, unexpected diversity and significant differences in species compositions between western and eastern North America. Persoonia 46: 216-239. https://doi.org/10.3767/persoonia.2021.46.08.},
}
@article {pmid35935886,
year = {2021},
author = {Zhang, W and Groenewald, JZ and Lombard, L and Schumacher, RK and Phillips, AJL and Crous, PW},
title = {Evaluating species in Botryosphaeriales.},
journal = {Persoonia},
volume = {46},
number = {},
pages = {63-115},
pmid = {35935886},
issn = {0031-5850},
abstract = {The Botryosphaeriales (Dothideomycetes) includes numerous endophytic, saprobic, and plant pathogenic species associated with a wide range of symptoms, most commonly on woody plants. In a recent phylogenetic treatment of 499 isolates in the culture collection (CBS) of the Westerdijk Institute, we evaluated the families and genera accommodated in this order of important fungi. The present study presents multigene phylogenetic analyses for an additional 230 isolates, using ITS, tef1, tub2, LSU and rpb2 loci, in combination with morphological data. Based on these data, 58 species are reduced to synonymy, and eight novel species are described. They include Diplodia afrocarpi (Afrocarpus, South Africa), Dothiorella diospyricola (Diospyros, South Africa), Lasiodiplodia acaciae (Acacia, Indonesia), Neofusicoccum podocarpi (Podocarpus, South Africa), N. rapaneae (Rapanea, South Africa), Phaeobotryon ulmi (Ulmus, Germany), Saccharata grevilleae (Grevillea, Australia) and S. hakeiphila (Hakea, Australia). The results have clarified the identity of numerous isolates that lacked Latin binomials or had been deposited under incorrect names in the CBS collection in the past. They also provide a solid foundation for more in-depth future studies on taxa in the order. Sequences of the tef1, tub2 and rpb2 genes proved to be the most reliable markers. At the species level, results showed that the most informative genes were inconsistent, but that a combination of four candidate barcodes (ITS, tef1, tub2 and rpb2) provided reliable resolution. Furthermore, given the large number of additional isolates included in this study, and newly generated multigene DNA datasets, several species could also be reduced to synonymy. The study illustrates the value of reassessing the identity of older collections in culture collections utilising modern taxonomic frameworks and methods. Citation: Zhang W, Groenewald JZ, Lombard L, et al. 2021. Evaluating species in Botryosphaeriales. Persoonia 46: 63-115. https://doi.org/10.3767/persoonia.2021.46.03.},
}
@article {pmid35990087,
year = {2021},
author = {Feng, J and Dewitt, WS and McKenna, A and Simon, N and Willis, AD and Matsen, FA},
title = {ESTIMATION OF CELL LINEAGE TREES BY MAXIMUM-LIKELIHOOD PHYLOGENETICS.},
journal = {The annals of applied statistics},
volume = {15},
number = {1},
pages = {343-362},
pmid = {35990087},
issn = {1932-6157},
support = {R00 HG010152/HG/NHGRI NIH HHS/United States ; F31 AI150163/AI/NIAID NIH HHS/United States ; K99 HG010152/HG/NHGRI NIH HHS/United States ; T32 HG000035/HG/NHGRI NIH HHS/United States ; DP5 OD019820/OD/NIH HHS/United States ; R01 AI146028/AI/NIAID NIH HHS/United States ; R01 GM113246/GM/NIGMS NIH HHS/United States ; },
abstract = {CRISPR technology has enabled cell lineage tracing for complex multicellular organisms through insertion-deletion mutations of synthetic genomic barcodes during organismal development. To reconstruct the cell lineage tree from the mutated barcodes, current approaches apply general-purpose computational tools that are agnostic to the mutation process and are unable to take full advantage of the data's structure. We propose a statistical model for the CRISPR mutation process and develop a procedure to estimate the resulting tree topology, branch lengths, and mutation parameters by iteratively applying penalized maximum likelihood estimation. By assuming the barcode evolves according to a molecular clock, our method infers relative ordering across parallel lineages, whereas existing techniques only infer ordering for nodes along the same lineage. When analyzing transgenic zebrafish data from McKenna, Findlay and Gagnon et al. (2016), we find that our method recapitulates known aspects of zebrafish development and the results are consistent across samples.},
}
@article {pmid35368910,
year = {2022},
author = {Taleb, M and Tail, G and Açıkgöz, HN},
title = {Molecular identification of the potentially forensically relevant cluster flies Pollenia rudis (Fabricius) and Pollenia vagabunda (Meigen) (Diptera: Polleniidae) - non-recorded species in Algeria.},
journal = {Forensic sciences research},
volume = {7},
number = {1},
pages = {69-77},
pmid = {35368910},
issn = {2471-1411},
abstract = {Cluster flies are represented by the genus Pollenia Robineau-Desvoidy, 1830 of the family Polleniidae Brauer and Bergenstamm, 1889. Their larvae are known to be internal parasites or predators of earthworms. Herein, we report for the first time the occurrence of the cluster flies Pollenia rudis Fabricius, 1794 and Pollenia vagabunda (Meigen, 1826) (Diptera: Polleniidae) on carcasses in Algeria and identify them through DNA barcoding. A region of the mitochondrial cytochrome c oxidase I gene (COI) was amplified and sequenced. Genetic distances were determined. A phylogenetic tree was constructed with the maximum parsimony method using 10 000 bootstrap replicates. A total number of 157 adults of P. rudis were collected together with 325 adults of Pollenia vagabunda. The occurrence of Pollenia on animal carcasses does not seem to be correlated with a particular stage of decomposition. All the sequences were correctly identified using the BLASTn tool from the GenBank database and the BOLD identification engine. Intra- and interspecific sequence divergence values were less than 1% and greater than 3%, respectively. COI barcodes obtained from this study were robust enough to identify and distinguish unambiguously between P. rudis and P. vagabunda. In the tree-based analysis, the cluster flies were all assigned to their respective species separately from each other confirming the morphological identification. These results provide DNA barcodes that contribute to the growth of reference databases and allow fast and accurate identification.},
}
@article {pmid35619733,
year = {2021},
author = {Hoffman, JC and Meredith, C and Pilgrim, E and Trebitz, A and Hatzenbuhler, C and Kelly, JR and Peterson, G and Lietz, J and Okum, S and Martinson, J},
title = {Comparison of Larval Fish Detections Using Morphology-Based Taxonomy versus High-Throughput Sequencing for Invasive Species Early Detection.},
journal = {Canadian journal of fisheries and aquatic sciences. Journal canadien des sciences halieutiques et aquatiques},
volume = {78},
number = {6},
pages = {752-764},
pmid = {35619733},
issn = {0706-652X},
support = {EPA999999/ImEPA/Intramural EPA/United States ; },
abstract = {When first introduced, invasive species typically evade detection; DNA barcoding coupled with high-throughput sequencing (HTS) may be more sensitive and accurate than morphology-based taxonomy, and thereby improve invasive (or rare) species detection. We quantified the relative error of species detection between morphology-based and HTS-based taxonomic identification of ichthyoplankton collections from the Port of Duluth, Minnesota, an aquatic non-native species introduction 'hot-spot' in the Laurentian Great Lakes. We found HTS-based taxonomy identified 28 species and morphology-based taxonomy 30 species, of which 27 were common to both. Among samples, 76% of family-level taxonomic assignments agreed; however, only 42% of species assignments agreed. Most errors were attributed to morphology-based taxonomy, whereas HTS-based taxonomy error was low. For this study system, for most non-native fishes, the detection probability by randomized survey for larvae was similar to that by a survey that is optimized for non-native species early detection of juveniles and adults. We conclude that classifying taxonomic errors by comparing HTS results against morphology-based taxonomy is an important step toward incorporating HTS-based taxonomy into biodiversity surveys.},
}
@article {pmid36120171,
year = {2020},
author = {Yang, L and Feng, C and Cai, MM and Chen, JH and Ding, P},
title = {Complete chloroplast genome sequence of Amomum villosum and comparative analysis with other Zingiberaceae plants.},
journal = {Chinese herbal medicines},
volume = {12},
number = {4},
pages = {375-383},
pmid = {36120171},
issn = {2589-3610},
abstract = {OBJECTIVE: Amomum villosum (AV) is an herb whose dried fruit has been extensively used in modern medicine to treat digestive system diseases such as dysentery, vomiting and abdominal pain. This paper aims to supplement chloroplast (cp) genomic resources and to be used in phylogenetic studies and identification of AV related plants.<br><br>METHODS: High-throughput sequencing technology was used to determine the complete sequence of the AV cp genome, and the sequence was then compared with three related species.<br><br>RESULTS: The genome size of AV we obtained was 163,968&#xa0;bp with an obvious tetrad structure. The AV cp genome was observed to contain 125 unique genes and 81 simple sequence repeat (SSRs) had been determined and the majority of which were adenine-thymine (AT)-rich. Comparative analysis of genome sequence of four ginger plants showed that the atpF, clpP and rpl32 genes are potential markers for identifying Amomum species. Phylogenetic analysis suggested that AV was closely related to A. kravanh and A. compactum.<br><br>CONCLUSION: These results have brought useful genetic resources for further identification researches, DNA barcoding, resolving taxonomy and understanding the evolutionary mode of Zingiberaceae cp genome.},
}
@article {pmid34857981,
year = {2020},
author = {Scharhauser, F and Zimmermann, J and Ott, JA and Leisch, N and Gruber-Vodicka, HR},
title = {Morphology of obligate ectosymbionts reveals Paralaxus gen. nov.: A new circumtropical genus of marine stilbonematine nematodes.},
journal = {Zoologica scripta},
volume = {49},
number = {3},
pages = {379-394},
pmid = {34857981},
issn = {0300-3256},
support = {P 31594/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Stilbonematinae are a subfamily of conspicuous marine nematodes, distinguished by a coat of sulphur-oxidizing bacterial ectosymbionts on their cuticle. As most nematodes, the worm hosts have a relatively simple anatomy and few taxonomically informative characters, and this has resulted in numerous taxonomic reassignments and synonymizations. Recent studies using a combination of morphological and molecular traits have helped to improve the taxonomy of Stilbonematinae but also raised questions on the validity of several genera. Here, we describe a new circumtropically distributed genus Paralaxus (Stilbonematinae) with three species: Paralaxus cocos sp. nov., P. bermudensis sp. nov. and P. columbae sp. nov. We used single worm metagenomes to generate host 18S rRNA and cytochrome c oxidase I (COI) as well as symbiont 16S rRNA gene sequences. Intriguingly, COI alignments and primer matching analyses suggest that the COI is not suitable for PCR-based barcoding approaches in Stilbonematinae as the genera have a highly diverse base composition and no conserved primer sites. The phylogenetic analyses of all three gene sets, however, confirm the morphological assignments and support the erection of the new genus Paralaxus as well as corroborate the status of the other stilbonematine genera. Paralaxus most closely resembles the stilbonematine genus Laxus in overlapping sets of diagnostic features but can be distinguished from Laxus by the morphology of the genus-specific symbiont coat. Our re-analyses of key parameters of the symbiont coat morphology as character for all Stilbonematinae genera show that with amended descriptions, including the coat, highly reliable genus assignments can be obtained.},
}
@article {pmid35493641,
year = {2020},
author = {Li, D and Song, Q and Li, T and Shu, C and Ji, S and Su, C and Su, Y and Ding, L},
title = {An LC-MS/MS method for protein detection based on a mass barcode and dual-target recognition strategy.},
journal = {RSC advances},
volume = {10},
number = {27},
pages = {16094-16100},
pmid = {35493641},
issn = {2046-2069},
abstract = {A mass barcode mediated signal amplification strategy was developed and applied to the determination of protein. A new compound, N'-((2-aminopyridin-3-yl)methylene)-5-(1,2-dithiolan-3-yl)pentanehydrazide (TAPA), was synthesized from the linker and the signal barcode, and used as the bonding barcode. For the realization of signal transduction, TAPAs and the target catcher aptamers, were both modified on gold nanoparticles (AuNPs) to establish the relationship between TAPAs and the target. Owing to the fact that the amount of TAPAs was much greater than the target, the signal of the target was not only transduced to the signal of the mass barcodes, but also amplified greatly. Thrombin, an important biomarker for coagulation abnormality diseases, was selected as a model analyte. Two kinds of thrombin recognition aptamers, aptamer 29 (apt29) and aptamer 15 (apt15), were modified onto the magnetic beads (MBs) and AuNPs, respectively. The modified AuNPs were further functionalized with lots of TAPA and formed apt15-AuNPs-TAPA. MBs-apt29 and apt15-AuNPs-TAPA could both recognize the target thrombin and form the sandwich complex (MBs-apt29/thrombin/apt15-AuNPs-TAPA). After the complex was separated by an extra magnetic field, NaClO oxidant solution was added to release the signal barcodes, 2-Amino-3-pyridinecarboxaldehyde (APA), which were then collected after centrifuging and analyzed by LC-MS/MS. Under optimized conditions, the mass response intensity was proportional to thrombin concentration in the range of 0.05-10 nM, with a 0.007 nM detection limit. This method was applied to the determination of thrombin in spiked serum samples, and the average recoveries ranged from 89.6% to 110.4%, which confirmed the applicability of this method.},
}
@article {pmid35541422,
year = {2019},
author = {Zou, D and Wu, W and Zhang, J and Ma, Q and Fan, S and Cheng, J and Li, D and Niu, J and Qian, X and Li, W and Cui, D},
title = {Multiplex detection of miRNAs based on aggregation-induced emission luminogen encoded microspheres.},
journal = {RSC advances},
volume = {9},
number = {68},
pages = {39976-39985},
pmid = {35541422},
issn = {2046-2069},
abstract = {Herein, we report a multiplex detection platform based on a suspension array with aggregation-induced emission luminogen (AIEgen) barcodes for simultaneous quantitative measurement of let-7b-5p, miR-16-5p and miR-19b-3p, which are associated with gastric cancer. A detection strategy by using a flow cytometer is proposed, which utilizes AIEgen-encoded microspheres to quantify the target miRNAs, and phycoerythrin as a fluorescence reporter on the detection probes to provide quantitative signals. This multiplex assay shows good specificity for recognizing single base mismatch, and possesses excellent sensitivity with limits of detection (LODs) ranging from 0.43 to 0.76 nM for the three miRNAs. The approach could be extended to the simultaneous detection of more target miRNAs by designing specific detection probes and increasing the number of fluorescence barcodes. We could foresee it holding great potential in future laboratory research and clinical applications due to its flexibility, strong multiplexed ability and good detection performance.},
}
@article {pmid35021504,
year = {2019},
author = {Kohll, AX and Koch, J and Chen, WD and O'Dwyer, C and Mikutis, G and Stark, WJ and Grass, RN},
title = {DNA Barcode Quantification As a Robust Tool for Measuring Mixing Ratios in Two-Component Systems.},
journal = {ACS applied bio materials},
volume = {2},
number = {11},
pages = {5062-5068},
doi = {10.1021/acsabm.9b00735},
pmid = {35021504},
issn = {2576-6422},
abstract = {For many manufacturing processes, correct mixing compositions are crucial to guarantee product quality. However, the analysis of mixing ratios based on component balances can be challenging and requires extensive infrastructure. DNA barcodes have been previously proposed as low-cost markers for product authenticity, and we show here that the quantification of such barcodes via a quantitative real-time polymerase chain reaction (PCR) enables the determination of mixing ratios in a range of liquid and polymeric products. To enable the distribution of the DNA within the various matrixes, the biochemical is encapsulated in silica nanoparticles and distributed within the matrix of the raw material. If both raw materials of a two-component mixture contain such barcodes, the composition of the mixture can be determined from the relative concentration of the barcodes via multiplex PCR reactions, irrespective of the sampling volume and for a wide range of initial barcode concentrations (10 ppm to 10 ppb). As an application example, we use the barcodes to determine the mixing ratios of cross-linked and multicomponent polysilicon products.},
}
@article {pmid35542252,
year = {2019},
author = {Jiang, K and Xu, D and Liu, Z and Zhao, W and Ji, H and Zhang, J and Li, M and Zheng, T and Feng, H},
title = {An invisible private 2D barcode design and implementation with tunable fluorescent nanoparticles.},
journal = {RSC advances},
volume = {9},
number = {64},
pages = {37292-37299},
pmid = {35542252},
issn = {2046-2069},
abstract = {The popularity of 2D barcodes is playing a key role in simplifying people's daily life activities, such as identification, quick payment, checking in and checking out, etc. However, relevant issues have emerged as their popularity has soared. The most urgent and representative problem is decryption, which may lead to serious information leakage and substantial damage to organizations, such as governments and international enterprises. This issue is mainly due to the visibility of 2D barcodes. In order to prevent potential privacy violation and sensitive information leakage through easy access of those visible 2D barcodes, we have designed and fabricated invisible 2D barcodes that will only be visible under UV illumination. This approach provides a promising solution to address the previous problem by transferring 2D barcodes into an invisible state. We have employed a typical micro-emulsion method to fabricate polystyrene (PS) fluorescent nanoparticles due to its simplicity. The invisible patterns can and will only be accessed and recognized under UV light illumination to protect personal private information. These invisible 2D barcodes provide a feasible solution for personal information protection and fit with a patient's privacy protection scenario very well, as we have demonstrated.},
}
@article {pmid35514483,
year = {2019},
author = {Wang, P and Zhang, J and Zhang, Y and Su, H and Qiu, X and Gong, L and Huang, J and Bai, J and Huang, Z and Xu, W},
title = {Chemical and genetic discrimination of commercial Guangchenpi (Citrus reticulata 'Chachi') by using UPLC-QTOF-MS/MS based metabolomics and DNA barcoding approaches.},
journal = {RSC advances},
volume = {9},
number = {40},
pages = {23373-23381},
pmid = {35514483},
issn = {2046-2069},
abstract = {CRP (Citri Reticulatae Pericarpium), a famous traditional Chinese medicine, has also been extensively used in foods and condiments in dietary practice for centuries. According to the Chinese Pharmacopeia (2015 edition) it contains two subtypes, Guangchenpi (GCP) and Chenpi (CP). GCP exclusively originates from the pericarp of Citrus reticulata 'Chachi' cultivar and it's generally believed that GCP has superior qualities compared with the other main cultivars (CP). In the present study, an integrated approach combining LC-QTOF MS-based untargeted metabolomics analysis and DNA barcoding molecular identification was conducted to study the genetic diversity and chemical differences between GCP and CP. A validated UPLC-QTOF MS metabolomics method was established to identify markers by using PCA and OPLS-DA models. 34 identified metabolites could be used as chemical markers to distinguish effectively between the two subtypes. Among them polymethoxyflavones (PMF) such as hexamethoxyflavone (nobiletin and natsudaidain), pentamethoxyflavone (tangeretin and sinensetin), and tetramethoxyflavone are the most influential markers. Support vector machines were employed to classify all the samples and these markers showed good prediction accuracy (100%). The results of DNA barcoding showed that the secondary structure of the ITS2 sequences were significantly different among GCP and other three cultivars. The study indicated the integrated method could be a powerful and reliable analytical tool for differentiating GCP from CP.},
}
@article {pmid34732017,
year = {2016},
author = {Meier, R and Wong, W and Srivathsan, A and Foo, M},
title = {$1 DNA barcodes for reconstructing complex phenomes and finding rare species in specimen-rich samples.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {32},
number = {1},
pages = {100-110},
doi = {10.1111/cla.12115},
pmid = {34732017},
issn = {1096-0031},
support = {R-154-000-526-490//PUB-NUS Project/ ; R-154-000-648-646//NUS Strategic Research/ ; R-154-000-648-733//NUS Strategic Research/ ; },
abstract = {Several of the biggest challenges in taxonomy and systematics are related to a toxic mixture of small size, abundance, and rarity. There are too many species in groups with too few taxonomists and many of these species are very rare and hard to find because they are hidden in mass samples. To make matters worse, these species often have life-history stages that are morphologically so different that it is difficult to identify them as semaphoronts of the same species. We demonstrate that these biodiversity challenges can be addressed with cost-effective molecular markers. Here, we describe a next-generation-sequencing protocol that can yield barcodes at a chemical cost of < 0.40 USD per specimen. We use this protocol to generate molecular markers for 1015 specimens of tropical midges (Diptera: Chironomidae). The barcodes cluster into 52-61 molecular operational taxonomic units (OTUs) depending on whether Objective Clustering (OC), Generalized Mixed Yule Coalescent (GMYC), or Poisson Tree Process (PTP) is used. More than half of the putative species are rare (< 10 specimens) and we are able to match larvae and adults for 24 of these OTUs. We argue that the proposed protocol will help with processing specimen-rich biodiversity samples at low cost.},
}
@article {pmid34814375,
year = {2013},
author = {Gruenstaeudl, M and Santos-Guerra, A and Jansen, RK},
title = {Phylogenetic analyses of Tolpis Adans. (Asteraceae) reveal patterns of adaptive radiation, multiple colonization and interspecific hybridization.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {29},
number = {4},
pages = {416-434},
doi = {10.1111/cla.12005},
pmid = {34814375},
issn = {1096-0031},
abstract = {The plant genus Tolpis (Asteraceae) has been the subject of several investigations on the evolution of oceanic island plants. Its insular species were utilized in studies of artificial hybrid fertility, testing the validity of Baker's law, the application of DNA barcodes, and the phylogenetic utility of inter-simple sequence repeat markers. Despite this considerable interest in Tolpis, little is known about its phylogenetic history. Past investigations were unable to resolve most of the interspecific relationships, especially within the Canary Islands, where the genus is particularly diverse. Incomplete taxon sampling, the use of ambiguous outgroups and the limited utility of slowly evolving chloroplast DNA markers precluded detailed reconstructions. The present investigation presents a comprehensive molecular phylogeny of Tolpis. By utilizing highly variable nuclear DNA markers and a comprehensive taxon set, we have resolved the majority of interspecific relationships in the genus. Evaluations of competing tree topologies and ancestral area reconstructions complemented the analyses. Our results highlight the presence of three dominant mechanisms of island plant evolution-island colonization, adaptive radiation and interspecific hybridization-in Tolpis: (i) the extant distribution of the genus is the result of two independent colonization pathways, (ii) Tolpis has colonized at least one archipelago multiple times, (iii) the present insular diversity is the product of adaptive radiation, (iv) potential hybridization was detected between species now inhabiting different islands and archipelagoes, indicating sympatric historical distributions, and (v) several undescribed species await taxonomic recognition.},
}
@article {pmid34856738,
year = {2012},
author = {Kwong, S and Srivathsan, A and Meier, R},
title = {An update on DNA barcoding: low species coverage and numerous unidentified sequences.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {28},
number = {6},
pages = {639-644},
doi = {10.1111/j.1096-0031.2012.00408.x},
pmid = {34856738},
issn = {1096-0031},
abstract = {DNA barcoding was proposed in 2003, the Consortium for the Barcode of Life was established in 2004, and the movement has since attracted more than $80 million funding. Here we investigate how many species of multicellular animals have been barcoded. We compare the numbers in a public database (GenBank as of January 2012) with those in the Barcode of Life Database (BOLD) and find that GenBank contains COI (cytochrome c oxidase subunit 1) sequences for ca. 60 000 species while BOLD reports barcodes for ca. 150 000 species. The discrepancy is likely due to a large amount of unpublished data in BOLD. Overall, the species coverage remains sparse, growth rates are low, and the barcode accumulation curve for Metazoa is linear with only 4788 species having been added in 2011. In addition, the vast majority of species in the public database (73%) were barcoded by projects that are unlikely to be related to the DNA barcoding movement. Particularly surprising was the large number of DNA barcodes in GenBank that were not identified to species (Jan 2012: 74%), with insect barcodes often being identified only to order. Of these several hundred thousand have since been suppressed by NCBI because they did not satisfy the iBOL/GenBank early release agreement. Species coverage is considerably better for target taxa of DNA barcoding campaigns (e.g. birds, fishes, Lepidoptera), although it also falls short of published campaign targets. © The Willi Hennig Society 2012.},
}
@article {pmid34861759,
year = {2012},
author = {Gibbs, J and Albert, J and Packer, L},
title = {Dual origins of social parasitism in North American Dialictus (Hymenoptera: Halictidae) confirmed using a phylogenetic approach.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {28},
number = {2},
pages = {195-207},
doi = {10.1111/j.1096-0031.2011.00373.x},
pmid = {34861759},
issn = {1096-0031},
abstract = {The bee subgenus Dialictus (Halictidae: Lasioglossum) displays a large array of behaviours including solitary behaviour, eusociality, and social parasitism. Socially parasitic Dialictus share a suite of morphological traits; these could result from shared ancestry, but given their functional significance, could also have resulted from adaptive convergence. A combined morphological and molecular phylogenetic approach was used to test for monophyly of North American socially parasitic Dialictus. Two data sets were used in the phylogenetic analyses. First, short mitochondrial DNA sequences from previous taxonomic studies of North American Dialictus, including six social parasites, were used because of the broad taxon sampling they provide. These data were analysed in combination with a set of 40 morphological characters, including a large proportion of characters associated with social parasitism. Phylogenetic analysis of the combined DNA barcode and morphology data set resolves two distinct lineages of social parasite. The second data set was based on three genes (cytochrome c oxidase subunit 1, elongation factor 1α, and long-wavelength rhodopsin), but with sparser taxon sampling, including one representative from each putative social parasite-lineage. This also supported dual origins of social parasitism among North American Dialictus. The evolution of social parasitism is discussed. © The Willi Hennig Society 2011.},
}
@article {pmid34861755,
year = {2012},
author = {Srivathsan, A and Meier, R},
title = {On the inappropriate use of Kimura-2-parameter (K2P) divergences in the DNA-barcoding literature.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {28},
number = {2},
pages = {190-194},
doi = {10.1111/j.1096-0031.2011.00370.x},
pmid = {34861755},
issn = {1096-0031},
abstract = {Here we present evidence, based on 10 datasets comprising 5283 sequences for 200 genera, that the use of the Kimura-2-parameter (K2P) model in DNA-barcoding studies is poorly justified. We demonstrate that K2P is neither expected nor confirmed to be an appropriate model for closely related COI sequences. In addition, we show that the use of uncorrected distances yields higher or similar identification success rates for neighbour-joining trees and distance-based identification techniques. K2P also does not widen the barcoding gap for closely related sequences. We conclude that the spread of K2P through the barcoding literature is difficult to explain, and urge the use of evidence-based approaches to DNA barcoding. © The Willi Hennig Society 2011.},
}
@article {pmid34875802,
year = {2011},
author = {Ebach, MC and Valdecasas, AG and Wheeler, QD},
title = {Impediments to taxonomy and users of taxonomy: accessibility and impact evaluation.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {27},
number = {5},
pages = {550-557},
doi = {10.1111/j.1096-0031.2011.00348.x},
pmid = {34875802},
issn = {1096-0031},
abstract = {There has been much discussion of the "taxonomic impediment". This phrase confuses two kinds of impediment: an impediment to end users imposed by lack of reliable information; and impediments to taxonomy itself, which vary from insufficient funding to low citation rates of taxonomic monographs. In order to resolve both these types of impediment, taxonomy needs to be revitalized through funding and training taxonomists, as well as investing in taxonomic revisions and monographs rather than technological surrogates such as DNA barcoding. © The Willi Hennig Society 2011.},
}
@article {pmid34875777,
year = {2011},
author = {Nicolalde-Morejón, F and Vergara-Silva, F and González-Astorga, J and Stevenson, DW and Vovides, AP and Sosa, V},
title = {A character-based approach in the Mexican cycads supports diverse multigene combinations for DNA barcoding.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {27},
number = {2},
pages = {150-164},
doi = {10.1111/j.1096-0031.2010.00321.x},
pmid = {34875777},
issn = {1096-0031},
abstract = {A DNA barcoding study was conducted to determine the optimal combination of loci needed for successful species-level molecular identification in three extant cycad genera-Ceratozamia, Dioon, and Zamia-that occur in Mexico. Based on conclusions of a previous multigene study in representative species of all genera in the Cycadales, we tested the DNA barcoding performance of seven chloroplast coding (matK, rpoB, rpoC1, and rbcL) and non-coding (atpF/H, psbK/I, and trnH-psbA) regions, plus sequences of the nuclear internal transcribed spacer. We analysed data under the assumptions of the "character attributes organization system" (CAOS), a character-based approach in which species are identified through the presence of 'DNA diagnostics'. In Ceratozamia, four chloroplast regions and one nuclear region were needed to achieve > 70% unique species identification. In contrast, the two-gene combination atpF/H + psbK/I and the four-gene combination atpF/H + psbK/I + rpoC1 + ITS2 were needed to reach 79% and 75% unique species identification in Dioon and Zamia, respectively. The combinations atpF/H + psbK/I and atpF/H + psbK/I + rpoC1 + ITS2 include loci previously considered by the international DNA barcoding community. However, none of the three combinations of potential DNA barcoding loci found to be optimal with a character-based approach in the Mexican cycads coincides with the 'core barcode' of chloroplast markers (matK + rbcL) recently proposed for universal use in the plant kingdom.},
}
@article {pmid34875771,
year = {2011},
author = {Pang, X and Song, J and Zhu, Y and Xu, H and Huang, L and Chen, S},
title = {Applying plant DNA barcodes for Rosaceae species identification.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {27},
number = {2},
pages = {165-170},
doi = {10.1111/j.1096-0031.2010.00328.x},
pmid = {34875771},
issn = {1096-0031},
abstract = {© The Willi Hennig Society 2010. ABSTRACT: The Consortium for the Barcode of Life (CBOL) Plant Working Group (PWG) established the use of matK+rbcL as core barcodes and ITS2 as one of the supplementary loci for differentiating plants at the Third International Barcoding Conference. Here, we tested the applicability of four DNA regions (rbcL, matK, rpoC1 and ITS2) as the barcodes for identifying species within Rosaceae. Based on assessments of the success rates of PCR amplifications, the sequence quality, extent of specific genetic divergence, DNA barcoding gap and ability for species discrimination, our results suggest that ITS2 is the best of the four loci tested for barcoding Rosaceae. We further evaluated the effectiveness of ITS2 for identifying a wide range of species within Rosaceae. Of the 1410 plant samples collected from 893 species in 96 diverse genera, ITS2 successfully identified 78 and 100% of them at the species and genus levels, respectively. Therefore, our research indicated that the ITS2 region is a powerful, though not perfect, barcode for Rosaceae identification that also contributes valuable information for identifying closely related species in other plant taxonomic groups.},
}
@article {pmid34879601,
year = {2009},
author = {Wedin, M and Westberg, M and Crewe, AT and Tehler, A and Purvis, OW},
title = {Species delimitation and evolution of metal bioaccumulation in the lichenized Acarospora smaragdula (Ascomycota, Fungi) complex.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {25},
number = {2},
pages = {161-172},
doi = {10.1111/j.1096-0031.2009.00240.x},
pmid = {34879601},
issn = {1096-0031},
abstract = {The crustose lichenized fungi in the Acarosporaceae are splendid examples of organisms managing to survive in extremely harsh environments, such as highly mineralized rocks and low-pH habitats. Some representatives of the Acarospora smaragdula complex are known to accumulate substantial amounts of potentially toxic metals including iron and copper, resulting in populations with highly divergent coloration and morphology. These populations have often been treated as distinct species by lichen taxonomists. Parsimony and parsimony jackknifing analyses of β-tubulin, nuclear ITS rDNA, and mtSSU rDNA sequence data sets was used to investigate the evolution of iron and copper accumulation and the production of the secondary compound norstictic acid in populations within the A. smaragdula species complex in Sweden, with additional samples mainly from Norway and the UK. Phylogenetic species recognition (concordance of single-gene phylogenies) was used to investigate species delimitations. Seven species are recognized in the complex. Atypically green, copper-accumulating samples, often given species rank, do not form a distinct group but are nested within A. smaragdula s. str., indicating that this ability is widespread in this species. Rust-coloured, iron-accumulating samples form two well supported separate groups, indicating that two morphologically distinct, obligate, iron-accumulating species are present, but facultatively iron-accumulating populations occur in at least one additional species. Norstictic acid, sometimes claimed to characterize the whole A. smaragdula complex, is only present in A. smaragdula s. str. The evolutionary significance of metal accumulation in Acarospora is discussed, as is the significance of our results for the application of phylogenetic species recognition/gene tree concordance-based species recognition, and DNA barcoding. © The Willi Hennig Society 2009.},
}
@article {pmid34905841,
year = {2007},
author = {Little, DP and Stevenson, DW},
title = {A comparison of algorithms for the identification of specimens using DNA barcodes: examples from gymnosperms.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {23},
number = {1},
pages = {1-21},
doi = {10.1111/j.1096-0031.2006.00126.x},
pmid = {34905841},
issn = {1096-0031},
abstract = {In order to use DNA sequences for specimen identification (e.g., barcoding, fingerprinting) an algorithm to compare query sequences with a reference database is needed. Precision and accuracy of query sequence identification was estimated for hierarchical clustering (parsimony and neighbor joining), similarity methods (BLAST, BLAT and megaBLAST), combined clustering/similarity methods (BLAST/parsimony and BLAST/neighbor joining), diagnostic methods (DNA-BAR and DOME ID), and a new method (ATIM). We offer two novel alignment-free algorithmic solutions (DOME ID and ATIM) to identify query sequences for the purposes of DNA barcoding. Publicly available gymnosperm nrITS 2 and plastid matK sequences were used as test data sets. On the test data sets, almost all of the methods were able to accurately identify sequences to genus; however, no method was able to accurately identify query sequences to species at a frequency that would be considered useful for routine specimen identification (42-71% unambiguously correct). Clustering methods performed the worst (perhaps due to alignment issues). Similarity methods, ATIM, DNA-BAR, and DOME ID all performed at approximately the same level. Given the relative precision of the algorithms (median = 67% unambiguous), the low accuracy of species-level identification observed could be ascribed to the lack of correspondence between patterns of allelic similarity and species delimitations. Application of DNA barcoding to sequences of CITES listed cycads (Cycadopsida) provides an example of the potential application of DNA barcoding to enforcement of conservation laws.},
}
@article {pmid34892966,
year = {2005},
author = {Wheeler, QD},
title = {Losing the plot: DNA "barcodes" and taxonomy.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {21},
number = {4},
pages = {405-407},
doi = {10.1111/j.1096-0031.2005.00075.x},
pmid = {34892966},
issn = {1096-0031},
}
@article {pmid34892971,
year = {2004},
author = {Will, KW and Rubinoff, D},
title = {Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {20},
number = {1},
pages = {47-55},
pmid = {34892971},
issn = {1096-0031},
abstract = {So-called DNA barcodes have recently been proposed to answer the problem of specimen identification and to quantify global biodiversity. We show that this proposition is wanting in terms of rationale, methodology and interpretation of results. In addition to falling short of all its stated goals, the method abandons the benefits of morphological studies in favor of a limited molecular identification system that would ultimately impede our understanding of biodiversity.},
}
@article {pmid34664552,
year = {2021},
author = {Öztürk, BE and Johnson, ME and Kleyman, M and Turunç, S and He, J and Jabalameli, S and Xi, Z and Visel, M and Dufour, VL and Iwabe, S and Pompeo Marinho, LFL and Aguirre, GD and Sahel, JA and Schaffer, DV and Pfenning, AR and Flannery, JG and Beltran, WA and Stauffer, WR and Byrne, LC},
title = {scAAVengr, a transcriptome-based pipeline for quantitative ranking of engineered AAVs with single-cell resolution.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
pmid = {34664552},
issn = {2050-084X},
support = {UG3 MH120094/MH/NIMH NIH HHS/United States ; R01 EY006855/EY/NEI NIH HHS/United States ; DP2 MH113095/MH/NIMH NIH HHS/United States ; P30 EY001583/EY/NEI NIH HHS/United States ; R24 EY022012/EY/NEI NIH HHS/United States ; R01 EY017549/EY/NEI NIH HHS/United States ; F32 EY023891/EY/NEI NIH HHS/United States ; },
mesh = {Animals ; Dependovirus/*physiology ; Gene Expression Profiling/*methods ; Genetic Vectors ; Macaca fascicularis/*physiology ; Retina/*physiology ; *Transcriptome ; *Transduction, Genetic ; },
abstract = {BACKGROUND: Adeno-associated virus (AAV)-mediated gene therapies are rapidly advancing to the clinic, and AAV engineering has resulted in vectors with increased ability to deliver therapeutic genes. Although the choice of vector is critical, quantitative comparison of AAVs, especially in large animals, remains challenging.<br><br>METHODS: Here, we developed an efficient single-cell AAV engineering pipeline (scAAVengr) to simultaneously quantify and rank efficiency of competing AAV vectors across all cell types in the same animal.<br><br>RESULTS: To demonstrate proof-of-concept for the scAAVengr workflow, we quantified - with cell-type resolution - the abilities of naturally occurring and newly engineered AAVs to mediate gene expression in primate retina following intravitreal injection. A top performing variant identified using this pipeline, K912, was used to deliver SaCas9 and edit the rhodopsin gene in macaque retina, resulting in editing efficiency similar to infection rates detected by the scAAVengr workflow. scAAVengr was then used to identify top-performing AAV variants in mouse brain, heart, and liver following systemic injection.<br><br>CONCLUSIONS: These results validate scAAVengr as a powerful method for development of AAV vectors.<br><br>FUNDING: This work was supported by funding from the Ford Foundation, NEI/NIH, Research to Prevent Blindness, Foundation Fighting Blindness, UPMC Immune Transplant and Therapy Center, and the Van Sloun fund for canine genetic research.},
}
@article {pmid34663862,
year = {2021},
author = {Marco-Herrero, E and Cuesta, JA and González-Gordillo, JI},
title = {DNA barcoding allows identification of undescribed crab megalopas from the open sea.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {20573},
pmid = {34663862},
issn = {2045-2322},
mesh = {Animals ; Brachyura/*genetics ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; Larva ; Phylogeny ; Plankton ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; },
abstract = {Megalopas of 15 brachyuran crab species collected in the open sea plankton, and unknown until now, were identified using DNA barcodes (COI and 16S rRNA). Specimens belonging to the families Portunidae, Pseudorhombilidae and Xanthidae (Crustacea, Decapoda, Brachyura), and corresponding to the species Achelous floridanus, Arenaeus mexicanus, Callinectes amnicola, C. arcuatus, C. ornatus, C. toxones, Charybdis (Charybdis) hellerii, Portunus hastatus, Thalamita admete, Scopolius nuttingi, Etisus odhneri, Liomera cinctimanus, Neoliomera cerasinus, Pseudoliomera variolosa, and Williamstimpsonia stimpsoni, are described and illustrated, and compared with other congeneric species previously described. We also provide a new geographical record for N. cerasinus and the most remarkable features for each species.},
}
@article {pmid34662396,
year = {2021},
author = {Jessurun, JG and Hunfeld, NGM and Van Rosmalen, J and Van Dijk, M and Van Den Bemt, PMLA},
title = {Effect of automated unit dose dispensing with barcode scanning on medication administration errors: an uncontrolled before-and-after study.},
journal = {International journal for quality in health care : journal of the International Society for Quality in Health Care},
volume = {33},
number = {4},
pages = {},
pmid = {34662396},
issn = {1464-3677},
mesh = {Hospitals, University ; Humans ; Medication Errors/prevention &amp; control ; *Medication Systems, Hospital ; *Pharmaceutical Preparations ; Prospective Studies ; },
abstract = {BACKGROUND: Medication administration errors (MAEs) occur frequently in hospitals and may compromise patient safety. Preventive strategies are needed to reduce the risk of MAEs.<br><br>OBJECTIVE: The primary aim of this study was to assess the effect of central automated unit dose dispensing with barcode-assisted medication administration on the prevalence of MAEs. Secondary aims were to assess the effect on the type and potential severity of MAEs. Furthermore, compliance with procedures regarding scanning of patient and medication barcodes and nursing staff satisfaction with the medication administration system were assessed.<br><br>METHODS: We performed a prospective uncontrolled before-and-after study in six clinical wards in a Dutch university hospital from 2018 to 2020. MAE data were collected by observation. The primary outcome was the proportion of medication administrations with one or more MAEs. Secondary outcomes were the type and potential severity of MAEs, rates of compliance with patient identification and signing of administered medication by scanning and nursing staff satisfaction with the medication administration system. Multivariable mixed-effects logistic regression analyses were used for the primary outcome to adjust for confounding and for clustering on nurse and patient level.<br><br>RESULTS: One or more MAEs occurred in 291 of 1490 administrations (19.5%) pre-intervention and in 258 of 1630 administrations (15.8%) post-intervention (adjusted odds ratio 0.70, 95% confidence interval 0.51-0.96). The rate of omission fell from 4.6% to 2.0% and of wrong dose from 3.8% to 2.1%, whereas rates of other MAE types were similar. The rate of potentially harmful MAEs fell from 3.0% (n&#x2009;=&#x2009;44) to 0.3% (n&#x2009;=&#x2009;5). The rates of compliance with scanning of patient and medication barcode post-intervention were 13.6% and 55.9%, respectively.The median overall satisfaction score of the nurses with the medication administration system on a 100-point scale was 70 (interquartile range 63-75, n&#x2009;=&#x2009;193) pre-intervention and 70 (interquartile range 60-78, n&#x2009;=&#x2009;145) post-intervention (P&#x2009;=&#x2009;0.626, Mann-Whitney U test).<br><br>CONCLUSION: The implementation of central automated unit dose dispensing with barcode-assisted medication administration was associated with a lower probability of MAEs, including potentially harmful errors, but more compliance with scanning procedures is needed. Nurses were moderately satisfied with the medication administration system, both before and after implementation. In conclusion, despite low compliance with scanning procedures, this study shows that this intervention contributes to the improvement of medication safety in hospitals.},
}
@article {pmid34661730,
year = {2021},
author = {Wiedermann, S and Harl, J and Fuehrer, HP and Mayr, S and Schmid, J and Hinney, B and Rehbein, S},
title = {DNA barcoding of rumen flukes (Paramphistomidae) from bovines in Germany and Austria.},
journal = {Parasitology research},
volume = {120},
number = {12},
pages = {4061-4066},
pmid = {34661730},
issn = {1432-1955},
mesh = {Animals ; Austria/epidemiology ; Cattle ; *Cattle Diseases/epidemiology ; DNA Barcoding, Taxonomic ; Female ; Germany/epidemiology ; *Paramphistomatidae/genetics ; Rumen ; Sheep ; *Trematoda ; *Trematode Infections/epidemiology/veterinary ; },
abstract = {Rumen flukes have received growing veterinary attention in western and central Europe during the past two decades because of an increase in prevalence of infection in cattle and sheep, including cases of severe clinical disease. Historically, rumen fluke infections in Europe were assumed to be caused mainly by Paramphistomum cervi (or species, which were later considered to be synonymous with P. cervi), but more recently molecular studies demonstrated Calicophoron daubneyi to be the predominating species. For the present investigation, adult rumen flukes isolated from 23 cattle originating from ten farms in Germany (Saxony [1], Baden-Württemberg [4], Bavaria [5]) and one farm in Austria (Tyrol) were analyzed to establish partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) and the complete sequence of the nuclear internal transcribed spacer 2 (ITS2). Flukes of five animals (dairy cows from three farms in Bavaria) were determined as P. leydeni, and flukes of 18 animals (dairy cows or cattle from cow-calf operations from eight farms in Saxony [1], Baden-Württemberg [4], Bavaria [2], and Tyrol [1]) were identified as C. daubneyi. Based on the molecular analysis of adult rumen flukes collected from cattle, the results of this investigation confirm the common occurrence of C. daubneyi in Germany and reveal the first definitive findings of P. leydeni in Germany and C. daubneyi in Austria.},
}
@article {pmid34661674,
year = {2022},
author = {Laurito, M and Ayala, AM and Arias-Builes, DL and Almirón, WR},
title = {Improving the DNA Barcode Library of Mosquito Species With New Identifications and Discoveries in North-Central Argentina.},
journal = {Journal of medical entomology},
volume = {59},
number = {1},
pages = {173-183},
doi = {10.1093/jme/tjab160},
pmid = {34661674},
issn = {1938-2928},
mesh = {*Animal Distribution ; Animals ; Argentina ; Culicidae/*classification/growth &amp; development ; *DNA Barcoding, Taxonomic ; Female ; Larva/classification/growth &amp; development ; Male ; Phylogeny ; Pupa/classification/growth &amp; development ; },
abstract = {The family Culicidae is represented by 244 species in Argentina, many of them with epidemiological importance. DNA barcodes are effective tools for identifying mosquito species, for knowing genetic variability, and for establishing phylogenetic relationships. This work aims to explore mosquito diversity employing different species delimitation approaches and to establish formally a DNA barcode library for the Argentinian mosquito fauna. Barcode fragments of 80 specimens of Argentinian mosquitoes of 28 species of the genera Aedeomyia Theobald (Diptera: Culicidae), Anopheles Meigen (Diptera: Culicidae), Coquillettidia Dyar (Diptera: Culicidae), Culex L. (Diptera: Culicidae), Haemagogus Williston (Diptera: Culicidae), Mansonia Blanchard (Diptera: Culicidae), Nyssorhynchus Blanchard (Diptera: Culicidae), Ochlerotatus Lynch-Arribálzaga (Diptera: Culicidae), Psorophora Robinneau-Desvoidy (Diptera: Culicidae) and Uranotaenia Lynch-Arribálzaga (Diptera: Culicidae) were sequenced. Another 82 sequences were obtained from public databases to establish the phylogenetic relationships using Maximum Likelihood and Bayesian Inference, and the species boundaries based on three approaches (ABGD, GMYC, and mPTP). Sixteen of the 28 species sequenced were recovered as monophyletic, of which 12 were also recognized as molecular operational taxonomic units according to the three methodologies. The disparity between morphology and barcode-based identifications could be explained by synonymy, species complexes occurrence, hybridization, incomplete lineage sorting, or the effect of the geographical scale of sampling. Twenty of the 28 sequenced species are new barcodes for Argentina and 11 are the first for science. This increases from 31 to 52 (12.7 to 21.31%) and from six to 10 (28.57 to 47.62%) the number of species and genera, respectively, with barcode sequences in Argentina. New species records are provided.},
}
@article {pmid34661331,
year = {2021},
author = {Bayat, S and Lysak, MA and Mandáková, T},
title = {Genome structure and evolution in the cruciferous tribe Thlaspideae (Brassicaceae).},
journal = {The Plant journal : for cell and molecular biology},
volume = {108},
number = {6},
pages = {1768-1785},
doi = {10.1111/tpj.15542},
pmid = {34661331},
issn = {1365-313X},
mesh = {Biological Evolution ; Brassicaceae/*genetics ; Chromosome Inversion ; *Chromosomes, Plant ; DNA, Plant/genetics ; DNA, Ribosomal/genetics ; Diploidy ; *Genome, Plant ; Karyotype ; Repetitive Sequences, Nucleic Acid ; Thlaspi/genetics ; },
abstract = {Whole-genome duplications (WGDs) and chromosome rearrangements (CRs) play the key role in driving the diversification and evolution of plant lineages. Although the direct link between WGDs and plant diversification is well documented, relatively few studies focus on the evolutionary significance of CRs. The cruciferous tribe Thlaspideae represents an ideal model system to address the role of large-scale chromosome alterations in genome evolution, as most Thlaspideae species share the same diploid chromosome number (2n = 2x = 14). Here we constructed the genome structure in 12 Thlaspideae species, including field pennycress (Thlaspi arvense) and garlic mustard (Alliaria petiolata). We detected and precisely characterized genus- and species-specific CRs, mostly pericentric inversions, as the main genome-diversifying drivers in the tribe. We reconstructed the structure of seven chromosomes of an ancestral Thlaspideae genome, identified evolutionary stable chromosomes versus chromosomes prone to CRs, estimated the rate of CRs, and uncovered an allohexaploid origin of garlic mustard from diploid taxa closely related to A. petiolata and Parlatoria cakiloidea. Furthermore, we performed detailed bioinformatic analysis of the Thlaspideae repeatomes, and identified repetitive elements applicable as unique species- and genus-specific barcodes and chromosome landmarks. This study deepens our general understanding of the evolutionary role of CRs, particularly pericentric inversions, in plant genome diversification, and provides a robust base for follow-up whole-genome sequencing efforts.},
}
@article {pmid34652616,
year = {2021},
author = {Myburgh, MM and Thabang Madisha, M and Coetzer, WG},
title = {South Africa's contribution of insect records on the BOLD system.},
journal = {Molecular biology reports},
volume = {48},
number = {12},
pages = {8211-8220},
pmid = {34652616},
issn = {1573-4978},
mesh = {Animals ; Biodiversity ; Classification/*methods ; DNA Barcoding, Taxonomic/methods/*standards ; Databases, Genetic/trends ; Insecta ; Phylogeny ; South Africa ; },
abstract = {South Africa is the third most biodiverse country in the world and insects represent a large part of its faunal diversity, as is seen globally. With more than 65,000 described animal species in South Africa, insects represent 44,088 species. While there are still a lot of species yet to be identified, progress may be hindered by the few insect taxonomists available in South Africa and subsequently, the time-consuming nature and costs of the methods used during species identification. DNA barcoding, on the other hand, has become a valuable tool for documenting biodiversity with the use of a small DNA fragment such as cytochrome oxidase subunit 1 (COI). This paper aims to assess South Africa's contribution to the Barcode of Life Database (BOLD) as well as highlight the regions that are under-represented on BOLD. From the 4,984,215 Insecta records on BOLD, South Africa contributed 56,392 insect records, with only 16.85% of that total identified to species level. The Gauteng Province had the most represented insect samples submitted to BOLD with 63.57% followed by Kwazulu-Natal (15.74%), and Mpumalanga (5.73%). However, the Free State, Limpopo, and the Northern Cape provinces are all under-represented on BOLD. This is evident as both the Northern Cape and Limpopo provinces contain one or more biodiversity hotspots which in turn displays the high levels of biodiversity that could still be recorded on BOLD. Improving our understanding with regards to DNA barcoding data linked to geographical regions, as well as specific insect groups, can highlight the areas in need of more research.},
}
@article {pmid34652142,
year = {2021},
author = {Banal, JL and Bathe, M},
title = {Scalable Nucleic Acid Storage and Retrieval Using Barcoded Microcapsules.},
journal = {ACS applied materials &amp; interfaces},
volume = {13},
number = {42},
pages = {49729-49736},
doi = {10.1021/acsami.1c14985},
pmid = {34652142},
issn = {1944-8252},
mesh = {Animals ; Capsules ; DNA/*chemistry/genetics ; Fluorescence ; Humans ; Materials Testing ; Polymerase Chain Reaction ; RNA/*chemistry/genetics ; Temperature ; },
abstract = {Rapid advances in nucleic acid sequencing and synthesis technologies have spurred a major need to collect, store, and sequence the DNA and RNA from viral, bacterial, and mammalian sources and organisms. However, current approaches to storing nucleic acids rely on a low-temperature environment and require robotics for access, posing challenges for scalable and low-cost nucleic acid storage. Here, we present an alternative method for storing nucleic acids, termed Preservation and Access of Nucleic aciDs using barcOded micRocApsules (PANDORA). Nucleic acids spanning kilobases to gigabases and from different sources, including animals, bacteria, and viruses, are encapsulated into silica microcapsules to protect them from environmental denaturants at room temperature. Molecular barcodes attached to each microcapsule enable sample pooling and subsequent identification and retrieval using fluorescence-activated sorting. We demonstrate quantitative storage and rapid access to targeted nucleic acids from a pool emulating standard retrieval operations implemented in conventional storage systems, including recovery of 100,000-200,000 samples and Boolean logic selection using four unique barcodes. Quantitative polymerase chain reaction and short-read sequencing of the retrieved samples validated the sorting experiments and the integrity of the released nucleic acids. Our proposed approach offers a scalable long-term, room-temperature storage and retrieval of nucleic acids with high sample fidelity.},
}
@article {pmid34649597,
year = {2021},
author = {Xu, FF and Niu, YF and Chen, WQ and Liu, SS and Li, JR and Jiang, P and Wang, ZQ and Cui, J and Zhang, X},
title = {Hookworm infection in central China: morphological and molecular diagnosis.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {537},
pmid = {34649597},
issn = {1756-3305},
support = {212300410070//Natural Science Foundation of Henan Province/ ; },
mesh = {Aged ; Ancylostomiasis/*epidemiology ; Animals ; China/epidemiology ; DNA, Helminth/genetics ; Female ; *Genome, Helminth ; Humans ; *Molecular Diagnostic Techniques ; Necator americanus/*genetics/isolation &amp; purification ; Necatoriasis/*diagnosis/*epidemiology ; },
abstract = {BACKGROUND: Necator americanus is one of the major etiological agents of human ancylostomiasis. Historically, the epidemiology of ancylostomiasis in Henan Province of central China and the molecular characteristics of N. americanus have been poorly understood.<br><br>METHODS: In this study, we report a case of ancylostomiasis in Zhengzhou city of Henan Province. We also review the epidemiology of ancylostomiasis in Henan Province from 1949 to 2020. In addition, the complete mitochondrial (mt) genome of one clinical isolate is fully characterized using Illumina sequencing. All available mt genomes of hookworms in GenBank were included to reconstruct the phylogeny using both maximum likelihood (ML) and Bayesian inference (BI) methods.<br><br>RESULTS: A total of three worms were collected from the patient. These worms were identified as N. americanus based on morphological characteristics as well as confirmed by genotyping with the barcoding gene cox1. Although ancylostomiasis cases have dropped substantially in recent years, hookworm infection is still a public health problem in underdeveloped areas and remote rural areas in Henan Province. The mt genome features of the N. americanus contained 12 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a major non-coding region. The nad1 gene showed high sequence variability among isolates, which is worth considering for future genetic studies of N. americanus. Phylogenetic analyses support the monophyly of hookworm isolates from different hosts and distinct geographical locations.<br><br>CONCLUSIONS: The mt genome of N. americanus presented here will serve as a useful data set for studying population genetics and phylogenetic relationships of hookworms. Positive measures for preventing and controlling ancylostomiasis are required by both health services and individuals in Henan Province.},
}
@article {pmid34648822,
year = {2022},
author = {Ringlander, J and Andersson, ME and Prakash, K and Larsson, SB and Lindh, M},
title = {Deep sequencing of hepatitis B virus using Ion Torrent fusion primer method.},
journal = {Journal of virological methods},
volume = {299},
number = {},
pages = {114315},
doi = {10.1016/j.jviromet.2021.114315},
pmid = {34648822},
issn = {1879-0984},
mesh = {DNA, Viral/genetics ; Drug Resistance, Viral/genetics ; Genotype ; *Hepatitis B ; Hepatitis B virus/genetics ; *Hepatitis B, Chronic ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Liver Neoplasms ; },
abstract = {BACKGROUND: Hepatitis B virus (HBV) infection is worldwide a major cause of liver cirrhosis and hepatocellular carcinoma. Thousands of years ago, several HBV genotypes (A-I) evolved and have, as a result of human migration, become globally disseminated. Sequencing of HBV is used for genotyping, and investigation of outbreaks or of antiviral resistance. The present study describes a simplified deep sequencing of the whole HBV genome.<br><br>METHODS: Sequencing by Ion Torrent was evaluated and its performance compared with Sanger sequencing on clinical samples.<br><br>RESULTS: Amplification of overlapping segments spanning the entire HBV genome was successful at HBV DNA levels in serum as low as 100 IU/mL. The use of primers carrying adapter tags generated libraries without the need for fragmentation and ligation steps, and inclusion of barcode sequences allowed parallel analysis of multiple samples. A streamlined bioinformatic platform generated consensus sequences and superior mutation assessment as compared with Sanger sequencing, with which there was a 99.8 % average agreement.<br><br>CONCLUSION: Deep sequencing of the whole HBV genome by using PCR primers tagged with adapters that prepare overlapping amplicons for Ion Torrent analysis was efficient and accurate.},
}
@article {pmid34647739,
year = {2021},
author = {Liao, J and Zhou, J and Song, Y and Liu, B and Lu, J and Jin, D},
title = {Optical Fingerprint Classification of Single Upconversion Nanoparticles by Deep Learning.},
journal = {The journal of physical chemistry letters},
volume = {12},
number = {41},
pages = {10242-10248},
doi = {10.1021/acs.jpclett.1c02923},
pmid = {34647739},
issn = {1948-7185},
abstract = {Highly controlled synthesis of upconversion nanoparticles (UCNPs) can be achieved in the heterogeneous design, so that a library of optical properties can be arbitrarily produced by depositing multiple lanthanide ions. Such a control offers the potential in creating nanoscale barcodes carrying high-capacity information. With the increasing creation of optical information, it poses more challenges in decoding them in an accurate, high-throughput, and speedy fashion. Here, we reported that the deep-learning approach can recognize the complexity of the optical fingerprints from different UCNPs. Under a wide-field microscope, the lifetime profiles of hundreds of single nanoparticles can be collected at once, which offers a sufficient amount of data to develop deep-learning algorithms. We demonstrated that high accuracies of over 90% can be achieved in classifying 14 kinds of UCNPs. This work suggests new opportunities in handling the diverse properties of nanoscale optical barcodes toward the establishment of vast luminescent information carriers.},
}
@article {pmid34646477,
year = {2021},
author = {Hurtado, G and Mayer, G and Mabry, KE},
title = {Does urbanization ameliorate the effect of endoparasite infection in kangaroo rats?.},
journal = {Ecology and evolution},
volume = {11},
number = {19},
pages = {13390-13400},
pmid = {34646477},
issn = {2045-7758},
support = {R25 GM061222/GM/NIGMS NIH HHS/United States ; },
abstract = {Urban development can fragment and degrade remnant habitat. Such habitat alterations can have profound impacts on wildlife, including effects on population density, parasite infection status, parasite prevalence, and body condition. We investigated the influence of urbanization on populations of Merriam's kangaroo rat (Dipodomys merriami) and their parasites. We predicted that urban development would lead to reduced abundance, increased parasite prevalence in urban populations, increased probability of parasite infection for individual animals, and decreased body condition of kangaroo rats in urban versus wildland areas. We live trapped kangaroo rats at 5 urban and 5 wildland sites in and around Las Cruces, NM, USA from 2013 to 2015, collected fecal samples from 209 kangaroo rats, and detected endoparasites using fecal flotation and molecular barcoding. Seven parasite species were detected, although only two parasitic worms, Mastophorus dipodomis and Pterygodermatites dipodomis, occurred frequently enough to allow for statistical analysis. We found no effects of urbanization on population density or probability of parasite infection. However, wildland animals infected with P. dipodomis had lower body condition scores than infected animals in urban areas or uninfected animals in either habitat. Our results suggest that urban environments may buffer Merriam's kangaroo rats from the detrimental impacts to body condition that P. dipodomis infections can cause.},
}
@article {pmid34646474,
year = {2021},
author = {Vasconcelos, S and Nunes, GL and Dias, MC and Lorena, J and Oliveira, RRM and Lima, TGL and Pires, ES and Valadares, RBS and Alves, R and Watanabe, MTC and Zappi, DC and Hiura, AL and Pastore, M and Vasconcelos, LV and Mota, NFO and Viana, PL and Gil, ASB and Simões, AO and Imperatriz-Fonseca, VL and Harley, RM and Giulietti, AM and Oliveira, G},
title = {Unraveling the plant diversity of the Amazonian canga through DNA barcoding.},
journal = {Ecology and evolution},
volume = {11},
number = {19},
pages = {13348-13362},
pmid = {34646474},
issn = {2045-7758},
abstract = {The canga of the Serra dos Carajás, in Eastern Amazon, is home to a unique open plant community, harboring several endemic and rare species. Although a complete flora survey has been recently published, scarce to no genetic information is available for most plant species of the ironstone outcrops of the Serra dos Carajás. In this scenario, DNA barcoding appears as a fast and effective approach to assess the genetic diversity of the Serra dos Carajás flora, considering the growing need for robust biodiversity conservation planning in such an area with industrial mining activities. Thus, after testing eight different DNA barcode markers (matK, rbcL, rpoB, rpoC1, atpF-atpH, psbK-psbI, trnH-psbA, and ITS2), we chose rbcL and ITS2 as the most suitable markers for a broad application in the regional flora. Here we describe DNA barcodes for 1,130 specimens of 538 species, 323 genera, and 115 families of vascular plants from a highly diverse flora in the Amazon basin, with a total of 344 species being barcoded for the first time. In addition, we assessed the potential of using DNA metabarcoding of bulk samples for surveying plant diversity in the canga. Upon achieving the first comprehensive DNA barcoding effort directed to a complete flora in the Brazilian Amazon, we discuss the relevance of our results to guide future conservation measures in the Serra dos Carajás.},
}
@article {pmid34645404,
year = {2021},
author = {Liu, Y and Zhang, M and Chen, X and Chen, X and Hu, Y and Gao, J and Pan, W and Xin, Y and Wu, J and Du, Y and Zhang, X},
title = {Developing an efficient DNA barcoding system to differentiate between Lilium species.},
journal = {BMC plant biology},
volume = {21},
number = {1},
pages = {465},
pmid = {34645404},
issn = {1471-2229},
mesh = {DNA Barcoding, Taxonomic/*methods ; *Endangered Species ; *Genetic Markers ; Genetic Variation ; *Genome, Chloroplast ; Lilium/*classification/*genetics ; Phylogeny ; Plants, Medicinal/*genetics ; *Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND: Lilium is an important ornamental bulb, possesses medicinal properties, and is also edible. Species within the Lilium genus share very similar morphology and macroscopic characteristics, thus they cannot be easily and clearly distinguished from one another. To date, no efficient species-specific markers have been developed for classifying wild lily species, which poses an issue with further characterizing its medicinal properties.<br><br>RESULTS: To develop a simple and reliable identification system for Lilium, 45 representative species from 6 sections were used to develop a DNA barcoding system, which was based on DNA sequence polymorphisms. In this study, we assessed five commonly used DNA barcode candidates (ITS, rbcL, ycf1b, matK and psbA-trnH) and five novel barcode candidates obtained from highly variable chloroplast genomic regions (trnL-trnF, trnS-trnG, trnF-ndhJ, trnP-psaJ-rpI33 and psbB-psbH). We showed that a set of three novel DNA barcodes (ITS + trnP-psaJ-rpI33 + psbB-psbH) could be efficiently used as a genetic marker to distinguish between lily species, as assessed by methods including DNAsp, BI and ML tree, and Pair Wise Group (PWG).<br><br>CONCLUSIONS: A rapid and reliable DNA barcoding method was developed for all 45 wild Lilium species by using ITS, trnP-psaJ-rpI33, and psbB-psbH as DNA barcoding markers. The method can be used in the classification of wild Lilium species, especially endangered species, and also provides an effective method for selective lily breeding.},
}
@article {pmid34644670,
year = {2022},
author = {Herholt, A and Sahoo, VK and Popovic, L and Wehr, MC and Rossner, MJ},
title = {Dissecting intercellular and intracellular signaling networks with barcoded genetic tools.},
journal = {Current opinion in chemical biology},
volume = {66},
number = {},
pages = {102091},
doi = {10.1016/j.cbpa.2021.09.002},
pmid = {34644670},
issn = {1879-0402},
mesh = {*Genomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Signal Transduction ; Transcriptome ; },
abstract = {The power of next-generation sequencing has stimulated the development of many analysis techniques for transcriptomics and genomics. More recently, the concept of 'molecular barcoding' has broadened the spectrum of sequencing-based applications to dissect different aspects of intracellular and intercellular signaling. In these assay formats, barcode reporters replace standard reporter genes. The virtually infinitive number of expressed barcode sequences allows high levels of multiplexing, hence accelerating experimental progress. Furthermore, reporter barcodes are used to quantitatively monitor a variety of biological events in living cells which has already provided much insight into complex cellular signaling and will further increase our knowledge in the future.},
}
@article {pmid34643419,
year = {2021},
author = {Langat, SK and Eyase, F and Bulimo, W and Lutomiah, J and Oyola, SO and Imbuga, M and Sang, R},
title = {Profiling of RNA Viruses in Biting Midges (Ceratopogonidae) and Related Diptera from Kenya Using Metagenomics and Metabarcoding Analysis.},
journal = {mSphere},
volume = {6},
number = {5},
pages = {e0055121},
pmid = {34643419},
issn = {2379-5042},
mesh = {Animals ; Ceratopogonidae/*virology ; DNA Barcoding, Taxonomic/*methods ; Insect Vectors ; Kenya ; Metagenomics/*methods ; Phylogeny ; RNA Viruses/*genetics ; },
abstract = {Vector-borne diseases (VBDs) cause enormous health burden worldwide, as they account for more than 17% of all infectious diseases and over 700,000 deaths each year. A significant number of these VBDs are caused by RNA virus pathogens. Here, we used metagenomics and metabarcoding analysis to characterize RNA viruses and their insect hosts among biting midges from Kenya. We identified a total of 15 phylogenetically distinct insect-specific viruses. These viruses fall into six families, with one virus falling in the recently proposed negevirus taxon. The six virus families include Partitiviridae, Iflaviridae, Tombusviridae, Solemoviridae, Totiviridae, and Chuviridae. In addition, we identified many insect species that were possibly associated with the identified viruses. Ceratopogonidae was the most common family of midges identified. Others included Chironomidae and Cecidomyiidae. Our findings reveal a diverse RNA virome among Kenyan midges that includes previously unknown viruses. Further, metabarcoding analysis based on COI (cytochrome c oxidase subunit 1 mitochondrial gene) barcodes reveal a diverse array of midge species among the insects used in the study. Successful application of metagenomics and metabarcoding methods to characterize RNA viruses and their insect hosts in this study highlights a possible simultaneous application of these two methods as cost-effective approaches to virus surveillance and host characterization. IMPORTANCE The majority of the viruses that currently cause diseases in humans and animals are RNA viruses, and more specifically arthropod-transmitted viruses. They cause diseases such as dengue, West Nile infection, bluetongue disease, Schmallenberg disease, and yellow fever, among others. Several sequencing investigations have shown us that a diverse array of RNA viruses among insect vectors remain unknown. Some of these could be ancient lineages that could aid in comprehensive studies on RNA virus evolution. Such studies may provide us with insights into the evolution of the currently pathogenic viruses. Here, we applied metagenomics to field-collected midges and we managed to characterize several RNA viruses, where we recovered complete and nearly complete genomes of these viruses. We also characterized the insect host species that are associated with these viruses. These results add to the currently known diversity of RNA viruses among biting midges as well as their associated insect hosts.},
}
@article {pmid34643250,
year = {2021},
author = {Wang, MY and Zhou, Y and Lai, GS and Huang, Q and Cai, WQ and Han, ZW and Wang, Y and Ma, Z and Wang, XW and Xiang, Y and Fang, SX and Peng, XC and Xin, HW},
title = {DNA barcode to trace the development and differentiation of cord blood stem cells (Review).},
journal = {Molecular medicine reports},
volume = {24},
number = {6},
pages = {},
pmid = {34643250},
issn = {1791-3004},
mesh = {Adult Stem Cells ; Animals ; Antigens, CD34 ; CRISPR-Cas Systems ; Cell Differentiation/*genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; *DNA Barcoding, Taxonomic ; *Fetal Blood ; Humans ; *Stem Cells ; T-Lymphocytes ; Tissue Engineering ; },
abstract = {Umbilical cord blood transplantation was first reported in 1980. Since then, additional research has indicated that umbilical cord blood stem cells (UCBSCs) have various advantages, such as multi‑lineage differentiation potential and potent renewal activity, which may be induced to promote their differentiation into a variety of seed cells for tissue engineering and the treatment of clinical and metabolic diseases. Recent studies suggested that UCBSCs are able to differentiate into nerve cells, chondrocytes, hepatocyte‑like cells, fat cells and osteoblasts. The culture of UCBSCs has developed from feeder‑layer to feeder‑free culture systems. The classical techniques of cell labeling and tracing by gene transfection and fluorescent dye and nucleic acid analogs have evolved to DNA barcode technology mediated by transposon/retrovirus, cyclization recombination‑recombinase and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR‑associated protein 9 strategies. DNA barcoding for cell development tracing has advanced to include single cells and single nucleic acid mutations. In the present study, the latest research findings on the development and differentiation, culture techniques and labeling and tracing of UCBSCs are reviewed. The present study may increase the current understanding of UCBSC biology and its clinical applications.},
}
@article {pmid34637755,
year = {2021},
author = {Gopalan, S and Wang, Y and Harper, NW and Garber, M and Fazzio, TG},
title = {Simultaneous profiling of multiple chromatin proteins in the same cells.},
journal = {Molecular cell},
volume = {81},
number = {22},
pages = {4736-4746.e5},
pmid = {34637755},
issn = {1097-4164},
support = {R01 HD072122/HD/NICHD NIH HHS/United States ; R01 HD093783/HD/NICHD NIH HHS/United States ; R21 CA236594/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Chromatin/*chemistry ; Chromatin Immunoprecipitation ; Chromosome Mapping ; Cluster Analysis ; DNA-Directed RNA Polymerases/*chemistry ; Embryonic Stem Cells/cytology ; Epigenesis, Genetic ; Epigenomics ; Epitopes/chemistry ; Gene Regulatory Networks ; Genome-Wide Association Study ; Histone Code ; Histones/chemistry ; Mice ; RNA Polymerase II/metabolism ; Sensitivity and Specificity ; },
abstract = {Methods derived from CUT&amp;RUN and CUT&amp;Tag enable genome-wide mapping of the localization of proteins on chromatin from as few as one cell. These and other mapping approaches focus on one protein at a time, preventing direct measurements of co-localization of different chromatin proteins in the same cells and requiring prioritization of targets where samples are limiting. Here, we describe multi-CUT&amp;Tag, an adaptation of CUT&amp;Tag that overcomes these hurdles by using antibody-specific barcodes to simultaneously map multiple proteins in the same cells. Highly specific multi-CUT&amp;Tag maps of histone marks and RNA Polymerase II uncovered sites of co-localization in the same cells, active and repressed genes, and candidate cis-regulatory elements. Single-cell multi-CUT&amp;Tag profiling facilitated identification of distinct cell types from a mixed population and characterization of cell-type-specific chromatin architecture. In sum, multi-CUT&amp;Tag increases the information content per cell of epigenomic maps, facilitating direct analysis of the interplay of different chromatin proteins.},
}
@article {pmid34637435,
year = {2021},
author = {Spatz, JM and Ko, FC and Ayturk, UM and Warman, ML and Bouxsein, ML},
title = {RNAseq and RNA molecular barcoding reveal differential gene expression in cortical bone following hindlimb unloading in female mice.},
journal = {PloS one},
volume = {16},
number = {10},
pages = {e0250715},
pmid = {34637435},
issn = {1932-6203},
support = {R21 AR057522/AR/NIAMS NIH HHS/United States ; R01 AR053237/AR/NIAMS NIH HHS/United States ; },
mesh = {Animals ; Bone Density/genetics ; Cortical Bone/*physiology ; Female ; Femur/physiology ; Gene Expression/*genetics ; Hindlimb Suspension/physiology ; Mice ; Mice, Inbred C57BL ; Osteoporosis/genetics ; RNA/*genetics ; Sequence Analysis, RNA/methods ; Weightlessness ; X-Ray Microtomography/methods ; },
abstract = {Disuse-induced bone loss is seen following spinal cord injury, prolonged bed rest, and exposure to microgravity. We performed whole transcriptomic profiling of cortical bone using RNA sequencing (RNAseq) and RNA molecular barcoding (NanoString) on a hindlimb unloading (HLU) mouse model to identify genes whose mRNA transcript abundances change in response to disuse. Eleven-week old female C57BL/6 mice were exposed to ambulatory loading or HLU for 7 days (n = 8/group). Total RNA from marrow-flushed femoral cortical bone was analyzed on HiSeq and NanoString platforms. The expression of several previously reported genes associated with Wnt signaling and metabolism was altered by HLU. Furthermore, the increased abundance of transcripts, such as Pfkfb3 and Mss51, after HLU imply these genes also have roles in the cortical bone's response to altered mechanical loading. Our study demonstrates that an unbiased approach to assess the whole transcriptomic profile of cortical bone can reveal previously unidentified mechanosensitive genes and may eventually lead to novel targets to prevent disuse-induced osteoporosis.},
}
@article {pmid34636322,
year = {2021},
author = {Hullahalli, K and Waldor, MK},
title = {Pathogen clonal expansion underlies multiorgan dissemination and organ-specific outcomes during murine systemic infection.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
pmid = {34636322},
issn = {2050-084X},
support = {F31 AI156949/AI/NIAID NIH HHS/United States ; R01 AI042347/AI/NIAID NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; Bacteremia/microbiology/*pathology ; Escherichia coli/physiology ; Escherichia coli Infections/microbiology/*pathology ; Mice ; Models, Animal ; },
abstract = {The dissemination of pathogens through blood and their establishment within organs lead to severe clinical outcomes. However, the within-host dynamics that underlie pathogen spread to and clearance from systemic organs remain largely uncharacterized. In animal models of infection, the observed pathogen population results from the combined contributions of bacterial replication, persistence, death, and dissemination, each of which can vary across organs. Quantifying the contribution of each these processes is required to interpret and understand experimental phenotypes. Here, we leveraged STAMPR, a new barcoding framework, to investigate the population dynamics of extraintestinal pathogenic Escherichia coli, a common cause of bacteremia, during murine systemic infection. We show that while bacteria are largely cleared by most organs, organ-specific clearance failures are pervasive and result from dramatic expansions of clones representing less than 0.0001% of the inoculum. Clonal expansion underlies the variability in bacterial burden between animals, and stochastic dissemination of clones profoundly alters the pathogen population structure within organs. Despite variable pathogen expansion events, host bottlenecks are consistent yet highly sensitive to infection variables, including inoculum size and macrophage depletion. We adapted our barcoding methodology to facilitate multiplexed validation of bacterial fitness determinants identified with transposon mutagenesis and confirmed the importance of bacterial hexose metabolism and cell envelope homeostasis pathways for organ-specific pathogen survival. Collectively, our findings provide a comprehensive map of the population biology that underlies bacterial systemic infection and a framework for barcode-based high-resolution mapping of infection dynamics.},
}
@article {pmid34630493,
year = {2021},
author = {Chen, J and Zang, Y and Shang, S and Liang, S and Zhu, M and Wang, Y and Tang, X},
title = {Comparative Chloroplast Genomes of Zosteraceae Species Provide Adaptive Evolution Insights Into Seagrass.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {741152},
pmid = {34630493},
issn = {1664-462X},
abstract = {Seagrasses are marine flowering plants found in tropical and sub-tropical areas that live in coastal regions between the sea and land. All seagrass species evolved from terrestrial monocotyledons, providing the opportunity to study plant adaptation to sea environments. Here, we sequenced the chloroplast genomes (cpGenomes) of three Zostera species, then analyzed and compared their cpGenome structures and sequence variations. We also performed a phylogenetic analysis using published seagrass chloroplasts and calculated the selection pressure of 17 species within seagrasses and nine terrestrial monocotyledons, as well as estimated the number of shared genes of eight seagrasses. The cpGenomes of Zosteraceae species ranged in size from 143,877 bp (Zostera marina) to 152,726 bp (Phyllospadix iwatensis), which were conserved and displayed similar structures and gene orders. Additionally, we found 17 variable hotspot regions as candidate DNA barcodes for Zosteraceae species, which will be helpful for studying the phylogenetic relationships and interspecies differences between seagrass species. Interestingly, nine genes had positive selection sites, including two ATP subunit genes (atpA and atpF), two ribosome subunit genes (rps4 and rpl20), two DNA-dependent RNA polymerase genes (rpoC1 and rpoC2), as well as accD, clpP, and ycf2. These gene regions may have played key roles in the seagrass adaptation to diverse environments. The Branch model analysis showed that seagrasses had a higher rate of evolution than terrestrial monocotyledons, suggesting that seagrasses experienced greater environmental pressure. Moreover, a branch-site model identified positively selected sites (PSSs) in ccsA, suggesting their involvement in the adaptation to sea environments. These findings are valuable for further investigations on Zosteraceae cpGenomes and will serve as an excellent resource for future studies on seagrass adaptation to sea environments.},
}
@article {pmid34628046,
year = {2022},
author = {Krosch, MN and Silva, FL and Ekrem, T and Baker, AM and Bryant, LM and Stur, E and Cranston, PS},
title = {A new molecular phylogeny for the Tanypodinae (Diptera: Chironomidae) places the Australian diversity in a global context.},
journal = {Molecular phylogenetics and evolution},
volume = {166},
number = {},
pages = {107324},
doi = {10.1016/j.ympev.2021.107324},
pmid = {34628046},
issn = {1095-9513},
mesh = {Animals ; Australia ; Bayes Theorem ; *Chironomidae/genetics ; Geography ; Phylogeny ; },
abstract = {The non-biting midge subfamily Tanypodinae (Diptera: Chironomidae) is species-rich, ecologically diverse, and near-globally distributed. Within the subfamily, aspects of generic and species-level taxonomy remain poorly understood, in particular the validity of assignment of Australian and New Zealand taxa to genera erected for northern hemisphere (Holarctic) fauna. Here, we place the austral diversity within this global context by extensive geographical and taxonomic sampling in concert with a multilocus phylogenetic approach. We incorporated sequence data for mitochondrial COI, and nuclear 28S and CAD, and conducted Bayesian and maximum likelihood phylogenetic inferences and Bayesian divergence time estimation. The resolved phylogeny supported many associations of Australian taxa with their proposed Holarctic congeners, with the exception of Apsectrotanypus Fittkau, and validates several taxa as endemic. Three of four New Zealand sampled taxa had their sister groups in Australia; New Zealand Monopelopia Fittkau was sister to a German congener. This included the first record of Procladius Kieffer from New Zealand. Most nodes connecting austral and Holarctic taxa clustered around the Cretaceous-Tertiary boundary (60-80 mya), whereas New Zealand-Australia nodes were generally slightly younger (53-57 mya). Together, these data contribute substantially to our understanding of the taxonomy, systematics and biogeography of the Australian Tanypodinae and more broadly to knowledge of Australia's aquatic insect biodiversity.},
}
@article {pmid34627793,
year = {2021},
author = {Loeffelholz, J and Stahl, L and Momeni, S and Turberville, C and Pienaar, J},
title = {Trichoderma infection of limno-terrestrial tardigrades.},
journal = {Journal of invertebrate pathology},
volume = {186},
number = {},
pages = {107677},
doi = {10.1016/j.jip.2021.107677},
pmid = {34627793},
issn = {1096-0805},
mesh = {Animals ; *Host-Pathogen Interactions ; Tardigrada/*microbiology ; Trichoderma/classification/*physiology ; },
abstract = {Interactions between fungi and tardigrades have scarcely been described. The few studies that address such relationships suggest a primarily parasitic nature for various fungal taxa, including the infectious chytridiomycetes. The aim of this study was to determine the identity of a fungus growing on a tardigrade of the genus Diaforobiotus and if it could infect other tardigrade genera. Using morphological analysis and ITS barcoding, we identified a mold isolate belonging to the Trichoderma harzianum species complex and found that it infected Diaforobiotus tardigrades, as well as animals in the eutardigrade genus Milnesium, and heterotardigrade genus Viridiscus.},
}
@article {pmid34627624,
year = {2021},
author = {Giersing, B and Shah, N and Kristensen, D and Amorij, JP and Kahn, AL and Gandrup-Marino, K and Jarrahian, C and Zehrung, D and Menozzi-Arnaud, M},
title = {Strategies for vaccine-product innovation: Creating an enabling environment for product development to uptake in low- and middle-income countries.},
journal = {Vaccine},
volume = {39},
number = {49},
pages = {7208-7219},
pmid = {34627624},
issn = {1873-2518},
support = {001/WHO_/World Health Organization/International ; },
mesh = {Developing Countries ; Humans ; Immunization ; *Immunization Programs ; Vaccination ; *Vaccines ; },
abstract = {Vaccine-product innovations that address barriers to immunization are urgently needed to achieve equitable vaccine coverage, as articulated in the new Immunization Agenda 2030 and the Gavi 5.0 strategy. In 2020, the Vaccine Innovation Prioritisation Strategy (VIPS) prioritized three innovations, namely microarray patches (MAPs), heat-stable and controlled-temperature chain (CTC) enabled liquid vaccine formulations and barcodes on primary packaging. These innovations were prioritized based on the priority immunization barriers that they may help overcome in resource constrained contexts, as well as by considering their potential impact on health, coverage and equity, safety, economic costs and their technical readiness and commercial feasibility. VIPS is now working to accelerate the development and lay the foundation for future uptake of the three priority vaccine-product innovations, with the long term-goal to ensure equitable vaccine coverage and increased impact of vaccines in low- and middle- income countries. To inform our strategic planning, we analyzed four commercially available vaccine product-innovations and conducted interviews with individuals from 17 immunization organizations, and/or independent immunization experts. The findings are synthesized into an 'innovation conundrum' that describes the challenges encountered in developing vaccine-product innovations and a vaccine-product innovation 'theory of change', which highlights actions that should be undertaken in parallel to product development to incentivize sustainable investment and prepare the pathway for uptake and impact.},
}
@article {pmid34626511,
year = {2022},
author = {Govender, A and Singh, S and Groeneveld, J and Pillay, S and Willows-Munro, S},
title = {Experimental validation of taxon-specific mini-barcode primers for metabarcoding of zooplankton.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {32},
number = {1},
pages = {e02469},
doi = {10.1002/eap.2469},
pmid = {34626511},
issn = {1051-0761},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Ecosystem ; Fishes ; Genetic Markers ; *Zooplankton/genetics ; },
abstract = {Metabarcoding to determine the species composition and diversity of marine zooplankton communities is a fast-developing field in which the standardization of methods is yet to be fully achieved. The selection of genetic markers and primer choice are particularly important because they substantially influence species detection rates and accuracy. Validation is therefore an important step in the design of metabarcoding protocols. We developed taxon-specific mini-barcode primers for the cytochrome c oxidase subunit I (COI) gene region and used an experimental approach to test species detection rates and primer accuracy of the newly designed primers for prawns, shrimps and crabs and published primers for marine lobsters and fish. Artificially assembled mock communities (with known species ratios) and unsorted coastal tow-net zooplankton samples were sequenced and the detected species were compared with those seeded in mock communities to test detection rates. Taxon-specific primers increased detection rates of target taxa compared with a universal primer set. Primer cocktails (multiple primer sets) significantly increased species detection rates compared with single primer pairs and could detect up to 100% of underrepresented target taxa in mock communities. Taxon-specific primers recovered fewer false-positive or false-negative results than the universal primer. The methods used to design taxon-specific mini-barcodes and the experimental mock community validation protocols shown here can easily be applied to studies on other groups and will allow for a level of standardization among studies undertaken in different ecosystems or geographic locations.},
}
@article {pmid34622153,
year = {2021},
author = {Samarasinghe, H and Lu, Y and Aljohani, R and Al-Amad, A and Yoell, H and Xu, J},
title = {Global patterns in culturable soil yeast diversity.},
journal = {iScience},
volume = {24},
number = {10},
pages = {103098},
pmid = {34622153},
issn = {2589-0042},
abstract = {Yeasts, broadly defined as unicellular fungi, fulfill essential roles in soil ecosystems as decomposers and nutrition sources for fellow soil-dwellers. Broad-scale investigations of soil yeasts pose a methodological challenge as metagenomics are of limited use for identifying this group of fungi. Here we characterize global soil yeast diversity using fungal DNA barcoding on 1473 yeasts cultured from 3826 soil samples obtained from nine countries in six continents. We identify mean annual precipitation and international air travel as two significant correlates with soil yeast community structure and composition worldwide. Evidence for anthropogenic influences on soil yeast communities, directly via travel and indirectly via altered rainfall patterns resulting from climate change, is concerning as we found common infectious yeasts frequently distributed in soil in several countries. Our discovery of 41 putative novel species highlights the continued need for culture-based studies to advance our knowledge of environmental yeast diversity.},
}
@article {pmid34620214,
year = {2021},
author = {Rebboah, E and Reese, F and Williams, K and Balderrama-Gutierrez, G and McGill, C and Trout, D and Rodriguez, I and Liang, H and Wold, BJ and Mortazavi, A},
title = {Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq.},
journal = {Genome biology},
volume = {22},
number = {1},
pages = {286},
pmid = {34620214},
issn = {1474-760X},
support = {T32 GM136624/GM/NIGMS NIH HHS/United States ; U01 AR073159/AR/NIAMS NIH HHS/United States ; UM1 HG009443/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; Cell Differentiation/genetics ; Cell Line ; Cell Nucleus/genetics ; Chromatin/metabolism ; Genomics ; Mice ; Models, Genetic ; Myogenin/genetics ; PAX7 Transcription Factor/genetics ; RNA Isoforms/*metabolism ; RNA-Seq/*methods ; Single-Cell Analysis/*methods ; Transcription Initiation Site ; Transcription, Genetic ; },
abstract = {The rise in throughput and quality of long-read sequencing should allow unambiguous identification of full-length transcript isoforms. However, its application to single-cell RNA-seq has been limited by throughput and expense. Here we develop and characterize long-read Split-seq (LR-Split-seq), which uses combinatorial barcoding to sequence single cells with long reads. Applied to the C2C12 myogenic system, LR-split-seq associates isoforms to cell types with relative economy and design flexibility. We find widespread evidence of changing isoform expression during differentiation including alternative transcription start sites (TSS) and/or alternative internal exon usage. LR-Split-seq provides an affordable method for identifying cluster-specific isoforms in single cells.},
}
@article {pmid34616621,
year = {2021},
author = {Sakata, Y and Shirahama, N and Uechi, A and Okano, K},
title = {Variability in deer diet and plant vulnerability to browsing among forests with different establishment years of sika deer.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e12165},
pmid = {34616621},
issn = {2167-8359},
abstract = {Increased ungulate browsing alters the composition of plant communities and modifies forest ecosystems worldwide. Ungulates alter their diet following changes in availability of plant species; however, we know little about how browse selection and plant community composition change with different stages of deer establishment. Here, we provide insight into this area of study by combining multiple approaches: comparison of the understory plant community, analysis of records of browsing damage, and DNA barcoding of sika deer feces at 22 sites in forests in northern Japan varying in when deer were first established. The coverage of vegetation and number of plant species were only lower at sites where deer were present for more than 20 years, while the difference in plant coverage among deer establishment years varied among plant species. Deer diet differed across establishment years, but was more affected by the site, thereby indicating that food selection by deer could change over several years after deer establishment. Plant life form and plant architecture explained the difference in plant coverage across establishment years, but large variability was observed in deer diet within the two categories. Integrating these results, we categorized 98 plant taxa into six groups that differed in vulnerability to deer browsing (degree of damage and coverage). The different responses to browsing among plant species inferred from this study could be a first step in predicting the short- and long-term responses of forest plant communities to deer browsing.},
}
@article {pmid34616214,
year = {2021},
author = {Kousteni, V and Papageorgiou, M and Rovatsos, M and Thasitis, I and Hadjioannou, L},
title = {First genetically confirmed records of the little gulper shark Centrophorusuyato (Squaliformes: Centrophoridae) from Cypriot waters.},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e71837},
pmid = {34616214},
issn = {1314-2828},
abstract = {The taxonomy within the genus Centrophorus has been controversial almost since its origin, raising uncertainties about the identification, the phylogenetic placement and the geographical distribution of several species. The partial nucleotide sequences of two mitochondrial DNA gene regions, the cytochrome c oxidase subunit I and the 16S ribosomal RNA, genetically confirmed the presence of the little gulper shark in Cypriot waters. The species presence in the Mediterranean Sea is revised and discussed.},
}
@article {pmid34616211,
year = {2021},
author = {Jovanović, M and Haring, E and Sattmann, H and Grosser, C and Pesic, V},
title = {DNA barcoding for species delimitation of the freshwater leech genus Glossiphonia from the Western Balkan (Hirudinea, Glossiphoniidae).},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e66347},
pmid = {34616211},
issn = {1314-2828},
abstract = {Glossiphoniid leeches are a diverse group and sometimes abundant elements of the aquatic fauna inhabiting various types of freshwater habitats. In this study, we sampled leeches of the genus Glossiphonia from the Western Balkan in order to test the suitability of the mitochondrial cytochrome c oxidase subunit 1 (COI) marker sequence for species delimitation. Morphological analysis revealed the presence of four taxa, G.complanata with two subspecies, G.c.complanata and G.c.maculosa, the latter an endemic of Ohrid Lake, G.nebulosa and endemic G.balcanica. In total, 29 new barcodes of Glossiphonia were sequenced in the course of this study and compared with the available molecular dataset of the latter genus from GenBank/BOLD databases. The applied ASAP distance-based species delimitation method for the analysed dataset revealed an interspecific threshold between 4-8% K2P distance as suitable for species identification purposes of the Western Balkan Glossiphonia species. Our study revealed that morphologically identified taxa as G.nebulosa and G.concolor each consists of more than one clearly different phylogenetic clade. This study contributes to a better knowledge of the taxonomy of glossiphoniid leeches and emphasises future work on the revision of this genus using a standard molecular COI marker in species identification.},
}
@article {pmid34614003,
year = {2021},
author = {Rinkert, A and Misiewicz, TM and Carter, BE and Salmaan, A and Whittall, JB},
title = {Bird nests as botanical time capsules: DNA barcoding identifies the contents of contemporary and historical nests.},
journal = {PloS one},
volume = {16},
number = {10},
pages = {e0257624},
pmid = {34614003},
issn = {1932-6203},
mesh = {Animals ; Botany ; Computational Biology ; DNA Barcoding, Taxonomic ; DNA, Plant/analysis/genetics ; *Ecosystem ; *Nesting Behavior ; Plants/classification/*genetics ; *Sparrows/physiology ; },
abstract = {Bird nests in natural history collections are an abundant yet vastly underutilized source of genetic information. We sequenced the nuclear ribosomal internal transcribed spacer to identify plant species used as nest material in two contemporary (2003 and 2018) and two historical (both 1915) nest specimens constructed by Song Sparrows (Melospiza melodia) and Savannah Sparrows (Passerculus sandwichensis). A total of 13 (22%) samples yielded single, strong bands that could be identified using GenBank resources: six plants (Angiospermae), six green algae (Chlorophyta), and one ciliate (Ciliophora). Two native plant species identified in the nests included Festuca microstachys, which was introduced to the nest collection site by restoration practitioners, and Rosa californica, identified in a nest collected from a lost habitat that existed about 100 years ago. Successful sequencing was correlated with higher sample mass and DNA quality, suggesting future studies should select larger pieces of contiguous material from nests and materials that appear to have been fresh when incorporated into the nest. This molecular approach was used to distinguish plant species that were not visually identifiable, and did not require disassembling the nest specimens as is a traditional practice with nest material studies. The many thousands of nest specimens in natural history collections hold great promise as sources of genetic information to address myriad ecological questions.},
}
@article {pmid34613959,
year = {2021},
author = {Di Bernardo, M and Crombie, TA and Cook, DE and Andersen, EC},
title = {easyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application.},
journal = {PloS one},
volume = {16},
number = {10},
pages = {e0254293},
pmid = {34613959},
issn = {1932-6203},
mesh = {Computers, Handheld ; Data Collection/*methods ; Ecology/*methods ; Environment ; Mobile Applications ; Software ; Specimen Handling/*methods ; },
abstract = {Large-scale ecological sampling can be difficult and costly, especially for organisms that are too small to be easily identified in a natural environment by eye. Typically, these microscopic floral and fauna are sampled by collecting substrates from nature and then separating organisms from substrates in the laboratory. In many cases, diverse organisms can be identified to the species-level using molecular barcodes. To facilitate large-scale ecological sampling of microscopic organisms, we used a geographic data-collection platform for mobile devices called Fulcrum that streamlines the organization of geospatial sampling data, substrate photographs, and environmental data at natural sampling sites. These sampling data are then linked to organism isolation data from the laboratory. Here, we describe the easyFulcrum R package, which can be used to clean, process, and visualize ecological field sampling and isolation data exported from the Fulcrum mobile application. We developed this package for wild nematode sampling, but it can be used with other organisms. The advantages of using Fulcrum combined with easyFulcrum are (1) the elimination of transcription errors by replacing manual data entry and/or spreadsheets with a mobile application, (2) the ability to clean, process, and visualize sampling data using a standardized set of functions in the R software environment, and (3) the ability to join disparate data to each other, including environmental data from the field and the molecularly defined identities of individual specimens isolated from samples.},
}
@article {pmid34611511,
year = {2021},
author = {Levesque-Beaudin, V and Sinclair, BJ},
title = {Louse fly (Diptera, Hippoboscidae) associations with raptors in southern Canada, with new North American and European records.},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {16},
number = {},
pages = {168-174},
pmid = {34611511},
issn = {2213-2244},
abstract = {Louse flies (Diptera, Hippoboscidae) are ectoparasites often found on birds. As they spend most of their life on their host, they are not often collected or studied. Hence, little is known about their species richness and prevalence on raptors in Canada. In this study, louse flies were collected from 184 out of 1467 raptors examined during the 2020 fall migration in southern Ontario, Canada, giving an overall prevalence of 12.5%. In total, 256 louse fly specimens were collected (mean intensity = 1.41) representing four species (identified morphologically, with support of DNA barcoding): Icosta americana (91.9%), Ornithomya anchineuria (0.3%), O. avicularia (7.3%) and O. bequaerti (0.3%). Mite clusters were found on 42% of O. avicularia. This study also presents the first North American record for O. avicularia and the presence of O. bequaerti in Europe was confirmed for the first time. Based on the different parameters recorded during banding, it appears that the host species and the month play a part in the presence of louse flies on the host. Further study of louse flies is needed to better understand their prevalence across different bird groups and geographic distribution.},
}
@article {pmid34611455,
year = {2021},
author = {Pohjoismäki, J and Haarto, A},
title = {Scenopinusjerei, a new species of window fly (Diptera, Scenopinidae) from Finland.},
journal = {ZooKeys},
volume = {1059},
number = {},
pages = {135-156},
pmid = {34611455},
issn = {1313-2989},
abstract = {A new species of window fly (Diptera: Scenopinidae), Scenopinusjerei sp. nov., with characteristic bicoloured legs and completely black halteres, is described from Finland. To exclude potential previously named species, a survey of the relevant type specimens as well as original descriptions of the Palearctic and Nearctic Scenopinus species has been conducted, including old Scenopinusfenestralis (Linnaeus) synonyms. Scenopinusjerei sp. nov. is likely to be an overlooked, boreal forest specialist living in the nests of cavity-nesting birds. An identification key to the European species is provided.},
}
@article {pmid34611275,
year = {2021},
author = {Matra, DD and Fathoni, MAN and Majiidu, M and Wicaksono, H and Sriyono, A and Gunawan, G and Susanti, H and Sari, R and Fitmawati, F and Siregar, IZ and Widodo, WD and Poerwanto, R},
title = {The genetic variation and relationship among the natural hybrids of Mangifera casturi Kosterm.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {19766},
pmid = {34611275},
issn = {2045-2322},
mesh = {Alleles ; Chimera/*genetics ; DNA, Plant ; *Genetic Variation ; *Hybridization, Genetic ; Mangifera/classification/*genetics ; Microsatellite Repeats ; Phenotype ; Phylogeny ; Plant Breeding ; },
abstract = {Mangifera casturi Kosterm., a mango plant from Kalimantan Selatan, Indonesia, has limited genetic information, severely limiting the research on its genetic variation and phylogeny. We collected M. casturi's genomic information using next-generation sequencing, developed microsatellite markers and performed Sanger sequencing for DNA barcoding analysis. These markers were used to confirm parental origin and genetic diversity of M. casturi hybrids. The clean reads of the Kasturi accession were assembled de novo, producing 259 872 scaffolds (N50 = 1 445 bp). Fourteen polymorphic microsatellite markers were developed from 11 040 microsatellite motif-containing sequences. In total, 58 alleles were produced with a mean of 4.14 alleles per locus. Microsatellite marker analysis revealed broad genetic variation in M. casturi. Phylogenetic analysis was performed using internal transcribed spacers (ITS), matK, rbcL, and trnH-psbA. The phylogenetic tree of chloroplast markers placed Kasturi, Cuban, Pelipisan, Pinari, and Hambawang in one group, with M. indica as the female ancestor. Meanwhile, the phylogenetic tree of ITS markers indicated several Mangifera species as ancestors of M. casturi. Thus, M. casturi very likely originated from the cross-hybridization of multiple ancestors. Furthermore, crossing the F1 hybrids of M. indica and M. quadrifida with other Mangifera spp. may have generated much genetic variation. The genetic information for M. casturi will be a resource for breeding improvement, and conservation studies.},
}
@article {pmid34609923,
year = {2021},
author = {Paradiso, L and Little, DP},
title = {Authentication of garlic (Allium sativum L.) supplements using a trnL[UAA] mini-barcode.},
journal = {Genome},
volume = {64},
number = {11},
pages = {1021-1028},
doi = {10.1139/gen-2021-0001},
pmid = {34609923},
issn = {1480-3321},
mesh = {*DNA Barcoding, Taxonomic ; Dietary Supplements/*standards ; Garlic/*genetics ; Introns ; },
abstract = {Garlic (Allium sativum), a widely distributed plant with great cultural and medicinal significance, is one of the most popular herbal dietary supplements in Europe and North America. Garlic supplements are consumed for a variety of reasons, including for their purported antihypertensive, antibacterial, and anticarcinogenic effects. The steady increase in the global herbal dietary supplement market paired with a global patchwork of regulatory frameworks makes the development of assays for authentication of these products increasingly important. A DNA mini-barcode assay was developed using the P6 loop of the plastid trnL[UAA] intron to positively identify A. sativum products. Analysis of 43 commercially available garlic herbal dietary supplements produced mini-barcode sequences for 33 supplements, all of which contained detectable amounts of A. sativum. The trnL[UAA] P6 mini-barcode can be highly useful for specimen identification, particularly for samples that may contain degraded DNA.},
}
@article {pmid34604529,
year = {2021},
author = {Zhou, J and Du, Q and Jiang, M and Liu, S and Wang, L and Chen, H and Wang, B and Liu, C},
title = {Characterization and comparative analysis of the plastome sequence from Justicia ventricosa (Lamiales: Acanthaceae).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {6},
number = {10},
pages = {2896-2902},
pmid = {34604529},
issn = {2380-2359},
abstract = {Justicia ventricosa is a characteristic ethnic herb commonly used to treat Orthopedic pains. Here, to confirm its phylogenetic position and to develop molecular markers that can distinguish different Justicia species, we obtained and analyzed the plastome of Justicia ventricosa. The plastome was sequenced using the Illumina HiSeq sequencing platform, assembled with NOVOPlasty, and annotated with CPGAVAS2. The genome has a circular structure of 149,700 bp, containing a large single-copy region of 82,324 bp, a small single-copy region of 17,260 bp, and two reverse repeat regions of 25,058 bp each. It encodes 112 unique genes, including 76 protein-coding genes, eight ribosomal RNA genes, and 28 transfer RNA genes. Twenty cis-splicing genes were found. In total, we predicted 19 microsatellite repeats and 13 tandem repeat sequences. For distributed repeats, four were palindrome repeats and five were direct repeats. To find the highly variable intergenic spacer (IGS) regions, we calculated the K2P distances for IGS regions from four Justicia species. The K2P values ranged from 6.11 to 57.82. The largest K2P distances were found for ccsA-ndhD, petB-petD, psbK-psbI, and ycf4-cemA. Phylogenetic analysis results showed that J. ventricosa was most closely related to J. leptostachya. To determine how Justicia species adapt to the environment, we performed selection pressure analysis. Nine genes were found to have undergone positive selection. Lastly, we performed a genome-wise DNA barcode prediction, seven pairs of primers were found. The results provide valuable information that can be used for molecular marker development and bioprospecting in Justicia species.},
}
@article {pmid34602838,
year = {2021},
author = {Awad, J and Vasilita, C and Wenz, S and Alkarrat, H and Zimmermann, O and Zebitz, C and Krogmann, L},
title = {New records of German Scelionidae (Hymenoptera: Platygastroidea) from the collection of the State Museum of Natural History Stuttgart.},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e69856},
pmid = {34602838},
issn = {1314-2828},
abstract = {BACKGROUND: Scelionid wasps are arthropod egg parasitoids, many of which are relevant to global biosecurity. However, the scelionid fauna of Germany has not received much attention from professional taxonomists.<br><br>NEW INFORMATION: Eleven species and four genera are recorded for the first time from Germany, including species of interest to agriculture and biological control. First genus records include Baryconus F&#xf6;rster, Macroteleia Westwood, Paratelenomus Dodd and Probaryconus Kieffer. First species records include B.europaeus (Kieffer), Idrisnigroclavatus (Kieffer), Idrissemiflavus (Kieffer), M.bicolora Kieffer, M.pannonica Szabo, Paratelenomussaccharalis (Dodd), Trimorusvaricornis (Walker), Trissolcusbasalis (Wollaston), Trissolcusbelenus (Walker), Trissolcuscolemani (Crawford) and Trissolcusflavipes (Thompson). COI barcodes are identified for the first time from B.europaeus and M.bicolora. Each species is illustrated and updated world distributions are provided. Implications for agriculture are discussed.},
}
@article {pmid34601868,
year = {2021},
author = {Velázquez, E and Al-Ramahi, Y and Tellechea-Luzardo, J and Krasnogor, N and de Lorenzo, V},
title = {Targetron-Assisted Delivery of Exogenous DNA Sequences into Pseudomonas putida through CRISPR-Aided Counterselection.},
journal = {ACS synthetic biology},
volume = {10},
number = {10},
pages = {2552-2565},
pmid = {34601868},
issn = {2161-5063},
mesh = {*CRISPR-Cas Systems ; DNA/*administration &amp; dosage/genetics ; DNA Barcoding, Taxonomic ; Gene Editing/methods ; Genes, Bacterial ; Introns ; Plasmids ; Pseudomonas putida/*genetics ; },
abstract = {Genome editing methods based on group II introns (known as targetron technology) have long been used as a gene knockout strategy in a wide range of organisms, in a fashion independent of homologous recombination. Yet, their utility as delivery systems has typically been suboptimal due to the reduced efficiency of insertion when carrying exogenous sequences. We show that this limitation can be tackled and targetrons can be adapted as a general tool in Gram-negative bacteria. To this end, a set of broad-host-range standardized vectors were designed for the conditional expression of the Ll.LtrB intron. After establishing the correct functionality of these plasmids in Escherichia coli and Pseudomonas putida, we created a library of Ll.LtrB variants carrying cargo DNA sequences of different lengths, to benchmark the capacity of intron-mediated delivery in these bacteria. Next, we combined CRISPR/Cas9-facilitated counterselection to increase the chances of finding genomic sites inserted with the thereby engineered introns. With these novel tools, we were able to insert exogenous sequences of up to 600 bp at specific genomic locations in wild-type P. putida KT2440 and its ΔrecA derivative. Finally, we applied this technology to successfully tag P. putida with an orthogonal short sequence barcode that acts as a unique identifier for tracking this microorganism in biotechnological settings. These results show the value of the targetron approach for the unrestricted delivery of small DNA fragments to precise locations in the genomes of Gram-negative bacteria, which will be useful for a suite of genome editing endeavors.},
}
@article {pmid34601593,
year = {2021},
author = {Olivieri, L and Saville, RJ and Gange, AC and Xu, X},
title = {Apple endophyte community in relation to location, scion and rootstock genotypes and susceptibility to European canker.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {10},
pages = {},
pmid = {34601593},
issn = {1574-6941},
support = {BB/P007899/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Endophytes/genetics ; Genotype ; *Hypocreales ; *Malus ; Plant Diseases ; },
abstract = {European apple canker, caused by Neonectria ditissima, is a severe disease of apple. Achieving effective control is difficult with the currently available pesticides. Specific apple endophytes associated with cultivars may partially contribute to the cultivar response to the pathogen and thus could be used for disease management. We sought to determine whether the overall endophyte community differed among cultivars differing in their susceptibility to N. ditissima and to identify specific microbial groups associated with the susceptibility. Using Illumina MiSeq meta-barcoding, we profiled apple tree endophytes in 16 scion-rootstock combinations at two locations and quantified the relative contribution of scion, rootstock and location to the observed variability in the endophyte communities. Endophyte diversity was primarily affected by the orchard location (accounting for 29.4% and 85.9% of the total variation in the PC1 for bacteria and fungi, respectively), followed by the scion genotype (24.3% and 19.5% of PC2), whereas rootstock effects were small (<3% of PC1 and PC2). There were significant differences in the endophyte community between canker-resistant and -susceptible cultivars. Several bacterial and fungal endophyte groups had different relative abundance between susceptible and resistant cultivars. These endophyte groups included putative pathogen antagonists as well as plant pathogens. Their possible ecological roles in the N. ditissima pathosystem are discussed.},
}
@article {pmid34600494,
year = {2021},
author = {Huang, R and Xie, X and Chen, A and Li, F and Tian, E and Chao, Z},
title = {The chloroplast genomes of four Bupleurum (Apiaceae) species endemic to Southwestern China, a diversity center of the genus, as well as their evolutionary implications and phylogenetic inferences.},
journal = {BMC genomics},
volume = {22},
number = {1},
pages = {714},
pmid = {34600494},
issn = {1471-2164},
support = {30650652//National Natural Science Foundation of China/ ; 81373905//National Natural Science Foundation of China/ ; 2014A030313321//Guangdong Provincial Natural Science Foundation/ ; 2021M691482//china postdoctoral science foundation/ ; },
mesh = {*Apiaceae ; *Bupleurum/genetics ; China ; Ecosystem ; *Genome, Chloroplast ; Phylogeny ; },
abstract = {BACKGROUND: As one of the largest genera in Apiaceae, Bupleurum L. is well known for its high medicinal value. The genus has frequently attracted the attention of evolutionary biologist and taxonomist for its distinctive characteristics in the Apiaceae family. Although some chloroplast genomes data have been now available, the changes in the structure of chloroplast genomes and selective pressure in the genus have not been fully understood. In addition, few of the species are endemic to Southwest China, a distribution and diversity center of Chinese Bupleurum. Endemic species are key components of biodiversity and ecosystems, and investigation of the chloroplast genomes features of endemic species in Bupleurum will be helpful to develop a better understanding of evolutionary process and phylogeny of the genus. In this study, we analyzed the sequences of whole chloroplast genomes of 4 Southwest China endemic Bupleurum species in comparison with the published data of 17 Bupleurum species to determine the evolutionary characteristics of the genus and the phylogenetic relationships of Asian Bupleurum.<br><br>RESULTS: The complete chloroplast genome sequences of the 4 endemic Bupleurum species are 155,025&#x2009;bp to 155,323&#x2009;bp in length including a SSC and a LSC region separated by a pair of IRs. Comparative analysis revealed an identical chloroplast gene content across the 21 Bupleurum species, including a total of 114 unique genes (30 tRNA genes, 4 rRNA genes and 80 protein-coding genes). Chloroplast genomes of the 21 Bupleurum species showed no rearrangements and a high sequence identity (96.4-99.2%). They also shared a similar tendency of SDRs and SSRs, but differed in number (59-83). In spite of their high conservation, they contained some mutational hotspots, which can be potentially exploited as high-resolution DNA barcodes for species discrimination. Selective pressure analysis showed that four genes were under positive selection. Phylogenetic analysis revealed that the 21 Bupleurum formed two major clades, which are likely to correspond to their geographical distribution.<br><br>CONCLUSIONS: The chloroplast genome data of the four endemic Bupleurum species provide important insights into the characteristics and evolution of chloroplast genomes of this genu, and the phylogeny of Bupleurum.},
}
@article {pmid34599889,
year = {2021},
author = {Singh, OP and Sindhania, A and Sharma, G and Mishra, S and Sharma, SK and Singh, PK and Das, MK},
title = {Are members of the Anopheles fluviatilis complex conspecific?.},
journal = {Acta tropica},
volume = {224},
number = {},
pages = {106149},
doi = {10.1016/j.actatropica.2021.106149},
pmid = {34599889},
issn = {1873-6254},
mesh = {Animals ; *Anopheles/genetics ; DNA, Ribosomal ; *Malaria ; Mosquito Vectors/genetics ; Polymerase Chain Reaction ; },
abstract = {Anopheles fluviatilis sensu lato, a primary malaria vector in India, has been identified to be comprised of four cryptic species, provisionally designated as species S, T, U and V. However, Kumar et al. (Mol Ecol Resour, 2013;13:354-61) considered all of the then known three members of this species complex (S, T and U) conspecific. The specific status of species S and T was refuted based on the lack of sufficient barcode gap in mitochondrial-CO1 and the perceived presence of heterozygotes in populations as detected through one of the two species-specific PCR assays employed for the cryptic species identification. The existence of species U was refuted claiming that earlier investigations have already refuted their existence. Here we discuss problems associated with the CO1-based barcode approach for delimitation of cryptic species, the perceived heterozygosity between species S and T based on a species-specific PCR assay, and interpretation of published reports. We demonstrated that fixed differences do exist in the ITS2-rDNA sequence of species S and T with no evidence of heterozygotes in sympatric populations and, that the observed heterozygosity by Kumar et al. in the ITS2-based species diagnostic PCR is due to the high mispriming tendency of the T-specific primer with species S. We infer that mitochondrial DNA-based 'barcoding gap', an arbitrary threshold recommended for species delimitation, alone, is inadequate to delimit the members of An. fluviatilis complex.},
}
@article {pmid34595064,
year = {2021},
author = {Santana, DJ and da Silva, LA and Sant'Anna, AC and Shepard, DB and Mângia, S},
title = {A new species of Proceratophrys Miranda-Ribeiro, 1920 (Anura, Odontophrynidae) from Southern Amazonia, Brazil.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e12012},
pmid = {34595064},
issn = {2167-8359},
abstract = {Based on concordant differences in morphology, male advertisement call, and 16S mtDNA barcode distance, we describe a new species of Proceratophrys from southern Amazonia, in the states of Mato Grosso and Pará, Brazil. The new species is most similar to P. concavitympanum and P. ararype but differs from these species by its proportionally larger eyes and features of the advertisement call. Additionally, genetic distance between the new species and its congeners is 3.0-10.4% based on a fragment of the 16S rRNA gene, which is greater than the threshold typically characterizing distinct species of anurans. Using an integrative approach (molecular, bioacoustics, and adult morphology), we were able to distinguish the new species from other congeneric species. The new species is known only from the type locality where it is threatened by illegal logging and gold mining as well as hydroelectric dams.},
}
@article {pmid34594153,
year = {2021},
author = {Young, RG and Gill, R and Gillis, D and Hanner, RH},
title = {Molecular Acquisition, Cleaning and Evaluation in R (MACER) - A tool to assemble molecular marker datasets from BOLD and GenBank.},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e71378},
pmid = {34594153},
issn = {1314-2828},
abstract = {Molecular sequence data is an essential component for many biological fields of study. The strength of these data is in their ability to be centralised and compared across research studies. There are many online repositories for molecular sequence data, some of which are very large accumulations of varying data types like NCBI's GenBank. Due to the size and the complexity of the data in these repositories, challenges arise in searching for data of interest. While data repositories exist for molecular markers, taxa and other specific research interests, repositories may not contain, or be suitable for, more specific applications. Manually accessing, searching, downloading, accumulating, dereplicating and cleaning data to construct project-specific datasets is time-consuming. In addition, the manual assembly of datasets presents challenges with reproducibility. Here, we present the MACER package to assist researchers in assembling molecular datasets and provide reproducibility in the process.},
}
@article {pmid34590264,
year = {2021},
author = {Bakkeren, E and Newson, JPM and Hardt, WD},
title = {Analysis of Salmonella Persister Population Sizes, Dynamics of Gut Luminal Seeding, and Plasmid Transfer in Mouse Models of Salmonellosis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2357},
number = {},
pages = {253-272},
pmid = {34590264},
issn = {1940-6029},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Disease Models, Animal ; Mice ; Plasmids/genetics ; Population Density ; Salmonella/genetics ; *Salmonella Infections ; },
abstract = {A previously unappreciated link between persisters and the emergence and spread of antibiotic resistance has been recently established. The bulk of this research has been conducted in vitro, but some studies are beginning to elucidate the importance of persister reservoirs in both antibiotic treatment failure and the spread of antibiotic resistance using in vivo models. In order to further this research, careful analyses of the mechanisms of persister reservoir formation as well as the dynamics of persister survival and postantibiotic regrowth are of importance. Here, we present a mouse model to quantitatively study Salmonella persisters in vivo. By using neutral unique sequence barcodes, we describe the quantitative analysis of rare events (aka bottlenecks) associated with persister reservoir formation, survival, and reseeding of the gut lumen. This provides quantitative data for persister-fueled plasmid transfer in vivo. Although this chapter describes analysis of Salmonella persisters in a mouse model, these concepts can be applied to any experimental system provided that tractable experimental systems are present.},
}
@article {pmid34589293,
year = {2021},
author = {Lawley, JW and Gamero-Mora, E and Maronna, MM and Chiaverano, LM and Stampar, SN and Hopcroft, RR and Collins, AG and Morandini, AC},
title = {The importance of molecular characters when morphological variability hinders diagnosability: systematics of the moon jellyfish genus Aurelia (Cnidaria: Scyphozoa).},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e11954},
pmid = {34589293},
issn = {2167-8359},
abstract = {Cryptic species have been detected across Metazoa, and while no apparent morphological features distinguish them, it should not impede taxonomists from formal descriptions. We accepted this challenge for the jellyfish genus Aurelia, which has a long and confusing taxonomic history. We demonstrate that morphological variability in Aurelia medusae overlaps across very distant geographic localities. Even though some morphological features seem responsible for most of the variation, regional geographic patterns of dissimilarities are lacking. This is further emphasized by morphological differences found when comparing lab-cultured Aurelia coerulea medusae with the diagnostic features in its recent redescription. Previous studies have also highlighted the difficulties in distinguishing Aurelia polyps and ephyrae, and their morphological plasticity. Therefore, mostly based on genetic data, we recognize 28 species of Aurelia, of which seven were already described, 10 are formally described herein, four are resurrected and seven remain undescribed. We present diagnostic genetic characters for all species and designate type materials for newly described and some resurrected species. Recognizing moon jellyfish diversity with formal names is vital for conservation efforts and other studies. This work clarifies the practical implications of molecular genetic data as diagnostic characters, and sheds light on the patterns and processes that generate crypsis.},
}
@article {pmid34588970,
year = {2021},
author = {Liang, D and Xia, S and Zhang, X and Zhang, W},
title = {Analysis of Brain Functional Connectivity Neural Circuits in Children With Autism Based on Persistent Homology.},
journal = {Frontiers in human neuroscience},
volume = {15},
number = {},
pages = {745671},
pmid = {34588970},
issn = {1662-5161},
abstract = {Autism spectrum disorder (ASD) is a complex neuropsychiatric disorder with a complex and unknown etiology. Statistics demonstrate that the number of people diagnosed with ASD is increasing in countries around the world. Currently, although many neuroimaging studies indicate that ASD is characterized by abnormal functional connectivity (FC) patterns within brain networks rather than local functional or structural abnormalities, the FC characteristics of ASD are still poorly understood. In this study, a Vietoris-Rips (VR) complex filtration model of the brain functional network was established by using resting-state functional magnetic resonance imaging (fMRI) data of children aged 6-13 years old [including 54 ASD patients and 52 typical development (TD) controls] from the Autism Brain Imaging Data Exchange (ABIDE) public database. VR complex filtration barcodes are calculated by using persistent homology to describe the changes in the FC neural circuits of brain networks. The number of FC neural circuits with different length ranges at different threshold values is calculated by using the barcodes, the different brain regions participating in FC neural circuits are discussed, and the connectivity characteristics of brain FC neural circuits in the two groups are compared and analyzed. Our results show that the number of FC neural circuits with lengths of 8-12 is significantly decreased in the ASD group compared with the TD control group at threshold values of 0.7, 0.8 and 0.9, and there is no significant difference in the number of FC neural circuits with lengths of 4-7 and 13-16 and lengths 16. When the thresholds are 0.7, 0.8, and 0.9, the number of FC neural circuits in some brain regions, such as the right orbital part of the superior frontal gyrus, the left supplementary motor area, the left hippocampus, and the right caudate nucleus, involved in the study is significantly decreased in the ASD group compared with the TD control group. The results of this study indicate that there are significant differences in the FC neural circuits of brain networks in the ASD group compared with the TD control group.},
}
@article {pmid34587965,
year = {2021},
author = {Srivathsan, A and Lee, L and Katoh, K and Hartop, E and Kutty, SN and Wong, J and Yeo, D and Meier, R},
title = {ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone.},
journal = {BMC biology},
volume = {19},
number = {1},
pages = {217},
pmid = {34587965},
issn = {1741-7007},
mesh = {*Biodiversity ; Computational Biology ; DNA Barcoding, Taxonomic ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; Software ; },
abstract = {BACKGROUND: DNA barcodes are a useful tool for discovering, understanding, and monitoring biodiversity which are critical tasks at a time of rapid biodiversity loss. However, widespread adoption of barcodes requires cost-effective and simple barcoding methods. We here present a workflow that satisfies these conditions. It was developed via "innovation through subtraction" and thus requires minimal lab equipment, can be learned within days, reduces the barcode sequencing cost to < 10 cents, and allows fast turnaround from specimen to sequence by using the portable MinION sequencer.<br><br>RESULTS: We describe how tagged amplicons can be obtained and sequenced with the real-time MinION sequencer in many settings (field stations, biodiversity labs, citizen science labs, schools). We also provide amplicon coverage recommendations that are based on several runs of the latest generation of MinION flow cells ("R10.3") which suggest that each run can generate barcodes for >&#x2009;10,000 specimens. Next, we present a novel software, ONTbarcoder, which overcomes the bioinformatics challenges posed by MinION reads. The software is compatible with Windows 10, Macintosh, and Linux, has a graphical user interface (GUI), and can generate thousands of barcodes on a standard laptop within hours based on only two input files (FASTQ, demultiplexing file). We document that MinION barcodes are virtually identical to Sanger and Illumina barcodes for the same specimens (>&#x2009;99.99%) and provide evidence that MinION flow cells and reads have improved rapidly since 2018.<br><br>CONCLUSIONS: We propose that barcoding with MinION is the way forward for government agencies, universities, museums, and schools because it combines low consumable and capital cost with scalability. Small projects can use the flow cell dongle ("Flongle") while large projects can rely on MinION flow cells that can be stopped and re-used after collecting sufficient data for a given project.},
}
@article {pmid34587213,
year = {2021},
author = {Wilkinson, DA and Edwards, M and Benschop, J and Nisa, S},
title = {Identification of pathogenic Leptospira species and serovars in New Zealand using metabarcoding.},
journal = {PloS one},
volume = {16},
number = {9},
pages = {e0257971},
pmid = {34587213},
issn = {1932-6203},
mesh = {Animals ; Cattle ; Cattle Diseases/*microbiology ; DNA Barcoding, Taxonomic ; Environmental Monitoring ; Leptospira/*genetics ; Leptospirosis/microbiology/*veterinary ; New Zealand ; *Serogroup ; },
abstract = {Leptospirosis is a zoonotic disease of global importance. The breadth of Leptospira diversity associated with both human and animal disease poses major logistical challenges to the use of classical diagnostic techniques, and increasingly molecular diagnostic tools are used for their detection. In New Zealand, this has resulted in an increase in positive cases reported nationally that have not been attributed to the infecting serovar or genomospecies. In this study, we used data from all pathogenic Leptospira genomes to identify a partial region of the glmU gene as a suitable locus for the discrimination of the infecting species and serovars of New Zealand-endemic Leptospira. This method can be used in culture and culture-independent scenarios making it flexible for diagnostics in humans, animals, and environmental samples. We explored the use of this locus as a molecular barcoding tool via the Oxford Nanopore Technology (ONT) sequencing platform MinION. Sequences obtained by this method allowed specific identification of Leptospira species in mixed and enriched environmental cultures, however read error inherent in the MinION sequencing system reduced the accuracy of strain/variant identification. Using this approach to characterise Leptospira in enriched environmental cultures, we detected the likely presence of Leptospira genomospecies that have not been reported in New Zealand to date. This included a strain of L. borgpetersenii that has recently been identified in dairy cattle and sequences similar to those of L. mayottensis. L. tipperaryensis, L. dzianensis and L. alstonii.},
}
@article {pmid34586776,
year = {2021},
author = {Ivanov, AV and Safenkova, IV and Zherdev, AV and Dzantiev, BB},
title = {Multiplex Assay of Viruses Integrating Recombinase Polymerase Amplification, Barcode-Anti-Barcode Pairs, Blocking Anti-Primers, and Lateral Flow Assay.},
journal = {Analytical chemistry},
volume = {93},
number = {40},
pages = {13641-13650},
doi = {10.1021/acs.analchem.1c03030},
pmid = {34586776},
issn = {1520-6882},
mesh = {DNA Primers ; Gold ; *Metal Nanoparticles ; Nucleic Acid Amplification Techniques ; *Plant Viruses ; Recombinases ; Sensitivity and Specificity ; },
abstract = {A multiplex assay based on recombinase polymerase amplification (RPA) and lateral flow test (LFT) is a desirable tool for many areas. This multiplex assay could be efficiently realized using single-stranded (ss) DNAs located in separate zones on the test strip and bound complementary ssDNA tags of double-stranded (ds) DNA amplicons. Here, we investigate how to enrich multiplex assay capabilities using ssDNAs. Bifunctional oligonucleotide probes integrating (1) a forward primer for RPA, (2) a C9 spacer to stop polymerase, and (3) a ssDNA tag for binding at test strip are developed. The amplicons have a unique individual ssDNA tag at one end and a universal label of fluorescein introducing through a reverse primer at the other end. A conjugate of gold nanoparticles (GNP) with antibodies to fluorescein is used to detect all amplicons. The remainder of primers after RPA interacting with GNP conjugate was found to be a limiting factor for sensitive and specific multiplex assay. The addition of anti-RPA-primers before the use of test strips was proposed to simply and effectively eliminate remaining primers. This approach was successfully applied for the detection of three priority plant RNA viruses: potato virus Y (PVY), -S (PVS) and potato leafroll virus (PLRV). The total time of the assay is 30 min. The multiplex RPA-LFT detected at least 4 ng of PVY per g of plant leaves, 0.04 ng/g for PVS, and 0.04 ng/g for PLRV. The testing of healthy and infected potato samples showed concordance between the developed assay and reverse transcription-polymerase chain reaction. Thus, the capabilities of the proposed universal modules (ssDNA anchors, bifunctional probes, and blocking anti-primers) for multiplex detection of RNA analytes with high specificity and sensitivity were demonstrated.},
}
@article {pmid34579429,
year = {2021},
author = {Mustafa, AA and Derise, MR and Yong, WTL and Rodrigues, KF},
title = {A Concise Review of Dendrocalamus asper and Related Bamboos: Germplasm Conservation, Propagation and Molecular Biology.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {9},
pages = {},
pmid = {34579429},
issn = {2223-7747},
support = {Niche Grant (DN20091) entitled "Identification and Selection of Endemic Bamboo Varieties of Sabah for Mass Propagation using Tissue Culture"//Pusat Penyelidikan dan Inovasi, Universiti Malaysia Sabah/ ; },
abstract = {Bamboos represent an emerging forest resource of economic significance and provide an avenue for sustainable development of forest resources. The development of the commercial bamboo industry is founded upon efficient molecular and technical approaches for the selection and rapid multiplication of elite germplasm for its subsequent propagation via commercial agro-forestry business enterprises. This review will delve into the micropropagation of Dendrocalamus asper, one of the most widely cultivated commercial varieties of bamboo, and will encompass the selection of germplasm, establishment of explants in vitro and micropropagation techniques. The currently available information pertaining to molecular biology, DNA barcoding and breeding, has been included, and potential areas for future research in the area of genetic engineering and gene regulation have been highlighted. This information will be of relevance to both commercial breeders and molecular biologists who have an interest in establishing bamboo as a crop of the future.},
}
@article {pmid34578199,
year = {2021},
author = {Becchimanzi, A and Zimowska, B and Nicoletti, R},
title = {Cryptic Diversity in Cladosporium cladosporioides Resulting from Sequence-Based Species Delimitation Analyses.},
journal = {Pathogens (Basel, Switzerland)},
volume = {10},
number = {9},
pages = {},
pmid = {34578199},
issn = {2076-0817},
abstract = {Cladosporium cladosporioides is an extremely widespread fungus involved in associations ranging from mutualistic to pathogenic and is the most frequently represented Cladosporium species in sequence databases, such as Genbank. The taxonomy of Cladosporium species, currently based on the integration of molecular data with morphological and cultural characters, is in frequent need of revision. Hence, the recently developed species delimitation methods can be helpful to explore cryptic diversity in this genus. Considering a previous study that reported several hypothetical species within C. cladosporioides, we tested four methods of species delimitation using the combined DNA barcodes internal transcribed spacers, translation elongation factor 1-α and actin 1. The analyses involved 105 isolates, revealing that currently available sequences of C. cladosporioides in GenBank actually represent more than one species. Moreover, we found that eight isolates from this set should be ascribed to Cladosporium anthropophilum. Our results revealed a certain degree of discordance among species delimitation methods, which can be efficiently treated using conservative approaches in order to minimize the risk of considering false positives.},
}
@article {pmid34575872,
year = {2021},
author = {Palumbo, F and Vannozzi, A and Barcaccia, G},
title = {Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies.},
journal = {International journal of molecular sciences},
volume = {22},
number = {18},
pages = {},
pmid = {34575872},
issn = {1422-0067},
mesh = {Apiaceae/*genetics ; Cell Nucleus/metabolism ; Chromosome Mapping ; *Crops, Agricultural ; Cytoplasm/metabolism ; Genes, Plant ; Genetic Markers ; *Genome, Plant ; Genomics ; Genotype ; Microsatellite Repeats ; Phylogeny ; *Plant Breeding ; Polymorphism, Single Nucleotide ; RNA-Seq ; *Transcriptome ; },
abstract = {The Apiaceae taxon is one of the most important families of flowering plants and includes thousands of species used for food, flavoring, fragrance, medical and industrial purposes. This study had the specific intent of reviewing the main genomics and transcriptomic data available for this family and their use for the constitution of new varieties. This was achieved starting from the description of the main reproductive systems and barriers, with particular reference to cytoplasmic (CMS) and nuclear (NMS) male sterility. We found that CMS and NMS systems have been discovered and successfully exploited for the development of varieties only in Foeniculum vulgare, Daucus carota, Apium graveolens and Pastinaca sativa; whereas, strategies to limit self-pollination have been poorly considered. Since the constitution of new varieties benefits from the synergistic use of marker-assisted breeding in combination with conventional breeding schemes, we also analyzed and discussed the available SNP and SSR marker datasets (20 species) and genomes (8 species). Furthermore, the RNA-seq studies aimed at elucidating key pathways in stress tolerance or biosynthesis of the metabolites of interest were limited and proportional to the economic weight of each species. Finally, by aligning 53 plastid genomes from as many species as possible, we demonstrated the precision offered by the super barcoding approach to reconstruct the phylogenetic relationships of Apiaceae species. Overall, despite the impressive size of this family, we documented an evident lack of molecular data, especially because genomic and transcriptomic resources are circumscribed to a small number of species. We believe that our contribution can help future studies aimed at developing molecular tools for boosting breeding programs in crop plants of the Apiaceae family.},
}
@article {pmid34575804,
year = {2021},
author = {Paloi, S and Mhuantong, W and Luangsa-Ard, JJ and Kobmoo, N},
title = {Using High-Throughput Amplicon Sequencing to Evaluate Intragenomic Variation and Accuracy in Species Identification of Cordyceps Species.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {7},
number = {9},
pages = {},
pmid = {34575804},
issn = {2309-608X},
support = {P1950231//National Center for Genetic Engineering and Biotechnology/ ; },
abstract = {While recent sequencing technologies (third generation sequencing) can successfully sequence all copies of nuclear ribosomal DNA (rDNA) markers present within a genome and offer insights into the intragenomic variation of these markers, high intragenomic variation can be a source of confusion for high-throughput species identification using such technologies. High-throughput (HT) amplicon sequencing via PacBio SEQUEL I was used to evaluate the intragenomic variation of the ITS region and D1-D2 LSU domains in nine Cordyceps species, and the accuracy of such technology to identify these species based on molecular phylogenies was also assessed. PacBio sequences within strains showed variable level of intragenomic variation among the studied Cordyceps species with C. blackwelliae showing greater variation than the others. Some variants from a mix of species clustered together outside their respective species of origin, indicative of intragenomic variation that escaped concerted evolution shared between species. Proper selection of consensus sequences from HT amplicon sequencing is a challenge for interpretation of correct species identification. PacBio consensus sequences with the highest number of reads represent the major variants within a genome and gave the best results in terms of species identification.},
}
@article {pmid34574328,
year = {2021},
author = {Zhu, X and Wu, M and Deng, R and Rizwan Khan, M and Deng, S and Wang, X and Busquets, R and Deng, W and Luo, A},
title = {Amplification Refractory Mutation System (ARMS)-PCR for Waxy Sorghum Authentication with Single-Nucleotide Resolution.},
journal = {Foods (Basel, Switzerland)},
volume = {10},
number = {9},
pages = {},
pmid = {34574328},
issn = {2304-8158},
support = {No. 2019CDLZ-02//Sichuan-Luzhou strategic cooperation project/ ; No. 2019ZHCG0073//Sichuan technological transformation program/ ; RSP-2021/138//King Saud University, Riyadh, Saudi Arabia/ ; },
abstract = {Waxy sorghum has greater economic value than wild sorghum in relation to their use in food processing and the brewing industry. Thus, the authentication of the waxy sorghum species is an important issue. Herein, a rapid and sensitive Authentication Amplification Refractory Mutation System-PCR (aARMS-PCR) method was employed to identify sorghum species via its ability to resolve single-nucleotide in genes. As a proof of concept, we chose a species of waxy sorghum containing the wx[c] mutation which is abundantly used in liquor brewing. The aARMS-PCR can distinguish non-wx[c] sorghum from wx[c] sorghum to guarantee identification of specific waxy sorghum species. It allowed to detect as low as 1% non-wx[c] sorghum in sorghum mixtures, which ar one of the most sensitive tools for food authentication. Due to its ability for resolving genes with single-nucleotide resolution and high sensitivity, aARMS-PCR may have wider applicability in monitoring food adulteration, offering a rapid food authenticity verification in the control of adulteration.},
}
@article {pmid34573887,
year = {2021},
author = {Ruenchit, P},
title = {State-of-the-Art Techniques for Diagnosis of Medical Parasites and Arthropods.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {11},
number = {9},
pages = {},
pmid = {34573887},
issn = {2075-4418},
support = {MRG6280087//Research Grant for New Scholar/ ; },
abstract = {Conventional methods such as microscopy have been used to diagnose parasitic diseases and medical conditions related to arthropods for many years. Some techniques are considered gold standard methods. However, their limited sensitivity, specificity, and accuracy, and the need for costly reagents and high-skilled technicians are critical problems. New tools are therefore continually being developed to reduce pitfalls. Recently, three state-of-the-art techniques have emerged: DNA barcoding, geometric morphometrics, and artificial intelligence. Here, data related to the three approaches are reviewed. DNA barcoding involves an analysis of a barcode sequence. It was used to diagnose medical parasites and arthropods with 95.0% accuracy. However, this technique still requires costly reagents and equipment. Geometric morphometric analysis is the statistical analysis of the patterns of shape change of an anatomical structure. Its accuracy is approximately 94.0-100.0%, and unlike DNA barcoding, costly reagents and equipment are not required. Artificial intelligence technology involves the analysis of pictures using well-trained algorithms. It showed 98.8-99.0% precision. All three approaches use computer programs instead of human interpretation. They also have the potential to be high-throughput technologies since many samples can be analyzed at once. However, the limitation of using these techniques in real settings is species coverage.},
}
@article {pmid34570467,
year = {2021},
author = {Pan, V and Wang, W and Heaven, I and Bai, T and Cheng, Y and Chen, C and Ke, Y and Wei, B},
title = {Monochromatic Fluorescent Barcodes Hierarchically Assembled from Modular DNA Origami Nanorods.},
journal = {ACS nano},
volume = {15},
number = {10},
pages = {15892-15901},
doi = {10.1021/acsnano.1c03796},
pmid = {34570467},
issn = {1936-086X},
mesh = {DNA/genetics ; Fluorescent Dyes ; Microscopy, Fluorescence ; *Nanotubes ; *Nucleic Acids ; },
abstract = {With the rapid advancement of fluorescence microscopy, there is a growing interest in the multiplexed detection and identification of various bioanalytes (e.g., nucleic acids and proteins) for efficient sample processing and analysis. We introduce in this work a simple and robust method to provide combinations for micrometer-scale fluorescent DNA barcodes of hierarchically assembled DNA origami superstructures for multiplexed molecular probing. In addition to optically resolvable dots, we placed fluorescent loci on adjacent origami within the diffraction limit of each other, rendering them as unresolvable bars of measurable lengths. We created a basic set of barcodes and trained a machine learning algorithm to process and identify individual barcodes from raw images with high accuracy. Moreover, we demonstrated that the number of combinations can be increased exponentially by generating longer barcodes, by controlling the number of incorporated fluorophores to create multiple levels of fluorescence intensity, and by employing super-resolution imaging. To showcase the readiness of the barcodes for applications, we used our barcodes to capture and identify target nucleic acid sequences and for simultaneous multiplexed characterization of binding kinetics of several orthogonal complementary nucleic acids.},
}
@article {pmid34567032,
year = {2021},
author = {Boivin, S and Mahé, F and Debellé, F and Pervent, M and Tancelin, M and Tauzin, M and Wielbo, J and Mazurier, S and Young, P and Lepetit, M},
title = {Genetic Variation in Host-Specific Competitiveness of the Symbiont Rhizobium leguminosarum Symbiovar viciae.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {719987},
pmid = {34567032},
issn = {1664-462X},
abstract = {Legumes of the Fabeae tribe form nitrogen-fixing root nodules resulting from symbiotic interaction with the soil bacteria Rhizobium leguminosarum symbiovar viciae (Rlv). These bacteria are all potential symbionts of the Fabeae hosts but display variable partner choice when co-inoculated in mixture. Because partner choice and symbiotic nitrogen fixation mostly behave as genetically independent traits, the efficiency of symbiosis is often suboptimal when Fabeae legumes are exposed to natural Rlv populations present in soil. A core collection of 32 Rlv bacteria was constituted based on the genomic comparison of a collection of 121 genome sequences, representative of known worldwide diversity of Rlv. A variable part of the nodD gene sequence was used as a DNA barcode to discriminate and quantify each of the 32 bacteria in mixture. This core collection was co-inoculated on a panel of nine genetically diverse Pisum sativum, Vicia faba, and Lens culinaris genotypes. We estimated the relative Early Partner Choice (EPC) of the bacteria with the Fabeae hosts by DNA metabarcoding on the nodulated root systems. Comparative genomic analyses within the bacterial core collection identified molecular markers associated with host-dependent symbiotic partner choice. The results revealed emergent properties of rhizobial populations. They pave the way to identify genes related to important symbiotic traits operating at this level.},
}
@article {pmid34567021,
year = {2021},
author = {Cheng, S and Zeng, W and Wang, J and Liu, L and Liang, H and Kou, Y and Wang, H and Fan, D and Zhang, Z},
title = {Species Delimitation of Asteropyrum (Ranunculaceae) Based on Morphological, Molecular, and Ecological Variation.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {681864},
pmid = {34567021},
issn = {1664-462X},
abstract = {Objectively evaluating different lines of evidence within a formalized framework is the most efficient and theoretically grounded approach for defining robust species hypotheses. Asteropyrum Drumm. et Hutch. is a small genus of perennial herb containing two species, A. cavaleriei and A. peltatum. The distinction of these two species mainly lies in the shape and size of leaf blades. However, these characters have been considered labile and could not differentiate the two species reliably. In this study, we investigated the variation of the leaf blades of 28 populations across the whole range of Asteropyrum using the landmark-based geometric morphometrics (GMM), sought genetic gaps within this genus using DNA barcoding, phylogenetic reconstruction and population genetic methods, and compared the predicted ecological niches of the two species. The results showed that the leaf form (shape and size) was overlapped between the two species; barcode gap was not detected within the genus Asteropyrum; and little ecological and geographical differentiation was found between the two taxa. Two genetic clusters detected by population genetic analysis did not match the two morphospecies. The results suggest that there are no distinct boundaries between the two species of Asteropyrum in terms of morphology, genetics and ecology and this present classification should be abandoned. We anticipate that range-wide population genomic studies would properly delineate the species boundaries and help to understand the evolution and speciation within Asteropyrum.},
}
@article {pmid34566452,
year = {2021},
author = {Murillo-Ramos, L and Sihvonen, P and Brehm, G and Ríos-Malaver, IC and Wahlberg, N},
title = {A database and checklist of geometrid moths (Lepidoptera) from Colombia.},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e68693},
pmid = {34566452},
issn = {1314-2828},
abstract = {BACKGROUND: Molecular DNA sequence data allow unprecedented advances in biodiversity assessments, monitoring schemes and taxonomic works, particularly in poorly-explored areas. They allow, for instance, the sorting of material rapidly into operational taxonomic units (such as BINs - Barcode Index Numbers), sequences can be subject to diverse analyses and, with linked metadata and physical vouchers, they can be examined further by experts. However, a prerequisite for their exploitation is the construction of reference libraries of DNA sequences that represent the existing biodiversity. To achieve these goals for Geometridae (Lepidoptera) moths in Colombia, expeditions were carried out to 26 localities in the northern part of the country in 2015-2019. The aim was to collect specimens and sequence their DNA barcodes and to record a fraction of the species richness and occurrences in one of the most biodiversity-rich countries. These data are the beginning of an identification guide to Colombian geometrid moths, whose identities are currently often provisional only, being morpho species or operational taxonomic units (OTUs). Prior to the current dataset, 99 Geometridae sequences forming 44 BINs from Colombia were publicly available on the Barcode of Life Data System (BOLD), covering 20 species only.<br><br>NEW INFORMATION: We enrich the Colombian Geometridae database significantly by including DNA barcodes, two nuclear markers, photos of vouchers and georeferenced occurrences of 281 specimens of geometrid moths from different localities. These specimens are classified into 80 genera. Analytical tools on BOLD clustered 157 of the mentioned sequences to existing BINs identified to species level, identified earlier by experts. Another 115 were assigned to BINs that were identified to genus or tribe level only. Eleven specimens did not match any existing BIN on BOLD and are, therefore, new additions to the database. It is likely that many BINs represent undescribed species. Nine short sequences (< 500bp) were not assigned to BINs, but identified to the lowest taxonomic category by expert taxonomists and with comparisons of type material photos. The released new genetic information will help to further progress the systematics of Geometridae. An illustrated catalogue of all new records allows validation of our identifications; it is also the first document of this kind for Colombian Geometridae. All specimens are deposited at the Museo de Zoolog&#xed;a of Universidad de Sucre (MZUS), North Colombia. DNA BINs are reported in this study through dx.doi.org/10.5883/DS-GEOCO, the species occurrences are available on SIB Colombia https://sibcolombia.net/ and the Global Biodiversity Information Facility (GBIF) https://www.gbif.org/ through https://doi.org/10.15472/ucfmkh.},
}
@article {pmid34564270,
year = {2021},
author = {Hlaka, V and Guilbert, &#xc9; and Smit, SJ and van Noort, S and Allsopp, E and Langley, J and van Asch, B},
title = {Species Diversity and Phylogenetic Relationships of Olive Lace Bugs (Hemiptera: Tingidae) Found in South Africa.},
journal = {Insects},
volume = {12},
number = {9},
pages = {},
pmid = {34564270},
issn = {2075-4450},
support = {131741//National Research Foundation/ ; },
abstract = {Olive lace bugs (Hemiptera: Tingidae) are small sap-sucking insects that feed on wild and cultivated Olea europaea. The diversity of olive lace bug species in South Africa, the most important olive producer on the continent, has been incompletely surveyed. Adult specimens were collected in the Western Cape province for morphological and DNA-based species identification, and sequencing of complete mitogenomes. Cysteochila lineata, Plerochila australis, Neoplerochila paliatseasi and Neoplerochila sp. were found at 12 sites. Intra- and interspecific genetic divergences and phylogenetic clustering in 30 species in 18 genera of Tingidae using new and publicly available DNA barcodes showed high levels of congruity between taxonomic and genetic data. The phylogenetic position of the four species found in South Africa was inferred using new and available mitogenomes of Tingidae. Notably, olive lace bugs formed a cluster of closely related species. However, Cysteochila was non-monophyletic as C. lineata was recovered as a sister species to P. australis whereas Cysteochila chiniana, the other representative of the genus, was grouped with Trachypeplus jacobsoni and Tingis cardui in a different cluster. This result suggests that feeding on O. europaea may have a common origin in Tingidae and warrants future research on potential evolutionary adaptations of olive lace bugs to this plant host.},
}
@article {pmid34564218,
year = {2021},
author = {Chen, HY and Yao, JM and Huang, SB and Pang, H},
title = {Ophelimus bipolaris sp. n. (Hymenoptera, Eulophidae), a New Invasive Eucalyptus Pest and Its Host Plants in China.},
journal = {Insects},
volume = {12},
number = {9},
pages = {},
pmid = {34564218},
issn = {2075-4450},
support = {No. 201904020041//Science and Technology Planning Project of Guangzhou/ ; },
abstract = {Eucalyptus species have become one of the most commonly planted trees worldwide, including China, due to their fast growth and various commercial applications. However, the productivity of Eucalyptus plantations has been threatened by exotic invasive insect pests in recent years. Among these pests, gall inducers of the genus Ophelimus of the Eulophidae family are among the most important invasive species in Eucalyptus plantations. We report here for the first time the presence of a new invasive Eucalyptus gall wasp, Ophelimus bipolaris sp. n., in Guangzhou, China, which also represents the first species of the genus reported from China. The identity of the new species was confirmed by an integrative approach combing biological, morphological and molecular evidence. The new species is described and illustrated. This wasp induces galls only on the leaf blade surface of four Eucalyptus species: E. grandis, E. grandis × E. urophylla, E. tereticornis and E. urophylla. Our preliminary observation showed that O. bipolaris could complete a life cycle on E. urophylla in approximately 2 months under local climatic conditions (23.5-30 °C). Considering the severe damage it may cause to Eucalyptus production, further investigations of its biology and control are urgently needed in China.},
}
@article {pmid34564202,
year = {2021},
author = {Bout, A and Tortorici, F and Hamidi, R and Warot, S and Tavella, L and Thomas, M},
title = {First Detection of the Adventive Egg Parasitoid of Halyomorpha halys (Stål) (Hemiptera: Pentatomidae) Trissolcus mitsukurii (Ashmead) (Hymenoptera: Scelionidae) in France.},
journal = {Insects},
volume = {12},
number = {9},
pages = {},
pmid = {34564202},
issn = {2075-4450},
support = {n&#xb0;7838010//REPLIK (2019-2022) (N&#xb0;7838010) - FEDER/ ; },
abstract = {We report the first detection of Trissolcus mitsukurii in France. More than 1860 sentinel egg masses of Halyomorpha halys (BMSB) were exposed in the field during the 2018-2020 period, and 12 specimens of T. mitsukurii emerged from one egg mass. Their taxonomic identification was confirmed both by morphological and molecular analysis. Trissolcus mitsukurii, similar to T. japonicus, is an egg parasitoid of BMSB in its area of origin in Asia, and both species are considered to be candidates for a classical biological control strategy against BMSB. Trissolcus mitsukurii was previously recorded in Italy where it is well established and widespread, and this may be the source of the French population. Possible permanent establishment and dispersion of T. mitsukurii in France should be monitored with emphasis on its potential effect on BMSB populations.},
}
@article {pmid34562422,
year = {2021},
author = {Fujisawa, Y and Homat, T and Thepparat, A and Changbunjong, T and Sutummaporn, K and Kornmatitsuk, S and Kornmatitsuk, B},
title = {DNA barcode identification and molecular detection of bluetongue virus in Culicoides biting midges (Diptera: Ceratopogonidae) from western Thailand.},
journal = {Acta tropica},
volume = {224},
number = {},
pages = {106147},
doi = {10.1016/j.actatropica.2021.106147},
pmid = {34562422},
issn = {1873-6254},
mesh = {Animals ; *Bluetongue ; *Bluetongue virus/genetics ; *Ceratopogonidae/genetics ; DNA Barcoding, Taxonomic ; Insect Vectors/genetics ; Seroepidemiologic Studies ; Sheep ; Thailand ; },
abstract = {Biting midges of the genus Culicoides Latreille are biological vectors of bluetongue virus (BTV), a member of family Reoviridae, genus Orbivirus. About 30 species of Culicoides have been identified as competent BTV vectors worldwide. Even though high seroprevalence of BTV has been reported among livestock ruminants from western Thailand, the Culicoides species which contribute to BTV transmission remain unclear. In the present study, Culicoides were collected from eight sampling sites, located in two BTV prevalent provinces in western Thailand. Adult Culicoides were identified using wing morphology and cytochrome c oxidase subunit I (COI) mtDNA molecular marker. A total of 9,677 Culicoides specimens belonging to 7 subgenera, 3 species groups, and 23 species were identified. After comparing sequencing results with available data from GenBank, COI sequences of five species were reported for the first time from Thailand. The most abundant potential BTV vector species collected were C. peregrinus, followed by C. orientalis, C. imicola, C. oxystoma, and C. fulvus. Out of 72 Culicoides pools, 9 pools (4 from C. orientalis, 2 from C. imicola, 2 from C. oxystoma, and 1 from C. fulvus) were positive by BTV RT-PCR analyses. These results are new to Culicoides BTV vector knowledge in Thailand and will contribute to further BTV studies in this particular region.},
}
@article {pmid34562055,
year = {2022},
author = {Roslin, T and Somervuo, P and Pentinsaari, M and Hebert, PDN and Agda, J and Ahlroth, P and Anttonen, P and Aspi, J and Blagoev, G and Blanco, S and Chan, D and Clayhills, T and deWaard, J and deWaard, S and Elliot, T and Elo, R and Haapala, S and Helve, E and Ilmonen, J and Hirvonen, P and Ho, C and Itämies, J and Ivanov, V and Jakovlev, J and Juslén, A and Jussila, R and Kahanpää, J and Kaila, L and Jari-PekkaKaitila, and Kakko, A and Kakko, I and Karhu, A and Karjalainen, S and Kjaerandsen, J and Koskinen, J and Laasonen, EM and Laasonen, L and Laine, E and Lampila, P and Levesque-Beaudin, V and Lu, L and Lähteenaro, M and Majuri, P and Malmberg, S and Manjunath, R and Martikainen, P and Mattila, J and McKeown, J and Metsälä, P and Miklasevskaja, M and Miller, M and Miskie, R and Muinonen, A and Veli-MattiMukkala, and Naik, S and Nikolova, N and Nupponen, K and Ovaskainen, O and Österblad, I and Paasivirta, L and Pajunen, T and Parkko, P and Paukkunen, J and Penttinen, R and Perez, K and Pohjoismäki, J and Prosser, S and Raekunnas, M and Rahulan, M and Rannisto, M and Ratnasingham, S and Raukko, P and Rinne, A and Rintala, T and Miranda Romo, S and Salmela, J and Salokannel, J and Savolainen, R and Schulman, L and Sihvonen, P and Soliman, D and Sones, J and Steinke, C and Ståhls, G and Tabell, J and Tiusanen, M and Várkonyi, G and Vesterinen, EJ and Viitanen, E and Vikberg, V and Viitasaari, M and Vilen, J and Warne, C and Wei, C and Winqvist, K and Zakharov, E and Mutanen, M},
title = {A molecular-based identification resource for the arthropods of Finland.},
journal = {Molecular ecology resources},
volume = {22},
number = {2},
pages = {803-822},
doi = {10.1111/1755-0998.13510},
pmid = {34562055},
issn = {1755-0998},
mesh = {Animals ; *Arthropods/classification ; Biodiversity ; DNA Barcoding, Taxonomic ; Finland ; Gene Library ; },
abstract = {To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.},
}
@article {pmid34561535,
year = {2021},
author = {Park, N and Yeom, J and Jeong, R and Lee, W},
title = {Novel attempt at discrimination of a bullet-shaped siphonophore (Family Diphyidae) using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-ToF MS).},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {19077},
pmid = {34561535},
issn = {2045-2322},
abstract = {One major difficulty in identifying the gelatinous bodied bullet-shaped Siphonophore, Diphyids, is that their shape is deformed following ethanol fixation. Ethanol often is preferred over other fixatives, since samples fixed in ethanol can be used for molecular studies that can supplement morphological findings. To overcome this problem, we obtained protein mass spectra of ten species of Diphyidae found in the waters of the Kuroshio Current (Northwest Pacific and South Coast of South Korea) to test whether MALDI-ToF MS could be used as a methodology for species identification. In addition, a number of morphological characteristics that can be used with ethanol-treated samples was summarized. Concatenated phylogenetic analysis was also performed to determine the phylogenetic relationship by obtaining partial sequences of four genes (mtCOI, 16S rRNA, 18S rRNA, and ITS regions). Based on our integrative analysis, MALDI-ToF MS was evaluated as a potentially fast, inexpensive, and accurate tool for species identification along with conventional morphological and DNA barcoding for Diphyidae.},
}
@article {pmid34559903,
year = {2022},
author = {Degrandmaison, J and Grisé, O and Parent, JL and Gendron, L},
title = {Differential barcoding of opioid receptors trafficking.},
journal = {Journal of neuroscience research},
volume = {100},
number = {1},
pages = {99-128},
doi = {10.1002/jnr.24949},
pmid = {34559903},
issn = {1097-4547},
support = {PJT-162103//CIHR/Canada ; },
mesh = {Analgesics/therapeutic use ; Analgesics, Opioid ; Animals ; *Chronic Pain/drug therapy ; Opioid Peptides/physiology ; *Receptors, Opioid/physiology ; Receptors, Opioid, mu ; },
abstract = {Over the past several years, studies have highlighted the δ-opioid receptor (DOPr) as a promising therapeutic target for chronic pain management. While exhibiting milder undesired effects than most currently prescribed opioids, its specific agonists elicit effective analgesic responses in numerous animal models of chronic pain, including inflammatory, neuropathic, diabetic, and cancer-related pain. However, as compared with the extensively studied μ-opioid receptor, the molecular mechanisms governing its trafficking remain elusive. Recent advances have denoted several significant particularities in the regulation of DOPr intracellular routing, setting it apart from the other members of the opioid receptor family. Although they share high homology, each opioid receptor subtype displays specific amino acid patterns potentially involved in the regulation of its trafficking. These precise motifs or "barcodes" are selectively recognized by regulatory proteins and therefore dictate several aspects of the itinerary of a receptor, including its anterograde transport, internalization, recycling, and degradation. With a specific focus on the regulation of DOPr trafficking, this review will discuss previously reported, as well as potential novel trafficking barcodes within the opioid and nociceptin/orphanin FQ opioid peptide receptors, and their impact in determining distinct interactomes and physiological responses.},
}
@article {pmid34556035,
year = {2021},
author = {Bravo, H and Cheng, CLY and Iannucci, A and Natali, C and Quadros, A and Rhodes, M and Yip, MML and Cannicci, S and Fratini, S},
title = {A DNA barcode library for mangrove gastropods and crabs of Hong Kong and the Greater Bay Area reveals an unexpected faunal diversity associated with the intertidal forests of Southern China.},
journal = {BMC ecology and evolution},
volume = {21},
number = {1},
pages = {180},
pmid = {34556035},
issn = {2730-7182},
mesh = {Animals ; Bayes Theorem ; *Brachyura/genetics ; China ; DNA Barcoding, Taxonomic ; Forests ; *Gastropoda/genetics ; Hong Kong ; Phylogeny ; Reproducibility of Results ; },
abstract = {BACKGROUND: Mangroves are tropical and subtropical intertidal forests colonising sheltered coasts across the world. They host a unique faunal community, dominated by brachyuran crabs and gastropods. These invertebrates strongly contribute to the functionality of the entire forest. The reliable assessment of mangrove faunal diversity is, thus, a crucial step for efficient management and conservation plans, but it is hindered by difficulties in species identification. Here we provide a verified DNA barcode library for brachyuran crabs and gastropods inhabiting the mangroves of the Greater Bay Area, Southern China. In particular, we collected and morphologically identified 1100 specimens of mangrove associated brachyuran crabs and gastropods. The partial sequences of the mtDNA cytochrome oxidase subunit I gene were obtained from 275 specimens. Barcode sequences were then used to delineate Molecular Operational Taxonomic Units (MOTUs), employing three different delimitation methods: the automatic barcode gap discovery (ABGD) method, the general mixed Yule coalescent (GMYC) model and a Bayesian implementation of the Poisson tree processes (bPTP) model.<br><br>RESULTS: By integrating DNA barcodes with morphology, we identified 44 gastropod species and 58 brachyuran species associated with Hong Kong mangroves, with five and seven new records, for gastropods and crabs, respectively, for the Greater Bay Area. The delineation of MOTUs based on barcode sequences revealed a strong congruence between morphological and molecular identification for both taxa, showing the high reliability of the barcode library.<br><br>CONCLUSIONS: This study provides the first reference barcode library for mangrove-associated macrobenthic fauna in the Greater Bay Area and represents a reliable tool to management and conservation plans. Our molecular analyses resolved long lasting taxonomic misidentifications and inconsistencies and updated the knowledge on the geographical distribution of Asian mangrove associated fauna, ultimately highlighting a level of biodiversity higher than previously thought for Southern China.},
}
@article {pmid34552011,
year = {2021},
author = {Johansson, G and Berndsen, M and Lindskog, S and Österlund, T and Fagman, H and Muth, A and Ståhlberg, A},
title = {Monitoring Circulating Tumor DNA During Surgical Treatment in Patients with Gastrointestinal Stromal Tumors.},
journal = {Molecular cancer therapeutics},
volume = {20},
number = {12},
pages = {2568-2576},
pmid = {34552011},
issn = {1538-8514},
mesh = {Aged ; Circulating Tumor DNA/*metabolism ; Female ; Gastrointestinal Stromal Tumors/*genetics/*surgery ; Humans ; Male ; Middle Aged ; Protein Kinase Inhibitors/pharmacology/*therapeutic use ; },
abstract = {The majority of patients diagnosed with advanced gastrointestinal stromal tumors (GISTs) are successfully treated with a combination of surgery and tyrosine kinase inhibitors (TKIs). However, it remains challenging to monitor treatment efficacy and identify relapse early. Here, we utilized a sequencing strategy based on molecular barcodes and developed a GIST-specific panel to monitor tumor-specific and TKI resistance mutations in cell-free DNA and applied the approach to patients undergoing surgical treatment. Thirty-two patients with GISTs were included, and 161 blood plasma samples were collected and analyzed at routine visits before and after surgery and at the beginning, during, and after surgery. Patients were included regardless of their risk category. Our GIST-specific sequencing approach allowed detection of tumor-specific mutations and TKI resistance mutations with mutant allele frequency < 0.1%. Circulating tumor DNA (ctDNA) was detected in at least one timepoint in nine of 32 patients, ranging from 0.04% to 93% in mutant allele frequency. High-risk patients were more often ctDNA positive than other risk groups (P < 0.05). Patients with detectable ctDNA also displayed higher tumor cell proliferation rates (P < 0.01) and larger tumor sizes (P < 0.01). All patients who were ctDNA positive during surgery became negative after surgery. Finally, in two patients who progressed on TKI treatment, we detected multiple resistance mutations. Our data show that ctDNA may become a clinically useful biomarker in monitoring treatment efficacy in patients with high-risk GISTs and can assist in treatment decision making.},
}
@article {pmid34547157,
year = {2021},
author = {Strobel, EJ},
title = {Efficient Linear dsDNA Tagging Using Deoxyuridine Excision*.},
journal = {Chembiochem : a European journal of chemical biology},
volume = {22},
number = {22},
pages = {3214-3224},
doi = {10.1002/cbic.202100425},
pmid = {34547157},
issn = {1439-7633},
support = {//University at Buffalo/ ; //Cornell University Genomics Innovation Hub Seed/ ; //Cornell University/ ; //Northwestern University/ ; },
mesh = {Cloning, Molecular ; DNA/genetics/*metabolism ; Deoxyuridine/*metabolism ; Gene Library ; Oligonucleotides/genetics/metabolism ; },
abstract = {Site-specific strategies for exchanging segments of dsDNA are important for DNA library construction and molecular tagging. Deoxyuridine (dU) excision is an approach for generating 3' ssDNA overhangs in gene assembly and molecular cloning procedures. Unlike approaches that use a multi-base pair motif to specify a DNA cut site, dU excision requires only a dT→dU substitution. Consequently, excision sites can be embedded in biologically active DNA sequences by placing dU substitutions at non-perturbative positions. In this work, I describe a molecular tagging method that uses dU excision to exchange a segment of a dsDNA strand with a long synthetic oligonucleotide. The core workflow of this method, called deoxyUridine eXcision-tagging (dUX-tagging), is an efficient one-pot reaction: strategically positioned dU nucleotides are excised from dsDNA to generate a 3' overhang so that additional sequence can be appended by annealing and ligating a tagging oligonucleotide. The tagged DNA is then processed by one of two procedures to fill the 5' overhang and remove excess tagging oligo. To facilitate its widespread use, all dUX-tagging procedures exclusively use commercially available reagents. As a result, dUX-tagging is a concise and easily implemented approach for high-efficiency linear dsDNA tagging.},
}
@article {pmid34546501,
year = {2021},
author = {Wang, Q and Huang, Z and Gao, C and Ge, Y and Cheng, R},
title = {The complete chloroplast genome sequence of Rubus hirsutus Thunb. and a comparative analysis within Rubus species.},
journal = {Genetica},
volume = {149},
number = {5-6},
pages = {299-311},
pmid = {34546501},
issn = {1573-6857},
support = {1/CX/CSRD VA/United States ; 1/CX/CSRD VA/United States ; 1/CX/CSRD VA/United States ; },
mesh = {Chloroplasts/*genetics ; Genome, Chloroplast/*genetics ; Phylogeny ; Rubus/*classification/cytology/*genetics ; },
abstract = {Rubus hirsutus is a type of tonifying kidney-essence herb that belongs to the Rosaceae family, and has been commonly used to treat multiple diseases, such as polyuria, impotence, and infertility. In this study, we determined the complete chloroplast sequence of R. hirsutus and conduced a comparative analysis within the genus Rubus. The assembled chloroplast (cp.) genome is 156,380 bp in length with a GC content of 37.0% and shares a conserved quadripartite structure within the other cp. genomes in this genus. A total of 132 unique genes were annotated in the cp. genome of R. hirsutus, which contained 87 protein-coding genes, 37 tRNAs, and eight rRNAs. Seventeen duplicated genes were identified in the inverted repeats region. Furthermore, 70 simple sequence repeats and 35 long repeats were detected in total in the R. hirsutus chloroplast genome. Eight mutational hotspots were identified in the cp. genome of this species with higher nucleotide variations in non-coding regions than those of coding regions. Furthermore, the gene order, codon usage, and repeat sequence distribution were highly consistent in Rubus according to the results of a comparative analysis. A phylogenetic analysis indicated that there was a sister relationship between R. hirsutus and R. chingii. Overall, the complete chloroplast genome of R. hirsutus and the comparative analysis will help to further the evolutionary study, conservation, phylogenetic reconstruction, and development of molecular barcodes for the genus Rubus.},
}
@article {pmid34546335,
year = {2021},
author = {Koch, RW and Shannon, RP and Detwiler, JT and Bolek, MG},
title = {MOLECULAR IDENTIFICATION OF JUVENILE NEOECHINORHYNCHUS SPP. (PHYLUM: ACANTHOCEPHALA) INFECTING OSTRACOD AND SNAIL HOSTS PROVIDES INSIGHT INTO ACANTHOCEPHALAN HOST USE.},
journal = {The Journal of parasitology},
volume = {107},
number = {5},
pages = {739-761},
doi = {10.1645/20-130},
pmid = {34546335},
issn = {1937-2345},
mesh = {Acanthocephala/anatomy &amp; histology/*genetics/isolation &amp; purification/pathogenicity ; Animals ; Crustacea/*parasitology ; DNA, Helminth/chemistry/isolation &amp; purification ; Female ; Fresh Water ; Male ; Seasons ; Snails/*parasitology ; Spatial Analysis ; Turtles/*parasitology ; },
abstract = {The role of invertebrates in some acanthocephalan life cycles is unclear because juvenile acanthocephalans are difficult to identify to species using morphology. Most reports suggest acanthocephalans from turtle definitive hosts use ostracods as intermediate hosts and snails as paratenic hosts. However, laboratory studies of the life cycle suggest that ostracods and snails are both required hosts in the life cycle. To elucidate the role of ostracods and snails in acanthocephalan life cycles better, we collected 558 freshwater snails of 2 species, including Planorbella cf. Planorbella trivolvis and Physa acuta, from 23 wetlands in Oklahoma, U.S.A., and examined them for acanthocephalan infections. Additionally, we examined 37,208 ostracods of 4 species, Physocypria sp. (morphotype 1), Cypridopsis sp., Stenocypris sp., and Physocypria sp. (morphotype 2) for juvenile acanthocephalans from 2 wetlands in Oklahoma. Juvenile acanthocephalans were morphologically characterized, and the complete internal transcribed spacer (ITS) region of nuclear rDNA was sequenced from acanthocephalans infecting 11 ostracod and 13 snail hosts. We also sampled 10 red-eared slider turtles, Trachemys scripta elegans, and 1 common map turtle, Graptemys geographica, collected from Oklahoma, Arkansas, and Texas and recovered 1,854 adult acanthocephalans of 4 species. The ITS of 17 adult acanthocephalans of 4 species from turtle hosts were sequenced and compared to juvenile acanthocephalan sequences from ostracod and snail hosts from this study and GenBank to determine conspecificity. Of the 23 locations sampled for snails, 7 (30%) were positive for juvenile acanthocephalans in the genus Neoechinorhynchus. The overall prevalence and mean intensity of acanthocephalans in Planorbella cf. P. trivolvis and P. acuta were 20% and 2 (1-6) and 2% and 1 (1), respectively. In contrast, only 1 of 4 species of ostracods, Physocypria sp. (morphotype 1), was infected with larval/juvenile Neoechinorhynchus spp. with an overall prevalence of 0.1% and a mean intensity of 1 (1-2). Although 4 species of acanthocephalans infected turtle definitive hosts, including Neoechinorhynchus chrysemydis, Neoechinorhynchus emydis, Neoechinorhynchus emyditoides, and Neoechinorhynchus pseudemydis, all the ITS sequences from cystacanths infecting snail hosts were conspecific with N. emydis. In contrast, the ITS sequences from larval/juvenile acanthocephalans from ostracods were conspecific with 2 species of acanthocephalans from turtles (N. emydis and N. pseudemydis) and 1 species of acanthocephalan from fish (Neoechinorhynchus cylindratus). These results indicate that N. emydis infects freshwater snails, whereas other species of Neoechinorhynchus appear not to infect snail hosts. We document new ostracod and snail hosts for Neoechinorhynchus species, including the first report of an ostracod host for N. pseudemydis, and we provide novel molecular barcodes that can be used to determine larva, juvenile, and adult conspecificity of Neoechinorhynchus species.},
}
@article {pmid34545683,
year = {2021},
author = {Suetsugu, K and Okada, H},
title = {Symbiotic germination and development of fully mycoheterotrophic plants convergently targeting similar Glomeraceae taxa.},
journal = {Environmental microbiology},
volume = {23},
number = {10},
pages = {6328-6343},
doi = {10.1111/1462-2920.15781},
pmid = {34545683},
issn = {1462-2920},
mesh = {Germination ; *Glomeromycota/genetics ; *Mycorrhizae/genetics ; Plants ; Symbiosis ; },
abstract = {Plants producing dust seeds often meet their carbon demands by exploiting fungi at the seedling stage. This germination strategy (i.e. mycoheterotrophic germination) has been investigated among orchidaceous and ericaceous plants exploiting Ascomycota or Basidiomycota. Although several other angiosperm lineages have evolved fully mycoheterotrophic relationships with Glomeromycota, the fungal identities involved in mycoheterotrophic germination remain largely unknown. Here, we conducted in situ seed baiting and high-throughput DNA barcoding to identify mycobionts associated with seedlings of Burmannia championii (Burmanniaceae: Dioscoreales) and Sciaphila megastyla (Triuridaceae: Pandanales), which have independently evolved full mycoheterotrophy. Subsequently, we revealed that both seedlings and adults in B. championii and S. megastyla predominantly associate with Glomeraceae. However, mycorrhizal communities are somewhat distinct between seedling and adult stages, particularly in S. megastyla. Notably, the dissimilarity of mycorrhizal communities between S. megastyla adult samples and S. megastyla seedling samples is significantly higher than that between B. championi adult samples and S. megastyla adult samples, based on some indices. This pattern is possibly due to both mycorrhizal shifts during ontogenetic development and convergent recruitment of cheating-susceptible fungi. The extensive fungal overlap in two unrelated mycoheterotrophic plants indicates that both species convergently exploit specific AM fungal phylotypes.},
}
@article {pmid34545138,
year = {2021},
author = {Ruíz-Rivero, O and Garcia-Lor, A and Rojas-Panadero, B and Franco, JC and Khamis, FM and Kruger, K and Cifuentes, D and Bielza, P and Tena, A and Urbaneja, A and Pérez-Hedo, M},
title = {Insights into the origin of the invasive populations of Trioza erytreae in Europe using microsatellite markers and mtDNA barcoding approaches.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {18651},
pmid = {34545138},
issn = {2045-2322},
mesh = {Animals ; Citrus/chemistry ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Europe ; Hemiptera/*genetics ; Insect Vectors ; Introduced Species/trends ; Microsatellite Repeats/*genetics ; Mitochondria/genetics ; Phylogeny ; Plant Diseases ; },
abstract = {The African citrus psyllid Trioza erytreae is one of the major threats to citrus industry as the vector of the incurable disease known as huanglongbing (HLB) or citrus greening. The psyllid invaded the northwest of the Iberian Peninsula 6 years ago. The invasion alarmed citrus growers in the Mediterranean basin, the largest citrus producing area in Europe, which is still free of HLB. Before our study, no research had been carried out on the genetic diversity of T. erytreae populations that have invaded the Iberian Peninsula and the archipelagos of the Macaronesia (Madeira and the Canary Islands). In this study, combining microsatellites markers and mtDNA barcoding analysis, we characterize the genetic diversity, structure and maternal relationship of these new invasive populations of T. erytreae and those from Africa. Our results suggest that the outbreaks of T. erytreae in the Iberian Peninsula may have derived from the Canary Islands. The populations of T. erytreae that invaded Macaronesia and the Iberian Peninsula are likely to have originated from southern Africa. We anticipate our results to be a starting point for tracking the spread of this invasive pest outside of Africa and to be important for optimizing contingency and eradication plans in newly invaded and free areas.},
}
@article {pmid34544910,
year = {2021},
author = {Azizi, MMF and Lau, HY and Abu-Bakar, N},
title = {Integration of advanced technologies for plant variety and cultivar identification.},
journal = {Journal of biosciences},
volume = {46},
number = {},
pages = {},
pmid = {34544910},
issn = {0973-7138},
mesh = {Biosensing Techniques ; Crops, Agricultural/classification/*genetics ; DNA, Plant/*genetics ; Genetic Markers ; Nucleic Acid Denaturation ; Plants/*classification/*genetics ; },
abstract = {Identification of plant variety and cultivar is pivotal in the agricultural sector due to the abundance of plant varieties and cultivars developed in many crop species. However, plant variety and cultivar identification via basic morphological features is problematic and challenging when differentiating closely related species not only due to their limited differences but also due to technical limitations of the process being time-consuming, labour-intensive and costly, and statistically imprecise information being available due to phenotypic plasticity. Therefore, it is imperative to have rapid and highly efficient techniques to mitigate these limitations. This review provides an overview and summarization of the development and application of molecular markers such as Random Amplified Polymorphic DNA (RAPD), Restriction Fragment Length Polymorphism (RFLP), Simple Sequence Repeats (SSR), Inter-simple sequence repeats (ISSR), Amplified Fragment Length Polymorphism (AFLP), Single nucleotide polymorphism (SNP) and DNA barcoding, High-resolution melting (HRM) and biosensor technology as potential tools in the identification of plant variety and cultivar.},
}
@article {pmid34544862,
year = {2021},
author = {Timmers, MA and Jury, CP and Vicente, J and Bahr, KD and Webb, MK and Toonen, RJ},
title = {Biodiversity of coral reef cryptobiota shuffles but does not decline under the combined stressors of ocean warming and acidification.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {39},
pages = {},
pmid = {34544862},
issn = {1091-6490},
mesh = {Acids/*adverse effects ; Animals ; Anthozoa/*physiology ; *Biodiversity ; *Climate Change ; *Coral Reefs ; *Ecosystem ; Hydrogen-Ion Concentration ; Oceans and Seas ; *Stress, Physiological ; },
abstract = {Ocean-warming and acidification are predicted to reduce coral reef biodiversity, but the combined effects of these stressors on overall biodiversity are largely unmeasured. Here, we examined the individual and combined effects of elevated temperature (+2 °C) and reduced pH (-0.2 units) on the biodiversity of coral reef communities that developed on standardized sampling units over a 2-y mesocosm experiment. Biodiversity and species composition were measured using amplicon sequencing libraries targeting the cytochrome oxidase I (COI) barcoding gene. Ocean-warming significantly increased species richness relative to present-day control conditions, whereas acidification significantly reduced richness. Contrary to expectations, species richness in the combined future ocean treatment with both warming and acidification was not significantly different from the present-day control treatment. Rather than the predicted collapse of biodiversity under the dual stressors, we find significant changes in the relative abundance but not in the occurrence of species, resulting in a shuffling of coral reef community structure among the highly species-rich cryptobenthic community. The ultimate outcome of altered community structure for coral reef ecosystems will depend on species-specific ecological functions and community interactions. Given that most species on coral reefs are members of the understudied cryptobenthos, holistic research on reef communities is needed to accurately predict diversity-function relationships and ecosystem responses to future climate conditions.},
}
@article {pmid34544191,
year = {2022},
author = {Parveen, I and Techen, N and Handy, SM and Li, J and Wu, C and Chittiboyina, AG and Khan, IA},
title = {The Low Copy Nuclear Gene Region, Granule Bound Starch Synthase (GBSS1), as a Novel Mini-DNA Barcode for the Identification of Different Sage (Salvia) Species.},
journal = {Planta medica},
volume = {88},
number = {12},
pages = {985-993},
doi = {10.1055/a-1618-6496},
pmid = {34544191},
issn = {1439-0221},
support = {Center for Drug Evaluation and Research, FDA//HHSF223201810175/ ; },
mesh = {DNA Barcoding, Taxonomic/methods ; DNA, Plant/genetics ; Phylogeny ; Powders ; *Salvia/genetics ; *Starch Synthase/genetics ; },
abstract = {Morphological similarity within species makes the identification and authentication of Salvia species challenging, especially in dietary supplements that contain processed root or leaf powder of different sage species. In the present study, the species discriminatory power of 2 potential DNA barcode regions from the nuclear genome was evaluated in 7 medicinally important Salvia species from the family Lamiaceae. The nuclear internal transcribed spacer 2 and the exon 9 - 14 region of low copy nuclear gene WAXY coding for granule-bound starch synthase 1 were tested for their species discrimination ability using distance, phylogenetic, and BLAST-based methods. A novel 2-step PCR method with 2 different annealing temperatures was developed to achieve maximum amplification from genomic DNA. The granule-bound starch synthase 1 region showed higher amplification and sequencing success rates, higher interspecific distances, and a perfect barcode gap for the tested species compared to the nuclear internal transcribed spacer 2. Hence, these novel mini-barcodes generated from low copy nuclear gene regions (granule-bound starch synthase) that were proven to be effective barcodes for identifying 7 Salvia species have potential for identification and authentication of other Salvia species.},
}
@article {pmid34539196,
year = {2021},
author = {Casalla, R and Scheffrahn, RH and Korb, J},
title = {Rugitermesursulae (Isoptera, Kalotermitidae), a new drywood termite from the Caribbean coast of Colombia.},
journal = {ZooKeys},
volume = {1057},
number = {},
pages = {23-36},
pmid = {34539196},
issn = {1313-2989},
abstract = {Rugitermesursulae sp. nov. is described from a sample collected inside a dead branch in a tropical dry forest of Colombia's Caribbean coast using molecular information and external morphological characters of the imago and soldier castes. Rugitermesursulae sp. nov. soldiers and imagoes are the smallest among all described Rugitermes species. The imago's head capsule coloration is dark castaneous, while the pronotum is contrastingly pale yellow. Our description includes soldier characters, such as subflangular elevation and shape of the antennal sockets, that can help in identification of samples lacking imagoes.},
}
@article {pmid34537175,
year = {2021},
author = {Ori, F and Menotta, M and Leonardi, M and Amicucci, A and Zambonelli, A and Covès, H and Selosse, MA and Schneider-Maunoury, L and Pacioni, G and Iotti, M},
title = {Effect of slug mycophagy on Tuber aestivum spores.},
journal = {Fungal biology},
volume = {125},
number = {10},
pages = {796-805},
doi = {10.1016/j.funbio.2021.05.002},
pmid = {34537175},
issn = {1878-6146},
mesh = {Animals ; *Ascomycota ; *Gastropoda ; Mice ; *Mycorrhizae ; Spores, Fungal ; },
abstract = {Truffles in the genus Tuber produce subterranean fruiting bodies that are not able to actively discharge their spores in the environment. For this reason, truffles depend on mycophagous animals for reproduction. Fungus consumption (mycophagy) is a behaviour typical of both vertebrates and invertebrates. Mammals, especially rodents, are the most studied group of mycophagists and have been found to consume a great variety of fungi. Among invertebrates, mycophagy is documented in arthropods, but rarely in molluscs. In our study we assessed the effect on the morphology and mycorrhizal colonization of Tuber aestivum spores after passage through the gut of slugs (Deroceras invadens) and, for comparison, of a house mouse (Mus musculus). Light, scanning electron and atomic force microscopy revealed that the digestion, especially by slugs, freed spores from the asci and modified their morphology. These are believed to be the reasons why we observed an improvement in oak mycorrhization with the slug and rodent ingested spores in comparison to a fresh spore inoculation. We also demonstrated by molecular barcoding that slugs' guts sampled on a Tuber melanosporum truffle ground contain spores from this species and Tuber brumale, further suggesting that some invertebrates are efficient Tuber spore dispersers.},
}
@article {pmid34534656,
year = {2022},
author = {Waki, T and Nakao, M and Sasaki, M and Ikezawa, H and Inoue, K and Ohari, Y and Kameda, Y and Asada, M and Furusawa, H and Miyazaki, S},
title = {Brachylaima phaedusae n. sp. (Trematoda: Brachylaimidae) from door snails in Japan.},
journal = {Parasitology international},
volume = {86},
number = {},
pages = {102469},
doi = {10.1016/j.parint.2021.102469},
pmid = {34534656},
issn = {1873-0329},
mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/analysis ; Female ; Japan ; Mice, Inbred ICR ; Snails/*parasitology ; Trematoda/anatomy &amp; histology/*classification/genetics ; Mice ; },
abstract = {The metacercarial infections of door snails (Gastropoda: Clausiliidae) with unknown species of the genus Brachylaima (Trematoda: Brachylaimidae) have recently been reported in eastern Honshu and Kyushu, Japan. A large scale snail survey was carried out to clarify their taxonomic status. From the period of 2015 to 2020, a total of 1239 land snails (768 door snails and 471 others) were collected from 32 localities in Honshu, Shikoku, and Kyushu. The resulting trematode isolates were identified as Brachylaima sp. by mitochondrial DNA barcoding. The sporocysts were found only a few from Megalophaedusa sublunellata (Clausiliidae), Tauphaedusa subaculus (Clausiliidae), and Aegista trochula (Camaenidae), while the metacercariae were frequently detected from 14 species of Clausiliidae and 2 species of other families. Although Brachylaima sp. showed a broad range of intermediate hosts, door snails seem to be very important to drive the life cycle. The gravid adults of Brachylaima sp. was experimentally raised from metacercariae using immunosuppressed mice. Morphological, phylogenetical, and ecological considerations prompted us to propose Brachylaima phaedusae n. sp. for this unknown species. The definitive hosts of the new species are completely unknown. The wide geographic distribution and high genetic diversity of the new species suggest a possibility that the definitive host is ground-foraging birds, which prefer door snails.},
}
@article {pmid34534243,
year = {2021},
author = {Yanaso, S and Phrutivorapongkul, A and Hongwiset, D and Piyamongkol, S and Intharuksa, A},
title = {Verification of Thai ethnobotanical medicine "Kamlang Suea Khrong" driven by multiplex PCR and powerful TLC techniques.},
journal = {PloS one},
volume = {16},
number = {9},
pages = {e0257243},
pmid = {34534243},
issn = {1932-6203},
mesh = {Chromatography, Thin Layer/methods ; DNA Barcoding, Taxonomic/*methods ; DNA Primers ; DNA, Plant/*genetics ; Ethnobotany/*methods ; Multiplex Polymerase Chain Reaction/methods ; Pharmaceutical Preparations/*analysis ; Plant Bark ; Plant Stems ; Plants, Medicinal/*chemistry ; Quality Control ; Species Specificity ; Thailand ; },
abstract = {Kamlang Suea Khrong (KSK) crude drug, a traditional Thai medicine used for oral tonic and analgesic purposes, is obtained from three origins: the inner stem bark of Betula alnoides (BA) or the stems of Strychnos axillaris (SA) or Ziziphus attopensis (ZA). According to the previous reports, SA contains strychnine-type alkaloids that probably cause poisoning; however, only organoleptic approaches are insufficient to differentiate SA from the other plant materials. To ensure the botanical origin of KSK crude drug, powerful and reliable tools are desperately needed. Therefore, molecular and chemical identification methods, DNA barcoding and thin-layer chromatography (TLC), were investigated. Reference databases, i.e., the ITS region and phytochemical profile of the authentic plant species, were conducted. In case of molecular analysis, multiplex polymerase chain reaction (PCR) based on species-specific primers was applied. Regarding species-specific primers designation, the suitability of three candidate barcode regions (ITS, ITS1, and ITS2) was evaluated by genetic distance using K2P model. ITS2 presented the highest interspecific variability was verified its discrimination power by tree topology. Accordingly, ITS2 was used to create primers that successfully specified plant species of authentic samples. For chemical analysis, TLC with toluene:ethyl acetate:ammonia (1:9:0.025) and hierarchical clustering were operated to identify the authentic crude drugs. The developed multiplex PCR and TLC methods were then applied to identify five commercial KSK crude drugs (CK1-CK5). Both methods correspondingly indicated that CK1-CK2 and CK3-CK5 were originated from BA and ZA, respectively. Molecular and chemical approaches are convenient and effective identification methods that can be performed for the routine quality-control of the KSK crude drugs for consumer reliance. According to chemical analysis, the results indicated BA, SA, and ZA have distinct chemical profiles, leading to differences in pharmacological activities. Consequently, further scientific investigations are required to ensure the quality and safety of Thai ethnobotanical medicine known as KSK.},
}
@article {pmid34531539,
year = {2022},
author = {Chang, MT and Shanahan, F and Nguyen, TTT and Staben, ST and Gazzard, L and Yamazoe, S and Wertz, IE and Piskol, R and Yang, YA and Modrusan, Z and Haley, B and Evangelista, M and Malek, S and Foster, SA and Ye, X},
title = {Identifying transcriptional programs underlying cancer drug response with TraCe-seq.},
journal = {Nature biotechnology},
volume = {40},
number = {1},
pages = {86-93},
pmid = {34531539},
issn = {1546-1696},
mesh = {*Antineoplastic Agents/pharmacology/therapeutic use ; ErbB Receptors/genetics/metabolism ; Humans ; *Lung Neoplasms/drug therapy/genetics ; Protein Kinase Inhibitors/pharmacology/therapeutic use ; Single-Cell Analysis/methods ; },
abstract = {Genetic and non-genetic heterogeneity within cancer cell populations represent major challenges to anticancer therapies. We currently lack robust methods to determine how preexisting and adaptive features affect cellular responses to therapies. Here, by conducting clonal fitness mapping and transcriptional characterization using expressed barcodes and single-cell RNA sequencing (scRNA-seq), we have developed tracking differential clonal response by scRNA-seq (TraCe-seq). TraCe-seq is a method that captures at clonal resolution the origin, fate and differential early adaptive transcriptional programs of cells in a complex population in response to distinct treatments. We used TraCe-seq to benchmark how next-generation dual epidermal growth factor receptor (EGFR) inhibitor-degraders compare to standard EGFR kinase inhibitors in EGFR-mutant lung cancer cells. We identified a loss of antigrowth activity associated with targeted degradation of EGFR protein and an essential role of the endoplasmic reticulum (ER) protein processing pathway in anti-EGFR therapeutic efficacy. Our results suggest that targeted degradation is not always superior to enzymatic inhibition and establish TraCe-seq as an approach to study how preexisting transcriptional programs affect treatment responses.},
}
@article {pmid34531498,
year = {2021},
author = {Arjona, MI and González-Manchón, C and Durán, S and Duch, M and Del Real, RP and Kadambi, A and Agusil, JP and Redondo-Horcajo, M and Pérez-García, L and Gómez, E and Suárez, T and Plaza, JA},
title = {Integrating magnetic capabilities to intracellular chips for cell trapping.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {18495},
pmid = {34531498},
issn = {2045-2322},
abstract = {Current microtechnologies have shown plenty of room inside a living cell for silicon chips. Microchips as barcodes, biochemical sensors, mechanical sensors and even electrical devices have been internalized into living cells without interfering their cell viability. However, these technologies lack from the ability to trap and preconcentrate cells in a specific region, which are prerequisites for cell separation, purification and posterior studies with enhanced sensitivity. Magnetic manipulation of microobjects, which allows a non-contacting method, has become an attractive and promising technique at small scales. Here, we show intracellular Ni-based chips with magnetic capabilities to allow cell enrichment. As a proof of concept of the potential to integrate multiple functionalities on a single device of this technique, we combine coding and magnetic manipulation capabilities in a single device. Devices were found to be internalized by HeLa cells without interfering in their viability. We demonstrated the tagging of a subpopulation of cells and their subsequent magnetic trapping with internalized barcodes subjected to a force up to 2.57 pN (for magnet-cells distance of 4.9 mm). The work opens the venue for future intracellular chips that integrate multiple functionalities with the magnetic manipulation of cells.},
}
@article {pmid34530118,
year = {2022},
author = {Borges, LMS and Treneman, NC and Haga, T and Shipway, JR and Raupach, MJ and Altermark, B and Carlton, JT},
title = {Out of taxonomic crypsis: A new trans-arctic cryptic species pair corroborated by phylogenetics and molecular evidence.},
journal = {Molecular phylogenetics and evolution},
volume = {166},
number = {},
pages = {107312},
doi = {10.1016/j.ympev.2021.107312},
pmid = {34530118},
issn = {1095-9513},
mesh = {Animals ; *Bivalvia/genetics ; Ecology ; Phylogeny ; Poaceae/genetics ; RNA, Ribosomal, 18S/genetics ; },
abstract = {Cryptic species are a common phenomenon in cosmopolitan marine species. The use of molecular tools has often uncovered cryptic species occupying a fraction of the geographic range of the original morphospecies. Shipworms (Teredinidae) are marine bivalves, living in drift and fixed wood, many of which have a conserved morphology across cosmopolitan distributions. Herein novel and GenBank mitochondrial (cytochrome c oxidase subunit I) and nuclear (18S rRNA) DNA sequences are employed to produce a phylogeny of the Teredinidae and delimit a cryptic species pair in the Psiloteredo megotara complex. The anatomy, biogeography, and ecology of P. megotara, Psiloteredo sp. and Nototeredo edax are compared based on private and historic museum collections and a thorough literature review. Morphological and anatomical characters of P. megotara from the North Atlantic and Psiloteredo sp. from Japan were morphologically indistinguishable, and differ in pallet architecture and soft tissue anatomy from N. edax. The two Psiloteredo species were then delimited as genetically distinct species using four molecular-based methods. Consequently, the Northwest Pacific species, Psiloteredo pentagonalis, first synonymized with N. edax and then with P. megotara, is resurrected. Nototeredo edax, P. megotara and P. pentagonalis are redescribed based upon morphological and molecular characters. Phylogenetic analysis further revealed cryptic species complexes within the cosmopolitan species Bankia carinata and possibly additional cryptic lineages within the cosmopolitan Lyrodus pedicellatus.},
}
@article {pmid34528760,
year = {2021},
author = {Larsson, I and Dalmo, E and Elgendy, R and Niklasson, M and Doroszko, M and Segerman, A and Jörnsten, R and Westermark, B and Nelander, S},
title = {Modeling glioblastoma heterogeneity as a dynamic network of cell states.},
journal = {Molecular systems biology},
volume = {17},
number = {9},
pages = {e10105},
pmid = {34528760},
issn = {1744-4292},
mesh = {*Brain Neoplasms/genetics ; Cell Line, Tumor ; *Glioblastoma/genetics ; Humans ; Neoplasm Recurrence, Local ; Single-Cell Analysis ; },
abstract = {Tumor cell heterogeneity is a crucial characteristic of malignant brain tumors and underpins phenomena such as therapy resistance and tumor recurrence. Advances in single-cell analysis have enabled the delineation of distinct cellular states of brain tumor cells, but the time-dependent changes in such states remain poorly understood. Here, we construct quantitative models of the time-dependent transcriptional variation of patient-derived glioblastoma (GBM) cells. We build the models by sampling and profiling barcoded GBM cells and their progeny over the course of 3 weeks and by fitting a mathematical model to estimate changes in GBM cell states and their growth rates. Our model suggests a hierarchical yet plastic organization of GBM, where the rates and patterns of cell state switching are partly patient-specific. Therapeutic interventions produce complex dynamic effects, including inhibition of specific states and altered differentiation. Our method provides a general strategy to uncover time-dependent changes in cancer cells and offers a way to evaluate and predict how therapy affects cell state composition.},
}
@article {pmid34527436,
year = {2021},
author = {Díaz, JA and Ramírez-Amaro, S and Ordines, F},
title = {Sponges of Western Mediterranean seamounts: new genera, new species and new records.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e11879},
pmid = {34527436},
issn = {2167-8359},
abstract = {BACKGROUND: The seamounts Ses Olives (SO), Ausias March (AM) and Emile Baudot (EB) at the Mallorca Channel (Balearic Islands, western Mediterranean), are poorly explored areas containing rich and singular sponge communities. Previous works have shown a large heterogeneity of habitats, including rhodolith beds, rocky, gravel and sandy bottoms and steeped slopes. This diversity of habitats provides a great opportunity for improving the knowledge of the sponges from Mediterranean seamounts.<br><br>METHODS: Sponges were collected during several surveys carried out by the Balearic Center of the Spanish Institute of Oceanography at the Mallorca Channel seamounts. Samples were obtained using a beam-trawl, rock dredge and remote operated vehicle. Additional samples were obtained from fishing grounds of the Balearic Islands continental shelf, using the sampling device GOC-73. Sponges were identified through the analysis of morphological and molecular characters.<br><br>RESULTS: A total of 60 specimens were analyzed, from which we identified a total of 19 species. Three species and one genus are new to science: Foraminospongia balearica gen. nov. sp. nov., Foraminospongia minuta gen. nov. sp. nov. and Paratimea massutii sp. nov. Heteroxya cf. beauforti represents the first record of the genus Heteroxya in the Mediterranean Sea. Additionally, this is the second report of Axinella spatula and Haliclona (Soestella) fimbriata since their description. Moreover, the species Petrosia (Petrosia) raphida, Calyx cf. tufa and Lanuginella pupa are reported for the first time in the Mediterranean Sea. Petrosia (Strongylophora) vansoesti is reported here for the first time in the western Mediterranean Sea. Haliclona (S.) fimbriata is reported here for the first time in the north-western Mediterranean Sea. Hemiasterella elongata is reported here for the second time in the Mediterranean Sea. The species Melonanchora emphysema, Rhabdobaris implicata, Polymastia polytylota, Dragmatella aberrans, Phakellia ventilabrum and Pseudotrachya hystrix are reported for first time off Balearic Islands. Following the Sponge Barcoding project goals, we have sequenced the Cytochrome Oxidase subunit I (COI) and the 28S ribosomal fragment (C1-D2 domains) for Foraminospongia balearica sp. nov., Foraminospongia minuta sp. nov., H. cf. beauforti and C. cf. tufa, and the COI for Paratimea massuti sp. nov. We also provide a phylogenetic analysis to discern the systematic location of Foraminospongia gen. nov., which, in accordance to skeletal complement, is placed in the Hymerhabdiidae family. A brief biogeographical discussion is provided for all these species, with emphasis on the sponge singularity of SO, AM and the EB seamounts and the implications for their future protection.},
}
@article {pmid34526361,
year = {2021},
author = {Mizuno, K and Sumiyoshi, T and Okegawa, T and Terada, N and Ishitoya, S and Miyazaki, Y and Kojima, T and Katayama, H and Fujimoto, N and Hatakeyama, S and Shiota, M and Yoshimura, K and Matsui, Y and Narita, S and Matsumoto, H and Kurahashi, R and Kanno, H and Ito, K and Kimura, H and Kamiyama, Y and Sunada, T and Goto, T and Kobayashi, T and Yamada, H and Tsuchiya, N and Kamba, T and Matsuyama, H and Habuchi, T and Eto, M and Ohyama, C and Ito, A and Nishiyama, H and Okuno, H and Kamoto, T and Fujimoto, A and Ogawa, O and Akamatsu, S},
title = {Clinical Impact of Detecting Low-Frequency Variants in Cell-Free DNA on Treatment of Castration-Resistant Prostate Cancer.},
journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},
volume = {27},
number = {22},
pages = {6164-6173},
doi = {10.1158/1078-0432.CCR-21-2328},
pmid = {34526361},
issn = {1557-3265},
mesh = {Biomarkers, Tumor/genetics/therapeutic use ; *Cell-Free Nucleic Acids/genetics ; Cohort Studies ; Humans ; Male ; Prospective Studies ; *Prostatic Neoplasms, Castration-Resistant/diagnosis/drug therapy/genetics ; },
abstract = {PURPOSE: Although cell-free DNA (cfDNA) testing is expected to drive cancer precision medicine, little is known about the significance of detecting low-frequency variants in circulating cell-free tumor DNA (ctDNA) in castration-resistant prostate cancer (CRPC). We aimed to identify genomic profile including low-frequency variants in ctDNA from patients with CRPC and investigate the clinical utility of detecting variants with variant allele frequency (VAF) below 1%.<br><br>EXPERIMENTAL DESIGN: This prospective, multicenter cohort study enrolled patients with CRPC eligible for treatment with abiraterone or enzalutamide. We performed targeted sequencing of pretreatment cfDNA and paired leukocyte DNA with molecular barcodes, and ctDNA variants with a VAF &#x2265;0.1% were detected using an in-house pipeline. We investigated progression-free survival (PFS) and overall survival (OS) after different ctDNA fraction cutoffs were applied.<br><br>RESULTS: One hundred patients were analyzed (median follow-up 10.7 months). We detected deleterious ATM, BRCA2, and TP53 variants even in samples with ctDNA fraction below 2%. When the ctDNA fraction cutoff value of 0.4% was applied, significant differences in PFS and OS were found between patients with and without defects in ATM or BRCA2 [HR, 2.52; 95% confidence interval (CI), 1.24-5.11; P = 0.0091] and TP53 (HR, 3.74; 95% CI, 1.60-8.71; P = 0.0014). However, these differences were no longer observed when the ctDNA fraction cutoff value of 2% was applied, and approximately 50% of the samples were classified as ctDNA unquantifiable.<br><br>CONCLUSIONS: Detecting low-frequency ctDNA variants with a VAF <1% is important to identify clinically informative genomic alterations in CRPC.},
}
@article {pmid34525767,
year = {2022},
author = {Suarez-Montes, D and Borrell, YJ and Gonzalez, JM and Rico, JM},
title = {Isolation and identification of microalgal strains with potential as carotenoids producers from a municipal solid waste landfill.},
journal = {The Science of the total environment},
volume = {802},
number = {},
pages = {149755},
doi = {10.1016/j.scitotenv.2021.149755},
pmid = {34525767},
issn = {1879-1026},
mesh = {Carotenoids ; *Microalgae/genetics ; Phylogeny ; Solid Waste ; Spain ; Waste Disposal Facilities ; },
abstract = {Derived from their great capacity of adaptation, microalgae have several industrial applications, including pigment production for nutraceutical sector. However, the scarcity of studies on the diversity and life histories from several environments, highlight the need for more research on new species and habitats. Based on this, the present study assessed the microalgal diversity in water bodies of a municipal solid waste (MSW) landfill in Asturias (Spain). A total of 14 strains were successfully isolated and scaled up in liquid monocultures. They were identified through a combination of morphologic features with molecular assignation by DNA barcoding via the 18S and ITS1-5.8S-ITS2 genes. The results of the genetic procedures (BLAST assignments and the 18S and ITS1-5.8S-ITS2 genealogies) showed that 10 of the 14 assayed isolates were identified at the species level. The available genetic data were not sufficient for species classifications of the remaining isolates. It is possible that some might be new species not previously studied or described. Indeed, a new species, Coelastrella cogersae, was proposed in this study. Moreover, 3 of the 14 isolates (including the newly proposed species) exhibited caretogenic activity under specific conditions during the culture. These results are a great step forward in both the screening of lesser-known environments and the discovery of new sources of bioactive compounds. The study could be of great value to the nutraceutical industries and markets.},
}
@article {pmid34524452,
year = {2022},
author = {Yang, B and Zhang, Z and Yang, CQ and Wang, Y and Orr, MC and Wang, H and Zhang, AB},
title = {Identification of Species by Combining Molecular and Morphological Data Using Convolutional Neural Networks.},
journal = {Systematic biology},
volume = {71},
number = {3},
pages = {690-705},
doi = {10.1093/sysbio/syab076},
pmid = {34524452},
issn = {1076-836X},
mesh = {Animals ; Biodiversity ; *Butterflies/genetics ; DNA/genetics ; DNA Barcoding, Taxonomic/methods ; Neural Networks, Computer ; Phylogeny ; },
abstract = {Integrative taxonomy is central to modern taxonomy and systematic biology, including behavior, niche preference, distribution, morphological analysis, and DNA barcoding. However, decades of use demonstrate that these methods can face challenges when used in isolation, for instance, potential misidentifications due to phenotypic plasticity for morphological methods, and incorrect identifications because of introgression, incomplete lineage sorting, and horizontal gene transfer for DNA barcoding. Although researchers have advocated the use of integrative taxonomy, few detailed algorithms have been proposed. Here, we develop a convolutional neural network method (morphology-molecule network [MMNet]) that integrates morphological and molecular data for species identification. The newly proposed method (MMNet) worked better than four currently available alternative methods when tested with 10 independent data sets representing varying genetic diversity from different taxa. High accuracies were achieved for all groups, including beetles (98.1% of 123 species), butterflies (98.8% of 24 species), fishes (96.3% of 214 species), and moths (96.4% of 150 total species). Further, MMNet demonstrated a high degree of accuracy ($>$98%) in four data sets including closely related species from the same genus. The average accuracy of two modest subgenomic (single nucleotide polymorphism) data sets, comprising eight putative subspecies respectively, is 90%. Additional tests show that the success rate of species identification under this method most strongly depends on the amount of training data, and is robust to sequence length and image size. Analyses on the contribution of different data types (image vs. gene) indicate that both morphological and genetic data are important to the model, and that genetic data contribute slightly more. The approaches developed here serve as a foundation for the future integration of multimodal information for integrative taxonomy, such as image, audio, video, 3D scanning, and biosensor data, to characterize organisms more comprehensively as a basis for improved investigation, monitoring, and conservation of biodiversity. [Convolutional neural network; deep learning; integrative taxonomy; single nucleotide polymorphism; species identification.].},
}
@article {pmid34522368,
year = {2021},
author = {Lin, XL and Jiang, K and Liu, WB and Liu, W and Bu, WJ and Wang, XH and Mo, L},
title = {Toward a global DNA barcode reference library of the intolerant nonbiting midge genus Rheocricotopus Brundin, 1956.},
journal = {Ecology and evolution},
volume = {11},
number = {17},
pages = {12161-12172},
pmid = {34522368},
issn = {2045-7758},
abstract = {Environmental DNA metabarcoding is becoming a predominant tool in biodiversity assessment, as this time- and cost-efficient tactics have the ability to increase monitoring accuracy. As a worldwide distributed genus, Rheocricotopus Brundin, 1956 still does not possess a complete and comprehensive global DNA barcode reference library for biodiversity monitoring. In the present study, we compiled a cytochrome c oxidase subunit 1 (COI) DNA barcode library of Rheocricotopus with 434 barcodes around the world, including 121 newly generated DNA barcodes of 32 morphospecies and 313 public barcodes. Automatic Barcode Gap Discovery (ABGD) was applied on the 434 COI barcodes to provide a comparison between the operational taxonomic units (OTU) number calculated from the Barcode Index Number (BIN) with the "Barcode Gap Analysis" and neighbor-joining (NJ) tree analysis. Consequently, these 434 COI barcodes were clustered into 78 BINs, including 42 new BINs. ABGD yielded 51 OTUs with a prior intraspecific divergence of Pmax = 7.17%, while NJ tree revealed 52 well-separated clades. Conservatively, 14 unknown species and one potential synonym were uncovered with reference to COI DNA barcodes. Besides, based on our ecological analysis, we discovered that annual mean temperature and annual precipitation could be considered as key factors associated with distribution of certain members from this genus. Our global DNA barcode reference library of Rheocricotopus provides one fundamental database for accurate species delimitation in Chironomidae taxonomy and facilitates the biodiversity monitoring of aquatic biota.},
}
@article {pmid34522329,
year = {2021},
author = {Liu, Y and Xu, C and Sun, Y and Chen, X and Dong, W and Yang, X and Zhou, S},
title = {Method for quick DNA barcode reference library construction.},
journal = {Ecology and evolution},
volume = {11},
number = {17},
pages = {11627-11638},
pmid = {34522329},
issn = {2045-7758},
abstract = {DNA barcoding has become one of the most important techniques in plant species identification. Successful application of this technology is dependent on the availability of reference database of high species coverage. Unfortunately, there are experimental and data processing challenges to construct such a library within a short time. Here, we present our solutions to these challenges. We sequenced six conventional DNA barcode fragments (ITS1, ITS2, matK1, matK2, rbcL1, and rbcL2) of 380 flowering plants on next-generation sequencing (NGS) platforms (Illumina Hiseq 2500 and Ion Torrent S5) and the Sanger sequencing platform. After comparing the sequencing depths, read lengths, base qualities, and base accuracies, we conclude that Illumina Hiseq2500 PE250 run is suitable for conventional DNA barcoding. We developed a new "Cotu" method to create consensus sequences from NGS reads for longer output sequences and more reliable bases than the other three methods. Step-by-step instructions to our method are provided. By using high-throughput machines (PCR and NGS), labeling PCR, and the Cotu method, it is possible to significantly reduce the cost and labor investments for DNA barcoding. A regional or even global DNA barcoding reference library with high species coverage is likely to be constructed in a few years.},
}
@article {pmid34521395,
year = {2021},
author = {Yeo, D and Srivathsan, A and Puniamoorthy, J and Maosheng, F and Grootaert, P and Chan, L and Guénard, B and Damken, C and Wahab, RA and Yuchen, A and Meier, R},
title = {Mangroves are an overlooked hotspot of insect diversity despite low plant diversity.},
journal = {BMC biology},
volume = {19},
number = {1},
pages = {202},
pmid = {34521395},
issn = {1741-7007},
mesh = {Animals ; *Biodiversity ; Ecosystem ; Forests ; *Insecta ; *Plants ; Wetlands ; },
abstract = {BACKGROUND: The world's fast disappearing mangrove forests have low plant diversity and are often assumed to also have a species-poor insect fauna. We here compare the tropical arthropod fauna across a freshwater swamp and six different forest types (rain-, swamp, dry-coastal, urban, freshwater swamp, mangroves) based on 140,000 barcoded specimens belonging to ca. 8500 species.<br><br>RESULTS: We find that the globally imperiled habitat "mangroves" is an overlooked hotspot for insect diversity. Our study reveals a species-rich mangrove insect fauna (>3000 species in Singapore alone) that is distinct (>50% of species are mangrove-specific) and has high species turnover across Southeast and East Asia. For most habitats, plant diversity is a good predictor of insect diversity, but mangroves are an exception and compensate for a comparatively low number of phytophagous and fungivorous insect species by supporting an unusually rich community of predators whose larvae feed in the productive mudflats. For the remaining tropical habitats, the insect communities have diversity patterns that are largely congruent across guilds.<br><br>CONCLUSIONS: The discovery of such a sizeable and distinct insect fauna in a globally threatened habitat underlines how little is known about global insect biodiversity. We here show how such knowledge gaps can be closed quickly with new cost-effective NGS barcoding techniques.},
}
@article {pmid34521041,
year = {2021},
author = {Gao, Y and Yan, L and Qiu, D and Huang, Z and Hu, D and Zhang, D},
title = {First mitogenome of moniezia sichuanensis from forest musk deer with comparative analyses within cyclophyllidea.},
journal = {Veterinary parasitology},
volume = {299},
number = {},
pages = {109575},
doi = {10.1016/j.vetpar.2021.109575},
pmid = {34521041},
issn = {1873-2550},
mesh = {Animals ; *Cestoda/genetics ; *Deer/parasitology ; Forests ; *Genome, Mitochondrial ; Phylogeny ; },
abstract = {We characterised, for the first time, the whole mitogenome of a unique tapeworm, Moniezia sichuanensis (Cyclophyllidea, Anoplocephalidae) of forest musk deer (Moschus berezovskii). The total length of the circular mitogenome was 13,652 bp. It consisted of 12 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes, which are typical of the mitogenomes of Moniezia. By comparing the available mitogenomes of PCGs for Cyclophyllidea in GenBank, nad6 and cox1 showed the highest and lowest evolutionary rates, respectively, and cox2 could be used as a potential DNA barcoding marker. The phylogenetic analyses of Cyclophyllidea confirmed the monophyly of the genus Moniezia and the family Anoplocephalidae; they then formed a clade with species of Hymenolepididae. Moreover, two novel gene arrangements of Cyclophyllidea were observed.},
}
@article {pmid34516547,
year = {2021},
author = {Wong, TKF and Li, T and Ranjard, L and Wu, SH and Sukumaran, J and Rodrigo, AG},
title = {An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes.},
journal = {PLoS computational biology},
volume = {17},
number = {9},
pages = {e1008949},
pmid = {34516547},
issn = {1553-7358},
mesh = {Algorithms ; Bayes Theorem ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Humans ; Markov Chains ; Monte Carlo Method ; *Phylogeny ; Polymorphism, Single Nucleotide ; },
abstract = {A current strategy for obtaining haplotype information from several individuals involves short-read sequencing of pooled amplicons, where fragments from each individual is identified by a unique DNA barcode. In this paper, we report a new method to recover the phylogeny of haplotypes from short-read sequences obtained using pooled amplicons from a mixture of individuals, without barcoding. The method, AFPhyloMix, accepts an alignment of the mixture of reads against a reference sequence, obtains the single-nucleotide-polymorphisms (SNP) patterns along the alignment, and constructs the phylogenetic tree according to the SNP patterns. AFPhyloMix adopts a Bayesian inference model to estimate the phylogeny of the haplotypes and their relative abundances, given that the number of haplotypes is known. In our simulations, AFPhyloMix achieved at least 80% accuracy at recovering the phylogenies and relative abundances of the constituent haplotypes, for mixtures with up to 15 haplotypes. AFPhyloMix also worked well on a real data set of kangaroo mitochondrial DNA sequences.},
}
@article {pmid34512092,
year = {2021},
author = {Wang, YL and Li, Q and Toda, MJ and Gao, JJ},
title = {The genus Dettopsomyia Lamb, 1914 (Diptera, Drosophilidae) from southern China.},
journal = {ZooKeys},
volume = {1056},
number = {},
pages = {73-94},
pmid = {34512092},
issn = {1313-2989},
abstract = {The genus Dettopsomyia was established by Lamb in 1914 for a single species, De.formosa described therein. It contains 13 known species recorded from the Old World (the Oriental, Australasian, Palearctic and Afrotropical regions). In the present paper, five new species discovered from southern China are described as members of Dettopsomyia: De.acutipenis Wang &amp; Gao, sp. nov., De.serripenis Wang &amp; Gao, sp. nov., De.discontinua Wang &amp; Gao, sp. nov., De.camelonota Wang, Li &amp; Gao, sp. nov. and De.paranigrovittata Wang, Li &amp; Gao, sp. nov. The new species were delimitated, based on not only morphological characters but also molecular data.},
}
@article {pmid34512087,
year = {2021},
author = {Sharkey, MJ and Janzen, DH and Hallwachs, W and Chapman, EG and Smith, MA and Dapkey, T and Brown, A and Ratnasingham, S and Naik, S and Manjunath, R and Perez, K and Milton, M and Hebert, P and Shaw, SR and Kittel, RN and Solis, MA and Metz, MA and Goldstein, PZ and Brown, JW and Quicke, DLJ and van Achterberg, C and Brown, BV and Burns, JM},
title = {Minimalist revision and description of 403 new species in 11 subfamilies of Costa Rican braconid parasitoid wasps, including host records for 219 species.},
journal = {ZooKeys},
volume = {1013},
number = {},
pages = {1-665},
pmid = {34512087},
issn = {1313-2989},
abstract = {Three new genera are described: Michener (Proteropinae), Bioalfa (Rogadinae), and Hermosomastax (Rogadinae). Keys are given for the New World genera of the following braconid subfamilies: Agathidinae, Braconinae, Cheloninae, Homolobinae, Hormiinae, Ichneutinae, Macrocentrinae, Orgilinae, Proteropinae, Rhysipolinae, and Rogadinae. In these subfamilies 416 species are described or redescribed. Most of the species have been reared and all but 13 are new to science. A consensus sequence of the COI barcodes possessed by each species is employed to diagnose the species, and this approach is justified in the introduction. Most descriptions consist of a lateral or dorsal image of the holotype, a diagnostic COI consensus barcode, the Barcode Index Number (BIN) code with a link to the Barcode of Life Database (BOLD), and the holotype specimen information required by the International Code of Zoological Nomenclature. The following species are treated and those lacking authorship are newly described here with authorship attributable to Sharkey except for the new species of Macrocentrinae which are by Sharkey &amp; van Achterberg: AGATHIDINAE: Aerophiluspaulmarshi, Mesocoelusdavidsmithi, Neothlipsisbobkulai, Plesiocoelusvanachterbergi, Pneumagathiserythrogastra (Cameron, 1905), Therophilusbobwhartoni, T.donaldquickei, T.gracewoodae, T.maetoi, T.montywoodi, T.penteadodiasae, Zacremnopsbrianbrowni, Z.coatlicue Sharkey, 1990, Zacremnopscressoni (Cameron, 1887), Z.ekchuah Sharkey, 1990, Z.josefernandezi, Zelomorphasarahmeierottoae. BRACONINAE: Braconalejandromarini, B.alejandromasisi, B.alexamasisae, B.andresmarini, B.andrewwalshi, B.anniapicadoae, B.anniemoriceae, B.barryhammeli, B.bernardoespinozai, B.carlossanabriai, B.chanchini, B.christophervallei, B.erasmocoronadoi, B.eugeniephillipsae, B.federicomatarritai, B.frankjoycei, B.gerardovegai, B.germanvegai, B.isidrochaconi, B.jimlewisi, B.josejaramilloi, B.juanjoseoviedoi, B.juliodiazi, B.luzmariaromeroae, B.manuelzumbadoi, B.marialuisariasae, B.mariamartachavarriae, B.mariorivasi, B.melissaespinozae, B.nelsonzamorai, B.nicklaphami, B.ninamasisae, B.oliverwalshi, B.paulamarinae, B.rafamoralesi, B.robertofernandezi, B.rogerblancoi, B.ronaldzunigai, B.sigifredomarini, B.tihisiaboshartae, B.wilberthbrizuelai, Digonogastramontylloydi, D.montywoodi, D.motohasegawai, D.natwheelwrighti, D.nickgrishini. CHELONINAE: Adeliusadrianguadamuzi, A.gauldi Shimbori &amp; Shaw, 2019, A.janzeni Shimbori &amp; Shaw, 2019, Ascogastergloriasihezarae, A.grettelvegae, A.guillermopereirai, A.gustavoecheverrii, A.katyvandusenae, A.luisdiegogomezi, Chelonusalejandrozaldivari, C.gustavogutierrezi, C.gustavoinduni, C.harryramirezi, C.hartmanguidoi, C.hazelcambroneroae, C.iangauldi, C.isidrochaconi, C.janecheverriae, C.jeffmilleri, C.jennyphillipsae, C.jeremydewaardi, C.jessiehillae, C.jesusugaldei, C.jimlewisi, C.jimmilleri, C.jimwhitfieldi, C.johanvalerioi, C.johnburnsi, C.johnnoyesi, C.jorgebaltodanoi, C.jorgehernandezi, C.josealfredohernandezi, C.josefernandeztrianai, C.josehernandezcortesi, C.josemanuelperezi, C.josephinerodriguezae, C.juanmatai, C.junkoshimurae, C.kateperezae, C.luciariosae, C.luzmariaromeroae, C.manuelpereirai, C.manuelzumbadoi, C.marianopereirai, C.maribellealvarezae, C.markmetzi, C.markshawi, C.martajimenezae, C.mayrabonillae, C.meganmiltonae, C.melaniamunozae, C.michaelstroudi, C.michellevanderbankae, C.mingfangi, C.minorcarmonai, C.monikaspringerae, C.moniquegilbertae, C.motohasegawai, C.nataliaivanovae, C.nelsonzamorai, C.normwoodleyi, C.osvaldoespinozai, C.pamelacastilloae, C.paulgoldsteini, C.paulhansoni, C.paulheberti, C.petronariosae, C.ramyamanjunathae, C.randallgarciai, C.rebeccakittelae, C.robertoespinozai, C.robertofernandezi, C.rocioecheverriae, C.rodrigogamezi, C.ronaldzunigai, C.rosibelelizondoae, C.rostermoragai, C.ruthfrancoae, C.scottmilleri, C.scottshawi, C.sergioriosi, C.sigifredomarini, C.stevearonsoni, C.stevestroudi, C.sujeevanratnasinghami, C.sureshnaiki, C.torbjornekremi, C.yeimycedenoae, Leptodrepanaalexisae, L.erasmocoronadoi, L.felipechavarriai, L.freddyquesadai, L.gilbertfuentesi, L.manuelriosi, Phanerotomaalmasolisae, P.alvaroherrerai, P.anacordobae, P.anamariamongeae, P.andydeansi, P.angelagonzalezae, P.angelsolisi, P.barryhammeli, P.bernardoespinozai, P.calixtomoragai, P.carolinacanoae, P.christerhanssoni, P.christhompsoni, P.davesmithi, P.davidduthiei, P.dirksteinkei, P.donquickei, P.duniagarciae, P.duvalierbricenoi, P.eddysanchezi, P.eldarayae, P.eliethcantillanoae, P.jenopappi, Pseudophanerotomaalanflemingi, Ps.albanjimenezi, Ps.alejandromarini, Ps.alexsmithi, Ps.allisonbrownae, Ps.bobrobbinsi. HOMOLOBINAE: Exasticolusjennyphillipsae, E.randallgarciai, E.robertofernandezi, E.sigifredomarini, E.tomlewinsoni. HORMIINAE: Hormiusanamariamongeae, H.angelsolisi, H.anniapicadoae, H.arthurchapmani, H.barryhammeli, H.carmenretanae, H.carloswalkeri, H.cesarsuarezi, H.danbrooksi, H.eddysanchezi, H.erikframstadi, H.georgedavisi, H.grettelvegae, H.gustavoinduni, H.hartmanguidoi, H.hectoraritai, H.hesiquiobenitezi, H.irenecanasae, H.isidrochaconi, H.jaygallegosi, H.jimbeachi, H.jimlewisi, H.joelcracrafti, H.johanvalerioi, H.johnburleyi, H.joncoddingtoni, H.jorgecarvajali, H.juanmatai, H.manuelzumbadoi, H.mercedesfosterae, H.modonnellyae, H.nelsonzamorai, H.pamelacastilloae, H.raycypessi, H.ritacolwellae, H.robcolwelli, H.rogerblancosegurai, H.ronaldzunigai, H.russchapmani, H.virginiaferrisae, H.warrenbrighami, H.willsflowersi. ICHNEUTINAE: Oligoneuruskriskrishtalkai, O.jorgejimenezi, Paroligoneuruselainehoaglandae, P.julianhumphriesi, P.mikeiviei. MACROCENTRINAE: Austrozelejorgecampabadali, A.jorgesoberoni, Dolichozelegravitarsis (Muesebeck, 1938), D.josefernandeztrianai, D.josephinerodriguezae, Hymenochaoniakalevikulli, H.kateperezae, H.katherinebaillieae, H.katherineellisonae, H.katyvandusenae, H.kazumifukunagae, H.keithlangdoni, H.keithwillmotti, H.kenjinishidai, H.kimberleysheldonae, H.krisnorvigae, H.lilianamadrigalae, H.lizlangleyae, Macrocentrusfredsingeri, M.geoffbarnardi, M.gregburtoni, M.gretchendailyae, M.grettelvegae, M.gustavogutierrezi, M.hannahjamesae, M.harisridhari, M.hillaryrosnerae, M.hiroshikidonoi, M.iangauldi, M.jennyphillipsae, M.jesseausubeli, M.jessemaysharkae, M.jimwhitfieldi, M.johnbrowni, M.johnburnsi, M.jonathanfranzeni, M.jonathanrosenbergi, M.jorgebaltodanoi, M.lucianocapelli. ORGILINAE: Orgilusamyrossmanae, O.carrolyoonae, O.christhompsoni, O.christinemcmahonae, O.dianalipscombae, O.ebbenielsoni, O.elizabethpennisiae, O.evertlindquisti, O.genestoermeri, O.jamesriegeri, O.jeanmillerae, O.jeffmilleri, O.jerrypowelli, O.jimtiedjei, O.johnlundbergi, O.johnpipolyi, O.jorgellorentei, O.larryspearsi, O.marlinricei, O.mellissaespinozae, O.mikesmithi, O.normplatnicki, O.peterrauchi, O.richardprimacki, O.sandraberriosae, O.sarahmirandae, O.scottmilleri, O.scottmorii, Stantoniabillalleni, S.brookejarvisae, S.donwilsoni, S.erikabjorstromae, S.garywolfi, S.henrikekmani, S.luismirandai, S.miriamzunzae, S.quentinwheeleri, S.robinkazmierae, S.ruthtifferae. PROTEROPINAE: Hebichneutestricolor Sharkey &amp; Wharton, 1994, Proteropsiangauldi, P.vickifunkae, Michenercharlesi. RHYSIPOLINAE: Pseudorhysipolisluisfonsecai, P. mailyngonzalezaeRhysipolisjulioquirosi. ROGADINAE: Aleiodesadrianaradulovae, A.adrianforsythi, A.agnespeelleae, A.alaneaglei, A.alanflemingi, A.alanhalevii, A.alejandromasisi, A.alessandracallejae, A.alexsmithi, A.alfonsopescadori, A.alisundermieri, A.almasolisae, A.alvarougaldei, A.alvaroumanai, A.angelsolisi, A.annhowdenae, A.bobandersoni, A.carolinagodoyae, A.charlieobrieni, A.davefurthi, A.donwhiteheadi, A.doylemckeyi, A.frankhovorei, A.henryhowdeni, A.inga Shimbori &amp; Shaw, 2020, A.johnchemsaki, A.johnkingsolveri, A.gonodontovorus Shimbori &amp; Shaw, 2020, A.manuelzumbadoi, A.mayrabonillae, A.michelledsouzae, A.mikeiviei, A.normwoodleyi, A.pammitchellae, A.pauljohnsoni, A.rosewarnerae, A.steveashei, A.terryerwini, A.willsflowersi, Bioalfapedroleoni, B.alvarougaldei, B.rodrigogamezi, Choreborogasandydeansi, C.eladiocastroi, C.felipechavarriai, C.frankjoycei, Clinocentrusandywarreni, Cl.angelsolisi, Cystomastaxalexhausmanni, Cy.angelagonzalezae, Cy.ayaigarashiae, Hermosomastaxclavifemorus Quicke sp. nov., Heterogamusdonstonei, Pseudoyeliconesbernsweeneyi, Stiropiusbencrairi, S.berndkerni, S.edgargutierrezi, S.edwilsoni, S.ehakernae, Triraphisbillfreelandi, T.billmclarneyi, T.billripplei, T.bobandersoni, T.bobrobbinsi, T.bradzlotnicki, T.brianbrowni, T.brianlaueri, T.briannestjacquesae, T.camilocamargoi, T.carlosherrerai, T.carolinepalmerae, T.charlesmorrisi, T.chigiybinellae, T.christerhanssoni, T.christhompsoni, T.conniebarlowae, T.craigsimonsi, T.defectus Valerio, 2015, T.danielhubi, T.davidduthiei, T.davidwahli, T.federicomatarritai, T.ferrisjabri, T.mariobozai, T.martindohrni, T.matssegnestami, T.mehrdadhajibabaei, T.ollieflinti, T.tildalauerae, Yeliconesdirksteinkei, Y.markmetzi, Y.monserrathvargasae, Y.tricolor Quicke, 1996. Y.woldai Quicke, 1996. The following new combinations are proposed: Neothlipsissmithi (Ashmead), new combination for Microdussmithi Ashmead, 1894; Neothlipsispygmaeus (Enderlein), new combination for Microduspygmaeus Enderlein, 1920; Neothlipsisunicinctus (Ashmead), new combination for Microdusunicinctus Ashmead, 1894; Therophilusanomalus (Bortoni and Penteado-Dias) new combination for Plesiocoelusanomalus Bortoni and Penteado-Dias, 2015; Aerophilusareolatus (Bortoni and Penteado-Dias) new combination for Plesiocoelusareolatus Bortoni and Penteado-Dias, 2015; Pneumagathiserythrogastra (Cameron) new combination for Agathiserythrogastra Cameron, 1905. Dolichozelecitreitarsis (Enderlein), new combination for Paniscozelecitreitarsis Enderlein, 1920. Dolichozelefuscivertex (Enderlein) new combination for Paniscozelefuscivertex Enderlein, 1920. Finally, Bassusbrooksi Sharkey, 1998 is synonymized with Agathiserythrogastra Cameron, 1905; Paniscozelegriseipes Enderlein, 1920 is synonymized with Dolichozelekoebelei Viereck, 1911; Paniscozelecarinifrons Enderlein, 1920 is synonymized with Dolichozelefuscivertex (Enderlein, 1920); and Paniscozelenigricauda Enderlein,1920 is synonymized with Dolichozelequaestor (Fabricius, 1804). (originally described as Ophionquaestor Fabricius, 1804).},
}
@article {pmid34502319,
year = {2021},
author = {Hassan, JJ and Lieske, A and Dörpmund, N and Klatt, D and Hoffmann, D and Kleppa, MJ and Kustikova, OS and Stahlhut, M and Schwarzer, A and Schambach, A and Maetzig, T},
title = {A Multiplex CRISPR-Screen Identifies PLA2G4A as Prognostic Marker and Druggable Target for HOXA9 and MEIS1 Dependent AML.},
journal = {International journal of molecular sciences},
volume = {22},
number = {17},
pages = {},
pmid = {34502319},
issn = {1422-0067},
support = {MA 7010/1//Deutsche Forschungsgemeinschaft/ ; SFB738//Deutsche Forschungsgemeinschaft/ ; MWK: ZN3440//State of Lower Saxony, Germany/ ; REBIRTH EXC62/2//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Apoptosis ; Biomarkers, Tumor/genetics/*metabolism ; *CRISPR-Cas Systems ; Cell Proliferation ; *Gene Expression Regulation, Neoplastic ; Group IV Phospholipases A2/*antagonists &amp; inhibitors/genetics ; High-Throughput Screening Assays ; Homeodomain Proteins/genetics/*metabolism ; Humans ; Leukemia, Myeloid, Acute/genetics/metabolism/*pathology ; Myeloid Ecotropic Viral Integration Site 1 Protein/genetics/*metabolism ; Tumor Cells, Cultured ; },
abstract = {HOXA9 and MEIS1 are frequently upregulated in acute myeloid leukemia (AML), including those with MLL-rearrangement. Because of their pivotal role in hemostasis, HOXA9 and MEIS1 appear non-druggable. We, thus, interrogated gene expression data of pre-leukemic (overexpressing Hoxa9) and leukemogenic (overexpressing Hoxa9 and Meis1; H9M) murine cell lines to identify cancer vulnerabilities. Through gene expression analysis and gene set enrichment analyses, we compiled a list of 15 candidates for functional validation. Using a novel lentiviral multiplexing approach, we selected and tested highly active sgRNAs to knockout candidate genes by CRISPR/Cas9, and subsequently identified a H9M cell growth dependency on the cytosolic phospholipase A2 (PLA2G4A). Similar results were obtained by shRNA-mediated suppression of Pla2g4a. Remarkably, pharmacologic inhibition of PLA2G4A with arachidonyl trifluoromethyl ketone (AACOCF3) accelerated the loss of H9M cells in bulk cultures. Additionally, AACOCF3 treatment of H9M cells reduced colony numbers and colony sizes in methylcellulose. Moreover, AACOCF3 was highly active in human AML with MLL rearrangement, in which PLA2G4A was significantly higher expressed than in AML patients without MLL rearrangement, and is sufficient as an independent prognostic marker. Our work, thus, identifies PLA2G4A as a prognostic marker and potential therapeutic target for H9M-dependent AML with MLL-rearrangement.},
}
@article {pmid34497930,
year = {2021},
author = {Yang, D and Li, Z and Gao, G and Li, X and Liao, Z and Wang, Y and Li, W and Zhang, Y and Liu, W},
title = {Combined Analysis of Surface Protein Profile and microRNA Expression Profile of Exosomes Derived from Brain Microvascular Endothelial Cells in Early Cerebral Ischemia.},
journal = {ACS omega},
volume = {6},
number = {34},
pages = {22410-22421},
pmid = {34497930},
issn = {2470-1343},
abstract = {Endothelial cell damage is an important pathological basis for the deterioration of acute ischemia stroke. Our previous studies have been exploring the mechanism of blood-brain barrier (BBB) endothelial cell injury in the early stage of cerebral ischemia. Exosomes act as an important intercellular player in neurovascular communication. However, the characteristic of exosomes derived from BBB endothelial cells in early ischemic stroke is poorly understood. We exposed cultured brain microvascular endothelial cells (bEnd.3) to 3 h oxygen glucose deprivation (OGD) to mimic early cerebral ischemia in vitro and compared miRome and surface protein contents of exosomes derived from bEnd.3 cells by miRNA sequencing and the proximity barcoding assay (PBA). A total of 346 differentially miRNA (159 upregulated and 187 downregulated) were identified via miRNA-Seq in bEnd.3 cells after exposure to OGD for 3 h. Moreover, Gene Ontology (GO) and KEGG pathway analyses showed that cell proliferation- and angiogenesis-associated miRNAs were significantly affected. The abnormal changes in top eight miRNAs were further verified by a quantitative polymerase chain reaction (qPCR). PBA experiments showed that the numbers of exosomes carrying the following proteins increased significantly under ischemia, including bFGF, CD146, EPHA2, ABCB5, and ITGB2. These proteins were related to angiogenesis, cell proliferation, and cell inflammation. The network analysis combining PBA data with miRNA-Seq data showed that 79 miRNAs were related to 24 membrane proteins and predicted that there were surface proteins associated with a variety of miRNA molecules, such as ITGA9, XIAP, ADAM1, ITGA2, ITGA3, PDPN, and ITGB1. Meanwhile, there were miRNAs related to various surface proteins including miR-410-3p, miR-378b, and miR-1960. Taken together, our data demonstrated for the first time the changes of exosomal miRNAs and surface protein profiles derived from ischemic microvascular endothelial cells, which may provide new therapeutic targets for BBB protection in ischemic stroke.},
}
@article {pmid34497385,
year = {2021},
author = {Sufi, J and Qin, X and Rodriguez, FC and Bu, YJ and Vlckova, P and Zapatero, MR and Nitz, M and Tape, CJ},
title = {Multiplexed single-cell analysis of organoid signaling networks.},
journal = {Nature protocols},
volume = {16},
number = {10},
pages = {4897-4918},
pmid = {34497385},
issn = {1750-2799},
support = {C416/A25145/CRUK_/Cancer Research UK/United Kingdom ; C60693/A23783/CRUK_/Cancer Research UK/United Kingdom ; C7893/A26233/CRUK_/Cancer Research UK/United Kingdom ; MR/T028270/1/MRC_/Medical Research Council/United Kingdom ; 23783/CRUK_/Cancer Research UK/United Kingdom ; },
mesh = {*Organoids/metabolism/cytology ; *Single-Cell Analysis/methods ; *Signal Transduction ; Humans ; Animals ; Protein Processing, Post-Translational ; Fibroblasts/metabolism/cytology ; Mice ; Coculture Techniques/methods ; Leukocytes/metabolism/cytology ; },
abstract = {Organoids are biomimetic tissue models comprising multiple cell types and cell states. Post-translational modification (PTM) signaling networks control cellular phenotypes and are frequently dysregulated in diseases such as cancer. Although signaling networks vary across cell types, there are limited techniques to study cell type-specific PTMs in heterocellular organoids. Here, we present a multiplexed mass cytometry (MC) protocol for single-cell analysis of PTM signaling and cell states in organoids and organoids co-cultured with fibroblasts and leukocytes. We describe how thiol-reactive organoid barcoding in situ (TOBis) enables 35-plex and 126-plex single-cell comparison of organoid cultures and provide a cytometry by time of flight (CyTOF) signaling analysis pipeline (CyGNAL) for computing cell type-specific PTM signaling networks. The TOBis MC protocol takes ~3 d from organoid fixation to data acquisition and can generate single-cell data for >40 antibodies from millions of cells across 126 organoid cultures in a single MC run.},
}
@article {pmid34496132,
year = {2022},
author = {Creedy, TJ and Andújar, C and Meramveliotakis, E and Noguerales, V and Overcast, I and Papadopoulou, A and Morlon, H and Vogler, AP and Emerson, BC and Arribas, P},
title = {Coming of age for COI metabarcoding of whole organism community DNA: Towards bioinformatic harmonisation.},
journal = {Molecular ecology resources},
volume = {22},
number = {3},
pages = {847-861},
pmid = {34496132},
issn = {1755-0998},
support = {810729//Horizon 2020 Framework Programme/ ; },
mesh = {Animals ; Biodiversity ; *Computational Biology ; DNA/genetics ; *DNA Barcoding, Taxonomic/methods ; Ecology ; },
abstract = {Metabarcoding of DNA extracted from community samples of whole organisms (whole organism community DNA, wocDNA) is increasingly being applied to terrestrial, marine and freshwater metazoan communities to provide rapid, accurate and high resolution data for novel molecular ecology research. The growth of this field has been accompanied by considerable development that builds on microbial metabarcoding methods to develop appropriate and efficient sampling and laboratory protocols for whole organism metazoan communities. However, considerably less attention has focused on ensuring bioinformatic methods are adapted and applied comprehensively in wocDNA metabarcoding. In this study we examined over 600 papers and identified 111 studies that performed COI metabarcoding of wocDNA. We then systematically reviewed the bioinformatic methods employed by these papers to identify the state-of-the-art. Our results show that the increasing use of wocDNA COI metabarcoding for metazoan diversity is characterised by a clear absence of bioinformatic harmonisation, and the temporal trends show little change in this situation. The reviewed literature showed (i) high heterogeneity across pipelines, tasks and tools used, (ii) limited or no adaptation of bioinformatic procedures to the nature of the COI fragment, and (iii) a worrying underreporting of tasks, software and parameters. Based upon these findings we propose a set of recommendations that we think the metabarcoding community should consider to ensure that bioinformatic methods are appropriate, comprehensive and comparable. We believe that adhering to these recommendations will improve the long-term integrative potential of wocDNA COI metabarcoding for biodiversity science.},
}
@article {pmid34493747,
year = {2021},
author = {Zainal Abidin, DH and Mohd Nor, SA and Lavoué, S and A Rahim, M and Jamaludin, NA and Mohammed Akib, NA},
title = {DNA-based taxonomy of a mangrove-associated community of fishes in Southeast Asia.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {17800},
pmid = {34493747},
issn = {2045-2322},
mesh = {Animals ; Biodiversity ; Conservation of Natural Resources ; DNA/genetics ; *DNA Barcoding, Taxonomic ; *Ecosystem ; Estuaries ; Fishes/*classification/genetics ; Gene Library ; Malaysia ; Reference Standards ; Rhizophoraceae ; Species Specificity ; },
abstract = {The Merbok Estuary comprises one of the largest remaining mangrove forests in Peninsular Malaysia. Its value is significant as it provides important services to local and global communities. It also offers a unique opportunity to study the structure and functioning of mangrove ecosystems. However, its biodiversity is still partially inventoried, limiting its research value. A recent checklist based on morphological examination, reported 138 fish species residing, frequenting or subject to entering the Merbok Estuary. In this work, we reassessed the fish diversity of the Merbok Estuary by DNA barcoding 350 specimens assignable to 134 species initially identified based on morphology. Our results consistently revealed the presence of 139 Molecular Operational Taxonomic Units (MOTUs). 123 of them are congruent with morphology-based species delimitation (one species = one MOTU). In two cases, two morphological species share the same MOTU (two species = one MOTU), while we unveiled cryptic diversity (i.e. COI-based genetic variability > 2%) within seven other species (one species = two MOTUs), calling for further taxonomic investigations. This study provides a comprehensive core-list of fish taxa in Merbok Estuary, demonstrating the advantages of combining morphological and molecular evidence to describe diverse but still poorly studied tropical fish communities. It also delivers a large DNA reference collection for brackish fishes occurring in this region which will facilitate further biodiversity-oriented research studies and management activities.},
}
@article {pmid34493337,
year = {2021},
author = {Escobar-Zepeda, A and Rosas-Escobar, P and Marquez Valdelamar, L and de la Torre, P and Partida-Martinez, LP and Remegaldo, R and Sanchez-Flores, A and Vergara, F},
title = {Distinctive prokaryotic microbiomes in sympatric plant roots from a Yucatan cenote.},
journal = {BMC research notes},
volume = {14},
number = {1},
pages = {333},
pmid = {34493337},
issn = {1756-0500},
mesh = {Mexico ; *Microbiota/genetics ; Plant Roots ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil Microbiology ; },
abstract = {OBJECTIVE: Cenotes are flooded caves in Mexico's Yucatan peninsula. Many cenotes are interconnected in an underground network of pools and streams forming a vast belowground aquifer across most of the peninsula. Many plants in the peninsula grow roots that reach the cenotes water and live submerged in conditions similar to hydroponics. Our objective was to study the microbial community associated with these submerged roots of the Sac Actun cenote. We accomplished this objective by profiling the root prokaryotic community using 16S rRNA gene amplification and sequencing.<br><br>RESULTS: We identified plant species by DNA barcoding the total genomic DNA of each root. We found a distinctive composition of the root and water bacterial and archaeal communities. Prokaryotic diversity was higher in all plant roots than in the surrounding freshwater, suggesting that plants in the cenotes may attract and select microorganisms from soil and freshwater, and may also harbor vertically transmitted lineages. The reported data are of interest for studies targeting biodiversity in general and root-microbial ecological interactions specifically.},
}
@article {pmid34488860,
year = {2021},
author = {Zhang, C and Yang, R and Wu, L and Luo, C and Guo, X and Deng, Y and Zhou, H and Zhang, Y},
title = {Molecular phylogeny of the Anopheles hyrcanus group (Diptera: Culicidae) based on rDNA-ITS2 and mtDNA-COII.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {454},
pmid = {34488860},
issn = {1756-3305},
support = {31601002//national natural science foundation of china/ ; 81160357//national natural science foundation of china/ ; 30960327//national natural science foundation of china/ ; 30660160//national natural science foundation of china/ ; 2014YNPHXT03//yunnan provincial collaborative innovation center for public health and disease prevention and control/ ; },
mesh = {Animals ; Anopheles/*classification/*genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Intergenic/genetics ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/*genetics ; Mosquito Vectors/*classification/*genetics ; *Phylogeny ; },
abstract = {BACKGROUND: The Anopheles hyrcanus group, which includes 25 species, is widely distributed in the Oriental and Palaearctic regions. Given the difficulty in identifying cryptic or sibling species based on their morphological characteristics, molecular identification is regarded as an important complementary approach to traditional morphological taxonomy. The aim of this study was to reconstruct the phylogeny of the Hyrcanus group using DNA barcoding markers in order to determine the phylogenetic correlations of closely related taxa and to compare these markers in terms of identification efficiency and genetic divergence among species.<br><br>METHODS: Based on data extracted from the GenBank database and data from the&#xa0;present&#xa0;study, we used 399 rDNA-ITS2 sequences of 19 species and 392 mtDNA-COII sequences of 14 species to reconstruct the molecular phylogeny of the Hyrcanus group across its worldwide range. We also compared the performance of rDNA-ITS2 against that of mtDNA-COII to assess the genetic divergence of closely related species within the Hyrcanus group.<br><br>RESULTS: Average interspecific divergence for the rDNA-ITS2 sequence (0.376) was 125-fold higher than the average intraspecies divergence (0.003), and average interspecific divergence for the mtDNA-COII sequence (0.055) was eightfold higher than the average intraspecies divergence (0.007). The barcoding gap ranged from 0.015 to 0.073 for rDNA-ITS2, and from 0.017 to 0.025 for mtDNA-COII. Two sets of closely related species, namely, Anophels lesteri and An. paraliae, and An. sinensis, An. belenrae and An. kleini, were resolved by rDNA-ITS2. In contrast, the relationship of An. sinensis/An. belenrae/An. kleini was poorly defined in the COII tree. The neutrality test and mismatch distribution revealed that An. peditaeniatus, An. hyrcanus, An. sinensis and An. lesteri were likely to undergo hitchhiking or population expansion in accordance with both markers. In addition, the population of an important vivax malaria vector, An. sinensis, has experienced an expansion after a bottleneck in northern and southern Laos.<br><br>CONCLUSIONS: The topology of the Hyrcanus group rDNA-ITS2 and mtDNA-COII trees conformed to the morphology-based taxonomy for species classification rather than for that for subgroup division. rDNA-ITS2 is considered to be a more reliable diagnostic tool than mtDNA-COII in terms of investigating the phylogenetic correlation between closely related mosquito species in the Hyrcanus group. Moreover, the population expansion of an important vivax malaria vector, An. sinensis, has underlined a potential risk of malaria transmission in northern and southern Laos. This study contributes to the molecular identification of the Anopheles hyrcanus group in vector surveillance.},
}
@article {pmid34488648,
year = {2021},
author = {Prazeres, M and Roberts, TE and Ramadhani, SF and Doo, SS and Schmidt, C and Stuhr, M and Renema, W},
title = {Diversity and flexibility of algal symbiont community in globally distributed larger benthic foraminifera of the genus Amphistegina.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {243},
pmid = {34488648},
issn = {1471-2180},
mesh = {Coral Reefs ; DNA Barcoding, Taxonomic ; Diatoms/genetics ; *Ecosystem ; Foraminifera/classification/*genetics ; *Genetic Variation ; High-Throughput Nucleotide Sequencing ; Oceans and Seas ; Phylogeny ; *Symbiosis ; },
abstract = {BACKGROUND: Understanding the specificity and flexibility of the algal symbiosis-host association is fundamental for predicting how species occupy a diverse range of habitats. Here we assessed the algal symbiosis diversity of three species of larger benthic foraminifera from the genus Amphistegina and investigated the role of habitat and species identity in shaping the associated algal community.<br><br>RESULTS: We used next-generation sequencing to identify the associated algal community, and DNA barcoding to identify the diatom endosymbionts associated with species of A. lobifera, A. lessonii, and A. radiata, collected from shallow habitats (<&#x2009;15&#x2009;m) in 16 sites, ranging from the Mediterranean Sea to French Polynesia. Next-generation sequencing results showed the consistent presence of Ochrophyta as the main algal phylum associated with all species and sites analysed. A significant proportion of phylotypes were classified as Chlorophyta and Myzozoa. We uncovered unprecedented diversity of algal phylotypes found in low abundance, especially of the class Bacillariophyta (i.e., diatoms). We found a significant influence of sites rather than host identity in shaping algal communities in all species. DNA barcoding revealed the consistent presence of phylotypes classified within the order Fragilariales as the diatoms associated with A. lobifera and A. lessonii, while A. radiata specimens host predominately diatoms of the order Triceratiales.<br><br>CONCLUSIONS: We show that local habitat is the main factor influencing the overall composition of the algal symbiont community. However, host identity and the phylogenetic relationship among hosts is relevant in shaping the specific endosymbiont diatom community, suggesting that the relationship between diatom endosymbiont and hosts plays a crucial role in the evolutionary history of the genus Amphistegina. The capacity of Amphistegina species to associate with a diverse array of diatoms, and possibly other algal groups, likely underpins the ecological success of these crucial calcifying organisms across their extensive geographic range.},
}
@article {pmid34487362,
year = {2022},
author = {Meier, R and Blaimer, BB and Buenaventura, E and Hartop, E and von Rintelen, T and Srivathsan, A and Yeo, D},
title = {A re-analysis of the data in Sharkey et al.'s (2021) minimalist revision reveals that BINs do not deserve names, but BOLD Systems needs a stronger commitment to open science.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {38},
number = {2},
pages = {264-275},
doi = {10.1111/cla.12489},
pmid = {34487362},
issn = {1096-0031},
support = {R-154-000-A22-112//Ministry of Education/ ; },
abstract = {Halting biodiversity decline is one of the most critical challenges for humanity, but monitoring biodiversity is hampered by taxonomic impediments. One impediment is the large number of undescribed species (here called "dark taxon impediment") whereas another is caused by the large number of superficial species descriptions, that can only be resolved by consulting type specimens ("superficial description impediment"). Recently, Sharkey et al. (2021) proposed to address the dark taxon impediment for Costa Rican braconid wasps by describing 403 species based on COI barcode clusters ("BINs") computed by BOLD Systems. More than 99% of the BINs (387 of 390) were converted into species by assigning binominal names (e.g. BIN "BOLD:ACM9419" becomes Bracon federicomatarritai) and adding a minimal diagnosis (consisting only of a consensus barcode for most species). We here show that many of Sharkey et al.'s species are unstable when the underlying data are analyzed using different species delimitation algorithms. Add the insufficiently informative diagnoses, and many of these species will become the next "superficial description impediment" for braconid taxonomy because they will have to be tested and redescribed after obtaining sufficient evidence for confidently delimiting species. We furthermore show that Sharkey et al.'s approach of using consensus barcodes as diagnoses is not functional because it cannot be applied consistently. Lastly, we reiterate that COI alone is not suitable for delimiting and describing species, and voice concerns over Sharkey et al.'s uncritical use of BINs because they are calculated by a proprietary algorithm (RESL) that uses a mixture of public and private data. We urge authors, reviewers and editors to maintain high standards in taxonomy by only publishing new species that are rigorously delimited with open-access tools and supported by publicly available evidence.},
}
@article {pmid34486815,
year = {2022},
author = {Günther, B and Marre, S and Defois, C and Merzi, T and Blanc, P and Peyret, P and Arnaud-Haond, S},
title = {Capture by hybridization for full-length barcode-based eukaryotic and prokaryotic biodiversity inventories of deep sea ecosystems.},
journal = {Molecular ecology resources},
volume = {22},
number = {2},
pages = {623-637},
doi = {10.1111/1755-0998.13500},
pmid = {34486815},
issn = {1755-0998},
support = {Contract no. 9194 TOTAL FR0000//Total/ ; 678760//European Union 2020 Research and Innovation Programme/ ; },
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Ribosomal ; *Ecosystem ; *Eukaryota ; Phylogeny ; },
abstract = {Biodiversity inventory of marine systems remains limited due to unbalanced access to the three ocean dimensions. The use of environmental DNA (eDNA) for metabarcoding allows fast and effective biodiversity inventory and is forecast as a future biodiversity research and biomonitoring tool. However, in poorly understood ecosystems, eDNA results remain difficult to interpret due to large gaps in reference databases and PCR bias limiting the detection of some major phyla. Here, we aimed to circumvent these limitations by avoiding PCR and recollecting larger DNA fragments to improve assignment of detected taxa through phylogenetic reconstruction. We applied capture by hybridization (CBH) to enrich DNA from deep-sea sediment samples and compared the results with those obtained through an up-to-date metabarcoding PCR-based approach (MTB). Originally developed for bacterial communities and targeting 16S rDNA, the CBH approach was applied to 18S rDNA to improve the detection of species forming benthic communities of eukaryotes, with a particular focus on metazoans. The results confirmed the possibility of extending CBH to metazoans with two major advantages: (i) CBH revealed a broader spectrum of prokaryotic, eukaryotic, and particularly metazoan diversity, and (ii) CBH allowed much more robust phylogenetic reconstructions of full-length barcodes with up to 1900 base pairs. This is particularly important for taxa whose assignment is hampered by gaps in reference databases. This study provides a database and probes to apply 18S CBH to diverse marine systems, confirming this promising new tool to improve biodiversity assessments in data-poor ecosystems such as those in the deep sea.},
}
@article {pmid34485968,
year = {2021},
author = {Shan, KJ and Wei, C and Wang, Y and Huan, Q and Qian, W},
title = {Host-specific asymmetric accumulation of mutation types reveals that the origin of SARS-CoV-2 is consistent with a natural process.},
journal = {Innovation (Cambridge (Mass.))},
volume = {2},
number = {4},
pages = {100159},
pmid = {34485968},
issn = {2666-6758},
abstract = {The capacity of RNA viruses to adapt to new hosts and rapidly escape the host immune system is largely attributable to de novo genetic diversity that emerges through mutations in RNA. Although the molecular spectrum of de novo mutations-the relative rates at which various base substitutions occur-are widely recognized as informative toward understanding the evolution of a viral genome, little attention has been paid to the possibility of using molecular spectra to infer the host origins of a virus. Here, we characterize the molecular spectrum of de novo mutations for SARS-CoV-2 from transcriptomic data obtained from virus-infected cell lines, enabled by the use of sporadic junctions formed during discontinuous transcription as molecular barcodes. We find that de novo mutations are generated in a replication-independent manner, typically on the genomic strand, and highly dependent on mutagenic mechanisms specific to the host cellular environment. De novo mutations will then strongly influence the types of base substitutions accumulated during SARS-CoV-2 evolution, in an asymmetric manner favoring specific mutation types. Consequently, similarities between the mutation spectra of SARS-CoV-2 and the bat coronavirus RaTG13, which have accumulated since their divergence strongly suggest that SARS-CoV-2 evolved in a host cellular environment highly similar to that of bats before its zoonotic transfer into humans. Collectively, our findings provide data-driven support for the natural origin of SARS-CoV-2.},
}
@article {pmid34481081,
year = {2021},
author = {Nitta, M},
title = {Capsalids (Platyhelminthes: Monogenea) from marine fishes off Okinawa in Japan with the proposal of two new genera.},
journal = {Parasitology international},
volume = {85},
number = {},
pages = {102448},
doi = {10.1016/j.parint.2021.102448},
pmid = {34481081},
issn = {1873-0329},
mesh = {Animals ; Female ; Fish Diseases/*epidemiology/parasitology ; Japan/epidemiology ; Male ; Prevalence ; Species Specificity ; Trematoda/anatomy &amp; histology/*classification/isolation &amp; purification ; Trematode Infections/epidemiology/parasitology/*veterinary ; },
abstract = {Molecular studies of the Capsalidae suggested that the genus Benedenia is polyphyletic, but a taxonomic organization of the genus that reflects molecular data has not yet been proposed. As a result of molecular analysis (28S rDNA, ITS1-5.8S-ITS2, and cox1 data) including specimens of Benedeniinae newly obtained from Okinawa-jima Island in Japan, two new genera and the revival of Tareenia independent to the genus Benedenia are proposed. Gracilobenedenia n. gen. is distinguished from the other genera of Benedeniinae based on morphological characteristics. This new genus comprises 6 species: G. lutjani n. comb. (type species), G. anticavaginata n. comb., G. rohdei n. comb., G. beverleyburtonae n. comb., G. kuremibai n. gen., n. sp., and G. hichi n. gen., n. sp. Armatobenedenia n. gen. is a monotypic genus for A. armata n. comb. The present molecular phylogenetic analysis showed the independence of Tareenia, and it can be morphologically separated from the other benedeniines. Four species including two new species obtained from Okinawa-jima Island are reported: G. kuremibai n. sp., G. hichi n. sp., G. lutjani n. comb., and Metabenedeniella parva. Furthermore, in the species identification and phylogenetic analysis of capsalids, the usefulness of not only the 28S rDNA but also ITS and the cox1 regions was suggested. These genes were evaluated the efficacy of those regions in DNA barcoding, and the ITS and cox1 regions shown to be useful for DNA barcoding in capsalids compared to the 28S rDNA sequence.},
}
@article {pmid34480131,
year = {2021},
author = {Alcántara-Hernández, M and Idoyaga, J},
title = {Mass cytometry profiling of human dendritic cells in blood and tissues.},
journal = {Nature protocols},
volume = {16},
number = {10},
pages = {4855-4877},
pmid = {34480131},
issn = {1750-2799},
support = {R21 AI163775/AI/NIAID NIH HHS/United States ; R01 AI158808/AI/NIAID NIH HHS/United States ; DP2 AR069953/AR/NIAMS NIH HHS/United States ; S10 OD016318/OD/NIH HHS/United States ; R01 CA219994/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Dendritic Cells/cytology/immunology ; *Flow Cytometry/methods ; Single-Cell Analysis/methods ; },
abstract = {The immune system comprises distinct functionally specialized cell populations, which can be characterized in depth by mass cytometry protein profiling. Unfortunately, the low-throughput nature of mass cytometry has made it challenging to analyze minor cell populations. This is the case for dendritic cells, which represent 0.2-2% of all immune cells in tissues and yet perform the critical task of initiating and modulating immune responses. Here, we provide an optimized step-by-step protocol for the characterization of well-known and emerging human dendritic cell populations in blood and tissues using mass cytometry. We provide detailed instructions for the generation of single-cell suspensions, sample enrichment, staining, acquisition and data analysis. We also include a barcoding option that reduces acquisition variability and allows the analysis of low numbers of dendritic cells, i.e., ~20,000. In contrast to other protocols, we emphasize the use of negative selection approaches to enrich for minor populations of immune cells while avoiding their activation. The entire procedure can be completed in 2-3 d and can be conveniently paused at several stages. The procedure described in this robust and reliable protocol allows the analysis of human dendritic cells in health and disease and during vaccination.},
}
@article {pmid34476739,
year = {2021},
author = {Negi, RK and Nautiyal, P and Bhatia, R and Verma, R},
title = {rbcL, a potential candidate DNA barcode loci for aconites: conservation of himalayan aconites.},
journal = {Molecular biology reports},
volume = {48},
number = {10},
pages = {6769-6777},
pmid = {34476739},
issn = {1573-4978},
support = {FRI-619/Bot-81//Indian Council of Forestry Research and Education (ICFRE)/ ; },
mesh = {Aconitum/*genetics ; Base Sequence ; *Conservation of Natural Resources ; *DNA Barcoding, Taxonomic ; Geography ; India ; Phylogeny ; Polymorphism, Genetic ; Ribulose-Bisphosphate Carboxylase ; },
abstract = {BACKGROUND: Aconitum heterophyllum Wall. ex Royle and Aconitum balfourii Stapf, are two highly important, threatened medicinal plants of the Indian Himalayan Region. Root-tubers of Aconites have occupied an important place in Indian pharmacopoeia from very ancient times. India is a hub of the wild-collected medicinal herbs industry in Asia and these two aconites are known to have been heavily traded from the region in illicit manner. Prosecution of these illegal trading crimes is hampered by lack of pharma-forensic expertise and tools.<br><br>METHODS AND RESULTS: Present study was conducted to evaluate the discriminatory potential of rbcL, a Chloroplast based DNA barcode marker for the authentication of these two Himalayan Aconites. Fresh plant samples were collected from their natural distributional range as well as raw materials were procured from herbal market and a total of 32 sequences were generated for the rbcL region. Analysis demonstrated that rbcL region can successfully be used for authentication and importantly, both the aconites, were successfully discriminated by rbcL locus with high bootstrap support (>&#x2009;50%).<br><br>CONCLUSION: Molecular markers could certainly be relied upon morphological and chemical markers being tissue specific, having a higher discriminatory power and not age dependent. Phylogenetic analysis using Maximum Likelihood Method revealed that the rbcL gene could successfully discriminate Himalayan Aconites to species level and have potential to be used in pharma-forensic applications as well as to curb illicit trade of these invaluable medicinal plants.},
}
@article {pmid34475451,
year = {2021},
author = {Choi, EH and Yeo, MY and Kim, G and Park, B and Shin, CR and Baek, SY and Hwang, UW},
title = {Liolophura species discrimination with geographical distribution patterns and their divergence and expansion history on the northwestern Pacific coast.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {17602},
pmid = {34475451},
issn = {2045-2322},
abstract = {The chiton Liolophura japonica (Lischke 1873) is distributed in intertidal areas of the northwestern Pacific. Using COI and 16S rRNA, we found three genetic lineages, suggesting separation into three different species. Population genetic analyses, the two distinct COI barcoding gaps albeit one barcoding gap in the 16S rRNA, and phylogenetic relationships with a congeneric species supported this finding. We described L. koreana, sp. nov. over ca. 33°24' N (JJ), and L. sinensis, sp. nov. around ca. 27°02'-28°00' N (ZJ). We confirmed that these can be morphologically distinguished by lateral and dorsal black spots on the tegmentum and the shape of spicules on the perinotum. We also discuss species divergence during the Plio-Pleistocene, demographic expansions following the last interglacial age in the Pleistocene, and augmentation of COI haplotype diversity during the Pleistocene. Our study sheds light on the potential for COI in examining marine invertebrate species discrimination and distribution in the northwestern Pacific.},
}
@article {pmid34471500,
year = {2021},
author = {Luan, MW and Lin, JL and Wang, YF and Liu, YX and Xiao, CL and Wu, R and Xie, SQ},
title = {SCSit: A high-efficiency preprocessing tool for single-cell sequencing data from SPLiT-seq.},
journal = {Computational and structural biotechnology journal},
volume = {19},
number = {},
pages = {4574-4580},
pmid = {34471500},
issn = {2001-0370},
abstract = {SPLiT-seq provides a low-cost platform to generate single-cell data by labeling the cellular origin of RNA through four rounds of combinatorial barcoding. However, an automatic and rapid method for preprocessing and classifying single-cell sequencing (SCS) data from SPLiT-seq, which directly identified and labeled combinatorial barcoding reads and distinguished special cell sequencing data, is currently lacking. Here, we develop a high-efficiency preprocessing tool for single-cell sequencing data from SPLiT-seq (SCSit), which can directly identify combinatorial barcodes and UMI of cell types and obtain more labeled reads, and remarkably enhance the retained data from SCS due to the exact alignment of insertion and deletion. Compared with the original method used in SPLiT-seq, the consistency of identified reads from SCSit increases to 97%, and mapped reads are twice than the original. Furthermore, the runtime of SCSit is less than 10% of the original. It can accurately and rapidly analyze SPLiT-seq raw data and obtain labeled reads, as well as effectively improve the single-cell data from SPLiT-seq platform. The data and source of SCSit are available on the GitHub website https://github.com/shang-qian/SCSit.},
}
@article {pmid34471179,
year = {2021},
author = {Mohammad Rahimi, H and Mirjalali, H and Zali, MR},
title = {Molecular epidemiology and genotype/subtype distribution of Blastocystis sp., Enterocytozoon bieneusi, and Encephalitozoon spp. in livestock: concern for emerging zoonotic infections.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {17467},
pmid = {34471179},
issn = {2045-2322},
mesh = {Animals ; Blastocystis/genetics/*physiology ; Blastocystis Infections/epidemiology/parasitology ; Cattle ; Chickens ; Encephalitozoon/genetics/*physiology ; Encephalitozoonosis/epidemiology/microbiology ; Enterocytozoon/genetics/*physiology ; Genotype ; Horses ; Iran/epidemiology ; Livestock ; Microsporidiosis/epidemiology/microbiology ; Molecular Epidemiology ; Phylogeny ; Prevalence ; Sheep ; Zoonoses/*epidemiology/microbiology/parasitology ; },
abstract = {Intestinal parasitic infections have high prevalence rate in many regions especially in developing countries. The aim of this study was to determine the presence and genotype/subtype of some intestinal protozoa in livestock in Iran. Stool samples were collected from cattle, sheep, chickens, and horses. The presence of targeted parasites was evaluated using real-time PCR. Genotyping/subtyping of positive samples was characterized using sequencing of the ITS and barcoding region, respectively. Blastocystis sp., 27.7% (48/173) and Enterocytozoon bieneusi 26.0% (45/173) were the most frequent protozoa followed by Encephalitozoon spp., 0.57% (1/173). Cryptosporidium spp. were not detected among samples. Encephalitozoon spp., was detected only in chickens 2.2% (1/45). A statistically correlation was seen between animals and the prevalence of targeted protozoa. E. bieneusi genotypes I (9/38; 23.68%), BEB6 (22/38; 57.89%), D (6/38; 15.79%), and horse1 (1/38; 2.63%) were detected among samples. A statistically significant correlation was seen between the genotypes and animals (P ≤ 0.05). Blastocystis sp., ST1 (1/45; 2.22%), ST5 3/45; 6.66%), ST7 (1/45; 2.22%), ST10 (24/45; 53.33%), and ST14 (16/45; 35.55%) were characterized among samples. There was no significant correlation between certain subtypes and animals (P = 0.173). The presence of zoonotic potential genotypes of E. bieneusi in animals and zoonotic potential subtypes ST1 and ST7 among our samples provide a clue about the transmission dynamic of E. bieneusi and Blastocystis sp. between animals-animals and humans-animals.},
}
@article {pmid34466168,
year = {2021},
author = {Crous, PW and Lombard, L and Sandoval-Denis, M and Seifert, KA and Schroers, HJ and Chaverri, P and Gené, J and Guarro, J and Hirooka, Y and Bensch, K and Kema, GHJ and Lamprecht, SC and Cai, L and Rossman, AY and Stadler, M and Summerbell, RC and Taylor, JW and Ploch, S and Visagie, CM and Yilmaz, N and Frisvad, JC and Abdel-Azeem, AM and Abdollahzadeh, J and Abdolrasouli, A and Akulov, A and Alberts, JF and Araújo, JPM and Ariyawansa, HA and Bakhshi, M and Bendiksby, M and Ben Hadj Amor, A and Bezerra, JDP and Boekhout, T and Câmara, MPS and Carbia, M and Cardinali, G and Castañeda-Ruiz, RF and Celis, A and Chaturvedi, V and Collemare, J and Croll, D and Damm, U and Decock, CA and de Vries, RP and Ezekiel, CN and Fan, XL and Fernández, NB and Gaya, E and González, CD and Gramaje, D and Groenewald, JZ and Grube, M and Guevara-Suarez, M and Gupta, VK and Guarnaccia, V and Haddaji, A and Hagen, F and Haelewaters, D and Hansen, K and Hashimoto, A and Hernández-Restrepo, M and Houbraken, J and Hubka, V and Hyde, KD and Iturriaga, T and Jeewon, R and Johnston, PR and Jurjević, &#x17d; and Karalti, I and Korsten, L and Kuramae, EE and Kušan, I and Labuda, R and Lawrence, DP and Lee, HB and Lechat, C and Li, HY and Litovka, YA and Maharachchikumbura, SSN and Marin-Felix, Y and Matio Kemkuignou, B and Matočec, N and McTaggart, AR and Mlčoch, P and Mugnai, L and Nakashima, C and Nilsson, RH and Noumeur, SR and Pavlov, IN and Peralta, MP and Phillips, AJL and Pitt, JI and Polizzi, G and Quaedvlieg, W and Rajeshkumar, KC and Restrepo, S and Rhaiem, A and Robert, J and Robert, V and Rodrigues, AM and Salgado-Salazar, C and Samson, RA and Santos, ACS and Shivas, RG and Souza-Motta, CM and Sun, GY and Swart, WJ and Szoke, S and Tan, YP and Taylor, JE and Taylor, PWJ and Tiago, PV and Váczy, KZ and van de Wiele, N and van der Merwe, NA and Verkley, GJM and Vieira, WAS and Vizzini, A and Weir, BS and Wijayawardene, NN and Xia, JW and Yáñez-Morales, MJ and Yurkov, A and Zamora, JC and Zare, R and Zhang, CL and Thines, M},
title = {Fusarium: more than a node or a foot-shaped basal cell.},
journal = {Studies in mycology},
volume = {98},
number = {},
pages = {100116},
pmid = {34466168},
issn = {0166-0616},
abstract = {Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).},
}
@article {pmid34464589,
year = {2021},
author = {Pramual, P and Jomkumsing, P and Wongpakam, K and Wongwian, P},
title = {DNA barcoding of tropical black flies (Diptera: Simuliidae) in Thailand: One decade of progress.},
journal = {Acta tropica},
volume = {224},
number = {},
pages = {106116},
doi = {10.1016/j.actatropica.2021.106116},
pmid = {34464589},
issn = {1873-6254},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Humans ; Phylogeny ; *Simuliidae/genetics ; Thailand ; },
abstract = {Black flies (Diptera: Simuliidae) are important blood sucking insects because they are the vectors of disease agents transmitted to human and other animals. Rapid and correct species identifications are necessary for all aspects of the study of black flies. DNA barcodes based on mitochondrial cytochrome c oxidase I (COI) have been effectively used for the determination of black fly species. However, the success of this method requires a large and reliable COI sequence library. In this study, 171 DNA barcoding sequences from 17 black fly species were added to NCBI GenBank database, six of these species were reported for the first time. Efficacy of DNA barcodes for species identification was examined using 1,286 sequences representing 89 nominal species of black flies in Thailand. A considerable level of success (90%) was achieved but efficiency of COI sequences for species identification was very low in the following species-groups; Simulium asakoae, S. feuerborni, S. multistriatum and S. striatum. Incomplete lineage sorting or inadequate variation of this genetic marker for differentiation of recently diverged species are the more likely explanations, and thus, more variable genetic markers are needed. Other reasons for unsuccessful DNA barcoding are imperfect taxonomy and the misidentification of sources of reference sequences. Because many new black fly species in Thailand were described recently, a reassessment of the COI sequences reported previously is necessary.},
}
@article {pmid34458843,
year = {2021},
author = {Gavins, GC and Gröger, K and Reimann, M and Bartoschek, MD and Bultmann, S and Seitz, O},
title = {Orthogonal coiled coils enable rapid covalent labelling of two distinct membrane proteins with peptide nucleic acid barcodes.},
journal = {RSC chemical biology},
volume = {2},
number = {4},
pages = {1291-1295},
pmid = {34458843},
issn = {2633-0679},
abstract = {Templated chemistry offers the prospect of addressing specificity challenges occurring in bioconjugation reactions. Here, we show two peptide-templated amide-bond forming reactions that enable the concurrent labelling of two different membrane proteins with two different peptide nucleic acid (PNA) barcodes. The reaction system is based on the mutually selective coiled coil interaction between two thioester-linked PNA-peptide conjugates and two cysteine peptides serving as genetically encoded peptide tags. Orthogonal coiled coil templated covalent labelling is highly specific, quantitative and proceeds within a minute. To demonstrate the usefulness, we evaluated receptor internalisation of two membranous receptors EGFR (epidermal growth factor) and ErbB2 (epidermal growth factor receptor 2) by first staining PNA-tagged proteins with fluorophore-DNA conjugates and then erasing signals from non-internalized receptors via toehold-mediated strand displacement.},
}
@article {pmid34458090,
year = {2021},
author = {Gao, Y and Fu, Y and Yan, L and Hu, D and Jiang, B and Zhang, D},
title = {First record of traumatic myiasis obtained from forest musk deer (Moschus berezovskii).},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {16},
number = {},
pages = {70-74},
pmid = {34458090},
issn = {2213-2244},
abstract = {Myiasis is an infestation of maggots on living tissue in humans and animals all over the world. It is known to occur in wild animals, while no information is reported in forest musk deer (Moschus berezovskii). During our research on the conservation of forest musk deer, we found a new record of traumatic myiasis of an injured forest musk deer. The flies are likely Lucilia caesar (Linnaeus, 1758) according to the results of DNA barcoding technology. We report traumatic myiasis of forest musk deer for the first time, which expands the information on parasite and myiasis of forest musk deer and confirms the potential risk of traumatic myiasis of forest musk deer.},
}
@article {pmid34456379,
year = {2020},
author = {Crous, PW and Cowan, DA and Maggs-Kölling, G and Yilmaz, N and Larsson, E and Angelini, C and Brandrud, TE and Dearnaley, JDW and Dima, B and Dovana, F and Fechner, N and García, D and Gené, J and Halling, RE and Houbraken, J and Leonard, P and Luangsa-Ard, JJ and Noisripoom, W and Rea-Ireland, AE and Ševčíková, H and Smyth, CW and Vizzini, A and Adam, JD and Adams, GC and Alexandrova, AV and Alizadeh, A and Duarte, E&#xc1; and Andjic, V and Antonín, V and Arenas, F and Assabgui, R and Ballarà, J and Banwell, A and Berraf-Tebbal, A and Bhatt, VK and Bonito, G and Botha, W and Burgess, TI and Caboň, M and Calvert, J and Carvalhais, LC and Courtecuisse, R and Cullington, P and Davoodian, N and Decock, CA and Dimitrov, R and Di Piazza, S and Drenth, A and Dumez, S and Eichmeier, A and Etayo, J and Fernández, I and Fiard, JP and Fournier, J and Fuentes-Aponte, S and Ghanbary, MAT and Ghorbani, G and Giraldo, A and Glushakova, AM and Gouliamova, DE and Guarro, J and Halleen, F and Hampe, F and Hernández-Restrepo, M and Iturrieta-González, I and Jeppson, M and Kachalkin, AV and Karimi, O and Khalid, AN and Khonsanit, A and Kim, JI and Kim, K and Kiran, M and Krisai-Greilhuber, I and Kučera, V and Kušan, I and Langenhoven, SD and Lebel, T and Lebeuf, R and Liimatainen, K and Linde, C and Lindner, DL and Lombard, L and Mahamedi, AE and Matočec, N and Maxwell, A and May, TW and McTaggart, AR and Meijer, M and Mešić, A and Mileto, AJ and Miller, AN and Molia, A and Mongkolsamrit, S and Cortés, CM and Muñoz-Mohedano, J and Morte, A and Morozova, OV and Mostert, L and Mostowfizadeh-Ghalamfarsa, R and Nagy, LG and Navarro-Ródenas, A and Örstadius, L and Overton, BE and Papp, V and Para, R and Peintner, U and Pham, THG and Pordel, A and Pošta, A and Rodríguez, A and Romberg, M and Sandoval-Denis, M and Seifert, KA and Semwal, KC and Sewall, BJ and Shivas, RG and Slovák, M and Smith, K and Spetik, M and Spies, CFJ and Syme, K and Tasanathai, K and Thorn, RG and Tkalčec, Z and Tomashevskaya, MA and Torres-Garcia, D and Ullah, Z and Visagie, CM and Voitk, A and Winton, LM and Groenewald, JZ},
title = {Fungal Planet description sheets: 1112-1181.},
journal = {Persoonia},
volume = {45},
number = {},
pages = {251-409},
pmid = {34456379},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Austroboletus asper on soil, Cylindromonium alloxyli on leaves of Alloxylon pinnatum, Davidhawksworthia quintiniae on leaves of Quintinia sieberi, Exophiala prostantherae on leaves of Prostanthera sp., Lactifluus lactiglaucus on soil, Linteromyces quintiniae (incl. Linteromyces gen. nov.) on leaves of Quintinia sieberi, Lophotrichus medusoides from stem tissue of Citrus garrawayi, Mycena pulchra on soil, Neocalonectria tristaniopsidis (incl. Neocalonectria gen. nov.) and Xyladictyochaeta tristaniopsidis on leaves of Tristaniopsis collina, Parasarocladium tasmanniae on leaves of Tasmannia insipida, Phytophthora aquae-cooljarloo from pond water, Serendipita whamiae as endophyte from roots of Eriochilus cucullatus, Veloboletus limbatus (incl. Veloboletus gen. nov.) on soil. Austria, Cortinarius glaucoelotus on soil. Bulgaria, Suhomyces rilaensis from the gut of Bolitophagus interruptus found on a Polyporus sp. Canada, Cantharellus betularum among leaf litter of Betula, Penicillium saanichii from house dust. Chile, Circinella lampensis on soil, Exophiala embothrii from rhizosphere of Embothrium coccineum. China, Colletotrichum cycadis on leaves of Cycas revoluta. Croatia, Phialocephala melitaea on fallen branch of Pinus halepensis. Czech Republic, Geoglossum jirinae on soil, Pyrenochaetopsis rajhradensis from dead wood of Buxus sempervirens. Dominican Republic, Amanita domingensis on litter of deciduous wood, Melanoleuca dominicana on forest litter. France, Crinipellis nigrolamellata (Martinique) on leaves of Pisonia fragrans, Talaromyces pulveris from bore dust of Xestobium rufovillosum infesting floorboards. French Guiana, Hypoxylon hepaticolor on dead corticated branch. Great Britain, Inocybe ionolepis on soil. India, Cortinarius indopurpurascens among leaf litter of Quercus leucotrichophora. Iran, Pseudopyricularia javanii on infected leaves of Cyperus sp., Xenomonodictys iranica (incl. Xenomonodictys gen. nov.) on wood of Fagus orientalis. Italy, Penicillium vallebormidaense from compost. Namibia, Alternaria mirabibensis on plant litter, Curvularia moringae and Moringomyces phantasmae (incl. Moringomyces gen. nov.) on leaves and flowers of Moringa ovalifolia, Gobabebomyces vachelliae (incl. Gobabebomyces gen. nov.) on leaves of Vachellia erioloba, Preussia procaviae on dung of Procavia capensis. Pakistan, Russula shawarensis from soil on forest floor. Russia, Cyberlindnera dauci from Daucus carota. South Africa, Acremonium behniae on leaves of Behnia reticulata, Dothiora aloidendri and Hantamomyces aloidendri (incl. Hantamomyces gen. nov.) on leaves of Aloidendron dichotomum, Endoconidioma euphorbiae on leaves of Euphorbia mauritanica, Eucasphaeria proteae on leaves of Protea neriifolia, Exophiala mali from inner fruit tissue of Malus sp., Graminopassalora geissorhizae on leaves of Geissorhiza splendidissima, Neocamarosporium leipoldtiae on leaves of Leipoldtia schultzii, Neocladosporium osteospermi on leaf spots of Osteospermum moniliferum, Neometulocladosporiella seifertii on leaves of Combretum caffrum, Paramyrothecium pituitipietianum on stems of Grielum humifusum, Phytopythium paucipapillatum from roots of Vitis sp., Stemphylium carpobroti and Verrucocladosporium carpobroti on leaves of Carpobrotus quadrifolius, Suttonomyces cephalophylli on leaves of Cephalophyllum pilansii. Sweden, Coprinopsis rubra on cow dung, Elaphomyces nemoreus from deciduous woodlands. Spain, Polyscytalum pini-canariensis on needles of Pinus canariensis, Pseudosubramaniomyces septatus from stream sediment, Tuber lusitanicum on soil under Quercus suber. Thailand, Tolypocladium flavonigrum on Elaphomyces sp. USA, Chaetothyrina spondiadis on fruits of Spondias mombin, Gymnascella minnisii from bat guano, Juncomyces patwiniorum on culms of Juncus effusus, Moelleriella puertoricoensis on scale insect, Neodothiora populina (incl. Neodothiora gen. nov.) on stem cankers of Populus tremuloides, Pseudogymnoascus palmeri from cave sediment. Vietnam, Cyphellophora vietnamensis on leaf litter, Tylopilus subotsuensis on soil in montane evergreen broadleaf forest. Morphological and culture characteristics are supported by DNA barcodes.},
}
@article {pmid34455348,
year = {2021},
author = {Kim, HJ and Park, JS and Lee, TK and Kang, D and Kang, JH and Shin, K and Jung, SW},
title = {Dynamics of marine bacterial biofouling communities after initial Alteromonas genovensis biofilm attachment to anti-fouling paint substrates.},
journal = {Marine pollution bulletin},
volume = {172},
number = {},
pages = {112895},
doi = {10.1016/j.marpolbul.2021.112895},
pmid = {34455348},
issn = {1879-3363},
mesh = {Alteromonas ; Bacteria ; Biofilms ; *Biofouling/prevention &amp; control ; Paint ; },
abstract = {To determine how bacterial communities succeed after the initial attachment of the bacterial biofilm adhesion using 16S rDNA meta-barcoding in plates coated with copper-based anti-fouling (AF) and non-AF (control) coatings as well as ambient seawater, coated plates were submerged in a marine environment in situ. Alteromonas genovensis (Gammaproteobacteria) in AF coating and Pacificibacter sp. (Alphaproteobacteria) in the control plate were initially abundant. In the AF coating, the abundance of A. genovensis decreased rapidly, whereas that of genus Phaeobacter (Alphaproteobacteria), Serratia (Gammaproteobacteria) and Cupriavidus (Betaproteobacteria) increased. Bacterial community in the control plate had a strong connection to pathogenic Vibrio spp. associated with the growth of invertebrates. Therefore, in the in situ AF coating experiment, A. genovensis accumulation was initially and intensively increased, and the bacteria responded to chemical antagonism, induced the proliferation of specific biofilm bacteria and influenced the interactions and recruitment of additional bacterial communities.},
}
@article {pmid34450040,
year = {2021},
author = {Dunn, A and Cai, Y and Iwasawa, K and Kimura, M and Takebe, T},
title = {POLYseq: A poly(β-amino ester)-based vector for multifunctional cellular barcoding.},
journal = {Stem cell reports},
volume = {16},
number = {9},
pages = {2149-2158},
pmid = {34450040},
issn = {2213-6711},
support = {DP2 DK128799/DK/NIDDK NIH HHS/United States ; P30 DK078392/DK/NIDDK NIH HHS/United States ; UH3 DK119982/DK/NIDDK NIH HHS/United States ; },
mesh = {Cell Culture Techniques ; Cell Differentiation/genetics ; DNA Barcoding, Taxonomic/*methods ; Flow Cytometry ; Fluorescent Dyes ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Induced Pluripotent Stem Cells/cytology/metabolism ; Organoids ; Polymers/*chemistry ; Single-Cell Analysis/methods ; Staining and Labeling/*methods ; },
abstract = {Despite evolving biological application of next-generation sequencing (NGS) at single-cell level, current techniques in NGS library preparation restrict multiplexing, necessitating the costly preparation of distinct libraries for each sample. Here, we report the development of a novel poly(β-amino) ester labeling system synthesized with inexpensive, common reagents, termed POLYseq, capable of efficiently delivering fluorescent molecules or sample-distinguishing DNA barcodes through non-covalent binding enabling rapid creation of custom sample pools. Chemical formulation was found to determine cellular labeling propensity. Live image-based tracking of fluorescent conjugated POLYseq vectors demonstrated lysosomal compartmentalization. Barcode labeling was uniformly detected across 90% of cells by single-cell RNA sequencing, allowing for the successful identification of human and mouse cultured cell lines from a single pool. These findings highlight the multifunctional applications of POLYseq in live cell imaging and NGS in a scalable and cost-effective manner.},
}
@article {pmid34448497,
year = {2021},
author = {Pestana, EMDS and Nunes, JMC and Cassano, V and Lyra, GM},
title = {Taxonomic revision of the Peyssonneliales (Rhodophyta): Circumscribing the authentic Peyssonnelia clade and proposing four new genera and seven new species.},
journal = {Journal of phycology},
volume = {57},
number = {6},
pages = {1749-1767},
doi = {10.1111/jpy.13207},
pmid = {34448497},
issn = {1529-8817},
mesh = {Biodiversity ; Biological Evolution ; Brazil ; Phylogeny ; *Rhodophyta/genetics ; },
abstract = {The Peyssonneliaceae represents the only family in the order Peyssonneliales, a clade of red encrusting algae distributed worldwide, including 136 species in eleven currently accepted genera. Delineation of genera in the Peyssonneliaceae has mostly been based on vegetative characteristics. Previous molecular phylogenies have shown that some traditionally circumscribed genera are not monophyletic and relationships among them are uncertain. We contribute to the knowledge of the evolutionary history of this clade, presenting a robust rbcL phylogeny that provides new insights on the origin and diversification of the Peyssonneliales. Based on a broad dataset and morphological analyses, we propose a revised taxonomic scheme for the Peyssonneliales resolved as monophyletic with well-supported main lineages. Our results show that Peyssonnelia is polyphyletic, and, therefore, we propose three new genera, Agissea, Olokunia, and Rhodowynnea to accommodate species currently assigned to Peyssonnelia, but distantly related to the clade with the type species of the genus. Additionally, barcoding techniques and analyzed criteria for specific delimitation supported the establishment of one new genus, Brasilophycus, and seven new species, from northeastern Brazil: Agissea amadoi, A. densissima, A. taberniforma, A. villatlantica, A. yemonjasagbae, Brasilophycus similis, and B. roseomarginatus. Our integrative taxonomic approach reveals underestimated diversity of Brazilian Peyssonneliales. Investment in broader sampling along the Brazilian coast and other tropical areas may reveal that its marine biodiversity can be expanded, enlightening our knowledge about this ecologically important group of red algae.},
}
@article {pmid34447921,
year = {2021},
author = {Meredith, C and Hoffman, J and Trebitz, A and Pilgrim, E and Okum, S and Martinson, J and Cameron, ES},
title = {Evaluating the performance of DNA metabarcoding for assessment of zooplankton communities in Western Lake Superior using multiple markers.},
journal = {Metabarcoding and metagenomics},
volume = {50},
number = {},
pages = {83-97},
pmid = {34447921},
issn = {2534-9708},
support = {EPA999999/ImEPA/Intramural EPA/United States ; },
abstract = {For DNA metabarcoding to attain its potential as a community assessment tool, we need to better understand its performance versus traditional morphological identification and work to address any remaining performance gaps in incorporating DNA metabarcoding into community assessments. Using fragments of the 18S nuclear and 16S mitochondrial rRNA genes and two fragments of the mitochondrial COI marker, we examined the use of DNA metabarcoding and traditional morphological identification for understanding the diversity and composition of crustacean zooplankton at 42 sites across western Lake Superior. We identified 51 zooplankton taxa (genus or species, depending on the finest resolution of the taxon across all identification methods), of which 17 were identified using only morphological traits, 13 using only DNA and 21 using both methods. The taxa found using only DNA metabarcoding included four species and one genus-level identification not previously known to occur in Lake Superior, the presence of which still needs to be confirmed. A substantial portion of taxa that were identified to genus or species by morphological identification, but not identified using DNA metabarcoding, had zero ("no record") or ≤ 2 ("underrepresented records") reference barcodes in the BOLD or NCBI databases (63% for COI, 80% for 16S, 74% for 18S). The two COI marker fragments identified the most genus- and species-level taxa, whereas 18S was the only marker whose family-level percent sequence abundance patterns showed high correlation to composition patterns from morphological identification, based on a NMDS analysis of Bray-Curtis similarities. Multiple replicates were collected at a subset of sites and an occupancy analysis was performed, which indicated that rare taxa were more likely to be detected using DNA metabarcoding than traditional morphology. Our results support that DNA metabarcoding can augment morphological identification for estimating zooplankton diversity and composition of zooplankton over space and time, but may require use of multiple markers. Further addition of taxa to reference DNA databases will improve our ability to use DNA metabarcoding to identify zooplankton and other invertebrates in aquatic surveys.},
}
@article {pmid34442789,
year = {2021},
author = {Cheutin, MC and Villéger, S and Hicks, CC and Robinson, JPW and Graham, NAJ and Marconnet, C and Restrepo, CXO and Bettarel, Y and Bouvier, T and Auguet, JC},
title = {Microbial Shift in the Enteric Bacteriome of Coral Reef Fish Following Climate-Driven Regime Shifts.},
journal = {Microorganisms},
volume = {9},
number = {8},
pages = {},
pmid = {34442789},
issn = {2076-2607},
abstract = {Replacement of coral by macroalgae in post-disturbance reefs, also called a "coral-macroalgal regime shift", is increasing in response to climate-driven ocean warming. Such ecosystem change is known to impact planktonic and benthic reef microbial communities but few studies have examined the effect on animal microbiota. In order to understand the consequence of coral-macroalgal shifts on the coral reef fish enteric bacteriome, we used a metabarcoding approach to examine the gut bacteriomes of 99 individual fish representing 36 species collected on reefs of the Inner Seychelles islands that, following bleaching, had either recovered to coral domination, or shifted to macroalgae. While the coral-macroalgal shift did not influence the diversity, richness or variability of fish gut bacteriomes, we observed a significant effect on the composition (R2 = 0.02; p = 0.001), especially in herbivorous fishes (R2 = 0.07; p = 0.001). This change is accompanied by a significant increase in the proportion of fermentative bacteria (Rikenella, Akkermensia, Desulfovibrio, Brachyspira) and associated metabolisms (carbohydrates metabolism, DNA replication, and nitrogen metabolism) in relation to the strong turnover of Scarinae and Siganidae fishes. Predominance of fermentative metabolisms in fish found on macroalgal dominated reefs indicates that regime shifts not only affect the taxonomic composition of fish bacteriomes, but also have the potential to affect ecosystem functioning through microbial functions.},
}
@article {pmid34442321,
year = {2021},
author = {Rector, BG and Gagné, RJ and Perilla López, JM and Tonkel, KC and Bon, MC and Guermache, F and Cristofaro, M},
title = {Taxonomic Description of Stenodiplosis tectori n. sp. (Diptera: Cecidomyiidae), a Seed Parasite of Cheatgrass, Anisantha tectorum, Based on Morphological and Mitochondrial DNA Data.},
journal = {Insects},
volume = {12},
number = {8},
pages = {},
pmid = {34442321},
issn = {2075-4450},
support = {Interagency Agreement L16PG00228//U.S. Bureau of Land Management/ ; },
abstract = {Cheatgrass is an annual grass species from Eurasia that has become invasive in much of western North America. It has been implicated in recent increases in the frequency, size, and intensity of wildfires, contributing to severe economic, environmental, and social destruction. In order to reduce this damage, the USDA-ARS established a classical biological control program against cheatgrass. In 2018 and 2019, adult gall midges were collected emerging from cheatgrass seed heads collected at several sites in Bulgaria and Greece; this is the first gall midge ever recorded from cheatgrass. Morphological comparisons with related midge species recorded from other plant hosts revealed that this midge from cheatgrass is a new species, described here as Stenodiplosis tectori n. sp. This status was supported by sequence comparisons of a barcode region of the gene encoding the mitochondrial cytochrome c subunit I (CO1) protein in Stenodiplosis tectori n. sp. and three congeners. The present study is the first to report MT-CO1 data in the genus Stenodiplosis. The ingroup Stenodiplosis tectori n. sp. collected in the Balkans grouped in one phylogenetic supported clade, with an average K2P-distance from its closest related congener, S. sorghicola, of 7.73% (SD = 1.10). The findings indicated relatively high year-to-year within-population diversity. Implications for this gall midge's utility as a biological control agent of cheatgrass are discussed.},
}
@article {pmid34442227,
year = {2021},
author = {Vendetti, JE and Sandig, K and Sahakyan, A and Granados, A},
title = {Multiple Introductions of the Pestiferous Land Snail Theba pisana (Müller, 1774) (Gastropoda: Helicidae) in Southern California.},
journal = {Insects},
volume = {12},
number = {8},
pages = {},
pmid = {34442227},
issn = {2075-4450},
abstract = {The terrestrial land snail Theba pisana is circum-Mediterranean in native range and widely introduced and pestiferous in regions around the world. In California, USA, T. pisana has been recorded intermittently since 1914, but its source population(s) are unknown, and no morphological or molecular analyses within or between California populations have been published. Therefore, we compared molecular data (CO1, 16S, ITS2) and internal morphology (jaw, radula, reproductive system) in T. pisana collected from Los Angeles and San Diego counties in 2019-2020. DNA barcode (CO1 mtDNA) analysis revealed that T. pisana from Los Angeles County was most similar to T. pisana from the Mediterranean island of Malta, and northern San Diego County-collected specimens were most similar to T. pisana from Morocco. Morphology of the jaw and mucous glands also differed between Los Angeles and San Diego populations, but it is unclear if traits are lineage-specific or artifacts of ontogeny. Several pathways of introduction into Southern California are possible for this species, but evidence for intentional vs. accidental introduction of present populations is lacking. Subsequent investigation(s) could use the data generated herein to assess the provenance of T. pisana elsewhere in California and/or worldwide and inform analyses of reproductive biology and systematics in this widespread species.},
}
@article {pmid34440312,
year = {2021},
author = {Abeynayake, SW and Fiorito, S and Dinsdale, A and Whattam, M and Crowe, B and Sparks, K and Campbell, PR and Gambley, C},
title = {A Rapid and Cost-Effective Identification of Invertebrate Pests at the Borders Using MinION Sequencing of DNA Barcodes.},
journal = {Genes},
volume = {12},
number = {8},
pages = {},
pmid = {34440312},
issn = {2073-4425},
mesh = {Animals ; *Cost-Benefit Analysis ; DNA Barcoding, Taxonomic/*methods ; Insecta/*classification/genetics ; Invertebrates/*classification/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {The rapid and accurate identification of invertebrate pests detected at the border is a challenging task. Current diagnostic methods used at the borders are mainly based on time consuming visual and microscopic examinations. Here, we demonstrate a rapid in-house workflow for DNA extraction, PCR amplification of the barcode region of the mitochondrial cytochrome oxidase subunit I (COI) gene and Oxford Nanopore Technologies (ONT) MinION sequencing of amplified products multiplexed after barcoding on ONT Flongle flow cells. A side-by-side comparison was conducted of DNA barcode sequencing-based identification and morphological identification of both large (>0.5 mm in length) and small (<0.5 mm in length) invertebrate specimens intercepted at the Australian border. DNA barcode sequencing results supported the morphological identification in most cases and enabled immature stages of invertebrates and their eggs to be identified more confidently. Results also showed that sequencing the COI barcode region using the ONT rapid sequencing principle is a cost-effective and field-adaptable approach for the rapid and accurate identification of invertebrate pests. Overall, the results suggest that MinION sequencing of DNA barcodes offers a complementary tool to the existing morphological diagnostic approaches and provides rapid, accurate, reliable and defendable evidence for identifying invertebrate pests at the border.},
}
@article {pmid34439977,
year = {2021},
author = {Zhang, ZK and Wang, XC and Zhuang, WY and Cheng, XH and Zhao, P},
title = {New Species of Talaromyces (Fungi) Isolated from Soil in Southwestern China.},
journal = {Biology},
volume = {10},
number = {8},
pages = {},
pmid = {34439977},
issn = {2079-7737},
support = {31750001//National Natural Science Foundation of China/ ; QYZDY-SSW-SMC029//Key Research Program of Frontier Science, Chinese Academy of Sciences/ ; },
abstract = {Southwestern China belongs among the global biodiversity hotspots and the Daba Mountains are recognized as one of the priority conservation areas. During the exploration of fungal biodiversity from soil samples collected from Mount Daba, two species of Talaromyces were discovered as new to science based on phylogenetic analyses and morphological comparisons. Talaromyces chongqingensis sp. nov. is a sister taxon of T. minioluteus and T. minnesotensis in the section Trachyspermi; and T. wushanicus sp. nov., affiliated to the section Talaromyces, is closely related to T. cnidii and T. siamensis. The new species differ from their sisters in DNA sequences, growth rates, and morphological characteristics. Descriptions and illustrations of them are provided in detail.},
}
@article {pmid34439341,
year = {2021},
author = {Dujardin, P and Baginska, AK and Urban, S and Grüner, BM},
title = {Unraveling Tumor Heterogeneity by Using DNA Barcoding Technologies to Develop Personalized Treatment Strategies in Advanced-Stage PDAC.},
journal = {Cancers},
volume = {13},
number = {16},
pages = {},
pmid = {34439341},
issn = {2072-6694},
support = {DFG, GR4575/1-1//Emmy Noether Award from the German Research Foundation/ ; n.a.//Cusanuswerk e.V./ ; },
abstract = {Tumor heterogeneity is a hallmark of many solid tumors, including pancreatic ductal adenocarcinoma (PDAC), and an inherent consequence of the clonal evolution of cancers. As such, it is considered the underlying concept of many characteristics of the disease, including the ability to metastasize, adapt to different microenvironments, and to develop therapy resistance. Undoubtedly, the high mortality of PDAC can be attributed to a high extent to these properties. Despite its apparent importance, studying tumor heterogeneity has been a challenging task, mainly due to its complexity and lack of appropriate methods. However, in recent years molecular DNA barcoding has emerged as a sophisticated tool that allows mapping of individual cells or subpopulations in a cell pool to study heterogeneity and thus devise new personalized treatment strategies. In this review, we provide an overview of genetic and non-genetic inter- and intra-tumor heterogeneity and its impact on (personalized) treatment strategies in PDAC and address how DNA barcoding technologies work and can be applied to study this clinically highly relevant question.},
}
@article {pmid34435116,
year = {2021},
author = {Shan, Y and Pei, X and Yong, S and Li, J and Qin, Q and Zeng, S and Yu, J},
title = {Analysis of the complete chloroplast genomes of Scutellaria tsinyunensis and Scutellaria tuberifera (Lamiaceae).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {6},
number = {9},
pages = {2672-2680},
pmid = {34435116},
issn = {2380-2359},
abstract = {Scutellaria Linn. is a perennial herb with about 300 species. This genus has high medicinal value and many are used in Traditional Chinese Medicine (TCM). In this study, we sequenced and assembled the complete chloroplast genomes of Scutellaria tsinyunensis and S. tuberifera. Subsequently, we conducted a comprehensive comparative genomics analysis with 12 other published Scutellaria species. These genomes all had a conserved quartile structure, and the gene contents, gene sequences and GC contents are highly similar. The study on the genetic characteristics and nucleotide substitution rate of different genes found that the protein-coding genes of chloroplasts have differed greatly. Most genes are under purifying selection, but the rps12 gene may have undergone positive selection. Besides, we identified three hypervariable regions as potential markers for Scutellaria taxa, which could play an important role in species identification of Scutellaria. Phylogenetic analysis showed that the 14 Scutellaria taxa were divided into two major clades. Moreover, the variation of IR regions is closely related to the evolutionary history as was reconstructed based on SNPs. In conclusion, we provided two high-quality chloroplast reference genomes of Scutellaria, this reliable information and genomic resources are valuable for developing of efficient DNA barcodes as reconstruction of chloroplast evolutionary history of the genus.},
}
@article {pmid34434823,
year = {2021},
author = {Oliver, AE and Newbold, LK and Gweon, HS and Read, DS and Woodcock, BA and Pywell, RF},
title = {Integration of DNA extraction, metabarcoding and an informatics pipeline to underpin a national citizen science honey monitoring scheme.},
journal = {MethodsX},
volume = {8},
number = {},
pages = {101303},
pmid = {34434823},
issn = {2215-0161},
abstract = {Worldwide honeybees (Apis mellifera L.) are one of the most widely kept domesticated animals, supporting domestic and commercial livelihoods through the production of honey and wax, as well as in the delivery of pollination services to crops. Quantifying which plant species are foraged upon by honeybees provides insights into their nutritional status as well as patterns of landscape scale habitat utilization. Here we outline a rapid and reproducible methodology for identifying environmental DNA (eDNA) originating principally from pollen grains suspended within honey. The process is based on a DNA extraction incorporating vacuum filtration prior to universal eukaryotic internal transcribed spacer 2 region (ITS2) amplicon generation, sequencing and identification. To provide a pre-cursor to sequence phylotyping, we outline systems for error-corrected processing amplicon sequence variant abundance tables that removes chimeras. This methodology underpins the new UK National Honey Monitoring Scheme.•We compare the efficacy and speed of centrifugation and filtration systems for removing pollen from honey samples as a precursor to plant DNA barcoding.•We introduce the 'HONEYPI' informatics pipeline, an open access resource implemented in python 2.7, to ensure long-term reproducibility during the process of amplicon sequence variant classification.},
}
@article {pmid34434778,
year = {2021},
author = {Marín, DV and Castillo, DK and López-Lavalle, LAB and Chalarca, JR and Pérez, CR},
title = {An optimized high-quality DNA isolation protocol for spodoptera frugiperda J. E. smith (Lepidoptera: Noctuidae).},
journal = {MethodsX},
volume = {8},
number = {},
pages = {101255},
pmid = {34434778},
issn = {2215-0161},
abstract = {An optimized high-quality DNA isolation protocol was developed using body segment tissue from the Fall Armyworm (Spodoptera frugiperda), that will allow documenting genetic variability based on biotypes, facilitating studies on the appearance, distribution and population dynamics of the fall armyworm at the molecular level. The resulting protocol is an easy-to-use, timesaving method that can rapidly achieve high quality, high-yielding total genomic DNA, using chemicals and everyday consumables available in a molecular laboratory. This new method of DNA extraction avoids the contamination of polysaccharides, salts, phenols, proteins and other cellular by-products that can interfere with subsequent reactions. DNA purity estimates reveal A260: A280 ratios greater than 1.9, which were evidenced by quality test on agarose gel, observing complete integrity and high purity of the resulting samples, and yielded 30-99 µg/g of total DNA. Therefore, the quality of the DNA produced from this extraction is suitable for subsequent molecular applications: (i) next generation whole genome sequencing, (ii) conventional polymerase chain reaction for genotyping, (iii) barcodes and (iv) gene cloning. In addition, to become an anticipating diagnostic tool for invasive lepidopteran larval stages:•The resulting protocol is an easy-to-use time-saving method.•This new extraction method prevents contamination from polysaccharides, salts, phenols, proteins, and other cellular sub-products.•DNA purity estimations reveal A260:A280 ratios above 1.9.},
}
@article {pmid34433967,
year = {2021},
author = {Park, S and Mali, NM and Kim, R and Choi, JW and Lee, J and Lim, J and Park, JM and Park, JW and Kim, D and Kim, T and Yi, K and Choi, JH and Kwon, SG and Hong, JH and Youk, J and An, Y and Kim, SY and Oh, SA and Kwon, Y and Hong, D and Kim, M and Kim, DS and Park, JY and Oh, JW and Ju, YS},
title = {Clonal dynamics in early human embryogenesis inferred from somatic mutation.},
journal = {Nature},
volume = {597},
number = {7876},
pages = {393-397},
pmid = {34433967},
issn = {1476-4687},
mesh = {Cell Lineage/*genetics ; Clone Cells/*metabolism ; DNA, Mitochondrial/genetics ; Embryo, Mammalian/*cytology/embryology/*metabolism ; Embryonic Development/*genetics ; Female ; Humans ; Male ; *Mutation ; Mutation Rate ; },
abstract = {Cellular dynamics and fate decision in early human embryogenesis remain largely unknown owing to the challenges of performing studies in human embryos[1]. Here, we explored whole-genomes of 334 single-cell colonies and targeted deep sequences of 379 bulk tissues obtained from various anatomical locations of seven recently deceased adult human donors. Using somatic mutations as an intrinsic barcode, we reconstructed early cellular phylogenies that demonstrate (1) an endogenous mutational rate that is higher in the first cell division but decreases to approximately one per cell per cell division later in life; (2) universal unequal contribution of early cells to embryo proper, resulting from early cellular bottlenecks that stochastically set aside epiblast cells within the embryo; (3) examples of varying degrees of early clonal imbalances between tissues on the left and right sides of the body, different germ layers and specific anatomical parts and organs; (4) emergence of a few ancestral cells that will substantially contribute to adult cell pools in blood and liver; and (5) presence of mitochondrial DNA heteroplasmy in the fertilized egg. Our approach also provides insights into the age-related mutational processes and loss of sex chromosomes in normal somatic cells. In sum, this study provides a foundation for future studies to complete cellular phylogenies in human embryogenesis.},
}
@article {pmid34430929,
year = {2021},
author = {Yan, F and Zhao, Z and Simon, LM},
title = {EmptyNN: A neural network based on positive and unlabeled learning to remove cell-free droplets and recover lost cells in scRNA-seq data.},
journal = {Patterns (New York, N.Y.)},
volume = {2},
number = {8},
pages = {100311},
pmid = {34430929},
issn = {2666-3899},
support = {R01 DE030122/DE/NIDCR NIH HHS/United States ; R01 LM012806/LM/NLM NIH HHS/United States ; },
abstract = {Droplet-based single-cell RNA sequencing (scRNA-seq) has significantly increased the number of cells profiled per experiment and revolutionized the study of individual transcriptomes. However, to maximize the biological signal, robust computational methods are needed to distinguish cell-free from cell-containing droplets. Here, we introduce a novel cell-calling algorithm called EmptyNN, which trains a neural network based on positive-unlabeled learning for improved filtering of barcodes. For benchmarking purposes, we leveraged cell hashing and genetic variation to provide ground truth. EmptyNN accurately removed cell-free droplets while recovering lost cell clusters, and achieved an area under the receiver operating characteristics of 94.73% and 96.30%, respectively. Comparisons to current state-of-the-art cell-calling algorithms demonstrated the superior performance of EmptyNN. EmptyNN was further applied to a single-nucleus RNA sequencing (snRNA-seq) dataset and showed good performance. Therefore, EmptyNN represents a powerful tool to enhance both scRNA-seq and snRNA-seq quality control analyses.},
}
@article {pmid34430912,
year = {2021},
author = {Marand, AP and Zhang, X and Nelson, J and Braga Dos Reis, PA and Schmitz, RJ},
title = {Profiling single-cell chromatin accessibility in plants.},
journal = {STAR protocols},
volume = {2},
number = {3},
pages = {100737},
pmid = {34430912},
issn = {2666-1667},
mesh = {Cell Culture Techniques ; *Chromatin/chemistry/genetics ; Chromatin Immunoprecipitation Sequencing/*methods ; Plant Cells/*chemistry ; Seedlings/cytology ; Single-Cell Analysis/*methods ; Zea mays/cytology ; },
abstract = {Coupling assay for transposase-accessible chromatin sequencing (ATAC-seq) with microfluidic separation and cellular barcoding has emerged as a powerful approach to investigate chromatin accessibility of individual cells. Here, we define a protocol for constructing single-cell ATAC-seq libraries from maize seedling nuclei and the preliminary computational steps for assessing data quality. This protocol can be readily adapted to other plant species or tissues with minor changes to reveal chromatin accessibility variation among individual cells. For complete details on the use and execution of this protocol, please refer to Marand et al. (2021).},
}
@article {pmid34430077,
year = {2021},
author = {Prieto, C and Faynel, C and Robbins, R and Hausmann, A},
title = {Congruence between morphology-based species and Barcode Index Numbers (BINs) in Neotropical Eumaeini (Lycaenidae).},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e11843},
pmid = {34430077},
issn = {2167-8359},
abstract = {BACKGROUND: With about 1,000 species in the Neotropics, the Eumaeini (Theclinae) are one of the most diverse butterfly tribes. Correct morphology-based identifications are challenging in many genera due to relatively little interspecific differences in wing patterns. Geographic infraspecific variation is sometimes more substantial than variation between species. In this paper we present a large DNA barcode dataset of South American Lycaenidae. We analyze how well DNA barcode BINs match morphologically delimited species.<br><br>METHODS: We compare morphology-based species identifications with the clustering of molecular operational taxonomic units (MOTUs) delimitated by the RESL algorithm in BOLD, which assigns Barcode Index Numbers (BINs). We examine intra- and interspecific divergences for genera represented by at least four morphospecies. We discuss the existence of local barcode gaps in a genus by genus analysis. We also note differences in the percentage of species with barcode gaps in groups of lowland and high mountain genera.<br><br>RESULTS: We identified 2,213 specimens and obtained 1,839 sequences of 512 species in 90 genera. Overall, the mean intraspecific divergence value of CO1 sequences was 1.20%, while the mean interspecific divergence between nearest congeneric neighbors was 4.89%, demonstrating the presence of a barcode gap. However, the gap seemed to disappear from the entire set when comparing the maximum intraspecific distance (8.40%) with the minimum interspecific distance (0.40%). Clear barcode gaps are present in many genera but absent in others. From the set of specimens that yielded COI fragment lengths of at least 650 bp, 75% of the a priori morphology-based identifications were unambiguously assigned to a single Barcode Index Number (BIN). However, after a taxonomic a posteriori review, the percentage of matched identifications rose to 85%. BIN splitting was observed for 17% of the species and BIN sharing for 9%. We found that genera that contain primarily lowland species show higher percentages of local barcode gaps and congruence between BINs and morphology than genera that contain exclusively high montane species. The divergence values to the nearest neighbors were significantly lower in high Andean species while the intra-specific divergence values were significantly lower in the lowland species. These results raise questions regarding the causes of observed low inter and high intraspecific genetic variation. We discuss incomplete lineage sorting and hybridization as most likely causes of this phenomenon, as the montane species concerned are relatively young and hybridization is probable. The release of our data set represents an essential baseline for a reference library for biological assessment studies of butterflies in mega diverse countries using modern high-throughput technologies an highlights the necessity of taxonomic revisions for various genera combining both molecular and morphological data.},
}
@article {pmid34429936,
year = {2021},
author = {Chen, W and Zhu, S and Yang, J and Li, X and Li, Y and Li, J},
title = {DNA barcoding reveals the temporal community composition of drifting fish eggs in the lower Hongshui River, China.},
journal = {Ecology and evolution},
volume = {11},
number = {16},
pages = {11507-11514},
pmid = {34429936},
issn = {2045-7758},
abstract = {Determining the temporal community composition of fish eggs in particular regions and understanding the reproductive times of regional fish taxa are key aspects of the management and regulation of regional fish stocks. However, it is extremely difficult to accurately identify fish eggs due to the absence of diagnostic morphological characters. We sampled fish eggs in the lower Hongshuihe River (an upper mainstem of the Pearl River) between May and September 2020. We then used DNA barcoding to determine the species composition of the egg pool and to predict the spawning periods of the identified species. A total of 641 eggs and 17 larvae were chosen for molecular identification; 397 eggs and 17 larvae yielded high-quality barcoding sequences. The high failure rate (~38%) was most likely due to long-term storage in low concentrations of ethanol prior to molecular analysis. We successfully classified 392 eggs into 10 species and 13 larvae into four species using public databases. Most of the species identified in the egg pool were small and/or benthic, and migratory species were rare. This may partially reflect the adverse effects of hydropower cascade development in this river section. We also found that spawning periods tended to be species-specific. Our study provides a reference for the conservation and management of regional fishery stocks.},
}
@article {pmid34429905,
year = {2021},
author = {Leavitt, SD and Hollinger, J and Summerhays, S and Munger, I and Allen, J and Smith, B},
title = {Alpine lichen diversity in an isolated sky island in the Colorado Plateau, USA-Insight from an integrative biodiversity inventory.},
journal = {Ecology and evolution},
volume = {11},
number = {16},
pages = {11090-11101},
pmid = {34429905},
issn = {2045-7758},
abstract = {Lichens are major components of high altitude/latitude ecosystems. However, accurately characterizing their biodiversity is challenging because these regions and habitats are often underexplored, there are numerous poorly known taxonomic groups, and morphological variation in extreme environments can yield conflicting interpretations. Using an iterative taxonomic approach based on over 800 specimens and incorporating both traditional morphology-based identifications and information from the standard fungal DNA barcoding marker, we compiled a voucher-based inventory of biodiversity of lichen-forming fungi in a geographically limited and vulnerable alpine community in an isolated sky island in the Colorado Plateau, USA-the La Sal Mountains. We used the newly proposed Assemble Species by Automatic Partitioning (ASAP) approach to empirically delimit candidate species-level lineages from family-level multiple sequence alignments. Specimens comprising DNA-based candidate species were evaluated using traditional taxonomically diagnostic phenotypic characters to identify specimens to integrative species hypotheses and link these, where possible, to currently described species. Despite the limited alpine habitat (ca. 3,250 ha), we document the most diverse alpine lichen community known to date from the southern Rocky Mountains, with up to 240 candidate species/species-level lineages of lichen-forming fungi. 139 species were inferred using integrative taxonomy, plus an additional 52 candidate species within 29 different putative species complexes. Over 68% of sequences could not be assigned to species-level rank with statistical confidence, corroborating the limited utility of current sequence repositories for species-level DNA barcoding of lichen-forming fungi. By integrating vouchered specimens, DNA sequence data, and photographic documentation, we provide an important baseline of lichen-forming fungal diversity for the limited alpine habitat in the Colorado Plateau. These data provide an important resource for subsequent research in the ecology and evolution of lichens alpine habitats, including DNA barcodes for most putative species/species-level lineages occurring in the La Sal Mountains, and vouchered collections representing any potentially undescribed species that can be used for future taxonomic studies.},
}
@article {pmid34426703,
year = {2022},
author = {Arrastia, MV and Jachowicz, JW and Ollikainen, N and Curtis, MS and Lai, C and Quinodoz, SA and Selck, DA and Ismagilov, RF and Guttman, M},
title = {Single-cell measurement of higher-order 3D genome organization with scSPRITE.},
journal = {Nature biotechnology},
volume = {40},
number = {1},
pages = {64-73},
pmid = {34426703},
issn = {1546-1696},
support = {U01 DA040612/DA/NIDA NIH HHS/United States ; U01 HG007910/HG/NHGRI NIH HHS/United States ; U01 HL130007/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; *Cell Nucleus/genetics ; Chromatin ; DNA/genetics ; *Genome/genetics ; Mice ; Mouse Embryonic Stem Cells ; },
abstract = {Although three-dimensional (3D) genome organization is central to many aspects of nuclear function, it has been difficult to measure at the single-cell level. To address this, we developed 'single-cell split-pool recognition of interactions by tag extension' (scSPRITE). scSPRITE uses split-and-pool barcoding to tag DNA fragments in the same nucleus and their 3D spatial arrangement. Because scSPRITE measures multiway DNA contacts, it generates higher-resolution maps within an individual cell than can be achieved by proximity ligation. We applied scSPRITE to thousands of mouse embryonic stem cells and detected known genome structures, including chromosome territories, active and inactive compartments, and topologically associating domains (TADs) as well as long-range inter-chromosomal structures organized around various nuclear bodies. We observe that these structures exhibit different levels of heterogeneity across the population, with TADs representing dynamic units of genome organization across cells. We expect that scSPRITE will be a critical tool for studying genome structure within heterogeneous populations.},
}
@article {pmid34426136,
year = {2022},
author = {Cabral, L and Giovanella, P and Pellizzer, EP and Teramoto, EH and Kiang, CH and Sette, LD},
title = {Microbial communities in petroleum-contaminated sites: Structure and metabolisms.},
journal = {Chemosphere},
volume = {286},
number = {Pt 2},
pages = {131752},
doi = {10.1016/j.chemosphere.2021.131752},
pmid = {34426136},
issn = {1879-1298},
mesh = {Biodegradation, Environmental ; Hydrocarbons ; *Microbiota ; *Petroleum ; *Petroleum Pollution/analysis ; Soil Microbiology ; *Soil Pollutants/analysis ; },
abstract = {Over recent decades, hydrocarbon concentrations have been augmented in soil and water, mainly derived from accidents or operations that input crude oil and petroleum into the environment. Different techniques for remediation have been proposed and used to mitigate oil contamination. Among the available environmental recovery approaches, bioremediation stands out since these hydrocarbon compounds can be used as growth substrates for microorganisms. In turn, microorganisms can play an important role with significant contributions to the stabilization of impacted areas. In this review, we present the current knowledge about responses from natural microbial communities (using DNA barcoding, multiomics, and functional gene markers) and bioremediation experiments (microcosm and mesocosm) conducted in the presence of petroleum and chemical dispersants in different samples, including soil, sediment, and water. Additionally, we present metabolic mechanisms for aerobic/anaerobic hydrocarbon degradation and alternative pathways, as well as a summary of studies showing functional genes and other mechanisms involved in petroleum biodegradation processes.},
}
@article {pmid34423264,
year = {2021},
author = {Gironda-Martínez, A and Donckele, EJ and Samain, F and Neri, D},
title = {DNA-Encoded Chemical Libraries: A Comprehensive Review with Succesful Stories and Future Challenges.},
journal = {ACS pharmacology &amp; translational science},
volume = {4},
number = {4},
pages = {1265-1279},
pmid = {34423264},
issn = {2575-9108},
abstract = {DNA-encoded chemical libraries (DELs) represent a versatile and powerful technology platform for the discovery of small-molecule ligands to protein targets of biological and pharmaceutical interest. DELs are collections of molecules, individually coupled to distinctive DNA tags serving as amplifiable identification barcodes. Thanks to advances in DNA-compatible reactions, selection methodologies, next-generation sequencing, and data analysis, DEL technology allows the construction and screening of libraries of unprecedented size, which has led to the discovery of highly potent ligands, some of which have progressed to clinical trials. In this Review, we present an overview of diverse approaches for the generation and screening of DEL molecular repertoires. Recent success stories are described, detailing how novel ligands were isolated from DEL screening campaigns and were further optimized by medicinal chemistry. The goal of the Review is to capture some of the most recent developments in the field, while also elaborating on future challenges to further improve DEL technology as a therapeutic discovery platform.},
}
@article {pmid34422006,
year = {2021},
author = {Tian, C and Li, X and Wu, Z and Li, Z and Hou, X and Li, FY},
title = {Characterization and Comparative Analysis of Complete Chloroplast Genomes of Three Species From the Genus Astragalus (Leguminosae).},
journal = {Frontiers in genetics},
volume = {12},
number = {},
pages = {705482},
pmid = {34422006},
issn = {1664-8021},
abstract = {Astragalus is the largest genus in Leguminosae. Several molecular studies have investigated the potential adulterants of the species within this genus; nonetheless, the evolutionary relationships among these species remain unclear. Herein, we sequenced and annotated the complete chloroplast genomes of three Astragalus species-Astragalus adsurgens, Astragalus mongholicus var. dahuricus, and Astragalus melilotoides using next-generation sequencing technology and plastid genome annotator (PGA) tool. All species belonged to the inverted repeat lacking clade (IRLC) and had similar sequences concerning gene contents and characteristics. Abundant simple sequence repeat (SSR) loci were detected, with single-nucleotide repeats accounting for the highest proportion of SSRs, most of which were A/T homopolymers. Using Astragalus membranaceus var. membranaceus as reference, the divergence was evident in most non-coding regions of the complete chloroplast genomes of these species. Seven genes (atpB, psbD, rpoB, rpoC1, trnV, rrn16, and rrn23) showed high nucleotide variability (Pi), and could be used as DNA barcodes for Astragalus sp. cemA and rpl33 were found undergoing positive selection by the section patterns in the coded protein. Phylogenetic analysis showed that Astragalus is a monophyletic group closely related to the genus Oxytropis within the tribe Galegeae. The newly sequenced chloroplast genomes provide insight into the unresolved evolutionary relationships within Astragalus spp. and are expected to contribute to species identification.},
}
@article {pmid34420293,
year = {2021},
author = {Han, P and Ma, Y and Fu, Z and Guo, Z and Xie, J and Wu, Y and Yuan, YJ},
title = {A DNA Inversion System in Eukaryotes Established via Laboratory Evolution.},
journal = {ACS synthetic biology},
volume = {10},
number = {9},
pages = {2222-2230},
doi = {10.1021/acssynbio.1c00132},
pmid = {34420293},
issn = {2161-5063},
mesh = {DNA Nucleotidyltransferases/genetics/metabolism ; DNA, Bacterial/genetics/*metabolism ; *Directed Molecular Evolution ; HEK293 Cells ; Humans ; Plasmids/genetics/metabolism ; Saccharomyces cerevisiae/genetics/*metabolism ; Salmonella/genetics ; },
abstract = {DNA inversion is a type of site-specific recombination system that plays an important role in the generation of genetic diversity and phenotypic adaptation by programmed rearrangements in bacteria. However, no such inversion system exhibiting a strong directionality bias has been identified or developed in eukaryotes yet. Here, using directed evolution of Rci recombinase, a tyrosine recombinase from a bacterial DNA inversion system, we identified a mutant Rci8 with a ratio of inversion/deletion up to ∼4320 in yeast. Based on Rci8 recombinase and sfxa101 sites, we have established a DNA inversion system in yeast and mammalian cells, enabling specificity for DNA inversions between inverted sites over deletions between directly repeated sites. Our results validated that the reversible DNA inversion system can act as an on/off transcriptional switch. Moreover, we demonstrate that the inversion system can also work on linear chromosomes. The eukaryotic DNA inversion system would provide a new tool for fields of genetic circuits, cellular barcoding, and synthetic genomes.},
}
@article {pmid34419430,
year = {2021},
author = {Mielinis, P and Sukackaitė, R and Serapinaitė, A and Samoilovas, F and Alzbutas, G and Matjošaitis, K and Lubys, A},
title = {MuA-based Molecular Indexing for Rare Mutation Detection by Next-Generation Sequencing.},
journal = {Journal of molecular biology},
volume = {433},
number = {19},
pages = {167209},
doi = {10.1016/j.jmb.2021.167209},
pmid = {34419430},
issn = {1089-8638},
mesh = {High-Throughput Nucleotide Sequencing ; Humans ; *Mutation ; Sequence Analysis, DNA/*methods ; Transposases/*metabolism ; },
abstract = {Detection of low-frequency mutations in cancer genomes or other heterogeneous cell populations requires high-fidelity sequencing. Molecular barcoding is one of the key technologies that enables the differentiation of true mutations from errors, which can be caused by sequencing or library preparation processes. However, current approaches where barcodes are introduced via primer extension or adaptor ligation do not utilize the full power of barcoding, due to complicated library preparation workflows and biases. Here we demonstrate the remarkable tolerance of MuA transposase to the presence of multiple replacements in transposon sequence, and explore this unique feature to engineer the MuA transposome complex with randomised nucleotides in 12 transposon positions, which can be introduced as a barcode into the target molecule after transposition event. We applied the approach of Unique MuA-based Molecular Indexing (UMAMI) to assess the power of rare mutation detection by shortgun sequencing on the Illumina platform. Our results show that UMAMI allows detection of rare mutations readily and reliably, and in this paper we report error rate values for the number of thermophilic DNA polymerases measured by using UMAMI.},
}
@article {pmid34418424,
year = {2022},
author = {Zbären, N and Brigger, D and Bachmann, D and Helbling, A and Jörg, L and Horn, MP and Schmid, JM and Hoffmann, HJ and Kinet, JP and Kaufmann, T and Eggel, A},
title = {A novel functional mast cell assay for the detection of allergies.},
journal = {The Journal of allergy and clinical immunology},
volume = {149},
number = {3},
pages = {1018-1030.e11},
doi = {10.1016/j.jaci.2021.08.006},
pmid = {34418424},
issn = {1097-6825},
mesh = {Allergens/metabolism ; Animals ; Humans ; *Hypersensitivity/diagnosis/metabolism ; Immunoglobulin E/metabolism ; *Mast Cells ; Mice ; Receptors, IgE/metabolism ; },
abstract = {BACKGROUND: Clinical management of allergic diseases has been hampered by the lack of safe and convenient tests to reliably identify culprit allergens and to closely follow changes in disease activity over time. Because allergy diagnosis is a complex and laborious multistep procedure, there is an urgent need for simpler but still functionally accurate ex vivo assays allowing objective diagnosis, substantiating treatment choices, and quantifying therapeutic responses.<br><br>OBJECTIVE: In this study, we sought to develop a novel functional cell-based assay that relies on passive sensitization of allergic effector cells with patient serum, circumventing current limitations in allergy diagnosis.<br><br>METHODS: We genetically engineered a conditional homeobox B8 (Hoxb8)-immortalized progenitor line from the bone marrow of mice that are transgenic for the human high-affinity IgE receptor (Fc&#x3b5;RI&#x3b1;). These cells can be reproducibly differentiated into mature Hoxb8 mast cells within 5 days of culture in virtually unlimited numbers.<br><br>RESULTS: We demonstrate that the established Hoxb8 mast cell assay can be used to accurately measure total IgE levels, identify culprit allergens, longitudinally monitor allergen-specific immunotherapy, and potentially determine the time point of tolerance induction upon allergen-specific immunotherapy in patients with allergy. To facilitate the analysis of large testing volumes, we demonstrate a proof-of-concept for a high-throughput screening application based on fluorescent cell barcoding using the engineered Hoxb8 mast cells.<br><br>CONCLUSIONS: Our results indicate that this novel mast cell assay could represent a valuable tool to support clinicians in the identification of IgE-mediated allergies and in the quantification of treatment efficacy as well as duration of therapeutic response.},
}
@article {pmid34417480,
year = {2021},
author = {Mahlerová, K and Jakubec, P and Novák, M and Růžička, J},
title = {Description of larval morphology and phylogenetic relationships of Heterotemna tenuicornis (Silphidae).},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {16973},
pmid = {34417480},
issn = {2045-2322},
mesh = {Animals ; Bayes Theorem ; Coleoptera/*anatomy &amp; histology/*classification/genetics/ultrastructure ; Larva/anatomy &amp; histology/classification/genetics/ultrastructure ; *Phylogeny ; Species Specificity ; },
abstract = {Providing clear and detailed morphological descriptions of endemic species in limited areas enables new knowledge of their biology and ecology to be obtained through citizen science. This information can be further used for their protection. Our study presents the first morphological description of the larvae of all three instars of Heterotemna tenuicornis (Brullé, 1836), an endemic species of the Canary Islands that, together with H. britoi García &amp; Pérez, 1996 and H. figurata (Brullé, 1839), belongs to the peculiar genus Heterotemna Wollaston, 1864. Furthermore, we present the first sequences of two mitochondrial genes (COI, 16S) obtained from larval specimens, and cross reference them with sequences from an adult specimen. Phylogenetic analysis of molecular data placed the genus Heterotemna within the genus Silpha Linnaeus, 1758, suggesting paraphyly of Silpha. In our study, we underline the importance of using a combination of morphological description and molecular data, that can be used for barcoding developmental stages which could not otherwise be definitely associated.},
}
@article {pmid34417123,
year = {2021},
author = {Gao, X and Mo, W and Shi, J and Song, N and Liang, P and Chen, J and Shi, Y and Guo, W and Li, X and Yang, X and Xin, B and Zhao, H and Song, W and Lai, J},
title = {HITAC-seq enables high-throughput cost-effective sequencing of plasmids and DNA fragments with identity.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {48},
number = {8},
pages = {671-680},
doi = {10.1016/j.jgg.2021.05.009},
pmid = {34417123},
issn = {1673-8527},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Zea mays/genetics ; *Plasmids/genetics ; *Sequence Analysis, DNA/methods ; Cost-Benefit Analysis ; Retroelements/genetics ; },
abstract = {DNA sequencing is vital for many aspects of biological research and diagnostics. Despite the development of second and third generation sequencing technologies, Sanger sequencing has long been the only choice when required to precisely track each sequenced plasmids or DNA fragments. Here, we report a complete set of novel barcoding and assembling system, Highly-parallel Indexed Tagmentation-reads Assembled Consensus sequencing (HITAC-seq), that could massively sequence and track the identities of each individual sequencing sample. With the cost of much less than that of single read of Sanger sequencing, HITAC-seq can generate high-quality contiguous sequences of up to 10 kilobases or longer. The capability of HITAC-seq was confirmed through large-scale sequencing of thousands of plasmid clones and hundreds of amplicon fragments using approximately 100 pg of input DNAs. Due to its long synthetic length, HITAC-seq was effective in detecting relatively large structural variations, as demonstrated by the identification of a ∼1.3 kb Copia retrotransposon insertion in the upstream of a likely maize domestication gene. Besides being a practical alternative to traditional Sanger sequencing, HITAC-seq is suitable for many high-throughput sequencing and genotyping applications.},
}
@article {pmid34415825,
year = {2021},
author = {Shin, D and Kang, HS and Park, EM and Kim, J and Kwon, J and Suh, J and Moon, G},
title = {Authentication of tejocote (Crataegus mexicana) dietary supplements based on DNA barcoding and chemical profiling.},
journal = {Food additives &amp; contaminants. Part A, Chemistry, analysis, control, exposure &amp; risk assessment},
volume = {38},
number = {12},
pages = {1985-1994},
doi = {10.1080/19440049.2021.1964701},
pmid = {34415825},
issn = {1944-0057},
mesh = {Cardenolides/administration &amp; dosage/adverse effects/*analysis ; Crataegus/adverse effects/*chemistry ; *DNA Barcoding, Taxonomic ; Dietary Supplements ; Digitoxigenin/administration &amp; dosage/adverse effects/*analysis ; Plant Extracts/administration &amp; dosage/adverse effects/*analysis ; },
abstract = {Tejocote (Crataegus mexicana, Mexican hawthorn), known as a weight-loss supplement, has been marketed online and is easily available for overseas direct purchase. Alipotec (brand name) is known as one of the most popular products containing tejocote in Mexico and other countries. However, adverse effects have been reported by users of these supplements. Therefore it is necessary to find the reason for the side effect. Dietary supplement samples labelled as containing tejocote were analysed using mass spectrometry and DNA barcoding analysis. Our results demonstrate that Alipotec samples contained ingredients from different species, yellow oleander instead of tejocote. The rpoB barcode region was able to differentiate between tejocote and yellow oleander species. Moreover, it was also observed that three compounds, including thevetin B, neriifolin, and digitoxigenin, clearly distinguish between tejocote and yellow oleander samples. This is the first and preliminary investigation to use an integrated approach of both chemical and genomic profiling for the authentication of dietary supplement containing tejocote.},
}
@article {pmid34414024,
year = {2021},
author = {Cutler Ii, WD and Bradshaw, AJ and Dentinger, BTM},
title = {What's for dinner this time?: DNA authentication of "wild mushrooms" in food products sold in the USA.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e11747},
pmid = {34414024},
issn = {2167-8359},
abstract = {Mushrooms have been consumed by humans for thousands of years, and while some have gastronomic and nutritional value, it has long been recognized that only select species of mushrooms are suitable for consumption. Adverse health effects of consuming poisonous mushrooms range from mild illness to death. Many valuable edible mushrooms are either impractical or unable to be grown commercially, requiring them to be harvested from the wild. In the U.S., products containing these wild-collected mushrooms are often sold with the nonspecific and undefined label "wild mushrooms," although in some cases particular species are listed in the ingredients. However, the ambiguity of the definition of "wild mushrooms" in foods makes it impossible to know which species are involved or whether they are truly wild-collected or cultivated varieties. As a consequence, any individual adverse reactions to consuming the mushrooms in these products cannot be traced to the source due to the minimal regulations around the harvest and sale of wild mushrooms. For this study, we set out to shed light on what species of fungi are being sold as "wild mushrooms" using DNA metabarcoding to identify fungal contents of various food products acquired from locally sourced grocers and a large online retail site. Twenty-eight species of mushroom were identified across 16 food products, ranging from commonly cultivated species to wild species not represented in global DNA databases. Our results demonstrate that "wild mushroom" ingredients often consist entirely or in part of cultivated species such as the ubiquitous white and brown "button" mushrooms and portabella (Agaricus bisporus), oyster (Pleurotus spp.) and shiitake (Lentinula edodes). In other cases truly wild mushrooms were detected but they were not always consistent with the species on the label. More alarmingly, a few products with large distribution potential contained species whose edibility is at best dubious, and at worst potentially toxic.},
}
@article {pmid34413445,
year = {2021},
author = {Sheraliev, B and Peng, Z},
title = {Molecular diversity of Uzbekistan's fishes assessed with DNA barcoding.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {16894},
pmid = {34413445},
issn = {2045-2322},
mesh = {Animals ; Bayes Theorem ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Fishes/classification/*genetics ; *Genetic Variation ; Geography ; Phylogeny ; Sample Size ; Species Specificity ; Uzbekistan ; },
abstract = {Uzbekistan is one of two doubly landlocked countries in the world, where all rivers are endorheic basins. Although fish diversity is relatively poor in Uzbekistan, the fish fauna of the region has not yet been fully studied. The aim of this study was to establish a reliable barcoding reference database for fish in Uzbekistan. A total of 666 specimens, belonging to 59 species within 39 genera, 17 families, and 9 orders, were subjected to polymerase chain reaction amplification in the barcode region and sequenced. The length of the 666 barcodes was 682 bp. The average K2P distances within species, genera, and families were 0.22%, 6.33%, and 16.46%, respectively. The average interspecific distance was approximately 28.8 times higher than the mean intraspecific distance. The Barcode Index Number (BIN) discordance report showed that 666 specimens represented 55 BINs, of which five were singletons, 45 were taxonomically concordant, and five were taxonomically discordant. The barcode gap analysis demonstrated that 89.3% of the fish species examined could be discriminated by DNA barcoding. These results provide new insights into fish diversity in the inland waters of Uzbekistan and can provide a basis for the development of further studies on fish fauna.},
}
@article {pmid34413171,
year = {2021},
author = {Parvez, S and Herdman, C and Beerens, M and Chakraborti, K and Harmer, ZP and Yeh, JJ and MacRae, CA and Yost, HJ and Peterson, RT},
title = {MIC-Drop: A platform for large-scale in vivo CRISPR screens.},
journal = {Science (New York, N.Y.)},
volume = {373},
number = {6559},
pages = {1146-1151},
pmid = {34413171},
issn = {1095-9203},
support = {R01 GM134069/GM/NIGMS NIH HHS/United States ; UM1 HL098160/HL/NHLBI NIH HHS/United States ; U01 HL098160/HL/NHLBI NIH HHS/United States ; U54 NS112107/NS/NINDS NIH HHS/United States ; R24 OD017870/OD/NIH HHS/United States ; },
mesh = {Animals ; *CRISPR-Cas Systems ; Cardiovascular System/growth &amp; development ; Cell Culture Techniques ; *Genetic Testing ; High-Throughput Nucleotide Sequencing ; *Microfluidic Analytical Techniques ; Zebrafish/*genetics/growth &amp; development ; },
abstract = {CRISPR-Cas9 can be scaled up for large-scale screens in cultured cells, but CRISPR screens in animals have been challenging because generating, validating, and keeping track of large numbers of mutant animals is prohibitive. Here, we introduce Multiplexed Intermixed CRISPR Droplets (MIC-Drop), a platform combining droplet microfluidics, single-needle en masse CRISPR ribonucleoprotein injections, and DNA barcoding to enable large-scale functional genetic screens in zebrafish. The platform can efficiently identify genes responsible for morphological or behavioral phenotypes. In one application, we showed that MIC-Drop could identify small-molecule targets. Furthermore, in a MIC-Drop screen of 188 poorly characterized genes, we discovered several genes important for cardiac development and function. With the potential to scale to thousands of genes, MIC-Drop enables genome-scale reverse genetic screens in model organisms.},
}
@article {pmid34408017,
year = {2021},
author = {Mueller, HS and Fowler, CE and Dalin, S and Moiso, E and Udomlumleart, T and Garg, S and Hemann, MT and Lees, JA},
title = {Acquired resistance to PRMT5 inhibition induces concomitant collateral sensitivity to paclitaxel.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {34},
pages = {},
pmid = {34408017},
issn = {1091-6490},
support = {T32 GM007287/GM/NIGMS NIH HHS/United States ; P01 CA042063/CA/NCI NIH HHS/United States ; P30 CA014051/CA/NCI NIH HHS/United States ; R01 CA233477/CA/NCI NIH HHS/United States ; T32 CA009216/CA/NCI NIH HHS/United States ; },
mesh = {Adenocarcinoma of Lung/drug therapy/metabolism ; Animals ; Antineoplastic Agents/*pharmacology ; Cell Line, Tumor ; Cell Proliferation ; *Drug Resistance, Neoplasm ; Drug Synergism ; Epigenesis, Genetic ; Gene Expression Regulation, Neoplastic ; Gene Knockdown Techniques ; Humans ; Lung Neoplasms/drug therapy/metabolism ; Mice ; Mutation ; Paclitaxel/*pharmacology ; Protein-Arginine N-Methyltransferases/*antagonists &amp; inhibitors ; Stathmin/genetics/metabolism ; },
abstract = {Epigenetic regulators play key roles in cancer and are increasingly being targeted for treatment. However, for many, little is known about mechanisms of resistance to the inhibition of these regulators. We have generated a model of resistance to inhibitors of protein arginine methyltransferase 5 (PRMT5). This study was conducted in Kras[G12D];Tp53-null lung adenocarcinoma (LUAD) cell lines. Resistance to PRMT5 inhibitors (PRMT5i) arose rapidly, and barcoding experiments showed that this resulted from a drug-induced transcriptional state switch, not selection of a preexisting population. This resistant state is both stable and conserved across variants arising from distinct LUAD lines. Moreover, it brought with it vulnerabilities to other chemotherapeutics, especially the taxane paclitaxel. This paclitaxel sensitivity depended on the presence of stathmin 2 (STMN2), a microtubule regulator that is specifically expressed in the resistant state. Remarkably, STMN2 was also essential for resistance to PRMT5 inhibition. Thus, a single gene is required for both acquisition of resistance to PRMT5i and collateral sensitivity to paclitaxel in our LUAD cells. Accordingly, the combination of PRMT5i and paclitaxel yielded potent and synergistic killing of the murine LUAD cells. Importantly, the synergy between PRMT5i and paclitaxel also extended to human cancer cell lines. Finally, analysis of The Cancer Genome Atlas patient data showed that high STMN2 levels correlate with complete regression of tumors in response to taxane treatment. Collectively, this study reveals a recurring mechanism of PRMT5i resistance in LUAD and identifies collateral sensitivities that have potential clinical relevance.},
}
@article {pmid34407880,
year = {2021},
author = {Lessard, BD and Kurucz, N and Rodriguez, J and Carter, J and Hardy, CM},
title = {Detection of the Japanese encephalitis vector mosquito Culex tritaeniorhynchus in Australia using molecular diagnostics and morphology.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {411},
pmid = {34407880},
issn = {1756-3305},
support = {RG 18-19//Australian Biological Resources Study/ ; },
mesh = {Animals ; Australia ; Culex/*classification/*genetics/virology ; Electron Transport Complex IV/genetics ; Encephalitis Virus, Japanese/pathogenicity ; Encephalitis, Japanese/transmission/virology ; Female ; Insect Vectors/*classification/*genetics/virology ; },
abstract = {BACKGROUND: Culex (Culex) tritaeniorhynchus is an important vector of Japanese encephalitis virus (JEV) affecting feral pigs, native mammals and humans. The mosquito species is widely distributed throughout Southeast Asia, Africa and Europe, and thought to be absent in Australia.<br><br>METHODS: In February and May, 2020 the Medical Entomology unit of the Northern Territory (NT) Top End Health Service collected Cx. tritaeniorhynchus female specimens (n&#x2009;=&#x2009;19) from the Darwin and Katherine regions. Specimens were preliminarily identified morphologically as the Vishnui subgroup in subgenus Culex. Molecular identification was performed using cytochrome c oxidase subunit 1 (COI) barcoding, including sequence percentage identity using BLAST and tree-based identification using maximum likelihood analysis in the IQ-TREE software package. Once identified using COI, specimens were reanalysed for diagnostic morphological characters to inform a new taxonomic key to related species from the NT.<br><br>RESULTS: Sequence percentage analysis of COI revealed that specimens from the NT shared 99.7% nucleotide identity to a haplotype of Cx. tritaeniorhynchus from Dili, Timor-Leste. The phylogenetic analysis showed that the NT specimens formed a monophyletic clade with other Cx. tritaeniorhynchus from Southeast Asia and the Middle East. We provide COI barcodes for most NT species from the Vishnui subgroup to aid future identifications, including the first genetic sequences for Culex (Culex) crinicauda and the undescribed species Culex (Culex) sp. No. 32 of Marks. Useful diagnostic morphological characters were identified and are presented in a taxonomic key to adult females to separate Cx. tritaeniorhynchus from other members of the Vishnui subgroup from the NT.<br><br>CONCLUSIONS: We report the detection of Cx. tritaeniorhynchus in Australia from the Darwin and Katherine regions of the NT. The vector is likely to be already established in northern Australia, given the wide geographical spread throughout the Top End of the NT. The establishment of Cx. tritaeniorhynchus in Australia is a concern to health officials as the species is an important vector of JEV and is now the sixth species from the subgenus Culex capable of vectoring JEV in Australia. We suggest that the species must now be continuously monitored during routine mosquito surveillance programmes to determine its current geographical spread and prevent the potential transmission of exotic JEV throughout Australia.},
}
@article {pmid34407123,
year = {2021},
author = {Su, HJ and Liang, SL and Nickrent, DL},
title = {Plastome variation and phylogeny of Taxillus (Loranthaceae).},
journal = {PloS one},
volume = {16},
number = {8},
pages = {e0256345},
pmid = {34407123},
issn = {1932-6203},
mesh = {DNA, Ribosomal/chemistry/classification/metabolism ; Evolution, Molecular ; Genome, Plastid ; Loranthaceae/*classification/genetics ; Mitochondria/genetics ; NADH Dehydrogenase/classification/genetics ; Phylogeny ; Plastids/*genetics ; RNA, Transfer/genetics ; Ribosomal Proteins/classification/genetics ; },
abstract = {Several molecular phylogenetic studies of the mistletoe family Loranthaceae have been published such that now the general pattern of relationships among the genera and their biogeographic histories are understood. Less is known about species relationships in the larger (> 10 species) genera. This study examines the taxonomically difficult genus Taxillus composed of 35-40 Asian species. The goal was to explore the genetic diversity present in Taxillus plastomes, locate genetically variable hotspots, and test these for their utility as potential DNA barcodes. Using genome skimming, complete plastomes, as well as nuclear and mitochondrial rDNA sequences, were newly generated for eight species. The plastome sequences were used in conjunction with seven publicly available Taxillus sequences and three sequences of Scurrula, a close generic relative. The Taxillus plastomes ranged from 121 to 123 kbp and encoded 90-93 plastid genes. In addition to all of the NADH dehydrogenase complex genes, four ribosomal genes, infA and four intron-containing tRNA genes were lost or pseudogenized in all of the Taxillus and Scurrula plastomes. The topologies of the plastome, mitochondrial rDNA and nuclear rDNA trees were generally congruent, though with discordance at the position of T. chinensis. Several variable regions in the plastomes were identified that have sufficient numbers of parsimony informative sites as to recover the major clades seen in the complete plastome tree. Instead of generating complete plastome sequences, our study showed that accD alone or the concatenation of accD and rbcL can be used in future studies to facilitate identification of Taxillus samples and to generate a molecular phylogeny with robust sampling within the genus.},
}
@article {pmid34406688,
year = {2021},
author = {von Beeren, C and Blüthgen, N and Hoenle, PO and Pohl, S and Brückner, A and Tishechkin, AK and Maruyama, M and Brown, BV and Hash, JM and Hall, WE and Kronauer, DJC},
title = {A remarkable legion of guests: Diversity and host specificity of army ant symbionts.},
journal = {Molecular ecology},
volume = {30},
number = {20},
pages = {5229-5246},
doi = {10.1111/mec.16101},
pmid = {34406688},
issn = {1365-294X},
mesh = {Animals ; *Ants/genetics ; Biodiversity ; *Coleoptera ; Host Specificity/genetics ; Symbiosis/genetics ; },
abstract = {Tropical rainforests are among the most diverse biomes on Earth. While species inventories are far from complete for any tropical rainforest, even less is known about the intricate species interactions that form the basis of these ecological communities. One fascinating but poorly studied example are the symbiotic associations between army ants and their rich assemblages of parasitic arthropod guests. Hundreds of these guests, or myrmecophiles, have been taxonomically described. However, because previous work has mainly been based on haphazard collections from disjunct populations, it remains challenging to define species boundaries. We therefore know little about the species richness, abundance and host specificity of most guests in any given population, which is crucial to understand co-evolutionary and ecological dynamics. Here, we report a quantitative community survey of myrmecophiles parasitizing the six sympatric Eciton army ant species in a Costa Rican rainforest. Combining DNA barcoding with morphological identification of over 2,000 specimens, we discovered 62 species, including 49 beetles, 11 flies, one millipede and one silverfish. At least 14 of these species were new to science. Ecological network analysis revealed a clear signal of host partitioning, and each Eciton species was host to both specialists and generalists. These varying degrees in host specificities translated into a moderate level of network specificity, highlighting the system's level of biotic pluralism in terms of biodiversity and interaction diversity. By providing vouchered DNA barcodes for army ant guest species, this study provides a baseline for future work on co-evolutionary and ecological dynamics in these species-rich host-symbiont networks across the Neotropical realm.},
}
@article {pmid34403833,
year = {2021},
author = {Gutierrez-Liberato, GA and Lotta-Arévalo, IA and González, LP and Vargas-Ramírez, M and Rodríguez-Fandiño, O and Cepeda, AS and Ortiz-Moreno, ML and Matta, NE},
title = {The genetic and morphological diversity of Haemogregarina infecting turtles in Colombia: Are mitochondrial markers useful as barcodes for these parasites?.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {95},
number = {},
pages = {105040},
doi = {10.1016/j.meegid.2021.105040},
pmid = {34403833},
issn = {1567-7257},
mesh = {Animals ; Coccidiosis/diagnosis/*veterinary ; Colombia ; *DNA Barcoding, Taxonomic ; Eucoccidiida/classification/genetics/*physiology ; *Genome, Mitochondrial ; Phylogeny ; RNA, Protozoan/analysis ; RNA, Ribosomal, 18S/analysis ; *Turtles ; },
abstract = {Adeleorinid parasites commonly infect turtles and tortoises in nature. Currently, our knowledge about such parasites is extremely poor. Their characterization is based on morphological and molecular approaches using the 18S rDNA molecular marker. However, there is a limitation with the 18S rDNA due to its slow rate of evolution. For that reason, the goals of this study were to 1) design primers for new molecular mitochondrial markers to improve the phylogenetic reconstructions of adeleorinid parasites and 2) to determine the morphological and genetic diversity of Haemogregarina infecting turtles and tortoises in Colombia. Turtles from 16 species representing six families were examined for the presence of haemoparasites. We analyzed 457 samples using PCR, and 203 of them were also analyzed by microscopy. Using a mitochondrial genome of Haemogregarina sequenced in this study, we designed primers to amplify fragments of the cytochrome oxidase I (coxI), cytochrome oxidase III (coxIII), and cytochrome b (cytb) mitochondrial markers in adeleorinid parasites. Lineages obtained from nuclear and mitochondrial molecular markers clustered according to the turtle lineages from which they were isolated. It is noteworthy that we found different evolutionary lineages within the same morphotype, which may indicate heteroplasmy and/or cryptic diversity in Haemogregarina. Due to this situation, we could not make a species delimitation, even when integrating the different lines of evidence we had in this study. However, the primers presented here are useful for diagnosis and, moreover, according to the available information, all three genes retain phylogenetic signals; thereby fragments amplified can be used in reconstructing evolutionary relationships. This effort contributes to the knowledge of the diversity of these parasites infecting continental turtles from Colombia.},
}
@article {pmid34402636,
year = {2021},
author = {Hullahalli, K and Pritchard, JR and Waldor, MK},
title = {Refined Quantification of Infection Bottlenecks and Pathogen Dissemination with STAMPR.},
journal = {mSystems},
volume = {6},
number = {4},
pages = {e0088721},
pmid = {34402636},
issn = {2379-5077},
support = {//National Science Foundation (NSF)/ ; R01 AI042347/AI/NIAID NIH HHS/United States ; //Howard Hughes Medical Institute (HHMI)/ ; F31 AI156949/AI/NIAID NIH HHS/United States ; AI-R01-042347//HHS | National Institutes of Health (NIH)/ ; },
abstract = {Pathogen population dynamics during infection are critical determinants of infection susceptibility and define patterns of dissemination. However, deciphering these dynamics, particularly founding population sizes in host organs and patterns of dissemination between organs, is difficult because measuring bacterial burden alone is insufficient to observe these patterns. Introduction of allelic diversity into otherwise identical bacteria using DNA barcodes enables sequencing-based measurements of these parameters, in a method known as STAMP (Sequence Tag-based Analysis of Microbial Populations). However, bacteria often undergo unequal expansion within host organs, resulting in marked differences in the frequencies of barcodes in input and output libraries. Here, we show that these differences confound STAMP-based analyses of founding population sizes and dissemination patterns. We present STAMPR, a successor to STAMP, which accounts for such population expansions. Using data from systemic infection of barcoded extraintestinal pathogenic E. coli, we show that this new framework, along with the metrics it yields, enhances the fidelity of measurements of bottlenecks and dissemination patterns. STAMPR was also validated on an independent barcoded Pseudomonas aeruginosa data set, uncovering new patterns of dissemination within the data. This framework (available at https://github.com/hullahalli/stampr_rtisan), when coupled with barcoded data sets, enables a more complete assessment of within-host bacterial population dynamics. IMPORTANCE Barcoded bacteria are often employed to monitor pathogen population dynamics during infection. The accuracy of these measurements is diminished by unequal bacterial expansion rates. Here, we develop computational tools to circumvent this limitation and establish additional metrics that collectively enhance the fidelity of measuring within-host pathogen founding population sizes and dissemination patterns. These new tools will benefit future studies of the dynamics of pathogens and symbionts within their respective hosts and may have additional barcode-based applications beyond host-microbe interactions.},
}
@article {pmid34402614,
year = {2021},
author = {Jeong, SM and Yang, J and Pak, JH and Seo, K and Lim, T and Ju, S},
title = {Real-Time Information-Variable Invisible Barcode Comprising Freely Deformable Infrared-Emitting Yarns.},
journal = {ACS applied materials &amp; interfaces},
volume = {13},
number = {34},
pages = {41046-41055},
doi = {10.1021/acsami.1c10052},
pmid = {34402614},
issn = {1944-8252},
abstract = {Barcodes are utilized for product information management in shops, offices, hospitals, passenger facilities, and factories because they enable substantial amounts of data to be processed quickly and accurately. However, a limited amount of information can be loaded on the currently used monochrome barcodes that are based on thin-film coatings. Therefore, these barcodes require constant replacement with new barcodes to update the information; furthermore, they cannot be applied to textile products. This study demonstrated the performance of wearable invisible infrared (IR)-emitting barcodes by using twisted yarns that comprised five highly elastic/conductive spandex fibers. The barcode information can be actively updated via the selective IR emission from specific yarns of the barcode by controlling the applied voltage to the IR-emitting yarns. Therefore, the IR barcode required a relatively small number of bars to express a higher volume of information compared to the existing monochrome barcodes. Because the emitted IR light from the yarns was invisible to the human eye and was only recognized by an IR camera, the information-variable IR-emitting yarn-based barcode exhibited an aesthetic design and was composed of a sustainable fabric-type material that could be easily applied to clothes, bags, and shoes. It is expected that the fabricated barcode will be widely utilized as wearable invisible barcodes, whose information will remain invisible to humans and can be updated in real time to ensure information fluidity.},
}
@article {pmid34399186,
year = {2021},
author = {Schroeder, A and Pallavicini, A and Edomi, P and Pansera, M and Camatti, E},
title = {Suitability of a dual COI marker for marine zooplankton DNA metabarcoding.},
journal = {Marine environmental research},
volume = {170},
number = {},
pages = {105444},
doi = {10.1016/j.marenvres.2021.105444},
pmid = {34399186},
issn = {1879-0291},
mesh = {Animals ; Biodiversity ; DNA ; *DNA Barcoding, Taxonomic ; *Zooplankton/genetics ; },
abstract = {As DNA metabarcoding has become an emerging tool for surveying biodiversity, including its application in legally binding assessments, reliable and efficient barcodes are requested, especially for the highly diverse group of zooplankton. This study focuses on comparing the efficiency of two mitochondrial COI barcodes based on the internal primers mlCOIintF and mlCOIintR utilizing mesozooplankton samples collected in a Mediterranean lagoon. Our results indicate that after a slight adjustment, the mlCOIintR primer performs in combination with jdgLCO1490 (herein) very comparably to the much more widely used primer system mlCOIintF/jgHCO2198+dgHCO2198, in terms of level of taxonomic resolution, species detection and their relative abundance in terms of numbers of reads. As for some groups, like Ctenophora, this barcode is not suitable; a combination of them may be the best option to rely on the Folmer region in its entirety without the risk of losing information for a limited primer match.},
}
@article {pmid34398521,
year = {2021},
author = {Madeira, S and Duarte, A and Boinas, F and Costa Osório, H},
title = {A DNA barcode reference library of Portuguese mosquitoes.},
journal = {Zoonoses and public health},
volume = {68},
number = {8},
pages = {926-936},
doi = {10.1111/zph.12885},
pmid = {34398521},
issn = {1863-2378},
mesh = {Animals ; *Culicidae/classification/genetics ; *DNA Barcoding, Taxonomic/methods/veterinary ; Electron Transport Complex IV/genetics ; Mosquito Vectors/genetics ; Phylogeny ; Portugal ; },
abstract = {Mosquitoes are important biological vectors of pathogens and species identification in all life stages is the first step for effective monitoring and control of mosquito-borne diseases. Molecular methods for species identification have been developed over the last years to overcome the limitations of the taxonomic identification based on morphology. DNA barcoding, using a fragment of the mitochondrial cytochrome oxidase I (COI) gene, can be used for species identification but a reliable and comprehensive reference database of verified sequences is required. In this study, we aimed to generate a DNA barcode reference library for the identification of mosquito species from Portuguese mosquito fauna, including most relevant vector species. Mosquitoes captured under the National Vector Surveillance Program (REVIVE) were processed for DNA extraction, COI gene fragment amplification and sequencing. Nighty-eight barcode sequences were obtained, representing 26 species and 6 genera. Sequences were submitted to GenBank and BOLD and were used for validation of phenetic classification. Barcode Index Number (BIN) assignment and Automatic Barcode Gap Discovery (ABGD) were used and clustered COI sequences into twenty-five molecular operational taxonomic units (MOTUs). This is the first comprehensive study that combines morphological and molecular identification of most mosquito species present in Portugal aiming to offer a reliable framework for mosquito species identification.},
}
@article {pmid34396748,
year = {2021},
author = {Wang, L and Zhang, XS and Zhang, CL},
title = {[Research progress on Pheretima and earthworms with related origin].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {46},
number = {13},
pages = {3298-3302},
doi = {10.19540/j.cnki.cjcmm.20210317.102},
pmid = {34396748},
issn = {1001-5302},
mesh = {Animals ; Chromatography, High Pressure Liquid ; Cyclooxygenase 2 ; DNA ; Fibroblasts ; Mice ; *Oligochaeta ; },
abstract = {Through literature analysis of Pheretima and its origin-related earthworm,this study summarized the progress on Pheretima in textual criticism of origin,origin identification,effective components,detection of harmful components,and pharmacological effects,which can lay a basis for further research on Pheretima. Through literature research,the authors found that Pheretima was first recorded in Secret Formulary for Traumatology and Fracture Taught by Immortal written by LIN Daoren in Tang Dynasty rather than the Taiping Holy Prescriptions for Universal Relief in Song Dynasty. The latest techniques for origin identification include microscopic trait identification,DNA barcoding,and HPLC. The main effective components of Pheretima are proteins,polypeptides,enzymes,nucleotides,amino acids,and trace elements. According to recent studies,Pheretima has anti-pulmonary and anti-renal interstitial fibrosis,respiratory syncytial virus-inhibiting,human hypertrophic scar fibroblast proliferation-suppressing,and mouse embryonic fibroblast proliferation-promoting effects. Moreover,Pheretima can prevent colitis-induced colon cancer by inhibiting the activation of COX-2/PGE2/β-catenin signaling pathway. METHODS:: for detecting the harmful components and their residues(organic pollutant polychlorinated biphenyl,heavy metals) and bacteria in Pheretima,have been established. Pheretima,mainly derived from wild earthworms,has remarkable clinical efficacy. However,the wild resource is in short supply and artificial culture is expected to be a promising solution.},
}
@article {pmid34396379,
year = {2021},
author = {Fan, X and Nie, J and Ying, W and Xu, S and Gu, J and Liu, S},
title = {Cryogenic enabled multicolor upconversion luminescence of KLa(MoO4)2:Yb[3+]/Ho[3+] for dual-mode anti-counterfeiting.},
journal = {Dalton transactions (Cambridge, England : 2003)},
volume = {50},
number = {35},
pages = {12234-12241},
doi = {10.1039/d1dt01727f},
pmid = {34396379},
issn = {1477-9234},
abstract = {The rational development of multicolor upconversion (UC) luminescent materials is particularly promising for achieving high-tech anti-counterfeiting and security applications. Here, an Ho[3+] and Yb[3+] ion co-doped KLa(MoO4)2 material can achieve multicolored UC luminescence by thermally manipulating the electron transition process, which could be developed to execute advanced optical anti-counterfeiting applications. The emission color of this material turns from bright green to deep orange with the temperature controlled from 85 K to 240 K in a cryogenic environment. The maximum absolute sensitivity and relative sensitivity of this temperature-sensing material based on non-thermally coupled levels of Ho[3+] ions reached 0.049 K[-1] and 4.6% K[-1]. And utilizing the thermochromic luminescence properties and high sensitivity for low temperature of the KLa(MoO4)2:Yb[3+]/Ho[3+] UC material, we created KLa(MoO4)2:Yb[3+]/Ho[3+] fluorescent security inks and UC photonic barcodes to realize novel visual reading and digital recognition dual-mode anti-counterfeiting in a secure manner. These results may provide useful enlightenment for the design and modulation of high-sensitivity temperature-sensing materials for high-level anti-counterfeiting applications.},
}
@article {pmid34396089,
year = {2021},
author = {Barnes, D and Polanco, L and Perea, JA},
title = {A Comparative Study of Machine Learning Methods for Persistence Diagrams.},
journal = {Frontiers in artificial intelligence},
volume = {4},
number = {},
pages = {681174},
pmid = {34396089},
issn = {2624-8212},
abstract = {Many and varied methods currently exist for featurization, which is the process of mapping persistence diagrams to Euclidean space, with the goal of maximally preserving structure. However, and to our knowledge, there are presently no methodical comparisons of existing approaches, nor a standardized collection of test data sets. This paper provides a comparative study of several such methods. In particular, we review, evaluate, and compare the stable multi-scale kernel, persistence landscapes, persistence images, the ring of algebraic functions, template functions, and adaptive template systems. Using these approaches for feature extraction, we apply and compare popular machine learning methods on five data sets: MNIST, Shape retrieval of non-rigid 3D Human Models (SHREC14), extracts from the Protein Classification Benchmark Collection (Protein), MPEG7 shape matching, and HAM10000 skin lesion data set. These data sets are commonly used in the above methods for featurization, and we use them to evaluate predictive utility in real-world applications.},
}
@article {pmid34395092,
year = {2021},
author = {Catlett, D and Son, K and Liang, C},
title = {ensembleTax: an R package for determinations of ensemble taxonomic assignments of phylogenetically-informative marker gene sequences.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e11865},
pmid = {34395092},
issn = {2167-8359},
abstract = {BACKGROUND: High-throughput sequencing of phylogenetically informative marker genes is a widely used method to assess the diversity and composition of microbial communities. Taxonomic assignment of sampled marker gene sequences (referred to as amplicon sequence variants, or ASVs) imparts ecological significance to these genetic data. To assign taxonomy to an ASV, a taxonomic assignment algorithm compares the ASV to a collection of reference sequences (a reference database) with known taxonomic affiliations. However, many taxonomic assignment algorithms and reference databases are available, and the optimal algorithm and database for a particular scientific question is often unclear. Here, we present the ensembleTax R package, which provides an efficient framework for integrating taxonomic assignments predicted with any number of taxonomic assignment algorithms and reference databases to determine ensemble taxonomic assignments for ASVs.<br><br>METHODS: The ensembleTax R package relies on two core algorithms: taxmapper and assign.ensembleTax. The taxmapper algorithm maps taxonomic assignments derived from one reference database onto the taxonomic nomenclature (a set of taxonomic naming and ranking conventions) of another reference database. The assign.ensembleTax algorithm computes ensemble taxonomic assignments for each ASV in a data set based on any number of taxonomic assignments determined with independent methods. Various parameters allow analysts to prioritize obtaining either more ASVs with more predicted clade names or more robust clade name predictions supported by multiple independent methods in ensemble taxonomic assignments.<br><br>RESULTS: The ensembleTax R package is used to compute two sets of ensemble taxonomic assignments for a collection of protistan ASVs sampled from the coastal ocean. Comparisons of taxonomic assignments predicted by individual methods with those predicted by ensemble methods show that conservative implementations of the ensembleTax package minimize disagreements between taxonomic assignments predicted by individual and ensemble methods, but result in ASVs with fewer ranks assigned taxonomy. Less conservative implementations of the ensembleTax package result in an increased fraction of ASVs classified at all taxonomic ranks, but increase the number of ASVs for which ensemble assignments disagree with those predicted by individual methods.<br><br>DISCUSSION: We discuss how implementation of the ensembleTax R package may be optimized to address specific scientific objectives based on the results of the application of the ensembleTax package to marine protist communities. While further work is required to evaluate the accuracy of ensemble taxonomic assignments relative to taxonomic assignments predicted by individual methods, we also discuss scenarios where ensemble methods are expected to improve the accuracy of taxonomy prediction for ASVs.},
}
@article {pmid34395083,
year = {2021},
author = {Elbrecht, V and Lindner, A and Manerus, L and Steinke, D},
title = {A bright idea-metabarcoding arthropods from light fixtures.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e11841},
pmid = {34395083},
issn = {2167-8359},
abstract = {Arthropod communities in buildings have not been extensively studied, although humans have always shared their homes with them. In this study we explored if arthropod DNA can be retrieved and metabarcoded from indoor environments through the collection of dead specimens in light fixtures to better understand what shapes arthropod diversity in our homes. Insects were collected from 45 light fixtures at the Centre for Biodiversity Genomics (CBG, Guelph, Canada), and by community scientists at 12 different residential homes in Southern Ontario. The CBG ground floor of the CBG showed the greatest arthropod diversity, especially in light fixtures that were continuously illuminated. The community scientist samples varied strongly by light fixture type, lightbulb used, time passed since lamp was last cleaned, and specimen size. In all cases, the majority of OTUs was not shared between samples even within the same building. This study demonstrates that light fixtures might be a useful resource to determine arthropod diversity in our homes, but individual samples are likely not representative of the full diversity.},
}
@article {pmid34393582,
year = {2021},
author = {Sousa, P and Grosso-Silva, JM and Andrade, R and Chaves, C and Pinto, J and Paupério, J and Beja, P and Ferreira, S},
title = {The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Hemiptera 01.},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e65314},
pmid = {34393582},
issn = {1314-2828},
abstract = {BACKGROUND: The InBIO Barcoding Initiative (IBI) Hemiptera 01 dataset contains records of 131 specimens of Hemiptera. Most specimens have been morphologically identified to species or subspecies level and represent 88 species in total. The species of this dataset correspond to about 7.3% of continental Portuguese hemipteran species diversity. All specimens were collected in continental Portugal. Sampling took place from 2015 to 2019 and specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources.<br><br>NEW INFORMATION: This dataset increases the knowledge on the DNA barcodes and distribution of 88 species of Hemiptera from Portugal. Six species, from five different families, were new additions to the Barcode of Life Data System (BOLD), with another twenty five species barcodes' added from under-represented taxa in BOLD. All specimens have their DNA barcodes publicly accessible through BOLD online database and the distribution data can be accessed through the Global Biodiversity Information Facility (GBIF). Eutettix variabilis and Fieberiella florii are recorded for the first time for Portugal and Siphanta acuta, an invasive species, previously reported from the Portuguese Azores archipelago, is recorded for the first time for continental Portugal.},
}
@article {pmid34393564,
year = {2021},
author = {Wu, R and Liu, X and Kondo, T and Ouyang, S and Wu, X},
title = {New species of the genus Inversidens Haas, 1911 (Unionoida, Unionidae, Gonideinae) from Jiangxi Province, China.},
journal = {ZooKeys},
volume = {1054},
number = {},
pages = {85-93},
pmid = {34393564},
issn = {1313-2989},
abstract = {We diagnose and describe a new freshwater mussel species of the genus Inversidens, I.rentianensis sp. nov. from Jiangxi Province, China based on morphological characters and molecular data. This paper includes a morphological description and photograph of the holotype, and partial sequences of mitochondrial COI as DNA barcode data.},
}
@article {pmid34393563,
year = {2021},
author = {Oliveira, D and Chaves, C and Pinto, J and Paupério, J and Fonseca, N and Beja, P and Ferreira, S},
title = {DNA Barcoding of Portuguese Lacewings (Neuroptera) and Snakeflies (Raphidioptera) (Insecta, Neuropterida).},
journal = {ZooKeys},
volume = {1054},
number = {},
pages = {67-84},
pmid = {34393563},
issn = {1313-2989},
abstract = {The orders Neuroptera and Raphidioptera include the species of insects known as lacewings and snakeflies, respectively. In Portugal, these groups account for over 100 species, some of which are very difficult to identify by morphological analysis. This work is the first to sample and DNA sequence lacewings and snakeflies of Portugal. A reference collection was built with captured specimens that were identified morphologically. DNA barcode sequences of 658 bp were obtained from 243 specimens of 54 species. The results showed that most species can be successfully identified through DNA barcoding, with the exception of seven species of Chrysopidae (Neuroptera). Additionally, the first published distribution data are presented for Portugal for the neuropterans Gymnocnemiavariegata (Schneider, 1845) and Myrmecaelurus (Myrmecaelurus) trigrammus (Pallas, 1771).},
}
@article {pmid34393560,
year = {2021},
author = {Shepherd, B and Pinheiro, HT and Phelps, TAY and Pérez-Matus, A and Rocha, LA},
title = {Pseudanthiashangapiko, a new anthiadine serranid (Teleostei, Serranidae, Anthiadinae) from Rapa Nui (Easter Island).},
journal = {ZooKeys},
volume = {1054},
number = {},
pages = {1-13},
pmid = {34393560},
issn = {1313-2989},
abstract = {Pseudanthiashangapiko sp. nov. (Teleostei, Serranidae, Anthiadinae) is herein described from three specimens collected from a depth of 83 m in a mesophotic coral ecosystem off Hanga Piko, Rapa Nui (Easter Island), Chile. Pseudanthiashangapiko sp. nov. can be distinguished from its congeners in live coloration and by the following combination of characters: dorsal-fin rays X, 17; anal-fin rays III, 8; pectoral-fin rays 16 (left side of one specimen 17); vertebrae 10+16; scales relatively large, two scales above lateral-line to base of fifth dorsal spine, and 16-17 circumpeduncular scales; gill rakers 11+23; and a slender body, with greatest body depth 3.6 (3.4-3.8) in SL. The most similar DNA barcodes (mitochondrial COI gene) are from Pseudanthiasventralis Randall, 1979 and Pseudanthiashawaiiensis Randall, 1979, with 16.8% and 17.0% uncorrected divergence, respectively. This fish is one of four new species that were documented from a pair of technical dives at a single location in Rapa Nui, emphasizing the high number of undescribed species likely still unknown in mesophotic coral ecosystems, especially in geographically remote locations. Pseudanthiashangapiko sp. nov. adds to the Rapa Nui ichthyofauna, which hosts the second-highest level of endemism in both shallow and deep-water fishes.},
}
@article {pmid34393558,
year = {2021},
author = {Pohjoismäki, J and Bergström, C},
title = {Review of the Nordic Gymnocheta Robineau-Desvoidy (Diptera, Tachinidae) with report of two species new to Europe.},
journal = {ZooKeys},
volume = {1053},
number = {},
pages = {145-184},
pmid = {34393558},
issn = {1313-2989},
abstract = {The genus Gymnocheta Robineau-Desvoidy, 1830 (Diptera, Tachinidae) has until now been represented by two species in Europe, G.viridis (Fallén, 1810) and G.magna Zimin, 1958. Two species are newly recorded from Finland and Sweden, Gymnochetalucida Zimin, 1958 and G.zhelochovtsevi Zimin, 1958, both previously known only from the Russian Far East and Japan. These four European species are redescribed and illustrated, including the first description of the female of G.zhelochovtsevi. A key is provided to seven of the eight described species of Palaearctic Gymnocheta. The holotype of G.viridis was examined and found to differ from the present concept of the species, instead matching the concept of the more recently described G.magna. In the interests of nomenclatural stability, the two names are maintained in their current usage pending a request to the International Commission on Zoological Nomenclature to replace the current holotype of G.viridis with a neotype that corresponds to the long-established concept of that species.},
}
@article {pmid34389656,
year = {2022},
author = {Pfeiffer, S and Herzmann, C and Gaede, KI and Kovacevic, D and Krauss-Etschmann, S and Schloter, M},
title = {Different responses of the oral, nasal and lung microbiomes to cigarette smoke.},
journal = {Thorax},
volume = {77},
number = {2},
pages = {191-195},
pmid = {34389656},
issn = {1468-3296},
mesh = {Humans ; Lung ; *Microbiota ; Prospective Studies ; *Smoke ; Smoking/adverse effects ; },
abstract = {To examine the role of smoking on the bacterial community composition of the upper and the lower respiratory tract, a monocentric, controlled prospective study was performed, including healthy smokers, ex-smokers and never-smokers. Smokers were further grouped according to their smoking history. Bacterial diversity was analysed using a molecular barcoding approach based on directly extracted DNA. Our study shows for the first time distinct bacterial response patterns in the upper and lower respiratory tract to cigarette smoking leading to a higher abundance of opportunistic pathogens. The clinical significance of these dysbioses for health needs to be further explored.},
}
@article {pmid34389172,
year = {2021},
author = {Raijada, D and Wac, K and Greisen, E and Rantanen, J and Genina, N},
title = {Integration of personalized drug delivery systems into digital health.},
journal = {Advanced drug delivery reviews},
volume = {176},
number = {},
pages = {113857},
doi = {10.1016/j.addr.2021.113857},
pmid = {34389172},
issn = {1872-8294},
mesh = {Digital Technology/*methods ; Dose-Response Relationship, Drug ; Drug Administration Schedule ; *Drug Delivery Systems ; Drug Liberation ; Humans ; Medication Adherence ; Pharmaceutical Preparations/administration &amp; dosage/chemistry ; Precision Medicine/*methods ; Technology, Pharmaceutical ; },
abstract = {Personalized drug delivery systems (PDDS), implying the patient-tailored dose, dosage form, frequency of administration and drug release kinetics, and digital health platforms for diagnosis and treatment monitoring, patient adherence, and traceability of drug products, are emerging scientific areas. Both fields are advancing at a fast pace. However, despite the strong complementary nature of these disciplines, there are only a few successful examples of merging these areas. Therefore, it is important and timely to combine PDDS with an increasing number of high-end digital health solutions to create an interactive feedback loop between the actual needs of each patient and the drug products. This review provides an overview of advanced design solutions for new products such as interactive personalized treatment that would interconnect the pharmaceutical and digital worlds. Furthermore, we discuss the recent advancements in the pharmaceutical supply chain (PSC) management and related limitations of the current mass production model. We summarize the current state of the art and envision future directions and potential development areas.},
}
@article {pmid34387804,
year = {2022},
author = {Haq, SAU and Mir, MA and Lone, SM and Banoo, A and Shafi, F and Mir, SA and Bhat, JIA and Rashid, R and Wani, SH and Masoodi, TH and Khan, MN and Nehvi, FA and Masoodi, KZ},
title = {Explicating genetic diversity based on ITS characterization and determination of antioxidant potential in sea buckthorn (Hippophae spp.).},
journal = {Molecular biology reports},
volume = {49},
number = {6},
pages = {5229-5240},
pmid = {34387804},
issn = {1573-4978},
mesh = {Animals ; Antioxidants/analysis ; Fruit/chemistry ; Genetic Variation ; *Hippophae/chemistry/genetics ; Phylogeny ; Plant Extracts/chemistry ; },
abstract = {BACKGROUND: Sea buckthorn (Hippophae) is in the focus of interest mainly for its positive effects on health of both human and animal organisms. Due to the similarities in vegetative morphology, Hippophae species are often misidentified. Therefore, current study was focused on ITS based sequence characterization of sea buckthorn species and comparative biochemical evaluation for its antioxidant properties.<br><br>METHODS AND RESULTS: DNA was extracted from leaf samples. Primer pairs K-Lab-SeaBukRhm-ITS1F1- K-Lab-SeaBukRhm-ITS1R1 and K-LabSeaBukTib- ITSF1- K-LabSeaBukTib-ITSR1 were used for PCR amplification. The purified PCR products were outsourced for sequencing. Phylogenetic tree was constructed based on neighbor-joining (NJ) method. Moreover, comparison of antioxidant potential of leaves of two sea buckthorn species (Hippophae rhamnoides and Hippophae tibetana) collected from different regions of Ladakh viz., Stakna, Nubra, DRDO Leh and Zanskar was determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2-azino-bis (3- ethylbenzothiazoline-6-sulphonic acid) diammonium salt (ABTS), and Total antioxidant capacity (TAC) by phosphomolybdenum assays. The present investigation led to the differentiation of two sea buckthorn species viz., H. rhamnoides and H. tibetana based on Internal Transcribed Spacer (ITS) region. Moreover, significant variation was observed in antioxidant potential of leaf extracts collected from different regions.<br><br>CONCLUSIONS: Primary ITS sequence analysis was found to be powerful tool for identification and genetic diversity studies in sea buckthorn. Leaves of sea buckthorn have pronounced antioxidant properties and can be used in food, neutraceuticals and pharmaceutical industries etc. The current study will pave the way to discover small bioactive molecules responsible for antioxidant and anticancer properties in sea buckthorn.},
}
@article {pmid34386040,
year = {2021},
author = {Xu, J and Liu, C and Song, Y and Li, M},
title = {Comparative Analysis of the Chloroplast Genome for Four Pennisetum Species: Molecular Structure and Phylogenetic Relationships.},
journal = {Frontiers in genetics},
volume = {12},
number = {},
pages = {687844},
pmid = {34386040},
issn = {1664-8021},
abstract = {The genus Pennisetum (Poaceae) is both a forage crop and staple food crop in the tropics. In this study, we obtained chloroplast genome sequences of four species of Pennisetum (P. alopecuroides, P. clandestinum, P. glaucum, and P. polystachion) using Illumina sequencing. These chloroplast genomes have circular structures of 136,346-138,119 bp, including a large single-copy region (LSC, 79,380-81,186 bp), a small single-copy region (SSC, 12,212-12,409 bp), and a pair of inverted repeat regions (IRs, 22,284-22,372 bp). The overall GC content of these chloroplast genomes was 38.6-38.7%. The complete chloroplast genomes contained 110 different genes, including 76 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analysis of nucleotide variability identified nine intergenic spacer regions (psbA-matK, matK-rps16, trnN-trnT, trnY-trnD-psbM, petN-trnC, rbcL-psaI, petA-psbJ, psbE-petL, and rpl32-trnL), which may be used as potential DNA barcodes in future species identification and evolutionary analysis of Pennisetum. The phylogenetic analysis revealed a close relationship between P. polystachion and P. glaucum, followed by P. clandestinum and P. alopecuroides. The completed genomes of this study will help facilitate future research on the phylogenetic relationships and evolution of Pennisetum species.},
}
@article {pmid34386020,
year = {2021},
author = {Park, I and Song, JH and Yang, S and Chae, S and Moon, BC},
title = {Plastid Phylogenomic Data Offers Novel Insights Into the Taxonomic Status of the Trichosanthes kirilowii Complex (Cucurbitaceae) in South Korea.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {559511},
pmid = {34386020},
issn = {1664-462X},
abstract = {Trichosanthes is a genus in Cucurbitaceae comprising 90-100 species. Trichosanthes species are valuable as herbaceous medicinal ingredients. The fruits, seeds, and roots of species such as T. kirilowii and T. rosthornii are used in Korean traditional herbal medicines. T. rosthornii is only found in China, whereas in South Korea two varieties, T. kirilowii var. kirilowii and T. kirilowii var. japonica, are distributed. T. kirilowii var. kirilowii and T. kirilowii var. japonica have different fruit and leaf shapes but are recognized as belonging to the same species. Furthermore, although its members have herbal medicine applications, genomic information of the genus is still limited. The broad goals of this study were (i) to evaluate the taxonomy of Trichosanthes using plastid phylogenomic data and (ii) provide molecular markers specific for T. kirilowii var. kirilowii and T. kirilowii var. japonica, as these have differences in their pharmacological effectiveness and thus should not be confused and adulterated. Comparison of five Trichosanthes plastid genomes revealed locally divergent regions, mainly within intergenic spacer regions (trnT-UGU-trnL-UAA: marker name Tri, rrn4.5-rrn5: TRr, trnE-UUC-trnT-GGU: TRtt). Using these three markers as DNA-barcodes for important herbal medicine species in Trichosanthes, the identity of Trichosanthes material in commercial medicinal products in South Korea could be successfully determined. Phylogenetic analysis of the five Trichosanthes species revealed that the species are clustered within tribe Sicyoeae. T. kirilowii var. kirilowii and T. rosthornii formed a clade with T. kirilowii var. japonica as their sister group. As T. kirilowii in its current circumscription is paraphyletic and as the two varieties can be readily distinguished morphologically (e.g., in leaf shape), T. kirilowii var. japonica should be treated (again) as an independent species, T. japonica.},
}
@article {pmid34385880,
year = {2021},
author = {Hofmann, S and Masroor, R and Jablonski, D},
title = {Morphological and molecular data on tadpoles of the westernmost Himalayan spiny frog Allopaa hazarensis (Dubois &amp; Khan, 1979).},
journal = {ZooKeys},
volume = {1049},
number = {},
pages = {67-77},
pmid = {34385880},
issn = {1313-2989},
abstract = {Little is known about the life history, ecology, and distribution of the genus Allopaa (Dicroglossidae) and far less recent data are available about the larvae of this taxon. Here, we provide data on the larval stage of Allopaa hazarensis (Dubois &amp; Khan, 1979) from northern Pakistan based on the examination of three tadpoles. Specimens were obtained from two sites in Buner, Khyber Pakhtunkhwa province, Pakistan. Morphological and genetic analysis (mtDNA and nDNA) confirmed the identity of the tadpoles as A. hazarensis. Tadpole characterizations were illustrated by detailed imagery. Basic measurements and details on oral apparatus provide relevant taxonomic characteristics to distinguish the tadpoles of this species from other spiny frogs. The illustration and description of the tadpole of A. hazarensis should facilitate the identification of this species in the field.},
}
@article {pmid34385692,
year = {2022},
author = {Cardozo, N and Zhang, K and Doroschak, K and Nguyen, A and Siddiqui, Z and Bogard, N and Strauss, K and Ceze, L and Nivala, J},
title = {Multiplexed direct detection of barcoded protein reporters on a nanopore array.},
journal = {Nature biotechnology},
volume = {40},
number = {1},
pages = {42-46},
pmid = {34385692},
issn = {1546-1696},
support = {P30 CA015704/CA/NCI NIH HHS/United States ; },
mesh = {Bacteria ; Humans ; *Nanopores ; },
abstract = {Detection of specific proteins using nanopores is currently challenging. To address this challenge, we developed a collection of over twenty nanopore-addressable protein tags engineered as reporters (NanoporeTERs, or NTERs). NTERs are constructed with a secretion tag, folded domain and a nanopore-targeting C-terminal tail in which arbitrary peptide barcodes can be encoded. We demonstrate simultaneous detection of up to nine NTERs expressed in bacterial or human cells using MinION nanopore sensor arrays.},
}
@article {pmid34385576,
year = {2021},
author = {Lim, TS and Montague-Cardoso, K},
title = {Glycans housed by a bacteriophage enable rapid identification of glycan recognition patterns.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {976},
pmid = {34385576},
issn = {2399-3642},
mesh = {Animals ; Bacterial Proteins/chemistry/genetics/metabolism ; Bacteriophage M13/*chemistry/genetics/metabolism ; Mice ; Polysaccharides/*chemistry/genetics/metabolism ; },
abstract = {Glycans are a major composition of the cell surface that interacts with the surrounding environment. The ability to carry out glycan-binding profile studies has been mainly done with glycan arrays. However, glycan arrays are not easily adaptable for cell surface and in vivo glycan recognition assays. The Liquid Glycan Array (LiGA) reported recently by Sojitra et al. is an alternative glycan recognition assay that employs DNA barcoding, bioorthogonal ligation and deep sequencing technology. In LiGA, barcoded M13 virions are used to present glycans to allow rapid identification of binding partners based on sequence identity. This physical link between the glycan to the DNA sequence fitted in the phage genome provides an ingenious approach to maneuver glycan binding profile studies in various conditions.},
}
@article {pmid34384346,
year = {2021},
author = {Schäffer, AA and McVeigh, R and Robbertse, B and Schoch, CL and Johnston, A and Underwood, BA and Karsch-Mizrachi, I and Nawrocki, EP},
title = {Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation.},
journal = {BMC bioinformatics},
volume = {22},
number = {1},
pages = {400},
pmid = {34384346},
issn = {1471-2105},
mesh = {DNA, Ribosomal ; *Databases, Nucleic Acid ; Phylogeny ; *RNA, Ribosomal ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, RNA ; },
abstract = {BACKGROUND: The DNA sequences encoding ribosomal RNA genes (rRNAs) are commonly used as markers to identify species, including in metagenomics samples that may combine many organismal communities. The 16S small subunit ribosomal RNA (SSU rRNA) gene is typically used to identify bacterial and archaeal species. The nuclear 18S SSU rRNA gene, and 28S large subunit (LSU) rRNA gene have been used as DNA barcodes and for phylogenetic studies in different eukaryote taxonomic groups. Because of their popularity, the National Center for Biotechnology Information (NCBI) receives a disproportionate number of rRNA sequence submissions and BLAST queries. These sequences vary in quality, length, origin (nuclear, mitochondria, plastid), and organism source and can represent any region of the ribosomal cistron.<br><br>RESULTS: To improve the timely verification of quality, origin and loci boundaries, we developed Ribovore, a software package for sequence analysis of rRNA sequences. The ribotyper and ribosensor programs are used to validate incoming sequences of bacterial and archaeal SSU rRNA. The ribodbmaker program is used to create high-quality datasets of rRNAs from different taxonomic groups. Key algorithmic steps include comparing candidate sequences against rRNA sequence profile hidden Markov models (HMMs) and covariance models of rRNA sequence and secondary-structure conservation, as well as other tests. Nine freely available blastn rRNA databases created and maintained with Ribovore are used for checking incoming GenBank submissions and used by the blastn browser interface at NCBI. Since 2018, Ribovore has been used to analyze more than 50 million prokaryotic SSU rRNA sequences submitted to GenBank, and to select at least 10,435 fungal rRNA RefSeq records from type material of 8350 taxa.<br><br>CONCLUSION: Ribovore combines single-sequence and profile-based methods to improve GenBank processing and analysis of rRNA sequences. It is a standalone, portable, and extensible software package for the alignment, classification and validation of rRNA sequences. Researchers planning on submitting SSU rRNA sequences to GenBank are encouraged to download and use Ribovore to analyze their sequences prior to submission to determine which sequences are likely to be automatically accepted into GenBank.},
}
@article {pmid34383793,
year = {2021},
author = {Riengvirodkij, N and Roytrakul, S and Jaresitthikunchai, J and Phaonakrop, N and Charoenlappanich, S and Sakcamduang, W},
title = {Peptide barcodes in dogs affected by mitral valve disease with and without pulmonary hypertension using MALDI-TOF MS and LC-MS/MS.},
journal = {PloS one},
volume = {16},
number = {8},
pages = {e0255611},
pmid = {34383793},
issn = {1932-6203},
mesh = {Animals ; Case-Control Studies ; Chromatography, Liquid/*methods ; Dogs ; Female ; Heart Valve Diseases/*diagnosis/etiology/metabolism ; Hypertension, Pulmonary/*complications ; Male ; Peptide Fragments/*analysis/*metabolism ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; Tandem Mass Spectrometry/*methods ; },
abstract = {Mitral valve disease (MVD) is an important and most frequently acquired heart disease found in dogs. MVD is classified into different stages according to its severity. There is a challenge in differentiation between asymptomatic and symptomatic stages of the MVD. Moreover, pulmonary hypertension (PH) is a common complication in dogs affected by MVD. In clinical practice, there are also some limitations to identify PH. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a technique that can characterize specific patterns of peptide mass called peptide barcodes from various samples. Besides, in combination with liquid chromatography-tandem mass spectrometry (LC-MS/MS), potential peptide sequences associated with specific conditions could be identified. The present study aimed to use MALDI-TOF coupled with LC-MS/MS to characterize specific peptide barcodes and potential peptide candidates in serum samples from healthy dogs, dogs with MVD stage B (MVD B, asymptomatic stage), MVD stage C (MVD C, symptomatic stage), MVD stage B with PH (MVD B PH), and MVD stage C with PH (MVD C PH). Discrete clusters of the 5 sample groups were identified by 3D plot analysis. Peptide barcodes also revealed differences in peptide patterns among the 5 groups. Six amino acid sequences of peptide candidates at 1,225.60, 1,363.85, 1,688.71, 1789.52, 2020.21, and 2156.42 Da were identified as part of the proteins CLCN1, CLUL1, EDNRA, PTEN, SLC39A7, and CLN6, respectively. The network interactions between these discovered proteins and common cardiovascular drugs were also investigated. These results demonstrate that MALDI-TOF MS has promise as an optional technique for diagnosing dogs affected by asymptomatic and symptomatic stages of MVD with and without PH. Further studies are required to identify peptide barcodes in dogs with other diseases to create peptide barcode databases in veterinary medicine before using this method as a novel diagnostic tool in the future.},
}
@article {pmid34378141,
year = {2022},
author = {Liao, B and Hu, H and Xiao, S and Zhou, G and Sun, W and Chu, Y and Meng, X and Wei, J and Zhang, H and Xu, J and Chen, S},
title = {Global Pharmacopoeia Genome Database is an integrated and mineable genomic database for traditional medicines derived from eight international pharmacopoeias.},
journal = {Science China. Life sciences},
volume = {65},
number = {4},
pages = {809-817},
pmid = {34378141},
issn = {1869-1889},
mesh = {Herbal Medicine ; Humans ; Medicine, Traditional ; Phytotherapy ; *Plant Breeding ; *Plants, Medicinal/genetics ; },
abstract = {Genomic data have demonstrated considerable traction in accelerating contemporary studies in traditional medicine. However, the lack of a uniform format and dispersed storage limits the full potential of herb genomic data. In this study, we developed a Global Pharmacopoeia Genome Database (GPGD). The database contains 34,346 records for 903 herb species from eight global pharmacopoeias (Brazilian, Egyptian, European, Indian, Japanese, Korean, the Pharmacopoeia of the People's Republic of China, and U.S. Pharmacopoeia's Herbal Medicines Compendium). In particular, the GPGD contains 21,872 DNA barcodes from 867 species, 2,203 organelle genomes from 674 species, 55 whole genomes from 49 species, 534 genomic sequencing datasets from 366 species, and 9,682 transcriptome datasets from 350 species. Among the organelle genomes, 534 genomes from 366 species were newly generated in this study. Whole genomes, organelle genomes, genomic fragments, transcriptomes, and DNA barcodes were uniformly formatted and arranged by species. The GPGD is publicly accessible at http://www.gpgenome.com and serves as an essential resource for species identification, decomposition of biosynthetic pathways, and molecular-assisted breeding analysis. Thus, the database is an invaluable resource for future studies on herbal medicine safety, drug discovery, and the protection and rational use of herbal resources.},
}
@article {pmid34375357,
year = {2021},
author = {Kruger, MS and Kanzaki, N and Giblin-Davis, RM and Greeff, JM},
title = {Molecular diversity and relationships of fig associated nematodes from South Africa.},
journal = {PloS one},
volume = {16},
number = {8},
pages = {e0255451},
pmid = {34375357},
issn = {1932-6203},
mesh = {Animals ; *Ficus/parasitology/genetics ; South Africa ; *Phylogeny ; *Nematoda/genetics/classification ; Genetic Variation ; DNA Barcoding, Taxonomic ; },
abstract = {Nematodes of figs and fig wasps have received limited attention in Africa since their discovery in 1973. Sixteen of the 25 species of native South African figs were sampled for nematode associates using molecular barcoding with three loci (SSU, LSU D2-D3 and mtCOI) and fourteen (93%) were positive for at least one nematode species. Thirty-three putative species of nematodes were identified and classified according to the loci that were amplified and successfully sequenced. Fourteen putative nematode species were classified as Aphelenchoididae, of which nine were identified as Ficophagus from four species of Ficus from the section Galoglychia (i.e., five ex F. burkei including one shared with F. natalensis, one ex F. glumosa, one ex F. lutea, and one ex F. stuhlmannii) and one species ex F. sur from the section Sycomorus. In addition, there were four nematode species classified as Schistonchus s.s. from section Galoglychia figs (i.e., one ex F. burkei, two ex F. trichopoda, and one ex F. glumosa). There was also one species of Bursaphelenchus nematode recovered from F. sur from the section Sycomorus. Sixteen putative nematode species were classified as Diplogastridae, of which eight occurred in two clades of what is currently called Parasitodiplogaster with one (P. salicifoliae) being recovered from two Ficus species in the section Urostigma (F. salicifolia and F. ingens) and seven diplogastrids being associated with six species of Ficus from the section Galoglychia (i.e., two ex F. burkei including P. sycophilon, one ex F. stuhlmannii, one ex F. burtt-davyi, one ex F. trichopoda, one ex F. abutilifolia and one ex F. sansibarica). Three Acrostichus spp., a Teratodiplogaster and a Pristionchus species were recovered from F. sur and two Teratodiplogaster spp. and Pristionchus sycomori were recovered from F. sycomorus with both Ficus species belonging to the subgenus and section Sycomorus. The identities of the previously described T. martini and Parasitodiplogaster doliostoma (= Pristionchus sp. 35) are discussed. Lastly, there was a panagrolaimid identified from F. petersii.},
}
@article {pmid34375267,
year = {2021},
author = {Pérez-Burillo, J and Trobajo, R and Leira, M and Keck, F and Rimet, F and Sigró, J and Mann, DG},
title = {DNA metabarcoding reveals differences in distribution patterns and ecological preferences among genetic variants within some key freshwater diatom species.},
journal = {The Science of the total environment},
volume = {798},
number = {},
pages = {149029},
doi = {10.1016/j.scitotenv.2021.149029},
pmid = {34375267},
issn = {1879-1026},
mesh = {*DNA Barcoding, Taxonomic ; *Diatoms/genetics ; Ecosystem ; Environmental Monitoring ; Rivers ; },
abstract = {Our study evaluates differences in the distribution and ecology of genetic variants within several ecologically important diatom species that are also key for Water Framework Directive monitoring of European rivers: Fistulifera saprophila (FSAP), Achnanthidium minutissimum (ADMI), Nitzschia inconspicua (NINC) and Nitzschia soratensis (NSTS). We used DADA2 to infer amplicon sequence variants (ASVs) of a short rbcL barcode in 531 environmental samples from biomonitoring campaigns in Catalonia and France. ASVs within each species showed different distribution patterns. Threshold Indicator Taxa ANalysis revealed three ecological groupings of ASVs in both ADMI and FSAP. Two of these in each species were separated by opposite responses to calcium and conductivity. Boosted regression trees additionally showed that both variables greatly influenced the occurrence of these groupings. A third grouping in FSAP was characterized by a negative response to total organic carbon and hence was better represented in waters with higher ecological status than the other FSAP ASVs, contrasting with what is generally assumed for the species. In the two Nitzschia species, our analyses confirmed earlier studies: NINC preferred higher levels of calcium and conductivity. Our findings suggest that the broad ecological tolerance of some diatom species results from overlapping preferences among genetic variants, which individually show much more restricted preferences and distributions. This work shows the importance of studying the ecological preferences of genetic variants within species complexes, now possible with DNA metabarcoding. The results will help reveal and understand biogeographical distributions and facilitate the development of more accurate biological indexes for biomonitoring programmes.},
}
@article {pmid34373560,
year = {2021},
author = {Kolmann, MA and Kalacska, M and Lucanus, O and Sousa, L and Wainwright, D and Arroyo-Mora, JP and Andrade, MC},
title = {Hyperspectral data as a biodiversity screening tool can differentiate among diverse Neotropical fishes.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {16157},
pmid = {34373560},
issn = {2045-2322},
mesh = {Animals ; *Biodiversity ; Characiformes/*classification/genetics/metabolism ; DNA Barcoding, Taxonomic ; Hyperspectral Imaging/*methods ; Phenotype ; Pigmentation ; South America ; },
abstract = {Hyperspectral data encode information from electromagnetic radiation (i.e., color) of any object in the form of a spectral signature; these data can then be used to distinguish among materials or even map whole landscapes. Although hyperspectral data have been mostly used to study landscape ecology, floral diversity and many other applications in the natural sciences, we propose that spectral signatures can be used for rapid assessment of faunal biodiversity, akin to DNA barcoding and metabarcoding. We demonstrate that spectral signatures of individual, live fish specimens can accurately capture species and clade-level differences in fish coloration, specifically among piranhas and pacus (Family Serrasalmidae), fishes with a long history of taxonomic confusion. We analyzed 47 serrasalmid species and could distinguish spectra among different species and clades, with the method sensitive enough to document changes in fish coloration over ontogeny. Herbivorous pacu spectra were more like one another than they were to piranhas; however, our method also documented interspecific variation in pacus that corresponds to cryptic lineages. While spectra do not serve as an alternative to the collection of curated specimens, hyperspectral data of fishes in the field should help clarify which specimens might be unique or undescribed, complementing existing molecular and morphological techniques.},
}
@article {pmid34371019,
year = {2022},
author = {Landaverde-González, P and Osgood, J and Montenegro Quiñonez, CA and Monzón, V and Rodas, A and Monroy, C},
title = {The effect of landscape and human settlement on the genetic differentiation and presence of Paragonimus species in Mesoamerica.},
journal = {International journal for parasitology},
volume = {52},
number = {1},
pages = {13-21},
doi = {10.1016/j.ijpara.2021.05.010},
pmid = {34371019},
issn = {1879-0135},
mesh = {Animals ; *Foodborne Diseases ; Humans ; *Paragonimiasis/epidemiology/parasitology ; *Paragonimus/genetics ; Rivers ; },
abstract = {Foodborne diseases are a neglected research area, and despite the existence of many tools for diagnosis and genetic studies, very little is known about the effect of the landscape on the genetic diversity and presence of parasites. One of these foodborne disease is paragonimiasis, caused by trematodes of the genus Paragonimus, which is responsible for a high number of infections in humans and wild animals. The main Paragonimus sp reported in Mesoamerica is Paragonimus mexicanus, yet there are doubts about its correct identification as a unique species throughout the region. This, together with a lack of detailed knowledge about their ecology, evolution and differentiation, may complicate the implementation of control strategies across the Mesoamerican region. We had the goal of delimiting the species of P. mexicanus found throughout Mesoamerica and determining the effect of landscape and geology on the diversity and presence of the parasite. We found support for the delimitation of five genetic groups. The genetic differentiation among these groups was positively affected by elevation and the isolation of river basins, while the parasite's presence was affected negatively only by the presence of human settlements. These results suggest that areas with lower elevation, connected rivers basins, and an absence of human settlements have low genetic differentiation and high P. mexicanus presence, which may increase the risk of Paragonimus infection. These demonstrate the importance of accurate species delimitation and consideration of the effect of landscape on Paragonimus in the proposal of adequate control strategies. However, other landscape variables cannot be discarded, including temperature, rainfall regime, and spatial scale (local, landscape and regional). These additional variables were not explored here, and should be considered in future studies.},
}
@article {pmid34370086,
year = {2021},
author = {Urumarudappa, SKJ and Gogna, N and Newmaster, SG and Venkatarangaiah, K and Subramanyam, R and Saroja, SG and Gudasalamani, R and Dorai, K and Ramanan, US},
title = {Correction to: DNA barcoding and NMR spectroscopy-based assessment of species adulteration in the raw herbal trade of Saraca asoca (Roxb.) Willd, an important medicinal plant.},
journal = {International journal of legal medicine},
volume = {135},
number = {6},
pages = {2681},
doi = {10.1007/s00414-021-02669-x},
pmid = {34370086},
issn = {1437-1596},
}
@article {pmid34368889,
year = {2021},
author = {de Oliveira Bustamante, F and do Nascimento, TH and Montenegro, C and Dias, S and do Vale Martins, L and Braz, GT and Benko-Iseppon, AM and Jiang, J and Pedrosa-Harand, A and Brasileiro-Vidal, AC},
title = {Oligo-FISH barcode in beans: a new chromosome identification system.},
journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik},
volume = {134},
number = {11},
pages = {3675-3686},
pmid = {34368889},
issn = {1432-2242},
support = {313527/2017-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 310804/2017-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 421968/2018-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 433931/2018-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 442019/2019-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; APQ-0390-2.02/19//Funda&#xe7;&#xe3;o de Amparo &#xe0; Ci&#xea;ncia e Tecnologia do Estado de Pernambuco/ ; },
mesh = {Centromere ; Chromosomes, Plant/genetics ; DNA Barcoding, Taxonomic/*methods ; *In Situ Hybridization, Fluorescence ; Karyotyping/*methods ; Molecular Probes ; Phaseolus/*genetics ; Vigna/*genetics ; },
abstract = {An Oligo-FISH barcode system was developed for two model legumes, allowing the identification of all cowpea and common bean chromosomes in a single FISH experiment, and revealing new chromosome rearrangements. The FISH barcode system emerges as an effective tool to understand the chromosome evolution of economically important legumes and their related species. Current status on plant cytogenetic and cytogenomic research has allowed the selection and design of oligo-specific probes to individually identify each chromosome of the karyotype in a target species. Here, we developed the first chromosome identification system for legumes based on oligo-FISH barcode probes. We selected conserved genomic regions between Vigna unguiculata (Vu, cowpea) and Phaseolus vulgaris (Pv, common bean) (diverged ~ 9.7-15 Mya), using cowpea as a reference, to produce a unique barcode pattern for each species. We combined our oligo-FISH barcode pattern with a set of previously developed FISH probes based on BACs and ribosomal DNA sequences. In addition, we integrated our FISH maps with genome sequence data. Based on this integrated analysis, we confirmed two translocation events (involving chromosomes 1, 5, and 8; and chromosomes 2 and 3) between both species. The application of the oligo-based probes allowed us to demonstrate the participation of chromosome 5 in the translocation complex for the first time. Additionally, we detailed a pericentric inversion on chromosome 4 and identified a new paracentric inversion on chromosome 10. We also detected centromere repositioning associated with chromosomes 2, 3, 5, 7, and 9, confirming previous results for chromosomes 2 and 3. This first barcode system for legumes can be applied for karyotyping other Phaseolinae species, especially non-model, orphan crop species lacking genomic assemblies and cytogenetic maps, expanding our understanding of the chromosome evolution and genome organization of this economically important legume group.},
}
@article {pmid34368852,
year = {2021},
author = {Liu, H and Yin, H and Li, G and Li, J and Wang, X},
title = {Aperture: alignment-free detection of structural variations and viral integrations in circulating tumor DNA.},
journal = {Briefings in bioinformatics},
volume = {22},
number = {6},
pages = {},
doi = {10.1093/bib/bbab290},
pmid = {34368852},
issn = {1477-4054},
mesh = {Algorithms ; Circulating Tumor DNA/*chemistry ; Humans ; Neoplasms/blood/genetics ; *Nucleic Acid Conformation ; *Virus Integration ; },
abstract = {The identification of structural variations (SVs) and viral integrations in circulating tumor DNA (ctDNA) is a key step in precision oncology that may assist clinicians in treatment selection and monitoring. However, due to the short fragment size of ctDNA, it is challenging to accurately detect low-frequency SVs or SVs involving complex junctions in ctDNA sequencing data. Here, we describe Aperture, a new fast SV caller that applies a unique strategy of $k$-mer-based searching, binary label-based breakpoint detection and candidate clustering to detect SVs and viral integrations with high sensitivity, especially when junctions span repetitive regions. Aperture also employs a barcode-based filter to ensure specificity. Compared with existing methods, Aperture exhibits superior sensitivity and specificity in simulated, reference and real data tests, especially at low dilutions. Additionally, Aperture is able to predict sites of viral integration and identify complex SVs involving novel insertions and repetitive sequences in real patient data. Aperture is freely available at https://github.com/liuhc8/Aperture.},
}
@article {pmid34368447,
year = {2021},
author = {Hebbar, P and Anand, A and K V, G},
title = {DNA barcoding indicates the range extension in an endemic frog Nyctibatrachus jog, from the Western Ghats, India.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {6},
number = {9},
pages = {2468-2474},
pmid = {34368447},
issn = {2380-2359},
abstract = {The frogs of genus Nyctibatrachus from the Western Ghats are endemic, with some taxa showing a narrow distribution range. Nyctibatrachus jog was known only from the type locality, Jog falls from Sharavathi river basin suggesting a restricted distribution. In this study, using DNA barcoding, we studied the distribution patterns of N. jog by sampling multiple river basins. 16S rRNA and Cytochrome b genes were used to distinguish N. jog from its congeners as well as to infer intra-species relationships. The results from the 16S rRNA gene showed 99% similarity of the collected individuals with the type specimen from Jog Falls confirming the identity of N. jog. The results indicate that N. jog has wide distribution extending its range in multiple river basins in the Western Ghats, India. This study also provides the Area of Occurrence and Extent of Occurrence of N. jog which could help in developing strategies for its conservation.},
}
@article {pmid34367592,
year = {2021},
author = {Zhou, CJ and Feng, MX and Tang, YT and Yang, CX and Meng, XL and Nie, GX},
title = {Species diversity of freshwater shrimp in Henan Province, China, based on morphological characters and COI mitochondrial gene.},
journal = {Ecology and evolution},
volume = {11},
number = {15},
pages = {10502-10514},
pmid = {34367592},
issn = {2045-7758},
abstract = {Freshwater shrimp are a rich species group, with a long and problematic taxonomic history attributed to their wide distribution and similar morphological characteristics. Shrimp diversity and species identification are important cornerstones for fisheries management. However, identification based on morphological characteristics is a difficult task for a nonspecialist. Abundant freshwater shrimp species are distributed in the waters of Henan Province, but investigations of freshwater shrimp are limited in this region, especially concerning molecular features. Here, we combined morphology and DNA barcodes to reveal the species diversity of freshwater shrimp in Henan province. A total of 1,200 freshwater shrimp samples were collected from 46 sampling sites, and 222 samples were chosen for further microscopic examination and molecular delimitation. We used tree-based methods (NJ, ML, and bPTP) and distance-based methods (estimation of the paired genetic distances and ABGD) to delimit species. The results showed that there were nine morphospecies based on morphological characteristics; all could effectively be defined by molecular methods, among which bPTP and ABGD defined 13 and 8 MOTUs, respectively. The estimation of the paired genetic distances of K2P and the p-distances had similar results. Mean K2P distances and p-distances within species were both equal to 1.2%. The maximum intraspecific genetic distances of all species were less than 2%, with the exception of Palaemon modestus and M. maculatum. Various analyses have shown that P. modestus and M. maculatum have a large genetic differentiation, which may indicate the existence of cryptic species. By contrast, DNA barcoding could unambiguously discriminate 13 species and detect cryptic diversity. Our results demonstrate the high efficiency of DNA barcoding to delimit freshwater shrimp diversity and detect the presence of cryptic species.},
}
@article {pmid34367578,
year = {2021},
author = {Lukic, D and Eberle, J and Thormann, J and Holzschuh, C and Ahrens, D},
title = {Excluding spatial sampling bias does not eliminate oversplitting in DNA-based species delimitation analyses.},
journal = {Ecology and evolution},
volume = {11},
number = {15},
pages = {10327-10337},
pmid = {34367578},
issn = {2045-7758},
abstract = {DNA barcoding and DNA-based species delimitation are major tools in DNA taxonomy. Sampling has been a central debate in this context, because the geographical composition of samples affects the accuracy and performance of DNA barcoding. Performance of complex DNA-based species delimitation is to be tested under simpler conditions in absence of geographic sampling bias. Here, we present an empirical dataset sampled from a single locality in a Southeast-Asian biodiversity hotspot (Laos: Phou Pan mountain). We investigate the performance of various species delimitation approaches on a megadiverse assemblage of herbivorous chafer beetles (Coleoptera: Scarabaeidae) to infer whether species delimitation suffers in the same way from exaggerate infraspecific variation despite the lack of geographic genetic variation that led to inconsistencies between entities from DNA-based and morphology-based species inference in previous studies. For this purpose, a 658 bp fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) was analyzed for a total of 186 individuals of 56 morphospecies. Tree-based and distance-based species delimitation methods were used. All approaches showed a rather limited match ratio (max. 77%) with morphospecies. Poisson tree process (PTP) and statistical parsimony network analysis (TCS) prevailingly over-splitted morphospecies, while 3% clustering and Automatic Barcode Gap Discovery (ABGD) also lumped several species into one entity. ABGD revealed the highest congruence between molecular operational taxonomic units (MOTUs) and morphospecies. Disagreements between morphospecies and MOTUs have to be explained by historically acquired geographic genetic differentiation, incomplete lineage sorting, and hybridization. The study once again highlights how important morphology still is in order to correctly interpret the results of molecular species delimitation.},
}
@article {pmid34367512,
year = {2021},
author = {Suriani, C and Prasetya, E and Harsono, T and Manurung, J and Prakasa, H and Handayani, D and Jannah, M and Rachmawati, Y},
title = {DNA Barcoding of Andaliman (Zanthoxylum acanthopodium DC) from North Sumatra Province of Indonesia Using Maturase K Gene.},
journal = {Tropical life sciences research},
volume = {32},
number = {2},
pages = {15-28},
pmid = {34367512},
issn = {1985-3718},
abstract = {Andaliman (Zanthoxylum acanthopodium DC) is a native plant of North Sumatra province. Zanthoxylum acanthopodium is a member of Rutaceae family widely found in northern Sumatra, Indonesia. The aim of this study was to barcode Z. acanthopodium in North Sumatra province, Indonesia based on cpDNA maturase K (matK). Samples were collected in seven localities across six regions of North Sumatra province. Phylogenetic analysis was conducted using Maximum Likelihood method. The results of phylogenetic analysis indicate that Z. acanthopodium is a monophyletic group that is derived from a common ancestor. The results of the phylogenetic tree construction show that there is a grouping of accession between Z. acanthopodium species separate from other species in the Zanthoxylum genus as well as those of the Rutaceae family. The results showed that cpDNA matK marker can effectively be used as DNA barcoding to identify Z. acanthopodium.},
}
@article {pmid34362980,
year = {2021},
author = {Chen, Y and Zhu, X and Loukopoulos, P and Weston, LA and Albrecht, DE and Quinn, JC},
title = {Genotypic identification of Panicum spp. in New South Wales, Australia using DNA barcoding.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {16055},
pmid = {34362980},
issn = {2045-2322},
mesh = {Crops, Agricultural/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/analysis/*genetics ; Genotype ; Panicum/*classification/*genetics ; *Phylogeny ; },
abstract = {Australia has over 30 Panicum spp. (panic grass) including several non-native species that cause crop and pasture loss and hepatogenous photosensitisation in livestock. It is critical to correctly identify them at the species level to facilitate the development of appropriate management strategies for efficacious control of Panicum grasses in crops, fallows and pastures. Currently, identification of Panicum spp. relies on morphological examination of the reproductive structures, but this approach is only useful for flowering specimens and requires significant taxonomic expertise. To overcome this limitation, we used multi-locus DNA barcoding for the identification of ten selected Panicum spp. found in Australia. With the exception of P. buncei, other native Australian Panicum were genetically separated at the species level and distinguished from non-native species. One nuclear (ITS) and two chloroplast regions (matK and trnL intron-trnF) were identified with varying facility for DNA barcode separation of the Panicum species. Concatenation of sequences from ITS, matK and trnL intron-trnF regions provided clear separation of eight regionally collected species, with a maximum intraspecific distance of 0.22% and minimum interspecific distance of 0.33%. Two of three non-native Panicum species exhibited a smaller genome size compared to native species evaluated, and we speculate that this may be associated with biological advantages impacting invasion of non-native Panicum species in novel locations. We conclude that multi-locus DNA barcoding, in combination with traditional taxonomic identification, provides an accurate and cost-effective adjunctive tool for further distinguishing Panicum spp. at the species level.},
}
@article {pmid34362388,
year = {2021},
author = {Lee, DE and Kim, HC and Chong, ST and Klein, TA and Kim, JH and Lee, SH},
title = {Prediction of species composition ratios in pooled specimens of the Anopheles Hyrcanus group using quantitative sequencing.},
journal = {Malaria journal},
volume = {20},
number = {1},
pages = {338},
pmid = {34362388},
issn = {1475-2875},
support = {HG18C0046//Government-wide R&amp;D Fund project for infectious disease research (GFID), Republic of Korea/ ; #P0131-20-ME-03//armed forces health surveillance branch/ ; Brain Korea 21 Plus//Brain Korea 21 Plus/ ; },
mesh = {Animals ; Anopheles/classification/genetics/*parasitology ; Cost-Benefit Analysis ; DNA/genetics/isolation &amp; purification ; Electron Transport Complex IV/genetics ; Linear Models ; Mosquito Vectors/classification/genetics/*parasitology ; Phylogeny ; RNA, Ribosomal/genetics ; Republic of Korea ; Sequence Alignment ; Species Specificity ; },
abstract = {BACKGROUND: Plasmodium vivax is transmitted by members of the Anopheles Hyrcanus Group that includes six species in the Republic of Korea: Anopheles sinensis sensu stricto (s.s.), Anopheles pullus, Anopheles kleini, Anopheles belenrae, Anopheles lesteri, and Anopheles sineroides. Individual Anopheles species within the Hyrcanus Group demonstrate differences in their geographical distributions, vector competence and insecticide resistance, making it crucial for accurate species identification. Conventional species identification conducted using individual genotyping (or barcoding) based on species-specific molecular markers requires extensive time commitment and financial resources.<br><br>RESULTS: A population-based quantitative sequencing (QS) protocol developed in this study provided a rapid estimate of species composition ratios among pooled mosquitoes as a cost-effective alternative to individual genotyping. This can be accomplished by using species- or group-specific nucleotide sequences of the mitochondrial cytochrome C oxidase subunit I (COI) and the ribosomal RNA internal transcribed spacer 2 (ITS2) region as species identification alleles in a two-step prediction protocol. Standard genomic DNA fragments of COI and ITS2 genes were amplified from each Anopheles species using group-specific universal primer sets. Following sequencing of the COI or ITS2 amplicons generated from sets of standard DNA mixtures, equations were generated via linear regression to predict species-specific nucleotide sequence frequencies at different positions. Species composition ratios between An. sineroides, An. pullus and An. lesteri were estimated from QS of the COI amplicons based on the mC.260A, mC.122C and mC.525C alleles at the first step, followed by the prediction of species composition ratios between An. sinensis, An. kleini and An. belenrae based on QS of the ITS2 amplicons using the rI.370G and rI.389T alleles. The COI copy number was not significantly different between species, suggesting the reliability of COI-based prediction. In contrast, ITS2 showed a slightly but significantly higher copy number in An. belenrae, requiring an adjustment of its predicted composition ratio. A blind test proved that predicted species composition ratios either from pooled DNA specimens or pooled mosquito specimens were not statistically different from the actual values, demonstrating that the QS-based prediction is accurate and reliable.<br><br>CONCLUSIONS: This two-step prediction protocol will facilitate rapid estimation of the species composition ratios in field-collected Anopheles Hyrcanus Group populations and is particularly useful for studying the vector ecology of Anopheles population and epidemiology of malaria.},
}
@article {pmid34359514,
year = {2021},
author = {Fanelli, V and Mascio, I and Miazzi, MM and Savoia, MA and De Giovanni, C and Montemurro, C},
title = {Molecular Approaches to Agri-Food Traceability and Authentication: An Updated Review.},
journal = {Foods (Basel, Switzerland)},
volume = {10},
number = {7},
pages = {},
pmid = {34359514},
issn = {2304-8158},
abstract = {In the last decades, the demand for molecular tools for authenticating and tracing agri-food products has significantly increased. Food safety and quality have gained an increased interest for consumers, producers, and retailers, therefore, the availability of analytical methods for the determination of food authenticity and the detection of major adulterations takes on a fundamental role. Among the different molecular approaches, some techniques such as the molecular markers-based methods are well established, while some innovative approaches such as isothermal amplification-based methods and DNA metabarcoding have only recently found application in the agri-food sector. In this review, we provide an overview of the most widely used molecular techniques for fresh and processed agri-food authentication and traceability, showing their recent advances and applications and discussing their main advantages and limitations. The application of these techniques to agri-food traceability and authentication can contribute a great deal to the reassurance of consumers in terms of transparency and food safety and may allow producers and retailers to adequately promote their products.},
}
@article {pmid34359446,
year = {2021},
author = {Muñoz-Tebar, N and González-Navarro, EJ and López-Díaz, TM and Santos, JA and Elguea-Culebras, GO and García-Martínez, MM and Molina, A and Carmona, M and Berruga, MI},
title = {Biological Activity of Extracts from Aromatic Plants as Control Agents against Spoilage Molds Isolated from Sheep Cheese.},
journal = {Foods (Basel, Switzerland)},
volume = {10},
number = {7},
pages = {},
pmid = {34359446},
issn = {2304-8158},
support = {RTA2015-00018-C03-02//Instituto Nacional de Investigaci&#xf3;n y Tecnolog&#xed;a Agraria y Alimentaria/ ; Nuria Mu&#xf1;oz-Tebar grant UCLM/ESF//European Social Fund/ ; Ortiz de Elguea-Culebras G grant JCCM/ESF//European Social Fund/ ; RyC-2014-16307//Ministerio de Ciencia e Innovaci&#xf3;n/ ; },
abstract = {The aim of this work was to assess the antifungal and antioxidant activity of essential oils and ethanolic extracts from distilled solid by-products from aromatic plants (Artemisia&amp;nbsp;dracunculus, Hyssopus&amp;nbsp;officinalis, Lavandula&amp;nbsp;stoechas, Origanum&amp;nbsp;vulgare and Satureja&amp;nbsp;montana) against 14 fungi strains isolated from sheep cheese and identified at species level using DNA barcoding based on β-tubulin sequence analysis. In addition, capacity of fungi to produce ochratoxin A, patulin, cyclopiazonic acid and sterigmatocystin was analyzed. Of the isolates, 85.7% belonged to Penicillium (P. commune/biforme, P. crustosum) and 14.3% to Aspergillus (A. puulaauensis and A. jensenii), the first time that these Aspergillus species have been found in sheep's cheese. All P. commune isolates were producers of cyclopiazonic acid, and the two Aspergillus strains produced sterigmatocystin, but the others did not produce any tested mycotoxin. Among the essential oils tested, oregano, savory and tarragon had a significant antifungal activity against all the isolated strains, but no ethanolic extract showed antifungal activity. By contrast, ethanolic extracts showed great potential as antioxidants. The identification of new molds in cheese will help the dairy industry to know more about those molds affecting the sector, and the use of aromatic plants in the control of fungal spoilage could be a suitable alternative to chemical preservatives used in the agri-food industry.},
}
@article {pmid34356944,
year = {2021},
author = {Lahiri, A and Murphy, BR and Hodkinson, TR},
title = {Assessing Genotypic and Environmental Effects on Endophyte Communities of Fraxinus (Ash) Using Culture Dependent and Independent DNA Sequencing.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {7},
number = {7},
pages = {},
pmid = {34356944},
issn = {2309-608X},
support = {2019R578//Department of Agriculture, Food and the Marine, Ireland/ ; },
abstract = {Fraxinus excelsior populations are in decline due to the ash dieback disease Hymenoscyphus fraxineus. It is important to understand genotypic and environmental effects on its fungal microbiome to develop disease management strategies. To do this, we used culture dependent and culture independent approaches to characterize endophyte material from contrasting ash provenances, environments, and tissues (leaves, roots, seeds). Endophytes were isolated and identified using nrITS, LSU, or tef DNA loci in the culture dependent assessments, which were mostly Ascomycota and assigned to 37 families. Few taxa were shared between roots and leaves. The culture independent approach used high throughput sequencing (HTS) of nrITS amplicons directly from plant DNA and detected 35 families. Large differences were found in OTU diversity and community composition estimated by the contrasting approaches and these data need to be combined for estimations of the core endophyte communities. Species richness and Shannon index values were highest for the leaf material and the French population. Few species were shared between seed and leaf tissue. PCoA and NMDS of the HTS data showed that seed and leaf microbiome communities were highly distinct and that there was a strong influence of Fraxinus species identity on their fungal community composition. The results will facilitate a better understanding of ash fungal ecology and are a step toward identifying microbial biocontrol systems to minimize the impact of the disease.},
}
@article {pmid34356524,
year = {2021},
author = {Osorio-Pulgarin, MI and Higuera, A and Beltran-Álzate, JC and Sánchez-Jiménez, M and Ramírez, JD},
title = {Epidemiological and Molecular Characterization of Blastocystis Infection in Children Attending Daycare Centers in Medellín, Colombia.},
journal = {Biology},
volume = {10},
number = {7},
pages = {},
pmid = {34356524},
issn = {2079-7737},
support = {130-2016//Departamento Administrativo de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n (COLCIENCIAS)/ ; },
abstract = {BACKGROUND: The present study aims to perform an epidemiological and molecular characterization of Blastocystis infection in a child population attending daycare centers of Medellín, Colombia.<br><br>METHODS: A total of 265 children aged 0-5 years were enrolled in five children's centers in urban sectors of Medell&#xed;n, northwestern Colombia. Stool samples were taken to identify intestinal parasites by direct examination, Ritchie-Frick concentration, and molecular identification of Blastocystis by conventional PCR and subtype (ST) identification by PCR barcoding with subsequent phylogenetic reconstruction. Kappa index was calculated to evaluate the agreement between microscopy and PCR for the diagnosis of Blastocystis.<br><br>RESULTS: The prevalence of intestinal protozoa was 36.6% (97/265), with Blastocystis as the most frequent parasitic protozoan at 15.8% (42/265), followed by Giardia intestinalis at 15.5% (41/265) and Endolimax nana at 15.1% (40/265). The prevalence of Blastocystis by PCR was 53.2% (141/265), the subtypes identified were ST3 at 30.5% (18/59), ST2 at 23.7% (14/59), ST1 at 20.3% (12/59), and with less frequency, ST4 at 5.1% (3/59), ST6 at 1.7% (1/59) and ST16 at 15.3% (9/59) allele 162.<br><br>CONCLUSION: This study provides the first genetic characterization of Blastocystis subtypes circulating in a population of Medell&#xed;n, Colombia, and also updates the epidemiology of Blastocystis subtypes in the world with the first identification of ST16 in humans.},
}
@article {pmid34355716,
year = {2021},
author = {Cai, Q and Wang, R and Qiao, Z and Yang, W},
title = {Single-digit Salmonella detection with the naked eye using bio-barcode immunoassay coupled with recombinase polymerase amplification and a CRISPR-Cas12a system.},
journal = {The Analyst},
volume = {146},
number = {17},
pages = {5271-5279},
doi = {10.1039/d1an00717c},
pmid = {34355716},
issn = {1364-5528},
mesh = {CRISPR-Cas Systems ; Gold ; Immunoassay ; *Metal Nanoparticles ; Nucleic Acid Amplification Techniques ; *Recombinases/genetics ; Salmonella typhimurium/genetics ; },
abstract = {The ability to visually detect low numbers of Salmonella in food samples is highly valuable but remains a challenge. Here we present a novel platform for ultrasensitive and visual detection of Salmonella Typhimurium by integrating the bio-barcode immunoassay (BCA), recombinase polymerase amplification (RPA), and CRISPR-Cas12a cleavage in a single reaction system (termed as BCA-RPA-Cas12a). In the system, the target bacteria were separated by immunomagnetic nanoparticles and labeled with numerous barcode AuNPs, which carry abundant bio-barcode DNA molecules to amplify the signal. Afterwards, the bio-barcode DNA molecules were amplified by RPA and subsequently triggered the cleavage activity of Cas12a to generate the fluorescence signal. Due to this triplex signal amplification, the BCA-RPA-Cas12a system can selectively detect Salmonella Typhimurium at the single-digit level with the naked eye under blue light within 60 min. Meanwhile, this novel platform was successfully applied to detect Salmonella Typhimurium in spiked milk samples with a similar sensitivity and satisfactory recovery, indicating its potential application in real samples. Furthermore, in virtue of the versatility of the antibody in the stage of BCA, the BCA-RPA-Cas12a system can be extended to further application in other bacteria detection and food safety monitoring.},
}
@article {pmid34354295,
year = {2021},
author = {Hwang, B and Lee, DS and Tamaki, W and Sun, Y and Ogorodnikov, A and Hartoularos, GC and Winters, A and Yeung, BZ and Nazor, KL and Song, YS and Chow, ED and Spitzer, MH and Ye, CJ},
title = {SCITO-seq: single-cell combinatorial indexed cytometry sequencing.},
journal = {Nature methods},
volume = {18},
number = {8},
pages = {903-911},
pmid = {34354295},
issn = {1548-7105},
support = {P30 DK063720/DK/NIDDK NIH HHS/United States ; DP5 OD023056/OD/NIH HHS/United States ; T32 EB009383/EB/NIBIB NIH HHS/United States ; P30 AR070155/AR/NIAMS NIH HHS/United States ; R01 AR071522/AR/NIAMS NIH HHS/United States ; S10 OD018040/OD/NIH HHS/United States ; T32 GM007175/GM/NIGMS NIH HHS/United States ; R35 GM134922/GM/NIGMS NIH HHS/United States ; S10 OD021822/OD/NIH HHS/United States ; R01 AI136972/AI/NIAID NIH HHS/United States ; R01 HG011239/HG/NHGRI NIH HHS/United States ; },
mesh = {Case-Control Studies ; Flow Cytometry/*methods ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Microfluidics/*methods ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis/*methods ; *Transcriptome ; },
abstract = {The development of DNA-barcoded antibodies to tag cell surface molecules has enabled the use of droplet-based single-cell sequencing (dsc-seq) to profile protein abundances from thousands of cells simultaneously. As compared to flow and mass cytometry, the high per cell cost of current dsc-seq-based workflows precludes their use in clinical applications and large-scale pooled screens. Here, we introduce SCITO-seq, a workflow that uses splint oligonucleotides (oligos) to enable combinatorially indexed dsc-seq of DNA-barcoded antibodies from over 10[5] cells per reaction using commercial microfluidics. By encoding sample barcodes into splint oligos, we demonstrate that multiplexed SCITO-seq produces reproducible estimates of cellular composition and surface protein expression comparable to those from mass cytometry. We further demonstrate two modified splint oligo designs that extend SCITO-seq to achieve compatibility with commercial DNA-barcoded antibodies and simultaneous expression profiling of the transcriptome and surface proteins from the same cell. These results demonstrate SCITO-seq as a flexible and ultra-high-throughput platform for sequencing-based single-cell protein and multimodal profiling.},
}
@article {pmid34354202,
year = {2021},
author = {Stüder, F and Petit, JL and Engelen, S and Mendoza-Parra, MA},
title = {Real-time SARS-CoV-2 diagnostic and variants tracking over multiple candidates using nanopore DNA sequencing.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {15869},
pmid = {34354202},
issn = {2045-2322},
mesh = {COVID-19/*diagnosis/virology ; COVID-19 Nucleic Acid Testing/instrumentation/methods ; Genome, Viral ; Humans ; Nanopores ; RNA, Viral/genetics ; SARS-CoV-2/*genetics ; Sequence Analysis, DNA/instrumentation/*methods ; Spike Glycoprotein, Coronavirus/genetics ; },
abstract = {Since December 2019, a novel coronavirus responsible for a severe acute respiratory syndrome (SARS-CoV-2) is accountable for a major pandemic situation. The emergence of the B.1.1.7 strain, as a highly transmissible variant has accelerated the world-wide interest in tracking SARS-CoV-2 variants' occurrence. Similarly, other extremely infectious variants, were described and further others are expected to be discovered due to the long period of time on which the pandemic situation is lasting. All described SARS-CoV-2 variants present several mutations within the gene encoding the Spike protein, involved in host receptor recognition and entry into the cell. Hence, instead of sequencing the whole viral genome for variants' tracking, herein we propose to focus on the SPIKE region to increase the number of candidate samples to screen at once; an essential aspect to accelerate diagnostics, but also variants' emergence/progression surveillance. This proof of concept study accomplishes both at once, population-scale diagnostics and variants' tracking. This strategy relies on (1) the use of the portable MinION DNA sequencer; (2) a DNA barcoding and a SPIKE gene-centered variant's tracking, increasing the number of candidates per assay; and (3) a real-time diagnostics and variant's tracking monitoring thanks to our software RETIVAD. This strategy represents an optimal solution for addressing the current needs on SARS-CoV-2 progression surveillance, notably due to its affordable implementation, allowing its implantation even in remote places over the world.},
}
@article {pmid34354125,
year = {2021},
author = {Young, MR and deWaard, JR and Hebert, PDN},
title = {DNA barcodes enable higher taxonomic assignments in the Acari.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {15922},
pmid = {34354125},
issn = {2045-2322},
mesh = {Acari/*genetics ; Animals ; Biodiversity ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; Ecosystem ; Electron Transport Complex IV/*genetics ; Gene Library ; Genetic Techniques ; Mites/genetics ; },
abstract = {Although mites (Acari) are abundant in many terrestrial and freshwater ecosystems, their diversity is poorly understood. Since most mite species can be distinguished by variation in the DNA barcode region of cytochrome c oxidase I, the Barcode Index Number (BIN) system provides a reliable species proxy that facilitates large-scale surveys. Such analysis reveals many new BINs that can only be identified as Acari until they are examined by a taxonomic specialist. This study demonstrates that the Barcode of Life Datasystem's identification engine (BOLD ID) generally delivers correct ordinal and family assignments from both full-length DNA barcodes and their truncated versions gathered in metabarcoding studies. This result was demonstrated by examining BOLD ID's capacity to assign 7021 mite BINs to their correct order (4) and family (189). Identification success improved with sequence length and taxon coverage but varied among orders indicating the need for lineage-specific thresholds. A strict sequence similarity threshold (86.6%) prevented all ordinal misassignments and allowed the identification of 78.6% of the 7021 BINs. However, higher thresholds were required to eliminate family misassignments for Sarcoptiformes (89.9%), and Trombidiformes (91.4%), consequently reducing the proportion of BINs identified to 68.6%. Lineages with low barcode coverage in the reference library should be prioritized for barcode library expansion to improve assignment success.},
}
@article {pmid34353338,
year = {2021},
author = {Zhou, GR and Liao, BS and Li, QS and Xu, J and Chen, SL},
title = {Establishing a genomic database for the medicinal plants in the Brazilian Pharmacopoeia.},
journal = {Chinese medicine},
volume = {16},
number = {1},
pages = {71},
pmid = {34353338},
issn = {1749-8546},
abstract = {BACKGROUND: Brazil is exceptionally abundant in medicinal plant resources and has a rich ethnopharmacological history. Brazilian Pharmacopoeia (BP) acts as a national standard that regulates drug quality and has six published editions. Recent genomic approaches have led to a resurgence of interest in herbal drugs. The genomic data of plants has been used for pharmaceutical applications, protecting natural resources, and efficiently regulating the market. However, there are few genomic databases specifically for medicinal plants, and the establishment of a database that focuses on the herbs contained in the BP is urgently required.<br><br>METHODS: The medicinal plant species included in each edition of the BP were analyzed to understand the evolution of the Brazilian herbal drugs. The data of 82 plants in the BP were collected and categorized into four sections: DNA barcodes, super-barcodes, genomes, and sequencing data. A typical web server architecture pattern was used to build the database and website. Furthermore, the cp-Gs of the Aloe genus in the database were analyzed as an illustration.<br><br>RESULTS: A new database, the Brazilian Pharmacopoeia Genomic Database (BPGD) was constructed and is now publicly accessible. A BLAST server for species identification and sequence searching with the internal transcribed spacer 2 (ITS2), the intergenic region (psbA-trnH), and the chloroplast genome (cp-G) of Brazilian medicinal plants was also embedded in the BPGD. The database has 753 ITS2 of 76 species, 553 psbA-trnH and 190 genomes (whole genome and chloroplast genome) of 57 species. In addition, it contains 37 genome sequence data sets of 24 species and 616 transcriptome sequence data sets of 34 species and also includes 187 cp-Gs representing 57 medicinal species in the BP. Analyses of the six cp-Gs of three Aloe species identified the variable regions in the cp-Gs. These can be used to identify species and understand the intraspecific relationships.<br><br>CONCLUSIONS: This study presents the first genomic database of medicinal plants listed in the latest BP. It serves as an efficient platform to obtain and analyze genomic data, accelerate studies regarding Brazilian medicinal plants and facilitate the rational development on their market regulation.},
}
@article {pmid34348091,
year = {2021},
author = {Johnson, KL and Qi, Z and Yan, Z and Wen, X and Nguyen, TC and Zaleta-Rivera, K and Chen, CJ and Fan, X and Sriram, K and Wan, X and Chen, ZB and Zhong, S},
title = {Revealing protein-protein interactions at the transcriptome scale by sequencing.},
journal = {Molecular cell},
volume = {81},
number = {19},
pages = {4091-4103.e9},
pmid = {34348091},
issn = {1097-4164},
support = {DP1 DK126138/DK/NIDDK NIH HHS/United States ; R01 GM138852/GM/NIGMS NIH HHS/United States ; R01 HL145170/HL/NHLBI NIH HHS/United States ; },
mesh = {*Computational Biology ; Databases, Genetic ; Female ; *Gene Expression Profiling ; Genes, Lethal ; HEK293 Cells ; Human Umbilical Vein Endothelial Cells/metabolism ; Humans ; Jurkat Cells ; Karyopherins/genetics/metabolism ; Kidney/metabolism ; Male ; Nuclear Matrix-Associated Proteins/genetics/metabolism ; Poly (ADP-Ribose) Polymerase-1/genetics/metabolism ; *Protein Interaction Mapping ; *Protein Interaction Maps ; Proteins/*genetics/*metabolism ; RNA-Binding Proteins/genetics/metabolism ; *RNA-Seq ; Receptors, Cytoplasmic and Nuclear/genetics/metabolism ; Software ; T-Lymphocytes/metabolism ; Transcription Factors/genetics/metabolism ; *Transcriptome ; beta Karyopherins/genetics/metabolism ; Exportin 1 Protein ; },
abstract = {We describe PROPER-seq (protein-protein interaction sequencing) to map protein-protein interactions (PPIs) en masse. PROPER-seq first converts transcriptomes of input cells into RNA-barcoded protein libraries, in which all interacting protein pairs are captured through nucleotide barcode ligation, recorded as chimeric DNA sequences, and decoded at once by sequencing and mapping. We applied PROPER-seq to human embryonic kidney cells, T lymphocytes, and endothelial cells and identified 210,518 human PPIs (collected in the PROPER v.1.0 database). Among these, 1,365 and 2,480 PPIs are supported by published co-immunoprecipitation (coIP) and affinity purification-mass spectrometry (AP-MS) data, 17,638 PPIs are predicted by the prePPI algorithm without previous experimental validation, and 100 PPIs overlap human synthetic lethal gene pairs. In addition, four previously uncharacterized interaction partners with poly(ADP-ribose) polymerase 1 (PARP1) (a critical protein in DNA repair) known as XPO1, MATR3, IPO5, and LEO1 are validated in vivo. PROPER-seq presents a time-effective technology to map PPIs at the transcriptome scale, and PROPER v.1.0 provides a rich resource for studying PPIs.},
}
@article {pmid34342956,
year = {2021},
author = {Okanishi, M and Kohtsuka, H},
title = {Description of a New Brooding Species of Ophiodelos (Echinodermata: Ophiuroidea) from Japan.},
journal = {Zoological science},
volume = {38},
number = {4},
pages = {352-358},
doi = {10.2108/zs200101},
pmid = {34342956},
issn = {0289-0003},
mesh = {Animals ; Echinodermata/*physiology ; Japan ; Pacific Ocean ; Reproduction/*physiology ; },
abstract = {A new species of brittle star, Ophiodelos okayoshitakai, is described from two specimens collected in Sagami Bay, central-eastern Japan. Photographic examination of the holotype specimen of the sole other congener, Ophiodelos insignis Koehler, 1930, indicates that Ophiodelos okayoshitakai sp. nov. is distinguished from O. insignis by i) the disc stumps covering on the dorsal side of the disc, ii) the dorsal and ventral arm plates being separated from each other on the proximal arm regions, iii) the dorsal arm plate being smooth, iv) the arm spines at proximal portion of the arm being six in number and smooth in shape, and v) the number and shape of the tentacle scales at proximal portion of the arm being up to two and spine-shaped adradially and oval abradially. Detailed morphological observations of this new species suggest the inclusion of Ophiodelos, whose familial affiliation remains unclear, in the suborder Ophiacanthina. More than 10 juveniles of various sizes were found in the disc of Ophiodelos okayoshitakai sp. nov., indicating a brooding reproduction. This is the first report of the genus Ophiodelos from Japanese waters. We also provided a nucleotide sequence for part of the cytochrome c oxidase subunit I (COI) gene in O. okayoshitakai sp. nov. for future studies of DNA barcoding and phylogeny.},
}
@article {pmid34340031,
year = {2021},
author = {Ardura, A and Gonzalez-Sanz, A and Clusa, L and Planes, S and Garcia-Vazquez, E},
title = {Beware of oysters. Rapid advance of non-native species in tropical Pacific islands.},
journal = {Marine environmental research},
volume = {170},
number = {},
pages = {105436},
doi = {10.1016/j.marenvres.2021.105436},
pmid = {34340031},
issn = {1879-0291},
mesh = {Animals ; Ecosystem ; *Introduced Species ; Islands ; *Ostreidae ; Pacific Islands ; Polynesia ; },
abstract = {Non-indigenous species can become a problem for the ecosystem health, especially when their distribution grows to the detriment of native species. In this moment, they can become invasive species. In marine ecosystems, the maritime transport is the principal gate and corridor for the movement of alien species. The genetic identification, using barcoding tools, of different oyster species in ports of the remote French Polynesia islands and atolls, showed a significant increase of exotic versus native oyster species between 2011 and 2018. This supports the spread of exotic species with the maritime traffic as the main cause. Moreover, the 11% of inaccurate identification at species level obtained in this study shows the need to complete the genetic databases.},
}
@article {pmid34339426,
year = {2021},
author = {Habib, KA and Neogi, AK and Rahman, M and Oh, J and Lee, YH and Kim, CG},
title = {DNA barcoding of brackish and marine water fishes and shellfishes of Sundarbans, the world's largest mangrove ecosystem.},
journal = {PloS one},
volume = {16},
number = {8},
pages = {e0255110},
pmid = {34339426},
issn = {1932-6203},
mesh = {Animals ; *Avicennia ; Base Sequence ; *DNA Barcoding, Taxonomic ; *Ecosystem ; Electron Transport Complex IV/genetics ; Fishes/*classification/*genetics ; Genetic Variation ; Geography ; Mollusca/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Seawater ; Shellfish/*classification ; },
abstract = {The present study aims to apply a DNA barcoding tool through amplifying two mitochondrial candidate genes i.e., COI and 16S rRNA for accurate identification of fish, aquatic molluscs and crustaceans of Sundarbans mangrove wetland, to build a reference library of fish and shellfishes of this unique ecosystems. A total of 185 mitochondrial COI barcode sequences and 59 partial sequences of the 16S rRNA gene were obtained from 120 genera, 65 families and 21 orders of fish, crustaceans and molluscs. The collected samples were first identified by examining morphometric characteristics and then assessed by DNA barcoding. The COI and 16S rRNA sequences of fishes and crustaceans were clearly discriminated among genera in their phylogenies. The average Kimura two-parameter (K2P) distances of COI barcode sequences within species, genera, and families of fishes are 1.57±0.06%, 15.16±0.23%, and 17.79±0.02%, respectively, and for 16S rRNA sequences, these values are 1.74±.8%, 0.97±.8%, and 4.29±1.3%, respectively. The minimum and maximum K2P distance based divergences in COI sequences of fishes are 0.19% and 36.27%, respectively. In crustaceans, the K2P distances within genera, families, and orders are 1.4±0.03%, 17.73±0.15%, and 22.81±0.02%, respectively and the minimum and maximum divergences are 0.2% and 33.93%, respectively. Additionally, the present study resolves the misidentification of the mud crab species of the Sundarbans as Scylla olivacea which was previously stated as Scylla serrata. In case of molluscs, values of interspecific divergence ranges from 17.43% to 66.3% in the barcoded species. The present study describes the development of a molecular and morphometric cross-referenced inventory of fish and shellfish of the Sundarbans. This inventory will be useful in future biodiversity studies and in forming future conservation plan.},
}
@article {pmid34339093,
year = {2021},
author = {Gao, Z and Yang, S and Xu, B and Zhang, T and Chen, S and Zhang, W and Sun, X and Wang, Z and Wang, X and Meng, X and Zhao, YS},
title = {Laterally Engineering Lanthanide-MOFs Epitaxial Heterostructures for Spatially Resolved Planar 2D Photonic Barcoding.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {60},
number = {46},
pages = {24519-24525},
doi = {10.1002/anie.202109336},
pmid = {34339093},
issn = {1521-3773},
support = {2017YFA0204502//ministry of science and technology of china/ ; 21905145//the national natural science foundation of china/ ; 11774188//the national natural science foundation of china/ ; 03010304//incubation program of universities' preponderant discipline of shandong province/ ; 23170504//mountain tai young scholarship/ ; JQ201802//excellent youth foundation of shandong's natural scientific committee/ ; },
abstract = {Metal-organic frameworks (MOFs) heterostructures with domain-controlled emissive colors have shown great potential for achieving high-throughput sensing, anti-counterfeit and information security. Here, a strategy based on steric-hindrance effect is proposed to construct lateral lanthanide-MOFs (Ln-MOFs) epitaxial heterostructures, where the channel-directed guest molecules are introduced to rebalance in-plane and out-of-plane growth rates of the Ln-MOFs microrods and eventually generate lateral MOF epitaxial heterostructures with controllable aspect ratios. A library of lateral Ln-MOFs heterostructures are acquired through a stepwise epitaxial growth procedure, from which rational modulation of each domain with specific lanthanide doping species allows for definition of photonic barcodes in a two-dimensional (2D) domain with remarkably enlarged encoding capacity. The results provide molecular-level insight into the use of modulators in governing crystallite morphology for spatially assembling multifunctional heterostructures.},
}
@article {pmid34337851,
year = {2021},
author = {Salo, HM and Nguyen, N and Alakärppä, E and Klavins, L and Hykkerud, AL and Karppinen, K and Jaakola, L and Klavins, M and Häggman, H},
title = {Authentication of berries and berry-based food products.},
journal = {Comprehensive reviews in food science and food safety},
volume = {20},
number = {5},
pages = {5197-5225},
doi = {10.1111/1541-4337.12811},
pmid = {34337851},
issn = {1541-4337},
support = {//European Regional Development Fund through Interreg Baltic Sea Region Programme/ ; //European Regional Development Fund through Interreg Nord/ ; },
mesh = {Diet ; *Flavonoids ; *Fruit ; Humans ; },
abstract = {Berries represent one of the most important and high-valued group of modern-day health-beneficial "superfoods" whose dietary consumption has been recognized to be beneficial for human health for a long time. In addition to being delicious, berries are rich in nutrients, vitamins, and several bioactive compounds, including carotenoids, flavonoids, phenolic acids, and hydrolysable tannins. However, due to their high value, berries and berry-based products are often subject to fraudulent adulteration, commonly for economical gain, but also unintentionally due to misidentification of species. Deliberate adulteration often comprises the substitution of high-value berries with lower value counterparts and mislabeling of product contents. As adulteration is deceptive toward customers and presents a risk for public health, food authentication through different methods is applied as a countermeasure. Although many authentication methods have been developed in terms of fast, sensitive, reliable, and low-cost analysis and have been applied in the authentication of a myriad of food products and species, their application on berries and berry-based products is still limited. The present review provides an overview of the development and application of analytical chemistry methods, such as isotope ratio analysis, liquid and gas chromatography, spectroscopy, as well as DNA-based methods and electronic sensors, for the authentication of berries and berry-based food products. We provide an overview of the earlier use and recent advances of these methods, as well as discuss the advances and drawbacks related to their application.},
}
@article {pmid34335651,
year = {2021},
author = {Ji, Y and Yang, J and Landis, JB and Wang, S and Yang, Z and Zhang, Y},
title = {Deciphering the Taxonomic Delimitation of Ottelia acuminata (Hydrocharitaceae) Using Complete Plastomes as Super-Barcodes.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {681270},
pmid = {34335651},
issn = {1664-462X},
abstract = {Accurate species delimitation and identification, which is a challenging task in traditional morphology-based taxonomy, is crucial to species conservation. Ottelia acuminata (Hydrocharitaceae) is a severely threatened submerged macrophyte endemic to southwestern China. The taxonomy of O. acuminata, which has long been in dispute, remains unresolved, impeding effective conservation and management practices. Here, we aim to address the long-standing issues concerning species boundary and intraspecific subdivision of O. acuminata using complete plastome sequences as super-barcodes. The taxonomic delimitation of O. acuminata was explored using phylogenetic inference and two independent sequence-based species delimitation schemes: automatic barcode gap discovery (ABGD) and multi-rate Poisson tree processes (mPTP). The reciprocally reinforcing results support the reduction of the closely related congeneric species, O. balansae and O. guanyangensis, as two conspecific varieties of O. acuminata. Within the newly defined O. acuminata, accurate varietal identification can be achieved using plastome super-barcodes. These findings will help inform future decisions regarding conservation, management and restoration of O. acuminata. This case study suggests that the use of plastome super-barcodes can provide a solution for species delimitation and identification in taxonomically difficult plant taxa, thus providing great potential to lessen the challenges of inventorying biodiversity, as well as biologically monitoring and assessing threatened species.},
}
@article {pmid34335532,
year = {2021},
author = {Zhang, Y and Wang, S and Li, H and Liu, C and Mi, F and Wang, R and Mo, M and Xu, J},
title = {Evidence for Persistent Heteroplasmy and Ancient Recombination in the Mitochondrial Genomes of the Edible Yellow Chanterelles From Southwestern China and Europe.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {699598},
pmid = {34335532},
issn = {1664-302X},
abstract = {Mitochondrial genes and genomes have patterns of inheritance that are distinctly different from those of nuclear genes and genomes. In nature, the mitochondrial genomes in eukaryotes are generally considered non-recombining and homoplasmic. If heteroplasmy and recombination exist, they are typically very limited in both space and time. Here we show that mitochondrial heteroplasmy and recombination may not be limited to a specific population nor exit only transiently in the basidiomycete Cantharellus cibarius and related species. These edible yellow chanterelles are an ecologically very important group of fungi and among the most prominent wild edible mushrooms in the Northern Hemisphere. At present, very little is known about the genetics and population biology of these fungia cross large geographical distances. Our study here analyzed a total of 363 specimens of edible yellow chanterelles from 24 geographic locations in Yunnan in southwestern China and six geographic locations in five countries in Europe. For each mushroom sample, we obtained the DNA sequences at two genes, one in the nuclear genome and one in the mitochondrial genome. Our analyses of the nuclear gene, translation elongation factor 1-alpha (tef-1) and the DNA barcode of C. cibarius and related species, suggested these samples belong to four known species and five potential new species. Interestingly, analyses of the mitochondrial ATP synthase subunit 6 (atp6) gene fragment revealed evidence of heteroplasmy in two geographic samples in Yunnan and recombination within the two new putative species in Yunnan. Specifically, all four possible haplotypes at two polymorphic nucleotide sites within the mitochondrial atp6 gene were found distributed across several geographic locations in Yunnan. Furthermore, these four haplotypes were broadly distributed across multiple phylogenetic clades constructed based on nuclear tef-1 sequences. Our results suggest that heteroplasmy and mitochondrial recombination might have happened repeatedly during the evolution of the yellow chanterelles. Together, our results suggest that the edible yellow chanterelles represent an excellent system from which to study the evolution of mitochondrial-nuclear genome relationships.},
}
@article {pmid34328872,
year = {2021},
author = {Oberprieler, S and Rees, G and Nielsen, D and Shackleton, M and Watson, G and Chandler, L and Davis, J},
title = {Connectivity, not short-range endemism, characterises the groundwater biota of a northern Australian karst system.},
journal = {The Science of the total environment},
volume = {796},
number = {},
pages = {148955},
doi = {10.1016/j.scitotenv.2021.148955},
pmid = {34328872},
issn = {1879-1026},
mesh = {Animals ; Australia ; Biota ; *Ecosystem ; *Groundwater ; Phylogeny ; RNA, Ribosomal, 16S ; },
abstract = {Groundwater ecosystems have a diverse and unique fauna, often dominated by Crustacea and generally characterised by short range endemics confined to single aquifers. Much of this knowledge has come from studies conducted either in fractured rock aquifers or alluvial aquifers. Karstic subterranean environments are present in the Cambrian Limestone Aquifer (CLA) in the Northern Territory, Australia, a freshwater aquifer which spans an area of ~28,000 km[2]. The presence of underground caverns and channels potentially allows extensive connectivity within this groundwater system. The emerging shale gas industry in the Beetaloo region, which underlies the CLA, provided the impetus to undertake the first survey of the potential existence of a stygofaunal community. Twenty-six groundwater wells (bores) and two springs were sampled in August and October 2019, across a distance of ~500 km, from the sub-tropical Mataranka region in the north to the semi-arid Barkly Tablelands in the south. Plankton nets and motorised pumps were used to collect water samples and conventional microscope-based morphological examinations in conjunction with environmental DNA (eDNA) were used to determine the presence of stygofauna. COI barcoding and 16S rRNA regions were also used for phylogenetic analysis. All stygofaunal communities were dominated by crustaceans, namely shrimps, amphipods, ostracods, copepods and syncarids. This fauna showed little affinity with the stygofauna recorded from more extensively sampled aquifers in north-western Australia, with new genera and species present in the CLA. eDNA analysis showed the presence of diverse biota at sites where direct water sampling for intact animals was difficult. COI and 16S analysis confirmed that a species of blind shrimp, Parisia unguis, occurred extensively throughout the aquifer, over a distance of at least ~300 km. The presence of Pa. unguis at widely separated sites across the CLA is consistent with substantial connectivity within the aquifer. This connectivity indicates that the risk of groundwater contamination from fracking chemicals needs to be adequately mitigated to prevent widespread effects.},
}
@article {pmid34327320,
year = {2021},
author = {Zhu, W and Xu, J and Chen, S and Chen, J and Liang, Y and Zhang, C and Li, Q and Lai, J and Li, L},
title = {Large-scale translatome profiling annotates the functional genome and reveals the key role of genic 3' untranslated regions in translatomic variation in plants.},
journal = {Plant communications},
volume = {2},
number = {4},
pages = {100181},
pmid = {34327320},
issn = {2590-3462},
mesh = {*3' Untranslated Regions ; Gene Expression Profiling ; *Genome, Plant ; *Quantitative Trait Loci ; Zea mays/*genetics ; },
abstract = {The translatome, a profile of the translational status of genetic information within cells, provides a new perspective on gene expression. Although many plant genomes have been sequenced, comprehensive translatomic annotations are not available for plants due to a lack of efficient translatome profiling techniques. Here, we developed a new technique termed 3' ribosome-profiling sequencing (3'Ribo-seq) for reliable, robust translatomic profiling. 3'Ribo-seq combines polysome profiling and 3' selection with a barcoding and pooling strategy. Systematic translatome profiling of different tissues of Arabidopsis, rice, and maize using conventional ribosome profiling (Ribo-seq) and 3'Ribo-seq revealed many novel translational genomic loci, thereby complementing functional genome annotation in plants. Using the low-cost, efficient 3'Ribo-seq technique and genome-wide association mapping of translatome expression (eGWAS), we performed a population-level dissection of the translatomes of 159 diverse maize inbred lines and identified 1,777 translational expression quantitative trait loci (eQTLs). Notably, local eQTLs are significantly enriched in the 3' untranslated regions of genes. Detailed eQTL analysis suggested that sequence variation around the polyadenylation (polyA) signal motif plays a key role in translatomic variation. Our study provides a comprehensive translatome annotation of plant functional genomes and introduces 3'Ribo-seq, which paves the way for deep translatomic analysis at the population level.},
}
@article {pmid34326549,
year = {2021},
author = {Fan, C and Deng, Q and Zhu, TF},
title = {Bioorthogonal information storage in L-DNA with a high-fidelity mirror-image Pfu DNA polymerase.},
journal = {Nature biotechnology},
volume = {39},
number = {12},
pages = {1548-1555},
pmid = {34326549},
issn = {1546-1696},
mesh = {*DNA/chemistry/genetics ; *DNA-Directed DNA Polymerase ; Information Storage and Retrieval ; Stereoisomerism ; },
abstract = {Natural DNA is exquisitely evolved to store genetic information. The chirally inverted L-DNA, possessing the same informational capacity but resistant to biodegradation, may serve as a robust, bioorthogonal information repository. Here we chemically synthesize a 90-kDa high-fidelity mirror-image Pfu DNA polymerase that enables accurate assembly of a kilobase-sized mirror-image gene. We use the polymerase to encode in L-DNA an 1860 paragraph by Louis Pasteur that first proposed a mirror-image world of biology. We realize chiral steganography by embedding a chimeric D-DNA/L-DNA key molecule in a D-DNA storage library, which conveys a false or secret message depending on the chirality of reading. Furthermore, we show that a trace amount of an L-DNA barcode preserved in water from a local pond remains amplifiable and sequenceable for 1 year, whereas a D-DNA barcode under the same conditions could not be amplified after 1 day. These next-generation mirror-image molecular tools may transform the development of advanced mirror-image biology systems and pave the way for the realization of the mirror-image central dogma and exploration of their applications.},
}
@article {pmid34324752,
year = {2021},
author = {Barbosa da Costa, N and Fugère, V and Hébert, MP and Xu, CCY and Barrett, RDH and Beisner, BE and Bell, G and Yargeau, V and Fussmann, GF and Gonzalez, A and Shapiro, BJ},
title = {Resistance, resilience, and functional redundancy of freshwater bacterioplankton communities facing a gradient of agricultural stressors in a mesocosm experiment.},
journal = {Molecular ecology},
volume = {30},
number = {19},
pages = {4771-4788},
doi = {10.1111/mec.16100},
pmid = {34324752},
issn = {1365-294X},
mesh = {*Aquatic Organisms ; Bacteria/genetics ; Biodiversity ; *Fresh Water ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Agricultural pollution with fertilizers and pesticides is a common disturbance to freshwater biodiversity. Bacterioplankton communities are at the base of aquatic food webs, but their responses to these potentially interacting stressors are rarely explored. To test the extent of resistance and resilience in bacterioplankton communities faced with agricultural stressors, we exposed freshwater mesocosms to single and combined gradients of two commonly used pesticides: the herbicide glyphosate (0-15 mg/L) and the neonicotinoid insecticide imidacloprid (0-60 μg/L), in high or low nutrient backgrounds. Over the 43-day experiment, we tracked variation in bacterial density with flow cytometry, carbon substrate use with Biolog EcoPlates, and taxonomic diversity and composition with environmental 16S rRNA gene amplicon sequencing. We show that only glyphosate (at the highest dose, 15 mg/L), but not imidacloprid, nutrients, or their interactions measurably changed community structure, favouring members of the Proteobacteria including the genus Agrobacterium. However, no change in carbon substrate use was detected throughout, suggesting functional redundancy despite taxonomic changes. We further show that communities are resilient at broad, but not fine taxonomic levels: 24 days after glyphosate application the precise amplicon sequence variants do not return, and tend to be replaced by phylogenetically close taxa. We conclude that high doses of glyphosate - but still within commonly acceptable regulatory guidelines - alter freshwater bacterioplankton by favouring a subset of higher taxonomic units (i.e., genus to phylum) that transiently thrive in the presence of glyphosate. Longer-term impacts of glyphosate at finer taxonomic resolution merit further investigation.},
}
@article {pmid34324525,
year = {2021},
author = {Vasquez, AA and Mohiddin, O and Li, Z and Bonnici, BL and Gurdziel, K and Ram, JL},
title = {Molecular diet studies of water mites reveal prey biodiversity.},
journal = {PloS one},
volume = {16},
number = {7},
pages = {e0254598},
pmid = {34324525},
issn = {1932-6203},
support = {R25 GM058905/GM/NIGMS NIH HHS/United States ; RL5 GM118981/GM/NIGMS NIH HHS/United States ; TL4 GM118983/GM/NIGMS NIH HHS/United States ; UL1 GM118982/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Predatory Behavior ; *Biodiversity ; DNA Barcoding, Taxonomic ; Mites/physiology/genetics ; Diet ; Electron Transport Complex IV/genetics ; Phylogeny ; Chironomidae/genetics/physiology ; },
abstract = {Water mites are diverse aquatic invertebrates that provide potentially important ecosystem and economic services as bioindicators and mosquito biocontrol; however, little is known about water mite digestive physiology, including their diet in nature. Water mites, much like their spider relatives, liquefy their prey upon consumption. This results in the absence of morphologically identifiable prey in water mite mid-gut. Previous studies have reported associations in the field of water mites with presumed prey and laboratory observations of water mites feeding on specific organisms offered for ingestion; however, the present work aims to determine what water mites have ingested in nature based on molecular studies of gut contents from freshly collected organisms from the field. To elucidate water mite prey, we used next-generation sequencing to detect diverse cytochrome oxidase I DNA barcode sequences of putative prey in the guts of 54 specimens comprising two species of Lebertia and a few specimens of Arrenurus (2) and Limnesia (1). To our knowledge this is the first molecular study of the diets of water mites as they feed in nature. While the presence of chironomid DNA confirmed previous observations of midge larvae as part of the diets of Lebertia, we also found the DNA of diverse organisms in all four species of water mites, including the DNA of mosquitoes in 6 specimens of Lebertia and a large number of previously unknown prey, especially from oligochaete worms. These studies thereby reveal a greater diversity of prey and a potentially broader significance than previously appreciated for water mites in aquatic food webs. Molecular studies like this can detect water mite predators of mosquito larvae and add knowledge of water mite predatory contributions to freshwater food webs.},
}
@article {pmid34322181,
year = {2020},
author = {Liu, QL and Li, JQ and Wingfield, MJ and Duong, TA and Wingfield, BD and Crous, PW and Chen, SF},
title = {Reconsideration of species boundaries and proposed DNA barcodes for Calonectria.},
journal = {Studies in mycology},
volume = {97},
number = {},
pages = {100106},
pmid = {34322181},
issn = {0166-0616},
abstract = {Calonectria represents a genus of phytopathogenic ascomycetous fungi with a worldwide distribution. In recent years, there has been an increase in the number of taxonomic studies on these fungi. Currently, there are 169 described species of Calonectria based on comparisons of DNA sequence data, combined with morphological characteristics. However, for some of these species, the sequence data utilised at the time of their description were relatively limited. This has justified an urgent need to reconsider the species boundaries for Calonectria based on robust genus-wide phylogenetic analyses. In this study, we utilised 240 available isolates including the ex-types of 128 Calonectria species, and re-sequenced eight gene regions (act, cmdA, his3, ITS, LSU, rpb2, tef1 and tub2) for them. Sequences for 44 Calonectria species, for which cultures could not be obtained, were downloaded from GenBank. DNA sequence data of all the 169 Calonectria species were then used to determine their phylogenetic relationships. As a consequence, 51 species were reduced to synonymy, two new species were identified, and the name Ca. lauri was validated. This resulted in the acceptance of 120 clearly defined Calonectria spp. The overall data revealed that the genus includes 11 species complexes, distributed across the Prolate and Sphaero-Naviculate Groups known to divide Calonectria. The results also made it possible to develop a robust set of DNA barcodes for Calonectria spp. To accomplish this goal, we evaluated the outcomes of each of the eight candidate DNA barcodes for the genus, as well as for each of the 11 species complexes. No single gene region provided a clear identity for all Calonectria species. Sequences of the tef1 and tub2 genes were the most reliable markers; those for the cmdA, his3, rpb2 and act gene regions also provided a relatively effective resolution for Calonectria spp., while the ITS and LSU failed to produce useful barcodes for species discrimination. At the species complex level, results showed that the most informative barcodes were inconsistent, but that a combination of six candidate barcodes (tef1, tub2, cmdA, his3, rpb2 and act) provided stable and reliable resolution for all 11 species complexes. A six-gene combined phylogeny resolved all 120 Calonectria species, and revealed that tef1, tub2, cmdA, his3, rpb2 and act gene regions are effective DNA barcodes for Calonectria.},
}
@article {pmid34319984,
year = {2021},
author = {Rosin, LF and Gil, J and Drinnenberg, IA and Lei, EP},
title = {Oligopaint DNA FISH reveals telomere-based meiotic pairing dynamics in the silkworm, Bombyx mori.},
journal = {PLoS genetics},
volume = {17},
number = {7},
pages = {e1009700},
pmid = {34319984},
issn = {1553-7404},
mesh = {Animals ; Bombyx/*genetics ; Cell Cycle Proteins/genetics ; Centromere/metabolism ; Chromosomal Proteins, Non-Histone/genetics ; Chromosome Pairing/*genetics ; Chromosome Segregation/genetics ; Chromosomes/genetics ; DNA/genetics ; Female ; Male ; Meiosis/genetics ; Microtubules/metabolism ; Synaptonemal Complex/metabolism ; Telomere/*genetics ; },
abstract = {Accurate chromosome segregation during meiosis is essential for reproductive success. Yet, many fundamental aspects of meiosis remain unclear, including the mechanisms regulating homolog pairing across species. This gap is partially due to our inability to visualize individual chromosomes during meiosis. Here, we employ Oligopaint FISH to investigate homolog pairing and compaction of meiotic chromosomes and resurrect a classical model system, the silkworm Bombyx mori. Our Oligopaint design combines multiplexed barcoding with secondary oligo labeling for high flexibility and low cost. These studies illustrate that Oligopaints are highly specific in whole-mount gonads and on meiotic squashes. We show that meiotic pairing is robust in both males and females and that pairing can occur through numerous partially paired intermediate structures. We also show that pairing in male meiosis occurs asynchronously and seemingly in a transcription-biased manner. Further, we reveal that meiotic bivalent formation in B. mori males is highly similar to bivalent formation in C. elegans, with both of these pathways ultimately resulting in the pairing of chromosome ends with non-paired ends facing the spindle pole. Additionally, microtubule recruitment in both C. elegans and B. mori is likely dependent on kinetochore proteins but independent of the centromere-specifying histone CENP-A. Finally, using super-resolution microscopy in the female germline, we show that homologous chromosomes remain associated at telomere domains in the absence of chiasma and after breakdown and modification to the synaptonemal complex in pachytene. These studies reveal novel insights into mechanisms of meiotic homolog pairing both with or without recombination.},
}
@article {pmid34313772,
year = {2021},
author = {Deblauwe, I and Ibáñez-Justicia, A and De Wolf, K and Smitz, N and Schneider, A and Stroo, A and Jacobs, F and Vanslembrouck, A and Gombeer, S and Dekoninck, W and Müller, R and Van Bortel, W},
title = {First Detections of Culiseta longiareolata (Diptera: Culicidae) in Belgium and the Netherlands.},
journal = {Journal of medical entomology},
volume = {58},
number = {6},
pages = {2524-2532},
doi = {10.1093/jme/tjab127},
pmid = {34313772},
issn = {1938-2928},
mesh = {*Animal Distribution ; Animals ; Belgium ; Culicidae/growth &amp; development/*physiology ; Female ; Larva/growth &amp; development/physiology ; Male ; Mosquito Vectors/*physiology ; Netherlands ; Pupa/growth &amp; development/physiology ; },
abstract = {Culiseta (Allotheobaldia) longiareolata (Macquart) (Diptera: Culicidae) is an ornithophilic mosquito species that occurs in the southern Palaearctic Region from the Azores to Central Asia, the Ethiopian Region, India, and Pakistan. Although it has a widespread distribution range, the species was only recently reported in Western and Central Europe. Between 2017 and 2020, larvae, pupae, and adults of Cs. longiareolata (n = 161) were found at 13 distinct locations in Belgium (n = 4) and The Netherlands (n = 9). Collected mosquitoes were morphologically identified and the identification was then validated by COI DNA barcoding. These are the first records of the species in the above-mentioned countries. The present results suggest that Cs. longiareolata could be increasing its distribution range in temperate regions, indicating a warming climate. As the species might be a potential vector of bird pathogens (e.g., West Nile virus), its spread in Western Europe is noteworthy.},
}
@article {pmid34312709,
year = {2022},
author = {de Los Ríos, A and Garrido-Benavent, I and Limón, A and Cason, ED and Maggs-Kölling, G and Cowan, D and Valverde, A},
title = {Novel lichen-dominated hypolithic communities in the Namib Desert.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {1036-1048},
pmid = {34312709},
issn = {1432-184X},
support = {CTM2015-64728-C2-2-R//(MINECO/FEDER, EU)/ ; PID2019-105469RB-C22//MICINN-AEI/ ; },
mesh = {*Cyanobacteria/genetics ; Desert Climate ; Ecosystem ; *Lichens ; Soil Microbiology ; },
abstract = {The ventral surfaces of translucent rocks from hot desert pavements often harbor hypolithic microbial communities, which are mostly dominated by cyanobacteria. The Namib Desert fog belt supports extensive hypolithic colonization of quartz rocks, which are also colonized by lichens on their dorsal surfaces. Here, we aim to evaluate whether lichens colonize the ventral surface of the rocks (i.e., show hypolithic lifestyle) and compare the bacterial composition of these coastal hypolithic communities with those found inland. Fungal DNA barcoding and fungal and bacterial Illumina metabarcoding were combined with electron microscopy to characterize the composition and spatial structure of hypolithic communities from two (coastal and inland) areas in the Namib Desert. We report, for the first time, the structure and composition of lichen-dominated hypolithic communities found in the coastal zone of the Namib Desert with extensive epilithic lichen cover. Lichen modified areoles with inverted morphology of the genus Stellarangia (three lineages) and Buellia (two lineages) were the main components of these hypolithic communities. Some of these lineages were also found in epilithic habitats. These lichen-dominated hypolithic communities differed in structural organization and bacterial community composition from those found in inland areas. The hypolithic lichen colonization characterized here seems not to be an extension of epilithic or biological soil crust lichen growths but the result of specific sublithic microenvironmental conditions. Moisture derived from fog and dew could be the main driver of this unique colonization.},
}
@article {pmid34312385,
year = {2021},
author = {Fischer, DS and Ansari, M and Wagner, KI and Jarosch, S and Huang, Y and Mayr, CH and Strunz, M and Lang, NJ and D'Ippolito, E and Hammel, M and Mateyka, L and Weber, S and Wolff, LS and Witter, K and Fernandez, IE and Leuschner, G and Milger, K and Frankenberger, M and Nowak, L and Heinig-Menhard, K and Koch, I and Stoleriu, MG and Hilgendorff, A and Behr, J and Pichlmair, A and Schubert, B and Theis, FJ and Busch, DH and Schiller, HB and Schober, K},
title = {Single-cell RNA sequencing reveals ex vivo signatures of SARS-CoV-2-reactive T cells through 'reverse phenotyping'.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {4515},
pmid = {34312385},
issn = {2041-1723},
mesh = {Aged ; Aged, 80 and over ; CD4-Positive T-Lymphocytes/metabolism/virology ; COVID-19/epidemiology/*immunology/virology ; Cells, Cultured ; Cohort Studies ; Female ; Gene Expression Profiling/*methods ; Humans ; Male ; Middle Aged ; Pandemics ; Receptors, Antigen, T-Cell/genetics/immunology/metabolism ; SARS-CoV-2/physiology ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis/*methods ; T-Lymphocytes/*metabolism/virology ; },
abstract = {The in vivo phenotypic profile of T cells reactive to severe acute respiratory syndrome (SARS)-CoV-2 antigens remains poorly understood. Conventional methods to detect antigen-reactive T cells require in vitro antigenic re-stimulation or highly individualized peptide-human leukocyte antigen (pHLA) multimers. Here, we use single-cell RNA sequencing to identify and profile SARS-CoV-2-reactive T cells from Coronavirus Disease 2019 (COVID-19) patients. To do so, we induce transcriptional shifts by antigenic stimulation in vitro and take advantage of natural T cell receptor (TCR) sequences of clonally expanded T cells as barcodes for 'reverse phenotyping'. This allows identification of SARS-CoV-2-reactive TCRs and reveals phenotypic effects introduced by antigen-specific stimulation. We characterize transcriptional signatures of currently and previously activated SARS-CoV-2-reactive T cells, and show correspondence with phenotypes of T cells from the respiratory tract of patients with severe disease in the presence or absence of virus in independent cohorts. Reverse phenotyping is a powerful tool to provide an integrated insight into cellular states of SARS-CoV-2-reactive T cells across tissues and activation states.},
}
@article {pmid34311008,
year = {2021},
author = {Monteiro, CS and Deconinck, D and Eljasik, P and Sobczak, M and Derycke, S and Panicz, R and Kane, N and Mazloomrezaei, M and H Devlin, R and Faria, MA},
title = {A fast HRMA tool to authenticate eight salmonid species in commercial food products.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {156},
number = {},
pages = {112440},
doi = {10.1016/j.fct.2021.112440},
pmid = {34311008},
issn = {1873-6351},
mesh = {Animals ; Fish Products/*analysis ; Real-Time Polymerase Chain Reaction ; Reproducibility of Results ; Salmonidae/*classification/genetics ; Species Specificity ; },
abstract = {Atlantic and Pacific salmon are frequently consumed species with very different economic values: farmed Atlantic salmon is cheaper than wild-caught Pacific salmons. Species replacements occur with the high valued Pacific species (Oncorhynchus keta, O. gorbuscha, O. kisutch, O. nerka and O. tshawytscha) substituted by cheaper farmed Atlantic salmon (Salmo salar) and Atlantic salmon by rainbow trout (Oncorhynchus mykiss) and brown trout (Salmo trutta). Here we use High-Resolution Melting Analysis (HRMA) to identify eight salmonid species. We designed primers to generate short amplicons of 72 and 116 bp from the fish barcode genes CO1 and CYTB. The time of analysis was under 70 min, after DNA extraction. Food processing of Atlantic salmon (fresh, "Bellevue", "gravadlax", frozen and smoked) did not impact the HRMA profiles allowing reliable identification. A blind test was conducted by three different institutes, showing correct species identifications irrespective of the laboratory conducting the analysis. Finally, a total of 82 retail samples from three European countries were analyzed and a low substitution rate of 1.2% was found. The developed tool provides a quick way to investigate salmon fraud and contributes to safeguard consumers.},
}
@article {pmid34310886,
year = {2021},
author = {Harvey, ML and Lin, AS and Sun, L and Koyama, T and Shuman, JHB and Loh, JT and Algood, HMS and Scholz, MB and McClain, MS and Cover, TL},
title = {Enhanced Fitness of a Helicobacter pylori babA Mutant in a Murine Model.},
journal = {Infection and immunity},
volume = {89},
number = {10},
pages = {e0072520},
pmid = {34310886},
issn = {1098-5522},
support = {P30 DK058404/DK/NIDDK NIH HHS/United States ; T32 AI007281/AI/NIAID NIH HHS/United States ; P01 CA116087/CA/NCI NIH HHS/United States ; R01 AI118932/AI/NIAID NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; R01 AI039657/AI/NIAID NIH HHS/United States ; I01 BX004447/BX/BLRD VA/United States ; },
mesh = {Adhesins, Bacterial/*genetics ; Animals ; Bacterial Adhesion/genetics ; Bacterial Outer Membrane Proteins/genetics ; Disease Models, Animal ; Helicobacter Infections/*microbiology ; Helicobacter pylori/*genetics ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Mutation/*genetics ; },
abstract = {Helicobacter pylori genomes encode over 60 predicted outer membrane proteins (OMPs). Several OMPs in the Hop family act as adhesins, but the functions of most Hop proteins are unknown. To identify hop mutant strains exhibiting differential fitness in vivo compared to in vitro, we used a genetic barcoding method that allowed us to track changes in the proportional abundance of H. pylori strains within a mixed population. We generated a library of hop mutant strains, each containing a unique nucleotide barcode, as well as a library of control strains, each containing a nucleotide barcode in an intergenic region predicted to be a neutral locus unrelated to bacterial fitness. We orogastrically inoculated each of the libraries into mice and analyzed compositional changes in the populations over time in vivo compared to changes detected in the populations during library passage in vitro. The control library proliferated as a relatively stable community in vitro, but there was a reduction in the population diversity of this library in vivo and marked variation in the dominant strains recovered from individual animals, consistent with the existence of a nonselective bottleneck in vivo. We did not identify any OMP mutants exhibiting fitness defects exclusively in vivo without corresponding fitness defects in vitro. Conversely, a babA mutant exhibited a strong fitness advantage in vivo but not in vitro. These findings, when taken together with results of other studies, suggest that production of BabA may have differential effects on H. pylori fitness depending on the environmental conditions.},
}
@article {pmid34310851,
year = {2022},
author = {Fu, CN and Mo, ZQ and Yang, JB and Cai, J and Ye, LJ and Zou, JY and Qin, HT and Zheng, W and Hollingsworth, PM and Li, DZ and Gao, LM},
title = {Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron.},
journal = {Molecular ecology resources},
volume = {22},
number = {1},
pages = {404-414},
doi = {10.1111/1755-0998.13479},
pmid = {34310851},
issn = {1755-0998},
support = {2017-LSFGBOWS-02//Large-scale Scientific Facilities of the Chinese Academy of Sciences/ ; 31670213//National Natural Science Foundation of China/ ; 91631101//National Natural Science Foundation of China/ ; 2017HA014//Program of Science and Technology Talents Training of Yunnan Province, China/ ; XDB31000000//Strategic Priority Research Program of Chinese Academy of Sciences/ ; E0295111Q1//Special Research Assistant Funding Project of the Chinese Academy of Sciences/ ; },
mesh = {Humans ; *Rhododendron/genetics ; },
abstract = {Standard plant DNA barcodes based on 2-3 plastid regions, and nrDNA ITS show variable levels of resolution, and fail to discriminate among species in many plant groups. Genome skimming to recover complete plastid genome sequences and nrDNA arrays has been proposed as a solution to address these resolution limitations. However, few studies have empirically tested what gains are achieved in practice. Of particular interest is whether adding substantially more plastid and nrDNA characters will lead to an increase in discriminatory power, or whether the resolution limitations of standard plant barcodes are fundamentally due to plastid genomes and nrDNA not tracking species boundaries. To address this, we used genome skimming to recover near-complete plastid genomes and nuclear ribosomal DNA from Rhododendron species and compared discrimination success with standard plant barcodes. We sampled 218 individuals representing 145 species of this species-rich and taxonomically difficult genus, focusing on the global biodiversity hotspots of the Himalaya-Hengduan Mountains. Only 33% of species were distinguished using ITS+matK+rbcL+trnH-psbA. In contrast, 55% of species were distinguished using plastid genome and nrDNA sequences. The vast majority of this increase is due to the additional plastid characters. Thus, despite previous studies showing an asymptote in discrimination success beyond 3-4 plastid regions, these results show that a demonstrable increase in discriminatory power is possible with extensive plastid genome data. However, despite these gains, many species remain unresolved, and these results also reinforce the need to access multiple unlinked nuclear loci to obtain transformative gains in species discrimination in plants.},
}
@article {pmid34309916,
year = {2021},
author = {Dang, J and Li, H and Zhang, L and Li, S and Zhang, T and Huang, S and Li, Y and Huang, C and Ke, Y and Shen, G and Zhi, X and Ding, X},
title = {New Structure Mass Tag based on Zr-NMOF for Multiparameter and Sensitive Single-Cell Interrogating in Mass Cytometry.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {33},
number = {35},
pages = {e2008297},
doi = {10.1002/adma.202008297},
pmid = {34309916},
issn = {1521-4095},
support = {81871448//National Science Foundation of China/ ; 31771088//National Science Foundation of China/ ; 31971327//National Science Foundation of China/ ; 81971736//National Science Foundation of China/ ; 32071405//National Science Foundation of China/ ; 2017SHZDZX01//National Science Foundation of China/ ; 18430760500//National Science Foundation of China/ ; ZH2018QNA51//Medical-Engineering Cross Foundation of Shanghai Jiao Tong University/ ; YG2021QN58//Medical-Engineering Cross Foundation of Shanghai Jiao Tong University/ ; },
mesh = {*Zirconium/chemistry ; Animals ; Mice ; *Single-Cell Analysis/methods ; Metal-Organic Frameworks/chemistry ; Spleen/cytology ; Flow Cytometry/methods ; Polymers/chemistry ; Humans ; Immunoassay/methods ; Biomarkers ; },
abstract = {Mass cytometry, also called cytometry by time-of-flight (CyTOF), is an emerging powerful proteomic analysis technique that utilizes metal chelated polymer (MCP) as mass tags for interrogating high-dimensional biomarkers simultaneously on millions of individual cells. However, under the typical polymer-based mass tag system, the sensitivity and multiplexing detection ability has been highly restricted. Herein, a new structure mass tag based on a nanometal organic framework (NMOF) is reported for multiparameter and sensitive single-cell biomarker interrogating in CyTOF. A uniform-sized Zr-NMOF (33 nm) carrying 10[5] metal ions is synthesized under modulator/reaction time coregulation, which is monodispersed and colloidally stable in water for over one-year storage. On functionalization with an antibody, the Zr mass tag exhibits specific molecular recognition properties and minimal cross-reaction toward nontargeted cells. In addition, the Zr-mass tag is compatible with MCP mass tags in a multiparameter assay for mouse spleen cells staining, which exploits four additional channels, m/z = 90, 91, 92, 94, for single-cell immunoassays in CyTOF. Compared to the MCP mass tag, the Zr-mass tag provides an additional fivefold signal amplification. This work provides the fundamental technical capability for exploiting NMOF-based mass tags for CyTOF application, which opens up possibility of high-dimensional single-cell immune profiling, low abundant antigen detection, and development of new barcoding systems.},
}
@article {pmid34309016,
year = {2021},
author = {Sung, JY and Lee, YJ and Cho, YJ and Shin, MN and Lee, SJ and Lee, HS and Koh, H and Bae, JW and Shin, JH and Kim, HJ and Lee, DW},
title = {A large-scale metagenomic study for enzyme profiles using the focused identification of the NGS-based definitive enzyme research (FINDER) strategy.},
journal = {Biotechnology and bioengineering},
volume = {118},
number = {11},
pages = {4360-4374},
doi = {10.1002/bit.27904},
pmid = {34309016},
issn = {1097-0290},
mesh = {*DNA Barcoding, Taxonomic ; Enzymes/*genetics ; *High-Throughput Nucleotide Sequencing ; *Metagenomics ; },
abstract = {Excavating the molecular details of many diverse enzymes from metagenomes remains challenging in agriculture, food, health, and environmental fields. We present a versatile method that accelerates metabolic enzyme discovery for highly selective gene capture in metagenomes using next-generation sequencing. Culture-independent enzyme mining of environmental DNA is based on a set of short identifying degenerate sequences specific for a wide range of enzyme superfamilies, followed by multiplexed DNA barcode sequencing. A strategy of 'focused identification of next-generation sequencing-based definitive enzyme research' enabled us to generate targeted enzyme datasets from metagenomes, resulting in minimal hands-on obtention of high-throughput biological diversity and potential function profiles, without being time-consuming. This method also provided a targeted inventory of predicted proteins and molecular features of metabolic activities from several metagenomic samples. We suggest that the efficiency and sensitivity of this method will accelerate the decryption of microbial diversity and the signature of proteins and their metabolism from environmental samples.},
}
@article {pmid34304051,
year = {2021},
author = {Rad, HS and Rad, HS and Shiravand, Y and Radfar, P and Arpon, D and Warkiani, ME and O'Byrne, K and Kulasinghe, A},
title = {The Pandora's box of novel technologies that may revolutionize lung cancer.},
journal = {Lung cancer (Amsterdam, Netherlands)},
volume = {159},
number = {},
pages = {34-41},
doi = {10.1016/j.lungcan.2021.06.022},
pmid = {34304051},
issn = {1872-8332},
mesh = {*Carcinoma, Non-Small-Cell Lung/diagnosis/genetics/therapy ; Humans ; Immunohistochemistry ; Immunotherapy ; *Lung Neoplasms/diagnosis/genetics/therapy ; Tumor Microenvironment ; },
abstract = {Non-small cell lung cancer (NSCLC) is one of the most common cancers globally and has a 5-year survival rate ~20%. Immunotherapies have demonstrated long-term and durable responses in NSCLC patients, although they appear to be effective in only a subset of patients. A more comprehensive understanding of the underlying tumour biology may contribute to identifying those patients likely to achieve optimal outcomes. Profiling the tumour microenvironment (TME) has shown to be beneficial in addressing fundamental tumour-immune cell interactions. Advances in multiplexing immunohistochemistry and molecular barcoding has led to recent advances in profiling genes and proteins in NSCLC. Here, we review the recent advancements in spatial profiling technologies for the analysis of NSCLC tissue samples to gain new insights and therapeutic options for NSCLC. The combination of spatial transcriptomics combined with advanced imaging is likely to lead to deep insights into NSCLC tissue biology, which can be a powerful tool to predict likelihood of response to therapy.},
}
@article {pmid34301787,
year = {2021},
author = {},
title = {Genome-Wide Screens Reveal Potential Biomarkers of NK-cell Sensitivity.},
journal = {Cancer discovery},
volume = {11},
number = {9},
pages = {2125},
doi = {10.1158/2159-8290.CD-RW2021-105},
pmid = {34301787},
issn = {2159-8290},
abstract = {DNA barcoding and CRISPR screens identified genes in cancer cells that modulate response to NK cells.},
}
@article {pmid34299949,
year = {2021},
author = {Vindigni, G and Pulvirenti, A and Alaimo, S and Monaco, C and Spina, D and Peri, I},
title = {Bioinformatics Approach to Mitigate Mislabeling in EU Seafood Market and Protect Consumer Health.},
journal = {International journal of environmental research and public health},
volume = {18},
number = {14},
pages = {},
pmid = {34299949},
issn = {1660-4601},
mesh = {Animals ; *Computational Biology ; *DNA Barcoding, Taxonomic ; Fisheries ; Fishes ; Humans ; Seafood ; },
abstract = {Fisheries products are some of the most traded commodities world-wide and the potential for fraud is a serious concern. Fish fraud represents a threat to human health and poses serious concerns due to the consumption of toxins, highly allergenic species, contaminates or zoonotic parasites, which may be present in substituted fish. The substitution of more expensive fish by cheaper species, with similar morphological characteristics but different origins, reflects the need for greater transparency and traceability upon which which the security of the entire seafood value-chain depends. Even though EU regulations have made significant progress in consumer information by stringent labelling requirements, fraud is still widespread. Many molecular techniques such as DNA barcoding provide valuable support to enhance the Common Fisheries Policy (CFP) in the protection of consumer interests by unequivocally detecting any kind of fraud. This paper aims to highlight both the engagement of EU fishery policy and the opportunity offered by new biotechnology instruments to mitigate the growing fraud in the globalized fish market and to enforce the food security system to protect consumers' health. In this paper, after a presentation of EU rules on fish labeling and a general overview on the current state of the global fish market, we discuss the public health implications and the opportunities offered by several techniques based on genetics, reporting a case study to show the efficacy of the DNA barcoding methodology in assessing fish traceability and identification, comparing different species of the Epinephelus genus, Mottled Grouper (Mycteroperca rubra) and Wreckfish (Polyprion americanus), often improperly sold with the commercial name of "grouper".},
}
@article {pmid34298128,
year = {2021},
author = {Kondratov, O and Kondratova, L and Mandel, RJ and Coleman, K and Savage, MA and Gray-Edwards, HL and Ness, TJ and Rodriguez-Lebron, E and Bell, RD and Rabinowitz, J and Gamlin, PD and Zolotukhin, S},
title = {A comprehensive study of a 29-capsid AAV library in a non-human primate central nervous system.},
journal = {Molecular therapy : the journal of the American Society of Gene Therapy},
volume = {29},
number = {9},
pages = {2806-2820},
pmid = {34298128},
issn = {1525-0024},
support = {R01 HL097088/HL/NHLBI NIH HHS/United States ; },
mesh = {Algorithms ; Animals ; Capsid Proteins/*genetics ; Central Nervous System/*chemistry/virology ; DNA, Viral/genetics ; Databases, Genetic ; Dependovirus/genetics/*physiology ; Drug Administration Routes ; Genetic Vectors/*administration &amp; dosage ; High-Throughput Nucleotide Sequencing ; Primates ; RNA, Messenger/genetics ; RNA, Viral/genetics ; Tissue Distribution ; Transduction, Genetic ; },
abstract = {Non-human primates (NHPs) are a preferred animal model for optimizing adeno-associated virus (AAV)-mediated CNS gene delivery protocols before clinical trials. In spite of its inherent appeal, it is challenging to compare different serotypes, delivery routes, and disease indications in a well-powered, comprehensive, multigroup NHP experiment. Here, a multiplex barcode recombinant AAV (rAAV) vector-tracing strategy has been applied to a systemic analysis of 29 distinct, wild-type (WT), AAV natural isolates and engineered capsids in the CNS of eight macaques. The report describes distribution of each capsid in 15 areas of the macaques' CNS after intraparenchymal (putamen) injection, or cerebrospinal fluid (CSF)-mediated administration routes (intracisternal, intrathecal, or intracerebroventricular). To trace the vector biodistribution (viral DNA) and targeted tissues transduction (viral mRNA) of each capsid in each of the analyzed CNS areas, quantitative next-generation sequencing analysis, assisted by the digital-droplet PCR technology, was used. The report describes the most efficient AAV capsid variants targeting specific CNS areas after each route of administration using the direct side-by-side comparison of WT AAV isolates and a new generation of rationally designed capsids. The newly developed bioinformatics and visualization algorithms, applicable to the comparative analysis of several mammalian brain models, have been developed and made available in the public domain.},
}
@article {pmid34295214,
year = {2021},
author = {Pedraza-Lara, C and Gutiérrez-Yurrita, PJ and Jesus-Bonilla, VS},
title = {A new species of Procambarus (Decapoda, Cambaridae) from the State of Querétaro, Mexico.},
journal = {ZooKeys},
volume = {1048},
number = {},
pages = {1-21},
pmid = {34295214},
issn = {1313-2989},
abstract = {With a Nearctic distribution, the family Cambaridae harbors a high species richness in Mexico, which is also evident along the Pánuco River catchment. A series of surveys carried on in five populations from the Sierra Gorda Biosphere Reserve in the State of Querétaro resulted in localizing a putative new species for science. A molecular phylogenetic study and species delimitation analyses including all the known Procambarus species from the Pánuco River catchment were conducted based on three mitochondrial genes (16S rDNA, 12S rDNA, and COI; 2,462 bp in total). Phylogeny recovered all species as monophyletic, including the populations under study. All delimitation results based on barcoding, ABGD, GMYC, bPTP, and gonopod differentiation agree in the recognition of a new taxon, to which the name Procambarus xihui sp. nov. is given, and its diagnosis and description are provided. The new species can be distinguished from the remaining species in the genus, among other characters, by a unique configuration of the terminal elements of the first pleopod of form I male, which includes a central projection lamellate, hood-like, forming a concave blade-like structure mesially directed, as well as a caudal process crest-like, mesiodistally directed, forming a lateral side of the concavity.},
}
@article {pmid34294911,
year = {2021},
author = {Kurtz, DM and Soo, J and Co Ting Keh, L and Alig, S and Chabon, JJ and Sworder, BJ and Schultz, A and Jin, MC and Scherer, F and Garofalo, A and Macaulay, CW and Hamilton, EG and Chen, B and Olsen, M and Schroers-Martin, JG and Craig, AFM and Moding, EJ and Esfahani, MS and Liu, CL and Dührsen, U and Hüttmann, A and Casasnovas, RO and Westin, JR and Roschewski, M and Wilson, WH and Gaidano, G and Rossi, D and Diehn, M and Alizadeh, AA},
title = {Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA.},
journal = {Nature biotechnology},
volume = {39},
number = {12},
pages = {1537-1547},
pmid = {34294911},
issn = {1546-1696},
support = {R01 CA254179/CA/NCI NIH HHS/United States ; T32 CA009302/CA/NCI NIH HHS/United States ; R43 CA199142/CA/NCI NIH HHS/United States ; R01 CA229766/CA/NCI NIH HHS/United States ; U01 CA194389/CA/NCI NIH HHS/United States ; R01 CA233975/CA/NCI NIH HHS/United States ; R01 CA244526/CA/NCI NIH HHS/United States ; K08 CA241076/CA/NCI NIH HHS/United States ; R01 CA188298/CA/NCI NIH HHS/United States ; R01 CA257655/CA/NCI NIH HHS/United States ; },
mesh = {Biomarkers, Tumor/genetics ; *Circulating Tumor DNA/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Mutation/genetics ; Neoplasm, Residual/diagnosis/genetics ; },
abstract = {Circulating tumor-derived DNA (ctDNA) is an emerging biomarker for many cancers, but the limited sensitivity of current detection methods reduces its utility for diagnosing minimal residual disease. Here we describe phased variant enrichment and detection sequencing (PhasED-seq), a method that uses multiple somatic mutations in individual DNA fragments to improve the sensitivity of ctDNA detection. Leveraging whole-genome sequences from 2,538 tumors, we identify phased variants and their associations with mutational signatures. We show that even without molecular barcodes, the limits of detection of PhasED-seq outperform prior methods, including duplex barcoding, allowing ctDNA detection in the ppm range in participant samples. We profiled 678 specimens from 213 participants with B cell lymphomas, including serial cell-free DNA samples before and during therapy for diffuse large B cell lymphoma. In participants with undetectable ctDNA after two cycles of therapy using a next-generation sequencing-based approach termed cancer personalized profiling by deep sequencing, an additional 25% have ctDNA detectable by PhasED-seq and have worse outcomes. Finally, we demonstrate the application of PhasED-seq to solid tumors.},
}
@article {pmid34294857,
year = {2021},
author = {Akahori, D and Inoue, Y and Inui, N and Karayama, M and Yasui, H and Hozumi, H and Suzuki, Y and Furuhashi, K and Fujisawa, T and Enomoto, N and Nakamura, Y and Suda, T},
title = {Comparative assessment of NOIR-SS and ddPCR for ctDNA detection of EGFR L858R mutations in advanced L858R-positive lung adenocarcinomas.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {14999},
pmid = {34294857},
issn = {2045-2322},
mesh = {Adenocarcinoma of Lung/genetics/*pathology ; Aged ; Aged, 80 and over ; *Amino Acid Substitution ; Circulating Tumor DNA/*genetics ; ErbB Receptors/genetics ; Female ; Humans ; Liquid Biopsy ; Lung Neoplasms/genetics/*pathology ; Male ; Middle Aged ; Neoplasm Staging ; Polymerase Chain Reaction ; Prospective Studies ; Sensitivity and Specificity ; Sequence Analysis, DNA/*methods ; },
abstract = {Genotyping epidermal growth factor receptor (EGFR) is an essential process to indicate lung adenocarcinoma patients for the most appropriate treatment. Liquid biopsy using circulating tumor DNA (ctDNA) potentially complements the use of tumor tissue biopsy for identifying genotype-specific mutations in cancer cells. We assessed the performance of a high-fidelity sequencing method that uses molecular barcodes called the nonoverlapping integrated read sequencing system (NOIR-SS) for detecting EGFR L858R-mutated alleles in 33 advanced or recurrent patients with L858R mutation-positive lung adenocarcinoma revealed by matched tissue biopsy. We compared NOIR-SS with site-specific droplet digital PCR (ddPCR), which was taken as the reference, in terms of sensitivity and ability to quantify L858R variant allele fractions (VAFs). NOIR-SS and ddPCR had sensitivities of 87.9% (29/33) and 78.8% (26/33) for detecting L858R alleles, respectively. The VAFs measured by each assay were strongly correlated. Notably, one specimen was positive with a VAF of 30.12% for NOIR-SS but marginally positive with that of 0.05% for ddPCR because of a previously poorly recognized mechanism: two-base substitution-induced L858R (c.2573_2574delinsGA). These results indicate that NOIR-SS is a useful method for detecting ctDNA, potentially overcoming a limitation of ddPCR which highly depends on the binding ability of primers to specific targeting sequences.},
}
@article {pmid34293865,
year = {2021},
author = {Bai, M and Cao, X and Chen, F and Xue, J and Zhao, Y and Zhao, Y},
title = {Bioorthogonal Chemical Signature Enabling Amplified Visualization of Cellular Oxidative Thymines.},
journal = {Analytical chemistry},
volume = {93},
number = {30},
pages = {10495-10501},
doi = {10.1021/acs.analchem.1c01285},
pmid = {34293865},
issn = {1520-6882},
mesh = {*Azides ; Click Chemistry ; DNA ; Oxidative Stress ; *Thymine ; },
abstract = {Cellular oxidative thymines, 5-hydroxymethyluracil (5hmU) and 5-formyluracil (5fU), are found in the genomes of a diverse range of organisms, the distribution of which profoundly influence biological processes and living systems. However, the distribution of cellular oxidative thymines has not been explored because of lacking both specific bioorthogonal labeling and sensitivity methods for single-cell analysis. Herein, we report a bioorthogonal chemical signature enabling amplified visualization of cellular oxidative thymines in single cells. The synthesized ATP-γ-alkyne, an ATP analogue with bioorthogonal tag modified on γ-phosphate can be specifically linked to cellular 5hmU by chemoenzymatic labeling. DNA with 5-alkynephosphomethyluracil were then clicked with azide (N3)-modified 5hmU-primer. Identification of 5fU is based on selective reduction from 5fU to 5hmU, subsequent chemoenzymatic labeling of the newly generated 5hmU, and cross-linking with N3-modified 5fU-primer via click chemistry. Then, all of the 5hmU and 5fU sites are encoded with respective circularized barcodes. These barcodes are simultaneously amplified for multiplexed single-molecule imaging. The above two kinds of barcodes can be simultaneously amplified for differentiated visualization of 5hmU and 5fU in single cells. We find these two kinds of cellular oxidative thymines are spatially organized in a cell-type-dependent style with cell-to-cell heterogeneity. We also investigate their multilevel subcellular information and explore their dynamic changes during cell cycles. Further, using DNA sequencing instead of fluorescence imaging, our proposed bioorthogonal chemical signature holds great potential to offer the sequence information of these oxidative thymines in cells and may provide a reliable chemical biology approach for studying the whole-genome oxidative thymines profiles and insights into their functional role and dynamics in biology.},
}
@article {pmid34289883,
year = {2021},
author = {Șuleșco, T and Erisoz Kasap, O and Halada, P and Oğuz, G and Rusnac, D and Gresova, M and Alten, B and Volf, P and Dvorak, V},
title = {Phlebotomine sand fly survey in the Republic of Moldova: species composition, distribution and host preferences.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {371},
pmid = {34289883},
issn = {1756-3305},
mesh = {Animals ; Female ; Haplotypes ; Host Specificity ; Humans ; Insect Vectors/*classification/genetics/parasitology ; Leishmaniasis/*transmission ; Male ; Moldova/epidemiology ; Phlebotomus/classification/genetics/physiology ; Phylogeny ; Psychodidae/*classification/genetics/physiology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {BACKGROUND: Phlebotomine sand flies (Diptera: Psychodiae) in the Republic of Moldova have been understudied for decades. Our study provides a first update on their occurrence, species composition and bloodmeal sources after 50 years.<br><br>METHODS: During 5 seasons (2013-2017), 58 localities from 20 regions were surveyed for presence of sand flies using CDC light traps and manual aspirators. Species identification was done by a combination of morphological and molecular approaches (DNA barcoding, MALDI-TOF MS protein profiling). In engorged females, host blood was identified by three molecular techniques (RFLP, cytb sequencing and MALDI-TOF peptide mass mapping). Population structure of most abundant species was studied by cox1 haplotyping; phylogenetic analyses of ITS2 and cox1 genetic markers were used to resolve relationships of other detected species.<br><br>RESULTS: In total, 793 sand flies were collected at 30 (51.7%) localities from 12 regions of Moldova. Three species were identified by an integrative morphological and molecular approach: Phlebotomus papatasi, P. perfiliewi and Phlebotomus sp. (Adlerius), the first being the most abundant and widespread, markedly anthropophilic based on bloodmeal analyses, occurring also indoors and showing low population structure with only five haplotypes of cox1 detected. Distinct morphological and molecular characters of Phlebotomus sp. (Adlerius) specimens suggest the presence of a yet undescribed species.<br><br>CONCLUSIONS: Our study revealed the presence of stable sand fly populations of three species in Moldova that represent a biting nuisance as well as a potential threat of pathogen transmission and shall be further studied.},
}
@article {pmid34286850,
year = {2021},
author = {Kraft, D and Meyer, L and Webb, M and Scidmore-Rossing, K and Huveneers, C and Clua, E and Meyer, C},
title = {Development and successful real-world use of a transfer DNA technique to identify species involved in shark bite incidents.},
journal = {Journal of forensic sciences},
volume = {66},
number = {6},
pages = {2438-2443},
doi = {10.1111/1556-4029.14808},
pmid = {34286850},
issn = {1556-4029},
support = {//Hawaii Department of Land and Natural Resources/ ; //Save Our Seas Foundation/ ; },
mesh = {Animals ; *Bites and Stings ; DNA/*genetics ; DNA Barcoding, Taxonomic/*methods ; Forensic Genetics/*methods ; Humans ; Sequence Analysis, DNA ; Sharks/*genetics ; Species Specificity ; },
abstract = {Identifying the species involved in shark bite incidents is an ongoing challenge but is important to mitigate risk. We developed a sampling protocol to identify shark species from DNA transferred to inanimate objects during bite incidents. To develop and refine the technique, we swabbed shark bite impressions on surfboards and wetsuit neoprene collected under semicontrolled conditions. Methods were tested experimentally and then successfully used to identify the species involved in a real-world shark bite incident. Thirty-two of 33 bite impressions yielded sufficient DNA sequences for species identification, producing barcodes from five test species, including dusky, Galapagos, bull, tiger, and white shark. The latter three species collectively account for a majority of shark bites worldwide. Our method successfully identified the species (Galeocerdo cuvier) responsible for a fatal shark bite on December 8th, 2020 on the island of Maui, from swab samples collected from the victim's surfboard 49 h after the bite incident. Our experimental results demonstrate that shark species can be accurately identified from transfer DNA recovered from bite impressions on surfboards and wetsuit neoprene. The successful use of our method in the real-world incident shows great potential for the practicality of this tool. We recommend DNA swabbing as a routine part of the forensic analysis of shark bites to help identify the species involved in human-shark interactions.},
}
@article {pmid34286104,
year = {2021},
author = {Wilkins, OG and Capitanchik, C and Luscombe, NM and Ule, J},
title = {Ultraplex: A rapid, flexible, all-in-one fastq demultiplexer.},
journal = {Wellcome open research},
volume = {6},
number = {},
pages = {141},
pmid = {34286104},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; FC001002/ARC_/Arthritis Research UK/United Kingdom ; },
abstract = {Background: The first step of virtually all next generation sequencing analysis involves the splitting of the raw sequencing data into separate files using sample-specific barcodes, a process known as "demultiplexing". However, we found that existing software for this purpose was either too inflexible or too computationally intensive for fast, streamlined processing of raw, single end fastq files containing combinatorial barcodes. Results: Here, we introduce a fast and uniquely flexible demultiplexer, named Ultraplex, which splits a raw FASTQ file containing barcodes either at a single end or at both 5' and 3' ends of reads, trims the sequencing adaptors and low-quality bases, and moves unique molecular identifiers (UMIs) into the read header, allowing subsequent removal of PCR duplicates. Ultraplex is able to perform such single or combinatorial demultiplexing on both single- and paired-end sequencing data, and can process an entire Illumina HiSeq lane, consisting of nearly 500 million reads, in less than 20 minutes. Conclusions: Ultraplex greatly reduces computational burden and pipeline complexity for the demultiplexing of complex sequencing libraries, such as those produced by various CLIP and ribosome profiling protocols, and is also very user friendly, enabling streamlined, robust data processing. Ultraplex is available on PyPi and Conda and via Github.},
}
@article {pmid34285053,
year = {2021},
author = {Lee, D and Kapoor, A and Lee, C and Mudgett, M and Beer, MA and Chakravarti, A},
title = {Sequence-based correction of barcode bias in massively parallel reporter assays.},
journal = {Genome research},
volume = {31},
number = {9},
pages = {1638-1645},
pmid = {34285053},
issn = {1549-5469},
support = {R01 GM104469/GM/NIGMS NIH HHS/United States ; R01 HL086694/HL/NHLBI NIH HHS/United States ; R01 HL128782/HL/NHLBI NIH HHS/United States ; },
mesh = {Bias ; Biological Assay ; *Gene Expression Regulation ; Genes, Reporter ; *Regulatory Sequences, Nucleic Acid ; },
abstract = {Massively parallel reporter assays (MPRAs) are a high-throughput method for evaluating in vitro activities of thousands of candidate cis-regulatory elements (CREs). In these assays, candidate sequences are cloned upstream or downstream from a reporter gene tagged by unique DNA sequences. However, tag sequences may themselves affect reporter gene expression and lead to major potential biases in the measured cis-regulatory activity. Here, we present a sequence-based method for correcting tag-sequence-specific effects and show that our method can significantly reduce this source of variation and improve the identification of functional regulatory variants by MPRAs. We also show that our model captures sequence features associated with post-transcriptional regulation of mRNA. Thus, this new method helps not only to improve detection of regulatory signals in MPRA experiments but also to design better MPRA protocols.},
}
@article {pmid34283110,
year = {2021},
author = {Hussein, BR and Malik, OA and Ong, WH and Slik, JWF},
title = {Automated Extraction of Phenotypic Leaf Traits of Individual Intact Herbarium Leaves from Herbarium Specimen Images Using Deep Learning Based Semantic Segmentation.},
journal = {Sensors (Basel, Switzerland)},
volume = {21},
number = {13},
pages = {},
pmid = {34283110},
issn = {1424-8220},
mesh = {*Deep Learning ; Image Processing, Computer-Assisted ; Plant Leaves ; Plants ; Semantics ; },
abstract = {With the increase in the digitization efforts of herbarium collections worldwide, dataset repositories such as iDigBio and GBIF now have hundreds of thousands of herbarium sheet images ready for exploration. Although this serves as a new source of plant leaves data, herbarium datasets have an inherent challenge to deal with the sheets containing other non-plant objects such as color charts, barcodes, and labels. Even for the plant part itself, a combination of different overlapping, damaged, and intact individual leaves exist together with other plant organs such as stems and fruits, which increases the complexity of leaf trait extraction and analysis. Focusing on segmentation and trait extraction on individual intact herbarium leaves, this study proposes a pipeline consisting of deep learning semantic segmentation model (DeepLabv3+), connected component analysis, and a single-leaf classifier trained on binary images to automate the extraction of an intact individual leaf with phenotypic traits. The proposed method achieved a higher F1-score for both the in-house dataset (96%) and on a publicly available herbarium dataset (93%) compared to object detection-based approaches including Faster R-CNN and YOLOv5. Furthermore, using the proposed approach, the phenotypic measurements extracted from the segmented individual leaves were closer to the ground truth measurements, which suggests the importance of the segmentation process in handling background noise. Compared to the object detection-based approaches, the proposed method showed a promising direction toward an autonomous tool for the extraction of individual leaves together with their trait data directly from herbarium specimen images.},
}
@article {pmid34280697,
year = {2021},
author = {Liberska, J and Michalik, J and Pers-Kamczyc, E and Wierzbicka, A and Lane, RS and Rączka, G and Opalińska, P and Skorupski, M and Dabert, M},
title = {Prevalence of Babesia canis DNA in Ixodes ricinus ticks collected in forest and urban ecosystems in west-central Poland.},
journal = {Ticks and tick-borne diseases},
volume = {12},
number = {5},
pages = {101786},
doi = {10.1016/j.ttbdis.2021.101786},
pmid = {34280697},
issn = {1877-9603},
mesh = {Animals ; Babesia/*isolation &amp; purification ; Cities ; DNA, Protozoan/*analysis ; Ecosystem ; Forests ; Ixodes/*parasitology ; Poland ; },
abstract = {Babesia canis, a widely distributed European tick-borne protozoan haemoparasite, causes canine babesiosis, the most important tick-borne disease afflicting dogs worldwide. The meadow tick, Dermacentor reticulatus, is considered to be the primary vector of this parasite in central Europe. Females of the more broadly distributed and medically important castor bean tick, Ixodes ricinus, also commonly feed upon dogs, but their role in the enzootic transmission cycle of B. canis is unclear. Here, we screened 1,598 host-seeking I. ricinus ticks collected from two different ecosystems, forest stands vs. urban recreational forests, for the presence of B. canis DNA. Ticks were sampled during their two seasonal peaks of activity, spring (May/June) and late summer (September). Babesia species were identified by amplification and sequencing of a hypervariable 18S rRNA gene fragment. Babesia canis was the only piroplasm detected in 13% of 200 larvae and 8.2% of 324 nymphs in the forest ecosystems. In urban recreational areas, B. canis DNA was found in 1.5% of 460 nymphs, 3.5% of 289 females and 3.2% of 280 males. Additionally, three samples, including one female, one male, and one nymph, were co-infected with B. venatorum and one nymph with B. divergens or B. capreoli. Our findings implicate that B. canis can be transmitted transovarially and maintained transstadially within populations of I. ricinus, but the vector competence of I. ricinus for transmitting B. canis remains to be investigated.},
}
@article {pmid34279655,
year = {2021},
author = {Xu, X and Coquilleau, MP and Ridland, PM and Umina, PA and Yang, Q and Hoffmann, AA},
title = {Molecular Identification of Leafmining Flies From Australia Including New Liriomyza Outbreaks.},
journal = {Journal of economic entomology},
volume = {114},
number = {5},
pages = {1983-1990},
doi = {10.1093/jee/toab143},
pmid = {34279655},
issn = {1938-291X},
mesh = {Animals ; Australia ; *Diptera/genetics ; *Plant Diseases ; },
abstract = {Some leafmining fly species are pests of agricultural and ornamental plants but they also include many species with little economic importance. The taxonomy of leafmining flies is often challenging because of putative cryptic species. Following new outbreaks of Liriomyza (Diptera:Agromyzidae) in Australia, we here characterize 13 dipteran leafminer species collected from Australia based on cytochrome c oxidase subunit 1 (COI) DNA barcodes, and we compare these with overseas data. We confirm barcodes of nine species from the Agromyzidae (Liriomyza sativae, L. huidobrensis, L. trifolii, L. bryoniae, L. chinensis, L. brassicae, L. chenopodii, Phytomyza plantaginis and P. syngenesiae) and one species from the Drosophilidae (Scaptomyza flava); we describe new haplotypes for some of these species. Furthermore, we provide the first DNA barcodes for two species (Cerodontha milleri and Phytoliriomyza praecellens) from the Agromyzidae and one species (Scaptomyza australis) from the Drosophilidae. These findings provide a baseline for DNA-based identification of pest Liriomyza incursions spreading across the Australian east coast in relation to other species already present in Australia.},
}
@article {pmid34277664,
year = {2021},
author = {Lau, RP and Kim, TH and Rao, J},
title = {Advances in Imaging Modalities, Artificial Intelligence, and Single Cell Biomarker Analysis, and Their Applications in Cytopathology.},
journal = {Frontiers in medicine},
volume = {8},
number = {},
pages = {689954},
pmid = {34277664},
issn = {2296-858X},
abstract = {Several advances in recent decades in digital imaging, artificial intelligence, and multiplex modalities have improved our ability to automatically analyze and interpret imaging data. Imaging technologies such as optical coherence tomography, optical projection tomography, and quantitative phase microscopy allow analysis of tissues and cells in 3-dimensions and with subcellular granularity. Improvements in computer vision and machine learning have made algorithms more successful in automatically identifying important features to diagnose disease. Many new automated multiplex modalities such as antibody barcoding with cleavable DNA (ABCD), single cell analysis for tumor phenotyping (SCANT), fast analytical screening technique fine needle aspiration (FAST-FNA), and portable fluorescence-based image cytometry analyzer (CytoPAN) are under investigation. These have shown great promise in their ability to automatically analyze several biomarkers concurrently with high sensitivity, even in paucicellular samples, lending themselves well as tools in FNA. Not yet widely adopted for clinical use, many have successfully been applied to human samples. Once clinically validated, some of these technologies are poised to change the routine practice of cytopathology.},
}
@article {pmid34277335,
year = {2021},
author = {Nyman, T and Papadopoulou, E and Ylinen, E and Wutke, S and Michell, CT and Sromek, L and Sinisalo, T and Andrievskaya, E and Alexeev, V and Kunnasranta, M},
title = {DNA barcoding reveals different cestode helminth species in northern European marine and freshwater ringed seals.},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {15},
number = {},
pages = {255-261},
pmid = {34277335},
issn = {2213-2244},
abstract = {Three subspecies of the ringed seal (Pusa hispida) are found in northeastern Europe: P. h. botnica in the Baltic Sea, P. h saimensis in Lake Saimaa in Finland, and P. h. ladogensis in Lake Ladoga in Russia. We investigated the poorly-known cestode helminth communities of these closely related but ecologically divergent subspecies using COI barcode data. Our results show that, while cestodes from the Baltic Sea represent Schistocephalus solidus, all worms from the two lakes are identified as Ligula intestinalis, a species that has previously not been reported from seals. The observed shift in cestode communities appears to be driven by differential availability of intermediate fish host species in marine vs. freshwater environments. Both observed cestode species normally infect fish-eating birds, so further work is required to elucidate the health and conservation implications of cestode infections in European ringed seals, whether L. intestinalis occurs also in marine ringed seals, and whether the species is able to reproduce in seal hosts. In addition, a deep barcode divergence found within S. solidus suggests the presence of cryptic diversity under this species name.},
}
@article {pmid34276367,
year = {2021},
author = {Xu, H and Li, P and Ren, G and Wang, Y and Jiang, D and Liu, C},
title = {Authentication of Three Source Spices of Arnebiae Radix Using DNA Barcoding and HPLC.},
journal = {Frontiers in pharmacology},
volume = {12},
number = {},
pages = {677014},
pmid = {34276367},
issn = {1663-9812},
abstract = {Arnebia decumbens (Vent.) Coss. et Kralik, A. euchroma (Royle) Johnst and A. guttata Bunge, three commonly used traditional Chinese medicinal plants have been widely used for the clinical treatment of inflammatory diseases caused by fungal, bacterial, oxidation, and other related pathogens. However, precise identification at the similar species level is usually challenging due to the influence of the source of medicinal materials, traditional ethnic medicine and medicinal habits. Here we developed a comprehensive and efficient identification system for three source spices of Arnebiae Radix based on DNA barcoding and HPLC fingerprinting. A total of 599 samples from thirty-five wild populations were collected and identified by using DNA barcodes of ITS2 regions, and the chemotypes of seven naphthoquinoneswere revealed by HPLC quantitative analysis including principal component analysis and hierarchical clustering analysis. Our results showed that the ITS2 sequences can distinguish three source spices of Arnebiae Radix from adulterants. However, it was difficult to identify them by HPLC-specific chromatograms combined with chemometric analysis. These results indicated that DNA barcoding was a more powerful method than HPLC fingerprinting for the identification of related species that were genetically similar. DNA barcoding analysis could be a promising and reliable tool to accurately confirm the identities of medicinal materials, especially for those whose sources are multiple and difficult to be identified by conventional chromatography.},
}
@article {pmid34273309,
year = {2021},
author = {Valença-Barbosa, C and Finamore-Araujo, P and Moreira, OC and Vergara-Meza, JG and Alvarez, MVN and Nascimento, JR and Borges-Veloso, A and Viana, MC and Lilioso, M and Miguel, DC and Gadelha, FR and Teixeira, MMG and Almeida, CE},
title = {Genotypic Trypanosoma cruzi distribution and parasite load differ ecotypically and according to parasite genotypes in Triatoma brasiliensis from endemic and outbreak areas in Northeastern Brazil.},
journal = {Acta tropica},
volume = {222},
number = {},
pages = {106054},
doi = {10.1016/j.actatropica.2021.106054},
pmid = {34273309},
issn = {1873-6254},
mesh = {Animals ; Brazil/epidemiology ; *Chagas Disease/epidemiology ; Disease Outbreaks ; Genotype ; Humans ; Parasite Load ; Real-Time Polymerase Chain Reaction ; *Triatoma/parasitology ; *Trypanosoma cruzi/genetics ; },
abstract = {This study aimed to identify the Trypanosoma cruzi genotypes and their relationship with parasitic load in distinct geographic and ecotypic populations of Triatoma brasiliensis in two sites, including one where a Chagas disease (ChD) outbreak occurred in Rio Grande do Norte state, Brazil. Triatomine captures were performed in peridomestic and sylvatic ecotopes in two municipalities: Marcelino Vieira - affected by the outbreak; and Currais Novos - where high pressure of peridomestic triatomine infestation after insecticide spraying have been reported. The kDNA-PCR was used to select 124 T. cruzi positive triatomine samples, of which 117 were successfully genotyped by fluorescent fragment length barcoding (FFLB). Moreover, the T. cruzi load quantification was performed using a multiplex TaqMan qPCR. Our findings showed a clear ecotypic segregation between TcI and TcII harboured by T. brasiliensis (p<0.001). Although no genotypes were ecotypically exclusive, TcI was predominant in peridomestic ecotopes (86%). In general, T. brasiliensis from Rio Grande do Norte had a higher T. cruzi load varying from 3.94 to 7.66 x 10[6]T. cruzi per insect. Additionally, TcII (median value=299,504 T. cruzi/intestine unit equivalents) had more than twice (p=0.1) the parasite load of TcI (median value=149,077 T. cruzi/intestine unit equivalents), which can be attributed to a more ancient co-evolution with T. brasiliensis. The higher prevalence of TcII in the sylvatic T. brasiliensis (70%) could be associated with a more diversified source of bloodmeals for wild insect populations. Either TcI or TcII may have been responsible for the ChD outbreak that occurred in the city of Marcelino Vieira. On the other hand, a smaller portion of T. brasiliensis was infected by TcIII (3%) in the peridomicile, in addition to T. rangeli genotype A (1%), often found in mixed infections. Our results highlight the need of understanding the patterns of T. cruzi genotype´s development and circulation in insect vectors and reservoirs as a mode of tracking situations of epidemiologic importance, as the ChD outbreak recently recorded for Northeastern Brazil.},
}
@article {pmid34270854,
year = {2022},
author = {Manzanilla, V and Teixidor-Toneu, I and Martin, GJ and Hollingsworth, PM and de Boer, HJ and Kool, A},
title = {Using target capture to address conservation challenges: Population-level tracking of a globally-traded herbal medicine.},
journal = {Molecular ecology resources},
volume = {22},
number = {1},
pages = {212-224},
doi = {10.1111/1755-0998.13472},
pmid = {34270854},
issn = {1755-0998},
support = {606895//EU FP7 Marie Curie Actions/ ; },
mesh = {Animals ; *Asteraceae ; Endangered Species ; Herbal Medicine ; *Magnoliopsida ; *Plants, Medicinal ; },
abstract = {The promotion of responsible and sustainable trade in biological resources is widely proposed as one solution to mitigate current high levels of global biodiversity loss. Various molecular identification methods have been proposed as appropriate tools for monitoring global supply chains of commercialized animals and plants. Here, we demonstrate the efficacy of target capture genomic barcoding in identifying and establishing the geographic origin of samples traded as Anacyclus pyrethrum, a medicinal plant assessed as globally vulnerable in the IUCN Red List of Threatened Species. Samples collected from national and international supply chains were identified through target capture sequencing of 443 low-copy nuclear makers and compared to results derived from genome skimming of plastome and DNA barcoding of standard plastid regions and ITS. Both target capture and genome skimming provided approximately 3.4 million reads per sample, but target capture largely outperformed standard plant barcodes and entire plastid genome sequences. We were able to discern the geographical origin of Anacyclus samples collected in Moroccan, Indian and Sri Lankan markets, differentiating between plant materials originally harvested from diverse populations in Algeria and Morocco. Dropping costs of analysing samples enables the potential of target capture to routinely identify commercialized plant species and determine their geographic origin. It promises to play an important role in monitoring and regulation of plant species in trade, supporting biodiversity conservation efforts, and in ensuring that plant products are unadulterated, contributing to consumer protection.},
}
@article {pmid34270452,
year = {2021},
author = {Nydahl, TK and Ahorhorlu, SY and Ndiaye, M and Das, MK and Hansson, H and Bravo, MC and Wang, CW and Lusingu, J and Theisen, M and Singh, SK and Singh, S and Campino, S and Lund, O and Roper, C and Alifrangis, M},
title = {Identification of Single-Nucleotide Polymorphisms in the Mitochondrial Genome and Kelch 13 Gene of Plasmodium falciparum in Different Geographical Populations.},
journal = {The American journal of tropical medicine and hygiene},
volume = {105},
number = {4},
pages = {1085-1092},
pmid = {34270452},
issn = {1476-1645},
mesh = {DNA, Protozoan/*genetics ; *Genome, Mitochondrial ; Haplotypes ; Humans ; India/epidemiology ; Malaria, Falciparum/epidemiology/parasitology ; Plasmodium falciparum/*genetics ; *Polymorphism, Single Nucleotide ; },
abstract = {The emergence of artemisinin-resistant Plasmodium falciparum parasites in Southeast Asia threatens malaria control and elimination. The interconnectedness of parasite populations may be essential to monitor the spread of resistance. Combining a published barcoding system of geographically restricted single-nucleotide polymorphisms (SNPs), mainly mitochondria of P. falciparum with SNPs in the K13 artemisinin resistance marker, could elucidate the parasite population structure and provide insight regarding the spread of drug resistance. We explored the diversity of mitochondrial SNPs (bp position 611-2825) and identified K13 SNPs from malaria patients in the districts of India (Ranchi), Tanzania (Korogwe), and Senegal (Podor, Richard Toll, Kaolack, and Ndoffane). DNA was amplified using a nested PCR and Sanger-sequenced. Overall, 199 K13 sequences (India: N = 92; Tanzania: N = 48; Senegal: N = 59) and 237 mitochondrial sequences (India: N = 93; Tanzania: N = 48; Senegal: N = 96) were generated. SNPs were identified by comparisons with reference genomes. We detected previously reported geographically restricted mitochondrial SNPs (T2175C and G1367A) as markers for parasites originating from the Indian subcontinent and several geographically unrestricted mitochondrial SNPs. Combining haplotypes with published P. falciparum mitochondrial genome data suggested possible regional differences within India. All three countries had G1692A, but Tanzanian and Senegalese SNPs were well-differentiated. Some mitochondrial SNPs are reported here for the first time. Four nonsynonymous K13 SNPs were detected: K189T (India, Tanzania, Senegal); A175T (Tanzania); and A174V and R255K (Senegal). This study supports the use of mitochondrial SNPs to determine the origin of the parasite and suggests that the P. falciparum populations studied were susceptible to artemisinin during sampling because all K13 SNPs observed were outside the propeller domain for artemisinin resistance.},
}
@article {pmid34270090,
year = {2021},
author = {Zheng, YJ and Li, XQ and Yang, ZX and Cai, WX and Lou, QS and Tao, W},
title = {The identification of fish eggs of two species, the ovate sole Solea ovata and black porgy Acanthopagrus schlegelii.},
journal = {Journal of fish biology},
volume = {99},
number = {5},
pages = {1746-1751},
doi = {10.1111/jfb.14854},
pmid = {34270090},
issn = {1095-8649},
support = {FEEL-2020-3//Guangdong Provincial Key Laboratory of Fishery Ecology and Environment/ ; 41776172//Natural Science Foundation of China/ ; },
mesh = {Animals ; *Flatfishes ; *Perciformes/genetics ; },
abstract = {Fish eggs of the ovate sole Solea ovata and black porgy Acanthopagrus schlegelii were identified through DNA barcoding of cytochrome c oxidase subunit I (COX1). Visual taxonomic features were achieved, and photographs of the eggs of both species at different developmental stages were reported for the first time. In addition, the dissolution of oil globules caused by ethanol as egg fixatives was observed. This result showed the importance of using formalin as egg fixatives in the case of morphometric analysis and the necessity of combining molecular and visual taxonomic method for morphological study.},
}
@article {pmid34268901,
year = {2021},
author = {Bik, HM},
title = {Just keep it simple? Benchmarking the accuracy of taxonomy assignment software in metabarcoding studies.},
journal = {Molecular ecology resources},
volume = {21},
number = {7},
pages = {2187-2189},
doi = {10.1111/1755-0998.13473},
pmid = {34268901},
issn = {1755-0998},
mesh = {Animals ; *Benchmarking ; Biodiversity ; *DNA Barcoding, Taxonomic ; Humans ; Phylogeny ; RNA, Ribosomal, 16S ; Software ; },
abstract = {How do you put a name on an unknown piece of DNA? From microbes to mammals, high-throughput metabarcoding studies provide a more objective view of natural communities, overcoming many of the inherent limitations of traditional field surveys and microscopy-based observations (Deiner et al., 2017). Taxonomy assignment is one of the most critical aspects of any metabarcoding study, yet this important bioinformatics task is routinely overlooked. Biodiversity surveys and conservation efforts often depend on formal species inventories: the presence (or absence) of species, and the number of individuals reported across space and time. However, computational workflows applied in eukaryotic metabarcoding studies were originally developed for use with bacterial/archaeal data sets, where microbial researchers rely on one conserved locus (nuclear 16S rRNA) and have access to vast databases with good coverage across most prokaryotic lineages - a situation not mirrored in most multicellular taxa. In this issue of Molecular Ecology Resources, Hleap et al. (2021) carry out an extensive benchmarking exercise focused on taxonomy assignment strategies for eukaryotic metabarcoding studies utilizing the mitochondrial Cytochrome C oxidase I marker gene (COI). They assess the performance and accuracy of software tools representing diverse methodological approaches: from "simple" strategies based on sequence similarity and composition, to model-based phylogenetic and probabilistic classification tools. Contrary to popular assumptions, less complex approaches (BLAST and the QIIME2 feature classifier) consistently outperformed more sophisticated mathematical algorithms and were highly accurate for assigning taxonomy at higher levels (e.g. family). Lower-level assignments at the genus and species level still pose significant challenge for most existing algorithms, and sparse eukaryotic reference databases further limit software performance. This study illuminates current best practices for metabarcoding taxonomy assignments, and underscores the need for community-driven efforts to expand taxonomic and geographic representation in reference DNA barcode databases.},
}
@article {pmid34263282,
year = {2021},
author = {Cho, CH and Cho, M and Park, JK},
title = {Biomarker barcodes: multiplexed microfluidic immunohistochemistry enables high-throughput analysis of tissue microarray.},
journal = {Lab on a chip},
volume = {21},
number = {18},
pages = {3471-3482},
doi = {10.1039/d1lc00375e},
pmid = {34263282},
issn = {1473-0189},
mesh = {Biomarkers, Tumor ; *Breast Neoplasms/diagnosis ; Female ; Humans ; Immunohistochemistry ; *Microfluidics ; Receptor, ErbB-2/genetics ; Reproducibility of Results ; Tissue Array Analysis ; },
abstract = {We present a multiplexed microfluidic immunohistochemistry (IHC) technology that enables high-throughput analysis of tissue microarrays (TMAs) using the patterns of biomarker barcodes, which consist of a series of expressed linear patterns of specific biomarkers. A multichannel poly(dimethylsiloxane) microfluidic device was reversibly assembled by the pressure of simple equipment for multiplexed IHC on each core of TMA or cell microarray (CMA) section slides. By injecting primary antibodies from different biomarkers independently into each channel, multiplexed immunostaining can be performed on each core of TMA. We confirmed the equal immunostaining quality regardless of the channel orders and core positions in the slide. Four different biomarkers (ER, PR, HER2, and Ki67) were used for the demonstration of distinctive expression patterns on CMAs which consist of six different breast cancer cell lines, and it was confirmed that these bar-like signals could be a biomarker barcode for the TMA core. A biomarker barcode of breast cancer patient-derived TMA was quickly scanned by a slide scanner and compared to the conventional method for breast cancer diagnosis. This "barcode-IHC" concept, which has been verified by performing multiplexed microfluidic IHC on CMA and TMA samples, provides high reproducibility and the potential of high-throughput screening with molecular diagnostic capability.},
}
@article {pmid34259241,
year = {2021},
author = {Zhang, B and Tang, WS and Ding, SN},
title = {Rational design of fluorescent barcodes for suspension array through a simple simulation strategy.},
journal = {The Analyst},
volume = {146},
number = {15},
pages = {4796-4802},
doi = {10.1039/d1an01052b},
pmid = {34259241},
issn = {1364-5528},
mesh = {Coloring Agents ; Flow Cytometry ; Microspheres ; *Quantum Dots ; Suspensions ; },
abstract = {Quantum dot (QD)-encoded microbeads as optical barcode with high fluorescence intensity and fluorescence uniformity, excellent stability and dispersity are greatly important for suspension array (SA). However, the size distribution of the microbeads mass-produced by the membrane emulsification method usually shows polydispersity, which leads to obstacles, imposing labour-intensive experimental iterations for the application of fluorescence-encoded microbeads as a distinguishable barcode. Herein, a simple simulation strategy based on a multicolor fluorescence model (MFM) was used to predict the influence of the microbeads' size distribution on the barcode signals. The point L and S respectively represent the two end points of the barcode, and the line segment LS can be considered as a cluster of the QD-encoded microbeads (simulated barcode). Experimental clusters of fluorescent microbeads were found to be in good agreement with the simulated barcodes. This simple simulation strategy can effectively simplify the experimental iteration process because the fluorescence-encoded microbeads are not decoded by a flow cytometer. Moreover, when applied for the high-throughput ultrasensitive detection of three tumor markers (CEA, CA125 and CA199) in a single sample, these barcodes exhibit superior detection performance. Detection limits of 0.028 ± 0.001 ng mL-1 for CEA, 1.5 ± 0.02 KU L-1 for CA125 and 0.8 ± 0.1 KU L-1 for CA199 are achieved, which meet the sensitivity criteria of tumor marker analysis. Therefore, this simple simulation strategy helps to overcome technical and economic obstacles for the widespread application of SA.},
}
@article {pmid34257929,
year = {2021},
author = {Jang-Liaw, NH},
title = {A barcoding-based scat-analysis assessment of Eurasian otter Lutra lutra diet on Kinmen Island.},
journal = {Ecology and evolution},
volume = {11},
number = {13},
pages = {8795-8813},
pmid = {34257929},
issn = {2045-7758},
abstract = {While it is well known that Eurasian otters principally feed on fishes and crustaceans, their detailed diet taxonomies are not fully understood. This is partly due to their nocturnal behavior and the limited resolving power of traditional morphological identification from scat. A suitable, reliable molecular method for diet studies is therefore needed.I performed a series of Sanger-sequencing reactions, utilizing nine primer sets for Eurasian otter diet research. These are mainly based on the barcoding concept to determine the taxonomic composition of spraints. The primer sets target different types of animals, amplifying each separately. This procedure was used to detect the prey contents of 64 spraint samples collected from Kinmen Island. Through high-resolution gel electrophoresis and sequencing, it was evident that PCR products could be successfully amplified by the different primer sets and from spraint samples comprising multiple prey species.Extracted DNA from all spraint samples was PCR-amplified with 9 primer sets. In total, 16 prey types were identified across all 64 samples. Fourteen were identified at the species level.The aim of this study was to develop and apply a novel diet research method to Eurasian otters. Eight of the primers are universal primers designed for COI segments of different animal groups, and one primer set was designed specifically for tilapia groups. This method can be applied to study the diets of not only Kinmen Eurasian otter populations, but also other Eurasian otter populations and other small carnivorous animals.},
}
@article {pmid34257510,
year = {2021},
author = {Hansen, S and Addison, P and Benoit, L and Haran, JM},
title = {Barcoding pest species in a biodiversity hot-spot: the South African polyphagous broad-nosed weevils (Coleoptera, Curculionidae, Entiminae).},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e66452},
pmid = {34257510},
issn = {1314-2828},
abstract = {Polyphagous broad nosed weevils (Curculionidae: Entiminae) constitute a large and taxonomically challenging subfamily that contains economically significant agricultural pests worldwide. South Africa is a hot-spot for biodiversity and several species of indigenous and endemic genera of Entiminae have shifted on to cultivated plants, with some being phytosanitary pests. The sporadic pest status of many species (where the species has an occasional economic impact on the agricultural industry, but is not encountered often enough that is is readily recognisable by researchers and agricultural extension workers) and the presence of pest complexes and cryptic species represent an identification challenge to non-specialists. Furthermore, no comprehensive identification tools exist to identify immature stages that may be found in crops/soil. In this paper, a curated barcoding database with 70 COI sequences from 41 species (39 Entiminae, 2 Cyclominae) is initiated, to assist with the complexity of identification of species in this group.},
}
@article {pmid34254973,
year = {2021},
author = {Ribolli, J and Zaniboni Filho, E and Scaranto, BMS and Shibatta, OA and Machado, CB},
title = {Cryptic diversity and diversification processes in three cis-Andean Rhamdia species (Siluriformes: Heptapteridae) revealed by DNA barcoding.},
journal = {Genetics and molecular biology},
volume = {44},
number = {3},
pages = {e20200470},
pmid = {34254973},
issn = {1415-4757},
abstract = {The wide distribution of the Neotropical freshwater catfish Rhamdia offers an excellent opportunity to investigate the historical processes responsible for modeling South America's hydrogeological structure. We used sequences from cis-Andean and Mesoamerican Rhamdia species to reconstruct and estimate divergence times among cis-Andean lineages, correlating the results with known geological events. Species delimitation methods based on distance (DNA barcoding and BIN) and coalescence (GMYC) approaches identified nine well-supported lineages from the cis-Andean region from sequences available in the BOLD dataset. The cis-Andean Rhamdia lineages diversification process began in Eocene and represented the split between cis-Andean and Mesoamerican clades. The cis-Andean clade contains two principal groups: Northwest clade (MOTUs from Amazon, Essequibo, Paraguay, and Itapecuru basins) and Southeast clade (Eastern Brazilian shield basins (Paraná, Uruguay, Iguaçu, and São Francisco) plus eastern coastal basins). The diversification of the cis-Andean Rhamdia lineages results from vicariance and geodispersion events, which played a key role in the current intricate distribution pattern of the Rhamdia lineages. The wide geographical distribution and large size of the specimens make it attractive to cultivate in different countries of the Neotropical region. The lineages delimitation minimizes identification mistakes, unintentional crossings by aquaculture, and reduces natural stocks contamination.},
}
@article {pmid34253607,
year = {2021},
author = {Steele, MP and Neaves, LE and Klump, BC and St Clair, JJH and Fernandes, JRSM and Hequet, V and Shaw, P and Hollingsworth, PM and Rutz, C},
title = {DNA barcoding identifies cryptic animal tool materials.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {29},
pages = {},
pmid = {34253607},
issn = {1091-6490},
support = {BB/G023913/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/G023913/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; RPG-2015-273/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Crows ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Nesting Behavior/physiology ; Phylogeny ; Plant Structures/anatomy &amp; histology/classification/genetics ; Tool Use Behavior/*physiology ; },
abstract = {Some animals fashion tools or constructions out of plant materials to aid foraging, reproduction, self-maintenance, or protection. Their choice of raw materials can affect the structure and properties of the resulting artifacts, with considerable fitness consequences. Documenting animals' material preferences is challenging, however, as manufacture behavior is often difficult to observe directly, and materials may be processed so heavily that they lack identifying features. Here, we use DNA barcoding to identify, from just a few recovered tool specimens, the plant species New Caledonian crows (Corvus moneduloides) use for crafting elaborate hooked stick tools in one of our long-term study populations. The method succeeded where extensive fieldwork using an array of conventional approaches-including targeted observations, camera traps, radio-tracking, bird-mounted video cameras, and behavioral experiments with wild and temporarily captive subjects-had failed. We believe that DNA barcoding will prove useful for investigating many other tool and construction behaviors, helping to unlock significant research potential across a wide range of study systems.},
}
@article {pmid34250772,
year = {2021},
author = {Can, H and Köseoğlu, AE and Erkunt Alak, S and Güvendi, M and Ün, C and Karakavuk, M and Değirmenci Döşkaya, A and Aykur, M and Aksoy Gökmen, A and Gürüz, AY and Döşkaya, M},
title = {Molecular prevalence and subtyping of Blastocystis sp. isolates in stray cats of İzmir, Turkey: First report of "ST4 allele 42" in cats.},
journal = {Polish journal of veterinary sciences},
volume = {24},
number = {2},
pages = {217-223},
doi = {10.24425/pjvs.2021.137656},
pmid = {34250772},
issn = {2300-2557},
mesh = {Animals ; Blastocystis/*classification/genetics ; Blastocystis Infections/epidemiology/parasitology/*veterinary ; Cat Diseases/*parasitology ; Cats ; Phylogeny ; Turkey/epidemiology ; },
abstract = {Blastocystis sp. is one of the most frequently detected intestinal parasites in humans and can inhabit a wide range of animals. Close contact with animals is one of the transmission factors of Blastocystis sp. infection in humans. In this study, we aimed to investigate the molecular prevalence and subtypes of Blastocystis sp. in stray cats living in İzmir, Turkey. The PCR target- ing the barcode region in the SSU rRNA gene was performed with DNA samples isolated from feces (n:465) to investigate the presence of Blastocystis sp. PCR positive samples were sequen- ced for subtyping analysis. Among the samples analyzed, Blastocystis sp. DNA was detected in 17 (3.65%) of them and sequence data were obtained from only seven isolates. Phylogenetic analysis showed that seven Blastocystis sp. isolates clustered with the reference Blastocystis ST4 isolates. Similarity rates were between 83.22% and 99.25%. In addition, Blastocystis database results confirmed that all of these were "allele 42" corresponding to ST4. As a result, the present study shows for the first time the presence of "ST4 allele 42", the prevalent subtype in humans, in stray cats in İzmir, Turkey. This finding supports the notion that stray cats can be a source of Blastocystis sp. infection in humans.},
}
@article {pmid34250419,
year = {2021},
author = {Varghese, AM and Patel, J and Janjigian, YY and Meng, F and Selcuklu, SD and Iyer, G and Houck-Loomis, B and Harding, JJ and O'Reilly, EM and Abou-Alfa, GK and Lowery, MA and Berger, MF},
title = {Noninvasive Detection of Polyclonal Acquired Resistance to FGFR Inhibition in Patients With Cholangiocarcinoma Harboring FGFR2 Alterations.},
journal = {JCO precision oncology},
volume = {5},
number = {},
pages = {},
pmid = {34250419},
issn = {2473-4284},
support = {P30 CA008748/CA/NCI NIH HHS/United States ; },
mesh = {Antineoplastic Agents/*therapeutic use ; Bile Duct Neoplasms/*blood/*drug therapy/*genetics ; *Bile Ducts, Intrahepatic ; Cholangiocarcinoma/*blood/*drug therapy/*genetics ; Circulating Tumor DNA/*blood ; Drug Resistance, Neoplasm/*genetics ; Humans ; Mutation ; Receptor, Fibroblast Growth Factor, Type 2/*antagonists &amp; inhibitors/*genetics ; },
abstract = {PURPOSE: Fibroblast growth factor receptor (FGFR) 2 alterations, present in 5%-15% of intrahepatic cholangiocarcinomas (IHC), are targets of FGFR-directed therapies. Acquired resistance is common among patients who respond. Biopsies at the time of acquired resistance to targeted agents may not always be feasible and may not capture the genetic heterogeneity that could exist within a patient. We studied circulating tumor DNA (ctDNA) as a less invasive means of potentially identifying genomic mechanisms of resistance to FGFR-targeted therapies.<br><br>MATERIALS AND METHODS: Serial blood samples were collected from eight patients with FGFR-altered cholangiocarcinoma for ctDNA isolation and next-generation sequencing (NGS) throughout treatment and at resistance to anti-FGFR-targeted therapy. ctDNA was sequenced using a custom ultra-deep coverage NGS panel, incorporating dual index primers and unique molecular barcodes to enable high-sensitivity mutation detection.<br><br>RESULTS: Thirty-one acquired mutations in FGFR2, 30/31 located in the kinase domain, were identified at resistance in six of eight patients with detectable ctDNA. Up to 13 independent FGFR2 mutations were detected per patient, indicative of striking genomic concordance among resistant subclones.<br><br>CONCLUSION: ctDNA could be an effective means to longitudinally monitor for acquired resistance in FGFR2-altered IHC. The numerous acquired genetic alterations in FGFR2 suggest frequent polyclonal mechanisms of resistance that cannot be detected from single-site tissue biopsies.},
}
@article {pmid34250083,
year = {2021},
author = {Romila, CA and Townsend, S and Malecki, M and Kamrad, S and Rodríguez-López, M and Hillson, O and Cotobal, C and Ralser, M and Bähler, J},
title = {Barcode sequencing and a high-throughput assay for chronological lifespan uncover ageing-associated genes in fission yeast.},
journal = {Microbial cell (Graz, Austria)},
volume = {8},
number = {7},
pages = {146-160},
pmid = {34250083},
issn = {2311-2638},
support = {/WT_/Wellcome Trust/United Kingdom ; FC001134/ARC_/Arthritis Research UK/United Kingdom ; },
abstract = {Ageing-related processes are largely conserved, with simple organisms remaining the main platform to discover and dissect new ageing-associated genes. Yeasts provide potent model systems to study cellular ageing owing their amenability to systematic functional assays under controlled conditions. Even with yeast cells, however, ageing assays can be laborious and resource-intensive. Here we present improved experimental and computational methods to study chronological lifespan in Schizosaccharomyces pombe. We decoded the barcodes for 3206 mutants of the latest gene-deletion library, enabling the parallel profiling of ~700 additional mutants compared to previous screens. We then applied a refined method of barcode sequencing (Bar-seq), addressing technical and statistical issues raised by persisting DNA in dead cells and sampling bottlenecks in aged cultures, to screen for mutants showing altered lifespan during stationary phase. This screen identified 341 long-lived mutants and 1246 short-lived mutants which point to many previously unknown ageing-associated genes, including 46 conserved but entirely uncharacterized genes. The ageing-associated genes showed coherent enrichments in processes also associated with human ageing, particularly with respect to ageing in non-proliferative brain cells. We also developed an automated colony-forming unit assay to facilitate medium- to high-throughput chronological-lifespan studies by saving time and resources compared to the traditional assay. Results from the Bar-seq screen showed good agreement with this new assay. This study provides an effective methodological platform and identifies many new ageing-associated genes as a framework for analysing cellular ageing in yeast and beyond.},
}
@article {pmid34242004,
year = {2021},
author = {Huang, Q and Chen, B and Shen, J and Liu, L and Li, J and Shi, J and Li, Q and Zuo, X and Wang, L and Fan, C and Li, J},
title = {Encoding Fluorescence Anisotropic Barcodes with DNA Fameworks.},
journal = {Journal of the American Chemical Society},
volume = {143},
number = {28},
pages = {10735-10742},
doi = {10.1021/jacs.1c04942},
pmid = {34242004},
issn = {1520-5126},
mesh = {Animals ; DNA/*analysis ; *Fluorescence Polarization ; Fluorescent Dyes/*chemistry ; Mice ; Optical Imaging ; Tumor Cells, Cultured ; },
abstract = {Fluorescence anisotropy (FA) holds great potential for multiplexed analysis and imaging of biomolecules since it can effectively discriminate fluorophores with overlapping emission spectra. Nevertheless, its susceptibility to environmental variation hampers its widespread applications in biology and biotechnology. In this study, we design FA DNA frameworks (FAFs) by scaffolding fluorophores in a fluorescent protein-like microenvironment. We find that the FA stability of the fluorophores is remarkably improved due to the sequestration effects of FAFs. The FA level of the fluorophores can be finely tuned when placed at different locations on an FAF, analogous to spectral shifts of protein-bound fluorophores. The high programmability of FAFs further enables the design of a spectrum of encoded FA barcodes for multiplexed sensing of nucleic acids and multiplexed labeling of live cells. This FAF system thus establishes a new paradigm for designing multiplexing FA probes for cellular imaging and other biological applications.},
}
@article {pmid34240574,
year = {2021},
author = {Cheng, J and Liao, J and Shao, X and Lu, X and Fan, X},
title = {Multiplexing Methods for Simultaneous Large-Scale Transcriptomic Profiling of Samples at Single-Cell Resolution.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {8},
number = {17},
pages = {e2101229},
pmid = {34240574},
issn = {2198-3844},
support = {81973701//National Natural Science Foundation of China/ ; LZ20H290002//Natural Science Foundation of Zhejiang Province/ ; W02070098//National Youth Top-notch Talent Support Program/ ; },
mesh = {Animals ; COVID-19/genetics ; DNA Barcoding, Taxonomic/*methods ; Gene Expression Profiling/*methods ; Humans ; Sequence Analysis, RNA/methods ; Transcriptome/*genetics ; },
abstract = {Barcoding technology has greatly improved the throughput of cells and genes detected in single-cell RNA sequencing (scRNA-seq) studies. Recently, increasing studies have paid more attention to the use of this technology to increase the throughput of samples, as it has greatly reduced the processing time, technical batch effects, and library preparation costs, and lowered the per-sample cost. In this review, the various DNA-based barcoding methods for sample multiplexing are focused on, specifically, on the four major barcoding strategies. A detailed comparison of the barcoding methods is also presented, focusing on aspects such as sample/cell throughput and gene detection, and guidelines for choosing the most appropriate barcoding technique according to the personalized requirements are developed. Finally, the critical applications of sample multiplexing and technical challenges in combinatorial labeling, barcoding in vivo, and multimodal tagging at the spatially resolved resolution, as well as, the future prospects of multiplexed scRNA-seq, for example, prioritizing and predicting the severity of coronavirus disease 2019 (COVID-19) in patients of different gender and age are highlighted.},
}
@article {pmid34239341,
year = {2021},
author = {Yang, LL and Li, HH},
title = {First report of the genus Pelecystola Meyrick (Lepidoptera, Tineidae) in China, with description of a new species.},
journal = {ZooKeys},
volume = {1046},
number = {},
pages = {189-206},
pmid = {34239341},
issn = {1313-2989},
abstract = {The genus Pelecystola Meyrick, 1920 and the species Pelecystola strigosa (Moore, 1888) are newly recorded from China, and Pelecystola peculiaris sp. nov. is described as new to science. Adults, head, venation, and genitalia of the two species are illustrated. A molecular phylogenetic analysis is presented to ascertain the generic affiliation of the new species. Forty-four species of 38 genera in Tineidae are analyzed using maximum likelihood methods based on one mitochondrial (COI) and two nuclear gene fragments (CAD and wingless). DNA barcodes of the two species are provided, and the genetic distance of barcode divergence among four species of Pelecystola is calculated.},
}
@article {pmid34239338,
year = {2021},
author = {Ji, SJ and Lee, CW and Min, GS},
title = {A new species of Hangangbathynella (Crustacea, Bathynellacea, Parabathynellidae) from South Korea.},
journal = {ZooKeys},
volume = {1046},
number = {},
pages = {143-155},
pmid = {34239338},
issn = {1313-2989},
abstract = {A new parabathynellid bathynellacean species, Hangangbathynella mihoensis sp. nov., was found in the groundwater of the Geumgang River in South Korea. This is the first report of Hangangbathynella from a tributary of the Geumgang River. All previously-reported species were found in the Hangang River and the origins of the two rivers are distinct from each other. The new species can be distinguished from its congeners by the two-segmented mandibular palp and the absence of epipods on thoracopod II. In this study, we provide a description of the new species and an identification table for the genus Hangangbathynella. In addition, we obtained partial sequences of the mitochondrial cytochrome c oxidase subunit I gene for DNA barcoding.},
}
@article {pmid34239337,
year = {2021},
author = {Jordaens, K and Goergen, G and Skevington, JH and Kelso, S and Meyer, M},
title = {Revision of the Afrotropical species of the hover fly genus Mesembrius Rondani (Diptera, Syrphidae) using morphological and molecular data.},
journal = {ZooKeys},
volume = {1046},
number = {},
pages = {1-141},
pmid = {34239337},
issn = {1313-2989},
abstract = {The Afrotropical representatives of the hover fly genus Mesembrius Rondani, 1857 (Diptera) are divided into two subgenera, namely Mesembrius s.s. and Vadonimyia Séguy, 1951 and, in this present work, the subgenus Mesembrius s.s. is revised. A total of 23 Mesembrius s.s. species are recognised for the Afrotropics. Known species are re-described and six species new to science are described: Mesembrius arcuatus sp. nov., M. copelandi sp. nov., M. longipilosus sp. nov., M. sulcus sp. nov., M. tibialis sp. nov. and M. vockerothi sp. nov. Mesembrius africanus (Verrall, 1898) is considered a junior synonym of M. senegalensis (Macquart, 1842), M. ctenifer Hull, 1941 a junior synonym of M. caffer (Loew, 1858), M. lagopus (Loew, 1869) a junior synonym of M. capensis (Macquart, 1842) and M. platytarsis Curran, 1929 a junior synonym of M. simplicipes Curran, 1929. The females of Mesembrius chapini Curran, 1939, M. rex Curran, 1927 and M. regulus (Hull, 1937) are described for the first time. Lectotypes are designated for Mesembrius caffer, M. capensis, M. cyanipennis (Bezzi, 1915), M. minor (Bezzi, 1915), M. senegalensis, M. strigilatus (Bezzi, 1912) and M. tarsatus (Bigot, 1883). Separate identification keys for males and females are presented. We obtained 236 DNA barcodes for 18 species. The relationships amongst the different Mesembrius species are briefly discussed, based on morphological and DNA barcode data.},
}
@article {pmid34238969,
year = {2021},
author = {Wengrat, APGS and Coelho Junior, A and Parra, JRP and Takahashi, TA and Foerster, LA and Corrêa, AS and Polaszek, A and Johnson, NF and Costa, VA and Zucchi, RA},
title = {Integrative taxonomy and phylogeography of Telenomus remus (Scelionidae), with the first record of natural parasitism of Spodoptera spp. in Brazil.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {14110},
pmid = {34238969},
issn = {2045-2322},
mesh = {Animals ; Brazil ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Genitalia, Male/anatomy &amp; histology ; Haplotypes/genetics ; Hymenoptera/anatomy &amp; histology/*classification ; Male ; Parasites/anatomy &amp; histology/*classification ; *Phylogeography ; Spodoptera/*parasitology ; },
abstract = {The egg parasitoid Telenomus remus (Hymenoptera: Scelionidae) has been investigated for classical and applied biological control of noctuid pests, especially Spodoptera (Lepidoptera: Noctuidae) species. Although T. remus was introduced into Brazil over three decades ago for classical biological control of S. frugiperda, this wasp has not been recorded as established in corn or soybean crops. We used an integrative approach to identify T. remus, combining a taxonomic key based on the male genitalia with DNA barcoding, using a cytochrome c oxidase subunit I mitochondrial gene fragment. This is the first report of natural parasitism of T. remus on S. frugiperda and S. cosmioides eggs at two locations in Brazil. We also confirmed that the T. remus lineage in Brazil derives from a strain in Venezuela (originally from Papua New Guinea and introduced into the Americas, Africa, and Asia). The occurrence of T. remus parasitizing S. frugiperda and S. cosmioides eggs in field conditions, not associated with inundative releases, suggests that the species has managed to establish itself in the field in Brazil. This opens possibilities for future biological control programs, since T. remus shows good potential for mass rearing and egg parasitism of important agricultural pests such as Spodoptera species.},
}
@article {pmid34235285,
year = {2021},
author = {Wang, F and Zhuo, B and Wang, S and Lou, J and Zhang, Y and Chen, Q and Shi, Z and Song, Y and Tu, P},
title = {Atriplex canescens: A new host for Cistanche deserticola.},
journal = {Heliyon},
volume = {7},
number = {6},
pages = {e07368},
pmid = {34235285},
issn = {2405-8440},
abstract = {Cistanche deserticola has been historically used in traditional Chinese medicine for supplementing kidney (yang) function, benefiting blood and essence, and moistening intestines in order to pass stool. Its host, Haloxylon ammodendron, is an important pioneer plant used for windbreaks and sand dune fixation, which are strategies used for the control desertification. For a long time, it has been considered that C. deserticola can only parasitize H. ammodendron. In this study, morphological identification, gene barcoding identification and inoculation experiment were carried out, we finally found that C. deserticola can also parasitize Atriplex canescens. A. canescens is a species of Chenopodiaceae with a wide range of adaptability. Compared with H. ammodendron, it has more biomass and a wider range of ecological adaptability, making it more suitable for the industrial production of C. deserticola. In addition, we also found that the concentration of active components was higher in C. deserticola parasitized on A. canescens than in those parasitized on H. ammodendron; this finding further suggests that the application of C. deserticola on a larger scale warrants further exploration.},
}
@article {pmid34234748,
year = {2021},
author = {Wylezich, C and Höper, D},
title = {Meta-Ribosomalomics: RNA Sequencing Is an Unbiased Method for Parasite Detection of Different Sample Types.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {614553},
pmid = {34234748},
issn = {1664-302X},
abstract = {In this perspective article, we review the past use of ribosomal sequences to address scientific and diagnostic questions. We highlight a variety of sequencing approaches including metagenomics and DNA barcoding and their different demands and requirements. Meta-ribosomalomics is introduced as an unbiased approach to exploit high-throughput sequencing datasets for eukaryotic and prokaryotic ribosomal sequences. Prerequisites, benefits, drawbacks, and future perspectives are elaborated and compared to other sequencing approaches.},
}
@article {pmid34233875,
year = {2021},
author = {Berthelet, J and Wimmer, VC and Whitfield, HJ and Serrano, A and Boudier, T and Mangiola, S and Merdas, M and El-Saafin, F and Baloyan, D and Wilcox, J and Wilcox, S and Parslow, AC and Papenfuss, AT and Yeo, B and Ernst, M and Pal, B and Anderson, RL and Davis, MJ and Rogers, KL and Hollande, F and Merino, D},
title = {The site of breast cancer metastases dictates their clonal composition and reversible transcriptomic profile.},
journal = {Science advances},
volume = {7},
number = {28},
pages = {},
pmid = {34233875},
issn = {2375-2548},
mesh = {*Breast Neoplasms/genetics/pathology ; Female ; Humans ; *Liver Neoplasms/genetics/pathology ; *Lung Neoplasms/pathology ; Neoplasm Metastasis ; Transcriptome ; Tumor Microenvironment/genetics ; },
abstract = {Intratumoral heterogeneity is a driver of breast cancer progression, but the nature of the clonal interactive network involved in this process remains unclear. Here, we optimized the use of optical barcoding to visualize and characterize 31 cancer subclones in vivo. By mapping the clonal composition of thousands of metastases in two clinically relevant sites, the lungs and liver, we found that metastases were highly polyclonal in lungs but not in the liver. Furthermore, the transcriptome of the subclones varied according to their metastatic niche. We also identified a reversible niche-driven signature that was conserved in lung and liver metastases collected during patient autopsies. Among this signature, we found that the tumor necrosis factor-α pathway was up-regulated in lung compared to liver metastases, and inhibition of this pathway affected metastasis diversity. These results highlight that the cellular and molecular heterogeneity observed in metastases is largely dictated by the tumor microenvironment.},
}
@article {pmid34233085,
year = {2022},
author = {Jin, L and Liu, JJ and Xiao, TW and Li, QM and Lin, LX and Shao, XN and Ma, CX and Li, BH and Mi, XC and Ren, HB and Qiao, XJ and Lian, JY and Hao, G and Ge, XJ},
title = {Plastome-based phylogeny improves community phylogenetics of subtropical forests in China.},
journal = {Molecular ecology resources},
volume = {22},
number = {1},
pages = {319-333},
doi = {10.1111/1755-0998.13462},
pmid = {34233085},
issn = {1755-0998},
support = {31500335//National Natural Science Foundation of China/ ; XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
mesh = {China ; *Forests ; Phylogeny ; },
abstract = {Phylogenetic trees have been extensively used in community ecology. However, how the phylogeny construction affects ecological inferences is poorly understood. In this study, we constructed three different types of phylogenetic trees (a synthetic-tree generated using V.PhyloMaker, a barcode-tree generated using rbcL+matK+trnH-psbA, and a plastome-tree generated from plastid genomes) that represented an increasing level of phylogenetic resolution among 580 woody plant species from six forest dynamic plots in subtropical evergreen broadleaved forests of China. We then evaluated the performance of each phylogeny in estimations of community phylogenetic structure, turnover and phylogenetic signal in functional traits. As expected, the plastome-tree was most resolved and most supported for relationships among species. For local phylogenetic structure, the three trees showed consistent results with Faith's PD and MPD; however, only the synthetic-tree produced significant clustering patterns using MNTD for some plots. For phylogenetic turnover, contrasting results between the molecular trees and the synthetic-tree occurred only with nearest neighbor distance. The barcode-tree agreed more with the plastome-tree than the synthetic-tree for both phylogenetic structure and turnover. For functional traits, both the barcode-tree and plastome-tree detected phylogenetic signal in maximum height, but only the plastome-tree detected signal in leaf width. This is the first study that uses plastid genomes in large-scale community phylogenetics. Our results highlight the improvement of plastome-trees over barcode-trees and synthetic-trees for the analyses studied here. Our results also point to the possibility of type I and II errors in estimation of phylogenetic structure and turnover and detection of phylogenetic signal when using synthetic-trees.},
}
@article {pmid34225754,
year = {2021},
author = {Wu, L and Wu, M and Cui, N and Xiang, L and Li, Y and Li, X and Chen, S},
title = {Plant super-barcode: a case study on genome-based identification for closely related species of Fritillaria.},
journal = {Chinese medicine},
volume = {16},
number = {1},
pages = {52},
pmid = {34225754},
issn = {1749-8546},
support = {81903758//National Natural Science Foundation of China/ ; 31900258//National Natural Science Foundation of China/ ; No.2017YFB1002303//National key research and development plan/ ; No.ZZ10-007//Key Research Project of China Academy of Chinese Medical Sciences of the 13th Five-Year Plan/ ; No.2019ZX09731002//Major Scientific and Technological Special Project for "Major New Drug Creation"/ ; ZZ13-YQ-106-C1//Fundamental Research Funds for the Central public welfare research institutes/ ; },
abstract = {BACKGROUND: Although molecular analysis offers a wide range of options for species identification, a universal methodology for classifying and distinguishing closely related species remains elusive. This study validated the effectiveness of utilizing the entire chloroplast (cp) genome as a super-barcode to help identify and classify closely related species.<br><br>METHODS: We here compared 26 complete cp genomes of ten Fritillaria species including 18 new sequences sequenced in this study. Each species had repeats and the cp genomes were used as a whole DNA barcode to test whether they can distinguish Fritillaria species.<br><br>RESULTS: The cp genomes of Fritillaria medicinal plants were conserved in genome structure, gene type, and gene content. Comparison analysis of the Fritillaria cp genomes revealed that the intergenic spacer regions were highly divergent compared with other regions. By constructing the phylogenetic tree by the maximum likelihood and maximum parsimony methods, we found that the entire cp genome showed a high discrimination power for Fritillaria species with individuals of each species in a monophyletic clade. These results indicate that cp genome can be used to effectively differentiate medicinal plants from the genus Fritillaria at the species level.<br><br>CONCLUSIONS: This study implies that cp genome can provide distinguishing differences to help identify closely related Fritillaria species, and has the potential to be served as a universal super-barcode for plant identification.},
}
@article {pmid34224654,
year = {2022},
author = {Christianson, LM and Johnson, SB and Schultz, DT and Haddock, SHD},
title = {Hidden diversity of Ctenophora revealed by new mitochondrial COI primers and sequences.},
journal = {Molecular ecology resources},
volume = {22},
number = {1},
pages = {283-294},
pmid = {34224654},
issn = {1755-0998},
support = {R01 GM087198/GM/NIGMS NIH HHS/United States ; R01-GM087198/NH/NIH HHS/United States ; //David and Lucile Packard Foundation/ ; NSF-DEB 1542679//National Science Foundation/ ; },
mesh = {Animals ; *Ctenophora/genetics ; Phylogeny ; },
abstract = {The mitochondrial gene cytochrome-c-oxidase subunit 1 (COI) is useful in many taxa for phylogenetics, population genetics, metabarcoding, and rapid species identifications. However, the phylum Ctenophora (comb jellies) has historically been difficult to study due to divergent mitochondrial sequences and the corresponding inability to amplify COI with degenerate and standard COI "barcoding" primers. As a result, there are very few COI sequences available for ctenophores, despite over 200 described species in the phylum. Here, we designed new primers and amplified the COI fragment from members of all major groups of ctenophores, including many undescribed species. Phylogenetic analyses of the resulting COI sequences revealed high diversity within many groups that was not evident from more conserved 18S rDNA sequences, in particular among the Lobata (Ctenophora; Tentaculata; Lobata). The COI phylogenetic results also revealed unexpected community structure within the genus Bolinopsis, suggested new species within the genus Bathocyroe, and supported the ecological and morphological differences of some species such as Lampocteis cruentiventer and similar undescribed lobates (Lampocteis sp. "V" stratified by depth, and "A" differentiated by colour). The newly designed primers reported herein provide important tools to enable researchers to illuminate the diversity of ctenophores worldwide via quick molecular identifications, improve the ability to analyse environmental DNA by improving reference libraries and amplifications, and enable a new breadth of population genetic studies.},
}
@article {pmid34224097,
year = {2021},
author = {De Luca, G and Dono, M},
title = {The Opportunities and Challenges of Molecular Tagging Next-Generation Sequencing in Liquid Biopsy.},
journal = {Molecular diagnosis &amp; therapy},
volume = {25},
number = {5},
pages = {537-547},
pmid = {34224097},
issn = {1179-2000},
mesh = {*Cell-Free Nucleic Acids ; High-Throughput Nucleotide Sequencing ; Humans ; Laboratories, Clinical ; Liquid Biopsy ; *Skin Neoplasms ; },
abstract = {Liquid biopsy (LB) is a promising tool that is rapidly evolving as a standard of care in early and advanced stages of cancer settings. Next-generation sequencing (NGS) methods have become essential in molecular diagnostics and clinical laboratories dealing with LB analytes, i.e., cell-free DNA and RNA. The sensitivity and high-throughput capacity of NGS enable us to overcome technical issues that are mainly attributable to low-abundance (below 1% mutated allelic frequency) tumour genetic material circulating within biological fluids. In this context, the introduction of unique molecular identifiers (UMIs), also known as molecular barcodes, applied to various NGS platforms greatly improved the characterization of rare genetic alterations, as they resulted in a drastic reduction in background noise while maintaining high levels of positive predictive value and sensitivity. Different UMI strategies have been developed, such as single (e.g., safe-sequencing system, Safe-SeqS) or double (duplex-sequencing system, Duplex-Seq) strand-based labelling, and, currently, considerable results corroborate their potential implementation in a routine laboratory. Recently, the US Food and Drug Administration approved the clinical use of two comprehensive UMI-based NGS assays (FoundationOne Liquid CDx and Guardant360 CDx) in cfDNA mutational assessment. However, to definitively translate LB into clinical practice, UMI-based NGS protocols should meet certain feasibility requirements in terms of cost-effectiveness, wet laboratory performance and easy access to web-source and bioinformatic tools for downstream molecular data.},
}
@article {pmid34223816,
year = {2021},
author = {Alford, BD and Tassoni-Tsuchida, E and Khan, D and Work, JJ and Valiant, G and Brandman, O},
title = {ReporterSeq reveals genome-wide dynamic modulators of the heat shock response across diverse stressors.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
pmid = {34223816},
issn = {2050-084X},
support = {R01GM115968/NH/NIH HHS/United States ; 5 T32 GM007276/NH/NIH HHS/United States ; R01 GM115968/GM/NIGMS NIH HHS/United States ; T32 GM007276/GM/NIGMS NIH HHS/United States ; 1704417//National Science Foundation/ ; N00014-18-1-2295//Office of Naval Research/ ; 1813049//National Science Foundation/ ; },
mesh = {Gene Expression Regulation, Fungal/*genetics ; Genome, Fungal/*physiology ; Heat-Shock Response/*genetics ; Reverse Genetics ; Saccharomyces cerevisiae/genetics/*physiology ; Saccharomyces cerevisiae Proteins/*metabolism ; Transcription Factors/*metabolism ; },
abstract = {Understanding cellular stress response pathways is challenging because of the complexity of regulatory mechanisms and response dynamics, which can vary with both time and the type of stress. We developed a reverse genetic method called ReporterSeq to comprehensively identify genes regulating a stress-induced transcription factor under multiple conditions in a time-resolved manner. ReporterSeq links RNA-encoded barcode levels to pathway-specific output under genetic perturbations, allowing pooled pathway activity measurements via DNA sequencing alone and without cell enrichment or single-cell isolation. We used ReporterSeq to identify regulators of the heat shock response (HSR), a conserved, poorly understood transcriptional program that protects cells from proteotoxicity and is misregulated in disease. Genome-wide HSR regulation in budding yeast was assessed across 15 stress conditions, uncovering novel stress-specific, time-specific, and constitutive regulators. ReporterSeq can assess the genetic regulators of any transcriptional pathway with the scale of pooled genetic screens and the precision of pathway-specific readouts.},
}
@article {pmid34221719,
year = {2021},
author = {Gao, J and Chen, T and Jiang, C and Wang, T and Huang, O and Zhang, X and Liu, J},
title = {Comparative anatomical and transcriptomic analyses of the color variation of leaves in Aquilaria sinensis.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e11586},
pmid = {34221719},
issn = {2167-8359},
abstract = {Color variation in plant tissues is a common phenomenon accompanied with a series of biological changes. In this study, a special-phenotype Aquilaria sinensis (GS) with color variation of leaf was firstly reported, and DNA barcode sequences showed GS samples could not be discriminated clearly with the normal A. sinensis sample (NS), which suggested that the variety was not the cause of the GS formation. To reveal the characteristics of GS compared to NS, the anatomical and transcriptome sequencing studies were carried out. In microscopic observation, the leaves of golden-vein-leaf sample (LGS) and normal-vein-leaf sample (LNS) showed significant differences including the area of the included phloem in midrib and the thickness parameters of palisade and spongy tissues; the stems of golden-vein-leaf sample (SGS) and normal-vein-leaf sample (SNS) were also different in many aspects such as the area of vessels and included phloem. In addition, the structure of chloroplast was more complete in the midrib of LNS than that of LGS, and some particles suspected as virus were found through transmission electron microscope as well. Genes upregulated in LGS in contrast with LNS were mainly enriched in photosynthesis. As for stems, most of the genes upregulated in SGS compared to SNS were involved in translation and metabolism processes. The pathways about photosynthesis and chlorophyll metabolism as well as some important transcription factors may explain the molecular mechanism of the unique phenotypes of leaves and the genes related to suberin biosynthesis may result in the difference of stems. In addition, the genes about defense response especially biotic stress associated with numerous pathogenesis-related (PR) genes upregulated in LGS compared to LNS indicated that the pathogen may be the internal factor. Taken together, our results reveal the macro- and micro-phenotype variations as well as gene expression profiles between GS and NS, which could provide valuable clues for elucidating the mechanism of the color variation of Aquilaria.},
}
@article {pmid34221248,
year = {2021},
author = {Lukhtanov, VA and Gagarina, AV and Pazhenkova, EA},
title = {Chromosomal and DNA barcode analysis of the Melitaea ala Staudinger, 1881 species complex (Lepidoptera, Nymphalidae).},
journal = {Comparative cytogenetics},
volume = {15},
number = {2},
pages = {199-216},
pmid = {34221248},
issn = {1993-0771},
abstract = {The species of the Melitaea ala Staudinger, 1881 complex are distributed in Central Asia. Here we show that this complex is a monophyletic group including the species, M. ala, M. kotshubeji Sheljuzhko, 1929 and M. enarea Fruhstorfer, 1917. The haploid chromosome number n=29 is found in M. ala and M. kotshubeji and is, most likely, a symplesiomorphy of the M. ala complex. We show that M. ala consists of four subspecies: M. ala zaisana Lukhtanov, 1999 (=M. ala irtyshica Lukhtanov, 1999, syn. nov.) (South Altai, Zaisan Lake valley), M. ala ala (Dzhungarian Alatau), M. ala bicolor Seitz, 1908 (North, East, Central and West Tian-Shan) and M. ala determinata Bryk, 1940 (described from "Fu-Shu-Shi", China). We demonstrate that M. kotshubeji kotshubeji (Peter the Great Mts in Tajikistan) and M. kotshubeji bundeli Kolesnichenko, 1999 (Alai Mts in Tajikistan and Kyrgyzstan) are distinct taxa despite their geographic proximity in East Tajikistan. Melitaea enarea is widely distributed in the southern part of Central Asia and is sympatric with M. kotshubeji.},
}
@article {pmid34220145,
year = {2021},
author = {Dave, AR and Chaudhary, DF and Mankad, PM and Koringa, PG and Rank, DN},
title = {Genetic diversity among two native Indian chicken populations using cytochrome c oxidase subunit I and cytochrome b DNA barcodes.},
journal = {Veterinary world},
volume = {14},
number = {5},
pages = {1389-1397},
pmid = {34220145},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: India has large varieties (recognized, unrecognized) of native chickens (Desi) scattered throughout the country, managed under scavenging system different from commercial chicken breeds. However, they are less investigated for genetic diversity they harbor. The present study was planned to evaluate genetic diversity among two native chicken populations of North Gujarat (proposed Aravali breed) and South Gujarat (Ankleshwar breed). Aravali chicken, a distinct population with unique characters different from the registered chicken breeds of India is under process to be registered as a new chicken breed of Gujarat, India.<br><br>MATERIALS AND METHODS: Two mitochondrial markers, namely, cytochrome oxidase c subunit I (COX I) and cytochrome b (Cyt b) genes were studied across 10 birds from each population. Methodology included sample collection (blood), DNA isolation (manual), polymerase chain reaction amplification of mitochondrial genes, Sanger sequencing, and purification followed by data analysis using various softwares.<br><br>RESULTS: Haplotype analysis of the COX I gene unveiled a total eight and three haplotypes from the Aravali and Ankleshwar populations, respectively, with haplotype diversity (Hd) of 92.70 % for the Aravali and 34.50% for the Ankleshwar breed. Haplotype analysis of the Cyt b gene revealed a total of four haplotypes from the Aravali population with 60% Hd and no polymorphism in Ankleshwar breed. The phylogenetic analysis uncovered Red Jungle Fowl and Gray Jungle Fowl as prime roots for both populations and all domestic chicken breeds.<br><br>CONCLUSION: Study findings indicated high genetic variability in Aravali chicken populations with COX I mitochondrial marker being more informative for evaluating genetic diversity in chickens.},
}
@article {pmid34218439,
year = {2021},
author = {Krueger-Hadfield, SA and Byers, JE and Bonthond, G and Terada, R and Weinberger, F and Sotka, EE},
title = {Intraspecific diversity and genetic structure in the widespread macroalga Agarophyton vermiculophyllum.},
journal = {Journal of phycology},
volume = {57},
number = {5},
pages = {1403-1410},
doi = {10.1111/jpy.13195},
pmid = {34218439},
issn = {1529-8817},
mesh = {DNA, Mitochondrial ; Genetic Variation ; Microsatellite Repeats ; Phylogeny ; Phylogeography ; *Rhodophyta ; *Seaweed ; },
abstract = {Single-gene markers, such as the mitochondrial cox1, microsatellites, and single-nucleotide polymorphisms are powerful methods to describe diversity within and among taxonomic groups and characterize phylogeographic patterns. Large repositories of publicly-available, molecular data can be combined to generate and evaluate evolutionary hypotheses for many species, including algae. In the case of biological invasions, the combination of different molecular markers has enabled the description of the geographic distribution of invasive lineages. Here, we review the phylogeography of the widespread invasive red macroalga Agarophyton vermiculophyllum (synonym Gracilaria vermiculophylla). The cox1 barcoding provided the first description of the invasion history and hinted at a strong genetic bottleneck during the invasion. Yet, more recent microsatellite and SNP genotyping has not found evidence for bottlenecks and instead suggested that genetically diverse inocula arose from a highly diverse source population, multiple invasions, or some mix of these processes. The bottleneck evident from cox1 barcoding likely reflects the dominance of one mitochondrial lineage, and one haplotype in particular, in the northern source populations in Japan. Recent cox1 sequencing of A. vermiculophyllum has illuminated the complexity of phylogeographic structure in its native range of the northwest Pacific Ocean. For example, the western coast of Honshu in the Sea of Japan displays spatial patterns of haplotypic diversity with multiple lineages found together at the same geographic site. By consolidating the genetic data of this species, we clarify the phylogenetic relationships of a well-studied macroalga introduced to virtually every temperate estuary of the Northern Hemisphere.},
}
@article {pmid34217359,
year = {2021},
author = {Phuphisut, O and Nitatsukprasert, C and Pathawong, N and Jaichapor, B and Pongsiri, A and Adisakwattana, P and Ponlawat, A},
title = {Sand fly identification and screening for Leishmania spp. in six provinces of Thailand.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {352},
pmid = {34217359},
issn = {1756-3305},
support = {ProMIS ID: P0108_19_AF_05, Funding Year: 2019//Armed Forces Health Surveillance Branch/ ; },
mesh = {Animals ; DNA, Protozoan/analysis ; Female ; Insect Vectors/*parasitology ; Leishmania/*genetics/*isolation &amp; purification ; Leishmaniasis/prevention &amp; control/*transmission ; Male ; Psychodidae/*parasitology ; Thailand ; },
abstract = {BACKGROUND: Phlebotomine sand flies are vectors of Leishmania spp. At least 27 species of sand flies have been recorded in Thailand. Although human leishmaniasis cases in Thailand are mainly imported, autochthonous leishmaniasis has been increasingly reported in several regions of the country since 1999. Few studies have detected Leishmania infection in wild-caught sand flies, although these studies were carried out only in those areas reporting human leishmaniasis cases. The aim of this study was therefore to identity sand fly species and to investigate Leishmania infection across six provinces of Thailand.<br><br>METHODS: Species of wild-caught sand flies were initially identified based on morphological characters. However, problems identifying cryptic species complexes necessitated molecular identification using DNA barcoding in parallel with identification based on morphological characters. The wild-caught sand flies were pooled and the DNA isolated prior to the detection of Leishmania infection by a TaqMan real-time PCR assay.<br><br>RESULTS: A total of 4498 sand flies (1158 males and 3340 females) were caught by trapping in six provinces in four regions of Thailand. The sand flies were morphologically classified into eight species belonging to three genera (Sergentomyia, Phlebotomus and Idiophlebotomus). Sergentomyia iyengari was found at all collection sites and was the dominant species at most of these, followed in frequency by Sergentomyia barraudi and Phlebotomus stantoni, respectively. DNA barcodes generated from 68 sand flies allowed sorting into 14 distinct species with 25 operational taxonomic units, indicating a higher diversity (by 75%) than that based on morphological identification. Twelve barcoding sequences could not be assigned to any species for which cytochrome c oxidase subunit I sequences are available. All tested sand flies were negative for Leishmania DNA.<br><br>CONCLUSIONS: Our results confirm the presence of several sand fly species in different provinces of Thailand, highlighting the importance of using DNA barcoding as a tool to study sand fly species diversity. While all female sand flies tested in this study were negative for Leishmania, the circulation of Leishmania spp. in the investigated areas cannot be ruled out.},
}
@article {pmid34217058,
year = {2021},
author = {Oury, N and Jaquemet, S and Simon, G and Casalot, L and Vangrevelynghe, G and Landron, F and Magalon, H},
title = {Forensic genetic identification of sharks involved in human attacks.},
journal = {Forensic science international. Genetics},
volume = {54},
number = {},
pages = {102558},
doi = {10.1016/j.fsigen.2021.102558},
pmid = {34217058},
issn = {1878-0326},
mesh = {Animals ; *Bites and Stings ; DNA/genetics ; Forensic Genetics ; Humans ; *Sharks/genetics ; },
abstract = {Each year, 75-100 unprovoked shark attacks on humans are recorded, most of them resulting in no or minor injuries, while a few are fatal. Often, shark identification responsible for attacks relies on visual observations or bite wound characteristics, which limits species determination and preclude individual identification. Here, we provide two genetic approaches to reliably identify species and/or individuals involved in shark attacks on humans based on a non-invasive DNA sampling (i.e. DNA traces present on bite wounds on victims), depending on the knowledge of previous attack history at the site. The first approach uses barcoding techniques allowing species identification without any a priori, while the second relies on microsatellite genotyping, allowing species identification confirmation and individual identification, but requiring an a priori of the potential species involved in the attack. Both approaches were validated by investigating two shark attacks that occurred in Reunion Island (southwestern Indian Ocean). According to both methods, each incident was attributed to a bull shark (Carcharhinus leucas), in agreement with suggestions derived from bite wound characteristics. Both approaches appear thus suitable for the reliable identification of species involved in shark attacks on humans. Moreover, microsatellite genotyping reveals, in the studied cases, that two distinct individuals were responsible of the bites. Applying these genetic identification methods will resolve ambiguities on shark species involved in attacks and allow the collection of individual data to better understand and mitigate shark risk.},
}
@article {pmid34215850,
year = {2021},
author = {Xia, Y and Ji, X and Jang, IS and Surka, C and Hsu, C and Wang, K and Rolfe, M and Bence, N and Lu, G},
title = {Genetic and pharmacological interrogation of cancer vulnerability using a multiplexed cell line screening platform.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {834},
pmid = {34215850},
issn = {2399-3642},
mesh = {Antineoplastic Agents/*pharmacology ; *CRISPR-Cas Systems ; Cell Line, Tumor ; Cell Proliferation/drug effects/genetics ; Cell Survival/drug effects/genetics ; Drug Screening Assays, Antitumor/methods ; Early Detection of Cancer/*methods ; Gene Editing/*methods ; HEK293 Cells ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Neoplasms/diagnosis/*genetics ; },
abstract = {The multiplexed cancer cell line screening platform PRISM demonstrated its utility in testing hundreds of cell lines in a single run, possessing the potential to speed up anti-cancer drug discovery, validation and optimization. Here we described the development and implementation of a next-generation PRISM platform combining Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9-mediated gene editing, cell line DNA barcoding and next-generation sequencing to enable genetic and/or pharmacological assessment of target addiction in hundreds of cell lines simultaneously. Both compound and CRISPR-knockout PRISM screens well recapitulated the results from individual assays and showed high consistency with a public database.},
}
@article {pmid34215187,
year = {2021},
author = {Galanti, L and Shasha, D and Gunsalus, KC},
title = {Pheniqs 2.0: accurate, high-performance Bayesian decoding and confidence estimation for combinatorial barcode indexing.},
journal = {BMC bioinformatics},
volume = {22},
number = {1},
pages = {359},
pmid = {34215187},
issn = {1471-2105},
support = {ADHPG-CGSB//New York University/ ; },
mesh = {Bayes Theorem ; DNA Barcoding, Taxonomic ; *Electronic Data Processing ; *High-Throughput Nucleotide Sequencing ; Reproducibility of Results ; Sequence Analysis, DNA ; Software ; },
abstract = {BACKGROUND: Systems biology increasingly relies on deep sequencing with combinatorial index tags to associate biological sequences with their sample, cell, or molecule of origin. Accurate data interpretation depends on the ability to classify sequences based on correct decoding of these combinatorial barcodes. The probability of correct decoding is influenced by both sequence quality and the number and arrangement of barcodes. The rising complexity of experimental designs calls for a probability model that accounts for both sequencing errors and random noise, generalizes to multiple combinatorial tags, and can handle any barcoding scheme. The needs for reproducibility and community benchmark standards demand a peer-reviewed tool that preserves decoding quality scores and provides tunable control over classification confidence that balances precision and recall. Moreover, continuous improvements in sequencing throughput require a fast, parallelized and scalable implementation.<br><br>RESULTS AND DISCUSSION: We developed a flexible, robustly engineered software that performs probabilistic decoding and supports arbitrarily complex barcoding designs. Pheniqs computes the full posterior decoding error probability of observed barcodes by consulting basecalling quality scores and prior distributions, and reports sequences and confidence scores in Sequence Alignment/Map (SAM) fields. The product of posteriors for multiple independent barcodes provides an overall confidence score for each read. Pheniqs achieves greater accuracy than minimum edit distance or simple maximum likelihood estimation, and it scales linearly with core count to enable the classification of > 11 billion reads in 1&#xa0;h 15&#xa0;m using < 50 megabytes of memory. Pheniqs has been in production use for seven years in our genomics core facility.<br><br>CONCLUSION: We introduce a computationally efficient software that implements both probabilistic and minimum distance decoders and show that decoding barcodes using posterior probabilities is more accurate than available methods. Pheniqs allows fine-tuning of decoding sensitivity using intuitive confidence thresholds and is extensible with alternative decoders and new error models. Any arbitrary arrangement of barcodes is easily configured, enabling computation of combinatorial confidence scores for any barcoding strategy. An optimized multithreaded implementation assures that Pheniqs is faster and scales better with complex barcode sets than existing tools. Support for POSIX streams and multiple sequencing formats enables easy integration with automated analysis pipelines.},
}
@article {pmid34212080,
year = {2021},
author = {Kundu, S and Lalremsanga, HT and Biakzuala, L and Decemson, H and Muansanga, L and Tyagi, K and Chandra, K and Kumar, V},
title = {Genetic diversity of the Pegu Rice Frog, Microhyla berdmorei (Anura: Microhylidae) based on mitochondrial DNA.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {6},
number = {5},
pages = {1586-1591},
pmid = {34212080},
issn = {2380-2359},
abstract = {The Pegu Rice Frog, Microhyla berdmorei is distributed across ten Asian countries. However, the DNA barcoding information (COI gene) is restricted to only Southeast Asian countries. Here, we sampled a specimen of M. berdmorei in Mizoram state, northeast India to allow the genetic diversity of the species across its range. We generated both COI and 16S ribosomal RNA sequences of the studied species to check the population genetic diversity. The Bayesian analyses clearly discriminate M. berdmorei from its sister species Microhyla pulchra. The present datasets of M. berdmorei also revealed 11 and 19 haplotypes with high uncorrected pairwise genetic distances in COI (3.8-11.8%) and 16S rRNA (0-4.6%) gene, respectively. Owing to the high intra-species genetic distances and different haplotypes with sufficient mutational steps in both mitochondrial genes, this study affirms the existence of M. berdmorei species complex or cryptic diversity within its range distribution in South and Southeast Asia.},
}
@article {pmid34211161,
year = {2021},
author = {Philpott, M and Watson, J and Thakurta, A and Brown, T and Brown, T and Oppermann, U and Cribbs, AP},
title = {Nanopore sequencing of single-cell transcriptomes with scCOLOR-seq.},
journal = {Nature biotechnology},
volume = {39},
number = {12},
pages = {1517-1520},
pmid = {34211161},
issn = {1546-1696},
support = {MR/V010182/1/MRC_/Medical Research Council/United Kingdom ; /DH_/Department of Health/United Kingdom ; },
mesh = {High-Throughput Nucleotide Sequencing/methods ; *Nanopore Sequencing ; Protein Isoforms ; Transcriptome/genetics ; },
abstract = {Here we describe single-cell corrected long-read sequencing (scCOLOR-seq), which enables error correction of barcode and unique molecular identifier oligonucleotide sequences and permits standalone cDNA nanopore sequencing of single cells. Barcodes and unique molecular identifiers are synthesized using dimeric nucleotide building blocks that allow error detection. We illustrate the use of the method for evaluating barcode assignment accuracy, differential isoform usage in myeloma cell lines, and fusion transcript detection in a sarcoma cell line.},
}
@article {pmid34211145,
year = {2021},
author = {Bloom, JS and Sathe, L and Munugala, C and Jones, EM and Gasperini, M and Lubock, NB and Yarza, F and Thompson, EM and Kovary, KM and Park, J and Marquette, D and Kay, S and Lucas, M and Love, T and Sina Booeshaghi, A and Brandenberg, OF and Guo, L and Boocock, J and Hochman, M and Simpkins, SW and Lin, I and LaPierre, N and Hong, D and Zhang, Y and Oland, G and Choe, BJ and Chandrasekaran, S and Hilt, EE and Butte, MJ and Damoiseaux, R and Kravit, C and Cooper, AR and Yin, Y and Pachter, L and Garner, OB and Flint, J and Eskin, E and Luo, C and Kosuri, S and Kruglyak, L and Arboleda, VA},
title = {Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples.},
journal = {Nature biomedical engineering},
volume = {5},
number = {7},
pages = {657-665},
pmid = {34211145},
issn = {2157-846X},
support = {/HHMI/Howard Hughes Medical Institute/United States ; DP5 OD024579/OD/NIH HHS/United States ; T32 GM008042/GM/NIGMS NIH HHS/United States ; },
mesh = {High-Throughput Nucleotide Sequencing ; Humans ; RNA, Viral/*genetics ; SARS-CoV-2/genetics/*pathogenicity ; Saliva/*virology ; Sensitivity and Specificity ; },
abstract = {Frequent and widespread testing of members of the population who are asymptomatic for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for the mitigation of the transmission of the virus. Despite the recent increases in testing capacity, tests based on quantitative polymerase chain reaction (qPCR) assays cannot be easily deployed at the scale required for population-wide screening. Here, we show that next-generation sequencing of pooled samples tagged with sample-specific molecular barcodes enables the testing of thousands of nasal or saliva samples for SARS-CoV-2 RNA in a single run without the need for RNA extraction. The assay, which we named SwabSeq, incorporates a synthetic RNA standard that facilitates end-point quantification and the calling of true negatives, and that reduces the requirements for automation, purification and sample-to-sample normalization. We used SwabSeq to perform 80,000 tests, with an analytical sensitivity and specificity comparable to or better than traditional qPCR tests, in less than two months with turnaround times of less than 24 h. SwabSeq could be rapidly adapted for the detection of other pathogens.},
}
@article {pmid34210039,
year = {2021},
author = {Agyeman, NA and Blanco-Fernandez, C and Steinhaussen, SL and Garcia-Vazquez, E and Machado-Schiaffino, G},
title = {Illegal, Unreported, and Unregulated Fisheries Threatening Shark Conservation in African Waters Revealed from High Levels of Shark Mislabelling in Ghana.},
journal = {Genes},
volume = {12},
number = {7},
pages = {},
pmid = {34210039},
issn = {2073-4425},
mesh = {Animals ; DNA Barcoding, Taxonomic/standards ; Endangered Species/legislation &amp; jurisprudence/*statistics &amp; numerical data ; Fish Products/*standards ; Fisheries/standards ; Food Labeling/*standards ; Ghana ; Sharks/*genetics/physiology ; },
abstract = {Mislabelling of fish and fish products has attracted much attention over the last decades, following public awareness of the practice of substituting high-value with low-value fish in markets, restaurants, and processed seafood. In some cases, mislabelling includes illegal, unreported, and unregulated (IUU) fishing, contributing to overexploit substitute species that are undetectable when sold under wrong names. This is the first study of DNA barcoding to assess the level of mislabelling in fish marketed in Ghana, focusing on endangered shark species. Genetic identification was obtained from 650 base pair sequences within the cytochrome c oxidase I (COI) gene. All except one of 17 shark fillets analysed were wrongly labelled as compared with none of 28 samples of small commercial pelagic fish and 14 commercial shark samples purchased in Europe. Several substitute shark species in Ghana are endangered (Carcharhinussignatus and Isurusoxyrinchus) and critically endangered (Squatina aculeata). Shark products commercialized in Europe (n = 14) did not reveal mislabelling, thus specific shark mislabelling cannot be generalized. Although based on a limited number of samples and fish markets, the results that reveal trade of endangered sharks in Ghana markets encourage Ghanaian authorities to improve controls to enforce conservation measures.},
}
@article {pmid34209308,
year = {2021},
author = {Feldmann, F and Ardura, A and Blanco-Fernandez, C and Garcia-Vazquez, E},
title = {DNA Analysis Detects Different Mislabeling Trend by Country in European Cod Fillets.},
journal = {Foods (Basel, Switzerland)},
volume = {10},
number = {7},
pages = {},
pmid = {34209308},
issn = {2304-8158},
abstract = {Atlantic cod, Gadus morhua, is a highly appreciated fish in European seafood markets and is one of the most substituted fish species in the world. Fraud have been detected in European markets in the last decade, finding different substitute species sold as G. morhua or Atlantic cod on the label. In this study, we analyzed 252 samples of fresh and frozen cod fillets sold in Germany, the Netherlands, and France using DNA barcoding. Different trends were found in different countries: while the level of mislabeling found in Germany and the Netherlands remained at zero in the last years, a significant increase was found in the French markets comparing the current results with previous studies on fillets in France. On the one hand, this mislabeling proves the need to encourage European efforts to control seafood authenticity; on the other, zero mislabeling in two countries shows the success of current European regulations.},
}
@article {pmid34208444,
year = {2021},
author = {An, YY and Dayarathne, MC and Zeng, XY and Phillips, AJL and Hyde, KD and Wang, Y},
title = {Molecular and Morphological Assessment of Septoria Species Associated with Ornamental Plants in Yunnan Province, China.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {7},
number = {6},
pages = {},
pmid = {34208444},
issn = {2309-608X},
support = {31972222, 31560489//National Natural Science Foundation of China/ ; },
abstract = {The Karst landform is the main geographic characteristic in South China. Such areas are rich in vegetation and especially suitable for growth of shrubs and herbaceous plants. In this study, 11 Septoria strains were obtained from different plants' leaves collected in the Kunming Botanical Garden, Yunnan Province, China. Based on single-gene and multi-gene analyses of five gene loci (tef1, rpb2, tub2, ITS, and LSU) and four gene regions (without LSU), these strains were found to belong to three independent phylogenetic lineages representing five species, including four novel taxa, and one new record for China. Five single gene trees were also provided to evaluate the effectiveness of each gene for discriminating the species, as a result of which tub2 was found to have the most suitable DNA barcode for rapid identification. Morphological descriptions, illustrations, and comparisons are provided for a more comprehensive assessment. Genealogical Concordance Phylogenetic Species Recognition (GCPSR) with a pairwise homoplasy index (PHI) test was used to evaluate the conclusions of the phylogenetic analyses.},
}
@article {pmid34207673,
year = {2021},
author = {Høyer, AK and Hodkinson, TR},
title = {Hidden Fungi: Combining Culture-Dependent and -Independent DNA Barcoding Reveals Inter-Plant Variation in Species Richness of Endophytic Root Fungi in Elymus repens.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {7},
number = {6},
pages = {},
pmid = {34207673},
issn = {2309-608X},
support = {674964//Horizon 2020/ ; },
abstract = {The root endophyte community of the grass species Elymus repens was investigated using both a culture-dependent approach and a direct amplicon sequencing method across five sites and from individual plants. There was much heterogeneity across the five sites and among individual plants. Focusing on one site, 349 OTUs were identified by direct amplicon sequencing but only 66 OTUs were cultured. The two approaches shared ten OTUs and the majority of cultured endophytes do not overlap with the amplicon dataset. Media influenced the cultured species richness and without the inclusion of 2% MEA and full-strength MEA, approximately half of the unique OTUs would not have been isolated using only PDA. Combining both culture-dependent and -independent methods for the most accurate determination of root fungal species richness is therefore recommended. High inter-plant variation in fungal species richness was demonstrated, which highlights the need to rethink the scale at which we describe endophyte communities.},
}
@article {pmid34207329,
year = {2021},
author = {Furfaro, G and Mariottini, P},
title = {Looking at the Nudibranch Family Myrrhinidae (Gastropoda, Heterobranchia) from a Mitochondrial '2D Folding Structure' Point of View.},
journal = {Life (Basel, Switzerland)},
volume = {11},
number = {6},
pages = {},
pmid = {34207329},
issn = {2075-1729},
support = {AIM 1848751-2, Linea 2//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; AIM 1848751-2, Linea 2//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; },
abstract = {Integrative taxonomy is an evolving field of multidisciplinary studies often utilised to elucidate phylogenetic reconstructions that were poorly understood in the past. The systematics of many taxa have been resolved by combining data from different research approaches, i.e., molecular, ecological, behavioural, morphological and chemical. Regarding molecular analysis, there is currently a search for new genetic markers that could be diagnostic at different taxonomic levels and that can be added to the canonical ones. In marine Heterobranchia, the most widely used mitochondrial markers, COI and 16S, are usually analysed by comparing the primary sequence. The 16S rRNA molecule can be folded into a 2D secondary structure that has been poorly exploited in the past study of heterobranchs, despite 2D molecular analyses being sources of possible diagnostic characters. Comparison of the results from the phylogenetic analyses of a concatenated (the nuclear H3 and the mitochondrial COI and 16S markers) dataset (including 30 species belonging to eight accepted genera) and from the 2D folding structure analyses of the 16S rRNA from the type species of the genera investigated demonstrated the diagnostic power of this RNA molecule to reveal the systematics of four genera belonging to the family Myrrhinidae (Gastropoda, Heterobranchia). The "molecular morphological" approach to the 16S rRNA revealed to be a powerful tool to delimit at both species and genus taxonomic levels and to be a useful way of recovering information that is usually lost in phylogenetic analyses. While the validity of the genera Godiva, Hermissenda and Phyllodesmium are confirmed, a new genus is necessary and introduced for Dondice banyulensis, Nemesis gen. nov. and the monospecific genus Nanuca is here synonymised with Dondice, with Nanuca sebastiani transferred into Dondice as Dondice sebastiani comb. nov.},
}
@article {pmid34206502,
year = {2021},
author = {Filonzi, L and Vaghi, M and Ardenghi, A and Rontani, PM and Voccia, A and Nonnis Marzano, F},
title = {Efficiency of DNA Mini-Barcoding to Assess Mislabeling in Commercial Fish Products in Italy: An Overview of the Last Decade.},
journal = {Foods (Basel, Switzerland)},
volume = {10},
number = {7},
pages = {},
pmid = {34206502},
issn = {2304-8158},
abstract = {The problem of fish traceability in processed products is still an important issue in food safety. Major attention is nowadays dedicated to consumer health and prevention of possible frauds regulated by national and international laws. For this reason, a technical approach is fundamental in revealing mislabeling at different levels. In particular, the use of genetic markers has been standardized and DNA barcoding is considered the gold-standard strategy to examine and prevent species substitution. Considering the richness of available DNA databases, it is nowadays possible to rapidly reach a reliable taxonomy at the species level. Among different approaches, an innovative method based on DNA mini barcoding has recently been proposed at an international level. Starting from this evidence, we herein illustrate an investigation dealing with the evolution of this topic in Italy over the last decade. The molecular analysis of 71 commercial fish samples based on mini-COI sequencing with two different primer sets reached an amplification success rate of 87.3 and 97.2%. The investigation revealed four major frauds (5.8%) and four minor ones (5.8%). Results highlighted a decrease in incorrect labeling in Italy from 32% to 11.6% over the last decade, although a recurrent involvement of "endangered" species sensu IUCN was still observed.},
}
@article {pmid34206388,
year = {2021},
author = {Crobe, V and Ferrari, A and Hanner, R and Leslie, RW and Steinke, D and Tinti, F and Cariani, A},
title = {Molecular Taxonomy and Diversification of Atlantic Skates (Chondrichthyes, Rajiformes): Adding More Pieces to the Puzzle of Their Evolutionary History.},
journal = {Life (Basel, Switzerland)},
volume = {11},
number = {7},
pages = {},
pmid = {34206388},
issn = {2075-1729},
abstract = {Conservation and long-term management plans of marine species need to be based upon the universally recognized key-feature of species identity. This important assignment is particularly challenging in skates (Rajiformes) in which the phenotypic similarity between some taxa and the individual variability in others, hampers accurate species identification. Here, 432 individual skate samples collected from four major ocean areas of the Atlantic were barcoded and taxonomically analysed. A BOLD project ELASMO ATL was implemented with the aim of establishing a new fully available and well curated barcode library containing both biological and molecular information. The evolutionary histories of the 38 skate taxa were estimated with two concatenated mitochondrial markers (COI and NADH2) through Maximum Likelihood and Bayesian inference. New evolutionary lineages within the genus Raja were discovered off Angola, where paleogeographic history coupled with oceanographic discontinuities could have contributed to the establishment of isolated refugia, playing a fundamental role among skates' speciation events. These data successfully resolved many taxonomic ambiguities, identified cryptic diversity within valid species and demonstrated a highly cohesive monophyletic clustering among the order, laying the background for further inference of evolutionary patterns suitable for addressing management and conservation issues.},
}
@article {pmid34205814,
year = {2021},
author = {Yang, RS and Ni, MY and Gu, YJ and Xu, JS and Jin, Y and Zhang, JH and Wang, Y and Qin, L},
title = {Newly Emerging Pest in China, Rhynchaenusmaculosus (Coleoptera: Curculionidae): Morphology and Molecular Identification with DNA Barcoding.},
journal = {Insects},
volume = {12},
number = {6},
pages = {},
pmid = {34205814},
issn = {2075-4450},
support = {CARS-18//Agriculture Research System of China/ ; 2017001//Venture Foundation of National Silk Industry/ ; },
abstract = {The oak flea weevil, Rhynchaenusmaculosus Yang et Zhang 1991, is a newly emerging pest that severely damages oak (genus Quercus) in China. The first R. maculosus outbreak occurred in 2020 and caused spectacular damage to all oak forests in Jilin province, northeast China. The lack of key morphological characters complicates the identification of this native pest, especially in larva and pupa stages. This is problematic because quick and accurate species identification is crucial for early monitoring and intervention during outbreaks. Here, we provided the first detailed morphological description of R. maculosus at four life stages. Additionally, we used DNA barcodes from larva and pupa specimens collected from three remote locations for molecular identification. The average pairwise divergence of all sequences in this study was 0.51%, well below the 2% to 3% (K-2-parameter) threshold set for one species. All sample sequences matched the R. maculosus morphospecies (KX657706.1 and KX657707.1), with 99.23% to 100% (sequence identity, E value: 0.00) matching success. The tree based on barcodes placed the specimens into the Rhynchaenus group, and the phylogenetic relationship between 62 sequences (30 samples and 32 from GeneBank) had high congruence with the morphospecies taxa. The traditional DNA barcodes were successfully transformed into quick response codes with larger coding capacity for information storage. The results showed that DNA barcoding is reliable for R. maculosus identification. The integration of molecular and morphology-based methods contributes to accurate species identification of this newly emerging oak pest.},
}
@article {pmid34205462,
year = {2021},
author = {Willette, DA and Navarrete-Forero, G and Gold, Z and Lizano, AMD and Gonzalez-Smith, L and Sotil, G},
title = {Characterizing Industrial and Artisanal Fishing Vessel Catch Composition Using Environmental DNA and Satellite-Based Tracking Data.},
journal = {Foods (Basel, Switzerland)},
volume = {10},
number = {6},
pages = {},
pmid = {34205462},
issn = {2304-8158},
support = {xxx//United States Fulbright Global Scholar Program/ ; },
abstract = {The decline in wild-caught fisheries paired with increasing global seafood demand is pushing the need for seafood sustainability to the forefront of national and regional priorities. Validation of species identity is a crucial early step, yet conventional monitoring and surveillance tools are limited in their effectiveness because they are extremely time-consuming and require expertise in fish identification. DNA barcoding methods are a versatile tool for the genetic monitoring of wildlife products; however, they are also limited by requiring individual tissue samples from target specimens which may not always be possible given the speed and scale of seafood operations. To circumvent the need to individually sample organisms, we pilot an approach that uses forensic environmental DNA (eDNA) metabarcoding to profile fish species composition from the meltwater in fish holds on industrial and artisanal fishing vessels in Ecuador. Fish identified genetically as present were compared to target species reported by each vessel's crew. Additionally, we contrasted the geographic range of identified species against the satellite-based fishing route data of industrial vessels to determine if identified species could be reasonably expected in the catch.},
}
@article {pmid34205139,
year = {2021},
author = {Isola, D and Bartoli, F and Langone, S and Ceschin, S and Zucconi, L and Caneva, G},
title = {Plant DNA Barcode as a Tool for Root Identification in Hypogea: The Case of the Etruscan Tombs of Tarquinia (Central Italy).},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {6},
pages = {},
pmid = {34205139},
issn = {2223-7747},
support = {PGR01253//Ministero degli Affari Esteri e della Cooperazione Internazionale/ ; MIUR-323 Italy Departments of Excellence, Article 1, Comma 314-337, Law 232/2016//Universit&#xe0; degli Studi Roma Tre/ ; },
abstract = {Roots can produce mechanical and chemical alterations to building structures, especially in the case of underground historical artifacts. In archaeological sites, where vegetation plays the dual role of naturalistic relevance and potential threat, trees and bushes are under supervision. No customized measures can be taken against herbaceous plants lacking fast and reliable root identification methods that are useful to assess their dangerousness. In this study, we aimed to test the efficacy of DNA barcoding in identifying plant rootlets threatening the Etruscan tombs of the Necropolis of Tarquinia. As DNA barcode markers, we selected two sections of the genes rbcL and matK, the nuclear ribosomal internal transcribed spacer (nrITS), and the intergenic spacer psbA-trnH. All fourteen root samples were successfully sequenced and identified at species (92.9%) and genus level (7.01%) by GenBank matching and reference dataset implementation. Some eudicotyledons with taproots, such as Echium italicum L., Foeniculum vulgare Mill., and Reseda lutea L. subsp. lutea, showed a certain recurrence. Further investigations are needed to confirm this promising result, increasing the number of roots and enlarging the reference dataset with attention to meso-Mediterranean perennial herbaceous species. The finding of herbaceous plants roots at more than 3 m deep confirms their potential risk and underlines the importance of vegetation planning, monitoring, and management on archaeological sites.},
}
@article {pmid34204756,
year = {2021},
author = {Massaiu, I and Songia, P and Chiesa, M and Valerio, V and Moschetta, D and Alfieri, V and Myasoedova, VA and Schmid, M and Cassetta, L and Colombo, GI and D'Alessandra, Y and Poggio, P},
title = {Evaluation of Oxford Nanopore MinION RNA-Seq Performance for Human Primary Cells.},
journal = {International journal of molecular sciences},
volume = {22},
number = {12},
pages = {},
pmid = {34204756},
issn = {1422-0067},
support = {GR-2018-12366423//Ministero della Salute/ ; PICASSO-JTC-2018-042//Ministero della Salute/ ; FPF-14//Fondazione Gigi e Pupa Ferrari/ ; },
mesh = {Cells, Cultured ; Gene Expression Regulation ; Humans ; *Nanopore Sequencing ; Open Reading Frames/genetics ; RNA-Seq ; },
abstract = {Transcript sequencing is a crucial tool for gaining a deep understanding of biological processes in diagnostic and clinical medicine. Given their potential to study novel complex eukaryotic transcriptomes, long-read sequencing technologies are able to overcome some limitations of short-read RNA-Seq approaches. Oxford Nanopore Technologies (ONT) offers the ability to generate long-read sequencing data in real time via portable protein nanopore USB devices. This work aimed to provide the user with the number of reads that should be sequenced, through the ONT MinION platform, to reach the desired accuracy level for a human cell RNA study. We sequenced three cDNA libraries prepared from poly-adenosine RNA of human primary cardiac fibroblasts. Since the runs were comparable, they were combined in a total dataset of 48 million reads. Synthetic datasets with different sizes were generated starting from the total and analyzed in terms of the number of identified genes and their expression levels. As expected, an improved sensitivity was obtained, increasing the sequencing depth, particularly for the non-coding genes. The reliability of expression levels was assayed by (i) comparison with PCR quantifications of selected genes and (ii) by the implementation of a user-friendly multiplexing method in a single run.},
}
@article {pmid34196282,
year = {2021},
author = {Barry, DE and Veillard, M and James, CT and Brummelhuis, L and Pila, EA and Turnbull, A and Oploo, AO and Han, X and Hanington, PC},
title = {qPCR-based environmental monitoring of Myxobolus cerebralis and phylogenetic analysis of its tubificid hosts in Alberta, Canada.},
journal = {Diseases of aquatic organisms},
volume = {145},
number = {},
pages = {119-137},
doi = {10.3354/dao03608},
pmid = {34196282},
issn = {0177-5103},
mesh = {Alberta ; Animals ; Environmental Monitoring ; *Fish Diseases/epidemiology ; *Myxobolus/genetics ; *Oligochaeta ; Phylogeny ; },
abstract = {Myxobolus cerebralis is the causative agent of whirling disease in salmonid fishes. In 2016, this invasive parasite was detected in Alberta, Canada, for the first time, initiating a comprehensive 3 yr monitoring program to assess where the parasite had spread within the province. As part of this program, a qPCR-based test was developed to facilitate detection of the environmental stages of M. cerebralis and from the oligochaete host, Tubifex tubifex. During this program, ~1500 environmental samples were collected and tested over 3 yr. Fish were collected from the same watersheds over 2 yr and tested as part of the official provincial monitoring effort. Substrate testing identified sites positive for M. cerebralis in 3 of 6 watersheds that had been confirmed positive by fish-based testing and 3 novel detections where the parasite had not been detected previously. Testing of individually isolated Tubifex from each sample site was used to further confirm the presence of M. cerebralis. DNA barcoding of the cytochrome oxidase I (cox1) gene of 567 oligochaete specimens collected from 6 different watersheds yielded 158 unique sequences belonging to 21 genera and 37 putative species. Phylogenetic analyses of sequences assigned to the genus Tubifex predicted 5 species of Tubifex arising from this assessment. Based on our results, we propose that environmental and worm samples can be a valuable complement to the gold-standard fish testing and will be especially useful for monitoring in areas where fish collection is challenging or prohibitive because of site accessibility or vulnerability of the fish populations.},
}
@article {pmid34194941,
year = {2021},
author = {Gong, C and Qiao, Z and Yuan, Z and Huang, SH and Wang, W and Wu, PC and Chen, YC},
title = {Topological Encoded Vector Beams for Monitoring Amyloid-Lipid Interactions in Microcavity.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {8},
number = {12},
pages = {2100096},
pmid = {34194941},
issn = {2198-3844},
mesh = {Amyloid/*chemistry ; Biomimetics ; Biosensing Techniques/*methods ; Equipment Design/*methods ; Lipids/*chemistry ; Nanotechnology/*methods ; Optics and Photonics/*methods ; },
abstract = {Lasers are the pillars of modern photonics and sensing. Recent advances in microlasers have demonstrated its extraordinary lasing characteristics suitable for biosensing. However, most lasers utilized lasing spectrum as a detection signal, which can hardly detect or characterize nanoscale structural changes in microcavity. Here the concept of amplified structured light-molecule interactions is introduced to monitor tiny bio-structural changes in a microcavity. Biomimetic liquid crystal droplets with self-assembled lipid monolayers are sandwiched in a Fabry-Pérot cavity, where subtle protein-lipid membrane interactions trigger the topological transformation of output vector beams. By exploiting Amyloid β (Aβ)-lipid membrane interactions as a proof-of-concept, it is demonstrated that vector laser beams can be viewed as a topology of complex laser modes and polarization states. The concept of topological-encoded laser barcodes is therefore developed to reveal dynamic changes of laser modes and Aβ-lipid interactions with different Aβ assembly structures. The findings demonstrate that the topology of vector beams represents significant features of intracavity nano-structural dynamics resulted from structured light-molecule interactions.},
}
@article {pmid34191835,
year = {2021},
author = {Prahl, RE and Khan, S and Deo, RC},
title = {The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces.},
journal = {PloS one},
volume = {16},
number = {6},
pages = {e0253772},
pmid = {34191835},
issn = {1932-6203},
mesh = {Ascomycota/*classification/genetics/isolation &amp; purification ; DNA, Environmental/*genetics/isolation &amp; purification ; DNA, Fungal/*genetics/isolation &amp; purification ; DNA, Ribosomal Spacer/*genetics/isolation &amp; purification ; Genetic Markers ; Phylogeny ; Plant Diseases/*microbiology ; Sequence Analysis, DNA ; },
abstract = {Many fungi require specific growth conditions before they can be identified. Direct environmental DNA sequencing is advantageous, although for some taxa, specific primers need to be used for successful amplification of molecular markers. The internal transcribed spacer region is the preferred DNA barcode for fungi. However, inter- and intra-specific distances in ITS sequences highly vary among some fungal groups; consequently, it is not a solely reliable tool for species delineation. Ampelomyces, mycoparasites of the fungal phytopathogen order Erysiphales, can have ITS genetic differences up to 15%; this may lead to misidentification with other closely related unknown fungi. Indeed, Ampelomyces were initially misidentified as other pycnidial mycoparasites, but subsequent research showed that they differ in pycnidia morphology and culture characteristics. We investigated whether the ITS2 nucleotide content and secondary structure was different between Ampelomyces ITS2 sequences and those unrelated to this genus. To this end, we retrieved all ITS sequences referred to as Ampelomyces from the GenBank database. This analysis revealed that fungal ITS environmental DNA sequences are still being deposited in the database under the name Ampelomyces, but they do not belong to this genus. We also detected variations in the conserved hybridization model of the ITS2 proximal 5.8S and 28S stem from two Ampelomyces strains. Moreover, we suggested for the first time that pseudogenes form in the ITS region of this mycoparasite. A phylogenetic analysis based on ITS2 sequences-structures grouped the environmental sequences of putative Ampelomyces into a different clade from the Ampelomyces-containing clades. Indeed, when conducting ITS2 analysis, resolution of genetic distances between Ampelomyces and those putative Ampelomyces improved. Each clade represented a distinct consensus ITS2 S2, which suggested that different pre-ribosomal RNA (pre-rRNA) processes occur across different lineages. This study recommends the use of ITS2 S2s as an important tool to analyse environmental sequencing and unveiling the underlying evolutionary processes.},
}
@article {pmid34188886,
year = {2021},
author = {Shu, L and Ludwig, A and Peng, Z},
title = {Environmental DNA metabarcoding primers for freshwater fish detection and quantification: In silico and in tanks.},
journal = {Ecology and evolution},
volume = {11},
number = {12},
pages = {8281-8294},
pmid = {34188886},
issn = {2045-7758},
abstract = {Environmental DNA (eDNA) techniques refer to utilizing the organisms' DNA extracted from environment samples to genetically identify target species without capturing actual organisms. eDNA metabarcoding via high-throughput sequencing can simultaneously detect multiple fish species from a single water sample, which is a powerful tool for the qualitative detection and quantitative estimates of multiple fish species. However, sequence counts obtained from eDNA metabarcoding may be influenced by many factors, of which primer bias is one of the foremost causes of methodological error. The performance of 18 primer pairs for COI, cytb, 12S rRNA, and 16S rRNA mitochondrial genes, which are all frequently used in fish eDNA metabarcoding, were evaluated in the current study. The ribosomal gene markers performed better than the protein-coding gene markers during in silico screening, resulting in higher taxonomic coverage and appropriate barcode lengths. Four primer pairs-AcMDB07, MiFish-U, Ve16S1, and Ve16S3-designed for various regions of the 12S and 16S rRNA genes were screened for tank metabarcoding in a case study targeting six freshwater fish species. The four primer pairs were able to accurately detect all six species in different tanks, while only MiFish-U, Ve16S1, and Ve16S3 revealed a significant positive relationship between species biomass and read count for the pooled tank data. The positive relationship could not be found in all species within the tanks. Additionally, primer efficiency differed depending on the species while primer preferential species varied in different fish assemblages. This case study supports the potential for eDNA metabarcoding to assess species diversity in natural ecosystems and provides an alternative strategy to evaluate the performance of candidate primers before application of eDNA metabarcoding in natural ecosystems.},
}
@article {pmid34188853,
year = {2021},
author = {Abdullah, and Mehmood, F and Rahim, A and Heidari, P and Ahmed, I and Poczai, P},
title = {Comparative plastome analysis of Blumea, with implications for genome evolution and phylogeny of Asteroideae.},
journal = {Ecology and evolution},
volume = {11},
number = {12},
pages = {7810-7826},
pmid = {34188853},
issn = {2045-7758},
abstract = {The genus Blumea (Asteroideae, Asteraceae) comprises about 100 species, including herbs, shrubs, and small trees. Previous studies have been unable to resolve taxonomic issues and the phylogeny of the genus Blumea due to the low polymorphism of molecular markers. Therefore, suitable polymorphic regions need to be identified. Here, we de novo assembled plastomes of the three Blumea species B. oxyodonta, B. tenella, and B. balsamifera and compared them with 26 other species of Asteroideae after correction of annotations. These species have quadripartite plastomes with similar gene content, genome organization, and inverted repeat contraction and expansion comprising 113 genes, including 80 protein-coding, 29 transfer RNA, and 4 ribosomal RNA genes. The comparative analysis of codon usage, amino acid frequency, microsatellite repeats, oligonucleotide repeats, and transition and transversion substitutions has revealed high resemblance among the newly assembled species of Blumea. We identified 10 highly polymorphic regions with nucleotide diversity above 0.02, including rps16-trnQ, ycf1, ndhF-rpl32, petN-psbM, and rpl32-trnL, and they may be suitable for the development of robust, authentic, and cost-effective markers for barcoding and inference of the phylogeny of the genus Blumea. Among these highly polymorphic regions, five regions also co-occurred with oligonucleotide repeats and support use of repeats as a proxy for the identification of polymorphic loci. The phylogenetic analysis revealed a close relationship between Blumea and Pluchea within the tribe Inuleae. At tribe level, our phylogeny supports a sister relationship between Astereae and Anthemideae rooted as Gnaphalieae, Calenduleae, and Senecioneae. These results are contradictory to recent studies which reported a sister relationship between "Senecioneae and Anthemideae" and "Astereae and Gnaphalieae" or a sister relationship between Astereae and Gnaphalieae rooted as Calenduleae, Anthemideae, and then Senecioneae using nuclear genome sequences. The conflicting phylogenetic signals observed at the tribal level between plastidt and nuclear genome data require further investigation.},
}
@article {pmid34188828,
year = {2021},
author = {Ingala, MR and Simmons, NB and Wultsch, C and Krampis, K and Provost, KL and Perkins, SL},
title = {Molecular diet analysis of neotropical bats based on fecal DNA metabarcoding.},
journal = {Ecology and evolution},
volume = {11},
number = {12},
pages = {7474-7491},
pmid = {34188828},
issn = {2045-7758},
abstract = {Bat communities in the Neotropics are some of the most speciose assemblages of mammals on Earth, with regions supporting more than 100 sympatric species with diverse feeding ecologies. Because bats are small, nocturnal, and volant, it is difficult to directly observe their feeding habits, which has resulted in their classification into broadly defined dietary guilds (e.g., insectivores, carnivores, and frugivores). Apart from these broad guilds, we lack detailed dietary information for many species and therefore have only a limited understanding of interaction networks linking bats and their diet items. In this study, we used DNA metabarcoding of plants, arthropods, and vertebrates to investigate the diets of 25 bat species from the tropical dry forests of Lamanai, Belize. Our results report some of the first detection of diet items for the focal bat taxa, adding rich and novel natural history information to the field of bat ecology. This study represents a comprehensive first effort to apply DNA metabarcoding to bat diets at Lamanai and provides a useful methodological framework for future studies testing hypotheses about coexistence and niche differentiation in the context of modern high-throughput molecular data.},
}
@article {pmid34188222,
year = {2021},
author = {Ludwig, KU and Schmithausen, RM and Li, D and Jacobs, ML and Hollstein, R and Blumenstock, K and Liebing, J and Słabicki, M and Ben-Shmuel, A and Israeli, O and Weiss, S and Ebert, TS and Paran, N and Rüdiger, W and Wilbring, G and Feldman, D and Lippke, B and Ishorst, N and Hochfeld, LM and Beins, EC and Kaltheuner, IH and Schmitz, M and Wöhler, A and Döhla, M and Sib, E and Jentzsch, M and Moench, EC and Borrajo, JD and Strecker, J and Reinhardt, J and Cleary, B and Geyer, M and Hölzel, M and Macrae, R and Nöthen, MM and Hoffmann, P and Exner, M and Regev, A and Zhang, F and Schmid-Burgk, JL},
title = {LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding.},
journal = {Nature biotechnology},
volume = {39},
number = {12},
pages = {1556-1562},
pmid = {34188222},
issn = {1546-1696},
support = {LU-1944/3-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; R01 MH110049/MH/NIMH NIH HHS/United States ; EXC2151 - 390873048//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 01KX2021//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; DP1 HL141201/HL/NHLBI NIH HHS/United States ; R01 HG009761/HG/NHGRI NIH HHS/United States ; },
mesh = {*COVID-19/diagnosis ; COVID-19 Testing/*methods ; Humans ; Molecular Diagnostic Techniques/*methods ; Nucleic Acid Amplification Techniques/*methods ; },
abstract = {Frequent testing of large population groups combined with contact tracing and isolation measures will be crucial for containing Coronavirus Disease 2019 outbreaks. Here we present LAMP-Seq, a modified, highly scalable reverse transcription loop-mediated isothermal amplification (RT-LAMP) method. Unpurified biosamples are barcoded and amplified in a single heat step, and pooled products are analyzed en masse by sequencing. Using commercial reagents, LAMP-Seq has a limit of detection of ~2.2 molecules per µl at 95% confidence and near-perfect specificity for severe acute respiratory syndrome coronavirus 2 given its sequence readout. Clinical validation of an open-source protocol with 676 swab samples, 98 of which were deemed positive by standard RT-qPCR, demonstrated 100% sensitivity in individuals with cycle threshold values of up to 33 and a specificity of 99.7%, at a very low material cost. With a time-to-result of fewer than 24 h, low cost and little new infrastructure requirement, LAMP-Seq can be readily deployed for frequent testing as part of an integrated public health surveillance program.},
}
@article {pmid34186993,
year = {2021},
author = {Dey, P and Uniyal, VP and Hausmann, A and Stüning, D},
title = {Revision of the genus Prometopidia Hampson, 1902, with description of the new species P. joshimathensis sp. nov. from West-Himalaya and its subspecies P. j. yazakii ssp. nov. from Nepal (Lepidoptera: Geometridae, Ennominae).},
journal = {Zootaxa},
volume = {4980},
number = {1},
pages = {2844},
doi = {10.11646/zootaxa.4980.1.2},
pmid = {34186993},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; DNA Barcoding, Taxonomic ; Ecosystem ; Female ; Genitalia ; Moths/*classification ; Nepal ; },
abstract = {The genus Prometopidia Hampson, 1902 and its type-species P. conisaria Hampson, 1902 are redescribed and newly discovered morphological characters are explained. The female holotype of Prometopidia arenosa Wiltshire, 1961, was studied and the species redescribed, its correct position in Prometopidia is verified. The new species P. joshimathensis sp. nov. is described from Joshimath area in India, Uttarakhand province. Sympatric with P. conisaria at Joshimath, P. joshimathensis also occurs at Shimla, Punjab province, and in central and eastern Nepal. Morphological and genetic differences found in the specimens of Nepal are considered subspecific, justifying the new taxon P. joshimathensis yazakii ssp. nov. Types and specimens of Prometopidia across its whole range of distribution from Afghanistan to Nepal, habitats, genitalia, remarkable morphological characters and DNA barcoding-results are figured.},
}
@article {pmid34186945,
year = {2021},
author = {Sinclair, BJ and Shamshev, IV},
title = {World revision of Iteaphila with unbranched radial vein (Diptera: Empidoidea: Iteaphilidae).},
journal = {Zootaxa},
volume = {4968},
number = {1},
pages = {189},
doi = {10.11646/zootaxa.4968.1.1},
pmid = {34186945},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures ; Animals ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; Diptera/*classification ; Male ; },
abstract = {Iteaphila Zetterstedt is redefined to include species with both branched and unbranched radial vein (R4+5) on the basis of a morphological cladistic analysis and parsimony analysis of COI mitochondrial DNA barcode sequences. As a result, Anthepiscopus Becker is hypothesized as a junior synonym of Iteaphila and species of the Iteaphila setosa group are transferred to the new genus, Paraiteaphila gen. nov. The following new combinations are proposed: P. arundela (Shamshev Sinclair, 2009) comb. nov., P. caucasica (Shamshev Sinclair, 2009) comb. nov., P. italica (Loew, 1873) comb. nov., P. kubaniensis (Shamshev Sinclair, 2009) comb. nov., P. merzi (Shamshev Sinclair, 2009) comb. nov. and P. setosa (Bezzi, 1924) comb. nov. These two genera are assigned to the family Iteaphilidae stat. rev. Thirty-five species of Iteaphila with unbranched radial vein are revised, including 26 new species: bulbosa species group (I. beringiensis sp. nov., I. bifida sp. nov., I. recta sp. nov., I. tribulosa sp. nov.), macquarti species group (I. bartaki sp. nov., I. falki sp. nov., I. kyrgyzstanensis sp. nov., I. ribesii (Becker, 1891) comb. nov.), nitidula species group (I. longiphallus sp. nov.), nupta species group (I. arnaudi sp. nov., I. bayarea sp. nov., I. brooksi sp. nov., I. dichoptica sp. nov., I. flavipilosa (Coquillett, 1900) comb. nov., I. glabricula sp. nov., I. gracilis sp. nov., I. grandis sp. nov., I. lolo sp. nov., I. longipalpis (Melander, 1928) comb. nov., I. luteitibia sp. nov., I. nupta (Melander, 1928) comb. nov., I. sierrensis sp. nov., I. spinosa sp. nov., I. subnupta sp. nov.), oedalina species group (I. aktruensis sp. nov., I. incus sp. nov., I. miranda sp. nov., I. oedalina (Zetterstedt, 1838) comb. nov., I. polygyna (Melander, 1928) comb. nov., I. recurvata sp. nov., I. sakhalinensis sp. nov., I. zontaki (Nowicki, 1871) comb. nov.), stentor species group (I. parastentor sp. nov., I. stentor (Melander, 1902) comb. nov.) and unplaced to species group (I. caelebs (Becker, 1891) comb. nov.). The following new synonyms are proposed: I. flavicoxa (Melander, 1928) is a junior synonym of I. polygyna (Melander, 1928); I. hirsutus (Melander, 1928) is a junior synonym of I. oedalina (Zettersedt, 1838). Lectotypes are designated for the following species: I. flavipilosa, I. fraternella Zetterstedt, I. nigra Zetterstedt, I. nupta, I. oedalina, I. polygyna and I. ribesii. All species of Iteaphila with unbranched R4+5 are described, key to species presented, male terminalia illustrated, distributions plotted and flowers visited by these species are listed. COI mitochondrial DNA barcode sequences were obtained for 18 identified Nearctic species of Iteaphila with both branched and unbranched R4+5.},
}
@article {pmid34186920,
year = {2021},
author = {Freyhof, J and Kaya, C and Abdullah, YS and Geiger, MF},
title = {The Glyptothorax catfishes of the Euphrates and Tigris with the description of a new species (Teleostei: Sisoridae).},
journal = {Zootaxa},
volume = {4969},
number = {3},
pages = {453491},
doi = {10.11646/zootaxa.4969.3.2},
pmid = {34186920},
issn = {1175-5334},
mesh = {Animals ; Catfishes/*anatomy &amp; histology/*classification ; DNA, Mitochondrial ; Iran ; },
abstract = {The Glyptothorax species inhabiting the Euphrates and Tigris drainages are reviewed and six species are recognised, one of which is described herein as new species. Glyptothorax armeniacus is endemic to headwater streams in the Euphrates drainage. Glyptothorax kurdistanicus is endemic to the upper Tigris downstream to the Lesser Zab drainage. Glyptothorax cous and G. steindachneri are riverine species widespread in both the Euphrates and Tigris drainages. Glyptothorax silviae is endemic to Iran. Glyptothorax daemon, new species, from the Greater Zab and Yanarsu in the upper Tigris drainage, is distinguished by having the thoracic adhesive apparatus strongly elevated, 1.11.2 times longer than wide, without tubercles on the head, well developed anteromedial striae, the medial pit without striae, and a short adipose fin. Glyptothorax daemon is separated into two mitochondrial lineages, externally indistinguishable and separated by a minimum K2P distance of 2.0% in the DNA barcode region. These lineages are paraphyletic in our analysis indicating past introgressive hybridisation with G. cous. All six species are diagnosed and all, except unstudied G. steindachneri, form distinct mitochondrial clades with between 1.2% and 3.4% minimum K2P distance between them. Species from the Euphrates and Tigris form a monophyletic mitochondrial group separated from 53 other Glyptothorax species studied from India and areas further east.},
}
@article {pmid34186915,
year = {2021},
author = {Chen, Z and Yang, X and Menzel, F and Wu, H and Huang, J},
title = {Three Oriental species of Pseudoaerumnosa Rudzinski (Diptera, Sciaridae) &lt;br /&gt;from China.},
journal = {Zootaxa},
volume = {4969},
number = {3},
pages = {551562},
doi = {10.11646/zootaxa.4969.3.7},
pmid = {34186915},
issn = {1175-5334},
mesh = {Animals ; China ; DNA Barcoding, Taxonomic ; Nematocera/*classification ; Phylogeny ; },
abstract = {Three Oriental species of the genus Pseudoaerumnosa Rudzinski, 2006 from China are described and illustrated: P. regularis sp. n., P. tianmushana sp. n. and P. tkoci Vilkamaa, Halenius Ševčík, 2019. The morphological species concepts were supported by the DNA barcodes of COI sequences. The genetic distances of Pseudoaerumnosa species were analyzed and a neighbor-joining tree was constructed, based on 37 sequences of nine species.},
}
@article {pmid34186914,
year = {2021},
author = {Olmi, M and Mita, T and Guglielmino, A and Vollaro, M and Vári, G},
title = {Application of DNA barcoding confirms the female, male, larva and host of Bocchus scobiolae Nagy (Hymenoptera: Dryinidae).},
journal = {Zootaxa},
volume = {4969},
number = {3},
pages = {563572},
doi = {10.11646/zootaxa.4969.3.8},
pmid = {34186914},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; Female ; Hungary ; Larva/classification ; Male ; Wasps/*classification ; },
abstract = {Bocchus scobiolae Nagy (Hymenoptera: Dryinidae, Bocchinae) was reared in Szeged, Hungary. The female, male and immature larva were associated by mitochondrial COI sequences. B. scobiolae, previously known only from Romania, is recorded for the first time from Hungary, Moldova, and Turkey. Caliscelis wallengreni (Stål) (Hemiptera: Caliscelidae) is mentioned for the first time as host of B. scobiolae. B. vernieri Olmi is indicated for the first time from Hungary. Helegonatopus rasnitzyni (Trjapitzin, 1963) (Hymenoptera: Encyrtidae), recorded for the first time from Hungary, was reared from B. scobiolae (new record).},
}
@article {pmid34186852,
year = {2021},
author = {Lalronunga, S and Vanramliana, V and Lalramliana, L and Lalhmingliani, E},
title = {A new country record of Raorchestes cangyuanensis Wu, Suwannapoom, Xu, Murphy amp; Che 2019 and additional record of Kurixalus yangi Yu, Hui, Rao amp; Yang 2018 (Anura: Rhacophoridae: Rhacophorinae) from India.},
journal = {Zootaxa},
volume = {4974},
number = {2},
pages = {383390},
doi = {10.11646/zootaxa.4974.2.7},
pmid = {34186852},
issn = {1175-5334},
mesh = {Animals ; Anura/*classification ; DNA Barcoding, Taxonomic ; India ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Most studies on the diversity of amphibians in northeast India were based on classical morpho-taxonomy, which have a high probability of errors in species identification. DNA barcoding of amphibians using the mitochondrial 16S rRNA gene has been used successfully for the identification of species and detection of cryptic species. In the present study, we carry out DNA barcoding of two rhacophorid species of the genus Raorchestes and Kurixalus that are not readily identifiable to the species level based on their morphology. Our analysis on the 16S rRNA gene revealed that these species were Raorchestes cangyuanensis and Kurixalus yangi, species which were recorded for the first time and second time from India respectively. We discuss on the records of R. longchuanensis from Bangladesh and India, which were based on the misidentification of R. cangyuanensis. We therefore propose to delist this species from the faunal list of Bangladesh and India. We further raise a question as to why the population of Kurixalus from Motuo, Xizang province of China was assigned as K. naso and not the population described as K. yangi, which is morphologically similar to K. naso and is also recorded from a locality close to the type locality of K. naso.},
}
@article {pmid34186845,
year = {2021},
author = {Tong, Y and Hao, J and Liu, H and Li, S and Hou, Z},
title = {Floresorchestia xueli, a new terrestrial crustacean (Amphipoda, Talitridae) from Yunnan, China.},
journal = {Zootaxa},
volume = {4991},
number = {2},
pages = {318-330},
doi = {10.11646/zootaxa.4991.2.5},
pmid = {34186845},
issn = {1175-5334},
mesh = {Amphipoda/*anatomy &amp; histology/*classification ; Animals ; China ; DNA Barcoding, Taxonomic ; Ecosystem ; Mandible ; },
abstract = {A new species, Floresorchestia xueli Tong Hou, sp. nov. is described from high altitude habitats of Yunnan, China. The species differs morphologically from its congeners by left mandible lacinia mobilis having four teeth; coxal gills complexly lobed and convoluted; epimeral plates IIIII without slits; telson with one slender facial spine and two terminal spines on each lobe. Analysis of DNA barcode sequences and niche distinctiveness support recognition of the new species.},
}
@article {pmid34186813,
year = {2021},
author = {Habib, KA and Islam, MJ},
title = {Description of a new species of giant guitarfish, Glaucostegus younholeei sp. nov. (Rhinopristiformes: Glaucostegidae) from the northern Bay of Bengal, Bangladesh.},
journal = {Zootaxa},
volume = {4995},
number = {1},
pages = {129-146},
doi = {10.11646/zootaxa.4995.1.7},
pmid = {34186813},
issn = {1175-5334},
mesh = {Animals ; Bangladesh ; Bays ; DNA Barcoding, Taxonomic ; Male ; Phylogeny ; Skates, Fish/*anatomy &amp; histology/*classification ; },
abstract = {A new species of giant guitarfish, Glaucostegus younholeei sp. nov., is described from 13 specimens, 730933 mm total length, collected from fish landing center of Bangladesh Fisheries Development Corporation in Cox's Bazar district of Bangladesh. The new species is distinguished from congeners in having the following combination of characters: Body brownish or greyish in color with a narrowly wedge-shaped disc, and long narrow bluntly pointed snout (angle 3140°), and broad oblique nostrils with the narrow anterior opening. Nostrils about half of the mouth width, subequal (0.981.33) to internasal width; ~5557 nasal lamellae; anterior nasal flaps slightly penetrating into internasal space, their interspace 2.20 2.61 in length of the posterior nasal aperture. Orbit very small in adults, diameter 8.1911.62 in preorbital length, 2.252.69 in interorbital space. Rostral ridges almost joined along their entire length; margin of cranium sharply demarcated before eyes. Spiracular folds very short and widely separated. Skin rough, densely covered with small denticles, more coarsely granular on the dorsal surface than ventrally, enlarged between orbits and in a distinct band between nape and first dorsal fin. Tail relatively longer, length 1.151.48 in disc length; dorsal fins narrowly spaced, interspace 1.322.11 in base length of the first dorsal fin. Clasper length in adult male 4.375.70 in total length. Phylogenetic analysis of DNA barcode sequences also shows the clear divergence of Glaucostegus younholeei from other congeneric species obtained from GenBank. A key is provided to the 8 known members including new species of the genus Glaucostegus.},
}
@article {pmid34186805,
year = {2021},
author = {Chang, GD and Potapov, M and Park, KH},
title = {A new species of Anurophorus (Collembola: Isotomidae) from South Korea, with notes on its molecular data.},
journal = {Zootaxa},
volume = {4985},
number = {3},
pages = {345358},
doi = {10.11646/zootaxa.4985.3.2},
pmid = {34186805},
issn = {1175-5334},
mesh = {Animals ; Arthropods/*anatomy &amp; histology/*classification ; Genes, Mitochondrial ; RNA, Ribosomal, 28S ; Republic of Korea ; },
abstract = {A new species, Anurophorus hallaensis sp. nov. was collected from the withered leaves of Korean fir (Abies koreana Wilson), which is distributed at higher than 1,300 m in altitude on Mt. Hallasan (Jeju Island, South Korea). The morphology and two partial gene regions of this species are described herein. Anurophorus hallaensis sp. nov. showed the same formulas of macrochaetae and sensilla on thoracic segment II to abdominal segment IV as those exhibited by A. laricis Nicolet and A. palearcticus Potapov; however, this new species can be distinguished from them by the number of knobbed hairs on ventral side of legs. Partial DNA sequences of the mitochondrial Cytochrome c Oxidase subunit I (COI) gene and ribosomal DNA (28S rDNA) were used as DNA barcodes to distinguish between A. hallaensis sp. nov. and closely related congeners. The results of the present study indicate that the COI and rDNA are useful for species discrimination within the genus Anurophorus. An identification key to the Korean species of Anurophorus is provided.},
}
@article {pmid34186801,
year = {2021},
author = {Techakijvej, C and Sareein, N and Hwang, JM and Bae, YJ and Phalaraksh, C},
title = {A new species of Ephoron Williamson, 1802 (Ephemeroptera: Polymitarcyidae) from Thailand.},
journal = {Zootaxa},
volume = {4985},
number = {3},
pages = {392402},
doi = {10.11646/zootaxa.4985.3.6},
pmid = {34186801},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Ephemeroptera/anatomy &amp; histology/*classification ; Genes, Mitochondrial ; Larva ; Thailand ; },
abstract = {The genus Ephoron Williamson, 1802 is widely distributed around the world. In Thailand, only Ephoron indicus Pictet, 1843 was reported in 1961. In this study, a new Ephoron mayfly is described as Ephoron ookaewae sp. nov. In this new species description, the morphological characteristics of larvae and eggs in addition to adults are also shown in detail. Number of tubercles on mandibular tusks, and a median frontal process in larvae, distinguish Ephoron ookaewae sp. nov. from other Ephoron species. Their polar cap shape and a concave indentation in their eggs are also unusual. In addition, the mitochondrial DNA COI sequence data of the newly described Ephoron ookaewae sp. nov. is registered in GenBank. Registration of sequence data for the DNA barcode region of Ephoron mayflies inhabiting the Oriental region remains limited, however it will be useful for future research.},
}
@article {pmid34186773,
year = {2021},
author = {Laguerre, M},
title = {Partial revision of the genus Robinsonia Grote 1866: description of five new species for the Neotropical fauna (Lepidoptera, Erebidae, Arctiinae, Phaegopterina).},
journal = {Zootaxa},
volume = {4990},
number = {1},
pages = {65-80},
doi = {10.11646/zootaxa.4990.1.4},
pmid = {34186773},
issn = {1175-5334},
mesh = {Animals ; Central America ; Female ; Genitalia ; Male ; Moths/anatomy &amp; histology/*classification ; South America ; },
abstract = {The genus Robinsonia Grote, 1866 is partially reviewed following a large DNA barcode campaign. In the Robinsonia praphoea Dognin, 1906 group three new species are described: R. simulans sp. n. from French Guiana, up to now confused with R. praphoea itself and then R. decaensi sp. n. and R. maranhensis sp. n. both from the lower Amazon. R. drechseli sp. n. is described from Paraguay and R. inexpectata sp. n., a species close to R. mera (Schaus, 1910) from Costa Rica, is described as new from Peru and Bolivia. Finally the full species status is confirmed for R. flavicorpus Dognin, 1910 which is found to be differentiable from R. marginata Rothschild, 1909. All types are figured along with the male genitalia for most and some female genitalia for all studied species.},
}
@article {pmid34186772,
year = {2021},
author = {Han, WU and Tang, H and Ni, Z},
title = {DNA barcodes and morphology reveal two new species of Monodiamesa Kieffer (Diptera: Chironomidae: Prodiamesinae) in Tibetan Plateau.},
journal = {Zootaxa},
volume = {4990},
number = {1},
pages = {81-103},
doi = {10.11646/zootaxa.4990.1.5},
pmid = {34186772},
issn = {1175-5334},
mesh = {Animals ; Chironomidae/*classification ; DNA Barcoding, Taxonomic ; Ecosystem ; Female ; Male ; Tibet ; },
abstract = {Two Monodiamesa species collected in all stages and both sexes from the Tibetan Plateau are erected as M. secunditibetica Han and Tang, sp. n. and M. bonalpicola Han and Tang, sp. n. Molecular analysis of barcodes (COI-5P) for some related known species confirms the species validity and allows inference of internal relationships. Detailed description, habitat ecology and geographical information of two new species are provided. Additionally, brief comments on some known eastern Palaearctic species of Monodiamesa are made to give insights on further study.},
}
@article {pmid34186755,
year = {2021},
author = {Yang, L and Liu, H and Ren, Y},
title = {One new species of the genus Etielloides Shibuya, 1928 from China (Lepidoptera, Pyralidae, Phycitinae).},
journal = {Zootaxa},
volume = {4990},
number = {2},
pages = {361368},
doi = {10.11646/zootaxa.4990.2.9},
pmid = {34186755},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; China ; DNA Barcoding, Taxonomic ; Female ; Genitalia ; Head ; Male ; Moths/anatomy &amp; histology/*classification ; },
abstract = {One new species, Etielloides luniformis sp. nov. is described based on specimens collected from Mt. Leigong, Qiandongnan Miao and Dong Autonomous Prefecture, Guizhou of China. Adults, venation, head and genitalia structures of both sexes are described and illustrated, along with a key to all the known species of the genus Etielloides. DNA barcodes of the new species and its related species are provided for species delimitation.},
}
@article {pmid34186754,
year = {2021},
author = {Guerrero, JJ and Hausmann, A and Ortiz, AS},
title = {Description of Idaea josephinae sp. n. from the Iberian Peninsula (Lepidoptera: Geometridae).},
journal = {Zootaxa},
volume = {4990},
number = {2},
pages = {369377},
doi = {10.11646/zootaxa.4990.2.10},
pmid = {34186754},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Genes, Mitochondrial ; Genitalia ; Moths/anatomy &amp; histology/*classification ; Spain ; },
abstract = {Idaea josephinae sp. n. is described from the Iberian Peninsula. Differential characters from its North African sister species Idaea lobaria (Chrétien, 1909) in external appearance and genitalia, and in the 5' barcode fragment of the mitochondrial COI gene (the DNA barcode) are presented.},
}
@article {pmid34186684,
year = {2021},
author = {Naumova, M and Blagoev, G and Deltshev, C},
title = {Fifty spider species new to the Bulgarian fauna, with a review of some dubious species (Arachnida: Araneae).},
journal = {Zootaxa},
volume = {4984},
number = {1},
pages = {228257},
doi = {10.11646/zootaxa.4984.1.18},
pmid = {34186684},
issn = {1175-5334},
mesh = {Animals ; Bulgaria ; DNA Barcoding, Taxonomic ; Spiders/*classification ; },
abstract = {This study is a part of an ongoing comprehensive inventory of Bulgarian spiders. A total of fifty spider species belonging to thirteen families are reported for the first time from Bulgaria. Four species are rejected from the Bulgarian spider checklist due to misidentification: Callilepis concolor Simon, 1914, Centromerus capucinus (Simon, 1884), Hoplopholcus labyrinthi (Kulczyński, 1903) and Mansuphantes prope fragilis (Thorell, 1875). Another four species (Drassodes villosus (Thorell, 1856), Entelecara flavipes (Blackwall, 1834), Lepthyphantes notabilis Kulczyński, 1887 and Singa semiatra L. Koch, 1867) are rejected after a new interpretation of the locations. Six species were omitted from the list of Bulgarian spiders as obviously doubtful records (Dysdera nicaeensis Thorell, 1873, Haplodrassus rufipes (Lucas, 1846), Harpactea hispana (Simon, 1882), Macaroeris cata (Blackwall, 1867), Nomisia celerrima (Simon, 1914) and Tenuiphantes monachus (Simon, 1884)). A new synonymy is proposed for Cyclosa strandjae Drensky, 1915 (= Cyclosa sierrae Simon, 1870 syn. nov.). In addition, new images with essential taxonomic value are provided for twenty-five species to facilitate their identification or to illustrate their intraspecific variability. To ensure correct identification, DNA barcoding was additionally used in some species.},
}
@article {pmid34186666,
year = {2021},
author = {Chakraborty, RD and Gayathri, AP and Sreelakshmy, S and Aghana, M and Kuberan, G},
title = {DNA barcoding of deep-sea shrimp Sicyonia parajaponica Crosnier, 2003 (Crustacea: Decapoda: Sicyoniidae) from southwest coast of India.},
journal = {Zootaxa},
volume = {4985},
number = {1},
pages = {125130},
doi = {10.11646/zootaxa.4985.1.9},
pmid = {34186666},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Decapoda/*classification ; Genes, Mitochondrial ; India ; Phylogeny ; },
abstract = {The present work reports detailed taxonomic information on deep-sea shrimp Sicyonia parajaponica from southwest Indian waters. The samples were caught in bottom trawls conducted between the depths of 200 and 230 m from Sakthikulangara fishing harbour off Kollam, Kerala along the Arabian Sea during November 2019. DNA barcoding and a phylogenetic analysis was used to explore the relationship of the genus Sicyonia based on mitochondrial cytochrome c oxidase subunit 1 (COI: MN816389, MN816390) with the present specimen and sequences retrieved from NCBI GenBank. There is no difference in the intraspecies genetic distance (0%) while interspecies genetic distance (19.028.1%) revealed divergence between the species (COI) of the genus Sicyonia.},
}
@article {pmid34186641,
year = {2021},
author = {Tiunova, TM and Semenchenko, AA and Tong, X},
title = {Baetis majus sp. nov., new species of mayfly (Ephemeroptera: Baetidae) from Far East of Russia.},
journal = {Zootaxa},
volume = {4965},
number = {3},
pages = {541557},
doi = {10.11646/zootaxa.4965.3.8},
pmid = {34186641},
issn = {1175-5334},
mesh = {Animals ; Bayes Theorem ; DNA Barcoding, Taxonomic ; Ephemeroptera/anatomy &amp; histology/*classification ; Phylogeny ; Russia ; },
abstract = {A new species, Baetis majus Tiunova sp. nov., is described and illustrated based on larvae and reared adults discovered in the Russian Far East. The differential identification of this species was determined by the characteristics of other representatives of the genus Baetis Leach, including subgenera Baetis Leach and Tenuibaetis Kang Yang from Eastern and Western Palaearctic, Nearctic and Oriental regions. In addition to morphological studies, DNA barcoding of the described species with average intraspecific K2P distances to nearest neighbours is documented. We reconstructed the phylogenetic relationships of all available cytochrome c oxidase subunit I (COI) sequences of the subgenera of Baetis and Tenuibaetis from four regions. Bayesian analysis using 47 morphological characters additional to partial COI sequences did not allow to determine the species-group of the Baetis genus to which the described species belongs.},
}
@article {pmid34186640,
year = {2021},
author = {Mantelatto, FL and Miranda, I and Vera-Silva, AL and Negri, M and Buranelli, RC and Terossi, M and Magalhães, T and Costa, RRC and Zara, FJ and Castilho, AL},
title = {Checklist of decapod crustaceans from the coast of the São Paulo state (Brazil) supported by integrative molecular and morphological data: IV. Infraorder Anomura: Superfamilies Chirostyloidea, Galatheoidea, Hippoidea and Paguroidea.},
journal = {Zootaxa},
volume = {4965},
number = {3},
pages = {558600},
doi = {10.11646/zootaxa.4965.3.9},
pmid = {34186640},
issn = {1175-5334},
mesh = {Animals ; Anomura/*classification ; Brazil ; DNA, Mitochondrial ; Phylogeny ; },
abstract = {This checklist is the fourth contribution resulting from a long-term multidisciplinary project which combined morphological analyses and molecular techniques (mitochondrial DNA markers) for accurate identification of marine and coastal decapod crustaceans of São Paulo State (Brazil). We provide a list of 63 species of the following 11 families of 4 superfamilies of Anomura: Albuneidae (4 spp.), Blepharipodidae (1 sp.), Chirostylidae (1 sp.), Diogenidae (18 spp.), Hippidae (1 sp.), Munididae (8 spp.), Munidopsidae (1 sp.), Paguridae (13 spp.), Parapaguridae (2 spp.), Porcellanidae (13 spp.), and Pylochelidae (1 sp.). Seven species previously reported from the region were neither collected nor found in museum collections during our study, including one (Sympagurus dimorphus) that we suggest to be removed from São Paulo coast fauna lists. We generated new sequences of cytochrome oxidase subunit I (barcode region) and 16S genes of 44 species. This anomuran inventory may serve as guideline for future studies on taxonomy, conservation, population genetics, biogeography, and phylogenetics, which might flag species that deserve further investigations and concerns.},
}
@article {pmid34183875,
year = {2021},
author = {Kavanaugh, DH and Maddison, DR and Simison, WB and Schoville, SD and Schmidt, J and Faille, A and Moore, W and Pflug, JM and Archambeault, SL and Hoang, T and Chen, JY},
title = {Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data.},
journal = {ZooKeys},
volume = {1044},
number = {},
pages = {41-152},
pmid = {34183875},
issn = {1313-2989},
abstract = {The phylogeny of the carabid beetle supertribe Nebriitae is inferred from analyses of DNA sequence data from eight gene fragments including one nuclear ribosomal gene (28S), four nuclear-protein coding genes (CAD, topoisomerase 1, PEPCK, and wingless), and three mitochondrial gene fragments (16S + tRNA-Leu + ND1, COI ("barcode" region) and COI ("Pat/Jer" region)). Our taxon sample included 264 exemplars representing 241 species and subspecies (25% of the known nebriite fauna), 39 of 41 currently accepted genera and subgenera (all except Notiokasis and Archileistobrius), and eight outgroup taxa. Separate maximum likelihood (ML) analyses of individual genes, combined ML analyses of nuclear, nuclear protein-coding, and mitochondrial genes, and combined ML and Bayesian analyses of the eight-gene-fragment matrix resulted in a well-resolved phylogeny of the supertribe, with most nodes in the tree strongly supported. Within Nebriitae, 167 internal nodes of the tree (out of the maximum possible 255) are supported by maximum-likelihood bootstrap values of 90% or more. The tribes Notiophilini, Opisthiini, Pelophilini, and Nebriini are well supported as monophyletic but relationships among these are not well resolved. Nippononebria is a distinct genus more closely related to Leistus than Nebria. Archastes, Oreonebria, Spelaeonebria, and Eurynebria, previously treated as distinct genera by some authors, are all nested within a monophyletic genus Nebria. Within Nebria, four major clades are recognized: (1) the Oreonebria Series, including eight subgenera arrayed in two subgeneric complexes (the Eonebria and Oreonebria Complexes); (2) the Nebriola Series, including only subgenus Nebriola; (3) the Nebria Series, including ten subgenera arrayed in two subgeneric complexes, the Boreonebria and Nebria Complexes, with the latter further subdivided into three subgeneric subcomplexes (the Nebria, Epinebriola, and Eunebria Subcomplexes)); and (4) the Catonebria Series, including seven subgenera arrayed in two subgeneric complexes (the Reductonebria and Catonebria Complexes). A strong concordance of biogeography with the inferred phylogeny is noted and some evident vicariance patterns are highlighted. A revised classification, mainly within the Nebriini, is proposed to reflect the inferred phylogeny. Three genus-group taxa (Nippononebria, Vancouveria and Archastes) are given revised status and seven are recognized as new synonymies (Nebriorites Jeannel, 1941 and Marggia Huber, 2014 = Oreonebria Daniel, 1903; Pseudonebriola Ledoux &amp; Roux, 1989 = Boreonebria Jeannel, 1937; Patrobonebria Bänninger, 1923, Paranebria Jeannel, 1937 and Barbonebriola Huber &amp; Schmidt, 2017 = Epinebriola Daniel &amp; Daniel, 1904; and Asionebria Shilenkov, 1982 = Psilonebria Andrewes, 1923). Six new subgenera are proposed and described for newly recognized clades: Parepinebriola Kavanaugh subgen. nov. (type species: Nebria delicata Huber &amp; Schmidt, 2017), Insulanebria Kavanaugh subgen. nov. (type species: Nebria carbonaria Eschscholtz, 1829), Erwinebria Kavanaugh subgen. nov. (type species Nebria sahlbergii Fischer von Waldheim, 1828), Nivalonebria Kavanaugh subgen. nov. (type species: Nebria paradisi Darlington, 1931), Neaptenonebria Kavanaugh subgen. nov. (type species: Nebria ovipennis LeConte, 1878), and Palaptenonebria Kavanaugh subgen. nov. (type species: Nebria mellyi Gebler, 1847). Future efforts to better understand relationships within the supertribe should aim to expand the taxon sampling of DNA sequence data, particularly within subgenera Leistus and Evanoleistus of genus Leistus and the Nebria Complex of genus Nebria.},
}
@article {pmid34179490,
year = {2021},
author = {Peng, C and Yu, CC and Xing, YW},
title = {The complete chloroplast genome of Androsace erecta (Primulaceae) and its phylogenetic implication.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {6},
number = {7},
pages = {1987-1989},
pmid = {34179490},
issn = {2380-2359},
abstract = {With about 153 species, the genus Androsace (Primulaceae) is known for its horticultural and economic importance. In this study, we report the complete chloroplast genome of Androsace erecta Maximowicz, a morphologically distinct species of Sect. Orthocaulon native to the Western China. The plastome of A. erecta is highly conserved in genome size, structure, and content when compared to all previously published plastomes of the genus. The phylogenomic analysis strongly supported A. erecta as sister to a clade comprising species of Sections Aizoideia and Chamaejasme. Lastly, we selected the four most variable regions across the Androsace species plastomes (trnK[UUU]-rps16, trnS[GCU]-trnG[UCC] , psbE-petL, and infA-rps8), which were considered to be suitable candidate DNA barcodes for Androsace.},
}
@article {pmid34179350,
year = {2020},
author = {Cang, Z and Munch, E and Wei, GW},
title = {Evolutionary homology on coupled dynamical systems with applications to protein flexibility analysis.},
journal = {Journal of applied and computational topology},
volume = {4},
number = {4},
pages = {481-507},
pmid = {34179350},
issn = {2367-1734},
support = {R01 GM126189/GM/NIGMS NIH HHS/United States ; },
abstract = {While the spatial topological persistence is naturally constructed from a radius-based filtration, it has hardly been derived from a temporal filtration. Most topological models are designed for the global topology of a given object as a whole. There is no method reported in the literature for the topology of an individual component in an object to the best of our knowledge. For many problems in science and engineering, the topology of an individual component is important for describing its properties. We propose evolutionary homology (EH) constructed via a time evolution-based filtration and topological persistence. Our approach couples a set of dynamical systems or chaotic oscillators by the interactions of a physical system, such as a macromolecule. The interactions are approximated by weighted graph Laplacians. Simplices, simplicial complexes, algebraic groups and topological persistence are defined on the coupled trajectories of the chaotic oscillators. The resulting EH gives rise to time-dependent topological invariants or evolutionary barcodes for an individual component of the physical system, revealing its topology-function relationship. In conjunction with Wasserstein metrics, the proposed EH is applied to protein flexibility analysis, an important problem in computational biophysics. Numerical results for the B-factor prediction of a benchmark set of 364 proteins indicate that the proposed EH outperforms all the other state-of-the-art methods in the field.},
}
@article {pmid34178311,
year = {2021},
author = {Seth, S and Bhattacharya, A},
title = {DNA barcode by flossing through a cylindrical nanopore.},
journal = {RSC advances},
volume = {11},
number = {34},
pages = {20781-20787},
pmid = {34178311},
issn = {2046-2069},
support = {R21 HG011236/HG/NHGRI NIH HHS/United States ; },
abstract = {We report an accurate method to determine DNA barcodes from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive theoretical scheme which improves the measurements to almost 100% accuracy. The heavier protein tags along the DNA backbone introduce a large speed variation in the chain that can be understood using the idea of non-equilibrium tension propagation theory. However, from an initial rough characterization of velocities into "fast" (nucleotides) and "slow" (protein tags) domains, we introduce a physically motivated interpolation scheme that enables us to determine the barcode velocities rather accurately. Our theoretical analysis of the motion of the DNA through a cylindrical nanopore opens up the possibility of its experimental realization and carries over to multi-nanopore devices used for barcoding.},
}
@article {pmid34177308,
year = {2021},
author = {Cho, K and Park, C and Böttger-Schnack, R},
title = {Taxonomy of three species of the genus Spinoncaea (Copepoda, Oncaeidae) in the North Pacific Ocean with focus on morphological variability.},
journal = {ZooKeys},
volume = {1043},
number = {},
pages = {147-191},
pmid = {34177308},
issn = {1313-2989},
abstract = {Three species of Spinoncaea Böttger-Schnack, 2003 are newly recorded in three locations of the equatorial and temperate Pacific Ocean collected by using a net of 60 μm mesh size. For all three species, morphological characters and patterns of ornamentation were analyzed in detail and illustrations of both sexes, also including form variants of the females, are provided. For the first time, information about the variability of various continuous (morphometric) characters are given, such as the spine lengths on the rami of the swimming legs or the proportions of urosomites. The complementary morphological descriptions of the Pacific specimens focus on similarities or modifications of characters as compared to earlier descriptions of these species from the type locality and various other localities. For S. ivlevi (Shmeleva, 1966), originally but insufficiently described from the Adriatic Sea, the Pacific material is similar in most aspects to the comprehensive redescription of the species from the Red Sea and from the type locality, except for a difference in the morphometry of the distal endopod segment on the antenna, which is discussed here. For S. tenuis Böttger-Schnack, 2003, and S. humesi Böttger-Schnack, 2003, the Pacific material mostly coincides with the characteristic features as described in the original account from the Red Sea. For all three species, differences and/or additions in ornamentation details were found in Pacific specimens (e.g., on the intercoxal sclerite of the first swimming leg or on the genital somite of the male) and females with aberrant morphology were detected. Genetic analyses based on 12S srRNA revealed for two species, S. ivlevi and S. humesi, little or no differences in genetic sequences between Pacific specimens and those recorded from the Mediterranean Sea, thus demonstrating that specimens from both locations are conspecific. For S. tenuis, for which no comparable genetic data are available, 12S srRNA amplification was unsuccessful as was the amplification of mitochondrial COI (barcoding) for all three species. The applicability of using COI amplification for barcoding of oncaeid copepods is discussed.},
}
@article {pmid34174956,
year = {2021},
author = {Guarido, MM and Riddin, MA and Johnson, T and Braack, LEO and Schrama, M and Gorsich, EE and Brooke, BD and Almeida, APG and Venter, M},
title = {Aedes species (Diptera: Culicidae) ecological and host feeding patterns in the north-eastern parts of South Africa, 2014-2018.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {339},
pmid = {34174956},
issn = {1756-3305},
support = {5 NU2GGH001874-02-00/CC/CDC HHS/United States ; 2016.08//Gratama Stichting/ ; SUB.2016.12.08//Uyttenboogaart-Eliasen Stichting/ ; },
mesh = {Aedes/classification/genetics/*physiology ; Animals ; Ecosystem ; Electron Transport Complex IV/genetics ; *Feeding Behavior ; Female ; Insect Proteins/genetics ; Mosquito Vectors/classification/genetics/physiology ; South Africa ; Temperature ; },
abstract = {BACKGROUND: There is a paucity of recent data and knowledge on mosquito diversity and potential vectors of arboviruses in South Africa, with most of the available data dating back to the 1950s-1970s. Aedes and Culex species are the major vectors of some of the principal arboviruses which have emerged and re-emerged in the past few decades.<br><br>METHODS: In this study we used entomological surveillance in selected areas in the north-eastern parts of South Africa from 2014 to 2018 to assess mosquito diversity, with special emphasis on the Aedes species. The impact of trap types and environmental conditions was also investigated. Identification of the blood meal sources of engorged females collected during the study period was carried out, and DNA barcodes were generated for selected species.<br><br>RESULTS: Overall, 18.5% of the total Culicidae mosquitoes collected belonged to the genus Aedes, with 14 species recognised or suspected vectors of arboviruses. Species belonging to the Neomelaniconion subgenus were commonly collected in the Bushveld savanna at conservation areas, especially Aedes mcintoshi and Aedes circumluteolus. Aedes aegypti was present in all sites, albeit in low numbers. Temperature was a limiting factor for the Aedes population, and they were almost exclusively collected at temperatures between 18&#xa0;&#xb0;C and 27&#xa0;&#xb0;C. The cytochrome oxidase subunit I (COI) barcode fragment was amplified for 21 Aedes species, and for nine of these species it was the first sequence information uploaded on GenBank.<br><br>CONCLUSION: This study provides a better understanding of the diversity and relative abundance of Aedes species in the north-east of South Africa. The information provided here will contribute to future arboviral research and implementation of efficient vector control and prevention strategies.},
}
@article {pmid34174720,
year = {2021},
author = {Sandin, MM and Biard, T and Romac, S and O'Dogherty, L and Suzuki, N and Not, F},
title = {A Morpho-molecular Perspective on the Diversity and Evolution of Spumellaria (Radiolaria).},
journal = {Protist},
volume = {172},
number = {3},
pages = {125806},
doi = {10.1016/j.protis.2021.125806},
pmid = {34174720},
issn = {1618-0941},
mesh = {Biological Evolution ; DNA, Ribosomal ; Eukaryota ; Humans ; Phylogeny ; *Rhizaria/genetics ; },
abstract = {Spumellaria (Radiolaria, Rhizaria) are holoplanktonic amoeboid protists, ubiquitous and abundant in the global ocean. Their silicified skeleton preserves very well in sediments, displaying an excellent fossil record extremely valuable for paleo-environmental reconstruction studies, from where most of their extant diversity and ecology have been inferred. This study represents a comprehensive classification of Spumellaria based on the combination of ribosomal taxonomic marker genes (rDNA) and morphological characteristics. In contrast to established taxonomic knowledge, we demonstrate that symmetry of the skeleton takes more importance than internal structures at high classification ranks. Such reconsideration allows gathering different morphologies with concentric structure and spherical or radial symmetry believed to belong to other Radiolaria orders from the fossil record, as for some Entactinaria families. Our calibrated molecular clock dates the origin of Spumellaria in the middle Cambrian (ca. 515 Ma), among the first radiolarian representatives in the fossil record. This study allows a direct connection between living specimens and extinct morphologies from the Cambrian, bringing both a standpoint for future molecular environmental surveys and a better understanding for paleo-environmental reconstruction analysis.},
}
@article {pmid34170326,
year = {2021},
author = {Pedraza-Lara, C and Garduño-Sánchez, MA and Téllez-García, I and Rodríguez-González, S and Nuple-Juárez, E and Guardado-Estrada, M},
title = {Species Delimitation of Scavenger Flies in the Valley of Mexico.},
journal = {Journal of medical entomology},
volume = {58},
number = {6},
pages = {2206-2215},
doi = {10.1093/jme/tjab094},
pmid = {34170326},
issn = {1938-2928},
mesh = {*Animal Distribution ; Animals ; Calliphoridae/*classification ; DNA Barcoding, Taxonomic ; Diptera/*classification ; Electron Transport Complex IV/analysis ; Sarcophagidae/*classification ; },
abstract = {Identification of species involved in cadaveric decomposition, such as scavenger Diptera, is a fundamental step for the use of entomological evidence in court. Identification based on morphology is widely used in forensic cases; however, taxonomic knowledge of scavenger fauna is poor for many groups and for many countries, particularly Neotropical ones. A number of studies have documented the utility of a DNA barcoding strategy to assist in the identification of poorly known and diverse groups, particularly in cases involving immature states or fragmented organisms. To provide baseline knowledge of the diversity of scavenger Diptera in the Valley of Mexico, we generated a DNA barcode collection comprised of sequences of the cytochrome c oxidase subunit 1 (COI) gene for all families sampled at a nature reserve located in this region. We collected and identified specimens on the basis of morphology and a species delimitation analysis. Our analyses of 339 individuals delineated 42 species distributed across nine families of Diptera. The richest families were Calliphoridae (9 species), Sarcophagidae (7 species), and Phoridae (6 species). We found many of the species previously recorded for the Valley of Mexico, plus 18 new records for the region. Our study highlights the utility of DNA barcoding as a first-step strategy to assess species richness of poorly studied scavenger fly taxa.},
}
@article {pmid34168325,
year = {2021},
author = {Pandey, R and Chang, D and Smieja, M and Hoare, T and Li, Y and Soleymani, L},
title = {Integrating programmable DNAzymes with electrical readout for rapid and culture-free bacterial detection using a handheld platform.},
journal = {Nature chemistry},
volume = {13},
number = {9},
pages = {895-901},
pmid = {34168325},
issn = {1755-4349},
mesh = {Bacterial Load/instrumentation/*methods ; DNA, Catalytic/*chemistry ; DNA, Single-Stranded/chemistry/genetics ; Electrochemical Techniques/instrumentation/methods ; Escherichia coli/chemistry/*isolation &amp; purification ; Humans ; Lab-On-A-Chip Devices ; Microfluidic Analytical Techniques/instrumentation/methods ; Nucleic Acid Hybridization ; RNA, Bacterial/chemistry ; Smartphone ; Software ; Urine/microbiology ; },
abstract = {The detection and identification of bacteria currently rely on enrichment steps such as bacterial culture and nucleic acid amplification to increase the concentration of target analytes. These steps increase assay time, cost and complexity, making it difficult to realize a truly rapid point-of-care test. Here we report the development of an electrical assay that uses electroactive RNA-cleaving DNAzymes (e-RCDs) to identify specific bacterial targets and subsequently release a DNA barcode for transducing a signal onto an electrical chip. Integrating e-RCDs into a two-channel electrical chip with nanostructured electrodes provides the analytical sensitivity and specificity needed for clinical analysis. The e-RCD assay is capable of detecting 10 CFU (equivalent to 1,000 CFU ml[-1]) of Escherichia coli selectively from a panel containing multiple non-specific bacterial species. Clinical evaluation of this assay using 41 patient urine samples demonstrated a diagnostic sensitivity of 100% and specificity of 78% at an analysis time of less than one hour compared with the several hours needed for currently used culture-based methods.},
}
@article {pmid34164048,
year = {2021},
author = {Wang, X and Liu, J and Yan, Z and Liu, X and Liu, S and Suo, Y and Lu, W and Yue, J and Chen, K and Jiang, H and Zhao, Y and Zheng, M and Dai, D and Lu, X},
title = {Diversified strategy for the synthesis of DNA-encoded oxindole libraries.},
journal = {Chemical science},
volume = {12},
number = {8},
pages = {2841-2847},
pmid = {34164048},
issn = {2041-6520},
abstract = {DNA-encoded library technology (DELT) employs DNA as a barcode to track the sequence of chemical reactions and enables the design and synthesis of libraries with billions of small molecules through combinatorial expansion. This powerful technology platform has been successfully demonstrated for hit identification and target validation for many types of diseases. As a highly integrated technology platform, DEL is capable of accelerating the translation of synthetic chemistry by using on-DNA compatible reactions or off-DNA scaffold synthesis. Herein, we report the development of a series of novel on-DNA transformations based on oxindole scaffolds for the design and synthesis of diversity-oriented DNA-encoded libraries for screening. Specifically, we have developed 1,3-dipolar cyclizations, cyclopropanations, ring-opening of reactions of aziridines and Claisen-Schmidt condensations to construct diverse oxindole derivatives. The majority of these transformations enable a diversity-oriented synthesis of DNA-encoded oxindole libraries which have been used in the successful hit identification for three protein targets. We have demonstrated that a diversified strategy for DEL synthesis could accelerate the application of synthetic chemistry for drug discovery.},
}
@article {pmid34163769,
year = {2021},
author = {Som, A and Pahwa, M and Bawari, S and Saha, ND and Sasmal, R and Bosco, MS and Mondal, J and Agasti, SS},
title = {Multiplexed optical barcoding of cells via photochemical programming of bioorthogonal host-guest recognition.},
journal = {Chemical science},
volume = {12},
number = {15},
pages = {5484-5494},
pmid = {34163769},
issn = {2041-6520},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Modern chemical and biological studies are undergoing a paradigm shift, where understanding the fate of individual cells, in an apparently homogeneous population, is becoming increasingly important. This has inculcated a growing demand for developing strategies that label individual cells with unique fluorescent signatures or barcodes so that their spatiotemporal trajectories can be mapped in real time. Among various approaches, light-regulated methods employing photocaged fluorophores have received particular attention, owing to their fine spatiotemporal control over labelling. However, their multiplexed use to barcode large numbers of cells for interrogating cellular libraries or complex tissues remains inherently challenging, due to the lack of multiple spectrally distinct photoactivated states in the currently available photocaged fluorophores. We report here an alternative multiplexable strategy based on optically controlled host-guest recognition in the cucurbit[7]uril (CB[7]) system that provides spatial control over the positioning of fluorophores to generate distinct barcodes in 'user-defined' cells. Using a combination of three spectrally distinct CB[7]-conjugated fluorophores and by sequentially performing cycles of photoactivation and fluorophore encoding, we demonstrate 10-color barcoding in microtubule-targeted fixed cells as well as 7-color barcoding in cell surface glycan targeted live MCF7 cells.},
}
@article {pmid34160283,
year = {2021},
author = {Tiron, GV and Stancu, IG and Dinu, S and Prioteasa, FL and Fălcuță, E and Ceianu, CS and Cotar, AI},
title = {Characterization and Host-Feeding Patterns of Culex pipiens s.l. Taxa in a West Nile Virus-Endemic Area in Southeastern Romania.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {21},
number = {9},
pages = {713-719},
doi = {10.1089/vbz.2020.2739},
pmid = {34160283},
issn = {1557-7759},
mesh = {Animals ; *Culex ; Feeding Behavior ; Female ; Mosquito Vectors/genetics ; Romania/epidemiology ; *West Nile Fever/epidemiology/veterinary ; *West Nile virus/genetics ; },
abstract = {Culex pipiens sensu lato has been documented as West Nile virus (WNV) vector in southeastern Romania. Bucharest, the densely populated capital city of Romania, and the surrounding Ilfov county are WNV hotspots. In this area, the morphologically indistinguishable biotypes of Cx. pipiens, namely pipiens and molestus, are usually differentiated by their behavioral and physiological traits. Their involvement in WNV transmission, as suggested by entomological investigations, was not previously documented for each biotype. We used a Real-Time PCR assay based on CQ11 microsatellite to identify the Cx. pipiens biotypes and their hybrids collected in various habitats in the Bucharest metropolitan area. A sympatric distribution of both biotypes was observed, with a preference of green areas for pipiens, and human settings and animal farmlands for molestus. In the latter habitats, pipiens and molestus were found in mixed aboveground populations. A low number of hybrids was found suggesting existence of reproductive isolation. In subway tunnels molestus was dominant with a higher number of hybrids recorded than aboveground. Blood-engorged mosquitoes were identified to biotype and the blood meal source identified by DNA barcoding. Overall, Cx. pipiens s.l. fed mainly on birds, commonly on house sparrows, collared doves, and blackbirds, which are potential WNV-amplifying hosts. The preference for avian hosts was expressed strongest by pipiens biotype, while molestus was substantially less specific, feeding on avian and mammal hosts with similar frequency, with humans representing 20% of the hosts. Hybrids had a host choice closer to that of molestus. These findings highlight the role of pipiens biotype as enzootic/epizootic vector, and specifically show molestus as the bridge vector for WNV. The pipiens and molestus biotypes show important differences in habitat preferences, including oviposition; these findings demonstrate that targeted mosquito control to limit WNV transmission may be possible.},
}
@article {pmid34158103,
year = {2021},
author = {Wheeler, SS and Taff, CC and Reisen, WK and Townsend, AK},
title = {Mosquito blood-feeding patterns and nesting behavior of American crows, an amplifying host of West Nile virus.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {331},
pmid = {34158103},
issn = {1756-3305},
support = {13-2735//Division of Agriculture and Natural Resources, University of California/ ; },
mesh = {Animals ; Bird Diseases/*physiopathology/virology ; Crows/blood/*physiology/*virology ; Culex/*physiology/*virology ; Feeding Behavior ; Female ; Male ; Nesting Behavior ; West Nile Fever/physiopathology/*veterinary/virology ; West Nile virus/genetics/isolation &amp; purification/*physiology ; },
abstract = {BACKGROUND: Although American crows are a key indicator species for West Nile virus (WNV) and mount among the highest viremias reported for any host, the importance of crows in the WNV transmission cycle has been called into question because of their consistent underrepresentation in studies of Culex blood meal sources. Here, we test the hypothesis that this apparent underrepresentation could be due, in part, to underrepresentation of crow nesting habitat from mosquito sampling designs. Specifically, we examine how the likelihood of a crow blood meal changes with distance to and timing of active crow nests in a Davis, California, population.<br><br>METHODS: Sixty artificial mosquito resting sites were deployed from May to September 2014 in varying proximity to known crow nesting sites, and Culex blood meal hosts were identified by DNA barcoding. Genotypes from crow blood meals and local crows (72 nestlings from 30 broods and 389 local breeders and helpers) were used to match mosquito blood meals to specific local crows.<br><br>RESULTS: Among the 297 identified Culex blood meals, 20 (6.7%) were attributable to crows. The mean percentage of blood meals of crow origin was 19% in the nesting period (1 May-18 June 2014), but 0% in the weeks after fledging (19 June-1 September 2014), and the likelihood of a crow blood meal increased with proximity to an active nest: the odds that crows hosted a Culex blood meal were 38.07 times greater within 10&#xa0;m of an active nest than&#x2009;>&#x2009;10&#xa0;m from an active nest. Nine of ten crow blood meals that could be matched to a genotype of a specific crow belonged to either nestlings in these nests or their mothers. Six of the seven genotypes that could not be attributed to sampled birds belonged to females, a sex bias likely due to mosquitoes targeting incubating or brooding females.<br><br>CONCLUSION: Data herein indicate that breeding crows serve as hosts for Culex in the initial stages of the WNV spring enzootic cycle. Given their high viremia, infected crows could thereby contribute to the re-initiation and early amplification of the virus, increasing its availability as mosquitoes shift to other moderately competent later-breeding avian hosts.},
}
@article {pmid34153170,
year = {2021},
author = {Potowski, M and Kunig, VBK and Eberlein, L and Vakalopoulos, A and Kast, SM and Brunschweiger, A},
title = {Chemically Stabilized DNA Barcodes for DNA-Encoded Chemistry.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {60},
number = {36},
pages = {19744-19749},
pmid = {34153170},
issn = {1521-3773},
abstract = {DNA-encoded compound libraries are a widely used small molecule screening technology. One important aim in library design is the coverage of chemical space through structurally diverse molecules. Yet, the chemical reactivity of native DNA barcodes limits the toolbox of reactions for library design. Substituting the chemically vulnerable purines by 7-deazaadenine, which exhibits tautomerization stability similar to natural adenine with respect to the formation of stable Watson-Crick pairs, yielded ligation-competent, amplifiable, and readable DNA barcodes for encoded chemistry with enhanced stability against protic acid- and metal ion-promoted depurination. The barcode stability allowed for straightforward translation of 16 exemplary reactions that included isocyanide multicomponent reactions, acid-promoted Pictet-Spengler and Biginelli reactions, and metal-promoted pyrazole syntheses on controlled pore glass-coupled barcodes for diverse DEL design. The Boc protective group of reaction products offered a convenient handle for encoded compound purification.},
}
@article {pmid34153167,
year = {2022},
author = {Fort, A and McHale, M and Cascella, K and Potin, P and Perrineau, MM and Kerrison, PD and da Costa, E and Calado, R and Domingues, MDR and Costa Azevedo, I and Sousa-Pinto, I and Gachon, C and van der Werf, A and de Visser, W and Beniers, JE and Jansen, H and Guiry, MD and Sulpice, R},
title = {Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution.},
journal = {Molecular ecology resources},
volume = {22},
number = {1},
pages = {86-101},
doi = {10.1111/1755-0998.13453},
pmid = {34153167},
issn = {1755-0998},
support = {SW-GROW project number 366//European Commission/ ; 727892//Horizon 2020 Framework Programme/ ; //WOA Institution: National University of Ireland Galway/ ; //Blended DEAL: IReL/ ; 19/FFP/6841/SFI_/Science Foundation Ireland/Ireland ; },
mesh = {Europe ; *Geography ; },
abstract = {Accurate species identification often relies on public repositories to compare the barcode sequences of the investigated individual(s) with taxonomically assigned sequences. However, the accuracy of identifications in public repositories is often questionable, and the names originally given are rarely updated. For instance, species of the Sea Lettuce (Ulva spp.; Ulvophyceae, Ulvales, Ulvaceae) are frequently misidentified in public repositories, including herbaria and gene banks, making species identification based on traditional barcoding unreliable. We DNA barcoded 295 individual distromatic foliose strains of Ulva from the North-East Atlantic for three loci (rbcL, tufA, ITS1). Seven distinct species were found, and we compared our results with all worldwide Ulva spp. sequences present in the NCBI database for the three barcodes rbcL, tufA and the ITS1. Our results demonstrate a large degree of species misidentification, where we estimate that 24%-32% of the entries pertaining to foliose species are misannotated and provide an exhaustive list of NCBI sequences reannotations. An analysis of the global distribution of registered samples from foliose species also indicates possible geographical isolation for some species, and the absence of U. lactuca from Northern Europe. We extended our analytical framework to three other genera, Fucus, Porphyra and Pyropia and also identified erroneously labelled accessions and possibly new synonymies, albeit less than for Ulva spp. Altogether, exhaustive taxonomic clarification by aggregation of a library of barcode sequences highlights misannotations and delivers an improved representation of species diversity and distribution.},
}
@article {pmid34152504,
year = {2021},
author = {Ho, VT and Tran, TKP and Vu, TTT and Widiarsih, S},
title = {Comparison of matK and rbcL DNA barcodes for genetic classification of jewel orchid accessions in Vietnam.},
journal = {Journal, genetic engineering &amp; biotechnology},
volume = {19},
number = {1},
pages = {93},
pmid = {34152504},
issn = {2090-5920},
abstract = {BACKGROUND: Jewel orchid is the common name of several orchid species which can be alike in morphological characteristics, but variable in medicinal properties. At present, two DNA barcode loci, namely, maturase K (matK) and ribulose 1,5-biphosphate carboxylase (rbcL), are intensively utilized for plant identification. However, the discrimination effectiveness of these loci is variable among plant species. This study was carried out to compare the identifying efficacy of these two loci on jewel orchid population collected throughout Vietnam.<br><br>RESULTS: The results revealed that 21 jewel orchid accessions studied were segregated into four different species with significant variations. The discrimination power of matK and rbcL markers in this jewel orchid study displayed different efficiency level. The rbcL gene has higher distinguishing potential than either matK gene alone or the combination of both genes.<br><br>CONCLUSION: The findings of this project could provide valuable information that is necessary for classification, plant origin identification, breeding, and conservation program of jewel orchid in Vietnam.},
}
@article {pmid34149907,
year = {2020},
author = {Hsu, JW and Shih, HT},
title = {Diversity of Taiwanese Brackish Crabs Genus Ptychognathus Stimpson, 1858 (Crustacea: Brachyura: Varunidae) based on DNA Barcodes, with Descriptions of Two New Species.},
journal = {Zoological studies},
volume = {59},
number = {},
pages = {e59},
pmid = {34149907},
issn = {1810-522X},
abstract = {Species in the brackish crab genus Ptychognathus are common in the seashore and estuary habitats with freshwater input. Due to their similar morphologies and dull colorations, it is always difficult to distinguish the species in this genus. In this study, the DNA barcode gene COI (cytochrome c oxidase subunit I) was used to help identify Ptychognathus from Taiwan. The results showed that the 10 species can be identified successfully based on COI, with intraspecific distances below 1.54% and interspecific distances of 12.2%-19.57%. In addition, two new species of Ptychognathus are described from Taiwan. Ptychognathus makii sp. nov. from southern Taiwan is similar to P. altimanus (Rathbun, 1914), and P. stimpsoni sp. nov. from southern Taiwan and the southern Philippines resembles P. aff. barbatus (A. Milne-Edwards, 1873) and P. pusillus Heller, 1865. Both species can be distinguished from other congeners by a suite of characters, including the carapace, orbital region, frontal region, telson of male pleon, male first gonopod, and setae on ambulatory legs.},
}
@article {pmid34147656,
year = {2021},
author = {Szudarek-Trepto, N and Kazmierski, A and Dabert, J},
title = {Long-term stasis in acariform mites provides evidence for morphologically stable evolution: Molecular vs. morphological differentiation in Linopodes (Acariformes; Prostigmata).},
journal = {Molecular phylogenetics and evolution},
volume = {163},
number = {},
pages = {107237},
doi = {10.1016/j.ympev.2021.107237},
pmid = {34147656},
issn = {1095-9513},
mesh = {Animals ; DNA ; *Mites/genetics ; Phylogeny ; },
abstract = {Molecular species delimitation, usually by COI DNA barcoding, shows that cryptic speciation is a common phenomenon observed in most animal phyla. Cryptic species have frequently been observed among all major taxa of mites. The mites of the eupodoid genus Linopodes are cosmopolitan in distribution and are most often found in soil-related habitats. Currently, the genus consists of 22 morphologically similar species, which, in practice, are indistinguishable on the basis of their morphological features. The diagnostic issue of the Linopodes species may be caused by the poor delineation of the species, which need taxonomic revision, or the low morphological variability among cryptic species. In this paper, we present the results of molecular species delimitation carried out using sampled Linopodes populations and the level of morphological inter/intraspecific variation within defined groups. We compared COI, 18S and 28S sequence data together with morphological characters. The molecular delimitation revealed seven well-defined species of Linopodes based on DNA sequences. A well-supported phylogenetic tree revealed the same seven species, while morphological analysis showed negligible phenotypic differentiation among the species revealed. We demonstrate that mites can undergo changes in their DNA accompanied by morphological stasis lasting at least 80 MY.},
}
@article {pmid34147113,
year = {2021},
author = {Liu, K and Xie, L and Deng, M and Zhang, X and Luo, J and Li, X},
title = {Zoology, chemical composition, pharmacology, quality control and future perspective of Musk (Moschus): a review.},
journal = {Chinese medicine},
volume = {16},
number = {1},
pages = {46},
pmid = {34147113},
issn = {1749-8546},
support = {2020JC0038//Sichuan Provincial Administration of Traditional Chinese Medicine/ ; },
abstract = {Musk, the dried secretion from the musk sac gland which is located between the navel and genitals of mature male musk deer, is utilized as oriental medicine in east Asia. It has been utilized to treat conditions such as stroke, coma, neurasthenia, convulsions, and heart diseases in China since ancient times. This paper aims to provide a comprehensive overview of musk in zoology, chemical composition, pharmacology, clinical applications, and quality control according to the up-to-date literature. Studies found that musk mainly contains macrocyclic ketones, pyridine, steroids, fatty acids, amino acids, peptides, and proteins, whilst the main active ingredient is muscone. Modern pharmacological studies have proven that musk possesses potent anti-inflammatory effects, neuroprotective effects, anti-cancer effects, antioxidant effects, etc. Moreover, muscone, the main active ingredient, possesses anti-inflammatory, neuroprotective, antioxidant, and other pharmacological effects. In the quality control of musk, muscone is usually the main detection indicator, and the common analytical method is GC, and researchers have established novel and convenient methods such as HPLC-RI, RP-UPLC-ELSD, and Single-Sweep Polarography. In addition, quality evaluation methods based on steroids and the bioactivity of musk have been established. As for the identification of musk, due to various objective factors such as the availability of synthetic Muscone, it is not sufficient to rely on muscone alone as an identification index. To date, some novel technologies have also been introduced into the identification of musk, such as the electronic nose and DNA barcoding technology. In future research, more in vivo experiments and clinical studies are encouraged to fully explain the pharmacological effects and toxicity of musk, and more comprehensive methods are needed to evaluate and control the quality of musk.},
}
@article {pmid34145435,
year = {2021},
author = {Longo, SK and Guo, MG and Ji, AL and Khavari, PA},
title = {Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics.},
journal = {Nature reviews. Genetics},
volume = {22},
number = {10},
pages = {627-644},
pmid = {34145435},
issn = {1471-0064},
support = {R01 AR043799/AR/NIAMS NIH HHS/United States ; R01 AR049737/AR/NIAMS NIH HHS/United States ; R01 AR076965/AR/NIAMS NIH HHS/United States ; R01 CA142635/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; *Cell Communication ; Computational Biology/*methods ; Humans ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis/*methods ; *Software ; *Transcriptome ; },
abstract = {Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but does not capture their spatial distribution nor reveal local networks of intercellular communication acting in situ. A suite of recently developed techniques that localize RNA within tissue, including multiplexed in situ hybridization and in situ sequencing (here defined as high-plex RNA imaging) and spatial barcoding, can help address this issue. However, no method currently provides as complete a scope of the transcriptome as does scRNA-seq, underscoring the need for approaches to integrate single-cell and spatial data. Here, we review efforts to integrate scRNA-seq with spatial transcriptomics, including emerging integrative computational methods, and propose ways to effectively combine current methodologies.},
}
@article {pmid34144599,
year = {2021},
author = {Vu, NS and Hertz, JC and Martin, NJ and Tran, TC and Fiorenzano, JM and Tran, PV and Nguyen, HV and Dang, AD and Tran, DN and Motoki, MT},
title = {Mosquitoes (Diptera: Culicidae) from Villages and Forest Areas of Rural Communes in Khanh Hoa and Binh Phuoc Provinces, Vietnam.},
journal = {Journal of medical entomology},
volume = {58},
number = {6},
pages = {2264-2273},
pmid = {34144599},
issn = {1938-2928},
mesh = {*Animal Distribution ; Animals ; Culicidae/classification/growth &amp; development/*physiology ; Larva/classification/growth &amp; development/physiology ; Vietnam ; },
abstract = {This study presents the diversity of mosquitoes collected from communes, endemic with malaria and dengue, located in Khanh Hoa and Binh Phuoc Provinces, Vietnam. A total of 10,288 mosquitoes were collected in the village and forested sites using standard larval dippers, cow-baited traps, ultra-violet light traps, and mechanical aspirators. Mosquito taxa were identified morphologically and species complexes/groups were further characterized molecularly. Five genera of mosquitoes were morphologically identified: Anopheles Meigen (21 species), Aedes Meigen (2 species), Culex Linnaeus (5 species), Mansonia Blanchard sp., and Armigeres Theobald sp. The PCR-based identification methods allowed the distinction of members of Maculatus Group, Funestus Group, and Dirus Complex; and DNA barcodes enabled the further identification of the Barbirostris Complex. Data reported here include the first report of An. saeungae Taai &amp; Harbach and An. wejchoochotei Taai &amp; Harbach from Vietnam, and re-emphasizes the significance of using molecular data in an integrated systematic approach to identify cryptic species and better understand their role in disease transmission.},
}
@article {pmid34142864,
year = {2022},
author = {Anabalón, L and Solano, J and Encina-Montoya, F and Bustos, M and Figueroa, A and Gangitano, D},
title = {Cannabis Seeds Authentication by Chloroplast and Nuclear DNA Analysis Coupled with High-Resolution Melting Method for Quality Control Purposes.},
journal = {Cannabis and cannabinoid research},
volume = {7},
number = {4},
pages = {548-556},
pmid = {34142864},
issn = {2378-8763},
mesh = {*Cannabis/genetics ; Chloroplasts/genetics ; *DNA Barcoding, Taxonomic/methods ; DNA, Intergenic ; DNA, Plant/genetics ; Quality Control ; Seeds/genetics ; },
abstract = {Background: Cannabis plants and their seed have been used in many cultures as a source of medicine and feeding during history. Today, there is an increasing demand for cannabis seeds for medical use. Moreover, a seed sales market with no legal regulations has also grown. This may pose some issues if a quality control is not set in place. Identification of cannabis strains is important for quality control purposes in a nonregulated growing market and in cases of illegal traffic and medical use. Owing to the high price as a pharmacological drug, commercial products of cannabis plants and seeds for medical users are often subjected to adulterations, either when packing or distributing certified seeds in the market. Materials and Methods: Cannabis commercial seeds and cannabis seeds for medical use were analyzed with high-resolution melting (HRM) analysis using barcoding markers. Humulus lupulus L. plants from a local market were used as outgroup control. DNA barcoding uses specific regions of the genome to identify differences in the genetic sequence of conserved regions such as internal transcribed spacer (ITS) and rbcL. DNA barcoding data can be generated with real-time polymerase chain reaction combined with HRM analysis to distinguish specific conserved DNA regions of closely related species. HRM analysis is the method of choice for rapid analysis of sequence variation. Results: The melting temperature (Tm) of homogeneous packages was consistent with single genotypes. However, packages containing contaminating seeds showed Tm differences of 0.2°C on average. Conclusions: An effective, rapid, and low-cost method based on ITS nuclear DNA and on chloroplast rbcL regions for screening and detection of contamination in commercial cannabis seeds was developed and applied for the analysis of different samples. This approach can be used as a quality control tool for cannabis seeds or other plant material.},
}
@article {pmid34142479,
year = {2021},
author = {Xia, RC and Zhang, XC and Wang, XX and Yang, Q and Chen, C and Yu, H and Qu, YL and Wang, ZW and Shi, Y and Xiang, P and Zhang, SH and Li, CT},
title = {Identification of Cannabis Sativa L. Based on rbcL Sequence.},
journal = {Fa yi xue za zhi},
volume = {37},
number = {2},
pages = {187-191},
doi = {10.12116/j.issn.1004-5619.2020.501004},
pmid = {34142479},
issn = {1004-5619},
mesh = {*Cannabis/genetics ; Genetic Markers ; Sequence Analysis, DNA ; },
abstract = {Objective To assess the feasibility of the rbcL sequence of chloroplast DNA as a genetic marker to identify Cannabis sativa L. Methods The rbcL sequences in 62 Cannabis sativa L. samples, 10 Humulus lupulus samples and 10 Humulus scandens DNA samples were detected, and 96 rbcL sequences of the Cannabaceae family were downloaded from Genbank. Sequence alignment was performed by MEGA X software, the intraspecific and interspecific Kimura-2-Parameter （K2P） genetic distances were calculated, and the system clustering tree was constructed. Results The rbcL sequence length acquired by sequencing of Cannabis sativa L. and Humulus scandens were 617 bp and 649 bp, respectively, and two haplotypes of Cannabis sativa L. were observed in the samples. The BLAST similarity search results showed that the highest similarity between the sequences acquired by sequencing and Cannabis sativa L. rbcL sequences available from Genbank was 100%. The genetic distance analysis showed that the maximum intraspecific genetic distance （0.004 9） of Cannabis sativa L. was less than the minimum interspecific genetic distance （0.012 9）. The results of median-joining network and system clustering tree analysis showed that Cannabis sativa L. and other members of the Cannabaceae family were located in different branches. Conclusion The rbcL sequence could be used as a DNA barcode for identifying Cannabis sativa L., and combined with comparative analysis of the rbcL sequence and system cluster analysis could be a reliable and effective detection method for Cannabis sativa L. identification in forensic investigation.},
}
@article {pmid34142101,
year = {2021},
author = {Del Priore, I and Ma, S and Strecker, J and Jacks, T and LaFave, LM and Buenrostro, JD},
title = {Protocol for single-cell ATAC sequencing using combinatorial indexing in mouse lung adenocarcinoma.},
journal = {STAR protocols},
volume = {2},
number = {2},
pages = {100583},
pmid = {34142101},
issn = {2666-1667},
support = {P01 CA042063/CA/NCI NIH HHS/United States ; P30 CA014051/CA/NCI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Adenocarcinoma of Lung/*genetics ; Animals ; Computational Biology/methods ; Epigenesis, Genetic ; Lung Neoplasms/*genetics ; Mice ; Single-Cell Analysis/*methods ; },
abstract = {Single-cell ATAC sequencing using combinatorial indexing (sciATAC-seq) enables the identification of chromatin accessibility profiles at single-cell resolution with a dual-barcoding approach during transposition and library construction. Unlike commercial droplet-based approaches, sciATAC-seq is a cost-effective, extensible strategy that permits flexibility in the experimental scale via multiplexed barcoding across samples or perturbations. In contrast, droplet-based approaches have higher cell recovery and may be advantageous when cell input is limited. The step-by-step sciATAC-seq protocol described here is amenable to diverse cell types and fixed samples. For complete details on the use and execution of this protocol, please refer to LaFave et al. (2020).},
}
@article {pmid34141497,
year = {2021},
author = {Powell, C and Shaw, J},
title = {Performant barcode decoding for herbarium specimen images using vector-assisted region proposals (VARP).},
journal = {Applications in plant sciences},
volume = {9},
number = {5},
pages = {},
pmid = {34141497},
issn = {2168-0450},
abstract = {PREMISE: The scale and associated costs of herbarium digitization make process automation appealing. One such process for many workflows is the association of specimen image files with barcode values stored with the specimen. Here, an innovation is presented that improves the speed and accuracy of decoding barcodes from specimen images.<br><br>METHODS AND RESULTS: Geometric features common in barcodes are used to identify the regions of specimen images that are likely to contain a barcode. The proposed regions are then combined into a significantly reduced composite image that is decoded using traditional barcode reading libraries. Tested against existing solutions, this method demonstrated the highest success rate (96.5%) and the second fastest processing time (617 ms).<br><br>CONCLUSIONS: This method was developed to support a larger effort to automate specimen image post-processing in real-time, highlighting the importance of execution time. Although initially designed for herbarium digitization, this method may be useful for other high-resolution applications.},
}
@article {pmid34141262,
year = {2021},
author = {Vogel, S and Prinzing, A and Bußler, H and Müller, J and Schmidt, S and Thorn, S},
title = {Abundance, not diversity, of host beetle communities determines abundance and diversity of parasitoids in deadwood.},
journal = {Ecology and evolution},
volume = {11},
number = {11},
pages = {6881-6888},
pmid = {34141262},
issn = {2045-7758},
abstract = {Most parasites and parasitoids are adapted to overcome defense mechanisms of their specific hosts and hence colonize a narrow range of host species. Accordingly, an increase in host functional or phylogenetic dissimilarity is expected to increase the species diversity of parasitoids. However, the local diversity of parasitoids may be driven by the accessibility and detectability of hosts, both increasing with increasing host abundance. Yet, the relative importance of these two mechanisms remains unclear. We parallelly reared communities of saproxylic beetle as potential hosts and associated parasitoid Hymenoptera from experimentally felled trees. The dissimilarity of beetle communities was inferred from distances in seven functional traits and from their evolutionary ancestry. We tested the effect of host abundance, species richness, functional, and phylogenetic dissimilarities on the abundance, species richness, and Shannon diversity of parasitoids. Our results showed an increase of abundance, species richness, and Shannon diversity of parasitoids with increasing beetle abundance. Additionally, abundance of parasitoids increased with increasing species richness of beetles. However, functional and phylogenetic dissimilarity showed no effect on the diversity of parasitoids. Our results suggest that the local diversity of parasitoids, of ephemeral and hidden resources like saproxylic beetles, is highest when resources are abundant and thereby detectable and accessible. Hence, in some cases, resources do not need to be diverse to promote parasitoid diversity.},
}
@article {pmid34140973,
year = {2020},
author = {Zając, KS and Stec, D},
title = {Molecular Approach to Identifying Three Closely Related Slug Species of the genus Deroceras (Gastropoda: Eupulmonata: Agriolimacidae).},
journal = {Zoological studies},
volume = {59},
number = {},
pages = {e55},
pmid = {34140973},
issn = {1810-522X},
abstract = {Some species of slugs belonging to the genus Deroceras are invasive and cause severe agricultural damage. Despite extensive knowledge about their invasiveness, data on the molecular differentiation of these morphologically similar species are lacking. Here we present a molecular approach to identifying three closely related species of the genus Deroceras-D. agreste (L., 1758), D. reticulatum (O. F. Müller, 1774) and D. turcicum (Simroth, 1894) (Gastropoda: Eupulmonata: Agriolimacidae)-based on sequences of multiple molecular markers: cytochrome c oxidase subunit I (COI), cytochrome b (cyt-b), internal transcribed spacer 2 (ITS-2) and 28S ribosomal RNA (28S rRNA). We also provide detailed photomicrographs of the penis and penial gland of the three species, as it is the latter that holds the most important phenotypic characters for distinguishing between these taxa. Since identification of the studied species based solely on morphology is considered challenging, contributing a means of molecular differentiation will aid further ecological and biodiversity surveys of these important pests.},
}
@article {pmid34140825,
year = {2021},
author = {Brunke, AJ and Pentinsaari, M and Klimaszewski, J},
title = {Integrative taxonomy of Nearctic and Palaearctic Aleocharinae: new species, synonymies, and records (Coleoptera, Staphylinidae).},
journal = {ZooKeys},
volume = {1041},
number = {},
pages = {27-99},
pmid = {34140825},
issn = {1313-2989},
abstract = {A long tradition of separate Nearctic and Palaearctic taxonomic studies of the diverse aleocharine rove beetles (Coleoptera: Staphylinidae) has obscured the recognition of Holarctic species and detection of adventive species in both regions. Recently, integrated study of the two regions through detailed morphological comparisons and development of an authoritatively identified DNA barcode reference library has revealed the degree to which these two aleocharine faunas are interconnected, both naturally and through human activity. Here this approach is adopted to recognize new species, reveal Holarctic species, and recognize adventive species in both North America and Europe. The following new species are described: Isoglossa triangularis Klimaszewski, Brunke &amp; Pentinsaari, sp. nov. from British Columbia; Gnypeta impressicollis Klimaszewski, Brunke &amp; Pentinsaari, sp. nov., from Ontario, Maryland and North Carolina; Aloconota pseudogregaria Klimaszewski, Brunke &amp; Pentinsaari, sp. nov., from Ontario and Virginia; and Philhygra pseudolaevicollis Klimaszewski, Brunke &amp; Pentinsaari, sp. nov. from eastern Canada. Dasygnypeta velata and Philhygra angusticauda are revealed to be Holarctic species, resulting in the following synonymies: Dasygnypeta velata (Erichson, 1839) = Gnypeta minuta Klimaszewski &amp; Webster, 2008, syn. nov. and Philhygra angusticauda (Bernhauer, 1909) = Atheta (Philhygra) pinegensis Muona, 1983, syn. nov. The Nearctic species Hylota ochracea (and genus Hylota), Thecturota tenuissima, and Trichiusa robustula are newly reported from the Palaearctic region as adventive, resulting in the following synonymies: Hylota ochracea Casey, 1906 = Stichoglossa (Dexiogyia) forticornis Strand, 1939, syn. nov.; Thecturota tenuissima Casey, 1893 = Atheta marchii Dodero, 1922, syn. nov.; and Trichiusa robustula Casey, 1893 = T. immigrata Lohse, 1984, syn. nov. The Palaearctic species Amarochara forticornis, Anomognathus cuspidatus, Oligota pumilio, and Parocyusa rubicunda are newly confirmed from the Nearctic region as adventive, resulting in the following synonymies: Parocyusa rubicunda (Erichson, 1837) = Chilopora americana Casey, 1906, syn. nov. and Anomognathus cuspidatus (Erichson, 1839) = Thectura americana Casey, 1893, syn. nov. The genus Dasygnypeta, sensu nov. is newly reported from North America, Paradilacra is newly reported from eastern North America, and Haploglossa is newly reported from Canada, resulting in the following synonymy: Paradilacra densissima (Bernhauer, 1909) = Gnypeta saccharina Klimaszewski &amp; Webster, 2008, syn. nov. Native Cyphea wallisi is newly reported from across Canada and C. curtula is removed from the Nearctic fauna. The status of both Gyrophaena affinis and Homalota plana is uncertain but these species are no longer considered to be adventive in North America. Three new combinations are proposed: Dasygnypeta baranowskii (Klimaszewski, 2020) and D. nigrella (LeConte, 1863) (both from Gnypeta) and Mocyta scopula (Casey, 1893) (from Acrotona). Dolosota Casey, 1910, syn. nov. (type species Eurypronota scopula Casey), currently a subgenus of Acrotona, is therefore synonymized with Mocyta Mulsant &amp; Rey, 1874. Additionally, four new Canadian records and 18 new provincial and state records are reported.},
}
@article {pmid34139894,
year = {2021},
author = {Lieske, A and Ha, TC and Schambach, A and Maetzig, T},
title = {An Improved Lentiviral Fluorescent Genetic Barcoding Approach Distinguishes Hematopoietic Stem Cell Properties in Multiplexed In Vivo Experiments.},
journal = {Human gene therapy},
volume = {32},
number = {19-20},
pages = {1280-1294},
doi = {10.1089/hum.2021.042},
pmid = {34139894},
issn = {1557-7422},
mesh = {Animals ; Genetic Vectors/genetics ; *Hematopoietic Stem Cell Transplantation ; *Hematopoietic Stem Cells ; Immunophenotyping ; Mice ; },
abstract = {Hematopoietic stem cells (HSCs) represent a rare cell population of particular interest for biomedical research and regenerative medicine. Various marker combinations enable the isolation of HSCs, but fail to reach purity in transplantation assays. To reduce animal consumption, we developed a multiplexing system based on lentiviral fluorescent genetic barcoding (FGB) to enable the parallel characterization of multiple HSC samples within single animals. While previous FGB-mediated HSC multiplexing experiments achieved high in vitro gene marking rates, in vivo persistence of transduced cells remained suboptimal. Thus, we aimed to optimize vector design and gene transfer protocols to demonstrate the applicability of FGB for functional characterization of two highly similar HSC populations in a reduced number of mice. We developed a set of six new lentiviral FGB vectors, utilizing individual and combinatorial expression of Azami Green, mCherry, and YFP derivatives. Gene transfer rates were optimized by overnight transduction of prestimulated HSCs with titrated vector doses. Populations for competitive transplantation experiments were identified by immunophenotyping murine HSCs. This identified an LSK-SLAM[-] (Lin[-]Sca-1[+]cKit[+]CD48[-]CD150[+]EPCR[-]) cell subpopulation that lacks EPCR expression and exhibits prospectively reduced self-renewal potential compared with prototypical ESLAM (CD45[+]EPCR[+]CD48[-]CD150[+]) HSCs. We monitored 30 data points per HSC-subpopulation in two independent experiments (each n = 5) after cotransplantation of three uniquely color-coded ESLAM and LSK-SLAM[-] samples per recipient. While the first experiment was hampered by data fluctuations, increasing cell numbers and exchange of the internal promoter in the second experiment led to 74.4% chimerism, with 87.1% of fluorescent cells derived from ESLAM HSCs. Furthermore, ESLAM-derived cells produced 88.1% of myeloid cells, which is indicative of their origin from long-term repopulating HSCs. This work verifies the importance of EPCR for long-term repopulating HSCs and demonstrates the applicability of our optimized FGB-driven multiplexing approach for the efficient characterization of blood cell populations in biomedical research.},
}
@article {pmid34137377,
year = {2021},
author = {Lewisch, E and Arnold, F and Fuehrer, HP and Harl, J and Reichart, U and Handschuh, S and Thielen, F and El-Matbouli, M},
title = {First description of freshwater mite Unionicola sauerensis sp. nov. infesting thick-shelled river mussel Unio crassus.},
journal = {Diseases of aquatic organisms},
volume = {145},
number = {},
pages = {63-77},
doi = {10.3354/dao03596},
pmid = {34137377},
issn = {0177-5103},
mesh = {Animals ; *Bivalvia ; Female ; Fresh Water ; *Mites ; Rivers ; *Unio ; },
abstract = {A sample of 30 thick-shelled river mussels Unio crassus Philipsson (Unionida: Unionidae) was collected from the River Sauer in Luxembourg to acquire data on parasitic infestations of the mussels. Among other parasites, different development stages of freshwater mites were collected from the gills and the mantle of the mussels and were documented with bright-field, stereo, and confocal laser scanning microscopy and microscopic X-ray computed tomography. The retrieved data allowed a morphological description of larvae and female adults of the mites and assigning them to the genus Unionicola Haldeman (Trombidiformes: Unionicolidae) and the subgenus Pentatax Thor. Additionally, adult stages and larvae were barcoded by sequencing a section of the mitochondrial COI and 18S rRNA genes. This resulted in 4 new, similar Unionicola lineages from the adult stages, which differ in at least 14.7% (uncorrected p distance) from those already published. Barcoding of larval DNA was not successful. The comparison with known European species of the genus Unionicola and analysis of the barcoding results allowed the proposal of a new species of the genus Unionicola. The species was named Unionicola sauerensis sp. nov. after the River Sauer in Luxembourg, where the infested mussels were collected.},
}
@article {pmid34135660,
year = {2021},
author = {Lin, XL and Yu, HJ and Wang, XH and Bu, WJ and Yan, CC and Liu, WB},
title = {New or little-known Boreoheptagyia (Diptera, Chironomidae) in China inferred from morphology and DNA barcodes.},
journal = {ZooKeys},
volume = {1040},
number = {},
pages = {187-200},
pmid = {34135660},
issn = {1313-2989},
abstract = {The male adult of Boreoheptagyia zhengi Lin &amp; Liu, sp. nov. is described and illustrated based on material collected in China. Associated morphological characteristics and reference to its DNA barcode are provided. Boreoheptagyia kurobebrevis (Sasa &amp; Okazawa, 1992) is newly recorded from China based on both a male and female, with additional associated data on the DNA barcode of the male adult. A neighbor-joining tree based on available Boreoheptagyia DNA barcodes and a key to the adults of Boreoheptagyia from China are given.},
}
@article {pmid34134047,
year = {2021},
author = {Smart, U and Cihlar, JC and Budowle, B},
title = {International Wildlife Trafficking: A perspective on the challenges and potential forensic genetics solutions.},
journal = {Forensic science international. Genetics},
volume = {54},
number = {},
pages = {102551},
doi = {10.1016/j.fsigen.2021.102551},
pmid = {34134047},
issn = {1878-0326},
mesh = {Animals ; *Animals, Wild ; Crime ; *Forensic Genetics ; Genetic Markers ; Humans ; },
abstract = {International wildlife trafficking (IWT) is a thriving and pervasive illegal enterprise that adversely affects modern societies. Yet, despite being globally recognized as a threat to biodiversity, national security, economy, and biosecurity, IWT remains largely unabated and is proliferating at an alarming rate. The increase in IWT is generally attributed to a lack of prioritization to curb wildlife crime through legal and scientific infrastructure. This review: (1) lays out the damaging scope and influence of IWT; (2) discusses the potential of DNA marker systems, barcodes, and emerging molecular technologies, such as long-read portable sequencing, to facilitate rapid, in situ identification of species and individuals; and (3) encourages initiatives that promote quality and innovation. Interdisciplinary collaboration promises to be one of the most effective ways forward to surmounting the complex scientific and legal challenges posed by IWT.},
}
@article {pmid34133074,
year = {2021},
author = {Zhu, J and Ermann, N and Chen, K and Keyser, UF},
title = {Image Encoding Using Multi-Level DNA Barcodes with Nanopore Readout.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {17},
number = {28},
pages = {e2100711},
doi = {10.1002/smll.202100711},
pmid = {34133074},
issn = {1613-6829},
mesh = {DNA ; DNA Barcoding, Taxonomic ; Glass ; *Nanopores ; },
abstract = {Deoxyribonucleic acid (DNA) nanostructure-based data encoding is an emerging information storage mode, offering rewritable, editable, and secure data storage. Herein, a DNA nanostructure-based storage method established on a solid-state nanopore sensing platform to save and encrypt a 2D grayscale image is proposed. DNA multi-way junctions of different sizes are attached to a double strand of DNA carriers, resulting in distinct levels of current blockades when passing through a glass nanopore with diameters around 14 nm. The resulting quaternary encoding doubles the capacity relative to a classical binary system. Through toehold-mediated strand displacement reactions, the DNA nanostructures can be precisely added to and removed from the DNA carrier. By encoding the image into 16 DNA carriers using the quaternary barcodes and reading them in one simultaneous measurement, the image is successfully saved, encrypted, and recovered. Avoiding any proteins or enzymatic reactions, the authors thus realize a pure DNA storage system on a nanopore platform with increased capacity and programmability.},
}
@article {pmid34132353,
year = {2021},
author = {Igwe, AN and Quasem, B and Liu, N and Vannette, RL},
title = {Plant phenology influences rhizosphere microbial community and is accelerated by serpentine microorganisms in Plantago erecta.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {7},
pages = {},
doi = {10.1093/femsec/fiab085},
pmid = {34132353},
issn = {1574-6941},
mesh = {*Microbiota ; Plant Roots ; *Plantago ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil ; Soil Microbiology ; },
abstract = {Serpentine soils are drought-prone and rich in heavy metals, and plants growing on serpentine soils host distinct microbial communities that may affect plant survival and phenotype. However, whether the rhizosphere communities of plants from different soil chemistries are initially distinct or diverge over time may help us understand drivers of microbial community structure and function in stressful soils. Here, we test the hypothesis that rhizosphere microbial communities will converge over time (plant development), independent of soil chemistry and microbial source. We grew Plantago erecta in serpentine or nonserpentine soil, with serpentine or nonserpentine microbes and tracked plant growth and root phenotypes. We used 16S rRNA gene barcoding to compare bacterial species composition at seedling, vegetative, early- and late-flowering phases. Plant phenotype and rhizosphere bacterial communities were mainly structured by soil type, with minor contributions by plant development, microbe source and their interactions. Serpentine microorganisms promoted early flowering in plants on nonserpentine soils. Despite strong effects of soil chemistry, the convergence in bacterial community composition across development demonstrates the importance of the plant-microbe interactions in shaping microbial assembly processes across soil types.},
}
@article {pmid34131518,
year = {2021},
author = {Seabra, SG and Rodrigues, ASB and Silva, SE and Neto, AC and Pina-Martins, F and Marabuto, E and Thompson, V and Wilson, MR and Yurtsever, S and Halkka, A and Rebelo, MT and Borges, PAV and Quartau, JA and Jiggins, CD and Paulo, OS},
title = {Population structure, adaptation and divergence of the meadow spittlebug, Philaenus spumarius (Hemiptera, Aphrophoridae), revealed by genomic and morphological data.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e11425},
pmid = {34131518},
issn = {2167-8359},
abstract = {Understanding patterns of population differentiation and gene flow in insect vectors of plant diseases is crucial for the implementation of management programs of disease. We investigated morphological and genome-wide variation across the distribution range of the spittlebug Philaenus spumarius (Linnaeus, 1758) (Hemiptera, Auchenorrhyncha, Aphrophoridae), presently the most important vector of the plant pathogenic bacterium Xylella fastidiosa Wells et al., 1987 in Europe. We found genome-wide divergence between P. spumarius and a very closely related species, P. tesselatus Melichar, 1899, at RAD sequencing markers. The two species may be identified by the morphology of male genitalia but are not differentiated at mitochondrial COI, making DNA barcoding with this gene ineffective. This highlights the importance of using integrative approaches in taxonomy. We detected admixture between P. tesselatus from Morocco and P. spumarius from the Iberian Peninsula, suggesting gene-flow between them. Within P. spumarius, we found a pattern of isolation-by-distance in European populations, likely acting alongside other factors restricting gene flow. Varying levels of co-occurrence of different lineages, showing heterogeneous levels of admixture, suggest other isolation mechanisms. The transatlantic populations of North America and Azores were genetically closer to the British population analyzed here, suggesting an origin from North-Western Europe, as already detected with mitochondrial DNA. Nevertheless, these may have been produced through different colonization events. We detected SNPs with signatures of positive selection associated with environmental variables, especially related to extremes and range variation in temperature and precipitation. The population genomics approach provided new insights into the patterns of divergence, gene flow and adaptation in these spittlebugs and led to several hypotheses that require further local investigation.},
}
@article {pmid34128770,
year = {2021},
author = {Bustamante, DE and Calderon, MS and Leiva, S and Mendoza, JE and Arce, M and Oliva, M},
title = {Three new species of Trichoderma in the Harzianum and Longibrachiatum lineages from Peruvian cacao crop soils based on an integrative approach.},
journal = {Mycologia},
volume = {113},
number = {5},
pages = {1056-1072},
doi = {10.1080/00275514.2021.1917243},
pmid = {34128770},
issn = {1557-2536},
mesh = {Bayes Theorem ; *Cacao ; Humans ; Peru ; Phylogeny ; Soil ; *Trichoderma/genetics ; },
abstract = {The hyperdiverse genus Trichoderma is one of most useful groups of microbes for a number of human activities, and their accurate identification is crucial. The structural simplicity and lack of distinctive phenotypic variation in this group enable the use of DNA-based species delimitation methods in combination with phylogenies (and morphology when feasible) to establish well-supported boundaries among species. Our study employed a multilocus phylogeny and four DNA-based methods (automated barcode gap discovery [ABGD], statistical parsimony [SPN], generalized mixed Yule coalescent [GMYC], and Bayesian phylogenetics and phylogeography [BPP]) for four molecular markers (acl1, act, rpb2, and tef1) to delimit species of two lineages of Trichoderma. Although incongruence among these methods was observed in our analyses, the genetic distance (ABGD) and coalescence (BPP) methods and the multilocus phylogeny strongly supported and confirmed recognition of 108 and 39 different species in the Harzianum and Longibrachiatum lineages, including three new species associated with cacao farms in northern Peru, namely, T.awajun, sp. nov., T.jaklitschii, sp. nov., and T.peruvianum, sp. nov. Morphological distinctions between the new species and their close relatives are primarily related to growth rates, colony appearance, and size of phialides and conidia. This study confirmed that an integrative approach (DNA-based methods, multilocus phylogeny, and phenotype) is more likely to reliably verify supported species boundaries in Trichoderma.},
}
@article {pmid34127714,
year = {2021},
author = {Ogbede, JU and Giaever, G and Nislow, C},
title = {A genome-wide portrait of pervasive drug contaminants.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {12487},
pmid = {34127714},
issn = {2045-2322},
mesh = {Arginine/biosynthesis ; Biosynthetic Pathways/drug effects/genetics ; DNA Damage/drug effects ; DNA Repair/drug effects ; DNA, Fungal/drug effects/isolation &amp; purification ; *Drug Contamination ; Genetic Fitness/drug effects ; Genome, Fungal/drug effects ; Mitochondria/drug effects/metabolism ; Nitrosamines/*toxicity ; Saccharomyces cerevisiae/*drug effects/genetics/growth &amp; development/metabolism ; Sequence Deletion ; *Toxicity Tests, Acute ; },
abstract = {Using a validated yeast chemogenomic platform, we characterized the genome-wide effects of several pharmaceutical contaminants, including three N-nitrosamines (NDMA, NDEA and NMBA), two related compounds (DMF and 4NQO) and several of their metabolites. A collection of 4800 non-essential homozygous diploid yeast deletion strains were screened in parallel and the strain abundance was quantified by barcode sequencing. These data were used to rank deletion strains representing genes required for resistance to the compounds to delineate affected cellular pathways and to visualize the global cellular effects of these toxins in an easy-to-use searchable database. Our analysis of the N-nitrosamine screens uncovered genes (via their corresponding homozygous deletion mutants) involved in several evolutionarily conserved pathways, including: arginine biosynthesis, mitochondrial genome integrity, vacuolar protein sorting and DNA damage repair. To investigate why NDMA, NDEA and DMF caused fitness defects in strains lacking genes of the arginine pathway, we tested several N-nitrosamine metabolites (methylamine, ethylamine and formamide), and found they also affected arginine pathway mutants. Notably, each of these metabolites has the potential to produce ammonium ions during their biotransformation. We directly tested the role of ammonium ions in N-nitrosamine toxicity by treatment with ammonium sulfate and we found that ammonium sulfate also caused a growth defect in arginine pathway deletion strains. Formaldehyde, a metabolite produced from NDMA, methylamine and formamide, and which is known to cross-link free amines, perturbed deletion strains involved in chromatin remodeling and DNA repair pathways. Finally, co-administration of N-nitrosamines with ascorbic or ferulic acid did not relieve N-nitrosamine toxicity. In conclusion, we used parallel deletion mutant analysis to characterize the genes and pathways affected by exposure to N-nitrosamines and related compounds, and provide the data in an accessible, queryable database.},
}
@article {pmid34124627,
year = {2021},
author = {Crous, PW and Hernández-Restrepo, M and Schumacher, RK and Cowan, DA and Maggs-Kölling, G and Marais, E and Wingfield, MJ and Yilmaz, N and Adan, OCG and Akulov, A and Duarte, E&#xc1; and Berraf-Tebbal, A and Bulgakov, TS and Carnegie, AJ and de Beer, ZW and Decock, C and Dijksterhuis, J and Duong, TA and Eichmeier, A and Hien, LT and Houbraken, JAMP and Khanh, TN and Liem, NV and Lombard, L and Lutzoni, FM and Miadlikowska, JM and Nel, WJ and Pascoe, IG and Roets, F and Roux, J and Samson, RA and Shen, M and Spetik, M and Thangavel, R and Thanh, HM and Thao, LD and van Nieuwenhuijzen, EJ and Zhang, JQ and Zhang, Y and Zhao, LL and Groenewald, JZ},
title = {New and Interesting Fungi. 4.},
journal = {Fungal systematics and evolution},
volume = {7},
number = {},
pages = {255-343},
pmid = {34124627},
issn = {2589-3831},
abstract = {An order, family and genus are validated, seven new genera, 35 new species, two new combinations, two epitypes, two lectotypes, and 17 interesting new host and / or geographical records are introduced in this study. Validated order, family and genus: Superstratomycetales and Superstratomycetaceae (based on Superstratomyces). New genera: Haudseptoria (based on Haudseptoria typhae); Hogelandia (based on Hogelandia lambearum); Neoscirrhia (based on Neoscirrhia osmundae); Nothoanungitopsis (based on Nothoanungitopsis urophyllae); Nothomicrosphaeropsis (based on Nothomicrosphaeropsis welwitschiae); Populomyces (based on Populomyces zwinianus); Pseudoacrospermum (based on Pseudoacrospermum goniomae). New species: Apiospora sasae on dead culms of Sasa veitchii (Netherlands); Apiospora stipae on dead culms of Stipa gigantea (Spain); Bagadiella eucalyptorum on leaves of Eucalyptus sp. (Australia); Calonectria singaporensis from submerged leaf litter (Singapore); Castanediella neomalaysiana on leaves of Eucalyptus sp. (Malaysia); Colletotrichum pleopeltidis on leaves of Pleopeltis sp. (South Africa); Coniochaeta deborreae from soil (Netherlands); Diaporthe durionigena on branches of Durio zibethinus (Vietnam); Floricola juncicola on dead culm of Juncus sp. (France); Haudseptoria typhae on leaf sheath of Typha sp. (Germany); Hogelandia lambearum from soil (Netherlands); Lomentospora valparaisensis from soil (Chile); Neofusicoccum mystacidii on dead stems of Mystacidium capense (South Africa); Neomycosphaerella guibourtiae on leaves of Guibourtia sp. (Angola); Niesslia neoexosporioides on dead leaves of Carex paniculata (Germany); Nothoanungitopsis urophyllae on seed capsules of Eucalyptus urophylla (South Africa); Nothomicrosphaeropsis welwitschiae on dead leaves of Welwitschia mirabilis (Namibia); Paracremonium bendijkiorum from soil (Netherlands); Paraphoma ledniceana on dead wood of Buxus sempervirens (Czech Republic); Paraphoma salicis on leaves of Salix cf. alba (Ukraine); Parasarocladium wereldwijsianum from soil (Netherlands); Peziza ligni on masonry and plastering (France); Phyllosticta phoenicis on leaves of Phoenix reclinata (South Africa); Plectosphaerella slobbergiarum from soil (Netherlands); Populomyces zwinianus from soil (Netherlands); Pseudoacrospermum goniomae on leaves of Gonioma kamassi (South Africa); Pseudopyricularia festucae on leaves of Festuca californica (USA); Sarocladium sasijaorum from soil (Netherlands); Sporothrix hypoxyli in sporocarp of Hypoxylon petriniae on Fraxinus wood (Netherlands); Superstratomyces albomucosus on Pycnanthus angolensis (Netherlands); Superstratomyces atroviridis on Pinus sylvestris (Netherlands); Superstratomyces flavomucosus on leaf of Hakea multilinearis (Australia); Superstratomyces tardicrescens from human eye specimen (USA); Taeniolella platani on twig of Platanus hispanica (Germany), and Tympanis pini on twigs of Pinus sylvestris (Spain). Citation: Crous PW, Hernández-Restrepo M, Schumacher RK, Cowan DA, Maggs-Kölling G, Marais E, Wingfield MJ, Yilmaz N, Adan OCG, Akulov A, Álvarez Duarte E, Berraf-Tebbal A, Bulgakov TS, Carnegie AJ, de Beer ZW, Decock C, Dijksterhuis J, Duong TA, Eichmeier A, Hien LT, Houbraken JAMP, Khanh TN, Liem NV, Lombard L, Lutzoni FM, Miadlikowska JM, Nel WJ, Pascoe IG, Roets F, Roux J, Samson RA, Shen M, Spetik M, Thangavel R, Thanh HM, Thao LD, van Nieuwenhuijzen EJ, Zhang JQ, Zhang Y, Zhao LL, Groenewald JZ (2021). New and Interesting Fungi. 4. Fungal Systematics and Evolution 7: 255-343. doi: 10.3114/fuse.2021.07.13.},
}
@article {pmid34124219,
year = {2021},
author = {Roy, L and Giangaspero, A and Sleeckx, N and Øines, &#xd8;},
title = {Who Is Dermanyssus gallinae? Genetic Structure of Populations and Critical Synthesis of the Current Knowledge.},
journal = {Frontiers in veterinary science},
volume = {8},
number = {},
pages = {650546},
pmid = {34124219},
issn = {2297-1769},
abstract = {Despite the economic and animal welfare importance of the Poultry Red Mite Dermanyssus gallinae, its genetic structure has been studied in a scattered way so far. The prophylaxis and control of such a globally distributed ectoparasite can be significantly improved by understanding its genetic population structure (composition in species and intraspecific variants). The present study aims to establish a rigorous framework for characterizing the neutral genetic structure of D. gallinae based on a literature review combined with an integrative analysis of the data available in GenBank on population-level nucleotide sequence diversity supplemented by a new dataset. The integrative analysis was conducted on sequence data extracted from GenBank coupled with new sequences of two fragments of the mitochondrial gene encoding Cytochrome Oxidase I (CO1) as well as of an intron of the nuclear gene encoding Tropomyosin (Tpm) from several PRM populations sampled from European poultry farms. Emphasis was placed on using the mitochondrial gene encoding CO1 on which the main universal region of DNA barcoding in animals is located. The species D. gallinae sensu lato is a species complex, encompassing at least two cryptic species, i.e., not distinguishable by morphological characters: D. gallinae sensu stricto and D. gallinae L1. Only D. gallinae s.s. has been recorded among the populations sampled in poultry farms worldwide. Current knowledge suggests they are structured in three mitochondrial groups (haplogroups A, B, and C). Haplogroup A is cosmopolitan, and the other two present slightly contrasted distributions (B rather in the northern part of Europe, C most frequently found in the southern part). Recent data indicate that a dynamic geographic expansion of haplogroup C is underway in Europe. Our results also show that NUMT (nuclear mitochondrial DNA) pseudogenes have generated artifactual groups (haplogroups E and F). It is important to exclude these artifact groups from future analyses to avoid confusion. We provide an operational framework that will promote consistency in the analysis of subsequent results using the CO1 fragment and recommendations for future analyses.},
}
@article {pmid34123584,
year = {2021},
author = {Sampieri, BR and Vieira, PE and Teixeira, MAL and Seixas, VC and Pagliosa, PR and Amaral, ACZ and Costa, FO},
title = {Molecular diversity within the genus Laeonereis (Annelida, Nereididae) along the west Atlantic coast: paving the way for integrative taxonomy.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e11364},
pmid = {34123584},
issn = {2167-8359},
abstract = {The polychaete genus Laeonereis (Annelida, Nereididae) occurs over a broad geographic range and extends nearly across the entire Atlantic coast of America, from the USA to Uruguay. Despite the research efforts to clarify its diversity and systematics, mostly by morphological and ecological evidence, there is still uncertainty, mainly concerning the species Laeonereis culveri, which constitutes an old and notorious case of taxonomic ambiguity. Here, we revised the molecular diversity and distribution of Laeonereis species based on a multi-locus approach, including DNA sequence analyses of partial segments of the cytochrome c oxidase subunit I (COI), 16S rRNA, and 28S rRNA genes. We examined Laeonereis specimens collected from 26 sites along the American Atlantic coast from Massachusetts (USA) to Mar del Plata (Argentina). Although no comprehensive morphological examination was performed between different populations, the COI barcodes revealed seven highly divergent MOTUs, with a mean K2P genetic distance of 16.9% (from 6.8% to 21.9%), which was confirmed through four clustering algorithms. All MOTUs were geographically segregated, except for MOTUs 6 and 7 from southeastern Brazil, which presented partially overlapping ranges between Rio de Janeiro and São Paulo coast. Sequence data obtained from 16S rRNA and 28S rRNA markers supported the same MOTU delimitation and geographic segregation as those of COI, providing further evidence for the existence of seven deeply divergent lineages within the genus. The extent of genetic divergence between MOTUs observed in our study fits comfortably within the range reported for species of polychaetes, including Nereididae, thus providing a strong indication that they might constitute separate species. These results may therefore pave the way for integrative taxonomic studies, aiming to clarify the taxonomic status of the Laeonereis MOTUs herein reported.},
}
@article {pmid34122513,
year = {2021},
author = {Tsagiopoulou, M and Maniou, MC and Pechlivanis, N and Togkousidis, A and Kotrová, M and Hutzenlaub, T and Kappas, I and Chatzidimitriou, A and Psomopoulos, F},
title = {UMIc: A Preprocessing Method for UMI Deduplication and Reads Correction.},
journal = {Frontiers in genetics},
volume = {12},
number = {},
pages = {660366},
pmid = {34122513},
issn = {1664-8021},
abstract = {A recent refinement in high-throughput sequencing involves the incorporation of unique molecular identifiers (UMIs), which are random oligonucleotide barcodes, on the library preparation steps. A UMI adds a unique identity to different DNA/RNA input molecules through polymerase chain reaction (PCR) amplification, thus reducing bias of this step. Here, we propose an alignment free framework serving as a preprocessing step of fastq files, called UMIc, for deduplication and correction of reads building consensus sequences from each UMI. Our approach takes into account the frequency and the Phred quality of nucleotides and the distances between the UMIs and the actual sequences. We have tested the tool using different scenarios of UMI-tagged library data, having in mind the aspect of a wide application. UMIc is an open-source tool implemented in R and is freely available from https://github.com/BiodataAnalysisGroup/UMIc.},
}
@article {pmid34121037,
year = {2021},
author = {Yabuki, A and Kawato, M and Nagano, Y and Tsuchida, S and Yoshida, T and Fujiwara, Y},
title = {Structural Comparison of Diplonemid Communities around the Izu Peninsula, Japan.},
journal = {Microbes and environments},
volume = {36},
number = {2},
pages = {},
pmid = {34121037},
issn = {1347-4405},
mesh = {Euglenozoa/*classification/genetics/*isolation &amp; purification ; Japan ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Seawater/parasitology ; },
abstract = {Diplonemea (diplonemids) is one of the most abundant and species-rich protist groups in marine environments; however, their community structures among local and seasonal samples have not yet been compared. In the present study, we analyzed four diplonemid community structures around the Izu Peninsula, Japan using barcode sequences amplified from environmental DNA. These sequences and the results of statistical analyses indicated that communities at the same site were more similar to each other than those in the same season. Environmental variables were also measured, and their influence on diplonemid community structures was examined. Salinity, electrical conductivity, and temperature, and their correlated variables, appeared to influence the structures of diplonemid communities, which was consistent with previous findings; however, since the results obtained did not reach statistical significance, further studies are required. A comparison of each diplonemid community indicated that some lineages were unique to specific samples, while others were consistently detected in all samples. Members of the latter type are cosmopolitan candidates and may be better adapted to the environments of the studied area. Future studies that focus on the more adaptive members will provide a more detailed understanding of the mechanisms by which diplonemids are widely distributed in marine environments and will facilitate their utilization as indicator organisms to monitor environmental changes.},
}
@article {pmid34119461,
year = {2021},
author = {Saraiva, JF and Scarpassa, VM},
title = {Anopheles (Nyssorhynchus) tadei: A new species of the Oswaldoi-konderi complex (Diptera, Anophelinae) and its morphological and molecular distinctions from An. konderi sensu stricto.},
journal = {Acta tropica},
volume = {221},
number = {},
pages = {106004},
doi = {10.1016/j.actatropica.2021.106004},
pmid = {34119461},
issn = {1873-6254},
mesh = {Animals ; *Anopheles/genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Female ; Larva/genetics ; Male ; Pupa ; },
abstract = {The Oswaldoi-konderi Complex (Anopheles, Nyssorhynchus) is composed of five species that have been distinguished and delimited using DNA sequences of mitochondrial and nuclear genes. At least two species of the complex have been formally described, namely Anopheles oswaldoi s.s. and An. konderi; however, the identity of An. konderi s.s. is unclear because two morphologically similar species co-exist in the type-locality in the municipality of Coari, Amazonas state, Brazil. Moreover, the study of resurrection and designation of the neotype of An. konderi s.s. included a mixture of both forms. In the present study, mosquitoes were collected in Coari to establish the molecular identity of An. konderi s.s. and describe a new species based on morphological and molecular data. Six females were collected and separated individually for oviposition. The parental progenies were obtained from field collected females, fourth-instar larva, pupa, and female and male were employed for morphological characterization. Genomic DNA from one fourth-instar larva of each progeny was extracted and sequenced for the mtDNA COI barcode region, CAD gene, and the ITS2 rDNA nuclear region to establish the molecular identity of the two morphological forms of An. konderi s.l. The An. konderi neotype was re-examined. The morphological and molecular analyses revealed two distinct groups: the first group was identical to the neotype of An. konderi s.s., whereas the second was found to belong to the group informally referred to as An. sp. near konderi or An. konderi B, herein described as Anopheles tadei n. sp.},
}
@article {pmid34117960,
year = {2021},
author = {Nitta, JH and Watkins, JE and Holbrook, NM and Wang, TW and Davis, CC},
title = {Ecophysiological differentiation between life stages in filmy ferns (Hymenophyllaceae).},
journal = {Journal of plant research},
volume = {134},
number = {5},
pages = {971-988},
pmid = {34117960},
issn = {1618-0860},
support = {DEB-1311169//Directorate for Biological Sciences/ ; Research Grant for Graduate Students//American Society of Plant Taxonomists/ ; Award in Tropical Botany//Garden Club of America/ ; Graduate Student Research Award//Society of Systematic Biologists/ ; Systematics Research Fund//Systematics Association/ ; },
mesh = {*Ferns ; Germ Cells, Plant ; Photosynthesis ; Photosystem II Protein Complex ; Water ; },
abstract = {Desiccation tolerance was a key trait that allowed plants to colonize land. However, little is known about the transition from desiccation tolerant non-vascular plants to desiccation sensitive vascular ones. Filmy ferns (Hymenophyllaceae) represent a useful system to investigate how water-stress strategies differ between non-vascular and vascular stages within a single organism because they have vascularized sporophytes and nonvascular gametophytes that are each capable of varying degrees of desiccation tolerance. To explore this, we surveyed sporophytes and gametophytes of 19 species (22 taxa including varieties) of filmy ferns on Moorea (French Polynesia) and used chlorophyll fluorescence to measure desiccation tolerance and light responses. We conducted phylogenetically informed analyses to identify differences in physiology between life stages and growth habits. Gametophytes had similar or less desiccation tolerance (ability to recover from 2 days desiccation at - 86 MPa) and lower photosynthetic optima (maximum electron transport rate of photosystem II and light level at 95% of that rate) than sporophytes. Epiphytes were more tolerant of desiccation than terrestrial species in both life stages. Despite their lack of greater physiological tolerances, gametophytes of several species occurred over a wider elevational range than conspecific sporophytes. Our results demonstrate that filmy fern gametophytes and sporophytes differ in their physiology and niche requirements, and point to the importance of microhabitat in shaping the evolution of water-use strategies in vascular plants.},
}
@article {pmid34117319,
year = {2021},
author = {Muftuoglu, M and Li, L and Liang, S and Mak, D and Lin, AJ and Fang, J and Burks, JK and Chen, K and Andreeff, M},
title = {Extended live-cell barcoding approach for multiplexed mass cytometry.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {12388},
pmid = {34117319},
issn = {2045-2322},
support = {P30 CA016672/CA/NCI NIH HHS/United States ; R50 CA243707/CA/NCI NIH HHS/United States ; },
mesh = {Cell Separation/*methods ; Cells, Cultured ; Humans ; Immunoassay/methods ; Leukocytes, Mononuclear/classification/*cytology ; Mass Spectrometry/*methods ; Single-Cell Analysis/methods ; },
abstract = {Sample barcoding is essential in mass cytometry analysis, since it can eliminate potential procedural variations, enhance throughput, and allow simultaneous sample processing and acquisition. Sample pooling after prior surface staining termed live-cell barcoding is more desirable than intracellular barcoding, where samples are pooled after fixation and permeabilization, since it does not depend on fixation-sensitive antigenic epitopes. In live-cell barcoding, the general approach uses two tags per sample out of a pool of antibodies paired with five palladium (Pd) isotopes in order to preserve appreciable signal-to-noise ratios and achieve higher yields after sample deconvolution. The number of samples that can be pooled in an experiment using live-cell barcoding is limited, due to weak signal intensities associated with Pd isotopes and the relatively low number of available tags. Here, we describe a novel barcoding technique utilizing 10 different tags, seven cadmium (Cd) tags and three Pd tags, with superior signal intensities that do not impinge on lanthanide detection, which enables enhanced pooling of samples with multiple experimental conditions and markedly enhances sample throughput.},
}
@article {pmid34116106,
year = {2021},
author = {Deconinck, D and Hostens, K and Taverniers, I and Volckaert, FAM and Robbens, J and Derycke, S},
title = {Identification and semi-quantification of Atlantic salmon in processed and mixed seafood products using Droplet Digital PCR (ddPCR).},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {154},
number = {},
pages = {112329},
doi = {10.1016/j.fct.2021.112329},
pmid = {34116106},
issn = {1873-6351},
mesh = {Animals ; Cooking ; DNA/*analysis ; Food Contamination/*analysis ; Freezing ; Limit of Detection ; Oncorhynchus mykiss ; Polymerase Chain Reaction/methods ; *Salmo salar ; Seafood/*analysis ; },
abstract = {Fishery products are often subject to substitution fraud, which is hard to trace due to a lack of morphologic traits when processed, gutted, or decapitated. Traditional molecular methods (DNA barcoding) fail to identify products containing multiple species and cannot estimate original weight percentages. As a proof of concept, an Atlantic salmon (Salmo salar) specific ddPCR assay was designed to authenticate mixed food products. The method proved to be specific and able to accurately quantify S. salar when using DNA extracts, even in the presence of DNA from closely related salmon species. The ddPCR estimates correlated well with the percentage of S. salar in artificially assembled tissue mixtures. The effect of common salmon processing techniques (freezing, smoking, poaching with a "Bellevue" recipe and marinating with a 'Gravad lax' recipe) on the ddPCR output was investigated and freezing and marinating appeared to lower the copies detected by the ddPCR. Finally, the assay was applied to 46 retail products containing Atlantic or Pacific salmon, and no indications of substitution fraud were detected. The method allows for a semi-quantitative evaluation of the S. salar content in processed food products and can rapidly screen Atlantic salmon products and flag potentially tampered samples for further investigation.},
}
@article {pmid34115987,
year = {2021},
author = {Simeonov, KP and Byrns, CN and Clark, ML and Norgard, RJ and Martin, B and Stanger, BZ and Shendure, J and McKenna, A and Lengner, CJ},
title = {Single-cell lineage tracing of metastatic cancer reveals selection of hybrid EMT states.},
journal = {Cancer cell},
volume = {39},
number = {8},
pages = {1150-1162.e9},
pmid = {34115987},
issn = {1878-3686},
support = {R00 HG010152/HG/NHGRI NIH HHS/United States ; T32 AI070077/AI/NIAID NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; F30 DK120135/DK/NIDDK NIH HHS/United States ; T32 HD083185/HD/NICHD NIH HHS/United States ; P30 CA023108/CA/NCI NIH HHS/United States ; R01 CA168654/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; CRISPR-Cas Systems ; Cell Line, Tumor ; Cell Lineage ; Cell Proliferation/genetics ; *Epithelial-Mesenchymal Transition/genetics ; *Gene Expression Regulation, Neoplastic ; Humans ; Male ; Mice, Inbred NOD ; Pancreatic Neoplasms/genetics/*pathology ; S100 Proteins/genetics ; Sequence Analysis, RNA ; Single-Cell Analysis/*methods ; Stem Cells/pathology ; Xenograft Model Antitumor Assays ; Mice ; },
abstract = {The underpinnings of cancer metastasis remain poorly understood, in part due to a lack of tools for probing their emergence at high resolution. Here we present macsGESTALT, an inducible CRISPR-Cas9-based lineage recorder with highly efficient single-cell capture of both transcriptional and phylogenetic information. Applying macsGESTALT to a mouse model of metastatic pancreatic cancer, we recover ∼380,000 CRISPR target sites and reconstruct dissemination of ∼28,000 single cells across multiple metastatic sites. We find that cells occupy a continuum of epithelial-to-mesenchymal transition (EMT) states. Metastatic potential peaks in rare, late-hybrid EMT states, which are aggressively selected from a predominately epithelial ancestral pool. The gene signatures of these late-hybrid EMT states are predictive of reduced survival in both human pancreatic and lung cancer patients, highlighting their relevance to clinical disease progression. Finally, we observe evidence for in vivo propagation of S100 family gene expression across clonally distinct metastatic subpopulations.},
}
@article {pmid34115981,
year = {2021},
author = {Cho, CS and Xi, J and Si, Y and Park, SR and Hsu, JE and Kim, M and Jun, G and Kang, HM and Lee, JH},
title = {Microscopic examination of spatial transcriptome using Seq-Scope.},
journal = {Cell},
volume = {184},
number = {13},
pages = {3559-3572.e22},
pmid = {34115981},
issn = {1097-4172},
support = {R01 DK114131/DK/NIDDK NIH HHS/United States ; T32 AG000114/AG/NIA NIH HHS/United States ; R01 DK102850/DK/NIDDK NIH HHS/United States ; P30 CA046592/CA/NCI NIH HHS/United States ; P30 AG024824/AG/NIA NIH HHS/United States ; K01 AG061236/AG/NIA NIH HHS/United States ; R01 DK118631/DK/NIDDK NIH HHS/United States ; P30 DK089503/DK/NIDDK NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; P30 AR069620/AR/NIAMS NIH HHS/United States ; R03 HD098552/HD/NICHD NIH HHS/United States ; U01 HL137182/HL/NHLBI NIH HHS/United States ; U2C DK110768/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Cell Nucleus/genetics ; Colon/pathology ; Gene Expression Regulation ; Hepatocytes/metabolism ; Inflammation/genetics ; Liver/metabolism ; Male ; Mice, Inbred C57BL ; *Microscopy ; Mitochondria/genetics ; RNA/metabolism ; Single-Cell Analysis ; Transcriptome/*genetics ; Mice ; },
abstract = {Spatial barcoding technologies have the potential to reveal histological details of transcriptomic profiles; however, they are currently limited by their low resolution. Here, we report Seq-Scope, a spatial barcoding technology with a resolution comparable to an optical microscope. Seq-Scope is based on a solid-phase amplification of randomly barcoded single-molecule oligonucleotides using an Illumina sequencing platform. The resulting clusters annotated with spatial coordinates are processed to expose RNA-capture moiety. These RNA-capturing barcoded clusters define the pixels of Seq-Scope that are ∼0.5-0.8 μm apart from each other. From tissue sections, Seq-Scope visualizes spatial transcriptome heterogeneity at multiple histological scales, including tissue zonation according to the portal-central (liver), crypt-surface (colon) and inflammation-fibrosis (injured liver) axes, cellular components including single-cell types and subtypes, and subcellular architectures of nucleus and cytoplasm. Seq-Scope is quick, straightforward, precise, and easy-to-implement and makes spatial single-cell analysis accessible to a wide group of biomedical researchers.},
}
@article {pmid34115787,
year = {2021},
author = {Mascarello, M and Amalfi, M and Asselman, P and Smets, E and Hardy, OJ and Beeckman, H and Janssens, SB},
title = {Genome skimming reveals novel plastid markers for the molecular identification of illegally logged African timber species.},
journal = {PloS one},
volume = {16},
number = {6},
pages = {e0251655},
pmid = {34115787},
issn = {1932-6203},
mesh = {Genetic Markers ; *Plastids/genetics ; High-Throughput Nucleotide Sequencing ; Trees/genetics ; Genome, Chloroplast ; Forests ; Conservation of Natural Resources/methods ; Africa ; Phylogeny ; DNA Barcoding, Taxonomic/methods ; },
abstract = {Tropical forests represent vast carbon stocks and continue to be key carbon sinks and buffer climate changes. The international policy constructed several mechanisms aiming at conservation and sustainable use of these forests. Illegal logging is an important threat of forests, especially in the tropics. Several laws and regulations have been set up to combat illegal timber trade. Despite significant enforcement efforts of these regulations, illegal logging continues to be a serious problem and impacts for the functioning of the forest ecosystem and global biodiversity in the tropics. Microscopic analysis of wood samples and the use of conventional plant DNA barcodes often do not allow to distinguish closely-related species. The use of novel molecular technologies could make an important contribution for the identification of tree species. In this study, we used high-throughput sequencing technologies and bioinformatics tools to obtain the complete de-novo chloroplast genome of 62 commercial African timber species using the genome skimming method. Then, we performed a comparative genomic analysis that revealed new candidate genetic regions for the discrimination of closely-related species. We concluded that genome skimming is a promising method for the development of plant genetic markers to combat illegal logging activities supporting CITES, FLEGT and the EU Timber Regulation.},
}
@article {pmid34114084,
year = {2021},
author = {Kappel, K and Fafińska, J and Fischer, M and Fritsche, J},
title = {A DNA microarray for the authentication of giant tiger prawn (Penaeus monodon) and whiteleg shrimp (Penaeus (Litopenaeus) vannamei): a proof-of-principle.},
journal = {Analytical and bioanalytical chemistry},
volume = {413},
number = {19},
pages = {4837-4846},
pmid = {34114084},
issn = {1618-2650},
support = {18667 N//Forschungskreis der Ern&#xe4;hrungsindustrie/ ; },
mesh = {Animals ; Astacoidea/genetics ; DNA/*genetics ; Oligonucleotide Array Sequence Analysis/*methods ; Penaeidae/*genetics ; RNA/genetics ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; },
abstract = {This proof-of-principle study describes the development of a rapid and easy-to-use DNA microarray assay for the authentication of giant tiger prawns and whiteleg shrimp. Following DNA extraction and conventional end-point PCR of a 16S rDNA segment, the PCR products are hybridised to species-specific oligonucleotide probes on DNA microarrays located at the bottom of centrifuge tubes (ArrayTubes) and the resulting signal patterns are compared to those of reference specimens. A total of 21 species-specific probes were designed and signal patterns were recorded for 47 crustacean specimens belonging to 16 species of seven families. A hierarchical clustering of the signal patterns demonstrated the specificity of the DNA microarray for the two target species. The DNA microarray can easily be expanded to other important crustaceans. As the complete assay can be performed within half a day and does not require taxonomic expertise, it represents a rapid and simple alternative to tedious DNA barcoding and could be used by crustacean trading companies as well as food control authorities for authentication of crustacean commodities.},
}
@article {pmid34112975,
year = {2021},
author = {Banal, JL and Shepherd, TR and Berleant, J and Huang, H and Reyes, M and Ackerman, CM and Blainey, PC and Bathe, M},
title = {Random access DNA memory using Boolean search in an archival file storage system.},
journal = {Nature materials},
volume = {20},
number = {9},
pages = {1272-1280},
pmid = {34112975},
issn = {1476-4660},
support = {F32 CA236425/CA/NCI NIH HHS/United States ; },
mesh = {Archives ; DNA/*chemistry ; Fluorescence ; *Information Storage and Retrieval ; Plasmids ; Polymerase Chain Reaction ; Silicon Dioxide/chemistry ; Synthetic Biology ; },
abstract = {DNA is an ultrahigh-density storage medium that could meet exponentially growing worldwide demand for archival data storage if DNA synthesis costs declined sufficiently and if random access of files within exabyte-to-yottabyte-scale DNA data pools were feasible. Here, we demonstrate a path to overcome the second barrier by encapsulating data-encoding DNA file sequences within impervious silica capsules that are surface labelled with single-stranded DNA barcodes. Barcodes are chosen to represent file metadata, enabling selection of sets of files with Boolean logic directly, without use of amplification. We demonstrate random access of image files from a prototypical 2-kilobyte image database using fluorescence sorting with selection sensitivity of one in 10[6] files, which thereby enables one in 10[6N] selection capability using N optical channels. Our strategy thereby offers a scalable concept for random access of archival files in large-scale molecular datasets.},
}
@article {pmid34112698,
year = {2021},
author = {Penter, L and Gohil, SH and Lareau, C and Ludwig, LS and Parry, EM and Huang, T and Li, S and Zhang, W and Livitz, D and Leshchiner, I and Parida, L and Getz, G and Rassenti, LZ and Kipps, TJ and Brown, JR and Davids, MS and Neuberg, DS and Livak, KJ and Sankaran, VG and Wu, CJ},
title = {Longitudinal Single-Cell Dynamics of Chromatin Accessibility and Mitochondrial Mutations in Chronic Lymphocytic Leukemia Mirror Disease History.},
journal = {Cancer discovery},
volume = {11},
number = {12},
pages = {3048-3063},
pmid = {34112698},
issn = {2159-8290},
support = {P01 CA229092/CA/NCI NIH HHS/United States ; R01 HL131768/HL/NHLBI NIH HHS/United States ; U24 CA224331/CA/NCI NIH HHS/United States ; R01 CA155010/CA/NCI NIH HHS/United States ; UG1 CA233338/CA/NCI NIH HHS/United States ; R01 CA258924/CA/NCI NIH HHS/United States ; P01 CA206978/CA/NCI NIH HHS/United States ; R01 CA213442/CA/NCI NIH HHS/United States ; R01 DK103794/DK/NIDDK NIH HHS/United States ; R50 CA251956/CA/NCI NIH HHS/United States ; },
mesh = {Chromatin/genetics ; Clonal Evolution/genetics ; Clone Cells ; DNA Copy Number Variations ; Humans ; *Leukemia, Lymphocytic, Chronic, B-Cell/genetics ; Mutation ; },
abstract = {UNLABELLED: While cancers evolve during disease progression and in response to therapy, temporal dynamics remain difficult to study in humans due to the lack of consistent barcodes marking individual clones in vivo. We employ mitochondrial single-cell assay for transposase-accessible chromatin with sequencing to profile 163,279 cells from 9 patients with chronic lymphocytic leukemia (CLL) collected across disease course and utilize mitochondrial DNA (mtDNA) mutations as natural genetic markers of cancer clones. We observe stable propagation of mtDNA mutations over years in the absence of strong selective pressure, indicating clonal persistence, but dramatic changes following tight bottlenecks, including disease transformation and relapse posttherapy, paralleled by acquisition of copy-number variants and changes in chromatin accessibility and gene expression. Furthermore, we link CLL subclones to distinct chromatin states, providing insight into nongenetic sources of relapse. mtDNA mutations thus mirror disease history and provide naturally occurring genetic barcodes to enable patient-specific study of cancer subclonal dynamics.<br><br>SIGNIFICANCE: Single-cell multi-omic profiling of CLL reveals the utility of somatic mtDNA mutations as in vivo barcodes, which mark subclones that can evolve over time along with changes in accessible chromatin and gene expression profiles to capture dynamics of disease evolution. See related commentary by Hilton and Scott, p. 2965. This article is highlighted in the In This Issue feature, p. 2945.},
}
@article {pmid34110166,
year = {2021},
author = {Zhang, Y and Malekjahani, A and Udugama, BN and Kadhiresan, P and Chen, H and Osborne, M and Franz, M and Kucera, M and Plenderleith, S and Yip, L and Bader, GD and Tran, V and Gubbay, JB and McGeer, A and Mubareka, S and Chan, WCW},
title = {Surveilling and Tracking COVID-19 Patients Using a Portable Quantum Dot Smartphone Device.},
journal = {Nano letters},
volume = {21},
number = {12},
pages = {5209-5216},
doi = {10.1021/acs.nanolett.1c01280},
pmid = {34110166},
issn = {1530-6992},
mesh = {*COVID-19 ; Humans ; Immunoassay ; *Quantum Dots ; SARS-CoV-2 ; Sensitivity and Specificity ; Seroepidemiologic Studies ; Smartphone ; },
abstract = {The ability to rapidly diagnose, track, and disseminate information for SARS-CoV-2 is critical to minimize its spread. Here, we engineered a portable smartphone-based quantum barcode serological assay device for real-time surveillance of patients infected with SARS-CoV-2. Our device achieved a clinical sensitivity of 90% and specificity of 100% for SARS-CoV-2, as compared to 34% and 100%, respectively, for lateral flow assays in a head-to-head comparison. The lateral flow assay misdiagnosed ∼2 out of 3 SARS-CoV-2 positive patients. Our quantum dot barcode device has ∼3 times greater clinical sensitivity because it is ∼140 times more analytically sensitive than lateral flow assays. Our device can diagnose SARS-CoV-2 at different sampling dates and infectious severity. We developed a databasing app to provide instantaneous results to inform patients, physicians, and public health agencies. This assay and device enable real-time surveillance of SARS-CoV-2 seroprevalence and potential immunity.},
}
@article {pmid34110016,
year = {2021},
author = {Luo, W and Ni, M and Wang, Y and Lan, R and Eissenstat, DM and Cahill, JF and Li, B and Chu, C},
title = {Limited evidence of vertical fine-root segregation in a subtropical forest.},
journal = {The New phytologist},
volume = {231},
number = {6},
pages = {2308-2318},
doi = {10.1111/nph.17546},
pmid = {34110016},
issn = {1469-8137},
mesh = {Forests ; *Plant Roots ; Soil ; *Trees ; Wood ; },
abstract = {Vertical root segregation and the resulting niche partitioning can be a key underpinning of species coexistence. This could result from substantial interspecific variations in root profiles and rooting plasticity in response to soil heterogeneity and neighbours, but they remain largely untested in forest communities. In a diverse forest in subtropical China, we randomly sampled > 4000 root samples from 625 0-30 cm soil profiles. Using morphological and DNA-based methods, we identified 109 woody plant species, determined the degree of vertical fine-root segregation, and examined rooting plasticity in response to soil heterogeneity and neighbour structure. We found no evidence of vertical fine-root segregation among cooccurring species. By contrast, root abundance of different species tended to be positively correlated within soil zones. Underlying these findings was a lack of interspecific variation in fine-root profiles with over 90% of species concentrated in the 0-10 cm soil zone with only one species dominating in the 10-20 cm soil zone. Root profiles exhibited low responsiveness to root neighbours but tended to be shallow in soils with low phosphorus and copper content. These findings suggest that if there is niche differentiation leading to coexistence in this diverse forest, it would be occurring by mechanisms other than vertical fine-root segregation.},
}
@article {pmid34108980,
year = {2021},
author = {Faller, AC and Shanmughanandhan, D and Ragupathy, S and Zhang, Y and Lu, Z and Chang, P and Swanson, G and Newmaster, SG},
title = {Validation of a Triplex Quantitative Polymerase Chain Reaction Assay for Detection and Quantification of Traditional Protein Sources, Pisum sativum L. and Glycine max (L.) Merr., in Protein Powder Mixtures.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {661770},
pmid = {34108980},
issn = {1664-462X},
abstract = {Several botanicals have been traditionally used as protein sources, including the leguminous Pisum sativum L. and Glycine max (L.) Merr. While a rich history exists of cultivating these plants for their whole, protein-rich grain, modern use as powdered supplements present a new challenge in material authentication. The absence of clear morphological identifiers of an intact plant and the existence of long, complex supply chains behoove industry to create quick, reliable analytical tools to identify the botanical source of a protein product (many of which contain multiple sources). The utility of molecular tools for plant-based protein powder authentication is gaining traction, but few validated tools exist. Multiplex quantitative polymerase chain reaction (qPCR) can provide an economical means by which sources can be identified and relative proportions quantified. We followed established guidelines for the design, optimization, and validation of qPCR assay, and developed a triplex qPCR assay that can amplify and quantify pea and soy DNA targets, normalized by a calibrator. The assay was evaluated for analytical specificity, analytical sensitivity, efficiency, precision, dynamic range, repeatability, and reproducibility. We tested the quantitative ability of the assay using pea and soy DNA mixtures, finding exceptional quantitative linearity for both targets - 0.9983 (p < 0.0001) for soy and 0.9915 (p < 0.0001) for pea. Ratios based on mass of protein powder were also tested, resulting in non-linear patterns in data that suggested the requirement of further sample preparation optimization or algorithmic correction. Variation in fragment size within different lots of commercial protein powder samples was also analyzed, revealing low SD among lots. Ultimately, this study demonstrated the utility of qPCR in the context of protein powder mixtures and highlighted key considerations to take into account for commercial implementation.},
}
@article {pmid34101998,
year = {2021},
author = {Hahn, MW and Huemer, A and Pitt, A and Hoetzinger, M},
title = {Opening a next-generation black box: Ecological trends for hundreds of species-like taxa uncovered within a single bacterial &gt;99% 16S rRNA operational taxonomic unit.},
journal = {Molecular ecology resources},
volume = {21},
number = {7},
pages = {2471-2485},
pmid = {34101998},
issn = {1755-0998},
support = {P 27160/FWF_/Austrian Science Fund FWF/Austria ; 27160-B22//Austrian Science Fund/ ; },
mesh = {Bacteria/genetics ; *Burkholderiaceae/genetics ; DNA, Bacterial/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Current knowledge on environmental distribution and taxon richness of free-living bacteria is mainly based on cultivation-independent investigations employing 16S rRNA gene sequencing methods. Yet, 16S rRNA genes are evolutionarily rather conserved, resulting in limited taxonomic and ecological resolutions provided by this marker. The faster evolving protein-encoding gene priB was used to reveal ecological patterns hidden within a single operational taxonomic unit (OTU) defined by >99% 16S rRNA sequence similarity. The studied subcluster PnecC of the genus Polynucleobacter represents a ubiquitous group of abundant freshwater bacteria with cosmopolitan distribution, which is very frequently detected by diversity surveys of freshwater systems. Based on genome taxonomy and a large set of genome sequences, a sequence similarity threshold for delineation of species-like taxa could be established. In total, 600 species-like taxa were detected in 99 freshwater habitats scattered across three regions representing a latitudinal range of 3,400 km (42°N to 71°N) and a pH gradient of 4.2 to 8.6. In addition to the unexpectedly high richness, the increased taxonomic resolution revealed structuring of Polynucleobacter communities by a couple of macroecological trends, which was previously only demonstrated for phylogenetically much broader groups of bacteria. An unexpected pattern was the almost complete compositional separation of Polynucleobacter communities of Ca[2+] -rich and Ca[2+] -poor habitats. This compositional pattern strongly resembled the vicariance of plant species on silicate and limestone soils. The new cultivation-independent approach presented opened a window to an incredible, previously unseen diversity, and enables investigations aiming on deeper understanding of how environmental conditions shape bacterial communities and drive evolution of free-living bacteria.},
}
@article {pmid34097924,
year = {2021},
author = {Kim, J and Vaughan, HJ and Zamboni, CG and Sunshine, JC and Green, JJ},
title = {High-throughput evaluation of polymeric nanoparticles for tissue-targeted gene expression using barcoded plasmid DNA.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {337},
number = {},
pages = {105-116},
pmid = {34097924},
issn = {1873-4995},
support = {T32 CA130840/CA/NCI NIH HHS/United States ; T32 CA153952/CA/NCI NIH HHS/United States ; R01 EY031097/EY/NEI NIH HHS/United States ; R01 CA228133/CA/NCI NIH HHS/United States ; P41 EB028239/EB/NIBIB NIH HHS/United States ; },
mesh = {Animals ; DNA/genetics ; Gene Expression ; Mice ; *Nanoparticles ; Plasmids/genetics ; Tissue Distribution ; Transfection ; },
abstract = {Successful systemic gene delivery requires specific tissue targeting as well as efficient intracellular transfection. Increasingly, research laboratories are fabricating libraries of novel nanoparticles, engineering both new biomaterial structures and composition ratios of multicomponent systems. Yet, methods for screening gene delivery vehicles directly in vivo are often low-throughout, limiting the number of candidate nanoparticles that can be investigated. Here, we report a comprehensive, high-throughput method to evaluate a library of polymeric nanoparticles in vivo for tissue-specific gene delivery. The method involves pairing each nanoparticle formulation with a plasmid DNA (pDNA) that harbors a unique nucleotide sequence serving as the identifying "barcode". Using real time quantitative PCR (qPCR) for detection of the barcoded pDNA and quantitative reverse transcription PCR (RT-qPCR) for transcribed barcoded mRNA, we can quantify accumulation and transfection in tissues of interest. The barcode pDNA and primers were designed with sufficient sensitivity and specificity to evaluate multiple nanoparticle formulations per mouse, improving screening efficiency. Using this platform, we evaluated the biodistribution and transfection of 8 intravenously administered poly(beta-amino ester; PBAE) nanoparticle formulations, each with a PBAE polymer of differential structure. Significant levels of nanoparticle accumulation and gene transfection were observed mainly in organs involved in clearance, including spleen, liver, and kidneys. Interestingly, higher levels of transfection of select organs did not necessarily correlate with higher levels of tissue accumulation, highlighting the importance of directly measuring in vivo transfection efficiency as the key barcoded parameter in gene delivery vector optimization. To validate this method, nanoparticle formulations were used individually for luciferase pDNA delivery in vivo. The distribution of luciferase expression in tissues matched the transfection analysis by the barcode qPCR method, confirming that this platform can be used to accurately evaluate systemic gene delivery.},
}
@article {pmid34097821,
year = {2021},
author = {Attiná, N and Núñez Bustos, EO and Lijtmaer, DA and Hebert, PDN and Tubaro, PL and Lavinia, PD},
title = {Genetic variation in neotropical butterflies is associated with sampling scale, species distributions, and historical forest dynamics.},
journal = {Molecular ecology resources},
volume = {21},
number = {7},
pages = {2333-2349},
doi = {10.1111/1755-0998.13441},
pmid = {34097821},
issn = {1755-0998},
support = {//Fundaci&#xf3;n Bosques Nativos Argentinos/ ; //Fundaci&#xf3;n Temaik&#xe8;n/ ; //Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas (CONICET)/ ; //Richard Lounsbery Foundation/ ; //Natural Sciences and Engineering Resarch Council of Canada/ ; //Agencia Nacional de Promoci&#xf3;n de la Investigaci&#xf3;n, el Desarrollo Tecnol&#xf3;gico y la Innovaci&#xf3;n (Agencia I+D+i)/ ; //Fundaci&#xf3;n Williams/ ; },
mesh = {Animals ; Brazil ; *Butterflies/genetics ; Forests ; Genetic Variation ; Phylogeny ; Phylogeography ; },
abstract = {Previous studies of butterfly diversification in the Neotropics have focused on Amazonia and the tropical Andes, while southern regions of the continent have received little attention. To address the gap in knowledge about the Lepidoptera of temperate South America, we analysed over 3000 specimens representing nearly 500 species from Argentina for a segment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Representing 42% of the country's butterfly fauna, collections targeted species from the Atlantic and Andean forests, and biodiversity hotspots that were previously connected but are now isolated. We assessed COI effectiveness for species discrimination and identification and how its performance was affected by geographic distances and taxon coverage. COI data also allowed to study patterns of genetic variation across Argentina, particularly between populations in the Atlantic and Andean forests. Our results show that COI discriminates species well, but that identification success is reduced on average by ~20% as spatial and taxonomic coverage rises. We also found that levels of genetic variation are associated with species' spatial distribution type, a pattern which might reflect differences in their dispersal and colonization abilities. In particular, intraspecific distance between populations in the Atlantic and Andean forests was significantly higher in species with disjunct distributions than in those with a continuous range. All splits between lineages in these forests dated to the Pleistocene, but divergence dates varied considerably, suggesting that historical connections between the Atlantic and Andean forests have differentially affected their shared butterfly fauna. Our study supports the fact that large-scale assessments of mitochondrial DNA variation are a powerful tool for evolutionary studies.},
}
@article {pmid34096866,
year = {2021},
author = {Bouguerche, C and Tazerouti, F and Gey, D and Justine, JL},
title = {Triple barcoding for a hyperparasite, its parasitic host, and the host itself: a study of Cyclocotyla bellones (Monogenea) on Ceratothoa parallela (Isopoda) on Boops boops (Teleostei).},
journal = {Parasite (Paris, France)},
volume = {28},
number = {},
pages = {49},
pmid = {34096866},
issn = {1776-1042},
mesh = {Algeria ; Animals ; *Fish Diseases ; Fishes ; *Isopoda ; Mediterranean Sea ; *Parasites/genetics ; *Perciformes ; *Trematoda/genetics ; },
abstract = {Cyclocotyla bellones Otto, 1823 (Diclidophoridae) is a monogenean characterised by an exceptional way of life. It is a hyperparasite that attaches itself to the dorsal face of isopods, themselves parasites in the buccal cavity of fishes. In this study, Cy. bellones was found on Ceratothoa parallela (Otto, 1828), a cymothoid isopod parasite of the sparid fish Boops boops off Algeria in the Mediterranean Sea. We provide, for the first time, molecular barcoding information of a hyperparasitic monogenean, the parasitic crustacean host, and the fish host, with COI sequences.},
}
@article {pmid34096765,
year = {2021},
author = {Xu, D and Adkar-Purushothama, CR and Lemoyne, P and Perreault, JP and Fall, M},
title = {First report of Grapevine yellow speckle viroid 1 infecting grapevine (Vitis vinifera L.) in Canada.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-04-21-0863-PDN},
pmid = {34096765},
issn = {0191-2917},
abstract = {Quebec is the third largest wine grape producer in Canada in acreage, tonnage, and wine grape sales (Carisse et al. 2017; Ben Moussa et al. 2019). To evaluate the diversity of viruses infecting grapevine in Quebec, a total of 77 leaf tissue samples (cv. Vidal) were collected from July to October in 2020 in three different vineyards located in Frelighsburg, Hemmingford and Saint-Jacques-le-Mineur in Quebec, Canada. Double-stranded RNA was extracted from each sample and used for cDNA library preparation with the Nextera XT DNA Library Preparation Kit (Illumina) as described previously (Kesanakurti et al. 2016). High-throughput sequencing (HTS, 2x300 bp) was conducted on dual-indexed libraries in a v3 flow cell using the Illumina MiSeq platform (Adkar-Purushothama et al. 2020). The obtained raw FASTQ data was de-multiplexed into 154 separate sequence files, and the adapters and barcode sequences were trimmed. The quality of the sequences was verified using Trimmomatic V.0.32 and the "clean" sequences were analyzed using Virtool and VirFind virus detection pipelines described elsewhere (Ho and Tzanetakis 2014; Rott et al. 2017) to screen for all possible viruses in the databases. Over 100,000 reads per sample were obtained with a percentage of mapped viral reads ranging from 1.47 to 19.43% of total number of reads. Out of 77 samples, 16 revealed the sequence of grapevine yellow speckle viroid 1 (GYSVd-1), for which the length coverage ranged from 98.5 to 99.1%; the depth ranged from 2X to 856X. The GYSVd-1 positive sequence files were subjected to whole genome assembly on CLC genomics Workbench v20.0.4 with the isolate SY-BR from Brazil (KU880715) used as reference. Seven complete genomes of GYSVd-1 of 366-368 nucleotides (nt) in size were deposited (GenBank Acc. MW732682 to MW732688). BLASTN analysis of the sequences showed 98-100% nt identities with isolate SY-BR. Other viruses and viroids such as Grapevine fleck virus, Grapevine rupestris stem pitting-associated virus, Grapevine rupestris vein feathering virus and Hop stunt viroid were also detected. To confirm GYSVd-1 presence in Quebec vineyards, seven of the 16 HTS-positive grapevine leaf tissue samples were subjected to total RNA extraction, followed by RT-PCR assay as before (Adkar-Purushothama et al. 2015; Sahana et al. 2013); all were positive by RT-PCR. The PCR products were directly Sanger-sequenced, and they showed 100% nt identity to the HTS derived sequences. Three of the seven GYSVd-1 positive grapevines exhibited yellow leaf spots and flecks and tiny yellow leaves, but their mixed infection status makes definitive symptoms association difficult to determine. Previously, Hop stunt viroid was reported from grapevines in Canada (Xiao et al. 2019; Fall et al. 2020) but to the best of our knowledge, this is the first report of GYSVd-1 infecting grapevines in Canada, specifically in the province of Quebec. Further research is required to assess the GYSVd-1 related yield loss. Monitoring and testing for GYSVd-1 infection is necessary to prevent propagation of infected materials, spread, and potential negative impact for the Canadian grapevine industry.},
}
@article {pmid34096689,
year = {2021},
author = {Suárez Casanova, VM and Shumskaya, M},
title = {Exploring DNA in biochemistry lab courses: DNA barcoding and phylogenetic analysis.},
journal = {Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology},
volume = {49},
number = {5},
pages = {789-799},
doi = {10.1002/bmb.21551},
pmid = {34096689},
issn = {1539-3429},
mesh = {Biochemistry ; DNA/genetics ; *DNA Barcoding, Taxonomic ; Humans ; *Laboratories ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {DNA structure has been leveraged in a variety of facets that allow scientists to perform a range of assays, including ones for identification of species, establishing evolutionary relationships between taxa, or even identifying individuals. Here, we present a DNA barcoding method as practical, hands-on approach that connects several experimental techniques in one sequence to teach the principles behind DNA isolation, purification, PCR, sequencing, and phylogeny analysis. Our set of exercises is designed for a teaching university laboratory setting. The three laboratory class assignments utilize DNA from a mushroom (can be purchased at a supermarket) and provide a pipeline to guide students through the process of identifying an unknown sample, like in many research laboratories. The third assignment can be used as a stand-alone exercise on phylogeny analysis and can be taught remotely. Students explore the theory behind the standard molecular techniques and apply it in a hands-on setting that involves experimental design, sample preparation, and use of hallmark molecular instruments.},
}
@article {pmid34095587,
year = {2021},
author = {Lea-Charris, E and Castro, LR and Villamizar, N},
title = {DNA barcoding reveals fraud in commercial common snook (Centropomus undecimalis) products in Santa Marta, Colombia.},
journal = {Heliyon},
volume = {7},
number = {5},
pages = {e07095},
pmid = {34095587},
issn = {2405-8440},
abstract = {The common snook Centropomus undecimalis is one of the main commercial fish species in the Caribbean region, including Colombia, where its populations have drastically decreased due to overfishing and environmental degradation. Thus, there is a market imbalance between the availability of snook products and their demand by consumers, which creates an opening for fraudulent actions such as species substitutions. Legislation in Colombia (and most Caribbean countries) lacks effective tools for the easy and rapid detection of frauds. Furthermore, there are very few studies published in scientific journals addressing this issue, of which none include C. undecimalis as the target species. Therefore, in order to investigate the existence of mislabeling in common snook products in Santa Marta, the present study analysed 44 frozen snook fillets from the five commercial brands available in the city. Moreover, 15 fresh snook fillets from six of the main fish markets were also analysed. To discover the frequency of possible frauds in labeling, samplings were carried out in July, September and November of 2019. Sample analyses involved the identification of each fillet at species level through molecular barcodes (16S-rRNA and COI), whose sequences were verified using BLAST and BOLD, and corroborated by a phylogenetic analysis. As a result, an astonishing 98% of the supermarkets fillets were found to be fraudulent, contrasting with a single case registered in the fish shop samples. The species used to substitute snook include the Pacific bearded brotula Brotula clarkae (38 samples), the Nile perch Lates niloticus (4 samples) and the acoupa weakfish Cynoscion acoupa (1 sample). Based on these results, there is a high rate of fraudulent labeling in the marketing of common snook in the city of Santa Marta, which calls for urgent actions to be taken by the corresponding authorities.},
}
@article {pmid34093980,
year = {2021},
author = {Bolshakov, VV and Prokin, AA},
title = {Karyotype and COI sequences of Chironomus sokolovae Istomina, Kiknadze et Siirin, 1999 (Diptera,Chironomidae) from the bay of Orkhon River, Mongolia.},
journal = {Comparative cytogenetics},
volume = {15},
number = {2},
pages = {149-157},
pmid = {34093980},
issn = {1993-0771},
abstract = {Chironomus sokolovae Istomina, Kiknadze et Siirin, 1999 (Diptera, Chironomidae) is recorded from Mongolia for the first time. Eleven banding sequences determined in the Mongolian population were previously known from Altai and Yenisei populations: sokA1, sokB1, sokB2, sokC1, sokC2, sokD1, sokD2, sokE1, sokF1, sokF2 and sokG1. The additional B-chromosomes are absent. DNA-barcoding of COI gene was carried out for this species for the first time. The phylogenetic tree estimated by Bayesian inference showed a high similarity of the studied species with Ch. acutiventris Wülker, Ryser et Scholl, 1983 from the Chironomus obtusidens-group. The estimated genetic distance K2P between Ch. sokolovae and Ch. acutiventris is much lower (0.38%) than the commonly accepted threshold of 3% for species of genus Chironomus Meigen, 1803. Our results show that the accepted cytogenetic criteria of species level in the genus Chironomus are more in accordance with morphological ones of the same level, than with molecular-genetic criteria accepted for species COI genetic distance.},
}
@article {pmid34093488,
year = {2021},
author = {Pjevac, P and Hausmann, B and Schwarz, J and Kohl, G and Herbold, CW and Loy, A and Berry, D},
title = {An Economical and Flexible Dual Barcoding, Two-Step PCR Approach for Highly Multiplexed Amplicon Sequencing.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {669776},
pmid = {34093488},
issn = {1664-302X},
abstract = {In microbiome research, phylogenetic and functional marker gene amplicon sequencing is the most commonly-used community profiling approach. Consequently, a plethora of protocols for the preparation and multiplexing of samples for amplicon sequencing have been developed. Here, we present two economical high-throughput gene amplification and sequencing workflows that are implemented as standard operating procedures at the Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna. These workflows are based on a previously-published two-step PCR approach, but have been updated to either increase the accuracy of results, or alternatively to achieve orders of magnitude higher numbers of samples to be multiplexed in a single sequencing run. The high-accuracy workflow relies on unique dual sample barcoding. It allows the same level of sample multiplexing as the previously-published two-step PCR approach, but effectively eliminates residual read missasignments between samples (crosstalk) which are inherent to single barcoding approaches. The high-multiplexing workflow is based on combinatorial dual sample barcoding, which theoretically allows for multiplexing up to 299,756 amplicon libraries of the same target gene in a single massively-parallelized amplicon sequencing run. Both workflows presented here are highly economical, easy to implement, and can, without significant modifications or cost, be applied to any target gene of interest.},
}
@article {pmid34093459,
year = {2021},
author = {Zhao, P and Ji, SP and Cheng, XH and Bau, T and Dong, HX and Gao, XX},
title = {DNA Barcoding Mushroom Spawn Using EF-1α Barcodes: A Case Study in Oyster Mushrooms (Pleurotus).},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {624347},
pmid = {34093459},
issn = {1664-302X},
abstract = {Oyster mushrooms (genus Pleurotus) are widespread and comprise the most commonly cultivated edible mushrooms in the world. Species identification of oyster mushroom spawn based on cultural, morphological, and cultivated characteristics is time consuming and can be extraordinarily difficult, which has impeded mushroom breeding and caused economic loss for mushroom growers. To explore a precise and concise approach for species identification, the nuclear ribosomal internal transcribed spacer (ITS), 28S rDNA, and the widely used protein-coding marker translation elongation factor 1α (EF-1α) gene were evaluated as candidate DNA barcode markers to investigate their feasibility in identifying 13 oyster mushroom species. A total of 160 sequences of the candidate loci were analyzed. Intra- and interspecific divergences and the ease of nucleotide sequence acquisition were the criteria used to evaluate the candidate genes. EF-1α showed the best intra- and interspecific variation among the candidate markers and discriminated 84.6% of the species tested, only being unable to distinguish two closely related species Pleurotus citrinopileatus and Pleurotus cornucopiae. Furthermore, EF-1α was more likely to be acquired than ITS or 28S rDNA, with an 84% success rate of PCR amplification and sequencing. For ITS and 28S rDNA, the intraspecific differences of several species were distinctly larger than the interspecific differences, and the species identification efficiency of the two candidate markers was worse (61.5 and 46.2%, respectively). In addition, these markers had some sequencing problems, with 55 and 76% success rates of sequencing, respectively. Hence, we propose EF-1α as a possible DNA barcode marker for oyster mushroom spawn.},
}
@article {pmid34093054,
year = {2021},
author = {Riedel, M and Humala, AE and Schwarz, M and Schnee, H and Schmidt, S},
title = {Checklist of the Ichneumonidae of Germany (Insecta, Hymenoptera).},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e64267},
pmid = {34093054},
issn = {1314-2828},
abstract = {BACKGROUND: A revised checklist of the Ichneumonidae of Germany is provided. The list represents an updated version of an earlier checklist published in 2001. The present list includes several records of species that are new for the German fauna and species that were discovered since the last checklist was published. The present checklist was compiled as part of the DNA barcoding projects at the Zoologische Staatssammlung München.<br><br>NEW INFORMATION: The checklist includes 3,644 species of Ichneumonidae from Germany, with 48 species recorded for the first time. Compared to the checklist published 20 years ago, the number of ichneumonid species recorded from Germany has increased by 312 species.},
}
@article {pmid34090343,
year = {2021},
author = {Ishitsuka, K and Sasaki, S and Mezawa, H and Konishi, M and Igarashi, M and Yamamoto-Hanada, K and Nakayama, SF and Ohya, Y},
title = {Dietary supplement use in elementary school children: a Japanese web-based survey.},
journal = {Environmental health and preventive medicine},
volume = {26},
number = {1},
pages = {63},
pmid = {34090343},
issn = {1347-4715},
support = {NA//Ministry of the Environment/ ; },
mesh = {Adult ; Amino Acids/therapeutic use ; Child ; Cross-Sectional Studies ; *Dietary Supplements ; Female ; Humans ; Internet ; Japan ; Male ; Middle Aged ; Mothers ; Nutrition Surveys ; Schools ; Socioeconomic Factors ; Students ; Vitamins/therapeutic use ; },
abstract = {BACKGROUND: A variety of dietary supplements are commercially available. However, the efficacy and safety of dietary supplement use in children are not well established. Understanding dietary supplement use is important for developing public health policy regarding dietary supplements. This study aimed to investigate the types of dietary supplements used and characteristics of dietary supplement users among Japanese elementary school children.<br><br>METHOD: We conducted a cross-sectional web-based questionnaire study. Dietary supplement use, socio-demographics, and health-related behaviors were assessed through mother-reported questionnaire. Types of dietary supplements were identified based on ingredient using product barcodes and brand names. Multivariate logistic regression analysis was conducted to investigate the socio-demographics and health-related behaviors associated with supplement use.<br><br>RESULTS: Among 4933 children, 333 (6.8%) were identified as dietary supplement users. The most common supplement was amino acids or protein (1.4%), followed by n-3 fatty acids or fish oil (1.0%), probiotics (1.0%), multivitamins (0.9%), multivitamin-minerals (0.8%), and botanicals (0.8%). Overall, any dietary supplement use was significantly associated with the highest frequency of sports participation (odds ratio [OR], 2.58; 95% confidence interval [CI], 1.65-4.02), highest household income (OR, 1.87; 95% CI, 1.13-3.10), highest maternal educational level (OR, 1.82; 95% CI, 1.31-2.52), and male sex (OR, 1.38; 95% CI, 1.09-1.75). The highest frequency of sports participation was significantly associated with higher odds of use of amino acids or protein (OR, 6.06; 95% CI, 1.78-20.6) and multivitamins (OR, 3.56; 95% CI, 1.11-11.5), compared to the lowest frequency of sports participation.<br><br>CONCLUSION: This study showed that Japanese children primarily use non-vitamin, non-mineral supplements. Non-vitamin, non-mineral supplements should thus be included in future studies aimed at monitoring dietary supplement use. We also found that dietary supplement use in children was associated with sports participation. Guidelines for dietary supplement use for children, in particular sport participants, are needed.},
}
@article {pmid34084068,
year = {2021},
author = {Pulgarín-R, PC and Olivera-Angel, M and Ortíz, L and Nanclares, D and Velásquez-Restrepo, S and Díaz-Nieto, JF},
title = {DNA barcodes of birds from northern Colombia.},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e64842},
pmid = {34084068},
issn = {1314-2828},
abstract = {DNA barcode datasets are a useful tool for conservation and aid in taxonomic identification, particularly in megadiverse tropical countries seeking to document and describe its biota, which is dropping at an alarming rate during recent decades. Here we report the barcodes for several low elevation bird species from northern Colombia with the goal to provide tools for species identification in this region of South America. We blood-sampled birds in a lowland tropical forest with various degrees of intervention using standard 3 × 12 m mist-nets. We extracted DNA and sequenced the COI barcode gene using standard primers and laboratory methods. We obtained 26 COI sequences from 18 species, 10 families and three orders and found that barcodes largely matched (but not always) phenotypic identification (> 90%) and they also facilitated the identification of several challenging passerine species. Despite our reduced sampling, our study represents the first attempt to document COI barcodes for birds (from blood samples) in this part of Colombia, which fills a considerable gap of sampling in this part of South America.},
}
@article {pmid34082296,
year = {2021},
author = {Chen, G and Liu, G and Jia, H and Cui, X and Wang, Y and Li, D and Zheng, W and She, Y and Xu, D and Huang, X and Abd El-Aty, AM and Sun, J and Liu, H and Zou, Y and Wang, J and Jin, M and Hammock, BD},
title = {A sensitive bio-barcode immunoassay based on bimetallic Au@Pt nanozyme for detection of organophosphate pesticides in various agro-products.},
journal = {Food chemistry},
volume = {362},
number = {},
pages = {130118},
pmid = {34082296},
issn = {1873-7072},
support = {P42 ES004699/ES/NIEHS NIH HHS/United States ; },
mesh = {Catalysis ; Chlorpyrifos/analysis ; Chromatography, Liquid ; Food Analysis/methods ; Food Contamination/*analysis ; Gold/chemistry ; Immunoassay/instrumentation/*methods ; Limit of Detection ; Metal Nanoparticles/*chemistry ; Organophosphorus Compounds/analysis ; Organothiophosphates/analysis ; Oxazines/chemistry ; Parathion/analysis ; Pesticide Residues/*analysis ; Platinum/chemistry ; Tandem Mass Spectrometry ; Triazoles/analysis ; },
abstract = {Organophosphate pesticides (OPs) are often used as insecticides and acaricides in agriculture, thus improving yields. OP residues may pose a serious threat, duetoinhibitionof the enzymeacetylcholinesterase(AChE). Therefore, a competitive bio-barcode immunoassay was designed for simultaneous quantification of organophosphate pesticide residues using AuNP signal amplification technology and Au@Pt catalysis. The AuNP probes were labelled with antibodies and corresponding bio-barcodes (ssDNAs), MNP probes coated with ovalbumin pesticide haptens and Au@Pt probes functionalized with the complementary ssDNAs were then prepared. Subsequently, pesticides competed with MNP probes to bind the AuNP probes. The recoveries of the developed assay were ranged from 71.26 to 117.47% with RSDs from 2.52 to 14.52%. The LODs were 9.88, 3.91, and 1.47 ng·kg[-1], for parathion, triazophos, and chlorpyrifos, respectively. The assay was closely correlated with the data obtained from LC-MS/MS. Therefore, the developed method has the potential to be used as an alternative approach for detection of multiple pesticides.},
}
@article {pmid34078895,
year = {2021},
author = {Lin, D and Hsieh, CL and Hsu, KC and Liao, PH and Qiu, S and Gong, T and Yong, KT and Feng, S and Kong, KV},
title = {Geometrically encoded SERS nanobarcodes for the logical detection of nasopharyngeal carcinoma-related progression biomarkers.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {3430},
pmid = {34078895},
issn = {2041-1723},
mesh = {Biomarkers, Tumor/blood/chemistry ; Biosensing Techniques/*methods ; Disease Progression ; Matrix Metalloproteinases/blood/chemistry ; Metal Nanoparticles/chemistry ; Nanogels/chemistry ; Nasopharyngeal Carcinoma/blood/*diagnosis/pathology ; Nasopharyngeal Neoplasms/blood/*diagnosis/pathology ; Organometallic Compounds/chemistry ; Sensitivity and Specificity ; *Spectrum Analysis, Raman ; Surface Properties ; },
abstract = {The limited availability of nasopharyngeal carcinoma-related progression biomarker array kits that offer physicians comprehensive information is disadvantageous for monitoring cancer progression. To develop a biomarker array kit, systematic identification and differentiation of a large number of distinct molecular surface-enhanced Raman scattering (SERS) reporters with high spectral temporal resolution is a major challenge. To address this unmet need, we use the chemistry of metal carbonyls to construct a series of unique SERS reporters with the potential to provide logical and highly multiplex information during testing. In this study, we report that geometric control over metal carbonyls on nanotags can produce 14 distinct barcodes that can be decoded unambiguously using commercial Raman spectroscopy. These metal carbonyl nanobarcodes are tested on human blood samples and show strong sensitivity (0.07 ng/mL limit of detection, average CV of 6.1% and >92% degree of recovery) and multiplexing capabilities for MMPs.},
}
@article {pmid34077477,
year = {2021},
author = {Siriwut, W and Jeratthitikul, E and Panha, S and Chanabun, R and Ngor, PB and Sutcharit, C},
title = {Evidence of cryptic diversity in freshwater Macrobrachium prawns from Indochinese riverine systems revealed by DNA barcode, species delimitation and phylogenetic approaches.},
journal = {PloS one},
volume = {16},
number = {6},
pages = {e0252546},
pmid = {34077477},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Ecosystem ; Genetic Variation/genetics/physiology ; Palaemonidae/classification/*genetics ; Phylogeny ; },
abstract = {The diversity of Indochinese prawns in genus Macrobrachium is enormous due to the habitat diversification and broad tributary networks of two river basins: the Chao Phraya and the Mekong. Despite long-standing interest in SE-Asian decapod diversity, the subregional Macrobrachium fauna is still not yet comprehensively clarified in terms of taxonomic identification or genetic diversification. In this study, integrative taxonomic approaches including morphological examination, DNA barcoding, and molecular species delimitation were used to emphasize the broad scale systematics of Macrobrachium prawns in Indochina. Twenty-seven nominal species were successfully re-verified by traditional and molecular taxonomy. Barcode gap analysis supported broad overlapping of species boundaries. Taxonomic ambiguity of several deposited samples in the public database is related to inter- and intraspecific genetic divergence as indicated by BOLD discordance. Diagnostic nucleotide positions were found in six Macrobrachium species. Eighteen additional putative lineages are herein assigned using the consensus of species delimitation methods. Genetic divergence indicates the possible existence of cryptic species in four morphologically complex and wide-ranging species: M. lanchesteri, M. niphanae, M. sintangense, and some members of the M. pilimanus group. The geographical distribution of some species supports the connections and barriers attributed to paleo-historical events of SE-Asian rivers and land masses. Results of this study show explicitly the importance of freshwater ecosystems in Indochinese subregions, especially for the Mekong River Basin due to its high genetic diversity and species composition found throughout its tributaries.},
}
@article {pmid34073265,
year = {2021},
author = {Bonnefoy, F and Bernier, M and Perret, E and Barbot, N and Siragusa, R and Hely, D and Kato, E and Garet, F},
title = {Video-Rate Identification of High-Capacity Low-Cost Tags in the Terahertz Domain.},
journal = {Sensors (Basel, Switzerland)},
volume = {21},
number = {11},
pages = {},
pmid = {34073265},
issn = {1424-8220},
support = {ANR-18-CE39-0002//Agence Nationale de la Recherche/ ; C2019 - 086//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; },
abstract = {In this article, we report on video-rate identification of very low-cost tags in the terahertz (THz) domain. Contrary to barcodes, Radio Frequency Identification (RFID) tags, or even chipless RFID tags, operate in the Ultra-Wide Band (UWB). These THz labels are not based on a planar surface pattern but are instead embedded, thus hidden, in the volume of the product to identify. The tag is entirely made of dielectric materials and is based on a 1D photonic bandgap structure, made of a quasi-periodic stack of two different polyethylene-based materials presenting different refractive indices. The thickness of each layer is of the order of the THz wavelength, leading to an overall tag thickness in the millimetre range. More particularly, we show in this article that the binary information coded within these tags can be rapidly and reliably identified using a commercial terahertz Time Domain Spectroscopy (THz-TDS) system as a reader. More precisely, a bit error rate smaller than 1% is experimentally reached for a reading duration as short as a few tens of milliseconds on an 8 bits (~40 bits/cm[2]) THID tag. The performance limits of such a tag structure are explored in terms of both dielectric material properties (losses) and angular acceptance. Finally, realistic coding capacities of about 60 bits (~300 bits/cm[2]) can be envisaged with such tags.},
}
@article {pmid34072252,
year = {2021},
author = {Gadoin, E and Durand, L and Guillou, A and Crochemore, S and Bouvier, T and Roque, E and Dagorn, L and Auguet, JC and Adingra, A and Desnues, C and Bettarel, Y},
title = {Does the Composition of the Gut Bacteriome Change during the Growth of Tuna?.},
journal = {Microorganisms},
volume = {9},
number = {6},
pages = {},
pmid = {34072252},
issn = {2076-2607},
abstract = {In recent years, a growing number of studies sought to examine the composition and the determinants of the gut microflora in marine animals, including fish. For tropical tuna, which are among the most consumed fish worldwide, there is scarce information on their enteric bacterial communities and how they evolve during fish growth. In this study, we used metabarcoding of the 16S rDNA gene to (1) describe the diversity and composition of the gut bacteriome in the three most fished tuna species (skipjack, yellowfin and bigeye), and (2) to examine its intra-specific variability from juveniles to larger adults. Although there was a remarkable convergence of taxonomic richness and bacterial composition between yellowfin and bigeyes tuna, the gut bacteriome of skipjack tuna was distinct from the other two species. Throughout fish growth, the enteric bacteriome of yellowfin and bigeyes also showed significant modifications, while that of skipjack tuna remained relatively homogeneous. Finally, our results suggest that the gut bacteriome of marine fish may not always be subject to structural modifications during their growth, especially in species that maintain a steady feeding behavior during their lifetime.},
}
@article {pmid34069990,
year = {2021},
author = {Ansorge, R and Birolo, G and James, SA and Telatin, A},
title = {Dadaist2: A Toolkit to Automate and Simplify Statistical Analysis and Plotting of Metabarcoding Experiments.},
journal = {International journal of molecular sciences},
volume = {22},
number = {10},
pages = {},
pmid = {34069990},
issn = {1422-0067},
support = {BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; BB/R506552/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/T030062/1//UK Research and Innovation/ ; },
mesh = {Algorithms ; Cluster Analysis ; Computational Biology/methods ; DNA Barcoding, Taxonomic/*statistics &amp; numerical data ; Data Interpretation, Statistical ; High-Throughput Nucleotide Sequencing ; Metadata ; Metagenomics/*statistics &amp; numerical data ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Software ; },
abstract = {The taxonomic composition of microbial communities can be assessed using universal marker amplicon sequencing. The most common taxonomic markers are the 16S rDNA for bacterial communities and the internal transcribed spacer (ITS) region for fungal communities, but various other markers are used for barcoding eukaryotes. A crucial step in the bioinformatic analysis of amplicon sequences is the identification of representative sequences. This can be achieved using a clustering approach or by denoising raw sequencing reads. DADA2 is a widely adopted algorithm, released as an R library, that denoises marker-specific amplicons from next-generation sequencing and produces a set of representative sequences referred to as 'Amplicon Sequence Variants' (ASV). Here, we present Dadaist2, a modular pipeline, providing a complete suite for the analysis that ranges from raw sequencing reads to the statistics of numerical ecology. Dadaist2 implements a new approach that is specifically optimised for amplicons with variable lengths, such as the fungal ITS. The pipeline focuses on streamlining the data flow from the command line to R, with multiple options for statistical analysis and plotting, both interactive and automatic.},
}
@article {pmid34065552,
year = {2021},
author = {Kartavtsev, YP},
title = {Some Examples of the Use of Molecular Markers for Needs of Basic Biology and Modern Society.},
journal = {Animals : an open access journal from MDPI},
volume = {11},
number = {5},
pages = {},
pmid = {34065552},
issn = {2076-2615},
abstract = {Application of molecular genetic markers appeared to be very fruitful in achieving many goals, including (i) proving the theoretic basements of general biology and (ii) assessment of worldwide biodiversity. Both are provided in the present meta-analysis and a review as the main signal. One of the basic current challenges in modern biology in the face of new demands in the 21st century is the validation of its paradigms such as the synthetic theory of evolution (STE) and biological species concept (BSC). Another of most valuable goals is the biodiversity assessment for a variety of social needs including free web-based information resources about any living being, renovation of museum collections, nature conservation that recognized as a global project, iBOL, as well as resolving global trading problems such as false labeling of species specimens used as food, drug components, entertainment, etc. The main issues of the review are focused on animals and combine four items. (1) A combination of nDNA and mtDNA markers best suits the identification of hybrids and estimation of genetic introgression. (2) The available facts on nDNA and mtDNA diversity seemingly make introgression among many taxa obvious, although it is evident, that introgression may be quite restricted or asymmetric, thus, leaving at least the "source" taxon (taxa) intact. (3) If we consider sexually reproducing species in marine and terrestrial realms introgressed, as it is still evident in many cases, then we should recognize that the BSC, in view of the complete lack of gene flow among species, is inadequate because many zoological species are not biological ones yet. However, vast modern molecular data have proven that sooner or later they definitely become biological species. (4) An investigation into the fish taxa divergence using the BOLD database shows that most gene trees are basically monophyletic and interspecies reticulations are quite rare.},
}
@article {pmid34065394,
year = {2021},
author = {Adams, SJ and Robicheau, BM and LaRue, D and Browne, RD and Walker, AK},
title = {Foliar Endophytic Fungi from the Endangered Eastern Mountain Avens (Geum peckii, Rosaceae) in Canada.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {5},
pages = {},
pmid = {34065394},
issn = {2223-7747},
support = {Discovery Grant 2017-04325//Natural Sciences and Engineering Research Council of Canada/ ; Martin-Baker Research Award//Mycological Society of America/ ; Habitat Conservation Fund//Nova Scotia Department of Natural Resources/ ; Research Grant//Nova Scotia Museum/ ; Research Grant//SAGE Environmental Fund/ ; Honours Student Research Award//Acadia University/ ; Student Scholarship//Arthur Irving Academy for the Environment/ ; },
abstract = {Eastern Mountain Avens (Geum peckii Pursh, Rosaceae) is a globally rare and endangered perennial plant found only at two coastal bogs within Digby County (Nova Scotia, Canada) and at several alpine sites in the White Mountains of New Hampshire (USA). In Canada, the G. peckii population has declined over the past forty years due in part to habitat degradation. We investigated the culturable foliar fungi present in G. peckii leaves at five locations with varying degrees of human impact within this plant species' Canadian range. Fungal identifications were made using ITS rDNA barcoding of axenic fungal cultures isolated from leaf tissue. Differences in foliar fungal communities among sites were documented, with a predominance of Gnomoniaceae (Class: Sordariomycetes, Phylum: Ascomycota). Habitats with more human impact showed lower endophytic diversities (10-16 species) compared to the pristine habitat (27 species). Intriguingly, several fungi may represent previously unknown taxa. Our work represents a significant step towards understanding G. peckii's mycobiome and provides relevant data to inform conservation of this rare and endangered plant.},
}
@article {pmid34062846,
year = {2021},
author = {Tian, Y and Zhou, J and Zhang, Y and Wang, S and Wang, Y and Liu, H and Wang, Z},
title = {Research Progress in Plant Molecular Systematics of Lauraceae.},
journal = {Biology},
volume = {10},
number = {5},
pages = {},
pmid = {34062846},
issn = {2079-7737},
abstract = {Lauraceae is a large family of woody plants with high ecological and economic value. The tribal and generic division and phylogenetic relationship of Lauraceae have long been controversial. Based on morphological and molecular evidence, phylogenetic relationships within the Cinnamomeae, Laureae and Perseeae tribes, also called 'the Core Lauraceae', have arisen particular attention. In this review, we comprehensively collated the literatures on the phylogeny of Lauraceae published in recent years and summarized progress made in molecular systematic researches employing gene fragments, chloroplast genomes and DNA barcodings analyses. We clarified the phylogenetic relationships and main controversies of 'the Core Lauraceae', the systemic position of fuzzy genera (Neocinnamomum, Caryodaphnopsis and Cassytha) and the development of chloroplast genome and DNA barcodes. We further suggested and proposed the whole genome analysis and different inflorescence types would be possible to provide more information for further research on phylogenetic relationships and taxonomy of Lauraceae.},
}
@article {pmid34062023,
year = {2021},
author = {Zhang, Y and Zheng, Y and Meana, Y and Raymo, FM},
title = {BODIPYs with Photoactivatable Fluorescence.},
journal = {Chemistry (Weinheim an der Bergstrasse, Germany)},
volume = {27},
number = {44},
pages = {11257-11267},
doi = {10.1002/chem.202101628},
pmid = {34062023},
issn = {1521-3765},
support = {CHE-1954430//National Science Foundation/ ; },
mesh = {*Boron Compounds ; Fluorescence ; *Fluorescent Dyes ; },
abstract = {The borondipyrromethene (BODIPY) chromophore is a versatile platform for the construction of photoresponsive dyes with unique properties. Specifically, its covalent connection to a photocleavable group can be exploited to engineer compounds with photoswitchable fluorescence. The resulting photoactivatable fluorophores can increase their emission intensity or shift their emission wavelengths in response to switching. Such changes permit the spatiotemporal control of fluorescence with optical stimulations and the implementation of imaging strategies that would be impossible to replicate with conventional fluorophores. Indeed, BODIPYs with photoactivatable fluorescence enable the selective highlighting of intracellular targets, the nanoscaled visualization of sub-cellular components, the real-time monitoring of dynamic events and the photochemical writing of optical barcodes.},
}
@article {pmid34057730,
year = {2021},
author = {Tak, T and Eisele, AS and Perié, L},
title = {In Vivo Tracking of Hematopoietic Stem and Progenitor Cell Ontogeny by Cellular Barcoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2308},
number = {},
pages = {281-300},
pmid = {34057730},
issn = {1940-6029},
mesh = {Animals ; *Cell Lineage ; Cell Proliferation ; Cell Separation ; *Cell Tracking ; Genetic Vectors ; HEK293 Cells ; *Hematopoiesis ; *Hematopoietic Stem Cell Transplantation ; Hematopoietic Stem Cells/*physiology ; *High-Throughput Nucleotide Sequencing ; Humans ; Lentivirus/genetics ; Mice ; Mice, Transgenic ; Phenotype ; Polymerase Chain Reaction ; *Transduction, Genetic ; },
abstract = {Cellular barcoding is a powerful technique that allows for high-throughput mapping of the fate of single cells, notably hematopoietic stem and progenitor cells (HSPCs) after transplantation. Unique artificial DNA fragments, termed barcodes, are stably inserted into HSPCs using lentiviral transduction, making sure that each individual cell receives a single unique barcode. Barcoded HSPCs are transplanted into sublethally irradiated mice where they reconstitute the hematopoietic system through proliferation and differentiation. During this process, the barcode of each HSPC is inherited by all of its daughter cells and their subsequent mature hematopoietic cell progeny. After sorting mature hematopoietic cell subsets, their barcodes can be retrieved from genomic DNA through nested PCR and sequencing. Analysis of barcode sequencing results allows for determination of clonal relationships between the mature cells, that is, which cell types were produced by a single barcoded HSPC, as well as the heterogeneity of the initial HSPC population. Here, we give a detailed protocol of a complete HSPC cellular barcoding experiment, starting with barcode lentivirus production, isolation, transduction, and transplantation of HSPCs, isolation of target cells followed by PCR amplification and sequencing of DNA barcodes. Finally, we describe the basic filtering and analysis steps of barcode sequencing data to ensure high-quality results.},
}
@article {pmid34057354,
year = {2021},
author = {Munakata, M and Tanaka, H and Kakui, K},
title = {Heterocypris spadix sp. nov. (Crustacea: Ostracoda: Cypridoidea) from Japan, with Information on Its Reproductive Mode.},
journal = {Zoological science},
volume = {38},
number = {3},
pages = {287-296},
doi = {10.2108/zs200127},
pmid = {34057354},
issn = {0289-0003},
mesh = {Animals ; Crustacea/classification/*genetics/physiology/ultrastructure ; Female ; Japan ; Male ; Reproduction ; Species Specificity ; },
abstract = {We describe the cypridoidean ostracod Heterocypris spadix sp. nov. from brackish water on Okinawa Island, Japan. The species closely resembles Heterocypris salina (Brady, 1868) but differs in that (1) the marginal infolds on valves are less developed, (2) the tubercles on the anterior margin of the right valve are completely covered by the selvage and invisible in inner view, and (3) the calcified inner lamella on the ventral margin of the left and right valves is scarcely evident in inner view, as the ventral margins of the valves bend inwardly. We determined partial sequences for the cytochrome c oxidase subunit I (COI; cox1) and 18S rRNA genes in H. spadix for future DNA barcoding and phylogenetic analyses. Our sample contained only females. A breeding experiment revealed that H. spadix females reproduce parthenogenetically. Another experiment showed that H. spadix has low tolerance to desiccation, with all individuals at 25°C dying between 1-2 hours after removal from water. We amplified and sequenced a partial 16S rRNA sequence for the endosymbiotic bacterium Cardinium from H. spadix. Infection by Cardinium may be related to the parthenogenetic reproductive mode we observed in H. spadix.},
}
@article {pmid34057346,
year = {2021},
author = {Watanabe, HK and Senokuchi, R and Nomaki, H and Kitahashi, T and Uyeno, D and Shimanaga, M},
title = {Distribution and Genetic Divergence of Deep-Sea Hydrothermal Vent Copepods (Dirivultidae: Siphonostomatoida: Copepoda) in the Northwestern Pacific.},
journal = {Zoological science},
volume = {38},
number = {3},
pages = {223-230},
doi = {10.2108/zs200153},
pmid = {34057346},
issn = {0289-0003},
mesh = {*Animal Distribution ; Animals ; Copepoda/*genetics ; *Genetic Variation ; *Hydrothermal Vents ; Pacific Ocean ; Phylogeny ; },
abstract = {Copepods in the family Dirivultidae are one of the most successful meiofauna in deep-sea hydrothermal vent fields and are abundant near venting fluid. Although vents are spatially limited ocean habitats, they are distributed widely in the Atlantic, Pacific, and Indian Oceans. However, knowledge of dirivultid biogeography and phylogeography remains limited, especially in the northwestern Pacific. Here, we obtained partial mitochondrial COI gene sequences of three dirivultids from the northwestern Pacific-Stygiopontius senokuchiae and an unidentified Chasmatopontius species from vent fields in the Izu-Bonin Arc and Stygiopontius senckenbergi associated with the squat lobster Shinkaia crosnieri in the Okinawa Trough-and analyzed them in comparison with existing data. The among-species sequence diversity exceeded 80 out of 560 bp (14% or 0.166 in Kimura 2-parameter distance), whereas the within-species diversity was less than 10 bp (2% or 0.018 in Kimura 2-parameter distance), with no genetic saturation. Each species formed a monophyletic clade and the genetic region targeted is deemed reliable for identifying species and populations for these copepods. Among the three genera targeted, only Chasmatopontius formed a monophyletic cluster, while Aphotopontius and Stygiopontius did not. Species delimitation analyses suggested the existence of cryptic species in Chasmatopontius. Subdivision among local populations was observed in Aphotopontius, but not in Stygiopontius in the same distribution, implying potential differences in dispersal ability among different genera of dirivultids. Further sampling is required, to fill the spatial gaps to elucidate the biogeography and evolution of dirivultids in the global deep ocean.},
}
@article {pmid34054773,
year = {2021},
author = {Aigle, A and Bourgeois, E and Marjolet, L and Houot, S and Patureau, D and Doelsch, E and Cournoyer, B and Galia, W},
title = {Relative Weight of Organic Waste Origin on Compost and Digestate 16S rRNA Gene Bacterial Profilings and Related Functional Inferences.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {667043},
pmid = {34054773},
issn = {1664-302X},
abstract = {Even though organic waste (OW) recycling via anaerobic digestion (AD) and composting are increasingly used, little is known about the impact of OW origin (fecal matters and food and vegetable wastes) on the end products' bacterial contents. The hypothesis of a predictable bacterial community structure in the end products according to the OW origin was tested. Nine OW treatment plants were selected to assess the genetic structure of bacterial communities found in raw OW according to their content in agricultural and urban wastes and to estimate their modifications through AD and composting. Two main bacterial community structures among raw OWs were observed and matched a differentiation according to the occurrences of urban chemical pollutants. Composting led to similar 16S rRNA gene OTU profiles whatever the OW origin. With a significant shift of about 140 genera (representing 50% of the bacteria), composting was confirmed to largely shape bacterial communities toward similar structures. The enriched taxa were found to be involved in detoxification and bioremediation activities. This process was found to be highly selective and favorable for bacterial specialists. Digestates showed that OTU profiles differentiated into two groups according to their relative content in agricultural (manure) and urban wastes (mainly activated sludge). About one third of the bacterial taxa was significantly affected by AD. In digestates of urban OW, this sorting led to an enrichment of 32 out of the 50 impacted genera, while for those produced from agricultural or mixed urban/agricultural OW (called central OW), a decay of 54 genera over 60 was observed. Bacteria from activated sludge appeared more fit for AD than those of other origins. Functional inferences showed AD enriched genera from all origins to share similar functional traits, e.g., chemoheterotrophy and fermentation, while being often taxonomically distinct. The main functional traits among the dominant genera in activated sludge supported a role in AD. Raw OW content in activated sludge was found to be a critical factor for predicting digestate bacterial contents. Composting generated highly predictable and specialized community patterns whatever the OW origin. AD and composting bacterial changes were driven by functional traits selected by physicochemical factors such as temperature and chemical pollutants.},
}
@article {pmid34051839,
year = {2021},
author = {Kniha, E and Milchram, M and Dvořák, V and Halada, P and Obwaller, AG and Poeppl, W and Mooseder, G and Volf, P and Walochnik, J},
title = {Ecology, seasonality and host preferences of Austrian Phlebotomus (Transphlebotomus) mascittii Grassi, 1908, populations.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {291},
pmid = {34051839},
issn = {1756-3305},
support = {DOC Fellowship//&#xd6;sterreichischen Akademie der Wissenschaften/ ; BIOCEV CZ.1.05/1.1.00/02.0109//Interreg/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//Interreg/ ; },
mesh = {Animals ; Austria ; Chickens ; *Ecology ; Europe ; Female ; Horses ; *Insect Vectors/parasitology ; Leishmania infantum ; Male ; *Phlebotomus/genetics ; Psychodidae ; Retrospective Studies ; *Seasons ; Sequence Analysis, DNA ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {BACKGROUND: Sand flies are principal vectors of the protozoan parasites Leishmania spp. and are widely distributed in all warmer regions of the world, including the Mediterranean parts of Europe. In Central European countries, the sand fly fauna is still under investigation. Phlebotomus mascittii, a suspected but unproven vector of Leishmania infantum, is regarded as the most widely distributed species in Europe. However, many aspects of its biology and ecology remain poorly known. The aim of this study was to provide new data on the biology and ecology of Ph. mascittii in Austria to better understand its current distribution and potential dispersal.<br><br>METHODS: Sand flies were collected by CDC light traps at four localities in Austria for 11 (2018) and 15&#xa0;weeks (2019) during the active sand fly season. Climatic parameters (temperature, relative humidity, barometric pressure and wind speed) were retrospectively obtained for the trapping periods. Sand flies were identified by a combined approach (morphology, DNA barcoding, MALDI-TOF protein profiling), and blood meals of engorged females were analysed by DNA sequencing and MALDI-TOF mass spectrometry.<br><br>RESULTS: In total, 450 individuals of Ph. mascittii were caught. Activity was observed to start at the beginning of June and end at the end of August with peaks in mid-July at three locations and early August at one location. Increased activity was associated with relatively high temperatures and humidity. Also, more individuals were caught on nights with low barometric pressure. Analysis of five identified blood meals revealed chicken (Gallus gallus) and equine (Equus spp.) hosts. Sand fly abundance was generally associated with availability of hosts.<br><br>CONCLUSION: This study reports unexpectedly high numbers of Ph. mascittii at selected Austrian localities and provides the first detailed analysis of its ecology to date. Temperature and humidity were shown to be good predictors for sand fly activity. Blood meal analyses support the assumption that Ph. mascittii feeds on mammals as well as birds. The study significantly contributes to understanding the ecology of this sand fly species in Central Europe and facilitates prospective entomological surveys.},
}
@article {pmid34051130,
year = {2021},
author = {Bakran-Lebl, K and Zittra, C and Harl, J and Shahi-Barogh, B and Grätzl, A and Ebmer, D and Schaffner, F and Fuehrer, HP},
title = {Arrival of the Asian tiger mosquito, Aedes albopictus (Skuse, 1895) in Vienna, Austria and initial monitoring activities.},
journal = {Transboundary and emerging diseases},
volume = {68},
number = {6},
pages = {3145-3150},
doi = {10.1111/tbed.14169},
pmid = {34051130},
issn = {1865-1682},
mesh = {*Aedes/genetics ; Animals ; Austria ; Cities ; Haplotypes ; },
abstract = {Aedes albopictus was recorded in Vienna, Austria, in August 2020 for the first time. The species was found to occur in three sites within the city; morphology-based monitoring was followed by DNA-barcoding. Mitochondrial COI barcode sequences recovered three different haplotypes, however this data does not reveal whether single or multiple introduction events have occurred. The vicinity of Viennese Ae. albopictus sites to major traffic routes highlights the importance of passive transport for range expansion of this species.},
}
@article {pmid34050232,
year = {2021},
author = {Everts, T and Halfmaerten, D and Neyrinck, S and De Regge, N and Jacquemyn, H and Brys, R},
title = {Accurate detection and quantification of seasonal abundance of American bullfrog (Lithobates catesbeianus) using ddPCR eDNA assays.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {11282},
pmid = {34050232},
issn = {2045-2322},
mesh = {Animals ; Biodiversity ; DNA, Environmental/genetics ; Environmental Monitoring/*methods ; Europe ; Fresh Water ; Introduced Species/trends ; Polymerase Chain Reaction/methods ; Ponds ; Rana catesbeiana/*genetics ; Seasons ; },
abstract = {The invasive American bullfrog (Lithobates catesbeianus) imperils freshwater biodiversity worldwide. Effective management hinges on early detection of incipient invasions and subsequent rapid response, as established populations are extremely difficult to eradicate. Although environmental DNA (eDNA) detection methods provide a highly sensitive alternative to conventional surveillance techniques, extensive testing is imperative to generate reliable output. Here, we tested and compared the performance of two primer/probe assays to detect and quantify the abundance of bullfrogs in Western Europe in silico and in situ using digital droplet PCR (ddPCR). Although both assays proved to be equally target-specific and sensitive, one outperformed the other in ddPCR detection resolution (i.e., distinguishing groups of target-positive and target-negative droplets), and hence was selected for further analyses. Mesocosm experiments revealed that tadpole abundance and biomass explained 99% of the variation in eDNA concentration. Because per individual eDNA emission rates did not differ significantly among tadpoles and juveniles, and adults mostly reside out of the water, eDNA concentration can be used as an approximation of local bullfrog abundance in natural populations. Seasonal eDNA patterns in three colonized ponds showed parallel fluctuations in bullfrog eDNA concentration. An increase in eDNA concentration was detected in spring, followed by a strong peak coinciding with the breeding season (August, September or October), and continuously low eDNA concentrations during winter. With this study, we report the validation process required for appropriately implementing eDNA barcoding analyses in lentic systems. We demonstrate that this technique can serve as a solid and reliable tool to detect the early stages of bullfrog invasions and to quantify temporal changes in abundance that will be useful in coordinating large-scale bullfrog eradication programs and evaluating their efficiency.},
}
@article {pmid34048789,
year = {2021},
author = {Gutierrez, MAC and Lopez, ROH and Ramos, AT and Vélez, ID and Gomez, RV and Arrivillaga-Henríquez, J and Uribe, S},
title = {DNA barcoding of Lutzomyia longipalpis species complex (Diptera: Psychodidae), suggests the existence of 8 candidate species.},
journal = {Acta tropica},
volume = {221},
number = {},
pages = {105983},
doi = {10.1016/j.actatropica.2021.105983},
pmid = {34048789},
issn = {1873-6254},
mesh = {Animals ; Bayes Theorem ; Brazil ; *DNA Barcoding, Taxonomic ; Humans ; *Leishmaniasis, Cutaneous ; *Leishmaniasis, Visceral/transmission ; Mosquito Vectors ; Phylogeny ; *Psychodidae/genetics ; },
abstract = {The sand fly Lutzomyia (L.) longipalpis has been implicated as the primary vector of Leishmania infantum, the causative agent of visceral leishmaniasis VL. In addition, it has been associated with atypical cutaneous leishmaniasis transmission in the Neotropic and Central America, respectively. The existence of a L. longipalpis complex species has been suggested with important implications for leishmaniasis epidemiology; however, the delimitation of species conforming it remains a topic of controversy. The DNA Barcoding Initiative based on cox1 sequence variation was used to identify the MOTUs in L. longipalpis including previously described L. pseudolongipalpis. The genetic variation was analyzed based on tree and distance methods. Fifty-five haplotypes were obtained from 103 sequences which were assigned to MOTUs, with a clear separation and a high correspondence of individuals to the groups. Maximum likelihood and Bayesian phylogenetic analysis showed eight MOTUs (100% bootstrap) with high genetic divergence (12.6%). Data obtained in the present study suggest that L. longipalpis complex consists of at least 8 lineages that may represent species. It would be desirable perform additional morphological and molecular analysis of L. longipalpis from Colosó (Caribbean ecoregion) considering that specimens from that area were grouped with L. pseudolongipalpis one of the complex species previously described from Venezuela, which has not been registered in Colombia.},
}
@article {pmid34047286,
year = {2021},
author = {Maheswari, P and Kunhikannan, C and Yasodha, R},
title = {Chloroplast genome analysis of Angiosperms and phylogenetic relationships among Lamiaceae members with particular reference to teak (Tectona grandis L.f).},
journal = {Journal of biosciences},
volume = {46},
number = {},
pages = {},
pmid = {34047286},
issn = {0973-7138},
mesh = {Biological Evolution ; Chloroplasts/*genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Intergenic/genetics ; Genetic Variation ; Genome Size ; *Genome, Chloroplast ; *Genome, Plant ; Lamiaceae/classification/*genetics ; Microsatellite Repeats ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Availability of comprehensive phylogenetic tree for flowering plants which includes many of the economically important crops and trees is one of the essential requirements of plant biologists for diverse applications. It is the first study on the use of chloroplast genome of 3265 Angiosperm taxa to identify evolutionary relationships among the plant species. Sixty genes from chloroplast genome was concatenated and utilized to generate the phylogenetic tree. Overall the phylogeny was in correspondence with Angiosperm Phylogeny Group (APG) IV classification with very few taxa occupying incongruous position either due to ambiguous taxonomy or incorrect identification. Simple sequence repeats (SSRs) were identified from almost all the taxa indicating the possibility of their use in various genetic analyses. Large proportion (95.6%) of A/T mononucleotide was recorded while the di, tri, tetra, penta and hexanucleotide amounted to less than 5%. Ambiguity of the taxonomic status of Tectona grandis L.f was assessed by comparing the chloroplast genome with closely related Lamiaceae members through nucleotide diversity and contraction/expansion of inverted repeat regions. Although the gene content was highly conserved, structural changes in the genome was evident. Phylogenetic analysis suggested that Tectona could qualify for a subfamily Tectonoideae. Nucleotide diversity in intergenic and genic sequences revealed prominent hyper-variable regions such as, rps16-trnQ, atpH-atpI, psc4-psbJ, ndhF, rpl32 and ycf1 which have high potential in DNA barcoding applications.},
}
@article {pmid34047118,
year = {2021},
author = {Zhang, Y and Song, MF and Li, HT and Sun, HF and Zhang, ZL},
title = {[DNA barcoding identification of original plants of a rare medicinal material Resina Draconis and related Dracaena species].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {46},
number = {9},
pages = {2173-2181},
doi = {10.19540/j.cnki.cjcmm.20210124.104},
pmid = {34047118},
issn = {1001-5302},
mesh = {China ; DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; *Dracaena/genetics ; Plants ; Resins, Plant ; Sequence Analysis, DNA ; },
abstract = {Resina Draconis, a rare and precious traditional medicine in China, is known as the "holy medicine for promoting blood circulation". According to the national drug standard, it's derived from the resin extracted from the wood of Dracaena cochinchinensis, a Liliaceae plant. In addition, a variety of Dracaena species all over the world can form red resins, and there is currently no molecular identification method that can efficiently identify the origin of Dracaena medicinal materials. In this study, seven species of Dracaena distributed in China were selected as the research objects. Four commonly used DNA barcodes(ITS2, matK, rbcL and psbA-trnH), and four highly variable regions(trnP-psaJ, psbK-psbI, trnT-trnL, clpP) in chloroplast genome were used to evaluate the identification efficiency of Dracaena species. The results showed that clpP sequence fragment could accurately identify seven species of Dracaena plants. However, due to the long sequence of clpP fragment, there were potential problems in the practical application process. We found that the combined fragment "psbK-psbI+ trnP-psaJ" can also be used for accurate molecular identification of the Resina Draconis origin plants and relative species of Dracaena, which were both relatively short sequences in the combined fragment, showing high success rates of amplification and sequencing. Therefore, the "psbK-psbI+ trnP-psaJ" combined fragment can be used as the DNA barcode fragments for molecular identification of Resina Dracon's origin plants and relative species of Dracaena. Research on the identification of Dracaena species, the results of this study can be used to accurately identify the original material of Resina Draconis, and providing effective means for identification, rational development and application of Resina Draconis base source.},
}
@article {pmid34046252,
year = {2021},
author = {Moraes, SS and Montebello, Y and Stanton, MA and Yamaguchi, LF and Kato, MJ and Freitas, AVL},
title = {Description of three new species of Geometridae (Lepidoptera) using species delimitation in an integrative taxonomy approach for a cryptic species complex.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e11304},
pmid = {34046252},
issn = {2167-8359},
abstract = {The genus Eois Hbner (Geometridae: Larentiinae) comprises 254 valid species, 217 of which were described from the Neotropics and 31 of those having their type locality in Brazil. Since this species rich genus has never been revised, and may potentially include many cryptic undescribed species, Eois embodies a problematic taxonomic scenario. The actual diversity of Eois is greatly underestimated and the Brazilian fauna is poorly known, both because of inadequate sampling and because of the potential existence of cryptic species "hidden" within some nominal taxa. In this study we investigated the diversity within a cryptic species complexes associated to the E. pallidicosta and E. odatis clades. We describe three new species Eois oya Moraes &amp; Montebello sp. nov., Eois ewa Moraes &amp; Stanton sp. nov., and Eois oxum Moraes &amp; Freitas sp. nov., in an integrative taxonomy approach, using morphology, host plant use and species delimitation tools.},
}
@article {pmid34046055,
year = {2021},
author = {Letiagina, AE and Omelina, ES and Ivankin, AV and Pindyurin, AV},
title = {MPRAdecoder: Processing of the Raw MPRA Data With a priori Unknown Sequences of the Region of Interest and Associated Barcodes.},
journal = {Frontiers in genetics},
volume = {12},
number = {},
pages = {618189},
pmid = {34046055},
issn = {1664-8021},
abstract = {Massively parallel reporter assays (MPRAs) enable high-throughput functional evaluation of numerous DNA regulatory elements and/or their mutant variants. The assays are based on the construction of reporter plasmid libraries containing two variable parts, a region of interest (ROI) and a barcode (BC), located outside and within the transcription unit, respectively. Importantly, each plasmid molecule in a such a highly diverse library is characterized by a unique BC-ROI association. The reporter constructs are delivered to target cells and expression of BCs at the transcript level is assayed by RT-PCR followed by next-generation sequencing (NGS). The obtained values are normalized to the abundance of BCs in the plasmid DNA sample. Altogether, this allows evaluating the regulatory potential of the associated ROI sequences. However, depending on the MPRA library construction design, the BC and ROI sequences as well as their associations can be a priori unknown. In such a case, the BC and ROI sequences, their possible mutant variants, and unambiguous BC-ROI associations have to be identified, whereas all uncertain cases have to be excluded from the analysis. Besides the preparation of additional "mapping" samples for NGS, this also requires specific bioinformatics tools. Here, we present a pipeline for processing raw MPRA data obtained by NGS for reporter construct libraries with a priori unknown sequences of BCs and ROIs. The pipeline robustly identifies unambiguous (so-called genuine) BCs and ROIs associated with them, calculates the normalized expression level for each BC and the averaged values for each ROI, and provides a graphical visualization of the processed data.},
}
@article {pmid34045917,
year = {2021},
author = {Chen, Z and Li, D and Li, D and Xu, X},
title = {Three new species of the primitively segmented spider genus Songthela (Araneae, Mesothelae) from Guizhou Province, China.},
journal = {ZooKeys},
volume = {1037},
number = {},
pages = {57-71},
pmid = {34045917},
issn = {1313-2989},
abstract = {We diagnose and describe three new species of the primitively segmented spider genus Songthela from Guizhou Province, China, based on morphological characters and molecular data: S. liui sp. nov. (♂♀), S. tianzhu sp. nov. (♂♀), and S. yuping sp. nov. (♂♀). We provide the genetic distances within and among the three new species based on the DNA barcode gene, cytochrome c oxidase subunit I (COI) to support our descriptions. We also provide the COI GenBank accession codes for the three new species for future identification.},
}
@article {pmid34044886,
year = {2021},
author = {Stec, D and Vecchi, M and Dudziak, M and Bartels, PJ and Calhim, S and Michalczyk, &#x141;},
title = {Integrative taxonomy resolves species identities within the Macrobiotus pallarii complex (Eutardigrada: Macrobiotidae).},
journal = {Zoological letters},
volume = {7},
number = {1},
pages = {9},
pmid = {34044886},
issn = {2056-306X},
support = {2018/31/N/NZ8/03096//Narodowe Centrum Nauki/ ; 2016/22/E/NZ8/00417//Narodowe Centrum Nauki/ ; },
abstract = {The taxonomy of many groups of meiofauna is challenging due to their low number of diagnostic morphological characters and their small body size. Therefore, with the advent of molecular techniques that provide a new source of traits, many cryptic species have started to be discovered. Tardigrades are not an exception, and many once thought to be cosmopolitan taxa are being found to be complexes of phenotypically similar species. Macrobiotus pallarii Maucci, 1954 was originally described in South Italy and has been subsequently recorded in Europe, America, and Asia. This allegedly wide geographic range suggests that multiple species may be hidden under this name. Moreover, recently, genetic evidence to support this was put forward, and the Macrobiotus pallarii complex has been proposed to accommodate putative species related to M. pallarii. Here, we describe three new pseudocryptic species based on populations that would have been all classified as Macrobiotus pallarii if molecular methods were not employed. Using an integrative taxonomy approach, we analyzed animals and eggs from the topotypic population of Macrobiotus pallarii, together with four other populations of the complex. We recovered four distinct phylogenetic lineages that, despite the overlap of morphometric traits, can be separated phenotypically by subtle but discrete morphological characters. One lineage corresponds to Macrobiotus pallarii, whereas the other three are newly described as Macrobiotus margoae Stec, Vecchi &amp; Bartels, sp. nov. from the USA, Macrobiotus ripperi Stec, Vecchi &amp; Michalczyk, sp. nov. from Poland and Finland, and Macrobiotus pseudopallarii Stec, Vecchi &amp; Michalczyk, sp. nov. from Montenegro. To facilitate species identification, we provide a dichotomous key for species of the M. pallarii complex. Delimitation of these pseudocryptic taxa highlights the need for an integrative approach to uncover the phylum's diversity in full.},
}
@article {pmid34043636,
year = {2021},
author = {Lehikoinen, A and Pohjola, P and Valkama, J and Mutanen, M and Pohjoismäki, JLO},
title = {Promiscuous specialists: Host specificity patterns among generalist louse flies.},
journal = {PloS one},
volume = {16},
number = {5},
pages = {e0247698},
pmid = {34043636},
issn = {1932-6203},
mesh = {Animals ; Birds/*parasitology ; DNA Barcoding, Taxonomic ; Diptera/classification/genetics/*physiology ; Ecosystem ; Finland ; Host Specificity/*physiology ; Phylogeny ; },
abstract = {Ectoparasites such as louse flies (Diptera: Hippoboscidae) have tendency for host specialization, which is driven by adaptation to host biology as well as competition avoidance between parasites of the same host. However, some louse fly species, especially in genera attacking birds, show wide range of suitable hosts. In the presented study, we have surveyed the current status of bird specific louse flies in Finland to provide comprehensive host association data to analyse the ecological requirements of the generalist species. A thorough sampling of 9342 birds, representing 134 species, recovered 576 specimens of louse flies, belonging to six species: Crataerina hirundinis, C. pallida, Ornithomya avicularia, O. chloropus, O. fringillina and Ornithophila metallica. Despite some overlapping hosts, the three Ornithomya species showed a notable pattern in their host preference, which was influenced not only by the host size but also by the habitat and host breeding strategy. We also provide DNA barcodes for ten Finnish species of Hippoboscidae, which can be used as a resource for species identification as well as metabarcoding studies in the future.},
}
@article {pmid34040896,
year = {2021},
author = {Zangl, L and Glatzhofer, E and Schmid, R and Randolf, S and Koblmüller, S},
title = {DNA barcoding of Austrian snow scorpionflies (Mecoptera, Boreidae) reveals potential cryptic diversity in Boreus westwoodi.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e11424},
pmid = {34040896},
issn = {2167-8359},
abstract = {BACKGROUND: Snow scorpionflies (genus Boreus) belong to a family of Mecoptera, Boreidae, that has been vastly neglected by entomological researchers due to their shift in seasonality to the winter months. Their activity during this time is regarded as a strategy for predator avoidance and regular sightings on snow fields suggest that this also facilitates dispersal. However, many aspects about snow scorpionflies, especially systematics, taxonomy, distribution of species, phylogenetics and phylogeography have remained fairly unexplored until today. In this study, we fill some of these gaps by generating a reference DNA barcode database for Austrian snow scorpionflies in the frame of the Austrian Barcode of Life initiative and by characterising morphological diversity in the study region.<br><br>METHODS: Initial species assignment of all 67 specimens was based on male morphological characters previously reported to differ between Boreus species and, for females, the shape of the ovipositor. DNA barcoding of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene was carried out for all 67 samples and served as a basis for BIN assignment, genetic distance calculations, as well as alternative species delimitation analyses (ABGD, GMYC, bGMYC, bPTP) and a statistical parsimony network to infer phylogenetic relationships among individual samples/sampling sites.<br><br>RESULTS: Morphological investigations suggested the presence of both Boreus hyemalis and Boreus westwoodi in Austria. DNA barcoding also separated the two species, but resulted in several divergent clades, the paraphyly of B. westwoodi in Austria, and high levels of phylogeographic structure on a small geographic scale. Even though the different molecular species delimitation methods disagreed on the exact number of species, they unequivocally suggested the presence of more than the traditionally recognized two Boreus species in Austria, thus indicating potential cryptic species within the genus Boreus in general and especially in B. westwoodi.},
}
@article {pmid34040491,
year = {2021},
author = {Herrera Mesías, F and Weigand, AM},
title = {Updates to the checklist of the wild bee fauna of Luxembourg as inferred from revised natural history collection data and fieldwork.},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e64027},
pmid = {34040491},
issn = {1314-2828},
abstract = {BACKGROUND: Museums and other institutions curating natural history collections (NHCs) are fundamental entities to many scientific disciplines, as they house data and reference material for varied research projects. As such, biological specimens preserved in NHCs represent accessible physical records of the living world's history. They provide useful information regarding the presence and distribution of different taxonomic groups through space and time. Despite the importance of biological museum specimens, their potential to answer scientific questions, pertinent to the necessities of our current historical context, is often under-explored.The currently-known wild bee fauna of Luxembourg comprises 341 registered species distributed amongst 38 different genera. However, specimens stored in the archives of local NHCs represent an untapped resource to update taxonomic lists, including potentially overlooked findings relevant to the development of national conservation strategies.<br><br>NEW INFORMATION: We re-investigated the wild bee collection of the Zoology Department of the National Museum of Natural History Luxembourg by using morphotaxonomy and DNA barcoding. The collection revision led to the discovery of four species so far not described for the country: Andrena lagopus (Latreille, 1809), Nomada furva (Panzer, 1798), Hoplitis papaveris (Latreille, 1799) and Sphecodes majalis (P&#xe9;rez, 1903). Additionally, the presence of Nomada sexfasciata (Panzer, 1799), which inexplicably had been omitted by the most current species list, can be re-confirmed. Altogether, our findings increase the number of recorded wild bee species in Luxembourg to 346. Moreover, the results highlight the crucial role of NHCs as repositories of our knowledge of the natural world.},
}
@article {pmid34040000,
year = {2021},
author = {Patwardhan, GA and Marczyk, M and Wali, VB and Stern, DF and Pusztai, L and Hatzis, C},
title = {Treatment scheduling effects on the evolution of drug resistance in heterogeneous cancer cell populations.},
journal = {NPJ breast cancer},
volume = {7},
number = {1},
pages = {60},
pmid = {34040000},
issn = {2374-4677},
support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; },
abstract = {The effect of scheduling of targeted therapy combinations on drug resistance is underexplored in triple-negative breast cancer (TNBC). TNBC constitutes heterogeneous cancer cell populations the composition of which can change dynamically during treatment resulting in the selection of resistant clones with a fitness advantage. We evaluated crizotinib (ALK/MET inhibitor) and navitoclax (ABT-263; Bcl-2/Bcl-xL inhibitor) combinations in a large design consisting of 696 two-cycle sequential and concomitant treatment regimens with varying treatment dose, duration, and drug holiday length over a 26-day period in MDA-MB-231 TNBC cells and found that patterns of resistance depend on the schedule and sequence in which the drugs are given. Further, we tracked the clonal dynamics and mechanisms of resistance using DNA-integrated barcodes and single-cell RNA sequencing. Our study suggests that longer formats of treatment schedules in vitro screening assays are required to understand the effects of resistance and guide more realistically in vivo and clinical studies.},
}
@article {pmid34036265,
year = {2021},
author = {Liu, P and Mu, Z and Ji, M and Liu, X and Gu, H and Peng, Y and Yang, J and Xie, Z and Zheng, F},
title = {Robust Carbonated Structural Color Barcodes with Ultralow Ontology Fluorescence as Biomimic Culture Platform.},
journal = {Research (Washington, D.C.)},
volume = {2021},
number = {},
pages = {9851609},
pmid = {34036265},
issn = {2639-5274},
abstract = {Photonic crystal (PC) barcodes are a new type of spectrum-encoding microcarriers used in multiplex high-throughput bioassays, such as broad analysis of biomarkers for clinical diagnosis, gene expression, and cell culture. Unfortunately, most of these existing PC barcodes suffered from undesired features, including difficult spectrum-signal acquisition, weak mechanical strength, and high ontology fluorescence, which limited their development to real applications. To address these limitations, we report a new type of structural color-encoded PC barcodes. The barcodes are fabricated by the assembly of monodisperse polydopamine- (PDA-) coated silica (PDA@SiO2) nanoparticles using a droplet-based microfluidic technique and followed by pyrolysis of PDA@SiO2 (C@SiO2) barcodes. Because of the templated carbonization of adhesive PDA, the prepared C@SiO2 PC beads were endowed with simultaneous easy-to-identify structural color, high mechanical strength, and ultralow ontology fluorescence. We demonstrated that the structural colored C@SiO2 barcodes not only maintained a high structural stability and good biocompatibility during the coculturing with fibroblasts and tumor cells capture but also achieved an enhanced fluorescent-reading signal-to-noise ratio in the fluorescence-reading detection. These features make the C@SiO2 PC barcodes versatile for expansive application in fluorescence-reading-based multibioassays.},
}
@article {pmid34031609,
year = {2021},
author = {Ferrari, S and Beretta, S and Jacob, A and Cittaro, D and Albano, L and Merelli, I and Naldini, L and Genovese, P},
title = {BAR-Seq clonal tracking of gene-edited cells.},
journal = {Nature protocols},
volume = {16},
number = {6},
pages = {2991-3025},
pmid = {34031609},
issn = {1750-2799},
support = {Grant E4//Fondazione Telethon (Telethon Foundation)/ ; Grant E3//Fondazione Telethon (Telethon Foundation)/ ; PE-2016-02363691//Ministero della Salute (Ministry of Health, Italy)/ ; E-Rare-3 JTC 2017//Ministero della Salute (Ministry of Health, Italy)/ ; GR-2013-02358956//Ministero della Salute (Ministry of Health, Italy)/ ; PRIN 2017 Prot. 20175XHBN//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca (Ministry of Education, University and Research)/ ; UPGRADE//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 2019 Jeantet-Collen Prize for Translational Medicine//Louis-Jeantet Foundation (Fondation Louis-Jeantet)/ ; },
mesh = {Cell Tracking/*methods ; *Clone Cells ; DNA Barcoding, Taxonomic ; *Gene Editing ; *Software ; },
abstract = {Gene editing by engineered nucleases has revolutionized the field of gene therapy by enabling targeted and precise modification of the genome. However, the limited availability of methods for clonal tracking of edited cells has resulted in a paucity of information on the diversity, abundance and behavior of engineered clones. Here we detail the wet laboratory and bioinformatic BAR-Seq pipeline, a strategy for clonal tracking of cells harboring homology-directed targeted integration of a barcoding cassette. We present the BAR-Seq web application, an online, freely available and easy-to-use software that allows performing clonal tracking analyses on raw sequencing data without any computational resources or advanced bioinformatic skills. BAR-Seq can be applied to most editing strategies, and we describe its use to investigate the clonal dynamics of human edited hematopoietic stem/progenitor cells in xenotransplanted hosts. Notably, BAR-Seq may be applied in both basic and translational research contexts to investigate the biology of edited cells and stringently compare editing protocols at a clonal level. Our BAR-Seq pipeline allows library preparation and validation in a few days and clonal analyses of edited cell populations in 1 week.},
}
@article {pmid34031050,
year = {2021},
author = {Rovira-Vallbona, E and Van Hong, N and Kattenberg, JH and Huan, RM and Binh, NTH and Ngọc, NTH and Guetens, P and Hieu, NL and Hien, NTT and Sang, VT and Long, ND and Sauve, E and Duong, TT and Xa, NX and Erhart, A and Rosanas-Urgell, A},
title = {High Proportion of Genome-Wide Homology and Increased Pretreatment pvcrt Levels in Plasmodium vivax Late Recurrences: a Chloroquine Therapeutic Efficacy Study.},
journal = {Antimicrobial agents and chemotherapy},
volume = {65},
number = {8},
pages = {e0009521},
pmid = {34031050},
issn = {1098-6596},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Adult ; *Antimalarials/pharmacology/therapeutic use ; Chloroquine/therapeutic use ; Drug Resistance/genetics ; Humans ; *Malaria, Vivax/drug therapy ; Plasmodium vivax/genetics ; Recurrence ; Young Adult ; },
abstract = {Chloroquine (CQ) is the first-line treatment for Plasmodium vivax malaria in most countries where malaria is endemic. Monitoring P. vivax CQ resistance (CQR) is critical but remains challenged by the difficulty to distinguish real treatment failure from reinfection or liver relapse. The therapeutic efficacy of CQ against uncomplicated P. vivax malaria was evaluated in Gia Lai Province, Vietnam. Sixty-seven patients were enrolled and followed for 42 days using microscopy and quantitative PCR. Adequate clinical and parasitological response (ACPR) was 100% (66/66) on day 28 but 75.4% (49/65) on day 42. Eighteen recurrences (27.7%) were detected, with a median time to recurrence of 42 days (interquartile range [IQR], 35 to 42) and blood CQ concentration of <100 ng/ml. Primary infections leading to recurrence occurred in younger individuals (median age for ACPR = 25 years [IQR, 20 to 28]; recurrences = 18 [16 to 21]; P = 0.002) had a longer parasite clearance time (PCT for ACPR = 47.5 h [IQR, 36.2 to 59.8 h]; recurrences = 54.2 [48.4 to 62.0]; P = 0.035) and higher pvcrt gene expression (median relative expression ratio for ACPR = 0.09 [IQR, 0.05 to 0.22]; recurrences = 0.20 [0.15 to 0.56]; P = 0.002), but showed no differences in ex vivo CQ sensitivity. Parasite genotyping by microsatellites, single nucleotide polymorphism (SNP) barcoding, and whole-genome sequencing (WGS) identified a majority of homologous recurrences, with 80% (8/10) showing >98% identity by descent to paired day 0 samples. This study shows that CQ remained largely efficacious to treat P. vivax in Gia Lai; i.e., recurrences occurred late (>day 28) and in the presence of low blood CQ concentrations. However, the combination of both WGS and gene expression analysis (pvcrt) data with clinical data (PCT) allowed us to identify potential emergence of low-grade CQR, which should be closely monitored. (This study has been registered at ClinicalTrials.gov under identifier NCT02610686.).},
}
@article {pmid34030983,
year = {2021},
author = {Miller, KE and Polaszek, A and Evans, DM},
title = {A dearth of data: fitting parasitoids into ecological networks.},
journal = {Trends in parasitology},
volume = {37},
number = {10},
pages = {863-874},
doi = {10.1016/j.pt.2021.04.012},
pmid = {34030983},
issn = {1471-5007},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Databases, Genetic ; *Ecosystem ; *Host-Parasite Interactions/physiology ; },
abstract = {Studying parasitoids can provide insights into global diversity estimates, climate change impacts, and agroecosystem service provision. However, this potential remains largely untapped due to a lack of data on how parasitoids interact with other organisms. Ecological networks are a useful tool for studying and exploiting the impacts of parasitoids, but their construction is hindered by the magnitude of undescribed parasitoid species, a sparse knowledge of host ranges, and an under-representation of parasitoids within DNA-barcode databases (we estimate <5% have a barcode). Here, we advocate the use of DNA metabarcoding to construct the host-parasitoid component of multilayer networks. While the incorporation of parasitoids into network-based analyses has far ranging applications, we focus on its potential for assessing ecosystem service provision within agroecosystems.},
}
@article {pmid34027489,
year = {2021},
author = {Su, G and Qin, X and Enninful, A and Bai, Z and Deng, Y and Liu, Y and Fan, R},
title = {Spatial multi-omics sequencing for fixed tissue via DBiT-seq.},
journal = {STAR protocols},
volume = {2},
number = {2},
pages = {100532},
pmid = {34027489},
issn = {2666-1667},
support = {R01 CA245313/CA/NCI NIH HHS/United States ; U54 CA209992/CA/NCI NIH HHS/United States ; UG3 CA257393/CA/NCI NIH HHS/United States ; UH3 CA257393/CA/NCI NIH HHS/United States ; },
mesh = {DNA/analysis/chemistry/genetics ; DNA Barcoding, Taxonomic/methods ; Equipment Design ; Gene Expression Profiling/*methods ; Genomics/instrumentation/*methods ; Microfluidic Analytical Techniques/instrumentation/methods ; Sequence Analysis, DNA/*methods ; Transcriptome/genetics ; },
abstract = {This protocol describes the use of the deterministic barcoding in tissue for spatial omics sequencing platform to construct a multi-omics atlas on fixed frozen tissue samples. This approach uses a microfluidic-based method to introduce combinatorial DNA oligo barcodes directly to the cells in a tissue section fixed on a glass slide. This technique does not directly resolve single cells but can achieve a near-single-cell resolution for spatial transcriptomics and spatial analysis of a targeted panel of proteins. For complete details on the use and execution of this protocol, please refer to Liu et al. (2020).},
}
@article {pmid34026038,
year = {2021},
author = {Ge, Y and Xia, C and Wang, J and Zhang, X and Ma, X and Zhou, Q},
title = {The efficacy of DNA barcoding in the classification, genetic differentiation, and biodiversity assessment of benthic macroinvertebrates.},
journal = {Ecology and evolution},
volume = {11},
number = {10},
pages = {5669-5681},
pmid = {34026038},
issn = {2045-7758},
abstract = {Macroinvertebrates have been recognized as key ecological indicators of aquatic environment and are the most commonly used approaches for water quality assessment. However, species identification of macroinvertebrates (especially of aquatic insects) proves to be very difficult due to the lack of taxonomic expertise in some regions and can become time-consuming. In this study, we evaluated the feasibility of DNA barcoding for the classification of benthic macroinvertebrates and investigated the genetic differentiation in seven orders (Insecta: Ephemeroptera, Plecoptera, Trichoptera, Diptera, Hemiptera, Coleoptera, and Odonata) from four large transboundary rivers of northwest China and further explored its potential application to biodiversity assessment. A total of 1,144 COI sequences, belonging to 176 species, 112 genera, and 53 families were obtained and analyzed. The barcoding gap analysis showed that COI gene fragment yielded significant intra- and interspecific divergences and obvious barcoding gaps. NJ phylogenetic trees showed that all species group into monophyletic species clusters whether from the same population or not, except two species (Polypedilum. laetum and Polypedilum. bullum). The distance-based (ABGD) and tree-based (PTP and MPTP) methods were utilized for grouping specimens into Operational Taxonomic Units (OTUs) and delimiting species. The ABGD, PTP, and MPTP analysis were divided into 177 (p = .0599), 197, and 195 OTUs, respectively. The BIN analysis generated 186 different BINs. Overall, our study showed that DNA barcoding offers an effective framework for macroinvertebrate species identification and sheds new light on the biodiversity assessment of local macroinvertebrates. Also, the construction of DNA barcode reference library of benthic macroinvertebrates in Eurasian transboundary rivers provides a solid backup for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future.},
}
@article {pmid34026031,
year = {2021},
author = {Evans, HK and Bunch, AJ and Schmitt, JD and Hoogakker, FJ and Carlson, KB},
title = {High-throughput sequencing outperforms traditional morphological methods in Blue Catfish diet analysis and reveals novel insights into diet ecology.},
journal = {Ecology and evolution},
volume = {11},
number = {10},
pages = {5584-5597},
pmid = {34026031},
issn = {2045-7758},
abstract = {Blue Catfish Ictalurus furcatus are an invasive, yet economically important species in the Chesapeake Bay. However, their impact on the trophic ecology of this system is not well understood. In order to provide in-depth analysis of predation by Blue Catfish, we identified prey items using high-throughput DNA sequencing (HTS) of entire gastrointestinal tracts from 134 samples using two genetic markers, mitochondrial cytochrome c oxidase I (COI) and the nuclear 18S ribosomal RNA gene. We compared our HTS results to a more traditional "hybrid" approach that coupled morphological identification with DNA barcoding. The hybrid study was conducted on additional Blue Catfish samples (n = 617 stomachs) collected from the same location and season in the previous year. Taxonomic representation with HTS vastly surpassed that achieved with the hybrid methodology in Blue Catfish. Significantly, our HTS study identified several instances of at-risk and invasive species consumption not identified using the hybrid method, supporting the hypothesis that previous studies using morphological methods may greatly underestimate consumption of critical species. Finally, we report the novel finding that Blue Catfish diet diversity inversely correlates to daily flow rates, perhaps due to higher mobility and prey-seeking behaviors exhibited during lower flow.},
}
@article {pmid34026027,
year = {2021},
author = {Couton, M and Baud, A and Daguin-Thiébaut, C and Corre, E and Comtet, T and Viard, F},
title = {High-throughput sequencing on preservative ethanol is effective at jointly examining infraspecific and taxonomic diversity, although bioinformatics pipelines do not perform equally.},
journal = {Ecology and evolution},
volume = {11},
number = {10},
pages = {5533-5546},
pmid = {34026027},
issn = {2045-7758},
abstract = {High-throughput sequencing of amplicons (HTSA) has been proposed as an effective approach to evaluate taxonomic and genetic diversity at the same time. However, there are still uncertainties as to how the results produced by different bioinformatics treatments impact the conclusions drawn on biodiversity and population genetics indices.We evaluated the ability of six bioinformatics pipelines to recover taxonomic and genetic diversity from HTSA data obtained from controlled assemblages. To that end, 20 assemblages were produced using 354 colonies of Botrylloides spp., sampled in the wild in ten marinas around Brittany (France). We used DNA extracted from preservative ethanol (ebDNA) after various time of storage (3, 6, and 12 months), and from a bulk of preserved specimens (bulkDNA). DNA was amplified with primers designed for targeting this ascidian genus. Results obtained from HTSA data were compared with Sanger sequencing on individual zooids (i.e., individual barcoding).Species identification and relative abundance determined with HTSA data from either ebDNA or bulkDNA were similar to those obtained with traditional individual barcoding. However, after 12 months of storage, the correlation between HTSA and individual-based data was lower than after shorter durations. The six bioinformatics pipelines were able to depict accurately the genetic diversity using standard population genetics indices (HS and FST), despite producing false positives and missing rare haplotypes. However, they did not perform equally and dada2 was the only pipeline able to retrieve all expected haplotypes.This study showed that ebDNA is a nondestructive alternative for both species identification and haplotype recovery, providing storage does not last more than 6 months before DNA extraction. Choosing the bioinformatics pipeline is a matter of compromise, aiming to retrieve all true haplotypes while avoiding false positives. We here recommend to process HTSA data using dada2, including a chimera-removal step. Even if the possibility to use multiplexed primer sets deserves further investigation to expand the taxonomic coverage in future similar studies, we showed that primers targeting a particular genus allowed to reliably analyze this genus within a complex community.},
}
@article {pmid34024368,
year = {2021},
author = {Filipe, D and Parreira, R and Pereira, A and Galvão, N and Cristóvão, JM and Nunes, M and Vieira, ML and Campino, L and Maia, C},
title = {Preliminary comparative analysis of the resolving power of COX1 and 16S-rDNA as molecular markers for the identification of ticks from Portugal.},
journal = {Veterinary parasitology, regional studies and reports},
volume = {24},
number = {},
pages = {100551},
doi = {10.1016/j.vprsr.2021.100551},
pmid = {34024368},
issn = {2405-9390},
mesh = {Animals ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; Phylogeny ; Portugal ; RNA, Ribosomal, 16S/genetics ; *Ticks/genetics ; },
abstract = {The utility of mitochondrial cytochrome oxidase subunit I (COX1) and 16S ribosomal DNA (16S-rDNA) sequence analyses as a complementary/alternative tool to classical taxonomy, for the identification of some of the most prevalent hard tick species from Portugal was evaluated using BOLD-ID (COX1 only), BLASTn and phylogenetic tree reconstruction based on multiple nucleotide sequence alignments. Both molecular markers proved suitable for identifying ticks to a species level, but specific aspects that limit their resolving power must be considered. Their accuracy of tick identification in all life stages and of the other tick species described in the South of Europe is required.},
}
@article {pmid34022059,
year = {2022},
author = {Talavera, G and Lukhtanov, V and Pierce, NE and Vila, R},
title = {DNA Barcodes Combined with Multilocus Data of Representative Taxa Can Generate Reliable Higher-Level Phylogenies.},
journal = {Systematic biology},
volume = {71},
number = {2},
pages = {382-395},
pmid = {34022059},
issn = {1076-836X},
mesh = {Animals ; DNA ; *DNA Barcoding, Taxonomic/methods ; *Lepidoptera ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Taxa are frequently labeled incertae sedis when their placement is debated at ranks above the species level, such as their subgeneric, generic, or subtribal placement. This is a pervasive problem in groups with complex systematics due to difficulties in identifying suitable synapomorphies. In this study, we propose combining DNA barcodes with a multilocus backbone phylogeny in order to assign taxa to genus or other higher-level categories. This sampling strategy generates molecular matrices containing large amounts of missing data that are not distributed randomly: barcodes are sampled for all representatives, and additional markers are sampled only for a small percentage. We investigate the effects of the degree and randomness of missing data on phylogenetic accuracy using simulations for up to 100 markers in 1000-tips trees, as well as a real case: the subtribe Polyommatina (Lepidoptera: Lycaenidae), a large group including numerous species with unresolved taxonomy. Our simulation tests show that when a strategic and representative selection of species for higher-level categories has been made for multigene sequencing (approximately one per simulated genus), the addition of this multigene backbone DNA data for as few as 5-10% of the specimens in the total data set can produce high-quality phylogenies, comparable to those resulting from 100% multigene sampling. In contrast, trees based exclusively on barcodes performed poorly. This approach was applied to a 1365-specimen data set of Polyommatina (including ca. 80% of described species), with nearly 8% of representative species included in the multigene backbone and the remaining 92% included only by mitochondrial COI barcodes, a phylogeny was generated that highlighted potential misplacements, unrecognized major clades, and placement for incertae sedis taxa. We use this information to make systematic rearrangements within Polyommatina, and to describe two new genera. Finally, we propose a systematic workflow to assess higher-level taxonomy in hyperdiverse groups. This research identifies an additional, enhanced value of DNA barcodes for improvements in higher-level systematics using large data sets. [Birabiro; DNA barcoding; incertae sedis; Kipepeo; Lycaenidae; missing data; phylogenomic; phylogeny; Polyommatina; supermatrix; systematics; taxonomy].},
}
@article {pmid34016280,
year = {2021},
author = {Kidd, SE and Crawford, LC and Halliday, CL},
title = {Antifungal Susceptibility Testing and Identification.},
journal = {Infectious disease clinics of North America},
volume = {35},
number = {2},
pages = {313-339},
doi = {10.1016/j.idc.2021.03.004},
pmid = {34016280},
issn = {1557-9824},
mesh = {Antifungal Agents/pharmacology/*therapeutic use ; *Drug Resistance, Fungal ; Endpoint Determination ; Fungi/classification/*drug effects/isolation &amp; purification ; Humans ; Microbial Sensitivity Tests/*methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {The requirement for antifungal susceptibility testing is increasing given the availability of new drugs, increasing populations of individuals at risk for fungal infection, and emerging multiresistant fungi. Rapid and accurate fungal identification remains at the forefront of laboratory efforts to guide empiric therapy. Antifungal susceptibility testing methods have greatly improved, but are subject to variation in results between methods. Careful standardization, validation, and extensive training of users is essential to ensure susceptibility results are clinically useful and interpreted appropriately. Interpretive criteria for many drugs and species are still lacking, but this will continue to evolve.},
}
@article {pmid34011275,
year = {2021},
author = {Porter, TM and Hajibabaei, M},
title = {Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets.},
journal = {BMC bioinformatics},
volume = {22},
number = {1},
pages = {256},
pmid = {34011275},
issn = {1471-2105},
mesh = {Cell Nucleus ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; *Pseudogenes/genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Pseudogenes are non-functional copies of protein coding genes that typically follow a different molecular evolutionary path as compared to functional genes. The inclusion of pseudogene sequences in DNA barcoding and metabarcoding analysis can lead to misleading results. None of the most widely used bioinformatic pipelines used to process marker gene (metabarcode) high throughput sequencing data specifically accounts for the presence of pseudogenes in protein-coding marker genes. The purpose of this study is to develop a method to screen for nuclear mitochondrial DNA segments (nuMTs) in large COI datasets. We do this by: (1) describing gene and nuMT characteristics from an artificial COI barcode dataset, (2) show the impact of two different pseudogene removal methods on perturbed community datasets with simulated nuMTs, and (3) incorporate a pseudogene filtering step in a bioinformatic pipeline that can be used to process Illumina paired-end COI metabarcode sequences. Open reading frame length and sequence bit scores from hidden Markov model (HMM) profile analysis were used to detect pseudogenes.<br><br>RESULTS: Our simulations showed that it was more difficult to identify nuMTs from shorter amplicon sequences such as those typically used in metabarcoding compared with full length DNA barcodes that are used in the construction of barcode libraries. It was also more difficult to identify nuMTs in datasets where there is a high percentage of nuMTs. Existing bioinformatic pipelines used to process metabarcode sequences already remove some nuMTs, especially in the rare sequence removal step, but the addition of a pseudogene filtering step can remove up to 5% of sequences even when other filtering steps are in place.<br><br>CONCLUSIONS: Open reading frame length filtering alone or combined with hidden Markov model profile analysis can be used to effectively screen out apparent pseudogenes from large datasets. There is more to learn from COI nuMTs such as their frequency in DNA barcoding and metabarcoding studies, their taxonomic distribution, and evolution. Thus, we encourage the submission of verified COI nuMTs to public databases to facilitate future studies.},
}
@article {pmid34002354,
year = {2021},
author = {Sawarkar, AD and Shrimankar, DD and Kumar, M and Kumar, P and Kumar, S and Singh, L},
title = {Traditional System Versus DNA Barcoding in Identification of Bamboo Species: A Systematic Review.},
journal = {Molecular biotechnology},
volume = {63},
number = {8},
pages = {651-675},
pmid = {34002354},
issn = {1559-0305},
mesh = {Bambusa/*classification/genetics ; Codon, Initiator ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Genetic Markers ; Microsatellite Repeats ; Polymorphism, Restriction Fragment Length ; Polymorphism, Single Nucleotide ; Species Specificity ; },
abstract = {Bamboo, a gramineous plant belonging to the family Poaceae, comprises of 1575 species from 116 genera across the globe. It has the ability to grow and evolve on degraded land and hence, can be utilized in the various applications as an alternative for plastic and wood. DNA barcoding, a long genomic sequence, identifies barcode region which shows species-specific nucleotide differences. This technology is considered as advanced molecular technique utilized for characterization and classification of the various species by applying distinctive molecular markers. Recent investigations revealed the potential application of various barcode regions such as matK, rbcL, rpoB, rpoC1, psbA-trnH, and ITS2, in identification of many bamboo species from different genus. In this review we comprehensively discussed the relevance of DNA barcoding as a tool in classification/identification of various bamboo species. We highlighted the methodology, how this advance technology overcomes the challenges associated with traditional methods along with prospects for future research.},
}
@article {pmid34002268,
year = {2021},
author = {Akpomie, OO and Okonkwo, KE and Gbemre, AC and Akpomie, KG and Ghosh, S and Ahmadi, S and Banach, AM},
title = {Thermotolerance and Cellulolytic Activity of Fungi Isolated from Soils/Waste Materials in the Industrial Region of Nigeria.},
journal = {Current microbiology},
volume = {78},
number = {7},
pages = {2660-2671},
pmid = {34002268},
issn = {1432-0991},
mesh = {*Cellulase ; Fungi/genetics ; Hypocreales ; Nigeria ; Soil ; Soil Microbiology ; *Thermotolerance ; },
abstract = {The current study aimed on isolating thermotolerant, cellulolytic fungi from different tropical soil/waste materials samples such as wood waste, sawmill, decomposing straw and compost pit sites in Abraka, Southern Nigeria and assessing their applications in diverse cellulolytic processes. Fungal isolates were identified based on cultural, morphological, ITS-5.8S barcoding, reproductive structures and thereafter screened for thermotolerance and cellulolytic activities [carboxy methyl cellulase (CMC-ase) and filter paperase (FP-ase)] by cultivating at 45, 50, 60, 70, 80° and 45 °C, respectively. The highest fungal abundance (44.4%) was observed in the compost pit while the lowest (11.1%) was recorded for sawmill. Nine thermotolerant fungal isolates were identified: Aspergillus flavus (4), Blakeslea sp. (3), and Trichoderma asperellum (2). Among them only five, including three A. flavus, one Blakeslea sp. and one T. asperellum, exhibited cellulolytic activity ranging from 12.11 ± 0.01 to 18.42 ± 5.39 µg/mL and 0.36 ± 0.01-9.21 ± 2.52 µg/mL for CMC-ase and filter paperase FP-ase assay, respectively. The low Michaelis-Menten constants of 1.137 for CMC-ase and 1.195 for FP-ase were obtained, indicated a strong affinity for the substrate. The thermotolerance coupled with cellulolytic activity of these isolates make them attractive for potential application in industries where they can be of economic and environmental benefits as against the use of chemicals.},
}
@article {pmid34000616,
year = {2021},
author = {Liu, Y and Xu, C and Dong, W and Yang, X and Zhou, S},
title = {Determination of a criminal suspect using environmental plant DNA metabarcoding technology.},
journal = {Forensic science international},
volume = {324},
number = {},
pages = {110828},
doi = {10.1016/j.forsciint.2021.110828},
pmid = {34000616},
issn = {1872-6283},
mesh = {Chloroplasts/genetics ; Criminals ; *DNA Barcoding, Taxonomic ; DNA, Environmental/*genetics ; DNA, Plant/*genetics ; Female ; Forensic Genetics/*methods ; High-Throughput Nucleotide Sequencing ; Homicide ; Humans ; Ribulose-Bisphosphate Carboxylase/genetics ; Soil/*chemistry ; },
abstract = {There are criminal cases that no frequently used evidence, for example, human DNAs from the criminal, is available. Such cases usually are unresolvable. With the advent of DNA metabarcoding, evidences are mined from environmental DNA and such cases become resolvable. This study reports how a criminal suspect was determined by environmental plant DNA metabarcoding technology. A girl was killed in a rural wet area in China without a witness or video record. Pants with dried mud was found from one of her classmate's house. The mud was removed from the pants and 11 more mud or soil samples surrounding murder scene were collected. DNA was extracted from the soil. Chloroplast rbcL gene were amplified and sequenced on a next generation sequencing platform. After bioinformatics analysis, ZOTU composition of 12 samples demonstrated that the mud on the suspect's pants was from the criminal scene. The suspect finally made a clean breast of his crime. This case implies that plant DNA in the environment soil is a new source of evidence in determination of suspects using DNA metabarcoding technology and has high potentials of extensive applications in criminal cases.},
}
@article {pmid34000509,
year = {2021},
author = {Ratnayake, AS and Flanagan, ME and Foley, TL and Hultgren, SL and Bellenger, J and Montgomery, JI and Lall, MS and Liu, B and Ryder, T and Kölmel, DK and Shavnya, A and Feng, X and Lefker, B and Byrnes, LJ and Sahasrabudhe, PV and Farley, KA and Chen, S and Wan, J},
title = {Toward the assembly and characterization of an encoded library hit confirmation platform: Bead-Assisted Ligand Isolation Mass Spectrometry (BALI-MS).},
journal = {Bioorganic &amp; medicinal chemistry},
volume = {41},
number = {},
pages = {116205},
doi = {10.1016/j.bmc.2021.116205},
pmid = {34000509},
issn = {1464-3391},
mesh = {Combinatorial Chemistry Techniques ; DNA/*chemistry ; *Drug Discovery ; *Gene Library ; Ligands ; Mass Spectrometry/*methods ; Molecular Structure ; Small Molecule Libraries/chemistry ; },
abstract = {The ability to predict chemical structure from DNA sequence has to date been a necessary cornerstone of DNA-encoded library technology. DNA-encoded libraries (DELs) are typically screened by immobilized affinity selection and enriched library members are identified by counting the number of times an individual compound's sequence is observed in the resultant dataset. Those with high signal reads (DEL hits) are subsequently followed up through off-DNA synthesis of the predicted small molecule structures. However, hits followed-up in this manner often fail to translate to confirmed ligands. To address this low conversion rate of DEL hits to off-DNA ligands, we have developed an approach that eliminates the reliance on chemical structure prediction from DNA sequence. Here we describe our method of combining non-combinatorial resynthesis on-DNA following library procedures as a rapid means to assess the probable molecules attached to the DNA barcode. Furthermore, we apply our Bead-Assisted Ligand Isolation Mass Spectrometry (BALI-MS) technique to identify the true binders found within the mixtures of on-DNA synthesis products. Finally, we describe a Normalized Enrichment (NE) metric that allows for the quantitative assessment of affinity selection in these studies. We exemplify how this combined approach enables the identification of putative hit matter against a clinically relevant therapeutic target bisphosphoglycerate mutase, BPGM.},
}
@article {pmid33999185,
year = {2021},
author = {Duan, J and Hon, GC},
title = {FBA: feature barcoding analysis for single cell RNA-Seq.},
journal = {Bioinformatics (Oxford, England)},
volume = {37},
number = {22},
pages = {4266-4268},
pmid = {33999185},
issn = {1367-4811},
support = {DP2 GM128203/GM/NIGMS NIH HHS/United States ; },
mesh = {RNA-Seq ; *Gene Expression Profiling ; Sequence Analysis, RNA ; *Software ; Single-Cell Analysis ; },
abstract = {MOTIVATION: Single cell RNA-Seq (scRNA-Seq) has broadened our understanding of cellular heterogeneity and provided valuable insights into cellular functions. Recent experimental strategies extend scRNA-Seq readouts to include additional features, including cell surface proteins and genomic perturbations. These 'feature barcoding' strategies rely on converting molecular and cellular features to unique sequence barcodes, which are then detected with the transcriptome.<br><br>RESULTS: Here, we introduce FBA, a flexible and streamlined package to perform quality control, quantification, demultiplexing, multiplet detection, clustering and visualization of feature barcoding assays.<br><br>FBA is available on PyPi at https://pypi.org/project/fba and on GitHub at https://github.com/jlduan/fba.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid33992328,
year = {2021},
author = {Barbosa, AJ and Sampaio, I and Santos, S},
title = {Re-visiting the occurrence of mislabeling in frozen "pescada-branca" (Cynoscion leiarchus and Plagioscion squamosissimus - Sciaenidae) sold in Brazil using DNA barcoding and octaplex PCR assay.},
journal = {Food research international (Ottawa, Ont.)},
volume = {143},
number = {},
pages = {110308},
doi = {10.1016/j.foodres.2021.110308},
pmid = {33992328},
issn = {1873-7145},
mesh = {Animals ; Blood Coagulation Factors ; Brazil ; *DNA Barcoding, Taxonomic ; *Perciformes ; Polymerase Chain Reaction ; },
abstract = {In Brazil, Cynoscion leiarchus and Plagioscion squamosissimus are the species allowed to be labeled as "pescada-branca". These species have high economic value, especially when sold in the form of fillets. Therefore, when morphological traits are removed, fish are highly prone to be substituted, which has been reported for species of the family Sciaenidae sold in Brazil, including "pescada-branca". We have sequenced 618 bp of the COI of 143 samples to re-evaluate the occurrence of substitutions in frozen "pescada-branca" marketed in Brazil. We observed more than 73% of mislabeling, with only 26.57% being P. squamosissimus, and none, C. leiarchus. In general, the substitutes were closely related Sciaenidae, but cheaper species, which indicates commercial fraud. Based on these results we used 1.2 kb of COI to develop an octaplex PCR assay that unequivocally identified the target species and six substitute species through the banding pattern. Specific reverse primers combined with a universal forward primer were used in the protocol and identified the species C. leiarchus (~290 bp), N. microps (~340 bp), M. ancylodon (~470 bp), C. acoupa (~540 bp), C. microlepidotus (~850 bp), P. auratus (~950 bp), C. virescens (~1050 bp), and P. squamosissimus (~1140 bp). The DNA barcoding and the multiplex PCR were accurate and specific to authenticate processed products labeled as "pescada-branca". The multiplex assay constitutes a cost-effective alternative for the authentication of these products and other sciaenids. Additionally, we suggest that the multiplex assay can be adopted by both companies and regulatory agencies to prevent commercial fraud in the marketing of processed fishery products in Brazil and other countries where these products are commercialized.},
}
@article {pmid33992095,
year = {2021},
author = {Zhang, XF and Landis, JB and Wang, HX and Zhu, ZX and Wang, HF},
title = {Comparative analysis of chloroplast genome structure and molecular dating in Myrtales.},
journal = {BMC plant biology},
volume = {21},
number = {1},
pages = {219},
pmid = {33992095},
issn = {1471-2229},
mesh = {*Evolution, Molecular ; *Genome, Chloroplast ; *Genome, Plant ; *Molecular Structure ; Myrtales/*genetics ; *Phylogeny ; *Whole Genome Sequencing ; },
abstract = {BACKGROUND: Myrtales is a species rich branch of Rosidae, with many species having important economic, medicinal, and ornamental value. At present, although there are reports on the chloroplast structure of Myrtales, a comprehensive analysis of the chloroplast structure of Myrtales is lacking. Phylogenetic and divergence time estimates of Myrtales are mostly constructed by using chloroplast gene fragments, and the support for relationships is low. A more reliable method to reconstruct the species divergence time and phylogenetic relationships is by using whole chloroplast genomes. In this study, we comprehensively analyzed the structural characteristics of Myrtales chloroplasts, compared variation hotspots, and reconstructed the species differentiation time of Myrtales with four fossils and one secondary calibration point.<br><br>RESULTS: A total of 92 chloroplast sequences of Myrtales, representing six families, 16 subfamilies and 78 genera, were obtained including nine newly sequenced chloroplasts by whole genome sequencing. Structural analyses showed that the chloroplasts range in size between 152,214-171,315&#x2009;bp and exhibit a typical four part structure. The IR region is between 23,901-36,747&#x2009;bp, with the large single copy region spanning 83,691-91,249&#x2009;bp and the small single copy region spanning 11,150-19,703&#x2009;bp. In total, 123-133 genes are present in the chloroplasts including 77-81 protein coding genes, four rRNA genes and 30-31 tRNA genes. The GC content was 36.9-38.9%, with the average GC content being 37%. The GC content in the LSC, SSC and IR regions was 34.7-37.3%, 30.6-36.8% and 39.7-43.5%, respectively. By analyzing nucleotide polymorphism of the chloroplast, we propose 21 hypervariable regions as potential DNA barcode regions for Myrtales. Phylogenetic analyses showed that Myrtales and its corresponding families are monophyletic, with Combretaceae and the clade of Onagraceae + Lythraceae (BS&#x2009;=&#x2009;100%, PP&#x2009;=&#x2009;1) being sister groups. The results of molecular dating showed that the crown of Myrtales was most likely to be 104.90&#x2009;Ma (95% HPD&#x2009;=&#x2009;87.88-114.18&#x2009;Ma), and differentiated from the Geraniales around 111.59&#x2009;Ma (95% HPD&#x2009;=&#x2009;95.50-118.62&#x2009;Ma).<br><br>CONCLUSIONS: The chloroplast genome structure of Myrtales is similar to other angiosperms and has a typical four part structure. Due to the expansion and contraction of the IR region, the chloroplast genome sizes in this group are slightly different. The variation of noncoding regions of the chloroplast genome is larger than those of coding regions. Phylogenetic analysis showed that Combretaceae and Onagraceae + Lythraceae were well supported as sister groups. Molecular dating indicates that the Myrtales crown most likely originated during the Albian age of the Lower Cretaceous. These chloroplast genomes contribute to the study of genetic diversity and species evolution of Myrtales, while providing useful information for taxonomic and phylogenetic studies of Myrtales.},
}
@article {pmid33987777,
year = {2021},
author = {Liu, X and Ge, Y and Wang, R and Dong, H and Yang, X and Zhang, L},
title = {First report of Blastocystis infection in Pallas's squirrels (Callosciurus erythraeus) in China.},
journal = {Veterinary research communications},
volume = {45},
number = {4},
pages = {441-445},
pmid = {33987777},
issn = {1573-7446},
support = {2020M672230//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; Blastocystis/*isolation &amp; purification ; Blastocystis Infections/epidemiology/parasitology/*veterinary ; China/epidemiology ; Prevalence ; *Sciuridae ; },
abstract = {Blastocystis, an intestinal anaerobic protist with high genetic diversity, inhabits a variety of hosts worldwide, including rodents. However, there have been few studies on squirrel Blastocystis infections in China to date. Herein, 171 fecal samples from Pallas's squirrels (Callosciurus erythraeus) sold as pets were collected to investigate the prevalence and genetic characteristics of Blastocystis. A total of 10 Blastocystis-positive samples (10/171, 5.9%) were obtained by PCR amplification and DNA sequencing of the barcode region of the SSU rRNA gene. Blastocystis subtype analysis revealed four known subtypes, namely, ST1, ST3, ST5 and ST6, with ST5 and ST6 being predominant. Phylogenetic analysis was performed to identify each subtype. To our knowledge, this study is the first to explore Blastocystis infection in Pallas's squirrels, expanding the host range of this parasite. Moreover, multiple zoonotic subtypes were found in Pallas's squirrels, suggesting that these animals may serve as reservoirs for pathogens of human Blastocystis infections.},
}
@article {pmid33986998,
year = {2021},
author = {Kim, HK and Chan, BKK and Song, SJ and Khim, JS},
title = {DNA-based diversity assessment reveals a new coral barnacle, Cantellius alveoporae sp. nov. (Balanomorpha: Pyrgomatidae) exclusively associated with the high latitude coral Alveopora japonica in the waters of southern Korea.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e11284},
pmid = {33986998},
issn = {2167-8359},
abstract = {In the present study, the Indo-Pacific coral associated barnacle Cantellius euspinulosum (Broch, 1931) was found to have cryptic species in Korea, Taiwan and other regions based on molecular studies. However, the original specimens of C. euspinulosum from Broch have not been previously described or illustrated, making it difficult to assign which cryptic species to the original C. euspinulosum. The original specimen of C. euspinulosum was examined and illustrated here, and the species identity of C. cf. euspinulosum collected from Jejudo Island in the present study and other cryptic species (based on literature illustrations) in the Indo-Pacific were evaluated.C. euspinulosum from Singapore, Java, Mergui Archipelago in Andaman Sea and Nha Trang represented the C. euspinulosum identified by Broch (1931). It is a generalist on Acropora, Favia, Favites, Leptoria, Montipora, Pachyseris and Pocillipora corals and distributed in the Indo-Pacific region. Morphological examination and DNA sequencing (COI, 12S DNA sequences) in the present study showed that C. cf. euspinulosum from Jejudo Island, Korea represents a distinct species, herein named C. alveoporae sp. nov. Cantellius alveroporae sp. nov. is a specialist species that only grows on Alveopora and also present in Palau, and Ogasawara Island in Japan. Cantellius cf. euspinuloum in Taiwan, the Moscos Island, and Australia belong to several other distinct species awaiting further morphological and molecular studies. At least five cryptic species of C. euspinulosum were identified in the present study, including both specialist and generalists.},
}
@article {pmid33986985,
year = {2021},
author = {Geiger, M and Koblmüller, S and Assandri, G and Chovanec, A and Ekrem, T and Fischer, I and Galimberti, A and Grabowski, M and Haring, E and Hausmann, A and Hendrich, L and Koch, S and Mamos, T and Rothe, U and Rulik, B and Rewicz, T and Sittenthaler, M and Stur, E and Tończyk, G and Zangl, L and Moriniere, J},
title = {Coverage and quality of DNA barcode references for Central and Northern European Odonata.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e11192},
pmid = {33986985},
issn = {2167-8359},
abstract = {BACKGROUND: Dragonflies and damselflies (Odonata) are important components in biomonitoring due to their amphibiotic lifecycle and specific habitat requirements. They are charismatic and popular insects, but can be challenging to identify despite large size and often distinct coloration, especially the immature stages. DNA-based assessment tools rely on validated DNA barcode reference libraries evaluated in a supraregional context to minimize taxonomic incongruence and identification mismatches.<br><br>METHODS: This study reports on findings from the analysis of the most comprehensive DNA barcode dataset for Central European Odonata to date, with 103 out of 145 recorded European species included and publicly deposited in the Barcode of Life Data System (BOLD). The complete dataset includes 697 specimens (548 adults, 108 larvae) from 274 localities in 16 countries with a geographic emphasis on Central Europe. We used BOLD to generate sequence divergence metrics and to examine the taxonomic composition of the DNA barcode clusters within the dataset and in comparison with all data on BOLD.<br><br>RESULTS: Over 88% of the species included can be readily identified using their DNA barcodes and the reference dataset provided. Considering the complete European dataset, unambiguous identification is hampered in 12 species due to weak mitochondrial differentiation and partial haplotype sharing. However, considering the known species distributions only two groups of five species possibly co-occur, leading to an unambiguous identification of more than 95% of the analysed Odonata via DNA barcoding in real applications. The cases of small interspecific genetic distances and the observed deep intraspecific variation in Cordulia aenea (Linnaeus, 1758) are discussed in detail and the corresponding taxa in the public reference database are highlighted. They should be considered in future applications of DNA barcoding and metabarcoding and represent interesting evolutionary biological questions, which call for in depth analyses of the involved taxa throughout their distribution ranges.},
}
@article {pmid33986447,
year = {2021},
author = {Inglis, GAS},
title = {BABEL: using deep learning to translate between single-cell datasets.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {591},
pmid = {33986447},
issn = {2399-3642},
mesh = {*Deep Learning ; Humans ; },
abstract = {Recent advances in sequencing and barcoding technologies have enabled researchers to simultaneously profile gene expression, chromatin accessibility, and/or protein levels in single cells. However, these multiomic techniques often pose technical and financial barriers that limit their practicality. Kevin Wu and colleagues recently developed BABEL, a deep learning algorithm that can effectively translate between transcriptomic and chromatin profiles in single cells, thereby enabling researchers to perform multiomic analyses from an individual dataset.},
}
@article {pmid33983440,
year = {2022},
author = {Baker, WJ and Bailey, P and Barber, V and Barker, A and Bellot, S and Bishop, D and Botigué, LR and Brewer, G and Carruthers, T and Clarkson, JJ and Cook, J and Cowan, RS and Dodsworth, S and Epitawalage, N and Françoso, E and Gallego, B and Johnson, MG and Kim, JT and Leempoel, K and Maurin, O and Mcginnie, C and Pokorny, L and Roy, S and Stone, M and Toledo, E and Wickett, NJ and Zuntini, AR and Eiserhardt, WL and Kersey, PJ and Leitch, IJ and Forest, F},
title = {A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life.},
journal = {Systematic biology},
volume = {71},
number = {2},
pages = {301-319},
pmid = {33983440},
issn = {1076-836X},
mesh = {Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; *Magnoliopsida/genetics ; Phylogeny ; },
abstract = {The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this article are to (i) document our methods, (ii) describe our first data release, and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic data set for angiosperms to date, comprising 3099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96$\%$) and 2333 genera (17$\%$). A "first pass" angiosperm tree of life was inferred from the data, which totaled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated data set, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone toward a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardized nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world's natural history collections. [Angiosperms; Angiosperms353; genomics; herbariomics; museomics; nuclear phylogenomics; open access; target sequence capture; tree of life.].},
}
@article {pmid33982270,
year = {2021},
author = {Heddergott, M and Frantz, AC},
title = {First Record of the Sinus Worm Skrjabingylus petrowi (Nematoda: Metastrongyloidea) in a Pine Marten Martes martes from Poland.},
journal = {Acta parasitologica},
volume = {66},
number = {4},
pages = {1570-1573},
pmid = {33982270},
issn = {1896-1851},
mesh = {Animals ; Europe ; Male ; *Metastrongyloidea ; *Mustelidae ; *Paranasal Sinuses ; Poland ; },
abstract = {BACKGROUND: Skrjabingylus spp. are nematodes that parasitize in the frontal and nasal sinuses of small mustelids. In Europe, the two species S. nasicola and S. petrowi are known, although records of S. petrowi are extremely rare, except in the former part of the USSR. The aim of the present study was to screen pine martens (Martes martes) from Poland for the first time for the presence of S. petrowi.<br><br>METHODS: Three road-killed pine martens were collected in 2018 and 2020 in the province Lower Silesian in southwestern Poland. A complete necropsy was performed on the fresh pine marten heads and especially the frontal sinuses and paranasal sinuses were examined for the presence of Skrjabingylus spp. The species identity of the recovered nematodes was determined by morphological measurements and genetic barcoding.<br><br>RESULTS: One of three pine martens examined showed infection with 12 Skrjabingylus spp. in the right frontal sinus. Measurements of the spicule length of the males revealed a range of 480-521 &#xb5;m which is characteristic of S. petrowi. There was a close match between the COI sequence reported here and of S. petrowi sequences reported from Germany.<br><br>CONCLUSION: This is the first report of infection of a pine marten with the sinus worm S. petrowi in Poland.},
}
@article {pmid33981819,
year = {2021},
author = {Mann, BC and Bezuidenhout, JJ and Swanevelder, ZH and Grobler, AF},
title = {MinION 16S datasets of a commercially available microbial community enables the evaluation of DNA extractions and data analyses.},
journal = {Data in brief},
volume = {36},
number = {},
pages = {107036},
pmid = {33981819},
issn = {2352-3409},
abstract = {New advances in sequencing technology and bioinformatics analysis tools have significantly supported the culture-independent analysis of complex microbial communities associated with environmental, plant, animal and human samples. However, previous work has shown that DNA extraction can have a major influence in the community profile. As such there is a constant need for new methods to efficiently and rapidly prepare and analyze DNA for microbiome research, especially in the case new and emerging technology like the Oxford Nanopore Technologies (ONT) MinION. A commercial standard was used, in triplicate, to evaluate three DNA extraction protocols, including two commercially available and one "in-house" DNA extraction method. All DNA extractions were done as per manufacturer's instructions and prepared with the same commercial ONT 16S sample preparation kit, prior to being analysed using MinION sequencing. Eight MinION 16S datasets of this microbial reference community were obtained. Reads were initially base called and demultiplexed using ONT's Guppy™ sequencing software (version 3.2.4), filtered using NanoFilt and then classified using Usearch. A set of R scripts are presented to process sintax files generated from Usearch and produce an OTU table that can be used for further analyses. All datasets were deposited into the SRA (NCBI) database. These datasets will allow future extraction kit comparisons using MinION sequencing since a standardize laboratory process using commercially available components, such as the MinION 16S sample preparation kit, microbial reference community and extraction kits, were used. The current ONT 16S workflow making use of the Epi2me agent only provides QC metrics and the ID's of the main genera identified and does not provide any tools currently for further downstream community comparison. The analyses scripts provided in the supplementary material will thus further enable the testing of new datasets against these reference sets and provide users the ability to compare their workflows with ours, thus standardizing comparisons and workflows.},
}
@article {pmid33981037,
year = {2021},
author = {Spencer Chapman, M and Ranzoni, AM and Myers, B and Williams, N and Coorens, THH and Mitchell, E and Butler, T and Dawson, KJ and Hooks, Y and Moore, L and Nangalia, J and Robinson, PS and Yoshida, K and Hook, E and Campbell, PJ and Cvejic, A},
title = {Lineage tracing of human development through somatic mutations.},
journal = {Nature},
volume = {595},
number = {7865},
pages = {85-90},
pmid = {33981037},
issn = {1476-4687},
support = {MC_PC_17230/MRC_/Medical Research Council/United Kingdom ; 203151/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; /ERC_/European Research Council/International ; MR/M008975/1/MRC_/Medical Research Council/United Kingdom ; MR/R006237/1/MRC_/Medical Research Council/United Kingdom ; 23917/CRUK_/Cancer Research UK/United Kingdom ; },
mesh = {Blood Cells/cytology/metabolism ; Cell Lineage/*genetics ; Clone Cells/cytology/metabolism ; DNA Mutational Analysis ; Embryonic Development/*genetics ; Fetus/cytology/embryology/metabolism ; Germ Layers/cytology/metabolism ; Health ; Hematopoietic System/cytology/*embryology/*metabolism ; Humans ; Karyotyping ; Male ; Mesoderm/cytology/embryology/metabolism ; *Mutation ; Mutation Rate ; Organ Specificity/genetics ; Time Factors ; Whole Genome Sequencing ; Workflow ; },
abstract = {The ontogeny of the human haematopoietic system during fetal development has previously been characterized mainly through careful microscopic observations[1]. Here we reconstruct a phylogenetic tree of blood development using whole-genome sequencing of 511 single-cell-derived haematopoietic colonies from healthy human fetuses at 8 and 18 weeks after conception, coupled with deep targeted sequencing of tissues of known embryonic origin. We found that, in healthy fetuses, individual haematopoietic progenitors acquire tens of somatic mutations by 18 weeks after conception. We used these mutations as barcodes and timed the divergence of embryonic and extra-embryonic tissues during development, and estimated the number of blood antecedents at different stages of embryonic development. Our data support a hypoblast origin of the extra-embryonic mesoderm and primitive blood in humans.},
}
@article {pmid33976967,
year = {2021},
author = {D'Ercole, J and Dincă, V and Opler, PA and Kondla, N and Schmidt, C and Phillips, JD and Robbins, R and Burns, JM and Miller, SE and Grishin, N and Zakharov, EV and DeWaard, JR and Ratnasingham, S and Hebert, PDN},
title = {A DNA barcode library for the butterflies of North America.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e11157},
pmid = {33976967},
issn = {2167-8359},
abstract = {Although the butterflies of North America have received considerable taxonomic attention, overlooked species and instances of hybridization continue to be revealed. The present study assembles a DNA barcode reference library for this fauna to identify groups whose patterns of sequence variation suggest the need for further taxonomic study. Based on 14,626 records from 814 species, DNA barcodes were obtained for 96% of the fauna. The maximum intraspecific distance averaged 1/4 the minimum distance to the nearest neighbor, producing a barcode gap in 76% of the species. Most species (80%) were monophyletic, the others were para- or polyphyletic. Although 15% of currently recognized species shared barcodes, the incidence of such taxa was far higher in regions exposed to Pleistocene glaciations than in those that were ice-free. Nearly 10% of species displayed high intraspecific variation (>2.5%), suggesting the need for further investigation to assess potential cryptic diversity. Aside from aiding the identification of all life stages of North American butterflies, the reference library has provided new perspectives on the incidence of both cryptic and potentially over-split species, setting the stage for future studies that can further explore the evolutionary dynamics of this group.},
}
@article {pmid33976851,
year = {2021},
author = {Downie, J and Taylor, AFS and Iason, G and Moore, B and Silvertown, J and Cavers, S and Ennos, R},
title = {Location, but not defensive genotype, determines ectomycorrhizal community composition in Scots pine (Pinus sylvestris L.) seedlings.},
journal = {Ecology and evolution},
volume = {11},
number = {9},
pages = {4826-4842},
pmid = {33976851},
issn = {2045-7758},
abstract = {For successful colonization of host roots, ectomycorrhizal (EM) fungi must overcome host defense systems, and defensive phenotypes have previously been shown to affect the community composition of EM fungi associated with hosts. Secondary metabolites, such as terpenes, form a core part of these defense systems, but it is not yet understood whether variation in these constitutive defenses can result in variation in the colonization of hosts by specific fungal species.We planted seedlings from twelve maternal families of Scots pine (Pinus sylvestris) of known terpene genotype reciprocally in the field in each of six sites. After 3 months, we characterized the mycorrhizal fungal community of each seedling using a combination of morphological categorization and molecular barcoding, and assessed the terpene chemodiversity for a subset of the seedlings. We examined whether parental genotype or terpene chemodiversity affected the diversity or composition of a seedling's mycorrhizal community.While we found that terpene chemodiversity was highly heritable, we found no evidence that parental defensive genotype or a seedling's terpene chemodiversity affected associations with EM fungi. Instead, we found that the location of seedlings, both within and among sites, was the only determinant of the diversity and makeup of EM communities.These results show that while EM community composition varies within Scotland at both large and small scales, variation in constitutive defensive compounds does not determine the EM communities of closely cohabiting pine seedlings. Patchy distributions of EM fungi at small scales may render any genetic variation in associations with different species unrealizable in field conditions. The case for selection on traits mediating associations with specific fungal species may thus be overstated, at least in seedlings.},
}
@article {pmid33976803,
year = {2021},
author = {Takamura, K and Ueno, R and Kondo, NI and Ohbayashi, K},
title = {Pond chironomid communities revealed by molecular species delimitation reflect eutrophication.},
journal = {Ecology and evolution},
volume = {11},
number = {9},
pages = {4193-4204},
pmid = {33976803},
issn = {2045-7758},
abstract = {Farm ponds, a valued habitat for freshwater organisms, are being negatively affected by the recent changes in the environment as well as anthropological activities. In these ponds, biodiversity researchers have tended to focus on species that prefer natural habitats and/or can be identified based on morphological characters. In contrast, this study focused on the insect family Chironomidae, which is widely distributed from clear to polluted waters of ponds, but is hard to identify morphologically as an aquatic larva. We adopted DNA barcoding and molecular species delimitation to identify every single specimen of quantitative collections. From bottom sediments of 17 ponds in summer in the Banshu Plain of Japan, a total of 62 species were delimited based on the DNA sequences of the mitochondrial COI region. Chironomid communities from these ponds were classified into four groups in a two-dimensional ordination of multivariate analysis (NMDS). One of the dimensions was well correlated with the gradient of eutrophication, while another dimension was not clearly assigned to any general feature of the environmental gradient, but rice cultivation could possibly be involved.},
}
@article {pmid33976769,
year = {2021},
author = {Ahmed, MS and Datta, SK and Saha, T and Hossain, Z},
title = {Molecular characterization of marine and coastal fishes of Bangladesh through DNA barcodes.},
journal = {Ecology and evolution},
volume = {11},
number = {9},
pages = {3696-3709},
pmid = {33976769},
issn = {2045-7758},
abstract = {This study describes the molecular characterization of marine and coastal fishes of Bangladesh based on the mitochondrial cytochrome c oxidase subunit I (COI) gene as a marker. A total of 376 mitochondrial COI barcode sequences were obtained from 185 species belonging to 146 genera, 74 families, 21 orders, and two classes of fishes. The mean length of the sequences was 652 base pairs. In Elasmobranchii (Sharks and rays), the average Kimura two parameter (K2P) distances within species, genera, families, and orders were 1.20%, 6.07%, 11.08%, and 14.68%, respectively, and for Actinopterygii, the average K2P distances within species, genera, families, and orders were 0.40%, 6.36%, 14.10%, and 24.07%, respectively. The mean interspecies distance was 16-fold higher than the mean intraspecies distance. The K2P neighbor-joining (NJ) trees based on the sequences generally clustered species in accordance with their taxonomic position. A total of 21 species were newly recorded in Bangladesh. High efficiency and fidelity in species identification and discrimination were demonstrated in the present study by DNA barcoding, and we conclude that COI sequencing can be used as an authentic identification marker for Bangladesh marine fish species.},
}
@article {pmid33974138,
year = {2021},
author = {Azizi, R and Bouguerche, C and Santoro, M and Gey, D and Tazerouti, F and Justine, JL and Bahri, S},
title = {Redescription and molecular characterization of two species of Pauciconfibula (Monogenea, Microcotylidae) from trachinid fishes in the Mediterranean Sea.},
journal = {Parasitology research},
volume = {120},
number = {7},
pages = {2363-2377},
pmid = {33974138},
issn = {1432-1955},
mesh = {Algeria ; Animals ; DNA Barcoding, Taxonomic ; Female ; Fish Diseases/*parasitology ; Gills/parasitology ; Italy ; Male ; Mediterranean Sea ; Perciformes/classification/genetics/*parasitology ; Phylogeny ; Species Specificity ; Trematoda/anatomy &amp; histology/*classification/genetics ; Trematode Infections/parasitology/*veterinary ; Tunisia ; },
abstract = {Many Pauciconfibula spp. have a long and complicated taxonomic history. The remaining unsolved taxonomic confusion in this genus is impelled by the host range and status of Pauciconfibula spp. from trachinid fishes: Pauciconfibula trachini and Pauciconfibula draconis, from Trachinus radiatus and Trachinus draco (Trachinidae), respectively. Pauciconfibula trachini was reported on Trachinus draco, type host of Pauciconfibula draconis suggesting thus a stenoxenic specificity for the former monogenean and the occurrence of two congeneric polyopisthocotyleans on a single host. Moreover, the validity of Pauciconfibula draconis was repeatedly questioned by several authors, unjustified synonymy between the two species was proposed, and the delimitations between the two species remained unsolved. Original descriptions were also incomplete and poorly illustrated. In this study, we provide a detailed illustrated redescription of both species based on newly collected specimens of Pauciconfibula trachini and Pauciconfibula draconis collected from their type hosts from off three Mediterranean localities: Algeria, Tunisia, and Italy. Integrative taxonomy using COI sequences was applied to resolve the delimitation between Pauciconfibula trachini and P. draconis. This study provides the first DNA barcoding for members of this genus.},
}
@article {pmid33972472,
year = {2021},
author = {Chang, J},
title = {MHC multimer: A Molecular Toolbox for Immunologists.},
journal = {Molecules and cells},
volume = {44},
number = {5},
pages = {328-334},
pmid = {33972472},
issn = {0219-1032},
mesh = {Allergy and Immunology/*standards ; Humans ; Major Histocompatibility Complex/*immunology ; },
abstract = {The advent of the major histocompatibility complex (MHC) multimer technology has led to a breakthrough in the quantification and analysis of antigen-specific T cells. In particular, this technology has dramatically advanced the measurement and analysis of CD8 T cells and is being applied more widely. In addition, the scope of application of MHC multimer technology is gradually expanding to other T cells such as CD4 T cells, natural killer T cells, and mucosal-associated invariant T cells. MHC multimer technology acts by complementing the T-cell receptor-MHC/peptide complex affinity, which is relatively low compared to antigen-antibody affinity, through a multivalent interaction. The application of MHC multimer technology has expanded to include various functions such as quantification and analysis of antigen-specific T cells, cell sorting, depletion, stimulation to replace antigen-presenting cells, and single-cell classification through DNA barcodes. This review aims to provide the latest knowledge of MHC multimer technology, which is constantly evolving, broaden understanding of this technology, and promote its widespread use.},
}
@article {pmid33971606,
year = {2021},
author = {Nistal-García, A and García-García, P and García-Girón, J and Borrego-Ramos, M and Blanco, S and Bécares, E},
title = {DNA metabarcoding and morphological methods show complementary patterns in the metacommunity organization of lentic epiphytic diatoms.},
journal = {The Science of the total environment},
volume = {786},
number = {},
pages = {147410},
doi = {10.1016/j.scitotenv.2021.147410},
pmid = {33971606},
issn = {1879-1026},
mesh = {DNA ; DNA Barcoding, Taxonomic ; *Diatoms/genetics ; Ecosystem ; Fresh Water ; },
abstract = {Diatoms are important organisms in freshwater ecosystems due to their position as primary producers and therefore, analyzing their assemblages provides relevant information on ecosystem functioning. Diatoms have historically been identified based on morphological traits, which is time-consuming and requires well-trained specialists. Nevertheless, DNA barcoding offers an alternative approach to overcome some limitations of the morphological method. Here, we assess if both approaches are comparable methods to study patterns and mechanisms (including environmental filtering and dispersal limitation) of epiphytic diatom metacommunities using a comprehensive dataset from 22 Mediterranean ponds at different taxonomic resolutions. We used a fragment of rbcL barcode gene combined with High-Throughput Sequencing to infer diatom community composition. The overall degree of correspondence between both approaches was assessed by Procrustean rotation analysis and Procrustean randomization tests, whereas the role of local environmental variables and geographical distances was studied using a comprehensive combination of BIOENV, Mantel tests and distance-based redundancy analysis. Our results showed a relatively poor correspondence in the compositional variation of diatom metacommunity between both approaches. We speculate that the incompleteness of the reference database and the bioinformatics processing are the biases most likely affecting the molecular approach, whereas the limited counting effort and the presence of cryptic species are presumably the major biases related with the morphological method. On the other hand, variation in diatom community composition detected with both approaches was strongly related to the environmental template, which may be related with the narrow community-environment relationships in diatoms. Nevertheless, we found no significant relationship between compositional variation and geographical distances. Overall, our work shows the complementary nature of both approaches and highlights the importance of DNA metabarcoding to address empirical research questions of community ecology in freshwaters, especially once the reference databases include most genotypes of occurring taxa and bioinformatics biases are overcome.},
}
@article {pmid33969211,
year = {2021},
author = {Kang, Y},
title = {Molecular identification of Aquilaria species with distribution records in China using DNA barcode technology.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {6},
number = {4},
pages = {1525-1535},
pmid = {33969211},
issn = {2380-2359},
abstract = {Aquilaria species is one of the main plant resources that produce agarwood, which containing black resin with important economic and medicinal values. There are about 15 species known to the genus around the world, but only two can be found in China, i.e. A. sinensis and A. yunnanensis. In this study, A. sinensis and A. yunnanensis that endemic respectively to Hainan and Yunnan were sampled, on the basis of the investigation and observation of their main morphological features in plantation. Five primers, i.e. ITS2, matK, trnL-trnF1, trnL-trnF2, and trnH-psbA, were eventually selected for DNA barcoding. The results showed that the seed surface of A. sinensis is smooth or sparsely pubescent, and the seed appendages were long. While the seed surface of A. yunnanensis is densely covered with yellow hairs and the seed appendages are short. The trnL-trnF1 sequence fragment has significant intraspecific and interspecific genetic distances. However, the species identification success rate of ITS2+matK combination was finally screened to be the highest, which was verified by the BBA method of TaxonDNA. The phylogenetic trees cluster analysis revealed that the classification of A. sinensis and A. yunnanensis is significant, and there is geographic isolation between the two species. Therefore, on the premise of accurate identification of plant morphological characters, ITS2+matK combination can be used to accurately identify the Aquilaria species in China.},
}
@article {pmid33969207,
year = {2021},
author = {Jiang, M and Li, Y and Chen, H and Wang, B and Liu, C},
title = {Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Lactuca raddeana and Lactuca sativa.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {6},
number = {4},
pages = {1498-1506},
pmid = {33969207},
issn = {2380-2359},
abstract = {Lactuca raddeana is a biennial plant of the Lactuca genus belonging to the Asteraceae family. The classification of Lactuca is controversial, and no consistent conclusions have been reached based on the analysis of morphological characters and different molecular markers. Here, we sequenced and assembled the complete chloroplast genome of L. raddeana. This genome has a total length of 152,339 bp, a conservative quartile structure that is composed of a large single-copy (LSC) region of 83,976 bp, a small-copy (SSC) region of 18,521 bp, and a pair of inverted repeats (IRs) of 24,921 bp. The genome contains 112 unique genes, including 79 protein-coding, four rRNA, and 29 tRNA genes. Repeat analysis obtained 17 microsatellite, 16 tandem, and 17 interspersed repeats. Comparison of sequence divergence between L. raddeana and L. sativa found the intergenic spacer trnC-petN exhibited the highest degree of variation. Three phylogenetic trees based on the 72 shared protein, matK gene, and rbcL gene sequences showed that L. raddeana and L. sativa are clustered together. The acquisition and comparative analysis of the chloroplast genome provide a valuable resource for the taxonomic and phylogenetic studies of Lactuca.},
}
@article {pmid33967582,
year = {2021},
author = {Zeng, Z and Wang, D and Song, W and Yu, H and Zhong, Y},
title = {Clubiona jiugong sp. nov., the fifth species of C. zilla-group from China (Araneae: Clubionidae).},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e66260},
pmid = {33967582},
issn = {1314-2828},
abstract = {BACKGROUND: The Clubiona zilla-group is a relatively small species group, distributed exclusively in East Asia, with only three species clearly documented so far.<br><br>NEW INFORMATION: Clubiona hooda Dong &amp; Zhang, 2016, which was previously placed in the C. trivialis-group, is assigned to the C. zilla-group in the present paper. A new spider of the C. zilla-group from Jiugong Mountain in China is described under the name of C. jiugong sp. nov. Detailed descriptions and photographs of the new species are provided.},
}
@article {pmid33967581,
year = {2021},
author = {Javal, M and Terblanche, JS and Conlong, DE and Delahaye, N and Grobbelaar, E and Benoit, L and Lopez-Vaamonde, C and Haran, JM},
title = {DNA barcoding for bio-surveillance of emerging pests and species identification in Afrotropical Prioninae (Coleoptera, Cerambycidae).},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e64499},
pmid = {33967581},
issn = {1314-2828},
abstract = {DNA barcoding has been succesfully used for bio-surveillance of forest and agricultural pests in temperate areas, but has few applications in the tropics and particulary in Africa. Cacosceles newmannii (Coleoptera: Cerambycidae) is a Prioninae species that is locally causing extensive damage in commercially-grown sugarcane in the KwaZulu-Natal Province in South Africa. Due to the risk of spread of this species to the rest of southern Africa and to other sugarcane growing regions, clear and easy identification of this pest is critical for monitoring and for phytosanitary services. The genus Cacosceles Newman, 1838 includes four species, most being very similar in morphology. The damaging stage of the species is the larva, which is inherently difficult to distinguish morphologically from other Cerambycidae species. A tool for rapid and reliable identification of this species was needed by plant protection and quarantine agencies to monitor its potential abundance and spread. Here, we provide newly-generated barcodes for C. newmannii that can be used to reliably identify any life stage, even by non-trained taxonomists. In addition, we compiled a curated DNA barcoding reference library for 70 specimens of 20 named species of Afrotropical Prioninae to evaluate DNA barcoding as a valid tool to identify them. We also assessed the level of deeply conspecific mitochondrial lineages. Sequences were assigned to 42 different Barcode Index Numbers (BINs), 28 of which were new to BOLD. Out of the 20 named species barcoded, 11 (52.4%) had their own unique Barcode Index Number (BIN). Eight species (38.1%) showed multiple BINs with no morphological differentiation. Amongst them, C. newmannii showed two highly divergent genetic clusters which co-occur sympatrically, but further investigation is required to test whether they could represent new cryptic species.},
}
@article {pmid33965834,
year = {2021},
author = {Bruňáková, K and Bálintová, M and Henzelyová, J and Kolarčik, V and Kimáková, A and Petijová, L and Čellárová, E},
title = {Phytochemical profiling of several Hypericum species identified using genetic markers.},
journal = {Phytochemistry},
volume = {187},
number = {},
pages = {112742},
doi = {10.1016/j.phytochem.2021.112742},
pmid = {33965834},
issn = {1873-3700},
mesh = {Chromatography, High Pressure Liquid ; Genetic Markers ; *Hypericum ; Phloroglucinol ; Phytochemicals ; Plant Extracts ; },
abstract = {In the present study, we performed phytochemical profiling of several under-exploited Hypericum representatives taxonomically belonging to the sections Ascyreia, Androsaemum, Inodora, Hypericum, Coridium, Myriandra, and Adenosepalum. The authenticity of the starting plant material was confirmed using the nuclear ribosomal internal transcribed spacer as a molecular marker, DNA content and chromosome number. Phenolic constituents were analyzed using high-performance liquid chromatography to complement species-specific metabolic profiles. In several Hypericum representatives, the pharmacologically important compounds, including naphthodianthrones; phloroglucinol derivatives; chlorogenic acid; and some classes of flavonoids, particularly the flavonols rutin and hyperoside, flavanol catechin, and flavanones naringenin and naringin, were reported for the first time. Comparative multivariate analysis of chemometric data for seedlings cultured in vitro and acclimated to the outdoor conditions revealed a strong genetically predetermined interspecific variability in phenolic compound content. In addition to hypericins, which are the most abundant chemomarkers for the genus Hypericum, rarely employed phenolic metabolites, including phloroglucinol derivatives, chlorogenic acid, catechin, naringenin, naringin, and kaempferol-3-O-glucoside, were shown to be useful for discriminating between closely related species. Given the increasing interest in natural products of the genus Hypericum, knowledge of the spectrum of phenolic compounds in shoot cultures is a prerequisite for future biotechnological applications. In addition, phytochemical profiling should be considered as an additional part of the integrated plant authentication system, which predominantly relies upon genetic markers.},
}
@article {pmid33963199,
year = {2021},
author = {Seth, S and Bhattacharya, A},
title = {DNA barcodes using a double nanopore system.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {9799},
pmid = {33963199},
issn = {2045-2322},
support = {R21 HG011236/HG/NHGRI NIH HHS/United States ; 1R21HG011236-01/HG/NHGRI NIH HHS/United States ; },
mesh = {DNA/*genetics ; *DNA Barcoding, Taxonomic ; *Nanopores ; },
abstract = {The potential of a double nanopore system to determine DNA barcodes has been demonstrated experimentally. By carrying out Brownian dynamics simulation on a coarse-grained model DNA with protein tag (barcodes) at known locations along the chain backbone, we demonstrate that due to large variation of velocities of the chain segments between the tags, it is inevitable to under/overestimate the genetic lengths from the experimental current blockade and time of flight data. We demonstrate that it is the tension propagation along the chain's backbone that governs the motion of the entire chain and is the key element to explain the non uniformity and disparate velocities of the tags and DNA monomers under translocation that introduce errors in measurement of the length segments between protein tags. Using simulation data we further demonstrate that it is important to consider the dynamics of the entire chain and suggest methods to accurately decipher barcodes. We introduce and validate an interpolation scheme using simulation data for a broad distribution of tag separations and suggest how to implement the scheme experimentally.},
}
@article {pmid33962655,
year = {2021},
author = {Uiterwijk, M and Ibáñez-Justicia, A and van de Vossenberg, B and Jacobs, F and Overgaauw, P and Nijsse, R and Dabekaussen, C and Stroo, A and Sprong, H},
title = {Imported Hyalomma ticks in the Netherlands 2018-2020.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {244},
pmid = {33962655},
issn = {1756-3305},
mesh = {Animal Migration ; Animals ; Bird Diseases/epidemiology/parasitology ; Birds/*parasitology ; Cross-Sectional Studies ; Female ; Horse Diseases/epidemiology/parasitology ; Horses/parasitology ; Humans ; Ixodidae/*classification/genetics ; Male ; Netherlands/epidemiology ; Phylogeny ; Tick Infestations/epidemiology/*parasitology/*veterinary ; },
abstract = {BACKGROUND: Ticks of the genus Hyalomma, which are vectors for several tick-borne diseases, are occasionally found in areas outside their endemic range including northern parts of Europe. The objective of this study was to analyse adult Hyalomma ticks that were recently found in the Netherlands.<br><br>METHODS: Hyalomma ticks were morphologically identified. Cluster analysis, based upon sequence data (cox1 barcoding) for molecular identification, and pathogen detection&#xa0;were performed. Additionally, a cross-sectional survey of horses was conducted to actively search for Hyalomma ticks in summer 2019. Analysis of temperature was done to assess the possibility of (i) introduced engorged nymphs moulting to adults and (ii) establishment of populations in the Netherlands.<br><br>RESULTS: Seventeen adult Hyalomma ticks (one in 2018, eleven in 2019, five in 2020) were found by citizens and reported. Fifteen ticks were detected on horses and two on humans. Twelve were identified as H. marginatum, one as H. rufipes and four, of which only photographic images were available, as Hyalomma sp. No Crimean-Congo haemorrhagic fever virus or Babesia/Theileria parasites were detected. One adult tick tested positive for Rickettsia aeschlimannii. In the cross-sectional horse survey, no Hyalomma ticks were found. Analysis of temperatures showed that engorged nymphs arriving on migratory birds in spring were able to moult to adults in 2019 and 2020, and that cumulative daily temperatures in the Netherlands were lower than in areas with established H. marginatum populations.<br><br>CONCLUSIONS: Our results show that Hyalomma ticks are regularly introduced in the Netherlands as nymphs. Under the Dutch weather conditions,&#xa0;these nymphs&#xa0;are able to develop to the adult stage, which&#xa0;can be sighted by vigilant citizens. Only one human pathogen, Rickettsia aeschlimannii, was found in one of the ticks. The risk of introduction of tick-borne diseases via Hyalomma ticks on migratory birds is considered to be low. Establishment of permanent Hyalomma populations is considered unlikely under the current Dutch climatic conditions.},
}
@article {pmid33960644,
year = {2021},
author = {Reisman, BJ and Barone, SM and Bachmann, BO and Irish, JM},
title = {DebarcodeR increases fluorescent cell barcoding capacity and accuracy.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {99},
number = {9},
pages = {946-953},
pmid = {33960644},
issn = {1552-4930},
support = {P30 DK058404/DK/NIDDK NIH HHS/United States ; U01 TR002625/TR/NCATS NIH HHS/United States ; T32 GM152284/GM/NIGMS NIH HHS/United States ; R01 GM092218/GM/NIGMS NIH HHS/United States ; U54 CA217450/CA/NCI NIH HHS/United States ; R01 CA226833/CA/NCI NIH HHS/United States ; T32 GM007347/GM/NIGMS NIH HHS/United States ; F30 CA236131/CA/NCI NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; T32 GM065086/GM/NIGMS NIH HHS/United States ; },
mesh = {Cell Line ; Flow Cytometry ; *Fluorescent Dyes ; Reproducibility of Results ; },
abstract = {Fluorescent cell barcoding (FCB) enables efficient collection of tens to hundreds of flow cytometry samples by covalently marking cells with varying concentration of spectrally distinct dyes. A key consideration in FCB is to balance the density of dye barcodes, the complexity of cells in the sample, and the desired accuracy of the debarcoding. Unfortunately, barcoding bench and computational methods have not benefited from the high dimensional revolution in cytometry due to a lack of automated computational tools that effectively balance these common cytometry needs. DebarcodeR addresses these unmet needs by providing a framework for computational debarcoding augmented by improvements to experimental methods. Adaptive regression modeling accounted for differential dye uptake between different cell types and Gaussian mixture modeling provided a robust method to probabilistically assign cells to samples. Assignment tolerance parameters are available to allow users to balance high cell recovery with accurate assignments. Improvements to experimental methods include: (1) inclusion of an "external standard" control where a pool of all cells was stained a single level of each barcoding dyes and (2) an "internal standard" where each cell is stained with a single level of a separate dye. DebarcodeR significantly improved speed, accuracy, and reproducibility of FCB while avoiding selective loss of unusual cell subsets when debarcoding microtiter plates of cell lines and heterogenous mixtures of primary cells. DebarcodeR is available on Github as an R package that works with flowCore and Cytoverse packages at github.com/cytolab/DebarcodeR.},
}
@article {pmid33958935,
year = {2021},
author = {Jang, JE and Park, JS and Jung, JY and Kim, DK and Yang, S and Choi, HJ},
title = {Notes on Allium section Rhizirideum (Amaryllidaceae) in South Korea and northeastern China: with a new species from Ulleungdo Island.},
journal = {PhytoKeys},
volume = {176},
number = {},
pages = {1-19},
pmid = {33958935},
issn = {1314-2011},
abstract = {Allium section Rhizirideum is reviewed for South Korea and neighboring northeastern China based on critical observation of wild populations and herbarium materials. Species delimitations are re-evaluated on the basis of morphological and somatic chromosome numbers, resulting in the recognition of five species. Allium dumebuchum from Ulleungdo Island, South Korea, is described as a new species. This species is most similar to A. senescens due to its habits, but is clearly distinguished particularly by its rhomboid scapes in cross-secion, light purple perianth color, entire and narrowly triangular inner filaments, and flowering season from late September. One previously recognized species is placed into synonymy: A. pseudosenescens (under A. senescens). Photographs and a key to species of Allium section Rhizirideum in South Korea and northeastern China are provided in addition to information on nomenclatural types, synonymies, chromosome numbers, distribution, and specimens examined.},
}
@article {pmid33958928,
year = {2021},
author = {Zhang, J and Yu, H and Li, S},
title = {Taxonomic studies on the sac spider genus Clubiona (Araneae, Clubionidae) from Xishuangbanna Rainforest, China.},
journal = {ZooKeys},
volume = {1034},
number = {},
pages = {1-163},
pmid = {33958928},
issn = {1313-2989},
abstract = {Spiders of the genus Clubiona Latreille, 1804 from Xishuangbanna, Yunnan Province, China are studied. A total of 47 species is reported and illustrated, including 14 new species and two new synonyms. Twelve of the new species belong to four species groups: C. dengpao Yu &amp; Li, sp. nov., C. subdidentata Yu &amp; Li, sp. nov., C. tixing Yu &amp; Li, sp. nov., C. xiaoci Yu &amp; Li, sp. nov., C. xiaokong Yu &amp; Li, sp. nov., C. yejiei Yu &amp; Li, sp. nov., C. zhaoi Yu &amp; Li, sp. nov. and C. zhigangi Yu &amp; Li, sp. nov. from the C. corticalis group; C. mii Yu &amp; Li, sp. nov. and C. subtongi Yu &amp; Li, sp. nov. from the C. ternatensis group; C. banna Yu &amp; Li, sp. nov. from the C. filicata group; and C. menglun Yu &amp; Li, sp. nov. from the C. trivialis group. The remaining two new species, C. shuangsi Yu &amp; Li, sp. nov. and C. wangchengi Yu &amp; Li, sp. nov., are not readily assignable to any of the existing species groups. The female of C. cochlearis Yu &amp; Li, 2019, the female of C. tiane Yu &amp; Li, 2019, the female of C. bicornis Yu &amp; Li, 2019, the male of C. lala Jäger &amp; Dankittipakul, 2010 and the true female of C. suthepica Dankittipakul, 2008 are described for the first time. Two new synonyms are: C. vukomi Jäger &amp; Dankittipakul, 2010 syn. nov. = C. circulata Zhang &amp; Yin, 1998; C. melanothele Thorell, 1895 syn. nov. = Clubiona melanosticta Thorell, 1890. A checklist of Clubiona species from Xishuangbanna is provided. The DNA barcodes of almost all of the species were obtained for species delimitation, matching of sexes and future use.},
}
@article {pmid33958913,
year = {2021},
author = {Decaëns, T and Bénéluz, F and Ballesteros-Mejia, L and Bonilla, D and Rougerie, R},
title = {Description of three new species of Automeris Hübner, 1819 from Colombia and Brazil (Lepidoptera, Saturniidae, Hemileucinae).},
journal = {ZooKeys},
volume = {1031},
number = {},
pages = {183-204},
pmid = {33958913},
issn = {1313-2989},
abstract = {The Saturniidae is one of the most emblematic families of moths, comprising nearly 3000 species distributed globally. In this study, DNA barcode analysis and comparative morphology were combined to describe three new species within the genus Automeris, which is the most diverse genus in the family. Automeris llaneros Decaëns, Rougerie &amp; Bonilla, sp. nov., Automeris mineros Decaëns, Rougerie &amp; Bonilla, sp. nov., and Automeris belemensis Decaëns, Rougerie &amp; Bénéluz, sp. nov. are described from the Colombian Orinoco watershed, the Colombian Eastern Cordillera, and the area of endemism of Belém in the Brazilian Amazonia, respectively. They all belong to the Automeris bilinea (Walker, 1855) species subgroup, which comprises a number of species that are sometimes difficult to distinguish from each other using morphology alone. Here, the description of these three new species is based on significant differences from their closest relatives, either in terms of wing patterns, genitalia, DNA barcodes or a combination of these features.},
}
@article {pmid33958792,
year = {2021},
author = {Sojitra, M and Sarkar, S and Maghera, J and Rodrigues, E and Carpenter, EJ and Seth, S and Ferrer Vinals, D and Bennett, NJ and Reddy, R and Khalil, A and Xue, X and Bell, MR and Zheng, RB and Zhang, P and Nycholat, C and Bailey, JJ and Ling, CC and Lowary, TL and Paulson, JC and Macauley, MS and Derda, R},
title = {Genetically encoded multivalent liquid glycan array displayed on M13 bacteriophage.},
journal = {Nature chemical biology},
volume = {17},
number = {7},
pages = {806-816},
pmid = {33958792},
issn = {1552-4469},
support = {R01 AI118842/AI/NIAID NIH HHS/United States ; R01 AI050143/AI/NIAID NIH HHS/United States ; P01 HL107151/HL/NHLBI NIH HHS/United States ; R01 AI132790/AI/NIAID NIH HHS/United States ; R01 AI099141/AI/NIAID NIH HHS/United States ; R01 GM061126/GM/NIGMS NIH HHS/United States ; U54 GM062116/GM/NIGMS NIH HHS/United States ; P01 AI058113/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Bacterial Proteins/chemistry/genetics/metabolism ; Bacteriophage M13/*chemistry/genetics/metabolism ; Mice ; *Microarray Analysis ; Polysaccharides/*chemistry/genetics/metabolism ; },
abstract = {The central dogma of biology does not allow for the study of glycans using DNA sequencing. We report a liquid glycan array (LiGA) platform comprising a library of DNA 'barcoded' M13 virions that display 30-1,500 copies of glycans per phage. A LiGA is synthesized by acylation of the phage pVIII protein with a dibenzocyclooctyne, followed by ligation of azido-modified glycans. Pulldown of the LiGA with lectins followed by deep sequencing of the barcodes in the bound phage decodes the optimal structure and density of the recognized glycans. The LiGA is target agnostic and can measure the glycan-binding profile of lectins, such as CD22, on cells in vitro and immune cells in a live mouse. From a mixture of multivalent glycan probes, LiGAs identify the glycoconjugates with optimal avidity necessary for binding to lectins on living cells in vitro and in vivo.},
}
@article {pmid33958790,
year = {2021},
author = {Xiong, H and Luo, Y and Wang, Q and Yu, X and He, A},
title = {Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions.},
journal = {Nature methods},
volume = {18},
number = {6},
pages = {652-660},
pmid = {33958790},
issn = {1548-7105},
mesh = {Animals ; Chromatin/*metabolism ; DNA/genetics ; *Epigenomics ; HEK293 Cells ; Humans ; Mice ; Mouse Embryonic Stem Cells/metabolism ; NIH 3T3 Cells ; RNA/genetics ; Single-Cell Analysis/*methods ; *Transcriptome ; },
abstract = {Deciphering mechanisms in cell-fate decisions requires single-cell holistic reconstructions of multidimensional epigenomic states in transcriptional regulation. Here we develop CoTECH, a combinatorial barcoding method allowing high-throughput single-cell joint detection of chromatin occupancy and transcriptome. We used CoTECH to examine bivalent histone marks (H3K4me3 and H3K27me3) with transcription from naive to primed mouse embryonic stem cells. We also derived concurrent bivalent marks in pseudosingle cells using transcriptome as an anchor for resolving pseudotemporal bivalency trajectories and disentangling a context-specific interplay between H3K4me3/H3K27me3 and transcription level. Next, we revealed the regulatory basis of endothelial-to-hematopoietic transition in two waves of hematopoietic cells and distinctive enhancer-gene-linking schemes guiding hemogenic endothelial cell emergence, indicating a unique epigenetic control of transcriptional regulation for hematopoietic stem cell priming. CoTECH provides an efficient framework for single-cell coassay of chromatin occupancy and transcription, thus enabling higher-dimensional epigenomic reconstructions.},
}
@article {pmid33957777,
year = {2021},
author = {Mark, K and Cornejo, C and Keller, C and Flück, D and Scheidegger, C},
title = {Correction: Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation.},
journal = {Genome},
volume = {64},
number = {6},
pages = {591-594},
doi = {10.1139/gen-2021-0032},
pmid = {33957777},
issn = {1480-3321},
}
@article {pmid33952762,
year = {2021},
author = {Waki, T and Ohari, Y and Hayashi, K and Moribe, J and Matsuo, K and Takashima, Y},
title = {The first detection of Dicrocoelium chinensis sporocysts from the land snail Aegista vulgivaga in Gifu Prefecture, Japan.},
journal = {The Journal of veterinary medical science},
volume = {83},
number = {6},
pages = {957-961},
pmid = {33952762},
issn = {1347-7439},
mesh = {Animals ; *Deer ; *Dicrocoelium ; Japan/epidemiology ; Oocysts ; Snails ; },
abstract = {Trematodes of the genus Dicrocoelium are one of the most common parasites in ruminant animals; however, their life cycles in Japan are unclear. To find the sporocysts of D. chinensis in the natural field, we sampled 269 land snails (14 species) at a location with high level infection of sika deer in Gifu Prefecture, Honshu Island, Japan in autumn between 2017 and 2019. During the sampling period, we found mother sporocysts in the hepatopancreas of Aegista vulgivaga and Cyclophorus herklotsi. DNA barcoding based on the sequences of cytochrome c oxidase subunit 1 showed that the sporocysts from A. vulgivaga belonged to D. chinensis, indicating that this snail has potential as the first intermediate host of D. chinensis at this location.},
}
@article {pmid33951420,
year = {2021},
author = {Pramual, P and Jomkumsing, P and Piraonapicha, K and Jumpato, W},
title = {Integrative taxonomy uncovers a new Culicoides (Diptera: Ceratopogonidae) biting midge species from Thailand.},
journal = {Acta tropica},
volume = {220},
number = {},
pages = {105941},
doi = {10.1016/j.actatropica.2021.105941},
pmid = {33951420},
issn = {1873-6254},
mesh = {Animals ; Biodiversity ; Ceratopogonidae/classification/*genetics ; DNA Barcoding, Taxonomic ; Female ; Male ; Phylogeny ; Thailand ; },
abstract = {Fully understanding biodiversity often requires an integrated approach especially for small insects because species diagnostic morphological characters are limited. In this study, morphological characters and DNA barcodes were used to examine previously recognized genetically divergent lineages detected in the biting midge, Culicoides arakawae (Arakawa), from Thailand. Morphological examinations revealed that specimens belonging to one lineage are morphologically different from C. arakawae in shape of the paramere in males, and in the leg color pattern of both sexes. Therefore, a formal description is provided for this new species, Culicoides mahasarakhamense sp. nov. Based on morphological characters including a large and shallow palpal pit, one sac like spermatheca and male with parameres bent at base with large basal knob, the new species was assigned into the subgenus Meijerehelea Wirth and Hubert. Morphological differentiation including wing pattern and shape of spermatheca of the new species are discussed and compared with other members of this subgenus. Mitochondrial cytochrome c oxidase I sequence analysis indicated that this new species is different from other members of the subgenus Meijerehelea with minimum interspecific genetic divergence of 3.92%. Automatic Barcode Gap Discovery species delimitation analysis also supported the recognition of a new species. Phylogenetic analyses revealed that the new species is closely related to C. arakawae, consistent with morphological similarity of these species. Results of this study highlight the necessity of using integrated approach for Culicoides taxonomy.},
}
@article {pmid33945952,
year = {2021},
author = {Adolfsson, E and Qvick, A and Gréen, H and Kling, D and Gunnarsson, C and Jonasson, J and Gréen, A},
title = {Technical in-depth comparison of two massive parallel DNA-sequencing methods for formalin-fixed paraffin-embedded tissue from victims of sudden cardiac death.},
journal = {Forensic science international. Genetics},
volume = {53},
number = {},
pages = {102522},
doi = {10.1016/j.fsigen.2021.102522},
pmid = {33945952},
issn = {1878-0326},
mesh = {*DNA Mutational Analysis ; Death, Sudden, Cardiac/*etiology ; Formaldehyde ; Genetic Testing/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Paraffin Embedding ; Sequence Analysis, DNA ; },
abstract = {Sudden cardiac death (SCD) is a tragic and traumatic event. SCD is often associated with hereditary genetic disease and in such cases, sequencing of stored formalin fixed paraffin embedded (FFPE) tissue is often crucial in trying to find a causal genetic variant. This study was designed to compare two massive parallel sequencing assays for differences in sensitivity and precision regarding variants related to SCD in FFPE material. From eight cases of SCD where DNA from blood had been sequenced using HaloPlex, corresponding FFPE samples were collected six years later. DNA from FFPE samples were amplified using HaloPlex HS, sequenced on MiSeq, representing the first method, as well as amplified using modified Twist and sequenced on NextSeq, representing the second method. Molecular barcodes were included to distinguish artefacts from true variants. In both approaches, read coverage, uniformity and variant detection were compared using genomic DNA isolated from blood and corresponding FFPE tissue, respectively. In terms of coverage uniformity, Twist performed better than HaloPlex HS for FFPE samples. Despite higher overall coverage, amplicon-based HaloPlex technologies, both for blood and FFPE tissue, suffered from design and/or performance issues resulting in genes lacking complete coverage. Although Twist had considerably lower overall mean coverage, high uniformity resulted in equal or higher fraction of genes covered at ≥ 20X. By comparing variants found in the matched samples in a pre-defined cardiodiagnostic gene panel, HaloPlex HS for FFPE material resulted in high sensitivity, 98.0% (range 96.6-100%), and high precision, 99.9% (range 99.5-100%) for moderately fragmented samples, but suffered from reduced sensitivity (range 74.2-91.1%) in more severely fragmented samples due to lack of coverage. Twist had high sensitivity, 97.8% (range 96.8-98.7%) and high precision, 99.9% (range 99.3-100%) in all analyzed samples, including the severely fragmented samples.},
}
@article {pmid33945437,
year = {2021},
author = {Nguyen, HDT and McCormick, W and Eyres, J and Eggertson, Q and Hambleton, S and Dettman, JR},
title = {Development and evaluation of a target enrichment bait set for phylogenetic analysis of oomycetes.},
journal = {Mycologia},
volume = {113},
number = {4},
pages = {856-867},
doi = {10.1080/00275514.2021.1889276},
pmid = {33945437},
issn = {1557-2536},
mesh = {Fungi/genetics ; High-Throughput Nucleotide Sequencing ; *Oomycetes/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Target enrichment is a term that encompasses multiple related approaches where desired genomic regions are captured by molecular baits, leaving behind redundant or non-target regions in the genome, followed by amplification and next-generation sequencing of those captured regions. A molecular bait set was developed based on 426 single-copy, oomycete-specific orthologs and 3 barcoding genes. The bait set was tested on 27 oomycete samples (belonging to the Saprolegniales, Albuginales, and Peronosporales) derived from live and herbarium specimens, as well as control samples of true fungi and plants. Results show that (i) our method greatly enriches for the targeted orthologs on oomycete samples, but insignificantly on fungal and plant samples; (ii) an average of 263 out of 429 orthologs (61%) were recovered from oomycete live and herbarium specimens; (iii) sequencing roughly 100 000 read pairs per sample is sufficient for optimal ortholog recovery while maintaining low sequencing costs; and (iv) the expected relationships were recovered by phylogenetic analysis from the data generated. This is the first report of an oomycete-specific target enrichment method with broad potential applications for evolutionary and taxonomic studies. A key benefit of our target enrichment method is that it allows researchers to easily unlock the vast and unexplored oomycete genomic diversity stored in natural history collections.},
}
@article {pmid33944583,
year = {2021},
author = {van der Merwe, R and Halleen, F and van Dyk, M and Jacobs, VG and Mostert, L},
title = {Occurrence of Canker and Wood Rot Pathogens on Stone Fruit Propagation Material and Nursery Trees in the Western Cape of South Africa.},
journal = {Plant disease},
volume = {105},
number = {11},
pages = {3586-3599},
doi = {10.1094/PDIS-10-20-2124-RE},
pmid = {33944583},
issn = {0191-2917},
mesh = {*Fruit ; Phylogeny ; Plant Diseases ; South Africa ; *Wood ; },
abstract = {Dieback and canker of young stone fruit trees can cause suboptimal growth and even death under severe conditions. One source of inoculum of canker pathogens could be through nursery trees harboring latent infections that would not be visible to inspections done according to the deciduous fruit scheme. The objectives of this study were to identify the canker and wood rot fungal pathogens present in nursery stone fruit trees as well as in propagation material and to evaluate their pathogenicity. Isolations were made from scion and rootstock propagation material and from certified nursery stone fruit trees. The plant material sampled did not have any external symptoms. The certified nursery trees when cross-sectioned displayed brown discoloration from the pruning wound, the bud union, and often the crown. Fungal species isolated were identified by sequencing of the relevant barcoding genes and phylogenetic analyses thereof. Canker- and wood rot-associated fungi were identified. Buds used for budding had low levels of infection, with 1.2% of dormant buds infected and 0.4% of green buds infected. The dormant rootstock shoots had a canker pathogen incidence of 6.2% before they were planted in the nursery fields and increased inasmuch as the ungrafted, rooted rootstock plants had 11.1% infection with canker and wood rot pathogens. Out of 1,080 nursery trees, the canker- and wood rot-associated fungi infected 21.8% of trees. The canker-causing pathogens that were isolated the most were Cadophora luteo-olivacea and Diplodia seriata. A low incidence of wood rot fungi was found, with only 1.5% of nursery trees infected. In total, 26 new reports of fungal species on stone fruit in South Africa were made. Of these, 22 have not been found on stone fruit worldwide. The pathogenicity trials' results confirmed the pathogenic status of these newly reported species. All of the isolates tested formed lesions significantly longer than the control, 4 months after wound inoculation of 2-year-old shoots of two plum orchards. Lasiodiplodia theobromae was the most virulent species on both plum cultivars. The results of this research showed that nursery stone fruit trees and propagation material can harbor latent infections. Different management practices need to be evaluated to prevent these infections to ensure healthier stone fruit nursery trees.},
}
@article {pmid33942871,
year = {2021},
author = {Dietschler, NJ and Bittner, TD and Trotter, RT and Fahey, TJ and Whitmore, MC},
title = {Biological Control of Hemlock Woolly Adelgid: Implications of Adult Emergence Patterns of Two Leucopis spp. (Diptera: Chamaemyiidae) and Laricobius nigrinus (Coleoptera: Derodontidae) Larval Drop.},
journal = {Environmental entomology},
volume = {50},
number = {4},
pages = {803-813},
doi = {10.1093/ee/nvab037},
pmid = {33942871},
issn = {1938-2936},
mesh = {Animals ; *Coleoptera ; *Diptera ; *Hemiptera ; *Hemlock ; Larva ; Predatory Behavior ; Tsuga ; Washington ; },
abstract = {The hemlock woolly adelgid (Hemiptera: Adelgidae Adelges tsugae Annand) poses a serious threat to hemlocks in eastern North America, and ongoing research is focused on the identification and development of biological controls to protect and manage hemlock resources. Three predators native to the Pacific Northwest of North America that have been the focus of much research are Leucopis argenticollis (Zetterstedt), Leucopis piniperda (Malloch) (Diptera: Chamaemyiidae), and Laricobius nigrinus (Fender) (Coleoptera: Derodontidae). This study addresses the knowledge gap of adult Leucopis spp. emergence patterns, with comparisons to the timing of larval La. nigrinus drop for pupation. Adult Leucopis spp. emergence was observed in the lab from field-collected, adelgid-infested foliage from Washington state in 2019 and 2020. Adult Leucopis spp. were collected daily as they emerged from foliage collections and identified to species using morphological features; a subset was validated using DNA barcoding. Accumulated heating degree days were calculated to compare a standardized emergence timing across collections made at different locations and temperature regimes. The abundance of the two Leucopis spp. and of the combined Leucopis spp. and La. nigrinus varied among sites and years, and no species was consistently more abundant than the other. Evaluations of seasonal emergence trends of the three species determine the predator complex behaves in a temporally stratified and predictable way. Emergence of adult Le. argenticollis was observed first, followed by La. nigrinus larval drop, with Le. piniperda emerging at the end of larval drop, and finally a second emergence of Le. argenticollis.},
}
@article {pmid33942522,
year = {2021},
author = {Arida, E and Ashari, H and Dahruddin, H and Fitriana, YS and Hamidy, A and Irham, M and Kadarusman, and Riyanto, A and Wiantoro, S and Zein, MSA and Hadiaty, RK and Apandi, and Krey, F and Kurnianingsih, and Melmambessy, EHP and Mulyadi, and Ohee, HL and Saidin, and Salamuk, A and Sauri, S and Suparno, and Supriatna, N and Suruwaky, AM and Laksono, WT and Warikar, EL and Wikanta, H and Yohanita, AM and Slembrouck, J and Legendre, M and Gaucher, P and Cochet, C and Delrieu-Trottin, E and Thébaud, C and Mila, B and Fouquet, A and Borisenko, A and Steinke, D and Hocdé, R and Semiadi, G and Pouyaud, L and Hubert, N},
title = {Exploring the vertebrate fauna of the Bird's Head Peninsula (Indonesia, West Papua) through DNA barcodes.},
journal = {Molecular ecology resources},
volume = {21},
number = {7},
pages = {2369-2387},
doi = {10.1111/1755-0998.13411},
pmid = {33942522},
issn = {1755-0998},
support = {Internal//Fondation Veolia Environnement/ ; Internal//COLAS/ ; Internal//Bollor&#xe9;/ ; Internal//Total foundation/ ; },
mesh = {Animals ; *Biodiversity ; Birds/genetics ; DNA ; *DNA Barcoding, Taxonomic ; Indonesia ; Phylogeny ; Vertebrates/genetics ; },
abstract = {Biodiversity knowledge is widely heterogeneous across the Earth's biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA-based inventory of aquatic and terrestrial vertebrate communities, which was the objective of a multidisciplinary expedition to the Bird's Head Peninsula (West Papua, Indonesia) conducted between 17 October and 20 November 2014. This expedition resulted in the assembly of 1005 vertebrate DNA barcodes. Based on the use of multiple species-delimitation methods (GMYC, PTP, RESL, ABGD), 264 molecular operational taxonomic units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird's Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed.},
}
@article {pmid33941929,
year = {2021},
author = {Cohen, JD and Douville, C and Dudley, JC and Mog, BJ and Popoli, M and Ptak, J and Dobbyn, L and Silliman, N and Schaefer, J and Tie, J and Gibbs, P and Tomasetti, C and Papadopoulos, N and Kinzler, KW and Vogelstein, B},
title = {Detection of low-frequency DNA variants by targeted sequencing of the Watson and Crick strands.},
journal = {Nature biotechnology},
volume = {39},
number = {10},
pages = {1220-1227},
pmid = {33941929},
issn = {1546-1696},
support = {U01 CA200469/CA/NCI NIH HHS/United States ; U01 CA152753/CA/NCI NIH HHS/United States ; P50 CA228991/CA/NCI NIH HHS/United States ; U01 CA230691/CA/NCI NIH HHS/United States ; R37 CA230400/CA/NCI NIH HHS/United States ; T32 GM007309/GM/NIGMS NIH HHS/United States ; T32 GM136577/GM/NIGMS NIH HHS/United States ; },
mesh = {Biomarkers, Tumor/blood/genetics ; DNA Mutational Analysis/*methods ; DNA, Neoplasm/blood/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Mutation ; Mutation Rate ; Polymerase Chain Reaction ; },
abstract = {Identification and quantification of low-frequency mutations remain challenging despite improvements in the baseline error rate of next-generation sequencing technologies. Here, we describe a method, termed SaferSeqS, that addresses these challenges by (1) efficiently introducing identical molecular barcodes in the Watson and Crick strands of template molecules and (2) enriching target sequences with strand-specific PCR. The method achieves high sensitivity and specificity and detects variants at frequencies below 1 in 100,000 DNA template molecules with a background mutation rate of <5 × 10[-7] mutants per base pair (bp). We demonstrate that it can evaluate mutations in a single amplicon or simultaneously in multiple amplicons, assess limited quantities of cell-free DNA with high recovery of both strands and reduce the error rate of existing PCR-based molecular barcoding approaches by >100-fold.},
}
@article {pmid33941896,
year = {2021},
author = {Song, P and Chen, SX and Yan, YH and Pinto, A and Cheng, LY and Dai, P and Patel, AA and Zhang, DY},
title = {Selective multiplexed enrichment for the detection and quantitation of low-fraction DNA variants via low-depth sequencing.},
journal = {Nature biomedical engineering},
volume = {5},
number = {7},
pages = {690-701},
pmid = {33941896},
issn = {2157-846X},
support = {R01 CA203964/CA/NCI NIH HHS/United States ; U01 CA233364/CA/NCI NIH HHS/United States ; },
mesh = {Carcinoma, Non-Small-Cell Lung/genetics/pathology ; Cell Line ; DNA/*analysis/genetics/metabolism ; Databases, Genetic ; Gene Frequency ; Gene Library ; Genetic Heterogeneity ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Lung Neoplasms/genetics/pathology ; Melanoma/genetics/pathology ; Multiplex Polymerase Chain Reaction/methods ; Mutation ; Polymorphism, Single Nucleotide ; },
abstract = {DNA sequence variants with allele fractions below 1% are difficult to detect and quantify by sequencing owing to intrinsic errors in sequencing-by-synthesis methods. Although molecular-identifier barcodes can detect mutations with a variant-allele frequency (VAF) as low as 0.1% using next-generation sequencing (NGS), sequencing depths of over 25,000× are required, thus hampering the detection of mutations at high sensitivity in patient samples and in most samples used in research. Here we show that low-frequency DNA variants can be detected via low-depth multiplexed NGS after their amplification, by a median of 300-fold, using polymerase chain reaction and rationally designed 'blocker' oligonucleotides that bind to the variants. Using an 80-plex NGS panel and a sequencing depth of 250×, we detected single nucleotide polymorphisms with a VAF of 0.019% and contamination in human cell lines at a VAF as low as 0.07%. With a 16-plex NGS panel covering 145 mutations across 9 genes involved in melanoma, we detected low-VAF mutations (0.2-5%) in 7 out of the 19 samples of freshly frozen tumour biopsies, suggesting that tumour heterogeneity could be notably higher than previously recognized.},
}
@article {pmid33940603,
year = {2021},
author = {Weaver, KD and De Los Santos, Y and Gaffar, M and Zona, MC and Gennaro, T and Shenoy, A and Flax, S and Chamala, S and Seifert, RP and Esnakula, AK},
title = {Wrong Tissue in Block.},
journal = {American journal of clinical pathology},
volume = {156},
number = {4},
pages = {700-707},
doi = {10.1093/ajcp/aqab011},
pmid = {33940603},
issn = {1943-7722},
mesh = {*Clinical Laboratory Information Systems ; Humans ; Medical Errors/prevention &amp; control ; Pathology, Surgical/*organization &amp; administration ; Specimen Handling/*standards ; Workflow ; },
abstract = {OBJECTIVES: Maintaining specimen identity during surgical pathology tissue processing is critical. Epic Beaker Laboratory Information System requires sequential scanning of specimen label and grossed blocks (block confirmation) to ensure specimen identity. We report our institution's experience with wrong tissue in block (WTIB) grossing errors before and after adopting block confirmation.<br><br>METHODS: During the first 18 months of Beaker implementation, block confirmation was not required. We then mandated block confirmation for a 3-month period. To ensure compliance, we then built a "hard stop" feature that prevents scanning any unconfirmed blocks onto a packing list. We reviewed WTIB incidents pre- and postimplementation of these solutions.<br><br>RESULTS: Before using block confirmation, we had WTIB incidents involving 17 (0.043%) of 38,848 cases. When we mandated block confirmation use, we had WTIB involving 2 (0.043%) of 4,646 cases. After implementing the hard stop feature, we had WTIB incidents involving 2 (0.005%) of 42,411 cases. Overall, there was an 88.4% (0.043% vs 0.005%; P < .001) reduction in WTIB incidents using block confirmation with a hard stop.<br><br>CONCLUSIONS: Beaker is a customizable platform that can be tailored to a laboratory's workflow. By using barcoding, implementing custom-built features, and improving workflow protocols, we significantly reduced WTIB errors.},
}
@article {pmid33935549,
year = {2021},
author = {Xu, H and Zhang, X and Yao, Z and Ali, A and Li, S},
title = {Thirty-five new species of the spider genus Pimoa (Araneae, Pimoidae) from Pan-Himalaya.},
journal = {ZooKeys},
volume = {1029},
number = {},
pages = {1-92},
pmid = {33935549},
issn = {1313-2989},
abstract = {Thirty-five new species of the Pimoa Chamberlin &amp; Ivie, 1943 are described from Pan-Himalaya: P. anning Zhang &amp; Li, sp. nov. (♂♀), P. bomi Zhang &amp; Li, sp. nov. (♂♀), P. cawarong Zhang &amp; Li, sp. nov. (♀), P. daman Zhang &amp; Li, sp. nov. (♀), P. danba Zhang &amp; Li, sp. nov. (♀), P. deqen Zhang &amp; Li, sp. nov. (♀), P. dongjiu Zhang &amp; Li, sp. nov. (♂♀), P. guiqing Zhang &amp; Li, sp. nov. (♀), P. gyaca Zhang &amp; Li, sp. nov. (♀), P. gyara Zhang &amp; Li, sp. nov. (♂♀), P. gyirong Zhang &amp; Li, sp. nov. (♂♀), P. heishui Zhang &amp; Li, sp. nov. (♂♀), P. jinchuan Zhang &amp; Li, sp. nov. (♂♀), P. khaptad Zhang &amp; Li, sp. nov. (♀), P. koshi Zhang &amp; Li, sp. nov. (♀), P. lhatog Zhang &amp; Li, sp. nov. (♀), P. mechi Zhang &amp; Li, sp. nov. (♂♀), P. miandam Zhang &amp; Li, sp. nov. (♂♀), P. miero Zhang &amp; Li, sp. nov. (♂♀), P. mude Zhang &amp; Li, sp. nov. (♀), P. muli Zhang &amp; Li, sp. nov. (♂♀), P. naran Zhang &amp; Li, sp. nov. (♀), P. ninglang Zhang &amp; Li, sp. nov. (♀), P. nyalam Zhang &amp; Li, sp. nov. (♂♀), P. phaplu Zhang &amp; Li, sp. nov. (♂♀), P. putou Zhang &amp; Li, sp. nov. (♀), P. rara Zhang &amp; Li, sp. nov. (♀), P. sangri Zhang &amp; Li, sp. nov. (♂♀), P. shigatse Zhang &amp; Li, sp. nov. (♀), P. tengchong Zhang &amp; Li, sp. nov. (♂♀), P. xiahe Zhang &amp; Li, sp. nov. (♂♀), P. yejiei Zhang &amp; Li, sp. nov. (♀), P. yele Zhang &amp; Li, sp. nov. (♂♀), P. zayu Zhang &amp; Li, sp. nov. (♂♀), P. zhigangi Zhang &amp; Li, sp. nov. (♀). The DNA barcodes of the thirty-five new species are provided.},
}
@article {pmid33932143,
year = {2021},
author = {Wei, X and Li, X and Chen, T and Chen, Z and Jin, Y and Malik, K and Li, C},
title = {Complete chloroplast genomes of Achnatherum inebrians and comparative analyses with related species from Poaceae.},
journal = {FEBS open bio},
volume = {11},
number = {6},
pages = {1704-1718},
pmid = {33932143},
issn = {2211-5463},
mesh = {China ; Genome, Chloroplast/*genetics ; Microsatellite Repeats ; Phylogeny ; Poaceae/*genetics ; },
abstract = {This article reports the complete chloroplast genome of Achnatherum inebrians, a poisonous herb that is widely distributed in the rangelands of Northern China. The genome is 137 714 bp in total and consists of a large single-copy (81 758 bp) region and small single-copy (12 682 bp) region separated by a pair of inverted repeats (21 637 bp). The genome contains 130 genes, including 84 protein-coding genes, 38 tRNA genes and 8 ribosomal RNA genes, and the guanine + cytosine content is 36.17%. We subsequently performed comparative analysis of complete genomes from A. inebrians and other Poaceae-related species from GenBank. Thirty-eight simple sequence repeats were identified, further demonstrating rapid evolution in Poaceae. Finally, the phylogenetic trees of 37 species of Poaceae and 2 species of Amaranthaceae were constructed by using maximum likelihood and Bayesian inference methods, based on the genes of the complete chloroplast genome. We identified hotspots that can be used as molecular markers and barcodes for phylogenetic analysis, as well as for species identification. Phylogenetic analysis indicated that A. inebrians is a member of the genus Stipa rather than Achnatherum.},
}
@article {pmid33930740,
year = {2021},
author = {Chaliha, C and Kaladhar, VC and Doley, R and Verma, PK and Kumar, A and Kalita, E},
title = {Bipartite molecular approach for species delimitation and resolving cryptic speciation of Exobasidium vexans within the Exobasidium genus.},
journal = {Computational biology and chemistry},
volume = {92},
number = {},
pages = {107496},
doi = {10.1016/j.compbiolchem.2021.107496},
pmid = {33930740},
issn = {1476-928X},
mesh = {Basidiomycota/*genetics ; Bayes Theorem ; DNA, Fungal/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Exobasidium vexans, a basidiomycete pathogen, is the causal organism of blister blight disease in tea. The molecular identification of the pathogen remains a challenge due to the limited availability of genomic data in sequence repositories and cryptic speciation within its genus Exobasidium. In this study, the nuclear internal transcribed spacer rDNA region (ITS) based DNA barcode was developed for E. vexans, to address the problem of molecular identification within the background of cryptic speciation. The isolation of E. vexans strain was confirmed through morphological studies followed by molecular identification utilizing the developed ITS barcode. Phylogenetic analysis based on Maximum Parsimony (MP), Maximum Likelihood (ML) and Bayesian Inference (BI) confirmed the molecular identification of the pathogen as E. vexans strain. Further, BI analysis using BEAST mediated the estimation of the divergence time and evolutionary relationship of E. vexans within genus Exobasidium. The speciation process followed the Yule diversification model wherein the genus Exobasidium is approximated to have diverged in the Paleozoic era. The study thus sheds light on the molecular barcode-based species delimitation and evolutionary relationship of E. vexans within its genus Exobasidium.},
}
@article {pmid33927337,
year = {2021},
author = {Park, HS and Jayakodi, M and Lee, SH and Jeon, JH and Lee, HO and Park, JY and Moon, BC and Kim, CK and Wing, RA and Newmaster, SG and Kim, JY and Yang, TJ},
title = {Author Correction: Mitochondrial plastid DNA can cause DNA barcoding paradox in plants.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {9599},
doi = {10.1038/s41598-021-89266-5},
pmid = {33927337},
issn = {2045-2322},
}
@article {pmid33927222,
year = {2021},
author = {Stenvers, VI and Hauss, H and Osborn, KJ and Neitzel, P and Merten, V and Scheer, S and Robison, BH and Freitas, R and Hoving, HJT},
title = {Distribution, associations and role in the biological carbon pump of Pyrosoma atlanticum (Tunicata, Thaliacea) off Cabo Verde, NE Atlantic.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {9231},
pmid = {33927222},
issn = {2045-2322},
abstract = {Gelatinous zooplankton are increasingly acknowledged to contribute significantly to the carbon cycle worldwide, yet many taxa within this diverse group remain poorly studied. Here, we investigate the pelagic tunicate Pyrosoma atlanticum in the waters surrounding the Cabo Verde Archipelago. By using a combination of pelagic and benthic in situ observations, sampling, and molecular genetic analyses (barcoding, eDNA), we reveal that: P. atlanticum abundance is most likely driven by local island-induced productivity, that it substantially contributes to the organic carbon export flux and is part of a diverse range of biological interactions. Downward migrating pyrosomes actively transported an estimated 13% of their fecal pellets below the mixed layer, equaling a carbon flux of 1.96-64.55 mg C m[-2] day[-1]. We show that analysis of eDNA can detect pyrosome material beyond their migration range, suggesting that pyrosomes have ecological impacts below the upper water column. Moribund P. atlanticum colonies contributed an average of 15.09 ± 17.89 (s.d.) mg C m[-2] to the carbon flux reaching the island benthic slopes. Our pelagic in situ observations further show that P. atlanticum formed an abundant substrate in the water column (reaching up to 0.28 m[2] substrate area per m[2]), with animals using pyrosomes for settlement, as a shelter and/or a food source. In total, twelve taxa from four phyla were observed to interact with pyrosomes in the midwater and on the benthos.},
}
@article {pmid33922516,
year = {2021},
author = {Grzywacz, A and Jarmusz, M and Walczak, K and Skowronek, R and Johnston, NP and Szpila, K},
title = {DNA Barcoding Identifies Unknown Females and Larvae of Fannia R.-D. (Diptera: Fanniidae) from Carrion Succession Experiment and Case Report.},
journal = {Insects},
volume = {12},
number = {5},
pages = {},
pmid = {33922516},
issn = {2075-4450},
support = {0146/IP1/2015/73//Polish Ministry of Science and Higher Education/ ; 823827 SYNTHESYS+//European Union's Horizon 2020/ ; },
abstract = {Application of available keys to European Fanniidae did not facilitate unequivocal species identification for third instar larvae and females of Fannia Robineau-Desvoidy, 1830 collected during a study of arthropod succession on pig carrion. To link these samples to known species, we took the advantage of molecular identification methods and compared newly obtained cytochrome oxidase subunit I (COI) barcode sequences against sequences deposited in reference databases. As an outcome of the results obtained, we describe for the first time a third instar larva of Fannia nigra Malloch, 1910 and Fannia pallitibia (Rondani, 1866) and a female of Fannia collini d'Assis-Fonseca, 1966. We provide combinations of characters allowing for discrimination of described insects from other Fanniidae. We provide an update for the key by Rozkošný et al. 1997, which allows differentiation between females of F. collini and other species of Fanniidae. Additionally, we provide a case of a human cadaver discovered in Southern Poland and insect fauna associated with it as the first report of F. nigra larvae developing on a human body.},
}
@article {pmid33920593,
year = {2021},
author = {Zhang, Y and Mo, M and Yang, L and Mi, F and Cao, Y and Liu, C and Tang, X and Wang, P and Xu, J},
title = {Exploring the Species Diversity of Edible Mushrooms in Yunnan, Southwestern China, by DNA Barcoding.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {7},
number = {4},
pages = {},
pmid = {33920593},
issn = {2309-608X},
support = {31870009//National Natural Science Foundation of China/ ; C176280107//Yunnan University/ ; },
abstract = {Yunnan Province, China, is famous for its abundant wild edible mushroom diversity and a rich source of the world's wild mushroom trade markets. However, much remains unknown about the diversity of edible mushrooms, including the number of wild edible mushroom species and their distributions. In this study, we collected and analyzed 3585 mushroom samples from wild mushroom markets in 35 counties across Yunnan Province from 2010 to 2019. Among these samples, we successfully obtained the DNA barcode sequences from 2198 samples. Sequence comparisons revealed that these 2198 samples likely belonged to 159 known species in 56 different genera, 31 families, 11 orders, 2 classes, and 2 phyla. Significantly, 51.13% of these samples had sequence similarities to known species at lower than 97%, likely representing new taxa. Further phylogenetic analyses on several common mushroom groups including 1536 internal transcribed spacer (ITS) sequences suggested the existence of 20 new (cryptic) species in these groups. The extensive new and cryptic species diversity in wild mushroom markets in Yunnan calls for greater attention for the conservation and utilization of these resources. Our results on both the distinct barcode sequences and the distributions of these sequences should facilitate new mushroom species discovery and forensic authentication of high-valued mushrooms and contribute to the scientific inventory for the management of wild mushroom markets.},
}
@article {pmid33918119,
year = {2021},
author = {Pappalardo, AM and Raffa, A and Calogero, GS and Ferrito, V},
title = {Geographic Pattern of Sushi Product Misdescription in Italy-A Crosstalk between Citizen Science and DNA Barcoding.},
journal = {Foods (Basel, Switzerland)},
volume = {10},
number = {4},
pages = {},
pmid = {33918119},
issn = {2304-8158},
abstract = {The food safety of sushi and the health of consumers are currently of high concern for food safety agencies across the world due to the globally widespread consumption of these products. The microbiological and toxicological risks derived from the consumption of raw fish and seafood have been highlighted worldwide, while the practice of species substitution in sushi products has attracted the interest of researchers more than food safety agencies. In this study, samples of sushi were processed for species authentication using the Cytochrome Oxidase I (COI) gene as a DNA barcode. The approach of Citizen Science was used to obtain the sushi samples by involving people from eighteen different Italian cities (Northern, Central and Southern Italy). The results indicate that a considerable rate of species substitution exists with a percentage of misdescription ranging from 31.8% in Northern Italy to 40% in Central Italy. The species most affected by replacement was Thunnus thynnus followed by the flying fish roe substituted by eggs of Mallotus villosus. These results indicate that a standardization of fish market names should be realized at the international level and that the indication of the scientific names of species should be mandatory for all products of the seafood supply chain.},
}
@article {pmid33917172,
year = {2021},
author = {Tarmizi, AAA and Wagiran, A and Mohd Salleh, F and Chua, LS and Abdullah, FI and Hasham, R and Binte Mostafiz, S},
title = {Integrated Approach for Species Identification and Quality Analysis for Labisia pumila Using DNA Barcoding and HPLC.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {4},
pages = {},
pmid = {33917172},
issn = {2223-7747},
support = {GUP-Tier 1 Grant (Q.J130000.2545.18H17).//Universiti Teknologi Malaysia/ ; },
abstract = {Labisia pumila is a precious herb in Southeast Asia that is traditionally used as a health supplement and has been extensively commercialized due to its claimed therapeutic properties in boosting a healthy female reproductive system. Indigenous people used these plants by boiling the leaves; however, in recent years it has been marketed as powdered or capsuled products. Accordingly, accuracy in determination of the authenticity of these modern herbal products has faced great challenges. Lack of authenticity is a public health risk because incorrectly used herbal species can cause adverse effects. Hence, any measures that may aid product authentication would be beneficial. Given the widespread use of Labisia herbal products, the current study focuses on authenticity testing via an integral approach of DNA barcoding and qualitative analysis using HPLC. This study successfully generated DNA reference barcodes (ITS2 and rbcL) for L. pumila var. alata and pumila. The DNA barcode that was generated was then used to identify species of Labisia pumila in herbal medicinal products, while HPLC was utilized to determine their quality. The findings through the synergistic approach (DNA barcode and HPLC) implemented in this study indicate the importance of both methods in providing the strong evidence required for the identification of true species and to examine the authenticity of such herbal medicinal products.},
}
@article {pmid33913586,
year = {2021},
author = {Faridi, E and Ghaderian, A and Honarasa, F and Shafie, A},
title = {Next generation of chemistry and biochemistry conference posters: Animation, augmented reality, visitor statistics, and visitors' attention.},
journal = {Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology},
volume = {49},
number = {4},
pages = {619-624},
doi = {10.1002/bmb.21520},
pmid = {33913586},
issn = {1539-3429},
mesh = {Audiovisual Aids/*statistics &amp; numerical data ; *Augmented Reality ; Biochemistry/*education ; Chemistry/*education ; *Communication ; Congresses as Topic ; Humans ; Information Dissemination/*methods ; Posters as Topic ; Video Recording/*methods ; },
abstract = {Every branch of science needs visitors' attention during the poster presentation session at conferences, symposiums, seminars, etc. In particular, participants in the chemistry and biochemistry conference need more visual tools to explain their research work in detail. Presence of smartphones and the ability of 2D barcodes will allow chemical reactions or processes to be shown in the form of a movie, animation or augmented reality (AR). Therefore, the next generation of posters will be more interested in this view. Here, the ability of 2D barcodes or QR codes to help researchers to catch more attention in their research work was presented during a poster presentation session. In this way, the visitors showed positive attitudes to the applicability of such tools. Also, some information including the number of poster visitors and interesting topics in the conference can be collected easily which is useful for the scientific and organizing committee of conferences. As a result, biochemistry conference posters can be presented in new ways, based on animation images or video, to capture the attention of viewers and deepen their understanding of poster concepts.},
}
@article {pmid33913162,
year = {2021},
author = {Tang, CN and Ho, HC},
title = {Description of a new perchlet, Chelidoperca formosa, from southwestern Taiwan (Peciformes: Serranidae).},
journal = {Journal of fish biology},
volume = {99},
number = {3},
pages = {844-855},
doi = {10.1111/jfb.14767},
pmid = {33913162},
issn = {1095-8649},
mesh = {Animals ; *Bass ; Gills ; *Perciformes ; Phylogeny ; Taiwan ; },
abstract = {A new perchlet species is described on the basis of four specimens collected from southwestern Taiwan. It is similar to congeners with relatively few lateral-line scales (35-38) and can be distinguished by having third to sixth dorsal-fin spines notably long; eighth and ninth dorsal-fin spines notably short; developed gill rakers 1 + 7-8; scale rows between lateral line and sixth dorsal-fin spine 4 (the dorsalmost half-sized); tip of upper corner of caudal fin reddish; four reddish bands midlaterally on body with groups of melanophores in these bands. DNA barcoding analysis reveals the new species is a distinct lineage and closest to Chelidoperca microdon. The average interspecific genetic distance calculated by the K2P model is 15.4%, whereas the mean distance from the new species to C. microdon is 18.3%. The inferred phylogenetic tree supports monophyly of Chelidoperca. Including the new species, six nominal species of Chelidoperca are recognized in Taiwanese waters.},
}
@article {pmid33913093,
year = {2021},
author = {Thakur, VV and Tripathi, N and Tiwari, S},
title = {DNA barcoding of some medicinally important plant species of Lamiaceae family in India.},
journal = {Molecular biology reports},
volume = {48},
number = {4},
pages = {3097-3106},
pmid = {33913093},
issn = {1573-4978},
mesh = {Classification ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Genetic Techniques ; Genetic Variation ; India ; *Lamiaceae/classification/genetics ; Phylogeny ; *Plants, Medicinal/classification/genetics ; },
abstract = {Several species of the Lamiaceae family are the primary source of bioactive aromatic oils and secondary metabolites, having broader applications in the cosmetics, pharmaceuticals, food, confectionery and liquor industries. Due to the scarcity of raw materials and high costs of this family's economically vital species, its products often adulterated to cater to the market's high demand. The present study provides a DNA based approach for identifying different species of this family. Henceforth, the performance of three already proposed barcode loci (matK, trnH-psbA and trnL) was examined for their PCR amplification and species recognition efficacy on various Lamiaceae species and cultivars using three different approaches such as pairwise genetic distance method, BLASTn and phylogenetic tree based on maximum likelihood (ML) analysis. Results illustrate that among all the DNA barcoding loci, matK locus can accurately and efficiently distinguish all the studied species followed by trnH-psbA and trnL. Present investigation may help diminish the illegal trade and events of adulteration of medicinally important plants species in genus Mentha, Ocimum and Plectranthus. This investigation will also help fulfil the scarcity of sequences of barcode loci of these species in the NCBI database. Apart from providing a molecular level reference for identifying processed herbal products, this technique also offers a convenient method for species identification and germplasm conservation of the Lamiaceae family.},
}
@article {pmid33911943,
year = {2021},
author = {Alabdali, EAA and Ghramh, HA and Ibrahim, EH and Ahmad, Z and Asiri, AN},
title = {Characterization of the native honey bee (Apis mellifera jemenitica) in the south western region of Saudi Arabia using morphometric and genetic (mtDNA COI) characteristics.},
journal = {Saudi journal of biological sciences},
volume = {28},
number = {4},
pages = {2278-2284},
pmid = {33911943},
issn = {1319-562X},
abstract = {Apis mellifera jemenitica incorporates a few perceived subspecies that vary in their natural properties and farming qualities. Mitochondrial COI gene sequence (mtCOI) has not been used before for bee identification in the southwestern region of Saudi Arabia. The aim of this work was to study the morphometry and analyzing the mtCOI of all collected bees. The nucleotide sequence of the mtCOI gene was analyzed. Similarity searches and distances between each obtained DNA and sequences available in GenBank were made. Morphometric analysis revealed close similarities among the studied bees, but these similarities are different from those previously indicated in earlier studies of the same region. Molecular studies revealed that the collected bees are similar to each other and some other sequences found in GenBank, but these bees are a new hybrid or subspecies that are different from those previously reported in the same region, indicating the emergence of a new hybrid.},
}
@article {pmid33908604,
year = {2021},
author = {Bernaola, L and Darlington, M and Britt, K and Prade, P and Roth, M and Pekarcik, A and Boone, M and Ricke, D and Tran, A and King, J and Carruthers, K and Thompson, M and Ternest, JJ and Anderson, SE and Gula, SW and Hauri, KC and Pecenka, JR and Grover, S and Puri, H and Vakil, SG},
title = {Technological Advances to Address Current Issues in Entomology: 2020 Student Debates.},
journal = {Journal of insect science (Online)},
volume = {21},
number = {2},
pages = {},
pmid = {33908604},
issn = {1536-2442},
mesh = {Animals ; Classification/methods ; *Entomology ; Grasshoppers ; Pest Control, Biological ; Plants, Genetically Modified ; },
abstract = {The 2020 Student Debates of the Entomological Society of America (ESA) were live-streamed during the Virtual Annual Meeting to debate current, prominent entomological issues of interest to members. The Student Debates Subcommittee of the National ESA Student Affairs Committee coordinated the student efforts throughout the year and hosted the live event. This year, four unbiased introductory speakers provided background for each debate topic while four multi-university teams were each assigned a debate topic under the theme 'Technological Advances to Address Current Issues in Entomology'. The two debate topics selected were as follows: 1) What is the best taxonomic approach to identify and classify insects? and 2) What is the best current technology to address the locust swarms worldwide? Unbiased introduction speakers and debate teams began preparing approximately six months before the live event. During the live event, teams shared their critical thinking and practiced communication skills by defending their positions on either taxonomical identification and classification of insects or managing the damaging outbreaks of locusts in crops.},
}
@article {pmid33903572,
year = {2021},
author = {Čiampor, F and Kodada, J and Bozáňová, J and Čiamporová-Zaťovičová, Z},
title = {Disersus otongachi/ a new species of Larainae riffle beetles from Ecuador (Coleoptera: Elmidae).},
journal = {Zootaxa},
volume = {4963},
number = {1},
pages = {zootaxa.4963.1.12},
doi = {10.11646/zootaxa.4963.1.12},
pmid = {33903572},
issn = {1175-5334},
mesh = {Animals ; Arthropod Antennae/anatomy &amp; histology ; *Coleoptera/anatomy &amp; histology/classification ; Ecuador ; Genitalia, Male/anatomy &amp; histology ; Male ; Species Specificity ; },
abstract = {We describe here a new species in the genus Disersus Sharp, 1882 from the Otongachi Reserve in Ecuador. Disersus otongachi sp.nov. is externally similar to other representatives of the genus, however, this species can be clearly distinguished for significantly longer antennae and the unique shape of the male genitalia.},
}
@article {pmid33903518,
year = {2021},
author = {Narita, K and Mita, T},
title = {A review of the subfamily Methochinae from Taiwan (Hymenoptera: Tiphiidae) with description of a new species and redescription of the known species.},
journal = {Zootaxa},
volume = {4964},
number = {2},
pages = {zootaxa.4964.2.4},
doi = {10.11646/zootaxa.4964.2.4},
pmid = {33903518},
issn = {1175-5334},
mesh = {Animals ; Female ; *Hymenoptera/anatomy &amp; histology/classification ; Male ; Species Specificity ; Taiwan ; },
abstract = {Eleven species of Methocha Latreille from Taiwan are revised. Methocha cirrhocrus Narita Mita, sp. nov. is described and illustrated. The previously unknown male of M. maai Lin, 1966 is described. Methocha taoi Lin, 1966 is newly synonymized under Methocha areolata Lin, 1966. The genus Karlissa Krombein, 1979 is newly recorded from Taiwan, and a new combination is proposed for Methoca (sic!) tricha Strand, 1913, which is transferred to the genus Karlissa Krombein. A key to the species based on males and females is given.},
}
@article {pmid33903496,
year = {2021},
author = {Volcan, MV and Barbosa, C and Robe, LJ and Lanés, LEK},
title = {Molecular phylogeny of the Austrolebias/ adloffi/ group (Cyprinodontiformes, Rivulidae), with description of two new endangered and highly endemic species of annual killifishes from the Laguna dos Patos system, southern Brazil.},
journal = {Zootaxa},
volume = {4965},
number = {1},
pages = {zootaxa.4965.1.4},
doi = {10.11646/zootaxa.4965.1.4},
pmid = {33903496},
issn = {1175-5334},
mesh = {Animals ; Brazil ; Endangered Species ; Fish Proteins/genetics ; *Killifishes/classification/genetics ; Male ; *Phylogeny ; Pigmentation ; Species Specificity ; Uruguay ; },
abstract = {The Austrolebias adloffi species group encompasses a diverse lineage of annual killifishes that occurs along the Laguna dos Patos/Lagoa Mirim system, in both Brazilian and Uruguayan territories. We herein employ an integrative taxonomy approach to describe two new species of the group, inferring their phylogenetic relationships and evaluating their conservation status. Austrolebias cheffei sp. nov. and Austrolebias lourenciano sp. nov. are herein described from the western portion of the Laguna dos Patos system. Austrolebias cheffei is distinguished from the remaining species of the A. adloffi species group by presenting a yellowish green or yellowish blue dorsal fin, with wide black to dark brown bars extending from the base to the middle portion of the dorsal and anal fins in the males. Austrolebias lourenciano is distinguished from the remaining species of the A. adloffi species group by presenting a yellowish green dorsal fin, with light yellow or light bluish bars forming small triangles, interspersed with small dark brown rows of blotches in the dorsal fin base, and greenish blue anal fin, sometimes with lighter elongated yellowish iridescent blotches, limited to the basal region. According to mitochondrial cytb sequences, both species are reciprocally monophyletic relative to other species of the A. adloffi species group, and present positive barcoding gap values. Interestingly, both new species form a grade that is closely related to Austrolebias aff. minuano 1, an undescribed species that occurs at the opposite margin of the Laguna dos Patos. Among the other evaluated species, A. bagual, A. aff. minuano 1, A. nigrofasciatus, A. pelotapes, A. pongondo, A. arachan, and A. viarius also revealed to be reciprocally monophyletic, whereas A. minuano and A. adloffi revealed to be paraphyletic in regard to A. charrua and A. aff. minuano 2, respectively, and A. nachtigalli is subdivided in two clades, one of which including A. reicherti, which points to the need of a taxonomic review of the group. In addition, we discussed the conservation status of the new species, corrected the type locality of A. pongondo, and provided a dichotomous identification key of the A. adloffi species group.},
}
@article {pmid33903396,
year = {2021},
author = {Moore, MD and Beaver, EP and Velasco-Castrillón, A and Stevens, MI},
title = {Two new endemic species of emAbantiades/em Herrich-Schäffer (Lepidoptera: Hepialidae) from Kangaroo Island, Australia.},
journal = {Zootaxa},
volume = {4951},
number = {3},
pages = {zootaxa.4951.3.9},
doi = {10.11646/zootaxa.4951.3.9},
pmid = {33903396},
issn = {1175-5334},
mesh = {Animals ; Australia ; DNA, Mitochondrial ; Islands ; *Lepidoptera/classification ; Moths ; },
abstract = {Abantiades penneshawensis Moore Beaver sp. nov. and Abantiades rubrus Moore Beaver sp. nov. are described as new. Both species are endemic to Kangaroo Island, and although both are related to species that occur on the Australian mainland and other islands, they are distinguished from those sister and phenotypically similar species by morphology and mtDNA (COI) barcodes. These two new species raise the number of Abantiades species on Kangaroo Island to six, three being endemic, and 45 species in the genus for the whole of Australia. There are now 13 species of Hepialidae (one undescribed) known from Kangaroo Island and we discuss the potential effects of recent catastrophic fire on some distributions.},
}
@article {pmid33903395,
year = {2021},
author = {Makarchenko, EA and Semenchenko, AA and Palatov, DM},
title = {New species and findings of emPagastia/em Oliver (Diptera: Chironomidae: Diamesinae) from Central Asia, with DNA barcoding of known species of the genus.},
journal = {Zootaxa},
volume = {4951},
number = {3},
pages = {zootaxa.4951.3.8},
doi = {10.11646/zootaxa.4951.3.8},
pmid = {33903395},
issn = {1175-5334},
mesh = {Animals ; Bayes Theorem ; *Chironomidae/classification/genetics ; DNA Barcoding, Taxonomic ; Diptera ; Male ; Phylogeny ; },
abstract = {Chironomids of the genus Pagastia Oliver (Diamesinae, Diamesini) from the mountains of Central Asia are revised using both morphological characters and molecular data. Illustrated descriptions of the adult male Pagastia (P.) caelestomontana sp. nov. from Kirgizstan and Tajikistan, P. (P.) hanseni sp. nov. from Tajikistan, and record of a finding apparently a new species P. (P.) aff. lanceolata (Tokunaga) from Tajikistan as well as an updated a key to the determination of the adult males of all known species of Pagastia are provided. A phylogenetic framework is reconstructed based on two mitochondrial genes cytochrome oxidase subunit I (COI) sequences of 34 samples belonging to 7 species of the genus Pagastia and cytochrome oxidase subunit II (COII) available for most samples. Phylogenetic trees of some known species of the genus Pagastia were reconstructed using the combined dataset and Bayesian inference (BI) and Maximum Likelihood (ML) methods. The interspecific K2P distances between seven Pagastia species including P. (P.) caelestomontana sp. nov., P. (P.) hanseni sp. nov. and undescribed P. (P.) aff. lanceolata (Tokunaga) are 6.3-13.2 which corresponding to species level.},
}
@article {pmid33903378,
year = {2021},
author = {Grebennikov, VV and Anderson, RS},
title = {Late Miocene eastwards transatlantic dispersal of flightless anchonine weevils (Coleoptera: Curculionidae: Molytinae).},
journal = {Zootaxa},
volume = {4952},
number = {1},
pages = {zootaxa.4952.1.3},
doi = {10.11646/zootaxa.4952.1.3},
pmid = {33903378},
issn = {1175-5334},
mesh = {Animals ; Coleoptera ; Fossils ; Phylogeny ; Phylogeography ; *Weevils/classification/genetics ; },
abstract = {The weevil genera Aethiopacorep Voisin and Titilayo Cristóvão Lyal are the only native African members of the nearly pantropical and poorly known tribe Anchonini. All Anchonini are flightless, a trait likely limiting dispersal, yet these weevils are found on both sides of the Atlantic Ocean. A phylogenetic analysis of 79 terminals and 3248 aligned positions from one mitochondrial and two nuclear ribosomal fragments supports a clade of West African Anchonini nested within American Anchonini. As suggested by previous authors, the Asian genera Himalanchonus Zherikhin and Otibazo Morimoto do not form a clade with the tribe's core, and along with Cycloterinus Kolbe, Euthycodes Pascoe, Leptanchonus Morimoto, Nepalanchonus Zherikhin, and Tanyomus Champion, are here removed from Anchonini and placed as Molytinae incertae sedis. So defined, the monophyletic tribe Anchonini contains 36 genus-group names, all but two denoting American taxa. Using molecular clock analysis, we estimate the separation of the West African Anchonini from its American sister at 9.5-5.2 million years ago (Ma). This date greatly postdates the Cretaceous opening of the Atlantic Ocean (about 100 Ma) and, therefore, evokes a single transatlantic dispersal to West Africa, likely by over-water rafting, leading to subsequent diversification. We postulate this to be the first documented eastwards crossing of the Atlantic Ocean by terrestrial non-volant arthropods based on morphological and molecular data.},
}
@article {pmid33903369,
year = {2021},
author = {Schmidt, RC and Knobloch, EC and Barrientos, C},
title = {Cast netting new species: Integrative taxonomy of emDistichodus/em emnotospilus/em (Characiformes: Distichodontidae) discovers new species and overlooked areas of endemism in Central Africa.},
journal = {Zootaxa},
volume = {4952},
number = {2},
pages = {zootaxa.4952.2.5},
doi = {10.11646/zootaxa.4952.2.5},
pmid = {33903369},
issn = {1175-5334},
mesh = {Animals ; *Characiformes/classification ; Rivers ; },
abstract = {Distichodus notospilus was described from the Ogooué River and is considered to occur throughout the Lower Guinea ichthyofaunal province and the western tributaries of the middle and lower Congo River. Recent expeditions in Equatorial Guinea collected D. notospilus specimens in the Mbini River drainage and the Mbia River; a small coastal river that is located between the Ntem and Mbini river drainages. Detailed morphological analyses and multilocus molecular analyses confirm that these two populations are distinct from one another. Topotypic populations of D. notospilus were included in the analyses and demonstrated that populations in the Mbini and Mbia rivers are distinct and these two new species are described herein. Distichodus microps sp. nov. is endemic to the Mbia River drainage and is distinguished from D. notospilus in having more scales along the lateral line (41, rarely 40 versus 37-39, rarely 40), a nearly inferior mouth versus subterminal in D. notospilus, a curved posterolateral margin of the opercle versus straight in D. notospilus, a smaller eye (56.7-80.4 versus 70.1-104.3 % of snout length), and a less prominent elongated spot at the base of the caudal fin. Distichodus mbiniensis sp. nov. is endemic to the upper Mbini River drainage and distinguished from D. notospilus in having more scales along the lateral line (41-42, rarely 40 versus 37-39, rarely 40), a much less prominent elongated dark spot at the base of the caudal fin, and a shorter dorsal fin (21.4-27.2 versus 22.7-34.2% standard length). Distichodus microps is distinguished from D. mbiniensis in having a shallower body (usually six scales from lateral line to the pelvic fin versus seven), fewer anal-fin rays (usually 12 total rays versus 13 or 14), a more inferior mouth, a deeper and longer caudal peduncle, a smaller eye, and differences in several features associated with the head. In addition to the two new species described this study also revealed potential undescribed diversity in the D. notospilus species complex in the Ntem River and Dja River (Congo R. basin) in Cameroon. The biogeography of these fishes in the rivers of Lower Guinea suggests that the Mbini River and smaller coastal rivers are overlooked areas of endemism. Studies of other reported widespread species will likely reveal additional diversity and further elucidate the processes promoting and maintaining freshwater diversity in Central Africa.},
}
@article {pmid33903357,
year = {2021},
author = {Chagnon, ME and Sinclair, BJ},
title = {Revision of Nearctic species of emAcerocnema/em Becker (Diptera: Scathophagidae).},
journal = {Zootaxa},
volume = {4952},
number = {3},
pages = {zootaxa.4952.3.5},
doi = {10.11646/zootaxa.4952.3.5},
pmid = {33903357},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; DNA, Mitochondrial ; *Diptera/classification/genetics ; Male ; },
abstract = {The Nearctic species of the genus Acerocnema Becker are revised. Four species are recorded including two new species: A. fasciventris (Malloch), A. merga sp. nov., A. rufula (Curran) and A. vanga sp. nov. Species descriptions, diagnoses and distribution maps are presented, including images of the male terminalia. A key to the Nearctic species is provided. COI mitochondrial DNA barcode sequences were obtained for two named and one unidentified species of Acerocnema.},
}
@article {pmid33903336,
year = {2021},
author = {Wang, J and Duffels, JP and Wei, C},
title = {Description of a new species of the genus emMaua/em Distant (Hemiptera, Cicadidae) from China.},
journal = {Zootaxa},
volume = {4949},
number = {3},
pages = {zootaxa.4949.3.8},
doi = {10.11646/zootaxa.4949.3.8},
pmid = {33903336},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; China ; Genes, Mitochondrial ; *Hemiptera/classification/genetics/physiology ; Male ; },
abstract = {A new species, Maua squeala sp. nov., is described from China. This species is similar to M. affinis Distant, 1905 and M. palawanensis Duffels, 2009, but can be distinguished by the shorter and more slender body of the new species, the lateral fasciae on the mesonotum and the shape of the male genitalia. The intraspecific variation of this species is discussed based on morphological observation combined with sequences of partial mitochondrial COI gene (DNA barcoding) of individuals exhibiting different morphological characters.},
}
@article {pmid33899938,
year = {2021},
author = {Kim, H and Martín-Vega, D and Shin, SE and Wang, AR and Park, SH},
title = {First report of the forensically important fly, Stearibia nigriceps (Diptera: Piophilidae) in South Korea: Confirmation of specimens from human corpses based on cytochrome c oxidase subunit I barcodes.},
journal = {Journal of forensic sciences},
volume = {66},
number = {4},
pages = {1538-1544},
doi = {10.1111/1556-4029.14721},
pmid = {33899938},
issn = {1556-4029},
support = {PA-G000001//Projects for Research and Development of Police Science and Technology under the Center for Research and Development of Police Science and Technology and the Korean National Police Agency/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Diptera/*genetics ; *Electron Transport Complex IV ; Feeding Behavior ; *Forensic Entomology ; Humans ; Larva ; Phylogeny ; Postmortem Changes ; Republic of Korea ; Sequence Analysis, DNA ; },
abstract = {Piophilidae are a relatively small family of Diptera that is frequently associated with cadavers at advanced stages of decomposition and are, therefore, considered potentially useful forensic indicators. However, their use in forensic investigations is typically hampered by a deficiency in reliable identification tools. This is particularly evident in countries such as South Korea, where forensic entomology is still in its infancy and the diversity of forensically relevant insect taxa remains largely undocumented. In the present study, we used cytochrome c oxidase subunit I (COI) barcodes to identify samples of piophilid larvae collected during medicolegal investigations performed in South Korea. A total of 174 COI sequences were obtained and have been made publicly available, thus augmenting the reference barcode library for forensically important Piophilidae species. Of the 174 sequenced samples, 172 were identified as Stearibia nigriceps (Meigen), whereas the two remaining samples may represent a previously unsequenced piophilid species. Stearibia nigriceps is recorded from South Korea for the first time, and our results suggest that it might be a particularly relevant forensic indicator in certain case types and scenarios in that country. The findings of this study highlight the utility of COI barcodes for achieving accurate identification of entomological samples, even by non-specialist forensic practitioners. They also contribute to the further development and consolidation of forensic entomology in South Korea and eastern Asia.},
}
@article {pmid33898833,
year = {2021},
author = {Peterson, AM and McBride, GE and Jhita, SK and Hellberg, RS},
title = {An investigation into country of origin labeling, species authentication and short weighting of commercially sold frozen fish fillets.},
journal = {Heliyon},
volume = {7},
number = {4},
pages = {e06713},
pmid = {33898833},
issn = {2405-8440},
abstract = {Proper labeling of seafood is important to prevent economic deception and protect public health. The goal of this research was to investigate prepackaged frozen fish for Country of Origin Labeling (COOL) compliance, species labeling, net weights/short weighting, and percent glaze. A total of 111 frozen prepackaged fish fillets were purchased from grocery stores in Southern California (USA). Samples were designated as COOL compliant if they displayed both procurement method and country of origin in accordance with COOL requirements. Species labeling was examined by comparing the species identified with DNA barcoding to the acceptable market names provided in the FDA Seafood List. Net weights and percent glaze were determined by recording the weight of each product before and after deglazing. Of the 111 samples, only 1 was noncompliant with COOL and 10 samples (9%) were short-weighted. The average percent glaze was 5%, with seven samples having >10% glaze. Most fish (95.5%) were correctly labeled with regards to species. Species substitution was discovered in two samples and three samples had unacceptable market names. The results of this study indicate high COOL compliance and minimal species mislabeling in prepackaged frozen fish fillets. However, there is a need for increased focus on short weighting and/or overglazing of frozen fish products.},
}
@article {pmid33894643,
year = {2021},
author = {Aguilar, A and Gutierrez, E and Seira, E},
title = {The effectiveness of sin food taxes: Evidence from Mexico.},
journal = {Journal of health economics},
volume = {77},
number = {},
pages = {102455},
doi = {10.1016/j.jhealeco.2021.102455},
pmid = {33894643},
issn = {1879-1646},
mesh = {*Beverages ; Commerce ; Consumer Behavior ; Dietary Supplements ; Humans ; Mexico ; *Taxes ; },
abstract = {We measure the effect of a large nationwide tax reform on sugar-added drinks and caloric-dense food introduced in Mexico in 2014. Using scanner data containing weekly purchases of 47,973 barcodes by 8,130 households and an RD design, we find that calories purchased from taxed drinks and taxed food decreased respectively by 2.7% and 3%. However, this was compensated by increases from untaxed categories, such that total calories purchased did not change. We find increases in cholesterol (12.6%), sodium (5.8%), saturated fat (3.1%), carbohydrates (2%), and proteins (3.8%).},
}
@article {pmid33893552,
year = {2021},
author = {Maharana, BR and Gupta, S and Gupta, S and Ganguly, A and Kumar, B and Chandratre, GA and Bisla, RS},
title = {First report of molecular and phylogenetic analysis of Physaloptera praeputialis in naturally infected stray cats from India.},
journal = {Parasitology research},
volume = {120},
number = {6},
pages = {2047-2056},
pmid = {33893552},
issn = {1432-1955},
mesh = {Animals ; Cats/*parasitology ; DNA, Helminth/genetics ; DNA, Ribosomal/genetics ; Genes, Mitochondrial/genetics ; India ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Spiruroidea/*classification/genetics/isolation &amp; purification ; },
abstract = {Nematodes of the genus Physaloptera are globally distributed and infect a multitude of hosts. Their life cycle involves orthopterans and coleopterans as intermediate hosts. The morphological characters alone are inadequate to detect and differentiate Physaloptera spp. from its congeners. Moreover, molecular studies are limited to compare them precisely. The present communication reports the first molecular phylogenetic characterization of feline Physaloptera spp. from India based on mitochondrial cytochrome c oxidase subunit 1 (COX1) and small subunit ribosomal DNA (18S rDNA). The nematodes were first isolated from the stomach of adult stray cats during necropsy examination. Based on the gross and microscopic characters, the worms were identified as P. praeputialis. Morphological identification was further confirmed through PCR targeting the barcode region of the mitochondrial cytochrome c oxidase subunit I (MT-COI) gene, using nematode-specific primers cocktail followed by species specific primers targeting partial COX1 and 18S rRNA genes. Generated sequences were submitted in NCBI GenBank (MW517846, MW410927, MW411349), and phylogenetic trees were constructed using the maximum likelihood method. When compared with other sequences of Physaloptera species across the globe, the present isolates showed 85.6-97.7% and 97.3-99% nucleotide homology based on COX1 and 18S rRNA gene, respectively. BLASTn analysis revealed a strong identity to other Physaloptera spp., and the phylogenetic tree placed all Physaloptera spp. in the same cluster. This study again indicates the usefulness of molecular techniques to substantiate the identity of species that may lack adequate descriptions and impart new insight for the potentially overlooked significance of P. praeputialis infections in felines.},
}
@article {pmid33893548,
year = {2021},
author = {Bernotienė, R and Bartkevičienė, G and Bukauskaitė, D},
title = {The flying activity of biting midges (Ceratopogonidae: Culicoides) in Verkiai Regional Park, southeastern Lithuania.},
journal = {Parasitology research},
volume = {120},
number = {7},
pages = {2323-2332},
pmid = {33893548},
issn = {1432-1955},
support = {S-MIP-17-27//Lietuvos Mokslo Taryba/ ; },
mesh = {Animals ; Ceratopogonidae/classification/*physiology ; Cluster Analysis ; Female ; Flight, Animal/*physiology ; Insect Vectors/classification/*physiology ; Lithuania ; Seasons ; Temperature ; },
abstract = {Culicoides biting midges are small dipterous insects (Diptera: Ceratopogonidae) which are known to be vectors of arboviruses, bacteria, protozoan and helminth parasites that can cause disease and mortality in livestock and poultry globally. Detailed knowledge of the Culicoides species composition and biology is essential to assess the risk of the introduction and transmission of pathogens. The aim of this study was to obtain data on Culicoides species composition and flying activity in southeastern Lithuania and to determine the meteorological variables related to the abundance of Culicoides biting midges. Biting midges were collected in Verkiai Regional Park, southeastern Lithuania, using an Onderstepoort trap once a week from April to October 2016 and 2018, and from April to July 2019; 7332 Culicoides females belonging to 22 species were identified. Both morphology and DNA barcoding were used for identification. The number of specimens trapped was highest for the Obsoletus Group, followed by Culicoides kibunensis and Culicoides impunctatus. The highest relative abundance and diversity of biting midges were found in May and June. The number of trapped biting midges correlated positively with the mean air temperature. The first biting midges in spring were caught when the mean daily temperature rose higher than 10 °C. No Culicoides were detected when the air temperature dropped below 5 °C in autumn. Wind speed and air humidity had no statistically significant effect on Culicoides abundance.},
}
@article {pmid33892518,
year = {2021},
author = {Papa, Y and Le Bail, PY and Covain, R},
title = {Genetic landscape clustering of a large DNA barcoding data set reveals shared patterns of genetic divergence among freshwater fishes of the Maroni Basin.},
journal = {Molecular ecology resources},
volume = {21},
number = {6},
pages = {2109-2124},
doi = {10.1111/1755-0998.13402},
pmid = {33892518},
issn = {1755-0998},
mesh = {Animals ; *Biodiversity ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; *Electron Transport Complex IV/genetics ; Fishes/*classification/genetics ; French Guiana ; Fresh Water ; Genetic Variation ; Phylogeny ; Suriname ; },
abstract = {The Maroni is one of the most speciose basins of the Guianas and hosts a megadiverse freshwater fish community. Although taxonomic references based on morphological identification exist for both the Surinamese and Guianese parts of the basin, there are still taxonomic uncertainties concerning the status of several species. We used COI sequences of 1284 fish in conjunction with morphological and biogeographical evidence to assist with species delineation and discovery in order to validate and standardize the current taxonomy. This resulted in a final DNA barcode data set of 199 fish species (125 genera, 36 families and eight orders; 68.86% of strictly freshwater fishes from the basin), among which 25 are new putative candidate species flagged as requiring taxonomic update. DNA barcoding delineation through Barcode Index Numbers (BINs) revealed further cryptic diversity (230 BINs in total). To explore global genetic patterns across the basin, genetic divergence landscapes were computed for 128 species, showing a global trend of high genetic divergence between the Surinamese southwest (Tapanahony and Paloemeu), the Guianese southeast (Marouini, Litany, Tampok, etc.), and the river outlet in the north. This could be explained by lower levels of connectivity between these three main areas and/or the exchange of individuals between these areas and the neighbouring basins. A new method of ordination of genetic landscapes successfully assigned species into cluster groups based on their respective pattern of genetic divergence across the Maroni Basin: genetically homogeneous species were effectively discriminated from species showing high spatial genetic fragmentation and possible lower capacity for dispersal.},
}
@article {pmid33891613,
year = {2021},
author = {Zeinalabedini, M and Khoshkholgh Sima, NA and Ghaffari, MR and Ebadi, A and Farsi, M},
title = {Application of DNA barcodes and spatial analysis in conservation genetics and modeling of Iranian Salicornia genetic resources.},
journal = {PloS one},
volume = {16},
number = {4},
pages = {e0241162},
pmid = {33891613},
issn = {1932-6203},
mesh = {Chenopodiaceae/*genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Plant/*genetics ; Genetics ; Iran ; Phylogeny ; Sequence Analysis, DNA/methods ; Spatial Analysis ; Species Specificity ; },
abstract = {Iran is one of the origins of some Salicornia species. Nevertheless, comprehensive research has not been conducted on genetic potential, distribution, selection of populations, and the economic utilization of Salicornia in Iran. In the current study, Salicornia was collected based on the previous data available for 26 different geographical locations of provinces in Iran. We examined Salicornia plants' universality DNA barcodes, including rbcL, matK, trnH-psbA, and ITS, and their species identification abilities and identified six species groups. Subsequently, accurate modeling of distributed areas was provided with MAXENT and highlighted the valuable information on the diversity of specific geographical regions, conservation status of existing species, prioritization of conservation areas, and selection of Agro-Ecological areas. Together, this type of integrative study will provide useful information for managing and utilizing Salicornia genetic resources in Iran.},
}
@article {pmid33890353,
year = {2021},
author = {Li, Y and Johnson, AJ and Gao, L and Wu, C and Hulcr, J},
title = {Two new invasive Ips bark beetles (Coleoptera: Curculionidae) in mainland China and their potential distribution in Asia.},
journal = {Pest management science},
volume = {77},
number = {9},
pages = {4000-4008},
doi = {10.1002/ps.6423},
pmid = {33890353},
issn = {1526-4998},
support = {19DZ1204102//Key Project of Science and Technology Commission of Shanghai Municipality/ ; 19ZR1451300//Natural Science Foundation of Shanghai/ ; },
mesh = {Animals ; *Coleoptera ; Humans ; Insect Control ; Pheromones ; Plant Bark ; *Weevils ; },
abstract = {BACKGROUND: Ips is a bark beetle genus of 45 species, many of which are pests of conifer forests and plantations under stress. Twelve Ips species are recorded from China and presumably native there. From 2016 to 2018, specimens suspected to be Ips calligraphus and Ips grandicollis, were collected from traps with ethanol as a sole lure in Zhuhai, Guangdong, China. Both species originate in North America and infest various species of native or introduced pines. Since Ips species are known to cause or exacerbate problems in pine plantations, and a regional survey using traps baited with attractants were implemented in this study to investigate the extent of the introduction.<br><br>RESULTS: Both I. calligraphus and I. grandicollis have been collected repeatedly from several traps with Ips attractants in Zhuhai, Guangdong, China since 2016. Potential distributions of these two species in Asia, inferred using MaxEnt, is extensive, given the high projected environmental suitability in North America, South America, Mediterranean Europe, Northern Africa, and Eastern Asia. The host plant of I. calligraphus from Zhuhai was identified as slash pine Pinus elliottii using DNA barcoding of gut contents from trapped individuals.<br><br>CONCLUSION: This is the first report of the establishment of two American pine bark beetles, I. calligraphus and I. grandicollis in continental Asia. The gut content of both species suggests that these pest feeds on a non-native host. Whether the two species present high-risk to Asian forests will become clear with more research on their interactions with native pines.},
}
@article {pmid33889047,
year = {2021},
author = {Yang, W and Dong, R and Song, X and Yu, H},
title = {The genus Syntozyga Lower (Lepidoptera, Tortricidae) in China, with descriptions of two new species.},
journal = {ZooKeys},
volume = {1028},
number = {},
pages = {95-111},
pmid = {33889047},
issn = {1313-2989},
abstract = {Species of the genus Syntozyga Lower, 1901 (Lepidoptera, Tortricidae, Olethreutinae) from China are studied. Syntozyga apicispinata sp. nov. and S. similispirographa sp. nov. are described, S. pedias (Meyrick, 1920) is recorded for the first time from China, and S. spirographa (Diakonoff, 1968) is newly recorded from the Chinese mainland. Adults and genitalia are illustrated, and a distribution map of the Chinese species is given. Keys to identify the Chinese species of Syntozyga are provided. Species of the genus are well clustered in a neighbor-joining tree based on the sequence data of the COI gene. COI sequences corresponding to the new species and S. spirographa (Diakonoff, 1968) are submitted to BOLD.},
}
@article {pmid33888110,
year = {2021},
author = {Ziegler, A and Sagorny, C},
title = {Holistic description of new deep sea megafauna (Cephalopoda: Cirrata) using a minimally invasive approach.},
journal = {BMC biology},
volume = {19},
number = {1},
pages = {81},
pmid = {33888110},
issn = {1741-7007},
mesh = {Animals ; *Octopodiformes ; X-Ray Microtomography ; },
abstract = {BACKGROUND: In zoology, species descriptions conventionally rely on invasive morphological techniques, frequently leading to damage of the specimens and thus only a partial understanding of their structural complexity. More recently, non-destructive imaging techniques have successfully been used to describe smaller fauna, but this approach has so far not been applied to identify or describe larger animal species. Here, we present a combination of entirely non-invasive as well as minimally invasive methods that permit taxonomic descriptions of large zoological specimens in a more comprehensive manner.<br><br>RESULTS: Using the single available representative of an allegedly novel species of deep-sea cephalopod (Mollusca: Cephalopoda), digital photography, standardized external measurements, high-field magnetic resonance imaging, micro-computed tomography, and DNA barcoding were combined to gather all morphological and molecular characters relevant for a full species description. The results show that this specimen belongs to the cirrate octopod (Octopoda: Cirrata) genus Grimpoteuthis&#xa0;Robson, 1932. Based on the number of suckers, position of web nodules, cirrus length, presence of a radula, and various shell characters, the specimen is designated as the holotype of a new species of dumbo octopus, G. imperator sp. nov. The digital nature of the acquired data permits a seamless online deposition of raw as well as derived morphological and molecular datasets in publicly accessible repositories.<br><br>CONCLUSIONS: Using high-resolution, non-invasive imaging systems intended for the analysis of larger biological objects, all external as well as internal morphological character states relevant for the identification of a new megafaunal species were obtained. Potentially harmful effects on this unique deep-sea cephalopod specimen were avoided by scanning the fixed animal without admixture of a contrast agent. Additional support for the taxonomic placement of the new dumbo octopus species was obtained through DNA barcoding, further underlining the importance of combining morphological and molecular datasets for a holistic description of zoological specimens.},
}
@article {pmid33887480,
year = {2021},
author = {Hosie, AM and Fromont, J and Munyard, K and Wilson, NG and Jones, DS},
title = {Surveying keratose sponges (Porifera, demospongiae, Dictyoceratida) reveals hidden diversity of host specialist barnacles (Crustacea, Cirripedia, Balanidae).},
journal = {Molecular phylogenetics and evolution},
volume = {161},
number = {},
pages = {107179},
doi = {10.1016/j.ympev.2021.107179},
pmid = {33887480},
issn = {1095-9513},
mesh = {Animals ; *Host Specificity ; *Phylogeny ; *Porifera ; Thoracica/*classification ; Western Australia ; },
abstract = {Sponges represent one of the most species-rich hosts for commensal barnacles yet host utilisation and diversity have not been thoroughly examined. This study investigated the diversity and phylogenetic relationships of sponge-inhabiting barnacles within a single, targeted host group, primarily from Western Australian waters. Specimens of the sponge order Dictyoceratida were surveyed and a total of 64 host morphospecies, representing four families, were identified as barnacle hosts during the study. Utilising molecular (COI, 12S) and morphological methods 42 molecular operational taxonomic units (MOTUs) of barnacles, representing Acasta, Archiacasta, Euacasta and Neoacasta were identified. Comparing inter- and intra-MOTU genetic distances showed a barcode gap between 2.5% and 5% for COI, but between 1% and 1.5% in the 12S dataset, thus demonstrating COI as a more reliable barcoding region. These sponge-inhabiting barnacles were demonstrated to show high levels of host specificity with the majority being found in a single sponge species (74%), a single genus (83%) or a single host family (93%). Phylogenetic relationships among the barnacles were reconstructed using mitochondrial (12S, COI) and nuclear (H3, 28S) markers. None of the barnacle genera were recovered as monophyletic. Euacasta was paraphyletic in relation to the remaining Acastinae genera, which were polyphyletic. Six well-supported clades of molecular operational taxonomic units, herein considered to represent species complexes, were recovered, but relationships between them were not well supported. These complexes showed differing patterns of host usage, though most were phylogenetically conserved with sister lineages typically occupying related hosts within the same genus or family of sponge. The results show that host specialists are predominant, and the dynamics of host usage have played a significant role in the evolutionary history of the Acastinae.},
}
@article {pmid33887182,
year = {2021},
author = {Siano, R and Lassudrie, M and Cuzin, P and Briant, N and Loizeau, V and Schmidt, S and Ehrhold, A and Mertens, KN and Lambert, C and Quintric, L and Noël, C and Latimier, M and Quéré, J and Durand, P and Penaud, A},
title = {Sediment archives reveal irreversible shifts in plankton communities after World War II and agricultural pollution.},
journal = {Current biology : CB},
volume = {31},
number = {12},
pages = {2682-2689.e7},
doi = {10.1016/j.cub.2021.03.079},
pmid = {33887182},
issn = {1879-0445},
mesh = {Biodiversity ; *Dinoflagellida/genetics ; Ecosystem ; Geologic Sediments ; Humans ; *Plankton/genetics ; Retrospective Studies ; World War II ; },
abstract = {To evaluate the stability and resilience[1] of coastal ecosystem communities to perturbations that occurred during the Anthropocene,[2] pre-industrial biodiversity baselines inferred from paleoarchives are needed.[3][,][4] The study of ancient DNA (aDNA) from sediments (sedaDNA)[5] has provided valuable information about past dynamics of microbial species[6-8] and communities[9-18] in relation to ecosystem variations. Shifts in planktonic protist communities might significantly affect marine ecosystems through cascading effects,[19-21] and therefore the analysis of this compartment is essential for the assessment of ecosystem variations. Here, sediment cores collected from different sites of the Bay of Brest (northeast Atlantic, France) allowed ca. 1,400 years of retrospective analyses of the effects of human pollution on marine protists. Comparison of sedaDNA extractions and metabarcoding analyses with different barcode regions (V4 and V7 18S rDNA) revealed that protist assemblages in ancient sediments are mainly composed of species known to produce resting stages. Heavy-metal pollution traces in sediments were ascribed to the World War II period and coincided with community shifts within dinoflagellates and stramenopiles. After the war and especially from the 1980s to 1990s, protist genera shifts followed chronic contaminations of agricultural origin. Community composition reconstruction over time showed that there was no recovery to a Middle Ages baseline composition. This demonstrates the irreversibility of the observed shifts after the cumulative effect of war and agricultural pollutions. Developing a paleoecological approach, this study highlights how human contaminations irreversibly affect marine microbial compartments, which contributes to the debate on coastal ecosystem preservation and restoration.},
}
@article {pmid33884571,
year = {2021},
author = {Chakraborty, C and Sharma, AR and Sharma, G and Bhattacharya, M and Patra, BC and Sarkar, BK and Banerjee, S and Banerjee, K and Lee, SS},
title = {Understanding the molecular evolution of tiger diversity through DNA barcoding marker ND4 and NADH dehydrogenase complex using computational biology.},
journal = {Genes &amp; genomics},
volume = {43},
number = {7},
pages = {759-773},
pmid = {33884571},
issn = {2092-9293},
mesh = {Animals ; Computational Biology ; DNA Barcoding, Taxonomic/*veterinary ; *Evolution, Molecular ; Genetic Markers ; Genetic Variation ; NADH Dehydrogenase/*genetics ; Phylogeny ; Tigers/classification/*genetics ; },
abstract = {BACKGROUND: Currently, Tigers (the top predator of an ecosystem) are on the list of endangered species. Thus the need is to understand the tiger's population genomics to design their conservation strategies.<br><br>OBJECTIVE: We analyzed the molecular evolution of tiger diversity using NADH dehydrogenase subunit 4 (ND4), a significant electron transport chain component.<br><br>METHODS: We have analyzed nucleotide composition and distribution pattern of ND genes, molecular evolution, evolutionary conservation pattern and conserved blocks of NADH, phylogenomics of ND4, and estimating species divergence, etc., using different bioinformatics tools and software, and MATLAB programming and computing environment.<br><br>RESULTS: The nucleotide composition and distribution pattern of ND genes in the tiger genome demonstrated an increase in the number of adenine (A) and a lower trend of A+T content in some place of the distribution analysis. However, the observed distributions were not significant (P > 0.05). Evolutionary conservation analysis showed three highly align blocks (186 to 198, 406 to 416, and 527 to 545). On mapping the molecular evolution of ND4 among model species (n = 30), we observed its presence in a broader range of species. ND4 based molecular evolution of tiger diversity and time divergence for a tiger (20 different other species) shows that genus Panthera originated more or less at a similar time.<br><br>CONCLUSIONS: The nucleotide composition and nucleotide distribution pattern of tiger ND genes showed the evolutionary pattern and origin of tiger and Panthera lineage concerning the molecular clock, which will help to understand their adaptive evolution.},
}
@article {pmid33880891,
year = {2021},
author = {Liu, JL and Dujsebayeva, TN and Chirikova, MA and Gong, X and Li, DJ and Guo, XG},
title = {Does the Dzungarian racerunner (Eremias dzungarica Orlova, Poyarkov, Chirikova, Nazarov, Munkhbaatar, Munkhbayar &amp; Terbish, 2017) occur in China? Species delimitation and identification with DNA barcoding and morphometric analyses.},
journal = {Zoological research},
volume = {42},
number = {3},
pages = {287-293},
pmid = {33880891},
issn = {2095-8137},
mesh = {*Animal Distribution ; Animals ; China ; DNA/genetics ; *DNA Barcoding, Taxonomic ; Lizards/classification/genetics/*physiology ; Phylogeny ; Species Specificity ; },
abstract = {The Eremias multiocellata-przewalskii species complex is a viviparous group in the genus Eremias, and a well-known representative of taxonomically complicated taxa. Within this complex, a new species - E. dzungarica (Orlova et al., 2017) - has been described recently from western Mongolia and eastern Kazakhstan, with an apparent distribution gap in northwestern China. In this study, we used an integrative taxonomic framework to address whether E. dzungarica indeed occurs in China. Thirty specimens previously classified as E. multiocellata were collected in eastern Kazakhstan and the adjacent Altay region in China. The cytochrome c oxidase I (COI) barcodes were sequenced and compiled with those from Orlova et al. (2017) and analyzed with the standard and diverse barcoding techniques. We detected an absence of a barcoding gap in this complex, which indicates potential cryptic species in Eremias sp. 3 with high intraspecific diversity and multiple recently evolved species in Clade A. Both BIN and GMYC suggested an unrealistically large number of species (23 and 26, respectively), while ABGD, mPTP and BPP indicated a more conservative number of species (10, 12, and 15, respectively), largely concordant with the previously defined species-level lineages according to phylogenetic trees. Based on molecular phylogeny and morphological examination, all 30 individuals collected in this study were reliably identified as E. dzungarica - a distinct species - confirming the occurrence of this species in the Altay region, Xinjiang, China. Potentially owing to the larger sample size in this study, our morphological analyses revealed many inconsistencies with the original descriptions of E. dzungarica, which were primarily associated with sexual dimorphism and a broader range of values for various traits.},
}
@article {pmid33878299,
year = {2021},
author = {Bado, IL and Zhang, W and Hu, J and Xu, Z and Wang, H and Sarkar, P and Li, L and Wan, YW and Liu, J and Wu, W and Lo, HC and Kim, IS and Singh, S and Janghorban, M and Muscarella, AM and Goldstein, A and Singh, P and Jeong, HH and Liu, C and Schiff, R and Huang, S and Ellis, MJ and Gaber, MW and Gugala, Z and Liu, Z and Zhang, XH},
title = {The bone microenvironment increases phenotypic plasticity of ER[+] breast cancer cells.},
journal = {Developmental cell},
volume = {56},
number = {8},
pages = {1100-1117.e9},
pmid = {33878299},
issn = {1878-1551},
support = {R01 CA251950/CA/NCI NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; R01 CA183878/CA/NCI NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; U01 CA253553/CA/NCI NIH HHS/United States ; R01 CA221946/CA/NCI NIH HHS/United States ; },
mesh = {*Adaptation, Physiological ; Animals ; Bone Neoplasms/secondary ; Bone and Bones/*pathology ; Breast Neoplasms/metabolism/*pathology ; Cell Communication ; Clonal Evolution ; Disease Models, Animal ; Down-Regulation ; Enhancer of Zeste Homolog 2 Protein/metabolism ; Female ; Gap Junctions/metabolism ; Genes, Reporter ; Green Fluorescent Proteins/metabolism ; Humans ; MCF-7 Cells ; Mice ; Neoplasm Micrometastasis ; Osteogenesis ; Receptors, Estrogen/*metabolism ; Signal Transduction ; *Tumor Microenvironment ; },
abstract = {Estrogen receptor-positive (ER[+]) breast cancer exhibits a strong bone tropism in metastasis. How the bone microenvironment (BME) impacts ER signaling and endocrine therapy remains poorly understood. Here, we discover that the osteogenic niche transiently and reversibly reduces ER expression and activities specifically in bone micrometastases (BMMs), leading to endocrine resistance. As BMMs progress, the ER reduction and endocrine resistance may partially recover in cancer cells away from the osteogenic niche, creating phenotypic heterogeneity in macrometastases. Using multiple approaches, including an evolving barcoding strategy, we demonstrated that this process is independent of clonal selection, and represents an EZH2-mediated epigenomic reprogramming. EZH2 drives ER[+] BMMs toward a basal and stem-like state. EZH2 inhibition reverses endocrine resistance. These data exemplify how epigenomic adaptation to BME promotes phenotypic plasticity of metastatic seeds, fosters intra-metastatic heterogeneity, and alters therapeutic responses. Our study provides insights into the clinical enigma of ER+ metastatic recurrences despite endocrine therapies.},
}
@article {pmid33878297,
year = {2021},
author = {Kang, Y and Kuperwasser, C},
title = {Evolving barcodes shed light into evolving metastases.},
journal = {Developmental cell},
volume = {56},
number = {8},
pages = {1077-1079},
doi = {10.1016/j.devcel.2021.03.029},
pmid = {33878297},
issn = {1878-1551},
mesh = {Bone and Bones ; *Breast Neoplasms ; Female ; Humans ; *Tumor Microenvironment ; },
abstract = {Selective pressure and signals from the tissue microenvironment drive metastasis and determine the survival of metastatic tumor cells at distant organs. Zhang et al. and Bado et al. apply CRISPR-mediated evolving barcode technology to elucidate the role of the bone microenvironment in the evolution of breast cancer metastasis.},
}
@article {pmid33878291,
year = {2021},
author = {Zhang, W and Bado, IL and Hu, J and Wan, YW and Wu, L and Wang, H and Gao, Y and Jeong, HH and Xu, Z and Hao, X and Lege, BM and Al-Ouran, R and Li, L and Li, J and Yu, L and Singh, S and Lo, HC and Niu, M and Liu, J and Jiang, W and Li, Y and Wong, STC and Cheng, C and Liu, Z and Zhang, XH},
title = {The bone microenvironment invigorates metastatic seeds for further dissemination.},
journal = {Cell},
volume = {184},
number = {9},
pages = {2471-2486.e20},
pmid = {33878291},
issn = {1097-4172},
support = {S10 OD016167/OD/NIH HHS/United States ; R01 CA251950/CA/NCI NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; U01 CA253553/CA/NCI NIH HHS/United States ; R01 CA221946/CA/NCI NIH HHS/United States ; R01 CA183878/CA/NCI NIH HHS/United States ; R01 CA227904/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Apoptosis ; Biomarkers, Tumor/genetics/metabolism ; Bone Neoplasms/genetics/metabolism/*secondary ; Breast Neoplasms/genetics/metabolism/*pathology ; Cell Proliferation ; Disease Progression ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Inbred NOD ; Mice, Nude ; Mice, SCID ; *Neoplasm Metastasis ; Prostatic Neoplasms/genetics/metabolism/*pathology ; Tumor Cells, Cultured ; *Tumor Microenvironment ; Xenograft Model Antitumor Assays ; },
abstract = {Metastasis has been considered as the terminal step of tumor progression. However, recent genomic studies suggest that many metastases are initiated by further spread of other metastases. Nevertheless, the corresponding pre-clinical models are lacking, and underlying mechanisms are elusive. Using several approaches, including parabiosis and an evolving barcode system, we demonstrated that the bone microenvironment facilitates breast and prostate cancer cells to further metastasize and establish multi-organ secondary metastases. We uncovered that this metastasis-promoting effect is driven by epigenetic reprogramming that confers stem cell-like properties on cancer cells disseminated from bone lesions. Furthermore, we discovered that enhanced EZH2 activity mediates the increased stemness and metastasis capacity. The same findings also apply to single cell-derived populations, indicating mechanisms distinct from clonal selection. Taken together, our work revealed an unappreciated role of the bone microenvironment in metastasis evolution and elucidated an epigenomic reprogramming process driving terminal-stage, multi-organ metastases.},
}
@article {pmid33877495,
year = {2021},
author = {Pereira, LHG and Castro, JRC and Vargas, PMH and Gomez, JAM and Oliveira, C},
title = {The use of an integrative approach to improve accuracy of species identification and detection of new species in studies of stream fish diversity.},
journal = {Genetica},
volume = {149},
number = {2},
pages = {103-116},
pmid = {33877495},
issn = {1573-6857},
support = {137/2018/PRPPG; 80/2019/PRPPG//Universidade Federal da Integra&#xe7;&#xe3;o Latino-Americana - UNILA/ ; 306054/2006-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2018/20610-1, 2016/09204-6, 2014/26508-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
mesh = {Animals ; Brazil ; DNA Barcoding, Taxonomic/*methods/standards ; Fishes/classification/*genetics ; Phylogeny ; *Polymorphism, Genetic ; Rivers ; Sensitivity and Specificity ; },
abstract = {In this study, we made an inventory of the stream and headwater ichthyofauna of the left bank of the Itaipu Dam Reservoir, located in the lower part of the Upper Paraná River basin, using an integrative approach of molecular and morphological data. The area is located in the western portion of the Paraná state in Brazil, in an area of about 8,000 km[2] highly impacted by deforestation and intensive agriculture. For taxonomic identification of species, we used an identification key combined with the DNA barcoding approach. We found 48 species belonging to six orders, 13 families, and 37 genera. The Siluriformes and Characiformes were the most representative orders (75%) and the Characidae was the most representative family (20.8%). Nine species prevailed in this region, making up to 86% of all specimens collected. The integrative approach proved to be useful by allowing the unambiguous identification of all species, including those cases in which morphological characters were not conclusive for species identification, cases of cryptic species, and species with high morphological plasticity. In addition, the integrative approach highlighted six to 13 new putative species depending on the approach considered. Our study provides a relevant contribution to the knowledge of fish diversity in a poorly studied area of the Paraná River basin. We showed that the use of an integrative approach in inventory studies improves species identification and the discovery of new, cryptic, and overlooked species, being a powerful and necessary tool to quantify biodiversity.},
}
@article {pmid33875688,
year = {2021},
author = {Moles, J and Derkarabetian, S and Schiaparelli, S and Schrödl, M and Troncoso, JS and Wilson, NG and Giribet, G},
title = {An approach using ddRADseq and machine learning for understanding speciation in Antarctic Antarctophilinidae gastropods.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {8473},
pmid = {33875688},
issn = {2045-2322},
mesh = {Animals ; Antarctic Regions ; *Ecosystem ; Gastropoda/*classification/*genetics ; Gene Expression Profiling ; *Gene Expression Regulation ; *Genetic Speciation ; *Machine Learning ; Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {Sampling impediments and paucity of suitable material for molecular analyses have precluded the study of speciation and radiation of deep-sea species in Antarctica. We analyzed barcodes together with genome-wide single nucleotide polymorphisms obtained from double digestion restriction site-associated DNA sequencing (ddRADseq) for species in the family Antarctophilinidae. We also reevaluated the fossil record associated with this taxon to provide further insights into the origin of the group. Novel approaches to identify distinctive genetic lineages, including unsupervised machine learning variational autoencoder plots, were used to establish species hypothesis frameworks. In this sense, three undescribed species and a complex of cryptic species were identified, suggesting allopatric speciation connected to geographic or bathymetric isolation. We further observed that the shallow waters around the Scotia Arc and on the continental shelf in the Weddell Sea present high endemism and diversity. In contrast, likely due to the glacial pressure during the Cenozoic, a deep-sea group with fewer species emerged expanding over great areas in the South-Atlantic Antarctic Ridge. Our study agrees on how diachronic paleoclimatic and current environmental factors shaped Antarctic communities both at the shallow and deep-sea levels, promoting Antarctica as the center of origin for numerous taxa such as gastropod mollusks.},
}
@article {pmid33867801,
year = {2021},
author = {Darshetkar, AM and Maurya, S and Lee, C and Bazarragchaa, B and Batdelger, G and Janchiv, A and Jeong, EJ and Choi, S and Choudhary, RK and Kim, SY},
title = {Plastome analysis unveils Inverted Repeat (IR) expansion and positive selection in Sea Lavenders (Limonium, Plumbaginaceae, Limonioideae, Limonieae).},
journal = {PhytoKeys},
volume = {175},
number = {},
pages = {89-107},
pmid = {33867801},
issn = {1314-2011},
abstract = {The genus Limonium, commonly known as Sea Lavenders, is one of the most species-rich genera of the family Plumbaginaceae. In this study, two new plastomes for the genus Limonium, viz. L. tetragonum and L. bicolor, were sequenced and compared to available Limonium plastomes, viz. L. aureum and L. tenellum, to understand the gene content and structural variations within the family. The loss of the rpl16 intron and pseudogenisation of rpl23 was observed. This study reports, for the first time, expansion of the IRs to include the ycf1 gene in Limonium plastomes, incongruent with previous studies. Two positively selected genes, viz. ndhF and ycf2, were identified. Furthermore, putative barcodes are proposed for the genus, based on the nucleotide diversity of four Limonium plastomes.},
}
@article {pmid33863944,
year = {2021},
author = {Nydam, ML and Lemmon, AR and Cherry, JR and Kortyna, ML and Clancy, DL and Hernandez, C and Cohen, CS},
title = {Phylogenomic and morphological relationships among the botryllid ascidians (Subphylum Tunicata, Class Ascidiacea, Family Styelidae).},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {8351},
pmid = {33863944},
issn = {2045-2322},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Life Cycle Stages ; Marine Biology ; *Phylogeny ; Species Specificity ; Tropical Climate ; Urochordata/*anatomy &amp; histology/classification/*genetics/physiology ; },
abstract = {Ascidians (Phylum Chordata, Class Ascidiacea) are a large group of invertebrates which occupy a central role in the ecology of marine benthic communities. Many ascidian species have become successfully introduced around the world via anthropogenic vectors. The botryllid ascidians (Order Stolidobranchia, Family Styelidae) are a group of 53 colonial species, several of which are widespread throughout temperate or tropical and subtropical waters. However, the systematics and biology of this group of ascidians is not well-understood. To provide a systematic framework for this group, we have constructed a well-resolved phylogenomic tree using 200 novel loci and 55 specimens. A Principal Components Analysis of all species described in the literature using 31 taxonomic characteristics revealed that some species occupy a unique morphological space and can be easily identified using characteristics of adult colonies. For other species, additional information such as larval or life history characteristics may be required for taxonomic discrimination. Molecular barcodes are critical for guiding the delineation of morphologically similar species in this group.},
}
@article {pmid33862015,
year = {2021},
author = {Tian, L and Tomei, S and Schreuder, J and Weber, TS and Amann-Zalcenstein, D and Lin, DS and Tran, J and Audiger, C and Chu, M and Jarratt, A and Willson, T and Hilton, A and Pang, ES and Patton, T and Kelly, M and Su, S and Gouil, Q and Diakumis, P and Bahlo, M and Sargeant, T and Kats, LM and Hodgkin, PD and O'Keeffe, M and Ng, AP and Ritchie, ME and Naik, SH},
title = {Clonal multi-omics reveals Bcor as a negative regulator of emergency dendritic cell development.},
journal = {Immunity},
volume = {54},
number = {6},
pages = {1338-1351.e9},
doi = {10.1016/j.immuni.2021.03.012},
pmid = {33862015},
issn = {1097-4180},
mesh = {Animals ; Cell Differentiation/genetics ; Cell Line ; Cell Lineage/genetics ; Dendritic Cells/*metabolism ; Female ; Gene Expression/genetics ; HEK293 Cells ; Humans ; Male ; Membrane Proteins/genetics/metabolism ; Mice, Inbred C57BL ; Proto-Oncogene Proteins/*genetics/*metabolism ; Repressor Proteins/*genetics/*metabolism ; Stem Cells/metabolism ; Mice ; },
abstract = {Despite advances in single-cell multi-omics, a single stem or progenitor cell can only be tested once. We developed clonal multi-omics, in which daughters of a clone act as surrogates of the founder, thereby allowing multiple independent assays per clone. With SIS-seq, clonal siblings in parallel "sister" assays are examined either for gene expression by RNA sequencing (RNA-seq) or for fate in culture. We identified, and then validated using CRISPR, genes that controlled fate bias for different dendritic cell (DC) subtypes. This included Bcor as a suppressor of plasmacytoid DC (pDC) and conventional DC type 2 (cDC2) numbers during Flt3 ligand-mediated emergency DC development. We then developed SIS-skew to examine development of wild-type and Bcor-deficient siblings of the same clone in parallel. We found Bcor restricted clonal expansion, especially for cDC2s, and suppressed clonal fate potential, especially for pDCs. Therefore, SIS-seq and SIS-skew can reveal the molecular and cellular mechanisms governing clonal fate.},
}
@article {pmid33860245,
year = {2021},
author = {Phan, KL and LE, TML and Nguyen, HT and Nguyen, TD and Trinh, QP},
title = {First report and new molecular and morphological characterizations of root-knot nematode, Meloidogyne javanica, infecting ginger and long coriander in Vietnam.},
journal = {Journal of nematology},
volume = {53},
number = {},
pages = {},
pmid = {33860245},
issn = {0022-300X},
abstract = {Ginger (Zingiber officinale Roscoe) and long coriander (Eryngium foetidum L.) are commonly grown and used as important spices and medicinal plants in Vietnam. Our study recovered for the first time one of the most damaging tropical root-knot nematodes, Meloidogyne javanica, associated with these plants in the Western Highlands of Vietnam. In this study, M. javanica was characterized based on morphology and molecular characterization of D2-D3 fragment of 28S rRNA, ITS, and Nad5 mtDNA regions. The identification of this species was done based on a combination of morphology, multiplex-PCR with specific primer, network haplotype analysis, and PPNID program.},
}
@article {pmid33860235,
year = {2021},
author = {Denham, AN and Hughes, MR and Dowler, RC and Negovetich, NJ and Ammerman, LK},
title = {Genetic variation within a species of parasitic nematode, Skrjabingylus chitwoodorum, in skunks.},
journal = {Journal of nematology},
volume = {53},
number = {},
pages = {},
pmid = {33860235},
issn = {0022-300X},
abstract = {Carnivores in the families Mustelidae and Mephitidae are essential hosts for the cranial roundworm genus Skrjabingylus. A high prevalence of Skrjabingylus chitwoodorum has been observed in the striped skunk, Mephitis mephitis. Genetic barcoding studies of other nematodes have successfully used the cytochrome oxidase I (COI) mitochondrial gene to analyze genetic variation and divergence. We tested the hypothesis that low population structuring occurs within S. chitwoodorum because M. mephitis is widespread across much of North America and has high levels of gene flow. We extracted DNA from 38 samples of Skrjabingylus removed from the sinuses of M. mephitis and one from the plains spotted skunk, Spilogale putorius interrupta, for amplification and sequencing of COI. Analysis of 492 base pairs confirmed all samples were S. chitwoodorum and showed low genetic divergence (1.0%) within Texas, but high haplotype diversity. Supporting our hypothesis, no obvious divergent lineages based on geographic location were recovered within the samples based on Maximum Likelihood analysis and median joining haplotype network analysis. In fact, samples of Skrjabingylus from New York and South Dakota showed little difference compared with samples from Texas.},
}
@article {pmid33860102,
year = {2021},
author = {Takano, S and Fukasawa, M and Shindo, H and Takahashi, E and Fukasawa, Y and Kawakami, S and Hayakawa, H and Kuratomi, N and Kadokura, M and Maekawa, S and Enomoto, N},
title = {Digital next-generation sequencing of cell-free DNA for pancreatic cancer.},
journal = {JGH open : an open access journal of gastroenterology and hepatology},
volume = {5},
number = {4},
pages = {508-516},
pmid = {33860102},
issn = {2397-9070},
abstract = {BACKGROUND AND AIM: The clinical applicability of digital next-generation sequencing (dNGS), which eliminates polymerase chain reaction (PCR) and sequencing error-derived noise by using molecular barcodes (MBs), has not been fully evaluated. We evaluated the utility of dNGS of cell-free DNA (cfDNA) in liquid biopsies obtained from patients with pancreatic cancer.<br><br>METHODS: Fifty-eight patients with pancreatic cancer undergoing endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) were included. Samples were subjected to sequencing of 50 cancer-related genes using next-generation sequencing (NGS). The results were used as reference gene alterations. NGS of cfDNA from plasma was performed for patients with a mutant allele frequency (MAF) >1% and an absolute mutant number&#x2009;>&#x2009;10 copies/plasma mL in KRAS or GNAS by digital PCR. Sequence readings with and without MBs were compared with reference to EUS-FNA-derived gene alterations.<br><br>RESULTS: The concordance rate between dNGS of cfDNA and EUS-FNA-derived gene alterations was higher with than without MBs (p = 0.039), and MAF cut-off values in dNGS could be decreased to 0.2%. dNGS using MBs eliminated PCR and sequencing error by 74% and 68% for TP53 and all genes, respectively. Overall, dNGS detected mutations in KRAS (45%) and TP53 (26%) and copy number alterations in CCND2, CCND3, CDK4, FGFR1, and MYC, which are targets of molecular-targeted drugs.<br><br>CONCLUSIONS: dNGS of cfDNA using MBs is useful for accurate detection of gene alterations even with low levels of MAFs. These results may be used to inform the development of diagnostics and therapeutics that can improve the prognosis of pancreatic cancer.},
}
@article {pmid33859870,
year = {2021},
author = {Schuster, A and Pomponi, SA and Pisera, A and Cárdenas, P and Kelly, M and Wörheide, G and Erpenbeck, D},
title = {Systematics of 'lithistid' tetractinellid demosponges from the Tropical Western Atlantic-implications for phylodiversity and bathymetric distribution.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e10775},
pmid = {33859870},
issn = {2167-8359},
abstract = {BACKGROUND: Among all present demosponges, lithistids represent a polyphyletic group with exceptionally well-preserved fossils dating back to the Cambrian. Knowledge of their recent diversity, particularly in the Tropical Western Atlantic Ocean (TWA) where they are common in deep waters, is scarce making any comparison between present and past major 'lithistid' faunas difficult. In addition, the lack of sufficient molecular and morphological data hamper any predictions on phylogenetic relationships or phylodiversity from this region. The Harbor Branch Oceanographic Institute (HBOI, Fort Pierce, Florida) holds the largest collection of TWA lithistid sponges worldwide, however, the majority remain to be taxonomically identified and revised.<br><br>PRINCIPAL FINDINGS: In this study we provide sequences of 249 lithistid demosponges using two independent molecular markers (28S rDNA (C1-D2) and cox1 mtDNA). In addition, a morphological documentation of 70 lithistid specimens is provided in the database of the Sponge Barcoding Project (SBP). This integrated dataset represents the largest and most comprehensive of the TWA lithistids to date. The phylogenetic diversity of 'lithistid' demosponges in the Bahamas and Jamaica are high in comparison to other TWA regions; Theonellidae and Corallistidae dominate the fauna, while Neopeltidae and Macandrewiidae are rare. A proposed tetractinellid suborder, one undescribed genus and several undescribed species are recognized and the Pacific 'lithistid' genera, Herengeria and Awhiowhio, are reported from the TWA for the first time. The higher-taxa relationships of desma-bearing tetractinellids are discussed and topics for revision suggested.<br><br>CONCLUSION: This first integrative approach of TWA 'lithistid' demosponges contributes to a better understanding of their phylogenetic affinities, diversity and bathymetric distribution patterns within the TWA. As in the Pacific, the TWA 'lithistid' demosponges dominate deep-water habitats. Deeper taxonomic investigations will undoubtedly contribute to a better comparison between present major 'lithistid' faunas and their fossil record in the Mesozoic.},
}
@article {pmid33857749,
year = {2021},
author = {Orkun, &#xd6; and Vatansever, Z},
title = {Rediscovery and first genetic description of some poorly known tick species: Haemaphysalis kopetdaghica Kerbabaev, 1962 and Dermacentor raskemensis Pomerantzev, 1946.},
journal = {Ticks and tick-borne diseases},
volume = {12},
number = {4},
pages = {101726},
doi = {10.1016/j.ttbdis.2021.101726},
pmid = {33857749},
issn = {1877-9603},
mesh = {Animals ; Animals, Wild ; Female ; Goat Diseases/*parasitology ; *Goats ; Ixodidae/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Larva/anatomy &amp; histology/classification/growth &amp; development ; Male ; Nymph/anatomy &amp; histology/classification/growth &amp; development ; Tick Infestations/parasitology/*veterinary ; Turkey ; },
abstract = {This study aimed to provide novel information for some poorly known/rare tick species collected from wild goats (Capra aegagrus) in the mountains of Eastern Anatolia, Turkey and to expand upon the available genetic data. The collected ticks were morphologically identified as Haemaphysalis kopetdaghica (all active stages, n = 140), Dermacentor raskemensis (adults, n = 7), Ixodes gibbosus (adults, n = 15), Rhipicephalus kohlsi (female, n = 1), and R. bursa (nymphs, n = 2). A total of 32 engorged ticks (6 larvae, 6 nymphs, and 20 females) collected were allowed to molt to the next stage or for egg laying and larval hatching, respectively. In addition, one R. kohlsi female (previously confirmed by SEM microscopy) collected from a wild goat in the neighboring province of Erzurum was included in this study for further genetic comparison. The partial mitochondrial 16S rDNA and cytochrome c oxidase subunit 1 (barcoding regions) genes of each tick species were sequenced. All DNA samples obtained from the ticks were checked by PCR for the presence of Anaplasma spp., Babesia spp., Borrelia burgdorferi sensu lato, spotted fever group rickettsiae, and Theileria spp., but were found to be negative. Phylogenetic analyses of the 16S rDNA and cox1 genes were performed using the ML method to determine their genetic relationship with related ticks. As a result, this study has: i) rediscovered and provided two new tick records (H. kopetdaghica and D. raskemensis) for Turkey, ii) provided the first genetic data for H. kopetdaghica and D. raskemensis and revealed their phylogenetic relationships, iii) characterized the cox1 region of I. gibbosus for the first time, and iv) revealed significant genetic diversity between R. kohlsi from Anatolia and R. kohlsi from Oman, suggesting that R. kohlsi could include a cryptic species.},
}
@article {pmid33857537,
year = {2021},
author = {Deonath, A},
title = {Evolution of eukaryotes as a story of survival and growth of mitochondrial DNA over two billion years.},
journal = {Bio Systems},
volume = {206},
number = {},
pages = {104426},
doi = {10.1016/j.biosystems.2021.104426},
pmid = {33857537},
issn = {1872-8324},
mesh = {Animals ; *Biological Evolution ; Cell Survival/physiology ; DNA, Mitochondrial/*physiology ; Eukaryota/genetics/*growth &amp; development ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; Humans ; Mitochondria/physiology ; Time Factors ; },
abstract = {Mitochondria's significance in human diseases and in functioning, health and death of eukaryotic cell has been acknowledged widely. Yet our perspective in cell biology and evolution remains nucleocentric. Mitochondrial DNA, by virtue of its omnipresence and species-level conservation, is used as a barcode in animal taxonomy. This article analyses various levels of containment structures that enclose mitochondrial DNA and advocates a fresh perspective wherein evolution of organic structures of the eukarya domain seem to support and facilitate survival and proliferation of mitochondrial DNA by splitting containers as they age and by directing them along two distinct pathways: destruction of containers with more mutant mitochondrial DNA and rejuvenation of containers with less mutant mitochondrial DNA.},
}
@article {pmid33857177,
year = {2021},
author = {Kenmotsu, H and Ishikawa, M and Nitta, T and Hirose, Y and Eki, T},
title = {Distinct community structures of soil nematodes from three ecologically different sites revealed by high-throughput amplicon sequencing of four 18S ribosomal RNA gene regions.},
journal = {PloS one},
volume = {16},
number = {4},
pages = {e0249571},
pmid = {33857177},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Helminth/genetics ; DNA, Ribosomal/genetics ; Ecosystem ; High-Throughput Nucleotide Sequencing ; Nematoda/*classification/genetics ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA ; Soil/*parasitology ; },
abstract = {Quantitative taxonomic compositions of nematode communities help to assess soil environments due to their rich abundance and various feeding habitats. DNA metabarcoding by the 18S ribosomal RNA gene (SSU) regions were preferentially used for analyses of soil nematode communities, but the optimal regions for high-throughput amplicon sequencing have not previously been well investigated. In this work, we performed Illumina-based amplicon sequencing of four SSU regions (regions 1-4) to identify suitable regions for nematode metabarcoding using the taxonomic structures of nematodes from uncultivated field, copse, and cultivated house garden soils. The fewest nematode-derived sequence variants (SVs) were detected in region 3, and the total nematode-derived SVs were comparable in regions 1 and 4. The relative abundances of reads in regions 1 and 4 were consistent in both orders and feeding groups with prior studies, thus suggesting that region 4 is a suitable target for the DNA barcoding of nematode communities. Distinct community structures of nematodes were detected in the taxon, feeding habitat, and life-history strategy of each sample; i.e., Dorylamida- and Rhabditida-derived plant feeders were most abundant in the copse soil, Rhabditida-derived bacteria feeders in the house garden soil, and Mononchida- and Dorylamida-derived omnivores and predators and Rhabditida-derived bacteria feeders in the field soil. Additionally, low- and high-colonizer-persister (cp) groups of nematodes dominated in the house garden and copse soils, respectively, whereas both groups were found in the field soil, suggesting bacteria-rich garden soil, undisturbed and plant-rich copse soil, and a transient status of nematode communities in the field soil. These results were also supported by the maturity indices of the three sampling sites. Finally, the influence of the primer tail sequences was demonstrated to be insignificant on amplification. These findings will be useful for DNA metabarcoding of soil nematode communities by amplicon sequencing.},
}
@article {pmid33854287,
year = {2021},
author = {Unnikrishnan, R and Sumod, M and Jayaraj, R and Sujanapal, P and Dev, SA},
title = {The efficacy of machine learning algorithm for raw drug authentication in Coscinium fenestratum (Gaertn.) Colebr. employing a DNA barcode database.},
journal = {Physiology and molecular biology of plants : an international journal of functional plant biology},
volume = {27},
number = {3},
pages = {605-617},
pmid = {33854287},
issn = {0971-5894},
abstract = {Medicinal plants are a valuable resource for traditional as well as modern medicine. Consequently huge demand has exerted a heavy strain on the existing natural resources. Due to over exploitation and unscientific collection most of the commercially traded ayurvedic plants are in the phase of depletion. Adulteration of expensive raw drugs with inferior taxa has become a common practice to meet the annual demand of the ayurvedic industry. Although there are several recommended methods for proper identification varying from the traditional taxonomic to organoleptic and physiochemical, it is difficult to authenticate ayurvedic raw drugs available in extremely dried, powdered or shredded forms. In this regard, the study addresses proper authentication and illicit trade in Coscinium fenestratum (Gaertn.) Colebr. using CBOL recommended standard barcode regions viz. nuclear ribosomal-Internally Transcribed Spacer (nrDNA- ITS), maturase K (matK), ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL), and psbA-trnH spacer regions. Further, an integrated analytical approach employing Maximum Likelihood phylogenetic tree and Machine Learning Approach, Waikato Environment for Knowledge Analysis was employed to prove efficacy of the method. The automated species identification technique, Artificial Intelligence uses the ability of computers to build models that can receive the input data and then conduct statistical analyses which significantly reduces the human labour. Concurrently, scientific management, restoration, cultivation and conservation measures should be given utmost priority to reduce the depletion of wild resources as well as to meet the rapidly increasing demand of the herbal industries.},
}
@article {pmid33854030,
year = {2021},
author = {Toropov, N and Vollmer, F},
title = {Whispering-gallery microlasers for cell tagging and barcoding: the prospects for in vivo biosensing.},
journal = {Light, science &amp; applications},
volume = {10},
number = {1},
pages = {77},
pmid = {33854030},
issn = {2047-7538},
abstract = {Researchers in the field of whispering-gallery-mode (WGM) microresonators have proposed biointegrated low-threshold WGM lasers, to enable large-scale parallel single-cell tracking and barcoding. Although the reported devices have so far been primarily investigated in model applications, most recent results represent important steps towards the development of in vivo tags and sensors that utilize the unique and narrow spectral features of miniature WGM lasers.},
}
@article {pmid33853847,
year = {2021},
author = {Ku, WL and Pan, L and Cao, Y and Gao, W and Zhao, K},
title = {Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencing.},
journal = {Genome research},
volume = {31},
number = {10},
pages = {1831-1842},
pmid = {33853847},
issn = {1549-5469},
mesh = {*Chromatin/genetics ; Chromatin Immunoprecipitation/methods ; *Histone Code ; Protein Processing, Post-Translational ; Sequence Analysis, DNA/methods ; },
abstract = {Recently, multiple single-cell assays were developed for detecting histone marks at the single-cell level. These techniques are either limited by the low cell throughput or sparse reads which limit their applications. To address these problems, we introduce indexing single-cell immunocleavage sequencing (iscChIC-seq), a multiplex indexing method based on TdT terminal transferase and T4 DNA ligase-mediated barcoding strategy and single-cell ChIC-seq, which is capable of readily analyzing histone modifications across tens of thousands of single cells in one experiment. Application of iscChIC-seq to profiling H3K4me3 and H3K27me3 in human white blood cells (WBCs) enabled successful detection of more than 10,000 single cells for each histone modification with 11 K and 45 K nonredundant reads per cell, respectively. Cluster analysis of these data allowed identification of monocytes, T cells, B cells, and NK cells from WBCs. The cell types annotated from H3K4me3 single-cell data are specifically correlated with the cell types annotated from H3K27me3 single-cell data. Our data indicate that iscChIC-seq is a reliable technique for profiling histone modifications in a large number of single cells, which may find broad applications in studying cellular heterogeneity and differentiation status in complex developmental and disease systems.},
}
@article {pmid33853671,
year = {2021},
author = {Shen, S and Liu, SL and Jiang, JH and Zhou, LW},
title = {Addressing widespread misidentifications of traditional medicinal mushrooms in Sanghuangporus (Basidiomycota) through ITS barcoding and designation of reference sequences.},
journal = {IMA fungus},
volume = {12},
number = {1},
pages = {10},
pmid = {33853671},
issn = {2210-6340},
support = {31970012//National Natural Science Foundation of China/ ; 2017240//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; KFJ-BRP-017-12//Biological Resources Programme, Chinese Academy of Sciences/ ; },
abstract = {"Sanghuang" refers to a group of important traditionally-used medicinal mushrooms belonging to the genus Sanghuangporus. In practice, species of Sanghuangporus referred to in medicinal studies and industry are now differentiated mainly by a BLAST search of GenBank with the ITS barcoding region as a query. However, inappropriately labeled ITS sequences of "Sanghuang" in GenBank restrict accurate species identification and, to some extent, the utilization of these species as medicinal resources. We examined all available 271 ITS sequences related to "Sanghuang" in GenBank including 31 newly submitted sequences from this study. Of these sequences, more than half were mislabeled so we have now corrected the corresponding species names. The mislabeled sequences mainly came from strains utilized by non-taxonomists. Based on the analyses of ITS sequences submitted by taxonomists as well as morphological characters, we separate the newly described Sanghuangporus subbaumii from S. baumii and treat S. toxicodendri as a later synonym of S. quercicola. Fourteen species of Sanghuangporus are accepted, with intraspecific distances up to 1.30% (except in S. vaninii, S. weirianus and S. zonatus) and interspecific distances above 1.30% (except between S. alpinus and S. lonicerinus, and S. baumii and S. subbaumii). To stabilize the concept of these 14 species of Sanghuangporus, their taxonomic information and reliable ITS reference sequences are provided. Moreover, ten potential diagnostic sequences are provided for Hyperbranched Rolling Circle Amplification to rapidly confirm three common commercial species, viz. S. baumii, S. sanghuang, and S. vaninii. Our results provide a practical method for ITS barcoding-based species identification of Sanghuangporus and will promote medicinal studies and commercial development from taxonomically correct material.},
}
@article {pmid33852820,
year = {2021},
author = {Turanov, SV and Kartavtsev, YP},
title = {A complement to DNA barcoding reference library for identification of fish from the Northeast Pacific.},
journal = {Genome},
volume = {64},
number = {10},
pages = {927-936},
doi = {10.1139/gen-2020-0192},
pmid = {33852820},
issn = {1480-3321},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; *Fishes/classification ; Gene Library ; Pacific Ocean ; Phylogeny ; },
abstract = {The seas of the North Pacific Ocean are characterized by a large variety of fish fauna, including endemic species. Molecular genetic methods, often based on DNA barcoding approaches, have been recently used to determine species boundaries and identify cryptic diversity within these species. This study complements the DNA barcode library of fish from the Northeast Pacific area. A library based on 154 sequences of the mitochondrial COI gene from 44 species was assembled and analyzed. It was found that 39 species (89%) can be unambiguously identified by the clear thresholds forming a barcoding gap. Deviations from the standard 2% threshold value resulted in detection of the species Enophrys lucasi in the sample, which is not typical for the eastern part of the Bering Sea. This barcoding gap also made it possible to identify naturally occurring low values of interspecific divergence of eulittoral taxa Aspidophoroides and the deep-sea genus Coryphaenoides. Synonymy of the genus Albatrossia in favor of the genus Coryphaenoides is suggested based on both the original and previously published data.},
}
@article {pmid33852067,
year = {2021},
author = {Costa, JCR and Marchi, GH and Santos, CS and Andrade, MCM and Chaves Junior, SP and Silva, MAN and Melo, MN and Andrade, AJ},
title = {First molecular evidence of frogs as a food source for sand flies (Diptera: Phlebotominae) in Brazilian caves.},
journal = {Parasitology research},
volume = {120},
number = {5},
pages = {1571-1582},
pmid = {33852067},
issn = {1432-1955},
mesh = {Animals ; Anura/*parasitology ; Brazil ; DNA/genetics ; Feeding Behavior ; Female ; Food ; Male ; Parks, Recreational ; Phlebotomus/*classification/*physiology ; Polymerase Chain Reaction ; },
abstract = {Genus and species of phlebotomine sand flies have been recorded and described in caves in Brazil, but no study has provided the food source used by sand flies in these environments. Herein, we identified the blood source used by sand fly species in caves located at "Quadrilátero Ferrífero" (QF), Minas Gerais state. Specimens were manually collected near or on anurans inside ferruginous caves in Serra do Gandarela National Park and Serra do Rola Moça State Park. Males and females were placed in vials with 70% alcohol and stored at -10°C. Females engorged, after specific identification, had DNA extracted and followed for PCR amplification using specific primers. Sequencing was analyzed in the GenBank and Barcode of Life. A total of 198 specimens were collected (107 females and 91 males), all of them belonging to species Sciopemyia aff. microps (88.89%), Sciopemyia sordellii (10.61%), or Martinsmyia oliveirai (0.50%). When it comes to the females, 89 were S. aff. microps and 18 S. sordellii. Nineteen engorged females of S. aff. microps were analyzed and most of them (n=18) presented blood from Bokermannohyla martinsi and one contained blood from Scinax fuscovarius. The blood present in engorged females of S. sordellii (n=4) was from B. martinsi. Sciopemyia genus specimens are commonly found in collections carried out inside natural caves, but this was the first study to prove that females of this genus feed on cold-blooded animals in nature. HIGHLIGHTS: • Here we proved that sand flies feed in cold-blooded animals in in Brazilian caves. • Females of the Sciopemyia genus were for the first time found feeding in natural habitats. • Anurans of the family Hylidae were identified as source by molecular analyzes. • Insect bloodmeal identification can help assessing the fauna in several biomes. • This is the first record of S. aff. microps in caves of Brazil.},
}
@article {pmid33852063,
year = {2021},
author = {Suetsugu, K and Yamato, M and Matsubayashi, J and Tayasu, I},
title = {Partial and full mycoheterotrophy in green and albino phenotypes of the slipper orchid Cypripedium debile.},
journal = {Mycorrhiza},
volume = {31},
number = {3},
pages = {301-312},
pmid = {33852063},
issn = {1432-1890},
support = {17H05016//Japan Society for the Promotion of Science/ ; 16H02524//Japan Society for the Promotion of Science/ ; },
mesh = {*Basidiomycota/genetics ; Carbon Isotopes/analysis ; *Mycorrhizae/chemistry/genetics ; *Orchidaceae ; Phenotype ; Phylogeny ; Symbiosis ; },
abstract = {Most green orchids form mycorrhizal associations with rhizoctonia fungi, a polyphyletic group including Serendipitaceae, Ceratobasidiaceae, and Tulasnellaceae. Although accumulating evidence indicated that partial mycoheterotrophy occurs in such so-called rhizoctonia-associated orchids, it remains unclear how much nutrition rhizoctonia-associated orchids obtain via mycoheterotrophic relationships. We investigated the physiological ecology of green and albino individuals of a rhizoctonia-associated orchid Cypripedium debile, by using molecular barcoding of the mycobionts and stable isotope ([13]C and [15] N) analysis. Molecular barcoding of the mycobionts indicated that the green and albino individuals harbored Tulasnella spp., which formed a clade with the previously reported C. debile mycobionts. In addition, stable isotope analysis showed that both phenotypes were significantly enriched in [13]C but not in [15] N. Therefore, green and albino individuals were recognized as partial and full mycoheterotrophs, respectively. The green variants were estimated to obtain 42.5 ± 8.2% of their C from fungal sources, using the [13]C enrichment factor of albino individuals as a mycoheterotrophic endpoint. The proportion of fungal-derived C in green C. debile was higher than that reported in other rhizoctonia-associated orchids. The high fungal dependence may facilitate the emergence of albino mutants. Our study provides the first evidence of partial mycoheterotrophy in the subfamily Cypripedioideae. Partial mycoheterotrophy may be more general than previously recognized in the family Orchidaceae.},
}
@article {pmid33851248,
year = {2021},
author = {Zhang, T and Vďačný, P},
title = {A discovery of two new Tetrahymena species parasitizing slugs and mussels: morphology and multi-gene phylogeny of T. foissneri sp. n. and T. unionis sp. n.},
journal = {Parasitology research},
volume = {120},
number = {7},
pages = {2595-2616},
pmid = {33851248},
issn = {1432-1955},
support = {APVV-19-0076//Agent&#xfa;ra na Podporu V&#xfd;skumu a V&#xfd;voja/ ; VEGA 1/0013/21//Vedeck&#xe1; Grantov&#xe1; Agent&#xfa;ra M&#x160;VVa&#x160; SR a SAV/ ; },
mesh = {Animals ; Bivalvia/*parasitology ; Ciliophora/classification ; Cyclooxygenase 1/genetics ; Europe ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Seafood ; Slovakia ; Snails/*parasitology ; Tetrahymena/*classification/genetics/growth &amp; development ; },
abstract = {The presence of parasitic ciliates of the hymenostome genus Tetrahymena was examined in 150 mollusks belonging to six bivalve and 13 gastropod species in Slovakia, Central Europe. Tetrahymenids were detected only in two species, viz., in the invasive Lusitanian slug (Arion vulgaris) and in the native swollen river mussel (Unio tumidus). Although only 10.52% of the examined mollusk taxa were positive, their Tetrahymena infections were very intensive accounting for several hundreds of ciliates per host. Phylogenetic analyses of the 16S and 18S rRNA genes as well as of the barcoding region of the gene encoding for cytochrome c oxidase subunit I revealed that both isolates represent new taxa, T. foissneri sp. n. and T. unionis sp. n. The former species belongs to the 'borealis' clade and its nearest relative is T. limacis, a well-known parasite of slugs and snails. Besides molecular data, T. foissneri can be distinguished from T. limacis also morphologically by the body shape of the parasitic-phase form, dimensions of micronuclei, and the silverline system. On the other hand, T. unionis was classified within the 'paravorax' clade along with T. pennsylvaniensis, T. glochidiophila, and T. nigricans. Although these four species are genetically distinct, T. unionis could be morphologically separated only from T. nigricans by body shape and size. The present study suggests that both aquatic and terrestrial mollusks represent interesting hosts for the discovery of novel Tetrahymena lineages.},
}
@article {pmid33850416,
year = {2021},
author = {Zhao, Y and Li, Y and Liu, Z},
title = {Revision of the Conwentzia Enderlein, 1905 (Neuroptera, Coniopterygidae) of China, combining morphological and molecular characters.},
journal = {ZooKeys},
volume = {1026},
number = {},
pages = {1-15},
pmid = {33850416},
issn = {1313-2989},
abstract = {The Chinese species of Conwentzia Enderlein are revised by integrating morphological characters and molecular data. Conwentzia yunguiana Liu &amp; Yang, 1993 is proposed as a junior synonym of Conwentzia nietoi Monserrat, 1982, syn. nov. and Conwentzia orthotibia Yang, 1974 is proposed as a junior synonym of Conwentzia pineticola Enderlein, 1905, syn. nov. Moreover, a key to the adult males of the Conwentzia from China and DNA barcodes are provided.},
}
@article {pmid33850233,
year = {2021},
author = {Gallegos-Monterrosa, R and Christensen, MN and Barchewitz, T and Koppenhöfer, S and Priyadarshini, B and Bálint, B and Maróti, G and Kempen, PJ and Dragoš, A and Kovács, &#xc1;T},
title = {Impact of Rap-Phr system abundance on adaptation of Bacillus subtilis.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {468},
pmid = {33850233},
issn = {2399-3642},
mesh = {Adaptation, Physiological/*genetics ; Bacillus subtilis/enzymology/genetics/*physiology ; Gene Expression Regulation, Bacterial ; *Genes, Bacterial ; *Multigene Family ; Phosphoric Monoester Hydrolases/*metabolism ; Quorum Sensing ; },
abstract = {Microbes commonly display great genetic plasticity, which has allowed them to colonize all ecological niches on Earth. Bacillus subtilis is a soil-dwelling organism that can be isolated from a wide variety of environments. An interesting characteristic of this bacterium is its ability to form biofilms that display complex heterogeneity: individual, clonal cells develop diverse phenotypes in response to different environmental conditions within the biofilm. Here, we scrutinized the impact that the number and variety of the Rap-Phr family of regulators and cell-cell communication modules of B. subtilis has on genetic adaptation and evolution. We examine how the Rap family of phosphatase regulators impacts sporulation in diverse niches using a library of single and double rap-phr mutants in competition under 4 distinct growth conditions. Using specific DNA barcodes and whole-genome sequencing, population dynamics were followed, revealing the impact of individual Rap phosphatases and arising mutations on the adaptability of B. subtilis.},
}
@article {pmid33848300,
year = {2021},
author = {Wang, H and Jiang, B and Gu, J and Wei, T and Lin, L and Huang, Y and Liang, D and Huang, J},
title = {Molecular phylogeny and species delimitation of the genus Tonkinacris (Orthoptera, Acrididae, Melanoplinae) from China.},
journal = {PloS one},
volume = {16},
number = {4},
pages = {e0249431},
pmid = {33848300},
issn = {1932-6203},
mesh = {Animals ; *Phylogeny ; China ; Bayes Theorem ; Grasshoppers/genetics/classification ; Species Specificity ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; },
abstract = {Tonkinacris is a small group in Acrididae. While a few species were occasionally sampled in some previous molecular studies, there is no revisionary research devoted to the genus. In this study, we explored the phylogeny of and the relationships among Chinese species of the genus Tonkinacris using the mitochondrial COI barcode and the complete sequences of ITS1 and ITS2 of the nuclear ribosomal DNA. The phylogeny was reconstructed in maximum likelihood and Bayesian inference frameworks, respectively. The overlap range between intraspecific variation and interspecific divergence was assessed via K2P distances. Species boundaries were delimitated using phylogenetic species concept, NJ tree, K2P distance, the statistical parsimony network as well as the GMYC model. The results demonstrate that the Chinese Tonkinacris species is a monophyletic group and the phylogenetic relationship among them is (T. sinensis, (T. meridionalis, (T. decoratus, T. damingshanus))). While T. sinensis, T. meridionalis and T. decoratus were confirmed being good independent species strongly supported by both morphological and molecular evidences, the validity of T. damingshanus was not perfectly supported by molecular evidence in this study.},
}
@article {pmid33846382,
year = {2021},
author = {Batovska, J and Piper, AM and Valenzuela, I and Cunningham, JP and Blacket, MJ},
title = {Developing a non-destructive metabarcoding protocol for detection of pest insects in bulk trap catches.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {7946},
pmid = {33846382},
issn = {2045-2322},
mesh = {Animals ; Aphids/*genetics ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; Genetic Loci ; Hemiptera/*genetics ; Larva/physiology ; Phylogeny ; },
abstract = {Metabarcoding has the potential to revolutionise insect surveillance by providing high-throughput and cost-effective species identification of all specimens within mixed trap catches. Nevertheless, incorporation of metabarcoding into insect diagnostic laboratories will first require the development and evaluation of protocols that adhere to the specialised regulatory requirements of invasive species surveillance. In this study, we develop a multi-locus non-destructive metabarcoding protocol that allows sensitive detection of agricultural pests, and subsequent confirmation using traditional diagnostic techniques. We validate this protocol for the detection of tomato potato psyllid (Bactericera cockerelli) and Russian wheat aphid (Diuraphis noxia) within mock communities and field survey traps. We find that metabarcoding can reliably detect target insects within mixed community samples, including specimens that morphological identification did not initially detect, but sensitivity appears inversely related to community size and is impacted by primer biases, target loci, and sample indexing strategy. While our multi-locus approach allowed independent validation of target detection, lack of reference sequences for 18S and 12S restricted its usefulness for estimating diversity in field samples. The non-destructive DNA extraction proved invaluable for resolving inconsistencies between morphological and metabarcoding identification results, and post-extraction specimens were suitable for both morphological re-examination and DNA re-extraction for confirmatory barcoding.},
}
@article {pmid33844840,
year = {2021},
author = {Mohammadi, S and Lutermann, H and Hoffmann, S and Emami-Khoyi, A and Webster, HJ and Fagir, D and Bennett, NC and van Vuuren, BJ},
title = {MORPHOLOGICAL AND MOLECULAR CHARACTERIZATION OF THE PLAGUE VECTOR XENOPSYLLA BRASILIENSIS.},
journal = {The Journal of parasitology},
volume = {107},
number = {2},
pages = {289-294},
doi = {10.1645/20-44},
pmid = {33844840},
issn = {1937-2345},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Flea Infestations/parasitology/veterinary ; Genetic Variation ; Haplotypes ; Insect Vectors/*anatomy &amp; histology/*genetics ; Male ; Mitochondria/enzymology ; Murinae/parasitology ; Plague/*transmission ; South Africa ; Xenopsylla/*anatomy &amp; histology/*genetics ; },
abstract = {Members of the flea family Pulicidae have been the focus of many studies due to their significance as diseases vectors of medical and veterinary importance and their cosmopolitan distribution. They often exhibit variation in morphological features that can make correct species identification and management challenging. This may also apply to Xenopsylla brasiliensis (Baker, 1904), an important plague vector. In the current study, we aimed to provide genetic tools for reliable species identification using a DNA barcoding approach. A total of 73 flea specimens was collected from a native host (Namaqua rock mouse, Micaelamys namaquensis) in South Africa and identified morphologically. In addition, we took measurements of 7 morphological characteristics. Subsequently, we successfully generated barcodes of the mitochondrial cytochrome c oxidase subunit I (COI) gene for X. brasiliensis. We validated this approach by comparing our data to COI sequences from Rwandan X. brasiliensis. While sequences from both regions suggested a close relationship between the 2 X. brasiliensis populations, both haplotype and nucleotide diversity were substantially larger for the South African specimens. This may be attributed to human-assisted spread, differences in habitat, and/or host species sampled and merits further study in the future.},
}
@article {pmid33840596,
year = {2021},
author = {Yagi, N and Hamamoto, K and Thi Bui, KN and Ueda, S and Tawata, S and Le, DT and Thi Bui, MH and Hirai, I},
title = {A high-throughput sequencing determination method for upstream genetic structure (UGS) of ISEcp1-blaCTX-M transposition unit and application of the UGS to classification of bacterial isolates possessing blaCTX-M.},
journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy},
volume = {27},
number = {9},
pages = {1288-1294},
doi = {10.1016/j.jiac.2021.04.001},
pmid = {33840596},
issn = {1437-7780},
mesh = {Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics ; *Escherichia coli Infections ; High-Throughput Nucleotide Sequencing ; Humans ; Plasmids/genetics ; beta-Lactamases/genetics ; },
abstract = {INTRODUCTION: Because blaCTX-M is responsible for resistance of bacteria to the third generation cephalosporins, location of blaCTX-M could be a good indicator for classifying bacterial isolates harboring blaCTX-M in molecular epidemiology. However, determination of blaCTX-M location has been difficult when multiple copies of ISEcp1 were found on bacterial genome. We aimed to establish a high-throughput analytical method for upstream genetic structures (UGS) of ISEcp1 to facilitate determination of blaCTX-M location.<br><br>METHODS: Extracted DNA samples obtained from 168 Escherichia coli isolates possessing blaCTX-M were digested by restriction enzyme, HaeIII, and the digested DNA fragments were ligated with homemade barcode adaptors. Then, DNA fragments containing UGS of ISEcp1 were amplified and subjected to the Nanopore sequencer.<br><br>RESULTS: Nucleotide sequences and locations of 168 UGSs obtained from the examined E.&#xa0;coli isolates were determined. Among the 168 determined UGSs, 150 (89.3%) UGS were confirmed on plasmid and classified into eight types. Interestingly, coding sequence of ISEcp1 transposase gene in seven of the eight types were disrupted by IS26 insertion. The remaining 18 (10.7%) UGSs were observed in identical chromosomal region. The obtained nucleotide sequences the locations of UGSs were confirmed by conventional capillary sequencer and Southern blotting, respectively, and any discrepant result was not observed with these confirmation procedures.<br><br>CONCLUSIONS: Our results indicated that the established method was efficient for simultaneously determining at least 100 different UGS, and suggested that the determined UGSs of ISEcp1-blaCTX-M transposition unit was useful for classification of bacterial isolates harboring blaCTX-M.},
}
@article {pmid33838948,
year = {2021},
author = {Pagliusi, S and Hayman, B and Jarrett, S},
title = {Vaccines for a healthy future: 21st DCVMN Annual General Meeting 2020 report.},
journal = {Vaccine},
volume = {39},
number = {18},
pages = {2479-2488},
pmid = {33838948},
issn = {1873-2518},
mesh = {*COVID-19 ; COVID-19 Vaccines ; Developing Countries ; Global Health ; Humans ; International Cooperation ; Pandemics ; SARS-CoV-2 ; *Vaccines ; },
abstract = {The Developing Countries Vaccine Manufacturers' Network held its 21st Annual General Meeting virtually in November 2020 given the COVID-19 pandemic. Vaccine manufacturing experts, leaders from local and global public health organizations and multilateral organizations, through diverse presentations, questions and answers, focused on the pandemic and the response of vaccine manufacturers where many are engaged in research and development and production agreements. The pandemic is expanding rapidly which makes the global availability and equitable access to safe and effective COVID-19 vaccines critical. Strategies put in place include the establishment of the Access to COVID-19 Tools Accelerator (ACT-A) within which the COVAX facility aims to distribute 2 billion COVID-19 vaccine doses by the end of 2021, with procurement mechanisms already being established. At the same time, regulatory authorities have emergency use authorizations aimed at the rapid approval of safe and effective vaccines, with a push for harmonization in regulatory approaches being advocated. The Meeting was also apprised of other innovations being developed for vaccines including multi-array patches for easier vaccine application, increased heat stability for mitigating cold chain and storage challenges, the barcoding of primary packaging for enhancing vaccine traceability, and gathering data for decision-making. Over time, these innovations will facilitate the widespread availability and equitable access of vaccines including those addressing epidemics and pandemics. In addition, a number of manufacturers described technologies they have for accelerating vaccine manufacturing and supply globally. Overall, there was agreement that manufacturers from developing countries play a critical role in the global research, development and supply of vaccines for a healthy future, with increasing collaboration and partnering between them a growing strength.},
}
@article {pmid33838361,
year = {2021},
author = {Yung, L and Bertheau, C and Tafforeau, F and Zappelini, C and Valot, B and Maillard, F and Selosse, MA and Viotti, C and Binet, P and Chiapusio, G and Chalot, M},
title = {Partial overlap of fungal communities associated with nettle and poplar roots when co-occurring at a trace metal contaminated site.},
journal = {The Science of the total environment},
volume = {782},
number = {},
pages = {146692},
doi = {10.1016/j.scitotenv.2021.146692},
pmid = {33838361},
issn = {1879-1026},
mesh = {*Mycobiome ; *Mycorrhizae ; Plant Roots ; Soil Microbiology ; *Urtica dioica ; },
abstract = {Stinging nettle (Urtica dioica L.) raises growing interest in phytomanagement because it commonly grows under poplar Short Rotation Coppices (SRC) set up at trace-metal (TM) contaminated sites and provides high-quality herbaceous fibres. The mycobiome of this non-mycorhizal plant and its capacity to adapt to TM-contaminated environments remains unknown. This study aimed at characterizing the mycobiome associated with nettle and poplar roots co-occurring at a TM-contaminated site. Plant root barcoding using the fungi-specific ITS1F-ITS2 primers and Illumina MiSeq technology revealed that nettle and poplar had distinct root fungal communities. The nettle mycobiome was dominated by Pezizomycetes from known endophytic taxa and from the supposedly saprotrophic genus Kotlabaea (which was the most abundant). Several ectomycorrhizal fungi such as Inocybe (Agaricomycetes) and Tuber (Pezizomycetes) species were associated with the poplar roots. Most of the Pezizomycetes taxa were present in the highly TM-contaminated area whereas Agaricomycetes tended to be reduced. Despite being a known non-mycorrhizal plant, nettle was associated with a significant proportion of ectomycorrhizal OTU (9.7%), suggesting some connexions between the poplar and the nettle root mycobiomes. Finally, our study raised the interest in reconsidering the fungal networking beyond known mycorrhizal interactions.},
}
@article {pmid33837131,
year = {2021},
author = {Heiser, CN and Wang, VM and Chen, B and Hughey, JJ and Lau, KS},
title = {Automated quality control and cell identification of droplet-based single-cell data using dropkick.},
journal = {Genome research},
volume = {31},
number = {10},
pages = {1742-1752},
pmid = {33837131},
issn = {1549-5469},
support = {P50 CA236733/CA/NCI NIH HHS/United States ; R01 DK103831/DK/NIDDK NIH HHS/United States ; R35 GM124685/GM/NIGMS NIH HHS/United States ; U54 CA217450/CA/NCI NIH HHS/United States ; },
mesh = {Gene Expression Profiling/methods ; Quality Control ; RNA/genetics ; Sequence Analysis, RNA/methods ; *Single-Cell Analysis/methods ; *Software ; },
abstract = {A major challenge for droplet-based single-cell sequencing technologies is distinguishing true cells from uninformative barcodes in data sets with disparate library sizes confounded by high technical noise (i.e., batch-specific ambient RNA). We present dropkick, a fully automated software tool for quality control and filtering of single-cell RNA sequencing (scRNA-seq) data with a focus on excluding ambient barcodes and recovering real cells bordering the quality threshold. By automatically determining data set-specific training labels based on predictive global heuristics, dropkick learns a gene-based representation of real cells and ambient noise, calculating a cell probability score for each barcode. Using simulated and real-world scRNA-seq data, we benchmarked dropkick against conventional thresholding approaches and EmptyDrops, a popular computational method, showing greater recovery of rare cell types and exclusion of empty droplets and noisy, uninformative barcodes. We show for both low- and high-background data sets that dropkick's weakly supervised model reliably learns which genes are enriched in ambient barcodes and draws a multidimensional boundary that is more robust to data set-specific variation than existing filtering approaches. dropkick provides a fast, automated tool for reproducible cell identification from scRNA-seq data that is critical to downstream analysis and compatible with popular single-cell Python packages.},
}
@article {pmid33835714,
year = {2022},
author = {Florentin, AS and Garcia Perez, HA and Rodrigues, CMF and Dubois, EF and Monzón, CM and Teixeira, MMG},
title = {Molecular epidemiological insights into Trypanosoma vivax in Argentina: From the endemic Gran Chaco to outbreaks in the Pampas.},
journal = {Transboundary and emerging diseases},
volume = {69},
number = {3},
pages = {1364-1374},
doi = {10.1111/tbed.14103},
pmid = {33835714},
issn = {1865-1682},
support = {INCT-EpiAmo//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CRAI/DEER/078-27/2018//Programa de Movilidad en el Posgrado de la Red de Macrouniversidades de Am&#xe9;rica Latina y El Caribe/ ; 2016/03028-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
mesh = {Animals ; Argentina/epidemiology ; *Cattle/parasitology ; *Disease Outbreaks/veterinary ; Female ; Genotype ; Livestock ; *Trypanosoma vivax/genetics ; *Trypanosomiasis, African/veterinary ; },
abstract = {Argentina is a home to millions of beef and dairy cattle and is one of the world's major exporters of meat. In the present study, Trypanosoma vivax was prevalent (2016-2018) in two major livestock farming regions, the Gran Chaco and the Pampas. In the Gran Chaco, 29% and 51% of animals (n = 72, taurine x zebuine crossbreed) were, respectively, positive by TviCATL-PCR and the more sensitive fluorescent fragment length barcoding (FFLB) method. While 18.4/38.8% of breeding cows (n = 49) tested positive by PCR/FFLB, infection increased to 52.2/78.3% in an outbreak of acute infection in steers (n = 23, taurine breed) brought from a non-endemic area. In the Pampas, overall infection rates in dairy cows (n = 54, taurine breed) were comparable (p > .01) between PCR (66.7%) and FFLB (62.9%) and showed a remarkable increase (PCR / FFLB) from 48.3/44.8% in 2017 to 88/84% in 2018. Infected dairy cattle exhibited anaemia, fever, anorexia, enlarged lymph nodes, emaciation and neurological signs. In contrast, beef cows (taurine x zebuine crossbreed) from the Pampas (n = 30) were asymptomatic despite exhibiting 16.7% (PCR) and 53.3% (FFLB) infection rates. Microsatellite genotyping revealed a remarkable microheterogeneity, seven genotypes in the Gran Chaco, nine in the Pampas and five shared between both regions, consistent with regular movement of T. vivax infected livestock. Data gathered in our study support the Gran Chaco being an endemic area for T. vivax, whereas the Pampas emerged as an outbreak area of acute infection in dairy cattle with critical negative impact in milk production. To the best of our knowledge, this is the first molecular study of T. vivax in Argentina, and results indicated the need for preventive measures to control T. vivax spread from the Gran Chaco to vast livestock farming areas across Argentina.},
}
@article {pmid33835712,
year = {2021},
author = {Brandt, MI and Trouche, B and Quintric, L and Günther, B and Wincker, P and Poulain, J and Arnaud-Haond, S},
title = {Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding.},
journal = {Molecular ecology resources},
volume = {21},
number = {6},
pages = {1904-1921},
doi = {10.1111/1755-0998.13398},
pmid = {33835712},
issn = {1755-0998},
support = {AP2016-228//Ifremer/ ; ANR-10-INBS-09//France G&#xe9;nomique/ ; //Genoscope-CEA/ ; },
mesh = {Animals ; Archaea/*classification ; Bacteria/*classification ; Bayes Theorem ; Biodiversity ; Cluster Analysis ; *Computational Biology ; *DNA Barcoding, Taxonomic ; *DNA, Environmental ; Ecosystem ; Eukaryota/*classification ; Geologic Sediments ; Seawater ; },
abstract = {Environmental DNA metabarcoding is a powerful tool for studying biodiversity. However, bioinformatic approaches need to adjust to the diversity of taxonomic compartments targeted as well as to each barcode gene specificities. We built and tested a pipeline based on read correction with DADA2 allowing analysing metabarcoding data from prokaryotic (16S) and eukaryotic (18S, COI) life compartments. We implemented the option to cluster amplicon sequence variants (ASVs) into operational taxonomic units (OTUs) with swarm, a network-based clustering algorithm, and the option to curate ASVs/OTUs using LULU. Finally, taxonomic assignment was implemented via the Ribosomal Database Project Bayesian classifier (RDP) and BLAST. We validated this pipeline with ribosomal and mitochondrial markers using metazoan mock communities and 42 deep-sea sediment samples. The results show that ASVs and OTUs describe different levels of biotic diversity, the choice of which depends on the research questions. They underline the advantages and complementarity of clustering and LULU-curation for producing metazoan biodiversity inventories at a level approaching the one obtained using morphological criteria. While clustering removes intraspecific variation, LULU effectively removes spurious clusters, originating from errors or intragenomic variability. Swarm clustering affected alpha and beta diversity differently depending on genetic marker. Specifically, d-values > 1 appeared to be less appropriate with 18S for metazoans. Similarly, increasing LULU's minimum ratio level proved essential to avoid losing species in sample-poor data sets. Comparing BLAST and RDP underlined that accurate assignments of deep-sea species can be obtained with RDP, but highlighted the need for a concerted effort to build comprehensive, ecosystem-specific databases.},
}
@article {pmid33834455,
year = {2021},
author = {Wang, C and Chen, C and Wang, X and Zhao, X and Zhao, G and Liu, L and Kong, X},
title = {[Non-invasive prenatal detection of ocutaneous albinism type I based on cfDNA barcode-enabled single-molecule test].},
journal = {Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics},
volume = {38},
number = {4},
pages = {317-320},
doi = {10.3760/cma.j.cn511374-20200214-00077},
pmid = {33834455},
issn = {1003-9406},
mesh = {*Albinism ; *Albinism, Oculocutaneous/genetics ; Amniocentesis ; *Cell-Free Nucleic Acids ; Female ; Humans ; Pregnancy ; Prenatal Diagnosis ; },
abstract = {OBJECTIVE: To assess the value of non-invasive prenatal testing based on cfDNA barcode-enabled single-molecule test (cfBEST) for the prenatal diagnosis of oculocutaneous albinism type I in a family.<br><br>METHODS: Prenatal genetic diagnosis was carried out by using the cfBEST-based method as well as invasive prenatal diagnosis through amniocentesis. The outcome of the pregnancy was followed up.<br><br>RESULTS: Non-invasive prenatal testing based on cfBEST showed a fetal DNA concentration of 6.6%, with the proportion of c.929_930insC (p.Arg311Lysfs*7) and c.1037-7T>A mutations being 45.7% and 0%, respectively. The posterior frequency of the negative results was 1, suggesting that the fetus carried neither of the two mutations. The result was consistent with that of invasive prenatal diagnosis, and the follow-up found that the fetus was normal.<br><br>CONCLUSION: Non-invasive prenatal testing based on cfBEST can be used to detect maternal and fetal genotypes in maternal cell-free DNA, which is clinically feasible.},
}
@article {pmid33831346,
year = {2021},
author = {Snyman, J and Snyman, LP and Labuschagne, K and Venter, GJ and Venter, M},
title = {The utilisation of CytB and COI barcodes for the identification of bloodmeals and Culicoides species (Diptera: Ceratopogonidae) reveals a variety of novel wildlife hosts in South Africa.},
journal = {Acta tropica},
volume = {219},
number = {},
pages = {105913},
doi = {10.1016/j.actatropica.2021.105913},
pmid = {33831346},
issn = {1873-6254},
mesh = {Animals ; Arboviruses/physiology ; Blood/*parasitology ; Ceratopogonidae/*classification/genetics ; Cytochromes b/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Female ; Host Specificity ; Humans ; Insect Vectors/genetics ; South Africa ; },
abstract = {Biting midges in the genus Culicoides (Diptera; Ceratopogonidae) are vectors of pathogens that can cause diseases of major economic importance in humans and animals. Identifying host ranges of these biting midges might aid in understanding the complex epidemiology of such diseases, often involving reservoir hosts and multiple species. In this study, we aim to identify bloodmeal origin from engorged female Culicoides biting midges. All bloodfed females were opportunistically collected as part of an ongoing surveillance programme using Onderstepoort light traps in two provinces in South Africa. DNA of individuals was extracted and subjected to PCR targeting the cytochrome B (CytB) gene region of mammals and avians as well as cytochrome oxidase I (COI) for species identification. In total, 21 new reference barcodes were generated for C. bedfordi, C imicola, C. leucosticus, C. magnus, and C. pycnostictus. Seventy-four blood meals were identified, originating from 12 mammal and three avian species. COI sequence data performed well for species delimitation and 54 Culicoides specimens were identified with C. imicola the predominant species identified (41.8%). Generally, Culicoides species feed on a variety of hosts and host availability might be an important factor when selecting a host. Culicoides species thus appear to be opportunistic feeders rather than specialists. This implicates Culicoides as transfer vectors and demonstrates possible transmission routes of arboviruses and other pathogens from wildlife onwards to domestic animals and humans.},
}
@article {pmid33830624,
year = {2021},
author = {Gumińska, N and Łukomska-Kowalczyk, M and Chaber, K and Zakryś, B and Milanowski, R},
title = {Evaluation of V2 18S rDNA barcode marker and assessment of sample collection and DNA extraction methods for metabarcoding of autotrophic euglenids.},
journal = {Environmental microbiology},
volume = {23},
number = {6},
pages = {2992-3008},
pmid = {33830624},
issn = {1462-2920},
mesh = {DNA Barcoding, Taxonomic ; DNA Primers ; DNA, Ribosomal/genetics ; *Euglenida/genetics ; Reproducibility of Results ; },
abstract = {Even though the interest in metabarcoding in environmental studies is growing, euglenids are still underrepresented in both sea and freshwater bodies researches. The reason for this situation could be the unsuitability of universal eukaryotic DNA barcodes and primers as well as the lack of a verified protocol, suitable to assess euglenid diversity. In this study, using specific primers for the V2 hypervariable region of 18S rDNA for metabarcoding resulted in obtaining a high fraction (85%) of euglenid reads and species-level identification of almost 90% of them. Fifty species were detected by the metabarcoding method, including almost all species observed using a light microscope. We investigated three biomass harvesting methods (filtering, centrifugation and scraping the side of a collection vessel) and determined that centrifugation and filtration outperformed scrapes, but the choice between them is not crucial for the reliability of the analysis. In addition, eight DNA extraction methods were evaluated. We compared five commercially available DNA isolation kits, two CTAB-based protocols and a chelating resin. For this purpose, the efficiency of extraction, quality of obtained DNA, preparation time and generated costs were taken into consideration. After examination of the aforementioned criteria, we chose the GeneMATRIX Soil DNA Purification Kit as the most suitable for DNA isolation.},
}
@article {pmid33830383,
year = {2021},
author = {Lin, X and Dong, J and Yang, Q and Zhou, W and Wang, Y and Zhang, Y and Ahmad, M and Sun, Y and Wang, Y and Ling, J},
title = {Identification of three seagrass species in coral reef ecosystem by using multiple genes of DNA barcoding.},
journal = {Ecotoxicology (London, England)},
volume = {30},
number = {5},
pages = {919-928},
doi = {10.1007/s10646-021-02397-3},
pmid = {33830383},
issn = {1573-3017},
support = {XDA13020300//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 41676107, 41676163, 41276114//National Natural Science Foundation of China/ ; },
mesh = {*Coral Reefs ; DNA ; DNA Barcoding, Taxonomic ; Ecosystem ; Humans ; *Hydrocharitaceae ; },
abstract = {Seagrasses constitute a significant part of coral reef ecosystems, representing high primary productivity and one of the most important coastal habitats in marine ecosystems. Though seagrasses possess irreplaceable ecological services to the marine environment, taxonomical ambiguity still exists due to similar morphological characters and phenotypic plasticity. As an emerging technology, DNA barcoding can effectively identify cryptic species using a short orthologous DNA region. In this study, we collected samples from five different locations (Daya Bay, Xincun Bay, Sanya Bay, Xisha Islands, and Nansha Islands), and three seagrass species Cymodocea rotundata, Thalassia hemprichii and Halophila ovalis was evaluated. Moreover, ITS, matK and rbcL genes were used as DNA barcodes. The results indicated that single ITS and concatenated ITS/matK/rbcL both conducted better species resolution than single matK and rbcL. Nevertheless, single ITS was more convenient. Furthermore, in all the four topology trees, three species resolved as 3 clusters as well H. ovalis and T. hemprichii grouped as sister clade. In the meantime, differentiation lay in intra-species based on the result of single ITS and three-locus analysis. Within H. ovalis and T. hemprichii separately, individuals from Xisha Islands first group together, then grouped with individuals from Nansha Islands and/or Xincun Bay and/or Sanya Bay and/or Daya Bay, which indicated that geographical distribution influenced population evolution. However, intra-species differentiation did not emerge in the tree of matK or rbcL.},
}
@article {pmid33829188,
year = {2020},
author = {Le, TML and Nguyen, HT and Nguyen, TD and Trinh, QP},
title = {First report of Paratylenchus lepidus Raski, 1975 associated with green tea (Camellia sinensis (L.) Kuntze) in Vietnam.},
journal = {Journal of nematology},
volume = {52},
number = {},
pages = {},
pmid = {33829188},
issn = {0022-300X},
abstract = {The pin nematodes, Paratylenchus spp., are relatively small nematodes that can feed on a wide range of host plants. The morphological identification of this nematode is greatly hampered by their small size and variable characters. This study provides the first report of Paratylenchus lepidus from Vietnam with a combination of morphological and molecular characterizations. The 28S rDNA phylogenetic tree of the genus and the first COI mtDNA barcode of this species are also provided.},
}
@article {pmid33827654,
year = {2021},
author = {García-Castro, H and Kenny, NJ and Iglesias, M and Álvarez-Campos, P and Mason, V and Elek, A and Schönauer, A and Sleight, VA and Neiro, J and Aboobaker, A and Permanyer, J and Irimia, M and Sebé-Pedrós, A and Solana, J},
title = {ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics.},
journal = {Genome biology},
volume = {22},
number = {1},
pages = {89},
pmid = {33827654},
issn = {1474-760X},
support = {BB/M011224/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/M000133/1/MRC_/Medical Research Council/United Kingdom ; MR/T028165/1/MRC_/Medical Research Council/United Kingdom ; MR/S007849/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; Cryopreservation ; Gene Expression Profiling/*methods/standards ; High-Throughput Nucleotide Sequencing ; Planarians/cytology/genetics ; Sequence Analysis, RNA ; Single-Cell Analysis/*methods/standards ; *Transcriptome ; Workflow ; },
abstract = {Single-cell sequencing technologies are revolutionizing biology, but they are limited by the need to dissociate live samples. Here, we present ACME (ACetic-MEthanol), a dissociation approach for single-cell transcriptomics that simultaneously fixes cells. ACME-dissociated cells have high RNA integrity, can be cryopreserved multiple times, and are sortable and permeable. As a proof of principle, we provide single-cell transcriptomic data of different species, using both droplet-based and combinatorial barcoding single-cell methods. ACME uses affordable reagents, can be done in most laboratories and even in the field, and thus will accelerate our knowledge of cell types across the tree of life.},
}
@article {pmid33826801,
year = {2021},
author = {Liu, L and Chen, R and Fugina, CJ and Siegel, B and Jackson, D},
title = {High-Throughput and Low-Cost Genotyping Method for Plant Genome Editing.},
journal = {Current protocols},
volume = {1},
number = {4},
pages = {e100},
doi = {10.1002/cpz1.100},
pmid = {33826801},
issn = {2691-1299},
support = {IOS-1546837//National Science Foundation/ ; },
mesh = {*Gene Editing ; Genome, Plant/genetics ; Genotype ; Genotyping Techniques ; Humans ; *Plant Breeding ; },
abstract = {Genome editing technologies have revolutionized genetic studies in the life sciences community in recent years. The application of these technologies allows researchers to conveniently generate mutations in almost any gene of interest. This is very useful for species such as maize that have complex genomes and lack comprehensive mutant collections. With the improvement of genome editing tools and transformation methods, these technologies are also widely used to assist breeding research and implementation in maize. However, the detection and genotyping of genomic edits rely on low-throughput, high-cost methods, such as traditional agarose gel electrophoresis and Sanger sequencing. This article describes a method to barcode the target regions of genomic edits from many individuals by low-cost polymerase chain reaction (PCR) amplification. It also employs next-generation sequencing (NGS) to genotype the genome-edited plants at high throughput and low cost. This protocol can be used for initial screening of genomic edits as well as derived population genotyping on a small or large scale, at high efficiency and low cost. © 2021 Wiley Periodicals LLC. Basic Protocol 1: A fast genomic DNA preparation method from genome edited plants Basic Protocol 2: Barcoding the amplicons of edited regions from each individual by two rounds of PCR Basic Protocol 3: Bioinformatics analysis.},
}
@article {pmid33826666,
year = {2021},
author = {Martín, MP and Daniëls, PP and Erickson, D and Spouge, JL},
title = {Correction: Figures of merit and statistics for detecting faulty species identification with DNA barcodes: A case study in Ramaria and related fungal genera.},
journal = {PloS one},
volume = {16},
number = {4},
pages = {e0250030},
pmid = {33826666},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0237507.].},
}
@article {pmid33826013,
year = {2021},
author = {Paiva, DNA and Perdiz, RO and Almeida, TE},
title = {Using near-infrared spectroscopy to discriminate closely related species: a case study of neotropical ferns.},
journal = {Journal of plant research},
volume = {134},
number = {3},
pages = {509-520},
pmid = {33826013},
issn = {1618-0860},
support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
mesh = {Discriminant Analysis ; *Ferns ; Least-Squares Analysis ; Spectroscopy, Fourier Transform Infrared ; *Spectroscopy, Near-Infrared ; },
abstract = {Identifying plant species requires considerable knowledge and can be difficult without complete specimens. Fourier-transform near-infrared spectroscopy (FT-NIR) is an effective technique for discriminating plant species, especially angiosperms. However, its efficacy has never been tested on ferns. Here we tested the accuracy of FT-NIR at discriminating species of the genus Microgramma. We obtained 16 spectral readings per individual from the adaxial and abaxial surfaces of 100 specimens belonging to 13 species. The analyses included all 1557 spectral variables. We tested different datasets (adaxial + abaxial, adaxial, and abaxial) to compare the correct identification of species through the construction of discriminant models (Linear discriminant analysis and partial least squares discriminant analysis) and cross-validation techniques (leave-one-out, K-fold). All analyses recovered an overall high percentage (> 90%) of correct predictions of specimen identifications for all datasets, regardless of the model or cross-validation used. On average, there was > 95% accuracy when using partial least squares discriminant analysis and both cross-validations. Our results show the high predictive power of FT-NIR at correctly discriminating fern species when using leaves of dried herbarium specimens. The technique is sensitive enough to reflect species delimitation problems and possible hybridization, and it has the potential of helping better delimit and identify fern species.},
}
@article {pmid33822094,
year = {2021},
author = {Avanesyan, A and Sutton, H and Lamp, WO},
title = {Choosing an Effective PCR-Based Approach for Diet Analysis of Insect Herbivores: A Systematic Review.},
journal = {Journal of economic entomology},
volume = {114},
number = {3},
pages = {1035-1046},
doi = {10.1093/jee/toab057},
pmid = {33822094},
issn = {1938-291X},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Diet ; *Herbivory ; Insecta ; Polymerase Chain Reaction ; },
abstract = {Identification of ingested plant species using polymerase chain reaction (PCR)-based methods is an increasingly useful yet challenging approach to accurately determine the diet composition of insect herbivores and thus their trophic interactions. A typical process of detection of DNA of ingested plants involves the choice of a DNA extraction method, a genomic target region, and/or the best approach for an accurate plant species identification. The wide range of available techniques makes the choice of the most appropriate method for an accurately and timely identification of ingested plants from insect guts difficult. In our study, we reviewed the commonly used PCR-based approaches in studies published from 1977 to 2019, to provide researchers with the information on the tools which have been shown to be effective for obtaining and identifying ingested plants. Our results showed that among five insect orders used in the retrieved studies Coleoptera and Hemiptera were prevalent (33 and 28% of all the records, respectively). In 79% of the studies a DNA barcoding approach was employed. In a substantial number of studies Qiagen DNA extraction kits and CTAB protocol were used (43 and 23%, respectively). Of all records, 65% used a single locus as a targeted plant DNA fragment; trnL, rbcL, and ITS regions were the most frequently used loci. Sequencing was the dominant type of among DNA verification approaches (70% of all records). This review provides important information on the availability of successfully used PCR-based approaches to identify ingested plant DNA in insect guts, and suggests potential directions for future studies on plant-insect trophic interactions.},
}
@article {pmid33821571,
year = {2021},
author = {Fang, L and Li, G and Sun, Z and Zhu, Q and Cui, H and Li, Y and Zhang, J and Liang, W and Wei, W and Hu, Y and Chen, W},
title = {CASB: a concanavalin A-based sample barcoding strategy for single-cell sequencing.},
journal = {Molecular systems biology},
volume = {17},
number = {4},
pages = {e10060},
pmid = {33821571},
issn = {1744-4292},
mesh = {Animals ; Cell Line, Tumor ; Cell Nucleus/metabolism ; Concanavalin A/*chemistry ; DNA/metabolism ; *DNA Barcoding, Taxonomic ; Gene Expression Regulation, Neoplastic ; Humans ; Mice ; *RNA-Seq ; *Single-Cell Analysis ; Transcriptome/genetics ; },
abstract = {Sample multiplexing facilitates single-cell sequencing by reducing costs, revealing subtle difference between similar samples, and identifying artifacts such as cell doublets. However, universal and cost-effective strategies are rather limited. Here, we reported a concanavalin A-based sample barcoding strategy (CASB), which could be followed by both single-cell mRNA and ATAC (assay for transposase-accessible chromatin) sequencing techniques. The method involves minimal sample processing, thereby preserving intact transcriptomic or epigenomic patterns. We demonstrated its high labeling efficiency, high accuracy in assigning cells/nuclei to samples regardless of cell type and genetic background, and high sensitivity in detecting doublets by three applications: 1) CASB followed by scRNA-seq to track the transcriptomic dynamics of a cancer cell line perturbed by multiple drugs, which revealed compound-specific heterogeneous response; 2) CASB together with both snATAC-seq and scRNA-seq to illustrate the IFN-γ-mediated dynamic changes on epigenome and transcriptome profile, which identified the transcription factor underlying heterogeneous IFN-γ response; and 3) combinatorial indexing by CASB, which demonstrated its high scalability.},
}
@article {pmid33819114,
year = {2021},
author = {Braga, GSF and Ferreira, DC and Marques, DKS and Centofante, L and Carvalho, FR and Venere, PC},
title = {Gymnotus paraguensis, a Good Example of Phenotypic Plasticity in the Pantanal Biome, Brazil.},
journal = {Zebrafish},
volume = {18},
number = {2},
pages = {162-173},
doi = {10.1089/zeb.2020.1908},
pmid = {33819114},
issn = {1557-8542},
mesh = {Adaptation, Physiological ; Animals ; Brazil ; Ecosystem ; *Gymnotiformes/genetics ; },
abstract = {Gymnotus is the most studied genus of the order Gymnotiformes, but the morphological similarities of the different species make it difficult to identify taxa reliably. The present study is a continuation of the ongoing research into the taxonomic diversity of the stocks of Gymnotus sold as live bait in the Pantanal, Brazil. These studies have been based on cytogenetic analyses, DNA barcoding, and the analysis of coloration patterns. The results of the cytogenetic analysis confirmed the presence of three distinct strains, recognized as Gymnotus paraguensis, G. sylvius, and G. pantanal. However, the results revealed that the molecular operational taxonomic units identified as G. paraguensis actually include a relatively diverse set of fish, separated by considerable genetic distances. As the G. paraguensis specimens also presented considerable variation in coloration patterns, further genetic diversity analyses were conducted on these individuals, to test the hypothesis that more than one species is present in this cytotaxonomic unit. The haplotype network revealed a regional pattern in the distribution of this species. The results indicate that the observed variation in coloration patterns is associated with a high degree of phenotypic plasticity in G. paraguensis. These findings emphasize the importance of using an integrative approach for a more accurate diagnosis of Gymnotus, in particular, the species marketed as live bait for the fisheries of the upper Paraguay River basin in the Brazilian Pantanal.},
}
@article {pmid33818911,
year = {2021},
author = {Gajera, CR and Fernandez, R and Montine, KS and Fox, EJ and Mrdjen, D and Postupna, NO and Keene, CD and Bendall, SC and Montine, TJ},
title = {Mass-tag barcoding for multiplexed analysis of human synaptosomes and other anuclear events.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {99},
number = {9},
pages = {939-945},
pmid = {33818911},
issn = {1552-4930},
support = {RF1 AG053959/AG/NIA NIH HHS/United States ; P30 AG066515/AG/NIA NIH HHS/United States ; U01 AG006781/AG/NIA NIH HHS/United States ; P50 AG047366/AG/NIA NIH HHS/United States ; R01 AG056287/AG/NIA NIH HHS/United States ; R01 AG057915/AG/NIA NIH HHS/United States ; U19 AG065156/AG/NIA NIH HHS/United States ; P50 NS062684/NS/NINDS NIH HHS/United States ; P30 AG066509/AG/NIA NIH HHS/United States ; DP2 EB024246/EB/NIBIB NIH HHS/United States ; U19 AG066567/AG/NIA NIH HHS/United States ; },
mesh = {*Antibodies ; Flow Cytometry ; Humans ; *Synaptosomes ; },
abstract = {Mass-tag cell barcoding has increased the throughput, multiplexing, and robustness of multiple cytometry approaches. Previously, we adapted mass cytometry for cells to analyze synaptosome preparations (mass synaptometry or SynTOF), extending mass cytometry to these smaller, anuclear particles. To improve throughput and individual event resolution, we report here the application of palladium-based barcoding in human synaptosomes. Up to 20 individual samples, each with a unique combinatorial barcode, were pooled for labeling with an antibody cocktail. Our synaptosome protocol used six palladium-based barcoding reagents, and in combination with sequential gating increased the identification of presynaptic events approximately fourfold. These same parameters also efficiently resolved two other anuclear particles: human red blood cells and platelets. The addition of palladium-based mass-tag barcoding to our approach improves mass cytometry of synaptic particles.},
}
@article {pmid33818189,
year = {2021},
author = {Fujioka, H and Abe, MS and Okada, Y},
title = {Individual Ants Do Not Show Activity-Rest Rhythms in Nest Conditions.},
journal = {Journal of biological rhythms},
volume = {36},
number = {3},
pages = {297-310},
doi = {10.1177/07487304211002934},
pmid = {33818189},
issn = {1552-4531},
mesh = {Animals ; *Ants ; Circadian Rhythm ; Locomotion ; Motor Activity ; Rest ; },
abstract = {Circadian rhythms, which respond to the day-night cycle on the earth, arise from the endogenous timekeeping system within organisms, called the "biological clock." For accurate circadian rhythms, daily fluctuations in light and temperature are considered one of the important time cues. In social insects, both abiotic and biotic factors (i.e., social interactions) play a significant role in activity-rest rhythm regulation. However, it is challenging to monitor individual activity-rest rhythms in a colony because of the large group size and small body size. Therefore, it is unclear whether individuals in a colony exhibit activity-rest rhythms and how social interactions regulate their activity-rest rhythms in the colony. This study developed an image-based tracking system using 2D barcodes for Diacamma cf. indicum from Japan (a monomorphic ant) and measured the locomotor activities of all colony members under laboratory colony conditions. We also investigated the effect of broods on activity-rest rhythms by removing all broods under colony conditions. Activity-rest rhythms appeared only in isolated ants, not under colony conditions. In addition, workers showed arrhythmic activities after brood removal. These results suggested that a mixture of social interactions, and not light and temperature, induces the loss of activity-rest rhythms. These results contribute to the knowledge of a diverse pattern of circadian activity rhythms in social insects.},
}
@article {pmid33817970,
year = {2021},
author = {Wang, Y and Chen, C and He, J and Cao, Y and Fang, X and Chi, X and Yi, J and Wu, J and Guo, Q and Masoomi, H and Wu, C and Ye, J and Gu, H and Xu, H},
title = {Precisely Encoded Barcodes through the Structure-Fluorescence Combinational Strategy: A Flexible, Robust, and Versatile Multiplexed Biodetection Platform with Ultrahigh Encoding Capacities.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {17},
number = {19},
pages = {e2100315},
doi = {10.1002/smll.202100315},
pmid = {33817970},
issn = {1613-6829},
mesh = {Electronic Data Processing ; Flow Cytometry ; Microspheres ; *Nanoparticles ; *Quantum Dots ; },
abstract = {With the rapid development of suspension array technology, microbeads-based barcodes as the core element with sufficient encoding capacity are urgently required for high-throughput multiplexed detection. Here, a novel structure-fluorescence combinational encoding strategy is proposed for the first time to establish a barcode library with ultrahigh encoding capacities. Based on the never revealed transformability of the structural parameters (e.g., porosity and matrix component) of mesoporous microbeads into scattering signals in flow cytometry, the enlargement of codes number has been successfully realized in combination with two other fluorescent elements of fluorescein isothiocyanate isomer I (FITC) and quantum dots (QDs). The barcodes are constructed with precise architectures including FITC encapsulated within mesopores and magnetic nanoparticles as well as QDs immobilized on the outer surface to achieve the ultrahigh encoding level of 300 accompanied with superparamagnetism. To the best of knowledge, it is the highest record of single excitation laser-based encoding capacity up to now. Moreover, a ten-plexed tumor markers bioassay based on the tailored-designed barcodes has been evaluated to confirm their feasibility and effectiveness, and the results indicate that the barcodes platform is a promising and robust tool for practical multiplexed biodetection.},
}
@article {pmid33817583,
year = {2021},
author = {Giraldo-Perez, P and Raw, V and Greven, M and Goddard, MR},
title = {A small effect of conservation agriculture on soil biodiversity that differs between biological kingdoms and geographic locations.},
journal = {iScience},
volume = {24},
number = {4},
pages = {102280},
pmid = {33817583},
issn = {2589-0042},
abstract = {Larger easily visible animals and plants are negatively affected by agrochemicals used for intensive food production, but we do not understand the general spatial and temporal effects of agrochemicals on the multitudes of bacteria, fungi, and small invertebrate animals that underpin ecosystem productivity. We sequenced the 16S, ITS2, and COI DNA barcode regions from 648 New Zealand vineyard soil samples managed under either conventional or low-agrochemical-input conservation approaches across two regions and three seasons in 1 year and discovered at least 170,000 phylotypes (taxa) with >97% genetic identity. Management approach correlated with a significant 2%-10% difference in the abundances of phylotypes that differed over regions and seasons. Although the data show that agrochemicals do not have a large effect on soil biodiversity on average, the important finding is that the magnitude of impact differs between taxa types and locations, and some taxa most affected also influence the quality of agricultural produce.},
}
@article {pmid33815469,
year = {2021},
author = {Guo, J and Shi, C and Chen, X and Wang, O and Liu, P and Yang, H and Xu, X and Zhang, W and Zhu, H},
title = {stLFRsv: A Germline Structural Variant Analysis Pipeline Using Co-barcoded Reads.},
journal = {Frontiers in genetics},
volume = {12},
number = {},
pages = {636239},
pmid = {33815469},
issn = {1664-8021},
abstract = {Co-barcoded reads originating from long DNA fragments (mean length >30 kbp) maintain both single base level accuracy and long-range genomic information. We propose a pipeline, stLFRsv, to detect structural variation using co-barcoded reads. stLFRsv identifies abnormal large gaps between co-barcoded reads to detect potential breakpoints and reconstruct complex structural variants (SVs). Haplotype phasing by co-barcoded reads increases the signal to noise ratio, and barcode sharing profiles are used to filter out false positives. We integrate the short read SV caller smoove for smaller variants with stLFRsv. The integrated pipeline was evaluated on the well-characterized genome HG002/NA24385, and 74.5% precision and a 22.4% recall rate were obtained for deletions. stLFRsv revealed some large variants not included in the benchmark set that were verified by long reads or assembly. For the HG001/NA12878 genome, stLFRsv also achieved the best performance for both resource usage and the detection of large variants. Our work indicates that co-barcoded read technology has the potential to improve genome completeness.},
}
@article {pmid33811913,
year = {2021},
author = {Piot, N and Eeraerts, M and Pisman, M and Claus, G and Meeus, I and Smagghe, G},
title = {More is less: mass-flowering fruit tree crops dilute parasite transmission between bees.},
journal = {International journal for parasitology},
volume = {51},
number = {9},
pages = {777-785},
doi = {10.1016/j.ijpara.2021.02.002},
pmid = {33811913},
issn = {1879-0135},
mesh = {Animals ; Bees ; Crops, Agricultural ; Fruit ; *Parasites ; Pollen ; Trees ; },
abstract = {Parasites influence wild bee population dynamics and are regarded as one of the main drivers of wild bee decline. Most of these parasites are mainly transmitted between bee species via the use of shared floral resources. Disturbance of the plant-pollinator network at a location can hence disturb the transmission of these parasites. Expansion and intensification of agriculture, another major driver of wild bee decline, often disturbs local plant-pollinator networks by altering the availability and diversity of floral resources. Mass-flowering crops are an extreme example as they provide an abundance of floral resources for a short period of time, substantially altering the present plant-pollinator network. This likely has repercussions on parasite transmission in the pollinator community. Using the bloom of mass-flowering crops we tested the hypothesis that an increase in floral resources can dilute parasite transmission in the pollinator community. To test this, we analysed the presence of parasites in the pollen of the brood cell provisions of Osmia spp., collected from trap nests placed in apple and sweet cherry orchards. We collected pollen at several time intervals during and after mass bloom, and found that pollen collected during mass bloom had significantly lower parasite prevalence compared with pollen collected after mass bloom. Furthermore, using pollen barcoding data we found that the presence of MFCs in pollen was a good predictor for lower parasite prevalence. Taken together, our results indicate that an increase in flower availability can reduce parasite transmission between bees.},
}
@article {pmid33810458,
year = {2021},
author = {Chen, HY and Li, HL and Pang, H and Zhu, CD and Zhang, YZ},
title = {Investigating the Parasitoid Community Associated with the Invasive Mealybug Phenacoccus solenopsis in Southern China.},
journal = {Insects},
volume = {12},
number = {4},
pages = {},
pmid = {33810458},
issn = {2075-4450},
support = {31872296, 31572296//National Natural Science Foundation of China/ ; },
abstract = {The cotton mealybug Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae), is an emerging invasive insect pest in China. Hymenopteran parasitoids are the key organisms for suppressing populations of P. solenopsis in the field, and therefore could be used as biological agents. Accurate identification of the associated parasitoids is the critical step to assess their potential role in biological control. In this study, we facilitated the identification of the parasitoid composition of P. solenopsis using an integrated approach of species delimitation, combining morphology with molecular data. Eighteen Hymenoptera parasitoid species belonging to 11 genera of four families are recognized based on morphological examination and molecular species delimitation of the mitochondrial cytochrome c oxidase 1 (COI) gene and the 28S rDNA using the automatic barcode gap discovery (ABGD) and the Bayesian Poisson tree processes model (bPTP). Among these species, eight species are primary parasitoids with Aenasius arizonensis (Girault) (Hymenoptera: Encyrtidae) being the dominant taxon, while the other 10 species are probably hyperparasitoids, with a prevalence of Cheiloneurus nankingensis Li &amp; Xu (Hymenoptera: Encyrtidae). These results indicate that parasitoid wasps associated with P. solenopsis from China are diverse and the integrated taxonomic approach applied in this study could enhance the accurate identification of these parasitoids that should be assessed in future biological control programs.},
}
@article {pmid33809525,
year = {2021},
author = {Zhao, P and Du, Z and Zhao, Q and Li, D and Shao, X and Li, H and Cai, W},
title = {Integrative Taxonomy of the Spinous Assassin Bug Genus Sclomina (Heteroptera: Reduviidae: Harpactorinae) Reveals Three Cryptic Species Based on DNA Barcoding and Morphological Evidence.},
journal = {Insects},
volume = {12},
number = {3},
pages = {},
pmid = {33809525},
issn = {2075-4450},
support = {No. 31760634//National Natural Science Foundation of China/ ; },
abstract = {Sclomina Stål, 1861 (Heteroptera: Reduviidae: Harpactorinae) is endemic to China and Vietnam, with only two species, Sclomina erinacea Stål, 1861 and Sclomina guangxiensis Ren, 2001, characterized by spinous body and dentate abdominal connexivum. However, due to variable morphological characteristics, Sclomina erinacea, which is widely distributed in South China, is possibly a complex of cryptic species, and Sclomina guangxiensis was suspected to be an extreme group of the S. erinacea cline. In the present study, we conducted species delimitation and phylogenetic analyses based on the mitochondrial cytochrome c oxidase subunit I (COI) gene sequences of 307 Sclomina specimens collected from 30 sampling localities combined with morphological evidence. The result showed that all samples used in this study were identified as five species: Sclomina guangxiensis is a valid species, and Sclomina erinacea actually includes three cryptic species: Sclomina xingrensis P. Zhao and Cai sp. nov., Sclomina pallens P. Zhao and Cai sp. nov., and Sclomina parva P. Zhao and Cai sp. nov. In this paper, the genus Sclomina is systematically revised, and the morphological characteristics of the five species are compared, described, and photographed in detail. We elucidate the evolutionary history of Sclomina based on results of estimated divergence time. The body shape and coloration (green in nymph and brown in adult) of Sclomina match their environment and mimic the Rubus plants on which they live. The symbiotic relationship between Sclomina and spinous Rubus plants is presented and discussed.},
}
@article {pmid33808078,
year = {2021},
author = {Michalski, M and Gadawski, P and Klemm, J and Szpila, K},
title = {New Species of Soldier Fly-Sargus bipunctatus (Scopoli, 1763) (Diptera: Stratiomyidae), Recorded from a Human Corpse in Europe-A Case Report.},
journal = {Insects},
volume = {12},
number = {4},
pages = {},
pmid = {33808078},
issn = {2075-4450},
support = {2016/23/NZ8/02123, 2018/31/B/NZ8/02113//National Science Center of Poland/ ; },
abstract = {The only European Stratiomyidae species known for feeding on human corpses was the black soldier fly Hermetia illucens (Linnaeus, 1758). Analysis of fauna found on a human corpse, discovered in central Poland, revealed the presence of feeding larvae of another species from this family: the twin-spot centurion fly Sargus bipunctatus (Scopoli, 1763). The investigated corpse was in a stage of advanced decomposition. The larvae were mainly observed in the adipocere formed on the back and lower limbs of the corpse, and in the mixture of litter and lumps of adipocere located under the corpse. Adult specimens and larvae were identified based on morphological characters, and final identification was confirmed using DNA barcoding. Implementing a combination of morphological and molecular methods provided a reliable way for distinguishing the larvae of S. bipunctatus and H. illucens. The potential of S. bipunctatus for practical applications in forensic entomology is currently difficult to assess. Wide and reliable use of S. bipunctatus in the practice of forensic entomology requires further studies of the bionomy of this fly.},
}
@article {pmid33805452,
year = {2021},
author = {Xavier, JKAM and Maia, L and Figueiredo, PLB and Folador, A and Ramos, AR and Andrade, EH and Maia, JGS and Setzer, WN and da Silva, JKR},
title = {Essential Oil Composition and DNA Barcode and Identification of Aniba species (Lauraceae) Growing in the Amazon Region.},
journal = {Molecules (Basel, Switzerland)},
volume = {26},
number = {7},
pages = {},
pmid = {33805452},
issn = {1420-3049},
mesh = {Brazil ; DNA Barcoding, Taxonomic/*methods ; *DNA, Plant ; *Lauraceae/chemistry/classification ; Oils, Volatile/*analysis ; Phylogeny ; Species Specificity ; },
abstract = {Lauraceae species are widely represented in the Amazon, presenting a significant essential oil yield, large chemical variability, various biological applications, and high economic potential. Its taxonomic classification is difficult due to the accentuated morphological uniformity, even among taxa from a different genus. For this reason, the present work aimed to find chemical and molecular markers to discriminate Aniba species collected in the Pará State (Brazil). The chemical composition of the essential oils from Aniba canelilla, A. parviflora, A. rosaeodora, and A. terminalis were grouped by multivariate statistical analysis. The major compounds were rich in benzenoids and terpenoids such as 1-nitro-2-phenylethane (88.34-70.85%), linalool (15.2-75.3%), α-phellandrene (36.0-51.8%), and β-phellandrene (11.6-25.6%). DNA barcodes were developed using the internal transcribed spacer (ITS) nuclear region, and the matK, psbA-trnH, rbcL, and ycf1 plastid regions. The markers psbA-trnH and ITS showed the best discrimination for the species, and the phylogenic analysis in the three- (rbcL + matK + trnH - psbA and rbcL + matK + ITS) and four-locus (rbcL + matK + trnH - psbA + ITS) combination formed clades with groups strongly supported by the Bayesian inference (BI) (PP:1.00) and maximum likelihood (ML) (BS ≥ 97%). Therefore, based on statistical multivariate and phylogenetic analysis, the results showed a significant correlation between volatile chemical classes and genetic characteristics of Aniba species.},
}
@article {pmid33805110,
year = {2021},
author = {Lemire, P and Temam, S and Lyon-Caen, S and Quinot, C and Sévin, E and Remacle, S and Supernant, K and Slama, R and Dumas, O and Siroux, V and Le Moual, N and Sepages Study Group, T},
title = {Comparison of a Barcode-Based Smartphone Application to a Questionnaire to Assess the Use of Cleaning Products at Home and Their Association with Asthma Symptoms.},
journal = {International journal of environmental research and public health},
volume = {18},
number = {7},
pages = {},
pmid = {33805110},
issn = {1660-4601},
support = {N 311765-E-DOHaD/ERC_/European Research Council/International ; },
mesh = {*Asthma/epidemiology ; *Disinfectants ; Female ; Humans ; Odds Ratio ; Smartphone ; Surveys and Questionnaires ; },
abstract = {Household disinfectant and cleaning products (HDCPs) assessment is challenging in epidemiological research. We hypothesized that a newly-developed smartphone application was more objective than questionnaires in assessing HDCPs. Therefore, we aimed to compare both methods, in terms of exposure assessments and respiratory health effects estimates. The women of the SEPAGES birth cohort completed repeated validated questionnaires on HDCPs and respiratory health and used an application to report HDCPs and scan products barcodes, subsequently linked with an ingredients database. Agreements between the two methods were assessed by Kappa coefficients. Logistic regression models estimated associations of HDCP with asthma symptom score. The 101 participants (18 with asthma symptom score ≥1) scanned 617 different products (580 with available ingredients list). Slight to fair agreements for sprays, bleach and scented HDCP were observed (Kappa: 0.35, 0.25, 0.11, respectively). Strength of the associations between HDCP and asthma symptom score varied between both methods but all odds ratios (OR) were greater than one. The number of scanned products used weekly was significantly associated with the asthma symptom score (adjusted-OR [CI 95%]: 1.15 [1.00-1.32]). This study shows the importance of using novel tools in epidemiological research to objectively assess HDCP and therefore reduce exposure measurement errors.},
}
@article {pmid33804838,
year = {2021},
author = {Mar Htun, Z and Laikul, A and Pathomsakulwong, W and Yurayart, C and Lohnoo, T and Yingyong, W and Kumsang, Y and Payattikul, P and Sae-Chew, P and Rujirawat, T and Jittorntam, P and Jaturapaktrarak, C and Chongtrakool, P and Krajaejun, T},
title = {Identification and Biotyping of Pythium insidiosum Isolated from Urban and Rural Areas of Thailand by Multiplex PCR, DNA Barcode, and Proteomic Analyses.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {7},
number = {4},
pages = {},
pmid = {33804838},
issn = {2309-608X},
support = {CF_61007//Mahidol University/ ; RSA6280092//Thailand Research Fund/ ; },
abstract = {Pythium insidiosum causes pythiosis, a fatal infectious disease of humans and animals worldwide. Prompt diagnosis and treatment are essential to improve the clinical outcome of pythiosis. Diagnosis of P. insidiosum relies on immunological, molecular, and proteomic assays. The main treatment of pythiosis aims to surgically remove all affected tissue to prevent recurrent infection. Due to the marked increase in case reports, pythiosis has become a public health concern. Thailand is an endemic area of human pythiosis. To obtain a complete picture of how the pathogen circulates in the environment, we surveyed the presence of P. insidiosum in urban (Bangkok) and rural areas of Thailand. We employed the hair-baiting technique to screen for P. insidiosum in 500 water samples. Twenty-seven culture-positive samples were identified as P. insidiosum by multiplex PCR, multi-DNA barcode (rDNA, cox1, cox2), and mass spectrometric analyses. These environmental strains of P. insidiosum fell into Clade-II and -III genotypes and exhibited a close phylogenetic/proteomic relationship with Thai clinical strains. Biodiversity of the environmental strains also existed in a local habitat. In conclusion, P. insidiosum is widespread in Thailand. A better understanding of the ecological niche of P. insidiosum could lead to the effective prevention and control of this pathogen.},
}
@article {pmid33804021,
year = {2021},
author = {Simoglou, KB and Avtzis, DN and Baixeras, J and Sarigkoli, I and Roditakis, E},
title = {Hylotelephium spectabile, a New Host for Carnation Tortrix Moth (Cacoecimorpha pronubana) and Molecular Characterization in Greece.},
journal = {Insects},
volume = {12},
number = {3},
pages = {},
pmid = {33804021},
issn = {2075-4450},
abstract = {Cacoecimorpha pronubana (Hübner) (Lepidoptera, Tortricidae) is a highly polyphagous pest of a wide range of crop and ornamental plants. It is of Mediterranean origin and widespread in European and Mediterranean Plant Protection Organization (EPPO) region. For the first time, infestations of Hylotelephium spectabile (Boreau) Ohba (syn.: Sedum spectabile Boreau) (Saxifragales, Crassulaceae) ornamental plants by C. pronubana larvae, in private gardens in urban area of Drama, Greece, were found. Species identification was conducted based on morphology of female genitalia. In addition, due to reports on occurrence of cryptic C. pronubana species within Europe, DNA barcoding was carried out to determine the molecular status of the pest. This communication reports a new host of C. pronubana and places the Greek pest population along with European species clade.},
}
@article {pmid33802818,
year = {2021},
author = {Katsi, P and Kosma, IS and Michailidou, S and Argiriou, A and Badeka, AV and Kontominas, MG},
title = {Characterization of Artisanal Spontaneous Sourdough Wheat Bread from Central Greece: Evaluation of Physico-Chemical, Microbiological, and Sensory Properties in Relation to Conventional Yeast Leavened Wheat Bread.},
journal = {Foods (Basel, Switzerland)},
volume = {10},
number = {3},
pages = {},
pmid = {33802818},
issn = {2304-8158},
abstract = {In the present study, both yeast leavened bread (YLB) and artisanal sourdough wheat bread (SDB) were prepared. The physico-chemical, microbiological, and sensory properties of breads were monitored as a function of storage time (T = 25 °C). As expected, the titratable acidity (TA) values of SDB were higher than those of YLB. The aroma profile of SDB was similar to that of YLB, including classes of compounds such as alcohols, aldehydes, ketones, esters, organic acids, terpenes, and sulfur compounds; however, the concentrations between the two were different. Aroma deterioration of bread during storage was partly related to the loss of several volatiles. Texture and sensory analysis showed that SDB was harder, less elastic, but richer in aroma and light sour taste than YLB. Mold growth was apparent when the population of yeasts/molds reached approximately 4 log cfu/g. This yeast/mold count was reached on days 4-5 for YLB and day 18 + for SDB. A 16S amplicon meta-barcoding analysis showed that the bacterial profile of SDB was dominated by a single genus, (Lactobacillus). Analysis of the eukaryotic load showed that at the genus level, Saccharomyces and Alternaria were the most abundant genera, independently of the gene sequenced (18S or ITS). Based primarily on mold growth and texture data, which proved to be the most sensitive quality parameters, the shelf life was ca. 4-5 days for YLB and 10 days for SDB.},
}
@article {pmid33802000,
year = {2021},
author = {Ceruso, M and Mascolo, C and De Luca, P and Venuti, I and Biffali, E and Ambrosio, RL and Smaldone, G and Sordino, P and Pepe, T},
title = {Dentex dentex Frauds: Establishment of a New DNA Barcoding Marker.},
journal = {Foods (Basel, Switzerland)},
volume = {10},
number = {3},
pages = {},
pmid = {33802000},
issn = {2304-8158},
abstract = {The common dentex (Dentex dentex (Linnaeus, 1758)) is an iconic fish in the Mediterranean diet. Due to its commercial and organoleptic importance, this sparid is highly appreciated in European markets and is often subjected to species substitution frauds. Comparative mitogenomics is a suitable approach for identifying new and effective barcode markers. This study aimed to find a molecular tag useful for unequivocally discriminating the sparid species D. dentex. The comparison of the complete mitochondrial DNA (mtDNA) sequences of 16 sparid species allowed us to highlight the potential of the NAD2 gene for direct identification purposes. Common dentex-specific primers were created and successfully evaluated by end-point and real-rime PCR (Polymerase Chain Reaction) for several fish species, achieving amplification only in the D. dentex. The method proposed in this study appears fast, simple, and inexpensive and requires affordable instrumentation. This approach provides unambiguous results for the common dentex authentication without the sequencing step. The presence/absence assay for D. dentex can be executed in a few hours of lab work. Therefore, national authorities responsible for food safety and traceability could apply and make full use of DNA-testing methods for deterring operators from false seafood declarations.},
}
@article {pmid33798862,
year = {2021},
author = {Jiang, G and Chen, P and Bao, Y and Wang, X and Yang, T and Mei, X and Banerjee, S and Wei, Z and Xu, Y and Shen, Q},
title = {Isolation of a novel psychrotrophic fungus for efficient low-temperature composting.},
journal = {Bioresource technology},
volume = {331},
number = {},
pages = {125049},
doi = {10.1016/j.biortech.2021.125049},
pmid = {33798862},
issn = {1873-2976},
mesh = {China ; *Composting ; Fungi ; *Oryza ; Penicillium ; Soil ; Temperature ; },
abstract = {This study aimed to isolate psychrotrophic cellulose-degrading fungi and to investigate their application potential for composting in cold climate regions in China. One out of five psychrotrophic cellulose-degrading fungal isolates was identified as a novel fungal species, Aureobasidium paleasum sp. nov., with a strong straw degradation potential. Enzyme activity assays and FITR spectroscopy revealed high cellulolytic activities of this psychrotrophic fungus at lower temperatures, with high thermal adaptability from 5 °C to 50 °C (optimum at 10 °C). A. paleasum efficiently decomposed rice straws and cellulose at 10 °C compared to the common cellulose-degrading fungus Penicillium oxalicum. In comparison to P. oxalicum, A. paleasum shortened the thermophilic stage, enhanced compost maturity and improved compost quality. Our work suggests that the psychrotrophic fungus A. paleasum is efficient for rice straw degradation and composting at low temperatures, highlighting its application potential for composting in colder regions.},
}
@article {pmid33796758,
year = {2021},
author = {Yang, J and Sun, Z and Wei, M and Niu, G},
title = {The complete mitochondrial genome of Allantus togatus (Panzer, 1801), in view of possible cryptic species.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {6},
number = {3},
pages = {1114-1115},
pmid = {33796758},
issn = {2380-2359},
abstract = {The complete Allantus togatus (Panzer, 1801) mitogenome was determined and analyzed. The mitogenome contains typical 37 genes with identical order to Allantoides luctifer mitogenomes. Phylogenetic analysis revealed that A. togatus clustered together with A. viennensis. The wide genetic distances found between lineages of A. togatus lead to the assumption of cryptic species. These complete mitogenomes provide valuable information at the genomic level that can be utilized to sustain bioresources to deepen the understanding of cryptic diversity within Allantinae.},
}
@article {pmid33795864,
year = {2021},
author = {Chiou, J and Zeng, C and Cheng, Z and Han, JY and Schlichting, M and Miller, M and Mendez, R and Huang, S and Wang, J and Sui, Y and Deogaygay, A and Okino, ML and Qiu, Y and Sun, Y and Kudtarkar, P and Fang, R and Preissl, S and Sander, M and Gorkin, DU and Gaulton, KJ},
title = {Single-cell chromatin accessibility identifies pancreatic islet cell type- and state-specific regulatory programs of diabetes risk.},
journal = {Nature genetics},
volume = {53},
number = {4},
pages = {455-466},
pmid = {33795864},
issn = {1546-1718},
support = {U01 DK105541/DK/NIDDK NIH HHS/United States ; R01 DK114650/DK/NIDDK NIH HHS/United States ; U01 DK120429/DK/NIDDK NIH HHS/United States ; R01 DK068471/DK/NIDDK NIH HHS/United States ; U01 DK105554/DK/NIDDK NIH HHS/United States ; },
mesh = {Blood Glucose/metabolism ; Cell Differentiation ; Chromatin/*chemistry/metabolism ; Diabetes Mellitus, Type 2/*genetics/metabolism/pathology ; Epigenomics ; Fasting ; Gene Expression Profiling ; Genome-Wide Association Study ; Glucagon-Secreting Cells/*metabolism/pathology ; High-Throughput Nucleotide Sequencing ; Human Embryonic Stem Cells/cytology ; Humans ; Insulin-Secreting Cells/*metabolism/pathology ; KCNQ1 Potassium Channel/*genetics/metabolism ; Multigene Family ; Pancreatic Polypeptide-Secreting Cells/*metabolism/pathology ; Polymorphism, Genetic ; Single-Cell Analysis ; Somatostatin-Secreting Cells/*metabolism/pathology ; Transcription Factors/classification/genetics/metabolism ; },
abstract = {Single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) creates new opportunities to dissect cell type-specific mechanisms of complex diseases. Since pancreatic islets are central to type 2 diabetes (T2D), we profiled 15,298 islet cells by using combinatorial barcoding snATAC-seq and identified 12 clusters, including multiple alpha, beta and delta cell states. We cataloged 228,873 accessible chromatin sites and identified transcription factors underlying lineage- and state-specific regulation. We observed state-specific enrichment of fasting glucose and T2D genome-wide association studies for beta cells and enrichment for other endocrine cell types. At T2D signals localized to islet-accessible chromatin, we prioritized variants with predicted regulatory function and co-accessibility with target genes. A causal T2D variant rs231361 at the KCNQ1 locus had predicted effects on a beta cell enhancer co-accessible with INS and genome editing in embryonic stem cell-derived beta cells affected INS levels. Together our findings demonstrate the power of single-cell epigenomics for interpreting complex disease genetics.},
}
@article {pmid33792830,
year = {2021},
author = {Lebedeva, D and Muñoz, G and Lumme, J},
title = {New Salinity Tolerant Species of Gyrodactylus (Platyhelminthes, Monogenea) on Intertidal and Supratidal Fish Species from the Chilean Coast.},
journal = {Acta parasitologica},
volume = {66},
number = {3},
pages = {1021-1030},
pmid = {33792830},
issn = {1896-1851},
support = {0218-2019-0075//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {Animals ; Chile ; *Fish Diseases/epidemiology ; Fishes ; Phylogeny ; Salinity ; *Trematoda ; },
abstract = {PURPOSE: The intertidal and supratidal coastal zone challenges the osmoregulatory capacity of aquatic inhabitants. Four new species of Gyrodactylus ectoparasites on two intertidal fishes from Chile are described based on molecular and morphological analyses.<br><br>METHODS: Monogeneans were found from two fish species, the clingfish Sicyases sanguineus M&#xfc;ller &amp; Troschel, 1843 and the combtooth blenny Scartichthys viridis Valenciennes, 1836. The morphology was described by drawings, and minimal measurements. The parasites were barcoded via the sequencing of the ribosomal DNA over ITS1-5.8S-ITS2.<br><br>RESULTS: The air-breathing clingfish S. sanguineus carried Gyrodactylus amphibius sp. nov., hiding in the ventral sucker formed by the modified pectoral fins of the fish. The intertidal combtooth blenny S. viridis carried three other new species: Gyrodactylus scartichthi sp. nov., Gyrodactylus viridae sp. nov., and Gyrodactylus zietarae sp. nov.<br><br>CONCLUSION: The four new species were all phylogenetically related with the previously described G. chileani Zi&#x119;tara et al. 2012 on triplefin Helcogrammoides chilensis Cancino, 1960 in the same habitat. Thus, the five Chilean Pacific Gyrodactylus species formed a statistically well-supported (100%) monophyletic clade together with three geographically distant species recorded in Europe. The Chilean Pacific parasites are not related to G. salinae and G. magadiensis, parasites described in extreme osmotic stress environments earlier.},
}
@article {pmid33792827,
year = {2021},
author = {El Khodary, YA and Ayoub, IM and El-Ahmady, SH and Ibrahim, N},
title = {Molecular and phytochemical variability among genus Albizia: a phylogenetic prospect for future breeding.},
journal = {Molecular biology reports},
volume = {48},
number = {3},
pages = {2619-2628},
pmid = {33792827},
issn = {1573-4978},
mesh = {Albizzia/*classification/*genetics ; Cluster Analysis ; Microsatellite Repeats/genetics ; Multivariate Analysis ; Phenols/analysis ; *Phylogeny ; Phytochemicals/*genetics ; *Plant Breeding ; Spectrophotometry, Ultraviolet ; },
abstract = {Fabaceae, the third-largest Angiosperm family, exhibits great morphological diversity with significantly high species diversification rate. Albizia, one of the largest genera of the legume family, possesses high ecological, economical and medicinal application prospects and displays a global distribution. The taxonomic classification among Albizia remains, however, unclear and has been subjected to changes. The resolution of phylogenetic relationships among members of genus Albizia is a priority. Nine Albizia species cultivated in Egypt; Albizia lebbeck, A. julibrissin, A. odoratissima, A. procera, A. anthelmintica, A. guachapele, A. myriophylla, A. richardiana and A. lucida were subjected to molecular classification via DNA fingerprinting techniques viz. Inter Simple Sequence Repeat (ISSR) and Start Codon Targeted polymorphism (SCoT) using ten primers, five for each technique. The total number of bands produced by ISSR and SCoT primers was 28 and 40, respectively. The percentage of polymorphism varied from 64.28% in ISSR to 67.50% in SCoT analysis. Additionally, chemotaxonomic analysis was implemented based on UV spectroscopic profiling and total phenolic content coupled to unsupervised chemometric tools; Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA). Interspecific relationships were confirmed via molecular and phytochemical analyses between A. procera and A. guachapele; A. lebbeck and A. odoratissima; and A. julibrissin and A. lucida. The study reveals that chemotaxonomic data can reflect phylogenetic relationships among examined Albizia species and provides insights to the significance of utilizing the strengths of both molecular taxonomy and chemotaxonomy to resolve phylogenetic relationship among this genus which offers baseline for breeding programs. Future strategies to enrich taxonomic classification among Albizia includes extensive morphological characterization, DNA barcoding techniques and metabolomic profiling.},
}
@article {pmid33792750,
year = {2021},
author = {González-Recio, O and Gutiérrez-Rivas, M and Peiró-Pastor, R and Aguilera-Sepúlveda, P and Cano-Gómez, C and Jiménez-Clavero, M&#xc1; and Fernández-Pinero, J},
title = {Sequencing of SARS-CoV-2 genome using different nanopore chemistries.},
journal = {Applied microbiology and biotechnology},
volume = {105},
number = {8},
pages = {3225-3234},
pmid = {33792750},
issn = {1432-0614},
mesh = {*Genome, Viral ; *Nanopores ; SARS-CoV-2/*genetics ; Sequence Analysis, RNA/*methods ; },
abstract = {Nanopore sequencing has emerged as a rapid and cost-efficient tool for diagnostic and epidemiological surveillance of SARS-CoV-2 during the COVID-19 pandemic. This study compared the results from sequencing the SARS-CoV-2 genome using R9 vs R10 flow cells and a Rapid Barcoding Kit (RBK) vs a Ligation Sequencing Kit (LSK). The R9 chemistry provided a lower error rate (3.5%) than R10 chemistry (7%). The SARS-CoV-2 genome includes few homopolymeric regions. Longest homopolymers were composed of 7 (TTTTTTT) and 6 (AAAAAA) nucleotides. The R10 chemistry resulted in a lower rate of deletions in thymine and adenine homopolymeric regions than the R9, at the expenses of a larger rate (~10%) of mismatches in these regions. The LSK had a larger yield than the RBK, and provided longer reads than the RBK. It also resulted in a larger percentage of aligned reads (99 vs 93%) and also in a complete consensus genome. The results from this study suggest that the LSK preparation library provided longer DNA fragments which contributed to a better assembly of the SARS-CoV-2, despite an impaired detection of variants in a R10 flow cell. Nanopore sequencing could be used in epidemiological surveillance of SARS-CoV-2. KEY POINTS: • Sequencing SARS-CoV-2 genome is of great importance for the pandemic surveillance. • Nanopore offers a low cost and accurate method to sequence SARS-CoV-2 genome. • Ligation sequencing is preferred rather than the rapid kit using transposases.},
}
@article {pmid33790382,
year = {2021},
author = {Garcia-Vazquez, E and Georges, O and Fernandez, S and Ardura, A},
title = {eDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {7224},
pmid = {33790382},
issn = {2045-2322},
mesh = {Animals ; *Biodiversity ; *Biomass ; *DNA Barcoding, Taxonomic ; Environmental Monitoring ; *Food Chain ; *High-Throughput Nucleotide Sequencing ; Oceans and Seas ; Zooplankton/classification/*genetics/growth &amp; development ; },
abstract = {Zooplankton community inventories are the basis of fisheries management for containing fish larvae and their preys; however, the visual identification of early-stage larvae (the "missing biomass") is difficult and laborious. Here, eDNA metabarcoding was employed to detect zooplankton species of interest for fisheries from open and coastal waters. High-Throughput sequencing (HTS) from environmental samples using small water volumes has been proposed to detect species of interest whose DNA is the most abundant. We analyzed 6-L water samples taken from subtropical and tropical waters using Cytochrome oxidase I (COI) gene as metabarcode. In the open ocean, several commercial fish larvae and invertebrate species important in fish diet were found from metabarcodes and confirmed from individual barcoding. Comparing Atlantic, Mediterranean, Red Sea, and Pacific samples we found a lower taxonomic depth of OTU assignments in samples from tropical waters than in those from temperate ones, suggesting large gaps in reference databases for those areas; thus a higher effort of zooplankton barcoding in tropical oceans is highly recommended. This and similar simplified sampling protocols could be applied in early detection of species important for fisheries.},
}
@article {pmid33790354,
year = {2021},
author = {Singh, RA and Boscaro, V and James, ER and Karnkowska, A and Kolisko, M and Gavelis, GS and Okamoto, N and Del Campo, J and Fiorito, R and Hehenberger, E and Irwin, NAT and Mathur, V and Scheffrahn, RH and Keeling, PJ},
title = {Characterization of new cristamonad species from kalotermitid termites including a novel genus, Runanympha.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {7270},
pmid = {33790354},
issn = {2045-2322},
mesh = {Animals ; *Isoptera ; *Parabasalidea/classification/physiology ; *Symbiosis ; },
abstract = {Cristamonadea is a large class of parabasalian protists that reside in the hindguts of wood-feeding insects, where they play an essential role in the digestion of lignocellulose. This group of symbionts boasts an impressive array of complex morphological characteristics, many of which have evolved multiple times independently. However, their diversity is understudied and molecular data remain scarce. Here we describe seven new species of cristamonad symbionts from Comatermes, Calcaritermes, and Rugitermes termites from Peru and Ecuador. To classify these new species, we examined cells by light and scanning electron microscopy, sequenced the symbiont small subunit ribosomal RNA (rRNA) genes, and carried out barcoding of the mitochondrial large subunit rRNA gene of the hosts to confirm host identification. Based on these data, five of the symbionts characterized here represent new species within described genera: Devescovina sapara n. sp., Devescovina aymara n. sp., Macrotrichomonas ashaninka n. sp., Macrotrichomonas secoya n. sp., and Macrotrichomonas yanesha n. sp. Additionally, two symbionts with overall morphological characteristics similar to the poorly-studied and probably polyphyletic 'joeniid' Parabasalia are classified in a new genus Runanympha n. gen.: Runanympha illapa n. sp., and Runanympha pacha n. sp.},
}
@article {pmid33789960,
year = {2021},
author = {Bogaerts, B and Delcourt, T and Soetaert, K and Boarbi, S and Ceyssens, PJ and Winand, R and Van Braekel, J and De Keersmaecker, SCJ and Roosens, NHC and Marchal, K and Mathys, V and Vanneste, K},
title = {A Bioinformatics Whole-Genome Sequencing Workflow for Clinical Mycobacterium tuberculosis Complex Isolate Analysis, Validated Using a Reference Collection Extensively Characterized with Conventional Methods and In Silico Approaches.},
journal = {Journal of clinical microbiology},
volume = {59},
number = {6},
pages = {},
pmid = {33789960},
issn = {1098-660X},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Computational Biology ; Computer Simulation ; Genome, Bacterial/genetics ; Humans ; *Mycobacterium tuberculosis/genetics ; Polymorphism, Single Nucleotide ; Whole Genome Sequencing ; Workflow ; },
abstract = {The use of whole-genome sequencing (WGS) for routine typing of bacterial isolates has increased substantially in recent years. For Mycobacterium tuberculosis (MTB), in particular, WGS has the benefit of drastically reducing the time required to generate results compared to most conventional phenotypic methods. Consequently, a multitude of solutions for analyzing WGS MTB data have been developed, but their successful integration in clinical and national reference laboratories is hindered by the requirement for their validation, for which a consensus framework is still largely absent. We developed a bioinformatics workflow for (Illumina) WGS-based routine typing of MTB complex (MTBC) member isolates allowing complete characterization, including (sub)species confirmation and identification (16S, csb/RD, hsp65), single nucleotide polymorphism (SNP)-based antimicrobial resistance (AMR) prediction, and pathogen typing (spoligotyping, SNP barcoding, and core genome multilocus sequence typing). Workflow performance was validated on a per-assay basis using a collection of 238 in-house-sequenced MTBC isolates, extensively characterized with conventional molecular biology-based approaches supplemented with public data. For SNP-based AMR prediction, results from molecular genotyping methods were supplemented with in silico modified data sets, allowing us to greatly increase the set of evaluated mutations. The workflow demonstrated very high performance with performance metrics of >99% for all assays, except for spoligotyping, where sensitivity dropped to ∼90%. The validation framework for our WGS-based bioinformatics workflow can aid in the standardization of bioinformatics tools by the MTB community and other SNP-based applications regardless of the targeted pathogen(s). The bioinformatics workflow is available for academic and nonprofit use through the Galaxy instance of our institute at https://galaxy.sciensano.be.},
}
@article {pmid33787097,
year = {2021},
author = {Li, RJ and Xin, TY and Song, LK and Yan, HX and Liao, H and Zhou, JY and Song, JY},
title = {[Research progress in original species identification in industry chain of Rhei Radix et Rhizoma].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {46},
number = {5},
pages = {1060-1066},
doi = {10.19540/j.cnki.cjcmm.20201207.601},
pmid = {33787097},
issn = {1001-5302},
mesh = {Animals ; Anthraquinones ; *Drugs, Chinese Herbal ; Plant Roots ; *Rheum ; Rhizome ; },
abstract = {Rhei Radix et Rhizoma is a kind of commonly used Chinese medicinal materials. Due to the overharvesting, the wild resource is endangering. Large market demand caused severely adulterant of commercial Rhei Radix et Rhizoma medicinal materials and decoction pieces. This manuscript reviewed the advances of the original species authentication in the industrial chain of Rhei Radix et Rhizoma during the latest decade, including characteristics and microscopic features, phytochemical analysis on anthraquinones, and molecular authentication based on DNA barcoding. Accordingly, an original species authentication route for the industrial chain of Rhei Radix et Rhizoma was summarized:(1)the identification of seeds and seedlings by DNA barcoding;(2) the selection of high variable sites based on the chloroplast genome;(3)biomonitoring of the Rhei Radix et Rhizoma medicinal materials and decoction pieces by two-dimensional DNA barcode;(4)traceability of Chinese patent medicines by third-generation sequencing. In conclusion, the combination of molecular identification and traditional identification methods provides a new idea for the identification of the original species of Rhei Radix et Rhizoma in the industrial chain and a essential guidance for the research of drug safety and efficacy of Rhei Radix et Rhizoma.},
}
@article {pmid33785750,
year = {2021},
author = {Chen, F and Bai, M and Cao, X and Xue, J and Zhao, Y and Wu, N and Wang, L and Zhang, D and Zhao, Y},
title = {Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {1965},
pmid = {33785750},
issn = {2041-1723},
mesh = {Cellular Microenvironment/*genetics ; Chromatin/*genetics/metabolism ; DNA/*genetics/metabolism ; *Epigenesis, Genetic ; Genetic Techniques ; High-Throughput Nucleotide Sequencing/methods ; Histones/metabolism ; Humans ; Molecular Biology/methods ; Protein Processing, Post-Translational ; Reproducibility of Results ; Transcription Factors/genetics/metabolism ; },
abstract = {Exploring spatial organization and relationship of diverse biomolecules within cellular nanoenvironments is important to elucidate the fundamental processes of life. However, it remains methodologically challenging. Herein, we report a molecular recognition mechanism cellular macromolecules-tethered DNA walking indexing (Cell-TALKING) to probe the nanoenvironments containing diverse chromatin modifications. As an example, we characterize the nanoenvironments of three DNA modifications around one histone posttranslational modification (PTM). These DNA modifications in fixed cells are labeled with respective DNA barcoding probes, and then the PTM site is tethered with a DNA walking probe. Cell-TALKING can continuously produce cleavage records of any barcoding probes nearby the walking probe. New 3'-OH ends are generated on the cleaved barcoding probes to induce DNA amplification for downstream detections. Combining fluorescence imaging, we identify various combinatorial chromatin modifications and investigate their dynamic changes during cell cycles. We also explore the nanoenvironments in different cancer cell lines and clinical specimens. In principle, using high-throughput sequencing instead of fluorescence imaging may allow the detection of complex cellular nanoenvironments containing tens of biomolecules such as transcription factors.},
}
@article {pmid33784084,
year = {2021},
author = {Ekanayake, AI and Sobze, L and Kelich, P and Youk, J and Bennett, NJ and Mukherjee, R and Bhardwaj, A and Wuest, F and Vukovic, L and Derda, R},
title = {Genetically Encoded Fragment-Based Discovery from Phage-Displayed Macrocyclic Libraries with Genetically Encoded Unnatural Pharmacophores.},
journal = {Journal of the American Chemical Society},
volume = {143},
number = {14},
pages = {5497-5507},
doi = {10.1021/jacs.1c01186},
pmid = {33784084},
issn = {1520-5126},
mesh = {*Peptide Library ; *Macrocyclic Compounds/chemistry ; Drug Discovery ; Carbonic Anhydrases/genetics/metabolism/chemistry ; Carbonic Anhydrase Inhibitors/chemistry/pharmacology ; },
abstract = {Genetically encoded macrocyclic peptide libraries with unnatural pharmacophores are valuable sources for the discovery of ligands for many targets of interest. Traditionally, generation of such libraries employs "early stage" incorporation of unnatural building blocks into the chemically or translationally produced macrocycles. Here, we describe a divergent late-stage approach to such libraries starting from readily available starting material: genetically encoded libraries of peptides. A diketone linchpin 1,5-dichloropentane-2,4-dione converts peptide libraries displayed on phage to 1,3-diketone bearing macrocyclic peptides (DKMP): shelf-stable precursors for Knorr pyrazole synthesis. Ligation of diverse hydrazine derivatives onto DKMP libraries displayed on phage that carries silent DNA-barcodes yields macrocyclic libraries in which the amino acid sequence and the pharmacophore are encoded by DNA. Selection of this library against carbonic anhydrase enriched macrocycles with benzenesulfonamide pharmacophore and nanomolar Kd. The methodology described in this manuscript can graft diverse pharmacophores into many existing genetically encoded phage libraries and significantly increase the value of such libraries in molecular discoveries.},
}
@article {pmid33783328,
year = {2021},
author = {Wang, N and Xing, RR and Zhou, MY and Sun, RX and Han, JX and Zhang, JK and Zheng, WJ and Chen, Y},
title = {Application of DNA barcoding and metabarcoding for species identification in salmon products.},
journal = {Food additives &amp; contaminants. Part A, Chemistry, analysis, control, exposure &amp; risk assessment},
volume = {38},
number = {5},
pages = {754-768},
doi = {10.1080/19440049.2020.1869324},
pmid = {33783328},
issn = {1944-0057},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Fish Products/*analysis ; *Food Analysis ; Food Contamination/*analysis ; Salmon ; },
abstract = {Mislabelling is a significant manifestation of food fraud. Traditional Sanger sequencing technology is the gold standard for seafood species identification. However, this method is not suitable for analysing processed samples that may contain more than one species. This study tested the feasibility of next-generation sequencing in identifying mixed salmon products. Salmon samples containing up to eight species were amplified using 16S rRNA mini-barcode primers, and sequenced on an Illumina HiSeq2500 platform. All species were accurately identified, and mixtures as low as 1% (w/w) could be detected. Furthermore, this study conducted a market survey of 32 products labelled as salmon. For pure and mixed fish products, Sanger and next-generation sequencing techniques were respectively used for species identification, and for NGS results, we also used real-time PCR method to cross-validate the mixed products to further verify the accuracy of the DNA metabarcoding technology established in this study. DNA barcoding and metabarcoding of commercial salmon food products revealed the presence of mislabelling in 16 of 32 (50%) samples. The developed DNA barcoding and metabarcoding methods are useful for the identification of salmon species in food and can be used for quality control of various types of salmon products.},
}
@article {pmid33780549,
year = {2021},
author = {Kolaříková, Z and Slavíková, R and Krüger, C and Krüger, M and Kohout, P},
title = {PacBio sequencing of Glomeromycota rDNA: a novel amplicon covering all widely used ribosomal barcoding regions and its applicability in taxonomy and ecology of arbuscular mycorrhizal fungi.},
journal = {The New phytologist},
volume = {231},
number = {1},
pages = {490-499},
doi = {10.1111/nph.17372},
pmid = {33780549},
issn = {1469-8137},
mesh = {DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; Fungi/genetics ; *Glomeromycota/genetics ; *Mycorrhizae/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {There is no consensus barcoding region for determination of arbuscular mycorrhizal fungal (AMF) taxa. To overcome this obstacle, we have developed an approach to sequence an AMF marker within the ribosome-encoding operon (rDNA) that covers all three widely applied variable molecular markers. Using a nested PCR approach specific to AMF, we amplified a part (c. 2.5 kb) of the rDNA spanning the majority of the small subunit rRNA (SSU) gene, the complete internal transcribed spacer (ITS) region and a part of the large subunit (LSU) rRNA gene. The PCR products were sequenced on the PacBio platform utilizing Single Molecule Real Time (SMRT) sequencing. Employing this method for selected environmental DNA samples, we were able to describe complex AMF communities consisting of various glomeromycotan lineages. We demonstrate the applicability of this new 2.5 kb approach to provide robust phylogenetic assignment of AMF lineages without known sequences from pure cultures and to consolidate information about AMF taxon distributions coming from three widely used barcoding regions into one integrative dataset.},
}
@article {pmid33780458,
year = {2021},
author = {Šturm, MB and Smith, S and Ganbaatar, O and Buuveibaatar, B and Balint, B and Payne, JC and Voigt, CC and Kaczensky, P},
title = {Isotope analysis combined with DNA barcoding provide new insights into the dietary niche of khulan in the Mongolian Gobi.},
journal = {PloS one},
volume = {16},
number = {3},
pages = {e0248294},
pmid = {33780458},
issn = {1932-6203},
support = {P 24231/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Animals ; Animals, Wild/*genetics/physiology ; Carbon Isotopes/chemistry ; *DNA Barcoding, Taxonomic ; *Diet ; Equidae/*genetics/physiology ; Humans ; Livestock/genetics ; Mongolia ; Poaceae/growth &amp; development ; Seasons ; },
abstract = {With increasing livestock numbers, competition and avoidance are increasingly shaping resource availability for wild ungulates. Shifts in the dietary niche of wild ungulates are likely and can be expected to negatively affect their fitness. The Mongolian Gobi constitutes the largest remaining refuge for several threatened ungulates, but unprecedentedly high livestock numbers are sparking growing concerns over rangeland health and impacts on threatened ungulates like the Asiatic wild ass (khulan). Previous stable isotope analysis of khulan tail hair from the Dzungarian Gobi suggested that they graze in summer but switch to a poorer mixed C3 grass / C4 shrub diet in winter, most likely in reaction to local herders and their livestock. Here we attempt to validate these findings with a different methodology, DNA metabarcoding. Further, we extend the scope of the original study to the South Gobi Region, where we expect higher proportions of low-quality browse in the khulan winter diet due to a higher human and livestock presence. Barcoding confirmed the assumptions behind the seasonal diet change observed in the Dzungarian Gobi isotope data, and new isotope analysis revealed a strong seasonal pattern and higher C4 plant intake in the South Gobi Region, in line with our expectations. However, DNA barcoding revealed C4 domination of winter diet was due to C4 grasses (rather than shrubs) for the South Gobi Region. Slight climatic differences result in regional shifts in the occurrence of C3 and C4 grasses and shrubs, which do not allow for an isotopic separation along the grazer-browser continuum over the entire Gobi. Our findings do not allow us to confirm human impacts upon dietary preferences in khulan as we lack seasonal samples from the South Gobi Region. However, these data provide novel insight into khulan diet, raise new questions about plant availability versus preference, and provide a cautionary tale about indirect analysis methods if used in isolation or extrapolated to the landscape level. Good concordance between relative read abundance of C4 genera from barcoding and proportion of C4 plants from isotope analysis adds to a growing body of evidence that barcoding is a promising quantitative tool to understand resource partitioning in ungulates.},
}
@article {pmid33778029,
year = {2020},
author = {Hernández-Triana, LM and Garza-Hernández, JA and Ortega Morales, AI and Prosser, SWJ and Hebert, PDN and Nikolova, NI and Barrero, E and de Luna-Santillana, EJ and González-Alvarez, VH and Mendez-López, R and Chan-Chable, RJ and Fooks, AR and Rodríguez-Pérez, MA},
title = {An Integrated Molecular Approach to Untangling Host-Vector-Pathogen Interactions in Mosquitoes (Diptera: Culicidae) From Sylvan Communities in Mexico.},
journal = {Frontiers in veterinary science},
volume = {7},
number = {},
pages = {564791},
pmid = {33778029},
issn = {2297-1769},
abstract = {There are ~240 species of Culicidae in Mexico, of which some are vectors of arthropod-borne viruses such as Zika virus, dengue virus, chikungunya virus, and West Nile virus. Thus, the identification of mosquito feeding preferences is paramount to understanding of vector-host-pathogen interactions that, in turn, can aid the control of disease outbreaks. Typically, DNA and RNA are extracted separately for animal (insects and blood meal hosts) and viral identification, but this study demonstrates that multiple organisms can be analyzed from a single RNA extract. For the first time, residual DNA present in standard RNA extracts was analyzed by DNA barcoding in concert with Sanger and next-generation sequencing (NGS) to identify both the mosquito species and the source of their meals in blood-fed females caught in seven sylvan communities in Chiapas State, Mexico. While mosquito molecular identification involved standard barcoding methods, the sensitivity of blood meal identification was maximized by employing short primers with NGS. In total, we collected 1,634 specimens belonging to 14 genera, 25 subgenera, and 61 morphospecies of mosquitoes. Of these, four species were new records for Mexico (Aedes guatemala, Ae. insolitus, Limatus asulleptus, Trichoprosopon pallidiventer), and nine were new records for Chiapas State. DNA barcode sequences for >300 bp of the COI gene were obtained from 291 specimens, whereas 130 bp sequences were recovered from another 179 specimens. High intraspecific divergence values (>2%) suggesting cryptic species complexes were observed in nine taxa: Anopheles eiseni (5.39%), An. pseudopunctipennis (2.79%), Ae. podographicus (4.05%), Culex eastor (4.88%), Cx. erraticus (2.28%), Toxorhynchites haemorrhoidalis (4.30%), Tr. pallidiventer (4.95%), Wyeomyia adelpha/Wy. guatemala (7.30%), and Wy. pseudopecten (4.04%). The study increased the number of mosquito species known from 128 species to 138 species for Chiapas State, and 239 for Mexico as a whole. Blood meal analysis showed that Aedes angustivittatus fed on ducks and chicken, whereas Psorophora albipes fed on humans. Culex quinquefasciatus fed on diverse hosts including chicken, human, turkey, and Mexican grackle. No arbovirus RNA was detected by reverse transcriptase-polymerase chain reaction in the surveyed specimens. This study demonstrated, for the first time, that residual DNA present in RNA blood meal extracts can be used to identify host vectors, highlighting the important role of molecular approaches in both vector identification and revealing host-vector-pathogen interactions.},
}
@article {pmid33777526,
year = {2021},
author = {Soledispa, P and Santos-Ordóñez, E and Miranda, M and Pacheco, R and Gutiérrez Gaiten, YI and Scull, R},
title = {Molecular barcode and morphological analysis of Smilax purhampuy Ruiz, Ecuador.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e11028},
pmid = {33777526},
issn = {2167-8359},
abstract = {Smilax plants are distributed in tropical, subtropical, and temperate regions in both hemispheres of the world. They are used extensively in traditional medicines in a number of countries. However, morphological and molecular barcodes analysis, which may assist in the taxonomic identification of species, are lacking in Ecuador. In order to evaluate the micromorphological characteristics of these plants, cross sections of Smilax purhampuy leaves were obtained manually. The rhizome powder, which is typically used in traditional medicines, was analyzed for micromorphological characteristics. All samples were clarified with 1% sodium hypochlorite. Tissues were colored with 1% safranin in water and were fixed with glycerinated gelatin. DNA was extracted from the leaves using a modified CTAB method for molecular barcode characterization and PCR was performed using primers to amplify the different loci including the plastid genome regions atpF-atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK-psbI spacer, and trnH-psbA spacer; and the nuclear DNA sequence ITS2. A DNA sequence similarity search was performed using BLAST in the GenBank nr database and phylogenetic analysis was performed using the maximum likelihood method according to the best model identified by MEGAX using a bootstrap test with 1,000 replicates. Results showed that the micromorphological evaluation of a leaf cross section depicted a concave arrangement of the central vein, which was more pronounced in the lower section and had a slight protuberance. The micromorphological analysis of the rhizome powder allowed the visualization of a group of cells with variable sizes in the parenchyma and revealed thickened xylematic vessels associated with other elements of the vascular system. Specific amplicons were detected in DNA barcoding for all the barcodes tested except for the trnH-psbA spacer. BLAST analysis revealed that the Smilax species was predominant in all the samples for each barcode; therefore, the genus Smilax was confirmed through DNA barcode analysis. The barcode sequences psbK-psbI, atpF-atpH, and ITS2 had a better resolution at the species level in phylogenetic analysis than the other barcodes we tested.},
}
@article {pmid33776521,
year = {2021},
author = {Savage, J and Sorokina, VS},
title = {Review of the North American fauna of Drymeia Meigen (Diptera, Muscidae) and evaluation of DNA barcodes for species-level identification in the genus.},
journal = {ZooKeys},
volume = {1024},
number = {},
pages = {31-89},
pmid = {33776521},
issn = {1313-2989},
abstract = {The North American fauna of Drymeia Meigen was studied. Four new species are described (Drymeia hucketti sp. nov., Drymeia ponti sp. nov., Drymeia vockerothi sp. nov., Drymeia woodorum sp. nov.), and three new synonymies are proposed: Drymeia amnicola (Huckett, 1966) (= Drymeia rivalis (Huckett, 1966), syn. nov.); Drymeia glacialis (Rondani, 1866) (= Drymeia alpicola (Rondani, 1871), syn. nov.); and Drymeia spinitarsis (Aldrich, 1918) (= Drymeia longiseta Sorokina &amp; Pont, 2015, syn. nov.). An annotated checklist, DNA barcodes (when available), and keys for each sex of the 24 named species of North American Drymeia are provided. The utility of DNA barcodes for the identification of Drymeia species across a wide geographical range was explored using sequences from five countries. A match between morphology and DNA barcodes was found for 71% (22/31) of species studied (including three unnamed taxa). The remaining nine species clustered into two groups of taxa with very little interspecific variation within clusters (groups of two and seven species). Caution is advised against using DNA barcoding as the only determination tool for Drymeia material without prior knowledge of its limitations for certain species groups.},
}
@article {pmid33776519,
year = {2021},
author = {Matsui, Y and Naka, H and Jinbo, U},
title = {DNA barcoding and morphology reveal a new cryptic species of Nagiella (Lepidoptera, Crambidae, Spilomelinae) from Japan.},
journal = {ZooKeys},
volume = {1023},
number = {},
pages = {171-192},
pmid = {33776519},
issn = {1313-2989},
abstract = {Nagiella tristalis Matsui &amp; Naka, sp. nov. is described from Japan, based on DNA barcoding and morphological evidence. The two species previously known from Japan, N. quadrimaculalis and N. inferior, are diagnosed. Photographs of adults, including male and female genitalia of the three species, are provided.},
}
@article {pmid33776517,
year = {2021},
author = {Tiutenko, A and Zinenko, O},
title = {A new species of Leptopelis (Anura, Arthroleptidae) from the south-eastern slope of the Ethiopian Highlands, with notes on the Leptopelis gramineus species complex and the revalidation of a previously synonymised species.},
journal = {ZooKeys},
volume = {1023},
number = {},
pages = {119-150},
pmid = {33776517},
issn = {1313-2989},
abstract = {A new ground-dwelling species of treefrog in the genus Leptopelis is described from the Harenna Forest in south-eastern Ethiopia. The description is based on morphology and acoustics and is supported by molecular data. The new species has a small body size, and the digital discs on fingers and toes are significantly more conspicuous than in other semi-fossorial members of the L. gramineus complex. It occupies forest habitats at lower altitudes and is separated ecologically and geographically from high-altitude species of the complex. One of them, a parapatric cryptic species from Bale and Arsi Mountains, is resurrected from synonymy of L. gramineus and given a new name, L. montanus. Genetic barcoding of specimens from both populations showed that they belong to two distinct lineages that had been revealed by recent phylogenetic research. To confirm the geographic separation of the studied populations, the collection area of L. gramineus types was verified through analysis of the diary and the final report of the 2[nd] expedition of V. Bottego, and through matching of the route described in it with modern maps. The type locality of L. gramineus sensu stricto is restricted to Gamo Gofa, Ethiopia. Following the results of recent phylogenetic studies, the range of L. gramineus is limited to west of the Great Rift Valley. An identification key to the named Ethiopian species of the genus is provided.},
}
@article {pmid33773100,
year = {2021},
author = {Kawachi, M and Nakayama, T and Kayama, M and Nomura, M and Miyashita, H and Bojo, O and Rhodes, L and Sym, S and Pienaar, RN and Probert, I and Inouye, I and Kamikawa, R},
title = {Rappemonads are haptophyte phytoplankton.},
journal = {Current biology : CB},
volume = {31},
number = {11},
pages = {2395-2403.e4},
doi = {10.1016/j.cub.2021.03.012},
pmid = {33773100},
issn = {1879-0445},
mesh = {*Haptophyta/genetics ; Phylogeny ; *Phytoplankton/genetics ; Plastids/genetics ; RNA, Ribosomal, 16S ; },
abstract = {Rapidly accumulating genetic data from environmental sequencing approaches have revealed an extraordinary level of unsuspected diversity within marine phytoplankton,[1-11] which is responsible for around 50% of global net primary production.[12][,][13] However, the phenotypic identity of many of the organisms distinguished by environmental DNA sequences remains unclear. The rappemonads represent a plastid-bearing protistan lineage that to date has only been identified by environmental plastid 16S rRNA sequences.[14-17] The phenotypic identity of this group, which does not confidently cluster in any known algal clades in 16S rRNA phylogenetic reconstructions,[15] has remained unknown since the first report of environmental sequences over two decades ago. We show that rappemonads are closely related to a haptophyte microalga, Pavlomulina ranunculiformis gen. nov. et sp. nov., and belong to a new haptophyte class, the Rappephyceae. Organellar phylogenomic analyses provide strong evidence for the inclusion of this lineage within the Haptophyta as a sister group to the Prymnesiophyceae. Members of this new class have a cosmopolitan distribution in coastal and oceanic regions. The relative read abundance of Rappephyceae in a large environmental barcoding dataset was comparable to, or greater than, those of major haptophyte species, such as the bloom-forming Gephyrocapsa huxleyi and Prymnesium parvum, and this result indicates that they likely have a significant impact as primary producers. Detailed characterization of Pavlomulina allowed for reconstruction of the ancient evolutionary history of the Haptophyta, a group that is one of the most important components of extant marine phytoplankton communities.},
}
@article {pmid33770699,
year = {2021},
author = {Vasiljevic, N and Lim, M and Humble, E and Seah, A and Kratzer, A and Morf, NV and Prost, S and Ogden, R},
title = {Developmental validation of Oxford Nanopore Technology MinION sequence data and the NGSpeciesID bioinformatic pipeline for forensic genetic species identification.},
journal = {Forensic science international. Genetics},
volume = {53},
number = {},
pages = {102493},
doi = {10.1016/j.fsigen.2021.102493},
pmid = {33770699},
issn = {1878-0326},
mesh = {Animals ; Birds/genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Deer/genetics ; *Forensic Genetics ; High-Throughput Nucleotide Sequencing/*instrumentation ; Humans ; Lynx/genetics ; Nanopores ; Panthera/genetics ; Reproducibility of Results ; Rupicapra/genetics ; Sequence Analysis, DNA/*instrumentation ; *Species Specificity ; Sus scrofa/genetics ; },
abstract = {Species identification of non-human biological evidence through DNA nucleotide sequencing is routinely used for forensic genetic analysis to support law enforcement. The gold standard for forensic genetics is conventional Sanger sequencing; however, this is gradually being replaced by high-throughput sequencing (HTS) approaches which can generate millions of individual reads in a single experiment. HTS sequencing, which now dominates molecular biology research, has already been demonstrated for use in a number of forensic genetic analysis applications, including species identification. However, the generation of HTS data to date requires expensive equipment and is cost-effective only when large numbers of samples are analysed simultaneously. The Oxford Nanopore Technologies (ONT) MinION™ is an affordable and small footprint DNA sequencing device with the potential to quickly deliver reliable and cost effective data. However, there has been no formal validation of forensic species identification using high-throughput (deep read) sequence data from the MinION making it currently impractical for many wildlife forensic end-users. Here, we present a MinION deep read sequence data validation study for species identification. First, we tested whether the clustering-based bioinformatics pipeline NGSpeciesID can be used to generate an accurate consensus sequence for species identification. Second, we systematically evaluated the read variation distribution around the generated consensus sequences to understand what confidence we have in the accuracy of the resulting consensus sequence and to determine how to interpret individual sample results. Finally, we investigated the impact of differences between the MinION consensus and Sanger control sequences on correct species identification to understand the ability and accuracy of the MinION consensus sequence to differentiate the true species from the next most similar species. This validation study establishes that ONT MinION sequence data used in conjunction with the NGSpeciesID pipeline can produce consensus DNA sequences of sufficient accuracy for forensic genetic species identification.},
}
@article {pmid33765921,
year = {2021},
author = {Guo, L and Xu, M and Wang, W and Gu, S and Zhao, X and Chen, F and Wang, O and Xu, X and Seim, I and Fan, G and Deng, L and Liu, X},
title = {SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme.},
journal = {BMC bioinformatics},
volume = {22},
number = {1},
pages = {158},
pmid = {33765921},
issn = {1471-2105},
support = {2018YFD0900301-05//the National Key Research and Development Program of China/ ; 19-6-2-33-cg//the Qingdao Applied Basic Research Projects/ ; },
mesh = {Algorithms ; Genomics ; *High-Throughput Nucleotide Sequencing ; Humans ; Sequence Analysis, DNA ; *Software ; },
abstract = {BACKGROUND: Synthetic long reads (SLR) with long-range co-barcoding information are now widely applied in genomics research. Although several tools have been developed for each specific SLR technique, a robust standalone scaffolder with high efficiency is warranted for hybrid genome assembly.<br><br>RESULTS: In this work, we developed a standalone scaffolding tool, SLR-superscaffolder, to link together contigs in draft assemblies using co-barcoding and paired-end read information. Our top-to-bottom scheme first builds a global scaffold graph based on Jaccard Similarity to determine the order and orientation of contigs, and then locally improves the scaffolds with the aid of paired-end information. We also exploited a screening algorithm to reduce the negative effect of misassembled contigs in the input assembly. We applied SLR-superscaffolder to a human single tube long fragment read sequencing dataset and increased the scaffold NG50 of its corresponding draft assembly 1349 fold. Moreover, benchmarking on different input contigs showed that this approach overall outperformed existing SLR scaffolders, providing longer contiguity and fewer misassemblies, especially for short contigs assembled by next-generation sequencing data. The open-source code of SLR-superscaffolder is available at https://github.com/BGI-Qingdao/SLR-superscaffolder .<br><br>CONCLUSIONS: SLR-superscaffolder can dramatically improve the contiguity of a draft assembly by integrating a hybrid assembly strategy.},
}
@article {pmid33764987,
year = {2021},
author = {Nibouche, S and Costet, L and Medina, RF and Holt, JR and Sadeyen, J and Zoogones, AS and Brown, P and Blackman, RL},
title = {Morphometric and molecular discrimination of the sugarcane aphid, Melanaphis sacchari, (Zehntner, 1897) and the sorghum aphid Melanaphis sorghi (Theobald, 1904).},
journal = {PloS one},
volume = {16},
number = {3},
pages = {e0241881},
pmid = {33764987},
issn = {1932-6203},
mesh = {Animals ; Aphids/*genetics/physiology ; Arthropod Antennae/physiology ; Bayes Theorem ; Cluster Analysis ; DNA-Binding Proteins/chemistry/genetics/metabolism ; Electron Transport Complex IV/chemistry/genetics/metabolism ; Genotype ; Haplotypes ; Insect Proteins/chemistry/genetics/metabolism ; Microsatellite Repeats ; Mitochondria/genetics ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; *Sorghum ; },
abstract = {Melanaphis sacchari (Zehntner, 1897) and Melanaphis sorghi (Theobald, 1904) are major worldwide crop pests causing direct feeding damage on sorghum and transmitting viruses to sugarcane. It is common in the scientific literature to consider these two species as synonyms, referred to as the 'sugarcane aphid', although no formal study has validated this synonymy. In this study, based on the comparison of samples collected from their whole distribution area, we use both morphometric and molecular data to better characterize the discrimination between M. sacchari and M. sorghi. An unsupervised multivariate analysis of morphometric data clearly confirmed the separation of the two species. The best discriminating characters separating these species were length of the antenna processus terminalis relative to length of hind tibia, siphunculus or cauda. However, those criteria sometimes do not allow an unambiguous identification. Bayesian clustering based on microsatellite data delimited two clusters, which corresponded to the morphological species separation. The DNA sequencing of three nuclear and three mitochondrial regions revealed slight divergence between species. In particular, the COI barcode region proved to be uninformative for species separation because one haplotype is shared by both species. In contrast, one SNP located on the nuclear EF1-α gene was diagnostic for species separation. Based on morphological and molecular evidence, the invasive genotype damaging to sorghum in the US, Mexico and the Caribbean since 2013 is found to be M. sorghi.},
}
@article {pmid33764469,
year = {2021},
author = {Pilgrim, J and Thongprem, P and Davison, HR and Siozios, S and Baylis, M and Zakharov, EV and Ratnasingham, S and deWaard, JR and Macadam, CR and Smith, MA and Hurst, GDD},
title = {Torix Rickettsia are widespread in arthropods and reflect a neglected symbiosis.},
journal = {GigaScience},
volume = {10},
number = {3},
pages = {},
pmid = {33764469},
issn = {2047-217X},
support = {BB/M011186/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *Arthropods/genetics ; Base Sequence ; Humans ; Phylogeny ; *Rickettsia/genetics ; Symbiosis ; },
abstract = {BACKGROUND: Rickettsia are intracellular bacteria best known as the causative agents of human and animal diseases. Although these medically important Rickettsia are often transmitted via haematophagous arthropods, other Rickettsia, such as those in the Torix group, appear to reside exclusively in invertebrates and protists with no secondary vertebrate host. Importantly, little is known about the diversity or host range of Torix group Rickettsia.<br><br>RESULTS: This study describes the serendipitous discovery of Rickettsia amplicons in the Barcode of Life Data System (BOLD), a sequence database specifically designed for the curation of mitochondrial DNA barcodes. Of 184,585 barcode sequences analysed, Rickettsia is observed in &#x223c;0.41% of barcode submissions and is more likely to be found than Wolbachia (0.17%). The Torix group of Rickettsia are shown to account for 95% of all unintended amplifications from the genus. A further targeted PCR screen of 1,612 individuals from 169 terrestrial and aquatic invertebrate species identified mostly Torix strains and supports the "aquatic hot spot" hypothesis for Torix infection. Furthermore, the analysis of 1,341 SRA deposits indicates that Torix infections represent a significant proportion of all Rickettsia symbioses found in arthropod genome projects.<br><br>CONCLUSIONS: This study supports a previous hypothesis that suggests that Torix Rickettsia are overrepresented in aquatic insects. In addition, multiple methods reveal further putative hot spots of Torix Rickettsia infection, including in phloem-feeding bugs, parasitoid wasps, spiders, and vectors of disease. The unknown host effects and transmission strategies of these endosymbionts make these newly discovered associations important to inform future directions of investigation involving the understudied Torix Rickettsia.},
}
@article {pmid33763596,
year = {2021},
author = {Wu, J and Lei, C and Zhao, J and Jin, F and Gao, H and Fu, S and Zhou, R and Luo, Y and Leng, Y and Xue, S and Zhang, W and Li, G},
title = {The complete mitochondrial genome of Silurus grahami Regan, 1907 (Siluriformes: Siluridae), a native catfish in Fuxian Lake.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {6},
number = {3},
pages = {835-836},
pmid = {33763596},
issn = {2380-2359},
abstract = {In this study, the whole mitochondrial genome of Silurus grahami was reported to be 16,518 bp in length, including 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and one control region. The phylogenetic analysis based on 13 protein-coding genes showed that S. grahami was sister to clade of S. meridionalis and S. lanzhouensis. A total of 81 bases differences were identified in COI barcoding region, which could be used for species identification in catfish.},
}
@article {pmid33763089,
year = {2021},
author = {Braglia, L and Lauria, M and Appenroth, KJ and Bog, M and Breviario, D and Grasso, A and Gavazzi, F and Morello, L},
title = {Duckweed Species Genotyping and Interspecific Hybrid Discovery by Tubulin-Based Polymorphism Fingerprinting.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {625670},
pmid = {33763089},
issn = {1664-462X},
abstract = {Duckweeds (Lemnaceae) are the smallest and fastest-growing angiosperms. This feature, together with high starch production and good nutritional properties, makes them suitable for several applications, including wastewater treatment, bioenergy production, or feed and food supplement. Due to their reduced morphology and great similarity between diverse species, taxonomic identification of duckweeds is a challenging issue even for experts. Among molecular genotyping methods, DNA barcoding is the most useful tool for species identification without a need for cluster analysis. The combination of two plastid barcoding loci is now considered the gold standard for duckweed classification. However, not all species can be defined with confidence by these markers, and a fast identification method able to solve doubtful cases is missing. Here we show the potential of tubulin-based polymorphism (TBP), a molecular marker based on the intron length polymorphisms of β-tubulin loci, in the genomic profiling of the genera Spirodela, Landoltia, and Lemna. Ninety-four clones were analyzed, including at least two representatives of each species of the three genera, with a special focus on the very heterogeneous species Lemna minor. We showed that a single PCR amplification with universal primers, followed by agarose gel analysis, was able to provide distinctive fingerprinting profiles for 10 out of 15 species. Cluster analysis of capillary electrophoresis-TBP data provided good separation for the remaining species, although the relationship between L. minor and Lemna japonica was not fully resolved. However, an accurate comparison of TBP profiles provided evidence for the unexpected existence of intraspecific hybrids between Lemna turionifera and L. minor, as further confirmed by amplified fragment length polymorphism and sequence analysis of a specific β-tubulin locus. Such hybrids could possibly correspond to L. japonica, as originally suggested by E. Landolt. The discovery of interspecific hybrids opens a new perspective to understand the speciation mechanisms in the family of duckweeds.},
}
@article {pmid33762644,
year = {2021},
author = {Tungphatthong, C and Urumarudappa, SKJ and Awachai, S and Sooksawate, T and Sukrong, S},
title = {Differentiation of Mitragyna speciosa, a narcotic plant, from allied Mitragyna species using DNA barcoding-high-resolution melting (Bar-HRM) analysis.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {6738},
pmid = {33762644},
issn = {2045-2322},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer ; Mitragyna/*classification/*genetics ; *Nucleic Acid Amplification Techniques ; Plants, Medicinal ; Polymerase Chain Reaction ; },
abstract = {Mitragyna speciosa (Korth.) Havil. [MS], or "kratom" in Thai, is the only narcotic species among the four species of Mitragyna in Thailand, which also include Mitragyna diversifolia (Wall. ex G. Don) Havil. [MD], Mitragyna hirsuta Havil. [MH], and Mitragyna rotundifolia (Roxb.) O. Kuntze [MR]. M. speciosa is a tropical tree belonging to the Rubiaceae family and has been prohibited by law in Thailand. However, it has been extensively covered in national and international news, as its abuse has become more popular. M. speciosa is a narcotic plant and has been used as an opium substitute and traditionally used for the treatment of chronic pain and various illnesses. Due to morphological disparities in the genus, the identification of plants in various forms, including fresh leaves, dried leaf powder, and finished products, is difficult. In this study, DNA barcoding combined with high-resolution melting (Bar-HRM) analysis was performed to differentiate M. speciosa from allied Mitragyna and to assess the capability of Bar-HRM assays to identify M. speciosa in suspected kratom or M. speciosa-containing samples. Bar-HRM analysis of PCR amplicons was based on the ITS2, rbcL, trnH-psbA, and matK DNA barcode regions. The melting profiles of ITS2 amplicons were clearly distinct, which enabled the authentication and differentiation of Mitragyna species from allied species. This study reveals that DNA barcoding coupled with HRM is an efficient tool with which to identify M. speciosa and M. speciosa-containing samples and ensure the safety and quality of traditional Thai herbal medicines.},
}
@article {pmid33758781,
year = {2020},
author = {Gan, Z and Lokugamage, MP and Hatit, MZC and Loughrey, D and Paunovska, K and Sato, M and Cristian, A and Dahlman, JE},
title = {Nanoparticles containing constrained phospholipids deliver mRNA to liver immune cells in vivo without targeting ligands.},
journal = {Bioengineering &amp; translational medicine},
volume = {5},
number = {3},
pages = {e10161},
pmid = {33758781},
issn = {2380-6761},
support = {R01 DE026941/DE/NIDCR NIH HHS/United States ; R01 GM132985/GM/NIGMS NIH HHS/United States ; UG3 TR002855/TR/NCATS NIH HHS/United States ; UH3 TR002855/TR/NCATS NIH HHS/United States ; },
abstract = {Once inside the cytoplasm of a cell, mRNA can be used to treat disease by upregulating the expression of any gene. Lipid nanoparticles (LNPs) can deliver mRNA to hepatocytes in humans, yet systemic non-hepatocyte delivery at clinical doses remains difficult. We noted that LNPs have historically been formulated with phospholipids containing unconstrained alkyl tails. Based on evidence that constrained adamantyl groups have unique properties that can improve small molecule drug delivery, we hypothesized that a phospholipid containing an adamantyl group would facilitate mRNA delivery in vivo. We quantified how 109 LNPs containing "constrained phospholipids" delivered mRNA to 16 cell types in mice, then using a DNA barcoding-based analytical pipeline, related phospholipid structure to in vivo delivery. By analyzing delivery mediated by constrained phospholipids, we identified a novel LNP that delivers mRNA to immune cells at 0.5 mg/kg. Unlike many previous LNPs, these (a) did not preferentially target hepatocytes and (b) delivered mRNA to immune cells without targeting ligands. These data suggest constrained phospholipids may be useful LNP components.},
}
@article {pmid33757429,
year = {2021},
author = {McGlincy, NJ and Meacham, ZA and Reynaud, KK and Muller, R and Baum, R and Ingolia, NT},
title = {A genome-scale CRISPR interference guide library enables comprehensive phenotypic profiling in yeast.},
journal = {BMC genomics},
volume = {22},
number = {1},
pages = {205},
pmid = {33757429},
issn = {1471-2164},
support = {DP2CA195768//NIH Office of the Director/ ; R01GM130996/GM/NIGMS NIH HHS/United States ; R01 GM130996/GM/NIGMS NIH HHS/United States ; R01 GM135233/GM/NIGMS NIH HHS/United States ; DP2 CA195768/CA/NCI NIH HHS/United States ; },
mesh = {CRISPR-Cas Systems/genetics ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Phenotype ; *RNA, Guide, CRISPR-Cas Systems/genetics ; Saccharomyces cerevisiae/genetics ; },
abstract = {BACKGROUND: CRISPR/Cas9-mediated transcriptional interference (CRISPRi) enables programmable gene knock-down, yielding loss-of-function phenotypes for nearly any gene. Effective, inducible CRISPRi has been demonstrated in budding yeast, and genome-scale guide libraries enable systematic, genome-wide genetic analysis.<br><br>RESULTS: We present a comprehensive yeast CRISPRi library, based on empirical design rules, containing 10 distinct guides for most genes. Competitive growth after pooled transformation revealed strong fitness defects for most essential genes, verifying that the library provides comprehensive genome coverage. We used the relative growth defects caused by different guides targeting essential genes to further refine yeast CRISPRi design rules. In order to obtain more accurate and robust guide abundance measurements in pooled screens, we link guides with random nucleotide barcodes and carry out linear amplification by in vitro transcription.<br><br>CONCLUSIONS: Taken together, we demonstrate a broadly useful platform for comprehensive, high-precision CRISPRi screening in yeast.},
}
@article {pmid33757098,
year = {2021},
author = {Rajaei, H and Gelbrecht, J and Schulz, N and Hausmann, A},
title = {Minoa lutea Schwingenschuss, 1954 (Lepidoptera: Geometridae: Larentiinae) recognized as bona species.},
journal = {Zootaxa},
volume = {4903},
number = {2},
pages = {zootaxa.4903.2.5},
doi = {10.11646/zootaxa.4903.2.5},
pmid = {33757098},
issn = {1175-5334},
mesh = {Animals ; Female ; *Lepidoptera ; Male ; *Moths/genetics ; },
abstract = {The species Minoa murinata (Scopoli, 1763) sensu lato is examined throughout its distribution range. Specimens from central Europe (Germany, Italy, France) are compared with those from Serbia, Croatia, Slovenia and newly collected specimens from eastern Turkey, Armenia, Georgia and Russia. The study is based on a combination of behavioural observations, morphological characters (size, wing coloration, structure of male and female genitalia) as well as genetic data (DNA barcoding). The taxon Minoa murinata var. monochroaria Herrich-Schäffer, 1848 is downgraded from subspecies rank to synonymy of M. murinata. Morphological study of the populations from eastern Turkey, Armenia, Georgia and Russia confirm the taxon Minoa murinata f./ssp. lutea Schwingenschuss, 1954 as a bona species. It is herewith upgraded from synonymy of M. murinata to species level. The results of DNA barcoding are discussed. Wing pattern, male and female genitalia of both species are illustrated.},
}
@article {pmid33757097,
year = {2021},
author = {Hu, FS and Liang, WR},
title = {The first record of the subfamily Dasycerinae in Taiwan, with description of a new species (Coleoptera: Staphylinidae).},
journal = {Zootaxa},
volume = {4903},
number = {2},
pages = {zootaxa.4903.2.4},
doi = {10.11646/zootaxa.4903.2.4},
pmid = {33757097},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; *Coleoptera/genetics ; Taiwan ; X-Ray Microtomography ; },
abstract = {Dasycerus poseidon Hu Liang, sp. nov. is described and illustrated based on fresh specimens from central and southern Taiwan, which filled in the disjunct distribution between the Japanese archipelago and south-eastern Asia. The new species represents the first record of the subfamily Dasycerinae in Taiwan. The barcoding sequence of the holotype of D. poseidon Hu Liang, sp. nov.is provided, and revealed a surprisingly large genetic distance within the genus. Detailed illustrations of D. poseidon Hu Liang, sp. nov. by scanning electron micrograph and micro-computed tomography are also provided. Living individuals of D. poseidon Hu Liang, sp. nov. were observed eating the mycelium of Pleurotus ostreatus in lab conditions, which represents the first direct evidence of mycophagous habits of Dasycerinae.},
}
@article {pmid33757090,
year = {2021},
author = {Psomadakis, PN and Yoshinaga, T and Wah, ZZ and Ida, H},
title = {Description of two new species of sandlances, genus Bleekeria (Perciformes, Ammodytidae) from the Andaman Sea (northeastern Indian Ocean).},
journal = {Zootaxa},
volume = {4903},
number = {3},
pages = {zootaxa.4903.3.7},
doi = {10.11646/zootaxa.4903.3.7},
pmid = {33757090},
issn = {1175-5334},
mesh = {Animals ; Indian Ocean ; *Perciformes/genetics ; },
abstract = {Two new species of Bleekeria Günther, 1862 are described from specimens collected in the Andaman Sea off the coast of Myanmar during bottom surveys conducted by the R/V Dr Fridtjof Nansen in 2015 and 2018. They are distinguished from each other and from congeners by a combination of morphological and meristic characters as well as fin coloration and genetic variance. Bleekeria albicauda sp. nov. has pelvic fins, 40-41 dorsal-fin rays, 54-55 total vertebrae, no teeth in jaws, 4 scale rows between dorsal-fin origin and lateral line, a single row of about 10 scales on mid-upper part of opercle, scales on central part of body clearly shorter than their height, caudal fin with white upper and lower lobes when fresh (unique within the genus). Bleekeria nigrilinea sp. nov. has no pelvic fins, 37-39 dorsal-fin rays, 49-50 total vertebrae, 2½ scale rows between dorsal-fin origin and lateral line (the smallest count within the genus with B. estuaria of Mozambique brackish water), 5-6 scales on mid-upper part of opercle arranged in a single row, scales on central part of body clearly longer than their height, upper and lower margins of caudal fin black when fresh (unique within the genus). The COI gene sequences of the two new species showed clear genetic divergence (pairwise K2P, >10 %) from Bleekeria estuaria Randall Ida, 2014 and Bleekeria mitsukurii (Jordan Evermann, 1902). A key to the species of Bleekeria is provided.},
}
@article {pmid33757063,
year = {2021},
author = {Elsayed, AK and Yukawa, J and Mochizuki, KO and Tokuda, M and Kawakita, A},
title = {Three new species of Ametrodiplosis (Diptera: Cecidomyiidae) from Japan, with a key to the Japanese species and a molecular phylogenetic analysis.},
journal = {Zootaxa},
volume = {4942},
number = {2},
pages = {zootaxa.4942.2.1},
doi = {10.11646/zootaxa.4942.2.1},
pmid = {33757063},
issn = {1175-5334},
mesh = {Animals ; *Diptera/genetics ; Japan ; Nematocera ; Phylogeny ; Plants ; },
abstract = {Ametrodiplosis Rübsaamen (Diptera: Cecidomyiidae: Clinodiplosini) is a mostly Holarctic gall midge genus whose species are associated with a wide range of seed plant families, either as gall-inducers or inquilines. In this study, we describe three species of Ametrodiplosis from Japan: A. adetos n. sp. feeding in the flowers of Tylophora aristolochioides Miq. (Apocynaceae); A. aeroradicis n. sp. inducing aerial root galls on Trachelospermum asiaticum (Sieb. et Zucc.) Nakai and T. gracilipes var. liukiuense (Apocynaceae); and A. stellariae n. sp. forming leaf bud galls on Stellaria uliginosa Murray var. undulata (Thunb.) Ohwi (Caryophyllaceae). A molecular phylogenetic analysis using mitochondrial COI and ribosomal 16S genes and nuclear ribosomal 28S gene were conducted for the three new Ametrodiplisis species and other clinodiplosine taxa sequences available in GenBank. The analysis supported the monophyly of Ametrodiplosis despite the variable life history of the three species. In addition, it indicated very low intraspecific genetic divergence among the individuals from different localities and/or host plants. A taxonomic key to the three new Japanese species of Ametrodiplosis is provided.},
}
@article {pmid33757056,
year = {2021},
author = {Cock, MJW and Rougerie, R},
title = {Gamelia bennetti sp. nov., a new Saturniidae species from Trinidad and Tobago (Lepidoptera: Bombycoidea).},
journal = {Zootaxa},
volume = {4942},
number = {3},
pages = {zootaxa.4942.3.2},
doi = {10.11646/zootaxa.4942.3.2},
pmid = {33757056},
issn = {1175-5334},
mesh = {Animals ; *Lepidoptera ; Trinidad and Tobago ; },
abstract = {Gamelia bennetti sp. nov. is described from Trinidad, Trinidad and Tobago, West Indies, and compared with members of the Gamelia abas species group: G. abas (Cramer, [1775]), G. berliozi Lemaire, 1967, G. lichyi Lemaire, 1973, G. rubriluna (Walker, 1862) and G. septentrionalis (Bouvier, 1936). A photographic record suggests G. bennetti sp. nov. may also occur in Tobago.},
}
@article {pmid33757055,
year = {2021},
author = {DE Figueiredo-Filho, JM and Marceniuk, AP and Feijó, A and Siccha-Ramirez, R and Ribeiro, GS and Oliveira, C and Rosa, RS},
title = {Taxonomy of Centropomus Lacépède, 1802 (Perciformes: Centropomidae), with focus on the Atlantic species of the genus.},
journal = {Zootaxa},
volume = {4942},
number = {3},
pages = {zootaxa.4942.3.1},
doi = {10.11646/zootaxa.4942.3.1},
pmid = {33757055},
issn = {1175-5334},
mesh = {Animals ; Fishes ; *Perciformes/genetics ; },
abstract = {Centropomus Lacépède, 1802 comprises 13 species of the fishes popularly knows as snooks, distributed in both Atlantic and Pacific coasts of America. Despite several studies on the group, conflicting taxonomic classifications still exist, including overlapping diagnostic characters, rendering species diagnoses extremely difficult. Herein, we review the taxonomy of Centropomus to elucidate species identities, redefine their diagnoses and to assess interspecific relationships based on the examination of 376 specimens. The study included complementary approaches, as analyses of external morphologic characters, linear and geometric morphometrics, and molecular analyses. Forty-nine characters were used for external morphology, 17 discrete plus 32 linear measurements. Shape and size were analyzed through geometric morphometrics of 185 specimens in lateral view. Partial sequences of the gene cytochrome c oxidase I were obtained for 129 specimens representing 11 species. Based on the consistent results retrieved from the morphologic and molecular analyses, we recognized six species of Centropomus from the Atlantic coast (C. ensiferus, C. irae, C. parallelus, C. pectinatus, C. poeyi and C. undecimalis). Centropomus mexicanus is treated as a junior synonym of C. parallelus. Six species from the Pacific coast are also tentatively recognized (C. armatus, C. medius, C. nigrescens, C. robalito, C. unionensis, and C. viridis), however further studies on the Pacific species are still needed. Information on type material, diagnosis, distribution, and taxonomic comments are provided for each species. An identification key to the species of Centropomus is presented.},
}
@article {pmid33757039,
year = {2021},
author = {Liu, T and Wang, E and Jiang, Y and Jiang, Z and Jiang, B and Teng, K},
title = {First report of the leaf-mining genus Parornix Spuler from China, with descriptions of two new species (Lepidoptera, Gracillariidae, Parornichinae).},
journal = {Zootaxa},
volume = {4948},
number = {1},
pages = {zootaxa.4948.1.8},
doi = {10.11646/zootaxa.4948.1.8},
pmid = {33757039},
issn = {1175-5334},
mesh = {Animals ; China ; Female ; Genitalia ; *Lepidoptera ; Male ; *Moths/genetics ; Plants ; *Rosaceae ; },
abstract = {The subfamily Parornichinae and thus the genus Parornix Spuler, 1910 are reported for the first time in China. Two new species, P. sinensis Liu, sp. n. feeding on Amygdalus davidiana and P. yuliella Liu Teng, sp. n. on Cerasus japonica, are described herein. Both host plant species belong to Rosaceae. Adult, genitalia of both sexes, and leaf mines are described and illustrated for both species. A Maximum Likelihood tree based on DNA barcodes available for Parornix is also provided for species separation. Reference barcodes for both new species are generated.},
}
@article {pmid33757007,
year = {2021},
author = {Kikuchi, N and Konishi, K},
title = {A taxonomic revision of the genus Linycus Cameron, 1903 from Japan.},
journal = {Zootaxa},
volume = {4948},
number = {4},
pages = {zootaxa.4948.4.3},
doi = {10.11646/zootaxa.4948.4.3},
pmid = {33757007},
issn = {1175-5334},
mesh = {Animals ; *Hymenoptera ; Japan ; },
abstract = {The Japanese species of the genus Linycus Cameron are examined with two species recognized. A Holarctic species, L. exhortator (Fabricius) is newly collected from Japan [Hokkaido, Honshû, Shikoku, Kyûshû], and a new species, L. kyoheii sp. nov., is described from Yamanshi Pref., Honshû. The two Japanese species can be distinguished by a white spot on scutellum (present in L. kyoheii vs. absent in L. exhorator), and sculpture of area between gastrocoeli (weakly rugose-punctate in L. kyoheii vs. clearly rugose in L. exhortator). We also compared the Cytochrome c oxidase subunit I (CO1) of Japanese L. exhortator with European L. exhortator. The p-distances between Japanese and European subspecies exhortator were about 2%, whereas between Japanese and Nearctic ssp. thoracius (Cresson) were about 5%. Here we provisionally treat Japanese L. exhorator as nominotypical subspecies. The intra-specific DNA barcode divergence and allopatric color variations are discussed.},
}
@article {pmid33757003,
year = {2021},
author = {Qi, M and Zuo, X},
title = {A new species of Minooa Yamanaka, 1996 (Lepidoptera, Pyralidae) from Xizang, China.},
journal = {Zootaxa},
volume = {4949},
number = {1},
pages = {zootaxa.4949.1.12},
doi = {10.11646/zootaxa.4949.1.12},
pmid = {33757003},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; China ; Genitalia ; Genitalia, Male ; *Lepidoptera ; Male ; *Moths/genetics ; },
abstract = {A new species of the genus Minooa Yamanaka, 1996 is described from Xizang Autonomous Region, China. Minooa longisacca sp. nov. can be easily distinguished from its congeners in the male genitalia by the sclerotized, short, bifurcated process at the base of the sacculus and the medial ridge connecting the apex of sacculus and base of costa of valva dentate and with a short thorn-like process at apex of ridge. DNA barcodes of all the Chinese species are provided along with illustrations of adult and genitalia and an updated key to all the species of Minooa worldwide.},
}
@article {pmid33756995,
year = {2021},
author = {Fagan-Jeffries, EP and Austin, AD},
title = {Four new species of parasitoid wasp (Hymenoptera: Braconidae) described through a citizen science partnership with schools in regional South Australia.},
journal = {Zootaxa},
volume = {4949},
number = {1},
pages = {zootaxa.4949.1.4},
doi = {10.11646/zootaxa.4949.1.4},
pmid = {33756995},
issn = {1175-5334},
mesh = {Animals ; *Citizen Science ; *Hymenoptera ; Schools ; South Australia ; *Wasps ; },
abstract = {Involving the community in taxonomic research has the potential to increase the awareness, appreciation and value of taxonomy in the public sphere. We report here on a trial citizen science project, Insect Investigators, which partners taxonomists with school students to monitor Malaise traps and prioritise the description of new species collected. In this initial trial, four schools in regional South Australia participated in the program and all collected new species of the braconid subfamily Microgastrinae (Hymenoptera: Braconidae). These four species are here described as new, with the names being chosen in collaboration with the participating school students: Choeras ramcomarmorata Fagan-Jeffries Austin sp. nov., Glyptapanteles drioplanetus Fagan-Jeffries Austin sp. nov., Dolichogenidea franklinharbourensis Fagan-Jeffries Austin sp. nov. and Miropotes waikerieyeties Fagan-Jeffries Austin sp. nov. All four species are diagnosed against the known members of the genera from Australia, New Zealand, Fiji, Samoa and Papua New Guinea, and images and COI DNA barcodes are provided of the holotypes. Students had positive feedback about their experiences of the program, and there is significant potential for it to be expanded and used as a means to connect communities with taxonomic science.},
}
@article {pmid33756956,
year = {2021},
author = {Booysen, R and Haddad, CR},
title = {Revision and molecular phylogeny of the spider genus Micaria Westring, 1851 (Araneae: Gnaphosidae) in the Afrotropical Region.},
journal = {Zootaxa},
volume = {4940},
number = {1},
pages = {zootaxa.4940.1.1},
doi = {10.11646/zootaxa.4940.1.1},
pmid = {33756956},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Bayes Theorem ; Female ; Male ; Phylogeny ; South Africa ; *Spiders/genetics ; },
abstract = {The genus Micaria Westring, 1851 (Araneae, Gnaphosidae) is a group of small (1.85-5 mm) ant-like spiders that can be distinguished from other gnaphosids by their piriform gland spigots that are similar in size to the major ampullate gland spigots. According to the World Spider Catalog, there are 105 species of Micaria in the world, of which only three species are known from the African part of the Afrotropical Region, namely M. chrysis (Simon, 1910), M. tersissima Simon, 1910 and M. beaufortia (Tucker, 1923). The objectives of this study were to revise Micaria in the Afrotropical Region, providing new and updated records for each of the species, evaluating the relationships between them using COI barcoding data, and providing information on their biology, mimetic relationships and feeding ecology. These objectives were met by collecting fresh material from the KwaZulu-Natal, Western Cape, Northern Cape and Free State provinces in South Africa. Fresh material of M. tersissima and M. chrysis were collected from their type localities, Komaggas and Port Nolloth (Northern Cape Province), respectively, for identification and DNA analyses. COI sequences generated, together with those sourced from Barcode of Life Data Systems (BOLD) and GenBank, were aligned using the CulstalW alignment algorithm in the Mega X software, and molecular phylogenetic analyses were performed using MrBayes for Bayesian Inference (BI) and RaxML for maximum likelihood (ML) analyses. Morphological examination of the collected and voucher material yielded 17 new species for the Afrotropical Region, namely M. basaliducta sp. nov. (♀, ♂, South Africa), M. bimaculata sp. nov. (♀, ♂, Mauritania), M. bispicula sp. nov. (♀, ♂, Namibia, South Africa), M. durbana sp. nov. (♀, ♂, South Africa, Zambia), M. felix sp. nov. (♀, ♂, Cameroon, Ethiopia, Malawi, Mozambique, Namibia, South Africa, Zambia, Zimbabwe), M. gagnoa sp. nov. (♀, ♂, Côte d'Ivoire, Mozambique, Mozambique, Tanzania), M. koingnaas sp. nov. (♂, South Africa), M. lata sp. nov. (♂, Namibia, South Africa), M. laxa sp. nov. (♀, South Africa), M. mediospina sp. nov. (♂, South Africa), M. parvotibialis sp. nov. (♀, ♂, Senegal), M. plana sp. nov. (♀, ♂, Ethiopia), M. quadrata sp. nov. (♀, Ethiopia), M. quinquemaculosa sp. nov. (♀, ♂, Namibia, South Africa), M. rivonosy sp. nov. (♀, ♂, Madagascar), M. sanipass sp. nov. (♂, South Africa) and M. scutellata sp. nov. (♂, South Africa). Furthermore, both sexes of M. beaufortia, as well as the male of M. tersissima, are redescribed. Both sexes of M. chrysis are described for the first time, as this species was only known from a juvenile. Of the previously known species, M. beaufortia (Botswana, Ethiopia, Lesotho, Namibia, South Africa, Zimbabwe) and M. chrysis (Côte d'Ivoire, Ethiopia, Lesotho, Namibia, South Africa, Tanzania) are widespread in the Afroptropics, while M. tersissima is only known from South Africa. Both the Bayesian inference and the maximum likelihood analysess recovered Micaria (sensu lato) as monophyletic with the inclusion of the subopaca group. The pulicaria species group was recovered as polyphyletic in both the BI and ML analyses. Four Afrotropical species, as well as the M. rossica Thorell, 1875/M. foxi Gertsch, 1933 group, formed a clade sister to M. formicaria (Sundevall, 1831). Eight of the Afrotropical species now have COI barcoding data uploaded to BOLD.},
}
@article {pmid33756933,
year = {2021},
author = {Pellinen, MJ and Wahlberg, N},
title = {Changes in the genus Beana Walker (Beaninae Zahiri amp; Holloway) with two new species and removing Beana nitida Tams to a new genus Beanoides (gen. nov.).},
journal = {Zootaxa},
volume = {4941},
number = {3},
pages = {zootaxa.4941.3.6},
doi = {10.11646/zootaxa.4941.3.6},
pmid = {33756933},
issn = {1175-5334},
mesh = {Animals ; *Lepidoptera ; },
abstract = {Two new Beana species (B. mutaneni sp. nov and B. penniuncus sp. nov) are described here. Based on molecular data, Beana nitida Tams is removed to its own genus Beanoides gen. nov. and placed in the subfamily Chloephorinae. Morphological characteristics and DNA barcodes are provided for the new species, with a comparison of morphological structures and genetic distances to Beana terminigera Walker. The current number of valid species in the genus is six.},
}
@article {pmid33756930,
year = {2021},
author = {Bahder, BW and Gore-Francis, J and Bartlett, CR},
title = {A new species of planthopper in the genus Patara (Hemiptera: Derbidae) on coconut palm (Cocos nucifera) from the island of Barbuda.},
journal = {Zootaxa},
volume = {4941},
number = {3},
pages = {zootaxa.4941.3.3},
doi = {10.11646/zootaxa.4941.3.3},
pmid = {33756930},
issn = {1175-5334},
mesh = {Animals ; Antigua and Barbuda ; *Cocos ; *Hemiptera/genetics ; Islands ; Phylogeny ; },
abstract = {The island of Barbuda was recently surveyed for the presence of Haplaxius crudus to establish the risk of Lethal Yellowing to palms on the island. After extensive collecting, H. crudus was not found on the island. A new species of Patara Westwood was found on coconut palms on the southwest portion of Barbuda. Herein, we describe the new species as Patara cooki sp. n. and provide DNA sequence data for cytochrome c oxidase subunit I (COI) and 18S genes for it and Patara guttata Westwood. Patara cooki differed from Patara guttata sp. n. by 1.8% for 18S and 7.8% for COI, similar to intrageneric differences reported for other taxa. A phylogenetic analysis of available Otiocerinae near Patara using found Patara cooki sp. n. nested among other Patara species. We also offer commentary regarding the interpretation of forewing venation in Patara.},
}
@article {pmid33756928,
year = {2021},
author = {Huemer, P and VAN Nieukerken, EJ},
title = {Identity of some recently described Lepidoptera from France-re-assessed with DNA barcodes and morphology.},
journal = {Zootaxa},
volume = {4941},
number = {3},
pages = {zootaxa.4941.3.1},
doi = {10.11646/zootaxa.4941.3.1},
pmid = {33756928},
issn = {1175-5334},
mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic ; France ; *Lepidoptera/genetics ; *Moths/genetics ; },
abstract = {Seventy-three species of Lepidoptera described from France since 2000, particularly by Jacques Nel and Thierry Varenne, are re-assessed from largely unpublished molecular data. We tried to obtain DNA barcode sequences from 62 holotypes, supplemented by paratypes of eight species and on one case by non-type material, whereas one previously synonymized species was not sequenced. Altogether we obtained 78 DNA barcode sequences for 65 nominal taxa while sequencing failed for six holotypes. An integrative analysis from molecular data and morphology supports the validity of the majority of species but also resulted in the re-assessment of several taxa. The following 13 new synonymies are established: Stigmella cyrneorolandi Nel Varenne, 2013 syn. nov. of Stigmella rolandi van Nieukerken, 1990; Stigmella thibaulti Varenne Nel, 2019 syn. nov. of Stigmella nivenburgensis (Preissecker, 1942) (Nepticulidae); Nemapogon peslieri Varenne Nel, 2017 syn. nov. of Nemapogon inexpectata Varenne Nel, 2017 (Tineidae); Phyllonorycter acericorsica Varenne Nel, 2015 syn. nov. of Phyllonorycter ochreojunctella (Klimesch, 1942) (Gracillariidae); Ancylis paraobtusana Varenne, Nel, Peslier, 2020 syn. nov. of Ancylis comptana (Frölich, 1828) (Tortricidae); Celypha paludicolella Varenne Nel, 2017 syn. nov. of Celypha doubledayana (Barrett, 1872) (Tortricidae); Cydia oxytropidana Nel Varenne, 2016 syn. nov. of Cydia oxytropidis (Martini, 1912) (Tortricidae); Sorhagenia orocorsa Varenne Nel, 2016 syn. nov. of Sorhagenia janiszewskae Riedl, 1962 (Cosmopterigidae); Chionodes cerdanica Peslier, Nel Varenne, 2020 syn. nov. of Chionodes distinctella (Zeller, 1839) (Gelechiidae); Elachista bidentata Varenne Nel, 2019 syn. nov. of Elachista orstadii Palm, 1943; Elachista karsticola Varenne Nel, 2018 syn. nov. of Elachista maculosella Chrétien, 1896 (Elachistidae); Scythris chablaisensis Delmas, 2018 syn. nov. of Scythris laminella ([Denis Schiffermüller], 1775) (Scythrididae); Epermenia pumila (Buvat Nel, 2000) syn. nov. of Epermenia profugella (Stainton, 1856) (Epermeniidae). Finally, the status of some taxa still remains unclear due to the lack of DNA barcodes of closely related species and the absence of convincing diagnostic characters in morphology.},
}
@article {pmid33756919,
year = {2021},
author = {Tabell, J and Wikström, BO and Mutanen, M and Bruckner, H and Sihvonen, P},
title = {Subspecies of Pleurota bicostella (Clerck, 1759) revisited and descriptions of nine new species in the P. bicostella species group (Lepidoptera: Gelechioidea: Oecophoridae: Pleurotinae).},
journal = {Zootaxa},
volume = {4941},
number = {4},
pages = {zootaxa.4941.4.1},
doi = {10.11646/zootaxa.4941.4.1},
pmid = {33756919},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Female ; Genitalia ; *Lepidoptera ; Male ; *Moths ; },
abstract = {The identities of five subspecies of Pleurota bicostella (Clerck, 1759) are studied, and each is raised from subspecies to species: P. andalusica Back, 1973, stat. nov.; P. aragonella Chrétien, 1925, stat. rev.; P. asiatica Back, 1973, stat. nov.; P. illucidella Chrétien, 1915, stat. rev.; P. lepigrei Lucas, 1937, stat. rev. Nine new Pleurota species which all belong to the P. bicostella species group are described: P. agadirensis Tabell, sp. nov.; P. aprilella Tabell, sp. n.; P. karsholti Tabell, sp. nov.; P. kullbergi Tabell, sp. nov.; P. monochroma Tabell, sp. nov.; P. murina Tabell, sp. nov.; P. paragallicella Tabell, sp. nov; P. phaeolepida Tabell, sp. nov., all from Morocco; and P. dalilae Tabell, sp. nov. from Tunisia. Adult males and females, and their genitalia are illustrated. DNA barcodes of the aforementioned species are compared with those of all other Pleurotinae available to us in the BOLD database. Each of the presented and barcoded species has a unique BIN (Barcode Index Number).},
}
@article {pmid33756910,
year = {2021},
author = {Haddad, CR and Jin, C and Platnick, NI and Booysen, R},
title = {Capobula gen. nov., a new Afrotropical dark sac spider genus related to Orthobula Simon, 1897 (Araneae: Trachelidae).},
journal = {Zootaxa},
volume = {4942},
number = {1},
pages = {zootaxa.4942.1.2},
doi = {10.11646/zootaxa.4942.1.2},
pmid = {33756910},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Female ; Male ; Phylogeny ; South Africa ; *Spiders/genetics ; },
abstract = {A new genus of the spider family Trachelidae L. Koch, 1872 from the Afrotropical Region is described. Capobula gen. nov. is represented by five species, known from South Africa and Lesotho only. Adults of both sexes of Orthobula infima Simon, 1896a, which is widely distributed in the Western Cape, South Africa, are described for the first time, and this species is transferred to Capobula gen. nov. as its type species. Four new species are described: C. capensis spec. nov. and C. neethlingi spec. nov. (South Africa: Western Cape), C. montana spec. nov. (Lesotho and South Africa: Eastern Cape, Free State and KwaZulu-Natal) and C. ukhahlamba spec. nov. (South Africa: KwaZulu-Natal). A phylogenetic analysis based on the cytochrome oxidase subunit I (COI) gene, including 14 genera of Trachelidae, one genus of Clubionidae Wagner, 1887 and three genera of Phrurolithidae Banks, 1892, supports the placement of Capobula gen. nov. in Trachelidae, with Orthobula Simon, 1897 as its likely closest relative.},
}
@article {pmid33756901,
year = {2020},
author = {Makarchenko, EA and Semenchenko, AA and Palatov, DM},
title = {Review of the genus Shilovia Makarchenko (Diptera: Chironomidae: Diamesinae: Boreoheptagyiini) from the mountains of Central Asia, with morphological description and DNA barcoding of known species.},
journal = {Zootaxa},
volume = {4895},
number = {2},
pages = {zootaxa.4895.2.2},
doi = {10.11646/zootaxa.4895.2.2},
pmid = {33756901},
issn = {1175-5334},
mesh = {Animals ; Bayes Theorem ; *Chironomidae/genetics ; DNA Barcoding, Taxonomic ; *Diptera ; Male ; Phylogeny ; },
abstract = {Chironomids of the genus Shilovia Makarchenko (Diamesinae, Boreoheptagyiini) from the mountains of Central Asia are revised using both morphological characters and molecular data. Illustrated descriptions of the adult male Shilovia xinhuawangi sp. nov. from Xinjiang Uygur Autonomous Region of China, S. yakovlevi sp. nov. from East Kazakhstan and redescription of S. rara Makarchenko from Tajikistan and Kyrgyzstan are provided. The result of morphological study is congruent with DNA barcoding analyses using COI sequences. The average K2P interspecific nucleotide distances within S. xinhuawangi sp. nov. and S. yakovlevi sp. nov. are 0.03% and 0.3% respectively. The nucleotide distances between the two new species and S. rara can be considered interspecific. Phylogenetic analysis using Maximum likelihood (ML) and Bayesian inferences (BI) support the placement of S. xinhuawangi sp. nov. and S. yakovlevi sp. nov. within the monophyletic genus Shilovia.},
}
@article {pmid33756873,
year = {2020},
author = {Yakovlev, RV and Shapoval, NA and Ivonin, VV and Knyazev, SA and Kuftina, GN and Masharskiy, AE},
title = {A new species of Carpenter Moths (Lepidoptera, Cossidae) from Tarbagatai (NE Kazakhstan) and Altai (SW Siberia, Russia) Mountains.},
journal = {Zootaxa},
volume = {4896},
number = {1},
pages = {zootaxa.4896.1.3},
doi = {10.11646/zootaxa.4896.1.3},
pmid = {33756873},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Kazakhstan ; *Lepidoptera ; Male ; *Moths/genetics ; Russia ; Siberia ; },
abstract = {We described a new cossid species, Dyspessa ulgen sp. nov. from the Tarbagatai and Altai Mountains and compared it to other taxa of Dyspessa reported from the region (D. tristis, D. saldaitisi, D. saissanica), as well as to morphologically similar D. ulula. The new species is most closely related to D. ulula but differs from the latter in the characteristics of the male genitalia, wing pattern, and molecular data (a 658 bp fragment of the mitochondrial COI gene).},
}
@article {pmid33756863,
year = {2020},
author = {Mukherjee, B and Mukherjee, T and Hazra, N},
title = {A new species of the genus Cryptotendipes Beck et Beck, 1969 (Diptera: Chironomidae) from India, with a world key to the males and tentative phylogenetic relationship.},
journal = {Zootaxa},
volume = {4896},
number = {2},
pages = {zootaxa.4896.2.3},
doi = {10.11646/zootaxa.4896.2.3},
pmid = {33756863},
issn = {1175-5334},
mesh = {Animals ; *Chironomidae/genetics ; *Diptera ; India ; Male ; Phylogeny ; },
abstract = {A new species of the genus Cryptotendipes Beck et Beck is described on the basis of adult male. It is the third species from India and ninth from the Oriental region. The Chinese species, C. nodus Yan, Tang et Wang, 2005 is recorded firstly from India. The molecular barcoding of two species, Cryptotendipes disparilis Pal et Hazra, 2018 and C. nodus is provided. Additional information and revision of two Indian species Cryptotendipes aculeatus Pal et Hazra, 2018 and C. disparilis Pal et Hazra, 2018 are furnished for erroneous description. A tentative cladistic relationship based on the morphological data of adult males and a revised world key to the adult males of the genus Cryptotendipes are also provided.},
}
@article {pmid33756859,
year = {2020},
author = {Samaai, T and Kelly, M and Ngwakum, B and Payne, R and Teske, PR and Janson, L and Kerwath, S and Parker, D and Gibbons, MJ},
title = {New Latrunculiidae (Demospongiae, Poecilosclerida) from the Agulhas ecoregion of temperate southern Africa.},
journal = {Zootaxa},
volume = {4896},
number = {3},
pages = {zootaxa.4896.3.4},
doi = {10.11646/zootaxa.4896.3.4},
pmid = {33756859},
issn = {1175-5334},
mesh = {Africa, Southern ; Animals ; DNA ; *Porifera ; },
abstract = {Sixteen species of Latrunculiidae Topsent, 1922, belonging to the genera Latrunculia du Bocage, 1869, Strongylodesma Lévi, 1969, Cyclacanthia Samaai Kelly, 2004, Samaai Kelly, 2002, are currently known from the temperate waters of South Africa. Extensive new sponge collections from the Amathole region of South Africa revealed the existence of three new species of Tsitsikamma, T. amatholensis sp. nov., T. madiba sp. nov., and T. beukesi sp. nov., and a new species of the endemic South African genus Cyclacanthia, C. rethahofmeyri sp. nov. With the recent addition of two new species of Tsitsikamma from Algoa Bay and Tsitsikamma National Park (T. michaeli Parker-Nance, 2019; T. nguni Parker-Nance, 2019) the total number of known South African Latrunculiidae is now 20 species in four genera. Here we propose two new subgenera of Tsitsikamma, Tsitsikamma Samaai Kelly, 2002 and Clavicaulis subgen. nov., based on the morphological groups "favus" and "pedunculata" hypothesized by Parker-Nance et al. (2019). Species in the nominotypical subgenus Tsitsikamma, containing the type species, are thick encrusting to hemispherical with a rigid honeycombed choanosome, while species in the new subgenus Clavicaulis subgen. nov. have a purse or sac-like morphology with little choanosomal structure. Despite the obvious species-level differences in morphology, multivariate analysis based on spicule measurements (anisostyle length, discorhabd length, shaft and whorl length) was not able to distinguish between the proposed Tsitsikamma species, but separated known species T. favus Samaai Kelly, 2002, T. pedunculata Samaai Kelly, 2003, and T. scurra Samaai Kelly, 2003, from each other. Similarly, DNA barcoding of the mitochondrial COI and the nuclear ITS of Tsitsikamma specimens failed to clearly differentiate between species, but was able to differentiate sister taxon relationships within the Latrunculiidae.},
}
@article {pmid33756834,
year = {2020},
author = {Magalhaes, ILF and Stockmann, M and Marusik, YM and Zonstein, SL},
title = {On Sahastata (Araneae: Filistatidae): complementary description of the generotype and two new species from Oman and Morocco.},
journal = {Zootaxa},
volume = {4899},
number = {1},
pages = {zootaxa.4899.1.12},
doi = {10.11646/zootaxa.4899.1.12},
pmid = {33756834},
issn = {1175-5334},
mesh = {Animals ; Male ; Morocco ; Oman ; *Spiders/genetics ; },
abstract = {The Filistatinae genus Sahastata Benoit, 1968 is distributed in arid and semi-arid areas, from westernmost Sahara to India, and includes seven known species. Four of these are only known from one sex, including Sahastata nigra (Simon, 1897), the type species. Here we present the first description of a male of this species collected near the type locality in Muscat, Oman. Additionally, two new species are described: S. wunderlichi sp. nov. (♂♀, Morocco) and S. wesolowskae sp. nov. (♂♀, Oman). Sahastata infuscata (Kulczyński, 1901) is newly recorded from Kenya and Yemen and S. nigra is newly recorded from the United Arab Emirates. DNA barcodes are given for S. nigra and the two new species. We observed some details of the life cycle of three Sahastata species, including clutch size, time to maturation, and a biased sex ratio for individuals raised from egg sacs, indicating that only 20-25% of specimens reaching adulthood are males. We provide SEM images of spiders of this genus, some observations on the morphology of spinnerets and male palps, and a distribution map of the species included in the genus.},
}
@article {pmid33756762,
year = {2021},
author = {Srinivasan, P and Sivaruban, T and Barathy, S and Malzacher, P and Isack, R},
title = {A new charismatic Caenis Stephens, 1835 (Ephemeroptera: Caenidae) from Southern India.},
journal = {Zootaxa},
volume = {4926},
number = {1},
pages = {zootaxa.4926.1.7},
doi = {10.11646/zootaxa.4926.1.7},
pmid = {33756762},
issn = {1175-5334},
mesh = {Animals ; *Ephemeroptera ; Female ; India ; Larva ; Male ; Parthenogenesis ; Phylogeny ; },
abstract = {Caenis americani sp. nov. is described based on larvae and female imagoes from the Mangalamkombu stream of Southern India. Caenis americani is most likely a parthenogenetic species, in the light of the fact that only females have been collected. The larva can be distinguished from other species of Caenis by the i) shape of the sternum IX and its shagreen field, ii) shape and denticulation of hind claws and iii) lateral lobes of mesonotum distinctly bulged. The phylogenetic relationships of the new species remain unknown, as molecular records of Caenis throughout the Oriental region are largely unknown, and the taxonomically important males are absent.},
}
@article {pmid33756760,
year = {2021},
author = {Sidharthan, A and Raghavan, R and Anoop, VK and Keskar, A and Dahanukar, N},
title = {Phylogenetic position and relationships of mountain loaches (Teleostei: Balitoridae) of the Western Ghats as revealed by CO1 sequences.},
journal = {Zootaxa},
volume = {4926},
number = {1},
pages = {zootaxa.4926.1.5},
doi = {10.11646/zootaxa.4926.1.5},
pmid = {33756760},
issn = {1175-5334},
mesh = {Animals ; Biological Evolution ; *Cypriniformes/genetics ; Phylogeny ; },
abstract = {The teleostean family Balitoridae comprises small-sized freshwater fishes adapted to swift-flowing torrential mountain streams in South and South-East Asia. Little is known about their molecular phylogenetics and evolutionary biogeography, and much of the scientific literature that references them is focused on morphological taxonomy. In this paper, we generate CO1 sequences for the endemic balitorid lineages of the Western Ghats (WG) Hotspot in India, particularly for the endemic genera, Bhavania, Ghatsa and Travancoria. Integration of these data into a phylogeny revealed that the endemic WG genera together form a well-supported monophyletic clade that shows, subject to our limited taxon sampling, a sister-group relationship to the Southeast Asian genus Pseudohomaloptera. Three WG endemic species of the genus Balitora, namely B. chipkali, B. jalpalli and B. laticauda, though morphologically distinct, have low genetic divergence and barcode gap, suggestive of recent speciation. Interestingly, a fourth WG endemic, B. mysorensis, formed a clade with two species of Balitora from Eastern-Himalaya and Indo-Burma. We also show that all available CO1 sequences assigned to WG endemic balitorid genera in GenBank are misidentifications, and provide diagnostic characters for the accurate identification of these taxa in the future.},
}
@article {pmid33756740,
year = {2021},
author = {Henry, SC and Cameron, SL and Smolenski, A and McQuillan, P},
title = {Polyzosteria cockroaches in Tasmania (Blattodea: Blattidae: Polyzosteriinae) represent a new, endemic species, with allopatric alpine and coastal sub-populations.},
journal = {Zootaxa},
volume = {4926},
number = {3},
pages = {zootaxa.4926.3.4},
doi = {10.11646/zootaxa.4926.3.4},
pmid = {33756740},
issn = {1175-5334},
mesh = {Animals ; Australia ; *Cockroaches ; Tasmania ; },
abstract = {We describe the endemic Tasmanian cockroach, Polyzosteria yingina sp. nov. (Henry), 78 years after it was first documented. Evidence from morphology, biogeography and CO1 barcodes is used to distinguish this species from related mainland Australian taxa it has previously been confused with. Polyzosteria yingina sp. nov. has two strongly allopatric populations: a compact alpine population above 1000m and a dispersed east coastal one at sealevel. However, mitochondrial Control Region D-loop molecular analysis suggests a single species identity for these disparate populations. Detailed internal and external morphological descriptions and photographs of living and preserved type material are presented. We also speculate on some hypotheses which could account for the unusual distribution of this charismatic insect.},
}
@article {pmid33756731,
year = {2021},
author = {Zhang, AO and Zhou, X},
title = {The larvae of Chinese Hydropsychidae (Insecta: Trichoptera), Part II: Potamyia chinensis and Cheumatopsyche trifascia.},
journal = {Zootaxa},
volume = {4926},
number = {4},
pages = {zootaxa.4926.4.5},
doi = {10.11646/zootaxa.4926.4.5},
pmid = {33756731},
issn = {1175-5334},
mesh = {Animals ; China ; *Holometabola ; *Insecta ; Larva ; },
abstract = {The larvae of Chinese caddisflies Potamyia chinensis and Cheumatopsyche trifascia were successfully associated with identifiable adults using independent DNA markers, mitochondrial COI barcodes and nuclear ribosomal 28S D2 genes. A total of 49 specimens collected in China were employed in the molecular analyses. The two markers were congruent on species boundaries for 11 distinctive haplogroups, while D2 failed in differentiating two closely related species. A brief summary for larval studies of both genera is given, followed by an introduction to the generic morphological characteristics, and detailed morphological descriptions and illustrations for the two successfully associated species. The larva of P. chinensis is re-described here based on Chinese materials, following the previous larval description for P. echigoensis, which was recently synonymized with P. chinensis.},
}
@article {pmid33756723,
year = {2021},
author = {Saldaitis, A and Volynkin, AV and Zahiri, R},
title = {Lasianobia nainysi, a new species from Sichuan, China (Lepidoptera, Noctuidae, Noctuinae).},
journal = {Zootaxa},
volume = {4927},
number = {1},
pages = {zootaxa.4927.1.7},
doi = {10.11646/zootaxa.4927.1.7},
pmid = {33756723},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; China ; Female ; *Lepidoptera ; Male ; *Moths/genetics ; },
abstract = {A new species of the genus Lasianobia Hampson, 1905, Lasianobia nainysi Saldaitis, Volynkin Zahiri, sp. nov. is described from highlands of western Sichuan Province of China. The new species is closely related to Lasianobia albilinea (Draudt, 1950). Adults, male and female genitalia as well as DNA barcode data of the new and related species are presented.},
}
@article {pmid33756722,
year = {2021},
author = {Laguerre, M and Vincentcent, B},
title = {Pairing of two highly sexually dimorphic species within the genus Lophocampa Harris, 1841 (Lepidoptera: Erebidae: Arctiini).},
journal = {Zootaxa},
volume = {4927},
number = {1},
pages = {zootaxa.4927.1.6},
doi = {10.11646/zootaxa.4927.1.6},
pmid = {33756722},
issn = {1175-5334},
mesh = {Animals ; Female ; *Lepidoptera ; Male ; *Moths/genetics ; },
abstract = {Two Lophocampa species previously known only by females are paired with morphologically highly different male specimens. This pairing was initiated after the discovery of a mosaic gynandromorph specimen and then confirmed using the mitochondrial COI gene (the so-called DNA barcode). Following the discovery of a labeling error by Rothschild during the original description of two species, two recombinations are proposed. Pairs for each species are illustrated and the male specimens are described for the first time.},
}
@article {pmid33756720,
year = {2021},
author = {Lo, YY and Cheng, RC and Lin, CP},
title = {Species delimitation and taxonomic revision of Oxyopes (Araneae: Oxyopidae) of Taiwan, with description of two new species.},
journal = {Zootaxa},
volume = {4927},
number = {1},
pages = {zootaxa.4927.1.4},
doi = {10.11646/zootaxa.4927.1.4},
pmid = {33756720},
issn = {1175-5334},
mesh = {Animals ; Bayes Theorem ; *DNA Barcoding, Taxonomic ; Phylogeny ; *Spiders/genetics ; Taiwan ; },
abstract = {This study revised the spider genus Oxyopes Latreille, 1804 in Taiwan and delineated the species boundaries based on morphological and molecular characters. A total of seven Oxyopes spiders were recognized, including two newly described species, O. hasta sp. nov. and O. taiwanensis sp. nov. Oxyopes fujianicus Song Zhu 1993 from Yilan County, Nantou County, and Kaohsuing City, and O. striagatus Song 1999 from New Taipei City, Taichung City, Nantou County, and Kaohsiung City were recorded for the first time in Taiwan. An identification key and a distributional map of Taiwanese Oxyopes species were provided. Partial COI sequences were obtained for molecular phylogenetic and species delimitation analyses. Maximum likelihood and Bayesian phylogenies, and DNA barcoding gap analysis supported morphologically defined species. However, molecular species delimitation based on Automatic Barcode Gap Discovery (ABGD), PID (Liberal), and generalized mixed Yule coalescent (GMYC) were incongruent in species assignment. The results showed that the interspecific genetic divergence between O. sertatus and O. taiwanensis was relatively low (1.28 ± 0.43%), and the intraspecific genetic divergence of O. striagatus was relatively high (1.69 ± 0.35%). Ecological data, additional samples and genetic loci are required to further examine the level of reproductive isolation and patterns of population genetic structure in Taiwanese Oxyopes.},
}
@article {pmid33756717,
year = {2021},
author = {Michalova, P and Lencioni, V and Nenov, M and Nikolov, S},
title = {Can DNA barcoding be used to identify closely related Clunio Haliday, 1855 species (Diptera: Chironomidae, Orthocladiinae)?.},
journal = {Zootaxa},
volume = {4927},
number = {1},
pages = {zootaxa.4927.1.1},
doi = {10.11646/zootaxa.4927.1.1},
pmid = {33756717},
issn = {1175-5334},
mesh = {Animals ; *Chironomidae/genetics ; DNA ; DNA Barcoding, Taxonomic ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {DNA barcoding based on a fragment of mitochondrial Cytochrome C Oxidase subunit 1 gene (COI) was applied to the two chironomids Clunio balticus Heimbach (690 base pairs) and C. ponticus Michailova (691 base pairs). The two species differed by one deletion in the nucleotide sequence Adenine. However, the 658-nucleotide long sequences of DNA from the mitochondrial Cytochrome C Oxidase subunit 1 gene (COI) of C. balticus and C. ponticus were identical upon comparison. Further, they compared with homologous sequences for C. marinus Holiday and C. tsushimensis Tokunaga from the Barcode of Life (BOLD) database and the results plotted as a weighted graph, where C. tsushimensis, C. marinus and C. balticus C. ponticus formed three almost equidistant groups. From this, we established that the genetic distance between the respective COI sequences of C. balticus and C. ponticus is minimal, indicating a close relationship between the species indicative of recent common origin. However, the comparative analysis between C. tsushimensis, C. marinus, C. balticus and C. ponticus showed a wider divergence in their respective nucleotide sequences. Overall, our results emphasized that the COI region does not work well as a DNA barcode to identify species within the Clunio genus. Either longer sequences or a multifaceted methodological approach, including morphology, cytogenetic and ecology is needed to distinguish some members of Clunio genus.},
}
@article {pmid33756706,
year = {2021},
author = {Salmela, J and Härmä, O and Taylor, DJ},
title = {Chaoborus flavicans Meigen (Diptera, Chaoboridae) is a complex of lake and pond dwelling species: a revision.},
journal = {Zootaxa},
volume = {4927},
number = {2},
pages = {zootaxa.4927.2.1},
doi = {10.11646/zootaxa.4927.2.1},
pmid = {33756706},
issn = {1175-5334},
mesh = {Animals ; *Diptera ; Lakes ; Larva ; Ponds ; },
abstract = {Chaoborus flavicans (Meigen) is a widespread and much studied lacustrine phantom midge. As larvae, these insects are important aquatic predators. Based on the available type material, morphology of immature stages and adults, their aquatic habitat, and DNA barcodes, C. flavicans is shown to be a composite of at least four species, with three of these named here. Chaoborus flavicans is primarily a lake-dwelling species with a Holarctic range. Chaoborus albipes (Johannsen, 1903 stat. rev.) and C. posio Salmela sp. n. are pond-dwelling Holarctic and north European species, respectively. The position of the larval subordinate mandibular tooth at the vertex of the second and fourth teeth is a synapomorphy of the Chaoborus flavicans species complex. We present an identification key to fourth instar larvae, pupae, and adult males. We also designate the lectotype and paralectotypes of Sayomyia rotundifolia Felt, 1904 (syn. nov. of C. albipes). We hypothesize that a fourth species of the species complex is present in Japan. Our revision indicates that Holarctic shallow ponds contain a hidden diversity of predators (C. albipes and C. posio sp. n.).},
}
@article {pmid33756692,
year = {2021},
author = {Timossi, G and Huemer, P},
title = {Megacraspedus laseni sp. nov. (Lepidoptera: Gelechiidae) from the Dolomites of north-eastern Italy.},
journal = {Zootaxa},
volume = {4927},
number = {4},
pages = {zootaxa.4927.4.6},
doi = {10.11646/zootaxa.4927.4.6},
pmid = {33756692},
issn = {1175-5334},
mesh = {Animals ; Calcium Carbonate ; Female ; Genitalia, Male ; Italy ; *Lepidoptera ; Magnesium ; Male ; *Moths/genetics ; },
abstract = {Megacraspedus laseni sp. nov. is described from Dolomiti Bellunesi (Veneto Region, Prov. Belluno, Italy). The habitus of the adult and male genitalia are described and illustrated whereas the female sex remains unknown. The new species belongs to the Megacraspedus pentheres species group and is closely related to the southern alpine M. eburnellus Huemer Karsholt, 2001 from which it differs in morphological characters and in DNA barcode sequence. Megacraspedus carolustertius Gastón Vives, 2020 is synonymized with M. quadristictus Lhomme, 1946, syn. nov.},
}
@article {pmid33756679,
year = {2021},
author = {DE Wolf, K and Vanderheyden, A and Deblauwe, I and Smitz, N and Gombeer, S and Vanslembrouck, A and Meganck, K and Dekoninck, W and DE Meyer, M and Backeljau, T and Müller, R and VAN Bortel, W},
title = {First record of the West Nile virus bridge vector Culex modestus Ficalbi (Diptera: Culicidae) in Belgium, validated by DNA barcoding.},
journal = {Zootaxa},
volume = {4920},
number = {1},
pages = {zootaxa.4920.1.7},
doi = {10.11646/zootaxa.4920.1.7},
pmid = {33756679},
issn = {1175-5334},
mesh = {Animals ; Belgium ; *Culex/genetics ; *Culicidae ; DNA ; DNA Barcoding, Taxonomic ; Mosquito Vectors/genetics ; *West Nile virus/genetics ; },
abstract = {A thorough knowledge of the presence and spatio-temporal distribution patterns of vector species are pivotal to assess the risk of mosquito-borne diseases in Europe. In 2018, a Culex larva was collected during routine monitoring activities to intercept exotic Aedes mosquito species in the port of Antwerp (Kallo, Belgium). The larva, collected from a pond in mid-September, was morphologically identified as Culex modestus, and this identification was subsequently confirmed by COI barcoding. It is the first confirmed record of this West Nile virus bridge vector in Belgium. The present study also demonstrates the value of DNA-based identification techniques to validate the presence of potential vector species.},
}
@article {pmid33756678,
year = {2021},
author = {Yu, T and Gao, L and Kallies, A and Arita, Y and Wang, M},
title = {A new species of the genus Paranthrenella Strand, 1916 (Lepidoptera: Sesiidae) from China.},
journal = {Zootaxa},
volume = {4920},
number = {1},
pages = {zootaxa.4920.1.6},
doi = {10.11646/zootaxa.4920.1.6},
pmid = {33756678},
issn = {1175-5334},
mesh = {Animals ; China ; *Cinnamomum ; Genitalia ; *Lauraceae ; *Lepidoptera ; *Moths/genetics ; Trees ; },
abstract = {A new clearwing moth, Paranthrenella cinnamoma sp. nov., is described from southern China. Adults and genitalia are illustrated, DNA barcodes provided, and potential damage to Cinnamomum trees (Lauraceae) is described. Paranthrenella mushana (Matsumura, 1931) comb. nov. is transferred from Synanthedon Hübner, [1819]. A checklist of the species of Paranthrenella Strand, 1916 of China is provided.},
}
@article {pmid33756646,
year = {2021},
author = {Nada, B and Ballantyne, LA and Jusoh, WFA},
title = {Description of the larva of a firefly species, Pygoluciola dunguna Nada (Coleoptera: Lampyridae).},
journal = {Zootaxa},
volume = {4920},
number = {4},
pages = {zootaxa.4920.4.4},
doi = {10.11646/zootaxa.4920.4.4},
pmid = {33756646},
issn = {1175-5334},
mesh = {Animals ; *Coleoptera/genetics ; Ecosystem ; Female ; *Fireflies ; Larva ; Male ; },
abstract = {Pygoluciola dunguna Nada, 2018 was described from Peninsular Malaysia, using males and reliably associated females. This paper details description of the larva which has been conclusively identified as Pygoluciola dunguna based on DNA barcoding technique and uses morphology, brief habitat and behavioural data. A total of 70 larval specimens were measured and their main features described. The larvae exhibit a riparian or semi-aquatic behaviour, observed crawling on the sandy edge of shallow streams. The stake-like projections along the length of the body suggest a form of defensive mechanism from falling prey to aquatic predators.},
}
@article {pmid33756637,
year = {2021},
author = {Weinzierl, A and Malicky, H and Waringer, J},
title = {The larva of Rhyacophila albardana McLachlan 1879, including a discriminatory matrix to the Rhyacophila larvae with comb-shaped gills of Austria, Germany and Switzerland (Rhyacophilidae, Trichoptera).},
journal = {Zootaxa},
volume = {4908},
number = {1},
pages = {zootaxa.4908.1.9},
doi = {10.11646/zootaxa.4908.1.9},
pmid = {33756637},
issn = {1175-5334},
mesh = {Animals ; Austria ; Germany ; *Gills ; *Insecta ; Larva ; Switzerland ; },
abstract = {Final instar larvae collected in the Rißbach (Isar catchment, Bavaria) were positively associated with adults of Rhyacophila albardana by barcoding; final instar larvae and adults of this species also were collected at the same time and site in the Lech River (Austria) in the absence of confusing species. These collections and associations enabled a description of the hitherto unknown larva of this species. We present information on the morphology of the larva and illustrate the most important diagnostic features. This dataset is included in a discriminatory matrix of the other larvae with comb-shaped gills (Rhyacophila Hyperrhyacophila Group) known so far from Austria, Germany, and Switzerland. Species can be separated by coloration patterns of the head and prosternum morphology. Rhyacophila albardana is known from Austria, France, Germany, Italy, and Switzerland (Neu et al. 2018).},
}
@article {pmid33756587,
year = {2021},
author = {Álvarez, Y and Núñez, R},
title = {A new subspecies of Calisto disjunctus Núñez amp; Barro (Lepidoptera: Nymphalidae: Satyrinae) from Western Cuba, with a key to the Cuban members of the genus.},
journal = {Zootaxa},
volume = {4915},
number = {1},
pages = {zootaxa.4915.1.7},
doi = {10.11646/zootaxa.4915.1.7},
pmid = {33756587},
issn = {1175-5334},
mesh = {Animals ; *Butterflies ; Cuba ; },
abstract = {Calisto disjunctus hersheyi ssp. n. is described from western Cuba. Additionally, a dichotomous key including all described Cuban taxa of the herophile species group of Calisto is given together with illustrations of live specimens of most taxa.},
}
@article {pmid33756569,
year = {2021},
author = {Shashank, PR and Singh, N and Harshana, A and Sinha, T and Kirichenko, N},
title = {First report of the poplar leaf miner, Phyllonorycter populifoliella (Treitschke) (Lepidoptera: Gracillariidae) from India.},
journal = {Zootaxa},
volume = {4915},
number = {3},
pages = {zootaxa.4915.3.11},
doi = {10.11646/zootaxa.4915.3.11},
pmid = {33756569},
issn = {1175-5334},
mesh = {Animals ; Female ; India ; *Lepidoptera ; Male ; *Moths ; *Populus ; },
abstract = {Here we report about the discovery of the poplar leaf miner, Phyllonorycter populifoliella (Treitschke) in India. The mines of this micromoth were found in noticeable density on the leaves of poplar, Populus sp. (Salicaceae) in the northern mountainous region Ladakh in 2017-2018. We provide short morphological diagnosis, describe bionomics and analyze molecular data of Ph. populifoliella from India comparing sequences with those from other countries in Eurasia where the species is known as native. We also illustrate male and female genitalia, an adult of the moth, the leaf mines and the infestation plot in Ladakh, and discuss the occurrence of the species in the country.},
}
@article {pmid33754638,
year = {2021},
author = {Pedersen, CA and Schneider, PJ and Ganio, MC and Scheckelhoff, DJ},
title = {ASHP national survey of pharmacy practice in hospital settings: Dispensing and administration-2020.},
journal = {American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists},
volume = {78},
number = {12},
pages = {1074-1093},
doi = {10.1093/ajhp/zxab120},
pmid = {33754638},
issn = {1535-2900},
mesh = {Child ; Hospitals ; Humans ; Medication Systems, Hospital ; Pharmacists ; *Pharmacy ; *Pharmacy Service, Hospital ; Surveys and Questionnaires ; United States ; },
abstract = {PURPOSE: Results of the 2020 ASHP national survey of pharmacy practice in hospital settings are presented.<br><br>METHODS: Pharmacy directors at 1,437 general and children's medical/surgical hospitals in the United States were surveyed using a mixed-mode method of contact by email and mail. Survey completion was online. IQVIA supplied data on hospital characteristics; the survey sample was drawn from the IQVIA hospital database.<br><br>RESULTS: The response rate was 18.7%. Almost all hospitals (92.5%) have a method for pharmacists to review medication orders on demand. Most hospitals (74.5%) use automated dispensing cabinets (ADCs) as their primary method for drug distribution. A third of hospitals use barcodes to verify doses during dispensing in the pharmacy and to verify ingredients when intravenous medications are compounded. More than 80% scan barcodes when restocking ADCs. Sterile workflow management technology is used in 21.3% of hospitals. Almost three-quarters of hospitals outsource some sterile preparations. Pharmacists can independently prescribe in 21.1% of hospitals. Pharmacist practice in ambulatory clinics in 46.2% of health systems and provide telepharmacy services in 28.4% of health systems.<br><br>CONCLUSION: Pharmacists continue their responsibility in their traditional role in preparation and dispensing of medications. They have successfully employed technology to improve safety and efficiency in performance of these duties and have employed emerging technologies to improve the safety, timeliness, and efficiency of the administration of drugs to patients. As pharmacists continue to expand their role to all aspects of medication use, new opportunities highlighted in ASHP's Practice Advancement Initiative 2030 have been identified.},
}
@article {pmid33754469,
year = {2021},
author = {Clemmensen, KE and Durling, MB and Michelsen, A and Hallin, S and Finlay, RD and Lindahl, BD},
title = {A tipping point in carbon storage when forest expands into tundra is related to mycorrhizal recycling of nitrogen.},
journal = {Ecology letters},
volume = {24},
number = {6},
pages = {1193-1204},
doi = {10.1111/ele.13735},
pmid = {33754469},
issn = {1461-0248},
support = {2011-1747//Swedish Research Council Formas/ ; 2013-655//Swedish Research Council Formas/ ; 221056//Marie Curie Intra European Fellowship within the 7th European Community Framework Programme/ ; },
mesh = {Arctic Regions ; *Carbon ; Ecosystem ; Forests ; *Mycorrhizae ; Nitrogen ; Soil ; Tundra ; },
abstract = {Tundra ecosystems are global belowground sinks for atmospheric CO2 . Ongoing warming-induced encroachment by shrubs and trees risks turning this sink into a CO2 source, resulting in a positive feedback on climate warming. To advance mechanistic understanding of how shifts in mycorrhizal types affect long-term carbon (C) and nitrogen (N) stocks, we studied small-scale soil depth profiles of fungal communities and C-N dynamics across a subarctic-alpine forest-heath vegetation gradient. Belowground organic stocks decreased abruptly at the transition from heath to forest, linked to the presence of certain tree-associated ectomycorrhizal fungi that contribute to decomposition when mining N from organic matter. In contrast, ericoid mycorrhizal plants and fungi were associated with organic matter accumulation and slow decomposition. If climatic controls on arctic-alpine forest lines are relaxed, increased decomposition will likely outbalance increased plant productivity, decreasing the overall C sink capacity of displaced tundra.},
}
@article {pmid33750912,
year = {2021},
author = {Dincă, V and Dapporto, L and Somervuo, P and Vodă, R and Cuvelier, S and Gascoigne-Pees, M and Huemer, P and Mutanen, M and Hebert, PDN and Vila, R},
title = {High resolution DNA barcode library for European butterflies reveals continental patterns of mitochondrial genetic diversity.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {315},
pmid = {33750912},
issn = {2399-3642},
mesh = {Animals ; Butterflies/classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Europe ; *Gene Library ; *Genetic Variation ; Haplotypes ; Species Specificity ; },
abstract = {The study of global biodiversity will greatly benefit from access to comprehensive DNA barcode libraries at continental scale, but such datasets are still very rare. Here, we assemble the first high-resolution reference library for European butterflies that provides 97% taxon coverage (459 species) and 22,306 COI sequences. We estimate that we captured 62% of the total haplotype diversity and show that most species possess a few very common haplotypes and many rare ones. Specimens in the dataset have an average 95.3% probability of being correctly identified. Mitochondrial diversity displayed elevated haplotype richness in southern European refugia, establishing the generality of this key biogeographic pattern for an entire taxonomic group. Fifteen percent of the species are involved in barcode sharing, but two thirds of these cases may reflect the need for further taxonomic research. This dataset provides a unique resource for conservation and for studying evolutionary processes, cryptic species, phylogeography, and ecology.},
}
@article {pmid33749162,
year = {2021},
author = {Jones, L and Twyford, AD and Ford, CR and Rich, TCG and Davies, H and Forrest, LL and Hart, ML and McHaffie, H and Brown, MR and Hollingsworth, PM and de Vere, N},
title = {Barcode UK: A complete DNA barcoding resource for the flowering plants and conifers of the United Kingdom.},
journal = {Molecular ecology resources},
volume = {21},
number = {6},
pages = {2050-2062},
doi = {10.1111/1755-0998.13388},
pmid = {33749162},
issn = {1755-0998},
support = {//Welsh Government's Enabling Natural Resources and Well-being in Wales Grants/ ; //Welsh Government Rural Communities - Rural Development Programme 2014-2020, which is funded by the European Agricultural Fund for Rural Development and the Welsh Government/ ; },
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; *Magnoliopsida/classification/genetics ; *Tracheophyta/classification/genetics ; United Kingdom ; },
abstract = {DNA barcoding and metabarcoding provide new avenues for investigating biological systems. These techniques require well-curated reference libraries with extensive coverage. Generating an exhaustive national DNA barcode reference library can open up new avenues of research in ecology, evolution and conservation, yet few studies to date have created such a resource. In plant DNA barcoding, herbarium collections provide taxonomically robust material but also pose challenges in lab processing. Here, we present a national DNA barcoding resource covering all of the native flowering plants and conifers of the United Kingdom. This represents 1,482 plant species, with the majority of specimens (81%) sourced from herbaria. Using Sanger sequencing of the plant DNA barcode markers, rbcL, matK, and ITS2, at least one DNA barcode was retrieved from 98% of the UK flora. We sampled from multiple individuals, resulting in a species coverage for rbcL of 96% (4,477 sequences), 90% for matK (3,259 sequences) and 75% for ITS2 (2,585 sequences). Sequence recovery was lower for herbarium material compared to fresh collections, with the age of the specimen having a significant effect on the success of sequence recovery. Species level discrimination was highest with ITS2, however, the ability to successfully retrieve a sequence was lowest for this region. Analyses of the genetic distinctiveness of species across a complete flora showed DNA barcoding to be informative for all but the most taxonomically complex groups. The UK flora DNA barcode reference library provides an important resource for many applications that require plant identification from DNA.},
}
@article {pmid33749132,
year = {2021},
author = {Nugent, CM and Elliott, TA and Ratnasingham, S and Hebert, PDN and Adamowicz, SJ},
title = {Debar: A sequence-by-sequence denoiser for COI-5P DNA barcode data.},
journal = {Molecular ecology resources},
volume = {21},
number = {8},
pages = {2832-2846},
doi = {10.1111/1755-0998.13384},
pmid = {33749132},
issn = {1755-0998},
support = {//Ontario Ministry of Economic Development, Job Creation and Trade/ ; },
mesh = {Animals ; *Biodiversity ; DNA ; *DNA Barcoding, Taxonomic ; High-Throughput Nucleotide Sequencing ; Phylogeny ; },
abstract = {DNA barcoding and metabarcoding are now widely used to advance species discovery and biodiversity assessments. High-throughput sequencing (HTS) has expanded the volume and scope of these analyses, but elevated error rates introduce noise into sequence records that can inflate estimates of biodiversity. Denoising -the separation of biological signal from instrument (technical) noise-of barcode and metabarcode data currently employs abundance-based methods which do not capitalize on the highly conserved structure of the cytochrome c oxidase subunit I (COI) region employed as the animal barcode. This manuscript introduces debar, an R package that utilizes a profile hidden Markov model to denoise indel errors in COI sequences introduced by instrument error. In silico studies demonstrated that debar recognized 95% of artificially introduced indels in COI sequences. When applied to real-world data, debar reduced indel errors in circular consensus sequences obtained with the Sequel platform by 75%, and those generated on the Ion Torrent S5 by 94%. The false correction rate was less than 0.1%, indicating that debar is receptive to the majority of true COI variation in the animal kingdom. In conclusion, the debar package improves DNA barcode and metabarcode workflows by aiding the generation of more accurate sequences aiding the characterization of species diversity.},
}
@article {pmid33749016,
year = {2021},
author = {Elkinton, JS and Boettner, GH and Broadley, HJ},
title = {Successful biological control of winter moth, Operophtera brumata, in the northeastern United States.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {31},
number = {5},
pages = {e02326},
doi = {10.1002/eap.2326},
pmid = {33749016},
issn = {1051-0761},
mesh = {Animals ; Europe ; Humans ; Massachusetts ; *Moths ; New England ; Seasons ; },
abstract = {Winter moth, Operophtera brumata, native to Europe, invaded the northeastern United States in the late 1990s, where it caused widespread defoliation of forests and shade trees ranging from 2,266 to 36,360 ha/yr between 2003 and 2015 in Massachusetts. In 2005, we initiated a biological control effort based on the specialist tachinid parasitoid Cyzenis albicans, which had previously been introduced along with the generalist ichneumonid parasitoid Agrypon flaveolatum to control winter moth in Nova Scotia in the 1950s and British Columbia in the 1970s. Due to concerns of possible non-target impacts by A. flaveolatum, we focused entirely on the specialist C. albicans. Each year for 14 yr, we collected several thousand individuals of C. albicans from British Columbia and released them in widely spaced sites in the northeastern United States. As of 2020, we had established C. albicans at 41 of 44 sites from coastal Maine to southeastern Connecticut. By 2016, winter moth densities (pupae/m[2]) had declined from 100-500 to 0-10 pupae/m[2] at six release sites at least 10 km apart and this was coincident with the onset of 10-40% parasitism. At one site in Wellesley, Massachusetts, the decline occurred in 2012 and winter moth densities have remained low for seven subsequent years. Defoliation in Massachusetts has been reduced to undetectable levels by aerial survey since 2016. DNA sequencing of the barcoding region of the mitochondrial gene CO1 confirmed that all C. albicans reared from winter moth matched the C. albicans collected from Vancouver Island and were distinct from parasitic flies (presumably a native species) reared from a native congener of winter moth, Bruce spanworm (O. bruceata). Successful establishment of C. albicans on winter moth represents a rare, if not the only, example of the biological control of a major forest defoliator that attacks a wide range of tree species anywhere in the world by the establishment of a single specialist natural enemy.},
}
@article {pmid33742406,
year = {2021},
author = {Dujardin, P and Grüner, BM},
title = {Barcoding Technology for Multiplexed Analysis of Metastatic Ability In Vivo.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2294},
number = {},
pages = {239-251},
pmid = {33742406},
issn = {1940-6029},
mesh = {Animals ; Cell Line, Tumor ; Drug Screening Assays, Antitumor/*methods ; HEK293 Cells ; High-Throughput Screening Assays/*methods ; Humans ; Mice ; Multiplex Polymerase Chain Reaction/*methods ; Neoplasm Metastasis ; Neoplasms/drug therapy/*genetics/pathology ; RNA-Seq/*methods ; },
abstract = {DNA barcoding allows the quantitative, biomarker-free tracking of individual cell populations in mixed/heterogeneous cell pools. Here, we describe a multiplexed in vivo screening platform based on DNA barcoding technology to interrogate compound libraries for their effect on metastatic seeding in vivo. We apply next-generation sequencing (NGS) technology to quantitatively analyze high-throughput compound screening in mice. Up to 96 compounds and controls can be screened for their effect on metastatic ability in a single mouse.},
}
@article {pmid33742356,
year = {2021},
author = {Amer, MA},
title = {DNA barcoding of the spider crab Menaethius monoceros (Latreille, 1825) from the Red Sea, Egypt.},
journal = {Journal, genetic engineering &amp; biotechnology},
volume = {19},
number = {1},
pages = {42},
pmid = {33742356},
issn = {2090-5920},
support = {331946//Cultural Affairs and Missions Sector, Ministry of Higher Education/ ; },
abstract = {BACKGROUND: Most spider crab species inhabiting the Red Sea have not been characterized genetically, in addition to the variation and complexity of morphological identification of some cryptic species. The present study was conducted to verify the identification of two morphotypes of the spider crab Menaethius monoceros (Latreille, 1825) in the family Epialtidae Macleay, 1838, collected from the Red Sea, Egypt. DNA barcoding of two mitochondrial markers, cytochrome oxidase subunit I (COI) and 16S, was used successfully to differentiate between these morphotypes.<br><br>RESULTS: DNA barcoding and genetic analyses combined with morphological identification showed that the two morphotypes were clustered together with low genetic distances ranged from 1.1 to 1.7% COI and from 0.0 to 0.06% 16S. Hence, this morphological variation is considered as individual variation within the same species.<br><br>CONCLUSION: The present study successively revealed that genetic analyses are important to confirm the spider crab's identification in case of morphological overlapping and accelerate the accurate identification of small-sized crab species. Also, DNA barcoding for spider crabs is important for better future evaluation and status records along the Red Sea coast.},
}
@article {pmid33742019,
year = {2021},
author = {Calzolari, M and Desiato, R and Albieri, A and Bellavia, V and Bertola, M and Bonilauri, P and Callegari, E and Canziani, S and Lelli, D and Mosca, A and Mulatti, P and Peletto, S and Ravagnan, S and Roberto, P and Torri, D and Pombi, M and Di Luca, M and Montarsi, F},
title = {Mosquitoes of the Maculipennis complex in Northern Italy.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {6421},
pmid = {33742019},
issn = {2045-2322},
mesh = {Animals ; Anopheles/*classification/*genetics ; DNA Barcoding, Taxonomic/methods ; *Ecosystem ; Female ; Haplotypes ; Italy/epidemiology ; Malaria/epidemiology/microbiology/*transmission ; Male ; Mosquito Vectors/*microbiology ; Phylogeny ; *Plasmodium/classification ; Polymorphism, Genetic ; Sequence Analysis, DNA ; },
abstract = {The correct identification of mosquito vectors is often hampered by the presence of morphologically indiscernible sibling species. The Maculipennis complex is one of these groups that include both malaria vectors of primary importance and species of low/negligible epidemiological relevance, of which distribution data in Italy are outdated. Our study was aimed at providing an updated distribution of Maculipennis complex in Northern Italy through the sampling and morphological/molecular identification of specimens from five regions. The most abundant species was Anopheles messeae (2032), followed by Anopheles maculipennis s.s. (418), Anopheles atroparvus (28) and Anopheles melanoon (13). Taking advantage of ITS2 barcoding, we were able to finely characterize tested mosquitoes, classifying all the Anopheles messeae specimens as Anopheles daciae, a taxon with debated rank to which we referred as species inquirenda (sp. inq.). The distribution of species was characterized by Ecological Niche Models (ENMs), fed by recorded points of presence. ENMs provided clues on the ecological preferences of the detected species, with An. daciae sp. inq. linked to stable breeding sites and An. maculipennis s.s. more associated to ephemeral breeding sites. We demonstrate that historical Anopheles malaria vectors are still present in Northern Italy.},
}
@article {pmid33741537,
year = {2021},
author = {Bober, S and Glaubrecht, M and Hausdorf, B and Neiber, MT},
title = {One, two or three? Integrative species delimitation of short-range endemic Hemicycla species (Gastropoda: Helicidae) from the Canary Islands based on morphology, barcoding, AFLP and ddRADseq data.},
journal = {Molecular phylogenetics and evolution},
volume = {161},
number = {},
pages = {107153},
doi = {10.1016/j.ympev.2021.107153},
pmid = {33741537},
issn = {1095-9513},
mesh = {*Amplified Fragment Length Polymorphism Analysis ; Animals ; *DNA Barcoding, Taxonomic ; Mitochondria/genetics ; *Phylogeny ; Polymorphism, Single Nucleotide/*genetics ; Snails/*anatomy &amp; histology/classification/*genetics ; Spain ; },
abstract = {Hemicycla mascaensis and H. diegoi are short-range endemics that occur allopatrically in small areas in the Teno Mountains in the western part of Tenerife (Canary Islands). Both taxa have been recognised as distinct species based on differences in shell morphology and genital anatomy. Preliminary molecular analyses using mitochondrial markers suggested a potential paraphyly of H. diegoi with regard to H. mascaensis. We here use multilocus AFLP data and ddRADseq data as well as distribution data, data on shell morphology and genital anatomy to assess the status of these taxa using phylogenetic analyses, species tree reconstruction and molecular species delimitation based on the multispecies coalescent as implemented in BFD* and BPP in an integrative approach. Our analyses show that, based on the analysis of multilocus data, the two taxa are reciprocally monophyletic. Species delimitation methods, however, tend to recognise all investigated populations as distinct species, albeit neither lending unambiguous support to any of the species hypotheses. The comparison of the anatomy of distal genital organs further suggests differentiation within H. mascaensis. This highlights the need for a balanced weighting of arguments from different lines of evidence to determine species status and calls for cautious interpretations of the results of molecular species delimitation analyses, especially in organisms with low active dispersal capacities and expected distinct population structuring such as land snails. Taking all available evidence into account, we favour to recognise H. mascaensis and H. diegoi as distinct species, acknowledging, though, that the recognition of both taxa as subspecies (with possibly a third yet undescribed) would also be an option as morphological differentiation is within the limits of other land snail species that are traditionally subdivided into subspecies.},
}
@article {pmid33740473,
year = {2021},
author = {Pham, K and Nikish, A and Phillips-Cremins, JE},
title = {See(quence) and ye shall find: higher-order genome folding in intact single cells.},
journal = {Molecular cell},
volume = {81},
number = {6},
pages = {1130-1132},
pmid = {33740473},
issn = {1097-4164},
support = {R01 MH120269/MH/NIMH NIH HHS/United States ; T32 GM007170/GM/NIGMS NIH HHS/United States ; U01 DA052715/DA/NIDA NIH HHS/United States ; U01 DK127405/DK/NIDDK NIH HHS/United States ; R01 NS114226/NS/NINDS NIH HHS/United States ; U01 HL129998/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Base Sequence ; *Genome ; Mice ; },
abstract = {Payne et al. (2020) combine in situ imaging and ex situ sequencing via spatially resolved unique molecular barcodes to query higher-order genome folding patterns in intact single nuclei from mouse embryos and human fibroblasts.},
}
@article {pmid33738325,
year = {2021},
author = {Srivastava, SK and Truitt, LL and Wu, C and Glaser, A and Nolan, DJ and Ginsberg, M and Espinoza, DA and Koelle, S and Yabe, IM and Yu, KR and Hong, S and Sellers, S and Krouse, A and Bonifacino, A and Metzger, M and Dagur, PK and Donahue, RE and Dunbar, CE and Panch, SR},
title = {Comparative engraftment and clonality of macaque HSPCs expanded on human umbilical vein endothelial cells versus non-expanded cells.},
journal = {Molecular therapy. Methods &amp; clinical development},
volume = {20},
number = {},
pages = {703-715},
pmid = {33738325},
issn = {2329-0501},
abstract = {Ex vivo hematopoietic stem and progenitor cell (HSPC) expansion platforms are under active development, designed to increase HSPC numbers and thus engraftment ability of allogeneic cord blood grafts or autologous HSPCs for gene therapies. Murine and in vitro models have not correlated well with clinical outcomes of HSPC expansion, emphasizing the need for relevant pre-clinical models. Our rhesus macaque HSPC competitive autologous transplantation model utilizing genetically barcoded HSPC allows direct analysis of the relative short and long-term engraftment ability of lentivirally transduced HSPCs, along with additional critical characteristics such as HSPC clonal diversity and lineage bias. We investigated the impact of ex vivo expansion of macaque HSPCs on the engineered endothelial cell line (E-HUVECs) platform regarding safety, engraftment of transduced and E-HUVEC-expanded HSPC over time compared to non-expanded HSPC for up to 51 months post-transplantation, and both clonal diversity and lineage distribution of output from each engrafted cell source. Short and long-term engraftment were comparable for E-HUVEC expanded and the non-expanded HSPCs in both animals, despite extensive proliferation of CD34[+] cells during 8 days of ex vivo culture for the E-HUVEC HSPCs, and optimization of harvesting and infusion of HSPCs co-cultured on E-HUVEC in the second animal. Long-term hematopoietic output from both E-HUVEC expanded and unexpanded HSPCs was highly polyclonal and multilineage. Overall, the comparable HSPC kinetics of macaques to humans, the ability to study post-transplant clonal patterns, and simultaneous multi-arm comparisons of grafts without the complication of interpreting allogeneic effects makes our model ideal to test ex vivo HSPC expansion platforms, particularly for gene therapy applications.},
}
@article {pmid33737485,
year = {2021},
author = {Bizzotto, S and Dou, Y and Ganz, J and Doan, RN and Kwon, M and Bohrson, CL and Kim, SN and Bae, T and Abyzov, A and , and Park, PJ and Walsh, CA},
title = {Landmarks of human embryonic development inscribed in somatic mutations.},
journal = {Science (New York, N.Y.)},
volume = {371},
number = {6535},
pages = {1249-1253},
pmid = {33737485},
issn = {1095-9203},
support = {R01 NS032457/NS/NINDS NIH HHS/United States ; U01 MH106883/MH/NIMH NIH HHS/United States ; T32 HG002295/HG/NHGRI NIH HHS/United States ; U54 HD090255/HD/NICHD NIH HHS/United States ; P50 CA165962/CA/NCI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Adolescent ; Adult ; Cell Division ; *Cell Lineage ; Clone Cells/cytology ; Embryonic Development/genetics ; Female ; Gastrula/cytology ; *Gastrulation ; Genetic Variation ; Germ Layers/cytology ; Humans ; Male ; *Mutation ; Neural Stem Cells/*cytology ; Neurons/cytology ; Organogenesis ; Polymorphism, Single Nucleotide ; Prosencephalon/*cytology/embryology ; Single-Cell Analysis ; Whole Genome Sequencing ; },
abstract = {Although cell lineage information is fundamental to understanding organismal development, very little direct information is available for humans. We performed high-depth (250×) whole-genome sequencing of multiple tissues from three individuals to identify hundreds of somatic single-nucleotide variants (sSNVs). Using these variants as "endogenous barcodes" in single cells, we reconstructed early embryonic cell divisions. Targeted sequencing of clonal sSNVs in different organs (about 25,000×) and in more than 1000 cortical single cells, as well as single-nucleus RNA sequencing and single-nucleus assay for transposase-accessible chromatin sequencing of ~100,000 cortical single cells, demonstrated asymmetric contributions of early progenitors to extraembryonic tissues, distinct germ layers, and organs. Our data suggest onset of gastrulation at an effective progenitor pool of about 170 cells and about 50 to 100 founders for the forebrain. Thus, mosaic mutations provide a permanent record of human embryonic development at very high resolution.},
}
@article {pmid33736847,
year = {2021},
author = {Fuentes-López, A and Pedreño Sala, A and Romera, E and Galián, J},
title = {DNA-based and taxonomic identification of forensically important Sarcophagidae (Diptera) in southeastern Spain.},
journal = {Science &amp; justice : journal of the Forensic Science Society},
volume = {61},
number = {2},
pages = {150-159},
doi = {10.1016/j.scijus.2020.11.003},
pmid = {33736847},
issn = {1876-4452},
mesh = {Animals ; Cadaver ; DNA, Mitochondrial/genetics ; *Diptera/genetics ; Electron Transport Complex IV/genetics ; Entomology ; Female ; Humans ; Phylogeny ; *Sarcophagidae/genetics ; Sequence Analysis, DNA ; Spain ; },
abstract = {Studying dipterans at the scene of a death can provide essential information for interpreting the evidence and help to reconstruct the events happened to a corpse in the past. Molecular tools have been employed for identification at specific levels in the cases of cryptic species or poorly conserved specimens. Identification of specimens is essential in forensic entomology since each species has a specific growth rate, which determines the calculation of the minimum post mortem interval (minPMI). In addition, phylogeographic reconstruction within a species can help to differentiate the haplotypes from a geographic area, thereby helping to clarify the possible relocation of a corpse. The morphological identification of Sarcophagidae species is often difficult, especially for the females. This is an important Diptera family since some of its species are among the first to reach a corpse, especially in warm areas. In this study, we compared the sarcophagids found in human corpses in forensic cases in Alicante (southeast of Spain) with specimens collected from baited traps in the same area and surrounding provinces. In total, 189 specimens were collected, comprising 72 from forensic cases and 117 from baited traps. Molecular identification was conducted by sequencing the cox1 mitochondrial gene and analyzing the sequences using ABGD, GMYC, and BIN species delimitation methods. The median joining algorithm in the PopART program was used to construct phylogeographic networks. Eight species in the family Sarcophagidae were identified. The most widely collected species were Sarcophaga argyrostoma and Sarcophaga tibialis. The haplotype networks obtained for these species did not indicate a clear geographic distribution of haplotypes. The S. argyrostoma samples from Alcoy were clearly isolated. The results demonstrated that this method is useful for identifying Sarcophagidae samples in forensic investigations and it can be employed for minPMI estimation.},
}
@article {pmid33736731,
year = {2021},
author = {Jirsa, F and Reier, S and Smales, L},
title = {Helminths of the mallard Anas platyrhynchos Linnaeus, 1758 from Austria, with emphasis on the morphological variability of Polymorphus minutus Goeze, 1782.},
journal = {Journal of helminthology},
volume = {95},
number = {},
pages = {e16},
doi = {10.1017/S0022149X21000079},
pmid = {33736731},
issn = {1475-2697},
mesh = {*Acanthocephala ; Animals ; Austria ; DNA Barcoding, Taxonomic ; Ducks/*parasitology ; *Nematoda ; *Trematoda ; },
abstract = {The mallard Anas platyrhynchos is the most abundant water bird species in Austria, but there is no record of its helminth community. Therefore, this work aimed to close that gap by recording and analysing the parasite community of a large number of birds from Austria for the first time. A total of 60 specimens shot by hunters in autumn were examined for intestinal parasites. The following taxa were recovered (prevalence given in parentheses): Cestoda: Diorchis sp. (31.7%) and Fimbriarioides intermedia (1.7%); Acanthocephala: Filicollis anatis (5%), Polymorphus minutus (30%) and one cystacanth unidentified (1.7%); Trematoda: Apatemon gracilis (3.3%), Echinostoma grandis (6.7%), Echinostoma revolutum (6.7%) and Notocotylus attenuatus (23.3%); Nematoda: Porrocaecum crassum (1.7%) and one not identified (1.7%). The frequency distribution of parasites showed a typical pattern in which 39 birds (65%) were either not parasitized or were harbouring up to five worms, whereas more intense infestations occurred in a lesser number of hosts. Compared to other studies from central and eastern Europe, an extremely depauperate helminth community, particularly of the cestodes and nematodes, was found. Polymorphus minutus was observed as having highly variable morphology and, therefore, molecular genetic characterization by DNA barcoding was carried out. Species identification was confirmed by comparing data with the reference cytochrome c oxidase subunit 1 gene sequence from P. minutus available in GenBank.},
}
@article {pmid33736466,
year = {2021},
author = {Lu, X and Shang, J and Niu, L and Sun, X and Su, Z and Dong, L and Guo, Q and Li, S and Ma, P},
title = {First Report of Verticillium Wilt of Watermelon Caused by Verticillium dahliae in China.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-01-21-0045-PDN},
pmid = {33736466},
issn = {0191-2917},
abstract = {Watermelon (Citrullus lanatus T.) is one of the most important economic crops in China. Soil-borne diseases are becoming more and more serious with longer growing seasons and continuous cropping of watermelon in greenhouses. In May 2020, symptoms were observed on plants in greenhouses located at Xingtai, Hebei province of China and included wilted leaves, chlorosis and plant death. Among the 26 greenhouses examined, symptomatic plants were observed in 17 greenhouses. The incidences of infected plants ranged from 1% to 35%, and caused an average 10% yield loss. Symptoms began on lower part of the plants and progressed upward to the vines and leaves. At the early stage of infection, the edge of watermelon leaves changed from green to yellow, and became soft. As the disease progressed, infected leaves wilted and desicated. The vascular tissue of the stem exhibited a uniform brown discoloration that often extended throughout the vine. To identify the causal agent, small pieces approximate 3.0×3.0 mm size of infected stem tissues were collected and sterilized with 0.5% sodium hypochlorite solution for 1 min, rinsed three times with sterile water and transferred onto potato dextrose agar (PDA) medium amended with 100 μg·mL-1 of chloramphenicol. The plates were incubated at 25°C for 3 days in the dark and fungal isolates were purified using the single-spore isolation method. A total of 22 fungal isolates with identical colony morphology were collected from diseased plants. The color of the fungal colonies on PDA medium was creamy-white with an abundance of mycelia that darken after 5 days growth due to the formation of microsclerotia. Fungal colonies consisted of fine, hyaline hyphae with verticillate conidiophores producing hyaline, ellipsoidal to oval conidia with an average size of 5.12×3.41 μm (n=50). The morphological characters of the fungal isolates were identical to those of Verticillium dahliae Kleb. described by Hawksworth and Talboys (Hawksworth, D. and Talboys, P, 1970). Pathogenicity tests were performed by soaking 30 watermelon seedlings with wounded root tips in the fungal conidial suspension (1x107 conidium/mL) for 30 min (Ma, et al, 2004). The same number of non-inoculated watermelon seedlings was used as a control. All plants were kept in a greenhouse at 25°C and 90%-95% relative humidity. Seven days post-inoculation (dpi), leaves of treated plants began to show symptoms of wilt. At 10-dpi, lower leaves wilted and dry and by 15-dpi, whole plants were dead. Pathogenicity tests were repeated three times with consistent results. The pathogen was re-isolated from the diseased plants and displayed identical morphological characteristics to the original isolates. To further identity the pathogens, the ribosomal DNA Internal Transcribed Spacer (rDNA-ITS) region was amplified by PCR (White et al., 1990; Liu et al., 1999; Bellemain et al.. 2010). The amplicon was sequenced and showed 99%-100% identity to the ITS region of the V. dahliae reference strains deposited in the NCBI database (MK093977.1, MK287620.1, MT348570.1 and LC549667.1, respectively). Based on morphological and ITS sequence information, the fungal pathogen was identified as V. dahliae. V. dahliae is an economically important pathogen with a wide host range worldwide. The discovery of Verticillium wilt on watermelons indicates that there might be a risk of Verticillium wilt when watermelons are planted in subsequent crops of the host plants of the disease, such as cotton or eggplant. To our knowledge, this is the first report of V. dahliae causing Verticillium wilt of watermelon in China. Financed: the Special Fund for Agro-scientific Research in the Public Interest, China (201503109) References: Hawksworth, D. and Talboys, P. 1970. Description of Pathogenic Fungi and Bacteria, CMI, Surrey. Ma, P., et al. 2004. A New Inoculation Method for Verticillium Wilt on Cotton and Its Application in Evaluating Pathogenesis and Host Resistance. Acta Phytopathologica Sinica, 34(6): 536-541. White, T. J., et al. 1990. Amplification and Direct Sequencing of Fungal Ribosomal RNA Genes for Phylogenetics. PCR protocols: a guide to methods and applications, 18(1), 315-322. Bellemain, E., et al. 2010. ITS as an Environmental DNA Barcode for Fungi: an in Silico Approach Reveals Potential PCR Biases. BMC microbiology, 10(1), 1-9. Liu, Y. J., et al. 1999. Phylogenetic Relationships Among Ascomycetes: Evidence from an RNA Polymerse II SubunitMol. Biol. Evol. 16:1799-1808.},
}
@article {pmid33732519,
year = {2021},
author = {Kim, KJ and Jung, YS and You, DM and Lee, SH and Lee, G and Kwon, KB and Kim, DO},
title = {Neuroprotective effects of ethanolic extract from dry Rhodiola rosea L. rhizomes.},
journal = {Food science and biotechnology},
volume = {30},
number = {2},
pages = {287-297},
pmid = {33732519},
issn = {2092-6456},
abstract = {UNLABELLED: Rhodiola rosea L. rhizome has been used as a traditional medicine to treat fatigue, depression, and cognitive dysfunction. We aimed to authenticate R. rosea L. rhizome using the DNA barcoding technique and to quantify its main compounds, total phenolics, total flavonoids, and antioxidant capacity, and then to investigate their neuroprotective effects. The sequences of internal transcribed spacer and trnH-psbA of R. rosea L. rhizomes showed a 99% identity with those of NCBI GenBank database according to BLAST searches. Analysis using reversed-phase HPLC revealed five main compounds in R. rosea L. rhizome. Rhodiola rosea L. rhizome and two bioactive compounds, salidroside and tyrosol, showed free radical scavenging activity. Rhodiola rosea L. rhizome and its identified compounds protected neuronal PC-12 cells against oxidative stress and showed moderate acetylcholinesterase inhibition. Taken together, these results suggest that R. rosea L. rhizomes with bioactives can be used as a functional ingredient with potential for neuroprotection.<br><br>SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1007/s10068-020-00868-7) contains supplementary material, which is available to authorized users.},
}
@article {pmid33732078,
year = {2021},
author = {Hashim, AM and Alatawi, A and Altaf, FM and Qari, SH and Elhady, ME and Osman, GH and Abouseadaa, HH},
title = {Phylogenetic relationships and DNA barcoding of nine endangered medicinal plant species endemic to Saint Katherine protectorate.},
journal = {Saudi journal of biological sciences},
volume = {28},
number = {3},
pages = {1919-1930},
pmid = {33732078},
issn = {1319-562X},
abstract = {A high degree of endemism has been recorded for several plant groups collectively in Saint Katherine Protectorate (SKP) in the Sinai Peninsula. Nine endangered endemic plant species in SKP were selected to test the variable abilities of three different DNA barcodes; Riboluse-1,5- Biphosphate Carboxylase/Oxygenase Large subunit (rbcL), Internal Transcribed Spacer (ITS), and the two regions of the plastid gene (ycf1) as well as Start Codon Targeted (SCoT) Polymorphism to find the phylogenetic relationships among them. The three barcodes were generally more capable of finding the genetic relationships among the plant species under study, new barcodes were introduced to the National Centre for Biotechnology Information (NCBI) for the first time through our work. The barcode sequences were efficient in finding the genetic relationships between the nine species. However, SCoT polymorphism could only cluster plant species belonging to the same genus together in one group, but it could not cluster plant species belonging to the same families except for some primers solely. RbcL was the most easily amplified and identified barcode in eight out of the nine species at the species level and the ninth barcode to the genus level. ITS identified all the species to the genus level. Finally, ycf1 identified six out of the eight species, but it could not identify two of the eight species to the genus level.},
}
@article {pmid33731803,
year = {2021},
author = {Maeshiro, M and Shinriki, S and Liu, R and Nakachi, Y and Komohara, Y and Fujiwara, Y and Ohtsubo, K and Yoshida, R and Iwamoto, K and Nakayama, H and Matsui, H},
title = {Colonization of distant organs by tumor cells generating circulating homotypic clusters adaptive to fluid shear stress.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {6150},
pmid = {33731803},
issn = {2045-2322},
mesh = {Animals ; Cell Line ; Head and Neck Neoplasms/*pathology ; Humans ; Mice ; Neoplasm Metastasis/*pathology ; Neoplastic Cells, Circulating/*pathology ; Squamous Cell Carcinoma of Head and Neck/*pathology ; },
abstract = {Once disseminated tumor cells (DTCs) arrive at a metastatic organ, they remain there, latent, and become seeds of metastasis. However, the clonal composition of DTCs in a latent state remains unclear. Here, we applied high-resolution DNA barcode tracking to a mouse model that recapitulated the metastatic dormancy of head and neck squamous cell carcinoma (HNSCC). We found that clones abundantly circulated peripheral blood dominated DTCs. Through analyses of multiple barcoded clonal lines, we identified specific subclonal population that preferentially generated homotypic circulating tumor cell (CTC) clusters and dominated DTCs. Despite no notable features under static conditions, this population significantly generated stable cell aggregates that were resistant to anoikis under fluid shear stress (FSS) conditions in an E-cadherin-dependent manner. Our data from various cancer cell lines indicated that the ability of aggregate-constituting cells to regulate cortical actin-myosin dynamics governed the aggregates' stability in FSS. The CTC cluster-originating cells were characterized by the expression of a subset of E-cadherin binding factors enriched with actin cytoskeleton regulators. Furthermore, this expression signature was associated with locoregional and metastatic recurrence in HNSCC patients. These results reveal a biological selection of tumor cells capable of generating FSS-adaptive CTC clusters, which leads to distant colonization.},
}
@article {pmid33728458,
year = {2022},
author = {Legon, L and Rallis, C},
title = {Genome-wide screens in yeast models towards understanding chronological lifespan regulation.},
journal = {Briefings in functional genomics},
volume = {21},
number = {1},
pages = {4-12},
pmid = {33728458},
issn = {2041-2657},
mesh = {Longevity/genetics ; Saccharomyces cerevisiae/genetics ; *Schizosaccharomyces/genetics/metabolism ; *Schizosaccharomyces pombe Proteins/genetics/metabolism ; },
abstract = {Cellular models such as yeasts are a driving force in biogerontology studies. Their simpler genome, short lifespans and vast genetic and genomics resources make them ideal to characterise pro-ageing and anti-ageing genes and signalling pathways. Over the last three decades, yeasts have contributed to the understanding of fundamental aspects of lifespan regulation including the roles of nutrient response, global protein translation rates and quality, DNA damage, oxidative stress, mitochondrial function and dysfunction as well as autophagy. In this short review, we focus on approaches used for competitive and non-competitive cell-based screens using the budding yeast Saccharomyces cerevisiae, and the fission yeast Schizosaccharomyces pombe, for deciphering the molecular mechanisms underlying chronological ageing. Automation accompanied with appropriate computational tools allowed manipulation of hundreds of thousands of colonies, generation, processing and analysis of genome-wide lifespan data. Together with barcoding and modern mutagenesis technologies, these approaches have allowed to take decisive steps towards a global, comprehensive view of cellular ageing.},
}
@article {pmid33727886,
year = {2021},
author = {Wang, YS and Chen, R and Jin, DT and Che, YL and Wang, ZQ},
title = {New record of Cyrtonotula Uvarov, 1939 (Blaberidae, Epilamprinae) from China, with three new species based on morphological and COI data.},
journal = {ZooKeys},
volume = {1021},
number = {},
pages = {127-143},
pmid = {33727886},
issn = {1313-2989},
abstract = {The genus Cyrtonotula Uvarov, 1939 (Blaberidae, Epilamprinae) is recorded for the first time from Hainan Island, China. Three new species, Cyrtonotula epunctata Wang &amp; Wang, sp. nov., C. maculosa Wang &amp; Wang, sp. nov., and C. longialata Wang &amp; Wang, sp. nov., are described based on morphological data and a molecular analysis using Automatic Barcode Gap Discovery (ABGD). Additional barcode data of blaberid species, including these three new species, are provided to facilitate future species identification. Morphological photographs and habitat photos of these new species, as well as a key to the known species, are provided.},
}
@article {pmid33723654,
year = {2021},
author = {Garrigues, S and Kun, RS and de Vries, RP},
title = {Genetic barcodes allow traceability of CRISPR/Cas9-derived Aspergillus niger strains without affecting their fitness.},
journal = {Current genetics},
volume = {67},
number = {4},
pages = {673-684},
pmid = {33723654},
issn = {1432-0983},
support = {15807//Stichting voor de Technische Wetenschappen/ ; },
mesh = {Antigens, Fungal/*genetics ; Aspergillus niger/*genetics ; CRISPR-Cas Systems/*genetics ; *DNA Barcoding, Taxonomic ; Gene Editing ; Gene Expression Regulation, Fungal/genetics ; },
abstract = {Safe use of genetically modified organisms (GMOs) in biotechnology requires the ability to track the presence of these strains in any environment in which they are applied. For this, introduction of genetic barcodes within the editing site represents a valuable tool for the identification of microbial strains that have undergone genetic modifications. However, it is not known whether these barcodes would have any unexpected effect in the resulting strains or affect the efficiency of the genetic modification. CRISPR/Cas9 has become one of the fastest-growing technologies for genome editing in a range of organisms, including fungi. However, this technology enables the generation of scarless GMOs that are very difficult to distinguish from naturally occurring mutants or other modified organisms. In this study, we address this issue using the industrial workhorse Aspergillus niger as a test case. We applied CRISPR/Cas9 technology to delete the genes encoding the transcriptional regulators XlnR and AraR, involved in the production of plant biomass-degrading enzymes. We generated 20-bp barcoded and non-barcoded ΔxlnR and ΔaraR mutants and analyzed the traceability and fitness of the resulting strains, as well as the efficiency of the genetic modification. Results showed that both barcoded and non-barcoded mutants can be traced by routine PCR reactions when the specific CRISPR/Cas9 modification is known. Additionally, barcodes neither affected the efficiency of the genetic modification nor the growth or protein production of the resulting strains. These results confirm the suitability of genetic barcodes to trace CRISPR-derived GMOs without affecting the performance of the resulting strains.},
}
@article {pmid33722637,
year = {2021},
author = {Wang, W and Wang, W and Wei, S and Huang, W and Qi, B and Wang, Q and Li, Y},
title = {Design of potentially universal SSU primers in myxomycetes using next-generation sequencing.},
journal = {Journal of microbiological methods},
volume = {184},
number = {},
pages = {106203},
doi = {10.1016/j.mimet.2021.106203},
pmid = {33722637},
issn = {1872-8359},
mesh = {DNA Primers/*genetics ; Fungal Proteins/*genetics ; Genetic Variation ; High-Throughput Nucleotide Sequencing/*methods ; Myxomycetes/classification/*genetics/isolation &amp; purification ; Phylogeny ; },
abstract = {Unlike fungi, which have a universally accepted barcode marker, universal primers still lack in myxomycetes. Typically, DNA barcode primers were designed based on comparing existing myxomycetes sequences and targeting the conserved regions. However, the extreme genetic diversity within major myxomycetes groups and the frequent occurrence of group I introns have made the development of universal DNA barcode a severe challenge. The emergence of next-generation sequencing provides an opportunity to address this problem. We sequenced the mixed genomic DNA of 81 myxomycetes and extracted the SSU gene's reads using next-generation sequencing. After alignment and assembly, we designed a set of SSU primers that matched all potential SNPs, avoided all known group I intron insertion sites, and were highly conserved between major myxomycetes orders. This set of SSU primers has the potential to become one of the universal primer combinations. Due to the high genetic divergence caused by long and complicated evolutionary histories, the lack of universal barcode primers is common in protists. Our research provides a new method to solve this problem.},
}
@article {pmid33719288,
year = {2021},
author = {Wang, Y and Lv, H and Xiang, X and Yang, A and Feng, Q and Dai, P and Li, Y and Jiang, X and Liu, G and Zhang, X},
title = {Construction of a SNP Fingerprinting Database and Population Genetic Analysis of Cigar Tobacco Germplasm Resources in China.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {618133},
pmid = {33719288},
issn = {1664-462X},
abstract = {Cigar tobacco is an important economic crop that is widely grown around the world. In recent years, varietal identification has become a frequent problem in germplasm preservation collections, which causes considerable inconvenience and uncertainty in the cataloging and preservation of cigar germplasm resources, in the selection of parental lines for breeding, and in the promotion and use of high quality varieties. Therefore, the use of DNA fingerprints to achieve rapid and accurate identification of varieties can play an important role in germplasm identification and property rights disputes. In this study, we used genotyping-by-sequencing (GBS) on 113 cigar tobacco accessions to develop SNP markers. After filtering, 580,942 high-quality SNPs were obtained. We used the 580,942 SNPs to perform principal component analysis (PCA), population structure analysis, and neighbor joining (NJ) cluster analysis on the 113 cigar tobacco accessions. The results showed that the accessions were not completely classified based on their geographical origins, and the genetic backgrounds of these cigar resources are complex and diverse. We further selected from these high-quality SNPs to obtained 163 SNP sites, 133 of which were successfully converted into KASP markers. Finally, 47 core KASP markers and 24 candidate core markers were developed. Using the core markers, we performed variety identification and fingerprinting in 216 cigar germplasm accessions. The results of SNP fingerprinting, 2D barcoding, and genetic analysis of cigar tobacco germplasm in this study provide a scientific basis for screening and identifying high-quality cigar tobacco germplasm, mining important genes, and broadening the basis of cigar tobacco genetics and subsequent breeding work at the molecular level.},
}
@article {pmid33717437,
year = {2021},
author = {Milián-García, Y and Young, R and Madden, M and Bullas-Appleton, E and Hanner, RH},
title = {Optimization and validation of a cost-effective protocol for biosurveillance of invasive alien species.},
journal = {Ecology and evolution},
volume = {11},
number = {5},
pages = {1999-2014},
pmid = {33717437},
issn = {2045-7758},
abstract = {Environmental DNA (eDNA) metabarcoding has revolutionized biodiversity monitoring and invasive pest biosurveillance programs. The introduction of insect pests considered invasive alien species (IAS) into a non-native range poses a threat to native plant health. The early detection of IAS can allow for prompt actions by regulating authorities, thereby mitigating their impacts. In the present study, we optimized and validated a fast and cost-effective eDNA metabarcoding protocol for biosurveillance of IAS and characterization of insect and microorganism diversity. Forty-eight traps were placed, following the CFIA's annual forest insect trapping survey, at four locations in southern Ontario that are high risk for forest IAS. We collected insects and eDNA samples using Lindgren funnel traps that contained a saturated salt (NaCl) solution in the collection jar. Using cytochrome c oxidase I (COI) as a molecular marker, a modified Illumina protocol effectively identified 2,535 Barcode Index Numbers (BINs). BINs were distributed among 57 Orders and 304 Families, with the vast majority being arthropods. Two IAS (Agrilus planipennis and Lymantria dispar) are regulated by the Canadian Food Inspection Agency (CFIA) as plant health pests, are known to occur in the study area, and were identified through eDNA in collected traps. Similarly, using 16S ribosomal RNA and nuclear ribosomal internal transcribed spacer (ITS), five bacterial and three fungal genera, which contain species of regulatory concern across several Canadian jurisdictions, were recovered from all sampling locations. Our study results reaffirm the effectiveness and importance of integrating eDNA metabarcoding as part of identification protocols in biosurveillance programs.},
}
@article {pmid33716539,
year = {2021},
author = {Skarżyński, D and Smolis, A and Kováč, &#x13d; and Porco, D},
title = {A new European species of Ceratophysella (Collembola, Hypogastruridae) revealed by morphological data and DNA barcodes.},
journal = {ZooKeys},
volume = {1021},
number = {},
pages = {1-18},
pmid = {33716539},
issn = {1313-2989},
abstract = {A new species, Ceratophysella stachi, from Denmark, Germany, Luxembourg, Norway, Poland, and Ukraine is described based on morphological data and DNA barcodes. It belongs to a small European group of species with type B chaetotaxy and strong tegumentary granulation with distinct fields of coarse granules: C. granulata Stach, 1949, C. lawrencei (Gisin, 1963), C. neomeridionalis (Nosek &amp; Červek, 1970), C. scotica (Carpenter &amp; Evans, 1899), and C. silvatica Rusek, 1964. It differs from all of them in the chaetotaxy of lateral parts of thoracic terga II-III (setae m6 present and one additional seta outside lateral sensillum m7 present or absent) that is exceptional within the whole C. armata-group. Notes on closely related species C. granulata are also given.},
}
@article {pmid33714808,
year = {2021},
author = {Dunham-Cheatham, SM and Klingler, KB and Estrada, MV and Gustin, MS},
title = {Using a next-generation sequencing approach to DNA metabarcoding for identification of adulteration and potential sources of mercury in commercial cat and dog foods.},
journal = {The Science of the total environment},
volume = {778},
number = {},
pages = {146102},
doi = {10.1016/j.scitotenv.2021.146102},
pmid = {33714808},
issn = {1879-1026},
mesh = {Animal Feed ; Animals ; Cats ; DNA ; DNA Barcoding, Taxonomic ; Dogs ; High-Throughput Nucleotide Sequencing ; *Mercury ; *Methylmercury Compounds ; },
abstract = {Studies have demonstrated that some commercial pet (i.e., cat and dog) food products contain high concentrations of mercury (Hg), and some products have Hg concentrations that are higher than expected based on the ingredients included in the package ingredient list. Additionally, concentrations of methylmercury, a particularly toxic form of Hg commonly associated with fish-based ingredients, are largely unstudied despite the widespread use of such ingredients in pet food products. This study aimed to quantify total Hg and methylmercury in a variety of commercial pet food products (n = 127), and use genetic tools to determine if specific ingredients contributed to high Hg concentrations in the final product. Results indicate that total Hg concentrations were above suggested maximum tolerable limits in three of the tested pet food products, and that methylmercury concentrations were at safe levels in all tested products. Next-generation amplicon sequencing using ten barcode primers was conducted to target distinct taxa and to determine if one primer set outperformed the others in amplifying the often heavily degraded DNA found in pet food products. The 16sUniF_16sUniR primer set generated a relatively higher number of reads across the broadest set of taxa, although several of the primer sets were useful in identifying common animal- and plant-based ingredients in commercial pet food products. Combined with the Hg results, it was demonstrated that pet food product ingredients are consistent among and between product lots. However, these results also revealed that adulteration is prevalent in pet food products.},
}
@article {pmid33714776,
year = {2021},
author = {Ardura, A and Fernandez, S and Haguenauer, A and Planes, S and Garcia-Vazquez, E},
title = {Ship-driven biopollution: How aliens transform the local ecosystem diversity in Pacific islands.},
journal = {Marine pollution bulletin},
volume = {166},
number = {},
pages = {112251},
doi = {10.1016/j.marpolbul.2021.112251},
pmid = {33714776},
issn = {1879-3363},
mesh = {Biodiversity ; *Ecosystem ; Introduced Species ; Islands ; Oceans and Seas ; Pacific Islands ; *Ships ; },
abstract = {Ships moving species across the oceans mix marine communities throughout latitudes. The introduction of new species may be changing the ecosystems even in remote islands. In tropical Pacific islands where maritime traffic is principally local, eDNA metabarcoding and barcoding revealed 75 introduced species, accounting in average for 28% of the community with a minimum of 13% in the very remote Rangiroa atoll. The majority of non-native species were primary producers -from diatoms to red algae, thus the ecosystem is being transformed from the bottom. Primary producers were more shared among sites than other exotics, confirming ship-mediated dispersal in Pacific marine ecosystems. Limited alien share and an apparent saturation of aliens (similar proportion in ports of very different size) suggests the occurrence of "alien drift" in port communities, or random retention of newly introduced aliens that reminds genetic drift of new mutations in a population.},
}
@article {pmid33704738,
year = {2021},
author = {Pizzolla, A and Keam, SP and D'Souza, C and Semple, T and Neeson, PJ},
title = {Single-Cell Gene Expression, Clonality, and Feature Barcoding of Melanoma Tumor-Infiltrating Lymphocytes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2265},
number = {},
pages = {529-541},
pmid = {33704738},
issn = {1940-6029},
mesh = {Humans ; Lymphocytes, Tumor-Infiltrating/*immunology ; *Melanoma/genetics/immunology ; *RNA-Seq ; *Receptors, Antigen, T-Cell/immunology ; *Single-Cell Analysis ; },
abstract = {We describe here a protocol to measure gene expression, T cell receptor (TCR) sequence, and protein expression by single T cells extracted from melanoma, using 10× Chromium technology. This method includes freezing and thawing of the melanoma infiltrating lymphocytes, staining of cells with fluorescent and barcode-conjugated antibodies, sorting of T cells, and loading the cells on the 10× Chromium Controller. After sequencing, analysis includes quality control, genetic demultiplexing to resolve genetically different samples, and T cell clonality and clustering analysis. Single cell RNA sequencing paints the complete portrait of individual T cells, including their clonality and phenotype, and it reconstructs a complete picture of the T cell infiltrate in a tumor that is represented as cell clustering similar to a pointillism painting.},
}
@article {pmid33693880,
year = {2021},
author = {Gao, W and Ku, WL and Pan, L and Perrie, J and Zhao, T and Hu, G and Wu, Y and Zhu, J and Ni, B and Zhao, K},
title = {Multiplex indexing approach for the detection of DNase I hypersensitive sites in single cells.},
journal = {Nucleic acids research},
volume = {49},
number = {10},
pages = {e56},
pmid = {33693880},
issn = {1362-4962},
mesh = {Chromatin/metabolism ; Deoxyribonuclease I/metabolism ; *Epigenesis, Genetic ; *Gene Expression ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Sequence Analysis, DNA/*methods ; Single-Cell Analysis/*methods ; },
abstract = {Single cell chromatin accessibility assays reveal epigenomic variability at cis-regulatory elements among individual cells. We previously developed a single-cell DNase-seq assay (scDNase-seq) to profile accessible chromatin in a limited number of single cells. Here, we report a novel indexing strategy to resolve single-cell DNase hypersensitivity profiles based on bulk cell analysis. This new technique, termed indexing single-cell DNase sequencing (iscDNase-seq), employs the activities of terminal DNA transferase (TdT) and T4 DNA ligase to add unique cell barcodes to DNase-digested chromatin ends. By a three-layer indexing strategy, it allows profiling genome-wide DHSs for >15 000 single-cells in a single experiment. Application of iscDNase-seq to human white blood cells accurately revealed specific cell types and inferred regulatory transcription factors (TF) specific to each cell type. We found that iscDNase-seq detected DHSs with specific properties related to gene expression and conservation missed by scATAC-seq for the same cell type. Also, we found that the cell-to-cell variation in accessibility computed using iscDNase-seq data is significantly correlated with the cell-to-cell variation in gene expression. Importantly, this correlation is significantly higher than that between scATAC-seq and scRNA-seq, suggesting that iscDNase-seq data can better predict the cellular heterogeneity in gene expression compared to scATAC-seq. Thus, iscDNase-seq is an attractive alternative method for single-cell epigenomics studies.},
}
@article {pmid33693773,
year = {2021},
author = {Liu, S and Punthambaker, S and Iyer, EPR and Ferrante, T and Goodwin, D and Fürth, D and Pawlowski, AC and Jindal, K and Tam, JM and Mifflin, L and Alon, S and Sinha, A and Wassie, AT and Chen, F and Cheng, A and Willocq, V and Meyer, K and Ling, KH and Camplisson, CK and Kohman, RE and Aach, J and Lee, JH and Yankner, BA and Boyden, ES and Church, GM},
title = {Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses.},
journal = {Nucleic acids research},
volume = {49},
number = {10},
pages = {e58},
pmid = {33693773},
issn = {1362-4962},
support = {R01 MH113279/MH/NIMH NIH HHS/United States ; R35 GM119772/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; RM1 HG008525/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; Cell Line ; Gene Expression Profiling/*methods ; Humans ; In Situ Hybridization, Fluorescence/*methods ; Mice ; Oligonucleotides/*chemistry ; RNA/*analysis ; Single-Cell Analysis/*methods ; },
abstract = {We present barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel insitu analyses (BOLORAMIS), a reverse transcription-free method for spatially-resolved, targeted, in situ RNA identification of single or multiple targets. BOLORAMIS was demonstrated on a range of cell types and human cerebral organoids. Singleplex experiments to detect coding and non-coding RNAs in human iPSCs showed a stem-cell signature pattern. Specificity of BOLORAMIS was found to be 92% as illustrated by a clear distinction between human and mouse housekeeping genes in a co-culture system, as well as by recapitulation of subcellular localization of lncRNA MALAT1. Sensitivity of BOLORAMIS was quantified by comparing with single molecule FISH experiments and found to be 11%, 12% and 35% for GAPDH, TFRC and POLR2A, respectively. To demonstrate BOLORAMIS for multiplexed gene analysis, we targeted 96 mRNAs within a co-culture of iNGN neurons and HMC3 human microglial cells. We used fluorescence in situ sequencing to detect error-robust 8-base barcodes associated with each of these genes. We then used this data to uncover the spatial relationship among cells and transcripts by performing single-cell clustering and gene-gene proximity analyses. We anticipate the BOLORAMIS technology for in situ RNA detection to find applications in basic and translational research.},
}
@article {pmid33693521,
year = {2021},
author = {López, MG and Fass, M and Rivas, JG and Carbonell-Caballero, J and Vera, P and Puebla, A and Defacio, R and Dopazo, J and Paniego, N and Hopp, HE and Lia, VV},
title = {Plastome genomics in South American maize landraces: chloroplast lineages parallel the geographical structuring of nuclear gene pools.},
journal = {Annals of botany},
volume = {128},
number = {1},
pages = {115-125},
pmid = {33693521},
issn = {1095-8290},
mesh = {Bayes Theorem ; Chloroplasts ; *Gene Pool ; Genetic Variation ; Genomics ; Phylogeny ; Phylogeography ; South America ; *Zea mays/genetics ; },
abstract = {BACKGROUND AND AIMS: The number of plastome sequences has increased exponentially during the last decade. However, there is still little knowledge of the levels and distribution of intraspecific variation. The aims of this study were to estimate plastome diversity within Zea mays and analyse the distribution of haplotypes in connection with the landrace groups previously delimited for South American maize based on nuclear markers.<br><br>METHODS: We obtained the complete plastomes of 30 South American maize landraces and three teosintes by means of next-generation sequencing (NGS) and used them in combination with data from public repositories. After quality filtering, the curated data were employed to search for single-nucleotide polymorphisms, indels and chloroplast simple sequence repeats. Exact permutational contingency tests were performed to assess associations between plastome and nuclear variation. Network and Bayesian phylogenetic analyses were used to infer evolutionary relationships among haplotypes.<br><br>KEY RESULTS: Our analyses identified a total of 124 polymorphic plastome loci, with the intergenic regions psbE-rps18, petN-rpoB, trnL_UAG-ndhF and rpoC2-atpI exhibiting the highest marker densities. Although restricted in number, these markers allowed the discrimination of 27 haplotypes in a total of 51 Zea mays individuals. Andean and lowland South American landraces differed significantly in haplotype distribution. However, overall differentiation patterns were not informative with respect to subspecies diversification, as evidenced by the scattered distribution of maize and teosinte plastomes in both the network and Bayesian phylogenetic reconstructions.<br><br>CONCLUSIONS: Knowledge of intraspecific plastome variation provides the framework for a more comprehensive understanding of evolutionary processes at low taxonomic levels and may become increasingly important for future plant barcoding efforts. Whole-plastome sequencing provided useful variability to contribute to maize phylogeographic studies. The structuring of haplotype diversity in the maize landraces examined here clearly reflects the distinction between the Andean and South American lowland gene pools previously inferred based on nuclear markers.},
}
@article {pmid33692551,
year = {2021},
author = {Leeper, K and Kalhor, K and Vernet, A and Graveline, A and Church, GM and Mali, P and Kalhor, R},
title = {Lineage barcoding in mice with homing CRISPR.},
journal = {Nature protocols},
volume = {16},
number = {4},
pages = {2088-2108},
pmid = {33692551},
issn = {1750-2799},
support = {R01 GM123313/GM/NIGMS NIH HHS/United States ; R01 MH103910/MH/NIMH NIH HHS/United States ; },
mesh = {Animals ; CRISPR-Cas Systems/*genetics ; DNA Barcoding, Taxonomic/*methods ; Mice ; Mutation/genetics ; *Phylogeny ; RNA, Guide, CRISPR-Cas Systems/genetics ; },
abstract = {Classic approaches to mapping the developmental history of cells in vivo have relied on techniques that require complex interventions and often capture only a single trajectory or moment in time. We have previously described a developmental barcoding system to address these issues using synthetically induced mutations to record information about each cell's lineage in its genome. This system uses MARC1 mouse lines, which have multiple homing guide RNAs that each generate hundreds of mutant alleles and combine to produce an exponential diversity of barcodes. Here, we detail two MARC1 lines that are available from a public repository. We describe strategies for using MARC1 mice and experimental design considerations. We provide a protocol for barcode retrieval and sequencing as well as the analysis of the sequencing data. This protocol generates barcodes based on synthetically induced mutations in mice to enable lineage analysis.},
}
@article {pmid33690726,
year = {2021},
author = {Zoia, L and Salanti, A and Giorgione, C and Gentili, R and Citterio, S and Gandolfi, I and Franzetti, A and Orlandi, M},
title = {Integrated biological and chemical characterisation of a pair of leonardesque canal lock gates.},
journal = {PloS one},
volume = {16},
number = {3},
pages = {e0247478},
pmid = {33690726},
issn = {1932-6203},
mesh = {Chromatography, Gel ; Construction Materials/*history ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; Fagus/classification/genetics ; History, Ancient ; Italy ; Lignin/analysis ; Phylogeny ; Picea/classification/genetics ; Wood/*chemistry/*classification/genetics ; },
abstract = {The Museo Nazionale della Scienza e della Tecnologia "Leonardo da Vinci" in Milan is exposing two pairs of canal lock gates, used to control the water flow in Milan canal system, whose design appears in the Leonardo's Codex Atlanticus. The wood present in the gates has been deeply characterised by mean of a multidisciplinary investigation involving i) DNA barcoding of wood fragments; ii) microbial community characterisation, and iii) chemical analyses. DNA barcoding revealed that two fragments of the gates belonged to wood species widely used in the middle age: Fagus sylvatica and Picea abies. The chemical characterisations were based on the use of ionic liquid as dissolving medium in order to analyse the entire cell wall material by means of Gel Permeation Chromatography (GPC) and 2D-NMR-HSQC techniques. This multidisciplinary analytical approach was able to highlight the complex nature of the degradation occurred during the gate operation (XVI-XVIII centuries): an intricate interplay between microbial populations (i.e. Shewanella), inorganic factors (i.e. iron from nails), physical factors and the lignocellulosic material.},
}
@article {pmid33690223,
year = {2021},
author = {Charmsaz, S and Gross, N and Jaffee, E and Ho, WJ},
title = {A global live cell barcoding approach for multiplexed mass cytometry profiling of mouse tumors.},
journal = {JCI insight},
volume = {6},
number = {7},
pages = {},
pmid = {33690223},
issn = {2379-3708},
support = {P01 CA247886/CA/NCI NIH HHS/United States ; R01 CA197296/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; B7-H1 Antigen/metabolism ; Biomarkers, Tumor/analysis/*metabolism ; Cell Line, Tumor ; Flow Cytometry/methods ; Fusion Regulatory Protein-1/analysis/*metabolism ; Integrin beta1/analysis/*metabolism ; Leukocyte Common Antigens/analysis ; Mice, Inbred C57BL ; Neoplasms, Experimental/metabolism/*pathology ; Programmed Cell Death 1 Receptor/metabolism ; Reproducibility of Results ; Single-Cell Analysis ; Tumor Microenvironment ; Mice ; },
abstract = {With the advent of cancer immunology, mass cytometry has been increasingly employed to characterize the responses to cancer therapies and the tumor microenvironment (TME). One of its most notable applications is efficient multiplexing of samples into batches by dedicating a number of metal isotope channels to barcodes, enabling robust data acquisition and analysis. Barcoding is most effective when markers are present in all cells of interest. While CD45 has been shown to be a reliable marker for barcoding all immune cells in a given sample, a strategy to reliably barcode mouse cancer cells has not been demonstrated. To this end, we identified CD29 and CD98 as markers widely expressed by commonly used mouse cancer cell lines. We conjugated anti-CD29 and anti-CD98 antibodies to cadmium or indium metals and validated their utility in 10-plex barcoding of live cells. Finally, we established a potentially novel barcoding system incorporating the combination of CD29, CD98, and CD45 to multiplex 10 tumors from s.c. MC38 and KPC tumor models, while successfully recapitulating the known contrast in the PD1-PDL1 axis between the 2 models. The ability to barcode tumor cells along with immune cells empowers the interrogation of the tumor-immune interactions in mouse TME studies.},
}
@article {pmid33689826,
year = {2021},
author = {Sasaki, M and Kobayashi, M and Yoshino, T and Asakawa, M and Nakao, M},
title = {Notocotylus ikutai n. sp. (Digenea: Notocotylidae) from lymnaeid snails and anatid birds in Hokkaido, Japan.},
journal = {Parasitology international},
volume = {83},
number = {},
pages = {102318},
doi = {10.1016/j.parint.2021.102318},
pmid = {33689826},
issn = {1873-0329},
mesh = {Animals ; Animals, Wild ; Bird Diseases/*epidemiology/parasitology ; *Ducks ; Japan/epidemiology ; Microscopy, Electron, Scanning ; Phylogeny ; Prevalence ; RNA, Helminth/analysis ; RNA, Ribosomal, 28S/analysis ; Snails/*parasitology ; Trematoda/*classification/cytology/genetics/ultrastructure ; Trematode Infections/epidemiology/parasitology/*veterinary ; },
abstract = {An unknown species of the genus Notocotylus (Digenea: Notocotylidae) was found as the larval stage from the lymnaeid snail, Radix auricularia, in a static water area of the Chubetsu River, Hokkaido, the northernmost island of Japan. A DNA barcoding identification system was applied to detect the adult stage. Through the inspection of anatid game birds in Hokkaido, Anas crecca, Anas platyrhynchos, Anas zonorhyncha, and Mareca penelope were demonstrated to serve as the definitive hosts. The detailed morphological features of the species were characterized using adults raised experimentally in immunosuppressed mice and naturally developed larvae in R. auricularia. Although the species is morphologically similar to Notocotylus attenuatus and Notocotylus magniovatus in both adult and larval stages, its taxonomic independence was confirmed by a comprehensive study based on molecular phylogeny, morphology, and ecology. Here we propose Notocotylus ikutai n. sp. for this species. The migratory behavior of the anatid hosts and the North-Eurasian distribution of R. auricularia suggest that the new species is widely distributed in the northern Far East.},
}
@article {pmid33688651,
year = {2021},
author = {Credle, JJ and Gunn, J and Sangkhapreecha, P and Monaco, DR and Zheng, XA and Tsai, HJ and Wilbon, A and Morgenlander, WR and Dong, Y and Jayaraman, S and Tosi, L and Parekkadan, B and Baer, AN and Roederer, M and Bloch, EM and Tobian, AAR and Zyskind, I and Silverberg, JI and Rosenberg, AZ and Cox, AL and Lloyd, T and Mammen, AL and Larman, HB},
title = {Neutralizing IFNL3 Autoantibodies in Severe COVID-19 Identified Using Molecular Indexing of Proteins by Self-Assembly.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {33688651},
issn = {2692-8205},
support = {K23 HL151826/HL/NHLBI NIH HHS/United States ; T32 GM136577/GM/NIGMS NIH HHS/United States ; },
abstract = {Unbiased antibody profiling can identify the targets of an immune reaction. A number of likely pathogenic autoreactive antibodies have been associated with life-threatening SARS-CoV-2 infection; yet, many additional autoantibodies likely remain unknown. Here we present Molecular Indexing of Proteins by Self Assembly (MIPSA), a technique that produces ORFeome-scale libraries of proteins covalently coupled to uniquely identifying DNA barcodes for analysis by sequencing. We used MIPSA to profile circulating autoantibodies from 55 patients with severe COVID-19 against 11,076 DNA-barcoded proteins of the human ORFeome library. MIPSA identified previously known autoreactivities, and also detected undescribed neutralizing interferon lambda 3 (IFN-λ3) autoantibodies. At-risk individuals with anti- IFN-λ3 antibodies may benefit from interferon supplementation therapies, such as those currently undergoing clinical evaluation.},
}
@article {pmid33687214,
year = {2021},
author = {Ko, J and Wang, Y and Sheng, K and Weitz, DA and Weissleder, R},
title = {Sequencing-Based Protein Analysis of Single Extracellular Vesicles.},
journal = {ACS nano},
volume = {15},
number = {3},
pages = {5631-5638},
pmid = {33687214},
issn = {1936-086X},
support = {K99 CA256353/CA/NCI NIH HHS/United States ; P01 CA069246/CA/NCI NIH HHS/United States ; R01 CA204019/CA/NCI NIH HHS/United States ; R21 CA236561/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Biomarkers ; *Extracellular Vesicles ; Humans ; *Nanostructures ; },
abstract = {Circulating extracellular vesicles (EVs)-biological nanomaterials shed from most mammalian cells-have emerged as promising biomarkers, drug delivery vesicles, and treatment modulators. While different types of vesicles are being explored for these applications, it is becoming clear that human EVs are quite heterogeneous even in homogeneous or monoclonal cell populations. Since it is the surface EV protein composition that will largely dictate their biological behavior, high-throughput single EV profiling methods are needed to better define EV subpopulations. Here, we present an antibody-based immunosequencing method that allows multiplexed measurement of protein molecules from individual nanometer-sized EVs. We use droplet microfluidics to compartmentalize and barcode individual EVs. The barcodes/antibody-DNA are then sequenced to determine protein composition. Using this highly sensitive technology, we detected specific proteins at the single EV level. We expect that this technology can be further adapted for multiplexed protein analysis of any nanoparticle.},
}
@article {pmid33686765,
year = {2022},
author = {Mhaidi, I and Ait Kbaich, M and El Kacem, S and Daoui, O and Akarid, K and Spitzova, T and Halada, P and Dvorak, V and Lemrani, M},
title = {Entomological study in an anthroponotic cutaneous leishmaniasis focus in Morocco: Fauna survey, Leishmania infection screening, molecular characterization and MALDI-TOF MS protein profiling of relevant Phlebotomus species.},
journal = {Transboundary and emerging diseases},
volume = {69},
number = {3},
pages = {1073-1083},
doi = {10.1111/tbed.14064},
pmid = {33686765},
issn = {1865-1682},
support = {//Institut Pasteur du Maroc/ ; 778298//H2020-MSCA-RAISE-2017/ ; },
mesh = {Animals ; DNA, Kinetoplast ; Female ; Insect Vectors ; *Leishmania/genetics ; *Leishmaniasis, Cutaneous/epidemiology/veterinary ; Male ; Morocco/epidemiology ; *Phlebotomus ; *Psychodidae ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/veterinary ; },
abstract = {In Morocco, leishmaniases are a major public health problem due to their genetic diversity and geographical distribution. Cutaneous leishmaniasis (CL) is an infectious disease caused by various species of Leishmania and transmitted typically by bite of phlebotomine sand flies. This study identifies sand fly fauna in Ibaraghen village, province of Azilal, which is a focus of CL, by combination of morphological and molecular methods (sequencing of COI gene, MALDI-TOF MS protein profiling). Nested-kDNA PCR was used to detect and identify Leishmania species within potential vector species. 432 CDC light traps were placed at different heights above ground level at four capture sites during a whole year. Traps at 1.5 m above the ground yielded capture of sand flies almost double compared to above ground level (29.33%), while the collection reached 55.09% when the traps were placed 2.5 m above ground. A total of 2,830 sand flies were collected, 2,213 unfed specimens were morphologically identified, 990 males (44.73%) and 1,223 females (55.26%) of 13 species; ten Phlebotomus species and three Sergentomyia species. Six species were analysed by MALDI-TOF MS protein profiling (4 Phlebotomus and 2 Sergentomiya species), and their identification was confirmed by COI sequencing. 1,375 unfed females were screened for the presence of Leishmania by nested-kDNA PCR in pools, 11/30 pools of P. sergenti showing a single band of 750 bp corresponding to L. tropica. Our results confirm the role of P. sergenti as a proven vector in Azilal focus of cutaneous leishmaniasis; however, the relative abundance of other species known as vectors of Leishmania species emphasizes the risk of introduction of L. infantum and L. major in this province. For the first time in Morocco, a combined approach to identify sand flies by both morphology and molecular methods based on DNA barcoding and MALDI-TOF MS protein profiling was applied.},
}
@article {pmid33684872,
year = {2021},
author = {Zhang, Y and Li, S and Liang, Y and Liu, R and Lv, X and Zhang, Q and Xu, H and Bi, K and Li, Z and Li, Q},
title = {A systematic strategy for uncovering quality marker of Asari Radix et Rhizoma on alleviating inflammation based chemometrics analysis of components.},
journal = {Journal of chromatography. A},
volume = {1642},
number = {},
pages = {461960},
doi = {10.1016/j.chroma.2021.461960},
pmid = {33684872},
issn = {1873-3778},
mesh = {Animals ; Anti-Inflammatory Agents, Non-Steroidal/*analysis/pharmacology/therapeutic use ; Asarum/*chemistry ; Chromatography, High Pressure Liquid ; Cytokines/analysis ; DNA Barcoding, Taxonomic ; Discriminant Analysis ; Drugs, Chinese Herbal/*analysis/pharmacology/therapeutic use ; Gas Chromatography-Mass Spectrometry ; Inflammation/drug therapy ; Least-Squares Analysis ; Male ; Mice ; Oils, Volatile/*analysis ; Phylogeny ; },
abstract = {Asari Radix et Rhizoma (Asarum), a traditional Chinese medicine (TCM), has been applied in clinical generally. However, due to the lack of valid methods for Asarum quality control, inhomogenous quality and therapy issues have become severe with each passing day. In this study, we aimed to establish a comprehensive multi-system to explore the quality control markers underlying pharmaceutical effects based on chemometrics analysis on the total ingredients of Asarum. In brief, DNA barcoding technology was used to screen out the unadulterated herbs in the 15 batches Asarum collected from different origins. Then, the chemical profiles of volatile/nonvolatile components of 10 batches Asarum with definite resource were obtained by HPLC Q-TOF/MS and GC/MS. Combination with chemometrics methods, 14 characteristic ingredients and 4 qualitative and quantitative markers were figured out preliminarily. Moreover, correlation analysis between the characteristic ingredients and the cytokines integrating the virtual targets prediction of network pharmacology, 3 potential bioactive substance were ascertained. In conclusion, l-asarinin, 2-Methoxy-4-vinylphenol and safrole were considered as the potent candidates for quality control markers based on the comprehensive understanding for therapeutic effects and the chemical information of Asarum, which provided a novel perspective of the development for the quality control of TCM.},
}
@article {pmid33683835,
year = {2021},
author = {Lambert, S and Wilkinson, D},
title = {Trust, efficacy and ethicacy when testing prisoners for COVID-19.},
journal = {International journal of prisoner health},
volume = {17},
number = {3},
pages = {233-244},
doi = {10.1108/IJPH-10-2020-0084},
pmid = {33683835},
issn = {1744-9219},
mesh = {Humans ; COVID-19 Testing ; Trust ; *COVID-19/diagnosis/epidemiology ; *Prisoners ; Prisons ; },
abstract = {PURPOSE: The outbreak of the severe acute respiratory syndrome coronavirus 2 virus and subsequent COVID-19 illness has had a major impact on all levels of society internationally. The extent of the impact of COVID-19 on prison staff and prisoners in England and Wales is unknown. Testing for COVID-19 both asymptomatic and symptomatic, as well as for antibodies, to date, has been minimal. The purpose of this paper is to explore the widespread testing of COVID-19 in prisons poses philosophical and ethical questions around trust, efficacy and ethicacy.<br><br>DESIGN/METHODOLOGY/APPROACH: This paper is both descriptive, providing an overview of the widespread testing of COVID-19 in prisoners in England and Wales, and conceptual in that it discusses and argues the issues associated with large-scale testing. This paper provides a discussion, using comparative studies, of the issues associated with large-scale testing of prisoners across the prison estate in England and Wales (120 prisons). The issues identified in this paper are contextualised through the lens of COVID-19, but they are equally transferrable to epidemiological studies of any pandemic. Given the prevalence of COVID-19 globally and the lack of information about its spread in prisons, at the time of writing this paper, there is a programme of asymptomatic testing of prisoners. However, there remains a paucity of data on the spread of COVID-19 in prisons because of the progress with the ongoing testing programme.<br><br>FINDINGS: The authors argue that the widespread testing of prisoners requires careful consideration of the details regarding who is included in testing, how consent is gained and how tests are administered. This paper outlines and argues the importance of considering the complex nuance of power relationships within the prison system, among prisoner officers, medical staff and prisoners and the detrimental consequences.<br><br>PRACTICAL IMPLICATIONS: The widespread testing of COVID-19 presents ethical and practical challenges. Careful planning is required when considering the ethics of who should be included in COVID-19 testing, how consent will be gained, who and how tests will be administered and very practical challenges around the recording and assigning of COVID-19 test kits inside the prison. The current system for the general population requires scanning of barcodes and registration using a mobile number; these facilities are not permitted inside a prison.<br><br>ORIGINALITY/VALUE: This paper looks at the issues associated with mass testing of prisoners for COVID-19. According to the authors' knowledge, there has not been any research that looks at the issues of testing either in the UK or internationally. The literature available details countries' responses to the pandemic rather and scientific papers on the development of vaccines. Therefore, this paper is an original review of some of the practicalities that need to be addressed to ensure that testing can be as successful as possible.},
}
@article {pmid33683557,
year = {2021},
author = {Pacheco da Silva, VC and Aquino, DA and Crochard, D and Malausa, T and Botton, M and Palero, F},
title = {Parasitoids (Hymenoptera) of Mealybug Pests (Hemiptera: Pseudococcidae) from Southern Brazil: Molecular and Morphological Characterization.},
journal = {Neotropical entomology},
volume = {50},
number = {5},
pages = {759-766},
pmid = {33683557},
issn = {1678-8052},
mesh = {Animals ; Brazil ; Fruit ; *Hemiptera/parasitology ; *Hymenoptera/anatomy &amp; histology/classification ; },
abstract = {Parasitoids of three mealybug pests (Hemiptera: Pseudococcidae), Planococcus ficus (Signoret), Pseudococcus sociabilis Hambleton, and Pseudococcus viburni (Signoret) have been identified for the first time in Brazil. Mealybugs were collected in fruit-growing areas along southern Brazil during 2013-2016. An integrative approach, combining morphological and molecular methods, was used to identify the Brazilian parasitoids to the species level. Fifteen species were recorded, including 14 primary parasitoids belonging to Encyrtidae and Platygastridae and a single secondary parasitoid species belonging to Signiphoridae. The encyrtid parasitoids Acerophagus flavidulus (Brèthes), Anagyrus calyxtoi Noyes and Zaplatycerus sp., and the signiphorid secondary parasitoid Chartocerus axillaris De Santis are reported for the first time in Brazil.},
}
@article {pmid33683395,
year = {2021},
author = {Tripathi, A and Rai, A and Dubey, SC and Akhtar, J and Kumar, P},
title = {DNA barcode, multiplex PCR and qPCR assay for diagnosis of pathogens infecting pulse crops to facilitate safe exchange and healthy conservation of germplasm.},
journal = {Archives of microbiology},
volume = {203},
number = {5},
pages = {2575-2589},
pmid = {33683395},
issn = {1432-072X},
support = {BT/PR18939/PFN/20/1211/2016//Department of Biotechnology , Ministry of Science and Technology/ ; },
mesh = {Alternaria/classification/genetics/isolation &amp; purification ; Ascomycota/classification/genetics/isolation &amp; purification ; Crops, Agricultural/*microbiology ; *DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; Fabaceae/*microbiology ; Fungi/*classification/genetics/isolation &amp; purification ; Fusarium/classification/genetics/isolation &amp; purification ; Multiplex Polymerase Chain Reaction ; Phylogeny ; Plant Diseases/*microbiology ; *Polymerase Chain Reaction ; Real-Time Polymerase Chain Reaction ; Rhizoctonia/classification/genetics/isolation &amp; purification ; },
abstract = {The DNA barcodes were developed from ITS region for the identification of fungal plant pathogens namely, Alternaria alternata and A. tenuissima both causing leaf spots, Ascochyta rabiei causing Ascochyta blight, Fusarium oxysporum f. sp. ciceris causing wilt, Macrophomina phaseolina causing dry root rot, Rhizoctonia solani causing web blight and wet root rot, Sclerotium (Athelia) rolfsii causing collar rot, Sclerotinia sclerotiorum causing stem rot and Cercospora canescens and Pseudocercospora cruenta both causing leaf spots in pulse crops. Barcode compliance for A. alternata (DBTPQ001-18), A. tenuissima (DBTPQ002-18), A. rabiei (DBTPQ003-18), F. oxysporum f. sp. ciceris (DBTPQ004-18), M. phaseolina (DBTPQ005-18), R. solani (DBTPQ006-18), S. rolfsii (DBTPQ007-18), S. sclerotiorum (DBTPQ008-18), C. canescens (DBTPQ009-18) and P. cruenta (DBTPQ029-20) have been generated based on the Barcode of Life Data System (BOLD) system. In addition to ITS, other genomic regions were also explored and on the basis of sequence variation they were ranked as TEF-α > SSU > LSU > β-tubulin. These genes could be considered for secondary barcode and phylogenetic relatedness. ITS-based markers for the detection of A. alternata (BAA2aF and BAA2aR) and R. solani (BRS17cF and BRS17cR) were developed which provided 400 bp and 220 bp amplicons, respectively. While, for F. oxysporum f. sp. ciceris, COX1-based marker (FOCox1F and FOCox3R) was developed which amplified 150 bp. The markers proved highly specific and sensitive with detection limit of 0.0001 ng of template DNA using qPCR and simultaneously detected these three pathogens. The DNA barcodes and diagnostics developed are suitable for quick and reliable detection of these pathogens during quarantine processing and field diagnostics.},
}
@article {pmid33682949,
year = {2021},
author = {Wanjiku, C and Tchouassi, DP and Sole, CL and Pirk, C and Torto, B},
title = {Plant sugar feeding patterns of wild-caught Aedes aegypti from dengue endemic and non-endemic areas of Kenya.},
journal = {Medical and veterinary entomology},
volume = {35},
number = {3},
pages = {417-425},
doi = {10.1111/mve.12514},
pmid = {33682949},
issn = {1365-2915},
mesh = {*Aedes ; Animals ; *Dengue/veterinary ; Feeding Behavior ; Kenya/epidemiology ; Mosquito Vectors ; Sugars ; },
abstract = {A fundamental understanding of plant sugar feeding behaviour in vector populations can lead to the development of ecologically effective vector monitoring and control strategies. Despite previous studies on mosquito-plant interactions, relatively few have been conducted on the dengue vector Aedes aegypti (Diptera: Culicidae). The authors studied Ae. aegypti-plant interactions at two sites of varying dengue endemicity in Kenya: Kilifi (endemic) and Isiolo (non-endemic). Using chemical and molecular assays [DNA barcoding targeting the chloroplast ribulose-1,5 bisphosphate carboxylase/oxygenase large chain (rbcL) gene], the authors show that at the two sites plant feeding in this mosquito species: (a) varies by sex and season; (b) results in the acquisition of diverse sugars, and (c) is associated with diverse host plants in the families Fabaceae, Malvaceae, Poaceae and Rosaceae. These results reveal insights into the plant sugar feeding patterns of wild-caught Ae. aegypti and provide a baseline for future studies on the olfactory basis for host plant attraction for the development of vector monitoring and control tools.},
}
@article {pmid33680700,
year = {2021},
author = {Neeragunda Shivaraj, Y and Plancot, B and Ramdani, Y and Gügi, B and Kambalagere, Y and Jogaiah, S and Driouich, A and Ramasandra Govind, S},
title = {Physiological and biochemical responses involved in vegetative desiccation tolerance of resurrection plant Selaginella brachystachya.},
journal = {3 Biotech},
volume = {11},
number = {3},
pages = {135},
pmid = {33680700},
issn = {2190-572X},
abstract = {UNLABELLED: The vegetative desiccation tolerance of Selaginella brachystachya has been evaluated for its ability to revive from a desiccation (air dry) state and start normal functioning when rehydrated. In this study, S. brachystachya was identified by DNA barcoding. Experiments were conducted using the detached hydrated, desiccated and rehydrated fronds under laboratory conditions to understand the mechanism of revival upon the water availability. Scanning Electron Microscope images during desiccation showed closed stomata and inside curled leaves. Chlorophyll concentration decreased by 1.1 fold in desiccated state and recovered completely upon rehydration. However, the total carotenoid content decreased 4.5 fold while the anthocyanin concentration increased 5.98 fold and the CO2 exchange rate became negative during desiccation. Lipid peroxidation and superoxide radical production were enhanced during desiccation by 68.32 and 73.4%, respectively. Relative electrolyte leakage was found to be minimal during desiccation. Activities of antioxidant enzymes, namely peroxidase (158.33%), glutathione reductase (107.70%), catalase (92.95%) and superoxide dismutase (184.70%) were found to be higher in the desiccated state. The proline concentration increased by 1.4 fold, starch concentration decreased 3.9 fold and sucrose content increased 2.8 fold during desiccation. Upon rehydration, S. brachystachya recovered its original morphology, physiological and biochemical functions. Our results demonstrate that S. brachystachya minimizes desiccation stress through a range of morphological, physiological and biochemical mechanisms. These results provide useful insights into desiccation tolerance mechanisms for potential utilization in enhancing stress tolerance in crop plants.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02667-1.},
}
@article {pmid33680576,
year = {2021},
author = {Cornman, RS and McKenna, JE and Fike, JA},
title = {Composition and distribution of fish environmental DNA in an Adirondack watershed.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e10539},
pmid = {33680576},
issn = {2167-8359},
abstract = {BACKGROUND: Environmental DNA (eDNA) surveys are appealing options for monitoring aquatic biodiversity. While factors affecting eDNA persistence, capture and amplification have been heavily studied, watershed-scale surveys of fish communities and our confidence in such need further exploration.<br><br>METHODS: We characterized fish eDNA compositions using rapid, low-volume filtering with replicate and control samples scaled for a single Illumina MiSeq flow cell, using the mitochondrial 12S ribosomal RNA locus for taxonomic profiling. Our goals were to determine: (1) spatiotemporal variation in eDNA abundance, (2) the filtrate needed to achieve strong sequencing libraries, (3) the taxonomic resolution of 12S ribosomal sequences in the study environment, (4) the portion of the expected fish community detectable by 12S sequencing, (5) biases in species recovery, (6) correlations between eDNA compositions and catch per unit effort (CPUE) and (7) the extent that eDNA profiles reflect major watershed features. Our bioinformatic approach included (1) estimation of sequencing error from unambiguous mappings and simulation of taxonomic assignment error under various mapping criteria; (2) binning of species based on inferred assignment error rather than by taxonomic rank; and (3) visualization of mismatch distributions to facilitate discovery of distinct haplotypes attributed to the same reference. Our approach was implemented within the St. Regis River, NY, USA, which supports tribal and recreational fisheries and has been a target of restoration activities. We used a large record of St. Regis-specific observations to validate our assignments.<br><br>RESULTS: We found that 300 mL drawn through 25-mm cellulose nitrate filters yielded greater than 5 ng/&#xb5;L DNA at most sites in summer, which was an approximate threshold for generating strong sequencing libraries in our hands. Using inferred sequence error rates, we binned 12S references for 110 species on a state checklist into 85 single-species bins and seven multispecies bins. Of 48 bins observed by capture survey in the St. Regis, we detected eDNA consistent with 40, with an additional four detections flagged as potential contaminants. Sixteen unobserved species detected by eDNA ranged from plausible to implausible based on distributional data, whereas six observed species had no 12S reference sequence. Summed log-ratio compositions of eDNA-detected taxa correlated with log(CPUE) (Pearson's R = 0.655, P < 0.001). Shifts in eDNA composition of several taxa and a genotypic shift in channel catfish (Ictalurus punctatus) coincided with the Hogansburg Dam, NY, USA. In summary, a simple filtering apparatus operated by field crews without prior expertise gave useful summaries of eDNA composition with minimal evidence of field contamination. 12S sequencing achieved useful taxonomic resolution despite the short marker length, and data exploration with standard bioinformatic tools clarified taxonomic uncertainty and sources of error.},
}
@article {pmid33680033,
year = {2020},
author = {Katoziyan, A and Imani Fooladi, AA and Taheri, RA and Vatanpour, S},
title = {Multi-drug resistance of Staphylococcus aureus Strains in Baqiyatallah hospital: a Primary Step Towards Digital Health Biomonitoring Systems.},
journal = {Iranian journal of pharmaceutical research : IJPR},
volume = {19},
number = {3},
pages = {321-328},
pmid = {33680033},
issn = {1735-0328},
abstract = {The aim of the study was to evaluate the drug-resistance patterns of Staphylococcus aureus infections in Baqiyatallah hospital within 2010-2019 and to present a novel monitoring and detection system making use of molecular laboratory methods teamed with molecular delimitation analyses. This in turn is a primary step to establishment of a digital health system within Baqiyatallah hospital as a perfect pilot instance for other hospitals to follow upon. Totally, 100 patients of Baqiyatallah hospital suspicious of Staphylococcus aureus infections were sampled. Bacterial identity confirmations were done using routine biochemical test. Antibiograms were made for all the patients in this study. Consequently, bacterial total DNA was extracted and 16S rDNA gene amplified and sequenced for all patients. To uncover any cryptic strain grouping within the samples, a molecular delimitation method, i.e. automated barcode gap discovery (ABGD), was done. Our results showed Ceftaroline to be the most and Erythromycin and Oxacillin the least effective drugs. Delimitation uncovered 19 groups out of which group 19 seemed to have location-specific genetic signals in regards to susceptibility of Erythromycin and Oxacillin. Our results indicate the importance of genetic identification of bacteria with respect to their genetic patterns before antibiotic administration in order to both reduce unnecessary medicine use and to biomonitor the bacterial patterns in respect to their behavior towards general antibiotics.},
}
@article {pmid33679170,
year = {2021},
author = {Wang, C and Gan, J and Mi, X},
title = {On four species of the genus Argiope Audouin, 1826 (Araneae, Araneidae) from China.},
journal = {ZooKeys},
volume = {1019},
number = {},
pages = {15-34},
pmid = {33679170},
issn = {1313-2989},
abstract = {Based on morphological and molecular evidence, Argiope macrochoera Thorell, 1891 from China is found to be the unknown female of A. cameloides Zhu &amp; Song, 1994, the known male of A. perforata Schenkel, 1963 is mismatched and provisionally suggested to be the male of A. boesenbergi Levi, 1983, and the true male of A. perforata Schenkel, 1963 is described for the first time. Argiope abramovi Logunov &amp; Jäger, 2015 is suggested to be a synonym of A. perforata Schenkel, 1963. Argiope chloreides Chrysanthus, 1961 and A. vietnamensis Ono, 2010 are newly recorded from China. The unknown male of A. vietnamensis Ono, 2010 is described for the first time.},
}
@article {pmid33676415,
year = {2021},
author = {Wen, F and Wu, X and Li, T and Jia, M and Liu, X and Liao, L},
title = {The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China.},
journal = {BMC genomics},
volume = {22},
number = {1},
pages = {161},
pmid = {33676415},
issn = {1471-2164},
support = {31560075//National Natural Science Foundation of China/ ; 31760047//National Natural Science Foundation of China/ ; 31960041//National Natural Science Foundation of China/ ; 20202BABL203045//Natural Science Foundation of Jiangxi Province/ ; 2017B070//Foundation of Chinese medicine research of health and family planning commission of Jiangxi province/ ; },
mesh = {Bayes Theorem ; China ; Evolution, Molecular ; *Genome, Chloroplast ; Phylogeny ; },
abstract = {BACKGROUND: Stauntonia chinensis DC. belongs to subfamily Lardizabaloideae, which is widely grown throughout southern China. It has been used as a traditional herbal medicinal plant, which could synthesize a number of triterpenoid saponins with anticancer and anti-inflammatory activities. However, the wild resources of this species and its relatives were threatened by over-exploitation before the genetic diversity and evolutionary analysis were uncovered. Thus, the complete chloroplast genome sequences of Stauntonia chinensis and comparative analysis of chloroplast genomes of Lardizabaloideae species are necessary and crucial to understand the plastome evolution of this subfamily.<br><br>RESULTS: A series of analyses including genome structure, GC content, repeat structure, SSR component, nucleotide diversity and codon usage were performed by comparing chloroplast genomes of Stauntonia chinensis and its relatives. Although the chloroplast genomes of eight Lardizabaloideae plants were evolutionary conserved, the comparative analysis also showed several variation hotspots, which were considered as highly variable regions. Additionally, pairwise Ka/Ks analysis showed that most of the chloroplast genes of Lardizabaloideae species underwent purifying selection, whereas 25 chloroplast protein coding genes were identified with positive selection in this subfamily species by using branch-site model. Bayesian and ML phylogeny on CCG (complete chloroplast genome) and CDs (coding DNA sequences) produced a well-resolved phylogeny of Lardizabaloideae plastid lineages.<br><br>CONCLUSIONS: This study enhanced the understanding of the evolution of Lardizabaloideae and its relatives. All the obtained genetic resources will facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of subfamily Lardizabaloideae.},
}
@article {pmid33675464,
year = {2021},
author = {Bhargavi, M and Maneesha, K and Withanawasam, DM and Aratikatla, KR and Himabindu, S and Prashanth, M and Shanthi, P and Kommana, ML and Reddy, DM and Reddy, BR and Vemireddy, LR},
title = {A novel barcode system for rapid identification of rice (Oryza sativa L.) varieties using agro-morphological descriptors and molecular markers.},
journal = {Molecular biology reports},
volume = {48},
number = {3},
pages = {2209-2221},
pmid = {33675464},
issn = {1573-4978},
mesh = {*Agriculture ; *DNA Barcoding, Taxonomic ; DNA Fingerprinting ; Genetic Markers ; Genotype ; Oryza/*anatomy &amp; histology/*genetics ; Plant Breeding ; },
abstract = {Rice varietal identification is a crucial aspect in breeding, seed production and trade in order to protect the interests of the farmers and consumers. As the number of varieties released is rising every year, the need to identify them unambiguously also increases. Here, we developed a novel barcode system to identify 62 rice genotypes using agro-morphological descriptors and molecular markers. In all, 62 rice genotypes, for 22 agro-morphological traits were recorded. In addition, 19 molecular markers were used for developing genotype-specific DNA fingerprints. The descriptor notes of 10 essential agro-morphological traits and allele codes of the polymorphic markers were used to generate two-dimensional (2-D) barcodes for the rice genotypes. Using agro-morphological traits, 31 rice genotypes were unambiguously distinguished while, with the polymorphic markers we were able to distinguish all rice genotypes except BPT2295 and Jaya. However, using both agro-morphological descriptors and molecular markers in combination, it was possible to distinguish all the rice genotypes used in the present study. These agro-morphological notes and allele codes from the molecular marker data together were used to develop QR (Quick Response) codes for rapid identification of rice genotypes as they facilitate storage of more data. In the present investigation, we have demonstrated the potentiality of agro-morphological traits and molecular markers in distinguishing rice genotypes. The novel QR code system proposed in the present study can also be extended to other crops not only for varietal identification but also for germplasm management and trade.},
}
@article {pmid33673865,
year = {2021},
author = {Binkienė, R and Chagas, CRF and Bernotienė, R and Valkiūnas, G},
title = {Molecular and morphological characterization of three new species of avian Onchocercidae (Nematoda) with emphasis on circulating microfilariae.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {137},
pmid = {33673865},
issn = {1756-3305},
support = {S-MIP-17-27//Lietuvos Mokslo Taryba/ ; },
mesh = {Animals ; Animals, Wild/parasitology ; Bayes Theorem ; Birds/*parasitology ; Female ; Filariasis/blood/parasitology/*veterinary ; Filarioidea/*anatomy &amp; histology/classification/*genetics/isolation &amp; purification ; Male ; Microfilariae/*anatomy &amp; histology/classification/*genetics/isolation &amp; purification ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Blood parasites have been the subject of much research, with numerous reports of the presence of microfilariae in the peripheral blood (circulating microfilariae) of birds belonging to many orders. Current limitations in molecular characterization methods and species identification using morphological characters of circulating microfilariae are major obstacles to improving our understanding the biology of Filarioidea species, particularly in wildlife. The aim of this study was to partially fill these gaps, with particular emphasis on morphological features of microfilariae, which are the most readily accessible stages of these pathogens.<br><br>METHODS: Peripheral blood samples of 206 birds belonging to genera Acrocephalus (five species) and Sylvia (five species) were examined using the buffy coat method to process the blood samples for the presence of microfilariae. Positive birds were dissected to collect adult nematodes. Microfilariae and adult nematodes were described, and sequences of their mitochondrial cytochrome c oxidase subunit I and nuclear 28S rDNA gene fragments were obtained and used for molecular characterization and Bayesian phylogenetic inferences.<br><br>RESULTS: Overall prevalence of microfilariae was 2.9%. Microfilariae were found in the blood samples from six birds (2 Acrocephalus scirpaceus and 1 each of A. arundinaceus, Sylvia atricapilla, S. borin and S. curruca), which were dissected. All parasite species observed were new. Eufilaria acrocephalusi sp. n. and Eufilaria sylviae sp. n. were present in subcutaneous, peritracheal and periesophageal connective tissues in A. scirpaceus and S. borin, respectively. Splendidofilaria bartletti sp. n. was found in finger joins of S. atricapilla. Illustrations of microfilariae and adult nematodes are shown, and morphological and phylogenetic analyses identified the DNA barcode haplotypes that are associated with these species. Phylogenetic analysis places the parasites of different genera in different closely related clades.<br><br>CONCLUSIONS: Adult nematode morphological characters, which have been traditionally used in the taxonomy of Filarioidea species, have a phylogenetic value. Importantly, in our study parasites of different genera were readily distinguishable based on the morphology of their microfilariae. The link between molecular and morphology data requires more study in Filarioidea species research, particularly because this approach provides new knowledge on species identity using only readily accessible blood stages (microfilariae), thereby avoiding host dissection and thus minimizing harm to wildlife during research.},
}
@article {pmid33671838,
year = {2021},
author = {Wawrzyniak, R and Wasiak, W and Jasiewicz, B and Bączkiewicz, A and Buczkowska, K},
title = {Chemical Fingerprinting of Cryptic Species and Genetic Lineages of Aneura pinguis (L.) Dumort. (Marchantiophyta, Metzgeriidae).},
journal = {Molecules (Basel, Switzerland)},
volume = {26},
number = {4},
pages = {},
pmid = {33671838},
issn = {1420-3049},
support = {2011/01/B/NZ8/00364; 2013/09/B/NZ8/03274//Narodowe Centrum Nauki/ ; },
mesh = {Gas Chromatography-Mass Spectrometry ; Genetic Speciation ; Marchantia/*genetics ; Phylogeny ; },
abstract = {Aneura pinguis (L.) Dumort. is a representative of the simple thalloid liverworts, one of the three main types of liverwort gametophytes. According to classical taxonomy, A. pinguis represents one morphologically variable species; however, genetic data reveal that this species is a complex consisting of 10 cryptic species (named by letters from A to J), of which four are further subdivided into two or three evolutionary lineages. The objective of this work was to develop an efficient method for the characterisation of plant material using marker compounds. The volatile chemical constituents of cryptic species within the liverwort A. pinguis were analysed by GC-MS. The compounds were isolated from plant material using the HS-SPME technique. Of the 66 compounds examined, 40 were identified. Of these 40 compounds, nine were selected for use as marker compounds of individual cryptic species of A. pinguis. A guide was then developed that clarified how these markers could be used for the rapid identification of the genetic lineages of A. pinguis. Multivariate statistical analyses (principal component and cluster analysis) revealed that the chemical compounds in A. pinguis made it possible to distinguish individual cryptic species (including genetic lineages), with the exception of cryptic species G and H. The classification of samples based on the volatile compounds by cluster analysis reflected phylogenetic relationships between cryptic species and genetic lineages of A. pinguis revealed based on molecular data.},
}
@article {pmid33671787,
year = {2021},
author = {Singh, PR and Karssen, G and Couvreur, M and Subbotin, SA and Bert, W},
title = {Integrative Taxonomy and Molecular Phylogeny of the Plant-Parasitic Nematode Genus Paratylenchus (Nematoda: Paratylenchinae): Linking Species with Molecular Barcodes.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {2},
pages = {},
pmid = {33671787},
issn = {2223-7747},
support = {UGent BOF01D05918//Universiteit Gent/ ; Plant Pest Diagnostic Center//California Department of Food and Agriculture/ ; },
abstract = {Pin nematodes of the genus Paratylenchus are obligate ectoparasites of a wide variety of plants that are distributed worldwide. In this study, individual morphologically vouchered nematode specimens of fourteen Paratylenchus species, including P. aculentus, P. elachistus, P. goodeyi, P. holdemani, P. idalimus, P. microdorus, P. nanus, P. neoamblycephalus, P. straeleni and P. veruculatus, are unequivocally linked to the D2-D3 of 28S, ITS, 18S rRNA and COI gene sequences. Combined with scanning electron microscopy and a molecular analysis of an additional nine known and thirteen unknown species originating from diverse geographic regions, a total of 92 D2-D3 of 28S, 41 ITS, 57 18S rRNA and 111 COI new gene sequences are presented. Paratylenchus elachistus, P. holdemani and P. neoamblycephalus are recorded for the first time in Belgium and P. idalimus for the first time in Europe. Paratylenchus is an excellent example of an incredibly diverse yet morphologically minimalistic plant-parasitic genus, and this study provides an integrated analysis of all available data, including coalescence-based molecular species delimitation, resulting in an updated Paratylenchus phylogeny and the corrective reassignment of 18 D2-D3 of 28S, 3 ITS, 3 18S rRNA and 25 COI gene sequences that were previously unidentified or incorrectly classified.},
}
@article {pmid33670984,
year = {2021},
author = {McLennan, K and Ruvindy, R and Ostrowski, M and Murray, S},
title = {Assessing the Use of Molecular Barcoding and qPCR for Investigating the Ecology of Prorocentrum minimum (Dinophyceae), a Harmful Algal Species.},
journal = {Microorganisms},
volume = {9},
number = {3},
pages = {},
pmid = {33670984},
issn = {2076-2607},
support = {Project FA002//Food Agility CRC/ ; Marine Microbes Project//Bioplatforms Australia/ ; },
abstract = {Prorocentrum minimum is a species of marine dinoflagellate that occurs worldwide and can be responsible for harmful algal blooms (HABs). Some studies have reported it to produce tetrodotoxin; however, results have been inconsistent. qPCR and molecular barcoding (amplicon sequencing) using high-throughput sequencing have been increasingly applied to quantify HAB species for ecological analyses and monitoring. Here, we isolated a strain of P. minimum from eastern Australian waters, where it commonly occurs, and developed and validated a qPCR assay for this species based on a region of ITS rRNA in relation to abundance estimates from the cultured strain as determined using light microscopy. We used this tool to quantify and examine ecological drivers of P. minimum in Botany Bay, an estuary in southeast Australia, for over ~14 months in 2016-2017. We compared abundance estimates using qPCR with those obtained using molecular barcoding based on an 18S rRNA amplicon. There was a significant correlation between the abundance estimates from amplicon sequencing and qPCR, but the estimates from light microscopy were not significantly correlated, likely due to the counting method applied. Using amplicon sequencing, ~600 unique actual sequence variants (ASVs) were found, much larger than the known phytoplankton diversity from this region. P. minimum abundance in Botany Bay was found to be significantly associated with lower salinities and higher dissolved CO2 levels.},
}
@article {pmid33670956,
year = {2021},
author = {Siedlecki, I and Gorczak, M and Okrasińska, A and Wrzosek, M},
title = {Chance or Necessity-The Fungi Co-Occurring with Formica polyctena Ants.},
journal = {Insects},
volume = {12},
number = {3},
pages = {},
pmid = {33670956},
issn = {2075-4450},
support = {2016/23/B/NZ8/00897//National Science Center Poland/ ; },
abstract = {Studies on carton nesting ants and domatia-dwelling ants have shown that ant-fungi interactions may be much more common and widespread than previously thought. Until now, studies focused predominantly on parasitic and mutualistic fungi-ant interactions occurring mostly in the tropics, neglecting less-obvious interactions involving the fungi common in ants' surroundings in temperate climates. In our study, we characterized the mycobiota of the surroundings of Formica polyctena ants by identifying nearly 600 fungal colonies that were isolated externally from the bodies of F. polyctena workers. The ants were collected from mounds found in northern and central Poland. Isolated fungi were assigned to 20 genera via molecular identification (ITS rDNA barcoding). Among these, Penicillium strains were the most frequent, belonging to eight different taxonomic sections. Other common and widespread members of Eurotiales, such as Aspergillus spp., were isolated very rarely. In our study, we managed to characterize the genera of fungi commonly present on F. polyctena workers. Our results suggest that Penicillium, Trichoderma, Mucor, Schwanniomyces and Entomortierella are commonly present in F. polyctena surroundings. Additionally, the high diversity and high frequency of Penicillium colonies isolated from ants in this study suggest that representatives of this genus may be adapted to survive in ant nests environment better than the other fungal groups, or that they are preferentially sustained by the insects in nests.},
}
@article {pmid33664667,
year = {2021},
author = {Liu, J and Mu, W and Shi, M and Zhao, Q and Kong, W and Xie, H and Shi, L},
title = {The Species Identification in Traditional Herbal Patent Medicine, Wuhu San, Based on Shotgun Metabarcoding.},
journal = {Frontiers in pharmacology},
volume = {12},
number = {},
pages = {607200},
pmid = {33664667},
issn = {1663-9812},
abstract = {Traditional herbal patent medicine typically consists of multiple ingredients, making it challenging to supervise contamination by impurities and the improper use of raw materials. This study employed shotgun metabarcoding for the species identification of biological ingredients in traditional herbal patent medicine, Wuhu San. The five prescribed herbal materials found in Wuhu San were collected, and their reference sequences were obtained by traditional DNA barcoding using Sanger sequencing. Two lab-made and three commercial Wuhu San samples were collected, and a total of 37.14 Gb of shotgun sequencing data was obtained for these five samples using the Illumina sequencing platform. A total of 1,421,013 paired-end reads were enriched for the Internal Transcribed Spacer 2 (ITS2), psbA and trnH intergenic spacer region (psbA-trnH), maturase k (matK), and ribulose-1, 5-bisphosphate carboxylase (rbcL) regions. Furthermore, 80, 11, 9, and 8 operational taxonomic units were obtained for the ITS2, psbA-trnH, matK, and rbcL regions, respectively, after metagenomic assembly, annotation, and chimeric detection. In the two lab-made mock samples, all labeled ingredients in the Wuhu San prescription were successfully detected, and the positive control, Panax quinquefolius L., was detected in the HSZY172 mock sample. Three species, namely Angelica sinensis (Oliv.) Diels, Saposhnikovia divaricata (Turcz. ex Ledeb.) Schischk., and Carthamus tinctorius L., belonging to three labeled ingredients, Angelicae Sinensis Radix (Danggui), Saposhnikoviae Radix (Fangfeng), and Carthami Flos (Honghua), were detected in the three commercial samples. Angelica dahurica (Hoffm.) Benth. &amp; Hook. f. ex Franch. &amp; Sav., the original Angelicae Dahuricae Radix (Baizhi) species, was only detected in WHS003. Arisaema erubescens (Wall.) Schott, Arisaema heterophyllum Blume, or Arisaema amurense Maxim., the original Arisaematis Rhizoma (Tiannanxing) species, were not detected in any of the commercial samples, which could be attributed to the fact that this medicinal material underwent extensive processing. In addition, the Saposhnikovia divaricata adulterant was detected in all the commercial samples, while 24 fungal genera, including Aspergillus, were identified in both the lab-made and commercial samples. This study showed that shotgun metabarcoding provided alternative strategy and technical means for identifying prescribed ingredients in traditional herbal patent medicine and displayed the potential to effectively complement traditional methods.},
}
@article {pmid33661555,
year = {2021},
author = {Dobrowolski, C and Paunovska, K and Hatit, MZC and Lokugamage, MP and Dahlman, JE},
title = {Therapeutic RNA Delivery for COVID and Other Diseases.},
journal = {Advanced healthcare materials},
volume = {10},
number = {15},
pages = {e2002022},
pmid = {33661555},
issn = {2192-2659},
support = {R01 GM132985/GM/NIGMS NIH HHS/United States ; UG3 TR002855/TR/NCATS NIH HHS/United States ; UH3 TR002855/TR/NCATS NIH HHS/United States ; },
mesh = {Animals ; *COVID-19 ; Drug Delivery Systems ; Humans ; Lipids ; *Nanoparticles ; RNA, Small Interfering/genetics ; SARS-CoV-2 ; },
abstract = {RNA can alter the expression of endogenous genes and can be used to express therapeutic proteins. As a result, RNA-based therapies have recently mitigated disease in patients. Yet most potential RNA therapies cannot currently be developed, in large part because delivering therapeutic quantities of RNA drugs to diseased cells remains difficult. Here, recent studies focused on the biological hurdles that make in vivo drug delivery challenging are described. Then RNA drugs that have overcome these challenges in humans, focusing on siRNA to treat liver disease and mRNA to vaccinate against COVID, are discussed. Finally, research centered on improving drug delivery to new tissues is highlighted, including the development of high-throughput in vivo nanoparticle DNA barcoding assays capable of testing over 100 distinct nanoparticles in a single animal.},
}
@article {pmid33660477,
year = {2020},
author = {Zhan, YJ and Zhang, LX and Sun, MT and Li, XM and Wang, Y and Li, MZ and Tao, DD and Sun, ET},
title = {[DNA barcoding of 4 species of cheyletid mites based on COI and 18S rRNA gene sequences].},
journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control},
volume = {33},
number = {1},
pages = {66-70},
doi = {10.16250/j.32.1374.2020154},
pmid = {33660477},
issn = {1005-6661},
support = {31870352//National Natural Science Foundation of China/ ; Wyqnyx201902//2019 Young Outstanding Talents Funded Project of Wannan Medical College/ ; S201910368114//Anhui Provincial College Students Innovation and Entrepreneurship Project/ ; MK201907//MedicalSystem Science and Technology Innovation Fund for Students in Wannan Medical College/ ; },
mesh = {Animals ; DNA ; *DNA Barcoding, Taxonomic ; Genes, rRNA ; *Mites/genetics ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; },
abstract = {OBJECTIVE: To analyze the sequences of mitochondrial cytochrome C oxidase subunit I gene (COI) and 18S ribosomal RNA gene (18S rRNA), so as to identify the feasible DNA barcodes for 4 species of cheyletid mites and improve the DNA barcoding database for cheyletid mites.<br><br>METHODS: Cheyletid mite samples were collected from small-scale flour mills in Fuyang, Wuhu and Tongling cities of Anhui Province from May 2018 to July 2019, extracted and morphologically identified. Then, genomic DNA was extracted from a single cheyletid mite, and the COI and 18S rRNA gene sequences were obtained by PCR amplification, cloning and sequencing. The obtained sequences were aligned using the BLAST software. Multiple sequence alignment was done using the software ClustalX version 1.83 using the known gene sequences from cheyletid mites. The genetic distance was calculated using the software MEGA X, and the phylogenetic tree was created using the maximum likelihood method.<br><br>RESULTS: The DNA barcoding results of Cheyletus malaccensis, C. carnifex and Cheletomorpha lepidopterorum were consistent with the morphological identification, while no sequences pertaining to Eucheyletia reticulate were retrieved in the GenBank database. The proportions of A + T were 69.6% and 55.1% in the COI and 18S rRNA sequences of 4 cheyletid mites species, respectively, and the numbers of base substitutions were 137 and 46, respectively. There were 154 to 321 and 58 to 99 inter-species variation loci in the COI and 18S rRNA gene sequences of 4 cheyletid mites species, respectively, and the intra-species genetic distance was all 0.020 or less in the COI and 18S rRNA gene sequences of 4 cheyletid mites species, with inter-species genetic distance of 0.235 to 0.583 and 0.078 to 0.114, respectively. Phylogenetic analysis based on COI and 18S rRNA genes showed that all four species of cheyletid mites were clustered into a branch with a 100% supportive rate, which was consistent with the morphological identification.<br><br>CONCLUSIONS: Mitochondrial COI gene is superior to 18S rRNA gene as DNA barcodes for 4 species of cheyletid mites, which is more suitable to be used to investigate the phylogenetic relationship of at genus and species levels.},
}
@article {pmid33659853,
year = {2020},
author = {Romanov, DA and Zakharov, IA and Shaikevich, EV},
title = {Wolbachia, Spiroplasma, and Rickettsia symbiotic bacteria in aphids (Aphidoidea).},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {24},
number = {6},
pages = {673-682},
doi = {10.18699/VJ20.661},
pmid = {33659853},
issn = {2500-0462},
abstract = {Aphids are a diverse family of crop pests. Aphids formed a complex relationship with intracellular bacteria. Depending on the region of study, the species composition of both aphids and their facultative endosymbionts varies. The aim of the work was to determine the occurrence and genetic diversity of Wolbachia, Spiroplasma and Rickettsia symbionts in aphids collected in 2018-2019 in Moscow. For these purposes, 578 aphids from 32 collection sites were tested by PCR using specific primers. At least 21 species of aphids from 14 genera and four families were identified by barcoding method, of which 11 species were infected with endosymbionts. Rickettsia was found in six species, Wolbachia in two species, Spiroplasma in one species. The presence of Rickettsia in Impatientinum asiaticum, Myzus cerasi, Hyalopterus pruni, Eucallipterus tiliae, Chaitophorus tremulae and Wolbachia in Aphis pomi and C. tremulae has been described for the first time. A double infection with Rickettsia and Spiroplasma was detected in a half of pea aphid (Acyrthosiphon pisum) individuals. For the first time was found that six species of aphids are infected with Rickettsia that are genetically different from previously known. It was first discovered that A. pomi is infected with two Wolbachia strains, one of which belongs to supergroup B and is genetically close to Wolbachia from C. tremulae. The second Wolbachia strain from A. pomi belongs to the supergroup M, recently described in aphid species. Spiroplasma, which we observed in A. pisum, is genetically close to male killing Spiroplasma from aphids, ladybirds and moths. Both maternal inheritance and horizontal transmission are the pathways for the distribution of facultative endosymbiotic bacteria in aphids.},
}
@article {pmid33659795,
year = {2020},
author = {Kryukov, AA and Gorbunova, AO and Machs, EM and Mikhaylova, YV and Rodionov, AV and Zhurbenko, PM and Yurkov, AP},
title = {Perspectives of using Illumina MiSeq for identification of arbuscular mycorrhizal fungi.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {24},
number = {2},
pages = {158-167},
doi = {10.18699/VJ19.38-o},
pmid = {33659795},
issn = {2500-0462},
abstract = {Arbuscular mycorrhiza fungi (AMF) form one of the most common symbiosis with the majority of land plants. AMF supply the plant with various mineral elements, primarily phosphorus, and improve the water supply. The search for the most effective AMF strains for symbiosis and the creation of microbial preparations on that basis is an important task for modern biology. Owing to the difficulties of cultivation without a host plant and their high genetic polymorphism, identifying AMF is very difficult. A high number of cryptic species often makes morphological identification unreliable. Recent years have seen a growth in the number of AMF biodiversity studies performed by modern NGS-based methods, Illumina MiSeq in particular. Currently, there are still many questions that remain for the identification of AМF. The most important are whether conservative or variable sequences should be used to select a marker for barcoding and whether universal primers or those specific to AMF should be used. In our work, we have successfully used universal primers ITS3 and ITS4 for the sequencing in Illumina MiSeq of the 5.8S rDNA - ITS2 region of the 35S rRNA genes, which contain both a conservative and variable regions. The molecular genetic approach for AMF identification was quite effective and allowed us to reliably identify eight of nine isolates to the species level: five isolates of Rhizophagus irregularis, and one isolate of R. invermaius, Paraglomus laccatum, and Claroideoglomus etunicatum, respectively. For all five R. irregularis isolates, high variability in the ITS region and the absence of ecotopic-related molecular characters in the ITS2 region were demonstrated. The NCBI data is still insufficient for accurate AMF identification of Acaulospora sp. isolates from the genus to the species level.},
}
@article {pmid33659709,
year = {2021},
author = {Zhang, Y and Xu, S and Sun, C and Dumont, H and Han, BP},
title = {A new set of highly efficient primers for COI amplification in rotifers.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {6},
number = {2},
pages = {636-640},
pmid = {33659709},
issn = {2380-2359},
abstract = {Rotifers are a small-sized but key group of freshwater zooplankters with high species richness, linking primary producers to higher consumers in aquatic food webs. DNA barcoding has been widely used in exploring its biodiversity, cryptic speciation and phylogeny. However, the inefficiency of universal primers to amplify COI of rotifers hinders our understanding of their species richness and genetic diversity. Here, we develop a new pair of primers, 30 F and 885 R, to amplify the COI gene of rotifers. We used 22 species to test their PCR success rate and found that the new pair of primers was more efficient (86%) than two pairs of universal primers, namely, dgLCO and dgHCO (32%), and Folmer primers (59%). The new primers will allow the barcoding of groups that were so far difficult to sequence and will contribute to clarify species diversity and phylogeny of rotifers.},
}
@article {pmid33659463,
year = {2020},
author = {Landskron, L and Bonnay, F and Burkard, TR and Knoblich, JA},
title = {DigiTAG-a RNA Sequencing Approach to Analyze Transcriptomes of Rare Cell Populations in Drosophila melanogaster.},
journal = {Bio-protocol},
volume = {10},
number = {21},
pages = {e3809},
pmid = {33659463},
issn = {2331-8325},
abstract = {Cell-type specific transcriptional programs underlie the development and maintenance of organs. Not only distinct cell types within a tissue, even cells with supposedly identical cell fates show a high degree of transcriptional heterogeneity. Inevitable, low cell numbers are a major hurdle to study transcriptomes of pure cell populations. Here we describe DigiTAG, a high-throughput method that combines transposase fragmentation and molecular barcoding to retrieve high quality transcriptome data of rare cell types in Drosophila melanogaster. The protocol showcases how DigiTAG can be used to analyse the transcriptome of rare neural stem cells (type II neuroblasts) of Drosophila larval brains, but can also be utilized for other cell types or model systems.},
}
@article {pmid33659418,
year = {2020},
author = {Yazaki, J},
title = {Novel Protein-oligonucleotide Conjugation Method Involving a High-affinity Capture HaloTag.},
journal = {Bio-protocol},
volume = {10},
number = {18},
pages = {e3759},
pmid = {33659418},
issn = {2331-8325},
abstract = {Highly sensitive quantitative protein profiling can play a key role in the early diagnosis of diseases, such as autoimmune diseases and cancer. We developed a modified protein-oligonucleotide conjugation method termed HaloTag-mediated barcoding, for quantifying protein molecules at a higher sensitivity than conventional protein quantification methods. This novel and efficient conjugation method can be used to prepare HaloTag-barcoded proteins using a click chemistry-based labeling technique. Here, we describe the preparation of protein-DNA complexes and detection of protein-protein interactions which can be used in a HaloTag protein barcode assay to detect an antibody. The protocol includes procedures for preparing the ligand-oligonucleotide complex, plasmid DNA preparation for protein expression, and preparation of the protein-oligonucleotide complex. The described click reaction-based protocols simplify the conventional amine-ester reaction methods which require additional steps for chromatography purification.},
}
@article {pmid33656329,
year = {2021},
author = {Rezaei, M and Radfar, P and Winter, M and McClements, L and Thierry, B and Warkiani, ME},
title = {Simple-to-Operate Approach for Single Cell Analysis Using a Hydrophobic Surface and Nanosized Droplets.},
journal = {Analytical chemistry},
volume = {93},
number = {10},
pages = {4584-4592},
doi = {10.1021/acs.analchem.0c05026},
pmid = {33656329},
issn = {1520-6882},
mesh = {High-Throughput Nucleotide Sequencing ; *Microfluidics ; Polymerase Chain Reaction ; *Single-Cell Analysis ; },
abstract = {Microfluidics-based technologies for single-cell analysis are becoming increasingly important tools in biological studies. With the increasing sophistication of microfluidics, cellular barcoding techniques, and next-generation sequencing, a more detailed picture of cellular subtype is emerging. Unfortunately, the majority of the methods developed for single-cell analysis are high-throughput and not suitable for rare cell analysis as they require a high input cell number. Here, we report a low-cost and reproducible method for rare single-cell analysis using a highly hydrophobic surface and nanosized static droplets. Our method allows rapid and efficient on-chip single-cell lysis and subsequent collection of genetic materials in nanoliter droplets using a micromanipulator or a laboratory pipette before subsequent genetic analysis. We show precise isolation of single cancer cells with high purity using two different strategies (i- cytospin and ii- static droplet array) for subsequent RNA analysis using droplet digital polymerase chain reaction (PCR) and real-time PCR. Our highly controlled isolation method opens a new avenue for the study of subcellular functional mechanisms, enabling the identification of rare cells of potential functional or pathogenic consequence.},
}
@article {pmid33655639,
year = {2021},
author = {Burian, A and Mauvisseau, Q and Bulling, M and Domisch, S and Qian, S and Sweet, M},
title = {Improving the reliability of eDNA data interpretation.},
journal = {Molecular ecology resources},
volume = {21},
number = {5},
pages = {1422-1433},
doi = {10.1111/1755-0998.13367},
pmid = {33655639},
issn = {1755-0998},
support = {//Global Challenges Research Fund, UK/ ; J45/2018//Leibniz Competition/ ; },
mesh = {*Biodiversity ; Conservation of Natural Resources ; *DNA Barcoding, Taxonomic ; DNA, Environmental/*analysis ; Environmental Monitoring ; Reproducibility of Results ; },
abstract = {Global declines in biodiversity highlight the need to effectively monitor the density and distribution of threatened species. In recent years, molecular survey methods detecting DNA released by target-species into their environment (eDNA) have been rapidly on the rise. Despite providing new, cost-effective tools for conservation, eDNA-based methods are prone to errors. Best field and laboratory practices can mitigate some, but the risks of errors cannot be eliminated and need to be accounted for. Here, we synthesize recent advances in data processing tools that increase the reliability of interpretations drawn from eDNA data. We review advances in occupancy models to consider spatial data-structures and simultaneously assess rates of false positive and negative results. Further, we introduce process-based models and the integration of metabarcoding data as complementing approaches to increase the reliability of target-species assessments. These tools will be most effective when capitalizing on multi-source data sets collating eDNA with classical survey and citizen-science approaches, paving the way for more robust decision-making processes in conservation planning.},
}
@article {pmid33651639,
year = {2021},
author = {},
title = {Trends in DNA Barcoding and Metabarcoding 2020.},
journal = {Genome},
volume = {64},
number = {3},
pages = {iii},
doi = {10.1139/gen-2021-0013},
pmid = {33651639},
issn = {1480-3321},
mesh = {Animals ; *DNA/genetics ; *DNA Barcoding, Taxonomic ; Genetic Techniques ; Humans ; },
}
@article {pmid33651354,
year = {2021},
author = {Angeli, D},
title = {Urinary Nucleic Acid in Tumor: Bioinformatics Approaches.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2292},
number = {},
pages = {95-104},
pmid = {33651354},
issn = {1940-6029},
mesh = {Animals ; Biomarkers, Tumor/genetics/urine ; Cell-Free Nucleic Acids/genetics/*urine ; DNA Copy Number Variations ; DNA Methylation ; Epigenesis, Genetic ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Liquid Biopsy/methods ; Neoplasms/genetics/*urine ; },
abstract = {Application of next generation sequencing techniques in the field of liquid biopsy, in particular urine, requires specific bioinformatics methods in order to deal with its peculiarity. Many aspects of cancer can be explored starting from nucleic acids, especially from cell-free DNA and circulating tumor DNA in order to characterize cancer. It is possible to detect small mutations, as single nucleotide variants, small insertions and deletions, copy-number alterations, and epigenetic profiles. Due to the low fraction of circulating tumor DNA over the whole cell-free DNA, some methods have been exploited. One of them is the application of unique barcodes to each DNA fragment in order to lower the limit of detection of cancer-related variants. Some bioinformatics workflows and tools are the same of a classic analysis of tumor tissue, but there are some steps in which specific algorithms have to be introduced.},
}
@article {pmid33649477,
year = {2021},
author = {Lin, DS and Tian, L and Tomei, S and Amann-Zalcenstein, D and Baldwin, TM and Weber, TS and Schreuder, J and Stonehouse, OJ and Rautela, J and Huntington, ND and Taoudi, S and Ritchie, ME and Hodgkin, PD and Ng, AP and Nutt, SL and Naik, SH},
title = {Single-cell analyses reveal the clonal and molecular aetiology of Flt3L-induced emergency dendritic cell development.},
journal = {Nature cell biology},
volume = {23},
number = {3},
pages = {219-231},
pmid = {33649477},
issn = {1476-4679},
mesh = {Animals ; Cell Lineage ; Cell Proliferation/*drug effects ; Cells, Cultured ; Dendritic Cells/*drug effects/immunology/metabolism ; Female ; Gene Expression Regulation, Developmental ; Hematopoiesis/*drug effects ; Hematopoietic Stem Cells/*drug effects/immunology/metabolism ; Interferon Regulatory Factors/genetics/metabolism ; Male ; Membrane Proteins/*pharmacology ; Mice, Inbred C57BL ; Mice, Transgenic ; Phenotype ; *RNA-Seq ; *Single-Cell Analysis ; Transcriptome/*drug effects ; Mice ; },
abstract = {Regulation of haematopoietic stem and progenitor cell (HSPC) fate is crucial during homeostasis and under stress conditions. Here we examine the aetiology of the Flt3 ligand (Flt3L)-mediated increase of type 1 conventional dendritic cells (cDC1s). Using cellular barcoding we demonstrate this occurs through selective clonal expansion of HSPCs that are primed to produce cDC1s and not through activation of cDC1 fate by other HSPCs. In particular, multi/oligo-potent clones selectively amplify their cDC1 output, without compromising the production of other lineages, via a process we term tuning. We then develop Divi-Seq to simultaneously profile the division history, surface phenotype and transcriptome of individual HSPCs. We discover that Flt3L-responsive HSPCs maintain a proliferative 'early progenitor'-like state, leading to the selective expansion of multiple transitional cDC1-primed progenitor stages that are marked by Irf8 expression. These findings define the mechanistic action of Flt3L through clonal tuning, which has important implications for other models of 'emergency' haematopoiesis.},
}
@article {pmid33648451,
year = {2021},
author = {Bernhards, CB and Lux, MW and Katoski, SE and Goralski, TDP and Liem, AT and Gibbons, HS},
title = {barCoder: a tool to generate unique, orthogonal genetic tags for qPCR detection.},
journal = {BMC bioinformatics},
volume = {22},
number = {1},
pages = {98},
pmid = {33648451},
issn = {1471-2105},
support = {CB3654//Defense Threat Reduction Agency/ ; },
mesh = {Algorithms ; *Bacillus anthracis/genetics ; *DNA Barcoding, Taxonomic ; *DNA Primers ; Genome ; Real-Time Polymerase Chain Reaction ; },
abstract = {BACKGROUND: Tracking dispersal of microbial populations in the environment requires specific detection methods that discriminate between the target strain and all potential natural and artificial interferents, including previously utilized tester strains. Recent work has shown that genomic insertion of short identification tags, called "barcodes" here, allows detection of chromosomally tagged strains by real-time PCR. Manual design of these barcodes is feasible for small sets, but expansion of the technique to larger pools of distinct and well-functioning assays would be significantly aided by software-guided design.<br><br>RESULTS: Here we introduce barCoder, a bioinformatics tool that facilitates the process of creating sets of uniquely identifiable barcoded strains. barCoder utilizes the genomic sequence of the target strain and a set of user-specified PCR parameters to generate a list of suggested barcode "modules" that consist of binding sites for primers and probes, and appropriate spacer sequences. Each module is designed to yield optimal PCR amplification and unique identification. Optimal amplification includes metrics such as ideal melting temperature and G+C content, appropriate spacing, and minimal stem-loop formation; unique identification includes low BLAST hits against the target organism, previously generated barcode modules, and databases (such as NCBI). We tested the ability of our algorithm to suggest appropriate barcodes by generating 12 modules for Bacillus thuringiensis serovar kurstaki-a simulant for the potential biowarfare agent Bacillus anthracis-and three each for other potential target organisms with variable G+C content. Real-time PCR detection assays directed at barcodes were specific and yielded minimal cross-reactivity with a panel of near-neighbor and potential contaminant materials.<br><br>CONCLUSIONS: The barCoder algorithm facilitates the generation of synthetically barcoded biological simulants by (a) eliminating the task of creating modules by hand, (b) minimizing optimization of PCR assays, and (c) reducing effort wasted on non-unique barcode modules.},
}
@article {pmid33647116,
year = {2020},
author = {Chan-Chable, RJ and Martínez-Arce, A and Ortega-Morales, AI and Mis-Ávila, PC},
title = {New Records and Updated Checklist of Mosquito Species in Quintana Roo, Mexico, Using DNA-Barcoding.},
journal = {Journal of the American Mosquito Control Association},
volume = {36},
number = {4},
pages = {264-268},
doi = {10.2987/20-6941.1},
pmid = {33647116},
issn = {1943-6270},
mesh = {Animals ; Biodiversity ; *Checklist ; *Culicidae ; DNA Barcoding, Taxonomic ; Female ; Mexico ; },
abstract = {Collections of mosquitoes were conducted as part of the entomological vector surveillance in Quintana Roo State, Mexico, during September 2015. Species collected included Anopheles gabaldoni, An. darlingi, Psorophora columbiae, Culex inflictus, Cx. trifidus, Cx. lactator, and Wyeomyia guatemala s.l. All the specimens were identified by morphological and molecular characters (DNA-barcoding). This is the 1st time these species are reported in the Mexican state of Quintana Roo. This research updates and increases the list of species of mosquitoes in Quintana Roo from 79 to 86.},
}
@article {pmid33647037,
year = {2021},
author = {Bulusheva, I and Belova, V and Nikashin, B and Korostin, D},
title = {BC-store: A program for MGISEQ barcode sets analysis.},
journal = {PloS one},
volume = {16},
number = {3},
pages = {e0247532},
pmid = {33647037},
issn = {1932-6203},
mesh = {Algorithms ; Base Sequence/genetics ; DNA Barcoding, Taxonomic/*instrumentation/*methods ; High-Throughput Nucleotide Sequencing/*instrumentation/*methods ; Humans ; *Software ; },
abstract = {Here we present the devised BC-store-a program for analyzing and selecting sets of barcodes for sequencing on platforms manufactured by MGI Tech (China). The app is available as an open source in Python3 and as a desktop version. The application allows analyzing the compatibility of barcodes on a single lane of a flow cell in a set in the case of equal and arbitrary fractions. In addition, with the help of this tool barcodes can be added to an existing set with custom share options. In this paper we describe how BC-store works for different tasks and consider the effectiveness of using BC-store in sequence lab routine tasks.},
}
@article {pmid33643301,
year = {2020},
author = {Hada-Neeman, S and Weiss-Ottolenghi, Y and Wagner, N and Avram, O and Ashkenazy, H and Maor, Y and Sklan, EH and Shcherbakov, D and Pupko, T and Gershoni, JM},
title = {Domain-Scan: Combinatorial Sero-Diagnosis of Infectious Diseases Using Machine Learning.},
journal = {Frontiers in immunology},
volume = {11},
number = {},
pages = {619896},
pmid = {33643301},
issn = {1664-3224},
mesh = {AIDS Serodiagnosis/methods ; Amino Acid Sequence ; Antigen-Antibody Reactions ; Base Sequence ; Communicable Diseases/*diagnosis ; DNA Barcoding, Taxonomic ; DNA, Recombinant/immunology ; Epitopes/genetics/immunology ; Genetic Vectors ; HIV Antibodies/*blood ; HIV Core Protein p24/genetics/*immunology ; HIV Envelope Protein gp160/*immunology ; HIV Infections/*diagnosis ; Hepatitis C/*diagnosis ; Hepatitis C Antibodies/*blood ; Hepatitis C Antigens/genetics/*immunology ; High-Throughput Nucleotide Sequencing ; Humans ; *Machine Learning ; Oligonucleotides/genetics/immunology ; Peptide Fragments/genetics/immunology ; *Peptide Library ; Polymerase Chain Reaction/methods ; Serologic Tests/*methods ; },
abstract = {The presence of pathogen-specific antibodies in an individual's blood-sample is used as an indication of previous exposure and infection to that specific pathogen (e.g., virus or bacterium). Measurement of the diagnostic antibodies is routinely achieved using solid phase immuno-assays such as ELISA tests and western blots. Here, we describe a sero-diagnostic approach based on phage-display of epitope arrays we term "Domain-Scan". We harness Next-generation sequencing (NGS) to measure the serum binding to dozens of epitopes derived from HIV-1 and HCV simultaneously. The distinction of healthy individuals from those infected with either HIV-1 or HCV, is modeled as a machine-learning classification problem, in which each determinant ("domain") is considered as a feature, and its NGS read-out provides values that correspond to the level of determinant-specific antibodies in the sample. We show that following training of a machine-learning model on labeled examples, we can very accurately classify unlabeled samples and pinpoint the domains that contribute most to the classification. Our experimental/computational Domain-Scan approach is general and can be adapted to other pathogens as long as sufficient training samples are provided.},
}
@article {pmid33642472,
year = {2021},
author = {Tanaka, S and Ito, M},
title = {Quantitative Analysis of Ent-Kaurane Diterpenoids in Isodon Herb (Enmei-So) by HPLC-UV.},
journal = {Chemical &amp; pharmaceutical bulletin},
volume = {69},
number = {3},
pages = {246-252},
doi = {10.1248/cpb.c20-00769},
pmid = {33642472},
issn = {1347-5223},
mesh = {Chromatography, High Pressure Liquid ; Diterpenes/chemistry ; Diterpenes, Kaurane/*chemistry/pharmacology ; Drug Evaluation, Preclinical ; Flowers/*chemistry ; Humans ; Isodon/*chemistry ; Plant Extracts/*chemistry/pharmacology ; Plant Leaves/*chemistry ; Plant Stems/*chemistry ; Solvents/chemistry ; Tandem Mass Spectrometry ; Temperature ; },
abstract = {The terrestrial plants, Isodon japonicus (Burm. f.) H. Hara and Isodon trichocarpus (Maxim.) Kudô (Labiatae), are native to Japan. Different parts of these plants have been used as a traditional bitter stomachic, under the name Isodon herb (Enmei-so). Ent-kaurane diterpenoids are the major constituents of Isodon herb that contribute to the herb's medicinal properties. However, large variability with respect to the composition of these diterpenoids limits the suitability of Isodon herb as a pharmaceutical ingredient. Thus, an investigation of the factors that affect its chemical composition is required. In this study, the DNA-barcoding method, using internal transcribed spacer sequences of nuclear ribosomal DNA, was applied to cultivated and commercial samples of Isodon herb. Further, each such sample was separated into leaves, stems, and flowers and analyzed for diterpenoid content by HPLC. Moreover, the diterpenoid content in coarsely cut and powdered samples was evaluated. Results confirmed that the source species of these samples was I. japonicus or I. trichocarpus. The three major diterpenoids in Isodon herb were enmein, oridonin, and ponicidin. The diterpenoid content was affected by milling process. Moreover, the diterpenoid content was greatly affected by the ratio between leaves and stems in each sample. Thus, to accurately quantify the diterpenoids in Isodon herb, the use specific conditions such as drying using mild temperature conditions and avoiding milling of the samples might be necessary. This may help in regulating variations in the herb's composition, in turn, providing better quality and a safe herbal product for pharmaceutical use.},
}
@article {pmid33641980,
year = {2021},
author = {Soltani Firouz, M and Mohi-Alden, K and Omid, M},
title = {A critical review on intelligent and active packaging in the food industry: Research and development.},
journal = {Food research international (Ottawa, Ont.)},
volume = {141},
number = {},
pages = {110113},
doi = {10.1016/j.foodres.2021.110113},
pmid = {33641980},
issn = {1873-7145},
mesh = {Food Microbiology ; *Food Packaging ; *Food Preservation ; Food-Processing Industry ; Research ; },
abstract = {The emergence of many new food products on the market with need of consumers to constantly monitor their quality until consuming, in addition to the necessity for reducing food corruption during preservation time, have led to the development of some modern packaging technologies such as intelligent packaging (IP) and active packaging (AP). The benefits of IP are detecting defects, quality monitoring and tracking the packaged food products to control the storage conditions from the production stage to the consumption stage by using various sensors and indicators such as time-temperature indicators (TTIs), gas indicators, humidity sensors, optical, calorimetric and electrochemical biosensors. While, AP helps to increase the shelf-life of products by using absorbing and diffusion systems for various materials like carbon dioxide, oxygen, and ethanol. However, there are some important issues over these emerging technologies including cost, marketability, consumer acceptance, safety and organoleptic quality of the food and emphatically environmental safety concerns. Therefore, future researches should be conducted to solve these problems and to prompt applications of IP and AP in the food industry. This paper reviews the latest innovations in these advanced packaging technologies and their applications in food industry. The IP systems namely indicators, barcoding techniques, radio frequency identification systems, sensors and biosensor are reviewed and then the latest innovations in AP methods including scavengers, diffusion systems and antimicrobial packaging are reviewed in detail.},
}
@article {pmid33641956,
year = {2021},
author = {Naaum, AM and Cusa, M and Singh, M and Bleicher, Z and Elliott, C and Goodhead, IB and Hanner, RH and Helyar, SJ and Mariani, S and Rice, JE and Wangh, LJ and Sanchez, JA},
title = {Validation of FASTFISH-ID: A new commercial platform for rapid fish species authentication via universal closed-tube barcoding.},
journal = {Food research international (Ottawa, Ont.)},
volume = {141},
number = {},
pages = {110035},
doi = {10.1016/j.foodres.2020.110035},
pmid = {33641956},
issn = {1873-7145},
mesh = {Animals ; *DNA/genetics ; *DNA Barcoding, Taxonomic ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Seafood represents up to 20% of animal protein consumption in global food consumption and is a critical dietary and income resource for the world's population. Currently, over 30% of marine fish stocks are harvested at unsustainable levels, and the industry faces challenges related to Illegal, Unregulated and Unreported (IUU) fishing. Accurate species identification is one critical component of successful stock management and helps combat fraud. Existing DNA-based technologies permit identification of seafood even when morphological features are removed, but are either too time-consuming, too expensive, or too specific for widespread use throughout the seafood supply chain. FASTFISH-ID is an innovative commercial platform for fish species authentication, employing closed-tube barcoding in a portable device. This method begins with asymmetric PCR amplification of the full length DNA barcode sequence and subsequently interrogates the resulting single-stranded DNA with a universal set of Positive/Negative probes labeled in two fluorescent colors. Each closed-tube reaction generates two species-specific fluorescent signatures that are then compared to a cloud-based library of previously validated fluorescent signatures. This novel approach results in rapid, automated species authentication without the need for complex, time consuming, identification by DNA sequencing, or repeated analysis with a panel of species-specific tests. Performance of the FASTFISH-ID platform was assessed in a blinded study carried out in three laboratories located in the UK and North America. The method exhibited a 98% success rate among the participating laboratories when compared to species identification via conventional DNA barcoding by sequencing. Thus, FASTFISH-ID is a promising new platform for combating seafood fraud across the global seafood supply chain.},
}
@article {pmid33637824,
year = {2021},
author = {Villalta, I and Ledet, R and Baude, M and Genoud, D and Bouget, C and Cornillon, M and Moreau, S and Courtial, B and Lopez-Vaamonde, C},
title = {A DNA barcode-based survey of wild urban bees in the Loire Valley, France.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {4770},
pmid = {33637824},
issn = {2045-2322},
mesh = {Animals ; Bees/classification/*genetics ; Cities ; DNA Barcoding, Taxonomic ; Ecosystem ; Endangered Species ; France ; Gene Library ; Sequence Analysis, DNA ; },
abstract = {The current decline of wild bees puts important ecosystem services such as pollination at risk. Both inventory and monitoring programs are needed to understand the causes of wild bee decline. Effective insect monitoring relies on both mass-trapping methods coupled with rapid and accurate identifications. Identifying wild bees using only morphology can be challenging, in particular, specimens from mass-trapped samples which are often in poor condition. We generated DNA barcodes for 2931 specimens representing 157 species (156 named and one unnamed species) and 28 genera. Automated cluster delineation reveals 172 BINs (Barcodes Index Numbers). A total of 36 species (22.93%) were found in highly urbanized areas. The majority of specimens, representing 96.17% of the species barcoded form reciprocally exclusive groups, allowing their unambiguous identification. This includes several closely related species notoriously difficult to identify. A total of 137 species (87.26%) show a "one-to-one" match between a named species and the BIN assignment. Fourteen species (8.92%) show deep conspecific lineages with no apparent morphological differentiation. Only two species pairs shared the same BIN making their identification with DNA barcodes alone uncertain. Therefore, our DNA barcoding reference library allows reliable identification by non-experts for the vast majority of wild bee species in the Loire Valley.},
}
@article {pmid33635552,
year = {2021},
author = {Mazungula, DN and Chakona, A},
title = {An integrative taxonomic review of the Natal mountain catfish, Amphilius natalensis Boulenger 1917 (Siluriformes, Amphiliidae), with description of four new species.},
journal = {Journal of fish biology},
volume = {99},
number = {1},
pages = {219-239},
doi = {10.1111/jfb.14714},
pmid = {33635552},
issn = {1095-8649},
support = {//Funding for this research was provided by the Rhodes University Research Council Grant and the National Research Foundation (NRF) of South Africa under the Foundational Biodiversity Information Programme: Biodiversity surveys in priority inland areas (FBIP) grants (grant reference no. IBIP-BS13100251309). The University of Zimbabwe is acknowledged for providing the research vehicle used for surveys in the Eastern Highlands of Zimbabwe. We hereby acknowledge the use of infrastructure, equipment and specimens provided by the NRF-SAIAB's Aquatic Genomics Research Platform, Margaret Smith Library, Collections Division Platform, and the funding channelled through the NRF-SAIAB Institutional Support System./ ; },
mesh = {Africa, Southern ; Animal Distribution ; Animals ; *Catfishes/genetics ; Phylogeny ; Rivers ; South Africa ; },
abstract = {An integrative taxonomic analysis combining mitochondrial cytochrome oxidase subunit I sequences, morphology, colour pattern and two species delimitation approaches revealed the existence of five lineages within the Natal mountain catfish, Amphilius natalensis, in southern Africa. These lineages are separated by substantial genetic divergences (1.6%-9.46%), and they can be consistently distinguished from one another based on a combination of morphology and colour pattern differences. Additionally, the lineages are allopatrically distributed and confined to isolated river systems draining discrete mountain ranges, which makes gene flow among them unlikely. One of these lineages is A. natalensis s.s., which is confined to the uMngeni and Tukela river systems in KwaZulu Natal (KZN) Province in South Africa. The other four lineages represent new species to science which are described as Amphilius zuluorum sp. nov., endemic to the uMkhomazi River system in KZN, Amphilius engelbrechti sp. nov., endemic to the Inkomati River system in Mpumalanga Province in South Africa, Amphilius marshalli sp. nov., endemic to the Pungwe and Lower Zambezi river systems in Zimbabwe and Mozambique, and Amphilius leopardus sp. nov., endemic to the Ruo River in Malawi. The results show that Amphilius laticaudatus which is endemic to the Buzi River system in Zimbabwe and Mozambique, belongs to the A. natalensis s.l. complex. A redescription of A. laticaudatus is presented and an updated identification key for the mountain catfishes of southern Africa is provided.},
}
@article {pmid33633762,
year = {2021},
author = {Han, S and Sebastin, R and Wang, X and Lee, KJ and Cho, GT and Hyun, DY and Chung, JW},
title = {Identification of Vicia Species Native to South Korea Using Molecular and Morphological Characteristics.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {608559},
pmid = {33633762},
issn = {1664-462X},
abstract = {Recently, within the Fabaceae family, the Vicia genus has been recognized for its vital role in sustainable agriculture. Vicia species are economically important grain and forage crops. However, the presence of complex morphological characteristics makes identification and recognition of native species difficult. In this study, the possibility of using DNA barcoding regions (ITS2, matK, and rbcL) to distinguish among 19 Vicia taxa (59 accessions) found in South Korea was evaluated. The sequence alignment analysis revealed considerable nucleotide diversity (π) between the loci, in which ITS2 showed the highest mean interspecific distance, whereas there was no intraspecific variability among the barcode regions in 12 of the 19 taxa. Phylogenetic analysis of combined barcoding regions revealed well-resolved phylogeny with the highest species level discrimination. Combinations of barcode loci were also used in classification at the subgenera and section levels. The results revealed that the combined barcoding regions can be used effectively to differentiate the following species: Vicia angustifolia var. segetilis, Vicia bungei, Vicia villosa, Vicia cracca, Vicia dasycarpa, Vicia hirsuta, Vicia tetrasperma, Vicia amurensis, Vicia hirticalycina, and Vicia chosenensis. However, it is difficult to differentiate the species of Vicia unijuga, Vicia unijuga var. kaussanensis, Vicia linearifolia, Vicia unijuga f. angustifolia, Vicia nipponica, Vicia amoena, Vicia venosa var. cuspidata, Vicia pseudo-orobus, and Vicia japonica with the tested barcode regions. These species come under sect. Vicilla and are found to be closely related or species that have recently undergone speciation; thus, it has limitation to distinguish with recommended barcodes. Hence, to differentiate the unclassified species, 39 morphological characteristics were investigated, in which 16 useful characteristics were selected for efficient classification. Finally, the 16 selected morphological useful traits efficiently differentiated all the Vicia species. In conclusion, a combination of barcoding loci together with morphological characteristics of this study efficiently discriminated all the Korean Vicia species.},
}
@article {pmid33631371,
year = {2021},
author = {Satz, AL and Kuai, L and Peng, X},
title = {Selections and screenings of DNA-encoded chemical libraries against enzyme and cellular targets.},
journal = {Bioorganic &amp; medicinal chemistry letters},
volume = {39},
number = {},
pages = {127851},
doi = {10.1016/j.bmcl.2021.127851},
pmid = {33631371},
issn = {1464-3405},
mesh = {Animals ; Cell Line ; DNA/*pharmacology ; Deoxyribonucleases/*antagonists &amp; inhibitors/metabolism ; Drug Evaluation, Preclinical ; Humans ; Molecular Structure ; Small Molecule Libraries/chemistry/*pharmacology ; },
abstract = {The use of DNA-encoded libraries (DELs) has increased greatly over the last decade, and today a majority of pharmaceutical companies employ the technology. The technology may be applied to most soluble and purified targets. However, standard DEL technology has limitations; some targets are challenging to purify, and it is not possible to directly screen for cellular or biochemical activity. Numerous creative methods have been reported to overcome these limitations and expand DEL target scope. Reported proof-of-concept experiments include DEL selections of cell surfaces, and inside of living cells. Additional alternatives include the construction and biochemical screening of one-bead-one-compound (OBOC) DELs using picoliter aqueous droplets or microfabricated wells as containers. In these cases, the small-molecule moiety of the library member is liberated from its DNA barcode, and able to interact freely with the desired target. Lastly, patent literature suggests the ability to conduct cellular functional screens using OBOC DELs.},
}
@article {pmid33631274,
year = {2021},
author = {Kiran, KR and Swathy, PS and Paul, B and Shama Prasada, K and Radhakrishna Rao, M and Joshi, MB and Rai, PS and Satyamoorthy, K and Muthusamy, A},
title = {Untargeted metabolomics and DNA barcoding for discrimination of Phyllanthus species.},
journal = {Journal of ethnopharmacology},
volume = {273},
number = {},
pages = {113928},
doi = {10.1016/j.jep.2021.113928},
pmid = {33631274},
issn = {1872-7573},
mesh = {Chromatography, Liquid ; Cluster Analysis ; DNA Barcoding, Taxonomic ; Metabolomics ; Phyllanthus/*chemistry/*classification/metabolism ; Phylogeny ; Plant Extracts/*chemistry/*classification/metabolism ; Plant Leaves/chemistry/metabolism ; Principal Component Analysis ; Tandem Mass Spectrometry ; },
abstract = {Phyllanthus species is extensively cultivated and used as edible fruits and herbal drugs. The Phyllanthus species are used extensively as ethnopharmacologically important materials in several countries, especially in Asia. Various Phyllanthus species are broadly used in the Ayurvedic system of medicine and deliberated as bitter, astringent, stomachic, diuretic, febrifuge, deobstruent, and antiseptic, and used for the treatment of digestive, genitourinary, respiratory, skin diseases, hepatopathy, jaundice, and renal calculus in India. Precise authentification of Phyllanthus species is a challenge due to morphological similarities and is important to avoid adulteration found in herbal drugs. Hence, there is a need to establish comprehensive methods for the identification of Phyllanthus species.<br><br>AIM OF THE STUDY: In this study, we attempted to integrate untargeted metabolomics to identify species-specific metabolites with traditional phylogenetic analysis for identification and discrimination of nine Phyllanthus species.<br><br>MATERIALS AND METHODS: Phyllanthus species such as P. acidus, P. amarus, P. debilis, P. emblica, P. virgatus, P. urinaria, P. lawii, P. myrtifolius, and P. reticulatus were collected. The liquid chromatography coupled mass spectrometry (LC-MS) was performed for untargeted metabolite profiling and MS/MS fragmentation analysis was performed for selected compounds. Further, the barcoding analysis was executed using plastid loci, rpoC1 to integrate with metabolite profiling data.<br><br>RESULTS: The Principal Component Analysis (PCA) of leaf metabolites showed distinct clusters in different species. Through further analysis, we have also identified the qualitative and quantitative status of unique metabolites across the species, and the majority of the selected compounds were annotated. The metabolic fingerprinting and the hierarchical clustering indicated that though the P. deblis and P. virgatus are distantly related to each other, they are closely associated with their metabolic profiling. Similarly, P. myrtifolius and P. urinaria are closely related to each other with their metabolic fingerprints than the genetic alignment. Further, we performed barcoding with rpoC1 across nine Phyllanthus species (P. acidus, P. amarus, P. debilis, P. emblica, P. virgatus, P. urinaria, P. lawii, P. myrtifolius, and P. reticulatus). Sequence similarity search in the GenBank database showed rpoC1 barcode loci from nine Phyllanthus species showed significant identity (>97%) with the sequences of various Phyllanthus species.<br><br>CONCLUSIONS: The bioactive metabolites and their abundance can be assigned to specific species thereby serving as a biological signature and indicators for potential therapeutic use. This study identified differential expression of 14 secondary metabolites from nine Phyllanthus species. Alkaloid compound zeatin was found specific to P. virgatus and delphinidin-3-O- &#x3b2; -D-glucoside was not found in P. myrtifolius. Barcoding and phylogenetic analysis showed P. acidus is the most genetically distinct among the groups and the sequence pair between P.emblica-P.reticulatus and P.emblica-P.urinaria showed the least difference.},
}
@article {pmid33630764,
year = {2021},
author = {Okoye, AA and Duell, DD and Fukazawa, Y and Varco-Merth, B and Marenco, A and Behrens, H and Chaunzwa, M and Selseth, AN and Gilbride, RM and Shao, J and Edlefsen, PT and Geleziunas, R and Pinkevych, M and Davenport, MP and Busman-Sahay, K and Nekorchuk, M and Park, H and Smedley, J and Axthelm, MK and Estes, JD and Hansen, SG and Keele, BF and Lifson, JD and Picker, LJ},
title = {CD8+ T cells fail to limit SIV reactivation following ART withdrawal until after viral amplification.},
journal = {The Journal of clinical investigation},
volume = {131},
number = {8},
pages = {},
pmid = {33630764},
issn = {1558-8238},
support = {P51 OD011092/OD/NIH HHS/United States ; 75N91019D00024/CA/NCI NIH HHS/United States ; UM1 AI126611/AI/NIAID NIH HHS/United States ; UM1 AI124377/AI/NIAID NIH HHS/United States ; R37 AI054292/AI/NIAID NIH HHS/United States ; HHSN261200800001E/CA/NCI NIH HHS/United States ; HHSN261200800001C/CA/NCI NIH HHS/United States ; S10 OD025002/OD/NIH HHS/United States ; },
mesh = {Animals ; Anti-Retroviral Agents/*pharmacology ; CD8-Positive T-Lymphocytes/*immunology/pathology ; Female ; *Lymphocyte Depletion ; Macaca mulatta ; Male ; Simian Acquired Immunodeficiency Syndrome/drug therapy/*immunology/pathology ; Simian Immunodeficiency Virus/*physiology ; Virus Activation/drug effects/*immunology ; },
abstract = {To define the contribution of CD8+ T cell responses to control of SIV reactivation during and following antiretroviral therapy (ART), we determined the effect of long-term CD8+ T cell depletion using a rhesusized anti-CD8β monoclonal antibody on barcoded SIVmac239 dynamics on stable ART and after ART cessation in rhesus macaques (RMs). Among the RMs with full CD8+ T cell depletion in both blood and tissue, there were no significant differences in the frequency of viral blips in plasma, the number of SIV RNA+ cells and the average number of RNA copies/infected cell in tissue, and levels of cell-associated SIV RNA and DNA in blood and tissue relative to control-treated RMs during ART. Upon ART cessation, both CD8+ T cell-depleted and control RMs rebounded in fewer than 12 days, with no difference in the time to viral rebound or in either the number or growth rate of rebounding SIVmac239M barcode clonotypes. However, effectively CD8+ T cell-depleted RMs showed a stable, approximately 2-log increase in post-ART plasma viremia relative to controls. These results indicate that while potent antiviral CD8+ T cell responses can develop during ART-suppressed SIV infection, these responses effectively intercept post-ART SIV rebound only after systemic viral replication, too late to limit reactivation frequency or the early spread of reactivating SIV reservoirs.},
}
@article {pmid33629364,
year = {2021},
author = {Azevedo, FM and Zawadzki, CH and Soria, TV and Fabrin, TMC and Oliveira, AV and Prioli, SMAP and Prioli, AJ},
title = {Integrative taxonomy reveals the historically poorly defined armoured catfish Hypostomus variipictus (Ihering 1911), from the upper rio Paraná basin, Brazil (Siluriformes, Loricariidae).},
journal = {Journal of fish biology},
volume = {99},
number = {1},
pages = {143-152},
doi = {10.1111/jfb.14706},
pmid = {33629364},
issn = {1095-8649},
support = {313623/2017-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Animals ; Brazil ; *Catfishes/genetics ; },
abstract = {In a recent expedition to the rio Grande basin, a tributary of the rio Paraná in southern Brazil, individuals of the armoured catfish genus Hypostomus with a peculiar and beautiful colour pattern composed of pale vermiculations on the head and four to five horizontal stripes on the flanks were collected. Initially, the specimens were identified as a colour morph of the pale-spotted H. margaritifer. However, when we compared their partial cytochrome C oxidase subunit I (COI) mitochondrial gene to sequences of some typically pale-spotted H. margaritifer, the striped specimens were genetically distinct. Further analysis of the striped individuals revealed that they are the poorly known but valid species Hypostomus variipictus, which was described by Ihering in 1911 from the rio Pardo, a tributary of the rio Grande, upper rio Paraná basin, in São Paulo State, Brazil. Since its descriptions, no robust taxonomic work has been published concerning this species. In this study, the newly sampled population was compared to the original description and to the holotype of H. variipictus, providing the foundation for a complete redescription, proper diagnosis, and first live colour illustration and description of the previously hidden H. variipictus.},
}
@article {pmid33628081,
year = {2021},
author = {Colihueque, N and Gantz, A and Parraguez, M},
title = {Revealing the biodiversity of Chilean birds through the COI barcode approach.},
journal = {ZooKeys},
volume = {1016},
number = {},
pages = {143-161},
pmid = {33628081},
issn = {1313-2989},
abstract = {The mitochondrial cytochrome c oxidase subunit I (COI) gene is an effective molecular tool for the estimation of genetic variation and the identification of bird species. This molecular marker is used to differentiate among Chilean bird species by analyzing barcodes for 76 species (197 individuals), comprising 28 species with no previous barcode data and 48 species with sequences retrieved from the BOLD and GenBank databases. The DNA barcodes correctly identified 94.7% of the species analyzed (72 of 76 species). Mean intraspecific K2P distance was 0.3% (range 0-8.7%). Within the intraspecific divergence range, three species, Phrygilus gayi, Sephanoides sephanoides and Curaeus curaeus, showed relatively high intraspecific divergence (1.5-8.7%), possibly due to the presence of a species complex or geographic isolation of sub-populations. Mean interspecific K2P distance was 24.7% (range 1.3-43.5%). Consequently, the intraspecific K2P distance showed limited overlap with interspecific K2P distance. The mean intraspecific divergence in our study was similar to that found in temperate regions of South America (0.24%). However, it was approximately one order of magnitude lower than values reported for bird species in tropical regions of northern South America (1.8-2.13%). This result suggests that bird species from Chile show low levels of genetic structure and divergence. The small overlap between intra- and inter-specific distances implies that COI barcodes could be used as an effective tool to identify nearly all the Chilean bird species analyzed.},
}
@article {pmid33627984,
year = {2020},
author = {Gupta, S and Fauzdar, A and Singh, VJ and Srivastava, A and Sharma, K and Singh, S},
title = {A Preliminary Experience of Integration of an Electronic Witness System, its Validation, Efficacy on Lab Performance, and Staff Satisfaction Assessment in a Busy Indian in vitro Fertilization Laboratory.},
journal = {Journal of human reproductive sciences},
volume = {13},
number = {4},
pages = {333-339},
pmid = {33627984},
issn = {0974-1208},
abstract = {BACKGROUND: Electronic witness system (EWS) is one of the recent advancements in the field of in vitro fertilization (IVF) that uses radiofrequency identification (RFID) technology to monitor all critical work carried out in each stage of IVF procedures cycle.<br><br>OBJECTIVE: The main objective of the study was validation and integration of electronic witnessing system, assessment of its efficacy on lab performance, and staff satisfaction in a busy tertiary IVF center.<br><br>MATERIALS AND METHODS: The study data included analysis of 187 consecutive cycles for installation and validation of EWS. The laboratory outcomes were analyzed for development of good-quality embryos followed up for the pregnancy outcome.<br><br>RESULTS: A total of 751 RFIG tags were involved with 77 patient-assigned barcodes for the all the analyzed cycles. During validation of EWS, a total of 02 (0.46%) red flags were highlighted by EWS from pre-allocated tags within the frequency range of the reader. The maturation rate (83.1%), fertilization rate (74.3%), cleavage rate (93.5%), day 3 grade-A embryo development rate (64.6%), good grade blastocyst development rate (26.4%) were observed in EWS group that was comparable to other groups with no significant difference (P > 0.005). Frozen embryo transfer of EWS cases observed a clinical pregnancy rate (50.0%) that was higher than other groups though statistically not significant as sample size was small.<br><br>CONCLUSIONS: Our preliminary study suggests that EWS does not affect the gametes, embryos, and pregnancy rate, however a larger randomized clinical trials should be undertaken to evaluate the safety and efficacy of EWS.},
}
@article {pmid33626067,
year = {2021},
author = {Gold, Z and Sprague, J and Kushner, DJ and Zerecero Marin, E and Barber, PH},
title = {eDNA metabarcoding as a biomonitoring tool for marine protected areas.},
journal = {PloS one},
volume = {16},
number = {2},
pages = {e0238557},
pmid = {33626067},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; Biological Monitoring/*methods ; California ; DNA/analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Environmental/*analysis ; Ecological Parameter Monitoring/methods ; Ecosystem ; Environmental Monitoring/methods ; Fishes/genetics ; Pacific Ocean ; },
abstract = {Monitoring of marine protected areas (MPAs) is critical for marine ecosystem management, yet current protocols rely on SCUBA-based visual surveys that are costly and time consuming, limiting their scope and effectiveness. Environmental DNA (eDNA) metabarcoding is a promising alternative for marine ecosystem monitoring, but more direct comparisons to visual surveys are needed to understand the strengths and limitations of each approach. This study compares fish communities inside and outside the Scorpion State Marine Reserve off Santa Cruz Island, CA using eDNA metabarcoding and underwater visual census surveys. Results from eDNA captured 76% (19/25) of fish species and 95% (19/20) of fish genera observed during pairwise underwater visual census. Species missed by eDNA were due to the inability of MiFish 12S barcodes to differentiate species of rockfishes (Sebastes, n = 4) or low site occupancy rates of crevice-dwelling Lythrypnus gobies. However, eDNA detected an additional 23 fish species not recorded in paired visual surveys, but previously reported from prior visual surveys, highlighting the sensitivity of eDNA. Significant variation in eDNA signatures by location (50 m) and site (~1000 m) demonstrates the sensitivity of eDNA to address key questions such as community composition inside and outside MPAs. Results demonstrate the utility of eDNA metabarcoding for monitoring marine ecosystems, providing an important complementary tool to visual methods.},
}
@article {pmid33625849,
year = {2021},
author = {Choo, XY and Lim, YM and Katwadi, K and Yap, L and Tryggvason, K and Sun, AX and Li, S and Handoko, L and Ouyang, JF and Rackham, OJL},
title = {Evaluating Capture Sequence Performance for Single-Cell CRISPR Activation Experiments.},
journal = {ACS synthetic biology},
volume = {10},
number = {3},
pages = {640-645},
doi = {10.1021/acssynbio.0c00499},
pmid = {33625849},
issn = {2161-5063},
mesh = {Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; Human Embryonic Stem Cells ; Humans ; RNA, Guide, CRISPR-Cas Systems/metabolism ; RNA, Messenger/metabolism ; Single-Cell Analysis/*methods ; Transcription Factors/genetics/metabolism ; },
abstract = {The combination of single-cell RNA sequencing with CRISPR inhibition/activation provides a high-throughput approach to simultaneously study the effects of hundreds if not thousands of gene perturbations in a single experiment. One recent development in CRISPR-based single-cell techniques introduces a feature barcoding technology that allows for the simultaneous capture of mRNA and guide RNA (gRNA) from the same cell. This is achieved by introducing a capture sequence, whose complement can be incorporated into each gRNA and that can be used to amplify these features prior to sequencing. However, because the technology is in its infancy, there is little information available on how such experimental parameters can be optimized. To overcome this, we varied the capture sequence, capture sequence position, and gRNA backbone to identify an optimal gRNA scaffold for CRISPR activation gene perturbation studies. We provide a report on our screening approach along with our observations and recommendations for future use.},
}
@article {pmid33620710,
year = {2021},
author = {Pyrcz, TW and Stachowicz, I and Zubek, A and Espeland, M and Jiménez, OM and Lachowska-Cierlik, D and Florczyk, K},
title = {A New Species of Butterfly of the Genus Protopedaliodes from the Isolated Tramen Tepui in the Guyana Shield (Lepidoptera, Nymphalidae, Satyrinae).},
journal = {Neotropical entomology},
volume = {50},
number = {2},
pages = {218-228},
pmid = {33620710},
issn = {1678-8052},
mesh = {Animals ; *Butterflies/anatomy &amp; histology/classification ; Environment ; Female ; Guyana ; Venezuela ; },
abstract = {A new species of Protopedaliodes Viloria &amp; Pyrcz, a satyrine butterfly genus endemic to the highest part of the Guyana Shield, P. arekuna Pyrcz &amp; Stachowicz n. sp., is described from the summit area, ca. 2400 m, of Tramen Tepui, an isolated mountain situated on the Venezuela-Guyana border. It is a remarkable finding as it is probably a narrow endemic, and only the fourth known member of the genus. Morphologically it most closely resembles P. kukenani Viloria &amp; Pyrcz from the Roraima-Kukenán twin peaks. COI barcode analysis shows, however, high genetic distances between these two species, 9-10%. Protopedaliodes taxonomy is briefly revised, from the perspective of the monophyly of the genus based on preliminary molecular and morphological comparative data, including the female genitalia described for the first time for P. kukenani and P. ridouti Viloria &amp; Pyrcz.},
}
@article {pmid33619394,
year = {2021},
author = {Emert, BL and Cote, CJ and Torre, EA and Dardani, IP and Jiang, CL and Jain, N and Shaffer, SM and Raj, A},
title = {Variability within rare cell states enables multiple paths toward drug resistance.},
journal = {Nature biotechnology},
volume = {39},
number = {7},
pages = {865-876},
pmid = {33619394},
issn = {1546-1696},
support = {T32 DK007780/DK/NIDDK NIH HHS/United States ; R01 HG009283/HG/NHGRI NIH HHS/United States ; T32 HL007439/HL/NHLBI NIH HHS/United States ; DP5 OD028144/OD/NIH HHS/United States ; R01 CA238237/CA/NCI NIH HHS/United States ; F30 CA236129/CA/NCI NIH HHS/United States ; T32 GM007170/GM/NIGMS NIH HHS/United States ; R01 CA232256/CA/NCI NIH HHS/United States ; F30 HD103378/HD/NICHD NIH HHS/United States ; P50 CA174523/CA/NCI NIH HHS/United States ; U01 CA227550/CA/NCI NIH HHS/United States ; F30 HG010822/HG/NHGRI NIH HHS/United States ; RM1 HG007743/HG/NHGRI NIH HHS/United States ; P30 CA016520/CA/NCI NIH HHS/United States ; U01 DK127405/DK/NIDDK NIH HHS/United States ; R01 GM137425/GM/NIGMS NIH HHS/United States ; U01 HL129998/HL/NHLBI NIH HHS/United States ; T32 HG000046/HG/NHGRI NIH HHS/United States ; },
mesh = {Antineoplastic Agents/*pharmacology ; Cell Line ; Cell Survival/*drug effects ; *Drug Resistance, Neoplasm ; Extracellular Signal-Regulated MAP Kinases/genetics/metabolism ; Gene Expression Regulation, Neoplastic/drug effects ; Humans ; Integrin alpha3/genetics/metabolism ; Melanoma ; Phosphorylation ; Single-Cell Analysis ; Vemurafenib/*pharmacology ; },
abstract = {Molecular differences between individual cells can lead to dramatic differences in cell fate, such as death versus survival of cancer cells upon drug treatment. These originating differences remain largely hidden due to difficulties in determining precisely what variable molecular features lead to which cellular fates. Thus, we developed Rewind, a methodology that combines genetic barcoding with RNA fluorescence in situ hybridization to directly capture rare cells that give rise to cellular behaviors of interest. Applying Rewind to BRAF[V600E] melanoma, we trace drug-resistant cell fates back to single-cell gene expression differences in their drug-naive precursors (initial frequency of ~1:1,000-1:10,000 cells) and relative persistence of MAP kinase signaling soon after drug treatment. Within this rare subpopulation, we uncover a rich substructure in which molecular differences among several distinct subpopulations predict future differences in phenotypic behavior, such as proliferative capacity of distinct resistant clones after drug treatment. Our results reveal hidden, rare-cell variability that underlies a range of latent phenotypic outcomes upon drug exposure.},
}
@article {pmid33619390,
year = {2021},
author = {Mateo, LJ and Sinnott-Armstrong, N and Boettiger, AN},
title = {Tracing DNA paths and RNA profiles in cultured cells and tissues with ORCA.},
journal = {Nature protocols},
volume = {16},
number = {3},
pages = {1647-1713},
pmid = {33619390},
issn = {1750-2799},
support = {DP2 GM132935/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Cell Line ; Cell Nucleus/genetics ; Cells, Cultured ; Chromatin/metabolism ; Chromatin Immunoprecipitation/methods ; Chromosomes/genetics ; DNA/chemistry/genetics ; DNA Probes ; Fluorescent Dyes/chemistry ; Genetic Techniques ; Genome/genetics ; Genomics/methods ; Humans ; Image Processing, Computer-Assisted/methods ; In Situ Hybridization, Fluorescence/*methods ; Microscopy, Fluorescence/*methods ; Optical Restriction Mapping/*methods ; RNA/chemistry/genetics ; },
abstract = {Chromatin conformation capture (3C) methods and fluorescent in situ hybridization (FISH) microscopy have been used to investigate the spatial organization of the genome. Although powerful, both techniques have limitations. Hi-C is challenging for low cell numbers and requires very deep sequencing to achieve its high resolution. In contrast, FISH can be done on small cell numbers and capture rare cell populations, but typically targets pairs of loci at a lower resolution. Here we detail a protocol for optical reconstruction of chromatin architecture (ORCA), a microscopy approach to trace the 3D DNA path within the nuclei of fixed tissues and cultured cells with a genomic resolution as fine as 2 kb and a throughput of ~10,000 cells per experiment. ORCA can identify structural features with comparable resolution to Hi-C while providing single-cell resolution and multimodal measurements characteristic of microscopy. We describe how to use this DNA labeling in parallel with multiplexed labeling of dozens of RNAs to relate chromatin structure and gene expression in the same cells. Oligopaint probe design, primary probe making, sample collection, cryosectioning and RNA/DNA primary probe hybridization can be completed in 1.5 weeks, while automated RNA/DNA barcode hybridization and RNA/DNA imaging typically takes 2-6 d for data collection and 2-7 d for the automated steps of image analysis.},
}
@article {pmid33618378,
year = {2021},
author = {Pyrka, I and Stefanaki, A and Vlachonasios, KE},
title = {DNA Barcoding of St. John's wort (Hypericum spp.) Growing Wild in North-Eastern Greece.},
journal = {Planta medica},
volume = {87},
number = {7},
pages = {528-537},
doi = {10.1055/a-1379-3249},
pmid = {33618378},
issn = {1439-0221},
support = {European Regional Development Fund//MIS 5002803/ ; National Strategic Reference Framework (NSRF), Research Funding Programme of the Action RESEARCH - CREATE - INNOVATE//AROMADISTIL - 95783/ ; },
mesh = {DNA Barcoding, Taxonomic ; Greece ; *Hypericum/genetics ; Plant Extracts ; *Plants, Medicinal ; },
abstract = {Plants of the genus Hypericum, commonly known as "St. John's wort" ("spathohorto" or "valsamo" in Greek), have been used since antiquity for their therapeutic properties. Wild-harvested Hypericum plants are still popular today in herbal medicines, commercially exploited due to their bioactive compounds, hypericin and hyperforin, which have antidepressant, antimicrobial and antiviral activity. Species identification of commercial products is therefore important and DNA barcoding, a molecular method that uses small sequences of organisms' genome as barcodes, can be useful in this direction. In this study, we collected plants of the genus Hypericum that grow wild in North-Eastern Greece and explored the efficiency of matK, and trnH-psbA regions as DNA barcodes for their identification. We focused on 5 taxa, namely H. aucheri, H. montbretii, H. olympicum, H. perforatum subsp. perforatum, and H. thasium, the latter a rare Balkan endemic species collected for the first time from mainland Greece. matK (using the genus-specific primers designed herein), trnH-psbA, and their combination were effectively used for the identification of the 5 Hypericum taxa and the discrimination of different H. perforatum subsp. perforatum populations. These barcodes were also able to discriminate Greek populations of H. perforatum, H. aucheri, H. montbretii, and H. olympicum from populations of the same species growing in other countries.},
}
@article {pmid33617379,
year = {2021},
author = {Zhang, W and Cheng, J and Zhao, Y and Niu, D and Guo, H},
title = {Molecular identification and DNA barcode screening of acaroid mites in ground flour dust.},
journal = {Genome},
volume = {64},
number = {9},
pages = {869-877},
doi = {10.1139/gen-2020-0099},
pmid = {33617379},
issn = {1480-3321},
mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; DNA Primers ; Dust ; *Flour ; *Mites/genetics ; Phylogeny ; },
abstract = {Molecular identification of acaroid mites is difficult because of the scarcity of molecular data in GenBank. Here, acaroid mites collected from ground flour dust in Xi'an, China, were preliminarily morphologically classified/grouped. Universal primers were then designed to amplify and screen suitable DNA barcodes for identifying these mites. Sixty mite samples were morphologically classified into six groups. Groups 1-2 were identified to Dermatophagoides farinae and Tyrophagus putrescentiae, while Groups 3-6 were not identified to the species level. ITS2 exhibited higher efficiency in molecular identification in comparison with COI, 12S, and 16S. Groups 1-6 were identified as D. farinae, T. putrescentiae, Suidasia nesbitti, Chortoglyphus arcuatus, Lepidoglyphus destructor, and Gohieria sp., respectively. The phylogenetic results were consistent with the morphological classification. Group 6 was further identified as G. fusca according to the morphology of the reproductive foramen. We conclude that the use of ITS2 and the availability of universal primers provide an ideal DNA barcode for molecular identification of acaroid mites. The use of multiple target genetic markers in conjunction with morphological approaches will improve the accuracy of Acaridida identification.},
}
@article {pmid33615949,
year = {2022},
author = {Dahm, OJ and Sampson, GL and Silva, AJ and Hellberg, RS},
title = {Use of Molecular Methods to Authenticate Animal Species and Tissue in Bovine Liver Dietary Supplements.},
journal = {Journal of dietary supplements},
volume = {19},
number = {3},
pages = {381-394},
doi = {10.1080/19390211.2021.1887424},
pmid = {33615949},
issn = {1939-022X},
mesh = {Animals ; Cattle ; *DNA ; Dietary Supplements ; Horses ; Liver ; *MicroRNAs/genetics ; Real-Time Polymerase Chain Reaction/methods ; Sheep ; Species Specificity ; },
abstract = {Dietary supplements containing bovine (subfamily Bovinae) liver are susceptible to fraud due to their high value and the lack of modern detection methods available for processed animal tissues. The objective of this research was to use molecular methods to authenticate dietary supplements claiming to contain bovine liver or beef liver through the verification of animal species and tissue type. A total of 53 bovine/beef liver dietary supplements were purchased from online sources. The presence of liver was verified with reverse transcription and real-time PCR testing for microRNA-122 (miR-122), which is highly expressed in liver tissue. Multiplex real-time PCR targeting domestic cattle (Bos taurus), horse (Equus caballus), sheep (Ovis aries), and pork (Sus scrofa) was used to verify species. Samples that failed species identification with multiplex real-time PCR underwent DNA mini-barcoding. Overall, bovine species were detected in 48/53 liver supplements: 35 samples were confirmed as domestic cattle with multiplex real-time PCR and an additional 13 samples were confirmed as domestic cattle or Bos spp. with DNA mini-barcoding. One of these samples was also positive for sheep/lamb, which was declared on the label. One product contained undeclared pork in addition to beef. MiR-122 was detected in 51 out of 53 supplements, suggesting the presence of liver. While this study demonstrates the potential use of tissue-specific microRNAs in verifying tissues in dietary supplements, more research is needed to evaluate the specificity of these markers.},
}
@article {pmid33614291,
year = {2021},
author = {Pumkaeo, P and Takahashi, J and Iwahashi, H},
title = {Detection and monitoring of insect traces in bioaerosols.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e10862},
pmid = {33614291},
issn = {2167-8359},
abstract = {Studies on bioaerosols have primarily focused on their chemical and biological compositions and their impact on public health and the ecosystem. However, most bioaerosol studies have only focused on viruses, bacteria, fungi, and pollen. To assess the diversity and composition of airborne insect material in particulate matter (PM) for the first time, we attempted to detect DNA traces of insect origin in dust samples collected over a two-year period. These samples were systematically collected at one-month intervals and categorized into two groups, PM2.5 and PM10, based on the aerodynamic diameter of the aerosol particles. Cytochrome-c oxidase I (COI) was the barcoding region used to identify the origins of the extracted DNA. The airborne insect community in these samples was analyzed using the Illumina MiSeq platform. The most abundant insect sequences belonged to the order Hemiptera (true bugs), whereas order Diptera were also detected in both PM2.5 and PM10 samples. Additionally, we inferred the presence of particulates of insect origin, such as brochosomes and integument particles, using scanning electron microscopy (SEM). This provided additional confirmation of the molecular results. In this study, we demonstrated the benefits of detection and monitoring of insect information in bioaerosols for understanding the source and composition. Our results suggest that the PM2.5 and PM10 groups are rich in insect diversity. Lastly, the development of databases can improve the identification accuracy of the analytical results.},
}
@article {pmid33614280,
year = {2021},
author = {Niu, Y and Gao, C and Liu, J},
title = {Comparative analysis of the complete plastid genomes of Mangifera species and gene transfer between plastid and mitochondrial genomes.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e10774},
pmid = {33614280},
issn = {2167-8359},
abstract = {Mango is an important commercial fruit crop belonging to the genus Mangifera. In this study, we reported and compared four newly sequenced plastid genomes of the genus Mangifera, which showed high similarities in overall size (157,780-157,853 bp), genome structure, gene order, and gene content. Three mutation hotspots (trnG-psbZ, psbD-trnT, and ycf4-cemA) were identified as candidate DNA barcodes for Mangifera. These three DNA barcode candidate sequences have high species identification ability. We also identified 12 large fragments that were transferred from the plastid genome to the mitochondrial genome, and found that the similarity was more than 99%. The total size of the transferred fragment was 35,652 bp, accounting for 22.6% of the plastid genome. Fifteen intact chloroplast genes, four tRNAs and numerous partial genes and intergenic spacer regions were identified. There are many of these genes transferred from mitochondria to the chloroplast in other species genomes. Phylogenetic analysis based on whole plastid genome data provided a high support value, and the interspecies relationships within Mangifera were resolved well.},
}
@article {pmid33614006,
year = {2021},
author = {Vu, JP and Vasquez, MF and Feng, Z and Lombardo, K and Haagensen, S and Bozinovic, G},
title = {Relative genetic diversity of the rare and endangered Agave shawii ssp. shawii and associated soil microbes within a southern California ecological preserve.},
journal = {Ecology and evolution},
volume = {11},
number = {4},
pages = {1829-1842},
pmid = {33614006},
issn = {2045-7758},
abstract = {Shaw's Agave (Agave shawii ssp. shawii) is an endangered maritime succulent growing along the coast of California and northern Baja California. The population inhabiting Point Loma Peninsula has a complicated history of transplantation without documentation. The low effective population size in California prompted agave transplanting from the U.S. Naval Base site (NB) to Cabrillo National Monument (CNM). Since 2008, there are no agave sprouts identified on the CNM site, and concerns have been raised about the genetic diversity of this population. We sequenced two barcoding loci, rbcL and matK, of 27 individual plants from 5 geographically distinct populations, including 12 individuals from California (NB and CNM). Phylogenetic analysis revealed the three US and two Mexican agave populations are closely related and have similar genetic variation at the two barcoding regions, suggesting the Point Loma agave population is not clonal. Agave-associated soil microbes used significantly more carbon sources in CNM soil samples than in NB soil likely due to higher pH and moisture content; meanwhile, soil type and soil chemistry analysis including phosphorus, nitrate nitrogen, organic matter, and metals revealed significant correlations between microbial diversity and base saturation (p < 0.05, r [2] = 0.3676), lime buffer capacity (p < 0.01, r [2] = 0.7055), equilibrium lime buffer capacity (p < 0.01, r [2] = 0.7142), and zinc (p < 0.01, r [2] = 0.7136). Soil microbiome analysis within the CNM population revealed overall expected richness (H' = 5.647-6.982) for Agave species, while the diversity range (1 - D = 0.003392-0.014108) suggests relatively low diversity marked by high individual variation. The most prominent remaining US population of this rare species is not clonal and does not seem to be threatened by a lack of genetic and microbial diversity. These results prompt further efforts to investigate factors affecting Agave's reproduction and fitness.},
}
@article {pmid33613989,
year = {2021},
author = {Young, RG and Milián-García, Y and Yu, J and Bullas-Appleton, E and Hanner, RH},
title = {Biosurveillance for invasive insect pest species using an environmental DNA metabarcoding approach and a high salt trap collection fluid.},
journal = {Ecology and evolution},
volume = {11},
number = {4},
pages = {1558-1569},
pmid = {33613989},
issn = {2045-7758},
abstract = {With the increase in global trade and warming patterns, the movement, introduction, and establishment of non-native insect species has increased. A rapid and effective early detection biosurveillance program to identify species of concern is needed to reduce future impacts and costs associated with introduced non-native species. One of the challenges facing insect surveillance trapping methods is the sheer volume of individual specimens in the collections. Although molecular identification methods are improving, they currently have limitations (e.g., destructive processing of specimens) and a protocol addressing these limitations can support regulatory applications that need morphological evidence to corroborate molecular data.The novel protocol presented here uses a metabarcoding approach to amplify environmental DNA from a saturated salt solution trap fluid, which retains trap specimens for downstream morphological identifications. The use of a saturated salt solution to preserve specimens in traps addresses issues with the high evaporation rate of ethanol in traps, and public safety concerns with other fluid preservation options with unattended traps in public settings.Using a metabarcoding approach, a 407-nucleotide segment of the cytochrome c oxidase subunit 1 (COI) animal barcode region was successfully amplified from Lindgren funnel trap collection fluids. These traps were placed in forested areas to survey for wood-boring beetles of regulatory concern. Our results displayed successful amplification of target taxa, including the molecular identification of the Japanese Beetle Popillia japonica, a species regulated in Canada. A second species, Anisandrus maiche, recently introduced to North America, was identified in every trap. The genus Lymantria, which contains numerous species of concern to North American woodlands, was also detected. Also, there were six other species identified of interest due to their potential impacts on native and crop flora and fauna.Our results show how this protocol can be used as an efficient method for the surveillance of insects using a trap with a saturated salt solution and eDNA metabarcoding to detect species of regulatory concern.},
}
@article {pmid33613869,
year = {2021},
author = {Mahmutovic, A and Gillman, AN and Lauksund, S and Robson Moe, NA and Manzi, A and Storflor, M and Abel Zur Wiesch, P and Abel, S},
title = {RESTAMP - Rate estimates by sequence-tag analysis of microbial populations.},
journal = {Computational and structural biotechnology journal},
volume = {19},
number = {},
pages = {1035-1051},
pmid = {33613869},
issn = {2001-0370},
abstract = {Microbial division rates determine the speed of mutation accumulation and thus the emergence of antimicrobial resistance. Microbial death rates are affected by antibiotic action and the immune system. Therefore, measuring these rates has advanced our understanding of host-pathogen interactions and antibiotic action. Several methods based on marker-loss or few inheritable neutral markers exist that allow estimating microbial division and death rates, each of which has advantages and limitations. Technical bottlenecks, i.e., experimental sampling events, during the experiment can distort the rate estimates and are typically unaccounted for or require additional calibration experiments. In this work, we introduce RESTAMP (Rate Estimates by Sequence Tag Analysis of Microbial Populations) as a method for determining bacterial division and death rates. This method uses hundreds of fitness neutral sequence barcodes to measure the rates and account for experimental bottlenecks at the same time. We experimentally validate RESTAMP and compare it to established plasmid loss methods. We find that RESTAMP has a number of advantages over plasmid loss or previous marker based techniques. (i) It enables to correct the distortion of rate estimates by technical bottlenecks. (ii) Rate estimates are independent of the sequence tag distribution in the starting culture allowing the use of an arbitrary number of tags. (iii) It introduces a bottleneck sensitivity measure that can be used to maximize the accuracy of the experiment. RESTAMP allows studying microbial population dynamics with great resolution over a wide dynamic range and can thus advance our understanding of host-pathogen interactions or the mechanisms of antibiotic action.},
}
@article {pmid33613042,
year = {2021},
author = {Chen, J and Schmelz, RM and Xie, Z},
title = {Description of Hemienchytraeus wuhanensis sp. nov. (Annelida, Clitellata, Enchytraeidae) from central China, with comments on species records of Hemienchytraeus from China.},
journal = {ZooKeys},
volume = {1015},
number = {},
pages = {87-97},
pmid = {33613042},
issn = {1313-2989},
abstract = {Hemienchytraeus wuhanensis sp. nov. is described from hardwood forest soil in Wuhan, China. This moderately sized enchytraeid species of 6-9 mm body length is characterized by: (1) an oesophageal appendage with tertiary branches, (2) three pairs of secondary pharyngeal gland lobes in V, VI, VII, (3) five pairs preclitellar nephridia, from 5/6 to 9/10, (4) dorsal vessel originating in clitellar segments, (5) a girdle-shaped clitellum, (6) a relatively small male reproductive apparatus without seminal vesicle, and (7) spermathecae that extend to VI-VII. DNA barcodes of paratype specimens of the new species are provided. Previous species records of Hemienchytraeus from China are critically discussed.},
}
@article {pmid33611842,
year = {2021},
author = {Hawlitschek, O and Scherz, MD and Webster, KC and Ineich, I and Glaw, F},
title = {Morphological, osteological, and genetic data support a new species of Madatyphlops (Serpentes: Typhlopidae) endemic to Mayotte Island, Comoros Archipelago.},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {304},
number = {10},
pages = {2249-2263},
doi = {10.1002/ar.24589},
pmid = {33611842},
issn = {1932-8494},
mesh = {Animals ; Comoros ; Indian Ocean ; *Osteology ; Phylogeny ; *Snakes/genetics ; },
abstract = {Blind snakes (Typhlopidae) are an enigmatic group of small burrowing snakes whose anatomy, phylogenetics, and biodiversity remain poorly known. Madatyphlops comorensis (Boulenger, 1889), endemic to the Comoros Archipelago in the Western Indian Ocean, is one of many species whose phylogenetic placement and generic assignment is unclear. We used DNA barcoding, external morphological examination, and osteological data from 3D reconstruction with micro-CT to study specimens of Madatyphlops from the Comoros Archipelago. Our results support the placement of M. comorensis in Madatyphlops and the recognition of the specimens from Mayotte Island as a closely related but distinct species, which we describe as Madatyphlops eudelini sp. nov. In this context, we present the first detailed osteological descriptions of any species of Madatyphlops, which we hope will serve as groundwork for further osteological studies in this genus and contribute to our limited but growing understanding of the osteology of typhlopid snakes.},
}
@article {pmid33608006,
year = {2021},
author = {Sy, M and Badiane, AS and Deme, AB and Gaye, A and Ndiaye, T and Fall, FB and Siddle, KJ and Dieye, B and Ndiaye, YD and Diallo, MA and Diongue, K and Seck, MC and Ndiaye, IM and Cissé, M and Gueye, AB and Sène, D and Dieye, Y and Souané, T and MacInnis, B and Volkman, SK and Wirth, DF and Ndiaye, D},
title = {Genomic investigation of atypical malaria cases in Kanel, northern Senegal.},
journal = {Malaria journal},
volume = {20},
number = {1},
pages = {103},
pmid = {33608006},
issn = {1475-2875},
support = {MR/P028071/1/MRC_/Medical Research Council/United Kingdom ; R21 AI141843/AI/NIAID NIH HHS/United States ; U54 HG007480/HG/NHGRI NIH HHS/United States ; },
mesh = {Adolescent ; Child ; Child, Preschool ; Female ; *Genome, Protozoan ; Humans ; Malaria, Falciparum/*classification/diagnosis/parasitology ; Male ; Plasmodium falciparum/*genetics ; Senegal ; Young Adult ; },
abstract = {BACKGROUND: The diagnosis of malaria cases in regions where the malaria burden has decreased significantly and prevalence is very low is more challenging, in part because of reduced clinical presumption of malaria. The appearance of a cluster of malaria cases with atypical symptoms in Mbounguiel, a village in northern Senegal where malaria transmission is low, in September 2018 exemplifies this scenario. The collaboration between the National Malaria Control Programme (NMCP) at the Senegal Ministry of Health and the Laboratory of Parasitology and Mycology at Cheikh Anta Diop University worked together to evaluate this cluster of malaria cases using molecular and serological tools.<br><br>METHODS: Malaria cases were diagnosed primarily by rapid diagnostic test (RDT), and confirmed by photo-induced electron transfer-polymerase chain reaction (PET-PCR). 24 single nucleotide polymorphisms (SNPs) barcoding was used for Plasmodium falciparum genotyping. Unbiased metagenomic sequencing and Luminex-based multi-pathogen antibody and antigen profiling were used to assess exposure to other pathogens.<br><br>RESULTS: Nine patients, of 15 suspected cases, were evaluated, and all nine samples were found to be positive for P. falciparum only. The 24 SNPs molecular barcode showed the predominance of polygenomic infections, with identifiable strains being different from one another. All patients tested positive for the P. falciparum antigens. No other pathogenic infection was detected by either the serological panel or metagenomic sequencing.<br><br>CONCLUSIONS: This work, undertaken locally within Senegal as a collaboration between the NMCP and a research laboratory at University of Cheikh Anta Diop (UCAD) revealed that a cluster of malaria cases were caused by different strains of P. falciparum. The public health response in real time demonstrates the value of local molecular and genomics capacity in affected countries for disease control and elimination.},
}
@article {pmid33607064,
year = {2021},
author = {Jomkumsing, P and Surapinit, A and Saengpara, T and Pramual, P},
title = {Genetic variation, DNA barcoding and blood meal identification of Culicoides Latreille biting midges (Diptera: Ceratopogonidae) in Thailand.},
journal = {Acta tropica},
volume = {217},
number = {},
pages = {105866},
doi = {10.1016/j.actatropica.2021.105866},
pmid = {33607064},
issn = {1873-6254},
mesh = {Animals ; Cattle ; Ceratopogonidae/*classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA Mutational Analysis ; Female ; *Genetic Variation ; Insect Vectors/genetics ; Phylogeny ; Thailand ; },
abstract = {Biting midges of the genus Culicoides Latreille are blood sucking insects of medical and veterinary importance. Many species are vectors of disease agents transmitted to humans and other animals. Therefore, rapid and accurate species identification is essential for appreciation of all aspects of these insects. In this study, DNA barcode efficacy and molecular identification of host blood sources were examined in biting midges from Thailand. A total of 203 barcoding sequences were obtained from 16 Culicoides taxa. Intraspecific genetic divergence varied from 0.28% to 9.90% for specimens collected in Thailand. Despite this high level of genetic variation, DNA barcode identifications in the Barcoding of Life Data System had a considerable success rate (90%). Phylogenetic analyses and distance-based species delimitation methods indicated the possibility of cryptic species in four taxa, namely, Culicoides actoni Smit, C. arakawae Arakawa, C. huffi Causey and C. jacobsoni Macfie. Further investigations will be required to examine the species status of these lineages. Host blood meal identifications from 42 blood engorged females of 10 Culicoides taxa revealed three animal hosts: chicken, cattle and buffalo. Most of this information agrees with previous knowledge but this is the first report of C. actoni, C. fulvus and C. huffi feeding on chicken.},
}
@article {pmid33604719,
year = {2021},
author = {Choudhary, P and Singh, BN and Chakdar, H and Saxena, AK},
title = {DNA barcoding of phytopathogens for disease diagnostics and bio-surveillance.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {37},
number = {3},
pages = {54},
pmid = {33604719},
issn = {1573-0972},
mesh = {Aspergillus/classification/genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal ; Fungi/classification/*genetics/*isolation &amp; purification ; Fusarium/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/methods ; Oomycetes/genetics/isolation &amp; purification ; Phylogeny ; Plant Diseases/*microbiology ; Plants/microbiology ; },
abstract = {DNA barcoding has proven to be a versatile tool for plant disease diagnostics in the genomics era. As the mass parallel and next generation sequencing techniques gained importance, the role of specific barcodes came under immense scrutiny. Identification and accurate classification of phytopathogens need a universal approach which has been the main application area of the concept of barcode. The present review entails a detailed description of the present status of barcode application in plant disease diagnostics. A case study on the application of Internal Transcribed Spacer (ITS) as barcode for Aspergillus and Fusarium spp. sheds light on the requirement of other potential candidates as barcodes for accurate identification. The challenges faced while barcoding novel pathogens have also been discussed with a comprehensive outline of integrating more recent technologies like meta-barcoding and genome skimming for detecting plant pathogens.},
}
@article {pmid33604694,
year = {2021},
author = {Cheng, YC and Houston, R},
title = {Evaluation of the trnK-matK-trnK, ycf3, and accD-psal chloroplast regions to differentiate crop type and biogeographical origin of Cannabis sativa.},
journal = {International journal of legal medicine},
volume = {135},
number = {4},
pages = {1235-1244},
pmid = {33604694},
issn = {1437-1596},
mesh = {Canada ; Cannabis/*classification/*genetics ; Chile ; DNA Barcoding, Taxonomic/*methods ; DNA, Chloroplast/*genetics ; Genetic Markers ; *Genome, Chloroplast ; Genotype ; *Genotyping Techniques ; *Haplotypes ; INDEL Mutation ; Mexico ; Microsatellite Repeats ; Phylogeny ; Phylogeography ; Polymorphism, Single Nucleotide ; Principal Component Analysis ; United States ; },
abstract = {Cannabis sativa (marijuana and hemp) is one of the most controversial crops worldwide. In the USA, the state-specific legalization of marijuana and recently legalized hemp pose a problem for law enforcement. This study seeks to utilize chloroplast hSTRs, INDEL, and SNPs markers to develop genotyping methods to aid in the differentiation of legal hemp from illicit marijuana and also for tracking the flow of trafficked marijuana. Three polymorphic regions: trnK-matK-trnK, ycf3, and accD-psal, of the C. sativa chloroplast genome were evaluated in order to distinguish crop type and biogeographic origin. A total of nine polymorphic sites were genotyped from five distinct populations (hemp from the USA and Canada, marijuana from Chile and USA-Mexico, and medical marijuana from Chile) with a custom fragment and SNaPshot[TM] assay. The study also combined genotype results from the same sample set using 21 additional polymorphic markers from previous studies. The effectiveness of these multi-locus assays to distinguish sample groups was assessed using haplotype analysis, phylogenetic analysis, pairwise comparisons, and principal component analysis. Results indicated a clear separation of Canadian hemp using only the nine polymorphic sites developed in this study. The additional 21 markers were able to separate US hemp from both marijuana groups to a significant level (p < 0.05) when assessing average Fixation Indices (FST). This study demonstrated the applicability of these organelle markers for the determination of crop type and biogeographic origin of C. sativa. However, a more extensive database is needed to evaluate the true discriminatory power of these markers.},
}
@article {pmid33603059,
year = {2021},
author = {Salonna, M and Gasparini, F and Huchon, D and Montesanto, F and Haddas-Sasson, M and Ekins, M and McNamara, M and Mastrototaro, F and Gissi, C},
title = {An elongated COI fragment to discriminate botryllid species and as an improved ascidian DNA barcode.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {4078},
pmid = {33603059},
issn = {2045-2322},
mesh = {Animals ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Electron Transport Complex IV/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Urochordata/classification/*genetics ; },
abstract = {Botryllids are colonial ascidians widely studied for their potential invasiveness and as model organisms, however the morphological description and discrimination of these species is very problematic, leading to frequent specimen misidentifications. To facilitate species discrimination and detection of cryptic/new species, we developed new barcoding primers for the amplification of a COI fragment of about 860 bp (860-COI), which is an extension of the common Folmer's barcode region. Our 860-COI was successfully amplified in 177 worldwide-sampled botryllid colonies. Combined with morphological analyses, 860-COI allowed not only discriminating known species, but also identifying undescribed and cryptic species, resurrecting old species currently in synonymy, and proposing the assignment of clade D of the model organism Botryllus schlosseri to Botryllus renierii. Importantly, within clade A of B. schlosseri, 860-COI recognized at least two candidate species against only one recognized by the Folmer's fragment, underlining the need of further genetic investigations on this clade. This result also suggests that the 860-COI could have a greater ability to diagnose cryptic/new species than the Folmer's fragment at very short evolutionary distances, such as those observed within clade A. Finally, our new primers simplify the amplification of 860-COI even in non-botryllid ascidians, suggesting their wider usefulness in ascidians.},
}
@article {pmid33602311,
year = {2021},
author = {Lumsden, GA and Zakharov, EV and Dolynskyj, S and Weese, JS and Lindsay, LR and Jardine, CM},
title = {The application of next-generation sequence-based DNA barcoding for bloodmeal detection in host-seeking wild-caught Ixodes scapularis nymphs.},
journal = {BMC research notes},
volume = {14},
number = {1},
pages = {67},
pmid = {33602311},
issn = {1756-0500},
mesh = {Animals ; Cattle ; DNA ; DNA Barcoding, Taxonomic ; Humans ; *Ixodes/genetics ; Nymph/genetics ; Vertebrates ; },
abstract = {OBJECTIVE: Our objective was to apply next-generation sequence-based DNA barcoding to identify the remnant larval bloodmeals in wild-caught host-seeking (unengorged) Ixodes scapularis nymphs (n = 216). To infer host species identification, vertebrate DNA was amplified using universal primers for cytochrome c oxidase subunit I (COI) and sequenced using next-generation sequencing (NGS) for comparison against known barcode references.<br><br>RESULTS: Bloodmeal identification was unsuccessful in most samples (99% of 216 specimens) demonstrating a very low detection rate of this assay. Sequences that surpassed quality thresholds were obtained for 41.7% of nymphs (n&#x2009;=&#x2009;90) and of those, confident species identification was obtained for 15.6% of nymphs (n&#x2009;=&#x2009;14). Wild host identifications were only obtained from 2 specimens, where DNA from the eastern grey squirrel (Sciurus carolinensis) was identified. Human and bovine DNA was identified in remaining nymphs and considered to be contaminants. Further optimization of the technique is required to improve detection of remnant bloodmeals in host-seeking nymphs.},
}
@article {pmid33600481,
year = {2021},
author = {Yang, IS and Bae, SW and Park, B and Kim, S},
title = {Development of a program for in silico optimized selection of oligonucleotide-based molecular barcodes.},
journal = {PloS one},
volume = {16},
number = {2},
pages = {e0246354},
pmid = {33600481},
issn = {1932-6203},
mesh = {Computer Simulation ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; Gene Expression Profiling/methods ; Models, Statistical ; Mutation/genetics ; Oligonucleotides/*genetics ; Single-Cell Analysis/methods ; },
abstract = {Short DNA oligonucleotides (~4 mer) have been used to index samples from different sources, such as in multiplex sequencing. Presently, longer oligonucleotides (8-12 mer) are being used as molecular barcodes with which to distinguish among raw DNA molecules in many high-tech sequence analyses, including low-frequent mutation detection, quantitative transcriptome analysis, and single-cell sequencing. Despite some advantages of using molecular barcodes with random sequences, such an approach, however, makes it impossible to know the exact sequences used in an experiment and can lead to inaccurate interpretation due to misclustering of barcodes arising from the occurrence of unexpected mutations in the barcodes. The present study introduces a tool developed for selecting an optimal barcode subset during molecular barcoding. The program considers five barcode factors: GC content, homopolymers, simple sequence repeats with repeated units of dinucleotides, Hamming distance, and complementarity between barcodes. To evaluate a selected barcode set, penalty scores for the factors are defined based on their distributions observed in random barcodes. The algorithm employed in the program comprises two steps: i) random generation of an initial set and ii) optimal barcode selection via iterative replacement. Users can execute the program by inputting barcode length and the number of barcodes to be generated. Furthermore, the program accepts a user's own values for other parameters, including penalty scores, for advanced use, allowing it to be applied in various conditions. In many test runs to obtain 100000 barcodes with lengths of 12 nucleotides, the program showed fast performance, efficient enough to generate optimal barcode sequences with merely the use of a desktop PC. We also showed that VFOS has comparable performance, flexibility in program running, consideration of simple sequence repeats, and fast computation time in comparison with other two tools (DNABarcodes and FreeBarcodes). Owing to the versatility and fast performance of the program, we expect that many researchers will opt to apply it for selecting optimal barcode sets during their experiments, including next-generation sequencing.},
}
@article {pmid33600318,
year = {2022},
author = {Yang, CH and Wu, KC and Chuang, LY and Chang, HW},
title = {DeepBarcoding: Deep Learning for Species Classification Using DNA Barcoding.},
journal = {IEEE/ACM transactions on computational biology and bioinformatics},
volume = {19},
number = {4},
pages = {2158-2165},
doi = {10.1109/TCBB.2021.3056570},
pmid = {33600318},
issn = {1557-9964},
mesh = {DNA/genetics ; *DNA Barcoding, Taxonomic/methods ; *Deep Learning ; Neural Networks, Computer ; Sequence Analysis, DNA ; },
abstract = {DNA barcodes with short sequence fragments are used for species identification. Because of advances in sequencing technologies, DNA barcodes have gradually been emphasized. DNA sequences from different organisms are easily and rapidly acquired. Therefore, DNA sequence analysis tools play an increasingly crucial role in species identification. This study proposed deep barcoding, a deep learning framework for species classification by using DNA barcodes. Deep barcoding uses raw sequence data as the input to represent one-hot encoding as a one-dimensional image and uses a deep convolutional neural network with a fully connected deep neural network for sequence analysis. It can achieve an average accuracy of >90 percent for both simulation and real datasets. Although deep learning yields outstanding performance for species classification with DNA sequences, its application remains a challenge. The deep barcoding model can be a potential tool for species classification and can elucidate DNA barcode-based species identification.},
}
@article {pmid33598139,
year = {2021},
author = {Sahlin, K and Lim, MCW and Prost, S},
title = {NGSpeciesID: DNA barcode and amplicon consensus generation from long-read sequencing data.},
journal = {Ecology and evolution},
volume = {11},
number = {3},
pages = {1392-1398},
pmid = {33598139},
issn = {2045-7758},
abstract = {Third-generation sequencing technologies, such as Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), have gained popularity over the last years. These platforms can generate millions of long-read sequences. This is not only advantageous for genome sequencing projects, but also advantageous for amplicon-based high-throughput sequencing experiments, such as DNA barcoding. However, the relatively high error rates associated with these technologies still pose challenges for generating high-quality consensus sequences. Here, we present NGSpeciesID, a program which can generate highly accurate consensus sequences from long-read amplicon sequencing technologies, including ONT and PacBio. The tool includes clustering of the reads to help filter out contaminants or reads with high error rates and employs polishing strategies specific to the appropriate sequencing platform. We show that NGSpeciesID produces consensus sequences with improved usability by minimizing preprocessing and software installation and scalability by enabling rapid processing of hundreds to thousands of samples, while maintaining similar consensus accuracy as current pipelines.},
}
@article {pmid33597941,
year = {2021},
author = {Wahdan, SFM and Heintz-Buschart, A and Sansupa, C and Tanunchai, B and Wu, YT and Schädler, M and Noll, M and Purahong, W and Buscot, F},
title = {Targeting the Active Rhizosphere Microbiome of Trifolium pratense in Grassland Evidences a Stronger-Than-Expected Belowground Biodiversity-Ecosystem Functioning Link.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {629169},
pmid = {33597941},
issn = {1664-302X},
abstract = {The relationship between biodiversity and ecosystem functioning (BEF) is a central issue in soil and microbial ecology. To date, most belowground BEF studies focus on the diversity of microbes analyzed by barcoding on total DNA, which targets both active and inactive microbes. This approach creates a bias as it mixes the part of the microbiome currently steering processes that provide actual ecosystem functions with the part not directly involved. Using experimental extensive grasslands under current and future climate, we used the bromodeoxyuridine (BrdU) immunocapture technique combined with pair-end Illumina sequencing to characterize both total and active microbiomes (including both bacteria and fungi) in the rhizosphere of Trifolium pratense. Rhizosphere function was assessed by measuring the activity of three microbial extracellular enzymes (β-glucosidase, N-acetyl-glucosaminidase, and acid phosphatase), which play central roles in the C, N, and P acquisition. We showed that the richness of overall and specific functional groups of active microbes in rhizosphere soil significantly correlated with the measured enzyme activities, while total microbial richness did not. Active microbes of the rhizosphere represented 42.8 and 32.1% of the total bacterial and fungal taxa, respectively, and were taxonomically and functionally diverse. Nitrogen fixing bacteria were highly active in this system with 71% of the total operational taxonomic units (OTUs) assigned to this group detected as active. We found the total and active microbiomes to display different responses to variations in soil physicochemical factors in the grassland, but with some degree of resistance to a manipulation mimicking future climate. Our findings provide critical insights into the role of active microbes in defining soil ecosystem functions in a grassland ecosystem. We demonstrate that the relationship between biodiversity-ecosystem functioning in soil may be stronger than previously thought.},
}
@article {pmid33596239,
year = {2021},
author = {Bhoyar, RC and Jain, A and Sehgal, P and Divakar, MK and Sharma, D and Imran, M and Jolly, B and Ranjan, G and Rophina, M and Sharma, S and Siwach, S and Pandhare, K and Sahoo, S and Sahoo, M and Nayak, A and Mohanty, JN and Das, J and Bhandari, S and Mathur, SK and Kumar, A and Sahlot, R and Rojarani, P and Lakshmi, JV and Surekha, A and Sekhar, PC and Mahajan, S and Masih, S and Singh, P and Kumar, V and Jose, B and Mahajan, V and Gupta, V and Gupta, R and Arumugam, P and Singh, A and Nandy, A and P V, R and Jha, RM and Kumari, A and Gandotra, S and Rao, V and Faruq, M and Kumar, S and Reshma G, B and Varma G, N and Roy, SS and Sengupta, A and Chattopadhyay, S and Singhal, K and Pradhan, S and Jha, D and Naushin, S and Wadhwa, S and Tyagi, N and Poojary, M and Scaria, V and Sivasubbu, S},
title = {High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing.},
journal = {PloS one},
volume = {16},
number = {2},
pages = {e0247115},
pmid = {33596239},
issn = {1932-6203},
mesh = {COVID-19/*epidemiology/genetics/*virology ; Genome, Viral/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; India/epidemiology ; Molecular Epidemiology/methods ; Multiplex Polymerase Chain Reaction/methods ; Pandemics ; Phylogeny ; RNA, Viral/genetics/isolation &amp; purification ; SARS-CoV-2/*genetics/*isolation &amp; purification ; Sensitivity and Specificity ; },
abstract = {The rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance, and determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding, and sequencing of samples for high-throughput detection and deciphering the genetic epidemiology of SARS-CoV-2. We used the approach on 752 clinical samples in duplicates, amounting to a total of 1536 samples which could be sequenced on a single S4 sequencing flow cell on NovaSeq 6000. Our analysis suggests a high concordance between technical duplicates and a high concordance of detection of SARS-CoV-2 between the COVIDSeq as well as RT-PCR approaches. An in-depth analysis revealed a total of six samples in which COVIDSeq detected SARS-CoV-2 in high confidence which were negative in RT-PCR. Additionally, the assay could detect SARS-CoV-2 in 21 samples and 16 samples which were classified inconclusive and pan-sarbeco positive respectively suggesting that COVIDSeq could be used as a confirmatory test. The sequencing approach also enabled insights into the evolution and genetic epidemiology of the SARS-CoV-2 samples. The samples were classified into a total of 3 clades. This study reports two lineages B.1.112 and B.1.99 for the first time in India. This study also revealed 1,143 unique single nucleotide variants and added a total of 73 novel variants identified for the first time. To the best of our knowledge, this is the first report of the COVIDSeq approach for detection and genetic epidemiology of SARS-CoV-2. Our analysis suggests that COVIDSeq could be a potential high sensitivity assay for the detection of SARS-CoV-2, with an additional advantage of enabling the genetic epidemiology of SARS-CoV-2.},
}
@article {pmid33596120,
year = {2021},
author = {Marín, MA and López-Rubio, A and Clavijo, A and Pyrcz, TW and Freitas, AVL and Uribe, SI and Álvarez, CF},
title = {Use of species delimitation approaches to tackle the cryptic diversity of an assemblage of high Andean butterflies (Lepidoptera: Papilionoidea).},
journal = {Genome},
volume = {64},
number = {10},
pages = {937-949},
doi = {10.1139/gen-2020-0100},
pmid = {33596120},
issn = {1480-3321},
mesh = {Animals ; Biodiversity ; *Butterflies/classification ; Colombia ; *DNA Barcoding, Taxonomic ; *Genetic Speciation ; *Phylogeny ; },
abstract = {Cryptic biological diversity has generated ambiguity in taxonomic and evolutionary studies. Single-locus methods and other approaches for species delimitation are useful for addressing this challenge, enabling the practical processing of large numbers of samples for identification and inventory purposes. This study analyzed an assemblage of high Andean butterflies using DNA barcoding and compared the identifications based on the current morphological taxonomy with three methods of species delimitation (automatic barcode gap discovery, generalized mixed Yule coalescent model, and Poisson tree processes). Sixteen potential cryptic species were recognized using these three methods, representing a net richness increase of 11.3% in the assemblage. A well-studied taxon of the genus Vanessa, which has a wide geographical distribution, appeared with the potential cryptic species that had a higher genetic differentiation at the local level than at the continental level. The analyses were useful for identifying the potential cryptic species in Pedaliodes and Forsterinaria complexes, which also show differentiation along altitudinal and latitudinal gradients. This genetic assessment of an entire assemblage of high Andean butterflies (Papilionoidea) provides baseline information for future research in a region characterized by high rates of endemism and population isolation.},
}
@article {pmid33595803,
year = {2021},
author = {Chen, J and Li, S and Wu, W and Xie, J and Cheng, X and Ye, Z and Yin, X and Liu, Y and Huang, Z},
title = {Molecular Identification and Phylogenetic Analysis of the Traditional Chinese Medicinal Plant Kochia scoparia Using ITS2 Barcoding.},
journal = {Interdisciplinary sciences, computational life sciences},
volume = {13},
number = {1},
pages = {128-139},
pmid = {33595803},
issn = {1867-1462},
support = {20161139//the Traditional Chinese Medicine Bureau Foundation of Guangdong Province, China/ ; 2019268//the higher education reform project of Guangdong Province/ ; GDMUM201834//the General Program of Guangdong Medical University, China/ ; 201710571056//the National University Students Innovation and Entrepreneurship Training Project, China/ ; 201710571096//the National University Students Innovation and Entrepreneurship Training Project, China/ ; 201810571042//the National University Students Innovation and Entrepreneurship Training Project, China/ ; },
mesh = {*Bassia scoparia/genetics ; China ; DNA Barcoding, Taxonomic ; DNA, Plant ; DNA, Ribosomal Spacer ; *Phylogeny ; *Plants, Medicinal ; },
abstract = {Kochia scoparia has high medicinal and economic value. However, with similar morphological features, adulterants and some closely related species of K. scoparia are increasingly sold in the medicinal markets, leading to potential safety risks. In this study, 128 internal transcribed spacer 2 (ITS2) sequences were collected to distinguish K. scoparia from its closely related species and adulterants. Then, sequence alignment, sequence characteristics analysis, and genetic distance calculations were performed using MEGA 6.06 software, and the phylogenetic trees were reconstructed using both MEGA 6.06 and IQ-Tree software. Finally, the secondary structure of ITS2 was modeled using the prediction tool in the ITS2 database. The results showed that ITS2 sequences of K. scoparia ranged in length from 226 to 227 bp, with a mean GC content of 55.3%. The maximum intraspecific distance was zero, while the minimum interspecific distance from closely related species and adulterants was 0.009 and 0.242, respectively. Kochia scoparia formed an independent clade in the phylogenetic trees, and its secondary structure exhibited enough variation to be separated from that of other species. In summary, ITS2 can be used as a mini-barcode for distinguishing K. scoparia from closely related species and adulterants. Its phylogenetic trees could illustrate the evolutionary process of K. scoparia in the Camphorosmeae. The phylogenetic results using ITS2 barcode further supported the internationally recognized revised classifications of Kochia and Bassia genera as a combined Bassia genus, together with the establishment of new genera Grubovia and Sedobassia, which we suggest is accepted by the Flora of China. Graphical abstract .},
}
@article {pmid33595417,
year = {2021},
author = {Réblová, M and Nekvindová, J and Kolařík, M and Hernández-Restrepo, M},
title = {Delimitation and phylogeny of Dictyochaeta, and introduction of Achrochaeta and Tubulicolla, genera nova.},
journal = {Mycologia},
volume = {113},
number = {2},
pages = {390-433},
doi = {10.1080/00275514.2020.1822095},
pmid = {33595417},
issn = {1557-2536},
mesh = {Ascomycota/*classification/*genetics ; Cluster Analysis ; DNA, Fungal/*genetics ; DNA, Ribosomal Spacer/genetics ; *Phylogeny ; RNA, Ribosomal, 28S/genetics ; RNA, Ribosomal, 5.8S/genetics ; Sequence Analysis, DNA ; },
abstract = {Dictyochaeta (Chaetosphaeriaceae) is a phialidic dematiaceous hyphomycete with teleomorphs classified in Chaetosphaeria. It is associated with significant variability of asexual morphological traits, which led to its broad delimitation. In the present study, six loci: nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode), nuc 18S rDNA (18S), nuc 28S rDNA (28S), DNA-directed RNA polymerase II second largest subunit gene (RPB2), translation elongation factor 1-α (TEF1-α), and β-tubulin (TUB2), along with comparative morphological and cultivation studies, are used to reevaluate the concept of Dictyochaeta and establish species boundaries. Based on revised species, morphological characteristics of conidia (shape, septation, absence or presence of setulae), collarettes (shape), and setae (presence or absence) and an extension of the conidiogenous cell proved to be important at the generic level. The dual DNA barcoding using ITS and TEF1-α, together with TUB2, facilitated accurate identification of Dictyochaeta species. Thirteen species are accepted, of which seven are characterized in this study; an identification key is provided. It was revealed that D. fuegiana, the type species, is a complex of three distinct species including D. querna and the newly described D. stratosa. Besides, a new species, D. detriticola, and two new combinations, D. callimorpha and D. montana, are proposed. An epitype of D. montana is selected. Dictyochaeta includes saprobes on decaying wood, bark, woody fruits, and fallen leaves. Dictyochaeta is shown to be distantly related to the morphologically similar Codinaea, which is resolved as paraphyletic. Chaetosphaeria talbotii with a Dictyochaeta anamorph represents a novel lineage in the Chaetosphaeriaceae; it is segregated from Dictyochaeta, and a new genus Achrochaeta is proposed. Multigene phylogenetic analysis revealed that D. cylindrospora belongs to the Vermiculariopsiellales, and a new genus Tubulicolla is introduced.},
}
@article {pmid33594128,
year = {2021},
author = {Shain, DH and Novis, PM and Cridge, AG and Zawierucha, K and Geneva, AJ and Dearden, PK},
title = {Five animal phyla in glacier ice reveal unprecedented biodiversity in New Zealand's Southern Alps.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {3898},
pmid = {33594128},
issn = {2045-2322},
support = {R01 CA031615/CA/NCI NIH HHS/United States ; },
abstract = {Glacier ice is an extreme environment in which most animals cannot survive. Here we report the colonization of high elevation, climate-threatened glaciers along New Zealand's southwestern coast by species of Arthropoda, Nematoda, Platyhelminthes, Rotifera and Tardigrada. Based on DNA barcoding and haplotype-inferred evidence for deep genetic variability, at least 12 undescribed species are reported, some of which have persisted in this niche habitat throughout the Pleistocene. These findings identify not only an atypical biodiversity hotspot but also highlight the adaptive plasticity of microinvertebrate Animalia.},
}
@article {pmid33589768,
year = {2021},
author = {De Luca, D and Piredda, R and Sarno, D and Kooistra, WHCF},
title = {Resolving cryptic species complexes in marine protists: phylogenetic haplotype networks meet global DNA metabarcoding datasets.},
journal = {The ISME journal},
volume = {15},
number = {7},
pages = {1931-1942},
pmid = {33589768},
issn = {1751-7370},
mesh = {*DNA Barcoding, Taxonomic ; *Eukaryota ; Haplotypes ; Oceans and Seas ; Phylogeny ; },
abstract = {Marine protists have traditionally been assumed to be lowly diverse and cosmopolitan. Yet, several recent studies have shown that many protist species actually consist of cryptic complexes of species whose members are often restricted to particular biogeographic regions. Nonetheless, detection of cryptic species is usually hampered by sampling coverage and application of methods (e.g. phylogenetic trees) that are not well suited to identify relatively recent divergence and ongoing gene flow. In this paper, we show how these issues can be overcome by inferring phylogenetic haplotype networks from global metabarcoding datasets. We use the Chaetoceros curvisetus (Bacillariophyta) species complex as study case. Using two complementary metabarcoding datasets (Ocean Sampling Day and Tara Oceans), we equally resolve the cryptic complex in terms of number of inferred species. We detect new hypothetical species in both datasets. Gene flow between most of species is absent, but no barcoding gap exists. Some species have restricted distribution patterns whereas others are widely distributed. Closely related taxa occupy contrasting biogeographic regions, suggesting that geographic and ecological differentiation drive speciation. In conclusion, we show the potential of the analysis of metabarcoding data with evolutionary approaches for systematic and phylogeographic studies of marine protists.},
}
@article {pmid33588011,
year = {2021},
author = {Zhu, S and Liu, Q and He, J and Nakajima, N and Samarakoon, SP and Swe, S and Zaw, K and Komatsu, K},
title = {Genetic identification of medicinally used Salacia species by nrDNA ITS sequences and a PCR-RFLP assay for authentication of Salacia-related health foods.},
journal = {Journal of ethnopharmacology},
volume = {274},
number = {},
pages = {113909},
doi = {10.1016/j.jep.2021.113909},
pmid = {33588011},
issn = {1872-7573},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Chloroplast/analysis/genetics ; DNA, Plant/*genetics ; DNA, Ribosomal Spacer/analysis/*genetics/*isolation &amp; purification ; Dietary Supplements/analysis ; Food Analysis ; Phylogeny ; Polymerase Chain Reaction/*methods ; Polymorphism, Restriction Fragment Length ; Salacia/*classification/*genetics ; },
abstract = {The roots and stems of several Salacia species have been used as traditional medicines, especially in Ayurvedic medical system for the treatment of diabetes, rheumatism, gonorrhea, amenorrhea, skin diseases, etc. Due to reported evidence supporting Salacia's beneficial effects in early-stage diabetes and other lifestyle-related diseases, Salacia-based dietary supplements and health foods have been gaining popularity in Japan and other countries in recent years. However, due to the morphological similarities between Salacia plants, particularly in the medicinally used parts (roots and stems), the authentication of the botanical identities of Salacia-derived products is challenging.<br><br>AIM OF THIS STUDY: This study aims to develop a genetic approach to authenticate the medicinally used Salacia species and to determine the botanical sources of the commercially available Salacia-derived products.<br><br>MATERIALS AND METHODS: The sequences of nuclear DNA internal transcribed spacer (ITS) and chloroplast trnK-rps16 region were determined and compared between 10 plant specimens from three medicinally used Salacia species as well as 48 samples of commercial crude drugs. Moreover, a PCR-restriction fragment length polymorphism (RFLP) assay was developed for rapid identification based on the ITS sequences.<br><br>RESULTS: The plant specimens from the three medicinally used Salacia species showed three main types of sequences in both ITS (types I, II, III) and trnK-rps16 (i, ii, iii) regions. Combined the sequences of ITS and trnK-rps16 regions, S. reticulata and S. oblonga had type I-i and type III-iii or similar sequences, respectively. S. chinensis had type II-ii or II(536M)-i sequences. Forty-eight samples of commercial crude drugs were identified based on ITS and trnK-rps16 DNA barcode. A convenient PCR-RFLP assay using Cac8I restriction enzyme was established and applied to identify the botanical sources of health food products purchased from online retailers. All the twelve samples were identified as S. chinensis.<br><br>CONCLUSION: The nrDNA ITS sequences provided useful information to authenticate Salacia species and to elucidate the phylogenetic relationship within the Salacia genus. Genetic identification results revealed that S. chinensis and S. reticulata are the major sources of commercially available Salacia-products. Based on the ITS sequences, a convenient PCR-RFLP assay was established for the identification of the medicinally used Salacia species as well as their derived health food products.},
}
@article {pmid33586985,
year = {2021},
author = {Kim, SH and Kim, H and Jeong, H and Yoon, TY},
title = {Encoding Multiple Virtual Signals in DNA Barcodes with Single-Molecule FRET.},
journal = {Nano letters},
volume = {21},
number = {4},
pages = {1694-1701},
doi = {10.1021/acs.nanolett.0c04502},
pmid = {33586985},
issn = {1530-6992},
mesh = {DNA/genetics ; *DNA Barcoding, Taxonomic ; *Fluorescence Resonance Energy Transfer ; Fluorescent Dyes ; Nanotechnology ; },
abstract = {DNA barcoding provides a way to label a myriad of different biological molecules using the extreme programmability in DNA sequence synthesis. Fluorescence imaging is presumably the most easy-to-access method for DNA barcoding, yet large spectral overlaps between fluorescence dyes severely limit the numbers of barcodes that can be detected simultaneously. We here demonstrate the use of single-molecule fluorescence resonance energy transfer (FRET) to encode virtual signals in DNA barcodes using conventional two-color fluorescence microscopy. By optimizing imaging and biochemistry conditions for weak DNA hybridization events, we markedly enhanced accuracy in our determination of the single-molecule FRET efficiency exhibited by each binding event between DNA barcode sequences. This allowed us to unambiguously differentiate six DNA barcodes encoding different FRET values without involving any probe sequence exchanges. Our method can be directly incorporated with previous DNA barcode techniques, and may thus be widely adopted to expand the signal space of DNA barcoding.},
}
@article {pmid33584940,
year = {2021},
author = {Kerr, M and Breitbart, M},
title = {DNA Detectives: Outreach Activity Teaching Students to Identify Fish Eggs Using DNA Barcoding.},
journal = {Journal of microbiology &amp; biology education},
volume = {22},
number = {1},
pages = {},
pmid = {33584940},
issn = {1935-7877},
}
@article {pmid33584760,
year = {2020},
author = {Chen, J and Wu, G and Shrestha, N and Wu, S and Guo, W and Yin, M and Li, A and Liu, J and Ren, G},
title = {Phylogeny and Species Delimitation of Chinese Medicago (Leguminosae) and Its Relatives Based on Molecular and Morphological Evidence.},
journal = {Frontiers in plant science},
volume = {11},
number = {},
pages = {619799},
pmid = {33584760},
issn = {1664-462X},
abstract = {Medicago and its relatives, Trigonella and Melilotus comprise the most important forage resources globally. The alfalfa selected from the wild relatives has been cultivated worldwide as the forage queen. In the Flora of China, 15 Medicago, eight Trigonella, and four Melilotus species are recorded, of which six Medicago and two Trigonella species are introduced. Although several studies have been conducted to investigate the phylogenetic relationship within the three genera, many Chinese naturally distributed or endemic species are not included in those studies. Therefore, the taxonomic identity and phylogenetic relationship of these species remains unclear. In this study, we collected samples representing 18 out of 19 Chinese naturally distributed species of these three genera and three introduced Medicago species, and applied an integrative approach by combining evidences from population-based morphological clusters and molecular data to investigate species boundaries. A total of 186 individuals selected from 156 populations and 454 individuals from 124 populations were collected for genetic and morphological analyses, respectively. We sequenced three commonly used DNA barcodes (trnH-psbA, trnK-matK, and ITS) and one nuclear marker (GA3ox1) for phylogenetic analyses. We found that 16 out of 21 species could be well delimited based on phylogenetic analyses and morphological clusters. Two Trigonella species may be merged as one species or treated as two subspecies, and Medicago falcata should be treated as a subspecies of the M. sativa complex. We further found that major incongruences between the chloroplast and nuclear trees mainly occurred among the deep diverging lineages, which may be resulted from hybridization, incomplete lineage sorting and/or sampling errors. Further studies involving a finer sampling of species associated with large scale genomic data should be employed to better understand the species delimitation of these three genera.},
}
@article {pmid33583039,
year = {2021},
author = {Hammer, MP and Taillebois, L and King, AJ and Crook, DA and Wedd, D and Adams, M and Unmack, PJ and Hoese, DF and Bertozzi, T},
title = {Unravelling the taxonomy and identification of a problematic group of benthic fishes from tropical rivers (Gobiidae: Glossogobius).},
journal = {Journal of fish biology},
volume = {99},
number = {1},
pages = {87-100},
doi = {10.1111/jfb.14701},
pmid = {33583039},
issn = {1095-8649},
support = {TTC216-14//Australian Biological Resources Study/ ; //Northern Australia Environmental Resources Hub (AU)/ ; },
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic ; Fishes/genetics ; *Perciformes/genetics ; Phylogeny ; *Rivers ; },
abstract = {Flathead gobies (genus Glossogobius) include c. 40 small- to medium-sized benthic fishes found primarily in freshwater habitats across the Indo-Pacific, having biodiversity value as well as cultural and economic value as food fishes, especially in developing countries. To help resolve considerable confusion regarding the identification of some of the larger-growing Glossogobius species, a systematic framework was established using nuclear genetic markers, mitochondrial DNA barcoding and phenotypic evidence for a geographically widespread collection of individuals from the waterways of tropical northern Australia. Species boundaries and distribution patterns were discordant with those previously reported, most notably for the tank goby Glossogobius giuris, which included a cryptic species. Genetic divergence was matched with accompanying unique visual characters that aid field identification. Additional taxonomic complexity was also evident, by comparison with DNA barcodes from international locations, suggesting that the specific names applicable for two of the candidate species in Australia remain unresolved due to confusion surrounding type specimens. Although flathead gobies are assumed to be widespread and common, this study demonstrates that unrealised taxonomic and ecological complexity is evident, and this will influence assessments of tropical biodiversity and species conservation. This study supports the need for taxonomic studies of freshwater fishes to underpin management in areas subject to significant environmental change.},
}
@article {pmid33581527,
year = {2021},
author = {Dai, Y and Hacker, CE and Cao, Y and Cao, H and Xue, Y and Ma, X and Liu, H and Zahoor, B and Zhang, Y and Li, D},
title = {Implementing a comprehensive approach to study the causes of human-bear (Ursus arctos pruinosus) conflicts in the Sanjiangyuan region, China.},
journal = {The Science of the total environment},
volume = {772},
number = {},
pages = {145012},
doi = {10.1016/j.scitotenv.2021.145012},
pmid = {33581527},
issn = {1879-1026},
mesh = {Animals ; China ; Humans ; Seasons ; *Ursidae ; },
abstract = {Personal injury and property loss caused by wildlife often deteriorates the relationship between humans and animals, prompting retaliatory killings that threaten species survival. Conflicts between humans and Tibetan brown bears (Ursus arctos pruinosus) (Human-Bear Conflicts, HBC) in the Sanjiangyuan region have recently dramatically increased, seriously affecting community enthusiasm for brown bears and the conservation of other species. In order to understand the driving mechanisms of HBC, we proposed six potential drivers leading to increased occurrences of HBC. We conducted field research in Zhiduo County of the Sanjiangyuan region from 2017 to 2019 to test hypotheses through semi-constructed interviews, marmot (Marmota himalayana) density surveys and brown bear diet analysis based on metagenomic sequencing. Analysis of herder perceptions revealed that the driving factors of HBC were related to changes in their settlement practice and living habits, changes in foraging behavior of brown bears and recovery of the brown bear population. Since the establishment of winter homes, brown bears have gradually learned to utilize the food in unattended homes. Although 91.4% (n = 285) of the respondents no longer store food in unattended homes, brown bears were reported to still frequently approach winter homes for food due to improper disposal of dead livestock and household garbage. The frequency and abundance of marmots were found to be high in brown bear diet, indicating that marmots were the bears' primary food. However, marmot density had no significant effect on brown bears utilizing human food (P = 0.329), and HBC appears to not be caused by natural food shortages. Distance to rocky outcrops (P = 0.022) and winter homes (P = 0.040) were the key factors linked to brown bears pursuing human food. The number of brown bears has increased over the past decade, and HBC is likely linked to its population recovery. Our findings will provide scientific basis for formulating effective mitigation measures and protection countermeasures for brown bears.},
}
@article {pmid33579697,
year = {2021},
author = {Wu, Q and Suo, C and Brown, T and Wang, T and Teichmann, SA and Bassett, AR},
title = {INSIGHT: A population-scale COVID-19 testing strategy combining point-of-care diagnosis with centralized high-throughput sequencing.},
journal = {Science advances},
volume = {7},
number = {7},
pages = {},
pmid = {33579697},
issn = {2375-2548},
support = {/WT_/Wellcome Trust/United Kingdom ; WT206194/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*COVID-19/diagnosis/genetics ; *COVID-19 Nucleic Acid Testing ; *High-Throughput Nucleotide Sequencing ; Humans ; *Point-of-Care Testing ; SARS-CoV-2/*genetics ; },
abstract = {We present INSIGHT [isothermal NASBA (nucleic acid sequence-based amplification) sequencing-based high-throughput test], a two-stage coronavirus disease 2019 testing strategy, using a barcoded isothermal NASBA reaction. It combines point-of-care diagnosis with next-generation sequencing, aiming to achieve population-scale testing. Stage 1 allows a quick decentralized readout for early isolation of presymptomatic or asymptomatic patients. It gives results within 1 to 2 hours, using either fluorescence detection or a lateral flow readout, while simultaneously incorporating sample-specific barcodes. The same reaction products from potentially hundreds of thousands of samples can then be pooled and used in a highly multiplexed sequencing-based assay in stage 2. This second stage confirms the near-patient testing results and facilitates centralized data collection. The 95% limit of detection is <50 copies of viral RNA per reaction. INSIGHT is suitable for further development into a rapid home-based, point-of-care assay and is potentially scalable to the population level.},
}
@article {pmid33575654,
year = {2021},
author = {Povysil, G and Heinzl, M and Salazar, R and Stoler, N and Nekrutenko, A and Tiemann-Boege, I},
title = {Increased yields of duplex sequencing data by a series of quality control tools.},
journal = {NAR genomics and bioinformatics},
volume = {3},
number = {1},
pages = {lqab002},
pmid = {33575654},
issn = {2631-9268},
support = {P 30867/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Duplex sequencing is currently the most reliable method to identify ultra-low frequency DNA variants by grouping sequence reads derived from the same DNA molecule into families with information on the forward and reverse strand. However, only a small proportion of reads are assembled into duplex consensus sequences (DCS), and reads with potentially valuable information are discarded at different steps of the bioinformatics pipeline, especially reads without a family. We developed a bioinformatics toolset that analyses the tag and family composition with the purpose to understand data loss and implement modifications to maximize the data output for the variant calling. Specifically, our tools show that tags contain polymerase chain reaction and sequencing errors that contribute to data loss and lower DCS yields. Our tools also identified chimeras, which likely reflect barcode collisions. Finally, we also developed a tool that re-examines variant calls from raw reads and provides different summary data that categorizes the confidence level of a variant call by a tier-based system. With this tool, we can include reads without a family and check the reliability of the call, that increases substantially the sequencing depth for variant calling, a particular important advantage for low-input samples or low-coverage regions.},
}
@article {pmid33575611,
year = {2020},
author = {Chen, X and Qian, W and Song, Z and Li, QX and Guo, S},
title = {Authentication, characterization and contamination detection of cell lines, xenografts and organoids by barcode deep NGS sequencing.},
journal = {NAR genomics and bioinformatics},
volume = {2},
number = {3},
pages = {lqaa060},
pmid = {33575611},
issn = {2631-9268},
abstract = {Misidentification and contamination of biobank samples (e.g. cell lines) have plagued biomedical research. Short tandem repeat (STR) and single-nucleotide polymorphism assays are widely used to authenticate biosamples and detect contamination, but with insufficient sensitivity at 5-10% and 3-5%, respectively. Here, we describe a deep NGS-based method with significantly higher sensitivity (≤1%). It can be used to authenticate human and mouse cell lines, xenografts and organoids. It can also reliably identify and quantify contamination of human cell line samples, contaminated with only small amount of other cell samples; detect and quantify species-specific components in human-mouse mixed samples (e.g. xenografts) with 0.1% sensitivity; detect mycoplasma contamination; and infer population structure and gender of human samples. By adopting DNA barcoding technology, we are able to profile 100-200 samples in a single run at per-sample cost comparable to conventional STR assays, providing a truly high-throughput and low-cost assay for building and maintaining high-quality biobanks.},
}
@article {pmid33575589,
year = {2020},
author = {Senabouth, A and Andersen, S and Shi, Q and Shi, L and Jiang, F and Zhang, W and Wing, K and Daniszewski, M and Lukowski, SW and Hung, SSC and Nguyen, Q and Fink, L and Beckhouse, A and Pébay, A and Hewitt, AW and Powell, JE},
title = {Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA-sequencing.},
journal = {NAR genomics and bioinformatics},
volume = {2},
number = {2},
pages = {lqaa034},
pmid = {33575589},
issn = {2631-9268},
abstract = {The libraries generated by high-throughput single cell RNA-sequencing (scRNA-seq) platforms such as the Chromium from 10× Genomics require considerable amounts of sequencing, typically due to the large number of cells. The ability to use these data to address biological questions is directly impacted by the quality of the sequence data. Here we have compared the performance of the Illumina NextSeq 500 and NovaSeq 6000 against the BGI MGISEQ-2000 platform using identical Single Cell 3' libraries consisting of over 70 000 cells generated on the 10× Genomics Chromium platform. Our results demonstrate a highly comparable performance between the NovaSeq 6000 and MGISEQ-2000 in sequencing quality, and the detection of genes, cell barcodes, Unique Molecular Identifiers. The performance of the NextSeq 500 was also similarly comparable to the MGISEQ-2000 based on the same metrics. Data generated by both sequencing platforms yielded similar analytical outcomes for general single-cell analysis. The performance of the NextSeq 500 and MGISEQ-2000 were also comparable for the deconvolution of multiplexed cell pools via variant calling, and detection of guide RNA (gRNA) from a pooled CRISPR single-cell screen. Our study provides a benchmark for high-capacity sequencing platforms applied to high-throughput scRNA-seq libraries.},
}
@article {pmid33575131,
year = {2021},
author = {Munguia-Vega, A and Weaver, AH and Domínguez-Contreras, JF and Peckham, H},
title = {Multiple drivers behind mislabeling of fish from artisanal fisheries in La Paz, Mexico.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e10750},
pmid = {33575131},
issn = {2167-8359},
abstract = {Seafood mislabeling has the potential to mask changes in the supply of species due to overfishing, while also preventing consumers from making informed choices about the origin, quality and sustainability of their food. Thus, there is a need to understand mislabeling and analyze the potential causes behind it to propose solutions. We conducted a COI DNA barcoding study in La Paz, Baja California Sur, Mexico, with 74 samples from fish markets and 50 samples from restaurants. We identified 38 species sold under 19 commercial names, from which at least ∼80% came from local small-scale fisheries. Overall, 49 samples, representing 40% (95% CI [31.4-48.3]) were considered mislabeled in our samples. Based on analyses where species were assigned to three price categories, economic incentives were associated with approximately half of the mislabeling events observed, suggesting that other motivating factors might simultaneously be at play. Using a network approach to describe both mislabeling (when species are mislabeled as the focal species) and substitution (when the focal species is used as substitute for others), we calculated proxies for the net availability of each species in the market. We found that local fish landings were a significant predictor of the net availability of the 10 most important commercial species at retail, but this true availability was masked to the eyes of the final consumer by both mislabeling and substitution. We hypothesize that the level of supply of each species could help explain mislabeling and substitution rates, where species in low supply and high demand could show higher mislabeling rates and rarely be used as substitutes, while species in high supply and low demand could be used as substitutes for the preferred species. Other factors affecting mislabeling include national regulations that restrict the fishing or commercialization of certain species and local and global campaigns that discourage specific patterns of consumption. We discuss how these factors might influence mislabeling and propose some solutions related to communication and education efforts to this local and global challenge.},
}
@article {pmid33574410,
year = {2021},
author = {Hami, A and Rasool, RS and Khan, NA and Mansoor, S and Mir, MA and Ahmed, N and Masoodi, KZ},
title = {Morpho-molecular identification and first report of Fusarium equiseti in causing chilli wilt from Kashmir (Northern Himalayas).},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {3610},
pmid = {33574410},
issn = {2045-2322},
mesh = {Capsicum/*microbiology ; DNA Barcoding, Taxonomic ; DNA, Intergenic/*genetics ; Fusarium/*genetics/pathogenicity ; Genetic Variation/genetics ; Plant Diseases/*genetics/microbiology ; Plant Roots/microbiology ; Plant Stems/microbiology ; },
abstract = {Chilli (Capsicum annuum L.) is one of the most significant vegetable and spice crop. Wilt caused by Fusarium Sp. has emerged as a serious problem in chilli production. Internal transcribed spacer (ITS) region is widely used as a DNA barcoding marker to characterize the diversity and composition of Fusarium communities. ITS regions are heavily used in both molecular methods and ecological studies of fungi, because of its high degree of interspecific variability, conserved primer sites and multiple copy nature in the genome. In the present study we focused on morphological and molecular characterization of pathogen causing chilli wilt. Chilli plants were collected from four districts of Kashmir valley of Himalayan region. Pathogens were isolated from infected root and stem of the plants. Isolated pathogens were subjected to DNA extraction and PCR amplification. The amplified product was sequenced and three different wilt causing fungal isolates were obtained which are reported in the current investigation. In addition to Fusarium oxysporum and Fusarium solani, a new fungal species was found in association with the chilli wilt in Kashmir valley viz., Fusarium equiseti that has never been reported before from this region. The studies were confirmed by pathogenicity test and re-confirmation by DNA barcoding.},
}
@article {pmid33573201,
year = {2021},
author = {Alzahrani, DA},
title = {Complete Chloroplast Genome of Abutilon fruticosum: Genome Structure, Comparative and Phylogenetic Analysis.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {2},
pages = {},
pmid = {33573201},
issn = {2223-7747},
support = {DF-295-130-1441//DEANSHIP OF SCIENTIFIC RESEARCH (DSR), KING ABDULAZIZ UNIVERSITY/ ; },
abstract = {Abutilon fruticosum is one of the endemic plants with high medicinal and economic value in Saudi Arabia and belongs to the family Malvaceae. However, the plastome sequence and phylogenetic position have not been reported until this study. In this research, the complete chloroplast genome of A. fruticosum was sequenced and assembled, and comparative and phylogenetic analyses within the Malvaceae family were conducted. The chloroplast genome (cp genome) has a circular and quadripartite structure with a total length of 160,357 bp and contains 114 unique genes (80 protein-coding genes, 30 tRNA genes and 4 rRNA genes). The repeat analyses indicate that all the types of repeats (palindromic, complement, forward and reverse) were present in the genome, with palindromic occurring more frequently. A total number of 212 microsatellites were identified in the plastome, of which the majority are mononucleotides. Comparative analyses with other species of Malvaceae indicate a high level of resemblance in gene content and structural organization and a significant level of variation in the position of genes in single copy and inverted repeat borders. The analyses also reveal variable hotspots in the genomes that can serve as barcodes and tools for inferring phylogenetic relationships in the family: the regions include trnH-psbA, trnK-rps16, psbI-trnS, atpH-atpI, trnT-trnL, matK, ycf1 and ndhH. Phylogenetic analysis indicates that A. fruticosum is closely related to Althaea officinalis, which disagrees with the previous systematic position of the species. This study provides insights into the systematic position of A. fruticosum and valuable resources for further phylogenetic and evolutionary studies of the species and the Malvaceae family to resolve ambiguous issues within the taxa.},
}
@article {pmid33573084,
year = {2021},
author = {Dalmon, A and Diévart, V and Thomasson, M and Fouque, R and Vaissière, BE and Guilbaud, L and Le Conte, Y and Henry, M},
title = {Possible Spillover of Pathogens between Bee Communities Foraging on the Same Floral Resource.},
journal = {Insects},
volume = {12},
number = {2},
pages = {},
pmid = {33573084},
issn = {2075-4450},
abstract = {Viruses are known to contribute to bee population decline. Possible spillover is suspected from the co-occurrence of viruses in wild bees and honey bees. In order to study the risk of virus transmission between wild and managed bee species sharing the same floral resource, we tried to maximize the possible cross-infections using Phacelia tanacetifolia, which is highly attractive to honey bees and a broad range of wild bee species. Virus prevalence was compared over two years in Southern France. A total of 1137 wild bees from 29 wild bee species (based on COI barcoding) and 920 honey bees (Apis mellifera) were checked for the seven most common honey bee RNA viruses. Halictid bees were the most abundant. Co-infections were frequent, and Sacbrood virus (SBV), Black queen cell virus (BQCV), Acute bee paralysis virus (ABPV) and Israeli acute paralysis virus (IAPV) were widespread in the hymenopteran pollinator community. Conversely, Deformed wing virus (DWV) was detected at low levels in wild bees, whereas it was highly prevalent in honey bees (78.3% of the samples). Both wild bee and honey bee virus isolates were sequenced to look for possible host-specificity or geographical structuring. ABPV phylogeny suggested a specific cluster for Eucera bees, while isolates of DWV from bumble bees (Bombus spp.) clustered together with honey bee isolates, suggesting a possible spillover.},
}
@article {pmid33572950,
year = {2021},
author = {Zhang, X and Yu, H and Yang, Q and Wang, Z and Xia, R and Chen, C and Qu, Y and Tan, R and Shi, Y and Xiang, P and Zhang, S and Li, C},
title = {A Forensic Detection Method for Hallucinogenic Mushrooms via High-Resolution Melting (HRM) Analysis.},
journal = {Genes},
volume = {12},
number = {2},
pages = {},
pmid = {33572950},
issn = {2073-4425},
mesh = {Agaricales/*chemistry ; DNA, Intergenic/*genetics/isolation &amp; purification ; *Forensic Genetics ; Genetic Techniques ; Hallucinogens/chemistry/*isolation &amp; purification ; Humans ; Psilocybe/*chemistry/isolation &amp; purification ; Temperature ; },
abstract = {In recent years, trafficking and abuse of hallucinogenic mushrooms have become a serious social problem. It is therefore imperative to identify hallucinogenic mushrooms of the genus Psilocybe for national drug control legislation. An internal transcribed spacer (ITS) is a DNA barcoding tool utilized for species identification. Many methods have been used to discriminate the ITS region, but they are often limited by having a low resolution. In this study, we sought to analyze the ITS and its fragments, ITS1 and ITS2, by using high-resolution melting (HRM) analysis, which is a rapid and sensitive method for evaluating sequence variation within PCR amplicons. The ITS HRM assay was tested for specificity, reproducibility, sensitivity, and the capacity to analyze mixture samples. It was shown that the melting temperatures of the ITS, ITS1, and ITS2 of Psilocybe cubensis were 83.72 ± 0.01, 80.98 ± 0.06, and 83.46 ± 0.08 °C, and for other species, we also obtained species-specific results. Finally, we performed ITS sequencing to validate the presumptive taxonomic identity of our samples, and the sequencing output significantly supported our HRM data. Taken together, these results indicate that the HRM method can quickly distinguish the DNA barcoding of Psilocybe cubensis and other fungi, which can be utilized for drug trafficking cases and forensic science.},
}
@article {pmid33568962,
year = {2021},
author = {Liu, WB and Yao, Y and Yan, CC and Wang, XH and Lin, XL},
title = {A new species of Polypedilum (Cerobregma) (Diptera, Chironomidae) from Oriental China.},
journal = {ZooKeys},
volume = {1011},
number = {},
pages = {139-148},
pmid = {33568962},
issn = {1313-2989},
abstract = {Polypedilum (Cerobregma) huapingensis Liu &amp; Lin, sp. nov. is described and illustrated based on an adult male from Huaping National Nature Reserve, Guangxi, China. A DNA barcode analysis, including the known partial COI sequences of species in the Cerobregma subgenus, was conducted. An updated key to adult males of the subgenus Cerobregma is provided.},
}
@article {pmid33568247,
year = {2021},
author = {Lashkari, M and Burckhardt, D and Kashef, S},
title = {Molecular, morphometric and digital automated identification of three Diaphorina species (Hemiptera: Liviidae).},
journal = {Bulletin of entomological research},
volume = {111},
number = {4},
pages = {411-419},
doi = {10.1017/S0007485321000043},
pmid = {33568247},
issn = {1475-2670},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Hemiptera/anatomy &amp; histology/*classification/genetics ; Image Processing, Computer-Assisted ; Wings, Animal/anatomy &amp; histology ; },
abstract = {Diaphorina is a species-rich genus, native to the tropics and subtropics of the Old World, particularly of more arid regions. One of the species, Diaphorina citri, is the economically most important pest of citrus. Diaphorina species are morphologically similar which makes their identification difficult. In this study, the accuracy of DNA barcoding, using mitochondrial cytochrome c oxidase subunit 1 (COI), geometric morphometrics of the forewing and digital image processing methods were tested for identification of the three Diaphorina species: D. chobauti, D. citri and D. zygophylli. Moreover, the published COI sequences of D. citri, D. communis and D. lycii obtained from Genbank were used for cluster analyses. DNA barcodes for D. chobauti and D. zygophylli are deposited in Genbank for the first time. The results of the molecular and geometric morphometric analyses are congruent and place D. chobauti as the sister taxon of the other Diaphorina species. The geometric morphometric analysis shows that in D. zygophylli the fore margin is slightly curved proximally and sharply bent distally, while in D. chobauti and D. citri it is straight proximally and weakly bent distally. The results of digital image processing show that the distribution of the dark pattern differs consistently in the three studied species.},
}
@article {pmid33566825,
year = {2021},
author = {Chandrasekara, CHWMRB and Naranpanawa, DNU and Bandusekara, BS and Pushpakumara, DKNG and Wijesundera, DSA and Bandaranayake, PCG},
title = {Universal barcoding regions, rbcL, matK and trnH-psbA do not discriminate Cinnamomum species in Sri Lanka.},
journal = {PloS one},
volume = {16},
number = {2},
pages = {e0245592},
pmid = {33566825},
issn = {1932-6203},
mesh = {*Base Sequence ; Cinnamomum/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics/isolation &amp; purification ; Phylogeny ; Polymorphism, Single Nucleotide ; Species Specificity ; Sri Lanka ; },
abstract = {The genus Cinnamomum consists of about 250 species spread globally. Out of these, C. verum (C. zeylanicum), also known as true cinnamon or Ceylon cinnamon, has gained worldwide attention due to its culinary uses and medicinal values. Sri Lanka is the largest true cinnamon producer in the world and accounts for about 80-90% of global production. Other than the cultivated species, Sri Lankan natural vegetation is home to seven endemic wild species of the genus Cinnamomum. While these are underutilized, proper identification and characterization are essential steps in any sustainable conservation and utilization strategies. Currently, species identification is purely based on morphological traits, and intraspecific diversity has made it more challenging. In this study, all the eight Cinnamomum species found in Sri Lanka, C. capparu-coronde, C. citriodorum C. dubium, C. litseifolium, C. ovalifolium, C. rivulorum, C. sinharajaense, and C. verum were collected in triplicates and identified using typical morphological traits. DNA extracted with the same collection was assessed with universal barcoding regions, rbcL, matK, and trnH-psbA. While no intraspecific sequence differences were observed in C. citriodorum, C. rivulorum, and C. verum, the others had polymorphic sites in one, two, or all regions assessed. Interestingly, two individuals of C. sinharajaense had identical barcodes to the cultivated species C. verum, while the other one had one variable cite in matK region and three cites in trnH-psbA reigon. Further, one C. dubium and one C. capparu-coronde accession each had identical, rbcL, and trnH-psbA sequences while those had only a single nucleotide variation observed in matK region. Overall, the phylogeny of Cinnamomum species found in Sri Lanka could not be completely resolved with DNA barcoding regions studied.},
}
@article {pmid33566818,
year = {2021},
author = {Landry, B and Whitton, J and Bazzicalupo, AL and Ceska, O and Berbee, ML},
title = {Phylogenetic analysis of the distribution of deadly amatoxins among the little brown mushrooms of the genus Galerina.},
journal = {PloS one},
volume = {16},
number = {2},
pages = {e0246575},
pmid = {33566818},
issn = {1932-6203},
mesh = {Agaricales/*classification/*genetics ; Amanitins/genetics ; Humans ; Likelihood Functions ; Phylogeny ; },
abstract = {Some but not all of the species of 'little brown mushrooms' in the genus Galerina contain deadly amatoxins at concentrations equaling those in the death cap, Amanita phalloides. However, Galerina's ~300 species are notoriously difficult to identify by morphology, and the identity of toxin-containing specimens has not been verified with DNA barcode sequencing. This left open the question of which Galerina species contain toxins and which do not. We selected specimens for toxin analysis using a preliminary phylogeny of the fungal DNA barcode region, the ribosomal internal transcribed spacer (ITS) region. Using liquid chromatography/mass spectrometry, we analyzed amatoxins from 70 samples of Galerina and close relatives, collected in western British Columbia, Canada. To put the presence of toxins into a phylogenetic context, we included the 70 samples in maximum likelihood analyses of 438 taxa, using ITS, RNA polymerase II second largest subunit gene (RPB2), and nuclear large subunit ribosomal RNA (LSU) gene sequences. We sequenced barcode DNA from types where possible to aid with applications of names. We detected amatoxins only in the 24 samples of the G. marginata s.l. complex in the Naucoriopsis clade. We delimited 56 putative Galerina species using Automatic Barcode Gap Detection software. Phylogenetic analysis showed moderate to strong support for Galerina infrageneric clades Naucoriopsis, Galerina, Tubariopsis, and Sideroides. Mycenopsis appeared paraphyletic and included Gymnopilus. Amatoxins were not detected in 46 samples from Galerina clades outside of Naucoriopsis or from outgroups. Our data show significant quantities of toxin in all mushrooms tested from the G. marginata s.l. complex. DNA barcoding revealed consistent accuracy in morphology-based identification of specimens to G. marginata s.l. complex. Prompt and careful morphological identification of ingested G. marginata s.l. has the potential to improve patient outcomes by leading to fast and appropriate treatment.},
}
@article {pmid33564041,
year = {2021},
author = {Wu, HY and Chan, KT and But, GW and Shaw, PC},
title = {Assessing the reliability of medicinal Dendrobium sequences in GenBank for botanical species identification.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {3439},
pmid = {33564041},
issn = {2045-2322},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; *Databases, Nucleic Acid ; *Dendrobium/classification/genetics ; *Sequence Analysis, DNA ; },
abstract = {DNA-based method is a promising tool in species identification and is widely used in various fields. DNA barcoding method has already been included in different pharmacopoeias for identification of medicinal materials or botanicals. Accuracy and validity of DNA-based methods rely on the accuracy and taxonomic reliability of the DNA sequences in the database to be compared against. Here we evaluated the annotation quality and taxonomic reliability of selected barcode loci (rbcL, matK, psbA-trnH, trnL-trnF and ITS) of 41 medicinal Dendrobium species downloaded from GenBank. Annotations of most accessions are incomplete. Only 53.06% of the 2041 accessions downloaded contain a reference to a voucher specimen. Only 31.60% and 4.8% of the entries are annotated with country of origin and collector or assessor, respectively. Taxonomic reliability of the sequences was evaluated by a Megablast search based on similarity to sequences submitted by other research groups. A small number of sequences (211, 7.14%) was regarded as highly doubted. Moreover, 10 out of 60 complete chloroplast genomes contain highly doubted sequences. Our findings suggest that sequences of GenBank should be used with caution for species-level identification. The scientific community should provide more important information regarding identity and traceability of the sample when they deposit sequences to public databases.},
}
@article {pmid33562113,
year = {2021},
author = {Scales, ZM and Narbay, E and Hellberg, RS},
title = {Use of DNA Barcoding Combined with PCR-SFLP to Authenticate Species in Bison Meat Products.},
journal = {Foods (Basel, Switzerland)},
volume = {10},
number = {2},
pages = {},
pmid = {33562113},
issn = {2304-8158},
abstract = {American bison (Bison bison) meat is susceptible to species mislabeling due to its high value and similar appearance to meat from domestic cattle (Bos taurus). DNA barcoding is commonly used to identify animal species. However, as a result of the historical hybridization of American bison and domestic cattle, additional genetic testing is required for species confirmation. The objective of this study was to perform a market survey of bison meat products and verify the species using DNA barcoding combined with polymerase chain reaction-satellite fragment length polymorphism (PCR-SFLP). Bison products (n = 45) were purchased from a variety of retailers. Samples that were positive for domestic cattle with DNA barcoding were further analyzed with PCR-SFLP. DNA barcoding identified bison in 41 products, red deer (Cervus elaphus) in one product, and domestic cattle in three products. PCR-SFLP confirmed the identification of domestic cattle in two samples, while the third sample was identified as bison with ancestral cattle DNA. Overall, mislabeling was detected in 3 of the 45 samples (6.7%). This study revealed that additional DNA testing of species that have undergone historical hybridization provides improved identification results compared to DNA barcoding alone.},
}
@article {pmid33559966,
year = {2021},
author = {Chen, J and Zhang, X and Yi, F and Gao, X and Song, W and Zhao, H and Lai, J},
title = {MP3RNA-seq: Massively parallel 3' end RNA sequencing for high-throughput gene expression profiling and genotyping.},
journal = {Journal of integrative plant biology},
volume = {63},
number = {7},
pages = {1227-1239},
doi = {10.1111/jipb.13077},
pmid = {33559966},
issn = {1744-7909},
support = {31421005//National Natural Science Foundation of China/ ; 2016YFD0100404//National Key Research and Development Program/ ; 2016YFD0101804//National Key Research and Development Program/ ; BX201600149//National Postdoctoral Program for Innovative Talents/ ; 2017M611049//China Postdoctoral Science Foundation/ ; },
mesh = {Genotype ; Quantitative Trait Loci/*genetics ; RNA-Seq ; Zea mays/*genetics ; },
abstract = {Transcriptome deep sequencing (RNA-seq) has become a routine method for global gene expression profiling. However, its application to large-scale experiments remains limited by cost and labor constraints. Here we describe a massively parallel 3' end RNA-seq (MP3RNA-seq) method that introduces unique sample barcodes during reverse transcription to permit sample pooling immediately following this initial step. MP3RNA-seq allows for handling of hundreds of samples in a single experiment, at a cost of about $6 per sample for library construction and sequencing. MP3RNA-seq is effective for not only high-throughput gene expression profiling, but also genotyping. To demonstrate its utility, we applied MP3RNA-seq to 477 double haploid lines of maize. We identified 19,429 genes expressed in at least 50% of the lines and 35,836 high-quality single nucleotide polymorphisms for genotyping analysis. Armed with these data, we performed expression and agronomic trait quantitative trait locus (QTL) mapping and identified 25,797 expression QTLs for 15,335 genes and 21 QTLs for plant height, ear height, and relative ear height. We conclude that MP3RNA-seq is highly reproducible, accurate, and sensitive for high-throughput gene expression profiling and genotyping, and should be generally applicable to most eukaryotic species.},
}
@article {pmid33559305,
year = {2021},
author = {Wolf, KKE and Hoppe, CJM and Leese, F and Weiss, M and Rost, B and Neuhaus, S and Gross, T and Kühne, N and John, U},
title = {Revealing environmentally driven population dynamics of an Arctic diatom using a novel microsatellite PoolSeq barcoding approach.},
journal = {Environmental microbiology},
volume = {23},
number = {7},
pages = {3809-3824},
doi = {10.1111/1462-2920.15424},
pmid = {33559305},
issn = {1462-2920},
mesh = {Arctic Regions ; *Diatoms/genetics ; Ecosystem ; Microsatellite Repeats/genetics ; Population Dynamics ; },
abstract = {Ecological stability under environmental change is determined by both interspecific and intraspecific processes. Particularly for planktonic microorganisms, it is challenging to follow intraspecific dynamics over space and time. We propose a new method, microsatellite PoolSeq barcoding (MPB), for tracing allele frequency changes in protist populations. We successfully applied this method to experimental community incubations and field samples of the diatom Thalassiosira hyalina from the Arctic, a rapidly changing ecosystem. Validation of the method found compelling accuracy in comparison with established genotyping approaches within different diversity contexts. In experimental and environmental samples, we show that MPB can detect meaningful patterns of population dynamics, resolving allelic stability and shifts within a key diatom species in response to experimental treatments as well as different bloom phases and years. Through our novel MPB approach, we produced a large dataset of populations at different time-points and locations with comparably little effort. Results like this can add insights into the roles of selection and plasticity in natural protist populations under stable experimental but also variable field conditions. Especially for organisms where genotype sampling remains challenging, MPB holds great potential to efficiently resolve eco-evolutionary dynamics and to assess the mechanisms and limits of resilience to environmental stressors.},
}
@article {pmid33556892,
year = {2021},
author = {Nithaniyal, S and Majumder, S and Umapathy, S and Parani, M},
title = {Forensic application of DNA barcoding in the identification of commonly occurring poisonous plants.},
journal = {Journal of forensic and legal medicine},
volume = {78},
number = {},
pages = {102126},
doi = {10.1016/j.jflm.2021.102126},
pmid = {33556892},
issn = {1878-7487},
mesh = {*DNA Barcoding, Taxonomic ; Forensic Toxicology ; *Gene Library ; *Genetic Markers ; Plants, Toxic/*genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; },
abstract = {Exposure to poisonous plants is hazardous to health; thus, reliable species identification is required to decide the most appropriate treatment. Since ingested plants are too much degraded for visual observation, DNA barcoding can be used as a molecular tool for species identification. Considering the universal primers, PCR and sequencing success rate, and diversity of the poisonous plants, the rbcL DNA marker was selected for molecular identification. A reference DNA barcode library for 100 poisonous plant species was created using rbcL DNA barcodes. For the poisonous plants represented in the library, 100% and 89% species differentiation was observed at the genus and species level, respectively. All the undifferentiated species were congeneric species. Mapping the metabolites of the poisonous plants to the DNA based phylogenetic tree indicated that the phylogenetically related species also had related toxic compounds. Therefore, genus-level identification may be sufficient in the practical application of DNA barcoding in poisoning cases. We conclude that rbcL can be used as a primary marker, and if required, ITS2 or trnH-psbA may be used as a secondary marker to identify the poisonous plants. The present study provides the foundation to develop a reliable molecular method to identify the poisonous species from the vomit samples of poisoning cases.},
}
@article {pmid33555972,
year = {2021},
author = {Camacho-Sánchez, FY and Aguirre, AA and Narváez-Zapata, JA and Zavala-Norzagaray, AA and Ley-Quiñónez, CP and Acosta-Sánchez, HH and Rodriguez-González, H and Delgado-Trejo, C and Reyes-López, MA},
title = {DNA barcode analysis of the endangered green turtle (Chelonia mydas) in Mexico[1].},
journal = {Genome},
volume = {64},
number = {9},
pages = {879-891},
doi = {10.1139/gen-2019-0213},
pmid = {33555972},
issn = {1480-3321},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Endangered Species ; Haplotypes ; Mexico ; *Turtles/genetics ; },
abstract = {Technological and analytical advances to study evolutionary biology, ecology, and conservation of green turtles (Chelonia mydas) are realized through molecular approaches including DNA barcoding. We characterized the usefulness of COI DNA barcodes in green turtles in Mexico to better understand genetic divergence and other genetic parameters of this species. We analyzed 63 sequences, including 25 from green turtle field specimens collected from the Gulf of Mexico and from the Mexican Pacific and 38 already present in the Barcode of Life Data Systems (BOLD). A total of 13 haplotypes were identified with four novel haplotypes from the Pacific Ocean and three novel haplotypes from the Atlantic Ocean. Intraspecific distance values among COI gene sequences by two different models were 0.01, demonstrating that there is not a subdivision for green turtle species. Otherwise, the interspecific distance interval ranged from 0.07 to 0.13, supporting a clear subdivision among all sea turtle species. Haplotype and total nucleotide diversity values of the COI gene reflect a medium genetic diversity average. Green turtles of the Mexican Pacific showed common haplotypes to some Australian and Chinese turtles, but different from the haplotypes of the Mexican Atlantic. COI analysis revealed new haplotypes and confirmed that DNA barcodes were useful for evaluation of the population diversity of green turtles in Mexico.},
}
@article {pmid33552747,
year = {2021},
author = {Herzog, SA and Latvis, M},
title = {Examining the utility of DNA barcodes for the identification of tallgrass prairie flora.},
journal = {Applications in plant sciences},
volume = {9},
number = {1},
pages = {e11405},
pmid = {33552747},
issn = {2168-0450},
abstract = {PREMISE: The tallgrass prairies of North America are one of the most threatened ecosystems in the world, making efficient species identification essential for understanding and managing diversity. Here, we assess DNA barcoding with high-throughput sequencing as a method for rapid plant species identification.<br><br>METHODS: Using herbarium collections representing the tallgrass prairie flora of Oak Lake Field Station, South Dakota, USA, we amplified and examined four common nuclear and plastid barcode regions (ITS, matK, psbA-trnH, and rbcL), individually and in combination, to test their success in identifying samples to family, genus, and species levels using BLAST searches of three databases of varying size.<br><br>RESULTS: Concatenated barcodes increased performance, although none were significantly different than single-region barcodes. The plastid region psbA-trnH performed significantly more poorly than the others, while barcodes containing ITS performed best. Database size significantly affected identification success at all three taxonomic levels. Confident species-level identification ranged from 8-44% for the global database, 13-56% for the regional database, and 21-80% for the sampled species database, depending on the barcode used.<br><br>DISCUSSION: Barcoding was generally successful in identifying tallgrass prairie genera and families, but was of limited use in species-level identifications. Database size was an important factor in successful plant identification. We discuss future directions and considerations for improving the performance of DNA barcoding in tallgrass prairies.},
}
@article {pmid33551656,
year = {2021},
author = {Vargas, HA},
title = {Iridopsis socoromaensis sp. n., a geometrid moth (Lepidoptera, Geometridae) from the Andes of northern Chile.},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e61592},
pmid = {33551656},
issn = {1314-2828},
abstract = {BACKGROUND: Iridopsis Warren, 1894 (Lepidoptera: Geometridae: Ennominae: Boarmiini) is a New World moth genus mainly diversified in the Neotropical Region. It is represented in Chile by two described species, both from the Atacama Desert.<br><br>NEW INFORMATION: Iridopsis socoromaensis sp. n. (Lepidoptera: Geometridae: Ennominae: Boarmiini) is described and illustrated from the western slopes of the Andes of northern Chile. Its larvae were found feeding on leaves of the Chilean endemic shrub Dalea pennellii (J.F. Macbr.) J.F. Macbr. var. chilensis Barneby (Fabaceae). Morphological differences of I. socoromaensis sp. n. with the two species of the genus previously known from Chile are discussed. A DNA barcode fragment of I. socoromaensis sp. n. showed 93.7-94.3% similarity with the Nearctic I. sanctissima (Barnes &amp; McDunnough, 1917). However, the morphology of the genitalia suggests that these two species are distantly related. The discovery of I. socoromaensis sp. n. highlights the need for additional surveys in underexplored areas to understand better the taxonomic diversity and evolutionary relationships of the mainly Neotropical moth genus Iridopsis.},
}
@article {pmid33551655,
year = {2021},
author = {Aghayeva, P and Cozzolino, S and Cafasso, D and Ali-Zade, V and Fineschi, S and Aghayeva, D},
title = {DNA barcoding of native Caucasus herbal plants: potentials and limitations in complex groups and implications for phylogeographic patterns.},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e61333},
pmid = {33551655},
issn = {1314-2828},
abstract = {DNA barcoding has rapidly become a useful complementary tool in floristic investigations particularly for identifying specimens that lack diagnostic characters. Here, we assess the capability of three DNA barcode markers (chloroplast rpoB, accD and nuclear ITS) for correct species assignment in a floristic survey on the Caucasus. We focused on two herbal groups with potential for ornamental applications, namely orchids and asterids. On these two plant groups, we tested whether our selection of barcode markers allows identification of the "barcoding gap" in sequence identity and to distinguish between monophyletic species when employing distance-based methods. All markers successfully amplified most specimens, but we found that the rate of species-level resolution amongst selected markers largely varied in the two plant groups. Overall, for both lineages, plastid markers had a species-level assignment success rate lower than the nuclear ITS marker. The latter confirmed, in orchids, both the existence of a barcoding gap and that all accessions of the same species clustered together in monophyletic groups. Further, it also allowed the detection of a phylogeographic signal.The ITS marker resulted in its being the best performing barcode for asterids; however, none of the three tested markers showed high discriminatory ability. Even if ITS were revealed as the most promising plant barcode marker, we argue that the ability of this barcode for species assignment is strongly dependent on the evolutionary history of the investigated plant lineage.},
}
@article {pmid33551652,
year = {2021},
author = {Xiao, JG and Yu, ZS and Song, N and Gao, TX},
title = {Description of a new species, Sillago nigrofasciata sp. nov. (Perciformes, Sillaginidae) from the southern coast of China.},
journal = {ZooKeys},
volume = {1011},
number = {},
pages = {85-100},
pmid = {33551652},
issn = {1313-2989},
abstract = {A new Sillago species, the black-banded sillago, Sillago nigrofasciata sp. nov., is described based on 302 specimens sampled from the southern coast of China. Morphological comparisons have been conducted between the new species and ten other Sillago species. The results show that the new species is characterized by a black mid-lateral band below the lateral line when fresh; other characteristics are similar to those of Sillago sihama but subtle differences exist on the swim bladder between Sillago nigrofasciata sp. nov. and S. sihama. A detailed description and illustrations are provided for the new species. The validity of this new species is also supported by a genetic comparison using sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene.},
}
@article {pmid33551466,
year = {2020},
author = {Balsamo, M and Artois, T and Smith, JPS and Todaro, MA and Guidi, L and Leander, BS and Van Steenkiste, NWL},
title = {The curious and neglected soft-bodied meiofauna: Rouphozoa (Gastrotricha and Platyhelminthes).},
journal = {Hydrobiologia},
volume = {847},
number = {12},
pages = {2613-2644},
pmid = {33551466},
issn = {0018-8158},
support = {P20 GM103499/GM/NIGMS NIH HHS/United States ; },
abstract = {Gastrotricha and Platyhelminthes form a clade called Rouphozoa. Representatives of both taxa are main components of meiofaunal communities, but their role in the trophic ecology of marine and freshwater communities is not sufficiently studied. Traditional collection methods for meiofauna are optimized for Ecdysozoa, and include the use of fixatives or flotation techniques that are unsuitable for the preservation and identification of soft-bodied meiofauna. As a result, rouphozoans are usually underestimated in conventional biodiversity surveys and ecological studies. Here, we give an updated outline of their diversity and taxonomy, with some phylogenetic considerations. We describe successfully tested techniques for their recovery and study, and emphasize current knowledge on the ecology, distribution and dispersal of freshwater gastrotrichs and microturbellarians. We also discuss the opportunities and pitfalls of (meta)barcoding studies as a means of overcoming the taxonomic impediment. Finally, we discuss the importance of rouphozoans in aquatic ecosystems and provide future research directions to fill in crucial gaps in the biology of these organisms needed for understanding their basic role in the ecology of benthos and their place in the trophic networks linking micro-, meio- and macrofauna of freshwater ecosystems.},
}
@article {pmid33549873,
year = {2021},
author = {Yik, MH and Lo, YT and Lin, X and Sun, W and Chan, TF and Shaw, PC},
title = {Authentication of Hedyotis products by adaptor ligation-mediated PCR and metabarcoding.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {196},
number = {},
pages = {113920},
doi = {10.1016/j.jpba.2021.113920},
pmid = {33549873},
issn = {1873-264X},
mesh = {China ; DNA Barcoding, Taxonomic ; *Hedyotis ; Oligonucleotides ; Polymerase Chain Reaction ; },
abstract = {DNA barcoding is a widely used tool for species identification and authentication. However, it may not be applicable to highly processed herbal products due to severe DNA fragmentation. The emergence of DNA metabarcoding provides an alternative way to solve the problem. In this study, we are the first to combine the use of adaptor ligation-mediated PCR method and metabarcoding to reveal species identities in herbal products. As an illustration, we applied the method on three Hedyotis herbal products collected from China and Thailand. Results showed that H. diffusa and H. corymbosa were present in the products which were consistent with their label claims. Our study indicated that the adaptor ligation-mediated PCR with metabarcoding approach is useful for authentication of highly processed herbal products.},
}
@article {pmid33549322,
year = {2021},
author = {Fish, M and Ellis, R and Bishop, C and Todd, K and Petrov, N and Singer, M and Swanson, CM and Shankar-Hari, M},
title = {Utilising mass cytometry with CD45 barcoding and standardised leucocyte phenotyping for immune trajectory assessment in critically ill patients.},
journal = {British journal of anaesthesia},
volume = {126},
number = {4},
pages = {e149-e152},
doi = {10.1016/j.bja.2021.01.006},
pmid = {33549322},
issn = {1471-6771},
mesh = {*Critical Illness ; Flow Cytometry/*methods ; Humans ; Immunity, Cellular/genetics/*immunology ; Leukocyte Common Antigens/genetics/*immunology ; Leukocytes, Mononuclear/*immunology ; *Phenotype ; Sequence Analysis, DNA/methods ; },
}
@article {pmid33548142,
year = {2021},
author = {Kennedy-Darling, J and Bhate, SS and Hickey, JW and Black, S and Barlow, GL and Vazquez, G and Venkataraaman, VG and Samusik, N and Goltsev, Y and Schürch, CM and Nolan, GP},
title = {Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction.},
journal = {European journal of immunology},
volume = {51},
number = {5},
pages = {1262-1277},
pmid = {33548142},
issn = {1521-4141},
support = {UG3 DK114937/DK/NIDDK NIH HHS/United States ; U19 AI100627/AI/NIAID NIH HHS/United States ; R01 HL120724/HL/NHLBI NIH HHS/United States ; U54 HG010426/HG/NHGRI NIH HHS/United States ; 27145/CRUK_/Cancer Research UK/United Kingdom ; F99 CA212231/CA/NCI NIH HHS/United States ; U01 AI140498/AI/NIAID NIH HHS/United States ; T32 CA196585/CA/NCI NIH HHS/United States ; R33 CA183692/CA/NCI NIH HHS/United States ; U19 AI135976/AI/NIAID NIH HHS/United States ; P01 AI131374/AI/NIAID NIH HHS/United States ; U19 AI057229/AI/NIAID NIH HHS/United States ; U2C CA233238/CA/NCI NIH HHS/United States ; C27165/A29073/CRUK_/Cancer Research UK/United Kingdom ; U01 AI101984/AI/NIAID NIH HHS/United States ; F32 CA233203/CA/NCI NIH HHS/United States ; P01 HL108797/HL/NHLBI NIH HHS/United States ; U2C CA233195/CA/NCI NIH HHS/United States ; R01 HL128173/HL/NHLBI NIH HHS/United States ; },
mesh = {*Antibodies ; Cell Communication ; Cell Count ; Histocytochemistry/*methods ; Humans ; In Situ Hybridization/methods ; Lymphoid Tissue ; Molecular Imaging/*methods ; *Oligonucleotides ; Organ Specificity ; Reproducibility of Results ; Sensitivity and Specificity ; Single-Cell Analysis/methods ; },
abstract = {Multiparameter tissue imaging enables analysis of cell-cell interactions in situ, the cellular basis for tissue structure, and novel cell types that are spatially restricted, giving clues to biological mechanisms behind tissue homeostasis and disease. Here, we streamlined and simplified the multiplexed imaging method CO-Detection by indEXing (CODEX) by validating 58 unique oligonucleotide barcodes that can be conjugated to antibodies. We showed that barcoded antibodies retained their specificity for staining cognate targets in human tissue. Antibodies were visualized one at a time by adding a fluorescently labeled oligonucleotide complementary to oligonucleotide barcode, imaging, stripping, and repeating this cycle. With this we developed a panel of 46 antibodies that was used to stain five human lymphoid tissues: three tonsils, a spleen, and a LN. To analyze the data produced, an image processing and analysis pipeline was developed that enabled single-cell analysis on the data, including unsupervised clustering, that revealed 31 cell types across all tissues. We compared cell-type compositions within and directly surrounding follicles from the different lymphoid organs and evaluated cell-cell density correlations. This sequential oligonucleotide exchange technique enables a facile imaging of tissues that leverages pre-existing imaging infrastructure to decrease the barriers to broad use of multiplexed imaging.},
}
@article {pmid33547272,
year = {2021},
author = {Liao, J and Yang, L},
title = {Optical whispering-gallery mode barcodes for high-precision and wide-range temperature measurements.},
journal = {Light, science &amp; applications},
volume = {10},
number = {1},
pages = {32},
pmid = {33547272},
issn = {2047-7538},
support = {ECCS1711451//National Science Foundation (NSF)/ ; W911NF1710189//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; W911NF1910234//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; },
abstract = {Temperature is one of the most fundamental physical properties to characterize various physical, chemical, and biological processes. Even a slight change in temperature could have an impact on the status or dynamics of a system. Thus, there is a great need for high-precision and large-dynamic-range temperature measurements. Conventional temperature sensors encounter difficulties in high-precision thermal sensing on the submicron scale. Recently, optical whispering-gallery mode (WGM) sensors have shown promise for many sensing applications, such as thermal sensing, magnetic detection, and biosensing. However, despite their superior sensitivity, the conventional sensing method for WGM resonators relies on tracking the changes in a single mode, which limits the dynamic range constrained by the laser source that has to be fine-tuned in a timely manner to follow the selected mode during the measurement. Moreover, we cannot derive the actual temperature from the spectrum directly but rather derive a relative temperature change. Here, we demonstrate an optical WGM barcode technique involving simultaneous monitoring of the patterns of multiple modes that can provide a direct temperature readout from the spectrum. The measurement relies on the patterns of multiple modes in the WGM spectrum instead of the changes of a particular mode. It can provide us with more information than the single-mode spectrum, such as the precise measurement of actual temperatures. Leveraging the high sensitivity of WGMs and eliminating the need to monitor particular modes, this work lays the foundation for developing a high-performance temperature sensor with not only superior sensitivity but also a broad dynamic range.},
}
@article {pmid33542589,
year = {2020},
author = {Fawley, MW and Fawley, KP},
title = {Identification of Eukaryotic Microalgal Strains.},
journal = {Journal of applied phycology},
volume = {32},
number = {5},
pages = {2699-2709},
pmid = {33542589},
issn = {0921-8971},
support = {P20 GM103429/GM/NIGMS NIH HHS/United States ; },
abstract = {Proper identification and documentation of microalgae is often lacking in publications of applied phycology, algal physiology and biochemistry. Identification of many eukaryotic microalgae can be very daunting to the non-specialist. We present a systematic process for identifying eukaryotic microalgae using morphological evidence and DNA sequence analysis. Our intent was to provide an identification method that could be used by non-taxonomists, but which is grounded in the current techniques used by algal taxonomists. Central to the identification is database searches with DNA sequences of appropriate loci. We provide usable criteria for identification at the genus or species level, depending on the availability of sequence data in curated databases and repositories. Particular attention is paid to dealing with possible misidentifications in DNA databases and utilizing current taxonomy.},
}
@article {pmid33541261,
year = {2021},
author = {Wang, Y and Wang, S and Liu, Y and Yuan, Q and Sun, J and Guo, L},
title = {Chloroplast genome variation and phylogenetic relationships of Atractylodes species.},
journal = {BMC genomics},
volume = {22},
number = {1},
pages = {103},
pmid = {33541261},
issn = {1471-2164},
support = {No.81891014//National Natural Science Foundation of China/ ; No.81874337//National Natural Science Foundation of China/ ; },
mesh = {*Atractylodes/genetics ; Chloroplasts ; *Genome, Chloroplast ; Microsatellite Repeats ; Phylogeny ; },
abstract = {BACKGROUND: Atractylodes DC is the basic original plant of the widely used herbal medicines "Baizhu" and "Cangzhu" and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing.<br><br>RESULTS: The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294&#x2009;bp (A. carlinoides) to 153,261&#x2009;bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT[(GGU)], and trnT[(UGU)]-trnL, and a total of 42-47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus.<br><br>CONCLUSIONS: Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.},
}
@article {pmid33540601,
year = {2021},
author = {Čadež, N and Dlauchy, D and Tome, M and Péter, G},
title = {Novakomyces olei sp. nov., the First Member of a Novel Taphrinomycotina Lineage.},
journal = {Microorganisms},
volume = {9},
number = {2},
pages = {},
pmid = {33540601},
issn = {2076-2607},
support = {no grant number//Hungarian Ministry for Innovation and Technology/ ; EFOP-3.6.3-VEKOP-16-2017-00005//European Union and co-financed by the European Social Fund/ ; P4-0116, and MRIC-UL ZIM, IP-0510//Slovenian Research Agency/ ; C3330-19-952047//Republic of Slovenia Ministry of Education/ ; },
abstract = {Taphrinomycotina is the smallest subphylum of the phylum Ascomycota. It is an assemblage of distantly related early diverging lineages of the phylum, comprising organisms with divergent morphology and ecology; however, phylogenomic analyses support its monophyly. In this study, we report the isolation of a yeast strain, which could not be assigned to any of the currently recognised five classes of Taphrinomycotina. The strain of the novel budding species was recovered from extra virgin olive oil and characterised phenotypically by standard methods. The ultrastructure of the cell wall was investigated by transmission electron microscopy. Comparisons of barcoding DNA sequences indicated that the investigated strain is not closely related to any known organism. Tentative phylogenetic placement was achieved by maximum-likelihood analysis of the D1/D2 domain of the nuclear LSU rRNA gene. The genome of the investigated strain was sequenced, assembled, and annotated. Phylogenomic analyses placed it next to the fission Schizosaccharomyces species. To accommodate the novel species, Novakomyces olei, a novel genus Novakomyces, a novel family Novakomycetaceae, a novel order Novakomycetales, and a novel class Novakomycetes is proposed as well. Functional analysis of genes missing in N. olei in comparison to Schizosaccharomyces pombe revealed that they are biased towards biosynthesis of complex organic molecules, regulation of mRNA, and the electron transport chain. Correlating the genome content and physiology among species of Taphrinomycotina revealed some discordance between pheno- and genotype. N. olei produced ascospores in axenic culture preceded by conjugation between two cells. We confirmed that N. olei is a primary homothallic species lacking genes for different mating types.},
}
@article {pmid33540579,
year = {2021},
author = {Conti, A and Corte, L and Casagrande Pierantoni, D and Robert, V and Cardinali, G},
title = {What Is the Best Lens? Comparing the Resolution Power of Genome-Derived Markers and Standard Barcodes.},
journal = {Microorganisms},
volume = {9},
number = {2},
pages = {},
pmid = {33540579},
issn = {2076-2607},
abstract = {Fungal species delimitation was traditionally carried out with multicopy ribosomal RNA (rRNA) genes, principally for their ease of amplification. Since the efficacy of these markers has been questioned, single-copy protein-encoding genes have been proposed alone or in combination for Multi-Locus Sequence Typing (MLST). In this context, the role of the many sequences obtained with Next-Generation Sequencing (NGS) techniques, in both genomics and metagenomics, further pushes toward an analysis of the efficacy of NGS-derived markers and of the metrics to evaluate the marker efficacy in discriminating fungal species. This paper aims at proposing MeTRe (Mean Taxonomic Resolution), a novel index that could be used both for measuring marker efficacy and for assessing the actual resolution (i.e., the level of separation) between species obtained with different markers or their combinations. In this paper, we described and then employed this index to compare the efficacy of two rRNAs and four single-copy markers obtained from public databases as both an amplicon-based approach and genome-derived sequences. Two different groups of species were used, one with a pathogenic species of Candida that was characterized by relatively well-separated taxa, whereas the other, comprising some relevant species of the sensu stricto group of the genus Saccharomyces, included close species and interspecific hybrids. The results showed the ability of MeTRe to evaluate marker efficacy in general and genome-derived markers specifically.},
}
@article {pmid33530758,
year = {2021},
author = {Nehal, N and Choudhary, B and Nagpure, A and Gupta, RK},
title = {DNA barcoding: a modern age tool for detection of adulteration in food.},
journal = {Critical reviews in biotechnology},
volume = {41},
number = {5},
pages = {767-791},
doi = {10.1080/07388551.2021.1874279},
pmid = {33530758},
issn = {1549-7801},
mesh = {*DNA Barcoding, Taxonomic ; *Food Safety ; Fruit ; Meat ; Quality Control ; },
abstract = {Globalization of the food trade requires precise and exact information about the origin, methods of production, transformation technologies, authentication, and the traceability of foodstuffs. New challenges in food supply chains such as deliberate fraudulent substitution, tampering or mislabeling of food and its ingredients or food packaging incapacitates the market and eventually the national economy. Currently, no proper standards have been established for the authentication of most of the food materials. However, in order to control food fraud, various robust and cost-effective technologies have been employed, like a spectrophotometer, GC-MS, HPLC, and DNA barcoding. Among these techniques, DNA barcoding is a biotechnology advantage with the principle of using 400-800 bp long standardized unique DNA sequences of mitochondrial (e.g. COI) or plastidial (e.g. rbcL) of nuclear origin (e.g. ITS) to analyze and classify the food commodities. This review covers several traded food commodities like legumes, seafood, oils, herbal products, spices, fruits, cereals, meat, and their unique barcodes which are critically analyzed to detect adulteration or fraud. DNA barcoding is a global initiative and it is being accepted as a global standard/marker for species identification or authentication. The research laboratories and industries should collaborate to realize its potential in setting standards for quality assurance, quality control, and food safety for different food products.},
}
@article {pmid33529467,
year = {2021},
author = {Erasmus, DJ},
title = {DNA barcoding: A different perspective to introducing undergraduate students to DNA sequence analysis.},
journal = {Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology},
volume = {49},
number = {3},
pages = {416-421},
doi = {10.1002/bmb.21492},
pmid = {33529467},
issn = {1539-3429},
mesh = {Animals ; Biochemistry/*education ; DNA Barcoding, Taxonomic/*methods ; Education, Medical, Undergraduate/*methods ; Lepidoptera/*genetics ; Molecular Biology/*education ; Sequence Analysis, DNA/*methods ; },
abstract = {Education in biochemistry teaching laboratories focus primarily on applying biochemical techniques to understanding human disease, biochemistry, and biotechnology. With anthropogenic climate change, there is a renewed interest in quantifying biodiversity, especially with the use of molecular-based approaches such as DNA barcoding. This 3-week laboratory exercise allowed undergraduate students to explore DNA sequencing, analysis, and DNA barcoding. Students extracted DNA from insect legs and amplified a 650 bp section of Cytochrome C oxidase I gene by PCR, and confirmed the success of their PCR by DNA gel electrophoresis. The PCR products were submitted for sequencing and students analyzed the sequences using FinchTV, Genbank, and the Barcode of Life Database. Based on the DNA sequences of their PCR products students were able to identify the species of insects. This lab exercise provides a different context to introducing students to analyzing DNA sequences and using DNA databases.},
}
@article {pmid33529182,
year = {2021},
author = {Swenson, SJ and Gemeinholzer, B},
title = {Testing the effect of pollen exine rupture on metabarcoding with Illumina sequencing.},
journal = {PloS one},
volume = {16},
number = {2},
pages = {e0245611},
pmid = {33529182},
issn = {1932-6203},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/*methods ; Plants/*genetics ; Pollen/*genetics ; Reproducibility of Results ; Species Specificity ; },
abstract = {Pollen metabarcoding has received much attention recently for its potential to increase taxonomic resolution of the identifications of pollen grains necessary for various public health, ecological and environmental inquiry. However, methodologies implemented are widely varied across studies confounding comparisons and casting uncertainty on the reliability of results. In this study, we investigated part of the methodology, the effects of level of exine rupture and lysis incubation time, on the performance of DNA extraction and Illumina sequencing. We examined 15 species of plants from 12 families with pollen that varies in size, shape, and aperture number to evaluate effort necessary for exine rupture. Then created mock communities of 14 of the species from DNA extractions at 4 levels of exine rupture (0, 33, 67, and 100%) and two levels of increased lysis incubation time without exine rupture (2 or 24 hours). Quantities of these DNA extractions displayed a positive correlation between increased rupture and DNA yield, however increasing time of lysis incubation was associated with decreased DNA yield. Illumina sequencing was performed with these artificial community treatments with three common plant DNA barcode regions (rbcL, ITS1, ITS2) with two different primer pairings for ITS2 and rbcL. We found decreased performance in treatments with 0% or 100% exine rupture compared to 33% and 67% rupture, based on deviation from expected proportions and species retrieval, and increased lysis incubation was found to be detrimental to results.},
}
@article {pmid33527609,
year = {2021},
author = {Pandit, R and Travadi, T and Sharma, S and Joshi, C and Joshi, M},
title = {DNA meta-barcoding using rbcL based mini-barcode revealed presence of unspecified plant species in Ayurvedic polyherbal formulations.},
journal = {Phytochemical analysis : PCA},
volume = {32},
number = {5},
pages = {804-810},
doi = {10.1002/pca.3026},
pmid = {33527609},
issn = {1099-1565},
support = {GSBTM/JDRD/584/2018/204//Gujarat State Biotechnology Mission (GSBTM)/ ; },
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Medicine, Ayurvedic ; *Plants, Medicinal/genetics ; Quality Control ; },
abstract = {INTRODUCTION: Ayurveda takes advantage of the beneficial properties of medicinal plants. High demands in combination with inadequate availability of botanicals and a lack of knowledge with respect to their precise identification lead to adulterations in herbal products. Identification becomes more difficult in complex herbal formulations. Four different polyherbal formulations have been analyzed for the present paper. The targeted plants have different pharmacological properties for various ailments.<br><br>OBJECTIVE: We aimed to examine the rbcL gene based plant DNA mini-barcode to identify target and non-target plants in polyherbal formulations by using high-throughput next generation sequencing.<br><br>METHODS: Degenerate primers of the selected mini-barcode region have been identified from the literature. A blend of 30 authentic medicinal plant species was used to examine the species resolution capacity of the mini-barcode. DNA was isolated from herbal formulations, an amplicon library was prepared, and sequencing was performed on an IonS5 system. Data were analyzed using various bioinformatics tools.<br><br>RESULTS: Analysis of control pooled samples revealed the optimum resolving power of the DNA mini-barcode. Data analysis of the commercial samples revealed that only one herbal formulation contained all plants and matched with listed contents. In two formulations, only 10 out of 21 and 11 out of 20 plants were detected, respectively. Additionally, several non-listed plants were also detected in these formulations. Two formulations contained >20% reads assigned to non-target plants. Overall, 21.98% of the reads were assigned to non-target plants.<br><br>CONCLUSION: The present study clearly demonstrated the successful application and potential of meta-barcoding in the quality control of complex herbal matrices. The results strongly suggest that this approach can be used in pharmacovigilance of processed herbal products.},
}
@article {pmid33524844,
year = {2021},
author = {Anaz K, M and N, S and A, R and M V, D},
title = {ITS 2 and RNA secondary structure-based analysis reveals a clear picture on phylogeny of South Indian Salacia spp.},
journal = {Computational biology and chemistry},
volume = {91},
number = {},
pages = {107438},
doi = {10.1016/j.compbiolchem.2021.107438},
pmid = {33524844},
issn = {1476-928X},
mesh = {DNA Barcoding, Taxonomic ; *Genes, Plant ; *Genetic Markers ; India ; *Nucleic Acid Conformation ; *Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Plant/*chemistry/genetics ; Salacia/*classification/genetics ; },
abstract = {The genus Salacia (Celastraceae) consists of many important medicinal plants used mainly against type II diabetes. Segregation and delimitation of species is difficult based on morphological features alone. DNA barcoding is the most effective and emerging method of molecular identification. It was reported that ITS2 has better discriminating power in the genus Salacia in comparison to other barcode loci. This paper describe the analysis of sequence and structural information of ITS2 to discriminate the species of Salacia. A total of 8 species of Salacia in South India and the available sequences in NCBI database were taken for the present study. NJ method based phylogenetic trees were constructed using MEGAX with primary sequence as well as using sequence and secondary structural information. Primary structure based phylogeny did not give much information whereas the dendrogram based on sequence and structural information was more informative to decipher the phylogeny of South Asian species of Salacia. The present study revealed some interesting facts regarding the genus. Secondary structure of the ITS2 sequence of S. chinensis reported from Kerala differs consistently from that of S. chinensis reported from other parts of India and of South Asia. Probably the S. chinensis in Kerala, India has diverged a lot from the original S. chinensis. ITS2 sequence of S. reticulata reported from Sri Lanka was identical to S. chinensis reported by other groups from Thailand and Udupi, India. The molecular level identity of ITS2 sequence of S. chinensis with S. reticulata suggest merger of the two species. ITS2 sequence of S. beddomei is only reported from Kerala, India showed it to be identical to S. macrosperma. This observation points to a mistaken identity of S. beddomei which could be elusive from Kerala. Phylogenetic trees constructed based on sequence and structural features of ITS2 suggest that the ancestor species of S.chinensis diversified in two evolutionary lines. One line leads to the present day S. chinensis and the other line further diversified and lead to the rest of the present day Salacia species.},
}
@article {pmid33522947,
year = {2021},
author = {Wat'senga Tezzo, F and Fasine, S and Manzambi Zola, E and Marquetti, MDC and Binene Mbuka, G and Ilombe, G and Mundeke Takasongo, R and Smitz, N and Bisset, JA and Van Bortel, W and Vanlerberghe, V},
title = {High Aedes spp. larval indices in Kinshasa, Democratic Republic of Congo.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {92},
pmid = {33522947},
issn = {1756-3305},
support = {FA4//Directorate-General for Development Co-operation/ ; ORT//Departement Economie, Wetenschap en Innovatie/ ; BOPCO//Belgian Federal Science Policy Office/ ; },
mesh = {Aedes/classification/*physiology ; Animals ; Cross-Sectional Studies ; Democratic Republic of the Congo ; Family Characteristics ; Larva/*physiology ; Mosquito Control/methods ; Mosquito Vectors/*physiology ; Seasons ; Virus Diseases/*transmission ; },
abstract = {BACKGROUND: Dengue, yellow fever, chikungunya and Zika are among the most important emerging infectious vector-borne diseases worldwide. In the Democratic Republic of Congo (DRC), increases in cases of dengue and outbreaks of yellow fever and chikungunya have been reported since 2010. The main vectors of these arboviruses, Aedes aegypti and Aedes albopictus, have been reported in DRC, but there is a lack of detailed information on their presence and spread to guide disease control efforts.<br><br>METHODS: In 2018, two cross-sectional surveys were conducted in Kinshasa province (DRC), one in the rainy (January/February) and one in the dry season (July). Four hundred houses were visited in each of the four selected communes (N'Djili, Mont Ngafula, Lingwala and Kalamu). Within the peri-domestic area of each household, searches were conducted for larval habitats, which were then surveyed for the presence of Aedes larvae and pupae. A subset of the immature specimens were reared to adults for morphological identification followed by DNA barcoding of the specimens to validate identifications.<br><br>RESULTS: The most rural commune (Mont Ngafula) had the highest pupal index (number of Aedes spp. pupae per 100 inspected houses) at 246 (20) pupae/100 houses, and Breteau index (BI; number of containers positive for immature stages of Aedes spp. per 100 households) at 82.2 (19.5) positive containers/100 houses for the rainy (and dry) season, respectively. The BI was 21.5 (4.7), 36.7 (9.8) and 41.7 (7.5) in Kalamu, Lingwala and N'Djili in the rainy (and dry) season, respectively. The house index (number of houses positive for at least one container with immature stages of Aedes spp. per 100 inspected houses) was, on average, across all communes, 27.5% (7.6%); and the container index (number of containers positive for immature stages of Aedes spp. per 100 inspected containers) was 15.0% (10.0%) for the rainy (and dry) season, respectively. The vast majority of Aedes-positive containers were found outside the houses [adjusted odds ratio 27.4 (95% confidence interval 14.9-50.1)]. During the dry season, the most productive containers were the ones used for water storage, whereas in the rainy season rubbish and tires constituted key habitats. Both Ae. aegypti and Ae. albopictus were found. Anopheles larvae were found in different types of Aedes larval habitats, especially during the rainy season.<br><br>CONCLUSIONS: In both surveys and in all communes, the larval indices (BI) were higher than the arbovirus transmission threshold values established by the World Health Organization. Management strategies for controlling Aedes in Kinshasa need to target the key types of containers for Aedes larvae, which are mainly located in outdoor spaces, for larval habitat destruction or reduction.},
}
@article {pmid33520432,
year = {2021},
author = {D'Ercole, J and Prosser, SWJ and Hebert, PDN},
title = {A SMRT approach for targeted amplicon sequencing of museum specimens (Lepidoptera)-patterns of nucleotide misincorporation.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e10420},
pmid = {33520432},
issn = {2167-8359},
abstract = {Natural history collections are a valuable resource for molecular taxonomic studies and for examining patterns of evolutionary diversification, particularly in the case of rare or extinct species. However, the recovery of sequence information is often complicated by DNA degradation. This article describes use of the Sequel platform (Pacific Biosciences) to recover the 658 bp barcode region of the mitochondrial cytochrome c oxidase I (COI) gene from 380 butterflies with an average age of 50 years. Nested multiplex PCR was employed for library preparation to facilitate sequence recovery from extracts with low concentrations of highly degraded DNA. By employing circular consensus sequencing (CCS) of short amplicons (circa 150 bp), full-length barcodes could be assembled without a reference sequence, an important advance from earlier protocols which required reference sequences to guide contig assembly. The Sequel protocol recovered COI sequences (499 bp on average) from 318 of 380 specimens (84%), much higher than for Sanger sequencing (26%). Because each read derives from a single molecule, it was also possible to quantify the incidence of substitutions arising from DNA damage. In agreement with past work on sequence changes induced by DNA degradation, the transition C/G → T/A was the most prevalent category of change, but its rate of occurrence (4.58E-4) was so low that it did not impede the recovery of reliable sequences. Because the current protocol recovers COI sequence from most museum specimens, and because sequence fidelity is unaffected by nucleotide misincorporations, large-scale sequence characterization of museum specimens is feasible.},
}
@article {pmid33520158,
year = {2021},
author = {Ludoški, J and Francuski, L and Lukač, M and Dekić, R and Milankov, V},
title = {Toward the conservation of the endemic monotypic fish genus Aulopyge from the Balkan Dinaric karst: Integrative assessment of introduced and natural population.},
journal = {Ecology and evolution},
volume = {11},
number = {2},
pages = {688-699},
pmid = {33520158},
issn = {2045-7758},
abstract = {The complex biogeographical history of the Balkan Peninsula caused remarkable freshwater fish diversity and endemism, among which Cyprinidae fish dominate. The Dinaric karst was a Pleistocene refugium and it harbors ancient and endemic cyprinids, including Aulopyge huegelii, a sole representative of its genus. Being highly distributionally restricted, it faces various threats that promote a critical decline in population abundance and even population extinction. Phenotypic and molecular diversity of the introduced (Šator Lake, Šator Mountain) and natural (Studena River, Duvanjsko Polje) populations of Dalmatian barbelgudgeon from Bosnia and Herzegovina was studied by using two mitochondrial genes and morphometric traits (linear and geometric morphometrics). Nonparametric ANOVA showed that two analyzed populations significantly differed in six linear measurements, except snout length and postorbital head length. Contrary to centroid size, two populations were found to be significantly different in body shape. Deformation grids indicated that individuals from Studena River are characterized by wider and slightly shorter body comparing to individuals from Šator Lake. Incongruence in cytochrome c oxidase subunit I (COI) and cytochrome b (cyt b) mitochondrial DNA (mtDNA) variation was observed since a common COI haplotype was observed, while four and three cyt b haplotypes were registered in Šator Lake and Studena River, respectively. Since it was demonstrated that cyt b mtDNA was a faster evolving gene, we encourage its use in intraspecies studies, especially for evaluating the connectivity of fragmented populations and for studying the evolutionary footprint of the processes incorporated into the distinctive evolution of Aulopyge. Finally, findings herewith provide a firm basis for designing a long-term sustainable conservation strategy for endemic species in Dinaric karst.},
}
@article {pmid33519856,
year = {2020},
author = {Zhao, K and Li, L and Quan, H and Yang, J and Zhang, Z and Liao, Z and Lan, X},
title = {Comparative Analyses of Chloroplast Genomes From 14 Zanthoxylum Species: Identification of Variable DNA Markers and Phylogenetic Relationships Within the Genus.},
journal = {Frontiers in plant science},
volume = {11},
number = {},
pages = {605793},
pmid = {33519856},
issn = {1664-462X},
abstract = {Zanthoxylum L. is an economic crop with a long history of cultivation and domestication and has important economic, ecological, and medicinal value. To solve the classification problems caused by the similar morphological characteristics of Zanthoxylum and establish a credible phylogenetic relationship, we sequenced and annotated six Zanthoxylum chloroplast (cp) genomes (Z. piasezkii, Z. armatum, Z. motuoense, Z. oxyphyllum, Z. multijugum, and Z. calcicola) and combined them with previously published genomes for the Zanthoxylum species. We used bioinformatics methods to analyze the genomic characteristics, contraction, and expansion of inverted repeat (IR) regions; differences in simple sequence repeats (SSRs) and long repeat sequences; species pairwise Ka/Ks ratios; divergence hotspots; and phylogenetic relationships of the 14 Zanthoxylum species. The results revealed that cp genomes of Zanthoxylum range in size from 158,071 to 158,963 bp and contain 87 protein-coding, 37 tRNA, and 8 rRNA genes. Seven mutational hotspots were identified as candidate DNA barcode sequences to distinguish Zanthoxylum species. The phylogenetic analysis strongly supported the genus Fagara as a subgenus of Zanthoxylum and proposed the possibility of a new subgenus in Zanthoxylum. The availability of these genomes will provide valuable information for identifying species, molecular breeding, and evolutionary analysis of Zanthoxylum.},
}
@article {pmid33519262,
year = {2021},
author = {Freitag, H and de Vries, R and Paterno, M and Maestri, S and Delledonne, M and Thompson, CG and Lamed, H and Lambert, R and Fox, MF and Gonzalez, MC and Delocado, ED and Sabordo, MR and Pangantihon, CV and Njunjić, I},
title = {Hydraena (s.str.) dinarica, new species (Coleoptera: Hydraenidae) along with further records of Hydraena spp. from Durmitor National Park, Montenegro and comments on the DNA barcoding problem with the genus.},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e59892},
pmid = {33519262},
issn = {1314-2828},
abstract = {BACKGROUND: Long-palped Water Beetles were collected during a taxon expedition in Montenegro which involved citizen scientists, students and taxonomists. The material was collected from springs, brooks, fens and the Tara River, at altitudes between 600 m and 1450 m above sea level, using fine-meshed hand-nets and by manual checking of submerged substrates. The morphological species delimitation was supplemented and congruent with mtDNA sequences mainly obtained in the field using the newly-developed MinION-based ONTrack pipeline.<br><br>NEW INFORMATION: The new species Hydraena dinarica Freitag &amp; de Vries, sp. n. from Durmitor Mt. is described, illustrated and compared in detail to closely-related congeners of the H. saga d'Orchymont, 1930/H. emarginata Rey, 1885 species complex. Five additional species and female specimens of two unidentified morphospecies of the genus were also recorded in the vicinity of Durmitor National Park. New records and the first DNA barcodes for Hydraena biltoni J&#xe4;ch &amp; D&#xed;az, 2012 (endemic to Montenegro) and H. morio Kiesenwetter, 1849 are provided. Further records of H. nigrita Germar, 1824, H. minutissima Stephens, 1829, H. subintegra Ganglbauer, 1901 and females of two unidentified morphospecies are commented upon. The resulting inter- and intraspecific genetic distances and some observations of low or zero sequence divergence between recently-diverged species of Hydraena Kugelann, 1794 are briefly discussed.},
}
@article {pmid33519257,
year = {2021},
author = {Yu, L and Liu, F and Zhang, Z and Li, D and Xu, X},
title = {Three new species of the segmented spider genus Qiongthela (Mesothelae, Liphistiidae) from Hainan Island, China.},
journal = {ZooKeys},
volume = {1009},
number = {},
pages = {123-138},
pmid = {33519257},
issn = {1313-2989},
abstract = {We report three new species of the segmented trapdoor spider genus Qiongthela Xu &amp; Kuntner, 2015 collected from Hainan Island, China based on morphological characters: Q. dongfang sp. nov. (♂♀), Q. nankai sp. nov. (♂♀), Q. yalin sp. nov. (♂♀). We also provide the GenBank accession codes of the DNA barcode gene, cytochrome c oxidase subunit I (COI), of the type specimens of all three new species to aid future identification.},
}
@article {pmid33515000,
year = {2021},
author = {Nachtigall, PG and Grazziotin, FG and Junqueira-de-Azevedo, ILM},
title = {MITGARD: an automated pipeline for mitochondrial genome assembly in eukaryotic species using RNA-seq data.},
journal = {Briefings in bioinformatics},
volume = {22},
number = {5},
pages = {},
doi = {10.1093/bib/bbaa429},
pmid = {33515000},
issn = {1477-4054},
mesh = {Animals ; Bothrops/classification/*genetics ; Eukaryotic Cells ; *Genome, Mitochondrial ; *RNA-Seq ; *Software ; },
abstract = {MOTIVATION: Over the past decade, the field of next-generation sequencing (NGS) has seen dramatic advances in methods and a decrease in costs. Consequently, a large expansion of data has been generated by NGS, most of which have originated from RNA-sequencing (RNA-seq) experiments. Because mitochondrial genes are expressed in most eukaryotic cells, mitochondrial mRNA sequences are usually co-sequenced within the target transcriptome, generating data that are commonly underused or discarded. Here, we present MITGARD, an automated pipeline that reliably recovers the mitochondrial genome from RNA-seq data from various sources. The pipeline identifies mitochondrial sequence reads based on a phylogenetically related reference, assembles them into contigs, and extracts a complete mtDNA for the target species.<br><br>RESULTS: We demonstrate that MITGARD can reconstruct the mitochondrial genomes of several species throughout the tree of life. We noticed that MITGARD can recover the mitogenomes in different sequencing schemes and even in a scenario of low-sequencing depth. Moreover, we showed that the use of references from congeneric species diverging up to 30 million years ago (MYA) from the target species is sufficient to recover the entire mitogenome, whereas the use of species diverging between 30 and 60 MYA allows the recovery of most mitochondrial genes. Additionally, we provide a case study with original data in which we estimate a phylogenetic tree of snakes from the genus Bothrops, further demonstrating that MITGARD is suitable for use on biodiversity projects. MITGARD is then a valuable tool to obtain high-quality information for studies focusing on the phylogenetic and evolutionary aspects of eukaryotes and provides data for easily identifying a sample using barcoding, and to check for cross-contamination using third-party tools.},
}
@article {pmid33514820,
year = {2021},
author = {Ramond, P and Siano, R and Schmitt, S and de Vargas, C and Marié, L and Memery, L and Sourisseau, M},
title = {Phytoplankton taxonomic and functional diversity patterns across a coastal tidal front.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {2682},
pmid = {33514820},
issn = {2045-2322},
abstract = {Oceanic physics at fine scale; e.g. eddies, fronts, filaments; are notoriously difficult to sample. However, an increasing number of theoretical approaches hypothesize that these processes affect phytoplankton diversity which have cascading effects on regional ecosystems. In 2015, we targeted the Iroise Sea (France) and evidenced the setting up of the Ushant tidal front from the beginning of spring to late summer. Seawater samples were taken during three sampling cruises and DNA-barcoding allowed us to investigate patterns of eukaryotic phytoplankton diversity across this front. First focusing on patterns of taxonomic richness, we evidenced that the front harbored a hotspot of eukaryotic phytoplankton diversity sustained throughout summer. We then detail the ecological processes leading to the formation of this hotspot by studying shifts in community composition across the Iroise Sea. Physical mixing mingled the communities surrounding the front, allowing the formation of a local ecotone, but it was cycles of disturbances and nutrient inputs over the front that allowed a decrease in competitive exclusion, which maintained a higher diversity of rare phytoplankton taxa. These processes did not select a specific ecological strategy as inferred by a trait approach coupled to our taxonomic approach. Instead the front favored higher richness within widespread strategies, resulting in functional redundancy. We detail how fine-scale ocean physics affect phytoplankton diversity and suppose that this interplay is a major control on regional ecosystems.},
}
@article {pmid33514375,
year = {2021},
author = {Cheloni, S and Hillje, R and Luzi, L and Pelicci, PG and Gatti, E},
title = {XenoCell: classification of cellular barcodes in single cell experiments from xenograft samples.},
journal = {BMC medical genomics},
volume = {14},
number = {1},
pages = {34},
pmid = {33514375},
issn = {1755-8794},
support = {MINSAL-TRANSCAN//Ministero della Salute (IT)/ ; FUV2018//Fondazione Umberto Veronesi (IT)/ ; AIRC-IG-2017-20162//Associazione Italiana per la Ricerca sul Cancro/ ; grant no. 341131/ERC_/European Research Council/International ; fellowship FUV2020//Fondazione Umberto Veronesi/ ; },
mesh = {*Single-Cell Analysis/methods ; Humans ; Animals ; Mice ; DNA Barcoding, Taxonomic/methods ; Software ; Heterografts ; Computational Biology/methods ; },
abstract = {BACKGROUND: Single-cell sequencing technologies provide unprecedented opportunities to deconvolve the genomic, transcriptomic or epigenomic heterogeneity of complex biological systems. Its application in samples from xenografts of patient-derived biopsies (PDX), however, is limited by the presence of cells originating from both the host and the graft in the analysed samples; in fact, in the bioinformatics workflows it is still a challenge discriminating between host and graft sequence reads obtained in a single-cell experiment.<br><br>RESULTS: We have developed XenoCell, the first stand-alone pre-processing tool that performs fast and reliable classification of host and graft cellular barcodes from single-cell sequencing experiments. We show its application on a mixed species 50:50 cell line experiment from 10&#xd7;&#x2009;Genomics platform, and on a publicly available PDX dataset obtained by Drop-Seq.<br><br>CONCLUSIONS: XenoCell accurately dissects sequence reads from any host and graft combination of species as well as from a broad range of single-cell experiments and platforms. It is open source and available at https://gitlab.com/XenoCell/XenoCell .},
}
@article {pmid33510577,
year = {2021},
author = {An, YY and Zeng, XY and Geng, K and Hyde, KD and Wang, Y},
title = {One new species and one new record of Zasmidium in China.},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e59001},
pmid = {33510577},
issn = {1314-2828},
abstract = {BACKGROUND: Two hyphomycetous species were collected from leaves of Smilax china (Liliales, Smilacaceae) and Cremastra appendiculata (Asparagales, Orchidaceae). ITS barcoding indicated that they belong to the genus Zasmidium.<br><br>NEW INFORMATION: Morphological data in combination with molecular phylogenetic analyses based on ITS, LSU and rpb2 confirmed that our Chinese strains represented a new species, Zasmidium liboense and a new record of Z. citri-griseum.},
}
@article {pmid33505833,
year = {2021},
author = {Chen, W and Wang, P and Wang, L and Zhang, D and Han, M and Han, M and Song, L},
title = {Low-complexity and highly robust barcodes for error-rich single molecular sequencing.},
journal = {3 Biotech},
volume = {11},
number = {2},
pages = {78},
pmid = {33505833},
issn = {2190-572X},
abstract = {DNA barcodes are frequently corrupted due to insertion, deletion, and substitution errors during DNA synthesis, amplification and sequencing, resulting in index hopping. In this paper, we propose a new DNA barcode construction scheme that combines a cyclic block code with a predetermined pseudo-random sequence bit by bit to form bit pairs, and then converts the bit pairs to bases, i.e., the DNA barcodes. Then, we present a barcode identification scheme for noisy sequencing reads, which uses a combination of cyclic shifting and traditional dynamic programming to mark the insertion and deletion positions, and then performs erasure-and-error-correction decoding on the corrupted codewords. Furthermore, we verify the identification error rate of barcodes for multiple errors and evaluate the reliability of the barcodes in DNA context. This method can be easily generalized for constructing long barcodes, which may be used in scenarios with serious errors. Simulation results show that the bit error rate after identifying insertions/deletions is greatly reduced using the combination of cyclic shift and dynamic programming compared to using dynamic programming only. It indicates that the proposed method can effectively improve the accuracy for estimating insertion/deletion errors. And the overall identification error rate of the proposed method is lower than 10 - 5 when the probability of each base mutation is less than 0.1, which is the typical scenario in third-generation sequencing.},
}
@article {pmid33505635,
year = {2021},
author = {Lukhtanov, VA and Dantchenko, AV},
title = {Chromosomal and DNA barcode analysis of the Polyommatus (Agrodiaetus) damone (Eversmann, 1841) species complex (Lepidoptera, Lycaenidae).},
journal = {Comparative cytogenetics},
volume = {15},
number = {1},
pages = {1-22},
pmid = {33505635},
issn = {1993-0771},
abstract = {The Polyommatus (Agrodiaetus) damone (Eversmann, 1841) species complex comprises from 5 to 8 species distributed in southeastern Europe and southern Siberia. Here we used chromosomal and DNA-barcode markers in order to test the taxonomic hypotheses previously suggested for this complex. We revealed that all taxa within this group demonstrate chromosomal stasis and share the same or very similar haploid chromosome number (n = 66 or n = 67). This finding is unexpected since the karyotypes are known to be very diverse and species-specific within the other taxa of the subgenus Agrodiaetus Hübner, 1822. Analysis of the mitochondrial gene COI revealed six diverged clusters of individuals within the complex. Each cluster has a specific geographic distribution and is characterized by distinct morphological features in the wing pattern. The clusters mostly (but not always) correlate with traditionally recognized species. As a result of our study, we describe a new subspecies P. (A.) iphigenides zarmitanussubsp. nov. from Uzbekistan and Tajikistan and show that the taxon originally described as Lycaena kindermanni var. melania Staudinger, 1886 represents a subspecies P. (A.) iphigenides melanius (Staudinger, 1886). Polyommatus (A.) samusi Korb, 2017 (syn. nov.) and P. (A.) melanius komarovi Korb, 2017 (syn. nov.) are considered here as junior subjective synonyms of P. (A.) iphigenides iphigenides (Staudinger, 1886).},
}
@article {pmid33505187,
year = {2020},
author = {Chang, SC and Chan, TY and Kumar, AB},
title = {Deep-sea clawed lobster Nephropsis stewarti Wood-Mason, 1872 species complex in the Indo-West Pacific (Crustacea, Decapoda, Nephropidae), with description of a new species.},
journal = {ZooKeys},
volume = {1008},
number = {},
pages = {37-60},
pmid = {33505187},
issn = {1313-2989},
abstract = {Nephropsis stewarti Wood-Mason, 1872 is the most common species of the deep-sea clawed lobster genus Nephropsis Wood-Mason, 1872 in the Indo-West Pacific. Morphological comparisons and genetic analyses of extensive material referred to this lobster revealed the presence of three species. The three species differ mainly in body size, development of the intermediate carina on the carapace, position of the lateral pair of rostral teeth, whether the pleonal tergum is granulate, and the spination on the large chelipeds. Nephropsis stewarti is restricted to the western central Indian Ocean, and a neotype is selected to fix its identity. The name Nephropsis grandis Zarenkov, 2006 is revived with neotype selection for the large form found in the West Pacific and northwestern Australia. The smaller form from southern Taiwan and the Philippines is described as Nephropsis pygmaea sp. nov.},
}
@article {pmid33502284,
year = {2021},
author = {Ekanayake, H and Perera, N and Ukuwela, KD and Walpita, CN and Kodithuwakku, SP and Perera, SJ},
title = {Cryptic species diversity and molecular diagnosis of Channa orientalis; an endemic freshwater fish of Sri Lanka.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {32},
number = {3},
pages = {77-84},
doi = {10.1080/24701394.2021.1876040},
pmid = {33502284},
issn = {2470-1408},
mesh = {Animals ; DNA ; *Fishes/classification/genetics ; Fresh Water ; *Genome, Mitochondrial ; Polymorphism, Restriction Fragment Length ; Sri Lanka ; },
abstract = {Fish genetic resources and diversity are very important aspects of environmental management and fisheries and are vital for making decisions on their commercial exploitation as well as conservation. The snakehead fishes in the world have significant economic importance as food and ornamental fish. A clear understanding of species' taxonomic status and genetic diversity is important for the utilization and implementation of conservation and management practices. Channa orientalis is a snakehead endemic to Sri Lanka that is heavily utilized in the ornamental fish export trade. Its genetic diversity has not yet been fully understood and it is difficult to distinguish it from closely resembling species. Therefore, we examined the genetic diversity of C. orientalis and developed a DNA-based marker that permits accurate, low cost, and reliable identification of C. orientalis. Determination of genetic diversity was mainly carried out through genetic analysis of the mitochondrial cytochrome c oxidase subunit 1 (MT-CO1) gene. The development of the DNA-based marker for the identification of C. orientalis was done through Polymerase Chain Reaction and Restriction Fragment Length Polymorphism (PCR-RFLP) analysis. Our analyses confirmed the presence of two distinct genetically divergent and geographically separated lineages of C. orientalis in Sri Lanka. The fast cost-effective gel-based PCR-RFLP marker method developed by us was successful in diagnosing C. orientalis from its closely resembling species. Thus, we believe our findings on the cryptic diversity and diagnostic methods will have important implications for the conservation and management of this endemic species.},
}
@article {pmid33502010,
year = {2021},
author = {Catarino, D and Stefanni, S and Porteiro, FM and Rosa, A and Giacomello, E},
title = {First record of the pencil cardinal Epigonus denticulatus (Perciformes: Epigonidae) in the Azores archipelago.},
journal = {Journal of fish biology},
volume = {99},
number = {1},
pages = {253-257},
doi = {10.1111/jfb.14689},
pmid = {33502010},
issn = {1095-8649},
support = {//Molecular analyses were supported by the Demersais project ("Monitoriza&#xe7;&#xe3;o Anual das Abund&#xe2;ncias Relativas das Esp&#xe9;cies Demersais dos A&#xe7;ores", funded by the Azorean Regional Government). This study had the support of Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia through the strategic project UIDB/05634/2020 granted to Okeanos-UAc and the grant awarded to DC (MARE-BI-2017-Peixes_Demersais)./ ; },
mesh = {Animals ; Azores ; *Fishes ; *Perciformes/genetics ; },
abstract = {The pencil cardinal Epigonus denticulatus is a small deep-water fish inhabiting continental slopes usually between 300 and 600 m depth. We report the first record of E. denticulatus in the Azores archipelago, where one specimen was found floating by fisherman off Faial island. Meristic and morphometric characters are in accordance with those reported for the species and molecular analyses further supported species identity. The record of E. denticulatus as a native species in the Azores increases the number of Epigonus species in the region to a total of three.},
}
@article {pmid33500478,
year = {2021},
author = {Ivanov, V and Marusik, Y and Pétillon, J and Mutanen, M},
title = {Relevance of ddRADseq method for species and population delimitation of closely related and widely distributed wolf spiders (Araneae, Lycosidae).},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {2177},
pmid = {33500478},
issn = {2045-2322},
mesh = {Animals ; Databases, Genetic ; Electron Transport Complex IV/genetics ; Haplotypes/genetics ; Likelihood Functions ; *Phylogeny ; Principal Component Analysis ; *Restriction Mapping ; Sequence Analysis, DNA/*methods ; Species Specificity ; Spiders/*genetics ; },
abstract = {Although species delimitation is often controversial, emerging DNA-based and classical morphology-based methods are rarely compared using large-scale samplings, even less in the case of widely distributed species that have distant, allopatric populations. In the current study, we examined species boundaries within two wolf spider species of the genus Pardosa (Araneae, Lycosidae), P. riparia and P. palustris. Wolf spiders constitute an excellent model for testing the relevance of traditional vs. modern methods in species and population delimitation because several closely related species are distributed over cross-continental geographic ranges. Allopatric populations of the two Pardosa species were sampled across Europe to Far East Russia (latitudinal range > 150°) and several dozen individuals were studied using morphological characters (morphometry of three measures for both sexes, plus five in males only and two in females only), DNA barcoding (COI sequencing) and double-digest restriction site associated DNA sequencing (ddRADseq). The results obtained allow for changing the taxonomic status of two Far East Russian populations to subspecies and ddRADseq proved to be a powerful tool for taxonomic research despite scarce sampling and inherent subjectivity of species delimitation in allopatry. Overall, this study pleads for both multi-criteria and more population-based studies in taxonomy.},
}
@article {pmid33499871,
year = {2021},
author = {Łuczaj, &#x141; and Lamxay, V and Tongchan, K and Xayphakatsa, K and Phimmakong, K and Radavanh, S and Kanyasone, V and Pietras, M and Karbarz, M},
title = {Wild food plants and fungi sold in the markets of Luang Prabang, Lao PDR.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {17},
number = {1},
pages = {6},
pmid = {33499871},
issn = {1746-4269},
mesh = {Agaricales/*classification ; *Commerce ; Flowers ; Fruit ; Laos ; Plants, Edible/*classification ; Vegetables ; },
abstract = {BACKGROUND: Open air markets hold an important position for ethnobiologists. In Southeast Asia, they are seriously understudied, in spite of their incredible biocultural diversity. In order to fill this gap we recorded plants and fungi sold in the open air markets of Luang Prabang, Lao PDR.<br><br>METHODS: The markets were visited 38 times in four seasons: the dry season, early monsoon, mid-monsoon, and end-of-monsoon, at least 8 times per season. All items were photographed and voucher specimens were collected. Fungi were identified using DNA barcoding techniques.<br><br>RESULTS: We recorded 110 species of wild edible plants and 54 species of fungi, including 49 wild-collected species. The sold plants included 86 species of green vegetables, 18 species of fruits and 3 species of flowers. Products from woody species constitute around half of all taxa sold. These include the young shoots of tree leaves, which are used for salads-an interesting feature of Lao cuisine. A large number of extremely rare Russula, with no reference sequences represented in databases or even species unknown to science is present on sale in the markets.<br><br>CONCLUSIONS: Luang Prabang markets are some of the richest in species of wild edible plants and fungi in Asia, and indeed in the whole world. It is worth pointing out the exceptionally long list of wild edible mushrooms which are sold in Luang Prabang (and probably elsewhere in Laos). We view the Morning Market of Luang Prabang as a cultural treasure that unites the traditions of eating a large number of living species with very diverse flora and fauna. Measures should be taken to strike a balance between local foraging traditions and nature conservation priorities.},
}
@article {pmid33497838,
year = {2021},
author = {Mirfendereski, R and Hashemi, S and Shirali, S and Shemshadi, B and Lawton, SP},
title = {DNA barcoding of Iranian radicine freshwater snails begins to untangle the taxonomy and phylogeography of intermediate hosts of schistosomiasis and fasciolosis from the Middle East and across Central Asia.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {89},
number = {},
pages = {104728},
doi = {10.1016/j.meegid.2021.104728},
pmid = {33497838},
issn = {1567-7257},
mesh = {Animals ; Asia ; *DNA Barcoding, Taxonomic ; Fasciola/*parasitology ; Fresh Water ; Iran ; Middle East ; *Phylogeography ; Schistosomiasis/*parasitology ; },
abstract = {In the Middle East radicine snails are of considerable medical and veterinary importance acting as vectors of trematodes. In Iran, such snails are responsible for the transmission of the zoonotic trematodes Schistosoma turkestanicum and Fasciola gigantica. Historically, Radix gedrosiana has been incriminated as an important intermediate host for both trematodes, however, controversy remains over the snail's true taxonomic status. This species has been determined using morphological characters that has resulted in erroneous identification of species, affecting understanding of population biology, and ultimately affecting vector incrimination. In this current study DNA barcoding using cox1 and phylogenetic analyses revealed that snails identified as R. gedrosiana from Iran split into two separate species, Radix euphratica and Ampullaceana sp. The cox1 also provided useful insights into the evolutionary history of R. euphratica populations. Phylogeographic analyses indicated that R. euphratica had an Iraqi/Iranian origin approximately 3.3 MYA and exists as a large stable population across the Middle East and Central Asia, and a lack of genetic differentiation between geographical isolates. Such molecular barcoding techniques are crucial for the identification of radicine snails of Iran being invaluable for the monitoring of zoonotic flukes, understanding the distribution of infection and the accurate incrimination of snail vectors.},
}
@article {pmid33497618,
year = {2021},
author = {Nascimento, JMC and Hamada, N and Andrade-Souza, V and Huerta, H and Garza, JA and Frontado, H and Frontado, CQ and Grillet, ME},
title = {Back from the past: Molecular and morphological support for Simulium mutucuna Nunes de Mello &amp; Vieira da Silva, 1974 (Diptera: Simuliidae) as a valid species.},
journal = {Acta tropica},
volume = {216},
number = {},
pages = {105846},
doi = {10.1016/j.actatropica.2021.105846},
pmid = {33497618},
issn = {1873-6254},
mesh = {Animals ; Female ; Larva/anatomy &amp; histology ; Male ; Pupa/anatomy &amp; histology ; Simuliidae/*anatomy &amp; histology/classification/genetics ; },
abstract = {Simulium mutucuna, a species described based on a single female from Roraima state, was previously synonymized with Simulium paynei and currently is considered a synonym of Simulium rubrithorax. In the present paper we present morphological and molecular evidence supporting the validity of S. mutucuna based on analysis of specimens from Brazil, Venezuela and Mexico. We redescribe the female and describe, for the first time, the male, pupa and larva of S. mutucuna and discuss the morphological differences between this species and the others that are already considered as its senior synonyms. Currently, the distribution of S. mutucuna is restricted to Roraima state. The distribution record for S. rubrithorax in Brazil's North region needs to be removed, since the previous records were based on occurrence of S. mutucuna. Finally, we present new evidence of cryptic diversity in the S. paynei complex based on molecular information.},
}
@article {pmid33494189,
year = {2021},
author = {Onore, ME and Torella, A and Musacchia, F and D'Ambrosio, P and Zanobio, M and Del Vecchio Blanco, F and Piluso, G and Nigro, V},
title = {Linked-Read Whole Genome Sequencing Solves a Double DMD Gene Rearrangement.},
journal = {Genes},
volume = {12},
number = {2},
pages = {},
pmid = {33494189},
issn = {2073-4425},
mesh = {Child ; Comparative Genomic Hybridization ; Dystrophin/*genetics ; *Gene Rearrangement ; Genetic Association Studies ; Genetic Predisposition to Disease ; Humans ; Male ; Muscular Dystrophy, Duchenne/*genetics ; Mutation ; Pedigree ; Polymorphism, Single Nucleotide ; *Whole Genome Sequencing ; },
abstract = {Next generation sequencing (NGS) has changed our approach to diagnosis of genetic disorders. Nowadays, the most comprehensive application of NGS is whole genome sequencing (WGS) that is able to detect virtually all DNA variations. However, even after accurate WGS, many genetic conditions remain unsolved. This may be due to the current NGS protocols, based on DNA fragmentation and short reads. To overcome these limitations, we applied a linked-read sequencing technology that combines single-molecule barcoding with short-read WGS. We were able to assemble haplotypes and distinguish between alleles along the genome. As an exemplary case, we studied the case of a female carrier of X-linked muscular dystrophy with an unsolved genetic status. A deletion of exons 16-29 in DMD gene was responsible for the disease in her family, but she showed a normal dosage of these exons by Multiplex Ligation-dependent Probe Amplification (MLPA) and array CGH. This situation is usually considered compatible with a "non-carrier" status. Unexpectedly, the girl also showed an increased dosage of flanking exons 1-15 and 30-34. Using linked-read WGS, we were able to distinguish between the two X chromosomes. In the first allele, we found the 16-29 deletion, while the second allele showed a 1-34 duplication: in both cases, linked-read WGS correctly mapped the borders at single-nucleotide resolution. This duplication in trans apparently restored the normal dosage of exons 16-29 seen by quantitative assays. This had a dramatic impact in genetic counselling, by converting a non-carrier into a double carrier status prediction. We conclude that linked-read WGS should be considered as a valuable option to improve our understanding of unsolved genetic conditions.},
}
@article {pmid33489824,
year = {2020},
author = {Matter, MS and Chijioke, O and Savic, S and Bubendorf, L},
title = {Narrative review of molecular pathways of kinase fusions and diagnostic approaches for their detection in non-small cell lung carcinomas.},
journal = {Translational lung cancer research},
volume = {9},
number = {6},
pages = {2645-2655},
pmid = {33489824},
issn = {2218-6751},
abstract = {The discovery of actionable oncogenic driver alterations has significantly improved treatment options for patients with advanced non-small cell lung cancer (NSCLC). In lung adenocarcinoma (LUAD), approved drugs or drugs in clinical development can target more than half of these altered oncogenic driver genes. In particular, several gene fusions have been discovered in LUAD, including ALK, ROS1, NTRK, RET, NRG1 and FGFR. All these fusions involve tyrosine kinases (TK), which are activated due to structural rearrangements on the DNA level. Although the overall prevalence of these fusions in LUAD is rare, their detection is extremely important, as they are linked to an excellent response to TK inhibitors. Therefore, reliable screening methods applicable to small tumor samples (biopsies and cytology specimens) are required in the diagnostic workup of advanced NSCLC. Several methods are at disposal in a routine laboratory to demonstrate, directly or indirectly, the presence of a gene fusion. These methods include immunohistochemistry (IHC), fluorescence in-situ hybridization (FISH), reverse transcriptase-polymerase chain reaction (RT-PCR), multiplex digital color-coded barcode technology or next-generation sequencing (NGS) either on DNA or RNA level. In our review, we will summarize the increasing number of relevant fusion genes in NSCLC, point out their underlining molecular mechanisms and discuss different methods for the detection of fusion genes.},
}
@article {pmid33487022,
year = {2021},
author = {Crous, PW and Rossman, AY and Aime, MC and Allen, WC and Burgess, T and Groenewald, JZ and Castlebury, LA},
title = {Names of Phytopathogenic Fungi: A Practical Guide.},
journal = {Phytopathology},
volume = {111},
number = {9},
pages = {1500-1508},
doi = {10.1094/PHYTO-11-20-0512-PER},
pmid = {33487022},
issn = {0031-949X},
mesh = {*Fungi ; *Plant Diseases ; },
abstract = {Using the correct name for phytopathogenic fungi and oomycetes is essential for communicating knowledge about species and their biology, control, and quarantine as well as for trade and research purposes. However, many plant pathogenic fungi are pleomorphic, meaning they produce different asexual (anamorph) and sexual (teleomorph) morphs in their life cycles. Therefore, more than one name has been applied to different morphs of the same species, which has confused users. The onset of DNA technologies makes it possible to connect different morphs of the same species, resulting in a move to a more natural classification system for fungi in which a single name for a genus and species can now be used. This move to a single nomenclature, coupled with the advent of molecular systematics and the introduction of polythetic taxonomic approaches, has been the main driving force for a reclassification of fungi, including pathogens. Nonetheless, finding the correct name for species remains challenging. In this article we outline a series of steps or considerations to greatly simplify this process and provide links to various online databases and resources to aid in determining the correct name. Additionally, a list of accurate names is provided for the most common genera and species of phytopathogenic fungi.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.},
}
@article {pmid33486177,
year = {2021},
author = {Berger, E and Bossenbroek, L and Beermann, AJ and Schäfer, RB and Znari, M and Riethmüller, S and Sidhu, N and Kaczmarek, N and Benaissa, H and Ghamizi, M and Plicht, S and Ben Salem, S and El Qorchi, F and Naimi, M and Leese, F and Frör, O},
title = {Social-ecological interactions in the Draa River Basin, southern Morocco: Towards nature conservation and human well-being using the IPBES framework.},
journal = {The Science of the total environment},
volume = {769},
number = {},
pages = {144492},
doi = {10.1016/j.scitotenv.2020.144492},
pmid = {33486177},
issn = {1879-1026},
mesh = {Animals ; Conservation of Natural Resources ; *Ecosystem ; Humans ; Morocco ; *Rivers ; Water Resources ; },
abstract = {Water is essential to human societies and a prerequisite for flourishing nature, especially in arid regions. Yet, climate change and socio-economic developments are expected to exacerbate current and future stresses on water resources, demanding innovative approaches to balance water needs for society and nature conservation. In this study, we use the IPBES conceptual framework to combine ecological and socio-economic insights and analyse the connections between people and nature in the water scarce Draa River Basin, southern Morocco. We study the diversity of desert benthic macroinvertebrates as one component of nature using DNA barcoding and their potential to serve as bioindicators of human impact by relating species occurrences to environmental parameters. Furthermore, based on 87 interviews with farmers and key institutional stakeholders, we investigate how farmers perceive water related changes and how water is managed in the basin. Regarding benthic macroinvertebrates, 41 families were identified, 475 DNA barcodes generated and assigned to 118 putative species (Barcode Index Numbers) of which 60 were first records. This indicates a lack of reference sequences for known, but also a potentially high number of undescribed species. Environmental parameters, which are partly influenced by human activities, such as aquatic stages, salinity and intermittency, were the most important variables explaining invertebrate richness and community composition in generalized linear models. We further describe farmers' perceptions of decreasing water quality and quantity. Farmers generally believe that they are able to cope with water related changes, although perceptions are regionally differentiated with farmers downstream being less optimistic. With growing concerns, water policies currently focus on increasing water supply and less on reducing water demands. Based on these findings, the usefulness of the IPBES framework for understanding social-ecological system dynamics is reflected, and recommendations for future freshwater management and research are derived.},
}
@article {pmid33484348,
year = {2021},
author = {Barrow, LN and Bauernfeind, SM and Cruz, PA and Williamson, JL and Wiley, DL and Ford, JE and Baumann, MJ and Brady, SS and Chavez, AN and Gadek, CR and Galen, SC and Johnson, AB and Mapel, XM and Marroquin-Flores, RA and Martinez, TE and McCullough, JM and McLaughlin, JE and Witt, CC},
title = {Detecting turnover among complex communities using null models: a case study with sky-island haemosporidian parasites.},
journal = {Oecologia},
volume = {195},
number = {2},
pages = {435-451},
pmid = {33484348},
issn = {1432-1939},
support = {DEB-1146491//National Science Foundation/ ; NSF DBI-1611710//National Science Foundation/ ; },
mesh = {Animals ; *Bird Diseases ; *Haemosporida/genetics ; Islands ; *Parasites ; Phylogeny ; *Plasmodium ; Southwestern United States ; },
abstract = {Turnover in species composition between sites, or beta diversity, is a critical component of species diversity that is typically influenced by geography, environment, and biotic interactions. Quantifying turnover is particularly challenging, however, in multi-host, multi-parasite assemblages where undersampling is unavoidable, resulting in inflated estimates of turnover and uncertainty about its spatial scale. We developed and implemented a framework using null models to test for community turnover in avian haemosporidian communities of three sky islands in the southwestern United States. We screened 776 birds for haemosporidian parasites from three genera (Parahaemoproteus, Plasmodium, and Leucocytozoon) by amplifying and sequencing a mitochondrial DNA barcode. We detected infections in 280 birds (36.1%), sequenced 357 infections, and found a total of 99 parasite haplotypes. When compared to communities simulated from a regional pool, we observed more unique, single-mountain haplotypes and fewer haplotypes shared among three mountain ranges than expected, indicating that haemosporidian communities differ to some degree among adjacent mountain ranges. These results were robust even after pruning datasets to include only identical sets of host species, and they were consistent for two of the three haemosporidian genera. The two more distant mountain ranges were more similar to each other than the one located centrally, suggesting that the differences we detected were due to stochastic colonization-extirpation dynamics. These results demonstrate that avian haemosporidian communities of temperate-zone forests differ on relatively fine spatial scales between adjacent sky islands. Null models are essential tools for testing the spatial scale of turnover in complex, undersampled, and poorly known systems.},
}
@article {pmid33484178,
year = {2021},
author = {Appleyard, SA and Maher, S and Pogonoski, JJ and Bent, SJ and Chua, XY and McGrath, A},
title = {Assessing DNA for fish identifications from reference collections: the good, bad and ugly shed light on formalin fixation and sequencing approaches.},
journal = {Journal of fish biology},
volume = {98},
number = {5},
pages = {1421-1432},
doi = {10.1111/jfb.14687},
pmid = {33484178},
issn = {1095-8649},
mesh = {Animal Identification Systems/*methods/standards ; Animals ; Australia ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Fishes/*classification/*genetics ; Formaldehyde/*chemistry ; High-Throughput Nucleotide Sequencing/standards ; Phylogeography ; Specimen Handling/*standards ; },
abstract = {Natural history collections are repositories of biodiversity and are potentially used by molecular ecologists for comparative taxonomic, phylogenetic, biogeographic and forensic purposes. Specimens in fish collections are preserved using a combination of methods with many fixed in formalin and then preserved in ethanol for long-term storage. Formalin fixation damages DNA, thereby limiting genetic analyses. In this study, the authors compared the DNA barcoding and identification success for frozen and formalin-fixed tissues obtained from specimens in the CSIRO Australian National Fish Collection. They studied 230 samples from fishes (consisting of >160 fish species). An optimized formalin-fixed, paraffin-embedded DNA extraction method resulted in usable DNA from degraded tissues. Four mini barcoding assays of the mitochondrial DNA (mtDNA) were characterized with Sanger and Illumina amplicon sequencing. In the good quality DNA (without exposure to formalin), up to 88% of the specimens were correctly matched at the species level using the cytochrome oxidase subunit 1 (COI) mini barcodes, whereas up to 58% of the specimens exposed to formalin for less than 8 weeks were correctly identified to species. In contrast, 16S primers provided higher amplification success with formalin-exposed tissues, although the COI gene was more successful for identification. Importantly, the authors found that DNA of a certain size and quality can be amplified and sequenced despite exposure to formalin, and Illumina sequencing provided them with greater power of resolution for taxa identification even when there was little DNA present. Overall, within parameter constraints, this study highlights the possibilities of recovering DNA barcodes for identification from formalin-fixed fish specimens, and the authors provide guidelines for when successful identification could be expected.},
}
@article {pmid33481325,
year = {2021},
author = {He, X and Gilmore, SR and Sutherland, TF and Hajibabaei, M and Miller, KM and Westfall, KM and Pawlowski, J and Abbott, CL},
title = {Biotic signals associated with benthic impacts of salmon farms from eDNA metabarcoding of sediments.},
journal = {Molecular ecology},
volume = {30},
number = {13},
pages = {3158-3174},
doi = {10.1111/mec.15814},
pmid = {33481325},
issn = {1365-294X},
mesh = {Animals ; Aquaculture ; Biodiversity ; British Columbia ; *DNA Barcoding, Taxonomic ; Environmental Monitoring ; Geologic Sediments ; Humans ; *Salmon/genetics ; },
abstract = {Environmental DNA (eDNA) metabarcoding can rapidly characterize the composition and diversity of benthic communities, thus it has high potential utility for routine assessments of benthic impacts of marine finfish farming. In this study, 126 sediment grab samples from 42 stations were collected at six salmon farms in British Columbia, Canada. Benthic community changes were assessed by both eDNA metabarcoding of metazoans and macrofaunal polychaete surveys. The latter was done by analysing 11,466 individuals using a combination of morphology-based taxonomy and DNA barcoding. Study objectives were to: (i) compare biotic signals associated with benthic impacts of salmon farming in the two data sources, and (ii) identify potential eDNA indicators to facilitate monitoring in Canada. Alpha diversity parameters were consistently reduced near fish cage edge and negatively correlated with pore-water sulphide concentration, with coefficients ranging from -0.62 to -0.48. Although Polychaeta are a common indicator group, the negative correlation with pore-water sulphide concentration was much stronger for Nematoda OTU richness (correlation coefficient: -0.86) than for Polychaeta (correlation coefficient: -0.38). Presence/absence of Capitella generally agreed well between the two methods despite that they differed in the volume of sediments sampled and the molecular marker used. Multiple approaches were used to identify OTUs related to organic enrichment statuses. We demonstrate that eDNA metabarcoding generates biotic signals that could be leveraged for environmental assessment of benthic impacts of fish farms in multiple ways: both alpha diversity and Nematoda OTU richness could be used to assess the spatial extent of impact, and OTUs related to organic enrichment could be used to develop local biotic indices.},
}
@article {pmid33478160,
year = {2021},
author = {Paill, W and Koblmüller, S and Friess, T and Gereben-Krenn, BA and Mairhuber, C and Raupach, MJ and Zangl, L},
title = {Relicts from Glacial Times: The Ground Beetle Pterostichus adstrictus Eschscholtz, 1823 (Coleoptera: Carabidae) in the Austrian Alps.},
journal = {Insects},
volume = {12},
number = {1},
pages = {},
pmid = {33478160},
issn = {2075-4450},
support = {18146388//&#xd6;sterreichische Forschungsf&#xf6;rderungsgesellschaft/ ; Establishing DNA-Barcoding Pipelines at Austrian Universities//Bundesministerium f&#xfc;r Wissenschaft, Forschung und Wirtschaft/ ; },
abstract = {The last ice age considerably influenced distribution patterns of extant species of plants and animals, with some of them now inhabiting disjunct areas in the subarctic/arctic and alpine regions. This arctic-alpine distribution is characteristic for many cold-adapted species with a limited dispersal ability and can be found in many invertebrate taxa, including ground beetles. The ground beetle Pterostichus adstrictus Eschscholtz, 1823 of the subgenus Bothriopterus was previously known to have a holarctic-circumpolar distribution, in Europe reaching its southern borders in Wales and southern Scandinavia. Here, we report the first findings of this species from the Austrian Ötztal Alps, representing also the southernmost edge of its currently known distribution, confirmed by the comparison of morphological characters to other Bothriopterus species and DNA barcoding data. Molecular data revealed a separation of the Austrian and Finish specimens with limited to no gene flow at all. Furthermore, we present the first data on habitat preference and seasonality of P. adstrictus in the Austrian Alps.},
}
@article {pmid33477439,
year = {2021},
author = {Park, SH and Kim, JS and Kim, HT},
title = {A Small Number of Gametophytes with Gametangia and Stunted Sporophytes of Antrophyum obovatum Baker (Pteridaceae): The Suppression of Functional Sporophyte Production by Prezygotic and Postzygotic Sterility.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {1},
pages = {},
pmid = {33477439},
issn = {2223-7747},
support = {2018R1D1A3B07048213//National Research Foundation of Korea/ ; },
abstract = {Ferns have conspicuous sporophytes as the dominant phase in their life cycle; however, the gametophytes are completely separated from the sporophytes and supply their own nutrition, unlike in bryophytes and seed plants. Among the gametophytes, some maintain their populations in the gametophyte phase without progressing to sporophyte production and are known as independent gametophytes. Independent gametophytes of Antrophyum obovatum Baker were recently reported in one population on Jeju Island, Korea. In the present study, we surveyed more places to find new independent gametophyte populations of A. obovatum using the rbcL gene sequence-based DNA barcoding technique. We identified two new sites inhabited by independent gametophytes. Archegonia and juvenile sporophytes were independently observed in each location under slightly different environmental conditions. Consequently, in the case of this species, functional sporophyte production is likely suppressed by prezygotic and postzygotic sterility, depending on microenvironmental factors.},
}
@article {pmid33475384,
year = {2021},
author = {Rietsch, P and Zeyat, M and Hübner, O and Hoffmann, K and Kutter, M and Paskin, A and Uhlig, J and Lentz, D and Resch-Genger, U and Eigler, S},
title = {Substitution Pattern-Controlled Fluorescence Lifetimes of Fluoranthene Dyes.},
journal = {The journal of physical chemistry. B},
volume = {125},
number = {4},
pages = {1207-1213},
doi = {10.1021/acs.jpcb.0c08851},
pmid = {33475384},
issn = {1520-5207},
abstract = {The absorption and emission properties of organic dyes are generally tuned by altering the substitution pattern. However, tuning the fluorescence lifetimes over a range of several 10 ns while barely affecting the spectral features and maintaining a moderate fluorescence quantum yield is challenging. Such properties are required for lifetime multiplexing and barcoding applications. Here, we show how this can be achieved for the class of fluoranthene dyes, which have substitution-dependent lifetimes between 6 and 33 ns for single wavelength excitation and emission. We explore the substitution-dependent emissive properties in the crystalline solid state that would prevent applications. Furthermore, by analyzing dye mixtures and embedding the dyes in carboxy-functionalized 8 μm-sized polystyrene particles, the unprecedented potential of these dyes as labels and encoding fluorophores for time-resolved fluorescence detection techniques is demonstrated.},
}
@article {pmid33470099,
year = {2021},
author = {Zhang, K and Liang, J and Brun, NR and Zhao, Y and Werdich, AA},
title = {Rapid Zebrafish Behavioral Profiling Assay Accelerates the Identification of Environmental Neurodevelopmental Toxicants.},
journal = {Environmental science &amp; technology},
volume = {55},
number = {3},
pages = {1919-1929},
doi = {10.1021/acs.est.0c06949},
pmid = {33470099},
issn = {1520-5851},
mesh = {Animals ; Biological Assay ; *Chlorpyrifos/toxicity ; Embryo, Nonmammalian ; Neurotoxins ; *Zebrafish ; },
abstract = {Rapid and cost-effective in vivo assays to screen potential environmental neurodevelopmental toxicants are necessary to address the limitations of in vitro platforms, such as the inability to fully recapitulate the developmental and physiological processes of whole organisms. In the present study, a rapid zebrafish behavioral profiling assay was developed to characterize the neurodevelopmental effects of environmental substances by quantitatively evaluating multiple spontaneous movement features of zebrafish embryos. This video analysis-based assay automatically segmented every embryo and thus was able to accurately quantify spontaneous movement features, including frequency, duration, intensity, interval, and the number of continuous movements. When tested with eight environmental substances known to be neurodevelopmental toxicants, such as chlorpyrifos and bisphenol A, the assay successfully captured frequency alterations that were well-documented in previous studies while also providing additional information. Using an optimized procedure, we further assessed 132 potential neurotoxins that spanned a wide range of molecular targets, many of which were previously detected in environmental waterbodies. The distinct altered behavioral barcodes indicated that the spontaneous movement was impacted by diverse neuroactive substances, and the effects could be effectively evaluated with the developed assay. The web-based tool, named EMAnalysis, is further provided at http://www.envh.sjtu.edu.cn/zebrafish_contraction.jsp. Thus, this assay provides an efficient platform to accelerate the pace of neurotoxic environmental contaminant discoveries.},
}
@article {pmid33468607,
year = {2021},
author = {Griesemer, SB and Van Slyke, G and St George, K},
title = {Assessment of Sample Pooling for Clinical SARS-CoV-2 Testing.},
journal = {Journal of clinical microbiology},
volume = {59},
number = {4},
pages = {},
pmid = {33468607},
issn = {1098-660X},
mesh = {*COVID-19 ; COVID-19 Testing ; Clinical Laboratory Techniques ; Humans ; Pandemics ; *SARS-CoV-2 ; Specimen Handling ; },
abstract = {Accommodating large increases in sample workloads has presented a major challenge to clinical laboratories during the coronavirus disease 2019 (COVID-19) pandemic. Despite the implementation of automated detection systems and previous efficiencies, including barcoding, electronic data transfer, and extensive robotics, capacities have struggled to meet the demand. Sample pooling has been suggested as an additional strategy to address this need. The greatest concern with this approach in clinical settings is the potential for reduced sensitivity, particularly detection failures with weakly positive samples. To investigate this possibility, detection rates in pooled samples were evaluated, with a focus on pools containing weakly positive specimens. Additionally, the frequencies of occurrence of weakly positive samples during the pandemic were reviewed. Weakly positive specimens, with threshold cycle (CT) values of 33 or higher, were detected in 95% of 60 five-sample pools but only 87% of 39 nine-sample pools. The proportion of positive samples with very low viral loads rose markedly during the first few months of the pandemic, peaking in June, decreasing thereafter, and remaining level since August. At all times, weakly positive specimens comprised a significant component of the sample population, ranging from 29% to >80% for CT values above 31. In assessing the benefits of pooling strategies, however, other aspects of the testing process must be considered. Accessioning, result data management, electronic data transfer, reporting, and billing are not streamlined and may be complicated by pooling procedures. Therefore, the impact on the entire laboratory process needs to be carefully assessed prior to implementing such a strategy.},
}
@article {pmid33467716,
year = {2021},
author = {Yik, MH and Kong, BL and Siu, TY and Lau, DT and Cao, H and Shaw, PC},
title = {Differentiation of Hedyotis diffusa and Common Adulterants Based on Chloroplast Genome Sequencing and DNA Barcoding Markers.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {1},
pages = {},
pmid = {33467716},
issn = {2223-7747},
abstract = {Chinese herbal tea, also known as Liang Cha or cooling beverage, is popular in South China. It is regarded as a quick-fix remedy to relieve minor health problems. Hedyotis diffusa Willd. (colloquially Baihuasheshecao) is a common ingredient of cooling beverages. H. diffusa is also used to treat cancer and bacterial infections. Owing to the high demand for H. diffusa, two common adulterants, Hedyotis brachypoda (DC.) Sivar and Biju (colloquially Nidingjingcao) and Hedyotis corymbosa (L.) Lam. (colloquially Shuixiancao), are commonly encountered in the market. Owing to the close similarity of their morphological characteristics, it is difficult to differentiate them. Here, we sequenced the complete chloroplast genomes of the three species of Hedyotis using next-generation sequencing (NGS). By comparing the complete chloroplast genomes, we found that they are closely related in the subfamily Rubioideae. We also discovered that there are significant differences in the number and repeating motifs of microsatellites and complex repeats and revealed three divergent hotspots, rps16-trnQ intergenic spacer, ndhD and ycf1. By using these species-specific sequences, we propose new DNA barcoding markers for the authentication of H. diffusa and its two common adulterants.},
}
@article {pmid33465147,
year = {2021},
author = {Santiago, JC and Goldman, JD and Zhao, H and Pankow, AP and Okuku, F and Schmitt, MW and Chen, LH and Hill, CA and Casper, C and Phipps, WT and Mullins, JI},
title = {Intra-host changes in Kaposi sarcoma-associated herpesvirus genomes in Ugandan adults with Kaposi sarcoma.},
journal = {PLoS pathogens},
volume = {17},
number = {1},
pages = {e1008594},
pmid = {33465147},
issn = {1553-7374},
support = {K23 CA150931/CA/NCI NIH HHS/United States ; P30 AI027757/AI/NIAID NIH HHS/United States ; T32 AI007140/AI/NIAID NIH HHS/United States ; U54 CA190146/CA/NCI NIH HHS/United States ; },
mesh = {Adult ; Cohort Studies ; DNA, Viral/*analysis/genetics ; Female ; *Genome, Viral ; Genomics ; Herpesvirus 8, Human/classification/*genetics/isolation &amp; purification ; *Host Specificity ; Humans ; Male ; Middle Aged ; Polymorphism, Genetic ; Sarcoma, Kaposi/epidemiology/*virology ; Uganda/epidemiology ; },
abstract = {Intra-host tumor virus variants may influence the pathogenesis and treatment responses of some virally-associated cancers. However, the intra-host variability of Kaposi sarcoma-associated herpesvirus (KSHV), the etiologic agent of Kaposi sarcoma (KS), has to date been explored with sequencing technologies that possibly introduce more errors than that which occurs in the viral population, and these studies have only studied variable regions. Here, full-length KSHV genomes in tumors and/or oral swabs from 9 Ugandan adults with HIV-associated KS were characterized. Furthermore, we used deep, short-read sequencing using duplex unique molecular identifiers (dUMI)-random double-stranded oligonucleotides that barcode individual DNA molecules before library amplification. This allowed suppression of PCR and sequencing errors to ~10-9/base as well as afforded accurate determination of KSHV genome numbers sequenced in each sample. KSHV genomes were assembled de novo, and rearrangements observed were confirmed by PCR and Sanger sequencing. 131-kb KSHV genome sequences, excluding major repeat regions, were successfully obtained from 23 clinical specimens, averaging 2.3x104 reads/base. Strikingly, KSHV genomes were virtually identical within individuals at the point mutational level. The intra-host heterogeneity that was observed was confined to tumor-associated KSHV mutations and genome rearrangements, all impacting protein-coding sequences. Although it is unclear whether these changes were important to tumorigenesis or occurred as a result of genomic instability in tumors, similar changes were observed across individuals. These included inactivation of the K8.1 gene in tumors of 3 individuals and retention of a region around the first major internal repeat (IR1) in all instances of genomic deletions and rearrangements. Notably, the same breakpoint junctions were found in distinct tumors within single individuals, suggesting metastatic spread of rearranged KSHV genomes. These findings define KSHV intra-host heterogeneity in vivo with greater precision than has been possible in the past and suggest the possibility that aberrant KSHV genomes may contribute to aspects of KS tumorigenesis. Furthermore, study of KSHV with use of dUMI provides a proof of concept for utilizing this technique for detailed study of other virus populations in vivo.},
}
@article {pmid33461115,
year = {2021},
author = {Wang, Y and Du, P and Abd El-Aty, AM and Chen, G and Jia, H and Cui, X and Oz, E and Zhang, Y and Zhang, X and Qin, G and Yan, F and Wang, J and Jin, M and Hammock, BD},
title = {A visual bio-barcode immunoassay for sensitive detection of triazophos based on biochip silver staining signal amplification.},
journal = {Food chemistry},
volume = {347},
number = {},
pages = {129024},
pmid = {33461115},
issn = {1873-7072},
support = {P42 ES004699/ES/NIEHS NIH HHS/United States ; },
mesh = {Gold ; Immunoassay/*methods ; Malus/*chemistry ; Metal Nanoparticles/chemistry ; Organothiophosphates/*analysis ; Silver Staining ; Triazoles/*analysis ; Water/*chemistry ; },
abstract = {Herein, a novel visual method for detecting triazophos based on competitive bio-barcode immunoassay was described. The competitive immunoassay was established by gold nanoparticles (AuNPs), magnetic microparticle (MMPs) and triazophos, combined with biochip hybridization system to detect the residual of triazophos in water and apple. Because AuNPs carried many bio-barcodes, which hybridized with labeled DNA on the biochip, catalyzed signal amplification using silver staining was detected by grayscale values as well as the naked eye. Notably, the grayscale values decreases with increasing the concentrations of triazophos, and the color change weakened gradually. The detection range was in between 0.05 and 10 ng/mL and the minimum detection limit was set at 0.04 ng/mL. Percent recovery calculated from spiked water and apple samples ranged between 55.4 and 107.8% with relative standard deviations (RSDs) of 12.4-24.9%. It has therefore been shown that this protocol provides a new insight for rapid detection of small molecule pesticides in various matrices.},
}
@article {pmid33460338,
year = {2021},
author = {Gonçalves, LT and Bianchi, FM and Deprá, M and Calegaro-Marques, C},
title = {Barcoding a can of worms: testing cox1 performance as a DNA barcode of Nematoda.},
journal = {Genome},
volume = {64},
number = {7},
pages = {705-717},
doi = {10.1139/gen-2020-0140},
pmid = {33460338},
issn = {1480-3321},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Helminth ; *Electron Transport Complex IV/genetics ; *Nematoda/genetics ; Phylogeny ; },
abstract = {Accurate taxonomic identifications and species delimitations are a fundamental problem in biology. The complex taxonomy of Nematoda is primarily based on morphology, which is often dubious. DNA barcoding emerged as a handy tool to identify specimens and assess diversity, but its applications in Nematoda are incipient. We evaluated cytochrome c oxidase subunit I (cox1) efficiency as a DNA barcode for nematodes scrutinising 5241 sequences retrieved from BOLD and GenBank. The samples included genera with medical, agricultural, or ecological relevance: Anguillicola, Caenorhabditis, Heterodera, Meloidogyne, Onchocerca, Strongyloides, and Trichinella. We assessed cox1 performance through barcode gap and Probability of Correct Identification (PCI) analyses, and estimated species richness through Automatic Barcode Gap Discovery (ABGD). Each genus presented distinct gap ranges, mirroring the evolutionary diversity within Nematoda. Thus, to survey the diversity of the phylum, a careful definition of thresholds for lower taxonomic levels should be considered. PCIs were around 70% for both databases, highlighting operational biases and challenges in nematode taxonomy. ABGD inferred higher richness than the taxonomic labels informed by databases. The prevalence of specimen misidentifications and dubious species delimitations emphasise the value of integrative approaches to nematode taxonomy and systematics. Overall, cox1 is a relevant tool for integrative taxonomy of nematodes.},
}
@article {pmid33458206,
year = {2020},
author = {Zhou, GC and Wang, JY and Li, W and Zhang, M and Meng, GQ and Wang, HY and Chen, X and Wu, YH and Wu, P and Wang, YL},
title = {Complete chloroplast genome sequence of Chimonanthus praecox link (Calycanthaceae): an endemic plant species in China.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {5},
number = {3},
pages = {3469-3471},
pmid = {33458206},
issn = {2380-2359},
abstract = {Chimonanthus praecox, a deciduous shrub tree, is endemic to China and widely cultivated in the world as a popular garden and ornamental plant. Here, we have reported its complete chloroplast genome with a length of 153,181 bp, containing a large single copy (LSC) region of 86,916 bp, a small single copy (SSC) region of 19,767 bp and two identical inverted repeat regions (IRs) of 23,249 bp. The overall GC contents of the plastome were 39.27%. A total of 114 unique genes were successfully annotated consisting of 80 protein-coding genes, 30 tRNA genes and four rRNA genes. Sixteen genes each possessed one intron and three genes had two introns. The ML phylogenetic analysis supports Chimonanthus as sister to Calycanthus. This result will be helpful for genetic breeding and population genetics of C. praecox, DNA barcoding of Chimonanthus, and phylogenetic studies of Calycanthaceae.},
}
@article {pmid33458131,
year = {2020},
author = {Shrestha, S and Bashyal, A and Dhakal, A and McGreevy, TJ and Buffum, B and Joshi, J and Chaudhary, HK and Khanal, SN},
title = {Mitochondrial DNA analysis of critically endangered Chinese Pangolins (Manis pentadactyla) from Nepal.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {5},
number = {3},
pages = {3257-3261},
pmid = {33458131},
issn = {2380-2359},
abstract = {Chinese Pangolins (Manis pentadactyla) are Critically Endangered and one of the most illegally traded mammals globally. We generated first COI sequences from five individuals of this species from Nepal. BLASTn search of our 600 bp sequences at GenBank showed pair-wise identity between 99.17% and 100% to M. pentadactyla. There were three haplotypes and a total of five variable sites among five M. pentadactyla sequences. Neighbor-joining tree revealed that all M. pentadactyla from Nepal clustered into same group further splitting into two sub-groups albeit with low bootstrap value, suggesting potential multiple geographic origins. The K2P distance was 0.3% within group and 0.7% between four sequences from Bhaktapur and Kavrepalanchok districts (Mape2, Mape3, Mape5 and Mape6) and museum sample (Mape10). This study has generated reference samples for M. pentadactyla from Nepal and will be helpful in understanding dynamics of illegal trade of this species and in successful identification of M. pentadactyla from Nepal even in the absence of intact specimens.},
}
@article {pmid33458121,
year = {2020},
author = {Kundu, S and Lalremsanga, HT and Biakzuala, L and Chandra, K and Kumar, V},
title = {DNA barcoding reveals distinct population of Dopasia gracilis (Squamata: Anguidae) in Mizoram, Northeast India.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {5},
number = {3},
pages = {3229-3233},
pmid = {33458121},
issn = {2380-2359},
abstract = {The DNA barcode data of Asian Glass Lizard, Dopasia gracilis, is limited in the global database, especially from India. The present study aimed to generate a barcode sequence of morphologically identified D. gracilis from the Mizoram state in northeast India and compared with other Anguidae species. The studied species showed monophyletic clustering in the Bayesian analysis (BA) phylogeny with strong posterior probability support and also discriminated sufficient Kimura 2 parameter genetic distances. The barcode data of D. gracilis revealed high intra-species genetic variability and formed two clusters in BA phylogeny. The Templeton, Crandall, and Sing network also depicted four different haplotypes within the barcode sequences of D. gracilis. The DNA sequences generated from northeast India showed 6.5-6.6% and 7.3% genetic distances with the sequences generated from Yunnan Province and Tibetan Plateau, respectively. Considering the high genetic distances, multiple clustering, and distinct haplotypes, the present study assumed the presence of possible cryptic diversity of D. gracilis in the Indochina sub-region and a distinct population in northeast India. We recommended the generation of more DNA information from different localities to elucidate the actual diversity of D. gracilis within the known range distribution.},
}
@article {pmid33458118,
year = {2020},
author = {Mahapatra, S and A, R and Dwivedy, P and E, S and S A, S and A, K},
title = {Character-based identification system of scombrids from Indian waters for authentication and conservation purposes.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {5},
number = {3},
pages = {3221-3224},
pmid = {33458118},
issn = {2380-2359},
abstract = {Scombrids are the important component of pelagic fishery resources which include 54 species under 15 genera commonly known as mackerels, bonitos, and tunas. Due to the high commercial value attained, there are real chances of fraudulent substitution by species of inferior value. DNA based species identification methods can be applied to detect product adulteration, as well as to better contribute to the conservation and management of these species by providing accurate species identification independently of the age of the individuals or the tissue processed. In this study, a total of 15 commercially important scombrid species from Indian waters were analyzed. Due to the inadequacy of mitochondrial COI barcoding gene in discriminating between some Thunnus species, cytochrome b sequences were used instead. For all the 15 species, we propose a DNA character-based keys which uses a diagnostic combination of nucleotides and respective probes, including the first character-based keys and probes to differentiate between Thunnus albacares and T. obsesus.},
}
@article {pmid33458033,
year = {2020},
author = {Naeem, Z and Masud, S and Hassan, S and Naeem, M},
title = {Molecular approach for identification of Catla catla using mitochondrial CO1 from Pakistan.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {5},
number = {3},
pages = {3000-3003},
pmid = {33458033},
issn = {2380-2359},
abstract = {DNA barcoding is a rapid, precise, and effective way of species identification. A short and standard target gene marker is used to create sequence profile of identified species. Specific tag or marker is used, which is derived from mitochondrial COI for identification. Effectiveness of this method axes the degree of divergence among species. Identification is necessary for their representation. In the present work, Catla catla was used to study by using Cytochrome C Oxidase 1.The genetic distances were computed, and Neighbor Joining tree was constructed based on the Kimura 2 Parameter method. GenBank and BOLD revealed definitive identity matches. Conspecific and congeneric K2P nucleotide divergence was estimated. Evolutionary tree was analyzed clearly by relating their species to phylogenetic tree, as same as species were bunched under same tree node, while species were differently clustered under distinct nodes. These findings conclude that the gene sequence may serve as a milestone for identification and phylogenetic history of related species at molecular level.},
}
@article {pmid33457858,
year = {2020},
author = {Liu, Z and Zhang, J and Zhou, Y and Liu, Y and Hu, Z and Zheng, G and Shi, Z},
title = {The complete chloroplast genome of Aesculus chinensis var. wilsonii.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {5},
number = {3},
pages = {2547-2549},
pmid = {33457858},
issn = {2380-2359},
abstract = {In this study, we sequenced the complete chloroplast (cp) genome of Aesculus chinensis Bunge var. wilsonii (Rehder) Turland &amp; N. H. Xia and compared it with cp genomes of congeneric species. The cp genome of A. chinensis var. wilsonii is a circular molecule, 156,211 bp in length, with typical quadripartite structure. It has one large single copy (LSC) region of 85,211 bp and one small single copy (SSC) region of 18,124 bp that are separated by two inverted repeat regions (IR) of 26,438 bp. The cp genome encodes 133 genes comprising 85 protein-coding genes, 40 tRNA genes, and eight rRNA ribosomal genes. The overall GC content of the cp genome of A. chinensis var. wilsonii is 37.93%. We conducted amaximum likelihood phylogenetic analysis, which revealed that A. chinensis var. wilsonii is sister to A. wangii and has a close relationship with Acer L. (maples). We expect that the cp genome of A. chinensis var. wilsonii will be useful for DNA barcoding and species delimitation for this species as well as future studies on the conservation, taxonomy, and evolutionary relationships of Aesculus L.},
}
@article {pmid33452897,
year = {2021},
author = {Dahl, MB and Peršoh, D and Jentsch, A and Kreyling, J},
title = {Root-Associated Mycobiomes of Common Temperate Plants (Calluna vulgaris and Holcus lanatus) Are Strongly Affected by Winter Climate Conditions.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {403-415},
pmid = {33452897},
issn = {1432-184X},
support = {DFG JE 282/5-1//Deutsche Forschungsgemeinschaft/ ; RTG 2010//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Ascomycota ; *Calluna ; Climate Change ; *Holcus ; *Mycobiome ; Seasons ; Soil ; },
abstract = {Winter temperatures are projected to increase in Central Europe. Subsequently, snow cover will decrease, leading to increased soil temperature variability, with potentially different consequences for soil frost depending on e.g. altitude. Here, we experimentally evaluated the effects of increased winter soil temperature variability on the root associated mycobiome of two plant species (Calluna vulgaris and Holcus lanatus) at two sites in Germany; a colder and wetter upland site with high snow accumulation and a warmer and drier lowland site, with low snow accumulation. Mesocosm monocultures were set-up in spring 2010 at both sites (with soil and plants originating from the lowland site). In the following winter, an experimental warming pulse treatment was initiated by overhead infrared heaters and warming wires at the soil surface for half of the mesocosms at both sites. At the lowland site, the warming treatment resulted in a reduced number of days with soil frost as well as increased the average daily temperature amplitude. Contrary, the treatment caused no changes in these parameters at the upland site, which was in general a much more frost affected site. Soil and plant roots were sampled before and after the following growing season (spring and autumn 2011). High-throughput sequencing was used for profiling of the root-associated fungal (ITS marker) community (mycobiome). Site was found to have a profound effect on the composition of the mycobiome, which at the upland site was dominated by fast growing saprotrophs (Mortierellomycota), and at the lowland site by plant species-specific symbionts (e.g. Rhizoscyphus ericae and Microdochium bolleyi for C. vulgaris and H. lanatus respectively). The transplantation to the colder upland site and the temperature treatment at the warmer lowland site had comparable consequences for the mycobiome, implying that winter climate change resulting in higher temperature variability has large consequences for mycobiome structures regardless of absolute temperature of a given site.},
}
@article {pmid33452280,
year = {2021},
author = {Grealy, A and Langmore, NE and Joseph, L and Holleley, CE},
title = {Genetic barcoding of museum eggshell improves data integrity of avian biological collections.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {1605},
pmid = {33452280},
issn = {2045-2322},
mesh = {Animals ; Birds/*genetics ; DNA/chemistry/isolation &amp; purification/metabolism ; *DNA Barcoding, Taxonomic ; Egg Shell/*metabolism ; Museums ; Parrots/*genetics ; Specimen Handling ; },
abstract = {Natural history collections are often plagued by missing or inaccurate metadata for collection items, particularly for specimens that are difficult to verify or rare. Avian eggshell in particular can be challenging to identify due to extensive morphological ambiguity among taxa. Species identifications can be improved using DNA extracted from museum eggshell; however, the suitability of current methods for use on small museum eggshell specimens has not been rigorously tested, hindering uptake. In this study, we compare three sampling methodologies to genetically identify 45 data-poor eggshell specimens, including a putatively extinct bird's egg. Using an optimised drilling technique to retrieve eggshell powder, we demonstrate that sufficient DNA for molecular identification can be obtained from even the tiniest eggshells without significant alteration to the specimen's appearance or integrity. This method proved superior to swabbing the external surface or sampling the interior; however, we also show that these methods can be viable alternatives. We then applied our drilling method to confirm that a purported clutch of Paradise Parrot eggs collected 40 years after the species' accepted extinction date were falsely identified, laying to rest a 53-year-old ornithological controversy. Thus, even the smallest museum eggshells can offer new insights into old questions.},
}
@article {pmid33448409,
year = {2021},
author = {Li, M and Hong, X and Qiu, X and Yang, C and Mao, Y and Li, Y and Liu, Z and Du, D},
title = {Ultrasensitive monitoring strategy of PCR-like levels for zearalenone contamination based DNA barcode.},
journal = {Journal of the science of food and agriculture},
volume = {101},
number = {11},
pages = {4490-4497},
doi = {10.1002/jsfa.11089},
pmid = {33448409},
issn = {1097-0010},
support = {//Collaborative Innovation Center for Water Treatment Technology and Materials/ ; 31701687//National Natural Science Foundation of China/ ; 31700108//National Natural Science Foundation of China/ ; BK20170537//Natural Science Foundation of Jiangsu Province/ ; PAPD-2018-87//Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; 16JDG035//Senior Talent Scientific Research Initial Funding Project of Jiangsu University/ ; //Youth Talent Cultivation Program of Jiangsu University/ ; },
mesh = {DNA/chemistry/genetics ; DNA Barcoding, Taxonomic ; Food Contamination/analysis ; Gold/chemistry ; Metal Nanoparticles/chemistry ; Real-Time Polymerase Chain Reaction/instrumentation/*methods ; Sensitivity and Specificity ; Zearalenone/analysis/*genetics ; },
abstract = {BACKGROUND: The ultrasensitive monitoring strategy of zearalenone (ZEN) is essential and desirable for food safety and human health. In the present study, a coupling of gold nanoparticles-DNA barcode and direct competitive immunoassay-based real-time polymerase chain reaction signal amplification (RT-IPCR) for ZEN close to the sensitivity of PCR-like levels is described and evaluated.<br><br>RESULTS: The RT-IPCR benefited from the use of a DNA barcode and RT-PCR detection strategy, thus resulting in ultrasensitive and simple detection for ZEN. Under the optimal RT-IPCR, the linear range of detection was from 0.5 to 1000&#x2009;pg&#x2009;mL[-1] and the limit of detection was 0.5&#xa0;pg&#x2009;mL[-1] , which was 400-fold lower than the enzyme-linked immunosorbent assay. The detection procedure was simplified and the detection time was shortened. The specificity, accuracy and precision of the RT-IPCR confirmed a high performance. ZEN-positive contamination levels were from 0.056 to 152.12&#x2009;ng&#x2009;g[-1] by the RT-IPCR, which was demonstrated to be highly reliable by liquid chromatography-tandem mass spectrometry.<br><br>CONCLUSION: The proposed RT-IPCR could be used as an alternative for detecting ZEN with satisfactory ultrasensitivity, simplicity, low cost and high-throughput. The present study could provide a strategy for the ultrasensitive detection of the small molecule with a simple and practical approach, which has significant appeal and application prospects.},
}
@article {pmid33448375,
year = {2020},
author = {Emerson, BC and Jiménez-García, E and Suárez, D},
title = {Revealing community assembly through barcoding: Mediterranean butterflies and dispersal variation.},
journal = {The Journal of animal ecology},
volume = {89},
number = {9},
pages = {1992-1996},
doi = {10.1111/1365-2656.13316},
pmid = {33448375},
issn = {1365-2656},
mesh = {Africa, Northern ; Animals ; *Butterflies/genetics ; DNA, Mitochondrial/genetics ; Europe ; Genetic Variation ; Italy ; Phylogeny ; },
abstract = {In Focus: Scalercio, S., Cini, A., Menchetti, M., Vodă, R., Bonelli, S., Bordoni, A., … Dapporto, L. (2020). How long is 3 km for a butterfly? Ecological constraints and functional traits explain high mitochondrial genetic diversity between Sicily and the Italian Peninsula. Journal of Animal Ecology. https://doi.org/10.1111/1365-2656.13196. Biotic and abiotic factors can shape geographical patterns of genetic variation within species, but few studies have addressed how this might generate common patterns at the level of communities of species. Scalercio et al. (2020) have combined mtDNA sequence data and life-history traits, to reveal a repeated pattern of genetic structure between Sicilian and southern Italian butterfly populations, which are separated by only 3 km of ocean. They reveal how intrinsic species traits and extrinsic environmental constraints explain this pattern, demonstrating an important role for wind. Moreover, the inclusion of almost 8,000 georeferenced sequences reveals that, in spite of also being present in southern Italy, almost half of Sicilian butterfly species are more closely related to populations from other parts of Europe, Asia or North Africa. We provide further discussion on the biogeographic barrier they identify, and the potential of community-level DNA barcoding to identify processes that structure genetic variation across communities.},
}
@article {pmid33446865,
year = {2021},
author = {Li, H and Xiao, W and Tong, T and Li, Y and Zhang, M and Lin, X and Zou, X and Wu, Q and Guo, X},
title = {The specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {1424},
pmid = {33446865},
issn = {2045-2322},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Chloroplast/*genetics ; *Evolution, Molecular ; *Genes, Chloroplast ; *Genetic Variation ; Orchidaceae/*genetics ; },
abstract = {DNA barcoding is currently an effective and widely used tool that enables rapid and accurate identification of plant species. The Orchidaceae is the second largest family of flowering plants, with more than 700 genera and 20,000 species distributed nearly worldwide. The accurate identification of Orchids not only contributes to the safe utilization of these plants, but also it is essential to the protection and utilization of germplasm resources. In this study, the DNA barcoding of 4 chloroplast genes (matK, rbcL, ndhF and ycf1) were used to provide theoretical basis for species identification, germplasm conservation and innovative utilization of orchids. By comparing the nucleotide replacement saturation of the single or combined sequences among the 4 genes, we found that these sequences reached a saturation state and were suitable for phylogenetic relationship analysis. The phylogenetic analyses based on genetic distance indicated that ndhF and ycf1 sequences were competent to identification at genus and species level of orchids in a single gene. In the combined sequences, matK + ycf1 and ndhF + ycf1 were qualified for identification at the genera and species levels, suggesting the potential roles of ndhF, ycf1, matK + ycf1 and ndhF + ycf1 as candidate barcodes for orchids. Based on the SNP sites, candidate genes were used to obtain the specific barcode of orchid plant species and generated the corresponding DNA QR code ID card that could be immediately recognized by electronic devices. This study provides innovative research methods for efficient species identification of orchids. The standardized and accurate barcode information of Orchids is provided for researchers. It lays the foundation for the conservation, evaluation, innovative utilization and protection of Orchidaceae germplasm resources.},
}
@article {pmid33445185,
year = {2021},
author = {Handy, SM and Pawar, RS and Ottesen, AR and Ramachandran, P and Sagi, S and Zhang, N and Hsu, E and Erickson, DL},
title = {HPLC-UV, Metabarcoding and Genome Skims of Botanical Dietary Supplements: A Case Study in Echinacea.},
journal = {Planta medica},
volume = {87},
number = {4},
pages = {314-324},
doi = {10.1055/a-1336-1685},
pmid = {33445185},
issn = {1439-0221},
mesh = {Chromatography, High Pressure Liquid ; DNA Barcoding, Taxonomic ; Dietary Supplements/analysis ; *Echinacea ; *Genome, Chloroplast ; High-Throughput Nucleotide Sequencing ; },
abstract = {The use of DNA-based methods to authenticate botanical dietary supplements has been vigorously debated for a variety of reasons. More comparisons of DNA-based and chemical methods are needed, and concordant evaluation of orthogonal approaches on the same products will provide data to better understand the strengths and weaknesses of both approaches. The overall application of DNA-based methods is already firmly integrated into a wide array of continually modernizing stand alone and complementary authentication protocols. Recently, the use of full-length chloroplast genome sequences provided enhanced discriminatory capacity for closely related species of Echinacea compared to traditional DNA barcoding approaches (matK and rbcL). Here, two next-generation sequencing approaches were used: (1) genome skimming and (2) PCR amplicon (metabarcoding). The two genetic approaches were then combined with HPLC-UV to evaluate 20 commercially available dietary supplements of Echinacea representing "finished" products. The trade-offs involved in different DNA approaches were discussed, with a focus on how DNA methods support existing, accepted chemical methods. In most of the products (19/20), HPLC-UV suggested the presence of Echinacea spp. While metabarcoding was not useful with this genus and instead only resolved 7 products to the family level, genome skimming was able to resolve to species (9) or genus (1) with the 10/20 products where it was successful. Additional ingredients that HPLC-UV was unable to identify were also found in four products along with the relative sequence proportion of the constituents. Additionally, genome skimming was able to identify one product that was a different Echinacea species entirely.},
}
@article {pmid33441696,
year = {2021},
author = {Varotto, C and Pindo, M and Bertoni, E and Casarotto, C and Camin, F and Girardi, M and Maggi, V and Cristofori, A},
title = {A pilot study of eDNA metabarcoding to estimate plant biodiversity by an alpine glacier core (Adamello glacier, North Italy).},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {1208},
pmid = {33441696},
issn = {2045-2322},
mesh = {Biodiversity ; Climate Change ; DNA Barcoding, Taxonomic/methods ; DNA, Environmental/*genetics ; DNA, Plant/*genetics ; Ecosystem ; Environmental Monitoring/methods ; Ice Cover ; Italy ; Pilot Projects ; Plants/*genetics ; },
abstract = {Current biodiversity loss is a major concern and thus biodiversity assessment of modern ecosystems is compelling and needs to be contextualized on a longer timescale. High Throughput Sequencing (HTS) is progressively becoming a major source of data on biodiversity time series. In this multi proxy study, we tested, for the first time, the potential of HTS to estimate plant biodiversity archived in the surface layers of a temperate alpine glacier, amplifying the trnL barcode for vascular plants from eDNA of firn samples. A 573 cm long core was drilled by the Adamello glacier and cut into sections; produced samples were analyzed for physical properties, stable isotope ratio, and plant biodiversity by eDNA metabarcoding and conventional light microscopy analysis. Results highlighted the presence of pollen and plant remains within the distinct layers of snow, firn and ice. While stable isotope ratio showed a scarcely informative pattern, DNA metabarcoding described distinct plant species composition among the different samples, with a broad taxonomic representation of the biodiversity of the catchment area and a high-ranking resolution. New knowledge on climate and plant biodiversity changes of large catchment areas can be obtained by this novel approach, relevant for future estimates of climate change effects.},
}
@article {pmid33441647,
year = {2021},
author = {Hadj-Henni, L and Djerada, Z and Millot, C and Augot, D},
title = {Comprehensive characterisation of Culicoides clastrieri and C. festivipennis (Diptera: Ceratopogonidae) according to morphological and morphometric characters using a multivariate approach and DNA barcode.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {521},
pmid = {33441647},
issn = {2045-2322},
mesh = {Animals ; Ceratopogonidae/anatomy &amp; histology/classification/*genetics ; *DNA Barcoding, Taxonomic ; *Phylogeny ; Species Specificity ; },
abstract = {Biting midges are widespread around the world and play an essential role in the epidemiology of over 100 veterinary and medical diseases. For taxonomists, it is difficult to correctly identify species because of affinities among cryptic species and species complexes. In this study, species boundaries were examined for C. clastrieri and C. festivipennis and compared with six other Culicoides species. The classifiers are partial least squares discriminant analysis (PLS-DA) and sparse partial least squares discriminant analysis (sPLS-DA).The performance of the proposed method was evaluated using four models: (i) geometric morphometrics applied to wings; (ii) morphological wing characters, (iii) "Full wing" (landmarks and morphological characters) and (iv) "Full model" (morphological characters-wing, head, abdomen, legs-and wing landmarks). Double cross-validation procedures were used to validate the predictive ability of PLS-DA and sPLS-DA models. The AUC (area under the ROC curve) and the balanced error rate showed that the sPLS-DA model performs better than the PLS-DA model. Our final sPLS-DA analysis on the full wing and full model, with nine and seven components respectively, managed to perfectly classify our specimens. The C. clastrieri and C. festivipennis sequences, containing both COI and 28S genes, revealed our markers' weak discrimination power, with an intraspecific and interspecific divergence of 0.4% and 0.1% respectively. Moreover, C. clastrieri and C. festivipennis are grouped in the same clade. The morphology and wing patterns of C. clastrieri and C. festivipennis can be used to clearly distinguish them. Our study confirms C. clastrieri and C. festivipennis as two distinct species. Our results show that caution should be applied when relying solely on DNA barcodes for species identification or discovery.},
}
@article {pmid33441587,
year = {2021},
author = {Palumbo, F and Squartini, A and Barcaccia, G and Macolino, S and Pornaro, C and Pindo, M and Sturaro, E and Ramanzin, M},
title = {A multi-kingdom metabarcoding study on cattle grazing Alpine pastures discloses intra-seasonal shifts in plant selection and faecal microbiota.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {889},
pmid = {33441587},
issn = {2045-2322},
mesh = {Animal Nutritional Physiological Phenomena/physiology ; Animals ; Biodiversity ; Cattle ; DNA Barcoding, Taxonomic/*methods ; Diet/veterinary ; Feces/*microbiology ; Feeding Behavior/*physiology ; Female ; Gastrointestinal Microbiome/genetics ; Grassland ; Herbivory ; Lactation ; Livestock ; Microbiota/genetics ; Plant Breeding ; Plants/genetics ; Seasons ; },
abstract = {Diet selection by grazing livestock may affect animal performance as well as the biodiversity of grazed areas. Recent DNA barcoding techniques allow to assess dietary plant composition in faecal samples, which may be additionally integrated by the description of gut microbiota. In this high throughput metabarcoding study, we investigated the diversity of plant, fungal and bacterial taxa in faecal samples of lactating cows of two breeds grazing an Alpine semi-natural grassland during summer. The estimated plant composition of the diet comprised 67 genera and 39 species, which varied remarkably during summer, suggesting a decline of the diet forage value with the advancing of the vegetative season. The fungal community included Neocallimastigomycota gut symbionts, but also Ascomycota and Basidiomycota plant parasite and coprophilous taxa, likely ingested during grazing. The proportion of ingested fungi was remarkably higher than in other studies, and varied during summer, although less than that observed for plants. Some variation related to breed was also detected. The gut bacterial taxa remained stable through the summer but displayed a breed-specific composition. The study provided insights in the reciprocal organisms' interactions affecting, and being affected by, the foraging behaviour: plants showed a high temporal variation, fungi a smaller one, while bacteria had practically none; conversely, the same kingdoms showed the opposite gradient of variation as respect to the animal host breed, as bacteria revealed to be the group mostly characterized by host-specificity.},
}
@article {pmid33437429,
year = {2021},
author = {Liu, M and Shoukouhi, P and Bisson, KR and Wyka, SA and Broders, KD and Menzies, JG},
title = {Sympatric divergence of the ergot fungus, Claviceps purpurea, populations infecting agricultural and nonagricultural grasses in North America.},
journal = {Ecology and evolution},
volume = {11},
number = {1},
pages = {273-293},
pmid = {33437429},
issn = {2045-7758},
abstract = {The ergot diseases of agricultural and nonagricultural grasses are caused by the infection of Claviceps spp. (Hypocreales, Ascomycota) on florets, producing dark spur-like sclerotia on spikes that are toxic to humans and animals, leading to detrimental impacts on agriculture and economy due to the downgrading of cereal grains, import-export barriers, reduced yield, and ecological concerns. At least seven phylogenetic lineages (phylogenetic species) were identified within the premolecular concept of C. purpurea s.l. (sensu lato) in agricultural areas and vicinities in Canada and the Western United States. Claviceps purpurea s.s (sensu stricto) remained as the most prevalent species with a wide host range, including cereal crops, native, invasive, and weedy grasses. The knowledge on genetic diversity and distribution of C. purpurea s.s. in North America is lacking. The objective of the present study was to shed light on genetic differentiation and evolution of the natural populations of C. purpurea s.s. Multilocus DNA sequences of samples from Canada and the Western USA were analyzed using a phylogenetic network approach, and population demographic parameters were investigated. Results showed that three distinct genetically subdivided populations exist, and the subdivision is not correlated with geographic or host differentiations. Potential intrinsic mechanisms that might play roles in leading to the cessation of gene flows among the subpopulations, that is, mating and/or vegetative incompatibility, genomic adaptation, were discussed. The neutrality of two house-keeping genes that are widely used for DNA barcoding, that is, translation elongation factor 1-α (TEF1-α) and RNA polymerase II second largest subunit (RPB2), was challenged and discussed.},
}
@article {pmid33437054,
year = {2021},
author = {De Luca, D and Kooistra, WHCF and Sarno, D and Biffali, E and Piredda, R},
title = {Empirical evidence for concerted evolution in the 18S rDNA region of the planktonic diatom genus Chaetoceros.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {807},
pmid = {33437054},
issn = {2045-2322},
mesh = {DNA, Ribosomal/*genetics ; DNA, Ribosomal Spacer/genetics ; Diatoms/*genetics ; Evolution, Molecular ; Genetic Variation ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; },
abstract = {Concerted evolution is a process of homogenisation of repetitive sequences within a genome through unequal crossing over and gene conversion. This homogenisation is never fully achieved because mutations always create new variants. Classically, concerted evolution has been detected as "noise" in electropherograms and these variants have been characterised through cloning and sequencing of subsamples of amplified products. However, this approach limits the number of detectable variants and provides no information about the abundance of each variant. In this study, we investigated concerted evolution by using environmental time-series metabarcoding data, single strain high-throughput sequencing (HTS) and a collection of Sanger reference barcode sequences. We used six species of the marine planktonic diatom genus Chaetoceros as study system. Abundance plots obtained from environmental metabarcoding and single strain HTS showed the presence of a haplotype far more abundant than all the others (the "dominant" haplotype) and identical to the reference sequences of that species obtained with Sanger sequencing. This distribution fitted best with Zipf's law among the rank abundance/ dominance models tested. Furthermore, in each strain 99% of reads showed a similarity of 99% with the dominant haplotype, confirming the efficiency of the homogenisation mechanism of concerted evolution. We also demonstrated that minor haplotypes found in the environmental samples are not only technical artefacts, but mostly intragenomic variation generated by incomplete homogenisation. Finally, we showed that concerted evolution can be visualised inferring phylogenetic networks from environmental data. In conclusion, our study provides an important contribution to the understanding of concerted evolution and to the interpretation of DNA barcoding and metabarcoding data based on multigene family markers.},
}
@article {pmid33435339,
year = {2021},
author = {Bielecka, M and Pencakowski, B and Stafiniak, M and Jakubowski, K and Rahimmalek, M and Gharibi, S and Matkowski, A and Ślusarczyk, S},
title = {Metabolomics and DNA-Based Authentication of Two Traditional Asian Medicinal and Aromatic Species of Salvia subg. Perovskia.},
journal = {Cells},
volume = {10},
number = {1},
pages = {},
pmid = {33435339},
issn = {2073-4409},
mesh = {Asia ; Base Sequence ; DNA, Plant/*metabolism ; Likelihood Functions ; *Medicine, Traditional ; *Metabolomics ; Phylogeny ; Plant Extracts/metabolism ; Plant Leaves/metabolism ; Plant Roots/metabolism ; Principal Component Analysis ; Salvia/genetics/*metabolism ; Species Specificity ; },
abstract = {Subgenus Perovskia of the extended genus of Salvia comprises several Central Asian medicinal and aromatic species, of which S. yangii and S. abrotanoides are the most widespread. These plants are cultivated in Europe as robust ornamentals, and several cultivars are available. However, their medicinal potential remains underutilized because of limited information about their phytochemical and genetic diversity. Thus, we combined an ultra-high performance liquid chromatography quadrupole time of flight mass spectrometry (UHPLC-QTOF-MS) based metabolomics with DNA barcoding approach based on trnH-psbA and ITS2 barcodes to clarify the relationships between these two taxa. Metabolomic analysis demonstrated that aerial parts are more similar than roots and none of the major compounds stand out as distinct. Sugiol in S. yangii leaves and carnosic acid quinone in S. abrotanoides were mostly responsible for their chemical differentiation, whereas in roots the distinction was supported by the presence of five norditerpenoids in S. yangii and two flavonoids and one norditerpenoid in S. abrotanoides. To verify the metabolomics-based differentiation, we performed DNA authentication that revealed S. yangii and S. abrotanoides to be very closely related but separate species. We demonstrated that DNA barcoding coupled with parallel LC-MS profiling constitutes a powerful tool in identification of taxonomically close Salvia species.},
}
@article {pmid33434383,
year = {2021},
author = {Vernette, C and Henry, N and Lecubin, J and de Vargas, C and Hingamp, P and Lescot, M},
title = {The Ocean barcode atlas: A web service to explore the biodiversity and biogeography of marine organisms.},
journal = {Molecular ecology resources},
volume = {21},
number = {4},
pages = {1347-1358},
doi = {10.1111/1755-0998.13322},
pmid = {33434383},
issn = {1755-0998},
support = {ANR-11-BTBR-0008//French Government 'Investissements d'Avenir' programmes OCEANOMICS/ ; ANR-10-INBS-09-08//FRANCE GENOMIQUE/ ; ANR-11-INBS-0013//Institut Fran&#xe7;ais de Bioinformatique (IFB)/ ; ANR-10-LABX-54//MEMO LIFE/ ; ANR-11-IDEX-0001-02//PSL* Research University/ ; ANR-19-CE45-0008//ANR SeqDigger/ ; },
mesh = {*Aquatic Organisms/classification ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Data Visualization ; Internet ; Oceans and Seas ; Plankton ; RNA, Ribosomal, 18S ; Software ; },
abstract = {The Ocean Barcode Atlas (OBA) is a user friendly web service designed for biologists who wish to explore the biodiversity and biogeography of marine organisms locked in otherwise difficult to mine planetary scale DNA metabarcode data sets. Using just a web browser, a comprehensive picture of the diversity of a taxon or a barcode sequence is visualized graphically on world maps and interactive charts. Interactive results panels allow dynamic threshold adjustments and the display of diversity results in their environmental context measured at the time of sampling (temperature, oxygen, latitude, etc). Ecological analyses such as alpha and beta-diversity plots are produced via publication quality vector graphics representations. Currently, the Ocean Barcode Altas is deployed online with the (i) Tara Oceans eukaryotic 18S-V9 rDNA metabarcodes; (ii) Tara Oceans 16S/18S rRNA mi Tags; and (iii) 16S-V4 V5 metabarcodes collected during the Malaspina-2010 expedition. Additional prokaryotic or eukaryotic plankton barcode data sets will be added upon availability, given they provide the required complement of barcodes (including raw reads to compute barcode abundance) associated with their contextual environmental variables. Ocean Barcode Atlas is a freely-available web service at: http://oba.mio.osupytheas.fr/ocean-atlas/.},
}
@article {pmid33432352,
year = {2021},
author = {Alfonso-Toledo, JA and Paredes-León, R},
title = {Molecular and Morphological Identification of Dermanyssoid Mites (Parasitiformes: Mesostigmata: Dermanyssoidea) Causatives of a Parasitic Outbreak on Captive Snakes.},
journal = {Journal of medical entomology},
volume = {58},
number = {1},
pages = {246-251},
doi = {10.1093/jme/tjaa164},
pmid = {33432352},
issn = {1938-2928},
mesh = {Animals ; Disease Outbreaks/*veterinary ; Mexico/epidemiology ; Mite Infestations/classification/epidemiology/parasitology/*veterinary ; Mites/anatomy &amp; histology/*classification/genetics/physiology ; *Snakes ; },
abstract = {A parasitic outbreak caused by dermanyssoid mites in a herpetarium of the Metropolitan area of the Valley of Mexico is revealed. This outbreak was caused by Hemilaelaps triangulus (Ewing), but a second mite species, Ophionyssus natricis (Gervais), was found in low abundance. The parasitic load is analyzed, and the morphological and molecular diagnostic characters to identify each of the two species involved are given. A barcode analysis is presented, and two more molecular markers are presented and analyzed. Hemilaelaps triangulus is recorded for the first time in Mexico, and this is the first record of massive infestation on captive snakes caused by ixodorhynchid mites, and DNA sequences of ixodorhynchid mites are publicly available for the first time.},
}
@article {pmid33431855,
year = {2021},
author = {Oki, T and Mercier, F and Kato, H and Jung, Y and McDonald, TO and Spencer, JA and Mazzola, MC and van Gastel, N and Lin, CP and Michor, F and Kitamura, T and Scadden, DT},
title = {Imaging dynamic mTORC1 pathway activity in vivo reveals marked shifts that support time-specific inhibitor therapy in AML.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {245},
pmid = {33431855},
issn = {2041-1723},
support = {R01 CA194596/CA/NCI NIH HHS/United States ; U54 CA193461/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Apoptosis Regulatory Proteins/metabolism ; Cell Line, Tumor ; Disease Progression ; Down-Regulation ; Drug Resistance, Neoplasm/genetics ; Gene Expression Regulation, Leukemic ; Leukemia, Myeloid, Acute/*drug therapy/genetics/pathology ; Mechanistic Target of Rapamycin Complex 1/*antagonists &amp; inhibitors/metabolism ; Mice ; Models, Biological ; NIH 3T3 Cells ; RNA-Binding Proteins/metabolism ; Signal Transduction ; Transcriptome/genetics ; Treatment Outcome ; },
abstract = {Acute myeloid leukemia (AML) is a high remission, high relapse fatal blood cancer. Although mTORC1 is a master regulator of cell proliferation and survival, its inhibitors have not performed well as AML treatments. To uncover the dynamics of mTORC1 activity in vivo, fluorescent probes are developed to track single cell proliferation, apoptosis and mTORC1 activity of AML cells in the bone marrow of live animals and to quantify these activities in the context of microanatomical localization and intra-tumoral heterogeneity. When chemotherapy drugs commonly used clinically are given to mice with AML, apoptosis is rapid, diffuse and not preferentially restricted to anatomic sites. Dynamic measurement of mTORC1 activity indicated a decline in mTORC1 activity with AML progression. However, at the time of maximal chemotherapy response, mTORC1 signaling is high and positively correlated with a leukemia stemness transcriptional profile. Cell barcoding reveals the induction of mTORC1 activity rather than selection of mTORC1 high cells and timed inhibition of mTORC1 improved the killing of AML cells. These data define the real-time dynamics of AML and the mTORC1 pathway in association with AML growth, response to and relapse after chemotherapy. They provide guidance for timed intervention with pathway-specific inhibitors.},
}
@article {pmid33429942,
year = {2021},
author = {Tanruean, K and Poolprasert, P and Suwannarach, N and Kumla, J and Lumyong, S},
title = {Phytochemical Analysis and Evaluation of Antioxidant and Biological Activities of Extracts from Three Clauseneae Plants in Northern Thailand.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {1},
pages = {},
pmid = {33429942},
issn = {2223-7747},
abstract = {This study established the DNA barcoding sequences (matK and rbcL) of three plant species identified in the tribe Clauseneae, namely Clausena excavata, C. harmandiana and Murraya koenigii. The total phenolic and total flavonoid contents, together with the biological activities of the derived essential oils and methanol extracts, were also investigated. Herein, the success of obtaining sequences of these plant using two different barcode genes matK and rbcL were 62.5% and 100%, respectively. Both regions were discriminated by around 700 base pairs and these had resemblance with those of the Clausenae materials earlier deposited in Genbank at a 99-100% degree of identity. Additionally, the use of matK DNA sequences could positively confirm the identity as monophyletic. The highest total phenolic and total flavonoid content values (p < 0.05) were observed in the methanol extract of M. koenigii at 43.50 mg GAE/g extract and 66.13 mg QE/g extract, respectively. Furthermore, anethole was detected as the dominant compound in C. excavata (86.72%) and C. harmandiana (46.09%). Moreover, anethole (26.02%) and caryophyllene (21.15%) were identified as the major phytochemical compounds of M. koenigii. In terms of the biological properties, the M. koenigii methanol extract was found to display the greatest amount of antioxidant activity (DPPH; IC50 95.54 µg/mL, ABTS value 118.12 mg GAE/g extract, FRAP value 48.15 mg GAE/g extract), and also revealed the highest α-glucosidase and antihypertensive inhibitory activities with percent inhibition values of 84.55 and 84.95. Notably, no adverse effects on human peripheral blood mononuclear cells were observed with regard to all of the plant extracts. Furthermore, M. koenigii methanol extract exhibited promise against human lung cancer cells almost at 80% after 24 h and 90% over 48 h.},
}
@article {pmid33429137,
year = {2021},
author = {Woerner, AE and Mandape, S and King, JL and Muenzler, M and Crysup, B and Budowle, B},
title = {Reducing noise and stutter in short tandem repeat loci with unique molecular identifiers.},
journal = {Forensic science international. Genetics},
volume = {51},
number = {},
pages = {102459},
doi = {10.1016/j.fsigen.2020.102459},
pmid = {33429137},
issn = {1878-0326},
mesh = {DNA Fingerprinting ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Microsatellite Repeats ; Sequence Analysis, DNA/*methods ; },
abstract = {Unique molecular identifiers (UMIs) are a promising approach to contend with errors generated during PCR and massively parallel sequencing (MPS). With UMI technology, random molecular barcodes are ligated to template DNA molecules prior to PCR, allowing PCR and sequencing error to be tracked and corrected bioinformatically. UMIs have the potential to be particularly informative for the interpretation of short tandem repeats (STRs). Traditional MPS approaches may simply lead to the observation of alleles that are consistent with the hypotheses of stutter, while with UMIs stutter products bioinformatically may be re-associated with their parental alleles and subsequently removed. Herein, a bioinformatics pipeline named strumi is described that is designed for the analysis of STRs that are tagged with UMIs. Unlike other tools, strumi is an alignment-free machine learning driven algorithm that clusters individual MPS reads into UMI families, infers consensus super-reads that represent each family and provides an estimate the resulting haplotype's accuracy. Super-reads, in turn, approximate independent measurements not of the PCR products, but of the original template molecules, both in terms of quantity and sequence identity. Provisional assessments show that naïve threshold-based approaches generate super-reads that are accurate (∼97 % haplotype accuracy, compared to ∼78 % when UMIs are not used), and the application of a more nuanced machine learning approach increases the accuracy to ∼99.5 % depending on the level of certainty desired. With these features, UMIs may greatly simplify probabilistic genotyping systems and reduce uncertainty. However, the ability to interpret alleles at trace levels also permits the interpretation, characterization and quantification of contamination as well as somatic variation (including somatic stutter), which may present newfound challenges.},
}
@article {pmid33425245,
year = {2021},
author = {Lopez Leyva, L and Brereton, NJB and Koski, KG},
title = {Emerging frontiers in human milk microbiome research and suggested primers for 16S rRNA gene analysis.},
journal = {Computational and structural biotechnology journal},
volume = {19},
number = {},
pages = {121-133},
pmid = {33425245},
issn = {2001-0370},
abstract = {Human milk is the ideal food for infants due to its unique nutritional and immune properties, and more recently human milk has also been recognized as an important source of bacteria for infants. However, a substantial amount of fundamental human milk microbiome information remains unclear, such as the origin, composition and function of the community and its members. There is emerging evidence to suggest that the diversity and composition of the milk microbiome might differ between lactation stages, due to maternal factors and diet, agrarian and urban lifestyles, and geographical location. The evolution of the methods used for studying milk microbiota, transitioning from culture dependent-approaches to include culture-independent approaches, has had an impact on findings and, in particular, primer selection within 16S rRNA gene barcoding studies have led to discrepancies in observed microbiota communities. Here, the current state-of-the-art is reviewed and emerging frontiers essential to improving our understanding of the human milk microbiome are considered.},
}
@article {pmid33424154,
year = {2020},
author = {Sherif, NA and Senthil Kumar, T and Rao, MV},
title = {DNA barcoding and genetic fidelity assessment of micropropagated Aenhenrya rotundifolia (Blatt.) C.S. Kumar and F.N. Rasm.: a critically endangered jewel orchid.},
journal = {Physiology and molecular biology of plants : an international journal of functional plant biology},
volume = {26},
number = {12},
pages = {2391-2405},
pmid = {33424154},
issn = {0971-5894},
abstract = {Aenhenrya rotundifolia is a critically endangered terrestrial jewel orchid. It is monotypic and endemic to evergreen forests of southern western ghats of India. In the present study, identification of this plant species is validated with DNA barcoding using matK and rbcL chloroplast markers. Further, germ-free juvenile axillary bud explants were cultured on Mitra medium supplemented with different kinds of cytokinins like 6-benzyladenine, 6-furfurylaminopurine, N[6]-(Δ[2]-isopentyl) adenine, thidiazuron, zeatin and meta-topolin as well as auxins such as α-naphthaleneacetic acid, indole-3-acetic acid and indole-3-butyric acid at different concentrations and combinations for successful proliferation and establishment in vitro. After 12 weeks of culture, axillary bud explants produced an average of 30.12 ± 0.71 shoots per explant, 3.87 ± 0.06 cm shoot length, 1671 ± 2.82 mg fresh mass of proliferated shoots with a proliferation frequency of 100% on Mitra medium supplemented with 6.20 µM meta-topolin and 2.25 µM thidiazuron. No root formation was observed in in vitro proliferated microshoots. However, tiny hair like projections were observed in some elongated shoots on Mitra medium pertaining to 5.37 µM NAA. The tiny hair like structure bearing plantlets were hardened and acclimatized with 100% survival rate in the polytunnel chamber. After 8-10 months of establishment ex vitro, flowering was observed. Additionally, the genetic fidelity of in vitro derived plants was tested with ISSR and SCoT marker profiling. The test results revealed that the plants derived from the protocol has 99% genetic similarity to that of the donor mother plant. This study can be applied in forensic interventions of this species, describes the maintenance of germplasm in vitro and establishment of new viable population in its original habitats by restoring existing sites of this critically endangered jewel orchid.},
}
@article {pmid33421259,
year = {2021},
author = {Drahun, I and Wiebe, KF and Koloski, CW and van Herk, WG and Cassone, BJ},
title = {Genetic structure and population demographics of Hypnoidus bicolor (Coleoptera: Elateridae) in the Canadian Prairies.},
journal = {Pest management science},
volume = {77},
number = {5},
pages = {2282-2291},
doi = {10.1002/ps.6255},
pmid = {33421259},
issn = {1526-4998},
support = {#1000210140//Manitoba Pulse &amp; Soybean Growers, Western Grain Research Foundation and Canadian Agricultural Partnership/ ; },
mesh = {Animals ; Canada ; *Coleoptera/genetics ; Demography ; Asia, Eastern ; Genetic Structures ; Grassland ; },
abstract = {BACKGROUND: Following banning of the pesticide lindane in most counties, wireworms (i.e., the soil-living larval stages of click beetles) have become major pests of a variety of economically important field crops. Hypnoidus bicolor is a common pest species in the Canadian Prairies. However, little is known about its life history, which impedes the development of effective integrated pest management (IPM) strategies. Population genetic approaches have the potential to assist in the development of IPM.<br><br>RESULTS: We sequenced a 622-bp fragment of the COX1 gene from 326 H. bicolor wireworm and click beetles collected from 13 localities on the Canadian Prairies. Two genetically distinct (>4.66% sequence divergence) clades were identified, suggesting that they may be part of a species complex. Clade A predominated and increased in prevalence the further east samples were collected, whereas the opposite was true for clade B. Clade B appears to be comprised of two mitochondrial DNA groups, however, one group was represented by only one haplotype. Both clades were characterized by uneven gene flow among populations with low levels of regional genetic structuring. Clade A appeared to have undergone population and range expansions, which may coincide with the advent of intensive agriculture practices in the prairies.<br><br>CONCLUSION: Knowledge of species composition and population structure is important for the development of effective IPM strategies but is often lacking for wireworms. Our study fills these knowledge gaps for a predominant pest species in the prairies, H. bicolor, by providing robust evidence for cryptic forms and characterizing its dispersal patterns and population dynamics. &#xa9; 2021 Society of Chemical Industry.},
}
@article {pmid33419206,
year = {2021},
author = {Antonetti, M and Nin, S and Burchi, G and Biricolti, S and Gori, M},
title = {Himantoglossum adriaticum H. Baumann × Himantoglossum robertianum (Loisel.) P. Delforge: A New Interspecific Hybrid Assessed by Barcoding Analysis.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {1},
pages = {},
pmid = {33419206},
issn = {2223-7747},
support = {DM 20380, 17.7.2017 and DM 9037962, 03.08.2020//MiPAAF (Italian Ministry of Agricultural, Food and Forestry Policies)/ ; },
abstract = {Most cultivated orchids, contributing to a worldwide highly profitable industry, are originated from tropic regions. Conversely, a considerable number of spontaneous orchids, belonging to the terrestrial orchids and widely diffused throughout the European continent, are not considered for trading due to their less gorgeous appearance and for technical difficulties in seed propagation. However, a breeding programme was undertaken aimed at developing a new hybrid between Himantoglossum adriaticum H. Baumann and H. robertianum (Loisel.) P. Delforge [syn. Barlia robertiana (Loisel.) Greuter] by applying techniques of anther conservation, manual pollination and in vitro asymbiotic germination of the obtained seeds. The plantlets that originated from the protocorms after seed germination were successfully acclimatised after potting in a proper medium. The parentage of the progenies of the hybridisation experiment was assessed by sequencing the Internal Transcribed Spacer assembly (ITS) and plastid barcoding markers of the parental lines and of the hybrids. The method proved to be effective in revealing the origin of the hybrids and to validate the maternal inheritance of the plastid DNA.},
}
@article {pmid33418885,
year = {2021},
author = {Borland, EM and Kading, RC},
title = {Modernizing the Toolkit for Arthropod Bloodmeal Identification.},
journal = {Insects},
volume = {12},
number = {1},
pages = {},
pmid = {33418885},
issn = {2075-4450},
abstract = {Understanding vertebrate-vector interactions is vitally important for understanding the transmission dynamics of arthropod-vectored pathogens and depends on the ability to accurately identify the vertebrate source of blood-engorged arthropods in field collections using molecular methods. A decade ago, molecular techniques being applied to arthropod blood meal identification were thoroughly reviewed, but there have been significant advancements in the techniques and technologies available since that time. This review highlights the available diagnostic markers in mitochondrial and nuclear DNA and discusses their benefits and shortcomings for use in molecular identification assays. Advances in real-time PCR, high resolution melting analysis, digital PCR, next generation sequencing, microsphere assays, mass spectrometry, and stable isotope analysis each offer novel approaches and advantages to bloodmeal analysis that have gained traction in the field. New, field-forward technologies and platforms have also come into use that offer promising solutions for point-of-care and remote field deployment for rapid bloodmeal source identification. Some of the lessons learned over the last decade, particularly in the fields of DNA barcoding and sequence analysis, are discussed. Though many advancements have been made, technical challenges remain concerning the prevention of sample degradation both by the arthropod before the sample has been obtained and during storage. This review provides a roadmap and guide for those considering modern techniques for arthropod bloodmeal identification and reviews how advances in molecular technology over the past decade have been applied in this unique biomedical context.},
}
@article {pmid33417860,
year = {2021},
author = {Rehman, SK and Haynes, J and Collignon, E and Brown, KR and Wang, Y and Nixon, AML and Bruce, JP and Wintersinger, JA and Singh Mer, A and Lo, EBL and Leung, C and Lima-Fernandes, E and Pedley, NM and Soares, F and McGibbon, S and He, HH and Pollet, A and Pugh, TJ and Haibe-Kains, B and Morris, Q and Ramalho-Santos, M and Goyal, S and Moffat, J and O'Brien, CA},
title = {Colorectal Cancer Cells Enter a Diapause-like DTP State to Survive Chemotherapy.},
journal = {Cell},
volume = {184},
number = {1},
pages = {226-242.e21},
pmid = {33417860},
issn = {1097-4172},
support = {FDN-148479//CIHR/Canada ; R01 CA148761/CA/NCI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; MOP-142375//CIHR/Canada ; 420231//CIHR/Canada ; },
mesh = {Animals ; Antineoplastic Agents/pharmacology/*therapeutic use ; Autophagy/drug effects/genetics ; Cell Line, Tumor ; Clone Cells ; Colorectal Neoplasms/*drug therapy/genetics/pathology ; *Diapause ; *Drug Resistance, Neoplasm/drug effects ; Embryo, Mammalian/drug effects/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic/drug effects ; Genetic Heterogeneity/drug effects ; Humans ; Irinotecan/pharmacology/therapeutic use ; Mice, Inbred NOD ; Mice, SCID ; Models, Biological ; Signal Transduction/drug effects ; Up-Regulation/drug effects/genetics ; Xenograft Model Antitumor Assays ; Mice ; },
abstract = {Cancer cells enter a reversible drug-tolerant persister (DTP) state to evade death from chemotherapy and targeted agents. It is increasingly appreciated that DTPs are important drivers of therapy failure and tumor relapse. We combined cellular barcoding and mathematical modeling in patient-derived colorectal cancer models to identify and characterize DTPs in response to chemotherapy. Barcode analysis revealed no loss of clonal complexity of tumors that entered the DTP state and recurred following treatment cessation. Our data fit a mathematical model where all cancer cells, and not a small subpopulation, possess an equipotent capacity to become DTPs. Mechanistically, we determined that DTPs display remarkable transcriptional and functional similarities to diapause, a reversible state of suspended embryonic development triggered by unfavorable environmental conditions. Our study provides insight into how cancer cells use a developmentally conserved mechanism to drive the DTP state, pointing to novel therapeutic opportunities to target DTPs.},
}
@article {pmid33413130,
year = {2021},
author = {Li, J and Tang, J and Zeng, S and Han, F and Yuan, J and Yu, J},
title = {Comparative plastid genomics of four Pilea (Urticaceae) species: insight into interspecific plastid genome diversity in Pilea.},
journal = {BMC plant biology},
volume = {21},
number = {1},
pages = {25},
pmid = {33413130},
issn = {1471-2229},
support = {31772260//National Natural Science Foundation of China/ ; cx2019052//Chongqing Study Abroad Innovation Project/ ; },
mesh = {China ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Plant ; *Genome, Plastid ; Phylogeny ; Plants, Medicinal/*genetics ; Sequence Analysis, DNA ; Urticaceae/*genetics ; },
abstract = {BACKGROUND: Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis, Pilea glauca 'Greizy', Pilea peperomioides and Pilea serpyllacea 'Globosa') and performed comprehensive comparative analysis.<br><br>RESULTS: The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398&#x2009;bp to 152,327&#x2009;bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified (petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae.<br><br>CONCLUSION: Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.},
}
@article {pmid33410911,
year = {2021},
author = {Tompkins, KJ and Houtti, M and Litzau, LA and Aird, EJ and Everett, BA and Nelson, AT and Pornschloegl, L and Limón-Swanson, LK and Evans, RL and Evans, K and Shi, K and Aihara, H and Gordon, WR},
title = {Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering.},
journal = {Nucleic acids research},
volume = {49},
number = {2},
pages = {1046-1064},
pmid = {33410911},
issn = {1362-4962},
support = {T32 GM008347/GM/NIGMS NIH HHS/United States ; T32 AR007612/AR/NIAMS NIH HHS/United States ; P30 GM124165/GM/NIGMS NIH HHS/United States ; R35 GM119483/GM/NIGMS NIH HHS/United States ; R35 GM118047/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Circoviridae/enzymology ; Conserved Sequence ; Crystallography, X-Ray ; DNA Helicases/chemistry/*metabolism ; DNA, Single-Stranded/chemistry/*metabolism ; Deoxyribonuclease I/chemistry/*metabolism ; Gene Library ; Models, Molecular ; Molecular Docking Simulation ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Plant Viruses/enzymology ; Protein Binding ; *Protein Conformation ; Protein Engineering/*methods ; Recombinant Fusion Proteins/chemistry/metabolism ; Replication Origin ; Sequence Alignment ; Sequence Homology, Amino Acid ; Single-Strand Specific DNA and RNA Endonucleases/chemistry/*metabolism ; Substrate Specificity ; Trans-Activators/chemistry/*metabolism ; Viral Proteins/chemistry/*metabolism ; },
abstract = {Replication initiator proteins (Reps) from the HUH-endonuclease superfamily process specific single-stranded DNA (ssDNA) sequences to initiate rolling circle/hairpin replication in viruses, such as crop ravaging geminiviruses and human disease causing parvoviruses. In biotechnology contexts, Reps are the basis for HUH-tag bioconjugation and a critical adeno-associated virus genome integration tool. We solved the first co-crystal structures of Reps complexed to ssDNA, revealing a key motif for conferring sequence specificity and for anchoring a bent DNA architecture. In combination, we developed a deep sequencing cleavage assay, termed HUH-seq, to interrogate subtleties in Rep specificity and demonstrate how differences can be exploited for multiplexed HUH-tagging. Together, our insights allowed engineering of only four amino acids in a Rep chimera to predictably alter sequence specificity. These results have important implications for modulating viral infections, developing Rep-based genomic integration tools, and enabling massively parallel HUH-tag barcoding and bioconjugation applications.},
}
@article {pmid33410308,
year = {2021},
author = {Pardo-Seco, J and Gómez-Carballa, A and Bello, X and Martinón-Torres, F and Salas, A},
title = {Pitfalls of barcodes in the study of worldwide SARS-CoV-2 variation and phylodynamics.},
journal = {Zoological research},
volume = {42},
number = {1},
pages = {87-93},
pmid = {33410308},
issn = {2095-8137},
mesh = {Algorithms ; COVID-19/*virology ; DNA Barcoding, Taxonomic ; Genetic Variation ; Genome, Viral ; Humans ; Mutation ; Phylogeny ; Phylogeography ; SARS-CoV-2/*classification/*genetics/isolation &amp; purification ; },
abstract = {Analysis of SARS-CoV-2 genome variation using a minimal number of selected informative sites conforming a genetic barcode presents several drawbacks. We show that purely mathematical procedures for site selection should be supervised by known phylogeny (i) to ensure that solid tree branches are represented instead of mutational hotspots with poor phylogeographic proprieties, and (ii) to avoid phylogenetic redundancy. We propose a procedure that prevents information redundancy in site selection by considering the cumulative informativeness of previously selected sites (as a proxy for phylogenetic-based criteria). This procedure demonstrates that, for short barcodes (e.g., 11 sites), there are thousands of informative site combinations that improve previous proposals. We also show that barcodes based on worldwide databases inevitably prioritize variants located at the basal nodes of the phylogeny, such that most representative genomes in these ancestral nodes are no longer in circulation. Consequently, coronavirus phylodynamics cannot be properly captured by universal genomic barcodes because most SARS-CoV-2 variation is generated in geographically restricted areas by the continuous introduction of domestic variants.},
}
@article {pmid33408400,
year = {2021},
author = {Tang, L},
title = {Multiomics sequencing goes spatial.},
journal = {Nature methods},
volume = {18},
number = {1},
pages = {31},
pmid = {33408400},
issn = {1548-7105},
mesh = {Gene Expression ; *Gene Expression Profiling ; Sequence Analysis ; },
abstract = {Microfluidic channels provide a means to deliver barcodes encoding spatial information to a tissue, which allows co-profiling of gene expression and proteins of interest in a spatially resolved manner.},
}
@article {pmid33403773,
year = {2021},
author = {Victorious, A and Saha, S and Pandey, R and Soleymani, L},
title = {Enhancing the Sensitivity of Photoelectrochemical DNA Biosensing Using Plasmonic DNA Barcodes and Differential Signal Readout.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {60},
number = {13},
pages = {7316-7322},
doi = {10.1002/anie.202014329},
pmid = {33403773},
issn = {1521-3773},
mesh = {*Biosensing Techniques ; DNA/*analysis ; *DNA Barcoding, Taxonomic ; *Electrochemical Techniques ; Photochemical Processes ; },
abstract = {Photoelectrochemical biosensors hold great promise for sensitive bioanalysis; however, similar to their electrochemical analogues, they are highly affected by the variable backgrounds caused by biological matrices. We developed a new PEC biosensing strategy that uses differential signal generation, combining signals from two separate but correlated binding events on the biosensor, for improving the limit-of-detection, sensitivity, and specificity of PEC DNA biosensors in biological samples. In this assay, the binding of unlabeled target DNA is followed by the capture of a signal amplification barcode featuring a plasmonic nanoparticle. The interaction of the plasmonic barcode with the semiconductive building blocks of the biosensor results in significant signal amplification, and together with differential signal processing enhances the limit of detection and sensitivity of the assay by up to 15- and three-fold, respectively, compared to the previously-used PEC assays with a single binding event, demonstrating a limit of detection of 3 fM.},
}
@article {pmid33401907,
year = {2021},
author = {Chen, C and Ding, Y and Wang, Y and Jiang, Q and Wang, F and Lu, C and Zhang, L and Zhu, C},
title = {High-Resolution Melting Analysis of COI Sequences Distinguishes Pufferfish Species (Takifugu spp.) in China.},
journal = {Journal of agricultural and food chemistry},
volume = {69},
number = {2},
pages = {794-804},
doi = {10.1021/acs.jafc.0c06584},
pmid = {33401907},
issn = {1520-5118},
mesh = {Animals ; China ; DNA/chemistry/*genetics ; Discriminant Analysis ; Electron Transport Complex IV/*genetics ; Fish Proteins/*genetics ; *Genetic Techniques ; Takifugu/classification/*genetics ; Transition Temperature ; },
abstract = {Pufferfish is a traditional, delicious dish in Asia. However, eating wild or improperly processed pufferfish causes serious poisoning. This study aimed to exploit the high-resolution melting (HRM) method for authenticating four species of Takifugu pufferfish (Takifugu xanthopterus, T. fasciatus, T. flavidus, and T. rubripes). Candidate DNA barcodes, including the cytochrome c oxidase subunit I (COI), cytochrome oxidase b (Cytb), and the control region (D-loop), were analyzed, with COI selected as the optimal DNA barcode. An HRM method was developed to identify 57 commercial fish samples in China, including 33 commercial pufferfish products and 24 unlabeled fish products. The findings revealed that the pufferfish products were T. rubripes or T. fasciatus, and four T. xanthopterus samples were detected in unlabeled fish products. These results showed that DNA barcode coupled with HRM analysis was a rapid and efficient tool to identify pufferfish, which might aid in the prevention of consumer fraud or mislabeling of fish products.},
}
@article {pmid33401773,
year = {2021},
author = {Neto, L and Pinto, N and Proença, A and Amorim, A and Conde-Sousa, E},
title = {4SpecID: Reference DNA Libraries Auditing and Annotation System for Forensic Applications.},
journal = {Genes},
volume = {12},
number = {1},
pages = {},
pmid = {33401773},
issn = {2073-4425},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Databases, Nucleic Acid ; Datasets as Topic ; Felidae/genetics ; Forensic Genetics/*methods ; *Gene Library ; Molecular Sequence Annotation/methods ; Ruminants/genetics ; *Software ; },
abstract = {Forensic genetics is a fast-growing field that frequently requires DNA-based taxonomy, namely, when evidence are parts of specimens, often highly processed in food, potions, or ointments. Reference DNA-sequences libraries, such as BOLD or GenBank, are imperative tools for taxonomic assignment, particularly when morphology is inadequate for classification. The auditing and curation of these datasets require reliable mechanisms, preferably with automated data preprocessing. Software tools were developed to grade these datasets considering as primary criterion the number of records, which is not compliant with forensic standards, where the priority is validation from independent sources. Moreover, 4SpecID is an efficient software tool developed to audit and annotate reference libraries, specifically designed for forensic applications. Its intuitive user-friendly interface virtually accesses any database and includes specific data mining functions tuned for the widespread BOLD repositories. The built tool was evaluated in laptop MacBook and a dual-Xeon server with a large BOLD dataset (Culicidae, 36,115 records), and the best execution time to grade the dataset on the laptop was 0.28 s. Datasets of Bovidae and Felidae families were used to evaluate the quality of the tool and the relevance of independent sources validation.},
}
@article {pmid33397448,
year = {2021},
author = {Nyasembe, VO and Tchouassi, DP and Muturi, MN and Pirk, CWW and Sole, CL and Torto, B},
title = {Plant nutrient quality impacts survival and reproductive fitness of the dengue vector Aedes aegypti.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {4},
pmid = {33397448},
issn = {1756-3305},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Aedes/chemistry/*genetics/*physiology ; Animals ; Dengue/transmission ; *Feeding Behavior ; Female ; Fertility ; *Genetic Fitness ; Mosquito Vectors/genetics/physiology ; *Nutrients ; Ovum/physiology ; Plants/*chemistry/classification ; },
abstract = {BACKGROUND: In a recent study using DNA barcoding, we identified the plants fed upon by four Afro-tropical mosquito species that vector dengue, malaria, and Rift Valley fever. Herein, we have expanded on this study by investigating the role of three of the plants, Pithecellobium dulce (Fabaceae), Leonotis nepetifolia (Lamiaceae), and Opuntia ficus-indica (Cactaceae), on the survival, fecundity, and egg viability of the dengue vector Aedes aegypti.<br><br>METHODS: We tested these effects using females that received (i) an initial three rations of blood meals and (ii) no blood meal at all. Two controls were included: age-matched females fed on glucose solution with or without an initial blood meal and those fed exclusively on blood meals. Data were collected daily over a 30-day period. The amino acid contents of Ae. aegypti guts and their respective diets were detected by coupled liquid chromatography-mass spectrometry.<br><br>RESULTS: Females fed on P. dulce and an exclusively blood meal diet had a shorter survival than those fed on glucose. On the other hand, females fed on L. nepetifolia survived longer than those fed exclusively on blood meals, whereas those fed on O. ficus-indica had the shortest survival time. With an initial blood meal, females fed on L. nepetifolia laid 1.6-fold more eggs while those fed on the other diets laid fewer eggs compared to those fed exclusively on blood meals. Hatching rates of the eggs laid varied with the diet. Mass spectroscopic analysis of gut contents of mosquitoes exposed to the different diets showed qualitative and quantitative differences in their amino acid levels.<br><br>CONCLUSION: Our findings highlight the central role of plant nutrients in the reproductive fitness of dengue vectors, which may impact their disease transmission potential.},
}
@article {pmid33396023,
year = {2021},
author = {Yu, J and Wu, X and Liu, C and Newmaster, S and Ragupathy, S and Kress, WJ},
title = {Progress in the use of DNA barcodes in the identification and classification of medicinal plants.},
journal = {Ecotoxicology and environmental safety},
volume = {208},
number = {},
pages = {111691},
doi = {10.1016/j.ecoenv.2020.111691},
pmid = {33396023},
issn = {1090-2414},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; High-Throughput Nucleotide Sequencing ; Plants, Medicinal/*genetics ; },
abstract = {DNA barcoding is an emerging molecular identification and classification technology that has been applied to medicinal plants since 2008. The application of this technique has greatly ensured the safety and effectiveness of medicinal materials. In this paper, we review the application of DNA barcoding and some related technologies over the past 10 years with respect to improving our knowledge of medicinal plant identification and authentication. From single locus-based DNA barcodes to combined markers to genome-scale levels, DNA barcodes contribute more and more genetic information. At the same time, other technologies, such as high-resolution melting (HRM), have been combined with DNA barcoding. With the development of next-generation sequencing (NGS), metabarcoding technology has also been shown to identify species in mixed samples successfully. As a widely used and effective tool, DNA barcoding will become more useful over time in the field of medicinal plants.},
}
@article {pmid33395693,
year = {2021},
author = {Behrens-Chapuis, S and Herder, F and Geiger, MF},
title = {Adding DNA barcoding to stream monitoring protocols - What's the additional value and congruence between morphological and molecular identification approaches?.},
journal = {PloS one},
volume = {16},
number = {1},
pages = {e0244598},
pmid = {33395693},
issn = {1932-6203},
mesh = {Animals ; Aquatic Organisms/classification/*genetics ; Biodiversity ; *DNA Barcoding, Taxonomic ; Fishes/classification/*genetics ; Germany ; Invertebrates/classification/*genetics ; Rivers ; },
abstract = {Although aquatic macroinvertebrates and freshwater fishes are important indicators for freshwater quality assessments, the morphological identification to species-level is often impossible and thus especially in many invertebrate taxa not mandatory during Water Framework Directive monitoring, a pragmatism that potentially leads to information loss. Here, we focus on the freshwater fauna of the River Sieg (Germany) to test congruence and additional value in taxa detection and taxonomic resolution of DNA barcoding vs. morphology-based identification in monitoring routines. Prior generated morphological identifications of juvenile fishes and aquatic macroinvertebrates were directly compared to species assignments using the identification engine of the Barcode of Life Data System. In 18% of the invertebrates morphology allowed only assignments to higher systematic entities, but DNA barcoding lead to species-level assignment. Dissimilarities between the two approaches occurred in 7% of the invertebrates and in 1% of the fishes. The 18 fish species were assigned to 20 molecular barcode index numbers, the 104 aquatic invertebrate taxa to 113 molecular entities. Although the cost-benefit analysis of both methods showed that DNA barcoding is still more expensive (5.30-8.60€ per sample) and time consuming (12.5h), the results emphasize the potential to increase taxonomic resolution and gain a more complete profile of biodiversity, especially in invertebrates. The provided reference DNA barcodes help building the foundation for metabarcoding approaches, which provide faster sample processing and more cost-efficient ecological status determination.},
}
@article {pmid33395311,
year = {2021},
author = {Chandrasekaran, AR and MacIsaac, M and Vilcapoma, J and Hansen, CH and Yang, D and Wong, WP and Halvorsen, K},
title = {DNA Nanoswitch Barcodes for Multiplexed Biomarker Profiling.},
journal = {Nano letters},
volume = {21},
number = {1},
pages = {469-475},
pmid = {33395311},
issn = {1530-6992},
support = {R21 CA212827/CA/NCI NIH HHS/United States ; R35 GM124720/GM/NIGMS NIH HHS/United States ; },
mesh = {Biomarkers, Tumor/genetics ; *DNA/genetics ; *MicroRNAs/genetics ; },
abstract = {Molecular biomarkers play a key role in the clinic, aiding in diagnostics and prognostics, and in the research laboratory, contributing to our basic understanding of diseases. Detecting multiple and diverse molecular biomarkers within a single accessible assay would have great utility, providing a more comprehensive picture for clinical evaluation and research, but is a challenge with standard methods. Here, we report programmable DNA nanoswitches for multiplexed detection of up to 6 biomarkers at once with each combination of biomarkers producing a unique barcode signature among 64 possibilities. As a defining feature of our method, we show "mixed multiplexing" for simultaneous barcoded detection of different types of biomolecules, for example, DNA, RNA, antibody, and protein in a single assay. To demonstrate clinical potential, we show multiplexed detection of a prostate cancer biomarker panel in serum that includes two microRNA sequences and prostate specific antigen.},
}
@article {pmid33390955,
year = {2020},
author = {Yu, X and Tan, W and Gao, H and Miao, L and Tian, X},
title = {Development of a Specific Mini-Barcode From Plastome and its Application for Qualitative and Quantitative Identification of Processed Herbal Products Using DNA Metabarcoding Technique: A Case Study on Senna.},
journal = {Frontiers in pharmacology},
volume = {11},
number = {},
pages = {585687},
pmid = {33390955},
issn = {1663-9812},
abstract = {Herbal products play an important role globally in the pharmaceutical and healthcare industries. However, some specific groups of herbal products are easily adulterated by confused materials on the market, which seriously reduces the products' quality. Universal conventional DNA barcodes would function poorly since the processed herbal products generally suffer from varying degrees of DNA degradation and DNA mixing during processing or manufacturing. For quality control purposes, an accurate and effective method should be provided for species identification of these herbal products. Here, we provided a strategy of developing the specific mini-barcode using Senna as an example, and by coupling with the metabarcoding technique, it realized the qualitative and quantitative identification of processed herbal products. The plastomes of Senna obtusifolia (L.) H.S.Irwin &amp; Barneby and Senna occidentalis (L.) Link were newly assembled, and the hypervariable coding-regions were identified by comparing their genomes. Then, the specific mini-barcodes were developed based on the identified hypervariable regions. Finally, we applied the DNA metabarcoding technique to the developed mini-barcodes. Results showed that the lengths of plastomes of S. obtusifolia and S. occidentalis were 162,426 and 159,993 bp, respectively. Four hypervariable coding-regions ycf1, rpl23, petL, and matK were identified. Two specific mini-barcodes were successfully developed from matK, and the mini-barcode of primer 647F-847R was proved to be able to qualitatively and quantitatively identify these two processed Senna seeds. Overall, our study established a valuable way to develop the specific mini-barcode, which may provide a new idea for the quality control of processed herbal products.},
}
@article {pmid33390091,
year = {2020},
author = {Selva Pandiyan, A and Siva Ganesa Karthikeyan, R and Rameshkumar, G and Sen, S and Lalitha, P},
title = {Identification of Bacterial and Fungal Pathogens by rDNA Gene Barcoding in Vitreous Fluids of Endophthalmitis Patients.},
journal = {Seminars in ophthalmology},
volume = {35},
number = {7-8},
pages = {358-364},
doi = {10.1080/08820538.2020.1864416},
pmid = {33390091},
issn = {1744-5205},
mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bacteria/genetics/isolation &amp; purification ; Child ; DNA, Bacterial/*analysis ; DNA, Fungal/*genetics ; DNA, Ribosomal/*genetics ; Endophthalmitis/*diagnosis/microbiology ; Eye Infections, Bacterial/*diagnosis/microbiology ; Eye Infections, Fungal/*diagnosis/microbiology ; Female ; Follow-Up Studies ; Fungi/genetics/isolation &amp; purification ; Humans ; Male ; Middle Aged ; Retrospective Studies ; Vitreous Body/*microbiology ; Young Adult ; },
abstract = {Purpose: To identify the bacterial and fungal pathogens in ocular samples of clinically suspected endophthalmitis patients by conventional culture methods and 16S and 28S rDNA gene sequencing respectively. Methods: A total of 88 patients with clinically suspected endophthalmitis were included in this study. Under sterile operating conditions, a vitreous fluid (0.1-0.2 ml) was obtained by pars plana vitrectomy procedure. The samples were processed for conventional microbiology methods and PCR. PCR targeting 16S rDNA gene for bacteria and 28S rDNA gene for fungus were performed individually using the MightyAmp DNA Polymerase Ver. 2 (TaKaRa China) kit. The PCR amplified samples were sequenced and aligned using CLUSTAL-W tool. The phylogenetic tree was constructed by Neighborhood joining along with the reference sequences downloaded from NCBI database using MEGA X software. Results: 67 Post-operative, 12 Endogenous and 9 traumatic endophthalmitis patients were included as study subjects. By the direct culturing bacterial growth was observed in 17 samples and fungal growth in three samples. PCR was positive for all the culture positive samples, in addition 14 were positive in culture negative samples. The predominant species identified in gram-positive bacteria were Staphylococcus spp., and Pseudomonas spp. in the gram-negative group. Both PCR and culture identified only three samples positive for fungal pathogens which were identified as Aspergillus fumigatus, Candida albicans, and Exerohilum rostratum. Conclusions: PCR based molecular diagnosis is more sensitive than the conventional gold standard culture methods in endophthalmitis. Bacterial pathogens were found to be the predominant in causing endophthalmitis than fungal pathogens.},
}
@article {pmid33389626,
year = {2021},
author = {Azmiera, N and Low, VL and Heo, CC},
title = {Colonization of Rabbit Carcasses by Drain Fly Larvae, Psychoda sp. (Diptera: Psychodidae): The First Report.},
journal = {Acta parasitologica},
volume = {66},
number = {2},
pages = {706-709},
pmid = {33389626},
issn = {1896-1851},
support = {600-IRMI 5/3/GIP (017/2018)//Universiti Teknologi MARA/ ; MO002-2019//Universiti Malaya/ ; },
mesh = {Animals ; Cadaver ; *Diptera ; Ecosystem ; Larva ; Postmortem Changes ; *Psychodidae ; Rabbits ; },
abstract = {INTRODUCTION: Psychoda sp. is often collected from patchy habitats such as sewers, drains and decomposing organic matters. The discovery of Psychoda sp. in forensic studies indicated that it might have noteworthy value in assisting death investigations.<br><br>PURPOSE: This study reports on the first finding of Psychoda larvae collected from decomposing rabbit carcasses placed in Cameron Highlands, Pahang, Malaysia.<br><br>METHODS: The larvae were first observed on rabbit carcasses and were collected using tweezers and carefully preserved in 70% ethanol. They were subsequently mounted on microscopy slides using Hoyer's medium and identified as Psychoda sp. morphologically. The identification was also confirmed through a DNA barcoding analysis.<br><br>RESULTS: Psychoda sp. larvae were collected on day-10 post-mortem where the rabbit carcasses were at the advanced decay stage of decomposition. The cytochrome c oxidase I (COI) gene sequences of the larvae had 90% similarity with the Psychoda spp. in the database.<br><br>CONCLUSION: The finding of these larvae on carrion may provide additional valuable insights into forensic entomology and may assist in death investigations.},
}
@article {pmid33387300,
year = {2021},
author = {de Boer, HJ and Ichim, MC and Newmaster, SG},
title = {Correction to: DNA Barcoding and Pharmacovigilance of Herbal Medicines.},
journal = {Drug safety},
volume = {44},
number = {3},
pages = {397},
doi = {10.1007/s40264-020-01029-9},
pmid = {33387300},
issn = {1179-1942},
}
@article {pmid33385843,
year = {2021},
author = {Rivera, SF and Vasselon, V and Mary, N and Monnier, O and Rimet, F and Bouchez, A},
title = {Exploring the capacity of aquatic biofilms to act as environmental DNA samplers: Test on macroinvertebrate communities in rivers.},
journal = {The Science of the total environment},
volume = {763},
number = {},
pages = {144208},
doi = {10.1016/j.scitotenv.2020.144208},
pmid = {33385843},
issn = {1879-1026},
mesh = {Animals ; Biodiversity ; Biofilms ; Comoros ; DNA ; DNA, Environmental ; Ecosystem ; Environmental Monitoring ; France ; *Invertebrates/genetics ; *Rivers ; },
abstract = {Aquatic biofilms are heterogeneous assemblages of microorganisms surrounded by a matrix of extracellular polymeric substances (EPS). Recent studies suggest that aquatic biofilms can physically act as sorptive sponges of DNA. We took the opportunity from already available samples of stone biofilms and macroinvertebrates specimens collected in parallel at the same sites to test the capacity of biofilms to act as DNA samplers of macroinvertebrate communities in streams. Macroinvertebrate communities are usually studied with metabarcoding using the DNA extracted from their bodies bulk samples, which remains a time-consuming approach and involves the destruction of all individual specimens from the samples. The ability of biofilms to capture DNA was explored on 19 rivers sites of a tropical island (Mayotte Island, France). First, macroinvertebrate specimens were identified based on their morphological characteristics. Second, DNA was extracted from biofilms, and macroinvertebrate communities were targeted using a standard COI barcode. The resulting morphological and molecular inventories were compared. They provided comparable structures and diversities for macroinvertebrate communities when one is working with the unassigned OTU data. After taxonomic assignment of the OTU data, diversity and richness were no longer correlated. The ecological assessment derived from morphological bulk samples was conserved by the biofilms samples. We also showed that the biofilm method allows to detect a higher diversity for some organisms (Cnidaria), that is hardly accessible with the morphological method. The results of this study exploring the DNA signal captured by natural biofilms are encouraging. However, a more detailed study integrating more replicates and comparing the biodiversity signal based on both morphological and molecular bulk macroinvertebrate samples to the one captured by biofilms will be necessary. Better understanding how the DNA signal captured by natural biofilms represents the biodiversity of a given sampling site is necessary before considering its use for bioassessment applications.},
}
@article {pmid33384563,
year = {2020},
author = {Meyer, M and Goergen, G and Jordaens, K},
title = {Taxonomic revision of the Afrotropical hover fly genus Senaspis Macquart (Diptera, Syrphidae).},
journal = {ZooKeys},
volume = {1003},
number = {},
pages = {83-160},
pmid = {33384563},
issn = {1313-2989},
abstract = {The representatives of the Afrotropical hover fly genus Senaspis Macquart (Diptera) are revised. In total, ten species are recognized. Senaspis apophysata (Bezzi) is herewith placed as junior synonym of S. flaviceps Macquart, S. livida (Bezzi) is herewith placed as junior synonym of S. dentipes (Macquart) and S. griseifacies (Bezzi) is herewith placed as junior synonym of S. haemorrhoa (Gerstaecker). All species are redescribed and an identification key is provided. DNA barcoding analysis (7 species, 64 barcodes) showed that the technique can be used to unambiguously identify the species. The relationships among the different Senaspis species are discussed based on morphological and DNA data.},
}
@article {pmid33384561,
year = {2020},
author = {Kodada, J and Jäch, MA and Freitag, H and Čiamporová-Zaťovičová, Z and Goffová, K and Selnekovič, D and Jr, F&#x10c;},
title = {Ancyronyx lianlabangorum sp. nov., a new spider riffle beetle from Sarawak, and new distribution records for A. pulcherrimus Kodada, Jäch &amp; Čiampor based on DNA barcodes (Coleoptera, Elmidae).},
journal = {ZooKeys},
volume = {1003},
number = {},
pages = {31-55},
pmid = {33384561},
issn = {1313-2989},
abstract = {Ancyronyx lianlabangorum sp. nov. (Coleoptera, Elmidae), a new spider riffle beetle from the Kelabit Highlands (Sarawak, northern Borneo), is described. Illustrations of the habitus and diagnostic characters of the new species and the similar, polymorphic A. pulcherrimus Kodada et al. are presented. Differences to closely related species, based on COI nucleotide sequences and morphological characters, are discussed. Ancyronyx pulcherrimus is here recorded from Sarawak for the first time, based on DNA barcoding.},
}
@article {pmid33382725,
year = {2020},
author = {Estrada-Franco, JG and Fernández-Santos, NA and Adebiyi, AA and López-López, MJ and Aguilar-Durán, JA and Hernández-Triana, LM and Prosser, SWJ and Hebert, PDN and Fooks, AR and Hamer, GL and Xue, L and Rodríguez-Pérez, MA},
title = {Vertebrate-Aedes aegypti and Culex quinquefasciatus (Diptera)-arbovirus transmission networks: Non-human feeding revealed by meta-barcoding and next-generation sequencing.},
journal = {PLoS neglected tropical diseases},
volume = {14},
number = {12},
pages = {e0008867},
pmid = {33382725},
issn = {1935-2735},
mesh = {Aedes/*virology ; Animals ; Arbovirus Infections/blood/transmission/*veterinary ; Arboviruses/*physiology ; Culex/*virology ; DNA Barcoding, Taxonomic ; Feeding Behavior ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions ; Models, Biological ; Mosquito Vectors/virology ; Species Specificity ; Vertebrates/blood/*virology ; },
abstract = {BACKGROUND: Aedes aegypti mosquito-borne viruses including Zika (ZIKV), dengue (DENV), yellow fever (YFV), and chikungunya (CHIKV) have emerged and re-emerged globally, resulting in an elevated burden of human disease. Aedes aegypti is found worldwide in tropical, sub-tropical, and temperate areas. The characterization of mosquito blood meals is essential to understand the transmission dynamics of mosquito-vectored pathogens.<br><br>Here, we report Ae. aegypti and Culex quinquefasciatus host feeding patterns and arbovirus transmission in Northern Mexico using a metabarcoding-like approach with next-generation deep sequencing technology. A total of 145 Ae. aegypti yielded a blood meal analysis result with 107 (73.8%) for a single vertebrate species and 38 (26.2%) for two or more. Among the single host blood meals for Ae. aegypti, 28.0% were from humans, 54.2% from dogs, 16.8% from cats, and 1.0% from tortoises. Among those with more than one species present, 65.9% were from humans and dogs. For Cx. quinquefasciatus, 388 individuals yielded information with 326 (84%) being from a single host and 63 (16.2%) being from two or more hosts. Of the single species blood meals, 77.9% were from dogs, 6.1% from chickens, 3.1% from house sparrows, 2.4% from humans, while the remaining 10.5% derived from other 12 host species. Among those which had fed on more than one species, 11% were from dogs and humans, and 89% of other host species combinations. Forage ratio analysis revealed dog as the most over-utilized host by Ae. aegypti (= 4.3) and Cx. quinquefasciatus (= 5.6) and the human blood index at 39% and 4%, respectively. A total of 2,941 host-seeking female Ae. aegypti and 3,536 Cx. quinquefasciatus mosquitoes were collected in the surveyed area. Of these, 118 Ae. aegypti pools and 37 Cx. quinquefasciatus pools were screened for seven arboviruses (ZIKV, DENV 1-4, CHIKV, and West Nile virus (WNV)) using qRT-PCR and none were positive (point prevalence = 0%). The 95%-exact upper limit confidence interval was 0.07% and 0.17% for Ae. aegypti and Cx. quinquefasciatus, respectively.<br><br>CONCLUSIONS/SIGNIFICANCE: The low human blood feeding rate in Ae. aegypti, high rate of feeding on mammals by Cx. quinquefasciatus, and the potential risk to transmission dynamics of arboviruses in highly urbanized areas of Northern Mexico is discussed.},
}
@article {pmid33380315,
year = {2020},
author = {Bratzel, F and Heller, S and Cyrannek, N and Paule, J and Leme, EMC and Loreth, A and Nowotny, A and Kiefer, M and Till, W and Barfuss, MHJ and Lexer, C and Koch, MA and Zizka, G},
title = {Correction to: The low-copy nuclear gene Agt1 as a novel DNA barcoding marker for Bromeliaceae.},
journal = {BMC plant biology},
volume = {20},
number = {1},
pages = {567},
pmid = {33380315},
issn = {1471-2229},
}
@article {pmid33379064,
year = {2021},
author = {Zhu, YL and Lian, YM and Wang, JK and Chen, ZP and Yu, RQ},
title = {Ultrasensitive detection of protein biomarkers by MALDI-TOF mass spectrometry based on ZnFe2O4 nanoparticles and mass tagging signal amplification.},
journal = {Talanta},
volume = {224},
number = {},
pages = {121848},
doi = {10.1016/j.talanta.2020.121848},
pmid = {33379064},
issn = {1873-3573},
mesh = {Biomarkers ; Humans ; Magnetics ; *Nanoparticles ; Peptides ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {A facile MALDI-TOF mass spectrometric platform for quantitative analysis of protein biomarkers was developed based on magnetic ZnFe2O4 nanoparticles and mass tagging signal amplification. In this platform, magnetic ZnFe2O4 nanoparticles functionalized with an aptamer of the biomarker of interest was used to magnetically separate silica nanoparticles modified with another aptamer of the target biomarker and a barcoding peptide from solution phase in the presence of the biomarker of interest. After the silica nanoparticles were dissolved by KHF2, the released barcoding peptide was detected by MALDI-TOF mass spectrometry with magnetic ZnFe2O4 nanoparticles used as assisting matrix of laser desorption ionization. Since the mass spectral intensity of the barcoding peptide is directly related to the concentration of the target biomarker, the proposed platform can be applied to the quantification of the target biomarker in complex biological samples. The effectiveness of the proposed platform was tested on the detection of carcinoembryonic antigen (CEA) in serum. Experimental results revealed that the proposed platform could achieve quite reliable quantitative results for CEA in human serum samples with accuracy comparable to a commercial CEA ELISA Kit. Its limit of detection and limit of quantification for CEA were estimated to be 0.6 × 10[-3] and 1.8 × 10[-3] ng/mL, respectively, considerably lower than the corresponding values reported in literature. Due to its features of simplicity in design, extremely low background signal, high sensitivity and selectivity, the proposed method can be further developed to be a competitive alternative for the quantification of CEA and other protein biomarkers as well.},
}
@article {pmid33376440,
year = {2020},
author = {Hansson, C and Schmidt, S},
title = {A revision of European species of the genus Tetrastichus Haliday (Hymenoptera: Eulophidae) using integrative taxonomy.},
journal = {Biodiversity data journal},
volume = {8},
number = {},
pages = {e59177},
pmid = {33376440},
issn = {1314-2828},
abstract = {BACKGROUND: The European species of the genus Tetrastichus (Insecta, Hymenoptera, Eulophidae, Tetrastichinae) are revised with 93 species, including 50 species described as new. The revision was conducted using an integrative taxonomic approach, based on DNA barcoding in combination with morphological characters. The Tetrastichinae are a biologically diverse and species-rich group of parasitoid wasps with numerous complexes of morphologically often very similar species that attack a wide range of hosts in over 100 insect families in 10 different orders. The genus Tetrastichus is, with almost 500 described species, the third largest genus of Tetrastichinae. Although biological information is lacking for most species, current data indicate that Tetrastichus species are gregarious koinobiont endoparasitoids developing on juvenile stages of mainly holometabolous insects. Due to their host specificity, several species of Tetrastichus are used as biological control agents.<br><br>NEW INFORMATION: The European species of Tetrastichus Haliday (Hymenoptera: Eulophidae) are revised using a combination of externo-morphological and DNA barcoding data. This is the first integrative approach for any of the large genera of the Tetrastichinae. A total of 93 species are included, of which 50 are described as new: T. agonus sp. n., T. antonjanssoni sp. n., T. argei sp. n., T. argutus sp. n., T. asilis sp. n., T. ballotus sp. n., T. bledius sp. n., T. broncus sp. n., T. calcarius sp. n., T. calmius sp. n., T. clisius sp. n., T. cosidis sp. n., T. cumulus sp. n., T. cyprus sp. n., T. delvarei sp. n., T. doczkali sp. n., T. elanus sp. n., T. elodius sp. n., T. ennis sp. n., T. enodis sp. n., T. erinus sp. n., T. evexus sp. n., T. fadus sp. n., T. fenrisi sp. n., T. flaccius sp. n., T. gredius sp. n., T. iasi sp. n., T. illydris sp. n., T. incanus sp. n., T. inscitus sp. n., T. intruitus sp. n., T. johnnoyesi sp. n., T. lacustrinus sp. n., T. ladrus sp. n., T. lanius sp. n., T. lazius sp. n., T. lixalius sp. n., T. lycus sp. n., T. marcusgrahami sp. n., T. minius sp. n., T. mixtus sp. n., T. nataliedaleskeyae sp. n., T. nymphae sp. n., T. pixius sp. n., T. scardiae sp. n., T. splendens sp. n., T. sti sp. n., T. suecus sp. n., T. tacitus sp. n. and T. tartus sp. n. Two keys for the identification of species are presented, one for females and one for males. Based on DNA barcode sequences for 70 of the species, a Maximum Likelihood tree to assess phylogenetic relationships within the genus is presented. These 70 species are also characterised by a combination of CO1 and morphological data. The remaining 23 species, without a DNA barcode, are characterised by morphological data. Using a combination of data from the morphology and CO1 or morphological data only, the species are separated into three species groups (clito-, hylotomarum-, murcia-groups) with 41 unplaced species outside these groups. Hosts are known for 27 of the species and they are gregarious, koinobiont endoparasitoids on a wide range of immature stages of holometabolous insects and appear to be very host specific. The first host record for Lepidoptera (Tineidae) in Europe is included.},
}
@article {pmid33375950,
year = {2020},
author = {Lwande, OW and Mohamed, N and Bucht, G and Ahlm, C and Olsson, G and Evander, M},
title = {Seewis hantavirus in common shrew (Sorex araneus) in Sweden.},
journal = {Virology journal},
volume = {17},
number = {1},
pages = {198},
pmid = {33375950},
issn = {1743-422X},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Disease Reservoirs/*veterinary/*virology ; Genetic Variation ; Orthohantavirus/classification/*genetics/*isolation &amp; purification ; Hantavirus Infections/*veterinary/*virology ; Phylogeny ; RNA, Viral/analysis/genetics ; Sequence Analysis, DNA ; Shrews/*virology ; Sweden ; },
abstract = {BACKGROUND: Rodent borne hantaviruses are emerging viruses infecting humans through inhalation. They cause hemorrhagic fever with renal syndrome and hemorrhagic cardiopulmonary syndrome. Recently, hantaviruses have been detected in other small mammals such as Soricomorpha (shrews, moles) and Chiroptera (bats), suggested as reservoirs for potential pandemic viruses and to play a role in the evolution of hantaviruses. It is important to study the global virome in different reservoirs, therefore our aim was to investigate whether shrews in Sweden carried any hantaviruses. Moreover, to accurately determine the host species, we developed a molecular method for identification of shrews.<br><br>METHOD: Shrews (n&#x2009;=&#x2009;198), caught during 1998 in Sweden, were screened with a pan-hantavirus PCR using primers from a conserved region of the large genome segment. In addition to morphological typing of shrews, we developed a molecular based typing method using sequencing of the mitochondrial cytochrome C oxidase I (COI) and cytochrome B (CytB) genes. PCR amplified hantavirus and shrew fragments were sequenced and phylogenetically analysed.<br><br>RESULTS: Hantavirus RNA was detected in three shrews. Sequencing identified the virus as Seewis hantavirus (SWSV), most closely related to previous isolates from Finland and Russia. All three SWSV sequences were retrieved from common shrews (Sorex araneus) sampled in V&#xe4;sterbotten County, Sweden. The genetic assay for shrew identification was able to identify native Swedish shrew species, and the genetic typing of the Swedish common shrews revealed that they were most similar to common shrews from Russia.<br><br>CONCLUSION: We detected SWSV RNA in Swedish common shrew samples and developed a genetic assay for shrew identification based on the COI and CytB genes. This was the first report of presence of hantavirus in Swedish shrews.},
}
@article {pmid33370342,
year = {2020},
author = {Ramirez, JL and Rosas-Puchuri, U and Cañedo, RM and Alfaro-Shigueto, J and Ayon, P and Zelada-Mázmela, E and Siccha-Ramirez, R and Velez-Zuazo, X},
title = {DNA barcoding in the Southeast Pacific marine realm: Low coverage and geographic representation despite high diversity.},
journal = {PloS one},
volume = {15},
number = {12},
pages = {e0244323},
pmid = {33370342},
issn = {1932-6203},
mesh = {Animals ; Aquatic Organisms/*classification/*genetics ; Biodiversity ; DNA ; DNA Barcoding, Taxonomic/*methods ; Ecosystem ; Fishes/classification/genetics ; Gene Library ; Invertebrates/classification/genetics ; Pacific Ocean/epidemiology ; Phylogeny ; South America ; },
abstract = {The Southeast Pacific comprises two Large Marine Ecosystems, the Pacific Central-American Coastal and the Humboldt Current System; and is one of the less well known in the tropical subregions in terms of biodiversity. To address this, we compared DNA barcoding repositories with the marine biodiversity species for the Southeast Pacific. We obtained a checklist of marine species in the Southeast Pacific (i.e. Colombia, Ecuador, Chile, and Peru) from the Ocean Biodiversity Information System (OBIS) database and compared it with species available at the Barcoding of Life Data System (BOLD) repository. Of the 5504 species records retrieved from OBIS, 42% of them had at least one registered specimen in BOLD (including specimens around the world); however, only 4.5% of records corresponded to publicly available DNA barcodes including specimens collected from a Southeast Pacific country. The low representation of barcoded species does not vary much across the different taxonomic groups or within countries, but we observed an asymmetric distribution of DNA barcoding records for taxonomic groups along the coast, being more abundant for the Humboldt Current System than the Pacific Central-American Coastal. We observed high-level of barcode records with Barcode Index Number (BIN) incongruences, particularly for fishes (Actinopterygii = 30.27% and Elasmobranchii = 24.71%), reflecting taxonomic uncertainties for fishes, whereas for Invertebrates and Mammalia more than 85% of records were classified as data deficient or inadequate procedure for DNA barcoding. DNA barcoding is a powerful tool to study biodiversity, with a great potential to increase the knowledge of the Southeast Pacific marine biodiversity. Our results highlight the critical need for increasing taxonomic sampling effort, the number of trained taxonomic specialists, laboratory facilities, scientific collections, and genetic reference libraries.},
}
@article {pmid33370106,
year = {2021},
author = {Palla, M and Punthambaker, S and Stranges, B and Vigneault, F and Nivala, J and Wiegand, D and Ayer, A and Craig, T and Gremyachinskiy, D and Franklin, H and Sun, S and Pollard, J and Trans, A and Arnold, C and Schwab, C and Mcgaw, C and Sarvabhowman, P and Dalal, D and Thai, E and Amato, E and Lederman, I and Taing, M and Kelley, S and Qwan, A and Fuller, CW and Roever, S and Church, GM},
title = {Multiplex Single-Molecule Kinetics of Nanopore-Coupled Polymerases.},
journal = {ACS nano},
volume = {15},
number = {1},
pages = {489-502},
doi = {10.1021/acsnano.0c05226},
pmid = {33370106},
issn = {1936-086X},
support = {R01 HG007415/HG/NHGRI NIH HHS/United States ; },
mesh = {DNA ; DNA-Directed DNA Polymerase ; Kinetics ; *Nanopores ; Sequence Analysis, DNA ; },
abstract = {DNA polymerases have revolutionized the biotechnology field due to their ability to precisely replicate stored genetic information. Screening variants of these enzymes for specific properties gives the opportunity to identify polymerases with different features. We have previously developed a single-molecule DNA sequencing platform by coupling a DNA polymerase to an α-hemolysin pore on a nanopore array. Here, we use this approach to demonstrate a single-molecule method that enables rapid screening of polymerase variants in a multiplex manner. In this approach, barcoded DNA strands are complexed with polymerase variants and serve as templates for nanopore sequencing. Nanopore sequencing of the barcoded DNA reveals both the barcode identity and kinetic properties of the polymerase variant associated with the cognate barcode, allowing for multiplexed investigation of many polymerase variants in parallel on a single nanopore array. Further, we develop a robust classification algorithm that discriminates kinetic characteristics of the different polymerase mutants. As a proof of concept, we demonstrate the utility of our approach by screening a library of ∼100 polymerases to identify variants for potential applications of biotechnological interest. We anticipate our screening method to be broadly useful for applications that require polymerases with altered physical properties.},
}
@article {pmid33367080,
year = {2020},
author = {Choi, JH and Jeong, DG and Oh, JN and Kim, S and Lee, YH and UngChoi, Y and Myoung, JG and Kim, CG},
title = {DNA barcoding of coral reef fishes from Chuuk State, Micronesia.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {5},
number = {3},
pages = {3733-3738},
pmid = {33367080},
issn = {2380-2359},
abstract = {The fish diversity of Chuuk Micronesia is currently under threat due to rapid changes in the coral reef ecosystem. Thus, accurate fish identification using DNA barcodes is fundamental for exploring species biodiversity and resource protection. In this study, we analyzed 162 fish mitochondrial DNA cytochrome c oxidase I (COI) barcodes from Chuuk Micronesia. Consequently, we identified 95 species from 53 genera in 26 families and seven orders. The average Kimura 2-parameter genetic distances within species, genera, families, and orders were calculated as 0.17%, 11.78%, 15.63%, and 21.90%, respectively. Also, we have utilized DNA barcodes to perform genetic divergence and phylogenetic analysis of families recognized as dominant groups in Chuuk State. Our findings confirm that DNA barcodes using COI are an effective approach in identifying coral reef fish species. We anticipate that the results of this study will provide baseline data for the protection of coral reef fish biodiversity at Chuuk Micronesia.},
}
@article {pmid33367033,
year = {2020},
author = {Kundu, S and Kumar, H and Tyagi, K and Chandra, K and Kumar, V},
title = {DNA barcoding of selected short-horned grasshoppers (Orthoptera: Acrididae) from Indian Himalayan region.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {5},
number = {3},
pages = {3618-3623},
pmid = {33367033},
issn = {2380-2359},
abstract = {In the context of Indian zoogeography, the DNA barcode data of short-horned grasshoppers (family Acrididae) are limited in global databases. Hence, the present study was aimed to collect selected Acridid species from the Indian Himalayan regions and generate DNA barcode data to enrich the global database. The estimated K2P genetic distances, Bayesian analysis (BA) topology and multiple species delimitation methods (ABGD, bPTP, and GMYC) clearly discriminate all the studied species. Based on high genetic distance (7.5%), multiple clades, and more than one molecular operational taxonomic unit, the present study elucidates the allopatric speciation and presence of possible cryptic diversity of Oxya japonica within India, China, and Russia. The present study suggests the collection of multiple specimens from different geographical locations and the generation of more DNA barcode data would facilitate the actual diversity of this insect group.},
}
@article {pmid33366922,
year = {2020},
author = {Ali, W and Javid, A and Hussain, A and Hafeez-Ur-Rehman, M and Chabber, AL and Hemmatzadeh, F},
title = {First record of Euphlyctis kalasgramensis (Anura: Dicroglossidae) from Punjab, Pakistan.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {5},
number = {2},
pages = {1227-1231},
pmid = {33366922},
issn = {2380-2359},
abstract = {The present study documented the first record of Euphlyctis kalasgramensis from Punjab, Pakistan. The specimens were collected during field visits from June through August 2018. Various morphometric measurements of E. kalasgramensis were taken and compared with Euphlyctis cyanophlyctis. Snout-vent length (SVL) was 38.11 ± 0.87 mm (n = 5), snout length was 3% of SVL, foot length was 55% of SVL, head length was 32% of SVL and weight was 8.01 ± 0.12 g (n = 5). A few specimens (n = 2) were euthanized and preserved for molecular analysis through mitochondrial 16S rRNA gene sequences. The newly obtained DNA sequences of E. kalasgramensis were submitted to GenBank and accession numbers were obtained (MK881165.1 and MK920114.1). The Maximum likelihood and Neighbor-joining trees based on Kimura 2-parameter distance resulted in similar phylogenetic trees. Euphlyctis kalasgramensis was out group in both phylogenetic trees. The interspecific divergence of E. kalasgramensis and E. cyanophlyctis was high ranging from 4% to 6% as compared to low intraspecific divergence 0% and 1%. The diversity and distribution ranges of many amphibians species are not well known in Pakistan due to lack of taxonomic information. In our recommendation, a large scale DNA barcoding is required to report more cryptic or new species from Pakistan.},
}
@article {pmid33366818,
year = {2020},
author = {Bhaskar, R and Kanaparthi, P and Sakthivel, R},
title = {DNA barcode approaches to reveal interspecies genetic variation of Indian ungulates.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {5},
number = {1},
pages = {938-944},
pmid = {33366818},
issn = {2380-2359},
abstract = {In the past two decades, identification of species from noninvasive sampling has turned out to be an important tool for wildlife conservation. In this study a total 93 specimens representing 22 species of ungulates were analyzed from partial sequences of mtDNA COI and Cytb genes. All the species showed unique clades, and sequences divergence within species was between 0.01-3.9% in COI and 0.01-13.7 in Cytb, whereas divergence between species ranged from 2.2 to 29.5% in COI and 2.3 to 28.8% in Cytb. Highest intraspecific divergence was observed within the Ovis aries in COI and Porcula salvania in Cytb. Bayesian (BA) phylogeny analysis of both genes combined distinguishes all the studied species as monophyletic criteria. The Indian rhinoceros (Rhinoceros unicornis) exhibited closer relation to horse (Equus caballus). No barcode gap was observed between species in COI. This study demonstrates that even short fragments of COI and Cytb generated from fecal pellets can efficiently identify the Indian ungulates, thus demonstrating its high potential for use in wildlife conservation activities.},
}
@article {pmid33366445,
year = {2019},
author = {Singh, A and Jabin, G and Joshi, BD and Thakur, M and Sharma, LK and Chandra, K},
title = {DNA barcodes and ethnomedicinal use of Sharpnose guitarfish Glaucostegus granulatus by the locals at Keylong, Lahaul and Spiti, Himachal Pradesh.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {5},
number = {1},
pages = {113-114},
pmid = {33366445},
issn = {2380-2359},
abstract = {Illegal trade of fishes is common and has been in practice since ages for the support of livelihood and as dietary supplements. However, several species are protected in the Wildlife (Protection) Act, 1972 of India and their trade is restricted under CITES. In this article, we report trade of Sharpnose guitarfish (Glaucostegus granulatus) for the ethnomedicinal remedy, identified using DNA barcoding in the Keylong district of Lahaul and Spiti, Himachal Pradesh. This study provides the first DNA barcode of Sharpnose guitarfish. In order to handle wildlife offense cases we emphasize that a large reference database for other fishes in trade is needed.},
}
@article {pmid33366358,
year = {2019},
author = {Tahir, HM and Summer, M and Mehmood, S and Ashraf, S and Naseem, S},
title = {DNA barcoding of spiders from agricultural fields.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {4},
number = {2},
pages = {4144-4151},
pmid = {33366358},
issn = {2380-2359},
abstract = {In the present study, DNA barcoding was used to assess the percentage accuracy of morphological base identification of spiders from the agriculture fields of district Layyah, Punjab, Pakistan. A total of 872 spiders were captured from June to August of 2017. All the collected spiders were brought to molecular laboratory at GC University Lahore, preserved in 95% ethanol and stored at -20 °C until the DNA extraction. Spiders were evaluated morphologically on the basis of different identification Keys and Catalogs. Morphological identification revealed the presence of 12 families, 29 genra and 49 species. To evaluate the authenticity of morphological identification, tissue samples of 96 specimens were sent to Canadian Center for Biodiversity and Genomics, University of Guelph, Canada. A 658-base pair sequence of COI (Cytochrome c Oxidase Subunit I) of 90 specimens was retrieved successfully, which confirmed the presence of 11 families, 25 genra and 47 species. On the basis of molecular results, all the misidentified specimens were then allotted the correct taxon. Overall accuracy of morphological based identification was 88%. It is concluded from the present study that morphological investigations to identify a spider, are satisfactory but to enhance the accuracy, pace and credibility of results, molecular technique like DNA barcoding is considerable. Furthermore, to magnify authenticity of evaluation of spiders, integrated barcoding- combination of molecular methods and conventional taxonomy- is compulsory.},
}
@article {pmid33363519,
year = {2020},
author = {Lutz, H and Vangelatos, A and Gottel, N and Osculati, A and Visona, S and Finley, SJ and Gilbert, JA and Javan, GT},
title = {Effects of Extended Postmortem Interval on Microbial Communities in Organs of the Human Cadaver.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {569630},
pmid = {33363519},
issn = {1664-302X},
abstract = {Human thanatomicrobiota studies have shown that microorganisms inhabit and proliferate externally and internally throughout the body and are the primary mediators of putrefaction after death. Yet little is known about the source and diversity of the thanatomicrobiome or the underlying factors leading to delayed decomposition exhibited by reproductive organs. The use of the V4 hypervariable region of bacterial 16S rRNA gene sequences for taxonomic classification ("barcoding") and phylogenetic analyses of human postmortem microbiota has recently emerged as a possible tool in forensic microbiology. The goal of this study was to apply a 16S rRNA barcoding approach to investigate variation among different organs, as well as the extent to which microbial associations among different body organs in human cadavers can be used to predict forensically important determinations, such as cause and time of death. We assessed microbiota of organ tissues including brain, heart, liver, spleen, prostate, and uterus collected at autopsy from criminal casework of 40 Italian cadavers with times of death ranging from 24 to 432 h. Both the uterus and prostate had a significantly higher alpha diversity compared to other anatomical sites, and exhibited a significantly different microbial community composition from non-reproductive organs, which we found to be dominated by the bacterial orders MLE1-12, Saprospirales, and Burkholderiales. In contrast, reproductive organs were dominated by Clostridiales, Lactobacillales, and showed a marked decrease in relative abundance of MLE1-12. These results provide insight into the observation that the uterus and prostate are the last internal organs to decay during human decomposition. We conclude that distinct community profiles of reproductive versus non-reproductive organs may help guide the application of forensic microbiology tools to investigations of human cadavers.},
}
@article {pmid33363243,
year = {2020},
author = {Schols, R and Mudavanhu, A and Carolus, H and Hammoud, C and Muzarabani, KC and Barson, M and Huyse, T},
title = {Exposing the Barcoding Void: An Integrative Approach to Study Snail-Borne Parasites in a One Health Context.},
journal = {Frontiers in veterinary science},
volume = {7},
number = {},
pages = {605280},
pmid = {33363243},
issn = {2297-1769},
abstract = {Trematodes are snail-borne parasites of major zoonotic importance that infect millions of people and animals worldwide and frequently hybridize with closely related species. Therefore, it is desirable to study trematodiases in a One Health framework, where human and animal trematodes are considered equally important. It is within this framework that we set out to study the snail and trematode communities in four artificial lakes and an abattoir in Zimbabwe. Trematode infections in snails were detected through multiplex PCR protocols. Subsequently, we identified snails by sequencing a partial mitochondrial cytochrome c oxidase subunit I (COI) fragment, and trematodes (adults from the abattoir and larval stages detected in snails) using COI and nuclear rDNA markers. Of the 1,674 collected snails, 699 were molecularly analyzed, in which we identified 12 snail and 19 trematode species. Additionally, three parasite species were sampled from the abattoir. Merely four trematode species were identified to species level through COI-based barcoding. Moreover, identification of members of the superfamilies Opisthorchioidea and Plagiorchioidea required a phylogenetic inference using the highly conserved 18S rDNA marker, as no related COI reference sequences were present in public databases. These barcoding challenges demonstrate a severe barcoding void in the available databases, which can be attributed to the neglected status of trematodiases. Adding to this, many available sequences cannot be used as different studies use different markers. To fill this gap, more studies on African trematodes, using a standardized COI barcoding region, are desperately needed.},
}
@article {pmid33360727,
year = {2021},
author = {Ardura, A and Rick, J and Martinez, JL and Zaiko, A and Garcia-Vazquez, E},
title = {Stress resistance for unraveling potential biopollutants. Insights from ballast water community analysis through DNA.},
journal = {Marine pollution bulletin},
volume = {163},
number = {},
pages = {111935},
doi = {10.1016/j.marpolbul.2020.111935},
pmid = {33360727},
issn = {1879-3363},
mesh = {Animals ; DNA ; Introduced Species ; Phytoplankton ; *Ships ; Water/analysis ; *Zooplankton ; },
abstract = {In marine settings, anthropogenic disturbances and climate change increase the rate of biological invasions. Predicting still undescribed invasive alien species (IAS) is needed for preparing timely management responses. We tested a strategy for discovering new potential IAS using DNA in a trans-equatorial expedition onboard RV Polarstern. During one-month travel, species inside ballast water experienced oxygen depletion, warming, darkness and ammonium stress. Many organisms died but several phytoplankton and zooplankton survivors resisted and were detected through a robust combination of individual sampling, DNA barcoding and metabarcoding, new in ballast water studies. Ammonium was identified as an important influential factor to explain diversity changes in phytoplankton and zooplankton. Some species reproduced until the end of the travel. These species tolerant to travel stress could be targeted as potential IAS and prioritized for designing control measures. Introducing resistance to travel stress in biosecurity risk analysis would be recommended.},
}
@article {pmid33357446,
year = {2021},
author = {Cappelletti, V and Hauser, T and Piazza, I and Pepelnjak, M and Malinovska, L and Fuhrer, T and Li, Y and Dörig, C and Boersema, P and Gillet, L and Grossbach, J and Dugourd, A and Saez-Rodriguez, J and Beyer, A and Zamboni, N and Caflisch, A and de Souza, N and Picotti, P},
title = {Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ.},
journal = {Cell},
volume = {184},
number = {2},
pages = {545-559.e22},
pmid = {33357446},
issn = {1097-4172},
mesh = {Allosteric Regulation ; Amino Acid Sequence ; Escherichia coli/enzymology/metabolism ; Escherichia coli Proteins/*metabolism ; *Imaging, Three-Dimensional ; Mass Spectrometry ; Molecular Dynamics Simulation ; Osmotic Pressure ; Phosphorylation ; Proteolysis ; Proteome/*metabolism ; Reproducibility of Results ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/*metabolism ; Stress, Physiological ; },
abstract = {Biological processes are regulated by intermolecular interactions and chemical modifications that do not affect protein levels, thus escaping detection in classical proteomic screens. We demonstrate here that a global protein structural readout based on limited proteolysis-mass spectrometry (LiP-MS) detects many such functional alterations, simultaneously and in situ, in bacteria undergoing nutrient adaptation and in yeast responding to acute stress. The structural readout, visualized as structural barcodes, captured enzyme activity changes, phosphorylation, protein aggregation, and complex formation, with the resolution of individual regulated functional sites such as binding and active sites. Comparison with prior knowledge, including other 'omics data, showed that LiP-MS detects many known functional alterations within well-studied pathways. It suggested distinct metabolite-protein interactions and enabled identification of a fructose-1,6-bisphosphate-based regulatory mechanism of glucose uptake in E. coli. The structural readout dramatically increases classical proteomics coverage, generates mechanistic hypotheses, and paves the way for in situ structural systems biology.},
}
@article {pmid33357075,
year = {2021},
author = {Young, KT and Lahmers, KK and Sellers, HS and Stallknecht, DE and Poulson, RL and Saliki, JT and Tompkins, SM and Padykula, I and Siepker, C and Howerth, EW and Todd, M and Stanton, JB},
title = {Randomly primed, strand-switching, MinION-based sequencing for the detection and characterization of cultured RNA viruses.},
journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc},
volume = {33},
number = {2},
pages = {202-215},
pmid = {33357075},
issn = {1943-4936},
support = {HHSN272201400004C/AI/NIAID NIH HHS/United States ; },
mesh = {High-Throughput Nucleotide Sequencing/methods/*veterinary ; RNA Viruses/*isolation &amp; purification ; Sequence Analysis, RNA/methods/*veterinary ; Whole Genome Sequencing/methods/*veterinary ; },
abstract = {RNA viruses rapidly mutate, which can result in increased virulence, increased escape from vaccine protection, and false-negative detection results. Targeted detection methods have a limited ability to detect unknown viruses and often provide insufficient data to detect coinfections or identify antigenic variants. Random, deep sequencing is a method that can more fully detect and characterize RNA viruses and is often coupled with molecular techniques or culture methods for viral enrichment. We tested viral culture coupled with third-generation sequencing for the ability to detect and characterize RNA viruses. Cultures of bovine viral diarrhea virus, canine distemper virus (CDV), epizootic hemorrhagic disease virus, infectious bronchitis virus, 2 influenza A viruses, and porcine respiratory and reproductive syndrome virus were sequenced on the MinION platform using a random, reverse primer in a strand-switching reaction, coupled with PCR-based barcoding. Reads were taxonomically classified and used for reference-based sequence building using a stock personal computer. This method accurately detected and identified complete coding sequence genomes with a minimum of 20× coverage depth for all 7 viruses, including a sample containing 2 viruses. Each lineage-typing region had at least 26× coverage depth for all viruses. Furthermore, analyzing the CDV sample through a pipeline devoid of CDV reference sequences modeled the ability of this protocol to detect unknown viruses. Our results show the ability of this technique to detect and characterize dsRNA, negative- and positive-sense ssRNA, and nonsegmented and segmented RNA viruses.},
}
@article {pmid33355113,
year = {2021},
author = {Ebert, KM and Arnold, WG and Ebert, PR and Merritt, DJ},
title = {Hindgut microbiota reflects different digestive strategies in dung beetles (Coleoptera: Scarabaeidae: Scarabaeinae).},
journal = {Applied and environmental microbiology},
volume = {87},
number = {5},
pages = {},
pmid = {33355113},
issn = {1098-5336},
abstract = {Gut microbes play an important role in the biology and evolution of insects. Australian native dung beetles (Scarabaeinae) present an opportunity to study gut microbiota in an evolutionary context as they come from two distinct phylogenetic lineages and some species in each lineage have secondarily adapted to alternative or broader diets. In this study, we characterised the hindgut bacterial communities found in 21 species of dung beetles across two lineages using 16S rRNA sequencing. We found that gut microbial diversity was more dependent on host phylogeny and gut morphology than specific dietary preferences or environment. In particular, gut microbial diversity was highest in the endemic, flightless genus Cephalodesmius that feeds on a broad range of composted organic matter. The hindgut of Cephalodesmius harbours a highly conserved core set of bacteria suggesting that the bacteria are symbiotic. Symbiosis is supported by the persistence of the core microbiota across isolated beetle populations and between species in the genus. A co-evolutionary relationship is supported by the expansion of the hindgut to form a fermentation chamber and the fermentative nature of the core microbes. In contrast, Australian species of the widespread dung beetle genus Onthophagus, specialise on a single food resource such as dung or fungus, exhibit minimal food processing behaviour, have a short, narrow hindgut and a variable gut microbiota with relatively few core bacterial taxa. A conserved, complex gut microbiota is hypothesised to be unnecessary for this highly mobile genus.IMPORTANCE Dung beetles are a very important part of an ecosystem because of their role in the removal and decomposition of vertebrate dung. It has been suspected that symbiotic gut bacteria facilitate this role, a hypothesis that we have explored with high throughput barcoding. We found that differences in hindgut morphology had the greatest effect on the bacterial community composition. Species with a hindgut fermentation chamber harboured a distinctly different hindgut community compared to those species with a narrow, undifferentiated hindgut. Diet and phylogeny were also associated with differences in gut community. Further understanding of the relationships between dung beetles and their gut microbes will provide insights into the evolution of their behaviours and how gut communities contribute to their fitness.},
}
@article {pmid33354136,
year = {2020},
author = {Kolcsár, LP and Kato, D and Gamboa, M and Watanabe, K},
title = {Revision of Japanese species of Nipponomyia Alexander, 1924 (Diptera, Pediciidae).},
journal = {ZooKeys},
volume = {1000},
number = {},
pages = {71-105},
pmid = {33354136},
issn = {1313-2989},
abstract = {Japanese species of the genus Nipponomyia Alexander, 1924 are revised. Two new species, Nipponomyia okinawensis Kolcsár &amp; Kato, sp. nov. and N. yakushimensis Kolcsár &amp; Kato, sp. nov. are described from the Ryukyu Islands. Images of habitus and wings, illustrations of male and female terminalia, and distribution maps are provided for the Japanese species. A key to the world species of Nipponomyia is added. DNA barcodes of three Japanese Nipponomyia are provided, representing the first barcodes from the genus.},
}
@article {pmid33339962,
year = {2020},
author = {Oguchi, Y and Shintaku, H and Uemura, S},
title = {Development of a sequencing system for spatial decoding of DNA barcode molecules at single-molecule resolution.},
journal = {Communications biology},
volume = {3},
number = {1},
pages = {788},
pmid = {33339962},
issn = {2399-3642},
mesh = {DNA Barcoding, Taxonomic/instrumentation/*methods ; Gene Expression Profiling ; Gene Library ; Humans ; K562 Cells ; Sequence Analysis, DNA/instrumentation/*methods ; Single Molecule Imaging/instrumentation/*methods ; },
abstract = {Single-cell transcriptome analysis has been revolutionized by DNA barcodes that index cDNA libraries, allowing highly multiplexed analyses to be performed. Furthermore, DNA barcodes are being leveraged for spatial transcriptomes. Although spatial resolution relies on methods used to decode DNA barcodes, achieving single-molecule decoding remains a challenge. Here, we developed an in-house sequencing system inspired by a single-molecule sequencing system, HeliScope, to spatially decode DNA barcode molecules at single-molecule resolution. We benchmarked our system with 30 types of DNA barcode molecules and obtained an average read length of ~20 nt with an error rate of less than 5% per nucleotide, which was sufficient to spatially identify them. Additionally, we spatially identified DNA barcode molecules bound to antibodies at single-molecule resolution. Leveraging this, we devised a method, termed "molecular foot printing", showing potential for applying our system not only to spatial transcriptomics, but also to spatial proteomics.},
}
@article {pmid33339199,
year = {2020},
author = {Medlin, LK and Gamella, M and Mengs, G and Serafín, V and Campuzano, S and M Pingarrón, J},
title = {Advances in the Detection of Toxic Algae Using Electrochemical Biosensors.},
journal = {Biosensors},
volume = {10},
number = {12},
pages = {},
pmid = {33339199},
issn = {2079-6374},
support = {778069//Horizon 2020/ ; },
mesh = {Biosensing Techniques/methods ; Carbon ; Ecosystem ; Electrochemical Techniques ; Electrodes ; *Environmental Monitoring ; *Harmful Algal Bloom ; Humans ; Nucleic Acid Hybridization ; Water Pollutants/analysis ; },
abstract = {Harmful algal blooms (HABs) are more frequent as climate changes and tropical toxic species move northward, especially along the Iberian Peninsula, a rich aquaculture area. Monitoring programs, detecting the presence of toxic algae before they bloom, are of paramount importance to protect ecosystems, aquaculture, human health and local economies. Rapid, reliable species identification methods using molecular barcodes coupled to biosensor detection tools have received increasing attention as an alternative to the legally required but impractical microscopic counting-based techniques. Our electrochemical detection system has improved, moving from conventional sandwich hybridization protocols using different redox mediators and signal probes with different labels to a novel strategy involving the recognition of RNA heteroduplexes by antibodies further labelled with bacterial antibody binding proteins conjugated with multiple enzyme molecules. Each change has increased sensitivity. A 150-fold signal increase has been produced with our newest protocol using magnetic microbeads (MBs) and amperometric detection at screen-printed carbon electrodes (SPCEs) to detect the target RNA of toxic species. We can detect as few as 10 cells L[-1] for some species by using a fast (~2 h), simple (PCR-free) and cheap methodology (~2 EUR/determination) that will allow this methodology to be integrated into easy-to-use portable systems.},
}
@article {pmid33337241,
year = {2020},
author = {Pitman, TL and Philbrook, RN and Vetterli, MR and Warren, JG},
title = {First report of Pythium ultimum causing crown rot in greenhouse grown Cannabis sativa (L.) in California.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-10-20-2228-PDN},
pmid = {33337241},
issn = {0191-2917},
abstract = {In April of 2020 cuttings of Cannabis sativa (L.) in a greenhouse in San Mateo County, CA were observed collapsing, and further observation revealed: water-soaked stems, tan discoloration to the cortex, and discolored roots. The greenhouse irrigation system was supplied by a local stream. We collected one-liter water samples from: intake pond, reservoir tank, irrigation lines, and local potable water tap. Water samples were filtered and plated as described previously (Rollins et al., 2016). Filter papers were removed after 24 hours. Crown sections from four symptomatic plants and one asymptomatic plant were surfaced sterilized in 10% bleach for five minutes, rinsed in sterile deionized water, cut into four-millimeter long sections, and plated onto V8 media, then incubated at room temperature for three days. White mycelial growth was observed from foci within the print of the filter paper from all irrigation water samples but not the potable water supply sample. Similar mycelial growth was observed from plated crown tissue from symptomatic plants only. Observation under light microscope revealed characteristics congruent with P. ultimum, including aseptate hyphae and globose sporangia (Watanabe, 2002). Mycelia was collected for DNA extraction from each of the water and plant sample plates with DNA extractions performed using Quick DNA Fungi/Bacterial Kit (Zymo Research Irvine, CA, USA) and PCR amplified using primers ITS100/ITS4 as described by Riit et al. (2016). All amplicons were Sanger sequenced, aligned using SnapGene software (from GSL Biotech; available at snapgene.com), and compared to barcode referencPe sequences to identify the species using the BarCode of Life Database (BOLDsystems) within the National Center for Biotechnology Information nucleotide database. After trimming and aligning, all amplicons were found to be identical, yielding the 810-nucleotide long consensus ITS amplicon (accession MW114807), which aligned with Pythium ultimum ITS sequences (e.g., accession HQ643886.1) with 100% identity and homology. We then completed Koch's postulates by using pure cultures from root sections of P. ultimum to stem inoculate C. sativa plants. We used a three-millimeter corer to remove a disc of epidermis and applied a plug of pure culture to the wound. We inoculated 10 plants, with two plants mock-inoculated using clean V8 agar. Inoculation sites were wrapped in parafilm, and plants were grown in the greenhouse for 20 days. Stems of mock and oomycete inoculated plants were examined for callus formation and 30 centimeters of stem were excised from each plant. The mock inoculated plants had fully callused inoculation sites and were discolored only where wounded. P. ultimum inoculated plant inoculation sites were partially callused over and had tan discoloration of the cortex that extended 6.0 mm +/- 2.0 mm above and below the inoculation site. Stem segments above and below inoculation sites were surface sterilized and plated on V8 media as previously described and P. ultimum recovered from inoculated plants, confirmed as identical to the inoculum by ITS amplification and sequencing. Mock inoculated plant stem cultures yielded no oomycete growth. Together, these results indicate that P. ultimum has the ability to cause crown rot in C. sativa in greenhouse cultivation.},
}
@article {pmid33335803,
year = {2020},
author = {Oliveira, PV and de Almeida, FAN and Lugon, MD and Britto, KB and Oliveira-Costa, J and Santos, AR and Paneto, GG},
title = {Using high-resolution melting to identify Calliphoridae (blowflies) species from Brazil.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e9680},
pmid = {33335803},
issn = {2167-8359},
abstract = {Forensic entomology is the study of insects and other arthropods used in the solution of crimes. Most of entomological evidences strongly depend on accurate species identification. Therefore, new methods are being developed due to difficulties in morphological identification, including molecular methods such as High-Resolution Melting. In this study, we reported a new HRM primer set to identify forensically important Calliphoridae (blowflies) from Brazil. For such purpose, Calliphoridae species of forensic importance in Brazil were listed and confirmed by specialists. Mitochondrial COI sequences of those species were downloaded from databases and aligned, and polymorphic variations were selected for distinction between species. Based on it, HRM primers were designed. Forty-three fly samples representing six species were tested in the HRM assay. All samples had the COI gene sequenced to validate the result. Identifying and differentiating the six species proposed using a combination of two amplicons was possible. The protocol was effective even for old insect specimens, collected and preserved dried for more than ten years, unlike the DNA sequencing technique that failed for those samples. The HRM technique proved to be an alternative tool to DNA sequencing, with advantage of amplifying degraded samples and being fast and cheaper than the sequencing technique.},
}
@article {pmid33335607,
year = {2020},
author = {Rodrigues, AM and Beale, MA and Hagen, F and Fisher, MC and Terra, PPD and de Hoog, S and Brilhante, RSN and de Aguiar Cordeiro, R and de Souza Collares Maia Castelo-Branco, D and Rocha, MFG and Sidrim, JJC and de Camargo, ZP},
title = {The global epidemiology of emerging Histoplasma species in recent years.},
journal = {Studies in mycology},
volume = {97},
number = {},
pages = {100095},
pmid = {33335607},
issn = {0166-0616},
support = {MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {Histoplasmosis is a serious infectious disease in humans caused by Histoplasma spp. (Onygenales), whose natural reservoirs are thought to be soil enriched with bird and bat guano. The true global burden of histoplasmosis is underestimated and frequently the pulmonary manifestations are misdiagnosed as tuberculosis. Molecular data on epidemiology of Histoplasma are still scarce, even though there is increasing recognition of histoplasmosis in recent years in areas distant from the traditional endemic regions in the Americas. We used multi-locus sequence data from protein coding loci (ADP-ribosylation factor, H antigen precursor, and delta-9 fatty acid desaturase), DNA barcoding (ITS1/2+5.8s), AFLP markers and mating type analysis to determine the genetic diversity, population structure and recognise the existence of different phylogenetic species among 436 isolates of Histoplasma obtained globally. Our study describes new phylogenetic species and the molecular characteristics of Histoplasma lineages causing outbreaks with a high number of severe outcomes in Northeast Brazil between 2011 and 2015. Genetic diversity levels provide evidence for recombination, common ancestry and clustering of Brazilian isolates at different geographic scales with the emergence of LAm C, a new genotype assigned to a separate population cluster in Northeast Brazil that exhibited low diversity indicative of isolation. The global survey revealed that the high genetic variability among Brazilian isolates along with the presence of divergent cryptic species and/or genotypes may support the hypothesis of Brazil being the center of dispersion of Histoplasma in South America, possibly with the contribution of migratory hosts such as birds and bats. Outside Brazil, the predominant species depends on the region. We confirm that histoplasmosis has significantly broadened its area of occurrence, an important feature of emerging pathogens. From a practical point of view, our data point to the emergence of histoplasmosis caused by a plethora of genotypes, and will enable epidemiological analysis focused on understanding the processes that lead to histoplasmosis. Further, the description of this diversity opens avenues for comparative genomic studies, which will allow progress toward a consensus taxonomy, improve understanding of the presence of hybrids in natural populations of medically relevant fungi, test reproductive barriers and to explore the significance of this variation.},
}
@article {pmid33335438,
year = {2020},
author = {Ubagan, MD and Lee, T and Kim, P and Shin, S},
title = {A new species of the genus Henricia (Asteroidea, Spinulosida, Echinasteridae) from South Korea.},
journal = {ZooKeys},
volume = {997},
number = {},
pages = {1-15},
pmid = {33335438},
issn = {1313-2989},
abstract = {A new species of the genus Henricia Gray, 1840 that belongs to the family Echinasteridae is described from South Korea. Henricia epiphysialis sp. nov. has epiphyseal ossicles at the ends of the abactinal and lateral plates, and the abactinal and lateral spines form a hooked crown. The partial sequence of the mitochondrial COXI gene (537 bp) of H. epiphysialis sp. nov. was obtained, and the new species was morphologically and genetically compared with other related Henricia species.},
}
@article {pmid33335020,
year = {2021},
author = {Kuchina, A and Brettner, LM and Paleologu, L and Roco, CM and Rosenberg, AB and Carignano, A and Kibler, R and Hirano, M and DePaolo, RW and Seelig, G},
title = {Microbial single-cell RNA sequencing by split-pool barcoding.},
journal = {Science (New York, N.Y.)},
volume = {371},
number = {6531},
pages = {},
pmid = {33335020},
issn = {1095-9203},
support = {R01 DK104908/DK/NIDDK NIH HHS/United States ; R01 HG009136/HG/NHGRI NIH HHS/United States ; R01 HG009892/HG/NHGRI NIH HHS/United States ; },
mesh = {Anti-Bacterial Agents/biosynthesis ; Bacillus Phages/physiology ; Bacillus subtilis/*genetics/growth &amp; development/metabolism ; Carbon/metabolism ; Culture Media ; Escherichia coli/genetics ; Fermentation/genetics ; *Gene Expression Regulation, Bacterial ; Gluconeogenesis/genetics ; Glycolysis/genetics ; Heat-Shock Response/genetics ; Inositol/metabolism ; Ion Transport ; Metabolic Networks and Pathways/*genetics ; Metals/metabolism ; Movement ; Operon ; RNA, Bacterial/genetics ; RNA-Seq/*methods ; Single-Cell Analysis/*methods ; Stress, Physiological ; Transcription, Genetic ; Transcriptome ; Virus Activation ; },
abstract = {Single-cell RNA sequencing (scRNA-seq) has become an essential tool for characterizing gene expression in eukaryotes, but current methods are incompatible with bacteria. Here, we introduce microSPLiT (microbial split-pool ligation transcriptomics), a high-throughput scRNA-seq method for Gram-negative and Gram-positive bacteria that can resolve heterogeneous transcriptional states. We applied microSPLiT to >25,000 Bacillus subtilis cells sampled at different growth stages, creating an atlas of changes in metabolism and lifestyle. We retrieved detailed gene expression profiles associated with known, but rare, states such as competence and prophage induction and also identified unexpected gene expression states, including the heterogeneous activation of a niche metabolic pathway in a subpopulation of cells. MicroSPLiT paves the way to high-throughput analysis of gene expression in bacterial communities that are otherwise not amenable to single-cell analysis, such as natural microbiota.},
}
@article {pmid33334103,
year = {2020},
author = {Handy, SM and Ott, BM and Hunter, ES and Zhang, S and Erickson, DL and Wolle, MM and Conklin, SD and Lane, CE},
title = {Suitability of DNA Sequencing Tools for Identifying Edible Seaweeds Sold in the United States.},
journal = {Journal of agricultural and food chemistry},
volume = {68},
number = {52},
pages = {15516-15525},
doi = {10.1021/acs.jafc.0c03734},
pmid = {33334103},
issn = {1520-5118},
mesh = {DNA, Plant/genetics ; Food Labeling ; Food Safety ; Genome, Plant ; Seaweed/classification/*genetics ; Sequence Analysis, DNA ; United States ; Vegetables/classification/*genetics ; },
abstract = {Seaweeds have been consumed by billions of people around the world and are increasingly popular in United States (US) diets. Some seaweed species have been associated with adverse health effects-such as heavy metal toxicity-and higher priced seaweeds may be more prone to adulteration. Knowing which species of seaweeds are being marketed in the US is important for protecting human health and preventing economic adulteration. Therefore, the United States Food and Drug Administration is developing new DNA-based species identification tools to complement established chemical methods for verifying the accurate labeling of products. Here, seaweed products available in the United States were surveyed using a tiered approach to evaluate a variety of DNA extraction techniques followed by traditional DNA barcoding via Sanger sequencing; if needed, genome skimming of total extracted nuclear DNA via next-generation sequencing was performed. This two-tiered approach of DNA barcoding and genome skimming could identify most seaweed samples (41/46), even those in blends (2/2, 1 out of 3 labeled species in each). Only two commercial samples appeared to be mislabeled or to contain unintended algal species. Five samples, labeled as "hijiki" or "arame", could not be confirmed by these DNA-based identification methods.},
}
@article {pmid33333226,
year = {2021},
author = {Chen, W and Li, C and Yang, J and Zhu, S and Li, J and Li, Y and Li, X},
title = {Temporal species-level composition of larvae resources in the lower Pearl River drainage and implications for species' reproductive cycles.},
journal = {Gene},
volume = {776},
number = {},
pages = {145351},
doi = {10.1016/j.gene.2020.145351},
pmid = {33333226},
issn = {1879-0038},
mesh = {Animals ; Aquaculture/*methods ; China ; DNA Barcoding, Taxonomic/methods ; Electron Transport Complex IV/genetics ; Fishes/*genetics ; Genetics, Population/methods ; Larva/*genetics ; Phylogeny ; Reproduction/genetics/physiology ; Rivers ; Species Specificity ; },
abstract = {Resolving the temporal community composition of a larvae population can not only further our understanding of the regional species composition but also help us to infer the reproductive times of regional fish taxa, which can have implications on the development of effective monitoring and conservation policies for the regional fish stock. Nevertheless, correctly diagnosing the fish larvae is extremely challenging due to the paucity of diagnostic morphological characters at the species level. Based on daily larval samplings during March and October in 2018, this study combined morphological features with a DNA barcode technique to determine the species composition of fish larvae in the lower Pearl River drainage (LPR) and evaluate the spawning periods of identified species. Due to an absence of reference barcodes for LPR fishes, a DNA barcode library of adult fishes in the LPR was built for 384 individuals representing 78 morphological species. Analyses demonstrated the usability of the barcode library and uncovered many undetected mitochondrial lineages in 12 species. Morphological analyses performed on 81 temporal larval samples revealed 25 morphotypes and assigned 9 morphotypes into the species level. A total of 1624 larvae from 96 temporal larval samples were selected for molecular identification, and high quality barcoding sequences were obtained from 1391 larvae. We accurately assigned 1078 larvae to 37 species using our barcode library and published database. Among the identified species, a critically endangered species, namely, Ochetobius elongatus, and several invasive species were examined, providing a new perspective to assess the stock of regional endangered and invasive species. Furthermore, this study found high species diversity occurred primarily between May and September, and clarified the spawning periods of identified species inferred from the temporal occurrences of larvae. Above all, our study highlights the applicability to fish larval ecology to assist conservation and fishery management efforts.},
}
@article {pmid33331682,
year = {2020},
author = {Grazina, L and Amaral, JS and Mafra, I},
title = {Botanical origin authentication of dietary supplements by DNA-based approaches.},
journal = {Comprehensive reviews in food science and food safety},
volume = {19},
number = {3},
pages = {1080-1109},
doi = {10.1111/1541-4337.12551},
pmid = {33331682},
issn = {1541-4337},
mesh = {DNA Barcoding, Taxonomic/methods ; DNA, Plant ; Dietary Supplements/*standards ; Drug Contamination ; Plants, Medicinal/*classification/genetics ; },
abstract = {Herbal products, such as dietary supplements, have become a subject of increasing global importance for their health benefits and economic considerations. However, they have also been targets of adulteration practices, being the accurate identification of botanicals in herbal products of utmost importance to protect the health and expectations of consumers. Particularly, in the case of dietary supplements, which can have different types of formulations, the identification of plant material used in their production is often a research challenge. DNA-based techniques have played a crucial role on the development of a wide range of tools for the authentication of herbal products. Therefore, this review intends to describe their main progresses, critically discussing their advantages and drawbacks when applied to authenticate herbal products, focusing on dietary supplements. DNA barcoding is particularly emphasized because it has provided the highest number of applications, followed by the advances on high-resolution melting analysis combined with DNA barcodes. A special emphasis is also given to the promising approaches relying on DNA metabarcoding and isothermal amplification.},
}
@article {pmid33326438,
year = {2020},
author = {Schwabl, P and Maiguashca Sánchez, J and Costales, JA and Ocaña-Mayorga, S and Segovia, M and Carrasco, HJ and Hernández, C and Ramírez, JD and Lewis, MD and Grijalva, MJ and Llewellyn, MS},
title = {Culture-free genome-wide locus sequence typing (GLST) provides new perspectives on Trypanosoma cruzi dispersal and infection complexity.},
journal = {PLoS genetics},
volume = {16},
number = {12},
pages = {e1009170},
pmid = {33326438},
issn = {1553-7404},
support = {/WT_/Wellcome Trust/United Kingdom ; MR/R021430/1/MRC_/Medical Research Council/United Kingdom ; 204820/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Costs and Cost Analysis ; DNA Barcoding, Taxonomic/economics/*methods/standards ; Disease Vectors ; *Genome, Protozoan ; Hemiptera/parasitology ; *Metagenome ; Metagenomics/economics/*methods/standards ; Polymorphism, Genetic ; Trypanosoma cruzi/*genetics/pathogenicity ; Virulence/genetics ; Whole Genome Sequencing/economics/*methods/standards ; },
abstract = {Analysis of genetic polymorphism is a powerful tool for epidemiological surveillance and research. Powerful inference from pathogen genetic variation, however, is often restrained by limited access to representative target DNA, especially in the study of obligate parasitic species for which ex vivo culture is resource-intensive or bias-prone. Modern sequence capture methods enable pathogen genetic variation to be analyzed directly from host/vector material but are often too complex and expensive for resource-poor settings where infectious diseases prevail. This study proposes a simple, cost-effective 'genome-wide locus sequence typing' (GLST) tool based on massive parallel amplification of information hotspots throughout the target pathogen genome. The multiplexed polymerase chain reaction amplifies hundreds of different, user-defined genetic targets in a single reaction tube, and subsequent agarose gel-based clean-up and barcoding completes library preparation at under 4 USD per sample. Our study generates a flexible GLST primer panel design workflow for Trypanosoma cruzi, the parasitic agent of Chagas disease. We successfully apply our 203-target GLST panel to direct, culture-free metagenomic extracts from triatomine vectors containing a minimum of 3.69 pg/μl T. cruzi DNA and further elaborate on method performance by sequencing GLST libraries from T. cruzi reference clones representing discrete typing units (DTUs) TcI, TcIII, TcIV, TcV and TcVI. The 780 SNP sites we identify in the sample set repeatably distinguish parasites infecting sympatric vectors and detect correlations between genetic and geographic distances at regional (< 150 km) as well as continental scales. The markers also clearly separate TcI, TcIII, TcIV and TcV + TcVI and appear to distinguish multiclonal infections within TcI. We discuss the advantages, limitations and prospects of our method across a spectrum of epidemiological research.},
}
@article {pmid33323415,
year = {2020},
author = {Burgos, HL and Burgos, EF and Steinberger, AJ and Suen, G and Mandel, MJ},
title = {Multiplexed Competition in a Synthetic Squid Light Organ Microbiome Using Barcode-Tagged Gene Deletions.},
journal = {mSystems},
volume = {5},
number = {6},
pages = {},
pmid = {33323415},
issn = {2379-5077},
support = {R25 GM086262/GM/NIGMS NIH HHS/United States ; R35 GM119627/GM/NIGMS NIH HHS/United States ; },
abstract = {Beneficial symbioses between microbes and their eukaryotic hosts are ubiquitous and have widespread impacts on host health and development. The binary symbiosis between the bioluminescent bacterium Vibrio fischeri and its squid host Euprymna scolopes serves as a model system to study molecular mechanisms at the microbe-animal interface. To identify colonization factors in this system, our lab previously conducted a global transposon insertion sequencing (INSeq) screen and identified over 300 putative novel squid colonization factors in V. fischeri To pursue mechanistic studies on these candidate genes, we present an approach to quickly generate barcode-tagged gene deletions and perform high-throughput squid competition experiments with detection of the proportion of each strain in the mixture by barcode sequencing (BarSeq). Our deletion approach improves on previous techniques based on splicing by overlap extension PCR (SOE-PCR) and tfoX-based natural transformation by incorporating a randomized barcode that results in unique DNA sequences within each deletion scar. Amplicon sequencing of the pool of barcoded strains before and after colonization faithfully reports on known colonization factors and provides increased sensitivity over colony counting methods. BarSeq enables rapid and sensitive characterization of the molecular factors involved in establishing the Vibrio-squid symbiosis and provides a valuable tool to interrogate the molecular dialogue at microbe-animal host interfaces.IMPORTANCE Beneficial microbes play essential roles in the health and development of their hosts. However, the complexity of animal microbiomes and general genetic intractability of their symbionts have made it difficult to study the coevolved mechanisms for establishing and maintaining specificity at the microbe-animal host interface. Model symbioses are therefore invaluable for studying the mechanisms of beneficial microbe-host interactions. Here, we present a combined barcode-tagged deletion and BarSeq approach to interrogate the molecular dialogue that ensures specific and reproducible colonization of the Hawaiian bobtail squid by Vibrio fischeri The ability to precisely manipulate the bacterial genome, combined with multiplex colonization assays, will accelerate the use of this valuable model system for mechanistic studies of how environmental microbes-both beneficial and pathogenic-colonize specific animal hosts.},
}
@article {pmid33320535,
year = {2021},
author = {Delgado-Gonzalez, A and Sanchez-Martin, RM},
title = {Mass Cytometry Tags: Where Chemistry Meets Single-Cell Analysis.},
journal = {Analytical chemistry},
volume = {93},
number = {2},
pages = {657-664},
doi = {10.1021/acs.analchem.0c03560},
pmid = {33320535},
issn = {1520-6882},
mesh = {Antibodies ; Cytophotometry/*methods ; Mass Spectrometry/methods ; Metals/chemistry ; Proteomics/*methods ; Single-Cell Analysis/*methods ; Staining and Labeling ; },
abstract = {Mass cytometry is a highly multiparametric proteomic technology that allows the measurement and quantification of nearly 50 markers with single-cell resolution. Mass cytometry reagents are probes tagged with metal isotopes of defined mass and act as reporters. Metals are detected using inductively coupled plasma time-of-flight mass spectrometry (ICP-TOF-MS). Many different types of mass-tag reagents have been developed to afford myriad applications. We have classified these compounds into polymer-based mass-tag reagents, nonpolymer-based mass-tag reagents, and inorganic nanoparticles. Metal-chelating polymers (MCPs) are widely used to profile and quantify cellular biomarkers; however, both the range of metals that can be detected and the metal signals have to be improved. Several strategies such as the inclusion of chelating agents or highly branched polymers may overcome these issues. Biocompatible materials such as polystyrene and inorganic nanoparticles are also of profound interest in mass cytometry. While polystyrene allows the inclusion of a wide variety of metals, the high metal content of inorganic nanoparticles offers an excellent opportunity to increase the signal from the metals to detect low-abundance biomarkers. Nonpolymer-based mass-tag reagents offer multiple applications: cell detection, cell cycle property determination, biomarker detection, and mass-tag cellular barcoding (MCB). Recent developments have been achieved in live cell barcoding by targeting proteins (CD45, b2m, and CD298), by using small and nonpolar probes or by ratiometric barcoding. From this perspective, the principal applications, strengths, and shortcomings of mass-tag reagents are highlighted, summarized, and discussed, with special emphasis on mass-tag reagents for MCB. Thereafter, the future perspectives of mass-tag reagents are discussed considering the current state-of-the-art technologies.},
}
@article {pmid33320307,
year = {2021},
author = {Zhang, W and Sun, Y and Liu, J and Xu, C and Zou, X and Chen, X and Liu, Y and Wu, P and Yang, X and Zhou, S},
title = {Correction to: DNA barcoding of Oryza: conventional, specific, and super barcodes.},
journal = {Plant molecular biology},
volume = {105},
number = {3},
pages = {229},
doi = {10.1007/s11103-020-01094-9},
pmid = {33320307},
issn = {1573-5028},
}
@article {pmid33319856,
year = {2020},
author = {Chen, PY and Ho, CW and Chen, AC and Huang, CY and Liu, TY and Liang, KH},
title = {Investigating seafood substitution problems and consequences in Taiwan using molecular barcoding and deep microbiome profiling.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {21997},
pmid = {33319856},
issn = {2045-2322},
mesh = {Animals ; Confidence Intervals ; *DNA Barcoding, Taxonomic ; Food Labeling ; Microbiota/*genetics ; Restaurants ; Seafood/*microbiology ; Taiwan ; Tilapia ; },
abstract = {Seafood is commonly seen in cuisines of the Asia-Pacific regions. The rates and consequences of seafood substitution frauds in Taiwan were elusive. To address this, we conducted a consumer-centered study, collecting seafood dishes and cooking materials from restaurants and markets easily accessible to the residents in Taiwan. Seafood substitutions were evaluated using DNA barcodes in the mitochondrial MT-CO1 gene. Among the 127 samples collected, 24 samples were mislabeled (18.9%, 95% Confidence interval [CI] = [12.5-26.8%]). The mislabel rates vary in different fish and product types (snapper [84.6%, 54.6-98.1%], cod [25%, 5.5-57.2%], swordfish [16.7%, 2.1-48.4%], cobia [16.7%, 0.4-64.1%], surimi products [100.0%]). A deep microbiome profiling was performed in 8 correctly-labeled conventional sushi and 2 tilapia sashimi mislabeled as snapper, with sequencing depths greater than 100,000 reads for every sample. The relative abundance of Pseudomonas genus is significantly higher in tilapia sashimi than in conventional sushi (P = 0.044). In conclusion, the gross seafood mislabel rate in Taiwan is 18.9% (12.5-26.8%). Snapper, cod and surimi products are particularly vulnerable to fraudulent substitutions. The high abundance of Pseudomonas in tilapia sashimi mislabeled as snapper unveils a potential health issue pertaining to the consumption of raw mislabeled seafood.},
}
@article {pmid33318927,
year = {2020},
author = {Gordy, MA and Koprivnikar, J and McPhail, B and Hanington, PC},
title = {Environmental and ecological factors driving trematode parasite community assembly in central Alberta lakes.},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {13},
number = {},
pages = {283-291},
pmid = {33318927},
issn = {2213-2244},
abstract = {Parasites have been neglected from most biodiversity surveys even though they are an essential component of ecosystems and intimately associated with the free-living communities within them. Parasites with complex life cycles, such as digenean trematode flatworms, utilize at least two host species within an ecosystem for their development and transmission, taking advantage of species networks to complete their life cycles. Despite this knowledge, our understanding of the processes that contribute to parasite community assembly, and which limit their geographic distributions, are rudimentary, including the importance of host diversity. Utilizing recent advancements in the identification of cryptic trematode species through molecular barcoding, we examined patterns of community assembly involving 79 species in six Alberta lakes over three years. Specifically, we focused on spatiotemporal variation in trematode diversity within their snail first intermediate hosts (component communities), how this might relate to host diversity through the specificity of host-parasite relationships, and the role of certain environmental factors in structuring these communities. We found substantial natural fluctuations of trematode communities through space and time within these lakes. Trematode communities were diverse, showing an overall positive relationship with snail diversity, but were often dominated by a few common species. We found that ecoregion and lake trophic status were key predictors for the presence of these trematode species. Such information is key for understanding how biodiversity alterations may affect parasite community composition, as well as our ability to formulate predictive models, by considering how this could influence both species richness and evenness.},
}
@article {pmid33317631,
year = {2020},
author = {Napier, G and Campino, S and Merid, Y and Abebe, M and Woldeamanuel, Y and Aseffa, A and Hibberd, ML and Phelan, J and Clark, TG},
title = {Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies.},
journal = {Genome medicine},
volume = {12},
number = {1},
pages = {114},
pmid = {33317631},
issn = {1756-994X},
support = {D43TW009127//Foundation for the National Institutes of Health/ ; MR/N010469/1//Medical Research Council (GB)/ ; MR/M01360X/1/MRC_/Medical Research Council/United Kingdom ; MR/R025576/1/MRC_/Medical Research Council/United Kingdom ; MR/N010469/1/MRC_/Medical Research Council/United Kingdom ; BB/R013063/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/R020973/1/MRC_/Medical Research Council/United Kingdom ; D43 TW009127/TW/FIC NIH HHS/United States ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Genome, Bacterial ; Genomics ; Humans ; Mutation ; Mycobacterium tuberculosis/*genetics ; *Phylogeny ; Polymorphism, Single Nucleotide ; Tuberculosis/diagnosis/*epidemiology/*microbiology ; Virulence ; Whole Genome Sequencing ; },
abstract = {BACKGROUND: Tuberculosis, caused by bacteria in the Mycobacterium tuberculosis complex (MTBC), is a major global public health burden. Strain-specific genomic diversity in the known lineages of MTBC is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Fast and accurate tracking of MTBC strains is therefore crucial for infection control, and our previous work developed a 62-single nucleotide polymorphism (SNP) barcode to inform on the phylogenetic identity of 7 human lineages and 64 sub-lineages.<br><br>METHODS: To update this barcode, we analysed whole genome sequencing data from 35,298 MTBC isolates (~&#x2009;1 million SNPs) covering 9 main lineages and 3 similar animal-related species (M. tuberculosis var. bovis, M. tuberculosis var. caprae and M. tuberculosis var. orygis). The data was partitioned into training (N&#xa0;=&#x2009;17,903, 50.7%) and test (N&#xa0;=&#x2009;17,395, 49.3%) sets and were analysed using an integrated phylogenetic tree and population differentiation (FST) statistical approach.<br><br>RESULTS: By constructing a phylogenetic tree on the training MTBC isolates, we characterised 90 lineages or sub-lineages or species, of which 30 are new, and identified 421 robust barcoding mutations, of which a minimal set of 90 was selected that included 20 markers from the 62-SNP barcode. The barcoding SNPs (90 and 421) discriminated perfectly the 86 MTBC isolate (sub-)lineages in the test set and could accurately reconstruct the clades across the combined 35k samples.<br><br>CONCLUSIONS: The validated 90 SNPs can be used for the rapid diagnosis and tracking of MTBC strains to assist public health surveillance and control. To facilitate this, the SNP markers have now been incorporated into the TB-Profiler informatics platform (https://github.com/jodyphelan/TBProfiler).},
}
@article {pmid33312049,
year = {2020},
author = {Cerdeña, J and Farfán, J and Vargas, HA and Brito, R and Gonçalves, GL and Lazo, A and Moreira, GRP},
title = {Phyllocnistis furcata sp. nov.: a new species of leaf-miner associated with Baccharis (Asteraceae) from Southern Peru (Lepidoptera, Gracillariidae).},
journal = {ZooKeys},
volume = {996},
number = {},
pages = {121-145},
pmid = {33312049},
issn = {1313-2989},
abstract = {The southwestern Andes of Peru harbors a hidden taxonomic diversity of Lepidoptera. Here a new leaf-mining species of Gracillariidae (Lepidoptera) is described, Phyllocnistis furcata Vargas &amp; Cerdeña, sp. nov., from a dry Andean valley of southern Peru, at 2400 m above sea level. The morphological aspects of adults (male and female) and the immature stages associated with Baccharis alnifolia Meyen &amp; Walp. (Asteraceae) are given, under optical microscopy and scanning electron microscopy. DNA barcodes show that its nearest neighbor is the Atlantic Forest species Phyllocnistis ourea Brito &amp; Moreira, 2017 that feeds on Baccharis anomala DC. The importance of morphological characters from immature stages for diagnosis among congeneric species is also discussed. Phyllocnistis furcata represents the fourth species of Phyllocnistis Zeller for Peru, and first record from the south of Peru for the genus.},
}
@article {pmid33311407,
year = {2020},
author = {Sankaran, PM and Sebastian, PA},
title = {A new species of Carlogonus Demange, 1961 from southern India (Spirostreptida, Harpagophoridae, Harpagophorinae), with phylogenetic analysis and species-group divisions in the genus.},
journal = {Zootaxa},
volume = {4868},
number = {1},
pages = {zootaxa.4868.1.2},
doi = {10.11646/zootaxa.4868.1.2},
pmid = {33311407},
issn = {1175-5334},
mesh = {Animals ; *Arthropods ; DNA, Mitochondrial ; India ; Phylogeny ; },
abstract = {The genus Carlogonus Demange, 1961, is diagnosed, and its relationship with other members of the Harpurostreptini Hoffman, 1980 is discussed. A new species, Carlogonus gayathri sp. nov. is described and illustrated from the southern Indian State of Kerala, and its DNA barcoding data is presented. Phylogenetic analysis based on mtDNA sequence data revealed that Carlogonus is sister-taxon to Thyropygus Pocock, 1894. Two species-groups are recognised in Carlogonus: the exaratus-group is characterised by a single tibial spine on the gonopod, while the acifer-group has paired tibial spines. A dichotomous key is presented for the known Carlogonus spp., and the current distribution of the genus is mapped.},
}
@article {pmid33311330,
year = {2020},
author = {Latif, R and Malek, M and Aminjan, AR and Pasantes, JJ and Briones, MJI and Csuzdi, C},
title = {Integrative taxonomy of some Iranian peregrine earthworm species using morphology and barcoding (Annelida: Megadrili).},
journal = {Zootaxa},
volume = {4877},
number = {1},
pages = {zootaxa.4877.1.7},
doi = {10.11646/zootaxa.4877.1.7},
pmid = {33311330},
issn = {1175-5334},
mesh = {Animals ; Biological Evolution ; DNA Barcoding, Taxonomic ; Iran ; *Oligochaeta/genetics ; Phylogeny ; },
abstract = {Despite the biological and economic importance of earthworms, the taxonomic status and evolutionary relationships of most lumbricid genera are still under debate. Further complications arise from the recognition that earthworms also show a high cryptic diversity. Past and current field studies of Iranian earthworm fauna have resulted in the identification of a total number of 28 earthworm species. However, many specimens do not fully fit into their original descriptions, making the species assignation very difficult. In this study, we evaluated the genetic diversity using mitochondrial markers as a tool to assess the species occurrence of some problematic species in Iran. Four species with high morphological variation were selected: Aporrectodea caliginosa (Savigny, 1826), Aporrectodea trapezoides (Dugès, 1828), Dendrobaena byblica (Rosa, 1893) and Dendrobaena veneta (Rosa, 1886). Morphological identification was contrasted with the molecular information generated through COI and 16S barcoding and the COI and 16S sequences stored in the Genbank. The results of this first integrative taxonomic analysis revealed that D. veneta consisted of two separated clades and that a number of species assigned to D. byblica showed very close relationships with those belonging to the genus Philomontanus. The lack of taxonomic expertise and identification characters providing a clear and unambiguous identification of earthworms highlights the urgent need of new tools to identify species unequivocally. Therefore, it is concluded that more taxonomical studies are needed to clarify the diagnostic characters and taxonomic status of the species belonging to two genera, Aporrectodea and Dendrobaena (Lumbricidae), in Iran.},
}
@article {pmid33311275,
year = {2020},
author = {Sayyadzadeh, G and Esmaeili, HR},
title = {Oxynoemacheilus marunensis, a new loach species from the Persian Gulf basin with remarks on O. frenatus (Teleostei: Nemacheilidae).},
journal = {Zootaxa},
volume = {4885},
number = {2},
pages = {zootaxa.4885.2.2},
doi = {10.11646/zootaxa.4885.2.2},
pmid = {33311275},
issn = {1175-5334},
mesh = {Animals ; Color ; *Cypriniformes ; Indian Ocean ; Rivers ; },
abstract = {Oxynoemacheilus marunensis, new species, is described from the Marun, a tributary of the Jarrahi River, which flows just east of the Tigris River to the Persian Gulf. It belongs to a group of species (O. argyrogramma, O. euphraticus, O. hanae, O. karunensis, and O. kurdistanicus) having two bold, black, round, or comma-shaped black spots on the caudal-fin base. It is most similar to a newly described species from the Persian Gulf basin, O. karunensis, but distinguished from O. karunensis by having a longer distance between pelvic and anal-fin origins [22.3-23.8 vs. 19.5-22.3 (% SL)] and a K2P distance of 6% based on COI barcode region sequences.},
}
@article {pmid33311236,
year = {2020},
author = {Lei, QI and Chen, J and Song, C and Qi, X and Zhang, R},
title = {Description of larva and female of Polypedilum (Probolum) bullum Zhang Wang with DNA barcodes.},
journal = {Zootaxa},
volume = {4890},
number = {2},
pages = {zootaxa.4890.2.6},
doi = {10.11646/zootaxa.4890.2.6},
pmid = {33311236},
issn = {1175-5334},
mesh = {Animals ; *Chironomidae ; *DNA Barcoding, Taxonomic ; Female ; Larva ; },
abstract = {The larva and female of Polypedilum (Probolum) bullum Zhang Wang associated with morphological characteristics and DNA barcodes are described and illustrated for the first time. The female is characteristic with developed dorsomesal lobe and ventrolateral lobe both densely covered with apical setae, ventrolateral lobe partially covered by dorsomesal lobe. The larva is distinguished by the shape of mentum, pecten epipharyngis, labral SI and labral SII.},
}
@article {pmid33311228,
year = {2020},
author = {Jiang, XK and Hennen, DA and Chen, HM and Xie, ZC},
title = {First description of the male of Glyphiulus formosus (Pocock, 1895) (Diplopoda: Spirostreptida: Cambalopsidae) from China.},
journal = {Zootaxa},
volume = {4861},
number = {2},
pages = {zootaxa.4861.2.8},
doi = {10.11646/zootaxa.4861.2.8},
pmid = {33311228},
issn = {1175-5334},
mesh = {Animals ; *Arthropods ; China ; Male ; },
abstract = {The male of Glyphiulus formosus (Pocock, 1895) is described for the first time based on specimens collected from Shenzhen, Guangdong, China. According to the male sexual characters, this species is verified to be a member of the G. javanicus group. In addition, a DNA barcode of the partial COI gene of G. formosus is provided.},
}
@article {pmid33311178,
year = {2020},
author = {Shiraiwa, K and Grishin, NV},
title = {Welcome back Mr. Rudkin: differentiating Papilio zelicaon and Papilio polyxenes in Southern California (Lepidoptera: Papilionidae).},
journal = {Zootaxa},
volume = {4877},
number = {3},
pages = {zootaxa.4877.3.3},
doi = {10.11646/zootaxa.4877.3.3},
pmid = {33311178},
issn = {1175-5334},
support = {R35 GM127390/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Base Sequence ; *Butterflies/genetics ; California ; DNA, Mitochondrial ; Wings, Animal ; },
abstract = {We studied wing pattern characters to distinguish closely related sympatric species Papilio zelicaon Lucas, 1852 and Papilio polyxenes Fabricius, 1775 in Southern California, and developed a morphometric method based on the ventral black postmedian band. Application of this method to the holotype of Papilio [Zolicaon variety] Coloro W. G. Wright, 1905, the name currently applied to the P. polyxenes populations, revealed that it is a P. zelicaon specimen. The name for western US polyxenes subspecies thus becomes Papilio polyxenes rudkini (F. R. Chermock, 1981), reinstated status, and we place coloro as a junior subjective synonym of P. zelicaon. Furthermore, we sequenced mitochondrial DNA COI barcodes of rudkini and coloro holotypes and compared them with those of polyxenes and zelicaon specimens, confirming rudkini as polyxenes and coloro as zelicaon.},
}
@article {pmid33311137,
year = {2020},
author = {Qi, X and Song, C and Ge, K and Wang, X},
title = {Polypedilum (Cerobregma) paracyclus sp. n., a new species from Oriental China (Diptera: Chironomidae).},
journal = {Zootaxa},
volume = {4881},
number = {1},
pages = {zootaxa.4881.1.12},
doi = {10.11646/zootaxa.4881.1.12},
pmid = {33311137},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; China ; *Chironomidae ; Color ; *Diptera ; Male ; },
abstract = {Polypedilum (Cerobregma) paracyclus sp. n. Qi Song is described based on male imagines collected by light trap in Oriental China. The description is supported by both morphological and DNA barcode evidences. The new species is distinguished from its related congeners in having some atypical morphological characters: tibia and femur dark brown, knees yellow; abdominal segment VII distinctly triangular and tapered towards base; tergite IX broadly sub-trapezoidal, tapering posteriorly, anal tergite bands ending with a characteristic sub-oval area; superior volsella sickle-like shaped with pointed apex; inferior volsella with orally directed dorsal setae; distal inner margin of gonostylus without shortly branched setae.},
}
@article {pmid33311068,
year = {2020},
author = {Sciarretta, A and Hausmann, A},
title = {The Geometridae of Ethiopia III: genus Zamarada (Lepidoptera: Geometridae, Ennominae, Cassymini).},
journal = {Zootaxa},
volume = {4894},
number = {3},
pages = {zootaxa.4894.3.1},
doi = {10.11646/zootaxa.4894.3.1},
pmid = {33311068},
issn = {1175-5334},
mesh = {Animals ; Ethiopia ; Female ; *Lepidoptera ; Male ; *Moths ; },
abstract = {We present faunistic and taxonomic data for the genus Zamarada (Geometridae, Ennominae, Cassymini) in Ethiopia. With this contribution, the number of Zamarada species in Ethiopia increases from 16 to 23. One species Zamarada erugatoides sp. n. is described as new. Zamarada iobathra Prout, 1932 and Zamarada polyctemon Prout, 1932 are downgraded from species rank to subspecies of Zamarada euryscaphes Prout, 1915 (stat. n.). The female of Zamarada eurygnathus Fletcher, 1974 and Zamarada chrysothyra Hampson, 1909 and the male of Zamarada secutaria (Guenée, 1858) are described for the first time.},
}
@article {pmid33311060,
year = {2020},
author = {DA Silva, VCP and Kaydan, MB and Basso, C},
title = {Pseudococcidae (Hemiptera: Coccomorpha) in Uruguay: morphological identification and molecular characterization, with descriptions of two new species.},
journal = {Zootaxa},
volume = {4894},
number = {4},
pages = {zootaxa.4894.4.1},
doi = {10.11646/zootaxa.4894.4.1},
pmid = {33311060},
issn = {1175-5334},
mesh = {Animals ; Fruit ; *Hemiptera ; *Malus ; Uruguay ; *Vitis ; },
abstract = {Mealybugs (Hemiptera: Coccomorpha: Pseudococcidae) are important pests in fruit production in Uruguay; however, very little is known about the species involved. A survey of mealybugs associated especially with fruit crops (apple, citrus, figs, grapes, pears, quince and strawberry), and other crops like vegetables and sugar cane, ornamentals and weeds was performed between 2017 and 2019 in Uruguay, using integrated taxonomy (morphology and DNA analyses) for their identification. A total of 19 mealybug species were identified. The most common species were Planococcus ficus (Signoret), Pseudococcus scatoterrae Granara de Willink and Pseudococcus viburni (Signoret) on fruits, and Phenacoccus madeirensis Green, Phenacoccus peruvianus Granara de Willink and Planococcus citri (Risso) on ornamental plants, all of them causing damage to their hosts. This study presents nine new species records for Uruguay, besides the description of two new species. An identification key to the mealybugs in Uruguay is provided.},
}
@article {pmid33307272,
year = {2021},
author = {Rahman, MA and Murata, K and Burt, BD and Hirano, N},
title = {Changing the landscape of tumor immunology: novel tools to examine T cell specificity.},
journal = {Current opinion in immunology},
volume = {69},
number = {},
pages = {1-9},
doi = {10.1016/j.coi.2020.11.003},
pmid = {33307272},
issn = {1879-0372},
mesh = {Animals ; Cancer Vaccines/*immunology ; DNA Barcoding, Taxonomic ; HLA Antigens/genetics/metabolism ; High-Throughput Screening Assays ; Humans ; Immunotherapy, Adoptive/*methods ; Mass Spectrometry ; Neoplasms/immunology/*therapy ; Precision Medicine ; Single-Cell Analysis ; T-Lymphocytes/*immunology ; },
abstract = {Immunotherapy has established itself as a stalwart arm in patient care and with precision medicine forms the new paradigm in cancer treatment. T cells are an important group of immune cells capable of potent cancer immune surveillance and immunity. The advent of bioinformatics, particularly more recent advances incorporating algorithms employing machine learning, provide a seemingly limitless ability for T cell analysis and hypothesis generation. Such endeavors have become indispensable to research efforts accelerating and evolving to such an extent that there exists an appreciable gap between knowledge and proof of function and application. Exciting new technologies such as DNA barcoding, cytometry by time-of-flight (CyTOF), and peptide-exchangeable pHLA multimers inclusive of rare and difficult HLA alleles offer high-throughput cell-by-cell analytical capabilities. These outstanding recent contributions to T cell research will help close this gap and potentially bring practical benefit to patients.},
}
@article {pmid33304655,
year = {2020},
author = {Garibian, PG and Neretina, AN and Taylor, DJ and Kotov, AA},
title = {Partial revision of the neustonic genus Scapholeberis Schoedler, 1858 (Crustacea: Cladocera): decoding of the barcoding results.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e10410},
pmid = {33304655},
issn = {2167-8359},
abstract = {Water fleas (Crustacea: Cladocera) are among the most intensively studied freshwater invertebrates. However, ecologically important daphniids that live on the surface layer (neuston) remain taxonomically confused. Here we attempt to reconcile genetic and morphological information for the neustonic genus Scapholeberis Schoedler, 1858 (Cladocera: Daphniidae) and present the first revision of the Scapholeberis kingii species group. We analyzed new and existing mitochondrial DNA sequences (сytochrome C oxidase subunit I gene region) together with morphology for all but one of the known species of the neustonic daphniids. Morphological comparisons of available populations, belonging to the Scapholeberis kingii species group from several Australian, Asian and African localities, revealed, that they are almost identical according to parthenogenetic females. However, Australian populations can be reliably distinguished from Asian ones based on the morphology of gamogenetic females. Mitochondrial DNA data analyses revealed divergent lineages (>17% for the DNA barcoding COI region) for the three different species (Australia, Asia and Africa). Based on this set of data, we redescribed S. kingii Sars, 1888 from Australia, its terra typica, and described a new species, S. smirnovi sp.nov. from the Russian Far East, Korea and Japan. The status of populations from Ethiopia and the Republic of South Africa remained unclear, because in the African material and the putative type material, we found only parthenogenetic females. Our results provide an integrative revision of the S. kingii species group and improve the taxonomic scaffold used for barcoding and genomics for the remaining species groups in the daphniid genus Scapholeberis.},
}
@article {pmid33304185,
year = {2020},
author = {Ismail, M and Ahmad, A and Nadeem, M and Javed, MA and Khan, SH and Khawaish, I and Sthanadar, AA and Qari, SH and Alghanem, SM and Khan, KA and Khan, MF and Qamer, S},
title = {Development of DNA barcodes for selected Acacia species by using rbcL and matK DNA markers.},
journal = {Saudi journal of biological sciences},
volume = {27},
number = {12},
pages = {3735-3742},
pmid = {33304185},
issn = {1319-562X},
abstract = {Acacia species are very important tree species in tropical and subtropical countries of the World for their economic and medicinal benefits. Precise identification of Acacia is very important to distinguish the invasive species from rare species however, it is difficult to differentiate Acacia species based on morphological charcters. In addition, precise identification is also important for wood charcterization in the forest industry as these species are declining due to illegal logging and deforestation. To overcome thsese limitations of morphological identification, DNA barcoding is being used as an efficient and quick approach for precise identification of tree species. In this study, we selected two chloroplast and plastid base DNA markers (rbcL and matK) for the identification of five selected tree species of Acacia (A. albida, A. ampliceps, A. catechu, A. coriacea and A. tortilis). The genomic DNA of the selected Acacia species was extracted, amplified through PCR using specific primers and subsequently sequenced through Sanger sequencing. In matK DNA marker the average AT nucleotide contents were higher (59.46%) and GC contents were lower (40.44%) as compared to the AT (55.40%) and GC content (44.54%) in rbcL marker. The means genetic distance K2P between the Acacia species was higher in matK (0.704%) as compared to rbcL (0.230%). All Acacia species could be identified based on unique SNPs profile. Based on SNP data profiles, DNA sequence based scannable QR codes were developed for accurate identification of Acacia species. The phylogenetic analysis based on both markers (rbcL and matK) showed that both A. coriacea and A. tortilis were closely related with each other and clustered in the same group while other two species A. albida and A. catechu were grouped together. The specie A. ampliceps remained ungrouped distantly, compared with other four species. These finding highlights the potential of DNA barcoding for efficient and reproducible identification of Acacia species.},
}
@article {pmid33304160,
year = {2020},
author = {Maurya, S and Darshetkar, AM and Yi, DK and Kim, J and Lee, C and Ali, MA and Choi, S and Choudhary, RK and Kim, SY},
title = {Plastome comparison and evolution within the tribes of Plantaginaceae: Insights from an Asian gypsyweed.},
journal = {Saudi journal of biological sciences},
volume = {27},
number = {12},
pages = {3489-3498},
pmid = {33304160},
issn = {1319-562X},
abstract = {In spite of availability of several plastomes representing different tribes of Plantaginaceae, sparse attempts have been made to understand the plastome structure, evolution, and phylogenomics. In the present study, we have made an effort to understand the gene content and plastome evolution in the family Plantaginaceae using the newly generated plastome sequence of Veronica ovata subsp. kiusiana, a taxon native to SE Asia. In the first-ever attempt, plastomes of seven out of 10 tribes of Plantaginaceae have been compared to understand the evolution across the tribes of Plantaginaceae. The size of the plastome of V. ovata subsp. kiusiana is 152,249 bp, showing a typical quadripartite structure containing LSC, SSC, and two IRs with the sizes of 83,187, 17,704, and 25,679 respectively. The plastome comparison revealed the unique deletions in ycf2 and ndhF genes of members of different tribes, and also revealed high nucleotide variable hotspots. The study also revealed six highly variable genes and intergenic spacer viz. rps16, rps15-ycf1, ccsA-ndhD, ndhC-trnV, petN-psbM, and ycf1-trnN as potential DNA barcodes for the genus Veronica. The phylogenomic study revealed the sister relationship between V. ovata subsp. kiusiana and V. persica and also suggested the tentative placement of seven tribes in the family Plantaginaceae.},
}
@article {pmid33303786,
year = {2020},
author = {Phi, TCM and Chu, HH and Trieu Le, N and Nguyen, DB},
title = {Phylogenetic relationship of Paramignya trimera and its relatives: an evidence for the wide sexual compatibility.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {21662},
pmid = {33303786},
issn = {2045-2322},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic ; Genetic Variation ; *Phylogeny ; Rutaceae/anatomy &amp; histology/*classification/*genetics ; Vietnam ; },
abstract = {The genus Paramignya (Rutaceae) comprises about 30 species typically distributing in tropical Asia. Like other genera of the family Rutaceae, the significant variation in the morphology of Paramignya species makes the taxonomic study and accurate identification become difficult. In Vietnam, Paramignya species have been mostly found in Khanh Hoa and Lam Dong provinces and used as traditional medicines. Recently, Paramignya trimera, a species of the genus Paramignya with local name "Xao tam phan" has been drawn attention and intensively exploited to treat liver diseases and cancers. However, the significant variations in the morphology and different local names of P. trimera have caused confusion and difficulty in the accurate identification and application of this plant for medicine. In this study, the combination of both morphological and DNA sequence data has effectively supported the taxonomic identification of P. trimera and some relatives collected in Khanh Hoa and Lam Dong provinces. The comparison of the morphology and analysis of the phylogenetic trees suggested that there was a significant variation of P. trimera. In addition, some accessions of P. trimera with morphological characteristics similar and Atalantia buxifolia were likely the intergeneric hybrids between the two species. Analysis of genetic variation, interspecific and intraspecific distances using ITS, matK and rbcL sequences shown that P. trimera was closely related to A. buxifolia, Severinia monophylla and Luvunga scandens. In addition, matK sequences represented as the effective candidate DNA barcode to identify and distinguish Paramignya species from others of the family Rutaceae.},
}
@article {pmid33303588,
year = {2020},
author = {Muller, R and Meacham, ZA and Ferguson, L and Ingolia, NT},
title = {CiBER-seq dissects genetic networks by quantitative CRISPRi profiling of expression phenotypes.},
journal = {Science (New York, N.Y.)},
volume = {370},
number = {6522},
pages = {},
pmid = {33303588},
issn = {1095-9203},
support = {DP2 CA195768/CA/NCI NIH HHS/United States ; R01 GM130996/GM/NIGMS NIH HHS/United States ; R01 GM135233/GM/NIGMS NIH HHS/United States ; S10 OD018174/OD/NIH HHS/United States ; },
mesh = {Alcohol Oxidoreductases/genetics ; Aminohydrolases/genetics ; *CRISPR-Associated Protein 9 ; *CRISPR-Cas Systems ; Eukaryotic Initiation Factor-2/metabolism ; *Gene Expression ; Gene Expression Profiling/*methods ; *Gene Regulatory Networks ; Phenotype ; Phosphorylation ; Protein Serine-Threonine Kinases/metabolism ; Pyrophosphatases/genetics ; RNA, Guide, CRISPR-Cas Systems/genetics ; RNA, Transfer/genetics/metabolism ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; },
abstract = {To realize the promise of CRISPR-Cas9-based genetics, approaches are needed to quantify a specific, molecular phenotype across genome-wide libraries of genetic perturbations. We addressed this challenge by profiling transcriptional, translational, and posttranslational reporters using CRISPR interference (CRISPRi) with barcoded expression reporter sequencing (CiBER-seq). Our barcoding approach allowed us to connect an entire library of guides to their individual phenotypic consequences using pooled sequencing. CiBER-seq profiling fully recapitulated the integrated stress response (ISR) pathway in yeast. Genetic perturbations causing uncharged transfer RNA (tRNA) accumulation activated ISR reporter transcription. Notably, tRNA insufficiency also activated the reporter, independent of the uncharged tRNA sensor. By uncovering alternate triggers for ISR activation, we illustrate how precise, comprehensive CiBER-seq profiling provides a powerful and broadly applicable tool for dissecting genetic networks.},
}
@article {pmid33301092,
year = {2021},
author = {Besse, P and Da Silva, D and Grisoni, M},
title = {Plant DNA Barcoding Principles and Limits: A Case Study in the Genus Vanilla.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2222},
number = {},
pages = {131-148},
pmid = {33301092},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic ; *DNA, Plant ; Genes, Plant ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Quantitative Trait Loci ; Sequence Analysis, DNA ; Species Specificity ; Vanilla/*classification/*genetics ; },
abstract = {Powerful DNA barcodes have been much more difficult to define in plants than in animals. In 2009, the international Consortium for the Barcoding Of Life (CBOL) chose the combination of the chloroplast genes (rbcL + matK) as the proposed official barcode for plants. However, this system has got important limits. First, any barcode system will only be useful if there is a clear barcode gap and if species are monophyletic. Second, chloroplast and mitochondrial (COI gene used for animals) barcodes will not be usable for discriminating hybrid species. Moreover, it was also shown that, using chloroplast regions, maximum species discrimination would be around 70% and very variable among plant groups. This is why many authors have more recently advocated for the addition of the nuclear ITS region to this barcode because it reveals more variations and allows the resolution of hybrid or closely related species. We tested different chloroplast genes (rbcL, matK, psaB, psbC) and the nuclear ITS region in the genus Vanilla, a taxonomically complex group and therefore a good model to test for the efficiency of different barcode systems. We found that the CBOL official barcode system performed relatively poorly in Vanilla (76% species discrimination), and we demonstrate that adding ITS to this barcode system allows to increase resolution (for closely related species and to the subspecies level) and to identify hybrid species. The best species discrimination attained was 96.2% because of one paraphyletic species that could not be resolved.},
}
@article {pmid33301088,
year = {2021},
author = {Záveská Drábková, L},
title = {Herbarium Specimens: A Treasure for DNA Extraction, an Update.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2222},
number = {},
pages = {69-88},
pmid = {33301088},
issn = {1940-6029},
mesh = {Amplified Fragment Length Polymorphism Analysis ; Chemical Fractionation/methods ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Microsatellite Repeats ; Organ Specificity ; Plant Leaves/genetics ; Plants/*classification/*genetics ; Polymerase Chain Reaction ; Reagent Kits, Diagnostic ; Sequence Analysis, DNA ; },
abstract = {With the expansion of molecular techniques, the historical collections have become widely used. The last boom started with using next- and second-generation sequencing in which massive parallel sequencing replaced targeted sequencing and third-generation technology involves single molecule technology. Studying plant DNA using these modern molecular techniques plays an important role in understanding evolutionary relationships, identification through DNA barcoding, conservation status, and many other aspects of plant biology. Enormous herbarium collections are an important source of material especially for taxonomic long-standing issues, specimens from areas difficult to access or from taxa that are now extinct. The ability to utilize these specimens greatly enhances the research. However, the process of extracting DNA from herbarium specimens is often fraught with difficulty related to such variables as plant chemistry, drying method of the specimen, and chemical treatment of the specimen. The result of these applications is often fragmented DNA. The reason new sequencing approaches have been so successful is that the template DNA needs to be fragmented for proper library building, and herbarium DNA is exactly that. Although many methods have been developed for extraction of DNA from herbarium specimens, the most frequently used are modified CTAB and DNeasy Plant Mini Kit protocols. Nine selected protocols in this chapter have been successfully used for high-quality DNA extraction from different kinds of plant herbarium tissues. These methods differ primarily with respect to their requirements for input material (from algae to vascular plants), type of the plant tissue (leaves with incrustations, sclerenchyma strands, mucilaginous tissues, needles, seeds), and further possible applications (PCR-based methods, microsatellites, AFLP or next-generation sequencing).},
}
@article {pmid33299191,
year = {2020},
author = {Jin, X and Demere, Z and Nair, K and Ali, A and Ferraro, GB and Natoli, T and Deik, A and Petronio, L and Tang, AA and Zhu, C and Wang, L and Rosenberg, D and Mangena, V and Roth, J and Chung, K and Jain, RK and Clish, CB and Vander Heiden, MG and Golub, TR},
title = {A metastasis map of human cancer cell lines.},
journal = {Nature},
volume = {588},
number = {7837},
pages = {331-336},
pmid = {33299191},
issn = {1476-4687},
support = {P30 CA014051/CA/NCI NIH HHS/United States ; R01 CA208205/CA/NCI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R35 CA197442/CA/NCI NIH HHS/United States ; U01 CA220413/CA/NCI NIH HHS/United States ; R35 CA242379/CA/NCI NIH HHS/United States ; R35 CA197743/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Brain Neoplasms/genetics/metabolism/pathology/secondary ; Breast Neoplasms/genetics/metabolism/*pathology ; Cell Line, Tumor ; *Cell Movement ; Electronic Data Processing ; Female ; Heterografts ; Humans ; Lipid Metabolism/genetics ; Mice ; Molecular Typing ; Mutation ; Neoplasm Metastasis/genetics/*pathology ; Neoplasm Transplantation ; *Organ Specificity ; Pilot Projects ; },
abstract = {Most deaths from cancer are explained by metastasis, and yet large-scale metastasis research has been impractical owing to the complexity of in vivo models. Here we introduce an in vivo barcoding strategy that is capable of determining the metastatic potential of human cancer cell lines in mouse xenografts at scale. We validated the robustness, scalability and reproducibility of the method and applied it to 500 cell lines[1,2] spanning 21 types of solid tumour. We created a first-generation metastasis map (MetMap) that reveals organ-specific patterns of metastasis, enabling these patterns to be associated with clinical and genomic features. We demonstrate the utility of MetMap by investigating the molecular basis of breast cancers capable of metastasizing to the brain-a principal cause of death in patients with this type of cancer. Breast cancers capable of metastasizing to the brain showed evidence of altered lipid metabolism. Perturbation of lipid metabolism in these cells curbed brain metastasis development, suggesting a therapeutic strategy to combat the disease and demonstrating the utility of MetMap as a resource to support metastasis research.},
}
@article {pmid33297960,
year = {2020},
author = {Baeza, JA},
title = {Yes, we can use it: a formal test on the accuracy of low-pass nanopore long-read sequencing for mitophylogenomics and barcoding research using the Caribbean spiny lobster Panulirus argus.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {882},
pmid = {33297960},
issn = {1471-2164},
mesh = {Animals ; Caribbean Region ; *Nanopore Sequencing ; *Nanopores ; *Palinuridae/genetics ; Phylogeny ; },
abstract = {BACKGROUND: Whole mitogenomes or short fragments (i.e., 300-700 bp of the cox1 gene) are the markers of choice for revealing within- and among-species genealogies. Protocols for sequencing and assembling mitogenomes include 'primer walking' or 'long PCR' followed by Sanger sequencing or Illumina short-read low-coverage whole genome (LC-WGS) sequencing with or without prior enrichment of mitochondrial DNA. The aforementioned strategies assemble complete and accurate mitochondrial genomes but are time consuming and/or expensive. In this study, I first tested whether mitogenomes can be sequenced from long-read nanopore sequencing data exclusively. Second, I explored the accuracy of the long-read assembled genomes by comparing them to a 'gold' standard reference mitogenome retrieved from the same individual using Illumina sequencing. Third and lastly, I tested if the long-read assemblies are useful for mitophylogenomics and barcoding research. To accomplish these goals, I used the Caribbean spiny lobster Panulirus argus, an ecologically relevant species in shallow water coral reefs and target of the most lucrative fishery in the greater Caribbean region.<br><br>RESULTS: LC-WGS using a MinION ONT device and various de-novo and reference-based assembly pipelines retrieved a complete and highly accurate mitogenome for the Caribbean spiny lobster Panulirus argus. Discordance between each of the long-read assemblies and the reference mitogenome was mostly due to indels at the flanks of homopolymer regions. Although not 'perfect', phylogenetic analyses using entire mitogenomes or a fragment of the cox1 gene demonstrated that mitogenomes assembled using long reads reliably identify the sequenced specimen as belonging to P. argus and distinguish it from other related species in the same genus, family, and superorder.<br><br>CONCLUSIONS: This study serves as a proof-of-concept for the future implementation of in-situ surveillance protocols using the MinION to detect mislabeling in P. argus across its supply chain. Mislabeling detection will improve fishery management in this overexploited lobster. This study will additionally aid in decreasing costs for exploring meta-population connectivity in the Caribbean spiny lobster and will aid with the transfer of genomics technology to low-income countries.},
}
@article {pmid33296546,
year = {2021},
author = {Gálico, DA and Kitos, AA and Ovens, JS and Sigoli, FA and Murugesu, M},
title = {Lanthanide-Based Molecular Cluster-Aggregates: Optical Barcoding and White-Light Emission with Nanosized {Ln20 }
Compounds.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {60},
number = {11},
pages = {6130-6136},
doi = {10.1002/anie.202013867},
pmid = {33296546},
issn = {1521-3773},
abstract = {Counterfeit goods represent a major problem to companies, governments, and customers, affecting the global economy. In order to protect the authenticity of products and documents, optical anti-counterfeit technologies have widely been employed via the use of discrete molecular species, extended metal-organic frameworks (MOFs), and nanoparticles. Herein, for the first time we demonstrate the potential use of molecular cluster-aggregates (MCA) as optical barcodes via composition and energy transfer control. The tuneable optical properties for the [Ln20 (chp)30 (CO3)12 (NO3)6 (H2 O)6 ], where chp[-] =deprotonated 6-chloro-2-pyridinol, allow the fine control of the emission colour output, resulting in high-security level optical labelling with a precise read-out. Moreover, a unique tri-doped composition of Gd[III] , Tb[III] , and Eu[III] led to MCAs with white-light emission. The presented methodology is a unique approach to probe the effect of composition control on the luminescent properties of nanosized molecular material.},
}
@article {pmid33293886,
year = {2020},
author = {Wöger, R and Wöger, R and Nuss, M},
title = {DNA barcodes for Aotearoa New Zealand Pyraloidea (Lepidoptera).},
journal = {Biodiversity data journal},
volume = {8},
number = {},
pages = {e58841},
pmid = {33293886},
issn = {1314-2828},
abstract = {Identification of pyraloid species is often hampered by highly similar external morphology requiring microscopic dissection of genitalia. This becomes especially obvious when mass samples from ecological studies or insect monitoring have to be analysed. DNA barcode sequences could accelerate identification, but are not available for most pyraloid species from New Zealand. Hence, we are presenting a first DNA-barcode library for this group, providing 440 COI barcodes (cytochrome C oxidase I sequences) for 73 morphologically-identified species, which is 29% of Pyraloidea known from New Zealand. Results are analysed using the Barcode Index Number system (BIN) of BOLD and the Automatic Barcode Gap Discovery method (ABGD). Using BIN, the 440 barcodes reveal 82 clusters. A perfect match between BIN assignment and morphological identification was found for 63 species (86.3%). Four species (5.5%) share BINs, each with two species in one BIN, of which Glaucocharis epiphaea and Glaucocharis harmonica even share the same barcode. In contrast, six species (8.2%) split into two or more BINs, with the highest number of five BINs for Orocrambus ramosellus. The interspecific variation of all collected specimens of New Zealand Pyraloidea averages 12.54%. There are deep intraspecific divergences (> 2%) in seven species, for instance Orocrambus vulgaris with up to 6.6% and Scoparia ustimacula with 5.5%. Using ABGD, the 440 barcodes reveal 71 or 88 operational taxonomic units (OTUs), depending on the preferred partition. A perfect match between OTU and morphological identification was found for 56 species (76.7%) or 62 species (84.9%). ABGD delivers four or seven species sharing OTUs and four or ten species split into more than one OTU. Morphological re-examination, as well as the analysis of a concatenated dataset of COI and the nuclear markers EF1α and GADPH for species split into more than one BIN or OTU, do not support a higher number of species. Likewise, there is no evidence for Wolbachia infection as a trigger for these sequence variations.},
}
@article {pmid33283785,
year = {2020},
author = {Vendrame, E and McKechnie, JL and Ranganath, T and Zhao, NQ and Rustagi, A and Vergara, R and Ivison, GT and Kronstad, LM and Simpson, LJ and Blish, CA},
title = {Profiling of the Human Natural Killer Cell Receptor-Ligand Repertoire.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {165},
pages = {},
pmid = {33283785},
issn = {1940-087X},
support = {U19 AI057229/AI/NIAID NIH HHS/United States ; UM1 AI068634/AI/NIAID NIH HHS/United States ; R01 AI131798/AI/NIAID NIH HHS/United States ; DP1 DA046089/DA/NIDA NIH HHS/United States ; U01 AI068636/AI/NIAID NIH HHS/United States ; R21 AI135287/AI/NIAID NIH HHS/United States ; K08 AI138640/AI/NIAID NIH HHS/United States ; TL1 TR001084/TR/NCATS NIH HHS/United States ; T32 AI007502/AI/NIAID NIH HHS/United States ; T32 AI007290/AI/NIAID NIH HHS/United States ; U01 AI068634/AI/NIAID NIH HHS/United States ; UM1 AI068636/AI/NIAID NIH HHS/United States ; },
mesh = {Antibodies/metabolism ; Cell Line ; DNA/metabolism ; Freeze Drying ; Humans ; Intercalating Agents/metabolism ; Killer Cells, Natural/immunology ; Ligands ; Receptors, Natural Killer Cell/*metabolism ; Reproducibility of Results ; Staining and Labeling ; },
abstract = {Natural killer (NK) cells are among the first responders to viral infections. The ability of NK cells to rapidly recognize and kill virally infected cells is regulated by their expression of germline-encoded inhibitory and activating receptors. The engagement of these receptors by their cognate ligands on target cells determines whether the intercellular interaction will result in NK cell killing. This protocol details the design and optimization of two complementary mass cytometry (CyTOF) panels. One panel was designed to phenotype NK cells based on receptor expression. The other panel was designed to interrogate expression of known ligands for NK cell receptors on several immune cell subsets. Together, these two panels allow for the profiling of the human NK cell receptor-ligand repertoire. Furthermore, this protocol also details the process by which we stain samples for CyTOF. This process has been optimized for improved reproducibility and standardization. An advantage of CyTOF is its ability to measure over 40 markers in each panel, with minimal signal overlap, allowing researchers to capture the breadth of the NK cell receptor-ligand repertoire. Palladium barcoding also reduces inter-sample variation, as well as consumption of reagents, making it easier to stain samples with each panel in parallel. Limitations of this protocol include the relatively low throughput of CyTOF and the inability to recover cells after analysis. These panels were designed for the analysis of clinical samples from patients suffering from acute and chronic viral infections, including dengue virus, human immunodeficiency virus (HIV), and influenza. However, they can be utilized in any setting to investigate the human NK cell receptor-ligand repertoire. Importantly, these methods can be applied broadly to the design and execution of future CyTOF panels.},
}
@article {pmid33281472,
year = {2020},
author = {Palacios-Vargas, JG and Callohuari, YT},
title = {A new species of the genus Neotropiella Handschin, 1942 (Collembola: Neanuridae) from Peru.},
journal = {Biodiversity data journal},
volume = {8},
number = {},
pages = {e57743},
pmid = {33281472},
issn = {1314-2828},
abstract = {BACKGROUND: Neotropiella is a genus of springtails which can be of medium size (2 mm) or relatively long (5 mm). These springtails live in leaf litter, under the bark of dead trees or in decomposing wood, mainly in the Neotropical Region and are often collected by litter samples on Berlese funnels or by pitfall traps. Most species have been described, based on relatively few specimens and chaetotaxy of several species is incomplete.<br><br>NEW INFORMATION: A new species within Neotropiella was discovered in recent pitfall trap collections from Peru. Neotropiella peruana sp. n. was taxonomically treated and studied under both phase contrast and scanning electron microscopy. It is similar to N. insularis from Brazil, but smaller with only 4 mandibular teeth (vs. 5) and with well-developed unguis lateral teeth. Intraspecific variation of the new species is provided. We also present the first DNA barcodes for the genus.},
}
@article {pmid33281469,
year = {2020},
author = {Zhang, L and Zhang, J and Song, P and Liu, S and Liu, P and Liu, C and Lin, L and Li, Y},
title = {Reidentification of Decapterus macarellus and D. macrosoma (Carangidae) reveals inconsistencies with current morphological taxonomy in China.},
journal = {ZooKeys},
volume = {995},
number = {},
pages = {81-96},
pmid = {33281469},
issn = {1313-2989},
abstract = {Decapterus macarellus and D. macrosoma are economically important pelagic fish species that are widely distributed in tropical and subtropical seas. The two species are often mistakenly identified due to their morphological similarities as described in the Chinese literature on fish identification. In this study, D. macarellus and D. macrosoma samples were collected in the Eastern Indian Ocean and the South China Sea and reidentified using morphological and DNA barcoding techniques. The characteristics that distinguish the two species primarily include the scute coverage of the straight portion of the lateral line (the most indicative characteristic for classification), the shape of the predorsal scaled area and its location relative to the middle axis of the eye, and the shapes of the posterior margin of the maxilla and the posterior margin of the operculum. The results revealed a large number of misidentified sequences among the homologous cytochrome oxidase (COI) sequences of the two species in the NCBI database and that the genus Decapterus may include cryptic species. In terms of genetic structure, the Sundaland has not blocked genetic exchange between D. macarellus populations in the South China Sea and the Eastern Indian Ocean, giving rise to a high level of genetic diversity. In this study, we made corrections to the Chinese classification standards for D. macarellus and D. macrosoma and the erroneous reference sequences in the NCBI database, thereby providing accurate reference points for the future exploration of cryptic species in the genus Decapterus.},
}
@article {pmid33279914,
year = {2020},
author = {Zhang, X and Xu, Y and Abel, AK and Smith, LS and Watt, R and Hussain, A and Gao, C},
title = {Visual Speech Recognition with Lightweight Psychologically Motivated Gabor Features.},
journal = {Entropy (Basel, Switzerland)},
volume = {22},
number = {12},
pages = {},
pmid = {33279914},
issn = {1099-4300},
support = {EP/M026981/1//EPSRC/ ; },
abstract = {Extraction of relevant lip features is of continuing interest in the visual speech domain. Using end-to-end feature extraction can produce good results, but at the cost of the results being difficult for humans to comprehend and relate to. We present a new, lightweight feature extraction approach, motivated by human-centric glimpse-based psychological research into facial barcodes, and demonstrate that these simple, easy to extract 3D geometric features (produced using Gabor-based image patches), can successfully be used for speech recognition with LSTM-based machine learning. This approach can successfully extract low dimensionality lip parameters with a minimum of processing. One key difference between using these Gabor-based features and using other features such as traditional DCT, or the current fashion for CNN features is that these are human-centric features that can be visualised and analysed by humans. This means that it is easier to explain and visualise the results. They can also be used for reliable speech recognition, as demonstrated using the Grid corpus. Results for overlapping speakers using our lightweight system gave a recognition rate of over 82%, which compares well to less explainable features in the literature.},
}
@article {pmid33277555,
year = {2020},
author = {Agarwal, A and Cunningham, JP and Valenzuela, I and Blacket, MJ},
title = {A diagnostic LAMP assay for the destructive grapevine insect pest, phylloxera (Daktulosphaira vitifoliae).},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {21229},
pmid = {33277555},
issn = {2045-2322},
mesh = {Animals ; Aphids/*genetics/pathogenicity ; DNA Primers ; DNA, Mitochondrial/*genetics ; Genotype ; Microsatellite Repeats/genetics ; Molecular Diagnostic Techniques/*methods ; Nucleic Acid Amplification Techniques/*methods ; Plant Diseases/*parasitology ; Real-Time Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; Vitis/*parasitology ; },
abstract = {Grape phylloxera (Daktulosphaira vitifoliae) is a destructive insect pest of grapevines that is highly invasive worldwide, despite strict biosecurity containment measures in place at farm and regional levels. Current phylloxera identification by visual inspection and laboratory-based molecular methods is time-consuming and costly. More rapid and cost-effective methods for identification of this pest would benefit industry, growers, and biosecurity services. Loop mediated isothermal amplification (LAMP) is a new portable technology available for rapid and accurate in-field molecular diagnostics. This study outlines the development of a new LAMP assay to enable the identification of phylloxera specimens. New LAMP primers were developed to specifically amplify phylloxera mitochondrial DNA (5'-COI), which we have shown is effective as a DNA barcode for identification of phylloxera, using LAMP technology. Positive LAMP reactions, containing phylloxera DNA, amplified in less than twelve minutes with an anneal derivative temperature of approximately 79 °C to 80 °C compared to a newly designed synthetic DNA (gBlock) fragment which had an anneal derivative temperature of 82 °C. No LAMP amplification was detected in any of the non-target species tested, i.e. no false-positive identification resulted for these species. We also successfully optimised a non-destructive DNA extraction procedure, HotSHOT "HS6", for use in the field on phylloxera adults, nymphs and eggs, to retain physical specimens. DNA extracted using this method was also suitable for species and genotype molecular identification methods, such as DNA barcoding, qPCR and microsatellite genotyping. The new LAMP assay provides a novel visual molecular tool for accurate diagnostics of phylloxera in the laboratory and field.},
}
@article {pmid33276723,
year = {2020},
author = {Yang, C and Zheng, Y and Tan, S and Meng, G and Rao, W and Yang, C and Bourne, DG and O'Brien, PA and Xu, J and Liao, S and Chen, A and Chen, X and Jia, X and Zhang, AB and Liu, S},
title = {Efficient COI barcoding using high throughput single-end 400 bp sequencing.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {862},
pmid = {33276723},
issn = {1471-2164},
support = {NO. JCYJ20170817150755701//Shenzhen Municipal Government of China/ ; No. KQTD20150330171505310//Shenzhen Peacock Plan/ ; 31425023//China National Funds for Distinguished Young Scientists/ ; 2019M660051//Chinese Postdoctoral Science Foundation/ ; },
mesh = {Animals ; DNA ; *DNA Barcoding, Taxonomic ; *Ecosystem ; High-Throughput Nucleotide Sequencing ; Insecta ; },
abstract = {BACKGROUND: Over the last decade, the rapid development of high-throughput sequencing platforms has accelerated species description and assisted morphological classification through DNA barcoding. However, the current high-throughput DNA barcoding methods cannot obtain full-length barcode sequences due to read length limitations (e.g. a maximum read length of 300 bp for the Illumina's MiSeq system), or are hindered by a relatively high cost or low sequencing output (e.g. a maximum number of eight million reads per cell for the PacBio's SEQUEL II system).<br><br>RESULTS: Pooled cytochrome c oxidase subunit I (COI) barcodes from individual specimens were sequenced on the MGISEQ-2000 platform using the single-end 400&#x2009;bp (SE400) module. We present a bioinformatic pipeline, HIFI-SE, that takes reads generated from the 5' and 3' ends of the COI barcode region and assembles them into full-length barcodes. HIFI-SE is written in Python and includes four function modules of filter, assign, assembly and taxonomy. We applied the HIFI-SE to a set of 845 samples (30 marine invertebrates, 815 insects) and delivered a total of 747 fully assembled COI barcodes as well as 70 Wolbachia and fungi symbionts. Compared to their corresponding Sanger sequences (72 sequences available), nearly all samples (71/72) were correctly and accurately assembled, including 46 samples that had a similarity score of 100% and 25 of ca. 99%.<br><br>CONCLUSIONS: The HIFI-SE pipeline represents an efficient way to produce standard full-length barcodes, while the reasonable cost and high sensitivity of our method can contribute considerably more DNA barcodes under the same budget. Our method thereby advances DNA-based species identification from diverse ecosystems and increases the number of relevant applications.},
}
@article {pmid33276142,
year = {2021},
author = {Nakao, M and Sasaki, M},
title = {Frequent infections of mountain stream fish with the amphibian acanthocephalan, Pseudoacanthocephalus toshimai (Acanthocephala: Echinorhynchidae).},
journal = {Parasitology international},
volume = {81},
number = {},
pages = {102262},
doi = {10.1016/j.parint.2020.102262},
pmid = {33276142},
issn = {1873-0329},
mesh = {Acanthocephala/*isolation &amp; purification ; Animals ; Female ; Fish Diseases/*epidemiology/parasitology ; Helminthiasis, Animal/*epidemiology/parasitology ; Japan/epidemiology ; Male ; *Perciformes ; Prevalence ; *Salmonidae ; },
abstract = {Pseudoacanthocephalus toshimai is an intestinal acanthocephalan parasite of amphibians in Hokkaido, the northernmost island of Japan. In this study, common freshwater fish of the families Salmonidae and Cottidae in mountain streams around the Kamikawa basin of Hokkaido were examined for acanthocephalan infections with P. toshimai. A total of 160 salmonids and 14 cottids were caught in 4 streams by bait fishing during summer and autumn seasons of 2019. Adult acanthocephalans were found only from the salmonids, namely, Salvelinus leucomaenis leucomaenis, Salvelinus malma krascheninnikovi, Oncorhynchus masou, and Oncorhynchus mykiss. The maximum prevalence reached 58.1% in S. leucomaenis, but the mean worm burden was at low levels (e.g., 3.1 in S. leucomaenis and 2.2 in S. malma). All of the acanthocephalans were identified to P. toshimai by morphological observation and DNA barcoding. Although the male acanthocephalans became sexually mature, the females never reached the gravid adult stage, suggesting that salmonids are unsuitable or aberrant hosts for P. toshimai. The infected fish were found exclusively from a small stream with bush, in which a large habitat of amphibians is included. Ligidium japonicum, a terrestrial isopod, collected from the habitat was highly infected with cystacanth larvae of P. toshimai. The observation of fish stomach contents directly demonstrated that small salmonids eat L. japonicum. The terrestrial isopods, which are washed away by rain into a stream, seem to be a source of salmonid infections with P. toshimai. The habitat of intermediate hosts should be emphasized in the taxonomy of the closely related genera Acanthocephalus and Pseudoacanthocephalus.},
}
@article {pmid33274611,
year = {2020},
author = {Ko, J and Wang, Y and Carlson, JCT and Marquard, A and Gungabeesoon, J and Charest, A and Weitz, D and Pittet, MJ and Weissleder, R},
title = {Single Extracellular Vesicle Protein Analysis Using Immuno-Droplet Digital Polymerase Chain Reaction Amplification.},
journal = {Advanced biosystems},
volume = {4},
number = {12},
pages = {e1900307},
pmid = {33274611},
issn = {2366-7478},
support = {P01 CA069246/CA/NCI NIH HHS/United States ; R21CA236561/CA/NCI NIH HHS/United States ; R21 CA236561/CA/NCI NIH HHS/United States ; R01 CA204019/CA/NCI NIH HHS/United States ; R01CA204019/CA/NCI NIH HHS/United States ; P01CA069246/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Cell Line ; Equipment Design ; *Extracellular Vesicles/chemistry/metabolism ; Humans ; Mice ; Microfluidic Analytical Techniques/*instrumentation ; *Polymerase Chain Reaction/instrumentation/methods ; Single-Cell Analysis/instrumentation ; },
abstract = {There is a need for novel analytical techniques to study the composition of single extracellular vesicles (EV). Such techniques are required to improve the understanding of heterogeneous EV populations, to allow identification of unique subpopulations, and to enable earlier and more sensitive disease detection. Because of the small size of EV and their low protein content, ultrahigh sensitivity technologies are required. Here, an immuno-droplet digital polymerase chain reaction (iddPCR) amplification method is described that allows multiplexed single EV protein profiling. Antibody-DNA conjugates are used to label EV, followed by stochastic microfluidic incorporation of single EV into droplets. In situ PCR with fluorescent reporter probes converts and amplifies the barcode signal for subsequent read-out by droplet imaging. In these proof-of-principle studies, it is shown that multiplex protein analysis is possible in single EV, opening the door for future analyses.},
}
@article {pmid33273884,
year = {2020},
author = {Moravec, J and Lehr, E and Kodejš, K},
title = {A new species of Pristimantis (Amphibia, Anura, Strabomantidae) from the Pui Pui Protected Forest (central Peru), with comments on Pristimantis albertus Duellman &amp; Hedges, 2007.},
journal = {ZooKeys},
volume = {994},
number = {},
pages = {125-148},
pmid = {33273884},
issn = {1313-2989},
abstract = {We describe a new Pristimantis species from the eastern Andes, Región Junín, Peru following an integrative taxonomic approach. The description is based on three adult males (snout-vent length 25.7-28.8 mm) collected in two montane forests between 1615 and 1800 m a.s.l. in the Pui Pui Protected Forest and its close surroundings. The new species is mainly characterised by absence of tympanum, presence of inner tarsal fold, broad horizontal red band across iris, ventre mottled black and cream and ventral surfaces of thighs salmon and grey mottled. Amongst the Amazonian and montane forest Pristimantis that have the ventre and groin contrastingly black and cream mottled, P. sinschi sp. nov. is morphologically most similar to P. lindae and P. ventrimarmoratus. However, DNA barcoding revealed a clear distinction between these three species and placed P. sinschi sp. nov. as sister taxon of P. lindae. We designate a lectotype for P. ventrimarmoratus and restrict the type locality of this species to "El Topo, R. Pastaza, [Provincia Tungurahua,] E. Ecuador, 4200 feet". Pristimantis albertus and P. sagittulus are recorded for the first time in the Región Junín. Additional data on morphology and systematics are provided for P. albertus.},
}
@article {pmid33269870,
year = {2020},
author = {Fujita, H and Kawai, K and Taniguchi, R and Tomano, S and Sanchez, G and Kuramochi, T and Umino, T},
title = {Infestation of the Parasitic Isopod Mothocya parvostis on Juveniles of the Black Sea Bream Acanthopagrus schlegelii as an Optional Intermediate Host in Hiroshima Bay.},
journal = {Zoological science},
volume = {37},
number = {6},
pages = {544-553},
doi = {10.2108/zs190147},
pmid = {33269870},
issn = {0289-0003},
mesh = {Animals ; Beloniformes/parasitology ; Ectoparasitic Infestations/parasitology ; Electron Transport Complex IV/genetics ; Fish Diseases/*parasitology ; Isopoda/anatomy &amp; histology/*classification/*genetics ; Japan ; RNA, Ribosomal, 16S/genetics ; Sea Bream/growth &amp; development/parasitology ; Sequence Analysis, DNA ; },
abstract = {In Hiroshima Bay, parasitic isopods of the genus Mothocya infest the black sea bream Acanthopagrus schlegelii (Bleeker, 1854) and the Japanese halfbeak Hyporhamphus sajori (Temminck and Schlegel, 1846), two fish species that are abundant and commercially important in the Seto Inland Sea of Japan. Immature and mature Mothocya individuals can infect both juveniles and adults of H. sajori, while immature Mothocya are known to parasitize juveniles of A. schlegelii; i.e., no Mothocya parasites are found in adult A. schlegelii. The identification of the immature Mothocya parasitizing juveniles of A. schlegelii remains uncertain, because Mothocya species are morphologically identifiable only based on adult females. Also, the biological/ecological relationship between the hosts and parasites has not been studied. Here, we identified the parasites on A. schlegelii as Mothocya parvostis Bruce, 1986 by molecular sequence analyses along with other parasites obtained from H. sajori, the latter being morphologically confirmed by comparison with paratype materials of M. parvostis as well as the similar congener Mothocya sajori Bruce, 1986. The growth rates of the infected A. schlegelii juveniles from June to September in the years 2013-2015 and 2018 were significantly lower than those of the uninfected ones, suggesting a negative effect of the infection on the hosts. Our data on the prevalence and duration of the infection, as well as the body size gain of the hosts and parasites, corroborate a hypothesis that M. parvostis would utilize A. schlegelii as an optional intermediate host before it reaches the final host, H. sajori.},
}
@article {pmid33269869,
year = {2020},
author = {Hu, J and Roos, C and Lv, X and Kuang, W and Yu, L},
title = {Molecular Genetics Supports a Potential Fifth Asian Pangolin Species (Mammalia, Pholidota, Manis).},
journal = {Zoological science},
volume = {37},
number = {6},
pages = {538-543},
doi = {10.2108/zs200084},
pmid = {33269869},
issn = {0289-0003},
mesh = {Animals ; Cytochromes b/genetics ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial ; Molecular Biology ; Pangolins/*classification/*genetics ; *Phylogeny ; Species Specificity ; },
abstract = {Recently, two mitochondrial haplotypes, H4 and H8, of Manis sp. were found in two seizures in Hong Kong that do not correspond to Manis javanica, Manis pentadactyla or Manis crassicaudata of Asian pangolin species or any African pangolin species. It was proposed that both haplotypes derived from Manis culionensis, an unknown lineage of M. javanica, or a thus far unidentified Asian pangolin species (Manis sp.). To further investigate these three hypotheses, we used two mitochondrial genes of all eight known extant pangolin species and conducted phylogenetic tree reconstructions, divergence time estimation, and species delimitation analyses. All analyses consistently confirmed that these two haplotypes of Manis sp. constitute a distinct lineage, potentially representing a fifth Asian pangolin species, which originated around the Late Miocene to Early Pliocene (6.95 [4.64-9.85] million years ago). Our study provides genetic support for a potential fifth Asian pangolin species and helps to better understand species diversity of Asian pangolins, which is urgently needed for effective conservation work.},
}
@article {pmid33269564,
year = {2020},
author = {Malatyalı, E and Sankur, F and Akın, MN and Ertabaklar, H and Ertuğ, S},
title = {Subtype Distribution of Blastocystis in Pregnant Women and Analysis of Possible Risk Factors.},
journal = {Turkiye parazitolojii dergisi},
volume = {44},
number = {4},
pages = {221-225},
doi = {10.4274/tpd.galenos.2020.6624},
pmid = {33269564},
issn = {2146-3077},
mesh = {Adult ; Blastocystis/*genetics/*isolation &amp; purification ; Blastocystis Infections/diagnosis/epidemiology/*parasitology ; Feces/parasitology ; Female ; Genetic Variation ; Genotype ; Humans ; Pregnancy ; Pregnancy Complications, Infectious/diagnosis/epidemiology/*parasitology ; Pregnant People ; Risk Factors ; Turkey/epidemiology ; },
abstract = {OBJECTIVE: Since the identification of Blastocystis subtypes (ST) in the last decade, much has been learned about the genetic diversity of Blastocystis isolates in different populations, except pregnant women. The objective of this study is to investigate the genetic diversity of Blastocystis in pregnant women and analyse some demographic factors.<br><br>METHODS: The faecal samples from 100 pregnant women were collected at an Obstetrics and Gynecology Department in Mu&#x11f;la, Turkey. Thereafter, Blastocystis positivity was detected by direct microscopy and culture. The positive cultures were subjected to DNA isolation, and the Blastocystis barcode region was amplified with polymerase chain reaction. Next, the sequences were queried against GenBank nucleotide and Blastocystis STs (18S) databases.<br><br>RESULTS: Blastocystis was detected in 14% (14 out of 100) of the faecal samples by culture and 10% (10 out of 100) of the samples by direct microscopy. Nine of Blastocystis isolates (64.4%) were ST3, three (21.4%) were ST1 and two (14.2%) were ST2. Neither the demographic features nor the gastrointestinal symptoms were statistically related to Blastocystis infection.<br><br>CONCLUSION: The findings in this study agreed with the most of the previous human studies that found ST3 as the most abundant genotype. This study reported the frequency of Blastocystis in pregnant women and highlighted the importance of comprehensive studies with more cases of Blastocystis during pregnancy.},
}
@article {pmid33269011,
year = {2020},
author = {Shimizu, S and Broad, GR and Maeto, K},
title = {Integrative taxonomy and analysis of species richness patterns of nocturnal Darwin wasps of the genus Enicospilus Stephens (Hymenoptera, Ichneumonidae, Ophioninae) in Japan.},
journal = {ZooKeys},
volume = {990},
number = {},
pages = {1-144},
pmid = {33269011},
issn = {1313-2989},
abstract = {The predominantly tropical ophionine genus Enicospilus Stephens, 1835 is one of the largest genera of Darwin wasps (Hymenoptera, Ichneumonidae), with more than 700 extant species worldwide that are usually crepuscular or nocturnal and are parasitoids of Lepidoptera larvae. In the present study, the Japanese species of Enicospilus are revised using an integrative approach (combined morphology and DNA barcoding). On the basis of 3,110 specimens, 47 Enicospilus species are recognised in Japan, eight of which are new species (E. acutus Shimizu, sp. nov., E. kunigamiensis Shimizu, sp. nov., E. limnophilus Shimizu, sp. nov., E. matsumurai Shimizu, sp. nov., E. pseudopuncticulatus Shimizu, sp. nov., E. sharkeyi Shimizu, sp. nov., E. takakuwai Shimizu, sp. nov., and E. unctus Shimizu, sp. nov.), seven are new records from Japan (E. jilinensis Tang, 1990, E. laqueatus (Enderlein, 1921), E. multidens Chiu, 1954, stat. rev., E. puncticulatus Tang, 1990, E. stenophleps Cushman, 1937, E. vestigator (Smith, 1858), and E. zeugos Chiu, 1954, stat. rev.), 32 had already been recorded in Japan; three (E. biharensis Townes, Townes &amp; Gupta, 1961, E. flavicaput (Morley, 1912), and E. merdarius (Gravenhorst, 1829)) have been erroneously recorded from Japan based on misidentifications, and four names that were previously on the Japanese list are deleted through synonymy. The following taxonomic changes are proposed: E. vacuus Gauld &amp; Mitchell, 1981, syn. nov. (= E. formosensis (Uchida, 1928)); E. multidens stat. rev.; E. striatus Cameron, 1899, syn. nov. = E. lineolatus (Roman, 1913), syn. nov. = E. uniformis Chiu, 1954, syn. nov. = E. flatus Chiu, 1954, syn. nov. = E. gussakovskii Viktorov, 1957, syn. nov. = E. striolatus Townes, Townes &amp; Gupta, 1961, syn. nov. = E. unicornis Rao &amp; Nikam, 1969, syn. nov. = E. unicornis Rao &amp; Nikam, 1970, syn. nov. (= E. pungens (Smith, 1874)); E. iracundus Chiu, 1954, syn. nov. (= E. sakaguchii (Matsumura &amp; Uchida, 1926)); E. sigmatoides Chiu, 1954, syn. nov. (= E. shikokuensis (Uchida, 1928)); E. yamanakai (Uchida, 1930), syn. nov. (= E. shinkanus (Uchida, 1928)); E. ranunculus Chiu, 1954, syn. nov. (= E. yezoensis (Uchida, 1928)); and E. zeugos stat. rev. = E. henrytownesi Chao &amp; Tang, 1991, syn. nov. In addition, the following new regional and country records are also provided: E. flavocephalus (Kirby, 1900), E. puncticulatus, and E. vestigator from the Eastern Palaearctic region, E. laqueatus from the Eastern Palaearctic and Oceanic regions, and E. maruyamanus (Uchida, 1928) from the Oriental region; E. abdominalis (Szépligeti, 1906) from Nepal, E. flavocephalus from Laos, E. formosensis from Laos and Malaysia, E. insinuator (Smith, 1860) from Taiwan, E. maruyamanus from India and Philippines, E. nigronotatus Cameron, 1903, E. riukiuensis (Matsumura &amp; Uchida, 1926), and E. sakaguchii from Indonesia, E. pungens from 14 countries (Australia, Bhutan, Brunei, Indonesia, Laos, Malaysia, Nepal, New Caledonia, Papua New Guinea, Philippines, Solomon Islands, Sri Lanka, Tajikistan, and Taiwan), and E. yezoensis from South Korea. An identification key to all Japanese species of Enicospilus is proposed. Although 47 species are recognised in the present study, approximately 55 species could potentially be found in Japan based on ACE and Chao 1 estimators. The latitudinal diversity gradient of Enicospilus species richness is also tested in the Japanese archipelago based on the constructed robust taxonomic framework and extensive samples. Enicospilus species richness significantly increases towards the south, contrary to the 'anomalous' pattern of some other ichneumonid subfamilies.},
}
@article {pmid33265904,
year = {2020},
author = {Ramírez-Ahuja, ML and Garza-González, E and Talamas, EJ and Gómez-Govea, MA and Rodríguez-Pérez, MA and Zambrano-Robledo, P and Rebollar-Tellez, E and Rodríguez-Sanchez, IP},
title = {Parasitoids of Chrysopidae Eggs in Sinaloa Mexico.},
journal = {Insects},
volume = {11},
number = {12},
pages = {},
pmid = {33265904},
issn = {2075-4450},
abstract = {The eggs parasitoids Myartsevaia chrysopae (Crawford) (Hymenoptera: Encyrtidae), Telenomus lobatus Johnson, Telenomus tridentatus Johnson (Hymenoptera: Scelionidae) and Trichogramma atopovirilia Oatman and Platner (Hymenoptera: Trichogrammatidae) are reported for the first time or in new localities in Mexico. Their occurrence was first discovered in 2018 during a survey of parasitism on chrysopid eggs, conducted on Sorghum bicolor L. Moench (Poales: Poaceae) and Zea mays L. (Poales: Poaceae) in different locations in Sinaloa, Mexico. The identity of the parasitoids was determined by morphology and for both species of Telenomus the barcode region of the cytochrome oxidase 1 gene (CO1) was generated to facilitate molecular diagnosis of these species in future studies.},
}
@article {pmid33263903,
year = {2021},
author = {Grazina, L and Costa, J and Amaral, JS and Mafra, I},
title = {High-Resolution Melting Analysis as a Tool for Plant Species Authentication.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2264},
number = {},
pages = {55-73},
doi = {10.1007/978-1-0716-1201-9_5},
pmid = {33263903},
issn = {1940-6029},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*analysis/*genetics/isolation &amp; purification ; Food Analysis/*methods ; Plant Proteins/*genetics ; Plants, Medicinal/classification/*genetics ; Polymerase Chain Reaction/*methods ; Species Specificity ; },
abstract = {High-resolution melting (HRM) analysis is a cost-effective, specific, and rapid tool that allows distinguishing genetically related plants and other organisms based on the detection of small nucleotide variations, which are recognized from melting properties of the double-stranded DNA. It has been widely applied in several areas of research and diagnostics, including botanical authentication of several food commodities and herbal products. Generally, it consists of the main steps: (1) in silico sequence analysis and primer design; (2) DNA extraction from plant material; (3) amplification by real-time PCR with an enhanced fluorescent dye targeting a specific DNA barcode or other regions of taxonomic interest (100-200 bp); (4) melting curve analysis; and (5) statistical data analysis using a specific HRM software. This chapter presents an overview of HRM analysis and application, followed by the detailed description of all the required reagents, instruments, and protocols for the successful and easy implementation of a HRM method to differentiate closely related plant species.},
}
@article {pmid33262846,
year = {2020},
author = {Stec, D and Dudziak, M and Michalczyk, &#x141;},
title = {Integrative Descriptions of Two New Macrobiotidae Species (Tardigrada: Eutardigrada: Macrobiotoidea) from French Guiana and Malaysian Borneo.},
journal = {Zoological studies},
volume = {59},
number = {},
pages = {e23},
pmid = {33262846},
issn = {1810-522X},
abstract = {In this paper we describe two new tardigrade species, one representing the Macrobiotus hufelandi complex and the other from the Paramacrobiotus richtersi complex. The descriptions are based on a detailed morphological examination under light and scanning electron microscopy and analysis of four genetic markers (18S rRNA, 28S rRNA, ITS-2 and COI). Macrobiotus crustulus sp. nov. from French Guiana is the most similar to Macrobiotus martini Bartels, Pilato, Lisi and Nelson, 2009, Macrobiotus santoroi Pilato and D'Urso, 1976, but differs from them mainly by having the lissostomus type of the oral cavity armature (teeth not visible under light microscopy) and well-developed, convex terminal discs of egg processes covered with evident granulation. Paramacrobiotus filipi sp. nov. from the Malaysian part of Borneo is the most similar to Paramacrobiotus alekseevi (Tumanov, 2005), but differs from it primarily by the presence of body granulation visible under light microscopy as well as sculptured and porous areoles around egg processes.},
}
@article {pmid33261133,
year = {2020},
author = {Monkman, J and Taheri, T and Ebrahimi Warkiani, M and O'Leary, C and Ladwa, R and Richard, D and O'Byrne, K and Kulasinghe, A},
title = {High-Plex and High-Throughput Digital Spatial Profiling of Non-Small-Cell Lung Cancer (NSCLC).},
journal = {Cancers},
volume = {12},
number = {12},
pages = {},
pmid = {33261133},
issn = {2072-6694},
abstract = {Profiling the tumour microenvironment (TME) has been informative in understanding the underlying tumour-immune interactions. Multiplex immunohistochemistry (mIHC) coupled with molecular barcoding technologies have revealed greater insights into the TME. In this study, we utilised the Nanostring GeoMX Digital Spatial Profiler (DSP) platform to profile a non-small-cell lung cancer (NSCLC) tissue microarray for protein markers across immune cell profiling, immuno-oncology (IO) drug targets, immune activation status, immune cell typing, and pan-tumour protein modules. Regions of interest (ROIs) were selected that described tumour, TME, and normal adjacent tissue (NAT) compartments. Our data revealed that paired analysis (n = 18) of matched patient compartments indicate that the TME was significantly enriched in CD27, CD3, CD4, CD44, CD45, CD45RO, CD68, CD163, and VISTA relative to the tumour. Unmatched analysis indicated that the NAT (n = 19) was significantly enriched in CD34, fibronectin, IDO1, LAG3, ARG1, and PTEN when compared to the TME (n = 32). Univariate Cox proportional hazards indicated that the presence of cells expressing CD3 (hazard ratio (HR): 0.5, p = 0.018), CD34 (HR: 0.53, p = 0.004), and ICOS (HR: 0.6, p = 0.047) in tumour compartments were significantly associated with improved overall survival (OS). We implemented both high-plex and high-throughput methodologies to the discovery of protein biomarkers and molecular phenotypes within biopsy samples, and demonstrate the power of such tools for a new generation of pathology research.},
}
@article {pmid33260641,
year = {2020},
author = {Bautista, MAC and Zheng, Y and Hu, Z and Deng, Y and Chen, T},
title = {Comparative Analysis of Complete Chloroplast Genome Sequences of Wild and Cultivated Bougainvillea (Nyctaginaceae).},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {12},
pages = {},
pmid = {33260641},
issn = {2223-7747},
support = {GZY-KJS-2018-004//Fourth National Survey of Chinese Traditional Medicine Resources/ ; Chen, 2009//Shenzhen Urban Management Bureau/ ; },
abstract = {Bougainvillea (Nyctaginaceae) is a popular ornamental plant group primarily grown for its striking colorful bracts. However, despite its established horticultural value, limited genomic resources and molecular studies have been reported for this genus. Thus, to address this existing gap, complete chloroplast genomes of four species (Bougainvillea glabra, Bougainvillea peruviana, Bougainvillea pachyphylla, Bougainvillea praecox) and one Bougainvillea cultivar were sequenced and characterized. The Bougainvillea cp genomes range from 153,966 bp to 154,541 bp in length, comprising a large single-copy region (85,159 bp-85,708 bp) and a small single-copy region (18,014 bp-18,078 bp) separated by a pair of inverted repeats (25,377-25,427 bp). All sequenced plastomes have 131 annotated genes, including 86 protein-coding, eight rRNA, and 37 tRNA genes. These five newly sequenced Bougainvillea cp genomes were compared to the Bougainvillea spectabilis cp genome deposited in GeBank. The results showed that all cp genomes have highly similar structures, contents, and organization. They all exhibit quadripartite structures and all have the same numbers of genes and introns. Codon usage, RNA editing sites, and repeat analyses also revealed highly similar results for the six cp genomes. The amino acid leucine has the highest proportion and almost all favored synonymous codons have either an A or U ending. Likewise, out of the 42 predicted RNA sites, most conversions were from serine (S) to leucine (L). The majority of the simple sequence repeats detected were A/T mononucleotides, making the cp genomes A/T-rich. The contractions and expansions of the IR boundaries were very minimal as well, hence contributing very little to the differences in genome size. In addition, sequence variation analyses showed that Bougainvillea cp genomes share nearly identical genomic profiles though several potential barcodes, such as ycf1, ndhF, and rpoA were identified. Higher variation was observed in both B. peruviana and B. pachyphylla cp sequences based on SNPs and indels analysis. Phylogenetic reconstructions further showed that these two species appear to be the basal taxa of Bougainvillea. The rarely cultivated and wild species of Bougainvillea (B. pachyphylla, B. peruviana, B. praecox) diverged earlier than the commonly cultivated species and cultivar (B. spectabilis, B. glabra, B. cv.). Overall, the results of this study provide additional genetic resources that can aid in further phylogenetic and evolutionary studies in Bougainvillea. Moreover, genetic information from this study is potentially useful in identifying Bougainvillea species and cultivars, which is essential for both taxonomic and plant breeding studies.},
}
@article {pmid34290157,
year = {2020},
author = {Ruiling, Z and Zhong, Z},
title = {Hidden biodiversity revealed by DNA barcoding in black fly genus Simulium.},
journal = {Journal of vector borne diseases},
volume = {57},
number = {2},
pages = {128-138},
doi = {10.4103/0972-9062.310862},
pmid = {34290157},
issn = {0972-9062},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Haplotypes ; Humans ; Simuliidae/*classification/genetics ; },
abstract = {BACKGROUND &amp; OBJECTIVES: The black fly genus Simulium Latreille is one of the most important medical insect group of the family Simuliidae (Diptera) and many species of this genus are important pests of human and animals, while some of them also represent vectors of pathogens. Correct species identification is essential to the implementation of control measures for species of medical or agricultural importance.<br><br>METHODS: In this study, the usefulness of DNA barcoding was discussed in distinguishing species of Simulium.<br><br>RESULTS: Analysis showed hidden biodiversity, usually referred to in Simuliidae as cryptic species, which was detected in 15 species. Firstly, intraspecific divergences of eleven species was unexpectedly high and the maximum distances of them ranged from 5.1-16.8%. Based on the differential of K2P (Kimura 2-Parameter) distances, sequences were subdivided into two or three groups, respectively. Secondly, extremely low interspecific divergences were detected in eight groups of species, and shared haplotypes were also found among them. Furthermore, the subdivision within species and shared haplotypes among some species were all supported by the NJ (Neighbour-Joining) analysis.<br><br>Our results confirmed that DNA barcoding was a powerful tool for revealing hidden species diversity of black flies. Further work is needed to reveal ambiguous species delimitation in some problematic species groups.},
}
@article {pmid34122814,
year = {2020},
author = {Tang, Y and He, C and Zheng, X and Chen, X and Gao, T},
title = {Super-capacity information-carrying systems encoded with spontaneous Raman scattering.},
journal = {Chemical science},
volume = {11},
number = {11},
pages = {3096-3103},
pmid = {34122814},
issn = {2041-6520},
abstract = {Optical multiplex barcode systems have been significantly boosting the throughput of scientific discovery. A high volume of barcodes can be made from combinations of distinct spectral bands and intensity levels. However, the practical capacity often reaches a ceiling due to the overlaps of signal frequencies or intensities when massive information is written on individual carriers. In this paper, we built super-capacity information-carrying systems by tuning vibrational signals into octal numeral intensities in multiple bands of Raman-silent regions. This novel approach experimentally yielded the largest capacity of distinct optical barcodes to date. The experiments of encoding ASCII and Unicode systems to write and read languages indicate that the Raman coding method provides a new strategy for super-capacity data storage. In addition, multiplex screening of a cell-binding ligand was implemented to demonstrate the feasibility of this technology for fast and in situ high-throughput bio-discovery. These information-carrying systems may open new scenarios for the development of high-throughput screening, diagnostics and data storage.},
}
@article {pmid33816897,
year = {2020},
author = {Phillips, JD and French, SH and Hanner, RH and Gillis, DJ},
title = {HACSim: an R package to estimate intraspecific sample sizes for genetic diversity assessment using haplotype accumulation curves.},
journal = {PeerJ. Computer science},
volume = {6},
number = {},
pages = {e243},
pmid = {33816897},
issn = {2376-5992},
abstract = {Assessing levels of standing genetic variation within species requires a robust sampling for the purpose of accurate specimen identification using molecular techniques such as DNA barcoding; however, statistical estimators for what constitutes a robust sample are currently lacking. Moreover, such estimates are needed because most species are currently represented by only one or a few sequences in existing databases, which can safely be assumed to be undersampled. Unfortunately, sample sizes of 5-10 specimens per species typically seen in DNA barcoding studies are often insufficient to adequately capture within-species genetic diversity. Here, we introduce a novel iterative extrapolation simulation algorithm of haplotype accumulation curves, called HACSim (Haplotype Accumulation Curve Simulator) that can be employed to calculate likely sample sizes needed to observe the full range of DNA barcode haplotype variation that exists for a species. Using uniform haplotype and non-uniform haplotype frequency distributions, the notion of sampling sufficiency (the sample size at which sampling accuracy is maximized and above which no new sampling information is likely to be gained) can be gleaned. HACSim can be employed in two primary ways to estimate specimen sample sizes: (1) to simulate haplotype sampling in hypothetical species, and (2) to simulate haplotype sampling in real species mined from public reference sequence databases like the Barcode of Life Data Systems (BOLD) or GenBank for any genomic marker of interest. While our algorithm is globally convergent, runtime is heavily dependent on initial sample sizes and skewness of the corresponding haplotype frequency distribution.},
}
@article {pmid34222831,
year = {2020},
author = {Cang, Z and Wei, GW},
title = {Persistent Cohomology for Data With Multicomponent Heterogeneous Information.},
journal = {SIAM journal on mathematics of data science},
volume = {2},
number = {2},
pages = {396-418},
pmid = {34222831},
issn = {2577-0187},
support = {R01 GM126189/GM/NIGMS NIH HHS/United States ; },
abstract = {Persistent homology is a powerful tool for characterizing the topology of a data set at various geometric scales. When applied to the description of molecular structures, persistent homology can capture the multiscale geometric features and reveal certain interaction patterns in terms of topological invariants. However, in addition to the geometric information, there is a wide variety of nongeometric information of molecular structures, such as element types, atomic partial charges, atomic pairwise interactions, and electrostatic potential functions, that is not described by persistent homology. Although element-specific homology and electrostatic persistent homology can encode some nongeometric information into geometry based topological invariants, it is desirable to have a mathematical paradigm to systematically embed both geometric and nongeometric information, i.e., multicomponent heterogeneous information, into unified topological representations. To this end, we propose a persistent cohomology based framework for the enriched representation of data. In our framework, nongeometric information can either be distributed globally or reside locally on the datasets in the geometric sense and can be properly defined on topological spaces, i.e., simplicial complexes. Using the proposed persistent cohomology based framework, enriched barcodes are extracted from datasets to represent heterogeneous information. We consider a variety of datasets to validate the present formulation and illustrate the usefulness of the proposed method based on persistent cohomology. It is found that the proposed framework outperforms or at least matches the state-of-the-art methods in the protein-ligand binding affinity prediction from massive biomolecular datasets without resorting to any deep learning formulation.},
}
@article {pmid33597465,
year = {2019},
author = {Pramual, P and Bunchom, N and Saijuntha, W and Tada, I and Suganuma, N and Agatsuma, T},
title = {Genetic diversity and DNA barcoding of the black fly (Diptera: Simuliidae) vectors of parasites causing human onchocerciasis in Guatemala.},
journal = {Tropical biomedicine},
volume = {36},
number = {4},
pages = {938-957},
pmid = {33597465},
issn = {2521-9855},
mesh = {Animals ; DNA Barcoding, Taxonomic ; *Genetic Variation ; Guatemala ; Insect Vectors/genetics/parasitology ; Onchocerciasis/transmission ; *Phylogeny ; Simuliidae/*genetics/parasitology ; },
abstract = {Genetic variation based on mitochondrial cytochrome c oxidase I (COI) and II (COII) sequences was investigated for three black fly nominal species, Simulium metallicum Bellardi complex, S. callidum Dyar and Shannon, and S. ochraceum Walker complex, which are vectors of human onchocerciasis from Guatemala. High levels of genetic diversity were found in S. metallicum complex and S. ochraceum complex with maximum intraspecific genetic divergences of 11.39% and 4.25%, respectively. Levels of genetic diversity of these nominal species are consistent with species status for both of them as they are cytologically complexes of species. Phylogenetic analyses revealed that the S. metallicum complex from Guatemala divided into three distinct clades, two with members of this species from several Central and South American countries and another exclusively from Mexico. The Simulium ochraceum complex from Guatemala formed a clade with members of this species from Mexico and Costa Rica while those from Ecuador and Colombia formed another distinct clade. Very low diversity in S. callidum was found for both genes with maximum intraspecific genetic divergence of 0.68% for COI and 0.88% for COII. Low genetic diversity in S. callidum might be a consequence of the result being informative of only recent population history of the species.},
}
@article {pmid33575567,
year = {2020},
author = {de Oliveira Martins, L and Page, AJ and Mather, AE and Charles, IG},
title = {Taxonomic resolution of the ribosomal RNA operon in bacteria: implications for its use with long-read sequencing.},
journal = {NAR genomics and bioinformatics},
volume = {2},
number = {1},
pages = {lqz016},
pmid = {33575567},
issn = {2631-9268},
abstract = {DNA barcoding through the use of amplified regions of the ribosomal operon, such as the 16S gene, is a routine method to gain an overview of the microbial taxonomic diversity within a sample without the need to isolate and culture the microbes present. However, bacterial cells usually have multiple copies of this ribosomal operon, and choosing the 'wrong' copy could provide a misleading species classification. While this presents less of a problem for well-characterized organisms with large sequence databases to interrogate, it is a significant challenge for lesser known organisms with unknown copy number and diversity. Using the entire length of the ribosomal operon, which encompasses the 16S, 23S, 5S and internal transcribed spacer regions, should provide greater taxonomic resolution but has not been well explored. Here, we use publicly available reference genomes and explore the theoretical boundaries when using concatenated genes and the full-length ribosomal operons, which has been made possible by the development and uptake of long-read sequencing technologies. We quantify the issues of both copy choice and operon length in a phylogenetic context to demonstrate that longer regions improve the phylogenetic signal while maintaining taxonomic accuracy.},
}
@article {pmid33366185,
year = {2019},
author = {Wang, M and Cheng, F},
title = {The complete mitochondrial genome of the Ctenophore Beroe cucumis, a mitochondrial genome showing rapid evolutionary rates.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {4},
number = {2},
pages = {3774-3775},
pmid = {33366185},
issn = {2380-2359},
abstract = {We described the complete mitochondrial genome of the Ctenophore Beroe cucumis, which is a circular molecule of 10,487 bp in length. The new mitochondrial genome comprised only 12 genes, making it one of the smallest animals' mtDNA. Both nucleotide substitution and gene order rearrangements exhibited extreme high evolutionary rate in mitogenomes of Ctenophore. The phylogenetic analysis based on mitogenomics failed to reveal the basal position of Ctenophore within metazoan, owing to the extreme evolutionary rate. Based on the available Ctenophora mitogenomes, we found the optimized primers designed by Geller et al. for DNA barcoding suited for the taxon.},
}
@article {pmid33365864,
year = {2019},
author = {Wang, S and Guo, J and Hou, F},
title = {Identification of the original species of cubilose based on DNA barcode.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {4},
number = {2},
pages = {3079-3082},
pmid = {33365864},
issn = {2380-2359},
abstract = {Cubilose, a valuable traditional Chinese medicine, is mainly composed of the saliva by several species of Aerodramus or Collocalia in the Apodidae. Due to rarity, high economic value and huge market demand, its fake or adulteration is frequently found in the market. Therefore, it is urgent to establish a simple and accurate method for authenticating cubilose. DNA barcoding, which is an easy, quick and reliable method, is widely used to trace the origin of traditional Chinese medicine. For identifying the original species of cubilose, cytb gene of 18 cubilose samples including 15 officer cubilose and 3 feather cubilose were amplified and entered into the GenBank database using the BLAST search tool. The genetic distances among 18 cubilose samples were calculated based on the Kimura two parameter (K2P) model. To construct the reference database, 18 cytb sequences of Aerodramus or Collocalia were downloaded from GenBank. The neighbor-joining (NJ) and unweighted pair group method with arithmetic average (UPGMA) trees were constructed based on sequences from GenBank and our dataset. Blast analysis showed that all cubilose samples had the highest similarity with A. fuciphagus, and the sequence similarity reached over 99%. Genetic distance of 18 cubilose samples ranged from 0.000-0.010. Trees constructed by NJ and UPGMA gave similar topology: all cubilose samples clustered together with A. fuciphagus. These result demonstrated that the original species of all 18 cubilose samples were A. fuciphagus, and cytb gene is a good candidate for identifying cubilose.},
}
@article {pmid33365819,
year = {2019},
author = {Balakirev, ES and Kravchenko, AY and Cherepkova, EV and Saveliev, PA and Semenchenko, AA and Ayala, FJ},
title = {Complete mitochondrial genome of the Belligerent sculpin Megalocottus platycephalus (Cottoidei: Cottidae).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {4},
number = {2},
pages = {2980-2981},
pmid = {33365819},
issn = {2380-2359},
abstract = {The complete mitochondrial (mt) genome was sequenced in two specimens of the Belligerent sculpin Megalocottus platycephalus by high-throughput sequencing technology (Ion S5 platform). The sequences are 16,673 bp in size, and the gene arrangement, composition, and size are very similar to the other sculpin mt genomes published previously. Comparison of the two M. platycephalus mt genomes now obtained with other complete mt genomes available in GenBank reveals an affinity to the sculpin fishes from the genus Myoxocephalus. The intergeneric difference between the Megalocottus and Myoxocephalus is 0.0757 ± 0.0019, which is significantly less than the corresponding value, 0.1240 ± 0.0120, obtained previously for the sculpin fishes based on the COI barcoding marker.},
}
@article {pmid33597485,
year = {2019},
author = {Mashaly, AM and Al-Ajmi, RA and Rady, A and Al-Musawi, Z and Farrukh, A},
title = {Species richness of scavenger insects on different carcass types.},
journal = {Tropical biomedicine},
volume = {36},
number = {3},
pages = {630-639},
pmid = {33597485},
issn = {2521-9855},
mesh = {Animals ; *Cadaver ; Camelus ; Coleoptera/*classification ; Diptera/*classification ; Dogs ; *Food Chain ; Goats ; Saudi Arabia ; },
abstract = {The type and amount of resources available significantly influences the structure and dynamics of food webs. In this study, we analyzed differences in species richness of scavengers based on carcass type in Riyadh, Saudi Arabia. We collected insects from experimental carcasses of three different types, domestic dogs (Canidae, Canis lupus familiaris), Hijazi goats (Bovidae, Capra aegagrus hircus), and camels (Camelidae, Camelus dromedarius). Data collection was conducted during the decay stage in June, 2016. We used mitochondrial cytochrome c oxidase subunit I (mtCOI) barcodes as a marker for the molecular identification of the scavenger insects. The results showed that there were more insects on the camels and goats than the dogs. In total, seven species were found on all carrions. Six species were found on the camels and goats, but only five were found on the dog. Musca domestica was the most collected species of flies whereas, Necrobia rufipes was the most collected species of beetles. Overall, this study showed that carrion type had an effect on the type and number of insects attracted to the carrions. Thus, one of the significant factors that influence the associated scavenger assemblage is a carcass type.},
}
@article {pmid33365695,
year = {2019},
author = {Chakraborty, R and Singha, D and Kumar, V and Pakrashi, A and Kundu, S and Chandra, K and Patnaik, S and Tyagi, K},
title = {DNA barcoding of selected Scirtothrips species (Thysanoptera) from India.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {4},
number = {2},
pages = {2710-2714},
pmid = {33365695},
issn = {2380-2359},
abstract = {The members of the genus Scirtothrips are highly polyphagous, including major pest and vector species. We applied both morphology and molecular approaches to delimit the selected Scirtothrips species from India. Out of 43 generated barcode sequences, six sequences of three species (S. hitam, S. mangiferae, and S. malayensis) are the novel contribution in global database. The Bayesian (BA) phylogeny clearly distinguishes all the studied species with reciprocal monophyletic criteria and represents multiple clades in S. dorsalis and S. oligochaetus. The high Kimura-2-Parameter (K2P) genetic divergences were observed between the multiple clades of S. dorsalis (4.5-8.8%) and S. oligochaetus (6.4%), which indicating possible existence of cryptic diversity. The current study also provided the morphological keys for six Scirtothrips species including S. hitam as a new record to India.},
}
@article {pmid33365612,
year = {2019},
author = {Kundu, S and Tyagi, K and Pakrashi, A and Kumar, V and Kosygin, L and Rath, S and Das, U and Chandra, K},
title = {DNA barcoding of freshwater fishes from the transboundary river of Indo-Bhutan: multiple clades and cryptic diversity.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {4},
number = {2},
pages = {2527-2532},
pmid = {33365612},
issn = {2380-2359},
abstract = {The species diversity of freshwater fishes from the transboundary river, Jaldhaka is still unknown to the scientific communities. We generated 40 DNA barcode sequences of 16 morphologically identified freshwater fishes and compared genetically with the database sequences. Ten species (Acanthocobitis botia, Barilius bendelisis, Crossocheilus latius, Channa punctata, Channa quinquefasciata, Garra gotyla, Garra kempi, Opsarius barna, Psilorhynchus balitora, and Pseudecheneis sulcata) showed unique haplotypes in the studied riverine system. Further, the estimated genetic divergences, BA tree topology, and ABGD species delimitation methods revealed the presence of cryptic diversity in Badis badis, Garra annandalei, G. gotyla, G. kempi, P. balitora, Rasbora daniconius, and Pethia ticto. The study suggested more exhaustive sampling and generation of more molecular data to strengthen the fact. The aimed integrated approach will be helpful to detect the extant species diversity, helps to reevaluate the checklist and promote sustainable conservation management to protect this unparalleled ecosystem.},
}
@article {pmid33365582,
year = {2019},
author = {Kundu, S and Kumar, V and Tyagi, K and Rath, S and Pakrashi, A and Saren, PC and Laishram, K and Chandra, K},
title = {Mitochondrial DNA identified bat species in northeast India: electrocution mortality and biodiversity loss.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {4},
number = {2},
pages = {2454-2458},
pmid = {33365582},
issn = {2380-2359},
abstract = {Northeast India with two biodiversity hotspots is recognized as a biodiversity-rich region. However, several extant animals including chiropterans are currently at jeopardy due to habitat loss, electrocution mortality, and other anthropogenic threats. This study examines the efficacy of mitochondrial Cytochrome b (mtCytb) sequences for species-level identification of five electrocuted bat specimens from Manipur state. The similarity search results in the global database, Kimura 2 parameter (K2P) genetic distances, and neighbor-joining (NJ) tree identified all bat specimens into two species, Cynopterus sphinx and Megaerops niphanae. The detection of M. niphanae is the first record of this mammal from the state. In comparison with other Pteropodidae species, the genetic distances clearly discriminate both C. sphinx (7.9-30.2%) and M. niphanae (12.2-25.7%). In addition, the combined tree analysis of present and earlier genetic information of C. sphinx suggested the presence of cryptic lineages and sympatric population in India. This similar approach with more sampling from a wide distribution area could assist the future genetics research on chiropterans and their precise conservation.},
}
@article {pmid33365567,
year = {2019},
author = {Kundu, S and Chandra, K and Tyagi, K and Pakrashi, A and Kumar, V},
title = {DNA barcoding of freshwater fishes from Brahmaputra River in Eastern Himalaya biodiversity hotspot.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {4},
number = {2},
pages = {2411-2419},
pmid = {33365567},
issn = {2380-2359},
abstract = {The genetic diversity of freshwater fishes is still anonymous in several drainage systems in northeast India. Moreover, the comparative genetic analysis is largely sporadic to judge their actual diversity and true status. We generated 89 DNA barcodes of 40 morphologically identified fishes collected from two major tributaries of Brahmaputra River. The comparative study revealed that most of the species were clearly discriminated by their estimated genetic distances and monophyletic clustering in Bayesian (BA) tree. Considering the genetic divergence (2%) for species discrimination boundary, the high genetic diversity (2.36-10.73%) was detected in 11 species (Macrognathus pancalus, Channa punctata, Puntius terio, Bangana ariza, Garra arupi, Badis badis, Mystus vittatus, Rita rita, Gagata cenia, Mastacembelus armatus, and Danio dangila), which signified the occurrence of concealed genetic diversity in this ecozone. However, the insignificant genetic distances were also noticed in few reportedly valid species: Channa stiktos and C. ornatipinnis (1.43%); Mystus ngasep, M. rufescens, and M. carcio (0.4%); Glyptothorax trilineatus, G. churamanii, and G. verrucosus (0.4%); Botia almorhae, B. histrionica, B. lohachata, and B. rostrata (0-0.4%); Barilius barilia and B. vagra (0.4%); Batasio merianiensis and B. tengana (1.2%); Puntius chola and P. fraseri (0%), Schistura beavani and S. paucireticulata (0%); hence to validate this species, generation of more barcode data was required from their types or topotypes. The present study would help to develop conservation schemes for the native species and collegiate ecosystem, which associated with the livelihoods of millions of ethnic communities in this region.},
}
@article {pmid33365600,
year = {2019},
author = {Chan, AFO and Luczon, AU and Fontanilla, IKC and Ong, PS and Santos, MD and Willette, DA and Quilang, JP},
title = {DNA barcoding cannot discriminate between Sardinella tawilis and S. hualiensis (Clupeiformes: Clupeidae).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {4},
number = {2},
pages = {2499-2503},
pmid = {33365600},
issn = {2380-2359},
abstract = {Sardinella tawilis, the only known freshwater sardinella in the world, is endemic to Taal Lake, Philippines. Previous studies found the Taiwan sardinella, S. hualiensis, to be morphologically very similar to S. tawilis and identified it as the marine sister species of S. tawilis. In this study, DNA barcoding using the mitochondrial cytochrome c oxidase I (COI) gene was carried out to analyze species demarcation in the Sardinella genus, focusing primarily on the relationship between S. tawilis and S. hualiensis. The neighbour-joining (NJ) tree that was constructed using Kimura 2-parameter (K2P) model showed a single clade for the two species with 100% bootstrap support. K2P interspecific genetic divergence ranged from 0% to 0.522%, which is clearly below the suggested 3-3.5% cutoff for species discrimination. Recombination activating gene 1 (RAG1), mitochondrial control region (CR), cytochrome b, 16S rRNA, and S7 markers were used to further validate the results. Sardinella tawilis and S. hualiensis clustered together with a bootstrap support of 99-100% in each of the NJ trees. Low interspecific genetic distances between S. tawilis and S. hualiensis for all the markers except CR could be attributed to incipient allopatric speciation.},
}
@article {pmid33365583,
year = {2019},
author = {Peng, W and Yang, H and Cai, K and Zhou, L and Tan, Z and Wu, K},
title = {Molecular identification of the Danzhou chicken breed in China using DNA barcoding.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {4},
number = {2},
pages = {2459-2463},
pmid = {33365583},
issn = {2380-2359},
abstract = {Mitochondrial cytochrome C oxidase subunit I (COI) has been used as a DNA barcode to identify population genetic diversity and distinguish animal species as it is variable enough to distinguish between species, yet suitably conserved. A new native chicken breed, named Danzhou chicken was discovered in Hainan, China in 2014, although identification is difficult by morphological examination alone. The mitochondrial COI genes of six chicken breeds, including four local and two imported breeds (Danzhou, Wenchang, Bawang, Beijing-You, Hy-Line Brown, and Ross) were compared and assessed in terms of their efficacy for DNA barcoding. The results showed that the number of COI gene variants in Danzhou chickens was less than those of other breeds, except Bawang and the genetic structure was relatively stable. The Kimura 2-parameter genetic distance between Danzhou chickens and the five other breeds was from ∼0.001 to 0.734. The genetic distance of the six breeds was ∼0.001-0.339, with that of Danzhou being the highest (0.339). Danzhou chickens clustered with Bawang and Wenchang chickens in the phylogenetic tree due to geographic closeness. Danzhou chickens could be identified more accurately using COI barcoding. Multiple molecular markers combined with morphological differences were more persuasive for identifying species.},
}
@article {pmid33597400,
year = {2019},
author = {Fallatah, SA and Ghallab, EH and Khater, EI},
title = {Phylogenetic diversity and DNA barcoding of the camel tick Hyalomma dromedarii (Acari: Ixodidae) of the Eastern region of Saudi Arabia.},
journal = {Tropical biomedicine},
volume = {36},
number = {2},
pages = {390-401},
pmid = {33597400},
issn = {2521-9855},
abstract = {Hard ticks are causative agents of physical illness and vectors of important diseases of human and livestock. The hard tick Hyalomma dromedarii Koch, 1844 is a major ectoparasite of livestock in the Kingdom of Saudi Arabia (KSA), of which, the onehumped dromedaries Camelus dromedarius is the most economically and culturally important and a potential reservoir of Middle East respiratory syndrome coronavirus (MERSCoV) disease. Here we report on the molecular phylogenetic diversity of H. dromedarii collected from camels in the Eastern Province of KSA based on the mitochondrial cytochrome oxidase I (COI) gene. Maximum likelihood (ML) phylogenetic analysis of COI sequences of the studied ticks identified 11 haplotypes. All H. dromedarii ticks from KSA belonged to eight haplotypes diverged into two distinguished genetic clades (A-B). These results indicate that H. dromedarii ticks from KSA are monophyletic species with two distinguished lineages with low intra-specific genetic divergence and sharply structured isolated populations with high level of genetic differentiation. This is a first report of DNA barcode of H. dromedarii ticks from KSA and the Arabian Peninsula, which is an important step towards broader phylogenetic studies on larger tick samples from the region. The studies are important for better understanding its interactions with camels and other hosts and role in zoonotic disease transmission (e.g. MERS-CoV or Alkhurma virus) to pinpoint effective control strategies.},
}
@article {pmid33365413,
year = {2019},
author = {Kang, TH and Kim, S and Hong, KJ and Lee, HS},
title = {DNA barcoding in quarantine inspection: a case study on quarantine insect monitoring for Lepidoptera obtained through quarantine inspection on foreign vessels.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {4},
number = {1},
pages = {43-48},
pmid = {33365413},
issn = {2380-2359},
abstract = {We conducted quarantine insect species diversity monitoring using DNA barcoding with 517 lepidopteran samples that were obtained from quarantine inspections of foreign vessels entering Korea. For species delimitation and species identification of the analyzed samples, we applied a 2% cutoff rule. Consequently, 145 (368 samples) were considered taxonomically identified. Therefore the number of samples that were identified to the species level was relatively low, at approximately 71%. Thirty of 145 species were not known in Korea, three, i.e., Noctua pronuba (Noctuidae), Orthosia hibisci (Noctuidae), and Pieris brassicae (Pieridae), were checked as 'Regulated pests' in Korea.},
}
@article {pmid33601860,
year = {2018},
author = {Brandon-Mong, GJ and Ketzis, JK and Choy, JS and Boonroumkaew, P and Tooba, M and Sawangjaroen, N and Yasiri, A and Janwan, P and Tan, TC and Nissapatorn, V},
title = {DNA barcoding relates Trichuris species from a human and a man's best friend to non-human primate sources.},
journal = {Tropical biomedicine},
volume = {35},
number = {4},
pages = {1131-1139},
pmid = {33601860},
issn = {2521-9855},
abstract = {Trichuris trichiura, the whipworm of humans, is one of the most prevalent soiltransmitted helminths (STH) reported worldwide. According to a recent study, out of 289 STH studies in Southeast Asia, only three studies used molecular methods. Hence, the genetic assemblages of Trichuris in Southeast Asia are poorly understood. In this study, we used partial mitochondrial DNA (cytochrome c oxidase subunit 1 or COI) sequences for analysis. Trichuris grouped in a same clade with different hosts indicate the potential of cross infection between hosts. Based on COI, the adult Trichuris isolated from a Malaysian patient was most closely related to Trichuris isolated from Papio anubis (olive baboons) from the USA. The Trichuris isolated from the dog from Malaysia was genetically similar to a Trichuris species isolated from Macaca silenus (lion-tailed macaque) from Czech Republic. Both the human and dog isolated Trichuris grouped in clades with different hosts indicating the potential of cross infection between hosts. Specific PCR primers based on the partial COI of T. trichiura isolated from African green monkey and T. serrata were designed and successfully amplified using multiplex PCR of the pooled DNA samples. Our results suggest a complex parasite-host relationship, and support the theory of cross infection of Trichuris between humans and non-human primates as suggested in previous publications.},
}
@article {pmid33365412,
year = {2019},
author = {Singha, D and V, VK and Chakraborty, R and Kundu, S and Hosamani, A and Kumar, V and Tyagi, K},
title = {Molecular footprint of Frankliniella occidentalis from India: a vector of Tospoviruses.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {4},
number = {1},
pages = {39-42},
pmid = {33365412},
issn = {2380-2359},
abstract = {The western flower thrips, F. occidentalis is a vector of Tospoviruses and native to Western North America and Mexico. The present study is based on collected F. occidentalis specimens from Karnataka state in southern India and morphologically identified through available keys. The generated DNA barcode data show 99-100% similarity with the database sequences of F. occidentalis. The phylogenetic analysis (NJ, ML, and BA) shows three distinct clades of F. occidentalis in the present dataset with high bootstrap supports and posterior probabilities. The K2P genetic distances further depicted high similarity of the generated sequences from India and Netherlands. The Clade-1 (India + Netherlands) also shows a close relationship with Clade-2 (Kenya) rather than Clade-3 (Canada + USA). This study recorded the first genetic footprint of F. occidentalis in India and indicated the gene flow from the Netherlands to India. The similar molecular techniques may help to detect the invasion of many alien species in the near future and assists the quarantine regulations to protect the native ecosystem.},
}
@article {pmid33474439,
year = {2018},
author = {Lee, SY and Ng, WL and Mohamed, R and Terhem, R},
title = {The complete chloroplast genome of Aquilaria malaccensis Lam. (Thymelaeaceae), an important and threatened agarwood-producing tree species.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {3},
number = {2},
pages = {1120-1121},
pmid = {33474439},
issn = {2380-2359},
abstract = {Known for its valuable agarwood, Aquilaria malaccensis Lam. is an evergreen tropical forest tree species endemic to the Indo-malesian region. Indiscriminate damaging and harvesting of the trees in the wild have resulted in it being listed in the CITES Appendix II for controlled trade and in the IUCN Red List as 'Vulnerable (VU)'. In this study, the complete chloroplast genome of A. malaccensis was assembled using data from high-throughput Illumina sequencing. The chloroplast genome was 174,832 bp in size, which included two inverted repeat regions of 42,091 bp each, separated by a large single copy region of 87,302 bp and a small single copy region of 3,348 bp. A total of 139 genes were predicted, including 39 tRNA, 8 rRNA, and 92 protein-coding genes. Phylogenetic analysis placed A. malaccensis within the family Thymelaeaceae. The chloroplast genome sequence of A. malaccensis offers a useful resource for future studies on the taxonomy and conservation of the threatened Aquilaria trees.},
}
@article {pmid33474470,
year = {2018},
author = {Tahir, HM and Noor, A and Mehmood, S and Sherawat, SM and Qazi, MA},
title = {Evaluating the accuracy of morphological identification of insect pests of rice crops using DNA barcoding.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {3},
number = {2},
pages = {1220-1224},
pmid = {33474470},
issn = {2380-2359},
abstract = {Accurate identification of agricultural pests is key requirement for the successful integrated pest management (IPM) program. However, due to limitations of conventional morphological methods, other molecular method like DNA barcoding is used. The current study was designed to evaluate the accuracy of morphological identification of insect pests using DNA barcoding. Morphologically, a total of 247 insect pests, representing 10 families, 18 genera, 22 species were identified. However, molecular identifications confirmed the presence of 11 families, 16 genera, and 20 species of agricultural pests. A total of 59 specimens were processed for DNA barcoding but genomic sequences of mt COI gene up to 600 bp were revived from 48 samples. Specimens that were misidentified through morphological studies were placed to their appropriate taxon, using this molecular approach. Results revealed the existence of clear barcode gap for different pest species. Moreover, the values of distance with the nearest neighbour recorded were higher than the maximum intra-sequence divergences for all species. It is concluded that DNA barcoding is a reliable technique for identification of agricultural pests, especially for immature stages when morphometric studies are ambiguous and will be helpful in the development of more effective pest management options for regulating pest species.},
}
@article {pmid33474378,
year = {2018},
author = {Kundu, S and Rath, S and Tyagi, K and Chakraborty, R and Pakrashi, A and Kumar, V and Chandra, K},
title = {DNA barcoding of Cloridopsis immaculata: genetic distance and phylogeny of stomatopods.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {3},
number = {2},
pages = {955-958},
pmid = {33474378},
issn = {2380-2359},
abstract = {The changes of coastal topography might have genetically altered the extant species diversity in Chilika Lake. The genetic assessment of stomatopods has never been attempted from this ecosystem. The study generate the first genetic information (mtCOI) of Cloridopsis immaculata. DNA sequences of C. immaculata shows 12.9% genetic divergence with Harpiosquilla harpax and clade as sister species in NJ tree. Alima, Harpiosquilla, and Oratosquilla shows high congeneric/conspecific genetic divergence (20.9%, 15.7%, and 7.2%) and cladded separately in the phylogeny; correlate to their diverse populations. We recommend more extensive survey of stomatopods and generation of molecular data to resolve the taxonomic uncertainty.},
}
@article {pmid33474344,
year = {2018},
author = {Garg, S and Das, A and Kamei, RG and Biju, SD},
title = {Delineating Microhyla ornata (Anura, Microhylidae): mitochondrial DNA barcodes resolve century-old taxonomic misidentification.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {3},
number = {2},
pages = {856-861},
pmid = {33474344},
issn = {2380-2359},
abstract = {Microhyla ornata, a species originally described from the southwest coast of India in 1841, was long reported to be wide-ranging throughout South, Southeast, and East Asia. Although the name M. ornata is restricted to populations from South Asia, the species is still considered to occur widely in India and its neighboring regions. To clarify the identity and geographical distribution of M. 'ornata', we performed DNA barcoding using a fragment of the mitochondrial 16S rRNA gene from 62 newly obtained samples. Our results show that this taxon is restricted to Peninsular India and Sri Lanka, whereas, populations from the other parts represent three different species - M. mukhlesuri, M. mymensinghensis, and M. nilphamariensis, creating new country records for India. Our work reemphasizes the benefits of DNA barcoding for rapidly identifying populations of widespread species and provides insights into the patterns of genetic differentiation in the M. 'ornata' species complex of South Asia.},
}
@article {pmid33381678,
year = {2018},
author = {Wadhwa, RR and Williamson, DFK and Dhawan, A and Scott, JG},
title = {TDAstats: R pipeline for computing persistent homology in topological data analysis.},
journal = {Journal of open source software},
volume = {3},
number = {28},
pages = {},
pmid = {33381678},
issn = {2475-9066},
support = {K12 CA076917/CA/NCI NIH HHS/United States ; R37 CA244613/CA/NCI NIH HHS/United States ; },
abstract = {High-dimensional datasets are becoming more common in a variety of scientific fields. Well-known examples include next-generation sequencing in biology, patient health status in medicine, and computer vision in deep learning. Dimension reduction, using methods like principal component analysis (PCA), is a common preprocessing step for such datasets. However, while dimension reduction can save computing and human resources, it comes with the cost of significant information loss. Topological data analysis (TDA) aims to analyze the "shape" of high-dimensional datasets, without dimension reduction, by extracting features that are robust to small perturbations in data. Persistent features of a dataset can be used to describe it, and to compare it to other datasets. Visualization of persistent features can be done using topological barcodes or persistence diagrams (Figure 1). Application of TDA methods has granted greater insight into high-dimensional data (Lakshmikanth et al., 2017); one prominent example of this is its use to characterize a clinically relevant subgroup of breast cancer patients (Nicolau, Levine, &amp; Carlsson, 2011). This is a particularly salient study as Nicolau et al. (2011) used a topological method, termed Progression Analysis of Disease, to identify a patient subgroup with 100% survival using that remains invisible to other clustering methods.},
}
@article {pmid33474313,
year = {2018},
author = {Mota, TFM and Fabrin, TMC and Gasques, LS and Ortêncio Filho, H and Prioli, AJ and Prioli, SMAP},
title = {Extraction of DNA from micro-tissue for bat species identification.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {3},
number = {2},
pages = {758-762},
pmid = {33474313},
issn = {2380-2359},
abstract = {Bat populations are declining worldwide. Accurate identification is essential to promote species' conservation. However, minimal morphological differences and a high rate of cryptic species make identification difficult, unless voucher specimens are kept, a controversial issue today. The objective of this work was to standardize a method of extracting non-lethal DNA using bats' uropatagium micro-tissue, aiming the molecular identification of species that occur in the region of Maringá PR. The method standardized was efficient, and does not cause serious damage to bats. For future field studies, collection of micro-tissue and morphometry of the specimens will be sufficient for accurate identification.},
}
@article {pmid33490531,
year = {2018},
author = {Ruihua, Z and Ping, J and Chuanbo, S and Deyong, S and Feng, Z and Chaochao, H},
title = {The analysis of genetic variation in the mitochondrial genome and its application for the identification of Papilio species.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {3},
number = {2},
pages = {687-690},
pmid = {33490531},
issn = {2380-2359},
abstract = {Mitochondrial DNA (mtDNA) markers are ideal for evolutionary studies, including phylogeography, population genetics, phylogeny, etc. However, different mitochondrial genes always own different evolutionary rate. In this study, we analysed the genetic variation across the 16 complete mtDNA from 13 species in the genus Papilio and recognized the best DNA barcoding for Papilio species. The mitochondrial gene arrangement for each species shares a similar order, similar to the typical Papilionidae species, which indicated the relatively conservative state of gene arrangement in Papilio. The sliding window of genetic diversity showed that there was a significant difference in the genetic diversity of each gene in the mitochondrial genome of Papilio. The relatively mean clock rate of the ND1 was broadly lower than the other genes in mitochondrial genome of Papilio; while the ATP8 owns the largest values of mean clock rate. Those results suggested that the rate of evolution of each gene is not balanced and all mitochondrial genes except ND1 and ATP8 could act as barcoding for the identification of Papilio species. The phylogenetic analyses of complete mtDNA data for 13 Papilio species divided them into five major branches, which keep the same topological structure with previous studies.},
}
@article {pmid33601825,
year = {2018},
author = {Farah Haziqah, MT and Chandrawathani, P and Douadi, B and Suresh, K and Wilson, JJ and Mohd Khalid, MKN and Rajamanikam, A and Lewis, JW and Mohd Zain, SN},
title = {Impact of pH on the viability and morphology of Blastocystis isolates.},
journal = {Tropical biomedicine},
volume = {35},
number = {2},
pages = {501-510},
pmid = {33601825},
issn = {2521-9855},
abstract = {Blastocystis sp. is ubiquitous in avian, mammalian and human hosts and propagates in either neutral or slightly alkaline conditions within the host's gastro-intestinal tract. Of the few previous studies on this enteric protozoan parasite in feline and canine hosts, prevalence values have been shown to range between 0 to 70.8%. In view of the close association between humans, and canine and feline hosts as companion animals, faecal samples of 180 Felis catus and 82 Canis lupus, collected from Penang and Kuala Lumpur, Malaysia, were initially screened by in vitro cultivation followed by molecular characterization. No positive isolates were identified in culture but in 12 feline samples DNA barcoding detected a zoonotic subtype Blastocystis ST1 for the first time. Consequently, avian and human isolates, which had previously been successfully cultured, were used to investigate the impact of pH on the viability and morphology of Blastocystis sp. The use of Trypan blue showed that the number of viable cells increased when exposed to pH 4 and a significant increase in viability occurred in pH values of 5 to 7. Development of Blastocystis cells in both isolates was suppressed in media less than pH 5 followed by the disappearance of viable cells from avian isolates in more acidic media below pH 4. Morphologically at pH 4 cells from avian isolates were less rounded, and with wrinkled / shrunken surfaces, than the more normal rounded cells from human isolates. On the other hand, at values below pH 3, no viable cells in human isolates were visible. The present findings therefore confirm that gastro-intestinal pH is an important determinant of Blastocystis viability and consequently influences the epidemiology of infection within avian, mammalian and human hosts.},
}
@article {pmid33474223,
year = {2018},
author = {Kundu, S and Kumar, V and Laskar, BA and Tyagi, K and Chandra, K},
title = {Pet and turtle: DNA barcoding identified twelve Geoemydid species in northeast India.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {3},
number = {2},
pages = {513-518},
pmid = {33474223},
issn = {2380-2359},
abstract = {Geoemydid turtles are one of the most imperilled fauna on the planet, with nearly half of them are threatened with extinction due to bushmeat crisis, traditional medicine, and the illegal pet trade. Classical taxonomy often fails to identify the pet-kept turtle specimens due to amorphous form, unusual shell colouration owing to poor storage in captivity or intensely tinted for high demanding value. The DNA barcoding technique has evidenced as a supportive tool for accurate species identification in systematics research and discerned the nameless taxa in forensic sciences. We tested the effectiveness of DNA barcoding tools for identifying the pet-kept Geoemydid turtle in northeast India. The 36 generated sequences are readily delineated into 12 Geoemydid species using molecular data. The overall mean genetic distance of the studied Geoemydid turtles dataset is 15.3% and ranges from 3.4% to 22.6% between the species. The NJ, ML and Bayesian phylogeny also resulted monophyletic clustering and discriminated all the studied species. The present study contributes DNA barcode sequences of Geoemydid turtles in the global database and also affirms the on-going illegal pet trade of highly threatened species in northeast India.},
}
@article {pmid33817067,
year = {2018},
author = {Molina, J and Sherpa, C and Ng, J and Sonam, T and Stuhr, N},
title = {DNA Barcoding of Online Herbal Supplements: Crowd-sourcing Pharmacovigilance in High School.},
journal = {Open life sciences},
volume = {13},
number = {},
pages = {48-55},
pmid = {33817067},
issn = {2391-5412},
abstract = {Herbal medicinal products (HMPs) have grown increasingly popular in the United States, many of them with imported raw materials and sold online. Yet due to the lack of regulation from the US Food and Drug Administration (FDA), manufacturers of the products can substitute or add in other herbs that are not advertised on the label. In this study, as part of the Urban Barcode Research Program (UBRP), an education initiative to engage New York City high school students in science, we aimed to taxonomically authenticate single-ingredient online-sold HMPs containing non-native plants through DNA barcoding of the internal transcribed spacer 2 region (ITS2) and matK. We were able to successfully barcode 20 HMPs, but four of these did not match the expected species. It was concluded that the four HMPs advertising astragalus, epazote, ginseng, and chanca piedra were contaminated/ substituted because their ITS2 and matK DNA sequences did not match the expected taxonomy in GenBank, a government database. Our study highlights the importance of herbal pharmacovigilance in the absence of strict government regulation of herbal supplements and motivates crowd-sourced DNA barcoding to enable American consumers make informed choices and be more empowered to safeguard their health.},
}
@article {pmid33569520,
year = {2018},
author = {Zheng, S and Li, Y and Yang, X and Chen, J and Hua, J and Gao, Y},
title = {DNA barcoding identification of Pseudococcidae (Hemiptera: Coccoidea) using the mitochondrial COI gene.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {3},
number = {1},
pages = {419-423},
pmid = {33569520},
issn = {2380-2359},
abstract = {DNA barcoding is a recently developed technique for species-level identification that involves the use of short, standard DNA sequences as species labels. It is an effective complement to traditional taxonomic classification based on morphology. At present, research and applications involving the DNA barcoding of the Pseudococcidae are focused primarily on the cytochrome coxidase subunit I (COI) gene, but there is not yet a consensus on the preferred gene region for barcoding. The purpose of this study was to explore the effectiveness of identification of Pseudococcidae beetles using DNA barcoding technology. The COI gene sequences of 97 samples from 21 species of Asemini were analysed, followed by evaluation of the ability to identify species using a tree-building method and distance evaluation. The COI sequences (500 bp) exhibited distinct distributions of intra-specific and inter-specific variation and a significant barcoding gap. The success rate of identification was 97.84%. These results demonstrate the feasibility of using this segment of COI to identify most species of Pseudococcidae.},
}
@article {pmid33474185,
year = {2018},
author = {Kwun, HJ},
title = {Species identification of juvenile fishes of the genus Pseudoblennius using mitochondrial DNA barcoding.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {3},
number = {1},
pages = {405-408},
pmid = {33474185},
issn = {2380-2359},
abstract = {Species identification is important in natural science and should be precise. Six specimens of juvenile Pseudoblennius were collected from the eastern coastal waters of the Korean Peninsula and Jeju Island in 2016-2017, and identified for the first time using DNA barcoding based on mitochondrial DNA cytochrome oxidase subunit I sequences. DNA barcoding analysis supported three adult species of genus Pseudoblennius (P. cottoides, P. marmoratus, and P. percoides) being quite distinct from each other. Six juvenile specimens were completely identified: two as P. cottoides; two more as P. marmoratus; and the final two as P. percoides. Mitochondrial DNA COI can be effective as a means of species identification method for the genus Pseudoblennius.},
}
@article {pmid33474158,
year = {2018},
author = {Bhaskar, R and Mohindra, V},
title = {Variability in DNA COI sequences reveals new haplotypes in freshwater turtles from northern region of India.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {3},
number = {1},
pages = {317-323},
pmid = {33474158},
issn = {2380-2359},
abstract = {The chelonian represents a diverse order of turtles. Little is known about this group from India at molecular level. Cytochrome c oxidase I (COI) sequences of 125 individuals from nine species of freshwater turtles were generated and analyzed. A total of 118 nucleotide positions in COI gene as character-based DNA barcodes for each species were identified. Neighbour-joining (NJ) analyses tree well differentiated freshwater hard shell and softshell turtle. Overall species divergence (K2P) was 13.3%. Analysis of COI sequences from present study, combined with sequences downloaded from NCBI GenBank, revealed new COI haplotypes from Northern region of India.},
}
@article {pmid33601782,
year = {2018},
author = {Carrero-Sarmiento, D and Hoyos-López, R},
title = {Molecular identification and genetic diversity of Lutzomyia gomezi (Diptera: Psychodidae) using DNAbarcodes in Cordoba, Colombia.},
journal = {Tropical biomedicine},
volume = {35},
number = {1},
pages = {100-110},
pmid = {33601782},
issn = {2521-9855},
abstract = {Lutzomyia gomezi, a suspected vector of cutaneous leishmaniasis in Colombia is recorded for natural infection of Leishmania parasites, its anthrophilic behaviour and significant abundance supports its vectorial role. The difficulties associated with taxonomic identification due to lack of males require the use of molecular markers (DNA barcodes), which allows us to distinguish the species. In this study, the cytochrome oxidase I fragment was proposed as DNA barcode to identify specimens collected from Cordoba, Colombia (Planeta Rica: Arenoso/ Centro Alegre, Sahagún: Santiago Abajo/San Andresito) by using protocols for DNA extraction, PCR, and sequencing. These sequences allowed for testing the genetic diversity, genetic distance, population structure and gene flow. A phylogenetic analysis was performed with sequences registered in Genbank for this and related species such as Lutzomyia lichyi, Lutzomyia longipalpis and Lutzomyia bifoliata. In total, 24 PCR products were sequenced, resulting in an alignment of 677 nt in length, and 9 haplotypes were identified for L. gomezi. Values for polymorphic sites, haplotype and nucleotide diversity were high for specimens belonging to Sahagún and Planeta Rica. The genetic distances (TN93) and localities studied were significant (0,011-0,024), FST evidenced with mild and significant structure (0,10-0,52) and limited genetic flow (Nm=0,45-24,5). The phylogenetic analysis showns three lineages with significant distances (0,026-0,48) and sympatric between haplotypes from different zones; however, the limited sampling size and the absence of specimens belonging to other Colombian geographic areas implied more lineages. The DNA barcode methodology can answer questions about phylogeography, vector competence and genetic structuration between populations using a common marker for the scientific community.},
}
@article {pmid33474133,
year = {2018},
author = {Kumar, VP and Shukla, M and Rajpoot, A and Thakur, M and Nigam, P and Kumar, D and Mehta, AK and Goyal, SP},
title = {DNA barcoding as a tool for robust identification of cervids of India and its utility in wildlife forensics.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {3},
number = {1},
pages = {250-255},
pmid = {33474133},
issn = {2380-2359},
abstract = {DNA barcoding has become a popular method of choice for identification of specimen based on molecular techniques. Here, we present preliminary findings on generating robust DNA barcode library of Cervids of India. The dataset comprising the DNA barcode library of seven deer species included in the genus Cervus, Axis and Muntiacus classified under family Cervidae. Mitochondrial Cytochrome C Oxidase subunit I gene of ca. 710 bp accepted widely as DNA barcode region, was used for generating species specific signature from 31 known samples of seven Indian deer species. Expectedly, the NJ tree clustered three genera i.e. Cervus, Axis and Muntiacus of Cervids of India into three clades. Further, the intra- and interspecies distances based on Kimura 2 parameter model also supported the results. The average intra- and interspecies sequence divergence were 0.011 (±0.09) and 0.65 (±0.14), respectively. The present study has exhibited that DNA barcoding has discriminating power to delineate boundaries among the closely related species. The data generated are of high importance to the law enforcement agencies in effective identification of species in wildlife offence cases. The similar approach can be utilized for generating DNA barcodes for other Indian mammals for making effective management and conservation action decisions.},
}
@article {pmid33474105,
year = {2018},
author = {Kundu, S and Rath, S and Tyagi, K and Chakraborty, R and Kumar, V},
title = {Identification of penaeid shrimp from Chilika Lake through DNA barcoding.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {3},
number = {1},
pages = {161-165},
pmid = {33474105},
issn = {2380-2359},
abstract = {Chilika Lake is one of the prolific habitats of shrimps in India and offers tons of commercial trading every year. The genetic diversity of penaeid shrimp species in this oldest and largest brackish water lagoon is unknown so far. The DNA barcoding is emerging as an essential supportive tool for morphology-based species identification. In this study, we have generated DNA barcode data of morphologically identified six penaeid shrimps from Chilika Lake. Most of the generated sequences revealed 99-100% similarities with the conspecific database sequences (GenBank and BOLD). More than one distinct clade in NJ tree and high-genetic variability were resulted in P. monodon (6.5% to 8.8%), L. vannamei (3.2% to 5.8%) and M. monoceros (2.3% to 3.5%). The resulted genetic variation within the species depicted different population correlate with the different sampling locations. Thus, more extensive survey and generation of more DNA barcode data of penaeid shrimp from the diverse geographical area might resolve the uncertain genetic distance within the species.},
}
@article {pmid33592943,
year = {2017},
author = {Farah Haziqah, MT and Nur Asyiqin, MN and Mohd Khalid, MKN and Suresh, K and Rajamanikam, A and Chandrawathani, P and Mohd Zain, SN},
title = {Current status of Blastocystis in cockroaches.},
journal = {Tropical biomedicine},
volume = {34},
number = {3},
pages = {741-745},
pmid = {33592943},
issn = {2521-9855},
abstract = {There are few reports on Blastocystis spp. infections in invertebrate hosts namely, cockroaches. Due to their close proximity to humans especially to their dwellings prompted this study as these organisms could possibly play a role in human transmission. A total of 151 cockroaches consisted predominantly of nymph and adult stages were captured from several types of dwellings in the state of Perak and Selangor, Malaysia. Approximately half (40.4%) of the cockroach intestinal contents screened were positive and were found associated to two main factors, host-stage and types of dwellings. The granular and vacuolated forms were the most common cell form found in the in vitro cultures and were morphologically similar to B. hominis. However, the surface coat observed was thick with an electron lucent area observed in the central vacuole. The isolates grew in room temperature but optimal growth was observed at a 24ºC similar to the reptilian Blastocystis with a high number of cells were recovered. Using the DNA barcoding method, two isolates were identified as ST3 (allele 56), one isolate was consider as the new subtype with close relation to allele 114.},
}
@article {pmid33473902,
year = {2017},
author = {Guo, G and Yi, S and Wang, W},
title = {The complete mitochondrial genome of Yihe bream, Megalobrama amblycephala Yih.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {2},
number = {2},
pages = {566-567},
pmid = {33473902},
issn = {2380-2359},
abstract = {The evolutionary status and phylogenetic relationships of Megalobrama species remain unclear, despite the efforts. The genetic information of Yihe bream, a new member in Megalobrama, is quite limited. The complete mitochondrial genome of Yihe bream was urgent to reveal the genetic relationships and evolutionary status. In this study, we sequenced the mitochondrial genome of Yihe bream. The genome is 16,624bp in length and structurally identical to the other Megalobrama species. The phylogenetic tree showed that Yihe bream clustered with blunt snout bream, indicated the closer genetic relationships between these two species. The genome of Yihe bream would be useful for the future researches of population genetics, evolution and DNA barcoding of Megalobrama species.},
}
@article {pmid33473855,
year = {2017},
author = {Xu, L and Huang, Q and Xu, S and Wang, X and Zhang, P and Xu, L and Du, F},
title = {A new set of primers for COI amplification from purpleback flying squid (Sthenoteuthis oualaniensis).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {2},
number = {2},
pages = {439-443},
pmid = {33473855},
issn = {2380-2359},
abstract = {Despite the contribution of DNA barcoding towards understanding the biodiversity and distribution of species, the success of the mitochondrial cytochrome c oxidase subunit I gene (COI) amplification has been quite variable when it comes to Cephalopoda. Some species in this class such as Sthenoteuthis oualaniensis seem to be more difficult to amplify COI than others due to failed amplifications with universal primer and lack of specific set of primers. In this study, we developed new Sthenoteuthis - specific primer set, which significantly increased average amplification success. The new primer set will aid the recovery of barcodes from this difficult group and facilitate further studies in phylogeny and cryptic diversity of Sthenoteuthis oualaniensis.},
}
@article {pmid34541235,
year = {2017},
author = {Kristiansen, TA and Doyle, A and Yuan, J},
title = {Lentiviral Barcode Labeling and Transplantation of Fetal Liver Hematopoietic Stem and Progenitor Cells.},
journal = {Bio-protocol},
volume = {7},
number = {8},
pages = {e2242},
pmid = {34541235},
issn = {2331-8325},
abstract = {Cellular barcoding enables the dissection of clonal dynamics in heterogeneous cell populations through single cell lineage tracing. The labeling of hematopoietic stem and progenitor cells (HSPCs) with unique and heritable DNA barcodes, makes it possible to resolve donor cell heterogeneity in terms of differentiation potential and lineage bias at the single cell level, through subsequent transplantation and high-throughput sequencing. Furthermore, cellular barcoding allows for bona fide hematopoietic stem cells (HSCs) to be defined based on functional rather than immunophenotypic parameters. This protocol describes the work flow of lentiviral cellular barcoding, tracking 14.5 days post coitum (d.p.c.) fetal liver (FL) Lineage-Sca[+]cKit[+] (LSK) HSPCs following long-term reconstitution (Figure 1) (Kristiansen et al., 2016), but can be adapted to the cell type or time frame of choice. Figure 1.Summary of experimental workflow (Naik et al., 2013).},
}
@article {pmid33593004,
year = {2017},
author = {Mohd Zain, SN and Farah Haziqah, MT and Woh, PY and Fazly Ann, Z and Vickneshwaran, M and Mohd Khalid, MKN and Arutchelvan, R and Suresh, K},
title = {Morphological and molecular detection of Blastocystis in wildlife from Tioman Island, Malaysia.},
journal = {Tropical biomedicine},
volume = {34},
number = {1},
pages = {249-255},
pmid = {33593004},
issn = {2521-9855},
abstract = {Blastocystis infection is widely reported in wildlife, livestocks and in non-human primates however, occurrence in Malaysian wildlife is scarce. A wildlife survey on Tioman Island captured six water monitor lizard (Varanus salvator), four mouse-deer (Tragulus sp.) and one Malayan porcupine (Hystrix brachyura) based on convenience sampling. Intestinal contents from each animal were subjected to in vitro cultivation method using Jones medium supplemented with 10% horse serum. Low prevalence of infections was detected with only 1/6 (16.7%) water monitor lizard and 1/4 (25%) mouse-deer infected. The vacuolated form was the most common cell form found in both cultures with similar morphology to B. hominis. However, the monitor lizard isolate propagated well in the laboratory for several months using Jones medium while mouse-deer isolate could not be maintained for more than a week. The reptilian isolates grew optimally at a lower temperature of 24ºC compared to 37ºC for the mouse-deer isolate. Using the DNA barcoding method, both isolates were confirmed to be Blastocystis sp. Sequence obtained from a monitor lizard isolate has 94% sequence identity to B. lapemi, an isolate recovered from a reptile sea-snake whereas a mouse-deer isolate has 99% sequence identitical to B. hominis HJ01-7. The phylogenetic tree revealed that the monitor lizard isolate were positioned within the herptiles clade (clade VIII) while the mouse deer isolate located at the homoithermal clade (clade IV). The present paper is the first report on the presence as well as genetic characteristics of Blastocystis in wildlife captured from Tioman Island, Pahang.},
}
@article {pmid33384880,
year = {2017},
author = {Ad, M and D, B and B, A and M, Y and S, M and Sr, G},
title = {Frequent Association of Colletotrichum Species with Citrus Fruit and Leaf Spot Disease Symptoms and their Genetic Diversity in Ethiopia.},
journal = {Journal of plant pathology &amp; microbiology},
volume = {8},
number = {10},
pages = {},
pmid = {33384880},
issn = {2157-7471},
abstract = {Citrus leaf and fruit spot is one of the most important biotic constraints of citrus production in Ethiopia. The symptomatic leaf and fruit samples were collected from 29 orchards of 15 major citrus growing districts of Ethiopia. One hundred sixty-seven fungal isolates were recovered and identified to species level through DNA barcoding; and their relationships were established using multigene phylogeny. The internal transcribed spacers, long subunit and actin gene sequences revealed that those 167 isolates belonged to either Collectotrichum gloeosporioides or Collectotrichum boninense species complexes (sensu lato), but no recovery of Pseudocercospora angolensis, the primary causal agent of the citrus leaf and fruit spot disease. Detached leaf assays confirmed pathogenicity of isolates of both C. gloeosporioides and C. boninense species complexes on citrus. They reproduced disease symptoms and the pathogens were re-isolated from symptomatic tissues. This study reports frequent association of C. gloeosporioides and C. boninense species complexes with citrus fruit and leaf spot disease in Ethiopia. This finding suggests the need for in-depth studies to determine the roles of C. gloeosporioides and C. boninense species complexes in citrus fruit and leaf spot disease epidemiology.},
}
@article {pmid33473683,
year = {2016},
author = {Akhtar, T and Ali, G},
title = {DNA barcoding of Schizothorax species from the Neelum and Jhelum Rivers of Azad Jammu and Kashmir.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {1},
number = {1},
pages = {934-936},
pmid = {33473683},
issn = {2380-2359},
abstract = {The mitochondrial Cytochrome Oxidase 1 gene is used as a standardized, authenticated, and reliable genetic marker for a global species-level bio-identification system. The present study was conducted to determine whether barcoding can help accurate species identification in fishes. The overall base composition of Schizothorax species was 29.6% of T, 25.5% of C, 26.5% of A, and 18.4% of G, A + T content 56.1% and G + C content 43.9%. The Ts/Tv bias (R) was 2.51. Complete COI gene was amplified using PCR and sequenced from 17 samples collected from river Neelum and Jhelum, and identification of species were done by following Mirza (1991), Jhingran (1991) classification and also through BOLD (99.3 to 99.9%) and NCBI (99.6 to 99.9%) reference sequences of those species. Multiple alignments of CO1 mtDNA gene resulted in a range of 1535-1551 base pairs. Out of 1535 consensus sites, 1490 were constant, 61 characters were variable, in which 54 were parsimony informative, and 7 variables were parsimony uninformative. This is the very first study reported from a reservoir of cold water bodies of Azad Kashmir which have a great potential for conservation of cold water fish species. We emphasized that, DNA barcoding is an accurate, reliable and has the great potential for identification of freshwater fish species.},
}
@article {pmid33473620,
year = {2016},
author = {Luczon, AU and Ong, PS and Quilang, JP and Fontanilla, IKC},
title = {Determining species identity from confiscated pangolin remains using DNA barcoding.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {1},
number = {1},
pages = {763-766},
pmid = {33473620},
issn = {2380-2359},
abstract = {Illegal wildlife trade is one of the key threats to biodiversity. A requisite in combating illegal wildlife trade is through effective and efficient identification of confiscated wildlife or wildlife remains. This can be done through DNA barcoding. In this study, DNA barcoding was employed on several cases of poaching in the Philippines involving 85 unidentified pangolin remains. Of these, 73 specimens confiscated from Palawan were identified as the Palawan endemic Manis culionensis, but no deep divergences were observed, suggesting that the samples originated from a single locality. The other 12 individuals, which were part of a large haul of pangolin carcasses recovered from a foreign fishing vessel that ran aground in Tubattaha Reefs, Philippines, were identified as the Malayan Pangolin, M. javanica. They split into two groups with 3.3% mean genetic distance, suggesting at least two geographic origins.},
}
@article {pmid33473584,
year = {2016},
author = {Selvakumar, C and Sivaramakrishnan, KG and Janarthanan, S},
title = {DNA barcoding of mayflies (Insecta: Ephemeroptera) from South India.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {1},
number = {1},
pages = {651-655},
pmid = {33473584},
issn = {2380-2359},
abstract = {In this study, DNA barcodes were generated for 40 species belonging to 32 genera under 10 families of Ephemeroptera from South India. Nucleotide sequence divergences were calculated using the Kimura two-parameter distance model and a neighbour-joining analysis was performed to provide a graphic display of the patterns of divergence among the species. This study demonstrates that COI barcoding is effective in discriminating among the mayfly species of South India, and provides a reference library for their future molecular identification.},
}
@article {pmid33260209,
year = {2020},
author = {Keller, EL and Schall, JJ},
title = {A New Species of Monocystis (Apicomplexa: Gregarina: Monocystidae) from the Asian Invasive Earthworm Amynthas agrestis (Megascolecidae), with an Improved Standard for Monocystis Species Descriptions.},
journal = {The Journal of parasitology},
volume = {106},
number = {6},
pages = {735-741},
doi = {10.1645/20-20},
pmid = {33260209},
issn = {1937-2345},
mesh = {Animals ; Apicomplexa/*classification/genetics/growth &amp; development/isolation &amp; purification ; DNA, Protozoan/isolation &amp; purification ; Host Specificity ; Introduced Species ; Japan ; Oligochaeta/classification/*parasitology ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/genetics ; Seasons ; Sequence Alignment ; Soil ; Vermont ; },
abstract = {Monocystis perplexa n. sp., a parasite of an important invasive Japanese earthworm in North America, Amynthas agrestis, is described from a site in Vermont. An improved standard for Monocystis species descriptions is proposed including a standard nomenclature to reduce synonymies, a standard set of biometrics and shape descriptions for living cells, and a DNA genomic sequence for the 18S rRNA (∼1,700 base pairs). Comparing morphologies of Monocystis parasites in sympatric earthworm species indicates that M. perplexa is specific to A. agrestis in the study region. Also, polymerase chain reaction primers specific to M. perplexa amplified samples of A. agrestis earthworms taken from several sites in Japan. This suggests the parasite entered North America from Japan, the origin of the invasive Amynthas earthworm, and thus M. perplexa would be the first Monocystis described from the diverse Japanese Amynthas earthworms and the first from East Asia. Monocystis perplexa was found in every population of A. agrestis surveyed in Vermont, always reaching 100% prevalence by late summer (the host has an annual life cycle in Vermont). The 18S gene sequence differed from that of Monocystis agilis from the sympatric earthworm Lumbricus terrestris (the only other sequence available for Monocystis), and a genetic similarity tree places them closest among other gregarines. Many of the 95 described species of Monocystis are very similar in morphology (based on species descriptions), so the 18S gene can act as a barcode for Monocystis species and thus will help to eliminate both synonymies and reveal cryptic species.},
}
@article {pmid33256809,
year = {2020},
author = {Squarre, D and Nakamura, Y and Hayashida, K and Kawai, N and Chambaro, H and Namangala, B and Sugimoto, C and Yamagishi, J},
title = {Investigation of the piroplasm diversity circulating in wildlife and cattle of the greater Kafue ecosystem, Zambia.},
journal = {Parasites &amp; vectors},
volume = {13},
number = {1},
pages = {599},
pmid = {33256809},
issn = {1756-3305},
support = {JP20w m0125008//Japan Agency for Medical Research and Development/ ; },
mesh = {Alveolata/classification/genetics/*isolation &amp; purification ; Animals ; Animals, Wild/classification/*parasitology ; Biodiversity ; Buffaloes/parasitology ; Cattle ; Cattle Diseases/parasitology ; Dog Diseases/parasitology ; Dogs ; Phylogeny ; Protozoan Infections, Animal/epidemiology/*parasitology ; Zambia/epidemiology ; },
abstract = {BACKGROUND: Piroplasms are vector-borne intracellular hemoprotozoan parasites that infect wildlife and livestock. Wildlife species are reservoir hosts to a diversity of piroplasms and play an important role in the circulation, maintenance and evolution of these parasites. The potential for likely spillover of both pathogenic and non-pathogenic piroplasm parasites from wildlife to livestock is underlined when a common ecological niche is shared in the presence of a competent vector.<br><br>METHOD: To investigate piroplasm diversity in wildlife and the cattle population of the greater Kafue ecosystem, we utilized PCR to amplify the 18S rRNA V4 hyper-variable region and meta-barcoding strategy using the Illumina MiSeq sequencing platform and amplicon sequence variant (ASV)-based bioinformatics pipeline to generate high-resolution data that discriminate sequences down to a single nucleotide difference.<br><br>RESULTS: A parasite community of 45 ASVs corresponding to 23 species consisting of 4 genera of Babesia, Theileria, Hepatozoon and Colpodella, were identified in wildlife and the cattle population from the study area. Theileria species were detected in buffalo, impala, hartebeest, sable antelope, sitatunga, wild dog and cattle. In contrast, Babesia species were only observed in cattle and wild dog. Our results demonstrate possible spillover of these hemoprotozoan parasites from wildlife, especially buffalo, to the cattle population in the wildlife-livestock interface.<br><br>CONCLUSION: We demonstrated that the deep amplicon sequencing of the 18S rRNA V4 hyper-variable region for wildlife was informative. Our results illustrated the diversity of piroplasma and the specificity of their hosts. They led us to speculate a possible ecological cycle including transmission from wildlife to domestic animals in the greater Kafue ecosystem. Thus, this approach may contribute to the establishment of appropriate disease control strategies in wildlife-livestock interface areas.},
}
@article {pmid33255443,
year = {2020},
author = {Tatulli, G and Cecere, P and Maggioni, D and Galimberti, A and Pompa, PP},
title = {A Rapid Colorimetric Assay for On-Site Authentication of Cephalopod Species.},
journal = {Biosensors},
volume = {10},
number = {12},
pages = {},
pmid = {33255443},
issn = {2079-6374},
mesh = {Animals ; Cephalopoda/*genetics ; *Colorimetry ; DNA Barcoding, Taxonomic ; DNA Primers ; *Molecular Diagnostic Techniques ; *Nucleic Acid Amplification Techniques ; },
abstract = {A colorimetric assay, exploiting the combination of loop-mediated isothermal amplification (LAMP) with DNA barcoding, was developed to address the authentication of some cephalopod species, a relevant group in the context of seafood traceability, due to the intensive processing from the fishing sites to the shelf. The discriminating strategy relies on accurate design of species-specific LAMP primers within the conventional 5' end of the mitochondrial COI DNA barcode region and allows for the identification of Loligo vulgaris among two closely related and less valuable species. The assay, coupled to rapid genomic DNA extraction, is suitable for large-scale screenings and on-site applications due to its easy procedures, with fast (30 min) and visual readout.},
}
@article {pmid33244355,
year = {2020},
author = {Lukhtanov, VA and Dantchenko, AV and Balayan, KV and Gagarina, AV},
title = {Karyotype and DNA barcode of Polyommatus (Agrodiaetus) cyaneus (Staudinger, 1899) from its type locality: implication for taxonomic and evolutionary research in Polyommatus blue butterflies (Lepidoptera, Lycaenidae).},
journal = {Comparative cytogenetics},
volume = {14},
number = {4},
pages = {567-575},
pmid = {33244355},
issn = {1993-0771},
abstract = {Chromosomal and molecular analyses of rapidly evolving organisms such as Polyommatus Latreille, 1804 blue butterflies are essential for understanding their taxonomy and evolutionary history, and the studies of populations from their type localities are crucially important for resolving problems of nomenclature and species identity. Here we present data on the topotypical population of the blue butterfly species described as Lycaena damone var. cyanea Staudinger, 1899. This taxon was described from Khankendi (Nagorno-Karabakh, Caucasus), and rediscovered at the type locality for the first time since it was collected there in 1869. The specimens were found on dry stony meadows with a predominance of Onobrychis radiata Bieberstein, 1810, on upper border of oak forests. Their haploid chromosome number (n) was established as n = 17. Chromosomal and mitochondrial DNA barcode analyses of the studied samples from type-locality provided an opportunity for the critical taxonomic re-examination of Caucasian species of the subgenus Agrodiaetus Hübner, 1822 of the genus Polyommatus Latreille, 1804. The obtained data support the interpretation of the P. (A.) cyaneus (Staudinger, 1899) and P. (A.) carmon (Herrich-Schäffer, 1851) as two different, not closely related species complexes as previously hypothesized by Hugo de Lesse. On the contrary, the treatment by Walter Forster who considered these taxa as two groups of conspecific populations was not supported by our data.},
}
@article {pmid33244113,
year = {2020},
author = {Wu, CS and Sudianto, E and Hung, YM and Wang, BC and Huang, CJ and Chen, CT and Chaw, SM},
title = {Genome skimming and exploration of DNA barcodes for Taiwan endemic cypresses.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {20650},
pmid = {33244113},
issn = {2045-2322},
mesh = {Chamaecyparis/genetics ; Cupressus/*genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Plant/*genetics ; DNA, Ribosomal/genetics ; Genome, Plant/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Species Specificity ; Taiwan ; },
abstract = {Cypresses are characterized by their longevity and valuable timber. In Taiwan, two endemic cypress species, Chamaecyparis formosensis and C. obtusa var. formosana, are threatened by prevalent illegal logging. A DNA barcode system is urgently needed for reforestation and conservation of these two cypresses. In this study, both plastomes and 35S rDNAs from 16, 10, and 6 individuals of C. formosensis, C. obtusa var. formosana, and C. obtusa var. obtusa were sequenced, respectively. We show that the loss of plastid trnT-GGU readily distinguishes C. formosensis from its congeneric species. We demonstrate that entire sequences of plastomes or 35S rDNAs are capable of correctly identifying cypress species and varieties, suggesting that they are effective super-barcodes. We also discover three short hypervariable loci (i.e., 3'ETS, ITS1, and trnH-psbA) that are promising barcodes for identifying cypress species and varieties. Moreover, nine species-specific indels of > 100 bp were detected in the cypress plastomes. These indels, together with the three aforementioned short barcodes, constitute an alternative and powerful barcode system crucial for identifying specimens that are fragmentary or contain degraded/poor DNA. Our sequenced data and barcode systems not only enrich the genetic reference for cypresses, but also contribute to future reforestation, conservation, and forensic investigations.},
}
@article {pmid33241313,
year = {2021},
author = {Musunuri, R and Arora, K and Corvelo, A and Shah, M and Shelton, J and Zody, MC and Narzisi, G},
title = {Somatic variant analysis of linked-reads sequencing data with Lancet.},
journal = {Bioinformatics (Oxford, England)},
volume = {37},
number = {13},
pages = {1918-1919},
pmid = {33241313},
issn = {1367-4811},
support = {R21 CA220411/CA/NCI NIH HHS/United States ; 1R21CA220411-01A1//Informatics Technology for Cancer Research (ITCR) program of the National Institutes of Health/ ; },
mesh = {Algorithms ; Diploidy ; *High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; *Software ; },
abstract = {SUMMARY: We present a new version of the popular somatic variant caller, Lancet, that supports the analysis of linked-reads sequencing data. By seamlessly integrating barcodes and haplotype read assignments within the colored De Bruijn graph local-assembly framework, Lancet computes a barcode-aware coverage and identifies variants that disagree with the local haplotype structure.<br><br>Lancet is implemented in C++ and available for academic and non-commercial research purposes as an open-source package at https://github.com/nygenome/lancet.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid33240760,
year = {2020},
author = {Bassi, G and Favalli, N and Vuk, M and Catalano, M and Martinelli, A and Trenner, A and Porro, A and Yang, S and Tham, CL and Moroglu, M and Yue, WW and Conway, SJ and Vogt, PK and Sartori, AA and Scheuermann, J and Neri, D},
title = {A Single-Stranded DNA-Encoded Chemical Library Based on a Stereoisomeric Scaffold Enables Ligand Discovery by Modular Assembly of Building Blocks.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {7},
number = {22},
pages = {2001970},
pmid = {33240760},
issn = {2198-3844},
support = {R35 CA197582/CA/NCI NIH HHS/United States ; },
abstract = {A versatile and Lipinski-compliant DNA-encoded library (DEL), comprising 366 600 glutamic acid derivatives coupled to oligonucleotides serving as amplifiable identification barcodes is designed, constructed, and characterized. The GB-DEL library, constructed in single-stranded DNA format, allows de novo identification of specific binders against several pharmaceutically relevant proteins. Moreover, hybridization of the single-stranded DEL with a set of known protein ligands of low to medium affinity coupled to a complementary DNA strand results in self-assembled selectable chemical structures, leading to the identification of affinity-matured compounds.},
}
@article {pmid33240595,
year = {2020},
author = {Justine, JL and Gey, D and Thévenot, J and Gastineau, R and Jones, HD},
title = {The land flatworm Amaga expatria (Geoplanidae) in Guadeloupe and Martinique: new reports and molecular characterization including complete mitogenome.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e10098},
pmid = {33240595},
issn = {2167-8359},
abstract = {BACKGROUND: The land flatworm Amaga expatria Jones &amp; Sterrer, 2005 (Geoplanidae) was described from two specimens collected in Bermuda in 1963 and 1988 and not recorded since.<br><br>METHODS: On the basis of a citizen science project, we received observations in the field, photographs and specimens from non-professionals and local scientists in Martinique and Guadeloupe. We barcoded (COI) specimens from both islands and studied the histology of the reproductive organs of one specimen. Based on Next Generation Sequencing, we obtained the complete mitogenome of A. expatria and some information on its prey from contaminating DNA.<br><br>RESULTS: We add records from 2006 to 2019 in two French islands of the Caribbean arc, Guadeloupe (six records) and Martinique (14 records), based on photographs obtained from citizen science and specimens examined. A specimen from Martinique was studied for histology of the copulatory organs and barcoded for the COI gene; its anatomy was similar to the holotype, therefore confirming species identification. The COI gene was identical for several specimens from Martinique and Guadeloupe and differed from the closest species by more than 10%; molecular characterisation of the species is thus possible by standard molecular barcoding techniques. The mitogenome is 14,962 bp in length and contains 12 protein coding genes, two rRNA genes and 22 tRNA genes; for two protein genes it was not possible to determine the start codon. The mitogenome was compared with the few available mitogenomes from geoplanids and the most similar was Obama nungara, a species from South America. An analysis of contaminating DNA in the digestive system suggests that A. expatria preys on terrestrial molluscs, and citizen science observations in the field suggest that prey include molluscs and earthworms; the species thus could be a threat to biodiversity of soil animals in the Caribbean.},
}
@article {pmid33239733,
year = {2020},
author = {Zhang, T and Foreman, R and Wollman, R},
title = {Identifying chromatin features that regulate gene expression distribution.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {20566},
pmid = {33239733},
issn = {2045-2322},
support = {R01 EY024960/EY/NEI NIH HHS/United States ; R01 GM111404/GM/NIGMS NIH HHS/United States ; },
mesh = {Chromatin/*genetics/metabolism ; Epigenesis, Genetic/genetics ; Epigenomics/methods ; Gene Expression/genetics ; Gene Expression Regulation/*genetics/physiology ; Genome/genetics ; Genomics/methods ; Humans ; K562 Cells ; Transcription Factors/genetics/metabolism ; },
abstract = {Gene expression variability, differences in the number of mRNA per cell across a population of cells, is ubiquitous across diverse organisms with broad impacts on cellular phenotypes. The role of chromatin in regulating average gene expression has been extensively studied. However, what aspects of the chromatin contribute to gene expression variability is still underexplored. Here we addressed this problem by leveraging chromatin diversity and using a systematic investigation of randomly integrated expression reporters to identify what aspects of chromatin microenvironment contribute to gene expression variability. Using DNA barcoding and split-pool decoding, we created a large library of isogenic reporter clones and identified reporter integration sites in a massive and parallel manner. By mapping our measurements of reporter expression at different genomic loci with multiple epigenetic profiles including the enrichment of transcription factors and the distance to different chromatin states, we identified new factors that impact the regulation of gene expression distributions.},
}
@article {pmid33237411,
year = {2021},
author = {Yang, L and Wang, J},
title = {Antibody Arrays: Barcode Technology.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2237},
number = {},
pages = {93-102},
doi = {10.1007/978-1-0716-1064-0_8},
pmid = {33237411},
issn = {1940-6029},
mesh = {Antibodies/*chemistry/immunology ; DNA/*chemistry ; High-Throughput Screening Assays/methods ; Immunoassay/methods ; Microfluidics/*methods ; Protein Array Analysis/*methods ; Single-Cell Analysis/methods ; },
abstract = {Antibody microarray is a fundamental, high-content technology for analyzing biomarkers with a multiplexity even at the proteomic level. Recent advancement in this field has driven the antibody array into a new territory related with single-cell analysis. Here we describe a flow pattern-based method for producing a high-density barcode antibody microarray for the detection of proteins in fluidic samples and in single cells. The antibody microarray is fabricated by a perpendicularly oriented flow patterning of single-stranded barcode DNAs, which are then converted into DNA-antibody conjugates. Compared to conventional microarrays, this barcode antibody microarray features a simple and high-throughput assay while achieving both high sensitivity and specificity. This barcode technology provides new clues for developing next-generation antibody microarrays and can be widely used in protein biomarker discovery, cell signaling network analysis, and disease diagnosis and prognosis.},
}
@article {pmid33234154,
year = {2020},
author = {Feldman, D and Tsai, F and Garrity, AJ and O'Rourke, R and Brenan, L and Ho, P and Gonzalez, E and Konermann, S and Johannessen, CM and Beroukhim, R and Bandopadhayay, P and Blainey, PC},
title = {CloneSifter: enrichment of rare clones from heterogeneous cell populations.},
journal = {BMC biology},
volume = {18},
number = {1},
pages = {177},
pmid = {33234154},
issn = {1741-7007},
support = {R01 HG009283/HG/NHGRI NIH HHS/United States ; CA219943/NH/NIH HHS/United States ; HG009283/NH/NIH HHS/United States ; R01 CA215489/CA/NCI NIH HHS/United States ; 1U54CA224068-01/NH/NIH HHS/United States ; R00 CA201592/CA/NCI NIH HHS/United States ; CA188228/NH/NIH HHS/United States ; CA201592-02/NH/NIH HHS/United States ; },
mesh = {Cells, Cultured ; Clone Cells ; Cloning, Organism/*methods ; *Clustered Regularly Interspaced Short Palindromic Repeats ; RNA/*metabolism ; },
abstract = {BACKGROUND: Many biological processes, such as cancer metastasis, organismal development, and acquisition of resistance to cytotoxic therapy, rely on the emergence of rare sub-clones from a larger population. Understanding how the genetic and epigenetic features of diverse clones affect clonal fitness provides insight into molecular mechanisms underlying selective processes. While large-scale barcoding with NGS readout has facilitated cellular fitness assessment at the population level, this approach does not support characterization of clones prior to selection. Single-cell genomics methods provide high biological resolution, but are challenging to scale across large populations to probe rare clones and are destructive, limiting further functional analysis of important clones.<br><br>RESULTS: Here, we develop CloneSifter, a methodology for tracking and enriching rare clones throughout their response to selection. CloneSifter utilizes a CRISPR sgRNA-barcode library that facilitates the isolation of viable cells from specific clones within the barcoded population using a sequence-specific retrieval reporter. We demonstrate that CloneSifter can measure clonal fitness of cancer cell models in vitro and retrieve targeted clones at abundance as low as 1 in 1883 in a heterogeneous cell population.<br><br>CONCLUSIONS: CloneSifter provides a means to track and access specific and rare clones of interest across dynamic changes in population structure to comprehensively explore the basis of these changes.},
}
@article {pmid33233108,
year = {2020},
author = {Frigerio, J and Agostinetto, G and Galimberti, A and De Mattia, F and Labra, M and Bruno, A},
title = {Tasting the differences: Microbiota analysis of different insect-based novel food.},
journal = {Food research international (Ottawa, Ont.)},
volume = {137},
number = {},
pages = {109426},
doi = {10.1016/j.foodres.2020.109426},
pmid = {33233108},
issn = {1873-7145},
mesh = {Animals ; *Edible Insects ; Food Handling ; Insecta ; *Microbiota ; *Tenebrio ; },
abstract = {Traceability, quality and safety of edible insects are important both for the producers and the consumers. Today, alongside the burst of edible insects in western countries, we are facing a gap of knowledge of insect microbiota associated with the microbial ecosystems of insect-based products. In this context, High-Throughput DNA Sequencing (HTS) techniques can give insight into the carryover of insect microbiota into final food products. In this study, we investigated the microbiota composition of insect-based commercial food products, applying HTS techniques coupled with bioinformatic analysis. The work aimed to analyse the microbiota variability of different categories of some insect-based commercial food products made of A. domesticus (house cricket), T. molitor (mealworm beetle), and A. diaperinus (lesser mealworm or litter beetle), including commercial raw materials and processed food items, purchased via e-commerce from different companies. Our data revealed that samples cluster per insect species based on microbiota profile and preliminary results suggested that a small number of prevalent bacteria formed a "core microbiota" characterizing the products depending on the insect. This microbial signature can be recognized despite the different food processing levels, rearing conditions and selling companies. Furthermore, differences between raw and processed food made of the same insect or similar product produced by different companies was found. These results support the application of HTS analysis for studying the composition of insect-based commercial food products in a wider perspective, for food traceability and food quality control.},
}
@article {pmid33231343,
year = {2021},
author = {Schmidt, M and Kubyshkin, V},
title = {How To Quantify a Genetic Firewall? A Polarity-Based Metric for Genetic Code Engineering.},
journal = {Chembiochem : a European journal of chemical biology},
volume = {22},
number = {7},
pages = {1268-1284},
pmid = {33231343},
issn = {1439-7633},
support = {766975//European Commission's Horizon 2020/ ; 820699//BioRoboost/ ; },
mesh = {Algorithms ; Amino Acids/genetics ; Codon/genetics ; Genetic Code/*genetics ; *Genetic Engineering ; Models, Genetic ; },
abstract = {Genetic code engineering aims to produce organisms that translate genetic information in a different way from that prescribed by the standard genetic code. This endeavor could eventually lead to genetic isolation, where an organism that operates under a different genetic code will not be able to transfer functional genes with other living species, thereby standing behind a genetic firewall. It is not clear however, how distinct the code should be, or how to measure the distance. We have developed a metric (Δcode) where we assigned polarity indices (clog D7) to amino acids to calculate the distances between pairs of genetic codes. We then calculated the distance between a set of 204 genetic codes, including the 24 known distinct natural codes, 11 extreme-distance codes created computationally, nine theoretical special purpose codes from literature and 160 codes in which canonical amino acids were replaced by noncanonical chemical analogues. The metric can be used for building strategies towards creating semantically alienated organisms, and testing the strength of genetic firewalls. This metric provides the basis for a map of the genetic codes that could guide future efforts towards novel biochemical worlds, biosafety and deep barcoding applications.},
}
@article {pmid33230206,
year = {2020},
author = {Biffi, D and López-Mobilia, A and Kelez, S and Williams, DA and Chumchal, MM and Weinburgh, M},
title = {Mislabelling and high mercury content hampers the efforts of market-based seafood initiatives in Peru.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {20390},
pmid = {33230206},
issn = {2045-2322},
abstract = {Peru is experiencing a "gastronomic boom" that is increasing the demand for seafood. We investigated two implicit assumptions of two popular sustainable seafood consumer-based initiatives: (1) seafood is labelled correctly, and (2) the recommended species are healthy for consumers. We used DNA barcoding to determine the taxonomic identity of 449 seafood samples from markets and restaurants and analysed the concentration of total mercury (THg) in a sub-sample (271 samples) of these. We found that a third of seafood is mislabelled and that over a quarter of all samples had mercury levels above the upper limit recommended by the US EPA (300 ng/g ww). Additionally, 30% of samples were threatened and protected species. Mislabelling often occurred for economic reasons and the lack of unique common names. Mislabelled samples also had significantly higher mercury concentrations than correctly labelled samples. The "best choice" species compiled from two sustainable seafood guides had less mislabelling, and when identified correctly through DNA barcoding, had on average lower mercury than the other species. Nevertheless, some high mercury species are included in these lists. Mislabelling makes the efforts of seafood campaigns less effective as does the inclusion of threatened species and species high in mercury.},
}
@article {pmid33227787,
year = {2020},
author = {Ferreira, M and de Jesus, IS and Viana, PF and Garcia, C and Matoso, DA and Cioffi, MB and Bertollo, LAC and Feldberg, E},
title = {Chromosomal Evolution in Aspredinidae (Teleostei, Siluriformes): Insights on Intra- and Interspecific Relationships with Related Groups.},
journal = {Cytogenetic and genome research},
volume = {160},
number = {9},
pages = {539-553},
doi = {10.1159/000511125},
pmid = {33227787},
issn = {1424-859X},
mesh = {Animals ; Biological Evolution ; Brazil ; Catfishes/classification/*genetics ; Chromosomes/*genetics/ultrastructure ; DNA Barcoding, Taxonomic ; DNA, Ribosomal/genetics ; Diploidy ; Evolution, Molecular ; Female ; In Situ Hybridization, Fluorescence ; Karyotyping ; Male ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 5S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Sex Chromosomes/genetics/ultrastructure ; Species Specificity ; },
abstract = {The family Aspredinidae comprises a clade of complex systematic relationships, both from molecular and morphological approaches. In this study, conventional and molecular cytogenetic studies coupled with nucleotide sequencing were performed in 6 Aspredininae species (Amaralia hypsiura, Bunocephalus cf. aloikae, Bunocephalus amaurus, Bunocephalus aff. coracoideus, Bunocephalus verrucosus, and Platystacus cotylephorus) from different locations of the Amazon hydrographic basin. Our results showed highly divergent diploid numbers (2n) among the species, ranging from 49 to 74, including the occurrence of an XX/X0 sex chromosome system. A neighbor-joining phylogram based on the cytochrome c oxidase I (COI) showed that Bunocephalus coracoideus is not a monophyletic clade, but closely related to B. verrucosus. The karyotypic data associated with COI suggest an ancestral karyotype for Aspredinidae with a reduced 2n, composed of bi-armed chromosomes and a trend toward chromosomal fissions resulting in higher diploid number karyotypes, mainly composed of acrocentric chromosomes. Evolutionary relationships were discussed under a phylogenetic context with related species from different Siluriformes families. The karyotype features and chromosomal diversity of Aspredinidae show an amazing differentiation, making this family a remarkable model for investigating the evolutionary dynamics in siluriforms as well as in fish as a whole.},
}
@article {pmid33226939,
year = {2021},
author = {Barron, I and Yeh, HJ and Dinesh, K and Sharma, G},
title = {Dual Modulated QR Codes for Proximal Privacy and Security.},
journal = {IEEE transactions on image processing : a publication of the IEEE Signal Processing Society},
volume = {30},
number = {},
pages = {657-669},
doi = {10.1109/TIP.2020.3037524},
pmid = {33226939},
issn = {1941-0042},
abstract = {The ubiquitous presence of surveillance cameras severely compromises the security of private information (e.g. passwords) entered via a conventional keyboard interface in public places. We address this problem by proposing dual modulated QR (DMQR) codes, a novel QR code extension via which users can securely communicate private information in public places using their smartphones and a camera interface. Dual modulated QR codes use the same synchronization patterns and module geometry as conventional monochrome QR codes. Within each module, primary data is embedded using intensity modulation compatible with conventional QR code decoding. Specifically, depending on the bit to be embedded, a module is either left white or an elliptical black dot is placed within it. Additionally, for each module containing an elliptical dot, secondary data is embedded by orientation modulation; that is, by using different orientations for the elliptical dots. Because the orientation of the elliptical dots can only be reliably assessed when the barcodes are captured from a close distance, the secondary data provides "proximal privacy" and can be effectively used to communicate private information securely in public settings. Tests conducted using several alternative parameter settings demonstrate that the proposed DMQR codes are effective in meeting their objective- the secondary data can be accurately decoded for short capture distances (6 in.) but cannot be recovered from images captured over long distances (>12 in.). Furthermore, the proximal privacy can be adapted to application needs by varying the eccentricity of the elliptical dots used.},
}
@article {pmid33225354,
year = {2021},
author = {Reeves, LE and Medina, J and Miqueli, E and Sloyer, KE and Petrie, W and Vasquez, C and Burkett-Cadena, ND},
title = {Establishment of Aedes (Ochlerotatus) scapularis (Diptera: Culicidae) in Mainland Florida, With Notes on the Ochlerotatus Group in the United States.},
journal = {Journal of medical entomology},
volume = {58},
number = {2},
pages = {717-729},
doi = {10.1093/jme/tjaa250},
pmid = {33225354},
issn = {1938-2928},
mesh = {*Aedes/classification/genetics ; *Animal Distribution ; Animals ; Classification ; Culicidae/classification/genetics ; DNA Barcoding, Taxonomic ; DNA, Intergenic/genetics ; Electron Transport Complex IV/genetics ; Florida ; Genes, Insect ; Introduced Species ; Larva/classification/genetics ; Mosquito Vectors/classification/genetics ; *Ochlerotatus/classification/genetics ; Phylogeny ; },
abstract = {Aedes scapularis (Rondani), a widespread neotropical vector mosquito species, has been included in the mosquito fauna of Florida on the basis of just three larval specimens that were collected in the middle Florida Keys in 1945. Here, we report numerous recent collections of immature and adult Ae. scapularis from multiple locations in two counties of southern Florida. These specimens represent the first records of Ae. scapularis from mainland Florida and the first records of the species in the state since the initial detection of the species 75 yr ago. Collections of both larvae and adults across several years indicate that Ae. scapularis is now established in Broward and Miami-Dade Counties. These contemporary records of this species in Florida may represent novel dispersal and subsequent establishment events from populations outside the United States or a recent reemergence of undetected endemic populations. To confirm morphological identification of Ae. scapularis specimens from Florida, the DNA barcoding region of the cytochrome c oxidase subunit I gene (COI) was sequenced and compared to all other Ochlerotatus Group species from the United States, specifically Aedes condolescens Dyar and Knab (Diptera: Culicidae), Aedes infirmatus Dyar and Knab (Diptera: Culicidae), Aedes thelcter Dyar (Diptera: Culicidae), Aedes tortilis (Theobald) (Diptera: Culicidae), and Aedes trivittatus (Coquillett) (Diptera: Culicidae). Molecular assays and sequencing confirm morphological identification of Ae. scapularis specimens. Maximum likelihood phylogenetic analysis of COI and ITS2 sequences place Florida Ae. scapularis in a distinct clade, but was unable to produce distinct clades for Florida specimens of Ae. condolescens and Ae. tortilis.},
}
@article {pmid33224443,
year = {2020},
author = {Gorobeyko, UV and Kartavtseva, IV and Sheremetyeva, IN and Kazakov, DV and Guskov, VY},
title = {DNA-barcoding and a new data about the karyotype of Myotis petax (Chiroptera, Vespertilionidae) in the Russian Far East.},
journal = {Comparative cytogenetics},
volume = {14},
number = {4},
pages = {483-500},
pmid = {33224443},
issn = {1993-0771},
abstract = {The DNA-barcoding and chromosomal study of the eastern water bat, Myotis petax Hollister, 1912, from the earlier unexplored localities in the Russian Far East are carried out. The COI barcoding obtained for 18 from a total of 19 individuals captured in five localities in the Russian Far East showed the low nucleotide variability with the prevalence of the central, the most abundant haplotype. The chromosomal characteristics of eight M. petax specimens (2n = 44, NFa = 52) in the Russian Far East are clarified. The number and localization of NOR in karyotype of M. petax is described at the first time and differ from distributional patterns of NOR in the sibling species M. daubentonii Kuhl, 1819 that can be used as diagnostic feature. The considerable intraspecific variability in the distribution of heterochromatin material revealed is not typical of the genus Myotis, but it has been found in other species of the family Vespertilionidae.},
}
@article {pmid33223909,
year = {2020},
author = {Mutanen, M and Huemer, P and Autto, J and Karsholt, O and Kaila, L},
title = {Monopis jussii, a new species (Lepidoptera, Tineidae) inhabiting nests of the Boreal owl (Aegolius funereus).},
journal = {ZooKeys},
volume = {992},
number = {},
pages = {157-181},
pmid = {33223909},
issn = {1313-2989},
abstract = {Monopis jussii Kaila, Mutanen, Huemer, Karsholt &amp; Autto, sp. nov. (Lepidoptera, Tineidae) is described as a new species. It is closely related to the widespread and common M. laevigella ([Denis &amp; Schiffermüller], 1775), but differs in its distinct COI DNA barcode sequences, four examined nuclear loci as well as details in forewing coloration and pattern. Most reared specimens of M. jussii have emerged from the nest remnants of the Boreal owl (Aegolius funereus (Linnaeus, 1758)), but also nests of the Ural owl (Strix uralensis Pallas, 1771) and the Great tit (Parus major Linnaeus, 1758) have been observed as suitable habitats. Based on the present knowledge, the new species has a boreo-montane distribution as it is recorded only from northern Europe and the Alps. Several extensive rearing experiments from Strix spp. nest remnants from southern Finland did not produce any M. jussii, but thousands of M. laevigella, suggesting that the species is lacking in the area or, more unlikely, that the nest of these owl species do not serve as good habitat for the new species. This unexpected species discovery highlights, once again, the usefulness of DNA barcoding in revealing the cryptic layers of biodiversity. To serve stability we select a neotype for Tinea laevigella [Denis &amp; Schiffermüller], 1775, and discuss the complicated synonymy and nomenclature of this species.},
}
@article {pmid33223905,
year = {2020},
author = {Parapar, J and Capa, M and Nygren, A and Moreira, J},
title = {To name but a few: descriptions of five new species of Terebellides (Annelida, Trichobranchidae) from the North East Atlantic.},
journal = {ZooKeys},
volume = {992},
number = {},
pages = {1-58},
pmid = {33223905},
issn = {1313-2989},
abstract = {The number of described species of the genus Terebellides Sars, 1835 (Annelida, Trichobranchidae) has greatly increased in the last years, particularly in the North East Atlantic. In this context, this paper deals with several putative species recently delineated by molecular means within a well delimited clade of Terebellides. Species are characterised here by a combination of morphological characters, and a complementary nucleotide diagnostic approach. Three species were identified as the nominal species T. stroemii Sars, 1835, T. bigeniculatus Parapar, Moreira &amp; Helgason, 2011 and T. europaeaLavesque et al., 2019. Five species are described as new: T. bakkeni sp. nov., T. kongsrudi sp. nov., T. norvegica sp. nov., T. ronningae sp. nov. and T. scotica sp. nov. The distinctive morphological characters refer to the branchial shape, absence or presence of papillae on lamellae of anterior margin of branchial dorsal lobes, absence or presence of ciliated papillae dorsal to thoracic notopodia, geniculate chaetae in one or two chaetigers, and the morphology of thoracic and abdominal uncini teeth. Furthermore, the description of T. bigeniculatus is revised and complemented after examination of type specimens. An updated identification key to all species of the genus in NE Atlantic and a proposal of a classification of different types of abdominal uncini to be used in taxonomy are also included.},
}
@article {pmid33223891,
year = {2020},
author = {Li, Y and Lin, Y and Li, S},
title = {A review of Crassignatha (Araneae, Symphytognathidae).},
journal = {ZooKeys},
volume = {988},
number = {},
pages = {63-128},
pmid = {33223891},
issn = {1313-2989},
abstract = {Crassignatha Wunderlich, 1995 is redefined to include species with six eyes in three diads, chelicerae fused only near the base, sculpturing on the carapace, one or two clasping spurs on tibia II, a bilateral scutum of the male abdomen, and globular spermathecae and adjacent copulatory openings in the female. A key and distribution map are provided for 24 Crassignatha species in this paper. Diagnoses and illustrated photographs are provided for 22 species from China, Malaysia, Thailand, and Vietnam. Thirteen species are described and documented as new to science: C. baihua Y. Lin &amp; S. Li, sp. nov. (♂♀), C. bangbie Y. Lin &amp; S. Li, sp. nov. (♀), C. changyan Y. Lin &amp; S. Li, sp. nov. (♀), C. dongnai Y. Lin &amp; S. Li, sp. nov. (♀), C. gucheng Y. Lin &amp; S. Li, sp. nov. (♂♀), C. mengla Y. Lin &amp; S. Li, sp. nov. (♂♀), C. nantou Y. Lin &amp; S. Li, sp. nov. (♂♀), C. nasalis Y. Lin &amp; S. Li, sp. nov. (♂♀), C. rostriformis Y. Lin &amp; S. Li, sp. nov. (♂♀), C. shunani Y. Lin &amp; S. Li, sp. nov. (♂♀), C. si Y. Lin &amp; S. Li, sp. nov. (♂♀), C. thamphra Y. Lin &amp; S. Li, sp. nov. (♀), and C. xichou Y. Lin &amp; S. Li, sp. nov. (♀). Three new combinations are proposed: C. bicorniventris (Lin &amp; Li, 2009), comb. nov., C. quadriventris (Lin &amp; Li, 2009), comb. nov., and C. shiluensis (Lin &amp; Li, 2009), comb. nov. are transferred from Patu Marples, 1951. DNA barcodes and genetic distances of seventeen species are obtained to confirm correct identification. Types of seven known Chinese Crassignatha species are re-examined, and the taxonomic placement of C. longtou Miller, Griswold &amp; Yin, 2009 may be incorrect based on morphological and molecular data.},
}
@article {pmid33223876,
year = {2020},
author = {Martinez, JI},
title = {Revision of the South American genus Gaujonia Dognin (Noctuidae, Pantheinae) with descriptions of five new genera and twenty-one new species.},
journal = {ZooKeys},
volume = {985},
number = {},
pages = {71-126},
pmid = {33223876},
issn = {1313-2989},
abstract = {The endemic Neotropical genus Gaujonia Dognin is revised. Morphological characters and a phylogenetic analysis demonstrate paraphyletic relationships among the species. Four different groups are interpreted to represent four different genera. The G. arbosi group is the only remaining clade in the genus Gaujonia, and the other groups have been arranged into three new genera: Millerana gen. nov., Oculicattus gen. nov., and Cicadoforma gen. nov. Additionally, two other genera Cicadomorphus gen. nov., and Gaujoptera gen. nov. were found using morphological and molecular analyses based on some specimens that were misidentified as Gaujonia spp. A total of five new genera, three new combinations (Cicadoforma vau-nigrum Hampson, comb. nov., Oculicattus renifera Hampson, comb. nov., and Millerana arbosioides Dognin, comb. nov.) and 21 new species (Cicadoforma ocelotus sp. nov., Cicadomorphus chicharra sp. nov., Cicadomorphus chuya sp. nov., Cicadomorphus falkasiska sp. nov., Cicadomorphus lilianae sp. nov., Gaujonia bichu sp. nov., Gaujonia chiqyaq sp. nov., Gaujonia kanakusika sp. nov., Gaujonia sourakovi sp. nov., Gaujoptera amsa sp. nov., Millerana austini sp. nov., Millerana cajas sp. nov., Millerana cundinamarquensis sp. nov., Millerana matthewsae sp. nov., Millerana tigrina sp. nov., Oculicattus boliviana sp. nov., Oculicattus brehmi sp. nov., Oculicattus inca sp. nov., Oculicattus raizae sp. nov., Oculicattus schmidti sp. nov., and Oculicattus uturunku sp. nov.) are established.},
}
@article {pmid33223874,
year = {2020},
author = {Ericson, HC and Forbes, AA},
title = {Description of the new species Coptera tonic (Hymenoptera, Diapriidae), a pupal parasitoid of Rhagoletis juniperina Marcovitch (Diptera, Tephritidae), and revised partial keys to Nearctic Coptera Say.},
journal = {ZooKeys},
volume = {985},
number = {},
pages = {49-60},
pmid = {33223874},
issn = {1313-2989},
abstract = {A new species of the parasitic wasp Coptera Say was previously distinguished from other species via correspondence between ecological (host) differences and DNA barcodes. A description and figures for Coptera tonic sp. nov., along with revisions to existing keys that allow it to be distinguished from other Nearctic species without the aid of molecular characters, is provided in this work.},
}
@article {pmid33223873,
year = {2020},
author = {Barber-James, HM and Zrelli, S and Yanai, Z and Sartori, M},
title = {A reassessment of the genus Oligoneuriopsis Crass, 1947 (Ephemeroptera, Oligoneuriidae, Oligoneuriellini).},
journal = {ZooKeys},
volume = {985},
number = {},
pages = {15-47},
pmid = {33223873},
issn = {1313-2989},
abstract = {The distinction between the two closely related genera Oligoneuriella Ulmer, 1924 and Oligoneuriopsis Crass, 1947 has been much debated. First described from South Africa, Oligoneuriopsis seemed to be a clearly defined genus. However, as the known distribution of the genus widened and knowledge on it expanded, species delimitation based on morphology became less clear due to overlap in several apparently defining morphological characters, especially in the nymphs. This work attempts to reassess Oligoneuriopsis morphology in the context of all currently known species. The type species, Oligoneuriopsis lawrencei Crass, 1947 is redescribed at the imaginal and nymphal stages and a neotype is designated. The putative nymph of Oligoneuriopsis dobbsi (Eaton, 1912) is described based on material collected around Mt Elgon (Kenya). The adults of Oligoneuriella orontensis Koch, 1980 are described for the first time and the species is transferred to the genus Oligoneuriopsis (Oligoneuriopsis orontensis comb. nov.). Egg structure is also described for the first time for the species Oligoneuriopsis skhounate and O. orontensis. Some biogeographical considerations are also given. It is likely that more species will still be discovered, especially in Africa.},
}
@article {pmid33223869,
year = {2020},
author = {Sheffield, CS and Oram, R and Heron, JM},
title = {Bombus (Pyrobombus) johanseni Sladen, 1919, a valid North American bumble bee species, with a new synonymy and comparisons to other "red-banded" bumble bee species in North America (Hymenoptera, Apidae, Bombini).},
journal = {ZooKeys},
volume = {984},
number = {},
pages = {59-81},
pmid = {33223869},
issn = {1313-2989},
abstract = {The bumble bee (Hymenoptera, Apidae, Bombini, Bombus Latreille) fauna of the Nearctic and Palearctic regions are considered well known, with a few species occurring in both regions (i.e., with a Holarctic distribution), but much of the Arctic, especially in North America, remains undersampled or unsurveyed. Several bumble bee taxa have been described from northern North America, these considered either valid species or placed into synonymy with other taxa. However, some of these synonymies were made under the assumption of variable hair colour only, without detailed examination of other morphological characters (e.g., male genitalia, hidden sterna), and without the aid of molecular data. Recently, Bombus interacti Martinet, Brasero &amp; Rasmont, 2019 was described from Alaska where it is considered endemic; based on both morphological and molecular data, it was considered a taxon distinct from B. lapponicus (Fabricius, 1793). Bombus interacti was also considered distinct from B. gelidus Cresson, 1878, a taxon from Alaska surmised to be a melanistic form of B. lapponicus sylvicola Kirby, 1837, the North American subspecies (Martinet et al. 2019). Unfortunately, Martinet et al. (2019) did not have DNA barcode sequences (COI) for females of B. interacti, but molecular data for a melanistic female specimen matching the DNA barcode sequence of the holotype of B. interacti have been available in the Barcodes of Life Data System (BOLD) since 2011. Since then, additional specimens have been obtained from across northern North America. Also unfortunate was that B. sylvicola var. johanseni Sladen, 1919, another melanistic taxon described from far northern Canada, was not considered. Bombus johanseni is here recognized as a distinct taxon from B. lapponicus sylvicola Kirby, 1837 (sensuMartinet et al. 2019) in the Nearctic region, showing the closest affinity to B. glacialis Friese, 1902 of the Old World. As the holotype male of B. interacti is genetically identical to material identified here as B. johanseni, it is placed into synonymy. Thus, we consider B. johanseni a widespread species occurring across arctic and subarctic North America in which most females are dark, with rarer pale forms (i.e., "interacti") occurring in and seemingly restricted to Alaska. In addition to B. johanseni showing molecular affinities to B. glacialis of the Old World, both taxa also inhabit similar habitats in the arctic areas of both Nearctic and Palearctic, respectively. It is also likely that many of the specimens identified as B. lapponicus sylvicola from far northern Canada and Alaska might actually be B. johanseni, so that should be considered for future studies of taxonomy, distribution, and conservation assessment of North American bumble bees.},
}
@article {pmid33221881,
year = {2021},
author = {Mathis, AD and Otto, RM and Reynolds, KA},
title = {A simplified strategy for titrating gene expression reveals new relationships between genotype, environment, and bacterial growth.},
journal = {Nucleic acids research},
volume = {49},
number = {1},
pages = {e6},
pmid = {33221881},
issn = {1362-4962},
support = {R01 GM136842/GM/NIGMS NIH HHS/United States ; },
mesh = {CRISPR-Cas Systems/*genetics ; Cell Division/genetics ; Computational Biology/*methods ; Escherichia coli/*genetics/growth &amp; development ; *Gene Expression Regulation, Bacterial ; Gene-Environment Interaction ; Genetic Techniques ; Genotype ; Mutation ; RNA, Guide, CRISPR-Cas Systems ; },
abstract = {A lack of high-throughput techniques for making titrated, gene-specific changes in expression limits our understanding of the relationship between gene expression and cell phenotype. Here, we present a generalizable approach for quantifying growth rate as a function of titrated changes in gene expression level. The approach works by performing CRISPRi with a series of mutated single guide RNAs (sgRNAs) that modulate gene expression. To evaluate sgRNA mutation strategies, we constructed a library of 5927 sgRNAs targeting 88 genes in Escherichia coli MG1655 and measured the effects on growth rate. We found that a compounding mutational strategy, through which mutations are incrementally added to the sgRNA, presented a straightforward way to generate a monotonic and gradated relationship between mutation number and growth rate effect. We also implemented molecular barcoding to detect and correct for mutations that 'escape' the CRISPRi targeting machinery; this strategy unmasked deleterious growth rate effects obscured by the standard approach of ignoring escapers. Finally, we performed controlled environmental variations and observed that many gene-by-environment interactions go completely undetected at the limit of maximum knockdown, but instead manifest at intermediate expression perturbation strengths. Overall, our work provides an experimental platform for quantifying the phenotypic response to gene expression variation.},
}
@article {pmid33220912,
year = {2021},
author = {Audrézet, F and Zaiko, A and Lear, G and Wood, SA and Tremblay, LA and Pochon, X},
title = {Biosecurity implications of drifting marine plastic debris: Current knowledge and future research.},
journal = {Marine pollution bulletin},
volume = {162},
number = {},
pages = {111835},
doi = {10.1016/j.marpolbul.2020.111835},
pmid = {33220912},
issn = {1879-3363},
mesh = {Biodiversity ; *Ecosystem ; Humans ; *Plastics/analysis ; Ships ; },
abstract = {The introduction and spread of marine non-indigenous species (NIS) and pathogens into new habitats are a major threat to biodiversity, ecosystem services, human health, and can have substantial economic consequences. Shipping is considered the main vector for marine biological invasions; less well understood is the increased spread of marine NIS and pathogens rafting on marine plastic debris (MPD). Despite an increasing research interest and recent progress in characterizing the plastisphere, this manuscript highlights critical knowledge gaps and research priorities towards a better understanding of the biosecurity implications of MPD. We advocate for future research to (i) investigate plastisphere community succession and the factors influencing NIS propagules and pathogens recruitment through robust experimental investigations; (ii) combine microscopy and molecular approaches to effectively assess the presence of specific taxa; (iii) include additional genetic markers to thoroughly characterize the biodiversity associated with MPD and explore the presence of specific marine pests.},
}
@article {pmid33218119,
year = {2020},
author = {Sánchez, M and González-Burgos, E and Divakar, PK and Gómez-Serranillos, MP},
title = {DNA-Based Authentication and Metabolomics Analysis of Medicinal Plants Samples by DNA Barcoding and Ultra-High-Performance Liquid Chromatography/Triple Quadrupole Mass Spectrometry (UHPLC-MS).},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {11},
pages = {},
pmid = {33218119},
issn = {2223-7747},
abstract = {There is growing interest for medicinal plants in the world drug market. Particularly, Matricaria recutita L., Valeriana officinalis L., Tilia spp., and Camellia sinensis (L.) Kuntze are some of the most consumed medicinal plants for treatment of minor health problems. Medicinal plants are seen as natural and safe; however, they can cause interactions and produce adverse reactions. Moreover, there is lack of consensus in medicinal plants regulation worldwide. DNA barcoding and UHPLC-MS technique are increasingly used to correctly identify medicinal plants and guarantee their quality and therapeutic safety. We analyzed 33 samples of valerian, linden, tea, and chamomile acquired in pharmacies, supermarkets, and herbal shops by DNA barcoding and UHPLC-MS. DNA barcoding, using matk as a barcode marker, revealed that CH1 sold as Camellia sinensis was Blepharocalyx tweediei, and sample TS2 sold as linden belong to Malvales. On the other hand, UHPLC-MS analysis revealed the presence of bioactive compounds (apigenin-7-glucoside, acetoxy valerenic acid, valerenic acid, epigallocatechin, and tiliroside). However, none of samples met minimum content of these active principles (except for valerenic acid in VF3) according to the European Medicines Agency (EMA) and Real Spanish Pharmacopeia. In conclusion, this study revealed the need to incorporate DNA barcoding and HPLC-MS techniques in quality controls of medicinal plants.},
}
@article {pmid33216985,
year = {2021},
author = {Cordes, S and Wu, C and Dunbar, CE},
title = {Clonal tracking of haematopoietic cells: insights and clinical implications.},
journal = {British journal of haematology},
volume = {192},
number = {5},
pages = {819-831},
pmid = {33216985},
issn = {1365-2141},
support = {ZIA HL006063/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Animals ; Asymmetric Cell Division ; Cell Lineage ; Cell Tracking/*methods ; Cellular Senescence ; Clone Cells/cytology ; DNA Mutational Analysis ; DNA Transposable Elements/genetics ; DNA, Mitochondrial/genetics ; Genetic Markers ; Genomics/methods ; Hematopoiesis/physiology ; Hematopoietic Stem Cell Transplantation ; Hematopoietic Stem Cells/*cytology ; High-Throughput Nucleotide Sequencing ; Humans ; Killer Cells, Natural/cytology ; Regenerative Medicine/trends ; Single-Cell Analysis ; T-Lymphocyte Subsets/cytology ; },
abstract = {Recent advances in high-throughput genomics have enabled the direct tracking of outputs from many cell types, greatly accelerating the study of developmental processes and tissue regeneration. The capacity for long-term self-renewal with multilineage differentiation potential characterises the cellular dynamics of a special set of developmental states that are critical for maintaining homeostasis. In haematopoiesis, the archetypal model for development, lineage-tracing experiments have elucidated the roles of haematopoietic stem cells to ongoing blood production and the importance of long-lived immune cells to immunological memory. An understanding of the biology and clonal dynamics of these cellular fates and states can provide clues to the response of haematopoiesis to ageing, the process of malignant transformation, and are key to designing more efficacious and durable clinical gene and cellular therapies.},
}
@article {pmid33214981,
year = {2020},
author = {Meena, RK and Negi, N and Uniyal, N and Shamoon, A and Bhandari, MS and Pandey, S and Negi, RK and Sharma, R and Ginwal, HS},
title = {Chloroplast-based DNA barcode analysis indicates high discriminatory potential of matK locus in Himalayan temperate bamboos.},
journal = {3 Biotech},
volume = {10},
number = {12},
pages = {534},
pmid = {33214981},
issn = {2190-572X},
abstract = {The study was conducted to evaluate the discriminatory potential of selected chloroplast-based DNA barcode regions for identifying and resolving phylogeny of the Indian bamboos. Among 11 chloroplast markers screened, only four, namely matK, rbcL, psbK-I and rps16-trnQ showed successful amplification in 88 genotypes of 30 Indian bamboo taxa under Bambuseae and Arundinarieae tribes. A total of 244 sequences were generated for the four chloroplast regions. Tree-based analysis demonstrated that none of the tested regions successfully discriminated the taxa under Bambuseae tribe. Importantly, our highly concerned Himalayan temperate bamboo species under Arundinarieae tribe, were successfully discriminated by matK locus with high bootstrap support (>60%). Sequence comparisons revealed that the discriminatory power demonstrated by matK region actually lies in the few unique fixed nucleotides (UFNs) despite the overall DNA polymorphism. Although, rps16-trnQ region was found to be the most polymorphic and revealed high genetic divergence among different taxonomic levels, it could not successfully discriminated the taxa with strong statistical support. In a taxonomically difficult plant group like bamboos, whose genome is relatively more complex and has a slow rate of molecular evolution, it is difficult to get a universal marker. Further, highly variable barcode regions utilized in other species may not be informative, and thus, the development of DNA barcodes for different taxonomic levels, such as lineages or tribes could be a viable approach.},
}
@article {pmid33207061,
year = {2020},
author = {Baharmand, I and Coatsworth, H and Peach, DAH and Belton, P and Lowenberger, C},
title = {Molecular relationships of introduced Aedes japonicus (Diptera: Culicidae) populations in British Columbia, Canada using mitochondrial DNA.},
journal = {Journal of vector ecology : journal of the Society for Vector Ecology},
volume = {45},
number = {2},
pages = {285-296},
doi = {10.1111/jvec.12399},
pmid = {33207061},
issn = {1948-7134},
mesh = {Aedes/*genetics ; Animals ; British Columbia ; DNA, Mitochondrial/chemistry ; Electron Transport Complex IV/*genetics ; Haplotypes ; NADH Dehydrogenase/*genetics ; *Phylogeny ; },
abstract = {Aedes japonicus japonicus (Theobald) is a relatively recent immigrant to the Pacific Northwest, having been collected in Washington State in 2001 and in British Columbia (BC) since 2014. We applied a molecular barcoding approach to determine the phylogenetic relationship of Ae. j. japonicus populations in BC with those from around the world. We sequenced a 617 base-pair segment of the cytochrome c oxidase 1 gene and a 330 base-pair region of the NADH dehydrogenase 4 gene to find genetic variation and characterize phylogenetic and haplotypic relationships based on nucleotide divergences. Our results revealed low genetic diversity in the BC samples, suggesting that these populations arose from the same introduction event. However, our approach lacked the granularity to identify the exact country of origin of the Ae. j. japonicus collected in BC. Future efforts should focus on detecting and preventing new Ae. j. japonicus introductions, recognizing that current molecular techniques are unable to pin-point the precise source of an introduction.},
}
@article {pmid33206674,
year = {2020},
author = {Nitta, JH and Ebihara, A and Smith, AR},
title = {A taxonomic and molecular survey of the pteridophytes of the Nectandra Cloud Forest Reserve, Costa Rica.},
journal = {PloS one},
volume = {15},
number = {11},
pages = {e0241231},
pmid = {33206674},
issn = {1932-6203},
mesh = {Biodiversity ; *Conservation of Natural Resources ; Costa Rica ; DNA Barcoding, Taxonomic ; Ferns/*classification/*genetics/growth &amp; development ; *Forests ; Geography ; Likelihood Functions ; Phylogeny ; Species Specificity ; *Surveys and Questionnaires ; },
abstract = {Floristic surveys are crucial to the conservation of biodiversity, but the vast majority of such surveys are limited to listing species names, and few take into account the evolutionary history of species. Here, we combine classical taxonomic and molecular phylogenetic (DNA barcoding) approaches to catalog the biodiversity of pteridophytes (ferns and lycophytes) of the Nectandra Cloud Forest Reserve, Costa Rica. Surveys were carried out over three field seasons (2008, 2011, and 2013), resulting in 176 species representing 69 genera and 22 families of pteridophytes. Our literature survey of protected areas in Costa Rica shows that Nectandra has an exceptionally diverse pteridophyte flora for its size. Plastid rbcL was selected as a DNA barcode marker and obtained for >95% of pteridophyte taxa at this site. Combined molecular and morphological analyses revealed two previously undescribed taxa that appear to be of hybrid origin. The utility of rbcL for species identification was assessed by calculating minimum interspecific distances and found to have a failure rate of 18%. Finally we compared the distribution of minimum interspecific rbcL distances with two other areas that have been the focus of pteridophyte molecular surveys: Japan and Tahiti. The comparison shows that Nectandra is more similar to Japan than Tahiti, which may reflect the biogeographic history of these floras.},
}
@article {pmid33203446,
year = {2020},
author = {Pareyn, M and Dvorak, V and Halada, P and Van Houtte, N and Girma, N and de Kesel, W and Merdekios, B and Massebo, F and Leirs, H and Volf, P},
title = {An integrative approach to identify sand fly vectors of leishmaniasis in Ethiopia by morphological and molecular techniques.},
journal = {Parasites &amp; vectors},
volume = {13},
number = {1},
pages = {580},
pmid = {33203446},
issn = {1756-3305},
support = {NDOC2016PR003//Vlaamse Interuniversitaire Raad/ ; 731060//Infravec2/ ; BIOCEV CZ.1.05/1.1.00/02.0109//European Regional Development Fund/ ; LM2015043//MEYS CR/ ; },
mesh = {Animals ; Ethiopia/epidemiology ; Female ; Insect Vectors/*classification ; Leishmaniasis ; Male ; Phylogeny ; Psychodidae/*classification ; Species Specificity ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; },
abstract = {BACKGROUND: Ethiopia is affected by human leishmaniasis caused by several Leishmania species and transmitted by a variety of sand fly vectors of the genus Phlebotomus. The sand fly fauna in Ethiopia is highly diverse and some species are closely related and similar in morphology, resulting in difficulties with species identification that requires deployment of molecular techniques. DNA barcoding entails high costs, requires time and lacks reference sequences for many Ethiopian species. Yet, proper species identification is pivotal for epidemiological surveillance as species differ in their actual involvement in transmission cycles. Recently, protein profiling using MALDI-TOF mass spectrometry has been introduced as a promising technique for sand fly identification.<br><br>METHODS: In our study, we used an integrative taxonomic approach to identify most of the important sand fly vectors of leishmaniasis in Ethiopia, applying three complementary methods: morphological assessment, sequencing analysis of two genetic markers, and MALDI-TOF MS protein profiling.<br><br>RESULTS: Although morphological assessment resulted in some inconclusive identifications, both DNA- and protein-based techniques performed well, providing a similar hierarchical clustering pattern for the analyzed species. Both methods generated species-specific sequences or protein patterns for all species except for Phlebotomus pedifer and P. longipes, the two presumed vectors of Leishmania aethiopica, suggesting that they may represent a single species, P. longipes Parrot &amp; Martin. All three approaches also revealed that the collected specimens of Adlerius sp. differ from P. (Adlerius) arabicus, the only species of Adlerius currently reported in Ethiopia, and molecular comparisons indicate that it may represent a yet undescribed new species.<br><br>CONCLUSIONS: Our study uses three complementary taxonomical methods for species identification of taxonomically challenging and yet medically import Ethiopian sand flies. The generated MALDI-TOF MS protein profiles resulted in unambiguous identifications, hence showing suitability of this technique for sand fly species identification. Furthermore, our results contribute to the still inadequate knowledge of the sand fly fauna of Ethiopia, a country severely burdened with human leishmaniasis.},
}
@article {pmid33200313,
year = {2020},
author = {Nneji, LM and Adeola, AC and Ayoola, AO and Oladipo, SO and Wang, YY and Malann, YD and Anyaele, O and Nneji, IC and Rahman, MM and Olory, CS},
title = {DNA barcoding and species delimitation of butterflies (Lepidoptera) from Nigeria.},
journal = {Molecular biology reports},
volume = {47},
number = {12},
pages = {9441-9457},
doi = {10.1007/s11033-020-05984-5},
pmid = {33200313},
issn = {1573-4978},
support = {SAJC201611//Sino-Africa Joint Research Centre, Chinese Academy of Sciences/ ; 31750110480//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Base Sequence/*genetics ; Bayes Theorem ; Biodiversity ; Butterflies/*enzymology/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; Electron Transport Complex IV/*genetics ; *Genes, Mitochondrial ; Genetic Variation ; Haplotypes ; Nigeria ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Accurate identification of species is a prerequisite for successful biodiversity management and further genetic studies. Species identification techniques often require both morphological diagnostics and molecular tools, such as DNA barcoding, for correct identification. In particular, the use of the subunit I of the mitochondrial cytochrome c oxidase (COI) gene for DNA barcoding has proven useful in species identification for insects. However, to date, no studies have been carried out on the DNA barcoding of Nigerian butterflies. We evaluated the utility of DNA barcoding applied for the first time to 735 butterfly specimens from southern Nigeria. In total, 699 DNA barcodes, resulting in a record of 116 species belonging to 57 genera, were generated. Our study sample comprised 807 DNA barcodes based on sequences generated from our current study and 108 others retrieved from BOLD. Different molecular analyses, including genetic distance-based evaluation (Neighbor-Joining, Maximum Likelihood and Bayesian trees) and species delimitation tests (TaxonDNA, Automated Barcode Gap Discovery, General Mixed Yule-Coalescent, and Bayesian Poisson Tree Processes) were performed to accurately identify and delineate species. The genetic distance-based analyses resulted in 163 well-separated clusters consisting of 147 described and 16 unidentified species. Our findings indicate that about 90.20% of the butterfly species were explicitly discriminated using DNA barcodes. Also, our field collections reported the first country records of ten butterfly species-Acraea serena, Amauris cf. dannfelti, Aterica galena extensa, Axione tjoane rubescens, Charaxes galleyanus, Papilio lormieri lormeri, Pentila alba, Precis actia, Precis tugela, and Tagiades flesus. Further, DNA barcodes revealed a high mitochondrial intraspecific divergence of more than 3% in Bicyclus vulgaris vulgaris and Colotis evagore. Furthermore, our result revealed an overall high haplotype (gene) diversity (0.9764), suggesting that DNA barcoding can provide information at a population level for Nigerian butterflies. The present study confirms the efficiency of DNA barcoding for identifying butterflies from Nigeria. To gain a better understanding of regional variation in DNA barcodes of this biogeographically complex area, future work should expand the DNA barcode reference library to include all butterfly species from Nigeria as well as surrounding countries. Also, further studies, involving relevant genetic and eco-morphological datasets, are required to understand processes governing mitochondrial intraspecific divergences reported in some species complexes.},
}
@article {pmid33199705,
year = {2020},
author = {Naffar-Abu Amara, S and Kuiken, HJ and Selfors, LM and Butler, T and Leung, ML and Leung, CT and Kuhn, EP and Kolarova, T and Hage, C and Ganesh, K and Panayiotou, R and Foster, R and Rueda, BR and Aktipis, A and Spellman, P and Ince, TA and Xiu, J and Oberley, M and Gatalica, Z and Navin, N and Mills, GB and Bronson, RT and Brugge, JS},
title = {Transient commensal clonal interactions can drive tumor metastasis.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {5799},
pmid = {33199705},
issn = {2041-1723},
support = {P30 NS072030/NS/NINDS NIH HHS/United States ; R01 CA181543/CA/NCI NIH HHS/United States ; R33 CA214310/CA/NCI NIH HHS/United States ; T32 GM007133/GM/NIGMS NIH HHS/United States ; R50 CA221675/CA/NCI NIH HHS/United States ; },
mesh = {Amphiregulin/metabolism ; Animals ; Ascites/pathology ; Carcinogenesis/pathology ; Carcinoma, Renal Cell/genetics/pathology ; *Cell Communication ; Cell Line, Tumor ; Cell Proliferation ; Cell Separation ; Clone Cells/*pathology ; Cohort Studies ; DNA Copy Number Variations/genetics ; Epithelium/pathology ; Female ; Gene Amplification ; Humans ; Kidney Neoplasms/genetics/pathology ; Ligands ; Mice, SCID ; Models, Biological ; Neoplasm Metastasis/*pathology ; Peritoneal Neoplasms/secondary ; Phenotype ; Receptor, ErbB-2/genetics ; Time Factors ; },
abstract = {The extent and importance of functional heterogeneity and crosstalk between tumor cells is poorly understood. Here, we describe the generation of clonal populations from a patient-derived ovarian clear cell carcinoma model which forms malignant ascites and solid peritoneal tumors upon intraperitoneal transplantation in mice. The clonal populations are engineered with secreted Gaussia luciferase to monitor tumor growth dynamics and tagged with a unique DNA barcode to track their fate in multiclonal mixtures during tumor progression. Only one clone, CL31, grows robustly, generating exclusively malignant ascites. However, multiclonal mixtures form large solid peritoneal metastases, populated almost entirely by CL31, suggesting that transient cooperative interclonal interactions are sufficient to promote metastasis of CL31. CL31 uniquely harbors ERBB2 amplification, and its acquired metastatic activity in clonal mixtures is dependent on transient exposure to amphiregulin, which is exclusively secreted by non-tumorigenic clones. Amphiregulin enhances CL31 mesothelial clearance, a prerequisite for metastasis. These findings demonstrate that transient, ostensibly innocuous tumor subpopulations can promote metastases via "hit-and-run" commensal interactions.},
}
@article {pmid33199075,
year = {2020},
author = {Jarrett, S and Wilmansyah, T and Bramanti, Y and Alitamsar, H and Alamsyah, D and Krishnamurthy, KR and Yang, L and Pagliusi, S},
title = {The role of manufacturers in the implementation of global traceability standards in the supply chain to combat vaccine counterfeiting and enhance safety monitoring.},
journal = {Vaccine},
volume = {38},
number = {52},
pages = {8318-8325},
pmid = {33199075},
issn = {1873-2518},
mesh = {COVID-19 Vaccines/standards ; *Counterfeit Drugs ; Drug Industry/economics/methods/*standards ; Drug Labeling/methods/*standards ; *Electronic Data Processing ; Humans ; Indonesia ; International Cooperation ; Inventions ; Investments ; Organizational Innovation ; Pilot Projects ; Vaccines/*standards ; },
abstract = {The counterfeiting of vaccines is an increasing problem globally with the safety of persons vaccinated, the trust in vaccines generally and the associated reputation of vaccine manufacturers and regulatory agencies at risk. This risk is especially critical with the on-going development of COVID-19 vaccines. The ability to track and trace vaccines through the vaccine supply chain down to persons vaccinated has to be enhanced. In this context of traceability, the global immunization community has recently set the barcoding of the primary packaging of vaccines, specifically vaccine vials and pre-filled syringes, as a top priority. Emerging vaccine manufacturers are already engaged in investigating ways to incorporate barcoding in their labelling and packaging using GS1 international standards. A specific pilot taking place in Indonesia by the national vaccine manufacturer, Bio Farma, shows the innovation of barcoding on primary packaging already underway with a relatively modest level of investment and success at this stage. This article highlights the efforts of industry and governments on the value of traceability and introduction to 2D barcodes. Access to financial resources and support from the international immunization community would accelerate such innovations leading to enhanced security of the vaccine supply chain.},
}
@article {pmid33196455,
year = {2020},
author = {Jackson, AS and Nijman, V},
title = {DNA barcoding of primates and the selection of molecular markers using African Great Apes as a model.},
journal = {Journal of anthropological sciences = Rivista di antropologia : JASS},
volume = {98},
number = {},
pages = {},
doi = {10.4436/JASS.98017},
pmid = {33196455},
issn = {2037-0644},
mesh = {Animals ; Anthropology, Physical ; Bacterial Proteins/genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Genetic Markers/*genetics ; Hominidae/*genetics ; Humans ; *Models, Genetic ; NADH Dehydrogenase/genetics ; },
abstract = {Ambiguities within species description and identification may compromise research validity. Species identification has typically been based upon morphological characteristics, yet recent technological advances have led to identifications achieved via DNA approaches, including DNA barcoding. DNA barcoding studies typically use cytochrome c oxidase subunit I (COI) as the proposed universal molecular marker for animals. Here, we test 12 mitochondrial protein coding genes for the presence of a clear barcoding gap allowing us to unequivocally define species. Using the African Great Apes as our model group, we assess this at the species (Pan troglodytes), genus (Pan) and family (Hominidae) level. Based on 279 complete mitochondrial genomes, sequences were partitioned by gene for analysis and pairwise distances were calculated. No barcoding gap was observed at the within species level, i.e., the four recognised chimpanzee taxa were not distinguishable through DNA barcoding. However, NADH dehydrogenase subunit 5 (ND5) and cytochrome c oxidase subunit II (COII) produce the largest barcoding gaps at the genus (ND5 2%, COII 0.5%) and family (ND5 1.5%, COII 0.5%) level. Rather than focusing on COI, our analysis suggests that these two genes may be more, or at least as, appropriate markers in primate species delineation, with uses in the identification of extinct and extant species. Further use may be beneficial to taxonomists, providing additional evidence and new insights for these morphologically similar species.},
}
@article {pmid33194709,
year = {2020},
author = {D'Orazio, M and Corsi, F and Mencattini, A and Di Giuseppe, D and Colomba Comes, M and Casti, P and Filippi, J and Di Natale, C and Ghibelli, L and Martinelli, E},
title = {Deciphering Cancer Cell Behavior From Motility and Shape Features: Peer Prediction and Dynamic Selection to Support Cancer Diagnosis and Therapy.},
journal = {Frontiers in oncology},
volume = {10},
number = {},
pages = {580698},
pmid = {33194709},
issn = {2234-943X},
abstract = {Cell motility varies according to intrinsic features and microenvironmental stimuli, being a signature of underlying biological phenomena. The heterogeneity in cell response, due to multilevel cell diversity especially relevant in cancer, poses a challenge in identifying the biological scenario from cell trajectories. We propose here a novel peer prediction strategy among cell trajectories, deciphering cell state (tumor vs. nontumor), tumor stage, and response to the anticancer drug etoposide, based on morphology and motility features, solving the strong heterogeneity of individual cell properties. The proposed approach first barcodes cell trajectories, then automatically selects the good ones for optimal model construction (good teacher and test sample selection), and finally extracts a collective response from the heterogeneous populations via cooperative learning approaches, discriminating with high accuracy prostate noncancer vs. cancer cells of high vs. low malignancy. Comparison with standard classification methods validates our approach, which therefore represents a promising tool for addressing clinically relevant issues in cancer diagnosis and therapy, e.g., detection of potentially metastatic cells and anticancer drug screening.},
}
@article {pmid33194419,
year = {2020},
author = {Silva-Morales, I},
title = {Reinstatement of Phascolosoma (Phascolosoma) varians Keferstein, 1865 (Sipuncula: Phascolosomatidae) based on morphological and molecular data.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e10238},
pmid = {33194419},
issn = {2167-8359},
abstract = {Phascolosoma (P.) varians, a sipunculan species known from the Greater Caribbean, was designated as a synonym of Phascolosoma (P.) nigrescens, which was originally described from Fiji. Their synonymy was primarily based upon an interpretation that these two species were morphologically indistinguishable. After its designation as a synonym, no further detailed analyses of morphological or molecular characteristics were performed to corroborate the assumed widespread distribution of Phascolosoma (P.) nigrescens. In this study, Phascolosoma (P.) varians is redescribed, and notable differences between this species and its proposed senior synonym are presented. These two species differ in the shape of their hooks, the spatial attachment of nephridia to the body wall, and the morphology of the contractile vessel. Additionally, there is high genetic divergence between nucleotide sequences within their respective cytochrome c oxidase subunit 1 (COI) genes, which supports the morphological data. Herein, the synonymy of Phascolosoma (P.) varians with Phascolosoma (P.) nigrescens is rejected due to morphological and molecular differences. Furthermore, the assumed widespread distribution of Phascolosoma (P.) nigrescens is still considered as questionable.},
}
@article {pmid33193683,
year = {2020},
author = {Gao, C and Wu, C and Zhang, Q and Zhao, X and Wu, M and Chen, R and Zhao, Y and Li, Z},
title = {Characterization of Chloroplast Genomes From Two Salvia Medicinal Plants and Gene Transfer Among Their Mitochondrial and Chloroplast Genomes.},
journal = {Frontiers in genetics},
volume = {11},
number = {},
pages = {574962},
pmid = {33193683},
issn = {1664-8021},
abstract = {Salvia species have been widely used as medicinal plants and have played an important role in the treatment and recovery of individuals with COVID-19. In this study, we reported two newly identified whole chloroplast genome sequences of Salvia medicinal plants (Salvia yangii and Salvia miltiorrhiza f. alba) and compared them with those of seven other reported Salvia chloroplast genomes. These were proven to be highly similar in terms of overall size, genome structure, gene content, and gene order. We identified 10 mutation hot spots (trnK-rps16, atpH-atpI, psaA-ycf3, ndhC-trnV, ndhF, rpl32-trnL, ndhG-ndhI, rps15-ycf1, ycf1a, and ycf1b) as candidate DNA barcodes for Salvia. Additionally, we observed the transfer of nine large-sized chloroplast genome fragments, with a total size of 49,895 bp (accounting for 32.97% of the chloroplast genome), into the mitochondrial genome as they shared >97% sequence similarity. Phylogenetic analyses of the whole chloroplast genome provided a high resolution of Salvia. This study will pave the way for the identification and breeding of Salvia medicinal plants and further phylogenetic evolutionary research on them as well.},
}
@article {pmid33193599,
year = {2020},
author = {Lozoya, OA and McClelland, KS and Papas, BN and Li, JL and Yao, HH},
title = {Patterns, Profiles, and Parsimony: Dissecting Transcriptional Signatures From Minimal Single-Cell RNA-Seq Output With SALSA.},
journal = {Frontiers in genetics},
volume = {11},
number = {},
pages = {511286},
pmid = {33193599},
issn = {1664-8021},
support = {ZIA ES102965/ImNIH/Intramural NIH HHS/United States ; },
abstract = {Single-cell RNA sequencing (scRNA-seq) technologies have precipitated the development of bioinformatic tools to reconstruct cell lineage specification and differentiation processes with single-cell precision. However, current start-up costs and recommended data volumes for statistical analysis remain prohibitively expensive, preventing scRNA-seq technologies from becoming mainstream. Here, we introduce single-cell amalgamation by latent semantic analysis (SALSA), a versatile workflow that combines measurement reliability metrics with latent variable extraction to infer robust expression profiles from ultra-sparse sc-RNAseq data. SALSA uses a matrix focusing approach that starts by identifying facultative genes with expression levels greater than experimental measurement precision and ends with cell clustering based on a minimal set of Profiler genes, each one a putative biomarker of cluster-specific expression profiles. To benchmark how SALSA performs in experimental settings, we used the publicly available 10X Genomics PBMC 3K dataset, a pre-curated silver standard from human frozen peripheral blood comprising 2,700 single-cell barcodes, and identified 7 major cell groups matching transcriptional profiles of peripheral blood cell types and driven agnostically by < 500 Profiler genes. Finally, we demonstrate successful implementation of SALSA in a replicative scRNA-seq scenario by using previously published DropSeq data from a multi-batch mouse retina experimental design, thereby identifying 10 transcriptionally distinct cell types from > 64,000 single cells across 7 independent biological replicates based on < 630 Profiler genes. With these results, SALSA demonstrates that robust pattern detection from scRNA-seq expression matrices only requires a fraction of the accrued data, suggesting that single-cell sequencing technologies can become affordable and widespread if meant as hypothesis-generation tools to extract large-scale differential expression effects.},
}
@article {pmid33193015,
year = {2020},
author = {Leija-Salazar, M and Pittman, A and Mokretar, K and Morris, H and Schapira, AH and Proukakis, C},
title = {Investigation of Somatic Mutations in Human Brains Targeting Genes Associated With Parkinson's Disease.},
journal = {Frontiers in neurology},
volume = {11},
number = {},
pages = {570424},
pmid = {33193015},
issn = {1664-2295},
abstract = {Background: Somatic single nucleotide variant (SNV) mutations occur in neurons but their role in synucleinopathies is unknown. Aim: We aimed to identify disease-relevant low-level somatic SNVs in brains from sporadic patients with synucleinopathies and a monozygotic twin carrying LRRK2 G2019S, whose penetrance could be explained by somatic variation. Methods and Results: We included different brain regions from 26 Parkinson's disease (PD), one Incidental Lewy body, three multiple system atrophy cases, and 12 controls. The whole SNCA locus and exons of other genes associated with PD and neurodegeneration were deeply sequenced using molecular barcodes to improve accuracy. We selected 21 variants at 0.33-5% allele frequencies for validation using accurate methods for somatic variant detection. Conclusions: We could not detect disease-relevant somatic SNVs, however we cannot exclude their presence at earlier stages of degeneration. Our results support that coding somatic SNVs in neurodegeneration are rare, but other types of somatic variants may hold pathological consequences in synucleinopathies.},
}
@article {pmid33192140,
year = {2020},
author = {Raupach, MJ and Hannig, K and Morinière, J and Hendrich, L},
title = {A DNA barcode library for ground beetles of Germany: the genus Pterostichus Bonelli, 1810 and allied taxa (Insecta, Coleoptera, Carabidae).},
journal = {ZooKeys},
volume = {980},
number = {},
pages = {93-117},
pmid = {33192140},
issn = {1313-2989},
abstract = {Species of the ground beetle genus Pterostichus Bonelli, 1810 are some of the most common carabids in Europe. This publication provides a first comprehensive DNA barcode library for this genus and allied taxa including Abax Bonelli, 1810, Molops Bonelli, 1810, Poecilus Bonelli, 1810, and Stomis Clairville, 1806 for Germany and Central Europe in general. DNA barcodes were analyzed from 609 individuals that represent 51 species, including sequences from previous studies as well as more than 198 newly generated sequences. The results showed a 1:1 correspondence between BIN and traditionally recognized species for 44 species (86%), whereas two (4%) species were characterized by two BINs. Three BINs were found for one species (2%), while one BIN for two species was revealed for two species pairs (8%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for four species pairs. Haplotype sharing was found for two closely related species pairs: Pterostichus adstrictus Eschscholtz, 1823/Pterostichus oblongopunctatus (Fabricius, 1787) and Pterostichus nigrita Paykull, 1790/Pterostichus rhaeticus Heer, 1837. In contrast to this, high intraspecific sequence divergences with values above 2.2% were shown for three species (Molops piceus (Panzer, 1793), Pterostichus panzeri (Panzer, 1805), Pterostichus strenuus (Panzer, 1793)). Summarizing the results, the present DNA barcode library does not only allow the identification of most of the analyzed species, but also provides valuable information for alpha-taxonomy as well as for ecological and evolutionary research. This library represents another step in building a comprehensive DNA barcode library of ground beetles as part of modern biodiversity research.},
}
@article {pmid33190356,
year = {2021},
author = {Kamdem, MM and Ngakou, A and Yanou Njintang, N and Voua Otomo, P},
title = {Habitat components and population density drive plant litter consumption by Eudrilus eugeniae (Oligochaeta) under tropical conditions.},
journal = {Integrative zoology},
volume = {16},
number = {2},
pages = {255-269},
doi = {10.1111/1749-4877.12503},
pmid = {33190356},
issn = {1749-4877},
support = {110858//National Research Foundation of South Africa/ ; FBIS160602167227//SANBI-FBIP South Africa/ ; },
mesh = {Animals ; Cameroon ; DNA Barcoding, Taxonomic ; *Ecosystem ; Manure ; Oligochaeta/genetics/*physiology ; Population Density ; Refuse Disposal ; Soil/*chemistry/*classification ; Tithonia ; Tropical Climate ; },
abstract = {The ingestion of organic and mineral materials by earthworms is a prominent functional role that has profound consequences for the decomposition and stabilization of soil organic matter. To investigate the litter consumption of the African nightcrawler earthworm Eudrilus eugeniae under different tropical conditions, we used DNA barcoding to identify specimens of E. eugeniae collected from sites across the Adamawa region in Cameroon, and studied the influence of habitat suitability (soil properties), soil moisture, litter type, and population density on litter consumption. A total of four litter consumption experiments were carried out using soils collected from refuse disposal sites, agricultural lands, and savannahs dominated by the Mexican sunflower Tithonia diversifolia. The results revealed that litter consumption significantly increased in the refuse disposal and agricultural soils as opposed to the Mexican sunflower (T. diversifolia) soil, a cow dung enriched substrate, and a sterile soil horizon from the savannah (P < 0.05). The optimum moistures for litter consumption were between 24% and 50%. Litter type did not affect the consumption rate of the earthworms (P > 0.05). We observed a general positive density-dependent consumption with litter mass loss increasing with increasing density. Our results suggest that E. eugeniae has a strong direct effect on the decomposition of plant materials than expected from previous estimations, and that litter consumption rates are determined by several habitat components and population density.},
}
@article {pmid33188776,
year = {2020},
author = {Liu, Y and Yang, M and Deng, Y and Su, G and Enninful, A and Guo, CC and Tebaldi, T and Zhang, D and Kim, D and Bai, Z and Norris, E and Pan, A and Li, J and Xiao, Y and Halene, S and Fan, R},
title = {High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue.},
journal = {Cell},
volume = {183},
number = {6},
pages = {1665-1681.e18},
pmid = {33188776},
issn = {1097-4172},
support = {U54 CA209992/CA/NCI NIH HHS/United States ; R33 CA246711/CA/NCI NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; UG3 CA257393/CA/NCI NIH HHS/United States ; U54 DK106857/DK/NIDDK NIH HHS/United States ; R01 CA245313/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Automation ; Brain/embryology ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; DNA, Complementary/genetics ; Embryo, Mammalian/metabolism ; Eye/embryology ; Female ; Gene Expression Regulation, Developmental ; *Genomics ; Human Umbilical Vein Endothelial Cells/metabolism ; Humans ; Mice, Inbred C57BL ; Microfluidics ; Organ Specificity/*genetics ; RNA, Messenger/genetics/metabolism ; Reproducibility of Results ; Single-Cell Analysis ; Transcriptome/genetics ; },
abstract = {We present deterministic barcoding in tissue for spatial omics sequencing (DBiT-seq) for co-mapping of mRNAs and proteins in a formaldehyde-fixed tissue slide via next-generation sequencing (NGS). Parallel microfluidic channels were used to deliver DNA barcodes to the surface of a tissue slide, and crossflow of two sets of barcodes, A1-50 and B1-50, followed by ligation in situ, yielded a 2D mosaic of tissue pixels, each containing a unique full barcode AB. Application to mouse embryos revealed major tissue types in early organogenesis as well as fine features like microvasculature in a brain and pigmented epithelium in an eye field. Gene expression profiles in 10-μm pixels conformed into the clusters of single-cell transcriptomes, allowing for rapid identification of cell types and spatial distributions. DBiT-seq can be adopted by researchers with no experience in microfluidics and may find applications in a range of fields including developmental biology, cancer biology, neuroscience, and clinical pathology.},
}
@article {pmid33187472,
year = {2020},
author = {Garcia-Garcia, S and Perez-Arguello, A and Henares, D and Timoneda, N and Muñoz-Almagro, C},
title = {Rapid identification, capsular typing and molecular characterization of Streptococcus pneumoniae by using whole genome nanopore sequencing.},
journal = {BMC microbiology},
volume = {20},
number = {1},
pages = {347},
pmid = {33187472},
issn = {1471-2180},
support = {PI19/00104//Instituto de Salud Carlos III/ ; },
mesh = {Bacterial Capsules/*genetics ; DNA, Bacterial/genetics ; Genome, Bacterial/*genetics ; Humans ; Molecular Diagnostic Techniques ; Multilocus Sequence Typing ; Nanopore Sequencing ; Pneumococcal Infections/*diagnosis ; Sequence Analysis, DNA ; Serogroup ; Streptococcus pneumoniae/classification/genetics/*isolation &amp; purification ; },
abstract = {BACKGROUND: Whole genome sequencing has emerged as a useful tool for identification and molecular characterization of pathogens. MinION (Oxford Nanopore) is a real-time third generation sequencer whose portability, affordability and speed in data production make of it an attractive device for whole genome sequencing. The objective of this study is to evaluate MinION sequencer for pathogen identification and molecular characterization of Streptococcus pneumoniae isolated at a children's Hospital. Whole genome sequencing of 32 Streptococcus pneumoniae invasive isolates, previously characterized by standard methods (Quellung reaction, Multiplex PCR and Sanger-MLST), were performed. DNA was extracted using ZymoBIOMICS DNA Microprep kit. Quantification and purity of DNA was assessed by Qubit and Nanodrop, respectively. Library preparation was performed using the Rapid Barcoding Kit. Real-time workflow EPI2ME platform "What's it in my pot" was used for species identification. Fast5 sequences were converted into FASTQ by Albacore software. Reads were assembled using CANU software. PathogenWatch, genomic epidemiology and pubmlst online tools were used for capsular typing and/or whole genome-MLST profile.<br><br>RESULTS: Rapid identification of Streptococcus pneumoniae was achieved by "What's in my pot". Capsular typing was correctly assigned with PathogenWatch in all 32 isolates at serogroup level and 24 at serotype level. Whole genome-MLST results obtained by genomic epidemiology and pubmlst were consistent with double locus variant clonal complex obtained by Sanger-MLST in 31 isolates.<br><br>CONCLUSION: MinION sequencer provides a rapid, cost-effective and promising pathway for performing WGS by a pocked-sized device for epidemiological purposes but improving its sequencing accuracy will make it more appealing to be used in clinical microbiology laboratories.},
}
@article {pmid33183225,
year = {2020},
author = {Wang, T and Zhang, YP and Yang, ZY and Liu, Z and Du, YY},
title = {DNA barcoding reveals cryptic diversity in the underestimated genus Triplophysa (Cypriniformes: Cobitidae, Nemacheilinae) from the northeastern Qinghai-Tibet Plateau.},
journal = {BMC evolutionary biology},
volume = {20},
number = {1},
pages = {151},
pmid = {33183225},
issn = {1471-2148},
support = {31460560//National Natural Science Foundation of China/International ; },
mesh = {Animals ; *Cypriniformes/genetics ; DNA ; *DNA Barcoding, Taxonomic ; *Phylogeny ; Tibet ; },
abstract = {BACKGROUND: The northeastern part of the Qinghai-Tibet Plateau (QTP) presents a high number of plateau loach species. As one of the three major groups of fishes distributed on the QTP, plateau loach has high ecological value. However, the taxonomy and systematics of these fish are still controversial, and a large number of new species have been reported. The reason for this phenomenon is that the degree of morphological variation is low, the phylogenetic information provided by morphological and anatomical features used for species identification is relatively poor, and many cryptic species are observed. Based on the high-density sampling points from the biodiversity hotspots surveyed, this study aims to evaluate the biodiversity of plateau loach in the northeastern part of the QTP and reveal the hidden diversity by comparing morphological species with molecular operational taxonomic units (MOTUs).<br><br>RESULTS: After careful identification and comparison of the morphology and DNA barcoding of 1630 specimens, 22 species were identified, with 20 considered valid local species and two identified as new species that had not been previously described. Based on the combination of morphological and molecular methods, a total of 24 native species were found, two of which were cryptic species: Triplophysa robusta sp1 and Triplophysa minxianensis sp1. Fourteen of the 24 species form clusters of barcodes that allow them to be reliably identified. The remaining cases involved 10 closely related species, including rapidly differentiated species and species that seemed to have experienced incomplete lineage sorting or showed introgressions.<br><br>CONCLUSIONS: The results highlight the need to combine traditional taxonomies with molecular methods to correctly identify species, especially closely related species, such as the plateau loach. This study provides a basis for protecting the biodiversity of plateau loach.},
}
@article {pmid33182384,
year = {2020},
author = {Gou, W and Jia, SB and Price, M and Guo, XL and Zhou, SD and He, XJ},
title = {Complete Plastid Genome Sequencing of Eight Species from Hansenia, Haplosphaera and Sinodielsia (Apiaceae): Comparative Analyses and Phylogenetic Implications.},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {11},
pages = {},
pmid = {33182384},
issn = {2223-7747},
support = {31872647//National Natural Science Foundation of China/ ; 2005DKA21403-JK//The Chinese Ministry of Science and Technology throng the National Science and Technology Infrastructure Platform Project/ ; 2019PC002//The fourth national survey of traditional Chinese medicine resources/ ; },
abstract = {Hansenia Turcz., Haplosphaera Hand.-Mazz. and Sinodielsia H.Wolff are three Apiaceae genera endemic to the Hengduan Mountains and the Himalayas, which usually inhabit elevations greater than 2000 m. The phylogenetic relationships between and within the genera were uncertain, especially the placement of Hap. himalayensis and S. microloba. Therefore, we aimed to conduct comparative (simple sequence repeat (SSR) structure, codon usage bias, nucleotide diversity (Pi) and inverted repeat (IR) boundaries) and phylogenetic analyses of Hansenia, Haplosphaera and Sinodielsia (also compared with Chamaesium and Bupleurum) to reduce uncertainties in intergeneric and interspecific relationships. We newly assembled eight plastid genomes from Hansenia, Haplosphaera and Sinodielsia species, and analyzed them with two plastid genomes from GenBank of Hap. phaea,S. yunnanensis. Phylogenetic analyses used these ten genomes and another 22 plastid genome sequences of Apiaceae. We found that the newly assembled eight genomes ranged from 155,435 bp to 157,797 bp in length and all had a typical quadripartite structure. Fifty-five to 75 SSRs were found in Hansenia, Haplosphaera and Sinodielsia species, and the most abundant SSR was mononucleotide, which accounted for 58.47% of Hansenia, 60.21% of Haplosphaera and 48.01% of Sinodielsia. There was no evident divergence of codon usage frequency between the three genera, where codons ranged from 21,134 to 21,254. The Pi analysis showed that trnE(UUC)-trnT(GGU), trnH(GUG)-psbA and trnE(UUC)-trnT(GGU) spacer regions had the highest Pi values in the plastid genomes of Hansenia (0.01889), Haplosphaera (0.04333) and Sinodielsia (0.01222), respectively. The ndhG-ndhI spacer regions were found in all three genera to have higher diversity values (Pi values: 0.01028-0.2), and thus may provide potential DNA barcodes in phylogenetic analysis. IR boundary analysis showed that the length of rps19 and ycf1 genes entering IRs were usually stable in the same genus. Our phylogenetic tree demonstrated that Hap. himalayensis is sister to Han. weberbaueriana; meanwhile, Haplosphaera and Hansenia are nested together in the East Asia clade, and S. microloba is nested within individuals of S. yunnanensis in the Acronema clade. This study will enrich the complete plastid genome dataset of the Apiaceae genera and has provided a new insight into phylogeny reconstruction using complete plastid genomes of Hansenia, Haplosphaera and Sinodielsia.},
}
@article {pmid33180770,
year = {2020},
author = {Gunnels, T and Creswell, M and McFerrin, J and Whittall, JB},
title = {The ITS region provides a reliable DNA barcode for identifying reishi/lingzhi (Ganoderma) from herbal supplements.},
journal = {PloS one},
volume = {15},
number = {11},
pages = {e0236774},
pmid = {33180770},
issn = {1932-6203},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/*analysis/genetics ; Dietary Supplements/*analysis ; Ganoderma/*chemistry ; Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {The dietary supplement industry is rapidly growing yet, a recent study revealed that up to 60% of supplements may have substituted ingredients, some of which can be harmful contaminants or additives. When ingredients cannot be verified morphologically or biochemically, DNA barcoding complemented with a molecular phylogenetic analysis can be a powerful method for species authentication. We employed a molecular phylogenetic analysis for species authentication of the commonly used fungal supplement, reishi (Ganoderma lingzhi), by amplifying and sequencing the nuclear ribosomal internal transcribed spacer regions (ITS) with genus-specific primers. PCR of six powdered samples and one dried sample all sold as G. lucidum representing independent suppliers produced single, strong amplification products in the expected size-range for Ganoderma. Both best-hit BLAST and molecular phylogenetic analyses clearly identified the presence of G. lingzhi DNA in all seven herbal supplements. We detected variation in the ITS sequences among our samples, but all herbal supplement samples fall within a large clade of G. lingzhi ITS sequences. ITS-based phylogenetic analysis is a successful and cost-effective method for DNA-based species authentication that could be used in the herbal supplement industry for this and other fungal and plant species that are otherwise difficult to identify.},
}
@article {pmid33178298,
year = {2020},
author = {Hala, MNT and Mona, MIA and Heba, MA},
title = {Phylogenetical analysis of partially sequenced cytb gene of Haemoproteus columbae in pigeons and its pathological lesions in Egypt.},
journal = {Iranian journal of veterinary research},
volume = {21},
number = {3},
pages = {203-210},
pmid = {33178298},
issn = {1728-1997},
abstract = {BACKGROUND: Haemoproteus columbae is widely distributed in tropical and subtropical regions, causing pseudomalaria in pigeons.<br><br>AIMS: The current study aimed to characterize the phylogenetic position of H. columbae in pigeons in Sharkia province, Egypt, based on partial sequencing of the cytb gene as the conserved regions. The "DNA barcode" of the cytb gene helps in designing primers that can be used to amplify the same gene in the related haemosporidians. Methods: One hundered blood samples were collected from domestic pigeons to identify H. columbae by polymerase chain reaction (PCR) and detect its relationship with other related haemosporidians.<br><br>RESULTS: Weight losses of 60%, anemia 40%, low growth rates 26.67%, diarrhea 76.67%, dyspnea 66.67%, some neurological symptoms 33.33%, and death 16.67% were observed in the studied birds. Post-mortem examinations showed chocolate-brown appearance of the livers of the birds and congested parenchymatous organs. Microscopical examinations of Giemsa stained blood smears (n=100) revealed a 30% infection rate. The obtained infection percentages were more pronounced in males (35.71%) than females (16.66%) and more in adults (57.14%) than young pigeons (15.38%). The present sequence of H. columbae was deposited in GenBank under accession No.: MH345964 and shows 100% identity with other related Haemoproteus species in the Sao Paulo Zoo, Brazil (KU131585 and KU131583) and the UK (KX832581 and KX832586).<br><br>CONCLUSION: This study concluded that the accurate diagnosis of H. coulmbae infection in pigeons by specific primers will help with the early treatment of affected cases, especially in the presence of the immature forms, and can thus avoid the noticed clinical signs and the induced pathological lesions mentioned in our study.},
}
@article {pmid33177949,
year = {2020},
author = {Epitashvili, G and Geiger, M and Astrin, JJ and Herder, F and Japoshvili, B and Mumladze, L},
title = {Towards retrieving the Promethean treasure: a first molecular assessment of the freshwater fish diversity of Georgia.},
journal = {Biodiversity data journal},
volume = {8},
number = {},
pages = {e57862},
pmid = {33177949},
issn = {1314-2828},
abstract = {In this study, we provide a first estimation of the molecular diversity of the freshwater fishes of Georgia. In addition to field collections, we integrated DNA barcode data obtained from recent works and public databases (BOLD and NCBI GenBank). Currently, the DNA barcode reference library for freshwater fishes of Georgia comprises 352 DNA barcodes for 50 species, 36 genera and 15 families (52% of total Georgian freshwater fish diversity), from which 162 DNA barcodes belonging to 41 species were newly generated as part of this study. A total of 22 species are reported from the Caspian Sea basin and 31 from the Black Sea basin. Amongst the studied taxa, seven species were found with large interspecific divergences (> 2%) while 11 species were found to share DNA barcodes within our dataset. In the course of the study, we found the first evidence of the existence of Gymnocephalus cernua (Linnaeus, 1758) and also confirm the second occurrence of invasive Rhinogobius lindbergi (Berg, 1933) in Georgia. Based on the evaluation of currently-available barcode data for Georgian fishes, we highlighted major gaps and research needs to further progress DNA-based biodiversity studies in Georgia. Though this study lays a solid base for DNA, based biodiversity assessment and monitoring approaches, further efforts within the recently started CaBOL (Caucasus Barcode Of Life) project are needed to obtain reference data for the species still lacking DNA barcodes.},
}
@article {pmid33177943,
year = {2020},
author = {David, KJ and Hancock, DL and Salini, S and Gracy, RG and Sachin, K},
title = {Taxonomic notes on the genus Campiglossa Rondani (Diptera, Tephritidae, Tephritinae, Tephritini) in India, with description of three new species.},
journal = {ZooKeys},
volume = {977},
number = {},
pages = {75-100},
pmid = {33177943},
issn = {1313-2989},
abstract = {Three new species of Campiglossa Rondani are described from India: adults of both sexes and third instar larvae of C. ialong David, Salini &amp; Hancock, sp. nov. and C. sherlyae David &amp; Hancock, sp. nov., plus an adult female of C. shaktii David, Sachin &amp; Hancock, sp. nov., are described and illustrated. Postabdominal structures, cephalopharyngeal skeleton, and anterior and posterior spiracles of C. gemma (Hering, 1939) and C. sororcula (Wiedemann, 1830) are illustrated. DNA barcode sequences of C. ialong sp. nov., C. sherlyae sp. nov., and C. gemma were obtained and reported. Records of C. absinthii (Fabricius, 1805) and C. iracunda (Hering, 1938) are regarded as misidentifications of C. lyncea (Bezzi, 1913) and C. shaktii sp. nov., respectively, and excluded from the Indian fauna. A key to the known species of Campiglossa from India is provided. Results of preliminary phylogenetic analysis using COI revealed that C. ialong sp. nov. is paraphyletic to the Campiglossa misella group and C. C. sherlyae sp. nov. is a sister species of C. deserta.},
}
@article {pmid33177913,
year = {2020},
author = {Lee, JS and Shin, HD and Choi, YJ},
title = {Rediscovery of Seven Long-Forgotten Species of Peronospora and Plasmopara (Oomycota).},
journal = {Mycobiology},
volume = {48},
number = {5},
pages = {331-340},
pmid = {33177913},
issn = {1229-8093},
abstract = {The family Peronosporaceae, an obligate biotrophic group of Oomycota, causes downy mildew disease on many cultivated and ornamental plants such as beet, cucumber, grape, onion, rose, spinach, and sunflower. To investigate the diversity of Peronosporaceae species in Korea, we performed morphological analysis for dried plant herbariums with downy mildew infections by two largest genera, Peronospora and Plasmopara. As a result, it was confirmed that there are five species of Peronospora and two species of Plasmopara, which have been so far unrecorded in Korea, as well as rarely known in the world; Pl. angustiterminalis (ex Xanthium strumarium), Pl. siegesbeckiae (ex Siegesbeckia glabrescens), P. chenopodii-ambrosioidis (ex Chenopodium ambrosioides), P. chenopodii-ficifolii (ex Chenopodium ficifolium), P. clinopodii (ex Clinopodium cf. vulgare), P. elsholtziae (ex Elsholtzia ciliata), and P. lathyrina (ex Lathyrus japonicus). In addition, their phylogenetic relationship was inferred by molecular sequence analysis of ITS, LSU rDNA, and cox2 mtDNA. By rediscovering the seven missing species and barcoding their DNA sequences, this study provides valuable insights into the diversity and evolutionary studies of downy mildew pathogens.},
}
@article {pmid33176883,
year = {2020},
author = {Zhang, L and Fang, X and Liao, H and Zhang, Z and Zhou, X and Han, L and Chen, Y and Qiu, Q and Li, SC},
title = {A comprehensive investigation of metagenome assembly by linked-read sequencing.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {156},
pmid = {33176883},
issn = {2049-2618},
mesh = {High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: The human microbiota are complex systems with important roles in our physiological activities and diseases. Sequencing the microbial genomes in the microbiota can help in our interpretation of their activities. The vast majority of the microbes in the microbiota cannot be isolated for individual sequencing. Current metagenomics practices use short-read sequencing to simultaneously sequence a mixture of microbial genomes. However, these results are in ambiguity during genome assembly, leading to unsatisfactory microbial genome completeness and contig continuity. Linked-read sequencing is able to remove some of these ambiguities by attaching the same barcode to the reads from a long DNA fragment (10-100 kb), thus improving metagenome assembly. However, it is not clear how the choices for several parameters in the use of linked-read sequencing affect the assembly quality.<br><br>RESULTS: We first examined the effects of read depth (C) on metagenome assembly from linked-reads in simulated data and a mock community. The results showed that C positively correlated with the length of assembled sequences but had little effect on their qualities. The latter observation was corroborated by tests using real data from the human gut microbiome, where C demonstrated minor impact on the sequence quality as well as on the proportion of bins annotated as draft genomes. On the other hand, metagenome assembly quality was susceptible to read depth per fragment (CR) and DNA fragment physical depth (CF). For the same C, deeper CR resulted in more draft genomes while deeper CF improved the quality of the draft genomes. We also found that average fragment length (&#x3bc;FL) had marginal effect on assemblies, while fragments per partition (NF/P) impacted the off-target reads involved in local assembly, namely, lower NF/P values would lead to better assemblies by reducing the ambiguities of the off-target reads. In general, the use of linked-reads improved the assembly for contig N50 when compared to Illumina short-reads, but not when compared to PacBio CCS (circular consensus sequencing) long-reads.<br><br>CONCLUSIONS: We investigated the influence of linked-read sequencing parameters on metagenome assembly comprehensively. While the quality of genome assembly from linked-reads cannot rival that from PacBio CCS long-reads, the case for using linked-read sequencing remains persuasive due to its low cost and high base-quality. Our study revealed that the probable best practice in using linked-reads for metagenome assembly was to merge the linked-reads from multiple libraries, where each had sufficient CR but a smaller amount of input DNA. Video Abstract.},
}
@article {pmid33176862,
year = {2020},
author = {Sumruayphol, S and Chaiphongpachara, T and Samung, Y and Ruangsittichai, J and Cui, L and Zhong, D and Sattabongkot, J and Sriwichai, P},
title = {Seasonal dynamics and molecular differentiation of three natural Anopheles species (Diptera: Culicidae) of the Maculatus group (Neocellia series) in malaria hotspot villages of Thailand.},
journal = {Parasites &amp; vectors},
volume = {13},
number = {1},
pages = {574},
pmid = {33176862},
issn = {1756-3305},
support = {D43 TW006571/TW/FIC NIH HHS/United States ; U19 AI089672/AI/NIAID NIH HHS/United States ; D43TW006571/NH/NIH HHS/United States ; U19AI089672/NH/NIH HHS/United States ; },
mesh = {Animals ; Anopheles/*classification/physiology ; DNA, Ribosomal Spacer/genetics ; Feeding Behavior ; Female ; Humans ; Malaria/epidemiology/*transmission ; Male ; Mosquito Vectors/*classification ; Phylogeny ; *Seasons ; Social Planning ; Thailand/epidemiology ; },
abstract = {BACKGROUND: Anopheles sawadwongporni Rattanarithikul &amp; Green, Anopheles maculatus Theobald and Anopheles pseudowillmori (Theobald) of the Anopheles maculatus group (Diptera: Culicidae) are recognized as potential malaria vectors in many countries from the Indian subcontinent through Southeast Asia to Taiwan. A number of malaria vectors in malaria hotspot areas along the Thai-Myanmar border belong to this complex. However, the species distribution and dynamic trends remain understudied in this malaria endemic region.<br><br>METHODS: Mosquitoes of the Maculatus group were collected using CDC light traps every other week from four villages in Tha Song Yang District, Tak Province, Thailand from January to December 2015. Adult female mosquitoes were morphologically identified on site using taxonomic keys. Molecular species identification was performed by multiplex PCR based on the internal transcribed spacer 2 (ITS2) region of ribosomal DNA (rDNA) and sequencing of the cox1 gene at a DNA barcoding region in a subset of 29 specimens.<br><br>RESULTS: A total of 1328 An. maculatus (sensu lato) female mosquitoes were captured with An. maculatus, An. sawadwongporni and An. pseudowilmori accounting for 75.2, 22.1 and 2.7% respectively. The field captured mosquitoes of the Maculatus group were most abundant in the wet season and had a preferred distribution in villages at higher elevations. The phylogenetic relationships of 29 cox1 sequences showed a clear-cut separation of the three member species of the Maculatus group, with the An. pseudowillmori cluster being separated from An. sawadwongporni and An. maculatus.<br><br>CONCLUSIONS: This study provides updated information for the species composition, seasonal dynamics and microgeographical distribution of the Maculatus group in malaria-endemic areas of western Thailand. This information can be used to guide the planning and implementation of mosquito control measures in the pursuance of malaria transmission.},
}
@article {pmid33176144,
year = {2020},
author = {Leavitt, T and Hu, MS and Borrelli, MR and Januszyk, M and Garcia, JT and Ransom, RC and Mascharak, S and desJardins-Park, HE and Litzenburger, UM and Walmsley, GG and Marshall, CD and Moore, AL and Duoto, B and Adem, S and Foster, DS and Salhotra, A and Shen, AH and Griffin, M and Shen, EZ and Barnes, LA and Zielins, ER and Maan, ZN and Wei, Y and Chan, CKF and Wan, DC and Lorenz, HP and Chang, HY and Gurtner, GC and Longaker, MT},
title = {Prrx1 Fibroblasts Represent a Pro-fibrotic Lineage in the Mouse Ventral Dermis.},
journal = {Cell reports},
volume = {33},
number = {6},
pages = {108356},
pmid = {33176144},
issn = {2211-1247},
support = {RM1 HG007735/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 GM136659/GM/NIGMS NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; R01 GM116892/GM/NIGMS NIH HHS/United States ; R01 DE027346/DE/NIDCR NIH HHS/United States ; P50 HG007735/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; Dermis/*metabolism ; Fibroblasts/*metabolism ; Homeodomain Proteins/*metabolism ; Humans ; Mice ; },
abstract = {Fibroblast heterogeneity has been shown within the unwounded mouse dorsal dermis, with fibroblast subpopulations being identified according to anatomical location and embryonic lineage. Using lineage tracing, we demonstrate that paired related homeobox 1 (Prrx1)-expressing fibroblasts are responsible for acute and chronic fibroses in the ventral dermis. Single-cell transcriptomics further corroborated the inherent fibrotic characteristics of Prrx1 fibroblasts during wound repair. In summary, we identify and characterize a fibroblast subpopulation in the mouse ventral dermis with intrinsic scar-forming potential.},
}
@article {pmid33174830,
year = {2020},
author = {Lipworth, S and Pickford, H and Sanderson, N and Chau, KK and Kavanagh, J and Barker, L and Vaughan, A and Swann, J and Andersson, M and Jeffery, K and Morgan, M and Peto, TEA and Crook, DW and Stoesser, N and Walker, AS},
title = {Optimized use of Oxford Nanopore flowcells for hybrid assemblies.},
journal = {Microbial genomics},
volume = {6},
number = {11},
pages = {},
pmid = {33174830},
issn = {2057-5858},
support = {/WT_/Wellcome Trust/United Kingdom ; MR/T001151/1/MRC_/Medical Research Council/United Kingdom ; MRF_MRF-145-0004-TPG-AVISO/MRF/MRF/United Kingdom ; /DH_/Department of Health/United Kingdom ; },
mesh = {DNA, Bacterial/*genetics ; Enterobacteriaceae/*genetics ; Flow Cytometry/methods ; Genome, Bacterial/*genetics ; Interspersed Repetitive Sequences/*genetics ; Plasmids/*genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {Hybrid assemblies are highly valuable for studies of Enterobacteriaceae due to their ability to fully resolve the structure of mobile genetic elements, such as plasmids, which are involved in the carriage of clinically important genes (e.g. those involved in antimicrobial resistance/virulence). The widespread application of this technique is currently primarily limited by cost. Recent data have suggested that non-inferior, and even superior, hybrid assemblies can be produced using a fraction of the total output from a multiplexed nanopore [Oxford Nanopore Technologies (ONT)] flowcell run. In this study we sought to determine the optimal minimal running time for flowcells when acquiring reads for hybrid assembly. We then evaluated whether the ONT wash kit might allow users to exploit shorter running times by sequencing multiple libraries per flowcell. After 24 h of sequencing, most chromosomes and plasmids had circularized and there was no benefit associated with longer running times. Quality was similar at 12 h, suggesting that shorter running times are likely to be acceptable for certain applications (e.g. plasmid genomics). The ONT wash kit was highly effective in removing DNA between libraries. Contamination between libraries did not appear to affect subsequent hybrid assemblies, even when the same barcodes were used successively on a single flowcell. Utilizing shorter run times in combination with between-library nuclease washes allows at least 36 Enterobacteriaceae isolates to be sequenced per flowcell, significantly reducing the per-isolate sequencing cost. Ultimately this will facilitate large-scale studies utilizing hybrid assembly, advancing our understanding of the genomics of key human pathogens.},
}
@article {pmid33173395,
year = {2020},
author = {Pholyotha, A and Sutcharit, C and Tongkerd, P and Panha, S},
title = {Integrative taxonomic revision of the land snail genus Sarika Godwin-Austen, 1907 in Thailand, with descriptions of nine new species (Eupulmonata, Ariophantidae).},
journal = {ZooKeys},
volume = {976},
number = {},
pages = {1-100},
pmid = {33173395},
issn = {1313-2989},
abstract = {Members of the land snail genus SarikaGodwin-Austen 1907 are superficially similar and difficult to differentiate by their shell morphology so that their species limits are still unclear. In order to resolve the taxonomy of this group, a phylogenetic reconstruction of Sarika is presented, based on morphological and anatomical characters, as well as on partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene. In total, 23 species of Sarika are recognised in Thailand, and nine species are new to science, namely S. caligina Pholyotha &amp; Panha, sp. nov., S. gratesi Pholyotha &amp; Panha, sp. nov., S. inferospira Pholyotha &amp; Panha, sp. nov., S. lactospira Pholyotha &amp; Panha, sp. nov., S. megalogyne Pholyotha &amp; Panha, sp. nov., S. melanospira Pholyotha &amp; Panha, sp. nov., S. pellosa Pholyotha &amp; Panha, sp. nov., S. solemi Pholyotha &amp; Panha, sp. nov., and S. subheptagyra Pholyotha &amp; Panha, sp. nov. Results from genital examination and COI analyses confirm the monophyly of Sarika and its species. The intra- and inter-specific genetic distances of Sarika were 0-3.7% and 4.6-12.0%, respectively. Colour images of the living adults, shell, and genitalia along with SEM images of the spermatophore and radula are given. In addition, an identification key and a geographical distribution map of Sarika species are provided.},
}
@article {pmid33171859,
year = {2020},
author = {Webster, HJ and Emami-Khoyi, A and van Dyk, JC and Teske, PR and Jansen van Vuuren, B},
title = {Environmental DNA Metabarcoding as a Means of Estimating Species Diversity in an Urban Aquatic Ecosystem.},
journal = {Animals : an open access journal from MDPI},
volume = {10},
number = {11},
pages = {},
pmid = {33171859},
issn = {2076-2615},
abstract = {Adaptation to environments that are changing as a result of human activities is critical to species' survival. A large number of species are adapting to, and even thriving in, urban green spaces, but this diversity remains largely undocumented. In the current study, we explored the potential of environmental DNA (eDNA) to document species diversity in one of the largest green spaces in Johannesburg, South Africa. Using a novel metabarcoding approach that assembles short DNA fragments suitable for massively parallel sequencing platforms to the approximate standard ~710 bp COI barcoding fragment, we document the presence of 26 phyla, 52 classes, 134 orders, 289 families, 380 genera and 522 known species from the study site. Our results highlight the critical role that urban areas play in protecting the world's declining biodiversity.},
}
@article {pmid33170730,
year = {2021},
author = {Onah, IE and Sumner, S},
title = {DNA barcodes and new primers for nature's pest controllers: the social wasps.},
journal = {Genome},
volume = {64},
number = {5},
pages = {581-590},
doi = {10.1139/gen-2019-0193},
pmid = {33170730},
issn = {1480-3321},
mesh = {Animals ; Biodiversity ; DNA/analysis ; DNA Barcoding, Taxonomic/*methods ; *DNA Primers ; Insecta/genetics ; *Pest Control ; Phylogeny ; Polymerase Chain Reaction ; Wasps/classification/*genetics ; },
abstract = {Globally, biodiversity is declining because of anthropogenic pressures, and this could lead to extinction of some species before they are discovered. The loss of insect taxa is of prime concern, given recent reports of significant declines in the populations of many taxa across the globe. Efforts to document biodiversity have met with several challenges, amongst which are the difficulties in using morphological features to discriminate species, especially in insects. DNA barcoding is a rapid and reliable method for species identification and discovery but choosing appropriate primers to amplify the barcode region without co-amplifying contaminants remains a key challenge. We developed and tested a set of primers for PCR amplification of the DNA barcode region of the COI gene in polistine wasps. We tested their efficacy in 36 species of vespid wasps, and the solitary wasp Zethus miniatus Saussure. Samples were obtained from Africa, Americas, Asia, and Europe. The polistine-specific primers successfully amplified the barcode region for all polistines tested, without amplifying any Wolbachia present; they also worked with many species from the other Vespidae wasp subfamilies. The new primers are valuable for the discovery and accurate documentation of polistine wasps in the four continents.},
}
@article {pmid33170624,
year = {2020},
author = {Cao, X and Gao, Q and Li, S and Hu, S and Wang, J and Fischer, P and Stavrakis, S and deMello, AJ},
title = {Laminar Flow-Based Fiber Fabrication and Encoding via Two-Photon Lithography.},
journal = {ACS applied materials &amp; interfaces},
volume = {12},
number = {48},
pages = {54068-54074},
doi = {10.1021/acsami.0c14917},
pmid = {33170624},
issn = {1944-8252},
abstract = {In recent years, flow photolithography (FL) has emerged as a powerful synthetic tool for the creation of barcoded microparticles with complex morphologies and chemical compositions which have been shown to be useful in a range of multiplexed bioassay applications. More specifically, FL has been highly successful in producing micron-sized, encoded particles of bespoke shape, size, and color. That said, to date, FL has been restricted to generating barcoded microparticles and has lacked the ability to produce hybrid fibers which are structurally and spectrally encoded. To this end, we herein present a method that combines a continuous flow microfluidic system with two-photon polymerization (2PP) to fabricate microscale-encoded fibers and Janus strips in a high-throughput manner. Specifically, two co-flow liquid streams containing a monomer and initiator are introduced through a Y-shape channel to form a stable interface in the center of a microfluidic channel. The flow containing the (fluorescently labeled) monomer is then patterned by scanning the voxel of the 2PP laser across the interface to selectively polymerize different regions of the forming fiber/particle. Such a process allows for rapid spectral encoding at the single fiber level, with the resulting structurally coded fibers having obvious application in the fields of security identification and anticounterfeiting.},
}
@article {pmid33168830,
year = {2020},
author = {Saini, SK and Ørskov, AD and Bjerregaard, AM and Unnikrishnan, A and Holmberg-Thydén, S and Borch, A and Jensen, KV and Anande, G and Bentzen, AK and Marquard, AM and Tamhane, T and Treppendahl, MB and Gang, AO and Dufva, IH and Szallasi, Z and Ternette, N and Pedersen, AG and Eklund, AC and Pimanda, J and Grønbæk, K and Hadrup, SR},
title = {Human endogenous retroviruses form a reservoir of T cell targets in hematological cancers.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {5660},
pmid = {33168830},
issn = {2041-1723},
mesh = {CD8-Positive T-Lymphocytes ; Endogenous Retroviruses/*genetics ; Epigenesis, Genetic ; Epitopes, T-Lymphocyte ; Gene Expression Profiling ; Hematologic Neoplasms/genetics/therapy/*virology ; Humans ; Immunotherapy ; Monitoring, Immunologic ; Myeloid Cells ; Neoplasms ; T-Lymphocytes/*metabolism/*virology ; },
abstract = {Human endogenous retroviruses (HERV) form a substantial part of the human genome, but mostly remain transcriptionally silent under strict epigenetic regulation, yet can potentially be reactivated by malignant transformation or epigenetic therapies. Here, we evaluate the potential for T cell recognition of HERV elements in myeloid malignancies by mapping transcribed HERV genes and generating a library of 1169 potential antigenic HERV-derived peptides predicted for presentation by 4 HLA class I molecules. Using DNA barcode-labeled MHC-I multimers, we find CD8[+] T cell populations recognizing 29 HERV-derived peptides representing 18 different HERV loci, of which HERVH-5, HERVW-1, and HERVE-3 have more profound responses; such HERV-specific T cells are present in 17 of the 34 patients, but less frequently in healthy donors. Transcriptomic analyses reveal enhanced transcription of the HERVs in patients; meanwhile DNA-demethylating therapy causes a small and heterogeneous enhancement in HERV transcription without altering T cell recognition. Our study thus uncovers T cell recognition of HERVs in myeloid malignancies, thereby implicating HERVs as potential targets for immunotherapeutic therapies.},
}
@article {pmid33167987,
year = {2020},
author = {Si, YJ and Lee, YN and Cheon, SH and Park, YR and Baek, YG and Kye, SJ and Lee, MH and Lee, YJ},
title = {Isolation and characterization of low pathogenic H7N7 avian influenza virus from a red-crowned crane in a zoo in South Korea.},
journal = {BMC veterinary research},
volume = {16},
number = {1},
pages = {432},
pmid = {33167987},
issn = {1746-6148},
support = {B-1543418-2019-21-01//Animal and Plant Quarantine Agency/ ; },
mesh = {Animals ; Animals, Zoo/virology ; Birds ; Feces/virology ; Influenza A Virus, H7N7 Subtype/genetics/*isolation &amp; purification ; Influenza in Birds/*virology ; Republic of Korea ; },
abstract = {BACKGROUND: South Korea conducts annual national surveillance programs to detect avian influenza (AI) in domestic poultry, live bird markets, and wild birds. In March 2017, an AIV was isolated from fecal samples in an outdoor aviary flight cage in a zoo in Korea.<br><br>RESULTS: Nucleotide sequencing identified the isolate as low pathogenic avian influenza virus (LPAIV) H7N7, and DNA barcoding analysis identified the host species as red-crowned crane. This isolate was designated A/red-crowned crane/Korea/H1026/2017 (H7N7). Genetic analysis and gene constellation analysis revealed that A/red-crowned crane/Korea/H1026/2017 (H7N7) showed high similarity with four H7N7 LPAIVs isolated from wild bird habitats in Seoul and Gyeonggi in early 2017.<br><br>CONCLUSIONS: Considering the genetic similarity and similar collection dates of the viruses, and the fact that zoo bird cages are vulnerable to AIV, it is likely that fecal contamination from wild birds might have introduced LPAIV H7N7 into the red-crowned crane at the zoo. Therefore, our results emphasize that enhanced biosecurity measures should be employed during the wild bird migration season, and that continued surveillance should be undertaken to prevent potential threats to avian species in zoos and to humans.},
}
@article {pmid33165859,
year = {2021},
author = {Chapellier, M and Järås, M},
title = {Arrayed Molecular Barcoding of Leukemic Stem Cells.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2185},
number = {},
pages = {345-359},
doi = {10.1007/978-1-0716-0810-4_21},
pmid = {33165859},
issn = {1940-6029},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Heterografts ; Leukemia, Myeloid, Acute/*genetics/metabolism ; Mice ; Neoplasm Transplantation ; *Neoplastic Stem Cells ; },
abstract = {Functional screens on cancer cells using compound or protein libraries are usually performed in vitro. However, to assess the effects on leukemia stem cells (LSCs) in a screening setting, methodologies that allow for a high-throughput in vivo readout of leukemia-initiating activity are needed. One experimental approach to solve this issue is to genetically label, also referred to as "barcoding," the leukemia cells in an arrayed format prior to exposing them to separate experimental conditions. The cells can then be pooled and injected into mice for competitive readout of leukemia-initiating activity. Here, we describe a procedure for combining lentiviral arrayed molecular barcoding of leukemia cells with next-generation sequencing, to enable screens on leukemia cells ex vivo followed by an in vivo competitive readout of LSC function. This methodology can also be applied to other model systems in which a competitive in vivo readout of cells is needed.},
}
@article {pmid33165858,
year = {2021},
author = {Jacobs, S and Bystrykh, LV and Belderbos, ME},
title = {Clonal Analysis of Patient-Derived Samples Using Cellular Barcodes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2185},
number = {},
pages = {317-344},
doi = {10.1007/978-1-0716-0810-4_20},
pmid = {33165858},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic ; *Gene Library ; HEK293 Cells ; *Hematopoietic Stem Cells ; Humans ; *Sequence Analysis, DNA ; },
abstract = {Cellular barcoding is a relatively simple method that allows quantitative assessment of the clonal dynamics of normal, nonmalignant hematopoietic stem cells and of leukemia. Cellular barcodes are (semi-)random synthetic DNA sequences of a fixed length, which are used to uniquely mark and track cells over time. A successful barcoding experiment consists of several essential steps, including library production, transfection, transduction, barcode retrieval, and barcode data analysis. Key challenges are to obtain sufficient number of barcoded cells to conduct experiments and reliable barcode data analysis. This is especially relevant for experiments using primary leukemia cells (which are of limited availability and difficult to transduce), when studying low levels of chimerism, or when the barcoded cell population is sorted in different smaller subpopulations (e.g., lineage contribution of normal hematopoietic stem cells in murine xenografts). In these settings, retrieving accurate barcode data from low input material using standard PCR amplification techniques might be challenging and more sophisticated approaches are required. In this chapter we describe the procedures to transfect and transduce patient-derived leukemia cells, to retrieve barcoded data from both high and low input material, and to filter barcode data from sequencing noise prior to quantitative clonal analysis.},
}
@article {pmid33165788,
year = {2021},
author = {Rahimi, MJ and Cai, F and Grujic, M and Chenthamara, K and Druzhinina, IS},
title = {Molecular Identification of Trichoderma reesei.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2234},
number = {},
pages = {157-175},
doi = {10.1007/978-1-0716-1048-0_14},
pmid = {33165788},
issn = {1940-6029},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic ; DNA, Fungal/isolation &amp; purification ; *Genetic Techniques ; Hypocreales/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Spores, Fungal/cytology ; },
abstract = {Fungi comprise one of the most diverse groups of eukaryotes with many cryptic species that are difficult to identify. In this chapter, we detail a protocol for the molecular identification of the most industrially relevant species of Trichoderma-T. reesei. We first describe how a single spore culture should be isolated and used for the sequencing of the diagnostic fragment of the tef1 gene. Then, we provide two alternative methods that can be used for molecular identification and offer the diagnostic oligonucleotide hallmark of the tef1 sequence that is present in sequences of all T. reesei strains known to date and that is therefore suitable for reliable and straightforward identification.},
}
@article {pmid33164854,
year = {2021},
author = {Ortiz, D and Pekár, S and Bilat, J and Alvarez, N},
title = {Poor performance of DNA barcoding and the impact of RAD loci filtering on the species delimitation of an Iberian ant-eating spider.},
journal = {Molecular phylogenetics and evolution},
volume = {154},
number = {},
pages = {106997},
doi = {10.1016/j.ympev.2020.106997},
pmid = {33164854},
issn = {1095-9513},
mesh = {Animals ; Cell Nucleus/genetics ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Genetic Loci ; Genetics, Population ; Genomics ; Geography ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; *Restriction Mapping ; *Sequence Analysis, DNA ; Species Specificity ; Spiders/classification/*genetics ; },
abstract = {Genomic data provide unprecedented power for species delimitation. However, current implementations are still time and resource consuming. In addition, bioinformatic processing is contentious and its impact on downstream analyses is insufficiently understood. Here we employ ddRAD sequencing and a thorough sampling for species delimitation in Zodarion styliferum, a widespread Iberian ant-eating spider. We explore the influence of the loci filtering strategy on the downstream phylogenetic analyses, genomic clustering and coalescent species delimitation. We also assess the accuracy of one mitochondrial (COI) and one nuclear (ITS) barcode for fast and inexpensive species delineation in the group. Our genomic data strongly support two morphologically cryptic but ecologically divergent lineages, mainly restricted to the central-eastern and western parts of the Iberian Peninsula, respectively. Larger matrices with more missing data showed increased genomic diversity, supporting that bioinformatic strategies to maximize matrix completion disproportionately exclude loci with the highest mutation rates. Moderate loci filtering gave the best results across analyses: although larger matrices returned concatenated phylogenies with higher support, middle-sized matrices performed better in genetic structure analyses. COI displayed high diversity and a conspicuous barcode gap, revealing 13 mitochondrial lineages. Mitonuclear discordance is consistent with ancestral isolation in multiple groups, probably in glacial refugia, followed by range expansion and secondary contact that produced genomic homogenization. Several apparently (unidirectionally) introgressed specimens further challenge the accuracy of species identification through mitochondrial barcodes in the group. Conversely, ITS failed to separate both lineages of Z. styliferum. This study shows an extreme case of mitonuclear discordance that highlights the limitations of single molecular barcodes for species delimitation, even in presence of distinct barcode gaps, and brings new light on the effects of parameterization on shallow-divergence studies using RAD data.},
}
@article {pmid33164622,
year = {2021},
author = {Iketani, G and Pimentel, L and Torres, EDS and Rêgo, PSD and Sampaio, I},
title = {Mitochondrial heteroplasmy and pseudogenes in the freshwater prawn, Macrobrachium amazonicum (Heller, 1862): DNA barcoding and phylogeographic implications.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {32},
number = {1},
pages = {1-11},
doi = {10.1080/24701394.2020.1844677},
pmid = {33164622},
issn = {2470-1408},
mesh = {Animals ; Arthropod Proteins/genetics ; Brazil ; Cell Nucleus/*genetics ; Cloning, Molecular ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Genetics, Population ; Heteroplasmy ; Mitochondria/*genetics ; Palaemonidae/*classification/genetics ; Paraguay ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; },
abstract = {The mitochondrial cytochrome oxidase c subunit 1 (COI) gene has been widely used in phylogenetic studies of crustaceans and analyses in population genetics. As COI studies have become more popular, there has been an increase in the number of reports of the presence of nuclear insertions of mitochondrial DNA (Numts) and mitochondrial heteroplasmy. Here, we provide evidence of both types of event in the COI sequences of Macrobrachium amazonicum, an economically important freshwater prawn, which is widespread in South America. Heteroplasmy and Numts were confirmed by different methods of DNA extraction (genomic, mitochondrial, and nuclear-enriched DNA), cloning, and sequencing, and were observed in 11 of the 14 populations sampled, primarily in the Amazon region. We discuss how the occurrence of these events affects the interpretation of the genetic relationships among the M. amazonicum populations, and we recommend caution when using COI for genetic inferences in prawns of the genus Macrobrachium, and in particular that any analysis should include nuclear markers.},
}
@article {pmid33163293,
year = {2020},
author = {Sanderson, BJ and DiFazio, SP and Cronk, QCB and Ma, T and Olson, MS},
title = {A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae.},
journal = {Applications in plant sciences},
volume = {8},
number = {10},
pages = {e11394},
pmid = {33163293},
issn = {2168-0450},
abstract = {PREMISE: The family Salicaceae has proved taxonomically challenging, especially in the genus Salix, which is speciose and features frequent hybridization and polyploidy. Past efforts to reconstruct the phylogeny with molecular barcodes have failed to resolve the species relationships of many sections of the genus.<br><br>METHODS: We used the wealth of sequence data in the family to design sequence capture probes to target regions of 300-1200 bp of exonic regions of 972 genes.<br><br>RESULTS: We recovered sequence data for nearly all of the targeted genes in three species of Populus and three species of Salix. We present a species tree, discuss concordance among gene trees, and present population genomic summary statistics for these loci.<br><br>CONCLUSIONS: Our sequence capture array has extremely high capture efficiency within the genera Populus and Salix, resulting in abundant phylogenetic information. Additionally, these loci show promise for population genomic studies.},
}
@article {pmid33160040,
year = {2021},
author = {Wells, T and Maurin, O and Dodsworth, S and Friis, I and Cowan, R and Epitawalage, N and Brewer, G and Forest, F and Baker, WJ and Monro, AK},
title = {Combination of Sanger and target-enrichment markers supports revised generic delimitation in the problematic 'Urera clade' of the nettle family (Urticaceae).},
journal = {Molecular phylogenetics and evolution},
volume = {158},
number = {},
pages = {107008},
doi = {10.1016/j.ympev.2020.107008},
pmid = {33160040},
issn = {1095-9513},
mesh = {Biological Evolution ; Chloroplasts/classification/genetics ; DNA, Plant/*chemistry/isolation &amp; purification/metabolism ; DNA, Ribosomal/classification/genetics ; Ecosystem ; Flowers/anatomy &amp; histology/classification ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Urticaceae/anatomy &amp; histology/*classification/genetics ; },
abstract = {Urera Gaudich, s.l. is a pantropical genus comprising c. 35 species of trees, shrubs, and vines. It has a long history of taxonomic uncertainty, and is repeatedly recovered as polyphyletic within a poorly resolved complex of genera in the Urticeae tribe of the nettle family (Urticaceae). To provide generic delimitations concordant with evolutionary history, we use increased taxonomic and genomic sampling to investigate phylogenetic relationships among Urera and associated genera. A cost-effective two-tier genome-sampling approach provides good phylogenetic resolution by using (i) a taxon-dense sample of Sanger sequence data from two barcoding regions to recover clades of putative generic rank, and (ii) a genome-dense sample of target-enrichment data for a subset of representative species from each well-supported clade to resolve relationships among them. The results confirm the polyphyly of Urera s.l. with respect to the morphologically distinct genera Obetia, Poikilospermum and Touchardia. Afrotropic members of Urera s.l. are recovered in a clade sister to the xerophytic African shrubs Obetia; and Hawaiian ones with Touchardia, also from Hawaii. Combined with distinctive morphological differences between Neotropical and African members of Urera s.l., these results lead us to resurrect the previously synonymised name Scepocarpus Wedd. for the latter. The new species epiphet Touchardia oahuensis T.Wells &amp; A.K. Monro is offered as a replacement name for Touchardia glabra non H.St.John, and subgenera are created within Urera s.s. to account for the two morphologically distinct Neotropical clades. This new classification minimises taxonomic and nomenclatural disruption, while more accurately reflecting evolutionary relationships within the group.},
}
@article {pmid33159902,
year = {2021},
author = {Shahhosseini, N and Frederick, C and Racine, T and Kobinger, GP and Wong, G},
title = {Modeling host-feeding preference and molecular systematics of mosquitoes in different ecological niches in Canada.},
journal = {Acta tropica},
volume = {213},
number = {},
pages = {105734},
doi = {10.1016/j.actatropica.2020.105734},
pmid = {33159902},
issn = {1873-6254},
mesh = {Aedes/classification/genetics/physiology ; Algorithms ; Animals ; Blood ; Canada ; Culex/classification/genetics/physiology ; Culicidae/classification/genetics/*physiology ; Deer ; Ecosystem ; Feeding Behavior ; Female ; *Host Specificity ; Humans ; Phylogeny ; Swine ; },
abstract = {Several mosquito-borne viruses (mobovirus) cause infections in Canada. Ecological data on mosquito species and host range in Canada remains elusive. The main aim of the current study is to determine the host range and molecular systematics of mosquito species in Canada. Mosquitoes were collected using BG-Sentinel traps and aspirators at 10 trapping sites in Canada during 2018 and 2019. Mosquitoes collected were identified via morphology and molecular techniques. Mosquito sequences were aligned by MUSCLE algorithm and evolutionary systematics were drawn using MEGA and SDT software. Moreover, the source of blood meals was identified using a DNA barcoding technique. A total of 5,708 female mosquitoes over 34 different taxa were collected. DNA barcodes and evolutionary tree analysis confirmed the identification of mosquito species in Canada. Of the total collected samples, 201 specimens were blood-fed female mosquitoes in 20 different taxa. Four mosquito species represented about half (51.47%) of all collected blood-fed specimens: Aede cinereus (39 specimens, 19.11%), Aedes triseriatus (23, 11.27%), Culex pipiens (22, 10.78%), and Anopheles punctipennis (21, 10.29%). The most common blood meal sources were humans (49 mosquito specimens, 24% of all blood-fed mosquito specimen), pigs (44, 21.5%), American red squirrels (28, 13.7%), white-tailed deers (28, 13.7%), and American crows (16, 7.8%). Here, we present the first analysis of the host-feeding preference of different mosquito species in Canada via molecular techniques. Our results on mosquito distribution and behavior will aid in the development of effective mitigation and control strategies to prevent or reduce human/animal health issues in regards to moboviruses.},
}
@article {pmid33159897,
year = {2021},
author = {Maekawa, Y and Pemba, D and Kumala, J and Gowelo, S and Higa, Y and Futami, K and Sawabe, K and Tsuda, Y},
title = {DNA barcoding of mosquitoes collected through a nationwide survey in 2011 and 2012 in Malawi, Southeast Africa.},
journal = {Acta tropica},
volume = {213},
number = {},
pages = {105742},
doi = {10.1016/j.actatropica.2020.105742},
pmid = {33159897},
issn = {1873-6254},
mesh = {Africa, Southern ; Animals ; Asia ; Culex/classification/genetics ; Culicidae/*classification/genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Genetics, Population ; Insect Proteins/genetics ; Malawi ; Phylogeny ; Surveys and Questionnaires ; },
abstract = {We conducted a nationwide survey of mosquito distribution in Malawi from November 2011 to April 2012, and from July to September 2012. Using dried specimens of mosquito adults collected during the survey, we analyzed their cytochrome c oxidase subunit I (COI) gene sequences, prepared specimens, and registered the genetic information (658 bp) of 144 individuals belonging to 51 species of 10 genera in GenBank. Using the obtained genetic information, we analyzed the degree of intraspecific variation and investigated the various species from morphological and genetic perspectives. Moreover, we conducted phylogenetic analysis of the medically important species distributed from Africa to Asia and explored their geographical differentiation. Results showed that individuals morphologically classified as Culex univittatus complex included a individual of Cx. perexiguus which, to date, have not been reported in southern Africa. Furthermore, Mansonia uniformis, distributed in Africa and Asia, was revealed to belong to genetically distinct populations, with observed morphological differences of the samples suggesting that they are separate species. The results of genetic analysis further suggested that Cx. ethiopicus is not a synonym of Cx. bitaeniorhynchus, but that it is an independent species; although, in this study, the only definite morphological difference observed was in the shape of the wing scales. Further morphological and genetic investigation of individuals of these species, including larvae, is highly recommended.},
}
@article {pmid33159130,
year = {2020},
author = {Carter-Gates, M and Balestreri, C and Thorpe, SE and Cottier, F and Baylay, A and Bibby, TS and Moore, CM and Schroeder, DC},
title = {Implications of increasing Atlantic influence for Arctic microbial community structure.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {19262},
pmid = {33159130},
issn = {2045-2322},
mesh = {Arctic Regions ; Atlantic Ocean ; *Ecosystem ; *Microbiota ; Seawater/*microbiology ; *Water Microbiology ; },
abstract = {Increasing influence of Atlantic water in the Arctic Ocean has the potential to significantly impact regional water temperature and salinity. Here we use a rDNA barcoding approach to reveal how microbial communities are partitioned into distinct assemblages across a gradient of Atlantic-Polar Water influence in the Norwegian Sea. Data suggest that temperate adapted bacteria may replace cold water taxa under a future scenario of increasing Atlantic influence, but the eukaryote response is more complex. Some abundant eukaryotic cold water taxa could persist, while less abundant eukaryotic taxa may be replaced by warmer adapted temperate species. Furthermore, within lineages, different taxa display evidence of increased relative abundance in reaction to favourable conditions and we observed that rare microbial taxa are sample site rather than region specific. Our findings have significant implications for the vulnerability of polar associated community assemblages, which may change, impacting the ecosystem services they provide, under predicted increases of Atlantic mixing and warming within the Arctic region.},
}
@article {pmid33154449,
year = {2020},
author = {Todd, DA and Kellogg, JJ and Wallace, ED and Khin, M and Flores-Bocanegra, L and Tanna, RS and McIntosh, S and Raja, HA and Graf, TN and Hemby, SE and Paine, MF and Oberlies, NH and Cech, NB},
title = {Chemical composition and biological effects of kratom (Mitragyna speciosa): In vitro studies with implications for efficacy and drug interactions.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {19158},
pmid = {33154449},
issn = {2045-2322},
support = {U54 AT008909/AT/NCCIH NIH HHS/United States ; P30 GM122733/NH/NIH HHS/United States ; P30 GM122733/GM/NIGMS NIH HHS/United States ; F32 AT009816/AT/NCCIH NIH HHS/United States ; U54 AT008909/NH/NIH HHS/United States ; },
mesh = {Analgesics/*pharmacology ; Chromatography, Liquid ; Humans ; Metabolomics ; Microsomes, Liver/drug effects/metabolism ; Mitragyna/*chemistry ; Plant Extracts/*chemistry ; Receptors, Opioid, mu/*metabolism ; Secologanin Tryptamine Alkaloids/*pharmacology ; Tandem Mass Spectrometry ; },
abstract = {The safety and efficacy of kratom (Mitragyna speciosa) for treatment of pain is highly controversial. Kratom produces more than 40 structurally related alkaloids, but most studies have focused on just two of these, mitragynine and 7-hydroxymitragynine. Here, we profiled 53 commercial kratom products using untargeted LC-MS metabolomics, revealing two distinct chemotypes that contain different levels of the alkaloid speciofoline. Both chemotypes were confirmed with DNA barcoding to be M. speciosa. To evaluate the biological relevance of variable speciofoline levels in kratom, we compared the opioid receptor binding activity of speciofoline, mitragynine, and 7-hydroxymitragynine. Mitragynine and 7-hydroxymitragynine function as partial agonists of the human µ-opioid receptor, while speciofoline does not exhibit measurable binding affinity at the µ-, δ- or ƙ-opioid receptors. Importantly, mitragynine and 7-hydroxymitragynine demonstrate functional selectivity for G-protein signaling, with no measurable recruitment of β-arrestin. Overall, the study demonstrates the unique binding and functional profiles of the kratom alkaloids, suggesting potential utility for managing pain, but further studies are needed to follow up on these in vitro findings. All three kratom alkaloids tested inhibited select cytochrome P450 enzymes, suggesting a potential risk for adverse interactions when kratom is co-consumed with drugs metabolized by these enzymes.},
}
@article {pmid33154397,
year = {2020},
author = {Scherz, MD and Rasolonjatovo, SM and Köhler, J and Rancilhac, L and Rakotoarison, A and Raselimanana, AP and Ohler, A and Preick, M and Hofreiter, M and Glaw, F and Vences, M},
title = {'Barcode fishing' for archival DNA from historical type material overcomes taxonomic hurdles, enabling the description of a new frog species.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {19109},
pmid = {33154397},
issn = {2045-2322},
mesh = {Animals ; Anura/*genetics ; Body Size/genetics ; *DNA Barcoding, Taxonomic ; Genetic Markers/*genetics ; Madagascar ; *Phylogeny ; },
abstract = {Taxonomic progress is often hindered by intrinsic factors, such as morphologically cryptic species that require a broad suite of methods to distinguish, and extrinsic factors, such as uncertainties in the allocation of scientific names to species. These uncertainties can be due to a wide variety of factors, including old and poorly preserved type specimens (which contain only heavily degraded DNA or have lost important diagnostic characters), inappropriately chosen type specimens (e.g. juveniles without diagnostic characters) or poorly documented type specimens (with unprecise, incorrect, or missing locality data). Thanks to modern sequencing technologies it is now possible to overcome many such extrinsic factors by sequencing DNA from name-bearing type specimens of uncertain assignment and assigning these to known genetic lineages. Here, we apply this approach to frogs of the Mantidactylus ambreensis complex, which was recently shown to consist of two genetic lineages supported by concordant differentiation in mitochondrial and nuclear genes. These lineages co-occur on the Montagne d'Ambre Massif in northern Madagascar but appear to have diverged in allopatry. We use a recently published bait set based on three mitochondrial markers from all known Malagasy frog lineages to capture DNA sequences from the 127-year-old holotype of Mantidactylus ambreensis Mocquard, 1895. With the obtained sequences we are able to assign the name M. ambreensis to the lowland lineage, which is rather widespread in the rainforests of northern Madagascar, leaving the microendemic high-elevation lineage on Montagne d'Ambre in north Madagascar in need of description. We describe this species as Mantidactylus ambony sp. nov., differing from M. ambreensis in call parameters and a smaller body size. Thus, using target enrichment to obtain DNA sequence data from this old specimen, we were able to resolve the extrinsic (nomenclatural) hindrances to taxonomic resolution of this complex. We discuss the broad-scale versatility of this 'barcode fishing' approach, which can draw on the enormous success of global DNA barcoding initiatives to quickly and efficiently assign type specimens to lineages.},
}
@article {pmid33152263,
year = {2020},
author = {McDonald, D and Wu, Y and Dailamy, A and Tat, J and Parekh, U and Zhao, D and Hu, M and Tipps, A and Zhang, K and Mali, P},
title = {Defining the Teratoma as a Model for Multi-lineage Human Development.},
journal = {Cell},
volume = {183},
number = {5},
pages = {1402-1419.e18},
pmid = {33152263},
issn = {1097-4172},
support = {R01 GM123313/GM/NIGMS NIH HHS/United States ; R01 CA222826/CA/NCI NIH HHS/United States ; P30 CA023100/CA/NCI NIH HHS/United States ; T32 GM007198/GM/NIGMS NIH HHS/United States ; R01 HG009285/HG/NHGRI NIH HHS/United States ; U54 CA209891/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; *Cell Lineage ; HEK293 Cells ; Humans ; Male ; Mice, Inbred NOD ; Mice, SCID ; MicroRNAs/genetics/metabolism ; *Models, Biological ; Reproducibility of Results ; Teratoma/genetics/*pathology ; },
abstract = {We propose that the teratoma, a recognized standard for validating pluripotency in stem cells, could be a promising platform for studying human developmental processes. Performing single-cell RNA sequencing (RNA-seq) of 179,632 cells across 23 teratomas from 4 cell lines, we found that teratomas reproducibly contain approximately 20 cell types across all 3 germ layers, that inter-teratoma cell type heterogeneity is comparable with organoid systems, and teratoma gut and brain cell types correspond well to similar fetal cell types. Furthermore, cellular barcoding confirmed that injected stem cells robustly engraft and contribute to all lineages. Using pooled CRISPR-Cas9 knockout screens, we showed that teratomas can enable simultaneous assaying of the effects of genetic perturbations across all germ layers. Additionally, we demonstrated that teratomas can be sculpted molecularly via microRNA (miRNA)-regulated suicide gene expression to enrich for specific tissues. Taken together, teratomas are a promising platform for modeling multi-lineage development, pan-tissue functional genetic screening, and tissue engineering.},
}
@article {pmid33151757,
year = {2020},
author = {Collin, R and Venera-Pontón, DE and Paulay, G and Boyle, MJ},
title = {World Travelers: DNA Barcoding Unmasks the Origin of Cloning Asteroid Larvae from the Caribbean.},
journal = {The Biological bulletin},
volume = {239},
number = {2},
pages = {73-79},
doi = {10.1086/710796},
pmid = {33151757},
issn = {1939-8697},
mesh = {Animals ; Caribbean Region ; Cloning, Molecular ; *DNA Barcoding, Taxonomic ; Larva/genetics ; Panama ; Phylogeny ; },
abstract = {AbstractThe identity of wild cloning sea star larvae has been a mystery since they were first documented in the Caribbean. The most commonly collected cloning species was thought to belong to the Oreasteridae, on the basis of similarity with sequences from Oreaster reticulatus and Oreaster clavatus. This larval form has recently been linked to a rare benthic juvenile. As part of two larger DNA barcoding projects, we collected cloning asteroid larvae from the Caribbean coast of Panama and compared them to a large reference database of tropical echinoderms. Morphological and DNA barcode data from the cytochrome c oxidase subunit I gene demonstrated that Panamanian larvae belonged to the same operational taxonomic unit as those recovered in previous studies of cloning larvae from the Caribbean. Much to our surprise, sequences from these larvae clearly identified them as belonging to Valvaster striatus, a species typically considered to be endemic to the Indo-West Pacific. A lineage of Mithrodia clavigera that occurs in both the Caribbean and the Indo-West Pacific also has cloning larvae, suggesting that this unusual life history has allowed larvae to pass around the Cape of Good Hope and the Benguela upwelling region, which is a barrier to dispersal for most tropical marine invertebrates.},
}
@article {pmid33150513,
year = {2020},
author = {Reier, S and Haring, E and Billinger, F and Blatterer, H and Duda, M and Gorofsky, C and Grasser, HP and Heinisch, W and Hörweg, C and Kruckenhauser, L and Szucsich, NU and Wanka, A and Sattmann, H},
title = {First confirmed record of Trichobilharzia franki Müller &amp; Kimmig, 1994, from Radix auricularia (Linnaeus, 1758) for Austria.},
journal = {Parasitology research},
volume = {119},
number = {12},
pages = {4135-4141},
pmid = {33150513},
issn = {1432-1955},
mesh = {Animals ; Auricularia ; Austria ; Bird Diseases/parasitology ; Birds/parasitology ; Dermatitis/*parasitology ; Disease Outbreaks ; Schistosomatidae/genetics/*isolation &amp; purification ; Schistosomiasis/parasitology/*veterinary ; Skin Diseases, Parasitic/*parasitology/veterinary ; Snails/*parasitology ; },
abstract = {Avian schistosomes are of medical and veterinary importance as they are responsible for the annually occurring cercarial dermatitis outbreaks. For Austria, so far, only Trichobilharzia szidati Neuhaus 1952 was confirmed on species level as causative agent of cercarial dermatitis. Here we present the first record of Trichobilharzia franki Müller &amp; Kimmig 1994 in Austria. The species was detected during a survey of digenean trematodes in Upper Austrian water bodies. Furthermore, we provide DNA barcodes of T. franki as well as measurements of several parasite individuals to indicate the intraspecific diversity. We also recommend the usage of an alternative primer pair, since the "standard COI primer pair" previously used for Schistosomatidae amplified an aberrant fragment in the sequence of T. franki. Overall, our study shows how limited our knowledge about occurrence and distribution of avian schistosomes in Austria is and how important it is to acquire such a knowledge to estimate ecological and epidemiological risks in the future.},
}
@article {pmid33150374,
year = {2021},
author = {Shen, YJ and Mishima, Y and Shi, J and Sklavenitis-Pistofidis, R and Redd, RA and Moschetta, M and Manier, S and Roccaro, AM and Sacco, A and Tai, YT and Mercier, F and Kawano, Y and Su, NK and Berrios, B and Doench, JG and Root, DE and Michor, F and Scadden, DT and Ghobrial, IM},
title = {Progression signature underlies clonal evolution and dissemination of multiple myeloma.},
journal = {Blood},
volume = {137},
number = {17},
pages = {2360-2372},
pmid = {33150374},
issn = {1528-0020},
support = {R01 CA181683/CA/NCI NIH HHS/United States ; R01 CA205954/CA/NCI NIH HHS/United States ; },
mesh = {Adaptor Proteins, Signal Transducing/antagonists &amp; inhibitors/genetics/*metabolism ; Animals ; Apoptosis ; Biomarkers, Tumor/genetics/*metabolism ; Bone Marrow/metabolism/pathology ; CRISPR-Cas Systems ; Cell Adhesion ; Cell Movement ; Cell Proliferation ; Clonal Evolution ; *Disease Models, Animal ; Disease Progression ; Female ; *Gene Expression Regulation, Neoplastic ; HMGA1a Protein/antagonists &amp; inhibitors/genetics/*metabolism ; Humans ; Mice ; Mice, SCID ; Multiple Myeloma/genetics/metabolism/*pathology ; Neoplasm Recurrence, Local/genetics/metabolism/*pathology ; Prognosis ; RNA-Binding Proteins/antagonists &amp; inhibitors/genetics/*metabolism ; Survival Rate ; Tumor Cells, Cultured ; },
abstract = {Clonal evolution drives tumor progression, dissemination, and relapse in multiple myeloma (MM), with most patients dying of relapsed disease. This multistage process requires tumor cells to enter the circulation, extravasate, and colonize distant bone marrow (BM) sites. Here, we developed a fluorescent or DNA-barcode clone-tracking system on MM PrEDiCT (progression through evolution and dissemination of clonal tumor cells) xenograft mouse model to study clonal behavior within the BM microenvironment. We showed that only the few clones that successfully adapt to the BM microenvironment can enter the circulation and colonize distant BM sites. RNA sequencing of primary and distant-site MM tumor cells revealed a progression signature sequentially activated along human MM progression and significantly associated with overall survival when evaluated against patient data sets. A total of 28 genes were then computationally predicted to be master regulators (MRs) of MM progression. HMGA1 and PA2G4 were validated in vivo using CRISPR-Cas9 in the PrEDiCT model and were shown to be significantly depleted in distant BM sites, indicating their role in MM progression and dissemination. Loss of HMGA1 and PA2G4 also compromised the proliferation, migration, and adhesion abilities of MM cells in vitro. Overall, our model successfully recapitulates key characteristics of human MM disease progression and identified potential new therapeutic targets for MM.},
}
@article {pmid33150123,
year = {2020},
author = {Unnikrishnan, R and Dev, SA and Jayaraj, R},
title = {Pitfalls and promises of raw drug identification techniques in the ayurvedic industry: an overview.},
journal = {3 Biotech},
volume = {10},
number = {11},
pages = {497},
pmid = {33150123},
issn = {2190-572X},
abstract = {India, with a rich heritage of floral diversity, is well-known for its medicinal plant wealth and is the largest producer of medicinal herbs in the world. Ethnobiological Survey of Ministry of Environment and Forests (MOEF) could identify 8000 plant species utilized in various systems of medicine with approximately 25,000 effective herbal formulations. The extensive consumption to meet demand-supply ratio exerts a heavy strain on the existing resources. This subsequently led to the adulteration and substitution of medicinal plants with look-alike species. The consumer's faith on herbal medicine is in the phase of decline due to the extremities in adulteration/substitution and ensuing consequences. It is imperative to bring forth universally acceptable standard tools to authenticate raw drugs before being processed further into formulations. A vast array of techniques such as physical, chemical (analytical), biochemical, anatomical, organoleptic, and recently emerged DNA based molecular methods are widely used for plant species authentication. In recent years, DNA barcoding has made remarkable progress in the field of medicinal plants research. DNA metabarcoding is the latest development for qualitative evaluation of the herbal formulations, whereas for quantitative analysis, combination of pharmacognostic, pharmacovigilance and analytical methods are inevitable for authentication. This review addresses the overall strengths and shortcomings of the existing as well as recently emerged techniques in authenticating ayurvedic raw drugs.},
}
@article {pmid33150083,
year = {2020},
author = {Koroiva, R and Rodrigues, LRR and Santana, DJ},
title = {DNA barcoding for identification of anuran species in the central region of South America.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e10189},
pmid = {33150083},
issn = {2167-8359},
abstract = {The use of COI barcodes for specimen identification and species discovery has been a useful molecular approach for the study of Anura. Here, we establish a comprehensive amphibian barcode reference database in a central area of South America, in particular for specimens collected in Mato Grosso do Sul state (Brazil), and to evaluate the applicability of the COI gene for species-level identification. Both distance- and tree-based methods were applied for assessing species boundaries and the accuracy of specimen identification was evaluated. A total of 204 mitochondrial COI barcode sequences were evaluated from 22 genera and 59 species (19 newly barcoded species). Our results indicate that morphological and molecular identifications converge for most species, however, some species may present cryptic species due to high intraspecific variation, and there is a high efficiency of specimen identification. Thus, we show that COI sequencing can be used to identify anuran species present in this region.},
}
@article {pmid33147546,
year = {2020},
author = {Liu, M and Zhao, Y and Sun, Y and Li, Y and Wu, P and Zhou, S and Ren, L},
title = {Comparative study on diatom morphology and molecular identification in drowning cases.},
journal = {Forensic science international},
volume = {317},
number = {},
pages = {110552},
doi = {10.1016/j.forsciint.2020.110552},
pmid = {33147546},
issn = {1872-6283},
mesh = {Adult ; Child ; DNA/isolation &amp; purification ; *DNA Barcoding, Taxonomic ; Diatoms/*genetics ; Drowning/*diagnosis ; Female ; Forensic Medicine ; High-Throughput Nucleotide Sequencing ; Humans ; Kidney/pathology ; Liver/pathology ; Lung/pathology ; Male ; Polymerase Chain Reaction ; Reproducibility of Results ; },
abstract = {In the field of criminal investigations, in the event that a body is found in water, the ability to differentiate whether the cause of death was drowning or the body was murdered then dumped into water elsewhere is difficult but important for case detection. Detecting diatoms in human organs can be used to effectively identify if the cause of death was drowning. At present, diatom detection methods are roughly divided into morphological and molecular detection methods, but both methods have different limitations. In this study, a total of 79 samples from 23 victims in 19 known drowning deaths were collected. The diatom morphological identification combined with DNA metabarcoding technology was used to compare the reliability of the diatom detection method. Microscopic observations revealed that the positive detection rate of diatoms was 52.6 %, 26.3 % and 58.8 % respectively in the kidney, liver and lung samples. DNA metabarcoding analysis found that the positive detection rate of diatoms was 31.6 %, 31.6 % and 35.3 % respectively in kidney, liver and lung samples. When compared with barcode BacirbcL, barcode 18S605 detected more diatoms, while diatoms in BacirbcL were more consistent with environmental samples. The comparative analysis found that microscopic observations were not highly correlated with the identification results of DNA barcoding technology. There were no obvious differences in the effect of internal organs on diatom enrichment, and different organs should be tested at the same time. At present, the DNA barcode reference sequence is gravely insufficient and has many errors, which leads to restrictions in the application of this technology, resulting in many OTU not being accurately identified. This explains why the success rate of molecular identification is not higher than that of microscopic identification. Construction of a reliable diatom DNA barcode reference sequence database is an urgent task for drowning forensics.},
}
@article {pmid33144581,
year = {2020},
author = {Doroschak, K and Zhang, K and Queen, M and Mandyam, A and Strauss, K and Ceze, L and Nivala, J},
title = {Rapid and robust assembly and decoding of molecular tags with DNA-based nanopore signatures.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {5454},
pmid = {33144581},
issn = {2041-1723},
mesh = {Algorithms ; Computational Biology ; Computer Systems ; DNA/*genetics ; Electronic Data Processing ; Machine Learning ; *Nanopores ; Sequence Analysis, DNA ; Synthetic Biology/*methods ; },
abstract = {Molecular tagging is an approach to labeling physical objects using DNA or other molecules that can be used when methods such as RFID tags and QR codes are unsuitable. No molecular tagging method exists that is inexpensive, fast and reliable to decode, and usable in minimal resource environments to create or read tags. To address this, we present Porcupine, an end-user molecular tagging system featuring DNA-based tags readable within seconds using a portable nanopore device. Porcupine's digital bits are represented by the presence or absence of distinct DNA strands, called molecular bits (molbits). We classify molbits directly from raw nanopore signal, avoiding basecalling. To extend shelf life, decrease readout time, and make tags robust to environmental contamination, molbits are prepared for readout during tag assembly and can be stabilized by dehydration. The result is an extensible, real-time, high accuracy tagging system that includes an approach to developing highly separable barcodes.},
}
@article {pmid33141617,
year = {2021},
author = {Topstad, L and Guidetti, R and Majaneva, M and Ekrem, T},
title = {Multi-marker DNA metabarcoding reflects tardigrade diversity in different habitats.},
journal = {Genome},
volume = {64},
number = {3},
pages = {217-231},
doi = {10.1139/gen-2019-0218},
pmid = {33141617},
issn = {1480-3321},
mesh = {Animals ; Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Environmental ; Ecosystem ; Genetic Markers ; Tardigrada/anatomy &amp; histology/*classification/genetics ; },
abstract = {Like meiofauna in general, tardigrades are often neglected in ecological and environmental surveys. Tardigrades occur in all parts of the world, from deep marine sediments to alpine environments, and are present in most ecosystems. They are therefore potentially good candidates for biomonitoring programs. However, sampling of these minute animals is both tedious and time-consuming, impeding their inclusion in large-scale ecological surveys. In this study we argue that using a multi-marker metabarcoding approach on environmental DNA (eDNA) partly can overcome this barrier. Samples of moss, lichens, and leaf litter were investigated both by morphology-based methods and DNA metabarcoding, and the results were compared in terms of tardigrade diversity and community composition of the sampled microhabitats. DNA metabarcoding using three markers detected more species of tardigrades than identification by morphology in most samples. Also, metabarcoding detected the same community differences and microhabitat distribution patterns as morphology-based methods. In general, metabarcoding of litter samples was unreliable, with only one out of three markers consistently amplifying and detecting tardigrades. The low availability of tardigrade reference sequences in public databases restricts the taxonomic resolution in eDNA surveys, but this impediment is partly circumvented by utilizing multiple markers.},
}
@article {pmid33138012,
year = {2020},
author = {Soldi, E and Casey, C and Murphy, BR and Hodkinson, TR},
title = {Fungal Endophytes for Grass Based Bioremediation: An Endophytic Consortium Isolated from Agrostis stolonifera Stimulates the Growth of Festuca arundinacea in Lead Contaminated Soil.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {6},
number = {4},
pages = {},
pmid = {33138012},
issn = {2309-608X},
support = {CF 2017 0625-P//Enterprise Ireland/ ; },
abstract = {Bioremediation is an ecologically-friendly approach for the restoration of heavy metal-contaminated sites and can exploit environmental microorganisms such as bacteria and fungi. These microorganisms are capable of removing and/or deactivating pollutants from contaminated substrates through biological and chemical reactions. Moreover, they interact with the natural flora, protecting and stimulating plant growth in these harsh conditions. In this study, we isolated a group of endophytic fungi from Agrostis stolonifera grasses growing on toxic waste from an abandoned lead mine (up to 47,990 Pb mg/kg) and identified them using DNA sequencing (nrITS barcoding). The endophytes were then tested as a consortium of eight strains in a growth chamber experiment in association with the grass Festuca arundinacea at increasing concentrations of lead in the soil to investigate how they influenced several growth parameters. As a general trend, plants treated with endophytes performed better compared to the controls at each concentration of heavy metal, with significant improvements in growth recorded at the highest concentration of lead (800 galena mg/kg). Indeed, this set of plants germinated and tillered significantly earlier compared to the control, with greater production of foliar fresh and dry biomass. Compared with the control, endophyte treated plants germinated more than 1-day earlier and produced 35.91% more plant tillers at 35 days-after-sowing. Our results demonstrate the potential of these fungal endophytes used in a consortium for establishing grassy plant species on lead contaminated soils, which may result in practical applications for heavy metal bioremediation.},
}
@article {pmid33135308,
year = {2021},
author = {Xue, J and Chen, F and Su, L and Cao, X and Bai, M and Zhao, Y and Fan, C and Zhao, Y},
title = {Pairwise Proximity-Differentiated Visualization of Single-Cell DNA Epigenetic Marks.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {60},
number = {7},
pages = {3428-3432},
doi = {10.1002/anie.202011172},
pmid = {33135308},
issn = {1521-3773},
mesh = {5-Methylcytosine/*analogs &amp; derivatives/chemistry ; Cell Line ; Chromatin/chemistry/metabolism ; Cytosine/*analogs &amp; derivatives/chemistry ; DNA/*chemistry ; Humans ; Molecular Structure ; *Single-Cell Analysis ; },
abstract = {Spatial positioning and proximity of relevant biomolecules such as DNA epigenetic marks are fundamental to a deeper understanding of life. However, it remains poorly explored and technically challenging. Here we report the pairwise proximity-differentiated visualization of single-cell 5-formylcytosine (5fC) and 5-hydroxymethylcytosine (5hmC). These two marks on chromatin in fixed cells are successively labeled and crosslinked with their DNA primer probes via click chemistry. Based on a pairwise proximity-differentiated mechanism, proximal 5fC/5hmC sites and residual 5fC or 5hmC sites are encoded with respective circularized barcodes. These barcodes are simultaneously amplified for multiplexed single-molecule imaging. We thus demonstrate the differentiated visualization of 5fC or 5hmC spatial positioning and their pairwise proximity in single cells. Such multi-level subcellular information may provide insights into regulation functions and mechanisms of chromatin modifications, and the spatial proximity can expose the potential crosstalk or interaction between their reader proteins.},
}
@article {pmid33135166,
year = {2021},
author = {Schoenrock, KM and McHugh, TA and Krueger-Hadfield, SA},
title = {Revisiting the 'bank of microscopic forms' in macroalgal-dominated ecosystems.},
journal = {Journal of phycology},
volume = {57},
number = {1},
pages = {14-29},
doi = {10.1111/jpy.13092},
pmid = {33135166},
issn = {1529-8817},
mesh = {Aquaculture ; Ecosystem ; *Kelp ; *Phaeophyceae ; Pilot Projects ; },
abstract = {Theoretical ecological models, such as succession and facilitation, were defined in terrestrial habitats, and subsequently applied to marine and freshwater habitats in intertidal and then subtidal realms. One such model is the soil seed bank, defined as all viable seeds (or fruits) found near the soil surface that facilitate community restoration/recovery. "Banks of microscopic forms" have been hypothesized in aquatic habitats and recent work from aquaculture has highlighted dormancy in algal life cycle stages. To reinvigorate the discussions about these algal banks, we discuss differences in life cycles, dispersal, and summarize research on banks of macroalgal stages in aquatic ecosystems that may be easier to explore with modern advances in molecular technology. With focus on seminal work in global kelp forest ecosystems, we present a pilot study in northern California as proof of concept that Nereocystis luetkeana and Alaria marginata stages can be detected within kelp forests in the biofilm of rocks and bedrock using targeted primers long after zoospore release. Considering the increased interest in algae as an economic resource, [blue] carbon sink, and as ecosystem engineers, the potential for "banking" macroalgal forms could be a mechanism of resilience and recovery in aquatic populations that have complex life cycles and environmental cues for reproduction. Molecular barcoding is becoming an important tool for identifying banks of macroalgal forms in marine communities. Understanding banks of macroalgal stages, especially in deforested habitats with intense disturbance and grazer pressure, will allow researchers and marine resource managers to facilitate this natural process in recovery of the aquatic system.},
}
@article {pmid33134622,
year = {2020},
author = {Jiang, KW and Zhang, R and Zhang, ZF and Pan, B and Tian, B},
title = {DNA barcoding and molecular phylogeny of Dumasia (Fabaceae: Phaseoleae) reveals a cryptic lineage.},
journal = {Plant diversity},
volume = {42},
number = {5},
pages = {376-385},
pmid = {33134622},
issn = {2468-2659},
abstract = {Dumasia taxonomy and classification have long been problematic. Species within this genus have few morphological differences and plants without flowers or fruits are difficult to accurately identify. In this study, we evaluated the ability of six DNA barcoding sequences, one nuclear (ITS) and five chloroplast regions (trnH-psbA, matK, rbcL, trnL-trnF, psbB-psbF), to efficiently identify Dumasia species. Most single markers or their combinations identify obvious barcoding gaps between intraspecific and interspecific genetic variation. Most combined analyses including ITS showed good species resolution and identification efficiency. We therefore suggest that ITS alone or a combination of ITS with any cpDNA marker are most suitable for DNA barcoding of Dumasia. The phylogenetic analyses clearly indicated that Dumasia yunnanensis is not monophyletic and is separated as two independent branches, which may result from cryptic differentiation. Our results demonstrate that molecular data can deepen the comprehension of taxonomy of Dumasia and provide an efficient approach for identification of the species.},
}
@article {pmid33134616,
year = {2020},
author = {Mwanzia, VM and He, DX and Gichira, AW and Li, Y and Ngarega, BK and Karichu, MJ and Kamau, PW and Li, ZZ},
title = {The complete plastome sequences of five Aponogeton species (Aponogetonaceae): Insights into the structural organization and mutational hotspots.},
journal = {Plant diversity},
volume = {42},
number = {5},
pages = {334-342},
pmid = {33134616},
issn = {2468-2659},
abstract = {Members of the aquatic plant genus Aponogeton are widely used commercially in aquariums because of their variable leaf shape and unique inflorescences. However, due to extensive similarity between species in this genus, morphological characters are generally inadequate for taxonomic classification. Currently, molecular makers available for taxonomic and phylogenetic studies of Aponogeton are limited. One approach to clarifying relationships between species in these complex groups is to use divergence hotspot regions within the genome. Here, we sequenced and analyzed the plastomes of five Aponogeton species collected from China, Zambia, and Kenya, and subsequently screened these plastomes for divergent DNA hotspots. The five plastomes are circular structures with sizes ranging from 154,167 bp to 154,860 bp. The Large and the Small Single Copies are separated by two Inverted Repeats. One hundred and thirteen unique genes were identified including 79 protein-coding, 30 tRNA, and four rRNA genes. We found that the most abundant repeats in all but one species were mononucleotide repeats (A/T) and that there were 23 potential RNA ending sites. Interestingly, a ~3 kb inversion, which includes the accD gene, was detected within the Asian species of Aponogeton. The inversion may be related to more frequent exchanges between this region and the nuclear genome. Furthermore, we detected mutational hotspot sites among the five Aponogeton species. Three of these hotspots are intergenic spacer regions (accD-psaI, rbcL-accD and trnH-GUG-psbA) that might be suitable for use as barcodes to resolve intra-generic relationships. We also identified four highly variable protein-coding genes (ccsA, rpl22, rps16 and ycf1) may be used as barcodes to resolve the higher-level phylogenies. Our study will provide valuable molecular resources for the taxonomic and phylogenomic study of the complex genus Aponogeton.},
}
@article {pmid33132707,
year = {2020},
author = {Valuyskikh, OE and Teteryuk, LV and Pylina, YI and Sushentsov, OE and Martynenko, NA and Shadrin, DM},
title = {Phylogenetic relationships and status of taxa of Pulsatilla uralensis and P. patens s.str. (Ranunculaceae) in north-eastern European Russia.},
journal = {PhytoKeys},
volume = {162},
number = {},
pages = {113-130},
pmid = {33132707},
issn = {1314-2011},
abstract = {We studied the allopatric complex Pulsatilla patens (L.) Mill. s.lat. (Ranunculaceae) in north-eastern European Russia and the Urals. In this region, there are two kinds of P. patens with different perianth colours in monochrome and polychrome populations. To clarify their taxonomic boundaries, we used the sequences of chloroplast DNA (rbcL and matK) and nuclear DNA (ITS2), in addition to morphological characteristics. The combination of three markers (rbcL+matK+ITS2) was found to be the most effective for phylogenetic resolution. The samples of two morphologically-different taxa P. uralensis and P. patents s.str. were shown to form a single clade on the phylogenetic tree. Based on the molecular phylogenetic analysis, we were not able to unequivocally prove the independent existence of P. uralensis.},
}
@article {pmid33131434,
year = {2020},
author = {Webb, TJ and Vanhoorne, B},
title = {Linking dimensions of data on global marine animal diversity.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1814},
pages = {20190445},
pmid = {33131434},
issn = {1471-2970},
mesh = {Animals ; *Aquatic Organisms ; *Biodiversity ; Conservation of Natural Resources/*methods ; Databases, Factual ; Ecosystem ; *Invertebrates ; Oceans and Seas ; *Vertebrates ; },
abstract = {Recent decades have seen an explosion in the amount of data available on all aspects of biodiversity, which has led to data-driven approaches to understand how and why diversity varies in time and space. Global repositories facilitate access to various classes of species-level data including biogeography, genetics and conservation status, which are in turn required to study different dimensions of diversity. Ensuring that these different data sources are interoperable is a challenge as we aim to create synthetic data products to monitor the state of the world's biodiversity. One way to approach this is to link data of different classes, and to inventory the availability of data across multiple sources. Here, we use a comprehensive list of more than 200 000 marine animal species, and quantify the availability of data on geographical occurrences, genetic sequences, conservation assessments and DNA barcodes across all phyla and broad functional groups. This reveals a very uneven picture: 44% of species are represented by no record other than their taxonomy, but some species are rich in data. Although these data-rich species are concentrated into a few taxonomic and functional groups, especially vertebrates, data are spread widely across marine animals, with members of all 32 phyla represented in at least one database. By highlighting gaps in current knowledge, our census of marine diversity data helps to prioritize future data collection activities, as well as emphasizing the importance of ongoing sustained observations and archiving of existing data into global repositories. This article is part of the theme issue 'Integrative research perspectives on marine conservation'.},
}
@article {pmid33128928,
year = {2020},
author = {Solano, J and Anabalón, L and Figueroa, A and Gangitano, D},
title = {ITS barcoding using high resolution melting analysis of Cannabis sativa drug seizures in Chile: A forensic application.},
journal = {Forensic science international},
volume = {316},
number = {},
pages = {110550},
doi = {10.1016/j.forsciint.2020.110550},
pmid = {33128928},
issn = {1872-6283},
mesh = {Cannabis/*genetics ; Chile ; *DNA Barcoding, Taxonomic ; DNA, Intergenic/*genetics ; DNA, Plant/genetics ; Drug Trafficking ; Forensic Genetics/methods ; Humans ; Real-Time Polymerase Chain Reaction ; Transition Temperature ; },
abstract = {Cannabis sativa L. is a plant cultivated worldwide as a source of fiber, medicine, and intoxicant. Traditionally, C. sativa is divided into two main types: fiber type (hemp) and drug type. Drug-type C. sativa differs from hemp by the presence of a high quantity of the psychoactive drug, Δ[9]-tetrahydrocannabinol (Δ[9] THC). Cannabis sativa is the most commonly used used illicit controlled substance in Chile. Chile is the third greatest consumer of Cannabis in South America. The objective of this study was to determine the genetic composition of ten drug seizures of Cannabis spp. in the south of Chile using a high resolution melting (HRM) strategy combined with a barcoding marker, ITS. C. sativa samples were selected from previously processed more than a thousand crime cases at the, Araucania region crime lab, National Dept. of Health. Ten cases were selected. Sample collection was based on the following: a) dry and fresh samples with no evidence of decomposition or degradation, b) defined plant fragments such as flowers and leaves from individual plants and, c) samples with different content of THC, CBN and CBD. Five sub samples were randomly selected from each case (N=50). The commercial Silver Haze strain was used as a control. Two real-time PCR and HRM analyses were conducted. The first analysis was performed with a representative sample of each of the 10 cases studied. Then a second assay was performed with all subsamples of cases 1, 5 and 8. Results showed that real-time PCR combined with HRM analysis using ITS allowed to determine the genetic composition of cannabis in all cases studied. The derivative of melting and the analysis of the shape of the curve and the peak of Tm, showed that three groups can be clearly distinguished. A first group exhibited a peak of Tm close to 87.4°C and includes cases 7 and 8. A second group had a peak of Tm close to 87.6°C and includes case 5. A third group displayed a peak of Tm close to 87.9°C and includes case 1, 6 and Silver Haze strain. A second experiment was performed using subsamples of cases 1, 5 and 8. Case 1 displayed a unique composition of the drug suggesting that this seizure contained cannabis clonally propagated. In case 5, two genotypes were present, therefore this could be associated with two strain or two different origin. Case 8, was composed of a mixture of cannabis strains indicating the presence of various crop type and/or different biogeographic origin. In general, our results suggested genetically homogeneous seizures from Araucanía Region. The high latitude (37° 35' and 39° 37' South latitude) and the natural geographic borders that surround southern Chile helps the control of cannabis traffic into the country. Finally, HRM analysis coupled with the barcode ITS demonstrated to be a rapid and low-cost screening method.},
}
@article {pmid33126913,
year = {2020},
author = {Dos Santos, QM and Avenant-Oldewage, A},
title = {Review on the molecular study of the Diplozoidae: analyses of currently available genetic data, what it tells us, and where to go from here.},
journal = {Parasites &amp; vectors},
volume = {13},
number = {1},
pages = {539},
pmid = {33126913},
issn = {1756-3305},
support = {115343//National Research Foundation (ZA)/ ; },
mesh = {Africa ; Animals ; Asia ; Cyprinidae/*parasitology ; DNA, Ribosomal ; DNA, Ribosomal Spacer/genetics ; Europe ; Fresh Water/parasitology ; Phylogeny ; Trematoda/*classification/*genetics ; },
abstract = {The use of molecular tools in the study of parasite taxonomy and systematics have become a substantial and crucial component of parasitology. Having genetic characterisation at the disposal of researchers has produced mostly useful, and arguably more objective conclusions. However, there are several groups for which limited genetic information is available and, coupled with the lack of standardised protocols, renders molecular study of these groups challenging. The Diplozoidae are fascinating and unique monogeneans parasitizing mainly freshwater cyprinid fishes in Europe, Asia and Africa. This group was studied from a molecular aspect since the turn of the century and as such, limitations and variability concerning the use of these techniques have not been clearly defined. In this review, all literature and molecular information, primarily from online databases such as GenBank, were compiled and scrupulously analysed for the Diplozoidae. This was done to review the information, detect possible pitfalls, and provide a "checkpoint" for future molecular studies of the family. Hindrances detected are the availability of sequence data for only a limited number of species, frequently limited to a single sequence per species, and the heavy reliance on one non-coding ribosomal marker (ITS2 rDNA) which is difficult to align objectively and displays massive divergences between taxa. Challenging species identification and limited understanding of diplozoid species diversity and plasticity are also likely restricting factors, all of which hamper the accurate taxonomic and phylogenetic study of this group. Thus, a more integrated taxonomic approach through the inclusion of additional markers, application of more rigorous morphological assessment, more structured barcoding techniques, alongside thorough capturing of species descriptions including genetypes, genophore vouchers and reference collections in open sources are encouraged. The pitfalls highlighted are not singular to the Diplozoidae, and the study of other groups may benefit from the points raised here as well.},
}
@article {pmid33125641,
year = {2021},
author = {Wan, YK and Choi, GCG and Wong, ASL},
title = {High-Throughput Protein Engineering by Massively Parallel Combinatorial Mutagenesis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2199},
number = {},
pages = {3-12},
doi = {10.1007/978-1-0716-0892-0_1},
pmid = {33125641},
issn = {1940-6029},
mesh = {*High-Throughput Nucleotide Sequencing ; *Mutagenesis ; *Protein Engineering ; Recombinant Proteins/genetics ; },
abstract = {Exploring how combinatorial mutations can be combined to optimize protein functions is important to guide protein engineering. Given the vast combinatorial space of changing multiple amino acids, identifying the top-performing variants from a large number of mutants might not be possible without a high-throughput gene assembly and screening strategy. Here we describe the CombiSEAL platform, a strategy that allows for modularization of any protein sequence into multiple segments for mutagenesis and barcoding, and seamless single-pot ligations of different segments to generate a library of combination mutants linked with concatenated barcodes at one end. By reading the barcodes using next-generation sequencing, activities of each protein variant during the protein selection process can be easily tracked in a high-throughput manner. CombiSEAL not only allows the identification of better protein variants but also enables the systematic analyses to distinguish the beneficial, deleterious, and neutral effects of combining different mutations on protein functions.},
}
@article {pmid33125294,
year = {2020},
author = {Sohsah, GN and Ibrahimzada, AR and Ayaz, H and Cakmak, A},
title = {Scalable classification of organisms into a taxonomy using hierarchical supervised learners.},
journal = {Journal of bioinformatics and computational biology},
volume = {18},
number = {5},
pages = {2050026},
doi = {10.1142/S0219720020500262},
pmid = {33125294},
issn = {1757-6334},
mesh = {Algorithms ; Animals ; Birds/classification/genetics ; Chiroptera/classification/genetics ; Classification/*methods ; DNA Barcoding, Taxonomic/*methods ; Databases, Genetic ; *Deep Learning ; Ferns/classification/genetics ; Fungi/classification/genetics ; Phylogeny ; Rodentia/classification/genetics ; Support Vector Machine ; },
abstract = {Accurately identifying organisms based on their partially available genetic material is an important task to explore the phylogenetic diversity in an environment. Specific fragments in the DNA sequence of a living organism have been defined as DNA barcodes and can be used as markers to identify species efficiently and effectively. The existing DNA barcode-based classification approaches suffer from three major issues: (i) most of them assume that the classification is done within a given taxonomic class and/or input sequences are pre-aligned, (ii) highly performing classifiers, such as SVM, cannot scale to large taxonomies due to high memory requirements, (iii) mutations and noise in input DNA sequences greatly reduce the taxonomic classification score. In order to address these issues, we propose a multi-level hierarchical classifier framework to automatically assign taxonomy labels to DNA sequences. We utilize an alignment-free approach called spectrum kernel method for feature extraction. We build a proof-of-concept hierarchical classifier with two levels, and evaluated it on real DNA sequence data from barcode of life data systems. We demonstrate that the proposed framework provides higher f1-score than regular classifiers. Besides, hierarchical framework scales better to large datasets enabling researchers to employ classifiers with high classification performance and high memory requirement on large datasets. Furthermore, we show that the proposed framework is more robust to mutations and noise in sequence data than the non-hierarchical classifiers.},
}
@article {pmid33122728,
year = {2020},
author = {Csapó, H and Krzywoźniak, P and Grabowski, M and Wattier, R and Bącela-Spychalska, K and Mamos, T and Jelić, M and Rewicz, T},
title = {Successful post-glacial colonization of Europe by single lineage of freshwater amphipod from its Pannonian Plio-Pleistocene diversification hotspot.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {18695},
pmid = {33122728},
issn = {2045-2322},
mesh = {Amphipoda/classification/genetics/*growth &amp; development ; Animals ; Biological Evolution ; Europe ; *Fresh Water ; Haplotypes ; Phylogeography ; Species Specificity ; },
abstract = {Gammarus roeselii Gervais, 1835 is a morphospecies with a wide distribution range in Europe. The Balkan Peninsula is known as an area of pre-Pleistocene cryptic diversification within this taxon, resulting in at least 13 Molecular Operational Taxonomic Units (MOTUs). The morphospecies diversified there during Neogene and has probably invaded other parts of the continent very recently, in postglacial or even historical times. Thus, the detailed goals of our study were to (1) identify which lineage(s) colonized Central-Western Europe (CWE), (2) determine their possible geographical origin, (3) verify, whether the colonisation was associated with demographic changes. In total, 663 individuals were sequenced for the cytochrome oxidase I (COI) barcoding fragment and 137 individuals for the internal transcribed spacer II (ITS2). We identified two MOTUs in the study area with contrasting Barcode Index Number and haplotype diversities. The Pannonian Basin (PB) appeared to be a potential ice age refugium for the species, while CWE was colonised by a single lineage (also present in PB), displaying low genetic diversity. Our results suggest that G. roeselii is a relatively recent coloniser in CWE, starting demographic expansion around 10 kya.},
}
@article {pmid33118174,
year = {2021},
author = {Suetsugu, K and Matsubayashi, J},
title = {Evidence for mycorrhizal cheating in Apostasia nipponica, an early-diverging member of the Orchidaceae.},
journal = {The New phytologist},
volume = {229},
number = {4},
pages = {2302-2310},
doi = {10.1111/nph.17049},
pmid = {33118174},
issn = {1469-8137},
mesh = {*Basidiomycota ; Carbon ; *Mycorrhizae ; *Orchidaceae ; Phylogeny ; Symbiosis ; },
abstract = {Most land plants, from liverworts to angiosperms, form mutualistic mycorrhizal symbioses with fungal partners. However, several plants known as mycoheterotrophs exploit fungal partners by reversing the polarity of carbon movement, which usually moves from plant to fungus. We investigated the physiological ecology of a photosynthetic orchid, Apostasia nipponica, which belongs to the first branching group within the Orchidaceae, to improve our understanding of mycoheterotrophic evolution in orchids. The fungal symbionts and nutrition modes of A. nipponica were investigated using molecular barcoding and carbon-13 ([13] C) and nitrogen-15 ([15] N) measurements, respectively. Community profiling based on a metabarcoding technique revealed that A. nipponica associates with specific Ceratobasidium spp. within ectomycorrhizas-forming clades, whereas isotope analysis revealed that A. nipponica was similar to fully mycoheterotrophic orchids in its [13] C signature and was even more enriched in [15] N than most of the fully mycoheterotrophic orchids that exploit ectomycorrhizal fungi. Our molecular and mass-spectrometric approaches demonstrated, for the first time, that a member of the Apostasioideae, the earliest-diverging lineage of the Orchidaceae, gains carbon through both photosynthesis and fungal cheating (i.e. partial mycoheterotrophy) during the adult stage.},
}
@article {pmid33117077,
year = {2020},
author = {Jaturas, N and Sing, KW and Wilson, JJ and Dong, H},
title = {Butterflies in urban parks in the Bangkok Metropolitan Region, Thailand.},
journal = {Biodiversity data journal},
volume = {8},
number = {},
pages = {e56317},
pmid = {33117077},
issn = {1314-2828},
abstract = {BACKGROUND: For residents of East-Southeast Asia's megacities, interactions with "nature" may be largely limited to interactions taking place in urban parks. Urban parks provide refuges for ecologically-important biodiversity, such as insect pollinators. While residents may be unlikely to notice small insects, butterflies are more likely to be noticed and to provide positive human-"nature" interactions. Engaging residents and city planners in promoting habitat for butterflies is valid conservation practice and has well-understood educational and well-being benefits. Surveying and monitoring is an essential activity to corroborate, improve and communicate the outcomes of conservation practices amongst city governments, scientists and other stakeholders. Here we present the data from a survey of butterflies in urban parks in the megacity of the Bangkok Metropolitan Region as part of the "Urban biodiversity and human well-being in East-Southeast Asia's megacities" project organised by the "Urban Butterflies in Asia Research Network".<br><br>NEW INFORMATION: We recorded 51 species of butterflies from ten urban parks in the Bangkok Metropolitan Region. This was more than double the 25 species reported in Bangkok's City Biodiversity Index application. However, this was lower than that recorded in other megacities in Southeast Asia, such as Kuala Lumpur at 60 species. Most of the butterflies recorded were common and widespread species. DNA barcodes are provided for most of the butterflies sampled.},
}
@article {pmid33117067,
year = {2020},
author = {Yang, L and Ren, Y},
title = {A new species of Pima Hulst, 1888 from China (Lepidoptera, Pyralidae, Phycitinae), with a key to Holarctic species.},
journal = {ZooKeys},
volume = {975},
number = {},
pages = {111-124},
pmid = {33117067},
issn = {1313-2989},
abstract = {Pima tristriata sp. nov. is described as new to science based on specimens collected from the Ningxia Hui Autonomous Region, China, and P. boisduvaliella (Guenée, 1845) is also treated here for comparison. DNA barcodes of the two species are provided, together with a neighbor-joining tree for species delimitation. A key to the Holarctic species and a distribution map of the Chinese species are presented.},
}
@article {pmid33117065,
year = {2020},
author = {Yu, HJ and Lin, XL and Zhang, RL and Wang, Q and Wang, XH},
title = {Species delimitation and life stage association of Propsilocerus Kieffer, 1923 (Diptera, Chironomidae) using DNA barcodes.},
journal = {ZooKeys},
volume = {975},
number = {},
pages = {79-86},
pmid = {33117065},
issn = {1313-2989},
abstract = {The utility of COI DNA barcodes in species delimitation is explored as well as life stage associations of five closely related Propsilocerus species: Propsilocerus akamusi (Tokunaga, 1938), Propsilocerus paradoxus (Lundström, 1915), Propsilocerus saetheri Wang, Liu et Paasivirta, 2007, Propsilocerus sinicus Sæther et Wang, 1996, and Propsilocerus taihuensis (Wen, Zhou et Rong, 1994). Results revealed distinctly larger interspecific than intraspecific divergences and indicated a clear "barcode gap". In total, 42 COI barcode sequences including 16 newly generated DNA barcodes were applied to seven Barcode Index Numbers (BINs). A neighbor-joining (NJ) tree comprises five well-separated clusters representing five morphospecies. Comments on how to distinguish the larvae of P. akamusi and P. taihuensis are provided.},
}
@article {pmid33116344,
year = {2020},
author = {Crous, PW and Wingfield, MJ and Chooi, YH and Gilchrist, CLM and Lacey, E and Pitt, JI and Roets, F and Swart, WJ and Cano-Lira, JF and Valenzuela-Lopez, N and Hubka, V and Shivas, RG and Stchigel, AM and Holdom, DG and Jurjević, &#x17d; and Kachalkin, AV and Lebel, T and Lock, C and Martín, MP and Tan, YP and Tomashevskaya, MA and Vitelli, JS and Baseia, IG and Bhatt, VK and Brandrud, TE and De Souza, JT and Dima, B and Lacey, HJ and Lombard, L and Johnston, PR and Morte, A and Papp, V and Rodríguez, A and Rodríguez-Andrade, E and Semwal, KC and Tegart, L and Abad, ZG and Akulov, A and Alvarado, P and Alves, A and Andrade, JP and Arenas, F and Asenjo, C and Ballarà, J and Barrett, MD and Berná, LM and Berraf-Tebbal, A and Bianchinotti, MV and Bransgrove, K and Burgess, TI and Carmo, FS and Chávez, R and Čmoková, A and Dearnaley, JDW and de A Santiago, ALCM and Freitas-Neto, JF and Denman, S and Douglas, B and Dovana, F and Eichmeier, A and Esteve-Raventós, F and Farid, A and Fedosova, AG and Ferisin, G and Ferreira, RJ and Ferrer, A and Figueiredo, CN and Figueiredo, YF and Reinoso-Fuentealba, CG and Garrido-Benavent, I and Cañete-Gibas, CF and Gil-Durán, C and Glushakova, AM and Gonçalves, MFM and González, M and Gorczak, M and Gorton, C and Guard, FE and Guarnizo, AL and Guarro, J and Gutiérrez, M and Hamal, P and Hien, LT and Hocking, AD and Houbraken, J and Hunter, GC and Inácio, CA and Jourdan, M and Kapitonov, VI and Kelly, L and Khanh, TN and Kisło, K and Kiss, L and Kiyashko, A and Kolařík, M and Kruse, J and Kubátová, A and Kučera, V and Kučerová, I and Kušan, I and Lee, HB and Levicán, G and Lewis, A and Liem, NV and Liimatainen, K and Lim, HJ and Lyons, MN and Maciá-Vicente, JG and Magaña-Dueñas, V and Mahiques, R and Malysheva, EF and Marbach, PAS and Marinho, P and Matočec, N and McTaggart, AR and Mešić, A and Morin, L and Muñoz-Mohedano, JM and Navarro-Ródenas, A and Nicolli, CP and Oliveira, RL and Otsing, E and Ovrebo, CL and Pankratov, TA and Paños, A and Paz-Conde, A and Pérez-Sierra, A and Phosri, C and Pintos, &#xc1; and Pošta, A and Prencipe, S and Rubio, E and Saitta, A and Sales, LS and Sanhueza, L and Shuttleworth, LA and Smith, J and Smith, ME and Spadaro, D and Spetik, M and Sochor, M and Sochorová, Z and Sousa, JO and Suwannasai, N and Tedersoo, L and Thanh, HM and Thao, LD and Tkalčec, Z and Vaghefi, N and Venzhik, AS and Verbeken, A and Vizzini, A and Voyron, S and Wainhouse, M and Whalley, AJS and Wrzosek, M and Zapata, M and Zeil-Rolfe, I and Groenewald, JZ},
title = {Fungal Planet description sheets: 1042-1111.},
journal = {Persoonia},
volume = {44},
number = {},
pages = {301-459},
pmid = {33116344},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Antarctica, Cladosporium arenosum from marine sediment sand. Argentina, Kosmimatamyces alatophylus (incl. Kosmimatamyces gen. nov.) from soil. Australia, Aspergillus banksianus, Aspergillus kumbius, Aspergillus luteorubrus, Aspergillus malvicolor and Aspergillus nanangensis from soil, Erysiphe medicaginis from leaves of Medicago polymorpha, Hymenotorrendiella communis on leaf litter of Eucalyptus bicostata, Lactifluus albopicri and Lactifluus austropiperatus on soil, Macalpinomyces collinsiae on Eriachne benthamii, Marasmius vagus on soil, Microdochium dawsoniorum from leaves of Sporobolus natalensis, Neopestalotiopsis nebuloides from leaves of Sporobolus elongatus, Pestalotiopsis etonensis from leaves of Sporobolus jacquemontii, Phytophthora personensis from soil associated with dying Grevillea mccutcheonii. Brazil, Aspergillus oxumiae from soil, Calvatia baixaverdensis on soil, Geastrum calycicoriaceum on leaf litter, Greeneria kielmeyerae on leaf spots of Kielmeyera coriacea. Chile, Phytophthora aysenensis on collar rot and stem of Aristotelia chilensis. Croatia, Mollisia gibbospora on fallen branch of Fagus sylvatica. Czech Republic, Neosetophoma hnaniceana from Buxus sempervirens. Ecuador, Exophiala frigidotolerans from soil. Estonia, Elaphomyces bucholtzii in soil. France, Venturia paralias from leaves of Euphorbia paralias. India, Cortinarius balteatoindicus and Cortinarius ulkhagarhiensis on leaf litter. Indonesia, Hymenotorrendiella indonesiana on Eucalyptus urophylla leaf litter. Italy, Penicillium taurinense from indoor chestnut mill. Malaysia, Hemileucoglossum kelabitense on soil, Satchmopsis pini on dead needles of Pinus tecunumanii. Poland, Lecanicillium praecognitum on insects' frass. Portugal, Neodevriesia aestuarina from saline water. Republic of Korea, Gongronella namwonensis from freshwater. Russia, Candida pellucida from Exomias pellucidus, Heterocephalacria septentrionalis as endophyte from Cladonia rangiferina, Vishniacozyma phoenicis from dates fruit, Volvariella paludosa from swamp. Slovenia, Mallocybe crassivelata on soil. South Africa, Beltraniella podocarpi, Hamatocanthoscypha podocarpi, Coleophoma podocarpi and Nothoseiridium podocarpi (incl. Nothoseiridium gen. nov.) from leaves of Podocarpus latifolius, Gyrothrix encephalarti from leaves of Encephalartos sp., Paraphyton cutaneum from skin of human patient, Phacidiella alsophilae from leaves of Alsophila capensis, and Satchmopsis metrosideri on leaf litter of Metrosideros excelsa. Spain, Cladophialophora cabanerensis from soil, Cortinarius paezii on soil, Cylindrium magnoliae from leaves of Magnolia grandiflora, Trichophoma cylindrospora (incl. Trichophoma gen. nov.) from plant debris, Tuber alcaracense in calcareus soil, Tuber buendiae in calcareus soil. Thailand, Annulohypoxylon spougei on corticated wood, Poaceascoma filiforme from leaves of unknown Poaceae. UK, Dendrostoma luteum on branch lesions of Castanea sativa, Ypsilina buttingtonensis from heartwood of Quercus sp. Ukraine, Myrmecridium phragmiticola from leaves of Phragmites australis. USA, Absidia pararepens from air, Juncomyces californiensis (incl. Juncomyces gen. nov.) from leaves of Juncus effusus, Montagnula cylindrospora from a human skin sample, Muriphila oklahomaensis (incl. Muriphila gen. nov.) on outside wall of alcohol distillery, Neofabraea eucalyptorum from leaves of Eucalyptus macrandra, Diabolocovidia claustri (incl. Diabolocovidia gen. nov.) from leaves of Serenoa repens, Paecilomyces penicilliformis from air, Pseudopezicula betulae from leaves of leaf spots of Populus tremuloides. Vietnam, Diaporthe durionigena on branches of Durio zibethinus and Roridomyces pseudoirritans on rotten wood. Morphological and culture characteristics are supported by DNA barcodes.},
}
@article {pmid33116335,
year = {2020},
author = {Mayers, CG and Harrington, TC and Masuya, H and Jordal, BH and McNew, DL and Shih, HH and Roets, F and Kietzka, GJ},
title = {Patterns of coevolution between ambrosia beetle mycangia and the Ceratocystidaceae, with five new fungal genera and seven new species.},
journal = {Persoonia},
volume = {44},
number = {},
pages = {41-66},
pmid = {33116335},
issn = {0031-5850},
abstract = {Ambrosia beetles farm specialised fungi in sapwood tunnels and use pocket-like organs called mycangia to carry propagules of the fungal cultivars. Ambrosia fungi selectively grow in mycangia, which is central to the symbiosis, but the history of coevolution between fungal cultivars and mycangia is poorly understood. The fungal family Ceratocystidaceae previously included three ambrosial genera (Ambrosiella, Meredithiella, and Phialophoropsis), each farmed by one of three distantly related tribes of ambrosia beetles with unique and relatively large mycangium types. Studies on the phylogenetic relationships and evolutionary histories of these three genera were expanded with the previously unstudied ambrosia fungi associated with a fourth mycangium type, that of the tribe Scolytoplatypodini. Using ITS rDNA barcoding and a concatenated dataset of six loci (28S rDNA, 18S rDNA, tef1-α, tub, mcm7, and rpl1), a comprehensive phylogeny of the family Ceratocystidaceae was developed, including Inodoromyces interjectus gen. &amp; sp. nov., a non-ambrosial species that is closely related to the family. Three minor morphological variants of the pronotal disk mycangium of the Scolytoplatypodini were associated with ambrosia fungi in three respective clades of Ceratocystidaceae: Wolfgangiella gen. nov., Toshionella gen. nov., and Ambrosiella remansi sp. nov. Closely-related species that are not symbionts of ambrosia beetles are accommodated by Catunica adiposa gen. &amp; comb. nov. and Solaloca norvegica gen. &amp; comb. nov. The divergent morphology of the ambrosial genera and their phylogenetic placement among non-ambrosial genera suggest three domestication events in the Ceratocystidaceae. Estimated divergence dates for the ambrosia fungi and mycangia suggest that Scolytoplatypodini mycangia may have been the first to acquire Ceratocystidaceae symbionts and other ambrosial fungal genera emerged shortly after the evolution of new mycangium types. There is no evidence of reversion to a non-ambrosial lifestyle in the mycangial symbionts.},
}
@article {pmid33116134,
year = {2020},
author = {Weinmann, J and Weis, S and Sippel, J and Tulalamba, W and Remes, A and El Andari, J and Herrmann, AK and Pham, QH and Borowski, C and Hille, S and Schönberger, T and Frey, N and Lenter, M and VandenDriessche, T and Müller, OJ and Chuah, MK and Lamla, T and Grimm, D},
title = {Identification of a myotropic AAV by massively parallel in vivo evaluation of barcoded capsid variants.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {5432},
pmid = {33116134},
issn = {2041-1723},
mesh = {Animals ; Capsid ; Capsid Proteins/*genetics ; DNA Barcoding, Taxonomic ; Dependovirus/*genetics ; Female ; Gene Library ; Genetic Therapy/methods ; Genetic Variation ; *Genetic Vectors ; High-Throughput Nucleotide Sequencing ; Humans ; Mice ; Mice, Inbred C57BL ; Muscles/*metabolism/*virology ; Mutation ; Organ Specificity ; },
abstract = {Adeno-associated virus (AAV) forms the basis for several commercial gene therapy products and for countless gene transfer vectors derived from natural or synthetic viral isolates that are under intense preclinical evaluation. Here, we report a versatile pipeline that enables the direct side-by-side comparison of pre-selected AAV capsids in high-throughput and in the same animal, by combining DNA/RNA barcoding with multiplexed next-generation sequencing. For validation, we create three independent libraries comprising 183 different AAV variants including widely used benchmarks and screened them in all major tissues in adult mice. Thereby, we discover a peptide-displaying AAV9 mutant called AAVMYO that exhibits superior efficiency and specificity in the musculature including skeletal muscle, heart and diaphragm following peripheral delivery, and that holds great potential for muscle gene therapy. Our comprehensive methodology is compatible with any capsids, targets and species, and will thus facilitate and accelerate the stratification of optimal AAV vectors for human gene therapy.},
}
@article {pmid33111105,
year = {2020},
author = {Kulhanek, KR and Myers, DR and Ksionda, O and Vercoulen, Y and Romero-Moya, D and Roose, JP},
title = {Protocol for Barcoding T Cells Combined with Timed Stimulations.},
journal = {STAR protocols},
volume = {1},
number = {2},
pages = {100067},
pmid = {33111105},
issn = {2666-1667},
support = {P01 AI091580/AI/NIAID NIH HHS/United States ; R01 AI104789/AI/NIAID NIH HHS/United States ; R01 CA187318/CA/NCI NIH HHS/United States ; R01 HL120724/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Cells, Cultured ; Flow Cytometry/*methods ; *Fluorescent Dyes/chemistry/metabolism ; Mice ; *Molecular Probe Techniques ; Phosphorylation ; Receptors, Antigen, T-Cell/chemistry/metabolism ; Signal Transduction ; *T-Lymphocytes/chemistry/cytology/metabolism ; Time Factors ; },
abstract = {Stimulation of naive T lymphocytes via the T cell receptor (TCR) induces distinct phosphorylation patterns that can be used to explore various signaling pathways within the cell. This protocol can be used to characterize different perturbations to the signaling pathways and the variations in time of stimulation. Here, we provide a method of barcoding and consolidating a maximum of 24 different sample conditions using two florescent dyes. This single sample for phospho-staining and flow cytometry saves time and reagents. For complete details on the use and execution of this protocol, please refer to Krutzik and Nolan (2006), Krutzik et al. (2012), Vercoulen et al. (2017), Ksionda et al. (2018), and Myers et al. (2019).},
}
@article {pmid33111099,
year = {2020},
author = {Thrash, EM and Kleinsteuber, K and Hathaway, ES and Nazzaro, M and Haas, E and Hodi, FS and Severgnini, M},
title = {High-Throughput Mass Cytometry Staining for Immunophenotyping Clinical Samples.},
journal = {STAR protocols},
volume = {1},
number = {2},
pages = {100055},
pmid = {33111099},
issn = {2666-1667},
mesh = {Antibodies ; Flow Cytometry/*methods ; High-Throughput Screening Assays/*methods ; Humans ; Immunophenotyping/*methods ; Leukocytes, Mononuclear/chemistry/classification/cytology ; Mass Spectrometry/*methods ; Staining and Labeling ; },
abstract = {As mass cytometry (MC) is implemented in clinical settings, the need for robust, validated protocols that reduce batch effects between samples becomes increasingly important. Here, we present a streamlined MC workflow for high-throughput staining that generates reproducible data for up to 80 samples in a single experiment by combining reference sample spike-in and palladium-based mass-tag cell barcoding. Although labor intensive, this workflow decreases experimental variables and thus reduces technical error and mitigates batch effects.},
}
@article {pmid33108982,
year = {2020},
author = {Van Houtan, KS and Gagné, TO and Reygondeau, G and Tanaka, KR and Palumbi, SR and Jorgensen, SJ},
title = {Coastal sharks supply the global shark fin trade.},
journal = {Biology letters},
volume = {16},
number = {10},
pages = {20200609},
pmid = {33108982},
issn = {1744-957X},
mesh = {Animals ; Asia ; Australia ; Brazil ; Conservation of Natural Resources ; Europe ; Japan ; Mexico ; *Sharks/genetics ; },
abstract = {Progress in global shark conservation has been limited by constraints to understanding the species composition and geographic origins of the shark fin trade. Previous assessments that relied on earlier genetic techniques and official trade records focused on abundant pelagic species traded between Europe and Asia. Here, we combine recent advances in DNA barcoding and species distribution modelling to identify the species and source the geographic origin of fins sold at market. Derived models of species environmental niches indicated that shark fishing effort is concentrated within Exclusive Economic Zones, mostly in coastal Australia, Indonesia, the United States, Brazil, Mexico and Japan. By coupling two distinct tools, barcoding and niche modelling, our results provide new insights for monitoring and enforcement. They suggest stronger local controls of coastal fishing may help regulate the unsustainable global trade in shark fins.},
}
@article {pmid33106757,
year = {2020},
author = {Luo, G and Gao, Q and Zhang, S and Yan, B},
title = {Probing infectious disease by single-cell RNA sequencing: Progresses and perspectives.},
journal = {Computational and structural biotechnology journal},
volume = {18},
number = {},
pages = {2962-2971},
pmid = {33106757},
issn = {2001-0370},
abstract = {The increasing application of single-cell RNA sequencing (scRNA-seq) technology in life science and biomedical research has significantly increased our understanding of the cellular heterogeneities in immunology, oncology and developmental biology. This review will summarize the development of various scRNA-seq technologies; primarily discussing the application of scRNA-seq on infectious diseases, and exploring the current development, challenges, and potential applications of scRNA-seq technology in the future.},
}
@article {pmid33106579,
year = {2020},
author = {Urumarudappa, SKJ and Tungphatthong, C and Prombutara, P and Sukrong, S},
title = {DNA metabarcoding to unravel plant species composition in selected herbal medicines on the National List of Essential Medicines (NLEM) of Thailand.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {18259},
pmid = {33106579},
issn = {2045-2322},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/analysis/*genetics ; Herbal Medicine/*standards ; Plant Preparations/*classification/isolation &amp; purification/metabolism ; Plants, Medicinal/classification/*genetics ; Reproducibility of Results ; Thailand ; },
abstract = {Traditional medicines are widely traded across the globe and have received considerable attention in the recent past, with expectations of heightened demand in the future. However, there are increasing global concerns over admixture, which can affect the quality, safety, and efficacy of herbal medicinal products. In this study, we aimed to use DNA metabarcoding to identify 39 Thai herbal products on the Thai National List of Essential Medicines (NLEM) and assess species composition and admixture. Among the products, 24 samples were in-house-prepared formulations, and 15 samples were registered formulations. In our study, DNA metabarcoding analysis using ITS2 and rbcL barcode regions were employed to identify herbal ingredients mentioned in the products. The nuclear region, ITS2, was able to identify herbal ingredients in the products at the genus- and family-levels in 55% and 63% of cases, respectively. The chloroplast gene, rbcL, enabled genus- and family-level identifications in 58% and 73% of cases, respectively. In addition, plant species were detected in larger numbers (Family identified, absolute %) in registered herbal products than in in-house-prepared formulations. The level of fidelity increases concerns about the reliability of the products. This study highlights that DNA metabarcoding is a useful analytical tool when combined with advanced chemical techniques for the identification of plant species in highly processed, multi-ingredient herbal products.},
}
@article {pmid33106181,
year = {2020},
author = {Yeh, YM and Lin, PC and Lee, CT and Chen, SH and Lin, BW and Lin, SC and Chen, PC and Chan, RH and Shen, MR},
title = {Treatment monitoring of colorectal cancer by integrated analysis of plasma concentration and sequencing of circulating tumor DNA.},
journal = {Molecular cancer},
volume = {19},
number = {1},
pages = {150},
pmid = {33106181},
issn = {1476-4598},
mesh = {Aged ; Biomarkers, Tumor/blood/*genetics ; Circulating Tumor DNA/blood/*genetics ; Colorectal Neoplasms/blood/genetics/*pathology/surgery ; High-Throughput Nucleotide Sequencing ; Humans ; Lung Neoplasms/blood/genetics/*secondary/surgery ; Male ; *Mutation ; Neoplasm Recurrence, Local/blood/genetics/*pathology/surgery ; Prognosis ; },
abstract = {Circulating cell-free DNA (cfDNA) analysis is an important tool for cancer monitoring. The patient-specific mutations identified in colorectal cancer (CRC) tissues are usually used to design the cfDNA analysis. Despite high specificity in predicting relapse, the sensitivity in most studies is around 40-50%. To improve this weakness, we designed a cfDNA panel according to the CRC genomic landscape and recurrent-specific mutations. The pathological variants in cfDNA samples from 60 CRC patients were studied by a next-generation sequencing (NGS) method incorporating the dual molecular barcode. Interestingly, patients in the disease positive group had a significantly higher cfDNA concentration than those in the disease negative group. Based on receiver operating characteristic analysis, the cfDNA concentration of 7 ng/mL was selected into the analytical workflow. The sensitivity in determining the disease status was 72.4%, which represented a considerable improvement on prior studies, and the specificity remained high at 80.6%. Compared to standard imaging and laboratory studies, earlier detection of residual disease and clinical benefits were shown on two cases by this cfDNA assay. We conclude this integrative framework of cfDNA analytical pipeline with a satisfactory sensitivity and specificity could be used in postoperative CRC surveillance.},
}
@article {pmid33105814,
year = {2020},
author = {Park, I and Yang, S and Choi, G and Moon, BC and Song, JH},
title = {An Integrated Approach for Efficient and Accurate Medicinal Cuscutae Semen Identification.},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {11},
pages = {},
pmid = {33105814},
issn = {2223-7747},
support = {KSN2012320//Korea Institute of Oriental Medicine (KIOM)/ ; },
abstract = {To guarantee the safety and efficacy of herbal medicines, accurate identification and quality evaluation are crucial. The ripe dried seeds of Cuscuta australis R.Br. and C. chinensis Lam. are known as Cuscutae Semen (CS) and are widely consumed in Northeast Asia; however, the seeds of other species can be misidentified as CS owing to morphological similarities, leading to misuse. In this report, we propose a multilateral strategy combining microscopic techniques with statistical analysis and DNA barcoding using a genus-specific primer to facilitate the identification and authentication of CS. Morphology-based identification using microscopy revealed that the useful diagnostic characteristics included general shape, embryo exudation, hairiness, and testa ornamentation, which were used to develop an effective identification key. In addition, we conducted DNA barcoding-based identification to ensure accurate authentication. A novel DNA barcode primer was produced from the chloroplast rbcL gene by comparative analysis using Cuscuta chloroplast genome sequences, which allowed four Cuscuta species and adulterants to be discriminated completely. Therefore, this investigation overcame the limitations of universal DNA barcodes for Cuscuta species with high variability. We believe that this integrated approach will enable CS to be differentiated from other species, thereby improving its quality control and product safety in medicinal markets.},
}
@article {pmid33103674,
year = {2020},
author = {Zhang, P and Wang, W and Fu, H and Rich, J and Su, X and Bachman, H and Xia, J and Zhang, J and Zhao, S and Zhou, J and Huang, TJ},
title = {Deterministic droplet coding via acoustofluidics.},
journal = {Lab on a chip},
volume = {20},
number = {23},
pages = {4466-4473},
pmid = {33103674},
issn = {1473-0189},
support = {R33 CA223908/CA/NCI NIH HHS/United States ; R01 HD086325/HD/NICHD NIH HHS/United States ; R01 GM135486/GM/NIGMS NIH HHS/United States ; UG3 TR002978/TR/NCATS NIH HHS/United States ; R01 GM127714/GM/NIGMS NIH HHS/United States ; R01 GM132603/GM/NIGMS NIH HHS/United States ; },
mesh = {*Lab-On-A-Chip Devices ; *Microfluidics ; Water ; },
abstract = {Droplet microfluidics has become an indispensable tool for biomedical research and lab-on-a-chip applications owing to its unprecedented throughput, precision, and cost-effectiveness. Although droplets can be generated and screened in a high-throughput manner, the inability to label the inordinate amounts of droplets hinders identifying the individual droplets after generation. Herein, we demonstrate an acoustofluidic platform that enables on-demand, real-time dispensing, and deterministic coding of droplets based on their volumes. By dynamically splitting the aqueous flow using an oil jet triggered by focused traveling surface acoustic waves, a sequence of droplets with deterministic volumes can be continuously dispensed at a throughput of 100 Hz. These sequences encode barcoding information through the combination of various droplet lengths. As a proof-of-concept, we encoded droplet sequences into end-to-end packages (e.g., a series of 50 droplets), which consisted of an address barcode with binary volumetric combinations and a sample package with consistent volumes for hosting analytes. This acoustofluidics-based, deterministic droplet coding technique enables the tagging of droplets with high capacity and high error-tolerance, and can potentially benefit various applications involving single cell phenotyping and multiplexed screening.},
}
@article {pmid33101394,
year = {2020},
author = {Zheng, S and Poczai, P and Hyvönen, J and Tang, J and Amiryousefi, A},
title = {Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes.},
journal = {Frontiers in genetics},
volume = {11},
number = {},
pages = {576124},
pmid = {33101394},
issn = {1664-8021},
abstract = {Understanding the complexity of genomic structures and their unique architecture is linked with the power of visualization tools used to represent these features. Such tools should be able to provide a realistic and scalable version of genomic content. Here, we present an online organelle plotting tool focused on chloroplasts, which were developed to visualize the exclusive structure of these genomes. The distinguished unique features of this program include its ability to represent the Single Short Copy (SSC) regions in reverse complement, which allows the depiction of the codon usage bias index for each gene, along with the possibility of the minor mismatches between inverted repeat (IR) regions and user-specified plotting layers. The versatile color schemes and diverse functionalities of the program are specifically designed to reflect the accurate scalable representation of the plastid genomes. We introduce a Shiny app website for easy use of the program; a more advanced application of the tool is possible by further development and modification of the downloadable source codes provided online. The software and its libraries are completely coded in R, available at https://irscope.shinyapps.io/chloroplot/.},
}
@article {pmid33101393,
year = {2020},
author = {Peng, F and Zhao, Z and Xu, B and Han, J and Yang, Q and Lei, Y and Tian, B and Liu, ZL},
title = {Characteristics of Organellar Genomes and Nuclear Internal Transcribed Spacers in the Tertiary Relict Genus Dipelta and Their Phylogenomic Implications.},
journal = {Frontiers in genetics},
volume = {11},
number = {},
pages = {573226},
pmid = {33101393},
issn = {1664-8021},
abstract = {Dipelta (Caprifoliaceae) is a Tertiary relict genus endemic to China, comprising three species with horticultural and medicinal values. For the lack of genomic information, interspecific relationships and divergence times in the genus remain unresolved. In the present study, we assembled and characterized the complete plastomes, the partial mitogenomes, and nuclear internal transcribed spacer (ITS) fragments from genome skimming datasets of 14 Dipelta individuals. The plastomes were conserved in genomic structure, gene order, and gene content, but with highly variable repeat sequences. Three genes (rpl23, ycf1, ycf2) were examined with positive selection, and nine divergent hotpot regions (psbL, accD, rpl23, ycf2, ycf3, rbcL-accD, trnI-CAU-ycf2, ndhH-rps15, and rps18 intron) were potentially valuable for DNA barcodes. Contrasted to the variability in plastome sequences, mitogenomes contained 12 protein-coding genes with limited indels and nucleotide substitutions, and no gene was found under positive selection. Genes in organellar genomes tended to have a similar pattern of codon usage bias, with a preference of A/U ending codons. Phylogenetic trees constructed with plastomes, mitogenomes, and ITS sequences consistently supported that Dipelta was monophyletic, and Dipelta elegans was sister to the other two taxa. Interspecific divergences were estimated at about 33-37 Ma in the Eocene/Oligocene boundary, suggesting the paleo-endemism of the extant species as "living fossils" of the East Asian Flora. Our study well-exhibited that genome skimming could provide valuable genomic information to elucidate the evolutionary history of the complex group in a cost-efficient way.},
}
@article {pmid33101342,
year = {2020},
author = {Barcaccia, G and Palumbo, F and Scariolo, F and Vannozzi, A and Borin, M and Bona, S},
title = {Potentials and Challenges of Genomics for Breeding Cannabis Cultivars.},
journal = {Frontiers in plant science},
volume = {11},
number = {},
pages = {573299},
pmid = {33101342},
issn = {1664-462X},
abstract = {Cannabis (Cannabis sativa L.) is an influential yet controversial agricultural plant with a very long and prominent history of recreational, medicinal, and industrial usages. Given the importance of this species, we deepened some of the main challenges-along with potential solutions-behind the breeding of new cannabis cultivars. One of the main issues that should be fixed before starting new breeding programs is the uncertain taxonomic classification of the two main taxa (e.g., indica and sativa) of the Cannabis genus. We tried therefore to examine this topic from a molecular perspective through the use of DNA barcoding. Our findings seem to support a unique species system (C. sativa) based on two subspecies: C. sativa subsp. sativa and C. sativa subsp. indica. The second key issue in a breeding program is related to the dioecy behavior of this species and to the comprehension of those molecular mechanisms underlying flower development, the main cannabis product. Given the role of MADS box genes in flower identity, we analyzed and reorganized all the genomic and transcriptomic data available for homeotic genes, trying to decipher the applicability of the ABCDE model in Cannabis. Finally, reviewing the limits of the conventional breeding methods traditionally applied for developing new varieties, we proposed a new breeding scheme for the constitution of F1 hybrids, without ignoring the indisputable contribution offered by genomics. In this sense, in parallel, we resumed the main advances in the genomic field of this species and, ascertained the lack of a robust set of SNP markers, provided a discriminant and polymorphic panel of SSR markers as a valuable tool for future marker assisted breeding programs.},
}
@article {pmid33099700,
year = {2020},
author = {Matsuda, Y and Yamaguchi, Y and Matsuo, N and Uesugi, T and Ito, J and Yagame, T and Figura, T and Selosse, MA and Hashimoto, Y},
title = {Communities of mycorrhizal fungi in different trophic types of Asiatic Pyrola japonica sensu lato (Ericaceae).},
journal = {Journal of plant research},
volume = {133},
number = {6},
pages = {841-853},
doi = {10.1007/s10265-020-01233-9},
pmid = {33099700},
issn = {1618-0860},
support = {25304026//KAKENHI/ ; },
mesh = {DNA Barcoding, Taxonomic ; Heterotrophic Processes ; Japan ; *Mycorrhizae ; Phylogeny ; Plant Leaves ; Pyrola/*microbiology ; Rhizome ; Symbiosis ; },
abstract = {Mixotrophic plants obtain carbon by their own photosynthetic activity and from their root-associated mycorrhizal fungi. Mixotrophy is deemed a pre-adaptation for evolution of mycoheterotrophic nutrition, where plants fully depend on fungi and lose their photosynthetic activity. The aim of this study was to clarify mycorrhizal dependency and heterotrophy level in various phenotypes of mixotrophic Pyrola japonica (Ericaceae), encompassing green individuals, rare achlorophyllous variants (albinos) and a form with minute leaves, P. japonica f. subaphylla. These three phenotypes were collected in two Japanese forests. Phylogenetic analysis of both plants and mycorrhizal fungi was conducted based on DNA barcoding. Enrichment in [13]C among organs (leaves, stems and roots) of the phenotypes with reference plants and fungal fruitbodies were compared by measuring stable carbon isotopic ratio. All plants were placed in the same clade, with f. subaphylla as a separate subclade. Leaf [13]C abundances of albinos were congruent with a fully mycoheterotrophic nutrition, suggesting that green P. japonica leaves are 36.8% heterotrophic, while rhizomes are 74.0% heterotrophic. There were no significant differences in δ[13]C values among organs in both albino P. japonica and P. japonica f. subaphylla, suggesting full and high mycoheterotrophic nutrition, respectively. Among 55 molecular operational taxonomic units (OTUs) detected as symbionts, the genus Russula was the most abundant in each phenotype and its dominance was significantly higher in albino P. japonica and P. japonica f. subaphylla. Russula spp. detected in P. japonica f. subaphylla showed higher dissimilarity with other phenotypes. These results suggest that P. japonica sensu lato is prone to evolve mycoheterotrophic variants, in a process that changes its mycorrhizal preferences, especially towards the genus Russula for which this species has a marked preference.},
}
@article {pmid33096064,
year = {2021},
author = {Adeniran, AA and Hernández-Triana, LM and Ortega-Morales, AI and Garza-Hernández, JA and Cruz-Ramos, J and Chan-Chable, RJ and Vázquez-Marroquín, R and Huerta-Jiménez, H and Nikolova, NI and Fooks, AR and Rodríguez-Pérez, MA},
title = {Identification of mosquitoes (Diptera: Culicidae) from Mexico State, Mexico using morphology and COI DNA barcoding.},
journal = {Acta tropica},
volume = {213},
number = {},
pages = {105730},
doi = {10.1016/j.actatropica.2020.105730},
pmid = {33096064},
issn = {1873-6254},
mesh = {Aedes/anatomy &amp; histology/classification/genetics ; Animals ; Anopheles/anatomy &amp; histology/classification/genetics ; Culex/anatomy &amp; histology/classification/genetics ; Culicidae/anatomy &amp; histology/*classification/genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Genes, Mitochondrial ; Male ; Mexico ; Mitochondria/enzymology/genetics ; },
abstract = {Mosquitoes are commonly identified to species level using morphological traits, but complementary methods for identification are often necessary when specimens are collected as immature stages, stored inadequately, or when delineation of species complexes is problematic. DNA-barcoding using the mitochondrial cytochrome c oxidase subunit 1 (COI) gene is one such tool used for the morphological identification of species. A comprehensive entomological survey of mosquito species in Mexico State identified by COI DNA barcoding and morphology is documented in this paper. Specimens were collected from all the physiographic provinces in Mexico State between 2017 and 2019. Overall, 2,218 specimens were collected from 157 localities representing both subfamilies Anophelinae and Culicinae. A species checklist that consists of 6 tribes, 10 genera, 20 subgenera, and 51 species, 35 of which are new records for Mexico State, is provided. Three hundred and forty-two COI sequences of 46 species were analysed. Mean intraspecific and interspecific distances ranged between 0% to 3.9% and from 1.2% to 25.3%, respectively. All species groups were supported by high bootstraps values in a Neighbour-Joining analysis, and new COI sequences were generated for eight species: Aedes chionotum Zavortink, Ae. vargasi Schick, Ae. gabriel Schick, Ae. guerrero Berlin, Ae. ramirezi Vargas and Downs, Haemagogus mesodentatus Komp and Kumm, Culex restrictor Dyar and Knab, and Uranotaenia geometrica Theobald. This study provides a detailed inventory of the Culicidae from Mexico State and discusses the utility of DNA barcoding as a complementary tool for accurate mosquito species identification in Mexico.},
}
@article {pmid33095865,
year = {2021},
author = {Lumsden, GAM and Zakharov, EV and Dolynskyj, S and Weese, JS and Lindsay, LR and Jardine, C},
title = {Temporal Detection Limits of Remnant Larval Bloodmeals in Nymphal Ixodes scapularis (Say, Ixodida: Ixodidae) Using Two Next-Generation Sequencing DNA Barcoding Assays.},
journal = {Journal of medical entomology},
volume = {58},
number = {2},
pages = {821-829},
doi = {10.1093/jme/tjaa192},
pmid = {33095865},
issn = {1938-2928},
mesh = {Animals ; *Blood ; DNA Barcoding, Taxonomic/methods ; Electron Transport Complex IV/genetics ; *Feeding Behavior ; Genetic Techniques ; High-Throughput Nucleotide Sequencing ; Host-Parasite Interactions ; Ixodes/*physiology ; Larva/physiology ; Limit of Detection ; Nymph/physiology ; Rabbits ; Vertebrates/classification/*genetics ; },
abstract = {Using next-generation sequencing DNA barcoding, we aimed to determine: 1) if the larval bloodmeal can be detected in Ixodes scapularis nymphs and 2) the post-moult temporal window for detection of the larval bloodmeal. Subsets of 30 nymphs fed on a domestic rabbit (Oryctolagus cuniculus Linnaeus, Lagomorphia: Leporidae) as larvae were reared and frozen at 11 time points post-moult, up to 150 d. Vertebrate DNA was amplified using novel universal (UP) and species-specific primers (SSP) and sequenced for comparison against cytochrome c oxidase subunit I barcodes to infer host identification. Detectable bloodmeals decreased as time since moult increased for both assays. For the SSP assay, detection of bloodmeals decreased from 96.7% (n = 29/30) in day 0 nymphs to 3.3% (n = 1/30) and 6.7% (n = 2/30) at 4- and 5-mo post-moult, respectively. A shorter temporal detection period was achieved with the UP assay, declining from 16.7% (n = 5/30) in day 0 nymphs to 0/30 in 3-d-old nymphs. Bloodmeal detection was nonexistent for the remaining cohorts, with the exception of 1/30 nymphs at 2-mo post-moult. Host detection was significantly more likely using the SSP assay compared to the UP assay in the first three time cohorts (day 0: χ 2 = 39.1, P < 0.005; day 2: χ 2 = 19.2, P < 0.005; day 3: χ 2 = 23.3, P < 0.005). Regardless of the primer set used, the next-generation sequencing DNA barcoding assay was able to detect host DNA from a larval bloodmeal in the nymphal life stage; however, a short window with a high proportion of detection post-moult was achieved.},
}
@article {pmid33088623,
year = {2020},
author = {Fasanello, VJ and Liu, P and Botero, CA and Fay, JC},
title = {High-throughput analysis of adaptation using barcoded strains of Saccharomyces cerevisiae.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e10118},
pmid = {33088623},
issn = {2167-8359},
support = {R01 GM080669/GM/NIGMS NIH HHS/United States ; },
abstract = {BACKGROUND: Experimental evolution of microbes can be used to empirically address a wide range of questions about evolution and is increasingly employed to study complex phenomena ranging from genetic evolution to evolutionary rescue. Regardless of experimental aims, fitness assays are a central component of this type of research, and low-throughput often limits the scope and complexity of experimental evolution studies. We created an experimental evolution system in Saccharomyces cerevisiae that utilizes genetic barcoding to overcome this challenge.<br><br>RESULTS: We first confirm that barcode insertions do not alter fitness and that barcode sequencing can be used to efficiently detect fitness differences via pooled competition-based fitness assays. Next, we examine the effects of ploidy, chemical stress, and population bottleneck size on the evolutionary dynamics and fitness gains (adaptation) in a total of 76 experimentally evolving, asexual populations by conducting 1,216 fitness assays and analyzing 532 longitudinal-evolutionary samples collected from the evolving populations. In our analysis of these data we describe the strengths of this experimental evolution system and explore sources of error in our measurements of fitness and evolutionary dynamics.<br><br>CONCLUSIONS: Our experimental treatments generated distinct fitness effects and evolutionary dynamics, respectively quantified via multiplexed fitness assays and barcode lineage tracking. These findings demonstrate the utility of this new resource for designing and improving high-throughput studies of experimental evolution. The approach described here provides a framework for future studies employing experimental designs that require high-throughput multiplexed fitness measurements.},
}
@article {pmid33087755,
year = {2020},
author = {Milan, DT and Mendes, IS and Damasceno, JS and Teixeira, DF and Sales, NG and Carvalho, DC},
title = {New 12S metabarcoding primers for enhanced Neotropical freshwater fish biodiversity assessment.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {17966},
pmid = {33087755},
issn = {2045-2322},
mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/*genetics ; DNA, Ribosomal/*genetics ; Databases, Genetic ; Fishes/*genetics ; Gene Library ; Mitochondria/genetics ; Species Specificity ; },
abstract = {The megadiverse Neotropical fish fauna lacks a comprehensive and reliable DNA reference database, which hampers precise species identification and DNA based biodiversity assessment in the region. Here, we developed a mitochondrial 12S ribosomal DNA reference database for 67 fish species, representing 54 genera, 25 families, and six major Neotropical orders. We aimed to develop mini-barcode markers (i.e. amplicons with less than 200 bp) suitable for DNA metabarcoding by evaluating the taxonomic resolution of full-length and mini-barcodes and to determine a threshold value for fish species delimitation using 12S. Evaluation of the target amplicons demonstrated that both full-length library (565 bp) and mini-barcodes (193 bp) contain enough taxonomic resolution to differentiate all 67 fish species. For species delimitation, interspecific genetic distance threshold values of 0.4% and 0.55% were defined using full-length and mini-barcodes, respectively. A custom reference database and specific mini-barcode markers are important assets for ecoregion scale DNA based biodiversity assessments (such as environmental DNA) that can help with the complex task of conserving the megadiverse Neotropical ichthyofauna.},
}
@article {pmid33086048,
year = {2021},
author = {Shashkova, S and Nyström, T and Leake, MC and Wollman, AJM},
title = {Correlative single-molecule fluorescence barcoding of gene regulation in Saccharomyces cerevisiae.},
journal = {Methods (San Diego, Calif.)},
volume = {193},
number = {},
pages = {62-67},
pmid = {33086048},
issn = {1095-9130},
support = {BB/P000746/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Fluorescence ; Gene Expression Regulation ; Gene Expression Regulation, Fungal ; Repressor Proteins ; *Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Transcription Factors/genetics/metabolism ; },
abstract = {Most cells adapt to their environment by switching combinations of genes on and off through a complex interplay of transcription factor proteins (TFs). The mechanisms by which TFs respond to signals, move into the nucleus and find specific binding sites in target genes is still largely unknown. Single-molecule fluorescence microscopes, which can image single TFs in live cells, have begun to elucidate the problem. Here, we show that different environmental signals, in this case carbon sources, yield a unique single-molecule fluorescence pattern of foci of a key metabolic regulating transcription factor, Mig1, in the nucleus of the budding yeast, Saccharomyces cerevisiae. This pattern serves as a 'barcode' of the gene regulatory state of the cells which can be correlated with cell growth characteristics and other biological function.},
}
@article {pmid33083125,
year = {2020},
author = {Bozáňová, J and Čiamporová Zat'ovičová, Z and Čiampor, F and Mamos, T and Grabowski, M},
title = {The tale of springs and streams: how different aquatic ecosystems impacted the mtDNA population structure of two riffle beetles in the Western Carpathians.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e10039},
pmid = {33083125},
issn = {2167-8359},
abstract = {The Western Carpathians are a particularly interesting part of the Carpathian Arc. According to recent molecular data upon aquatic and terrestrial taxa, this mountain area is an important biodiversity hotspot of Europe. Moreover, the W Carpathians include rich systems of karst springs inhabited by specific fauna, where molecular diversity and phylogeographic patterns are yet to be fully explored. Our study aims to compare population genetic structure and molecular diversity of two related and commonly co-occurring riffle beetles, Elmis aenea (PWJ Müller, 1806) and Limnius perrisi (Dufour, 1843) in the springs and streams of the W Carpathians using the mitochondrial DNA barcoding fragment of the cytochrome c oxidase subunit I gene (COI). The relatively stable thermal and chemical conditions of springs throughout unfavourable climatic settings make these highly specific lotic systems potentially ideal for a long-term survival of some aquatic biota. Populations of both elmid species were relatively homogeneous genetically, with a single dominant haplotype. However, we revealed that E. aenea significantly dominated in the springs, while L. perrisi preferred streams. Relative isolation of the springs and their stable conditions were reflected in significantly higher molecular diversity of the E. aenea population in comparison to L. perrisi. The results of Bayesian Skyline Plot analysis also indicated the exceptional position of springs regarding maintaining the population size of E. aenea. On the other hand, it seems that streams in the W Carpathians provide more effective dispersal channels for L. perrisi, whose population expanded much earlier compared to E. aenea. Present study points out that different demographic histories of these two closely related elmid species are manifested by their different habitat preference and molecular diversity.},
}
@article {pmid33082418,
year = {2020},
author = {Palumbo, F and Scariolo, F and Vannozzi, A and Barcaccia, G},
title = {NGS-based barcoding with mini-COI gene target is useful for pet food market surveys aimed at mislabelling detection.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {17767},
pmid = {33082418},
issn = {2045-2322},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; *Food ; *Food Labeling ; *Food-Processing Industry ; *High-Throughput Nucleotide Sequencing ; Pets ; },
abstract = {Pet food industry has grown considerably in the last few years and it is expected to continue with this rate. Despite the economic impact of this sector and the consumer concerns for the increasing number of food and feed adulteration cases, few studies have been published on mislabelling in pet foods. We therefore investigated the capability of a next generation sequencing-based mini-barcoding approach to identify animal species in pet food products. In a preliminary analysis, a 127 bp fragment of the COI gene was tested on both individual specimens and ad hoc mixed fresh samples used as testers, to evaluate its discrimination power and primers effectiveness. Eighteen pet food products of different price categories and forms available on the market (i.e. kibbles, bites, pâté and strips) were analysed through an NGS approach in biological replicates. At least one of the species listed in the ingredients was not detected in half of the products, while seven products showed supplementary species in addition to those stated on the label. Due to the accuracy, sensitivity and specificity demonstrated, this method can be proposed as food genetic traceability system to evaluate both the feed and food quality timely along the supply chain.},
}
@article {pmid33081815,
year = {2020},
author = {Fola, AA and Kattenberg, E and Razook, Z and Lautu-Gumal, D and Lee, S and Mehra, S and Bahlo, M and Kazura, J and Robinson, LJ and Laman, M and Mueller, I and Barry, AE},
title = {SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics.},
journal = {Malaria journal},
volume = {19},
number = {1},
pages = {375},
pmid = {33081815},
issn = {1475-2875},
support = {U19 AI089686/AI/NIAID NIH HHS/United States ; },
mesh = {DNA Barcoding, Taxonomic/*methods ; Genetics, Population/*instrumentation ; Humans ; Malaria, Vivax/parasitology ; *Microsatellite Repeats ; Plasmodium vivax/*genetics ; *Polymorphism, Single Nucleotide ; },
abstract = {BACKGROUND: Genomic surveillance of malaria parasite populations has the potential to inform control strategies and to monitor the impact of interventions. Barcodes comprising large numbers of single nucleotide polymorphism (SNP) markers are accurate and efficient genotyping tools, however may need to be tailored to specific malaria transmission settings, since 'universal' barcodes can lack resolution at the local scale. A SNP barcode was developed that captures the diversity and structure of Plasmodium vivax populations of Papua New Guinea (PNG) for research and surveillance.<br><br>METHODS: Using 20 high-quality P. vivax genome sequences from PNG, a total of 178 evenly spaced neutral SNPs were selected for development of an amplicon sequencing assay combining a series of multiplex PCRs and sequencing on the Illumina MiSeq platform. For initial testing, 20 SNPs were amplified in a small number of mono- and polyclonal P. vivax infections. The full barcode was then validated by genotyping and population genetic analyses of 94 P. vivax isolates collected between 2012 and 2014 from four distinct catchment areas on the highly endemic north coast of PNG. Diversity and population structure determined from the SNP barcode data was then benchmarked against that of ten microsatellite markers used in previous population genetics studies.<br><br>RESULTS: From a total of 28,934,460 reads generated from the MiSeq Illumina run, 87% mapped to the PvSalI reference genome with deep coverage (median&#x2009;=&#x2009;563, range 56-7586) per locus across genotyped samples. Of 178 SNPs assayed, 146 produced high-quality genotypes (minimum coverage&#x2009;=&#x2009;56X) in more than 85% of P. vivax isolates. No amplification bias was introduced due to either polyclonal infection or whole genome amplification (WGA) of samples before genotyping. Compared to the microsatellite panels, the SNP barcode revealed greater variability in genetic diversity between populations and geographical population structure. The SNP barcode also enabled assignment of genotypes according to their geographic origins with a significant association between genetic distance and geographic distance at the sub-provincial level.<br><br>CONCLUSIONS: High-throughput SNP barcoding can be used to map variation of malaria transmission dynamics at sub-national resolution. The low cost per sample and genotyping strategy makes the transfer of this technology to field settings highly feasible.},
}
@article {pmid33080083,
year = {2021},
author = {Dal Forno, M and Lawrey, JD and Sikaroodi, M and Gillevet, PM and Schuettpelz, E and Lücking, R},
title = {Extensive photobiont sharing in a rapidly radiating cyanolichen clade.},
journal = {Molecular ecology},
volume = {30},
number = {8},
pages = {1755-1776},
doi = {10.1111/mec.15700},
pmid = {33080083},
issn = {1365-294X},
mesh = {*Agaricales ; *Lichens/genetics ; Phylogeny ; Symbiosis/genetics ; },
abstract = {Recent studies have uncovered remarkable diversity in Dictyonema s.lat. basidiolichens, here recognized as subtribe Dictyonemateae. This group includes five genera and 148 species, but hundreds more await description. The photobionts of these lichens belong to Rhizonema, a recently resurrected cyanobacterial genus known by a single species. To further investigate photobiont diversity within Dictyonemateae, we generated 765 new cyanobacterial sequences from 635 specimens collected from 18 countries. The ITS barcoding locus supported the recognition of 200 mycobiont (fungal) species among these samples, but the photobiont diversity was comparatively low. Our analyses revealed three main divisions of Rhizonema, with two repeatedly recovered as monophyletic (proposed as new species), and the third mostly paraphyletic. The paraphyletic lineage corresponds to R. interruptum and partnered with mycobionts from all five genera in Dictyonemateae. There was no evidence of photobiont-mycobiont co-speciation, but one of the monophyletic lineages of Rhizonema appears to partner predominantly with one of the two major clades of Cora (mycobiont) with samples collected largely from the northern Andes. Molecular clock estimations indicate the Rhizonema species are much older than the fungal species in the Dictyonemateae, suggesting that these basidiolichens obtained their photobionts from older ascolichen lineages and the photobiont variation in extant lineages of Dictyonemateae is the result of multiple photobiont switches. These results support the hypothesis of lichens representing "fungal farmers," in which diverse mycobiont lineages associate with a substantially lower diversity of photobionts by sharing those photobionts best suited for the lichen symbiosis among multiple and often unrelated mycobiont lineages.},
}
@article {pmid33079486,
year = {2020},
author = {Agusil, JP and Arjona, MI and Duch, M and Fusté, N and Plaza, JA},
title = {Multidimensional Anisotropic Architectures on Polymeric Microparticles.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {16},
number = {46},
pages = {e2004691},
doi = {10.1002/smll.202004691},
pmid = {33079486},
issn = {1613-6829},
mesh = {Anisotropy ; *Polymers ; *Printing ; Printing, Three-Dimensional ; },
abstract = {Next generation life science technologies will require the integration of building blocks with tunable physical and chemical architectures at the microscale. A central issue is to govern the multidimensional anisotropic space that defines these microparticle attributes. However, this control is limited to one or few dimensions due to profound fabrication tradeoffs, a problem that is exacerbated by miniaturization. Here, a vast number of anisotropic dimensions are integrated combining SU-8 photolithography with (bio)chemical modifications via soft-lithography. Microparticles in a 15-D anisotropic space are demonstrated, covering branching, faceting, fiducial, topography, size, aspect ratio, stiffness, (bio)molecular and quantum dot printing, top/bottom surface coverage, and quasi-0D, 1D, 2D, and 3D surface patterning. The strategy permits controlled miniaturization on physical dimensions below 1 µm and molecular patterns below 1 µm[2] . By combining building blocks, anisotropic microparticles detect pH changes, form the basis for a DNA-assay recognition platform, and obtain an extraordinary volumetric barcoding density up to 1093 codes µm[-3] in a 3 × 12 × 0.5 µm[3] volume.},
}
@article {pmid33077960,
year = {2021},
author = {Aksel, T and Yu, Z and Cheng, Y and Douglas, SM},
title = {Molecular goniometers for single-particle cryo-electron microscopy of DNA-binding proteins.},
journal = {Nature biotechnology},
volume = {39},
number = {3},
pages = {378-386},
pmid = {33077960},
issn = {1546-1696},
support = {S10 OD020054/OD/NIH HHS/United States ; F32 GM119322/GM/NIGMS NIH HHS/United States ; R01 HL134183/HL/NHLBI NIH HHS/United States ; R35 GM125027/GM/NIGMS NIH HHS/United States ; R01 GM098672/GM/NIGMS NIH HHS/United States ; S10 OD021741/OD/NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Cryoelectron Microscopy/*methods ; DNA/*chemistry ; DNA-Binding Proteins/chemistry/*ultrastructure ; Nucleic Acid Conformation ; Protein Conformation ; },
abstract = {Correct reconstruction of macromolecular structure by cryo-electron microscopy (cryo-EM) relies on accurate determination of the orientation of single-particle images. For small (<100 kDa) DNA-binding proteins, obtaining particle images with sufficiently asymmetric features to correctly guide alignment is challenging. We apply DNA origami to construct molecular goniometers-instruments that precisely orient objects-and use them to dock a DNA-binding protein on a double-helix stage that has user-programmable tilt and rotation angles. We construct goniometers with 14 different stage configurations to orient and visualize the protein just above the cryo-EM grid surface. Each goniometer has a distinct barcode pattern that we use during particle classification to assign angle priors to the bound protein. We use goniometers to obtain a 6.5-Å structure of BurrH, an 82-kDa DNA-binding protein whose helical pseudosymmetry prevents accurate image orientation using traditional cryo-EM. Our approach should be adaptable to other DNA-binding proteins as well as small proteins fused to DNA-binding domains.},
}
@article {pmid33077803,
year = {2020},
author = {Sauer, FG and Jaworski, L and Erdbeer, L and Heitmann, A and Schmidt-Chanasit, J and Kiel, E and Lühken, R},
title = {Geometric morphometric wing analysis represents a robust tool to identify female mosquitoes (Diptera: Culicidae) in Germany.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {17613},
pmid = {33077803},
issn = {2045-2322},
mesh = {Aedes/anatomy &amp; histology/genetics ; Animals ; Culicidae/*anatomy &amp; histology/genetics ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Germany ; Wings, Animal/*anatomy &amp; histology ; },
abstract = {Accurate species identification is the prerequisite to assess the relevance of mosquito specimens, but is often hindered by missing or damaged morphological features. The present study analyses the applicability of wing geometric morphometrics as a low-cost and practical alternative to identify native mosquitoes in Germany. Wing pictures were collected for 502 female mosquitoes of five genera and 19 species from 80 sampling sites. The reliable species identification based on interspecific wing geometry of 18 landmarks per specimen was tested. Leave-one-out cross validation revealed an overall accuracy of 99% for the genus and 90% for the species identification. Misidentifications were mainly due to three pairings of Aedes species: Aedes annulipes vs. Aedes cantans, Aedes cinereus vs. Aedes rossicus and Aedes communis vs. Aedes punctor. Cytochrome oxidase subunit I (COI) gene region was sequenced to validate the morphological and morphometric identification. Similar to the results of the morphometric analysis, the same problematic three Aedes-pairs clustered, but most other species could be well separated. Overall, our study underpins that morphometric wing analysis is a robust tool for reliable mosquito identification, which reach the accuracy of COI barcoding.},
}
@article {pmid33075070,
year = {2020},
author = {Egydio Brandão, APM and Yamaguchi, LF and Tepe, EJ and Salatino, A and Kato, MJ},
title = {Evaluation of DNA markers for molecular identification of three Piper species from Brazilian Atlantic Rainforest.},
journal = {PloS one},
volume = {15},
number = {10},
pages = {e0239056},
pmid = {33075070},
issn = {1932-6203},
mesh = {Brazil ; Cluster Analysis ; DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; DNA, Ribosomal Spacer/genetics ; Genetic Markers ; Genetic Variation ; Microsatellite Repeats ; Phylogeny ; Piper/*classification/*genetics ; Rainforest ; Species Specificity ; },
abstract = {Piper is one of two large genera in the Piperaceae, and with ca. 2600 species, is one of the largest plant genera in the world. Species delimitation and evaluation of genetic diversity among populations are important requisites for conservation and adequate exploitation of economically important species. DNA barcoding has been used as a powerful tool and a practical method for species characterization and delimitation. The present work aims to evaluate molecular markers for barcoding three Piper species native to Brazil: P. gaudichaudianum ("jaborandi" or "pariparoba"), P. malacophyllum ("pariparoba-murta") and P. regnellii ("caapeba" or "pariparoba"). A reference DNA barcode library was developed using sequences of three candidate regions: ITS2, trnH-psbA and rbcL. Transferability of the microsatellite (SSR) primers Psol 3, Psol 6 and Psol 10, designed originally for Piper solmsianum, to the three Piper species was also evaluated. The discriminatory power of the markers was based on the determination of inter- and intraspecific distances, phylogenetic reconstruction, and clustering analysis, as well as BLASTn comparison. Sequences of ITS2 enabled efficient species identification by means of the BLASTn procedure. Based on these sequences, intraspecific divergence was lower than interspecific variation. Maximum Parsimony analyses based on ITS2 sequences provided three resolved clades, each corresponding to one of the three analysed species. Sequences of trnH-psbA and rbcL had lower discriminatory value. Analyses combining sequences of these regions were less effective toward the attainment of resolved and strongly supported clades of all species. In summary, robustly supported clades of P. regnellii were obtained in most of the analyses, based either on isolated or combined sequences. The SSRs primers Psol 3, Psol 6 and Psol 10 were shown to be transferable to P. gaudichaudianum and P. regnellii, but not to P. malacophyllum. Preliminary cluster analyses based on the polymorphism of the amplified products suggested that Psol 3 has lower potential than Psol 6 and Psol 10 for discrimination of Piper species.},
}
@article {pmid33074148,
year = {2021},
author = {Kwak, ML and Chavatte, JM and Chew, KL and Lee, BPY},
title = {Emergence of the zoonotic tick Dermacentor (Indocentor) auratus Supino, 1897 (Acari: Ixodidae) in Singapore.},
journal = {Ticks and tick-borne diseases},
volume = {12},
number = {1},
pages = {101574},
doi = {10.1016/j.ttbdis.2020.101574},
pmid = {33074148},
issn = {1877-9603},
mesh = {*Animal Distribution ; Animals ; Child ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/analysis ; Dermacentor/enzymology/genetics/*physiology ; Electron Transport Complex IV/analysis ; Female ; Humans ; Male ; Middle Aged ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA ; Singapore ; Tick Infestations/*parasitology ; },
abstract = {Though ticks pose a significant public health risk, until recently, little research had focused on the diversity of ticks and tick-borne diseases in Singapore. To date, only fourteen tick species in five genera have been recorded there. For the first time, Dermacentor auratus is recorded from Singapore from a range of hosts, including humans. DNA sequences are provided at 2 loci, for D. auratus, the cytochrome c oxidase I (COI) for DNA barcoding and the 16S large subunit ribosomal RNA (16S lsu rRNA). The health risk posed by D. auratus in Singapore is discussed.},
}
@article {pmid33072904,
year = {2020},
author = {Chiou, CY and Shih, HC and Tsai, CC and Jin, XL and Ko, YZ and Mantiquilla, JA and Weng, IS and Chiang, YC},
title = {The genetic relationships of Indian jujube (Ziziphus mauritiana Lam.) cultivars using SSR markers.},
journal = {Heliyon},
volume = {6},
number = {10},
pages = {e05078},
pmid = {33072904},
issn = {2405-8440},
abstract = {The genetic relationships among 24 Indian jujube cultivars (Ziziphus mauritiana Lam.) were evaluated by genotyping the microsatellite loci using simple sequence repeat (SSR) markers. The SSR loci were scored by fluorescent labelling and automated detection systems for the high-throughput capillary electrophoresis and high-resolution gel electrophoresis. Out of the 29 newly characterized SSR loci, 26 were considered as polymorphic with a total of 181 alleles obtained. The number of alleles ranged from 2-12, while the polymorphism information content ranged from 0.08-0.83, and the expected and observed heterozygosity were 0.04-0.83 and 0.04-0.82, respectively. The allele pattern of Indian jujube for all SSR loci confirmed its karyotype as tetraploid. Similarity coefficients and UPGMA dendrogram revealed that the Taiwanese cultivars consisted of a large 'A' clade, which is further divided into 'A1' and 'A2' groups, and the 'B' clade where both are rooted by the wild accession, 'Chad native'. These four genetic clusters were supported by the results of PCoA and the assignment test. The excess of heterozygotes based on F-statistics was attributed to its mating system as outcrossing and self-incompatible, and the introgression of the presumed mutation-derived cultivars with genetic admixture. Based on this study, SSR markers offer valuable information on the genetic relationship of this tropical fruit tree which is basically in agreement with the genealogy of its breeding history.},
}
@article {pmid33072294,
year = {2020},
author = {Gaytán, &#xc1; and Bergsten, J and Canelo, T and Pérez-Izquierdo, C and Santoro, M and Bonal, R},
title = {DNA Barcoding and geographical scale effect: The problems of undersampling genetic diversity hotspots.},
journal = {Ecology and evolution},
volume = {10},
number = {19},
pages = {10754-10772},
pmid = {33072294},
issn = {2045-7758},
abstract = {DNA barcoding identification needs a good characterization of intraspecific genetic divergence to establish the limits between species. Yet, the number of barcodes per species is many times low and geographically restricted. A poor coverage of the species distribution range may hamper identification, especially when undersampled areas host genetically distinct lineages. If so, the genetic distance between some query sequences and reference barcodes may exceed the maximum intraspecific threshold for unequivocal species assignation. Taking a group of Quercus herbivores (moths) in Europe as model system, we found that the number of DNA barcodes from southern Europe is proportionally very low in the Barcoding of Life Data Systems. This geographical bias complicates the identification of southern query sequences, due to their high intraspecific genetic distance with respect to barcodes from higher latitudes. Pairwise intraspecific genetic divergence increased along with spatial distance, but was higher when at least one of the sampling sites was in southern Europe. Accordingly, GMYC (General Mixed Yule Coalescent) single-threshold model retrieved clusters constituted exclusively by Iberian haplotypes, some of which could correspond to cryptic species. The number of putative species retrieved was more reliable than that of multiple-threshold GMYC but very similar to results from ABGD and jMOTU. Our results support GMYC as a key resource for species delimitation within poorly inventoried biogeographic regions in Europe, where historical factors (e.g., glaciations) have promoted genetic diversity and singularity. Future European DNA barcoding initiatives should be preferentially performed along latitudinal gradients, with special focus on southern peninsulas.},
}
@article {pmid33071802,
year = {2020},
author = {Garcia-Gonzalez, I and Mühleder, S and Fernández-Chacón, M and Benedito, R},
title = {Genetic Tools to Study Cardiovascular Biology.},
journal = {Frontiers in physiology},
volume = {11},
number = {},
pages = {1084},
pmid = {33071802},
issn = {1664-042X},
support = {J 4358/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Progress in biomedical science is tightly associated with the improvement of methods and genetic tools to manipulate and analyze gene function in mice, the most widely used model organism in biomedical research. The joint effort of numerous individual laboratories and consortiums has contributed to the creation of a large genetic resource that enables scientists to image cells, probe signaling pathways activities, or modify a gene function in any desired cell type or time point, à la carte. However, as these tools significantly increase in number and become more sophisticated, it is more difficult to keep track of each tool's possibilities and understand their advantages and disadvantages. Knowing the best currently available genetic technology to answer a particular biological question is key to reach a higher standard in biomedical research. In this review, we list and discuss the main advantages and disadvantages of available mammalian genetic technology to analyze cardiovascular cell biology at higher cellular and molecular resolution. We start with the most simple and classical genetic approaches and end with the most advanced technology available to fluorescently label cells, conditionally target their genes, image their clonal expansion, and decode their lineages.},
}
@article {pmid33070327,
year = {2021},
author = {Mojekwu, TO and Cunningham, MJ and Bills, RI and Pretorius, PC and Hoareau, TB},
title = {Utility of DNA barcoding in native Oreochromis species.},
journal = {Journal of fish biology},
volume = {98},
number = {2},
pages = {498-506},
doi = {10.1111/jfb.14594},
pmid = {33070327},
issn = {1095-8649},
support = {//University of Pretoria/ ; },
mesh = {Animals ; DNA Barcoding, Taxonomic/*standards ; Fisheries ; Genes, Mitochondrial ; Genetic Variation ; Phylogeny ; Species Specificity ; Tilapia/*classification/*genetics ; },
abstract = {The importance of Oreochromis in worldwide aquaculture and regional fisheries motivates the study of their genetic diversity in their native range. In this article, all mitochondrial cytochrome c oxidase subunit I gene (COI) sequences of Oreochromis species are retrieved from Barcode of Life Data system to quantify the available DNA barcoding information from wild individuals collected within the native ranges of the respective species. It is found that 70% of the known species in the genus still lack a COI barcode, and only 15% of the available sequences are from within the respective native ranges. Many of the available sequences have been produced from specimens acquired from aquaculture and introduced, naturalized populations, making the assessment of variation within the original native range challenging. Analyses of the wild-collected fraction of available sequences indicated the presence of cryptic lineages within Nile tilapia Oreochromis niloticus and O. schwebischi, the occurrence of potential introgressive hybridization between O. niloticus and blue tilapia O. aureus, and potential ancestral polymorphism between Karonga tilapia O. karongae and black tilapia O. placidus. This article also reports a case of misidentification of O. mweruensis as longfin tilapia O. macrochir. These results stress the importance of improving the knowledge of genetic variation within the native ranges of Oreochromis species for better-informed conservation of these natural resources.},
}
@article {pmid33068532,
year = {2020},
author = {Raj, B and Farrell, JA and Liu, J and El Kholtei, J and Carte, AN and Navajas Acedo, J and Du, LY and McKenna, A and Relić, &#x110; and Leslie, JM and Schier, AF},
title = {Emergence of Neuronal Diversity during Vertebrate Brain Development.},
journal = {Neuron},
volume = {108},
number = {6},
pages = {1058-1074.e6},
pmid = {33068532},
issn = {1097-4199},
support = {R00 HG010152/HG/NHGRI NIH HHS/United States ; K99 HD091291/HD/NICHD NIH HHS/United States ; //CIHR/Canada ; R01 HD085905/HD/NICHD NIH HHS/United States ; K99 HD098298/HD/NICHD NIH HHS/United States ; DP1 HD094764/HD/NICHD NIH HHS/United States ; K99 HG010152/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; Brain/cytology/*growth &amp; development ; Cell Differentiation/physiology ; Cell Lineage/*physiology ; Gene Expression Regulation, Developmental ; Neurogenesis/*physiology ; Neurons/*cytology ; Zebrafish/*genetics ; },
abstract = {Neurogenesis comprises many highly regulated processes including proliferation, differentiation, and maturation. However, the transcriptional landscapes underlying brain development are poorly characterized. We describe a developmental single-cell catalog of ∼220,000 zebrafish brain cells encompassing 12 stages from embryo to larva. We characterize known and novel gene markers for ∼800 clusters and provide an overview of the diversification of neurons and progenitors across these time points. We also introduce an optimized GESTALT lineage recorder that enables higher expression and recovery of Cas9-edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post-embryonic stages. Reconstruction of cell specification trajectories reveals that late-stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis.},
}
@article {pmid33067865,
year = {2021},
author = {Martin, GK and Beisner, BE and Chain, FJJ and Cristescu, ME and Del Giorgio, PA and Derry, AM},
title = {Freshwater zooplankton metapopulations and metacommunities respond differently to environmental and spatial variation.},
journal = {Ecology},
volume = {102},
number = {1},
pages = {e03224},
doi = {10.1002/ecy.3224},
pmid = {33067865},
issn = {1939-9170},
mesh = {Animals ; Biodiversity ; Canada ; *Ecosystem ; Fresh Water ; *Zooplankton ; },
abstract = {Theory predicts that population genetic structure and metacommunity structure are linked by the common processes of drift and migration, but how population genetic structure and metacommunity structure are related in nature is still unknown. Deeper understanding of the processes influencing both genetic and community diversity is vital for better predicting how environmental change will impact biodiversity patterns. We examined how crustacean zooplankton and rotifer species' metapopulation genetic structure and metacommunities respond to environmental and spatial variation both within and across four regions of boreal Canada. Metapopulation and metacommunity variation partitioning results were compared within and across the four regions. Metapopulations and metacommunities responded differently to environmental variation and spatial structure both within and across regions, as metapopulations were influenced by different environmental variables compared to metacommunities. At larger spatial scales both metapopulations and metacommunities exhibited greater spatial and environmental structuring, again responding to a different subset of environmental variables. Our findings suggest that even though both genetic and species diversity are linked by the same processes, regional variation in environmental characteristics and spatial structure influence resulting biodiversity patterns differently. To date, no other empirical research has explored relationships between entire metapopulation and metacommunity assemblages at large regional spatial scales.},
}
@article {pmid33067509,
year = {2020},
author = {Davidov, K and Iankelevich-Kounio, E and Yakovenko, I and Koucherov, Y and Rubin-Blum, M and Oren, M},
title = {Identification of plastic-associated species in the Mediterranean Sea using DNA metabarcoding with Nanopore MinION.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {17533},
pmid = {33067509},
issn = {2045-2322},
mesh = {Aquatic Organisms/*classification ; Bacteria/classification ; Biodiversity ; Biota ; *DNA Barcoding, Taxonomic ; DNA, Intergenic/genetics ; *Ecosystem ; Environmental Monitoring/*methods ; Eukaryota/classification ; Fungi/classification ; Mediterranean Sea ; Microscopy, Electron, Scanning ; Nanopores ; *Plastics ; Polyethylene/chemistry ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; },
abstract = {Plastic debris in the ocean form a new ecosystem, termed 'plastisphere', which hosts a variety of marine organisms. Recent studies implemented DNA metabarcoding to characterize the taxonomic composition of the plastisphere in different areas of the world. In this study, we used a modified metabarcoding approach which was based on longer barcode sequences for the characterization of the plastisphere biota. We compared the microbiome of polyethylene food bags after 1 month at sea to the free-living biome in two proximal but environmentally different locations on the Mediterranean coast of Israel. We targeted the full 1.5 kb-long 16S rRNA gene for bacteria and 0.4-0.8 kb-long regions within the 18S rRNA, ITS, tufA and COI loci for eukaryotes. The taxonomic barcodes were sequenced using Oxford Nanopore Technology with multiplexing on a single MinION flow cell. We identified between 1249 and 2141 species in each of the plastic samples, of which 61 species (34 bacteria and 27 eukaryotes) were categorized as plastic-specific, including species that belong to known hydrocarbon-degrading genera. In addition to a large prokaryotes repertoire, our results, supported by scanning electron microscopy, depict a surprisingly high biodiversity of eukaryotes within the plastisphere with a dominant presence of diatoms as well as other protists, algae and fungi.},
}
@article {pmid33067488,
year = {2020},
author = {Mishra, P and Kumar, A and Sivaraman, G and Shukla, AK and Kaliamoorthy, R and Slater, A and Velusamy, S},
title = {Author Correction: Character-based DNA barcoding for authentication and conservation of IUCN Red listed threatened species of genus Decalepis (Apocynaceae).},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {17942},
doi = {10.1038/s41598-020-74406-0},
pmid = {33067488},
issn = {2045-2322},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}
@article {pmid33063681,
year = {2021},
author = {Chae, H and Sung, PS and Choi, H and Kwon, A and Kang, D and Kim, Y and Kim, M and Yoon, SK},
title = {Targeted Next-Generation Sequencing of Plasma Cell-Free DNA in Korean Patients with Hepatocellular Carcinoma.},
journal = {Annals of laboratory medicine},
volume = {41},
number = {2},
pages = {198-206},
pmid = {33063681},
issn = {2234-3814},
mesh = {Aged ; Biomarkers, Tumor ; *Carcinoma, Hepatocellular ; *Cell-Free Nucleic Acids ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; *Liver Neoplasms ; Male ; Middle Aged ; Mutation ; Republic of Korea ; },
abstract = {BACKGROUND: Hepatocellular carcinoma (HCC) is the second-most-common cause of cancer-related deaths worldwide, and an accurate and non-invasive biomarker for the early detection and monitoring of HCC is required. We assessed pathogenic variants of HCC driver genes in cell-free DNA (cfDNA) from HCC patients who had not undergone systemic therapy.<br><br>METHODS: Plasma cfDNA was collected from 20 HCC patients, and deep sequencing was performed using a customized cfDNA next-generation sequencing panel, targeting the major HCC driver genes (TP53, CTNNB1, TERT) that incorporates molecular barcoding.<br><br>RESULTS: In 13/20 (65%) patients, we identified at least one pathogenic variant of two major HCC driver genes (TP53 and CTNNB1), including 16 variants of TP53 and nine variants of CTNNB1. The TP53 and CTNNB1 variants showed low allele frequencies, with median values of 0.17% (range: 0.06%-6.99%) and 0.07% (range: 0.05%-0.96%), respectively. However, the molecular coverage of variants was sufficient, with median values of 5,543 (range: 2,317-9,088) and 7,568 (range: 2,400-9,633) for TP53 and CTNNB1 variants, respectively.<br><br>CONCLUSIONS: Our targeted DNA sequencing successfully identified low-frequency pathogenic variants in the cfDNA from HCC patients by achieving high coverage of unique molecular families. Our results support the utility of cfDNA analysis to identify somatic gene variants in HCC patients.},
}
@article {pmid33062688,
year = {2020},
author = {Kim, H and Shin, SE and Ko, KS and Park, SH},
title = {The Application of Mitochondrial COI Gene-Based Molecular Identification of Forensically Important Scuttle Flies (Diptera: Phoridae) in Korea.},
journal = {BioMed research international},
volume = {2020},
number = {},
pages = {6235848},
pmid = {33062688},
issn = {2314-6141},
mesh = {Animals ; Cadaver ; DNA Barcoding, Taxonomic ; *Diptera/classification/genetics ; Electron Transport Complex IV/*genetics ; Forensic Medicine/*methods ; Genes, Insect/*genetics ; Humans ; Larva/genetics ; Republic of Korea ; },
abstract = {Phoridae are a family of necrophagous flies commonly found in indoor death scene. They account for approximately 19.7% of the entomofauna in human cadavers in Korea. Additionally, this taxon is an indicator of indoor hygiene, and these flies appear in environments where access by other necrophagous insects is difficult, such as enclosed rooms. Thus, they are likely to be used as forensic evidence. Despite their importance in forensic investigations and environmental hygiene, detailed studies on the taxonomy and molecular barcoding for this family are scarce, including in Korea. Because accurate taxonomic information regarding necrophagous insects collected from a death-related scene is essential during medicolegal investigations, molecular barcoding data could be useful as well as reliable. In this paper, full-length nucleotide sequences of genes coding for the cytochrome c oxidase subunit I (COI) in 79 Phoridae larvae collected from 20 medicolegal autopsy cases in Korea were phylogenetically analyzed by comparing their sequences to the foreign barcoding data of Phoridae. Six mitochondrial haplogroups were identified, which two of them matched to foreign Phoridae fly species haplotypes, Megaselia scalaris (Loew, 1866) and M. spiracularis Schmitz 1938. Taxonomies of five other haplogroups, with nucleotide distances ranging from 1.68% to 2.26% from the M. scalaris group, could not be confirmed solely based on the molecular barcoding data. Further research should be performed to determine whether these five haplogroups are diverged conspecifics of M. scalaris or a closely related sister cryptic species of M. scalaris.},
}
@article {pmid33062439,
year = {2020},
author = {Liu, SYV and Kumara, TP and Hsu, CH},
title = {Genetic identification and hybridization in the seagrass genus Halophila (Hydrocharitaceae) in Sri Lankan waters.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e10027},
pmid = {33062439},
issn = {2167-8359},
abstract = {Seagrasses, as marine angiosperms, play important roles in coastal ecosystems. With increasing anthropogenic impacts, they are facing dramatic declines on a global scale. Halophila is well-known as a complex taxonomic challenge mainly due to high morphological plasticity. By using only a morphological approach, the genus could be over-split or similar species could be erroneously lumped, thus masking its true biodiversity. In the present study, we incorporated genetic identification with morphological examination to reveal the identity of Halophila plants in southern and northwestern Sri Lankan waters. The nuclear ribosomal internal transcribed spacer (ITS) region and chloroplast ribulose-bisphosphate carboxylase gene (rbcL) were used to identify plants collected from the Gulf of Mannar, Puttalam Lagoon, and Matara, Sri Lanka. Based on genetic identification, H. major (Zoll.) Miquel is reported for the first time from Sri Lanka, which might have been misidentified as H. ovalis in previous literature based on morphology alone. We also observed a first hybridization case of Halophila cross between H. ovalis and H. major. Two potential cryptic species were found, herein designated Halophila sp. 1 (allied to H. minor) and Halophila sp. 2 (closely related to H. decipiens). In order to clarify taxonomic ambiguity caused by morphological plasticity and the low resolution of genetic markers, further comparative phylogenomic approaches might be needed to solve species boundary issues in this genus.},
}
@article {pmid33062384,
year = {2019},
author = {Hagestad, OC and Andersen, JH and Altermark, B and Hansen, E and Rämä, T},
title = {Cultivable marine fungi from the Arctic Archipelago of Svalbard and their antibacterial activity.},
journal = {Mycology},
volume = {11},
number = {3},
pages = {230-242},
pmid = {33062384},
issn = {2150-1203},
abstract = {During a research cruise in 2016, we isolated fungi from sediments, seawater, driftwood, fruiting bodies, and macroalgae using three different media to assess species richness and potential bioactivity of cultivable marine fungi in the High Arctic region. Ten stations from the Svalbard archipelago (73-80 °N, 18-31 °E) were investigated and 33 fungal isolates were obtained. These grouped into 22 operational taxonomic units (OTUs) using nuc rDNA internal transcribed spacer regions (ITS1-5.8S-ITS2 = ITS) with acut-off set at 98% similarity. The taxonomic analysis showed that 17 OTUs belonged to Ascomycota, one to Basidiomycota, two to Mucoromycota and two were fungal-like organisms. The nuc rDNA V1-V5 regions of 18S (18S) and D1-D3 regions of 28S (28S) were sequenced from representative isolates of each OTU for comparison to GenBank sequences. Isolates of Lulworthiales and Eurotiales were the most abundant, with seven isolates each. Among the 22 OTUs, nine represent potentially undescribed species based on low similarity to GenBank sequences and 10 isolates showed inhibitory activity against Gram-positive bacteria in an agar diffusion plug assay. These results show promise for the Arctic region as asource of novel marine fungi with the ability to produce bioactive secondary metabolites with antibacterial properties.},
}
@article {pmid33058550,
year = {2021},
author = {Puillandre, N and Brouillet, S and Achaz, G},
title = {ASAP: assemble species by automatic partitioning.},
journal = {Molecular ecology resources},
volume = {21},
number = {2},
pages = {609-620},
doi = {10.1111/1755-0998.13281},
pmid = {33058550},
issn = {1755-0998},
support = {ANR-13-JSV7-0013-01//Agence Nationale de la Recherche/ ; },
mesh = {Algorithms ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; Monte Carlo Method ; Phylogeny ; Sequence Alignment ; *Software ; Species Specificity ; },
abstract = {Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough to split data sets as large 10[4] sequences into putative species in several minutes. Although grounded in evolutionary theory, ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity. ASAP is a stand-alone program that can be used either through a graphical web-interface or that can be downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP and GMYC) on 10 real COI barcode data sets representing various degrees of challenge (from small and easy cases to large and complicated data sets). We also used Monte-Carlo simulations of a multispecies coalescent framework to assess the strengths and weaknesses of ASAP and the other programs. Through these analyses, we demonstrate that ASAP has the potential to become a major tool for taxonomists as it proposes rapidly in a full graphical exploratory interface relevant species hypothesis as a first step of the integrative taxonomy process.},
}
@article {pmid33058218,
year = {2021},
author = {Kumar, RG and Charan, R and Krishnaprasoon, NP and Basheer, VS},
title = {Catfishes of the genus Sperata (Pisces:Bagridae) in India.},
journal = {Journal of fish biology},
volume = {98},
number = {2},
pages = {456-469},
doi = {10.1111/jfb.14590},
pmid = {33058218},
issn = {1095-8649},
mesh = {Animal Distribution ; Animals ; Catfishes/*classification/*genetics ; DNA Barcoding, Taxonomic ; India ; *Rivers ; },
abstract = {DNA barcode data of the South Asian bagrid catfish genus Sperata indicate the presence of at least five species in the Indian subcontinent. Those results, which are supported by morphological data, show a marked increase in species diversity from the recent taxonomic and fishery literature, although each of the five species had been previously named. Two species are restricted to rivers of peninsular India south of the Godavari: Sperata aorides from the Cauvery river basin and S. seenghala from the Krishna river basin. Most literature records of S. seenghala from the Ganges-Brahmaputra-Meghna river basins likely refer to S. lamarrii, a species which appears to also be present in the Indus river basin. Some genetic data reported as S. seenghala from the Ganges-Brahmaputra-Meghna river basins refer to S. aorella. S. aor is widespread in the Ganges-Brahmaputra-Surma river basins in India and Bangladesh, extending southwards to the Godavari river.},
}
@article {pmid33058146,
year = {2021},
author = {Bustamante, C and García-Cegarra, AM and Vargas-Caro, C},
title = {Observations of coastal aggregations of the broadnose sevengill shark (Notorynchus cepedianus) in Chilean waters.},
journal = {Journal of fish biology},
volume = {98},
number = {3},
pages = {870-873},
doi = {10.1111/jfb.14591},
pmid = {33058146},
issn = {1095-8649},
support = {MINEDUC-UA ANT-1755//Vicerrector&#xed;a de Investigaci&#xf3;n, Innovaci&#xf3;n y Postgrado; Universidad de Antofagasta/ ; },
mesh = {*Animal Distribution ; Animals ; Chile ; Cyclooxygenase 1/genetics ; Female ; *Fisheries/trends ; Pacific Ocean ; Sharks/*physiology ; Video Recording ; },
abstract = {The presence of four sharks was documented in coastal waters of Antofagasta (Chile) using an unmanned aerial video camera. Fishers took advantage of this aggregation to catch and sold three adult broadnose sevengill sharks Notorynchus cepedianus. Species identity was determined by using the cox1 gene. One additional video was later recorded 3000 km south of Antofagasta, and shows a large female interacting with a salmon farming facility. Shallow water records of N. cepedianus were previously undocumented in Chilean waters, yet historically have provided an opportunistic event to fishers in Chile.},
}
@article {pmid33056918,
year = {2020},
author = {Pinho, LC and DA Silva, FL},
title = {Description of two new species of Polypedilum (Asheum) and immature stages of Polypedilum (A.) curticaudatum (Diptera: Chironomidae).},
journal = {Zootaxa},
volume = {4759},
number = {2},
pages = {zootaxa.4759.2.2},
doi = {10.11646/zootaxa.4759.2.2},
pmid = {33056918},
issn = {1175-5334},
mesh = {Animals ; *Chironomidae ; Forests ; Larva ; Male ; Pupa ; },
abstract = {Two new species of Polypedilum (Asheum) (Diptera: Chironomidae: Chironominae) are described and figured as adult males, P. (A.) sofiae sp. n. collected in the states of Mato Grosso and Rondônia and P. (A.) mayrahu sp. n. collected in the state of Bahia, Brazil. In addition, the adult male of Polypedilum (Asheum) curticaudatum (Rempel) is redescribed based on material from some localities in the Brazilian Atlantic Forest and Pantanal, and its larva and pupa are described for the first time.},
}
@article {pmid33056776,
year = {2020},
author = {Wagner, R and Rada, T},
title = {Moth flies (Diptera, Psychodidae) living in the dark of caves in the Dinaric Karst.},
journal = {Zootaxa},
volume = {4845},
number = {2},
pages = {zootaxa.4845.2.8},
doi = {10.11646/zootaxa.4845.2.8},
pmid = {33056776},
issn = {1175-5334},
mesh = {Animals ; Female ; Male ; *Psychodidae ; },
abstract = {Seoda cavernicola sp. nov. and Psychoda glamocensis sp. nov., are new species and cave dwellers from Bosnia and Hercegovina, and Croatia. Adults of S. cavernicola are pale and small; the eye bridge is reduced, ommatidia irregularly arranged, epandrium with a pair of setose excrescences. The eye bridge of P. glamocensis is likewise reduced with 2 or 3 irregularly ordered facet rows, palpus segments of some individuals are malformed; its closest relative is Psychoda alticola Vaillant based on the morphology of male and female genitalia as well as on COI barcodes.},
}
@article {pmid33056752,
year = {2020},
author = {Twinkle, T and Shashank, PR and Chattopadhyay, PC},
title = {DNA barcoding and Taxonomic account on some selected species of subfamily Plusiinae (Lepidoptera: Noctuidae) from India.},
journal = {Zootaxa},
volume = {4845},
number = {4},
pages = {zootaxa.4845.4.1},
doi = {10.11646/zootaxa.4845.4.1},
pmid = {33056752},
issn = {1175-5334},
mesh = {Animals ; DNA ; *DNA Barcoding, Taxonomic ; India ; Larva ; *Moths ; },
abstract = {This study represents a detailed taxonomic account of 31 species of Plusiinae (Lepidoptera: Noctuidae) from India. The survey and collection of 39 localities from different regions of India between 2015 and 2018. The tribe Argyrogrammatini Eichlin Cunningham, 1978 with Ctenoplusia Dufey, 1970 was the most species rich genera with seven species, followed by Thysanoplusia Ichinose, 1973 and Chrysodeixis Hubner, 1821 with four and three species respectively. Among 31 species, 15 species are commonly found in Himalayan regions and while other species were distributed from subtropical to tropical region. Five species, T. orichalcea (Fabricius, 1775), Chrysodeixis eriosoma (Doubleday, 1843), C. acuta (Walker, 1858), C. chalcites (Esper, 1789), Trichoplusia ni (Hubner, 1803) are widespread throughout India and reported as serious crop pests. Present study also revealed range expansion of four species viz., Dactyloplusia impulsa (Walker, 1865), Ctenoplusia mutans (Walker, 1865), Ctenoplusia tarassota (Hampson, 1913) and Zonoplusia ochreata (Walker, 1865). Systematic accounts of all 31 species are discussed here with adult images, species diagnostic characters, collection localities, detailed distributions and reported larval host plants. In addition to morphological studies, for the first time, a preliminary barcode library for 25 species of Indian Plusiinae with average intra-specific distance (%), maximum intra-specific distance (%) and distance to nearest neighbor (%) for individual species is provided. Among 25 species, four species barcode data (Ctenoplusia mutans, C. kosemponesis, Plusiopalpa adrasta, Sclerogenia jessica) are novel to world and 18 species barcode sequences were novel to India.},
}
@article {pmid33056717,
year = {2020},
author = {Prasad, VK and Gautam, KB and Gupta, SK and Murthy, RS and Ramesh, K and Shinde, AD and DAS, A},
title = {Identification of anuran species diversity of the Panna Tiger Reserve, Central India, using an integrated approach.},
journal = {Zootaxa},
volume = {4851},
number = {3},
pages = {zootaxa.4851.3.2},
doi = {10.11646/zootaxa.4851.3.2},
pmid = {33056717},
issn = {1175-5334},
mesh = {Acoustics ; Animals ; *Anura ; India ; },
abstract = {We present a comprehensive inventory of amphibians from Panna Tiger Reserve in Madhya Pradesh based on morphological, molecular and bioacoustic data. Representatives of 15 anuran species were collected, corresponding to roughly four fifths of the known amphibian species of Madhya Pradesh. The main results of this study are: (1) Description of advertisement calls of eleven species, including the first-time description of advertisement calls of Sphaerotheca pashchima. (2) Identification of cryptic species using acoustic and molecular techniques. (3) Five new significant range extensions and new state records. (4) Description of geographical variation in call properties in three anuran species. This study also provides morphological descriptions with ecological and natural history notes for each species that may be useful in management planning for amphibian conservation in Panna Tiger Reserve.},
}
@article {pmid33056674,
year = {2020},
author = {Moore, MD and Beaver, EP and Velasco-CastrillÓn, A and Stevens, MI},
title = {Four new tri-forked species of the Australian genus Abantiades Herrich-Schäffer (Lepidoptera: Hepialidae) from the "dark obscura clade".},
journal = {Zootaxa},
volume = {4801},
number = {1},
pages = {zootaxa.4801.1.5},
doi = {10.11646/zootaxa.4801.1.5},
pmid = {33056674},
issn = {1175-5334},
mesh = {Animals ; Australia ; DNA, Mitochondrial ; *Lepidoptera ; },
abstract = {A distinct group of Abantiades Herrich-Schäffer species is here confirmed as a valid clade that we refer to as the "dark obscura clade" supported by morphological and mtDNA evidence. The clade is the sister group of A. obscura Simonsen of north-western Australia and comprises four new species: Abantiades centralia sp. nov., A. kayi sp. nov., A. zonatriticum sp. nov., and A. hutchinsoni sp. nov. These species together with A. obscura, are reciprocally allopatric and have a combined distribution spanning much of the western half of Australia and this distribution is consistent with their each differentiating locally from a widespread ancestor. The four new species raise the diversity of Abantiades to 42 species. [Zoobank urn:lsid:zoobank.org:pub:C05458D1-0D34-4432-8EC4-D031ED6B7BEF].},
}
@article {pmid33056612,
year = {2020},
author = {Wang, E and Li, W and Liu, T},
title = {Bucculatricidae associated with Asteraceae in China, with one new species (Lepidoptera: Gracillarioidea).},
journal = {Zootaxa},
volume = {4766},
number = {1},
pages = {zootaxa.4766.1.10},
doi = {10.11646/zootaxa.4766.1.10},
pmid = {33056612},
issn = {1175-5334},
mesh = {Animals ; *Artemisia ; China ; *Moths ; Plant Leaves ; Pupa ; },
abstract = {Asteraceae comprises one of the major host plant families for Bucculatricidae and Artemisia is the most exploited host genus, however, not a single record of Bucculatrix species feeding on Asteraceae is confirmed in China. One new species, B. duanwuia Liu, sp. nov., feeding on Artemisia princeps Pamp. (Asteraceae), is described from China, supplemented with illustrations of leaf mines and pupa, biology and DNA barcodes. Bucculatrix notella Seksjaeva, 1996 is recorded for the first time in China and DNA barcodes are provided aiding species separation for the first time.},
}
@article {pmid33056601,
year = {2020},
author = {Pogonoski, JJ and Gon, O and Appleyard, SA},
title = {&lt;p&gt;-Redescription and distributional range extension of the Speckled Siphonfish, Siphamia guttulata (Pisces: Apogonidae).},
journal = {Zootaxa},
volume = {4766},
number = {2},
pages = {zootaxa.4766.2.6},
doi = {10.11646/zootaxa.4766.2.6},
pmid = {33056601},
issn = {1175-5334},
mesh = {Animals ; Australia ; *Fishes ; *Perciformes ; },
abstract = {During seabed biodiversity surveys between 2003 and 2005 from the Torres Strait (Papua New Guinea) to the southern Great Barrier Reef (Queensland), hundreds of Siphamia specimens were collected. After Gon Allen's (2012) revision allowed greater interrogation of the Siphamia species present, a re-examination of preserved and frozen Siphamia specimens at the CSIRO Australian National Fish Collection (ANFC) was warranted. The material was re-identified as four commonly collected species (S. cuneiceps, S. roseigaster, S. tubifer, and S. tubulata) and a fifth unidentified species that appeared to key to S. guttulata, previously known only from the type locality. Further detailed investigations including an analysis of meristic, morphometric and COI barcoding data confirmed the identity of S. guttulata from almost the entire length of the Great Barrier Reef, Queensland, from the Torres Strait in the north to the Northumberland Islands Group in the south. This study provides a redescription of Siphamia guttulata and highlights the importance of re-assessing the taxonomic status of museum material after revisionary studies.},
}
@article {pmid33056589,
year = {2020},
author = {Grebennikov, VV},
title = {Tazarcus, a new phylogenetically unplaced genus of two flightless weevils &lt;br /&gt;with metapleural ridge from the Eastern Arc Mountains, Tanzania (Coleoptera: Curculionidae: Molytinae).},
journal = {Zootaxa},
volume = {4766},
number = {3},
pages = {zootaxa.4766.3.2},
doi = {10.11646/zootaxa.4766.3.2},
pmid = {33056589},
issn = {1175-5334},
mesh = {Animals ; *Coleoptera ; Phylogeny ; Tanzania ; *Weevils ; },
abstract = {This paper reports new flightless forest litter weevils discovered in Tanzania. They are classified into two species of the genus Tazarcus gen. nov.: T. aeaea sp. nov. (the type species; from South Pare and West Usambara) and T. ogygia sp. nov. (Rubeho). Both new species inhabit the archipelago-type Eastern Arc Mountain rainforests renowned for the high diversity of their biota. Adults of Tazarcus are recognizable by their relatively small size (length of pronotum and elytra in dorsal view 2.0-3.4 mm), the short and straight rostrum covered dorsally with dense velvety pilosity, an antennal funicle with seven segments, a prosternal canal, procoxae separated, a lack of hind wings and effaced elytral shoulders. Remarkably, adults of Tazarcus possess a short longitudinal ridge on each metapleuron, which bears a line of serration likely homologous to sclerolepidia. A phylogenetic analysis of 72 terminals and 3134 aligned positions from one mitochondrial and two nuclear ribosomal fragments corroborated the monophyly of the new genus, of both new species and of all three sampled populations but did not identify the sister group of Tazarcus. Three other weevil taxa with adults possessing a similarly shaped metapleural ridge (the African Thrombosternus Marshall and Allocycloteres Voss and an unidentified species of Molytinae from Madagascar) did not cluster with Tazarcus, suggesting multiple origins of this structure. Tazarcus is taxonomically classified as incertae sedis in a non-monophyletic subfamily "Molytinae". Images and DNA sequences of all 72 herein analysed specimens are available online at dx.doi.org/10.5883/DS-VGDS011.},
}
@article {pmid33056572,
year = {2020},
author = {Sugiura, K and Arakawa, K and Matsumoto, M},
title = {Distribution of Macrobiotus shonaicus Stec, Arakawa amp; Michalczyk, 2018 (Tardigrada: Eutardigrada: Macrobiotidae) in Japan.},
journal = {Zootaxa},
volume = {4767},
number = {1},
pages = {zootaxa.4767.1.2},
doi = {10.11646/zootaxa.4767.1.2},
pmid = {33056572},
issn = {1175-5334},
mesh = {Animals ; Haplotypes ; Japan ; Reproduction ; *Tardigrada ; },
abstract = {To date, only seven species of Macrobiotidae (Parachela; Eutardigrada; Tardigrada) have been reported from Japan, including the recently described Macrobiotus shonaicus Stec et al., 2018 from the Shonai region of Japan. This species has flexible filaments on the egg processes and is known to proliferate only through sexual reproduction. Here, we report a multifaceted analysis of nine populations of M. shonaicus found on four Japanese islands. DNA sequencing of the cytochrome oxidase subunit I (COI) and internal transcribed spacer 2 (ITS-2) of the nine populations revealed 8 and 11 haplotypes, respectively. The extensive morphometric analysis showed considerably greater variability in the morphology of eggs than of animals. In addition to the morphological and molecular data, we confirmed the karyotype and found that all populations had a chromosome number of n = 6. Moreover, we observed and filmed mating behaviour between all studied populations of M. shonaicus. Our results clearly indicated that M. shonaicus is widely distributed throughout Japan.},
}
@article {pmid33056545,
year = {2020},
author = {Bahder, BW and Barrantes, EAB and Echavarria, MAZ and Mou, DF and Helmick, EE and Bartlett, CR},
title = {A new species of planthopper in the genus Haplaxius (Hemiptera: Auchenorrhyncha: Fulgoroidea: Cixiidae) on palms in Costa Rica and a new country record for Haplaxius skarphion.},
journal = {Zootaxa},
volume = {4767},
number = {4},
pages = {zootaxa.4767.4.4},
doi = {10.11646/zootaxa.4767.4.4},
pmid = {33056545},
issn = {1175-5334},
mesh = {Animals ; *Arecaceae ; Cocos ; Costa Rica ; *Hemiptera ; },
abstract = {The genus Haplaxius is a large taxon of cixiid planthoppers that is of economic importance due to the ability of Haplaxius crudus to transmit lethal yellowing in coconut palms. Haplaxius dougwalshi sp. n. is established as a new taxon of Cixiidae in the tribe Oecleini collected from native palms in lowland tropical rainforest in Costa Rica. Placement in the genus Haplaxius is supported both by molecular evidence based on the COI and 18S genes as well as by morphological characters. This novel taxon was discovered during survey work in Costa Rica to look for phytoplasmas and document planthopper diversity on palms. Furthermore, Haplaxius skarphion was also collected from coconut palms during survey work and is reported for the first time in Costa Rica.},
}
@article {pmid33056529,
year = {2020},
author = {Lin, XL and Yu, HJ and Wang, Q and Bu, WJ and Wang, XH},
title = {DNA barcodes and morphology confirm a new species of Rheocricotopus (Psilocricotopus) orientalis group (Diptera: Chironomidae).},
journal = {Zootaxa},
volume = {4768},
number = {2},
pages = {zootaxa.4768.2.9},
doi = {10.11646/zootaxa.4768.2.9},
pmid = {33056529},
issn = {1175-5334},
mesh = {Animals ; *Chironomidae ; DNA Barcoding, Taxonomic ; Male ; },
abstract = {Morphology and DNA barcodes confirm a new chironomid species within the Rheocricotopus (Psilocricotopus) orientalis group (Diptera: Chironomidae). Rheocricotopus (Psilocricotopus) kongi Lin et Wang sp. n. is described and illustrated based on adult male from Hainan, China. Key to adult males of the R. orientalis group is given.},
}
@article {pmid33056515,
year = {2020},
author = {Majumder, A and Drumont, A and Bouyer, T and Chandra, K},
title = {Notes on the genus Sarmydus Pascoe, 1867 (Cerambycidae: Prioninae: Anacolini) from India with description of a new species.},
journal = {Zootaxa},
volume = {4780},
number = {3},
pages = {zootaxa.4780.3.6},
doi = {10.11646/zootaxa.4780.3.6},
pmid = {33056515},
issn = {1175-5334},
mesh = {Animals ; *Coleoptera ; Female ; India ; Male ; },
abstract = {A new species of Sarmydus Pascoe, 1867, S. bagh sp. nov., is described from north India and adjacent countries based on the habitus of both male and female, and male genitalia characters. Detailed taxonomic investigations reveal previous misidentification of several specimens from India of the new species as S. antennatus Pascoe, 1867. Accordingly, Sarmydus antennatus Pascoe, 1867 is removed from the Indian fauna. Photographs of the holotype of S. antennatus are provided, and the characters of this species discussed in detail. DNA barcoding analysis of the Himalayan Sarmydus species has been done for the confirmation of the new species. This analysis depicts significant genetic divergences of >14% between S. bagh sp. nov. and its congeners, thus, sufficiently supporting morphological interpretations.},
}
@article {pmid33056464,
year = {2020},
author = {Yosuva, M and Ho, HC and Jeyapragash, D and Saravanakuamr, A},
title = {Parapercis annamalai sp. nov., a new sandperch from southwestern India (Family Pinguipedidiae).},
journal = {Zootaxa},
volume = {4786},
number = {4},
pages = {zootaxa.4786.4.7},
doi = {10.11646/zootaxa.4786.4.7},
pmid = {33056464},
issn = {1175-5334},
mesh = {Animals ; Fishes ; Gills ; India ; *Perciformes ; },
abstract = {A new sandperch is described from 3 specimens from off Parangipettai, southeastern India. It can be separated from its congeners in having a combination of dorsal-fin rays V, 21‒22; anal-fin rays I, 17‒18; pectoral-fin rays 17‒18; pored lateral-line scales 53‒54; median predorsal scales 7; transverse scale rows 4/13; gill rakers on 1st gill arch 15‒17; single row of stout teeth on vomer; no teeth on palatine; 3 pairs of enlarged canines at front of lower jaw; opercle uniformly dark brownish; blade-like patch on cheek, the patch orange dorsally and reddish ventrally, fading entirely in preservative; dorsal fins light grayish with 2 rows of spots; a whitish longitudinal band just above lateral axis of body; dorsal surface of body with 8 irregular blackish saddles and lower half with 7 reddish bars and black dots on upper half of each bar; lower half of anal fin reddish; caudal fin grayish with upper and lower portion darker and vertical rows of orange dots on yellowish bands. The new species is most similar to Parapercis somaliensis and Parapercis kentingensis morphologically and genetically, but differs in coloration, serrations on the opercle, and body proportions. The establishment of the new species is also supported by DNA barcoding analysis.},
}
@article {pmid33056449,
year = {2020},
author = {Santa-Rita, JVP and Baixeras, J and Karsholt, O},
title = {The enigmatic case of the genus Argyresthia in the Azores Islands (Lepidoptera: Argyresthiidae).},
journal = {Zootaxa},
volume = {4789},
number = {1},
pages = {zootaxa.4789.1.7},
doi = {10.11646/zootaxa.4789.1.7},
pmid = {33056449},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Azores ; *Moths ; Wings, Animal ; },
abstract = {The species composition of the genus Argyresthia Hübner, 1825 in the Azores is examined. Argyresthia brumella, sp. nov., is described and illustrated from Terceira and Flores Islands. Argyresthia minusculella Rebel, 1940, syn. nov. and Tinea poecilella Rebel, 1940, syn. nov. are synonymized with Argyresthia atlanticella Rebel, 1940. The high variability of A. atlanticella is revealed through the polymorphic wing pattern and the intraspecific genetic divergence of the DNA barcode COI in the specimens examined.},
}
@article {pmid33056411,
year = {2020},
author = {Amini, S and Nozari, J and Smith, SM and Martinez, I and Hosseini, R and Faccoli, M},
title = {Morphological and molecular identification of the Iranian bark and ambrosia beetles (Coleoptera, Curculionidae, Scolytinae).},
journal = {Zootaxa},
volume = {4852},
number = {3},
pages = {zootaxa.4852.3.1},
doi = {10.11646/zootaxa.4852.3.1},
pmid = {33056411},
issn = {1175-5334},
mesh = {*Ambrosia ; Animals ; *Coleoptera ; Iran ; Plant Bark ; *Weevils ; },
abstract = {A faunal and molecular taxonomic study of Iranian bark and ambrosia beetle species based on field collections, museum specimens and literature data was carried out from in the period 2011-2016. A total of 29 genera and 84 species were found for Iran. A morphological key for species identification is provided. Molecular identification based on mitochondrial cytochrome c oxidase I (CO1) barcoding region gene was also performed for the collected specimens to confirm morphological identification, and an exclusive DNA barcode was provided and registered for the samples collected in this study. Host plants and distribution of each species in the Palearctic region and in Iran are reported in the key.},
}
@article {pmid33056366,
year = {2020},
author = {Chagnon, ME and Sinclair, BJ},
title = {Revision of the Nearctic species of Gimnomera Rondani (Diptera: Scathophagidae), with morphological phylogeny and DNA barcodes.},
journal = {Zootaxa},
volume = {4853},
number = {3},
pages = {zootaxa.4853.3.3},
doi = {10.11646/zootaxa.4853.3.3},
pmid = {33056366},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; *Diptera ; Male ; Phylogeny ; },
abstract = {The Nearctic species of Gimnomera Rondani are revised and includes eight species, of which three are new to science (G. aquilonia sp. nov., G. cerea (Coquillett), G. cuneiventris (Zetterstedt), G. incisurata Malloch, G. subvittata (Malloch), G. terrywheeleri sp. nov., G. tibialis (Malloch), G. vockerothi sp. nov.). Gimnomera cuneiventris is newly recognized as Holarctic in distribution. Gimnomera fasciventris Malloch is removed and transferred to the genus Acerocnema, comb. nov. An additional Nearctic species is recognized but not described due to lack of male specimens. Species descriptions, diagnoses and distribution maps are presented, including images of the male terminalia as well as additional diagnostic characters. A key to the Nearctic species is also provided. A morphological cladistic analysis of 12 species reveals that the Nearctic and Palearctic species do not form separate monophyletic groups. COI mitochondrial DNA barcode sequences were obtained for eight Nearctic species of Gimnomera.},
}
@article {pmid33056339,
year = {2020},
author = {Prieto, C and Hincapie, CF&#xc1; and Giraldo, AC and Uribe, S},
title = {DNA barcodes, morphology and geographic distribution confirm a new butterfly species in the genus Rhamma (Lepidoptera: Lycaenidae).},
journal = {Zootaxa},
volume = {4821},
number = {1},
pages = {zootaxa.4821.1.11},
doi = {10.11646/zootaxa.4821.1.11},
pmid = {33056339},
issn = {1175-5334},
mesh = {Animals ; *Butterflies ; DNA Barcoding, Taxonomic ; Female ; Wings, Animal ; },
abstract = {We diagnose a new butterfly species from the Belmira paramo in the central cordillera of the Colombian Andes. We infer from the barcoding analysis, wing pattern, morphology and distribution that this entity is not a geographical variation or subspecies of any named lycaenid, and it is described herein as Rhamma eleonorae sp. nov. Adult specimens and female genitalia are illustrated and compared with R. arria (Hewitson, 1870) and R. oxida (Hewitson, 1870), the most closely related taxa based on similarities of wing pattern and COI sequences.},
}
@article {pmid33056300,
year = {2020},
author = {Moore, MD and Beaver, EP and Velasco-CastrillÓn, A and Stevens, MI},
title = {Description of two new Australian species of Abantiades Herrich-Schäffer (Lepidoptera: Hepialidae) and females of two further species with notes on their biogeography.},
journal = {Zootaxa},
volume = {4822},
number = {1},
pages = {zootaxa.4822.1.3},
doi = {10.11646/zootaxa.4822.1.3},
pmid = {33056300},
issn = {1175-5334},
mesh = {Animals ; Australia ; DNA, Mitochondrial ; Female ; *Moths ; },
abstract = {Abantiades cephalocorvus sp. nov. and Abantiades tembyi sp. nov. are described, along with the previously undescribed females of A. macropusinsulariae Simonsen, 2018 and A. pallida Simonsen, 2018. All of these species belong to a triforked Abantiades Herrich-Schäffer clade that is loosely centred around the Nullarbor and other arid regions of Australia. We explore DNA barcodes (mtDNA COI gene) from these and other Abantiades and discuss their significance for species recognition. The species distributions are entirely or largely allopatric and we discuss their origins from a widespread common ancestor that was likely distributed over inland and coastal regions in the mid- to late-Mesozoic before the onset of desertification. Notes on new distributional data for all of the known species in this clade are included.},
}
@article {pmid33056279,
year = {2020},
author = {Shinohara, A and Yamasako, J},
title = {Hyperxiphia hirashimai, comb. n. (Hymenoptera, Xiphydriidae) from southern Japan: remarkable sexual dimorphism revealed by DNA barcodes and new distribution records.},
journal = {Zootaxa},
volume = {4822},
number = {3},
pages = {zootaxa.4822.3.5},
doi = {10.11646/zootaxa.4822.3.5},
pmid = {33056279},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Female ; *Hymenoptera ; Japan ; Male ; Phylogeny ; Sex Characteristics ; },
abstract = {Based on a study of the type material, Genaxiphia hirashimai Okutani, 1965, a southern Japanese xiphydriid showing remarkable sexual dimorphism, is newly combined with the genus Hyperxiphia Maa, 1949. The previously unknown female is described, and the male is redescribed with additional material. The sexes are associated by examination of specimens of both sexes that apparently emerged from the same piece of branch and by a molecular analysis using mitochondrial COI sequences. Hyperxiphia hirashimai, originally described from Amami-oshima Island, is newly recorded from Miyake-jima Island, southwestern Shikoku, southern Kyushu, Yakushima, Kuroshima and Okinawa-jima Islands.},
}
@article {pmid33056275,
year = {2020},
author = {Marceniuk, AP and Caires, RA and Rotundo, MM and Cerqueira, NNCD and Siccha-Ramirez, R and Wosiacki, WB and Oliveira, C},
title = {Taxonomic revision of the Menticirrhus americanus (Linnaeus, 1758) and M. littoralis (Holbrook, 1847) (Percomorphacea: Sciaenidae) species complexes from the western Atlantic.},
journal = {Zootaxa},
volume = {4822},
number = {3},
pages = {zootaxa.4822.3.1},
doi = {10.11646/zootaxa.4822.3.1},
pmid = {33056275},
issn = {1175-5334},
mesh = {Animals ; *Perciformes ; },
abstract = {The genus Menticirrhus is widely distributed in the Neotropical region, where its species are common and abundant in shallow coastal waters and estuaries. The diversity, biogeography, and evolutionary relationships of the Menticirrhus species are still poorly known, due primarily to the difficulty of differentiating the species, given the broad similarities in their external morphology. The present study is based on the analysis of morphological and molecular data, with the examination of type specimens and a comprehensive collection of non-type specimens from an ample geographic range. These analyses indicated that two widely distributed Western Atlantic species, Menticirrhus americanus and M. littoralis, represent species complexes. The M. littoralis species complex is characterized by the absence of dark bars on body side, and a smaller, light-colored pectoral fins, that barely reaching the tip of the depressed pelvic fins, with fewer pectoral-fin rays. This complex includes three species: M. littoralis, found in the Gulf of Mexico, M. gracilis, from the southeastern and southern coast of South America, and a new species, described here, from the northern to eastern Brazilian coast. The M. americanus species complex is characterized by the presence of dark bars on body side, and a large, dark pectoral fin, that surpass the tip of the depressed pelvic fin, with more pectoral-fin rays. This complex has two species, M. americanus, which occurs on the east coast of the United States and in the Gulf of Mexico, and M. martinicensis, found from Caribbean to Argentina, that represents a cryptic allopatric species. An identification key to all species of the genus is presented.},
}
@article {pmid33056261,
year = {2020},
author = {Jaschhof, M and Jaschhof, C},
title = {Reevaluation of species richness in Winnertzia (Diptera, Cecidomyiidae, Winnertziinae), with descriptions of 37 new species from Sweden, Peru and Australia.},
journal = {Zootaxa},
volume = {4829},
number = {1},
pages = {zootaxa.4829.1.1},
doi = {10.11646/zootaxa.4829.1.1},
pmid = {33056261},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures ; Animals ; Australia ; *Biodiversity ; Body Size ; *Diptera ; Male ; Organ Size ; Peru ; Sweden ; },
abstract = {Tentative studies of Malaise trap samples from different geographic regions and habitats indicate unanimously that Winnertzia, a genus of mycophagous gall midges (Cecidomyiidae), is exceptionally speciose, but hard data in proof of that were previously unavailable. A taxonomic inventory of mycophagous cecidomyiids in Sweden has now revealed that, of 751 species found in total, 93 are Winnertzia. A preliminary census in 2013 had identified only 26 different Winnertzia in Sweden. Two factors are responsible for this increment: the inclusion of large amounts of fresh material to study and the application of a narrower species concept. The latter results from the reevaluation of male morphological characters in the light of COI sequence (DNA barcoding) data. With the inclusion of 37 new Winnertzia described here, the genus now contains 136 extant species. New Winnertzia discovered in Sweden are described here under the following names: W. acutistylus sp. nov., W. angustistylus sp. nov., W. arctostylus sp. nov., W. bicolor sp. nov., W. brachytarsus sp. nov., W. dentata sp. nov., W. egregia sp. nov., W. ekdalensis sp. nov., W. fraxinophila sp. nov., W. grytsjoenensis sp. nov., W. hamatula sp. nov., W. hemisphaerica sp. nov., W. imbecilla sp. nov., W. incisa sp. nov., W. inornata sp. nov., W. lapponica sp. nov., W. lobata sp. nov., W. longicoxa sp. nov., W. normalis sp. nov., W. oelandica sp. nov., W. ombergensis sp. nov., W. parvidens sp. nov., W. pilosistylus sp. nov., W. pratensis sp. nov., W. pustulatula sp. nov., W. quercinophila sp. nov., W. rickebasta sp. nov., W. ruliki sp. nov., W. serri sp. nov., W. setosa sp. nov., W. silvestris sp. nov., W. smalandensis sp. nov., W. sundini sp. nov., W. tumidoides sp. nov., and W. upplandensis sp. nov. Additionally, W. panguana sp. nov. is the first Winnertzia described from the Neotropical region (Peru), and W. warraensis sp. nov. is the first member of the genus described from the Australasian region (Tasmania). Parwinnertzia Felt, 1920 syn. nov. is revealed to be a junior synonym of Winnertzia Rondani, 1860, implying the recombinations of Winnertzia notmani (Felt) comb. nov. and Winnertzia italiana (Mamaev Zaitzev) comb. nov. The intrageneric classification of Winnertzia is reviewed and developed further, with the W. setosa group introduced for species whose gonostylar claw is conspicuously long and exposed, and whose gonocoxal emargination is bordered by dense, large setae. Winnertzia feralis Mamaev, revived here from synonymy with W. tridens Panelius, and W. fusca Kieffer are new faunistic records in Sweden. Swedish records published in the past of W. brachypalpa Mamaev and W. pravdini Mamaeva Mamaev rest on misidentifications, and both species are deleted from the Swedish checklist.},
}
@article {pmid33056257,
year = {2020},
author = {Riyanto, A and Farajallah, A and Hamidy, A and Fitriana, YS and Munir, M and Kurniawan, N and Smith, EN},
title = {Taxonomic evaluation of two similar bent-toed geckos Squamata: Gekkonidae: Cyrtodactylus Gray, 1827) from East Java, Indonesia.},
journal = {Zootaxa},
volume = {4830},
number = {1},
pages = {zootaxa.4830.1.8},
doi = {10.11646/zootaxa.4830.1.8},
pmid = {33056257},
issn = {1175-5334},
mesh = {Animals ; Color ; Ecosystem ; Genetic Drift ; Indonesia ; *Lizards ; Male ; },
abstract = {The bent-toed geckos of the genus Cyrtodactylus are the most speciose land vertebrates of Southeast Asia (about 300 species so far) and new species continue to be recognized at a rapid rate. Within the last decade three new species were described from Java, Indonesia, C. semiadii, C. petani, and C. klakahensis. The latter two are very similar, except for differences in the precloacal depression in adult males. These two species have relatively close type localities, separated from each other by only about 50 km, and with similar habitat type and elevation. Our study aimed to evaluate the taxonomic status of C. klakahensis and C. petani using both morphological and genetic evidence. These two species are genetically similar, with a genetic divergence of only 1.5 to 1.6%. This divergence is well below the level of typically characterizes sister species of Cyrtodactylus (approximately 4% in the mitochondrial ND2 gene), and is more in line with population variation due to geographic distance. Further examination of specimens, from both type localities, showed no diagnostic morphological characters between the two species. Thus, we conclude that C. klakahensis and C. petani are conspecific, and following article 23 of the ICZN, C. klakahensis is herein considered a junior synonym of C. petani.},
}
@article {pmid33056256,
year = {2020},
author = {Kuroda, K and Konishi, K and Turrisi, GF and Yamasako, J},
title = {A revisional study of the genus Aulacus Jurine (Hymenoptera: Aulacidae) of Japan.},
journal = {Zootaxa},
volume = {4830},
number = {1},
pages = {zootaxa.4830.1.7},
doi = {10.11646/zootaxa.4830.1.7},
pmid = {33056256},
issn = {1175-5334},
mesh = {Animals ; *Hymenoptera ; Japan ; Male ; },
abstract = {Japanese species of the genus Aulacus Jurine are revised and seven species are recognized. Two new species, A. davidi sp. n. and A. shizukii sp. n. are described. In addition, A. flavigenis Alekseev and A. sinensis He Chen are newly recorded from the Japanese archipelago. Male genitalia of three species, i.e., A. davidi, A. flavigenis and A. sinensis, are described for the first time. An identification key for Japanese species and DNA barcoding data for A. davidi, A. machaerophorus Kuroda, Kikuchi Konishi and A. sinensis are also provided.},
}
@article {pmid33056253,
year = {2020},
author = {RadenkoviĆ, S and Likov, L and StÅhls, G and Rojo, S and PÉrez-BaÑÓn, C and Smit, J and Petanidou, T and VAN Steenis, W and VujiĆ, A},
title = {Three new hoverfly species from Greece (Diptera: Syrphidae).},
journal = {Zootaxa},
volume = {4830},
number = {1},
pages = {zootaxa.4830.1.4},
doi = {10.11646/zootaxa.4830.1.4},
pmid = {33056253},
issn = {1175-5334},
mesh = {Animals ; *Diptera ; Greece ; Mitochondria ; },
abstract = {An ongoing investigation on the Greek hoverfly fauna using adult morphology has revealed new species within three genera. In this study, the knowledge of the Mediterranean hoverfly fauna has been enhanced by describing the following species: Cheilosia candida Vujić et Radenković sp. n. (Pindos Mountains), Paragus thracusi Radenković, Likov et Vujić sp. n. (Rhodope Mountains) and Psilota aegeae Vujić, Ståhls et Smit sp. n. (Lesvos island). Diagnosis of new species, as well as identification keys to the Mediterranean species of the subgenus Convocheila Barkalov of Cheilosia Meigen and the European species of the genus Psilota Meigen have been provided. Additionally, mtDNA COI barcodes for the members of the Psilota atra group (except Psilota nana Smit et Vujić) have been given. In addition, the taxonomic status of Psilota anthracina Meigen has been discussed.},
}
@article {pmid33056237,
year = {2020},
author = {Stec, D and Michalczyk, &#x141;},
title = {Macrobiotus coronifer Richters, 1903 (type species for Richtersius Pilato amp; Binda, 1989): designating a new neotype from the original type locality described within the integrative taxonomy framework.},
journal = {Zootaxa},
volume = {4858},
number = {2},
pages = {zootaxa.4858.2.10},
doi = {10.11646/zootaxa.4858.2.10},
pmid = {33056237},
issn = {1175-5334},
mesh = {Animals ; Microscopy, Electron, Scanning ; *Tardigrada ; },
abstract = {The designation of a neotype for Macrobiotus coronifer Richters, 1903 (now the type species of the genus Richtersius Pilato Binda, 1989) by Maucci Ramazzotti (1981) with type locality Bodø in Norway is shown to be invalid as it does not comply with the International Code of Zoological Nomenclature (Article 75.3.4). Furthermore, the specimen selected by Maucci Ramazzotti (1981) is not from the original type locality, and the superficial and outdated documentation prevent a reliable identification of the species. A Code-compliant neotype is therefore designated. The new neotype was collected from the original locus typicus in Svalbard and described with standard light microscopy, detailed scanning electron microscopy imaging, DNA barcodes and a transcriptome, which makes it ideally suited for stabilising the taxonomy and nomenclature of Richtersius coronifer (Richters, 1903).},
}
@article {pmid33056219,
year = {2020},
author = {Ge, X and Wang, Y and Wang, B and Sun, C},
title = {Descriptions of larvae of three species of Hydropsyche Pictet 1834 (Trichoptera, Hydropsychidae) from China.},
journal = {Zootaxa},
volume = {4858},
number = {3},
pages = {zootaxa.4858.3.3},
doi = {10.11646/zootaxa.4858.3.3},
pmid = {33056219},
issn = {1175-5334},
mesh = {Animals ; China ; *Holometabola ; *Insecta ; Larva ; },
abstract = {Adults and larvae of the genus Hydropsyche from Yun-nan and Si-chuan Provinces, China, were examined and the COI barcode gene sequences were obtained and analyzed, adults and larvae of 3 species were successfully associated. Of them, H. uvana Mey 1995 is a new record for the Chinese caddisfly fauna. The larvae of H. cerva Li Tian 1990, H. penicillata Martynov 1931, and H. uvana Mey 1995 are described for the first time. The diagnostic features of the species are described and illustrated.},
}
@article {pmid33056187,
year = {2020},
author = {Mondal, D and Mukherjee, T and Hazra, N},
title = {A new species of the genus Larsia Fittkau (Diptera: Chironomidae) from India, with cladistic analysis and a world key to the known males.},
journal = {Zootaxa},
volume = {4859},
number = {3},
pages = {zootaxa.4859.3.2},
doi = {10.11646/zootaxa.4859.3.2},
pmid = {33056187},
issn = {1175-5334},
mesh = {Animals ; *Chironomidae ; India ; Male ; },
abstract = {A new species of the genus Larsia Fittkau, 1962 is described based on the adult males. It is the first species of this genus reported from India and second member from the Oriental region. The DNA barcode of this new species is provided. The cladistic analysis of the known species of Larsia using morphological data of both immature and male adult stages have supported monophyly of the genus. A world key to the known males of the genus Larsia is presented here.},
}
@article {pmid33056154,
year = {2020},
author = {Trofimova, T and Bidzilya, O and Budashkin, Y and Karolinskiy, E},
title = {Description of a new genus, a new species and a new subspecies of snout moths (Lepidoptera: Pyralidae: Phycitinae) from Eastern Europe and Central Asia.},
journal = {Zootaxa},
volume = {4830},
number = {2},
pages = {zootaxa.4830.2.5},
doi = {10.11646/zootaxa.4830.2.5},
pmid = {33056154},
issn = {1175-5334},
mesh = {Animals ; Asia, Central ; Europe, Eastern ; Female ; Male ; *Moths ; },
abstract = {Yelenka gen. nov. is established to accommodate two species initially described in the genus Nephopterix Hübner, [1825] 1816-Yelenka hastiferella (Ragonot, 1887) comb. nov. and Yelenka gengisella (Ragonot, 1893) comb. nov. Additionally, a new species Yelenka calciferella sp. nov. from Ukraine, Russia and Western Kazakhstan, and its mountain subspecies Yelenka calciferella uyghurica ssp. nov. from Eastern Kazakhstan and Mongolia are described. The new genus is placed into the subfamily Phycitinae. Yelenka gengisella (Ragonot, 1893) sp. rev. is taken out from synonymy with Myrlaea orcella (Ragonot, 1887). Yelenka gengisella and Y. hastiferella are redescribed based on type material and additional specimens. According to DNA barcode, Y. gengisella and Y. hastiferella are placed in the same BOLD BIN. However, these species exhibit pronounced morphological characters that clearly distinguish the two taxa on the species level. The lectotype is designated for Nephopteryx [sic] hastiferella Ragonot, 1887. Comparative diagnoses, a key to species, illustrations of external characters, also male and female genitalia are provided for all species.},
}
@article {pmid33056136,
year = {2020},
author = {KovaČiĆ, M and Wirtz, P and Schliewen, UK},
title = {A new species of Corcyrogobius (Teleostei: Gobiidae) from Île de Ngor, Senegal.},
journal = {Zootaxa},
volume = {4834},
number = {1},
pages = {zootaxa.4834.1.8},
doi = {10.11646/zootaxa.4834.1.8},
pmid = {33056136},
issn = {1175-5334},
mesh = {Animals ; Fishes ; Head ; *Perciformes ; Senegal ; },
abstract = {Corcyrogobius pulcher sp. nov. is described from off Île de Ngor, Dakar, Senegal. Corcyrogobius pulcher is distinguished from its two congeners by having the rear edge of the jaws ending posteriorly below mideye, second dorsal fin I/9, pectoral fin rays 17, pelvic fins oval or truncated posteriorly, scales in lateral series 26-27, anterior oculoscapular head canal with pore β, suborbital row b of sensory papillae anteriorly beginning below vertical of posterior edge of eye, dark vertical caudal bar, branchiostegal membrane without intense dark spot, cheek with two oblique whitish stripes, the first going from the eye downwards and forward to the posterior jaws, the second on the preopercular, alternating with brown oblique stripe going from behind the eye downwards and forward across the cheek. Furthermore, mitochondrial COI-barcoding data unambiguously support the species-level distinctiveness of the three Corcyrogobius species. A key to the species of Corcyrogobius is provided.},
}
@article {pmid33056133,
year = {2020},
author = {Matsuura, K and Bogorodsky, SV and Mal, AO and Alpermann, TJ},
title = {Canthigaster aziz, a new deep-dwelling toby fish (Tetraodontiformes: Tetraodontidae) from the Red Sea.},
journal = {Zootaxa},
volume = {4834},
number = {1},
pages = {zootaxa.4834.1.5},
doi = {10.11646/zootaxa.4834.1.5},
pmid = {33056133},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Indian Ocean ; *Perciformes ; Phylogeny ; *Tetraodontiformes ; },
abstract = {A new species of toby fish, Canthigaster aziz, is described based on a single specimen collected from the northern Red Sea off Saudi Arabia. The holotype was trawled from a depth of 315 m, the second deepest record for the genus. The new species is distinguished from other species of the genus by the following combination of characters: 8 dorsal-fin rays; 8 anal-fin rays; 15 pectoral-fin rays; dorsal-fin origin opposite to anal-fin origin; five diffuse, saddle-like, black blotches along dark yellowish dorsal edge of body between nape and dorsal-fin origin; dorsal half of body light brown with concentrated dark pigments just behind eye and with a longitudinal, irregular, pale golden stripe running from area just behind eye to dorsal side of caudal peduncle; ventral half of posterior part of body pinkish with tiny subcutaneous black spots; head and ventral half of body before anus white; and all fins uniformly pale grey. A phylogenetic analysis of the mitochondrial COI barcoding region resulted in a new and unique evolutionary lineage for the new species that is sister to a clade composed of C. leoparda, C. pygmaea and C. valentini. It also shows C. aziz to be evolutionary deeply divergent from its closest congeners. In addition to the description of the new species, comparisons with congeners and a revised key to the Indo-Pacific species are provided.},
}
@article {pmid33056104,
year = {2020},
author = {Uiblein, F and Gouws, G and Lisher, M and Malauene, BS},
title = {Upeneus floros, a new goatfish from South Africa and Mozambique, with updated taxonomic accounts for U. guttatus and U. pori and a key to Western Indian Ocean Upeneus species (Mullidae).},
journal = {Zootaxa},
volume = {4834},
number = {4},
pages = {zootaxa.4834.4.3},
doi = {10.11646/zootaxa.4834.4.3},
pmid = {33056104},
issn = {1175-5334},
mesh = {Animals ; *Fishes ; Indian Ocean ; Mozambique ; South Africa ; },
abstract = {The highly diverse goatfish genus Upeneus (Mullidae) requires enhanced attention regarding the possible occurrence of undescribed species in insufficiently explored regions. This study focuses on the South-Western Indian Ocean region (SWIO), and on the so-called japonicus-group, a taxonomic species group of Upeneus. Based on in-situ observations and collections in Sodwana Bay, KwaZulu-Natal, South Africa, the Floros goatfish, U. floros n. sp., is described. Detailed comparative studies of colour patterns and morphological characters of all other 13 japonicus-group species were undertaken as well as COI barcoding. The new species occurs in the coastal area between Angoche, N Mozambique and KwaZulu-Natal and partly overlaps in distribution with two similar species, U. guttatus, widely distributed in the Indo-W Pacific, and U. saiab, assumed to be endemic in a small area off Angoche. Two additional japonicus-group species occurring in the SWIO, U. seychellensis from the Seychelles Bank and U. pori from the Mediterranean Sea (as Lessepsian migrant), Northern Red Sea and Madagascar, were also compared. Because specimens as well as in-situ photographs of U. floros have been erroneously identified as either U. guttatus or U. pori during previous studies, updated taxonomic accounts and diagnoses are provided for these species taking size-related and population differences into account. For U. pori, of which a single preserved specimen from SW Madagascar was known so far, a new record from NE Madagascar is reported based on three specimens and a fresh-colour photo. Upeneus floros can be distinguished from U. guttatus and U. pori by a combination of three characters: head length, first dorsal-fin height and number of gill rakers. Upeneus guttatus can be distinguished from the other two species by disproportionally higher anterior dorsal-fin spines vs. a proportional decrease of dorsal-fin spines in height, barbels mostly yellow vs. white or creamy-white, and slightly fewer pectoral-fin rays. COI barcoding detected a clear distinction between U. guttatus and U. floros and U. pori, respectively, but no significant divergence between the two latter species. COI barcoding also failed to differentiate several other Upeneus species which are clearly distinguished morphologically. Possible interrelationships between species distribution patterns and physical oceanography are discussed. An identification key for the 22 WIO Upeneus species is provided.},
}
@article {pmid33056081,
year = {2020},
author = {Mukherjee, T and Mukherjee, B and Hazra, N},
title = {Revision of the Oriental species of Polypedilum Kieffer (Diptera: Chironomidae) with their phylogenetic relationship.},
journal = {Zootaxa},
volume = {4820},
number = {1},
pages = {zootaxa.4820.1.3},
doi = {10.11646/zootaxa.4820.1.3},
pmid = {33056081},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; *Chironomidae ; Phylogeny ; Pupa ; },
abstract = {Imagines and pupae of new species Polypedilum (Pentapedilum) retusum are described from India. Three species, P. (Polypedilum) tamanigrum Sasa, 1983, P. (Pentapedilum) anale (Freeman, 1954), and P. (Tripodura) conghuaense Zhang, Song, Qi and Wang, 2016 with pupa are recorded firstly in the subcontinent. Hypopygia of P. (P.) ascium Chaudhuri, Guha and Das Gupta, 1981, P. (T.) conghuaense, P. (T.) lineatum Chaudhuri, Guha and Das Gupta, 1981 and P. (P.) nudiceps Chaudhuri, Guha and Das Gupta, 1981 are redescribed. Polypedilum (P.) exterflexum Hazra, Sanyal and Brahma, 2015, P. clavipennae Hazra, Sanyal and Brahma, 2015 and P. aduncum Konar and Hazra, 2017 are proposed here to transfer to the genus Stictochironomus Kieffer, 1919. Polypedilum (P.) insolitum Chaudhuri, Guha and Das Gupta, 1981 is here stated as junior synonym of Zavreliella marmorata (Wulp, 1859). In addition, some biogeographic and taxonomic remarks including DNA barcoding for selected species are given. Cladistic analysis of the Oriental species of Polypedilum Kieffer is made to hypothesise their possible relationship. A new dichotomous key of the Oriental species of Polypedilum is presented here.},
}
@article {pmid33056068,
year = {2020},
author = {Tiunova, TM and Semenchenko, AA},
title = {Baetis (Rhodobaetis) molecularis sp. nov., a new mayfly species (Ephemeroptera: Baetidae) from the Russian Far East.},
journal = {Zootaxa},
volume = {4820},
number = {2},
pages = {zootaxa.4820.2.4},
doi = {10.11646/zootaxa.4820.2.4},
pmid = {33056068},
issn = {1175-5334},
mesh = {Animals ; Bayes Theorem ; *Ephemeroptera ; Asia, Eastern ; Phylogeny ; Russia ; },
abstract = {A new species Baetis (Rhodobaetis) molecularis sp. nov. is described and illustrated based on larvae and reared adults from the Far East of Russia. The differential diagnosis of this species is provided with regard to other representatives of the subgenus Rhodobaetis Jacob, 2003 from East Palaearctic and Nearctic Regions. A dataset including novel and publicly available COI mtDNA sequences of 16 species of Rhodobaetis has been assembled to provide a reference dataset for DNA barcoding. The comparison between Baetis (Rhodobaetis) molecularis sp. nov. and other species produced K2P genetic distances of 0.201 in average, values well above those associated with intraspecific variation. The closest species was Baetis foemina McDonough with a K2P distance value 0.114. A Bayesian phylogeny of available Rhodobaetis is also provided.},
}
@article {pmid33056053,
year = {2020},
author = {Krasheninnikov, AB and Makarchenko, EA and Semenchenko, AA and Gavrilo, MV and Vshivkova, KA},
title = {Morphological description and DNA barcoding of some Diamesinae (Diptera, Chironomidae) from the Severnaya Zemlya Archipelago and the Vaigach Island (Russian Arctic).},
journal = {Zootaxa},
volume = {4802},
number = {3},
pages = {zootaxa.4802.3.13},
doi = {10.11646/zootaxa.4802.3.13},
pmid = {33056053},
issn = {1175-5334},
mesh = {Animals ; *Chironomidae ; DNA Barcoding, Taxonomic ; Islands ; Male ; Phylogeny ; Russia ; },
abstract = {Chironomids of the Diamesinae subfamily from the Russian Arctic were studied using both morphological characters and molecular data. Adult males of Diamesa urvantsevi sp. nov., D. amplexivirilia Hansen, Arctodiamesa appendiculata (Lundström) from Severnaya Zemlya Archipelago and D. arctica (Boheman), Pseudokiefferiella sp. from Vaigach Island were described, redescribed, annotated and figured. A reference 658 bp barcode sequence from a fragment of the mitochondrial gene cytochrome oxidase I (COI) was used as a tool for species delimitation. For D. arctica (Boheman) and Pseudokiefferiella sp. close DNA barcodes from Norway were performed, which allowed to relate these specimens to the described species. Comparisons with corresponding regions of COI between each described species and close related congeneric species produced K2P genetic distances of 0.11-0.16, values well associated with interspecific variation. Phylogenetic relationships for genera Arctodiamesa Makarchenko and Pseudokiefferiella Zavřel were reconstructed for the first time.},
}
@article {pmid33056038,
year = {2020},
author = {Kim, S and Lee, S},
title = {New species, Agnoea digitiella sp. nov., of the family Lypusidae (Lepidoptera: Gelechioidea) based on morphology and COI sequences.},
journal = {Zootaxa},
volume = {4803},
number = {1},
pages = {zootaxa.4803.1.11},
doi = {10.11646/zootaxa.4803.1.11},
pmid = {33056038},
issn = {1175-5334},
mesh = {Animals ; Genitalia ; *Moths ; },
abstract = {In this study, Agnoea digitiella Kim sp. nov. of the little known family Lypusidae are new to science. New taxonomical description and illustrations of its adult and genitalia are provided. Additionally, intra- and inter genetic divergence within the genus, and Neighbor-joining analyses are also supported that A. digitiella sp. nov. is clearly distinguished from congeneric species in the COI gene.},
}
@article {pmid33056016,
year = {2020},
author = {DE Meyer, M and Goergen, G and Jordaens, K},
title = {Taxonomic revision of the Afrotropical Phytomia Guérin-Méneville (Diptera: Syrphidae).},
journal = {Zootaxa},
volume = {4803},
number = {2},
pages = {zootaxa.4803.2.1},
doi = {10.11646/zootaxa.4803.2.1},
pmid = {33056016},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; *Diptera ; },
abstract = {The Afrotropical representatives of the hoverfly genus Phytomia Guérin-Méneville (Diptera) are revised. In total, 19 species are recognized of which three are new to science: Phytomia austeni sp. nov., P. memnon sp. nov., and P. pallida sp. nov. Phytomia neavei Bezzi is considered a junior synonym of P. kroeberi (Bezzi), P. noctilio Speiser a junior synonym of P. pubipennis Bezzi, and P. ephippium Bezzi a junior synonym of P. melas (Bezzi). Lectotypes are designated for the following species: Megaspis bulligera Austen, Megaspis erratica Bezzi, and Megaspis poensis Bezzi. In addition, unpublished lectotype designations are hereby formally published for the following species: Megaspis bullata Loew, Megaspis curta Loew, and Megaspis capito Loew. Phytomia curta (Loew) is considered a valid species, and differentiated from P. natalensis (Macquart). Phytomia fronto Loew is tentatively considered to belong to the genus Simoides Loew. The relationship between the different Phytomia species, as well as the relationship between Phytomia and Simoides, is briefly discussed based on morphological and DNA data.},
}
@article {pmid33056012,
year = {2020},
author = {Ardila-Camacho, A and Martins, CC and Noriega, JA},
title = {Isostenosmylus ammirabilis sp. nov., a remarkable new species of lance lacewing (Neuroptera: Osmylidae) from the Colombian Andes.},
journal = {Zootaxa},
volume = {4803},
number = {3},
pages = {zootaxa.4803.3.10},
doi = {10.11646/zootaxa.4803.3.10},
pmid = {33056012},
issn = {1175-5334},
mesh = {Animals ; Colombia ; *Holometabola ; },
abstract = {Isostenosmylus Krüger, 1913 is the richest genus of Osmylidae of the Neotropical region, with 17 described species so far, which are distributed mainly in the Andean region and in the South of Brazil and Paraguay. A new remarkable Colombian species of Isostenosmylus-I. ammirabilis sp. nov.-is herein described and illustrated. DNA barcode of mitochondrial gene cytochrome c oxidase subunit I (COI) for this species is also provided. Taxonomic keys for the genus are updated.},
}
@article {pmid33055995,
year = {2020},
author = {DE Alvarenga, ADS and Magalhaes, ILF and DA Fonseca, RN and PÉrez-GonzÁlez, A},
title = {Rectifying the identities of the males of two Micrathena species (Araneae: Araneidae), with report of the first case of intersexuality in the genus.},
journal = {Zootaxa},
volume = {4808},
number = {1},
pages = {zootaxa.4808.1.9},
doi = {10.11646/zootaxa.4808.1.9},
pmid = {33055995},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures ; Animals ; Female ; Male ; *Spiders ; },
abstract = {Despite extensive taxonomic work on the Neotropical fauna of the spider genus Micrathena Sundevall, for 27 out of 117 (23%) species only the female morphology has been described, and some of the previously hypothesized male-female matches have been proven erroneous. This work provides new insight about sex matching in two species: Micrathena ruschii (Mello-Leitão, 1945) and Micrathena lata Chickering, 1960. For Micrathena ruschii, the male previously hypothesized to belong to this species was collected with females in Itatiaia; we here present morphologically different males, also collected with females, in Macaé, both in Rio de Janeiro, Brazil. Through a DNA barcoding approach, we present molecular evidence indicating conspecificity of M. ruschii females with the males collected in Macaé, proving the male from Itatiaia to be a misidentification. Therefore, a description of the correct male of Micrathena ruschii is herein provided. The male previously identified as M. ruschii probably represents an undescribed species but is not named here due to scarcity of material. We also describe for the first time the male of Micrathena lata based on one specimen collected in Misiones, Argentina. This male specimen belongs to the militaris species group, where M. lata is the only species from the Atlantic Forest previously only known by females. In addition, we detect an intersexual specimen of Micrathena ruschii, revealing the first case of intersexuality for the genus.},
}
@article {pmid33055983,
year = {2020},
author = {Chernyshev, AV and Polyakova, NE and Vignesh, MS and Jain, RP and Sanjeevi, P and Norenburg, JL and Rajesh, RP},
title = {A histology-free description of a new species of the genus Tetrastemma (Nemertea: Hoplonemertea: Monostilifera) from Hawaii and India.},
journal = {Zootaxa},
volume = {4808},
number = {2},
pages = {zootaxa.4808.2.10},
doi = {10.11646/zootaxa.4808.2.10},
pmid = {33055983},
issn = {1175-5334},
mesh = {*Acanthocephala ; Animals ; DNA ; Hawaii ; India ; },
abstract = {A new species of the genus Tetrastemma Ehrenberg, 1831, T. freyae sp. nov., is described and illustrated from Hawaii and India. The description is based on light microscopy examination of the external and internal morphology, as well as on two gene markers (cytochrome c oxidase subunit I and histone H3 DNA).},
}
@article {pmid33055982,
year = {2020},
author = {Frolov, AV and Akhmetova, LA and Vishnevskaya, MS},
title = {A new species of the endemic Madagascan scarab beetle genus, Madecorphnus grebennikovi (Coleoptera: Scarabaeidae: Orphninae): morphological description and DNA barcode.},
journal = {Zootaxa},
volume = {4808},
number = {2},
pages = {zootaxa.4808.2.9},
doi = {10.11646/zootaxa.4808.2.9},
pmid = {33055982},
issn = {1175-5334},
mesh = {Animals ; *Coleoptera ; DNA Barcoding, Taxonomic ; },
abstract = {A new species of the orphnine scarab beetle genus Madecorphnus Paulian, 1992, Madecorphnus grebennikovi Frolov, Akhmetova Vishnevskaya, new species, is described from the Marojejy National Park, Sava Region, northeastern Madagascar. The new species can be distinguished from the congeners by the parameres narrowly rounded in lateral view and having a small but distinct lateral teeth, and by the endophallic armature consisting of 1) a long straight sclerite with attached to its end a 2/3 shorted, somewhat curved sclerite, 2) separate smaller, elongate sclerite, and 3) a rather large area of microspinules. The 811 bp long fragment of the mitochondrial gene COI (DNA barcode) is provided as a part of the diagnosis of the new species. An updated key to the Madecorphnus species is given.},
}
@article {pmid33055922,
year = {2020},
author = {Beaver, EP and Moore, MD and Grehan, JR and Velasco-CastrillÓn, A and Stevens, MI},
title = {Four new species of Splendid Ghost Moths (Lepidoptera: Hepialidae: Aenetus) from Australia and Papua New Guinea.},
journal = {Zootaxa},
volume = {4809},
number = {3},
pages = {zootaxa.4809.3.2},
doi = {10.11646/zootaxa.4809.3.2},
pmid = {33055922},
issn = {1175-5334},
mesh = {Animals ; *Moths ; Papua New Guinea ; },
abstract = {Four new Aenetus Herrich-Schäffer species are described from northern Australasia; Aenetus simonseni sp. nov. from the top-end of the Northern Territory, Australia, A. maiasinus sp. nov. from the Kimberley region of Western Australia, A. trigonogrammus sp. nov. from south-eastern Queensland, Australia, and A. albadamanteum sp. nov. from eastern Papua New Guinea. Aenetus simonseni sp. nov. and A. maiasinus sp. nov. appear to belong to the tegulatus-group of species (sensu Grehan et al. 2018), A. trigonogrammus sp. nov. is part of the splendens-group of species (sensu Simonsen 2018), while A. albadamanteum sp. nov. shares morphological similarities with A. hampsoni (Joicey Noakes, 1914), A. crameri Viette, 1956, and A. toxopeusi Viette, 1956, from New Guinea, and A. cohici Viette, 1961 from New Caledonia. The four new species are illustrated and compared with superficially similar species in morphology and, for two species, molecular (mtDNA COI gene) sequences.},
}
@article {pmid33055890,
year = {2020},
author = {Habib, KA and Islam, MJ and Nahar, N and Neogi, AK},
title = {Pomacentrus bangladeshius, a new species of damselfish (Perciformes, Pomacentridae) from Saint Martin's Island, Bangladesh.},
journal = {Zootaxa},
volume = {4860},
number = {3},
pages = {zootaxa.4860.3.6},
doi = {10.11646/zootaxa.4860.3.6},
pmid = {33055890},
issn = {1175-5334},
mesh = {Animals ; Bangladesh ; Gills ; Islands ; *Perciformes ; Phylogeny ; },
abstract = {A new species of damselfish, Pomacentrus bangladeshius, is described from 3 specimens, 67-77 mm standard length (SL), collected from Saint Martin's Island, Bangladesh. The new species is distinguished from congeners in having the following combination of characters: XIV, 13 dorsal-fin elements; II, 14 anal-fin elements; 19 pectoral-fin rays; 18-19 lateral-line scales; 17-19 gill rakers on first arch; body depth 1.68-1.88 (1.88) in SL; snout 4.17-4.60 (4.17) in head length; head 2.91-3.09 (3.08) in SL; a prominent notch present between preorbital and suborbital; olive to dark brown body color, dark brown premaxilla, and yellow iris with a narrow bronze eye ring. The new species inhabits shallow reef flats around rock and coral outcrops. Phylogenetic analysis also shows the clear divergence of P. bangladeshius from other genetically closely related congeneric species retrieved from GenBank and that it represents a separate lineage.},
}
@article {pmid33055856,
year = {2020},
author = {Makarchenko, EA and Semenchenko, AA and Palatov, DM},
title = {Taxonomy of some Boreoheptagyiini Brundin (Diptera: Chironomidae: Diamesinae) from the mountains of Central Asia and the Middle East, with description and DNA barcoding of new taxa.},
journal = {Zootaxa},
volume = {4790},
number = {1},
pages = {zootaxa.4790.1.5},
doi = {10.11646/zootaxa.4790.1.5},
pmid = {33055856},
issn = {1175-5334},
mesh = {Animals ; Bayes Theorem ; *Chironomidae ; DNA ; DNA Barcoding, Taxonomic ; Male ; Middle East ; Phylogeny ; },
abstract = {Chironomids of the tribe Boreoheptagyiini from the mountains of Iran, China and East Kazakhstan are revised using both morphological characters and partial DNA sequences of the mitochondrial cytochrome c oxidase subunit I gene. Using adult males, Palatovia lorestanica gen. nov. sp. nov., as well as Boreoheptagyia iranica sp. nov. both from Iran (Lorestan Province, Zagros Mountains), B. joeli sp. nov. from China (Tien Shan Mountains), and B. sarymsactyensis sp. nov. from Eastern Kazakhstan (Kazakh Mountain Altai), are described and figured. A brief redescription of the rare species B. brevitarsis (Tokunaga) from Iran (Mazandaran Province), previously known only from Japan, is also given. The DNA barcoding analysis shows well-supported genetic divergence between all studied taxa (four species of the genus Boreoheptagyia and one of Palatovia). Combining DNA barcodes obtained in this study with available sequences in GenBank, the phylogenetic relationships of the tribe Boreoheptagyiini are reconstructed. In the resulting Bayesian and maximum likelihood (ML) tree the polyphyly of the genus Boreoheptagyia is recognized. B. iranica is placed as a sister species to P. lorestanica, despite the lack of confirmation of their morphological similarity.},
}
@article {pmid33055832,
year = {2020},
author = {Derycke, EG and Gottscho, AD and Gottscho, AD and Mulcahy, DG and DE Queiroz, K},
title = {A new cryptic species of fringe-toed lizards from southwestern Arizona with a revised taxonomy of the Uma notata species complex (Squamata: Phrynosomatidae).},
journal = {Zootaxa},
volume = {4778},
number = {1},
pages = {zootaxa.4778.1.3},
doi = {10.11646/zootaxa.4778.1.3},
pmid = {33055832},
issn = {1175-5334},
mesh = {Animals ; Arizona ; Biological Evolution ; *Lizards ; Phylogeny ; },
abstract = {Fringe-toed lizards (Uma) are among the most specialized lizards in North America, adapted to insular windblown sand habitats in the hyper-arid southwestern deserts, with allopatric distributions, subtle morphological variation, and an unstable taxonomic history. We analyzed a morphological dataset of 40 characters for 65 specimens and a molecular dataset of 2,286 bases from three mitochondrial loci for 92 individuals and interpreted these data alongside published analyses of multi-locus genetic data with the goal of revising the taxonomy of the Uma notata (Baird 1858) species complex. We confirmed that fringe-toed lizards from the Mohawk Dunes in southwestern Arizona (U. sp.) constitute a cryptic species sister to the rest of the complex that can be diagnosed with DNA barcoding and geography, so we describe and name this species Uma thurmanae sp. nov. We also confirmed the evolutionary distinctiveness of U. inornata (Cope 1895), an endangered species endemic to Coachella Valley in southern California. We designate a lectotype for the taxon U. "rufopunctata", but we put its name in quotation marks to reflect its uncertain taxonomic status with respect to its neighboring species U. cowlesi and U. notata.},
}
@article {pmid33055770,
year = {2020},
author = {Yu, T and Wang, M},
title = {A new species of the genus Sarcinodes Guenée, [1858] (Lepidoptera, Geometridae) from China.},
journal = {Zootaxa},
volume = {4779},
number = {4},
pages = {zootaxa.4779.4.6},
doi = {10.11646/zootaxa.4779.4.6},
pmid = {33055770},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; China ; Female ; Male ; *Moths ; },
abstract = {The genus Sarcinodes Guenée, [1858]of China is reviewed and totally 9 species are recognized with the description of Sarcinodes hainana sp. nov. from Hainan, China. Sarcinodes lilacina Moore, 1888 is reported for the first time from Yunnan, China. The external morphology of adults, particularly the male and female genitalia, are illustrated. COI sequences were obtained as DNA barcodes for identification of the new species. A key to the Chinese Sarcinodes species is provided.},
}
@article {pmid33055761,
year = {2020},
author = {Sankaran, PM and Sebastian, PA},
title = {A redescription and a synonym in the South Asian millipede genus Xenobolus Carl, 1919 (Spirobolida, Pachybolidae).},
journal = {Zootaxa},
volume = {4780},
number = {1},
pages = {zootaxa.4780.1.8},
doi = {10.11646/zootaxa.4780.1.8},
pmid = {33055761},
issn = {1175-5334},
mesh = {Animals ; *Arthropods ; },
abstract = {The South Asian spiroboloid species Xenobolus carnifex (Fabricius, 1775) is redescribed and illustrated in detail. The genus Xenobolus Carl, 1919 is diagnosed and its relationship and subfamily placement within Pachybolidae Cook, 1897 are discussed. The species Xenobolus acuticonus Attems, 1936 is synonymised with X. carnifex based on morphological and DNA barcoding data. Information on the natural history of X. carnifex is provided and its current distribution is mapped.},
}
@article {pmid33055755,
year = {2020},
author = {Uluar, O and Çiplak, B},
title = {Evolution, characterization and phylogenetic utility of ITS2 gene in Orthoptera and some Polyneoptera: Highly variable at the order level and highly conserved at the species level.},
journal = {Zootaxa},
volume = {4780},
number = {1},
pages = {zootaxa.4780.1.2},
doi = {10.11646/zootaxa.4780.1.2},
pmid = {33055755},
issn = {1175-5334},
mesh = {Animals ; Base Sequence ; DNA, Ribosomal Spacer ; Neoptera ; *Orthoptera ; Phylogeny ; },
abstract = {ITS2 is often suggested as a potential marker for evolutionary studies and species barcoding. However, there are many lineages have not been studied. This study focuses on ITS2 in Polyneoptera at the order and species levels. ITS2 sequences representing six polyneopteran orders and 15 species in the genus Anterastes are studied. We arrived at the following conclusions: (i) ITS2 is highly variable and contains little phylogenetic information in Polyneoptera, (ii) the shortest length and the highest GC content of ITS2 is found in Orthoptera among insects, (iii) the secondary structure exhibits general characteristics of eukaryotes especially in helices II and III, and with no order-specific architecture, (iv) ITS2 is highly conserved at the species level, both in linear sequences and secondary structures, (v) helices I, IA, II, IIA and III almost invariable in nucleotide sequence shared by all species in the genus. At the generic level, the most conspicuous result is the variable pattern in ITS2. It is highly conserved in helical sequences, but highly variable in non/peri-helical regions which we considered to be mutation islands. These frequently mutated regions contain a significant amount of molecular homoplasy, thus, the utility of ITS2 in phylogenetic analyses and species barcoding is low, at least in Polyneoptera.},
}
@article {pmid33055725,
year = {2020},
author = {Wanke, D and Hausmann, A and Krogmann, L and PetrÁnyi, G and Rajaei, H},
title = {Taxonomic revision of the genus Nychiodes Lederer, 1853 (Geometridae: Ennominae: Boarmiini) with description of three new species-an integrative approach.},
journal = {Zootaxa},
volume = {4812},
number = {1},
pages = {zootaxa.4812.1.1},
doi = {10.11646/zootaxa.4812.1.1},
pmid = {33055725},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Female ; Male ; *Moths ; },
abstract = {The non-European taxa of the genus Nychiodes Lederer, 1853 are revised. Type specimens of all described species and a large series of about 800 additional specimens were morphologically examined. More than 400 genitalia preparations were made and analyzed along with distributional and DNA barcode data. As a result of our integrative taxonomic approach, Nychiodes waltheri saerdabica Wehrli, 1938 syn. nov., is synonymized with N. waltheri Wagner, 1919; N. palaestinensis libanotica Zerny, 1933 syn. nov. is synonymized with N. palaestinensis Wagner, 1919 and the synonymy of N. persuavis Wehrli, 1929 syn. rev. with N. palaestinensis is confirmed; N. admirabila safidaria Wiltshire, 1943 syn. nov. is synonymized with N. admirabila Brandt, 1938; N. agatcha Brandt, 1938 syn. nov., N. subvirida disjuncta Wehrli, 1941 syn. nov. and N. subvirida taftana Brandt, 1941 syn. nov. are synonymized with N. subvirida Brandt, 1938. Also, N. variabila variabila Brandt, 1938 syn. nov., N. variabila opulenta Brandt, 1941 syn. nov., N. divergaria elbursica Wehrli, 1937 syn. nov., N. divergaria fallax Wehrli, 1939 syn. nov. and N. divergaria achtyca Wehrli, 1939 syn. nov. are synonymized with N. divergaria Staudinger, 1892. Nychiodes convergata sp. nov. from Israel, N. mirzayansi sp. nov. from the Iran and N. eberti sp. nov. from Turkey are described. Lecto- and paralectotypes are designated for N. palaestinensis, N. antiquaria, N. divergaria. Furthermore, N. antiquaria is reported as a new species for Pakistan, N. rayatica is reported as a new species for Iran and the hypothetical occurrence of N. amygdalaria in Iran is confirmed. Additionally, N. tyttha needs to be excluded from the genus. Wing pattern, male and female genitalia and diagnostic characters of all examined species are illustrated and distribution maps are provided. Illustrated keys based on genitalia, as well as a complete checklist of the genus is given here.},
}
@article {pmid33055707,
year = {2020},
author = {Sohail, K and Huang, W and Usman, M and Zhang, Y},
title = {First record of Tettigometridae (Hemiptera: Fulgoromorpha) from Pakistan: description of a new species including barcode identification.},
journal = {Zootaxa},
volume = {4816},
number = {2},
pages = {zootaxa.4816.2.7},
doi = {10.11646/zootaxa.4816.2.7},
pmid = {33055707},
issn = {1175-5334},
mesh = {Animals ; *Hemiptera ; Pakistan ; },
abstract = {Tettigometra ziaratensis sp. nov. is described from Ziarat, Baluchistan, Pakistan; it is the first record of the genus Tettigometra Latreille, 1804 and the family Tettigometridae from this country. Sequence data for the barcoding region of the mitochondrial gene COI for this new species was obtained and deposited in GenBank.},
}
@article {pmid33055661,
year = {2020},
author = {Golzarianpour, K and Malek, M and Golestaninasab, M and Sarafrazi, A and Kochmann, J and Klimpel, S},
title = {Insights into the Urogymnid whiprays (Chondrichthyes: Batoidea) in the Persian Gulf and the Gulf of Oman, with an amendment of their diagnostic characteristics and dispersal range.},
journal = {Zootaxa},
volume = {4819},
number = {2},
pages = {zootaxa.4819.2.5},
doi = {10.11646/zootaxa.4819.2.5},
pmid = {33055661},
issn = {1175-5334},
mesh = {Animals ; Bayes Theorem ; *Elasmobranchii ; Indian Ocean ; Oman ; *Skates, Fish ; },
abstract = {Correct identification of elasmobranch species is crucial for taxonomic and parasitological research. Although molecular barcoding may be the fastest choice to determine the identity of a given species, robust and fast species level identification in the field using morphological characters is essential. During this study, 389 specimens representing seven stingray species (Brevitrygon walga, Himantura leoparda, H. uarnak, Maculabatis randalli, M. arabica, M. gerrardi and Pateobatis fai) were examined from the Persian Gulf and the Gulf of Oman. A 1044 bp fragment of the NADH2 gene was generated for 50 specimens with representatives of all species. To verify the initial morphological identification and to compare intra- and interspecific differences a Neighbor-Joining analysis was conducted using uncorrected p-distances, whereas the Bayesian Inference was used to examine the relationships among taxa. Two species (M. arabica and M. gerrardi) are documented from the Persian Gulf for the first time. The molecular results provide the first known evidence of the sympatric distribution of M. randalli and M. arabica in the north and northwestern Indian Ocean. The results of the Bayesian Inference support the recent divergence of both species. Based on morphological comparisons and molecular support we suggest that the descriptions of M. randalli and M. arabica have been carried out on heterogeneous type series which has led to inconsistency between molecular identification and diagnostic morphological characteristics. Detailed morphological examination revealed that there is a relation between the type and number of denticles on the mid-dorsal surface of the disc and the color pattern of the tail. To address this taxonomic conflict all type materials should be re-examined. The Bayesian Inference tree showed that all specimens from the Persian Gulf and the Gulf of Oman morphologically resembling B. walga were found to group well outside those of the Indian species (B. imbricata) with an average p-distance of 0.097. The low nucleotide differences among the urogymnid taxa (P. fai and H. leoparda) from the Persian Gulf and the Gulf of Oman and their conspecific specimens in the Indo-West Pacific region revealed that philopatric behaviors may cause considerable gene flow among populations.},
}
@article {pmid33055617,
year = {2020},
author = {Kazerani, F and Mortelmans, J and Farashiani, ME and Thorn, S},
title = {A new species of Pherbellia (Diptera: Sciomyzidae) from Iran.},
journal = {Zootaxa},
volume = {4772},
number = {2},
pages = {zootaxa.4772.2.7},
doi = {10.11646/zootaxa.4772.2.7},
pmid = {33055617},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; *Diptera ; Female ; Forests ; Iran ; Male ; },
abstract = {Pherbellia jalili Mortelmans Kazerani sp. nov. is described based on 5 males and 4 females. The new species is associated with old deciduous forest and is found only in the Hyrcanean forest in Iran. It is compared with its sister species, P. annulipes (Zetterstedt, 1846), and a comprehensive distribution map for both species is given. The key to species of this group of Pherbellia is updated including the Japanese Pherbellia tricolor Sueyoshi, 2001. Barcodes are generated for P. jalili sp. nov., P. annulipes, and P. nana nana (Fallén, 1820).},
}
@article {pmid33053137,
year = {2021},
author = {Kheirallah, DA},
title = {DNA barcoding revels first records of three rare coleopteran genera in Northern lakes of Egypt.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {81},
number = {4},
pages = {1054-1060},
doi = {10.1590/1519-6984.234428},
pmid = {33053137},
issn = {1678-4375},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Egypt ; Electron Transport Complex IV/genetics ; *Lakes ; Phylogeny ; },
abstract = {One aquatic coleopteran species from family Dytiscidae and two aquatic coleopteran genera from family Hydrophilidae were recorded in the summer period and represent first records in the Egyptian lakes. Beetles were collected from two northern lakes, Lake Idku and Lake Burullus. They were identified by morphological characteristics as well as the mtDNA barcoding method. A molecular phylogenetic approach was used to determine the genetic identity of the collected samples based on the mitochondrial cytochrome oxidase I (COI). Prodaticus servillianus (Dytiscidae) from Egypt showed no significant difference in the COI region and they are highly similar to P. servillianus from Madagascar. The phylogenetic analysis revealed that the other two coleopteran genera belong to family Hydrophilidae. Based on COI only, there is no clear evidence for their genetic identity at the species level. So, we defined them to the closest taxon and denoted them as Cymbiodyta type A and B. The results indicated that resolving the molecular identity of the aquatic beetles from northern lakes of Egypt need more considerations in the field of biological conservation. We concluded that utilization of COI as a barcoding region for identifying some coleopteran species is not sufficient and additional molecular markers are required to uncover the molecular taxonomy at deep levels.},
}
@article {pmid33053130,
year = {2021},
author = {Viana, JBV and Querino, RB and Carvalho, LCB and Lima, PSC},
title = {Sequence analysis of the internal transcribed spacer 2 (ITS2) region of rDNA for identifying Trichogramma species and evaluating genetic diversity.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {81},
number = {4},
pages = {928-933},
doi = {10.1590/1519-6984.232362},
pmid = {33053130},
issn = {1678-4375},
mesh = {Animals ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; Genetic Variation/genetics ; *Hymenoptera/genetics ; Phylogeny ; Reproducibility of Results ; Sequence Analysis, DNA ; },
abstract = {Species of Trichogramma Westwood, 1833 (Hymenoptera: Trichogrammtidae) are frequently used as biological control agents against Lepidoptera, but practical application of these egg endoparasitoids are complicated because of their complex taxonomy. This study aimed to compare sequences of internal transcribed spacer regions of ribosomal DNA (ITS2-rDNA) of Trichogramma accessions with those deposited in GenBank in order to access the reliability of the ITS2 as a barcode for discriminating species and evaluating the genetic diversity. ITS2-rDNA sequences obtained from seventeen specimens of Trichogramma confirmed previous identifications based on morphological characteristics. Multiple sequence alignment revealed the existence of highly conserved regions in ITS2 sequences while the neighbour-joining dendrogram indicated that the specimens formed three clusters comprising T. manicobai and T. marandobai (group I), T. galloi (group II) and T. pretiosum (group III). The ITS2 marker was shown to be a powerful DNA barcode for discriminating Trichogramma species and could be used to complement the morphological approach.},
}
@article {pmid33053129,
year = {2021},
author = {Pires, WMM and Barros, MC and Fraga, EC},
title = {DNA Barcoding unveils cryptic lineages of Hoplias malabaricus from Northeastern Brazil.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {81},
number = {4},
pages = {917-927},
doi = {10.1590/1519-6984.231598},
pmid = {33053129},
issn = {1678-4375},
mesh = {Animals ; Brazil ; *Characiformes/genetics ; *DNA Barcoding, Taxonomic ; Genetic Variation/genetics ; Haplotypes/genetics ; Phylogeny ; Rivers ; },
abstract = {The trahira or wolf fish - Hoplias malabaricus- is a valid species, although recent cytogenetic and molecular studies have indicated the existence of a species complex. In this context, the present study analyzed the mitochondrial COI marker to determine the levels of genetic diversity of specimens from the Brazilian state of Maranhão, and verify the occurrence of distinct lineages within the study area. Samples were collected from the basins of the Turiaçu, Pindaré, Mearim, Itapecuru, and Parnaíba rivers. A 630-bp fragment was obtained from 211 specimens, with 484 conserved and 108 variable sites, and 60 haplotypes (Hd = 0,947; π = 0,033). The phylogenetic analyses indicated the existence of three distinct lineages of H. malabaricus from Maranhão. Genetic distances of 1.5-8.2% were found between all the populations analyzed, while the variation between haplogroups ranged from 2.1% to 7.7%. The AMOVA indicated that most of the molecular variation was found among groups, with high FST values. The high levels of genetic variability found in the present study are supported by the available cytogenetic data. These findings reinforce the need for the development of effective programs of conservation and management independently for each river basin, in order to preserve the genetic variability found in this taxon.},
}
@article {pmid33051931,
year = {2021},
author = {Rafique, S and Zahid, S and Ali, A and Tariq, M and Saeed, M and Iqbal Sahibzada, K and Ali Shahid, A and Idrees, M},
title = {Genome-wide methylation profiling of HCV pathogenesis to develop diabetes and diabetic complications.},
journal = {Journal of viral hepatitis},
volume = {28},
number = {2},
pages = {245-259},
doi = {10.1111/jvh.13417},
pmid = {33051931},
issn = {1365-2893},
mesh = {DNA Methylation ; *Diabetes Complications ; *Diabetes Mellitus, Type 2/genetics ; *Hepatitis C ; Humans ; *Liver Neoplasms ; Phosphatidylinositol 3-Kinases ; },
abstract = {HCV is key pathological factor for inducting insulin resistance. Such HCV-induced insulin resistance is linked with metabolic syndrome, type 2 diabetes mellitus, extrahepatic manifestations, hepatic fibrosis progression and development of hepatocellular carcinoma. DNA methylation alterations can cause developmental abnormalities, tumours and other diseases. In our study, PBMCs were isolated and genomic DNA was extracted. DNA fragmentation was achieved by sonication to 200-400 bp; subsequently, end repair and adenylation was performed. Manufacturer's guidelines were followed to ligate Cytosine-methylated barcodes to sonicated DNA. EZ DNA Methylation-GoldTM Kit was then employed to treat these DNA segments twice with bisulphite. A Library was maintained, sequenced on an Illumina platform and 150/125 bp paired-end reads generated. GO seq R package was used to perform Gene Ontology (GO) enrichment analysis for genes linked to DMRs and DMPs; gene length bias was corrected. We identified 12 945 significant hypermethylated DMRs among all samples that were screened as those with at least 0.1 methylation level differences and P-value less than 0.05. Fisher's exact test with FDR multiple test correction is used for identification of DMPs and DMRs. High throughput bisulphite sequencing (Illumina) was carried out, and bioinformatics analysis was performed to analyse methylation status. Gene ontology (GO) and KEGG pathway enrichment analysis showed differentially methylated regions enriched in various pathways that include PI3K-AKT/IRS1 signalling pathway, metabolic pathway, oxidative phosphorylation, Renin-angiotensin system that are all involved in developing type-2 diabetes (T2D). Our study provides supporting evidence for significant involvement of HCV infection in development of epigenetic modifications in regulation of metabolic disorders like T2D and its complications.},
}
@article {pmid33047543,
year = {2020},
author = {Wu, J and Gao, HY and Luo, L and Wen, ST and Chen, PY and Yu, J},
title = {DNA Barcode Technology and Its Application Prospects in Forensic Medicine.},
journal = {Fa yi xue za zhi},
volume = {36},
number = {4},
pages = {559-564},
doi = {10.12116/j.issn.1004-5619.2020.04.023},
pmid = {33047543},
issn = {1004-5619},
mesh = {DNA/genetics ; *DNA Barcoding, Taxonomic ; *Forensic Medicine ; },
abstract = {Traditional species identification has gone through five stages -- morphology, cytology, biochemistry, immunology and molecular biology. At present, the use of DNA technology for species identification has become a research hotspot. In the use of DNA for species identification, the presentation and application of DNA barcode is of epoch-making significance. With the successful application of new technology in species identification, forensic species identification has also made corresponding development, and is expected to play an important role in forensic related fields. This paper briefly describes the general situation and principles of DNA barcode technology as well as its advantages and limitations when applied to biological classification, and discusses the future significance and feasibility of DNA barcode technology in forensic applications, in order to provide new ideas for future forensic identification.},
}
@article {pmid33047508,
year = {2021},
author = {Ducotterd, C and Crovadore, J and Lefort, F and Rubin, JF and Ursenbacher, S},
title = {A powerful long metabarcoding method for the determination of complex diets from faecal analysis of the European pond turtle (Emys orbicularis, L. 1758).},
journal = {Molecular ecology resources},
volume = {21},
number = {2},
pages = {433-447},
pmid = {33047508},
issn = {1755-0998},
support = {//Schildkr&#xf6;ten-Interessengemeinschaft Schweiz/ ; //Canton de Vaud/ ; //Office F&#xe9;d&#xe9;ral de l'Environnement/ ; //Canton de Gen&#xe8;ve/ ; //Canton de Neuch&#xe2;tel/ ; //Fondation Gelbert/ ; //La Maison de la Rivi&#xe8;re/ ; //HES-SO University of Applied Sciences and Arts Western Switzerland/ ; //Soci&#xe9;t&#xe9; Acad&#xe9;mique Vaudoise/ ; //Protection et R&#xe9;cup&#xe9;ration des tortues/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Diet/*veterinary ; Feces ; High-Throughput Nucleotide Sequencing ; *Turtles ; },
abstract = {High-throughput sequencing has become an accurate method for the identification of species present in soil, water, faeces, gut or stomach contents. However, information at the species level is limited due to the choice of short barcodes and based on the idea that DNA is too degraded to allow longer sequences to be amplified. We have therefore developed a long DNA metabarcoding method based on the sequencing of short reads followed by de novo assembly, which can precisely identify the taxonomic groups of organisms associated with complex diets, such as omnivorous individuals. The procedure includes 11 different primer pairs targeting the COI gene, the large subunit of the ribulose-1,5-bisphosphate carboxylase gene, the maturase K gene, the 28S rRNA and the trnL-trnF chloroplastic region. We validated this approach using 32 faeces samples from an omnivorous reptile, the European pond turtle (Emys orbicularis, L. 1758). This metabarcoding approach was assessed using controlled experiments including mock communities and faecal samples from captive feeding trials. The method allowed us to accurately identify prey DNA present in the diet of the European pond turtles to the species level in most of the cases (82.4%), based on the amplicon lengths of multiple markers (168-1,379 bp, average 546 bp), and produced by de novo assembly. The proposed approach can be adapted to analyse various diets, in numerous conservation and ecological applications. It is consequently appropriate for detecting fine dietary variations among individuals, populations and species as well as for the identification of rare food items.},
}
@article {pmid33045364,
year = {2020},
author = {Rostami, M and Fasihi-Harandi, M and Shafiei, R and Aspatwar, A and Derakhshan, FK and Raeghi, S},
title = {Genetic diversity analysis of Blastocystis subtypes and their distribution among the domestic animals and pigeons in northwest of Iran.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {86},
number = {},
pages = {104591},
doi = {10.1016/j.meegid.2020.104591},
pmid = {33045364},
issn = {1567-7257},
mesh = {Animal Diseases/*epidemiology/*microbiology ; Animals ; *Animals, Domestic ; Blastocystis/*genetics ; Blastocystis Infections/*veterinary ; Cattle ; *Columbidae ; *Genetic Variation ; Iran/epidemiology ; Poultry ; Sheep ; Zoonoses ; },
abstract = {Blastocystis is a unicellular, anaerobic, eukaryotic protist, a common parasite found in the intestinal tracts of animals and humans. During the last few years, the host fecal DNA analysis by nucleic acid-based method has led to significant advances in Blastocystis diagnostics and enabled subtypes (STs). The zoonotic transmission of Blastocystis to humans is not well understood, therefore the present study was conducted to identify Blastocystis subtypes in Iran from different animal hosts from northwest of Iran. A total of 427 fresh fecal specimens were collected from cattle, sheep, poultry and pigeon (40,150,132,105 respectively). To detect the Blastocystis sp., each fecal specimen was examined microscopically. Total DNA from the samples that were positive for Blastocystis sp. was isolated, and the barcoding region of the small subunit of ribosomal rRNA (18S rRNA) was amplified and sequenced. Subsequently, sequence analyses, genetic diversity indices and evolutionary relationships of Blastocystis subtype populations were carried out. In total, 14.98% of the analyzed samples were positive for Blastocystis sp. and the subtypes detected were ST3,7,10 and 14. Among these, the ST10 was the main subtype that was found only in the cattle, sheep and poultry and the zoonotic subtype ST3 was present only from cattle. Our study shows the presence of Blastocystis subtypes in the sheep in north west of Iran and also demonstrated that the genetic approaches are crucial to understand the host specify of subtypes and the mode of infection. The study suggests that the genetic approaches will help us to understand the host specificity of subtypes and their role in infection if they are obtained from human and animals from the same geographical locations. Therefore, it is important to study the zoonotic aspects of this parasite with large number of samples from different groups of animals and from different geographical locations.},
}
@article {pmid33036978,
year = {2020},
author = {Guarecuco, R and Williams, RT and Baudrier, L and La, K and Passarelli, MC and Ekizoglu, N and Mestanoglu, M and Alwaseem, H and Rostandy, B and Fidelin, J and Garcia-Bermudez, J and Molina, H and Birsoy, K},
title = {Dietary thiamine influences l-asparaginase sensitivity in a subset of leukemia cells.},
journal = {Science advances},
volume = {6},
number = {41},
pages = {},
pmid = {33036978},
issn = {2375-2548},
support = {DP2 CA228042/CA/NCI NIH HHS/United States ; T32 GM007739/GM/NIGMS NIH HHS/United States ; F30 CA247026/CA/NCI NIH HHS/United States ; F30 CA247199/CA/NCI NIH HHS/United States ; F31 CA247528/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; *Antineoplastic Agents/therapeutic use ; Asparaginase/metabolism/pharmacology/therapeutic use ; Diet ; *Leukemia/drug therapy ; Membrane Transport Proteins ; Mice ; Thiamine/pharmacology ; },
abstract = {Tumor environment influences anticancer therapy response but which extracellular nutrients affect drug sensitivity is largely unknown. Using functional genomics, we determine modifiers of l-asparaginase (ASNase) response and identify thiamine pyrophosphate kinase 1 as a metabolic dependency under ASNase treatment. While thiamine is generally not limiting for cell proliferation, a DNA-barcode competition assay identifies leukemia cell lines that grow suboptimally under low thiamine and are characterized by low expression of solute carrier family 19 member 2 (SLC19A2), a thiamine transporter. SLC19A2 is necessary for optimal growth and ASNase resistance, when standard medium thiamine is lowered ~100-fold to human plasma concentrations. In addition, humanizing blood thiamine content of mice through diet sensitizes SLC19A2-low leukemia cells to ASNase in vivo. Together, our work reveals that thiamine utilization is a determinant of ASNase response for some cancer cells and that oversupplying vitamins may affect therapeutic response in leukemia.},
}
@article {pmid33036491,
year = {2020},
author = {Doh, EJ and Lee, G and Jung, HJ and Kwon, KB and Kim, JH},
title = {Chemotaxonomic Monitoring of Genetically Authenticated Amomi Fructus Using High-Performance Liquid Chromatography-Diode Array Detector with Chemometric Analysis.},
journal = {Molecules (Basel, Switzerland)},
volume = {25},
number = {19},
pages = {},
pmid = {33036491},
issn = {1420-3049},
support = {Project No.S2853477//project for Collabo R&amp;D between Industry, Academy, and Research Institute/ ; },
mesh = {Amomum/*chemistry/*classification ; Chromatography, High Pressure Liquid/*methods ; Phylogeny ; },
abstract = {Amomi Fructus is widely used to treat digestive disorders, and Amomum villosum, A. villosum var. xanthioides, and A. longiligulare are permitted medicinally in national pharmacopeias. However, there are a variety of adulterants present in herbal markets owing to their morphological similarities to the genuine Amomum species. Forty-two Amomi Fructus samples from various origins were identified using internal transcribed spacer and chloroplast barcoding analyses, and then their chromatographic profiles were compared using chemometric analysis for chemotaxonomic monitoring. Among the Amomi Fructus samples, A. villosum, A. longiligulare, A. ghaticum, and A. microcarpum were confirmed as single Amomum species, whereas a mixture of either these Amomum species or with another Amomum species was observed in 15 samples. Chemotaxonomic monitoring results demonstrated that two medicinal Amomum samples, A. villosum and A. longiligulare, were not clearly distinguished from each other, but were apparently separated from other non-medicinal Amomum adulterants. A. ghaticum and A. microcarpum samples were also chemically different from other samples and formed their own species groups. Amomum species mixtures showed diverse variations of chemical correlations according to constituent Amomum species. Genetic authentication-based chemotaxonomic monitoring methods are helpful in classifying Amomi Fructus samples by their original species and to distinguish genuine Amomum species from the adulterants.},
}
@article {pmid33035799,
year = {2021},
author = {Pekdemir, S and Ipekci, HH and Serhatlioglu, M and Elbuken, C and Onses, MS},
title = {SERS-active linear barcodes by microfluidic-assisted patterning.},
journal = {Journal of colloid and interface science},
volume = {584},
number = {},
pages = {11-18},
doi = {10.1016/j.jcis.2020.09.087},
pmid = {33035799},
issn = {1095-7103},
abstract = {Simple, low-cost, robust, and scalable fabrication of microscopic linear barcodes with high levels of complexity and multiple authentication layers is critical for emerging applications in information security and anti-counterfeiting. This manuscript presents a novel approach for fabrication of microscopic linear barcodes that can be visualized under Raman microscopy. Microfluidic channels are used as molds to generate linear patterns of end-grafted polymers on a substrate. These patterns serve as templates for area-selective binding of colloidal gold nanoparticles resulting in plasmonic arrays. The deposition of multiple taggant molecules on the plasmonic arrays via a second microfluidic mold results in a linear barcode with unique Raman fingerprints that are enhanced by the underlying plasmonic nanoparticles. The width of the bars is as small as 10 μm, with a total barcode length on the order of 100 μm. The simultaneous use of geometric and chemical security layers provides a high level of complexity challenging the counterfeiting of the barcodes. The additive, scalable, and inexpensive nature of the presented approach can be easily adapted to different colloidal nanomaterials and applications.},
}
@article {pmid33033825,
year = {2021},
author = {Motoki, MT and Linton, YM and Conn, JE and Ruiz-Lopez, F and Wilkerson, RC},
title = {Phylogenetic Network of Mitochondrial COI Gene Sequences Distinguishes 10 Taxa Within the Neotropical Albitarsis Group (Diptera: Culicidae), Confirming the Separate Species Status of Anopheles albitarsis H (Diptera: Culicidae) and Revealing a Novel Lineage, Anopheles albitarsis J.},
journal = {Journal of medical entomology},
volume = {58},
number = {2},
pages = {599-607},
pmid = {33033825},
issn = {1938-2928},
support = {R01 AI054139/AI/NIAID NIH HHS/United States ; U24 AI050139/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Anopheles/*classification/genetics ; Electron Transport Complex IV/genetics ; Genetic Variation ; *Phylogeny ; South America ; },
abstract = {The Neotropical Albitarsis Group is a complex assemblage of essentially isomorphic species which currently comprises eight recognized species-five formally described (Anopheles albitarsis Lynch-Arribalzaga, An. deaneorum Rosa-Freitas, An. janconnae Wilkerson and Sallum, An. marajoara Galvao and Damasceno, An. oryzalimnetes Wilkerson and Motoki) and three molecularly assigned (An. albitarsis F, G &amp; I)-and one mitochondrial lineage (An. albitarsis H). To further explore species recognition within this important group, 658 base pairs of the mitochondrial DNA cytochrome oxidase subunit I (COI) were analyzed from 988 specimens from South America. We conducted statistical parsimony network analysis, generated estimates of haplotype, nucleotide, genetic differentiation, divergence time, and tested the effect of isolation by distance (IBD). Ten clusters were identified, which confirmed the validity of the eight previously determined species, and confirmed the specific status of the previous mitochondrial lineage An. albitarsis H. High levels of diversity were highlighted in two samples from Pará (= An. albitarsis J), which needs further exploration through additional sampling, but which may indicate another cryptic species. The highest intra-specific nucleotide diversity was observed in An. deaneorum, and the lowest in An. marajoara. Significant correlation between genetic and geographical distance was observed only in An. oryzalimnetes and An. albitarsis F. Divergence time within the Albitarsis Group was estimated at 0.58-2.25 Mya, during the Pleistocene. The COI barcode region was considered an effective marker for species recognition within the Albitarsis Group and a network approach was an analytical method to discriminate among species of this group.},
}
@article {pmid33033309,
year = {2020},
author = {Park, E and Poulin, R},
title = {Widespread Torix Rickettsia in New Zealand amphipods and the use of blocking primers to rescue host COI sequences.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {16842},
pmid = {33033309},
issn = {2045-2322},
mesh = {Amphipoda/*genetics/*microbiology ; Animals ; *DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Genetics, Population ; *Host Microbial Interactions ; New Zealand ; Phylogeny ; Rickettsia/*genetics/physiology ; Symbiosis/genetics ; },
abstract = {Endosymbionts and intracellular parasites are common in arthropod hosts. As a consequence, (co)amplification of untargeted bacterial sequences has been occasionally reported as a common problem in DNA barcoding. While identifying amphipod species with universal COI primers, we unexpectedly detected rickettsial endosymbionts belonging to the Torix group. To map the distribution and diversity of Rickettsia species among amphipod hosts, we conducted a nationwide molecular screening of seven families of New Zealand freshwater amphipods. In addition to uncovering a diversity of Torix Rickettsia species across multiple amphipod populations from three different families, our research indicates that: (1) detecting Torix Rickettsia with universal primers is not uncommon, (2) obtaining 'Rickettsia COI sequences' from many host individuals is highly likely when a population is infected, and (3) obtaining 'host COI' may not be possible with a conventional PCR if an individual is infected. Because Rickettsia COI is highly conserved across diverse host taxa, we were able to design blocking primers that can be used in a wide range of host species infected with Torix Rickettsia. We propose the use of blocking primers to circumvent problems caused by unwanted amplification of Rickettsia and to obtain targeted host COI sequences for DNA barcoding, population genetics, and phylogeographic studies.},
}
@article {pmid33031471,
year = {2020},
author = {Galen, SC and Borner, J and Perkins, SL and Weckstein, JD},
title = {Phylogenomics from transcriptomic "bycatch" clarify the origins and diversity of avian trypanosomes in North America.},
journal = {PloS one},
volume = {15},
number = {10},
pages = {e0240062},
pmid = {33031471},
issn = {1932-6203},
mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Birds/*genetics/parasitology ; Contig Mapping ; DNA Barcoding, Taxonomic ; DNA, Protozoan/chemistry/metabolism ; Databases, Factual ; Haplotypes ; Humans ; North America ; Phylogeny ; RNA, Ribosomal, 18S/chemistry/classification/metabolism ; *Transcriptome ; Trypanosoma/classification/*genetics/pathogenicity ; Trypanosoma cruzi/classification ; },
abstract = {The eukaryotic blood parasite genus Trypanosoma includes several important pathogens of humans and livestock, but has been understudied in wildlife broadly. The trypanosomes that infect birds are in particular need of increased attention, as these parasites are abundant and globally distributed, yet few studies have addressed their evolutionary origins and diversity using modern molecular and analytical approaches. Of specific interest are the deep evolutionary relationships of the avian trypanosomes relative to the trypanosome species that are pathogenic in humans, as well as their species level diversity in regions where they have been understudied such as North America. Here, we address these unresolved areas of study using phylogenomic data for two species of avian trypanosomes that were isolated as "bycatch" from host transcriptome assemblies, as well as a large 18S DNA barcode sequence dataset that includes 143 novel avian Trypanosoma 18S sequences from North America. Using a phylogenomic approach, we find that the avian trypanosomes are nested within a clade of primarily mammalian trypanosomes that includes the human pathogen Trypanosoma cruzi, and are paraphyletic with respect to the ruminant trypanosome Trypanosoma theileri. DNA barcode sequences showed that T. avium and an unidentified small, non-striated trypanosome that was morphologically similar to T. everetti are each represented by highly abundant and divergent 18S haplotypes in North America. Community-level sampling revealed that additional species-level Trypanosoma lineages exist in this region. We compared the newly sequenced DNA barcodes from North America to a global database, and found that avian Trypanosoma 18S haplotypes generally exhibited a marked lack of host specificity with at least one T. avium haplotype having an intercontinental distribution. This highly abundant T. avium haplotype appears to have a remarkably high dispersal ability and cosmopolitan capacity to evade avian host immune defenses, which warrant further study.},
}
@article {pmid33029717,
year = {2020},
author = {Deepika, YS and Mahadevakumar, S and Amruthesh, KN and Sridhar, KR and Lakshmidevi, N},
title = {Dactuliophora mysorensis sp. nov.: A New Species of Mycelia Sterilia Causing Zonate Leaf Spot on Cowpea in India.},
journal = {Current microbiology},
volume = {77},
number = {12},
pages = {4140-4151},
doi = {10.1007/s00284-020-02229-3},
pmid = {33029717},
issn = {1432-0991},
support = {ViGha 04/35/2016-17 Dated 28/03/2017//University of Mysore/ ; File No. 09/119(0205)2018EMR-I//Council of Scientific and Industrial Research/ ; },
mesh = {*Ascomycota/genetics ; *Fungicides, Industrial ; India ; *Vigna ; },
abstract = {Cowpea is an important pulse crop extensively grown in arid and semi-arid tropics which is affected by a number of diseases. Fungi belonging to mycelia sterilia are known to cause many diseases on cereals and pulses. During the cowpea field survey in Mysore District of Karnataka (India), Dactuliophora sp. was identified as the major pathogen causing zonate leaf spot (ZLS) disease. The fungal pathogen was isolated from naturally infected cowpea leaves and identified as a member belongs to the genus Dactuliophora, which was previously described by CLA Leakey in the year 1964 on Vigna unguiculata from Africa. However, detailed morphological and cultural examinations of the pathogen revealed striking differences from that of D. tarrii. Based on differences in morphology with D. tarrii, a new species Dactuliophora mysorensis sp. nov. is described herein. The disease incidence as well as disease index was estimated for 3 years (2016-2018). The severity of the disease was high during August-November. High incidence and disease index of ZLS was recorded in Doddamaragowdanahally region. The pathogenicity tests demonstrated similar symptoms of ZLS. The ITS barcoding revealed that the pathogen is closely related to Rhizoctonia bataticola and Macrophomina phaseolina. Further, in vitro evaluation of fungicides was carried out by poisoned food technique. Among the five fungicides examined, only two systemic fungicides (Benomyl and Carbendazim) were effective against D. mysorensis. Thus, the present study recommends Benomyl and Carbendazim for management of ZLS disease caused by D. mysorensis.},
}
@article {pmid33029559,
year = {2020},
author = {Freed, NE and Vlková, M and Faisal, MB and Silander, OK},
title = {Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and Oxford Nanopore Rapid Barcoding.},
journal = {Biology methods &amp; protocols},
volume = {5},
number = {1},
pages = {bpaa014},
pmid = {33029559},
issn = {2396-8923},
abstract = {Rapid and cost-efficient whole-genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019, is critical for understanding viral transmission dynamics. Here we show that using a new multiplexed set of primers in conjunction with the Oxford Nanopore Rapid Barcode library kit allows for faster, simpler, and less expensive SARS-CoV-2 genome sequencing. This primer set results in amplicons that exhibit lower levels of variation in coverage compared to other commonly used primer sets. Using five SARS-CoV-2 patient samples with Cq values between 20 and 31, we show that high-quality genomes can be generated with as few as 10 000 reads (∼5 Mbp of sequence data). We also show that mis-classification of barcodes, which may be more likely when using the Oxford Nanopore Rapid Barcode library prep, is unlikely to cause problems in variant calling. This method reduces the time from RNA to genome sequence by more than half compared to the more standard ligation-based Oxford Nanopore library preparation method at considerably lower costs.},
}
@article {pmid33028881,
year = {2020},
author = {Floren, A and von Rintelen, T and Hebert, PDN and de Araujo, BC and Schmidt, S and Balke, M and Narakusumo, RP and Peggie, D and Ubaidillah, R and von Rintelen, K and Müller, T},
title = {Integrative ecological and molecular analysis indicate high diversity and strict elevational separation of canopy beetles in tropical mountain forests.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {16677},
pmid = {33028881},
issn = {2045-2322},
mesh = {Animals ; *Biodiversity ; Coleoptera/metabolism/*physiology ; DNA Barcoding, Taxonomic ; *Forests ; Trees ; Tropical Climate ; },
abstract = {Tropical mountain forests contribute disproportionately to terrestrial biodiversity but little is known about insect diversity in the canopy and how it is distributed between tree species. We sampled tree-specific arthropod communities from 28 trees by canopy fogging and analysed beetle communities which were first morphotyped and then identified by their DNA barcodes. Our results show that communities from forests at 1100 and 1700 m a.s.l. are almost completely distinct. Diversity was much lower in the upper forest while community structure changed from many rare, less abundant species to communities with a pronounced dominance structure. We also found significantly higher beta-diversity between trees at the lower than higher elevation forest where community similarity was high. Comparisons on tree species found at both elevations reinforced these results. There was little species overlap between sites indicating limited elevational ranges. Furthermore, we exploited the advantage of DNA barcodes to patterns of haplotype diversity in some of the commoner species. Our results support the advantage of fogging and DNA barcodes for community studies and underline the need for comprehensive research aimed at the preservation of these last remaining pristine forests.},
}
@article {pmid33027665,
year = {2020},
author = {Kim, IS and Wu, J and Rahme, GJ and Battaglia, S and Dixit, A and Gaskell, E and Chen, H and Pinello, L and Bernstein, BE},
title = {Parallel Single-Cell RNA-Seq and Genetic Recording Reveals Lineage Decisions in Developing Embryoid Bodies.},
journal = {Cell reports},
volume = {33},
number = {1},
pages = {108222},
pmid = {33027665},
issn = {2211-1247},
support = {DP1 CA216873/CA/NCI NIH HHS/United States ; R35 HG010717/HG/NHGRI NIH HHS/United States ; R01 HG009269/HG/NHGRI NIH HHS/United States ; F32 CA236432/CA/NCI NIH HHS/United States ; RM1 HG006193/HG/NHGRI NIH HHS/United States ; },
mesh = {Cell Differentiation ; Cell Lineage/*physiology ; DNA Methylation/*genetics ; Embryoid Bodies/*metabolism ; Humans ; RNA-Seq/*methods ; },
abstract = {Early developmental specification can be modeled by differentiating embryonic stem cells (ESCs) to embryoid bodies (EBs), a heterogeneous mixture of three germ layers. Here, we combine single-cell transcriptomics and genetic recording to characterize EB differentiation. We map transcriptional states along a time course and model cell fate trajectories and branchpoints as cells progress to distinct germ layers. To validate this inferential model, we propose an innovative inducible genetic recording technique that leverages recombination to generate cell-specific, timestamp barcodes in a narrow temporal window. We validate trajectory architecture and key branchpoints, including early specification of a primordial germ cell (PGC)-like lineage from preimplantation epiblast-like cells. We further identify a temporally defined role of DNA methylation in this PGC-epiblast decision. Our study provides a high-resolution lineage map for an organoid model of embryogenesis, insights into epigenetic determinants of fate specification, and a strategy for lineage mapping of rapid differentiation processes.},
}
@article {pmid33027282,
year = {2020},
author = {Kenmotsu, H and Uchida, K and Hirose, Y and Eki, T},
title = {Taxonomic profiling of individual nematodes isolated from copse soils using deep amplicon sequencing of four distinct regions of the 18S ribosomal RNA gene.},
journal = {PloS one},
volume = {15},
number = {10},
pages = {e0240336},
pmid = {33027282},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Nematoda/*classification/genetics ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA ; Software ; Soil/*parasitology ; },
abstract = {Nematodes are representative soil metazoans with diverged species that play crucial roles in nutrient recycling in the pedosphere. Qualitative and quantitative information on nematode communities is useful for assessing soil quality, and DNA barcode-mediated taxonomic analysis is a powerful tool to investigate taxonomic compositions and changes in nematode communities. Here, we investigated four regions (regions 1-4) of the 18S small subunit ribosomal RNA (SSU) gene as PCR targets of deep amplicon sequencing for the taxonomic profiling of individual soil nematodes. We determined the sequence variants (SVs) of 4 SSU regions for 96 nematodes (total 384 amplicons) isolated from copse soils and assigned their taxonomy using the QIIME2 software with dada2 or deblur algorithm and the SILVA database. Dada2 detected approximately 2-fold more nematode-derived SVs than deblur, and a larger number of SVs were obtained in regions 1 and 4 than those in other regions. These results and sufficient reference sequence coverage in region 4 indicated that DNA barcoding using a primer set for region 4 followed by dada2-based analysis would be most suitable for soil nematode taxonomic analysis. Eighteen SSU-derived operational taxonomic units (rOTUs) were obtained from 68 isolates, and their orders were determined based on the phylogenetic trees built by four regional sequences of rOTUs and 116 nematode reference species as well as the BLASTN search. The majority of the isolates were derived from three major orders Dorylaimida (6 rOTUs, 51.5% in 68 isolates), Rhabditida (4 rOTUs, 29.4%), and Triplonchida (7 rOTUs, 17.6%). The predicted feeding types of the isolates were fungivores (38.2% in total nematodes), plant feeders (32.4%), and 14.7% for both bacterivores and omnivores/predators. Additionally, we attempted to improve the branch structure of phylogenetic trees by using long nucleotide sequences artificially prepared by connecting regional sequences, but the effect was limited.},
}
@article {pmid33026144,
year = {2020},
author = {Traynor, SM and Wang, GA and Pandey, R and Li, F and Soleymani, L},
title = {Dynamic Bio-Barcode Assay Enables Electrochemical Detection of a Cancer Biomarker in Undiluted Human Plasma: A Sample-In-Answer-Out Approach.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {59},
number = {50},
pages = {22617-22622},
doi = {10.1002/anie.202009664},
pmid = {33026144},
issn = {1521-3773},
mesh = {Biomarkers, Tumor/*blood ; *Biosensing Techniques ; *Electrochemical Techniques ; Electrodes ; Humans ; *Point-of-Care Systems ; Prostate-Specific Antigen/*blood ; },
abstract = {There is a need for biosensing systems that can be operated at the point-of-care (POC) for disease screening and diagnostics and health monitoring. In spite of this, simple to operate systems with the required analytical sensitivity and specificity in clinical samples, using a sample-in-answer-out approach, remain elusive. Reported here is an electrochemical bio-barcode assay (e-biobarcode assay) that integrates biorecognition with signal transduction using molecular (DNA/protein) machines and signal readout using nanostructured electrodes. The e-biobarcode assay eliminates multistep processing and uses a single step for analysis following sample collection into the reagent tube. A clinically relevant performance for the analysis of prostate specific antigen (PSA) in undiluted and unprocessed human plasma: a log-linear range of 1 ng mL[-1] -200 ng mL[-1] and a LOD of 0.4 ng mL[-1] , was achieved. The e-biobarcode assay offers a realistic solution for biomarker analysis at the POC.},
}
@article {pmid33024639,
year = {2020},
author = {Kim, J and Nam, E and Lee, W},
title = {Quinquelaophonte enormis sp. nov., a new interstitial copepod (Harpacticoida: Laophontidae) from Korea.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e10007},
pmid = {33024639},
issn = {2167-8359},
abstract = {We collected an undescribed laophontid copepod from a coarse sand habitat on the east coast of Korea and named it Quinquelaophonte enormis sp. nov. We compared the detailed morphological characteristics of the new species with those of congeneric species. Among them, the new species shows a superficial resemblance to the Californian species Quinquelaophonte longifurcata Lang, 1965. However, the two species are easily distinguishable by the setation of the syncoxa on the maxilliped and the fourth swimming leg. The new species has the variable setation on the second to fourth swimming legs. The variations appear among individuals or between the left and right rami of a pair of legs in a single specimen. Although complex chaetotaxical polymorphism occur in this new species, we used myCOI and Cytb to confirm that the new species is not a species complex. Also, partial sequences of 18S and 28S ribosomal RNA genes were used to analyze the position of the new species within the family Laophontidae. The new speciesis the fourteenth Quinquelaophonte species in the world and the second species in Korea.},
}
@article {pmid33024635,
year = {2020},
author = {Andrade-Sossa, C and Buitron-Caicedo, L and Elías-Gutiérrez, M},
title = {A new species of Scapholeberis Schoedler, 1858 (Anomopoda: Daphniidae: Scapholeberinae) from the Colombian Amazon basin highlighted by DNA barcodes and morphology.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e9989},
pmid = {33024635},
issn = {2167-8359},
abstract = {BACKGROUND: The Amazon basin is recognized as one of the most complex and species-rich freshwater environments globally. The diversity of zooplankton here remains unknown, with many species undescribed.<br><br>METHODS: Here, we describe a new species of Scapholeberis Schoedler, 1858 (Cladocera: Anomopoda: Daphniidae: Scapholeberinae) from the Colombian Amazon Basin, collected with recently designed light traps. The description is based on detailed morphology (based on SEM and light microscopy) of parthenogenetic females, ephippial females, males, and molecular data based on the COI gene.<br><br>RESULTS: Scapholeberis yahuarcaquensis n. sp. has a combination of characters present in Scapholeberis kingi Sars, 1888 and Scapholeberis armata freyi Dumont &amp; Pensaert, 1983. These are a trilobate rostrum, with the middle lobe well developed with sides straight to relatively rounded, the presence of an elongated slit frontal head pore, a dorsal pore in the juncture of the cephalic shield and the valves, and a single denticulate membrane at the posterior rim of the valves, with stronger setae in the last third. The unique characters of the parthenogenetic females are ventral sucker with delicate triangles. Each has a filament-like projection in the lamellae's inner side and an external section forming convex folds with denticle-like projections in the middle zone of the sucker-plate. There is a peculiar pitted sculpture in the ephippial females and a strong projection in the front of it. The male hook on the limb I with a blunt tip, a quirky lamella-like outgrow in the proximal side, and a paddle with well-developed spines scattered on its surface. The ventral sucker-lamellae in the male is much more developed than the female. The COI gene sequences showed an interspecific mean genetic divergence of 16.4% between S. yahuarcaquensis n. sp. and the closest species S. freyi from Mexico, supporting our results. A coalescence analysis and Barcode Index Number also support the new species based on the DNA sequences. New methods of collecting and integrative biology will give important support to recognize the fauna from the Amazon Basin, one of the most important sources of fresh water in the world that remains unknown in many respects.},
}
@article {pmid33024234,
year = {2020},
author = {Ahmed, I and Tucci, FA and Aflalo, A and Smith, KGC and Bashford-Rogers, RJM},
title = {Author Correction: Ultrasensitive amplicon barcoding for next-generation sequencing facilitating sequence error and amplification-bias correction.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {17010},
doi = {10.1038/s41598-020-74321-4},
pmid = {33024234},
issn = {2045-2322},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}
@article {pmid33024224,
year = {2020},
author = {Wattier, R and Mamos, T and Copilaş-Ciocianu, D and Jelić, M and Ollivier, A and Chaumot, A and Danger, M and Felten, V and Piscart, C and Žganec, K and Rewicz, T and Wysocka, A and Rigaud, T and Grabowski, M},
title = {Continental-scale patterns of hyper-cryptic diversity within the freshwater model taxon Gammarus fossarum (Crustacea, Amphipoda).},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {16536},
pmid = {33024224},
issn = {2045-2322},
mesh = {Amphipoda/*classification/*genetics ; Animals ; DNA Barcoding, Taxonomic ; Ecotoxicology ; Europe ; Evolution, Molecular ; *Fresh Water ; Genetic Linkage ; *Genetic Variation ; *Hydrobiology ; Phylogeny ; },
abstract = {Traditional morphological diagnoses of taxonomic status remain widely used while an increasing number of studies show that one morphospecies might hide cryptic diversity, i.e. lineages with unexpectedly high molecular divergence. This hidden diversity can reach even tens of lineages, i.e. hyper cryptic diversity. Even well-studied model-organisms may exhibit overlooked cryptic diversity. Such is the case of the freshwater crustacean amphipod model taxon Gammarus fossarum. It is extensively used in both applied and basic types of research, including biodiversity assessments, ecotoxicology and evolutionary ecology. Based on COI barcodes of 4926 individuals from 498 sampling sites in 19 European countries, the present paper shows (1) hyper cryptic diversity, ranging from 84 to 152 Molecular Operational Taxonomic Units, (2) ancient diversification starting already 26 Mya in the Oligocene, and (3) high level of lineage syntopy. Even if hyper cryptic diversity was already documented in G. fossarum, the present study increases its extent fourfold, providing a first continental-scale insight into its geographical distribution and establishes several diversification hotspots, notably south-eastern and central Europe. The challenges of recording hyper cryptic diversity in the future are also discussed.},
}
@article {pmid33024134,
year = {2020},
author = {Sumner-Kalkun, JC and Highet, F and Arnsdorf, YM and Back, E and Carnegie, M and Madden, S and Carboni, S and Billaud, W and Lawrence, Z and Kenyon, D},
title = {'Candidatus Liberibacter solanacearum' distribution and diversity in Scotland and the characterisation of novel haplotypes from Craspedolepta spp. (Psyllidae: Aphalaridae).},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {16567},
pmid = {33024134},
issn = {2045-2322},
mesh = {Animals ; Apiaceae/*microbiology/*parasitology ; Crops, Agricultural/*microbiology ; *Haplotypes ; Hemiptera/*microbiology ; Liberibacter/*genetics/*isolation &amp; purification ; Plant Diseases/*microbiology/*parasitology ; Scotland ; Solanaceae/*microbiology/*parasitology ; Urtica dioica/*microbiology ; },
abstract = {The phloem limited bacterium 'Candidatus Liberibacter solanacearum' (Lso) is associated with disease in Solanaceous and Apiaceous crops. This bacterium has previously been found in the UK in Trioza anthrisci, but its impact on UK crops is unknown. Psyllid and Lso diversity and distribution among fields across the major carrot growing areas of Scotland were assessed using real-time PCR and DNA barcoding techniques. Four Lso haplotypes were found: C, U, and two novel haplotypes. Lso haplotype C was also found in a small percentage of asymptomatic carrot plants (9.34%, n = 139) from a field in Milnathort where known vectors of this haplotype were not found. This is the first report of Lso in cultivated carrot growing in the UK and raises concern for the carrot and potato growing industry regarding the potential spread of new and existing Lso haplotypes into crops. Trioza anthrisci was found present only in sites in Elgin, Moray with 100% of individuals harbouring Lso haplotype C. Lso haplotype U was found at all sites infecting Trioza urticae and at some sites infecting Urtica dioica with 77.55% and 24.37% average infection, respectively. The two novel haplotypes were found in Craspedolepta nebulosa and Craspedolepta subpunctata and named Cras1 and Cras2. This is the first report of Lso in psyllids from the Aphalaridae. These new haplotypes were most closely related to Lso haplotype H recently found in carrot and parsnip. Lso was also detected in several weed plants surrounding carrot and parsnip fields. These included two Apiaceous species Aegropodium podagraria (hap undetermined) and Anthriscus sylvestris (hap C); one Gallium sp. (Rubiaceae) (hap undetermined); and Chenopodium album (Amaranthaceae) (hap undetermined).},
}
@article {pmid33024122,
year = {2020},
author = {Walens, A and Lin, J and Damrauer, JS and McKinney, B and Lupo, R and Newcomb, R and Fox, DB and Mabe, NW and Gresham, J and Sheng, Z and Sibley, AB and De Buysscher, T and Kelkar, H and Mieczkowski, PA and Owzar, K and Alvarez, JV},
title = {Adaptation and selection shape clonal evolution of tumors during residual disease and recurrence.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {5017},
pmid = {33024122},
issn = {2041-1723},
support = {F31 CA220957/CA/NCI NIH HHS/United States ; R01 CA208042/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Breast Neoplasms/*pathology ; Cell Line, Tumor ; Crizotinib/pharmacology ; Doxycycline/pharmacology ; Epithelial-Mesenchymal Transition/genetics ; Female ; *Gene Expression Regulation, Neoplastic ; High-Throughput Nucleotide Sequencing ; Humans ; Lung Neoplasms/pathology/secondary ; Mice, Nude ; Neoplasm Recurrence, Local/drug therapy/*genetics/*pathology ; Proto-Oncogene Proteins c-met/antagonists &amp; inhibitors/genetics ; Receptor, ErbB-2/genetics ; Single-Cell Analysis ; Xenograft Model Antitumor Assays ; },
abstract = {The survival and recurrence of residual tumor cells following therapy constitutes one of the biggest obstacles to obtaining cures in breast cancer, but it remains unclear how the clonal composition of tumors changes during relapse. We use cellular barcoding to monitor clonal dynamics during tumor recurrence in vivo. We find that clonal diversity decreases during tumor regression, residual disease, and recurrence. The recurrence of dormant residual cells follows several distinct routes. Approximately half of the recurrent tumors exhibit clonal dominance with a small number of subclones comprising the vast majority of the tumor; these clonal recurrences are frequently dependent upon Met gene amplification. A second group of recurrent tumors comprises thousands of subclones, has a clonal architecture similar to primary tumors, and is dependent upon the Jak/Stat pathway. Thus the regrowth of dormant tumors proceeds via multiple routes, producing recurrent tumors with distinct clonal composition, genetic alterations, and drug sensitivities.},
}
@article {pmid33023115,
year = {2020},
author = {Ceruso, M and Mascolo, C and De Luca, P and Venuti, I and Smaldone, G and Biffali, E and Anastasio, A and Pepe, T and Sordino, P},
title = {A Rapid Method for the Identification of Fresh and Processed Pagellus erythrinus Species against Frauds.},
journal = {Foods (Basel, Switzerland)},
volume = {9},
number = {10},
pages = {},
pmid = {33023115},
issn = {2304-8158},
abstract = {The commercialization of porgies or seabreams of the family Sparidae has greatly increased in the last decade, and some valuable species have become subject to seafood substitution. DNA regions currently used for fish species identification in fresh and processed products belong to the mitochondrial (mt) genes cytochrome b (Cytb), cytochrome c oxidase I (COI), 16S and 12S. However, these markers amplify for fragments with lower divergence within and between some species, failing to provide informative barcodes. We adopted comparative mitogenomics, through the analysis of complete mtDNA sequences, as a compatible approach toward studying new barcoding markers. The intent is to develop a specific and rapid assay for the identification of the common pandora Pagellus erythrinus, a sparid species frequently subject to fraudulent replacement. The genetic diversity analysis (Hamming distance, p-genetic distance, gene-by-gene sequence variability) between 16 sparid mtDNA genomes highlighted the discriminating potential of a 291 bp NAD2 gene fragment. A pair of species-specific primers were successfully designed and tested by end-point and real-time PCR, achieving amplification only in P. erythrinus among several fish species. The use of the NAD2 barcoding marker provides a rapid presence/absence method for the identification of P. erythrinus.},
}
@article {pmid33017936,
year = {2020},
author = {Kang, ASW and Enright, AJ},
title = {Locating patterns in Nanopore currents using time-warped signal representation of consensus nucleotides for demultiplexing and motif detection.},
journal = {Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference},
volume = {2020},
number = {},
pages = {82-86},
doi = {10.1109/EMBC44109.2020.9176358},
pmid = {33017936},
issn = {2694-0604},
mesh = {Base Sequence ; Consensus ; DNA ; *Nanopores ; Nucleotides ; },
abstract = {Nanopore-based approaches for the sequencing of DNA and RNA molecules are promising technologies with potential applications in clinical genomics. These approaches have generated large numbers of time series objects over the years, however, it remains a challenge to accurately decipher the underlying nucleotide sequence corresponding to a given signal. By using a combination of consensus signal averaging and stream monitoring of variable-length motifs, we outline an online pattern matching framework that can efficiently locate consensus sequences in real world Nanopore datasets. We demonstrate the applicability of our proposed framework across two use-cases: demultiplexing of DNA barcodes and multiple motif site identification in RNA transcripts.},
}
@article {pmid33016319,
year = {2020},
author = {Borg Dahl, M and Krebs, M and Unterseher, M and Urich, T and Gaudig, G},
title = {Temporal dynamics in the taxonomic and functional profile of the Sphagnum-associated fungi (mycobiomes) in a Sphagnum farming field site in Northwestern Germany.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {11},
pages = {},
doi = {10.1093/femsec/fiaa204},
pmid = {33016319},
issn = {1574-6941},
mesh = {Agriculture ; Ecosystem ; Fungi/genetics ; Germany ; *Mycobiome ; *Sphagnopsida ; },
abstract = {The drainage of peatlands for their agricultural use leads to huge emissions of greenhouse gases. One sustainable alternative is the cultivation of peat mosses after rewetting ('Sphagnum farming'). Environmental parameters of such artificial systems may differ from those of natural Sphagnum ecosystems which host a rich fungal community. We studied the fungal community at a 4 ha Sphagnum farming field site in Northwestern Germany and compared it with that of natural Sphagnum ecosystems. Additionally, we asked if any fungi occur with potentially negative consequences for the commercial production and/or use of Sphagnum biomass. Samples were collected every 3 months within 1 year. High-throughput sequencing of the fungal ITS2 barcode was used to obtain a comprehensive community profile of the fungi. The dominant taxa in the fungal community of the Sphagnum farming field site were all commonly reported from natural Sphagnum ecosystems. While the taxonomic composition showed clear differences between seasons, a stable functional community profile was identified across seasons. Additionally, nutrient supply seems to affect composition of fungal community. Despite a rather high abundance of bryophyte parasites, and the occurrence of both Sphagnum-species-specific and general plant pathogens, their impact on the productivity and usage of Sphagnum biomass as raw material for growing media was considered to be low.},
}
@article {pmid33014994,
year = {2020},
author = {Munir, S and Ahmed, S and Ibrahim, M and Khalid, M and Ojha, SC},
title = {A Spellbinding Interplay Between Biological Barcoding and Nanotechnology.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {8},
number = {},
pages = {883},
pmid = {33014994},
issn = {2296-4185},
abstract = {Great scientific research with improved potential in probing biological locales has remained a giant stride. The use of bio-barcodes with the potential use of nanotechnology is a hallmark being developed among recent advanced techniques. Biobarcoding is a novel method used for screening biomolecules to identify and divulge ragbag biodiversity. It establishes successful barcoding projects in the field of nanomedical technology for massively testing disease diagnosis and treatment. Biobarcoding and nanotechnology are recently developed technologies that provide unique opportunities and challenges for multiplex detection such as DNAs, proteins and nucleic acids of animals, plants, viruses, and various other species. These technologies also clump drug delivery, gene delivery, and DNA sequencing. Bio-barcode amplification assay (BCA) is used at large for the detection and identification of proteins and DNAs. DNA barcoding combined with nanotechnology has been proven highly sensitive rendering fast uniplex and multiplex detection of pathogens in food, blood, and other specimens. This review takes a panoramic view of current advances in nano bio-barcodes which have been summarized to explore additional applications such as detection of cytokines, neurotransmitters, cancer markers, prostate-specific antigens, and allergens. In the future, it will also be possible to detect some fungi, algae, protozoa, and other pollutants in food, agriculture, and clinical samples. Using these technologies, specific and efficient sensors would possibly be developed that can perform swift detections of antigens, allergens, and other specimens.},
}
@article {pmid33014510,
year = {2020},
author = {Ma, Q and Chen, X and Zhang, K and Yao, D and Yang, L and Wang, H and Bulemasi, S and Huang, J and Wang, J},
title = {Chemical Fingerprint Analysis for Discovering Markers and Identifying Saussurea involucrata by HPLC Coupled with OPLS-DA.},
journal = {Journal of analytical methods in chemistry},
volume = {2020},
number = {},
pages = {7560710},
pmid = {33014510},
issn = {2090-8865},
abstract = {The quality control of Saussurea involucrata has been greatly improved by macroscopic and microscopic identification and chemical profiling described in Chinese Pharmacopoeia since 2005. However, these methods have their own limitations, e.g., their dependence on personal experience and expertise, and it is a huge challenge to identify closely related species that share similar or identical morphological characteristics and chemical profiles. A novel and generally accepted identification strategy is urgently needed as a complement to regulations for protecting the public health interests. In this work, a comprehensive chromatographic fingerprint method was developed and tested on 43 samples from four haplotypes of S. involucrata according to DNA barcoding. Three common patterns consisting of 20, 14, and 7 common peaks were generated by frequency filters of median, upper quartile, and 100%, respectively. Based on two formerly screened patterns, S. involucrata can be effectively identified from its five easily confused snow lotus species, including the most closely related plant (S. orgaadayi) in the orthogonal partial least-squares discriminant analysis (OPLS-DA) models. The model is supported by good R and Q coefficients. In addition, different haplotypes of S. involucrata can be discriminated in the OPLS-DA model using the 20 common peaks. Among them, peaks 9, 11, 16 (zaluzanin C), and 18 (dehydrocostus lactone) have been identified as fingerprint markers of S. involucrata via S-plots and VIP values (>1). Additionally, peaks 19 and 20 were identified as linolenic acid and linoleic acid with anti-inflammatory activity, and they were isolated from the herb for the first time. Collectively, the chromatographic fingerprint of S. involucrata can be an effective and integrated method for the identification of authentic herbs from adulterant species or related plants, and discrimination of its different haplotypes provides an objective and reliable tool for quality control.},
}
@article {pmid33014122,
year = {2020},
author = {Su, Y and Ding, D and Yao, M and Wu, L and Dong, G and Zhang, D and Chen, S and Xiang, L},
title = {Specific DNA mini-barcoding for identification of Gekko gecko and its products.},
journal = {Chinese medicine},
volume = {15},
number = {},
pages = {103},
pmid = {33014122},
issn = {1749-8546},
abstract = {BACKGROUND: The dry body of the Tokay Gecko (Gekko gecko) is the source of a valuable traditional Chinese medicine, it is therefore listed as a Class II protected animal species in China. Due to increasing market demand and a declining supply of the species, a considerable number of adulterants have emerged in the market. Thus, it is necessary to establish an accurate and rapid method of identification for distinguishing G. gecko from its adulterants and for separating it from highly processed products.<br><br>METHODS: A total of 274 COI sequences were analyzed by using MEGA 5.0 software. Several specific primers were designed to amplify mini-barcode regions and identify G. gecko from its counterfeits and products.<br><br>RESULTS: 274 COI sequences of G. gecko and 15 adulterants species were analyzed. G. gecko could be distinguished from its adulterants through BLAST analysis, intra- and inter-specific distance analyses, and an NJ tree based on COI sequences. Two pairs of specific primers designed for this study, COISF2/COISR2 and COISF3/COISR3, amplified 200- and 133-bp fragments of the COI region, respectively, both of which were suitable for the identification of G. gecko and its adulterants. Furthermore, COISF3/COISR3 detected G. gecko in 15 batches of products.<br><br>CONCLUSION: Therefore, the specific DNA mini-barcoding method developed here may be a powerful tool for the identification of G. gecko and counterfeits, and may also be used to distinguish G. gecko from its highly processed by-products.},
}
@article {pmid33013171,
year = {2020},
author = {Motamedinia, B and Skevington, JH and Kelso, S},
title = {Revision of Eudorylas Aczél, 1940 (Diptera, Pipunculidae) in the Middle East, with the description of four new species.},
journal = {Biodiversity data journal},
volume = {8},
number = {},
pages = {e53609},
pmid = {33013171},
issn = {1314-2828},
abstract = {BACKGROUND: The Middle Eastern species of Eudorylas Aczél, 1940 are revised through an integrative taxonomic approach by combining morphological and sequence data from the mitochondrial COI barcoding gene. Four new species of the genus Eudorylas are described, males and females of three species are associated, DNA sequence data of 11 Middle Eastern Eudorylas species are provided and 15 additional species are discussed. To facilitate their recognition, we provide diagnoses, descriptions, an identification key and distributional maps for all species.<br><br>NEW INFORMATION: The following new species are described from the Middle East: E. avis Motamedinia &amp; Skevington sp. n., E. bihamatus Motamedinia &amp; Skevington sp. n., E. corniculans Motamedinia &amp; Skevington sp. n., E. nasicus Motamedinia &amp; Skevington sp. n.},
}
@article {pmid33009923,
year = {2020},
author = {May, JA and Feng, Z and Orton, MG and Adamowicz, SJ},
title = {The Effects of Ecological Traits on the Rate of Molecular Evolution in Ray-Finned Fishes: A Multivariable Approach.},
journal = {Journal of molecular evolution},
volume = {88},
number = {8-9},
pages = {689-702},
pmid = {33009923},
issn = {1432-1432},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Environment ; *Evolution, Molecular ; *Fishes/classification/genetics ; Phenotype ; Phylogeny ; },
abstract = {Myriad environmental and biological traits have been investigated for their roles in influencing the rate of molecular evolution across various taxonomic groups. However, most studies have focused on a single trait, while controlling for additional factors in an informal way, generally by excluding taxa. This study utilized a dataset of cytochrome c oxidase subunit I (COI) barcode sequences from over 7000 ray-finned fish species to test the effects of 27 traits on molecular evolutionary rates. Environmental traits such as temperature were considered, as were traits associated with effective population size including body size and age at maturity. It was hypothesized that these traits would demonstrate significant correlations with substitution rate in a multivariable analysis due to their associations with mutation and fixation rates, respectively. A bioinformatics pipeline was developed to assemble and analyze sequence data retrieved from the Barcode of Life Data System (BOLD) and trait data obtained from FishBase. For use in phylogenetic regression analyses, a maximum likelihood tree was constructed from the COI sequence data using a multi-gene backbone constraint tree covering 71% of the species. A variable selection method that included both single- and multivariable analyses was used to identify traits that contribute to rate heterogeneity estimated from different codon positions. Our analyses revealed that molecular rates associated most significantly with latitude, body size, and habitat type. Overall, this study presents a novel and systematic approach for integrative data assembly and variable selection methodology in a phylogenetic framework.},
}
@article {pmid33007903,
year = {2020},
author = {Milam, J and Johnson, DE and Andersen, JC and Fassler, AB and Narango, DL and Elkinton, JS},
title = {Validating Morphometrics with DNA Barcoding to Reliably Separate Three Cryptic Species of Bombus Cresson (Hymenoptera: Apidae).},
journal = {Insects},
volume = {11},
number = {10},
pages = {},
pmid = {33007903},
issn = {2075-4450},
abstract = {Despite their large size and striking markings, the identification of bumble bees (Bombus spp.) is surprisingly difficult. This is particularly true for three North American sympatric species in the subgenus Pyrobombus that are often misidentified: B. sandersoni Franklin, B. vagans Smith B. perplexus Cresson. Traditionally, the identification of these cryptic species was based on observations of differences in hair coloration and pattern and qualitative comparisons of morphological characters including malar length. Unfortunately, these characteristics do not reliably separate these species. We present quantitative morphometric methods to separate these species based on the malar length to width ratio (MRL) and the ratios of the malar length to flagellar segments 1 (MR1) and 3 (MR3) for queens and workers, and validated our determinations based on DNA barcoding. All three measurements discriminated queens of B. sandersoni and B. vagans with 100% accuracy. For workers, we achieved 99% accuracy by combining both MR1 and MR3 measurements, and 100% accuracy differentiating workers using MRL. Moreover, measurements were highly repeatable within and among both experienced and inexperienced observers. Our results, validated by genetic evidence, demonstrate that malar measurements provide accurate identifications of B. vagans and B. sandersoni. There was considerable overlap in the measurements between B. perplexus and B. sandersoni. However, these species can usually be reliably separated by combining malar ratio measurements with other morphological features like hair color. The ability to identify bumble bees is key to monitoring the status and trends of their populations, and the methods we present here advance these efforts.},
}
@article {pmid33006183,
year = {2020},
author = {Guo, L and Wang, T and Wu, Z and Wang, J and Wang, M and Cui, Z and Ji, S and Cai, J and Xu, C and Chen, X},
title = {Portable Food-Freshness Prediction Platform Based on Colorimetric Barcode Combinatorics and Deep Convolutional Neural Networks.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {32},
number = {45},
pages = {e2004805},
doi = {10.1002/adma.202004805},
pmid = {33006183},
issn = {1521-4095},
support = {A18A1b0045//Agency for Science, Technology and Research/ ; NRF-NRFI2017-07//National Research Foundation-Prime Minister's office, Republic of Singapore/ ; MOE2017-T2-2-107//Ministry of Education - Singapore/ ; //NTU/ ; //China Scholarship Council/ ; },
mesh = {Cellulose/analogs &amp; derivatives/chemistry ; Chitosan/chemistry ; Colorimetry/*instrumentation ; Coloring Agents/chemistry ; *Deep Learning ; *Food Quality ; Nanocomposites/chemistry ; Porosity ; },
abstract = {Artificial scent screening systems (known as electronic noses, E-noses) have been researched extensively. A portable, automatic, and accurate, real-time E-nose requires both robust cross-reactive sensing and fingerprint pattern recognition. Few E-noses have been commercialized because they suffer from either sensing or pattern-recognition issues. Here, cross-reactive colorimetric barcode combinatorics and deep convolutional neural networks (DCNNs) are combined to form a system for monitoring meat freshness that concurrently provides scent fingerprint and fingerprint recognition. The barcodes-comprising 20 different types of porous nanocomposites of chitosan, dye, and cellulose acetate-form scent fingerprints that are identifiable by DCNN. A fully supervised DCNN trained using 3475 labeled barcode images predicts meat freshness with an overall accuracy of 98.5%. Incorporating DCNN into a smartphone application forms a simple platform for rapid barcode scanning and identification of food freshness in real time. The system is fast, accurate, and non-destructive, enabling consumers and all stakeholders in the food supply chain to monitor food freshness.},
}
@article {pmid33005736,
year = {2020},
author = {Wen, X and Ou, YC and Zarick, HF and Zhang, X and Hmelo, AB and Victor, QJ and Paul, EP and Slocik, JM and Naik, RR and Bellan, LM and Lin, EC and Bardhan, R},
title = {PRADA: Portable Reusable Accurate Diagnostics with nanostar Antennas for multiplexed biomarker screening.},
journal = {Bioengineering &amp; translational medicine},
volume = {5},
number = {3},
pages = {e10165},
pmid = {33005736},
issn = {2380-6761},
support = {R21 HD100685/HD/NICHD NIH HHS/United States ; },
abstract = {Precise monitoring of specific biomarkers in biological fluids with accurate biodiagnostic sensors is critical for early diagnosis of diseases and subsequent treatment planning. In this work, we demonstrated an innovative biodiagnostic sensor, portable reusable accurate diagnostics with nanostar antennas (PRADA), for multiplexed biomarker detection in small volumes (~50 μl) enabled in a microfluidic platform. Here, PRADA simultaneously detected two biomarkers of myocardial infarction, cardiac troponin I (cTnI), which is well accepted for cardiac disorders, and neuropeptide Y (NPY), which controls cardiac sympathetic drive. In PRADA immunoassay, magnetic beads captured the biomarkers in human serum samples, and gold nanostars (GNSs) "antennas" labeled with peptide biorecognition elements and Raman tags detected the biomarkers via surface-enhanced Raman spectroscopy (SERS). The peptide-conjugated GNS-SERS barcodes were leveraged to achieve high sensitivity, with a limit of detection (LOD) of 0.0055 ng/ml of cTnI, and a LOD of 0.12 ng/ml of NPY comparable with commercially available test kits. The innovation of PRADA was also in the regeneration and reuse of the same sensor chip for ~14 cycles. We validated PRADA by testing cTnI in 11 de-identified cardiac patient samples of various demographics within a 95% confidence interval and high precision profile. We envision low-cost PRADA will have tremendous translational impact and be amenable to resource-limited settings for accurate treatment planning in patients.},
}
@article {pmid33005350,
year = {2020},
author = {Voelker, MR and Schwarz, D and Thomas, A and Nelson, BW and Acevedo-Gutiérrez, A},
title = {Large-scale molecular barcoding of prey DNA reveals predictors of intrapopulation feeding diversity in a marine predator.},
journal = {Ecology and evolution},
volume = {10},
number = {18},
pages = {9867-9885},
pmid = {33005350},
issn = {2045-7758},
abstract = {Predator-prey interactions are critical in understanding how communities function. However, we need to describe intraspecific variation in diet to accurately depict those interactions. Harbor seals (Phoca vitulina) are an abundant marine predator that prey on species of conservation concern. We estimated intrapopulation feeding diversity (variation in feeding habits between individuals of the same species) of harbor seals in the Salish Sea. Estimates of feeding diversity were examined relative to sex, month, and location using a novel approach that combined molecular techniques, repeated cross-sectional sampling of scat, and a specialization metric (within-individual consistency in diet measured by the Proportional Similarity Index (P S i)). Based on 1,083 scat samples collected from five haul-out sites during four nonsequential years, we quantified diet using metabarcoding techniques and determined the sex of the scat depositor using a molecular assay. Results suggest that intrapopulation feeding diversity was present. Specialization was high over short periods (24-48 hr, P S i = 0.392, 95% CI = 0.013, R = 100,000) and variable in time and space. Females showed more specialization than males, particularly during summer and fall. Additionally, demersal and benthic prey species were correlated with more specialized diets. The latter finding suggests that this type of prey likely requires specific foraging strategies and that there are trade-offs between pelagic and benthic foraging styles for harbor seals. This differential feeding on prey species, as well as between sexes of harbor seals, indicates that predator-prey interactions in harbor seals are complex and that each sex may have a different impact on species of conservation concern. As such, describing intrapopulation feeding diversity may unravel hitherto unknown complex predator-prey interactions in the community.},
}
@article {pmid33005338,
year = {2020},
author = {Gaither, MR and Coker, DJ and Greaves, S and Sarigol, F and Payet, SD and Chaidez, V and Sinclair-Taylor, TH and DiBattista, JD and Berumen, ML},
title = {Does color matter? Molecular and ecological divergence in four sympatric color morphs of a coral reef fish.},
journal = {Ecology and evolution},
volume = {10},
number = {18},
pages = {9663-9681},
pmid = {33005338},
issn = {2045-7758},
abstract = {Non-sex-linked color polymorphism is common in animals and can be maintained in populations via balancing selection or, when under diversifying selection, can promote divergence. Despite their potential importance in ecological interactions and the evolution of biodiversity, their function and the mechanisms by which these polymorphisms are maintained are still poorly understood. Here, we combine field observations with life history and molecular data to compare four sympatric color morphs of the coral reef fish Paracirrhites forsteri (family Cirrhitidae) in the central Red Sea. Our findings verify that the color morphs are not sex-limited, inhabit the same reefs, and do not show clear signs of avoidance or aggression among them. A barcoding approach based on 1,276 bp of mitochondrial DNA could not differentiate the color morphs. However, when 36,769 SNPs were considered, we found low but significant population structure. Focusing on 1,121 F ST outliers, we recovered distinct population clusters that corresponded to shifts in allele frequencies with each color morph harboring unique alleles. Genetic divergence at these outlier loci is accompanied by differences in growth and marginal variation in microhabitat preference. Together, life history and molecular analysis suggest subtle divergence between the color morphs in this population, the causes for which remain elusive.},
}
@article {pmid33005195,
year = {2020},
author = {Salerno, D and Rosa, A},
title = {Identification of Molecular Signatures in Neural Differentiation and Neurological Diseases Using Digital Color-Coded Molecular Barcoding.},
journal = {Stem cells international},
volume = {2020},
number = {},
pages = {8852313},
pmid = {33005195},
issn = {1687-966X},
abstract = {Human pluripotent stem cells (PSCs), including embryonic stem cells and induced pluripotent stem cells, represent powerful tools for disease modeling and for therapeutic applications. PSCs are particularly useful for the study of development and diseases of the nervous system. However, generating in vitro models that recapitulate the architecture and the full variety of subtypes of cells that make the complexity of our brain remains a challenge. In order to fully exploit the potential of PSCs, advanced methods that facilitate the identification of molecular signatures in neural differentiation and neurological diseases are highly demanded. Here, we review the literature on the development and application of digital color-coded molecular barcoding as a potential tool for standardizing PSC research and applications in neuroscience. We will also describe relevant examples of the use of this technique for the characterization of the heterogeneous composition of the brain tumor glioblastoma multiforme.},
}
@article {pmid33005084,
year = {2020},
author = {Jiao, RJ and Bai, LH and Gao, JJ},
title = {Descriptions of two new species of the genus Colocasiomyia (Diptera, Drosophilidae) breeding on Rhaphidophora host plants in Yunnan, China.},
journal = {ZooKeys},
volume = {968},
number = {},
pages = {127-141},
pmid = {33005084},
issn = {1313-2989},
abstract = {The genus Colocasiomyia de Meijere (Diptera, Drosophilidae) is known to include 30 described and nearly 60 undescribed species classified into six species groups. Among these, the C. gigantea group of seven known species (two Southeast Asian and five Chinese) proved to be peculiar for its specificity on monsteroid (subfamily Monsteroideae, family Araceae) host plants. In this paper, two new species, C. todai Jiao &amp; Gao, sp. nov. and C. liae Jiao &amp; Gao, sp. nov., are described as members of the C. gigantea group with specimens collected from inflorescences of the monsteroid host species Rhaphidophora peepla (Roxb.) Schott and R. crassicaulis Engl. &amp; Krause, respectively, in Yunnan, China. The two new species are delimitated, in comparison with all known species, based on not only morphological but also DNA barcode (partial sequence of the mitochondrial COI, i.e., cytochrome c oxydase subunit I, gene) data. A revised key to all the nine species of the C. gigantea species group is provided.},
}
@article {pmid33005079,
year = {2020},
author = {Egger, C and Neusser, TP and Norenburg, J and Leasi, F and Buge, B and Vannozzi, A and Cunha, RL and Cox, CJ and Jörger, KM},
title = {Uncovering the shell game with barcodes: diversity of meiofaunal Caecidae snails (Truncatelloidea, Caenogastropoda) from Central America.},
journal = {ZooKeys},
volume = {968},
number = {},
pages = {1-42},
pmid = {33005079},
issn = {1313-2989},
abstract = {Caecidae is a species-rich family of microsnails with a worldwide distribution. Typical for many groups of gastropods, caecid taxonomy is largely based on overt shell characters. However, identification of species using shell characteristics is problematic due to their rather uniform, tubular shells, the presence of different growth stages, and a high degree of intraspecific variability. In the present study, a first integrative approach to caecid taxonomy is provided using light-microscopic investigation with microsculptural analyses and multi-marker barcoding, in conjunction with molecular species delineation analyses (ABGD, haplotype networks, GMYC, and bPTP). In total 132 specimens of Caecum and Meioceras collected during several sampling trips to Central America were analyzed and delineated into a minimum of 19 species to discuss putative synonyms, and supplement the original descriptions. Molecular phylogenetic analyses suggest Meioceras nitidum and M. cubitatum should be reclassified as Caecum, and the genus Meioceras might present a junior synonym of Caecum. Meiofaunal caecids morphologically resembling C. glabrum from the Northeast Atlantic are a complex of cryptic species with independent evolutionary origins, likely associated with multiple habitat shifts to the mesopsammic environment. Caecum invisibile Egger &amp; Jörger, sp. nov. is formally described based on molecular diagnostic characters. This first integrative approach towards the taxonomy of Caecidae increases the known diversity, reveals the need for a reclassification of the genus Caecum and serves as a starting point for a barcoding library of the family, thereby enabling further reliable identifications of these taxonomically challenging microsnails in future studies.},
}
@article {pmid33005000,
year = {2020},
author = {Tan, W and Gao, H and Jiang, W and Zhang, H and Yu, X and Liu, E and Tian, X},
title = {The complete chloroplast genome of Gleditsia sinensis and Gleditsia japonica: genome organization, comparative analysis, and development of taxon specific DNA mini-barcodes.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {16309},
pmid = {33005000},
issn = {2045-2322},
mesh = {Chloroplasts/*genetics ; Chromosome Mapping ; *DNA Barcoding, Taxonomic/methods ; Genes, Plant/genetics ; Genome, Chloroplast/*genetics ; Genome, Plant/genetics ; Gleditsia/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; },
abstract = {Chloroplast genomes have been widely considered an informative and valuable resource for molecular marker development and phylogenetic reconstruction in plant species. This study evaluated the complete chloroplast genomes of the traditional Chinese medicine Gleditsia sinensis and G. japonica, an adulterant of the former. The complete chloroplast genomes of G. sinensis and G. japonica were found to be of sizes 163,175 bp and 162,391 bp, respectively. A total of 111 genes were identified in each chloroplast genome, including 77 coding sequences, 30 tRNA, and 4 rRNA genes. Comparative analysis demonstrated that the chloroplast genomes of these two species were highly conserved in genome size, GC contents, and gene organization. Additionally, nucleotide diversity analysis of the two chloroplast genomes revealed that the two short regions of ycf1b were highly diverse, and could be treated as mini-barcode candidate regions. The mini-barcode of primers ZJ818F-1038R was proven to precisely discriminate between these two species and reflect their biomass ratio accurately. Overall, the findings of our study will shed light on the genetic evolution and guide species identification of G. sinensis and G. japonica.},
}
@article {pmid33003457,
year = {2020},
author = {Kocić, K and Petrović, A and Čkrkić, J and Kavallieratos, NG and Rakhshani, E and Arnó, J and Aparicio, Y and Hebert, PDN and Tomanović, &#x17d;},
title = {Resolving the Taxonomic Status of Potential Biocontrol Agents Belonging to the Neglected Genus Lipolexis Förster (Hymenoptera, Braconidae, Aphidiinae) with Descriptions of Six New Species.},
journal = {Insects},
volume = {11},
number = {10},
pages = {},
pmid = {33003457},
issn = {2075-4450},
support = {III43001//Ministry of Education, Science and Technological Development of the Republic of Serbia/ ; },
abstract = {Lipolexis is a small genus in the subfamily Aphidiinae represented by one species in Europe (Lipolexis gracilis Förster) and by four in Asia (Lipolexis wuyiensis Chen, L. oregmae Gahan, L. myzakkaiae Pramanik and Raychaudhuri and L. pseudoscutellaris Pramanik and Raychaudhuri). Although L. oregmae is employed in biological control programs against pest aphids, the last morphological study on the genus was completed over 50 years ago. This study employs an integrative approach (morphology and molecular analysis (COI barcode region)), to examine Lipolexis specimens that were sampled worldwide, including specimens from BOLD database. These results establish that two currently recognized species of Lipolexis (L. gracilis, L. oregmae) are actually a species complex and also reveal phylogenetic relationships within the genus. Six new species are described and a global key for the identification of Lipolexis species is provided.},
}
@article {pmid33003192,
year = {2021},
author = {Kang, TS},
title = {Identification and Authentication of Commercial Mi-iuy Croaker (Miichthys miiuy) Products by Two PCR-Based Methods.},
journal = {Journal of food protection},
volume = {84},
number = {3},
pages = {463-471},
doi = {10.4315/JFP-20-143},
pmid = {33003192},
issn = {1944-9097},
mesh = {Animals ; *Perciformes ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {ABSTRACT: Mi-iuy croaker (Miichthys miiuy) is one of the most important ingredients of Korean cuisine and, thus, has a high economic value. However, the similar morphological traits among croaker fish belonging to family Sciaenidae are often exploited for seafood fraud. In this study, an M. miiuy-specific primer set was designed and further improved by the development of a rapid and cost-effective duplex PCR method. The specificity of M. miiuy-specific duplex PCR was tested using 22 seafood species, and no cross-reactivity was observed. The sensitivity of the PCR assay was found to be 0.1 ng/μL. For the first time, labeling compliance of 43 commercial mi-iuy croaker products was verified using both full DNA barcoding and M. miiuy-specific duplex PCR methods. For species identification, BOLDSYSTEMS and GenBank database were screened with the consensus sequences of each PCR product as a query. This identification result was further confirmed using the M. miiuy-specific duplex PCR method. The findings of this study revealed that principal species substituted were law croaker (Pseudotolithus senegallus, n = 4), bigeye croaker (Micropogonias megalops, n = 3), whitemouth croaker (Micropogonias furnieri, n = 1), and tigertoothed croaker (Otolithes ruber, n = 1). A significant percentage (21%) of mislabeling was present in commercial mi-iuy products sold on the South Korean market.},
}
@article {pmid33002605,
year = {2020},
author = {Pacheco, MA and Ceríaco, LMP and Matta, NE and Vargas-Ramírez, M and Bauer, AM and Escalante, AA},
title = {A phylogenetic study of Haemocystidium parasites and other Haemosporida using complete mitochondrial genome sequences.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {85},
number = {},
pages = {104576},
doi = {10.1016/j.meegid.2020.104576},
pmid = {33002605},
issn = {1567-7257},
mesh = {Africa ; Biodiversity ; DNA, Protozoan ; *Genome, Mitochondrial ; *Genomics/methods ; Haemosporida/*classification/*genetics ; High-Throughput Nucleotide Sequencing ; *Phylogeny ; South America ; },
abstract = {Haemosporida are diverse vector-borne parasites associated with terrestrial vertebrates. Driven by the interest in species causing malaria (genus Plasmodium), the diversity of avian and mammalian haemosporidian species has been extensively studied, relying mostly on mitochondrial genes, particularly cytochrome b. However, parasites from reptiles have been neglected in biodiversity surveys. Reptilian haemosporidian parasites include Haemocystidium, a genus that shares morphological features with Plasmodium and Haemoproteus. Here, the first complete Haemocystidium mitochondrial DNA (mtDNA) genomes are studied. In particular, three mtDNA genomes from Haemocystidium spp. sampled in Africa, Oceania, and South America, are described. The Haemocystidium mtDNA genomes showed a high A + T content and a gene organization, including an extreme fragmentation of the rRNAs, found in other Haemosporida. These Haemocystidium mtDNA genomes were incorporated in phylogenetic and molecular clock analyses together with a representative sample of haemosporidian parasites from birds, mammals, and reptiles. The recovered phylogeny supported Haemocystidium as a monophyletic group apart from Plasmodium and other Haemosporida. Both the phylogenetic and molecular clock analyses yielded results consistent with a scenario in which haemosporidian parasites radiated with modern birds. Haemocystidium, like mammalian parasite clades, seems to originate from host switches by avian Haemosporida that allowed for the colonization of new vertebrate hosts. This hypothesis can be tested by investigating additional parasite species from all vertebrate hosts, particularly from reptiles. The mtDNA genomes reported here provide baseline data that can be used to scale up studies in haemosporidian parasites of reptiles using barcode approaches.},
}
@article {pmid33002384,
year = {2021},
author = {Boukhdoud, L and Saliba, C and Parker, LD and Rotzel McInerney, N and Ishak Mouawad, G and Kharrat, M and Kahale, R and Chahine, T and Maldonado, JE and Bou Dagher-Kharrat, M},
title = {First DNA sequence reference library for mammals and plants of the Eastern Mediterranean Region.},
journal = {Genome},
volume = {64},
number = {1},
pages = {39-49},
doi = {10.1139/gen-2019-0194},
pmid = {33002384},
issn = {1480-3321},
mesh = {Animals ; Base Sequence ; Biodiversity ; DNA Barcoding, Taxonomic ; Ecosystem ; *Gene Library ; Genetic Markers ; Mammals/*genetics ; Mediterranean Region ; Plant Leaves/genetics ; Plants/*genetics ; },
abstract = {The Mediterranean region is identified as one of the world's 36 biodiversity hotspots, with the Earth's most biologically rich yet threatened areas. Lebanon is a hub for Eastern Mediterranean Region (EMR) biodiversity with 9116 characterized plant and animal species (4486 fauna and 4630 flora). Using DNA barcoding as a tool has become crucial in the accurate identification of species in multiple contexts. It can also complement species morphological descriptions, which will add to our understanding of the biodiversity and richness of ecosystems and benefit conservation projects for endangered and endemic species. In this study, we create the first reference library of standard DNA markers for mammals and plants in the EMR, with a focus on endemic and endangered species. Plant leaves were collected from different nature reserves in Mount Lebanon, and mammal samples were obtained from taxidermized museum specimens or road kills. We generated the 12S rRNA sequences of 18 mammal species from 6 orders and 13 different families. We also obtained the trnL and rbcL barcode sequences of 52 plant species from 24 different families. Twenty-five plant species and two mammal species included in this study were sequenced for the first time using these markers.},
}
@article {pmid33000878,
year = {2021},
author = {Fontes, JT and Vieira, PE and Ekrem, T and Soares, P and Costa, FO},
title = {BAGS: An automated Barcode, Audit &amp; Grade System for DNA barcode reference libraries.},
journal = {Molecular ecology resources},
volume = {21},
number = {2},
pages = {573-583},
doi = {10.1111/1755-0998.13262},
pmid = {33000878},
issn = {1755-0998},
support = {NORTE-01-0145-FEDER-000032//European Regional Development Fund/ ; PTDC/BIA-BMA/29754/2017//Portuguese Foundation for Science and Technology/ ; },
mesh = {Animals ; *Biodiversity ; DNA ; *DNA Barcoding, Taxonomic ; *Gene Library ; Reproducibility of Results ; *Software ; },
abstract = {Biodiversity studies greatly benefit from molecular tools, such as DNA metabarcoding, which provides an effective identification tool in biomonitoring and conservation programmes. The accuracy of species-level assignment, and consequent taxonomic coverage, relies on comprehensive DNA barcode reference libraries. The role of these libraries is to support species identification, but accidental errors in the generation of the barcodes may compromise their accuracy. Here, we present an R-based application, Barcode, Audit &amp; Grade System (BAGS) (https://github.com/tadeu95/BAGS), that performs automated auditing and annotation of cytochrome c oxidase subunit I (COI) sequences libraries, for a given taxonomic group of animals, available in the Barcode of Life Data System (BOLD). This is followed by implementing a qualitative ranking system that assigns one of five grades (A to E) to each species in the reference library, according to the attributes of the data and congruency of species names with sequences clustered in barcode index numbers (BINs). Our goal is to allow researchers to obtain the most useful and reliable data, highlighting and segregating records according to their congruency. Different tests were performed to perceive its usefulness and limitations. BAGS fulfils a significant gap in the current landscape of DNA barcoding research tools by quickly screening reference libraries to gauge the congruence status of data and facilitate the triage of ambiguous data for posterior review. Thereby, BAGS has the potential to become a valuable addition in forthcoming DNA metabarcoding studies, in the long term contributing to globally improve the quality and reliability of the public reference libraries.},
}
@article {pmid32997595,
year = {2020},
author = {Taha, H and Shivanand, P and Khoo, H and Mohammad, YH and Matussin, NBA and Metali, F},
title = {Identification of culturable petroleum-degrading bacteria and fungi from petroleum-contaminated sites in Brunei Darussalam.},
journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances &amp; environmental engineering},
volume = {55},
number = {13},
pages = {1542-1547},
doi = {10.1080/10934529.2020.1826238},
pmid = {32997595},
issn = {1532-4117},
mesh = {Bacteria/isolation &amp; purification ; Biodegradation, Environmental ; Biotechnology ; Brunei ; Fungi/isolation &amp; purification ; Petroleum Pollution/*analysis ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/*analysis ; Water Pollutants, Chemical/*analysis ; },
abstract = {Microbes that can be cultured and degrade petroleum are of particular interest for biotechnology such as bioremediation. This study aims to isolate and identify culturable petroleum-degrading bacteria and fungi from Brunei Darussalam, which has not previously been explored. A total of eight bacterial and nine fungal isolates that could degrade petroleum were obtained from petroleum-contaminated water or soil samples. DNA barcoding using 16S rRNA gene sequence identified five different bacterial genera which were Bacillus, Enterobacter, Micrococcus, Pseudoaltermonas and Pseudomonas. DNA barcoding using rRNA-ITS gene sequence identified nine different fungal taxa which were Aspergillus, Cladosporium, Exophiala, Flavodon, Hypocreales, Nectriaceae, Penicillium, Peniophora and Trichoderma. Biolog provided additional support to the identification of some isolates. This study is the first to report these unique microbes from Brunei Darussalam, which are of ecological and biotechnological value.},
}
@article {pmid32996917,
year = {2020},
author = {Hlaváček, A and Křivánková, J and Pizúrová, N and Václavek, T and Foret, F},
title = {Photon-upconversion barcode for monitoring an enzymatic reaction with a fluorescence reporter in droplet microfluidics.},
journal = {The Analyst},
volume = {145},
number = {23},
pages = {7718-7723},
doi = {10.1039/d0an01667e},
pmid = {32996917},
issn = {1364-5528},
mesh = {*Fluorescent Dyes ; Galactose ; *Microfluidics ; beta-Galactosidase/genetics ; },
abstract = {We report luminescent photon-upconversion barcodes for indexing the chemical content of droplets. The barcode is compatible with the simultaneous detection of fluorescence. The encoding and decoding of the initial concentration of enzyme β-galactosidase and substrate 4-methylumbelliferyl β-d-galactopyranoside are described. The fluorescent product 4-methylumbelliferone is detected simultaneously with the barcode.},
}
@article {pmid32995546,
year = {2019},
author = {Currin, A and Swainston, N and Dunstan, MS and Jervis, AJ and Mulherin, P and Robinson, CJ and Taylor, S and Carbonell, P and Hollywood, KA and Yan, C and Takano, E and Scrutton, NS and Breitling, R},
title = {Highly multiplexed, fast and accurate nanopore sequencing for verification of synthetic DNA constructs and sequence libraries.},
journal = {Synthetic biology (Oxford, England)},
volume = {4},
number = {1},
pages = {ysz025},
pmid = {32995546},
issn = {2397-7000},
support = {BB/M017702/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {Synthetic biology utilizes the Design-Build-Test-Learn pipeline for the engineering of biological systems. Typically, this requires the construction of specifically designed, large and complex DNA assemblies. The availability of cheap DNA synthesis and automation enables high-throughput assembly approaches, which generates a heavy demand for DNA sequencing to verify correctly assembled constructs. Next-generation sequencing is ideally positioned to perform this task, however with expensive hardware costs and bespoke data analysis requirements few laboratories utilize this technology in-house. Here a workflow for highly multiplexed sequencing is presented, capable of fast and accurate sequence verification of DNA assemblies using nanopore technology. A novel sample barcoding system using polymerase chain reaction is introduced, and sequencing data are analyzed through a bespoke analysis algorithm. Crucially, this algorithm overcomes the problem of high-error rate nanopore data (which typically prevents identification of single nucleotide variants) through statistical analysis of strand bias, permitting accurate sequence analysis with single-base resolution. As an example, 576 constructs (6 × 96 well plates) were processed in a single workflow in 72 h (from Escherichia coli colonies to analyzed data). Given our procedure's low hardware costs and highly multiplexed capability, this provides cost-effective access to powerful DNA sequencing for any laboratory, with applications beyond synthetic biology including directed evolution, single nucleotide polymorphism analysis and gene synthesis.},
}
@article {pmid32995390,
year = {2020},
author = {Inai, K and Wakimura, K and Kato, M},
title = {Pairwise sequence comparison data of the DNA barcodes of aquatic insects.},
journal = {Data in brief},
volume = {32},
number = {},
pages = {106284},
pmid = {32995390},
issn = {2352-3409},
abstract = {This study compared the DNA sequences of cytochrome c oxidase subunit I (COI) and histone H3 of Ephemeroptera, Odonata, Plecoptera, and Trichoptera in a pairwise manner, and calculated the sequence similarities based on uncorrected P-distance (number of identical sites in both sequences per total number of the sites compared). Datasets of annotated sequences, the source organisms of which are identified at the species level in taxonomy, were retrieved from INSD (GenBank/ ENA/ DDBJ) as of the end of May 2020. Similarity scores of the pairwise comparison were sorted by the combinations of taxonomic groups; intraspecific variations, intrageneric-interspecific divergences, intrafamily-intergeneric divergences, and intraorder-interfamily divergences for Ephemeroptera, Odonata, Plecoptera, and Trichoptera. Similarity scores at the cumulative relative frequency points (1%, 5%, 10%, and median) may be used as the threshold to differentiate between the taxonomic groups based on sequence match. This is often done in the characterization of morphologically-unidentified specimens using barcode sequences, in the metabarcoding analysis of the local fauna, and environmental DNA analysis.},
}
@article {pmid32994210,
year = {2020},
author = {St John, N and Freedland, J and Baldino, H and Doyle, F and Cera, C and Begley, T and Fasullo, M},
title = {Genome Profiling for Aflatoxin B1 Resistance in Saccharomyces cerevisiae Reveals a Role for the CSM2/SHU Complex in Tolerance of Aflatoxin B1-Associated DNA Damage.},
journal = {G3 (Bethesda, Md.)},
volume = {10},
number = {11},
pages = {3929-3947},
pmid = {32994210},
issn = {2160-1836},
support = {F33 ES021133/ES/NIEHS NIH HHS/United States ; R15 ES023685/ES/NIEHS NIH HHS/United States ; R21 CA125064/CA/NCI NIH HHS/United States ; },
mesh = {Aflatoxin B1/toxicity ; *Carcinoma, Hepatocellular ; DNA Damage ; DNA-Binding Proteins/genetics ; Humans ; *Liver Neoplasms ; Saccharomyces cerevisiae/genetics ; *Saccharomyces cerevisiae Proteins/genetics ; },
abstract = {Exposure to the mycotoxin aflatoxin B1 (AFB1) strongly correlates with hepatocellular carcinoma (HCC). P450 enzymes convert AFB1 into a highly reactive epoxide that forms unstable 8,9-dihydro-8-(N7-guanyl)-9-hydroxyaflatoxin B1 (AFB1-N[7]-Gua) DNA adducts, which convert to stable mutagenic AFB1 formamidopyrimidine (FAPY) DNA adducts. In CYP1A2-expressing budding yeast, AFB1 is a weak mutagen but a potent recombinagen. However, few genes have been identified that confer AFB1 resistance. Here, we profiled the yeast genome for AFB1 resistance. We introduced the human CYP1A2 into ∼90% of the diploid deletion library, and pooled samples from CYP1A2-expressing libraries and the original library were exposed to 50 μM AFB1 for 20 hs. By using next generation sequencing (NGS) to count molecular barcodes, we initially identified 86 genes from the CYP1A2-expressing libraries, of which 79 were confirmed to confer AFB1 resistance. While functionally diverse genes, including those that function in proteolysis, actin reorganization, and tRNA modification, were identified, those that function in postreplication DNA repair and encode proteins that bind to DNA damage were over-represented, compared to the yeast genome, at large. DNA metabolism genes also included those functioning in checkpoint recovery and replication fork maintenance, emphasizing the potency of the mycotoxin to trigger replication stress. Among genes involved in postreplication repair, we observed that CSM2, a member of the CSM2(SHU) complex, functioned in AFB1-associated sister chromatid recombination while suppressing AFB1-associated mutations. These studies thus broaden the number of AFB1 resistance genes and have elucidated a mechanism of error-free bypass of AFB1-associated DNA adducts.},
}
@article {pmid32992465,
year = {2020},
author = {Pecoraro, C and Crobe, V and Ferrari, A and Piattoni, F and Sandionigi, A and Andrews, AJ and Cariani, A and Tinti, F},
title = {Canning Processes Reduce the DNA-Based Traceability of Commercial Tropical Tunas.},
journal = {Foods (Basel, Switzerland)},
volume = {9},
number = {10},
pages = {},
pmid = {32992465},
issn = {2304-8158},
abstract = {Canned tuna is one of the most widely traded seafood products internationally and is of growing demand. There is an increasing concern over the vulnerability of canned tuna supply chains to species mislabelling and fraud. Extensive processing conditions in canning operations can lead to the degradation and fragmentation of DNA, complicating product traceability. We here employed a forensically validated DNA barcoding tool (cytochrome b partial sequences) to assess the effects of canning processes on DNA degradation and the identification of four tropical tuna species (yellowfin, bigeye, skipjack and longtail tuna) collected on a global scale, along their commercial chains. Each species was studied under five different canning processes i.e., freezing, defrosting, cooking, and canning in oil and brine, in order to investigate how these affect DNA-based species identification and traceability. The highest percentage of nucleotide substitutions were observed after brine-canning operations and were greatest for yellowfin and skipjack tuna. Overall, we found that DNA degradation significantly increased along the tuna canning process for most specimens. Consequently, most of the specimens canned in oil or brine were misidentified due to the high rate of nucleotide substitution in diagnostic sequences.},
}
@article {pmid32990747,
year = {2020},
author = {Gyllborg, D and Langseth, CM and Qian, X and Choi, E and Salas, SM and Hilscher, MM and Lein, ES and Nilsson, M},
title = {Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue.},
journal = {Nucleic acids research},
volume = {48},
number = {19},
pages = {e112},
pmid = {32990747},
issn = {1362-4962},
mesh = {Animals ; Brain/metabolism ; Computational Biology ; Humans ; In Situ Hybridization, Fluorescence/*methods ; Mice ; RNA/*analysis ; Single-Cell Analysis/*methods ; *Transcriptome ; },
abstract = {Visualization of the transcriptome in situ has proven to be a valuable tool in exploring single-cell RNA-sequencing data, providing an additional spatial dimension to investigate multiplexed gene expression, cell types, disease architecture or even data driven discoveries. In situ sequencing (ISS) method based on padlock probes and rolling circle amplification has been used to spatially resolve gene transcripts in tissue sections of various origins. Here, we describe the next iteration of ISS, HybISS, hybridization-based in situ sequencing. Modifications in probe design allows for a new barcoding system via sequence-by-hybridization chemistry for improved spatial detection of RNA transcripts. Due to the amplification of probes, amplicons can be visualized with standard epifluorescence microscopes for high-throughput efficiency and the new sequencing chemistry removes limitations bound by sequence-by-ligation chemistry of ISS. HybISS design allows for increased flexibility and multiplexing, increased signal-to-noise, all without compromising throughput efficiency of imaging large fields of view. Moreover, the current protocol is demonstrated to work on human brain tissue samples, a source that has proven to be difficult to work with image-based spatial analysis techniques. Overall, HybISS technology works as a targeted amplification detection method for improved spatial transcriptomic visualization, and importantly, with an ease of implementation.},
}
@article {pmid32987804,
year = {2020},
author = {Chang, JJM and Ip, YCA and Ng, CSL and Huang, D},
title = {Takeaways from Mobile DNA Barcoding with BentoLab and MinION.},
journal = {Genes},
volume = {11},
number = {10},
pages = {},
pmid = {32987804},
issn = {2073-4425},
mesh = {Animals ; Aquatic Organisms/*genetics ; Biodiversity ; *Coral Reefs ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing/*methods ; *Nanopores ; Sequence Analysis, DNA/*methods ; *Software ; },
abstract = {Since the release of the MinION sequencer in 2014, it has been applied to great effect in the remotest and harshest of environments, and even in space. One of the most common applications of MinION is for nanopore-based DNA barcoding in situ for species identification and discovery, yet the existing sample capability is limited (n ≤ 10). Here, we assembled a portable sequencing setup comprising the BentoLab and MinION and developed a workflow capable of processing 32 samples simultaneously. We demonstrated this enhanced capability out at sea, where we collected samples and barcoded them onboard a dive vessel moored off Sisters' Islands Marine Park, Singapore. In under 9 h, we generated 105 MinION barcodes, of which 19 belonged to fresh metazoans processed immediately after collection. Our setup is thus viable and would greatly fortify existing portable DNA barcoding capabilities. We also tested the performance of the newly released R10.3 nanopore flow cell for DNA barcoding, and showed that the barcodes generated were ~99.9% accurate when compared to Illumina references. A total of 80% of the R10.3 nanopore barcodes also had zero base ambiguities, compared to 50-60% for R9.4.1, suggesting an improved homopolymer resolution and making the use of R10.3 highly recommended.},
}
@article {pmid32985685,
year = {2021},
author = {Wagner, M and Kovačić, M and Koblmüller, S},
title = {Unravelling the taxonomy of an interstitial fish radiation: Three new species of Gouania (Teleostei: Gobiesocidae) from the Mediterranean Sea and redescriptions of G. willdenowi and G. pigra.},
journal = {Journal of fish biology},
volume = {98},
number = {1},
pages = {64-88},
pmid = {32985685},
issn = {1095-8649},
support = {//Heinrich-J&#xf6;rg-Foundation (University of Graz)/ ; IP-2016-06-9884//Hrvatska Zaklada za Znanost (HR)/ ; IP-2016-06-5251//Hrvatska Zaklada za Znanost (HR)/ ; //&#xd6;sterreichische Forschungsgemeinschaft/ ; //&#xd6;sterreichischen Akademie der Wissenschaften/ ; //University of Graz (KUWI)/ ; //Croatian Science Foundation/ ; },
mesh = {Animal Distribution ; Animals ; Biodiversity ; Classification ; DNA Barcoding, Taxonomic ; Europe ; Fishes/anatomy &amp; histology/*classification/genetics ; Mediterranean Sea ; *Phylogeny ; Species Specificity ; X-Ray Microtomography ; },
abstract = {The clingfish (Gobiesocidae) genus Gouania Nardo, 1833 is endemic to the Mediterranean Sea and inhabits, unlike any other vertebrate species in Europe, the harsh intertidal environment of gravel beaches. Following up on a previous phylogenetic study, we revise the diversity and taxonomy of this genus by analysing a comprehensive set of morphological (meristics, morphometrics, microcomputed tomography imaging), geographical and genetic (DNA-barcoding) data. We provide descriptions of three new species, G. adriatica sp. nov., G. orientalis sp. nov. and G. hofrichteri sp. nov., as well as redescriptions of G. willdenowi (Risso, 1810) and G. pigra (Nardo, 1827) and assign neotypes for the latter two species. In addition to elucidating the complex taxonomic situation of Gouania, we discuss the potential of this enigmatic clingfish genus for further ecological, evolutionary and biodiversity studies that might unravel even more diversity in this unique Mediterranean fish radiation.},
}
@article {pmid32984598,
year = {2020},
author = {de Carvalho, SC and Sampaio, I and Santos, S},
title = {DNA barcoding reveals mislabeling and commercial fraud in the marketing of fillets of the genus Brachyplatystoma Bleeker, 1862, the Amazonian freshwater catfishes economically important in Brazil.},
journal = {Heliyon},
volume = {6},
number = {9},
pages = {e04888},
pmid = {32984598},
issn = {2405-8440},
abstract = {The substitution and mislabeling is facilitated by the processing of fish products. We employed a DNA barcoding to authenticate fillets labeled as "dourada" (Brachyplatystoma rousseauxii), and "piramutaba" (Brachyplatystoma vaillantii) marketed in the Brazil. A 615 bp of the Cytochrome oxidase subunit I (COI) was sequenced from 305 fillets and subsequently identified to species level by querying public databases and sequences of reference species. The results revealed a global mean substitution rate of 17%. The highest substitution rate was detected in "dourada" (26%), the most valuable species, followed by "piramutaba" (9%). The most cases of substitutions were by species of lower commercial value, suggesting fraud aimed at increased profits. Therefore, we suggest the improvement of food-labeling regulation, continued inspection, as well as the adoption of the DNA barcode for the molecular authentication of processed fish to prevent substitution of these products in Brazil.},
}
@article {pmid32982555,
year = {2020},
author = {Kjærandsen, J and Polevoi, A and Salmela, J},
title = {Coelosynapha, a new genus of the subfamily Gnoristinae (Diptera: Mycetophilidae) with a circumpolar, Holarctic distribution.},
journal = {Biodiversity data journal},
volume = {8},
number = {},
pages = {e54834},
pmid = {32982555},
issn = {1314-2828},
abstract = {BACKGROUND: The subfamily Gnoristinae is one of the most diverse and taxonomically difficult subfamilies of Mycetophilidae, with new species and genera being described almost every year from various parts of the world. Through inventories of fungus gnats in the Nordic Region and Russia, a genus and species new to science was discovered, yet with links back to an illustration made by the late French entomologist Loïc Matile in the 1980s. DNA barcoding aligned it with yet another species new to science, distributed across Canada and documented through The Barcode of Life Data System (BOLD) by Paul D. N. Hebert and colleagues at the BOLD team.<br><br>NEW INFORMATION: The new Holarctic genus, Coelosynapha gen. n. is described, consisting of two new species, the Palaearctic Coelosynapha loici sp. n. and the Nearctic Coelosynapha heberti sp. n. DNA-barcodes assign the two new species to distinctly separated (8.27% p-distance) Barcode Index Numbers (BINs) which are most closely aligned to unidentified species of Mycetophilidae from South Australia and Costa Rica on BOLD. The new genus shows morphological characteristics in between the two Holarctic genera Coelosia Winnertz, 1864 and Synapha Meigen, 1818 and further shows affinity to the southern continents genus Austrosynapha Tonnoir, 1929. The Palaearctic Coelosynapha loici sp. n., for which habitat requirements are best documented, is largely restricted to pristine, old-growth conifer (mostly spruce, Picea abies ssp. obovata) forests within the boreal vegetation zone, although it is also recorded from hummock tundra along the Anadyr River in Far East Russia.},
}
@article {pmid32981248,
year = {2020},
author = {S Dessoky, ED and Attia, AO and A Ismail, I and Alotaibi, SS and S Aljuaid, B},
title = {Molecular Assessment of Genetic Stability Using CDDP and DNA-barcoding Assays in Long-term Micropropagated Rose Plant.},
journal = {Pakistan journal of biological sciences : PJBS},
volume = {23},
number = {9},
pages = {1176-1183},
doi = {10.3923/pjbs.2020.1176.1183},
pmid = {32981248},
issn = {1812-5735},
mesh = {Chloroplasts/metabolism ; Cluster Analysis ; Computational Biology ; DNA Barcoding, Taxonomic/*methods ; DNA Primers ; DNA, Plant/*genetics ; Genetic Variation ; In Vitro Techniques ; Microsatellite Repeats ; Mutation ; Phylogeny ; Plants ; Polymerase Chain Reaction ; *Polymorphism, Genetic ; Rosa/*genetics ; Species Specificity ; },
abstract = {BACKGROUND AND OBJECTIVE: Roses are the world's best-known garden plants, established as ornamental plants cultivated for their blooms. Taif rose (Rosa damascena trigintipetala) refers to the Damascus Rose species and is regarded one of Taif Governorate's most significant financial goods, which produces an extremely fragrant commercially precious essential oil. The objective of current study was to assess the genetic stability of micropropagated Taif rose and to assess the usefulness of Conserved DNA Derived Polymorphism (CDDP) and DNA-barcoding genes such as; rpoC1 (chloroplast gene RNA polymerase1) in the detection of somaclonal variation.<br><br>MATERIALS AND METHODS: Ten combinations of CDDP PCR primers were employed and the rpoC1 gene region was sequenced for mother plant (control) and micropropagated plantlets of Taif rose plant.<br><br>RESULTS: Based on CDDP data, phylogenetic divergence indicated that the distinct specimens of Taif rose micro-propagated plantlets and control were genetically differentiated by a difference of 1% of genetic dissimilarity. Phylogenetic tree which developed using rpoC1 DNA showed that rpoC1 DNA sequencing discovered a genetic difference between the control and micro-propagated plantlets of Taif rose.<br><br>CONCLUSION: Furthermore, CDDP and DNA barcoding using rpoC1 gene have demonstrated their usefulness in investigating the genetic history of Rosa species and their ability to explore genetic mutation.},
}
@article {pmid32974106,
year = {2020},
author = {Santamaria, CA and Locascio, J and Greenan, TM},
title = {First report of lionfish prey from Western Florida waters as identified by DNA barcoding.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e9922},
pmid = {32974106},
issn = {2167-8359},
abstract = {DNA barcoding was used to identify prey fragments recovered from the stomachs of lionfish harvested during the 2016 Sarasota Lionfish Derby. A total of 305 prey fragments were recovered from 50 stomachs (mean = 4.6 per stomach), of which 184 (60.3%) fragments could be identified to either species or genus when Cytochrome Oxidase I (COI) sequences were queried against the Barcode of Life Database. We identified 21 fish prey species which represented fourteen families and accounted for 95.7% of genetically identifiable prey items. The remaining prey items identified corresponded to six crustacean species. The four most common prey taxa in lionfish stomachs were Ptereleotris calliura (24.3%), an unidentified Microgobius species (20.4%), Diplectum formosum (14.3%), and Apogon aurolineatus (12.2%). The most frequently observed crustacean species, Metapenaeopsis goodei, was found in only three stomachs (6.1%). We also report eleven taxa as putative novel lionfish prey species, most of which are common in Florida waters. Sixteen prey items were identified as lionfish (P. volitans); however, it was not definitive whether these detections were due to cross contamination or cannibalization. This represents the first report of lionfish diets from Florida waters in the Eastern Gulf of Mexico based on barcoding efforts. Our results are largely congruent with previous COI barcoding based studies of lionfish diets, indicating these predators to be generalists exhibiting preferences for specific prey traits but with regional differences in their diets.},
}
@article {pmid32973378,
year = {2020},
author = {Wang, X and Shaheen, S and He, Q and Yao, Z},
title = {Notes on two closely related spider species of the Pholcus phungiformes species group (Araneae, Pholcidae) from Beijing, China.},
journal = {ZooKeys},
volume = {965},
number = {},
pages = {1-16},
pmid = {32973378},
issn = {1313-2989},
abstract = {The Pholcus phungiformes species group is highly diverse and currently contains 53 species. In this study, Pholcus tongyaoi Wang &amp; Yao, sp. nov. (male, female) from Huairou District, Beijing, China is described while similar congener Pholcus lexuancanhi Yao, Pham &amp; Li, 2012 from neighboring Haidian District (type locality) is redescribed; the female of P. lexuancanhi is described for the first time. In addition, the DNA barcode COI for the two species was obtained to estimate p-distance.},
}
@article {pmid32972362,
year = {2020},
author = {Dhivya, S and Ashutosh, S and Gowtham, I and Baskar, V and Harini, AB and Mukunthakumar, S and Sathishkumar, R},
title = {Molecular identification and evolutionary relationships between the subspecies of Musa by DNA barcodes.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {659},
pmid = {32972362},
issn = {1471-2164},
support = {PDFWM -2015-17-TAM-34021//University Grants Commission/ ; },
mesh = {DNA Barcoding, Taxonomic/*methods ; *Evolution, Molecular ; Musa/classification/*genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; },
abstract = {BACKGROUND: The banana (Musa sp., AAA) genome is constantly increasing due to high-frequency of somaclonal variations. Due to its large diversity, a conventional numerical and morphological based taxonomic identification of banana cultivars is laborious, difficult and often leads to subject of disagreements.<br><br>RESULTS: Hence, in the present study, we used universal DNA barcode ITS2 region to identify and to find the genetic relationship between the cultivars and varieties of banana. Herein, a total of 16 banana cultivars were PCR amplified using ITS2 primer pair. In addition, 321 sequences which were retrieved from GenBank, USA, were used in this study. The sequences were then aligned using Clustal W and genetic distances were computed using MEGA V5.1. The study showed significant divergence between the intra- and inter-specific genetic distances in ITS2 region. BLAST1 and Distance methods proved that ITS2 DNA barcode region successfully identified and distinguished the cultivar and varieties of banana.<br><br>CONCLUSION: Thus, from the results of the present study, it is clear that ITS2 is not only an efficient DNA barcode to identify the banana species but also a potential candidate for enumerating the phylogenetic relationships between the subspecies and cultivars. This is the first comprehensive study to categorically distinguish the economically important banana subspecies and varieties using DNA barcodes and to understand its evolutionary relationship.},
}
@article {pmid32972089,
year = {2020},
author = {Sugiura, K and Minato, H and Matsumoto, M and Suzuki, AC},
title = {Milnesium (Tardigrada: Apochela) in Japan: The First Confirmed Record of Milnesium tardigradum s.s. and Description of Milnesium pacificum sp. nov.},
journal = {Zoological science},
volume = {37},
number = {5},
pages = {476-495},
doi = {10.2108/zs190154},
pmid = {32972089},
issn = {0289-0003},
mesh = {Animals ; Phylogeny ; Species Specificity ; Tardigrada/classification/*isolation &amp; purification ; },
abstract = {Presently, more than 40 species of the genus Milnesium Doyère, 1840 (Tardigrada: Eutardigrada: Apochela: Milnesiidae) have been described. In Japan, however, almost all records of milnesiid tardigrades should be re-examined with the current criteria on the taxonomy of this genus, except for one species, the recently described Milnesium inceptum Morek, Suzuki, Schill, Georgiev, Yankova, Marley, and Michalczyk, 2019. In this study, we found two species, Milnesium pacificum sp. nov. and Milnesium tardigradum Doyère, 1840, from three southern islands and two cold regions in Japan, respectively. Milnesium pacificum sp. nov., having dorsal sculpturing, exhibits an early positive change in claw configuration. On the other hand, M. tardigradum s.s. from Japan has an early negative claw configuration change, as has been reported in a recent study on the neotype population of this species. We performed DNA barcoding for both species, which indicated that M. pacificum sp. nov. has a close affinity with an undescribed Milnesium species collected from Brazil, and that M. tardigradum from Japan represents the recently described subclade that contains specimens from Poland, Hungary, and Russia. The chromosome numbers were 2n = 14 in M. pacificum sp. nov. and 2n = 10 in M. tardigradum. We detected at least three species of the genus Milnesium present in Japan. Our results advance the investigation of the relationship between phylogenetic position and characteristic morphology as well as expand the known geographic range of M. tardigradum.},
}
@article {pmid32971306,
year = {2021},
author = {Rossel, S and Barco, A and Kloppmann, M and Martínez Arbizu, P and Huwer, B and Knebelsberger, T},
title = {Rapid species level identification of fish eggs by proteome fingerprinting using MALDI-TOF MS.},
journal = {Journal of proteomics},
volume = {231},
number = {},
pages = {103993},
doi = {10.1016/j.jprot.2020.103993},
pmid = {32971306},
issn = {1876-7737},
mesh = {Animals ; *Conservation of Natural Resources ; Fisheries ; *Proteome ; Specimen Handling ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {Quantifying spawning biomass of commercially relevant fish species is important to generate fishing quotas. This will mostly rely on the annual or daily production of fish eggs. However, these have to be identified precisely to species level to obtain a reliable estimate of offspring production of the different species. Because morphological identification can be very difficult, recent developments are heading towards application of molecular tools. Methods such as COI barcoding have long handling times and cause high costs for single specimen identifications. In order to test MALDI-TOF MS, a rapid and cost-effective alternative for species identification, we identified fish eggs using COI barcoding and used the same specimens to set up a MALDI-TOF MS reference library. This library, constructed from two different MALDI-TOF MS instruments, was then used to identify unknown eggs from a different sampling occasion. By using a line of evidence from hierarchical clustering and different supervised identification approaches we obtained concordant species identifications for 97.5% of the unknown fish eggs, proving MALDI-TOF MS a good tool for rapid species level identification of fish eggs. At the same time we point out the necessity of adjusting identification scores of supervised methods for identification to optimize identification success. SIGNIFICANCE: Fish products are commercially highly important and many societies rely on them as a major food resource. Over many decades stocks of various relevant fish species have been reduced due to unregulated overfishing. Nowadays, to avoid overfishing and threatening of important fish species, fish stocks are regularly monitored. One component of this monitoring is the monitoring of spawning stock sizes. Whereas this is highly dependent on correct species identification of fish eggs, morphological identification is difficult because of lack of morphological features.},
}
@article {pmid32968111,
year = {2020},
author = {Zamani Kouhpanji, MR and Ghoreyshi, A and Visscher, PB and Stadler, BJH},
title = {Facile decoding of quantitative signatures from magnetic nanowire arrays.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {15482},
pmid = {32968111},
issn = {2045-2322},
abstract = {Magnetic nanoparticles have been proposed as contact-free minimal-background nanobarcodes, and yet it has been difficult to rapidly and reliably decode them in an assembly. Here, high aspect ratio nanoparticles, or magnetic nanowires (MNWs), are characterized using first-order reversal curves (FORC) to investigate quantitative decoding. We have synthesized four types of nanowires (differing in diameter) that might be used for barcoding, and identified four possible "signature" functions that might be used to quickly distinguish them. To test this, we have measured the signatures of several combination samples containing two or four different MNW types, and fit them to linear combinations of the individual type signatures to determine the volume ratios of the types. We find that the signature which determines the ratios most accurately involves only the slope of each FORC at its reversal field, which requires only 2-4 data points per FORC curve, reducing the measurement time by a factor of 10 to 50 compared to measuring the full FORC.},
}
@article {pmid32963488,
year = {2020},
author = {Pykälä, J and Kantelinen, A and Myllys, L},
title = {Taxonomy of Verrucaria species characterised by large spores, perithecia leaving pits in the rock and a pale thin thallus in Finland.},
journal = {MycoKeys},
volume = {72},
number = {},
pages = {43-92},
pmid = {32963488},
issn = {1314-4049},
abstract = {Species of Verrucaria, characterised by large spores (at least some spores exceeding 25 µm in length), perithecia leaving pits in the rock and a pale thin thallus, form a taxonomically-difficult and poorly-known group. In this study, such species occurring in Finland are revised, based on ITS sequences and morphology. Maximum likelihood analysis of ITS sequence data was used to examine if the species belong to the Thelidium group, as suggested by BLAST search. Twelve species are accepted in Finland: Verrucaria bifurcata sp. nov., V. cavernarum sp. nov., V. devergens, V. difficilis sp. nov., V. foveolata, V. fuscozonata sp. nov., V. karelica, V. kuusamoensis sp. nov., V. subdevergens sp. nov., V. subjunctiva, V. subtilis and V. vacillans sp. nov. Verrucaria foveolata is nested in V. subjunctiva in the phylogeny, but due to morphological and ecogeographical differences, the two taxa are treated as separate species pending further studies. Based on the analysis, the study species belong to the Thelidium group. The studied species show a rather high infraspecific morphological, but a low genetic variation. Furthermore, they show considerable overlap in their morphology and many specimens cannot be reliably identified, based on morphology only. All species are restricted to calcareous rocks. Verrucaria alpigena, V. cinereorufa and V. hochstetteri are excluded from the lichen flora of Finland. Verrucaria grossa is considered a species with unresolved identity. Verrucaria foveolata and V. subtilis are rather common on calcareous rocks of Finland while V. devergens and V. kuusamoensis are restricted to northern Finland. Verrucaria subjunctiva occurs mainly in northern Finland. Verrucaria bifurcata has been found only from southern Finland. Verrucaria difficilis has few localities both in SW and NE Finland. Verrucaria vacillans is restricted to calcareous rocks (dolomite) on the mountains of the NW corner of Finland. Verrucaria fuscozonata, V. karelica and V. subdevergens occur only in the Oulanka area in NE Finland. A lectotype is designated for V. subjunctiva. The morphology of the Finnish species was compared with 51 European species of Verrucaria presumably belonging to the Thelidium group.},
}
@article {pmid32961908,
year = {2020},
author = {Wang, Y and Wagner, E},
title = {Non-Viral Targeted Nucleic Acid Delivery: Apply Sequences for Optimization.},
journal = {Pharmaceutics},
volume = {12},
number = {9},
pages = {},
pmid = {32961908},
issn = {1999-4923},
support = {ID 201269156 SFB 1032 subproject B4//Deutsche Forschungsgemeinschaft/ ; 410149116//DFG-NSFC Joint Sino-German Research Project/ ; 91658575//Sino-German (CSC-DAAD) Postdoc Scholarship Program/ ; },
abstract = {In nature, genomes have been optimized by the evolution of their nucleic acid sequences. The design of peptide-like carriers as synthetic sequences provides a strategy for optimizing multifunctional targeted nucleic acid delivery in an iterative process. The optimization of sequence-defined nanocarriers differs for different nucleic acid cargos as well as their specific applications. Supramolecular self-assembly enriched the development of a virus-inspired non-viral nucleic acid delivery system. Incorporation of DNA barcodes presents a complementary approach of applying sequences for nanocarrier optimization. This strategy may greatly help to identify nucleic acid carriers that can overcome pharmacological barriers and facilitate targeted delivery in vivo. Barcode sequences enable simultaneous evaluation of multiple nucleic acid nanocarriers in a single test organism for in vivo biodistribution as well as in vivo bioactivity.},
}
@article {pmid32953072,
year = {2020},
author = {Gojković, N and Francuski, L and Ludoški, J and Milankov, V},
title = {DNA barcode assessment and population structure of aphidophagous hoverfly Sphaerophoria scripta: Implications for conservation biological control.},
journal = {Ecology and evolution},
volume = {10},
number = {17},
pages = {9428-9443},
pmid = {32953072},
issn = {2045-7758},
abstract = {With the advent of integrated pest management, the conservation of indigenous populations of natural enemies of pest species has become a relevant practice, necessitating the accurate identification of beneficial species and the inspection of evolutionary mechanisms affecting the long-time persistence of their populations. The long hoverfly, Sphaerophoria scripta, represents one of the most potent aphidophagous control agents due to a worldwide distribution and a favorable constellation of biological traits. Therefore, we assessed five European S. scripta populations by combining molecular (cytochrome c oxidase subunit I- COI, internal transcribed spacer 2- ITS2, and allozyme loci) and morphological (wing size and shape) characters. COI sequences retrieved in this study were conjointly analyzed with BOLD/GenBank sequences of the other Sphaerophoria species to evaluate whether COI possessed a sufficient diagnostic value as a DNA barcode marker to consistently delimit allospecific individuals. Additionally, the aforementioned characters were used to inspect the population structure of S. scripta in Europe using methods based on individual- and population-based genetic differences, as well as geometric morphometrics of wing traits. The results indicate numerous shared COI haplotypes among different Sphaerophoria species, thus disqualifying this marker from being an adequate barcoding region in this genus. Conversely, the analyses of population structuring revealed high population connectivity across Europe, therefore indicating strong tolerance of S. scripta to environmental heterogeneity. The results imply a multilocus approach as the next step in molecular identification of different Sphaerophoria species, while confirming the status of S. scripta as a powerful biocontrol agent of economically relevant aphid pests.},
}
@article {pmid32953045,
year = {2020},
author = {Hill, GE},
title = {Genetic hitchhiking, mitonuclear coadaptation, and the origins of mt DNA barcode gaps.},
journal = {Ecology and evolution},
volume = {10},
number = {17},
pages = {9048-9059},
pmid = {32953045},
issn = {2045-7758},
abstract = {DNA barcoding based on mitochondrial (mt) nucleotide sequences is an enigma. Neutral models of mt evolution predict DNA barcoding cannot work for recently diverged taxa, and yet, mt DNA barcoding accurately delimits species for many bilaterian animals. Meanwhile, mt DNA barcoding often fails for plants and fungi. I propose that because mt gene products must cofunction with nuclear gene products, the evolution of mt genomes is best understood with full consideration of the two environments that impose selective pressure on mt genes: the external environment and the internal genomic environment. Moreover, it is critical to fully consider the potential for adaptive evolution of not just protein products of mt genes but also of mt transfer RNAs and mt ribosomal RNAs. The tight linkage of genes on mt genomes that do not engage in recombination could facilitate selective sweeps whenever there is positive selection on any element in the mt genome, leading to the purging of mt genetic diversity within a population and to the rapid fixation of novel mt DNA sequences. Accordingly, the most important factor determining whether or not mt DNA sequences diagnose species boundaries may be the extent to which the mt chromosomes engage in recombination.},
}
@article {pmid32946982,
year = {2020},
author = {Jacobs, S and Ausema, A and Zwart, E and Weersing, E and de Haan, G and Bystrykh, LV and Belderbos, ME},
title = {Detection of chemotherapy-resistant patient-derived acute lymphoblastic leukemia clones in murine xenografts using cellular barcodes.},
journal = {Experimental hematology},
volume = {91},
number = {},
pages = {46-54},
doi = {10.1016/j.exphem.2020.09.188},
pmid = {32946982},
issn = {1873-2399},
mesh = {Adolescent ; Animals ; Clone Cells/*drug effects ; *DNA Barcoding, Taxonomic ; DNA, Neoplasm/genetics ; Dexamethasone/pharmacology ; *Drug Resistance, Neoplasm ; Heterografts ; Humans ; Interleukin Receptor Common gamma Subunit/deficiency ; Leukemia, B-Cell/*pathology ; Methotrexate/pharmacology ; Mice ; Mice, Inbred NOD ; Mice, SCID ; Neoplasm Transplantation ; Neoplastic Stem Cells/*drug effects ; Selection, Genetic ; Single-Cell Analysis ; Vincristine/pharmacology ; },
abstract = {Clonal heterogeneity fuels leukemia evolution, therapeutic resistance, and relapse. Upfront detection of therapy-resistant leukemia clones at diagnosis may allow adaptation of treatment and prevention of relapse, but this is hampered by a paucity of methods to identify and trace single leukemia-propagating cells and their clonal offspring. Here, we tested methods of cellular barcoding analysis, to trace the in vivo competitive dynamics of hundreds of patient-derived leukemia clones upon chemotherapy-mediated selective pressure. We transplanted Nod/Scid/Il2Rγ[-/-] (NSG) mice with barcoded patient-derived or SupB15 acute lymphoblastic leukemia (ALL) cells and assessed clonal responses to dexamethasone, methotrexate, and vincristine, longitudinally and across nine anatomic locations. We illustrate that chemotherapy reduces clonal diversity in a drug-dependent manner. At end-stage disease, methotrexate-treated patient-derived xenografts had significantly fewer clones compared with placebo-treated mice (100 ± 10 vs. 160 ± 15 clones, p = 0.0005), while clonal complexity in vincristine- and dexamethasone-treated xenografts was unaffected (115 ± 33 and 150 ± 7 clones, p = NS). Using tools developed to assess differential gene expression, we determined whether these clonal patterns resulted from random clonal drift or selection. We identified 5 clones that were reproducibly enriched in methotrexate-treated patient-derived xenografts, suggestive of pre-existent resistance. Finally, we found that chemotherapy-mediated selection resulted in a more asymmetric distribution of leukemia clones across anatomic sites. We found that cellular barcoding is a powerful method to trace the clonal dynamics of human patient-derived leukemia cells in response to chemotherapy. In the future, integration of cellular barcoding with single-cell sequencing technology may allow in-depth characterization of therapy-resistant leukemia clones and identify novel targets to prevent relapse.},
}
@article {pmid32944930,
year = {2020},
author = {Oladipo, SO and Nneji, LM and Anifowoshe, AT and Nneji, IC},
title = {Molecular characterization of Malapterurus minjiriya Sagua, 1987 and phylogenetic relationships within the genus Malapterurus (Silurifomes, Malapteruridae) from Nigerian inland water bodies.},
journal = {Journal of fish biology},
volume = {97},
number = {6},
pages = {1865-1869},
doi = {10.1111/jfb.14547},
pmid = {32944930},
issn = {1095-8649},
support = {//Kwara State University/ ; //Tertiary Education Trust Fund/ ; },
mesh = {Animals ; Biodiversity ; Catfishes/*classification/*genetics ; Electron Transport Complex IV/genetics ; Fresh Water ; Nigeria ; *Phylogeny ; },
abstract = {Molecular (mitochondrial cytochrome C oxidase subunit 1- COI) analysis was performed to characterize the poorly known Malapterurus minjiriya from Nigerian inland water bodies. Integrative taxonomy, involving morphological and molecular data, confirms the identity of M. minjiriya. Matrilineal genealogy reveals a sister relationship of M. minjiriya with Malapterurus electricus and Malapterurus microstoma. The genetic analysis further shows evidence of population divergence within M. electricus and Malapterurus beninensis. The findings of the study highlight the importance of the integration of DNA barcoding in biodiversity documentation of freshwater fish species in Nigeria.},
}
@article {pmid32943975,
year = {2020},
author = {Martínez-Domínguez, L and Nicolalde-Morejón, F and Lorea-Hernández, FG and Vergara-Silva, F and Stevenson, DW},
title = {A novelty in Ceratozamia (Zamiaceae, Cycadales) from the Sierra Madre del Sur, Mexico: biogeographic and morphological patterns, DNA barcoding and phenology.},
journal = {PhytoKeys},
volume = {156},
number = {},
pages = {1-25},
pmid = {32943975},
issn = {1314-2011},
abstract = {Ceratozamia is a genus of cycads occurring in eastern Mexico and Central America. In this study, we describe a new species from the Pacific region of Mexico in Guerrero state. This locality represents the most northwestern Mexico distribution for the genus. We focus the comparison of this species with the most geographically proximate and phenotypically relevant lineages for this taxon. We followed an integrative taxonomy approach to evaluate the classification of these species, including geographic location, morphology, DNA barcoding and phenology as primary sources of systematic data. Within the morphological dataset, reproductive structures are described in detail and new characters are proposed for microsporophylls. The comparative morphology of these structures facilitated the elucidation of differences in forms and species for identification. The two chosen DNA barcoding markers - namely, the chloroplast genome coding region matK and the nuclear ribosomal internal transcribed spacer (ITS) region - had low divergence, allowing only 61% of species identification, suggesting slow molecular evolutionary rates. Besides employing these three basic sources of evidence, we introduced phenology as additional information for species circumscription. In addition, this work includes a brief review of the genus at the species-level. This is therefore the most recent review for Ceratozamia across its full geographic range (latitudinal and elevational). Overall, this work further contributes to a comprehensive framework for systematic studies in Mexican cycads.},
}
@article {pmid32943824,
year = {2020},
author = {Tan, WH and Chai, LC and Chin, CF},
title = {Efficacy of DNA barcode internal transcribed spacer 2 (ITS 2) in phylogenetic study of Alpinia species from Peninsular Malaysia.},
journal = {Physiology and molecular biology of plants : an international journal of functional plant biology},
volume = {26},
number = {9},
pages = {1889-1896},
pmid = {32943824},
issn = {0971-5894},
abstract = {Alpinia belongs to a large genus with many species found in Peninsular Malaysia. Several species of Alpinia exhibit important medicinal potential. However, progressive studies on the genus Alpinia were hampered by difficulties encountered in species identification. With the advancement achieved in genomic technology, more sensitive tools such as DNA barcoding were developed, which can be used for species identification. Internal Transcribe Spacer 2 (ITS2) is a DNA barcode which has proven to be a promising tool for species identification. The criterions of ITS2 efficacy namely universality and efficacy for species identification were tested on Alpinia species collected from Peninsular Malaysia. The results showed that a success rate of 96.97% was achieved using ITS2 for screening 11 species of Alpinia and an outgroup sample (Zingiber specatabile). Combined with 15 additional sequences from the Genbank for five Alpinia species, ITS2 demonstrated high species identification efficacy with 88.2% of species identified using phylogenetic and distance analysis. The analysis was further improved with the use of ITS2 secondary structure. The results of both criterions demonstrated the ability of ITS2 to successfully discriminate Alpinia species, which will help to improve species identification of Alpinia species in Peninsular Malaysia.},
}
@article {pmid32943823,
year = {2020},
author = {Kurian, A and Dev, SA and Sreekumar, VB and Muralidharan, EM},
title = {The low copy nuclear region, RPB2 as a novel DNA barcode region for species identification in the rattan genus Calamus (Arecaceae).},
journal = {Physiology and molecular biology of plants : an international journal of functional plant biology},
volume = {26},
number = {9},
pages = {1875-1887},
pmid = {32943823},
issn = {0971-5894},
abstract = {Taxonomic complexities, like environmental plasticity and homoplasy, make precise identification challenging in Calamus, the genus of spiny climbing palms of the subfamily Calamoideae (Arecaceae). In the present study, the species discriminatory power of twelve potential DNA barcode regions (rbcL, matK, psbA-trnH, rpoC, rpoB, psbK-psbI, atpF-atpH, psbZ-trnfM, ITS1, ITS2, PRK, and RPB2) were evaluated in 21 species of Calamus from the Western Ghats region of India, using distance, tree, and similarity based statistical methods. Except for the low copy nuclear region, RPB2, none of the tested plastid loci or nuclear loci ITS, either singly or in combinations, could discriminate all the species of Calamus due to low substitution rate of plastid regions and multiple copies of ITS respectively. The RPB2 locus showed highest species resolution with 96% accuracy in similarity based analysis, indicating its potential and efficiency as a barcode locus for the genus. The putative "Calamus gamblei complex" based on overlapping morphology was successfully resolved as six distinct, though closely related, species. The analysis also indicates that C. delessertianus is a morphological variant of C. dransfieldii. In spite of being a low copy nuclear gene region, RPB2 provided an efficient barcode to delineate Calamus species and has the potential to further extend its use as a prospective barcode to other Palm genera.},
}
@article {pmid32939150,
year = {2020},
author = {Lu, XQ and Du, XC},
title = {Revision of Nagiella Munroe (Lepidoptera, Crambidae), with the description of a new species from China.},
journal = {ZooKeys},
volume = {964},
number = {},
pages = {143-159},
pmid = {32939150},
issn = {1313-2989},
abstract = {The genus Nagiella was studied using morphological and DNA barcode data. Nagiella bispina sp. nov. is described as a new species, and N. hortulatoides Munroe is recorded in China for the first time. The diagnosis of this genus is revised, and the genitalia description of N. quadrimaculalis (Kollar and Redtenbacher) and N. inferior (Hampson) are given in English for the first time. Nosophora incomitata (Swinhoe) stat. rev. is removed from the synonym of N. quadrimaculalis. Photographs of the habitus and genitalia as well as COI DNA Barcode data of these four species are provided.},
}
@article {pmid32934803,
year = {2020},
author = {Matumba, TG and Oliver, J and Barker, NP and McQuaid, CD and Teske, PR},
title = {Intraspecific mitochondrial gene variation can be as low as that of nuclear rRNA.},
journal = {F1000Research},
volume = {9},
number = {},
pages = {339},
pmid = {32934803},
issn = {2046-1402},
mesh = {Animals ; *Evolution, Molecular ; *Genes, Mitochondrial ; *Genetic Variation ; Phylogeny ; RNA, Ribosomal, 28S/*genetics ; Selection, Genetic ; Sequence Analysis, DNA ; Snails/classification/*genetics ; Species Specificity ; },
abstract = {Background: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. Methods: DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related rocky shore snails, and species-level variation was compared. Nuclear rRNA is not usually used to study intraspecific variation in species that are not spatially structured, presumably because this marker is assumed to evolve so slowly that it is more suitable for phylogenetics. Results: Even though high inter-specific divergence reflected the faster evolutionary rate of COI, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions differed between the two markers by millions of years. Conclusions: Assuming that 28S evolution is more clock-like, these findings can be explained by variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by diversifying selection between the two species. Although these two selective forces together make mtDNA suitable as a marker for species identifications by means of DNA barcoding because they create a 'barcoding gap', estimates of demographic change based on this marker can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA sequence data beyond DNA barcoding is limited.},
}
@article {pmid32931539,
year = {2020},
author = {Chen, TN and Gupta, A and Zalavadia, MD and Streets, A},
title = {μCB-seq: microfluidic cell barcoding and sequencing for high-resolution imaging and sequencing of single cells.},
journal = {Lab on a chip},
volume = {20},
number = {21},
pages = {3899-3913},
pmid = {32931539},
issn = {1473-0189},
support = {R35 GM124916/GM/NIGMS NIH HHS/United States ; },
mesh = {Gene Expression Profiling ; *Microfluidics ; Sequence Analysis, RNA ; Single-Cell Analysis ; *Software ; },
abstract = {Single-cell RNA sequencing (scRNA-seq) enables the investigation of complex biological processes in multicellular organisms with high resolution. However, many phenotypic features that are critical to understanding the functional role of cells in a heterogeneous tissue or organ are not directly encoded in the genome and therefore cannot be profiled with scRNA-seq. Quantitative optical microscopy has long been a powerful approach for characterizing diverse cellular phenotypes including cell morphology, protein localization, and chemical composition. Combining scRNA-seq with optical imaging has the potential to provide comprehensive single-cell analysis, allowing for functional integration of gene expression profiling and cell-state characterization. However, it is difficult to track single cells through both measurements; therefore, coupling current scRNA-seq protocols with optical measurements remains a challenge. Here, we report microfluidic cell barcoding and sequencing (μCB-seq), a microfluidic platform that combines high-resolution imaging and sequencing of single cells. μCB-seq is enabled by a novel fabrication method that preloads primers with known barcode sequences inside addressable reaction chambers of a microfluidic device. In addition to enabling multi-modal single-cell analysis, μCB-seq improves gene detection sensitivity, providing a scalable and accurate method for information-rich characterization of single cells.},
}
@article {pmid32929347,
year = {2020},
author = {Xing, S and Lu, Z and Huang, Q and Li, H and Wang, Y and Lai, Y and He, Y and Deng, M and Liu, W},
title = {An ultrasensitive hybridization chain reaction-amplified CRISPR-Cas12a aptasensor for extracellular vesicle surface protein quantification.},
journal = {Theranostics},
volume = {10},
number = {22},
pages = {10262-10273},
pmid = {32929347},
issn = {1838-7640},
mesh = {Aptamers, Nucleotide/*genetics ; Biomarkers, Tumor/genetics ; Biosensing Techniques/*methods ; CRISPR-Cas Systems/*genetics ; Cell Line, Tumor ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; Extracellular Vesicles/genetics ; Humans ; Membrane Proteins/*genetics ; Nucleic Acid Hybridization/*genetics ; },
abstract = {Tumor-derived extracellular vesicle (TEV) protein biomarkers facilitate cancer diagnosis and prognostic evaluations. However, the lack of reliable and convenient quantitative methods for evaluating TEV proteins prevents their clinical application. Methods: Here, based on dual amplification of hybridization chain reaction (HCR) and CRISPR-Cas12a, we developed the apta-HCR-CRISPR assay for direct high-sensitivity detection of TEV proteins. The TEV protein-targeted aptamer was amplified by HCR to produce a long-repeated sequence comprising multiple CRISPR RNA (crRNA) targetable barcodes, and the signals were further amplified by CRISPR-Cas12a collateral cleavage activities, resulting in a fluorescence signal. Results: The established strategy was verified by detecting the TEV protein markers nucleolin and programmed death ligand 1 (PD-L1). Both achieved limit of detection (LOD) values as low as 10[2] particles/µL, which is at least 10[4]-fold more sensitive than aptamer-ELISA and 10[2]-fold more sensitive than apta-HCR-ELISA. We directly applied our assay to a clinical analysis of circulating TEVs from 50 µL of serum, revealing potential applications of nucleolin[+] TEVs for nasopharyngeal carcinoma cancer (NPC) diagnosis and PD-L1[+] TEVs for therapeutic monitoring. Conclusion: The platform was simple and easy to operate, and this approach should be useful for the highly sensitive and versatile quantification of TEV proteins in clinical samples.},
}
@article {pmid32929225,
year = {2020},
author = {Lee, J and Hyeon, DY and Hwang, D},
title = {Single-cell multiomics: technologies and data analysis methods.},
journal = {Experimental &amp; molecular medicine},
volume = {52},
number = {9},
pages = {1428-1442},
pmid = {32929225},
issn = {2092-6413},
support = {NRF-2019M3A9B6066967//National Research Foundation of Korea (NRF)/ ; 2019R1A6A1A10073437//National Research Foundation of Korea (NRF)/ ; },
mesh = {Animals ; Biotechnology ; Computational Biology/methods/standards ; Epigenomics/methods ; Gene Expression Profiling/methods ; Genomics/*methods/standards ; Humans ; Organ Specificity/genetics ; Proteomics/methods ; Single-Cell Analysis/*methods/standards ; Transcriptome ; },
abstract = {Advances in single-cell isolation and barcoding technologies offer unprecedented opportunities to profile DNA, mRNA, and proteins at a single-cell resolution. Recently, bulk multiomics analyses, such as multidimensional genomic and proteogenomic analyses, have proven beneficial for obtaining a comprehensive understanding of cellular events. This benefit has facilitated the development of single-cell multiomics analysis, which enables cell type-specific gene regulation to be examined. The cardinal features of single-cell multiomics analysis include (1) technologies for single-cell isolation, barcoding, and sequencing to measure multiple types of molecules from individual cells and (2) the integrative analysis of molecules to characterize cell types and their functions regarding pathophysiological processes based on molecular signatures. Here, we summarize the technologies for single-cell multiomics analyses (mRNA-genome, mRNA-DNA methylation, mRNA-chromatin accessibility, and mRNA-protein) as well as the methods for the integrative analysis of single-cell multiomics data.},
}
@article {pmid32928097,
year = {2020},
author = {Martinsson, S and Klinth, M and Erséus, C},
title = {Testing species hypotheses for Fridericia magna, an enchytraeid worm (Annelida: Clitellata) with great mitochondrial variation.},
journal = {BMC evolutionary biology},
volume = {20},
number = {1},
pages = {116},
pmid = {32928097},
issn = {1471-2148},
mesh = {Animals ; Bayes Theorem ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Genetic Speciation ; Genetics, Population ; Oligochaeta/*classification ; *Phylogeny ; Scandinavian and Nordic Countries ; },
abstract = {BACKGROUND: Deep mitochondrial divergences were observed in Scandinavian populations of the terrestrial to semi-aquatic annelid Fridericia magna (Clitellata: Enchytraeidae). This raised the need for testing whether the taxon is a single species or a complex of cryptic species.<br><br>RESULTS: A total of 62 specimens from 38 localities were included in the study, 44 of which were used for species delimitation. First, the 44 specimens were divided into clusters using ABGD (Automatic Barcode Gap Discovery) on two datasets, consisting of sequences of the mitochondrial markers COI and 16S. For each dataset, the worms were divided into six not completely congruent clusters. When they were combined, a maximum of seven clusters, or species hypotheses, were obtained, and the seven clusters were used as input in downstream analyses. We tested these hypotheses by constructing haplowebs for two nuclear markers, H3 and ITS, and in both haplowebs the specimens appeared as a single species. Multi-locus species delimitation analyses performed with the Bayesian BPP program also mainly supported a single species. Furthermore, no apparent morphological differences were found between the clusters. Two of the clusters were partially separated from each other and the other clusters, but not strongly enough to consider them as separate species. All 62 specimens were used to visualise the Scandinavian distribution, of the species, and to compare with published COI data from other Fridericia species.<br><br>CONCLUSION: We show that the morphospecies Fridericia magna is a single species, harbouring several distinct mitochondrial clusters. There is partial genetic separation between some of them, which may be interpreted as incipient speciation. The study shows the importance of rigorous species delimitation using several independent markers when deep mitochondrial divergences might give the false impression of cryptic speciation.},
}
@article {pmid32922134,
year = {2020},
author = {Huemer, P and Karsholt, O and Wieser, C},
title = {Megacraspedus cottiensis sp. nov. (Lepidoptera, Gelechiidae) from northern Italy - a case of taxonomic confusion.},
journal = {ZooKeys},
volume = {963},
number = {},
pages = {141-152},
pmid = {32922134},
issn = {1313-2989},
abstract = {Megacraspedus cottiensis sp. nov. is described from the western Alps (prov. Torino, Italy). The dorsal habitus and genitalia for both the male and brachypterous female are provided. The new species belongs to the M. faunierensis species group based on genitalia morphology and DNA barcodes, and was hitherto confused with M. neli Huemer &amp; Karsholt, 2018 from the southwestern Alps. However, it clearly differs in morphology and DNA barcode sequences from that species and from M. faunierensis Huemer &amp; Karsholt, 2018. The new species is suspected of being a regional endemic of the Cottian Alps.},
}
@article {pmid32920194,
year = {2020},
author = {Rosas-Valdez, R and Morrone, JJ and Pinacho-Pinacho, CD and Domínguez-Domínguez, O and García-Varela, M},
title = {Genetic diversification of acanthocephalans of the genus Floridosentis Ward 1953 (Acanthocephala: Neoechinorhynchidae), parasites of mullets from the Americas.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {85},
number = {},
pages = {104535},
doi = {10.1016/j.meegid.2020.104535},
pmid = {32920194},
issn = {1567-7257},
mesh = {Acanthocephala/*classification/*genetics ; Americas ; Animals ; DNA Barcoding, Taxonomic ; DNA, Helminth ; DNA, Mitochondrial ; DNA, Ribosomal Spacer/genetics ; Fish Diseases/parasitology ; *Genetic Variation ; Phylogeny ; Smegmamorpha/*parasitology ; },
abstract = {Adult worms of the genus Floridosentis are endoparasites of marine fishes of the genus Mugil and are broadly distributed in the Americas. Currently, Floridosentis includes two species, F. mugilis, distributed in the Gulf of Mexico and along the Atlantic Ocean coast, and F. pacifica, restricted to the Pacific Ocean coast. The aim of this study was to explore the species limit of both species of the genus Floridosentis, collected in 37 localities in eight countries: Mexico, Guatemala, El Salvador, Honduras, Nicaragua, Costa Rica, Ecuador and Venezuela. We sequenced 253 specimens to build a comprehensive dataset for three genes: the cytochrome c oxidase subunit I (cox 1) from mitochondrial DNA, the internal transcribed spacers ITS1 and ITS2 including the 5.8S gene (ITS region), and the D2 + D3 domains of the large subunit (LSU) of nuclear DNA. Maximum likelihood and Bayesian analyses with the cox 1 and concatenated (cox 1 + ITS+LSU) datasets were conducted. Two species delimitation methods were implemented, the Automatic Barcode Gap Discovery (ABGD), and Bayesian species delimitation (BPP), plus a haplotype network inferred with 253 specimens, allowing us to validate two nominal species of Floridosentis., F. mugilis, plus one linage distributed in the Gulf of Mexico and along the Atlantic Ocean coast, and F. pacifica, plus two additional lineages distributed along the Pacific Ocean coast. All these lineages are shared by both species of mullet (Mugil curema and M. cephalus). The currents in the Atlantic Ocean, Pacific Ocean and Gulf of Mexico, in combination with the biology of the definitive hosts, have played a key role in the distribution of the two nominal species and of the three lineages of Floridosentis across the Americas.},
}
@article {pmid32917087,
year = {2020},
author = {Teske, D and Peters, A and Möllers, A and Fischer, M},
title = {Genomic Profiling: The Strengths and Limitations of Chloroplast Genome-Based Plant Variety Authentication.},
journal = {Journal of agricultural and food chemistry},
volume = {68},
number = {49},
pages = {14323-14333},
doi = {10.1021/acs.jafc.0c03001},
pmid = {32917087},
issn = {1520-5118},
mesh = {Chloroplasts/*genetics ; *Genome, Chloroplast ; *Genome, Plant ; Genomics ; Phylogeny ; Plants/classification/*genetics ; },
abstract = {Genomic profiling is a suitable tool for variety authentication and has applications in both operational quality and regulatory raw material control. It can be used to differentiate species or varieties and to identify admixtures as well as field contaminants. To establish a molecular profile, reliable and very accurate sequence data are required. As a result of the influence of the pollinator plant, nuclear genome-based authentication is in most cases not suitable for a direct application on the fruit. Sequences must be used that come exclusively from the localized mother plant. Parts of the fruit of maternal origin, e.g., components derived from the blossom, are suitable as a basis for this. Alternatively, DNA from cell organelles that are maternally inherited, such as mitochondria or chloroplasts, can be used. The latter will be discussed in this review in closer detail. Although individual gene segments on the chloroplast genome are already used for species differentiation in barcoding studies on plants, little is known about the usefulness of the entire chloroplast genome for intraspecies differentiation in general and for differentiation between modern varieties in particular. Results from the literature as well as from our own work suggest that chloroplast genome sequences are indeed very well-suited for the differentiation of old varieties. On the other hand, they are less or not suitable for the genetic differentiation of modern cultivars, because they are often too closely related.},
}
@article {pmid32916006,
year = {2020},
author = {Gueuning, M and Frey, JE and Praz, C},
title = {Ultraconserved yet informative for species delimitation: Ultraconserved elements resolve long-standing systematic enigma in Central European bees.},
journal = {Molecular ecology},
volume = {29},
number = {21},
pages = {4203-4220},
doi = {10.1111/mec.15629},
pmid = {32916006},
issn = {1365-294X},
mesh = {Animals ; Bees/genetics ; Biodiversity ; Cell Nucleus ; DNA Barcoding, Taxonomic ; *DNA, Mitochondrial/genetics ; Genomics ; *Mitochondria/genetics ; Phylogeny ; },
abstract = {Accurate and testable species hypotheses are essential for measuring, surveying and managing biodiversity. Taxonomists often rely on mitochondrial DNA barcoding to complement morphological species delimitations. Although COI-barcoding has largely proven successful in assisting identifications for most animal taxa, there are nevertheless numerous cases where mitochondrial barcodes do not reflect species hypotheses. For instance, what is regarded as a single species can be associated with two distinct DNA barcodes, which can point either to cryptic diversity or to within-species mitochondrial divergences without reproductive isolation. In contrast, two or more species can share barcodes, for instance due to mitochondrial introgression. These intrinsic limitations of DNA barcoding are commonly addressed with nuclear genomic markers, which are expensive, may have low repeatability and often require high-quality DNA. To overcome these limitations, we examined the use of ultraconserved elements (UCEs) as a quick and robust genomic approach to address such problematic cases of species delimitation in bees. This genomic method was assessed using six different species complexes suspected to harbour cryptic diversity, mitochondrial introgression or mitochondrial paraphyly. The sequencing of UCEs recovered between 686 and 1,860 homologous nuclear loci and provided explicit species delimitation in all investigated species complexes. These results provide strong evidence for the suitability of UCEs as a fast method for species delimitation even in recently diverged lineages. Furthermore, we provide the first evidence for both mitochondrial introgression among distinct bee species, and mitochondrial paraphyly within a single bee species.},
}
@article {pmid32915104,
year = {2020},
author = {Thakur, SS and Lone, AR and Tiwari, N and Yadav, S},
title = {Exploring new records of Eutyphoeus sp. (haplotaxida: Octochaetidae) from garo hills, Meghalaya, North Eastern state of India with use of DNA barcodes.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {31},
number = {7},
pages = {265-272},
doi = {10.1080/24701394.2020.1781834},
pmid = {32915104},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; India ; Oligochaeta/anatomy &amp; histology/*classification/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The work was aimed to investigate earthworms species particularly Eutyphoeus endemic to India with the use of DNA barcodes and usual morpho-anatomical standards of earthworm taxonomy from protected areas of Garo Hills, Meghalaya, the north-east region (NER) of India. The study revealed two new records Eutyphoeus kempi Stephenson, E. nepalensis Michaelsen and confirms availability of three known sp. namely E. callosus Gates, E. gammiei Beddard and E. turaensis Stephenson. The neighbor-joining tree was constructed using the K2P substitution model and the genomic signature of each species using COI-1 gene was generated for the first time and were used to reconfirm the identification of species.},
}
@article {pmid32914511,
year = {2020},
author = {Kankaanpää, T and Vesterinen, E and Hardwick, B and Schmidt, NM and Andersson, T and Aspholm, PE and Barrio, IC and Beckers, N and Bêty, J and Birkemoe, T and DeSiervo, M and Drotos, KHI and Ehrich, D and Gilg, O and Gilg, V and Hein, N and Høye, TT and Jakobsen, KM and Jodouin, C and Jorna, J and Kozlov, MV and Kresse, JC and Leandri-Breton, DJ and Lecomte, N and Loonen, M and Marr, P and Monckton, SK and Olsen, M and Otis, JA and Pyle, M and Roos, RE and Raundrup, K and Rozhkova, D and Sabard, B and Sokolov, A and Sokolova, N and Solecki, AM and Urbanowicz, C and Villeneuve, C and Vyguzova, E and Zverev, V and Roslin, T},
title = {Parasitoids indicate major climate-induced shifts in arctic communities.},
journal = {Global change biology},
volume = {26},
number = {11},
pages = {6276-6295},
pmid = {32914511},
issn = {1365-2486},
support = {//Parks Canada/ ; //University of Guelph/ ; //Societas pro Fauna et Flora Fennica/ ; 201500090//Maj ja Tor Nesslingin S&#xe4;&#xe4;ti&#xf6;/ ; 201600034//Maj ja Tor Nesslingin S&#xe4;&#xe4;ti&#xf6;/ ; 201700420//Maj ja Tor Nesslingin S&#xe4;&#xe4;ti&#xf6;/ ; //Polar Knowledge Canada/ ; 152468-051//Icelandic Centre for Research/ ; //Fonds Qu&#xe9;b&#xe9;cois de la Recherche sur la Nature et les Technologies/ ; //The Danish Environmental Protection Agency/ ; //Churchill Northern Studies Centre/ ; //Entomological Society of Canada/ ; //Canadian Polar Commission/ ; //Polar Continental Shelf Project/ ; 276671//Biotieteiden ja Ymp&#xe4;rist&#xf6;n Tutkimuksen Toimikunta/ ; 276909//Biotieteiden ja Ymp&#xe4;rist&#xf6;n Tutkimuksen Toimikunta/ ; 285803//Biotieteiden ja Ymp&#xe4;rist&#xf6;n Tutkimuksen Toimikunta/ ; //Natural Sciences and Engineering Research Council of Canada/ ; 276909//Academy of Finland/ ; 285803//Academy of Finland/ ; 276671//Academy of Finland/ ; 201700420//Nessling Foundation/ ; 201600034//Nessling Foundation/ ; 201500090//Nessling Foundation/ ; //Jane and Aatos Erkko Foundation/ ; //French Polar Institute/ ; //INTERACT/ ; 249902/F20//Research Council of Norway/ ; //ArcticNet/ ; 18-05-60261//Russian Foundation for Basic Research/ ; },
mesh = {Animals ; Arctic Regions ; *Ecosystem ; Greenland ; *Herbivory ; Host-Parasite Interactions ; Larva ; },
abstract = {Climatic impacts are especially pronounced in the Arctic, which as a region is warming twice as fast as the rest of the globe. Here, we investigate how mean climatic conditions and rates of climatic change impact parasitoid insect communities in 16 localities across the Arctic. We focus on parasitoids in a widespread habitat, Dryas heathlands, and describe parasitoid community composition in terms of larval host use (i.e., parasitoid use of herbivorous Lepidoptera vs. pollinating Diptera) and functional groups differing in their closeness of host associations (koinobionts vs. idiobionts). Of the latter, we expect idiobionts-as being less fine-tuned to host development-to be generally less tolerant to cold temperatures, since they are confined to attacking hosts pupating and overwintering in relatively exposed locations. To further test our findings, we assess whether similar climatic variables are associated with host abundances in a 22 year time series from Northeast Greenland. We find sites which have experienced a temperature rise in summer while retaining cold winters to be dominated by parasitoids of Lepidoptera, with the reverse being true for the parasitoids of Diptera. The rate of summer temperature rise is further associated with higher levels of herbivory, suggesting higher availability of lepidopteran hosts and changes in ecosystem functioning. We also detect a matching signal over time, as higher summer temperatures, coupled with cold early winter soils, are related to high herbivory by lepidopteran larvae, and to declines in the abundance of dipteran pollinators. Collectively, our results suggest that in parts of the warming Arctic, Dryas is being simultaneously exposed to increased herbivory and reduced pollination. Our findings point to potential drastic and rapid consequences of climate change on multitrophic-level community structure and on ecosystem functioning and highlight the value of collaborative, systematic sampling effort.},
}
@article {pmid32914470,
year = {2020},
author = {Chuctaya, J and Ohara, WM and Malabarba, LR},
title = {A new species of Odontostilbe cope (Characiformes: Cheirodontinae) from rio Madeira basin diagnosed based on morphological and molecular data.},
journal = {Journal of fish biology},
volume = {97},
number = {6},
pages = {1701-1712},
doi = {10.1111/jfb.14533},
pmid = {32914470},
issn = {1095-8649},
support = {//We thank the Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq) for financial support to J.C. and L.R.M./ ; //Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; },
mesh = {Animal Fins/anatomy &amp; histology ; Animals ; Brazil ; Characidae/anatomy &amp; histology/*classification/genetics ; Female ; Fish Proteins/genetics ; Male ; Mouth/anatomy &amp; histology ; Pigmentation ; Species Specificity ; Tooth/anatomy &amp; histology ; },
abstract = {A new species of Odontostilbe is described from the rio Jaciparaná, rio Madeira basin, Rondônia, Brazil. Odontostilbe pacaasnovos differs from all its congeners, except O. pequira, by the colour pattern. Additionally, it differs from its congeners by the terminal mouth, number of cusps in the teeth of the premaxilla (5-7), number of branched rays in the anal fin (19-22), by the shape of dentary teeth (5-7 cusps with central cusp larger and longer than laterals cusps) and by the number of lamellae of the olfactory rosette (17-18 in male and 14 in female). Morphological and molecular comparisons corroborate the distinctiveness between O. pacaasnovos and its congeners, justifying its recognition as a new species.},
}
@article {pmid32911871,
year = {2020},
author = {Mbareche, H and Dumont-Leblond, N and Bilodeau, GJ and Duchaine, C},
title = {An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists.},
journal = {Life (Basel, Switzerland)},
volume = {10},
number = {9},
pages = {},
pmid = {32911871},
issn = {2075-1729},
abstract = {High-throughput DNA sequencing (HTS) has changed our understanding of the microbial composition present in a wide range of environments. Applying HTS methods to air samples from different environments allows the identification and quantification (relative abundance) of the microorganisms present and gives a better understanding of human exposure to indoor and outdoor bioaerosols. To make full use of the avalanche of information made available by these sequences, repeated measurements must be taken, community composition described, error estimates made, correlations of microbiota with covariates (variables) must be examined, and increasingly sophisticated statistical tests must be conducted, all by using bioinformatics tools. Knowing which analysis to conduct and which tools to apply remains confusing for bioaerosol scientists, as a litany of tools and data resources are now available for characterizing microbial communities. The goal of this review paper is to offer a guided tour through the bioinformatics tools that are useful in studying the microbial ecology of bioaerosols. This work explains microbial ecology features like alpha and beta diversity, multivariate analyses, differential abundances, taxonomic analyses, visualization tools and statistical tests using bioinformatics tools for bioaerosol scientists new to the field. It illustrates and promotes the use of selected bioinformatic tools in the study of bioaerosols and serves as a good source for learning the "dos and don'ts" involved in conducting a precise microbial ecology study.},
}
@article {pmid32910470,
year = {2021},
author = {Heck, MA and Lüth, VM and van Gessel, N and Krebs, M and Kohl, M and Prager, A and Joosten, H and Decker, EL and Reski, R},
title = {Axenic in vitro cultivation of 19 peat moss (Sphagnum L.) species as a resource for basic biology, biotechnology, and paludiculture.},
journal = {The New phytologist},
volume = {229},
number = {2},
pages = {861-876},
doi = {10.1111/nph.16922},
pmid = {32910470},
issn = {1469-8137},
mesh = {Austria ; Biology ; Biotechnology ; Germany ; Russia ; *Sphagnopsida ; Sweden ; },
abstract = {Sphagnum farming can substitute peat with renewable biomass and thus help mitigate climate change. Large volumes of the required founder material can only be supplied sustainably by axenic cultivation in bioreactors. We established axenic in vitro cultures from sporophytes of 19 Sphagnum species collected in Austria, Germany, Latvia, the Netherlands, Russia, and Sweden: S. angustifolium, S. balticum, S. capillifolium, S. centrale, S. compactum, S. cuspidatum, S. fallax, S. fimbriatum, S. fuscum, S. lindbergii, S. medium/divinum, S. palustre, S. papillosum, S. rubellum, S. russowii, S. squarrosum, S. subnitens, S. subfulvum and S. warnstorfii. These species cover five of the six European Sphagnum subgenera; namely, Acutifolia, Cuspidata, Rigida, Sphagnum and Squarrosa. Their growth was measured in suspension cultures, whereas their ploidy was determined by flow cytometry and compared with the genome size of Physcomitrella patens. We identified haploid and diploid Sphagnum species, found that their cells are predominantly arrested in the G1 phase of the cell cycle, and did not find a correlation between plant productivity and ploidy. DNA barcoding was achieved by sequencing introns of the BRK1 genes. With this collection, high-quality founder material for diverse large-scale applications, but also for basic Sphagnum research, is available from the International Moss Stock Center.},
}
@article {pmid32909008,
year = {2021},
author = {Bloom, JS and Sathe, L and Munugala, C and Jones, EM and Gasperini, M and Lubock, NB and Yarza, F and Thompson, EM and Kovary, KM and Park, J and Marquette, D and Kay, S and Lucas, M and Love, T and Booeshaghi, AS and Brandenberg, OF and Guo, L and Boocock, J and Hochman, M and Simpkins, SW and Lin, I and LaPierre, N and Hong, D and Zhang, Y and Oland, G and Choe, BJ and Chandrasekaran, S and Hilt, EE and Butte, MJ and Damoiseaux, R and Kravit, C and Cooper, AR and Yin, Y and Pachter, L and Garner, OB and Flint, J and Eskin, E and Luo, C and Kosuri, S and Kruglyak, L and Arboleda, VA},
title = {Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {32909008},
support = {DP5 OD024579/OD/NIH HHS/United States ; T32 GM008042/GM/NIGMS NIH HHS/United States ; },
abstract = {The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is due to the high rates of transmission by individuals who are asymptomatic at the time of transmission[1,2]. Frequent, widespread testing of the asymptomatic population for SARS-CoV-2 is essential to suppress viral transmission. Despite increases in testing capacity, multiple challenges remain in deploying traditional reverse transcription and quantitative PCR (RT-qPCR) tests at the scale required for population screening of asymptomatic individuals. We have developed SwabSeq, a high-throughput testing platform for SARS-CoV-2 that uses next-generation sequencing as a readout. SwabSeq employs sample-specific molecular barcodes to enable thousands of samples to be combined and simultaneously analyzed for the presence or absence of SARS-CoV-2 in a single run. Importantly, SwabSeq incorporates an in vitro RNA standard that mimics the viral amplicon, but can be distinguished by sequencing. This standard allows for end-point rather than quantitative PCR, improves quantitation, reduces requirements for automation and sample-to-sample normalization, enables purification-free detection, and gives better ability to call true negatives. After setting up SwabSeq in a high-complexity CLIA laboratory, we performed more than 80,000 tests for COVID-19 in less than two months, confirming in a real world setting that SwabSeq inexpensively delivers highly sensitive and specific results at scale, with a turn-around of less than 24 hours. Our clinical laboratory uses SwabSeq to test both nasal and saliva samples without RNA extraction, while maintaining analytical sensitivity comparable to or better than traditional RT-qPCR tests. Moving forward, SwabSeq can rapidly scale up testing to mitigate devastating spread of novel pathogens.},
}
@article {pmid32907883,
year = {2020},
author = {Smith, MA and Ersavas, T and Ferguson, JM and Liu, H and Lucas, MC and Begik, O and Bojarski, L and Barton, K and Novoa, EM},
title = {Molecular barcoding of native RNAs using nanopore sequencing and deep learning.},
journal = {Genome research},
volume = {30},
number = {9},
pages = {1345-1353},
pmid = {32907883},
issn = {1549-5469},
mesh = {Algorithms ; *Deep Learning ; Nanopore Sequencing/*methods ; Sequence Analysis, RNA/*methods ; },
abstract = {Nanopore sequencing enables direct measurement of RNA molecules without conversion to cDNA, thus opening the gates to a new era for RNA biology. However, the lack of molecular barcoding of direct RNA nanopore sequencing data sets severely affects the applicability of this technology to biological samples, where RNA availability is often limited. Here, we provide the first experimental protocol and associated algorithm to barcode and demultiplex direct RNA nanopore sequencing data sets. Specifically, we present a novel and robust approach to accurately classify raw nanopore signal data by transforming current intensities into images or arrays of pixels, followed by classification using a deep learning algorithm. We demonstrate the power of this strategy by developing the first experimental protocol for barcoding and demultiplexing direct RNA sequencing libraries. Our method, DeePlexiCon, can classify 93% of reads with 95.1% accuracy or 60% of reads with 99.9% accuracy. The availability of an efficient and simple multiplexing strategy for native RNA sequencing will improve the cost-effectiveness of this technology, as well as facilitate the analysis of lower-input biological samples. Overall, our work exemplifies the power, simplicity, and robustness of signal-to-image conversion for nanopore data analysis using deep learning.},
}
@article {pmid32907717,
year = {2020},
author = {Ezgeta-Balić, D and Šantić, D and Šegvić-Bubić, T and Bojanić, N and Bužančić, M and Vidjak, O and Varezić, DB and Stagličić, N and Kundid, P and Peharda, M and Žužul, I and Grubišić, L and Briski, E},
title = {Competitive feeding interactions between native Ostrea edulis and non-native Crassostrea gigas with implications of introducing C. gigas into commercial aquaculture in the eastern Adriatic Sea.},
journal = {Marine environmental research},
volume = {160},
number = {},
pages = {105051},
doi = {10.1016/j.marenvres.2020.105051},
pmid = {32907717},
issn = {1879-0291},
mesh = {Animals ; *Aquaculture ; *Crassostrea ; Ecology ; *Feeding Behavior ; Food Chain ; Larva ; *Ostrea ; },
abstract = {In order to detect the possible regulatory effect of non-native C. gigas on the native O. edulis, under aquaculture conditions, feeding interactions between them were investigated in a highly productive environment of Lim Bay (Adriatic Sea). The present study uses a multi-methodological approach, including stomach content, DNA barcoding and stable isotope analysis to elucidate the feeding ecology of two oyster species. The research confirmed a high overlap throughout the year in the feeding traits among native and non-native oyster species. Competition for food was not the only relationship that exists between the investigated species as the presence of O. edulis larvae in C. gigas stomach content was confirmed by DNA analysis. Findings are not in favour of introducing C. gigas to commercial aquaculture in any new areas in the Adriatic Sea and support the need to improve the existing O. edulis aquaculture and conserve its wild stocks.},
}
@article {pmid32904192,
year = {2020},
author = {Crous, PW and Wingfield, MJ and Schumacher, RK and Akulov, A and Bulgakov, TS and Carnegie, AJ and Jurjević, &#x17d; and Decock, C and Denman, S and Lombard, L and Lawrence, DP and Stack, AJ and Gordon, TR and Bostock, RM and Burgess, T and Summerell, BA and Taylor, PWJ and Edwards, J and Hou, LW and Cai, L and Rossman, AY and Wöhner, T and Allen, WC and Castlebury, LA and Visagie, CM and Groenewald, JZ},
title = {New and Interesting Fungi. 3.},
journal = {Fungal systematics and evolution},
volume = {6},
number = {},
pages = {157-231},
pmid = {32904192},
issn = {2589-3831},
abstract = {Seven new genera, 26 new species, 10 new combinations, two epitypes, one new name, and 20 interesting new host and / or geographical records are introduced in this study. New genera are: Italiofungus (based on Italiofungus phillyreae) on leaves of Phillyrea latifolia (Italy); Neolamproconium (based on Neolamproconium silvestre) on branch of Tilia sp. (Ukraine); Neosorocybe (based on Neosorocybe pini) on trunk of Pinus sylvestris (Ukraine); Nothoseptoria (based on Nothoseptoria caraganae) on leaves of Caragana arborescens (Russia); Pruniphilomyces (based on Pruniphilomyces circumscissus) on Prunus cerasus (Russia); Vesiculozygosporium (based on Vesiculozygosporium echinosporum) on leaves of Muntingia calabura (Malaysia); Longiseptatispora (based on Longiseptatispora curvata) on leaves of Lonicera tatarica (Russia). New species are: Barrmaelia serenoae on leaf of Serenoa repens (USA); Chaetopsina gautengina on leaves of unidentified grass (South Africa); Chloridium pini on fallen trunk of Pinus sylvestris (Ukraine); Cadophora fallopiae on stems of Reynoutria sachalinensis (Poland); Coleophoma eucalyptigena on leaf litter of Eucalyptus sp. (Spain); Cylindrium corymbiae on leaves of Corymbia maculata (Australia); Diaporthe tarchonanthi on leaves of Tarchonanthus littoralis (South Africa); Elsinoe eucalyptorum on leaves of Eucalyptus propinqua (Australia); Exophiala quercina on dead wood of Quercus sp., (Germany); Fusarium californicum on cambium of budwood of Prunus dulcis (USA); Hypomyces gamsii on wood of Alnus glutinosa (Ukraine); Kalmusia araucariae on leaves of Araucaria bidwillii (USA); Lectera sambuci on leaves of Sambucus nigra (Russia); Melanomma populicola on fallen twig of Populus canadensis (Netherlands), Neocladosporium syringae on branches of Syringa vulgarishorus (Ukraine); Paraconiothyrium iridis on leaves of Iris pseudacorus (Ukraine); Pararoussoella quercina on branch of Quercus robur (Ukraine); Phialemonium pulveris from bore dust of deathwatch beetle (France); Polyscytalum pinicola on needles of Pinus tecunumanii (Malaysia); Acervuloseptoria fraxini on Fraxinus pennsylvanica (Russia); Roussoella arundinacea on culms of Arundo donax (Spain); Sphaerulina neoaceris on leaves of Acer negundo (Russia); Sphaerulina salicicola on leaves of Salix fragilis (Russia); Trichomerium syzygii on leaves of Syzygium cordatum (South Africa); Uzbekistanica vitis-viniferae on dead stem of Vitis vinifera (Ukraine); Vermiculariopsiella eucalyptigena on leaves of Eucalyptus sp. (Australia).},
}
@article {pmid32904189,
year = {2020},
author = {Hernández-Restrepo, M and Giraldo, A and van Doorn, R and Wingfield, MJ and Groenewald, JZ and Barreto, RW and Colmán, AA and Mansur, PSC and Crous, PW},
title = {The Genera of Fungi - G6: Arthrographis, Kramasamuha, Melnikomyces, Thysanorea, and Verruconis.},
journal = {Fungal systematics and evolution},
volume = {6},
number = {},
pages = {1-24},
pmid = {32904189},
issn = {2589-3831},
abstract = {The Genera of Fungi series, of which this is the sixth contribution, links type species of fungal genera to their morphology and DNA sequence data. Five genera of microfungi are treated in this study, with new species introduced in Arthrographis, Melnikomyces, and Verruconis. The genus Thysanorea is emended and two new species and nine combinations are proposed. Kramasamuha sibika, the type species of the genus, is provided with DNA sequence data for first time and shown to be a member of Helminthosphaeriaceae (Sordariomycetes). Aureoconidiella is introduced as a new genus representing a new lineage in the Dothideomycetes.},
}
@article {pmid32901359,
year = {2020},
author = {Zangl, L and Oberreiter, H and Huss, H and Stabentheiner, E and Sturmbauer, C and Koblmüller, S},
title = {Discriminating larvae of two syntopic Cychramus species (Coleoptera, Nitidulidae) by means of bar-HRM analysis.},
journal = {Molecular biology reports},
volume = {47},
number = {10},
pages = {8251-8257},
pmid = {32901359},
issn = {1573-4978},
mesh = {Animals ; Coleoptera/*genetics ; *DNA Barcoding, Taxonomic ; Larva/genetics ; Species Specificity ; },
abstract = {Molecular genetic methods are increasingly used to supplement or substitute classical morphology-based species identification. Here, we employ a COI mini-barcode coupled high-resolution melting analysis to quickly, cost-efficiently and reliably determine larvae of two closely related Cychramus (Coleoptera, Nitidulidae) species. Euclidean distance comparison (p < 0.01) and a Welch t-test of the melting point temperatures (p < 0.01) provide highly significant statistical evidence for species specific differences in melting and fluorescence curves, thus allowing the assignment of larvae to either of the two species. This protocol serves as a fast, low-cost and low-tech method to discriminate between pairs or groups of closely related species and can be adapted and applied to various ecological research questions.},
}
@article {pmid32901266,
year = {2021},
author = {Giangaspero, A and Barlaam, A and Pane, S and Marchili, MR and Onetti Muda, A and Putignani, L and Hall, MJR},
title = {Accidental Nasal Myiasis Caused by Megaselia rufipes (Diptera: Phoridae) in a Child.},
journal = {Journal of medical entomology},
volume = {58},
number = {1},
pages = {121-124},
doi = {10.1093/jme/tjaa184},
pmid = {32901266},
issn = {1938-2928},
mesh = {Animals ; Child, Preschool ; *Diptera/classification/genetics/pathogenicity ; Electron Transport Complex IV/genetics ; Genes, Insect ; Humans ; Italy ; Larva ; Myiasis/*diagnosis ; Nose/parasitology ; Phylogeny ; },
abstract = {A case of a nasal myiasis in a 3-yr-old Italian girl who was referred to Bambino Gesù Hospital in Rome, Italy, is reported. Larvae discharged with the nasal mucus were microscopically identified as Megaselia spp.; DNA barcoding analysis showed that they belonged to the 'scuttle fly' species Megaselia rufipes (Meigen). Based on the patient's history, she became infected when she played outside. This is the first report of myiasis in humans due to M. rufipes (Diptera: Phoridae).},
}
@article {pmid32901085,
year = {2020},
author = {Thongkhao, K and Pongkittiphan, V and Phadungcharoen, T and Tungphatthong, C and Urumarudappa, SKJ and Pengsuparp, T and Sutanthavibul, N and Wiwatcharakornkul, W and Kengtong, S and Sukrong, S},
title = {Differentiation of Cyanthillium cinereum, a smoking cessation herb, from its adulterant Emilia sonchifolia using macroscopic and microscopic examination, HPTLC profiles and DNA barcodes.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {14753},
pmid = {32901085},
issn = {2045-2322},
mesh = {Asteraceae/*classification/*genetics ; Chromatography, High Pressure Liquid/*methods ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*analysis/genetics ; Sequence Analysis, DNA/*methods ; Smoking Cessation ; Species Specificity ; },
abstract = {Cyanthillium cinereum (L.) H.Rob. is one of the most popular herbal smoking cessation aids currently used in Thailand, and its adulteration with Emilia sonchifolia (L.) DC. is often found in the herbal market. Therefore, the quality of the raw material must be considered. This work aimed to integrate macro- and microscopic, chemical and genetic authentication strategies to differentiate C. cinereum raw material from its adulterant. Different morphological features between C. cinereum and E. sonchifolia were simply recognized at the leaf base. For microscopic characteristics, trichome and pappus features were different between the two plants. HPTLC profiles showed a distinct band that could be used to unambiguously differentiate C. cinereum from E. sonchifolia. Four triterpenoid compounds, β-amyrin, taraxasterol, lupeol, and betulin, were identified from the distinct HPTLC band of C. cinereum. The use of core DNA barcode regions; rbcL, matK, ITS and psbA-trnH provided species-level resolution to differentiate the two plants. Taken together, the integration of macroscopic and microscopic characterization, phytochemical analysis by HPTLC and DNA barcoding distinguished C. cinereum from E. sonchifolia. The signatures of C. cinereum obtained here can help manufacturers to increase the quality control of C. cinereum raw material in commercialized smoking cessation products.},
}
@article {pmid32899738,
year = {2020},
author = {Howard, C and Lockie-Williams, C and Slater, A},
title = {Applied Barcoding: The Practicalities of DNA Testing for Herbals.},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {9},
pages = {},
pmid = {32899738},
issn = {2223-7747},
abstract = {DNA barcoding is a widely accepted technique for the identification of plant materials, and its application to the authentication of commercial medicinal plants has attracted significant attention. The incorporation of DNA-based technologies into the quality testing protocols of international pharmacopoeias represents a step-change in status, requiring the establishment of standardized, reliable and reproducible methods. The process by which this can be achieved for any herbal medicine is described, using Hypericum perforatum L. (St John's Wort) and potential adulterant Hypericum species as a case study. A range of practical issues are considered including quality control of DNA sequences from public repositories and the construction of individual curated databases, choice of DNA barcode region(s) and the identification of informative polymorphic nucleotide sequences. A decision tree informs the structure of the manuscript and provides a template to guide the development of future DNA barcode tests for herbals.},
}
@article {pmid32899282,
year = {2020},
author = {Gilligan, TM and Brown, JW and Baixeras, J},
title = {Immigrant Tortricidae: Holarctic versus Introduced Species in North America.},
journal = {Insects},
volume = {11},
number = {9},
pages = {},
pmid = {32899282},
issn = {2075-4450},
abstract = {In support of a comprehensive update to the checklist of the moths of North America, we attempt to determine the status of 151 species of Tortricidae present in North America that may be Holarctic, introduced, or sibling species of their European counterparts. Discovering the natural distributions of these taxa is often difficult, if not impossible, but several criteria can be applied to determine if a species that is present in both Europe and North America is natively Holarctic, introduced, or represented by different but closely related species on each continent. We use DNA barcodes (when available), morphology, host plants, and historical records (literature and museum specimens) to make these assessments and propose several taxonomic changes, as well as future areas of research. The following taxa are raised from synonymy to species status: Acleris ferrumixtana (Benander, 1934), stat. rev.; Acleris viburnana (Clemens, 1860), stat. rev.; Acleris pulverosana (Walker, 1863), stat. rev.; Acleris placidana (Robinson, 1869), stat. rev.; Lobesia spiraeae (McDunnough, 1938), stat. rev.; and Epiblema arctica Miller, 1985, stat. rev. Cydia saltitans (Westwood, 1858), stat. rev., is determined to be the valid name for the "jumping bean moth," and Phiaris glaciana (Möschler, 1860), comb. n., is placed in a new genus. We determine that the number of Holarctic species has been overestimated by at least 20% in the past, and that the overall number of introduced species in North America is unexpectedly high, with Tortricidae accounting for approximately 23-30% of the total number of Lepidoptera species introduced to North America.},
}
@article {pmid32898701,
year = {2020},
author = {Pereira, AC and Cunha, MV},
title = {An effective culturomics approach to study the gut microbiota of mammals.},
journal = {Research in microbiology},
volume = {171},
number = {8},
pages = {290-300},
doi = {10.1016/j.resmic.2020.09.001},
pmid = {32898701},
issn = {1769-7123},
mesh = {Animals ; Biodiversity ; Culture Media ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Herpestidae/*microbiology ; Male ; Mammals/microbiology ; *Metagenome ; Metagenomics/*methods ; Microbiological Techniques/*methods ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {The microbial characterization of the mammal's gut is an emerging research area, wherein culturomics methodologies applied to human samples are transposed to the animal context without improvement. In this work, using Egyptian mongoose as a model, we explore wet bench conditions to define an effective experimental design based on culturomics and DNA barcoding with potential application to different mammal species. After testing a battery of solid media and enrichments, we show that YCFA-based media, in aerobic and anaerobic conditions, together with PDA supplemented with chloramphenicol, are sufficient to maximize bacterial and fungal microbiota diversity. The pasteurization of the sample enrichment before cultivation is central to gain insight into sporogenic communities. We suggest the application of this optimized culturomics strategy to accurately expand knowledge on the microbial richness of mammals' gut, maximizing the application of common laboratory resources, without dramatic time and consumables expenditure but with high resolution of microbial landscapes. The analysis of ten fecal samples proved adequate to assess the core gastrointestinal microbiota of the mesocarnivore under analysis. This approach may empower most microbiology laboratories, particularly the veterinary, to perform studies on mammal's microbiota, and, in contrast with metagenomics, enabling the recovery of live bacteria for further studies.},
}
@article {pmid32897317,
year = {2020},
author = {Onetto, CA and Schmidt, SA and Roach, MJ and Borneman, AR},
title = {Comparative genome analysis proposes three new Aureobasidium species isolated from grape juice.},
journal = {FEMS yeast research},
volume = {20},
number = {6},
pages = {},
doi = {10.1093/femsyr/foaa052},
pmid = {32897317},
issn = {1567-1364},
mesh = {Aureobasidium/*classification/isolation &amp; purification ; Comparative Genomic Hybridization ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Fruit and Vegetable Juices/*microbiology ; Genome, Fungal ; *Phylogeny ; Sequence Analysis, DNA ; South Australia ; Vitis/*microbiology ; },
abstract = {Aureobasidium pullulans is the most abundant and ubiquitous species within the genus and is also considered a core component of the grape juice microflora. So far, a small number of other Aureobasidium species have been reported, that in contrast to A. pullulans, appear far more constrained to specific habitats. It is unknown whether grape juice is a reservoir of novel Aureobasidium species, overlooked in the course of conventional morphological and meta-barcoding analyses. In this study, eight isolates from grape juice taxonomically classified as Aureobasidium through ITS sequencing were subjected to whole-genome phylogenetic, synteny and nucleotide identity analyses, which revealed three isolates to likely represent newly discovered Aureobasidium species. Analyses of ITS and metagenomic sequencing datasets show that these species can be present in grape juice samples from different locations and vintages. Functional annotation revealed the Aureobasidium isolates possess the genetic potential to support growth on the surface of plants and grapes. However, the loss of several genes associated with tolerance to diverse environmental stresses suggest a more constrained ecological range than A. pullulans.},
}
@article {pmid32894458,
year = {2020},
author = {Artamonova, VS and Afanasyev, SA and Bardukov, NV and Golod, VM and Kokodiy, SV and Koulish, AV and Pashkov, AN and Pipoyan, SK and Reshetnikov, SI and Makhrov, AA},
title = {The Center of Origin and Colonization Routes of Noble Salmons of the Genus Salmo (Salmonidae, Actinopterigii).},
journal = {Doklady. Biochemistry and biophysics},
volume = {493},
number = {1},
pages = {171-177},
doi = {10.1134/S160767292004002X},
pmid = {32894458},
issn = {1608-3091},
mesh = {Animal Migration ; Animals ; Biological Evolution ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Europe ; Genes, Mitochondrial ; Genetic Variation ; Haplotypes ; Salmo salar/classification/genetics/*physiology ; },
abstract = {Genetic diversity and colonization routes of noble salmons were studied using a partial nucleotide sequence of the mitochondrial COI gene. The brown trout S. trutta, which is the most ancient species of the genus, was concluded to originate from the modern southeastern Pontic-Caspian area, which is currently inhabited by members of the subspecies S. trutta oxianus. Migrating westward while the Paratethys was in existence (5-34 million years ago), species of the genus colonized ancient water bodies in the modern Mediterranean basin and formed many isolated populations that survived desiccation of the Mediterranean Sea (5-6 million years ago). The Strait of Gibraltar mediated brown trout migrations to Northern Europe; the subspecies S. trutta trutta belongs to a relatively young phylogenetic lineage of the species. A separate brown trout lineage, currently classified as the subspecies S. trutta labrax, formed most likely in the area of the modern Danube basin, which was a relatively separate part of the Paratethys and was sometimes isolated as the Pannonian Lake. A highly divergent phylogenetic lineage of Atlantic salmon (S. salar) haplotypes originates from a haplotype of the brown trout that inhabited the area of the modern Strait of Gibraltar.},
}
@article {pmid32893839,
year = {2020},
author = {Sijimol, K and Arun Dev, S and Sreekumar, VB},
title = {DNA barcoding supports existence of morphospecies complex in endemic bamboo genus Ochlandra Thwaites of the Western Ghats, India.},
journal = {Journal of genetics},
volume = {99},
number = {},
pages = {},
pmid = {32893839},
issn = {0973-7731},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Intergenic/*genetics ; DNA, Plant/analysis/*genetics ; DNA, Ribosomal Spacer/*genetics ; India ; Poaceae/*classification/*genetics ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
abstract = {Ochlandra Thwaites, an economically exploited bamboo genus of the Western Ghats of India is severely affected by unsustainable extraction, natural habitat destruction and endangerment of species resources. This taxonomically challenging genus consists of a genetic mixture of 10 related polyploid species that are difficult to define and classify using traditional morphology. The present study investigated the probability of DNA barcoding using seven standard barcode regions recommended by CBOL as a supplementary tool to define true species boundaries. Distance (MEGA v.6.0) and sequence similarity (TaxonDNA) based approaches highlighted the discriminatory power of psbA-trnH intergenic spacer barcode region, but did not support true species entities. Neighbour-joining and Bayesian inference trees supported the existence of morphospecies complex in seven species of the genus owing to weak reproductive barriers amongnaturally coexisting species. Morphological affinities existing within genus might have stemmed from natural interspecific hybridization events and consequent reticulate evolution in morphospecies complex of genus Ochlandra.},
}
@article {pmid32893331,
year = {2020},
author = {Song, Z and Proctor, H},
title = {Application of DNA barcoding and morphometric analysis in differentiating cystacanths of Polymorphus species (Acanthocephala: Polymorphidae) from central Alberta, Canada.},
journal = {Parasitology research},
volume = {119},
number = {10},
pages = {3359-3368},
pmid = {32893331},
issn = {1432-1955},
support = {Supervisor: Dr. Heather Proctor//Alberta Conservation Association Grant in Biodiversity/ ; },
mesh = {Acanthocephala/anatomy &amp; histology/*classification/genetics ; Alberta ; Amphipoda/parasitology ; Animals ; DNA Barcoding, Taxonomic ; Fresh Water/parasitology ; Genes, Helminth/genetics ; Genes, Mitochondrial/genetics ; Larva/anatomy &amp; histology/classification/genetics ; Species Specificity ; },
abstract = {Acanthocephalans are multi-host endoparasites, many of which use freshwater amphipods as intermediate hosts for their larval stages (e.g., cystacanths) while adults live in the intestines of vertebrates, including waterfowl. In central Alberta, Canada, several co-occurring species of the acanthocephalan genus Polymorphus use the amphipod Gammarus lacustris Sars, 1863 as an intermediate host. We applied DNA barcoding and morphometric analysis to differentiate cystacanth larvae from G. lacustris sampled from 17 Albertan water bodies. We slide-mounted specimens and measured morphological traits relating to proboscis hooks. We sequenced the standard DNA barcoding region of the mitochondrial cytochrome c oxidase subunit I gene (COI). Morphometric analysis suggested that the acanthocephalans we collected belonged to four morphologically different groups that keyed to Polymorphus contortus (Bremser, 1821) Travassos, 1926; P. marilis Van Cleave, 1939; P. paradoxus Connel et Corner, 1957; and P. strumosoides (Lundström, 1942) Amin, 2013. Our Bayesian tree based on COI sequences generally corroborated the morphological results and supported that the specimens assigned to P. cf. contortus and P. cf. strumosoides belong to two distinct species. In contrast, the Bayesian tree showed that specimens of P. cf. marilis were nested as a cluster within the P. cf. paradoxus clade. Similarly, small pairwise genetic distance (< 2%) between specimens identified as P. cf. contortus and P. cf. strumosoides suggests that they are conspecific. Future studies should use morphology and sequence data from adult acanthocephalans to assess the taxonomic identity of the cystacanth-based Polymorphus taxa. Our study is the first to provide genetic information for the four Polymorphus taxa and emphasizes the importance of applying multiple approaches to differentiate parasite species.},
}
@article {pmid32892369,
year = {2021},
author = {Yao, L and Xin, H and Qu, M and Jiang, Y and Guo, Y and Li, F and Li, N and Tan, Z and Wang, L},
title = {Development of duplex real-time polymerase chain reaction for simultaneous detection of oilfish- and escolar-derived components.},
journal = {Journal of the science of food and agriculture},
volume = {101},
number = {5},
pages = {1792-1799},
doi = {10.1002/jsfa.10793},
pmid = {32892369},
issn = {1097-0010},
support = {2016YFF0201805//National Key Research and Development Program of China/ ; 2020TD71//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; },
mesh = {Animals ; DNA Primers/genetics ; Discriminant Analysis ; Fish Products/*analysis ; Fish Proteins/genetics ; Food Contamination/analysis ; Limit of Detection ; Perciformes/classification/*genetics ; Real-Time Polymerase Chain Reaction/*methods ; },
abstract = {BACKGROUND: Oilfish (Ruvettus pretiosus) and escolar (Lepidocybium flavobrunneum) are often used to adulterate high-value aquatic products, causing serious economic losses to consumers, and even keriorrhea in severe cases. It was difficult to identify them by morphological features for these two fish were processed into steak or fillet. The purpose of this study, therefore, is to develop an accurate and efficient method for detecting the oilfish- and escolar-derived components.<br><br>RESULTS: By comparing the mitochondrial 16S ribosomal RNA gene sequences of oilfish, escolar, and 16 varieties susceptible to adulteration, specific primers/probes were designed, and a duplex real-time polymerase chain reaction (PCR) method was established to detect oilfish- and escolar-derived components. The specificity and sensitivity of the method were analyzed, and the method was used to analyze 70 commercial samples to evalutate its applicability to actual samples in the market. The method developed was highly specific, without any cross-reaction on the other 16 species, with a limit of detection (LOD) for DNA of 0.0002&#x2009;ng&#x2009;&#x3bc;L[-1] for R. pretiosus and 0.002&#x2009;ng&#x2009;&#x3bc;L[-1] for L. flavobrunneum. In addition, the LOD for mixed muscle tissues was 0.1 g&#x2009;kg[-1] . Oilfish- and escolar-derived components were detected in 12 of the 70 commercial samples, a result that is consistent with the classic DNA barcoding test results.<br><br>CONCLUSION: The duplex real-time PCR method developed can be used to detect oilfish and escolar specifically, sensitively and accurately; it provides a good technical support for the identification of authentic aquatic products. &#xa9; 2020 Society of Chemical Industry.},
}
@article {pmid32891535,
year = {2021},
author = {Zheng, WY and Lichtner, V and Van Dort, BA and Baysari, MT},
title = {The impact of introducing automated dispensing cabinets, barcode medication administration, and closed-loop electronic medication management systems on work processes and safety of controlled medications in hospitals: A systematic review.},
journal = {Research in social &amp; administrative pharmacy : RSAP},
volume = {17},
number = {5},
pages = {832-841},
doi = {10.1016/j.sapharm.2020.08.001},
pmid = {32891535},
issn = {1934-8150},
mesh = {Electronic Data Processing ; Electronics ; Hospitals ; Humans ; *Medication Systems ; *Medication Therapy Management ; },
abstract = {BACKGROUND: Technology in the form of Automated Dispensing Cabinets (ADCs), Barcode Medication Administration (BCMA), and closed-loop Electronic Medication Management Systems (EMMS) are implemented in hospitals to assist with the supply, use and monitoring of medications. Although there is evidence to suggest that these technologies can reduce errors and improve monitoring of medications in general, little is known about their impact on controlled medications such as opioids.<br><br>OBJECTIVES: This review aimed to fill this knowledge gap by synthesising literature to determine the impact of ADCs, BCMA and closed-loop EMMS on clinical work processes, medication safety, and drug diversion associated with controlled medications in the inpatient setting.<br><br>METHODS: Eight databases (Medline, Pubmed, Embase, Scopus, Web of Science, PsycINFO, CINAHL, and ScienceDirect) were searched for relevant papers published between January 2000 and May 2019. Qualitative, quantitative, and mixed-methods empirical studies published in English that reported findings on the impact of ADCs, BCMA and/or closed-loop EMMS on controlled medications in the inpatient setting were included.<br><br>RESULTS: In total, 16 papers met the inclusion criteria. Eleven studies reported on ADCs, four on BCMA, and only one on closed-loop EMMS. Only four studies focused on controlled medications, with the remainder reporting only incidental findings. Studies reported the elimination of manual end-of-shift counts of controlled medications after ADC implementation but cases of drug diversion were reported despite introducing ADCs. Three quantitative studies reported reductions in medication errors after implementing BCMA, but medications labelled with wrong barcodes and unreadable barcodes led to confusion and administration errors.<br><br>CONCLUSIONS: More quality, targeted research is needed to provide evidence on the benefits and also risks of implementing technology to safeguard against inappropriate use of controlled medications in the inpatient setting. Processes need to be in place to supplement technological capabilities, and resources should be made available for post-implementation evaluations and interventions.},
}
@article {pmid32889152,
year = {2021},
author = {de Lorenzo, V and Krasnogor, N and Schmidt, M},
title = {For the sake of the Bioeconomy: define what a Synthetic Biology Chassis is!.},
journal = {New biotechnology},
volume = {60},
number = {},
pages = {44-51},
doi = {10.1016/j.nbt.2020.08.004},
pmid = {32889152},
issn = {1876-4347},
mesh = {Biotechnology/*economics ; Pseudomonas putida/*genetics ; Synthetic Biology/*economics ; },
abstract = {At the onset of the 4th Industrial Revolution, the role of synthetic biology (SynBio) as a fuel for the bioeconomy requires clarification of the terms typically adopted by this growing scientific-technical field. The concept of the chassis as a defined, reusable biological frame where non-native components can be plugged in and out to create new functionalities lies at the boundary between frontline bioengineering and more traditional recombinant DNA technology. As synthetic biology leaves academic laboratories and starts penetrating industrial and environmental realms regulatory agencies demand clear definitions and descriptions of SynBio constituents, processes and products. In this article, the state of the ongoing discussion on what is a chassis is reviewed, a non-equivocal nomenclature for the jargon used is proposed and objective criteria are recommended for distinguishing SynBio agents from traditional GMOs. The use of genomic barcodes as unique identifiers is strongly advocated. Finally the soil bacterium Pseudomonas putida is shown as an example of the roadmap that one environmental isolate may go through to become a bona fide SynBio chassis.},
}
@article {pmid32886759,
year = {2021},
author = {Pantanowitz, L and Michelow, P and Hazelhurst, S and Kalra, S and Choi, C and Shah, S and Babaie, M and Tizhoosh, HR},
title = {A Digital Pathology Solution to Resolve the Tissue Floater Conundrum.},
journal = {Archives of pathology &amp; laboratory medicine},
volume = {145},
number = {3},
pages = {359-364},
doi = {10.5858/arpa.2020-0034-OA},
pmid = {32886759},
issn = {1543-2165},
mesh = {*Algorithms ; *Artifacts ; Carcinoma, Renal Cell/diagnosis/*pathology ; Databases, Factual ; Diagnostic Errors/*prevention &amp; control ; Eosine Yellowish-(YS) ; Feasibility Studies ; Hematoxylin ; Humans ; Image Processing, Computer-Assisted ; Kidney Neoplasms/diagnosis/*pathology ; Pathologists ; *Pathology, Clinical ; Staining and Labeling ; },
abstract = {CONTEXT.&#x2014;: Pathologists may encounter extraneous pieces of tissue (tissue floaters) on glass slides because of specimen cross-contamination. Troubleshooting this problem, including performing molecular tests for tissue identification if available, is time consuming and often does not satisfactorily resolve the problem.<br><br>OBJECTIVE.&#x2014;: To demonstrate the feasibility of using an image search tool to resolve the tissue floater conundrum.<br><br>DESIGN.&#x2014;: A glass slide was produced containing 2 separate hematoxylin and eosin (H&amp;E)-stained tissue floaters. This fabricated slide was digitized along with the 2 slides containing the original tumors used to create these floaters. These slides were then embedded into a dataset of 2325 whole slide images comprising a wide variety of H&amp;E stained diagnostic entities. Digital slides were broken up into patches and the patch features converted into barcodes for indexing and easy retrieval. A deep learning-based image search tool was employed to extract features from patches via barcodes, hence enabling image matching to each tissue floater.<br><br>RESULTS.&#x2014;: There was a very high likelihood of finding a correct tumor match for the queried tissue floater when searching the digital database. Search results repeatedly yielded a correct match within the top 3 retrieved images. The retrieval accuracy improved when greater proportions of the floater were selected. The time to run a search was completed within several milliseconds.<br><br>CONCLUSIONS.&#x2014;: Using an image search tool offers pathologists an additional method to rapidly resolve the tissue floater conundrum, especially for those laboratories that have transitioned to going fully digital for primary diagnosis.},
}
@article {pmid32884673,
year = {2020},
author = {Abrego, N and Huotari, T and Tack, AJM and Lindahl, BD and Tikhonov, G and Somervuo, P and Martin Schmidt, N and Ovaskainen, O and Roslin, T},
title = {Higher host plant specialization of root-associated endophytes than mycorrhizal fungi along an arctic elevational gradient.},
journal = {Ecology and evolution},
volume = {10},
number = {16},
pages = {8989-9002},
pmid = {32884673},
issn = {2045-7758},
abstract = {How community-level specialization differs among groups of organisms, and changes along environmental gradients, is fundamental to understanding the mechanisms influencing ecological communities. In this paper, we investigate the specialization of root-associated fungi for plant species, asking whether the level of specialization varies with elevation. For this, we applied DNA barcoding based on the ITS region to root samples of five plant species equivalently sampled along an elevational gradient at a high arctic site. To assess whether the level of specialization changed with elevation and whether the observed patterns varied between mycorrhizal and endophytic fungi, we applied a joint species distribution modeling approach. Our results show that host plant specialization is not environmentally constrained in arctic root-associated fungal communities, since there was no evidence for changing specialization with elevation, even if the composition of root-associated fungal communities changed substantially. However, the level of specialization for particular plant species differed among fungal groups, root-associated endophytic fungal communities being highly specialized on particular host species, and mycorrhizal fungi showing almost no signs of specialization. Our results suggest that plant identity affects associated mycorrhizal and endophytic fungi differently, highlighting the need of considering both endophytic and mycorrhizal fungi when studying specialization in root-associated fungal communities.},
}
@article {pmid32883215,
year = {2020},
author = {King, J and Harder, T and Beer, M and Pohlmann, A},
title = {Rapid multiplex MinION nanopore sequencing workflow for Influenza A viruses.},
journal = {BMC infectious diseases},
volume = {20},
number = {1},
pages = {648},
pmid = {32883215},
issn = {1471-2334},
support = {"COMPARE" No. 643476//Horizon 2020 Framework Programme/ ; "DELTA-FLU" No. 727922//Horizon 2020 Framework Programme/ ; "VEO" No. 874735//Horizon 2020 Framework Programme/ ; },
mesh = {High-Throughput Nucleotide Sequencing/*methods ; Humans ; Influenza A virus/*genetics ; Nanopore Sequencing/*methods ; Polymerase Chain Reaction ; Reproducibility of Results ; Workflow ; },
abstract = {BACKGROUND: Due to the frequent reassortment and zoonotic potential of influenza A viruses, rapid gain of sequence information is crucial. Alongside established next-generation sequencing protocols, the MinION sequencing device (Oxford Nanopore Technologies) has become a serious competitor for routine whole-genome sequencing. Here, we established a novel, rapid and high-throughput MinION multiplexing workflow based on a universal RT-PCR.<br><br>METHODS: Twelve representative influenza A virus samples of multiple subtypes were universally amplified in a one-step RT-PCR and subsequently sequenced on the MinION instrument in conjunction with a barcoding library preparation kit from the rapid family and the MinIT performing live base-calling. The identical PCR products were sequenced on an IonTorrent platform and, after final consensus assembly, all data was compared for validation. To prove the practicability of the MinION-MinIT method in human and veterinary diagnostics, we sequenced recent and historical influenza strains for further benchmarking.<br><br>RESULTS: The MinION-MinIT combination generated over two million reads for twelve samples in a six-hour sequencing run, from which a total of 72% classified as quality screened, trimmed and mapped influenza reads to produce full genome sequences. Identities between the datasets of >&#x2009;99.9% were achieved, with 100% coverage of all segments alongside a sufficient confidence and 4492fold mean depth. From RNA extraction to finished sequences, only 14&#x2009;h were required.<br><br>CONCLUSIONS: Overall, we developed and validated a novel and rapid multiplex workflow for influenza A virus sequencing. This protocol suits both clinical and academic settings, aiding in real time diagnostics and passive surveillance.},
}
@article {pmid32883208,
year = {2020},
author = {An, J and Zheng, W and Liang, J and Xi, Q and Chen, R and Jia, J and Lu, X and Jakovlić, I},
title = {Disrupted architecture and fast evolution of the mitochondrial genome of Argeia pugettensis (Isopoda): implications for speciation and fitness.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {607},
pmid = {32883208},
issn = {1471-2164},
support = {31471970//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 2015FY210300//Program of Ministry of Science and Technology of the People's Republic of China/ ; 201901D111274//Natural Science Foundation of Shanxi Province/ ; },
mesh = {Animals ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Genetic Fitness ; Genetic Speciation ; *Genome, Mitochondrial ; Isopoda/classification/*genetics ; Phylogeny ; Selection, Genetic ; },
abstract = {BACKGROUND: Argeia pugettensis is an isopod species that parasitizes other crustaceans. Its huge native geographic range spans the Pacific from China to California, but molecular data are available only for a handful of specimens from North-American populations. We sequenced and characterised the complete mitogenome of a specimen collected in the Yellow Sea.<br><br>RESULTS: It exhibited a barcode (cox1) similarity level of only 87-89% with North-American populations, which is unusually low for conspecifics. Its mitogenome is among the largest in isopods (&#x2248;16.5 Kbp), mostly due to a large duplicated palindromic genomic segment (2 Kbp) comprising three genes. However, it lost a segment comprising three genes, nad4L-trnP-nad6, and many genes exhibited highly divergent sequences in comparison to isopod orthologues, including numerous mutations, deletions and insertions. Phylogenetic and selection analyses corroborated that this is one of the handful of most rapidly evolving available isopod mitogenomes, and that it evolves under highly relaxed selection constraints (as opposed to positive selection). However, its nuclear 18S gene is highly conserved, which suggests that rapid evolution is limited to its mitochondrial genome. The cox1 sequence analysis indicates that elevated mitogenomic evolutionary rates are not shared by North-American conspecifics, which suggests a breakdown of cox1 barcoding in this species.<br><br>CONCLUSIONS: A highly architecturally disrupted mitogenome and decoupling of mitochondrial and nuclear rates would normally be expected to have strong negative impacts on the fitness of the organism, so the existence of this lineage is a puzzling evolutionary question. Additional studies are needed to assess the phylogenetic breadth of this disrupted mitochondrial architecture and its impact on fitness.},
}
@article {pmid32881235,
year = {2021},
author = {Kim, J and Moon, JH and Um, SH},
title = {Short RNA Universal Coding for Topological Transformation Nano-barcoding Application.},
journal = {Chembiochem : a European journal of chemical biology},
volume = {22},
number = {2},
pages = {392-397},
doi = {10.1002/cbic.202000477},
pmid = {32881235},
issn = {1439-7633},
mesh = {Humans ; *Point-of-Care Testing ; RNA/*genetics ; *Reverse Transcriptase Polymerase Chain Reaction ; },
abstract = {With the advent of innovative genomic discovery toolkits such as RT-PCR, genetic information can be quickly decrypted, and this has resulted in significant progress in overcoming diseases. However, RT-PCR has the serious problem of frequent errors, and the demand for a new gene diagnostic system is emerging. Herein, we propose a universal coding system for the effective detection of short single-stranded DNA or RNA by using a topological transformation-based nano-barcoding technique (TNT). Our goal was to develop a dedicated diagnostic device that unifies the other gene groups, thus resulting in minimum testing. In a universal coding system consisting of two separate circulation structures, different gene groups become generalized into specific single genes with the same sequence by a strand-displacement reaction and are then amplified, eventually being quickly detected in one TNT system. Simple gene diagnostic systems like this make high-speed, point-of-care diagnostic technologies, and we are very confident that these will provide clinical gene detection in the near future.},
}
@article {pmid32880855,
year = {2021},
author = {Zhang, W and Sun, Y and Liu, J and Xu, C and Zou, X and Chen, X and Liu, Y and Wu, P and Yang, X and Zhou, S},
title = {DNA barcoding of Oryza: conventional, specific, and super barcodes.},
journal = {Plant molecular biology},
volume = {105},
number = {3},
pages = {215-228},
pmid = {32880855},
issn = {1573-5028},
support = {XDA 19050303//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDA 23080204//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2018JB001//Fundamental Research Funds for Central Universities of the Central South University (CN)/ ; },
mesh = {*DNA Barcoding, Taxonomic ; Likelihood Functions ; Oryza/*classification/*genetics ; Phylogeny ; Seeds/genetics ; Species Specificity ; Tissue Banks ; },
abstract = {We applied the phylogenomics to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity. Rice (genus Oryza) is one of the most important crops in the world, supporting half of the world's population. Breeding of high-yielding and quality cultivars relies on genetic resources from both cultivated and wild species, which are collected and maintained in seed banks. Unfortunately, numerous seeds are mislabeled due to taxonomic issues or misidentifications. Here, we applied the phylogenomics of 58 complete chloroplast genomes and two hypervariable nuclear genes to determine species identity in rice seeds. Twenty-one Oryza species were identified. Conspecific relationships were determined between O. glaberrima and O. barthii, O. glumipatula and O. longistaminata, O. grandiglumis and O. alta, O. meyeriana and O. granulata, O. minuta and O. malampuzhaensis, O. nivara and O. sativa subsp. indica, and O. sativa subsp. japonica and O. rufipogon. D and L genome types were not found and the H genome type was extinct. Importantly, we evaluated the performance of four conventional plant DNA barcodes (matK, rbcL, psbA-trnH, and ITS), six rice-specific chloroplast DNA barcodes (psaJ-rpl33, trnC-rpoB, rps16-trnQ, rpl22-rps19, trnK-matK, and ndhC-trnV), two rice-specific nuclear DNA barcodes (NP78 and R22), and a chloroplast genome super DNA barcode. The latter was the most reliable marker. The six rice-specific chloroplast barcodes revealed that 17% of the 53 seed accessions from rice seed banks or field collections were mislabeled. These results are expected to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity.},
}
@article {pmid32879616,
year = {2020},
author = {Benhadji, N and Sartori, M and Abdellaoui Hassaine, K and Gattolliat, JL},
title = {Reports of Baetidae (Ephemeroptera) species from Tafna Basin, Algeria and biogeographic affinities revealed by DNA barcoding.},
journal = {Biodiversity data journal},
volume = {8},
number = {},
pages = {e55596},
pmid = {32879616},
issn = {1314-2828},
abstract = {BACKGROUND: The Mediterranean basin is known to be the cradle of many endemic species. Within mayflies (Insecta, Ephemeroptera), North African species belonging to the family Baetidae remain poorly known and, traditionally, affinities to European fauna were proposed. Recent studies, based on molecular reconstructions, showed closer relationships to Mediterranean islands fauna.<br><br>NEW INFORMATION: Baetidae were sampled from North-West Algerian wadis (Tafna basin) and involved in COI barcoding reconstructions. Seven species were identified. The subgenus Rhodobaetis is represented by Baetis atlanticus known previously from Macaronesian islands, Europe and Morocco and the Maghrebian endemic Baetis sinespinosus. Specimens, previously identified as Cloeon cf. dipterum, correspond to Cloeon peregrinator and, until now, only reported from Macaronesia. Besides the confirmation of endemicity of some species, such as Procloen stagnicola and B. sinespinosus, our molecular study showed quite original results for relationships between European, insular and Algerian species. Baetis maurus stood out as a North African endemic sister clade to an Iberian clade. Furthermore, we found clear interspecific distances between Algerian and European clades for A. cf. sinaica and B. cf. pavidus, suggesting the presence of cryptic species in Algeria. However, additional studies are needed, as, for the moment, no clear morphological characters were found to separate the different clades and support them as valid species.},
}
@article {pmid32879612,
year = {2020},
author = {Huemer, P and Sohn, JC},
title = {Eidophasia assmanni sp. nov., the first alpine representative of the genus, detected in the Russian Altai Mountains (Lepidoptera, Plutellidae).},
journal = {ZooKeys},
volume = {959},
number = {},
pages = {99-111},
pmid = {32879612},
issn = {1313-2989},
abstract = {Eidophasia assmanni sp. nov., a new species of Plutellidae from the alpine zone of Russian Altai Mountains, is described from diagnostic morphology and DNA barcodes. Male adult and genitalia are illustrated, whereas the female sex remains unknown. The species inhabits alpine scree with patchy herbaceous plants and is considered as possible endemic species of the Altai Mountains. An updated checklist of the 13 global Eidophasia Stephens, 1842 species is provided. The likely polyphyly of the genus is discussed from molecular data of the barcode region of the mt COI gene.},
}
@article {pmid32879611,
year = {2020},
author = {Monjardim, M and Azevedo, CO and Fagundes, V},
title = {DNA barcoding and hypopygium shape support delimitation of sympatric Dissomphalus species (Hymenoptera, Bethylidae) from the Atlantic rainforest.},
journal = {ZooKeys},
volume = {959},
number = {},
pages = {87-97},
pmid = {32879611},
issn = {1313-2989},
abstract = {Dissomphalus is a cosmopolitan genus of Bethylidae and has 269 Neotropical species divided into 32 species-groups, mostly defined by the genital and the tergal process structures. Dissomphalus rectilineus and D. concavatus are sympatric species in the ulceratus species-group. Members of the species-group share many similarities in the morphology of the head, hypopygium, tergal process and genitalia, but may be distinguished by the structure of the hypopygium. Previous studies have found intermediate structures of the hypopygium in the sympatric areas and raised questions about the distinctiveness of these two species. We sequenced 340 bp of the mitochondrial gene cytochrome oxidase I of 29 specimens from Brazil and Paraguay, calculated the genetic divergence among specimens, and recovered the phylogenetic relationships between taxa. In addition, we compared the morphology of the hypopygium to evaluate its use as a species-specific diagnostic character using the genetic divergence values. We recovered three well-supported monophyletic groups (intraclade divergence from 1.3 to 13.4%) and three hypopygium morphologies associated with each clade, two of them associated with D. rectilineus and D. concavatus (as described in the literature); the third one is new, not associated with any known species. The divergence between the D. rectilineus and D. concavatus clades was 19%, while the third clade is divergent from each species by 19-20%. If fully described, the hypopygium shape associated with the COI sequence will represent an extremely promising approach to the diagnosis of Dissomphalus species.},
}
@article {pmid32879467,
year = {2021},
author = {Zaccaria, S and Raphael, BJ},
title = {Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL.},
journal = {Nature biotechnology},
volume = {39},
number = {2},
pages = {207-214},
pmid = {32879467},
issn = {1546-1696},
support = {P30 CA072720/CA/NCI NIH HHS/United States ; R01 HG007069/HG/NHGRI NIH HHS/United States ; U24 CA211000/CA/NCI NIH HHS/United States ; },
mesh = {*Algorithms ; *Alleles ; Breast Neoplasms/genetics ; Cell Line, Tumor ; DNA Copy Number Variations/genetics ; DNA, Neoplasm/genetics ; *Evolution, Molecular ; Female ; *Gene Dosage ; Genetic Heterogeneity ; Haplotypes/*genetics ; Humans ; Single-Cell Analysis ; },
abstract = {Single-cell barcoding technologies enable genome sequencing of thousands of individual cells in parallel, but with extremely low sequencing coverage (<0.05×) per cell. While the total copy number of large multi-megabase segments can be derived from such data, important allele-specific mutations-such as copy-neutral loss of heterozygosity (LOH) in cancer-are missed. We introduce copy-number haplotype inference in single cells using evolutionary links (CHISEL), a method to infer allele- and haplotype-specific copy numbers in single cells and subpopulations of cells by aggregating sparse signal across hundreds or thousands of individual cells. We applied CHISEL to ten single-cell sequencing datasets of ~2,000 cells from two patients with breast cancer. We identified extensive allele-specific copy-number aberrations (CNAs) in these samples, including copy-neutral LOHs, whole-genome duplications (WGDs) and mirrored-subclonal CNAs. These allele-specific CNAs affect genomic regions containing well-known breast-cancer genes. We also refined the reconstruction of tumor evolution, timing allele-specific CNAs before and after WGDs, identifying low-frequency subpopulations distinguished by unique CNAs and uncovering evidence of convergent evolution.},
}
@article {pmid32878171,
year = {2020},
author = {Chen, R and Yu, Y and Chen, J and Zhong, Y and Zhao, H and Hussain, A and Tan, HZ},
title = {Customized 2D Barcode Sensing for Anti-Counterfeiting Application in Smart IoT with Fast Encoding and Information Hiding.},
journal = {Sensors (Basel, Switzerland)},
volume = {20},
number = {17},
pages = {},
pmid = {32878171},
issn = {1424-8220},
support = {NO.61672008//the National Natural Science Foundation of China/ ; NO.2017KCXTD021//the Innovation Team Project of the Education Department of Guangdong Province/ ; NO.2018KTSCX120//the Project for Distinctive Innovation of Ordinary Universities of Guangdong Province/ ; NO.2016A030310335//the Ph.D. Start-up Fund of Natural Science Foundation of Guangdong Province/ ; NO.76120-42020022//the Science and Technology Planning Project of Guangdong Province/ ; NO. 2018KQNCX138//the Guangdong Colleges and Universities Young Innovative Talents Projects/ ; },
abstract = {With the development of commodity economy, the emergence of fake and shoddy products has seriously harmed the interests of consumers and enterprises. To tackle this challenge, customized 2D barcode is proposed to satisfy the requirements of the enterprise anti-counterfeiting certification. Based on information hiding technology, the proposed approach can solve these challenging problems and provide a low-cost, difficult to forge, and easy to identify solution, while achieving the function of conventional 2D barcodes. By weighting between the perceptual quality and decoding robustness in sensing recognition, the customized 2D barcode can maintain a better aesthetic appearance for anti-counterfeiting and achieve fast encoding. A new picture-embedding scheme was designed to consider 2D barcode, within a unit image block as a basic encoding unit, where the 2D barcode finder patterns were embedded after encoding. Experimental results demonstrated that the proposed customized barcode could provide better encoding characteristics, while maintaining better decoding robustness than several state-of-the-art methods. Additionally, as a closed source 2D barcode that could be visually anti-counterfeit, the customized 2D barcode could effectively prevent counterfeiting that replicate physical labels. Benefitting from the high-security, high information capacity, and low-cost, the proposed customized 2D barcode with sensing recognition scheme provide a highly practical, valuable in terms of marketing, and anti-counterfeiting traceable solution for future smart IoT applications.},
}
@article {pmid32878026,
year = {2020},
author = {Pappalardo, AM and Copat, C and Raffa, A and Rossitto, L and Grasso, A and Fiore, M and Ferrante, M and Ferrito, V},
title = {Fish-Based Baby Food Concern-From Species Authentication to Exposure Risk Assessment.},
journal = {Molecules (Basel, Switzerland)},
volume = {25},
number = {17},
pages = {},
pmid = {32878026},
issn = {1420-3049},
support = {#22722132134//University of Catania/ ; },
mesh = {DNA Barcoding, Taxonomic ; Fish Products/*analysis/classification ; Food Analysis ; Food Contamination/analysis ; *Food Quality ; Food Safety ; Infant Food/*analysis/*standards ; Metals/analysis ; Risk Assessment ; },
abstract = {In this work, two different but complementary approaches were used to evaluate the reliability of fish-based baby foods as a source of safe nourishment for babies. More specifically, barcoding analysis based on the Cytochrome Oxidase I sequences was used for fish species authentication and an analysis of metal/metalloid levels was performed to estimate the exposure risk assessment derived from consumption of selected fish-based baby food in infants and toddlers. COI DNA barcoding revealed that in three samples the species detected did not match the common name of the species shown on the label. In particular, G. chalcogrammus and M. australis were found in place of M. merluccius and O. mykiss was found in place of S. salar. The analysis of exposure risk assessment indicated a low risk for developing chronic systemic and carcinogenic effects in infants and toddler, under an exposure scenario based on daily consumption of a single box of fish-based baby food. However, it is important to highlight that in order to provide a comprehensive risk assessment it would be important to supplement the levels of exposure resulting from the total diet. Overall, our results suggest that more attention should be paid by authorities to ensure the safety of food for infants and toddlers.},
}
@article {pmid32877322,
year = {2020},
author = {Luande, VN and Eklöf, D and Lindström, A and Nyanjom, SG and Evander, M and Lilja, T},
title = {The Human Biting Culex pipiens Bioform molestus Detected in Several Areas in Southern Sweden.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {20},
number = {12},
pages = {936-938},
doi = {10.1089/vbz.2020.2631},
pmid = {32877322},
issn = {1557-7759},
mesh = {*Animal Distribution ; Animals ; Culex/classification/*physiology ; DNA/genetics ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Humans ; Microsatellite Repeats ; Species Specificity ; Sweden ; },
abstract = {Background: The mosquito species Culex pipiens is a known vector of several pathogens and occurs in two distinct bioforms, pipiens and molestus. The bioform molestus thrives in urban environments where there are below-ground habitats; it can mate in confined spaces and feed on mammals as well as birds. In contrast, the bioform pipiens is found above ground, is thought to require more space for mating, and mainly feeds on birds. The pipiens bioform is present in large parts of Sweden but the molestus bioform has previously only been found in major cities. Materials and Methods: People experiencing mosquito nuisance in southern Sweden submitted mosquito samples as part of a citizen science project, and these samples were analyzed to determine the geographical distribution of the molestus bioform of Cx. pipiens. Mosquito specimens were identified to the species level by DNA barcoding of the cytochrome C oxidase subunit I (COI) gene, and the bioforms were determined through the CQ11 microsatellite marker. Results:Culex pipiens f molestus was observed to be spread across large parts of Gothenburg as well as in the suburbs. This bioform was found both in urban and rural areas at several sites across southern Sweden. In one site, hybrids between the two bioforms were found. Conclusions: The detection of Cx. pipiens f molestus in several rural areas was surprising, indicating that it may be more widely spread than urban areas alone, where it has been previously reported.},
}
@article {pmid32876070,
year = {2020},
author = {Khalmuratova, I and Choi, DH and Woo, JR and Jeong, MJ and Oh, Y and Kim, YG and Lee, IJ and Choo, YS and Kim, JG},
title = {Diversity and Plant Growth-Promoting Effects of Fungal Endophytes Isolated from Salt-Tolerant Plants.},
journal = {Journal of microbiology and biotechnology},
volume = {30},
number = {11},
pages = {1680-1687},
pmid = {32876070},
issn = {1738-8872},
mesh = {Alternaria ; Ascomycota ; Basidiomycota ; Biodiversity ; Chenopodiaceae ; DNA, Fungal/genetics ; Endophytes/classification/genetics/*isolation &amp; purification/*physiology ; Fungi/genetics/isolation &amp; purification/physiology ; Gibberellins ; Oryza ; *Plant Development ; Plant Roots/microbiology ; Plumbaginaceae ; Republic of Korea ; Salt-Tolerant Plants/*microbiology ; Symbiosis ; },
abstract = {Fungal endophytes are symbiotic microorganisms that are often found in asymptomatic plants. This study describes the genetic diversity of the fungal endophytes isolated from the roots of plants sampled from the west coast of Korea. Five halophytic plant species, Limonium tetragonum, Suaeda australis, Suaeda maritima, Suaeda glauca Bunge, and Phragmites australis, were collected from a salt marsh in Gochang and used to isolate and identify culturable, root-associated endophytic fungi. The fungal internal transcribed spacer (ITS) region ITS1-5.8S-ITS2 was used as the DNA barcode for the classification of these specimens. In total, 156 isolates of the fungal strains were identified and categorized into 23 genera and two phyla (Ascomycota and Basidiomycota), with Dothideomycetes and Sordariomycetes as the predominant classes. The genus Alternaria accounted for the largest number of strains, followed by Cladosporium and Fusarium. The highest diversity index was obtained from the endophytic fungal group associated with the plant P. australis. Waito-C rice seedlings were treated with the fungal culture filtrates to analyze their plant growth-promoting capacity. A bioassay of the Sm-3-7-5 fungal strain isolated from S. maritima confirmed that it had the highest plant growth-promoting capacity. Molecular identification of the Sm-3-7-5 strain revealed that it belongs to Alternaria alternata and is a producer of gibberellins. These findings provided a fundamental basis for understanding the symbiotic interactions between plants and fungi.},
}
@article {pmid32873796,
year = {2020},
author = {Raveendran, M and Lee, AJ and Sharma, R and Wälti, C and Actis, P},
title = {Rational design of DNA nanostructures for single molecule biosensing.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {4384},
pmid = {32873796},
issn = {2041-1723},
support = {MR/N029976/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Aptamers, Nucleotide/*chemistry ; Biomarkers/analysis ; Biosensing Techniques/*instrumentation ; C-Reactive Protein/analysis ; DNA/*chemistry ; Equipment Design ; Humans ; Limit of Detection ; Nanostructures/*chemistry ; Nanotechnology/methods ; Single Molecule Imaging/*instrumentation ; },
abstract = {The ability to detect low concentrations of biomarkers in patient samples is one of the cornerstones of modern healthcare. In general, biosensing approaches are based on measuring signals resulting from the interaction of a large ensemble of molecules with the sensor. Here, we report a biosensor platform using DNA origami featuring a central cavity with a target-specific DNA aptamer coupled with a nanopore read-out to enable individual biomarker detection. We show that the modulation of the ion current through the nanopore upon the DNA origami translocation strongly depends on the presence of the biomarker in the cavity. We exploit this to generate a biosensing platform with a limit of detection of 3 nM and capable of the detection of human C-reactive protein (CRP) in clinically relevant fluids. Future development of this approach may enable multiplexed biomarker detection by using ribbons of DNA origami with integrated barcoding.},
}
@article {pmid32870109,
year = {2021},
author = {Eaton, MJ and Edwards, S and Inocencio, HA and Machado, FJ and Nuckles, EM and Farman, M and Gauthier, NA and Vaillancourt, LJ},
title = {Diversity and Cross-Infection Potential of Colletotrichum Causing Fruit Rots in Mixed-Fruit Orchards in Kentucky.},
journal = {Plant disease},
volume = {105},
number = {4},
pages = {1115-1128},
doi = {10.1094/PDIS-06-20-1273-RE},
pmid = {32870109},
issn = {0191-2917},
mesh = {*Colletotrichum/genetics ; Fruit ; Kentucky ; Phylogeny ; Plant Diseases ; },
abstract = {Fungi in the genus Colletotrichum cause apple, blueberry, and strawberry fruit rots, which can result in significant losses. Accurate identification is important because species differ in aggressiveness, fungicide sensitivity, and other factors affecting management. Multiple Colletotrichum species can cause similar symptoms on the same host, and more than one fruit type can be infected by a single Colletotrichum species. Mixed-fruit orchards may facilitate cross-infection, with significant management implications. Colletotrichum isolates from small fruits in Kentucky orchards were characterized and compared with apple isolates via a combination of morphotyping, sequencing of voucher loci and whole genomes, and cross-inoculation assays. Seven morphotypes representing two species complexes (C. acutatum and C. gloeosporioides) were identified. Morphotypes corresponded with phylogenetic species C. fioriniae, C. fructicola, C. nymphaeae, and C. siamense, identified by TUB2 or GAPDH barcodes. Phylogenetic trees built from nine single-gene sequences matched barcoding results with one exception, later determined to belong to an undescribed species. Comparison of single-gene trees with representative whole genome sequences revealed that CHS and ApMat were the most informative for diagnosis of fruit rot species and individual morphotypes within the C. acutatum or C. gloeosporioides complexes, respectively. All blueberry isolates belonged to C. fioriniae, and most strawberry isolates were C. nymphaeae, with a few C. siamense and C. fioriniae also recovered. All three species cause fruit rot on apples in Kentucky. Cross-inoculation assays on detached apple, blueberry, and strawberry fruits showed that all species were pathogenic on all three hosts but with species-specific differences in aggressiveness.},
}
@article {pmid32863726,
year = {2020},
author = {Sawant, M and Sarang, S and Modak, N},
title = {Finding the forgotten gems: revisiting the butterflies of Matheran after 125 years with introduction to novel colour barcode for depicting seasons and activity of the Indian butterflies.},
journal = {Biodiversity data journal},
volume = {8},
number = {},
pages = {e54333},
pmid = {32863726},
issn = {1314-2828},
abstract = {We present here an updated checklist for the butterflies of Matheran, Maharashtra, India, an eco-sensitive zone, with identification remarks for locally rare or very rare butterflies. This is the first dedicated checklist for butterflies of Matheran after 125 years. A total of 140 species of butterflies were recorded belonging to six families. Amongst them, 15 species were either listed under Schedule I, II or IV of the Indian Wildlife (Protection) Act, 1972. We also list the habitats of the species along with the data for their activity at the time of recording the observation. We propose a uniform colour code system for representing season and activity for the Indian butterflies. Examples of colour barcodes are provided with the images of rare and very rare butterflies. The lack of abundance data is a limitation of the study for which we propose long term monitoring with dedicated efforts.},
}
@article {pmid32863723,
year = {2020},
author = {Pannell, CM and Schnitzler, J and Muellner-Riehl, AN},
title = {Two new species and a new species record of Aglaia (Meliaceae) from Indonesia.},
journal = {PhytoKeys},
volume = {155},
number = {},
pages = {33-51},
pmid = {32863723},
issn = {1314-2011},
abstract = {Two new species of Aglaia from Indonesia are described, Aglaia monocaula restricted to West Papua, and Aglaia nyaruensis occurring on Borneo (Kalimantan, Brunei, Sabah and Sarawak). A phylogenetic analysis using nuclear ITS and ETS, and plastid rps15-ycf1 sequence data indicates that the two new species of Aglaia are also genetically distinct. Aglaia monocaula belongs to sectionAmoora, while A. nyaruensis is included in section Aglaia. A dichotomous key, drawings and three-locus DNA barcodes are provided as aids for the identification of the two new species of Aglaia. In addition, the geographic range of Aglaia mackiana (section Amoora) is expanded from a single previously known site in Papua New Guinea to West Papua, Indonesia.},
}
@article {pmid32863715,
year = {2020},
author = {Elsayed, AK and Skuhravá, M and Ohta, K and Yoshida, S and Tokuda, M},
title = {Revision of the birch-associated genus Massalongia (Diptera, Cecidomyiidae), with description of a new species from Japan and a taxonomic key to worldwide species.},
journal = {ZooKeys},
volume = {958},
number = {},
pages = {1-27},
pmid = {32863715},
issn = {1313-2989},
abstract = {Betula (Betulaceae), or birch, is a Holarctic genus of trees and shrubs whose species have ornamental, industrial, and medical importance. Gall midges of the genus Massalongia (Diptera: Cecidomyiidae: Cecidomyiidi) are exclusively associated with birches in the Palearctic region. In 2018, an undescribed Massalongia species was discovered forming leaf galls on the midveins of B. grossa on Mount Tara, Saga Prefecture, Kyushu, Japan. In this study the species is described as M. nakamuratetsui Elsayed &amp; Tokuda, sp. nov., and a DNA barcode provided for it. The other known species of Massalongia are redescribed because the original descriptions are outdated and insufficient. A lectotype is designated for M. bachmaieri. In addition, the monotypic genus Apagodiplosis, containing A. papyriferae associated with B. papyrifera in the Nearctic region, is synonymized here under Massalongia, resulting in M. papyriferae comb. nov., rendering Massalongia a Holarctic genus with six species. Comparing the sequence data of M. nakamuratetsui with all sequences available in The Barcode of Life Data (BOLD) system supports the occurrence of Massalongia in the Nearctic region and suggest that more species could be discovered there. Massalongia species form leaf or bud galls, and their mature larvae drop to the ground in autumn and overwinter in characteristic waterproof bottle-like cocoons, which is possibly a protective adaptation for pupation in wet and snowy lands. A taxonomic key to all Massalongia species is provided.},
}
@article {pmid32863714,
year = {2020},
author = {van Nieukerken, EJ and Eiseman, CS},
title = {Splitting the leafmining shield-bearer moth genus Antispila Hübner (Lepidoptera, Heliozelidae): North American species with reduced venation placed in Aspilanta new genus, with a review of heliozelid morphology.},
journal = {ZooKeys},
volume = {957},
number = {},
pages = {105-161},
pmid = {32863714},
issn = {1313-2989},
abstract = {The new genus Aspilanta gen. n. is described to harbour Nearctic heliozelid moths with reduced venation, previously placed in Antispila Hübner, 1825, with type species Antispila oinophylla van Nieukerken &amp; Wagner, 2012. The erection of this genus has become possible now that monophyly has been supported by a recent phylotranscriptomics analysis. Six species are combined in this genus: Aspilanta oinophylla (van Nieukerken &amp; Wagner, 2012), comb. n., A. hydrangaeella (Chambers, 1874), comb. n., A. ampelopsifoliella (Chambers, 1874), comb. n., A. voraginella (Braun, 1927), comb. n., A. argentifera (Braun, 1927), comb. n., A. viticordifoliella (Clemens, 1860), comb. n. and two candidate species are recognised. DNA barcode COI sequences of Malaise trapped specimens suggest a rich fauna of Aspilanta in Central America. All are leafminers, with Vitaceae as main host family, and single species feeding respectively on Hydrangeaceae and Myricaceae. The species are briefly diagnosed, and data on biology, DNA barcodes and distribution are provided. To place the genus in context, a review of heliozelid morphology and phylogeny is presented and a key to Nearctic genera is given. The genus is confined to North and Central America, possibly also occurring in South America. Aspilanta oinophylla is also an invasive species on grapevine in Italy. The genus is sister to Coptodisca Walsingham, 1895. Another species is removed from Antispila: Heliozela eugeniella (Busck, 1900), comb. n., feeding on Eugenia (Myrtaceae), from Florida.},
}
@article {pmid32860303,
year = {2021},
author = {Martins, FMS and Porto, M and Feio, MJ and Egeter, B and Bonin, A and Serra, SRQ and Taberlet, P and Beja, P},
title = {Modelling technical and biological biases in macroinvertebrate community assessment from bulk preservative using multiple metabarcoding markers.},
journal = {Molecular ecology},
volume = {30},
number = {13},
pages = {3221-3238},
pmid = {32860303},
issn = {1365-294X},
mesh = {Bias ; Biodiversity ; *DNA Barcoding, Taxonomic ; *Ecosystem ; Fresh Water ; Portugal ; },
abstract = {DNA metabarcoding from the ethanol used to store macroinvertebrate bulk samples is a convenient methodological option in molecular biodiversity assessment and biomonitoring of aquatic ecosystems, as it preserves specimens and reduces problems associated with sample sorting. However, this method may be affected by errors and biases, which need to be thoroughly quantified before it can be mainstreamed into biomonitoring programmes. Here, we used 80 unsorted macroinvertebrate samples collected in Portugal under a Water Framework Directive monitoring programme, to compare community diversity and taxonomic composition metrics estimated through morphotaxonomy versus metabarcoding from storage ethanol using three markers (COI-M19BR2, 16S-Inse01 and 18S-Euka02) and a multimarker approach. A preliminary in silico analysis showed that the three markers were adequate for the target taxa, with detection failures related primarily to the lack of adequate barcodes in public databases. Metabarcoding of ethanol samples retrieved far less taxa per site (alpha diversity) than morphotaxonomy, albeit with smaller differences for COI-M19BR2 and the multimarker approach, while estimates of taxa turnover (beta diversity) among sites were similar across methods. Using generalized linear mixed models, we found that after controlling for differences in read coverage across samples, the probability of detection of a taxon was positively related to its proportional abundance, and negatively so to the presence of heavily sclerotized exoskeleton (e.g., Coleoptera). Overall, using our experimental protocol with different template dilutions, the COI marker showed the best performance, but we recommend the use of a multimarker approach to detect a wider range of taxa in freshwater macroinvertebrate samples. Further methodological development and optimization efforts are needed to reduce biases associated with body armouring and rarity in some macroinvertebrate taxa.},
}
@article {pmid32855742,
year = {2020},
author = {Tanney, JB and Seifert, KA},
title = {Mollisiaceae: An overlooked lineage of diverse endophytes.},
journal = {Studies in mycology},
volume = {95},
number = {},
pages = {293-380},
pmid = {32855742},
issn = {0166-0616},
abstract = {Mollisia is a taxonomically neglected discomycete genus (Helotiales, Leotiomycetes) of commonly encountered saprotrophs on decaying plant tissues throughout temperate regions. The combination of indistinct morphological characters, more than 700 names in the literature, and lack of reference DNA sequences presents a major challenge when working with Mollisia. Unidentified endophytes, including strains that produced antifungal or antiinsectan secondary metabolites, were isolated from conifer needles in New Brunswick and placed with uncertainty in Phialocephala and Mollisia, necessitating a more comprehensive treatment of these genera. In this study, morphology and multigene phylogenetic analyses were used to explore the taxonomy of Mollisiaceae, including Mollisia, Phialocephala, and related genera, using new field collections, herbarium specimens, and accessioned cultures and sequences. The phylogeny of Mollisiaceae was reconstructed and compared using the nuc internal transcribed spacer rDNA (ITS) barcode and partial sequences of the 28S nuc rDNA (LSU) gene, largest subunit of RNA polymerase II (RPB1), DNA topoisomerase I (TOP1), and the hypothetical protein Lipin/Ned1/Smp2 (LNS2). The results show that endophytism is common throughout the Mollisiaceae lineage in a diverse range of hosts but is infrequently attributed to Mollisia because of a paucity of reference sequences. Generic boundaries within Mollisiaceae are poorly resolved and based on phylogenetic evidence the family included species placed in Acephala, Acidomelania, Barrenia, Bispora, Cheirospora, Cystodendron, Fuscosclera, Hysteronaevia, Loramyces, Mollisia, Neopyrenopeziza, Obtectodiscus, Ombrophila, Patellariopsis, Phialocephala, Pulvinata, Tapesia (=Mollisia), and Trimmatostroma. Taxonomic novelties included the description of five novel Mollisia species and five novel Phialocephala species and the synonymy of Fuscosclera with Phialocephala, Acidomelania with Mollisia, and Loramycetaceae with Mollisiaceae.},
}
@article {pmid32855741,
year = {2020},
author = {Visagie, CM and Houbraken, J},
title = {Updating the taxonomy of Aspergillus in South Africa.},
journal = {Studies in mycology},
volume = {95},
number = {},
pages = {253-292},
pmid = {32855741},
issn = {0166-0616},
abstract = {The taxonomy and nomenclature of the genus Aspergillus and its associated sexual (teleomorphic) genera have been greatly stabilised over the last decade. This was in large thanks to the accepted species list published in 2014 and associated metadata such as DNA reference sequences released at the time. It had a great impact on the community and it has never been easier to identify, publish and describe the missing Aspergillus diversity. To further stabilise its taxonomy, it is crucial to not only discover and publish new species but also to capture infraspecies variation in the form of DNA sequences. This data will help to better characterise and distinguish existing species and make future identifications more robust. South Africa has diverse fungal communities but remains largely unexplored in terms of Aspergillus with very few sequences available for local strains. In this paper, we re-identify Aspergillus previously accessioned in the PPRI and MRC culture collections using modern taxonomic approaches. In the process, we re-identify strains to 63 species, describe seven new species and release a large number of new DNA reference sequences.},
}
@article {pmid32855593,
year = {2020},
author = {Degtyarev, MI and Lebedev, IM and Kuznetsova, KG and Gongalsky, KB},
title = {A history of study and new records of terrestrial enchytraeids (Annelida, Clitellata, Enchytraeidae) from the Russian Far East.},
journal = {ZooKeys},
volume = {955},
number = {},
pages = {79-96},
pmid = {32855593},
issn = {1313-2989},
abstract = {A list of terrestrial enchytraeids of the Russian Far East is compiled based on literature and extensive field data collected by the authors in 2019. A database has been created consisting of geographic coordinates, habitat type, species, and data source. For some species collected by the authors, barcoding using COI, 16s, and 12s rRNA genes has been performed. In total, there are at least 62 species of enchytraeids belonging to 12 genera. Seven species (Achaeta macroampullacea, Cognettia sphagnetorum, Enchytraeus dichaetus, Fridericia cusanica, Globulidrilus riparius, Marionina southerni, Mesenchytraeus gigachaetus) are reported in the Russian Far East for the first time. Cognettia sphagnetorum and F. cusanica are most probably introduced. Taxonomic and biogeographical remarks on some of the species found and differences from the original descriptions are provided. Some of the specimens may be undescribed species, but this requires a more in-depth examination. The Russian Far East, especially its southeastern part, is of great interest as a possible location for new species of enchytraeids.},
}
@article {pmid32848176,
year = {2020},
author = {Costa, FF and da Silva, NM and Voidaleski, MF and Weiss, VA and Moreno, LF and Schneider, GX and Najafzadeh, MJ and Sun, J and Gomes, RR and Raittz, RT and Castro, MAA and de Muniz, GBI and de Hoog, GS and Vicente, VA},
title = {Environmental prospecting of black yeast-like agents of human disease using culture-independent methodology.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {14229},
pmid = {32848176},
issn = {2045-2322},
mesh = {Ascomycota/genetics/*isolation &amp; purification ; Brazil ; Chromoblastomycosis/*microbiology ; Datasets as Topic ; Environmental Monitoring/methods ; Humans ; Metagenomics ; },
abstract = {Melanized fungi and black yeasts in the family Herpotrichiellaceae (order Chaetothyriales) are important agents of human and animal infectious diseases such as chromoblastomycosis and phaeohyphomycosis. The oligotrophic nature of these fungi enables them to survive in adverse environments where common saprobes are absent. Due to their slow growth, they lose competition with common saprobes, and therefore isolation studies yielded low frequencies of clinically relevant species in environmental habitats from which humans are thought to be infected. This problem can be solved with metagenomic techniques which allow recognition of microorganisms independent from culture. The present study aimed to identify species of the family Herpotrichiellaceae that are known to occur in Brazil by the use of molecular markers to screen public environmental metagenomic datasets from Brazil available in the Sequence Read Archive (SRA). Species characterization was performed with the BLAST comparison of previously described barcodes and padlock probe sequences. A total of 18,329 sequences was collected comprising the genera Cladophialophora, Exophiala, Fonsecaea, Rhinocladiella and Veronaea, with a focus on species related to the chromoblastomycosis. The data obtained in this study demonstrated presence of these opportunists in the investigated datasets. The used techniques contribute to our understanding of environmental occurrence and epidemiology of black fungi.},
}
@article {pmid32846590,
year = {2020},
author = {Liu, K and Zhao, S and Yu, Z and Zhou, Y and Yang, J and Zhao, R and Yang, C and Ma, W and Wang, X and Feng, M and Tang, Y and Li, K and Zhou, C},
title = {Application of DNA barcoding in fish identification of supermarkets in Henan province, China: More and longer COI gene sequences were obtained by designing new primers.},
journal = {Food research international (Ottawa, Ont.)},
volume = {136},
number = {},
pages = {109516},
doi = {10.1016/j.foodres.2020.109516},
pmid = {32846590},
issn = {1873-7145},
mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; Fish Products/analysis ; Fishes/genetics ; Horses ; *Supermarkets ; },
abstract = {In recent years, DNA barcode technology has been widely used in food identification, especially in the identification of fish. In China, there are few studies on the authenticity of fish products in Henan province of China. In this study, 179 fish samples were collected from supermarkets in Zhengzhou city and Xinxiang city in Henan province, China. COI gene sequences were obtained with PCR technology by designing specific primers and universal primers. COI gene sequences of all samples were obtained to identify species, which is used to investigate species substitution and mislabeling of the fish sold in the two regional markets. The molecular identification results showed that 28.49% (51/179) fish samples were not consistent with the labels. Substitution of high-price fish by low-price fish was prevalent. For example, halibut (Pleuronectiformes) and cod (Gadus) are replaced by striped catfish (Pangasianodon hypophthalmus), and some merchants label bighead carp (Hypophthalmichthys nobilis) as cod (Gadus), there are also accidental labeling errors (such as labels for greenfin horse-faced filefish (Thamnaconus septentrionalis) have been identified as grass carp (Ctenopharyngodon idella) and Wuchang bream (Megalobrama amblycephala) etc. Most of the samples labeled correctly are the fish of low economic value and the fresh fish. This study shows that almost all the commercial fish can be identified by COI DNA barcoding by newly designed primers. Finally, this study also gives a reference of real species of fish fillet in Henan province in China.},
}
@article {pmid32845927,
year = {2020},
author = {Gu, J and Jiang, B and Wang, H and Wei, T and Lin, L and Huang, Y and Huang, J},
title = {Phylogeny and species delimitation of the genus Longgenacris and Fruhstorferiola viridifemorata species group (Orthoptera: Acrididae: Melanoplinae) based on molecular evidence.},
journal = {PloS one},
volume = {15},
number = {8},
pages = {e0237882},
pmid = {32845927},
issn = {1932-6203},
mesh = {Animals ; Electron Transport Complex IV/genetics ; Genetic Variation ; Grasshoppers/anatomy &amp; histology/*classification/*genetics ; Haplotypes/genetics ; Likelihood Functions ; Male ; Models, Theoretical ; *Phylogeny ; Species Specificity ; Tooth/anatomy &amp; histology ; },
abstract = {Phylogenetic positions of the genus Longgenacris and one of its members, i.e. L. rufiantennus are controversial. The species boundaries within both of L. rufiantennus+Fruhstorferiola tonkinensis and F. viridifemorata species groups are unclear. In this study, we explored the phylogenetic positions of the genus Longgenacris and the species L. rufiantennus and the relationships among F. viridifemorata group based on the 658-base fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) barcode and the complete sequences of the internal transcribed spacer regions (ITS1 and ITS2) of the nuclear ribosomal DNA. The phylogenies were reconstructed in maximum likelihood framework using IQ-TREE. K2P distances were used to assess the overlap range between intraspecific variation and interspecific divergence. Phylogenetic species concept and NJ tree, K2P distance, the statistical parsimony network as well as the generalized mixed Yule coalescent model (GMYC) were employed to delimitate the species boundaries in L. rufiantennus+F. tonkinensis and F. viridifemorata species groups. The results demonstrated that the genus Longgenacris should be placed in the subfamily Melanoplinae but not Catantopinae, and L. rufiantennus should be a member of the genus Fruhstorferiola but not Longgenacris. Species boundary delimitation confirmed the presence of oversplitting in L. rufiantennus+F. tonkinensis and F. viridifemorata species groups and suggested that each group should be treated as a single species.},
}
@article {pmid32844060,
year = {2020},
author = {Fadli, N and Mohd Nor, SA and Othman, AS and Sofyan, H and Muchlisin, ZA},
title = {DNA barcoding of commercially important reef fishes in Weh Island, Aceh, Indonesia.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e9641},
pmid = {32844060},
issn = {2167-8359},
abstract = {Knowledge on the precise identification of fish resources is critical for sustainable fisheries management. This study employs the DNA barcoding approach to generate a molecular taxonomic catalogue of commercially important reef fishes in the waters of Weh Island (Aceh Province), the most northerly inhabited island in the biodiverse Indonesian Archipelago. The waters not only support artisanal fisheries but also a feeder for the industry in the greater island of Aceh. In total, 230 specimens from 72 species belonging to 32 genera and 17 families were DNA barcoded, representing a major segment of the captured reef fish taxa and a quarter of fish species diversity that had previously been recorded. The sequence read lengths were 639 bp revealing 359 conserved sites, 280 variable sites, 269 parsimony informative and 11 singletons. Our molecular findings paralleled the morphological identification with no evidence of cryptic species or new species discovery. This study is a significant contribution to the fisheries statistics of this area, which would facilitate assessment of species catch composition and hence for strategizing management plans. It is an important input to the DNA barcode library of Indonesian marine fishes and to the global DNA barcode entries in general.},
}
@article {pmid32841689,
year = {2020},
author = {Guan, Q and Sadykov, M and Mfarrej, S and Hala, S and Naeem, R and Nugmanova, R and Al-Omari, A and Salih, S and Al Mutair, A and Carr, MJ and Hall, WW and Arold, ST and Pain, A},
title = {A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {100},
number = {},
pages = {216-223},
pmid = {32841689},
issn = {1878-3511},
mesh = {COVID-19/epidemiology/*virology ; *Genome, Viral ; High-Throughput Nucleotide Sequencing ; Humans ; *Molecular Typing ; Mutation ; Pandemics ; SARS-CoV-2/classification/*genetics ; Viral Proteins/genetics ; },
abstract = {OBJECTIVE: The SARS-CoV-2 pathogen has established endemicity in humans. This necessitates the development of rapid genetic surveillance methodologies to serve as an adjunct with existing comprehensive, albeit though slower, genome sequencing-driven approaches.<br><br>METHODS: A total of 21,789 complete genomes were downloaded from GISAID on May 28, 2020 for analyses. We have defined the major clades and subclades of circulating SARS-CoV-2 genomes. A rapid sequencing-based genotyping protocol was developed and tested on SARS-CoV-2-positive RNA samples by next-generation sequencing.<br><br>RESULTS: We describe 11 major mutations which defined five major clades (G614, S84, V251, I378 and D392) of globally circulating viral populations. The clades can specifically identify using an 11-nucleotide genetic barcode. An analysis of amino acid variation in SARS-CoV-2 proteins provided evidence of substitution events in the viral proteins involved in both host entry and genome replication.<br><br>CONCLUSION: Globally circulating SARS-CoV-2 genomes could be classified into 5 major clades based on mutational profiles defined by an 11-nucleotide barcode. We have successfully developed a multiplexed sequencing-based, rapid genotyping protocol for high-throughput classification of major clade types of SARS-CoV-2 in clinical samples. This barcoding strategy will be required to monitor decreases in genetic diversity as treatment and vaccine approaches become widely available.},
}
@article {pmid32840625,
year = {2022},
author = {Tessema, SK and Hathaway, NJ and Teyssier, NB and Murphy, M and Chen, A and Aydemir, O and Duarte, EM and Simone, W and Colborn, J and Saute, F and Crawford, E and Aide, P and Bailey, JA and Greenhouse, B},
title = {Sensitive, Highly Multiplexed Sequencing of Microhaplotypes From the Plasmodium falciparum Heterozygome.},
journal = {The Journal of infectious diseases},
volume = {225},
number = {7},
pages = {1227-1237},
pmid = {32840625},
issn = {1537-6613},
support = {R01 AI139520/AI/NIAID NIH HHS/United States ; K24 AI144048/AI/NIAID NIH HHS/United States ; K23 AI076614/AI/NIAID NIH HHS/United States ; 098051/WT_/Wellcome Trust/United Kingdom ; 090770/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Haplotypes ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Malaria, Falciparum/epidemiology ; *Plasmodium falciparum/genetics ; Whole Genome Sequencing/methods ; },
abstract = {BACKGROUND: Targeted next-generation sequencing offers the potential for consistent, deep coverage of information-rich genomic regions to characterize polyclonal Plasmodium falciparum infections. However, methods to identify and sequence these genomic regions are currently limited.<br><br>METHODS: A bioinformatic pipeline and multiplex methods were developed to identify and simultaneously sequence 100 targets and applied to dried blood spot (DBS) controls and field isolates from Mozambique. For comparison, whole-genome sequencing data were generated for the same controls.<br><br>RESULTS: Using publicly available genomes, 4465 high-diversity genomic regions suited for targeted sequencing were identified, representing the P. falciparum heterozygome. For this study, 93 microhaplotypes with high diversity (median expected heterozygosity&#x2005;=&#x2005;0.7) were selected along with 7 drug resistance loci. The sequencing method achieved very high coverage (median 99%), specificity (99.8%), and sensitivity (90% for haplotypes with 5% within sample frequency in dried blood spots with 100 parasites/&#xb5;L). In silico analyses revealed that microhaplotypes provided much higher resolution to discriminate related from unrelated polyclonal infections than biallelic single-nucleotide polymorphism barcodes.<br><br>CONCLUSIONS: The bioinformatic and laboratory methods outlined here provide a flexible tool for efficient, low-cost, high-throughput interrogation of the P. falciparum genome, and can be tailored to simultaneously address multiple questions of interest in various epidemiological settings.},
}
@article {pmid32840039,
year = {2020},
author = {Premont, RT},
title = {Keys to the Kingdom: GPCR phosphorylation patterns direct β-arrestin.},
journal = {EMBO reports},
volume = {21},
number = {9},
pages = {e51249},
pmid = {32840039},
issn = {1469-3178},
support = {P01 HL075443/HL/NHLBI NIH HHS/United States ; R01 DK113159/DK/NIDDK NIH HHS/United States ; P01 HL075443/GF/NIH HHS/United States ; R01 DK113159/GF/NIH HHS/United States ; },
mesh = {*Arrestins/genetics/metabolism ; *MAP Kinase Signaling System ; Phosphorylation ; beta-Arrestin 1 ; beta-Arrestins ; },
abstract = {The β-arrestin proteins are key regulators of G protein-coupled receptors, serving at least three distinct functions: inhibiting receptor signaling through G proteins, directing receptor trafficking from the cell surface after activation, and transmitting receptor-initiated signals directly. How the two β-arrestin proteins perform these many functions for hundreds of receptor types throughout the body, and specifically how β-arrestin-mediated signaling can be tuned to cellular conditions, remains an open question. Function-based evidence and recent structure-based evidence have suggested that patterns of receptor phosphorylation ("barcodes") may be a critical determinant of β-arrestin action. In this issue of EMBO Reports, Baidya and colleagues (Baidya et al, 2020a) report that specific receptor phosphorylation site clusters ("codes") determine whether β-arrestin 1 acts to promote or inhibit receptor activation of Erk mitogen-activated protein kinases. They provide direct evidence for a functional barcode system by transferring inhibitory and stimulatory codes between receptors, suggesting future work to understand just how code site location in a receptor and its phosphorylation status can lead to very different functions of bound β-arrestin proteins.},
}
@article {pmid32838560,
year = {2021},
author = {Fernandes, TJR and Amaral, JS and Mafra, I},
title = {DNA barcode markers applied to seafood authentication: an updated review.},
journal = {Critical reviews in food science and nutrition},
volume = {61},
number = {22},
pages = {3904-3935},
doi = {10.1080/10408398.2020.1811200},
pmid = {32838560},
issn = {1549-7852},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; RNA, Ribosomal, 16S ; Real-Time Polymerase Chain Reaction ; *Seafood/analysis ; Species Specificity ; },
abstract = {The world's seafood supply and trade have increased in the last decades, as well as the potential for marketed species substitution. Currently, seafood safety and authenticity assessment have become central issues, directly related with the identification of improper labeling of processed foods. To detect and prevent mislabeling issues, species identification using DNA barcodes has been widely used as effective molecular markers. Therefore, this review intends to present the current status on the application of DNA barcodes to seafood species authentication. In this regard, the barcode regions, reference databases and related methodologies are described, while applications are listed and summarized. Cytochrome c oxidase subunit I (COI) gene has been the preferential targeted DNA region in animal species identification, including fish and shellfish, though other mitochondrial (cytb, 12S rRNA, 16S rRNA) and nuclear genes have been used. DNA barcoding relying on Sanger's sequencing has been the most used approach for seafood authentication. Nevertheless, in recent years, noteworthy progresses have been advanced toward DNA barcoding strategies, involving next generation sequencing. Methods relying on real-time PCR using species-specific primers and probes or followed by high resolution melting analysis combined with DNA barcodes represent alternative and promising approaches for simple, cost-effective and high-throughput species discrimination in processed seafood. Still, polymerase chain reaction with restriction fragment length polymorphism detection, targeting DNA barcodes, continues to be a well-established and broadly accepted method in seafood authentication.},
}
@article {pmid32833963,
year = {2020},
author = {Hopfe, C and Ospina-Jara, B and Scheibel, T and Cabra-García, J},
title = {Ocrepeira klamt sp. n. (Araneae: Araneidae), a novel spider species from an Andean páramo in Colombia.},
journal = {PloS one},
volume = {15},
number = {8},
pages = {e0237499},
pmid = {32833963},
issn = {1932-6203},
mesh = {Animal Distribution ; Animal Structures/*anatomy &amp; histology/*physiology ; Animals ; Colombia ; DNA Barcoding, Taxonomic ; Ecosystem ; Electron Transport Complex IV/genetics ; Phylogeny ; Spiders/*anatomy &amp; histology/*classification/physiology ; },
abstract = {Herein we describe Ocrepeira klamt sp. n. (Araneae: Araneidae), a new orb-weaving spider species from a Colombian páramo, which was formerly inaccessible for scientific studies due to decades long armed conflicts. Both, phenotypic and molecular data are used to confirm genus affiliation, and the new species is placed into phylogenetic context with other araneid spiders. Morphological characteristics and ecological notes of Ocrepeira klamt sp. n. are reported together with the sequence of the barcoding region of cytochrome c oxidase subunit I (COI) to provide a comprehensive description of the spider, facilitating future identification beyond taxonomic experts. With this study we contribute to the taxonomic knowledge that is required to inventory the hyper diverse yet threatened ecosystem of the Colombian páramos.},
}
@article {pmid32832990,
year = {2020},
author = {Liu, M and Zhao, Y and Sun, Y and Wu, P and Zhou, S and Ren, L},
title = {Diatom DNA barcodes for forensic discrimination of drowning incidents.},
journal = {FEMS microbiology letters},
volume = {367},
number = {17},
pages = {},
doi = {10.1093/femsle/fnaa145},
pmid = {32832990},
issn = {1574-6968},
mesh = {*DNA Barcoding, Taxonomic ; Diatoms/classification/*genetics ; Drowning/*microbiology ; Forensic Pathology/*methods ; },
abstract = {The presence of diatoms in victim's internal organs has been regarded as a gold biological evidence of drowning. The idea becomes true at the advent of DNA metabarcoding. Unfortunately, the DNA barcode of diatoms are far from being applicable due to neither consensus on the barcode and nor reliable reference library.In this study we tested 23 pairs of primers, including two new primer pairs, Baci18S (V4 of 18S) and BacirbcL (central region of rbcL), for amplifying fragments of 16S/18S, 23S/28S, COI, ITS and rbcL. A total of five pairs of primers performed satisfactory for diatoms. We used three of them, 18S605 (V2 + V3 of 18S), Baci18S and BacirbcL, to barcode four water samples using next generation sequencing platform. The results showed that these primers worked well for NGS metabarcoding of diatoms. We suggest that 18S605, Baci18S and BacirbcL be barcodes of diatoms and the corresponding primer pairs be used. Considering a quite high proportion of sequences deposited in GenBank were mislabeled, the most urgent task for DNA barcoding of diatoms is to create standard sequences using correctly identified specimens, ideally type specimens.},
}
@article {pmid32828979,
year = {2020},
author = {Sah, GP and Wall, D},
title = {Kin recognition and outer membrane exchange (OME) in myxobacteria.},
journal = {Current opinion in microbiology},
volume = {56},
number = {},
pages = {81-88},
pmid = {32828979},
issn = {1879-0364},
support = {R01 GM101449/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacterial Proteins/genetics/*metabolism ; Cell Membrane/genetics/*metabolism ; Myxococcales/genetics/*metabolism ; Receptors, Cell Surface/genetics/*metabolism ; },
abstract = {Myxobacteria conduct complex social traits that requires populations to be highly related and devoid of exploiters. To enrich for clonal cells in populations, they employ kin discrimination mechanisms. One key system involves a polymorphic cell surface receptor, TraA, which recognizes self by homotypic interactions with neighboring myxobacterial cells. Recent studies revealed that TraA and its partner TraB are fluid outer membrane proteins that coalesce into foci upon recognition of kin. The formation of foci leads to transient membrane fusion junctions and the bidirectional exchange of outer membrane components that facilitates cooperative behaviors. Additionally, expansive suites of polymorphic lipoprotein toxins are exchanged, which act as self-identity barcodes that exquisitely discriminate against nonself to assemble homogenous populations.},
}
@article {pmid32825730,
year = {2020},
author = {Tanabe, K and Ikeda, M and Hayashi, M and Matsuo, K and Yasaka, M and Machida, H and Shida, M and Katahira, T and Imanishi, T and Hirasawa, T and Sato, K and Yoshida, H and Mikami, M},
title = {Comprehensive Serum Glycopeptide Spectra Analysis Combined with Artificial Intelligence (CSGSA-AI) to Diagnose Early-Stage Ovarian Cancer.},
journal = {Cancers},
volume = {12},
number = {9},
pages = {},
pmid = {32825730},
issn = {2072-6694},
support = {17H04340//Ministry of Education, Culture, Sports, Science and Technology/ ; 18K09274//Ministry of Education, Culture, Sports, Science and Technology/ ; 18K09300//Ministry of Education, Culture, Sports, Science and Technology/ ; 20lm0203004j0003//AMED/ ; },
abstract = {Ovarian cancer is a leading cause of deaths among gynecological cancers, and a method to detect early-stage epithelial ovarian cancer (EOC) is urgently needed. We aimed to develop an artificial intelligence (AI)-based comprehensive serum glycopeptide spectra analysis (CSGSA-AI) method in combination with convolutional neural network (CNN) to detect aberrant glycans in serum samples of patients with EOC. We converted serum glycopeptide expression patterns into two-dimensional (2D) barcodes to let CNN learn and distinguish between EOC and non-EOC. CNN was trained using 60% samples and validated using 40% samples. We observed that principal component analysis-based alignment of glycopeptides to generate 2D barcodes significantly increased the diagnostic accuracy (88%) of the method. When CNN was trained with 2D barcodes colored on the basis of serum levels of CA125 and HE4, a diagnostic accuracy of 95% was achieved. We believe that this simple and low-cost method will increase the detection of EOC.},
}
@article {pmid32825240,
year = {2020},
author = {Auychinda, C and Jacobus, LM and Sartori, M and Boonsoong, B},
title = {A New Species of Vietnamella Tshernova 1972 (Ephemeroptera: Vietnamellidae) from Thailand.},
journal = {Insects},
volume = {11},
number = {9},
pages = {},
pmid = {32825240},
issn = {2075-4450},
support = {BDC-PG2-161004//The Centre of Excellence on Biodiversity (BDC) Office of Higher Education Commission/ ; },
abstract = {The larva, male subimago, female imago, and eggs of V. nanensis sp. n. are described based on specimens from Mae Hong Son and Nan provinces, Thailand. The female subimago is described based on a photograph of a specimen reared to the imago stage. The species previously was distinguished only by DNA barcode data and designated as Vietnamella sp. C. Based on morphology, the larva of the new species can be distinguished with the following combination of characteristics: (i) pattern of serration on the ventral margin of the forefemur, (ii) posterolateral margins of abdominal terga with pairs of acute tubercles, especially terga VI and VII, (iii) a well-developed pair of median ridge projections on tergum X, (iv) the second segment of the maxillary palp being about 1.3× the length of the third segment, and (v) females containing eggs with prominent protuberances on the chorionic surface. A key to larvae of all known species in the genus is provided.},
}
@article {pmid32824262,
year = {2020},
author = {Roscini, L and Conti, A and Casagrande Pierantoni, D and Robert, V and Corte, L and Cardinali, G},
title = {Do Metabolomics and Taxonomic Barcode Markers Tell the Same Story about the Evolution of Saccharomyces sensu stricto Complex in Fermentative Environments?.},
journal = {Microorganisms},
volume = {8},
number = {8},
pages = {},
pmid = {32824262},
issn = {2076-2607},
abstract = {Yeast taxonomy was introduced based on the idea that physiological properties would help discriminate species, thus assuming a strong link between physiology and taxonomy. However, the instability of physiological characteristics within species configured them as not ideal markers for species delimitation, shading the importance of physiology and paving the way to the DNA-based taxonomy. The hypothesis of reconnecting taxonomy with specific traits from phylogenies has been successfully explored for Bacteria and Archaea, suggesting that a similar route can be traveled for yeasts. In this framework, thirteen single copy loci were used to investigate the predictability of complex Fourier Transform InfaRed spectroscopy (FTIR) and High-performance Liquid Chromatography-Mass Spectrometry (LC-MS) profiles of the four historical species of the Saccharomyces sensu stricto group, both on resting cells and under short-term ethanol stress. Our data show a significant connection between the taxonomy and physiology of these strains. Eight markers out of the thirteen tested displayed high correlation values with LC-MS profiles of cells in resting condition, confirming the low efficacy of FTIR in the identification of strains of closely related species. Conversely, most genetic markers displayed increasing trends of correlation with FTIR profiles as the ethanol concentration increased, according to their role in the cellular response to different type of stress.},
}
@article {pmid32821214,
year = {2020},
author = {Ferreira, S and Tierno de Figueroa, JM and Martins, FM and Verissimo, J and Quaglietta, L and Grosso-Silva, JM and Lopes, PB and Sousa, P and Paupério, J and Fonseca, NA and Beja, P},
title = {The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera.},
journal = {Biodiversity data journal},
volume = {8},
number = {},
pages = {e55137},
pmid = {32821214},
issn = {1314-2828},
abstract = {BACKGROUND: The use of DNA barcoding allows unprecedented advances in biodiversity assessments and monitoring schemes of freshwater ecosystems; nevertheless, it requires the construction of comprehensive reference collections of DNA sequences that represent the existing biodiversity. Plecoptera are considered particularly good ecological indicators and one of the most endangered groups of insects, but very limited information on their DNA barcodes is available in public databases. Currently, less than 50% of the Iberian species are represented in BOLD.<br><br>NEW INFORMATION: The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera dataset contains records of 71 specimens of Plecoptera. All specimens have been morphologically identified to species level and belong to 29 species in total. This dataset contributes to the knowledge on the DNA barcodes and distribution of Plecoptera from the Iberian Peninsula and it is one of the IBI database public releases that makes available genetic and distribution data for a series of taxa.The species represented in this dataset correspond to an addition to public databases of 17 species and 21 BINs. Fifty-eight specimens were collected in Portugal and 18 in Spain during the period of 2004 to 2018. All specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources and their DNA barcodes are publicly available in the Barcode of Life Data System (BOLD) online database. The distribution dataset can be freely accessed through the Global Biodiversity Information Facility (GBIF).},
}
@article {pmid32821211,
year = {2020},
author = {Rebelo, H and Ferreira, S and Amorim, F and Horta, P and Raposeira, H and Santos, H and Beja, P and Mata, VA},
title = {Hidden in our pockets: building of a DNA barcode library unveils the first record of Myotis alcathoe for Portugal.},
journal = {Biodiversity data journal},
volume = {8},
number = {},
pages = {e54479},
pmid = {32821211},
issn = {1314-2828},
abstract = {BACKGROUND: The advent and boom of DNA barcoding technologies have provided a powerful tool for the fields of ecology and systematics. Here, we present the InBIO Barcoding Initiative Database: Portuguese Bats (Chiroptera) dataset containing DNA sequences of 63 specimens representing the 25 bat species currently known for continental Portugal. For that, we sequenced tissues samples obtained in a vast array of projects spanning the last two decades.<br><br>NEW INFORMATION: We added four new Barcoding Index Numbers (BINs) to existing Chiroptera barcodes on BOLD, two belonging to Myotis escalerai, one to Plecotus auritus and the other to Rhinolophus hipposideros. Surprisingly, one of the samples initially identified in the field as Myotis mystacinus turned out to be Myotis alcathoe, which represents the first record of this species for Portugal. The presence of Nyctalus noctula in Portugal was also genetically confirmed for the first time. This case study shows the power and value of DNA barcoding initiatives to unravel new data that may be hidden on biological collections.},
}
@article {pmid32821204,
year = {2020},
author = {Pelingen, AL and Freitag, H},
title = {Description of Neoperla mindoroensis sp. nov., the first record of a stonefly from Mindoro, Philippines (Plecoptera, Perlidae), and identification of its life stages using COI barcodes.},
journal = {ZooKeys},
volume = {954},
number = {},
pages = {47-63},
pmid = {32821204},
issn = {1313-2989},
abstract = {The new stonefly species, Neoperla mindoroensis sp. nov. (Perlidae), from Mindoro island is described. The new species is assigned to the N. recta species complex of the N. montivaga group on account of its obvious T7 and T8 with pointed processes and the presence of basolateral lobes in the everted aedeagal sac. The male adult is distinguishable by its aedeagus with a slightly raised mediodorsal lobe, fully covered with fine spinules, while the female adult has comparably small eggs (240 × 220 μm) with a punctate, chorionic surface with punctae arranged in polygonal FCIs. The life stages and sexes were assigned using COI mtDNA barcodes (2.2% maximum intraspecific genetic distance), which were compared with available barcodes of congeners, which had interspecific genetic distances varying by at least 23.5%. Biogeographic aspects, ecological habitat requirements, and suitability as potential bioindicator of the species are also briefly discussed.},
}
@article {pmid32821201,
year = {2020},
author = {Liu, W and Golovatch, S},
title = {The first representatives of the millipede family Glomeridellidae (Diplopoda, Glomerida) recorded from China and Indochina.},
journal = {ZooKeys},
volume = {954},
number = {},
pages = {1-15},
pmid = {32821201},
issn = {1313-2989},
abstract = {A new species of glomeridellid millipede is described from Guizhou Province, southern China: Tonkinomeris huzhengkuni sp. nov. This new epigean species differs very clearly in many structural details, being sufficiently distinct morphologically and disjunct geographically from T. napoensis Nguyen, Sierwald &amp; Marek, 2019, the type and sole species of Tonkinomeris Nguyen, Sierwald &amp; Marek, 2019, which was described recently from northern Vietnam. The genus Tonkinomeris is formally relegated from Glomeridae and assigned to the family Glomeridellidae, which has hitherto been considered strictly Euro-Mediterranean in distribution and is thus new to the diplopod faunas of China and Indochina. Tonkinomeris is re-diagnosed and shown to have perhaps the basalmost position in the family Glomeridellidae. Its relationships are discussed, both morphological and zoogeographical, within and outside the Glomeridellidae, which can now be considered as relict and basically Oriental in origin. Because of the still highly limited array of DNA-barcoding sequences of the COI mitochondrial gene available in the GenBank, the first molecular phylogenetic analysis of Glomerida attempted here shows our phylogram to be too deficient to consider meaningful.},
}
@article {pmid32821195,
year = {2020},
author = {Song, HT and Fei, MH and Li, BP and Zhu, CD and Cao, HX},
title = {A new species of Oomyzus Rondani (Hymenoptera, Eulophidae) reared from the pupae of Coccinella septempunctata (Coleoptera, Coccinellidae) in China.},
journal = {ZooKeys},
volume = {953},
number = {},
pages = {49-60},
pmid = {32821195},
issn = {1313-2989},
abstract = {Oomyzus spiraculus Song, Fei &amp; Cao sp. nov. (Hymenoptera, Eulophidae) is described and illustrated as a gregarious larval-pupal endoparasitoid of Coccinella septempunctata L. (Coleoptera, Coccinellidae). Differentiation between O. spiraculus and its similar species is discussed and a key to differentiate the female and male of these species is provided. DNA barcodes of O. spiraculus and O. scaposus are analyzed and compared.},
}
@article {pmid32821193,
year = {2020},
author = {Wesener, T},
title = {Ecotone shifts in southern Madagascar: first barcoding data and six new species of the endemic millipede genus Riotintobolus (Spirobolida, Pachybolidae).},
journal = {ZooKeys},
volume = {953},
number = {},
pages = {1-29},
pmid = {32821193},
issn = {1313-2989},
abstract = {Six new species of the Spirobolida millipede genus Riotintobolus Wesener, 2009, are described from the spiny forest in southern Madagascar utilising genetic barcoding, drawings and scanning electron microscopy: Riotintobolus tsimelahy sp. nov., R. mangatsiaka sp. nov., R. lavanono sp. nov., R. bovinus sp. nov., R. antafoky sp. nov. and R. makayi sp. nov. One other Riotintobolus population from the spiny forest might represent an additional species based on genetic data, but it cannot be described as no male specimens were collected. At present, the genus Riotintobolus Wesener, 2009 has eight species from the spiny forest and two species from the littoral rainforest. A determination key to all ten species of the genus is provided. Molecular data reveal that the two critically endangered species from the humid littoral rainforest are not closely related to one another, but have their closest relative in the dry spiny forest ecosystem. Riotintobolus mandenensis Wesener, 2009, only known from the southern littoral rainforest of Mandena is related to R. tsimelahy sp. nov. from the nearby spiny forest at Tsimelahy with a p-distance of 11%, while R. minutus Wesener, 2009 from the littoral forest of Sainte Luce is more distant to all other Riotintobolus species, but more closely related to R. bovinus sp. nov. from the southwestern forest of the Makay.},
}
@article {pmid32820574,
year = {2020},
author = {Min, S and Jeon, YS and Jung, HJ and Khatua, C and Li, N and Bae, G and Choi, H and Hong, H and Shin, JE and Ko, MJ and Ko, HS and Jun, I and Fu, HE and Kim, SH and Thangam, R and Song, JJ and Dravid, VP and Kim, YK and Kang, H},
title = {Independent Tuning of Nano-Ligand Frequency and Sequences Regulates the Adhesion and Differentiation of Stem Cells.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {32},
number = {40},
pages = {e2004300},
doi = {10.1002/adma.202004300},
pmid = {32820574},
issn = {1521-4095},
support = {//National Research Foundation of Korea/ ; 2020R1C1C1011038//MSIT/ ; 2019R1A2C3006587//MSIT/ ; NSF ECCS-1542205//Soft and Hybrid Nanotechnology Experimental/ ; NSF DMR-1720139//MRSEC IRG2/ ; },
mesh = {Cell Adhesion/*drug effects ; Cell Differentiation/*drug effects ; Cell Line ; Extracellular Matrix/drug effects/metabolism ; Gold/chemistry ; Humans ; Iron/chemistry ; Ligands ; Nanotechnology/*methods ; Oligopeptides/chemistry/pharmacology ; Stem Cells/*cytology/*drug effects ; },
abstract = {The native extracellular matrix (ECM) can exhibit heterogeneous nano-sequences periodically displaying ligands to regulate complex cell-material interactions in vivo. Herein, an ECM-emulating heterogeneous barcoding system, including ligand-bearing Au and ligand-free Fe nano-segments, is developed to independently present tunable frequency and sequences in nano-segments of cell-adhesive RGD ligand. Specifically, similar exposed surface areas of total Fe and Au nano-segments are designed. Fe segments are used for substrate coupling of nanobarcodes and as ligand-free nano-segments and Au segments for ligand coating while maintaining both nanoscale (local) and macroscale (total) ligand density constant in all groups. Low nano-ligand frequency in the same sequences and terminally sequenced nano-ligands at the same frequency independently facilitate focal adhesion and mechanosensing of stem cells, which are collectively effective both in vitro and in vivo, thereby inducing stem cell differentiation. The Fe/RGD-Au nanobarcode implants exhibit high stability and no local and systemic toxicity in various tissues and organs in vivo. This work sheds novel insight into designing biomaterials with heterogeneous nano-ligand sequences at terminal sides and/or low frequency to facilitate cellular adhesion. Tuning the electrodeposition conditions can allow synthesis of unlimited combinations of ligand nano-sequences and frequencies, magnetic elements, and bioactive ligands to remotely regulate numerous host cells in vivo.},
}
@article {pmid32815545,
year = {2020},
author = {Harjes, J and Link, A and Weibulat, T and Triebel, D and Rambold, G},
title = {FAIR digital objects in environmental and life sciences should comprise workflow operation design data and method information for repeatability of study setups and reproducibility of results.},
journal = {Database : the journal of biological databases and curation},
volume = {2020},
number = {},
pages = {},
pmid = {32815545},
issn = {1758-0463},
mesh = {Computational Biology ; *Databases, Factual ; *Information Dissemination ; Reproducibility of Results ; *Research Design ; *Software ; Workflow ; },
abstract = {Repeatability of study setups and reproducibility of research results by underlying data are major requirements in science. Until now, abstract models for describing the structural logic of studies in environmental sciences are lacking and tools for data management are insufficient. Mandatory for repeatability and reproducibility is the use of sophisticated data management solutions going beyond data file sharing. Particularly, it implies maintenance of coherent data along workflows. Design data concern elements from elementary domains of operations being transformation, measurement and transaction. Operation design elements and method information are specified for each consecutive workflow segment from field to laboratory campaigns. The strict linkage of operation design element values, operation values and objects is essential. For enabling coherence of corresponding objects along consecutive workflow segments, the assignment of unique identifiers and the specification of their relations are mandatory. The abstract model presented here addresses these aspects, and the software DiversityDescriptions (DWB-DD) facilitates the management of thusly connected digital data objects and structures. DWB-DD allows for an individual specification of operation design elements and their linking to objects. Two workflow design use cases, one for DNA barcoding and another for cultivation of fungal isolates, are given. To publish those structured data, standard schema mapping and XML-provision of digital objects are essential. Schemas useful for this mapping include the Ecological Markup Language, the Schema for Meta-omics Data of Collection Objects and the Standard for Structured Descriptive Data. Data pipelines with DWB-DD include the mapping and conversion between schemas and functions for data publishing and archiving according to the Open Archival Information System standard. The setting allows for repeatability of study setups, reproducibility of study results and for supporting work groups to structure and maintain their data from the beginning of a study. The theory of 'FAIR++' digital objects is introduced.},
}
@article {pmid32813726,
year = {2020},
author = {Martín, MP and Daniëls, PP and Erickson, D and Spouge, JL},
title = {Figures of merit and statistics for detecting faulty species identification with DNA barcodes: A case study in Ramaria and related fungal genera.},
journal = {PloS one},
volume = {15},
number = {8},
pages = {e0237507},
pmid = {32813726},
issn = {1932-6203},
mesh = {Bayes Theorem ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/*analysis ; DNA, Ribosomal Spacer/*analysis ; Fungi/*classification/*genetics ; Models, Statistical ; Phylogeny ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
abstract = {DNA barcoding can identify biological species and provides an important tool in diverse applications, such as conserving species and identifying pathogens, among many others. If combined with statistical tests, DNA barcoding can focus taxonomic scrutiny onto anomalous species identifications based on morphological features. Accordingly, we put nonparametric tests into a taxonomic context to answer questions about our sequence dataset of the formal fungal barcode, the nuclear ribosomal internal transcribed spacer (ITS). For example, does DNA barcoding concur with annotated species identifications significantly better if expert taxonomists produced the annotations? Does species assignment improve significantly if sequences are restricted to lengths greater than 500 bp? Both questions require a figure of merit to measure of the accuracy of species identification, typically provided by the probability of correct identification (PCI). Many articles on DNA barcoding use variants of PCI to measure the accuracy of species identification, but do not provide the variants with names, and the absence of explicit names hinders the recognition that the different variants are not comparable from study to study. We provide four variant PCIs with a name and show that for fixed data they follow systematic inequalities. Despite custom, therefore, their comparison is at a minimum problematic. Some popular PCI variants are particularly vulnerable to errors in species annotation, insensitive to improvements in a barcoding pipeline, and unable to predict identification accuracy as a database grows, making them unsuitable for many purposes. Generally, the Fractional PCI has the best properties as a figure of merit for species identification. The fungal genus Ramaria provides unusual taxonomic difficulties. As a case study, it shows that a good taxonomic background can be combined with the pertinent summary statistics of molecular results to improve the identification of doubtful samples, linking both disciplines synergistically.},
}
@article {pmid32808922,
year = {2020},
author = {Bouguerche, C and Tazerouti, F and Gey, D and Justine, JL},
title = {No vagina, one vagina, or multiple vaginae? An integrative study of Pseudaxine trachuri (Monogenea, Gastrocotylidae) leads to a better understanding of the systematics of Pseudaxine and related genera.},
journal = {Parasite (Paris, France)},
volume = {27},
number = {},
pages = {50},
pmid = {32808922},
issn = {1776-1042},
mesh = {Algeria ; Animals ; *Classification ; Female ; France ; Male ; Perciformes/parasitology ; *Trematoda/anatomy &amp; histology/classification ; *Vagina/anatomy &amp; histology ; },
abstract = {The presence/absence and number of vaginae is a major characteristic for the systematics of the Monogenea. Three gastrocotylid genera share similar morphology and anatomy but are distinguished by this character: Pseudaxine Parona &amp; Perugia, 1890 has no vagina, Allogastrocotyle Nasir &amp; Fuentes Zambrano, 1983 has two vaginae, and Pseudaxinoides Lebedev, 1968 has multiple vaginae. In the course of a study of Pseudaxine trachuri Parona &amp; Perugia 1890, we found specimens with structures resembling "multiple vaginae"; we compared them with specimens without vaginae in terms of both morphology and molecular characterisitics (COI barcode), and found that they belonged to the same species. We also investigated the male copulatory organ (MCO) of this species, the accuracy of the original description of which is known to be a matter of debate. We found that the genital atrium is armed with 12 hooks arranged as a single circle and a central hollow stylet which is probably involved in traumatic insemination. We redescribed Pseudaxine trachuri based on newly collected specimens from off the coast of Algeria and Museum specimens from off France. Specimens from the type-host, Trachurus trachurus, were found to be similar, for both molecular sequences and morphology, to those found on Boops boops. We can therefore confirm, for the first time with molecular evidence, that B. boops is a host of this parasite. We consider that Pseudaxinoides was erected on the basis of an erroneous interpretation of structures which are not vaginae and, consequently, propose the transfer of most of its species to Pseudaxine, as P. australis (Lebedev, 1968) n. comb., P. bychowskyi (Lebedev, 1977) n. comb., P. caballeroi (Lebedev, 1977) n. comb., P. cariacoensis (Nasir &amp; Fuentes-Zambrano, 1983) n. comb., and P. vietnamensis (Lebedev, Parukhin &amp; Roitman, 1970) n. comb. We also propose Allogastrocotyle dillonhargisorum nom. nov. for Pseudaxine bivaginalis Dillon &amp; Hargis, 1965 to avoid a secondary homonymy.},
}
@article {pmid32804944,
year = {2020},
author = {Ong, WK and Courtney, DK and Pan, S and Andrade, RB and Kiley, PJ and Pfleger, BF and Reed, JL},
title = {Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4.},
journal = {PLoS computational biology},
volume = {16},
number = {8},
pages = {e1008137},
pmid = {32804944},
issn = {1553-7358},
support = {T32 GM008349/GM/NIGMS NIH HHS/United States ; },
mesh = {Anaerobiosis ; Genetic Fitness/*genetics ; Genome, Bacterial/*genetics ; Metabolic Engineering ; *Models, Genetic ; Mutation/*genetics ; *Zymomonas/genetics/metabolism ; },
abstract = {Genome-scale metabolic models have been utilized extensively in the study and engineering of the organisms they describe. Here we present the analysis of a published dataset from pooled transposon mutant fitness experiments as an approach for improving the accuracy and gene-reaction associations of a metabolic model for Zymomonas mobilis ZM4, an industrially relevant ethanologenic organism with extremely high glycolytic flux and low biomass yield. Gene essentiality predictions made by the draft model were compared to data from individual pooled mutant experiments to identify areas of the model requiring deeper validation. Subsequent experiments showed that some of the discrepancies between the model and dataset were caused by polar effects, mis-mapped barcodes, or mutants carrying both wild-type and transposon disrupted gene copies-highlighting potential limitations inherent to data from individual mutants in these high-throughput datasets. Therefore, we analyzed correlations in fitness scores across all 492 experiments in the dataset in the context of functionally related metabolic reaction modules identified within the model via flux coupling analysis. These correlations were used to identify candidate genes for a reaction in histidine biosynthesis lacking an annotated gene and highlight metabolic modules with poorly correlated gene fitness scores. Additional genes for reactions involved in biotin, ubiquinone, and pyridoxine biosynthesis in Z. mobilis were identified and confirmed using mutant complementation experiments. These discovered genes, were incorporated into the final model, iZM4_478, which contains 747 metabolic and transport reactions (of which 612 have gene-protein-reaction associations), 478 genes, and 616 unique metabolites, making it one of the most complete models of Z. mobilis ZM4 to date. The methods of analysis that we applied here with the Z. mobilis transposon mutant dataset, could easily be utilized to improve future genome-scale metabolic reconstructions for organisms where these, or similar, high-throughput datasets are available.},
}
@article {pmid32803835,
year = {2021},
author = {Ba Abduallah, MM and Hemida, MG},
title = {Comparative analysis of the genome structure and organization of the Middle East respiratory syndrome coronavirus (MERS-CoV) 2012 to 2019 revealing evidence for virus strain barcoding, zoonotic transmission, and selection pressure.},
journal = {Reviews in medical virology},
volume = {31},
number = {1},
pages = {1-12},
pmid = {32803835},
issn = {1099-1654},
support = {20-0004//King Abdul-Aziz City for Science and Technology (KACST)/International ; },
mesh = {Animals ; Camelus/*virology ; Coronavirus Infections/*epidemiology/transmission/*veterinary ; DNA Barcoding, Taxonomic ; Genome, Viral/genetics ; Humans ; Middle East Respiratory Syndrome Coronavirus/*genetics ; Polyproteins/genetics ; Saudi Arabia/epidemiology ; Spike Glycoprotein, Coronavirus/genetics ; Viral Envelope Proteins/genetics ; },
abstract = {The Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in late 2012 in Saudi Arabia. For this study, we conducted a large-scale comparative genome study of MERS-CoV from both human and dromedary camels from 2012 to 2019 to map any genetic changes that emerged in the past 8 years. We downloaded 1309 submissions, including 308 full-length genome sequences of MERS-CoV available in GenBank from 2012 to 2019. We used bioinformatics tools to describe the genome structure and organization of the virus and to map the most important motifs within various regions/genes throughout the genome over the past 8 years. We also monitored variations/mutations among these sequences since its emergence. Our phylogenetic analyses suggest that the cluster within African camels is derived by S gene. We identified some prominent motifs within the ORF1ab, S gene and ORF-5, which may be used for barcoding the African camel lineages of MERS-CoV. Furthermore, we mapped some sequence patterns that support the zoonotic origin of the virus from dromedary camels. Other sequences identified selection pressures, particularly within the N gene and the 5' UTR. Further studies are required for careful monitoring of the MERS-CoV genome to identify any potential significant mutations in the future.},
}
@article {pmid32802898,
year = {2020},
author = {Ogunlaja, A and Sharma, V and Ghai, M and Lin, J},
title = {Molecular characterization and DNA methylation profile of Libyodrilus violaceous from oil polluted soil.},
journal = {Molecular biology research communications},
volume = {9},
number = {2},
pages = {45-53},
pmid = {32802898},
issn = {2345-2005},
abstract = {Studies on earthworms using molecular markers are rare in Africa except a handful from South Africa. Reports on Libyodrilus violaceous, an earthworm found in West Africa are available including their metal tolerance and bioaccumulation capacity but their molecular characterization and ecotoxicology studies are scarce. In this study, triplicate L. violaceous specimens were collected from four locations within a petroleum polluted site and one in a control site, ≃1Km away from point of spill. DNA was extracted and 18S rRNA and 16S rRNA genes were amplified and sequenced. DNA methylation of their 18S rRNA gene was determined using Methylation specific PCR (MSP) method. Phylogenetic trees generated for 18S rRNA and 16S rRNA genes grouped L. violaceous within the Eudrilidae family concurrent with its conventional grouping and MSP results indicate no methylation in L. violaceous population from this site.},
}
@article {pmid32800126,
year = {2020},
author = {Hilton, SH and Hall, C and Nguyen, HT and Everitt, ML and DeShong, P and White, IM},
title = {Phenotypically distinguishing ESBL-producing pathogens using paper-based surface enhanced Raman sensors.},
journal = {Analytica chimica acta},
volume = {1127},
number = {},
pages = {207-216},
pmid = {32800126},
issn = {1873-4324},
support = {T32 CA154274/CA/NCI NIH HHS/United States ; },
mesh = {Anti-Bacterial Agents/pharmacology ; *Escherichia coli ; *Escherichia coli Infections ; Humans ; Microbial Sensitivity Tests ; beta-Lactamases ; },
abstract = {Antimicrobial stewardship practices are critical in preventing the further erosion of treatment options for bacterial infections. Yet, at the same time, determination of an infection's antimicrobial susceptibility requires multiple rounds of culture and expensive lab automation systems. In this work, we report the use of paper-based surface enhanced Raman spectroscopy (SERS) sensors and portable instrumentation to phenotypically discriminate multi-drug resistance with fewer culture steps than conventional clinical microbiology. Specifically, we demonstrate the identification of resistance to varying generations of β-lactam antibiotics by detecting the activity of particular β-lactamase enzymes in a multiplexed assay. The method utilizes molecular reporters that consist of β-lactams with SERS barcodes. Hydrolysis of the β-lactam by β-lactamase enzymes in the sample expels the barcode; the released sulfur-containing barcode is then detected via SERS. Using this approach, we demonstrate the differentiation of E. coli strains with (1) extended spectrum β-lactamase (ESBL), (2) narrow-spectrum β-lactamase, and (3) no resistance, using only a single measurement on a single sample. In addition, we experimentally validate an approach to expand the library of reporters through the simple chemical synthesis of new barcoded β-lactams. Importantly, the reported method determines the susceptibility based on phenotypic β-lactamase activity, which is aligned with current microbiology lab standards. This new method will enable the precise selection of effective β-lactam antibiotics (as opposed to defaulting to drugs of last resort) faster than current methods while using simple steps and low-cost portable instrumentation.},
}
@article {pmid32799680,
year = {2020},
author = {Da Silva Sanchez, A and Paunovska, K and Cristian, A and Dahlman, JE},
title = {Treating Cystic Fibrosis with mRNA and CRISPR.},
journal = {Human gene therapy},
volume = {31},
number = {17-18},
pages = {940-955},
pmid = {32799680},
issn = {1557-7422},
support = {T32 GM008433/GM/NIGMS NIH HHS/United States ; UG3 TR002855/TR/NCATS NIH HHS/United States ; UH3 TR002855/TR/NCATS NIH HHS/United States ; R01 GM132985/GM/NIGMS NIH HHS/United States ; },
mesh = {*CRISPR-Cas Systems ; Cystic Fibrosis/genetics/*therapy ; Cystic Fibrosis Transmembrane Conductance Regulator/*genetics ; Gene Editing/*methods ; Genetic Therapy/*methods ; Humans ; RNA, Messenger/*administration &amp; dosage/genetics ; },
abstract = {Less than 20% of the protein coding genome is thought to be targetable using small molecules. mRNA therapies are not limited in the same way since in theory, they can silence or edit any gene by encoding CRISPR nucleases, or alternatively, produce any missing protein. Yet not all mRNA therapies are equally likely to succeed. Over the past several years, an increasing number of clinical trials with siRNA- and antisense oligonucleotide-based drugs have revealed three key concepts that will likely extend to mRNA therapies delivered by nonviral systems. First, scientists have come to understand that some genes make better targets for RNA therapies than others. Second, scientists have learned that the type and position of chemical modifications made to an RNA drug can alter its therapeutic window, toxicity, and bioavailability. Third, scientists have found that safe and targeted drug delivery vehicles are required to ferry mRNA therapies into diseased cells. In this study, we apply these learnings to cystic fibrosis (CF). We also describe lessons learned from a subset of CF gene therapies that have already been tested in patients. Finally, we highlight the scientific advances that are still required for nonviral mRNA- or CRISPR-based drugs to treat CF successfully in patients.},
}
@article {pmid32798690,
year = {2020},
author = {Martyniuk, CJ},
title = {Perspectives on transcriptomics in animal physiology studies.},
journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology},
volume = {250},
number = {},
pages = {110490},
doi = {10.1016/j.cbpb.2020.110490},
pmid = {32798690},
issn = {1879-1107},
mesh = {Animals ; *Gene Expression Profiling ; Humans ; Physiology/*methods ; },
abstract = {Reductionist approaches in physiology and biochemistry are essential for understanding how animals cope and adapt to their environments. Transcriptomics is no longer restricted to a select few, and accessibility and affordability continue to facilitate its rapid growth as a science. More than 6000 publications (a conservative estimate) over the past decade quantify the response of the transcriptome to a wide breadth of questions in animal physiology. Transcriptomes have been quantified under conditions of hypoxia, climate change, salinity, drought, environmental pollution, and ultraviolet radiation among others; these studies have greatly improved understanding of the molecular machinery required for organismal adaptation. These "snapshots in time" however are never complete as the transcriptome is exquisitely sensitive to an individual's current physiologic state. Animal physiologists new to the field must recognize limitations of transcriptome technologies and consider experimental designs that strengthen physiologic interpretation. Current estimates suggest that a sample size of 6 or more are required for RNA-seq experiments in order to capture the majority of differentially expressed genes confidently. "Outside-the-box" approaches for statistical analyses of data derived from RNA-seq should be explored, as studies continue to point out that high false discoveries rates are pervasive with RNA-seq studies, reminiscent of the early days of microarrays. Incorporating biological variability, rather than reducing it (i.e. pooling strategies), into experimental designs is essential. Moreover, real-time PCR must not be viewed as a "validation step" to justify low samples sizes, but rather an orthogonal method to strengthen biological interpretation. The use of proper experimental controls in transcriptomics studies (i.e. spike-in controls and technical replication) are recommended and there is a pressing need for inter-laboratory tests (round robin experiments) to quantify repeatability and to identify sources of transcriptome variation within the context of animal physiology. Testing the reproducibility of transcriptome experiments in light of physiology in non-model organisms would be a significant contribution to the community. Single cell transcriptomics and multiplexing barcoding strategies such as decode-seq are poised to further advance the reductionist view of animal physiology; researchers are encouraged to consult literature herein and elsewhere for guidance on best practices and limitations of transcriptome technologies when studying the physiology of animals.},
}
@article {pmid32798614,
year = {2020},
author = {Mao, R and He, Z},
title = {Pinellia ternata (Thunb.) Breit: A review of its germplasm resources, genetic diversity and active components.},
journal = {Journal of ethnopharmacology},
volume = {263},
number = {},
pages = {113252},
doi = {10.1016/j.jep.2020.113252},
pmid = {32798614},
issn = {1872-7573},
mesh = {Alkaloids/genetics/isolation &amp; purification ; Animals ; China/ethnology ; Chromatography, High Pressure Liquid/methods ; Genetic Variation/*genetics ; Humans ; Japan/ethnology ; Pinellia/*genetics ; Plants, Medicinal/*genetics ; Republic of Korea/ethnology ; Seeds/*genetics ; },
abstract = {The medicinal plant Pinellia ternata has been widely used in China, Korea, and Japan and has been demonstrated to be highly effective for treating cough, vomiting, infection, and inflammatory diseases. Modern pharmacological investigations have demonstrated its multiple activities, such as antitussive, expectorant, antiemetic, antitumor, antibacterial, and sedative-hypnotic activities.<br><br>AIM OF THE REVIEW: This review aims to summarize the information about the biological traits, genetic diversity, active components, and continuous cropping obstacle of P. ternata in order to improve its use.<br><br>MATERIALS AND METHODS: In this review, the relevant literature was gathered by using Pinellia ternata, genetic diversity, active components, and continuous cropping obstacle as the keywords from Google Scholar, PubMed, Springer Link, the Wiley online library, SciFinder, SCOPUS, Baidu Scholar, China national knowledge infrastructure (CNKI), and WANFANF DATA (up to April 2020).<br><br>RESULTS: P. ternata is the most widely used herb in the Pinellia genus to treat several diseases. The genetic diversity of P. ternata has been extensively studied, and its high genetic diversity level in China has been demonstrated. Modern pharmacological research has indicated that amino acids, alkaloids, and polysaccharides are the main active components supporting P. ternata's medicinal effects. However, an efficient method for determining its active components is still unavailable. The method used to evaluate Pinelliae Rhizoma (PR) quality standards should be further optimized. The continuous cropping obstacle has a significant effect on the quantity and quality of P. ternata. The underlying mechanism of the continuous cropping obstacle needs to be further explored.<br><br>CONCLUSIONS: P. ternata has emerged as a valuable source of traditional medicine. Some uses of P. ternata in medicine have been validated by pharmacological investigations. However, a more efficient analytical method should be established to evaluate the quality of PR based on multiple quality markers. Furthermore, high-performance liquid chromatography (HPLC) and DNA barcoding should be introduced to identify the authenticity of PR. In addition, the genes involved in the metabolic synthesis pathways of the main active components, population genetic relationships, the quality control of processed PR, and the continuous cropping obstacle need to be further elucidated. We hope this review will allow for better utilization of this valuable herb.},
}
@article {pmid32797323,
year = {2020},
author = {Amar, MH},
title = {ycf1-ndhF genes, the most promising plastid genomic barcode, sheds light on phylogeny at low taxonomic levels in Prunus persica.},
journal = {Journal, genetic engineering &amp; biotechnology},
volume = {18},
number = {1},
pages = {42},
pmid = {32797323},
issn = {2090-5920},
abstract = {BACKGROUND: Chloroplast genome sequencing is becoming a valuable process for developing several DNA barcodes. At present, plastid DNA barcode for systematics and evolution in flowering plant rely heavily on the use of non-coding genes. The present study was performed to verify the novelty and suitability of the two hotspot barcode plastid coding gene ycf1 and ndhF, to estimate the rate of molecular evolution in the Prunus genus at low taxonomic levels.<br><br>RESULTS: Here, 25 chloroplast genomes of Prunus genus were selected for sequences annotation to search for the highly variable coding DNA barcode regions. Among them, 5 genera were of our own data, including the ornamental, cultivated, and wild haplotype, while 20 genera have been downloaded from the GenBank database. The results indicated that the two hotspot plastid gene ycf1 and ndhF were the most variable regions within the coding genes in Prunus with an average of 3268 to 3416 bp in length, which have been predicted to have the highest nucleotide diversity, with the overall transition/transversion bias (R = 1.06). The ycf1-ndhF structural domains showed a positive trend evident in structure variation among the 25 specimens tested, due to the variant overlap[']s gene annotation and insertion or deletion with a broad trend of the full form of IGS sequence. As a result, the principal component analysis (PCA) and the ML tree data drew an accurate monophyletic annotations cluster in Prunus species, offering unambiguous identification without overlapping groups between peach, almond, and cherry.<br><br>CONCLUSION: To this end, we put forward the domain of the two-locus ycf1-ndhF genes as the most promising coding plastid DNA barcode in P. persica at low taxonomic levels. We believe that the discovering of further variable loci with high evolutionary rates is extremely useful and potential uses as a DNA barcode in P. persica for further phylogeny study and species identification.},
}
@article {pmid32796084,
year = {2020},
author = {Westbrook, JI and Sunderland, NS and Woods, A and Raban, MZ and Gates, P and Li, L},
title = {Changes in medication administration error rates associated with the introduction of electronic medication systems in hospitals: a multisite controlled before and after study.},
journal = {BMJ health &amp; care informatics},
volume = {27},
number = {3},
pages = {},
pmid = {32796084},
issn = {2632-1009},
mesh = {*Drug Administration Schedule ; Efficiency, Organizational ; Hospitals, Teaching/*organization &amp; administration ; Humans ; *Medication Errors/prevention &amp; control/statistics &amp; numerical data ; *Medication Systems, Hospital ; *Pharmaceutical Preparations ; },
abstract = {BACKGROUND: Electronic medication systems (EMS) have been highly effective in reducing prescribing errors, but little research has investigated their effects on medication administration errors (MAEs).<br><br>OBJECTIVE: To assess changes in MAE rates and types associated with EMS implementation.<br><br>METHODS: This was a controlled before and after study (three intervention and three control wards) at two adult teaching hospitals. Intervention wards used an EMS with no bar-coding. Independent, trained observers shadowed nurses and recorded medications administered and compliance with 10 safety procedures. Observational data were compared against medication charts to identify errors (eg, wrong dose). Potential error severity was classified on a 5-point scale, with those scoring &#x2265;3 identified as serious. Changes in MAE rates preintervention and postintervention by study group, accounting for differences at baseline, were calculated.<br><br>RESULTS: 7451 administrations were observed (4176 pre-EMS and 3275 post-EMS). At baseline, 30.2% of administrations contained &#x2265;1 MAE, with wrong intravenous rate, timing, volume and dose the most frequent. Post-EMS, MAEs decreased on intervention wards relative to control wards by 4.2 errors per 100 administrations (95% CI 0.2 to 8.3; p=0.04). Wrong timing errors alone decreased by 3.4 per 100 administrations (95% CI 0.01 to 6.7; p<0.05). EMS use was associated with an absolute decline in potentially serious MAEs by 2.4% (95% CI 0.8 to 3.9; p=0.003), a 56% reduction in the proportion of potentially serious MAEs. At baseline, 74.1% of administrations were non-compliant with &#x2265;1 of 10 procedures and this rate did not significantly improve post-EMS.<br><br>CONCLUSIONS: Implementation of EMS was associated with a modest, but significant, reduction in overall MAE rate, but halved the proportion of MAEs rated as potentially serious.},
}
@article {pmid32788954,
year = {2020},
author = {Afriyie, G and Wang, Z and Dong, Z and Ayisi Larbi, C and Asiedu, B and Guo, Y},
title = {Complete mitochondrial genome and assembled DNA barcoding analysis of Lutjanus fulgens (Valenciennes, 1830) and its comparison with other Lutjanus species.},
journal = {Ecology and evolution},
volume = {10},
number = {15},
pages = {7971-7980},
pmid = {32788954},
issn = {2045-7758},
abstract = {Lutjanus fulgens (Valenciennes, 1830) is a teleost species classified under the family Lutjanidae which is a native of the Eastern Atlantic Ocean. Though highly commercialized due to its abundance and good taste, the production output has declined in recent years. This is an indication of the need for effective management and conservation measures. However, accurate species identification will ensure strategic management and conservation measure. DNA-based species identification has proven its reliability in this regard via precise species identification. Several researchers have confirmed the accuracy of DNAbarcode as a species identification tool as well as species phylogeny analysis based on both the complete mitogenome and COI gene. Currently, nine specimens of L. fulgens were sampled from Ghana and subjected to DNA-based analysis, namely, complete mitochondrial DNAand COI gene (DNA barcoding) analyses. The mitogenomic result revealed that L. fulgens is made up of a 16,500 base pairs (bp) mtDNA which consists of 22 transfer RNAs, 13 protein-coding genes, and two ribosomal RNAs (GenBank Accession Number: MN398650). Furthermore, a sequence polymorphism analysis of the COIgene (MN986442-MN986450) detected two haplotypes. These haplotypes were both collected from the same fish landing site which suggests a possible cryptic linage diversity in the L. fulgens population at Vodza. According to the phylogeny examination, a close taxonomic relationship exists between L. fulgens and Lutjanus buccanella caused by a recent evolution termed as sympatric speciation. This study serves as a novel study for this species, building the foundation for future molecular-based study for this species and as a DNA barcode reference data.},
}
@article {pmid32787940,
year = {2020},
author = {Kuchboev, A and Sobirova, K and Karimova, R and Amirov, O and von Samson-Himmelstjerna, G and Krücken, J},
title = {Molecular analysis of polymorphic species of the genus Marshallagia (Nematoda: Ostertagiinae).},
journal = {Parasites &amp; vectors},
volume = {13},
number = {1},
pages = {411},
pmid = {32787940},
issn = {1756-3305},
support = {57313677//Deutscher Akademischer Austauschdienst/ ; FA-&#x410;8-T004//Academy of Sciences Republic of Uzbekistan/ ; },
mesh = {Animals ; Classification ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Genes, Helminth ; Genitalia, Male/anatomy &amp; histology ; Male ; *Nematoda/anatomy &amp; histology/classification/genetics ; Nematode Infections/veterinary ; Pathology, Molecular ; Phylogeny ; Ruminants/*parasitology ; Sheep/parasitology ; Uzbekistan ; },
abstract = {BACKGROUND: The genus Marshallagia (Family Haemonchidae, subfamily Ostertagiinae) contains multiple species of nematodes parasitising the abomasum (or duodenum) of ruminants, in particular of Caprinae. Male specimens have been described to be polymorphic with the frequent/major morphotype initially described in the genus Marshallagia while the minor/rare morphotype was initially often placed in the genus Grossospicularia. Due to common morphological features, certain pairs of morphotypes were suggested to belong to the same species such as Marshallagia marshalli/M. occidentalis. However, molecular evidence to confirm these pairs of morphotypes belonging to the same species is missing.<br><br>METHODS: In the present study, Marshallagia sp. were collected from domestic sheep in Uzbekistan. Male specimens were morphologically described with particular emphasis on the structure of the bursa copulatrix. After DNA isolation from morphologically identified specimens, PCRs targeting the ribosomal internal transcribed spacer 2 (ITS2) and mitochondrial cytochrome c oxidase subunit 1 (cox1) regions were conducted. After Sanger sequencing, maximum likelihood phylogenetic analyses and pairwise identities between sequences were calculated.<br><br>RESULTS: The major morphotypes of M. marshalli, M. schumakovitschi and M. uzbekistanica and the minor morphotypes M. occidentalis, M. trifida and M. sogdiana were identified and their morphology was documented in detail. ITS2 sequences showed little variation and did not allow diagnosing species. In contrast, phylogenetic analysis of cox1 sequences identified highly supported clusters and verified that M. marshalli, M. occidentalis and M. uzbekistanica are different morphotypes of the species M. marshalli while M. schumakovitschi and M. trifida represent distinct morphotypes of M. trifida. For M. sogdiana no corresponding major morphotype could be identified in the present study. Due to a large barcoding gap, comparison of cox1 sequences in terms of percent identity was sufficient to reliably assign the sequences to a particular species without phylogenetic analysis.<br><br>CONCLUSIONS: The data presented here create a framework that will allow the classification of other members of the genus in the future and underline that parallel morphological and molecular analysis of specimens is crucial to improve the taxonomy of polymorphic species.},
}
@article {pmid32786110,
year = {2021},
author = {Erickson, KL and Pentico, A and Quattrini, AM and McFadden, CS},
title = {New approaches to species delimitation and population structure of anthozoans: Two case studies of octocorals using ultraconserved elements and exons.},
journal = {Molecular ecology resources},
volume = {21},
number = {1},
pages = {78-92},
doi = {10.1111/1755-0998.13241},
pmid = {32786110},
issn = {1755-0998},
support = {1457817//National Science Foundation/ ; 1457581//National Science Foundation/ ; },
mesh = {Animals ; *Anthozoa/classification/genetics ; Biological Evolution ; *Exons ; *Genetics, Population ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {As coral populations decline worldwide in the face of ongoing environmental change, documenting their distribution, diversity and conservation status is now more imperative than ever. Accurate delimitation and identification of species is a critical first step. This task, however, is not trivial as morphological variation and slowly evolving molecular markers confound species identification. New approaches to species delimitation in corals are needed to overcome these challenges. Here, we test whether target enrichment of ultraconserved elements (UCEs) and exons can be used for delimiting species boundaries and population structure within species of corals by focusing on two octocoral genera, Alcyonium and Sinularia, as exemplary case studies. We designed an updated bait set (29,181 baits) to target-capture 3,023 UCE and exon loci, recovering a mean of 1,910 ± 168 SD per sample with a mean length of 1,055 ± 208 bp. Similar numbers of loci were recovered from Sinularia (1,946 ± 227 SD) and Alcyonium (1,863 ± 177 SD). Species-level phylogenies were highly supported for both genera. Clustering methods based on filtered single nucleotide polymorphisms delimited species and populations that are congruent with previous allozyme, DNA barcoding, reproductive and ecological data for Alcyonium, and offered further evidence of hybridization among species. For Sinularia, results were congruent with those obtained from a previous study using restriction site associated DNA sequencing. Both case studies demonstrate the utility of target-enrichment of UCEs and exons to address a wide range of evolutionary and taxonomic questions across deep to shallow timescales in corals.},
}
@article {pmid32785466,
year = {2021},
author = {Karamat, S and Ashraf, N and Akhtar, T and Rahim, F and Shafi, N and Khalid, S and Shahid, B and Khawaja, S and Rahim, J and Majeed, Z and Lateef, Z and Mehmood, M},
title = {CO1-Based DNA barcoding for assessing diversity of Pteropus giganteus from the state of Azad Jammu Kashmir, Pakistan.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {81},
number = {3},
pages = {584-591},
doi = {10.1590/1519-6984.226466},
pmid = {32785466},
issn = {1678-4375},
mesh = {Animals ; *Chiroptera/genetics ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; Haplotypes/genetics ; Pakistan ; },
abstract = {The flying fox (Pteropus giganteus) also familiar with the name of the greater Indian fruit Bat belongs to the order Chiroptera and family Pteropodidae. Current research emphasis on the DNA barcoding of P. giganteus in Azad Jammu Kashmir. Bat sequences were amplified and PCR products were sequenced and examined by bioinformatics software. Congeneric and conspecific, nucleotide composition and K2P nucleotide deviation, haplotype diversity and the number of haplotypes were estimated. The analysis showed that all of the five studied samples of P. giganteus had low G contents (G 19.8%) than C (27.8%), A (25.1%) and T (27.3%) contents. The calculated haplotype diversity was 0.60% and the mean intraspecific K2P distance was 0.001% having a high number of transitional substitutions. The study suggested that P. giganteus (R=0.00) do not deviate from the neutral evolution. It was determined from the conclusion that this mtDNA gene is a better marker for identification of Bat species than nuclear genes due to its distinctive characteristics and may serve as a landmark for the identification of interconnected species at the molecular level and in the determination of population genetics.},
}
@article {pmid32785184,
year = {2020},
author = {Kunej, U and Dervishi, A and Laucou, V and Jakše, J and Štajner, N},
title = {The Potential of HTS Approaches for Accurate Genotyping in Grapevine (Vitis vinifera L.).},
journal = {Genes},
volume = {11},
number = {8},
pages = {},
pmid = {32785184},
issn = {2073-4425},
mesh = {Alleles ; Computational Biology ; DNA, Plant ; Genetic Markers ; Genotype ; *Genotyping Techniques ; *High-Throughput Nucleotide Sequencing ; Microsatellite Repeats ; Polymerase Chain Reaction ; Quantitative Trait Loci ; Vitis/*classification/*genetics ; },
abstract = {The main challenge associated with genotyping based on conventional length polymorphisms is the cross-laboratory standardization of allele sizes. This step requires the inclusion of standards and manual sizing to avoid false results. Capillary electrophoresis (CE) approaches limit the information to the length polymorphism and do not allow the determination of a complete marker sequence. As an alternative, high-throughput sequencing (HTS) offers complete information regarding marker sequences and their flanking regions. In this work, we investigated the suitability of a semi-quantitative sequencing approach for microsatellite genotyping using Illumina paired-end technology. Twelve microsatellite loci that are well established for grapevine CE typing were analysed on 96 grapevine samples from six different countries. We redesigned primers to the length of the amplicon for short sequencing (~100 bp). The primer pair was flanked with a 10 bp overhang for the introduction of barcodes on both sides of the amplicon to enable high multiplexing. The highest data peaks were determined as simple sequence repeat (SSR) alleles and compared with the CE dataset based on 12 reference samples. The comparison showed that HTS SSR genotyping can successfully replace the CE system in further experiments. We believe that, with next-generation sequencing, genotyping can be improved in terms of its speed, accuracy, and price.},
}
@article {pmid32783885,
year = {2020},
author = {Pei, W and Shang, F and Wang, X and Fanti, AK and Greco, A and Busch, K and Klapproth, K and Zhang, Q and Quedenau, C and Sauer, S and Feyerabend, TB and Höfer, T and Rodewald, HR},
title = {Resolving Fates and Single-Cell Transcriptomes of Hematopoietic Stem Cell Clones by PolyloxExpress Barcoding.},
journal = {Cell stem cell},
volume = {27},
number = {3},
pages = {383-395.e8},
doi = {10.1016/j.stem.2020.07.018},
pmid = {32783885},
issn = {1875-9777},
mesh = {Cell Differentiation/genetics ; Cell Lineage/genetics ; Clone Cells ; Hematopoiesis/genetics ; *Hematopoietic Stem Cells ; *Transcriptome/genetics ; },
abstract = {Lineage tracing reveals hematopoietic stem cell (HSC) fates, while single-cell RNA sequencing identifies snapshots of HSC transcriptomes. To obtain information on fate plus transcriptome in the same cell, we developed the PolyloxExpress allele, enabling Cre-recombinase-dependent RNA barcoding in situ. Linking fates to single HSC transcriptomes provided the information required to identify transcriptional signatures of HSC fates, which were not apparent in single-HSC transcriptomes alone. We find that differentiation-inactive, multilineage, and lineage-restricted HSC clones reside in distinct regions of the transcriptional landscape of hematopoiesis. Differentiation-inactive HSC clones are closer to the origin of the transcriptional trajectory, yet they are not characterized by a quiescent gene signature. Fate-specific gene signatures imply coherence of clonal HSC fates, and HSC output toward short-lived lineage progenitors indicates stability of HSC fates over time. These combined analyses of fate and transcriptome under physiological conditions may pave the way toward identifying molecular determinants of HSC fates.},
}
@article {pmid32781419,
year = {2020},
author = {Seabra, SG and Pina-Martins, F and Marabuto, E and Yurtsever, S and Halkka, O and Quartau, JA and Paulo, OS},
title = {Corrigendum to "Molecular phylogeny and DNA barcoding in the meadow-spittlebug Philaenus spumarius (Hemiptera, Cercopidae) and its related species" [Mol. Phylogenet. Evol. 56 (2010) 462-467].},
journal = {Molecular phylogenetics and evolution},
volume = {152},
number = {},
pages = {106888},
doi = {10.1016/j.ympev.2020.106888},
pmid = {32781419},
issn = {1095-9513},
}
@article {pmid32779738,
year = {2020},
author = {Reis, VJC and Dos Santos, SA and Britto, MR and de Assis Volpi, T and de Pinna, MCC},
title = {Iterative taxonomy reveals a new species of Trichomycterus Valenciennes 1832 (Siluriformes, Trichomycteridae) widespread in Rio Doce basin: a pseudocryptic of T. immaculatus.},
journal = {Journal of fish biology},
volume = {97},
number = {6},
pages = {1607-1623},
doi = {10.1111/jfb.14490},
pmid = {32779738},
issn = {1095-8649},
support = {//CAPES (PROAP-MZUSP to V.J.C.R.); CAPES/PROEX (proc. 88882.183278/2018-01 to S.A.S.); CNPq (proc. #310688/2019-1 to M.C.C.P. and proc. #309285/2018-6 to M.R.B.); FAPESP (proc. 2015/26804 -4 to M.C.C.P. and 2016/25467 -7 to V.J.C.R.)/ ; },
mesh = {Animal Distribution ; Animals ; Brazil ; Catfishes/*anatomy &amp; histology/*classification ; Pigmentation ; Rivers ; Species Specificity ; Spine/anatomy &amp; histology ; },
abstract = {This paper reports on a new species of Trichomycterus from the Rio Doce basin. Unusually for new taxa in the genus during the past few decades, the new species is not narrowly endemic but instead widely distributed in its major drainage, the Rio Doce. The species has been collected and deposited in scientific collections for some years, but has been systematically misidentified as the more abundant Trichomycterus immaculatus or, to a lesser degree, as other morphologically similar species from south-eastern Brazil such as T. nigricans and T. pradensis. A combination of several morphological characteristics, such as vertebral number, pectoral-fin ray counts, pigmentation pattern and barcoding distance, were iteratively used and unambiguously distinguish the new species from all congeners. The present case reveals a pattern of diversity-discovery in which rare and narrowly endemic morphologically conspicuous species are discovered and described before visually inconspicuous taxa, even when the latter are more abundant and widespread. The morphological similarities among south-eastern Brazilian species with a uniform dark-grey color serve as basis for a brief discussion about the concepts of cryptic and pseudo-cryptic species in Trichomycterus and their consequences for potentially hidden diversity in the genus.},
}
@article {pmid32778978,
year = {2020},
author = {Ghareb, HE and Ibrahim, SD and Hegazi, GAE},
title = {In vitro propagation and DNA barcode analysis of the endangered Silene schimperiana in Saint Katherine protectorate.},
journal = {Journal, genetic engineering &amp; biotechnology},
volume = {18},
number = {1},
pages = {41},
pmid = {32778978},
issn = {2090-5920},
abstract = {BACKGROUND: Anthropogenic activity, climate change, pollution, and exploitation of natural resources are some reasons that cause threatening of plant diversity. Silene schimperiana is an endangered plant species in Egypt and is endemic to the high mountain of Saint Katherine Protected Area in southern Sinai. The purpose of the study was the ex situ conservation of Silene schimperiana through in vitro propagation and DNA barcode analysis.<br><br>RESULTS: To develop an efficient ex situ conservation program of the plant, in vitro propagation protocol has been achieved from shoot tip and stem nodal segment explants of in vitro germinated seedlings. Explants were established in vitro on Murashige and Skoog (MS) medium supplemented with 2.89&#x2009;&#x3bc;M gibberellic acid (GA3), 1.08&#x2009;&#x3bc;M &#x3b1;-naphthaleneacetic acid (NAA), and 1.16&#x2009;&#x3bc;M kinetin (Kin). The highest number of axillary shoots (9.27) was obtained when they were transferred to MS medium supplemented with 4.48&#x2009;&#x3bc;M 6-benzyl adenine (BA). Hundred percent of multiple axillary shoots were rooted on quarter-strength MS medium supplemented with 4.92&#x2009;&#x3bc;M indole-3-butyric acid (IBA) and 10.75&#x2009;&#x3bc;M NAA. Rooted plants were transferred to pots containing a soil-peat mixture (1: 2&#x2009;v/v) and successfully acclimatized in the greenhouse. Plant identification is a crucial aspect to understand and conserve plant diversity from extinction. DNA barcode analysis of Silene schimperiana was carried out using two chloroplast DNA markers (cpDNA): 1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) and RNA polymerase subunit (rpoC1) and a nuclear ribosome DNA marker (ncDNA), internal transcribed spacer (ITS). Phylogenetic analysis revealed a successful identification of Silene schimperiana on the species and genus levels and supported the inclusion of Silene schimperiana in genus Silene.<br><br>CONCLUSIONS: In this study, a relevant in vitro propagation method was established to facilitate the recovery of Silene schimperiana, in addition to DNA barcoding of the plant as a tool for effective management and conservation of plant genetic resources.},
}
@article {pmid32778674,
year = {2020},
author = {Gogoi, B and Wann, SB and Saikia, SP},
title = {DNA barcodes for delineating Clerodendrum species of North East India.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {13490},
pmid = {32778674},
issn = {2045-2322},
mesh = {Biodiversity ; Clerodendrum/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Genes, Plant ; India ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The diversified genus of Clerodendrum with its complex evolutionary history leads to taxonomic mystification. Unlike traditional taxonomic methods, DNA barcoding could be a promising tool for the identification and conservation of Clerodendrum species. This study was attempted to develop an efficient barcode locus in Clerodendrum species of North East India. We evaluated four barcode candidates (ITS2, matK, rbcL, ycf1) and its combinations in different Clerodendrum species. The reliability of barcodes to distinguish the species were calculated using genetic pairwise distances, intra- and inter-specific diversity, barcode gap, and phylogenetic tree-based methods. The results exemplify that matK posse's maximum number of variables and parsimony-informative sites (103/100), intra- (0.021 ± 0.001) and inter- (0.086 ± 0.005) specific divergences and species resolution rate (89.1%) followed by ITS2, ycf1, and rbcL. Among the combinatorial locus, ITS2 + matK showed the best species discrimination with distinctive barcode gaps. Therefore, we tentatively suggest that the combination of ITS2 + matK as core barcode for Clerodendrum and converted into quick response (QR) code. Hence, this finding indicates that DNA barcoding could provide consistent resources for species discrimination and resolve taxonomic controversies of the genus as well as set a preliminary assessment toward its biodiversity.},
}
@article {pmid32770272,
year = {2021},
author = {Thongprem, P and Davison, HR and Thompson, DJ and Lorenzo-Carballa, MO and Hurst, GDD},
title = {Incidence and Diversity of Torix Rickettsia-Odonata Symbioses.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {203-212},
pmid = {32770272},
issn = {1432-184X},
support = {CGL2008-02799//Ministerio de Ciencia e Innovaci&#xf3;n/ ; },
mesh = {Animals ; DNA Barcoding, Taxonomic ; Female ; Infectious Disease Transmission, Vertical ; Odonata/*microbiology ; Ovary/microbiology ; Rickettsia/classification/genetics/*physiology ; Rickettsia Infections/*transmission ; Symbiosis/*physiology ; },
abstract = {Heritable microbes are an important component of invertebrate biology, acting both as beneficial symbionts and reproductive parasites. Whilst most previous research has focussed on the 'Wolbachia pandemic', recent work has emphasised the importance of other microbial symbionts. In this study, we present a survey of odonates (dragonflies and damselflies) for torix group Rickettsia, following previous research indicating that this clade can be common in other aquatic insect groups. PCR assays were used to screen a broad range of odonates from two continents and revealed 8 of 76 species tested were infected with Rickettsia. We then conducted further deeper screening of UK representatives of the Coenagrionidae damselfly family, revealing 6 of 8 UK coenagrionid species to be positive for torix Rickettsia. Analysis of Rickettsia gene sequences supported multiple establishments of symbiosis in the group. Some strains were shared between UK coenagrionid species that shared mtDNA barcodes, indicating a likely route for mitochondrial introgression between sister species. There was also evidence of coinfecting Rickettsia strains in two species. FISH analysis indicated Rickettsia were observed in the ovarioles, consistent with heritable symbiosis. We conclude that torix Rickettsia represent an important associate of odonates, being found in a broad range of species from both Europe and South America. There is evidence that coinfection can occur, vertical transmission is likely, and that symbiont movement following hybridisation may underpin the lack of 'barcoding gap' between well-established species pairs in the genus. Future work should establish the biological significance of the symbioses observed.},
}
@article {pmid32769631,
year = {2020},
author = {Bauer, AM and Bar, KJ},
title = {Advances in simian--human immunodeficiency viruses for nonhuman primate studies of HIV prevention and cure.},
journal = {Current opinion in HIV and AIDS},
volume = {15},
number = {5},
pages = {275-281},
doi = {10.1097/COH.0000000000000645},
pmid = {32769631},
issn = {1746-6318},
support = {P01 AI131338/AI/NIAID NIH HHS/United States ; UM1 AI126619/AI/NIAID NIH HHS/United States ; UM1 AI126620/AI/NIAID NIH HHS/United States ; P30 AI045008/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; *HIV Infections/prevention &amp; control ; *HIV-1/genetics ; Humans ; Macaca mulatta ; *Simian Acquired Immunodeficiency Syndrome/prevention &amp; control ; *Simian Immunodeficiency Virus/genetics ; Virus Replication ; },
abstract = {PURPOSE OF REVIEW: Simian--human immunodeficiency viruses (SHIVs), chimeric viruses that encode HIV-1 Env within an SIV backbone, are key reagents for nonhuman primate studies of antibody-based vaccines, broadly neutralizing antibodies (bnAbs), and other Env-targeting reagents. Here, we discuss the provenance and characteristics of currently relevant SHIVs, novel technical advances, recent discoveries enabled by SHIV challenge studies, and the continued development of SHIVs for persistence and cure experiments.<br><br>RECENT FINDINGS: SHIV SF162P3, SHIV AD8EO, and transmitter/founder SHIVs with Env375 mutations are now common reagents in nonhuman primate studies, with increased use and validation establishing their properties and potential applications. Genetic barcoding of SIV and SHIV, which allows tracing of individual lineages and elucidation of viral kinetics from transmission through latency has expanded the experimental capacity of SHIV models. SHIV challenge studies have determined the neutralizing antibody titers that correlate with protection for passive and active immunization and enabled complementary human and nonhuman primate studies of vaccine development. SHIV models of latency continue to evolve, aided by descriptions of SHIV persistence on ART and the proviral landscape.<br><br>SUMMARY: Recent advances and more thorough characterization of SHIVs allow for expanded applications and greater confidence in experimental results.},
}
@article {pmid32768166,
year = {2020},
author = {Lv, YN and Yang, CY and Shi, LC and Zhang, ZL and Xu, AS and Zhang, LX and Li, XL and Li, HT},
title = {Identification of medicinal plants within the Apocynaceae family using ITS2 and psbA-trnH barcodes.},
journal = {Chinese journal of natural medicines},
volume = {18},
number = {8},
pages = {594-605},
doi = {10.1016/S1875-5364(20)30071-6},
pmid = {32768166},
issn = {1875-5364},
mesh = {Apocynaceae/*classification/genetics ; China ; *DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; DNA, Ribosomal Spacer/*genetics ; Plant Leaves ; Plants, Medicinal/*classification/genetics ; },
abstract = {To ensure the safety of medications, it is vital to accurately authenticate species of the Apocynaceae family, which is rich in poisonous medicinal plants. We identified Apocynaceae species by using nuclear internal transcribed spacer 2 (ITS2) and psbA-trnH based on experimental data. The identification ability of ITS2 and psbA-trnH was assessed using specific genetic divergence, BLAST1, and neighbor-joining trees. For DNA barcoding, ITS2 and psbA-trnH regions of 122 plant samples of 31 species from 19 genera in the Apocynaceae family were amplified. The PCR amplification for ITS2 and psbA-trnH sequences was 100%. The sequencing success rates for ITS2 and psbA-trnH sequences were 81% and 61%, respectively. Additional data involved 53 sequences of the ITS2 region and 38 sequences of the psbA-trnH region were downloaded from GenBank. Moreover, the analysis showed that the inter-specific divergence of Apocynaceae species was greater than its intra-specific variations. The results indicated that, using the BLAST1 method, ITS2 showed a high identification efficiency of 97% and 100% of the samples at the species and genus levels, respectively, via BLAST1, and psbA-trnH successfully identified 95% and 100% of the samples at the species and genus levels, respectively. The barcode combination of ITS2/psbA-trnH successfully identified 98% and 100% of samples at the species and genus levels, respectively. Subsequently, the neighbor joining tree method also showed that barcode ITS2 and psbA-trnH could distinguish among the species within the Apocynaceae family. ITS2 is a core barcode and psbA-trnH is a supplementary barcode for identifying species in the Apocynaceae family. These results will help to improve DNA barcoding reference databases for herbal drugs and other herbal raw materials.},
}
@article {pmid32768164,
year = {2020},
author = {Yang, CH and Liu, X and Cui, YX and Nie, LP and Lin, YL and Wei, XP and Wang, Y and Yao, H},
title = {Molecular structure and phylogenetic analyses of the complete chloroplast genomes of three original species of Pyrrosiae Folium.},
journal = {Chinese journal of natural medicines},
volume = {18},
number = {8},
pages = {573-581},
doi = {10.1016/S1875-5364(20)30069-8},
pmid = {32768164},
issn = {1875-5364},
mesh = {China ; *Genome, Chloroplast ; *Phylogeny ; Plants, Medicinal/*classification ; Polypodiaceae/*classification ; },
abstract = {Pyrrosia petiolosa, Pyrrosia lingua and Pyrrosia sheareri are recorded as original plants of Pyrrosiae Folium (PF) and commonly used as Chinese herbal medicines. Due to the similar morphological features of PF and its adulterants, common DNA barcodes cannot accurately distinguish PF species. Knowledge of the chloroplast (cp) genome is widely used in species identification, molecular marker and phylogenetic analyses. Herein, we determined the complete cp genomes of three original species of PF via high-throughput sequencing technologies. The three cp genomes exhibited a typical quadripartite structure with sizes ranging from 158 165 to 163 026 bp. The cp genomes of P. petiolosa and P. lingua encoded 130 genes, whilst that of P. sheareri encoded 131 genes. The complete cp genomes were compared, and five highly divergent regions of petA-psbJ, matK-rps16, ndhC-trnM, psbM-petN and psaC-ndhE were screened as potential DNA barcodes for identification of Pyrrosia genus species. The phylogenetic tree we obtained indicated that P. petiolosa and P. lingua are clustered in a single clade and, thus, share a close relationship. This study provides invaluable information for further studies on the species identification, taxonomy and phylogeny of Pyrrosia genus species.},
}
@article {pmid32768163,
year = {2020},
author = {Cui, N and Liao, BS and Liang, CL and Li, SF and Zhang, H and Xu, J and Li, XW and Chen, SL},
title = {Complete chloroplast genome of Salvia plebeia: organization, specific barcode and phylogenetic analysis.},
journal = {Chinese journal of natural medicines},
volume = {18},
number = {8},
pages = {563-572},
doi = {10.1016/S1875-5364(20)30068-6},
pmid = {32768163},
issn = {1875-5364},
mesh = {China ; Codon/genetics ; DNA Barcoding, Taxonomic ; *Genes, Plant ; Genetic Variation ; *Genome, Chloroplast ; Phylogeny ; Plants, Medicinal/*genetics ; Salvia/*genetics ; },
abstract = {Salvia plebeia has been in use as traditional Chinese medicine (TCM) for more than 500 years. In this study, the complete chloroplast (cp) genome of S. plebeia was sequenced, assembled and compared to those of other five published Salvia cp genomes. It was found that the cp genome structure of S. plebeia was well conserved and had a total size of 151 062 bp. Four parameters were used to display the usage conditions of the codons of the amino acids in Salvia genus. Although the number of protein-coding genes in each species was the same, the total number of codons was different. Except for amino acids Trp and Met whose Relative Synonymous Codon Usage (RSCU) value of one condon was equal to 1, the remaining 19 amino acids had 1-3 preferred codons. The preferred codon names of each amino acid were coincident. The period size for the tandem repeats of six species ranged from 9 to 410 bp. Salvia cp genomes mainly possessed tandem repeats with a copy number less than or equal to 3. The sequence length of tandem repeats of the six species ranged from 25 to 824 bp. Highly viarable regions including four intergenic spacers and six partial genes were discovered as potential specific barcodes for Salvia species through cp genome-wide comparison. Finally, we performed phylogenetic analyses based on the complete cp genome and coding sequences respectively. These results provide information to help construct the cp genome library for Salvia, which may support studies of phylogenetics, DNA barcoding, population and transplastomics.},
}
@article {pmid32766673,
year = {2020},
author = {Tanaka, A and Ishida, S and Fuchigami, T and Hayashi, Y and Kuroda, A and Ikenaka, K and Fukazawa, Y and Hitoshi, S},
title = {Life-Long Neural Stem Cells Are Fate-Specified at an Early Developmental Stage.},
journal = {Cerebral cortex (New York, N.Y. : 1991)},
volume = {30},
number = {12},
pages = {6415-6425},
doi = {10.1093/cercor/bhaa200},
pmid = {32766673},
issn = {1460-2199},
mesh = {Animals ; Brain/*growth &amp; development ; *Cell Lineage ; Genetic Vectors ; Lentivirus/physiology ; Mice, Transgenic ; Neural Stem Cells/*physiology ; },
abstract = {The origin and life-long fate of quiescent neural stem cells (NSCs) in the adult mammalian brain remain largely unknown. A few neural precursor cells in the embryonic brain elongate their cell cycle time and subsequently become quiescent postnatally, suggesting the possibility that life-long NSCs are selected at an early embryonic stage. Here, we utilized a GFP-expressing lentivirus to investigate the fate of progeny from individual lentivirus-infected NSCs by identifying the lentiviral integration site. Our data suggest that NSCs become specified to two or more lineages prior to embryonic day 13.5 in mice: one NSC lineage produces cells only for the cortex and another provides neurons to the olfactory bulb. The majority of neurosphere-forming NSCs in the adult brain are relatively dormant and generate very few cells, if any, in the olfactory bulb or cortex, and this NSC population could serve as a reservoir that is occasionally reactivated later in life.},
}
@article {pmid32765452,
year = {2020},
author = {Kiss, L and Vaghefi, N and Bransgrove, K and Dearnaley, JDW and Takamatsu, S and Tan, YP and Marston, C and Liu, SY and Jin, DN and Adorada, DL and Bailey, J and Cabrera de Álvarez, MG and Daly, A and Dirchwolf, PM and Jones, L and Nguyen, TD and Edwards, J and Ho, W and Kelly, L and Mintoff, SJL and Morrison, J and Németh, MZ and Perkins, S and Shivas, RG and Smith, R and Stuart, K and Southwell, R and Turaganivalu, U and Váczy, KZ and Blommestein, AV and Wright, D and Young, A and Braun, U},
title = {Australia: A Continent Without Native Powdery Mildews? The First Comprehensive Catalog Indicates Recent Introductions and Multiple Host Range Expansion Events, and Leads to the Re-discovery of Salmonomyces as a New Lineage of the Erysiphales.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1571},
pmid = {32765452},
issn = {1664-302X},
abstract = {In contrast to Eurasia and North America, powdery mildews (Ascomycota, Erysiphales) are understudied in Australia. There are over 900 species known globally, with fewer than currently 60 recorded from Australia. Some of the Australian records are doubtful as the identifications were presumptive, being based on host plant-pathogen lists from overseas. The goal of this study was to provide the first comprehensive catalog of all powdery mildew species present in Australia. The project resulted in (i) an up-to-date list of all the taxa that have been identified in Australia based on published DNA barcode sequences prior to this study; (ii) the precise identification of 117 specimens freshly collected from across the country; and (iii) the precise identification of 30 herbarium specimens collected between 1975 and 2013. This study confirmed 42 species representing 10 genera, including two genera and 13 species recorded for the first time in Australia. In Eurasia and North America, the number of powdery mildew species is much higher. Phylogenetic analyses of powdery mildews collected from Acalypha spp. resulted in the transfer of Erysiphe acalyphae to Salmonomyces, a resurrected genus. Salmonomyces acalyphae comb. nov. represents a newly discovered lineage of the Erysiphales. Another taxonomic change is the transfer of Oidium ixodiae to Golovinomyces. Powdery mildew infections have been confirmed on 13 native Australian plant species in the genera Acacia, Acalypha, Cephalotus, Convolvulus, Eucalyptus, Hardenbergia, Ixodia, Jagera, Senecio, and Trema. Most of the causal agents were polyphagous species that infect many other host plants both overseas and in Australia. All powdery mildews infecting native plants in Australia were phylogenetically closely related to species known overseas. The data indicate that Australia is a continent without native powdery mildews, and most, if not all, species have been introduced since the European colonization of the continent.},
}
@article {pmid32765172,
year = {2020},
author = {Hoenle, PO and Lattke, JE and Donoso, DA and von Beeren, C and Heethoff, M and Schmelzle, S and Argoti, A and Camacho, L and Ströbel, B and Blüthgen, N},
title = {Odontomachus davidsoni sp. nov. (Hymenoptera, Formicidae), a new conspicuous trap-jaw ant from Ecuador.},
journal = {ZooKeys},
volume = {948},
number = {},
pages = {75-105},
pmid = {32765172},
issn = {1313-2989},
abstract = {One of the largest species in its genus, Odontomachus davidsoni Hoenle, Lattke &amp; Donoso, sp. nov. is described from workers and queens collected at lowland forests in the Chocó-Darién bioregion in coastal Ecuador. The workers are characterized by their uniform red coloration, their large size (16-18 mm body length), and their frontal head striation that reaches the occipital margin. DNA barcodes (COI) and high resolution 2D images of the type material are provided, as well as an updated key for the Neotropical species of Odontomachus. In addition, a three-dimensional digital model of the worker holotype and a paratype queen scanned with DISC3D based on photogrammetry is presented, for the first time in a species description. Findings of large and conspicuous new species are uncommon around the world and suggest that these Ecuadorian rainforests may conceal many more natural treasures that deserve conservation.},
}
@article {pmid32764752,
year = {2020},
author = {De León, LF and Cornejo, A and Gavilán, RG and Aguilar, C},
title = {Hidden biodiversity in Neotropical streams: DNA barcoding uncovers high endemicity of freshwater macroinvertebrates at small spatial scales.},
journal = {PloS one},
volume = {15},
number = {8},
pages = {e0231683},
pmid = {32764752},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; DNA/genetics ; DNA Barcoding, Taxonomic/methods ; Ecosystem ; Fresh Water ; Freshwater Biology/*methods ; Insecta/*classification/genetics ; Invertebrates/*genetics ; Panama ; Panama Canal Zone ; Phylogeny ; Rivers ; },
abstract = {Aquatic macroinvertebrates play a crucial role in freshwater ecosystems, but their diversity remains poorly known, particularly in the tropics. This "taxonomic void" limits our understanding of biodiversity patterns and processes in freshwater ecosystems, and the scale at which they operate. We used DNA barcoding to estimate lineage diversity (and the diversity of unique haplotypes) in 224 specimens of freshwater macroinvertebrates at a small spatial scale within the Panama Canal Watershed (PCW). In addition, we compiled available barcoding data to assess macroinvertebrate diversity at a broader spatial scale spanning the Isthmus of Panama. Consistently across two species delimitation algorithms (i.e., ABGD and GMYC), we found high lineage diversity within the PCW, with ~ 100-106 molecular operational taxonomic units (MOTUs) across 168 unique haplotypes. We also found a high lineage diversity along the Isthmus of Panama, but this diversity peaked within the PCW. However, our rarefaction/extrapolation approach showed that this diversity remains under-sampled. As expected, these results indicate that the diversity of Neotropical freshwater macroinvertebrates is higher than previously thought, with the possibility of high endemicity even at narrow spatial scales. Consistent with previous work on aquatic insects and other freshwater taxa in this region, geographic isolation is likely a main factor shaping these patterns of diversity. However, other factors such as habitat variability and perhaps local adaptation might be reshaping these patterns of diversity at a local scale. Although further research is needed to better understand the processes driving diversification in freshwater macroinvertebrates, we suggest that Neotropical streams hold a high proportion of hidden biodiversity. Understanding this diversity is crucial in the face of increasing human disturbance.},
}
@article {pmid32764380,
year = {2020},
author = {Verhagen, A and Kelarakis, A},
title = {Carbon Dots for Forensic Applications: A Critical Review.},
journal = {Nanomaterials (Basel, Switzerland)},
volume = {10},
number = {8},
pages = {},
pmid = {32764380},
issn = {2079-4991},
abstract = {Owing to their superior fluorescence performance, inexpensive synthesis and nontoxic nature, carbon dots (C-dots) are systematically explored in a variety of applications; in this review, we outline and critically discuss recent trends with respect to their potential exploitation in criminal investigation, forensic toxicology and anti-counterfeit interventions. Capitalising on their colour-tuneable behaviour (in the sense that they adopt different colours with respect to the incident radiation), C-dot-based compositions are ideal for the visual enhancement of latent fingerprints, affording improved contrast against multicoloured and patterned backgrounds. As highly sensitive and highly selective optical nanoprobes, C-dots show excellent analytical performance in detecting biological compounds, drugs, explosives, heavy metals and poisonous reactants. In addition, benefiting from their versatile structural and chemical composition, C-dots can be incorporated into ink and polymeric formulations capable of functioning as a new generation of cost-effective barcodes and security nanotags for object authentication and anti-counterfeit applications. Translating these encouraging research outcomes into real-life innovations with significant social and economic impact requires an open, multidisciplinary approach and a close synergy between materials scientists, biologists, forensic investigators and digital engineers.},
}
@article {pmid32764359,
year = {2020},
author = {Badr, A and El-Sherif, N and Aly, S and Ibrahim, SD and Ibrahim, M},
title = {Genetic Diversity among Selected Medicago sativa Cultivars Using Inter-Retrotransposon-Amplified Polymorphism, Chloroplast DNA Barcodes and Morpho-Agronomic Trait Analyses.},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {8},
pages = {},
pmid = {32764359},
issn = {2223-7747},
abstract = {Alfalfa (Medicago sativa L.) is a major forage crop of family Fabaceae and is frequently cultivated in Egypt. The present study is concerned with the genetic discrimination of fifteen alfalfa cultivars from three different countries (Egypt, Australia, and USA) using two molecular approaches: inter-retrotransposon-amplified polymorphism (IRAP) markers and two chloroplast DNA barcodes matK and the trnH in addition to the analysis of fifteen morpho-agronomic traits. The genetic relatedness, based on analysis of IRAP marker polymorphism and produced using eleven primers by clustering via principal component analysis (PCA) and multivariate heatmap biostatistical methods differentiated the two Egyptian cultivars EGY1-Ismailia1 and EGY2-Nubaria1 from the three Australian and seven American cultivars, with some distinction of the cv. USA6-SW9720 and cv. AUS4-SuperFast. The results were also supported by the sequence analysis of the matK and the trnH genes on the genetic relatedness between eight cultivars. Moreover, it might be suggested that breeding lines from M. sativa cultivars may provide novel insights and a better understanding of the domestication of M. sativa genetic diversity. The classification of the eight cultivars, as revealed by morpho-agronomic traits, confirmed the close genetic relationship between the two Egyptian cultivars and indicated some resemblance between them and the AUS2-Siri Nafa, whereas the two American cultivars, USA1-Super supreme and USA4-Cuf101, were clearly isolated from a cluster of other three cultivars USA7-SW9628, USA8-Magna901, and USA9-Perfect. The results are useful sources of genetic information for future breeding programs in crop development and open new possibilities of producing M. sativa lines harboring high forage quality, productivity, and resistance to biotic and abiotic stresses.},
}
@article {pmid32764268,
year = {2020},
author = {Cornara, L and Ambu, G and Trombetta, D and Denaro, M and Alloisio, S and Frigerio, J and Labra, M and Ghimire, G and Valussi, M and Smeriglio, A},
title = {Comparative and Functional Screening of Three Species Traditionally used as Antidepressants: Valeriana officinalis L., Valeriana jatamansi Jones ex Roxb. and Nardostachys jatamansi (D.Don) DC.},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {8},
pages = {},
pmid = {32764268},
issn = {2223-7747},
abstract = {The essential oils (EOs) of three Caprifoliaceae species, the Eurasiatic Valeriana officinalis (Vo), the Himalayan Valeriana jatamansi (Vj) and Nardostachys jatamansi (Nj), are traditionally used to treat neurological disorders. Roots/rhizomes micromorphology, DNA barcoding and EOs phytochemical characterization were carried out, while biological effects on the nervous system were assessed by acetylcholinesterase (AChE) inhibitory activity and microelectrode arrays (MEA). Nj showed the highest inhibitory activity on AChE (IC50 67.15 μg/mL) followed by Vo (IC50 127.30 μg/mL) and Vj (IC50 246.84 μg/mL). MEA analyses on rat cortical neurons, carried out by recording mean firing rate (MFR) and mean bursting rate (MBR), revealed stronger inhibition by Nj (IC50 18.8 and 11.1 μg/mL) and Vo (16.5 and 22.5 μg/mL), compared with Vj (68.5 and 89.3 μg/mL). These results could be related to different EO compositions, since sesquiterpenes and monoterpenes significantly contribute to the observed effects, but the presence of oxygenated compounds such as aldehydes and ketones is a discriminating factor in determining the order of potency. Our multidisciplinary approach represents an important tool to avoid the adulteration of herbal drugs and permits the evaluation of the effectiveness of EOs that could be used for a wide range of therapeutic applications.},
}
@article {pmid32762642,
year = {2020},
author = {Villacrés-Vallejo, J and Aranda-Ventura, J and Wallis, A and Cagle, R and Handy, SM and Davis, J and Reed, E and Zhang, S and Strain, E and Pava-Ripoll, M and Erickson, D and Ramachandran, P and Ottesen, A},
title = {Using full chloroplast genomes of 'red' and 'yellow' Bixa orellana (achiote) for kmer based identification and phylogenetic inference.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {544},
pmid = {32762642},
issn = {1471-2164},
mesh = {Animals ; *Bixaceae/genetics ; *Genome, Chloroplast ; Humans ; Phylogeny ; Plant Extracts ; },
abstract = {BACKGROUND: Full chloroplast genomes provide high resolution taxonomic discrimination between closely related plant species and are quickly replacing single and multi-locus barcoding regions as reference materials of choice for DNA based taxonomic annotation of plants. Bixa orellana, commonly known as "achiote" and "annatto" is a plant used for both human and animal foods and was thus identified for full chloroplast sequencing for the Center for Veterinary Medicine (CVM) Complete Chloroplast Animal Feed database. This work was conducted in collaboration with the Instituto de Medicina Tradicional (IMET) in Iquitos, Peru. There is a wide range of color variation in pods of Bixa orellana for which genetic loci that distinguish phenotypes have not yet been identified. Here we apply whole chloroplast genome sequencing of "red" and "yellow" individuals of Bixa orellana to provide high quality reference genomes to support kmer database development for use identifying this plant from complex mixtures using shotgun data. Additionally, we describe chloroplast gene content, synteny and phylogeny, and identify an indel and snp that may be associated with seed pod color.<br><br>RESULTS: Fully assembled chloroplast genomes were produced for both red and yellow Bixa orellana accessions (158,918 and 158,823&#x2009;bp respectively). Synteny and gene content was identical to the only other previously reported full chloroplast genome of Bixa orellana (NC_041550). We observed a 17 base pair deletion at position 58,399-58,415 in both accessions, relative to NC_041550 and a 6&#x2009;bp deletion at position 75,531-75,526 and a snp at position 86,493 in red Bixa orellana.<br><br>CONCLUSIONS: Our data provide high quality reference genomes of individuals of red and yellow Bixa orellana to support kmer based identity markers for use with shotgun sequencing approaches for rapid, precise identification of Bixa orellana from complex mixtures. Kmer based phylogeny of full chloroplast genomes supports monophylly of Bixaceae consistent with alignment based approaches. A potentially discriminatory indel and snp were identified that may be correlated with the red phenotype.},
}
@article {pmid32756607,
year = {2020},
author = {Horns, F and Quake, SR},
title = {Cloning antibodies from single cells in pooled sequence libraries by selective PCR.},
journal = {PloS one},
volume = {15},
number = {8},
pages = {e0236477},
pmid = {32756607},
issn = {1932-6203},
mesh = {Amino Acid Sequence/genetics ; Antibodies/*genetics ; Cell Surface Display Techniques ; Cloning, Molecular ; DNA, Complementary/genetics ; Gene Library ; Genetic Vectors/genetics ; Humans ; Immunoglobulin Heavy Chains/*genetics ; Immunoglobulin Variable Region/*genetics ; Polymerase Chain Reaction/*methods ; Single-Cell Analysis ; },
abstract = {Antibodies function by binding to antigens. Antibodies must be cloned and expressed to determine their binding characteristics, but current methods for high-throughput antibody sequencing yield antibody DNA pooled from many cells and do not readily permit cloning of antibodies from single B cells. We present a strategy for retrieving and cloning antibody DNA from single cells within a pooled library of cells. Our strategy, called selective PCR for antibody retrieval (SPAR), takes advantage of the unique sequence barcodes attached to individual cDNA molecules during sample preparation to enable specific amplification by PCR of antibody heavy- and light-chain cDNA originating from a single cell. We show through computational analysis that most human antibodies sequenced using typical high-throughput methods can be retrieved using SPAR, and experimentally demonstrate retrieval of full-length antibody variable region cDNA from three cells within pools of ~5,000 cells. SPAR enables rapid low-cost cloning and expression of native human antibodies from pooled single-cell sequence libraries for functional characterization.},
}
@article {pmid32755801,
year = {2020},
author = {Lara, E and Dumack, K and García-Martín, JM and Kudryavtsev, A and Kosakyan, A},
title = {Amoeboid protist systematics: A report on the "Systematics of amoeboid protists" symposium at the VIIIth ECOP/ISOP meeting in Rome, 2019.},
journal = {European journal of protistology},
volume = {76},
number = {},
pages = {125727},
doi = {10.1016/j.ejop.2020.125727},
pmid = {32755801},
issn = {1618-0429},
mesh = {Amoebozoa/*classification ; Biodiversity ; *Classification ; Research/trends ; Terminology as Topic ; },
abstract = {Amoeboid protists are extremely abundant and diverse in natural systems where they often play outstanding ecological roles. They can be found in almost all major eukaryotic divisions, and genomic approaches are bringing major changes in our perception of their deep evolutionary relationships. At fine taxonomic levels, the generalization of barcoding is revealing a considerable and unsuspected specific diversity that can be appreciated with careful morphometric analyses based on light and electron microscopic observations. We provide examples on the difficulties and advances in amoeboid protists systematics in a selection of groups that were presented at the VIIIth ECOP/ISOP meeting in Rome, 2019. We conclude that, in all studied groups, important taxonomical rearrangements will certainly take place in the next few years, and systematics must be adapted to incorporate these changes. Notably, nomenclature should be flexible enough to integrate many new high level taxa, and a unified policy must be adopted to species description and to the establishment of types.},
}
@article {pmid32755053,
year = {2021},
author = {Galimberti, A and Assandri, G and Maggioni, D and Ramazzotti, F and Baroni, D and Bazzi, G and Chiandetti, I and Corso, A and Ferri, V and Galuppi, M and Ilahiane, L and La Porta, G and Laddaga, L and Landi, F and Mastropasqua, F and Ramellini, S and Santinelli, R and Soldato, G and Surdo, S and Casiraghi, M},
title = {Italian odonates in the Pandora's box: A comprehensive DNA barcoding inventory shows taxonomic warnings at the Holarctic scale.},
journal = {Molecular ecology resources},
volume = {21},
number = {1},
pages = {183-200},
doi = {10.1111/1755-0998.13235},
pmid = {32755053},
issn = {1755-0998},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Evolution, Molecular ; *Haplotypes ; Italy ; Odonata/*classification ; Phylogeny ; },
abstract = {The Odonata are considered among the most endangered freshwater faunal taxa. Their DNA-based monitoring relies on validated reference data sets that are often lacking or do not cover important biogeographical centres of diversification. This study presents the results of a DNA barcoding campaign on Odonata, based on the standard 658-bp 5' end region of the mitochondrial COI gene, involving the collection of 812 specimens (409 of which barcoded) from peninsular Italy and its main islands (328 localities), belonging to all the 88 species (31 Zygoptera and 57 Anisoptera) known from the country. Additional BOLD and GenBank data from Holarctic samples expanded the data set to 1,294 DNA barcodes. A multi-approach species delimitation analysis involving two distance (OT and ABGD) and four tree-based (PTP, MPTP, GMYC and bGMYC) methods was used to explore these data. Of the 88 investigated morphospecies, 75 (85%) unequivocally corresponded to distinct molecular operational units, whereas the remaining ones were classified as 'warnings' (i.e. showing a mismatch between morphospecies assignment and DNA-based species delimitation). These results are in contrast with other DNA barcoding studies on Odonata showing up to 95% of identification success. The species causing warnings were grouped into three categories depending on if they showed low, high or mixed genetic divergence patterns. The analysis of haplotype networks revealed unexpected intraspecific complexity at the Italian, Palearctic and Holarctic scale, possibly indicating the occurrence of cryptic species. Overall, this study provides new insights into the taxonomy of odonates and a valuable basis for future DNA and eDNA-based monitoring studies.},
}
@article {pmid32755016,
year = {2020},
author = {Bruez, E and Vallance, J and Gautier, A and Laval, V and Compant, S and Maurer, W and Sessitsch, A and Lebrun, MH and Rey, P},
title = {Major changes in grapevine wood microbiota are associated with the onset of esca, a devastating trunk disease.},
journal = {Environmental microbiology},
volume = {22},
number = {12},
pages = {5189-5206},
doi = {10.1111/1462-2920.15180},
pmid = {32755016},
issn = {1462-2920},
support = {//French National Research Agency/ ; V90//Ministry of Agriculture/ ; },
mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Fungi/classification/genetics/isolation &amp; purification ; *Microbiota ; Plant Diseases/*microbiology ; Plant Structures/microbiology ; Seasons ; Vitis/*microbiology ; Wood/*microbiology ; },
abstract = {Esca, a major grapevine trunk disease in old grapevines, is associated with the colonization of woody tissues by a broad range of plant pathogenic fungi. To identify which fungal and bacterial species are involved in the onset of this disease, we analysed the microbiota from woody tissues of young (10-year-old) grapevines at an early stage of esca. Using meta-barcoding, 515 fungal and 403 bacterial operational taxonomic units (OTUs) were identified in woody tissues. In situ hybridization showed that these fungi and bacteria co-inhabited in grapevine woody tissues. In non-necrotic woody tissues, fungal and bacterial microbiota varied according to organs and seasons but not diseased plant status. Phaeomoniella chlamydospora, involved in the Grapevine trunk disease, was the most abundant species in non-necrotic tissues from healthy plants, suggesting a possible non-pathogenic endophytic behaviour. Most diseased plants (70%) displayed cordons, with their central white-rot necrosis colonized essentially by two plant pathogenic fungi (Fomitiporia mediterranea: 60%-90% and P. chlamydospora: 5%-15%) and by a few bacterial taxa (Sphingomonas spp. and Mycobacterium spp.). The occurrence of a specific association of fungal and bacterial species in cordons from young grapevines expressing esca-foliar symptoms strongly suggests that that microbiota is involved in the onset of this complex disease.},
}
@article {pmid32752172,
year = {2020},
author = {Marullo, R and Mercati, F and Vono, G},
title = {DNA Barcoding: A Reliable Method for the Identification of Thrips Species (Thysanoptera, Thripidae) Collected on Sticky Traps in Onion Fields.},
journal = {Insects},
volume = {11},
number = {8},
pages = {},
pmid = {32752172},
issn = {2075-4450},
abstract = {Several thrips species (Insecta, Thysanoptera) are globally known as important crop pests and vectors of viral diseases, but their identification is difficult because of their small body size and inconspicuous morphological differences. Sequencing variation in the mitochondrial cytochrome c oxidase I (COI) region has been proven to be useful for the identification of species of many groups of insect pests. Here, DNA barcoding has been used to identify thrips species collected with the use of sticky traps placed in an open onion field. A total of 238 thrips specimens were analyzed, 151 of which could be identified to species and 27 to genera belonging to the family Thripidae. Fifty-one specimens could not be assigned to any genus, with the closest BLAST match in the GenBank queries being below 98%, whilst six specimens were not recognized as Thysanoptera. The results indicate that, although there are a few pest thrips species not yet barcoded, most of the species that may cause damage to crops in Europe are represented in GenBank and other databases, enabling correct identification. Additionally, DNA barcoding can be considered a valuable alternative to the classic morphology method for identification of major thrips species.},
}
@article {pmid32750890,
year = {2021},
author = {Sikolenko, MA and Valentovich, LN},
title = {Barapost: Binning of Nucleotide Sequences According to Taxonomic Annotation.},
journal = {IEEE/ACM transactions on computational biology and bioinformatics},
volume = {18},
number = {6},
pages = {2766-2767},
doi = {10.1109/TCBB.2020.3009780},
pmid = {32750890},
issn = {1557-9964},
mesh = {Computational Biology ; DNA Barcoding, Taxonomic/*methods ; Molecular Sequence Annotation/*methods ; Nanopore Sequencing/*methods ; *Software ; },
abstract = {Contemporary sequencing technologies, Oxford Nanopore in particular, provide a way to sequence multiple samples during single run using molecular barcodes. Specific circumstances, however, can make barcoding undesirable or unaffordable. Here, we introduce Barapost: a command-line toolkit that demultiplexes long nucleotide sequences relying on taxonomic annotation instead of barcoding.},
}
@article {pmid32749270,
year = {2020},
author = {Wang, CH and Hwang, YS and Wang, HC and Wang, YL and Tsai, KY},
title = {Microstructure overlapping image application with optical decryption.},
journal = {Journal of the Optical Society of America. A, Optics, image science, and vision},
volume = {37},
number = {8},
pages = {1361-1368},
doi = {10.1364/JOSAA.393182},
pmid = {32749270},
issn = {1520-8532},
abstract = {Currently, valuable tickets are scanned and verified by embedding quick response (QR) codes, but few studies have embedded encrypted information into QR codes to prevent counterfeiting. In the existing literature on color image-based QR codes, there is room for improvement in image quality and anti-counterfeiting functions. We propose an optically decrypted microstructure overlapping image technology, hiding the information points of two-dimensional barcodes on the image reservation area in the ticket, and using the optical principle to use the lenticular lens as a decryption component, to make the image produce continuous dynamic effects and increase the difficulty of forgery. In addition, the distribution of embedded parameters and differences will also affect the distortion of hidden information, which may cause the QR code to fail to read, so the median edge detection predictor is proposed for distortion control comparison. The experimental results prove that our method provides low distortion of information-hiding technology.},
}
@article {pmid32742784,
year = {2020},
author = {Areces-Berazain, F and Wang, Y and Hinsinger, DD and Strijk, JS},
title = {Plastome comparative genomics in maples resolves the infrageneric backbone relationships.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e9483},
pmid = {32742784},
issn = {2167-8359},
abstract = {Maples (Acer) are among the most diverse and ecologically important tree genera of the north-temperate forests. They include species highly valued as ornamentals and as a source of timber and sugar products. Previous phylogenetic studies employing plastid markers have not provided sufficient resolution, particularly at deeper nodes, leaving the backbone of the maple plastid tree essentially unresolved. We provide the plastid genome sequences of 16 species of maples spanning the sectional diversity of the genus and explore the utility of these sequences as a source of information for genetic and phylogenetic studies in this group. We analyzed the distribution of different types of repeated sequences and the pattern of codon usage, and identified variable regions across the plastome. Maximum likelihood and Bayesian analyses using two partitioning strategies were performed with these and previously published sequences. The plastomes ranged in size from 155,212 to 157,023 bp and had structure and gene content except for Acer palmatum (sect. Palmata), which had longer inverted repeats and an additional copy of the rps19 gene. Two genes, rps2 and rpl22, were found to be truncated at different positions and might be non-functional in several species. Most dispersed repeats, SSRs, and overall variation were detected in the non-coding sequences of the LSC and SSC regions. Fifteen loci, most of which have not been used before in the genus, were identified as the most variable and potentially useful as molecular markers for barcoding and genetic studies. Both ML and Bayesian analyses produced similar results irrespective of the partitioning strategy used. The plastome-based tree largely supported the topology inferred in previous studies using cp markers while providing resolution to the backbone relationships but was highly incongruous with a recently published nuclear tree presenting an opportunity for further research to investigate the causes of discordance, and particularly the role of hybridization in the diversification of the genus. Plastome sequences are valuable tools to resolve deep-level relationships within Acer. The variable loci and SSRs identified in this study will facilitate the development of markers for ecological and evolutionary studies in the genus. This study underscores the potential of plastid genome sequences to improve our understanding of the evolution of maples.},
}
@article {pmid32741413,
year = {2020},
author = {Reier, S and Sattmann, H and Schwaha, T and Fuehrer, HP and Haring, E},
title = {Unravelling the hidden biodiversity - the establishment of DNA barcodes of fish-parasitizing Acanthocephala Koehlreuther, 1771 in view of taxonomic misidentifications, intraspecific variability and possible cryptic species.},
journal = {Parasitology},
volume = {147},
number = {13},
pages = {1499-1508},
pmid = {32741413},
issn = {1469-8161},
mesh = {Acanthocephala/*classification/genetics ; Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/*veterinary ; DNA, Helminth ; Fishes/*parasitology ; *Host-Parasite Interactions ; Phylogeny ; },
abstract = {Acanthocephalans are obligate parasites of vertebrates, mostly of fish. There is limited knowledge about the diversity of fish-parasitizing Acanthocephala in Austria. Seven determined species and an undetermined species are recorded for Austrian waters. Morphological identification of acanthocephalans remains challenging due to their sparse morphological characters and their high intraspecific variations. DNA barcoding is an effective tool for taxonomic assignment at the species level. In this study, we provide new DNA barcoding data for three genera of Acanthocephala (Pomphorhynchus Monticelli, 1905, Echinorhynchus Zoega in Müller, 1776 and Acanthocephalus Koelreuter, 1771) obtained from different fish species in Austria and provide an important contribution to acanthocephalan taxonomy and distribution in Austrian fish. Nevertheless, the taxonomic assignment of one species must remain open. We found indications for cryptic species within Echinorhynchus cinctulus Porta, 1905. Our study underlines the difficulties in processing reliable DNA barcodes and highlights the importance of the establishment of such DNA barcodes to overcome these. To achieve this goal, it is necessary to collect and compare material across Europe allowing a comprehensive revision of the phylum in Europe.},
}
@article {pmid32738110,
year = {2020},
author = {Reveillion, F and Wattier, R and Montuire, S and Carvalho, LS and Bollache, L},
title = {Cryptic diversity within three South American whip spider species (Arachnida, Amblypygi).},
journal = {Zoological research},
volume = {41},
number = {5},
pages = {595-598},
pmid = {32738110},
issn = {2095-8137},
mesh = {Animals ; DNA/genetics ; *Genetic Variation ; Phylogeny ; Species Specificity ; Spiders/*classification/*genetics ; },
abstract = {Cryptic diversity (CD), the presence of highly divergent phylogenetic lineages within closed morphological species, has been documented for many taxa. Great arachnid orders such as Araneae or Scorpiones are well studied and many cases of CD have been described therein; to date, however, related research on smaller arachnid orders, such as whip spiders (Amblypygi), remains lacking. In the current study, we investigated CD based on cytochrome oxidase 1 (COI) in three nominal species of the genus Heterophrynus (H. alces, H. batesii, and H. longicornis), represented by 65 specimens. The sequences were compared using three different methods. All three species showed geographically structured CD. Thus, given its existence in this genus, it is important that CD and its spatial distribution be considered in future studies and possible conservation projects.},
}
@article {pmid32737516,
year = {2020},
author = {You, X and Thiruppathi, S and Liu, W and Cao, Y and Naito, M and Furihata, C and Honma, M and Luan, Y and Suzuki, T},
title = {Detection of genome-wide low-frequency mutations with Paired-End and Complementary Consensus Sequencing (PECC-Seq) revealed end-repair-derived artifacts as residual errors.},
journal = {Archives of toxicology},
volume = {94},
number = {10},
pages = {3475-3485},
doi = {10.1007/s00204-020-02832-0},
pmid = {32737516},
issn = {1432-0738},
mesh = {Cell Line ; Consensus ; DNA Mutational Analysis/*methods ; Genome, Human ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Mutation ; *Mutation Rate ; Polymerase Chain Reaction ; Sensitivity and Specificity ; Sequence Analysis, DNA ; },
abstract = {To improve the accuracy and the cost-efficiency of next-generation sequencing in ultralow-frequency mutation detection, we developed the Paired-End and Complementary Consensus Sequencing (PECC-Seq), a PCR-free duplex consensus sequencing approach. PECC-Seq employed shear points as endogenous barcodes to identify consensus sequences from the overlap in the shortened, complementary DNA strand-derived paired-end reads for sequencing error correction. With the high accuracy of PECC-Seq, we identified the characteristic base substitution errors introduced by the end-repair process of mechanical fragmentation-based library preparations, which were prominent at the terminal 7 bp of the library fragments in the 5'-NpCpA-3' and 5'-NpCpT-3' trinucleotide context. As demonstrated at the human genome scale (TK6 cells), after removing these potential end-repair artifacts from the terminal 7 bp, PECC-Seq could reduce the sequencing error frequency to mid-10[-7] with a relatively low sequencing depth. For TA base pairs, the background error rate could be suppressed to mid-10[-8]. In mutagen-treated (6 μg/mL methyl methanesulfonate or 12 μg/mL N-nitroso-N-ethylurea) TK6, increases in mutagen treatment-related mutant frequencies could be detected, indicating the potential of PECC-Seq in detecting genome-wide ultra-rare mutations. In addition, our finding on the patterns of end-repair artifacts may provide new insights into further reducing technical errors not only for PECC-Seq, but also for other next-generation sequencing techniques.},
}
@article {pmid32735908,
year = {2020},
author = {Carrelha, J and Lin, DS and Rodriguez-Fraticelli, AE and Luis, TC and Wilkinson, AC and Cabezas-Wallscheid, N and Tremblay, CS and Haas, S},
title = {Single-cell lineage tracing approaches in hematology research: technical considerations.},
journal = {Experimental hematology},
volume = {89},
number = {},
pages = {26-36},
pmid = {32735908},
issn = {1873-2399},
support = {/WT_/Wellcome Trust/United Kingdom ; K99 HL146983/HL/NHLBI NIH HHS/United States ; K99 HL150218/HL/NHLBI NIH HHS/United States ; MC_UU_12009/5/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; Cell Differentiation ; Cell Lineage/genetics/immunology ; Cell Tracking/*methods ; Cell Transplantation/*methods ; Congresses as Topic ; DNA Barcoding, Taxonomic/methods ; Genetic Vectors/chemistry/metabolism ; Hematology/*methods ; Hematopoiesis/*genetics/immunology ; Hematopoietic Stem Cells/*cytology/immunology/virology ; Homeostasis/genetics/immunology ; Humans ; Lentivirus/genetics/metabolism ; Mice ; Single-Cell Analysis/methods ; Transgenes ; Transposases/genetics/immunology ; },
abstract = {The coordinated differentiation of hematopoietic stem and progenitor cells (HSPCs) into the various mature blood cell types is responsible for sustaining blood and immune system homeostasis. The cell fate decisions underlying this important biological process are made at the level of single cells. Methods to trace the fate of single cells are therefore essential for understanding hematopoietic system activity in health and disease and have had a major impact on how we understand and represent hematopoiesis. Here, we discuss the basic methodologies and technical considerations for three important clonal assays: single-cell transplantation, lentiviral barcoding, and Sleeping Beauty barcoding. This perspective is a synthesis of presentations and discussions from the 2019 International Society for Experimental Hematology (ISEH) Annual Meeting New Investigator Technology Session and the 2019 ISEH Winter Webinar.},
}
@article {pmid32735584,
year = {2020},
author = {Le, DT and Zhang, YQ and Xu, Y and Guo, LX and Ruan, ZP and Burgess, KS and Ge, XJ},
title = {The utility of DNA barcodes to confirm the identification of palm collections in botanical gardens.},
journal = {PloS one},
volume = {15},
number = {7},
pages = {e0235569},
pmid = {32735584},
issn = {1932-6203},
mesh = {Arecaceae/*classification/*genetics ; *DNA Barcoding, Taxonomic ; *Gardens ; },
abstract = {The palm family (Arecaceae) is of high ecological and economic value, yet identification in the family remains a challenge for both taxonomists and horticulturalists. The family consists of approximately 2600 species across 181 genera and DNA barcoding may be a useful tool for species identification within the group. However, there have been few systematic evaluations of DNA barcodes for the palm family. In the present study, five DNA barcodes (rbcL, matK, trnH-psbA, ITS, ITS2) were evaluated for species identification ability across 669 samples representing 314 species and 100 genera in the Arecaceae, employing four analytical methods. The ITS gene region was found to not be a suitable barcode for the palm family, due in part, to low recovery rates and paralogous gene copies. Among the four analyses used, species resolution for ITS2 was much higher than that achieved with the plastid barcodes alone (rbcL, matK, trnH-psbA), and the barcode combination ITS2 + matK + rbcL gave the highest resolution among all single barcodes and their combinations, followed by ITS2 + matK. Among 669 palm samples analyzed, 110 samples (16.3%) were found to be misidentified. The 2992 DNA barcode sequences generated in this study greatly enriches the existing identification toolbox available to plant taxonomists that are interested in researching genetic relationships among palm taxa as well as for horticulturalists that need to confirm palm collections for botanical garden curation and horticultural applications. Our results indicate that the use of the ITS2 DNA barcode gene region provides a useful and cost-effective tool to confirm the identity of taxa in the Palm family.},
}
@article {pmid32735043,
year = {2020},
author = {Veeranagouda, Y and Zachayus, JL and Guillemot, JC and Venier, O and Didier, M},
title = {High-Throughput Cellular RNA Sequencing (HiCAR-Seq): Cost-Effective, High-Throughput 3' mRNA-Seq Method Enabling Individual Sample Quality Control.},
journal = {Current protocols in molecular biology},
volume = {132},
number = {1},
pages = {e123},
doi = {10.1002/cpmb.123},
pmid = {32735043},
issn = {1934-3647},
mesh = {Animals ; Cell Line ; Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Quality Control ; Sequence Analysis, RNA/*methods ; },
abstract = {High-throughput screening is one of the pillars of drug development. Unbiased transcriptome profiling is now widely used for a deeper understanding of a drug's mechanisms of action, off target effects, and cytotoxicity. Although currently available high-throughput RNA-Seq (HT RNA-Seq) methods such as PLATE-Seq, DRUG-Seq, and BRB-Seq serve these purposes, the inherent nature of these methods does not allow sample-wise sequencing library quality control. Here, we describe an HTR method called High-throughput CellulAr RNA Sequencing (HiCAR-Seq). HiCAR-Seq was optimized to work directly on cultured cells (as little as 1,000 cells) or 10 ng of total RNA. HiCAR-Seq involves reverse transcription from cultured cells or total RNA using oligo-dT primers followed by the PCR amplification of full-length cDNAs using sample-specific barcode primers in individual plate wells. Amplification of cDNA from every sample can be verified using Bioanalyzer. This step not only reveals cDNA amplification but also provides greater precision for pooling equal concentrations of cDNA from different samples. A single pooled cDNA library is made suitable for sequencing on Illumina sequencers using a tagmentation kit. Because HiCAR-Seq targets a small region at the 3' of the mRNAs, as little as 3 to 4 million reads/sample are enough to infer changes in gene expression in human or mouse cells. We believe that HiCAR-Seq represents a robust and competitive addition to the existing set of transcriptome-based high-throughput screening methods. © 2020 Wiley Periodicals LLC. Basic Protocol 1: cDNA synthesis and barcoding/enrichment PCR Basic Protocol 2: Nextera tagmentation/amplification, quantification, and sequencing.},
}
@article {pmid32733543,
year = {2020},
author = {Wang, RN and Milne, RI and Du, XY and Liu, J and Wu, ZY},
title = {Characteristics and Mutational Hotspots of Plastomes in Debregeasia (Urticaceae).},
journal = {Frontiers in genetics},
volume = {11},
number = {},
pages = {729},
pmid = {32733543},
issn = {1664-8021},
abstract = {Debregeasia is an economically important genus of the nettle family (Urticaceae). Previous systematic studies based on morphology, or using up to four plastome regions, have not satisfactorily resolved relationships within the genus. Here, we report 25 new plastomes for Urticaceae, including 12 plastomes from five Debregeasia species and 13 plastomes from other genera. Together with the one published plastome for Debregeasia, we analyzed plastome structure and character, identified mutation hotspots and loci under selection, and constructed phylogenies. The plastomes of Debregeasia were found to be very conservative, with a size from 155,743 bp to 156,065 bp, and no structural variation. Eleven mutation hotspots were identified, including three (rpoB-trnC-GCA, trnT-GGU-psbD and ycf1) that are highly variable both within Debregeasia and among genera; these show high potential value for future DNA barcoding, population genetics and phylogenetic reconstruction. Selection pressure analysis revealed nine genes (clpP, ndhF, petB, psbA, psbK, rbcL, rpl23, ycf2, and ycf1) that may experience positive selection. Phylogenomic analyses results suggest that Debregeasia was monophyletic, and closest to Boehmeria among genera examined. Within Debregeasia, D. longifolia was sister to D. saeneb, whereas D. elliptica, D. orientalis with D. squamata formed the other subclade. This study enriches organelle genome resources for Urticaceae, and highlights the utility of plastome data for detecting mutation hotspots for evolutionary and systematic analysis.},
}
@article {pmid32733130,
year = {2020},
author = {Hrivniak, &#x13d; and Sroka, P and Bojková, J and Godunko, RJ and Namin, JI and Bagheri, S and Nejat, F and Abdoli, A and Staniczek, AH},
title = {Diversity and distribution of Epeorus (Caucasiron) (Ephemeroptera, Heptageniidae) in Iran, with descriptions of three new species.},
journal = {ZooKeys},
volume = {947},
number = {},
pages = {71-102},
pmid = {32733130},
issn = {1313-2989},
abstract = {Combining morphological and molecular data in an integrative approach, three new mayfly species of Epeorus (Caucasiron) are described. These include Epeorus (Caucasiron) alborzicus Hrivniak &amp; Sroka, sp. nov. and Epeorus (Caucasiron) shargi Hrivniak &amp; Sroka, sp. nov. from northern Iran, and Epeorus (Caucasiron) zagrosicus Hrivniak &amp; Sroka, sp. nov. from central Iran. They are unambiguously delimited using both distance-based and likelihood-based approaches in the analyses of barcode COI sequences. Each new species is compared with other species of the subgenus and morphological diagnostic characters are provided. Based on extensive sampling of streams throughout the country, the distribution and habitat preferences of all Caucasiron species in Iran are assessed. Altogether, there are now six species recorded, among them also E. (C.) nigripilosus Sinitshenkova, 1976 is reported for the first time in Iran. Five species are distributed in the Alborz Mts. in northern Iran, one species was found in the Zagros Mts. in central Iran.},
}
@article {pmid32731885,
year = {2020},
author = {Xin, H and Lian, Q and Jiang, Y and Luo, J and Wang, X and Erb, C and Xu, Z and Zhang, X and Heidrich-O'Hare, E and Yan, Q and Duerr, RH and Chen, K and Chen, W},
title = {GMM-Demux: sample demultiplexing, multiplet detection, experiment planning, and novel cell-type verification in single cell sequencing.},
journal = {Genome biology},
volume = {21},
number = {1},
pages = {188},
pmid = {32731885},
issn = {1474-760X},
support = {P01 AI106684/AI/NIAID NIH HHS/United States ; U01 DK062420/DK/NIDDK NIH HHS/United States ; R01 HL137709/HL/NHLBI NIH HHS/United States ; UL1 TR001857/TR/NCATS NIH HHS/United States ; },
mesh = {Bayes Theorem ; Humans ; Molecular Typing/*methods ; *Sequence Analysis, RNA ; *Single-Cell Analysis ; },
abstract = {Identifying and removing multiplets are essential to improving the scalability and the reliability of single cell RNA sequencing (scRNA-seq). Multiplets create artificial cell types in the dataset. We propose a Gaussian mixture model-based multiplet identification method, GMM-Demux. GMM-Demux accurately identifies and removes multiplets through sample barcoding, including cell hashing and MULTI-seq. GMM-Demux uses a droplet formation model to authenticate putative cell types discovered from a scRNA-seq dataset. We generate two in-house cell-hashing datasets and compared GMM-Demux against three state-of-the-art sample barcoding classifiers. We show that GMM-Demux is stable and highly accurate and recognizes 9 multiplet-induced fake cell types in a PBMC dataset.},
}
@article {pmid32729766,
year = {2020},
author = {Murugan, R and Ananthan, G and Arunkumar, A},
title = {DNA bar coding of Aplousobranchiata and Phlebobranchiata Ascidians (Phylum:Chordata) inferred from mitochondrial cytochrome oxidase subunit I (COI) gene sequence approach in Andaman and Nicobar Islands, India: a first report.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {31},
number = {7},
pages = {285-297},
doi = {10.1080/24701394.2020.1798417},
pmid = {32729766},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; India ; Islands ; Mitochondria/genetics ; Sequence Analysis, DNA ; Urochordata/*classification/genetics ; },
abstract = {Ascidians (Phylum: Chordata) are sessile and filter-feeding marine animal, species identification of ascidians is possible by observing various morphological and anatomical features in various stages of life span. However, this method is labor intensive, time-consuming and very difficult for non-specialists particularly when dealing with field collections. Suborder Aplousobranchiata and Phlebobranchiata is the largest group of tunicates within, morphological and molecular data suggest that Didemnidae and Ascidiidae are monophyletic, but the monophyly of each genus and their phylogenetic relationships are still poorly understood. Therefore, this study was aimed to develop DNA barcodes of ascidians belonging to the orders of Aplousobranchiata and Phlebobranchiata species namely Diplosoma listerianum, Lissoclinum fragile, Didemnum psammatode, Phallusia fumigata and Phallusia ingeria collected from Andaman and Nicobar Islands were sequenced and submitted in Gen Bank. Colony structure, Scanning Electron Microscope (SEM) for spicules of colonial ascidians, larval type and zooids formation were found to be the most useful morphological characters for discriminating the species. Our BLAST results proved D. Listerianum KP842724 (98%) L. fragile KP842726 (100%) D. psammatode KP779902 (99%), P. fumigata KP779904 (99%) and P. ingeria KP842727 (100%) similarity and this is the first report of mitochondrial COI gene of these ascidians from Andaman and Nicobar Islands. We explored the usefulness of CO1 gene sequences for molecular level identification and mtDNA data in assessing a phylogenetic relationship of ascidian species.},
}
@article {pmid32729709,
year = {2020},
author = {Hikosaka-Katayama, T and Watanuki, N and Niiho, S and Hikosaka, A},
title = {Geographical Distribution and Genetic Diversity of Praesagittifera naikaiensis (Acoelomorpha) in the Seto Inland Sea, Japan.},
journal = {Zoological science},
volume = {37},
number = {4},
pages = {314-322},
doi = {10.2108/zs190119},
pmid = {32729709},
issn = {0289-0003},
mesh = {*Animal Distribution ; Animals ; Haplotypes ; Japan ; Oceans and Seas ; *Phylogeny ; Platyhelminths/anatomy &amp; histology/classification/*genetics/*physiology ; Species Specificity ; },
abstract = {Acoel flatworms are simple bilaterians that lack digestive lumens and coelomic cavities. Although they are a significant taxon for evaluating the evolution of metazoans, suitable species for biological experiments are not available in Japan. We recently focused on Praesagittifera naikaiensis, which inhabits the sandy shores of intertidal zones in the Seto Inland Sea in Japan, as a candidate for a representative acoel species to be used in experiments. However, reports on its distribution range remain limited. Here, we surveyed the habitats of P. naikaiensis on 108 beaches along the Seto Inland Sea. Praesagittifera naikaiensis is reported here from 37 sites (six previously known and 31 newly discovered sites) spread over a wide area of the Seto Inland Sea, from Awaji Island in Hyogo Prefecture to Fukuoka Prefecture (364 km direct distance). Based on the mitochondrial cytochrome oxidase subunit I (COI) gene haplotypes, we evaluated the genetic diversity of 145 individuals collected from 33 sites. Out of 42 COI haplotypes, 13 haplotypes were shared by multiple individuals. The most frequent haplotype was observed in 67 individuals collected from 31 sites. Eight other haplotypes were detected at geographically distant locations (maximum of 299 km direct distance). Multiple haplotypes were found at 32 sites. These results demonstrate that sufficient genetic flow exists among P. naikaiensis populations throughout the Seto Inland Sea. Molecular phylogenetic analysis of the COI haplotypes of P. naikaiensis revealed that all specimens were grouped into one clade. The genetic homogeneity of the animals in this area favors their use as an experimental animal.},
}
@article {pmid32728339,
year = {2020},
author = {Hernández, D and Møller, PR and Casane, D and García-Machado, E},
title = {A new species of the cave-fish genus Lucifuga (Ophidiiformes, Bythitidae), from eastern Cuba.},
journal = {ZooKeys},
volume = {946},
number = {},
pages = {17-35},
pmid = {32728339},
issn = {1313-2989},
abstract = {Recently, a barcoding study and a molecular phylogenetic analysis of the Cuban species of the cave-fish genus Lucifuga Poey, 1858 revealed the existence of different evolutionary lineages that were previously unknown or passed unnoticed by morphological scrutiny (i.e., cryptic candidate species). In the present study, Lucifuga gibarensis is described as a new species restricted to anchialine caves in the northeastern karst region of the main island. The species was earlier described as a variety of Lucifuga dentata, but since the name was introduced as a variety after 1960, it is deemed to be infrasubspecific and unavailable according to the International Code of Zoological Nomenclature Art. 15.2. The new species differs from L. dentata by pigmented eyes vs. eyes absent and lack of palatine teeth vs. present. Lucifuga gibarensis seems to be most similar to the Bahamian species L. lucayana by showing pigmented eyes, 13 or 14 precaudal vertebrae and ten caudal fin rays. However, differs from it by a larger size of the pigmented eye (1.1-1.9 vs. 0.9-1.0% SL) and number of posterior lateral line neuromasts (30-33 vs. 34-35).},
}
@article {pmid32728217,
year = {2020},
author = {Meuleman, W and Muratov, A and Rynes, E and Halow, J and Lee, K and Bates, D and Diegel, M and Dunn, D and Neri, F and Teodosiadis, A and Reynolds, A and Haugen, E and Nelson, J and Johnson, A and Frerker, M and Buckley, M and Sandstrom, R and Vierstra, J and Kaul, R and Stamatoyannopoulos, J},
title = {Index and biological spectrum of human DNase I hypersensitive sites.},
journal = {Nature},
volume = {584},
number = {7820},
pages = {244-251},
pmid = {32728217},
issn = {1476-4687},
support = {R35 HG011317/HG/NHGRI NIH HHS/United States ; U54 HG007010/HG/NHGRI NIH HHS/United States ; UM1 HG009444/HG/NHGRI NIH HHS/United States ; },
mesh = {Chromatin/chemistry/*genetics/metabolism ; DNA/chemistry/genetics/*metabolism ; Deoxyribonuclease I/*metabolism ; Gene Expression Regulation ; Genes/genetics ; Genome, Human/genetics ; Humans ; *Molecular Sequence Annotation ; Promoter Regions, Genetic/genetics ; Regulatory Sequences, Nucleic Acid/genetics ; },
abstract = {DNase I hypersensitive sites (DHSs) are generic markers of regulatory DNA[1-5] and contain genetic variations associated with diseases and phenotypic traits[6-8]. We created high-resolution maps of DHSs from 733 human biosamples encompassing 438 cell and tissue types and states, and integrated these to delineate and numerically index approximately 3.6 million DHSs within the human genome sequence, providing a common coordinate system for regulatory DNA. Here we show that these maps highly resolve the cis-regulatory compartment of the human genome, which encodes unexpectedly diverse cell- and tissue-selective regulatory programs at very high density. These programs can be captured comprehensively by a simple vocabulary that enables the assignment to each DHS of a regulatory barcode that encapsulates its tissue manifestations, and global annotation of protein-coding and non-coding RNA genes in a manner orthogonal to gene expression. Finally, we show that sharply resolved DHSs markedly enhance the genetic association and heritability signals of diseases and traits. Rather than being confined to a small number of distal elements or promoters, we find that genetic signals converge on congruently regulated sets of DHSs that decorate entire gene bodies. Together, our results create a universal, extensible coordinate system and vocabulary for human regulatory DNA marked by DHSs, and provide a new global perspective on the architecture of human gene regulation.},
}
@article {pmid32727027,
year = {2020},
author = {Pédron, J and Guyon, L and Lecomte, A and Blottière, L and Chandeysson, C and Rochelle-Newall, E and Raynaud, X and Berge, O and Barny, MA},
title = {Comparison of Environmental and Culture-Derived Bacterial Communities through 16S Metabarcoding: A Powerful Tool to Assess Media Selectivity and Detect Rare Taxa.},
journal = {Microorganisms},
volume = {8},
number = {8},
pages = {},
pmid = {32727027},
issn = {2076-2607},
support = {Ec2co-CARTOBACTER//Centre National de la Recherche Scientifique/ ; CE32-2017-SPREE//Agence Nationale de la Recherche/ ; },
abstract = {To compare environmental and culture-derived microbial communities, we performed 16S metabarcoding of uncultured samples and their culture-derived bacterial lawns. Microbial communities were obtained from freshwater river samples representative of an anthropization gradient along a river stream. Their culture-derived bacterial lawns were obtained by growing aliquots of the samples on a broad range medium and on two different semi-selective media. The V3-V4 16S rRNA region was amplified and sequenced. The bacterial diversity of water samples decreased from the upper to lower stream sampling sites and, as expected, these differences were mostly suppressed by the culture step. Overall, the diversity of cultured-derived bacterial communities reflected selectivity of each tested medium. Comparison of treatments indicated that the culture selected both detected and rare undetected environmental species. Accurate detection of rare environmental bacteria of the Pectobacterium genus by 16S metabarcoding of the culture lawn was demonstrated. Interestingly, for abundant taxa, such as those of the Pseudomonas genus, the culture/environment ratio varied between sampled sites, indicating the difficulty of comparing cultured-derived taxa abundance between environmental sites. Finally, our study also highlighted media specificity and complementarity: bacterial communities grown on the two selective media, while selecting a small set of specific species, were mostly a subset of the bacterial community observed on the broad range medium.},
}
@article {pmid32722121,
year = {2020},
author = {Higuchi, R and Goto, T and Hirotsu, Y and Yokoyama, Y and Nakagomi, T and Otake, S and Amemiya, K and Oyama, T and Mochizuki, H and Omata, M},
title = {Primary Driver Mutations in GTF2I Specific to the Development of Thymomas.},
journal = {Cancers},
volume = {12},
number = {8},
pages = {},
pmid = {32722121},
issn = {2072-6694},
abstract = {Thymomas are rare mediastinal tumors that are difficult to treat and pose a major public health concern. Identifying mutations in target genes is vital for the development of novel therapeutic strategies. Type A thymomas possess a missense mutation in GTF2I (chromosome 7 c.74146970T>A) with high frequency. However, the molecular pathways underlying the tumorigenesis of other thymomas remain to be elucidated. We aimed to detect this missense mutation in GTF2I in other thymoma subtypes (types B). This study involved 22 patients who underwent surgery for thymomas between January 2014 and August 2019. We isolated tumor cells from formalin-fixed paraffin-embedded tissues from the primary lesions using laser-capture microdissection. Subsequently, we performed targeted sequencing to detect mutant GTF2I coupled with molecular barcoding. We used PyClone analysis to determine the fraction of tumor cells harboring mutant GTF2I. We detected the missense mutation (chromosome 7 c.74146970T>A) in GTF2I in 14 thymomas among the 22 samples (64%). This mutation was harbored in many type B thymomas as well as type A and AB thymomas. The allele fraction for the tumors containing the mutations was variable, primarily owing to the coexistence of normal lymphocytes in the tumors, especially in type B thymomas. PyClone analysis revealed a high cellular prevalence of mutant GTF2I in tumor cells. Mutant GTF2I was not detected in other carcinomas (lung, gastric, colorectal, or hepatocellular carcinoma) or lymphomas. In conclusion, the majority of thymomas harbor mutations in GTF2I that can be potentially used as a novel therapeutic target in patients with thymomas.},
}
@article {pmid32720487,
year = {2020},
author = {Ballesteros, I and Castillejo, P and Haro, AP and Montes, CC and Heinrich, C and Lobo, EA},
title = {Genetic barcoding of Ecuadorian epilithic diatom species suitable as water quality bioindicators.},
journal = {Comptes rendus biologies},
volume = {343},
number = {1},
pages = {41-52},
doi = {10.5802/crbiol.2},
pmid = {32720487},
issn = {1768-3238},
mesh = {DNA Barcoding, Taxonomic/methods ; Diatoms/*classification/genetics ; Ecosystem ; Ecuador ; *Environmental Biomarkers ; Eutrophication ; Phylogeny ; Rivers ; *Water Quality ; },
abstract = {Diatom identification is a key step in using these microorganisms as water quality bioindicators. Morphological diagnosis is a difficult task due to the enormous number of species and their microscopic size. This can be overcome using molecular tools to complement the diagnosis. The main goal of this work was to obtain the DNA barcode of Ecuadorian epilithic diatoms with a wide geographical distribution, a well-defined ecological range and characteristics that allow them to be reliable indicator species. Unialgal diatom cultures were obtained from environmental samples of Ecuadorian Andean streams. Morphological characterization of cultures was carried out under SEM microscopy. For molecular characterization, 18SV4 and rbcL barcodes were sequenced from each strain and blasted against a GenBank database. A phylogenetic tree for each barcode was constructed using the ML method including sequences of strains of the studied species from different geographical locations. The results showed the following five species to be suitable as bioindicators and these were isolated. Sellaphora seminulum (strain JA01b, c), Nitzschia fonticola (strain SP02a) and N. palea (strain CA01a) are tolerant to eutrophication; Eolimna minima (strain CH02a) is a mesotrophic water bioindicator, and Achnanthidium minutissimum (strain JA01a) is an oligotrophic water bioindicator. The comparison with the GenBank database of the barcoding regions supported the morphological identification. The barcoding sequences of the strains showed a high percentage of identity with the sequences reported in INSDC databases for the same species. The topology of the phylogenetic trees demonstrates that epilithic diatoms from Ecuador are closely related to those of same species isolated from other geographical regions. This study is a first attempt to establish a morphological and molecular taxonomic reference library for neotropical diatoms. This study demonstrates that it would be feasible to use the existing barcoding data for diatoms to develop molecular tools for the bioassessment of aquatic ecosystems in the Ecuadorian Andean region.},
}
@article {pmid32716260,
year = {2020},
author = {Liu, J and Haelewaters, D and Pfliegler, WP and Page, RA and Dick, CW and Aime, MC},
title = {A new species of Gloeandromyces from Ecuador and Panama revealed by morphology and phylogenetic reconstruction, with a discussion of secondary barcodes in Laboulbeniomycetes taxonomy.},
journal = {Mycologia},
volume = {112},
number = {6},
pages = {1192-1202},
doi = {10.1080/00275514.2020.1781496},
pmid = {32716260},
issn = {1557-2536},
mesh = {Animals ; Ascomycota/*classification/*genetics/isolation &amp; purification ; Chiroptera ; *DNA Barcoding, Taxonomic/methods ; DNA, Fungal/genetics ; Diptera/microbiology ; Ecuador ; Female ; Male ; Panama ; *Phylogeny ; },
abstract = {This paper describes and illustrates a new species of Laboulbeniales (Ascomycota, Laboulbeniomycetes) recovered from Mastoptera guimaraesi bat flies (Diptera, Streblidae) in Ecuador and Panama. Bat fly-associated Laboulbeniales are still unexplored in the Neotropics, with only four described species of Gloeandromyces and one species of Nycteromyces known. Morphological characteristics and phylogenetic analyses support placement of the new taxon in Gloeandromyces and its recognition as an undescribed species. Gloeandromyces hilleri sp. nov. is easily recognized by 2-3 longitudinal rows of undulations at its perithecial venter. Phylogenetic reconstructions of the large subunit (LSU) ribosomal DNA and the translation elongation factor 1α (TEF1) both resolve G. hilleri and G. nycteribiidarum as sister species. We discuss the utility of LSU and TEF1 as secondary barcodes in Laboulbeniomycetes taxonomy.},
}
@article {pmid32714773,
year = {2020},
author = {Lücking, R and Aime, MC and Robbertse, B and Miller, AN and Ariyawansa, HA and Aoki, T and Cardinali, G and Crous, PW and Druzhinina, IS and Geiser, DM and Hawksworth, DL and Hyde, KD and Irinyi, L and Jeewon, R and Johnston, PR and Kirk, PM and Malosso, E and May, TW and Meyer, W and Öpik, M and Robert, V and Stadler, M and Thines, M and Vu, D and Yurkov, AM and Zhang, N and Schoch, CL},
title = {Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?.},
journal = {IMA fungus},
volume = {11},
number = {},
pages = {14},
pmid = {32714773},
issn = {2210-6340},
abstract = {True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.},
}
@article {pmid32713859,
year = {2020},
author = {Oyebanji, OO and Chukwuma, EC and Bolarinwa, KA and Adejobi, OI and Adeyemi, SB and Ayoola, AO},
title = {Re-evaluation of the phylogenetic relationships and species delimitation of two closely related families (Lamiaceae and Verbenaceae) using two DNA barcode markers.},
journal = {Journal of biosciences},
volume = {45},
number = {},
pages = {},
pmid = {32713859},
issn = {0973-7138},
mesh = {Bayes Theorem ; *DNA Barcoding, Taxonomic ; Genetic Markers/genetics ; Lamiaceae/classification/*genetics ; *Phylogeny ; Species Specificity ; Verbenaceae/classification/*genetics ; },
abstract = {The families Lamiaceae and Verbenaceae comprise several closely related species that possess high morphological synapomorphic traits. Hence, there is a tendency of species misidentification using only the morphological characters. Herein, we evaluated the discriminatory power of the universal DNA barcodes (matK and rbcL) for 53 species spanning the two families. Using these markers, we inferred phylogenetic relationships and conducted species delimitation analysis using four delimitation methods: Automated Barcode Gap Discovery (ABGD), TaxonDNA, Bayesian Poisson Tree Processes (bPTP) and General Mixed Yule Coalescent (GMYC). The phylogenetic reconstruction based on the matK gene resolved the relationships between the families and further suggested the expansion of the Lamiaceae to include some core Verbanaceae genus, e.g., Gmelina. The rbcL marker using the TaxonDNA method displayed high species delimitation resolutions, while the ABGD, GMYC, and bPTP generated different number of Operational Taxonomic Units/genetic clusters. Our results underscored the efficiency of the matK and rbcL genes as reliable markers for resolving phylogenetic relationships and species delimitation of both families, respectively. The current study provides insights into the DNA barcode applications in these families, at the same time contributing to the current understanding of genetic divergence patterns in angiosperms.},
}
@article {pmid32712371,
year = {2020},
author = {Sakalauskaite, J and Marin, F and Pergolizzi, B and Demarchi, B},
title = {Shell palaeoproteomics: First application of peptide mass fingerprinting for the rapid identification of mollusc shells in archaeology.},
journal = {Journal of proteomics},
volume = {227},
number = {},
pages = {103920},
doi = {10.1016/j.jprot.2020.103920},
pmid = {32712371},
issn = {1876-7737},
mesh = {Animal Shells ; Animals ; *Archaeology ; *Bivalvia ; Peptide Mapping ; Peptides ; Phylogeny ; },
abstract = {Molluscs were one of the most widely-used natural resources in the past, and their shells are abundant among archaeological findings. However, our knowledge of the variety of shells that were circulating in prehistoric times (and thus their socio-economic and cultural value) is scarce due to the difficulty of achieving taxonomic determination of fragmented and/or worked remains. This study aims to obtain molecular barcodes based on peptide mass fingerprints (PMFs) of intracrystalline proteins, in order to obtain shell identification. Palaeoproteomic applications on shells are challenging, due to low concentration of molluscan proteins and an incomplete understanding of their sequences. We explore different approaches for protein extraction from small-size samples (<20 mg), followed by MALDI-TOF-MS analysis. The SP3 (single-pot, solid-phase) sample preparation method was found to be the most successful in retrieving the intracrystalline protein fraction from seven molluscan shell taxa, which belong to different phylogenetic groups, possess distinct microstructures and are relevant for archaeology. Furthermore, all the shells analysed, including a 7000-year-old specimen of the freshwater bivalve Pseudunio, yielded good-quality distinctive spectra, demonstrating that PMFs can be used for shell taxon determination. Our work suggests good potential for large-scale screening of archaeological molluscan remains. SIGNIFICANCE: We characterise for the first time the peptide mass fingerprints of the intracrystalline shell protein fraction isolated from different molluscan taxa. We demonstrate that these proteins yield distinctive PMFs, even for shells that are phylogenetically related and/or that display similar microstructures. Furthermore, we extend the range of sample preparation approaches for "shellomics" by testing the SP3 method, which proved to be well-suited to shell protein extraction from small-size and protein-poor samples. This work thus lays the foundations for future large-scale applications for the identification of mollusc shells and other invertebrate remains from the archaeological and palaeontological records.},
}
@article {pmid32711370,
year = {2020},
author = {Roman, MG and Houston, R},
title = {Investigation of chloroplast regions rps16 and clpP for determination of Cannabis sativa crop type and biogeographical origin.},
journal = {Legal medicine (Tokyo, Japan)},
volume = {47},
number = {},
pages = {101759},
doi = {10.1016/j.legalmed.2020.101759},
pmid = {32711370},
issn = {1873-4162},
mesh = {Canada ; Cannabis/chemistry/*classification/*genetics ; Chile ; Chloroplasts/*genetics ; *Crops, Agricultural ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant ; Forensic Genetics/*methods ; Genetic Loci ; Genome, Plant/genetics ; Genotype ; Haplotypes ; Mexico ; Phylogeny ; },
abstract = {Cannabis sativa can be classified as either hemp (a legal crop containing less than 0.3% delta-9-tetrahydrocannabinol, THC) or marijuana (an illegal drug containing more than 0.3% THC). Despite its legalization in 33 states for medicinal or recreational use, marijuana remains the most commonly used illicit drug in the USA, and it is heavily trafficked into and within the country. Discriminating between marijuana and hemp is critical to the legal process. Genetic analysis provides a means of analyzing samples unsuitable for chemical analysis, and in addition to discriminating between crop types, DNA may be able to determine the biogeographical origin of samples. In addition, the sharing of rare haplotypes between different seizures may be useful for linking cases and providing investigative leads to law enforcement. This study evaluates the potential of two highly polymorphic regions of the chloroplast genome of C. sativa, rps16 and clpP, to be used for determination of crop type and biogeographical origin. Custom fragment analysis and SNaPshot™ assays were developed to genotype nine polymorphic loci in hemp samples from the USA and Canada, marijuana samples from USA-Mexico and Chile, and medical marijuana samples from Chile. Haplotype analysis revealed eight haplotypes. Only Canadian hemp could be completely differentiated from the other sample groups by haplotype. Phylogenetic analysis and principal component analysis suggested a closer relationship among USA-Mexico marijuana, Chilean marijuana and medical marijuana, and USA hemp. Genotyping additional polymorphisms in future studies is expected to reveal further differences between these sample groups.},
}
@article {pmid32710387,
year = {2020},
author = {Matthes, N and Pietsch, K and Rullmann, A and Näumann, G and Pöpping, B and Szabo, K},
title = {The Barcoding Table of Animal Species (BaTAnS): a new tool to select appropriate methods for animal species identification using DNA barcoding.},
journal = {Molecular biology reports},
volume = {47},
number = {8},
pages = {6457-6461},
pmid = {32710387},
issn = {1573-4978},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Food Analysis/*methods ; Food Quality ; Meat/analysis ; },
abstract = {Food and feed products derived from animal materials have a long history of being adulterated. Methods for the identification of animal samples based on DNA barcoding are very potent tools to reveal species substitution. Since numerous DNA barcoding methods are available for different taxa, it is challenging to choose an appropriate and verified method for each sample in question. To overcome this obstacle the working group "Molecular biological methods for plant and animal species differentiation" developed the "Barcoding Table of Animal Species". This working group is established through the German food and feed law and is mandated to validate standard methods, especially for the official food and feed control laboratories in Germany. In this paper, a collection of currently available and verified DNA barcoding methods for the identification of animal species is presented as a Microsoft Excel[®] file-"The Barcoding Table of Animal Species (BaTAnS)". It consists of several components: The method collection, the results collection and a section for reporting new entries and problems. It is focusing on the validity and applicability of DNA barcoding methods to test food and feed products for correct species declaration. Each method is listed with its reference and is verified by at least two laboratories for their applicability. Since additional information will be available in future, this table will be updated regularly. The BaTAnS is an easy tool that helps to choose the right verified method to identify a certain specimen to taxon, genus or species level in food samples.},
}
@article {pmid32709929,
year = {2020},
author = {Arrigoni, L and Ferrari, F and Weller, J and Bella, C and Bönisch, U and Manke, T},
title = {AutoRELACS: automated generation and analysis of ultra-parallel ChIP-seq.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {12400},
pmid = {32709929},
issn = {2045-2322},
mesh = {Automation ; Cell Count ; Chromatin Immunoprecipitation/*methods ; Sequence Analysis, DNA/*methods ; },
abstract = {Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a method used to profile protein-DNA interactions genome-wide. Restriction Enzyme-based Labeling of Chromatin in Situ (RELACS) is a recently developed ChIP-seq protocol that deploys a chromatin barcoding strategy to enable standardized and high-throughput generation of ChIP-seq data. The manual implementation of RELACS is constrained by human processivity in both data generation and data analysis. To overcome these limitations, we have developed AutoRELACS, an automated implementation of the RELACS protocol using the liquid handler Biomek i7 workstation. We match the unprecedented processivity in data generation allowed by AutoRELACS with the automated computation pipelines offered by snakePipes. In doing so, we build a continuous workflow that streamlines epigenetic profiling, from sample collection to biological interpretation. Here, we show that AutoRELACS successfully automates chromatin barcode integration, and is able to generate high-quality ChIP-seq data comparable with the standards of the manual protocol, also for limited amounts of biological samples.},
}
@article {pmid32709120,
year = {2020},
author = {Rodríguez-Martínez, M and Hills, SA and Diffley, JFX and Svejstrup, JQ},
title = {Multiplex Cell Fate Tracking by Flow Cytometry.},
journal = {Methods and protocols},
volume = {3},
number = {3},
pages = {},
pmid = {32709120},
issn = {2409-9279},
support = {11567/CRUK_/Cancer Research UK/United Kingdom ; FC001166/CRUK_/Cancer Research UK/United Kingdom ; FC001166/WT_/Wellcome Trust/United Kingdom ; 693327/ERC_/European Research Council/International ; },
abstract = {Measuring differences in cell cycle progression is often essential to understand cell behavior under different conditions, treatments and environmental changes. Cell synchronization is widely used for this purpose, but unfortunately, there are many cases where synchronization is not an option. Many cell lines, patient samples or primary cells cannot be synchronized, and most synchronization methods involve exposing the cells to stress, which makes the method incompatible with the study of stress responses such as DNA damage. The use of dual-pulse labelling using EdU and BrdU can potentially overcome these problems, but the need for individual sample processing may introduce a great variability in the results and their interpretation. Here, we describe a method to analyze cell proliferation and cell cycle progression by double staining with thymidine analogues in combination with fluorescent cell barcoding, which allows one to multiplex the study and reduces the variability due to individual sample staining, reducing also the cost of the experiment.},
}
@article {pmid32698489,
year = {2020},
author = {Ekundayo, T and Okoh, A},
title = {Molecular Characterization, Intra-Species Diversity and Abundance of Freshwater Plesiomonas shigelloides Isolates.},
journal = {Microorganisms},
volume = {8},
number = {7},
pages = {},
pmid = {32698489},
issn = {2076-2607},
support = {99796 and 116382//South African Medical Research Council (SAMRC) and the National Research Foundation, The World Academy of Science (NRF-TWAS)/ ; },
abstract = {Molecular signatures of Plesiomonas shigelloides strain specific to pathogenic and nonpathogenic variants are not well established till present. There is a need for intra-species barcoding of P. shigelloides to aid infection control. This study aims at characterizing and assessing intra-species diversity and abundance of P. shigelloides isolated from three freshwaters in the Eastern Cape Province. The study used a Plesiomonas-specific PCR to characterize the isolates. Intra-species (dis)similarities were assessed using ERIC-PCR and (GTG)5-PCR techniques. The DNA fingerprints produced were electrophoresed, digitized, and documented via computer-assisted pattern analysis. The fingerprints were analyzed using neighbor-joining clustering (NJC) based on Euclidean similarity index. Results revealed 80%, 83.64%, and 80% of the water samples from Tyhume, Kat, and Kubusie rivers, respectively, positive for P. shigelloides isolation. The prevalence of P. shigelloides from sites ranged from 13.5% to 88.9%. NJC delineated 48 isolates to 8 clades (ERIC-fingerprints) and 34 isolates into 7 clades ((GTG)5-fingerprints). The relative abundance of unique strains ranged from 6.3% to 22.9% via the two methods. Both fingerprinting approaches have strain-differentiating potential for P. shigelloides, however ERIC-PCR possessed higher resolution (D = 37.46) advantage over (GTG)5-PCR (D = 29.64). In conclusion, the study achieved intra-species diversity and abundance of P. shigelloides from aquatic milieu and provide further opportunity for intra-species-specific barcoding.},
}
@article {pmid32695906,
year = {2020},
author = {Calvani, NED and Bell, L and Carney, A and De La Fuente, C and Stragliotto, T and Tunstall, M and Šlapeta, J},
title = {The molecular identity of fleas (Siphonaptera) carrying Rickettsia felis, Bartonella clarridgeiae and Bartonella rochalimae from dogs and cats in Northern Laos.},
journal = {Heliyon},
volume = {6},
number = {7},
pages = {e04385},
pmid = {32695906},
issn = {2405-8440},
abstract = {Cat fleas (Ctenocephalides felis) are the most commonly recognised ectoparasites of domestic pets globally and are frequently implicated in the transmission of a variety of zoonotic vector-borne pathogens. The aim of the present study was to investigate the morphological and molecular identity of fleas parasitising cats and dogs in Northern Laos and screen them for a range of bacterial pathogens. Fleas (n = 120) were collected from dogs and cats and morphologically identified as Ctenocephalides felis (115/120), Ctenocephalides orientis (4/120) and Pulex irritans (1/120). Molecular barcoding using the cytochrome c oxidase subunit I gene (cox1) was used to confirmed species identity of 21 selected fleas. The cat flea (C. felis) was the most dominant flea identified. Rickettsia and Bartonella spp. DNA was detected in 21/21 and 7/21 samples, respectively, via a multiplex real-time PCR targeting gltA and ssrA. Sequencing of the seven Bartonella-positive samples and ten Rickettsia-positive samples revealed Bartonella clarridgeiae, Bartonella rochalimae, Rickettsia felis and Rickettsia sp. genotype RF2125 DNA. Anaplasma platys DNA was detected in a single C. felis after 20 of the 21 DNA samples were screened using a commercial PCR panel for vector-borne pathogens. The detection of a range of bacterial pathogens in fleas from owned cats and dogs in Northern Laos provides further evidence to the importance of these ectoparasites as vectors of zoonotic diseases in the region.},
}
@article {pmid32694593,
year = {2020},
author = {Gostel, MR and Zúñiga, JD and Kress, WJ and Funk, VA and Puente-Lelievre, C},
title = {Author Correction: Microfluidic Enrichment Barcoding (MEBarcoding): a new method for high throughput plant DNA barcoding.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {12521},
doi = {10.1038/s41598-020-69598-4},
pmid = {32694593},
issn = {2045-2322},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}
@article {pmid32694527,
year = {2020},
author = {Sharaf, MR and Gotzek, D and Guénard, B and Fisher, BL and Aldawood, AS and Al Dhafer, HM and Mohamed, AA},
title = {Molecular phylogenetic analysis and morphological reassessments of thief ants identify a new potential case of biological invasions.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {12040},
pmid = {32694527},
issn = {2045-2322},
mesh = {Animals ; Ants/*anatomy &amp; histology/*classification/*genetics ; Florida ; Genes, Mitochondrial ; Geography ; Hawaii ; *Introduced Species ; *Phenotype ; *Phylogeny ; Saudi Arabia ; },
abstract = {Species delimitation offered by DNA-based approaches can provide important insights into the natural history and diversity of species, but the cogency of such processes is limited without multigene phylogenies. Recent attempts to barcode various Solenopsidini ant taxa (Hymenoptera: Formicidae: Myrmicinae), including the thief ant Solenopsis saudiensis Sharaf &amp; Aldawood, 2011 described from the Kingdom of Saudi Arabia (KSA), were precipitated by the unexpected existence of a closely related species, the Nearctic S. abdita Thompson, 1989 within the S. molesta species complex native to Florida. This finding left the species status of the former uncertain. Here, we investigated the taxonomy and phylogeny of these two species to determine whether or not S. abdita represents a new global tramp species. We inferred a phylogeny of the two species using DNA sequence data from four nuclear genes (Abd-A, EF1α-F1, EF1α-F2, and Wingless) and one mitochondrial gene (COI) sampled from populations in Florida, Guatemala, Hawaii, and Saudi Arabia. Both species clustered into one distinct and robust clade. The taxonomy of S. saudiensis was re-examined using morphometrics. A reassessment of the morphological characters used to diagnose the worker and queen castes were consistent with molecular evidence. Based on combined morphological and molecular evidences S. saudiensis is declared as a junior synonym of S. abdita (syn. nov.). In addition, our findings indicate that S. abdita is a novel global tramp species which has a far wider distribution than previously thought and has established itself in many new habitats and different geographic realms.},
}
@article {pmid32692749,
year = {2020},
author = {Ghazi, AR and Kong, X and Chen, ES and Edelstein, LC and Shaw, CA},
title = {Bayesian modelling of high-throughput sequencing assays with malacoda.},
journal = {PLoS computational biology},
volume = {16},
number = {7},
pages = {e1007504},
pmid = {32692749},
issn = {1553-7358},
support = {R01 HL128234/HL/NHLBI NIH HHS/United States ; },
mesh = {Bayes Theorem ; Computational Biology/*methods ; Genetic Variation/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Models, Statistical ; Sequence Analysis, DNA/*methods ; *Software ; },
abstract = {NGS studies have uncovered an ever-growing catalog of human variation while leaving an enormous gap between observed variation and experimental characterization of variant function. High-throughput screens powered by NGS have greatly increased the rate of variant functionalization, but the development of comprehensive statistical methods to analyze screen data has lagged. In the massively parallel reporter assay (MPRA), short barcodes are counted by sequencing DNA libraries transfected into cells and the cell's output RNA in order to simultaneously measure the shifts in transcription induced by thousands of genetic variants. These counts present many statistical challenges, including overdispersion, depth dependence, and uncertain DNA concentrations. So far, the statistical methods used have been rudimentary, employing transformations on count level data and disregarding experimental and technical structure while failing to quantify uncertainty in the statistical model. We have developed an extensive framework for the analysis of NGS functionalization screens available as an R package called malacoda (available from github.com/andrewGhazi/malacoda). Our software implements a probabilistic, fully Bayesian model of screen data. The model uses the negative binomial distribution with gamma priors to model sequencing counts while accounting for effects from input library preparation and sequencing depth. The method leverages the high-throughput nature of the assay to estimate the priors empirically. External annotations such as ENCODE data or DeepSea predictions can also be incorporated to obtain more informative priors-a transformative capability for data integration. The package also includes quality control and utility functions, including automated barcode counting and visualization methods. To validate our method, we analyzed several datasets using malacoda and alternative MPRA analysis methods. These data include experiments from the literature, simulated assays, and primary MPRA data. We also used luciferase assays to experimentally validate several hits from our primary data, as well as variants for which the various methods disagree and variants detectable only with the aid of external annotations.},
}
@article {pmid32690073,
year = {2020},
author = {Chan, AHE and Chaisiri, K and Morand, S and Saralamba, N and Thaenkham, U},
title = {Evaluation and utility of mitochondrial ribosomal genes for molecular systematics of parasitic nematodes.},
journal = {Parasites &amp; vectors},
volume = {13},
number = {1},
pages = {364},
pmid = {32690073},
issn = {1756-3305},
mesh = {Animals ; Classification ; DNA Barcoding, Taxonomic/*methods ; *Genes, Mitochondrial ; Genetic Markers ; Genome, Mitochondrial ; Humans ; *Nematoda/classification/genetics ; Parasites/classification/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Molecular advances have accelerated our understanding of nematode systematics and taxonomy. However, comparative analyzes between various genetic markers have led to discrepancies in nematode phylogenies. This study aimed to evaluate the suitability of using mitochondrial 12S and 16S ribosomal RNA genes for nematode molecular systematics.<br><br>METHODS: To study the suitability of mitochondrial 12S and 16S ribosomal RNA genes as genetic markers for nematode molecular systematics, we compared them with the other commonly used genetic markers, nuclear internal transcribed spacer 1 and 2 regions, nuclear 18S and 28S ribosomal RNA genes, and mitochondrial cytochrome c oxidase subunit 1 gene. After that, phylum-wide primers for mitochondrial 12S and 16S ribosomal RNA genes were designed, and parasitic nematodes of humans and animals from 75 taxa with 21 representative species were inferred through phylogenetic analyzes. Phylogenetic analyzes were carried out using maximum likelihood and Bayesian inference algorithms.<br><br>RESULTS: The phylogenetic relationships of nematodes based on the mitochondrial 12S rRNA gene supported the monophyly of nematodes in clades I, IV, and V, reinforcing the potential of this gene as a genetic marker for nematode systematics. In contrast, the mitochondrial 16S rRNA gene only supported the monophyly of clades I and V, providing evidence that the 12S rRNA gene is more suitable for nematode molecular systematics. In this study, subclades of clade III containing various nematode families were not monophyletic when the 16S or 12S rRNA gene was used as the genetic marker. This is similar to the phylogenetic relationship revealed by previous studies using whole mitochondrial genomes as genetic markers.<br><br>CONCLUSIONS: This study supports the use of the 12S rRNA gene as a genetic marker for studying the molecular systematics of nematodes to understand intra-phyla relationships. Phylum-wide primers for nematodes using mitochondrial ribosomal genes were prepared, which may enhance future studies. Furthermore, sufficient genetic variation in the mitochondrial 12S and 16S rRNA genes between species also allowed for accurate taxonomy to species level, revealing the potential of these two genes as genetic markers for DNA barcoding.},
}
@article {pmid32686876,
year = {2020},
author = {Juiz, N and Elkaoutari, A and Bigonnet, M and Gayet, O and Roques, J and Nicolle, R and Iovanna, J and Dusetti, N},
title = {Basal-like and classical cells coexist in pancreatic cancer revealed by single-cell analysis on biopsy-derived pancreatic cancer organoids from the classical subtype.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {34},
number = {9},
pages = {12214-12228},
doi = {10.1096/fj.202000363RR},
pmid = {32686876},
issn = {1530-6860},
mesh = {Biopsy ; Carcinoma, Pancreatic Ductal/*pathology ; Humans ; Organoids/*pathology ; Pancreatic Neoplasms/*pathology ; RNA-Seq ; Signal Transduction/physiology ; Single-Cell Analysis/*methods ; },
abstract = {Pancreatic ductal adenocarcinoma (PDAC) is composed of stromal, immune, and cancerous epithelial cells. Transcriptomic analysis of the epithelial compartment allows classification into different phenotypic subtypes as classical and basal-like. However, little is known about the intra-tumor heterogeneity particularly in the epithelial compartment. Growing evidences suggest that this phenotypic segregation is not so precise and different cancerous cell types may coexist in a single tumor. To test this hypothesis, we performed single-cell transcriptomic analyses using combinational barcoding exclusively on epithelial cells from six different classical PDAC patients obtained by Endoscopic Ultrasound (EUS) with Fine Needle Aspiration (FNA). To purify the epithelial compartment, PDAC were grown as biopsy-derived pancreatic cancer organoids. Single-cell transcriptomic analysis allowed the identification of four main cell clusters present in different proportions in all tumors. Remarkably, although all these tumors were classified as classical, one cluster present in all corresponded to a basal-like phenotype. These results reveal an unanticipated high heterogeneity of pancreatic cancers and demonstrate that basal-like cells, which have a highly aggressive phenotype, are more widespread than expected.},
}
@article {pmid32686820,
year = {2020},
author = {Čertnerová, D and Škaloud, P},
title = {Substantial intraspecific genome size variation in golden-brown algae and its phenotypic consequences.},
journal = {Annals of botany},
volume = {126},
number = {6},
pages = {1077-1087},
pmid = {32686820},
issn = {1095-8290},
mesh = {Biological Evolution ; *Chrysophyta ; Genome Size ; *Genome, Plant/genetics ; Ploidies ; },
abstract = {BACKGROUND AND AIMS: While nuclear DNA content variation and its phenotypic consequences have been well described for animals, vascular plants and macroalgae, much less about this topic is known regarding unicellular algae and protists in general. The dearth of data is especially pronounced when it comes to intraspecific genome size variation. This study attempts to investigate the extent of intraspecific variability in genome size and its adaptive consequences in a microalgal species.<br><br>METHODS: Propidium iodide flow cytometry was used to estimate the absolute genome size of 131 strains (isolates) of the golden-brown alga Synura petersenii (Chrysophyceae, Stramenopiles), identified by identical internal transcribed spacer (ITS) rDNA barcodes. Cell size, growth rate and genomic GC content were further assessed on a sub-set of strains. Geographic location of 67 sampling sites across the Northern hemisphere was used to extract climatic database data and to evaluate the ecogeographical distribution of genome size diversity.<br><br>KEY RESULTS: Genome size ranged continuously from 0.97 to 2.02 pg of DNA across the investigated strains. The genome size was positively associated with cell size and negatively associated with growth rate. Bioclim variables were not correlated with genome size variation. No clear trends in the geographical distribution of strains of a particular genome size were detected, and strains of different genome size occasionally coexisted at the same locality. Genomic GC content was significantly associated only with genome size via a quadratic relationship.<br><br>CONCLUSIONS: Genome size variability in S. petersenii was probably triggered by an evolutionary mechanism operating via gradual changes in genome size accompanied by changes in genomic GC content, such as, for example, proliferation of transposable elements. The variation was reflected in cell size and relative growth rate, possibly with adaptive consequences.},
}
@article {pmid32686307,
year = {2020},
author = {Catalano, M and Moroglu, M and Balbi, P and Mazzieri, F and Clayton, J and Andrews, KH and Bigatti, M and Scheuermann, J and Conway, SJ and Neri, D},
title = {Selective Fragments for the CREBBP Bromodomain Identified from an Encoded Self-assembly Chemical Library.},
journal = {ChemMedChem},
volume = {15},
number = {18},
pages = {1752-1756},
doi = {10.1002/cmdc.202000528},
pmid = {32686307},
issn = {1860-7187},
support = {BB/S507003/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Benzodiazepinones/chemical synthesis/chemistry/*pharmacology ; CREB-Binding Protein/*antagonists &amp; inhibitors/metabolism ; Cell Cycle Proteins/*antagonists &amp; inhibitors/metabolism ; Enzyme-Linked Immunosorbent Assay ; Humans ; Models, Molecular ; Molecular Structure ; Small Molecule Libraries/chemical synthesis/chemistry/*pharmacology ; Transcription Factors/*antagonists &amp; inhibitors/metabolism ; },
abstract = {DNA-encoded chemical libraries (DECLs) are collections of chemical moieties individually coupled to distinctive DNA barcodes. Compounds can be displayed either at the end of a single DNA strand (i. e., single-pharmacophore libraries) or at the extremities of two complementary DNA strands (i. e., dual-pharmacophore libraries). In this work, we describe the use of a dual-pharmacophore encoded self-assembly chemical (ESAC) library for the affinity maturation of a known 4,5-dihydrobenzodiazepinone ring (THBD) acetyl-lysine (KAc) mimic for the cyclic-AMP response element binding protein (CREB) binding protein (CREBBP or CBP) bromodomain. The new pair of fragments discovered from library selection showed a sub-micromolar affinity for the CREBBP bromodomain in fluorescence polarization and ELISA assays, and selectivity against BRD4(1).},
}
@article {pmid32684969,
year = {2020},
author = {Delrieu-Trottin, E and Durand, JD and Limmon, G and Sukmono, T and Kadarusman, and Sugeha, HY and Chen, WJ and Busson, F and Borsa, P and Dahruddin, H and Sauri, S and Fitriana, Y and Zein, MSA and Hocdé, R and Pouyaud, L and Keith, P and Wowor, D and Steinke, D and Hanner, R and Hubert, N},
title = {Biodiversity inventory of the grey mullets (Actinopterygii: Mugilidae) of the Indo-Australian Archipelago through the iterative use of DNA-based species delimitation and specimen assignment methods.},
journal = {Evolutionary applications},
volume = {13},
number = {6},
pages = {1451-1467},
pmid = {32684969},
issn = {1752-4571},
abstract = {DNA barcoding opens new perspectives on the way we document biodiversity. Initially proposed to circumvent the limits of morphological characters to assign unknown individuals to known species, DNA barcoding has been used in a wide array of studies where collecting species identity constitutes a crucial step. The assignment of unknowns to knowns assumes that species are already well identified and delineated, making the assignment performed reliable. Here, we used DNA-based species delimitation and specimen assignment methods iteratively to tackle the inventory of the Indo-Australian Archipelago grey mullets, a notorious case of taxonomic complexity that requires DNA-based identification methods considering that traditional morphological identifications are usually not repeatable and sequence mislabeling is common in international sequence repositories. We first revisited a DNA barcode reference library available at the global scale for Mugilidae through different DNA-based species delimitation methods to produce a robust consensus scheme of species delineation. We then used this curated library to assign unknown specimens collected throughout the Indo-Australian Archipelago to known species. A second iteration of OTU delimitation and specimen assignment was then performed. We show the benefits of using species delimitation and specimen assignment methods iteratively to improve the accuracy of specimen identification and propose a workflow to do so.},
}
@article {pmid32684778,
year = {2020},
author = {Wei, Z and Zhang, L and Shi, A},
title = {A note on the larva of Chalcophora japonica chinensis (Coleoptera, Buprestidae) based on morphological characters and molecular data.},
journal = {ZooKeys},
volume = {944},
number = {},
pages = {147-155},
pmid = {32684778},
issn = {1313-2989},
abstract = {Larvae of Chalcophora japonica chinensis Schaufuss, 1879 were collected from within dead trunks in Hubei Province, China, in February 2019. These specimens created an opportunity to provide the first description of the larval stage of this subspecies; The larva is described and illustrated based on morphological characters and DNA barcoding.},
}
@article {pmid32684775,
year = {2020},
author = {Chen, HY and Olmi, M and Pang, H and Liu, JX},
title = {Application of DNA barcoding confirms the host of Gonatopus viet Olmi, 1986 (Hymenoptera, Dryinidae).},
journal = {ZooKeys},
volume = {944},
number = {},
pages = {115-120},
pmid = {32684775},
issn = {1313-2989},
abstract = {Gonatopus viet Olmi, 1986 was originally described from Vietnam based on a single female. No further distribution records or hosts have been documented since its original discovery. In the present study, this species is newly recorded from China and its host is confirmed as Stirellus capitatus (Distant, 1918) using DNA barcoding techniques. The utility of DNA barcoding to discover host-Dryinidae associations is discussed.},
}
@article {pmid32683117,
year = {2020},
author = {Abdollahi, A and Roghani-Mamaqani, H and Salami-Kalajahi, M and Razavi, B},
title = {Encryption and authentication of security patterns by ecofriendly multi-color photoluminescent inks containing oxazolidine-functionalized nanoparticles.},
journal = {Journal of colloid and interface science},
volume = {580},
number = {},
pages = {192-210},
doi = {10.1016/j.jcis.2020.06.121},
pmid = {32683117},
issn = {1095-7103},
abstract = {Counterfeiting of confidential documents has been a costly challenge for banks, companies, and customers. Encryption of invisible security marks, such as barcodes, quick response codes, and logos, in national or international confidential documents by high-security anticounterfeiting inks is the most significant solution for counterfeiting problems. Ecofriendly multi-color photoluminescent anticounterfeiting inks based on highly-fluorescent polymer nanoparticles functionalized with new oxazolidine derivatives were developed for the fast and facile encryption of security labels on cellulosic documents, such as paper currency, passport, and certificate. Depending on the polarity of functionalized polymer nanoparticles, a wide range of colors and fluorescence emissions were observed as a result of polar-polar interactions between the oxazolidine molecules and surface functional groups of the nanoparticles. The fluorescent polymer nanoparticles showed spherical, vesicular, and cauliflower-like morphologies resulted from different surface functional groups. Functional polymer nanoparticles displayed high stability and printability on cellulosic substrates due to hydrogen bonding interactions. The highly-fluorescent polymer nanoparticles were also used to prepare anticounterfeiting inks with different colors and fluorescence emissions. All the ecofriendly polymeric anticounterfeiting inks were loaded to stamps with specific marks, and then applied to different confidential documents. Printed labels displayed highly intense fluorescence emission in different colors (green, orange, pink, and purple depending on the matrix polarity) under UV irradiation (365 nm). These water-based multi-color fluorescent anticounterfeiting inks with highly intense, bright, and sensitive fluorescence emission have potential applications in encryption and authentication of security patterns.},
}
@article {pmid32681513,
year = {2020},
author = {Morf, J and Wingett, SW},
title = {Proximity RNA-seq: A Sequencing Method to Identify Co-localization of RNA.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2161},
number = {},
pages = {175-194},
doi = {10.1007/978-1-0716-0680-3_13},
pmid = {32681513},
issn = {1940-6029},
mesh = {Animals ; Cell Line ; Cell Nucleus/metabolism ; Cells, Cultured ; Humans ; RNA/chemistry/metabolism ; RNA Transport ; RNA-Seq/*methods ; Transcriptome ; },
abstract = {RNA localization is an important regulatory layer of gene expression and cell functioning. The protocol guides through the Proximity RNA-seq method, in which RNA molecules are sequenced in their spatial, cellular context to derive RNA co-localization and transcriptome organization. Transcripts in individual subcellular particles from chemically crosslinked cells are tagged with the same, unique DNA barcode in water-in-oil emulsion droplets. First, single DNA barcodes are PCR amplified and immobilized on single, small magnetic beads in droplets. Subsequently, 3' ends of bead-bound barcode copies are tailed with random pentadecamers. Then beads are encapsulated again into droplets together with crosslinked subcellular particles containing RNA. Reverse transcription using random pentadecamers as primers is performed in droplets, which optimally contain one bead and one particle, in order to tag RNAs co-localized to the same particle. Sequencing such cDNA molecules identifies the RNA molecule and the barcode. Subsequent analysis of transcripts that share the same barcode, i.e., co-barcoding, reveals RNA co-localization and interactions. The technique is not restricted to pairs of RNAs but can as well detect groups of transcripts and estimates local RNA density or connectivity for individual transcripts. We provide here a detailed protocol to perform and analyze Proximity RNA-seq on cell nuclei to study spatial, nuclear RNA organization.},
}
@article {pmid32680870,
year = {2020},
author = {Dou, K and Lu, Z and Wu, Q and Ni, M and Yu, C and Wang, M and Li, Y and Wang, X and Xie, H and Chen, J and Zhang, C},
title = {MIST: a Multilocus Identification System for Trichoderma.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {18},
pages = {},
pmid = {32680870},
issn = {1098-5336},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic ; DNA, Fungal/analysis ; Multilocus Sequence Typing/*methods ; RNA, Fungal/*analysis ; RNA, Ribosomal/*analysis ; Species Specificity ; Trichoderma/*classification/genetics/*isolation &amp; purification ; },
abstract = {Due to the rapid expansion in microbial taxonomy, precise identification of common industrially and agriculturally relevant fungi such as Trichoderma species is challenging. In this study, we introduce the online multilocus identification system (MIST) for automated detection of 349 Trichoderma species based on a set of three DNA barcodes. MIST is based on the reference databases of validated sequences of three commonly used phylogenetic markers collected from public databases. The databases consist of 414 complete sequences of the nuclear rRNA internal transcribed spacers (ITS) 1 and 2, 583 sequence fragments of the gene encoding translation elongation factor 1-alpha (tef1), and 534 sequence fragments of the gene encoding RNA polymerase subunit 2 (rpb2). Through MIST, information from different DNA barcodes can be combined and the identification of Trichoderma species can be achieved based on the integrated parametric sequence similarity search (blastn) performed in the manner of a decision tree classifier. In the verification process, MIST provided correct identification for 44 Trichoderma species based on DNA barcodes consisting of tef1 and rpb2 markers. Thus, MIST can be used to obtain an automated species identification as well as to retrieve sequences required for manual identification by means of phylogenetic analysis.IMPORTANCE The genus Trichoderma is important to humankind, with a wide range of applications in industry, agriculture, and bioremediation. Thus, quick and accurate identification of Trichoderma species is paramount, since it is usually the first step in Trichoderma-based research. However, it frequently becomes a limitation, especially for researchers who lack taxonomic knowledge of fungi. Moreover, as the number of Trichoderma-based studies has increased, a growing number of unidentified sequences have been stored in public databases, which has made the species identification more ambiguous. In this study, we provide an easy-to-use tool, MIST, for automated species identification, a list of Trichoderma species, and corresponding sequences of reference DNA barcodes. Therefore, this study will facilitate the research on the biodiversity and applications of the genus Trichoderma.},
}
@article {pmid32680557,
year = {2020},
author = {Huang, X and Huang, D and Liang, Y and Zhang, L and Yang, G and Liu, B and Peng, Y and Deng, W and Dong, L},
title = {A new protocol for absolute quantification of haemosporidian parasites in raptors and comparison with current assays.},
journal = {Parasites &amp; vectors},
volume = {13},
number = {1},
pages = {354},
pmid = {32680557},
issn = {1756-3305},
support = {31772444//National Natural Science Foundation of China/ ; 31672297//National Natural Science Foundation of China/ ; 2019NTST13//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Animals ; Bird Diseases/parasitology ; Birds ; Genes, Protozoan ; Haemosporida/genetics/*isolation &amp; purification ; Pathology, Molecular/methods ; Plasmodium/genetics/isolation &amp; purification ; Raptors/*parasitology ; Real-Time Polymerase Chain Reaction/*methods ; },
abstract = {BACKGROUND: Accurate quantification of infection intensity is essential to estimate infection patterns of avian haemosporidian parasites in order to understand the evolution of host-parasite associations. Traditional microscopy is cost-effective but requires high-quality blood smears and considerable experience, while the widely used semi-quantitative qPCR methods are mostly employed with ideal, laboratory-based golden samples and standard curves, which may limit the comparison of parasitemia from different laboratories.<br><br>METHODS: Here we present a digital droplet PCR (ddPCR) protocol for absolute quantification of avian haemosporidians in raptors. Novel primers were designed that target a conserved fragment of a rRNA region of the mitochondrial genome of the parasites. Sensitivity and repeatability were evaluated compared to qPCR and other assays.<br><br>RESULTS: This ddPCR assay enables accurate quantification of haemosporidian parasites belonging to Plasmodium, Haemoproteus and Leucocytozoon with minimum infection quantities of 10[-5] (i.e. one parasite copy in 10[5] host genomes) without the use of standard curves. Quantities assessed by ddPCR were more accurate than qPCR using the same primers through reduction of non-specific amplification in low-intensity samples. The ddPCR technique was more consistent among technical duplicates and reactions, especially when infection intensities were low, and this technique demonstrated equal sensitivity with high correspondence (R[2]&#x2009;=&#x2009;0.97) compared to the widely used qPCR assay. Both ddPCR and qPCR identified more positive samples than the standard nested PCR protocol for the cytb gene used for barcoding avian haemosporidians.<br><br>CONCLUSIONS: We developed a novel ddPCR assay enabling accurate quantification of avian haemosporidians without golden samples or standard curves. This assay can be used as a robust method for investigating infection patterns in different host-parasite assemblages and can facilitate the comparison of results from different laboratories.},
}
@article {pmid32680458,
year = {2020},
author = {Zhang, X and Sun, Y and Landis, JB and Lv, Z and Shen, J and Zhang, H and Lin, N and Li, L and Sun, J and Deng, T and Sun, H and Wang, H},
title = {Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes.},
journal = {BMC plant biology},
volume = {20},
number = {1},
pages = {340},
pmid = {32680458},
issn = {1471-2229},
support = {U1802232//Key Projects of the Joint Fund of the National Natural Science Foundation of China/ ; 2019QZKK0502//Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; 2017YFC0505200//National Key R&amp;D Program of China/ ; XDA20050203//Strategic Priority Research Program of Chinese Academy of Sciences/ ; },
mesh = {DNA Barcoding, Taxonomic ; Evolution, Molecular ; *Genetic Heterogeneity ; Genetic Markers/genetics ; Genome, Plastid/*genetics ; Gentianaceae/*genetics ; Nucleotides/genetics ; Phylogeny ; Plastids/*genetics ; },
abstract = {BACKGROUND: Plastome-scale data have been prevalent in reconstructing the plant Tree of Life. However, phylogenomic studies currently based on plastomes rely primarily on maximum likelihood inference of concatenated alignments of plastid genes, and thus phylogenetic discordance produced by individual plastid genes has generally been ignored. Moreover, structural and functional characteristics of plastomes indicate that plastid genes may not evolve as a single locus and are experiencing different evolutionary forces, yet the genetic characteristics of plastid genes within a lineage remain poorly studied.<br><br>RESULTS: We sequenced and annotated 10 plastome sequences of Gentianeae. Phylogenomic analyses yielded robust relationships among genera within Gentianeae. We detected great variation of gene tree topologies and revealed that more than half of the genes, including one (atpB) of the three widely used plastid markers (rbcL, atpB and matK) in phylogenetic inference of Gentianeae, are likely contributing to phylogenetic ambiguity of Gentianeae. Estimation of nucleotide substitution rates showed extensive rate heterogeneity among different plastid genes and among different functional groups of genes. Comparative analysis suggested that the ribosomal protein (RPL and RPS) genes and the RNA polymerase (RPO) genes have higher substitution rates and genetic variations among plastid genes in Gentianeae. Our study revealed that just one (matK) of the three (matK, ndhB and rbcL) widely used markers show high phylogenetic informativeness (PI) value. Due to the high PI and lowest gene-tree discordance, rpoC2 is advocated as a promising plastid DNA barcode for taxonomic studies of Gentianeae. Furthermore, our analyses revealed a positive correlation of evolutionary rates with genetic variation of plastid genes, but a negative correlation with gene-tree discordance under purifying selection.<br><br>CONCLUSIONS: Overall, our results demonstrate the heterogeneity of nucleotide substitution rates and genetic characteristics among plastid genes providing new insights into plastome evolution, while highlighting the necessity of considering gene-tree discordance into phylogenomic studies based on plastome-scale data.},
}
@article {pmid32678985,
year = {2021},
author = {Ogwang, J and Bariche, M and Bos, AR},
title = {Genetic diversity and phylogenetic relationships of threadfin breams (Nemipterus spp.) from the Red Sea and eastern Mediterranean Sea.},
journal = {Genome},
volume = {64},
number = {3},
pages = {207-216},
doi = {10.1139/gen-2019-0163},
pmid = {32678985},
issn = {1480-3321},
mesh = {Animals ; Electron Transport Complex IV/genetics ; Fishes/*classification/*genetics ; Genetic Variation ; Haplotypes ; Indian Ocean ; Mediterranean Sea ; Phylogeny ; },
abstract = {The present work utilized partial sequences of cytochrome c oxidase subunit I (COI) to study Red Sea populations of threadfin breams (Nemipteridae), and compare their genetic diversity to that of Mediterranean Sea (Nemipterus randalli only) and Indo-Pacific populations. A Maximum Likelihood tree separated four fish species - N. randalli, N. japonicus, N. bipunctatus, and N. zysron - into four clades. Haplotype analyses revealed a strong case of the founder effect for the Lessepsian migrant N. randalli: Three haplotypes represented all sampled geographical ranges in the Mediterranean Sea and only one haplotype was shared with a Red Sea individual, presenting evidence that the colonizing population was founded by a small number of migrants. The Red Sea population of N. japonicus shared haplotypes with Persian Gulf and Indian Ocean populations, but South China Sea populations remained fully isolated. The haplotype networks of N. randalli and N. bipunctatus also revealed haplotype sharing between Red Sea and Indian Ocean populations. For N. zysron, one haplotype was shared between Indonesia and the Persian Gulf. We discuss the impact of continued usage of public database sequences of initially misidentified organisms and provide recommendations for avoiding distribution of sequences with incorrect scientific names.},
}
@article {pmid32670345,
year = {2020},
author = {Cheng, Z and Shu, H and Zhang, S and Luo, B and Gu, R and Zhang, R and Ji, Y and Li, F and Long, C},
title = {From Folk Taxonomy to Species Confirmation of Acorus (Acoraceae): Evidences Based on Phylogenetic and Metabolomic Analyses.},
journal = {Frontiers in plant science},
volume = {11},
number = {},
pages = {965},
pmid = {32670345},
issn = {1664-462X},
abstract = {Plants in Acorus have been used as herbal medicine by various linguistic groups for thousands of years. Arguments of taxonomy of Acorus among scientists resulted in confusions and misuses of Acorus plants. The present study used different methods to investigate the classification of the genus, based on folk taxonomy. The relationships among Acorus species were revealed through phylogenetic analyses by constructing the Maximum Likelihood and Bayesian phylogenetic analyses based on sequences of two chloroplast regions (trnL-trnF and rbcL). All samples named with two so-called synonyms, Acorus macrospadiceus (Yamam.) F. N. Wei and Y. K. Li and Acorus tatarinowii Schott collected from different habitats, were clustered into separate groups, which revealed that they represented two independent species. Multivariate statistical analysis of metabolites from different Acorus populations were carried out based on UPLC-QTOF-MS data. Three independent analysis, principal component analysis, heat-map analysis, and hierarchical cluster analysis, showed that A. macrospadiceus and A. tatarinowii are different from two recognized species in the genus, A. calamus L. and A. gramineus Aiton. The results of phylogenetics and chemotaxonomy, together with morphological and ecological evidences, were consistent with traditional knowledge of local people related to Acorus taxa, which proved the significance of parataxonomy. Multiple evidences including morphological, ecological, folk taxonomic, phylogenetic, and chemical taxonomic results suggested that there are four species in the genus Acorus.},
}
@article {pmid32669716,
year = {2020},
author = {Rodriguez-Fraticelli, AE and Weinreb, C and Wang, SW and Migueles, RP and Jankovic, M and Usart, M and Klein, AM and Lowell, S and Camargo, FD},
title = {Single-cell lineage tracing unveils a role for TCF15 in haematopoiesis.},
journal = {Nature},
volume = {583},
number = {7817},
pages = {585-589},
pmid = {32669716},
issn = {1476-4687},
support = {K99 HL146983/HL/NHLBI NIH HHS/United States ; R01 HL141402/HL/NHLBI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; P01 HL131477/HL/NHLBI NIH HHS/United States ; //Wellcome Trust/United Kingdom ; R33 CA212697/CA/NCI NIH HHS/United States ; P01HL13147/NH/NIH HHS/United States ; HL128850-01A1/NH/NIH HHS/United States ; MR/K017047/1/MRC_/Medical Research Council/United Kingdom ; R01 HL128850/HL/NHLBI NIH HHS/United States ; WT103789AIA/WT_/Wellcome Trust/United Kingdom ; R33CA212697-01/NH/NIH HHS/United States ; },
mesh = {Animals ; Basic Helix-Loop-Helix Transcription Factors/genetics/*metabolism ; CRISPR-Cas Systems ; *Cell Lineage ; Cell Self Renewal ; Female ; *Hematopoiesis ; Hematopoietic Stem Cells/*cytology/*metabolism ; Mice ; *Single-Cell Analysis ; },
abstract = {Bone marrow transplantation therapy relies on the life-long regenerative capacity of haematopoietic stem cells (HSCs)[1,2]. HSCs present a complex variety of regenerative behaviours at the clonal level, but the mechanisms underlying this diversity are still undetermined[3-11]. Recent advances in single-cell RNA sequencing have revealed transcriptional differences among HSCs, providing a possible explanation for their functional heterogeneity[12-17]. However, the destructive nature of sequencing assays prevents simultaneous observation of stem cell state and function. To solve this challenge, we implemented expressible lentiviral barcoding, which enabled simultaneous analysis of lineages and transcriptomes from single adult HSCs and their clonal trajectories during long-term bone marrow reconstitution. Analysis of differential gene expression between clones with distinct behaviour revealed an intrinsic molecular signature that characterizes functional long-term repopulating HSCs. Probing this signature through in vivo CRISPR screening, we found the transcription factor TCF15 to be required and sufficient to drive HSC quiescence and long-term self-renewal. In situ, Tcf15 expression labels the most primitive subset of true multipotent HSCs. In conclusion, our work elucidates clone-intrinsic molecular programmes associated with functional stem cell heterogeneity and identifies a mechanism for the maintenance of the self-renewing HSC state.},
}
@article {pmid32669109,
year = {2020},
author = {Eyler, CE and Matsunaga, H and Hovestadt, V and Vantine, SJ and van Galen, P and Bernstein, BE},
title = {Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance.},
journal = {Genome biology},
volume = {21},
number = {1},
pages = {174},
pmid = {32669109},
issn = {1474-760X},
support = {DP1 CA216873/CA/NCI NIH HHS/United States ; KL2 TR002542/TR/NCATS NIH HHS/United States ; },
mesh = {Antineoplastic Agents/pharmacology/*therapeutic use ; Clonal Evolution ; Dasatinib/*therapeutic use ; Drug Resistance, Neoplasm/*genetics ; Epigenesis, Genetic ; Glioblastoma/drug therapy/*genetics ; Humans ; Insulin Receptor Substrate Proteins/genetics ; Receptor, Platelet-Derived Growth Factor alpha/*antagonists &amp; inhibitors ; Sequence Analysis, RNA ; Single-Cell Analysis ; },
abstract = {BACKGROUND: Tumors can evolve and adapt to therapeutic pressure by acquiring genetic and epigenetic alterations that may be transient or stable. A precise understanding of how such events contribute to intratumoral heterogeneity, dynamic subpopulations, and overall tumor fitness will require experimental approaches to prospectively label, track, and characterize resistant or otherwise adaptive populations at the single-cell level. In glioblastoma, poor efficacy of receptor tyrosine kinase (RTK) therapies has been alternatively ascribed to genetic heterogeneity or to epigenetic transitions that circumvent signaling blockade.<br><br>RESULTS: We combine cell lineage barcoding and single-cell transcriptomics to trace the emergence of drug resistance in stem-like glioblastoma cells treated with RTK inhibitors. Whereas a broad variety of barcoded lineages adopt a Notch-dependent persister phenotype that sustains them through early drug exposure, rare subclones acquire genetic changes that enable their rapid outgrowth over time. Single-cell analyses reveal that these genetic subclones gain copy number amplifications of the insulin receptor substrate-1 and substrate-2 (IRS1 or IRS2) loci, which activate insulin and AKT signaling programs. Persister-like cells and genomic amplifications of IRS2 and other loci are evident in primary glioblastomas and may underlie the inefficacy of targeted therapies in this disease.<br><br>CONCLUSIONS: A method for combined lineage tracing and scRNA-seq reveals the interplay between complementary genetic and epigenetic mechanisms of resistance in a heterogeneous glioblastoma tumor model.},
}
@article {pmid32667717,
year = {2020},
author = {Gao, Z and Xu, B and Zhang, T and Liu, Z and Zhang, W and Sun, X and Liu, Y and Wang, X and Wang, Z and Yan, Y and Hu, F and Meng, X and Zhao, YS},
title = {Spatially Responsive Multicolor Lanthanide-MOF Heterostructures for Covert Photonic Barcodes.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {59},
number = {43},
pages = {19060-19064},
doi = {10.1002/anie.202009295},
pmid = {32667717},
issn = {1521-3773},
support = {2017YFA0204502//Ministry of Science and Technology of the People's Republic of China/ ; 21905145//National Natural Science Foundation of China/ ; 11774188//National Natural Science Foundation of China/ ; 03010304//Incubation Program of Universities' Preponderant Discipline of Shandong Province/ ; 23170504//Mountain Tai Young Scholarship/ ; JQ201802//Excellent Youth Foundation of Shandong's Natural Scientific Committee/ ; },
abstract = {Micro/nanoscale photonic barcodes based on multicolor luminescent segmented heterojunctions hold potential for applications in information security. However, such multicolor heterojunctions reported thus far are exclusively based on static luminescent signals, thus restricting their application in advanced confidential information protection. Reported here is a strategy to design responsive photonic barcodes with heterobimetallic (Tb[3+] /Eu[3+]) metal-organic framework multicolor heterostructures. The spatial colors could be precisely controlled by thermally manipulating the energy-transfer process between the two lanthanides, thus achieving responsive covert photonic barcodes. Also demonstrated is that spatially resolved responsive barcodes with multi-responsive features could be created in a single heterostructure. These findings offer unique opportunities to purposely design highly integrated responsive microstructures and smart devices toward advanced anti-counterfeiting applications.},
}
@article {pmid32664630,
year = {2020},
author = {Sipiczki, M},
title = {Metschnikowia pulcherrima and Related Pulcherrimin-Producing Yeasts: Fuzzy Species Boundaries and Complex Antimicrobial Antagonism.},
journal = {Microorganisms},
volume = {8},
number = {7},
pages = {},
pmid = {32664630},
issn = {2076-2607},
support = {K-124417//National Research, Development and Innovation Office of Hungary/ ; },
abstract = {Yeasts affiliated with the Metschnikowia pulcherrima clade (subclade) of the large ascomycetous genus Metschnikowia frequently turn out to produce the characteristic maroon-red pulcherrimin when tested for pigment production and prove to exert antagonistic effects on many types of microorganisms. The determination of the exact taxonomic position of the strains is hampered by the shortage of distinctive morphological and physiological properties of the species of the clade and the lack of rDNA barcode gaps. The rDNA repeats of the type strains of the species are not homogenized and are assumed to evolve by a birth-and-death mechanism combined with reticulation. The taxonomic division is further hampered by the incomplete biological (reproductive) isolation of the species: certain type strains can be hybridized and genome sequencing revealed chimeric genome structures in certain strains that might have evolved from interspecies hybrids (alloploid genome duplication). Various mechanisms have been proposed for the antimicrobial antagonism. One is related to pulcherrimin production. The diffusible precursor of pulcherrimin, the pulcherriminic acid is secreted by the cells into the environment where it forms the insoluble pulcherrimin with the ferric ions. The lack of free iron caused by the immobilization of ferric ions inhibits the growth of many microorganisms. Recent results of research into the complexity of the taxonomic division of the pulcherrimin-producing Metschnikowia yeasts and the mechanism(s) underlying their antimicrobial antagonism are discussed in this review.},
}
@article {pmid32661870,
year = {2020},
author = {Ali, FS and Ismail, M and Aly, W},
title = {DNA barcoding to characterize biodiversity of freshwater fishes of Egypt.},
journal = {Molecular biology reports},
volume = {47},
number = {8},
pages = {5865-5877},
pmid = {32661870},
issn = {1573-4978},
mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Egypt ; Electron Transport Complex IV/*genetics ; Fishes/classification/*genetics ; Fresh Water ; *Genes, Mitochondrial ; Genetic Variation ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {The current study represents the first molecular characterization of freshwater fish species in Egypt from two major fish resources; the River Nile and Lake Nasser. A total of 160 DNA barcodes using a 655-bp-long fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene were generated from 37 species belonging to 32 genera that represent 15 families from nine orders. The studied species were identified using different molecular-based identification approaches, in addition to the morphological identification, including neighbor-joining (NJ) trees, Barcode Index Number, and Automatic Barcode Gap Discovery (ABGD). The average genetic divergence based on the Kimura two-parameter model (K2P) within orders, families, genera, and species were 0.175, 0.067, 0.02, and 0.008, respectively. The minimum and maximum K2P distance-based genetic divergences were 0.0 and 0.154, respectively. Nucleotide diversity (π) varied among families and ranged between 0.0% for families Malapteruridae, Auchenoglanididae, Schilbeidae, Anguillidae, Centropomidae and Tetraodontidae and 17% for family Cyprinidae. The current study cautions against the lack of species coverage at public databases which limits the accurate identification of newly surveyed species and recommends that multiple methods are encouraged for accurate species identification. The findings of the current study also support that COI barcode enabled effective fish species identification in River Nile and Lake Nasser. Moreover, the results of the current study will establish a comprehensive DNA barcode library for freshwater fishes along the River Nile in Egypt. Egyptian freshwater fish DNA barcodes will contribute substantially to future efforts in monitoring, conservation, and management of fisheries in Egypt.},
}
@article {pmid32661501,
year = {2020},
author = {Harmsen, S and Coskun, AF and Ganesh, S and Nolan, GP and Gambhir, SS},
title = {Isotopically Encoded Nanotags for Multiplexed Ion Beam Imaging.},
journal = {Advanced materials technologies},
volume = {5},
number = {7},
pages = {},
pmid = {32661501},
issn = {2365-709X},
support = {K25 AI140783/AI/NIAID NIH HHS/United States ; R01 CA182043/CA/NCI NIH HHS/United States ; U19 AI057229/AI/NIAID NIH HHS/United States ; U54 CA199075/CA/NCI NIH HHS/United States ; },
abstract = {High-dimensional profiling of markers and analytes using approaches, such as barcoded fluorescent imaging with repeated labeling and mass cytometry has allowed visualization of biological processes at the single-cell level. To address limitations of sensitivity and mass-channel capacity, a nanobarcoding platform is developed for multiplexed ion beam imaging (MIBI) using secondary ion beam spectrometry that utilizes fabricated isotopically encoded nanotags. Use of combinatorial isotope distributions in 100 nm sized nanotags expands the labeling palette to overcome the spectral bounds of mass channels. As a proof-of-principle, a four-digit (i.e., 0001-1111) barcoding scheme is demonstrated to detect 16 variants of [2]H, [19]F, [79/81]Br, and [127]I elemental barcode sets that are encoded in silica nanoparticle matrices. A computational debarcoding method and an automated machine learning analysis approach are developed to extract barcodes for accurate quantification of spatial nanotag distributions in large ion beam imaging areas up to 0.6 mm[2]. Isotopically encoded nanotags should boost the performance of mass imaging platforms, such as MIBI and other elemental-based bioimaging approaches.},
}
@article {pmid32661429,
year = {2020},
author = {Verma, SK and Biswas, N},
title = {A novel nucleic acid extraction method from aromatic herbs and dried herbal powders using cow skim milk.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {11513},
pmid = {32661429},
issn = {2045-2322},
mesh = {Animals ; Cattle ; DNA Barcoding, Taxonomic/methods ; DNA Primers/genetics ; DNA, Plant/chemistry/*isolation &amp; purification ; Female ; Milk/*chemistry ; Plants, Medicinal/*chemistry/classification/genetics ; Polymerase Chain Reaction/methods ; Powders/chemistry ; RNA, Plant/chemistry/*isolation &amp; purification ; },
abstract = {Authenticity of dried aromatic herbs and herbal powders for the ASU (ayurvedic, siddha, unani) drug formulations is a key of their clinical success. The DNA based authentication is an answer; however, extraction of PCR quality DNA from such material is often problematic due to the presence of various co-extracted PCR inhibitors. Here, we report a novel DNA isolation and purification method utilizing cow skim milk that successfully yields PCR quality DNA from the aromatic herbs and dried herbal powders. The improved method presented in this study could be used as an alternative to successfully extract PCR quality DNA from such plant materials. Further, we present a set of robust matK primers which could be used as plant barcoding resource in future studies.},
}
@article {pmid32661410,
year = {2020},
author = {Aghebat Rafat, A and Sagredo, S and Thalhammer, M and Simmel, FC},
title = {Barcoded DNA origami structures for multiplexed optimization and enrichment of DNA-based protein-binding cavities.},
journal = {Nature chemistry},
volume = {12},
number = {9},
pages = {852-859},
pmid = {32661410},
issn = {1755-4349},
support = {694410/ERC_/European Research Council/International ; },
mesh = {Aptamers, Nucleotide/chemistry/metabolism ; DNA/chemistry/*metabolism ; Humans ; Microscopy, Atomic Force ; Nanostructures/chemistry ; Nucleic Acid Conformation ; Protein Binding ; Proteins/chemistry/*metabolism ; Streptavidin/chemistry/metabolism ; Thrombin/chemistry/metabolism ; },
abstract = {Simultaneous binding of molecules by multiple binding partners is known to strongly reduce the apparent dissociation constant of the corresponding molecular complexes, and can be used to achieve strong, non-covalent molecular interactions. Based on this principle, efficient binding of proteins to DNA nanostructures has been achieved previously by placing several aptamers in close proximity to each other onto DNA scaffolds. Here, we develop an approach for exploring design parameters, such as the geometric arrangement or the nanomechanical properties of the binding sites, that use two-dimensional DNA origami-based nanocavities that bear aptamers with known mechanical properties at defined distances and orientations. The origami structures are labelled with barcodes, which enables large numbers of binding cavities to be investigated in parallel and under identical conditions, and facilitates a direct and reliable quantitative comparison of their binding yields. We demonstrate that binding geometry and mechanical properties have a dramatic effect on origami-based multivalent binding sites, and that optimization of linker spacings and flexibilities can improve the effective binding strength of the sites substantially.},
}
@article {pmid32660038,
year = {2020},
author = {Celiński, K and Sokołowska, J and Zemleduch-Barylska, A and Kuna, R and Kijak, H and Staszak, AM and Wojnicka-Półtorak, A and Chudzińska, E},
title = {Seed Total Protein Profiling in Discrimination of Closely Related Pines: Evidence from the Pinus mugo Complex.},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {7},
pages = {},
pmid = {32660038},
issn = {2223-7747},
support = {NN304060339//the Ministry of Science and Higher Education in Poland/ ; },
abstract = {The Pinus mugo complex includes several dozen closely related European mountain pines. The discrimination of specific taxa within this complex is still extremely challenging, although numerous methodologies have been used to solve this problem, including morphological and anatomical analyses, cytological studies, allozyme variability, and DNA barcoding, etc. In this study, we used the seed total protein (STP) patterns to search for taxonomically interesting differences among three closely-related pine taxa from the Pinus mugo complex and five more distant species from the Pinaceae family. It was postulated that STP profiling can serve as the backup methodology for modern taxonomic research, in which more sophisticated analyses, i.e., based on the DNA barcoding approach, have been found to be useless. A quantitative analysis of the STP profiles revealed characteristic electrophoretic patterns for all the analyzed taxa from Pinaceae. STP profiling enabled the discrimination of closely-related pine taxa, even of those previously indistinguishable by chloroplast DNA barcodes. The results obtained in this study indicate that STP profiling can be very useful for solving complex taxonomic puzzles.},
}
@article {pmid32659949,
year = {2020},
author = {Skowron Volponi, M},
title = {A Vivid Orange New Genus and Species of Braconid-Mimicking Clearwing Moth (Lepidoptera: Sesiidae) Found Puddling on Plecoptera Exuviae.},
journal = {Insects},
volume = {11},
number = {7},
pages = {},
pmid = {32659949},
issn = {2075-4450},
support = {2019/32/C/NZ8/00523//Narodowe Centrum Nauki/ ; expedition funds//ClearWing Foundation for Biodiversity/ ; },
abstract = {A clearwing moth with a distinct orange, black and white colour pattern was found sucking up fluids from Plecoptera (stonefly) exuviae on rocks, surrounded by water, on a river bank in Thailand. During this process, known as puddling, the sesiid ejected brown liquid, indicating that it was not imbibing water alone. The behaviour was documented via video recording. Morphological and DNA analyses indicate that the moth is a new genus and species of the tribe Osminiini and it is described herein as Aurantiosphecia piotrii genus et species nova. Two species of Aschistophleps Hampson, 1893 have been transferred to the newly established genus. The barcode sequence of the cytochrome c oxidase I gene was obtained with universal invertebrate primers after two sets of standard Lepidoptera primers failed to generate a product. Sections on behaviour, conditions of occurrence and possible mimicry models are included. The unique colouration and body posture of A. piotrii suggest that it is a braconid wasp mimic, with the mimicry model potentially also being the sesiid's parasitoid.},
}
@article {pmid32659298,
year = {2020},
author = {Beneke, T and Gluenz, E},
title = {Bar-seq strategies for the LeishGEdit toolbox.},
journal = {Molecular and biochemical parasitology},
volume = {239},
number = {},
pages = {111295},
doi = {10.1016/j.molbiopara.2020.111295},
pmid = {32659298},
issn = {1872-9428},
support = {15/16_MSD_83633/MRC_/Medical Research Council/United Kingdom ; },
mesh = {CRISPR-Cas Systems ; *DNA Barcoding, Taxonomic ; DNA Primers ; Databases, Nucleic Acid ; *Gene Editing ; Genome, Protozoan ; Kinetoplastida/*genetics ; Leishmania/genetics ; Trypanosoma/genetics ; },
abstract = {The number of fully sequenced genomes increases steadily but the function of many genes remains unstudied. To accelerate dissection of gene function in Leishmania spp. and other kinetoplastids we previously developed a streamlined pipeline for CRISPR-Cas9 gene editing, which we termed LeishGEdit. To facilitate high-throughput mutant screens we have adapted this pipeline by barcoding mutants with unique 17-nucleotide barcodes, allowing loss-of-function screens in mixed populations. Here we present primer design and analysis tools that facilitate these bar-seq strategies. We have developed a standalone easy-to-use pipeline to design CRISPR primers suitable for the LeishGEdit toolbox for any given genome and have generated a list of 14,995 barcodes. Barcodes and oligo sequences are now accessible through our website www.leishgedit.net allowing researchers to pursue bar-seq experiments in all currently available TriTrypDB genomes (release 41). This will streamline CRISPR bar-seq assays in kinetoplastids, enabling pooled mutant screens across the community.},
}
@article {pmid32659282,
year = {2020},
author = {Rot, A and Meiswinkel, R and Fleker, M and Blum, SE and Behar, A},
title = {Towards modernizing the taxonomy of Mediterranean Culicoides using classical morphology, mtDNA barcoding, and MALDI-TOF MS protein profiling.},
journal = {Acta tropica},
volume = {211},
number = {},
pages = {105628},
doi = {10.1016/j.actatropica.2020.105628},
pmid = {32659282},
issn = {1873-6254},
mesh = {Animals ; Ceratopogonidae/anatomy &amp; histology/*classification/genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Insect Proteins/*chemistry/genetics ; *Phylogeny ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; },
abstract = {Culicoides biting midges (Diptera: Ceratopogonidae) are a highly successful group of small (1-3 mm) hematophagous flies, infamous for the role they play as biological vectors for numerous pathogens of veterinary significance. The principal aim of the national animal disease surveillance program of Israel is to be able to rapidly sort and identify live field-captured insects including Culicoides for arbovirus screening. In this exploratory study, three identification methods-classical morphology, DNA barcoding, and MALDI-TOF MS-were applied simultaneously to individuals of 10 Culicoides species that commonly attack livestock in Israel. The strengths and limitations of the three methods are compared and evaluated. In essence, the CO1 barcoding and MALDI-TOF MS results closely matched those of classical morphology. Furthermore, at a higher level and in strong accordance with recognized subgenera, the 10 species, in the reconstructed phylogenies, coalesced into multiple deeper-branched monophyletic clades. However, some discrepancies between the molecular and protein profiling results did occur and proved difficult to assess in terms of taxonomic significance. This difficulty underscores how tricky it is to establish clear species limits when methods involving borderline cutoff values and similarity indices are used as a taxonomic aid. An added shortcoming of the pluralistic triple-method approach is that a significant percentage of the species-level depositions in the GenBank and BOLD databases are misidentified, hindering structured comparison and interpretation of the morphological and molecular results obtained. Aspects of the unresolved taxonomy of various biting midge assemblages within the Mediterranean basin, including minor changes to the Israeli Culicoides checklist, are discussed in light of the methods applied. It is observed that the direct access that classical morphology provides to the external environment (or species niche) is indispensable to the full and correct interpretation (and application) of concomitant molecular and protein profiling results. The Culicoides taxonomy of the future ought to be fully integrative, during which the assimilation of modern methodological advances should strengthen-rather than undermine-the morphological foundations laid down during the 260-year Linnaean epoch.},
}
@article {pmid32658789,
year = {2020},
author = {Paul, B and Kavia Raj, K and Murali, TS and Satyamoorthy, K},
title = {Species-specific genomic sequences for classification of bacteria.},
journal = {Computers in biology and medicine},
volume = {123},
number = {},
pages = {103874},
doi = {10.1016/j.compbiomed.2020.103874},
pmid = {32658789},
issn = {1879-0534},
mesh = {Bacteria/genetics ; *Genome, Bacterial/genetics ; *Genomics ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Modern bacterial classification relies on genomic relatedness. Genetic variation in bacterial populations present a big challenge for taxonomic classification and recently several bacterial species have been reclassified based on the intra-species genome comparison. These were facilitated by next generation sequencing technologies and advances in genome comparison approaches which led to the rearrangement of diverse bacterial species and revolution in the microbial classification system. One of the outcome of these studies is the development of suitable DNA barcodes as reliable and cost-effective method for identifying various bacterial genera. Towards refining this further, we have applied a genome comparison approach in 1104 bacterial genome assemblies (excluding plasmids) to identify unique genomic segments among intra-species genome assemblies. Using extensive bioinformatics analysis, we have identified species-specific genomic regions and designed unique primers for 100 different species (belonging to 62 genera) which includes 62 pathogenic and 13 opportunistic pathogenic bacterial species and built a database (http://slsdb.manipal.edu/bact/). These species-specific genomic regions will have a major impact on in silico and molecular methods aimed at bacterial classification and identification. These may also serve as better DNA barcodes than the markers currently used for delineation of bacteria and may also find application in various translational research programs.},
}
@article {pmid32657574,
year = {2020},
author = {Xiang, Y and Yan, H and Zheng, B and Faheem, A and Hu, Y},
title = {Microorganism@UiO-66-NH2 Composites for the Detection of Multiple Colorectal Cancer-Related microRNAs with Flow Cytometry.},
journal = {Analytical chemistry},
volume = {92},
number = {18},
pages = {12338-12346},
doi = {10.1021/acs.analchem.0c02017},
pmid = {32657574},
issn = {1520-6882},
mesh = {Colorectal Neoplasms/*diagnosis ; Escherichia coli/*chemistry ; *Flow Cytometry ; Humans ; Metal-Organic Frameworks/*chemistry ; MicroRNAs/*analysis ; Organometallic Compounds/*chemistry ; Phthalic Acids/*chemistry ; },
abstract = {High-throughput analyses of multitarget markers can facilitate rapid and accurate clinical diagnosis. Suspension array assays, a flow cytometry-based analysis technology, are among some of the most promising multicomponent analysis methods for clinical diagnostics and research purposes. These assays are appropriate for examining low-volume, complex samples having trace amounts of analytes due to superior elimination of background. Physical shape is an important and promising code system, which uses a set of visually distinct patterns to identify different assay particles. Here, we presented a morphology recognizable suspension arrays based on the microorganisms with different morphologies. In this study, UiO-66-NH2 (UiO stands for University of Oslo) metal-organic frameworks (MOFs), was wrapped on the microorganism surface to form an innovative class of microorganism@UiO-66-NH2 composites for suspension array assays. The use of microorganisms endowed composites barcoding ability with their different morphology and size. Meanwhile, the UiO-66-NH2 provided a stable rigid shell, large specific surface area, and metal(IV) ions with multiple binding sites, which could simplify the protein immobilization procedure and enhance detection sensitivity. With this method, simultaneous detection of three colorectal cancer-related microRNA (miRNA), including miRNA-21, miRNA-17, and miRNA-182, could be easily achieved with femtomolar sensitivity by using a commercial flow cytometer. The synergy between microorganisms and MOFs make the composites a prospective barcoding candidate with excellent characteristics for multicomponent analysis, offering great potential for the development of high throughput and accurate diagnostics.},
}
@article {pmid32656919,
year = {2020},
author = {Hanafy, RA and Johnson, B and Youssef, NH and Elshahed, MS},
title = {Assessing anaerobic gut fungal diversity in herbivores using D1/D2 large ribosomal subunit sequencing and multi-year isolation.},
journal = {Environmental microbiology},
volume = {22},
number = {9},
pages = {3883-3908},
doi = {10.1111/1462-2920.15164},
pmid = {32656919},
issn = {1462-2920},
support = {1557102//National Science Foundation/International ; },
mesh = {Animals ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Herbivory ; Neocallimastigomycota/classification/genetics/*isolation &amp; purification ; Phylogeny ; Ribosome Subunits, Large/*genetics ; Sequence Analysis, DNA ; },
abstract = {The anaerobic gut fungi (AGF, Neocallimastigomycota) reside in the alimentary tracts of herbivores where they play a central role in the breakdown of plant material. Here, we report on the development of the hypervariable domains D1/D2 of the large ribosomal subunit (D1/D2 LSU) as a barcoding marker for the AGF. We generated a reference D1/D2 LSU database for all cultured AGF genera, as well as the majority of candidate genera encountered in prior internal transcribed spacer 1 (ITS1)-based surveys. Subsequently, a D1/D2 LSU-based diversity survey using long read PacBio SMRT sequencing was conducted on faecal samples from 21 wild and domesticated herbivores. Twenty-eight genera and candidate genera were identified, including multiple novel lineages that were predominantly, but not exclusively, identified in wild herbivores. Association between certain AGF genera and animal lifestyles, or animal host family was observed. Finally, to address the current paucity of AGF isolates, concurrent isolation efforts utilizing multiple approaches to maximize recovery yielded 216 isolates belonging to 12 different genera, several of which have no prior cultured-representatives. Our results establish the utility of D1/D2 LSU and PacBio sequencing for AGF diversity surveys, the culturability of multiple AGF taxa, and demonstrate that wild herbivores represent a yet-untapped reservoir of AGF diversity.},
}
@article {pmid32654508,
year = {2020},
author = {Fettke, H and Steen, JA and Kwan, EM and Bukczynska, P and Keerthikumar, S and Goode, D and Docanto, M and Ng, N and Martelotto, L and Hauser, C and Southey, MC and Azad, AA and Nguyen-Dumont, T},
title = {Analytical validation of an error-corrected ultra-sensitive ctDNA next-generation sequencing assay.},
journal = {BioTechniques},
volume = {69},
number = {2},
pages = {133-140},
doi = {10.2144/btn-2020-0045},
pmid = {32654508},
issn = {1940-9818},
mesh = {Cell-Free Nucleic Acids/blood ; Circulating Tumor DNA/*blood ; *High-Throughput Nucleotide Sequencing/methods/standards ; Humans ; Liquid Biopsy/methods/standards ; Male ; Prostatic Neoplasms/blood/pathology ; Sensitivity and Specificity ; *Sequence Analysis, DNA/methods/standards ; },
abstract = {Plasma circulating tumor DNA (ctDNA) analysis has emerged as a minimally invasive means to perform molecular tumor typing. Here we developed a custom ultra-sensitive ctDNA next-generation sequencing assay using molecular barcoding technology and off-the-shelf reagents combined with bioinformatics tools for enhanced ctDNA analysis. Assay performance was assessed via a spike-in experiment and the technique was applied to analyze 41 plasma samples from men with advanced prostate cancer. Orthogonal validation was performed using a commercial assay. Sensitivity and specificity of 93 and 99.5% were recorded for ultra-rare somatic variants (<1%), with high concordance observed between the in-house and commercial assays. The optimized protocol dramatically improved the efficiency of the assay and enabled the detection of low-frequency somatic variants from plasma cell-free DNA (cfDNA).},
}
@article {pmid32653928,
year = {2020},
author = {Lin, YL and Sewunet, T and Kk, S and Giske, CG and Westerlund, F},
title = {Optical maps of plasmids as a proxy for clonal spread of MDR bacteria: a case study of an outbreak in a rural Ethiopian hospital.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {75},
number = {10},
pages = {2804-2811},
pmid = {32653928},
issn = {1460-2091},
mesh = {Anti-Bacterial Agents/pharmacology ; Child ; *Disease Outbreaks ; *Escherichia coli Infections/epidemiology ; Hospitals ; Humans ; Infant ; Multilocus Sequence Typing ; *Plasmids ; beta-Lactamases/genetics ; },
abstract = {OBJECTIVES: MDR bacteria have become a prevailing health threat worldwide. We here aimed to use optical DNA mapping (ODM) as a rapid method to trace nosocomial spread of bacterial clones and gene elements. We believe that this method has the potential to be a tool of pivotal importance for MDR control.<br><br>METHODS: Twenty-four Escherichia coli samples of ST410 from three different wards were collected at an Ethiopian hospital and their plasmids were analysed by ODM. Plasmids were specifically digested with Cas9 targeting the antibiotic resistance genes, stained by competitive binding and confined in nanochannels for imaging. The resulting intensity profiles (barcodes) for each plasmid were compared to identify potential clonal spread of resistant bacteria.<br><br>RESULTS: ODM demonstrated that a large fraction of the patients carried bacteria with a plasmid of the same origin, carrying the ESBL gene blaCTX-M-15, suggesting clonal spread. The results correlate perfectly with core genome (cg)MLST data, where bacteria with the same plasmid also had very similar cgMLST profiles.<br><br>CONCLUSIONS: ODM is a rapid discriminatory method for identifying plasmids and antibiotic resistance genes. Long-range deletions/insertions, which are challenging for short-read next-generation sequencing, can be easily identified and used to trace bacterial clonal spread. We propose that plasmid typing can be a useful tool to identify clonal spread of MDR bacteria. Furthermore, the simplicity of the method enables possible future application in low- and middle-income countries.},
}
@article {pmid32649839,
year = {2021},
author = {Kolter, A and Gemeinholzer, B},
title = {Plant DNA barcoding necessitates marker-specific efforts to establish more comprehensive reference databases.},
journal = {Genome},
volume = {64},
number = {3},
pages = {265-298},
doi = {10.1139/gen-2019-0198},
pmid = {32649839},
issn = {1480-3321},
mesh = {*DNA Barcoding, Taxonomic ; *DNA, Plant ; DNA, Ribosomal Spacer ; Databases, Nucleic Acid ; Genetic Markers ; Plants/*classification/genetics ; },
abstract = {The problem of low species-level identification rates in plants by DNA barcoding is exacerbated by the fact that reference databases are far from being comprehensive. We investigate the impact of increased sampling depth on identification success by analyzing the efficacy of established plant barcode marker sequences (rbcL, matK, trnL-trnF, psbA-trnH, ITS). Adding sequences of the same species to the reference database led to an increase in correct species assignment of +10.9% for rbcL and +19.0% for ITS. Simultaneously, erroneous identification dropped from ∼40% to ∼12.5%. Despite its evolutionary constraints, ITS showed the highest identification rate and identification gain by increased sampling effort, which makes it a very suitable marker in the planning phase of a barcode study. The limited sequence availability of trnL-trnF is problematic for an otherwise very promising plastid plant barcoding marker. Future developments in machine learning algorithms have the potential to give new impetus to plant barcoding, but are dependent on extensive reference databases. We expect that our results will be incorporated into future plans for the development of DNA barcoding reference databases and will lead to these being developed with greater depth and taxonomic coverage.},
}
@article {pmid32648670,
year = {2019},
author = {Yuk, JS and Shin, SW and Chun, SH and Ku, BM and Choi, YJ and Lim, YT and Luo, D and Ahn, MJ and Um, SH},
title = {Topological Transformation-Based Nanobarcoding for Detection and Enumeration of MicroRNAs and Single Nucleotide Polymorphism.},
journal = {Advanced biosystems},
volume = {3},
number = {7},
pages = {e1900013},
doi = {10.1002/adbi.201900013},
pmid = {32648670},
issn = {2366-7478},
mesh = {*DNA Barcoding, Taxonomic ; ErbB Receptors/genetics ; *Graphite ; Humans ; MicroRNAs/*genetics ; *Mutation ; *Polymorphism, Single Nucleotide ; },
abstract = {RNA biomarkers have been recently reported to be associated tightly with the diagnosis and prognosis of many diseases. Particularly, cancers considered to be a serious threat to primates are known to be vastly dominated by genetic networks where RNA plays a key role. RNAs are thus recognized as a major target group that can be used for numerous cancer treatments and it is still required to identify and enumerate them in an effective manner. Here, a new topological transformation-based nanobarcoding technique (TNT) is first reported using fluorescence-DNA barcodes engaged with graphene oxide (GOx) for effectively discriminating short RNAs such as miRNAs and their single nucleotide polyporphisms in tissue and plasma. Through topological transformation into 3D DNA-RNA polygonal structures, various kinds of microRNAs have been read at the same time and analyzed quantitatively. Also, it positively discerned epidermal growth factor receptor (EGFR) mutations known as single base variations of typical lung cancer specific RNAs. A single variant of 0.785% in target EGFR mutations is explicitly detected. It is speculated that the TNT may be a versatile method for polymerase chain reaction (PCR)-free practical diagnosis of several clinical genetic deviations such as significant biotic RNA and genic fragments and would be a promising alternative to conventional PCR terrains.},
}
@article {pmid32645030,
year = {2020},
author = {Vancuren, SJ and Dos Santos, SJ and Hill, JE and , },
title = {Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling.},
journal = {PloS one},
volume = {15},
number = {7},
pages = {e0235682},
pmid = {32645030},
issn = {1932-6203},
support = {//CIHR/Canada ; },
mesh = {Bacteria/genetics ; Chaperonin 60/*genetics ; DNA Barcoding, Taxonomic/*methods ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Vagina/microbiology ; },
abstract = {Amplification and sequencing of conserved genetic barcodes such as the cpn60 gene is a common approach to determining the taxonomic composition of microbiomes. Exact sequence variant calling has been proposed as an alternative to previously established methods for aggregation of sequence reads into operational taxonomic units (OTU). We investigated the utility of variant calling for cpn60 barcode sequences and determined the minimum sequence length required to provide species-level resolution. Sequence data from the 5´ region of the cpn60 barcode amplified from the human vaginal microbiome (n = 45), and a mock community were used to compare variant calling to de novo assembly of reads, and mapping to a reference sequence database in terms of number of OTU formed, and overall community composition. Variant calling resulted in microbiome profiles that were consistent in apparent composition to those generated with the other methods but with significant logistical advantages. Variant calling is rapid, achieves high resolution of taxa, and does not require reference sequence data. Our results further demonstrate that 150 bp from the 5´ end of the cpn60 barcode sequence is sufficient to provide species-level resolution of microbiota.},
}
@article {pmid32641802,
year = {2020},
author = {Gordon, MG and Inoue, F and Martin, B and Schubach, M and Agarwal, V and Whalen, S and Feng, S and Zhao, J and Ashuach, T and Ziffra, R and Kreimer, A and Georgakopoulos-Soares, I and Yosef, N and Ye, CJ and Pollard, KS and Shendure, J and Kircher, M and Ahituv, N},
title = {lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements.},
journal = {Nature protocols},
volume = {15},
number = {8},
pages = {2387-2412},
pmid = {32641802},
issn = {1750-2799},
support = {U01 MH116438/MH/NIMH NIH HHS/United States ; T32 HL007093/HL/NHLBI NIH HHS/United States ; UM1 HG009408/HG/NHGRI NIH HHS/United States ; R21 HG010683/HG/NHGRI NIH HHS/United States ; R01 GM142112/GM/NIGMS NIH HHS/United States ; P30 AR070155/AR/NIAMS NIH HHS/United States ; R21 HG010065/HG/NHGRI NIH HHS/United States ; R01 MH116438/MH/NIMH NIH HHS/United States ; U01 HG012192/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; F31 HG011007/HG/NHGRI NIH HHS/United States ; R01 MH109907/MH/NIMH NIH HHS/United States ; T32 GM067547/GM/NIGMS NIH HHS/United States ; },
mesh = {Base Sequence ; Lentivirus/*genetics ; Regulatory Sequences, Nucleic Acid/*genetics ; Sequence Analysis, DNA/*methods ; *Workflow ; },
abstract = {Massively parallel reporter assays (MPRAs) can simultaneously measure the function of thousands of candidate regulatory sequences (CRSs) in a quantitative manner. In this method, CRSs are cloned upstream of a minimal promoter and reporter gene, alongside a unique barcode, and introduced into cells. If the CRS is a functional regulatory element, it will lead to the transcription of the barcode sequence, which is measured via RNA sequencing and normalized for cellular integration via DNA sequencing of the barcode. This technology has been used to test thousands of sequences and their variants for regulatory activity, to decipher the regulatory code and its evolution, and to develop genetic switches. Lentivirus-based MPRA (lentiMPRA) produces 'in-genome' readouts and enables the use of this technique in hard-to-transfect cells. Here, we provide a detailed protocol for lentiMPRA, along with a user-friendly Nextflow-based computational pipeline-MPRAflow-for quantifying CRS activity from different MPRA designs. The lentiMPRA protocol takes ~2 months, which includes sequencing turnaround time and data processing with MPRAflow.},
}
@article {pmid32641511,
year = {2020},
author = {Dawadi, S and Simmons, N and Miklossy, G and Bohren, KM and Faver, JC and Ucisik, MN and Nyshadham, P and Yu, Z and Matzuk, MM},
title = {Discovery of potent thrombin inhibitors from a protease-focused DNA-encoded chemical library.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {29},
pages = {16782-16789},
pmid = {32641511},
issn = {1091-6490},
support = {P01 HD087157/HD/NICHD NIH HHS/United States ; },
mesh = {Combinatorial Chemistry Techniques ; DNA/*chemistry/*metabolism ; *Drug Discovery ; *Gene Library ; Humans ; Protease Inhibitors/chemistry/*pharmacology ; Small Molecule Libraries/chemistry/*pharmacology ; Thrombin/*antagonists &amp; inhibitors ; },
abstract = {DNA-encoded chemical libraries are collections of compounds individually coupled to unique DNA tags serving as amplifiable identification barcodes. By bridging split-and-pool combinatorial synthesis with the ligation of unique encoding DNA oligomers, million- to billion-member libraries can be synthesized for use in hundreds of healthcare target screens. Although structural diversity and desirable molecular property ranges generally guide DNA-encoded chemical library design, recent reports have highlighted the utility of focused DNA-encoded chemical libraries that are structurally biased for a class of protein targets. Herein, a protease-focused DNA-encoded chemical library was designed that utilizes chemotypes known to engage conserved catalytic protease residues. The three-cycle library features functional moieties such as guanidine, which interacts strongly with aspartate of the protease catalytic triad, as well as mild electrophiles such as sulfonamide, urea, and carbamate. We developed a DNA-compatible method for guanidinylation of amines and reduction of nitriles. Employing these optimized reactions, we constructed a 9.8-million-membered DNA-encoded chemical library. Affinity selection of the library with thrombin, a common protease, revealed a number of enriched features which ultimately led to the discovery of a 1 nM inhibitor of thrombin. Thus, structurally focused DNA-encoded chemical libraries have tremendous potential to find clinically useful high-affinity hits for the rapid discovery of drugs for targets (e.g., proteases) with essential functions in infectious diseases (e.g., severe acute respiratory syndrome coronavirus 2) and relevant healthcare conditions (e.g., male contraception).},
}
@article {pmid32638553,
year = {2020},
author = {Egizi, A and Bulaga-Seraphin, L and Alt, E and Bajwa, WI and Bernick, J and Bickerton, M and Campbell, SR and Connally, N and Doi, K and Falco, RC and Gaines, DN and Greay, TL and Harper, VL and Heath, ACG and Jiang, J and Klein, TA and Maestas, L and Mather, TN and Occi, JL and Oskam, CL and Pendleton, J and Teator, M and Thompson, AT and Tufts, DM and Umemiya-Shirafuji, R and VanAcker, MC and Yabsley, MJ and Fonseca, DM},
title = {First glimpse into the origin and spread of the Asian longhorned tick, Haemaphysalis longicornis, in the United States.},
journal = {Zoonoses and public health},
volume = {67},
number = {6},
pages = {637-650},
doi = {10.1111/zph.12743},
pmid = {32638553},
issn = {1863-2378},
mesh = {*Animal Distribution ; Animals ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Gene Expression Regulation, Enzymologic ; Ixodidae/*physiology ; United States ; },
abstract = {Established populations of Asian longhorned ticks (ALT), Haemaphysalis longicornis, were first identified in the United States (US) in 2017 by sequencing the mitochondrial cytochrome c oxidase subunit I (cox1) 'barcoding' locus followed by morphological confirmation. Subsequent investigations detected ALT infestations in 12, mostly eastern, US states. To gain information on the origin and spread of US ALT, we (1) sequenced cox1 from ALT populations across 9 US states and (2) obtained cox1 sequences from potential source populations [China, Japan and Republic of Korea (ROK) as well as Australia, New Zealand and the Kingdom of Tonga (KOT)] both by sequencing and by downloading publicly available sequences in NCBI GenBank. Additionally, we conducted epidemiological investigations of properties near its initial detection locale in Hunterdon County, NJ, as well as a broader risk analysis for importation of ectoparasites into the area. In eastern Asian populations (China/Japan/ROK), we detected 35 cox1 haplotypes that neatly clustered into two clades with known bisexual versus parthenogenetic phenotypes. In Australia/New Zealand/KOT, we detected 10 cox1 haplotypes all falling within the parthenogenetic cluster. In the United States, we detected three differentially distributed cox1 haplotypes from the parthenogenetic cluster, supporting phenotypic evidence that US ALT are parthenogenetic. While none of the source populations examined had all three US cox1 haplotypes, a phylogeographic network analysis supports a northeast Asian source for the US populations. Within the United States, epidemiological investigations indicate ALT can be moved long distances by human transport of animals, such as horses and dogs, with smaller scale movements on wildlife. These results have relevant implications for efforts aimed at minimizing the spread of ALT in the United States and preventing additional exotic tick introductions.},
}
@article {pmid32636489,
year = {2020},
author = {Weber, J and Braun, CJ and Saur, D and Rad, R},
title = {In vivo functional screening for systems-level integrative cancer genomics.},
journal = {Nature reviews. Cancer},
volume = {20},
number = {10},
pages = {573-593},
pmid = {32636489},
issn = {1474-1768},
mesh = {Animals ; CRISPR-Cas Systems ; Cell Transformation, Neoplastic/genetics/metabolism ; Cell Transformation, Viral ; DNA Transposable Elements ; Early Detection of Cancer ; *Genetic Association Studies/methods ; *Genetic Predisposition to Disease ; Genetic Testing/methods ; *Genomics/methods ; Humans ; Mutagenesis/drug effects/radiation effects ; Neoplasms/*diagnosis/*genetics/therapy ; Translational Research, Biomedical ; },
abstract = {With the genetic portraits of all major human malignancies now available, we next face the challenge of characterizing the function of mutated genes, their downstream targets, interactions and molecular networks. Moreover, poorly understood at the functional level are also non-mutated but dysregulated genomes, epigenomes or transcriptomes. Breakthroughs in manipulative mouse genetics offer new opportunities to probe the interplay of molecules, cells and systemic signals underlying disease pathogenesis in higher organisms. Herein, we review functional screening strategies in mice using genetic perturbation and chemical mutagenesis. We outline the spectrum of genetic tools that exist, such as transposons, CRISPR and RNAi and describe discoveries emerging from their use. Genome-wide or targeted screens are being used to uncover genomic and regulatory landscapes in oncogenesis, metastasis or drug resistance. Versatile screening systems support experimentation in diverse genetic and spatio-temporal settings to integrate molecular, cellular or environmental context-dependencies. We also review the combination of in vivo screening and barcoding strategies to study genetic interactions and quantitative cancer dynamics during tumour evolution. These scalable functional genomics approaches are transforming our ability to interrogate complex biological systems.},
}
@article {pmid32634147,
year = {2020},
author = {Sherwood, AR and Huisman, JM and Paiano, MO and Williams, TM and Kosaki, RK and Smith, CM and Giuseffi, L and Spalding, HL},
title = {Taxonomic determination of the cryptogenic red alga, Chondria tumulosa sp. nov., (Rhodomelaceae, Rhodophyta) from Papahānaumokuākea Marine National Monument, Hawai'i, USA: A new species displaying invasive characteristics.},
journal = {PloS one},
volume = {15},
number = {7},
pages = {e0234358},
pmid = {32634147},
issn = {1932-6203},
mesh = {Classification/methods ; Hawaii ; Introduced Species ; Islands ; Phylogeny ; Rhodophyta/*classification/*genetics ; Seaweed ; Sequence Analysis, DNA/methods ; },
abstract = {Survey cruises by the National Oceanic and Atmospheric Administration (NOAA) in 2016 and 2019 yielded specimens of an undetermined red alga that rapidly attained alarming levels of benthic coverage at Pearl and Hermes Atoll, Papahānaumokuākea Marine National Monument, Hawai'i. By 2019 the seaweed had covered large expanses on the northeast side of the atoll with mat-like, extensive growth of entangled thalli. Specimens were analyzed using light microscopy and molecular analysis, and were compared to morphological descriptions in the literature for closely related taxa. Light microscopy demonstrated that the specimens likely belonged to the rhodomelacean genus Chondria, yet comparisons to taxonomic literature revealed no morphological match. DNA sequence analyses of the mitochondrial COI barcode marker, the plastidial rbcL gene, and the nuclear SSU gene confirmed its genus-level placement and demonstrated that this alga was unique compared to all other available sequences. Based on these data, this cryptogenic seaweed is here proposed as a new species: Chondria tumulosa A.R.Sherwood &amp; J.M.Huisman sp. nov. Chondria tumulosa is distinct from all other species of Chondria based on its large, robust thalli, a mat-forming tendency, large axial diameter in mature branches (which decreases in diameter with subsequent orders of branching), terete axes, and bluntly rounded apices. Although C. tumulosa does not meet the criteria for the definition of an invasive species given that it has not been confirmed as introduced to Pearl and Hermes Atoll, this seaweed is not closely related to any known Hawaiian native species and is of particular concern given its sudden appearance and rapid increase in abundance in the Papahānaumokuākea Marine National Monument; an uninhabited, remote, and pristine island chain to the northwest of the Main Hawaiian Islands.},
}
@article {pmid32632238,
year = {2020},
author = {Hu, KH and Eichorst, JP and McGinnis, CS and Patterson, DM and Chow, ED and Kersten, K and Jameson, SC and Gartner, ZJ and Rao, AA and Krummel, MF},
title = {ZipSeq: barcoding for real-time mapping of single cell transcriptomes.},
journal = {Nature methods},
volume = {17},
number = {8},
pages = {833-843},
pmid = {32632238},
issn = {1548-7105},
support = {T32 GM007810/GM/NIGMS NIH HHS/United States ; P30 DK063720/DK/NIDDK NIH HHS/United States ; R33 CA247744/CA/NCI NIH HHS/United States ; R01 GM135462/GM/NIGMS NIH HHS/United States ; R01 CA197363/CA/NCI NIH HHS/United States ; R01 AI038903/AI/NIAID NIH HHS/United States ; R01 AI114787/AI/NIAID NIH HHS/United States ; U01 CA217864/CA/NCI NIH HHS/United States ; T32 CA177555/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Computational Biology ; DNA Barcoding, Taxonomic/*methods ; Gene Expression Regulation ; Lymph Nodes ; Mice ; NIH 3T3 Cells ; Single-Cell Analysis/*methods ; T-Lymphocytes ; Transcriptome/*genetics ; Tumor Microenvironment ; },
abstract = {Spatial transcriptomics seeks to integrate single cell transcriptomic data within the three-dimensional space of multicellular biology. Current methods to correlate a cell's position with its transcriptome in living tissues have various limitations. We developed an approach, called 'ZipSeq', that uses patterned illumination and photocaged oligonucleotides to serially print barcodes ('zipcodes') onto live cells in intact tissues, in real time and with an on-the-fly selection of patterns. Using ZipSeq, we mapped gene expression in three settings: in vitro wound healing, live lymph node sections and a live tumor microenvironment. In all cases, we discovered new gene expression patterns associated with histological structures. In the tumor microenvironment, this demonstrated a trajectory of myeloid and T cell differentiation from the periphery inward. A combinatorial variation of ZipSeq efficiently scales in the number of regions defined, providing a pathway for complete mapping of live tissues, subsequent to real-time imaging or perturbation.},
}
@article {pmid32632001,
year = {2020},
author = {Weinreb, C and Klein, AM},
title = {Lineage reconstruction from clonal correlations.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {29},
pages = {17041-17048},
pmid = {32632001},
issn = {1091-6490},
mesh = {Animals ; *Cell Lineage/genetics/physiology ; DNA Barcoding, Taxonomic/*methods ; Decision Trees ; Dendritic Cells/cytology ; Erythrocytes/cytology ; Hematopoiesis/genetics/physiology ; Leukocytes/cytology ; Models, Biological ; Systems Biology ; },
abstract = {A central task in developmental biology is to learn the sequence of fate decisions that leads to each mature cell type in a tissue or organism. Recently, clonal labeling of cells using DNA barcodes has emerged as a powerful approach for identifying cells that share a common ancestry of fate decisions. Here we explore the idea that stochasticity of cell fate choice during tissue development could be harnessed to read out lineage relationships after a single step of clonal barcoding. By considering a generalized multitype branching process, we determine the conditions under which the final distribution of barcodes over observed cell types encodes their bona fide lineage relationships. We then propose a method for inferring the order of fate decisions. Our theory predicts a set of symmetries of barcode covariance that serves as a consistency check for the validity of the method. We show that broken symmetries may be used to detect multiple paths of differentiation to the same cell types. We provide computational tools for general use. When applied to barcoding data in hematopoiesis, these tools reconstruct the classical hematopoietic hierarchy and detect couplings between monocytes and dendritic cells and between erythrocytes and basophils that suggest multiple pathways of differentiation for these lineages.},
}
@article {pmid32631223,
year = {2020},
author = {Bendová, B and Piálek, J and Ďureje, &#x13d; and Schmiedová, L and Čížková, D and Martin, JF and Kreisinger, J},
title = {How being synanthropic affects the gut bacteriome and mycobiome: comparison of two mouse species with contrasting ecologies.},
journal = {BMC microbiology},
volume = {20},
number = {1},
pages = {194},
pmid = {32631223},
issn = {1471-2180},
support = {18-17796Y//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/International ; 1501218//Grantov&#xe1; Agentura, Univerzita Karlova (CZ)/International ; },
mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Ribosomal/genetics ; Ecology ; Feces/microbiology ; Fungi/*classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Mice ; Microbiota ; Mycobiome ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: The vertebrate gastrointestinal tract is colonised by microbiota that have a major effect on the host's health, physiology and phenotype. Once introduced into captivity, however, the gut microbial composition of free-living individuals can change dramatically. At present, little is known about gut microbial changes associated with adaptation to a synanthropic lifestyle in commensal species, compared with their non-commensal counterparts. Here, we compare the taxonomic composition and diversity of bacterial and fungal communities across three gut sections in synanthropic house mouse (Mus musculus) and a closely related non-synanthropic mound-building mouse (Mus spicilegus).<br><br>RESULTS: Using Illumina sequencing of bacterial 16S rRNA amplicons, we found higher bacterial diversity in M. spicilegus and detected 11 bacterial operational taxonomic units with significantly different proportions. Notably, abundance of Oscillospira, which is typically higher in lean or outdoor pasturing animals, was more abundant in non-commensal M. spicilegus. ITS2-based barcoding revealed low diversity and high uniformity of gut fungi in both species, with the genus Kazachstania clearly dominant.<br><br>CONCLUSIONS: Though differences in gut bacteria observed in the two species can be associated with their close association with humans, changes due to a move from commensalism to captivity would appear to have caused larger shifts in microbiota.},
}
@article {pmid32630777,
year = {2020},
author = {Stillson, PT and Szendrei, Z},
title = {Identifying Leafhopper Targets for Controlling Aster Yellows in Carrots and Celery.},
journal = {Insects},
volume = {11},
number = {7},
pages = {},
pmid = {32630777},
issn = {2075-4450},
abstract = {Aster yellows phytoplasma (Candidatus Phytoplasma asteris) is a multi-host plant pathogen and is transmitted by at least 24 leafhopper species. Pathogen management is complex and requires a thorough understanding of vector dynamics. In the American Midwest, aster yellows is of great concern for vegetable farmers who focus on controlling one vector, Macrosteles quadrilineatus-the aster leafhopper. However, vegetable-associated leafhopper communities can be diverse. To investigate whether additional species are important aster yellows vectors, we surveyed leafhopper communities at commercial celery and carrot farms in Michigan from 2018 to 2019 and conducted real-time PCR to determine infection status. Leafhoppers were collected within crop fields and field edges and identified with DNA barcoding. Overall, we collected 5049 leafhoppers, with the most abundant species being M. quadrilineatus (57%) and Empoasca fabae-the potato leafhopper (23%). Our results revealed the most abundant aster yellows vector in Michigan in both crops is M. quadrilineatus, but we also found that E. fabae may be a potential vector for this pathogen. While several taxa reside in and near these crops, we did not find strong evidence that they contribute to phytoplasma infection. These findings indicate that M. quadrilineatus should be the primary target for controlling this pathogen.},
}
@article {pmid32623815,
year = {2020},
author = {Merckelbach, LM and Borges, LMS},
title = {Make every species count: fastachar software for rapid determination of molecular diagnostic characters to describe species.},
journal = {Molecular ecology resources},
volume = {20},
number = {6},
pages = {1761-1768},
doi = {10.1111/1755-0998.13222},
pmid = {32623815},
issn = {1755-0998},
mesh = {DNA ; *Genetic Markers ; *Genetic Speciation ; Phylogeny ; *Software ; },
abstract = {Only a fraction of species found so far has been described, particularly cryptic species uncovered by molecular data. The latter might require the use of molecular data for its diagnosis, but it is important to make use of the diagnostic content of the molecular data itself. The molecular character-based model provides discrete molecular diagnostic characters within DNA sequences that can be used in species descriptions fulfilling the requirement of most codes of nomenclature for a character-based description of species. Here, we introduce fastachar, a software developed to extract molecular diagnostic characters from one or several taxonomically informative DNA markers of a selected taxon compared with those of other taxa in a single step. The input data consist of a single file with aligned sequences in the fasta format, which can be created using alignment software such as mega or geneious. fastachar is an easy-to-use software with a graphical interface. Thus, the software does not require the user to have any knowledge of the underlying programming environment (Python). We hope this software, based on the method proposed by Jörger and Schrödl (Frontiers in Zoology, 10, 59, 2013) to describe cryptic species, will encourage researchers to take the final step in taxonomy: the formal description of species. We propose the use of this method and fastachar also for the inclusion of molecular data in the description of any species. fastachar is released as open-source software under GNU General Public License V3 and is freely available for all major operating systems from https://github.com/smerckel/FastaChar.},
}
@article {pmid32623275,
year = {2020},
author = {Kalra, S and Tizhoosh, HR and Choi, C and Shah, S and Diamandis, P and Campbell, CJV and Pantanowitz, L},
title = {Yottixel - An Image Search Engine for Large Archives of Histopathology Whole Slide Images.},
journal = {Medical image analysis},
volume = {65},
number = {},
pages = {101757},
doi = {10.1016/j.media.2020.101757},
pmid = {32623275},
issn = {1361-8423},
mesh = {Algorithms ; Humans ; *Neoplasms ; *Search Engine ; Software ; },
abstract = {With the emergence of digital pathology, searching for similar images in large archives has gained considerable attention. Image retrieval can provide pathologists with unprecedented access to the evidence embodied in already diagnosed and treated cases from the past. This paper proposes a search engine specialized for digital pathology, called Yottixel, a portmanteau for "one yotta pixel," alluding to the big-data nature of histopathology images. The most impressive characteristic of Yottixel is its ability to represent whole slide images (WSIs) in a compact manner. Yottixel can perform millions of searches in real-time with a high search accuracy and low storage profile. Yottixel uses an intelligent indexing algorithm capable of representing WSIs with a mosaic of patches which are then converted into barcodes, called "Bunch of Barcodes" (BoB), the most prominent performance enabler of Yottixel. The performance of the prototype platform is qualitatively tested using 300 WSIs from the University of Pittsburgh Medical Center (UPMC) and 2,020 WSIs from The Cancer Genome Atlas Program (TCGA) provided by the National Cancer Institute. Both datasets amount to more than 4,000,000 patches of 1000 × 1000 pixels. We report three sets of experiments that show that Yottixel can accurately retrieve organs and malignancies, and its semantic ordering shows good agreement with the subjective evaluation of human observers.},
}
@article {pmid32623089,
year = {2020},
author = {Paranaiba, RTF and Carvalho, CBV and Paiva, RS and Trindade, BR and Barros, MG and Souza, EP and Gontijo, AB and Silveira, D},
title = {DNA from wood - A simple approach facing a challenging matrix - A preliminary study.},
journal = {Forensic science international},
volume = {314},
number = {},
pages = {110371},
doi = {10.1016/j.forsciint.2020.110371},
pmid = {32623089},
issn = {1872-6283},
mesh = {Aspidosperma/*genetics ; Brazil ; Conservation of Natural Resources ; DNA, Plant/*isolation &amp; purification ; Databases, Nucleic Acid ; Forensic Genetics/methods ; Humans ; Pilot Projects ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; Specimen Handling/methods ; Wood/*genetics ; },
abstract = {Plant DNA barcoding has proven to be a handy tool for identifying botanical species. However, extracting DNA from woody materials is often a challenging task. Forensic applications, therefore, must be able to overcome the technical difficulties of this nature. A simple and successful adaptation, through a widely used method in forensic laboratories, using chemistry based on magnetic DNA isolation technology and a robotic platform, is presented here. The model case was the application of this adapted DNA extraction method for the identification of Aspidosperma spp., a genus comprising several species in all biomes of Brazil, including Cerrado and Rain Forest. Such technology adaptation can aid in the identification of seized material and help in investigations involving illegal logging and deforestation, ultimately contributing to environmental protection.},
}
@article {pmid32620832,
year = {2020},
author = {Palecanda, S and Feller, KD and Porter, ML},
title = {Using larval barcoding to estimate stomatopod species richness at Lizard Island, Australia for conservation monitoring.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {10990},
pmid = {32620832},
issn = {2045-2322},
mesh = {Animals ; Arthropod Proteins/genetics ; Australia ; Conservation of Natural Resources ; Crustacea/*classification/genetics/*growth &amp; development ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Islands ; Larva/classification/genetics/growth &amp; development ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Stomatopods (Crustacea, Stomatopoda) are well studied for their aggressive behavior and unique visual system as well as their commercial importance in Asian and European countries. Like many crustaceans, stomatopods undergo indirect development, passing though several larval stages before reaching maturity. Adult stomatopods can be difficult to catch due to their inaccessible habitats and cryptic coloration. By sampling larvae from the planktonic community, less effort is required to obtain accurate measures of species richness within a region. Stomatopod larvae were collected between 2006 and 2015 from the waters around the Lizard Island reef platform in Eastern Australia. Cytochrome oxidase I (COI) mitochondrial DNA sequences were generated from each larval sample and compared to a database of COI sequences tied to adult specimens. Of the 20 species collected from Lizard Island as adults which have COI data available, 18 species were identified from larval sampling. One additional species identified from larval samples, Busquilla plantei, was previously unknown from Lizard Island. Nine larval OTUs were found not to match any published adult sequences. Sampling larval stomatopod populations provides a comparable picture of the adult population to benthic sampling methods and may include species richness beyond what is measurable by sampling adult populations.},
}
@article {pmid32619493,
year = {2020},
author = {El-Nachef, D and Shi, K and Beussman, KM and Martinez, R and Regier, MC and Everett, GW and Murry, CE and Stevens, KR and Young, JE and Sniadecki, NJ and Davis, J},
title = {A Rainbow Reporter Tracks Single Cells and Reveals Heterogeneous Cellular Dynamics among Pluripotent Stem Cells and Their Differentiated Derivatives.},
journal = {Stem cell reports},
volume = {15},
number = {1},
pages = {226-241},
pmid = {32619493},
issn = {2213-6711},
support = {R01 HL128362/HL/NHLBI NIH HHS/United States ; T32 EB001650/EB/NIBIB NIH HHS/United States ; R01 HL146868/HL/NHLBI NIH HHS/United States ; R01 HL128368/HL/NHLBI NIH HHS/United States ; U54 DK107979/DK/NIDDK NIH HHS/United States ; P30 DK017047/DK/NIDDK NIH HHS/United States ; DP2 HL137188/HL/NHLBI NIH HHS/United States ; R01 HL141187/HL/NHLBI NIH HHS/United States ; R01 HL142624/HL/NHLBI NIH HHS/United States ; },
mesh = {*Cell Differentiation ; Cell Engineering ; Cell Line ; Cell Proliferation ; *Cell Tracking ; Clone Cells ; *Genes, Reporter ; Germ Layers/cytology ; Humans ; Kinetics ; Models, Biological ; Morphogenesis ; Pluripotent Stem Cells/*cytology ; },
abstract = {Single-cell transcriptomic approaches have found molecular heterogeneities within populations of pluripotent stem cells (PSCs). A tool that tracks single-cell lineages and their phenotypes longitudinally would reveal whether heterogeneity extends beyond molecular identity. Hence, we generated a stable Cre-inducible rainbow reporter human PSC line that provides up to 18 unique membrane-targeted fluorescent barcodes. These barcodes enable repeated assessments of single cells as they clonally expand, change morphology, and migrate. Owing to the cellular resolution of this reporter, we identified subsets of PSCs with enhanced clonal expansion, synchronized cell divisions, and persistent localization to colony edges. Reporter expression was stably maintained throughout directed differentiation into cardiac myocytes, cortical neurons, and hepatoblasts. Repeated examination of neural differentiation revealed self-assembled cortical tissues derive from clonally dominant progenitors. Collectively, these findings demonstrate the broad utility and easy implementation of this reporter line for tracking single-cell behavior.},
}
@article {pmid32619423,
year = {2020},
author = {Huang, L and Kebschull, JM and Fürth, D and Musall, S and Kaufman, MT and Churchland, AK and Zador, AM},
title = {BRICseq Bridges Brain-wide Interregional Connectivity to Neural Activity and Gene Expression in Single Animals.},
journal = {Cell},
volume = {182},
number = {1},
pages = {177-188.e27},
pmid = {32619423},
issn = {1097-4172},
support = {U19 MH114821/MH/NIMH NIH HHS/United States ; R01 NS073129/NS/NINDS NIH HHS/United States ; R01 DA036913/DA/NIDA NIH HHS/United States ; R01 EY022979/EY/NEI NIH HHS/United States ; R01 MH049159/MH/NIMH NIH HHS/United States ; U01 MH109113/MH/NIMH NIH HHS/United States ; RF1 MH114132/MH/NIMH NIH HHS/United States ; },
mesh = {Animals ; Brain Mapping ; *Connectome ; Decision Making ; *Gene Expression Regulation ; Male ; Mice, Inbred C57BL ; Mice, Neurologic Mutants ; Nerve Net/*physiology ; Neurons/*physiology ; Reproducibility of Results ; *Sequence Analysis, DNA ; Task Performance and Analysis ; },
abstract = {Comprehensive analysis of neuronal networks requires brain-wide measurement of connectivity, activity, and gene expression. Although high-throughput methods are available for mapping brain-wide activity and transcriptomes, comparable methods for mapping region-to-region connectivity remain slow and expensive because they require averaging across hundreds of brains. Here we describe BRICseq (brain-wide individual animal connectome sequencing), which leverages DNA barcoding and sequencing to map connectivity from single individuals in a few weeks and at low cost. Applying BRICseq to the mouse neocortex, we find that region-to-region connectivity provides a simple bridge relating transcriptome to activity: the spatial expression patterns of a few genes predict region-to-region connectivity, and connectivity predicts activity correlations. We also exploited BRICseq to map the mutant BTBR mouse brain, which lacks a corpus callosum, and recapitulated its known connectopathies. BRICseq allows individual laboratories to compare how age, sex, environment, genetics, and species affect neuronal wiring and to integrate these with functional activity and gene expression.},
}
@article {pmid32617188,
year = {2020},
author = {Spencer, ET and Richards, E and Steinwand, B and Clemons, J and Dahringer, J and Desai, P and Fisher, M and Fussell, S and Gorman, O and Jones, D and Le, A and Long, K and McMahan, C and Moscarito, C and Pelay, C and Price, E and Smith, A and VanSant, A and Bruno, JF},
title = {A high proportion of red snapper sold in North Carolina is mislabeled.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e9218},
pmid = {32617188},
issn = {2167-8359},
abstract = {Seafood mislabeling occurs when a market label is inaccurate, primarily in terms of species identity, but also regarding weight, geographic origin, or other characteristics. This widespread problem allows cheaper or illegally-caught species to be marketed as species desirable to consumers. Previous studies have identified red snapper (Lutjanus campechanus) as one of the most frequently mislabeled seafood species in the United States. To quantify how common mislabeling of red snapper is across North Carolina, the Seafood Forensics class at the University of North Carolina at Chapel Hill used DNA barcoding to analyze samples sold as "red snapper" from restaurants, seafood markets, and grocery stores purchased in ten counties. Of 43 samples successfully sequenced and identified, 90.7% were mislabeled. Only one grocery store chain (of four chains tested) accurately labeled red snapper. The mislabeling rate for restaurants and seafood markets was 100%. Vermilion snapper (Rhomboplites aurorubens) and tilapia (Oreochromis aureus and O. niloticus) were the species most frequently substituted for red snapper (13 of 39 mislabeled samples for both taxa, or 26 of 39 mislabeled total). This study builds on previous mislabeling research by collecting samples of a specific species in a confined geographic region, allowing local vendors and policy makers to better understand the scope of red snapper mislabeling in North Carolina. This methodology is also a model for other academic institutions to engage undergraduate researchers in mislabeling data collection, sample processing, and analysis.},
}
@article {pmid32616799,
year = {2020},
author = {Carrasquilla, M and Adjalley, S and Sanderson, T and Marin-Menendez, A and Coyle, R and Montandon, R and Rayner, JC and Pance, A and Lee, MCS},
title = {Defining multiplicity of vector uptake in transfected Plasmodium parasites.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {10894},
pmid = {32616799},
issn = {2045-2322},
support = {/WT_/Wellcome Trust/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Biological Transport ; Calmodulin/genetics ; Clone Cells ; DNA Barcoding, Taxonomic ; DNA, Recombinant/*metabolism ; Electroporation ; Erythrocytes/parasitology ; Flow Cytometry ; Gene Library ; Genetic Vectors/genetics/*metabolism ; Humans ; Luminescent Proteins/genetics ; Plasmids/genetics/*metabolism ; Plasmodium falciparum/genetics/growth &amp; development/*metabolism ; Plasmodium knowlesi/genetics/growth &amp; development/metabolism ; Promoter Regions, Genetic ; Species Specificity ; Transfection/*methods ; },
abstract = {The recurrent emergence of drug resistance in Plasmodium falciparum increases the urgency to genetically validate drug resistance mechanisms and identify new targets. Reverse genetics have facilitated genome-scale knockout screens in Plasmodium berghei and Toxoplasma gondii, in which pooled transfections of multiple vectors were critical to increasing scale and throughput. These approaches have not yet been implemented in human malaria species such as P. falciparum and P. knowlesi, in part because the extent to which pooled transfections can be performed in these species remains to be evaluated. Here we use next-generation sequencing to quantitate uptake of a pool of 94 barcoded vectors. The distribution of vector acquisition allowed us to estimate the number of barcodes and DNA molecules taken up by the parasite population. Dilution cloning of P. falciparum transfectants showed that individual clones possess as many as seven episomal barcodes, revealing that an intake of multiple vectors is a frequent event despite the inefficient transfection efficiency. Transfection of three spectrally-distinct fluorescent reporters allowed us to evaluate different transfection methods and revealed that schizont-stage transfection limited the tendency for parasites to take up multiple vectors. In contrast to P. falciparum, we observed that the higher transfection efficiency of P. knowlesi resulted in near complete representation of the library. These findings have important implications for how reverse genetics can be scaled in culturable Plasmodium species.},
}
@article {pmid32615399,
year = {2020},
author = {Amorim, A and Pereira, F and Alves, C and García, O},
title = {Species assignment in forensics and the challenge of hybrids.},
journal = {Forensic science international. Genetics},
volume = {48},
number = {},
pages = {102333},
doi = {10.1016/j.fsigen.2020.102333},
pmid = {32615399},
issn = {1878-0326},
mesh = {Animals ; Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; *Forensic Genetics ; *Hybridization, Genetic ; *Species Specificity ; },
abstract = {Forensic identification of species is in growing demand, particularly from law enforcement authorities in the areas of wildlife, fisheries and hunting as well as food authentication. Within the non-human forensic genetics expanding applications' field, the major current difficulties result from the lack of standards and genetic databases as well as the poor or absent taxonomic definition of several groups. Here we focus on a forensically important and overlooked problem in species identification: the exclusive use of uniparental markers, a common practice in current genetic barcoding methodologies, may lead to incorrect or impossible assignment whenever hybrids can occur (frequently, not only in domesticates, but also in the wild). For example, if one of these cases involves a mammal, and mitochondrial DNA alone is used (which in instances may be the only type of DNA sequence available in databases), the sample will be wrongfully assigned to the female parental species, completely missing the detection of a possible hybrid animal. The importance of this issue in the forensic contributions to food authentication, wildlife and conservation genetics is analyzed. We present a cautionary guidance on the forensic reporting of results avoiding this error.},
}
@article {pmid32613204,
year = {2020},
author = {Corsello, SM and Nagari, RT and Spangler, RD and Rossen, J and Kocak, M and Bryan, JG and Humeidi, R and Peck, D and Wu, X and Tang, AA and Wang, VM and Bender, SA and Lemire, E and Narayan, R and Montgomery, P and Ben-David, U and Garvie, CW and Chen, Y and Rees, MG and Lyons, NJ and McFarland, JM and Wong, BT and Wang, L and Dumont, N and O'Hearn, PJ and Stefan, E and Doench, JG and Harrington, CN and Greulich, H and Meyerson, M and Vazquez, F and Subramanian, A and Roth, JA and Bittker, JA and Boehm, JS and Mader, CC and Tsherniak, A and Golub, TR},
title = {Discovering the anti-cancer potential of non-oncology drugs by systematic viability profiling.},
journal = {Nature cancer},
volume = {1},
number = {2},
pages = {235-248},
pmid = {32613204},
issn = {2662-1347},
support = {KL2 TR002542/TR/NCATS NIH HHS/United States ; K08 CA230220/CA/NCI NIH HHS/United States ; U54 HL127366/HL/NHLBI NIH HHS/United States ; U01 HG008699/HG/NHGRI NIH HHS/United States ; U54 HG008097/HG/NHGRI NIH HHS/United States ; },
mesh = {Cell Line ; Disulfiram ; Drug Repositioning ; Humans ; *Neoplasms/drug therapy ; },
abstract = {Anti-cancer uses of non-oncology drugs have occasionally been found, but such discoveries have been serendipitous. We sought to create a public resource containing the growth inhibitory activity of 4,518 drugs tested across 578 human cancer cell lines. We used PRISM, a molecular barcoding method, to screen drugs against cell lines in pools. An unexpectedly large number of non-oncology drugs selectively inhibited subsets of cancer cell lines in a manner predictable from the cell lines' molecular features. Our findings include compounds that killed by inducing PDE3A-SLFN12 complex formation; vanadium-containing compounds whose killing depended on the sulfate transporter SLC26A2; the alcohol dependence drug disulfiram, which killed cells with low expression of metallothioneins; and the anti-inflammatory drug tepoxalin, which killed via the multi-drug resistance protein ABCB1. The PRISM drug repurposing resource (https://depmap.org/repurposing) is a starting point to develop new oncology therapeutics, and more rarely, for potential direct clinical translation.},
}
@article {pmid32613104,
year = {2020},
author = {Nolorbe-Payahua, CD and de Freitas, AS and Roesch, LFW and Zanette, J},
title = {Environmental contamination alters the intestinal microbial community of the livebearer killifish Phalloceros caudimaculatus.},
journal = {Heliyon},
volume = {6},
number = {6},
pages = {e04190},
pmid = {32613104},
issn = {2405-8440},
abstract = {Intestinal microbiota perform important functions for the health of fishes. Knowing the microbial composition and evaluating the possible effects caused by anthropogenic pollution in the intestinal microbiota of fish populations might represent an important step in defining microbial biomarkers for water pollution. This study evaluated the impact of environmental contamination on the gut microbiota of the livebearer killifish Phalloceros caudimaculatus. The 16S survey using the V4 region of the 16S rRNA gene was used to characterize and compare the microbiota of two P. caudimaculatus populations from streams with different levels of environmental contamination in Rio Grande, RS, Brazil. Twelve bacterial operational taxonomic units (OTUs) (around one-third of the total) were shared between both fish populations. They represent the core microbiota of the gut in this species. The dominant phyla were Protebacteria and Firmicutes, with more than 80% of relative abundance. The dominant genus was Burkholderia with more than 35% of the relative abundance irrespective of the environmental condition. We detected a lower microbial diversity (Shannon index and observed OTUs) in fish from the polluted stream compared to the reference stream. The PERMANOVA analysis showed that the intestinal microbial communities from fish living in the polluted stream were distinct from those found in the reference stream (p < 0.05). Finally, we identified Luteolibacter, Methylocaldum and Rhodobacter genera, which correlated strongly with the polluted stream. These taxa might represent potential microbial biomarkers of exposure to environmental contaminants in the guts of fish. Confirmation of these findings in other polluted environments might allow the development of a microbiota-based screening approach for environmental evaluation in ecotoxicological studies in aquatic ecosystems.},
}
@article {pmid32611164,
year = {2020},
author = {Satish, A and Trivett, D and Sabra, KG},
title = {Omnidirectional passive acoustic identification tags for underwater navigation.},
journal = {The Journal of the Acoustical Society of America},
volume = {147},
number = {6},
pages = {EL517},
doi = {10.1121/10.0001444},
pmid = {32611164},
issn = {1520-8524},
abstract = {A class of passive acoustic identification (AID) tags with curved symmetry for underwater navigation is presented. These AID tags are composed of radially stratified shells designed to backscatter a unique specular reflection pattern independent of the incidence orientation in a monostatic configuration, thus acting as acoustic bar-codes. The AID tag's response can be uniquely engineered by selecting the thicknesses and material properties of the individual constitutive shells. Furthermore, in the high-frequency regime, the specular component of the AID tag's response can be simply predicted numerically assuming horizontally stratified layers. This approach is demonstrated using scaled experiments with an AID tag constructed from 3D printed hemispherical shells.},
}
@article {pmid32607145,
year = {2020},
author = {Rodrigues, NT and Saranholi, BH and Angeloni, TA and Pasqualotto, N and Chiarello, AG and Galetti, PM},
title = {DNA mini-barcoding of leporids using noninvasive fecal DNA samples and its significance for monitoring an invasive species.},
journal = {Ecology and evolution},
volume = {10},
number = {12},
pages = {5219-5225},
pmid = {32607145},
issn = {2045-7758},
abstract = {Introduced in South America at the end of the 19th century, the European hare population has expanded dramatically and now represents a risk to native Brazilian forest rabbits. Monitoring the invasive Lepus europaeus and its coexistence with native Sylvilagus brasiliensis is a challenge that can be efficiently addressed by the use of molecular tools. This work describes a set of primers useful for amplifying three mini-barcodes for the molecular identification of both invasive and native leporid species using degraded fecal DNA. In addition, tests in silico indicate that these mini-barcodes can successfully amplify the DNA sequences of a number of leporids. These mini-barcodes constitute a powerful tool for the monitoring and management of the invasive L. europaeus and the conservation of native rabbits.},
}
@article {pmid32607056,
year = {2020},
author = {Iturrieta-González, I and Gené, J and Wiederhold, N and García, D},
title = {Three new Curvularia species from clinical and environmental sources.},
journal = {MycoKeys},
volume = {68},
number = {},
pages = {1-21},
pmid = {32607056},
issn = {1314-4049},
abstract = {Curvularia is a Pleosporalean monophyletic genus with a great diversity of species, including relevant phytopathogenic, animal and human pathogenic fungi. However, their microscopic identification is difficult due to overlapping morphological features amongst species. In recent years, multi-locus sequence analysis using the ITS region of the rDNA and fragments of the genes gapdh and tef1 revealed numerous cryptic species, especially in isolates that commonly produced 3-septate conidia. Therefore, based on sequence analysis of the above-mentioned DNA barcodes recommended for species delineation in Curvularia, we propose three novel species, C. paraverruculosa, C. suttoniae and C. vietnamensis, isolated from soil, human clinical specimens and plant material, respectively, collected in different countries. These new species are morphologically characterised and illustrated in the present study. Curvularia paraverruculosa differs from its counterparts, C. americana and C. verruculosa, mainly by its narrower conidia. Curvularia suttoniae and C. vietnamensis are closely related to C. petersonii, but the former two have larger conidia.},
}
@article {pmid32604846,
year = {2020},
author = {Kirik, H and Tummeleht, L and Lilja, T and Kurina, O},
title = {Novel Mitochondrial DNA Lineage Found among Ochlerotatus communis (De Geer, 1776) of the Nordic-Baltic Region.},
journal = {Insects},
volume = {11},
number = {6},
pages = {},
pmid = {32604846},
issn = {2075-4450},
support = {IUT21-1//Eesti Teadusagentuur/ ; 8P160014VLVP//Eesti Maa&#xfc;likool/ ; },
abstract = {The Ochlerotatus (Oc.) communis complex consist of three Northern American species as well as a common Holarctic mosquito (Diptera: Culicidae) Oc. communis (De Geer, 1776). These sister species exhibit important ecological differences and are capable of transmitting various pathogens, but cannot always be differentiated by morphological traits. To investigate the Oc. communis complex in Europe, we compared three molecular markers (COI, ND5 and ITS2) from 54 Estonian mosquitoes as well as two COI marker sequences from Sweden. These sequences were subjected to phylogenetic analysis and screened for Wolbachia Hertig and Wolbach symbionts. Within and between groups, distances were calculated for each marker to better understand the relationships among individuals. Results demonstrate that a group of samples, extracted from adult female mosquitoes matching the morphology of Oc. communis, show a marked difference from the main species when comparing the mitochondrial markers COI and ND5. However, there is no variance between the same specimens when considering the nuclear ITS2. We conclude that Oc. communis encompasses two distinct mitochondrial DNA lineages in the Nordic-Baltic region. Further research is needed to investigate the origin and extent of these genetic differences.},
}
@article {pmid32601433,
year = {2020},
author = {Ferrari, S and Jacob, A and Beretta, S and Unali, G and Albano, L and Vavassori, V and Cittaro, D and Lazarevic, D and Brombin, C and Cugnata, F and Kajaste-Rudnitski, A and Merelli, I and Genovese, P and Naldini, L},
title = {Efficient gene editing of human long-term hematopoietic stem cells validated by clonal tracking.},
journal = {Nature biotechnology},
volume = {38},
number = {11},
pages = {1298-1308},
pmid = {32601433},
issn = {1546-1696},
mesh = {Animals ; Base Sequence ; Cell Lineage ; *Cell Tracking ; Clone Cells ; Dependovirus/metabolism ; G2 Phase ; *Gene Editing ; HEK293 Cells ; Hematopoietic Stem Cells/*cytology ; Humans ; Mice ; Recombinational DNA Repair ; Reproducibility of Results ; S Phase ; Transcription, Genetic ; Transplantation, Heterologous ; Tumor Suppressor Protein p53/metabolism ; Up-Regulation ; Viral Proteins/metabolism ; Xenograft Model Antitumor Assays ; },
abstract = {Targeted gene editing in hematopoietic stem cells (HSCs) is a promising treatment for several diseases. However, the limited efficiency of homology-directed repair (HDR) in HSCs and the unknown impact of the procedure on clonal composition and dynamics of transplantation have hampered clinical translation. Here, we apply a barcoding strategy to clonal tracking of edited cells (BAR-Seq) and show that editing activates p53, which substantially shrinks the HSC clonal repertoire in hematochimeric mice, although engrafted edited clones preserve multilineage and self-renewing capacity. Transient p53 inhibition restored polyclonal graft composition. We increased HDR efficiency by forcing cell-cycle progression and upregulating components of the HDR machinery through transient expression of the adenovirus 5 E4orf6/7 protein, which recruits the cell-cycle controller E2F on its target genes. Combined E4orf6/7 expression and p53 inhibition resulted in HDR editing efficiencies of up to 50% in the long-term human graft, without perturbing repopulation and self-renewal of edited HSCs. This enhanced protocol should broaden applicability of HSC gene editing and pave its way to clinical translation.},
}
@article {pmid32601361,
year = {2020},
author = {Ahmed, I and Tucci, FA and Aflalo, A and Smith, KGC and Bashford-Rogers, RJM},
title = {Ultrasensitive amplicon barcoding for next-generation sequencing facilitating sequence error and amplification-bias correction.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {10570},
pmid = {32601361},
issn = {2045-2322},
support = {/WT_/Wellcome Trust/United Kingdom ; WT106068AIA/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Bias ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Nucleic Acid Amplification Techniques/methods ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA/methods ; },
abstract = {The ability to accurately characterize DNA variant proportions using PCR amplification is key to many genetic studies, including studying tumor heterogeneity, 16S microbiome, viral and immune receptor sequencing. We develop a novel generalizable ultrasensitive amplicon barcoding approach that significantly reduces the inflation/deflation of DNA variant proportions due to PCR amplification biases and sequencing errors. This method was applied to immune receptor sequencing, where it significantly improves the quality and estimation of diversity of the resulting library.},
}
@article {pmid32599938,
year = {2020},
author = {Xu, ZB and Wang, YY and Condamine, FL and Cotton, AM and Hu, SJ},
title = {Are the Yellow and Red Marked Club-Tail Losaria coon the Same Species?.},
journal = {Insects},
volume = {11},
number = {6},
pages = {},
pmid = {32599938},
issn = {2075-4450},
support = {41761011; SDZXWJZ01013//the NSFC Programme of China; the Biodiversity Conservation Programme of the Ministry of Ecology and Environment, China/ ; },
abstract = {Losaria coon (Fabricius, 1793) is currently comprised of ten subspecies, which were originally described under two names, Papilio coon and P. doubledayi before 1909, when they were combined as one species. The main difference between them is the colour of abdomen and hindwing subterminal spots-yellow in coon and red in doubledayi. Wing morphology, male and female genitalia, and molecular evidence (DNA barcodes) were analysed for multiple subspecies of L. coon and three other Losaria species-rhodifer, neptunus, and palu. Our molecular data support the separation of L. coon and L. doubledayi stat. rev. as two distinct species, with L. rhodifer positioned between them in phylogenetic analyses. Wing morphology and genitalic structures also confirm the molecular conclusions. Our findings divide L. coon into two species occupying different geographic ranges: with L. coon restricted to southern Sumatra, Java, and Bawean Island, while L. doubledayi occurs widely in regions from North India to northern Sumatra, including Hainan and Nicobar Islands. Hence, future conservation efforts must reassess the status and threat factors of the two species to form updated strategies.},
}
@article {pmid32599078,
year = {2020},
author = {Xu, X and Kuntner, M and Bond, JE and Ono, H and Ho, SYW and Liu, F and Yu, L and Li, D},
title = {Molecular species delimitation in the primitively segmented spider genus Heptathela endemic to Japanese islands.},
journal = {Molecular phylogenetics and evolution},
volume = {151},
number = {},
pages = {106900},
doi = {10.1016/j.ympev.2020.106900},
pmid = {32599078},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Geography ; *Islands ; Japan ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; Probability ; Species Specificity ; Spiders/*genetics ; },
abstract = {Determining species boundaries forms an important foundation for biological research. However, the results of molecular species delimitation can vary with the data sets and methods that are used. Here we use a two-step approach to delimit species in the genus Heptathela, a group of primitively segmented trapdoor spiders that are endemic to Japanese islands. Morphological evidence suggests the existence of 19 species in the genus. We tested this initial species hypothesis by using six molecular species-delimitation methods to analyse 180 mitochondrial COI sequences of Heptathela sampled from across the known range of the genus. We then conducted a set of more focused analyses by sampling additional genetic markers from the subset of taxa that were inconsistently delimited by the single-locus analyses of mitochondrial DNA. Multilocus species delimitation was performed using two Bayesian approaches based on the multispecies coalescent. Our approach identified 20 putative species among the 180 sampled individuals of Heptathela. We suggest that our two-step approach provides an efficient strategy for delimiting species while minimizing costs and computational time.},
}
@article {pmid32598919,
year = {2020},
author = {Ullah, H and Qadeer, A and Giri, BR},
title = {Detection of circulating cell-free DNA to diagnose Schistosoma japonicum infection.},
journal = {Acta tropica},
volume = {211},
number = {},
pages = {105604},
doi = {10.1016/j.actatropica.2020.105604},
pmid = {32598919},
issn = {1873-6254},
mesh = {Animals ; Biomarkers/blood ; Cell-Free Nucleic Acids/*blood ; Cercaria/isolation &amp; purification ; DNA, Intergenic/blood ; Humans ; Male ; Mice ; Mice, Inbred BALB C ; Molecular Diagnostic Techniques ; Rabbits ; Schistosoma japonicum/*genetics/isolation &amp; purification ; Schistosomiasis/*diagnosis/*genetics ; Schistosomiasis japonica/*genetics/*parasitology ; Serum/*parasitology ; Snails ; },
abstract = {Schistosomiasis occurs in 240 million people worldwide and is a major public health concern. Thus, early diagnosis and monitoring of schistosomiasis progression are needed to treat patients. Cell-free DNA (cfDNA) is present as fragments of parasite-derived DNA in host body fluids. Detection of this cfDNA in host blood may be a promising diagnostic marker of schistosomiasis. Therefore, in this study, we investigated the potential of internal transcribed spacer 2 (ITS2), a molecular taxonomy and barcoding marker, in diagnosing schistosomiasis using infected rabbit and mice sera. A 192 bp fragment of ITS2 was detected in the serum-isolated DNA from the infected host on different days after infection. We also determined the sensitivity of detecting ITS2 in mice with varying numbers of cercaria: cfDNA was present even in mice with low abundance of the parasite. Overall, our results show that cfDNA may be a potential tool for the early diagnosis and therapeutic evaluation of S. japonicum infection.},
}
@article {pmid32596108,
year = {2020},
author = {Sevim, S and Franco, C and Chen, XZ and Sorrenti, A and Rodríguez-San-Miguel, D and Pané, S and deMello, AJ and Puigmartí-Luis, J},
title = {SERS Barcode Libraries: A Microfluidic Approach.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {7},
number = {12},
pages = {1903172},
pmid = {32596108},
issn = {2198-3844},
abstract = {Microfluidic technologies have emerged as advanced tools for surface-enhanced Raman spectroscopy (SERS). They have proved to be particularly appealing for in situ and real-time detection of analytes at extremely low concentrations and down to the 10 × 10[-15] m level. However, the ability to prepare reconfigurable and reusable devices endowing multiple detection capabilities is an unresolved challenge. Herein, a microfluidic-based method that allows an extraordinary spatial control over the localization of multiple active SERS substrates in a single microfluidic channel is presented. It is shown that this technology provides for exquisite control over analyte transport to specific detection points, while avoiding cross-contamination; a feature that enables the simultaneous detection of multiple analytes within the same microfluidic channel. Additionally, it is demonstrated that the SERS substrates can be rationally designed in a straightforward manner and that they allow for the detection of single molecules (at concentrations as low as 10[-14] m). Finally, it is shown that rapid etching and reconstruction of SERS substrates provides for reconfigurable and reusable operation.},
}
@article {pmid32596045,
year = {2020},
author = {Teshome, GE and Mekbib, Y and Hu, G and Li, ZZ and Chen, J},
title = {Comparative analyses of 32 complete plastomes of Tef (Eragrostis tef) accessions from Ethiopia: phylogenetic relationships and mutational hotspots.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e9314},
pmid = {32596045},
issn = {2167-8359},
abstract = {Eragrostis tef is an important cereal crop in Ethiopia with excellent storage properties, high-quality food, and the unique ability to thrive in extreme environmental conditions. However, the application of advanced molecular tools for breeding and conservation of these species is extremely limited. Therefore, developing chloroplast genome resources and high-resolution molecular markers are valuable to E. tef population and biogeographic studies. In the current study, we assembled and compared the complete plastomes of 32 E. tef accessions. The size of the plastomes ranged from 134,349 to 134,437 bp with similar GC content (∼38.3%). Genomes annotations revealed 112 individual genes, including 77 protein-coding, 31 tRNA, and 4 rRNA genes. Comparison of E. tef plastomes revealed a low degree of intraspecific sequence variations and no structural differentiations. Furthermore, we found 34 polymorphic sites (13 cpSSRs, 12 InDels, and 9 SNPs) that can be used as valuable DNA barcodes. Among them, the majority (88%) of the polymorphic sites were identified in the noncoding genomic regions. Nonsynonymous (ka) and synonymous (ks) substitution analysis showed that all PCGs were under purifying selection (ka/ks <1). The phylogenetic analyses of the whole plastomes and polymorphic region sequences were able to distinguish the accession from the southern population, indicating its potential to be used as a super-barcode. In conclusion, the newly generated plastomes and polymorphic markers developed here could be a useful genomic resource in molecular breeding, population genetics and the biogeographical study of E. tef.},
}
@article {pmid32593782,
year = {2020},
author = {Naik, SH},
title = {Dendritic cell development at a clonal level within a revised 'continuous' model of haematopoiesis.},
journal = {Molecular immunology},
volume = {124},
number = {},
pages = {190-197},
doi = {10.1016/j.molimm.2020.06.012},
pmid = {32593782},
issn = {1872-9142},
mesh = {Animals ; Cell Differentiation/immunology ; Cell Lineage/immunology ; Dendritic Cells/*cytology ; *Hematopoiesis ; Humans ; },
abstract = {Understanding development of the dendritic cell (DC) subtypes continues to evolve. The origin and relationship of conventional DC type 1 (cDC1), cDC type 2 (cDC2) and plasmacytoid DCs (pDCs) to each other, and in relation to classic myeloid and lymphoid cells, has had a long and controversial history and is still not fully resolved. This review summarises the technological developments and findings that have been achieved at a clonal level, and how that has enhanced our knowledge of the process. It summarises the single cell lineage tracing technologies that have emerged, their application in in vitro and in vivo studies, in both mouse and human settings, and places the findings in a wider context of understanding haematopoiesis at a single cell or clonal level. In particular, it addresses the fate heterogeneity observed in many phenotypically defined progenitor subsets and how these findings have led to a departure from the classic ball-and-stick models of haematopoiesis to the emerging continuous model. Prior contradictions in DC development may be reconciled if they are framed within this revised model, where commitment to a lineage or cell type does not occur in an all-or-nothing process in defined progenitors but rather can occur at many stages of haematopoiesis in a dynamic process.},
}
@article {pmid32591495,
year = {2020},
author = {Liu, WP and Huan, D and Wang, JG and Lv, QL and Ibrahim, U and Jin, XX and Tao, ZY},
title = {Esophageal Scab Mimicking a Parasite: A Case Report.},
journal = {The American journal of case reports},
volume = {21},
number = {},
pages = {e925199},
pmid = {32591495},
issn = {1941-5923},
mesh = {Aged ; Esophageal Diseases/*diagnosis ; *Esophagus ; Foreign Bodies/*diagnosis ; Gastroscopy ; Humans ; Male ; Parasitology/methods ; Ulcer/*diagnosis ; *Wound Healing ; },
abstract = {BACKGROUND Parasitic helminths in the esophagus are rare. Here, we report a case of esophageal scab mimicking a parasite. CASE REPORT A 65-year-old man was admitted to our hospital because after choking on food. Gastroscopy showed 2 foreign bodies adherent to the esophagus wall 28 and 34 cm from the incisor, which appeared to be a fluke. Two fluke-like foreign bodies (1.5 and 1.8 cm in length) were removed from the esophageal ulcer with forceps. After fixation with alcohol, the suspected fluke-like foreign bodies were noted to be brown and woody. Under a light microscope, the structure of the foreign body was not apparent, and no typical flatworm tegument structure was demonstrated on pathologic sections, but it had a blood clot-like structure. Administration of albendazole did not expel any helminths. A stool examination showed no eggs of the putative flukes. The genomic DNA of the suspected flukes was extracted and a 700 bp fragment was amplified by universal barcoding primers. The sequencing showed that the homology with human cytochrome c oxidase subunit I gene was 98.8%. CONCLUSIONS The scab formed by the esophageal ulcer was identified based on clinical manifestations, anti-helminth and stool examinations, parasite morphology, and molecular biology. Our experience with this case suggests that the universal barcoding technique can be used for identification of foreign bodies suspected to be parasites.},
}
@article {pmid32590882,
year = {2021},
author = {Ding, MY and Chen, W and Ma, XC and Lv, BW and Jiang, SQ and Yu, YN and Rahimi, MJ and Gao, RW and Zhao, Z and Cai, F and Druzhinina, IS},
title = {Emerging salt marshes as a source of Trichoderma arenarium sp. nov. and other fungal bioeffectors for biosaline agriculture.},
journal = {Journal of applied microbiology},
volume = {130},
number = {1},
pages = {179-195},
pmid = {32590882},
issn = {1365-2672},
support = {P25613-B20//Austrian Science Fund/ ; BK20180533//Ministry of Science &amp; Technology of Jiangsu Province/ ; 2018M630567//China Postdoctoral Science Foundation/ ; LS13-048//Vienna Science and Technology Fund/ ; 201910307044Z//National Innovation Training Programs/ ; S20190038//National Innovation Training Programs/ ; },
mesh = {Agriculture/*methods ; Antibiosis ; China ; Fungi/classification/genetics/metabolism ; Solanum lycopersicum/growth &amp; development/microbiology ; Rhizosphere ; *Saline Waters ; Seedlings/growth &amp; development/microbiology ; Soil Microbiology ; Trichoderma/classification/genetics/metabolism/*physiology ; *Wetlands ; },
abstract = {AIMS: Sustainable agriculture requires effective and safe biofertilizers and biofungicides with low environmental impact. Natural ecosystems that closely resemble the conditions of biosaline agriculture may present a reservoir for fungal strains that can be used as novel bioeffectors.<br><br>METHODS AND RESULTS: We isolated a library of fungi from the rhizosphere of three natural halotolerant plants grown in the emerging tidal salt marshes on the south-east coast of China. DNA barcoding of 116 isolates based on the rRNA ITS1 and 2 and other markers (tef1 or rpb2) revealed 38 fungal species, including plant pathogenic (41%), saprotrophic (24%) and mycoparasitic (28%) taxa. The mycoparasitic fungi were mainly species from the hypocrealean genus Trichoderma, including at least four novel phylotypes. Two of them, representing the taxa Trichoderma arenarium sp. nov. (described here) and T. asperelloides, showed antagonistic activity against five phytopathogenic fungi, and significant growth promotion on tomato seedlings under the conditions of saline agriculture.<br><br>CONCLUSIONS: Trichoderma spp. of salt marshes play the role of natural biological control in young soil ecosystems with a putatively premature microbiome.<br><br>The saline soil microbiome is a rich source of halotolerant bioeffectors that can be used in biosaline agriculture.},
}
@article {pmid32590879,
year = {2020},
author = {Rodrigues, BL and Baton, LA and Shimabukuro, PHF},
title = {Single-locus DNA barcoding and species delimitation of the sandfly subgenus Evandromyia (Aldamyia).},
journal = {Medical and veterinary entomology},
volume = {34},
number = {4},
pages = {420-431},
doi = {10.1111/mve.12458},
pmid = {32590879},
issn = {1365-2915},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Phylogeny ; *Psychodidae/classification/genetics ; },
abstract = {Sandfly specimens from the subgenus Evandromyia (Aldamyia) Galati, 2003 (Diptera: Psychodidae: Phlebotominae) were collected between 2012 and 2019 from nine localities in seven Brazilian states, morphologically-identified, and then DNA barcoded by sequencing the mitochondrial cytochrome c oxidase subunit I (coi) gene. Forty-four new barcode sequences generated from 10 morphospecies were combined with 49 previously published sequences from the same subgenus and analysed using sequence-similarity methods (best-match criteria) to assess their ability at specimen identification, while four different species delimitation methods (ABGD, GMYC, PTP and TCS) were used to infer molecular operational taxonomic units (MOTUs). Overall, seven of the 11 morphospecies analysed were congruent with both the well-supported clades identified by phylogenetic analysis and the MOTUs inferred by species delimitation, while the remaining four morphospecies - E. carmelinoi, E. evandroi, E. lenti and E. piperiformis - were merged into a single well-supported clade/MOTU. Although E. carmelinoi, E. evandroi and E. lenti were indistinguishable using coi DNA barcodes, E. piperiformis did form a distinct phylogenetic cluster and could be correctly identified using best-match criteria. Despite their apparent morphological differences, we propose on the basis of the molecular similarity of their DNA barcodes that these latter four morphospecies should be considered members of a recently-diverged species complex.},
}
@article {pmid32585770,
year = {2020},
author = {Horn, IR and Verleg, PA and Ibrahim, NZ and Soeleman, K and van Kampen, F and Ruesen, MO and Reulen, NM and Breij, H and Bakker, RJ and Gravendeel, B},
title = {Mushroom DNA barcoding project: Sequencing a segment of the 28S rRNA gene.},
journal = {Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology},
volume = {48},
number = {4},
pages = {404-410},
pmid = {32585770},
issn = {1539-3429},
mesh = {Agaricales/classification/*genetics ; Base Sequence ; DNA Barcoding, Taxonomic/*methods ; Genes, rRNA/*genetics ; Humans ; Phylogeny ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 28S/*analysis/*genetics ; Sequence Analysis, DNA/*methods ; Sequence Homology ; },
abstract = {DNA barcoding is an important molecular methodology for species identification that was developed over the last two decades and it should be covered in the biology bachelor curriculum. Here, we present an example of DNA barcoding by sequencing a segment of the 28S nuclear ribosomal large subunit rRNA gene of wild mushrooms and framing the education in a project form for undergraduate students in biology. Students perform this project in 6-8 weeks, which also includes preparing a poster, writing a report and presenting a paper related to the work in a journal club format. First, fieldwork in the Netherlands was carried out, during which students collected mushrooms under supervision of a professional mycologist with the goal to (a) verify morphologically based identifications with a molecular method and (b) assess phylogenetic relationships of the different species collected. Next, DNA extractions and quantitation were performed, PCR amplification was done, and samples were sent out for Sanger sequencing. Students aligned and analyzed the sequences using BLAST and Geneious and subsequently created a phylogenetic tree. In case of collecting DNA barcodes of an earlier sequenced species, students could upload the data to a repository established for facilitation of future research projects. The method described is very robust, reagents and equipment are readily available, and costs are relatively low. In addition, the results can be compared to published fungal phylogenetic trees.},
}
@article {pmid32584918,
year = {2020},
author = {Lima, MCC and Lima, SC and Savada, CS and Suzuki, KM and Orsi, ML and Almeida, FS},
title = {Use of DNA barcode in the identification of fish eggs in tributaries of the Paranapanema River basin.},
journal = {Genetics and molecular biology},
volume = {43},
number = {3},
pages = {e20190352},
pmid = {32584918},
issn = {1415-4757},
abstract = {Fish eggs are often excluded from identification analysis since at this stage of development there are few morphological characters. The correct identification of eggs can provide important information about spawning areas of species. The current work aimed to identify fish eggs in the Tibagi and Cinzas Rivers using the DNA barcode to obtain information on richness and diversity, adding to the existing data in the area. Of the 928 sequences analyzed using the BOLD Systems database, 99.78% were able to be identified at a specific level, demonstrating a high success rate for egg identification. The samples resulted in 25 species, 11 families, and 2 orders. Of the 25 species found, more than half (60%) present reproductive migration behavior, indicating that the tributaries of the Capivara reservoir are being used as a migratory route by these species. Eggs of rare and endangered species were found, indicating these tributaries as spawning grounds for these species. The results demonstrate the importance of identifying fish eggs in reservoir-influenced environments to recognize breeding areas of native and endangered species, as well as the importance of the Tibagi and Cinzas Rivers for the maintenance of native fish species in the Paranapanema River.},
}
@article {pmid32581632,
year = {2020},
author = {Zhang, X and Lan, T and Nie, L and Li, S},
title = {Eight new species of the spider genus Pimoa (Araneae, Pimoidae) from Tibet, China.},
journal = {ZooKeys},
volume = {940},
number = {},
pages = {79-104},
pmid = {32581632},
issn = {1313-2989},
abstract = {Eight new species of the spider genus Pimoa Chamberlin &amp; Ivie, 1943 are described from Tibet, China: P. cona Zhang &amp; Li, sp. nov. (♂♀), P. duiba Zhang &amp; Li, sp. nov. (♂♀), P. lemenba Zhang &amp; Li, sp. nov. (♀), P. mainling Zhang &amp; Li, sp. nov. (♂♀), P. nyingchi Zhang &amp; Li, sp. nov. (♂♀), P. rongxar Zhang &amp; Li, sp. nov. (♂♀), P. samyai Zhang &amp; Li, sp. nov. (♂♀), and P. yadong Zhang &amp; Li, sp. nov. (♂♀). The DNA barcodes of the eight new species are documented.},
}
@article {pmid32580761,
year = {2020},
author = {Tan, J and Wang, W and Wu, F and Li, Y and Fan, Q},
title = {Transcriptome profiling of venom gland from wasp species: de novo assembly, functional annotation, and discovery of molecular markers.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {427},
pmid = {32580761},
issn = {1471-2164},
mesh = {Animals ; Evolution, Molecular ; Gene Expression Profiling/*veterinary ; Gene Ontology ; *Genetic Markers ; High-Throughput Nucleotide Sequencing ; Insect Proteins/*genetics ; Microsatellite Repeats ; Molecular Sequence Annotation ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, RNA ; Wasp Venoms/*genetics ; Wasps/*classification/genetics ; },
abstract = {BACKGROUND: Vespa velutina, one of the most aggressive and fearful wasps in China, can cause grievous allergies and toxic reactions, leading to organ failure and even death. However, there is little evidence on molecular data regarding wasps. Therefore, we aimed to provide an insight into the transcripts expressed in the venom gland of wasps.<br><br>RESULTS: In our study, high-throughput RNA sequencing was performed using the venom glands of four wasp species. First, the mitochondrial cytochrome C oxidase submit I (COI) barcoding and the neighbor joining (NJ) tree were used to validate the unique identity and lineage of each individual species. After sequencing, a total of 127,630 contigs were generated and 98,716 coding domain sequences (CDS) were predicted from the four species. The Gene ontology (GO) enrichment analysis of unigenes revealed their functional role in important biological processes (BP), molecular functions (MF) and cellular components (CC). In addition, c-type, p1 type, p2 type and p3 type were the most commonly found simple sequence repeat (SSR) types in the four species of wasp transcriptome. There were differences in the distribution of SSRs and single nucleotide polymorphisms (SNPs) among the four wasp species.<br><br>CONCLUSIONS: The transcriptome data generated in this study will improve our understanding on bioactive proteins and venom-related genes in wasp venom gland and provide a basis for pests control and other applications. To our knowledge, this is the first study on the identification of large-scale genomic data and the discovery of microsatellite markers from V. tropica ducalis and V. analis fabricius.},
}
@article {pmid32579871,
year = {2020},
author = {Janzen, DH and Hallwachs, W and Pereira, G and Blanco, R and Masis, A and Chavarria, MM and Chavarria, F and Guadamuz, A and Araya, M and Smith, MA and Valerio, J and Guido, H and Sanchez, E and Bermudez, S and Perez, K and Manjunath, R and Ratnasingham, S and St Jacques, B and Milton, M and DeWaard, JR and Zakharov, E and Naik, S and Hajibabaei, M and Hebert, PDN and Hasegawa, M},
title = {Using DNA-barcoded Malaise trap samples to measure impact of a geothermal energy project on the biodiversity of a Costa Rican old-growth rain forest.},
journal = {Genome},
volume = {63},
number = {9},
pages = {407-436},
doi = {10.1139/gen-2020-0002},
pmid = {32579871},
issn = {1480-3321},
mesh = {Animals ; *Biodiversity ; Costa Rica ; DNA ; *DNA Barcoding, Taxonomic ; Ecology ; Entomology ; *Geothermal Energy ; Insecta/*genetics ; Moths/genetics ; *Rainforest ; Species Specificity ; },
abstract = {We report one year (2013-2014) of biomonitoring an insect community in a tropical old-growth rain forest, during construction of an industrial-level geothermal electricity project. This is the first-year reaction by the species-rich insect biodiversity; six subsequent years are being analyzed now. The site is on the margin of a UNESCO Natural World Heritage Site, Área de Conservación Guanacaste (ACG), in northwestern Costa Rica. This biomonitoring is part of Costa Rica's ongoing efforts to sustainably retain its wild biodiversity through biodevelopmental integration with its societies. Essential tools are geothermal engineering needs, entomological knowledge, insect species-rich forest, government-NGO integration, common sense, DNA barcoding for species-level identification, and Malaise traps. This research is tailored for integration with its society at the product level. We combine an academic view with on-site engineering decisions. This biomonitoring requires alpha-level DNA barcoding combined with centuries of morphology-based entomological taxonomy and ecology. Not all desired insect community analyses are performed; they are for data from subsequent years combined with this year. We provide enough analysis to be used by both guilds now. This biomonitoring has shown, for the first year, that the geothermal project impacts only the biodiversity within a zone less than 50 m from the project margin.},
}
@article {pmid32578684,
year = {2020},
author = {Boucinha, C and Caetano, AR and Santos, HL and Helaers, R and Vikkula, M and Branquinha, MH and Dos Santos, ALS and Grellier, P and Morelli, KA and d'Avila-Levy, CM},
title = {Analysing ambiguities in trypanosomatids taxonomy by barcoding.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {115},
number = {},
pages = {e200504},
pmid = {32578684},
issn = {1678-8060},
mesh = {*Biodiversity ; *DNA Barcoding, Taxonomic ; Phylogeny ; Trypanosomatina/*classification/*genetics ; },
abstract = {BACKGROUND: Biodiversity screens and phylogenetic studies are dependent on reliable DNA sequences in public databases. Biological collections possess vouchered specimens with a traceable history. Therefore, DNA sequencing of samples available at institutional collections can greatly contribute to taxonomy, and studies on evolution and biodiversity.<br><br>METHODS: We sequenced part of the glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH) and the SSU rRNA (V7/V8) genes from 102 trypanosomatid cultures, which are available on request at www.colprot.fiocruz.br.<br><br>OBJECTIVE: The main objective of this work was to use phylogenetic inferences, using the obtained DNA sequences and those from representatives of all Trypanosomatidae genera, to generate phylogenetic trees that can simplify new isolates screenings.<br><br>FINDINGS: A DNA sequence is provided for the first time for several isolates, the phylogenetic analysis allowed the classification or reclassification of several specimens, identification of candidates for new genera and species, as well as the taxonomic validation of several deposits.<br><br>MAIN CONCLUSIONS: This survey aimed at presenting a list of validated species and their associated DNA sequences combined with a short historical overview of each isolate, which can support taxonomic and biodiversity research and promote culture collections.},
}
@article {pmid32577820,
year = {2020},
author = {Mohammad Rahimi, H and Nemati, S and Mirjalali, H and Sharifdini, M and Zali, MR},
title = {Molecular characterization and identification of Blastocystis and its subtypes from raccoon (Procyon lotor) in north of Iran.},
journal = {Parasitology research},
volume = {119},
number = {8},
pages = {2741-2745},
pmid = {32577820},
issn = {1432-1955},
mesh = {Animals ; Base Sequence ; Blastocystis/classification/genetics/*isolation &amp; purification ; Blastocystis Infections/epidemiology/parasitology/transmission/*veterinary ; DNA, Protozoan/genetics ; Feces/parasitology ; Genetic Variation ; Genotype ; Iran/epidemiology ; Prevalence ; Protozoan Infections, Animal/epidemiology/*parasitology/transmission ; RNA, Ribosomal/genetics ; Raccoons/*parasitology ; Ribosome Subunits, Small/genetics ; },
abstract = {Blastocystis is a zoonotic protozoan parasite frequently identified in the intestinal tract of humans and a vast variety of animals, worldwide. Here, we assessed the prevalence of Blastocystis and its subtypes in stool samples of raccoons. Stool samples from 30 raccoons were collected. Total DNA was extracted, and the barcoding region of the small subunit ribosomal rRNA (SSU rRNA) gene was amplified and sequenced. Specific fragment for Blastocystis was successfully amplified in five samples (16.66%). Sequencing analysis revealed ST1, ST2, and ST3 among 1, 2, and 2 Blastocystis-positive samples. Our results documented the presence of Blastocystis subtypes 1-3 in raccoons. Subtype 1 showed higher similarity to the human isolates of Blastocystis. However, it seems that raccoons may emerge as reservoirs for Blastocystis and may be linked to zoonotic transmission of the protist.},
}
@article {pmid32577648,
year = {2020},
author = {Credle, JJ and Robinson, ML and Gunn, J and Monaco, D and Sie, B and Tchir, A and Hardick, J and Zheng, X and Shaw-Saliba, K and Rothman, RE and Eshleman, SH and Pekosz, A and Hansen, K and Mostafa, H and Steinegger, M and Larman, HB},
title = {Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {32577648},
issn = {2692-8205},
support = {T34 GM083688/GM/NIGMS NIH HHS/United States ; R21 CA202875/CA/NCI NIH HHS/United States ; U01 AI068613/AI/NIAID NIH HHS/United States ; UM1 AI068613/AI/NIAID NIH HHS/United States ; HHSN272201400007C/AI/NIAID NIH HHS/United States ; },
abstract = {The emergence of SARS-CoV-2 has caused the current COVID-19 pandemic with catastrophic societal impact. Because many individuals shed virus for days before symptom onset, and many show mild or no symptoms, an emergent and unprecedented need exists for development and deployment of sensitive and high throughput molecular diagnostic tests. RNA-mediated oligonucleotide Annealing Selection and Ligation with next generation DNA sequencing (RASL-seq) is a highly multiplexed technology for targeted analysis of polyadenylated mRNA, which incorporates sample barcoding for massively parallel analyses. Here we present a more generalized method, capture RASL-seq ("cRASL-seq"), which enables analysis of any targeted pathogen- (and/or host-) associated RNA molecules. cRASL-seq enables highly sensitive (down to ~1-100 pfu/ml or cfu/ml) and highly multiplexed (up to ~10,000 target sequences) detection of pathogens. Importantly, cRASL-seq analysis of COVID-19 patient nasopharyngeal (NP) swab specimens does not involve nucleic acid extraction or reverse transcription, steps that have caused testing bottlenecks associated with other assays. Our simplified workflow additionally enables the direct and efficient genotyping of selected, informative SARS-CoV-2 polymorphisms across the entire genome, which can be used for enhanced characterization of transmission chains at population scale and detection of viral clades with higher or lower virulence. Given its extremely low per-sample cost, simple and automatable protocol and analytics, probe panel modularity, and massive scalability, we propose that cRASL-seq testing is a powerful new surveillance technology with the potential to help mitigate the current pandemic and prevent similar public health crises.},
}
@article {pmid32574364,
year = {2020},
author = {Mann, JG and Washington, M and Guynup, T and Tarrand, C and Dewey, EM and Fredregill, C and Duguma, D and Pitts, RJ},
title = {Feeding Habits of Vector Mosquitoes in Harris County, TX, 2018.},
journal = {Journal of medical entomology},
volume = {57},
number = {6},
pages = {1920-1929},
doi = {10.1093/jme/tjaa117},
pmid = {32574364},
issn = {1938-2928},
mesh = {Aedes/physiology ; Animals ; Culex/physiology ; Culicidae/*physiology ; Feeding Behavior ; Female ; Mosquito Vectors/*physiology ; Texas ; },
abstract = {Mosquito-borne pathogens contribute significantly to the global burden of infectious diseases and are a continuing public health concern in the United States. Blood feeding by vector mosquitoes is a critical step in the transmission of human pathogens. Continuous surveillance of mosquito feeding patterns, especially in major population centers, is necessary for sustainable, effective control strategies. To better understand female feeding habits in Harris County, TX, we trapped mosquitoes from various locations, distributed among urban and semi-urban environments. Bloodmeal hosts were determined using a cytochrome C oxidase I DNA barcoding strategy. We identified a diverse array of vertebrate hosts with a high degree of avian host utilization, most surprisingly from anthropophilic species like Aedes aegypti (L.). We also detected sequences from two different vertebrate hosts in about half of specimens examined, suggesting that multiple bloodmeals had been acquired in the same feeding cycle by a sizable fraction of females in both urban and semi-urban locations. The high proportion of feeding on domestic chickens may indicate that a significant number of homeowners are rearing chickens within close proximity to study trap sites. As non-amplifying hosts, chickens may have a diluting effect on West Nile virus, as well as a zooprophylactic effect in their immediate vicinities. Ultimately, spatial and temporal host utilization patterns add insight into potential disease transmission dynamics, thereby informing vector control strategies in Harris County and other metropolitan areas.},
}
@article {pmid32574357,
year = {2020},
author = {Borland, EM and Hartman, DA and Hopken, MW and Piaggio, AJ and Kading, RC},
title = {Technical Limitations Associated With Molecular Barcoding of Arthropod Bloodmeals Taken From North American Deer Species.},
journal = {Journal of medical entomology},
volume = {57},
number = {6},
pages = {2002-2006},
doi = {10.1093/jme/tjaa112},
pmid = {32574357},
issn = {1938-2928},
mesh = {Animals ; Colorado ; Culicidae/*physiology ; DNA Barcoding, Taxonomic/*instrumentation ; Deer/*physiology ; Diet ; Electron Transport Complex IV/analysis ; Feeding Behavior ; *Food Chain ; Mosquito Control/instrumentation ; },
abstract = {Accurate species-level identification of the source of arthropod bloodmeals is important for deciphering blood feeding patterns of field-collected specimens. Cytochrome c oxidase I (COI) mitochondrial gene sequencing has been used for this purpose; however, species resolution can be difficult to obtain from certain vertebrate genera, including Odocoileus. Sanger sequencing of mitochondrial genes was employed to identify the bloodmeal source of wild-caught mosquitoes trapped in Greeley, Colorado. Initial sequencing of the COI gene of mitochondrial DNA in bloodmeals was inadequate for species-level resolution of bloodmeals from deer in the genus Odocoileus, with current databases returning low fidelity matches to multiple genera. The use of the hypervariable D loop of the control region provided species-level identification of white-tailed deer (Order: Artiodactyla, Family: Cervidae, Odocoileus virginianus); however, taxonomic identification was successful only to genus for mule (O. hemionus hemionus) and black-tailed deer (O. hemionus columbianus). We advocate the use of multiple loci for bloodmeal analysis and the buildout of available databases to include multiple mitochondrial reference genes for reliable host species identification.},
}
@article {pmid32572078,
year = {2020},
author = {Huang, W and Xie, X and Huo, L and Liang, X and Wang, X and Chen, X},
title = {An integrative DNA barcoding framework of ladybird beetles (Coleoptera: Coccinellidae).},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {10063},
pmid = {32572078},
issn = {2045-2322},
mesh = {Animals ; Coleoptera/*classification/genetics ; DNA Barcoding, Taxonomic/*veterinary ; DNA Primers/genetics ; Databases, Genetic ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {Even though ladybirds are well known as economically important biological control agents, an integrative framework of DNA barcoding research was not available for the family so far. We designed and present a set of efficient mini-barcoding primers to recover full DNA barcoding sequences for Coccinellidae, even for specimens collected 40 years ago. Based on these mini-barcoding primers, we obtained 104 full DNA barcode sequences for 104 species of Coccinellidae, in which 101 barcodes were newly reported for the first time. We also downloaded 870 COI barcode sequences (658 bp) from GenBank and BOLD database, belonging to 108 species within 46 genera, to assess the optimum genetic distance threshold and compare four methods of species delimitation (GMYC, bPTP, BIN and ABGD) to determine the most accurate approach for the family. The results suggested the existence of a 'barcode gap' and that 3% is likely an appropriate genetic distance threshold to delimit species of Coccinellidae using DNA barcodes. Species delimitation analyses confirm ABGD as an accurate and efficient approach, more suitable than the other three methods. Our research provides an integrative framework for DNA barcoding and descriptions of new taxa in Coccinellidae. Our results enrich DNA barcoding public reference libraries, including data for Chinese coccinellids. This will facilitate taxonomic identification and biodiversity monitoring of ladybirds using metabarcoding.},
}
@article {pmid32571207,
year = {2020},
author = {Kim, GB and Lim, CE and Kim, JS and Kim, K and Lee, JH and Yu, HJ and Mun, JH},
title = {Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: insights into evolutionary divergence and phylogenomic implications.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {415},
pmid = {32571207},
issn = {1471-2164},
support = {NIBR201922101//National Institute of Biological Resources/ ; PJ013194//Rural Development Administration/ ; 2020//Myongji University Research Year Grant/ ; },
mesh = {Artemisia/*classification/genetics ; Bayes Theorem ; Chloroplasts/classification/*genetics ; Evolution, Molecular ; Genetic Variation ; Genome Size ; Genome, Chloroplast ; High-Throughput Nucleotide Sequencing ; Interatrial Block ; Phylogeny ; Whole Genome Sequencing/*methods ; },
abstract = {BACKGROUND: Artemisia in East Asia includes a number of economically important taxa that are widely used for food, medicinal, and ornamental purposes. The identification of taxa, however, has been hampered by insufficient diagnostic morphological characteristics and frequent natural hybridization. Development of novel DNA markers or barcodes with sufficient resolution to resolve taxonomic issues of Artemisia in East Asia is significant challenge.<br><br>RESULTS: To establish a molecular basis for taxonomic identification and comparative phylogenomic analysis of Artemisia, we newly determined 19 chloroplast genome (plastome) sequences of 18 Artemisia taxa in East Asia, de novo-assembled and annotated the plastomes of two taxa using publicly available Illumina reads, and compared them with 11 Artemisia plastomes reported previously. The plastomes of Artemisia were 150,858-151,318 base pairs (bp) in length and harbored 87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNA genes in conserved order and orientation. Evolutionary analyses of whole plastomes and 80 non-redundant protein-coding genes revealed that the noncoding trnH-psbA spacer was highly variable in size and nucleotide sequence both between and within taxa, whereas the coding sequences of accD and ycf1 were under weak positive selection and relaxed selective constraints, respectively. Phylogenetic analysis of the whole plastomes based on maximum likelihood and Bayesian inference analyses yielded five groups of Artemisia plastomes clustered in the monophyletic subgenus Dracunculus and paraphyletic subgenus Artemisia, suggesting that the whole plastomes can be used as molecular markers to infer the chloroplast haplotypes of Artemisia taxa. Additionally, analysis of accD and ycf1 hotspots enabled the development of novel markers potentially applicable across the family Asteraceae with high discriminatory power.<br><br>CONCLUSIONS: The complete sequences of the Artemisia plastomes are sufficiently polymorphic to be used as super-barcodes for this genus. It will facilitate the development of new molecular markers and study of the phylogenomic relationships of Artemisia species in the family Asteraceae.},
}
@article {pmid32570618,
year = {2020},
author = {Cassarino, M and Galvan, C and Descalzo, J and Jerez, E and Smith, M and Luna, D},
title = {Experience Story: How Do We Re-Implement What Has Been Implemented?.},
journal = {Studies in health technology and informatics},
volume = {270},
number = {},
pages = {1279-1280},
doi = {10.3233/SHTI200401},
pmid = {32570618},
issn = {1879-8365},
mesh = {Electronic Data Processing ; Humans ; *Mobile Applications ; Nursing Staff ; Vital Signs ; },
abstract = {Since 2017, the Hospital Italiano de Buenos Aires, has a "Workstation on Wheels" project were nurses can access to a mobile application in order to register the drug's administration, vital signs and complete an early warning assessment scale of the hemodynamic state of the patient. Although the overall objective was to achieve at least 95% drug registration through this system, their use did not remain stable over time. Therefore, it was necessary to create an interdisciplinary team to make a diagnosis of the project situation and reasons for the low use rate. In this process, a re-implementation of the barcoding administration system was carried out, focusing on the nursing staff maintaining the use of the system over time. The aim of this paper is to describe the experience and lessons learned in the process of re-implementing the drug barcoding system at the patient's bedside.},
}
@article {pmid32569843,
year = {2020},
author = {Ricardo, PC and Françoso, E and Arias, MC},
title = {Mitochondrial DNA intra-individual variation in a bumblebee species: A challenge for evolutionary studies and molecular identification.},
journal = {Mitochondrion},
volume = {53},
number = {},
pages = {243-254},
doi = {10.1016/j.mito.2020.06.007},
pmid = {32569843},
issn = {1872-8278},
mesh = {Animals ; Bees/classification/*genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Heteroplasmy ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*veterinary ; },
abstract = {Mitochondrial DNA (mtDNA) regions have been widely used as molecular markers in evolutionary studies and species identification. However, the presence of heteroplasmy and NUMTs may represent obstacles. Heteroplasmy is a state where an organism has different mitochondrial haplotypes. NUMTs are nuclear pseudogenes originating from mtDNA sequences transferred to nuclear DNA. Evidences of heteroplasmy were already verified in the bumblebee Bombus morio in an earlier study. The present work investigated in more detail the presence of intra-individual haplotypes variation in this species. Heteroplasmy was detected in individuals from all the ten sampled locations, with an average of six heteroplasmic haplotypes per individual. In addition, some of these heteroplasmic haplotypes were shared among individuals from different locations, suggesting the existence of stable heteroplasmy in B. morio. These results demonstrated that heteroplasmy is likely to affect inferences based on mtDNA analysis, especially in phylogenetic, phylogeographic and population genetics studies. In addition, NUMTs were also detected. These sequences showed divergence of 2.7% to 12% in relation to the mitochondrial haplotypes. These levels of divergence could mislead conclusions in evolutionary studies and affect species identification through DNA barcoding.},
}
@article {pmid32569285,
year = {2020},
author = {Metfies, K and Hessel, J and Klenk, R and Petersen, W and Wiltshire, KH and Kraberg, A},
title = {Uncovering the intricacies of microbial community dynamics at Helgoland Roads at the end of a spring bloom using automated sampling and 18S meta-barcoding.},
journal = {PloS one},
volume = {15},
number = {6},
pages = {e0233921},
pmid = {32569285},
issn = {1932-6203},
mesh = {DNA Barcoding, Taxonomic ; Eukaryota/*classification/genetics ; High-Throughput Nucleotide Sequencing ; *Microbiota ; North Sea ; Phylogeny ; Phytoplankton/*classification/genetics/growth &amp; development ; RNA, Ribosomal, 18S/genetics ; Seasons ; Seawater ; },
abstract = {In May 2016, the remote-controlled Automated Filtration System for Marine Microbes (AUTOFIM) was implemented in parallel to the Long Term Ecological Research (LTER) observatory Helgoland Roads in the German Bight. We collected samples for characterization of dynamics within the eukaryotic microbial communities at the end of a phytoplankton bloom via 18S meta-barcoding. Understanding consequences of environmental change for key marine ecosystem processes, such as phytoplankton bloom dynamics requires information on biodiversity and species occurrences with adequate temporal and taxonomic resolution via time series observations. Sampling automation and molecular high throughput methods can serve these needs by improving the resolution of current conventional marine time series observations. A technical evaluation based on an investigation of eukaryotic microbes using the partial 18S rRNA gene suggests that automated filtration with the AUTOFIM device and preservation of the plankton samples leads to highly similar 18S community profiles, compared to manual filtration and snap freezing. The molecular data were correlated with conventional microscopic counts. Overall, we observed substantial change in the eukaryotic microbial community structure during the observation period. A simultaneous decline of diatom and ciliate sequences succeeded a peak of Miracula helgolandica, suggesting a potential impact of these oomycete parasites on diatom bloom dynamics and phenology in the North Sea. As oomycetes are not routinely counted at Helgoland Roads LTER, our findings illustrate the benefits of combining automated filtration with metabarcodingto augment classical time series observations, particularly for taxa currently neglected due to methodological constraints.},
}
@article {pmid32566672,
year = {2020},
author = {Wang, C and Zhang, Y and Han, S},
title = {Its2vec: Fungal Species Identification Using Sequence Embedding and Random Forest Classification.},
journal = {BioMed research international},
volume = {2020},
number = {},
pages = {2468789},
pmid = {32566672},
issn = {2314-6141},
mesh = {Algorithms ; Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; *DNA, Fungal/classification/genetics ; *Fungi/classification/genetics ; *Machine Learning ; Software ; },
abstract = {Fungi play essential roles in many ecological processes, and taxonomic classification is fundamental for microbial community characterization and vital for the study and preservation of fungal biodiversity. To cope with massive fungal barcode data, tools that can implement extensive volumes of barcode sequences, especially the internal transcribed spacer (ITS) region, are necessary. However, high variation in the ITS region and computational requirements for processing high-dimensional features remain challenging for existing predictors. In this study, we developed Its2vec, a bioinformatics tool for the classification of fungal ITS barcodes to the species level. An ITS database covering more than 25,000 species in a broad range of fungal taxa was assembled. For dimensionality reduction, a word embedding algorithm was used to represent an ITS sequence as a dense low-dimensional vector. A random forest-based classifier was built for species identification. Benchmarking results showed that our model achieved an accuracy comparable to that of several state-of-the-art predictors, and more importantly, it could implement large datasets and greatly reduce dimensionality. We expect the Its2vec model to be helpful for fungal species identification and, thus, for revealing microbial community structures and in deepening our understanding of their functional mechanisms.},
}
@article {pmid32565673,
year = {2020},
author = {Vitecek, S and Graf, W and Martini, J and Zittra, C and Handschuh, S and Kuhlmann, HC and Vieira, A and Hess, M and Heckes, U and Erzinger, F and Pauls, SU and Waringer, J},
title = {A new Drusinae species from the western Alps with comments on the subfamily and an updated key to filtering carnivore larvae of Drusinae species (Insecta: Trichoptera: Limnephilidae).},
journal = {Zootaxa},
volume = {4790},
number = {3},
pages = {491-504},
pmid = {32565673},
issn = {1175-5334},
support = {P 31258/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Animals ; *Holometabola ; *Insecta ; Larva ; Male ; },
abstract = {A new Drusinae species, Drusus katagelastos sp. nov., of the Drusus chapmani Species Complex, is described based on a male and associated larvae. Adult-larval association was achieved through DNA barcoding. The male of the new species differ from that of its congeners in the formation of the intermediate appendages and parameres. Information on the morphology of the larva is given, and important diagnostic features are discussed. In the context of filtering carnivore Drusinae, the larva of the new species can be separated from other filtering carnivore species by the dense cover of long translucent bristles within the frontal cavity surrounded by a circular corona of long bristles. Drusus katagelastos sp. nov. is known from only northwestern Italy (Piemonte).},
}
@article {pmid32565339,
year = {2020},
author = {Garcia Pérez, HA and Rodrigues, CMF and Pivat, IHV and Fuzato, ACR and Camargo, EP and Minervino, AHH and Teixeira, MMG},
title = {High Trypanosoma vivax infection rates in water buffalo and cattle in the Brazilian Lower Amazon.},
journal = {Parasitology international},
volume = {79},
number = {},
pages = {102162},
doi = {10.1016/j.parint.2020.102162},
pmid = {32565339},
issn = {1873-0329},
mesh = {Animals ; Brazil/epidemiology ; *Buffaloes ; Cattle ; Cattle Diseases/*epidemiology/parasitology ; Genotype ; Polymerase Chain Reaction ; Prevalence ; Trypanosoma vivax/*isolation &amp; purification ; Trypanosomiasis, African/epidemiology/parasitology/*veterinary ; },
abstract = {Highly sensitive and accurate molecular diagnostic methods have not yet been employed for livestock trypanosomosis in the Brazilian Lower Amazon although the first reports of Trypanosoma vivax and Trypanosoma evansi in Brazil were in water buffalo (Bubalus bubalis) in this region. The present study assessed trypanosomosis in buffalo and cattle raised in communal and seasonally flooding pastures in the state of Pará using the fluorescent fragment length barcoding (FFLB) method. T. evansi was not detected, but high infection rates of T. vivax and T. theileri were revealed by a simplified FFLB standardized in the present study that discriminates all trypanosome species infective to livestock in South America. T. vivax infection rates detected by TviCATL-PCR were 24.6% for cattle (n = 61) and 28.1% for buffalo (n = 89). Using the FFLB method, overall T. vivax infection rates increased to 59.6% and 44.3% for buffalo and cattle, respectively. Furthermore, the predominance of a single microsatellite-based genotype of T. vivax was reinforced in the Lower Amazon. Relevant T. vivax infection rates detected in clinically healthy buffalo and cattle through the sampled years (2008-2017) highlight the need for systematic studies to demonstrate the endemic steady state of T. vivax in this region. Our findings provide baseline information for livestock management, including control of T. vivax dispersal, and the introduction of naïve animals. The growing international trade of live livestock from this very important livestock breeding region represents a serious risk for T. vivax spreading outside Amazonia and Brazil.},
}
@article {pmid32564434,
year = {2020},
author = {Wang, MQ and Li, Y and Chesters, D and Bruelheide, H and Ma, K and Guo, PF and Zhou, QS and Staab, M and Zhu, CD and Schuldt, A},
title = {Host functional and phylogenetic composition rather than host diversity structure plant-herbivore networks.},
journal = {Molecular ecology},
volume = {29},
number = {14},
pages = {2747-2762},
doi = {10.1111/mec.15518},
pmid = {32564434},
issn = {1365-294X},
mesh = {Biodiversity ; DNA Barcoding, Taxonomic ; *Ecosystem ; *Herbivory ; *Phylogeny ; Plants/*classification/genetics ; Trees/classification/genetics ; },
abstract = {Declining plant diversity alters ecological networks, such as plant-herbivore interactions. However, our knowledge of the potential mechanisms underlying effects of plant species loss on plant-herbivore network structure is still limited. We used DNA barcoding to identify herbivore-host plant associations along declining levels of tree diversity in a large-scale, subtropical biodiversity experiment. We tested for effects of tree species richness, host functional and phylogenetic diversity, and host functional (leaf trait) and phylogenetic composition on species, phylogenetic and network composition of herbivore communities. We found that phylogenetic host composition and related palatability/defence traits but not tree species richness significantly affected herbivore communities and interaction network complexity at both the species and community levels. Our study indicates that evolutionary dependencies and functional traits of host plants determine the composition of higher trophic levels and corresponding interaction networks in species-rich ecosystems. Our findings highlight that characteristics of the species lost have effects on ecosystem structure and functioning across trophic levels that cannot be predicted from mere reductions in species richness.},
}
@article {pmid32564405,
year = {2020},
author = {Kennedy, SR and Krehenwinkel, H},
title = {DNA barcoding and community assembly-A simple solution to a complex problem.},
journal = {Molecular ecology},
volume = {29},
number = {13},
pages = {2318-2320},
doi = {10.1111/mec.15519},
pmid = {32564405},
issn = {1365-294X},
mesh = {Animals ; *Biodiversity ; China ; *DNA Barcoding, Taxonomic ; Insecta ; Phylogeny ; },
abstract = {Identifying the current and past processes driving community assembly is critical in the effort to understand the Earth's biodiversity and its response to future environmental change. But while studies on community assembly often emphasize the role of contemporary ecological drivers, it has been particularly challenging to account for the effects of past processes in shaping present-day communities. In this issue of Molecular Ecology, Hao et al. (2020) provide a holistic analysis of factors driving the assembly of diverse communities of Lepidoptera in two mountain ranges in northeastern China. The authors use an impressively large data set and exceptionally comprehensive analyses to test how processes of range expansion and gene flow, speciation and extinction, dispersal limitation, environmental filtering and competition have led to present-day diversity patterns. A key novelty of this work is the exhaustive use of DNA barcodes, relatively simple yet powerful molecular markers, to tackle complex biological questions. The authors elegantly show the utility of DNA barcoding data for research beyond simple taxonomic assignment. Their approach is remarkable as it manages to integrate population genetics, phylogenetic history, species diversity and ecology into a well-rounded picture of community assembly. With this work, Hao et al. demonstrate the great promise of DNA barcoding for exhaustive community analysis of even highly diverse and complex systems, raising the bar for future research.},
}
@article {pmid32560829,
year = {2020},
author = {Lin, S and Hu, Z and Deng, Y and Shang, L and Gobler, CJ and Tang, YZ},
title = {An assessment on the intrapopulational and intraindividual genetic diversity in LSU rDNA in the harmful algal blooms-forming dinoflagellate Margalefidinium (= Cochlodinium) fulvescens based on clonal cultures and bloom samples from Jiaozhou Bay, China.},
journal = {Harmful algae},
volume = {96},
number = {},
pages = {101821},
doi = {10.1016/j.hal.2020.101821},
pmid = {32560829},
issn = {1878-1470},
mesh = {Bays ; China ; DNA, Ribosomal/genetics ; *Dinoflagellida/genetics ; Genetic Variation ; *Harmful Algal Bloom ; },
abstract = {Large subunit ribosomal DNA (LSU rDNA) sequences have been increasingly used to infer the phylogeny and species identity of organisms, a few previous studies, however, have observed high intraspecific and even intraindividual variability in LSU rDNA in some dinoflagellate species due to, assumably, large copy numbers of rDNA in dinoflagellates. Since the copy number of LSU rDNA varies tremendously among dinoflagellate species, the intraspecific and intraindividual diversity for a species of particular interest thus needs to be investigated individually. As a toxic and HABs-forming dinoflagellate, Margalefidinium (= Cochlodinium) fulvescens has been observed to approach blooming density in Jiaozhou Bay, China since 2015 after numerous blooms having been reported from other countries. In trying to identify the source of this newly observed HABs-forming species in China by sequencing the LSU rDNA for both field samples and clonal cultures, we noticed and thus further investigated high intrapopulational and intraindividual genetic diversities of the dinoflagellate. The D1-D6 region of the LSU rDNA (1,435 bases) was amplified from 7 field samples (pooled cells) and 11 clonal cultures, cloned, sequenced, and analyzed phylogenetically for 2,341 sequences obtained. All the numbers of sequences obtained from each clonal culture were far less than the estimated rDNA copy number in M. fulvescens. In the clone library, only one unique sequence was contained in all samples as the most dominant sequence. We found high intrapopulational and intraindividual genetic diversity in M. fulvescens as reflected in the number of polymorphic sites and unique sequences in the clone library for different field samples and clonal cultures in comparison to other species. The mean number of nucleotide differences of each sequence from different field samples and clonal cultures were 6.43 and 4.42 bases, respectively, with the highest being 132 bases, nearly 10%. The sequences with highest variability may be easily annotated as different species if they were obtained from environmental genomic studies because sequence-based species identification in meta-barcoding studies often use "97% identity" threshold. Based on that the mean and overall intrapopulational genetic diversity calculated for 7 field samples was equivalent to the mean and overall intraindividual variability for 11 clonal cultures in indices of genetic diversity, together with the result of AMOVA analysis, we infer that the variability within individual cells (i.e. variability among LSU rDNA polymorphic copies) caused both the intraindividual and intrapopulational genetic diversities observed in the M. fulvescens population, and a higher interpopulational diversity may exist among different geographic populations. The results provide an insightful basis for such a comprehensive interpopulational comparison and important implications for identifying species and establishing new taxa based on the similarity comparison to reference sequences deposited in databases.},
}
@article {pmid32559020,
year = {2020},
author = {Hardulak, LA and Morinière, J and Hausmann, A and Hendrich, L and Schmidt, S and Doczkal, D and Müller, J and Hebert, PDN and Haszprunar, G},
title = {DNA metabarcoding for biodiversity monitoring in a national park: Screening for invasive and pest species.},
journal = {Molecular ecology resources},
volume = {20},
number = {6},
pages = {1542-1557},
doi = {10.1111/1755-0998.13212},
pmid = {32559020},
issn = {1755-0998},
support = {GBOL: BMBF FKZ 01LI1101//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 01LI1501//Bundesministerium f&#xfc;r Bildung und Forschung/ ; //Bayerisches Staatsministerium f&#xfc;r Wissenschaft, Forschung und Kunst/ ; },
mesh = {Animals ; *Arthropods/classification ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Germany ; Parks, Recreational ; },
abstract = {DNA metabarcoding was utilized for a large-scale, multiyear assessment of biodiversity in Malaise trap collections from the Bavarian Forest National Park (Germany, Bavaria). Principal component analysis of read count-based biodiversities revealed clustering in concordance with whether collection sites were located inside or outside of the National Park. Jaccard distance matrices of the presences of barcode index numbers (BINs) at collection sites in the two survey years (2016 and 2018) were significantly correlated. Overall similar patterns in the presence of total arthropod BINs, as well as BINs belonging to four major arthropod orders across the study area, were observed in both survey years, and are also comparable with results of a previous study based on DNA barcoding of Sanger-sequenced specimens. A custom reference sequence library was assembled from publicly available data to screen for pest or invasive arthropods among the specimens or from the preservative ethanol. A single 98.6% match to the invasive bark beetle Ips duplicatus was detected in an ethanol sample. This species has not previously been detected in the National Park.},
}
@article {pmid32555941,
year = {2020},
author = {Machado, LO and Vieira, LDN and Stefenon, VM and Faoro, H and Pedrosa, FO and Guerra, MP and Nodari, RO},
title = {Molecular relationships of Campomanesia xanthocarpa within Myrtaceae based on the complete plastome sequence and on the plastid ycf2 gene.},
journal = {Genetics and molecular biology},
volume = {43},
number = {2},
pages = {e20180377},
pmid = {32555941},
issn = {1415-4757},
abstract = {Plastomes are very informative structures for comparative phylogenetic and evolutionary analyses. We sequenced and analyzed the complete plastome of Campomanesia xanthocarpa and compared its gene order, structure, and evolutionary characteristics within Myrtaceae. Analyzing 48 species of Myrtaceae, we identified six genes representing 'hotspots' of variability within the plastomes (ycf2, atpA, rpoC2, pcbE, ndhH and rps16), and performed phylogenetic analyses based on: (i) the ycf2 gene, (ii) all the six genes identified as 'hotspots' of variability, and (iii) the genes identified as 'hotspots' of variability, except the ycf2 gene. The structure, gene order, and gene content of the C. xanthocarpa plastome are similar to other Myrtaceae species. Phylogenetic analyses revealed the ycf2 gene as a promissing region for barcoding within this family, having also a robust phylogenetic signal. The synonymous and nonsynonymous substitution rates and the Ka/Ks ratio revealed low values for the ycf2 gene among C. xanthocarpa and the other 47 analyzed species of Myrtaceae, with moderate purifying selection acting on this gene. The average nucleotide identity (ANI) analysis of the whole plastomes produced phylogenetic trees supporting the monophyly of three Myrtaceae tribes. The findings of this study provide support for planning conservation, breeding, and biotechnological programs for this species.},
}
@article {pmid32555294,
year = {2020},
author = {Huang, C and Shao, L and Qu, S and Rao, J and Cheng, T and Cao, Z and Liu, S and Hu, J and Liang, X and Shang, L and Chen, Y and Liang, Z and Zhang, J and Chen, P and Luo, D and Zhu, A and Yu, T and Zhang, W and Fan, G and Chen, F and Huang, J},
title = {An integrated Asian human SNV and indel benchmark established using multiple sequencing methods.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {9821},
pmid = {32555294},
issn = {2045-2322},
mesh = {Adult ; Asian People/*genetics ; Benchmarking ; Genome, Human/genetics ; Haplotypes ; High-Throughput Nucleotide Sequencing/*standards ; Humans ; INDEL Mutation/*genetics ; Male ; Polymorphism, Single Nucleotide/*genetics ; Reference Standards ; },
abstract = {Sequencing technologies have been rapidly developed recently, leading to the breakthrough of sequencing-based clinical diagnosis, but accurate and complete genome variation benchmark would be required for further assessment of precision medicine applications. Despite the human cell line of NA12878 has been successfully developed to be a variation benchmark, population-specific variation benchmark is still lacking. Here, we established an Asian human variation benchmark by constructing and sequencing a stabilized cell line of a Chinese Han volunteer. By using seven different sequencing strategies, we obtained ~3.88 Tb clean data from different laboratories, hoping to reach the point of high sequencing depth and accurate variation detection. Through the combination of variations identified from different sequencing strategies and different analysis pipelines, we identified 3.35 million SNVs and 348.65 thousand indels, which were well supported by our sequencing data and passed our strict quality control, thus should be high confidence variation benchmark. Besides, we also detected 5,913 high-quality SNVs which had 969 sites were novel and located in the high homologous regions supported by long-range information in both the co-barcoding single tube Long Fragment Read (stLFR) data and PacBio HiFi CCS data. Furthermore, by using the long reads data (stLFR and HiFi CCS), we were able to phase more than 99% heterozygous SNVs, which helps to improve the benchmark to be haplotype level. Our study provided comprehensive sequencing data as well as the integrated variation benchmark of an Asian derived cell line, which would be valuable for future sequencing-based clinical development.},
}
@article {pmid32554381,
year = {2020},
author = {Chuang, LY and Yang, CS and Yang, HS and Yang, CH},
title = {Identification of High-Order Single-Nucleotide Polymorphism Barcodes in Breast Cancer Using a Hybrid Taguchi-Genetic Algorithm: Case-Control Study.},
journal = {JMIR medical informatics},
volume = {8},
number = {6},
pages = {e16886},
pmid = {32554381},
issn = {2291-9694},
abstract = {BACKGROUND: Breast cancer has a major disease burden in the female population, and it is a highly genome-associated human disease. However, in genetic studies of complex diseases, modern geneticists face challenges in detecting interactions among loci.<br><br>OBJECTIVE: This study aimed to investigate whether variations of single-nucleotide polymorphisms (SNPs) are associated with histopathological tumor characteristics in breast cancer patients.<br><br>METHODS: A hybrid Taguchi-genetic algorithm (HTGA) was proposed to identify the high-order SNP barcodes in a breast cancer case-control study. A Taguchi method was used to enhance a genetic algorithm (GA) for identifying high-order SNP barcodes. The Taguchi method was integrated into the GA after the crossover operations in order to optimize the generated offspring systematically for enhancing the GA search ability.<br><br>RESULTS: The proposed HTGA effectively converged to a promising region within the problem space and provided excellent SNP barcode identification. Regression analysis was used to validate the association between breast cancer and the identified high-order SNP barcodes. The maximum OR was less than 1 (range 0.870-0.755) for two- to seven-order SNP barcodes.<br><br>CONCLUSIONS: We systematically evaluated the interaction effects of 26 SNPs within growth factor-related genes for breast carcinogenesis pathways. The HTGA could successfully identify relevant high-order SNP barcodes by evaluating the differences between cases and controls. The validation results showed that the HTGA can provide better fitness values as compared with other methods for the identification of high-order SNP barcodes using breast cancer case-control data sets.},
}
@article {pmid32552661,
year = {2020},
author = {Majidian, S and Kahaei, MH and de Ridder, D},
title = {Hap10: reconstructing accurate and long polyploid haplotypes using linked reads.},
journal = {BMC bioinformatics},
volume = {21},
number = {1},
pages = {253},
pmid = {32552661},
issn = {1471-2105},
mesh = {Algorithms ; Genome, Human/*genetics ; Haplotypes/*physiology ; Humans ; *Polyploidy ; },
abstract = {BACKGROUND: Haplotype information is essential for many genetic and genomic analyses, including genotype-phenotype associations in human, animals and plants. Haplotype assembly is a method for reconstructing haplotypes from DNA sequencing reads. By the advent of new sequencing technologies, new algorithms are needed to ensure long and accurate haplotypes. While a few linked-read haplotype assembly algorithms are available for diploid genomes, to the best of our knowledge, no algorithms have yet been proposed for polyploids specifically exploiting linked reads.<br><br>RESULTS: The first haplotyping algorithm designed for linked reads generated from a polyploid genome is presented, built on a typical short-read haplotyping method, SDhaP. Using the input aligned reads and called variants, the haplotype-relevant information is extracted. Next, reads with the same barcodes are combined to produce molecule-specific fragments. Then, these fragments are clustered into strongly connected components which are then used as input of a haplotype assembly core in order to estimate accurate and long haplotypes.<br><br>CONCLUSIONS: Hap10 is a novel algorithm for haplotype assembly of polyploid genomes using linked reads. The performance of the algorithms is evaluated in a number of simulation scenarios and its applicability is demonstrated on a real dataset of sweet potato.},
}
@article {pmid32552121,
year = {2020},
author = {Kim, P and Han, JH and An, SL},
title = {Genetic identification of species and natural hybridization determination based on mitochondrial DNA and nuclear DNA of genus Zacco in Korea.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {31},
number = {6},
pages = {221-227},
doi = {10.1080/24701394.2020.1777994},
pmid = {32552121},
issn = {2470-1408},
mesh = {Animals ; Breeding ; Cell Nucleus/*genetics ; Chimera ; Cyprinidae/*classification/genetics ; DNA/*genetics ; DNA Barcoding, Taxonomic ; Female ; Genes, RAG-1/genetics ; Genetic Variation ; Male ; Mitochondria/*genetics ; Phylogeny ; Republic of Korea ; },
abstract = {Genus Zacco specimens collected in this study were classified genetically as five species, Zacco platypus, Z. temminckii, Z. koreanus and two unidentified species, using DNA barcoding analysis based on 655 bp of mitochondrial cytochrome c oxidase subunit I (COI) gene. Two of unidentified species (Z. sp.1 and Z. sp.2) were considered to be unrecorded or new species of genus Zacco according to genetic distances between Zacco species. In addition, we determined a natural hybrid based on polymorphic base at the diagnostic positions displayed on nuclear recombination activating gene 1 (RAG1) gene (965 bp), and estimated paternal and maternal species of natural hybrid comparing phylogenetic tree between COI and RAG1, and Z. sp.1♀ × Z. koreanus♂, Z. sp.2♀ × Z. koreanus♂ and Z. koreanus♀ × Z. sp.1♂ individuals were confirmed. The habitat of natural hybrids of Z. koreanus between Z. sp.1 and Z. sp.2 was identified as Geum and Yeongsan River, respectively. In our data, only F1 hybrid generation was identified; however, generations after F1 hybrid or backcross were not demonstrated.},
}
@article {pmid32552081,
year = {2021},
author = {Guzik, MT and Stevens, MI and Cooper, SJB and Humphreys, WF and Austin, AD},
title = {Extreme genetic diversity among springtails (Collembola) in subterranean calcretes of arid Australia.},
journal = {Genome},
volume = {64},
number = {3},
pages = {181-195},
doi = {10.1139/gen-2019-0199},
pmid = {32552081},
issn = {1480-3321},
mesh = {Animals ; Arthropods/*classification/*genetics ; Biodiversity ; Calcium Carbonate ; Electron Transport Complex IV/genetics ; Genetic Variation ; Phylogeny ; Phylogeography ; Western Australia ; },
abstract = {The subterranean islands hypothesis for calcretes of the Yilgarn region in Western Australia applies to many stygobitic (subterranean-aquatic) species that are "trapped" evolutionarily within isolated aquifers due to their aquatic lifestyles. In contrast, little is known about the distribution of terrestrial-subterranean invertebrates associated with the calcretes. We used subterranean Collembola from the Yilgarn calcretes to test the hypothesis that troglobitic species, those inhabiting the subterranean unsaturated (non-aquatic) zone of calcretes, are also restricted in their distribution and represent reciprocally monophyletic and endemic lineages. We used the barcoding fragment of the mtDNA cytochrome c oxidase subunit 1 (COI) gene from 183 individuals to reconstruct the phylogenetic history of the genus Pseudosinella Schäffer (Collembola, Lepidocyrtidae) from 10 calcretes in the Yilgarn. These calcretes represent less than 5% of the total possible calcretes in this region, yet we show that their diversity for subterranean Collembola comprises a minimum of 25 new species. Regionally, multiple levels of diversity exist in Pseudosinella, indicative of a complex evolutionary history for this genus in the Yilgarn. These species have probably been impacted by climatic oscillations, facilitating their dispersal across the landscape. The results represent a small proportion of the undiscovered diversity in Australia's arid zone.},
}
@article {pmid32550269,
year = {2020},
author = {Frazzette, N and Khodadadi-Jamayran, A and Doudican, N and Santana, A and Felsen, D and Pavlick, AC and Tsirigos, A and Carucci, JA},
title = {Decreased cytotoxic T cells and TCR clonality in organ transplant recipients with squamous cell carcinoma.},
journal = {NPJ precision oncology},
volume = {4},
number = {},
pages = {13},
pmid = {32550269},
issn = {2397-768X},
abstract = {T-cell landscape differences between cutaneous squamous cell carcinoma (cSCC) tumors in immune competent (SCC in IC) and immunocompromised organ transplant recipients (TSCC in OTR) are unclear. We developed an analytical method to define tumor infiltrating lymphocyte (TIL) phenotype in cSCC from immune competent and immune suppressed patients using single-cell TCR sequencing and gene expression data. TSCC exhibits reduced proportions of cytotoxic and naïve TILs and similar numbers of regulatory TILs. Fewer, more heterogeneous TCR clonotypes are observed in TIL from OTR. Most TCR sequences for top ten clonotypes correspond to known antigens, while 24% correspond to putative neoantigens. OTR show increased cSCC events over 12 months possibly due to reduced cytotoxic T-cells. Our novel method of barcoding CD8+ T-cells is the first providing gene expression and TCR sequences in cSCC. Knowledge regarding putative antigens recognized by TCRs with phenotypic function of T-cells bearing those TCRs could facilitate personalized cSCC treatments.},
}
@article {pmid32549748,
year = {2020},
author = {Canty, R and Ruzzier, E and Cronk, QC and Percy, DM},
title = {Salix transect of Europe: records of willow-associated weevils (Coleoptera: Curculionoidea) from Greece to Arctic Norway, with insights from DNA barcoding.},
journal = {Biodiversity data journal},
volume = {8},
number = {},
pages = {e52881},
pmid = {32549748},
issn = {1314-2828},
abstract = {BACKGROUND: Curculionid beetles associated with willow (Salix spp.) were surveyed at 42 sites across Europe, from Greece (lat. 38.8 °N) to arctic Norway (lat. 69.7 °N). DNA sequence data provide additional verification of identifications and geographic clustering.<br><br>NEW INFORMATION: In all, 73 curculionid species were collected from willows, of which seven were particularly abundant. The most widespread species were: Acalyptus carpini Fabricius, 1793 at 15 sites; Tachyerges stigma Germar, 1821 at 13 sites; Phyllobius oblongus (Linnaeus, 1758) at 11 sites; Phyllobius maculicornis Germar, 1824 at 10 sites; and Archarius salicivorus (Paykull, 1792), Melanapion minimum (Herbst, 1797), and Phyllobius cf. pyri (Linnaeus, 1758) all at nine sites. The mean number of curculionid species collected on willow at each site was 5.5 (range 0-14). Compared to chrysomelids, curculionids were richer in species but the species had relatively low average abundance. Widespread curculionid species appear to have scattered and patchy observed distributions with limited geographical structuring in our data. However, deeper sampling (e.g. over multiple seasons and years), would give a better indication of distribution, and may increase apparent geographical structuring. There is some site-to-site variation in colour in a few taxa, but little notable size variation. DNA barcoding, performed on some of the more common species, provides clear species clusters and definitive separation of the taxonomically more challenging species, as well as some interesting geographic insights. Our northernmost sample of Phyllobius oblongus is unique in clustering with Canadian samples of this species. On the other hand, our samples of Acalyptus carpini cluster with European samples and are distinct from a separate Canadian cluster of this species. We provide the first available DNA sequences for Phyllobius thalassinus Gyllenhal, 1834 (Hungary).},
}
@article {pmid32549379,
year = {2020},
author = {Mehmood, F and Abdullah, and Ubaid, Z and Bao, Y and Poczai, P and Mirza, B},
title = {Comparative Plastomics of Ashwagandha (Withania, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants.},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {6},
pages = {},
pmid = {32549379},
issn = {2223-7747},
abstract = {Within the family Solanaceae, Withania is a small genus belonging to the Solanoideae subfamily. Here, we report the de novo assembled chloroplast genome sequences of W. coagulans, W. adpressa, and W. riebeckii. The length of these genomes ranged from 154,162 to 154,364 base pairs (bp). These genomes contained a pair of inverted repeats (IRa and IRb) ranging from 25,029 to 25,071 bp that were separated by a large single-copy (LSC) region of 85,635-85,765 bp and a small single-copy (SSC) region of 18,457-18,469 bp. We analyzed the structural organization, gene content and order, guanine-cytosine content, codon usage, RNA-editing sites, microsatellites, oligonucleotide and tandem repeats, and substitutions of Withania plastomes, which revealed high similarities among the species. Comparative analysis among the Withania species also highlighted 10 divergent hotspots that could potentially be used for molecular marker development, phylogenetic analysis, and species identification. Furthermore, our analyses showed that even three mutational hotspots (rps4-trnT, trnM-atpE, and rps15) were sufficient to discriminate the Withania species included in current study.},
}
@article {pmid32547302,
year = {2020},
author = {Lin, Y and Chen, HW},
title = {The genus Scaptodrosophila Duda (Diptera, Drosophilidae), part III: the riverata species group from China, with morphological and molecular evidence for five new species.},
journal = {ZooKeys},
volume = {937},
number = {},
pages = {139-162},
pmid = {32547302},
issn = {1313-2989},
abstract = {A new species group, the riverata species group, is established within the genus Scaptodrosophila based on morphological and molecular evidence for five known and five new species from China: S. abdentata sp. nov., S. cederholmi (Okada, 1988), S. crocata (Bock, 1976), S. paraclubata (Sundaran &amp; Gupta, 1991), S. platyrhina sp. nov., S. puncticeps (Okada, 1956), S. riverata (Singh &amp; Gupta, 1977), S. serrateifoliacea sp. nov., S. sinuata sp. nov. and S. tanyrhina sp. nov. A key to this group is provided. Furthermore, 51 mtDNA COI sequences belonging to S. puncticeps, S. riverata and the five new species are used for verifying species boundaries defined by the morphological data.},
}
@article {pmid32547296,
year = {2020},
author = {Li, D and Liu, F and Li, D and Xu, X},
title = {Two new species of the primitively segmented spider genus Songthela from Hunan Province, China (Mesothelae, Liphistiidae).},
journal = {ZooKeys},
volume = {937},
number = {},
pages = {1-19},
pmid = {32547296},
issn = {1313-2989},
abstract = {This study reports two new species of the primitively segmented spider genus Songthela from Hunan Province, China, based on morphological characters: S. huangyang sp. nov. (♂♀), S. xiangnan sp. nov. (♂♀). Additional material also facilitates a more accurate description of S. goulouensis (Yin, 2001) with the first description of the male. Nucleotide data for the barcoding gene, cytochrome c oxidase subunit I (COI), is also provided for these three species.},
}
@article {pmid32545846,
year = {2020},
author = {Guo, L and Gao, F and Cheng, Y and Gao, C and Chen, J and Li, Z and Wang, T and Xu, J},
title = {Mitochondrial COI Sequence Variations within and among Geographic Samples of the Hemp Pest Psylliodes attenuata from China.},
journal = {Insects},
volume = {11},
number = {6},
pages = {},
pmid = {32545846},
issn = {2075-4450},
support = {31701818//National Natural Science Foundation of China/ ; 2018JJ3582//Natural Science Foundation of&#xa0;Hunan Province/ ; CAAS-ASTIP-IBFC//Chinese Academy of Agricultural Sciences/ ; },
abstract = {The hemp flea beetle Psylliodes attenuata (Coleoptera: Chrysomelidae: Psylliodes) is a common pest of Cannabis sativa, including cultivars of both industrial hemp and medicinal marijuana. Both the larval and adult stages of this beetle can cause significant damages to C. sativa, resulting in substantial crop losses. At present, little is known about the populations of this pest, including its genetic diversity. In this study, we obtained 281 P. attenuata samples from nine field sites representing broad industrial hemp productions in China and analyzed their DNA sequences at the mitochondrial COI gene, the insect DNA barcode. Our analyses revealed a total of 48 haplotypes, with 28 being found only in one specimen each while the remaining 20 were shared by two or more specimens each. Of the 20 shared haplotypes, eight were shared among local populations often from far away locations, consistent with recent long-distance dispersals. However, the observed putative long-distance dispersals have not obscured the significant genetic differentiations among the regional populations from northeastern, eastern, central and southwestern China. Interestingly, haplotype network analyses suggest evidence for potential mitochondrial recombination in natural populations of this species. We briefly discuss the implications of our results on its evolution, center of diversity, route of spread, and pest management strategies in hemp fields.},
}
@article {pmid32545703,
year = {2020},
author = {Contreras, R and van den Brink, L and Burgos, B and González, M and Gacitúa, S},
title = {Genetic Characterization of an Endangered Chilean Endemic Species, Prosopis burkartii Muñoz, Reveals its Hybrids Parentage.},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {6},
pages = {},
pmid = {32545703},
issn = {2223-7747},
abstract = {The hybridization of Prosopis burkartii, a critically endangered endemic species, and the identification of its paternal species has not been genetically studied before. In this study we aimed to genetically confirm the origin of this species. To resolve the parental status of P. burkartii, inter-simple sequence repeat (ISSR), simple sequence repeats (SSR) and intron trnL molecular markers were used, and compared with Chilean species from the Algarobia and Strombocarpa sections. Out of seven ISSRs, a total of 70 polymorphic bands were produced in four species of the Strombocarpa section. An Multi-dimensional scaling (MDS) and Bayasian (STRUCTURE) analysis showed signs of introgression of genetic material in P. burkartii. Unweighted pair group method with arithmetic average (UPGMA) cluster analysis showed three clusters, and placed the P. burkartii cluster nested within the P. tamarugo group. Sequencing of the trnL intron showed a fragment of 535 bp and 529 bp in the species of the Algarobia and Strombocarpa sections, respectively. Using maximum parsimony (MP) and maximum likelihood (ML) trees with the trnL intron, revealed four clusters. A species-specific diagnostic method was performed, using the trnL intron Single Nucleotide Polymorphism (SNP). This method identified if individuals of P. burkartii inherited their maternal DNA from P. tamarugo or from P. strombulifera. We deduced that P. tamarugo and P. strombulifera are involved in the formation of P. burkartii.},
}
@article {pmid32542933,
year = {2020},
author = {Bohmann, K and Mirarab, S and Bafna, V and Gilbert, MTP},
title = {Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification.},
journal = {Molecular ecology},
volume = {29},
number = {14},
pages = {2521-2534},
pmid = {32542933},
issn = {1365-294X},
support = {R01 GM114362/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *DNA ; *DNA Barcoding, Taxonomic ; DNA Primers ; Databases, Genetic ; Genomics/*methods ; Polymerase Chain Reaction ; },
abstract = {Genetic tools are increasingly used to identify and discriminate between species. One key transition in this process was the recognition of the potential of the ca 658bp fragment of the organelle cytochrome c oxidase I (COI) as a barcode region, which revolutionized animal bioidentification and lead, among others, to the instigation of the Barcode of Life Database (BOLD), containing currently barcodes from >7.9 million specimens. Following this discovery, suggestions for other organellar regions and markers, and the primers with which to amplify them, have been continuously proposed. Most recently, the field has taken the leap from PCR-based generation of DNA references into shotgun sequencing-based "genome skimming" alternatives, with the ultimate goal of assembling organellar reference genomes. Unfortunately, in genome skimming approaches, much of the nuclear genome (as much as 99% of the sequence data) is discarded, which is not only wasteful, but can also limit the power of discrimination at, or below, the species level. Here, we advocate that the full shotgun sequence data can be used to assign an identity (that we term for convenience its "DNA-mark") for both voucher and query samples, without requiring any computationally intensive pretreatment (e.g. assembly) of reads. We argue that if reference databases are populated with such "DNA-marks," it will enable future DNA-based taxonomic identification to complement, or even replace PCR of barcodes with genome skimming, and we discuss how such methodology ultimately could enable identification to population, or even individual, level.},
}
@article {pmid32541427,
year = {2021},
author = {Evanson, HV and Reed, JH and Cox, R and Clinthorne, AD and Williams, WW and Vallero, J and Rodgers, L and Greene, M and Koeppl, P and Gerlach, K},
title = {Improving Staff Experience With Vaccine Data Entry With 2D Barcode Scanning.},
journal = {Journal of nursing care quality},
volume = {36},
number = {2},
pages = {143-148},
doi = {10.1097/NCQ.0000000000000495},
pmid = {32541427},
issn = {1550-5065},
mesh = {Electronic Data Processing ; Humans ; Surveys and Questionnaires ; *Vaccines ; },
abstract = {BACKGROUND: Small fonts on vaccine labels make manually recording vaccine data in patient records time-consuming and challenging. Vaccine 2-dimensional (2D) barcode scanning is a promising alternative to manually recording these data.<br><br>PROBLEM: While vaccine 2D barcode scanning assists in data entry, adoption of scanning technology is still low.<br><br>APPROACH: Pilot sites (n = 27) within a health system scanned 2D barcodes to record vaccine data for 6 months. The time to record through scanning and nonscanning methods was measured for 13 vaccinators at 9 sites. A survey was administered to participants across all sites about their experience.<br><br>OUTCOMES: On average, 22 seconds were saved per vaccine scanned versus entered manually (7 vs 29 seconds, respectively). Participants reported preference for scanning over other vaccine entry options and identified benefits of scanning.<br><br>CONCLUSION: Expanded use of 2D barcode scanning can meaningfully improve clinical practices by improving efficiency and staff satisfaction during vaccine data entry.},
}
@article {pmid32540955,
year = {2020},
author = {Chen, Z and Pham, L and Wu, TC and Mo, G and Xia, Y and Chang, PL and Porter, D and Phan, T and Che, H and Tran, H and Bansal, V and Shaffer, J and Belda-Ferre, P and Humphrey, G and Knight, R and Pevzner, P and Pham, S and Wang, Y and Lei, M},
title = {Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information.},
journal = {Genome research},
volume = {30},
number = {6},
pages = {898-909},
pmid = {32540955},
issn = {1549-5469},
support = {K12 GM068524/GM/NIGMS NIH HHS/United States ; },
mesh = {Computational Biology/methods ; DNA Barcoding, Taxonomic/methods ; *Gene Library ; Genetic Variation ; Genome, Human ; Genomics/methods ; HLA Antigens/genetics ; Haplotypes ; *High-Throughput Nucleotide Sequencing/methods/standards ; Humans ; *Sequence Analysis, DNA/methods/standards ; Workflow ; },
abstract = {Long-range sequencing information is required for haplotype phasing, de novo assembly, and structural variation detection. Current long-read sequencing technologies can provide valuable long-range information but at a high cost with low accuracy and high DNA input requirements. We have developed a single-tube Transposase Enzyme Linked Long-read Sequencing (TELL-seq) technology, which enables a low-cost, high-accuracy, and high-throughput short-read second-generation sequencer to generate over 100 kb of long-range sequencing information with as little as 0.1 ng input material. In a PCR tube, millions of clonally barcoded beads are used to uniquely barcode long DNA molecules in an open bulk reaction without dilution and compartmentation. The barcoded linked-reads are used to successfully assemble genomes ranging from microbes to human. These linked-reads also generate megabase-long phased blocks and provide a cost-effective tool for detecting structural variants in a genome, which are important to identify compound heterozygosity in recessive Mendelian diseases and discover genetic drivers and diagnostic biomarkers in cancers.},
}
@article {pmid32535016,
year = {2020},
author = {Pagliusi, S and Dennehy, M and Homma, A},
title = {Two decades of vaccine innovations for global public good: Report of the Developing Countries' Vaccine Manufacturers Network 20th meeting, 21-23 october 2019, Rio de Janeiro, Brazil.},
journal = {Vaccine},
volume = {38},
number = {36},
pages = {5851-5860},
pmid = {32535016},
issn = {1873-2518},
mesh = {Brazil ; *Developing Countries ; Global Health ; Humans ; Immunization Programs ; Vaccination ; *Vaccines ; },
abstract = {The Developing Countries' Vaccine Manufacturers Network, joined by global health organizations, held its 20th meeting celebrating two decades of vaccine innovations for global public good. Health leaders from industry, academia and global health organizations reviewed efforts to accelerate innovation, improve access to vaccines, overcome inequalities and strengthen technological and public-health management capabilities. Discussion topics included World Health Organization's immunization strategy, Pan American Health Organization's system-strengthening efforts, Gavi's evaluation of vaccine coverage in middle income countries and developments on public-market intelligence. Health market trends, delivery gaps, integration of system-wide needs, costs and benefits, and implications for stakeholder decision-making were areas of focus. Novel thinking was discussed on integration of policy, financing, regulatory pathways and alignment of innovation priorities to improve efficiency in vaccine development pathways. The Vaccine Innovation Prioritization Strategy collaboration presented nine global innovation priorities, and many other partners and members presented updates on their priorities. Novel technologies and platforms, such as RNA-based vaccines, adenoviral vectors, bioconjugation, blow-fill-seal and two-dimensional barcodes, provided opportunities to accelerate vaccine innovations. Challenges in planning and operations at global level included those in health security, polio eradication, re-emergence of diseases, disparities between forecasts and orders and heterogeneous regulatory requirements. Manufacturers were urged to accelerate innovation and prequalification of high-impact vaccines, such as pneumococcal, human papillomavirus and rotavirus vaccines, to strengthen immunization globally.},
}
@article {pmid32531457,
year = {2020},
author = {Pandey, PK and Singh, YS and Tripathy, PS and Kumar, R and Abujam, SK and Parhi, J},
title = {DNA barcoding and phylogenetics of freshwater fish fauna of Ranganadi River, Arunachal Pradesh.},
journal = {Gene},
volume = {754},
number = {},
pages = {144860},
doi = {10.1016/j.gene.2020.144860},
pmid = {32531457},
issn = {1879-0038},
mesh = {Animals ; *Biodiversity ; DNA/*analysis/genetics ; *DNA Barcoding, Taxonomic ; Fishes/*classification/*genetics ; Fresh Water ; *Genetic Variation ; *Phylogeny ; Rivers ; },
abstract = {Arunachal Pradesh, the largest state of North-East India covers almost 60.93% of the Eastern Himalayan hotspot. Fish diversity and species identification is utmost important for fisheries management. But, in some cases morphological characteristics based identification is difficult for a non-specialist to perform. In view of the above, the present study emphasized on the assessment of DNA barcoding, phylogenetics and genetic diversity of fish species in the Ranganadi River, Arunachal Pradesh, India. India. Arunachal Pradesh, the largest state of North-East India covers almost 60.93% of the Eastern Himalayan hotspot. Altogether 114 specimens, representing 22 species, belonging to 3 orders and 5 families were successfully barcoded and found to be 98-100% identical from both GenBank and BOLD databases. Out of these 22 fish species, it was found that one species assessed was Endangered, three species as Near Threatened and one species as Vulnerable. A Neighbour Joining (NJ) tree was constructed using Rstudio for the purpose of a phylogenetic analysis of the identified species. The barcoding gap analysis using K2P, P-distance and Jukes-Cantor was done to detect the presence of cryptic species and barcoding success. The nucleotide base composition and genetic distance analysis were also performed, using MEGA 6.0. DNA Sequence Polymorphism v6.12.03 analysis revealed the nucleotide diversity (p) and haplotype diversity (Hd). The Hd for the whole dataset was found to be 0.975, which showed high genetic diversity in the Ranganadi River. Both morphological key identifying characters and molecular data corroborated the phylogenetic analysis. This COI barcode library, generated in the present study, not only helped in species identification and molecular study, but also in cryptic species identification.},
}
@article {pmid32527930,
year = {2020},
author = {Zhang, P and Ganesamoorthy, D and Nguyen, SH and Au, R and Coin, LJ and Tey, SK},
title = {Nanopore sequencing as a scalable, cost-effective platform for analyzing polyclonal vector integration sites following clinical T cell therapy.},
journal = {Journal for immunotherapy of cancer},
volume = {8},
number = {1},
pages = {},
pmid = {32527930},
issn = {2051-1426},
mesh = {Cell Engineering/*methods ; Cell- and Tissue-Based Therapy/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Nanopore Sequencing/*methods ; },
abstract = {BACKGROUND: Analysis of vector integration sites in gene-modified cells can provide critical information on clonality and potential biological impact on nearby genes. Current short-read next-generation sequencing methods require specialized instruments and large batch runs.<br><br>METHODS: We used nanopore sequencing to analyze the vector integration sites of T cells transduced by the gammaretroviral vector, SFG.iCasp9.2A.&#x394;CD19. DNA from oligoclonal cell lines and polyclonal clinical samples were restriction enzyme digested with two 6-cutters, NcoI and BspHI; and the flanking genomic DNA amplified by inverse PCR or cassette ligation PCR. Following nested PCR and barcoding, the amplicons were sequenced on the Oxford Nanopore platform. Reads were filtered for quality, trimmed, and aligned. Custom tool was developed to cluster reads and merge overlapping clusters.<br><br>RESULTS: Both inverse PCR and cassette ligation PCR could successfully amplify flanking genomic DNA, with cassette ligation PCR showing less bias. The 4.8&#x2009;million raw reads were grouped into 12,186 clusters and 6410 clones. The 3'long terminal repeat (LTR)-genome junction could be resolved within a 5-nucleotide span for a majority of clusters and within one nucleotide span for clusters with &#x2265;5 reads. The chromosomal distributions of the insertional sites and their predilection for regions proximate to transcription start sites were consistent with previous reports for gammaretroviral vector integrants as analyzed by short-read next-generation sequencing.<br><br>CONCLUSION: Our study shows that it is feasible to use nanopore sequencing to map polyclonal vector integration sites. The assay is scalable and requires minimum capital, which together enable cost-effective and timely analysis. Further refinement is required to reduce amplification bias and improve single nucleotide resolution.},
}
@article {pmid32527315,
year = {2020},
author = {Na, D},
title = {DNA steganography: hiding undetectable secret messages within the single nucleotide polymorphisms of a genome and detecting mutation-induced errors.},
journal = {Microbial cell factories},
volume = {19},
number = {1},
pages = {128},
pmid = {32527315},
issn = {1475-2859},
support = {NRF-2019M3E5D4065682//National Research Foundation of Korea/ ; NRF-2018R1A5A1025077//National Research Foundation of Korea/ ; },
mesh = {Algorithms ; Animals ; Bacteria/genetics ; *DNA ; DNA Mutational Analysis/*methods ; Humans ; *Mutation ; Plants/genetics ; *Polymorphism, Single Nucleotide ; },
abstract = {BACKGROUND: As cell engineering technology advances, more complex synthetically designed cells and metabolically engineered cells are being developed. Engineered cells are important resources in industry. Similar to image watermarking, engineered cells should be watermarked for protection against improper use.<br><br>RESULTS: In this study, a DNA steganography methodology was developed to hide messages in variable regions (single nucleotide polymorphisms) of the genome to create hidden messages and thereby prevent&#xa0;from hacking. Additionally, to detect errors (mutations) within the encrypted messages, a block sum check algorithm was employed, similar to that used in network data transmission to detect noise-induced information changes.<br><br>CONCLUSIONS: This DNA steganography methodology could be used to hide secret messages in a genome and detect errors within the encrypted messages. This approach is expected to be useful for tracking cells and protecting biological assets (e.g., engineered cells).},
}
@article {pmid32526150,
year = {2021},
author = {Powers, TO and Harris, TS and Higgins, RS and Mullin, PG and Powers, KS},
title = {Nematode biodiversity assessments need vouchered databases: A BOLD reference library for plant-parasitic nematodes in the superfamily Criconematoidea.},
journal = {Genome},
volume = {64},
number = {3},
pages = {232-241},
doi = {10.1139/gen-2019-0196},
pmid = {32526150},
issn = {1480-3321},
mesh = {Animals ; Biodiversity ; Canada ; DNA Barcoding, Taxonomic ; Databases, Nucleic Acid ; Haplotypes ; Plants/parasitology ; Rhabditida/*classification/genetics ; United States ; },
abstract = {Nematodes are frequently cited as underrepresented in faunistic surveys using DNA barcoding with COI. This underrepresentation is generally attributed to a limited presence of nematodes in DNA databases which, in turn, is often ascribed to structural variability and high evolutionary rates in nematode mitochondrial genomes. Empirical evidence, however, indicates that many taxa are readily amplified with primer sets specifically targeted to different nematode families. Here we report the development of a COI reference library of 1726 specimens in the terrestrial plant parasitic nematode superfamily Criconematoidea. Specimens collected during an ecoregion survey of North America were individually photographed, measured, and PCR amplified to produce a 721 bp region of COI for taxonomic analysis. A neighbor-joining tree structured the dataset into 179 haplotype groups that generally conformed to morphospecies in traditional analysis or Barcode Index Numbers (BINs) in the BOLD system, although absent formal BIN membership due to insufficient overlap with the Folmer region of COI. Approximately one-third of the haplotype groups could be associated with previously described species. The geographic distribution of criconematid nematode species suggests a structure influenced by the major habitat types in the United States and Canada. All sequences collected in the ecoregion survey are deposited in BOLD.},
}
@article {pmid32523040,
year = {2020},
author = {Oke, AO and Oladigbolu, AA and Kunta, M and Alabi, OJ and Sétamou, M},
title = {First report of the occurrence of Asian citrus psyllid Diaphorina citri (Hemiptera: Liviidae), an invasive species in Nigeria, West Africa.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {9418},
pmid = {32523040},
issn = {2045-2322},
mesh = {Africa, Eastern ; Africa, Western ; Animals ; Citrus/*parasitology ; Hemiptera/*genetics ; Insect Vectors/genetics ; *Introduced Species ; Nigeria ; Nymph/genetics ; Plant Diseases/*parasitology ; Real-Time Polymerase Chain Reaction/methods ; Rhizobiaceae/genetics ; },
abstract = {The Asian citrus psyllid (ACP; Diaphorina citri) is the vector of Candidatus Liberibacter asiaticus (CLas) that is associated with the devastating Huanglongbing (HLB; citrus greening disease). This pest of Asian origin has spread into the Americas and more recently into a few countries in East Africa. During recent surveys, suspect ACP adults and nymphs were recorded for the first time infesting citrus trees in southwest Nigeria. Morphological identification and DNA barcoding confirmed the samples to be D. citri. Analysis of the obtained sequences revealed that the ACP recorded in Nigeria clustered with other taxa in the previously identified B1 clade that consists of populations from different continents. The presence of the endosymbionts Ca. Carsonella ruddii and Ca. Profftella armatura in ACP from Nigeria was also confirmed by PCR and Sanger sequencing. The ACP individuals were assayed for the presence of CLaf, CLam and CLas by qPCR, but none of the insects tested positive for any of the Liberibacters. The prolific nature of ACP and the tropical climate prevailing in the citrus-producing areas of Nigeria and other West African countries may favor its rapid spread and population increase, thus posing a grave threat to the sustainability of citriculture in these countries.},
}
@article {pmid32522020,
year = {2020},
author = {Bourque, DA and Morey, KC and Bradley, DL and Fost, B and Daley, JM and Jacobson, N and Naaum, AM and Hanner, RH},
title = {Dimethyldimethyl Hydantoin: An Alternative Fluid for Morphological and Genetic Preservation.},
journal = {Biopreservation and biobanking},
volume = {18},
number = {4},
pages = {283-289},
doi = {10.1089/bio.2020.0001},
pmid = {32522020},
issn = {1947-5543},
mesh = {Animals ; DNA/*analysis/drug effects ; DNA Barcoding, Taxonomic ; Dose-Response Relationship, Drug ; Fishes/*classification/genetics ; Hydantoins/*pharmacology ; North America ; Preservation, Biological ; Solutions ; Specimen Handling ; },
abstract = {Modern taxonomy requires the preservation of biospecimens for both morphological and molecular applications. The utility of a previously identified preservative, dimethyldimethylhydantoin hydantoin (Dekafald[®]), to retain both physical diagnostic traits and the DNA integrity of biological specimens remains unknown. Using 439 eggs and 414 larvae from two North American fish species, we compared three hydantoin solutions at different concentrations (5%, 10%, and 20%) with gold standard preservatives (10% buffered formalin, 95% ethanol) to evaluate morphological trait retention up to 90 days, and DNA barcoding success up to 56 days. While the 5% hydantoin solution had the most sequencing success by 56 days, the 10% hydantoin solution was the best multipurpose preservative. Future work should assess the performance of ∼10% hydantoin solution over longer time periods, and its applicability to other taxa such as Arthropoda.},
}
@article {pmid32519408,
year = {2020},
author = {Park, S and Lee, SS and Kim, SH},
title = {Photonic Multishells Composed of Cholesteric Liquid Crystals Designed by Controlled Phase Separation in Emulsion Drops.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {32},
number = {30},
pages = {e2002166},
doi = {10.1002/adma.202002166},
pmid = {32519408},
issn = {1521-4095},
support = {NRF-2020R1A2C2003245//National Science Foundation, United Arab Emirates/ ; NRF-2019K1A3A1A14012962//National Science Foundation, United Arab Emirates/ ; //Ministry of Science, ICT and Future Planning/ ; //Korea Institute of Science and Technology/ ; NRF-2020R1A2C2003245//NRF/ ; NRF-2019K1A3A1A14012962//NRF/ ; },
abstract = {Cholesteric liquid crystals (CLCs), also known as chiral nematic LCs, show a photonic stopband, which is promising for various optical applications. In particular, CLCs confined in microcompartments are useful for sensing, lasing, and optical barcoding at the microscale. The integration of distinct CLCs into single microstructures can provide advanced functionality. In this work, CLC multishells with multiple stopbands are created by liquid-liquid phase separation (LLPS) in a simple yet highly controlled manner. A homogeneous ternary mixture of LC, hydrophilic liquid, and co-solvent is microfluidically emulsified to form uniform oil-in-water drops, which undergo LLPS to form onion-like drops composed of alternating CLC-rich and CLC-depleted layers. The multiplicity is controlled from one to five by adjusting the initial composition of the ternary mixture, which dictates the number of consecutive steps of LLPS. Interestingly, the concentration of the chiral dopant becomes reduced from the outermost to the innermost CLC drop due to uneven partitioning during LLPS, which results in multiple stopbands. Therefore, the photonic multishells show multiple structural colors. In addition, dye-doped multishells provide band-edge lasing at two different wavelengths. This new class of photonic multishells will provide new opportunities for advanced optical applications.},
}
@article {pmid32517030,
year = {2020},
author = {Martoni, F and Taylor, GS and Blacket, MJ},
title = {Illuminating Insights into the Biodiversity of the Australian Psyllids (Hemiptera: Psylloidea) Collected Using Light Trapping.},
journal = {Insects},
volume = {11},
number = {6},
pages = {},
pmid = {32517030},
issn = {2075-4450},
abstract = {The superfamily Psylloidea includes numerous species which play a key role in Australian ecology and biodiversity, as well as pests and biological control agents, and sometimes threatened species of conservation concern. Different psyllid sampling and collection techniques are usually performed depending on the nature and aim of the study: from the beating and sweeping of psyllid host plants for conservation and biodiversity assessment, to suction and sticky traps in agriculture. Due to a general lack of information on its efficacy for psyllids, however, light trapping has not usually been employed. Here we present the results obtained trapping psyllids using different light sources and we discuss the strengths and weaknesses of this technique to assess psyllid biodiversity. In particular, we highlight the strength of using this methodology paired with DNA barcoding, to cast some light on psyllid biodiversity. The results obtained here suggest that the psyllid fauna of Australia is heavily understudied and the number of undescribed species might be many times higher than previously expected. Additionally, we report, for the first time, the species Trioza adventicia Tuthill 1952, and Cryptoneossa triangula Taylor 1990 in the state of Queensland.},
}
@article {pmid32516485,
year = {2020},
author = {Trzebny, A and Slodkowicz-Kowalska, A and Becnel, JJ and Sanscrainte, N and Dabert, M},
title = {A new method of metabarcoding Microsporidia and their hosts reveals high levels of microsporidian infections in mosquitoes (Culicidae).},
journal = {Molecular ecology resources},
volume = {20},
number = {6},
pages = {1486-1504},
pmid = {32516485},
issn = {1755-0998},
support = {//National Research Centre/ ; },
mesh = {Animals ; *Culicidae/microbiology ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal ; *Microsporidia/genetics ; *Microsporidiosis ; Phylogeny ; },
abstract = {DNA metabarcoding offers new perspectives, especially with regard to the high-throughput identification and diagnostics of pathogens. Microsporidia are an example of widely distributed, opportunistic and pathogenic microorganisms in which molecular identification is important for both environmental research and clinical diagnostics. We have developed a method for parallel detection of both microsporidian infection and the host species. We designed new primer sets: one specific for the classical Microsporidia (targeting the hypervariable V5 region of small subunit [ssu] rDNA), and a second one targeting a shortened fragment of the COI gene (standard metazoan DNA-barcode); both markers are well suited for next generation sequencing. Analysis of the ssu rDNA data set representing 607 microsporidian species (120 genera) indicated that the V5 region enables identification of >98% species in the data set (596/607). To test the method, we used microsporidians that infect mosquitoes in natural populations. Using mini-COI data, all field-collected mosquitoes were unambiguously assigned to seven species; among them almost 60% of specimens were positive for at least 11 different microsporidian species, including a new microsporidian ssu rDNA sequence (Microsporidium sp. PL01). Phylogenetic analysis showed that this species belongs to one of the two main clades in the Terresporidia. We found a high rate of microsporidian co-infections (9.4%). The numbers of sequence reads for the operational taxonomic units suggest that the occurrence of Nosema spp. in co-infections could benefit them; however, this observation should be retested using a more intensive host sampling. Our results show that DNA barcoding is a rapid and cost-effective method for deciphering sample diversity in greater resolution, including the hidden biodiversity that may be overlooked using classical methodology.},
}
@article {pmid32513247,
year = {2020},
author = {Ni, Z and Chen, S and Brown, J and Kendziorski, C},
title = {CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data.},
journal = {Genome biology},
volume = {21},
number = {1},
pages = {137},
pmid = {32513247},
issn = {1474-760X},
support = {R01 GM102756/GM/NIGMS NIH HHS/United States ; NIH GM102756/NH/NIH HHS/United States ; },
mesh = {*Cluster Analysis ; *DNA Barcoding, Taxonomic ; Humans ; Sequence Analysis, RNA ; Single-Cell Analysis ; },
abstract = {An important challenge in pre-processing data from droplet-based single-cell RNA sequencing protocols is distinguishing barcodes associated with real cells from those binding background reads. Existing methods test barcodes individually and consequently do not leverage the strong cell-to-cell correlation present in most datasets. To improve cell detection, we introduce CB2, a cluster-based approach for distinguishing real cells from background barcodes. As demonstrated in simulated and case study datasets, CB2 has increased power for identifying real cells which allows for the identification of novel subpopulations and improves the precision of downstream analyses.},
}
@article {pmid32513105,
year = {2020},
author = {Song, F and Li, T and Burgess, KS and Feng, Y and Ge, XJ},
title = {Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China.},
journal = {BMC plant biology},
volume = {20},
number = {1},
pages = {261},
pmid = {32513105},
issn = {1471-2229},
support = {No. 31770227, 31570210//National Natural Science Foundation of China/ ; },
mesh = {China ; DNA Barcoding, Taxonomic/methods ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Phylogeny ; Plastids/*genetics ; Polygonaceae/classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Calligonum (Polygonaceae) is distributed from southern Europe through northern Africa to central Asia, and is typically found in arid, desert regions. Previous studies have revealed that standard DNA barcodes fail to discriminate Calligonum species. In this study, the complete plastid genomes (plastome) for 32 accessions of 21 Calligonum species is sequenced to not only generate the first complete plastome sequence for the genus Calligonum but to also 1) Assess the ability of the complete plastome sequence to discern species within the group, and 2) screen the plastome sequence for a cost-effective DNA barcode that can be used in future studies to resolve taxonomic relationships within the group.<br><br>RESULTS: The whole plastomes of Calligonum species possess a typical quadripartite structure. The size of the Calligonum plastome is approximately 161 kilobase pairs (kbp), and encodes 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Based on ML phylogenetic tree analyses, the complete plastome has higher species identification (78%) than combinations of standard DNA barcodes (rbcL&#x2009;+&#x2009;matK&#x2009;+&#x2009;nrITS, 56%). Five newly screened gene regions (ndhF, trnS-G, trnC-petN, ndhF-rpl32, rpl32-trnL) had high species resolution, where ndhF and trnS-G were able to distinguish the highest proportion of Calligonum species (56%).<br><br>CONCLUSIONS: The entire plastid genome was the most effective barcode for the genus Calligonum, although other gene regions showed great potential as taxon-specific barcodes for species identification in Calligonum.},
}
@article {pmid32510236,
year = {2021},
author = {Fuhrmann, N and Kaiser, TS},
title = {The importance of DNA barcode choice in biogeographic analyses - a case study on marine midges of the genus Clunio.},
journal = {Genome},
volume = {64},
number = {3},
pages = {242-252},
doi = {10.1139/gen-2019-0191},
pmid = {32510236},
issn = {1480-3321},
mesh = {Animals ; Chironomidae/*classification/genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Europe ; Genome, Mitochondrial ; Haplotypes ; Phylogeography ; },
abstract = {DNA barcodes are widely used for species identification and biogeographic studies. Here, we compare the use of full mitochondrial genomes versus DNA barcodes and other mitochondrial DNA fragments for biogeographic and ecological analyses. Our dataset comprised 120 mitochondrial genomes from the genus Clunio (Diptera: Chironomidae), comprising five populations from two closely related species (Clunio marinus and Clunio balticus) and three ecotypes. We extracted cytochrome oxidase c subunit I (COI) barcodes and partitioned the mitochondrial genomes into non-overlapping windows of 750 or 1500 bp. Haplotype networks and diversity indices were compared for these windows and full mitochondrial genomes (15.4 kb). Full mitochondrial genomes indicate complete geographic isolation between populations, but do not allow for conclusions on the separation of ecotypes or species. COI barcodes have comparatively few polymorphisms, ideal for species identification, but do not resolve geographic isolation. Many of the similarly sized 750 bp windows have higher nucleotide and haplotype diversity than COI barcodes, but still do not resolve biogeography. Only when increasing the window size to 1500 bp, two windows resolve biogeography reasonably well. Our results suggest that the design and use of DNA barcodes in biogeographic studies must be carefully evaluated for each investigated species.},
}
@article {pmid32507771,
year = {2020},
author = {Teves, JM and Won, KJ},
title = {Mapping Cellular Coordinates through Advances in Spatial Transcriptomics Technology.},
journal = {Molecules and cells},
volume = {43},
number = {7},
pages = {591-599},
pmid = {32507771},
issn = {0219-1032},
mesh = {*Cell Communication/physiology ; Computational Biology/*methods ; Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing/*methods ; In Situ Hybridization, Fluorescence/*methods ; Single-Cell Analysis/*methods ; Spatial Analysis ; Transcriptome ; },
abstract = {Complex cell-to-cell communication underlies the basic processes essential for homeostasis in the given tissue architecture. Obtaining quantitative gene-expression of cells in their native context has significantly advanced through single-cell RNA sequencing technologies along with mechanical and enzymatic tissue manipulation. This approach, however, is largely reliant on the physical dissociation of individual cells from the tissue, thus, resulting in a library with unaccounted positional information. To overcome this, positional information can be obtained by integrating imaging and positional barcoding. Collectively, spatial transcriptomics strategies provide tissue architecture-dependent as well as position-dependent cellular functions. This review discusses the current technologies for spatial transcriptomics ranging from the methods combining mechanical dissociation and single-cell RNA sequencing to computational spatial re-mapping.},
}
@article {pmid32506392,
year = {2020},
author = {Najafzadeh, MJ and Dolatabadi, S and de Hoog, S and Esfahani, MK and Haghani, I and Aghili, SR and Ghazvini, RD and Rezaei-Matehkolaei, A and Abastabar, M and Al-Hatmi, AMS},
title = {Phylogenetic Analysis of Clinically Relevant Fusarium Species in Iran.},
journal = {Mycopathologia},
volume = {185},
number = {3},
pages = {515-525},
doi = {10.1007/s11046-020-00460-x},
pmid = {32506392},
issn = {1573-0832},
support = {IR.NIMAD.REC.971086//National Institute for Medical Research Development/ ; },
mesh = {Consensus Sequence ; DNA, Fungal/chemistry/isolation &amp; purification ; Fusariosis/*microbiology ; Fusarium/*classification/genetics ; Humans ; Iran ; Keratitis/*microbiology ; Likelihood Functions ; Onychomycosis/*microbiology ; Phylogeny ; },
abstract = {Fungi of the genus Fusarium are well known as major plant pathogens but also cause a broad spectrum of human infections. Sixty-three clinical isolates, collected during 2014-2017, were identified using a part of the TEF1 gene as barcoding marker. Fusarium fujikuroi species complex (FFSC, n = 41, 65%) showed to be the dominant etiological agent, followed by F. solani species complex (FSSC, n = 14, 22%) and F. oxysporum species complex (FOSC, n = 7, 11%). There was one strain belonging to F. lateritium species complex (FLSC, n = 1, 1.5%). For final identification, a phylogenetic tree was constructed including the type strains of each species complex. Most cases of fusariosis were due to nail infection (n = 38, 60.3%), followed by keratitis (n = 22, 34%). Fusarium infections are difficult to be treated due to their intrinsic resistance to different azoles; however, accurate and fast identification of etiological agents may enhance management of the infection. We present the first phylogenetic study on clinical Fusarium spp. from Iran.},
}
@article {pmid32502832,
year = {2020},
author = {Oliveira Carvalho, C and Pires Marceniuk, A and Oliveira, C and Wosiacki, WB},
title = {Integrative taxonomy of the species complex Haemulon steindachneri () (Eupercaria; Haemulidae) with a description of a new species from the western Atlantic.},
journal = {Zoology (Jena, Germany)},
volume = {141},
number = {},
pages = {125782},
doi = {10.1016/j.zool.2020.125782},
pmid = {32502832},
issn = {1873-2720},
mesh = {Animal Distribution ; Animals ; DNA/*genetics ; *DNA Barcoding, Taxonomic ; Fishes/*anatomy &amp; histology/classification/*genetics ; *Phylogeny ; Species Specificity ; },
abstract = {Haemulon steindachneri (Jordan and Gilbert) (Haemulidae), popularly known as "cocoroca-de-boca-larga", "latin-grunt" or "latin-burro", represents a species complex found on the Atlantic western coast and on the Pacific eastern coast, condition confirmed recently by molecular phylogenies. In the present study, DNA barcoding analysis recognizes two distinct clusters; the first includes Brazil and Caribbean, and the second is composed of Pacific specimens, with genetic distance of 7.4%, differentiated by 35 base pairs. In addition to the molecular evidence, our results show morphological differences that distinguish the Atlantic lineage from that of the Pacific: anal fin, usually, with eight rays (vs. generally nine rays in Pacific); 13-15 scales below the lateral line, rarely 12 (vs. 12 scales below the lateral line, rarely 13 in Pacific), posterior margin of the maxilla robust with a slightly angled end (vs. smaller maxilla with moderately convex extremity), and presence of a spot on the pre-operculum, broad and robust, with no definite shape (vs. narrow spot, with anterior extremity tuned and posterior straight, resembling a triangle in Pacific). Therefore, based on both molecular and morphological evidences, H. steindachneri is redescribed for the Pacific coast while a new species is described for the Atlantic coast.},
}
@article {pmid32502367,
year = {2021},
author = {Rewicz, T and Móra, A and Tończyk, G and Szymczak, A and Grabowski, M and Calleja, EJ and Pernecker, B and Csabai, Z},
title = {First records raise questions: DNA barcoding of Odonata in the middle of the Mediterranean.},
journal = {Genome},
volume = {64},
number = {3},
pages = {196-206},
doi = {10.1139/gen-2019-0226},
pmid = {32502367},
issn = {1480-3321},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Genetic Variation ; Malta ; Odonata/*classification/genetics ; Phylogeny ; },
abstract = {We present the results of the first-ever DNA barcoding study of odonates from the Maltese Islands. In total, 10 morphologically identified species were collected during a two-week long expedition in 2018. Eighty cytochrome c oxidase subunit I (COI) barcodes were obtained from the collected specimens. Intra- and interspecific distances ranged from 0.00% to 2.24% and 0.48% to 17.62%, respectively. Successful species identification based on ascribing a single morphological species to a single Barcode Index Number (BIN) was achieved for eight species (80%). In the case of two species, Ischnura genei and Anax parthenope, BINs were shared with other closely related species. The taxonomic status of I. genei is questionable and the phylogenetic relationship between A. imperator/parthenope is not clear. Further studies involving a series of adult specimens collected in a wide spatial range and nuclear markers are necessary to resolve these cases. Therefore, this dataset serves as an initial DNA barcode reference library for Maltese odonates, within a larger project: Aquatic Macroinvertebrates DNA Barcode Library of Malta.},
}
@article {pmid32501553,
year = {2020},
author = {Bañón, R and de Carlos, A and Ruiz-Pico, S and Baldó, F},
title = {Unexpected deep-sea fish species on the Porcupine Bank (NE Atlantic): Biogeographical implications.},
journal = {Journal of fish biology},
volume = {97},
number = {3},
pages = {908-913},
doi = {10.1111/jfb.14418},
pmid = {32501553},
issn = {1095-8649},
support = {//The Spanish Bottom Trawl Survey on the Porcupine Bank (SP-PORC-Q3) was funded in part by the EU through the European Maritime and Fisheries Fund (EMFF) within the Spanish National Program of collection, management and use of data in the fisheries sector and support for scientific advice regarding the Common Fisheries Policy./ ; //European Maritime and Fisheries Fund (EMFF)/ ; },
mesh = {*Animal Distribution ; Animal Migration ; Animals ; Atlantic Ocean ; Azores ; DNA Barcoding, Taxonomic ; Flatfishes/genetics/*physiology ; Gadiformes/genetics/*physiology ; },
abstract = {Four specimens corresponding to three rare deep-water fish species were caught on the Porcupine Bank (Northeast Atlantic) in September 2019. These catches include the new northernmost records of Azores rockling Gaidropsarus granti and deep-water dab Poecilopsetta beanii in the Atlantic Ocean and the second record of the latter species in its eastern zone. Three of the specimens were retained and their molecular identification also allowed the Cataetyx alleni DNA barcode to be obtained for the first time. The appearance of P. beanii, a West Atlantic species, in its eastern zone is discussed in relation to a possible phenomenon of transoceanic drift in the larval stage.},
}
@article {pmid32501542,
year = {2020},
author = {Bonani Mateussi, NT and Melo, BF and Oliveira, C},
title = {Molecular delimitation and taxonomic revision of the wimple piranha Catoprion (Characiformes: Serrasalmidae) with the description of a new species.},
journal = {Journal of fish biology},
volume = {97},
number = {3},
pages = {668-685},
doi = {10.1111/jfb.14417},
pmid = {32501542},
issn = {1095-8649},
support = {//NTBM was funded by Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq; Grant number:164213/2015-5) and Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/Programa de Doutorado Sandu&#xed;che no Exterior (CAPES/PDSE, Grant number: 88881.132950/2016-01); BFM and CO were funded by Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP, Grant numbers: 16/11313-8 and 14/26508-3, respectively)./ ; 164213/2015-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 88881.132950/2016-01//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/Programa de Doutorado Sandu&#xed;che no Exterior/ ; 16/11313-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 14/26508-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
mesh = {Animals ; Characiformes/anatomy &amp; histology/*classification/*genetics ; DNA, Mitochondrial/genetics ; Lateral Line System/anatomy &amp; histology ; Paraguay ; *Phylogeny ; Species Specificity ; },
abstract = {A taxonomic revision of wimple piranhas of the genus Catoprion is performed in combination with a molecular analysis using mtDNA. Molecular phylogenetic analyses of 49 specimens using genetic distances, conventional likelihood and four delimitation methods yielded two distinct lineages of Catoprion, with the morphological analyses of 198 specimens of Catoprion corroborating the molecular results. We provide a redescription of Catoprion mento, from the Paraguay, Orinoco, and tributaries of western Amazon basin, keeping Mylesinus macropterus as a junior synonym of C. mento, and the description of Catoprion absconditus n. sp., from the Amazon and Essequibo basins. C. absconditus n. sp. differs from C. mento by the presence of 86-94 perforated scales in the lateral line (vs. 65-86 scales) and the presence of 35-40 circumpeduncular scales (vs. 29-34 scales). The distribution of C. mento follows the Amazonas-Paraguay-Orinoco lowlands, whereas C. absconditus follows the eastern Amazon biogeographic pattern.},
}
@article {pmid32500776,
year = {2020},
author = {Servis, JA and Reid, BN and Timmers, MA and Stergioula, V and Naro-Maciel, E},
title = {Characterizing coral reef biodiversity: genetic species delimitation in brachyuran crabs of Palmyra Atoll, Central Pacific.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {31},
number = {5},
pages = {178-189},
doi = {10.1080/24701394.2020.1769087},
pmid = {32500776},
issn = {2470-1408},
mesh = {Animals ; Biodiversity ; Brachyura/*classification/genetics ; Coral Reefs ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Pacific Ocean ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
abstract = {Coral reefs are highly threatened ecosystems, yet there are numerous challenges in conducting inventories of their vanishing biodiversity, partly because many taxa remain difficult to detect and describe. Genetic species delimitation methods provide a standardized means for taxonomic classification including of cryptic, rare, or elusive groups, but results can vary by analytical method and genetic marker. In this study, a combination of morphological and genetic identification methods was used to estimate species richness and identify taxonomic units in true crabs (Infraorder Brachyura; n = 200) from coral reefs of Palmyra Atoll, Central Pacific. Genetic identification was based on matches between mitochondrial 16S ribosomal RNA (16S rRNA) and/or cytochrome c oxidase subunit I (COI) sequences to GenBank data, while morphological work relied on the taxonomic literature. Broad agreement in the number of candidate species delimited by genetic distance thresholds and tree-based approaches was found, although the multi-rate Poisson tree process (mPTP) was less appropriate for this dataset. The COI sequence data identified 30-32 provisional species and the 16S data revealed 34-35. The occurrence of 10 families, 20 genera, and 19 species of brachyurans at Palmyra was corroborated by at least two methods. Diversity levels within Chlorodiella laevissima indicated possible undescribed or cryptic species in currently lumped taxa. These results illustrate the efficacy of DNA sequences in identifying organisms and detecting cryptic variation, and underscore the importance of using appropriate genetic markers and multiple species delimitation analyses, with applications for future species descriptions.},
}
@article {pmid32497831,
year = {2020},
author = {Parks, KS and Janzen, DH and Hallwachs, W and Fernández-Triana, J and Dyer, LA and Rodriguez, JJ and Arias-Penna, DC and Whitfield, JB},
title = {A five-gene molecular phylogeny reveals Parapanteles Ashmead (Hymenoptera: Braconidae) to be polyphyletic as currently composed.},
journal = {Molecular phylogenetics and evolution},
volume = {150},
number = {},
pages = {106859},
doi = {10.1016/j.ympev.2020.106859},
pmid = {32497831},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Electron Transport Complex IV/classification/genetics ; Hymenoptera/*classification/genetics ; Insect Proteins/classification/genetics ; NADH Dehydrogenase/classification/genetics ; Phylogeny ; RNA, Ribosomal, 28S/classification/genetics ; },
abstract = {Parapanteles Ashmead (Braconidae: Microgastrinae) is a medium-sized genus of microgastrine wasps that was erected over a century ago and lacks a unique synapomorphic character, and its monophyly has not been tested by any means. Parapanteles usually are parasitoids of large, unconcealed caterpillars (macrolepidoptera) and have been reared from an unusually large diversity of hosts for a relatively small microgastrine genus. We used Cytochrome Oxidase I sequences ("DNA barcodes") available for Parapanteles and other microgastrines to sample the generic diversity of described and undescribed species currently placed in Parapanteles, and then sequenced four additional genes for this subsample (wingless, elongation factor 1-alpha, ribosomal subunit 28s, and NADH dehydrogenase subunit 1). We constructed individual gene trees and concatenated Bayesian and maximum-likelihood phylogenies for this 5-gene subsample. In these phylogenies, most Parapanteles species formed a monophyletic clade within another genus, Dolichogenidea, while the remaining Parapanteles species were recovered polyphyletically within several other genera. The latter likely represent misidentified members of other morphologically similar genera. Species in the monophyletic clade containing most Parapanteles parasitized caterpillars from only five families - Erebidae (Arctiinae), Geometridae, Saturniidae, Notodontidae, and Crambidae. We do not make any formal taxonomic decisions here because we were not able to include representatives of type species for Parapanteles or other relevant genera, and because we feel such decisions should be reserved until a comprehensive morphological analysis of the boundaries of these genera is accomplished.},
}
@article {pmid32497542,
year = {2020},
author = {Changbunjong, T and Weluwanarak, T and Sedwisai, P and Ruangsittichai, J and Duvallet, G and Chareonviriyaphap, T},
title = {New records and DNA barcoding of deer flies, Chrysops (Diptera: Tabanidae) in Thailand.},
journal = {Acta tropica},
volume = {210},
number = {},
pages = {105532},
doi = {10.1016/j.actatropica.2020.105532},
pmid = {32497542},
issn = {1873-6254},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Diptera/*classification ; Electron Transport Complex IV/genetics ; Entomology ; Mitochondria/genetics ; Thailand ; },
abstract = {Chrysops spp. or deer flies (Diptera: Tabanidae) are hematophagous flies of medical and veterinary importance and some species are important vectors of Trypanosoma evansi, the causative agent of surra in Thailand. However, data regarding deer fly species and their molecular identification are limited. Accurate species identification will indicate the appropriate control measures. In this study, an entomological survey of deer flies from different sites in Thailand between May 2018 and June 2019 were conducted. In addition, mitochondrial cytochrome oxidase subunit I (COI) barcoding region was used for species identification. A total of 82 females were collected and 6 species were identified. Of these, three species are new records for Thailand: C. designatus, C. fuscomarginalis and C. vanderwulpi bringing the species total found in Thailand to nine. The COI sequences revealed an intraspecific divergence of 0.0%-2.65% and an interspecific divergence of 7.03%-13.47%. Phylogenetic analysis showed that all deer fly species were clearly separated into distinct clusters according to morphologically identified species. These results indicated that COI barcodes were capable in discriminating between deer fly species on the basis of the barcoding gap and phylogenetic analysis. Therefore, DNA barcoding is a valuable tool for species identification of deer flies in Thailand.},
}
@article {pmid32497482,
year = {2020},
author = {Hernández-Guevara, LF and Sánchez-Rámos, FJ and Chan-Chable, RJ and Hernández-Triana, LM and Valdés-Perezgasga, MT and González-Acosta, C and Correa-Morales, F},
title = {First Record of Mansonia dyari in the State of Morelos, Mexico, Based on Morphology and COI DNA Barcoding.},
journal = {Journal of the American Mosquito Control Association},
volume = {36},
number = {1},
pages = {33-36},
doi = {10.2987/19-6909.1},
pmid = {32497482},
issn = {1943-6270},
mesh = {*Animal Distribution ; Animals ; Culicidae/*anatomy &amp; histology/enzymology/*genetics ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/analysis ; Female ; Insect Proteins/analysis ; Male ; Mexico ; },
abstract = {Collections of mosquitoes were conducted for the surveillance of species of medical importance in the state of Morelos, Mexico, in June 2017. Species collected included Mansonia (Mansonia) dyari, which was identified using morphological characters and cytochrome c oxidase I DNA barcoding. Although 3 species of genus Mansonia have been previously reported in Mexico, this is the 1st confirmed record of Ma. dyari in Morelos State, where no Mansonia species had been recorded. Historical records of Ma. dyari and Ma. indubitans in Mexico were reviewed. Therefore, this record increases the number of mosquito species occurring in Morelos to 46. The specimens collected in this study were deposited in the Culicidae collection of the Universidad Autónoma Agraria Antonio Narro, Unidad Laguna.},
}
@article {pmid32497465,
year = {2020},
author = {Hughes, KW and Matheny, PB and Miller, AN and Petersen, RH and Iturriaga, TM and Johnson, KD and Methven, AS and Raudabaugh, DB and Swenie, RA and Bruns, TD},
title = {Pyrophilous fungi detected after wildfires in the Great Smoky Mountains National Park expand known species ranges and biodiversity estimates.},
journal = {Mycologia},
volume = {112},
number = {4},
pages = {677-698},
doi = {10.1080/00275514.2020.1740381},
pmid = {32497465},
issn = {1557-2536},
mesh = {*Biodiversity ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; Fruiting Bodies, Fungal/classification/genetics/growth &amp; development ; Fungi/classification/genetics/*growth &amp; development ; *Parks, Recreational ; Phylogeny ; Pinus/microbiology ; United States ; *Wildfires ; },
abstract = {Following a late fall wildfire in 2016 in the Great Smoky Mountains National Park, pyrophilous fungi in burn zones were documented over a 2-y period with respect to burn severity and phenology. Nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) barcodes were obtained to confirm morphological evaluations. Forty-one taxa of Ascomycota and Basidiomycota were identified from burn sites and categorized as fruiting only in response to fire or fruiting enhanced by fire. Twenty-two species of Pezizales (Ascomycota) were among the earliest to form ascomata in severe burn zones, only one of which had previously been documented in the Great Smoky Mountains National Park. Nineteen species of Basidiomycota, primarily Agaricales, were also documented. Among these, only five species (Coprinellus angulatus, Gymnopilus decipiens, Lyophyllum anthracophilum, Pholiota carbonicola, and Psathyrella pennata) were considered to be obligate pyrophilous taxa, but fruiting of two additional taxa (Hygrocybe conica and Mycena galericulata) was clearly enhanced by fire. Laccaria trichodermophora was an early colonizer of severe burn sites and persisted through the winter of 2017 and into spring and summer of 2018, often appearing in close association with Pinus pungens seedlings. Fruiting of pyrophilous fungi peaked 4-6 mo post fire then diminished, but some continued to fruit up to 2.5 y after the fire. In all, a total of 27 previously unrecorded taxa were added to the All Taxa Biodiversity Inventory (ATBI) database (~0.9%). Most pyrophilous fungi identified in this study are either cosmopolitan or have a Northern Hemisphere distribution, but cryptic endemic lineages were detected in Anthracobia and Sphaerosporella. One new combination, Hygrocybe spadicea var. spadicea f. odora, is proposed.},
}
@article {pmid32497352,
year = {2020},
author = {Speare, L and Davies, SW and Balmonte, JP and Baumann, J and Castillo, KD},
title = {Patterns of environmental variability influence coral-associated bacterial and algal communities on the Mesoamerican Barrier Reef.},
journal = {Molecular ecology},
volume = {29},
number = {13},
pages = {2334-2348},
doi = {10.1111/mec.15497},
pmid = {32497352},
issn = {1365-294X},
mesh = {Animals ; Anthozoa/*microbiology ; *Bacteria/classification ; Belize ; Coral Reefs ; *Dinoflagellida/classification ; *Microbiota ; },
abstract = {A coral's capacity to alter its microbial symbionts may enhance its fitness in the face of climate change. Recent work predicts exposure to high environmental variability may increase coral resilience and adaptability to future climate conditions. However, how this heightened environmental variability impacts coral-associated microbial communities remains largely unexplored. Here, we examined the bacterial and algal symbionts associated with two coral species of the genus Siderastrea with distinct life history strategies from three reef sites on the Belize Mesoamerican Barrier Reef System with low or high environmental variability. Our results reveal bacterial community structure, as well as alpha- and beta-diversity patterns, vary by host species. Differences in bacterial communities between host species were partially explained by high abundance of Deltaproteobacteria and Rhodospirillales and high bacterial diversity in Siderastrea radians. Our findings also suggest Siderastrea spp. have dynamic core bacterial communities that likely drive differences observed in the entire bacterial community, which may play a critical role in rapid acclimatization to environmental change. Unlike the bacterial community, Symbiodiniaceae composition was only distinct between host species at high thermal variability sites, suggesting that different factors shape bacterial versus algal communities within the coral holobiont. Our findings shed light on how domain-specific shifts in dynamic microbiomes may allow for unique methods of enhanced host fitness.},
}
@article {pmid32497198,
year = {2021},
author = {Princepe, D and De Aguiar, MAM},
title = {Modeling Mito-nuclear Compatibility and Its Role in Species Identification.},
journal = {Systematic biology},
volume = {70},
number = {1},
pages = {133-144},
doi = {10.1093/sysbio/syaa044},
pmid = {32497198},
issn = {1076-836X},
mesh = {Cell Nucleus/genetics ; *DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; Geography ; Phylogeny ; },
abstract = {Mitochondrial genetic material (mtDNA) is widely used for phylogenetic reconstruction and as a barcode for species identification. The utility of mtDNA in these contexts derives from its particular molecular properties, including its high evolutionary rate, uniparental inheritance, and small size. But mtDNA may also play a fundamental role in speciation-as suggested by recent observations of coevolution with the nuclear DNA, along with the fact that respiration depends on coordination of genes from both sources. Here, we study how mito-nuclear interactions affect the accuracy of species identification by mtDNA, as well as the speciation process itself. We simulate the evolution of a population of individuals who carry a recombining nuclear genome and a mitochondrial genome inherited maternally. We compare a null model fitness landscape that lacks any mito-nuclear interaction against a scenario in which interactions influence fitness. Fitness is assigned to individuals according to their mito-nuclear compatibility, which drives the coevolution of the nuclear and mitochondrial genomes. Depending on the model parameters, the population breaks into distinct species and the model output then allows us to analyze the accuracy of mtDNA barcode for species identification. Remarkably, we find that species identification by mtDNA is equally accurate in the presence or absence of mito-nuclear coupling and that the success of the DNA barcode derives mainly from population geographical isolation during speciation. Nevertheless, selection imposed by mito-nuclear compatibility influences the diversification process and leaves signatures in the genetic content and spatial distribution of the populations, in three ways. First, speciation is delayed and the resulting phylogenetic trees are more balanced. Second, clades in the resulting phylogenetic tree correlate more strongly with the spatial distribution of species and clusters of more similar mtDNA's. Third, there is a substantial increase in the intraspecies mtDNA similarity, decreasing the number of alleles substitutions per locus and promoting the conservation of genetic information. We compare the evolutionary patterns observed in our model to empirical data from copepods (Tigriopus californicus). We find good qualitative agreement in the geographic patterns and the topology of the phylogenetic tree, provided the model includes selection based on mito-nuclear interactions. These results highlight the role of mito-nuclear compatibility in the speciation process and its reconstruction from genetic data.[Mito-nuclear coevolution; mtDNA barcode; parapatry; phylogeny.].},
}
@article {pmid32496601,
year = {2020},
author = {Hughes, KW and Case, A and Matheny, PB and Kivlin, S and Petersen, RH and Miller, AN and Iturriaga, T},
title = {Secret lifestyles of pyrophilous fungi in the genus Sphaerosporella.},
journal = {American journal of botany},
volume = {107},
number = {6},
pages = {876-885},
pmid = {32496601},
issn = {1537-2197},
mesh = {Fungi ; Life Style ; *Mycorrhizae ; *Pinus ; Plant Roots ; Seedlings ; },
abstract = {PREMISE: Pyrophilous fungi form aboveground fruiting structures (ascocarps) following wildfires, but their ecology, natural history, and life cycles in the absence of wildfires are largely unknown. Sphaerosporella is considered to be pyrophilous. This study explores Sphaerosporella ascocarp appearance following a rare 2016 wildfire in the Great Smoky Mountains National Park (GSMNP), compares the timing of ascocarp formation with recovery of Sphaerosporella DNA sequences in soils, and explores the association of Sphaerosporella with post-fire Table Mountain pine (Pinus pungens) seedlings.<br><br>METHODS: Burned sites in the GSMNP were surveyed for pyrophilous fungal ascocarps over 2 years. Ascocarps, mycorrhizae, and endophyte cultures were evaluated morphologically and by Sanger sequencing of the nuclear ribosomal ITS gene region (fungal barcode; Schoch et al., 2012). DNA from soil cores was subjected to Illumina sequencing.<br><br>RESULTS: The timing and location of post-fire Sphaerosporella ascocarp formation was correlated with recovery of Sphaerosporella DNA sequences in soils. Genetic markers (fungal barcode) of Sphaerosporella were also recovered from mycorrhizal root tips and endophyte cultures from seedlings of Pinus pungens.<br><br>CONCLUSIONS: This study demonstrates that Sphaerosporella species, in the absence of fire, are biotrophic, forming both mycorrhizal and endophytic associations with developing Pinus pungens seedlings and may persist in nature in the absence of wildfire as a conifer symbiont. We speculate that Sphaerosporella may fruit only after the host plant is damaged or destroyed and that after wildfires, deep roots, needle endophytes, or heat-resistant spores could serve as a source of soil mycelium.},
}
@article {pmid32490083,
year = {2020},
author = {Massaccesi, L and Rondoni, G and Tosti, G and Conti, E and Guiducci, M and Agnelli, A},
title = {Data on soil physicochemical properties and biodiversity from conventional, organic and organic mulch-based cropping systems.},
journal = {Data in brief},
volume = {31},
number = {},
pages = {105718},
pmid = {32490083},
issn = {2352-3409},
abstract = {The data presented here are related to the article entitled "Soil functions are affected by transition from conventional to organic mulch-based cropping system"[1]. Data were collected in 2016 in a processing tomato field located near Perugia, Italy. In details, data were collected in three differently managed processing tomato cropping systems: conventional integrated (INT); traditional organic with cover crops and conventional tillage (ORG); and organic coupled with conservation agriculture, with mulch-based cover crop and no-tillage (ORG+). We report data on the impact of each cropping system on crop biomass and yield, soil physicochemical properties, size and structure of soil microbial community, soil invertebrate biodiversity and habitat provision (predator-prey trophic interactions).},
}
@article {pmid32489032,
year = {2020},
author = {Liu, SS and Wei, SH and Zhu, JJ and Zhang, WW and Jiao, S and Guo, J and Yan, LH and Wang, ZM},
title = {[Herbal textural research, morphologic characteristics and DNA barcoding of botanical origins of Alismatis Rhizoma].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {45},
number = {7},
pages = {1536-1544},
doi = {10.19540/j.cnki.cjcmm.20200318.201},
pmid = {32489032},
issn = {1001-5302},
mesh = {*Alisma ; China ; DNA Barcoding, Taxonomic ; *Drugs, Chinese Herbal ; Medicine, Chinese Traditional ; *Rhizome ; },
abstract = {Alismatis Rhizoma(Zexie) is a commonly used traditional Chinese medicine, and it is separated into "Chuan Zexie"(Sichuan and Hubei provinces), "Jian Zexie"(Fujian and Jiangxi provinces) and "Guang Zexie"(Guangxi province) according to different producing areas. Alisma plantago-aquatica and A. orientale were listed as the original plants of Alismatis Rhizoma in different editions of Chinese Pharmacopoeia(Ch.P), respectively. The botanical origins of Alismatis Rhizoma caused much controversy during a period of time. This study aimed to define the botanical origins of Alismatis Rhizoma from different producing areas, and supply scientific evidence for Ch. P 2020 edition. In this paper, we summarized the descriptions of original plants and producing areas of Alismatis Rhizoma in ancient literatures. Flowers and fruits of original plants of Alismatis Rhizoma were collected from different typical areas, and compared with the morphological description of two species from Alisma genus in the Flora of China. Thirty-nine batches of leaves from 8 different areas were identified using DNA barcoding technology. The results showed that original plants of Alismatis Rhizoma from different areas could be distinguished from each other based on morphological characteristics and molecular characteristics. Then, "Jian Zexie" was identified as A. orientale, while "Chuan Zexie" and "Guang Zexie" were identified as A. plantago-aquatica. In conclusion, combining with herbal textural research, morphologic characteristics, DNA barcoding technology and market situation, this paper recommended that the botanical sources of Alismatis Rhizoma could be revised as Alisma orientale(Sam.) Juzep. and Alisma plantago-aquatica Linn. in the Ch. P 2020 edition.},
}
@article {pmid32483972,
year = {2020},
author = {Zhou, Y and Zhao, G and Bian, J and Tian, X and Cheng, X and Wang, H and Chen, H},
title = {Multiplexed SERS Barcodes for Anti-Counterfeiting.},
journal = {ACS applied materials &amp; interfaces},
volume = {12},
number = {25},
pages = {28532-28538},
doi = {10.1021/acsami.0c06272},
pmid = {32483972},
issn = {1944-8252},
abstract = {Forged signature threatens the authenticity of personal identity. Here, an effective SERS anti-counterfeiting system is designed for personal signatures. Mixed ligands improve the complexity of Raman spectra and expand the coding capacity. Fourteen distinct combinations are created from mere five ligands, and great expansion is possible with modest expansion of the ligand library. On the other hand, the (Au-aggregate)@Ag@PSPAA nanostructure significantly increases the surface-enhanced Raman scattering (SERS) intensity and stability so that excellent performance is achieved in SERS detection. By integrating these strategies, SERS inks are produced and applied in signature anti-counterfeiting. The resulting spectra are converted to barcodes that are readily detected through a smart phone APP. With these improvements, this work brings SERS one step closer toward practical applications in signature anti-counterfeiting.},
}
@article {pmid32479629,
year = {2020},
author = {Becker, M and Noll-Puchta, H and Amend, D and Nolte, F and Fuchs, C and Jeremias, I and Braun, CJ},
title = {CLUE: a bioinformatic and wet-lab pipeline for multiplexed cloning of custom sgRNA libraries.},
journal = {Nucleic acids research},
volume = {48},
number = {13},
pages = {e78},
pmid = {32479629},
issn = {1362-4962},
support = {681524/ERC_/European Research Council/International ; },
mesh = {Animals ; CRISPR-Cas Systems/genetics ; *Cloning, Molecular ; *Gene Library ; Genome ; Humans ; Mice ; Oligonucleotides/genetics ; RNA, Guide, CRISPR-Cas Systems/*genetics ; },
abstract = {The systematic perturbation of genomes using CRISPR/Cas9 deciphers gene function at an unprecedented rate, depth and ease. Commercially available sgRNA libraries typically contain tens of thousands of pre-defined constructs, resulting in a complexity challenging to handle. In contrast, custom sgRNA libraries comprise gene sets of self-defined content and size, facilitating experiments under complex conditions such as in vivo systems. To streamline and upscale cloning of custom libraries, we present CLUE, a bioinformatic and wet-lab pipeline for the multiplexed generation of pooled sgRNA libraries. CLUE starts from lists of genes or pasted sequences provided by the user and designs a single synthetic oligonucleotide pool containing various libraries. At the core of the approach, a barcoding strategy for unique primer binding sites allows amplifying different user-defined libraries from one single oligonucleotide pool. We prove the approach to be straightforward, versatile and specific, yielding uniform sgRNA distributions in all resulting libraries, virtually devoid of cross-contaminations. For in silico library multiplexing and design, we established an easy-to-use online platform at www.crispr-clue.de. All in all, CLUE represents a resource-saving approach to produce numerous high quality custom sgRNA libraries in parallel, which will foster their broad use across molecular biosciences.},
}
@article {pmid32474999,
year = {2020},
author = {Pan, Y and Sun, Y and Wang, Y and Zhang, Z},
title = {Barcode sequence could be a good target for developing a species-specific anti-parasite agent based on CRISPR-Cas9.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {34},
number = {7},
pages = {9393-9404},
doi = {10.1096/fj.202000118RR},
pmid = {32474999},
issn = {1530-6860},
mesh = {Animals ; *CRISPR-Cas Systems ; Ciliophora/*genetics/growth &amp; development/metabolism ; Ciliophora Infections/parasitology/*veterinary ; Fish Diseases/*parasitology ; *Gene Editing ; Protozoan Proteins/*genetics ; RNA, Guide, CRISPR-Cas Systems/*genetics ; },
abstract = {Parasitic infections are a severe issue in many regions of the world. We assume that if a chemical can destroy a DNA barcode sequence, then this chemical could be developed as a species-specific parasiticidal agent. To test this hypothesis, we designed sgRNAs that target the sequences of both a DNA barcode (ITS-2) and a control (5.8S rDNA) in Cryptocaryon irritans. In in vivo tests, we found that exposure to Cas9 mRNA mixed with sgRNAs was able to significantly reduce the hatching rate of tomont and the survival rate of theront. Quantitative Real-time PCR demonstrated that the DNAs of tomont and theront exposed to sgRNAs and Cas9 mRNA were significantly disrupted, no matter whether they were exposed to a single sgRNA or a mixture of two sgRNAs. DNA sequencing also suggested the test group that was exposed to a single sgRNA mixed with Cas9-induced mutation at sgRNA targeted fragments and the test group exposed to two sgRNAs combined with Cas9-induced deletion of large pieces. The findings and principles provided by this study contribute to the development of novel nucleic acid therapeutic drugs for cryptocaryoniasis and other parasitic diseases and provide insight into the development of species-specific parasiticidal agents.},
}
@article {pmid32473569,
year = {2020},
author = {Yoshinami, T and Kagara, N and Motooka, D and Nakamura, S and Miyake, T and Tanei, T and Naoi, Y and Shimoda, M and Shimazu, K and Kim, SJ and Noguchi, S},
title = {Detection of ctDNA with Personalized Molecular Barcode NGS and Its Clinical Significance in Patients with Early Breast Cancer.},
journal = {Translational oncology},
volume = {13},
number = {8},
pages = {100787},
pmid = {32473569},
issn = {1936-5233},
abstract = {We attempted to detect circulating tumor DNA (ctDNA), taking advantage of molecular barcode next-generation sequencing (MB-NGS), which can be more easily customized to detect a variety of mutations with a high sensitivity than PCR-based methods. Sequencing with a gene panel consisting of the 13 most frequently mutated genes in breast tumors from stage I or II patients revealed 95 somatic mutations in the 12 genes in 62% (62/100) of tumors. Then, plasma DNA from each patient (n = 62) before surgery was analyzed via MB-NGS customized to each somatic mutation, resulting in the detection of ctDNA in 16.1% (10/62) of patients. ctDNA was significantly associated with biologically aggressive phenotypes, including large tumor size (P = .004), positive lymph node (P = .009), high histological grade (P < .001), negative ER (P = .018), negative PR (P = .017), and positive HER2 (P = .046). Furthermore, distant disease-free survival was significantly worse in patients with ctDNA (n = 10) than those without ctDNA (n = 52) (P < .001). Our results demonstrate that MB-NGS personalized to each mutation can detect ctDNA with a high sensitivity in early breast cancer patients at diagnosis, and it seems to have a potential to serve as a clinically useful tumor marker for predicting their prognosis.},
}
@article {pmid32473295,
year = {2020},
author = {Toran, PT and Wohlfahrt, M and Foye, J and Kiem, HP and Wojchowski, DM},
title = {Assessment and streamlined preparation of low-cytotoxicity lentiviral vectors for mobilized human hematopoietic stem cell transduction.},
journal = {Experimental hematology},
volume = {86},
number = {},
pages = {28-42.e3},
pmid = {32473295},
issn = {1873-2399},
support = {P30 GM106391/GM/NIGMS NIH HHS/United States ; R01 HL044491/HL/NHLBI NIH HHS/United States ; P20 GM113131/GM/NIGMS NIH HHS/United States ; R01 DK089439/DK/NIDDK NIH HHS/United States ; P30 GM103392/GM/NIGMS NIH HHS/United States ; U54 DK106829/DK/NIDDK NIH HHS/United States ; },
mesh = {Cell Line ; *Erythropoietin/biosynthesis/genetics ; *Genetic Vectors ; *Hematopoietic Stem Cell Mobilization ; Humans ; *Lentivirus ; Peripheral Blood Stem Cells/cytology/*metabolism ; *Transduction, Genetic ; },
abstract = {As important vectors for ectopic protein expression, gene silencing, and progenitor cell barcoding, lentiviruses continue to emerge as versatile research and clinical tools. For studies employing cell types that are relatively resistant to transduction, high-titer lentivirus preparations with low cytotoxicity are required. During lentivirus production, carryover plasmid DNA endotoxins, transfection reagents, damaged packaging cells, and virus concentration procedures are potential sources of cytotoxicity. As an often unevaluated property of lentivirus preparations, cytotoxicity can unwittingly skew estimates of functional titers and complicate interpretations of transduced cell phenotypes. By employing hematopoietic UT7epo cells cultured in erythropoietin (EPO) below maximal dosing, we first define a sensitive flow cytometric bioassay for critically assessing the cytotoxicity (and titers) of lentivirus preparations. Bioassay of custom preparations of research-grade lentiviruses from six commercial sources unexpectedly revealed substantial cytotoxicity (with certain preparations additionally registering titers several log below designated values). To overcome such limiting properties, we further report on unique, efficient workflows for reproducibly preparing and processing high-titer, low-cytotoxicity (HTLC) lentiviruses at research scale. These HTLC lentiviruses reliably transduce peripheral blood hematopoietic stem/progenitor cells (PB-HSPCs) at frequencies ≥40%, with low cytotoxicity. In addition, by employing cyclosporin H (to inhibit IFITM3), PB-HSPCs can be transduced at heightened efficiency with nominal cytotoxicity. Overall, this work provides straightforward approaches to (1) critical assessment of the cytotoxicity of lentivirus preparations; (2) reproducible generation (and concentration) of high-quality lentiviruses via a streamlined workflow; and (3) transduction of PB-HSPCs at benchmark levels with nominal cytotoxicity.},
}
@article {pmid32472382,
year = {2020},
author = {Locke, SA and Drago, FB and Núñez, V and Souza, GTRE and Takemoto, RM},
title = {Phylogenetic position of Diplostomum spp. from New World herons based on complete mitogenomes, rDNA operons, and DNA barcodes, including a new species with partially elucidated life cycle.},
journal = {Parasitology research},
volume = {119},
number = {7},
pages = {2129-2137},
doi = {10.1007/s00436-020-06713-4},
pmid = {32472382},
issn = {1432-1955},
support = {2016-00080//Puerto Rico Science, Technology and Research Trust/ ; 1845021//National Science Foundation/ ; 597/16//Comisi&#xf3;n de Investigaciones Cient&#xed;ficas de la provincial de Buenos Aires/ ; 11/N896//Universidad de la Plata/ ; 13741-12-8//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 480180/2011-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Animals ; Birds/*parasitology ; Catfishes/parasitology ; DNA Barcoding, Taxonomic ; DNA, Ribosomal/genetics ; Genome, Mitochondrial/genetics ; *Life Cycle Stages ; Metacercariae/classification/genetics ; *Phylogeny ; Puerto Rico ; Trematoda/anatomy &amp; histology/*classification/genetics/*growth &amp; development ; },
abstract = {Diplostomum ardeae Dubois, 1969 has seldom been reported since its description from the great blue heron (Ardea herodias L., 1758) in the USA. Sequences obtained in this study from the barcode region of cytochrome c oxidase 1 (CO1) in diplostomids from black-crowned night heron (Nycticorax nycticorax (L., 1758)) in Puerto Rico matched data from D. ardeae from A. herodias in the type region. We also obtained DNA barcodes from morphologically similar diplostomids from a rufescent tiger heron (Tigrisoma lineatum (Boddaert, 1783)) and from metacercariae from eye lenses of Trachelyopterus galeatus (Linnaeus, 1766) from the Paraná River basin in Argentina and Brazil, respectively. Barcodes matched (97-100% identity) in these South American adult and larval specimens as well as in recently published sequences from metacercariae from 11 other siluriform fishes from the same region. Barcodes from the South American species, which we describe as Diplostomum lunaschiae n. sp., differed from those of D. ardeae by 7.2-9.8%, and the new species differs from D. ardeae in its size, pharynx:oral sucker length ratio, egg:body length ratio, and distribution of vitellaria. As in prior phylogenetic analysis of CO1 sequences, both D. ardeae and D. lunaschiae n. sp. were not associated with Diplostomum. In more character-rich analyses of nuclear rDNA and of mitochondrial genomes, D. ardeae was an early divergent member of clades of species of Diplostomum. Consequently, we continue to consider D. ardeae and D. lunaschiae n. sp. members of Diplostomum, in contrast to recent suggestions that these species may belong to a different genus.},
}
@article {pmid32471310,
year = {2020},
author = {Pallavicini, P and De Vita, L and Merlin, F and Milanese, C and Borzenkov, M and Taglietti, A and Chirico, G},
title = {Suitable Polymeric Coatings to Avoid Localized Surface Plasmon Resonance Hybridization in Printed Patterns of Photothermally Responsive Gold Nanoinks.},
journal = {Molecules (Basel, Switzerland)},
volume = {25},
number = {11},
pages = {},
pmid = {32471310},
issn = {1420-3049},
support = {BSR1774514//Universit&#xe0; degli Studi di Pavia/ ; },
mesh = {Gold/*chemistry ; Metal Nanoparticles/*chemistry ; Polymers/*chemistry ; Surface Plasmon Resonance ; },
abstract = {When using gold nanoparticle (AuNP) inks for writing photothermal readable secure information, it is of utmost importance to obtain a sharp and stable shape of the localized surface plasmon resonance (LSPR) absorption bands in the prints. The T increase at a given irradiation wavelength (DTl) is the retrieved information when printed patterns are interrogated with a laser source. As DTl is proportional to the absorbance at the wavelength l, any enlargement or change of the absorbance peak shape in a printed pattern would lead to wrong or unreliable reading. With the aim of preparing AuNP inks suitable for inkjet printing of patterns with stable and reliable photothermal reading, we prepared liquid solutions of spherical AuNP coated with a series of different polymers and with or without additional dispersant. The optical stability of the inks and of the printed patterns were checked by monitoring the shape changes of the sharp LSPR absorption band of AuNP in the visible (lmax 519 nm) along weeks of ageing. AuNP coated with neutral polyethylenglycol thiols (HS-PEG) of mw 2000-20,000 showed a strong tendency to rapidly agglomerate in the dry prints. The close contact between agglomerated AuNP resulted in the loss of the pristine shape of the LSPR band, that flattened and enlarged with the further appearance of a second maximum in the Near IR, due to plasmon hybridization. The tendency to agglomerate was found directly proportional to the PEG mw. Addition of the ethylcellulose (EC) dispersant to inks resulted in an even stronger and faster tendency to LSPR peak shape deformation in the prints due to EC hydrophobicity, that induced AuNP segregation and promoted agglomeration. The introduction of a charge on the AuNP coating revelead to be the correct way to avoid agglomeration and obtain printed patterns with a sharp LSPR absorption band, stable with ageing. While the use of a simple PEG thiol with a terminal negative charge, HS-PEGCOO(-) (mw 3000), was not sufficient, overcoating with the positively charged polyallylamine hydrochloride (PAH) and further overcoating with the negatively charged polystyrene sulfonate (PSS) yielded AuNP@HS-PEGCOO(-)/PAH(+) and AuNP@HS-PEGCOO(-)/PAH(+)/PSS(-), both giving stable prints. With these inks we have shown that it is possible to write photothermally readable secure information. In particular, the generation of reliable three-wavelength photothemal barcodes has been demonstrated.},
}
@article {pmid32468625,
year = {2020},
author = {Lagiotis, G and Stavridou, E and Bosmali, I and Osathanunkul, M and Haider, N and Madesis, P},
title = {Detection and quantification of cashew in commercial tea products using High Resolution Melting (HRM) analysis.},
journal = {Journal of food science},
volume = {85},
number = {6},
pages = {1629-1634},
doi = {10.1111/1750-3841.15138},
pmid = {32468625},
issn = {1750-3841},
support = {02/2019//Chiang Mai University/ ; },
mesh = {Anacardium/chemistry/*genetics ; Camellia sinensis/chemistry/*genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Plant/chemistry/genetics ; Food Contamination/*analysis/economics ; Genetic Markers ; Tea/*chemistry/economics ; Transition Temperature ; },
abstract = {Tea, a popular aromatic infusion and food supplement, prepared from Camellia sinensis (L.) Kuntze leaves, is often subjected to adulteration with various undeclared inorganic and plant-derived materials. Cashew (Anacardium occidentale L.) nut husk is one of the most common plant tea adulterants. To date, there are limited DNA-based technologies for tea authentication and quantitative detection of adulterants. Herein, we used a universal plant DNA barcoding marker coupled with High Resolution Melting (Bar-HRM) analysis to authenticate tea products from cashew ground nut. Additionally, cashew-specific markers coupled with HRM technology were used to detect and quantify adulteration of tea with cashew DNA. This methodology can reliably detect admixtures as low as 1% v/v cashew in commercial tea products. Overall, our results demonstrate that the HRM technology is a strong molecular approach in tea authentication, capable of detecting very low adulterations in DNA admixtures. PRACTICAL APPLICATION: In this study, we established the use of high-resolution DNA-based technologies for the detection of cashew adulteration in tea, even in very low quantities. The technology could be applied to a greater range of plant-based tea adulterants. This work is expected to facilitate the traceability and authenticity of tea products and form the basis for the development of strategies against fraudulent practices.},
}
@article {pmid32467922,
year = {2020},
author = {Løken, SB and Skrede, I and Schumacher, T},
title = {The Helvella corium species aggregate in Nordic countries - phylogeny and species delimitation.},
journal = {Fungal systematics and evolution},
volume = {5},
number = {},
pages = {169-186},
pmid = {32467922},
issn = {2589-3831},
abstract = {Mycologists have always been curious about the elaborate morphotypes and shapes of species of the genus Helvella. The small, black, cupulate Helvella specimens have mostly been assigned to Helvella corium, a broadly defined morpho-species. Recent phylogenetic analyses, however, have revealed an aggregate of species hidden under this name. We performed a multispecies coalescent analysis to re-assess species limits and evolutionary relationships of the Helvella corium species aggregate in the Nordic countries. To achieve this, we used morphology and phylogenetic evidence from five loci - heat shock protein 90 (hsp), translation elongation factor 1-alpha (tef), RNA polymerase II (rpb2), and the 5.8S and large subunit (LSU) of the nuclear ribosomal DNA. All specimens under the name Helvella corium in the larger university fungaria of Norway, Sweden and Denmark were examined and barcoded, using partial hsp and/or rpb2 as the preferential secondary barcodes in Helvella. Additional fresh specimens were collected in three years (2015-2018) to obtain in vivo morphological data to aid in species discrimination. The H. corium species aggregate consists of seven phylogenetically distinct species, nested in three divergent lineages, i.e. H. corium, H. alpina and H. pseudoalpina sp. nov. in the /alpina-corium lineage, H. alpestris, H. macrosperma and H. nannfeldtii in the /alpestris-nannfeldtii lineage, and H. alpicola as a weakly supported sister to the /alpestris-nannfeldtii lineage. Among the seven species, the ribosomal loci expressed substantial variation in evolutionary rates, suggesting care in the use of these regions alone in delimitation of Helvella species. Altogether, 469 out of 496 available fungarium specimens were successfully barcoded.},
}
@article {pmid32467915,
year = {2020},
author = {Crous, PW and Schumacher, RK and Wood, AR and Groenewald, JZ},
title = {The Genera of Fungi - G5: Arthrinium, Ceratosphaeria, Dimerosporiopsis, Hormodochis, Lecanostictopsis, Lembosina, Neomelanconium, Phragmotrichum, Pseudomelanconium, Rutola, and Trullula.},
journal = {Fungal systematics and evolution},
volume = {5},
number = {},
pages = {77-98},
pmid = {32467915},
issn = {2589-3831},
abstract = {The present paper represents the fifth contribution in the Genera of Fungi series, linking type species of fungal genera to their morphology and DNA sequence data. This paper focuses on 11 genera of microfungi, for seven of which the type species are neo- or epitypified here: Arthrinium (Arthrinium caricicola; Apiosporaceae, Xylariales, Sordariomycetes), Ceratosphaeria (Ceratosphaeria lampadophora; Magnaporthaceae, Magnaporthales, Sordariomycetes), Dimerosporiopsis (Dimerosporiopsis engleriana; Venturiaceae, Venturiales, Dothideomycetes), Hormodochis (Hormodochis melanochlora; Stictidaceae, Ostropales, Ostropomycetidae, OSLEUM clade, Lecanoromycetes), Lecanostictopsis (Lecanostictopsis kamatii; Mycosphaerellaceae, Capnodiales, Dothideomycetes), Lembosina (Lembosina aulographoides; Lembosinaceae fam. nov., Lembosinales ord. nov., Dothideomycetes), Neomelanconium (Neomelanconium gelatosporum; Cenangiaceae, Helotiales, Leotiomycetes), Phragmotrichum (Phragmotrichum chailletii; Melanommataceae, Pleosporales, Pleosporomycetidae, Dothideomycetes), Pseudomelanconium gen. nov. (Pseudomelanconium spartii; incertae sedis, Pezizomycotina), Rutola (Rutola graminis; Torulaceae, Pleosporales, Pleosporomycetidae, Dothideomycetes), and Trullula (Trullula oreoselini; incertae sedis, Pezizomycotina).},
}
@article {pmid32467898,
year = {2019},
author = {Crous, PW and Schumacher, RK and Akulov, A and Thangavel, R and Hernández-Restrepo, M and Carnegie, AJ and Cheewangkoon, R and Wingfield, MJ and Summerell, BA and Quaedvlieg, W and Coutinho, TA and Roux, J and Wood, AR and Giraldo, A and Groenewald, JZ},
title = {New and Interesting Fungi. 2.},
journal = {Fungal systematics and evolution},
volume = {3},
number = {},
pages = {57-134},
pmid = {32467898},
issn = {2589-3831},
abstract = {One order, seven families, 28 new genera, 72 new species, 13 new combinations, four epitypes, and interesting new host and / or geographical records are introduced in this study. Pseudorobillardaceae is introduced for Pseudorobillarda (based on P. phragmitis). New genera include: Jeremyomyces (based on J. labinae) on twigs of Salix alba (Germany); Neodothidotthia (based on N. negundinicola) on Acer negundo (Ukraine); Neomedicopsis (based on N. prunicola) on fallen twigs of Prunus padus (Ukraine); Neophaeoappendicospora (based on N. leucaenae) on Leucaena leucocephala (France) (incl. Phaeoappendicosporaceae); Paradevriesia (incl. Paradevriesiaceae) (based on P. americana) from air (USA); Phaeoseptoriella (based on P. zeae) on leaves of Zea mays (South Africa); Piniphoma (based on P. wesendahlina) on wood debris of Pinus sylvestris (Germany); Pseudoconiothyrium (based on P. broussonetiae) on branch of Broussonetia papyrifera (Italy); Sodiomyces (based on S. alkalinus) from soil (Mongolia), and Turquoiseomyces (incl. Turquoiseomycetales and Turquoiseomycetaceae) (based on T. eucalypti) on leaves of Eucalyptus leptophylla (Australia); Typhicola (based on T. typharum) on leaves of Typha sp. (Germany); Xenodevriesia (incl. Xenodevriesiaceae) (based on X. strelitziicola) on leaves of Strelitzia sp. (South Africa). New species include: Bacillicladium clematidis on branch of Clematis vitalbae (Austria); Cercospora gomphrenigena on leaves of Gomphrena globosa (South Africa); Cyphellophora clematidis on Clematis vitalba (Austria); Exophiala abietophila on bark of Abies alba (Norway); Exophiala lignicola on fallen decorticated trunk of Quercus sp. (Ukraine); Fuscostagonospora banksiae on Banksia sp. (Australia); Gaeumannomycella caricicola on dead leaf of Carex remota (Germany); Hansfordia pruni on Prunus persica twig (Italy) (incl. Hansfordiaceae); Microdochium rhopalostylidis on Rhopalostylis sapida (New Zealand); Neocordana malayensis on leaves of Musa sp. (Malaysia); Neocucurbitaria prunicola on fallen twigs of Prunus padus (Ukraine); Neocucurbitaria salicis-albae on Salix alba twig (Ukraine); Neohelicomyces deschampsiae on culm base of dead leaf sheath of Deschampsia cespitosa (Germany); Pararoussoella juglandicola on twig of Juglans regia (Germany); Pezicula eucalyptigena on leaves of Eucalyptus sp. (South Africa); Phlogicylindrium dunnii on leaves of Eucalyptus dunnii (Australia); Phyllosticta hagahagaensis on leaf litter of Carissa bispinosa (South Africa); Phyllosticta austroafricana on leaf spots of unidentified deciduous tree host (South Africa); Pseudosigmoidea alnicola on Alnus glutinosa leaf litter (Germany); Pseudoteratosphaeria africana on leaf spot on unidentified host (Angola); Porodiplodia vitis on canes of Vitis vinifera (USA); Sodiomyces alkalinus from soil (Mongolia), Sodiomyces magadiensis and Sodiomyces tronii from soil (Kenya), Sympodiella quercina on fallen leaf of Quercus robur (Germany) and Zasmidium hakeicola on leaves of Hakea corymbosa (Australia). Epitypes are designated for: Cryptostictis falcata on leaves of E. alligatrix (Australia), Hendersonia phormii on leaves of Phormium tenax (New Zealand), Sympodiella acicola on needles of Pinus sylvestris (Netherlands), and Sphaeria scirpicola var. typharum on leaf of Typha sp. (Germany). Several taxa originally described from rocks are validated in this study. New taxa include: Extremaceae fam. nov., and new genera, Arthrocatena, Catenulomyces, Constantinomyces, Extremus, Hyphoconis, Incertomyces, Lapidomyces, Lithophila, Monticola, Meristemomyces, Oleoguttula, Perusta, Petrophila, Ramimonilia, Saxophila and Vermiconidia. New species include: Arthrocatena tenebrosa, Catenulomyces convolutus, Constantinomyces virgultus, C. macerans, C. minimus, C. nebulosus, C. virgultus, Exophiala bonariae, Extremus adstrictus, E. antarcticus, Hyphoconis sterilis, Incertomyces perditus, Knufia karalitana, K. marmoricola, K. mediterranea, Lapidomyces hispanicus, Lithophila guttulata, Monticola elongata, Meristemomyces frigidus, M. arctostaphyli, Neodevriesia bulbillosa, N. modesta, N. sardiniae, N. simplex, Oleoguttula mirabilis, Paradevriesia compacta, Perusta inaequalis, Petrophila incerta, Rachicladosporium alpinum, R. inconspicuum, R. mcmurdoi, R. monterosanum, R. paucitum, Ramimonilia apicalis, Saxophila tyrrhenica, Vermiconidia antarctica, V. calcicola, V. foris, and V. flagrans.},
}
@article {pmid32466772,
year = {2020},
author = {Ślipiko, M and Myszczyński, K and Buczkowska, K and Bączkiewicz, A and Szczecińska, M and Sawicki, J},
title = {Molecular delimitation of European leafy liverworts of the genus Calypogeia based on plastid super-barcodes.},
journal = {BMC plant biology},
volume = {20},
number = {1},
pages = {243},
pmid = {32466772},
issn = {1471-2229},
support = {No.2015/19/B/NZ8/03970//The National Science Center Krak&#xf3;w, Poland/ ; },
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Genes, Plant/genetics ; Genome, Chloroplast/genetics ; Hepatophyta/anatomy &amp; histology/classification/*genetics ; Phylogeny ; Plastids/*genetics ; Polymorphism, Single Nucleotide/genetics ; },
abstract = {BACKGROUND: Molecular research revealed that some of the European Calypogeia species described on the basis of morphological criteria are genetically heterogeneous and, in fact, are species complexes. DNA barcoding is already commonly used for correct identification of difficult to determine species, to disclose cryptic species, or detecting new taxa. Among liverworts, some DNA fragments, recommend as universal plant DNA barcodes, cause problems in amplification. Super-barcoding based on genomic data, makes new opportunities in a species identification.<br><br>RESULTS: On the basis of 22 individuals, representing 10 Calypogeia species, plastid genome was tested as a super-barcode. It is not effective in 100%, nonetheless its success of species discrimination (95.45%) is still conspicuous. It is not excluded that the above outcome may have been upset by cryptic speciation in C. suecica, as our results indicate. Having the sequences of entire plastomes of European Calypogeia species, we also discovered that the ndhB and ndhH genes and the trnT-trnL spacer identify species in 100%.<br><br>CONCLUSIONS: This study shows that even if a super-barcoding is not effective in 100%, this method does not close the door to a traditional single- or multi-locus barcoding. Moreover, it avoids many complication resulting from the need to amplify selected DNA fragments. It seems that a good solution for species discrimination is a development of so-called "specific barcodes" for a given taxonomic group, based on plastome data.},
}
@article {pmid32466556,
year = {2020},
author = {Hong, Z and Wu, Z and Zhao, K and Yang, Z and Zhang, N and Guo, J and Tembrock, LR and Xu, D},
title = {Comparative Analyses of Five Complete Chloroplast Genomes from the Genus Pterocarpus (Fabacaeae).},
journal = {International journal of molecular sciences},
volume = {21},
number = {11},
pages = {},
pmid = {32466556},
issn = {1422-0067},
support = {CAFYBB2020SZ005//Central Non-profit Research Institution of Chinese Academy of Forestry/ ; 31500537//National Natural Science Foundation of China/ ; },
mesh = {Evolution, Molecular ; *Genome, Chloroplast ; Microsatellite Repeats ; Molecular Sequence Annotation ; Open Reading Frames ; *Phylogeny ; Pterocarpus/classification/*genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Selection, Genetic ; },
abstract = {Pterocarpus is a genus of trees mainly distributed in tropical Asia, Africa, and South America. Some species of Pterocarpus are rosewood tree species, having important economic value for timber, and for some species, medicinal value as well. Up to now, information about this genus with regard to the genomic characteristics of the chloroplasts has been limited. Based on a combination of next-generation sequencing (Illumina Hiseq) and long-read sequencing (PacBio), the whole chloroplast genomes (cp genomes) of five species (rosewoods) in Pterocarpus (Pterocarpus macrocarpus, P. santalinus, P. indicus, P. pedatus, P. marsupium) have been assembled. The cp genomes of five species in Pterocarpus have similar structural characteristics, gene content, and sequence to other flowering plants. The cp genomes have a typical four-part structure, containing 110 unique genes (77 protein coding genes, 4 rRNAs, 29 tRNAs). Through comparative genomic analysis, abundant simple sequence repeat (SSR)loci (333-349) were detected in Pterocarpus, among which A /T single nucleotide repeats accounted for the highest proportion (72.8-76.4%). In the five cp genomes of Pterocarpus, eight hypervariable regions, including trnH-GUG_psbA, trnS-UGA_psbC, accD-psaI, ndhI-exon2_ndhI-exon1, ndhG_ndhi-exon2, rpoC2-exon2, ccsA, and trnfM-CAU, are proposed for use as DNA barcode regions. In the comparison of gene selection pressures (P. santalinus as the reference genome), purifying selection was inferred as the primary mode of selection in maintaining important biological functions. Phylogenetic analysis shows that Pterocarpus is a monophyletic group. The species P. tinctorius is resolved as early diverging in the genus. Pterocarpus was resolved as sister to the genus Tipuana.},
}
@article {pmid32463383,
year = {2020},
author = {Martorelli, I and Helwerda, LS and Kerkvliet, J and Gomes, SIF and Nuytinck, J and van der Werff, CRA and Ramackers, GJ and Gultyaev, AP and Merckx, VSFT and Verbeek, FJ},
title = {Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB).},
journal = {Journal of integrative bioinformatics},
volume = {17},
number = {1},
pages = {},
pmid = {32463383},
issn = {1613-4516},
mesh = {Biodiversity ; *DNA Barcoding, Taxonomic ; *Ecosystem ; Fungi/genetics ; },
abstract = {Fungi have crucial roles in ecosystems, and are important associates for many organisms. They are adapted to a wide variety of habitats, however their global distribution and diversity remains poorly documented. The exponential growth of DNA barcode information retrieved from the environment is assisting considerably the traditional ways for unraveling fungal diversity and detection. The raw DNA data in association to environmental descriptors of metabarcoding studies are made available in public sequence read archives. While this is potentially a valuable source of information for the investigation of Fungi across diverse environmental conditions, the annotation used to describe environment is heterogenous. Moreover, a uniform processing pipeline still needs to be applied to the available raw DNA data. Hence, a comprehensive framework to analyses these data in a large context is still lacking. We introduce the MycoDiversity DataBase, a database which includes public fungal metabarcoding data of environmental samples for the study of biodiversity patterns of Fungi. The framework we propose will contribute to our understanding of fungal biodiversity and aims to become a valuable source for large-scale analyses of patterns in space and time, in addition to assisting evolutionary and ecological research on Fungi.},
}
@article {pmid32463089,
year = {2020},
author = {Neidermeier, AN and Ross, DW and Havill, NP and Wallin, KF},
title = {Temporal Asynchrony of Adult Emergence Between Leucopis argenticollis and Leucopis piniperda (Diptera: Chamaemyiidae), Predators of the Hemlock Woolly Adelgid (Hemiptera: Adelgidae), with Implications for Biological Control.},
journal = {Environmental entomology},
volume = {49},
number = {4},
pages = {823-828},
doi = {10.1093/ee/nvaa049},
pmid = {32463089},
issn = {1938-2936},
mesh = {Animals ; *Diptera ; *Hemiptera ; *Hemlock ; North America ; Northwestern United States ; Tsuga ; },
abstract = {Two species of silver fly, Leucopis argenticollis (Zetterstedt) and Leucopis piniperda (Malloch) (Diptera: Chamaemyiidae), from the Pacific Northwest region of North America have been identified as potential biological control agents of hemlock woolly adelgid (Hemiptera: Adelgidae: Adelges tsugae Annand) in eastern North America. The two predators are collectively synchronized with A. tsugae development. To determine whether adult emergence of the two species of silver fly are also synchronized with one another, we collected adult Leucopis which emerged from A. tsugae-infested western hemlock [Pinaceae: Tsuga heterophylla (Raf.) Sarg.] from four sites in the Pacific Northwest over a 29-d period. Specimens were collected twice daily in the laboratory and identified to species using DNA barcoding. The study found that more adult Leucopis were collected in the evening than the morning. Additionally, the daily emergences of adults over the 29-d sampling period exhibited sinusoidal-like fluctuations of peak abundance of each species, lending evidence to a pattern of temporal partitioning. This pattern could have logistical implications for their use as biological control agents in eastern North America, namely the need to release both species for maximum efficacy in decreasing A. tsugae populations.},
}
@article {pmid32458471,
year = {2020},
author = {Xiong, X and Huang, M and Xu, W and Li, Y and Cao, M and Xiong, X},
title = {Rainbow trout (Oncorhynchus mykiss) identification in processed fish products using loop-mediated isothermal amplification and polymerase chain reaction assays.},
journal = {Journal of the science of food and agriculture},
volume = {100},
number = {13},
pages = {4696-4704},
doi = {10.1002/jsfa.10526},
pmid = {32458471},
issn = {1097-0010},
support = {2018YFC1602800//National Key Research and Development Program of China/ ; 31701688//National Natural Science Foundation of China/ ; },
mesh = {Animals ; China ; DNA/genetics ; DNA Primers/genetics ; Discriminant Analysis ; Fish Products/*analysis ; Fishes/genetics ; Food Contamination/analysis ; Molecular Diagnostic Techniques/*methods ; Nucleic Acid Amplification Techniques/*methods ; Oncorhynchus mykiss/*genetics ; Polymerase Chain Reaction/*methods ; },
abstract = {BACKGROUND: Financial loss and health risk caused by the substitution of rainbow trout for other salmonid species have become a common issue around the world. The situation could be further exacerbated in China by the 'abused' common name of San Wen Yu (the corresponding Chinese ideogram) for salmonids, considering the absence of a standardized naming system for seafood species. To prevent such episodes, the present study aimed to develop novel loop-mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR) assays targeting the mitochondrial cytochrome b gene for rapid identification of rainbow trout in processed fish products.<br><br>RESULTS: Rainbow trout-specific primers (LAMP and PCR) were designed, and the specificity against 23 different fish species was confirmed. The minimum amount of detectable DNA for LAMP assay reached 500&#x2009;pg, up to 10-fold less than for PCR assay. In addition to agarose gel electrophoresis, naked-eye inspection of the LAMP-positive samples using SYBR Green I under daylight or ultraviolet light was also validated. Finally, commercial San Wen Yu products made from rainbow trout could be accurately identified using the newly developed LAMP and PCR assays, further cross-confirmed by mini DNA barcoding and neighbor-joining dendrograms.<br><br>CONCLUSIONS: The LAMP and PCR assays established in the study allow a fast and accurate identification of rainbow trout in processed fish products. &#xa9; 2020 Society of Chemical Industry.},
}
@article {pmid32458049,
year = {2020},
author = {McCart Reed, AE and Bennett, J and Kutasovic, JR and Kalaw, E and Ferguson, K and Yeong, J and Simpson, PT and Lakhani, SR},
title = {Digital spatial profiling application in breast cancer: a user's perspective.},
journal = {Virchows Archiv : an international journal of pathology},
volume = {477},
number = {6},
pages = {885-890},
doi = {10.1007/s00428-020-02821-9},
pmid = {32458049},
issn = {1432-2307},
support = {APP1113867//National Health and Medical Research Council/ ; },
mesh = {Biomarkers, Tumor/*analysis ; *Breast Neoplasms ; Female ; Gene Expression Profiling/*methods ; Humans ; Nanotechnology/*methods ; Tissue Array Analysis/*methods ; },
abstract = {The disciplines of oncology and pathology are at present experiencing a wave of changes as precision medicine becomes embedded as standard-of-care. Consequently, the need to assess increasing numbers of biomarkers simultaneously has become more urgent and recognising the vast intra-tumoural heterogeneity, including within the microenvironment, requires a complex dimensional understanding of the localisation of the biomarker expression. Digital spatial profiling (DSP; nanoString™) technology spatially resolves and digitally quantifies proteins in a highly multiplexed assay, underpinned by the nCounter® barcoding platform. We present the application of this technology to breast cancer samples. Applying the 'off the shelf' cancer panel and a custom-conjugated E-cadherin antibody, we quantify vast intra-tumoural heterogeneity in immunological and tumour markers, and demonstrate a need for focussed selection of target cell populations. The technology offers enormous potential not only for making research advances but also for improving standard operating procedures in diagnostic applications.},
}
@article {pmid32457375,
year = {2020},
author = {Gostel, MR and Zúñiga, JD and Kress, WJ and Funk, VA and Puente-Lelievre, C},
title = {Microfluidic Enrichment Barcoding (MEBarcoding): a new method for high throughput plant DNA barcoding.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {8701},
pmid = {32457375},
issn = {2045-2322},
mesh = {Cycadopsida/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*chemistry/genetics/metabolism ; Magnoliopsida/genetics ; Microfluidics ; Plants/*genetics ; Polymerase Chain Reaction ; },
abstract = {DNA barcoding is a valuable tool to support species identification with broad applications from traditional taxonomy, ecology, forensics, food analysis, and environmental science. We introduce Microfluidic Enrichment Barcoding (MEBarcoding) for plant DNA Barcoding, a cost-effective method for high-throughput DNA barcoding. MEBarcoding uses the Fluidigm Access Array to simultaneously amplify targeted regions for 48 DNA samples and hundreds of PCR primer pairs (producing up to 23,040 PCR products) during a single thermal cycling protocol. As a proof of concept, we developed a microfluidic PCR workflow using the Fluidigm Access Array and Illumina MiSeq. We tested 96 samples for each of the four primary DNA barcode loci in plants: rbcL, matK, trnH-psbA, and ITS. This workflow was used to build a reference library for 78 families and 96 genera from all major plant lineages - many currently lacking in public databases. Our results show that this technique is an efficient alternative to traditional PCR and Sanger sequencing to generate large amounts of plant DNA barcodes and build more comprehensive barcode databases.},
}
@article {pmid32456322,
year = {2020},
author = {Kirchgatter, K and de Oliveira Guimarães, L and Hugo Yañez Trujillano, H and Rafael Arias, F and Cáceres, AG and de Castro Duarte, AMR and Dos Santos Malafronte, R and Tubaki, RM and Mureb Sallum, MA},
title = {Phylogeny of Anopheles (Kerteszia) (Diptera: Culicidae) Using Mitochondrial Genes.},
journal = {Insects},
volume = {11},
number = {5},
pages = {},
pmid = {32456322},
issn = {2075-4450},
support = {Research code: 100101171//Universidad Nacional Mayor de San Marcos/ ; },
abstract = {Identification of mosquito species is necessary for determining the entomological components of malaria transmission, but it can be difficult in morphologically similar species. DNA sequences are largely used as an additional tool for species recognition, including those that belong to species complexes. Kerteszia mosquitoes are vectors of human and simian malaria in the Neotropical Region, but there are few DNA sequences of Kerteszia species in public databases. In order to provide relevant information about diversity and improve knowledge in taxonomy of Kerteszia species in Peru, we sequenced part of the mitochondrial genome, including the cytochrome c oxidase I (COI) barcode region. Phylogenetic analyses structured all species of mosquitoes collected in Peru into a single clade, separate from the Brazilian species. The Peruvian clade was composed of two lineages, encompassing sequences from Anopheles Kerteszia boliviensis and Anopheles Kerteszia pholidotus. An. pholidotus sequences were recorded for the first time in Peru, whereas An. boliviensis sequences were for the first time published in the GenBank database. Sequences generated from specimens morphologically identified as Anopheles Kerteszia cruzii clustered into three separate clades according to the collection localities of Serra do Mar, Serra da Mantiqueira, and Serra da Cantareira, confirming An. cruzii as a species complex, composed of at least three putative species.},
}
@article {pmid32456256,
year = {2020},
author = {Zittra, C and Wöss, G and Van der Vloet, L and Bakran-Lebl, K and Shahi Barogh, B and Sehnal, P and Fuehrer, HP},
title = {Barcoding of the Genus Culicoides (Diptera: Ceratopogonidae) in Austria-An Update of the Species Inventory Including the First Records of Three Species in Austria.},
journal = {Pathogens (Basel, Switzerland)},
volume = {9},
number = {5},
pages = {},
pmid = {32456256},
issn = {2076-0817},
support = {P 31258/FWF_/Austrian Science Fund FWF/Austria ; ABOL//Austrian Federal Ministry of Education, Science and Research/ ; P 31258-B29//Austrian Science Funds/ ; },
abstract = {Ceratopogonidae are small nematoceran Diptera with a worldwide distribution, consisting of more than 5400 described species, divided into 125 genera. The genus Culicoides is known to comprise hematophagous vectors of medical and veterinary importance. Diseases transmitted by Culicoides spp. Such as African horse sickness virus, Bluetongue virus, equine encephalitis virus (Reoviridae) and Schmallenberg virus (Bunyaviridae) affect large parts of Europe and are strongly linked to the spread and abundance of its vectors. However, Culicoides surveillance measures are not implemented regularly nor in the whole of Austria. In this study, 142 morphologically identified individuals were chosen for molecular analyses (barcoding) of the mitochondrial cytochrome c oxidase subunit I gene (mt COI). Molecular analyses mostly supported previous morphologic identification. Mismatches between results of molecular and morphologic analysis revealed three new Culicoides species in Austria, Culicoides gornostaevae Mirzaeva, 1984, which is a member of the Obsoletus group, C. griseidorsum Kieffer, 1918 and C. pallidicornis Kieffer, 1919 as well as possible cryptic species. We present here the first Austrian barcodes of the mt COI region of 26 Culicoides species and conclude that barcoding is a reliable tool with which to support morphologic analysis, especially with regard to the difficult to identify females of the medically and economically important genus Culicoides.},
}
@article {pmid32455920,
year = {2020},
author = {Cacciola, SO and Gilardi, G and Faedda, R and Schena, L and Pane, A and Garibaldi, A and Gullino, ML},
title = {Characterization of Colletotrichum ocimi Population Associated with Black Spot of Sweet Basil (Ocimum basilicum) in Northern Italy.},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {5},
pages = {},
pmid = {32455920},
issn = {2223-7747},
abstract = {Black spot is a major foliar disease of sweet basil (Ocimum basilicum) present in a typical cultivation area of northern Italy, including the Liguria and southern Piedmont regions, where this aromatic herb is an economically important crop. In this study, 15 Colletotrichum isolates obtained from sweet basil plants with symptoms of black spot sampled in this area were characterized morphologically and by nuclear DNA analysis using internal transcribed spacers (ITS) and intervening 5.8S nrDNA as well as part of the β-tubulin gene (TUB2) regions as barcode markers. Analysis revealed all but one isolate belonged to the recently described species C. ocimi of the C. destructivum species complex. Only one isolate was identified as C. destructivum sensu stricto (s.s.). In pathogenicity tests on sweet basil, both C. ocimi and C. destructivum s.s. isolates incited typical symptoms of black spot, showing that although C. ocimi prevails in this basil production area, it is not the sole causal agent of black spot in northern Italy. While no other hosts of C. ocimi are known worldwide, the close related species C. destructivum has a broad host range, suggesting a speciation process of C. ocimi within this species complex driven by adaptation to the host.},
}
@article {pmid32448524,
year = {2020},
author = {Pereira, AE and Uribe, N and Pointier, JP},
title = {Lymnaeidae from Santander and bordering departments of Colombia: Morphological characterization, molecular identification and natural infection with Fasciola hepatica.},
journal = {Veterinary parasitology, regional studies and reports},
volume = {20},
number = {},
pages = {100408},
doi = {10.1016/j.vprsr.2020.100408},
pmid = {32448524},
issn = {2405-9390},
mesh = {Animals ; Colombia ; Disease Vectors/classification ; Fasciola hepatica ; Snails/anatomy &amp; histology/*classification/genetics/parasitology ; },
abstract = {The Lymnaeidae constitute a family of freshwater gastropod molluscs whose diversity and ecology have been infrequently studied throughout Colombia. Some lymnaeid species act as intermediate hosts of trematode parasites, which are of great importance in both the veterinary and medical fields. Among trematode parasites, Fasciola hepatica is best known for being an important parasite of sheep and cattle for decades and causes significant economic losses in these livestock species. The main objective of this work is to identify the various species of lymnaeids that occupy different geographical regions of Santander and its bordering departments within Colombia. This will expand the knowledge of lymnaeid diversity in Colombia and provide further insight into their role in the transmission of F. hepatica. A total of 118 georeferenced sites between 126 m.a.s.l. and 3870 m.a.s.l. were sampled in Santander, Boyacá, Norte de Santander and Cundinamarca, respectively. Lymnaeid snails were identified according to the morphology of their shells and by several characteristics of their reproductive systems. Species identification was confirmed using DNA barcoding. Four lymnaeid species are reported in the study area: the native Galba cousini and three exotic species, Pseudosuccinea columella, G. truncatula and G. schirazensis. The four species were examined for natural infection with F. hepatica. Infected variants of the main snail host, G. cousini, were found in the Onzaga, Encino and Vetas municipalities of Santander, as well as in the Belén municipality of Boyacá. A second species, G. truncatula was also found naturally infected in Mutiscua municipality of Norte de Santander. The two other species, P. columella and G. schirazensis were found free of infection.},
}
@article {pmid32448128,
year = {2020},
author = {Ståhls, G and Meier, R and Sandrock, C and Hauser, M and Šašić Zorić, L and Laiho, E and Aracil, A and Doderović, J and Badenhorst, R and Unadirekkul, P and Mohd Adom, NAB and Wein, L and Richards, C and Tomberlin, JK and Rojo, S and Veselić, S and Parviainen, T},
title = {The puzzling mitochondrial phylogeography of the black soldier fly (Hermetia illucens), the commercially most important insect protein species.},
journal = {BMC evolutionary biology},
volume = {20},
number = {1},
pages = {60},
pmid = {32448128},
issn = {1471-2148},
support = {645636//H2020 Marie Sk&#x142;odowska-Curie Actions/International ; R-154-000-B46-114//National Research Foundation Singapore/International ; R-154-000-A94-592//National Research Foundation Singapore/International ; },
mesh = {Animals ; Breeding ; Diptera/genetics/*metabolism/physiology ; Genetic Variation ; Insect Proteins/*metabolism ; Larva/metabolism ; Mitochondria/*metabolism ; *Phylogeography ; Reproduction ; },
abstract = {BACKGROUND: The black soldier fly (Diptera: Stratiomyidae, Hermetia illucens) is renowned for its bioconversion ability of organic matter, and is the worldwide most widely used source of insect protein. Despite varying extensively in morphology, it is widely assumed that all black soldier flies belong to the same species, Hermetia illucens. We here screened about 600 field-collected and cultured flies from 39 countries and six biogeographic regions to test this assumption based on data for three genes (mitochondrial COI, nuclear ITS2 &amp; 28S rDNA) and in order to gain insights into the phylogeography of the species.<br><br>RESULTS: Our study reveals a surprisingly high level of intraspecific genetic diversity for the mitochondrial barcoding gene COI (divergences up to 4.9%). This level of variability is often associated with the presence of multiple species, but tested nuclear markers (ITS2 and 28S rDNA) were invariant and fly strain hybridization experiments under laboratory conditions revealed reproductive compatibility. COI haplotype diversity is not only very high in all biogeographic regions (56 distinct haplotypes in total), but also in breeding facilities and research centers from six continents (10 haplotypes: divergences up to 4.3%). The high genetic diversity in fly-breeding facilities is mostly likely due to many independent acquisitions of cultures via sharing and/or establishing new colonies from field-collected flies. However, explaining some of the observed diversity in several biogeographic regions is difficult given that the origin of the species is considered to be New World (32 distinct haplotypes) and one would expect severely reduced genetic diversity in the putatively non-native populations in the remaining biogeographic regions. However, distinct, private haplotypes are known from the Australasian (N&#x2009;=&#x2009;1), Oriental (N&#x2009;=&#x2009;4), and the Eastern Palearctic (N&#x2009;=&#x2009;4) populations. We reviewed museum specimen records and conclude that the evidence for introductions is strong for the Western Palearctic and Afrotropical regions which lack distinct, private haplotypes.<br><br>CONCLUSIONS: Based on the results of this paper, we urge the black soldier fly community to apply molecular characterization (genotyping) of the fly strains used in artificial fly-breeding and share these data in research publications as well as when sharing cultures. In addition, fast-evolving nuclear markers should be used to reconstruct the recent invasion history of the species.},
}
@article {pmid32443882,
year = {2020},
author = {Liu, L and Chen, D and Wang, J and Chen, J},
title = {Advances of Single-Cell Protein Analysis.},
journal = {Cells},
volume = {9},
number = {5},
pages = {},
pmid = {32443882},
issn = {2073-4409},
mesh = {Animals ; Biological Assay ; Dietary Proteins/*analysis ; Flow Cytometry ; Humans ; Microfluidics ; Proteomics ; Single-Cell Analysis/*trends ; },
abstract = {Proteins play a significant role in the key activities of cells. Single-cell protein analysis provides crucial insights in studying cellular heterogeneities. However, the low abundance and enormous complexity of the proteome posit challenges in analyzing protein expressions at the single-cell level. This review summarizes recent advances of various approaches to single-cell protein analysis. We begin by discussing conventional characterization approaches, including fluorescence flow cytometry, mass cytometry, enzyme-linked immunospot assay, and capillary electrophoresis. We then detail the landmark advances of microfluidic approaches for analyzing single-cell protein expressions, including microfluidic fluorescent flow cytometry, droplet-based microfluidics, microwell-based assay (microengraving), microchamber-based assay (barcoding microchips), and single-cell Western blotting, among which the advantages and limitations are compared. Looking forward, we discuss future research opportunities and challenges for multiplexity, analyte, throughput, and sensitivity of the microfluidic approaches, which we believe will prompt the research of single-cell proteins such as the molecular mechanism of cell biology, as well as the clinical applications for tumor treatment and drug development.},
}
@article {pmid32441499,
year = {2020},
author = {Pansare, AV and Chhatre, SY and Khairkar, SR and Bell, JG and Barbezat, M and Chakrabarti, S and Nagarkar, AA},
title = {"Shape-Coding": Morphology-Based Information System for Polymers and Composites.},
journal = {ACS applied materials &amp; interfaces},
volume = {12},
number = {24},
pages = {27555-27561},
doi = {10.1021/acsami.0c05314},
pmid = {32441499},
issn = {1944-8252},
abstract = {Fiber-reinforced composites have become the material of choice for aerospace structures because of their favorable strength-to-weight ratio. Given the increasing amounts of counterfeit composite parts showing up in the complex aerospace supply chain, it is absolutely vital to track a composite part throughout its lifecycle-from production to usage and to disposal. Existing barcoding methods are invasive, affect the structural properties of composites, and/or are vulnerable to tampering. We describe a universal method to store information in fiber-reinforced composites based on solid-state in situ reduction leading to embedded nanoparticles with controlled morphologies. This simple, cost-effective, mild, surfactant-free, and one-step protocol for the fabrication of embedded platinum nanostructures leads to morphology-based barcodes for polymeric composites. We also describe a coding methodology wherein a 1 × 1 cm code can represent 3.4 billion parts to 95 trillion parts, depending on the resolution required along with access to morphology-based chemical encryption systems.},
}
@article {pmid32440288,
year = {2020},
author = {Martínez-Aquino, A and Vidal-Martínez, VM and Ceccarelli, FS and Méndez, O and Soler-Jiménez, LC and Aguirre-Macedo, ML},
title = {Phylogeny, genetics, and the partial life cycle of Oncomegas wageneri in the Gulf of Mexico.},
journal = {Current zoology},
volume = {66},
number = {3},
pages = {275-283},
pmid = {32440288},
issn = {1674-5507},
abstract = {Despite the diversity and ecological importance of cestodes, there is a paucity of studies on their life stages (i.e., complete lists of intermediate, paratenic, and definitive hosts) and genetic variation. For example, in the Gulf of Mexico (GoM) 98 species of cestodes have been reported to date; however, data on their intraspecific genetic variation and population genetic studies are lacking. The trypanorhynch cestode, Oncomegas wageneri, is found (among other places) off the American Western Atlantic Coast, including the GoM, and has been reported as an adult from stingrays and from several teleost species in its larval form (as plerocerci). This study represents the first report of 2 previously unregistered definitive hosts for O. wageneri, namely the Atlantic sharpnose shark Rhizoprionodon terraenovae and the southern stingray Hypanus americanus. In this work, partial sequences of the 28S (region D1-D2) ribosomal DNA were analyzed to include O. wageneri within an eutetrarhynchoid phylogenetic framework. All O. wageneri individuals (which included plerocerci and adults) were recovered as monophyletic and Oncomegas celatus was identified as the sister species of O. wageneri. Furthermore, population genetic analyses of O. wageneri from the southern GoM were carried out using DNA sequences of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene, which reflected high genetic variation and a lack of genetic structure among the 9 oceanographic sampling sites. Based on these results, O. wageneri is panmictic in the southern GoM. More extensive sampling along the species entire distribution is necessary to make more accurate inferences of population genetics of O. wageneri.},
}
@article {pmid32437897,
year = {2020},
author = {Deconinck, D and Volckaert, FAM and Hostens, K and Panicz, R and Eljasik, P and Faria, M and Monteiro, CS and Robbens, J and Derycke, S},
title = {A high-quality genetic reference database for European commercial fishes reveals substitution fraud of processed Atlantic cod (Gadus morhua) and common sole (Solea solea) at different steps in the Belgian supply chain.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {141},
number = {},
pages = {111417},
doi = {10.1016/j.fct.2020.111417},
pmid = {32437897},
issn = {1873-6351},
mesh = {Animals ; Belgium ; Commerce ; DNA Barcoding, Taxonomic ; *Databases, Genetic ; Flatfishes/*genetics ; *Food Supply ; *Forensic Genetics ; *Fraud ; Gadus morhua/*genetics ; Species Specificity ; },
abstract = {Seafood is an important component of the human diet. With depleting fish stocks and increasing prices, seafood is prone to fraudulent substitution. DNA barcoding has illustrated fraudulent substitution of fishes in retail and restaurants. Whether substitution also occurs in other steps of the supply chain remains largely unknown. DNA barcoding relies on public reference databases for species identification, but these can contain incorrect identifications. The creation of a high quality genetic reference database for 42 European commercially important fishes was initiated containing 145 Cytochrome c oxidase subunit I (COI) and 152 Cytochrome b (cytB) sequences. This database was used to identify substitution rates of Atlantic cod (Gadus morhua) and common sole (Solea solea) along the fish supply chain in Belgium using DNA barcoding. Three out of 132 cod samples were substituted, in catering (6%), import (5%) and fishmongers (3%). Seven out of the 41 processed sole samples were substituted, in wholesale (100%), food services (50%), retailers (20%) and catering (8%). Results show that substitution of G. morhua and S. solea is not restricted to restaurants, but occurs in other parts of the supply chain, warranting for more stringent controls along the supply chain to increase transparency and trust among consumers.},
}
@article {pmid32437883,
year = {2020},
author = {Mohammed-Geba, K and Sheir, SK and El-Aziz Hamed, EA and Galal-Khallaf, A},
title = {Molecular and morphological signatures for extreme environmental adaptability of the invasive mussel Brachidontes pharaonis (Fischer, 1870).},
journal = {Molecular and cellular probes},
volume = {53},
number = {},
pages = {101594},
doi = {10.1016/j.mcp.2020.101594},
pmid = {32437883},
issn = {1096-1194},
mesh = {Adaptation, Physiological ; Animals ; DNA, Environmental/*genetics ; Egypt ; Electron Transport Complex IV/*genetics ; *Genetic Variation ; Genetics, Population ; Indian Ocean ; Introduced Species ; Mediterranean Sea ; Mytilidae/classification/genetics/*physiology ; Phylogeny ; Phylogeography ; Species Specificity ; },
abstract = {Brachidontes pharaonis (Bivalvia:Mytilidae) is one of the most successful Lessepsian migrants. Its extensive populations' expansion and phenotypic plasticity might reshape the Mediterranean biodiversity. Individuals of B. pharaonis were collected from various sites in the Mediterranean Sea and the Red Sea in Egypt. Species-specific primers for Cytochrome Oxidase Subunit 1 gene were designed. They were applied for analysis of mussel's population genetics and assessment of its aquatic environmental DNA (eDNA) abundance. Morphological, allometric and morphometric characteristics were also described. The newly designed primers could efficiently detect the species presence, abundance, and genetic diversity. The Northern Red Sea and north-westward populations exhibited higher nucleotide diversities than southwards. Phylogeny and principal coordinates' analysis (PCoA) detected three geographical categories for B. pharaonis: one of the Indian Ocean, other of the Middle Red Sea and southwards, and the other extends from the Northern Red Sea to the westernmost part of the Mediterranean. Intraspecific differences in the shell shape, colour, and biometrics were noted. The shells were significantly smaller and lighter in rocky habitats than in sandy ones. The morphometric indices and allometry were significantly different between rocky and sandy environments. In general, B. pharaonis genetic and morphological features appeared to contribute much to the species success in versatile habitats.},
}
@article {pmid32437469,
year = {2020},
author = {Salvi, D and Berrilli, E and D'Alessandro, P and Biondi, M},
title = {Sharpening the DNA barcoding tool through a posteriori taxonomic validation: The case of Longitarsus flea beetles (Coleoptera: Chrysomelidae).},
journal = {PloS one},
volume = {15},
number = {5},
pages = {e0233573},
pmid = {32437469},
issn = {1932-6203},
mesh = {Animals ; Coleoptera/classification/*genetics ; DNA/genetics/isolation &amp; purification ; *DNA Barcoding, Taxonomic/methods ; Databases, Nucleic Acid ; Evolution, Molecular ; },
abstract = {The accuracy of the DNA barcoding tool depends on the existence of a comprehensive archived library of sequences reliably determined at species level by expert taxonomists. However, misidentifications are not infrequent, especially following large-scale DNA barcoding campaigns on diverse and taxonomically complex groups. In this study we used the species-rich flea beetle genus Longitarsus, that requires a high level of expertise for morphological species identification, as a case study to assess the accuracy of the DNA barcoding tool following several optimization procedures. We built a cox1 reference database of 1502 sequences representing 78 Longitarsus species, among which 117 sequences (32 species) were newly generated using a non-invasive DNA extraction method that allows keeping reference voucher specimens. Within this dataset we identified 69 taxonomic inconsistencies using barcoding gap analysis and tree topology methods. Threshold optimisation and a posteriori taxonomic revision based on newly generated reference sequences and metadata allowed resolving 44 sequences with ambiguous and incorrect identification and provided a significant improvement of the DNA barcoding accuracy and identification efficacy. Unresolved taxonomic uncertainties, due to overlapping intra- and inter-specific levels of divergences, mainly regards the Longitarsus pratensis species complex and polyphyletic groups L. melanocephalus, L. nigrofasciatus and L. erro. Such type of errors indicates either poorly established taxonomy or any biological processes that make mtDNA groups poorly predictive of species boundaries (e.g. recent speciation or interspecific hybridisation), thus providing directions for further integrative taxonomic and evolutionary studies. Overall, this study underlines the importance of reference vouchers and high-quality metadata associated to sequences in reference databases and corroborates, once again, the key role of taxonomists in any step of the DNA barcoding pipeline in order to generate and maintain a correct and functional reference library.},
}
@article {pmid32437127,
year = {2020},
author = {Bai, Z and Deng, Y and Kim, D and Chen, Z and Xiao, Y and Fan, R},
title = {An Integrated Dielectrophoresis-Trapping and Nanowell Transfer Approach to Enable Double-Sub-Poisson Single-Cell RNA Sequencing.},
journal = {ACS nano},
volume = {14},
number = {6},
pages = {7412-7424},
doi = {10.1021/acsnano.0c02953},
pmid = {32437127},
issn = {1936-086X},
mesh = {Animals ; *High-Throughput Nucleotide Sequencing ; Mice ; *Microfluidics ; Sequence Analysis, RNA ; Single-Cell Analysis ; },
abstract = {Current technologies for high-throughput single-cell RNA sequencing (scRNA-seq) are based upon stochastic pairing of cells and barcoded beads in nanoliter droplets or wells. They are limited by the mathematical principle of the Poisson statistics such that the utilization of either cells or beads or both is no more than ∼33%. Despite the versatile design of microfluidics or microwells for high-yield loading of beads that beats the Poisson limit, subsequent encapsulation of single cells is still determined by stochastic pairing, representing a fundamental limitation in the field of single-cell sequencing. Here, we present dTNT-seq, an integrated dielectrophoresis (DEP)-trapping-nanowell-transfer (dTNT) approach to perform cell trapping and bead loading both in a sub-Poisson manner to facilitate scRNA-seq. A larger-sized 50 μm microwell array was prealigned precisely on top of the 20 μm DEP nanowell array such that single cells trapped by DEP can be readily transferred into the underneath larger wells by flipping the device, followed by subsequent hydrodynamic bead loading and coisolation with transferred single cells. Using a dTNT device composed of 3600 electroactive DEP-nanowell units, we demonstrated a single-cell trapping rate of 91.84%, a transfer efficiency of 82%, and a routine bead loading rate of >99%, which breaks the Poisson limit for the capture of both cells and beads, thus called double-sub-Poisson distribution, prior to encapsulating them in nanoliter wells for cellular mRNA barcoding. This approach was applied to human (HEK) and mouse (3T3) cells. Comparison with a non-DEP-based method through gene expression clustering and regulatory pathway analysis demonstrates consistent patterns and negligible alternation of cellular transcriptional states by DEP. We envision the dTNT-seq device can be modified for studying cell-cell interactions and enable other applications requiring active manipulation of single cells prior to transcriptome sequencing.},
}
@article {pmid32436499,
year = {2020},
author = {Gao, Z and Chen, Z and Han, Y and Wang, F},
title = {Cyanostilbene-based vapo-fluorochromic supramolecular assemblies for reversible 3D code encryption.},
journal = {Nanoscale horizons},
volume = {5},
number = {7},
pages = {1081-1087},
doi = {10.1039/d0nh00186d},
pmid = {32436499},
issn = {2055-6764},
abstract = {Scanning codes with the capability for stimuli-triggered decryption are urgently needed to prevent information leakage and counterfeiting. Compared to conventional 1D barcodes and 2D QR codes, 3D codes show promise in this field thanks to the presence of four different colors in the icon, with great information variability. Up to now, encrypted 3D code development has primarily focused on chemical reaction-based systems, leading to information decryption in an irreversible transformation manner. Herein, a novel and intelligent 3D code encryption system has been constructed with full reversibility and a fast response, taking advantage of the luminescent vapochromism of cyanostilbene-based supramolecular assemblies. Information in the inkjet-printed 3D code is specifically decrypted through vapor fuming with chlorinated solvents, while it is reversibly encrypted upon removing the vapor. Hence, this study provides a novel and effective strategy for obtaining high-performance smart scanning codes.},
}
@article {pmid32434592,
year = {2020},
author = {Mignotte, A and Garros, C and Gardès, L and Balenghien, T and Duhayon, M and Rakotoarivony, I and Tabourin, L and Poujol, L and Mathieu, B and Ibañez-Justicia, A and Deniz, A and Cvetkovikj, A and Purse, BV and Ramilo, DW and Stougiou, D and Werner, D and Pudar, D and Petrić, D and Veronesi, E and Jacobs, F and Kampen, H and Pereira da Fonseca, I and Lucientes, J and Navarro, J and de la Puente, JM and Stefanovska, J and Searle, KR and Khallaayoune, K and Culverwell, CL and Larska, M and Bourquia, M and Goffredo, M and Bisia, M and England, M and Robin, M and Quaglia, M and Miranda-Chueca, M&#xc1; and Bødker, R and Estrada-Peña, R and Carpenter, S and Tchakarova, S and Boutsini, S and Sviland, S and Schäfer, SM and Ozoliņa, Z and Segliņa, Z and Vatansever, Z and Huber, K},
title = {The tree that hides the forest: cryptic diversity and phylogenetic relationships in the Palaearctic vector Obsoletus/Scoticus Complex (Diptera: Ceratopogonidae) at the European level.},
journal = {Parasites &amp; vectors},
volume = {13},
number = {1},
pages = {265},
pmid = {32434592},
issn = {1756-3305},
support = {727393//H2020-PALE-Blu/ ; OC/EFSA/AHAW/2013/02-FWC1//VectorNet Project/ ; },
mesh = {Animals ; Ceratopogonidae/*classification/virology ; Cyclooxygenase 1/genetics ; DNA Barcoding, Taxonomic ; Europe ; Female ; *Genetic Variation ; Geography ; Insect Vectors/*classification/virology ; Livestock/virology ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Culicoides obsoletus is an abundant and widely distributed Holarctic biting midge species, involved in the transmission of bluetongue virus (BTV) and Schmallenberg virus (SBV) to wild and domestic ruminants. Females of this vector species are often reported jointly with two morphologically very close species, C. scoticus and C. montanus, forming the Obsoletus/Scoticus Complex. Recently, cryptic diversity within C. obsoletus was reported in geographically distant sites. Clear delineation of species and characterization of genetic variability is mandatory to revise their taxonomic status and assess the vector role of each taxonomic entity. Our objectives were to characterize and map the cryptic diversity within the Obsoletus/Scoticus Complex.<br><br>METHODS: Portion of the cox1 mitochondrial gene of 3763 individuals belonging to the Obsoletus/Scoticus Complex was sequenced. Populations from 20 countries along a Palaearctic Mediterranean transect covering Scandinavia to Canary islands (North to South) and Canary islands to Turkey (West to East) were included. Genetic diversity based on cox1 barcoding was supported by 16S rDNA mitochondrial gene sequences and a gene coding for ribosomal 28S rDNA. Species delimitation using a multi-marker methodology was used to revise the current taxonomic scheme of the Obsoletus/Scoticus Complex.<br><br>RESULTS: Our analysis showed the existence of three phylogenetic clades (C. obsoletus clade O2, C. obsoletus clade dark and one not yet named and identified) within C. obsoletus. These analyses also revealed two intra-specific clades within C. scoticus and raised questions about the taxonomic status of C. montanus.<br><br>CONCLUSIONS: To our knowledge, our study provides the first genetic characterization of the Obsoletus/Scoticus Complex on a large geographical scale and allows a revision of the current taxonomic classification for an important group of vector species of livestock viruses in the Palaearctic region.},
}
@article {pmid32433893,
year = {2021},
author = {Varadharajan, B and Parani, M},
title = {DMSO and betaine significantly enhance the PCR amplification of ITS2 DNA barcodes from plants.},
journal = {Genome},
volume = {64},
number = {3},
pages = {165-171},
doi = {10.1139/gen-2019-0221},
pmid = {32433893},
issn = {1480-3321},
mesh = {*Betaine ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant ; *DNA, Ribosomal Spacer ; *Dimethyl Sulfoxide ; Plants/*classification/genetics ; Polymerase Chain Reaction/*methods ; },
abstract = {ITS2 marker is highly efficient in species discrimination but its application in DNA barcoding is limited due to huge variations in the PCR success rate. We have hypothesized that higher GC content and the resultant secondary structures formed during annealing might hinder the PCR amplification of ITS2. To test this hypothesis, we selected 12 species from 12 different families in which ITS2 was not amplified under standard PCR reaction conditions. In these samples, DMSO, formamide, betaine, and 7-deaza-dGTP were evaluated for their ability to improve the PCR success rate. The highest PCR success rate (91.6%) was observed with 5% DMSO, followed by 1 M betaine (75%), 50 μM 7-deaza-dGTP (33.3%), and 3% formamide (16.6%). The one sample that did not amplify with DMSO was amplified by adding 1 M betaine. However, combining DMSO and betaine in the same reaction did not improve the PCR. Therefore, to achieve the highest PCR success rate for ITS2, it is recommended to include 5% DMSO by default and substitute it with 1 M betaine only in the case of failed reactions. When this strategy was tested in 50 species from 43 genera and 29 families, the PCR success rate of ITS2 increased from 42% to 100%.},
}
@article {pmid32431746,
year = {2020},
author = {Baird, HP and Moon, KL and Janion-Scheepers, C and Chown, SL},
title = {Springtail phylogeography highlights biosecurity risks of repeated invasions and intraregional transfers among remote islands.},
journal = {Evolutionary applications},
volume = {13},
number = {5},
pages = {960-973},
pmid = {32431746},
issn = {1752-4571},
abstract = {Human-mediated transport of species outside their natural range is a rapidly growing threat to biodiversity, particularly for island ecosystems that have evolved in isolation. The genetic structure underpinning island populations will largely determine their response to increased transport and thus help to inform biosecurity management. However, this information is severely lacking for some groups, such as the soil fauna. We therefore analysed the phylogeographic structure of an indigenous and an invasive springtail species (Collembola: Poduromorpha), each distributed across multiple remote sub-Antarctic islands, where human activity is currently intensifying. For both species, we generated a genome-wide SNP data set and additionally analysed all available COI barcodes. Genetic differentiation in the indigenous springtail Tullbergia bisetosa is substantial among (and, to a lesser degree, within) islands, reflecting low dispersal and historic population fragmentation, while COI patterns reveal ancestral signatures of postglacial recolonization. This pronounced geographic structure demonstrates the key role of allopatric divergence in shaping the region's diversity and highlights the vulnerability of indigenous populations to genetic homogenization via human transport. For the invasive species Hypogastrura viatica, nuclear genetic structure is much less apparent, particularly for islands linked by regular shipping, while diverged COI haplotypes indicate multiple independent introductions to each island. Thus, human transport has likely facilitated this species' persistence since its initial colonization, through the ongoing introduction and inter-island spread of genetic variation. These findings highlight the different evolutionary consequences of human transport for indigenous and invasive soil species. Crucially, both outcomes demonstrate the need for improved intraregional biosecurity among remote island systems, where the policy focus to date has been on external introductions.},
}
@article {pmid32429218,
year = {2020},
author = {Ibáñez-Justicia, A and Smitz, N and den Hartog, W and van de Vossenberg, B and De Wolf, K and Deblauwe, I and Van Bortel, W and Jacobs, F and Vaux, AGC and Medlock, JM and Stroo, A},
title = {Detection of Exotic Mosquito Species (Diptera: Culicidae) at International Airports in Europe.},
journal = {International journal of environmental research and public health},
volume = {17},
number = {10},
pages = {},
pmid = {32429218},
issn = {1660-4601},
mesh = {*Aedes ; Airports ; Animals ; *Culicidae ; Europe ; Introduced Species ; *Mosquito Vectors ; },
abstract = {In Europe, the air-borne accidental introduction of exotic mosquito species (EMS) has been demonstrated using mosquito surveillance schemes at Schiphol International Airport (Amsterdam, The Netherlands). Based upon these findings and given the increasing volume of air transport movements per year, the establishment of EMS after introduction via aircraft is being considered a potential risk. Here we present the airport surveillance results performed by the Centre for Monitoring of Vectors of the Netherlands, by the Monitoring of Exotic Mosquitoes (MEMO) project in Belgium, and by the Public Health England project on invasive mosquito surveillance. The findings of our study demonstrate the aircraft mediated transport of EMS into Europe from a wide range of possible areas in the world. Results show accidental introductions of Aedes aegypti and Ae. albopictus, as well as exotic Anopheles and Mansonia specimens. The findings of Ae. albopictus at Schiphol airport are the first evidence of accidental introduction of the species using this pathway in Europe. Furthermore, our results stress the importance of the use of molecular tools to validate the morphology-based species identifications. We recommend monitoring of EMS at airports with special attention to locations with a high movement of cargo and passengers.},
}
@article {pmid32428603,
year = {2020},
author = {Ren, Y and Zhang, Y and Wang, D and Liu, F and Fu, Y and Xiang, S and Su, L and Li, J and Dai, H and Huang, B},
title = {SinoDuplex: An Improved Duplex Sequencing Approach to Detect Low-frequency Variants in Plasma cfDNA Samples.},
journal = {Genomics, proteomics &amp; bioinformatics},
volume = {18},
number = {1},
pages = {81-90},
pmid = {32428603},
issn = {2210-3244},
mesh = {Algorithms ; Cell Line ; Cell-Free Nucleic Acids/*blood ; Circulating Tumor DNA/*blood ; DNA Mutational Analysis/*methods ; Humans ; Lung Neoplasms/*blood/*genetics ; Mutation ; Sensitivity and Specificity ; *Software ; },
abstract = {Accurate detection of low frequency mutations from plasma cell-free DNA in blood using targeted next generation sequencing technology has shown promising benefits in clinical settings. Duplex sequencing technology is the most commonly used approach in liquid biopsies. Unique molecular identifiers are attached to each double-stranded DNA template, followed by production of low-error consensus sequences to detect low frequency variants. However, high sequencing costs have hindered application of this approach in clinical practice. Here, we have developed an improved duplex sequencing approach called SinoDuplex, which utilizes a pool of adapters containing pre-defined barcode sequences to generate far fewer barcode combinations than with random sequences, and implemented a novel computational analysis algorithm to generate duplex consensus sequences more precisely. SinoDuplex increased the output of duplex sequencing technology, making it more cost-effective. We evaluated our approach using reference standard samples and cell-free DNA samples from lung cancer patients. Our results showed that SinoDuplex has high sensitivity and specificity in detecting very low allele frequency mutations. The source code for SinoDuplex is freely available at https://github.com/SinOncology/sinoduplex.},
}
@article {pmid32428090,
year = {2020},
author = {Briñoccoli, YF and Garrido, GG and Alvarez, A},
title = {DNA barcoding identifies three species of croakers (Pisces, Sciaenidae) in the ichthyoplankton of the High Paraná River.},
journal = {Anais da Academia Brasileira de Ciencias},
volume = {92},
number = {1},
pages = {e20180783},
doi = {10.1590/0001-3765202020180783},
pmid = {32428090},
issn = {1678-2690},
mesh = {Animals ; Argentina ; Base Sequence ; Biodiversity ; Brazil ; *DNA Barcoding, Taxonomic ; Paraguay ; Perciformes/*classification/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Rivers ; },
abstract = {In the province of Misiones (Argentina), the filling of the Yacyretá Reservoir (Argentina-Paraguay) to its final dimensions in 2011 formed new aquatic ecosystem, e.g., Garupá Stream was converted into a subreservoir. Reports have been made in this stream of adult individuals and spawning of the Family Sciaenidae, excellent colonizers of modified environments. The larvae of this family are morphologically similar, particularly among Pachyurus and Plagioscion species, making taxonomic differentiation difficult. In the present work, sciaenidae larvae were characterized molecularly at the cytochrome c oxidase subunit I gene in order to determine which species use this environment for reproduction. Additionally, genetic distances, Barcode Index Number (BIN) and Automatic Barcode Gap Discovery method (ABGD) were estimated and phylogenetic trees were reconstructed. The results indicated the presence of Plagioscion ternetzi and Pachyurus bonariensis larvae, and for the first time in tributaries of the region, Plagioscion squamosissimus. The incorporation of P. bonariensis and P. squamosissimus to the faunistic assemblage of ichthyoplankton in the Garupá Stream supports better characterization of the species richness of this secondary watercourse modified by the Yacyretá Reservoir, and advancement in our understanding of use of this area for reproduction.},
}
@article {pmid32428009,
year = {2020},
author = {Kim, J and Kang, S and Kim, HS and Kim, S and Lee, SS},
title = {Pilot plant study on nitrogen and phosphorus removal in marine wastewater by marine sediment with sequencing batch reactor.},
journal = {PloS one},
volume = {15},
number = {5},
pages = {e0233042},
pmid = {32428009},
issn = {1932-6203},
mesh = {Bacteria/*classification/genetics ; Biodegradation, Environmental ; Bioreactors/microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Geologic Sediments/*microbiology ; Nitrogen/*analysis ; Phosphorus/*analysis ; Phylogeny ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; Sewage/microbiology ; Wastewater/*analysis ; },
abstract = {Effective biological treatment of marine wastewater is not well-known. Accumulation of nitrogen and phosphorus from land-based effluent is a crucial cause of red-tide in marine systems. The purpose of the study is to reduce nitrogen and phosphorus in marine wastewater with a pilot plant-scale sequencing batch reactor (SBR) system by using marine sediment as eco-friendly and effective biological materials, and elucidate which bacterial strains in sludge from marine sediment influence the performance of SBR. By applying eco-friendly high efficiency marine sludge (eco-HEMS), the treatment performance was 15 m3 d-1 of treatment amount in 4.5 m3 of the reactor with the average removal efficiency of 89.3% for total nitrogen and 94.9% for total phosphorus at the optimal operation condition in summer. Moreover, the average removal efficiency was 84.0% for total nitrogen and 88.3% for total phosphorus in winter although biological treatment efficiency in winter is generally lower due to bacterial lower activity. These results were revealed by the DNA barcoding analysis of 16s rRNA amplicon sequencing of samples from the sludge in winter. The comparative analysis of the bacterial community composition in sludge at the high efficiency of the system showed the predominant genera Psychromonas (significantly increased to 45.6% relative abundance), Vibrio (13.3%), Gaetbulibacter (5.7%), and Psychroserpens (4.3%) in the 4 week adaptation after adding marine sediment, suggesting that those predominant bacteria influenced the treatment performance in winter.},
}
@article {pmid32424138,
year = {2020},
author = {Xie, Y and Arno, MC and Husband, JT and Torrent-Sucarrat, M and O'Reilly, RK},
title = {Manipulating the fluorescence lifetime at the sub-cellular scale via photo-switchable barcoding.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {2460},
pmid = {32424138},
issn = {2041-1723},
mesh = {A549 Cells ; Cell Survival ; Energy Transfer ; Fluorescence ; Humans ; Isomerism ; *Light ; Microscopy, Fluorescence/*methods ; Mitochondria/metabolism ; Nanogels/chemistry ; Polyethylene Glycols/chemistry ; Polyethyleneimine/chemistry ; Polymers/chemistry ; Subcellular Fractions ; },
abstract = {Fluorescent barcoding is a pivotal technique for the investigation of the microscale world, from information storage to the monitoring of dynamic biochemical processes. Using fluorescence lifetime as the readout modality offers more reproducible and quantitative outputs compared to conventional fluorescent barcoding, being independent of sample concentration and measurement methods. However, the use of fluorescence lifetime in this area has been limited by the lack of strategies that provide spatiotemporal manipulation of the coding process. In this study, we design a two-component photo-switchable nanogel that exhibits variable fluorescence lifetime upon photoisomerization-induced energy transfer processes through light irradiation. This remotely manipulated fluorescence lifetime property could be visually mapped using fluorescence lifetime imaging microscopy (FLIM), allowing selective storage and display of information at the microscale. Most importantly, the reversibility of this system further provides a strategy for minimizing the background influence in fluorescence lifetime imaging of live cells and sub-cellular organelles.},
}
@article {pmid32419363,
year = {2020},
author = {Liu, X and Liu, H and Zhang, C and Wei, A and Ao, H and Liu, F and Li, M and Guo, L and Ye, Q},
title = {Combination of c oxidase subunit I based deoxyribonucleic acid barcoding and HPLC techniques for the identification and quality evaluation of Pheretima aspergillum.},
journal = {Journal of separation science},
volume = {43},
number = {15},
pages = {2989-2995},
doi = {10.1002/jssc.202000283},
pmid = {32419363},
issn = {1615-9314},
support = {030041012//Innovation Team for Comprehensive Research and Application Development of the Genuine Crude Drugs in Sichuan/ ; },
mesh = {Animals ; Chromatography, High Pressure Liquid ; Cyclooxygenase 1/*metabolism ; DNA/*chemistry/metabolism ; Nucleosides/*analysis/genetics ; Oligochaeta/*chemistry/genetics ; Quality Control ; },
abstract = {This study aimed to identify Pheretima aspergillum (Guang-Pheretima) and its adulterants using the cytochrome c oxidase subunit I based deoxyribonucleic acid barcoding technology, and further to evaluate their quality using an optimized high-performance liquid chromatography method. For deoxyribonucleic acid barcoding identification, the Kimura-2-Parameter model was used to analyze genetic distance, and phylogenetic neighbor-joining tree was constructed for species identification of 20 labeled Guang-Pheretima samples. A high-performance liquid chromatography method was developed for the simultaneous determination of seven nucleoside components for quality evaluation. Compared with the GenBank database, 10 samples were identified as real Guang-Pheretima (P. aspergillum), and the others as the adulterants-Metaphire magna. The maximum intraspecific genetic distances of c oxidase subunit I sequence for P. aspergillum were smaller than the minimum interspecific genetic distances between P. aspergillum and M. magna. Ten P. aspergillum and 10 M. magna samples were clearly clustered in the neighbor-joining tree. The contents of seven nucleosides components in P. aspergillum were significantly higher than that in its adulterant-M. magna. The incidence of adulterants for Guang-Pheretima was high (up to 50%) with an alarming quality. This study provided a powerful idea for the quality evaluation of other highly valuable plant- or animal-derived products for safety concerns to avoid misidentification.},
}
@article {pmid32417496,
year = {2020},
author = {Grosse, M and Bakken, T and Nygren, A and Kongsrud, JA and Capa, M},
title = {Species delimitation analyses of NE Atlantic Chaetozone (Annelida, Cirratulidae) reveals hidden diversity among a common and abundant marine annelid.},
journal = {Molecular phylogenetics and evolution},
volume = {149},
number = {},
pages = {106852},
doi = {10.1016/j.ympev.2020.106852},
pmid = {32417496},
issn = {1095-9513},
mesh = {Animals ; Annelida/anatomy &amp; histology/*classification ; Aquatic Organisms/*classification ; Atlantic Ocean ; Bayes Theorem ; *Biodiversity ; Geography ; Phylogeny ; Species Specificity ; },
abstract = {The polychaetes of the family Cirratulidae (Annelida) are common inhabitants in continental shelf benthic environments and considered an important group of organisms in environmental monitoring surveys. The family represents a taxonomic and systematic challenge, as monophyly of genera and evolutionary relationships within the family remain to be explored in a proper phylogenetic framework. Bitentaculate cirratulids, especially the genus Chaetozone, form one of the most species-diverse group of polychaetes worldwide. In this study, we aimed at evaluating the species diversity of the genus Chaetozonein benthic environments in the North East Atlantic by molecular means. We tested whether traditional morphological diagnostic characters are able to discriminate between the species hypothesis after species delimitation analyses, and assessed monophyly of the genera involved. Two DNA markers were sequenced from about 200 specimens belonging to Chaetozone, Aphelochaeta, Dodecaceria, Cirriformia and Cirratulus - the universal mitochondrial barcoding region COI, and the D1-D2 regions of the nuclear 28S rRNA - and analyzed with Bayesian inference, Maximum Likelihood and the species delimitation methods mPTP and GMYC. The first phylogeny of the family Cirratulidae is inferred and the genera Chaetozone, Dodecaceria and Cirratulus are recovered monophyletic. A total of 14 clusters of sequences - corresponding to species of Chaetozone - were found in the study area, and only one of them is here referred to a nominal species, Chaetozone setosa. Our results reveal several species complexes in the genus Chaetozone, that some of these independent lineages are unnamed and undescribed, and that morphological diagnostic features are in most cases unable to discriminate between the most similar species.},
}
@article {pmid32416067,
year = {2020},
author = {Shu, S and Wu, HJ and Ge, JY and Zeid, R and Harris, IS and Jovanović, B and Murphy, K and Wang, B and Qiu, X and Endress, JE and Reyes, J and Lim, K and Font-Tello, A and Syamala, S and Xiao, T and Reddy Chilamakuri, CS and Papachristou, EK and D'Santos, C and Anand, J and Hinohara, K and Li, W and McDonald, TO and Luoma, A and Modiste, RJ and Nguyen, QD and Michel, B and Cejas, P and Kadoch, C and Jaffe, JD and Wucherpfennig, KW and Qi, J and Liu, XS and Long, H and Brown, M and Carroll, JS and Brugge, JS and Bradner, J and Michor, F and Polyak, K},
title = {Synthetic Lethal and Resistance Interactions with BET Bromodomain Inhibitors in Triple-Negative Breast Cancer.},
journal = {Molecular cell},
volume = {78},
number = {6},
pages = {1096-1113.e8},
pmid = {32416067},
issn = {1097-4164},
support = {R35 CA197623/CA/NCI NIH HHS/United States ; P01 CA080111/CA/NCI NIH HHS/United States ; F30 CA228208/CA/NCI NIH HHS/United States ; P50 CA168504/CA/NCI NIH HHS/United States ; U54 CA193461/CA/NCI NIH HHS/United States ; 20411/CRUK_/Cancer Research UK/United Kingdom ; },
mesh = {Animals ; Antineoplastic Agents/pharmacology ; Azepines/pharmacology ; Cell Cycle Proteins/metabolism ; Cell Line, Tumor ; Chromosomal Proteins, Non-Histone/metabolism ; Drug Resistance, Neoplasm/*genetics ; Female ; Gene Expression Regulation, Neoplastic/drug effects ; Humans ; Mice ; Mice, Inbred NOD ; Nuclear Proteins/metabolism ; Proteins/*antagonists &amp; inhibitors/metabolism ; Signal Transduction/drug effects ; Transcription Factors/metabolism ; Triazoles/pharmacology ; Triple Negative Breast Neoplasms/*drug therapy/genetics/metabolism ; },
abstract = {BET bromodomain inhibitors (BBDIs) are candidate therapeutic agents for triple-negative breast cancer (TNBC) and other cancer types, but inherent and acquired resistance to BBDIs limits their potential clinical use. Using CRISPR and small-molecule inhibitor screens combined with comprehensive molecular profiling of BBDI response and resistance, we identified synthetic lethal interactions with BBDIs and genes that, when deleted, confer resistance. We observed synergy with regulators of cell cycle progression, YAP, AXL, and SRC signaling, and chemotherapeutic agents. We also uncovered functional similarities and differences among BRD2, BRD4, and BRD7. Although deletion of BRD2 enhances sensitivity to BBDIs, BRD7 loss leads to gain of TEAD-YAP chromatin binding and luminal features associated with BBDI resistance. Single-cell RNA-seq, ATAC-seq, and cellular barcoding analysis of BBDI responses in sensitive and resistant cell lines highlight significant heterogeneity among samples and demonstrate that BBDI resistance can be pre-existing or acquired.},
}
@article {pmid32413320,
year = {2020},
author = {Bowling, S and Sritharan, D and Osorio, FG and Nguyen, M and Cheung, P and Rodriguez-Fraticelli, A and Patel, S and Yuan, WC and Fujiwara, Y and Li, BE and Orkin, SH and Hormoz, S and Camargo, FD},
title = {An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells.},
journal = {Cell},
volume = {181},
number = {6},
pages = {1410-1422.e27},
pmid = {32413320},
issn = {1097-4172},
support = {F31 CA235893/CA/NCI NIH HHS/United States ; R01 HL128850/HL/NHLBI NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; P01 HL131477/HL/NHLBI NIH HHS/United States ; U54 DK110805/DK/NIDDK NIH HHS/United States ; R01 DK123216/DK/NIDDK NIH HHS/United States ; R00 GM118910/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; CRISPR-Cas Systems/*genetics ; Cell Line ; Cell Lineage/*genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; Female ; Flow Cytometry/methods ; Hematopoietic Stem Cells/physiology ; Male ; Mice ; Transcriptome/*genetics ; Transduction, Genetic/methods ; },
abstract = {Tracing the lineage history of cells is key to answering diverse and fundamental questions in biology. Coupling of cell ancestry information with other molecular readouts represents an important goal in the field. Here, we describe the CRISPR array repair lineage tracing (CARLIN) mouse line and corresponding analysis tools that can be used to simultaneously interrogate the lineage and transcriptomic information of single cells in vivo. This model exploits CRISPR technology to generate up to 44,000 transcribed barcodes in an inducible fashion at any point during development or adulthood, is compatible with sequential barcoding, and is fully genetically defined. We have used CARLIN to identify intrinsic biases in the activity of fetal liver hematopoietic stem cell (HSC) clones and to uncover a previously unappreciated clonal bottleneck in the response of HSCs to injury. CARLIN also allows the unbiased identification of transcriptional signatures associated with HSC activity without cell sorting.},
}
@article {pmid32413273,
year = {2021},
author = {Parslow, BA and Schwarz, MP and Stevens, MI},
title = {Molecular diversity and species delimitation in the family Gasteruptiidae (Hymenoptera: Evanioidea).},
journal = {Genome},
volume = {64},
number = {3},
pages = {253-264},
doi = {10.1139/gen-2019-0186},
pmid = {32413273},
issn = {1480-3321},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Genetic Variation ; Phylogeny ; Wasps/*classification/genetics ; },
abstract = {Gasteruptiidae Ashmead is an easily recognised family of wasps with ∼589 described species worldwide. Although well characterised by traditional taxonomy, multiple authors have commented on the extreme morphological uniformity of the group, making species-level identification difficult. This problem is enhanced by the lack of molecular data and molecular phylogenetic research for the group. We used 187 cytochrome c oxidase subunit I (COI) barcodes to explore the efficiency of sequence data to delimitate species in Gasteruptiidae. We undertook a graphical and discussion-based comparison of six methods for species delimitation, with the success of methods judged based on known species boundaries and morphology. Both distance-based (ABGD and jMOTU threshold analysis) and tree-based (GMYC and PTP) methods compared across multiple parameters recovered variable molecular operational taxonomic units (MOTUs), ranging from 55 to 123 MOTUs. Tree-based methods tended to split known morphological species less than distance-based methods, with the single-threshold GMYC method the most concordant with known morphospecies. Our results suggest that the incorporation of molecular species delimitation techniques provides a powerful tool to assist in the interpretation of species and help direct informed decisions with taxonomic uncertainty in the family.},
}
@article {pmid32412006,
year = {2020},
author = {Camacho-Oliveira, RB and Daneluz, CM and do Prado, FD and Utsunomia, R and Rodrigues, CE and Foresti, F and Porto-Foresti, F},
title = {DNA barcode reveals the illegal trade of rays commercialized in fishmongers in Brazil.},
journal = {Forensic science international. Synergy},
volume = {2},
number = {},
pages = {95-97},
pmid = {32412006},
issn = {2589-871X},
abstract = {Sequences of the mitochondrial gene COI (DNA Barcode) were used to identify species of rays and skates commercialized in fishmongers in Brazil. The comparisons of the obtained sequences with previously published data available in NCBI and BOLD showed that the fish products corresponded to four species, Hypanus dipterurus, Potamotrygon motoro, Paratrygon ajereba and Gymnura altavela, the last of which is classified as vulnerable according to the IUCN Red List and therefore should not be marketed in accordance with the MMA ordinance 445/2015.},
}
@article {pmid32407998,
year = {2020},
author = {Uncu, AO and Uncu, AT},
title = {A barcode-DNA analysis method for the identification of plant oil adulteration in milk and dairy products.},
journal = {Food chemistry},
volume = {326},
number = {},
pages = {126986},
doi = {10.1016/j.foodchem.2020.126986},
pmid = {32407998},
issn = {1873-7072},
mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA, Plant/*analysis/genetics/metabolism ; Dairy Products/*analysis ; Electrophoresis, Capillary/*methods ; Milk/*chemistry ; Plant Oils/*chemistry/metabolism ; Plastids/genetics ; Polymerase Chain Reaction ; Glycine max/genetics ; Yogurt/analysis ; Zea mays/genetics ; },
abstract = {In the present work, a barcode-DNA analysis method is described for the detection of plant oil adulteration in milk and dairy products. The method relies on the fact that plant DNA should not be present in readily detectable amounts in a dairy product unless it contains undeclared plant material. Thus, a universal plant barcode is chosen as the target to be amplified from dairy samples. Accordingly, barcode PCR-CE (PCR-capillary electrophoresis) assays are described, which do not require preliminary information on the species source of the adulterant oil type. Two PCR-CE assays, one operating on the plastid trnL (UAA) intron and the other targeting its inner P6 loop in nested format, were shown to detect corn, soybean, rapeseed and sunflower oils in clarified butter, milk and yogurt. Both barcodes are robustly amplified with extremely conserved primers. While the intron provides the species discrimination ability, the P6 loop provides superior detection sensitivity.},
}
@article {pmid32406757,
year = {2020},
author = {Nugent, CM and Elliott, TA and Ratnasingham, S and Adamowicz, SJ},
title = {coil: an R package for cytochrome c oxidase I (COI) DNA barcode data cleaning, translation, and error evaluation.},
journal = {Genome},
volume = {63},
number = {6},
pages = {291-305},
doi = {10.1139/gen-2019-0206},
pmid = {32406757},
issn = {1480-3321},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Frameshift Mutation/genetics ; Humans ; *Phylogeny ; Pseudogenes/*genetics ; },
abstract = {Biological conclusions based on DNA barcoding and metabarcoding analyses can be strongly influenced by the methods utilized for data generation and curation, leading to varying levels of success in the separation of biological variation from experimental error. The 5' region of cytochrome c oxidase subunit I (COI-5P) is the most common barcode gene for animals, with conserved structure and function that allows for biologically informed error identification. Here, we present coil (https://CRAN.R-project.org/package=coil), an R package for the pre-processing and frameshift error assessment of COI-5P animal barcode and metabarcode sequence data. The package contains functions for placement of barcodes into a common reading frame, accurate translation of sequences to amino acids, and highlighting insertion and deletion errors. The analysis of 10 000 barcode sequences of varying quality demonstrated how coil can place barcode sequences in reading frame and distinguish sequences containing indel errors from error-free sequences with greater than 97.5% accuracy. Package limitations were tested through the analysis of COI-5P sequences from the plant and fungal kingdoms as well as the analysis of potential contaminants: nuclear mitochondrial pseudogenes and Wolbachia COI-5P sequences. Results demonstrated that coil is a strong technical error identification method but is not reliable for detecting all biological contaminants.},
}
@article {pmid32406148,
year = {2020},
author = {Kim, JB and Lee, SY and Min, NG and Lee, SY and Kim, SH},
title = {Plasmonic Janus Microspheres Created from Pickering Emulsion Drops.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {32},
number = {26},
pages = {e2001384},
doi = {10.1002/adma.202001384},
pmid = {32406148},
issn = {1521-4095},
support = {NRF-2019K1A3A1A14012962//National Research Foundation/ ; NRF-2015K1A1A2033054//National Research Foundation/ ; //Ministry of Science, ICT and Future Planning/ ; NRF-2015K1A1A2033054//National Research Foundation of Korea/ ; },
abstract = {Metal nanostructures have been created in a film format to develop unique plasmonic properties. Here, well-defined metal nanostructures are designed on the surface of microspheres to provide plasmonic microgranules. As conventional techniques are inadequate for nanofabrication on spherical surfaces, photocurable emulsion drops with a regular array of silica particles are employed at the interface to create periodic nanostructures. The silica particles, originating from the dispersed phase, fully cover the interface by forming a non-close-packed hexagonal array after drop generation, and slowly protrude to the continuous phase during aging while their interparticle separation decreases. Therefore, hexagonal arrays of spherical dimples with controlled geometry and separation are created on the surface of microspheres by photocuring the drops and removing the particles. Directional deposition of either aluminum or gold results in a continuous film with a hexagonal array of holes on the outermost surface and isolated curved disks in dimples, which renders the hemisphere of microspheres plasmonically colored. The resonant wavelength is controlled by adjusting the aging time, metal thickness, and size of silica particles, providing various plasmonic colors. This granular format of the plasmonic Janus microspheres will open a new avenue of optical applications including active color pixels, optical barcodes, and microsensors.},
}
@article {pmid32404192,
year = {2020},
author = {Zhao, Y and Zhang, WY and Wang, RL and Niu, DL},
title = {Divergent domains of 28S ribosomal RNA gene: DNA barcodes for molecular classification and identification of mites.},
journal = {Parasites &amp; vectors},
volume = {13},
number = {1},
pages = {251},
pmid = {32404192},
issn = {1756-3305},
support = {81471972//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Mites/*classification/*genetics ; *Phylogeny ; RNA, Ribosomal, 28S/*genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The morphological and molecular identification of mites is challenging due to the large number of species, the microscopic size of the organisms, diverse phenotypes of the same species, similar morphology of different species and a shortage of molecular data.<br><br>METHODS: Nine medically important mite species belonging to six families, i.e. Demodex folliculorum, D. brevis, D. canis, D. caprae, Sarcoptes scabiei canis, Psoroptes cuniculi, Dermatophagoides farinae, Cheyletus malaccensis and Ornithonyssus bacoti, were collected and subjected to DNA barcoding. Sequences of cox1, 16S and 12S mtDNA, as well as ITS, 18S and 28S rDNA from mites were retrieved from GenBank and used as candidate genes. Sequence alignment and analysis identified 28S rDNA as the suitable target gene. Subsequently, universal primers of divergent domains were designed for molecular identification of 125 mite samples. Finally, the universality of the divergent domains with high identification efficiency was evaluated in Acari to screen DNA barcodes for mites.<br><br>RESULTS: Domains D5 (67.65%), D6 (62.71%) and D8 (77.59%) of the 28S rRNA gene had a significantly higher sequencing success rate, compared to domains D2 (19.20%), D3 (20.00%) and D7 (15.12%). The successful divergent domains all matched the closely-related species in GenBank with an identity of 74-100% and a coverage rate of 92-100%. Phylogenetic analysis also supported this result. Moreover, the three divergent domains had their own advantages. D5 had the lowest intraspecies divergence (0-1.26%), D6 had the maximum barcoding gap (10.54%) and the shortest sequence length (192-241 bp), and D8 had the longest indels (241 bp). Further universality analysis showed that the primers of the three divergent domains were suitable for identification across 225 species of 40 families in Acari.<br><br>CONCLUSIONS: This study confirmed that domains D5, D6 and D8 of 28S rDNA are universal DNA barcodes for molecular classification and identification of mites. 28S rDNA, as a powerful supplement for cox1 mtDNA 5'-end 648-bp fragment, recommended by the International Barcode of Life (IBOL), will provide great potential in molecular identification of mites in future studies because of its universality.},
}
@article {pmid32403949,
year = {2020},
author = {Tucker, NR and Chaffin, M and Fleming, SJ and Hall, AW and Parsons, VA and Bedi, KC and Akkad, AD and Herndon, CN and Arduini, A and Papangeli, I and Roselli, C and Aguet, F and Choi, SH and Ardlie, KG and Babadi, M and Margulies, KB and Stegmann, CM and Ellinor, PT},
title = {Transcriptional and Cellular Diversity of the Human Heart.},
journal = {Circulation},
volume = {142},
number = {5},
pages = {466-482},
pmid = {32403949},
issn = {1524-4539},
support = {K24 HL105780/HL/NHLBI NIH HHS/United States ; R01 HL092577/HL/NHLBI NIH HHS/United States ; K01 HL140187/HL/NHLBI NIH HHS/United States ; R01 HL128914/HL/NHLBI NIH HHS/United States ; R01 HL105993/HL/NHLBI NIH HHS/United States ; },
mesh = {Adipocytes/metabolism ; Adult ; Aged ; Cardiovascular Agents/pharmacology/therapeutic use ; Endothelial Cells/classification/metabolism ; Fibroblasts/classification/metabolism ; Gene Ontology ; Heart/innervation ; Heart Atria/cytology ; Heart Diseases/drug therapy ; Heart Ventricles/cytology ; Homeostasis ; Humans ; Lymphocyte Subsets/metabolism ; Macrophages/classification/metabolism ; Microfluidic Analytical Techniques ; Middle Aged ; Myocardium/*cytology/metabolism ; Myocytes, Cardiac/metabolism ; Myocytes, Smooth Muscle/metabolism ; Pericytes/metabolism ; RNA-Seq ; Sex Characteristics ; Single-Cell Analysis ; *Transcription, Genetic ; Transcriptome ; },
abstract = {BACKGROUND: The human heart requires a complex ensemble of specialized cell types to perform its essential function. A greater knowledge of the intricate cellular milieu of the heart is critical to increase our understanding of cardiac homeostasis and pathology. As recent advances in low-input RNA sequencing have allowed definitions of cellular transcriptomes at single-cell resolution at scale, we have applied these approaches to assess the cellular and transcriptional diversity of the nonfailing human heart.<br><br>METHODS: Microfluidic encapsulation and barcoding was used to perform single nuclear RNA sequencing with samples from 7 human donors, selected for their absence of overt cardiac disease. Individual nuclear transcriptomes were then clustered based on transcriptional profiles of highly variable genes. These clusters were used as the basis for between-chamber and between-sex differential gene expression analyses and intersection with genetic and pharmacologic data.<br><br>RESULTS: We sequenced the transcriptomes of 287 269 single cardiac nuclei, revealing 9 major cell types and 20 subclusters of cell types within the human heart. Cellular subclasses include 2 distinct groups of resident macrophages, 4 endothelial subtypes, and 2 fibroblast subsets. Comparisons of cellular transcriptomes by cardiac chamber or sex reveal diversity not only in cardiomyocyte transcriptional programs but also in subtypes involved in extracellular matrix remodeling and vascularization. Using genetic association data, we identified strong enrichment for the role of cell subtypes in cardiac traits and diseases. Intersection of our data set with genes on cardiac clinical testing panels and the druggable genome reveals striking patterns of cellular specificity.<br><br>CONCLUSIONS: Using large-scale single nuclei RNA sequencing, we defined the transcriptional and cellular diversity in the normal human heart. Our identification of discrete cell subtypes and differentially expressed genes within the heart will ultimately facilitate the development of new therapeutics for cardiovascular diseases.},
}
@article {pmid32403314,
year = {2020},
author = {Monti, MM and Ruocco, M and Grobbelaar, E and Pedata, PA},
title = {Morphological and Molecular Characterization of Lema bilineata (Germar), a New Alien Invasive Leaf Beetle for Europe, with Notes on the Related Species Lema daturaphila Kogan &amp; Goeden.},
journal = {Insects},
volume = {11},
number = {5},
pages = {},
pmid = {32403314},
issn = {2075-4450},
support = {URCOFI Project//Regione Campania/ ; the Department of Science and Innovation and the Department of Agriculture, Land Reform and Rural Development//Agricultural Research Council/ ; },
abstract = {Lema bilineata (Germar) is an alien invasive leaf beetle (Coleoptera: Chrysomelidae) first recorded in Europe in the summer of 2017 in the province of Naples (Campania, Italy). It occurs on both cultivated plants (Nicotiana tabacum) and weeds (Salpichroa origanifolia and Datura spp.). Information on morphological characters, color variation and molecular data are deficient for L. bilineata, as is the case for most Lema species. These data could be useful to discriminate between this species and the closely related Lema daturaphila Kogan &amp; Goeden, which has the same potential to become an alien invasive species. In this paper, color variation in adults and the morphology of the aedeagi and spermathecae of the two species are documented and compared, including micrographic images. Additional data on the current distribution of L. bilineata in Campania is also provided. The cytochrome c oxidase I (COI) barcoding region of both Italian and South African specimens of L. bilineata, as well as South African specimens of L. daturaphila, was sequenced. A preliminary phylogenetic tree is provided, based on the sequences available for Lema species.},
}
@article {pmid32398457,
year = {2020},
author = {Nazaraliyev, A and Richard, E and Sawai, CM},
title = {In-vivo differentiation of adult hematopoietic stem cells from a single-cell point of view.},
journal = {Current opinion in hematology},
volume = {27},
number = {4},
pages = {241-247},
doi = {10.1097/MOH.0000000000000587},
pmid = {32398457},
issn = {1531-7048},
mesh = {Adult ; Adult Stem Cells/cytology/*metabolism ; *Cell Differentiation ; Genomics ; Hematopoietic Stem Cells/cytology/*metabolism ; Humans ; RNA-Seq ; },
abstract = {PURPOSE OF REVIEW: Although hematopoietic stem cell (HSC) function has long been studied by transplantation assays, this does not reflect what HSCs actually do in their native context. Here, we review recent technologic advances that facilitate the study of HSCs in their native context focusing on inducible HSC-specific lineage tracing and inference of hematopoietic trajectories through single-cell RNA sequencing (scRNA-Seq).<br><br>RECENT FINDINGS: Lineage tracing of HSCs at the population level using multiple systems has suggested that HSCs make a major contribution to steady-state hematopoiesis. Although several genetic systems and novel methods for lineage tracing individual hematopoietic clones have been described, the technology for tracking these cellular barcodes (in particular mutations or insertion sites) is still in its infancy. Thus, lineage tracing of HSC clones in the adult bone marrow remains elusive. Static snapshots of scRNA-Seq of hematopoietic populations have captured the heterogeneity of transcriptional profiles of HSCs and progenitors, with some cells displaying a unilineage signature as well as others with bi or multipotent lineage profiles. Kinetic analysis using HSC-specific lineage tracing combined with scRNA-Seq confirmed this heterogeneity of progenitor populations and revealed a rapid and early emergence of megakaryocytic progeny, followed by erythroid and myeloid lineages, whereas lymphoid differentiation emerged last.<br><br>SUMMARY: New approaches to study HSCs both in vivo through lineage tracing and at a high-resolution molecular level through scRNA-Seq are providing key insight into HSC differentiation in the absence of transplantation. Recent studies using these approaches are discussed here. These studies pave the way for integration of in-vivo clonal analysis of HSC behavior over time with single-cell sequencing data, including but not limited to transcriptomic, proteomic, and epigenomic, to establish a comprehensive molecular and cellular map of hematopoiesis.},
}
@article {pmid32394818,
year = {2020},
author = {Shi, R and Huang, M and Wang, J and He, C and Ying, X and Xiong, X and Xiong, X},
title = {Molecular identification of dried squid products sold in China using DNA barcoding and SYBR green real time PCR.},
journal = {Food additives &amp; contaminants. Part A, Chemistry, analysis, control, exposure &amp; risk assessment},
volume = {37},
number = {7},
pages = {1061-1074},
doi = {10.1080/19440049.2020.1746411},
pmid = {32394818},
issn = {1944-0057},
mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; Decapodiformes/*genetics ; *Real-Time Polymerase Chain Reaction ; Seafood/*analysis ; },
abstract = {Dried squid products are popular in China as a snack food, side dishes, or refreshments, and the market appeal can be reflected by the high price that occasionally reaches 497 RMB per kg. However, the absence of harmonisation around the definition of squid, as well as the problems with visual inspection for processed seafood products, make alternative species substitution for dried squid products a frequent occurrence. The aim of the present study was to apply a DNA barcoding approach for species identification of 48 dried squid products collected from the largest online shopping platform in China. Moreover, we also developed a novel SYBR green real-time PCR assay (simplex and duplex followed by a melting curve analysis) specific for Illex argentinus and Todarodes pacificus based on cytochrome C oxidase subunit I (COI) gene. Results highlighted the successful DNA extraction and PCR amplification of a 655 bp COI gene fragment from all products. A maximum similarity value in the range of 98-100% was obtained for all readable sequences using the BOLD and BLAST public databases and four species (Dosidicus gigas, Uroteuthis edulis, I. argentinus, and T. pacificus) were identified. The specificity of the designed primer sets was confirmed against 23 non-target species, and the newly developed methods were successfully applied to screen I. argentinus and T. pacificus in dried squid products. Overall, DNA barcoding is a robust tool for seafood species identification and the novel method is effective in screening I. argentinus and T. pacificus in food products.},
}
@article {pmid32394392,
year = {2020},
author = {Zollinger, DR and Lingle, SE and Sorg, K and Beechem, JM and Merritt, CR},
title = {GeoMx™ RNA Assay: High Multiplex, Digital, Spatial Analysis of RNA in FFPE Tissue.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2148},
number = {},
pages = {331-345},
pmid = {32394392},
issn = {1940-6029},
mesh = {Gene Expression Profiling/*methods ; Humans ; In Situ Hybridization/*methods ; Paraffin Embedding/methods ; RNA/*genetics/isolation &amp; purification ; Spatial Analysis ; Tissue Fixation/methods ; },
abstract = {RNA in situ hybridization (ISH) is a widely used technique for the localization of mRNA in tissues. Limitations to traditional ISH include the number of targets that can be analyzed concurrently and the ability for many of these assays to be used in formalin-fixed, paraffin-embedded tissues (FFPE). Here, we describe the GeoMx™ RNA assay that is capable of the highly multiplexed detection of mRNA targets in FFPE tissues. This assay utilizes ISH probes linked to indexing oligo barcodes via a photocleavable linker and the GeoMx Digital Spatial Profiler (DSP) Instrument to enable profiling of RNA targets in a region-of-interest-based method. In brief, 5 μm FFPE sections are dewaxed, target retrieved, digested with proteinase K, post-fixed, and then incubated overnight with GeoMx RNA detection probes. Stringent washes are performed followed by the addition of fluorescently labeled antibodies for use as morphology markers. User-defined regions of interest are then profiled on the GeoMx DSP through region-specific cleaving and collecting the photocleaved indexing oligos. Cleaved indices are then quantified using NanoString nCounter[®] Technology generating digital quantification of RNA expression with spatial context.},
}
@article {pmid32393766,
year = {2020},
author = {Ge, JY and Shu, S and Kwon, M and Jovanović, B and Murphy, K and Gulvady, A and Fassl, A and Trinh, A and Kuang, Y and Heavey, GA and Luoma, A and Paweletz, C and Thorner, AR and Wucherpfennig, KW and Qi, J and Brown, M and Sicinski, P and McDonald, TO and Pellman, D and Michor, F and Polyak, K},
title = {Acquired resistance to combined BET and CDK4/6 inhibition in triple-negative breast cancer.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {2350},
pmid = {32393766},
issn = {2041-1723},
support = {R35 CA197623/CA/NCI NIH HHS/United States ; P01 CA080111/CA/NCI NIH HHS/United States ; F30 CA228208/CA/NCI NIH HHS/United States ; R01 CA213404/CA/NCI NIH HHS/United States ; U54 CA193461/CA/NCI NIH HHS/United States ; P50 CA168504/CA/NCI NIH HHS/United States ; R01 CA202634/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Azepines/pharmacology ; Cell Cycle Checkpoints/drug effects ; Cell Proliferation/drug effects ; Clone Cells ; Cyclin-Dependent Kinase 4/*antagonists &amp; inhibitors/metabolism ; Cyclin-Dependent Kinase 6/*antagonists &amp; inhibitors/metabolism ; DNA, Neoplasm/metabolism ; *Drug Resistance, Neoplasm/drug effects ; Drug Synergism ; Female ; Gene Expression Regulation, Neoplastic/drug effects ; Mice ; Models, Biological ; Mutation/genetics ; Paclitaxel/pharmacology ; Piperazines/pharmacology ; Ploidies ; Proteins/*antagonists &amp; inhibitors/metabolism ; Pyridines/pharmacology ; Retinoblastoma Protein/genetics/metabolism ; Treatment Outcome ; Triazoles/pharmacology ; Triple Negative Breast Neoplasms/*drug therapy/genetics ; Up-Regulation/drug effects/genetics ; },
abstract = {BET inhibitors are promising therapeutic agents for the treatment of triple-negative breast cancer (TNBC), but the rapid emergence of resistance necessitates investigation of combination therapies and their effects on tumor evolution. Here, we show that palbociclib, a CDK4/6 inhibitor, and paclitaxel, a microtubule inhibitor, synergize with the BET inhibitor JQ1 in TNBC lines. High-complexity DNA barcoding and mathematical modeling indicate a high rate of de novo acquired resistance to these drugs relative to pre-existing resistance. We demonstrate that the combination of JQ1 and palbociclib induces cell division errors, which can increase the chance of developing aneuploidy. Characterizing acquired resistance to combination treatment at a single cell level shows heterogeneous mechanisms including activation of G1-S and senescence pathways. Our results establish a rationale for further investigation of combined BET and CDK4/6 inhibition in TNBC and suggest novel mechanisms of action for these drugs and new vulnerabilities in cells after emergence of resistance.},
}
@article {pmid32391031,
year = {2020},
author = {Ji, Y and Liu, C and Yang, J and Jin, L and Yang, Z and Yang, JB},
title = {Ultra-Barcoding Discovers a Cryptic Species in Paris yunnanensis (Melanthiaceae), a Medicinally Important Plant.},
journal = {Frontiers in plant science},
volume = {11},
number = {},
pages = {411},
pmid = {32391031},
issn = {1664-462X},
abstract = {Ultra-barcoding is a technique using whole plastomes and nuclear ribosomal DNA (nrDNA) sequences for plant species identification. Paris yunnanensis is a medicinal plant of great economic importance for the pharmaceutical industry. However, the alpha taxonomy of P. yunnanensis is still uncertain, hindering effective conservation and management of the germplasm. To resolve long-standing taxonomic disputes regarding this species, we newly generated the complete plastomes and nrDNA sequences from 22 P. yunnanensis accessions. Ultra-barcoding analyses suggest that P. yunnanensis as currently circumscribed is made up of two distinct genetic lineages, corresponding to the two phenotypes ("typical" and "high stem" form) identified early in our study. With distinct morphologies and distribution, the "high stem" form should be recognized as a previously unrecognized species; here it is described as a new species, P. liiana sp. nov. Moreover, the ultra-barcoding data do not support treatment of P. yunnanensis as a conspecific variety under Paris polyphylla. Our study represents a guiding practical application of ultra-barcoding for discovery of cryptic species in taxonomically challenging plant taxa. The findings highlight the great potential of ultra-barcoding as an effective tool for resolving perplexing problems in plant taxonomy.},
}
@article {pmid32390756,
year = {2020},
author = {Atherton, S and Jondelius, U},
title = {Biodiversity between sand grains: Meiofauna composition across southern and western Sweden assessed by metabarcoding.},
journal = {Biodiversity data journal},
volume = {8},
number = {},
pages = {e51813},
pmid = {32390756},
issn = {1314-2828},
abstract = {The meiofauna is an important part of the marine ecosystem, but its composition and distribution patterns are relatively unexplored. Here we assessed the biodiversity and community structure of meiofauna from five locations on the Swedish western and southern coasts using a high-throughput DNA sequencing (metabarcoding) approach. The mitochondrial cytochrome oxidase 1 (COI) mini-barcode and nuclear 18S small ribosomal subunit (18S) V1-V2 region were amplified and sequenced using Illumina MiSeq technology. Our analyses revealed a higher number of species than previously found in other areas: thirteen samples comprising 6.5 dm[3] sediment revealed 708 COI and 1,639 18S metazoan OTUs. Across all sites, the majority of the metazoan biodiversity was assigned to Arthropoda, Nematoda and Platyhelminthes. Alpha and beta diversity measurements showed that community composition differed significantly amongst sites. OTUs initially assigned to Acoela, Gastrotricha and the two Platyhelminthes sub-groups Macrostomorpha and Rhabdocoela were further investigated and assigned to species using a phylogeny-based taxonomy approach. Our results demonstrate that there is great potential for discovery of new meiofauna species even in some of the most extensively studied locations.},
}
@article {pmid32390740,
year = {2020},
author = {Fernandez-Triana, J and Shaw, MR and Boudreault, C and Beaudin, M and Broad, GR},
title = {Annotated and illustrated world checklist of Microgastrinae parasitoid wasps (Hymenoptera, Braconidae).},
journal = {ZooKeys},
volume = {920},
number = {},
pages = {1-1090},
pmid = {32390740},
issn = {1313-2989},
abstract = {A checklist of world species of Microgastrinae parasitoid wasps (Hymenoptera: Braconidae) is provided. A total of 81 genera and 2,999 extant species are recognized as valid, including 36 nominal species that are currently considered as species inquirendae. Two genera are synonymized under Apanteles. Nine lectotypes are designated. A total of 318 new combinations, three new replacement names, three species name amendments, and seven species status revised are proposed. Additionally, three species names are treated as nomina dubia, and 52 species names are considered as unavailable names (including 14 as nomina nuda). A total of three extinct genera and 12 extinct species are also listed. Unlike in many previous treatments of the subfamily, tribal concepts are judged to be inadequate, so genera are listed alphabetically. Brief diagnoses of all Microgastrinae genera, as understood in this paper, are presented. Illustrations of all extant genera (at least one species per genus, usually more) are included to showcase morphological diversity. Primary types of Microgastrinae are deposited in 108 institutions worldwide, although 76% are concentrated in 17 collections. Localities of primary types, in 138 countries, are reported. Recorded species distributions are listed by biogeographical region and by country. Microgastrine wasps are recorded from all continents except Antarctica; specimens can be found in all major terrestrial ecosystems, from 82°N to 55°S, and from sea level up to at least 4,500 m a.s.l. The Oriental (46) and Neotropical (43) regions have the largest number of genera recorded, whereas the Palaearctic region (28) is the least diverse. Currently, the highest species richness is in the Palearctic region (827), due to more historical study there, followed by the Neotropical (768) and Oriental (752) regions, which are expected to be the most species rich. Based on ratios of Lepidoptera and Microgastrinae species from several areas, the actual world diversity of Microgastrinae is expected to be between 30,000-50,000 species; although these ratios were mostly based on data from temperate areas and thus must be treated with caution, the single tropical area included had a similar ratio to the temperate ones. Almost 45,000 specimens of Microgastrinae from 67 different genera (83% of microgastrine genera) have complete or partial DNA barcode sequences deposited in the Barcode of Life Data System; the DNA barcodes represent 3,545 putative species or Barcode Index Numbers (BINs), as estimated from the molecular data. Information on the number of sequences and BINs per genus are detailed in the checklist. Microgastrinae hosts are here considered to be restricted to Eulepidoptera, i.e., most of the Lepidoptera except for the four most basal superfamilies (Micropterigoidea, Eriocranioidea, Hepialoidea and Nepticuloidea), with all previous literature records of other insect orders and those primitive Lepidoptera lineages being considered incorrect. The following nomenclatural acts are proposed: 1) Two genera are synonymyzed under Apanteles: Cecidobracon Kieffer &amp; Jörgensen, 1910, new synonym and Holcapanteles Cameron, 1905, new synonym; 2) Nine lectotype designations are made for Alphomelon disputabile (Ashmead, 1900), Alphomelon nigriceps (Ashmead, 1900), Cotesia salebrosa (Marshall, 1885), Diolcogaster xanthaspis (Ashmead, 1900), Dolichogenidea ononidis (Marshall, 1889), Glyptapanteles acraeae (Wilkinson, 1932), Glyptapanteles guyanensis (Cameron, 1911), Glyptapanteles militaris (Walsh, 1861), and Pseudapanteles annulicornis Ashmead, 1900; 3) Three new replacement names are a) Diolcogaster aurangabadensis Fernandez-Triana, replacing Diolcogaster indicus (Rao &amp; Chalikwar, 1970) [nec Diolcogaster indicus (Wilkinson, 1927)], b) Dolichogenidea incystatae Fernandez-Triana, replacing Dolichogenidea lobesia Liu &amp; Chen, 2019 [nec Dolichogenidea lobesia Fagan-Jeffries &amp; Austin, 2019], and c) Microplitis vitobiasi Fernandez-Triana, replacing Microplitis variicolor Tobias, 1964 [nec Microplitis varicolor Viereck, 1917]; 4) Three names amended are Apanteles irenecarrilloae Fernandez-Triana, 2014, Cotesia ayerzai (Brèthes, 1920), and Cotesia riverai (Porter, 1916); 5) Seven species have their status revised: Cotesia arctica (Thomson, 1895), Cotesia okamotoi (Watanabe, 1921), Cotesia ukrainica (Tobias, 1986), Dolichogenidea appellator (Telenga, 1949), Dolichogenidea murinanae (Capek &amp; Zwölfer, 1957), Hypomicrogaster acarnas Nixon, 1965, and Nyereria nigricoxis (Wilkinson, 1932); 6) New combinations are given for 318 species: Alloplitis congensis, Alloplitis detractus, Apanteles asphondyliae, Apanteles braziliensis, Apanteles sulciscutis, Choeras aper, Choeras apollion, Choeras daphne, Choeras fomes, Choeras gerontius, Choeras helle, Choeras irates, Choeras libanius, Choeras longiterebrus, Choeras loretta, Choeras recusans, Choeras sordidus, Choeras stenoterga, Choeras superbus, Choeras sylleptae, Choeras vacillatrix, Choeras vacillatropsis, Choeras venilia, Cotesia asavari, Cotesia bactriana, Cotesia bambeytripla, Cotesia berberidis, Cotesia bhairavi, Cotesia biezankoi, Cotesia bifida, Cotesia caligophagus, Cotesia cheesmanae, Cotesia compressithorax, Cotesia delphinensis, Cotesia effrena, Cotesia euphobetri, Cotesia elaeodes, Cotesia endii, Cotesia euthaliae, Cotesia exelastisae, Cotesia hiberniae, Cotesia hyperion, Cotesia hypopygialis, Cotesia hypsipylae, Cotesia jujubae, Cotesia lesbiae, Cotesia levigaster, Cotesia lizeri, Cotesia malevola, Cotesia malshri, Cotesia menezesi, Cotesia muzaffarensis, Cotesia neptisis, Cotesia nycteus, Cotesia oeceticola, Cotesia oppidicola, Cotesia opsiphanis, Cotesia pachkuriae, Cotesia paludicolae, Cotesia parbhanii, Cotesia parvicornis, Cotesia pratapae, Cotesia prozorovi, Cotesia pterophoriphagus, Cotesia radiarytensis, Cotesia rangii, Cotesia riverai, Cotesia ruficoxis, Cotesia senegalensis, Cotesia seyali, Cotesia sphenarchi, Cotesia sphingivora, Cotesia transuta, Cotesia turkestanica, Diolcogaster abengouroui, Diolcogaster agama, Diolcogaster ambositrensis, Diolcogaster anandra, Diolcogaster annulata, Diolcogaster bambeyi, Diolcogaster bicolorina, Diolcogaster cariniger, Diolcogaster cincticornis, Diolcogaster cingulata, Diolcogaster coronata, Diolcogaster coxalis, Diolcogaster dipika, Diolcogaster earina, Diolcogaster epectina, Diolcogaster epectinopsis, Diolcogaster grangeri, Diolcogaster heterocera, Diolcogaster homocera, Diolcogaster indica, Diolcogaster insularis, Diolcogaster kivuana, Diolcogaster mediosulcata, Diolcogaster megaulax, Diolcogaster neglecta, Diolcogaster nigromacula, Diolcogaster palpicolor, Diolcogaster persimilis, Diolcogaster plecopterae, Diolcogaster plutocongoensis, Diolcogaster psilocnema, Diolcogaster rufithorax, Diolcogaster semirufa, Diolcogaster seyrigi, Diolcogaster subtorquata, Diolcogaster sulcata, Diolcogaster torquatiger, Diolcogaster tristiculus, Diolcogaster turneri, Diolcogaster vulcana, Diolcogaster wittei, Distatrix anthedon, Distatrix cerales, Distatrix cuspidalis, Distatrix euproctidis, Distatrix flava, Distatrix geometrivora, Distatrix maia, Distatrix tookei, Distatrix termina, Distatrix simulissima, Dolichogenidea agamedes, Dolichogenidea aluella, Dolichogenidea argiope, Dolichogenidea atreus, Dolichogenidea bakeri, Dolichogenidea basiflava, Dolichogenidea bersa, Dolichogenidea biplagae, Dolichogenidea bisulcata, Dolichogenidea catonix, Dolichogenidea chrysis, Dolichogenidea coffea, Dolichogenidea coretas, Dolichogenidea cyane, Dolichogenidea diaphantus, Dolichogenidea diparopsidis, Dolichogenidea dryas, Dolichogenidea earterus, Dolichogenidea ensiger, Dolichogenidea eros, Dolichogenidea evadne, Dolichogenidea falcator, Dolichogenidea gelechiidivoris, Dolichogenidea gobica, Dolichogenidea hyalinis, Dolichogenidea iriarte, Dolichogenidea lakhaensis, Dolichogenidea lampe, Dolichogenidea laspeyresiella, Dolichogenidea latistigma, Dolichogenidea lebene, Dolichogenidea lucidinervis, Dolichogenidea malacosomae, Dolichogenidea maro, Dolichogenidea mendosae, Dolichogenidea monticola, Dolichogenidea nigra, Dolichogenidea olivierellae, Dolichogenidea parallelis, Dolichogenidea pelopea, Dolichogenidea pelops, Dolichogenidea phaenna, Dolichogenidea pisenor, Dolichogenidea roepkei, Dolichogenidea scabra, Dolichogenidea statius, Dolichogenidea stenotelas, Dolichogenidea striata, Dolichogenidea wittei, Exoryza asotae, Exoryza belippicola, Exoryza hylas, Exoryza megagaster, Exoryza oryzae, Glyptapanteles aggestus, Glyptapanteles agynus, Glyptapanteles aithos, Glyptapanteles amenophis, Glyptapanteles antarctiae, Glyptapanteles anubis, Glyptapanteles arginae, Glyptapanteles argus, Glyptapanteles atylana, Glyptapanteles badgleyi, Glyptapanteles bataviensis, Glyptapanteles bistonis, Glyptapanteles borocerae, Glyptapanteles cacao, Glyptapanteles cadei, Glyptapanteles cinyras, Glyptapanteles eryphanidis, Glyptapanteles euproctisiphagus, Glyptapanteles eutelus, Glyptapanteles fabiae, Glyptapanteles fulvigaster, Glyptapanteles fuscinervis, Glyptapanteles gahinga, Glyptapanteles globatus, Glyptapanteles glyphodes, Glyptapanteles guierae, Glyptapanteles horus, Glyptapanteles intricatus, Glyptapanteles lamprosemae, Glyptapanteles lefevrei, Glyptapanteles leucotretae, Glyptapanteles lissopleurus, Glyptapanteles madecassus, Glyptapanteles marquesi, Glyptapanteles melanotus, Glyptapanteles melissus, Glyptapanteles merope, Glyptapanteles naromae, Glyptapanteles nepitae, Glyptapanteles nigrescens, Glyptapanteles ninus, Glyptapanteles nkuli, Glyptapanteles parasundanus, Glyptapanteles penelope, Glyptapanteles penthocratus, Glyptapanteles philippinensis, Glyptapanteles philocampus, Glyptapanteles phoebe, Glyptapanteles phytometraduplus, Glyptapanteles propylae, Glyptapanteles puera, Glyptapanteles seydeli, Glyptapanteles siderion, Glyptapanteles simus, Glyptapanteles speciosissimus, Glyptapanteles spilosomae, Glyptapanteles subpunctatus, Glyptapanteles thespis, Glyptapanteles thoseae, Glyptapanteles venustus, Glyptapanteles wilkinsoni, Hypomicrogaster samarshalli, Iconella cajani, Iconella detrectans, Iconella jason, Iconella lynceus, Iconella pyrene, Iconella tedanius, Illidops azamgarhensis, Illidops lamprosemae, Illidops trabea, Keylimepie striatus, Microplitis adisurae, Microplitis mexicanus, Neoclarkinella ariadne, Neoclarkinella curvinervus, Neoclarkinella sundana, Nyereria ituriensis, Nyereria nioro, Nyereria proagynus, Nyereria taoi, Nyereria vallatae, Parapanteles aethiopicus, Parapanteles alternatus, Parapanteles aso, Parapanteles atellae, Parapanteles bagicha, Parapanteles cleo, Parapanteles cyclorhaphus, Parapanteles demades, Parapanteles endymion, Parapanteles epiplemicidus, Parapanteles expulsus, Parapanteles fallax, Parapanteles folia, Parapanteles furax, Parapanteles hemitheae, Parapanteles hyposidrae, Parapanteles indicus, Parapanteles javensis, Parapanteles jhaverii, Parapanteles maculipalpis, Parapanteles maynei, Parapanteles neocajani, Parapanteles neohyblaeae, Parapanteles nydia, Parapanteles prosper, Parapanteles prosymna, Parapanteles punctatissimus, Parapanteles regalis, Parapanteles sarpedon, Parapanteles sartamus, Parapanteles scultena, Parapanteles transvaalensis, Parapanteles turri, Parapanteles xanthopholis, Pholetesor acutus, Pholetesor brevivalvatus, Pholetesor extentus, Pholetesor ingenuoides, Pholetesor kuwayamai, Promicrogaster apidanus, Promicrogaster briareus, Promicrogaster conopiae, Promicrogaster emesa, Promicrogaster grandicula, Promicrogaster orsedice, Promicrogaster repleta, Promicrogaster typhon, Sathon bekilyensis, Sathon flavofacialis, Sathon laurae, Sathon mikeno, Sathon ruandanus, Sathon rufotestaceus, Venanides astydamia, Venanides demeter, Venanides parmula, and Venanides symmysta.},
}
@article {pmid32390312,
year = {2020},
author = {Tang, G and Chen, L and Wang, Z and Gao, S and Qu, Q and Xiong, R and Braeckmans, K and De Smedt, SC and Zhang, YS and Huang, C},
title = {Faithful Fabrication of Biocompatible Multicompartmental Memomicrospheres for Digitally Color-Tunable Barcoding.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {16},
number = {24},
pages = {e1907586},
doi = {10.1002/smll.201907586},
pmid = {32390312},
issn = {1613-6829},
mesh = {Biological Assay ; Coloring Agents ; *Nanoparticles ; },
abstract = {Barcodes have attracted widespread attention, especially for the multiplexed bioassays and anti-counterfeiting used toward medical and biomedical applications. An enabling gas-shearing approach is presented for generating 10-faced microspherical barcodes with precise control over the properties of each compartment. As such, the color of each compartment could be programmatically adjusted in the 10-faced memomicrospheres by using pregel solutions containing different combinations of fluorescent nanoparticles. During the process, three primary colors (red, green, and blue) are adopted to obtain up to seven merged fluorescent colors for constituting a large amount of coding as well as a magnetic compartment, capable of effective and robust high-throughput information-storage. More importantly, by using the biocompatible sodium alginate to construct the multicolor microspherical barcodes, the proposed technology is likely to advance the fields of food and pharmaceutics anti-counterfeiting. These remarkable properties point to the potential value of gas-shearing in engineering microspherical barcodes for biomedical applications in the future.},
}
@article {pmid32386812,
year = {2020},
author = {Bassi, G and Favalli, N and Oehler, S and Martinelli, A and Catalano, M and Scheuermann, J and Neri, D},
title = {Comparative evaluation of DNA-encoded chemical selections performed using DNA in single-stranded or double-stranded format.},
journal = {Biochemical and biophysical research communications},
volume = {533},
number = {2},
pages = {223-229},
pmid = {32386812},
issn = {1090-2104},
support = {182003/SNSF_/Swiss National Science Foundation/Switzerland ; 670603/ERC_/European Research Council/International ; },
mesh = {Binding Sites ; Combinatorial Chemistry Techniques ; DNA/chemical synthesis/*chemistry ; DNA, Single-Stranded/chemical synthesis/*chemistry ; Ligands ; Models, Molecular ; Small Molecule Libraries/chemical synthesis/*chemistry ; },
abstract = {DNA-encoded chemical libraries (DEL) are increasingly being used for the discovery and optimization of small organic ligands to proteins of biological or pharmaceutical interest. The DNA fragments, that serve as amplifiable identification barcodes for individual compounds in the library, are typically used in double-stranded DNA format. To the best of our knowledge, a direct comparison of DEL selections featuring DNA in either single- or double-stranded DNA format has not yet been reported. In this article, we describe a comparative evaluation of selections with two DEL libraries (named GB-DEL and NF-DEL), based on different chemical designs and produced in both single- and double-stranded DNA format. The libraries were selected in identical conditions against multiple protein targets, revealing comparable and reproducible fingerprints for both types of DNA formats. Surprisingly, selections performed with single-stranded DNA barcodes exhibited improved enrichment factors compared to double-stranded DNA. Using high-affinity ligands to carbonic anhydrase IX as benchmarks for selection performance, we observed an improved selectivity for the NF-DEL library (on average 2-fold higher enrichment factors) in favor of single-stranded DNA. The enrichment factors were even higher for the GB-DEL selections (approximately 5-fold), compared to the same library in double-stranded DNA format. Collectively, these results indicate that DEL libraries can conveniently be synthesized and screened in both single- and double-stranded DNA format, but single-stranded DNA barcodes typically yield enhanced enrichment factors.},
}
@article {pmid32382044,
year = {2020},
author = {O'Huallachain, M and Bava, FA and Shen, M and Dallett, C and Paladugu, S and Samusik, N and Yu, S and Hussein, R and Hillman, GR and Higgins, S and Lou, M and Trejo, A and Qin, L and Tai, YC and Kinoshita, SM and Jager, A and Lashkari, D and Goltsev, Y and Ozturk, S and Nolan, GP},
title = {Ultra-high throughput single-cell analysis of proteins and RNAs by split-pool synthesis.},
journal = {Communications biology},
volume = {3},
number = {1},
pages = {213},
pmid = {32382044},
issn = {2399-3642},
support = {P01 HL108797/HL/NHLBI NIH HHS/United States ; S10 OD018220/OD/NIH HHS/United States ; },
mesh = {Animals ; Antibodies/*analysis ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Mice ; Mice, Inbred C57BL ; Proteins/*analysis ; RNA/*analysis ; Single-Cell Analysis/*methods ; },
abstract = {Single-cell omics provide insight into cellular heterogeneity and function. Recent technological advances have accelerated single-cell analyses, but workflows remain expensive and complex. We present a method enabling simultaneous, ultra-high throughput single-cell barcoding of millions of cells for targeted analysis of proteins and RNAs. Quantum barcoding (QBC) avoids isolation of single cells by building cell-specific oligo barcodes dynamically within each cell. With minimal instrumentation (four 96-well plates and a multichannel pipette), cell-specific codes are added to each tagged molecule within cells through sequential rounds of classical split-pool synthesis. Here we show the utility of this technology in mouse and human model systems for as many as 50 antibodies to targeted proteins and, separately, >70 targeted RNA regions. We demonstrate that this method can be applied to multi-modal protein and RNA analyses. It can be scaled by expansion of the split-pool process and effectively renders sequencing instruments as versatile multi-parameter flow cytometers.},
}
@article {pmid32381359,
year = {2020},
author = {Li, J and Li, Y and Lu, F and Liu, L and Ji, Q and Song, K and Yin, Q and Lerner, RA and Yang, G and Xu, H and Ma, P},
title = {A DNA-encoded library for the identification of natural product binders that modulate poly (ADP-ribose) polymerase 1, a validated anti-cancer target.},
journal = {Biochemical and biophysical research communications},
volume = {533},
number = {2},
pages = {241-248},
doi = {10.1016/j.bbrc.2020.04.022},
pmid = {32381359},
issn = {1090-2104},
mesh = {Antineoplastic Agents/chemical synthesis/chemistry/pharmacology ; Biological Products/chemical synthesis/chemistry/pharmacology ; Cell Line, Tumor ; DNA/chemical synthesis/*chemistry ; Drug Discovery ; Drug Evaluation, Preclinical ; Humans ; Luteolin/chemical synthesis/chemistry/pharmacology ; Poly (ADP-Ribose) Polymerase-1/antagonists &amp; inhibitors/*metabolism ; Poly(ADP-ribose) Polymerase Inhibitors/chemical synthesis/*chemistry/*pharmacology ; Protein Binding ; Small Molecule Libraries/chemical synthesis/chemistry/pharmacology ; Surface Plasmon Resonance ; },
abstract = {Natural products have been an invaluable source of drug discovery, but their targets remain largely unknown. Natural products enriched DNA-encoded chemical libraries (nDELs) empower the researchers to rapidly and economically screen numerous natural products against various protein targets, and therefore promote the elucidation of the molecular mechanisms. In this work, we used poly (ADP-ribose) polymerase 1 (PARP1), as an example to explore the usage of nDEL for the functional natural products selection. We used late-stage modification approach to label three positive binders with unique DNA barcodes, whose dissociation constants range from sub-micromolar to micromolar. The selection criterion was set up according to the enrichment of these controls. Five natural products selected by this criterion directly bind to PARP1 in SPR, among which luteolin exhibits the highest inhibitory activity against PARP1. Moreover, luteolin selectively induces accumulation of DNA double-strand breaks and G2/M phase arrest in BRCA-deficient cells. All the findings from these investigations on luteolin support that PARP1 inhibition is one of the mechanisms for its anti-cancer activity.},
}
@article {pmid32381246,
year = {2020},
author = {Fuentes-López, A and Ruiz, C and Galián, J and Romera, E},
title = {Molecular identification of forensically important fly species in Spain using COI barcodes.},
journal = {Science &amp; justice : journal of the Forensic Science Society},
volume = {60},
number = {3},
pages = {293-302},
doi = {10.1016/j.scijus.2019.12.003},
pmid = {32381246},
issn = {1876-4452},
mesh = {Animals ; DNA Barcoding, Taxonomic ; *Diptera/genetics ; Electron Transport Complex IV/genetics ; Humans ; Sequence Analysis, DNA ; Spain ; },
abstract = {Species identification with DNA barcodes has been proven to be effective on different organisms and, particularly, has become a routinely used and quite accurate tool in forensic entomology to study necrophagous Diptera species. In this study, we analysed 215 specimens belonging to 42 species of 17 genera, from 9 different Diptera families. Flies were collected in 39 Spanish localities of the Iberian Peninsula sampled across three years in the four seasons. Intraspecific variation ranged from 0 to 2.46% whereas interspecific variation fluctuated from 3.07 to 14.59%, measuring 651 pb of the cytochrome oxidase subunit one (COI) gene. Neighbour-Joining analysis was carried out to investigate the molecular identification capabilities of the barcoding region, recovering almost all species as distinct monophyletic groups. The species groupings were generally consistent with morphological and molecular identifications. This work, which is the first with this intensive and extensive sampling in this area, shows that the COI barcode is an appropriate marker for unambiguous identification of forensically important Diptera in Spain.},
}
@article {pmid32380410,
year = {2020},
author = {Zia, Q and Alawami, M and Mokhtar, NFK and Nhari, RMHR and Hanish, I},
title = {Current analytical methods for porcine identification in meat and meat products.},
journal = {Food chemistry},
volume = {324},
number = {},
pages = {126664},
doi = {10.1016/j.foodchem.2020.126664},
pmid = {32380410},
issn = {1873-7072},
mesh = {Animals ; Biosensing Techniques ; Chromatography/methods ; DNA/analysis ; Food Analysis/instrumentation/*methods ; Food Contamination/*analysis ; Mass Spectrometry ; Meat/analysis ; Meat Products/*analysis ; Polymerase Chain Reaction ; Proteins/analysis ; Spectrum Analysis/methods ; *Swine/genetics ; },
abstract = {Authentication of meat products is critical in the food industry. Meat adulteration may lead to religious apprehensions, financial gain and food-toxicities such as meat allergies. Thus, empirical validation of the quality and constituents of meat is paramount. Various analytical methods often based on protein or DNA measurements are utilized to identify meat species. Protein-based methods, including electrophoretic and immunological techniques, are at times unsuitable for discriminating closely related species. Most of these methods have been replaced by more accurate and sensitive detection methods, such as DNA-based techniques. Emerging technologies like DNA barcoding and mass spectrometry are still in their infancy when it comes to their utilization in meat detection. Gold nanobiosensors have shown some promise in this regard. However, its applicability in small scale industries is distant. This article comprehensively reviews the recent developments in the field of analytical methods used for porcine identification.},
}
@article {pmid32379799,
year = {2020},
author = {Zhao, F and Li, B and Drew, BT and Chen, YP and Wang, Q and Yu, WB and Liu, ED and Salmaki, Y and Peng, H and Xiang, CL},
title = {Leveraging plastomes for comparative analysis and phylogenomic inference within Scutellarioideae (Lamiaceae).},
journal = {PloS one},
volume = {15},
number = {5},
pages = {e0232602},
pmid = {32379799},
issn = {1932-6203},
mesh = {Evolution, Molecular ; Genome, Plastid/*genetics ; Phylogeny ; Plastids/*genetics ; Scutellaria/*classification ; },
abstract = {Scutellaria, or skullcaps, are medicinally important herbs in China, India, Japan, and elsewhere. Though Scutellaria is the second largest and one of the more taxonomically challenging genera within Lamiaceae, few molecular systematic studies have been undertaken within the genus; in part due to a paucity of available informative markers. The lack of informative molecular markers for Scutellaria hinders our ability to accurately and robustly reconstruct phylogenetic relationships, which hampers our understanding of the diversity, phylogeny, and evolutionary history of this cosmopolitan genus. Comparative analyses of 15 plastomes, representing 14 species of subfamily Scutellarioideae, indicate that plastomes within Scutellarioideae contain about 151,000 nucleotides, and possess a typical quadripartite structure. In total, 590 simple sequence repeats, 489 longer repeats, and 16 hyper-variable regions were identified from the 15 plastomes. Phylogenetic relationships among the 14 species representing four of the five genera of Scutellarioideae were resolved with high support values, but the current infrageneric classification of Scutellaria was not supported in all analyses. Complete plastome sequences provide better resolution at an interspecific level than using few to several plastid markers in phylogenetic reconstruction. The data presented here will serve as a foundation to facilitate DNA barcoding, species identification, and systematic research within Scutellaria, which is an important medicinal plant resource worldwide.},
}
@article {pmid32377152,
year = {2020},
author = {Young, RG and Yu, J and Cote, MJ and Hanner, RH},
title = {The Molecular Data Organization for Publication (MDOP) R package to aid the upload of data to shared databases.},
journal = {Biodiversity data journal},
volume = {8},
number = {},
pages = {e50630},
pmid = {32377152},
issn = {1314-2828},
abstract = {Molecular identification methods, such as DNA barcoding, rely on centralized databases populated with morphologically identified individuals and their referential nucleotide sequence records. As molecular identification approaches have expanded in use to fields such as food fraud, environmental surveys, and border surveillance, there is a need for diverse international data sets. Although central data repositories, like the Barcode of Life Datasystems (BOLD), provided workarounds for formatting data for upload, these workarounds can be taxing on researchers with few resources and limited funding. To address these concerns, we present the Molecular Data Organization for Publication (MDOP) R package to assist researchers in uploading data to public databases. To illustrate the use of these scripts, we use the BOLD system as an example. The main intent of this writing is to assist in the movement of data, from academic, governmental, and other institutional computer systems, to public locations. The movement of these data can then better contribute to the global DNA barcoding initiative and other global molecular data efforts.},
}
@article {pmid32377148,
year = {2020},
author = {Tujuba, TF and Hausmann, A and Sciarretta, A},
title = {Revision of the Orbamia Herbulot, 1966 group of genera with description of two new genera, ten new species, and two new subspecies (Lepidoptera, Geometridae, Ennominae, Cassymini).},
journal = {ZooKeys},
volume = {929},
number = {},
pages = {53-77},
pmid = {32377148},
issn = {1313-2989},
abstract = {The genus Orbamia Herbulot, 1966 is revised. Two new genera are described: Rabomia Hausmann &amp; Tujuba, gen. nov. (type species: Ectropis ? subaurata Warren, 1899), and Morabia Hausmann &amp; Tujuba, gen. nov. (type species: Morabia politzari Hausmann &amp; Tujuba, sp. nov.). Ten new species and two new subspecies are described: Rabomia obscurior Hausmann &amp; Tujuba, sp. nov., from western Africa, Morabia politzari Hausmann &amp; Tujuba, sp. nov., from Kenya, Morabia brunnea Hausmann &amp; Tujuba, sp. nov., from Zambia, Orbamia marginata Hausmann &amp; Tujuba, sp. nov., from Tanzania, Orbamia clarissima Hausmann &amp; Tujuba, sp. nov., from Kenya, Orbamia clarior Hausmann &amp; Tujuba, sp. nov., from Kenya, Orbamia obliqua Hausmann &amp; Tujuba, sp. nov., from Zambia, Orbamia obliqua parva Hausmann &amp; Tujuba, subsp. nov., from South Africa, Orbamia abiyi Hausmann &amp; Tujuba, sp. nov., from Zambia, Tanzania, Ethiopia, Orbamia emanai Hausmann &amp; Tujuba, sp. nov., from Ethiopia, Orbamia emanai lenzi Hausmann &amp; Tujuba, subsp. nov., from Zambia and Malawi, and Orbamia balensis Hausmann &amp; Tujuba, sp. nov. from Ethiopia. The taxon Lepiodes ocellata Warren, 1897 is raised from synonymy of O. octomaculata (Wallengren, 1872) to species rank (Zambia, Tanzania, Rwanda). The taxonomical analysis is based on both morphological and genetic cytochrome oxidase I (COI) data. Adults and male and female genitalia of all species are illustrated.},
}
@article {pmid32376008,
year = {2020},
author = {Brom, T and Reddavide, FV and Heiden, S and Thompson, M and Zhang, Y},
title = {Influence of the geometry of fluorescently labelled DNA constructs on fluorescence anisotropy assay.},
journal = {Biochemical and biophysical research communications},
volume = {533},
number = {2},
pages = {230-234},
doi = {10.1016/j.bbrc.2020.04.025},
pmid = {32376008},
issn = {1090-2104},
mesh = {Binding Sites ; Combinatorial Chemistry Techniques ; DNA/chemical synthesis/*chemistry ; Drug Discovery ; Drug Evaluation, Preclinical ; Fluorescence Polarization ; Fluorescent Dyes/chemical synthesis/*chemistry ; Ligands ; Small Molecule Libraries/chemical synthesis/*chemistry/pharmacology ; },
abstract = {DNA-encoded chemical libraries (DECLs) are powerful tools for modern drug discovery. A DECL is a pooled mixture of small molecule compounds, each of which is tagged with a unique DNA sequence which functions as a barcode. After incubation with a drug target and washing to remove non-binders, the bound molecules are eluted and submitted for DNA sequencing to determine which molecules are binding the target. While the DECL technology itself is ultra-high throughput, the following re-synthesis of identified compounds for orthogonal validation experiments remains the bottleneck. Using existing DNA-small molecule conjugates directly for affinity measurements, as opposed to complete compound resynthesis, could accelerate the discovery process. To this end, we have tested various geometries of fluorescently-labelled DNA constructs for fluorescence anisotropy (FA) experiments. Minimizing the distance between the fluorescent moiety and ligand can maximize the correlation between ligand-protein interaction and corresponding change in fluorophore rotational freedom, thus leading to larger, easier to interpret changes in FA values. However, close proximity can also cause artifacts due to potentially promiscuous interactions between fluorophore and protein. By balancing these two opposite effects, we have identified applicable fluorescently labelled DNA constructs displaying either a single ligand or pairs of fragments for affinity measurement using a FA assay.},
}
@article {pmid32374816,
year = {2020},
author = {Boža, V and Perešíni, P and Brejová, B and Vinař, T},
title = {DeepNano-blitz: a fast base caller for MinION nanopore sequencers.},
journal = {Bioinformatics (Oxford, England)},
volume = {36},
number = {14},
pages = {4191-4192},
doi = {10.1093/bioinformatics/btaa297},
pmid = {32374816},
issn = {1367-4811},
mesh = {DNA ; High-Throughput Nucleotide Sequencing ; Humans ; *Nanopores ; Sequence Analysis, DNA ; Software ; },
abstract = {MOTIVATION: Oxford Nanopore MinION is a portable DNA sequencer that is marketed as a device that can be deployed anywhere. Current base callers, however, require a powerful GPU to analyze data produced by MinION in real time, which hampers field applications.<br><br>RESULTS: We have developed a fast base caller DeepNano-blitz that can analyze stream from up to two MinION runs in real time using a common laptop CPU (i7-7700HQ), with no GPU requirements. The base caller settings allow trading accuracy for speed and the results can be used for real time run monitoring (i.e. sample composition, barcode balance, species identification, etc.) or prefiltering of results for more detailed analysis (i.e. filtering out human DNA from human-pathogen runs).<br><br>DeepNano-blitz has been developed and tested on Linux and Intel processors and is available under MIT license at https://github.com/fmfi-compbio/deepnano-blitz.<br><br>CONTACT: vladimir.boza@fmph.uniba.sk.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid32368801,
year = {2020},
author = {Dueñas, JF and Camenzind, T and Roy, J and Hempel, S and Homeier, J and Suárez, JP and Rillig, MC},
title = {Moderate phosphorus additions consistently affect community composition of arbuscular mycorrhizal fungi in tropical montane forests in southern Ecuador.},
journal = {The New phytologist},
volume = {227},
number = {5},
pages = {1505-1518},
doi = {10.1111/nph.16641},
pmid = {32368801},
issn = {1469-8137},
mesh = {Ecosystem ; Ecuador ; Forests ; Fungi ; *Mycorrhizae ; Phosphorus ; Plant Roots ; Soil ; Soil Microbiology ; },
abstract = {Anthropogenic atmospheric deposition can increase nutrient supply in the most remote ecosystems, potentially affecting soil biodiversity. Arbuscular mycorrhizal fungal (AMF) communities rapidly respond to simulated soil eutrophication in tropical forests. Yet the limited spatio-temporal extent of such manipulations, together with the often unrealistically high fertilization rates employed, impedes generalization of such responses. We sequenced mixed root AMF communities within a seven year-long fully factorial nitrogen (N) and phosphorus (P) addition experiment, replicated at three tropical montane forests in southern Ecuador with differing environmental characteristics. We hypothesized: strong shifts in community composition and species richness after long-term fertilization, site- and clade-specific responses to N vs P additions depending on local soil fertility and clade life history traits respectively. Fertilization consistently shifted AMF community composition across sites, but only reduced richness of Glomeraceae. Compositional changes were mainly driven by increases in P supply while richness reductions were observed only after combined N and P additions. We conclude that moderate increases of N and P exert a mild but consistent effect on tropical AMF communities. To predict the consequences of these shifts, current results need to be supplemented with experiments that characterize local species-specific AMF functionality.},
}
@article {pmid32364092,
year = {2020},
author = {Montes, MM and Plaul, SE and Croci, Y and Waldbillig, M and Ferrari, W and Topa, E and Martorelli, SR},
title = {Pathology associated with three new Clinostomum metacercariae from Argentina with morphological and DNA barcode identification.},
journal = {Journal of helminthology},
volume = {94},
number = {},
pages = {e148},
doi = {10.1017/S0022149X20000292},
pmid = {32364092},
issn = {1475-2697},
mesh = {Animals ; Argentina ; *DNA Barcoding, Taxonomic ; DNA, Helminth/genetics ; DNA, Ribosomal Spacer/genetics ; Fish Diseases/parasitology ; Inflammation/parasitology ; Metacercariae/anatomy &amp; histology/classification ; Muscles/parasitology/pathology ; Phylogeny ; Trematoda/*anatomy &amp; histology/*classification ; Trematode Infections/*pathology/*veterinary ; },
abstract = {In the Laboratory of Parasites of Fishes, Crustaceans and Mollusks (CEPAVE), we undertook a parasitological study on three species of fish from the Espinal and Esteros del Iberá ecoregions of Argentina. Clinostomid metacercariae were found parasitizing Characidium rachovii, Crenicichla vittata and Gymnogeophagus balzanii. In this study, we analysed the damage that these parasites inflict on their hosts through the evaluation of histological sections. In addition, Clinostomum metacercariae were identified using morphological characters and DNA barcoding. In the pathological analysis, we observed that muscle tissue was the most affected. The inflammatory response showed vascular congestion areas and infiltration of numerous inflammatory cells, mainly lymphocytes. The molecular and morphological approach supports the presence of three new lineages of clinostomid metacercariae in Argentina. This could lead to the discovery of a high number of lineages or species of Clinostomum from South America.},
}
@article {pmid32362331,
year = {2020},
author = {Prati, L and Bigatti, M and Donckele, EJ and Neri, D and Samain, F},
title = {On-DNA hit validation methodologies for ligands identified from DNA-encoded chemical libraries.},
journal = {Biochemical and biophysical research communications},
volume = {533},
number = {2},
pages = {235-240},
doi = {10.1016/j.bbrc.2020.04.030},
pmid = {32362331},
issn = {1090-2104},
support = {670603/ERC_/European Research Council/International ; },
mesh = {Animals ; Carbonic Anhydrase II/metabolism ; Carbonic Anhydrase IX/metabolism ; Cattle ; Combinatorial Chemistry Techniques ; DNA/chemical synthesis/*chemistry ; Drug Discovery ; Drug Evaluation, Preclinical ; Enzyme-Linked Immunosorbent Assay ; Humans ; Ligands ; Models, Molecular ; Protein Binding ; Small Molecule Libraries/chemical synthesis/*chemistry/pharmacology ; },
abstract = {DNA-encoded chemical libraries (DECLs) are large compound collections attached to DNA fragments, serving as amplifiable barcodes, which can be screened on target proteins of pharmaceutical interest. In DECL selections, ligands are identified by high-throughput DNA sequencing, by comparing their frequency before and after the affinity capture step. Hits identified using this procedure need to be validated by resynthesis and by performing affinity measurements. Here we report novel on-DNA hit validation strategies, which enable the facile confirmation of ligand-protein interaction as well as the determination of equilibrium and kinetic binding constants. The experimental procedures, which had been inspired by enzyme-linked immunosorbent assays (ELISA), were validated using ligands of different affinity to carbonic anhydrase II and IX.},
}
@article {pmid32359176,
year = {2020},
author = {Dankworth, M and Heinrich, S and Fredriksen, S and Bartsch, I},
title = {DNA barcoding and mucilage ducts in the stipe reveal the presence of Hedophyllum nigripes (Laminariales, Phaeophyceae) in Kongsfjorden (Spitsbergen).},
journal = {Journal of phycology},
volume = {56},
number = {5},
pages = {1245-1254},
doi = {10.1111/jpy.13012},
pmid = {32359176},
issn = {1529-8817},
mesh = {DNA Barcoding, Taxonomic ; Ecosystem ; *Laminaria ; *Phaeophyceae ; Svalbard ; },
abstract = {The Arctic Ocean is a unique ecosystem hosting a biodiversity that has not yet been elucidated in full detail. There is increasing evidence that there are more kelp species constricted to Arctic/sub-Arctic habitats hitherto not well investigated, such as Hedophyllum nigripes, which is morphologically very similar to cold-temperate Laminaria digitata. Hedophyllum nigripes was originally described as L. nigripes by Agardh from Spitsbergen but has often been misidentified as L. digitata in the European Arctic. We initiated a systematic algal survey along a depth gradient (0-7.5 m) in Kongsfjorden (Spitsbergen) in June and July 2015 and thereby confirmed a predominant presence of H. nigripes (73%). Hedophyllum nigripes is occurring between 0 and 7.5 m while L. digitata was most abundant at 2.5 m depth. Hedophyllum nigripes individuals were generally younger (2.3 vs. 3.6 years) and stipe and blade length shorter (31 vs. 54 cm and 76 vs. 96 cm, respectively) compared to L. digitata. A combination of molecular (COI-5P) and morpho-anatomical tools (presence of sori and mucilage ducts in the stipe) was used to differentiate specimens of H. nigripes and L. digitata. Both kelp species were indistinguishable in most cases by external blade and stipe morphology. The different blade shapes represented different ontogenetic stages rather than phenotypic plasticity. The presence of mucilage ducts in the stipe was correlated with H. nigripes and changed with depth from 17%, 36%, and 85% at 2.5, 5, and 7.5 m, respectively. In addition, all summer fertile specimens were L. digitata.},
}
@article {pmid32358068,
year = {2020},
author = {Rowe, JB and Taghon, GJ and Kapolka, NJ and Morgan, WM and Isom, DG},
title = {CRISPR-addressable yeast strains with applications in human G protein-coupled receptor profiling and synthetic biology.},
journal = {The Journal of biological chemistry},
volume = {295},
number = {24},
pages = {8262-8271},
pmid = {32358068},
issn = {1083-351X},
support = {R03 TR002908/TR/NCATS NIH HHS/United States ; R35 GM119518/GM/NIGMS NIH HHS/United States ; },
mesh = {Autocrine Communication ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; Gene Dosage ; Genes, Reporter ; Humans ; Metabolic Engineering ; Pheromones/metabolism ; Receptors, G-Protein-Coupled/*metabolism ; Receptors, Mating Factor/metabolism ; Receptors, Somatostatin/metabolism ; Reproducibility of Results ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Signal Transduction ; Somatostatin/analogs &amp; derivatives/pharmacology ; *Synthetic Biology ; },
abstract = {Genome stability is essential for engineering cell-based devices and reporter systems. With the advent of CRISPR technology, it is now possible to build such systems by installing the necessary genetic parts directly into an organism's genome. Here, we used this approach to build a set of 10 versatile yeast-based reporter strains for studying human G protein-coupled receptors (GPCRs), the largest class of membrane receptors in humans. These reporter strains contain the necessary genetically encoded parts for studying human GPCR signaling in yeast, as well as four CRISPR-addressable expression cassettes, i.e. landing pads, installed at known safe-harbor sites in the yeast genome. We showcase the utility of these strains in two applications. First, we demonstrate that increasing GPCR expression by incrementally increasing GPCR gene copy number potentiates Gα coupling of the pharmacologically dark receptor GPR68. Second, we used two CRISPR-addressable landing pads for autocrine activation of a GPCR (the somatostatin receptor SSTR5) with its peptide agonist SRIF-14. The utility of these reporter strains can be extended far beyond these select examples to include applications such as nanobody development, mutational analysis, drug discovery, and studies of GPCR chaperoning. Additionally, we present a BY4741 yeast strain created for broad applications in the yeast and synthetic biology communities that contains only the four CRISPR-addressable landing pads. The general utility of these yeast strains provides an inexpensive, scalable, and easy means of installing and expressing genes directly from the yeast genome to build genome-barcoded sensors, reporter systems, and cell-based factories.},
}
@article {pmid32355868,
year = {2020},
author = {Adair, JE and Enstrom, MR and Haworth, KG and Schefter, LE and Shahbazi, R and Humphrys, DR and Porter, S and Tam, K and Porteus, MH and Kiem, HP},
title = {DNA Barcoding in Nonhuman Primates Reveals Important Limitations in Retrovirus Integration Site Analysis.},
journal = {Molecular therapy. Methods &amp; clinical development},
volume = {17},
number = {},
pages = {796-809},
pmid = {32355868},
issn = {2329-0501},
support = {P30 CA015704/CA/NCI NIH HHS/United States ; },
abstract = {In vivo tracking of retrovirus-tagged blood stem and progenitor cells is used to study hematopoiesis. Two techniques are used most frequently: sequencing the locus of retrovirus insertion, termed integration site analysis, or retrovirus DNA barcode sequencing. Of these, integration site analysis is currently the only available technique for monitoring clonal pools in patients treated with retrovirus-modified blood cells. A key question is how these two techniques compare in their ability to detect and quantify clonal contributions. In this study, we assessed both methods simultaneously in a clinically relevant nonhuman primate model of autologous, myeloablative transplantation. Our data demonstrate that both methods track abundant clones; however, DNA barcode sequencing is at least 5-fold more efficient than integration site analysis. Using computational simulation to identify the sources of low efficiency, we identify sampling depth as the major factor. We show that the sampling required for integration site analysis to achieve minimal coverage of the true clonal pool is likely prohibitive, especially in cases of low gene-modified cell engraftment. We also show that early subsampling of different blood cell lineages adds value to clone tracking information in terms of safety and hematopoietic biology. Our analysis demonstrates DNA barcode sequencing as a useful guide to maximize integration site analysis interpretation in gene therapy patients.},
}
@article {pmid32355612,
year = {2019},
author = {Marcelino, VR and Irinyi, L and Eden, JS and Meyer, W and Holmes, EC and Sorrell, TC},
title = {Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities - a proof of concept under laboratory conditions.},
journal = {IMA fungus},
volume = {10},
number = {},
pages = {12},
pmid = {32355612},
issn = {2210-6340},
abstract = {High-throughput sequencing (HTS) enables the generation of large amounts of genome sequence data at a reasonable cost. Organisms in mixed microbial communities can now be sequenced and identified in a culture-independent way, usually using amplicon sequencing of a DNA barcode. Bulk RNA-seq (metatranscriptomics) has several advantages over DNA-based amplicon sequencing: it is less susceptible to amplification biases, it captures only living organisms, and it enables a larger set of genes to be used for taxonomic identification. Using a model mock community comprising 17 fungal isolates, we evaluated whether metatranscriptomics can accurately identify fungal species and subspecies in mixed communities. Overall, 72.9% of the RNA transcripts were classified, from which the vast majority (99.5%) were correctly identified at the species level. Of the 15 species sequenced, 13 were retrieved and identified correctly. We also detected strain-level variation within the Cryptococcus species complexes: 99.3% of transcripts assigned to Cryptococcus were classified as one of the four strains used in the mock community. Laboratory contaminants and/or misclassifications were diverse, but represented only 0.44% of the transcripts. Hence, these results show that it is possible to obtain accurate species- and strain-level fungal identification from metatranscriptome data as long as taxa identified at low abundance are discarded to avoid false-positives derived from contamination or misclassifications. This study highlights both the advantages and current challenges in the application of metatranscriptomics in clinical mycology and ecological studies.},
}
@article {pmid32355211,
year = {2020},
author = {Zhang, M and Zou, Y and Xu, X and Zhang, X and Gao, M and Song, J and Huang, P and Chen, Q and Zhu, Z and Lin, W and Zare, RN and Yang, C},
title = {Highly parallel and efficient single cell mRNA sequencing with paired picoliter chambers.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {2118},
pmid = {32355211},
issn = {2041-1723},
mesh = {3T3 Cells ; Animals ; Antineoplastic Agents/pharmacology ; Cell Differentiation ; Cell-Free System ; Embryonic Stem Cells/metabolism ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Humans ; K562 Cells ; Mice ; Precision Medicine ; RNA, Messenger/*chemistry ; Reproducibility of Results ; *Sequence Analysis, RNA ; Single-Cell Analysis/*methods ; Stem Cells/*cytology ; },
abstract = {ScRNA-seq has the ability to reveal accurate and precise cell types and states. Existing scRNA-seq platforms utilize bead-based technologies uniquely barcoding individual cells, facing practical challenges for precious samples with limited cell number. Here, we present a scRNA-seq platform, named Paired-seq, with high cells/beads utilization efficiency, cell-free RNAs removal capability, high gene detection ability and low cost. We utilize the differential flow resistance principle to achieve single cell/barcoded bead pairing with high cell utilization efficiency (95%). The integration of valves and pumps enables the complete removal of cell-free RNAs, efficient cell lysis and mRNA capture, achieving highest mRNA detection accuracy (R = 0.955) and comparable sensitivity. Lower reaction volume and higher mRNA capture and barcoding efficiency significantly reduce the cost of reagents and sequencing. The single-cell expression profile of mES and drug treated cells reveal cell heterogeneity, demonstrating the enormous potential of Paired-seq for cell biology, developmental biology and precision medicine.},
}
@article {pmid32351753,
year = {2020},
author = {Yao, G and Ma, W and Huang, X and Jia, Q and Shen, J and Chang, Y and Ouyang, H and He, J},
title = {Identification and Quality Evaluation of Raw and Processed Asarum Species Using Microscopy, DNA Barcoding, and Gas Chromatography-Mass Spectrometry.},
journal = {Journal of analytical methods in chemistry},
volume = {2020},
number = {},
pages = {2690238},
pmid = {32351753},
issn = {2090-8865},
abstract = {Asarum (Aristolochiaceae) is one of the common herbs used to relieve exterior syndromes. Some volatile components of Asarum which have toxic effect may cause adverse reactions such as headache, general tension, unconsciousness, and respiratory paralysis. Therefore, Asarum is normally processed to reduce such toxicity and adverse effects. The bioactive ingredients contained in different Asarum herbs vary significantly; this variation may be attributed to their differences in species, origins, or processing methods. In this study, 16 batches of Asarum herbs were collected, and their species were identified using DNA barcoding, which is a method for distinguishing plant species, coupled with microscopy. A gas chromatography-mass spectrometry (GC-MS) method for simultaneous determination of 10 compounds was established to evaluate the contents of raw and processed Asarum herbs. Multivariate analysis was then applied to compare different batches of herbs based on the GC-MS data. DNA barcoding identified the herbs as being derived from four sources, and herbs from different origins showed different microscopic features. The results demonstrated that most of the samples were clearly clustered into distinct groups that corresponded to species types. All raw and processed samples were classified by partial least squares discriminant analysis (PLS-DA) based on the 10 analyzed compounds. The findings suggested that safrole and methyleugenol with a variable importance in the project (VIP) > 1 are unique compounds that can be used to differentiate between Asarum species. Safrole, methyleugenol, and 2,6,6-trimethylcyclohepta-2,4-dien-1-one were identified as significant constituents, the presence of which can be used to differentiate between raw and processed Asarum samples. These results indicate that species and processing methods show important effects on the composition of Asarum herbs.},
}
@article {pmid32351241,
year = {2020},
author = {Lewisch, E and Solymos, V and Waldner, K and van der Vloedt, L and Harl, J and Bakran-Lebl, K and El-Matbouli, M and Fuehrer, HP},
title = {Acanthocephalan parasites collected from Austrian fishes: molecular barcoding and pathological observations.},
journal = {Diseases of aquatic organisms},
volume = {139},
number = {},
pages = {103-111},
doi = {10.3354/dao03471},
pmid = {32351241},
issn = {0177-5103},
mesh = {*Acanthocephala ; Animals ; Austria ; *Fish Diseases/parasitology ; *Oncorhynchus mykiss ; },
abstract = {Acanthocephalan parasites were collected from the intestinal tracts of 137 predominantly wild fish (1 barbel Barbus barbus, 3 European chub Squalius cephalus, 13 rainbow trout Oncorhynchus mykiss and 120 brown trout Salmo trutta) from 12 localities. The condition factor, intensity of acanthocephalan infection and pathological lesions, if applicable, were documented. Routine bacteriology and virology were performed, and the brown trout were additionally tested for the presence of the myxozoan parasite Tetracapsolioides bryosalmonae by PCR. In total, 113 acanthocephalans were barcoded by sequencing a section of the mitochondrial cytochrome oxidase subunit I (COI) gene. Barcoding of the acanthocephalan tissues resulted in 77 sequences, of which 56 were assigned to Echinorhynchus truttae (3 genotypes), 11 to Pomphorhynchus tereticollis (9 genotypes), 9 to Acanthocephalus sp. (5 genotypes) and 1 to Neoechinorhynchida. Most of these genotypes were detected for the first time. Statistically, the acanthocephalan infection did not have an impact on the condition factor of the brown trout. Infection with P. tereticollis caused more severe pathological changes in the digestive tract than E. truttae. The present study provides new data regarding the distribution of acanthocephalan species in Austria and their impact on individual fish. In addition, new barcoding data from acanthocephalan parasites are presented, and the occurrence of P. tereticollis in European chub in Austria and in brown and rainbow trout in general was confirmed for the first time.},
}
@article {pmid32349369,
year = {2020},
author = {Masiero, E and Banik, D and Abson, J and Greene, P and Slater, A and Sgamma, T},
title = {Molecular Verification of the UK National Collection of Cultivated Liriope and Ophiopogon Plants.},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {5},
pages = {},
pmid = {32349369},
issn = {2223-7747},
abstract = {A collection of cultivated Liriope and Ophiopogon plants was established in 1996-1998 and subsequently hosted at a horticultural college. Uncertainties about the identification of the accessions, compounded by potential errors in propagation and labelling have led to waning confidence in the identities of the plants in the collection. The potential for using DNA barcoding to determine the species identities of the accessions was investigated. The DNA barcode regions of the plastid ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit gene (rbcL) and nuclear ribosomal internal transcribed spacer (nrITS) were amplified. DNA sequence analysis allowed the sequences of the accessions to be compared to reference sequences in public databases. A simple haplotype map of the characteristic polymorphic positions in the rbcL regions was used to clearly distinguish between the two genera and assign Ophiopogon accessions to individual species or sub-groups of species. The ITS sequence data confirmed these genus and species assignations and provided greater resolution to distinguish between closely related species. The combination of two DNA barcodes allowed most of the accessions to be assigned to individual species. This molecular verification confirmed the identity of about 70% of the accessions, with the remaining 30% demonstrating a range of mistaken identities at the species and genus levels.},
}
@article {pmid32348727,
year = {2020},
author = {Michels, BE and Mosa, MH and Streibl, BI and Zhan, T and Menche, C and Abou-El-Ardat, K and Darvishi, T and Członka, E and Wagner, S and Winter, J and Medyouf, H and Boutros, M and Farin, HF},
title = {Pooled In Vitro and In Vivo CRISPR-Cas9 Screening Identifies Tumor Suppressors in Human Colon Organoids.},
journal = {Cell stem cell},
volume = {26},
number = {5},
pages = {782-792.e7},
doi = {10.1016/j.stem.2020.04.003},
pmid = {32348727},
issn = {1875-9777},
mesh = {*CRISPR-Cas Systems/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Colon ; Genes, Tumor Suppressor ; Humans ; *Organoids ; },
abstract = {Colorectal cancer (CRC) is characterized by prominent genetic and phenotypic heterogeneity between patients. To facilitate high-throughput genetic testing and functional identification of tumor drivers, we developed a platform for pooled CRISPR-Cas9 screening in human colon organoids. Using transforming growth factor β (TGF-β) resistance as a paradigm to establish sensitivity and scalability in vitro, we identified optimal conditions and strict guide RNA (gRNA) requirements for screening in 3D organoids. We then screened a pan-cancer tumor suppressor gene (TSG) library in pre-malignant organoids with APC[-/-];KRAS[G12D] mutations, which were xenografted to study clonal advantages in context of a complex tumor microenvironment. We identified TGFBR2 as the most prevalent TSG, followed by known and previously uncharacterized mediators of CRC growth. gRNAs were validated in a secondary screen using unique molecular identifiers (UMIs) to adjust for clonal drift and to distinguish clone size and abundance. Together, these findings highlight a powerful organoid-based platform for pooled CRISPR-Cas9 screening for patient-specific functional genomics.},
}
@article {pmid32341676,
year = {2020},
author = {Huemer, P and Haxaire, J and Lee, KM and Mutanen, M and Pekarsky, O and Scalercio, S and Ronkay, L},
title = {Revision of the genus Hoplodrina Boursin, 1937 (Lepidoptera, Noctuidae, Xyleninae). I. Hoplodrina octogenaria (Goeze, 1781) and its sister species H. alsinides (Costantini, 1922) sp. rev. in Europe.},
journal = {ZooKeys},
volume = {927},
number = {},
pages = {75-97},
pmid = {32341676},
issn = {1313-2989},
abstract = {The taxonomic status of the European Hoplodrina octogenaria (Goeze, 1781) is discussed and its partly sympatric sister species, Hoplodrina alsinides (Costantini, 1922) sp. rev., is separated and re-described based on morphological and molecular taxonomic evidence. The adults and their genitalia are illustrated and DNA barcodes, as well as genome-wide single nucleotide polymorphism data collected by fractional genome sequencing (ddRAD), of the two species are provided.},
}
@article {pmid32341417,
year = {2020},
author = {Nneji, LM and Adeola, AC and Mustapha, MK and Oladipo, SO and Djagoun, CAMS and Nneji, IC and Adedeji, BE and Olatunde, O and Ayoola, AO and Okeyoyin, AO and Ikhimiukor, OO and Useni, GF and Iyiola, OA and Faturoti, EO and Matouke, MM and Ndifor, WK and Wang, YY and Chen, J and Wang, WZ and Kachi, JB and Ugwumba, OA and Ugwumba, AAA and Nwani, CD},
title = {DNA Barcoding Silver Butter Catfish (Schilbe intermedius) Reveals Patterns of Mitochondrial Genetic Diversity Across African River Systems.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {7097},
pmid = {32341417},
issn = {2045-2322},
mesh = {Animals ; Catfishes/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; *Genetic Variation ; Kenya ; Nigeria ; *Phylogeny ; Phylogeography ; Rivers ; },
abstract = {The silver butter catfish (Schilbe intermedius) is widely distributed across African river systems. To date, information on its mitochondrial genetic diversity, population structure, and historical demography are not well-established. Herein, we combined newly generated mitochondrial cytochrome c oxidase (COI) subunit I gene sequences with previously published COI sequences in the global databases to reconstruct its phylogeography, population genetic structure, and historical demography. Results from the mtDNA phylogeography and species delimitation tests (Cluster algorithm - Species Identifier, Automatic Barcode Gap Discovery and Poison Tree Process model) revealed that S. intermedius comprises at least seven geographically defined matrilines. Although the overall haplotype diversity of S. intermedius was high (h = 0.90), results showed that East (Kenya) and West (Nigeria) African populations had low levels of haplotype diversity (h = ~0.40). In addition, population genetic polymorphism and historical demographics showed that S. intermedius populations in both East and West Africa underwent severe contractions as a result of biogeographic influences. The patterns of genetic diversity and population structure were consistent with adaptive responses to historical biogeographic factors and contemporary environmental variations across African river systems. This is suggestive of the influence of historical biogeographic factors and climatic conditions on population divergence of S. intermedius across African river systems. Given our discovery of previously underappreciated diversity within S. intermedius, we recommend that this species be considered for increased conservation and management.},
}
@article {pmid32340081,
year = {2020},
author = {Cariou, M and Henri, H and Martinez, S and Duret, L and Charlat, S},
title = {How consistent is RAD-seq divergence with DNA-barcode based clustering in insects?.},
journal = {Molecular ecology resources},
volume = {20},
number = {5},
pages = {1294-1298},
doi = {10.1111/1755-0998.13178},
pmid = {32340081},
issn = {1755-0998},
support = {//Centre National de la Recherche Scientifique/ ; },
mesh = {Animals ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; *Insecta/classification/genetics ; Phylogeny ; *Sequence Analysis, DNA ; },
abstract = {Promoted by the barcoding approach, mitochondrial DNA is more than ever used as a molecular marker to identify species boundaries. Yet, it has been repeatedly argued that it may be poorly suited for this purpose, especially in insects where mitochondria are often associated with invasive intracellular bacteria that may promote their introgression. Here, we inform this debate by assessing how divergent nuclear genomes can be when mitochondrial barcodes indicate very high proximity. To this end, we obtained RAD-seq data from 92 barcode-based species-like units (operational taxonomic units [OTUs]) spanning four insect orders. In 100% of the cases, the observed median nuclear divergence was lower than 2%, a value that was recently estimated as one below which nuclear gene flow is not uncommon. These results suggest that although mitochondria may occasionally leak between species, this process is rare enough in insects to make DNA barcoding a reliable tool for clustering specimens into species-like units.},
}
@article {pmid32336926,
year = {2020},
author = {Chatzispyrou, A and Gubili, C and Laiaki, M and Mantopoulou-Palouka, D and Kavadas, S},
title = {First record of the marbled ray, Dasyatis marmorata (Elasmobranchii: Dasyatidae), from Greece (central Aegean Sea).},
journal = {Biodiversity data journal},
volume = {8},
number = {},
pages = {e51100},
pmid = {32336926},
issn = {1314-2828},
abstract = {BACKGROUND: Currently, seven dasyatid species have been described in the Mediterranean Sea: Bathytoshia lata, Dasyatis marmorata, Dasyatis pastinaca, Dasyatis tortonesei, Himantura uarnak, Pteroplatytrygon violacea and Taeniura grabata. Papaconstantinou (2014) listed four species of Dasyatidae occurring in Greece (P. violacea, D. pastinaca, D. tortonesei and D. centroura; the latter was a case of misidentification and it is currently identified as B. lata, according to genetic analysis). However, the marbled stingray (D. marmorata) was not amongst them. Here, the presence of D. marmorata was examined for the first time in Greece.<br><br>NEW INFORMATION: The present study provides updated information on the geographical distribution of D. marmorata in the Eastern Mediterranean Sea. A juvenile male stingray was captured in February 2019, during an onshore survey in Maliakos Gulf, located in the central Aegean Sea, Greece. The ray was examined at the Fisheries laboratory of the Hellenic Centre for Marine Research (HCMR) in Athens and was identified as D. marmorata. Morphological characters were recorded and DNA barcoding was applied to confirm the species identification. The combination of the two methods verified the occurrence of the marbled ray in the Greek waters. This is the first record of D. marmorata from the Aegean Sea.},
}
@article {pmid32336924,
year = {2020},
author = {Sheffield, C and Heron, J and Musetti, L},
title = {Xylocopa sonorina Smith, 1874 from Vancouver, British Columbia, Canada (Hymenoptera: Apidae, Xylocopinae) with comments on its taxonomy.},
journal = {Biodiversity data journal},
volume = {8},
number = {},
pages = {e49918},
pmid = {32336924},
issn = {1314-2828},
abstract = {BACKGROUND: Only one species of large carpenter bee, Xylocopa virginica (Linnaeus, 1771), has been recorded from Canada, albeit restricted to southern Ontario and Quebec. However, a single female specimen identified by Hurd in 1954 as X. varipuncta Patton, 1879 from British Columbia is in the C.A. Triplehorn Insect Collection at The Ohio State University (OSUC), suggesting that this species was accidentally introduced into coastal western Canada. As wood-nesters, many large carpenter bees are likely capable of expanding their range great distances by natural and unnatural transport methods while nesting inside suitable substrates, the presumed mode of transport into western Canada, and likely elsewhere. The ease at which the nests are transported has likely contributed to the nomenclatural and distributional ambiguity surrounding this species due to morphological similarities of specimens from North America, Hawaii, and several South Pacific islands.<br><br>NEW INFORMATION: By comparing DNA barcodes of specimens from the western United States to specimens from Hawaii, we confirm the early opinion of P.H. Timberlake (Timberlake 1922) that specimens long established on the Hawaiian Islands are the same X. varipuncta from continental North America. Furthermore, these DNA barcode sequences also match those of specimens identified as X. sonorina Smith, 1874 from the French Polynesian and Samoan Islands, thus fully supporting the opinion of Groom et al. (2017) that all are likely conspecific. As X. sonorina, a species described from and likely introduced to Hawaii is the oldest name available, X. varipuncta is here placed into synonymy. Additional research will be needed to trace the timing and pathway of introduction and establishment of X. sonorina; it is presumed that the species is native to the southwestern United States but has been established in Hawaii since the mid-1800s. It is also established in French Polynesia, the Samoan Islands, and likely other south Pacific islands, with additional records of occurrence from Java, New Zealand, and now Canada.},
}
@article {pmid32334210,
year = {2020},
author = {Pérez-Burillo, J and Trobajo, R and Vasselon, V and Rimet, F and Bouchez, A and Mann, DG},
title = {Evaluation and sensitivity analysis of diatom DNA metabarcoding for WFD bioassessment of Mediterranean rivers.},
journal = {The Science of the total environment},
volume = {727},
number = {},
pages = {138445},
doi = {10.1016/j.scitotenv.2020.138445},
pmid = {32334210},
issn = {1879-1026},
mesh = {DNA Barcoding, Taxonomic ; *Diatoms ; Environmental Monitoring ; *Rivers ; Spain ; Water ; },
abstract = {Our study of 164 diatom samples from Catalonia (NE Spain) is the first to evaluate the applicability of DNA metabarcoding, based on high throughput sequencing (HTS) using a 312-bp rbcL marker, for biomonitoring Mediterranean rivers. For this, we compared the values of a biotic index (IPS) and the ecological status classes derived from them, between light microscope-based (LM) and HTS methods. Very good correspondence between methods gives encouraging results concerning the applicability of DNA metabarcoding for Catalan rivers for the EU Water Framework Directive (WFD). However, in 10 sites, the ecological status class was downgraded from "Good"/"High" obtained by LM to "Moderate"/"Poor"/"Bad" by HTS; these "critical" sites are especially important, because the WFD requires remedial action by water managers for any river with Moderate or lower status. We investigated the contribution of each species to the IPS using a "leave-one-out" sensitivity analysis, paying special attention to critical sites. Discrepancies in IPS between LM and HTS were mainly due to the misidentification and overlooking in LM of a few species, which were better recovered by HTS. This bias was particularly important in the case of Fistulifera saprophila, whose clear underrepresentation in LM was important for explaining 8 out of the 10 critical sites and probably reflected destruction of weakly-silicified frustules during sample preparation. Differences between species in the rbcL copy number per cell affected the relative abundance obtained by HTS for Achnanthidium minutissimum, Nitzschia inconspicua and Ulnaria ulna, which were also identified by the sensitivity analysis as important for the WFD. Only minor IPS discrepancies were attributed to the incompleteness of the reference library, as most of the abundant and influential species (to the IPS) were well represented there. Finally, we propose that leave-one-out analysis is a good method for identifying priority species for isolation and barcoding.},
}
@article {pmid32333110,
year = {2020},
author = {Sikkel, PC and Pagan, JA and Santos, JL and Hendrick, GC and Nicholson, MD and Xavier, R},
title = {Molecular detection of apicomplexan blood parasites of coral reef fishes from free-living stages of ectoparasitic gnathiid isopods.},
journal = {Parasitology research},
volume = {119},
number = {6},
pages = {1975-1980},
pmid = {32333110},
issn = {1432-1955},
support = {OCE-1536794//National Science Foundation/ ; },
mesh = {Animals ; Apicomplexa/*isolation &amp; purification ; Caribbean Region ; Coral Reefs ; DNA Barcoding, Taxonomic ; Disease Vectors ; Fish Diseases/*parasitology ; Fishes/parasitology ; Isopoda/*parasitology ; },
abstract = {Gnathiid isopods are marine ectoparasites that feed on the blood of fishes that have been implicated as vectors of blood parasites, with transmission possibly occurring through biting during their parasitic life-stages, or through ingestion by fishes. However, evidence for their role as vectors is limited, reflecting the small number of research groups working on them. Here, we used a molecular barcode approach to identify fish hosts and apicomplexan parasites in free-living gnathiids from the eastern Caribbean Sea, with the goal of further evaluating their potential role as reservoirs and/or vectors for these parasites. Apicomplexa were only identified in 8% of the Gnathia analyzed, and in four cases we could identify both Apicomplexa and fish host DNA. The results further suggest that Gnathia spp. in this region may serve as reservoirs for Apicomplexa, but whether they are vectors for this parasite remains uncertain.},
}
@article {pmid32333022,
year = {2020},
author = {Low, VL and Srisuka, W and Saeung, A and Tan, TK and Ya'cob, Z and Yeong, YS and Takaoka, H},
title = {DNA Barcoding of Simulium asakoae (Diptera: Simuliidae) From Northern Thailand.},
journal = {Journal of medical entomology},
volume = {57},
number = {5},
pages = {1675-1678},
doi = {10.1093/jme/tjaa081},
pmid = {32333022},
issn = {1938-2928},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Diptera/*classification/genetics ; Electron Transport Complex IV/genetics ; Male ; },
abstract = {Previous studies suggested the presence of species complex in the so-called Simulium asakoae Takaoka &amp; Davies (Diptera: Simuliidae) in Thailand due to its high morphological variability and genetic divergence. To investigate whether the true S. asakoae is present in Thailand, we performed a detailed morphological identification of S. asakoae and compared its DNA barcodes with the morphospecies S. asakoae from Myanmar and the typical S. asakoae from Malaysia. Phylogenetic analysis revealed the Thai materials analyzed in this study were indeed genetically similar with those from Myanmar and Malaysia, though genetic distances 0-2.27% were observed. We tentatively regard this divergence as intraspecific variation, and the automatic barcode gap discovery analysis further supports them as a single species.},
}
@article {pmid32331381,
year = {2020},
author = {Li, J and Xie, DF and Guo, XL and Zheng, ZY and He, XJ and Zhou, SD},
title = {Comparative Analysis of the Complete Plastid Genome of Five Bupleurum Species and New Insights into DNA Barcoding and Phylogenetic Relationship.},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {4},
pages = {},
pmid = {32331381},
issn = {2223-7747},
support = {Grant Nos. 31872647 and 31570198//the National Natural Science Foundation of China/ ; Grant No. 2005DKA21403-JK//the Chinese Ministry of Science and Technology through the "National Science and Technology Infrastructure Platform" project/ ; Grant No. 2019PC002//the fourth national survey of traditional Chinese medicine resources/ ; },
abstract = {Bupleurum L. (Apiaceae) is a perennial and herbal genus, most species of which have high medicinal value. However, few studies have been performed using plastome data in this genus, and the phylogenetic relationships have always been controversial. In this study, the plastid genomes of Bupleurum chinense and Bupleurum commelynoideum were sequenced, and their gene content, order, and structure were counted and analyzed. The only three published Bupleurum species (B. boissieuanum, B. falcatum, and B. latissimum) and other fifteen allied species were selected to conduct a series of comparative and phylogenetic analyses. The genomes of B. chinense and B. commelynoideum were 155,869 and 155,629 bp in length, respectively, both of which had a typical quadripartite structure. The genome length, structure, guanine and cytosine (GC) content, and gene distribution were highly similar to the other three Bupleurum species. The five Bupleurum species had nearly the same codon usages, and eight regions (petN-psbM, rbcL-accD, ccsA-ndhD, trnK(UUU)-rps16, rpl32-trnL(UAG)-ccsA, petA-psbJ, ndhF-rpl32, and trnP(UGG)-psaJ-rpl33) were found to possess relatively higher nucleotide diversity, which may be the promising DNA barcodes in Bupleurum. Phylogenetic analysis revealed that all Bupleurum species clustered into a monophyletic clade with high bootstrap support and diverged after the Chamaesium clade. Overall, our study provides new insights into DNA barcoding and phylogenetic relationship between Bupleurum and its related genera, and will facilitate the population genomics, conservation genetics, and phylogenetics of Bupleurum in Apiaceae.},
}
@article {pmid32330378,
year = {2020},
author = {Bai, M and Qing, X and Qiao, K and Ning, X and Xiao, S and Cheng, X and Liu, G},
title = {Mitochondrial COI gene is valid to delimitate Tylenchidae (Nematoda: Tylenchomorpha) species.},
journal = {Journal of nematology},
volume = {52},
number = {},
pages = {1-12},
pmid = {32330378},
issn = {0022-300X},
abstract = {Tylenchidae is a widely distributed soil-inhabiting nematode family. Regardless their abundance, molecular phylogeny based on rRNA genes is problematic, and the delimitation of taxa in this group remains poorly documented and highly uncertain. Mitochondrial Cytochrome Oxidase I (COI) gene is an important barcoding gene that has been widely used species identifications and phylogenetic analyses. However, currently COI data are only available for one species in Tylenchidae. In present study, we newly obtained 27 COI sequences from 12 species and 26 sequences from rRNA genes. The results suggest that the COI gene is valid to delimitate Tylenchidae species but fails to resolve phylogenetic relationships. Tylenchidae is a widely distributed soil-inhabiting nematode family. Regardless their abundance, molecular phylogeny based on rRNA genes is problematic, and the delimitation of taxa in this group remains poorly documented and highly uncertain. Mitochondrial Cytochrome Oxidase I (COI) gene is an important barcoding gene that has been widely used species identifications and phylogenetic analyses. However, currently COI data are only available for one species in Tylenchidae. In present study, we newly obtained 27 COI sequences from 12 species and 26 sequences from rRNA genes. The results suggest that the COI gene is valid to delimitate Tylenchidae species but fails to resolve phylogenetic relationships.},
}
@article {pmid32328670,
year = {2020},
author = {Hanya, G and Tackmann, J and Sawada, A and Lee, W and Pokharel, SS and de Castro Maciel, VG and Toge, A and Kuroki, K and Otsuka, R and Mabuchi, R and Liu, J and Hatakeyama, M and Yamasaki, E and von Mering, C and Shimizu-Inatsugi, R and Hayakawa, T and Shimizu, KK and Ushida, K},
title = {Fermentation Ability of Gut Microbiota of Wild Japanese Macaques in the Highland and Lowland Yakushima: In Vitro Fermentation Assay and Genetic Analyses.},
journal = {Microbial ecology},
volume = {80},
number = {2},
pages = {459-474},
doi = {10.1007/s00248-020-01515-8},
pmid = {32328670},
issn = {1432-184X},
support = {15KK0256//MEXT Grant-in-Aid for Promotion of Joint International Research (Fostering Joint International Research)/ ; 19KK0186//MEXT Grant-in-Aid for Promotion of Joint International Research (Fostering Joint International Research)/ ; 25291100//MEXT Grant-in-Aid for Scientific Research B/ ; 18H02508//MEXT Grant-in-Aid for Scientific Research B/ ; },
mesh = {Animals ; Bacteria/genetics/*metabolism ; Diet ; *Digestion ; *Feeding Behavior ; Fermentation ; Gastrointestinal Microbiome/*physiology ; Macaca fuscata/*microbiology/*physiology ; Metagenome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; },
abstract = {Wild Japanese macaques (Macaca fuscata Blyth) living in the highland and lowland areas of Yakushima are known to have different diets, with highland individuals consuming more leaves. We aim to clarify whether and how these differences in diet are also reflected by gut microbial composition and fermentation ability. Therefore, we conduct an in vitro fermentation assay using fresh feces from macaques as inoculum and dry leaf powder of Eurya japonica Thunb. as a substrate. Fermentation activity was higher for feces collected in the highland, as evidenced by higher gas and butyric acid production and lower pH. Genetic analysis indicated separation of highland and lowland in terms of both community structure and function of the gut microbiota. Comparison of feces and suspension after fermentation indicated that the community structure changed during fermentation, and the change was larger for lowland samples. Analysis of the 16S rRNA V3-V4 barcoding region of the gut microbiota showed that community structure was clearly clustered between the two areas. Furthermore, metagenomic analysis indicated separation by gene and pathway abundance patterns. Two pathways (glycogen biosynthesis I and D-galacturonate degradation I) were enriched in lowland samples, possibly related to the fruit-eating lifestyle in the lowland. Overall, we demonstrated that the more leaf-eating highland Japanese macaques harbor gut microbiota with higher leaf fermentation ability compared with the more fruit-eating lowland ones. Broad, non-specific taxonomic and functional gut microbiome differences suggest that this pattern may be driven by a complex interplay between many taxa and pathways rather than single functional traits.},
}
@article {pmid32328429,
year = {2020},
author = {Wang, Y and Cao, T and Ko, J and Shen, Y and Zong, W and Sheng, K and Cao, W and Sun, S and Cai, L and Zhou, YL and Zhang, XX and Zong, C and Weissleder, R and Weitz, D},
title = {Dissolvable Polyacrylamide Beads for High-Throughput Droplet DNA Barcoding.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {7},
number = {8},
pages = {1903463},
pmid = {32328429},
issn = {2198-3844},
support = {R21 CA236561/CA/NCI NIH HHS/United States ; },
abstract = {Droplet-based single cell sequencing technologies, such as inDrop, Drop-seq, and 10X Genomics, are catalyzing a revolution in the understanding of biology. Barcoding beads are key components for these technologies. What is limiting today are barcoding beads that are easy to fabricate, can efficiently deliver primers into drops, and thus achieve high detection efficiency. Here, this work reports an approach to fabricate dissolvable polyacrylamide beads, by crosslinking acrylamide with disulfide bridges that can be cleaved with dithiothreitol. The beads can be rapidly dissolved in drops and release DNA barcode primers. The dissolvable beads are easy to synthesize, and the primer cost for the beads is significantly lower than that for the previous barcoding beads. Furthermore, the dissolvable beads can be loaded into drops with >95% loading efficiency of a single bead per drop and the dissolution of beads does not influence reverse transcription or the polymerase chain reaction (PCR) in drops. Based on this approach, the dissolvable beads are used for single cell RNA and protein analysis.},
}
@article {pmid32326237,
year = {2020},
author = {Jo, H and Choi, B and Park, K and Kim, WS and Kwak, IS},
title = {First Gut Content Analysis of 4th Instar Midge Larvae (Diptera: Chronomidae) In Large-Scale Weirs Using a DNA Meta-Barcoding Approach.},
journal = {International journal of environmental research and public health},
volume = {17},
number = {8},
pages = {},
pmid = {32326237},
issn = {1660-4601},
mesh = {Animals ; *Chironomidae/microbiology ; *DNA Barcoding, Taxonomic ; Ecosystem ; *Gastrointestinal Microbiome ; Larva ; Republic of Korea ; },
abstract = {Chironomidae larvae play an important role in the food chain of river ecosystems in Korea, where it is dominant. However, detailed information on the diet of Chironomidae larvae are still lacking. The purpose of this study was to identify the gut contents of 4th instar larvae of a Chironomidae inhabiting four large-scale weirs (Sejong Weir, Juksan Weir, Gangjeong-Goryeong Weir, and Dalseong Weir) using a DNA meta-barcoding approach. We found that dominant Operational Taxonomic Unit (OUT) was assigned to Paractinolaimus sp. (Nematoda), and the sub-dominant OTU was assigned to Dicrotendipes fumidus (Chironomidae). The most common OTUs among the individuals included phytoplankton, such as Tetrahymena sp., D. armatus, Pseudopediastrum sp., Tetradesmus dimorphus, Biddulphia tridens, and Desmodesmus spp. We calculated the selectivity index (E') and provided scientific evidence that Chironomidae larvae have a significant preference (E' > 0.5) for Desmodesmus armatus, E. minima, and T. dimorphus, while it does not show preference for other species found in its gut. Differences in physico-chemical factors, such as water quality, nutrients, Chl-a, and carbon concentrations, resulting from anthropogenic impacts (i.e., construction of large-scale weirs) as well as the particle size of prey organisms (small-sized single cell) and effects of chemicals (chemokinesis) could affect the feeding behavior of Chironomidae larvae.},
}
@article {pmid32325704,
year = {2020},
author = {Seah, A and Lim, MCW and McAloose, D and Prost, S and Seimon, TA},
title = {MinION-Based DNA Barcoding of Preserved and Non-Invasively Collected Wildlife Samples.},
journal = {Genes},
volume = {11},
number = {4},
pages = {},
pmid = {32325704},
issn = {2073-4425},
mesh = {Animals ; Animals, Wild/*genetics ; *Biodiversity ; Computational Biology/*methods ; *DNA Barcoding, Taxonomic ; Ducks/*genetics ; High-Throughput Nucleotide Sequencing ; Panthera/*genetics ; *Preservation, Biological ; },
abstract = {The ability to sequence a variety of wildlife samples with portable, field-friendly equipment will have significant impacts on wildlife conservation and health applications. However, the only currently available field-friendly DNA sequencer, the MinION by Oxford Nanopore Technologies, has a high error rate compared to standard laboratory-based sequencing platforms and has not been systematically validated for DNA barcoding accuracy for preserved and non-invasively collected tissue samples. We tested whether various wildlife sample types, field-friendly methods, and our clustering-based bioinformatics pipeline, SAIGA, can be used to generate consistent and accurate consensus sequences for species identification. Here, we systematically evaluate variation in cytochrome b sequences amplified from scat, hair, feather, fresh frozen liver, and formalin-fixed paraffin-embedded (FFPE) liver. Each sample was processed by three DNA extraction protocols. For all sample types tested, the MinION consensus sequences matched the Sanger references with 99.29%-100% sequence similarity, even for samples that were difficult to amplify, such as scat and FFPE tissue extracted with Chelex resin. Sequencing errors occurred primarily in homopolymer regions, as identified in previous MinION studies. We demonstrate that it is possible to generate accurate DNA barcode sequences from preserved and non-invasively collected wildlife samples using portable MinION sequencing, creating more opportunities to apply portable sequencing technology for species identification.},
}
@article {pmid32324995,
year = {2020},
author = {Crook, N and Ferreiro, A and Condiotte, Z and Dantas, G},
title = {Transcript Barcoding Illuminates the Expression Level of Synthetic Constructs in E. coli Nissle Residing in the Mammalian Gut.},
journal = {ACS synthetic biology},
volume = {9},
number = {5},
pages = {1010-1021},
pmid = {32324995},
issn = {2161-5063},
support = {DP2 DK098089/DK/NIDDK NIH HHS/United States ; R01 AT009741/AT/NCCIH NIH HHS/United States ; R01 GM099538/GM/NIGMS NIH HHS/United States ; T32 DK077653/DK/NIDDK NIH HHS/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; },
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Escherichia coli/genetics/*metabolism ; *Gastrointestinal Microbiome ; Green Fluorescent Proteins/genetics/metabolism ; Mice ; Mice, Inbred C57BL ; Probiotics ; Promoter Regions, Genetic ; },
abstract = {The development of robust engineered probiotic therapies demands accurate knowledge of genetic construct expression in the gut. However, the monetary and ethical costs of testing engineered strains in vertebrate hosts are incompatible with current high-throughput design-build-test cycles. To enable parallel measurement of multiple construct designs, we placed unique DNA barcodes in engineered transcripts and measured barcode abundances via sequencing. In standard curve experiments, the barcode sequences exhibited consistent relationships between input and measured abundances, which allowed us to use transcript barcoding to measure expression levels of 30 GFP-expressing strains of E. coli Nissle in parallel. Applying this technology in culture and in the mouse gut, we found that GFP expression in the gut could often be predicted from expression levels in culture, but several strains exhibited gut-specific expression. This work establishes the experimental design parameters and advantages of transcript barcoding to measure the performance of many engineered probiotic designs in mammalian hosts.},
}
@article {pmid32318929,
year = {2020},
author = {Ferreira da Silva, MJ and Paddock, C and Gerini, F and Borges, F and Aleixo-Pais, I and Costa, M and Colmonero-Costeira, I and Casanova, C and Lecoq, M and Silva, C and Bruford, MW and Varanda, J and Minhós, T},
title = {Chasing a ghost: notes on the present distribution and conservation of the sooty mangabey (Cercocebus atys) in Guinea-Bissau, West Africa.},
journal = {Primates; journal of primatology},
volume = {61},
number = {3},
pages = {357-363},
pmid = {32318929},
issn = {1610-7365},
support = {PTDC/IVC-ANT/3058/2014//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/AFR/100646/2008//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; POCI/ANT/57434/2004//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/CS/ANT/099184//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; CEECIND/01937/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BD/118444/2016//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BD/146509/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UID/ANT/04038/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; CASE Studentship NE/N007980/1//Natural Environment Research Council/ ; },
mesh = {*Animal Distribution ; Animals ; *Cercocebus atys ; *Conservation of Natural Resources ; Feces/chemistry ; Guinea-Bissau ; Photography ; },
abstract = {The West-African sooty mangabey (Cercocebus atys) is threatened by habitat loss, hunting for meat consumption, and mortality during crop-foraging events. The species' overall demographic trend is unknown. Presence and distribution in Guinea-Bissau, a country neighbored by Senegal and Republic of Guinea, was confirmed in 1946 but the species was declared extinct in 1989 and not observed in subsequent countrywide expeditions. Narratives of its presence across southern Guinea-Bissau are scattered in reports and occurrence in the eastern part was reported in 2017, but the limits of its distribution are currently unknown. Here, we present recent geo-referenced visual and molecular-based records of the sooty mangabey for three protected areas in southern Guinea-Bissau collected as part of a region-wide survey. Individuals were observed in Cufada Lagoons Natural Park (2015) and Dulombi National Park (NP) (2016) and photographed in Boé NP (2007, 2015 and 2020). Thirty-six samples collected in Boé NP (2017) were identified as sooty mangabey using a 402 base pair fragment of the mitochondrial cytochrome b gene. Our work suggests a wider distribution in Guinea-Bissau than previously described, augments knowledge of the populations' current habitat use and threats, and has implications for efforts to conserve the species in West Africa. Considering the sooty mangabey as the reservoir of the simian immunodeficiency virus that led to the human variant, HIV-2, confirmation that the Guinea-Bissau population is not extinct may lead to a better understanding of early viral jump to humans and consequent epidemic spread, specifically of the HIV-2 Subgroup A. We highlight the need for extra conservation measures by Guinea-Bissau authorities.},
}
@article {pmid32317663,
year = {2020},
author = {Acar, A and Nichol, D and Fernandez-Mateos, J and Cresswell, GD and Barozzi, I and Hong, SP and Trahearn, N and Spiteri, I and Stubbs, M and Burke, R and Stewart, A and Caravagna, G and Werner, B and Vlachogiannis, G and Maley, CC and Magnani, L and Valeri, N and Banerji, U and Sottoriva, A},
title = {Exploiting evolutionary steering to induce collateral drug sensitivity in cancer.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {1923},
pmid = {32317663},
issn = {2041-1723},
support = {22897/CRUK_/Cancer Research UK/United Kingdom ; RP-2016-07-28/DH_/Department of Health/United Kingdom ; 22909/CRUK_/Cancer Research UK/United Kingdom ; 202778/B/16/Z/WT_/Wellcome Trust/United Kingdom ; A22897/CRUK_/Cancer Research UK/United Kingdom ; A18052/CRUK_/Cancer Research UK/United Kingdom ; P01 CA091955/CA/NCI NIH HHS/United States ; 105104/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; R01 CA170595/CA/NCI NIH HHS/United States ; 11566/CRUK_/Cancer Research UK/United Kingdom ; 23110/CRUK_/Cancer Research UK/United Kingdom ; A22909/CRUK_/Cancer Research UK/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; R01 CA140657/CA/NCI NIH HHS/United States ; U54 CA217376/CA/NCI NIH HHS/United States ; A23110/CRUK_/Cancer Research UK/United Kingdom ; R01 CA185138/CA/NCI NIH HHS/United States ; 18052/CRUK_/Cancer Research UK/United Kingdom ; A25128/CRUK_/Cancer Research UK/United Kingdom ; A26815/CRUK_/Cancer Research UK/United Kingdom ; 202778/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; RP-2016-07-028/DH_/Department of Health/United Kingdom ; },
mesh = {Antineoplastic Agents/*pharmacology ; Clonal Evolution ; Computational Biology ; Computer Simulation ; *Drug Resistance, Neoplasm ; *Evolution, Molecular ; Gefitinib/pharmacology ; Genotype ; Humans ; Lung Neoplasms/*drug therapy/*genetics/pathology ; Models, Theoretical ; Molecular Medicine ; Pyridones/pharmacology ; Pyrimidinones/pharmacology ; Stochastic Processes ; },
abstract = {Drug resistance mediated by clonal evolution is arguably the biggest problem in cancer therapy today. However, evolving resistance to one drug may come at a cost of decreased fecundity or increased sensitivity to another drug. These evolutionary trade-offs can be exploited using 'evolutionary steering' to control the tumour population and delay resistance. However, recapitulating cancer evolutionary dynamics experimentally remains challenging. Here, we present an approach for evolutionary steering based on a combination of single-cell barcoding, large populations of 10[8]-10[9] cells grown without re-plating, longitudinal non-destructive monitoring of cancer clones, and mathematical modelling of tumour evolution. We demonstrate evolutionary steering in a lung cancer model, showing that it shifts the clonal composition of the tumour in our favour, leading to collateral sensitivity and proliferative costs. Genomic profiling revealed some of the mechanisms that drive evolved sensitivity. This approach allows modelling evolutionary steering strategies that can potentially control treatment resistance.},
}
@article {pmid32314625,
year = {2020},
author = {Chagas, ATA and Ludwig, S and Pimentel, JDSM and de Abreu, NL and Nunez-Rodriguez, DL and Leal, HG and Kalapothakis, E},
title = {Use of complete mitochondrial genome sequences to identify barcoding markers for groups with low genetic distance.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {31},
number = {4},
pages = {139-146},
doi = {10.1080/24701394.2020.1748609},
pmid = {32314625},
issn = {2470-1408},
mesh = {Animals ; Bayes Theorem ; Characiformes/*classification/genetics ; DNA Barcoding, Taxonomic ; *Genetic Markers ; Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Species Specificity ; },
abstract = {Complete mitochondrial sequences can be rapidly obtained and are widely available, providing a great source of species information and allowing for the discovery of new specific molecular markers. However, for some taxonomic groups, traditional approaches for species delimitation are impaired by the low genetic distance values. In these cases, other species-level markers are used. For Prochilodus, which includes important neotropical fish species, species-level delimitation usually results in poor phylogenetic resolution when using mitochondrial COI/cytB genes as barcoding markers because of low genetic variability and low species-level resolution. Thus, in this study, we developed an approach to design and validate new barcoding markers with high species-level resolution obtained from the D-loop region, using Prochilodus spp. as a model. For the new barcoding marker validation, the amplicon region was used to infer the phylogenetic relationships of Prochilodus spp. through three distinct methods: Bayesian inference (BI), Neighbor-Joining method (NJ), and Maximum Likelihood method (ML). The phylogenetic relationships of Prochilodus spp. revealed high resolution at species-level, nonoverlapping clades, and high branch support. The genetic distance results allied to two different clustering methods (Bayesian Poisson tree processes and automatic barcode gap discovery) revealed the existence of a barcoding gap, thus, validating the use of the barcoding markers designed in this study. The approach proposed here may, therefore, be expanded to other taxa to access and validate new barcoding markers with higher resolution at the species level.},
}
@article {pmid32312993,
year = {2020},
author = {Overall, SA and Toor, JS and Hao, S and Yarmarkovich, M and Sara M O'Rourke, and Morozov, GI and Nguyen, S and Japp, AS and Gonzalez, N and Moschidi, D and Betts, MR and Maris, JM and Smibert, P and Sgourakis, NG},
title = {High throughput pMHC-I tetramer library production using chaperone-mediated peptide exchange.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {1909},
pmid = {32312993},
issn = {2041-1723},
support = {U01 DK112217/DK/NIDDK NIH HHS/United States ; R35 GM125034/GM/NIGMS NIH HHS/United States ; R35 CA220500/CA/NCI NIH HHS/United States ; R01 AI143997/AI/NIAID NIH HHS/United States ; UC4 DK112232/DK/NIDDK NIH HHS/United States ; U54 CA232568/CA/NCI NIH HHS/United States ; R21 HG009748/HG/NHGRI NIH HHS/United States ; UC4 DK112217/DK/NIDDK NIH HHS/United States ; },
mesh = {Alleles ; Animals ; Carrier Proteins/*chemistry/genetics/metabolism ; Gene Library ; Histocompatibility Antigens Class I/*chemistry/genetics/metabolism ; Humans ; Immunity, Cellular ; Immunochemistry ; Membrane Transport Proteins/*chemistry/genetics/metabolism ; Mice ; Models, Molecular ; Molecular Chaperones/*chemistry/metabolism ; Peptides/*chemistry ; *Protein Interaction Domains and Motifs ; T-Lymphocytes ; },
abstract = {Peptide exchange technologies are essential for the generation of pMHC-multimer libraries used to probe diverse, polyclonal TCR repertoires in various settings. Here, using the molecular chaperone TAPBPR, we develop a robust method for the capture of stable, empty MHC-I molecules comprising murine H2 and human HLA alleles, which can be readily tetramerized and loaded with peptides of choice in a high-throughput manner. Alternatively, catalytic amounts of TAPBPR can be used to exchange placeholder peptides with high affinity peptides of interest. Using the same system, we describe high throughput assays to validate binding of multiple candidate peptides on empty MHC-I/TAPBPR complexes. Combined with tetramer-barcoding via a multi-modal cellular indexing technology, ECCITE-seq, our approach allows a combined analysis of TCR repertoires and other T cell transcription profiles together with their cognate antigen specificities in a single experiment. The new approach allows TCR/pMHC interactions to be interrogated easily at large scale.},
}
@article {pmid32312428,
year = {2020},
author = {Sui, J and Xie, P and Lin, Z and Javanmard, M},
title = {Electronic classification of barcoded particles for multiplexed detection using supervised machine learning analysis.},
journal = {Talanta},
volume = {215},
number = {},
pages = {120791},
doi = {10.1016/j.talanta.2020.120791},
pmid = {32312428},
issn = {1873-3573},
abstract = {Wearable biosensors are of great interest in recent years due to their potential in health related applications. Multiplex biomarker analysis is needed in wearable devices to improve the sensitivity and reliability. Electronic barcoding of micro-particles has the possibility to enable multiplexed biomarker analysis. Compared with traditional optical and plasmonic methods for barcoding, electronically barcoded particles can be classified using ultra-compact electronic readout platforms. Nano-electronic barcoding works by depositing a thin layer of oxide on the top half of a micro-particle. The thickness and dielectric property of the oxide layer can be tuned to modulate the frequency dependent impedance signature of the particles. A one to one correspondence between a target biomarker and each barcoded particle can potentially be established using this technique. The barcoded particles could be tested with wearable devices to enable multiplex analysis for portable point-of-care diagnostics and real-time monitoring. In this work, we fabricated nine barcoded particles by forming oxide layers of different thicknesses and different dielectric materials using atomic layer deposition and assessed the ability to accurately classify particle barcodes using multi-frequency impedance cytometry in conjunction with supervised machine learning.},
}
@article {pmid32310953,
year = {2020},
author = {, },
title = {Expression of Concern: Potential DNA barcodes for Melilotus species based on five single loci and their combinations.},
journal = {PloS one},
volume = {15},
number = {4},
pages = {e0230324},
pmid = {32310953},
issn = {1932-6203},
}
@article {pmid32305511,
year = {2020},
author = {Jaramillo, AF and De La Riva, I and Guayasamin, JM and Chaparro, JC and Gagliardi-Urrutia, G and Gutiérrez, RC and Brcko, I and Vilà, C and Castroviejo-Fisher, S},
title = {Vastly underestimated species richness of Amazonian salamanders (Plethodontidae: Bolitoglossa) and implications about plethodontid diversification.},
journal = {Molecular phylogenetics and evolution},
volume = {149},
number = {},
pages = {106841},
doi = {10.1016/j.ympev.2020.106841},
pmid = {32305511},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; *Biodiversity ; Brazil ; Central America ; DNA, Mitochondrial/genetics ; Geography ; Likelihood Functions ; Phylogeny ; Phylogeography ; Species Specificity ; Time Factors ; Caudata/*classification/genetics ; },
abstract = {We present data showing that the number of salamander species in Amazonia is vastly underestimated. We used DNA sequences of up to five genes (3 mitochondrial and 2 nuclear) of 366 specimens, 189 corresponding to 89 non-Amazonian nominal species and 177 Amazonian specimens, including types or topotypes, of eight of the nine recognized species in the region. By including representatives of all known species of Amazonian Bolitoglossa, except for one, and 73% of the currently 132 recognized species of the genus, our dataset represents the broadest sample of Bolitoglossa species, specimens, and geographic localities studied to date. We performed phylogenetic analyses using parsimony with tree-alignment and maximum likelihood (ML) with similarity alignment, with indels as binary characters. Our optimal topologies were used to delimit lineages that we assigned to nominal species and candidate new species following criteria that maximize the consilience of the current species taxonomy, monophyly, gaps in branch lengths, genetic distances, and geographic distribution. We contrasted the results of our species-delimitation protocol with those of Automated Barcode Gap Discovery (ABGD) and multi-rate Poisson Tree Processes (mPTP). Finally, we inferred the historical biogeography of South American salamanders by dating the trees and using dispersal-vicariance analysis (DIVA). Our results revealed a clade including almost all Amazonian salamanders, with a topology incompatible with just the currently recognized nine species. Following our species-delimitation criteria, we identified 44 putative species in Amazonia. Both ABGD and mPTP inferred more species than currently recognized, but their numbers (23-49) and limits vary. Our biogeographic analysis suggested a stepping-stone colonization of the Amazonian lowlands from Central America through the Chocó and the Andes, with several late dispersals from Amazonia back into the Andes. These biogeographic events are temporally concordant with an early land bridge between Central and South America (~10-15 MYA) and major landscape changes in Amazonia during the late Miocene and Pliocene, such as the drainage of the Pebas system, the establishment of the Amazon River, and the major orogeny of the northern Andes.},
}
@article {pmid32303959,
year = {2020},
author = {Chen, W and Wang, L and Han, M and Han, C and Li, B},
title = {Sequencing barcode construction and identification methods based on block error-correction codes.},
journal = {Science China. Life sciences},
volume = {63},
number = {10},
pages = {1580-1592},
doi = {10.1007/s11427-019-1651-3},
pmid = {32303959},
issn = {1869-1889},
mesh = {Algorithms ; Computer Simulation ; DNA/chemistry/genetics ; DNA Primers/chemistry/genetics ; High-Throughput Nucleotide Sequencing/*methods ; INDEL Mutation ; Models, Statistical ; Nucleic Acid Amplification Techniques ; Sequence Analysis, DNA/*methods ; },
abstract = {Multiplexed sequencing relies on specific sample labels, the barcodes, to tag DNA fragments belonging to different samples and to separate the output of the sequencers. However, the barcodes are often corrupted by insertion, deletion and substitution errors introduced during sequencing, which may lead to sample misassignment. In this paper, we propose a barcode construction method, which combines a block error-correction code with a predetermined pseudorandom sequence to generate a base sequence for labeling different samples. Furthermore, to identify the corrupted barcodes for assigning reads to their respective samples, we present a soft decision identification method that consists of inner decoding and outer decoding. The inner decoder establishes the hidden Markov model (HMM) for base insertion/deletion estimation with the pseudorandom sequence, and adapts the forward-backward (FB) algorithm to output the soft information of each bit in the block code. The outer decoder performs soft decision decoding using the soft information to effectively correct multiple errors in the barcodes. Simulation results show that the proposed methods are highly robust to high error rates of insertions, deletions and substitutions in the barcodes. In addition, compared with the inner decoding algorithm of the barcodes based on watermarks, the proposed inner decoding algorithm can greatly reduce the decoding complexity.},
}
@article {pmid32302591,
year = {2020},
author = {Roth, TL and Li, PJ and Blaeschke, F and Nies, JF and Apathy, R and Mowery, C and Yu, R and Nguyen, MLT and Lee, Y and Truong, A and Hiatt, J and Wu, D and Nguyen, DN and Goodman, D and Bluestone, JA and Ye, CJ and Roybal, K and Shifrut, E and Marson, A},
title = {Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies.},
journal = {Cell},
volume = {181},
number = {3},
pages = {728-744.e21},
pmid = {32302591},
issn = {1097-4172},
support = {F30 DK120213/DK/NIDDK NIH HHS/United States ; T32 GM007618/GM/NIGMS NIH HHS/United States ; L30 AI113413/AI/NIAID NIH HHS/United States ; L40 AI140341/AI/NIAID NIH HHS/United States ; S10 OD021822/OD/NIH HHS/United States ; P30 AR070155/AR/NIAMS NIH HHS/United States ; R01 DK119979/DK/NIDDK NIH HHS/United States ; P50 AI150476/AI/NIAID NIH HHS/United States ; DP2 DA042423/DA/NIDA NIH HHS/United States ; P30 DK063720/DK/NIDDK NIH HHS/United States ; DP3 DK111914/DK/NIDDK NIH HHS/United States ; T32 AI007334/AI/NIAID NIH HHS/United States ; T32 DK007418/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Blood Cells ; CRISPR-Cas Systems/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Gene Knock-In Techniques/*methods ; Genetic Engineering/*methods ; Humans ; Immunotherapy/*methods ; Mice ; Mice, Inbred NOD ; Mice, SCID ; RNA, Guide, CRISPR-Cas Systems/genetics ; Single-Cell Analysis/methods ; T-Lymphocytes ; Transcriptome/genetics ; },
abstract = {Adoptive transfer of genetically modified immune cells holds great promise for cancer immunotherapy. CRISPR knockin targeting can improve cell therapies, but more high-throughput methods are needed to test which knockin gene constructs most potently enhance primary cell functions in vivo. We developed a widely adaptable technology to barcode and track targeted integrations of large non-viral DNA templates and applied it to perform pooled knockin screens in primary human T cells. Pooled knockin of dozens of unique barcoded templates into the T cell receptor (TCR)-locus revealed gene constructs that enhanced fitness in vitro and in vivo. We further developed pooled knockin sequencing (PoKI-seq), combining single-cell transcriptome analysis and pooled knockin screening to measure cell abundance and cell state ex vivo and in vivo. This platform nominated a novel transforming growth factor β (TGF-β) R2-41BB chimeric receptor that improved solid tumor clearance. Pooled knockin screening enables parallelized re-writing of endogenous genetic sequences to accelerate discovery of knockin programs for cell therapies.},
}
@article {pmid32298457,
year = {2020},
author = {Miralles, A and Bruy, T and Wolcott, K and Scherz, MD and Begerow, D and Beszteri, B and Bonkowski, M and Felden, J and Gemeinholzer, B and Glaw, F and Glöckner, FO and Hawlitschek, O and Kostadinov, I and Nattkemper, TW and Printzen, C and Renz, J and Rybalka, N and Stadler, M and Weibulat, T and Wilke, T and Renner, SS and Vences, M},
title = {Repositories for Taxonomic Data: Where We Are and What is Missing.},
journal = {Systematic biology},
volume = {69},
number = {6},
pages = {1231-1253},
pmid = {32298457},
issn = {1076-836X},
mesh = {Animals ; *Classification ; Databases, Factual/*standards/trends ; },
abstract = {Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000-20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use of molecular data in species diagnosis and description. In 2018, of the 2661 papers published in specialized taxonomic journals, molecular data were widely used in mycology (94%), regularly in vertebrates (53%), but rarely in botany (15%) and entomology (10%). Images play an important role in taxonomic research on all taxa, with photographs used in >80% and drawings in 58% of the surveyed papers. The use of omics (high-throughput) approaches or 3D documentation is still rare. Improved archiving strategies for metabarcoding consensus reads, genome and transcriptome assemblies, and chemical and metabolomic data could help to mobilize the wealth of high-throughput data for alpha-taxonomy. Because long-term-ideally perpetual-data storage is of particular importance for taxonomy, energy footprint reduction via less storage-demanding formats is a priority if their information content suffices for the purpose of taxonomic studies. Whereas taxonomic assignments are quasifacts for most biological disciplines, they remain hypotheses pertaining to evolutionary relatedness of individuals for alpha-taxonomy. For this reason, an improved reuse of taxonomic data, including machine-learning-based species identification and delimitation pipelines, requires a cyberspecimen approach-linking data via unique specimen identifiers, and thereby making them findable, accessible, interoperable, and reusable for taxonomic research. This poses both qualitative challenges to adapt the existing infrastructure of data centers to a specimen-centered concept and quantitative challenges to host and connect an estimated $ \le $2 million images produced per year by alpha-taxonomic studies, plus many millions of images from digitization campaigns. Of the 30,000-40,000 taxonomists globally, many are thought to be nonprofessionals, and capturing the data for online storage and reuse therefore requires low-complexity submission workflows and cost-free repository use. Expert taxonomists are the main stakeholders able to identify and formalize the needs of the discipline; their expertise is needed to implement the envisioned virtual collections of cyberspecimens. [Big data; cyberspecimen; new species; omics; repositories; specimen identifier; taxonomy; taxonomic data.].},
}
@article {pmid32298447,
year = {2020},
author = {Seifert, B},
title = {The Gene and Gene Expression (GAGE) Species Concept: An Universal Approach for All Eukaryotic Organisms.},
journal = {Systematic biology},
volume = {69},
number = {5},
pages = {1033-1038},
doi = {10.1093/sysbio/syaa032},
pmid = {32298447},
issn = {1076-836X},
mesh = {Classification/*methods ; Eukaryota/*classification/*genetics ; *Gene Expression ; Genes/*genetics ; *Genetic Speciation ; },
abstract = {The Gene and Gene Expression (GAGE) species concept, a new version of the Pragmatic Species Concept of Seifert (2014), is proposed as a concept applicable to any described recent or fossil eukaryotic organism independent from its mode of reproduction or evolutionary history. In addition to presenting the concept as such, the article also provides practical recommendations for taxonomists when delimiting species and describing taxa. The wording of the new concept contains a heading core sentence plus five attached sentences addressing essential conditions for its translation into a sound taxonomic practice: "Species are separable clusters that have passed a threshold of evolutionary divergence and are exclusively defined by nuclear DNA sequences and/or their expression products. Nuclear DNA sequences and their expression products are different character systems but have a highly correlated indicative function. Character systems with the least risk of epigenetic or ontogenetic modification have superior indicative value when conflicts between character systems of integrative studies arise. All character systems have to be described by an adequate numerics allowing cluster formation and determination of thresholds. Thresholds for each character system should be fixed by consensus among the experts under the principle of avoiding oversplitting or lumping. Clusters must not be the expression of intraspecific polymorphism." Recognizing the distortions and conflicts caused to taxonomy through barcoding or through assessment on the basis of association with other organisms, the GAGE species concept strongly downgrades the use of cytoplasmic DNA of endosymbiotic origin (mtDNA, cpDNA) or DNA of closely associated microbes (e.g., Wolbachia bacteria) for final taxonomic decision-making. Recognizing the distortion of phylogenies by the high frequency of reticulate evolution, it is argued that delimiting and naming species has to be separated from constructing bifurcating phylogenetic trees. [Cytoplasmic DNA; lumping; nuclear DNA; numeric taxonomy; oversplitting; reticulate evolution.].},
}
@article {pmid32298363,
year = {2020},
author = {Pentinsaari, M and Ratnasingham, S and Miller, SE and Hebert, PDN},
title = {BOLD and GenBank revisited - Do identification errors arise in the lab or in the sequence libraries?.},
journal = {PloS one},
volume = {15},
number = {4},
pages = {e0231814},
pmid = {32298363},
issn = {1932-6203},
mesh = {Animals ; DNA/*genetics ; DNA Barcoding, Taxonomic ; Data Accuracy ; *Databases, Nucleic Acid ; Insecta/*genetics ; Phylogeny ; Scientific Experimental Error ; Species Specificity ; },
abstract = {Applications of biological knowledge, such as forensics, often require the determination of biological materials to a species level. As such, DNA-based approaches to identification, particularly DNA barcoding, are attracting increased interest. The capacity of DNA barcodes to assign newly encountered specimens to a species relies upon access to informatics platforms, such as BOLD and GenBank, which host libraries of reference sequences and support the comparison of new sequences to them. As parameterization of these libraries expands, DNA barcoding has the potential to make valuable contributions in diverse applied contexts. However, a recent publication called for caution after finding that both platforms performed poorly in identifying specimens of 17 common insect species. This study follows up on this concern by asking if the misidentifications reflected problems in the reference libraries or in the query sequences used to test them. Because this reanalysis revealed that missteps in acquiring and analyzing the query sequences were responsible for most misidentifications, a workflow is described to minimize such errors in future investigations. The present study also revealed the limitations imposed by the lack of a polished species-level taxonomy for many groups. In such cases, applications can be strengthened by mapping the geographic distributions of sequence-based species proxies rather than waiting for the maturation of formal taxonomic systems based on morphology.},
}
@article {pmid32298351,
year = {2020},
author = {Esmaeili, HR and Teimori, A and Zarei, F and Sayyadzadeh, G},
title = {DNA barcoding and species delimitation of the Old World tooth-carps, family Aphaniidae Hoedeman, 1949 (Teleostei: Cyprinodontiformes).},
journal = {PloS one},
volume = {15},
number = {4},
pages = {e0231717},
pmid = {32298351},
issn = {1932-6203},
mesh = {Animals ; Cyprinodontiformes/anatomy &amp; histology/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; History, 19th Century ; History, 20th Century ; Indian Ocean ; Iran ; Jordan ; Male ; Phylogeny ; Turkey ; },
abstract = {The fishes, which have currently named Aphanius Nardo, 1827 are the relict of the ancient ichthyofauna of the Tethys Sea. For a long time since 1827, the genus name has been subjected to revision by several researchers using mainly morphological features. Until recently, no comprehensive single- or multi-locus DNA barcoding study has been conducted on whole members of the family Aphaniidae. In the present study, by applying four conceptually different molecular species delimitation methods, including one distance-based method, one network-based and two topology-based methods, we examined a single-locus DNA barcode library (COI) diversity for the 268 sequences within the family Aphaniidae from the Old World (57 sequences are new in the present study and 211 sequences were retrieved from NCBI database). The molecular analyses revealed a clearer picture of intra-family relationships and allowed us to clarify the generic names, and also describe a new genus for the family Aphaniidae. Results supported distinction of three major clades related to three genera within this family: i) the first clade includes the A. mento group which are placed in a new genus, Paraphanius gen. nov., found in the Orontes (= Asi) and Tigris-Euphrates River drainage, the Levant in coastal waters and the Dead Sea basin, western Jordan, and in southern Turkey in the Mediterranean basins as well as in central Turkey. This clade positioned at the base of the phylogenetic tree, (ii) the second clade contains the A. dispar-like brackish water tooth-carps which are transferred to the genus Aphaniops Hoedeman, 1951 (type species, Lebias dispar), distributed in the coastal waters around the Red Sea and the Persian Gulf basins; and (iii) the third clade, the genus Aphanius Nardo, 1827 (type species Aphanius nanus = A. fasciatus) contains all the inland and inland-related tooth-carps, which are mainly distributed in the inland waters in Turkey and Iran and also in the inland-related drainages around the Mediterranean basin.},
}
@article {pmid32298321,
year = {2020},
author = {Timpano, EK and Scheible, MKR and Meiklejohn, KA},
title = {Optimization of the second internal transcribed spacer (ITS2) for characterizing land plants from soil.},
journal = {PloS one},
volume = {15},
number = {4},
pages = {e0231436},
pmid = {32298321},
issn = {1932-6203},
mesh = {Bryophyta/classification/genetics ; DNA Barcoding, Taxonomic/*methods/standards ; DNA, Intergenic/chemistry/*genetics ; DNA, Plant/chemistry/*genetics ; Ferns/classification/genetics ; Magnoliopsida/classification/genetics ; Metagenomics/*methods/standards ; Polymerase Chain Reaction/methods/standards ; Soil/chemistry ; },
abstract = {Molecular-based taxonomy, specifically DNA barcoding, has streamlined organism identification. For land plants, the recommended 2-locus barcode of rbcL and matK is not suitable for all groups, thus the second subunit of the nuclear internal transcribed spacer (ITS2) has received attention as a possible alternative. To date, evaluations of ITS2 have mostly been limited in scope to specific plant orders/families and single source material. Prior to using ITS2 to routinely characterize land plants present in environmental samples (i.e., DNA metabarcoding), a wet lab protocol optimized for bulk sample types is needed. To address this gap, in this study we determined the broad recoverability across land plants when using published ITS2 primer pairs, and subsequently optimized the PCR reaction constituents and cycling conditions for the best two performing primer pairs (ITS2F/ITSp4 and ITSp3/ITSu4). Using these conditions, both primer pairs were used to characterize land plants present in 17 diverse soils collected from across the US. The resulting PCR amplicons were prepared into libraries and pooled for sequencing on an Illumina® MiniSeq. Our existing bioinformatics workflow was used to process raw sequencing data and taxonomically assign unique ITS2 plant sequences by comparison to GenBank. Given strict quality criteria were imposed on sequences for inclusion in data analysis, only 43.6% and 7.5% of sequences from ITS2F/ITSp4 and ITSp3/ITSu4 respectively remained for taxonomic comparisons; ~7-11% of sequences originated from fungal co-amplification. The number of orders and families recovered did differ between primer pairs, with ITS2F/ITSp4 consistently outperforming ITSp3/ITSu4 by >15%. Primer pair bias was observed in the recovery of certain taxonomic groups; ITS2F/ITSp4 preferentially recovered flowering plants and grasses, whereas ITSp3/ITSu4 recovered more moss taxa. To maximize data recovery and reduce potential bias, we advocate that studies using ITS2 to characterize land plants from environmental samples such as soil use a multiple primer pair approach.},
}
@article {pmid32292273,
year = {2020},
author = {Bragança, PHN and van Zeeventer, RM and Bills, R and Tweddle, D and Chakona, A},
title = {Diversity of the southern Africa Lacustricola Myers, 1924 and redescription of Lacustricola johnstoni (Günther, 1894) and Lacustricola myaposae (Boulenger, 1908) (Cyprinodontiformes, Procatopodidae).},
journal = {ZooKeys},
volume = {923},
number = {},
pages = {91-113},
pmid = {32292273},
issn = {1313-2989},
abstract = {Through the analysis of a comprehensive database of COI sequences, with the sequencing of 48 specimens, a first insight into the genetic diversity, distribution and relationships between the southern Africa "Lacustricola" species is presented. Species from "Lacustricola" occur mainly in freshwater systems within the arid savanna, and are considered to be widely distributed in southern Africa, but most of them are data deficient taxa. Two species are redescribed, "Lacustricola" johnstoni (Günther, 1894) and "Lacustricola" myaposae (Boulenger, 1908), based on specimens collected at their respective type localities. Detailed osteological and life colouration information is presented for the first time. "Lacustricola" johnstoni was described from the Upper Shire River in Mangochi, Lake Malawi but is herein considered as widespread in the Okavango, Zambezi, southern Africa east coastal drainages and the Bangweulu in the Congo System. A sympatric similar species occurring in the Okavango is also identified. "Lacustricola" myaposae (Boulenger, 1908), was described from the Nseleni River in KwaZulu-Natal Province, South Africa and is herein considered to be endemic to the small coastal river drainages within this region. Lectotypes for both "L." johnstoni and "L." myaposae are designated. A new species from the Lualaba River in the Congo System, sister to "L." macrurus is identified, and the deep bodied "L." jubbi is considered sister taxon to a clade including "L." johnstoni and "L." myaposae.},
}
@article {pmid32292272,
year = {2020},
author = {Matson, TA and Wagner, DL},
title = {A new Stamnodes from the southwestern United States (Lepidoptera, Geometridae, Larentiinae).},
journal = {ZooKeys},
volume = {923},
number = {},
pages = {79-90},
pmid = {32292272},
issn = {1313-2989},
abstract = {Stamnodes fergusoni sp. nov. occurs from extreme southeastern Arizona through southern New Mexico east into western Texas, USA. Identity of the new species can be reliably determined by external features, genitalic characters, and COI haplotypes. Larvae are believed to be specialists on Salvia pinguifolia and S. ballotiflora. The adult and larval stages and male and female genitalia are illustrated, available DNA barcode data that support the recognition of the new Stamnodes are reviewed, and its life history briefly characterized.},
}
@article {pmid32291863,
year = {2020},
author = {Kim, J and Yoo, C and Moon, JH and Um, SH},
title = {EGFR Fragmentation for Topological Transformation Nanobarcoding.},
journal = {Chembiochem : a European journal of chemical biology},
volume = {21},
number = {17},
pages = {2533-2539},
doi = {10.1002/cbic.202000179},
pmid = {32291863},
issn = {1439-7633},
mesh = {Animals ; Cells, Cultured ; *DNA Barcoding, Taxonomic ; ErbB Receptors/*genetics ; Graphite/chemical synthesis/*chemistry ; Humans ; Mice ; *Polymerase Chain Reaction ; },
abstract = {As the market for personalized lung cancer medicine expands, the demand for molecular diagnostic tools in general, and methods of detecting multiple genes with qualitative, quantitative, and high specificity in particular, have grown. Here, we propose a system for the effective detection of lung cancer-specific, long-length epidermal growth factor receptor (EGFR) gene mutations by using a topological transformation nano-barcoding technique (TNT). In former TNT studies, EGFR was successfully detected in cell environments and at test stages in the presence of a reference gene. However, because typical EGFR target concentrations are significantly lower at the clinical stage and the probe-binding ability of long-length targets is lower that of short targets, our system employs polymerase chain reaction (PCR) amplification, restriction, and filtering (PRF) for EGFR fragmentation to maximize performance. In a PRF system, the target is amplified by PCR, cut to a suitable size by a restriction enzyme, and filtered by a magnetic bead. With detection limits of 0.3555 % and 1.500 % for EGFR Del 19 and L858R mutations, respectively, the proposed TNT with PRF can effectively distinguish mutant cell lines and efficiently detect various lengths of genetic variations in clinical trials.},
}
@article {pmid32290169,
year = {2020},
author = {Kulik, T and Bilska, K and Żelechowski, M},
title = {Promising Perspectives for Detection, Identification, and Quantification of Plant Pathogenic Fungi and Oomycetes through Targeting Mitochondrial DNA.},
journal = {International journal of molecular sciences},
volume = {21},
number = {7},
pages = {},
pmid = {32290169},
issn = {1422-0067},
support = {2015/19/B/NZ9/01329//National Science Center, Poland/ ; },
mesh = {DNA Barcoding, Taxonomic ; *DNA, Mitochondrial ; Fungi/*classification/*genetics ; Genome, Mitochondrial ; Genomics/methods ; Oomycetes/*classification/*genetics ; Plant Diseases/*microbiology ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {Fungi and oomycetes encompass many pathogens affecting crops worldwide. Their effective control requires screening pathogens across the local and international trade networks along with the monitoring of pathogen inocula in the field. Fundamentals to all of these concerns are their efficient detection, identification, and quantification. The use of molecular markers showed the best promise in the field of plant pathogen diagnostics. However, despite the unquestionable benefits of DNA-based methods, two significant limitations are associated with their use. The first limitation concerns the insufficient level of sensitivity due to the very low and uneven distribution of pathogens in plant material. The second limitation pertains to the inability of widely used diagnostic assays to detect cryptic species. Targeting mtDNA appears to provide a solution to these challenges. Its high copy number in microbial cells makes mtDNA an attractive target for developing highly sensitive assays. In addition, previous studies on different pathogen taxa indicated that mitogenome sequence variation could improve cryptic species delimitation accuracy. This review sheds light on the potential application of mtDNA for pathogen diagnostics. This paper covers a brief description of qPCR and DNA barcoding as two major strategies enabling the diagnostics of plant pathogenic fungi and oomycetes. Both strategies are discussed along with the potential use of mtDNA, including their strengths and weaknesses.},
}
@article {pmid32290139,
year = {2020},
author = {Nguyen, NH and Vu, HT and Le, ND and Nguyen, TD and Duong, HX and Tran, HD},
title = {Molecular Identification and Evaluation of the Genetic Diversity of Dendrobium Species Collected in Southern Vietnam.},
journal = {Biology},
volume = {9},
number = {4},
pages = {},
pmid = {32290139},
issn = {2079-7737},
abstract = {Dendrobium has been widely used not only as ornamental plants but also as food and medicines. The identification and evaluation of the genetic diversity of Dendrobium species support the conservation of genetic resources of endemic Dendrobium species. Uniquely identifying Dendrobium species used as medicines helps avoid misuse of medicinal herbs. However, it is challenging to identify Dendrobium species morphologically during their immature stage. Based on the DNA barcoding method, it is now possible to efficiently identify species in a shorter time. In this study, the genetic diversity of 76 Dendrobium samples from Southern Vietnam was investigated based on the ITS (Internal transcribed spacer), ITS2, matK (Maturase_K), rbcL (ribulose-bisphosphate carboxylase large subunit) and trnH-psbA (the internal space of the gene coding histidine transfer RNA (trnH) and gene coding protein D1, a polypeptide of the photosystem I reaction center (psaB)) regions. The ITS region was found to have the best identification potential. Nineteen out of 24 Dendrobium species were identified based on phylogenetic tree and Indel information of this region. Among these, seven identified species were used as medicinal herbs. The results of this research contributed to the conservation, propagation, and hybridization of indigenous Dendrobium species in Southern Vietnam.},
}
@article {pmid32283704,
year = {2020},
author = {Stavridou, E and Lagiotis, G and Karapetsi, L and Osathanunkul, M and Madesis, P},
title = {DNA Fingerprinting and Species Identification Uncovers the Genetic Diversity of Katsouni Pea in the Greek Islands Amorgos and Schinoussa.},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {4},
pages = {},
pmid = {32283704},
issn = {2223-7747},
support = {T1EDK- 04448//General Secretariat for Research and Technology/ ; 02/2019//Chiang Mai University/ ; },
abstract = {Pea (P. sativum L.), one of the most important legume crops worldwide, has been traditionally cultivated in Lesser Cyclades since ancient times. The commonly known traditional pea cultivar, 'Katsouni', is endemic to the islands of Amorgos and Schinoussa and is of great local economic importance. Despite the widespread cultivation of 'Katsouni' in both islands, it is still unknown whether the current Schinoussa and Amorgos pea populations are distinct landraces, and if they have common evolutionary origin. To assist conservation and breeding of the pea crop, the genetic diversity and phylogenetic relationships of 39 pea samples from Amorgos and 86 from Schinoussa were studied using DNA barcoding and ISSR marker analyses. The results indicate that both populations are different landraces with distinct geographical distribution and are more closely related to P. sativum subsp. elatius than the P. abyssinicum and P. fulvum species. Further characterization of the 'Katsouni' landraces for functional polymorphisms regarding pathogen resistance, revealed susceptibility to the powdery mildew (Erysiphe pisi DC.). This work represents the first investigation on the genetic diversity and population structure of the 'Katsouni' cultivar. Exploiting the local genetic diversity of traditional landraces is fundamental for conservation practices and crop improvement through breeding strategies.},
}
@article {pmid32281336,
year = {2020},
author = {Cai, ZC and Liu, XH and Wang, CC and Tan, MX and Chen, JL and Mei, YQ and Wei, LF and Chen, H and Yang, R and Chen, JJ},
title = {[Research progress in molecular biology of Lonicerae Japonicae Flos].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {45},
number = {6},
pages = {1272-1278},
doi = {10.19540/j.cnki.cjcmm.20200104.106},
pmid = {32281336},
issn = {1001-5302},
mesh = {Amplified Fragment Length Polymorphism Analysis ; Chromatography, High Pressure Liquid ; DNA Barcoding, Taxonomic ; Drugs, Chinese Herbal/*pharmacology ; Lonicera/*chemistry ; Medicine, Chinese Traditional ; Microsatellite Repeats ; Plants, Medicinal/chemistry ; Polymorphism, Restriction Fragment Length ; Polymorphism, Single Nucleotide ; Random Amplified Polymorphic DNA Technique ; Secondary Metabolism ; },
abstract = {Molecular biology is a new subject that clarifies the phenomena and nature of life at the molecular level. Its development provides new biotechnology and methods for the study of traditional pharmacognosy. The formation of molecular biology has brought the development of pharmacognosy into a new era of gene research. Lonicerae Japonicae Flos is a classical Chinese medicine. Many scholars of home and abroad have carried out relevant studies on its molecular biology on the basis of the in-depth study with traditional methods, and have achieved certain results. In order to provide references on the method, technical for promoting the modernization of Lonicerae Japonicae Flos, and the development, protection, and utilization of other traditional Chinese medicine resources. This article summarized the application status of molecular biology methods and techniques on the identification, biosynthesis of active constituents, and molecular mechanism of secondary metabolite under stress conditions of Lonicerae Japonicae Flos in recent years. In hybridization technology of tag(RFLP), molecular markers based on PCR(RAPD, AFLP, SSR and ISSR), based on DNA sequence analysis of SNP and DNA barcode for the variety identification, diagnosis, identification of Lonicerae Japonicae Flos, and so forth in detail. At the same time, it is proposed that multi-omics technology can be used to build systems biology technology and platforms, and establish related models of secondary metabolite biosynthesis, so as to deepen acknowledge the molecular mechanism of the active component biosynthesis of Lonicerae Japonicae Flos and the accumulation of metabolites, life activities of other medicinal plants under adverse environment, then to regulate them.},
}
@article {pmid32280726,
year = {2020},
author = {Meisen, WH and Nejad, ZB and Hardy, M and Zhao, H and Oliverio, O and Wang, S and Hale, C and Ollmann, MM and Collins, PJ},
title = {Pooled Screens Identify GPR108 and TM9SF2 as Host Cell Factors Critical for AAV Transduction.},
journal = {Molecular therapy. Methods &amp; clinical development},
volume = {17},
number = {},
pages = {601-611},
pmid = {32280726},
issn = {2329-0501},
abstract = {Adeno-associated virus (AAV) has been used extensively as a vector for gene therapy. Despite its widespread use, the mechanisms by which AAV enters the cell and is trafficked to the nucleus are poorly understood. In this study, we performed two pooled, genome-wide screens to identify positive and negative factors modulating AAV2 transduction. Genome-wide libraries directed against all human genes with four designs per gene or eight designs per gene were transduced into U-2 OS cells. These pools were transduced with AAV2 encoding EGFP and sorted based on the intensity of EGFP expression. Analysis of enriched and depleted barcodes in the sorted samples identified several genes that putatively decreased AAV2 transduction. A subset of screen hits was validated in flow cytometry and imaging studies. In addition to KIAA0319L (AAVR), we confirmed the role of two genes, GPR108 and TM9SF2, in mediating viral transduction in eight different AAV serotypes. Interestingly, GPR108 displayed serotype selectivity and was not required for AAV5 transduction. Follow-up studies suggested that GPR108 localized primarily to the Golgi, where it may interact with AAV and play a critical role in mediating virus escape or trafficking. Cumulatively, these results expand our understanding of the process of AAV transduction in different cell types and serotypes.},
}
@article {pmid32279439,
year = {2020},
author = {Ortega, A and Geraldi, NR and Díaz-Rúa, R and Ørberg, SB and Wesselmann, M and Krause-Jensen, D and Duarte, CM},
title = {A DNA mini-barcode for marine macrophytes.},
journal = {Molecular ecology resources},
volume = {20},
number = {4},
pages = {920-935},
doi = {10.1111/1755-0998.13164},
pmid = {32279439},
issn = {1755-0998},
support = {//King Abdullah University of Science and Technology/ ; 8021-00222 B//Independent Research Fund/ ; },
mesh = {Chlorophyta/genetics ; DNA Barcoding, Taxonomic/methods ; DNA Primers/genetics ; DNA, Plant/*genetics ; Gene Library ; Geologic Sediments/chemistry ; Phaeophyceae/genetics ; Phylogeny ; Rhodophyta/genetics ; Seaweed/*genetics ; },
abstract = {Studies focusing on marine macrophyte metabarcoding from environmental samples are scarce, due to the lack of a universal barcode for these taxa, and to their poor representation in DNA databases. Here, we searched for a short barcode able to identify marine macrophytes from tissue samples; then, we created a DNA reference library which was used to identify macrophytes in eDNA from coastal sediments. Barcoding of seagrasses, mangroves and marine macroalgae (Chlorophyta, Rhodophyta and Phaeophyceae) was tested using 18 primer pairs from six barcoding genes: the plant barcodes rbcL, matK and trnL, plus the genes ITS2, COI and 18S. The 18S gene showed the highest universality among marine macrophytes, amplifying 95%-100% of samples; amplification performance of the other barcodes was limited. Taxonomy was assigned using a phylogeny-based approach to create an 18S DNA reference library. Macrophyte tissue sequences were accurately identified within their phyla (88%), order (76%), genus (71%) and species (23%). Nevertheless, out of 86 macrophytes tested, only 48% and 15% had a reference sequence at genus and at species level, respectively. Identification at these levels can be improved by more inclusive reference libraries. Using the 18S mini-barcode and the reference library, we recovered eDNA from 21 marine macrophytes in sediments, demonstrating the barcode's ability to trace primary producers that contribute to blue carbon. We expect this barcode to also be useful for other ecological questions, such as tracing macro primary producers in marine food webs.},
}
@article {pmid32277166,
year = {2020},
author = {Kim, S and Lee, Y and Mutanen, M and Seung, J and Lee, S},
title = {High functionality of DNA barcodes and revealed cases of cryptic diversity in Korean curved-horn moths (Lepidoptera: Gelechioidea).},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {6208},
pmid = {32277166},
issn = {2045-2322},
mesh = {Animals ; DNA/genetics ; DNA Barcoding, Taxonomic ; Evolution, Molecular ; Female ; Genetic Variation ; Male ; Moths/classification/*genetics ; Phylogeny ; Republic of Korea ; Species Specificity ; },
abstract = {Curved-horn moths or gelechioid moths (Lepidoptera: Gelechioidea) represent one of the most diverse lepidopteran groups. Due to the large number of species, generally small size of adults and subtle morphological differences, their confident identification requires tenacious and long-term dedication on their diversity. Over the past decade, DNA barcoding has repeatedly been used to elucidate boundaries of species in many large and difficult groups. Here, we conducted a test of DNA barcoding with the diverse fauna of Korean Gelechioidea with very little prior information of COI gene region from the area. Altogether 509 specimens representing 154 morphospecies were included in the study. The species assignments of all three tested species delimitation methods (ABGD, bPTP and PTP) were consistent with morphological identifications for 117 species (75.97%). A threshold of 2.5% genetic divergence was observed to differentiate the morphological species efficiently. Careful morphological examination of morphospecies exceeding 2.5% intraspecific variability prove cryptic diversity in three species (Neoblastobasis biceratala, Evippe albidoesella and Promalactis atriplagata). One morphospecies, Promalactis odaiensis, showed high intraspecific divergence while consisted of only a single MOTU. Overall, DNA barcoding was shown to provide a powerful tool to discriminate species of Korean Gelechioidea and reveal cases of cryptic diversity.},
}
@article {pmid32274883,
year = {2020},
author = {Marchese, P and Garzoli, L and Gnavi, G and O'Connell, E and Bouraoui, A and Mehiri, M and Murphy, JM and Varese, GC},
title = {Diversity and bioactivity of fungi associated with the marine sea cucumber Holothuria poli: disclosing the strains potential for biomedical applications.},
journal = {Journal of applied microbiology},
volume = {129},
number = {3},
pages = {612-625},
doi = {10.1111/jam.14659},
pmid = {32274883},
issn = {1365-2672},
support = {//Fondazione CRT/ ; //Irish Research Council/ ; //Core/ ; //National University of Ireland/ ; /SFI_/Science Foundation Ireland/Ireland ; },
mesh = {Animals ; Biological Products/metabolism/*pharmacology ; Cell Survival/drug effects ; Fungi/classification/genetics/*isolation &amp; purification/*metabolism ; Hep G2 Cells ; Holothuria/*microbiology ; Humans ; Mesenchymal Stem Cells ; *Mycobiome ; Osteogenesis/drug effects ; },
abstract = {AIMS: Identification of the mycobiota associated to the marine echinoderm Holothuria poli and investigation of cytotoxic and pro-osteogenic potential of isolated strains.<br><br>METHODS AND RESULTS: Fungal strains were isolated from the animal's body-wall, intestine and faeces. The species identification was based on DNA barcoding and morphophysiological observations. Forty-seven species were identified, all are Ascomycota and mainly belonging to Aspergillus and Penicillium genera. Sixteen strains were grown on three media for chemical extraction. Cytotoxic activity was tested on a hepatic cancer cell line (HepG2), the cells viability was evaluated after treatment using a resazurin based assay (AlamarBlue). Pro-osteogenic activity was tested on human Mesenchymal stem cell, differentiation was measured as the alkaline phosphatase production through reaction with p-nitrophenylphosphate or as the cells ability to mineralize calcium using a colorimetric kit (StanBio). Cytotoxic activity was recorded for four fungal species while five of 48 extracts highlighted bioactivity towards human mesenchymal stem cells.<br><br>CONCLUSIONS: The presence of relevant animal-associated mycobiota was observed in H. poli and selected strains showed cytotoxic potential and pro-osteogenic activity.<br><br>Our work represents the first report of a Mediterranean Sea cucumber mycobiota and highlights the isolates potential to synthetize compounds of pharmaceutical interest for regenerative medicine.},
}
@article {pmid32274263,
year = {2020},
author = {Kannan, A and Rama Rao, S and Ratnayeke, S and Yow, YY},
title = {The efficiency of universal mitochondrial DNA barcodes for species discrimination of Pomacea canaliculata and Pomacea maculata.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e8755},
pmid = {32274263},
issn = {2167-8359},
abstract = {Invasive apple snails, Pomacea canaliculata and P. maculata, have a widespread distribution globally and are regarded as devastating pests of agricultural wetlands. The two species are morphologically similar, which hinders species identification via morphological approaches and species-specific management efforts. Advances in molecular genetics may contribute effective diagnostic tools to potentially resolve morphological ambiguity. DNA barcoding has revolutionized the field of taxonomy by providing an alternative, simple approach for species discrimination, where short sections of DNA, the cytochrome c oxidase subunit I (COI) gene in particular, are used as 'barcodes' to delineate species boundaries. In our study, we aimed to assess the effectiveness of two mitochondrial markers, the COI and 16S ribosomal deoxyribonucleic acid (16S rDNA) markers for DNA barcoding of P. canaliculata and P. maculata. The COI and 16S rDNA sequences of 40 Pomacea specimens collected from six localities in Peninsular Malaysia were analyzed to assess their barcoding performance using phylogenetic methods and distance-based assessments. The results confirmed both markers were suitable for barcoding P. canaliculata and P. maculata. The phylogenies of the COI and 16S rDNA markers demonstrated species-specific monophyly and were largely congruent with the exception of one individual. The COI marker exhibited a larger barcoding gap (6.06-6.58%) than the 16S rDNA marker (1.54%); however, the magnitude of barcoding gap generated within the barcoding region of the 16S rDNA marker (12-fold) was bigger than the COI counterpart (approximately 9-fold). Both markers were generally successful in identifying P. canaliculata and P. maculata in the similarity-based DNA identifications. The COI + 16S rDNA concatenated dataset successfully recovered monophylies of P. canaliculata and P. maculata but concatenation did not improve individual datasets in distance-based analyses. Overall, although both markers were successful for the identification of apple snails, the COI molecular marker is a better barcoding marker and could be utilized in various population genetic studies of P. canaliculata and P. maculata.},
}
@article {pmid32274008,
year = {2020},
author = {Franco-Sierra, ND and Díaz-Nieto, JF},
title = {Rapid mitochondrial genome sequencing based on Oxford Nanopore Sequencing and a proxy for vertebrate species identification.},
journal = {Ecology and evolution},
volume = {10},
number = {7},
pages = {3544-3560},
pmid = {32274008},
issn = {2045-7758},
abstract = {Molecular information is crucial for species identification when facing challenging morphology-based specimen identifications. The use of DNA barcodes partially solves this problem, but in some cases when PCR is not an option (i.e., primers are not available, problems in reaction standardization), amplification-free approaches could be an optimal alternative. Recent advances in DNA sequencing, like the MinION device from Oxford Nanopore Technologies (ONT), allow to obtain genomic data with low laboratory and technical requirements, and at a relatively low cost. In this study, we explore ONT sequencing for molecular species identification from a total DNA sample obtained from a neotropical rodent and we also test the technology for complete mitochondrial genome reconstruction via genome skimming. We were able to obtain "de novo" the complete mitogenome of a specimen from the genus Melanomys (Cricetidae: Sigmodontinae) with average depth coverage of 78X using ONT-only data and by combining multiple assembly routines. Our pipeline for an automated species identification was able to identify the sample using unassembled sequence data (raw) in a reasonable computing time, which was substantially reduced when a priori information related to the organism identity was known. Our findings suggest ONT sequencing as a suitable candidate to solve species identification problems in metazoan nonmodel organisms and generate complete mtDNA datasets.},
}
@article {pmid32274002,
year = {2020},
author = {Duke, EM and Burton, RS},
title = {Efficacy of metabarcoding for identification of fish eggs evaluated with mock communities.},
journal = {Ecology and evolution},
volume = {10},
number = {7},
pages = {3463-3476},
pmid = {32274002},
issn = {2045-7758},
abstract = {There is urgent need for effective and efficient monitoring of marine fish populations. Monitoring eggs and larval fish may be more informative than that traditional fish surveys since ichthyoplankton surveys reveal the reproductive activities of fish populations, which directly impact their population trajectories. Ichthyoplankton surveys have turned to molecular methods (DNA barcoding &amp; metabarcoding) for identification of eggs and larval fish due to challenges of morphological identification. In this study, we examine the effectiveness of using metabarcoding methods on mock communities of known fish egg DNA. We constructed six mock communities with known ratios of species. In addition, we analyzed two samples from a large field collection of fish eggs and compared metabarcoding results with traditional DNA barcoding results. We examine the ability of our metabarcoding methods to detect species and relative proportion of species identified in each mock community. We found that our metabarcoding methods were able to detect species at very low input proportions; however, levels of successful detection depended on the markers used in amplification, suggesting that the use of multiple markers is desirable. Variability in our quantitative results may result from amplification bias as well as interspecific variation in mitochondrial DNA copy number. Our results demonstrate that there remain significant challenges to using metabarcoding for estimating proportional species composition; however, the results provide important insights into understanding how to interpret metabarcoding data. This study will aid in the continuing development of efficient molecular methods of biological monitoring for fisheries management.},
}
@article {pmid32273993,
year = {2020},
author = {Limmon, G and Delrieu-Trottin, E and Patikawa, J and Rijoly, F and Dahruddin, H and Busson, F and Steinke, D and Hubert, N},
title = {Assessing species diversity of Coral Triangle artisanal fisheries: A DNA barcode reference library for the shore fishes retailed at Ambon harbor (Indonesia).},
journal = {Ecology and evolution},
volume = {10},
number = {7},
pages = {3356-3366},
pmid = {32273993},
issn = {2045-7758},
abstract = {The Coral Triangle (CT), a region spanning across Indonesia and Philippines, is home to about 4,350 marine fish species and is among the world's most emblematic regions in terms of conservation. Threatened by overfishing and oceans warming, the CT fisheries have faced drastic declines over the last decades. Usually monitored through a biomass-based approach, fisheries trends have rarely been characterized at the species level due to the high number of taxa involved and the difficulty to accurately and routinely identify individuals to the species level. Biomass, however, is a poor proxy of species richness, and automated methods of species identification are required to move beyond biomass-based approaches. Recent meta-analyses have demonstrated that species richness peaks at intermediary levels of biomass. Consequently, preserving biomass is not equal to preserving biodiversity. We present the results of a survey to estimate the shore fish diversity retailed at the harbor of Ambon Island, an island located at the center of the CT that display exceptionally high biomass despite high levels of threat, while building a DNA barcode reference library of CT shore fishes targeted by artisanal fisheries. We sampled 1,187 specimens and successfully barcoded 696 of the 760 selected specimens that represent 202 species. Our results show that DNA barcodes were effective in capturing species boundaries for 96% of the species examined, which opens new perspectives for the routine monitoring of the CT fisheries.},
}
@article {pmid32273595,
year = {2020},
author = {Park, HS and Jayakodi, M and Lee, SH and Jeon, JH and Lee, HO and Park, JY and Moon, BC and Kim, CK and Wing, RA and Newmaster, SG and Kim, JY and Yang, TJ},
title = {Mitochondrial plastid DNA can cause DNA barcoding paradox in plants.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {6112},
pmid = {32273595},
issn = {2045-2322},
mesh = {Cynanchum/classification/*genetics ; DNA Barcoding, Taxonomic/methods/*standards ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Phylogeny ; },
abstract = {The transfer of ancestral plastid genomes into mitochondrial genomes to generate mitochondrial plastid DNA (MTPT) is known to occur in plants, but its impacts on mitochondrial genome complexity and the potential for causing a false-positive DNA barcoding paradox have been underestimated. Here, we assembled the organelle genomes of Cynanchum wilfordii and C. auriculatum, which are indigenous medicinal herbs in Korea and China, respectively. In both species, it is estimated that 35% of the ancestral plastid genomes were transferred to mitochondrial genomes over the past 10 million years and remain conserved in these genomes. Some plastid barcoding markers co-amplified the conserved MTPTs and caused a barcoding paradox, resulting in mis-authentication of botanical ingredients and/or taxonomic mis-positioning. We identified dynamic and lineage-specific MTPTs that have contributed to mitochondrial genome complexity and might cause a putative barcoding paradox across 81 plant species. We suggest that a DNA barcoding guidelines should be developed involving the use of multiple markers to help regulate economically motivated adulteration.},
}
@article {pmid32273525,
year = {2020},
author = {Prakash, S and Ashley, BK and Doyle, PS and Hassan, U},
title = {Design of a Multiplexed Analyte Biosensor using Digital Barcoded Particles and Impedance Spectroscopy.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {6109},
pmid = {32273525},
issn = {2045-2322},
support = {P41 RR012408/RR/NCRR NIH HHS/United States ; T32 GM135141/GM/NIGMS NIH HHS/United States ; },
mesh = {Biosensing Techniques/*methods ; Cell Separation/methods ; Electric Impedance ; Microfluidics/*methods ; *Microspheres ; Spectrum Analysis/*methods ; },
abstract = {Multiplexing allows quantifying multiple analytes in a single step, providing advantages over individual testing through shorter processing time, lower sample volume, and reduced cost per test. Currently, flow cytometry is the gold standard for biomedical multiplexing, but requires technical training, extensive data processing, and expensive operational and capital costs. To solve this challenge, we designed digital barcoded particles and a microfluidic architecture for multiplexed analyte quantification. In this work, we simulate and model non-fluorescence-based microfluidic impedance detection with a single excitation and detection scheme using barcoded polymer microparticles. Our barcoded particles can be designed with specific coding regions and generate numerous distinct patterns enabling digital barcoding. We found that signals based on adhered microsphere position and relative orientation were evaluated and separated based on their associated electrical signatures and had a 7 µm microsphere limit of detection. Our proposed microfluidic system can enumerate micron-sized spheres in a single assay using barcoded particles of various configurations. As representation of blood cells, the microsphere concentrations may provide useful information on disease onset and progression. Such sensors may be used for diagnostic and management of common critical care diseases like sepsis, acute kidney injury, urinary tract infections, and HIV/AIDS.},
}
@article {pmid32268069,
year = {2021},
author = {Hobern, D},
title = {BIOSCAN: DNA barcoding to accelerate taxonomy and biogeography for conservation and sustainability.},
journal = {Genome},
volume = {64},
number = {3},
pages = {161-164},
doi = {10.1139/gen-2020-0009},
pmid = {32268069},
issn = {1480-3321},
mesh = {Animals ; *Biodiversity ; DNA ; *DNA Barcoding, Taxonomic ; Genomics ; Humans ; },
}
@article {pmid32265708,
year = {2020},
author = {Zhang, G and Liu, J and Gao, M and Kong, W and Zhao, Q and Shi, L and Wang, Q},
title = {Tracing the Edible and Medicinal Plant Pueraria montana and Its Products in the Marketplace Yields Subspecies Level Distinction Using DNA Barcoding and DNA Metabarcoding.},
journal = {Frontiers in pharmacology},
volume = {11},
number = {},
pages = {336},
pmid = {32265708},
issn = {1663-9812},
abstract = {Increased public awareness of nutritional and health issues has resulted in the increasing consumption of food and herbal products made from the root of Pueraria montana var. lobata (Willd.) Maesen &amp; S. M. Almeida ex Sanjappa &amp; Predeep (kudzu vine) and P. montana var. thomsonii (Benth.) M. R. Almeida. The famous herbal medicine Yufeng Ningxin, which is used to treat cardiovascular diseases, can be legally produced only using P. montana var. lobata. However, precise identification at the subspecies level is usually challenging when these products' ingredients lose their morphological characteristics after deep processing. Here, six herbarium specimens, 21 expert-identified original plant samples, 30 raw material samples, 10 food products and 12 herbal products were collected to test the subspecies-level authentication abilities of ITS2 sequences. The results showed that ITS2 sequences can distinguish P. montana var. lobata from P. montana var. thomsonii with stable single nucleotide polymorphism (SNP) sites. A total of 93.3% of raw material samples were consistent with the markings on their labels, but only 50% of Gegen Powder samples were made from P. montana var. lobata. High-quality ITS2 sequences were successfully obtained from nine of the 12 herbal products using Sanger sequencing. Substitution and fungal contamination were detected in 3 herbal products by further DNA metabarcoding, even though thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC) tests verified that the products met existing quality standards. This study demonstrated that DNA barcoding is a powerful tool for the identification of P. montana var. lobata and P. montana var. thomsonii at the subspecies level, and we conclude that DNA barcodes can be broadly applied to trace the raw materials of food and herbal products.},
}
@article {pmid32265692,
year = {2020},
author = {Cui, X and Li, W and Wei, J and Qi, Y and Li, R and Yang, Y and Shi, Y and Meng, X and Mi, Y and Huot, T and Sun, W and Zheng, X},
title = {Assessing the Identity of Commercial Herbs From a Cambodian Market Using DNA Barcoding.},
journal = {Frontiers in pharmacology},
volume = {11},
number = {},
pages = {244},
pmid = {32265692},
issn = {1663-9812},
abstract = {In Cambodia, medicinal plants are often used to treat various illnesses. However, the identities of many medicinal plants remain unknown. In this study, we collected 50 types of traditional Cambodian medicinal plants that could not be identified by their appearance from a domestic market. We utilized the DNA barcoding technique, combined with the literature survey, to trace their identities. In the end, 33 species were identified at the species level and 7 species were identified at the genus level. The ethnopharmacological information of 33 medicinal plants was documented. The DNA barcoding technique is useful in the identification of medicinal plants with no previous information.},
}
@article {pmid32256158,
year = {2020},
author = {Ferreira, SA and Andrade, R and Gonçalves, AR and Sousa, P and Paupério, J and Fonseca, NA and Beja, P},
title = {The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Diptera 01.},
journal = {Biodiversity data journal},
volume = {8},
number = {},
pages = {e49985},
pmid = {32256158},
issn = {1314-2828},
abstract = {BACKGROUND: The InBIO Barcoding Initiative (IBI) Diptera 01 dataset contains records of 203 specimens of Diptera. All specimens have been morphologically identified to species level, and belong to 154 species in total. The species represented in this dataset correspond to about 10% of continental Portugal dipteran species diversity. All specimens were collected north of the Tagus river in Portugal. Sampling took place from 2014 to 2018, and specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources.<br><br>NEW INFORMATION: This dataset contributes to the knowledge on the DNA barcodes and distribution of 154 species of Diptera from Portugal and is the first of the planned IBI database public releases, which will make available genetic and distribution data for a series of taxa. All specimens have their DNA barcodes made publicly available in the Barcode of Life Data System (BOLD) online database and the distribution dataset can be freely accessed through the Global Biodiversity Information Facility (GBIF).},
}
@article {pmid32256152,
year = {2020},
author = {Huemer, P and Karsholt, O and Aarvik, L and Berggren, K and Bidzilya, O and Junnilainen, J and Landry, JF and Mutanen, M and Nupponen, K and Segerer, A and Šumpich, J and Wieser, C and Wiesmair, B and Hebert, PDN},
title = {DNA barcode library for European Gelechiidae (Lepidoptera) suggests greatly underestimated species diversity.},
journal = {ZooKeys},
volume = {921},
number = {},
pages = {141-157},
pmid = {32256152},
issn = {1313-2989},
abstract = {For the first time, a nearly complete barcode library for European Gelechiidae is provided. DNA barcode sequences (COI gene - cytochrome c oxidase 1) from 751 out of 865 nominal species, belonging to 105 genera, were successfully recovered. A total of 741 species represented by specimens with sequences ≥ 500bp and an additional ten species represented by specimens with shorter sequences were used to produce 53 NJ trees. Intraspecific barcode divergence averaged only 0.54% whereas distance to the Nearest-Neighbour species averaged 5.58%. Of these, 710 species possessed unique DNA barcodes, but 31 species could not be reliably discriminated because of barcode sharing or partial barcode overlap. Species discrimination based on the Barcode Index System (BIN) was successful for 668 out of 723 species which clustered from minimum one to maximum 22 unique BINs. Fifty-five species shared a BIN with up to four species and identification from DNA barcode data is uncertain. Finally, 65 clusters with a unique BIN remained unidentified to species level. These putative taxa, as well as 114 nominal species with more than one BIN, suggest the presence of considerable cryptic diversity, cases which should be examined in future revisionary studies.},
}
@article {pmid32256151,
year = {2020},
author = {Huemer, P and Karsholt, O},
title = {Commented checklist of European Gelechiidae (Lepidoptera).},
journal = {ZooKeys},
volume = {921},
number = {},
pages = {65-140},
pmid = {32256151},
issn = {1313-2989},
abstract = {The checklist of European Gelechiidae covers 865 species, belonging to 109 genera, with three species records which require confirmation. Further, it is the first checklist to include a complete coverage of proved synonyms of species and at generic level. The following taxonomic changes are introduced: Pseudosophronia constanti (Nel, 1998) syn. nov. of Pseudosophronia exustellus (Zeller, 1847), Metzneria expositoi Vives, 2001 syn. nov. of Metzneria aestivella (Zeller, 1839); Sophronia ascalis Gozmány, 1951 syn. nov. of Sophronia grandii Hering, 1933, Aproaerema incognitana (Gozmány, 1957) comb. nov., Aproaerema cinctelloides (Nel &amp; Varenne, 2012) comb. nov., Aproaerema azosterella (Herrich-Schäffer, 1854) comb. nov., Aproaerema montanata (Gozmány, 1957) comb. nov., Aproaerema cincticulella (Bruand, 1851) comb. nov., Aproaerema buvati (Nel, 1995) comb. nov., Aproaerema linella (Chrétien, 1904) comb. nov., Aproaerema captivella (Herrich-Schäffer, 1854) comb. nov., Aproaerema semicostella (Staudinger, 1871) comb. nov., Aproaerema steppicola (Junnilainen, 2010) comb. nov., Aproaerema cottienella (Nel, 2012) comb. nov., Ptocheuusa cinerella (Chrétien, 1908) comb. nov., Pragmatodes melagonella (Constant, 1895) comb. nov., Pragmatodes albagonella (Varenne &amp; Nel, 2010) comb. nov., Pragmatodes parvulata (Gozmány, 1953) comb. nov., Oxypteryx nigromaculella (Millière, 1872) comb. nov., Oxypteryx wilkella (Linnaeus, 1758) comb. nov., Oxypteryx ochricapilla (Rebel, 1903) comb. nov., Oxypteryx superbella (Zeller, 1839) comb. nov., Oxypteryx mirusella (Huemer &amp; Karsholt, 2013) comb. nov., Oxypteryx baldizzonei (Karsholt &amp; Huemer, 2013) comb. nov., Oxypteryx occidentella (Huemer &amp; Karsholt, 2011) comb. nov., Oxypteryx libertinella (Zeller, 1872) comb. nov., Oxypteryx gemerensis (Elsner, 2013) comb. nov., Oxypteryx deserta (Piskunov, 1990) comb. nov., Oxypteryx unicolorella (Duponchel, 1843) comb. nov., Oxypteryx nigritella (Zeller, 1847) comb. nov., Oxypteryx plumbella (Heinemann, 1870) comb. nov., Oxypteryx isostacta (Meyrick, 1926) comb. nov., Oxypteryx helotella (Staudinger, 1859) comb. nov., Oxypteryx parahelotella (Nel, 1995) comb. nov., Oxypteryx graecatella (Šumpich &amp; Skyva, 2012) comb. nov.; Aproaerema genistae (Walsingham, 1908) comb. rev., Aproaerema thaumalea (Walsingham, 1905) comb. rev.; Dichomeris neatodes Meyrick, 1923 sp. rev.; Caryocolum horoscopa (Meyrick, 1926) stat. rev.; Ivanauskiella occitanica (Nel &amp; Varenne, 2013) sp. rev.; Apodia martinii Petry, 1911 sp. rev.; Caulastrocecis cryptoxena (Gozmány, 1952) sp. rev. Following Article 23.9.2 ICZN we propose Caryocolum blandella (Douglas, 1852) (Gelechia) nom. protectum and Caryocolum signatella (Eversmann, 1844) (Lita) nom. oblitum.},
}
@article {pmid32252306,
year = {2020},
author = {Prodinger, F and Endo, H and Gotoh, Y and Li, Y and Morimoto, D and Omae, K and Tominaga, K and Blanc-Mathieu, R and Takano, Y and Hayashi, T and Nagasaki, K and Yoshida, T and Ogata, H},
title = {An Optimized Metabarcoding Method for Mimiviridae.},
journal = {Microorganisms},
volume = {8},
number = {4},
pages = {},
pmid = {32252306},
issn = {2076-2607},
support = {203143100025//The Canon Foundation/ ; 26430184//Japan Society for the Promotion of Science/ ; 17H03850//Japan Society for the Promotion of Science/ ; 18H02279//Japan Society for the Promotion of Science/ ; 16H06279//Japan Society for the Promotion of Science/ ; 16H06429//Scientific Research on Innovative Areas from the Ministry of Education, Culture, Science, Sports and Technology (MEXT) of Japan/ ; 16K21723//Scientific Research on Innovative Areas from the Ministry of Education, Culture, Science, Sports and Technology (MEXT) of Japan/ ; 16H06437//Scientific Research on Innovative Areas from the Ministry of Education, Culture, Science, Sports and Technology (MEXT) of Japan/ ; 2019-33//The Kyoto University Foundation/ ; 2018-31//The Kyoto University Foundation/ ; 2017-25//The Kyoto University Foundation/ ; 2016-28//The Kyoto University Foundation/ ; },
abstract = {Mimiviridae is a group of viruses with large genomes and virions. Ecological relevance of Mimiviridae in marine environments has been increasingly recognized through the discoveries of novel isolates and metagenomic studies. To facilitate ecological profiling of Mimiviridae, we previously proposed a meta-barcoding approach based on 82 degenerate primer pairs (i.e., MEGAPRIMER) targeting the DNA polymerase gene of Mimiviridae. The method detected a larger number of operational taxonomic units (OTUs) in environmental samples than previous methods. However, it required large quantities of DNA and was laborious due to the use of individual primer pairs. Here, we examined coastal seawater samples using varying PCR conditions and purification protocols to streamline the MEGAPRIMER method. Mixing primer pairs in "cocktails" reduced the required amount of environmental DNA by 90%, while reproducing the results obtained by the original protocol. We compared the results obtained by the meta-barcoding approach with quantifications using qPCR for selected OTUs. This revealed possible amplification biases among different OTUs, but the frequency profiles for individual OTUs across multiple samples were similar to those obtained by qPCR. We anticipate that the newly developed MEGAPRIMER protocols will be useful for ecological investigation of Mimiviridae in a larger set of environmental samples.},
}
@article {pmid32247883,
year = {2020},
author = {Tremble, K and Suz, LM and Dentinger, BTM},
title = {Lost in translation: Population genomics and long-read sequencing reveals relaxation of concerted evolution of the ribosomal DNA cistron.},
journal = {Molecular phylogenetics and evolution},
volume = {148},
number = {},
pages = {106804},
doi = {10.1016/j.ympev.2020.106804},
pmid = {32247883},
issn = {1095-9513},
mesh = {Agaricales/*genetics ; DNA, Ribosomal/*genetics ; DNA, Ribosomal Spacer/genetics ; *Evolution, Molecular ; Gene Frequency/genetics ; Genetic Loci ; Genetic Variation ; Genetics, Population ; Genome, Fungal ; *Genomics ; Haplotypes/genetics ; Likelihood Functions ; Metagenomics ; Nanopore Sequencing ; Phylogeny ; *Sequence Analysis, DNA ; },
abstract = {Concerted evolution of the ribosomal DNA array has been studied in numerous eukaryotic taxa, yet is still poorly understood. rDNA genes are repeated dozens to hundreds of times in the eukaryotic genome (Eickbush and Eickbush, 2007) and it is believed that these arrays are homogenized through concerted evolution (Zimmer et al., 1980; Dover, 1993) preventing the accumulation of intragenomic, and intraspecific, variation. However, numerous studies have reported rampant intragenomic and intraspecific variation in the rDNA array (Ganley and Kobayashi, 2011; Naidoo et al., 2013; Hughes and Petersen, 2001; Lindner and Banik, 2011; Li et al., 2013; Lindner et al., 2013; Hughes et al., 2018), contradicting our current understanding of concerted evolution. The internal transcribed spacers (ITS) of the rDNA cistron are the most commonly used DNA barcoding region in Fungi (Schoch et al., 2012), and rely on concerted evolution to homogenize the rDNA array leading to a "barcode gap" (Puillandre et al., 2012). Here we show that in Boletus edulis Bull., ITS intragenomic variation persists at low allele frequencies throughout the rDNA array, this variation does not correlate with genomic relatedness between populations, and rDNA genes may not evolve in a strictly concerted fashion despite the presence of unequal recombination and gene conversion. Under normal assumptions, heterozygous positions found in ITS sequences represent hybridization between populations, yet through allelic mapping of the rDNA array we found numerous heterozygous alleles to be stochastically introgressed throughout, presenting a dishonest signal of gene flow. Moreover, despite the signal of gene flow in ITS, our organisms were highly inbred, indicating a disconnect between true gene flow and barcoding signals. In addition, we show that while the mechanisms of concerted evolution are ongoing in pseudo-heterozygous individuals, they are not fully homogenizing the ITS array. Concerted evolution of the rDNA array may insufficiently homogenize the ITS gene, allowing for misleading signals of gene flow to persist, vastly complicating the use of the ITS locus for DNA barcoding in Fungi.},
}
@article {pmid32246984,
year = {2021},
author = {Freitag, F and Wagner, E},
title = {Optimizing synthetic nucleic acid and protein nanocarriers: The chemical evolution approach.},
journal = {Advanced drug delivery reviews},
volume = {168},
number = {},
pages = {30-54},
doi = {10.1016/j.addr.2020.03.005},
pmid = {32246984},
issn = {1872-8294},
mesh = {Algorithms ; Chemistry, Pharmaceutical ; Computational Chemistry ; Drug Carriers/*chemistry ; *Evolution, Chemical ; Macromolecular Substances/administration &amp; dosage ; Nanoparticles/*chemistry ; Nucleic Acids/*chemistry ; Polymers/chemistry ; Proteins/*chemistry ; },
abstract = {Optimizing synthetic nanocarriers is like searching for a needle in a haystack. How to find the most suitable carrier for intracellular delivery of a specified macromolecular nanoagent for a given disease target location? Here, we review different synthetic 'chemical evolution' strategies that have been pursued. Libraries of nanocarriers have been generated either by unbiased combinatorial chemistry or by variation and novel combination of known functional delivery elements. As in natural evolution, definition of nanocarriers as sequences, as barcode or design principle, may fuel chemical evolution. Screening in appropriate test system may not only provide delivery candidates, but also a refined understanding of cellular delivery including novel, unpredictable mechanisms. Combined with rational design and computational algorithms, candidates can be further optimized in subsequent evolution cycles into nanocarriers with improved safety and efficacy. Optimization of nanocarriers differs for various cargos, as illustrated for plasmid DNA, siRNA, mRNA, proteins, or genome-editing nucleases.},
}
@article {pmid32246736,
year = {2020},
author = {Wu, LL and Zhang, ZL and Tang, M and Zhu, DL and Dong, XJ and Hu, J and Qi, CB and Tang, HW and Pang, DW},
title = {Spectrally Combined Encoding for Profiling Heterogeneous Circulating Tumor Cells Using a Multifunctional Nanosphere-Mediated Microfluidic Platform.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {59},
number = {28},
pages = {11240-11244},
doi = {10.1002/anie.201914468},
pmid = {32246736},
issn = {1521-3773},
mesh = {Biomarkers, Tumor/blood ; Cell Line, Tumor ; DNA Barcoding, Taxonomic ; Humans ; *Microfluidics ; Microscopy, Fluorescence ; *Nanospheres ; *Neoplastic Cells, Circulating ; Proof of Concept Study ; },
abstract = {Comprehensive phenotypic profiling of heterogeneous circulating tumor cells (CTCs) at single-cell resolution has great importance for cancer management. Herein, a novel spectrally combined encoding (SCE) strategy was proposed for multiplex biomarker profiling of single CTCs using a multifunctional nanosphere-mediated microfluidic platform. Different cellular biomarkers uniquely labeled by multifunctional nanosphere barcodes, possessing identical magnetic tags and distinct optical signatures, enabled isolation of heterogeneous CTCs with over 91.6 % efficiency and in situ SCE of phenotypes. By further trapping individual CTCs in ordered microstructures on chip, composite single-cell spectral signatures were conveniently and efficiently obtained, allowing reliable spectral-readout for multiplex biomarker profiling. This SCE strategy exhibited great potential in multiplex profiling of heterogeneous CTC phenotypes, offering new avenues for cancer study and precise medicine.},
}
@article {pmid32246716,
year = {2020},
author = {Zhang, T and Pilko, A and Wollman, R},
title = {Loci specific epigenetic drug sensitivity.},
journal = {Nucleic acids research},
volume = {48},
number = {9},
pages = {4797-4810},
pmid = {32246716},
issn = {1362-4962},
support = {R01 GM111404/GM/NIGMS NIH HHS/United States ; },
mesh = {Acetylation/drug effects ; Azacitidine/pharmacology ; Azepines/pharmacology ; Chromosomes, Human ; DNA Methylation/drug effects ; Epigenesis, Genetic/*drug effects ; Genes, Reporter ; Genetic Loci ; Genomics/methods ; Histones/metabolism ; Humans ; K562 Cells ; Sequence Analysis, DNA ; Triazoles/pharmacology ; },
abstract = {Therapeutic targeting of epigenetic modulators offers a novel approach to the treatment of multiple diseases. The cellular consequences of chemical compounds that target epigenetic regulators (epi-drugs) are complex. Epi-drugs affect global cellular phenotypes and cause local changes to gene expression due to alteration of a gene chromatin environment. Despite increasing use in the clinic, the mechanisms responsible for cellular changes are unclear. Specifically, to what degree the effects are a result of cell-wide changes or disease related locus specific effects is unknown. Here we developed a platform to systematically and simultaneously investigate the sensitivity of epi-drugs at hundreds of genomic locations by combining DNA barcoding, unique split-pool encoding, and single cell expression measurements. Internal controls are used to isolate locus specific effects separately from any global consequences these drugs have. Using this platform we discovered wide-spread loci specific sensitivities to epi-drugs for three distinct epi-drugs that target histone deacetylase, DNA methylation and bromodomain proteins. By leveraging ENCODE data on chromatin modification, we identified features of chromatin environments that are most likely to be affected by epi-drugs. The measurements of loci specific epi-drugs sensitivities will pave the way to the development of targeted therapy for personalized medicine.},
}
@article {pmid32246241,
year = {2020},
author = {Watanabe, K and Kobayashi, I and Hatakeyama, M and Kayukawa, T and Akiduki, G},
title = {Establishment and characterization of novel cell lines derived from six lepidopteran insects collected in the field.},
journal = {In vitro cellular &amp; developmental biology. Animal},
volume = {56},
number = {6},
pages = {425-429},
doi = {10.1007/s11626-020-00438-5},
pmid = {32246241},
issn = {1543-706X},
mesh = {Animals ; Cell Culture Techniques/*methods ; Cell Line/*cytology ; Cell Proliferation ; Cell Shape ; Green Fluorescent Proteins/metabolism ; Lepidoptera/*cytology ; Transfection ; },
abstract = {Insect cell lines are used to study cellular interactions and gene functions in vitro in several research areas. However, suitable cell lines for experiments are not always available, especially in non-model species. Here, we established novel cell lines derived from fat bodies of six lepidopteran insects: Cydia kurokoi (named NARO-Cyku), Cephonodes hylas (NARO-Cehy), Haritalodes basipunctalis (NARO-Haba), Theretra oldenlandiae (NARO-Thol), Lymantria dispar (NARO-Lydi), and Hyphantria cunea (NARO-Hycu) collected in the field. The larval fat body was a promising tissue for the starting material when samples were limited due to field collection. It was critical that the medium volume was kept to a minimum for primary culture to maintain adherence of the fat body cells to the flask. The flask was coated with poly-L-lysine for effective induction of adherence and cell division. The identities of cell lines were confirmed using DNA barcoding with the mitochondrial cytochrome c oxidase I gene after cultures were passaged over 50 times. All lines except for NARO-Lydi and NARO-Hycu are adherent cells, and population doubling time of six cell lines ranged from 1.03 to 2.49. Induction of gene expression was practicable in the four adherent cell lines as revealed by transfection of expression vectors and found the immediate early 2 and the Bombyx actin 3 were effective gene promoters. The results suggest that these cell lines are capable of gene functional analysis. Thus, establishments of cell line using our methods for non-model lepidopterans could make a practical contribution to pest management and insect utilization.},
}
@article {pmid32245364,
year = {2020},
author = {Wu, L and Deng, Q and Xu, Z and Zhou, S and Li, C and Li, YX},
title = {A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA.},
journal = {BMC bioinformatics},
volume = {21},
number = {1},
pages = {127},
pmid = {32245364},
issn = {1471-2105},
support = {2017YFA0505500//National Key R&amp;D Program of China/ ; },
mesh = {*Algorithms ; Circulating Tumor DNA/*chemistry ; Computer Simulation ; Humans ; Mutation ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: Hybrid capture-based next-generation sequencing of DNA has been widely applied in the detection of circulating tumor DNA (ctDNA). Various methods have been proposed for ctDNA detection, but low-allelic-fraction (AF) variants are still a great challenge. In addition, no panel-wide calling algorithm is available, which hiders the full usage of ctDNA based 'liquid biopsy'. Thus, we developed the VBCALAVD (Virtual Barcode-based Calling Algorithm for Low Allelic Variant Detection) in silico to overcome these limitations.<br><br>RESULTS: Based on the understanding of the nature of ctDNA fragmentation, a novel platform-independent virtual barcode strategy was established to eliminate random sequencing errors by clustering sequencing reads into virtual families. Stereotypical mutant-family-level background artifacts were polished by constructing AF distributions. Three additional robust fine-tuning filters were obtained to eliminate stochastic mutant-family-level noises. The performance of our algorithm was validated using cell-free DNA reference standard samples (cfDNA RSDs) and normal healthy cfDNA samples (cfDNA controls). For the RSDs with AFs of 0.1, 0.2, 0.5, 1 and 5%, the mean F1 scores were 0.43 (0.25~0.56), 0.77, 0.92, 0.926 (0.86~1.0) and 0.89 (0.75~1.0), respectively, which indicates that the proposed approach significantly outperforms the published algorithms. Among controls, no false positives were detected. Meanwhile, characteristics of mutant-family-level noise and quantitative determinants of divergence between mutant-family-level noises from controls and RSDs were clearly depicted.<br><br>CONCLUSIONS: Due to its good performance in the detection of low-AF variants, our algorithm will greatly facilitate the noninvasive panel-wide detection of ctDNA in research and clinical settings. The whole pipeline is available at https://github.com/zhaodalv/VBCALAVD.},
}
@article {pmid32244739,
year = {2020},
author = {Young, KI and Medwid, JT and Azar, SR and Huff, RM and Drumm, H and Coffey, LL and Pitts, RJ and Buenemann, M and Vasilakis, N and Perera, D and Hanley, KA},
title = {Identification of Mosquito Bloodmeals Collected in Diverse Habitats in Malaysian Borneo Using COI Barcoding.},
journal = {Tropical medicine and infectious disease},
volume = {5},
number = {2},
pages = {},
pmid = {32244739},
issn = {2414-6366},
support = {U01 AI115577/AI/NIAID NIH HHS/United States ; NIH T35 OD010956//Students Training in Advanced Research/ ; },
abstract = {Land cover and land use change (LCLUC) acts as a catalyst for spillover of arthropod-borne pathogens into novel hosts by shifting host and vector diversity, abundance, and distribution, ultimately reshaping host-vector interactions. Identification of bloodmeals from wild-caught mosquitoes provides insight into host utilization of particular species in particular land cover types, and hence their potential role in pathogen maintenance and spillover. Here, we collected 134 blood-engorged mosquitoes comprising 10 taxa across 9 land cover types in Sarawak, Malaysian Borneo, a region experiencing intense LCLUC and concomitant spillover of arthropod-borne pathogens. Host sources of blood were successfully identified for 116 (87%) mosquitoes using cytochrome oxidase subunit I (COI) barcoding. A diverse range of hosts were identified, including reptiles, amphibians, birds, and mammals. Sixteen engorged Aedes albopictus, a major vector of dengue virus, were collected from seven land cover types and found to feed exclusively on humans (73%) and boar (27%). Culex tritaeniohynchus (n = 2), Cx. gelidus (n = 3), and Cx. quiquefasciatus (n = 3), vectors of Japanese encephalitis virus, fed on humans and pigs in the rural built-up land cover, creating potential transmission networks between these species. Our data support the use of COI barcoding to characterize mosquito-host networks in a biodiversity hotspot.},
}
@article {pmid32244630,
year = {2020},
author = {Avanesyan, A and Lamp, WO},
title = {Use of Molecular Gut Content Analysis to Decipher the Range of Food Plants of the Invasive Spotted Lanternfly, Lycorma delicatula.},
journal = {Insects},
volume = {11},
number = {4},
pages = {},
pmid = {32244630},
issn = {2075-4450},
support = {191501-02//Maryland Department of Agriculture's Specialty Crop Block Grant Program/ ; MD-ENTM-1802//the Hatch Project/ ; },
abstract = {Spotted lanternfly, Lycorma delicatula (Hemiptera: Fulgoridae), is an introduced highly invasive insect pest in the US that poses a significant risk to forestry and agriculture. Assessing and predicting plant usage of the lanternfly has been challenging, and little is known regarding the lanternfly nymph association with its host plants. In this study, we focused on: (a) providing a protocol for using molecular markers for food plant identification of L. delicatula; (b) determining whether the ingested plant DNA corresponds with DNA of the plants from which the lanternfly was collected; and, (c) investigating the spectrum of ingested plants. We utilized gut contents of third and fourth instar nymphs that were collected from multiple plants; we isolated ingested plant DNA and identified consumed plants. We demonstrated that (a) up to 534 bp of the rbcL gene from ingested plants can be detected in L. delicatula guts, (b) ingested plants in ~93% of the nymphs did not correspond with the plants from which the nymphs were collected, and (c) both introduced and native plants, as well as woody and non-woody plants, were ingested. This information will aid effective the monitoring and management of the lanternfly, as well as predict the lanternfly host plants with range expansion.},
}
@article {pmid32244605,
year = {2020},
author = {Alsos, IG and Lavergne, S and Merkel, MKF and Boleda, M and Lammers, Y and Alberti, A and Pouchon, C and Denoeud, F and Pitelkova, I and Pușcaș, M and Roquet, C and Hurdu, BI and Thuiller, W and Zimmermann, NE and Hollingsworth, PM and Coissac, E},
title = {The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material.},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {4},
pages = {},
pmid = {32244605},
issn = {2223-7747},
support = {226134/F50//Norges Forskningsr&#xe5;d/ ; 14-14, 70184209//Norwegian Biodiversity Information Centre/ ; PhD internal funded//Universitetet i Troms&#xf8;/ ; FP7/2007-2013 281422//Seventh Framework Programme/ ; GOCE-CT-2007-036866//Sixth Framework Programme/ ; Grant 31003A_149508/1//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; NextBarcode project//Institut Fran&#xe7;ais de Bioinformatique/ ; ANR-07-BDIV-014//Agence Nationale de la Recherche/ ; ANR-13-ISV7-0004//Agence Nationale de la Recherche/ ; PN-II-ID-JRP-RO-FR-2012//Agence Nationale de la Recherche/ ; BRANCUSI No. 32660WB//Agence Nationale de la Recherche/ ; PN-II-CT-ROFR-2014-2-0011//Agence Nationale de la Recherche/ ; PN-II-RU-PD-2012-3-0636//Romanian Ministry of Education/ ; ANR-10-INBS-09-08//France G&#xe9;nomique/ ; },
abstract = {Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.},
}
@article {pmid32243090,
year = {2020},
author = {Allio, R and Schomaker-Bastos, A and Romiguier, J and Prosdocimi, F and Nabholz, B and Delsuc, F},
title = {MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics.},
journal = {Molecular ecology resources},
volume = {20},
number = {4},
pages = {892-905},
pmid = {32243090},
issn = {1755-0998},
support = {ERC-2015-CoG-683257//H2020 European Research Council/ ; ANR-10-LABX-0004//Agence Nationale de la Recherche/ ; ANR-10-LABX-25-01//Agence Nationale de la Recherche/ ; },
mesh = {Animals ; Ants/genetics ; Biological Evolution ; Computational Biology/*methods ; Conserved Sequence/genetics ; DNA, Mitochondrial/genetics ; Genome, Mitochondrial/genetics ; Genomics/*methods ; Phylogeny ; Sequence Analysis, DNA/methods ; Software ; Transcriptome/genetics ; },
abstract = {Thanks to the development of high-throughput sequencing technologies, target enrichment sequencing of nuclear ultraconserved DNA elements (UCEs) now allows routine inference of phylogenetic relationships from thousands of genomic markers. Recently, it has been shown that mitochondrial DNA (mtDNA) is frequently sequenced alongside the targeted loci in such capture experiments. Despite its broad evolutionary interest, mtDNA is rarely assembled and used in conjunction with nuclear markers in capture-based studies. Here, we developed MitoFinder, a user-friendly bioinformatic pipeline, to efficiently assemble and annotate mitogenomic data from hundreds of UCE libraries. As a case study, we used ants (Formicidae) for which 501 UCE libraries have been sequenced whereas only 29 mitogenomes are available. We compared the efficiency of four different assemblers (IDBA-UD, MEGAHIT, MetaSPAdes, and Trinity) for assembling both UCE and mtDNA loci. Using MitoFinder, we show that metagenomic assemblers, in particular MetaSPAdes, are well suited to assemble both UCEs and mtDNA. Mitogenomic signal was successfully extracted from all 501 UCE libraries, allowing us to confirm species identification using CO1 barcoding. Moreover, our automated procedure retrieved 296 cases in which the mitochondrial genome was assembled in a single contig, thus increasing the number of available ant mitogenomes by an order of magnitude. By utilizing the power of metagenomic assemblers, MitoFinder provides an efficient tool to extract complementary mitogenomic data from UCE libraries, allowing testing for potential mitonuclear discordance. Our approach is potentially applicable to other sequence capture methods, transcriptomic data and whole genome shotgun sequencing in diverse taxa. The MitoFinder software is available from GitHub (https://github.com/RemiAllio/MitoFinder).},
}
@article {pmid32240264,
year = {2020},
author = {Blekhman, A and Goryacheva, I and Schepetov, D and Zakharov, I},
title = {Variability of the mitochondrial CO1 gene in native and invasive populations of Harmonia axyridis Pall. comparative analysis.},
journal = {PloS one},
volume = {15},
number = {4},
pages = {e0231009},
pmid = {32240264},
issn = {1932-6203},
mesh = {Animals ; Biological Evolution ; Coleoptera/*genetics ; Genes, Mitochondrial/*genetics ; Genetic Variation/*genetics ; Genetics, Population/methods ; Haplotypes/genetics ; Introduced Species ; North America ; },
abstract = {Our study is focused on original and publicly accessible data on the intraspecific variability of the barcoding DNA fragment in ladybirds Harmonia axyridis Pall analysis. The complete dataset consists of 39 haplotypes, 16 of which we identified for the first time. The intra-population and geographical variability of the barcoding fragment was studied for seven populations of the western and eastern groups of the native range and in six invasive populations, in which 25 of the 39 haplotypes are found. Population structure inferred on base of molecular variability and haplotype frequencies showed a high level of differences between the eastern and western groups of native populations and confirm the hypothesis of the origin of all invasive populations from native populations of the eastern group. A comparative analysis of molecular variation indices testifies to various evolutionary scenarios of the formation of the western and eastern groups of native populations and confirms the hypothesis of the microevolutionary history of the species, previously suggested in morphological character based studies of the geographical variability of H. axyridis. A significant decrease in the molecular diversity of invasive populations confirms the hypothesis of a random nature of the primary invasion of this species in North America.},
}
@article {pmid32233825,
year = {2020},
author = {Li, R and Li, S and Yang, X and Guo, Y and Duan, B and Xu, L and Xia, C},
title = {Identification of Tibetan medicine Dida based on DNA barcoding.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {31},
number = {4},
pages = {131-138},
doi = {10.1080/24701394.2020.1741563},
pmid = {32233825},
issn = {2470-1408},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic/*methods ; DNA, Intergenic/genetics ; DNA, Plant/*genetics ; Databases, Factual ; Drugs, Chinese Herbal/*analysis/classification ; Medicine, Tibetan Traditional ; Phylogeny ; Polymerase Chain Reaction ; Swertia/*classification/genetics ; },
abstract = {The purpose of this study was to test the ability of DNA barcoding to identify the herbal raw trade of Tibetan medicine Dida in China. A reference database for plant-material DNA barcodes was successfully constructed and used to identify 36 commercially samples of Dida collected from Southwest China. The ITS sequence was amplified from these samples and the efficiency of the PCR amplification of ITS was 100%. The DNA sequencing results revealed that 3 samples (8.3%) were authenticated as Swertia chirayita, 2 sequences (5.6%) were authenticated as Swertia mussotii, 3 sequences (8.3%) were authenticated as Swertia ciliata, as recorded in the Tibetan Pharmacopeia. The other samples were authenticated as adulterants and all of them originated from common plants belonging to Saxifraga, Swertia and Halenia. This result indicates Dida pieces that are available in the market have complex origins and may indicate a potential safety issue and DNA barcoding is a convenient tool for market supervision.},
}
@article {pmid32231870,
year = {2020},
author = {Mesmin, X and Chartois, M and Genson, G and Rossi, JP and Cruaud, A and Rasplus, JY},
title = {Ooctonus vulgatus (Hymenoptera, Mymaridae), a potential biocontrol agent to reduce populations of Philaenus spumarius (Hemiptera, Aphrophoridae) the main vector of Xylella fastidiosa in Europe.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e8591},
pmid = {32231870},
issn = {2167-8359},
abstract = {As a vector of Xylella fastidiosa (Wells, 1987) in Europe, the meadow spittlebug Philaenus spumarius (Linnaeus, 1758) (Hemiptera, Aphrophoridae) is a species of major concern. Therefore, tools and agents to control this ubiquitous insect that develops and feeds on hundreds of plant species are wanted. We conducted a field survey of P. spumarius eggs in Corsica and provide a first report of Ooctonus vulgatus Haliday, 1833 (Hymenoptera, Mymaridae) as a potential biocontrol agent of P. spumarius in Europe. To allow species identification, we summarized the main characters distinguishing O. vulgatus from other European species of Ooctonus and generated COI DNA barcodes. Parasitism rates were variable in the four localities included in the survey but could reach 69% (for an average number of eggs that hatched per locality of 109). Based on the geographic occurrences of O. vulgatus obtained from the literature, we calibrated an ecological niche model to assess its potential distribution in the Holarctic. Obviously, several questions need to be addressed to determine whether O. vulgatus could become an effective biocontrol agent of P. spumarius in Europe. So far, O. vulgatus has been reared only from P. spumarius eggs, but its exact host-range should be evaluated to ensure efficiency and avoid non-target effect. The top-down impact of the parasitoid on vector populations should also be assessed on large data sets. Finally, the feasibility of mass rearing should be tested. We hope this report serves as a starting point to initiate research on this parasitoid wasp to assess whether it could contribute to reduce the spread and impact of X. fastidiosa in Europe.},
}
@article {pmid32231869,
year = {2020},
author = {Weng, J and Chen, T and Xie, Y and Xu, X and Zhang, G and Peters, BA and Drmanac, R},
title = {IterCluster: a barcode clustering algorithm for long fragment read analysis.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e8431},
pmid = {32231869},
issn = {2167-8359},
abstract = {Recent advances in long fragment read (LFR, also known as linked-read technologies or read-cloud) technologies, such as single tube long fragment reads (stLFR), 10X Genomics Chromium reads, and TruSeq synthetic long-reads, have enabled efficient haplotyping and genome assembly. However, in the case of stLFR and 10X Genomics Chromium reads, the long fragments of a genome are covered sparsely by reads in each barcode and most barcodes are contained in multiple long fragments from different regions, which results in inefficient assembly when using long-range information. Thus, methods to address these shortcomings are vital for capitalizing on the additional information obtained using these technologies. We therefore designed IterCluster, a novel, alignment-free clustering algorithm that can cluster barcodes from the same target region of a genome, using -mer frequency-based features and a Markov Cluster (MCL) approach to identify enough reads in a target region of a genome to ensure sufficient target genome sequence depth. The IterCluster method was validated using BGI stLFR and 10X Genomics chromium reads datasets. IterCluster had a higher precision and recall rate on BGI stLFR data compared to 10X Genomics Chromium read data. In addition, we demonstrated how IterCluster improves the de novo assembly results when using a divide-and-conquer strategy on a human genome data set (scaffold/contig N50 = 13.2 kbp/7.1 kbp vs. 17.1 kbp/11.9 kbp before and after IterCluster, respectively). IterCluster provides a new way for determining LFR barcode enrichment and a novel approach for de novo assembly using LFR data. IterCluster is OpenSource and available on https://github.com/JianCong-WENG/IterCluster.},
}
@article {pmid32230909,
year = {2020},
author = {Iturrieta-González, I and García, D and Guarro, J and Gené, J},
title = {Heliocephala variabilis and Pseudopenidiella vietnamensis: Two New Hyphomycetous Species in the Microthyriaceae (Dothideomycetes) from Vietnam.},
journal = {Microorganisms},
volume = {8},
number = {4},
pages = {},
pmid = {32230909},
issn = {2076-2607},
abstract = {In a survey of microfungi from plant debris collected in Vietnam, two new hyphomycetous species were found, which belong to the genera Heliocephala and Pseudopenidiella and the family Microthyriaceae (Microthyriales, Dothideomycetes). Maximum Likelihood and Bayesian Inference sequence analyses of the internal transcribed spacers (ITS) and large subunit (LSU) of the ribosomal DNA barcodes allowed assessing the phylogenetic relationships of the new species with other species of the respective genera. Heliocephala variabilis sp. nov. was closely related to Heliocephala elegans, Heliocephala gracilis, and Heliocephala zimbabweensis, from which it was morphologically distinguished by its smaller conidiophores and non-rostrate conidia of up to four septa on the natural substratum. Pseudopenidiella vietnamensis sp. nov. was related to Pseudopenidiella piceae and Pseudopenidiella podocarpi and differed from the former principally by its lack of microcondiophores and from P. podocarpi by having larger macroconidiophores and smooth conidia. Key morphological features to distinguish the accepted species in Heliocephala and Pseudopenidiella are also provided. In addition, Pseudopenidiella pini was excluded from the genus on the basis of its morphological features.},
}
@article {pmid32230691,
year = {2019},
author = {Cumming, JM and Cumming, HJ},
title = {Additional DNA barcodes confirm recent morphological species concepts and synonymies in Callomyia Meigen (Diptera: Platypezidae).},
journal = {Zootaxa},
volume = {4712},
number = {2},
pages = {zootaxa.4712.2.9},
doi = {10.11646/zootaxa.4712.2.9},
pmid = {32230691},
issn = {1175-5334},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Diptera/genetics ; Female ; },
abstract = {Cumming Wheeler (2016) revised the Nearctic species of the sexually dimorphic flat-footed fly genus Callomyia Meigen (Callomyiinae) recognizing 10 Nearctic species, including three newly described taxa, namely C. argentea Cumming, C. arnaudi Cumming, and C. browni Cumming. They also described the unknown female of C. velutina Johnson and proposed three new synonymies associating species previously described from one sex only with others described from the opposite sex (Kessel 1948; Kessel Buegler 1972). Callomyia cleta Kessel was considered a junior synonym of C. calla Kessel, C. clara Kessel was considered a junior synonym of C. corvina Kessel, and C. liardia Kessel Buegler was synonymized with C. proxima Johnson.},
}
@article {pmid32230632,
year = {2020},
author = {Quigg, SM and Lowe, CN and Butt, KR and Mitcham, T and Iyengar, A},
title = {A re-examination of the taxonomic status of Prostoma jenningsi-a Freshwater Nemertean.},
journal = {Zootaxa},
volume = {4722},
number = {2},
pages = {zootaxa.4722.2.4},
doi = {10.11646/zootaxa.4722.2.4},
pmid = {32230632},
issn = {1175-5334},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Electron Transport Complex IV ; Fresh Water ; Invertebrates ; Phylogeny ; },
abstract = {Prostoma jenningsi was first recorded at the Clay 'Ole pond in Lancashire, UK, in 1969 and was distinguished histologically from other Prostoma by the presence of 11 proboscidial nerves (with all other Prostoma species thought to have 9-10). P. jenningsi was considered to be the only species endemic to Lancashire and listed in the British Red Data Book as 'Insufficiently Known' as well as a 'Species of Principal Importance' under the UK Natural Environment and Rural Communities Act (2006). A limited number of Prostoma spp were recovered from the Clay 'Ole in 2011 (the first confirmation of the presence of Prostoma spp. since 1999). In 2015, further sampling was undertaken and expanded to other ponds in Lancashire resulting in the discovery of Prostoma spp. at a further 3 locations. Thereafter, DNA sequencing of nuclear 18S ribosomal RNA and mitochondrial Cytochrome Oxidase I (COI) genes were undertaken and phylogenetic analyses performed to establish the taxonomic status of recovered specimens. All available Prostoma sequences (Prostoma eilhardi and Prostoma graecense) were downloaded from GenBank® and Barcode of Life Data System (BOLD) databases for comparison. All 18S sequences from samples in Lancashire were identical to each other and to all downloaded Prostoma sequences, allowing no further analyses. With COI, 50 individuals were collected from 4 locations across Lancashire and sequenced, comparing a total of 480 base pairs. Average uncorrected p-distances between UK and European samples were low, although some more geographically distant samples from California, USA, displayed higher uncorrected p-distance values. Results suggest that the Prostoma recovered from the Clay 'Ole (and all other sampled locations in Lancashire) are not distinct from P. eilhardi and P. graecense (as downloaded from GenBank® and BOLD) suggesting that there is a strong case for the species status of P. jenningsi to be revoked. Further regional and national sampling is required to obtain a clearer evaluation of the distribution of Prostoma and the levels of genetic diversity present in the UK. In addition, results from this study indicate that thorough taxonomical re-evaluation of species within the Prostoma genus is required.},
}
@article {pmid32230628,
year = {2020},
author = {Song, C and Zheng, J and Wang, X and Qi, X},
title = {A new species of Limnophyes Eaton (Diptera: Chironomidae) from Xizang, China.},
journal = {Zootaxa},
volume = {4722},
number = {3},
pages = {zootaxa.4722.3.7},
doi = {10.11646/zootaxa.4722.3.7},
pmid = {32230628},
issn = {1175-5334},
mesh = {Animals ; China ; *Chironomidae ; *Diptera ; Male ; },
abstract = {A new species of the genus Limnophyes Eaton, 1875 from Xizang, China is described and figured based on adult males. Limnophyes nudus sp. nov. belongs to the minimus group and can be easily separated from other species by antenna with 13 flagellomeres, higher AR of 0.85-1.00, bluntly triangular anal point, phallapodeme with ring-like appendix, inferior volsella bare and gonostylus with bubble-like inner margin.},
}
@article {pmid32230610,
year = {2020},
author = {Timossi, G and Ruzzier, E},
title = {Description of the female of Sattleria sophiae Timossi, 2014 (Lepidoptera: Gelechiidae).},
journal = {Zootaxa},
volume = {4722},
number = {5},
pages = {zootaxa.4722.5.8},
doi = {10.11646/zootaxa.4722.5.8},
pmid = {32230610},
issn = {1175-5334},
mesh = {Animals ; Ecosystem ; Female ; *Lepidoptera ; *Moths ; },
abstract = {The female of Sattleria sophiae Timossi, 2014 is identified on the basis of DNA barcoding, described, illustrated and its habitat is discussed.},
}
@article {pmid32230605,
year = {2020},
author = {Langley, J and Cornwall, M and Powell, C and Costa, C and Allsopp, E and Noort, SV and Guilbert, E and Asch, BV},
title = {First report of the lace bug Neoplerochila paliatseasi (Rodrigues, 1981) (Hemiptera: Tingidae) infesting cultivated olive trees in South Africa, and its complete mitochondrial sequence.},
journal = {Zootaxa},
volume = {4722},
number = {5},
pages = {zootaxa.4722.5.3},
doi = {10.11646/zootaxa.4722.5.3},
pmid = {32230605},
issn = {1175-5334},
mesh = {Animals ; *Genome, Mitochondrial ; *Hemiptera ; *Heteroptera ; Phylogeny ; South Africa ; },
abstract = {Olive lace bugs are small phytophagous Hemipteran insects known to cause agricultural losses in olive production in South Africa. Plerochila australis (Distant, 1904) has been reported as the species responsible for damage to olive trees; however, the diversity of olive lace bug species in the region has lacked attention. Adult olive lace bugs were collected incidentally from wild and cultivated olive trees in the Western Cape Province, and identified as P. australis and Neoplerochila paliatseasi (Rodrigues, 1981). The complete mitochondrial genome of a representative specimen of N. paliatseasi was sequenced, and used for comparative mitogenomics and phylogenetic reconstruction within the family. Furthermore, the value of DNA barcodes for species identification in Tingidae was assessed using genetic clustering and estimates of genetic divergence. The patterns of genetic clustering and genetic divergence of COI sequences supported the morphological identification of N. paliatseasi, and the utility of DNA barcoding methods in Tingidae. The complete mitogenome sequence had the typical Metazoan gene content and order, including 13 PCGs, 22 tRNAs, two rRNAs, and an AT-rich non-coding region. A+T content was high, as commonly found in Tingidae. The phylogenetic reconstruction recovered Agramma hupehanum (Drake Maa 1954) as basal to Tingini, and as a sister species to N. paliatseasi. Stephanitis Stål 1873 and Corythucha Stål 1873 were monophyletic, but Metasalis populi (Takeya 1932) was not recovered as sister to Tingis cardui (Linnaeus 1746), as expected. The mitochondrial phylogeny of the family Tingidae has been recovered inconsistently across different studies, possibly due to sequence heterogeneity and high mutation rates. Species diversity of olive lace bugs in South Africa was previously underestimated. The presence of P. australis was confirmed in both wild and cultivated olives, and N. paliatseasi is reported in cultivated olives for the first time. These results warrant further investigation on the diversity and distribution of olive lace bugs in the Western Cape to inform pest control strategies.},
}
@article {pmid32230586,
year = {2020},
author = {Szpila, K and Wyborska, D and Bystrowski, C and Pape, T},
title = {Redescription of Sphecapatoclea excisa Villeneuve, 1909 (Diptera: Sarcophagidae).},
journal = {Zootaxa},
volume = {4728},
number = {1},
pages = {zootaxa.4728.1.5},
doi = {10.11646/zootaxa.4728.1.5},
pmid = {32230586},
issn = {1175-5334},
mesh = {Animals ; *Diptera ; Female ; Larva ; Male ; *Sarcophagidae ; },
abstract = {Sphecapatoclea excisa Villeneuve, 1909, the type species of the Palaearctic genus Sphecapatoclea Villeneuve, 1909, is redescribed based on a female syntype and on material from Makhtesh Ramon National Park, Israel, and its first instar larva is described for the first time. The species is sexually dimorphic, with much darker adult males. The male genital apparatus is unique by its compressed and sclerotised epiphallus. The morphology of the first instar larva is in accordance with the recently suggested position of the genus Sphecapatoclea in the Old World clade of the "lower" Miltogramminae. Two COI mini-barcodes are provided for S. excisa, and molecular data are in agreement with sequences for Sphecapatoclea spp. available in GenBank. Morphology supports a broad concept of the genus, as S. excisa presents a mixture of character states traditionally used to diagnose either Sphecapatoclea (s. str.) or Parthomyia Rohdendorf, 1925. Available morphological keys for genera of Palaearctic Miltogramminae are compared for functionality, and possible autapomorphies from both adult and larval morphology are discussed.},
}
@article {pmid32230576,
year = {2020},
author = {Shih, HT and Hsu, JW and Li, JJ and Ng, NK and Lee, JH},
title = {The identities of three species of Parahelice Sakai, Türkay amp; Yang, 2006 (Crustacea: Brachyura: Varunidae) from the western Pacific, based on morphological and molecular evidence.},
journal = {Zootaxa},
volume = {4728},
number = {2},
pages = {zootaxa.4728.2.6},
doi = {10.11646/zootaxa.4728.2.6},
pmid = {32230576},
issn = {1175-5334},
mesh = {Animals ; *Brachyura ; Female ; Male ; Mitochondria ; },
abstract = {Species of the varunid genus Parahelice Sakai, Türkay Yang, 2006, inhabit high intertidal areas of oceanic islands of the tropical Indo-West Pacific region. As several species of Parahelice and Pseudohelice subquadrata (Dana, 1851) were found to be sympatric in some places, and their morphological differences are minor, especially in females, the misidentification of species is not uncommon in the literature. In this study, the DNA barcoding marker, mitochondrial cytochrome c oxidase subunit I (COI), was applied to confirm species identities and this was correlated with the specific characters of males and females. Distributions of three species of Parahelice were also updated, with Par. daviei (Sakai, Türkay Yang, 2006), Par. pilimana (A. Milne-Edwards, 1873), and Par. pilosa (Sakai, Türkay Yang, 2006) being new records to Taiwan, and Par. pilosa new to Bali, Indonesia.},
}
@article {pmid32230559,
year = {2019},
author = {Weissman, DB and Gray, DA},
title = {Crickets of the genus Gryllus in the United States (Orthoptera: Gryllidae: Gryllinae).},
journal = {Zootaxa},
volume = {4705},
number = {1},
pages = {zootaxa.4705.1.1},
doi = {10.11646/zootaxa.4705.1.1},
pmid = {32230559},
issn = {1175-5334},
mesh = {Animals ; *Gryllidae ; United States ; },
abstract = {Gryllus field and wood crickets of the United States, mostly west of the Mississippi River, are reviewed and revised. We validate the following 18 Gryllus cricket names: G. armatus, G. assimilis, G. brevicaudus, G. cayensis, G. cohni, G. firmus, G. fultoni, G. integer, G. lineaticeps, G. multipulsator, G. ovisopis, G. pennsylvanicus, G. personatus, G. rubens, G. texensis, G. veletis, G. vernalis, and G. vocalis. We synonymize G. alogus under G. vocalis. We designate a lectotype for G. armatus. We describe the following 17 new Gryllus species: G. chisosensis, G. leei, G. lightfooti, G. longicercus, G. makhosica, G. montis, G. navajo, G. planeta, G. regularis, G. saxatilis, G. sotol, G. staccato, G. thinos, G. transpecos, G. veintinueve, G. veletisoides, and G. vulcanus. We present biology, distribution, and genetic analysis of all taxa and discuss their nearest relatives.},
}
@article {pmid32230503,
year = {2019},
author = {Yakovlev, RV and Shapoval, NA and Kuftina, GN and Gagarina, AV and Gorodilova, EY},
title = {A DNA-based description of a new carpenter moth species (Lepidoptera: Cossidae) from Morocco.},
journal = {Zootaxa},
volume = {4711},
number = {2},
pages = {zootaxa.4711.2.10},
doi = {10.11646/zootaxa.4711.2.10},
pmid = {32230503},
issn = {1175-5334},
mesh = {Animals ; DNA ; Genitalia ; *Lepidoptera ; Morocco ; *Moths ; },
abstract = {We used a combination of morphological data (genitalia structure) and a molecular marker (a 658bp fragment of the COI gene) to demonstrate that carpenter moth populations from central and southern Morocco, previously identified as Cossus cossus (Linnaeus, 1758) based on external morphology, represent a new species, described herein as C. romantsovi Yakovlev Shapoval, sp. n. The genetic divergence of the new species with respect to other members of genus Cossus is significant and includes at least 23 fixed nucleotide substitutions in the 658 bp of the COI barcode.},
}
@article {pmid32230492,
year = {2019},
author = {Saetung, T and Boonsoong, B},
title = {A review of genus Agriocnemis larva (Odonata: Coenagrionidae) from Thailand including a description of the final stadium larva of Agriocnemis minima Selys, 1877 with supporting molecular (COI) data.},
journal = {Zootaxa},
volume = {4711},
number = {3},
pages = {zootaxa.4711.3.9},
doi = {10.11646/zootaxa.4711.3.9},
pmid = {32230492},
issn = {1175-5334},
mesh = {Animals ; Genes, Mitochondrial ; Larva ; Male ; *Odonata/genetics ; Thailand ; },
abstract = {The larva of Agriocnemis minima Selys, 1879 is described and illustrated for the first time, based on reared specimens collected from Thailand. Selected larvae of Agrioncnemis Selys, 1877 were matched with their adults by DNA barcoding. The mitochondrial COI gene (658 bp) of three species (A. minima, A. femina femina (Brauer, 1868), and A. pygmaea (Rambur, 1842)) occurring in Thailand was analysed to confirm the species identification and to determine the association between the larva and adult stages. The larva of A. minima can be distinguished from known species by the following combination of characteristics: 1) long simple setae on the antennomeres I and II, 2) protrusion of the male cerci as long as 0.5× the S10, and 3) tufts of spiniform setae on the lateral occiput margin and on the ventral view of the compound eyes. Comparisons to known larvae of Agriocnemis and those of some other subfamily Agriocnemidinae members are also provided.},
}
@article {pmid32230491,
year = {2019},
author = {Huang, W and Zhang, Y},
title = {Two new species in the genus Destinoides (Hemiptera: Cicadellidae, Ledrinae) from China, with DNA barcoding data.},
journal = {Zootaxa},
volume = {4711},
number = {3},
pages = {zootaxa.4711.3.8},
doi = {10.11646/zootaxa.4711.3.8},
pmid = {32230491},
issn = {1175-5334},
mesh = {Animals ; China ; DNA Barcoding, Taxonomic ; *Hemiptera/genetics ; Male ; },
abstract = {Two new species in the genus Destinoides Cai He, D. hainanensis and D. rubeus spp. nov. from China are described and illustrated. A checklist and key to the known species of Destinoides are provided.},
}
@article {pmid32230470,
year = {2020},
author = {Hasan, ME and Durand, JD and Iwatsuki, Y},
title = {Acanthopagrus datnia (Hamilton, 1822), a senior synonym of Acanthopagrus longispinnis (Valenciennes, 1830) (Perciformes: Sparidae).},
journal = {Zootaxa},
volume = {4750},
number = {2},
pages = {zootaxa.4750.2.1},
doi = {10.11646/zootaxa.4750.2.1},
pmid = {32230470},
issn = {1175-5334},
mesh = {Animals ; *Perciformes ; },
abstract = {The taxonomic status of the Bay of Bengal nominal sparid species Coius datnia Hamilton, 1822 and Acanthopagrus longispinnis (Valenciennes, 1830) are reviewed and investigated both morphologically and genetically. Because of inadequate description and no type specimen, Coius datnia has recently been considered to belong to Sparidentex, a genus without molarifom teeth. Critical examination of the original description and examination of specimens from the type locality and adjacent areas reveal that Coius datnia belongs to Acanthopagrus, a genus with an inner series of molars. Furthermore, examination of specimens previously recognized as Acanthopagrus longispinnis (Valenciennes 1830), and recent collection of fresh specimens from lower Ganges estuary in Bangladesh, show that morphological differences between Acanthopagrus datnia and A. longispinnis are minor, and they are genetically identical. The longer second anal-fin spine in A. longispinnis (>21% SL) is, in fact, a feature of some younger A. datnia. Accordingly, A. datnia is regarded as a senior synonym of A. longispinnis, and is distinguished from its congeners by the presence of 12 dorsal-fin spines (rarely 11 or 13), 3½ scale rows between the fifth dorsal-fin spine base and lateral line, pelvic and anal-fins pale yellow to yellow with black streaks present in the interradial membranes of anal-fin rays, and caudal fin grey or yellowish grey. A neotype (and neogenotype) has been designated for Acanthopagrus datnia (Hamilton, 1822).},
}
@article {pmid32230423,
year = {2020},
author = {Chen, ZT and Jiang, C and Li, YS},
title = {DNA barcodes of Plecoptera from China: The preliminary dataset and its performance in species delimitation.},
journal = {Zootaxa},
volume = {4751},
number = {2},
pages = {zootaxa.4751.2.9},
doi = {10.11646/zootaxa.4751.2.9},
pmid = {32230423},
issn = {1175-5334},
mesh = {Animals ; Biodiversity ; China ; *DNA Barcoding, Taxonomic ; *Insecta ; Phylogeny ; },
abstract = {The DNA barcodes of Chinese Plecoptera project has a goal to promote species identification, life stage association, systematic, conservation, biodiversity, and population genetic studies for stoneflies of China. In this study, we sequenced and analyzed 19 DNA barcode sequences belonging to 19 stonefly species, increasing the Chinese barcoded stonefly species number to 53. Genetic distances were calculated and the gene trees constructed, suggesting the efficiency of delimiting Chinese stonefly species using DNA barcodes.},
}
@article {pmid32230410,
year = {2020},
author = {Jadhav, SS and Karuthapandi, M and Chandra, K and Jaiswal, D and Dinesh, KP and Narahari, A},
title = {Parapsilorhynchus alluriensis, a new species of cyprinid fish (Teleostei: Cyprinidae) from the Eastern Ghats, of India.},
journal = {Zootaxa},
volume = {4751},
number = {3},
pages = {zootaxa.4751.3.8},
doi = {10.11646/zootaxa.4751.3.8},
pmid = {32230410},
issn = {1175-5334},
mesh = {Animals ; *Cyprinidae ; India ; Phylogeny ; Rivers ; *Skates, Fish ; },
abstract = {A new species of cyprinid fish, Parapsilorhynchus alluriensis, is described from the Alluri Hills of Andhra Pradesh State, India. It is distinguished from its congeners by the combination of the following characters: A poorly-developed callous pad present behind lower lip; head deep (depth at occiput 47.3-72.3% head length, HL); body stout and deep (depth at dorsal fin origin 17.3-21.7 % standard length, SL); gape width 27.3-32.8% HL; inter-orbital space 33.9-43.2% HL; lower lip rounded; mouth opening situated very close to the anterior tip of snout; upper lip concealed by a poorly-developed rostral fold which is slightly fringed; minute papillae on rostral fold; 3 simple pectoral-fin rays; 33-34 lateral-line scales. A partial phylogeny based on the DNA Barcode COI gene suggests a sister-group relationship between the new species and P. prateri. Till date, the genus consists of four species from the Western Ghats, three from the Eastern Ghats, including the species described herein totaling it to seven from the peninsular India.},
}
@article {pmid32230384,
year = {2020},
author = {Afrand, M and Sourinejad, I and Fazeli, SAS and Akbarzadeh, A and Yeganeh, LP and Sadeghi, M and Azarbaijani, R},
title = {Morphological identification and molecular validation of anchovies (Engraulidae) in the Persian Gulf and Oman Sea.},
journal = {Zootaxa},
volume = {4742},
number = {2},
pages = {zootaxa.4742.2.10},
doi = {10.11646/zootaxa.4742.2.10},
pmid = {32230384},
issn = {1175-5334},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Fishes ; Indian Ocean ; Oman ; Phylogeny ; },
abstract = {Validation of species using independent lines of evidence is sometimes desirable when their identification using only one approach is difficult or questionable. The identification of anchovies (Engraulidae) are often challenging based on morphology because closely related species exhibit only slight morphological differentiation. This study utilized morphological characteristics and DNA barcodes for identification and validation of anchovies in the Persian Gulf and Oman Sea. Based on morphology, we identified eight species: Thryssa hamiltonii, T. setirostris, T. vitrirostris, T. whiteheadi, T. dussumieri, Encrasicholina punctifer, E. pseudoheteroloba and Stolephorus indicus. A 658 bp region of mitochondrial cytochrome oxidase subunit I (COI) was generated for 53 specimens from these eight species. From these sequences, we built a Maximum Likelihood phylogenetic tree. In this tree, each species forms a monophyletic group confirming our initial morphological identification. In addition, we provided (and registered in GenBank) the first barcode sequences for T. whiteheadi, an endemic species of this region. Interspecies genetic distances were comprised between 0.168 to 0.275. The largest genetic distance was found between T. vitrirostris and S. indicus and the smallest between T. dussumieri and T. whiteheadi. This study successfully identified eight species of anchovies in the Persian Gulf and Oman Sea based on both morphological and molecular characters.},
}
@article {pmid32230368,
year = {2020},
author = {Rahman, MM and Chen, JM and Wu, YH and Chen, HM and Lwin, YH and Murphy, RW and Li, GG and Che, J},
title = {New country records for three species of frog from Myanmar including two genera (Nasutixalus and Oreolalax).},
journal = {Zootaxa},
volume = {4742},
number = {3},
pages = {zootaxa.4742.3.7},
doi = {10.11646/zootaxa.4742.3.7},
pmid = {32230368},
issn = {1175-5334},
mesh = {Animals ; *Anura ; Myanmar ; Phylogeny ; },
abstract = {Myanmar, a biodiversity hotspot, harbors a striking diversity and endemism of species. Despite this, its herpetofauna remains one of the least explored in continental Asia due to restrictions of crossing political boundaries and infrastructure in remote regions. Many species in adjacent China and India are hypothesized to occur in Myanmar but records are wanting. Recent fieldwork found the frogs Polypedates braueri, Nasutixalus jerdonii and Oreolalax jingdongensis there, and the latter two species represent new generic records for Myanmar. All major morphological characters of these populations match the original descriptions. In addition, our matrilineal genealogy based on DNA barcoding confirms their identities. Overall, these findings confirm that the amphibian diversity is underestimated and this has important implications for conservation. Analyses indicate that northern Myanmar is a biogeographic corridor for the Himalayas, southern China, and northeastern India.},
}
@article {pmid32230314,
year = {2020},
author = {Gangan, SS and Pavan-Kumar, A and Jahageerdar, S and Jaiswar, AK},
title = {A new species of Stolephorus (Clupeiformes: Engraulidae) from the Bay of Bengal, India.},
journal = {Zootaxa},
volume = {4743},
number = {4},
pages = {zootaxa.4743.4.6},
doi = {10.11646/zootaxa.4743.4.6},
pmid = {32230314},
issn = {1175-5334},
mesh = {Animals ; Bays ; Fishes ; Gills ; India ; *Skates, Fish ; },
abstract = {A new fish species, Stolephorus tamilensis sp. nov., is described from the East coast of India. The major distinguishing characters are 5-6 small needle-like pre-pelvic scutes on belly; maxilla tip pointed, reaching to border of operculum, concave and indented in the preoperculum; 25-28 gill rakers on lower lobe of the first branchial arch; dorsal fin without spine; 17-19 anal-fin rays. Moreover, S. tamilensis sp. nov. present higher average genetic divergence values at mitochondrial cytochrome c oxidase subunit I and 16S rDNA loci in comparison with congeners. Also, nucleotide diagnostic characters exclusive to S. tamilensis are identified. Neighbor-joining analysis revealed close relation between S. tamilensis and S. andhraensis.},
}
@article {pmid32230296,
year = {2020},
author = {Scioli, JA and Anker, A},
title = {Description of Alpheus gallicus, a new deep-water snapping shrimp from Galicia Bank, northeastern Atlantic (Malacostraca, Decapoda, Alpheidae).},
journal = {Zootaxa},
volume = {4731},
number = {3},
pages = {zootaxa.4731.3.4},
doi = {10.11646/zootaxa.4731.3.4},
pmid = {32230296},
issn = {1175-5334},
mesh = {Animal Structures ; Animals ; *Decapoda ; },
abstract = {A new species of the snapping shrimp genus Alpheus Fabricius, 1798 is described based on material from Galicia Bank, an offshore seamount off northwestern Spain. The type series of Alpheus gallicus n. sp. was collected at a depth of 768-785 m, making it one of the deepest occurring snapping shrimps. The new species belongs to the Alpheus macrocheles species group and is morphologically most similar to several deep-water members of this group, viz. A. lentiginosus Anker Nizinski, 2011, A. platydactylus Coutière, 1897, A. romensky Burukovsky, 1990, as well as to the shallow-water A. macrocheles (Hailstone, 1835). The new species can be distinguished from all of them by some features on the minor cheliped and dactyli of the third to fifth pereiopods. In addition to morphology, DNA barcoding of the COI gene distinguished A. gallicus n. sp. from all related species with available barcode sequences.},
}
@article {pmid32230290,
year = {2020},
author = {Pérez, L and Rodríguez, M and Asenjo, A},
title = {A new Peruvian species of Megarthrus Curtis (Coleoptera: Staphylinidae: Proteininae).},
journal = {Zootaxa},
volume = {4731},
number = {4},
pages = {zootaxa.4731.4.11},
doi = {10.11646/zootaxa.4731.4.11},
pmid = {32230290},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; *Coleoptera ; Peru ; },
abstract = {A new species of Megarthrus Curtis is described from the Eastern slopes of the Andes in southeastern Peru (Department of Cuzco). Major diagnostic features are photographed and illustrated, and COI molecular barcode is given.},
}
@article {pmid32230283,
year = {2020},
author = {Hu, YL and Tsring, S and Wang, BX and Sun, CH},
title = {Descriptions of larvae of three Philopotamidae species from China (Insecta, Trichoptera).},
journal = {Zootaxa},
volume = {4731},
number = {4},
pages = {zootaxa.4731.4.4},
doi = {10.11646/zootaxa.4731.4.4},
pmid = {32230283},
issn = {1175-5334},
mesh = {Animals ; China ; *Holometabola ; *Insecta ; Larva ; Male ; },
abstract = {Adults and larvae of the family Philopotamidae from Zhejiang Province, China, were examined and mtCOI gene sequences were extracted and analyzed, males and larvae of 3 species were successfully associated. The larvae of Chimarra sadayu Malicky 1993, Dolophilodes bellatula Sun Malicky 2002, Wormaldia unispina Sun 1998 are described in detail and their diagnostic photographs and illustrations are presented. Diagnostic characters for genera and species are discussed.},
}
@article {pmid32230270,
year = {2020},
author = {Levesque-Beaudin, V and Mlynarek, JJ},
title = {Revision of Nearctic Paramyia Williston (Diptera: Milichiidae).},
journal = {Zootaxa},
volume = {4732},
number = {1},
pages = {zootaxa.4732.1.1},
doi = {10.11646/zootaxa.4732.1.1},
pmid = {32230270},
issn = {1175-5334},
mesh = {Animals ; *Diptera ; Female ; Male ; },
abstract = {The taxonomy of genus Paramyia Williston is revised for the Nearctic region north of Mexico, including the description (morphological and molecular) and illustration of 10 new species and re-description of Paramyia nitens. Morphological keys to the species of males and females are provided. The following new species are described: Paramyia anguliloba sp. n., P. brevikeraia sp. n., P. incrassatoloba sp. n., P. nigritarsi sp. n., P. lustrum sp. n., P. lutea sp. n., P. pseudonitens sp. n., P. silvestris sp. n., P. rectiloba sp. n., P. wheeleri sp. n.. Paramyia hungarica is also discussed in relation to the Nearctic species.},
}
@article {pmid32230246,
year = {2020},
author = {Beaver, EP and Moore, MD and Velasco-Castrillón, A and Stevens, MI},
title = {Three new ghost moths of the genus Oxycanus Walker, 1856 from Australia (Lepidoptera: Hepialidae).},
journal = {Zootaxa},
volume = {4732},
number = {3},
pages = {zootaxa.4732.3.1},
doi = {10.11646/zootaxa.4732.3.1},
pmid = {32230246},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Australia ; *Lepidoptera ; *Moths ; },
abstract = {Three new species of ghost moth, Oxycanus ephemerous sp. nov., O. flavoplumosus sp. nov., and O. petalous sp. nov. are described from South Australia, New South Wales, and south-west Western Australia, respectively. We illustrate these species and compare morphological and molecular (mtDNA COI gene) characters with similar Oxycanus Walker, 1856 species from Australia. Comparative images of Oxycanus subvaria (Walker, 1856), O. byrsa (Pfitzner, 1933), and O. determinata (Walker, 1856) are figured. The type material of the three new species are held in the Australian National Insect Collection, Canberra, the Western Australian Museum, Perth, and in the South Australian Museum, Adelaide. The type specimens of Oxycanus hildae Tindale, 1964 syn. n. were also examined and the taxon is here considered synonymous with O. subvaria. Concerns are raised about the conservation status of all three new species due to few or localised distribution records.},
}
@article {pmid32230120,
year = {2020},
author = {Sudasinghe, H and Adamson, EAS and Ranasinghe, RHT and Meegaskumbura, M and Ikebe, C and Britz, R},
title = {Unexpected species diversity within Sri Lanka's snakehead fishes of the Channa marulius group (Teleostei: Channidae).},
journal = {Zootaxa},
volume = {4747},
number = {1},
pages = {zootaxa.4747.1.4},
doi = {10.11646/zootaxa.4747.1.4},
pmid = {32230120},
issn = {1175-5334},
mesh = {Animals ; Color ; *Fishes ; *Skates, Fish ; Sri Lanka ; },
abstract = {The taxonomic status of the large snakeheads of the Channa marulius group that occur in Sri Lanka is reviewed and clarified. Two species are recognized from the island, based on both morphological and molecular (cytochrome c oxidase subunit 1: cox1) differentiation: C. marulius Hamilton from the northern dry zone and C. ara Deraniyagala from the middle and lower regions of the Mahaweli basin. Channa ara is endemic to Sri Lanka and can be distinguished from its Marulius group congeners, C. marulius, C. aurolineata and C. auroflammea, by having fewer dorsal- and anal-fin rays, fewer lateral-line scales and fewer vertebrae; from C. marulioides by a different adult colour pattern; and from C. pseudomarulius by having more vertebrae. At the cox1 barcoding locus, Channa ara is at least 3.6% genetically different from C. marulius, and at least 8% different from the other described species in the group. Specimens collected from the southwestern wet zone in Sri Lanka are a puzzling third component of the Marulius group's diversity, uncovered in this study, and identified here as C. cf. ara. Whilst genetically more similar to C. marulius, C. cf. ara possesses fewer dorsal- and anal-fin rays, fewer lateral-line scales and fewer vertebrae and is therefore morphologically more similar to C. ara. Channa ara can be distinguished from C. cf. ara, however, by differences in circumpeduncular scale count, adult colour pattern, and by an uncorrected pairwise genetic distance of 3.7% in cox1 sequences. A neotype is designated for Ophicephalus marulius ara Deraniyagala.},
}
@article {pmid32230118,
year = {2020},
author = {Valdez-Mondragón, A},
title = {COI mtDNA barcoding and morphology for species delimitation in the spider genus Ixchela Huber (Araneae: Pholcidae), with the description of two new species from Mexico.},
journal = {Zootaxa},
volume = {4747},
number = {1},
pages = {zootaxa.4747.1.2},
doi = {10.11646/zootaxa.4747.1.2},
pmid = {32230118},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; Female ; Male ; Mexico ; Phylogeny ; *Spiders ; },
abstract = {The spider genus Ixchela Huber 2000, is comprised of 22 species distributed from north-eastern Mexico to Central America, including the two new species described herein from Mexico: Ixchela panchovillai sp. nov. and Ixchela zapatai sp. nov., both from the state of Oaxaca and described for both sexes. DNA barcoding utilizing mitochondrial cytochrome c oxidase subunit 1 (COI) and morphology were used for species delimitation. Molecular analyses and species delimitation included four methods: 1) corrected p-distances under neighbor-joining (NJ), 2) general mixed yule coalescent model (GMYC), 3) automatic barcode gap discovery (ABGD), and 4) Poisson tree processes (bPTP). All molecular methods and morphology were consistent in delimiting and recognizing the two new species describing herein. The average inter-specific genetic distance (p-distance) within the genus Ixchela is 12%. Ixchela panchovillai sp. nov. is closely related in the NJ analysis with I. placida, with an average p-distance of 7.9%, whereas I. zapatai sp. nov. is closely related to I. taxco, with an average p-distance of 8.4% between both species. Additionally, identification keys for males and females of the genus Ixchela are presented.},
}
@article {pmid32230093,
year = {2020},
author = {Zhang, J and Brockmann, E and Cong, Q and Shen, J and Grishin, NV},
title = {A genomic perspective on the taxonomy of the subtribe Carcharodina (Lepidoptera: Hesperiidae: Carcharodini).},
journal = {Zootaxa},
volume = {4748},
number = {1},
pages = {zootaxa.4748.1.10},
pmid = {32230093},
issn = {1175-5334},
support = {R35 GM127390/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Butterflies ; Genomics ; *Lepidoptera ; Male ; *Moths ; Phylogeny ; },
abstract = {We obtained whole genome shotgun sequences and phylogenetically analyzed protein-coding regions of representative skipper butterflies from the genus Carcharodus Hübner, [1819] and its close relatives. Type species of all available genus-group names were sequenced. We find that species attributed to four exclusively Old World genera (Spialia Swinhoe, 1912, Gomalia Moore, 1879, Carcharodus Hübner, [1819] and Muschampia Tutt, 1906) form a monophyletic group that we call a subtribe Carcharodina Verity, 1940. In the phylogenetic trees built from various genomic regions, these species form 7 (not 4) groups that we treat as genera. We find that Muschampia Tutt, 1906 is not monophyletic, and the 5th group is formed by currently monotypic genus Favria Tutt, 1906 new status (type species Hesperia cribrellum Eversmann, 1841), which is sister to Gomalia. The 6th and 7th groups are composed of mostly African species presently placed in Spialia. These groups do not have names and are described here as Ernsta Grishin, gen. n. (type species Pyrgus colotes Druce, 1875) and Agyllia Grishin, gen. n. (type species Pyrgus agylla Trimen, 1889). Two subgroups are recognized in Ernsta: the nominal subgenus and a new one: Delaga Grishin, subgen. n. (type species Pyrgus delagoae Trimen, 1898). Next, we observe that Carcharodus is not monophyletic, and species formerly placed in subgenera Reverdinus Ragusa, 1919 and Lavatheria Verity, 1940 are here transferred to Muschampia. Furthermore, due to differences in male genitalia or DNA sequences, we reinstate Gomalia albofasciata Moore, 1879 and Gomalia jeanneli (Picard, 1949) as species, not subspecies or synonyms of Gomalia elma (Trimen, 1862), and Spialia bifida (Higgins, 1924) as a species, not subspecies of Spialia zebra (Butler, 1888). Sequencing of the type specimens reveals 2.2-3.2% difference in COI barcodes, the evidence that combined with wing pattern differences suggests a new status of a species for Spialia lugens (Staudinger, 1886) and Spialia carnea (Reverdin, 1927), formerly subspecies of Spialia orbifer (Hübner, [1823]).},
}
@article {pmid32230052,
year = {2020},
author = {Kovačić, M and Sadeghi, R and Esmaeili, HR},
title = {New species of Silhouettea (Teleostei: Gobiidae) from Qeshm Island, Iran and the DNA barcoding of the Persian Gulf and Oman Sea gobies.},
journal = {Zootaxa},
volume = {4750},
number = {1},
pages = {zootaxa.4750.1.3},
doi = {10.11646/zootaxa.4750.1.3},
pmid = {32230052},
issn = {1175-5334},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Indian Ocean ; Iran ; Islands ; Oman ; *Perciformes/genetics ; },
abstract = {Silhouettea ghazalae sp. nov. is described from Qeshm Island, Persian Gulf. Silhouettea ghazalae sp. nov. is distinguished from congeners by having: small mental fold present on chin, head length 31.4-32.4% of standard length, head width 24.5% of standard length, second dorsal fin I/11, anal fin I/13, breast with large cycloid scales, predorsal area naked, suborbital row b anteriorly beginning below anterior edge of pupil, posteriorly ending below pore β, suborbital row c anteriorly extending more than row b and posteriorly extending less than row b, suborbital row cp oblique with four papillae, body with four ill-defined midlateral blotches and the fifth a triangular mark on the caudal fin base, no clearly defined pale saddles on back, and the first dorsal fin pigmented with dots and with dark blotch present anteriorly. A key to Silhouettea species is provided. A dataset including novel and publicly available mtDNA COI sequences of 12 species from the Persian Gulf and Oman Sea gobies belonging to eight genera have been assembled in order to provide a reference dataset for DNA barcoding studies. The new species is further characterised by a minimum K2P distance of 21% to its closest relatives in our dataset, Cabillus tongarevae in the mtDNA COI barcode region.},
}
@article {pmid32230051,
year = {2020},
author = {McCOSKER, JE and Bogorodsky, SV and Mal, AO and Alpermann, TJ},
title = {Description of a new snake eel Ophichthus olivaceus (Teleostei: Anguilliformes, Ophichthidae) from the Red Sea.},
journal = {Zootaxa},
volume = {4750},
number = {1},
pages = {zootaxa.4750.1.2},
doi = {10.11646/zootaxa.4750.1.2},
pmid = {32230051},
issn = {1175-5334},
mesh = {Animals ; *Eels ; Indian Ocean ; Phylogeny ; },
abstract = {A new species of snake eel Ophichthus olivaceus is described based on two specimens trawled from a depth of 35-63 m from a soft substratum off Jizan, Red Sea coast of southern Saudi Arabia. It differs from its congeners by the following combination of characters: vertebrae 141-145; tail moderately short (2.15 in TL); head short (9.6-11.1 in TL); uniserial teeth in jaws and on vomer; pectoral fins slightly elongate, not lanceolate, upper rays longer than the lower; dorsal-fin origin above middle of pectoral fin; and a generally uniform, dark tan body with an olivaceous hue shading to tan or pale orange ventrally, with two pale yellow blotches above pectoral-fin base, snout and lower jaw dark brown, and olivaceous median fins. Its divergence from other mitochondrial-analyzed species is shown by phylogenetic analysis of the mitochondrial COI barcoding region. A key to the Indian Ocean species is provided.},
}
@article {pmid32230046,
year = {2020},
author = {Recuero, E and Rodríguez-Flores, PC},
title = {A new Mediterranean species of Dolistenus (Diplopoda, Platydesmida, Andrognathidae), with an updated key for the genus and the first contribution for a barcode database of European Platydesmida.},
journal = {Zootaxa},
volume = {4718},
number = {1},
pages = {zootaxa.4718.1.10},
doi = {10.11646/zootaxa.4718.1.10},
pmid = {32230046},
issn = {1175-5334},
mesh = {Animals ; *Arthropods ; DNA, Mitochondrial ; },
abstract = {Dolistenus Fanzago, 1874 is a widespread Mediterranean millipede genus of the order Platydesmida, currently including three valid species, each with relict distributions. Here we describe a fourth species of Dolistenus, and characterize it using morphological and molecular (mitochondrial DNA) characters. We provide an updated key to the species of Dolistenus and the first COI barcode sequences for the new species and several other European representatives of the Andrognathidae (Platydesmida).},
}
@article {pmid32230045,
year = {2020},
author = {Chang, G and Park, KH},
title = {Report on a new species of Plutomurus (Collembola, Tomoceridae) from a South Korean limestone cave, with notes on its DNA barcode.},
journal = {Zootaxa},
volume = {4718},
number = {1},
pages = {zootaxa.4718.1.9},
doi = {10.11646/zootaxa.4718.1.9},
pmid = {32230045},
issn = {1175-5334},
mesh = {Animals ; *Arthropods ; *Calcium Carbonate ; DNA ; DNA Barcoding, Taxonomic ; Republic of Korea ; },
abstract = {A new species of Plutomurus Yosii, 1956, P. jangamensis sp. nov., was found in a limestone cave of South Korea. The new species is very similar to P. gul (Yosii, 1966) in the general pattern of cephalic and body chaetotaxy, absence of eye, presence of pointed tenent hair, number of lateral macrochaetae in basal segment of dens, and number of mucronal intermediate tooth; however, the two species can be distinguished by the small spines arranged in-a-row along with dental spines and lighter body color. This species, however, shows variability and was not easily classified morphologically as P. jangamensis sp. nov. and P. gul., in terms of body color, formula of dental spine, or even the number of prelabral chaetae. Partial DNA sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene were used as DNA barcodes to distinguish the species. This result suggests that the COI gene is useful for discrimination of P. jangamensis sp. nov. with high support (bootstrap=100). An identification key to the world species of Plutomurus is also provided.},
}
@article {pmid32230035,
year = {2020},
author = {Tsyrlin, E and Carew, M and Alarie, Y},
title = {Re-description of larvae of Chostonectes nebulosus (Macleay, 1871) (Coleoptera: Dytiscidae, Hydroporinae, Hydroporini, Sternopriscina) with an identification key to the known larvae of Chostonectes Sharp, 1882.},
journal = {Zootaxa},
volume = {4718},
number = {3},
pages = {zootaxa.4718.3.11},
doi = {10.11646/zootaxa.4718.3.11},
pmid = {32230035},
issn = {1175-5334},
mesh = {Animals ; Australia ; *Coleoptera ; Extremities ; Head ; Larva ; },
abstract = {The second and third larval instars of the Australian endemic dytiscid Chostonectes nebulosus (Macleay, 1871) are described and illustrated for the first time including a detailed chaetotaxic analysis of head capsule and appendages, legs, last abdominal segment and urogomphi. Collected larvae were successfully associated with adults using rearing and a molecular approach. The identification key and COI barcodes for C. nebulosus, C. gigas (Boheman, 1858) and C. johnsonii (Clark, 1862) are provided.},
}
@article {pmid32229963,
year = {2019},
author = {Wright, BMOG and Wright, CD and Sole, CL and Lyle, R and Tippett, R and Sholto-Douglas, C and Verburgt, L and Engelbrecht, I},
title = {A new forest dwelling button spider from South Africa (Araneae, Theridiidae, Latrodectus).},
journal = {Zootaxa},
volume = {4700},
number = {4},
pages = {zootaxa.4700.4.12},
doi = {10.11646/zootaxa.4700.4.12},
pmid = {32229963},
issn = {1175-5334},
mesh = {Animals ; Ecosystem ; Female ; Forests ; Male ; South Africa ; *Spiders ; },
abstract = {The medically important spider genus Latrodectus Walckenaer 1805, commonly referred to as "button spiders" in South Africa, is represented by six species in the country. Using morphology and the COI barcoding gene we describe a new forest dwelling species, Latrodectus umbukwane n. sp. Wright, Wright, Lyle and Engelbrecht. Females have red markings on both the ventral and posterior dorsal surfaces of the abdomen, parallel spermathecae and three loops of the copulatory ducts. Males have an embolus with four loops and diagnostic white markings on the ventral surface of the abdomen that darken with age. Egg sacs are smooth, large, and bright purple when freshly laid, turning shiny grey with time. Latrodectus umbukwane n. sp. is known only from sand forest vegetation types in northern Zululand, KwaZulu-Natal, South Africa. A predicted geographic distribution for this species is provided based on cartographic mapping of known habitat and altitudinal preference, from which area of occupancy (AOO; 698 km2) and extent of occurrence (EOO; 4963 km2) were calculated to assess potential IUCN Red List status. Due to the uncertainty of the distribution of this species, a Red List status of Data Deficient (DD) is recommended. An updated key to the southern African species of Latrodectus is provided.},
}
@article {pmid32229937,
year = {2019},
author = {Foottit, RG and Maw, HEL},
title = {Geographic distribution, host preferences and molecular diversity within the genus Pentalonia (Hemiptera: Aphididae).},
journal = {Zootaxa},
volume = {4701},
number = {4},
pages = {zootaxa.4701.4.4},
doi = {10.11646/zootaxa.4701.4.4},
pmid = {32229937},
issn = {1175-5334},
mesh = {Animals ; *Aphids ; Phylogeny ; },
abstract = {Both Pentalonia nigronervosa and P. caladii are distributed throughout the tropics and subtropics wherever suitable hosts are grown. To clarify the host relationships of both species on a global scale, the morphology of museum specimens of Pentalonia comprising 447 samples from 77 countries was examined, and all available mitochondrial COI sequences were analysed. Pentalonia nigronervosa is confirmed to feed almost exclusively on Musaceae (sensu stricto), while P. caladii feeds on other Zingiberales and on Araceae. Heliconia is accepted by both species. Molecular evidence suggests that there is an additional widespread species.},
}
@article {pmid32229911,
year = {2019},
author = {Hibino, Y and Chiu, YC and Chen, HM and Shao, KT},
title = {Two new species of the genus Ophichthus from the western central Pacific Ocean, with a redescription of Ophichthus megalops Asano, 1987 (Anguilliformes: Ophichthidae).},
journal = {Zootaxa},
volume = {4702},
number = {1},
pages = {zootaxa.4702.1.17},
doi = {10.11646/zootaxa.4702.1.17},
pmid = {32229911},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; *Eels ; Pacific Ocean ; },
abstract = {Two new species similar to Ophichthus megalops Asano, 1987 with dark-tipped anal fins, are described on the basis of one specimen of each species. Ophichthus semilunatus sp. nov. from northeastern Taiwan is characterized by having 176 total vertebrae, three rows of teeth on the maxilla, one + three supraorbital pores, two preopercular pores, a brownish anterior-nostril tube, and a blotch on the anterior margin of anus. Ophichthus brevidorsalis sp. nov. from New Caledonia is characterized by having two preopercular pores, one + three supraorbital pores, smaller eyes 2.7 in head, a short head 9.5% of total length, a long tail 59.8% of total length, a slightly short snout 19.4% of head, and 43 predorsal vertebrae. A redescription of O. megalops is provided based on the holotype and 18 specimens newly collected from Taiwan. Selected characters of all nine Ophichthus with a dark-tipped anal fin are provided. In addition, partial COI sequences of five species is provided.},
}
@article {pmid32229910,
year = {2019},
author = {Ho, HC and Tsai, SY and Li, HH},
title = {The barracudina genera Lestidium and Lestrolepis of Taiwan, with descriptions of two new species (Aulopiformes: Paralepididae).},
journal = {Zootaxa},
volume = {4702},
number = {1},
pages = {zootaxa.4702.1.16},
doi = {10.11646/zootaxa.4702.1.16},
pmid = {32229910},
issn = {1175-5334},
mesh = {Animals ; *Fishes ; Head ; Luminescence ; Mandible ; Taiwan ; },
abstract = {Two genera of barracudinas with luminescent duct in abdominal cavity, Lestrolepis and Lestidium, collected from around Taiwan are studied. Two species in each genus are recognized in Taiwan, including one new species in each genus. New diagnostic characters are used to distinguish these species. Lestrolepis nigroventralis sp. nov. is similar to Lestrolepis intermedia and can be distinguished by having 32-35 prehaemal vertebrae; dorsal-fin origin slightly in front of midline of distance between origins of pelvic and anal fins, distance between origins of dorsal and pelvic fin 9.8-11.7% SL; and pelvic-fin origin at or slightly behind midline of body, prepelvic length 50.6-52.6% SL. Lestidium orientale sp. nov. is similar to Lestidium atlanticum and can be distinguished by having prehaemal vertebrae 37-40; caudal vertebrae 41-44; a relatively short and deep head, reflected by a shorter snout (9.7-10.4% SL), shorter upper jaw (8.6-10.1% SL), shorter lower jaw (11.9-13.7% SL) and a deeper head (31.2-33.9% HL). Data of Lestrolepis japonicus and Lestidium prolixium collected from Taiwan, as well as two Atlantic congeners, are provided. DNA barcoding is conducted to support the recognition of these new species.},
}
@article {pmid32229907,
year = {2019},
author = {Koeda, K and Muto, N},
title = {An unexpected distribution record of the cold water fish Pholis fangi (Pholidae) from southern Taiwan.},
journal = {Zootaxa},
volume = {4702},
number = {1},
pages = {zootaxa.4702.1.13},
doi = {10.11646/zootaxa.4702.1.13},
pmid = {32229907},
issn = {1175-5334},
mesh = {Animals ; *Fishes ; Taiwan ; },
abstract = {Gunnel species (family Pholidae), characterized by an elongated bar-like body and usually found in shallow coastal waters, are mostly restricted to temperate to subarctic waters in the Northern Pacific Ocean, although some in the Western Pacific are distributed southward to the northern East China Sea. Despite the absence of previous records from subtropical and tropical waters, a single specimen of the fish family Pholidae was recently trawled off southwestern Taiwan. Examination on the morphological characteristics and DNA barcoding revealed this is a Pholis fangi (Wang Wang 1935), a species previously recorded only from cold waters in the Bohai and Yellow seas. As a consequence, the present specimen represents the first record of the species from the subtropical South China Sea coast of Taiwan, as well as an isolated southernmost record of this species, more than 1,000 km southward from the otherwise known distribution. Detailed morphology and fresh coloration are described.},
}
@article {pmid32229876,
year = {2020},
author = {Shimbori, EM and Wengrat, APGS and Savaris, M and Galvão, WB and Nanini, F and Garcia, SSP and Corrêa, AS},
title = {Two new species of Nealiolus Mason (Hymenoptera, Braconidae, Brachistinae) reared from pest weevils (Coleoptera, Curculionidae).},
journal = {Zootaxa},
volume = {4729},
number = {1},
pages = {zootaxa.4729.1.8},
doi = {10.11646/zootaxa.4729.1.8},
pmid = {32229876},
issn = {1175-5334},
mesh = {Animals ; *Coleoptera ; *Hymenoptera ; *Weevils ; },
abstract = {Here, we present the first two South American species of Nealiolus Mason (Hymenoptera, Braconidae), both reared from weevils damaging plants of economic value: Nealiolus chayohtli Wengrat Shimbori sp. n. on Phymatophosus squameus feeding in stems of Sechium edule (chayote), and Nealiolus jaboticaba Shimbori Wengrat sp. n. on Conotrachelus sp. in fruits of Plinia cauliflora (jaboticaba). This parasitoid genus is poorly studied, despite its potential importance as a biological control agent of several pest weevils (Curculionidae), including the cotton boll weevil. With the addition of the two new species, nine species of Nealiolus are known, three of them occurring in the Neotropical region. We also present an identification key to species of Nealiolus and DNA barcoding information for the new species.},
}
@article {pmid32229875,
year = {2020},
author = {Friedrich, S and Lehmann, T},
title = {Taito adrik, a new harvestman species from the Área de Conservación Privada Panguana, Peruvian Amazonia (Opiliones: Laniatores: Cosmetidae).},
journal = {Zootaxa},
volume = {4729},
number = {1},
pages = {zootaxa.4729.1.7},
doi = {10.11646/zootaxa.4729.1.7},
pmid = {32229875},
issn = {1175-5334},
mesh = {Animals ; *Arachnida ; Male ; Peru ; },
abstract = {A new species of the cosmetid harvestman genus Taito Kury Barros 2014 is described from the Área de Conservación Privada (ACP) Panguana, Peruvian Amazonia, which extends the distribution range of the genus to the south-west. The herein described species Taito adrik sp. nov. differs from all other known species of the genus by the distinct shape of the equuleus, the armature of leg IV in males, and the structure of male genitalia, in combination with features of the chelicerae and the anal operculum. In addition, COI barcodes of the new species are provided.},
}
@article {pmid32229872,
year = {2020},
author = {Chan, TY and Hsu, CY and Kumar, AB and Chang, SC},
title = {On the "Plesionika martia" (A. Milne-Edwards, 1883) species group in Indian waters.},
journal = {Zootaxa},
volume = {4729},
number = {1},
pages = {zootaxa.4729.1.4},
doi = {10.11646/zootaxa.4729.1.4},
pmid = {32229872},
issn = {1175-5334},
mesh = {Animals ; *Decapoda ; *Pandalidae ; },
abstract = {Material of the "Plesionika martia" (A. Milne-Edwards, 1883) species group from India had been reported as either P. martia or P. semilaevis Bate, 1888. Recent collection, however, revealed that both P .martia and P. semilaevis occur in Indian waters. COI barcoding gene sequence comparisons of the Indian and topotypic material of the four known species of the "P. martia" group showed that the Andaman Sea specimen is most similar to the topotypic specimens of P. martia even though there is high genetic divergence between them. For P. semilaevis, large sequence divergence is found in the topotypic material from the Philippines while the Indian specimens are genetically similar to one of the topotypic specimens. The characteristics of the Indian material of both species are described and illustrated.},
}
@article {pmid32229849,
year = {2020},
author = {Gilligan, TM and Wright, DJ and Brown, RL and Augustinus, BA and Schaffner, U},
title = {Taxonomic issues related to biological control prospects for the ragweed borer, Epiblema strenuana (Lepidoptera: Tortricidae).},
journal = {Zootaxa},
volume = {4729},
number = {3},
pages = {zootaxa.4729.3.3},
doi = {10.11646/zootaxa.4729.3.3},
pmid = {32229849},
issn = {1175-5334},
mesh = {*Ambrosia ; Animals ; Female ; *Lepidoptera ; *Moths ; },
abstract = {The ragweed borer, Epiblema strenuana (Walker, 1863), has a long history of use as a biological control agent against important weed pests in the family Asteraceae. Recently, E. strenuana has been reported feeding on the invasive perennials Ambrosia confertiflora and A. tenuifolia in Israel. The geographic location of Israel has raised concern over the possibility that the moth may spread to areas such as Ethiopia where the oil-seed crop Guizotia abyssinica is cultivated, as this is a potential host for E. strenuana. However, the taxonomic status of E. strenuana and a current synonym, E. minutana (Kearfott, 1905) is unclear. These taxa have been treated as separate species in the past, and they potentially have different feeding habits and damage different parts of the plant. We analyzed DNA data and adult morphology and determined that E. minutana, stat. rev., is a valid species which we raise from synonymy with E. strenuana. Wing coloration, the shape of the female sterigma, and COI DNA barcodes are consistently different between the two species. We also determined that the species previously identified as E. strenuana in Israel is actually E. minutana. While detailed host range tests have been conducted on the E. strenuana populations released in Australia and China, the host range of E. minutana remains to be clarified. We discuss the history of biological control using E. strenuana and the implications for finding E. minutana in Israel. We also provide species redescriptions for E. strenuana and E. minutana and illustrate diagnostic characters.},
}
@article {pmid32229844,
year = {2020},
author = {Guerrero, JJ and Cuenca, ED and Barros, D and Ortiz, AS},
title = {Redescription and DNA barcoding of diurnal moth Athroolopha latimargo&lt;br /&gt;Rothschild, 1914 bona sp., stat. rev. from the southern Iberian Peninsula (Lepidoptera: Geometridae: Ennominae).},
journal = {Zootaxa},
volume = {4729},
number = {4},
pages = {zootaxa.4729.4.9},
doi = {10.11646/zootaxa.4729.4.9},
pmid = {32229844},
issn = {1175-5334},
mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic ; *Lepidoptera ; *Moths ; Sequence Analysis, DNA ; },
abstract = {The rare and diurnal geometrid moth Athroolopha latimargo Rothschild, 1914 bona sp., stat. rev. is re-discovered and redescribed from the furthest point of the south of the Iberian Peninsula, for the first time since its original description as a subspecies of Athroolopha chrysitaria (Hübner, 1813) from North Africa. The range of this taxon is questioned. A mitochondrial COI barcode sequence was generated for the specimens and compared with Iberian and Sicilian Athroolopha species.},
}
@article {pmid32227890,
year = {2020},
author = {Wei, X and Bian, F and Cai, X and Wang, Y and Cai, L and Yang, J and Zhu, Y and Zhao, Y},
title = {Multiplexed Detection Strategy for Bladder Cancer MicroRNAs Based on Photonic Crystal Barcodes.},
journal = {Analytical chemistry},
volume = {92},
number = {8},
pages = {6121-6127},
doi = {10.1021/acs.analchem.0c00630},
pmid = {32227890},
issn = {1520-6882},
mesh = {Biomarkers, Tumor/*analysis ; *Biosensing Techniques ; Humans ; MicroRNAs/*analysis ; *Nucleic Acid Hybridization ; Particle Size ; *Photons ; Surface Properties ; Urinary Bladder Neoplasms/*diagnosis ; },
abstract = {Bladder cancer is a complex and highly prevalent disease associated with substantial morbidity and mortality rates. Detection and surveillance of biomarkers for bladder cancer are particularly critical in clinical diagnosis and prognostic monitoring. The current detection methods are limited to low sensitivity, low throughput, and high operational cost. In this paper, we present a multiplexed detection strategy for microRNA (miRNA) related to bladder cancer by utilizing photonic crystal (PhC) barcodes. PhC barcodes have characteristic reflective peaks generated by periodic orderly porous nanostructures, providing an ideal choice for encoding element. Besides, owing to the larger surface area provided by the structure, PhC barcodes is an effective platform for probes ligation and miRNAs detection. Compared with the planar microarrays, PhC barcodes avoid the problem of steric hindrance, making it express more efficient reaction and higher detection sensitivity. By introducing hybridization chain reaction (HCR), the detection efficiency of this strategy is greatly improved, making the rapid, accurate, high sensitivity quantification of miRNAs possible. The results indicated that the multiplexed detection strategy based on PhC barcodes can be applied to the clinical analysis of tumor markers.},
}
@article {pmid32226429,
year = {2020},
author = {Hansen, UK and Ramskov, S and Bjerregaard, AM and Borch, A and Andersen, R and Draghi, A and Donia, M and Bentzen, AK and Marquard, AM and Szallasi, Z and Eklund, AC and Svane, IM and Hadrup, SR},
title = {Tumor-Infiltrating T Cells From Clear Cell Renal Cell Carcinoma Patients Recognize Neoepitopes Derived From Point and Frameshift Mutations.},
journal = {Frontiers in immunology},
volume = {11},
number = {},
pages = {373},
pmid = {32226429},
issn = {1664-3224},
mesh = {Antigens, Neoplasm/genetics/*immunology ; Carcinoma, Renal Cell/genetics/*immunology ; Epitopes, T-Lymphocyte/genetics/immunology ; Frameshift Mutation ; Humans ; Kidney Neoplasms/genetics/*immunology ; Lymphocytes, Tumor-Infiltrating/*immunology ; Point Mutation ; T-Lymphocytes/*immunology ; },
abstract = {Mutation-derived neoantigens are important targets for T cell-mediated reactivity toward tumors and, due to their unique tumor expression, an attractive target for immunotherapy. Neoepitope-specific T cells have been detected across a number of solid cancers with high mutational burden tumors, but neoepitopes have been mostly selected from single nucleotide variations (SNVs), and little focus has been given to neoepitopes derived from in-frame and frameshift indels, which might be equally important and potentially highly immunogenic. Clear cell renal cell carcinomas (ccRCCs) are medium-range mutational burden tumors with a high pan-cancer proportion of frameshift mutations. In this study, the mutational landscape of tumors from six RCC patients was analyzed by whole-exome sequencing (WES) of DNA from tumor fragments (TFs), autologous tumor cell lines (TCLs), and tumor-infiltrating lymphocytes (TILs, germline reference). Neopeptides were predicted using MuPeXI, and patient-specific peptide-MHC (pMHC) libraries were created for all neopeptides with a rank score < 2 for binding to the patient's HLAs. T cell recognition toward neoepitopes in TILs was evaluated using the high-throughput technology of DNA barcode-labeled pMHC multimers. The patient-specific libraries consisted of, on average, 258 putative neopeptides (range, 103-397, n = 6). In four patients, WES was performed on two different sources (TF and TCL), whereas in two patients, WES was performed only on TF. Most of the peptides were predicted from both sources. However, a fraction was predicted from one source only. Among the total predicted neopeptides, 16% were derived from frameshift indels. T cell recognition of 52 neoepitopes was detected across all patients (range, 4-18, n = 6) and spanning two to five HLA restrictions per patient. On average, 21% of the recognized neoepitopes were derived from frameshift indels (range, 0-43%, n = 6). Thus, frameshift indels are equally represented in the pool of immunogenic neoepitopes as SNV-derived neoepitopes. This suggests the importance of a broad neopeptide prediction strategy covering multiple sources of tumor material, and including different genetic alterations. This study, for the first time, describes the T cell recognition of frameshift-derived neoepitopes in RCC and determines their immunogenic profile.},
}
@article {pmid32223968,
year = {2020},
author = {Herholt, A and Galinski, S and Geyer, PE and Rossner, MJ and Wehr, MC},
title = {Multiparametric Assays for Accelerating Early Drug Discovery.},
journal = {Trends in pharmacological sciences},
volume = {41},
number = {5},
pages = {318-335},
doi = {10.1016/j.tips.2020.02.005},
pmid = {32223968},
issn = {1873-3735},
mesh = {*Drug Discovery ; Humans ; *Proteomics ; },
abstract = {Drug discovery campaigns are hampered by substantial attrition rates largely due to a lack of efficacy and safety reasons associated with candidate drugs. This is true in particular for genetically complex diseases, where insufficient knowledge of the modulatory actions of candidate drugs on targets and entire target pathways further adds to the problem of attrition. To better profile compound actions on targets, potential off-targets, and disease-linked pathways, new innovative technologies need to be developed that can elucidate the complex cellular signaling networks in health and disease. Here, we discuss progress in genetically encoded multiparametric assays and mass spectrometry (MS)-based proteomics, which both represent promising toolkits to profile multifactorial actions of drug candidates in disease-relevant cellular systems to promote drug discovery and personalized medicine.},
}
@article {pmid32222363,
year = {2020},
author = {do Nascimento, JMC and Hamada, N and Pepinelli, M},
title = {A new species in Simulium (Trichodagmia) (Diptera: Simuliidae) from Chapada Diamantina region, Brazil: cryptic diversity revealed by morphological and molecular evidence.},
journal = {Acta tropica},
volume = {206},
number = {},
pages = {105457},
doi = {10.1016/j.actatropica.2020.105457},
pmid = {32222363},
issn = {1873-6254},
mesh = {Animals ; Brazil ; Female ; Male ; Simuliidae/*anatomy &amp; histology/classification/genetics ; },
abstract = {We describe new species of black fly that had previously been identified as S. scutistriatum Lutz due to morphological similarities at the pupal stage. The description of the new species, Simulium (Trichogamia) itajara n. sp., is based on molecular and morphological evidences. The known distribution of the new species is currently restricted to the Paraguaçu River hydrographic basin in Chapada Diamantina National Park and the surrounded area in Bahia state, Brazil. The distribution record for S. scutistriatum in the northeast region of Brazil needs to be removed, since the previous records were based on occurrence of S. itajara n. sp.},
}
@article {pmid32217735,
year = {2020},
author = {Bush, A and Monk, WA and Compson, ZG and Peters, DL and Porter, TM and Shokralla, S and Wright, MTG and Hajibabaei, M and Baird, DJ},
title = {DNA metabarcoding reveals metacommunity dynamics in a threatened boreal wetland wilderness.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {15},
pages = {8539-8545},
pmid = {32217735},
issn = {1091-6490},
mesh = {Animals ; *Biodiversity ; DNA/*analysis ; DNA Barcoding, Taxonomic/*methods ; *Ecosystem ; Environmental Monitoring/*methods ; Invertebrates/*physiology ; *Wetlands ; Wilderness ; },
abstract = {The complexity and natural variability of ecosystems present a challenge for reliable detection of change due to anthropogenic influences. This issue is exacerbated by necessary trade-offs that reduce the quality and resolution of survey data for assessments at large scales. The Peace-Athabasca Delta (PAD) is a large inland wetland complex in northern Alberta, Canada. Despite its geographic isolation, the PAD is threatened by encroachment of oil sands mining in the Athabasca watershed and hydroelectric dams in the Peace watershed. Methods capable of reliably detecting changes in ecosystem health are needed to evaluate and manage risks. Between 2011 and 2016, aquatic macroinvertebrates were sampled across a gradient of wetland flood frequency, applying both microscope-based morphological identification and DNA metabarcoding. By using multispecies occupancy models, we demonstrate that DNA metabarcoding detected a much broader range of taxa and more taxa per sample compared to traditional morphological identification and was essential to identifying significant responses to flood and thermal regimes. We show that family-level occupancy masks high variation among genera and quantify the bias of barcoding primers on the probability of detection in a natural community. Interestingly, patterns of community assembly were nearly random, suggesting a strong role of stochasticity in the dynamics of the metacommunity. This variability seriously compromises effective monitoring at local scales but also reflects resilience to hydrological and thermal variability. Nevertheless, simulations showed the greater efficiency of metabarcoding, particularly at a finer taxonomic resolution, provided the statistical power needed to detect change at the landscape scale.},
}
@article {pmid32216466,
year = {2020},
author = {Rampazzo, F and Tosi, F and Tedeschi, P and Gion, C and Arcangeli, G and Brandolini, V and Giovanardi, O and Maietti, A and Berto, D},
title = {Preliminary multi analytical approach to address geographic traceability at the intraspecific level in Scombridae family.},
journal = {Isotopes in environmental and health studies},
volume = {56},
number = {3},
pages = {260-279},
doi = {10.1080/10256016.2020.1739671},
pmid = {32216466},
issn = {1477-2639},
mesh = {Animals ; Carbon Isotopes/*analysis ; DNA Barcoding, Taxonomic ; Fatty Acids/analysis ; Food Chain ; Geography ; Nitrogen Isotopes/*analysis ; Perciformes/classification/genetics/*growth &amp; development ; Principal Component Analysis ; Seafood/*analysis ; Species Specificity ; },
abstract = {Globalization of seafood product marketing caused the increase of request of an effective fish traceability that enhances the consumer confidence in food safety. In this study, an integrated multi analytical approach based on two different and independent analytical techniques (carbon and nitrogen stable isotopes and fatty acids analysis) was applied in order to identify different fish species and trace their geographical provenience. The investigation was focused on four species (Thunnus thynnus, Thunnus alalunga, Auxis rochei and Scomber scombrus) belonging to the Scombridae family. The DNA barcoding method confirmed genus and species for S. scombrus and A. rochei, but only genus for T. alalunga and T. thynnus. Carbon and nitrogen stable isotopes results evidenced different fish diets and trophic positions, whereas fatty acids analysis displayed that the unsaturated prevailed (∼60 %) over the saturated compounds with a variation among the species and the geographical area in particular for docosahexaenoic and eicosapentaenoic acids percentage. The principal component analysis applied to stable isotopes and fatty acids evidenced a good discrimination among species and their geographical catching area. This multi-disciplinary analytical approach could represent a promising tool to identify the commercial fish and trace their origin in order to guarantee the health of consumers.},
}
@article {pmid32214353,
year = {2020},
author = {Sumner-Kalkun, JC and Sjölund, MJ and Arnsdorf, YM and Carnegie, M and Highet, F and Ouvrard, D and Greenslade, AFC and Bell, JR and Sigvald, R and Kenyon, DM},
title = {A diagnostic real-time PCR assay for the rapid identification of the tomato-potato psyllid, Bactericera cockerelli (Šulc, 1909) and development of a psyllid barcoding database.},
journal = {PloS one},
volume = {15},
number = {3},
pages = {e0230741},
pmid = {32214353},
issn = {1932-6203},
support = {BBS/E/C/000J0200/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Computational Biology ; *DNA Barcoding, Taxonomic ; *Databases, Genetic ; Hemiptera/*classification/*genetics/physiology ; *Solanum lycopersicum ; Real-Time Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA ; Time Factors ; },
abstract = {The accurate and rapid identification of insect pests is an important step in the prevention and control of outbreaks in areas that are otherwise pest free. The potato-tomato psyllid Bactericera cockerelli (Šulc, 1909) is the main vector of 'Candidatus Liberibacter solanacearum' on potato and tomato crops in North America and New Zealand; and is considered a threat for introduction in Europe and other pest-free regions. This study describes the design and validation of the first species-specific TaqMan probe-based real-time PCR assay, targeting the ITS2 gene region of B. cockerelli. The assay detected B. cockerelli genomic DNA from adults, immatures, and eggs, with 100% accuracy. This assay also detected DNA from cloned plasmids containing the ITS2 region of B. cockerelli with 100% accuracy. The assay showed 0% false positives when tested on genomic and cloned DNA from 73 other psyllid species collected from across Europe, New Zealand, Mexico and the USA. This included 8 other species in the Bactericera genus and the main vectors of 'Candidatus Liberibacter solanacearum' worldwide. The limit of detection for this assay at optimum conditions was 0.000001ng DNA (~200 copies) of ITS2 DNA which equates to around a 1:10000 dilution of DNA from one single adult specimen. This assay is the first real-time PCR based method for accurate, robust, sensitive and specific identification of B. cockerelli from all life stages. It can be used as a surveillance and monitoring tool to further study this important crop pest and to aid the prevention of outbreaks, or to prevent their spread after establishment in new areas.},
}
@article {pmid32212593,
year = {2020},
author = {Karademir, GK and Usluğ, S and Okur, M and İnci, A and Yıldırım, A},
title = {Molecular Characterization and Phylogenetic Analyses of Oestrus ovis Larvae Causing Human Naso-pharyngeal Myiasis Based on CO1 Barcode Sequences.},
journal = {Turkiye parazitolojii dergisi},
volume = {44},
number = {1},
pages = {43-47},
doi = {10.4274/tpd.galenos.2020.6852},
pmid = {32212593},
issn = {2146-3077},
mesh = {Animals ; Cyclooxygenase 1/*genetics ; DNA Barcoding, Taxonomic ; Diptera/anatomy &amp; histology/classification/*genetics ; Female ; Haplotypes ; Humans ; Larva/anatomy &amp; histology/classification/genetics ; Middle Aged ; Myiasis/diagnosis/*parasitology ; Nasopharynx/*parasitology ; *Phylogeny ; Polymorphism, Genetic ; Turkey ; },
abstract = {OBJECTIVE: The identification and molecular characterization of the bot fly larvae from an infected human with naso-pharyngeal myiasis in Turkey were aimed in this study.<br><br>METHODS: A total of 8 bot fly larvae from a 49-year-old woman with naso-pharyngeal infection in Adana province constituted the materials of this study. Morphological identification was performed on the larvae according to described keys. The barcode region of the CO1 gene from the genomic DNA extracts of the larvae was amplified and sequence analyses were utilized. Haplotype and genetic distance analyses were performed in CO1 sequences and a phylogenetic tree was built revealing phylogenetic relationships.<br><br>RESULTS: All bot fly larvae were identified as second stage larvae of Oestrus ovis in terms of morphologic characteristics. There was no polymorphism among the CO1 sequences of all isolates leading to detection of a single novel haplotype. The newly characterized haplotype in this study clustered with the O. ovis haplotypes from Bosnia and Herzegovina, Croatia, Brazil, and Iran in a monophyletic clade with an overall identity of 99.5%. Interspecific genetic differences among the subfamilies of Oestridae were in the range of 19.8% to 30.8%.<br><br>CONCLUSION: This study has provided the first molecular characterization data on O. ovis larvae from an accidental human host in Turkey based on CO1 barcode sequences.},
}
@article {pmid32211163,
year = {2020},
author = {Schenk, J and Kleinbölting, N and Traunspurger, W},
title = {Comparison of morphological, DNA barcoding, and metabarcoding characterizations of freshwater nematode communities.},
journal = {Ecology and evolution},
volume = {10},
number = {6},
pages = {2885-2899},
pmid = {32211163},
issn = {2045-7758},
abstract = {Biomonitoring approaches and investigations of many ecological questions require assessments of the biodiversity of a given habitat. Small organisms, ranging from protozoans to metazoans, are of great ecological importance and comprise a major share of the planet's biodiversity but they are extremely difficult to identify, due to their minute body sizes and indistinct structures. Thus, most biodiversity studies that include small organisms draw on several methods for species delimitation, ranging from traditional microscopy to molecular techniques. In this study, we compared the efficiency of these methods by analyzing a community of nematodes. Specifically, we evaluated the performances of traditional morphological identification, single-specimen barcoding (Sanger sequencing), and metabarcoding in the identification of 1500 nematodes from sediment samples. The molecular approaches were based on the analysis of the 28S ribosomal large and 18S small subunits (LSU and SSU). The morphological analysis resulted in the determination of 22 nematode species. Barcoding identified a comparable number of operational taxonomic units (OTUs) based on 28S rDNA (n = 20) and fewer OTUs based on 18S rDNA (n = 12). Metabarcoding identified a higher OTU number but fewer amplicon sequence variants (AVSs) (n = 48 OTUs, n = 17 ASVs for 28S rDNA, and n = 31 OTUs, n = 6 ASVs for 18S rDNA). Between the three approaches (morphology, barcoding, and metabarcoding), only three species (13.6%) were shared. This lack of taxonomic resolution hinders reliable community identifications to the species level. Further database curation will ensure the effective use of molecular species identification.},
}
@article {pmid32210683,
year = {2020},
author = {Naim, DM and Nor, SAM and Mahboob, S},
title = {Reassessment of species distribution and occurrence of mud crab (Scylla spp., Portunidae) in Malaysia through morphological and molecular identification.},
journal = {Saudi journal of biological sciences},
volume = {27},
number = {2},
pages = {643-652},
pmid = {32210683},
issn = {1319-562X},
abstract = {This study utilized genetic and morphometric approaches to assess the molecular and morphometric differentiation among commercially important species of mud crab. Molecular investigations were derived from 542 bp mitochondrial DNA COI on 249 individuals within genus Scylla from nine states in Malaysia represents four marine regions; South China Sea, Sulu Sea, Straits of Singapore and Straits of Malacca. Four specimens were obtained from Indonesia to give a robust analysis in this study. For species delimitation, Automatic Barcode Gap Discovery (ABGD) method on a web interface was employed. Analysis on phylogenetics was implemented utilizing Neighbour joining (NJ) and Maximum Parsimony (MP) methods. The inter- and intraspecies genetic distances (Ds) was computed using Kimura 2-parameter distance and executed in MEGA version 5.05. All samples were genetically and morphologically identified and clustered into four distinct species. Among the species, S. olivacea was the most abundant (n = 111), on the other hand the occurrence of S. paramamosain in Malaysia was very low (n = 29). No single individual of S. serrata from Malaysia was recorded in this study. Both genetic distance and phylogenetic approaches exhibited a correlative monophyletic association among all specimens analysed. This present study is crucial as it reports the reassessment of all species within genus Scylla in Malaysia, eventually could be employed as a reference source for subsequent research mainly on mariculture and other conservation efforts for the species.},
}
@article {pmid32207239,
year = {2020},
author = {Mutanen, M and Ovaskainen, O and Várkonyi, G and Itämies, J and Prosser, SWJ and Hebert, PDN and Hanski, I},
title = {Dynamics of a host-parasitoid interaction clarified by modelling and DNA sequencing.},
journal = {Ecology letters},
volume = {23},
number = {5},
pages = {851-859},
pmid = {32207239},
issn = {1461-0248},
support = {223257//Norges Forskningsr&#xe5;d/ ; //Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada/ ; 284601//Academy of Finland/ ; 309581//Academy of Finland/ ; 277984//Academy of Finland/ ; 223257//Academy of Finland/ ; //Jane and Aatos Erkko Foundation/ ; //Research Council of Norway/ ; },
mesh = {Animals ; Finland ; Host-Parasite Interactions ; Larva ; *Moths ; Sequence Analysis, DNA ; *Wasps ; },
abstract = {It has been hypothesised that the 2-year oscillations in abundance of Xestia moths are mediated by interactions with 1-year Ophion parasitoid wasps. We tested this hypothesis by modelling a 35-year time series of Xestia and Ophion from Northern Finland. Additionally, we used DNA barcoding to ascertain the species diversity of Ophion and targeted amplicon sequencing of their gut contents to confirm their larval hosts. Modelling of the time-series data strongly supported the hypothesised host-parasitoid dynamics and that periodic occurrence of Xestia moths is mediated by Ophion. DNA barcodes revealed that Ophion included five species rather than just one while targeted amplicon sequencing verified that Ophion does parasitise Xestia. At least one Ophion species employs 1-year Syngrapha interrogationis as an alternate host, but it did not detectably affect Xestia-Ophion dynamics. We also demonstrate the previously unrecognised complexity of this system due to cryptic parasitoid diversity.},
}
@article {pmid32206021,
year = {2020},
author = {Cho, G and Liao, YC and Lee, S and Yang, MM},
title = {Anomoneura taiwanica sp. nov. (Hemiptera, Psylloidea, Psyllidae), a new jumping plant-louse species from Taiwan associated with Morus australis (Moraceae).},
journal = {ZooKeys},
volume = {917},
number = {},
pages = {117-126},
pmid = {32206021},
issn = {1313-2989},
abstract = {Anomoneura taiwanica sp. nov. (Hemiptera, Psylloidea, Psyllidae, Psyllinae) is described based on samples from Taiwan that were previously misidentified as A. mori Schwarz, 1896. Morphological and genetic differences between the two species, as well as their distribution, are detailed and discussed. Comments on the pest status of Anomoneura spp. in East Asia are also provided.},
}
@article {pmid32206018,
year = {2020},
author = {Moulin, N},
title = {A cryptic new species of Chlidonoptera Karsch, 1892 from the south west protected zone of the Central African Republic (Insecta, Mantodea, Hymenopodidae).},
journal = {ZooKeys},
volume = {917},
number = {},
pages = {63-83},
pmid = {32206018},
issn = {1313-2989},
abstract = {Between 1998 and 2012, several scientific expeditions in Dzanga-Sangha Special Reserve and Dzanga-Ndoki National Park led to the collection of many Mantodea specimens from Central African Republic (CAR). Among these specimens, several males of an undescribed species were discovered. Morphologically, this species most closely resembles to Chlidonoptera vexillum Karsch, 1892 and Chlidonoptera lestoni Roy, 1975. A new lineage was revealed by DNA barcoding. Therefore, a new species is described, Chlidonoptera roxanae sp. nov. Habitus images, genitalia illustrations and descriptions, measurement data, a key to species, natural history information, and locality data are provided. These results add to the evidence that cryptic species can be found in tropical regions, a critical issue in efforts to document global species richness. They also illustrate the value of DNA barcoding, especially when coupled with traditional taxonomic tools, in disclosing hidden diversity.},
}
@article {pmid32200760,
year = {2020},
author = {Li, Y and Yang, H and Zhang, H and Liu, Y and Shang, H and Zhao, H and Zhang, T and Tu, Q},
title = {Decode-seq: a practical approach to improve differential gene expression analysis.},
journal = {Genome biology},
volume = {21},
number = {1},
pages = {66},
pmid = {32200760},
issn = {1474-760X},
mesh = {Animals ; Female ; Humans ; Male ; Mice ; Oryzias/genetics ; RNA-Seq/*methods ; Sex Determination Processes/genetics ; },
abstract = {Many differential gene expression analyses are conducted with an inadequate number of biological replicates. We describe an easy and effective RNA-seq approach using molecular barcoding to enable profiling of a large number of replicates simultaneously. This approach significantly improves the performance of differential gene expression analysis. Using this approach in medaka (Oryzias latipes), we discover novel genes with sexually dimorphic expression and genes necessary for germ cell development. Our results also demonstrate why the common practice of using only three replicates in differential gene expression analysis should be abandoned.},
}
@article {pmid32089821,
year = {2019},
author = {Asiah, N and Junianto, J and Yustiati, A and Sukendi, S and Fahmi, MR and Muchlisin, ZA and Kadapi, M and Windarti, W},
title = {Biometric and genetic differences in kelabau (Osteochilus spp.) as revealed using cytochrome c oxidase subunit 1.},
journal = {F1000Research},
volume = {8},
number = {},
pages = {177},
pmid = {32089821},
issn = {2046-1402},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Electron Transport Complex IV ; *Fishes/genetics ; Indonesia ; Phylogeny ; },
abstract = {Background: Kelabau (Osteochilus spp.) is a freshwater fish commonly found in the rivers of Riau, Indonesia. Researchers believe that these are Osteochilus kelabau; however, accurate taxonomic determination of these fish in Riau waters has not been made. The purpose of this study was to facilitate the identification of the kelabau based on its morphology and genetics using biometric and cytochrome c oxidase subunit 1 (CO1) analyses, respectively. Methods: Fish samples were collected from the Siak, Kampar and Rokan rivers in Riau Province, Indonesia. The DNA of 90 fish was extracted from the caudal fins using a DNA extraction kit, after which it was amplified using primers Fish-F1 and Fish-R1. Sequencing was conducted by Applied Biosystems Macrogen Korea, and the DNA sequences were then edited and aligned using MEGA v. 7. All samples were BLAST-searched for identification using the National Center for Biotechnology Information and BOLD System. Phylogenetic trees were constructed, and the similarity index was calculated using accession numbers AP011385.1 and KC631202.1 in GenBank. Results: Analysis of the consensus barcode sequence for 86 species revealed a high percentage of barcode matches (96%-97% in GenBank and 96.6%-96.76% in the BOLD System). The nucleotide distance between groups of kelabau from the different rivers based on the Kimura 2-parameter model gave the following results: 0.05% between groups from the Siak and Kampar rivers, 0.09% between those from the Siak and Rokan rivers and 0.05% between those from the Kampar and Rokan rivers. The nucleotide distance between the groups in the Siak (0.09%), Kampar (0.00%) and Rokan (0.10%) Rivers indicated that the kelabau in those rivers were related to each other. Conclusions: Based on the results of the research data using CO1 and biometric analyses, the kelabau were confirmed to be O. melanopleurus.},
}
@article {pmid32199980,
year = {2020},
author = {Hess, JF and Kohl, TA and Kotrová, M and Rönsch, K and Paprotka, T and Mohr, V and Hutzenlaub, T and Brüggemann, M and Zengerle, R and Niemann, S and Paust, N},
title = {Library preparation for next generation sequencing: A review of automation strategies.},
journal = {Biotechnology advances},
volume = {41},
number = {},
pages = {107537},
doi = {10.1016/j.biotechadv.2020.107537},
pmid = {32199980},
issn = {1873-1899},
mesh = {Automation ; Gene Library ; *High-Throughput Nucleotide Sequencing ; Humans ; *RNA ; Reproducibility of Results ; },
abstract = {Next generation sequencing is in the process of evolving from a technology used for research purposes to one which is applied in clinical diagnostics. Recently introduced high throughput and benchtop instruments offer fully automated sequencing runs at a lower cost per base and faster assay times. In turn, the complex and cumbersome library preparation, starting with isolated nucleic acids and resulting in amplified and barcoded DNA with sequencing adapters, has been identified as a significant bottleneck. Library preparation protocols usually consist of a multistep process and require costly reagents and substantial hands-on-time. Considerable emphasis will need to be placed on standardisation to ensure robustness and reproducibility. This review presents an overview of the current state of automation of library preparation for next generation sequencing. Major challenges associated with library preparation are outlined and different automation strategies are classified according to their functional principle. Pipetting workstations allow high-throughput processing yet offer limited flexibility, whereas microfluidic solutions offer great potential due to miniaturisation and decreased investment costs. For the emerging field of single cell transcriptomics for example, microfluidics enable singularisation of tens of thousands of cells in nanolitre droplets and barcoding of the RNA to assign each nucleic acid sequence to its cell of origin. Finally, two applications, the characterisation of bacterial pathogens and the sequencing within human immunogenetics, are outlined and benefits of automation are discussed.},
}
@article {pmid32198992,
year = {2020},
author = {Bahrami, F and Haghighi, A and Zamini, G and Khademerfan, M},
title = {Molecular evidence for zoonotic transmission of Blastocystis subtypes in Kurdistan province, West of Iran.},
journal = {Annals of parasitology},
volume = {66},
number = {1},
pages = {19&#x2013;25},
doi = {10.17420/ap6601.234},
pmid = {32198992},
issn = {2299-0631},
mesh = {Animals ; *Blastocystis/classification/genetics ; *Blastocystis Infections/transmission ; DNA, Protozoan/genetics ; Feces/parasitology ; Genetic Variation ; Humans ; Iran ; *Phylogeny ; *Zoonoses/parasitology/transmission ; },
abstract = {Blastocystis sp. is one of the most prevalent human parasites with a vast variety of non-human hosts. The aim of the present study was to determine the subtype distribution of Blastocystis in humans and trace the route of transmission by molecular data and phylogenetic analysis. Stool samples were collected from patients who referred to 14 medical laboratories in Kurdistan, Iran. All the samples were examined using the direct wet mount and formalinether concentration techniques. DNA extraction was carried out for 30 microscopically positive isolates and 33 negative samples. DNA amplification and subtype identification were also performed using the barcoding method and sequencing techniques. Of 1383 stool samples, 239 (17.3%) were infected with Blastocystis sp. Out of the 24 sequenced isolates, two (8.3%), six (25%), and 16 (66.6 %) belonged to the ST1, ST2, and ST3 subtypes, respectively. Bioinformatics analysis indicated that all the isolates were genetically similar to animal isolates. Blastocystis sp. was very common and ST1, ST2, and ST3 subtypes were prevalent in the study population. Bioinformatics analysis suggests that zoonotic transmission plays an important role in Blastocystis sp. distribution in Kurdistan province.},
}
@article {pmid32198938,
year = {2021},
author = {Bryan, R and Aronson, JK and Williams, A and Jordan, S},
title = {The problem of look-alike, sound-alike name errors: Drivers and solutions.},
journal = {British journal of clinical pharmacology},
volume = {87},
number = {2},
pages = {386-394},
doi = {10.1111/bcp.14285},
pmid = {32198938},
issn = {1365-2125},
mesh = {Humans ; Male ; *Medical Order Entry Systems ; Medication Errors/prevention &amp; control ; *Pharmaceutical Preparations ; },
abstract = {Look-alike or sound-alike (LASA) medication names may be mistaken for each other, e.g. mercaptamine and mercaptopurine. If an error of this sort is not intercepted, it can reach the patient and may result in harm. LASA errors occur because of shared linguistic properties between names (phonetic or orthographic), and potential for error is compounded by similar packaging, tablet appearance, tablet strength, route of administration or therapeutic indication. Estimates of prevalence range from 0.00003 to 0.0022% of all prescriptions, 7% of near misses, and between 6.2 and 14.7% of all medication error events. Solutions to LASA errors can target people or systems, and include reducing interruptions or distractions during medication administration, typographic tweaks, such as selective capitalization (Tall Man letters) or boldface, barcoding, and computerized physician order entry.},
}
@article {pmid32197583,
year = {2020},
author = {Achari, SR and Kaur, J and Dinh, Q and Mann, R and Sawbridge, T and Summerell, BA and Edwards, J},
title = {Phylogenetic relationship between Australian Fusarium oxysporum isolates and resolving the species complex using the multispecies coalescent model.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {248},
pmid = {32197583},
issn = {1471-2164},
mesh = {Cell Nucleus/genetics ; Evolution, Molecular ; Fusarium/*classification/genetics/isolation &amp; purification ; Genome, Fungal ; Mitochondria/genetics ; Phylogeny ; Whole Genome Sequencing/*statistics &amp; numerical data ; },
abstract = {BACKGROUND: The Fusarium oxysporum species complex (FOSC) is a ubiquitous group of fungal species readily isolated from agroecosystem and natural ecosystem soils which includes important plant and human pathogens. Genetic relatedness within the complex has been studied by sequencing either the genes or the barcoding gene regions within those genes. Phylogenetic analyses have demonstrated a great deal of diversity which is reflected in the differing number of clades identified: three, five and eight. Genetic limitation within the species in the complex has been studied through Genealogical Concordance Phylogenetic Species Recognition (GCPSR) analyses with varying number of phylogenetic 'species' identified ranging from two to 21. Such differing views have continued to confuse users of these taxonomies.<br><br>RESULTS: The phylogenetic relationships between Australian F. oxysporum isolates from both natural and agricultural ecosystems were determined using three datasets: whole genome, nuclear genes, and mitochondrial genome sequences. The phylogenies were concordant except for three isolates. There were three concordant clades from all the phylogenies suggesting similar evolutionary history for mitochondrial genome and nuclear genes for the isolates in these three clades. Applying a multispecies coalescent (MSC) model on the eight single copy nuclear protein coding genes from the nuclear gene dataset concluded that the three concordant clades correspond to three phylogenetic species within the FOSC. There was 100% posterior probability support for the formation of three species within the FOSC. This is the first report of using the MSC model to estimate species within the F. oxysporum species complex. The findings from this study were compared with previously published phylogenetics and species delimitation studies.<br><br>CONCLUSION: Phylogenetic analyses using three different gene datasets from Australian F. oxysporum isolates have all supported the formation of three major clades which delineated into three species. Species 2 (Clade 3) may be called F. oxysporum as it contains the neotype for F. oxysporum.},
}
@article {pmid32197350,
year = {2020},
author = {Cheng, Y and Tang, X and Gao, C and Li, Z and Chen, J and Guo, L and Wang, T and Xu, J},
title = {Molecular Diagnostics and Pathogenesis of Fungal Pathogens on Bast Fiber Crops.},
journal = {Pathogens (Basel, Switzerland)},
volume = {9},
number = {3},
pages = {},
pmid = {32197350},
issn = {2076-0817},
abstract = {Bast fibers and products derived from them are undergoing a resurgence in demand in the global market. However, fungal diseases have become an important factor limiting their yield and quality, causing devastating consequences for the production of bast fiber crops in many parts of the world. Thus, there is a high demand for effective control and prevention strategies against fungal pathogens. Having rapid, specific, sensitive, and cost-effective tests that can be used for early and accurate diagnosis of disease agents is an essential step of such strategies. The objective of this study was to review the current status of research on molecular diagnosis of fungal pathogens on bast fiber crops. Our search of PubMed identified nearly 20 genera of fungal pathogens on bast fiber crops, among which the five most common genera were Colletotrichum, Pythium, Verticillium, Fusarium, and Golovinomyces. The gene regions that have been used for molecular identifications of these fungi include internal transcribed spacer (ITS), translation elongation factor 1-α (EF-1α), ß-tubulin, calmodulin (CAL), histone subunit 3 (H3), glyceraldehydes-3-phosphate dehydrogenase (GAPDH), etc. We summarize the molecular assays that have been used to identify these fungi and discuss potential areas of future development for fast, specific, and accurate diagnosis of fungal pathogens on bast fiber crops.},
}
@article {pmid32189977,
year = {2020},
author = {Mengual, X and Bot, S and Chkhartishvili, T and Reimann, A and Thormann, J and von der Mark, L},
title = {Checklist of hover flies (Diptera, Syrphidae) of the Republic of Georgia.},
journal = {ZooKeys},
volume = {916},
number = {},
pages = {1-123},
pmid = {32189977},
issn = {1313-2989},
abstract = {A checklist of the Syrphidae species of the Republic of Georgia is presented. New hover fly (Diptera: Syrphidae) records from Georgia are provided as a result of field work conducted in 2018. At the same time, published syrphid records for the country are here reviewed and updated. A total of 357 species of hoverflies are now documented from Georgia, 40 of which are reported for the first time. Moreover, DNA barcodes were sequenced for 238 specimens, representing 74 species from this country.},
}
@article {pmid32187448,
year = {2020},
author = {Akimov, Y and Bulanova, D and Timonen, S and Wennerberg, K and Aittokallio, T},
title = {Improved detection of differentially represented DNA barcodes for high-throughput clonal phenomics.},
journal = {Molecular systems biology},
volume = {16},
number = {3},
pages = {e9195},
pmid = {32187448},
issn = {1744-4292},
mesh = {Algorithms ; Cell Line, Tumor ; Clone Cells ; DNA Barcoding, Taxonomic/*methods ; HEK293 Cells ; High-Throughput Nucleotide Sequencing ; Humans ; Neoplasms/*genetics ; Phenomics/*methods ; Selection, Genetic ; Sequence Analysis, DNA ; },
abstract = {Cellular DNA barcoding has become a popular approach to study heterogeneity of cell populations and to identify clones with differential response to cellular stimuli. However, there is a lack of reliable methods for statistical inference of differentially responding clones. Here, we used mixtures of DNA-barcoded cell pools to generate a realistic benchmark read count dataset for modelling a range of outcomes of clone-tracing experiments. By accounting for the statistical properties intrinsic to the DNA barcode read count data, we implemented an improved algorithm that results in a significantly lower false-positive rate, compared to current RNA-seq data analysis algorithms, especially when detecting differentially responding clones in experiments with strong selection pressure. Building on the reliable statistical methodology, we illustrate how multidimensional phenotypic profiling enables one to deconvolute phenotypically distinct clonal subpopulations within a cancer cell line. The mixture control dataset and our analysis results provide a foundation for benchmarking and improving algorithms for clone-tracing experiments.},
}
@article {pmid32184993,
year = {2020},
author = {Rey, A and Basurko, OC and Rodriguez-Ezpeleta, N},
title = {Considerations for metabarcoding-based port biological baseline surveys aimed at marine nonindigenous species monitoring and risk assessments.},
journal = {Ecology and evolution},
volume = {10},
number = {5},
pages = {2452-2465},
pmid = {32184993},
issn = {2045-7758},
abstract = {Monitoring introduction and spread of nonindigenous species via maritime transport and performing risk assessments require port biological baseline surveys. Yet, the comprehensiveness of these surveys is often compromised by the large number of habitats present in a port, the seasonal variability, and the time-consuming morphological approach used for taxonomic identification. Metabarcoding represents a promising alternative for rapid comprehensive port biological baseline surveys, but its application in this context requires further assessments.We applied metabarcoding (based on barcodes of the cytochrome c oxidase subunit I and of the 18S ribosomal RNA gene) to 192 port samples collected (a) from diverse habitats (water column-including environmental DNA and zooplankton, sediment, and fouling structures), (b) at different sites (from inner to outer estuary), and iii) during the four seasons of the year.By comparing the biodiversity metrics derived from each sample group, we show that each sampling method resulted in a distinct community profile and that environmental DNA alone cannot substitute for organismal sampling, and that, although sampling at different seasons and locations resulted in higher observed biodiversity, operational results can be obtained by sampling selected locations and seasons.By assessing the taxonomic composition of the samples, we show that metabarcoding data allowed the detection of previously recorded nonindigenous species as well as to reveal presence of new ones, even if in low abundance. Synthesis and application. Our comprehensive assessment of metabarcoding for port biological baseline surveys sets the basics for cost-effective, standardized, and comprehensive monitoring of nonindigenous species and for performing risk assessments in ports. This development will contribute to the implementation of the recently entered into force International Convention for the Control and Management of Ships' Ballast Water and Sediments.},
}
@article {pmid32184986,
year = {2020},
author = {Zenker, MM and Specht, A and Fonseca, VG},
title = {Assessing insect biodiversity with automatic light traps in Brazil: Pearls and pitfalls of metabarcoding samples in preservative ethanol.},
journal = {Ecology and evolution},
volume = {10},
number = {5},
pages = {2352-2366},
pmid = {32184986},
issn = {2045-7758},
abstract = {Automated species identification based on data produced with metabarcoding offers an alternative for assessing biodiversity of bulk insect samples obtained with traps. We used a standard two-step PCR approach to amplify a 313 bp fragment of the barcoding region of the mitochondrial COI gene. The PCR products were sequenced on an Illumina MiSeq platform, and the OTUs production and taxonomic identifications were performed with a customized pipeline and database. The DNA used in the PCR procedures was extracted directly from the preservative ethanol of bulk insect samples obtained with automatic light traps in 12 sampling areas located in different biomes of Brazil, during wet and dry seasons. Agricultural field and forest edge habitats were collected for all sampling areas. A total of 119 insect OTUs and nine additional OTUs assigned to other arthropod taxa were obtained at a ≥97% sequence similarity level. The alpha and beta diversity analyses comparing biomes, habitats, and seasons were mostly inconclusive, except for a significant difference in beta diversity between biomes. In this study, we were able to metabarcode and HTS adult insects from their preservative medium. Notwithstanding, our results underrepresent the true magnitude of insect diversity expected from samples obtained with automatic light traps in Brazil. Although biological and technical factors might have impacted our results, measures to optimize and standardize eDNA HTS should be in place to improve taxonomic coverage of samples of unknown diversity and stored in suboptimal conditions, which is the case of most eDNA samples.},
}
@article {pmid32183077,
year = {2020},
author = {Stur, E and Ekrem, T},
title = {The Chironomidae (Diptera) of Svalbard and Jan Mayen.},
journal = {Insects},
volume = {11},
number = {3},
pages = {},
pmid = {32183077},
issn = {2075-4450},
support = {70184209//Norwegian Biodiversity Information Centre/ ; 226134/F50//Norges Forskningsr&#xe5;d/ ; },
abstract = {Non-biting midges of the fly family Chironomidae are extremely abundant and diverse in Arctic regions and are essential components of Arctic ecosystems. Modern identification tools based on documented records of Arctic chironomid species are therefore important for ecological research and environmental monitoring in the region. Here, we provide an updated review of the chironomid fauna of the Svalbard archipelago and the island of Jan Mayen, Norway. Our results show that a total of 73 species distributed across 24 genera in four subfamilies are known from these areas. Our review treats 109 taxa, including nomina dubia and misidentifications. It includes morphological identification keys to all known species as well as photographs of most taxa and DNA barcodes of 66 species. Taxonomic remarks are given for selected taxa, including previous misidentifications and erroneous records. Chironomus islandicus, Tvetenia bavarica, Limnophyes schnelli, Metriocnemus brusti and Metriocnemus fuscipes as well as the genera Allocladius, Corynoneura and Bryophaenocladius are reported from Svalbard for the first time, while Procladius (Holotanypus) frigidus, Stictochironomus psilopterus, Chaetocladius incertus, Orthocladius (Orthocladius) mixtus and Smittia longicosta, previously considered as junior synonyms or nomina dubia, are revived as valid species based on examination of type material or literature. Twenty species within eleven genera are introduced with interim names. Metriocnemus similis is regarded as a junior synonym of Metriocnemus ursinus, and Smittia incerta, Smittia flexinervis and Smittia spitzbergensis are regarded as nomina dubia. Valid taxa no longer considered as part of the Svalbard fauna are Parochlus kiefferi, Arctopelopia barbitarsis, Procladius (Holotanypus) crassinervis, Diamesa lindrothi, Diamesa incallida, Diamesa lundstromi, Chironomus hyperboreus, Sergentia coracina, Camptocladius stercorarius, Chaetocladius dissipatus, Chaetocladius dentiforceps, Chaetocladius laminatus, Chaetocladius perennis, Cricotopus (Cricotopus) humeralis, Cricotopus (Cricotopus) polaris, Hydrosmittia ruttneri, Limnophyes edwardsi, Metriocnemus picipes, Metriocnemus tristellus, Orthocladius (Eudactylocladius) gelidus, Orthocladius (Euorthocladius) thienemanni, Orthocladius (Orthocladius) obumbratus, Orthocladius (Orthocladius) rhyacobius, Paralimnophyes, Paraphaenocladius impensus, Psectrocladius (Monopsectrocladius) calcaratus, Psectrocladius (Psectrocladius) psilopterus, Psectrocladius (Psectrocladius) ventricosus, Smittia lasiophthalma, Smittia lasiops and Zalutschia tatrica.},
}
@article {pmid32181342,
year = {2020},
author = {Richards, JL and Sheng, V and Yi, CW and Ying, CL and Ting, NS and Sadovy, Y and Baker, D},
title = {Prevalence of critically endangered European eel (Anguilla anguilla) in Hong Kong supermarkets.},
journal = {Science advances},
volume = {6},
number = {10},
pages = {eaay0317},
pmid = {32181342},
issn = {2375-2548},
mesh = {Anguilla/classification/*genetics ; Animals ; Commerce/*ethics ; Conservation of Natural Resources/legislation &amp; jurisprudence ; DNA/*genetics ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; *Endangered Species ; Fish Proteins/*genetics ; Hong Kong ; Phylogeny ; Seafood/economics ; },
abstract = {European eel (Anguilla anguilla) is a critically endangered species requiring CITES permits for international trade. Despite the fact that no imports to Hong Kong were declared within the last 2 years, our study found that this species is still commonly sold in major supermarket chains across Hong Kong. In a COI barcoding survey of 49 retail vendors encompassing 13 brands, 9 of 13 carried A. anguilla, and 45% of all eel products available at retail outlets (n = 49) were unambiguously identified as A. anguilla. Considering the visual similarity of eel species and disproportionate amount of undeclared A. anguilla available for consumption, this finding raises urgent concerns regarding the enforcement of international CITES trade regulations. Furthermore, the prevalence of A. anguilla in supermarkets highlights how illicit wildlife products are not solely limited to specialized affluent buyers; some species have entered mainstream distribution networks for the average consumer.},
}
@article {pmid32179808,
year = {2020},
author = {Ouso, DO and Otiende, MY and Jeneby, MM and Oundo, JW and Bargul, JL and Miller, SE and Wambua, L and Villinger, J},
title = {Three-gene PCR and high-resolution melting analysis for differentiating vertebrate species mitochondrial DNA for biodiversity research and complementing forensic surveillance.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {4741},
pmid = {32179808},
issn = {2045-2322},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Animals, Wild/*genetics ; *Biodiversity ; Conservation of Natural Resources ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Elephants/genetics ; Forensic Genetics/*methods ; Giraffes/genetics ; High-Throughput Screening Assays/*methods ; Kenya ; Mitochondria/enzymology ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Vertebrates/*genetics ; },
abstract = {Reliable molecular identification of vertebrate species from morphologically unidentifiable tissue is critical for the prosecution of illegally-traded wildlife products, conservation-based biodiversity research, and identification of blood-meal hosts of hematophagous invertebrates. However, forensic identification of vertebrate tissue relies on sequencing of the mitochondrial cytochrome oxidase I (COI) 'barcode' gene, which remains costly for purposes of screening large numbers of unknown samples during routine surveillance. Here, we adapted a rapid, low-cost approach to differentiate 10 domestic and 24 wildlife species that are common in the East African illegal wildlife products trade based on their unique high-resolution melting profiles from COI, cytochrome b, and 16S ribosomal RNA gene PCR products. Using the approach, we identified (i) giraffe among covertly sampled meat from Kenyan butcheries, and (ii) forest elephant mitochondrial sequences among savannah elephant reference samples. This approach is being adopted for high-throughput pre-screening of potential bushmeat samples in East African forensic science pipelines.},
}
@article {pmid32178248,
year = {2020},
author = {Sawicki, J and Bączkiewicz, A and Buczkowska, K and Górski, P and Krawczyk, K and Mizia, P and Myszczyński, K and Ślipiko, M and Szczecińska, M},
title = {The Increase of Simple Sequence Repeats during Diversification of Marchantiidae, An Early Land Plant Lineage, Leads to the First Known Expansion of Inverted Repeats in the Evolutionarily-Stable Structure of Liverwort Plastomes.},
journal = {Genes},
volume = {11},
number = {3},
pages = {},
pmid = {32178248},
issn = {2073-4425},
mesh = {Embryophyta/*genetics/growth &amp; development ; Evolution, Molecular ; Genome, Chloroplast/genetics ; Hepatophyta/*genetics/growth &amp; development ; High-Throughput Nucleotide Sequencing ; Inverted Repeat Sequences/*genetics ; Microsatellite Repeats/*genetics ; Phylogeny ; },
abstract = {The chloroplast genomes of liverworts, an early land plant lineage, exhibit stable structure and gene content, however the known resources are very limited. The newly sequenced plastomes of Conocephalum, Riccia and Sphaerocarpos species revealed an increase of simple sequence repeats during the diversification of complex thalloid liverwort lineage. The presence of long TA motifs forced applying the long-read nanopore sequencing method for proper and dependable plastome assembly, since the length of dinucleotide repeats overcome the length of Illumina short reads. The accumulation of SSRs (simple sequence repeats) enabled the expansion of inverted repeats by the incorporation of rps12 and rps7 genes, which were part of large single copy (LSC) regions in the previously sequenced plastomes. The expansion of inverted repeat (IR) at the genus level is reported for the first time for non-flowering plants. Moreover, comparative analyses with remaining liverwort lineages revealed that the presence of SSR in plastomes is specific for simple thalloid species. Phylogenomic analysis resulted in trees confirming monophyly of Marchantiidae and partially congruent with previous studies, due to dataset-dependent results of Dumortiera-Reboulia relationships. Despite the lower evolutionary rate of Marchantiales plastomes, significant barcoding gap was detected, even for recently divergent holarctic Conocephalum species. The sliding window analyses revealed the presence of 18 optimal (500 bp long) barcodes that enable the molecular identification of all studied species.},
}
@article {pmid32174029,
year = {2020},
author = {Guo, Q and Wang, Y and Chen, C and Wei, D and Fu, J and Xu, H and Gu, H},
title = {Multiplexed Luminescence Oxygen Channeling Immunoassay Based on Dual-Functional Barcodes with a Host-Guest Structure: A Facile and Robust Suspension Array Platform.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {16},
number = {17},
pages = {e1907521},
doi = {10.1002/smll.201907521},
pmid = {32174029},
issn = {1613-6829},
mesh = {*Immunoassay/instrumentation/methods ; *Luminescence ; *Oxygen/metabolism ; Quantum Dots/chemistry ; Singlet Oxygen/chemistry ; },
abstract = {The development of a powerful immunoassay platform with capacities of both simplicity and high multiplexing is promising for disease diagnosis. To meet this urgent need, for the first time, a multiplexed luminescent oxygen channeling immunoassay (multi-LOCI) platform by implementation of LOCI with suspension array technology is reported. As the microcarrier of the platform, a unique dual-functional barcode with a host-guest structure composed of a quantum dot host bead (QDH) and LOCI acceptor beads (ABs) is designed, in which QDH provides function of high coding capacity while ABs facilitate the LOCI function. The analytes bridge QDH@ABs and LOCI donor beads (DBs) into a close proximity, forming a QDH@ABs-DBs "host-guest-satellite" superstructure that generates both barcode signal from QDH and LOCI signal induced by singlet oxygen channeling between ABs and DBs. Through imaging-based decoding, different barcodes are automatically distinguished and colocalized with LOCI signals. Importantly, the assay achieves simultaneous detection of multiple analytes within one reaction, simply by following a "mix-and-measure" protocol without the need for tedious washing steps. Furthermore, the multi-LOCI platform is validated for real sample measurements. With the advantages of robustness, simplicity, and high multiplexing, the platform holds great potential for the development of point-of-care diagnostics.},
}
@article {pmid32173285,
year = {2020},
author = {Ye, C and Chen, Z and Liu, Z and Wang, F and He, X},
title = {Defining endogenous barcoding sites for CRISPR/Cas9-based cell lineage tracing in zebrafish.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {47},
number = {2},
pages = {85-91},
doi = {10.1016/j.jgg.2019.11.012},
pmid = {32173285},
issn = {1673-8527},
mesh = {Animals ; CRISPR-Cas Systems/*genetics ; Cell Lineage/*genetics ; *DNA Barcoding, Taxonomic ; Genome/genetics ; Humans ; Single-Cell Analysis ; Transcriptome/genetics ; Zebrafish/classification/*genetics ; },
abstract = {There is a growing interest in developing experimental methods for tracking the developmental cell lineages of a complex organism. The recently developed CRISPR/Cas9-based barcoding method is, although highly promising, difficult to scale up because it relies on exogenous barcoding sequences that are engineered into the genome. In this study, we characterized 78 high-quality endogenous sites in the zebrafish genome that can be used as CRISPR/Cas9-based barcoding sites. The 78 sites are all highly expressed in most of the cell types according to single-cell RNA sequencing (scRNA-seq) data. Hence, the barcoding information of the 78 endogenous sites is recovered by the available scRNA-seq platforms, enabling simultaneous characterization of cell type and cell lineage information.},
}
@article {pmid32171299,
year = {2020},
author = {Dilthey, AT and Meyer, SA and Kaasch, AJ},
title = {Ultraplexing: increasing the efficiency of long-read sequencing for hybrid assembly with k-mer-based multiplexing.},
journal = {Genome biology},
volume = {21},
number = {1},
pages = {68},
pmid = {32171299},
issn = {1474-760X},
mesh = {*Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; Nanopore Sequencing/*methods ; Plasmids/genetics ; Staphylococcus aureus/genetics/isolation &amp; purification ; },
abstract = {Hybrid genome assembly has emerged as an important technique in bacterial genomics, but cost and labor requirements limit large-scale application. We present Ultraplexing, a method to improve per-sample sequencing cost and hands-on time of Nanopore sequencing for hybrid assembly by at least 50% compared to molecular barcoding while maintaining high assembly quality. Ultraplexing requires the availability of Illumina data and uses inter-sample genetic variability to assign reads to isolates, which obviates the need for molecular barcoding. Thus, Ultraplexing can enable significant sequencing and labor cost reductions in large-scale bacterial genome projects.},
}
@article {pmid32166968,
year = {2021},
author = {Yue, J and Zuo, Z and Huang, H and Wang, Y},
title = {Application of Identification and Evaluation Techniques for Ethnobotanical Medicinal Plant of Genus Panax: A Review.},
journal = {Critical reviews in analytical chemistry},
volume = {51},
number = {4},
pages = {373-398},
doi = {10.1080/10408347.2020.1736506},
pmid = {32166968},
issn = {1547-6510},
mesh = {Chromatography, High Pressure Liquid ; Chromatography, Liquid ; DNA Barcoding, Taxonomic ; Electrochemical Techniques ; Geography ; Humans ; Medicine, Chinese Traditional ; Microscopy ; Panax/*chemistry/*classification/genetics/metabolism ; Plants, Medicinal/*chemistry ; Quality Control ; Treatment Outcome ; },
abstract = {Genus Panax, as worldwide medicinal plants, has a medical history for thousands of years. Most of the entire genus are traditional ethnobotanical medicine in China, Myanmar, Thailand, Vietnam and Laos, which have given rise to international attention and use. This paper reviewed more than 210 articles and related books on the research of Panax medicinal plants and their Chinese patent medicines published in the last 30 years. The purpose was to review and summarize the species classification, geographical distribution, and ethnic minorities medicinal records of the genus Panax, and further to review the analytical tools and data analysis methods for the authentication and quality assessment of Panax medicinal materials and Chinese patent medicines. Five main technologies applied in the identification and evaluation of Panax have been introduced and summarized. Chromatography was the most widely used one. Further research and development of molecular identification technology had the potential to become a mainstream identification technology. In addition, some novel, controversial, and worthy methods including electronic noses, electronic eyes, and DNA barcoding were also introduced. At the same time, more than 80% of the researches were carried out by a combination of chemometric pattern-recognition technologies and multi-analysis technologies. All the technologies and methods applied can provide strong support and guarantee for the identification and evaluation of genus Panax, and also conduce to excellent reference value for the development and in-depth research of new technologies in Panax.},
}
@article {pmid32165853,
year = {2020},
author = {Bowser, ML and Brassfield, R and Dziergowski, A and Eskelin, T and Hester, J and Magness, DR and McInnis, M and Melvin, T and Morton, JM and Stone, J},
title = {Towards conserving natural diversity: A biotic inventory by observations, specimens, DNA barcoding and high-throughput sequencing methods.},
journal = {Biodiversity data journal},
volume = {8},
number = {},
pages = {e50124},
pmid = {32165853},
issn = {1314-2828},
abstract = {The Kenai National Wildlife Refuge has been given a broad conservation mandate to conserve natural diversity. A prerequisite for fulfilling this purpose is to be able to identify the species and communities that make up that biodiversity. We tested a set of varied methods for inventory and monitoring of plants, birds and terrestrial invertebrates on a grid of 40 sites in a 938 ha study area in the Slikok Creek watershed, Kenai Peninsula, Alaska. We sampled plants and lichens through observation and specimen-based methods. We surveyed birds using bird call surveys on variable circular plots. We sampled terrestrial arthropods by sweep net sampling, processing samples with High Throughput Sequencing methods. We surveyed for earthworms, using the hot mustard extraction method and identified worm specimens by morphology and DNA barcoding. We examined community membership using clustering methods and Nonmetric Multidimensional Scaling. We documented a total of 4,764 occurrences of 984 species and molecular operational taxonomic units: 87 vascular plants, 51 mosses, 12 liverworts, 111 lichens, 43 vertebrates, 663 arthropods, 9 molluscs and 8 annelid worms. Amongst these records, 102 of the arthropod species appeared to be new records for Alaska. We found three non-native species: Deroceras agreste (Linnaeus, 1758) (Stylommatophora: Agriolimacidae), Dendrobaena octaedra (Savigny, 1826) (Crassiclitellata: Lumbricidae) and Heterarthrus nemoratus (Fallén, 1808) (Hymenoptera: Tenthredinidae). Both D. octaedra and H. nemoratus were found at sites distant from obvious human disturbance. The 40 sites were grouped into five community groups: upland mixed forest, black spruce forest, open deciduous forest, shrub-sedge bog and willow. We demonstrated that, at least for a subset of species that could be detected using these methods, we were able to document current species distributions and assemblages in a way that could be efficiently repeated for the purposes of biomonitoring. While our methods could be improved and additional methods and groups could be added, our combination of techniques yielded a substantial portion of the data necessary for fulfilling Kenai National Wildlife Refuge's broad conservation purposes.},
}
@article {pmid32164546,
year = {2020},
author = {Bratzel, F and Heller, S and Cyrannek, N and Paule, J and Leme, EMC and Loreth, A and Nowotny, A and Kiefer, M and Till, W and Barfuss, MHJ and Lexer, C and Koch, MA and Zizka, G},
title = {The low-copy nuclear gene Agt1 as a novel DNA barcoding marker for Bromeliaceae.},
journal = {BMC plant biology},
volume = {20},
number = {1},
pages = {111},
pmid = {32164546},
issn = {1471-2229},
support = {Evo-BoGa//Bundesministerium f&#xfc;r Bildung und Forschung/ ; Evo-BoGa//Bundesministerium f&#xfc;r Bildung und Forschung/ ; },
mesh = {Bromeliaceae/classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; Plant Proteins/*genetics ; },
abstract = {BACKGROUND: The angiosperm family Bromeliaceae comprises over 3.500 species characterized by exceptionally high morphological and ecological diversity, but a very low genetic variation. In many genera, plants are vegetatively very similar which makes determination of non flowering bromeliads difficult. This is particularly problematic with living collections where plants are often cultivated over decades without flowering. DNA barcoding is therefore a very promising approach to provide reliable and convenient assistance in species determination. However, the observed low genetic variation of canonical barcoding markers in bromeliads causes problems.<br><br>RESULT: In this study the low-copy nuclear gene Agt1 is identified as a novel DNA barcoding marker suitable for molecular identification of closely related bromeliad species. Combining a comparatively slowly evolving exon sequence with an adjacent, genetically highly variable intron, correctly matching MegaBLAST based species identification rate was found to be approximately double the highest rate yet reported for bromeliads using other barcode markers.<br><br>CONCLUSION: In the present work, we characterize Agt1 as a novel plant DNA barcoding marker to be used for barcoding of bromeliads, a plant group with low genetic variation. Moreover, we provide a comprehensive marker sequence dataset for further use in the bromeliad research community.},
}
@article {pmid32163643,
year = {2020},
author = {Hao, M and Jin, Q and Meng, G and Yang, C and Yang, S and Shi, Z and Tang, M and Liu, S and Li, Y and Zhang, D and Su, X and Shih, C and Sun, Y and Zhou, X and Zhang, AB},
title = {Regional assemblages shaped by historical and contemporary factors: Evidence from a species-rich insect group.},
journal = {Molecular ecology},
volume = {29},
number = {13},
pages = {2492-2510},
doi = {10.1111/mec.15412},
pmid = {32163643},
issn = {1365-294X},
mesh = {Animals ; *Biodiversity ; China ; DNA Barcoding, Taxonomic ; Gene Flow ; Moths/*classification ; Phylogeny ; },
abstract = {Understanding diversity patterns requires accounting for the roles of both historical and contemporary factors in the assembly of communities. Here, we compared diversity patterns of two moth assemblages sampled from Taihang and Yanshan mountains in Northern China and performed ancestral range reconstructions using the Multi-State Speciation and Extinction model, to track the origins of these patterns. Further, we estimated diversification rates of the two moth assemblages and explored the effects of contemporary ecological factors. From 7,788 specimens we identified 835 species belonging to 23 families, using both DNA barcode analysis and morphology. Moths in Yanshan mountains showed higher species diversity than in Taihang mountains. Ancestral range analysis indicated Yanshan as the origin, with significant historical dispersals from Yanshan to Taihang. Asymmetrical diversification, population expansion, along with frequent and considerable gene flow were detected between communities. Moreover, dispersal limitation or the joint effect of environment filtering and dispersal limitation were inferred as main driving forces shaping current diversity patterns. In summary, we demonstrate that a multiscale (community, population and species level) analysis incorporating both historical and contemporary factors can be useful in delineating factors contributing to community assembly and patterning in diversity.},
}
@article {pmid32163447,
year = {2020},
author = {Zangl, L and Daill, D and Schweiger, S and Gassner, G and Koblmüller, S},
title = {A reference DNA barcode library for Austrian amphibians and reptiles.},
journal = {PloS one},
volume = {15},
number = {3},
pages = {e0229353},
pmid = {32163447},
issn = {1932-6203},
mesh = {Amphibians/*genetics ; Animals ; Austria ; *Biodiversity ; DNA/*genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; *Gene Library ; Phylogeny ; Reference Standards ; Reptiles/*genetics ; Species Specificity ; },
abstract = {In the last few years, DNA barcoding became an established method for species identification in biodiversity inventories and monitoring studies. Such studies depend on the access to a comprehensive reference data base, covering all relevant taxa. Here we present a comprehensive DNA barcode inventory of all amphibian and reptile species native to Austria, except for the putatively extinct Vipera ursinii rakosiensis and Lissotriton helveticus, which has been only recently reported for the very western edge of Austria. A total of 194 DNA barcodes were generated in the framework of the Austrian Barcode of Life (ABOL) initiative. Species identification via DNA barcodes was successful for most species, except for the hybridogenetic species complex of water frogs (Pelophylax spp.) and the crested newts (Triturus spp.), in areas of sympatry. However, DNA barcoding also proved powerful in detecting deep conspecific lineages, e.g. within Natrix natrix or the wall lizard (Podarcis muralis), resulting in more than one Barcode Index Number (BIN) per species. Moreover, DNA barcodes revealed the presence of Natrix helvetica, which has been elevated to species level only recently, and genetic signatures of the Italian water frog Pelophylax bergeri in Western Austria for the first time. Comparison to previously published DNA barcoding data of European amphibians and reptiles corroborated the results of the Austrian data but also revealed certain peculiarities, underlining the particular strengths and in the case of the genus Pelophylax also the limitations of DNA barcoding. Consequently, DNA barcoding is not only powerful for species identification of all life stages of most Austrian amphibian and reptile species, but also for the detection of new species, the monitoring of gene flow or the presence of alien populations and/or species. Thus, DNA barcoding and the data generated in this study may serve both scientific and national or even transnational conservation purposes.},
}
@article {pmid32163430,
year = {2020},
author = {Korzik, ML and Austin, HM and Cooper, B and Jasperse, C and Tan, G and Richards, E and Spencer, ET and Steinwand, B and Fodrie, FJ and Bruno, JF},
title = {Marketplace shrimp mislabeling in North Carolina.},
journal = {PloS one},
volume = {15},
number = {3},
pages = {e0229512},
pmid = {32163430},
issn = {1932-6203},
mesh = {Animals ; Aquaculture/*ethics/*methods ; Conservation of Natural Resources/methods ; DNA Barcoding, Taxonomic/methods ; Ecosystem ; North Carolina ; Penaeidae/classification/*genetics ; Seafood/analysis/economics ; Shellfish/analysis/classification ; },
abstract = {Seafood mislabeling occurs in a wide range of seafood products worldwide, resulting in public distrust, economic fraud, and health risks for consumers. We quantified the extent of shrimp mislabeling in coastal and inland North Carolina. We used standard DNA barcoding procedures to determine the species identity of 106 shrimp sold as "local" by 60 vendors across North Carolina. Thirty-four percent of the purchased shrimp was mislabeled, and surprisingly the percentage did not differ significantly between coastal and inland counties. One third of product incorrectly marketed as "local" was in fact whiteleg shrimp: an imported and globally farmed species native to the eastern Pacific, not found in North Carolina waters. In addition to the negative ecosystem consequences of shrimp farming (e.g., the loss of mangrove forests and the coastal buffering they provide), North Carolina fishers-as with local fishers elsewhere-are negatively impacted when vendors label farmed, frozen, and imported shrimp as local, fresh, and wild-caught.},
}
@article {pmid32162067,
year = {2020},
author = {Kamyabi, N and Abbasgholizadeh, R and Maitra, A and Ardekani, A and Biswal, SL and Grande-Allen, KJ},
title = {Isolation and mutational assessment of pancreatic cancer extracellular vesicles using a microfluidic platform.},
journal = {Biomedical microdevices},
volume = {22},
number = {2},
pages = {23},
pmid = {32162067},
issn = {1572-8781},
support = {P30 CA016672/CA/NCI NIH HHS/United States ; },
mesh = {Cell Line, Tumor ; Cell Separation/*instrumentation ; DNA Mutational Analysis/*instrumentation ; Extracellular Vesicles/*genetics/*pathology ; Genomics ; Humans ; *Lab-On-A-Chip Devices ; Pancreatic Neoplasms/*pathology ; Proto-Oncogene Proteins p21(ras)/genetics ; },
abstract = {Cancer cells release extracellular vesicles known as extracellular vesicles (EVs), containing tumor-derived DNA, RNA and proteins within their cargo, into the circulation. Circulating tumor-derived extracellular vesicles (TEV) can be used in the context of serial "liquid biopsies" for early detection of cancer, for monitoring disease burden in patients, and for assessing recurrence in the post-resection setting. Nonetheless, isolating sufficient TEV by ultracentrifugation-based approaches, in order to enable molecular assessment of EVs cargo, can be an arduous, time-consuming process and is inconsistent in the context of yield and purity among institutions. Herein, we describe a microfluidic platform, which we have named MITEV (Microfluidic Isolation of Tumor-derived Extracellular Vesicles) for the rapid isolation of TEV from the plasma of pancreatic cancer patients. The device, which has ~100,000 pillars placed in a zigzag pattern and is coated with antibodies against generic EV surface proteins (anti-CD63, -CD9, and -CD81 antibodies) or the TEV specific anti-Epithelial Cell Adhesion Molecule (EpCAM) antibody, is capable of high-throughput EVs isolation and yields sufficient DNA (total of ~2-14 ng from 2-ml plasma) for downstream genomic analysis. Using two independent quantitative platforms, droplet digital polymerase chain reaction (ddPCR) and molecular barcoding using nanoString nCounter® technology, we can reliably identify KRAS mutations within isolated TEV of treatment-naïve metastatic pancreatic cancer patients. Our study suggests that the MITEV device can be used for point-of-care applications, such as in the context of monitoring residual or recurrent tumor presence in pancreatic cancer patients undergoing therapy.},
}
@article {pmid32161577,
year = {2020},
author = {Betts, EL and Gentekaki, E and Tsaousis, AD},
title = {Exploring Micro-Eukaryotic Diversity in the Gut: Co-occurrence of Blastocystis Subtypes and Other Protists in Zoo Animals.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {288},
pmid = {32161577},
issn = {1664-302X},
support = {BB/M009971/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {Blastocystis is a genetically diverse microbial eukaryote thriving in the gut of humans and other animals. While Blastocystis has been linked with gastrointestinal disorders, its pathogenicity remains controversial. Previous reports have suggested that one out of six humans could be carrying Blastocystis in their gut, while the numbers could be even higher in animals. Most studies on Blastocystis are either exclusively targeting the organism itself and/or the associated prokaryotic microbiome, while co-occurrence of other microbial eukaryotes has been mainly ignored. Herein, we aimed to explore presence and genetic diversity of Blastocystis along with the commonly occurring eukaryotes Cryptosporidium, Eimeria, Entamoeba and Giardia in the gut of asymptomatic animals from two conservation parks in the United Kingdom. Building upon a previous study, a total of 231 fecal samples were collected from 38 vertebrates, which included 12 carnivorous and 26 non-carnivorous species. None of the animals examined herein showed gastrointestinal symptoms. The barcoding region of the small subunit ribosomal RNA was used for subtyping of Blastocystis. Overall, 47% of animal species were positive for Blastocystis. Twenty six percent of samples carried more than one subtypes, including the newly identified hosts Scottish wildcat, bongo and lynx. Fifty three percent of samples carried at least another microbial eukaryote. Herewith, we discuss potential implications of these findings and the increasingly blurred definition of microbial parasites.},
}
@article {pmid32156257,
year = {2020},
author = {Berry, LK and Thomas, GH and Thorpe, PH},
title = {CATS: Cas9-assisted tag switching. A high-throughput method for exchanging genomic peptide tags in yeast.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {221},
pmid = {32156257},
issn = {1471-2164},
support = {FC001003/ARC_/Arthritis Research UK/United Kingdom ; MC_UP_A252_1027/MRC_/Medical Research Council/United Kingdom ; FC001003/WT_/Wellcome Trust/United Kingdom ; },
mesh = {CRISPR-Associated Protein 9/*metabolism ; CRISPR-Cas Systems ; Gene Editing ; Green Fluorescent Proteins/*genetics/metabolism ; High-Throughput Screening Assays ; Peptides/*genetics/metabolism ; Plasmids/genetics ; RNA, Guide, CRISPR-Cas Systems/genetics ; Saccharomyces cerevisiae/genetics/*growth &amp; development ; Staining and Labeling ; },
abstract = {BACKGROUND: The creation of arrays of yeast strains each encoding a different protein with constant tags is a powerful method for understanding how genes and their proteins control cell function. As genetic tools become more sophisticated there is a need to create custom libraries encoding proteins fused with specialised tags to query gene function. These include protein tags that enable a multitude of added functionality, such as conditional degradation, fluorescent labelling, relocalization or activation and also DNA and RNA tags that enable barcoding of genes or their mRNA products. Tools for making new libraries or modifying existing ones are becoming available, but are often limited by the number of strains they can be realistically applied to or by the need for a particular starting library.<br><br>RESULTS: We present a new recombination-based method, CATS - Cas9-Assisted Tag Switching, that switches tags in any existing library of yeast strains. This method employs the reprogrammable RNA guided nuclease, Cas9, to both introduce endogenous double strand breaks into the genome as well as liberating a linear DNA template molecule from a plasmid. It exploits the relatively high efficiency of homologous recombination in budding yeast compared with non-homologous end joining.<br><br>CONCLUSIONS: The method takes less than 2 weeks, is cost effective and can simultaneously introduce multiple genetic changes, thus providing a rapid, genome-wide approach to genetic modification.},
}
@article {pmid32156073,
year = {2020},
author = {Vitale, SR and Groenendijk, FH and van Marion, R and Beaufort, CM and Helmijr, JC and Dubbink, HJ and Dinjens, WNM and Ewing-Graham, PC and Smolders, R and van Doorn, HC and Boere, IA and Berns, EMJJ and Helleman, J and Jansen, MPHM},
title = {TP53 Mutations in Serum Circulating Cell-Free Tumor DNA As Longitudinal Biomarker for High-Grade Serous Ovarian Cancer.},
journal = {Biomolecules},
volume = {10},
number = {3},
pages = {},
pmid = {32156073},
issn = {2218-273X},
mesh = {Adult ; Aged ; *Biomarkers, Tumor/genetics/metabolism ; *Circulating Tumor DNA/blood/genetics ; Female ; Humans ; Middle Aged ; *Mutation, Missense ; Neoplasm, Residual ; *Ovarian Neoplasms/blood/drug therapy/genetics ; Tumor Suppressor Protein p53/*genetics ; },
abstract = {The aim of this study was to determine an optimal workflow to detect TP53 mutations in baseline and longitudinal serum cell free DNA (cfDNA) from high-grade serous ovarian carcinomas (HGSOC) patients and to define whether TP53 mutations are suitable as biomarker for disease. TP53 was investigated in tissue and archived serum from 20 HGSOC patients by a next-generation sequencing (NGS) workflow alone or combined with digital PCR (dPCR). AmpliSeq™-focused NGS panels and customized dPCR assays were used for tissue DNA and longitudinal cfDNAs, and Oncomine NGS panel with molecular barcoding was used for baseline cfDNAs. TP53 missense mutations were observed in 17 tissue specimens and in baseline cfDNA for 4/8 patients by AmpliSeq, 6/9 patients by Oncomine, and 4/6 patients by dPCR. Mutations in cfDNA were detected in 4/6 patients with residual disease and 3/4 patients with disease progression within six months, compared to 5/11 patients with no residual disease and 6/13 patients with progression after six months. Finally, mutations were detected at progression in 5/6 patients, but not during chemotherapy. NGS with molecular barcoding and dPCR were most optimal workflows to detect TP53 mutations in baseline and longitudinal serum cfDNA, respectively. TP53 mutations were undetectable in cfDNA during treatment but re-appeared at disease progression, illustrating its promise as a biomarker for disease monitoring.},
}
@article {pmid32152714,
year = {2020},
author = {Rataj, M and Vďačný, P},
title = {Multi-gene phylogeny of Tetrahymena refreshed with three new histophagous species invading freshwater planarians.},
journal = {Parasitology research},
volume = {119},
number = {5},
pages = {1523-1545},
pmid = {32152714},
issn = {1432-1955},
support = {APVV-15-0147//Agent&#xfa;ra na Podporu V&#xfd;skumu a V&#xfd;voja/ ; VEGA 1/0041/17//Vedeck&#xe1; Grantov&#xe1; Agent&#xfa;ra M&#x160;VVa&#x160; SR a SAV/ ; UK/160/2020//Univerzita Komensk&#xe9;ho v Bratislave/ ; },
mesh = {Animals ; Biodiversity ; Fresh Water/parasitology ; Host Specificity ; Hymenostomatida/classification/genetics/physiology ; *Phylogeny ; Planarians/classification/*parasitology ; Protozoan Proteins/genetics ; RNA, Ribosomal/genetics ; Tetrahymena/*classification/genetics/physiology ; },
abstract = {Planarians represent an insufficiently explored group of aquatic invertebrates that might serve as hosts of histophagous ciliates belonging to the hymenostome genus Tetrahymena. During our extensive research on freshwater planarians, parasitic tetrahymenas were detected in two of the eight planarian species investigated, namely, in Dugesia gonocephala and Girardia tigrina. Using the 16S and 18S rRNA genes as well as the barcoding cytochrome oxidase subunit I, one ciliate species was identified as T. scolopax and three species were recognized as new forms: T. acanthophora, T. dugesiae, and T. nigricans. Thus, 25% of the examined planarian taxa are positive for Tetrahymena species and three of them represent new taxa, indicating a large undescribed ciliate diversity in freshwater planarians. According to phylogenetic analyses, histophagous tetrahymenas show a low phylogenetic host specificity. Although T. acanthophora, T. dugesiae, and T. scolopax clustered together within the "borealis" clade, the former species has been detected exclusively in G. tigrina, while the two latter species only in D. gonocephala. Tetrahymena nigricans, which has been isolated only from G. tigrina, was classified within the "paravorax" clade along with T. glochidiophila which feeds on glochidia. The present phylogenetic reconstruction of ancestral life strategies suggested that the last common ancestor of the family Tetrahymenidae was free-living, unlike the progenitor of the subclass Hymenostomatia which was very likely parasitic. Consequently, there were at least seven independent shifts back to parasitism/histophagy within Tetrahymena: one each in the "paravorax" and "australis" clades and at least five transfers back to parasitism in the "borealis" clade.},
}
@article {pmid32152386,
year = {2020},
author = {Kannangara, S and Karunarathne, S and Ranaweera, L and Ananda, K and Ranathunga, D and Jayarathne, H and Weebadde, C and Sooriyapathirana, S},
title = {Assessment of the applicability of wood anatomy and DNA barcoding to detect the timber adulterations in Sri Lanka.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {4352},
pmid = {32152386},
issn = {2045-2322},
mesh = {*DNA Barcoding, Taxonomic ; *DNA, Plant ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; Sri Lanka ; Wood/*anatomy &amp; histology/*classification/*genetics ; },
abstract = {The wood adulteration is a common problem and under-studied aspect in the timber industry of Sri Lanka. Hence we conducted a survey to assess the status of timber adulteration and check the applicability of morphometric parameters and DNA barcoding to detect the adulterated timber sources. We interviewed the stakeholders of the timber industry to collect information regarding timber adulterations. We measured the morphometric parameters; wood density and sizes of the xylem elements of the standard and adulterant species. For DNA barcoding, DNA was extracted from the wood of the selected standard and adulterant species and subjected to PCR using the markers, matK-trnT and atpB-rbcL. The PCR products were subjected to DNA sequencing. According to the survey, 92.5% of patrons, 73.7% of manufacturers and 96.7% of carpenters said timber adulteration is taking place in the country. The respondents said that the standard timber species; Tectona grandis, Artocarpus heterophyllus, and Swietenia macrophylla, profoundly undergo adulteration in Sri Lanka. The morphometric parameters did not discriminate the adulterant species from the standard species. The DNA barcodes matK-trnT and atpB-rbcL provided unique polymorphic DNA sequences with specific lengths for each species permitting the precise establishment of species identity and enabling the accurate detection of timber adulterations.},
}
@article {pmid32148769,
year = {2020},
author = {Kumar, A},
title = {Jump around: transposons in and out of the laboratory.},
journal = {F1000Research},
volume = {9},
number = {},
pages = {},
pmid = {32148769},
issn = {2046-1402},
mesh = {DNA Barcoding, Taxonomic ; *DNA Transposable Elements ; Genetic Therapy ; Humans ; *Mutagenesis, Insertional ; },
abstract = {Since Barbara McClintock's groundbreaking discovery of mobile DNA sequences some 70 years ago, transposable elements have come to be recognized as important mutagenic agents impacting genome composition, genome evolution, and human health. Transposable elements are a major constituent of prokaryotic and eukaryotic genomes, and the transposition mechanisms enabling transposon proliferation over evolutionary time remain engaging topics for study, suggesting complex interactions with the host, both antagonistic and mutualistic. The impact of transposition is profound, as over 100 human heritable diseases have been attributed to transposon insertions. Transposition can be highly mutagenic, perturbing genome integrity and gene expression in a wide range of organisms. This mutagenic potential has been exploited in the laboratory, where transposons have long been utilized for phenotypic screening and the generation of defined mutant libraries. More recently, barcoding applications and methods for RNA-directed transposition are being used towards new phenotypic screens and studies relevant for gene therapy. Thus, transposable elements are significant in affecting biology both in vivo and in the laboratory, and this review will survey advances in understanding the biological role of transposons and relevant laboratory applications of these powerful molecular tools.},
}
@article {pmid32148428,
year = {2020},
author = {Wang, WY and Yamada, A and Yamane, S},
title = {Maritime trap-jaw ants (Hymenoptera, Formicidae, Ponerinae) of the Indo-Australian region - redescription of Odontomachus malignus Smith and description of a related new species from Singapore, including first descriptions of males.},
journal = {ZooKeys},
volume = {915},
number = {},
pages = {137-174},
pmid = {32148428},
issn = {1313-2989},
abstract = {The maritime trap-jaw ant Odontomachus malignus Smith, 1859 is thought to be widespread throughout islands in the Indo-Pacific and parts of the Oriental realm. Because of its unique nesting preference for harsh littoral habitat and distinct morphology, O. malignus has usually been assumed to consist of only one species. We, however, describe a new species similar to O. malignus found in the mangroves of Singapore, Southeast Asia - Odontomachus litoralis sp. nov. We find strong evidence of both species existing in (near) sympatry, and also distinct morphological differences between O. malignus and the new species. Additional complementary DNA evidence in the form of COI barcodes (313 bp) supporting putative species identification and delimitation is provided. Defining morphological characteristics for the O. malignus species group (nested within the larger O. infandus clade) are given in detail for the first time. The worker and queen castes of the new species are described; a redescription of the worker caste of O. malignus, based on specimens from Singapore and the Philippines in addition to the holotype, is also given. The males of both species are also described for the first time, including male genitalia. A preliminary key to most known species of the O. infandus group based on the worker caste is provided.},
}
@article {pmid32148421,
year = {2020},
author = {LeMay, GA and Agnarsson, I},
title = {New species of smiley-faced spider Spintharus (Araneae, Theridiidae) from Brazil, and comments on unobserved diversity in South America.},
journal = {ZooKeys},
volume = {915},
number = {},
pages = {17-24},
pmid = {32148421},
issn = {1313-2989},
abstract = {Spintharus is a genus of spiders that contained only two species until 2018 when it was demonstrated that a 'widespread' species was instead composed of multiple short-range endemics. This note redescribes Spintharus gracilis Keyserling and describes a new species of Spintharus (Araneae, Theridiidae), S. leverger sp. nov., both based on specimens from Brazil. We also examine specimens from several additional localities in Brazil displaying variation consistent with patterns previously found within the Caribbean: geographically isolated and unique localities may contain independent species lineages. Given the limited number of specimens, profuse variation, and lack of DNA data from museum specimens, it is challenging to gauge the number of species in the observed material. Instead of describing these as new species here, we highlight this variation and hypothesize that in South America, a greater diversity of the genus across the geographical landscape will be found than predicted based on Levi's "widespread Spintharus flavidus" hypothesis. Our results suggest that continental efforts to sample the genus would be profitable, as this charismatic group likely harbors unappreciated diversity throughout the continent.},
}
@article {pmid32148145,
year = {2020},
author = {Hanchipura Mallesh, MS and Asokan, R and Gadad, H and Duleep Kumar, S and Kumar, R and Prakash, T},
title = {DNA barcoding and phylogenetic analysis of leafhoppers associated with Aster Yellow disease on China aster, Marigold and Chrysanthemum.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {31},
number = {2},
pages = {64-72},
doi = {10.1080/24701394.2020.1735378},
pmid = {32148145},
issn = {2470-1408},
mesh = {Animals ; Calendula/*genetics ; China ; Chrysanthemum/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics/metabolism ; Genome, Mitochondrial/genetics ; Hemiptera/*genetics ; Phylogeny ; Plant Diseases/*genetics ; },
abstract = {The Cicadellidae (Auchenorrhyncha: Hemiptera) are important agricultural, horticultural and ornamental pests. But it is very difficult to define nymphs and female adults using morphological characteristics. This research was aimed at understanding the variety of leafhoppers species and defining the prospective cause of the aster-yellow disease in China Aster, Marigold and Chrysanthemum. Two surveys were conducted in and around Pune, Maharashtra and Bengaluru, Karnataka between November 2016 and February 2017. The mitochondrial cytochrome oxidase subunit I (mtCOI) region marker was used in the species diagnosis and genetic diversity research. Through the use of mtCOI molecular marker eight different leafhoppers species were identified as Sogatella furcifera, Homalodisca insolita, Amrasca biguttula, Balclutha incise and Balclutha abdominalis and Japanagallia trifurcate. Whereas at genus level identified as Toya, Empoasca, Perkinsiella, Hishimonus, Tambocerus, Phaconeura, Curena, Psammotettix and Graphocophala species. These results are strongly corroborated with morphological identification. On the basis of multiple sequence alignment of the mtCOI gene, a species phylogenetic tree with the highest likelihood was drawn. All the leafhopper species clustered together in accordance with the species data collected from the database of the different geographic regions from the NCBI GenBank and Barcode of Life (BOLD). Such results suggest that it is important to use both molecular and morphological methods to ensure accurate identification of organisms. To conclude, this research contributes valuable knowledge to molecular biology and recognizes leafhopper species that serve as major phytoplasma vectors.},
}
@article {pmid32144638,
year = {2020},
author = {Vasquez, AA and Carmona-Galindo, V and Qazazi, MS and Walker, XN and Ram, JL},
title = {Water mite assemblages reveal diverse genera, novel DNA barcodes and transitional periods of intermediate disturbance.},
journal = {Experimental &amp; applied acarology},
volume = {80},
number = {4},
pages = {491-507},
pmid = {32144638},
issn = {1572-9702},
support = {1/CX/CSRD VA/United States ; R25GM058905//NIGMS R25GM058905/ ; 1/CX/CSRD VA/United States ; },
mesh = {Animals ; Biodiversity ; *DNA Barcoding, Taxonomic ; Ecosystem ; Michigan ; Mites/*classification ; *Rivers ; },
abstract = {Water mites are important constituents of aquatic ecosystems, but their biodiversity is poorly understood. The goal of this study was to improve knowledge of water mite assemblages in the Detroit River through combined use of morphological and cytochrome oxidase I (COI) DNA barcode data and to elucidate seasonal water mite diversity. The diversity of water mites collected from Blue Heron Lagoon at Belle Isle, an island in the Detroit River, is described. Novel DNA barcodes for Albia, Hydrochoreutes, Madawaska, and Axonopsis are reported with a species level barcode for Lebertia. Novel DNA barcodes may represent the presence of previously undescribed variants or new species of several genera. The prevalence of water mites is higher in the summer, but a different pattern is observed for diversity. The diversity of water mites, by several measures, varies seasonally with lower diversity in summer and winter months and higher diversity during seasonal transitions. For these organisms, we interpret seasonal change as an intermediate disturbance resulting in increased biodiversity.},
}
@article {pmid32138773,
year = {2020},
author = {Hollmann, J and Brecht, J and Goetzke, R and Franzen, J and Selich, A and Schmidt, M and Eipel, M and Ostrowska, A and Hapala, J and Fernandez-Rebollo, E and Müller-Newen, G and Rothe, M and Eggermann, T and Zenke, M and Wagner, W},
title = {Genetic barcoding reveals clonal dominance in iPSC-derived mesenchymal stromal cells.},
journal = {Stem cell research &amp; therapy},
volume = {11},
number = {1},
pages = {105},
pmid = {32138773},
issn = {1757-6512},
mesh = {Cell Differentiation ; Cells, Cultured ; DNA Copy Number Variations ; *Induced Pluripotent Stem Cells ; *Mesenchymal Stem Cells ; },
abstract = {BACKGROUND: The use of mesenchymal stromal cells (MSCs) for research and clinical application is hampered by cellular heterogeneity and replicative senescence. Generation of MSC-like cells from induced pluripotent stem cells (iPSCs) may circumvent these limitations, and such iPSC-derived MSCs (iMSCs) are already tested in clinical trials. So far, a comparison of MSCs and iMSCs was particularly addressed in bulk culture. Despite the high hopes in cellular therapy, only little is known how the composition of different subclones changes in these cell preparations during culture expansion.<br><br>METHODS: In this study, we used multicolor lentiviral genetic barcoding for the marking of individual cells within cell preparations. Based on this, we could track the clonal composition of syngenic MSCs, iPSCs, and iMSCs during culture expansion. Furthermore, we analyzed DNA methylation patterns at senescence-associated genomic regions by barcoded bisulfite amplicon sequencing. The proliferation and differentiation capacities of individual subclones within MSCs and iMSCs were investigated with limiting dilution assays.<br><br>RESULTS: Overall, the clonal composition of primary MSCs and iPSCs gradually declined during expansion. In contrast, iMSCs became oligoclonal early during differentiation, indicating that they were derived from few individual iPSCs. This dominant clonal outgrowth of iMSCs was not associated with changes in chromosomal copy number variation. Furthermore, clonal dynamics were not clearly reflected by stochastically acquired DNA methylation patterns. Limiting dilution assays revealed that iMSCs are heterogeneous in colony formation and in vitro differentiation potential, while this was even more pronounced in primary MSCs.<br><br>CONCLUSIONS: Our results indicate that the subclonal diversity of MSCs and iPSCs declines gradually during in vitro culture, whereas derivation of iMSCs may stem from few individual iPSCs. Differentiation regimen needs to be further optimized to achieve homogeneous differentiation of iPSCs towards iMSCs.},
}
@article {pmid32138187,
year = {2020},
author = {Jiang, S and Ma, X and Li, T and Zhu, C and You, X},
title = {Developing Single Nucleotide Polymorphisms for Identification of Cod Products by RAD-Seq.},
journal = {Animals : an open access journal from MDPI},
volume = {10},
number = {3},
pages = {},
pmid = {32138187},
issn = {2076-2615},
abstract = {The increase in the rate of seafood fraud, particularly in the expensive fishes, forces us to verify the identity of marine products. Meanwhile, the definition of cod lacks consistency at the international level, as few standards and effective application methods are capable of accurately detecting cod species. Genetic fingerprinting is important for both certifying authenticity and traceability of fish species. In this study, we developed a method that combines DNA barcoding and the restriction-site associated DNA sequencing (RAD-Seq) approach for the identification of cod products. We first obtained 6941 high-quality single nucleotide polymorphism (SNP)s from 65.6 gigabases (Gb) of RAD-Seq raw data, and two sequences that contain SNPs were finally used to successfully identify three different cod product species, which are Atlantic cod (Gadus morhua), Greenland turbot (Reinhardtius hippoglossoides), and Patagonian toothfish (Dissostichus eleginoides). This SNP-based method will help us to identify the products, which are sold under the name of "Xue Yu" (Cod) in China, and works in parallel with existing fish identification techniques to establish an efficient framework to detect and prevent fraud at all points of the seafood supply chain.},
}
@article {pmid32132854,
year = {2020},
author = {Zhang, J and Yu, H and Zhong, Y},
title = {Redescription of Pristidia cervicornuta (Araneae, Clubionidae), with a first description of the female.},
journal = {ZooKeys},
volume = {914},
number = {},
pages = {33-42},
pmid = {32132854},
issn = {1313-2989},
abstract = {Pristidia cervicornuta Yu, Zhang &amp; Chen, 2017 is redescribed based on new material from the type locality, Diaoluo Mountains of Hainan Island, China. The female is described and illustrated for the first time. In addition, this paper further illustrates the male, and provides a supplementary description.},
}
@article {pmid32132718,
year = {2020},
author = {Bramlett, C and Jiang, D and Nogalska, A and Eerdeng, J and Contreras, J and Lu, R},
title = {Clonal tracking using embedded viral barcoding and high-throughput sequencing.},
journal = {Nature protocols},
volume = {15},
number = {4},
pages = {1436-1458},
pmid = {32132718},
issn = {1750-2799},
support = {R00 HL113104/HL/NHLBI NIH HHS/United States ; R35 HL150826/HL/NHLBI NIH HHS/United States ; R01HL135292S//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/International ; R01HL135292//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/International ; R01 HL135292/HL/NHLBI NIH HHS/United States ; P30 CA014089/CA/NCI NIH HHS/United States ; R00HL113104//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/International ; R01 HL138225/HL/NHLBI NIH HHS/United States ; R01HL138225//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/International ; },
mesh = {Animals ; Cell Proliferation/genetics ; Cell Tracking/*methods ; Clone Cells/*cytology ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; Genetic Vectors/genetics ; HEK293 Cells ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Lentivirus/genetics ; Mice ; },
abstract = {Embedded viral barcoding in combination with high-throughput sequencing is a powerful technology with which to track single-cell clones. It can provide clonal-level insights into cellular proliferation, development, differentiation, migration, and treatment efficacy. Here, we present a detailed protocol for a viral barcoding procedure that includes the creation of barcode libraries, the viral delivery of barcodes, the recovery of barcodes, and the computational analysis of barcode sequencing data. The entire procedure can be completed within a few weeks. This barcoding method requires cells to be susceptible to viral transduction. It provides high sensitivity and throughput, and enables precise quantification of cellular progeny. It is cost efficient and does not require any advanced skills. It can also be easily adapted to many types of applications, including both in vitro and in vivo experiments.},
}
@article {pmid32131829,
year = {2020},
author = {Crowgey, EL and Mahajan, N and Wong, WH and Gopalakrishnapillai, A and Barwe, SP and Kolb, EA and Druley, TE},
title = {Error-corrected sequencing strategies enable comprehensive detection of leukemic mutations relevant for diagnosis and minimal residual disease monitoring.},
journal = {BMC medical genomics},
volume = {13},
number = {1},
pages = {32},
pmid = {32131829},
issn = {1755-8794},
support = {R01 CA211711/CA/NCI NIH HHS/United States ; },
mesh = {Adolescent ; Cell Line, Tumor ; Child ; Female ; *High-Throughput Nucleotide Sequencing ; Humans ; Leukemia/*diagnosis/*genetics/therapy ; Male ; *Mutation ; Neoplasm, Residual ; },
abstract = {BACKGROUND: Pediatric leukemias have a diverse genomic landscape associated with complex structural variants, including gene fusions, insertions and deletions, and single nucleotide variants. Routine karyotype and fluorescence in situ hybridization (FISH) techniques lack sensitivity for smaller genomic alternations. Next-generation sequencing (NGS) assays are being increasingly utilized for assessment of these various lesions. However, standard NGS lacks quantitative sensitivity for minimal residual disease (MRD) surveillance due to an inherently high error rate.<br><br>METHODS: Primary bone marrow samples from pediatric leukemia (n&#xa0;=&#x2009;32) and adult leukemia subjects (n&#xa0;=&#x2009;5), cell line MV4-11, and an umbilical cord sample were utilized for this study. Samples were sequenced using molecular barcoding with targeted DNA and RNA library enrichment techniques based on anchored multiplexed PCR (AMP&#xae;) technology, amplicon based error-corrected sequencing (ECS) or a human cancer transcriptome assay. Computational analyses were performed to quantitatively assess limit of detection (LOD) for various DNA and RNA lesions, which could be systematically used for MRD assays.<br><br>RESULTS: Matched leukemia patient samples were analyzed at three time points; diagnosis, end of induction (EOI), and relapse. Similar to flow cytometry for ALL MRD, the LOD for point mutations by these sequencing strategies was &#x2265;0.001. For DNA structural variants, FLT3 internal tandem duplication (ITD) positive cell line and patient samples showed a LOD of &#x2265;0.001 in addition to previously unknown copy number losses in leukemia genes. ECS in RNA identified multiple novel gene fusions, including a SPANT-ABL gene fusion in an ALL patient, which could have been used to alter therapy. Collectively, ECS for RNA demonstrated a quantitative and complex landscape of RNA molecules with 12% of the molecules representing gene fusions, 12% exon duplications, 8% exon deletions, and 68% with retained introns. Droplet digital PCR validation of ECS-RNA confirmed results to single mRNA molecule quantities.<br><br>CONCLUSIONS: Collectively, these assays enable a highly sensitive, comprehensive, and simultaneous analysis of various clonal leukemic mutations, which can be tracked across disease states (diagnosis, EOI, and relapse) with a high degree of sensitivity. The approaches and results presented here highlight the ability to use NGS for MRD tracking.},
}
@article {pmid32131723,
year = {2020},
author = {Stoler, N and Arbeithuber, B and Povysil, G and Heinzl, M and Salazar, R and Makova, KD and Tiemann-Boege, I and Nekrutenko, A},
title = {Family reunion via error correction: an efficient analysis of duplex sequencing data.},
journal = {BMC bioinformatics},
volume = {21},
number = {1},
pages = {96},
pmid = {32131723},
issn = {1471-2105},
support = {J 4096/FWF_/Austrian Science Fund FWF/Austria ; P 30867/FWF_/Austrian Science Fund FWF/Austria ; R01 GM116044/GM/NIGMS NIH HHS/United States ; T32 GM102057/GM/NIGMS NIH HHS/United States ; },
mesh = {Algorithms ; DNA/chemistry/metabolism ; Humans ; Sequence Alignment ; Sequence Analysis, DNA ; *User-Computer Interface ; },
abstract = {BACKGROUND: Duplex sequencing is the most accurate approach for identification of sequence variants present at very low frequencies. Its power comes from pooling together multiple descendants of both strands of original DNA molecules, which allows distinguishing true nucleotide substitutions from PCR amplification and sequencing artifacts. This strategy comes at a cost-sequencing the same molecule multiple times increases dynamic range but significantly diminishes coverage, making whole genome duplex sequencing prohibitively expensive. Furthermore, every duplex experiment produces a substantial proportion of singleton reads that cannot be used in the analysis and are thrown away.<br><br>RESULTS: In this paper we demonstrate that a significant fraction of these reads contains PCR or sequencing errors within duplex tags. Correction of such errors allows "reuniting" these reads with their respective families increasing the output of the method and making it more cost effective.<br><br>CONCLUSIONS: We combine an error correction strategy with a number of algorithmic improvements in a new version of the duplex analysis software, Du Novo 2.0. It is written in Python, C, AWK, and Bash. It is open source and readily available through Galaxy, Bioconda, and Github: https://github.com/galaxyproject/dunovo.},
}
@article {pmid32131042,
year = {2020},
author = {Ollinger, N and Lasinger, V and Probst, C and Pitsch, J and Sulyok, M and Krska, R and Weghuber, J},
title = {DNA barcoding for the identification of mold species in bakery plants and products.},
journal = {Food chemistry},
volume = {318},
number = {},
pages = {126501},
doi = {10.1016/j.foodchem.2020.126501},
pmid = {32131042},
issn = {1873-7072},
mesh = {Bread/microbiology ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/genetics ; Food Contamination/analysis ; Food Handling ; Fungi/genetics/*isolation &amp; purification/metabolism ; Mycotoxins/metabolism ; Polymerase Chain Reaction/*methods ; },
abstract = {Mold identification at the species level in environmental samples is a major challenge. Molecular techniques have been widely used for fungal classification, but as most primers are genus-specific, it is laborious to identify unknown samples. In this study, a PCR-based method for the identification of mold at the species level was developed. Therefore, common sequencing primers and combinations of them, targeting specific DNA regions, were tested. Here we present a combination of eight primer pairs to identify mold within a single PCR run. The approach correctly identified mold of unknown species from samples taken at a local bakery, including Penicillium chrysogenum, Penicillium citrinum, Cladosporium sphaerospermum, Paecilomyces formosus, Rhizopus oryzae and Aspergillus niger. Results obtained from the PCR method were successfully validated by chromatographic mycotoxin and microscopy analysis. Findings highlight DNA barcoding as an appropriate tool for mold identification; however, its efficacy is essentially dependent on DNA quality and primer selection.},
}
@article {pmid32126856,
year = {2020},
author = {Zou, R and Liang, C and Dai, M and Wang, X and Zhang, X and Song, Z},
title = {DNA barcoding and phylogenetic analysis of bagrid catfish in China based on mitochondrial COI gene.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {31},
number = {2},
pages = {73-80},
doi = {10.1080/24701394.2020.1735379},
pmid = {32126856},
issn = {2470-1408},
mesh = {Animals ; Catfishes/*classification/*genetics ; China ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics/metabolism ; Genes, Mitochondrial/*genetics ; Genome, Mitochondrial/*genetics ; Phylogeny ; },
abstract = {The family Bagridae is a collection of species widely distributed in Africa and Asia with a high diversity of morphology. The species identification and phylogenetic relationship in this family have been confused and controversial. In order to explore the effectiveness of DNA barcoding in species identification of Bagridae, sequences of mitochondrial cytochrome c oxidase I (COI) gene of 20 species in four genera of Bagridae were used to analyse barcoding gap and to reconstruct phylogenetic relationship. Both the barcoding gap and the phylogenetic tree analysis showed that the COI gene-based DNA barcoding is an effective molecular technique for most species recognition of Chinese Bagridae. However, the rapid speciation and incomplete lineage sorting may affect the accuracy of DNA barcoding in species identification in certain species, and adding additional genes, such as nuclear gene, may help to achieve accurate identification of these species. The phylogenetic tree showed that the monophyly of genera Pelteobagrus, Leiocassis and Pseudobagrus did not exist, which supports that the species of genera Pelteobagrus, Pseudobagrus and Leiocassis distributed in China should be revised into one genus.},
}
@article {pmid32126246,
year = {2020},
author = {Amritha, N and Bhooma, V and Parani, M},
title = {Authentication of the market samples of Ashwagandha by DNA barcoding reveals that powders are significantly more adulterated than roots.},
journal = {Journal of ethnopharmacology},
volume = {256},
number = {},
pages = {112725},
doi = {10.1016/j.jep.2020.112725},
pmid = {32126246},
issn = {1872-7573},
mesh = {DNA Barcoding, Taxonomic/methods ; DNA, Plant/*genetics ; Medicine, Ayurvedic/methods ; Plant Extracts/*genetics ; Plant Roots/*genetics ; Plants, Medicinal/genetics ; Powders/*metabolism ; Senna Plant/genetics ; Withania/genetics ; },
abstract = {Ashwagandha, also known as Indian Ginseng, is a highly traded medicinal plant, which is used in Ayurveda, Siddha and Unani systems of medicine to improve cognitive function, decrease inflammation, and to counter the ill-effects of aging. Withanolide A and Withaferin A from Ashwagandha were shown to improve immunity and have anti-cancer property, respectively.<br><br>AIM OF THE STUDY: Here, we aimed to create reference DNA barcodes for W.&#xa0;somnifera and to authenticate root and powder samples of Ashwagandha collected from markets.<br><br>MATERIALS AND METHODS: Three plant specimen of W.&#xa0;somnifera were collected, and reference DNA barcodes were generated using rbcL, matK, trnH-psbA, and ITS2 DNA barcode markers. Market samples in the form of root (n&#x202f;=&#x202f;33) and powder (n&#x202f;=&#x202f;70) were collected and authenticated using ITS2 and trnH-psbA DNA barcodes.<br><br>RESULTS: Genomic DNA was successfully isolated from all plant specimens and market samples. DNA barcoding showed that 77% of samples were authentic. About 22% of non-authentic samples were powder samples and only 1% were root samples. Among the non-authentic samples, 18% were completely substituted with single species (Mucuna pruriens (L.) DC., Trigonella foenum-graceum L., or Senna auriculata (L.) Roxb.) and 82% were mixed samples containing more than one species. About 63% of the mixed samples contained Ashwagandha as the major ingredient. Furthermore, we identified that six taxonomically divergent plant species from four families were present as adulterants in the mixed samples.<br><br>CONCLUSION: DNA barcoding revealed that botanical adulteration in the market samples of Ashwagandha is significant. Powder samples are more prone to adulteration than root samples. The adulterated samples contained plant material that is not related to Ashwagandha, which warrants strict quantity control and market surveillance to derive the true medicinal benefits of this medicinal plant.},
}
@article {pmid32124439,
year = {2020},
author = {Kaunisto, KM and Roslin, T and Forbes, MR and Morrill, A and Sääksjärvi, IE and Puisto, AIE and Lilley, TM and Vesterinen, EJ},
title = {Threats from the air: Damselfly predation on diverse prey taxa.},
journal = {The Journal of animal ecology},
volume = {89},
number = {6},
pages = {1365-1374},
doi = {10.1111/1365-2656.13184},
pmid = {32124439},
issn = {1365-2656},
mesh = {Animals ; *Chironomidae ; Food Chain ; Insecta ; Invertebrates ; *Odonata ; Predatory Behavior ; },
abstract = {To understand the diversity and strength of predation in natural communities, researchers must quantify the total amount of prey species in the diet of predators. Metabarcoding approaches have allowed widespread characterization of predator diets with high taxonomic resolution. To determine the wider impacts of predators, researchers should combine DNA techniques with estimates of population size of predators using mark-release-recapture (MRR) methods, and with accurate metrics of food consumption by individuals. Herein, we estimate the scale of predation exerted by four damselfly species on diverse prey taxa within a well-defined 12-ha study area, resolving the prey species of individual damselflies, to what extent the diets of predatory species overlap, and which fraction of the main prey populations are consumed. We identify the taxonomic composition of diets using DNA metabarcoding and quantify damselfly population sizes by MRR. We also use predator-specific estimates of consumption rates, and independent data on prey emergence rates to estimate the collective predation pressure summed over all prey taxa and specific to their main prey (non-biting midges or chironomids) of the four damselfly species. The four damselfly species collectively consumed a prey mass equivalent to roughly 870 (95% CL 410-1,800) g, over 2 months. Each individual consumed 29%-66% (95% CL 9.4-123) of its body weight during its relatively short life span (2.1-4.7 days; 95% CL 0.74-7.9) in the focal population. This predation pressure was widely distributed across the local invertebrate prey community, including 4 classes, 19 orders and c. 140 genera. Different predator species showed extensive overlap in diets, with an average of 30% of prey shared by at least two predator species. Of the available prey individuals in the widely consumed family Chironomidae, only a relatively small proportion (0.76%; 95% CL 0.35%-1.61%) were consumed. Our synthesis of population sizes, per-capita consumption rates and taxonomic distribution of diets identifies damselflies as a comparatively minor predator group of aerial insects. As the next step, we should add estimates of predation by larger odonate species, and experimental removal of odonates, thereby establishing the full impact of odonate predation on prey communities.},
}
@article {pmid32123501,
year = {2020},
author = {Espinoza-Donoso, S and Bobadilla, D and Huanca-Mamani, W and Vargas-Ortiz, M and Vargas, HA},
title = {A new species of Ithome Chambers (Lepidoptera, Cosmopterigidae, Chrysopeleiinae) from the Atacama Desert revealed by morphology and DNA barcodes.},
journal = {ZooKeys},
volume = {912},
number = {},
pages = {125-138},
pmid = {32123501},
issn = {1313-2989},
abstract = {Morphology and DNA barcode sequences were used to assess the taxonomic status of a micro-moth of the genus Ithome Chambers, 1875 (Lepidoptera, Cosmopterigidae, Chrysopeleiinae), whose larvae feed on inflorescences of Prosopis tamarugo Phil. (Fabaceae), a tree native to the Pampa del Tamarugal, Atacama Desert, northern Chile. As a result, Ithome tamarugensis Vargas, sp. nov. is described and illustrated. Its genitalia are remarkably similar to those of Ithome tiaynai Vargas, 2004 from coastal valleys of the Atacama Desert. However, the two species can be recognized by the shape of the phallus in males and the shape of the antrum and ductus bursae in females. The genetic distance between DNA barcodes of I. tamarugensis and I. tiaynai was 3.0-3.3% (K2P), and a maximum likelihood analysis indicated that they are in reciprocally monophyletic clusters, providing additional support for the heterospecific status suggested by morphology.},
}
@article {pmid32123499,
year = {2020},
author = {Kodada, J and Jäch, MA and Freitag, H and Čiamporová-Zaťovičová, Z and Goffová, K and Selnekovič, D and Jr, F&#x10c;},
title = {Ancyronyx clisteri, a new spider riffle beetle species from Borneo, redescription of A. sarawacensis Jäch including a description of the larva and new distribution data for A. procerus Jäch using DNA barcodes (Coleoptera, Elmidae).},
journal = {ZooKeys},
volume = {912},
number = {},
pages = {25-64},
pmid = {32123499},
issn = {1313-2989},
abstract = {Ancyronyx clisteri sp. nov. (Coleoptera, Elmidae) a new spider riffle beetle discovered from northern Borneo (Brunei; Sabah and Sarawak, Malaysia) and the larva of Ancyronyx sarawacensis Jäch are described. Illustrations of the habitus and diagnostic characters of the new species and the similar and highly variable A. sarawacensis are presented. Differences to closely related species, based on DNA barcodes and morphological characters, are discussed. Association of the larva and the imago of A. sarawacensis, and the occurrence of Ancyronyx procerus Jäch in Peninsular Malaysia and Sabah are confirmed by using COI mtDNA sequences.},
}
@article {pmid32121620,
year = {2020},
author = {Čkrkić, J and Petrović, A and Kocić, K and Mitrović, M and Kavallieratos, NG and van Achterberg, C and Hebert, PDN and Tomanović, &#x17d;},
title = {Phylogeny of the Subtribe Monoctonina (Hymenoptera, Braconidae, Aphidiinae).},
journal = {Insects},
volume = {11},
number = {3},
pages = {},
pmid = {32121620},
issn = {2075-4450},
support = {III43001//Ministarstvo Prosvete, Nauke i Tehnolo&#x161;kog Razvoja/ ; N/A//Canada First Research Excellence Fund to the Food From Thought research program/ ; },
abstract = {Members of the Monoctonina subtribe have long been neglected in applied studies of the subfamily Aphidiinae, due to their low economic importance, as they do not parasitize pests of cultivated plants. Consequently, data about this group are scarce, including its taxonomy and phylogeny. In the present study, we explore inter- and intraspecific genetic variation of Monoctonina species, including genera Monoctonus Haliday 1833, Monoctonia Starý 1962, Falciconus Mackauer 1959 and Harkeria Cameron 1900. We employ two molecular markers, the barcode region of the mitochondrial cytochrome c oxidase subunit I (COI) and the D2 region of the 28S nuclear gene (28S rDNA), to analyze genetic structuring and phylogeny of all available Monoctonina species, and combine them with morphological data for an integrative approach. We report one new species, and three potentially new species which can be formally described when further specimens are available. Analysis of phylogenetic relationships within the subtribe shows a basal position for the genera Falciconus and Monoctonia, and the close relatedness of Harkeria and Monoctonus.},
}
@article {pmid32121321,
year = {2020},
author = {Duran, DP and Laroche, RA and Gough, HM and Gwiazdowski, RA and Knisley, CB and Herrmann, DP and Roman, SJ and Egan, SP},
title = {Geographic Life History Differences Predict Genomic Divergence Better than Mitochondrial Barcodes or Phenotype.},
journal = {Genes},
volume = {11},
number = {3},
pages = {},
pmid = {32121321},
issn = {2073-4425},
mesh = {Animals ; Classification/*methods ; Coleoptera/classification/*genetics ; DNA, Mitochondrial/classification/*genetics ; Genetic Variation ; Genome, Insect/genetics ; Haplotypes/genetics ; Life History Traits ; Mitochondria/genetics ; Phenotype ; *Phylogeography ; Polymorphism, Single Nucleotide/genetics ; Species Specificity ; },
abstract = {Species diversity can be inferred using multiple data types, however, results based on genetic data can be at odds with patterns of phenotypic variation. Tiger beetles of the Cicindelidiapolitula (LeConte, 1875) species complex have been taxonomically problematic due to extreme phenotypic variation within and between populations. To better understand the biology and taxonomy of this group, we used mtDNA genealogies and multilocus nuclear analyses of 34,921 SNPs to elucidate its evolutionary history and evaluate the validity of phenotypically circumscribed species and subspecies. Genetic analyses recovered two divergent species that are also ecologically distinct, based on adult life history. These patterns are incongruous with the phenotypic variation that informed prior taxonomy, and most subspecies were not supported as distinct evolutionary lineages. One of the nominal subspecies was found to be a cryptic species; consequently, we elevate C. p.laetipennis (Horn, 1913) to a full species. Although nuclear and mtDNA datasets recovered broadly similar evolutionary units, mito-nuclear discordance was more common than expected, being observed between nearly all geographically overlapping taxonomic pairs. Additionally, a pattern of 'mitochondrial displacement' was observed, where mitochondria from one species unidirectionally displace others. Overall, we found that geographically associated life history factors better predict genomic divergence than phenotype and mitochondrial genealogies, and consequently taxon identifications based on mtDNA (e.g., DNA barcodes) may be misleading.},
}
@article {pmid32117126,
year = {2020},
author = {Vuorio, K and Mäki, A and Salmi, P and Aalto, SL and Tiirola, M},
title = {Consistency of Targeted Metatranscriptomics and Morphological Characterization of Phytoplankton Communities.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {96},
pmid = {32117126},
issn = {1664-302X},
abstract = {The composition of phytoplankton community is the basis for environmental monitoring and assessment of the ecological status of aquatic ecosystems. Community composition studies of phytoplankton have been based on time-consuming and expertise-demanding light microscopy analyses. Molecular methods have the potential to replace microscopy, but the high copy number variation of ribosomal genes and the lack of universal primers for simultaneous amplification of prokaryotic and eukaryotic genes complicate data interpretation. In this study, we used our previously developed directional primer-independent high-throughput sequencing (HTS) approach to analyze 16S and 18S rRNA community structures. Comparison of 83 boreal lake samples showed that the relative abundances of eukaryotic phytoplankton at class level and prokaryotic cyanobacteria at order level were consistent between HTS and microscopy results. At the genus level, the results had low correspondence, mainly due to lack of sequences in the reference library. HTS was superior to identify genera that are extensively represented in the reference databases but lack specific morphological characteristics. Targeted metatranscriptomics proved to be a feasible method to complement the microscopy analysis. The metatranscriptomics can also be applied without linking the sequences to taxonomy. However, direct indexing of the sequences to their environmental indicator values needs collections of more comprehensive sample sets, as long as the coverage of molecular barcodes of eukaryotic species remains insufficient.},
}
@article {pmid32116712,
year = {2020},
author = {Dalle Fratte, C and Guardascione, M and De Mattia, E and Borsatti, E and Boschetto, R and Farruggio, A and Canzonieri, V and Romanato, L and Borsatti, R and Gagno, S and Marangon, E and Polano, M and Buonadonna, A and Toffoli, G and Cecchin, E},
title = {Clonal Selection of a Novel Deleterious TP53 Somatic Mutation Discovered in ctDNA of a KIT/PDGFRA Wild-Type Gastrointestinal Stromal Tumor Resistant to Imatinib.},
journal = {Frontiers in pharmacology},
volume = {11},
number = {},
pages = {36},
pmid = {32116712},
issn = {1663-9812},
abstract = {The standard of care for the first-line treatment of advanced gastrointestinal stromal tumor (GIST) is represented by imatinib, which is given daily at a standard dosage until tumor progression. Resistance to imatinib commonly occurs through the clonal selection of genetic mutations in the tumor DNA, and an increase in imatinib dosage was demonstrated to be efficacious to overcome imatinib resistance. Wild-type GISTs, which do not display KIT or platelet-derived growth factor receptor alpha (PDGFRA) mutations, are usually primarily insensitive to imatinib and tend to rapidly relapse in course of treatment. Here we report the case of a 53-year-old male patient with gastric GIST who primarily did not respond to imatinib and that, despite the administration of an increased imatinib dose, led to patient death. By using a deep next-generation sequencing barcode-aware approach, we analyzed a panel of actionable cancer-related genes in the patient cfDNA to investigate somatic changes responsible for imatinib resistance. We identified, in two serial circulating tumor DNA (ctDNA) samples, a sharp increase in the allele frequency of a never described TP53 mutation (c.560-7_560-2delCTCTTAinsT) located in a splice acceptor site and responsible for a protein loss of function. The same TP53 mutation was retrospectively identified in the primary tumor by digital droplet PCR at a subclonal frequency (0.1%). The mutation was detected at a very high allelic frequency (99%) in the metastatic hepatic lesion, suggesting a rapid clonal selection of the mutation during tumor progression. Imatinib plasma concentration at steady state was above the threshold of 760 ng/ml reported in the literature for the minimum efficacious concentration. The de novo TP53 (c.560-7_560-2delCTCTTAinsT) mutation was in silico predicted to be associated with an aberrant RNA splicing and with an aggressive phenotype which might have contributed to a rapid disease spread despite the administration of an increased imatinib dosage. This result underlies the need of a better investigation upon the role of TP53 in the pathogenesis of GISTs and sustains the use of next-generation sequencing (NGS) in cfDNA for the identification of novel genetic markers in wild-type GISTs.},
}
@article {pmid32114251,
year = {2020},
author = {Kudryavtsev, A and Volkova, E},
title = {Cunea russae n. sp. (Amoebozoa, Dactylopodida), another cryptic species of Cunea Kudryavtsev and Pawlowski, 2015, inhabits a continental brackish-water biotope.},
journal = {European journal of protistology},
volume = {73},
number = {},
pages = {125685},
doi = {10.1016/j.ejop.2020.125685},
pmid = {32114251},
issn = {1618-0429},
mesh = {Amoebozoa/*classification/cytology/genetics ; Biodiversity ; Cold Temperature ; Genes, Protozoan/genetics ; Saline Waters ; Species Specificity ; },
abstract = {The genus Cunea Kudryavtsev and Pawlowski, 2015 (Amoebozoa, Dactylopodida) was initially described from the oceanic benthos: C. profundata, from over 5 km depth in the Atlantic Ocean, and C. thuwala from the Red Sea benthos at ca. 60 m depth. Both species are identical to each other in morphology (including cell coat ultrastructure), but differ significantly in the gene sequence data, including barcoding loci of small subunit ribosomal RNA and cytochrome oxidase subunit 1 gene, as well as actin. This paper describes the third species of Cunea, C. russae n. sp. isolated from a brackish water habitat without a direct connection to the ocean, a small spring of brackish water (19‰) emerging from a 246 m deep hole in the earth. This species is morphologically identical to the previous two amoebae, but differs from them significantly in the gene sequence data and ecological preferences. In particular, this species has the broadest salinity tolerance range, being able to reproduce well already at 2.5‰. It is also capable of resisting cold temperatures, like C. profundata. The data obtained suggest that the genus Cunea may comprise a significant taxonomic diversity represented by morphologically identical, but quickly diverging species with significant ecological plasticity.},
}
@article {pmid32110484,
year = {2020},
author = {Mbareche, H and Veillette, M and Bilodeau, G and Duchaine, C},
title = {Comparison of the performance of ITS1 and ITS2 as barcodes in amplicon-based sequencing of bioaerosols.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e8523},
pmid = {32110484},
issn = {2167-8359},
abstract = {This paper presents the performance of two eukaryotic genomic ribosomal regions, ITS1 and ITS2, in describing fungal diversity in aerosol samples using amplicon-based High-Throughput Sequencing (HTS). Composting sites, biomethanization facilities, and dairy farms, all affected by the presence of fungi, were visited to collect air samples. The amplicon-based HTS approach is a target enrichment method that relies on the amplification of a specific target using particular primers before sequencing. Thus, the results are highly dependent on the quality of amplification. For this reason, the authors of this paper used a shotgun metagenomic approach to compare its outcome with the amplicon-based method. Indeed, shotgun metagenomic does not rely on any amplification prior to sequencing, because all genes are sequenced without a specific target. In addition, culture methods were added to the analyses in biomethanization and dairy farms samples to validate their contribution to fungal diversity of aerosols. The results obtained are unequivocal towards ITS1 outperformance to ITS2 in terms of richness, and taxonomic coverage. The differential abundance analysis did demonstrate that some taxa were exclusively detected only by ITS2, and vice-versa for ITS1. However, the shotgun metagenomic approach showed a taxonomic profile more resembling to ITS1 than ITS2. Based on these results, neither of the barcodes evaluated is perfect in terms of distinguishing all species. Using both barcodes offers a broader view of the fungal aerosol population. However, with the actual knowledge, the authors strongly recommend using ITS1 as a universal fungal barcode for quick general analyses of diversity and when limited financial resources are available, primarily due its ability to capture taxonomic profiles similar to those obtained using the shotgun metagenomic. The culture comparison with amplicon-based sequencing showed the complementarity of both approaches in describing the most abundant taxa.},
}
@article {pmid32110483,
year = {2020},
author = {Motamedinia, B and Skevington, JH and Kelso, S},
title = {Taxonomic revision of Dasydorylas Skevington, 2001 (Diptera, Pipunculidae) in the Middle East.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e8511},
pmid = {32110483},
issn = {2167-8359},
abstract = {Species of the distinctive and cosmopolitan genus Dasydorylas Skevington, 2001 in the Middle East are revised. Seven species are documented, and three new species, Dasydorylas dactylos sp. nov., D. forcipus sp. nov. and D. parazardouei sp. nov., are described, and one synonym, D. derafshani Motamedinia &amp; Kehlmaier, 2017, syn. nov. is proposed, based on sequence information from the mitochondrial COI barcoding gene and morphological parameters. Diagnoses, illustrations and distributional data are provided for all studied species. Descriptions of new species as well as an identification key to all known species in the Middle East are also provided.},
}
@article {pmid32105989,
year = {2020},
author = {Masunaga, N and Kagara, N and Motooka, D and Nakamura, S and Miyake, T and Tanei, T and Naoi, Y and Shimoda, M and Shimazu, K and Kim, SJ and Noguchi, S},
title = {Molecular Barcode Sequencing of the Whole Ligand Binding Domain of the ESR1 Gene in Cell-Free DNA from Patients with Metastatic Breast Cancer.},
journal = {Translational oncology},
volume = {13},
number = {3},
pages = {100735},
pmid = {32105989},
issn = {1936-5233},
abstract = {ESR1 mutations in breast cancer are known as one of the mechanisms of resistance to aromatase inhibitors. These mutations often occur in the hotspot regions in the ligand binding domain (LBD), but comprehensive mutational analysis has shown that mutations are observed throughout the whole LBD. We previously developed a molecular barcode sequencing (MB-NGS) technique to detect ESR1 hotspot mutations in plasma with high sensitivity. In this study, we have developed a multiplex MB-NGS assay that covers the whole LBD of ESR1. The assay demonstrated that the background errors in the plasma DNA of 10 healthy controls were below 0.1%; thus, the limit of detection was set at 0.1%. We analyzed the plasma DNA of 54 patients with estrogen receptor-positive metastatic breast cancer. Seventeen mutations were detected in 13 patients (24%), with variant allele frequencies ranging from 0.13% to 10.67%, including six rare mutations with a variant allele frequency <1.0% and a novel nonhotspot mutation (A312V). Three patients had double mutations located in the same amplicons, and it was revealed that the double mutations were located in different alleles. ESR1 hotspot mutations were associated with a longer duration of aromatase inhibitor treatment under metastatic conditions and to liver metastasis. The multiplex MB-NGS assay is useful for the sensitive and comprehensive detection of mutations throughout the whole LBD of ESR1. Our assay can be applied to any specific target region of interest using tailor-made primers and can result in minimized sequencing volume and cost.},
}
@article {pmid32104992,
year = {2020},
author = {Akankunda, T and To, H and Rodriguez Lopez, C and Leijs, R and Hogendoorn, K},
title = {A method to generate multilocus barcodes of pinned insect specimens using MiSeq.},
journal = {Molecular ecology resources},
volume = {20},
number = {3},
pages = {},
doi = {10.1111/1755-0998.13143},
pmid = {32104992},
issn = {1755-0998},
support = {15-02-35//Department of Agriculture and Water Resources, Australian Government/ ; //Holsworth Wildlife Research Endowment/ ; },
mesh = {Animals ; Bees/*genetics ; Computational Biology/methods ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods ; },
abstract = {For molecular insect identification, amplicon sequencing methods are recommended because they offer a cost-effective approach for targeting small sets of informative genes from multiple samples. In this context, high-throughput multilocus amplicon sequencing has been achieved using the MiSeq Illumina sequencing platform. However, this approach generates short gene fragments of <500 bp, which then have to be overlapped using bioinformatics to achieve longer sequence lengths. This increases the risk of generating chimeric sequences or leads to the formation of incomplete loci. Here, we propose a modified nested amplicon sequencing method for targeting multiple loci from pinned insect specimens using the MiSeq Illumina platform. The modification exists in using a three-step nested PCR approach targeting near full-length loci in the initial PCR and subsequently amplifying short fragments of between 300 and 350 bp for high-throughput sequencing using Illumina chemistry. Using this method, we generated 407 sequences of three loci from 86% of all the specimens sequenced. Out of 103 pinned bee specimens of replicated species, 71% passed the 95% sequence similarity threshold between species replicates. This method worked best for pinned specimens aged between 0 and 5 years, with a limit of 10 years for pinned and 14 years for ethanol-preserved specimens. Hence, our method overcomes some of the challenges of amplicon sequencing using short read next generation sequencing and improves the possibility of creating high-quality multilocus barcodes from insect collections.},
}
@article {pmid32104138,
year = {2020},
author = {Yu, L and Liu, F and Zhang, Z and Wang, Y and Li, D and Xu, X},
title = {Four new species of the primitively segmented spider genus Qiongthela from Hainan Island, China (Mesothelae, Liphistiidae).},
journal = {ZooKeys},
volume = {911},
number = {},
pages = {51-66},
pmid = {32104138},
issn = {1313-2989},
abstract = {The primitively segmented spider genus Qiongthela Xu &amp; Kuntner, 2015 consists of seven species that are distributed in Hainan Island, China and southern Vietnam. Of the seven species, five are known from Hainan Island. In this study, four more Qiongthela species collected from Hainan Island are diagnosed and described as new to science based on morphological characters: Q. baoting sp. nov. (♂♀), Q. qiongzhong sp. nov. (♂♀), Q. sanya sp. nov. (♂♀), Q. yinggezui sp. nov. (♂♀). To facilitate future identification, the GenBank accession codes of the DNA barcode gene, cytochrome c oxidase subunit I (COI), for all the type specimens are also provided.},
}
@article {pmid32104137,
year = {2020},
author = {Angyal, D and Chávez-Solís, EM and Liévano-Beltrán, LA and Magaña, B and Simoes, N and Mascaró, M},
title = {New distribution records of subterranean crustaceans from cenotes in Yucatan (Mexico).},
journal = {ZooKeys},
volume = {911},
number = {},
pages = {21-49},
pmid = {32104137},
issn = {1313-2989},
abstract = {New records of 14 stygobiont crustacean species pertaining to six Malacostraca orders from 32 cenotes are presented, with their associated caves of the state of Yucatan, Mexico, together with an individual account for each species. Species composition of most of the investigated cenotes is examined for the first time. A thermosbaenacean and two amphipod species were not formally recorded to the cenote ecosystems of the state of Yucatan prior to our research. Distribution data of a cirolanid isopod previously known only from its type locality is also provided. Barcodes of mitochondrial cytochrome c oxidase subunit I for the reported peracarid species previously lacking this information have been included in present study as tools for species identification and a baseline of further molecular genetic analyses.},
}
@article {pmid32103211,
year = {2020},
author = {Li, C and Zhang, Y and Cai, Q and Jie, G and Li, C},
title = {A dendritically amplified fluorescent signal probe on SiO2 microspheres for the ultrasensitive detection of mercury ions.},
journal = {The Analyst},
volume = {145},
number = {7},
pages = {2805-2810},
doi = {10.1039/d0an00158a},
pmid = {32103211},
issn = {1364-5528},
mesh = {DNA/chemistry/metabolism ; DNA Nucleotidylexotransferase/metabolism ; Fluorescent Dyes/chemistry ; Fresh Water/analysis ; Gold/chemistry ; Mercury/*analysis/chemistry ; Metal Nanoparticles/chemistry ; *Microspheres ; Nucleic Acid Amplification Techniques ; Silicon Dioxide/*chemistry ; Spectrometry, Fluorescence/*methods ; Thymine/chemistry ; },
abstract = {In this work, a new kind of dendritically amplified fluorescent signal probe on SiO2 microspheres was controllably fabricated by the terminal deoxynucleotidyl transferase (TdT)-catalyzed incorporation of nucleotides combined with bio-barcode (BBC) amplification for the ultrasensitive detection of Hg[2+]. A thymine T-Hg[2+]-T hairpin structure was first formed and further initiated the strand displacement amplification (SDA) reaction, generating a mimic target (MT). MT hybridized with a capture probe 1 (C1) on SiO2 microspheres, and the 3'-hydroxyl (OH) termini of MT initiated TdT-based DNA extension, producing abundant poly-guanine sequences (G1). Then, G1 hybridized with a capture probe 2 (C2) with abundant cytosine (C) species to assemble multiple C2/reporter probe-AuNPs onto the SiO2 microspheres. The reporter DNA further initiated TdT-based extension with a poly-T sequence (T1) to link large numbers of signal probes, which generated a very high fluorescence signal for the ultrasensitive detection of target Hg[2+]. This TdT-based signal amplification method coupled with SDA exhibits extraordinary sensitivity for Hg[2+] assay with a limit down to 1.0 aM. The proposed highly sensitive fluorescence strategy holds great potential for detecting targets in environmental and biological fields.},
}
@article {pmid32099048,
year = {2020},
author = {Hirotsu, Y and Otake, S and Ohyama, H and Amemiya, K and Higuchi, R and Oyama, T and Mochizuki, H and Goto, T and Omata, M},
title = {Dual-molecular barcode sequencing detects rare variants in tumor and cell free DNA in plasma.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {3391},
pmid = {32099048},
issn = {2045-2322},
mesh = {Alleles ; Carcinoma, Non-Small-Cell Lung/*genetics/pathology ; Cell-Free Nucleic Acids/blood/*genetics ; DNA Barcoding, Taxonomic ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Lung Neoplasms/*genetics/pathology ; Mutation ; Pancreatic Neoplasms/*genetics/pathology ; },
abstract = {Conventional next generation sequencing analysis has provided important insights into cancer genetics. However, the detection of rare (low allele fraction) variants remains difficult because of the error-prone nucleotide changes derived from sequencing/PCR errors. To eliminate the false-positive variants and detect genuine rare variants, sequencing technology combined with molecular barcodes will be useful. Here, we used the newly developed dual-molecular barcode technology (Ion AmpliSeq HD) to analyze somatic mutations in 24 samples (12 tumor tissues and 12 plasma) from 12 patients with biliary-pancreatic and non-small cell lung cancers. We compared the results between next generation sequencing analysis with or without molecular barcode technologies. The variant allele fraction (VAF) between non-molecular barcode and molecular barcode sequencing was correlated in plasma DNA (R[2] = 0.956) and tumor (R[2] = 0.935). Both methods successfully detected high VAF mutations, however, rare variants were only identified by molecular barcode sequencing and not by non-molecular barcode sequencing. Some of these rare variants in tumors were annotated as pathogenic, and therefore subclonal driver mutations could be observed. Furthermore, the very low VAF down to 0.17% were identified in cell free DNA in plasma. These results demonstrate that the dual molecular barcode sequencing technologies can sensitively detect rare somatic mutations, and will be important in the investigation of the clonal and subclonal architectures of tumor heterogeneity.},
}
@article {pmid32098193,
year = {2020},
author = {Shipunov, A and Carr, S and Furniss, S and Pay, K and Pirani, JR},
title = {First Phylogeny of Bitterbush Family, Picramniaceae (Picramniales).},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {2},
pages = {},
pmid = {32098193},
issn = {2223-7747},
support = {2590//North Dakota INBRE/ ; },
abstract = {Picramniaceae is the only member of Picramniales which is sister to the clade (Sapindales (Huerteales (Malvales, Brassicales))) in the rosidsmalvids. Not much is known about most aspects of their ecology, geography, and morphology. The family is restricted to American tropics. Picramniaceae representatives are rich in secondary metabolites; some species are known to be important for pharmaceutical purposes. Traditionally, Picramniaceae was classified as a subfamily of Simaroubaceae, but from 1995 on, it has been segregated containing two genera, Picramnia and Alvaradoa, with the recent addition of a third genus, Nothotalisia, described in 2011. Only a few species of the family have been the subject of DNA-related research, and fewer than half of the species have been included in morphological phylogenetic analyses. It is clear that Picramniaceae remains a largely under-researched plant group. Here we present the first molecular phylogenetic tree of the group, based on both chloroplast and nuclear markers, widely adopted in the plant DNA barcoding. The main findings are: The family and its genera are monophyletic and Picramnia is sister to two other genera; some clades corroborate previous assumptions of relationships made on a morphological or geographical basis, while most parts of the molecular topology suggest high levels of homoplasy in the morphological evolution of Picramnia.},
}
@article {pmid32096585,
year = {2021},
author = {Martoni, F and Valenzuela, I and Blacket, MJ},
title = {On the complementarity of DNA barcoding and morphology to distinguish benign endemic insects from possible pests: the case of Dirioxa pornia and the tribe Acanthonevrini (Diptera: Tephritidae: Phytalmiinae) in Australia.},
journal = {Insect science},
volume = {28},
number = {1},
pages = {261-270},
pmid = {32096585},
issn = {1744-7917},
support = {//Improved Market Access for Horticulture (IMAH) program (Victoria)/ ; },
mesh = {Animal Distribution ; Animals ; Australia ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/analysis ; Insect Control/*methods ; Insect Proteins/analysis ; Larva/anatomy &amp; histology/genetics/growth &amp; development ; Tephritidae/*anatomy &amp; histology/*genetics/growth &amp; development ; },
abstract = {Fruit flies are considered economically important insects due to some species being agricultural pests. However, morphological identification of fruit fly adults and larvae can be difficult requiring a high level of taxonomic expertise, with misidentifications causing problematic false-positive/negative results. While destructive molecular techniques can assist with the identification process, these often cannot be applied where it is mandatory to retain a voucher reference specimen. In this work, we non-destructively (and partial-destructively) processed larvae and adults mostly belonging to the species Dirioxa pornia (Walker, 1849), of the poorly studied nonpest fruit fly tribe Acanthonevrini (Tephritidae) from Australia, to enable molecular identifications whilst retaining morphological vouchers. By retaining the morphological features of specimens, we confirmed useful characters for genus/species-level identification, contributing to improved accuracy for future diagnostics using both molecular and morphological approaches. We provide DNA barcode information for three species of Acanthonevrini known from Australia, which prior to our study was only available for a single species, D. pornia. Our specimen examinations provide new distribution records for three nonpest species: Acanthonevroides variegatus Permkam and Hancock, 1995 in South Australia, Acanthonevroides basalis (Walker, 1853) and D. pornia in Victoria, Australia; as well as new host plant records for D. pornia, from kangaroo apple, apricot and loquat.},
}
@article {pmid32095344,
year = {2020},
author = {Siozios, S and Massa, A and Parr, CL and Verspoor, RL and Hurst, GDD},
title = {DNA barcoding reveals incorrect labelling of insects sold as food in the UK.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e8496},
pmid = {32095344},
issn = {2167-8359},
abstract = {BACKGROUND: Insects form an established part of the diet in many parts of the world and insect food products are emerging into the European and North American marketplaces. Consumer confidence in product is key in developing this market, and accurate labelling of content identity is an important component of this. We used DNA barcoding to assess the accuracy of insect food products sold in the UK.<br><br>METHODS: We purchased insects sold for human consumption from online retailers in the UK and compared the identity of the material ascertained from DNA barcoding to that stated on the product packaging. To this end, the COI sequence of mitochondrial DNA was amplified and sequenced, and compared the sequences produced to reference sequences in NCBI and the Barcode of Life Data System (BOLD).<br><br>RESULTS: The barcode identity of all insects that were farmed was consistent with the packaging label. In contrast, disparity between barcode identity and package contents was revealed in two cases of foraged material (mopane worm and winged termites). One case of very broad family-level description was also highlighted, where material described as grasshopper was identified as Locusta migratoria from DNA barcode.<br><br>CONCLUSION: Overall these data indicate the need to establish tight protocols to validate product identity in this developing market. Maintaining biosafety and consumer confidence rely on accurate and consistent product labelling that provides a clear chain of information from producer to consumer.},
}
@article {pmid32094541,
year = {2020},
author = {Jasinska, W and Manhart, M and Lerner, J and Gauthier, L and Serohijos, AWR and Bershtein, S},
title = {Chromosomal barcoding of E. coli populations reveals lineage diversity dynamics at high resolution.},
journal = {Nature ecology &amp; evolution},
volume = {4},
number = {3},
pages = {437-452},
pmid = {32094541},
issn = {2397-334X},
mesh = {Anti-Bacterial Agents ; *Escherichia coli ; *Evolution, Molecular ; Mutation ; },
abstract = {Evolutionary dynamics in large asexual populations is strongly influenced by multiple competing beneficial lineages, most of which segregate at very low frequencies. However, technical barriers to tracking a large number of these rare lineages in bacterial populations have so far prevented a detailed elucidation of evolutionary dynamics. Here, we overcome this hurdle by developing a chromosomal-barcoding technique that allows simultaneous tracking of approximately 450,000 distinct lineages in Escherichia coli, which we use to test the effect of sub-inhibitory concentrations of common antibiotics on the evolutionary dynamics of low-frequency lineages. We find that populations lose lineage diversity at distinct rates that correspond to their antibiotic regimen. We also determine that some lineages have similar fates across independent experiments. By analysing the trajectory dynamics, we attribute the reproducible fates of these lineages to the presence of pre-existing beneficial mutations, and we demonstrate how the relative contribution of pre-existing and de novo mutations varies across drug regimens. Finally, we reproduce the observed lineage dynamics by simulations. Altogether, our results provide a valuable methodology for studying bacterial evolution as well as insights into evolution under sub-inhibitory antibiotic levels.},
}
@article {pmid32088900,
year = {2020},
author = {Busconi, M and Soffritti, G and Mozos Pascual, ML and Fernandez, JA},
title = {Epigenetic Barcodes for Detection of Adulterated Plants and Plant-Derived Products.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2093},
number = {},
pages = {227-242},
doi = {10.1007/978-1-0716-0179-2_16},
pmid = {32088900},
issn = {1940-6029},
mesh = {Amplified Fragment Length Polymorphism Analysis/methods ; Crocus/*genetics ; DNA Methylation/genetics ; DNA, Plant/genetics ; Epigenesis, Genetic/genetics ; Epigenomics/methods ; Flowers/genetics ; Plants/*genetics ; Polymorphism, Restriction Fragment Length/genetics ; },
abstract = {In this chapter, we report a possible alternative use of epigenetics by applying methylation-sensitive amplified fragment length polymorphisms (MS-AFLP) to saffron traceability. Saffron is the most expensive plant-derived product in the world and one of the most frequently adulterated. One of the most frequent adulteration is by adding to saffron stigmas different parts of the saffron flower itself to increase volumes. While DNA is the same in all the parts of the plant, the epigenetic state can vary according to the organ and/or tissue of origin, making it possible to discriminate the stigmas from the other parts of saffron flower. In the subsequent method, the protocol to carry out a MS-AFLP analysis of saffron DNA methylation patterns is described.},
}
@article {pmid32086315,
year = {2020},
author = {},
title = {Breast Cancer Drivers Can Be Distinguished Using Embryonic Barcoding.},
journal = {Cancer discovery},
volume = {10},
number = {4},
pages = {OF2},
doi = {10.1158/2159-8290.CD-RW2020-029},
pmid = {32086315},
issn = {2159-8290},
mesh = {Animals ; *Breast Neoplasms/diagnosis/genetics ; Humans ; Mice ; },
abstract = {A lentiviral-barcoding approach using mouse embryonic cells allows driver-mutation identification.},
}
@article {pmid32084695,
year = {2020},
author = {Zhang, X and Du, P and Cui, X and Chen, G and Wang, Y and Zhang, Y and Abd El-Aty, AM and Hacımüftüoğlu, A and Wang, J and He, H and Jin, M and Hammock, B},
title = {A sensitive fluorometric bio-barcodes immunoassay for detection of triazophos residue in agricultural products and water samples by iterative cycles of DNA-RNA hybridization and dissociation of fluorophores by Ribonuclease H.},
journal = {The Science of the total environment},
volume = {717},
number = {},
pages = {137268},
pmid = {32084695},
issn = {1879-1026},
support = {P42 ES004699/ES/NIEHS NIH HHS/United States ; },
mesh = {DNA ; Gold ; *Immunoassay ; Limit of Detection ; Metal Nanoparticles ; Organothiophosphates ; RNA ; Ribonuclease H ; Triazoles ; },
abstract = {Although the toxicity of triazophos is high and it has been pulled from the market in many countries; it is still widely used and frequently detected in agricultural products. While conventional analyses have been routinely used for the quantification and monitoring of triazophos residues, those for detecting low residual levels are deemed necessary. Therefore, we developed a novel and sensitive fluorometric signal amplification immunoassay employing bio-barcodes for the quantitative analysis of triazophos residues in foodstuffs and surface water. Herein, monoclonal antibodies (mAbs) attached to gold nanoparticles (AuNPs) were coated with DNA oligonucleotides (used as a signal generator), and a complementary fluorogenic RNA was used for signal amplification. The system generated detection signals through DNA-RNA hybridization and subsequent dissociation of fluorophores by Ribonuclease H (RNase H). It has to be noted that RNase H can only disintegrate the RNA in DNA-RNA duplex, but not cleave single or double-stranded DNA. Hence, with iterative cycles of DNA-RNA hybridization, sufficient strong signal was obtained for reliable detection of residues. Furthermore, this method enables quantitative detection of triazophos residues through fluorescence intensity measurements. The competitive immunoassay shows a wide linear range of 0.01-100 ng/mL with a limit of detection (LOD) of 0.0032 ng/mL. The assay substantially meets the demand for the low residue detection of triazophos residues in agricultural products and water samples. Accuracy (expressed as spiked recovery %) and coefficient of variation (CV) were ranged from 73.4% to 116% and 7.04% to 17.4%, respectively. The proposed bio-barcodes immunoassay has the advantages of being stable, reproducible, and reliable for residue detection. In sum, the present study provides a novel approach for detection of small molecules in various sample matrices.},
}
@article {pmid32084625,
year = {2020},
author = {Melo, LB and Alencar, RB and Scarpassa, VM},
title = {Molecular taxonomy and phylogenetic inferences of Bichromomyia flaviscutellata complex based on the COI gene DNA barcode region.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {81},
number = {},
pages = {104256},
doi = {10.1016/j.meegid.2020.104256},
pmid = {32084625},
issn = {1567-7257},
mesh = {Animals ; Bayes Theorem ; Brazil ; DNA Barcoding, Taxonomic/methods ; Genes, Insect/*genetics ; Haplotypes/genetics ; Insect Vectors/*classification/*genetics ; Insecta/*classification/*genetics ; Leishmania/pathogenicity ; Leishmaniasis/parasitology ; Phylogeny ; },
abstract = {Leishmaniasis is considered one of the six most important infectious diseases in the world. In spite of its importance, the leishmaniasis is one of the world's most neglected tropical diseases. Bichromomyia flaviscutellata sensu lato is a complex composed of at least three species: B. flaviscutellata sensu stricto, B. reducta and B. olmeca. The latter is composed of three subspecies: B. olmeca olmeca, B. olmeca bicolor and B. olmeca nociva, which are distributed from Central America to South America. Of these, B. flaviscutellata s.s. is recognized as the main vector of Leishmania amazonensis in Brazil. The present study aimed to identify molecularly the species and subspecies of the B. flaviscutellata complex using the 5' region of the COI gene (Barcode region). A total of 44 specimens, comprising 22 B. flaviscutellata s.s. and 22 B. olmeca nociva, were analyzed from six localities in the Brazilian Amazon: five in the State of Amazonas (Autazes, Manaus, Pitinga, Novo Airão, and Rio Preto da Eva), and one in the State of Pará (Serra do Cachorro). Three sequences from B. olmeca olmeca and one of B. olmeca bicolor from GenBank were also added to the dataset, totaling 48 sequences with a length of 549 base pairs (bp). The total dataset generated 28 haplotypes and four disconnected networks. Phylogenetic analyses using three algorithms (Neighbor-Joining [NJ], Maximum Likelihood [ML] and Bayesian Inference [BI]) generated similar topologies and most clades were from moderately to highly supported. The phylogenetic relationship, together with genetic distance values (1%) and haplotypes networks, confirm the position of B. olmeca bicolor as a subspecies of B. olmeca olmeca. However, B. olmeca nociva was closer phylogenetically to B. flaviscutellata s.s. than to B. olmeca olmeca and B. olmeca bicolor. Additionally, the haplotype network separated B. olmeca nociva from B. olmeca olmeca and B. olmeca bicolor. These findings, combined with previous morphological data, suggest that the B. olmeca nociva should be elevated to full-species status. The findings of this study also found that B. flaviscutellata s.s. populations may be in process of forming lineages.},
}
@article {pmid32084206,
year = {2020},
author = {Nix, DA and Hellwig, S and Conley, C and Thomas, A and Fuertes, CL and Hamil, CL and Bhetariya, PJ and Garrido-Laguna, I and Marth, GT and Bronner, MP and Underhill, HR},
title = {The stochastic nature of errors in next-generation sequencing of circulating cell-free DNA.},
journal = {PloS one},
volume = {15},
number = {2},
pages = {e0229063},
pmid = {32084206},
issn = {1932-6203},
support = {UL1 RR025764/RR/NCRR NIH HHS/United States ; R37 CA246183/CA/NCI NIH HHS/United States ; UL1 TR000105/TR/NCATS NIH HHS/United States ; S10 OD021644/OD/NIH HHS/United States ; UL1 TR001067/TR/NCATS NIH HHS/United States ; },
mesh = {Adult ; Circulating Tumor DNA/*genetics ; DNA Barcoding, Taxonomic ; Female ; Hematopoiesis/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Male ; Middle Aged ; },
abstract = {Challenges with distinguishing circulating tumor DNA (ctDNA) from next-generation sequencing (NGS) artifacts limits variant searches to established solid tumor mutations. Here we show early and random PCR errors are a principal source of NGS noise that persist despite duplex molecular barcoding, removal of artifacts due to clonal hematopoiesis of indeterminate potential, and suppression of patterned errors. We also demonstrate sample duplicates are necessary to eliminate the stochastic noise associated with NGS. Integration of sample duplicates into NGS analytics may broaden ctDNA applications by removing NGS-related errors that confound identification of true very low frequency variants during searches for ctDNA without a priori knowledge of specific mutations to target.},
}
@article {pmid32083020,
year = {2020},
author = {Imai, K and Nemoto, R and Kodana, M and Tarumoto, N and Sakai, J and Kawamura, T and Ikebuchi, K and Mitsutake, K and Murakami, T and Maesaki, S and Fujiwara, T and Hayakawa, S and Hoshino, T and Seki, M and Maeda, T},
title = {Rapid and Accurate Species Identification of Mitis Group Streptococci Using the MinION Nanopore Sequencer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {10},
number = {},
pages = {11},
pmid = {32083020},
issn = {2235-2988},
mesh = {*Bacterial Typing Techniques ; Genes, Bacterial ; Genome, Bacterial ; Humans ; Mouth Mucosa/microbiology ; Multilocus Sequence Typing ; *Nanopore Sequencing ; Phylogeny ; *Sequence Analysis, DNA ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Streptococcal Infections/microbiology ; Streptococcus/*classification/genetics/isolation &amp; purification ; Streptococcus mitis/classification/genetics/isolation &amp; purification ; Streptococcus oralis/classification/genetics/isolation &amp; purification ; Streptococcus pneumoniae/classification/genetics/isolation &amp; purification ; Streptococcus sanguis/classification/genetics/isolation &amp; purification ; Whole Genome Sequencing ; },
abstract = {Differentiation between mitis group streptococci (MGS) bacteria in routine laboratory tests has become important for obtaining accurate epidemiological information on the characteristics of MGS and understanding their clinical significance. The most reliable method of MGS species identification is multilocus sequence analysis (MLSA) with seven house-keeping genes; however, because this method is time-consuming, it is deemed unsuitable for use in most clinical laboratories. In this study, we established a scheme for identifying 12 species of MGS (S. pneumoniae, S. pseudopneumoniae, S. mitis, S. oralis, S. peroris, S. infantis, S. australis, S. parasanguinis, S. sinensis, S. sanguinis, S. gordonii, and S. cristatus) using the MinION nanopore sequencer (Oxford Nanopore Technologies, Oxford, UK) with the taxonomic aligner "What's in My Pot?" (WIMP; Oxford Nanopore's cloud-based analysis platform) and Kraken2 pipeline with the custom database adjusted for MGS species identification. The identities of the species in reference genomes (n = 514), clinical isolates (n = 31), and reference strains (n = 4) were confirmed via MLSA. The nanopore simulation reads were generated from reference genomes, and the optimal cut-off values for MGS species identification were determined. For 31 clinical isolates (S. pneumoniae = 8, S. mitis = 17 and S. oralis = 6) and 4 reference strains (S. pneumoniae = 1, S. mitis = 1, S. oralis = 1, and S. pseudopneumoniae = 1), a sequence library was constructed via a Rapid Barcoding Sequencing Kit for multiplex and real-time MinION sequencing. The optimal cut-off values for the identification of MGS species for analysis by WIMP and Kraken2 pipeline were determined. The workflow using Kraken2 pipeline with a custom database identified all 12 species of MGS, and WIMP identified 8 MGS bacteria except S. infantis, S. australis, S. peroris, and S. sinensis. The results obtained by MinION with WIMP and Kraken2 pipeline were consistent with the MGS species identified by MLSA analysis. The practical advantage of whole genome analysis using the MinION nanopore sequencer is that it can aid in MGS surveillance. We concluded that MinION sequencing with the taxonomic aligner enables accurate MGS species identification and could contribute to further epidemiological surveys.},
}
@article {pmid32080356,
year = {2020},
author = {Bleuven, C and Nguyen, GQ and Després, PC and Filteau, M and Landry, CR},
title = {Competition experiments in a soil microcosm reveal the impact of genetic and biotic factors on natural yeast populations.},
journal = {The ISME journal},
volume = {14},
number = {6},
pages = {1410-1421},
pmid = {32080356},
issn = {1751-7370},
mesh = {Biodiversity ; Quercus/growth &amp; development/microbiology ; Saccharomyces/*genetics/*growth &amp; development/isolation &amp; purification ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {The ability to measure microbial fitness directly in natural conditions and in interaction with other microbes is a challenge that needs to be overcome if we want to gain a better understanding of microbial fitness determinants in nature. Here we investigate the influence of the natural microbial community on the relative fitness of the North American populations SpB, SpC and SpC* of the wild yeast Saccharomyces paradoxus using DNA barcodes and a soil microcosm derived from soil associated with oak trees. We find that variation in fitness among these genetically distinct groups is influenced by the microbial community. Altering the microbial community load and diversity with an irradiation treatment significantly diminishes the magnitude of fitness differences among populations. Our findings suggest that microbial interactions could affect the evolution of yeast lineages in nature by modulating variation in fitness.},
}
@article {pmid32078768,
year = {2020},
author = {Tellechea-Luzardo, J and Winterhalter, C and Widera, P and Kozyra, J and de Lorenzo, V and Krasnogor, N},
title = {Linking Engineered Cells to Their Digital Twins: A Version Control System for Strain Engineering.},
journal = {ACS synthetic biology},
volume = {9},
number = {3},
pages = {536-545},
doi = {10.1021/acssynbio.9b00400},
pmid = {32078768},
issn = {2161-5063},
mesh = {Bacillus subtilis/genetics ; Biotechnology/*methods ; Clustered Regularly Interspaced Short Palindromic Repeats ; DNA Barcoding, Taxonomic ; Escherichia coli/genetics ; Genetic Engineering/*methods ; Microorganisms, Genetically-Modified ; Recombination, Genetic ; Sequence Analysis, DNA ; *Software ; },
abstract = {As DNA sequencing and synthesis become cheaper and more easily accessible, the scale and complexity of biological engineering projects is set to grow. Yet, although there is an accelerating convergence between biotechnology and digital technology, a deficit in software and laboratory techniques diminishes the ability to make biotechnology more agile, reproducible, and transparent while, at the same time, limiting the security and safety of synthetic biology constructs. To partially address some of these problems, this paper presents an approach for physically linking engineered cells to their digital footprint-we called it digital twinning. This enables the tracking of the entire engineering history of a cell line in a specialized version control system for collaborative strain engineering via simple barcoding protocols.},
}
@article {pmid32078092,
year = {2020},
author = {Wang, X and Xue, J and Zhang, Y and Xie, H and Wang, Y and Weng, W and Kang, Y and Huang, J},
title = {DNA barcodes for the identification of Stephania (Menispermaceae) species.},
journal = {Molecular biology reports},
volume = {47},
number = {3},
pages = {2197-2203},
pmid = {32078092},
issn = {1573-4978},
support = {31100238//National Natural Science Foundation of China/ ; },
mesh = {Computational Biology/methods ; *DNA Barcoding, Taxonomic ; DNA, Plant ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Stephania/*classification/*genetics ; },
abstract = {Stephania is a medicinal plants-rich genus of Menispermaceae. However, the identification of morphologically-similar species in Stephania is difficult using the currently reported methods. The indiscriminate overexploitation of Stephania plants has resulted in clinical misuse and endangerment of many species, which necessitates the development of an efficient and reliable method for species authentication. Therefore, six candidate DNA barcode sequences (ITS, ITS2, psbA-trnH, matK, rbcL, and trnL-F) were tested for their capacity to identify Stephania species. The barcodes were analyzed either as a single region or in combination by tree-based [neighbor-joining (NJ) and Bayesian inference (BI)], distance-based (PWG-distance), and sequence similarity-based (TaxonDNA) methods. Amplification and sequencing success rates were 100% for all six candidate barcodes. A comparison of six barcode regions showed that ITS exhibited the highest number of variable and informative sites (182/179), followed by psbA-trnH (173/162). DNA barcoding gap assessment showed that interspecific distances of the six barcodes were greater than intraspecific distances. The identification results showed that species discrimination rates of combination barcodes were higher than those of single-region barcodes. Based on best match and best close match methods, the ITS+psbA-trnH combination exhibited the highest discrimination power (93.93%). Further, all Stephania species could be resolved in the phylogenetic trees based on ITS+psbA-trnH (NJ, BI). This study demonstrates that DNA barcoding is an efficient method to identify Stephania species and recommends that the ITS+psbA-trnH combination is the best DNA barcode for the identification of Stephania species.},
}
@article {pmid32077619,
year = {2020},
author = {Quek, RZB and Jain, SS and Neo, ML and Rouse, GW and Huang, D},
title = {Transcriptome-based target-enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia).},
journal = {Molecular ecology resources},
volume = {20},
number = {3},
pages = {807-818},
pmid = {32077619},
issn = {1755-0998},
support = {MSRDP-P03//National Research Foundation Singapore/ ; },
mesh = {Animals ; Anthozoa/*genetics ; Bayes Theorem ; Evolution, Molecular ; Genetic Loci/genetics ; Phylogeny ; Transcriptome/*genetics ; },
abstract = {Despite the ecological and economic significance of stony corals (Scleractinia), a robust understanding of their phylogeny remains elusive due to patchy taxonomic and genetic sampling, as well as the limited availability of informative markers. To increase the number of genetic loci available for phylogenomic analyses in Scleractinia, we designed 15,919 DNA enrichment baits targeting 605 orthogroups (mean 565 ± SD 366 bp) over 1,139 exon regions. A further 236 and 62 barcoding baits were designed for COI and histone H3 genes respectively for quality and contamination checks. Hybrid capture using these baits was performed on 18 coral species spanning the presently understood scleractinian phylogeny, with two corallimorpharians as outgroup. On average, 74% of all loci targeted were successfully captured for each species. Barcoding baits were matched unambiguously to their respective samples and revealed low levels of cross-contamination in accordance with expectation. We put the data through a series of stringent filtering steps to ensure only scleractinian and phylogenetically informative loci were retained, and the final probe set comprised 13,479 baits, targeting 452 loci (mean 531 ± SD 307 bp) across 865 exon regions. Maximum likelihood, Bayesian and species tree analyses recovered maximally supported, topologically congruent trees consistent with previous phylogenomic reconstructions. The phylogenomic method presented here allows for consistent capture of orthologous loci among divergent coral taxa, facilitating the pooling of data from different studies and increasing the phylogenetic sampling of scleractinians in the future.},
}
@article {pmid32077485,
year = {2020},
author = {Sen, F and Uncu, AO and Uncu, AT and Erdeger, SN},
title = {The trnL (UAA)-trnF (GAA) intergenic spacer is a robust marker of green pea (Pisum sativum L.) adulteration in economically valuable pistachio nuts (Pistacia vera L.).},
journal = {Journal of the science of food and agriculture},
volume = {100},
number = {7},
pages = {3056-3061},
doi = {10.1002/jsfa.10336},
pmid = {32077485},
issn = {1097-0010},
mesh = {DNA, Intergenic/*genetics ; DNA, Plant/*genetics ; Discriminant Analysis ; Food Contamination/*analysis ; Genomics ; Pisum sativum/*genetics ; Pistacia/*genetics ; Plant Proteins/genetics ; Plastids/genetics ; Polymerase Chain Reaction ; },
abstract = {BACKGROUND: Pistachio (Pistacia vera L.) is an expensive culinary nut species; it is therefore susceptible to adulteration for economic profit. Green pea (Pisum sativum L.) kernels constitute the most common material used for adulterating chopped / ground pistachio nuts and pistachio paste. Food genomics enables the species composition of a food sample to be ascertained through DNA analysis. Accordingly, a barcode DNA genotyping approach was used to standardize a test method to identify green pea adulteration in pistachio nuts.<br><br>RESULTS: The trnL (UAA)-trnF (GAA) intergenic spacer in the plastid genome was the target analyte in the present study. The barcode locus displayed a significant, discriminatory size difference between pistachio and pea, with amplicon sizes of 449 and 179&#x2009;bp, respectively. Polymerase chain reaction-capillary electrophoresis (PCR-CE) analysis of the intergenic spacer resulted in the successful identification of species composition in the in-house admixtures, which contained 5% to 30% of green pea.<br><br>CONCLUSION: The present work describes a fast and straightforward DNA test that identifies green pea adulteration in pistachio nuts without requiring a statistical data interpretation process. The plastid trnL (UAA)-trnF (GAA) intergenic spacer length widely varies among plant taxa, so the PCR-CE protocol that operates on the intergenic spacer holds the potential to reveal adulteration with a plethora of adulterants. The PCR-CE assay described in the present work can be adopted readily by food-quality laboratories in the public sector or the food industry as an easy and reliable method to analyze pistachio authenticity. &#xa9; 2020 Society of Chemical Industry.},
}
@article {pmid32072355,
year = {2020},
author = {Erban, T and Klimov, P and Molva, V and Hubert, J},
title = {Whole genomic sequencing and sex-dependent abundance estimation of Cardinium sp., a common and hyperabundant bacterial endosymbiont of the American house dust mite, Dermatophagoides farinae.},
journal = {Experimental &amp; applied acarology},
volume = {80},
number = {3},
pages = {363-380},
pmid = {32072355},
issn = {1572-9702},
support = {17-12068S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; RO0418//Ministerstvo Zem&#x11b;d&#x11b;lstv&#xed;/ ; 19-14-00004//Russian Science Foundation/ ; },
mesh = {Animals ; Bacteroidetes/*isolation &amp; purification ; China ; Dermatophagoides farinae/*microbiology ; Dermatophagoides pteronyssinus/microbiology ; Europe ; Female ; *Genome, Bacterial ; Male ; Microbiota ; Symbiosis ; United States ; Whole Genome Sequencing ; },
abstract = {The two common species of house dust mites (HDMs), Dermatophagoides farinae and D. pteronyssinus, are major sources of allergens in human dwellings worldwide. Many allergens from HDMs have been described, but their extracts vary in immunogens. Mite strains may differ in their microbiomes, which affect mite allergen expression and contents of bacterial endotoxins. Some bacteria, such as the intracellular symbiont Cardinium, can affect both the sex ratio and biochemical pathways of mites, resulting in abundance variations of mite allergens/immunogens. Here, we investigated the bacterial microbiomes of D. farinae and D. pteronyssinus males and females using barcode 16S rDNA sequencing, qPCR, and genomic data analysis. We found a single species of Cardinium associated with D. farinae strains from the USA, China and Europe. Cardinium had high abundance relative to other bacterial taxa and represented 99% of all bacterial DNA reads from female mites from the USA. Cardinium was also abundant with respect to the number of host cells-we estimated 10.4-11.8 cells of Cardinium per single female mite cell. In a European D. farinae strain, Cardinium was more prevalent in females than in males (representing 92 and 67% of all bacterial taxa in females and males, respectively). In contrast, D. pteronyssinus lacked any Cardinium species, and the microbiomes of male and female mites were similar. We produced a Cardinium genome assembly (1.48 Mb; GenBank: PRJNA555788, GCA_007559345.1) associated with D. farinae. The ascertained ubiquity and abundance of Cardinium strongly suggest that this intracellular bacterium plays an important biological role in D. farinae.},
}
@article {pmid32071801,
year = {2020},
author = {Justine, JL and Winsor, L and Gey, D and Gros, P and Thévenot, J},
title = {Obama chez moi! The invasion of metropolitan France by the land planarian Obama nungara (Platyhelminthes, Geoplanidae).},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e8385},
pmid = {32071801},
issn = {2167-8359},
abstract = {BACKGROUND: Obama nungara is a species of land flatworm originating from South America; the species was recently described and distinguished from a similar species, Obama marmorata. Obama nungara has invaded several countries of Europe, but the extent of the invasion has not been thoroughly mapped.<br><br>METHODS: In this article, based on a five and a half-year survey undertaken by citizen science, which yielded 530 records from 2013 to 2018, we analysed information about the invasion of Metropolitan France by O. nungara. We also investigated the variability of newly obtained cytochrome c oxidase 1 (COI) sequences of specimens from France, Italy and Switzerland.<br><br>RESULTS: Obama nungara was recorded from 72 of the 96 Departments of Metropolitan France. The species is especially abundant along the Atlantic coast, from the Spanish border to Brittany, and along the Mediterranean coast, from the Spanish border to the Italian border. More than half of the records were from an altitude below 50 m, and no record was from above 500 m; mountainous regions such as the Alps, Pyrenees and Massif Central are not invaded. Local abundance can be impressive, with 100 of specimens found in a small garden. An analysis of our new COI sequences, combined with published sequences of specimens from several countries, confirmed that three clades comprise the species. The first clade, 'Brazil', is currently confined to this country in South America; the second clade, 'Argentina 2', was found in Argentina and in Europe, only in Spain; and the third, 'Argentina 1', was found in Argentina and in Europe, in Spain, Portugal, France, UK, Italy, Belgium, and Switzerland. This suggests that two clades of O. nungara from Argentina have invaded Europe, with one widely spread.<br><br>DISCUSSION: The present findings strongly suggest that O. nungara is a highly invasive species and that the population which has invaded several countries in Europe comes from Argentina. The wide dispersion of the species and its reported local abundance, combined with the predatory character of the species, make O. nungara a potential threat to the biodiversity and ecology of the native soil fauna in Europe, and probably the most threatening species of all invasive land planarians present in Europe.},
}
@article {pmid32071342,
year = {2020},
author = {Sholihah, A and Delrieu-Trottin, E and Sukmono, T and Dahruddin, H and Risdawati, R and Elvyra, R and Wibowo, A and Kustiati, K and Busson, F and Sauri, S and Nurhaman, U and Dounias, E and Zein, MSA and Fitriana, Y and Utama, IV and Muchlisin, ZA and Agnèse, JF and Hanner, R and Wowor, D and Steinke, D and Keith, P and Rüber, L and Hubert, N},
title = {Disentangling the taxonomy of the subfamily Rasborinae (Cypriniformes, Danionidae) in Sundaland using DNA barcodes.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {2818},
pmid = {32071342},
issn = {2045-2322},
mesh = {Animals ; Asia, Southeastern ; Biodiversity ; Cypriniformes/*classification ; DNA Barcoding, Taxonomic ; Fresh Water ; Phylogeny ; },
abstract = {Sundaland constitutes one of the largest and most threatened biodiversity hotspots; however, our understanding of its biodiversity is afflicted by knowledge gaps in taxonomy and distribution patterns. The subfamily Rasborinae is the most diversified group of freshwater fishes in Sundaland. Uncertainties in their taxonomy and systematics have constrained its use as a model in evolutionary studies. Here, we established a DNA barcode reference library of the Rasborinae in Sundaland to examine species boundaries and range distributions through DNA-based species delimitation methods. A checklist of the Rasborinae of Sundaland was compiled based on online catalogs and used to estimate the taxonomic coverage of the present study. We generated a total of 991 DNA barcodes from 189 sampling sites in Sundaland. Together with 106 previously published sequences, we subsequently assembled a reference library of 1097 sequences that covers 65 taxa, including 61 of the 79 known Rasborinae species of Sundaland. Our library indicates that Rasborinae species are defined by distinct molecular lineages that are captured by species delimitation methods. A large overlap between intraspecific and interspecific genetic distance is observed that can be explained by the large amounts of cryptic diversity as evidenced by the 166 Operational Taxonomic Units detected. Implications for the evolutionary dynamics of species diversification are discussed.},
}
@article {pmid32071310,
year = {2020},
author = {Aiello, LM and Quercia, D and Schifanella, R and Del Prete, L},
title = {Tesco Grocery 1.0, a large-scale dataset of grocery purchases in London.},
journal = {Scientific data},
volume = {7},
number = {1},
pages = {57},
pmid = {32071310},
issn = {2052-4463},
mesh = {Commerce ; *Consumer Behavior ; Energy Intake ; Food/*economics ; Humans ; London ; Nutritive Value ; },
abstract = {We present the Tesco Grocery 1.0 dataset: a record of 420 M food items purchased by 1.6 M fidelity card owners who shopped at the 411 Tesco stores in Greater London over the course of the entire year of 2015, aggregated at the level of census areas to preserve anonymity. For each area, we report the number of transactions and nutritional properties of the typical food item bought including the average caloric intake and the composition of nutrients. The set of global trade international numbers (barcodes) for each food type is also included. To establish data validity we: i) compare food purchase volumes to population from census to assess representativeness, and ii) match nutrient and energy intake to official statistics of food-related illnesses to appraise the extent to which the dataset is ecologically valid. Given its unprecedented scale and geographic granularity, the data can be used to link food purchases to a number of geographically-salient indicators, which enables studies on health outcomes, cultural aspects, and economic factors.},
}
@article {pmid32069124,
year = {2020},
author = {Ma, Q and He, K and Wang, X and Jiang, J and Zhang, X and Song, Z},
title = {Better Resolution for Cytochrome b than Cytochrome c Oxidase Subunit I to Identify Schizothorax Species (Teleostei: Cyprinidae) from the Tibetan Plateau and Its Adjacent Area.},
journal = {DNA and cell biology},
volume = {39},
number = {4},
pages = {579-598},
doi = {10.1089/dna.2019.5031},
pmid = {32069124},
issn = {1557-7430},
mesh = {Animals ; Base Sequence ; Cyprinidae/*classification/genetics ; Cytochromes b/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Variation/genetics ; Mitochondria/enzymology/genetics ; Molecular Typing/methods ; Sequence Analysis, DNA ; Tibet ; },
abstract = {The genus Schizothorax is one of the most diverse groups of schizothoracine fish. Many species within this genus possess highly similar morphological characters and are very difficult to be identified accurately only based on morphology. The present study aims to test the effectiveness of mitochondrial cytochrome c oxidase subunit I (COI) gene and cytochrome b (Cytb) gene for discriminating the Schizothorax fish. A total of 185 individuals of 11 species for COI gene and 264 individuals of 23 species for Cytb gene were used for analyzing, respectively. According to the genetic distances, only one species based on COI gene and five species based on Cytb gene had "barcoding gaps," respectively. The tree-based analysis displayed that four species based on COI gene and six species based on Cytb gene clustered monophyletic group with strong support, respectively. The optimal threshold value of Schizothorax is 0.005 based on COI gene and 0.008 based on Cytb gene. The results of genetic similarity tests performed through online BLAST showed that 108 of 185 similarity searches succeeded in identifying conspecific sequences based on COI gene and 199 of 264 succeeded in identifying conspecific sequences based on Cytb gene. Considering greater interspecific genetic distance in Kimura 2-parameter (K2P) analysis and many clades with higher supporting values in tree-based analysis, we suggest that Cytb gene has better resolution in discrimination of Schizothorax species than COI gene. However, there are still many confused clustering relationships based on molecular data currently available. Incomplete lineage sorting, the existence of possible cryptic species and problematic morphological identification, etc. might have greatly weakened the resolution of Cytb gene in discrimination of Schizothorax species.},
}
@article {pmid32066960,
year = {2020},
author = {Qin, X and Sufi, J and Vlckova, P and Kyriakidou, P and Acton, SE and Li, VSW and Nitz, M and Tape, CJ},
title = {Cell-type-specific signaling networks in heterocellular organoids.},
journal = {Nature methods},
volume = {17},
number = {3},
pages = {335-342},
pmid = {32066960},
issn = {1548-7105},
support = {19763/CRUK_/Cancer Research UK/United Kingdom ; 23783/CRUK_/Cancer Research UK/United Kingdom ; A23783/CRUK_/Cancer Research UK/United Kingdom ; },
mesh = {Animals ; *Biomimetics ; Cell Differentiation ; Coculture Techniques/methods ; Colorectal Neoplasms/metabolism/*pathology ; Cytophotometry/methods ; Enterocytes/cytology ; Enteroendocrine Cells/cytology ; Female ; Fibroblasts/cytology ; *Gene Expression Regulation ; Goblet Cells/cytology ; Humans ; Intestine, Small/*cytology ; Macrophages/cytology ; Mice ; Mice, Inbred C57BL ; Organ Culture Techniques ; Organoids/*metabolism ; Paneth Cells/cytology ; *Signal Transduction ; Single-Cell Analysis/methods ; Sulfhydryl Compounds/chemistry ; Tumor Suppressor Protein p53/metabolism ; },
abstract = {Despite the widespread adoption of organoids as biomimetic tissue models, methods to comprehensively analyze cell-type-specific post-translational modification (PTM) signaling networks in organoids are absent. Here, we report multivariate single-cell analysis of such networks in organoids and organoid cocultures. Simultaneous analysis by mass cytometry of 28 PTMs in >1 million single cells derived from small intestinal organoids reveals cell-type- and cell-state-specific signaling networks in stem, Paneth, enteroendocrine, tuft and goblet cells, as well as enterocytes. Integrating single-cell PTM analysis with thiol-reactive organoid barcoding in situ (TOBis) enables high-throughput comparison of signaling networks between organoid cultures. Cell-type-specific PTM analysis of colorectal cancer organoid cocultures reveals that shApc, Kras[G12D] and Trp53[R172H] cell-autonomously mimic signaling states normally induced by stromal fibroblasts and macrophages. These results demonstrate how standard mass cytometry workflows can be modified to perform high-throughput multivariate cell-type-specific signaling analysis of healthy and cancerous organoids.},
}
@article {pmid32066493,
year = {2020},
author = {Tomazatos, A and Jöst, H and Schulze, J and Spînu, M and Schmidt-Chanasit, J and Cadar, D and Lühken, R},
title = {Blood-meal analysis of Culicoides (Diptera: Ceratopogonidae) reveals a broad host range and new species records for Romania.},
journal = {Parasites &amp; vectors},
volume = {13},
number = {1},
pages = {79},
pmid = {32066493},
issn = {1756-3305},
mesh = {Animals ; *Blood ; Ceratopogonidae/*classification/*physiology ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Feeding Behavior ; *Host Specificity ; Insect Vectors/classification ; Mammals/parasitology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Romania ; Wetlands ; },
abstract = {BACKGROUND: Culicoides biting midges are potential vectors of different pathogens. However, especially for eastern Europe, there is a lack of knowledge on the host-feeding patterns of this vector group. Therefore, this study aimed to identify Culicoides spp. and their vertebrate hosts collected in a wetland ecosystem.<br><br>METHODS: Culicoides spp. were collected weekly from May to August 2017, using Biogents traps with UV light at four sites in the Danube Delta Biosphere Reserve, Romania. Vectors and hosts were identified with a DNA barcoding approach. The mitochondrial cytochrome c oxidase subunit 1 was used to identify Culicoides spp., while vertebrate hosts were determined targeting cytochrome b or 16S rRNA gene fragments. A maximum likelihood phylogenetic tree was constructed to verify the biting midge identity against other conspecific Palaearctic Culicoides species. A set of unfed midges was used for morphological confirmation of species identification using slide-mounted wings.<br><br>RESULTS: Barcoding allowed the species identification and detection of corresponding hosts for 1040 (82.3%) of the 1264 analysed specimens. Eight Culicoides spp. were identified with Culicoides griseidorsum, Culicoides puncticollis and Culicoides submaritimus as new species records for Romania. For 39 specimens no similar sequences were found in GenBank. This group of unknown Culicoides showed a divergence of 15.6-16.3% from the closest identified species and clustered in a monophyletic clade, i.e. a novel species or a species without reference sequences in molecular libraries. For all Culicoides spp., nine mammalian and 24 avian species were detected as hosts. With the exception of C. riethi (n&#x2009;=&#x2009;12), at least one avian host was detected for all Culicoides spp., but this host group only dominated for Culicoides kibunensis and the unknown Culicoides sp.. The most common host group were mammals (n&#x2009;=&#x2009;993, 87.6% of all identified blood sources) dominated by cattle (n&#x2009;=&#x2009;817, 70.6%).<br><br>CONCLUSIONS: Most Culicoides spp. showed a broad host-feeding pattern making them potential bridge vectors. At the same time, new records of biting midge species for Romania, as well as a potentially unknown Culicoides species, highlight the lack of knowledge regarding the biting midge species and their genetic diversity in eastern Europe.},
}
@article {pmid32065638,
year = {2020},
author = {Yeo, D and Srivathsan, A and Meier, R},
title = {Longer is Not Always Better: Optimizing Barcode Length for Large-Scale Species Discovery and Identification.},
journal = {Systematic biology},
volume = {69},
number = {5},
pages = {999-1015},
doi = {10.1093/sysbio/syaa014},
pmid = {32065638},
issn = {1076-836X},
mesh = {Animal Identification Systems/*methods/standards ; Base Sequence/genetics ; *Biological Monitoring ; DNA Barcoding, Taxonomic/*methods ; Species Specificity ; },
abstract = {New techniques for the species-level sorting of millions of specimens are needed in order to accelerate species discovery, determine how many species live on earth, and develop efficient biomonitoring techniques. These sorting methods should be reliable, scalable, and cost-effective, as well as being largely insensitive to low-quality genomic DNA, given that this is usually all that can be obtained from museum specimens. Mini-barcodes seem to satisfy these criteria, but it is unclear how well they perform for species-level sorting when compared with full-length barcodes. This is here tested based on 20 empirical data sets covering ca. 30,000 specimens (5500 species) and six clade-specific data sets from GenBank covering ca. 98,000 specimens ($>$20,000 species). All specimens in these data sets had full-length barcodes and had been sorted to species-level based on morphology. Mini-barcodes of different lengths and positions were obtained in silico from full-length barcodes using a sliding window approach (three windows: 100 bp, 200 bp, and 300 bp) and by excising nine mini-barcodes with established primers (length: 94-407 bp). We then tested whether barcode length and/or position reduces species-level congruence between morphospecies and molecular operational taxonomic units (mOTUs) that were obtained using three different species delimitation techniques (Poisson Tree Process, Automatic Barcode Gap Discovery, and Objective Clustering). Surprisingly, we find no significant differences in performance for both species- or specimen-level identification between full-length and mini-barcodes as long as they are of moderate length ($>$200 bp). Only very short mini-barcodes (<200 bp) perform poorly, especially when they are located near the 5$^\prime$ end of the Folmer region. The mean congruence between morphospecies and mOTUs was ca. 75% for barcodes $>$200 bp and the congruent mOTUs contain ca. 75% of all specimens. Most conflict is caused by ca. 10% of the specimens that can be identified and should be targeted for re-examination in order to efficiently resolve conflict. Our study suggests that large-scale species discovery, identification, and metabarcoding can utilize mini-barcodes without any demonstrable loss of information compared to full-length barcodes. [DNA barcoding; metabarcoding; mini-barcodes; species discovery.].},
}
@article {pmid32065512,
year = {2020},
author = {van der Heyde, M and Bunce, M and Wardell-Johnson, G and Fernandes, K and White, NE and Nevill, P},
title = {Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA metabarcoding.},
journal = {Molecular ecology resources},
volume = {20},
number = {3},
pages = {},
doi = {10.1111/1755-0998.13148},
pmid = {32065512},
issn = {1755-0998},
support = {ICI150100041//ARC Centre for Mine Site Restoration/ ; },
mesh = {Animals ; Arthropods/genetics ; Biodiversity ; Climate ; DNA/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Environmental/*genetics ; Ecosystem ; Environmental Monitoring/*methods ; Invertebrates/genetics ; Metagenomics/methods ; Plants/genetics ; Soil ; },
abstract = {Biological surveys based on visual identification of the biota are challenging, expensive and time consuming, yet crucial for effective biomonitoring. DNA metabarcoding is a rapidly developing technology that can also facilitate biological surveys. This method involves the use of next generation sequencing technology to determine the community composition of a sample. However, it is uncertain as to what biological substrate should be the primary focus of metabarcoding surveys. This study aims to test multiple sample substrates (soil, scat, plant material and bulk arthropods) to determine what organisms can be detected from each and where they overlap. Samples (n = 200) were collected in the Pilbara (hot desert climate) and Swan Coastal Plain (hot Mediterranean climate) regions of Western Australia. Soil samples yielded little plant or animal DNA, especially in the Pilbara, probably due to conditions not conducive to long-term preservation. In contrast, scat samples contained the highest overall diversity with 131 plant, vertebrate and invertebrate families detected. Invertebrate and plant sequences were detected in the plant (86 families), pitfall (127 families) and vane trap (126 families) samples. In total, 278 families were recovered from the survey, 217 in the Swan Coastal Plain and 156 in the Pilbara. Aside from soil, 22%-43% of the families detected were unique to the particular substrate, and community composition varied significantly between substrates. These results demonstrate the importance of selecting appropriate metabarcoding substrates when undertaking terrestrial surveys. If the aim is to broadly capture all biota then multiple substrates will be required.},
}
@article {pmid32063738,
year = {2020},
author = {Oliveira, CMG and Harakava, R and Rosa, JMO},
title = {On the First Occurrence of Xiphinema Santos in Brazil.},
journal = {Helminthologia},
volume = {57},
number = {1},
pages = {37-42},
pmid = {32063738},
issn = {0440-6605},
abstract = {Based on morphology, measurements of juveniles and female specimens and sequences of the D2/ D3 expansion 28S rDNA gene and ITS1 analysis by DNA barcode technique, a Xiphinema americanum group species associated with olive trees from state of Sao Paulo, Brazil was identifi ed as X. santos. This is the first report of X. santos in Southern Hemisphere and outside the European and African continents, thus extending its geographic range.},
}
@article {pmid32063727,
year = {2020},
author = {Léger, T and Kehlmaier, C and Vairappan, CS and Nuss, M},
title = {Twenty-six new species of Hoploscopa (Lepidoptera, Crambidae) from South-East Asia revealed by morphology and DNA barcoding.},
journal = {ZooKeys},
volume = {907},
number = {},
pages = {1-99},
pmid = {32063727},
issn = {1313-2989},
abstract = {Hoploscopa Meyrick (Lepidoptera: Crambidae) is a fern-feeding genus found in montane areas of South-East Asia and Melanesia, eastwards up to the Samoan Islands. It includes sixteen described species, with at least 70 further undescribed species known from scientific collections. An iterative approach including morphological and molecular characters was used in order to explore the diversity of Hoploscopa. The hitherto described species are revised, and descriptions authored by T. Léger and M. Nuss are provided for an additional 26 new species: H. agtuuganonensis sp. nov., H. albipuncta sp. nov., H. albomaculata sp. nov., H. anacantha sp. nov., H. boleta sp. nov., H. cynodonta sp. nov., H. danaoensis sp. nov., H. gombongi sp. nov., H. gracilis sp. nov., H. ignitamaculae sp. nov., H. isarogensis sp. nov., H. jubata sp. nov., H. kelama sp. nov., H. kinabaluensis sp. nov., H. mallyi sp. nov., H. marijoweissae sp. nov., H. matheae sp. nov., H. niveofascia sp. nov., H. pangrangoensis sp. nov., H. parvimacula sp. nov., H. pseudometacrossa sp. nov., H. sepanggi sp. nov., H. sumatrensis sp. nov., H. titika sp. nov., H. tonsepi sp. nov., H. ypsilon sp. nov. Using a protocol specific for the amplification of DNA from old museum specimens, we recovered 101 COI barcodes for all but one of the newly described species, with 76 being barcode compliant (>487 bp). Species delimitation analyses suggest cryptic diversity, with six cases reflecting allopatric divergence, and two further cases found in sympatry.},
}
@article {pmid32059806,
year = {2020},
author = {Ying, Z and Beronja, S},
title = {Embryonic Barcoding of Equipotent Mammary Progenitors Functionally Identifies Breast Cancer Drivers.},
journal = {Cell stem cell},
volume = {26},
number = {3},
pages = {403-419.e4},
pmid = {32059806},
issn = {1875-9777},
support = {K99 DE029229/DE/NIDCR NIH HHS/United States ; P30 CA015704/CA/NCI NIH HHS/United States ; R01 AR070780/AR/NIAMS NIH HHS/United States ; },
mesh = {Animals ; Cell Differentiation ; Cell Lineage/genetics ; Cells, Cultured ; Epithelial Cells ; *Mammary Glands, Animal ; Mice ; *Neoplasms ; Stem Cells ; },
abstract = {Identification of clinically relevant drivers of breast cancers in intact mammary epithelium is critical for understanding tumorigenesis yet has proven challenging. Here, we show that intra-amniotic lentiviral injection can efficiently transduce progenitor cells of the adult mammary gland and use that as a platform to functionally screen over 500 genetic lesions for functional roles in tumor formation. Targeted progenitors establish long-term clones of both luminal and myoepithelial lineages in adult animals, and via lineage tracing with stable barcodes, we found that each mouse mammary gland is generated from a defined number of ∼120 early progenitor cells that expand uniformly with equal growth potential. We then designed an in vivo screen to test genetic interactions in breast cancer and identified candidates that drove not only tumor formation but also molecular subtypes. Thus, this methodology enables rapid and high-throughput cancer driver discovery in mammary epithelium.},
}
@article {pmid32055372,
year = {2019},
author = {Potowski, M and Losch, F and Wünnemann, E and Dahmen, JK and Chines, S and Brunschweiger, A},
title = {Screening of metal ions and organocatalysts on solid support-coupled DNA oligonucleotides guides design of DNA-encoded reactions.},
journal = {Chemical science},
volume = {10},
number = {45},
pages = {10481-10492},
pmid = {32055372},
issn = {2041-6520},
abstract = {DNA-encoded compound libraries are a widely used technology for target-based small molecule screening. Generally, these libraries are synthesized by solution phase combinatorial chemistry requiring aqueous solvent mixtures and reactions that are orthogonal to DNA reactivity. Initiating library synthesis with readily available controlled pore glass-coupled DNA barcodes benefits from enhanced DNA stability due to nucleobase protection and choice of dry organic solvents for encoded compound synthesis. We screened the compatibility of solid-phase coupled DNA sequences with 53 metal salts and organic reagents. This screening experiment suggests design of encoded library synthesis. Here, we show the reaction optimization and scope of three sp[3]-bond containing heterocyclic scaffolds synthesized on controlled pore glass-connected DNA sequences. A ZnCl2-promoted aza-Diels-Alder reaction with Danishefsky's diene furnished diverse substituted DNA-tagged pyridones, and a phosphoric acid organocatalyst allowed for synthesis of tetrahydroquinolines by the Povarov reaction and pyrimidinones by the Biginelli reaction, respectively. These three reactions caused low levels of DNA depurination and cover broad and only partially overlapping chemical space though using one set of DNA-coupled starting materials.},
}
@article {pmid32054950,
year = {2020},
author = {Cai, R and Kayal, E and Alves-de-Souza, C and Bigeard, E and Corre, E and Jeanthon, C and Marie, D and Porcel, BM and Siano, R and Szymczak, J and Wolf, M and Guillou, L},
title = {Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {2531},
pmid = {32054950},
issn = {2045-2322},
mesh = {DNA, Ribosomal/genetics ; Dinoflagellida/classification/*genetics ; Operon ; Phenotype ; Protozoan Infections/parasitology ; Ribosomes/genetics ; Ribotyping ; Whole Genome Sequencing ; },
abstract = {As critical primary producers and recyclers of organic matter, the diversity of marine protists has been extensively explored by high-throughput barcode sequencing. However, classification of short metabarcoding sequences into traditional taxonomic units is not trivial, especially for lineages mainly known by their genetic fingerprints. This is the case for the widespread Amoebophrya ceratii species complex, parasites of their dinoflagellate congeners. We used genetic and phenotypic characters, applied to 119 Amoebophrya individuals sampled from the same geographic area, to construct practical guidelines for species delineation that could be applied in DNA/RNA based diversity analyses. Based on the internal transcribed spacer (ITS) regions, ITS2 compensatory base changes (CBC) and genome k-mer comparisons, we unambiguously defined eight cryptic species among closely related ribotypes that differed by less than 97% sequence identity in their SSU rDNA. We then followed the genetic signatures of these parasitic species during a three-year survey of Alexandrium minutum blooms. We showed that these cryptic Amoebophrya species co-occurred and shared the same ecological niche. We also observed a maximal ecological fitness for parasites having narrow to intermediate host ranges, reflecting a high cost for infecting a broader host range. This study suggests that a complete taxonomic revision of these parasitic dinoflagellates is long overdue to understand their diversity and ecological role in the marine plankton.},
}
@article {pmid32054859,
year = {2020},
author = {Lareau, CA and Ma, S and Duarte, FM and Buenrostro, JD},
title = {Inference and effects of barcode multiplets in droplet-based single-cell assays.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {866},
pmid = {32054859},
issn = {2041-1723},
support = {F31 CA232670/CA/NCI NIH HHS/United States ; },
mesh = {Artifacts ; Base Sequence ; DNA Barcoding, Taxonomic/*methods/statistics &amp; numerical data ; Data Interpretation, Statistical ; Databases, Genetic/statistics &amp; numerical data ; Genomics/methods/statistics &amp; numerical data ; Humans ; Lymphocytes/chemistry/cytology ; Single-Cell Analysis/*methods/statistics &amp; numerical data ; },
abstract = {A widespread assumption for single-cell analyses specifies that one cell's nucleic acids are predominantly captured by one oligonucleotide barcode. Here, we show that ~13-21% of cell barcodes from the 10x Chromium scATAC-seq assay may have been derived from a droplet with more than one oligonucleotide sequence, which we call "barcode multiplets". We demonstrate that barcode multiplets can be derived from at least two different sources. First, we confirm that approximately 4% of droplets from the 10x platform may contain multiple beads. Additionally, we find that approximately 5% of beads may contain detectable levels of multiple oligonucleotide barcodes. We show that this artifact can confound single-cell analyses, including the interpretation of clonal diversity and proliferation of intra-tumor lymphocytes. Overall, our work provides a conceptual and computational framework to identify and assess the impacts of barcode multiplets in single-cell data.},
}
@article {pmid32054368,
year = {2020},
author = {Ran, K and Li, Q and Qi, L and Li, W and Kong, L},
title = {Molecular identification of Cerithiidae (Mollusca: Gastropod) in Hainan island, China.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {31},
number = {2},
pages = {57-63},
doi = {10.1080/24701394.2020.1726898},
pmid = {32054368},
issn = {2470-1408},
mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics/metabolism ; Gastropoda/*classification/*genetics ; *Islands ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {A number of same species of Cerithiidae are morphologically unlike, whereas most of species in the same genus are morphologically similar and just exhibit subtle differences. It is difficult to identify them by morphological methods alone. DNA barcoding is a modern molecular technique that can be used to identify species accurately, and is particularly helpful when distinguishing morphologically similar species. In order to identify species of Cerithiidae using DNA barcoding technology based on mitochondrial cytochrome oxidase subunit I (COI) and 16S ribosomal RNA (16S rRNA) genes, this study calculated intraspecific and interspecific genetic distance and constructed the phylogenetic trees. A total of 80 COI and 16S rRNA barcode sequences were obtained from 10 species and 3 genera. Some unknown specimens were further identified and a cryptic species may exist in Cerithium traillii, showing that DNA barcoding technology has the potential to discover new species and cryptic species. The phylogenetic trees revealed that all of the cerithiids could converge upon a monophyly with high support values and two genera (Cerithium and Clypeomorus) maybe support the reclassification. It is necessary for traditional morphological methods to combine with the DNA barcoding for classification and identification of Cerithiidae.},
}
@article {pmid32053689,
year = {2020},
author = {Chen, Q and Wu, X and Zhang, D},
title = {Comparison of the abilities of universal, super, and specific DNA barcodes to discriminate among the original species of Fritillariae cirrhosae bulbus and its adulterants.},
journal = {PloS one},
volume = {15},
number = {2},
pages = {e0229181},
pmid = {32053689},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic ; Fraud/*prevention &amp; control ; Fritillaria/*classification/*genetics ; Genetic Variation ; Genome, Plastid/genetics ; Phylogeny ; },
abstract = {Fritillariae cirrhosae bulbus is a famous type of traditional Chinese medicine used for cough relief and eliminating phlegm. The medicine originates from dried bulbs of five species and one variety of Fritillaria. Recently, immature bulbs from other congeneric species, such as F. ussuriensis, have been sold as adulterants of Fritillariae cirrhosae bulbus in medicine markets owing to the high price and limited availability of the genuine medicine. However, it is difficult to accurately identify the bulbs from different original species of Fritillariae cirrhosae bulbus and its adulterants based on traditional methods, although such medicines have different prices and treatment efficacies. The present study adopted DNA barcoding to identify these different species and compared the discriminatory power of super, universal, and specific barcodes in Fritillaria. The results revealed that the super-barcode had strong discriminatory power (87.5%). Among universal barcodes, matK provided the best species resolution (87.5%), followed by ITS (62.5%), rbcL (62.5%), and trnH-psbA (25%). The combination of these four universal barcodes provided the highest discriminatory power (87.5%), which was equivalent to that of the super-barcode. Two plastid genes, ycf1 and psbM-psbD, had much better discriminatory power (both 87.5%) than did other plastid barcodes, and were suggested as potential specific barcodes for identifying Fritillaria species. Phylogenetic analyses indicated that F. cirrhosa was not a "good" species that was composed of multiple lineages, which might have affected the evaluation of the discriminatory ability. This study revealed that the complete plastid genome, as super barcode, was an efficient and reliable tool for identifying the original species of Fritillariae cirrhosae bulbus and its adulterants.},
}
@article {pmid32053607,
year = {2020},
author = {Diez Benavente, E and Campos, M and Phelan, J and Nolder, D and Dombrowski, JG and Marinho, CRF and Sriprawat, K and Taylor, AR and Watson, J and Roper, C and Nosten, F and Sutherland, CJ and Campino, S and Clark, TG},
title = {A molecular barcode to inform the geographical origin and transmission dynamics of Plasmodium vivax malaria.},
journal = {PLoS genetics},
volume = {16},
number = {2},
pages = {e1008576},
pmid = {32053607},
issn = {1553-7404},
support = {MR/M01360X/1/MRC_/Medical Research Council/United Kingdom ; MR/K000551/1/MRC_/Medical Research Council/United Kingdom ; MR/N010469/1/MRC_/Medical Research Council/United Kingdom ; MR/R020973/1/MRC_/Medical Research Council/United Kingdom ; BB/R013063/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Africa, Eastern ; Asia ; Datasets as Topic ; Disease Eradication/methods ; Disease Outbreaks/*prevention &amp; control ; Genetic Markers/genetics ; Genome, Protozoan/*genetics ; Genotype ; Genotyping Techniques/*methods ; Geography ; Humans ; Malaria, Vivax/epidemiology/parasitology/*transmission ; Metadata ; Microsatellite Repeats/genetics ; Plasmodium vivax/*genetics/isolation &amp; purification ; Polymorphism, Single Nucleotide/genetics ; Predictive Value of Tests ; South America ; Travel-Related Illness ; United Kingdom ; Whole Genome Sequencing ; },
abstract = {Although Plasmodium vivax parasites are the predominant cause of malaria outside of sub-Saharan Africa, they not always prioritised by elimination programmes. P. vivax is resilient and poses challenges through its ability to re-emerge from dormancy in the human liver. With observed growing drug-resistance and the increasing reports of life-threatening infections, new tools to inform elimination efforts are needed. In order to halt transmission, we need to better understand the dynamics of transmission, the movement of parasites, and the reservoirs of infection in order to design targeted interventions. The use of molecular genetics and epidemiology for tracking and studying malaria parasite populations has been applied successfully in P. falciparum species and here we sought to develop a molecular genetic tool for P. vivax. By assembling the largest set of P. vivax whole genome sequences (n = 433) spanning 17 countries, and applying a machine learning approach, we created a 71 SNP barcode with high predictive ability to identify geographic origin (91.4%). Further, due to the inclusion of markers for within population variability, the barcode may also distinguish local transmission networks. By using P. vivax data from a low-transmission setting in Malaysia, we demonstrate the potential ability to infer outbreak events. By characterising the barcoding SNP genotypes in P. vivax DNA sourced from UK travellers (n = 132) to ten malaria endemic countries predominantly not used in the barcode construction, we correctly predicted the geographic region of infection origin. Overall, the 71 SNP barcode outperforms previously published genotyping methods and when rolled-out within new portable platforms, is likely to be an invaluable tool for informing targeted interventions towards elimination of this resilient human malaria.},
}
@article {pmid32052030,
year = {2020},
author = {Shahhosseini, N and Wong, G and Frederick, C and Kobinger, GP},
title = {Mosquito Species Composition and Abundance in Quebec, Eastern Canada.},
journal = {Journal of medical entomology},
volume = {57},
number = {4},
pages = {1025-1031},
doi = {10.1093/jme/tjaa020},
pmid = {32052030},
issn = {1938-2928},
mesh = {Animals ; *Biodiversity ; *Culicidae ; Evolution, Molecular ; Female ; Mosquito Vectors ; Phylogeny ; Population Density ; Quebec ; },
abstract = {Given current and projected changes in the climate, the composition of mosquito species is predicted to shift geographically with implications for the transmission dynamics of vector-borne pathogens. Many mosquito species are rarely collected in Canada and their history is poorly understood; thus assessing their potential role as vectors for pathogenesis is difficult. Mosquitoes were collected from four trapping sites in Quebec Province, Canada, from June to September during 2018 and 2019 using BG sentinel traps. From all morphologically identified female mosquitoes, at least one specimen was selected for identification confirmation using the DNA-barcoding technique. Sequences were subjected to alignment and a Neighbor-Joining (NJ) tree was created using Geneious software. In total, 2,752 female mosquitoes belonging to 20 species over five genera: including Aedes (Ae.), Anopheles (An.), Culex (Cx.), Culiseta (Cu.), Coquillettidia (Cq.) were collected. The predominant mosquito was found to be Ae. cinereus. The highest number of mosquito species was captured in July, followed by August, September, and then June. Five genera were characterized by a distinctive set of cytochrome oxidase I (COI) sequences that formed well-supported clusters in the NJ-tree. The presence of Ae.japonicus in Quebec provides an initial look at the distribution of mosquito species in eastern Canada, which may put Canadians at risk of a wider range of arboviruses.},
}
@article {pmid32047649,
year = {2020},
author = {Stec, D and Krzywański, &#x141; and Arakawa, K and Michalczyk, &#x141;},
title = {A new redescription of Richtersius coronifer, supported by transcriptome, provides resources for describing concealed species diversity within the monotypic genus Richtersius (Eutardigrada).},
journal = {Zoological letters},
volume = {6},
number = {},
pages = {2},
pmid = {32047649},
issn = {2056-306X},
abstract = {Richtersius coronifer, the nominal species for the family Richtersiidae and a popular laboratory model, exemplifies a common problem in modern tardigrade taxonomy. Despite undeniable progress in the field, many old and incomplete descriptions of taxa hinder both species delimitation and the estimation of species diversity and distribution. Although for over a century this species has been recorded throughout the world, recent research indicates that records to date are likely to represent a species complex rather than a single cosmopolitan species. However, in order to recognise and name species diversity within the complex, an integrative redescription of the nominal species is first needed. Here, we describe an R. coronifer population collected from Spitsbergen, i.e., one of the two localities mentioned in the original description, with detailed morphological and morphometric data associated with standard DNA sequences of four standard genetic markers (18S rRNA, 28S rRNA, ITS-2, and COI) and supported by transcriptome sequencing. We propose replacement of the neotype designated in 1981 by Maucci and Ramazzotti, as it is impossible to verify whether the existing neotype is conspecific with specimens studied by Richters in 1903 and 1904. Finally, using newly obtained cytochrome c oxidase subunit I (COI) sequences of populations from Spitsbergen, Italy, Poland, and Greece together with sequences deposited in GenBank (China, Greenland, Italy, Mongolia), we performed genetic species delimitation, which indicated seven distinct potential species within the genus Richtersius, in addition to the nominal taxon. This study marks a starting point for further research on the taxonomy of and species diversity within the genus. Moreover, this work has the potential to be the first tardigrade redescription to provide both genetic barcodes and a transcriptome of the species in question.},
}
@article {pmid32046929,
year = {2020},
author = {Gillingham, EL and Hansford, KM and Meadows, S and Henney, J and Wieckowski, F and Hernández-Triana, LM and Muscat, I and Muscat, J and Beckert, C and Nikolova, NI and Cull, B and Medlock, JM},
title = {Ticks on the Channel Islands and implications for public health.},
journal = {Ticks and tick-borne diseases},
volume = {11},
number = {3},
pages = {101405},
doi = {10.1016/j.ttbdis.2020.101405},
pmid = {32046929},
issn = {1877-9603},
mesh = {*Animal Distribution ; Animals ; Channel Islands ; Ecosystem ; Female ; Humans ; Ixodes/growth &amp; development/*physiology ; Larva/growth &amp; development/physiology ; Male ; Nymph/growth &amp; development/physiology ; *Public Health ; },
abstract = {The Channel Islands are British Crown dependencies located in the English Channel to the west of the Normandy coast in northern France. Whilst there have been studies investigating tick occurrence and distribution in different habitats on the mainland of the UK and in France, the Channel Islands have been relatively understudied. As such, little is known about whether the sheep tick, Ixodes ricinus, is present, and whether there is a potential risk of Lyme borreliosis on the Channel Islands. To ascertain the presence of I. ricinus on the three largest islands in the archipelago: Jersey, Guernsey and Alderney, surveys of ticks questing in the vegetation and ticks feeding on hosts were undertaken during April and May 2016. Across all three islands, the highest numbers of ticks were found in woodland habitats. Ixodes ricinus was the predominant questing tick species found on Jersey, and Ixodes ventalloi the most common questing tick species on Alderney and Guernsey, with little or no evidence of questing I. ricinus on either island. During field studies on small mammals, I. ricinus was the predominant tick species feeding on Jersey bank voles (Myodes glareolus caesarius), with Ixodes hexagonus the most common species infesting hedgehogs on Guernsey. We propose that the greater diversity of small mammals on Jersey may be important in supporting immature stages of I. ricinus, in contrast to Guernsey and Alderney. Morphological identification of tick species was confirmed by PCR sequencing based on amplification of the cytochrome c oxidase subunit one (cox1) gene (COI DNA barcoding). To date, there have been few records of human tick bites in the Channel Islands, suggesting that the current risk from tick-borne disease may be low, but continued reporting of any human tick bites, along with reporting of cases of Lyme borreliosis will be important for continued assessment of the impact of tick-borne diseases in the Channel Islands.},
}
@article {pmid32042891,
year = {2020},
author = {Tian, X and Angioletti-Uberti, S and Battaglia, G},
title = {On the design of precision nanomedicines.},
journal = {Science advances},
volume = {6},
number = {4},
pages = {eaat0919},
pmid = {32042891},
issn = {2375-2548},
mesh = {Animals ; Blood-Brain Barrier/*cytology/*metabolism ; Cattle ; *Drug Delivery Systems ; Humans ; *Models, Biological ; *Nanoparticles ; Rats ; },
abstract = {Tight control on the selectivity of nanoparticles' interaction with biological systems is paramount for the development of targeted therapies. However, the large number of tunable parameters makes it difficult to identify optimal design "sweet spots" without guiding principles. Here, we combine superselectivity theory with soft matter physics into a unified theoretical framework and we prove its validity using blood brain barrier cells as target. We apply our approach to polymersomes functionalized with targeting ligands to identify the most selective combination of parameters in terms of particle size, brush length and density, as well as tether length, affinity, and ligand number. We show that the combination of multivalent interactions into multiplexed systems enable interaction as a function of the cell phenotype, that is, which receptors are expressed. We thus propose the design of a "bar-coding" targeting approach that can be tailor-made to unique cell populations enabling personalized therapies.},
}
@article {pmid32041961,
year = {2020},
author = {Manel, S and Guerin, PE and Mouillot, D and Blanchet, S and Velez, L and Albouy, C and Pellissier, L},
title = {Global determinants of freshwater and marine fish genetic diversity.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {692},
pmid = {32041961},
issn = {2041-1723},
mesh = {Animals ; Aquatic Organisms/classification/genetics ; *Biodiversity ; DNA, Mitochondrial/genetics ; Databases, Genetic ; Environment ; Fishes/classification/*genetics ; *Genetic Variation ; Geography ; },
abstract = {Genetic diversity is estimated to be declining faster than species diversity under escalating threats, but its spatial distribution remains poorly documented at the global scale. Theory predicts that similar processes should foster congruent spatial patterns of genetic and species diversity, but empirical studies are scarce. Using a mined database of 50,588 georeferenced mitochondrial DNA barcode sequences (COI) for 3,815 marine and 1,611 freshwater fish species respectively, we examined the correlation between genetic diversity and species diversity and their global distributions in relation to climate and geography. Genetic diversity showed a clear spatial organisation, but a weak association with species diversity for both marine and freshwater species. We found a predominantly positive relationship between genetic diversity and sea surface temperature for marine species. Genetic diversity of freshwater species varied primarily across the regional basins and was negatively correlated with average river slope. The detection of genetic diversity patterns suggests that conservation measures should consider mismatching spatial signals across multiple facets of biodiversity.},
}
@article {pmid32040713,
year = {2020},
author = {Kennedy, SR and Prost, S and Overcast, I and Rominger, AJ and Gillespie, RG and Krehenwinkel, H},
title = {High-throughput sequencing for community analysis: the promise of DNA barcoding to uncover diversity, relatedness, abundances and interactions in spider communities.},
journal = {Development genes and evolution},
volume = {230},
number = {2},
pages = {185-201},
pmid = {32040713},
issn = {1432-041X},
support = {KR4623//Deutsche Forschungsgemeinschaft/International ; DEB 1241253//National Science Foundation/International ; },
mesh = {Animals ; DNA/genetics ; DNA Barcoding, Taxonomic/*classification/methods ; Ecosystem ; Food Chain ; Genomics ; *High-Throughput Nucleotide Sequencing/methods ; Predatory Behavior ; Spiders/*classification/*genetics ; },
abstract = {Large-scale studies on community ecology are highly desirable but often difficult to accomplish due to the considerable investment of time, labor and, money required to characterize richness, abundance, relatedness, and interactions. Nonetheless, such large-scale perspectives are necessary for understanding the composition, dynamics, and resilience of biological communities. Small invertebrates play a central role in ecosystems, occupying critical positions in the food web and performing a broad variety of ecological functions. However, it has been particularly difficult to adequately characterize communities of these animals because of their exceptionally high diversity and abundance. Spiders in particular fulfill key roles as both predator and prey in terrestrial food webs and are hence an important focus of ecological studies. In recent years, large-scale community analyses have benefitted tremendously from advances in DNA barcoding technology. High-throughput sequencing (HTS), particularly DNA metabarcoding, enables community-wide analyses of diversity and interactions at unprecedented scales and at a fraction of the cost that was previously possible. Here, we review the current state of the application of these technologies to the analysis of spider communities. We discuss amplicon-based DNA barcoding and metabarcoding for the analysis of community diversity and molecular gut content analysis for assessing predator-prey relationships. We also highlight applications of the third generation sequencing technology for long read and portable DNA barcoding. We then address the development of theoretical frameworks for community-level studies, and finally highlight critical gaps and future directions for DNA analysis of spider communities.},
}
@article {pmid32037992,
year = {2020},
author = {Cho, G and Malenovský, I and Burckhardt, D and Inoue, H and Lee, S},
title = {DNA barcoding of pear psyllids (Hemiptera: Psylloidea: Psyllidae), a tale of continued misidentifications.},
journal = {Bulletin of entomological research},
volume = {110},
number = {4},
pages = {521-534},
doi = {10.1017/S0007485320000012},
pmid = {32037992},
issn = {1475-2670},
mesh = {Animals ; DNA Barcoding, Taxonomic/methods ; Genes, Insect ; Genes, Mitochondrial ; Hemiptera/*chemistry/*genetics ; Species Specificity ; },
abstract = {Pear psyllids (Hemiptera: Psylloidea: Psyllidae: Cacopsylla spp.) belong to the most serious pests of pear (Pyrus spp.). They damage pear trees by excessive removal of phloem sap, by soiling the fruits with honeydew which, in turn, provides a substrate for sooty mould, and by transmission of Candidatus Phytoplasma spp., the causal agents of the pear decline disease. The morphological similarity, the presence of seasonal dimorphism that affects adult colour, size and wing morphology and uncritical use of species names, led to much confusion in the taxonomy of pear psyllids. As a result, pear psyllids have been frequently misidentified. Many of the entries attributed to Cacopsylla pyricola and other species in the GenBank are misidentifications which led to additional, unnecessary confusion. Here we analysed DNA barcodes of 11 pear psyllid species from eastern Asia, Europe and Iran using four mitochondrial gene fragments (COI 658 bp, COI 403 bp, COI-tRNAleu-COII 580 bp and 16S rDNA 452 bp). The efficiency of identification was notably high and considerable barcoding gaps were observed in all markers. Our results confirm the synonymies of the seasonal forms of Cacopsylla jukyungi (= C. cinereosignata, winter form) and C. maculatili (= C. qiuzili, summer form) previously suggested based on morphology. Some previous misidentifications (C. chinensis from China, Japan and Korea = misidentification of C. jukyungi; C. pyricola and C. pyrisuga from East Asia = misidentification of C. jukyungi and C. burckhardti, respectively; C. pyricola from Iran = misidentification of C. bidens, C. pyri and Cacopsylla sp.) are also corrected. There is no evidence for the presence of European pear psyllid species in East Asia.},
}
@article {pmid32034234,
year = {2020},
author = {Teets, EM and Gregory, C and Shaffer, J and Blachly, JS and Blaser, BW},
title = {Quantifying Hematopoietic Stem Cell Clonal Diversity by Selecting Informative Amplicon Barcodes.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {2153},
pmid = {32034234},
issn = {2045-2322},
support = {K08 DK111920/DK/NIDDK NIH HHS/United States ; },
mesh = {Algorithms ; Animals ; *Clonal Evolution ; Genotyping Techniques/*methods/standards ; *Hematopoiesis ; Hematopoietic Stem Cells/cytology/*metabolism ; *Mutation ; Sequence Analysis, DNA/methods/standards ; Zebrafish ; },
abstract = {Hematopoietic stem cells (HSCs) are functionally and genetically diverse and this diversity decreases with age and disease. Numerous systems have been developed to quantify HSC diversity by genetic barcoding, but no framework has been established to empirically validate barcode sequences. Here we have developed an analytical framework, Selection of informative Amplicon Barcodes from Experimental Replicates (SABER), that identifies barcodes that are unique among a large set of experimental replicates. Amplicon barcodes were sequenced from the blood of 56 adult zebrafish divided into training and validation sets. Informative barcodes were identified and samples with a high fraction of informative barcodes were chosen by bootstrapping. There were 4.2 ± 1.8 barcoded HSC clones per sample in the training set and 3.5 ± 2.1 in the validation set (p = 0.3). SABER reproducibly quantifies functional HSCs and can accommodate a wide range of experimental group sizes. Future large-scale studies aiming to understand the mechanisms of HSC clonal evolution will benefit from this new approach to identifying informative amplicon barcodes.},
}
@article {pmid32030323,
year = {2020},
author = {Gutiérrez-Aguirre, MA and Cervantes-Martínez, A and Elías-Gutiérrez, M and Lugo-Vázquez, A},
title = {Remarks on Mastigodiaptomus (Calanoida: Diaptomidae) from Mexico using integrative taxonomy, with a key of identification and three new species.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e8416},
pmid = {32030323},
issn = {2167-8359},
abstract = {BACKGROUND: In Mexico, species of four families of free-living calanoid copepods have been recorded as inhabitants of several freshwater systems. These families are Centropagidae, Temoridae, Pseudodiaptomidae and Diaptomidae. The genera Leptodiaptomus and Mastigodiaptomus are the most speciose diaptomid genera in Mexico, and they inhabit natural and artificial lakes, ephemeral ponds, springs, and caverns. Leptodiaptomus is considered as an endemic Nearctic genus, whereas Mastigodiaptomus is a widely distributed Neotropical genus in the southern USA, Mexico, the Caribbean Islands and Central America. Based on new and recent evidence, Mastigodiaptomus diversity has been underestimated: six species of the genus were known before 2000. In this work three new Mastigodiaptomus species have been described from different regions of Mexico by using integrative taxonomy. We also gave amended diagnosis of M. nesus Bowman (1986) and M. patzcuarensis s. str. (Kiefer, 1938).<br><br>METHODS: In this work, the taxonomic status of the species was clarified using modern, integrative method based on the COI gene as a DNA marker, plus micro-structural analysis (based on SEM and ligth microscopy).<br><br>RESULTS: Three new species of Mastigodiaptomus were described based on genetic and morphological analyses: M. alexei sp. n., M. ha sp. n. and M. cihuatlan sp. n. Also amended description of M. nesus, morphological variation of M. patzcuarensis s. str., and a comparison of them with all known sequences within the genus are provided. These new findings show that in Mastigodiaptomus differences in several cuticular microstructures of several appendages (such as the antennules, the fifth legs, or the urosomites of these copepods) agree with the interspecific genetic divergence >3% observed in sequences of the COI gene, and the integration of this information is a powerful tool in species delineation.},
}
@article {pmid32029757,
year = {2020},
author = {Vivien, R and Apothéloz-Perret-Gentil, L and Pawlowski, J and Werner, I and Lafont, M and Ferrari, BJD},
title = {High-throughput DNA barcoding of oligochaetes for abundance-based indices to assess the biological quality of sediments in streams and lakes.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {2041},
pmid = {32029757},
issn = {2045-2322},
mesh = {*Animal Distribution ; Animals ; DNA Barcoding, Taxonomic ; Environmental Monitoring/*methods ; *Geologic Sediments ; Lakes ; Oligochaeta/*genetics ; Rivers ; Sentinel Species/*genetics ; },
abstract = {Aquatic oligochaete communities are valuable indicators of the biological quality of sediments in streams and lakes, but identification of specimens to the species level based on morphological features requires solid expertise in taxonomy and is possible only for a fraction of specimens present in a sample. The identification of aquatic oligochaetes using DNA barcodes would facilitate their use in biomonitoring and allow a wider use of this taxonomic group for ecological diagnoses. Previous approaches based on DNA metabarcoding of samples composed of total sediments or pools of specimens have been proposed for assessing the biological quality of ecosystems, but such methods do not provide precise information on species abundance, which limits the value of resulting ecological diagnoses. Here, we tested how a DNA barcoding approach based on high-throughput sequencing of sorted and genetically tagged specimens performed to assess oligochaete species diversity and abundance and the biological quality of sediments in streams and lakes. We applied both molecular and morphological approaches at 13 sites in Swiss streams and at 7 sites in Lake Geneva. We genetically identified 33 or 66 specimens per site. For both approaches, we used the same index calculations. We found that the ecological diagnoses derived from the genetic approach matched well with those of the morphological approach and that the genetic identification of only 33 specimens per site provided enough ecological information for correctly estimating the biological quality of sediments in streams and lakes.},
}
@article {pmid32028056,
year = {2020},
author = {Berrilli, E and Simbula, G},
title = {First molecular identification of the tapeworm Mesocestoides litteratus from an Italian wall lizard (Podarcis siculus).},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {81},
number = {},
pages = {104233},
doi = {10.1016/j.meegid.2020.104233},
pmid = {32028056},
issn = {1567-7257},
mesh = {Animals ; Cestoda/*genetics ; DNA Barcoding, Taxonomic/methods ; Europe ; Female ; Italy ; Life Cycle Stages/genetics ; Lizards/*parasitology ; Mesocestoides/*genetics ; Phylogeny ; },
abstract = {The cyclophyllidean cestodes of the genus Mesocestoides are parasites infecting a variety of carnivorous vertebrates. The complete life cycle of these tapeworms is not clear yet, but some reptiles, amphibians, birds and micro-mammals have been indicated as intermediate hosts. Although Mesocestoides spp. are considered endemic in Europe, infections by the metacestode form, the tetrathyridium, are reported less commonly than are infections by adult worms. In the present study, a peritoneal infection by Mesocestoides tetrathyridia in a wall lizard (Podarcis siculus) collected in central Italy is described. The phylogenetic position of the metacestodes was assessed using the barcode region COI and species delimitation methods, i.e. Automatic Barcode Gap Discovery (ABGD) and Bayesian implementation of the Poisson Tree Processes model (bPTP). COI sequence analysis assigned the isolates from the wall lizard to Mesocestoides litteratus, as confirmed by species delimitation and phylogenetic analyses. M. litteratus has been observed in Europe mainly in the definitive hosts (dogs, cats and foxes), and never identified in the Mediterranean region. This study represents the first evidence of parasitic infection by tetrathyridia of M. litteratus in P. siculus in Italy.},
}
@article {pmid32027722,
year = {2020},
author = {Iguchi, A and Nishijima, M and Yoshioka, Y and Miyagi, A and Miwa, R and Tanaka, Y and Kato, S and Matsui, T and Igarashi, Y and Okamoto, N and Suzuki, A},
title = {Deep-sea amphipods around cobalt-rich ferromanganese crusts: Taxonomic diversity and selection of candidate species for connectivity analysis.},
journal = {PloS one},
volume = {15},
number = {2},
pages = {e0228483},
pmid = {32027722},
issn = {1932-6203},
mesh = {Amphipoda/*classification/*genetics ; Animals ; Cobalt/*chemistry ; DNA Barcoding, Taxonomic/*methods ; Genetic Variation ; Geologic Sediments/*chemistry ; Iron/*chemistry ; Japan ; Manganese/*chemistry ; Oceans and Seas ; Phylogeny ; Sequence Analysis, DNA/veterinary ; Species Specificity ; Vanuatu ; },
abstract = {The aim of this study was to select a candidate deep-sea amphipod species suitable for connectivity analyses in areas around cobalt-rich ferromanganese crusts (CRCs). We applied DNA barcoding based on the mitochondrial protein-coding gene, cytochrome c oxidase subunit I (COI), to specimens collected from the Xufu Guyot (the JA06 Seamount) off southeastern Minami-Torishima Island in the North Pacific, where CRCs are distributed. We used baited traps to collect 37 specimens. Comparison of COI sequences with public reference databases (GenBank, BOLD) showed that almost all of the specimens belonged to the superfamily Lysianassoidea, which is known to be ubiquitous in deep-sea areas. In a molecular taxonomic analysis of these sequences, we detected 11 clades. One of these clades (group 9) composed of 18 sequences and was identified by DNA barcoding as a putative species belonging to Abyssorchomene, which has been reported from the New Hebrides Trench in the South Pacific. We considered this species to be a candidate for connectivity analysis and analyzed its genome by restriction site-associated DNA sequencing. The results showed that the genetic variation in this species is adequate for analyzing connectivity patterns in CRC areas in the future.},
}
@article {pmid32025771,
year = {2020},
author = {Hu, X and Liu, M and Liu, Y and Zhang, J and Tang, Y and Pei, H and Liu, H and Chen, S and Song, C and Hu, Z},
title = {A two-step approach for systematic identification and quality evaluation of wild and introduced Anemone flaccida Fr. Schmidt (Di Wu) based on DNA barcode and UPLC-QTOF-MS/MS.},
journal = {Analytical and bioanalytical chemistry},
volume = {412},
number = {8},
pages = {1807-1816},
doi = {10.1007/s00216-020-02426-w},
pmid = {32025771},
issn = {1618-2650},
support = {2019ZYYD063//the Central Government Guides Local Science and Technology Development Fund in Hubei Province/ ; },
mesh = {Anemone/*chemistry/classification/genetics ; Biomass ; Chromatography, High Pressure Liquid/*methods ; *DNA Barcoding, Taxonomic ; Quality Control ; Species Specificity ; Tandem Mass Spectrometry ; },
abstract = {Herbal materials have both medicinal and commercial values. As such, accurate species and content identification and verification are necessary to ensure the safe and effective use for medical and commodity purposes. Herein, we introduce a two-step approach for systematic identification and quality evaluation of wild and introduced Anemone flaccida Fr. Schmidt (aka Di Wu) using DNA barcode and ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS/MS). To begin, a precise and rapid identification method based on internal transcribed spacer 2 (ITS2) sequence was developed to ensure the authenticity of 'Di Wu' species. Next, the major active components were fully characterized utilizing a targeted profile of oleanane-type triterpenoid saponins, which was established via UPLC-QTOF-MS/MS. As a result, 34 oleanane-type triterpenoid saponins were identified or characterized in 'Di Wu.' The qualitative and relative quantitative analysis showed obvious differences between wild and introduced 'Di Wu.' Furthermore, dynamic changes in the contents of triterpenoid saponins throughout various harvesting periods were clearly explained and mid-April was identified as the appropriate harvest time. Moreover, results indicate that the contents of five main saponins (anhuienoside E, glycosideSt-I4a, hemsgiganoside B, flaccidoside II, and hederasaponin B) are more appropriate as a quality evaluation indicator than the current quality standard. The two-step approach provides a suitable strategy to evaluate the genuine quality of wild and introduced 'Di Wu,' and can be applied to the targeted analysis of other triterpenoid saponin analogues for quality evaluation. Graphical Abstract .},
}
@article {pmid32024835,
year = {2020},
author = {Strobel, B and Spöring, M and Klein, H and Blazevic, D and Rust, W and Sayols, S and Hartig, JS and Kreuz, S},
title = {High-throughput identification of synthetic riboswitches by barcode-free amplicon-sequencing in human cells.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {714},
pmid = {32024835},
issn = {2041-1723},
mesh = {Computational Biology/methods ; DNA Barcoding, Taxonomic ; DNA, Complementary ; Gene Expression Regulation/drug effects ; Guanine/pharmacology ; HEK293 Cells ; Hepatitis Delta Virus/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; RNA, Catalytic/genetics ; Ribonucleoprotein, U1 Small Nuclear/genetics ; Riboswitch/drug effects/*genetics ; Synthetic Biology/methods ; Tetracycline/pharmacology ; },
abstract = {Synthetic riboswitches mediating ligand-dependent RNA cleavage or splicing-modulation represent elegant tools to control gene expression in various applications, including next-generation gene therapy. However, due to the limited understanding of context-dependent structure-function relationships, the identification of functional riboswitches requires large-scale-screening of aptamer-effector-domain designs, which is hampered by the lack of suitable cellular high-throughput methods. Here we describe a fast and broadly applicable method to functionally screen complex riboswitch libraries (~1.8 × 10[4] constructs) by cDNA-amplicon-sequencing in transiently transfected and stimulated human cells. The self-barcoding nature of each construct enables quantification of differential mRNA levels without additional pre-selection or cDNA-manipulation steps. We apply this method to engineer tetracycline- and guanine-responsive ON- and OFF-switches based on hammerhead, hepatitis-delta-virus and Twister ribozymes as well as U1-snRNP polyadenylation-dependent RNA devices. In summary, our method enables fast and efficient high-throughput riboswitch identification, thereby overcoming a major hurdle in the development cascade for therapeutically applicable gene switches.},
}
@article {pmid32024384,
year = {2020},
author = {de Alencastro, G and Pekrun, K and Valdmanis, P and Tiffany, M and Xu, J and Kay, MA},
title = {Tracking Adeno-Associated Virus Capsid Evolution by High-Throughput Sequencing.},
journal = {Human gene therapy},
volume = {31},
number = {9-10},
pages = {553-564},
pmid = {32024384},
issn = {1557-7422},
support = {R01 AI116698/AI/NIAID NIH HHS/United States ; S10 OD010580/OD/NIH HHS/United States ; },
mesh = {Biodiversity ; Capsid/*metabolism ; Cell Line ; Dependovirus/*genetics ; Directed Molecular Evolution ; Gene Library ; Gene Transfer Techniques ; Genetic Vectors/*genetics ; Genome, Viral ; HaCaT Cells ; Helper Viruses ; High-Throughput Nucleotide Sequencing ; Humans ; Reproducibility of Results ; Transduction, Genetic ; Virus Replication ; },
abstract = {Despite early successes using recombinant adeno-associated virus (rAAV) vectors in clinical gene therapy trials, limitations remain making additional advancements a necessity. Some of the challenges include variable levels of pre-existing neutralizing antibodies and poor transduction in specific target tissues and/or diseases. In addition, readministration of an rAAV vector is in general not possible due to the immune response against the capsid. Recombinant adeno-associated virus (AAV) vectors with novel capsids can be isolated in nature or developed through different directed evolution strategies. However, in most cases, the process of AAV selection is not well understood and new strategies are required to define the best parameters to develop more efficient and functional rAAV capsids. Therefore, the use of barcoding for AAV capsid libraries, which can be screened by high-throughput sequencing, provides a powerful tool to track AAV capsid evolution and potentially improve AAV capsid library screens. In this study, we examined how different parameters affect the screen of two different AAV libraries in two human cell types. We uncovered new and unexpected insights in how to maximize the likelihood of obtaining AAV variants with the desired properties. The major findings of the study are the following. (1) Inclusion of helper-virus for AAV replication can selectively propagate variants that can replicate to higher titers, but are not necessarily better at transduction. (2) Competition between AAVs with specific capsids can take place in cells that have been infected with different AAVs. (3) The use of low multiplicity of infections for infection results in more variation between screens and is not optimal at selecting the most desired capsids. (4) Using multiple rounds of selection can be counterproductive. We conclude that each of these parameters should be taken into consideration when screening AAV libraries for enhanced properties of interest.},
}
@article {pmid32023871,
year = {2020},
author = {Panyukov, VV and Kiselev, SS and Ozoline, ON},
title = {Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling.},
journal = {International journal of molecular sciences},
volume = {21},
number = {3},
pages = {},
pmid = {32023871},
issn = {1422-0067},
support = {18-14-00348//Russian Science Foundation/ ; 18-07-00899//&#x420;&#x43e;&#x441;&#x441;&#x438;&#x439;&#x441;&#x43a;&#x438;&#x439; &#x424;&#x43e;&#x43d;&#x434; &#x424;&#x443;&#x43d;&#x434;&#x430;&#x43c;&#x435;&#x43d;&#x442;&#x430;&#x43b;&#x44c;&#x43d;&#x44b;&#x445; &#x418;&#x441;&#x441;&#x43b;&#x435;&#x434;&#x43e;&#x432;&#x430;&#x43d;&#x438;&#x439; (&#x420;&#x424;&#x424;&#x418;)/ ; },
mesh = {Algorithms ; Case-Control Studies ; Computational Biology ; Crohn Disease/*genetics/microbiology ; DNA Barcoding, Taxonomic/*methods ; Escherichia coli/classification/*genetics/isolation &amp; purification ; Escherichia coli Infections/*genetics/microbiology ; *Genes, Bacterial ; *Genome, Bacterial ; Humans ; Metagenome ; *Microbiota ; },
abstract = {The need for a comparative analysis of natural metagenomes stimulated the development of new methods for their taxonomic profiling. Alignment-free approaches based on the search for marker k-mers turned out to be capable of identifying not only species, but also strains of microorganisms with known genomes. Here, we evaluated the ability of genus-specific k-mers to distinguish eight phylogroups of Escherichia coli (A, B1, C, E, D, F, G, B2) and assessed the presence of their unique 22-mers in clinical samples from microbiomes of four healthy people and four patients with Crohn's disease. We found that a phylogenetic tree inferred from the pairwise distance matrix for unique 18-mers and 22-mers of 124 genomes was fully consistent with the topology of the tree, obtained with concatenated aligned sequences of orthologous genes. Therefore, we propose strain-specific "barcodes" for rapid phylotyping. Using unique 22-mers for taxonomic analysis, we detected microbes of all groups in human microbiomes; however, their presence in the five samples was significantly different. Pointing to the intraspecies heterogeneity of E. coli in the natural microflora, this also indicates the feasibility of further studies of the role of this heterogeneity in maintaining population homeostasis.},
}
@article {pmid32020432,
year = {2020},
author = {Shibayama, T and Low, SK and Ono, M and Kobayashi, T and Kobayashi, K and Fukada, I and Ito, Y and Ueno, T and Ohno, S and Nakamura, Y and Takahashi, S},
title = {Clinical significance of gene mutation in ctDNA analysis for hormone receptor-positive metastatic breast cancer.},
journal = {Breast cancer research and treatment},
volume = {180},
number = {2},
pages = {331-341},
doi = {10.1007/s10549-019-05512-5},
pmid = {32020432},
issn = {1573-7217},
mesh = {Aged ; Aged, 80 and over ; Biomarkers, Tumor/blood/*genetics ; Breast Neoplasms/blood/*genetics/pathology ; Circulating Tumor DNA/blood/*genetics ; Class I Phosphatidylinositol 3-Kinases/*genetics ; Estrogen Receptor alpha/*genetics ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Middle Aged ; Neoplasm Metastasis ; Prognosis ; Receptor, ErbB-2/metabolism ; Receptors, Estrogen/metabolism ; Receptors, Progesterone/metabolism ; Survival Rate ; Tumor Suppressor Protein p53/*genetics ; },
abstract = {PURPOSE: In this study, we aim to investigate the mutation spectrum of circulating tumor DNA among hormone receptor-positive metastatic breast cancer (HR-MBC) patients using ultradeep targeted resequencing. In addition, we also evaluate the correlation of mutations detected from this study with progression-free survival (PFS).<br><br>MATERIALS AND METHODS: A total of 56 HR-MBC patients were enrolled. Cell-free DNA (cfDNA) was extracted from plasma and sequenced by using Oncomine Breast cancer cfDNA assay in this study.<br><br>RESULT: Concentration of cfDNA is correlated with a number of metastatic organs and serum CEA levels (Spearman's rank correlation p&#x2009;=&#x2009;0.0018, p&#x2009;=&#x2009;0.0015 respectively). Cases with high cfDNA levels (&#x2265;&#x2009;2.6&#xa0;ng/&#x3bc;l of plasma) showed worse progression-free survival (PFS) and overall survival compared with cases with low cfDNA levels (p&#x2009;=&#x2009;0.043 and 0.046, respectively). Among these patients, 29 patients (51.7%) have TP53 mutations, 12 patients (30.3%) have PIK3CA mutations, and 9 patients (16.0%) have ESR1 mutations. Acquisition of ESR1 mutation increased according to the lines of hormone therapy. In addition, patients with ESR1 mutation showed shorter PFS than those without mutation (log-rank p&#x2009;=&#x2009;0.047). In the multivariate analysis, ESR1 mutation and cfDNA concentration were significant for PFS (p&#x2009;=&#x2009;0.027 and 0.006, respectively). In conclusion, assessment of ESR1 mutation and cfDNA concentration could be useful in predicting prognosis for HR-MBCs.},
}
@article {pmid32016319,
year = {2020},
author = {Banchi, E and Ametrano, CG and Greco, S and Stanković, D and Muggia, L and Pallavicini, A},
title = {PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding.},
journal = {Database : the journal of biological databases and curation},
volume = {2020},
number = {},
pages = {},
pmid = {32016319},
issn = {1758-0463},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Intergenic/*genetics ; DNA, Plant/*genetics ; Databases, Genetic ; Plants/classification/*genetics ; },
abstract = {DNA metabarcoding combines DNA barcoding with high-throughput sequencing to identify different taxa within environmental communities. The ITS has already been proposed and widely used as universal barcode marker for plants, but a comprehensive, updated and accurate reference dataset of plant ITS sequences has not been available so far. Here, we constructed reference datasets of Viridiplantae ITS1, ITS2 and entire ITS sequences including both Chlorophyta and Streptophyta. The sequences were retrieved from NCBI, and the ITS region was extracted. The sequences underwent identity check to remove misidentified records and were clustered at 99% identity to reduce redundancy and computational effort. For this step, we developed a script called 'better clustering for QIIME' (bc4q) to ensure that the representative sequences are chosen according to the composition of the cluster at a different taxonomic level. The three datasets obtained with the bc4q script are PLANiTS1 (100 224 sequences), PLANiTS2 (96 771 sequences) and PLANiTS (97 550 sequences), and all are pre-formatted for QIIME, being this the most used bioinformatic pipeline for metabarcoding analysis. Being curated and updated reference databases, PLANiTS1, PLANiTS2 and PLANiTS are proposed as a reliable, pivotal first step for a general standardization of plant DNA metabarcoding studies. The bc4q script is presented as a new tool useful in each research dealing with sequences clustering. Database URL: https://github.com/apallavicini/bc4q; https://github.com/apallavicini/PLANiTS.},
}
@article {pmid32015955,
year = {2020},
author = {Dev, SA and Sijimol, K and Prathibha, PS and Sreekumar, VB and Muralidharan, EM},
title = {DNA barcoding as a valuable molecular tool for the certification of planting materials in bamboo.},
journal = {3 Biotech},
volume = {10},
number = {2},
pages = {59},
pmid = {32015955},
issn = {2190-572X},
abstract = {DNA barcodes developed for selected commercially important bamboo species can be utilized for the certification of planting stock in bamboo nurseries in absence of discriminatory features at the juvenile stage. Planting materials such as micropropagated plantlets, rhizome transplants and culm cuttings, generated at nursery level are directly procured for establishment of commercial plantations without any further verification. Very often misidentification and mixing up occur at nursery level and the error is not discovered until several years have passed. The present study evaluated the potentiality of seven Consortium for Barcode of Life (CBOL) recommended standard DNA barcode regions in commercially important bamboo species of India. Among the analyzed barcode regions, multiple sequence alignment (MSA) of psbA-trnH barcode region showed species-specific nucleotide differences in the studied bamboo taxa. The major nucleotide changes observed were transitions/transversions as well as insertions/deletions of nucleotides. Even though species-specific mononucleotide differences could be identified for most of the studied bamboo taxa, a small amount of sequence similarities were found in some of the Dendrocalamus and Bambusa species, which were grouped together in tree-based analysis. In subtribe Melocanninae, Ochlandra travancorica, Melocanna baccifera and M. clarkei showed unique species-specific psbA-trnH barcodes. Similarly, in the genus Oxytenanthera, unique species-specific psbA-trnH barcodes were obtained for O. monadelpha and O. parvifolia. Thus psbA-trnH barcode region generated distinct species-specific barcodes for commercial bamboo species in genera Bambusa, Dendrocalamus, Melocanna, Oxytenanthera as well as Ochlandra. Any national certification agency set up for the purpose can utilize psbA-trnH DNA barcode region to tag species identity and to establish the authenticity of multiplied planting materials in bamboos.},
}
@article {pmid32015666,
year = {2020},
author = {Janssens, SB and Couvreur, TLP and Mertens, A and Dauby, G and Dagallier, LMJ and Vanden Abeele, S and Vandelook, F and Mascarello, M and Beeckman, H and Sosef, M and Droissart, V and van der Bank, M and Maurin, O and Hawthorne, W and Marshall, C and Réjou-Méchain, M and Beina, D and Baya, F and Merckx, V and Verstraete, B and Hardy, O},
title = {A large-scale species level dated angiosperm phylogeny for evolutionary and ecological analyses.},
journal = {Biodiversity data journal},
volume = {8},
number = {},
pages = {e39677},
pmid = {32015666},
issn = {1314-2828},
abstract = {Phylogenies are a central and indispensable tool for evolutionary and ecological research. Even though most angiosperm families are well investigated from a phylogenetic point of view, there are far less possibilities to carry out large-scale meta-analyses at order level or higher. Here, we reconstructed a large-scale dated phylogeny including nearly 1/8th of all angiosperm species, based on two plastid barcoding genes, matK (incl. trnK) and rbcL. Novel sequences were generated for several species, while the rest of the data were mined from GenBank. The resulting tree was dated using 56 angiosperm fossils as calibration points. The resulting megaphylogeny is one of the largest dated phylogenetic tree of angiosperms yet, consisting of 36,101 sampled species, representing 8,399 genera, 426 families and all orders. This novel framework will be useful for investigating different broad scale research questions in ecological and evolutionary biology.},
}
@article {pmid32013396,
year = {2020},
author = {Zhang, D and Cai, L and Bian, F and Kong, T and Zhao, Y},
title = {Label-Free Quantifications of Multiplexed Mycotoxins by G-Quadruplex Based on Photonic Barcodes.},
journal = {Analytical chemistry},
volume = {92},
number = {4},
pages = {2891-2895},
doi = {10.1021/acs.analchem.9b05213},
pmid = {32013396},
issn = {1520-6882},
mesh = {Aptamers, Nucleotide/chemistry ; Benzothiazoles/chemistry ; Biosensing Techniques ; Fluorescent Dyes/chemistry ; G-Quadruplexes ; Mycotoxins/*analysis ; Particle Size ; *Photons ; Surface Properties ; },
abstract = {Multiplexed quantification of mycotoxins is of great significance in food safety. Here, novel photonic crystal (PhC) barcodes with G-quadruplex aptamer encapsulated for label-free multiplex mycotoxins quantification are developed. The probes are immobilized on PhC barcodes to form a molecular beacon (MB), which contains the sequences of mycotoxin aptamers and a G-quadruplex. In the presence of the target, the hairpin structure of MB would open and the region of the G-quadruplex is exposed, which subsequently combines with Thioflavin T (ThT) to produce fluorescence. The relative fluorescence intensity increased as the mycotoxins concentration increased in a linear range from 1.0 pg/mL to 100 ng/mL. Moreover, the multiplexed mycotoxins quantification could be achieved by tuning the structural color of the PhC barcodes. We demonstrate that this method with high accuracy and specificity for multiplexed detection of mycotoxins, with the sensitivity of the detection as low as 0.70 pg/mL. Our results show that G-quadruplex-encapsulated PhC barcodes offer a novel simple and label-free pathway toward the multiplex screen assay of mycotoxins for food safety.},
}
@article {pmid32012388,
year = {2020},
author = {Dufresnes, C and Nicieza, AG and Litvinchuk, SN and Rodrigues, N and Jeffries, DL and Vences, M and Perrin, N and Martínez-Solano, &#xcd;},
title = {Are glacial refugia hotspots of speciation and cytonuclear discordances? Answers from the genomic phylogeography of Spanish common frogs.},
journal = {Molecular ecology},
volume = {29},
number = {5},
pages = {986-1000},
doi = {10.1111/mec.15368},
pmid = {32012388},
issn = {1365-294X},
mesh = {Animals ; Cell Nucleus/genetics ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; *Genetic Speciation ; *Genetics, Population ; Ice Cover ; *Phylogeography ; Polymorphism, Single Nucleotide ; Rana temporaria/*genetics ; *Refugium ; Spain ; },
abstract = {Subdivided Pleistocene glacial refugia, best known as "refugia within refugia", provided opportunities for diverging populations to evolve into incipient species and/or to hybridize and merge following range shifts tracking the climatic fluctuations, potentially promoting extensive cytonuclear discordances and "ghost" mtDNA lineages. Here, we tested which of these opposing evolutionary outcomes prevails in northern Iberian areas hosting multiple historical refugia of common frogs (Rana cf. temporaria), based on a genomic phylogeography approach (mtDNA barcoding and RAD-sequencing). We found evidence for both incipient speciation events and massive cytonuclear discordances. On the one hand, populations from northwestern Spain (Galicia and Asturias, assigned to the regional endemic R. parvipalmata), are deeply-diverged at mitochondrial and nuclear genomes (~4 My of independent evolution), and barely admix with northeastern populations (assigned to R. temporaria sensu stricto) across a narrow hybrid zone (~25 km) located in the Cantabrian Mountains, suggesting that they represent distinct species. On the other hand, the most divergent mtDNA clade, widespread in Cantabria and the Basque country, shares its nuclear genome with other R. temporaria s. s. lineages. Patterns of population expansions and isolation-by-distance among these populations are consistent with past mitochondrial capture and/or drift in generating and maintaining this ghost mitochondrial lineage. This remarkable case study emphasizes the complex evolutionary history that shaped the present genetic diversity of refugial populations, and stresses the need to revisit their phylogeography by genomic approaches, in order to make informed taxonomic inferences.},
}
@article {pmid32008996,
year = {2020},
author = {Schulz, A and Karger, A and Bettin, B and Eisenbarth, A and Sas, MA and Silaghi, C and Groschup, MH},
title = {Molecular discrimination of Hyalomma tick species serving as reservoirs and vectors for Crimean-Congo hemorrhagic fever virus in sub-Saharan Africa.},
journal = {Ticks and tick-borne diseases},
volume = {11},
number = {3},
pages = {101382},
doi = {10.1016/j.ttbdis.2020.101382},
pmid = {32008996},
issn = {1877-9603},
mesh = {Africa South of the Sahara ; Animals ; Arachnid Vectors/*classification/virology ; Disease Reservoirs/*classification/virology ; Hemorrhagic Fever Virus, Crimean-Congo/*physiology ; Hemorrhagic Fever, Crimean/transmission ; Ixodidae/*classification/genetics ; Mass Spectrometry/*veterinary ; Polymerase Chain Reaction/*veterinary ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*veterinary ; },
abstract = {The species identification of tick vectors of Crimean-Congo hemorrhagic fever virus (CCHFV), especially Hyalomma (H.) species, is a prerequisite to understand the eco-epidemiology of this disease and to reveal vector and virus reservoir species. However, the morphologic species discrimination can be difficult for damaged or blood-fed ticks and in case of species intercrosses. Therefore, we used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and restriction fragment length polymorphism (RFLP) analysis to distinguish the most common Hyalomma species from sub-Saharan Africa (H. truncatum, H. rufipes and H. dromedarii). Within the last years, MALDI-TOF MS analysis based on tick leg proteins has been shown to be a reliable method to distinguish several tick species. For this purpose, a reference spectral library of several European, American and African tick species was established. In this study, six different Hyalomma species were tested, all of which were all clearly distinguishable by mass spectrometric analyses. Moreover, MALDI TOF- MS was able to confirm morphologic findings where sequencing provided ambiguous results. In addition, a polymerase chain reaction (PCR) based on the CO1 gene amplification of ticks has been developed for the unequivocal species identification by amplicon sequencing and specific restriction endonuclease cleavage pattern analysis. RFLP proved to be a feasible auxiliary discrimination tool for selected Hyalomma species when access to sequencing methods is not available, as for instance during field studies.},
}
@article {pmid32006229,
year = {2020},
author = {Pérez-Bañón, C and Rojas, C and Vargas, M and Mengual, X and Rojo, S},
title = {A world review of reported myiases caused by flower flies (Diptera: Syrphidae), including the first case of human myiasis from Palpada scutellaris (Fabricius, 1805).},
journal = {Parasitology research},
volume = {119},
number = {3},
pages = {815-840},
pmid = {32006229},
issn = {1432-1955},
mesh = {Animals ; Costa Rica ; Diptera/classification/cytology/*physiology/ultrastructure ; Feces/parasitology ; Female ; Humans ; Larva/classification/cytology/physiology/ultrastructure ; Middle Aged ; Myiasis/*parasitology/pathology/physiopathology ; },
abstract = {Rat-tailed larvae of the syrphid species Palpada scutellaris (Fabricius, 1805) are documented causing an enteric human myiasis in Costa Rica. This is the first time that the genus Palpada is recorded as a human myiasis agent. We report a 68-year-old woman with intestinal pain and bloody diarrhea with several live Palpada larvae present in the stool. Using molecular techniques (DNA barcodes) and both electronic and optical microscopy to study the external morphology, the preimaginal stages of the fly were unambiguously identified. An identification key to all syrphid genera actually known as agents of human and animal myiases is provided for larvae, puparia, and adults. Moreover, a critical world review of more than 100 references of Syrphidae as myiasis agents is also given, with emphasis on the species with rat-tailed larvae.},
}
@article {pmid32005923,
year = {2020},
author = {Jacobs, S and Ausema, A and Zwart, E and Weersing, E and Kingma, MJ and El Menshawi, YAS and de Haan, G and Bystrykh, LV and Belderbos, ME},
title = {Correction: Quantitative distribution of patient-derived leukemia clones in murine xenografts revealed by cellular barcodes.},
journal = {Leukemia},
volume = {34},
number = {7},
pages = {1974},
doi = {10.1038/s41375-020-0722-3},
pmid = {32005923},
issn = {1476-5551},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}
@article {pmid32005143,
year = {2020},
author = {Duan, H and Guo, J and Xuan, L and Wang, Z and Li, M and Yin, Y and Yang, Y},
title = {Comparative chloroplast genomics of the genus Taxodium.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {114},
pmid = {32005143},
issn = {1471-2164},
support = {31700588//National Natural Science Foundation of China/ ; JSPKLB201842//Jiangsu Key Laboratory for the Research and Utilization of Plant Resources/ ; BK20160601//Natural Science Foundation of Jiangsu Province/ ; kfj-brsn-2018-6-003//Biological Resources Service Network/ ; },
mesh = {Chloroplasts/*genetics ; Evolution, Molecular ; Genetic Variation ; Genome Size ; Genome, Chloroplast ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Sequence Analysis, DNA/*methods ; Taxodium/*classification/genetics ; },
abstract = {BACKGROUND: Chloroplast (cp) genome information would facilitate the development and utilization of Taxodium resources. However, cp genome characteristics of Taxodium were poorly understood.<br><br>RESULTS: We determined the complete cp genome sequences of T. distichum, T. mucronatum, and T. ascendens. The cp genomes are 131,947&#x2009;bp to 132,613&#x2009;bp in length, encode 120 genes with the same order, and lack typical inverted repeat (IR) regions. The longest small IR, a 282&#x2009;bp trnQ-containing IR, were involved in the formation of isomers. Comparative analysis of the 3 cp genomes showed that 91.57% of the indels resulted in the periodic variation of tandem repeat (TR) motifs and 72.46% single nucleotide polymorphisms (SNPs) located closely to TRs, suggesting a relationship between TRs and mutational dynamics. Eleven hypervariable regions were identified as candidates for DNA barcode development. Hypothetical cp open reading frame 1(Ycf1) was the only one gene that has an indel in coding DNA sequence, and the indel is composed of a long TR. When extended to cupressophytes, ycf1 genes have undergone a universal insertion of TRs accompanied by extreme length expansion. Meanwhile, ycf1 also located in rearrangement endpoints of cupressophyte cp genomes. All these characteristics highlight the important role of repeats in the evolution of cp genomes.<br><br>CONCLUSIONS: This study added new evidence for the role of repeats in the dynamics mechanism of cp genome mutation and rearrangement. Moreover, the information of TRs and hypervariable regions would provide reliable molecular resources for future research focusing on the infrageneric taxa identification, phylogenetic resolution, population structure and biodiversity for the genus Taxodium and Cupressophytes.},
}
@article {pmid32004478,
year = {2020},
author = {Hurley, K and Ding, J and Villacorta-Martin, C and Herriges, MJ and Jacob, A and Vedaie, M and Alysandratos, KD and Sun, YL and Lin, C and Werder, RB and Huang, J and Wilson, AA and Mithal, A and Mostoslavsky, G and Oglesby, I and Caballero, IS and Guttentag, SH and Ahangari, F and Kaminski, N and Rodriguez-Fraticelli, A and Camargo, F and Bar-Joseph, Z and Kotton, DN},
title = {Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors.},
journal = {Cell stem cell},
volume = {26},
number = {4},
pages = {593-608.e8},
pmid = {32004478},
issn = {1875-9777},
support = {R01 HL128172/HL/NHLBI NIH HHS/United States ; R01 GM108807/GM/NIGMS NIH HHS/United States ; TL1 TR001410/TR/NCATS NIH HHS/United States ; T32 HL007035/HL/NHLBI NIH HHS/United States ; R01 GM122096/GM/NIGMS NIH HHS/United States ; P01 HL131477/HL/NHLBI NIH HHS/United States ; F30 HL142169/HL/NHLBI NIH HHS/United States ; R01 HL095993/HL/NHLBI NIH HHS/United States ; F31 HL134274/HL/NHLBI NIH HHS/United States ; U01 HL134766/HL/NHLBI NIH HHS/United States ; R01 HL122442/HL/NHLBI NIH HHS/United States ; UL1 TR001430/TR/NCATS NIH HHS/United States ; U01 TR001810/TR/NCATS NIH HHS/United States ; K99 HL146983/HL/NHLBI NIH HHS/United States ; U24 HL148865/HL/NHLBI NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; R24 HL123828/HL/NHLBI NIH HHS/United States ; OT2 OD026682/OD/NIH HHS/United States ; U01 HL134745/HL/NHLBI NIH HHS/United States ; },
mesh = {Alveolar Epithelial Cells ; Cell Differentiation ; Humans ; *Lung ; *Pluripotent Stem Cells ; Pulmonary Alveoli ; },
abstract = {Alveolar epithelial type 2 cells (AEC2s) are the facultative progenitors responsible for maintaining lung alveoli throughout life but are difficult to isolate from patients. Here, we engineer AEC2s from human pluripotent stem cells (PSCs) in vitro and use time-series single-cell RNA sequencing with lentiviral barcoding to profile the kinetics of their differentiation in comparison to primary fetal and adult AEC2 benchmarks. We observe bifurcating cell-fate trajectories as primordial lung progenitors differentiate in vitro, with some progeny reaching their AEC2 fate target, while others diverge to alternative non-lung endodermal fates. We develop a Continuous State Hidden Markov model to identify the timing and type of signals, such as overexuberant Wnt responses, that induce some early multipotent NKX2-1[+] progenitors to lose lung fate. Finally, we find that this initial developmental plasticity is regulatable and subsides over time, ultimately resulting in PSC-derived AEC2s that exhibit a stable phenotype and nearly limitless self-renewal capacity.},
}
@article {pmid32004351,
year = {2020},
author = {Bartolini, I and Rivera, J and Nolazco, N and Olórtegui, A},
title = {Towards the implementation of a DNA barcode library for the identification of Peruvian species of Anastrepha (Diptera: Tephritidae).},
journal = {PloS one},
volume = {15},
number = {1},
pages = {e0228136},
pmid = {32004351},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Phylogeny ; Tephritidae/*classification/genetics ; },
abstract = {The genus Anastrepha is a diverse lineage of fruit-damaging tephritid flies widespread across the Neotropical Region. Accurate taxonomic identification of these flies is therefore of paramount importance in agricultural contexts. DNA barcoding libraries are molecular-based tools based on a short sequence of the mitochondrial COI gene enabling rapid taxonomic identification of biological species. In this study, we evaluate the utility of this method for species identification of Peruvian species of Anastrepha and assemble a preliminary barcode profile for the group. We obtained 73 individual sequences representing the 15 most common species, 13 of which were either assigned to previously recognized or newly established BINs. Intraspecific genetic divergence between sampled species averaged 1.01% (range 0-3.3%), whereas maximum interspecific values averaged 8.67 (range 8.26-17.12%). DNA barcoding was found to be an effective method to discriminate between many Peruvian species of Anastrepha that were tested, except for most species of the fraterculus species group, which were all assigned to the same BIN as they shared similar and, in some cases, identical barcodes. We complemented this newly produced dataset with 86 published sequences to build a DNA barcoding library of 159 sequences representing 56 Peruvian species of Anastrepha (approx. 58% of species reported from that country). We conclude that DNA barcoding is an effective method to distinguish among Peruvian species of Anastrepha outside the fraterculus group, and that complementary methods (e.g., morphometrics, additional genetic markers) would be desirable to assist sensu stricto species identification for phytosanitary surveillance and management practices of this important group of pestiferous flies.},
}
@article {pmid32002333,
year = {2020},
author = {Janik, P and Ronikier, M and Ronikier, A},
title = {New protocol for successful isolation and amplification of DNA from exiguous fractions of specimens: a tool to overcome the basic obstacle in molecular analyses of myxomycetes.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e8406},
pmid = {32002333},
issn = {2167-8359},
abstract = {Herbarium collections provide an essential basis for a wide array of biological research and, with development of DNA-based methods, they have become an invaluable material for genetic analyses. Yet, the use of such material is hindered by technical limitations related to DNA degradation and to quantity of biological material. The latter is inherent for some biological groups, as best exemplified by myxomycetes which form minute sporophores. It is estimated that ca. two-thirds of myxomycete taxa are represented by extremely scanty material. As DNA isolation methods applied so far in myxomycete studies require destructive sampling of many sporophores, a large part of described diversity of the group remains unavailable for phylogenetic studies or barcoding. Here, we tested several procedures of DNA isolation and amplification to seek for an efficient and possibly non-destructive method of sampling. Tests were based on herbarium specimens of 19 species representing different taxonomic orders. We assayed several variants of isolation based on silica gel membrane columns, and a newly designed procedure using highly reduced amount of biological material (small portion of spores), based on fine disruption of spores and direct PCR. While the most frequently used column-based method led to PCR success in 89.5% of samples when a large amount of material was used, its performance dropped to 52% when based on single sporophores. Single sporophores provided amplicons in 89.5% of samples when using a kit dedicated to low-amount DNA samples. Our new procedure appeared the most effective (94.7%) while it used only a small fraction of spores, being nearly non-destructive; it was also the most cost-effective. We thus demonstrate that combination of adequate handling of spore micro-disruption coupled with application of direct PCR can be an efficient way to circumvent technical limitations for genetic studies in myxomycetes and thus can substantially improve taxon sampling for phylogeny and barcoding. Additionally, this approach gives a unique possibility to apply both molecular and morphological assays to the same structure (sporophore), which then can be further stored as documentation.},
}
@article {pmid32002013,
year = {2020},
author = {Goltz, NC and Awad, J and Moore, MR and Talamas, EJ},
title = {A fortuitous find: a unique haplotype of Ooencyrtus nezarae Ishii (Encyrtidae: Encyrtinae) discovered in Florida.},
journal = {Biodiversity data journal},
volume = {8},
number = {},
pages = {e36440},
pmid = {32002013},
issn = {1314-2828},
abstract = {The adventive arrival of biological control agents circumvents the regulatory process by introducing exotic species to control invasive pests and is generally followed by post hoc risk evaluation. The bean plataspid, Megacopta cribraria (Fabricius) (Hemiptera: Plataspidae), is an invasive pest of leguminous crops in the south-eastern United States that was eventually followed by two parasitoid wasps from its range in the eastern hemisphere, Paratelenomus saccharalis (Dodd) (Scelionidae) and Ooencyrtus nezarae Ishii (Encyrtidae). In North Central Florida, sentinel egg masses, intended to capture Paratelenomus saccharalis, instead yielded Ooencyrtus nezarae, which was previously known only from Alabama (Ademokoya et al. 2018). Two generations of O. nezarae were subsequently reared in the laboratory. COI sequences from the Florida population of O. nezarae differed by 1.3% from the Alabama population and the presence of a different haplotype suggests the possibility of a separate introduction. Laboratory parasitism rates, sex ratios, morphology, molecular diagnosis and implications for agriculture are discussed.},
}
@article {pmid32000838,
year = {2020},
author = {Jackson, JL and Finch, NA and Baker, MC and Kachergus, JM and DeJesus-Hernandez, M and Pereira, K and Christopher, E and Prudencio, M and Heckman, MG and Thompson, EA and Dickson, DW and Shah, J and Oskarsson, B and Petrucelli, L and Rademakers, R and van Blitterswijk, M},
title = {Elevated methylation levels, reduced expression levels, and frequent contractions in a clinical cohort of C9orf72 expansion carriers.},
journal = {Molecular neurodegeneration},
volume = {15},
number = {1},
pages = {7},
pmid = {32000838},
issn = {1750-1326},
support = {R35 NS097273/NS/NINDS NIH HHS/United States ; P01 NS084974/NH/NIH HHS/United States ; R35 NS097261/NS/NINDS NIH HHS/United States ; R21 NS099631/NS/NINDS NIH HHS/United States ; R35 NS097273/NH/NIH HHS/United States ; P01 NS084974/NS/NINDS NIH HHS/United States ; P01 NS099114/NH/NIH HHS/United States ; R35 NS097261/NH/NIH HHS/United States ; R21 NS099631/NH/NIH HHS/United States ; },
mesh = {Aged ; Amyotrophic Lateral Sclerosis/*genetics ; C9orf72 Protein/*genetics ; Cohort Studies ; DNA Methylation/genetics ; DNA Repeat Expansion ; Female ; Frontotemporal Dementia/*genetics ; Heterozygote ; Humans ; Male ; Middle Aged ; Promoter Regions, Genetic/genetics ; },
abstract = {BACKGROUND: A repeat expansion in the C9orf72-SMCR8 complex subunit (C9orf72) is the most common genetic cause of two debilitating neurodegenerative diseases: amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Currently, much remains unknown about which variables may modify these diseases. We sought to investigate associations between C9orf72 promoter methylation, RNA expression levels, and repeat length, their potential effects on disease features, as well as changes over time and within families.<br><br>METHODS: All samples were obtained through the ALS Center at Mayo Clinic Florida. Our primary cohort included 75 unrelated patients with an expanded C9orf72 repeat, 33 patients who did not possess this expansion, and 20 control subjects without neurodegenerative diseases. Additionally, 67 members from 17 independent C9orf72 families were selected of whom 33 harbored this expansion. Longitudinally collected samples were available for 35 C9orf72 expansion carriers. To increase our understanding of C9orf72-related diseases, we performed quantitative methylation-sensitive restriction enzyme-based assays, digital molecular barcoding, quantitative real-time PCR, and Southern blotting.<br><br>RESULTS: In our primary cohort, higher methylation levels were observed in patients with a C9orf72 repeat expansion than in patients without this expansion (p&#x2009;=&#x2009;1.7e-13) or in control subjects (p&#x2009;=&#x2009;3.3e-07). Moreover, we discovered that an increase in methylation levels was associated with a decrease in total C9orf72 transcript levels (p&#x2009;=&#x2009;5.5e-05). These findings aligned with our observation that C9orf72 expansion carriers had lower expression levels of total C9orf72 transcripts than patients lacking this expansion (p&#x2009;=&#x2009;3.7e-07) or control subjects (p&#x2009;=&#x2009;9.1e-05). We also detected an elevation of transcripts containing intron 1a (upstream of the repeat) in patients carrying a C9orf72 repeat expansion compared to (disease) controls (p&#x2009;&#x2264;&#x2009;0.01), an indication of abortive transcripts and/or a switch in transcription start site usage. While methylation and expression levels were relatively stable over time, fluctuations were seen in repeat length. Interestingly, contractions occurred frequently in parent-offspring transmissions (>&#x2009;50%), especially in paternal transmissions. Furthermore, smaller repeat lengths were detected in currently unaffected individuals than in affected individuals (p&#x2009;=&#x2009;8.9e-04) and they were associated with an earlier age at collection (p&#x2009;=&#x2009;0.008).<br><br>CONCLUSIONS: In blood from C9orf72 expansion carriers, we found elevated methylation levels, reduced expression levels, and unstable expansions that tend to contract in successive generations, arguing against anticipation.},
}
@article {pmid32000541,
year = {2020},
author = {Westhaus, A and Cabanes-Creus, M and Rybicki, A and Baltazar, G and Navarro, RG and Zhu, E and Drouyer, M and Knight, M and Albu, RF and Ng, BH and Kalajdzic, P and Kwiatek, M and Hsu, K and Santilli, G and Gold, W and Kramer, B and Gonzalez-Cordero, A and Thrasher, AJ and Alexander, IE and Lisowski, L},
title = {High-Throughput In Vitro, Ex Vivo, and In Vivo Screen of Adeno-Associated Virus Vectors Based on Physical and Functional Transduction.},
journal = {Human gene therapy},
volume = {31},
number = {9-10},
pages = {575-589},
pmid = {32000541},
issn = {1557-7422},
support = {104807/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; /DH_/Department of Health/United Kingdom ; },
mesh = {Animals ; Capsid/metabolism ; Cell Line ; Cell Line, Tumor ; Cells, Cultured ; DNA, Viral ; Dependovirus/*genetics ; Female ; Fibroblasts ; Gene Transfer Techniques ; Genetic Therapy ; Genetic Vectors/*genetics ; HeLa Cells ; High-Throughput Nucleotide Sequencing ; High-Throughput Screening Assays/*methods ; Humans ; Induced Pluripotent Stem Cells ; Male ; Mice ; Receptor, EphB2 ; T-Lymphocytes ; Transduction, Genetic ; Transgenes ; },
abstract = {Adeno-associated virus (AAV) vectors are quickly becoming the vectors of choice for therapeutic gene delivery. To date, hundreds of natural isolates and bioengineered variants have been reported. While factors such as high production titer and low immunoreactivity are important to consider, the ability to deliver the genetic payload (physical transduction) and to drive high transgene expression (functional transduction) remains the most important feature when selecting AAV variants for clinical applications. Reporter expression assays are the most commonly used methods for determining vector fitness. However, such approaches are time consuming and become impractical when evaluating a large number of variants. Limited access to primary human tissues or challenging model systems further complicates vector testing. To address this problem, convenient high-throughput methods based on next-generation sequencing (NGS) are being developed. To this end, we built an AAV Testing Kit that allows inherent flexibility in regard to number and type of AAV variants included, and is compatible with in vitro, ex vivo, and in vivo applications. The Testing Kit presented here consists of a mix of 30 known AAVs where each variant encodes a CMV-eGFP cassette and a unique barcode in the 3'-untranslated region of the eGFP gene, allowing NGS-barcode analysis at both the DNA and RNA/cDNA levels. To validate the AAV Testing Kit, individually packaged barcoded variants were mixed at an equal ratio and used to transduce cells/tissues of interest. DNA and RNA/cDNA were extracted and subsequently analyzed by NGS to determine the physical/functional transduction efficiencies. We were able to assess the transduction efficiencies of immortalized cells, primary cells, and induced pluripotent stem cells in vitro, as well as in vivo transduction in naïve mice and a xenograft liver model. Importantly, while our data validated previously reported transduction characteristics of individual capsids, we also identified novel previously unknown tropisms for some AAV variants.},
}
@article {pmid31999713,
year = {2020},
author = {Hausmann, A and Diller, J and Moriniere, J and Höcherl, A and Floren, A and Haszprunar, G},
title = {DNA barcoding of fogged caterpillars in Peru: A novel approach for unveiling host-plant relationships of tropical moths (Insecta, Lepidoptera).},
journal = {PloS one},
volume = {15},
number = {1},
pages = {e0224188},
pmid = {31999713},
issn = {1932-6203},
mesh = {Animals ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing ; Insecta/classification/genetics ; Larva/genetics ; Moths/classification/*genetics ; Peru ; *Phylogeny ; Plants/classification/genetics ; Species Specificity ; Tropical Climate ; },
abstract = {The present study aimed to perform molecular identification of lepidopteran larvae from canopy fogging including gut-content analyses. A total of 130 lepidopteran larvae were selected from 37 fogging samples at the Panguana station, district Yuyapichis, province Puerto Inca, department Huánuco, Peru. Target trees were pre-identified and subsequently submitted to molecular confirmation of identity with three markers (rbcL, psbA and trnL-F). The COI gene of 119 lepidopteran larvae was successfully sequenced and found to belong to 92 species: Comparison of DNA barcodes with the reference database of adult moths resulted in 65 (55%) matches at species level, 32 (27%) at genus level, 19 (16%) at subfamily or family level, three just to order level. Three larvae could not be assigned to a family. For these larvae the fogged target tree now suggests a potential host-plant relationship. Molecular gut content analysis, based on High-Throughput-Sequencing was successfully tested for ten larvae corroborating feeding on the target plant in some cases but elucidating several other cases of potential 'alternative feeding'. We propose a larger-scale approach using this rapid and efficient method including molecular gut-content analyses for comprehensively testing the ratio of 'alternative feeders' and pitfalls caused by collateral fogging of larvae from neighboring trees.},
}
@article {pmid31997886,
year = {2020},
author = {Englmaier, GK and Tesfaye, G and Bogutskaya, NG},
title = {A new species of Enteromius (Actinopterygii, Cyprinidae, Smiliogastrinae) from the Awash River, Ethiopia, and the re-establishment of E. akakianus.},
journal = {ZooKeys},
volume = {902},
number = {},
pages = {107-150},
pmid = {31997886},
issn = {1313-2989},
support = {M 2183/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {In the present study, populations of small-sized smiliogastrin barbs with a thickened and serrated last simple dorsal-fin ray distributed in the Main Ethiopian Rift were analysed. An integrated approach combining genetic markers and a variety of morphological methods based on a wide set of characters, including osteology and sensory canals, proved to be very productive for taxonomy in this group of fishes. The results showed that Ethiopian Enteromius species with a serrated dorsal-fin ray are distant from the true E. paludinosus (with E. longicauda as a synonym) and the so-called E. paludinosus complex involves several supposedly valid species with two distinct species occurring in the Main Ethiopian Rift area. A new species, Enteromius yardiensis sp. nov., is described from the Afar Depression in the north-eastern part of the Northern Main Ethiopian Rift. Enteromius akakianus is resurrected as a valid species including populations from the Central Main Ethiopian Rift (basins of lakes Langano, Ziway, and Awasa). No genetic data were available for E. akakianus from its type locality. Enteromius yardiensis sp. nov. is clearly distant from E. akakianus from the Central Main Ethiopian Rift by CO1 and cytb barcodes: pairwise distances between the new species and the Ethiopian congeners were 5.4 % to 11.0 %. Morphologically, the new species most clearly differs from all examined Ethiopian congeners by three specialisations which are unique in the group: the absence of the anterior barbel, the absence of the medial branch of the supraorbital sensory canal, and few, 1-3, commonly two, scale rows between the lateral line and the anus.},
}
@article {pmid31997112,
year = {2020},
author = {Zheng, G and Wei, L and Ma, L and Wu, Z and Gu, C and Chen, K},
title = {Comparative analyses of chloroplast genomes from 13 Lagerstroemia (Lythraceae) species: identification of highly divergent regions and inference of phylogenetic relationships.},
journal = {Plant molecular biology},
volume = {102},
number = {6},
pages = {659-676},
pmid = {31997112},
issn = {1573-5028},
support = {LY17C160003//Zhejiang Provincial Natural Science Foundation of China/ ; },
mesh = {Base Sequence ; Chloroplasts/*genetics ; Databases, Nucleic Acid ; Evolution, Molecular ; Genome, Chloroplast/*genetics ; Lagerstroemia/*classification/*genetics ; Molecular Sequence Annotation ; *Phylogeny ; Plant Proteins/genetics ; Plastids ; Sequence Analysis, DNA ; },
abstract = {Seven divergence hotspots as plastid markers for DNA barcoding was selected, and the phylogeny of 13 Lagerstroemia species based on the cp genome data was reconstructed within Myrtales. The Lagerstroemia species used in this study originated in China and have high economic and ecological value. The shared interspecific morphological characteristics and intraspecific morphological variation resulting from hybridization among Lagerstroemia taxa have made resolving their classification problems and phylogenetic relationships difficult. Systematic comparative genomic analysis has been shown to resolve phylogenetic relationships. We sequenced and annotated 6 Lagerstroemia cp genomes (Lagerstroemia excelsa, Lagerstroemia limii, Lagerstroemia siamica, Lagerstroemia tomentosa, Lagerstroemia venusta, and Lagerstroemia calyculata) for the first time and combined them with previously published genomes for Lagerstroemia species. Bioinformatics was used to analyse the 13 cp genomes in terms of gene structure and organization, codon usage, contraction and expansion of inverted repeat regions, repeat structure, divergence hotspots, species pairwise Ka/Ks ratios and phylogenetic relationships. The length varied between 152,049 bp in Lagerstroemia subcostata and 152,521 bp in L. venusta. We selected seven divergence hotspots in the cp genomes that had the potential to act as plastid markers to distinguish Lagerstroemia species. The phylogenetic relationships within Myrtales inferred from the cp genomes of 13 Lagerstroemia species and 27 other Myrtales species were highly supported, which illustrated several novel relationships within Myrtales. Taken together, our results provide comprehensive chloroplast genomic resources, which can be used further for species identification and molecular breeding of Lagerstroemia species.},
}
@article {pmid31996783,
year = {2020},
author = {Rahman, MM and Norén, M and Mollah, AR and Kullander, SO},
title = {Publisher Correction: Building a DNA barcode library for the freshwater fishes of Bangladesh.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {1719},
doi = {10.1038/s41598-020-58810-0},
pmid = {31996783},
issn = {2045-2322},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}
@article {pmid31995228,
year = {2020},
author = {Cabezas, MP and Lasso-Alcalá, OM and Xavier, R and Jowers, MJ},
title = {First genetic record of the non-native muzzled blenny Omobranchus punctatus (Teleostei: Blenniidae) in the Atlantic Coast of Central and South America.},
journal = {Journal of fish biology},
volume = {96},
number = {3},
pages = {841-846},
doi = {10.1111/jfb.14268},
pmid = {31995228},
issn = {1095-8649},
support = {//Financial support came from nonprofit organizations Conservation International (USA) and Fundaci&#xf3;n La Salle de Ciencias Naturales (Venezuela) to the project Biological Assessment and Socio Economical Aspects of the Aquatic Ecosystems of the Gulf of Paria and Orinoco Delta, Venezuela under the Program AquaRAP from 2002 to 2004. M.J.J. is supported by FCT (FCT, SFRH/BPD/109148/2015) and R.X. by FCT under the Programa Operacional Potencial Humano - Quadro de Refer&#xea;ncia Estrat&#xe9;gico Nacional funds from the European Social Fund and the Portuguese Minist&#xe9;rio da Educa&#xe7;&#xe3;o e Ci&#xea;ncia (IF-FCT contract IF/00359/2015)./ ; },
mesh = {Animals ; Atlantic Ocean ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Indian Ocean ; *Introduced Species ; Perciformes/classification/*genetics ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; South America ; Venezuela ; },
abstract = {In this study we sequenced two mitochondrial (COI and 16S rRNA) and one nuclear (18S rRNA) gene fragment of an introduced muzzled blenny (Omobranchus punctatus) specimen collected from the Orinoco Delta (Gulf of Paria estuary) in Venezuela. This is the first genetic data generated for this species' introduced range in Central and South America, suggesting an introduction from the Indian Ocean.},
}
@article {pmid31993050,
year = {2019},
author = {Looney, TJ and Topacio-Hall, D and Lowman, G and Conroy, J and Morrison, C and Oh, D and Fong, L and Zhang, L},
title = {TCR Convergence in Individuals Treated With Immune Checkpoint Inhibition for Cancer.},
journal = {Frontiers in immunology},
volume = {10},
number = {},
pages = {2985},
pmid = {31993050},
issn = {1664-3224},
support = {R01 CA194511/CA/NCI NIH HHS/United States ; R01 CA223484/CA/NCI NIH HHS/United States ; U01 CA233100/CA/NCI NIH HHS/United States ; },
mesh = {Antigens, Neoplasm/immunology ; CTLA-4 Antigen/immunology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Leukocytes, Mononuclear/immunology ; Neoplasms/*immunology ; Receptors, Antigen, T-Cell/*immunology ; Receptors, Antigen, T-Cell, alpha-beta/*immunology ; T-Lymphocytes/*immunology ; },
abstract = {Tumor antigen-driven selection may expand T cells having T cell receptors (TCRs) of shared antigen specificity but different amino acid or nucleotide sequence in a process known as TCR convergence. Substitution sequencing errors introduced by TCRβ (TCRB) repertoire sequencing may create artifacts resembling TCR convergence. Given the anticipated differences in substitution error rates across different next-generation sequencing platforms, the choice of platform could be consequential. To test this, we performed TCRB sequencing on the same peripheral blood mononuclear cells (PBMC) from individuals with cancer receiving anti-CTLA-4 or anti-PD-1 using an Illumina-based approach (Sequenta) and an Ion Torrent-based approach (Oncomine TCRB-LR). While both approaches found similar TCR diversity, clonality, and clonal overlap, we found that Illumina-based sequencing resulted in higher TCR convergence than with the Ion Torrent approach. To build upon this initial observation we conducted a systematic comparison of Illumina-based TCRB sequencing assays, including those employing molecular barcodes, with the Oncomine assay, revealing differences in the frequency of convergent events, purportedly artifactual rearrangements, and sensitivity of detection. Finally, we applied the Ion Torrent-based approach to evaluate clonality and convergence in a cohort of individuals receiving anti-CTLA-4 blockade for cancer. We found that clonality and convergence independently predicted response and could be combined to improve the accuracy of a logistic regression classifier. These results demonstrate the importance of the sequencing platform in assessing TCRB convergence.},
}
@article {pmid31993022,
year = {2019},
author = {Kidd, SE and Chen, SC and Meyer, W and Halliday, CL},
title = {A New Age in Molecular Diagnostics for Invasive Fungal Disease: Are We Ready?.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2903},
pmid = {31993022},
issn = {1664-302X},
abstract = {Invasive fungal diseases (IFDs) present an increasing global burden in immunocompromised and other seriously ill populations, including those caused by pathogens which are inherently resistant or less susceptible to antifungal drugs. Early diagnosis encompassing accurate detection and identification of the causative agent and of antifungal resistance is critical for optimum patient outcomes. Many molecular-based diagnostic approaches have good clinical utility although interpretation of results should be according to clinical context. Where an IFD is in the differential diagnosis, panfungal PCR assays allow the rapid detection/identification of fungal species directly from clinical specimens with good specificity; sensitivity is also high when hyphae are seen in the specimen including in paraffin-embedded tissue. Aspergillus PCR assays on blood fractions have good utility in the screening of high risk hematology patients with high negative predictive value (NPV) and positive predictive value (PPV) of 94 and 70%, respectively, when two positive PCR results are obtained. The standardization, and commercialization of Aspergillus PCR assays has now enabled direct comparison of results between laboratories with commercial assays also offering the simultaneous detection of common azole resistance mutations. Candida PCR assays are not as well standardized with the only FDA-approved commercial system (T2Candida) detecting only the five most common species; while the T2Candida outperforms blood culture in patients with candidemia, its role in routine Candida diagnostics is not well defined. There is growing use of Mucorales-specific PCR assays to detect selected genera in blood fractions. Quantitative real-time Pneumocystis jirovecii PCRs have replaced microscopy and immunofluorescent stains in many diagnostic laboratories although distinguishing infection may be problematic in non-HIV-infected patients. For species identification of isolates, DNA barcoding with dual loci (ITS and TEF1α) offer optimal accuracy while next generation sequencing (NGS) technologies offer highly discriminatory analysis of genetic diversity including for outbreak investigation and for drug resistance characterization. Advances in molecular technologies will further enhance routine fungal diagnostics.},
}
@article {pmid31992717,
year = {2020},
author = {Wingett, SW and Andrews, S and Fraser, P and Morf, J},
title = {RNA proximity sequencing data and analysis pipeline from a human neuroblastoma nuclear transcriptome.},
journal = {Scientific data},
volume = {7},
number = {1},
pages = {35},
pmid = {31992717},
issn = {2052-4463},
mesh = {Cell Line, Tumor ; DNA Barcoding, Taxonomic ; DNA, Complementary ; Humans ; Monte Carlo Method ; Neuroblastoma/*genetics ; *RNA-Seq ; *Transcriptome ; },
abstract = {We have previously developed and described a method for measuring RNA co-locations within cells, called Proximity RNA-seq, which promises insights into RNA expression, processing, storage and translation. Here, we describe transcriptome-wide proximity RNA-seq datasets obtained from human neuroblastoma SH-SY5Y cell nuclei. To aid future users of this method, we also describe and release our analysis pipeline, CloseCall, which maps cDNA to a custom transcript annotation and allocates cDNA-linked barcodes to barcode groups. CloseCall then performs Monte Carlo simulations on the data to identify pairs of transcripts, which are co-barcoded more frequently than expected by chance. Furthermore, derived co-barcoding frequencies for individual transcripts, dubbed valency, serve as proxies for RNA density or connectivity for that given transcript. We outline how this pipeline was applied to these sequencing datasets and openly share the processed data outputs and access to a virtual machine that runs CloseCall. The resulting data specify the spatial organization of RNAs and builds hypotheses for potential regulatory relationships between RNAs.},
}
@article {pmid31992185,
year = {2020},
author = {Zhang, Y and An, D and Li, C and Zhao, Z and Wang, W},
title = {The complete chloroplast genome of greater duckweed (Spirodela polyrhiza 7498) using PacBio long reads: insights into the chloroplast evolution and transcription regulation.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {76},
pmid = {31992185},
issn = {1471-2164},
support = {31670366//National Natural Science Foundation of China/ ; },
mesh = {Araceae/*genetics/metabolism ; Chloroplasts/genetics ; Computational Biology ; Evolution, Molecular ; Gene Expression Regulation, Plant ; Genes, Plant ; *Genome, Chloroplast ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Introns ; Molecular Sequence Annotation ; Operon ; Photosynthesis/genetics ; RNA Editing ; Reproducibility of Results ; Transcription, Genetic ; },
abstract = {BACKGROUND: Duckweeds (Lemnaceae) are aquatic plants distributed all over the world. The chloroplast genome, as an efficient solar-powered reactor, is an invaluable resource to study biodiversity and to carry foreign genes. The chloroplast genome sequencing has become routine and less expensive with the delivery of high-throughput sequencing technologies, allowing us to deeply investigate genomics and transcriptomics of duckweed organelles.<br><br>RESULTS: Here, the complete chloroplast genome of Spirodela polyrhiza 7498 (SpV2) is assembled by PacBio sequencing. The length of 168,956&#x2009;bp circular genome is composed of a pair of inverted repeats of 31,844&#x2009;bp, a large single copy of 91,210&#x2009;bp and a small single copy of 14,058&#x2009;bp. Compared to the previous version (SpV1) assembled from short reads, the integrity and quality of SpV2 are improved, especially with the retrieval of two repeated fragments in ycf2 gene. There are a number of 107 unique genes, including 78 protein-coding genes, 25 tRNA genes and 4 rRNA genes. With the evidence of full-length cDNAs generated from PacBio isoform sequencing, seven genes (ycf3, clpP, atpF, rpoC1, rpl2, rps12 and ndhA) are detected to contain type-II introns. The ndhA intron has 50% more sequence divergence than the species-barcoding marker of atpF-atpH, showing the potential power to discriminate close species. A number of 37 RNA editing sites are recognized to have cytosine (C) to uracil (U) substitutions, eight of which are newly defined including six from the intergenic regions and two from the coding sequences of rpoC2 and ndhA genes. In addition, nine operon classes are identified using transcriptomic data. It is found that the operons contain multiple subunit genes encoding the same functional complexes comprising of ATP synthase, photosynthesis system, ribosomal proteins, et.al., which could be simultaneously transcribed and coordinately translated in response to the cell stimuli.<br><br>CONCLUSIONS: The understanding of the chloroplast genomics and the transcriptomics of S.polyrhiza would greatly facilitate the study of phylogenetic evolution and the application of genetically engineering duckweeds.},
}
@article {pmid31990943,
year = {2020},
author = {Smidt, EC and Páez, MZ and Vieira, LDN and Viruel, J and de Baura, VA and Balsanelli, E and de Souza, EM and Chase, MW},
title = {Characterization of sequence variability hotspots in Cranichideae plastomes (Orchidaceae, Orchidoideae).},
journal = {PloS one},
volume = {15},
number = {1},
pages = {e0227991},
pmid = {31990943},
issn = {1932-6203},
mesh = {Base Composition ; Brazil ; Chromosome Mapping ; DNA Barcoding, Taxonomic/methods ; *Gene Expression Regulation, Plant ; Gene Ontology ; *Genetic Variation ; *Genome ; Molecular Sequence Annotation ; NADH Dehydrogenase/genetics/metabolism ; Orchidaceae/classification/*genetics/metabolism ; *Phylogeny ; Plant Leaves/genetics/metabolism ; Plant Proteins/genetics/metabolism ; Plastids/*genetics ; },
abstract = {This study reports complete plastome sequences for six species of Neotropical Cranichideae and focuses on identification of the most variable regions (hotspots) in this group of orchids. These structure of these six plastomes is relatively conserved, exhibiting lengths ranging between 142,599 to 154,562 bp with 36.7% GC on average and exhibiting typical quadripartite arrangement (LSC, SSC and two IRs). Variation detected in the LSC/IR and SSC/IR junctions is explained by the loss of ndhF and ycf1 length variation. For the two genera of epiphytic clade in Spiranthinae, almost whole sets of the ndh-gene family were missing. Eight mutation hotspots were identified based on nucleotide diversity, sequence variability and parsimony-informative sites. Three of them (rps16-trnQ, trnT-trnL, rpl32-trnL) seem to be universal hotspots in the family, and the other five (trnG-trnR, trnR-atpA, trnP-psaJ, rpl32-infA, and rps15-ycf1) are described for the first time as orchid molecular hotspots. These regions have much more variation than all those used previously in phylogenetics of the group and offer useful plastid markers for phylogenetic, barcoding and population genetic studies. The use of whole plastomes or exclusive no-gap matrices also positioned with high support the holomycotrophic Rhizanthella among Orchidoideae plastomes in model-based analyses, showing the utility of plastomes for phylogenetic placement of this unusual genus.},
}
@article {pmid31988471,
year = {2020},
author = {Askary, A and Sanchez-Guardado, L and Linton, JM and Chadly, DM and Budde, MW and Cai, L and Lois, C and Elowitz, MB},
title = {Publisher Correction: In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription.},
journal = {Nature biotechnology},
volume = {38},
number = {2},
pages = {245},
doi = {10.1038/s41587-020-0432-4},
pmid = {31988471},
issn = {1546-1696},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}
@article {pmid31988118,
year = {2020},
author = {Mullokandov, G and Vijayakumar, G and Leon, P and Henry, C and Wilson, PC and Krammer, F and Palese, P and Brown, BD},
title = {High-complexity extracellular barcoding using a viral hemagglutinin.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {6},
pages = {2767-2769},
pmid = {31988118},
issn = {1091-6490},
support = {HHSN272201400008C/AI/NIAID NIH HHS/United States ; P01 AI097092/AI/NIAID NIH HHS/United States ; R01 AI128821/AI/NIAID NIH HHS/United States ; R33 CA223947/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Antibodies, Monoclonal/*analysis ; Cell Tracking/instrumentation/*methods ; Female ; Flow Cytometry/methods ; HEK293 Cells ; Hemagglutinin Glycoproteins, Influenza Virus/*analysis/genetics/metabolism ; Humans ; Melanoma/chemistry/genetics/metabolism ; Mice ; Mice, Inbred C57BL ; Orthomyxoviridae/chemistry/genetics/metabolism ; },
abstract = {While single-cell sequencing technologies have revealed tissue heterogeneity, resolving mixed cellular libraries into cellular clones is essential for many pooled screens and clonal lineage tracing. Fluorescent proteins are limited in number, while DNA barcodes can only be read after cell lysis. To overcome these limitations, we used influenza virus hemagglutinins to engineer a genetically encoded cell-surface protein barcoding system. Using antibodies paired to hemagglutinins carrying combinations of escape mutations, we developed an exponential protein barcoding system which can label 128 clones using seven antibodies. This study provides a proof of principle for a strategy to create protein-level cell barcodes that can be used in vivo in mice to track clonal populations.},
}
@article {pmid31986139,
year = {2020},
author = {Bo, QK and Zheng, XD and Chen, ZW},
title = {Feeding intensity and molecular prey identification of the common long-armed octopus, Octopus minor (Mollusca: Octopodidae) in the wild.},
journal = {PloS one},
volume = {15},
number = {1},
pages = {e0220482},
pmid = {31986139},
issn = {1932-6203},
mesh = {Animals ; Animals, Wild/*physiology ; Crustacea ; *Ecosystem ; Feeding Behavior/*physiology ; Fisheries ; Gastrointestinal Contents ; Octopodiformes/*physiology ; Perciformes ; },
abstract = {The common long-armed octopus, Octopus minor, is an important component of systems and supports the local fisheries in the coastal areas of northern China. For the fishery management and artificial breeding, especially for the management of exclusive conservation reserves, its role in the ecosystem requires assessment. Therefore, the feeding intensity of O. minor was studied from April to July 2014 when females reaching ovary maturation, and prey composition was identified from stomach contents using a DNA barcoding method. Of the 172 sampled octopuses, 66 had stomach contents that were nearly digested into pulp. On the whole, the feeding intensity of octopus remained more or less the same during the first three months and significantly decreased in July. The changes of feeding intensity were different between females and males; in females, the intensity of feeding decreased from April to July; in case of males, however, the feeding activity increased from April to June and decreased thereafter. The feeding intensity of the females was extremely greater than that of the males. O. minor was a generalist predator and based on homology searches and phylogenetic analysis, a total of 10 different taxa were identified in the stomach contents. In terms of percent composition by frequency of occurrences (%N), fishes accounted for the most of the octopuses diet (50%), followed by cephalopod (25%), crustaceans (21.7%), annelid (1.7%) and nematode (1.7%). The families of Gobiidae and Octopodidae appeared in all months and Protunidae appeared in three months. The results confirmed that Gobiidae family (45.8%, by frequency of occurrences) was an important source of food during the time when females reaching ovarian maturation. From April to July, the observed cannibalism showed an increasing trend. Controlling and reducing fishing production of Gobiidae fishes in conservation area are recommended from April to June when female octopuses are actively feeding.},
}
@article {pmid31986025,
year = {2020},
author = {Chen, F and Xue, J and Zhang, J and Bai, M and Yu, X and Fan, C and Zhao, Y},
title = {Differentiated Visualization of Single-Cell 5-Hydroxymethylpyrimidines with Microfluidic Hydrogel Encoding.},
journal = {Journal of the American Chemical Society},
volume = {142},
number = {6},
pages = {2889-2896},
doi = {10.1021/jacs.9b11393},
pmid = {31986025},
issn = {1520-5126},
mesh = {5-Methylcytosine/*analogs &amp; derivatives/metabolism ; Breast Neoplasms/metabolism/pathology ; Cell Line, Tumor ; DNA/genetics ; Epigenesis, Genetic ; Female ; Humans ; Hydrogels/*chemistry ; *Microfluidics ; Neoplasm Invasiveness ; Pentoxyl/*analogs &amp; derivatives/metabolism ; Single-Cell Analysis/*methods ; },
abstract = {5-Hydroxymethyluracil (5hmU) is found in the genomes of a diverse range of organisms as another kind of 5-hydroxymethylpyrimidine, with the exception of 5-hydroxymethylcytosine (5hmC). The biological function of 5hmU has not been well explored due to lacking both specific 5hmU recognition and single-cell analysis methods. Here we report differentiated visualization of single-cell 5hmU and 5hmC with microfluidic hydrogel encoding (sc 5hmU / 5hmC -microgel). Single cells and their genomic DNA after cell lysis can be encapsulated in individual agarose microgels. The 5hmU sites are then specifically labeled with thiophosphate for the first time, followed by labeling 5hmC with azide glucose. These labeled bases are each encoded into respective DNA barcode primers by chemical cross-linking. In situ amplification is triggered for single-molecule fluorescence visualization of single-cell 5hmU and 5hmC . On the basis of the sc 5hmU / 5hmC -microgel, we reveal cell type-specific molecular signatures of these two bases with remarkable single-cell heterogeneity. Utilizing machine learning algorithms to decode four-dimensional signatures of 5hmU / 5hmC , we visualize the discrimination of nontumorigenic, carcinoma and highly invasive breast cell lines. This strategy provides a new route to analyze and decode single-cell DNA epigenetic modifications.},
}
@article {pmid31979389,
year = {2020},
author = {Cieniewicz, E and Poplaski, V and Brunelli, M and Dombroskie, J and Fuchs, M},
title = {Two Distinct Genotypes of Spissistilus festinus (Say, 1830) (Hemiptera, Membracidae) in the United States Revealed by Phylogenetic and Morphological Analyses.},
journal = {Insects},
volume = {11},
number = {2},
pages = {},
pmid = {31979389},
issn = {2075-4450},
support = {1004285//U.S. Department of Agriculture/ ; },
abstract = {Spissistilus festinus (Say, 1830) (Hemiptera: Membracidae) is a frequent pest of leguminous crops in the Southern United States, and a vector of grapevine red blotch virus. There is currently no information on the genetic diversity of S. festinus. In this study, populations of S. festinus were collected in 2015-2017 from various crops and geographic locations in the United States, and fragments of the mitochondrial cytochrome C oxidase 1 (mt-COI) gene and the nuclear internal transcribed spacer 2 (ITS2) region were characterized by polymerase chain reaction and sequencing. Maximum-likelihood and Bayesian analyses of the mt-COI and ITS2 sequences yielded similar phylogenetic tree topologies, revealing two distinct genetic S. festinus lineages with all of the specimens from California comprising one phylogenetic clade, alongside a single GenBank entry from Arizona, and all specimens from the Southeastern United States comprising a statistically-supported distinct clade, regardless of host and year of collection. The mt-COI gene fragment showed up to 10.8% genetic distance between the two phylogenetic clades. These results suggest the existence of two genotypes within S. festinus in the United States. The only distinct morphological trait between the two genotypes was a less elevated pronotum in the representative specimens from California, compared to the representative specimens from the Southeastern United States. Since this phenotypic feature is inconspicuous, a diagnostic polymerase chain reaction targeting a variable region of the mt-COI fragment was developed to reliably distinguish between the specimens of the two genotypes of S. festinus and to facilitate their specific identification.},
}
@article {pmid31974159,
year = {2020},
author = {Weinreb, C and Rodriguez-Fraticelli, A and Camargo, FD and Klein, AM},
title = {Lineage tracing on transcriptional landscapes links state to fate during differentiation.},
journal = {Science (New York, N.Y.)},
volume = {367},
number = {6479},
pages = {},
pmid = {31974159},
issn = {1095-9203},
support = {K99 HL146983/HL/NHLBI NIH HHS/United States ; R01 HL141402/HL/NHLBI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 HL128850/HL/NHLBI NIH HHS/United States ; P01 HL131477/HL/NHLBI NIH HHS/United States ; R33 CA212697/CA/NCI NIH HHS/United States ; },
mesh = {Algorithms ; Animals ; Cell Lineage/*genetics ; DNA Barcoding, Taxonomic ; *Gene Expression ; Hematopoiesis/*genetics ; Mice ; Monocytes/cytology ; RNA-Seq ; Single-Cell Analysis/methods ; *Transcriptome ; },
abstract = {A challenge in biology is to associate molecular differences among progenitor cells with their capacity to generate mature cell types. Here, we used expressed DNA barcodes to clonally trace transcriptomes over time and applied this to study fate determination in hematopoiesis. We identified states of primed fate potential and located them on a continuous transcriptional landscape. We identified two routes of monocyte differentiation that leave an imprint on mature cells. Analysis of sister cells also revealed cells to have intrinsic fate biases not detectable by single-cell RNA sequencing. Finally, we benchmarked computational methods of dynamic inference from single-cell snapshots, showing that fate choice occurs earlier than is detected by state-of the-art algorithms and that cells progress steadily through pseudotime with precise and consistent dynamics.},
}
@article {pmid31973113,
year = {2020},
author = {Huang, J and Yu, Y and Liu, YM and Xie, DF and He, XJ and Zhou, SD},
title = {Comparative Chloroplast Genomics of Fritillaria (Liliaceae), Inferences for Phylogenetic Relationships between Fritillaria and Lilium and Plastome Evolution.},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {2},
pages = {},
pmid = {31973113},
issn = {2223-7747},
support = {31570198, 31872647//the National Natural Science Foundation of China/ ; },
abstract = {Fritillaria is a genus that has important medicinal and horticultural values. The study involved the most comprehensive chloroplast genome samples referring to Old and New World clades of Fritillaria for marker selection and phylogenetic studies. We reported and compared eleven newly sequenced whole-plastome sequences of Fritillaria which proved highly similar in overall size (151,652-152,434 bp), genome structure, gene content, and order. Comparing them with other species of Liliales (6 out of 10 families) indicated the same similarity but showed some structural variations due to the contraction or expansion of the inverted repeat (IR) regions. A/T mononucleotides, palindromic, and forward repeats were the most common types. Six hypervariable regions (rps16-trnQ, rbcL-accD, accD-psaI, psaJ-rpl33, petD-rpoA, and rpl32-trnL) were discovered based on 26 Fritillaria whole-plastomes to be potential molecular markers. Based on the plastome data that were collected from 26 Fritillaria and 21 Lilium species, a phylogenomic study was carried out with three Cardiocrinum species as outgroups. Fritillaria was sister to Lilium with a high support value, and the interspecies relationships within subgenus Fritillaria were resolved very well. The six hypervariable regions can be used as candidate DNA barcodes of Fritillaria and the phylogenomic framework can guide extensive genomic sampling for further phylogenetic analyses.},
}
@article {pmid31971776,
year = {2020},
author = {Smith, LD and Liu, Y and Zahid, MU and Canady, TD and Wang, L and Kohli, M and Cunningham, BT and Smith, AM},
title = {High-Fidelity Single Molecule Quantification in a Flow Cytometer Using Multiparametric Optical Analysis.},
journal = {ACS nano},
volume = {14},
number = {2},
pages = {2324-2335},
pmid = {31971776},
issn = {1936-086X},
support = {R00 CA153914/CA/NCI NIH HHS/United States ; R01 CA212097/CA/NCI NIH HHS/United States ; R01 CA227699/CA/NCI NIH HHS/United States ; R01 NS100019/NS/NINDS NIH HHS/United States ; },
mesh = {*Flow Cytometry ; Humans ; MicroRNAs/*analysis/genetics ; Nucleic Acids/*analysis/genetics ; *Optical Imaging ; Particle Size ; Polymerase Chain Reaction ; Surface Properties ; },
abstract = {Microfluidic techniques are widely used for high-throughput quantification and discrete analysis of micron-scale objects but are difficult to apply to molecular-scale targets. Instead, single-molecule methods primarily rely on low-throughput microscopic imaging of immobilized molecules. Here we report that commercial-grade flow cytometers can detect single nucleic acid targets following enzymatic extension and dense labeling with multiple distinct fluorophores. We focus on microRNAs, short nucleic acids that can be extended by rolling circle amplification (RCA). We labeled RCA-extended microRNAs with multicolor fluorophores to generate repetitive nucleic acid products with submicron sizes and tunable multispectral profiles. By cross-correlating the multiparametric optical features, signal-to-background ratios were amplified 1600-fold to allow single-molecule detection across 4 orders of magnitude of concentration. The limit of detection was measured to be 47 fM, which is 100-fold better than gold-standard methods based on polymerase chain reaction. Furthermore, multiparametric analysis allowed discrimination of different microRNA sequences in the same solution using distinguishable optical barcodes. Barcodes can apply both ratiometric and colorimetric signatures, which could facilitate high-dimensional multiplexing. Because of the wide availability of flow cytometers, we anticipate that this technology can provide immediate access to high-throughput multiparametric single-molecule measurements and can further be adapted to the diverse range of molecular amplification methods that are continually emerging.},
}
@article {pmid31970959,
year = {2019},
author = {Liu, MY and Liu, YL and Wu, P and Chen, Q and Zhou, SL},
title = {Determination of Place of Residence Using the Gene Information of Plants Carried by the Human Body.},
journal = {Fa yi xue za zhi},
volume = {35},
number = {6},
pages = {710-715},
doi = {10.12116/j.issn.1004-5619.2019.06.012},
pmid = {31970959},
issn = {1004-5619},
mesh = {China ; *DNA Barcoding, Taxonomic ; *Human Body ; Humans ; Lung/pathology ; Phylogeny ; *Plants/classification/genetics ; *Residence Characteristics ; Sequence Analysis, DNA ; },
abstract = {Objective To identify the plant species using the DNA sequence of plant pollen from lung tissues of a unidentified body, infer the possible long-term places of residence of the deceased according to the distribution area of the pollen in the lung tissues, therefore narrow the scope of criminal investigation and provide clues for case solving. Methods Lung tissues were extracted from the deceased, total DNA was extracted by the mCTAB method. Gene fragments of the two plant DNA barcodes, matK and rbcL, were acquired using specific primers for amplification, then sequenced. The DNA sequences of target gene fragments were acquired through bioinformatics analysis. The sequences were combined with reference sequence data. Phylogenetic analysis was made to identify the species that the DNA sequences belonged to. The places where the deceased could have lived for a long time were inferred, according to the distribution information of plant species. Results Gene fragments of 32 plant species which belonged to 31 genera of 27 families were in the lung tissues of the deceased. Among them, plants of 9 genera that had certain indicative function were mainly endemic plants from Hainan, Guangdong, Guangxi and Yunnan. These results showed that the deceased may have stayed in these areas for a long time before death. After further investigation, the victim was confirmed to have come from a county in southern Guangxi, which was in accordance with the research results. Conclusion The method of using gene information of plants from lung tissues of human bodies to infer places of residence can assist inference of the places where the deceased could have lived for a long time. The present study may also provide new ideas for locating sources of the corpses in cases with unidentified victims.},
}
@article {pmid31966334,
year = {2019},
author = {Jung, J and Yoshida, R and Kim, W},
title = {Diversity of Parasitic Peltogastrid Barnacles (Crustacea: Cirripedia: Rhizocephala) on Hermit Crabs in Korea.},
journal = {Zoological studies},
volume = {58},
number = {},
pages = {e33},
pmid = {31966334},
issn = {1810-522X},
abstract = {We performed a diversity study on parasitic barnacles (Crustacea: Cirripedia: Rhizocephala: Peltogastridae) that parasitize hermit crabs in Korea. Their morphological, ecological, molecular (cytochrome c oxidase subunit I, 16S rRNA), and biogeographical characteristics were examined. Three species were identified based on GenBank sequences and the external morphology of the externa. In addition, this study proposes four new candidate species. This is the first report on the family Peltogastridae from Korea. Six hermit crab species were found to be new hosts to peltogastrids. Korean peltogastrids are less prevalent on their host hermit crabs than those from Japan are, especially in the west coast of Korea. Peltogasterella gracilis is widely distributed throughout Korea, Peltogaster lineata is located on the east coast, and Peltogaster postica is only located on Jeju Island.},
}
@article {pmid31966333,
year = {2019},
author = {Surmacz, B and Morek, W and Michalczyk, &#x141;},
title = {What If Multiple Claw Configurations Are Present in A Sample? A Case Study with the Description of Milnesium pseudotardigradum sp. nov. (Tardigrada) with Unique Developmental Variability.},
journal = {Zoological studies},
volume = {58},
number = {},
pages = {e32},
pmid = {31966333},
issn = {1810-522X},
abstract = {The tardigrade fauna of Iceland has been a subject of studies since mid XX century. So far, only a single species of the genus Milnesium has been reported from the island, M. tardigradum, which at the time was assumed to have a cosmopolitan distribution. However, the record comes from before the redescription of M. tardigradum, thus the validity of the Icelandic report is questionable. Some species of Milnesium are characterised by developmental variability, which is most pronounced in the morphology of secondary branches of claws, exhibited by shifts in the number of spurs. In this contribution, we present a case study in which multiple claw configurations (CC) were found in a single lichen sample from Iceland, indicating the presence of more than one species and/or ontogenetic variability. To elucidate this puzzle, we utilised a range of integrative tools, including detailed morphology, morphometry, barcoding and development tracking. We present the workflow, which enabled us to collect the data for each species/morphotype. In result, we revealed the presence of three species, two characterised by ontogenetic CC change (M. variefidum and a new species) and one with a stable CC (a new species). Here, we describe one of these new species, M. pseudotardigradum, which is extremely similar to M. tardigradum, but can be phenotypically differentiated by a unique, double CC change pattern.},
}
@article {pmid31966331,
year = {2019},
author = {Chu, C and Loh, KH and Ng, CC and Ooi, AL and Konishi, Y and Huang, SP and Chong, VC},
title = {Using DNA Barcodes to Aid the Identification of Larval Fishes in Tropical Estuarine Waters (Malacca Straits, Malaysia).},
journal = {Zoological studies},
volume = {58},
number = {},
pages = {e30},
pmid = {31966331},
issn = {1810-522X},
abstract = {Larval descriptions of tropical marine and coastal fishes are very few, and this taxonomic problem is further exacerbated by the high diversity of fish species in these waters. Nonetheless, accurate larval identification in ecological and early life history studies of larval fishes is crucial for fishery management and habitat protection. The present study aimed to evaluate the usefulness of DNA barcodes to support larval fish identification since conventional dichotomous keys based on morphological traits are not efficient due to the lack of larval traits and the rapid morphological changes during ontogeny. Our molecular analysis uncovered a total of 48 taxa (21 families) from the larval samples collected from the Klang Strait waters encompassing both spawning and nursery grounds of marine and estuarine fishes. Thirty-two (67%) of the larval taxa were identified at the species level, two taxa (4%) at the genus level, and 14 taxa (29%) at family level. The relatively low rate of species-level identification is not necessarily due to the DNA barcoding method per se, but a general lack of reference sequences for speciose and non- commercial fish families such as Gobiidae, Blenniidae, and Callionymidae. Larval morphology remains important in species diagnoses when molecular matches are ambiguous. A lower ethanol percentage (50%) for larva preservation is also useful to keep the body of larvae intact for morphological identification, and to preserve DNA for subsequent molecular analyses. The 10% Chelex resin used to extract DNA is also cost- effective for long term monitoring of larval fishes. Hence, the DNA barcoding method is an effective and easy way to aid the identification of estuarine larval fishes at the species level.},
}
@article {pmid31966311,
year = {2019},
author = {Lin, YJ and Qurban, MA and Shen, KN and Chao, NL},
title = {Delimitation of Tigertooth Croaker Otolithes Species (Teleostei: Sciaenidae) from the Western Arabian Gulf Using an Integrative Approach, with a Description of Otolithes arabicus sp. nov.},
journal = {Zoological studies},
volume = {58},
number = {},
pages = {e10},
pmid = {31966311},
issn = {1810-522X},
abstract = {Two species, Otolithes ruber and Otolithes cuvieri, are currently recognized in the sciaenid genus Otolithes. Recent findings suggest that Otolithes ruber likely has multiple genetically and morphologically distinct lineages and one of them, Otolithes sp. West Indian Ocean II group (WIO II group), has been previously identified in the Arabian Gulf. In this study, the specimens of Otolithes sp. collected from the western Arabian Gulf were examined using an integrative approach by combining mitochondrial cytochrome c oxidase 1 gene, morphological characteristics, and otolith-shape analyses. Three groups were found to have small within-group and large between-group genetic distance: the Otolithes sp. Western Arabian Gulf (WA) group, and the Otolithes sp. WIO II groups type A and type B. Accordingly, three primary species hypotheses were proposed. Evidence from conventional morphological comparisons, multivariate statistical analysis, geometric morphometric landmark analysis on morphological characteristics, and otolith shape analysis based on wavelet transformation all favor the hypothesis that the Otolithes sp. WA group is a distinct lineage. For this new species, the name Otolithes arabicus sp. nov. is proposed. A detailed description of Otolithes arabicus sp. nov. and a key to identifing species in the genus Otolithes are also provided. However, the primary species hypotheses for Otolithes sp. West Indian Ocean II group type A and type B cannot be fully supported because of partial congruence, which may result from recent divergence.},
}
@article {pmid31966290,
year = {2018},
author = {Benayahu, Y and van Ofwegen, LP and Dai, CF and Jeng, MS and Soong, K and Shlagman, A and Du, SW and Hong, P and Imam, NH and Chung, A and Wu, T and McFadden, CS},
title = {The Octocorals of Dongsha Atoll (South China Sea): An Iterative Approach to Species Identification Using Classical Taxonomy and Molecular Barcodes.},
journal = {Zoological studies},
volume = {57},
number = {},
pages = {e50},
pmid = {31966290},
issn = {1810-522X},
abstract = {Yehuda Benayahu, Leendert Pieter van Ofwegen, Chang-feng Dai, Ming-Shiou Jeng, Keryea Soong, Alex Shlagman, Samuel W. Du, Prudence Hong, Nimrah H. Imam, Alice Chung, Tiana Wu, and Catherine S. McFadden (2018) Surveys of octocorals from Dongsha Atoll, Taiwan were conducted during 2011, 2013 and 2015 by SCUBA at a depth range of 6-25 m. The collections yielded ~540 specimens, encompassing the variety of taxa occurring in the explored sites; estimates of their abundances were also recorded. Dongsha features a highly diverse octocoral fauna, and octocorals are the dominant benthic organisms in the surveyed reef sites, often covering the majority of the hard substratum. Specimens were identified to the genus and species levels based on an iterative approach that integrates classical taxonomy with character-based molecular barcodes. A total of 51 nominal species representing 20 genera belonging to seven families were recorded, plus ~30 colonies that could only be assigned to a genus. Members of the family Alcyoniidae were the most abundant and diverse taxa, with 27 nominal species plus at least one potentially new, undescribed species of Sinularia, and 5-7 species each of Cladiella, Lobophytum and Sarcophyton. Problems with the taxonomic identification and phylogenetic relationships of species in these genera are discussed. The peculiarity of the Dongsha octocoral species composition is noted, and the composition is also compared to the other Taiwanese reef systems.},
}
@article {pmid31966024,
year = {2020},
author = {Venera-Pontón, DE and Driskell, AC and De Grave, S and Felder, DL and Scioli, JA and Collin, R},
title = {Documenting decapod biodiversity in the Caribbean from DNA barcodes generated during field training in taxonomy.},
journal = {Biodiversity data journal},
volume = {8},
number = {},
pages = {e47333},
pmid = {31966024},
issn = {1314-2828},
abstract = {DNA barcoding is a useful tool to identify the components of mixed or bulk samples, as well as to determine individuals that lack morphologically diagnostic features. However, the reference database of DNA barcode sequences is particularly sparsely populated for marine invertebrates and for tropical taxa. We used samples collected as part of two field courses, focused on graduate training in taxonomy and systematics, to generate DNA sequences of the barcode fragments of cytochrome c oxidase subunit I (COI) and mitochondrial ribosomal 16S genes for 447 individuals, representing at least 129 morphospecies of decapod crustaceans. COI sequences for 36% (51/140) of the species and 16S sequences for 26% (37/140) of the species were new to GenBank. Automatic Barcode Gap Discovery identified 140 operational taxonomic units (OTUs) which largely coincided with the morphospecies delimitations. Barcode identifications (i.e. matches to identified sequences) were especially useful for OTUs within Synalpheus, a group that is notoriously difficult to identify and rife with cryptic species, a number of which we could not identify to species, based on morphology. Non-concordance between morphospecies and barcode OTUs also occurred in a few cases of suspected cryptic species. As mitochondrial pseudogenes are particularly common in decapods, we investigate the potential for this dataset to include pseudogenes and discuss the utility of these sequences as species identifiers (i.e. barcodes). These results demonstrate that material collected and identified during training activities can provide useful incidental barcode reference samples for under-studied taxa.},
}
@article {pmid31965295,
year = {2020},
author = {May, M and Jąkalski, M and Novotná, A and Dietel, J and Ayasse, M and Lallemand, F and Figura, T and Minasiewicz, J and Selosse, MA},
title = {Three-year pot culture of Epipactis helleborine reveals autotrophic survival, without mycorrhizal networks, in a mixotrophic species.},
journal = {Mycorrhiza},
volume = {30},
number = {1},
pages = {51-61},
pmid = {31965295},
issn = {1432-1890},
mesh = {Autotrophic Processes ; *Mycorrhizae ; *Orchidaceae ; Photosynthesis ; Plant Roots ; Symbiosis ; },
abstract = {Some mixotrophic plants from temperate forests use the mycorrhizal fungi colonizing their roots as a carbon source to supplement their photosynthesis. These fungi are also mycorrhizal on surrounding trees, from which they transfer carbon to mixotrophic plants. These plants are thus reputed difficult to transplant, even when their protection requires it. Here, we take profit of a successful ex situ pot cultivation over 1 to 3 years of the mixotrophic orchid Epipacis helleborine to investigate its mycorrhizal and nutrition status. Firstly, compared with surrounding autotrophic plants, it did not display the higher N content and higher isotopic ([13]C and [15]N) abundance that normally feature mixotrophic orchids because they incorporate N-, [13]C-, and [15]N-rich fungal biomass. Second, fungal barcoding by next-generation sequencing revealed that the proportion of ectomycorrhizal fungi (expressed as percentage of the total number of either reads or operational taxonomic units) was unusually low compared with E. helleborine growing in situ: instead, we found a high percentage of rhizoctonias, the usual mycorrhizal partners of autotrophic orchids. Altogether, this supports autotrophic survival. Added to the recently published evidence that plastid genomes of mixotrophic orchids have intact photosynthetic genes, this suggests that at least some of them have abilities for autotrophy. This adds to the ecological plasticity of mixotrophic plants, and may allow some reversion to autotrophy in their evolution.},
}
@article {pmid31961225,
year = {2020},
author = {Xiong, X and Yuan, F and Huang, M and Cao, M and Xiong, X},
title = {Comparative Evaluation of Web Page and Label Presentation for Imported Seafood Products Sold on Chinese E-Commerce Platform and Molecular Identification Using DNA Barcoding.},
journal = {Journal of food protection},
volume = {83},
number = {2},
pages = {256-265},
doi = {10.4315/0362-028X.JFP-19-309},
pmid = {31961225},
issn = {1944-9097},
abstract = {ABSTRACT: With the expansion of e-commerce, an increasing number of Chinese consumers are turning to online markets to purchase foreign seafood. When buying seafood online, customers cannot physically evaluate the product, and the market Web page instead of the seafood label conveys all of the product information. However, specific regulations concerning the information presented on the Web page have not been created, which may foster seafood fraud and misdescription. Because mislabeling of seafood has become a widely reported issue in the Chinese offline market, the online scenario must be investigated comprehensively. This study focused on various seafood products that originated from 20 countries and were sold by one of the largest e-commerce companies in China. For each country, only the product with the greatest overall monthly transaction volume was selected, and 5 samples were purchased per product for a total of 100 samples. The Web page description (including the heading of the Web page and the description of the commodity) and the label of the received products were compared to evaluate the description consistency. DNA barcoding technology was used for seafood species identification, and the scientific names retrieved from the sequence analysis after consulting the Barcode of Life Data systems and GenBank were compared with the expected species, genus, and family to determine the description authenticity. Only 25% of the samples had consistent descriptions on the Web page and on the label of the received product. Most of the inconsistency originated from the geographical origin, and only four products (G10, G50, G19, and G69) had inconsistent species, genus, and family descriptions. Molecular analysis revealed that in 65% of samples the species was correctly described. The online seafood market presents challenges regarding seafood fraud and opportunities for seafood species substitution.},
}
@article {pmid31960092,
year = {2020},
author = {Jongman, M and Carmichael, PC and Bill, M},
title = {Technological Advances in Phytopathogen Detection and Metagenome Profiling Techniques.},
journal = {Current microbiology},
volume = {77},
number = {4},
pages = {675-681},
pmid = {31960092},
issn = {1432-0991},
mesh = {Bacteria/*genetics/pathogenicity ; DNA Barcoding, Taxonomic ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Microbial Viability/genetics ; *Microbiota ; Oligonucleotide Array Sequence Analysis ; Plant Diseases/microbiology ; Plants/*microbiology ; },
abstract = {The use of advanced molecular methods in plant pathology and applied microbiology has necessitated for more accurate, rapid detection and identification of plant pathogens. This is particularly significant given accelerated emergence of virulence that leads to increased prevalence of plant pathogens. Thus, the capacity to contain plant pathogens and ultimately disease progression is key to ensuring crop biosecurity and overall food security. Of recent, research on pathogens utilizes a holistic approach focusing on elucidating growth dynamics within the entire biome rather than studying individual or closely related isolates in unison. This has advanced knowledge and information of microbial ecosystem within natural environments in the twenty first century. Applied technological platforms used for rapid detection and profiling microbial biomes in this regard include digital PCR, pyrosequencing, Illumina, DNA microarray and barcoding, Ion torrent, and nanopore. These technologies have been applied in various fields including human health and medicine, marine and animal biology, crop production and water quality research, to mention but a few. Although much has been done and achieved through the development of several technologies, more accuracy is required to circumvent the shortfalls still experienced. This includes integrating existing methods with new applications such as viability PCRs and microbial viability testing. Hence, this review provides critical analysis of some widely used latest technologies in rapid detection and identification of plant pathogens, and profiling plant associated microbiomes that reveal growth dynamics and population diversity. The advantages and limitations of the technologies are also discussed.},
}
@article {pmid31955731,
year = {2020},
author = {Frigerio, J and Agostinetto, G and Sandionigi, A and Mezzasalma, V and Berterame, NM and Casiraghi, M and Labra, M and Galimberti, A},
title = {The hidden 'plant side' of insect novel foods: A DNA-based assessment.},
journal = {Food research international (Ottawa, Ont.)},
volume = {128},
number = {},
pages = {108751},
doi = {10.1016/j.foodres.2019.108751},
pmid = {31955731},
issn = {1873-7145},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Edible Insects/*genetics ; Enzyme-Linked Immunosorbent Assay ; Flour/*analysis ; Food Contamination/*analysis ; Food Handling/*methods ; Food Hypersensitivity/*prevention &amp; control ; },
abstract = {In the context of novel foods, a category for which the market demand is increasing worldwide, the consumption of edible insects and related insect-based products is expected to grow in the next years. Insects represent an important source of energy for the human diet but there is a lack of scientific knowledge about their processing to ensure safe food items to the consumer. In this study we adopted a combined DNA-based approach to verify the identity of the declared species in five categories of commercial insect-based products (mt COI DNA barcoding) and to characterize plant declared ingredients or contaminants (nu ITS2 DNA metabarcoding) with particular attention to putative elements of allergenic concern belonging, for example to the insect rearing substrate. Moreover, the same approach has been used to assess its sensitivity to cases of contamination and counterfeits to insect flour with low cost (and potentially allergenic) vegetable flours like wheat and soybean. Results show the success of insect DNA barcoding authentication even for highly processed products. Furthermore, the DNA metabarcoding analysis revealed a high efficacy as a screening method to identify both plant ingredients and vegetal traces belonging to insect farming or possible adulteration events, also acting as an early warning strategy for the occurrence of allergens of human concern. This approach could support the development of new risk assessment procedures for novel foods by regulatory authorities to ensure their quality, safety, and acceptance which will become more required in order to face the challenge of feeding the world population in the next decades.},
}
@article {pmid31954510,
year = {2020},
author = {Eberle, J and Ahrens, D and Mayer, C and Niehuis, O and Misof, B},
title = {A Plea for Standardized Nuclear Markers in Metazoan DNA Taxonomy.},
journal = {Trends in ecology &amp; evolution},
volume = {35},
number = {4},
pages = {336-345},
doi = {10.1016/j.tree.2019.12.003},
pmid = {31954510},
issn = {1872-8383},
mesh = {Animals ; *DNA ; *DNA Barcoding, Taxonomic ; Mitochondria ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The ease of sequencing DNA barcodes promoted a species identification system universally applicable across animal phyla. However, relying on a single mitochondrial DNA fragment has a number of drawbacks that can mislead species delimitation and identification. Implementation of multiple nuclear markers would mitigate the limits of the current barcoding system if these markers are universally applicable across species, carry sufficient information to discriminate between closely related species, and if sequencing and analyzing these markers can be automatized. As sequencing costs continue to fall, we believe that the time is right to extend DNA barcoding. Here we argue that nearly universal single-copy nuclear protein-coding genes deliver the desired characteristics and could be used to reliably delimit and identify animal species.},
}
@article {pmid31953199,
year = {2020},
author = {Song, JH and Cha, JM and Moon, BC and Kim, WJ and Yang, S and Choi, G},
title = {Mantidis Oötheca (mantis egg case) original species identification via morphological analysis and DNA barcoding.},
journal = {Journal of ethnopharmacology},
volume = {252},
number = {},
pages = {112574},
doi = {10.1016/j.jep.2020.112574},
pmid = {31953199},
issn = {1872-7573},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Mantodea/classification/*genetics ; *Ovum ; Phylogeny ; },
abstract = {Mantidis Oötheca (mantis egg case; sangpiaoxiao) is a medicine from an insect source, which has been widely used in Asian countries. However, misidentification due to a lack of information given variations in the medicinal portion of the ootheca and morphological similarities of the ootheca as an egg chamber.<br><br>AIM OF THE STUDY: Thus, this study aims to provide the first comprehensive data for discriminating authentic of Mantidis O&#xf6;theca. Here, we provide detailed ootheca morphology and their molecular information to accurately identify Mantidis O&#xf6;theca.<br><br>MATERIALS AND METHODS: Oothecae of Tenodera angustipennis (Saussure, 1869), Tenodera sinensis (Saussure, 1871), Hierodula patellifera Serville, 1839, and Hierodula sp. were used in the comparative morphological, principal component analysis, and DNA barcoding.<br><br>RESULTS: The morphological analyses revealed that the emergence area, outline, angle of distal end, width of air-filled layer, and weight are useful diagnostic characters. Using these quantitative and qualitative characteristics, we developed the effective identification key. Furthermore, our CO1 sequences from all individuals were monophyletic with high bootstrap values at genus and species levels. Moreover, morphological identification using our developed key among all studied individuals agreed with molecular identification results using CO1 barcoding data.<br><br>CONCLUSIONS: These multilateral approaches, including morphological, statistical, and DNA barcoding methods are highly reliable identification tools. Moreover, our diagnostic key characteristics and molecular barcoding should aid in the accurate identification, authentication, and quality control of Mantidis O&#xf6;theca medicinal materials.},
}
@article {pmid31952556,
year = {2020},
author = {Loera-Sánchez, M and Studer, B and Kölliker, R},
title = {DNA barcode trnH-psbA is a promising candidate for efficient identification of forage legumes and grasses.},
journal = {BMC research notes},
volume = {13},
number = {1},
pages = {35},
pmid = {31952556},
issn = {1756-0500},
support = {n.a.//Bundesamt f&#xfc;r Landwirtschaft/ ; },
mesh = {Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Intergenic/*genetics ; DNA, Plant ; Ecosystem ; Fabaceae/*genetics ; Phylogeny ; Poaceae/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {OBJECTIVE: Grasslands are widespread ecosystems that fulfil many functions. Plant species richness (PSR) is known to have beneficial effects on such functions and monitoring PSR is crucial for tracking the effects of land use and agricultural management on these ecosystems. Unfortunately, traditional morphology-based methods are labor-intensive and cannot be adapted for high-throughput assessments. DNA barcoding could aid increasing the throughput of PSR assessments in grasslands. In this proof-of-concept work, we aimed at determining which of three plant DNA barcodes (rbcLa, matK and trnH-psbA) best discriminates 16 key grass and legume species common in temperate sub-alpine grasslands.<br><br>RESULTS: Barcode trnH-psbA had a 100% correct assignment rate (CAR) in the five analyzed legumes, followed by rbcLa (93.3%) and matK (55.6%). Barcode trnH-psbA had a 100% CAR in the grasses Cynosurus cristatus, Dactylis glomerata and Trisetum flavescens. However, the closely related Festuca, Lolium and Poa species were not always correctly identified, which led to an overall CAR in grasses of 66.7%, 50.0% and 46.4% for trnH-psbA, matK and rbcLa, respectively. Barcode trnH-psbA is thus the most promising candidate for PSR assessments in permanent grasslands and could greatly support plant biodiversity monitoring on a larger scale.},
}
@article {pmid31952076,
year = {2020},
author = {Nagarajan, RP and Goodbla, A and Graves, E and Baerwald, M and Holyoak, M and Schreier, A},
title = {Non-invasive genetic monitoring for the threatened valley elderberry longhorn beetle.},
journal = {PloS one},
volume = {15},
number = {1},
pages = {e0227333},
pmid = {31952076},
issn = {1932-6203},
mesh = {Animals ; California ; Coleoptera/*genetics/physiology ; DNA, Mitochondrial/genetics ; *Ecosystem ; Endangered Species ; *Environmental Monitoring ; Humans ; Larva/*genetics/physiology ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The valley elderberry longhorn beetle (VELB), Desmocerus californicus dimorphus (Coleoptera: Cerambycidae), is a federally threatened subspecies endemic to the Central Valley of California. The VELB range partially overlaps with that of its morphologically similar sister taxon, the California elderberry longhorn beetle (CELB), Desmocerus californicus californicus (Coleoptera: Cerambycidae). Current surveying methods are limited to visual identification of larval exit holes in the VELB/CELB host plant, elderberry (Sambucus spp.), into which larvae bore and excavate feeding galleries. Unbiased genetic approaches could provide a much-needed complementary approach that has more precision than relying on visual inspection of exit holes. In this study we developed a DNA sequencing-based method for indirect detection of VELB/CELB from frass (insect fecal matter), which can be easily and non-invasively collected from exit holes. Frass samples were collected from 37 locations and the 12S and 16S mitochondrial genes were partially sequenced using nested PCR amplification. Three frass-derived sequences showed 100% sequence identity to VELB/CELB barcode references from museum specimens sequenced for this study. Database queries of frass-derived sequences also revealed high similarity to common occupants of old VELB feeding galleries, including earwigs, flies, and other beetles. Overall, this non-invasive approach is a first step towards a genetic assay that could augment existing VELB monitoring and accurately discriminate between VELB, CELB, and other insects. Furthermore, a phylogenetic analysis of 12S and 16S data from museum specimens revealed evidence for the existence of a previously unrecognized, genetically distinct CELB subpopulation in southern California.},
}
@article {pmid31945184,
year = {2020},
author = {Güçlü, SS and Kalaycı, G and Küçük, F and Turan, D},
title = {Barbus xanthos, a new barbel from the Southern Aegean basin (Teleostei: Cyprinidae).},
journal = {Journal of fish biology},
volume = {96},
number = {6},
pages = {1309-1319},
doi = {10.1111/jfb.14259},
pmid = {31945184},
issn = {1095-8649},
support = {//This study was supported by a grant from the S&#xfc;leyman Demirel &#xdc;niversitesi Scientific Research Projects Coordination Unit (Project No: SD&#xdc;-BAP1987D09)./ ; },
mesh = {Animals ; Cyprinidae/anatomy &amp; histology/*classification/genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Pigmentation ; Rivers ; Species Specificity ; },
abstract = {Barbus xanthos, a new species, is described from the Eşen, Dalaman, Tersakan and Büyük Menderes rivers in south-western Anatolia. It differs from other Barbus species in the adjacent basins by having 53-60 lateral line scales, a weakly ossified last unbranched dorsal-fin ray (about 33-50%), numerous small irregular-shaped black or dark-brown spots smaller than scales, often forming large, black or dark-brown blotches on back and flank in juveniles and adults, and a straight or slightly convex posterior dorsal-fin margin. B. xanthos differs from its most closely related congener, B. pergamonensis, by nine nucleotide substitution sites in the mitochondrial DNA cytochrome oxidase I barcode region.},
}
@article {pmid31944524,
year = {2020},
author = {Fernández, S and Rodríguez-Muñiz, LJ and Molina, J and Muñiz-Rodríguez, L and Jiménez, J and García-Vázquez, E and Borrell, YJ},
title = {Lab experience with seafood control at the undergraduate level: Cephalopods as a case study.},
journal = {Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology},
volume = {48},
number = {3},
pages = {236-246},
doi = {10.1002/bmb.21332},
pmid = {31944524},
issn = {1539-3429},
support = {FC-GRUPIN-IDI/2018/000201//Principado de Asturias/International ; PINN-14-005//University of Oviedo/International ; },
mesh = {Animals ; Cephalopoda/classification ; Conservation of Natural Resources ; DNA Barcoding, Taxonomic ; Europe ; Female ; Fisheries ; Food Technology/methods ; Genetics/*education ; Humans ; Laboratories ; Male ; Motivation ; Polymerase Chain Reaction ; Problem-Based Learning/*methods ; Seafood/*classification ; Spain ; Students ; Surveys and Questionnaires ; *Teaching ; Universities ; },
abstract = {The correct labeling of seafood is important to protect nature and the rights of consumers. Given the certainty that the resources of the sea are not inexhaustible, only strict regulations and the implementation of sustainable fishing systems and reliable and traceable marketing systems can help ensure the long-term sustainability of fishery resources. Detecting mislabeling and seafood fraud is a useful resource for improving students' motivation and developing active learning methodologies in higher education. In the present study, we have proposed to the students a lab exercise consisting of exploring 25 different commercial cephalopod products from three major European supermarkets by using DNA barcoding and analyzing the results under the framework of EU and Spanish regulations. The problem is connected with the last theme (traceability) of the Conservation Genetics and Breeding course with the aim of providing students with a practical research lab experience about a real problem before going deeper into more theoretical contents. In this way, they can use the knowledge and the skills they acquired previously to better comprehend and think critically about the problem. Findings from students' answers to a survey revealed that the use of this approach generates useful information for communities, increases curiosity and feelings of benefit, and leads to high levels of satisfaction with lab practices compared with those in other courses. In conclusion, lab exercises focused on seafood control, in addition to being viable, can be used as a tool in classes to improve students' commitment to higher education.},
}
@article {pmid31943790,
year = {2020},
author = {Rachtman, E and Balaban, M and Bafna, V and Mirarab, S},
title = {The impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters.},
journal = {Molecular ecology resources},
volume = {20},
number = {3},
pages = {},
doi = {10.1111/1755-0998.13135},
pmid = {31943790},
issn = {1755-0998},
support = {IIS-1815485//NSF/ ; },
mesh = {DNA/genetics ; Databases, Genetic ; Genome/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Sequence Analysis, DNA/methods ; },
abstract = {The ability to detect the identity of a sample obtained from its environment is a cornerstone of molecular ecological research. Thanks to the falling price of shotgun sequencing, genome skimming, the acquisition of short reads spread across the genome at low coverage, is emerging as an alternative to traditional barcoding. By obtaining far more data across the whole genome, skimming has the promise to increase the precision of sample identification beyond traditional barcoding while keeping the costs manageable. While methods for assembly-free sample identification based on genome skims are now available, little is known about how these methods react to the presence of DNA from organisms other than the target species. In this paper, we show that the accuracy of distances computed between a pair of genome skims based on k-mer similarity can degrade dramatically if the skims include contaminant reads; i.e., any reads originating from other organisms. We establish a theoretical model of the impact of contamination. We then suggest and evaluate a solution to the contamination problem: Query reads in a genome skim against an extensive database of possible contaminants (e.g., all microbial organisms) and filter out any read that matches. We evaluate the effectiveness of this strategy when implemented using Kraken-II, in detailed analyses. Our results show substantial improvements in accuracy as a result of filtering but also point to limitations, including a need for relatively close matches in the contaminant database.},
}
@article {pmid31940408,
year = {2020},
author = {Parimuchová, A and Žurovcová, M and Papáč, V and Kováč, &#x13d;},
title = {Subterranean Deuteraphorura Absolon, 1901, (Hexapoda, Collembola) of the Western Carpathians - Troglomorphy at the northern distributional limit in Europe.},
journal = {PloS one},
volume = {15},
number = {1},
pages = {e0226966},
pmid = {31940408},
issn = {1932-6203},
mesh = {Adaptation, Physiological ; Animals ; Arthropods/*anatomy &amp; histology/*classification/genetics/physiology ; *Caves ; Ecosystem ; Electron Transport Complex IV/genetics ; Europe ; Female ; Male ; Slovakia ; },
abstract = {An integrative approach employing molecular, morphological and geographical data were applied to species delimitation among Deuteraphorura congeners occupying caves of the Western Carpathian Mts. A new species of Deuteraphorura from the Western Carpathians is described. D. muranensis sp. nov. belongs among species with 4 pso at the hind margin of the head and possesses highly troglomorphic features. It is conspicuous with its distinctly elongated claws and long, hair-like body chaetae. The status of the new species was confirmed by DNA barcoding based on the mitochondrial COI marker. Populations of D. kratochvili (Nosek, 1963), the most widespread species, were studied in detail. Both ABGD and PTP analyses brought results congruent with geography, i.e. the molecular and geographic distance of the populations were positively correlated. However, some molecular separation based on pairwise distance and the number of substitutions was indicated within two of the studied populations. Despite the indistinct morphological differences, the tested populations were well isolated both geographically and genetically, which indicates that each studied population may represent a cryptic species. The troglomorphy of cave Collembola at the northernmost border of the distribution of cave-adapted species in the Europe is discussed. It is clear that the level of troglomorphy is closely associated with conditions of the microhabitat occupied by the individual subterranean species. The results of our study enhance the importance of the Western Carpathians regarding the diversity pattern of obligate cave species in Europe.},
}
@article {pmid31938901,
year = {2020},
author = {Ou, Z and Li, K and Yang, T and Dai, Y and Chandra, M and Ning, J and Wang, Y and Xu, R and Gao, T and Xie, Y and He, Q and Li, Y and Lu, Q and Wang, L and Song, Z},
title = {Detection of bladder cancer using urinary cell-free DNA and cellular DNA.},
journal = {Clinical and translational medicine},
volume = {9},
number = {1},
pages = {4},
pmid = {31938901},
issn = {2001-1326},
support = {2017SK2173//The Key Research and Development Program of Hunan Province/ ; },
abstract = {BACKGROUND: The present study sought to identify a panel of DNA markers for noninvasive diagnosis using cell-free DNA (cfDNA) from urine supernatant or cellular DNA from urine sediments of hematuria patients. A panel of 48 bladder cancer-specific genes was selected. A next-generation sequencing-based assay with a cfDNA barcode-enabled single-molecule test was employed. Mutation profiles of blood, urine, and tumor sample from 16 bladder cancer patients were compared. Next, urinary cellular DNA and cfDNA were prospectively collected from 125 patients (92 bladder cancer cases and 33 controls) and analyzed using the 48-gene panel. The individual gene markers and combinations of markers were validated according to the pathology results. The mean areas under the receiver operating characteristic (ROC) curves (AUCs) obtained with the various modeling approaches were calculated and compared.<br><br>RESULTS: This pilot study of 16 bladder cancer patients demonstrated that gene mutations in urine supernatant and sediments had better concordance with cancer tissue as compared with plasma. Logistic analyses suggested two powerful combinations of genes for genetic diagnostic modeling: five genes for urine supernatant (TERT, FGFR3, TP53, PIK3CA, and KRAS) and seven genes for urine sediments (TERT, FGFR3, TP53, HRAS, PIK3CA, KRAS, and ERBB2). The accuracy of the five-gene panel and the seven-gene panel in the validation cohort yielded AUCs of 0.94 [95% confidence interval (CI) 0.91-0.97] and 0.91 (95% CI 0.86-0.96), respectively. With the addition of age and gender, the diagnostic power of the urine supernatant five-gene model and the urine sediment seven-gene model improved as the revised AUCs were 0.9656 (95% CI 0.9368-0.9944) and 0.9587 (95% CI 0.9291-0.9883).<br><br>CONCLUSIONS: cfDNA from urine bears great diagnostic potential. A five-gene panel for urine supernatant and a seven-gene panel for urine sediments are promising options for identifying bladder cancer in hematuria patients.},
}
@article {pmid31938848,
year = {2020},
author = {Sun, X and Fei, R and Zhang, L and Huo, B and Wang, Y and Peng, Y and Ning, B and He, J and Gao, Z and Hu, Y},
title = {Bio-barcode triggered isothermal amplification in a fluorometric competitive immunoassay for the phytotoxin abrin.},
journal = {Mikrochimica acta},
volume = {187},
number = {2},
pages = {127},
pmid = {31938848},
issn = {1436-5073},
mesh = {Abrin/*analysis/immunology/metabolism ; Antibodies/immunology ; Binding, Competitive ; DNA Barcoding, Taxonomic ; Fluorometry/methods/standards ; Gold ; Immunoassay/*methods/standards ; Limit of Detection ; Magnetics ; Metal Nanoparticles/chemistry ; Toxins, Biological/*analysis ; },
abstract = {Abrin is one of the most toxic phytotoxins to date, and is a potential biological warfare agent. A bio-barcode triggered isothermal amplification for fluorometric determination of abrin is described. Free abrin competes with abrin-coated magnetic microparticles (MMP) probes to bind to gold nanoparticle (AuNP) probes modified with abrin antibody and bio-barcoded DNA. Abundant barcodes are released from the MMP-AuNP complex via dithiothreitol treatment. This triggers an exponential amplification reaction (EXPAR) that is monitored by real-time fluorometry, at typical excitation/emission wavelengths of 495/520 nm. The EXPAR assay is easily operated, highly sensitive and specific. It was used to quantify abrin in spiked commercial samples. The detection limit (at S/N = 3; for n = 6) is 5.6 pg·mL[-1] which is considerably lower than previous reports. This assay provides a universal sensing platform and has great potential for determination of various analytes, including small molecules, proteins, DNA, and cells. Graphical abstract Schematic representation of the bio-barcode triggered exponential amplification reaction (EXPAR) for a fluorometric competitive immunoassay for abrin. The limit of detection is 5.6 pg mL[-1] with a large dynamic range from 10 pg mL[-1] to 1 µg mL[-1].},
}
@article {pmid31938523,
year = {2019},
author = {Bakker, J and Wangensteen, OS and Baillie, C and Buddo, D and Chapman, DD and Gallagher, AJ and Guttridge, TL and Hertler, H and Mariani, S},
title = {Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding.},
journal = {Ecology and evolution},
volume = {9},
number = {24},
pages = {14341-14355},
pmid = {31938523},
issn = {2045-7758},
abstract = {Our understanding of marine communities and their functions in an ecosystem relies on the ability to detect and monitor species distributions and abundances. Currently, the use of environmental DNA (eDNA) metabarcoding is increasingly being applied for the rapid assessment and monitoring of aquatic species. Most eDNA metabarcoding studies have either focussed on the simultaneous identification of a few specific taxa/groups or have been limited in geographical scope. Here, we employed eDNA metabarcoding to compare beta diversity patterns of complex pelagic marine communities in tropical coastal shelf habitats spanning the whole Caribbean Sea. We screened 68 water samples using a universal eukaryotic COI barcode region and detected highly diverse communities, which varied significantly among locations, and proved good descriptors of habitat type and environmental conditions. Less than 15% of eukaryotic taxa were assigned to metazoans, most DNA sequences belonged to a variety of planktonic "protists," with over 50% of taxa unassigned at the phylum level, suggesting that the sampled communities host an astonishing amount of micro-eukaryotic diversity yet undescribed or absent from COI reference databases. Although such a predominance of micro-eukaryotes severely reduces the efficiency of universal COI markers to investigate vertebrate and other metazoans from aqueous eDNA, the study contributes to the advancement of rapid biomonitoring methods and brings us closer to a full inventory of extant marine biodiversity.},
}
@article {pmid31936447,
year = {2020},
author = {Pentinsaari, M and Blagoev, GA and Hogg, ID and Levesque-Beaudin, V and Perez, K and Sobel, CN and Vandenbrink, B and Borisenko, A},
title = {A DNA Barcoding Survey of an Arctic Arthropod Community: Implications for Future Monitoring.},
journal = {Insects},
volume = {11},
number = {1},
pages = {},
pmid = {31936447},
issn = {2075-4450},
support = {NST-1819-0039//Polar Knowledge Canada/ ; },
abstract = {Accurate and cost-effective methods for tracking changes in arthropod communities are needed to develop integrative environmental monitoring programs in the Arctic. To date, even baseline data on their species composition at established ecological monitoring sites are severely lacking. We present the results of a pilot assessment of non-marine arthropod diversity in a middle arctic tundra area near Ikaluktutiak (Cambridge Bay), Victoria Island, Nunavut, undertaken in 2018 using DNA barcodes. A total of 1264 Barcode Index Number (BIN) clusters, used as a proxy for species, were recorded. The efficacy of widely used sampling methods was assessed. Yellow pan traps captured 62% of the entire BIN diversity at the study sites. When complemented with soil and leaf litter sifting, the coverage rose up to 74.6%. Combining community-based data collection with high-throughput DNA barcoding has the potential to overcome many of the logistic, financial, and taxonomic obstacles for large-scale monitoring of the Arctic arthropod fauna.},
}
@article {pmid31935649,
year = {2020},
author = {Susca, A and Villani, A and Moretti, A and Stea, G and Logrieco, A},
title = {Identification of toxigenic fungal species associated with maize ear rot: Calmodulin as single informative gene.},
journal = {International journal of food microbiology},
volume = {319},
number = {},
pages = {108491},
doi = {10.1016/j.ijfoodmicro.2019.108491},
pmid = {31935649},
issn = {1879-3460},
mesh = {Aspergillus/classification/genetics/metabolism ; Biodiversity ; Calmodulin/*genetics ; Food Contamination/analysis ; Food Safety ; Fungi/*classification/*genetics ; Fusarium/classification/genetics/metabolism ; Mycotoxins/*analysis ; Penicillium/classification/genetics/metabolism ; Plant Diseases/microbiology ; Polymerase Chain Reaction ; Talaromyces/classification/genetics/metabolism ; Zea mays/*microbiology ; },
abstract = {Accurate identification of fungi occurring on agrofood products is the key aspect of any prevention and pest management program, offering valuable information in leading crop health and food safety. Fungal species misidentification can dramatically impact biodiversity assessment, ecological studies, management decisions, and, concerning toxigenic fungi, health risk assessment, since they can produce a wide range of toxic secondary metabolites, referred to as mycotoxins. Since each toxigenic fungal species can have its own mycotoxin profile, a correct species identification, hereby attempted with universal DNA barcoding approach, could have a key role in mycotoxins prevention strategies. Currently, identification of single marker for species resolution in fungi has not been achieved and the analysis of multiple genes is used, with the advantage of an accurate species identification and disadvantage of difficult setting up of PCR-based diagnostic assays. In the present paper, we describe our strategy to set up a DNA-based species identification of fungal species associated with maize ear rot, combining DNA barcoding approach and species-specific primers design for PCR based assays. We have (i) investigated the appropriate molecular marker for species identification, limited to mycobiota possibly occurring on maize, identifying calmodulin gene as single taxonomically informative entity; (ii) designed 17 sets of primers for rapid identification of 14 Fusarium, 10 Aspergillus, 2 Penicillium, and 2 Talaromyces species or species groups, and finally (iii) tested specificity of the 17 set of primers, in combination with 3 additional sets previously developed.},
}
@article {pmid31935501,
year = {2020},
author = {Gui, L and Jiang, S and Xie, D and Yu, L and Huang, Y and Zhang, Z and Liu, Y},
title = {Analysis of complete chloroplast genomes of Curcuma and the contribution to phylogeny and adaptive evolution.},
journal = {Gene},
volume = {732},
number = {},
pages = {144355},
doi = {10.1016/j.gene.2020.144355},
pmid = {31935501},
issn = {1879-0038},
mesh = {Chloroplasts/genetics ; Curcuma/*classification/cytology/genetics ; Evolution, Molecular ; Genome Size ; *Genome, Chloroplast ; Microsatellite Repeats ; Phylogeny ; Whole Genome Sequencing/*methods ; },
abstract = {Curcuma is an important member of Zingiberaceae. Many species of this genus are widely used in traditional medicine and have important cultural value in East Asia. Among them, C. longa is considered to be the main source of curcumin and has a very wide range of uses. The rapid development of molecular phylogeny has deepened our understanding of taxonomy and evolution of Curcuma. However, little is known about the chloroplast genome phylogeny and the genetic bases of adaptative evolution. In this work, we sequenced the complete chloroplast genome of 4 Curcuma species. Curcuma chloroplast genomes showed highly conserved structures and the length ranged from 159,423 bp to 152,723 bp. A total of 133 genes were observed. Multiple repeats and simple sequence repeats (SSRs) were detected. By comparing with related species, 7 highly variable regions were identified as potential specific DNA barcodes for species identification. Phylogenetic analysis of complete plastome sequences and specific data sets revealed discordance with expected genus boundary. Chloroplast phylogenetic relationships were better predicted by geography than by morphological and nuclear DNA, indicating a substantial existence of introgression. 9 genes were proved to have high posteriori probability in positive selection analysis, and 4 of them (psbA, psbD, PetA and rbcL) closely related to photosynthesis, implying that chloroplast genes may had undergone positive selection pressure in evolution. These results are of great significance for us to understand the genetic basis, phylogeny and adaptive evolution of Curcuma chloroplast.},
}
@article {pmid31933272,
year = {2019},
author = {Khan, SA and Baeshen, MN and Ramadan, HA and Baeshen, NA},
title = {ITS2: An Ideal DNA Barcode for the Arid Medicinal Plant Rhazya Stricta.},
journal = {Pharmaceutical medicine},
volume = {33},
number = {1},
pages = {53-61},
pmid = {31933272},
issn = {1179-1993},
mesh = {Apocynaceae/*genetics ; Cell Nucleus/genetics ; Chloroplasts/genetics ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Plants, Medicinal/genetics ; },
abstract = {INTRODUCTION: In Saudi Arabia, Rhazya stricta is a widely used folkloric plant because of its various therapeutic properties. It is sold in herbal markets as a dried powder; however, the absence of visible phenotypic traits in the powder can mask its authenticity. Potential misidentification of this substance threatens consumer health. DNA barcoding could accurately identify this plant regardless of its physical state, however barcoding presents the challenge of variations in marker loci.<br><br>OBJECTIVES: The objective of this work was to assess barcode markers from the chloroplast and nuclear regions to determine their taxonomic accuracy in R. stricta barcoding, and select the best marker for this species that could fulfill the authentication test for its fresh and dried samples.<br><br>METHOD: In this study, we assessed seven barcode markers from the chloroplast (psbA-trnH, matK, rbcL, rpoB, and rpoC1) and nuclear regions (ITS1and ITS2). We compared DNA sequences of R. stricta from 50 fresh locally collected samples and 10 dried ground samples from the herbal market with the database sequences of R. stricta, R. orientalis, and eight other related species as controls. We utilized three methods (BLAST, nearest distance, and neighbor-joining tree) in this analysis.<br><br>RESULT: With the exception of psbA-trnH, all the chloroplast markers determined high similarity with other taxa. However, nuclear ITS2 best distinguished between R. stricta, R. orientalis, and other related species because of its secondary structures, which allowed for more accurate distinctions. A two-locus marker of ITS1&#x2009;+&#x2009;ITS2 sequences also showed promising results. A two-dimensional image of our proposed marker was generated to more easily handle DNA barcoding applications.<br><br>CONCLUSION: Our study indicates that ITS2 is a cost-effective barcoding marker capable of verifying the authenticity of R. stricta and other medicinal plants in order to protect consumer health.},
}
@article {pmid31920425,
year = {2019},
author = {Stonis, JR and Remeikis, A and Diškus, A and Orlovskytė, S and Vargas, SA and Solis, MA},
title = {A new leafmining pest of guava: Hesperolyra guajavifoliae sp. nov., with comments on the diagnostics of the endemic Neotropical genus Hesperolyra van Nieukerken (Lepidoptera, Nepticulidae).},
journal = {ZooKeys},
volume = {900},
number = {},
pages = {87-110},
pmid = {31920425},
issn = {1313-2989},
abstract = {We describe a new pest of guava (Psidium guajava L.), Hesperolyra guajavifoliae Stonis &amp; Vargas, sp. nov., that was recently discovered in western Colombia. Hesperolyra van Nieukerken is a small, Neotropical genus of pygmy moths (Nepticulidae). We re-examine and document the complex morphology of the male genitalia of the generic type species, H. diskusi (Puplesis &amp; Robinson). We discuss the diagnostics and composition of the genus and provide a simple pictorial differentiation scheme for all currently known representatives of the genus. The new species is illustrated with photographs of the adults, some of the immature stages, male and female genitalia, and leaf mines. A link to the COI barcodes of H. guajavifoliae sp. nov. is provided and the relationship of Hesperolyra to other genera is discussed.},
}
@article {pmid31919378,
year = {2020},
author = {de Kerdrel, GA and Andersen, JC and Kennedy, SR and Gillespie, R and Krehenwinkel, H},
title = {Rapid and cost-effective generation of single specimen multilocus barcoding data from whole arthropod communities by multiple levels of multiplexing.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {78},
pmid = {31919378},
issn = {2045-2322},
mesh = {Animals ; Arthropods/*classification/*genetics ; *Biodiversity ; *Cost-Benefit Analysis ; DNA Barcoding, Taxonomic/*economics/*methods ; *Ecosystem ; Hawaii ; Multiplex Polymerase Chain Reaction ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {In light of the current biodiversity crisis, molecular barcoding has developed into an irreplaceable tool. Barcoding has been considerably simplified by developments in high throughput sequencing technology, but still can be prohibitively expensive and laborious when community samples of thousands of specimens need to be processed. Here, we outline an Illumina amplicon sequencing approach to generate multilocus data from large collections of arthropods. We reduce cost and effort up to 50-fold, by combining multiplex PCRs and DNA extractions from pools of presorted and morphotyped specimens and using two levels of sample indexing. We test our protocol by generating a comprehensive, community wide dataset of barcode sequences for several thousand Hawaiian arthropods from 14 orders, which were collected across the archipelago using various trapping methods. We explore patterns of diversity across the Archipelago and compare the utility of different arthropod trapping methods for biodiversity explorations on Hawaii, highlighting undergrowth beating as highly efficient method. Moreover, we show the effects of barcode marker, taxonomy and relative biomass of the targeted specimens and sequencing coverage on taxon recovery. Our protocol enables rapid and inexpensive explorations of diversity patterns and the generation of multilocus barcode reference libraries across whole ecosystems.},
}
@article {pmid31917512,
year = {2020},
author = {Behbehani, GK and Finck, R and Samusik, N and Sridhar, K and Fantl, WJ and Greenberg, PL and Nolan, GP},
title = {Profiling myelodysplastic syndromes by mass cytometry demonstrates abnormal progenitor cell phenotype and differentiation.},
journal = {Cytometry. Part B, Clinical cytometry},
volume = {98},
number = {2},
pages = {131-145},
pmid = {31917512},
issn = {1552-4957},
support = {R33 CA183654/CA/NCI NIH HHS/United States ; U19 AI057229/AI/NIAID NIH HHS/United States ; U19 AI100627/AI/NIAID NIH HHS/United States ; R01 HL120724/HL/NHLBI NIH HHS/United States ; P01 HL108797/HL/NHLBI NIH HHS/United States ; HHSN268201000034C/HL/NHLBI NIH HHS/United States ; R33 CA183692/CA/NCI NIH HHS/United States ; R01 CA184968/CA/NCI NIH HHS/United States ; UH2 AR067676/AR/NIAMS NIH HHS/United States ; R21 CA183660/CA/NCI NIH HHS/United States ; U54 CA149145/CA/NCI NIH HHS/United States ; },
mesh = {Biopsy, Needle ; Bone Marrow/pathology ; Bone Marrow Cells/immunology/pathology/physiology ; Cell Differentiation ; Flow Cytometry/*methods ; Humans ; Immunophenotyping/methods ; Myelodysplastic Syndromes/*diagnosis/pathology/physiopathology ; Phenotype ; Pilot Projects ; Stem Cells/*pathology/*physiology ; },
abstract = {BACKGROUND: We sought to enhance the cytometric analysis of myelodysplastic syndromes (MDS) by performing a pilot study of a single cell mass cytometry (MCM) assay to more comprehensively analyze patterns of surface marker expression in patients with MDS.<br><br>METHODS: Twenty-three MDS and five healthy donor bone marrow samples were studied using a 34-parameter mass cytometry panel utilizing barcoding and internal reference standards. The resulting data were analyzed by both traditional gating and high-dimensional clustering.<br><br>RESULTS: This high-dimensional assay provided three major benefits relative to traditional cytometry approaches: First, MCM enabled detection of aberrant surface maker at high resolution, detecting aberrancies in 27/31 surface markers, encompassing almost every previously reported MDS surface marker aberrancy. Additionally, three previously unrecognized aberrancies in MDS were detected in multiple samples at least one developmental stage: increased CD321 and CD99; and decreased CD47. Second, analysis of the stem and progenitor cell compartment (HSPCs), demonstrated aberrant expression in 21 of the 23 MDS samples, which were not detected in three samples from patients with idiopathic cytopenia of undetermined significance. These immunophenotypically abnormal HSPCs were also the single most significant distinguishing feature between clinical risk groups. Third, unsupervised clustering of high-parameter MCM data allowed identification of abnormal differentiation patterns associated with immunophenotypically aberrant myeloid cells similar to myeloid derived suppressor cells.<br><br>CONCLUSIONS: These results demonstrate that high-parameter cytometry methods that enable simultaneous analysis of all bone marrow cell types could enhance the diagnostic utility of immunophenotypic analysis in MDS.},
}
@article {pmid31912756,
year = {2020},
author = {Marzal-Alfaro, M and Rodriguez-Gonzalez, CG and Escudero-Vilaplana, V and Revuelta-Herrero, JL and González-Haba, E and Ibáñez-Garcia, S and Iglesias-Peinado, I and Herranz-Alonso, A and Sanjurjo Saez, M},
title = {Risks and medication errors analysis to evaluate the impact of a chemotherapy compounding workflow management system on cancer patients' safety.},
journal = {Health informatics journal},
volume = {26},
number = {3},
pages = {1995-2010},
doi = {10.1177/1460458219895434},
pmid = {31912756},
issn = {1741-2811},
mesh = {Drug Compounding ; Humans ; Medication Errors/prevention &amp; control ; *Neoplasms ; *Pharmacy Service, Hospital ; Workflow ; },
abstract = {A failure modes, effects and criticality analysis was supported by an observational medication error rate study to analyze the impact of Phocus Rx[®], a new image-based workflow software system, on chemotherapy compounding error rates. Residual risks that should be a target for additional action were identified and prioritized and pharmacy staff satisfaction with the new system was evaluated. In total, 16 potential failure modes were recognized in the pre-implementation phase and 21 after Phocus Rx[®] implementation. The total reduction of the criticality index was 67 percent, with a reduction of 46 percent in material preparation, 76 percent in drug production and 48 percent in quality control subprocesses. The relative risk reduction of compounding error rate was 63 percent after the implementation of Phocus Rx[®], from 0.045 to 0.017 percent. The high-priority recommendations defined were identification of the product with batch and expiration date from scanned bidimensional barcodes on drug vials and process improvements in image-based quality control. Overall satisfaction index was 8.30 (SD 1.06) for technicians and 8.56 (SD 1.42) for pharmacists (p = 0.655). The introduction of a new workflow management software system was an effective approach to increasing safety in the compounding procedures in the pharmacy department, according to the failure modes, effects and criticality analysis method.},
}
@article {pmid31911810,
year = {2020},
author = {Nevill, PG and Zhong, X and Tonti-Filippini, J and Byrne, M and Hislop, M and Thiele, K and van Leeuwen, S and Boykin, LM and Small, I},
title = {Large scale genome skimming from herbarium material for accurate plant identification and phylogenomics.},
journal = {Plant methods},
volume = {16},
number = {},
pages = {1},
pmid = {31911810},
issn = {1746-4811},
abstract = {BACKGROUND: Herbaria are valuable sources of extensive curated plant material that are now accessible to genetic studies because of advances in high-throughput, next-generation sequencing methods. As an applied assessment of large-scale recovery of plastid and ribosomal genome sequences from herbarium material for plant identification and phylogenomics, we sequenced 672 samples covering 21 families, 142 genera and 530 named and proposed named species. We explored the impact of parameters such as sample age, DNA concentration and quality, read depth and fragment length on plastid assembly error. We also tested the efficacy of DNA sequence information for identifying plant samples using 45 specimens recently collected in the Pilbara.<br><br>RESULTS: Genome skimming was effective at producing genomic information at large scale. Substantial sequence information on the chloroplast genome was obtained from 96.1% of samples, and complete or near-complete sequences of the nuclear ribosomal RNA gene repeat were obtained from 93.3% of samples. We were able to extract sequences for the core DNA barcode regions rbcL and matK from 96 to 93.3% of samples, respectively. Read quality and DNA fragment length had significant effects on sequencing outcomes and error correction of reads proved essential. Assembly problems were specific to certain taxa with low GC and high repeat content (Goodenia, Scaevola, Cyperus, Bulbostylis, Fimbristylis) suggesting biological rather than technical explanations. The structure of related genomes was needed to guide the assembly of repeats that exceeded the read length. DNA-based matching proved highly effective and showed that the efficacy for species identification declined in the order cpDNA&#x2009;>>&#x2009;rDNA&#x2009;>&#x2009;matK&#x2009;>>&#x2009;rbcL.<br><br>CONCLUSIONS: We showed that a large-scale approach to genome sequencing using herbarium specimens produces high-quality complete cpDNA and rDNA sequences as a source of data for DNA barcoding and phylogenomics.},
}
@article {pmid31910332,
year = {2020},
author = {Montero-Vargas, M and Escudero-Leyva, E and Díaz-Valerio, S and Chaverri, P},
title = {Step-by-Step Pipeline for the Ecological Analysis of Endophytic Fungi using ITS nrDNA Data.},
journal = {Current protocols in microbiology},
volume = {56},
number = {1},
pages = {e96},
doi = {10.1002/cpmc.96},
pmid = {31910332},
issn = {1934-8533},
mesh = {DNA, Fungal/*genetics ; DNA, Ribosomal Spacer/*genetics ; Endophytes/classification/*genetics/isolation &amp; purification ; Fungi/classification/*genetics/isolation &amp; purification ; *Genetic Techniques ; Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {The nuclear ribosomal DNA internal transcribed spacer (ITS) is accepted as the genetic marker or barcode of choice for the identification of fungal samples. Here, we present a protocol to analyze fungal ITS data, from quality preprocessing of raw sequences to identification of operational taxonomic units (OTUs), taxonomic classification, and assignment of functional traits. The pipeline relies on well-established and manually curated data collections, namely the UNITE database and the FUNGuild script. As an example, real ITS data from culturable endophytic fungi were analyzed, providing detailed descriptions for every step, parameter, and downstream analysis, and finishing with a phylogenetic analysis of the sequences and assigned ecological roles. This article constitutes a comprehensive guide for researchers that have little familiarity with bioinformatic analysis of essential steps required in further ecological studies of fungal communities. © 2020 by John Wiley &amp; Sons, Inc. Basic Protocol 1: Raw sequencing data processing Support Protocol: Building a BLAST database Basic Protocol 2: Obtaining information from databases Basic Protocol 3: Phylogenetic analysis.},
}
@article {pmid31910130,
year = {2020},
author = {Liimatainen, K and Niskanen, T and San-Fabian, B and Mujic, AB and Peintner, U and Dresch, P and Furci, G and Nouhra, E and Matheny, PB and Smith, ME},
title = {Cortinarius section Thaumasti in South American Nothofagaceae forests.},
journal = {Mycologia},
volume = {112},
number = {2},
pages = {329-341},
doi = {10.1080/00275514.2019.1689763},
pmid = {31910130},
issn = {1557-2536},
mesh = {Agaricales/*classification/cytology/genetics/isolation &amp; purification ; DNA, Ribosomal Spacer ; Fagales/*microbiology ; Forests ; Genes, Fungal ; *Mycorrhizae ; New Zealand ; Phylogeny ; South America ; },
abstract = {We studied the South American species of Cortinarius section Thaumasti based on morphological and molecular data. Members of this group can easily be identified in the field because the basidiomata are small and Phlegmacium-like with a bulbous stipe and the universal veil in most species forms a distinct volva at the base of the stipe. The phylogenetic delimitation of the clade was mostly in concordance with the earlier, morphology-based grouping of the South American taxa except that C. chrysophaeus was resolved outside of the clade. Altogether nine species were recognized in the section. Four species, C. chlorophanus, C. coleopus, C. cosmoxanthus, and C. vaginatus, were previously described by other authors, whereas three species, C. chlorosplendidus, C. olivaceovaginatus, and C. subcosmoxanthus, are described here as new. We were able to identify two remaining taxa, but we do not have sufficient morphological data to allow for a formal description. All of the species in C. section Thaumasti form ectomycorrhizal associations with Nothofagaceae. They have been documented from South America and New Zealand. The Patagonian species are considered endemic to the region. A key to the described species is provided.},
}
@article {pmid31909084,
year = {2020},
author = {Schmit, PF and Pacouret, S and Zinn, E and Telford, E and Nicolaou, F and Broucque, F and Andres-Mateos, E and Xiao, R and Penaud-Budloo, M and Bouzelha, M and Jaulin, N and Adjali, O and Ayuso, E and Vandenberghe, LH},
title = {Cross-Packaging and Capsid Mosaic Formation in Multiplexed AAV Libraries.},
journal = {Molecular therapy. Methods &amp; clinical development},
volume = {17},
number = {},
pages = {107-121},
pmid = {31909084},
issn = {2329-0501},
abstract = {Generation and screening of libraries of adeno-associated virus (AAV) variants have emerged as a powerful method for identifying novel capsids for gene therapy applications. For the majority of libraries, vast population diversity requires multiplexed production, in which a library of inverted terminal repeat (ITR)-containing plasmid variants is transfected together into cells to generate the viral library. This process has the potential to be confounded by cross-packaging and mosaicism, in which particles are comprised of genomes and capsid monomers derived from different library members. Here, we investigate the prevalence of cross-packaging and mosaicism in simplified, minimal libraries using novel assays designed to assess capsid composition and packaging fidelity. We show that AAV library variants are prone to cross-packaging and capsid mosaic formation when produced at high plasmid levels, although to a lesser extent than in a recombinant context. We also provide experimental evidence that dilution of input library DNA significantly increases capsid monomer homogeneity and increases capsid:genome correlation in AAV libraries. Lastly, we determine that similar dilution methods yield higher-quality libraries when used for in vivo screens. Together, these findings quantitatively characterized the prevalence of cross-packaging and mosaicism in AAV libraries and established conditions that minimize related noise in subsequent screens.},
}
@article {pmid31907471,
year = {2020},
author = {Tang, L},
title = {Optically measuring barcodes.},
journal = {Nature methods},
volume = {17},
number = {1},
pages = {30},
doi = {10.1038/s41592-019-0716-0},
pmid = {31907471},
issn = {1548-7105},
}
@article {pmid31906844,
year = {2020},
author = {Bradshaw, M and Grewe, F and Thomas, A and Harrison, CH and Lindgren, H and Muggia, L and St Clair, LL and Lumbsch, HT and Leavitt, SD},
title = {Characterizing the ribosomal tandem repeat and its utility as a DNA barcode in lichen-forming fungi.},
journal = {BMC evolutionary biology},
volume = {20},
number = {1},
pages = {2},
pmid = {31906844},
issn = {1471-2148},
mesh = {Ascomycota/classification/*genetics ; Cell Nucleus/genetics ; *DNA Barcoding, Taxonomic/methods ; DNA, Fungal/genetics ; DNA, Intergenic ; DNA, Ribosomal ; DNA, Ribosomal Spacer/genetics ; High-Throughput Nucleotide Sequencing ; Lichens/classification/*genetics ; Phylogeny ; Symbiosis ; Tandem Repeat Sequences ; },
abstract = {BACKGROUND: Regions within the nuclear ribosomal operon are a major tool for inferring evolutionary relationships and investigating diversity in fungi. In spite of the prevalent use of ribosomal markers in fungal research, central features of nuclear ribosomal DNA (nrDNA) evolution are poorly characterized for fungi in general, including lichenized fungi. The internal transcribed spacer (ITS) region of the nrDNA has been adopted as the primary DNA barcode identification marker for fungi. However, little is known about intragenomic variation in the nrDNA in symbiotic fungi. In order to better understand evolution of nrDNA and the utility of the ITS region for barcode identification of lichen-forming fungal species, we generated nearly complete nuclear ribosomal operon sequences from nine species in the Rhizoplaca melanophthalma species complex using short reads from high-throughput sequencing.<br><br>RESULTS: We estimated copy numbers for the nrDNA operon, ranging from nine to 48 copies for members of this complex, and found low levels of intragenomic variation in the standard barcode region (ITS). Monophyly of currently described species in this complex was supported in phylogenetic inferences based on the ITS, 28S, intergenic spacer region, and some intronic regions, independently; however, a phylogenetic inference based on the 18S provided much lower resolution. Phylogenetic analysis of concatenated ITS and intergenic spacer sequence data generated from 496 specimens collected worldwide revealed previously unrecognized lineages in the nrDNA phylogeny.<br><br>CONCLUSIONS: The results from our study support the general assumption that the ITS region of the nrDNA is an effective barcoding marker for fungi. For the R. melanophthalma group, the limited amount of potential intragenomic variability in the ITS region did not correspond to fixed diagnostic nucleotide position characters separating taxa within this species complex. Previously unrecognized lineages inferred from ITS sequence data may represent undescribed species-level lineages or reflect uncharacterized aspects of nrDNA evolution in the R. melanophthalma species complex.},
}
@article {pmid31906128,
year = {2019},
author = {Vu, HT and Vu, QL and Nguyen, TD and Tran, N and Nguyen, TC and Luu, PN and Tran, DD and Nguyen, TK and Le, L},
title = {Genetic Diversity and Identification of Vietnamese Paphiopedilum Species Using DNA Sequences.},
journal = {Biology},
volume = {9},
number = {1},
pages = {},
pmid = {31906128},
issn = {2079-7737},
support = {312/2013/HD-SKHCN//Department of Science and Technology of Hochiminh City, Vietnam/ ; },
abstract = {Paphiopedilum is among the most popular ornamental orchid genera due to its unique slipper flowers and attractive leaf coloration. Most of the Paphiopedilum species are in critical danger due to over-exploitation. They were listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora, which prevents their being traded across borders. While most Paphiopedilum species are distinctive, owing to their respective flowers, their vegetative features are more similar and undistinguished. Hence, the conservation of these species is challenging, as most traded specimins are immature and non-flowered. An urgent need exists for effective identification methods to prevent further illegal trading of Paphiopedilum species. DNA barcoding is a rapid and sensitive method for species identification, at any developmental stage, using short DNA sequences. In this study, eight loci, i.e., ITS, LEAFY, ACO, matK, trnL, rpoB, rpoC1, and trnH-psbA, were screened for potential barcode sequences on the Vietnamese Paphiopedilum species. In total, 17 out of 22 Paphiopedilum species were well identified. The studied DNA sequences were deposited to GenBank, in which Paphiopedilum dalatense accessions were introduced for the first time. ACO, LEAFY, and trnH-psbA were limited in amplification rate for Paphiopedilum. ITS was the best single barcode. Single ITS could be used along with nucleotide polymorphism characteristics for species discrimination. The combination of ITS + matK was the most efficient identification barcode for Vietnamese Paphiopedilum species. This barcode also succeeded in recognizing misidentified or wrongly-named traded samples. Different bioinformatics programs and algorithms for establishing phylogenetic trees were also compared in the study to propose quick, simple, and effective tools for practical use. It was proved that both the Bayesian Inference method in the MRBAYES program and the neighbor-joining method in the MEGA software met the criteria. Our study provides a barcoding database of Vietnamese Paphiopedilum which may significantly contribute to the control and conservation of these valuable species.},
}
@article {pmid31904820,
year = {2020},
author = {Keller, A and Hohlfeld, S and Kolter, A and Schultz, J and Gemeinholzer, B and Ankenbrand, MJ},
title = {BCdatabaser: on-the-fly reference database creation for (meta-)barcoding.},
journal = {Bioinformatics (Oxford, England)},
volume = {36},
number = {8},
pages = {2630-2631},
doi = {10.1093/bioinformatics/btz960},
pmid = {31904820},
issn = {1367-4811},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Databases, Factual ; *Documentation ; *Software ; },
abstract = {SUMMARY: DNA barcoding and meta-barcoding have become irreplaceable in research and applications, where identification of taxa alone or within a mixture, respectively, becomes relevant. Pioneering studies were in the microbiological context, yet nowadays also plants and animals become targeted. Given the variety of markers used, formatting requirements for classifiers and constant growth of primary databases, there is a need for dedicated reference database creation. We developed a web and command-line interface to generate such on-the-fly for any applicable marker and taxonomic group with optional filtering, formatting and restriction specific for (meta-)barcoding purposes. Also, databases optionally receive a DOI, making them well-documented with meta-data, publicly sharable and citable.<br><br>source code: https://www.github.com/molbiodiv/bcdatabaser, webservice: https://bcdatabaser.molecular.eco, documentation: https://molbiodiv.github.io/bcdatabaser.},
}
@article {pmid31901140,
year = {2020},
author = {Ding, Y and Jiang, G and Huang, L and Chen, C and Sun, J and Zhu, C},
title = {DNA barcoding coupled with high-resolution melting analysis for nut species and walnut milk beverage authentication.},
journal = {Journal of the science of food and agriculture},
volume = {100},
number = {6},
pages = {2372-2379},
doi = {10.1002/jsfa.10241},
pmid = {31901140},
issn = {1097-0010},
support = {LR17C130001//Natural Science Foundation of Zhejiang Province/ ; LY19C020001//Natural Science Foundation of Zhejiang Province/ ; 31771698//National Natural Science Foundation of China/ ; },
mesh = {Arachis/chemistry/genetics ; Beverages/*analysis ; China ; Chloroplasts/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; Food Contamination/analysis ; Juglans/*chemistry/*genetics ; Nuts/chemistry ; Glycine max/chemistry/genetics ; },
abstract = {BACKGROUND: Walnut (Juglans regia L.) is one of the most widely cultivated nuts. Walnut milk beverage is very popular in China due to its nutritional value. However, adulterated walnut milk ingredients have been detected in the Chinese market. Peanut and soybean are sold at much lower prices than walnut and are reported to be commonly used for adulteration in the industrial chain of walnut milk production. The purpose of this study is therefore to develop an accurate and efficient method for detecting the authenticity of the raw materials used in walnut milk beverage.<br><br>RESULTS: DNA barcoding and high-resolution melting (HRM) analyses were used to identify common adulterated raw ingredients such as peanut and soybean in commercial walnut milk beverage samples. The chloroplast psbA-trnH gene was used for sequencing, and HRM analysis was performed. We also prepared experimental mixtures, in the laboratory, with different quantities of walnut, peanut, and soybean. High-resolution melting analysis of the experimental mixtures clearly distinguished all of them. The results revealed that most of the walnut milk beverage samples fell in the same cluster of walnut species. Several samples fell in the peanut cluster, confirming that they were adulterated products.<br><br>CONCLUSION: The results revealed that HRM analysis based on the psbA-trnH barcode sequence can be used to identify raw ingredients in walnut milk beverages. &#xa9; 2020 Society of Chemical Industry.},
}
@article {pmid31899899,
year = {2020},
author = {Xu, S and Böttcher, L and Chou, T},
title = {Diversity in biology: definitions, quantification and models.},
journal = {Physical biology},
volume = {17},
number = {3},
pages = {031001},
pmid = {31899899},
issn = {1478-3975},
support = {R01 HL146552/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; *Biodiversity ; Data Interpretation, Statistical ; Entropy ; Humans ; *Models, Biological ; },
abstract = {Diversity indices are useful single-number metrics for characterizing a complex distribution of a set of attributes across a population of interest. The utility of these different metrics or sets of metrics depends on the context and application, and whether a predictive mechanistic model exists. In this topical review, we first summarize the relevant mathematical principles underlying heterogeneity in a large population, before outlining the various definitions of 'diversity' and providing examples of scientific topics in which its quantification plays an important role. We then review how diversity has been a ubiquitous concept across multiple fields, including ecology, immunology, cellular barcoding experiments, and socioeconomic studies. Since many of these applications involve sampling of populations, we also review how diversity in small samples is related to the diversity in the entire population. Features that arise in each of these applications are highlighted.},
}
@article {pmid31899786,
year = {2020},
author = {Williams, SH and Levy, A and Yates, RA and Somaweera, N and Neville, PJ and Nicholson, J and Lindsay, MDA and Mackenzie, JS and Jain, K and Imrie, A and Smith, DW and Lipkin, WI},
title = {Discovery of Jogalong virus, a novel hepacivirus identified in a Culex annulirostris (Skuse) mosquito from the Kimberley region of Western Australia.},
journal = {PloS one},
volume = {15},
number = {1},
pages = {e0227114},
pmid = {31899786},
issn = {1932-6203},
support = {U19 AI109761/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Culex/*virology ; *Genome, Viral ; Hepacivirus/classification/*genetics/pathogenicity ; Mosquito Vectors/*virology ; *Phylogeny ; Viral Proteins/genetics ; Western Australia ; },
abstract = {The discovery of hepaciviruses in non-human hosts has accelerated following the advancement of high-throughput sequencing technology. Hepaciviruses have now been described in reptiles, fish, birds, and an extensive array of mammals. Using metagenomic sequencing on pooled samples of field-collected Culex annulirostris mosquitoes, we discovered a divergent hepacivirus-like sequence, named Jogalong virus, from the Kimberley region in northern Western Australia. Using PCR, we screened the same 300 individual mosquitoes and found just a single positive sample (1/300, 0.33%). Phylogenetic analysis of the hepacivirus NS5B protein places Jogalong virus within the genus Hepacivirus but on a distinct and deeply rooted monophyletic branch shared with duck hepacivirus, suggesting a notably different evolutionary history. Vertebrate barcoding PCR targeting two mitochondrial genes, cytochrome c oxidase subunit I and cytochrome b, indicated that the Jogalong virus-positive mosquito had recently fed on the tawny frogmouth (Podargus strigoides), although it is currently unknown whether this bird species contributes to the natural ecology of this virus.},
}
@article {pmid31897449,
year = {2019},
author = {Crawford, KHD and Bloom, JD},
title = {alignparse: A Python package for parsing complex features from high-throughput long-read sequencing.},
journal = {Journal of open source software},
volume = {4},
number = {44},
pages = {},
pmid = {31897449},
issn = {2475-9066},
support = {R01 AI140891/AI/NIAID NIH HHS/United States ; R01 AI141707/AI/NIAID NIH HHS/United States ; S10 OD020069/OD/NIH HHS/United States ; },
abstract = {Advances in sequencing technology have made it possible to generate large numbers of long, high-accuracy sequencing reads. For instance, the new PacBio Sequel platform can generate hundreds of thousands of high-quality circular consensus sequences in a single run (Hebert et al., 2018; Rhoads &amp; Au, 2015). Good programs exist for aligning these reads for genome assembly (Chaisson &amp; Tesler, 2012; Li, 2018). However, these long reads can also be used for other purposes, such as sequencing PCR amplicons that contain various features of interest. For instance, PacBio circular consensus sequences have been used to identify the mutations in influenza viruses in single cells (Russell et al, 2019), or to link barcodes to gene mutants in deep mutational scanning (Matreyek et al., 2018). For such applications, the alignment of the sequences to the targets may be fairly trivial, but it is not trivial to then parse specific features of interest (such as mutations, unique molecular identifiers, cell barcodes, and flanking sequences) from these alignments. Here we describe alignparse, a Python package for parsing complex sets of features from long sequences that map to known targets. Specifically, it allows the user to provide complex target sequences in Genbank Flat File format that contain an arbitrary number of user-defined sub-sequence features (Sayers et al., 2019). It then aligns the sequencing reads to these targets and filters alignments based on whether the user-specified features are present with the desired identities (which can be set to different thresholds for different features). Finally, it parses out the sequences, mutations, and/or accuracy (sequence quality) of these features as specified by the user. The flexibility of this package therefore fulfills the need for a tool to extract and analyze complex sets of features in large numbers of long sequencing reads.},
}
@article {pmid31893466,
year = {2020},
author = {Fost, B and Morey, K and Ferguson, B and Bourque, D and Naaum, A and Bradley, D and Hanner, R},
title = {Rapid cooling via dry ice preserves the genetic and morphological integrity of fish embryos.},
journal = {Journal of fish biology},
volume = {96},
number = {3},
pages = {820-824},
doi = {10.1111/jfb.14248},
pmid = {31893466},
issn = {1095-8649},
support = {//This study was funded by National Grid and the Electric Power Research Institute./ ; //National Grid/ ; },
mesh = {Animals ; DNA Barcoding, Taxonomic ; *Dry Ice ; Embryo, Nonmammalian/anatomy &amp; histology ; Fishes/*anatomy &amp; histology/*classification ; Preservation, Biological/*methods ; },
abstract = {Larval fishes provide a valuable metric for assessing and monitoring species, populations, and ecosystem trends and condition. However, taxonomic resolution for this life stage is inherently problematic because of their individual sizes, limited morphological characteristics and high tissue degradation rates. There is little research on methods that rapidly preserve larval tissues for later morphological and molecular identification. The goal of this study was to test methods of rapidly killing fish embryos that maintain both morphological and molecular integrity. Rapid cooling with dry ice successfully maintained morphological and molecular integrity and may offer a simple and cost-effective approach for larval fish identification.},
}
@article {pmid31892714,
year = {2019},
author = {Song, Y and Zhang, Y and Xu, J and Li, W and Li, M},
title = {Characterization of the complete chloroplast genome sequence of Dalbergia species and its phylogenetic implications.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {20401},
pmid = {31892714},
issn = {2045-2322},
mesh = {Chloroplasts/*genetics/metabolism ; DNA Barcoding, Taxonomic ; Dalbergia/*genetics/metabolism ; *Genome, Chloroplast ; Mutation ; *Phylogeny ; Whole Genome Sequencing ; },
abstract = {The pantropical plant genus Dalbergia comprises approximately 250 species, most of which have a high economic and ecological value. However, these species are among the most threatened due to illegal logging and the timber trade. To enforce protective legislation and ensure effective conservation of Dalbergia species, the identity of wood being traded must be accurately validated. For the rapid and accurate identification of Dalbergia species and assessment of phylogenetic relationships, it would be highly desirable to develop more effective DNA barcodes for these species. In this study, we sequenced and compared the chloroplast genomes of nine species of Dalbergia. We found that these chloroplast genomes were conserved with respect to genome size, structure, and gene content and showed low sequence divergence. We identified eight mutation hotspots, namely, six intergenic spacer regions (trnL-trnT, atpA-trnG, rps16-accD, petG-psaJ, ndhF-trnL, and ndhG-ndhI) and two coding regions (ycf1a and ycf1b), as candidate DNA barcodes for Dalbergia. Phylogenetic analyses based on whole chloroplast genome data provided the best resolution of Dalbergia, and phylogenetic analysis of the Fabaceae showed that Dalbergia was sister to Arachis. Based on comparison of chloroplast genomes, we identified a set of highly variable markers that can be developed as specific DNA barcodes.},
}
@article {pmid31889874,
year = {2020},
author = {Gaber, A and Hassan, MM and Boland, C and Alsuhaibany, A and Babbington, J and Pereira, J and Budd, J and Shobrak, M},
title = {Molecular identification of Todiramphus chloris subspecies on the Arabian Peninsula using three mitochondrial barcoding genes and ISSR markers.},
journal = {Saudi journal of biological sciences},
volume = {27},
number = {1},
pages = {480-488},
pmid = {31889874},
issn = {1319-562X},
abstract = {The Collared Kingfisher (Todiramphus chloris) is widely distributed across the Indian and western Pacific Oceans and consists of about 50 subspecies. Two different subspecies of T. chloris occur in the Arabian Peninsula: T. c. abyssinicus from the Red Sea coast and T. c. kalbaensis from the Arabian Sea coast in the United Arab Emirates and Oman. The aim of this study was to determine the molecular relationship between the two Arabian subspecies and to establish the first DNA barcodes from the Arabian Peninsula for this species. Three different mitochondrial genes were used: (i) cytochrome c oxidase subunit I (COI), (ii) 12S rRNA (12S) and (iii) NADH dehydrogenase-1 (ND1). The COI gene sequences of the two subspecies were 100% identical, while the 12S and ND1 gene sequences revealed a unique single nucleotide variation between the two subspecies. Thus, this single nucleotide variation can be used as a DNA barcode to discriminate between two subspecies. Furthermore, the genetic profile or fingerprint for both subspecies were compared using ten primers of the highly polymorphic nuclear markers (Inter Simple Sequence Repeat, ISSR). As expected, the DNA analysis of the ISSR markers was able to distinguish between the specimens of the two subspecies. These results suggest that T. c. abyssinicus and T. c. kalbaensis are not identical and thus belong to different subspecies. Besides, the sequences of the COI gene for T. c. abyssinicus and T. c. kalbaensis differs by only 1.28% from T. sanctus suggesting that the Arabian subspecies are closely related to the Sacred Kingfisher (T. sanctus).},
}
@article {pmid31889834,
year = {2020},
author = {Rasool, KG and Husain, M and Salman, S and Tufail, M and Sukirno, S and Aldawood, AS},
title = {DNA barcoding of the fire ant genus Solenopsis Westwood (Hymenoptera: Formicidae) from the Riyadh region, the Kingdom of Saudi Arabia.},
journal = {Saudi journal of biological sciences},
volume = {27},
number = {1},
pages = {184-188},
pmid = {31889834},
issn = {1319-562X},
abstract = {The ant genus Solenopsis Westwood, 1840 is the largest in Myrmicinae subfamily having almost 200 described species worldwide. They are commonly distributed in the tropics and temperate areas of the world. Some invasive Solenopsis species are very dreadful. We have already reported a fire ant species, Solenopsis saudiensis Sharaf &amp; Aldawood, 2011, identified using traditional morphometric approaches of species identification. Present study was carried out to develop DNA Barcoding to identify Solenopsis saudiensis and to elucidate genetic structure of the various S. saudiensis populations across their distribution range in Riyadh, Saudi Arabia. The comparison of DNA barcodes showed no genetic diversity among six populations and a queen from S. saudiensis analyzed from the Riyadh region. This genetic resemblance probably reflects their adaptation toward a specific habitat, thus constituting a single and strong gene pool. Our comprehensive field survey did not provide any evidence of Solenopsis species except S. saudiensis in the Riyadh region. Solenopsis saudiensis populations were only found around date palm trees indicating their strong association with date palm groves. Moreover, S. saudiensis has 83-86% sequence identity to other Solenopsis spp. from other parts of the world. Interestingly, the highest sequence identity of (86%) was with that of Solenopsis molesta Say, 1836, the thief ant, from the USA. This study provides a working laboratory procedure and a reference library for the identification of Solenopsis saudiensis.},
}
@article {pmid31886776,
year = {2019},
author = {Lukhtanov, VA and Iashenkova, Y},
title = {Linking karyotypes with DNA barcodes: proposal for a new standard in chromosomal analysis with an example based on the study of Neotropical Nymphalidae (Lepidoptera).},
journal = {Comparative cytogenetics},
volume = {13},
number = {4},
pages = {435-449},
pmid = {31886776},
issn = {1993-0771},
abstract = {Chromosomal data are important for taxonomists, cytogeneticists and evolutionary biologists; however, the value of these data decreases sharply if they are obtained for individuals with inaccurate species identification or unclear species identity. To avoid this problem, here we suggest linking each karyotyped sample with its DNA barcode, photograph and precise geographic data, providing an opportunity for unambiguous identification of described taxa and for delimitation of undescribed species. Using this approach, we present new data on chromosome number diversity in neotropical butterflies of the subfamily Biblidinae (genus Vila Kirby, 1871) and the tribe Ithomiini (genera Oleria Hübner, 1816, Ithomia Hübner, 1816, Godyris Boisduval, 1870, Hypothyris Hübner, 1821, Napeogenes Bates, 1862, Pseudoscada Godman et Salvin, 1879 and Hyposcada Godman et Salvin, 1879). Combining new and previously published data we show that the species complex Oleria onega (Hewitson, [1852]) includes three discrete chromosomal clusters (with haploid chromosome numbers n = 15, n = 22 and n = 30) and at least four DNA barcode clusters. Then we discuss how the incomplete connection between these chromosomal and molecular data (karyotypes and DNA barcodes were obtained for different sets of individuals) complicates the taxonomic interpretation of the discovered clusters.},
}
@article {pmid31886246,
year = {2019},
author = {Ma, Q and Wang, Y and Zhu, L and Bi, C and Li, S and Li, S and Wen, J and Yan, K and Li, Q},
title = {Characterization of the Complete Chloroplast Genome of Acer truncatum Bunge (Sapindales: Aceraceae): A New Woody Oil Tree Species Producing Nervonic Acid.},
journal = {BioMed research international},
volume = {2019},
number = {},
pages = {7417239},
pmid = {31886246},
issn = {2314-6141},
mesh = {Acer/*genetics ; Fatty Acids, Monounsaturated/*metabolism ; Genes, Plant ; Genetic Markers ; Genetic Variation ; *Genome, Chloroplast ; Likelihood Functions ; Microsatellite Repeats/genetics ; Phylogeny ; Plant Oils/*metabolism ; Trees/*genetics ; Wood/*genetics ; },
abstract = {Acer truncatum, which is a new woody oil tree species, is an important ornamental and medicinal plant in China. To assess the genetic diversity and relationships of A. truncatum, we analyzed its complete chloroplast (cp) genome sequence. The A. truncatum cp genome comprises 156,492 bp, with the large single-copy, small single-copy, and inverted repeat (IR) regions consisting of 86,010, 18,050, and 26,216 bp, respectively. The A. truncatum cp genome contains 112 unique functional genes (i.e., 4 rRNA, 30 tRNA, and 78 protein-coding genes) as well as 78 simple sequence repeats, 9 forward repeats, 1 reverse repeat, 5 palindromic repeats, and 7 tandem repeats. We analyzed the expansion/contraction of the IR regions in the cp genomes of six Acer species. A comparison of these cp genomes indicated the noncoding regions were more diverse than the coding regions. A phylogenetic analysis revealed that A. truncatum is closely related to A. miaotaiense. Moreover, a novel ycf4-cemA indel marker was developed for distinguishing several Acer species (i.e., A. buergerianum, A. truncatum, A. henryi, A. negundo, A. ginnala, and A. tonkinense). The results of the current study provide valuable information for future evolutionary studies and the molecular barcoding of Acer species.},
}
@article {pmid31884031,
year = {2020},
author = {Park, HJ and Kwak, M and Baek, SH},
title = {Neuroprotective effects of Dendropanax morbifera leaves on glutamate-induced oxidative cell death in HT22 mouse hippocampal neuronal cells.},
journal = {Journal of ethnopharmacology},
volume = {251},
number = {},
pages = {112518},
doi = {10.1016/j.jep.2019.112518},
pmid = {31884031},
issn = {1872-7573},
mesh = {Animals ; *Araliaceae ; Biphenyl Compounds/chemistry ; Cell Death/drug effects ; Cell Line ; Glutamic Acid/toxicity ; Hippocampus/cytology ; Mice ; Mitochondria/drug effects/physiology ; Neurons/*drug effects ; Neuroprotective Agents/chemistry/*pharmacology ; Oxidative Stress/drug effects ; Picrates/chemistry ; Plant Extracts/chemistry/*pharmacology ; Plant Leaves ; Reactive Oxygen Species/metabolism ; Superoxides/chemistry ; },
abstract = {Dendropanax morbifera (DM) has long been used as a traditional herbal medicine for migraines. Glutamate toxicity and oxidative stress have emerged as the possible triggers implicated in migraine pathogenesis.<br><br>AIM OF THE STUDY: We aimed to examine the neuroprotective effects of DM leaves (DML) on glutamate-induced oxidative cell death in HT22 mouse hippocampal neuronal cells.<br><br>MATERIALS AND METHODS: Molecular authentication of DML was assessed using DNA barcoding analysis. Four different solvent extracts of DML were prepared and subjected to antioxidant activity and phytochemical assays. Neuroprotective effects of DML extracts were evaluated using relevant biochemical and imaging assays that measure cell viability/death, ROS generation, Ca[2+] levels, mitochondrial dysfunction, and AIF nuclear translocation.<br><br>RESULTS: The sequences of matK, rbcL, atpF-H, and psbK-I in DML were identical with those in voucher specimens, confirming that DML was indeed D. morbifera. The ethyl acetate extract of DML (DMLE) showed the highest flavonoid and phenolic content, and prominent DPPH/superoxide radical scavenging and reducing power activities. In the HT22&#xa0;cell model, glutamate was shown to be the causative agent for apoptotic cell death via elevation of intracellular ROS and Ca[2+] levels, induction of mitochondrial depolarization and membrane permeabilization, and translocation of AIF to the nucleus. Of note, N-acetyl-L-cysteine and necrostatin-1, but not z-VAD-fmk, completely prevented glutamate-induced cell death, implying that oxidative stress and AIF translocation were pivotal in glutamate cytotoxicity. DMLE significantly recovered glutamate-induced apoptotic cell death in a concentration-dependent manner. It completely inhibited intracellular/mitochondrial ROS generation, the elevation of Ca[2+] levels, and mitochondrial dysfunction induced by glutamate during early exposure within 8&#xa0;h. It significantly reversed subsequent AIF nuclear translocation after 12&#xa0;h of treatment. Antioxidant activities of DMLE may be the protective mechanism that regulates homeostatic balance of ROS and Ca[2+] as well as maintains mitochondrial function.<br><br>CONCLUSIONS: DMLE shows significant neuroprotective effects against glutamate-induced oxidative neuronal cell death. Therefore, DM could be a potential therapeutic candidate for neurological disorders propagated by glutamate toxicity.},
}
@article {pmid31883048,
year = {2020},
author = {Nebel, C and Harl, J and Pajot, A and Weissenböck, H and Amar, A and Sumasgutner, P},
title = {High prevalence and genetic diversity of Haemoproteus columbae (Haemosporida: Haemoproteidae) in feral pigeons Columba livia in Cape Town, South Africa.},
journal = {Parasitology research},
volume = {119},
number = {2},
pages = {447-463},
pmid = {31883048},
issn = {1432-1955},
mesh = {Animals ; Bird Diseases/epidemiology/*parasitology ; Columbidae/*parasitology ; Cytochromes b/genetics ; *Genetic Variation ; Haemosporida/*genetics ; Prevalence ; Protozoan Infections, Animal/epidemiology/*parasitology ; South Africa/epidemiology ; },
abstract = {In this study, we explore blood parasite prevalence, infection intensity, and co-infection levels in an urban population of feral pigeons Columba livia in Cape Town. We analyze the effect of blood parasites on host body condition and the association between melanin expression in the host's plumage and parasite infection intensity and co-infection levels. Relating to the haemosporidian parasite itself, we study their genetic diversity by means of DNA barcoding (cytochrome b) and show the geographic and host distribution of related parasite lineages in pigeons worldwide. Blood from 195 C. livia individuals was collected from April to June 2018. Morphometric measurements and plumage melanism were recorded from every captured bird. Haemosporidian prevalence and infection intensity were determined by screening blood smears and parasite lineages by DNA sequencing. Prevalence of Haemoproteus spp. was high at 96.9%. The body condition of the hosts was negatively associated with infection intensity. However, infection intensity was unrelated to plumage melanism. The cytochrome b sequences revealed the presence of four Haemoproteus lineages in our population of pigeons, which show high levels of co-occurrence within individual birds. Three lineages (HAECOL1, COLIV03, COQUI05) belong to Haemoproteus columbae and differ only by 0.1% to 0.8% in the cytochrome b gene. Another lineage (COLIV06) differs by 8.3% from the latter ones and is not linked to a morphospecies, yet. No parasites of the genera Leucocytozoon and Plasmodium were detected.},
}
@article {pmid31881939,
year = {2019},
author = {Orr, RJS and Haugen, MN and Berning, B and Bock, P and Cumming, RL and Florence, WK and Hirose, M and Di Martino, E and Ramsfjell, MH and Sannum, MM and Smith, AM and Vieira, LM and Waeschenbach, A and Liow, LH},
title = {A genome-skimmed phylogeny of a widespread bryozoan family, Adeonidae.},
journal = {BMC evolutionary biology},
volume = {19},
number = {1},
pages = {235},
pmid = {31881939},
issn = {1471-2148},
mesh = {Animals ; Biological Evolution ; Bryozoa/*classification/*genetics ; Evolution, Molecular ; Genome, Mitochondrial ; Phylogeny ; Sequence Analysis, DNA ; rRNA Operon ; },
abstract = {BACKGROUND: Understanding the phylogenetic relationships among species is one of the main goals of systematic biology. Simultaneously, credible phylogenetic hypotheses are often the first requirement for unveiling the evolutionary history of traits and for modelling macroevolutionary processes. However, many non-model taxa have not yet been sequenced to an extent such that statistically well-supported molecular phylogenies can be constructed for these purposes. Here, we use a genome-skimming approach to extract sequence information for 15 mitochondrial and 2 ribosomal operon genes from the cheilostome bryozoan family, Adeonidae, Busk, 1884, whose current systematics is based purely on morphological traits. The members of the Adeonidae are, like all cheilostome bryozoans, benthic, colonial, marine organisms. Adeonids are also geographically widely-distributed, often locally common, and are sometimes important habitat-builders.<br><br>RESULTS: We successfully genome-skimmed 35 adeonid colonies representing 6 genera (Adeona, Adeonellopsis, Bracebridgia, Adeonella, Laminopora and Cucullipora). We also contributed 16 new, circularised mitochondrial genomes to the eight previously published for cheilostome bryozoans. Using the aforementioned mitochondrial and ribosomal genes, we inferred the relationships among these 35 samples. Contrary to some previous suggestions, the Adeonidae is a robustly supported monophyletic clade. However, the genera Adeonella and Laminopora are in need of revision: Adeonella is polyphyletic and Laminopora paraphyletically forms a clade with some Adeonella species. Additionally, we assign a sequence clustering identity using cox1 barcoding region of 99% at the species and 83% at the genus level.<br><br>CONCLUSIONS: We provide sequence data, obtained via genome-skimming, that greatly increases the resolution of the phylogenetic relationships within the adeonids. We present a highly-supported topology based on 17 genes and substantially increase availability of circularised cheilostome mitochondrial genomes, and highlight how we can extend our pipeline to other bryozoans.},
}
@article {pmid31880864,
year = {2021},
author = {Zhang, XM and Shi, ZY and Zhang, SQ and Zhang, P and Wilson, JJ and Shih, C and Li, J and Li, XD and Yu, GY and Zhang, AB},
title = {Plant-herbivorous insect networks: who is eating what revealed by long barcodes using high-throughput sequencing and Trinity assembly.},
journal = {Insect science},
volume = {28},
number = {1},
pages = {127-143},
doi = {10.1111/1744-7917.12749},
pmid = {31880864},
issn = {1744-7917},
support = {31772501//Natural Science Foundation of China/ ; //Academy for Multidisciplinary Studies, Capital Normal University/ ; IRT_17R75//Program for Changjiang Scholars and Innovative Research Team in University/ ; IDHT20180518//Support Project of High-level Teachers in Beijing Municipal Universities/ ; 31425023//China National Funds for Distinguished Young Scientists/ ; },
mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA, Plant/analysis ; Diet ; *Food Deprivation ; *Herbivory ; Larva/growth &amp; development/physiology ; Moths/growth &amp; development/*physiology ; *Pinus ; *Salix ; *Nicotiana ; *Vitis ; },
abstract = {Interactions between plants and insects are among the most important life functions for all organism at a particular natural community. Usually a large number of samples are required to identify insect diets in food web studies. Previously, Sanger sequencing and next generation sequencing (NGS) with short DNA barcodes were used, resulting in low species-level identification; meanwhile the costs of Sanger sequencing are expensive for metabarcoding together with more samples. Here, we present a fast and effective sequencing strategy to identify larvae of Lepidoptera and their diets at the same time without increasing the cost on Illumina platform in a single HiSeq run, with long-multiplex-metabarcoding (COI for insects, rbcL, matK, ITS and trnL for plants) obtained by Trinity assembly (SHMMT). Meanwhile, Sanger sequencing (for single individuals) and NGS (for polyphagous) were used to verify the reliability of the SHMMT approach. Furthermore, we show that SHMMT approach is fast and reliable, with most high-quality sequences of five DNA barcodes of 63 larvae individuals (54 species) recovered (full length of 100% of the COI gene and 98.3% of plant DNA barcodes) using Trinity assembly (up-sized to 1015 bp). For larvae diets identification, 95% are reliable; the other 5% failed because their guts were empty. The diets identified by SHMMT approach are 100% consistent with the host plants that the larvae were feeding on during our collection. Our study demonstrates that SHMMT approach is reliable and cost-effective for insect-plants network studies. This will facilitate insect-host plant studies that generally contain a huge number of samples.},
}
@article {pmid31880429,
year = {2020},
author = {Valastyan, JS and Tota, MR and Taylor, IR and Stergioula, V and Hone, GAB and Smith, CD and Henke, BR and Carson, KG and Bassler, BL},
title = {Discovery of PqsE Thioesterase Inhibitors for Pseudomonas aeruginosa Using DNA-Encoded Small Molecule Library Screening.},
journal = {ACS chemical biology},
volume = {15},
number = {2},
pages = {446-456},
pmid = {31880429},
issn = {1554-8937},
support = {/HHMI/Howard Hughes Medical Institute/United States ; F32 GM134583/GM/NIGMS NIH HHS/United States ; R37 GM065859/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacterial Proteins/*antagonists &amp; inhibitors ; Benzamides/chemical synthesis/pharmacology ; DNA/*chemistry ; Enzyme Inhibitors/chemical synthesis/*pharmacology ; Microbial Sensitivity Tests ; Molecular Structure ; Phthalic Acids/chemical synthesis/pharmacology ; Pseudomonas aeruginosa/*drug effects/enzymology ; Small Molecule Libraries/chemical synthesis/*pharmacology ; Structure-Activity Relationship ; Thiolester Hydrolases/*antagonists &amp; inhibitors ; },
abstract = {Pseudomonas aeruginosa is a leading cause of hospital-acquired infections in the United States. PqsE, a thioesterase enzyme, is vital for virulence of P. aeruginosa, making PqsE an attractive target for inhibition. Neither the substrate nor the product of PqsE catalysis has been identified. A library of 550 million DNA-encoded drug-like small molecules was screened for those that bind to the purified PqsE protein. The structures of the bound molecules were identified by high throughput sequencing of the attached DNA barcodes. Putative PqsE binders with the strongest affinity features were examined for inhibition of PqsE thioesterase activity in vitro. The most potent inhibitors were resynthesized off DNA and examined for the ability to alter PqsE thermal melting and for PqsE thioesterase inhibition. Here, we report the synthesis, biological activity, mechanism of action, and early structure-activity relationships of a series of 2-(phenylcarbamoyl)benzoic acids that noncompetitively inhibit PqsE. A small set of analogs designed to probe initial structure-activity relationships showed increases in potency relative to the original hits, the best of which has an IC50 = 5 μM. Compound refinement is required to assess their in vivo activities as the current compounds do not accumulate in the P. aeruginosa cytosol. Our strategy validates DNA-encoded compound library screening as a rapid and effective method to identify catalytic inhibitors of the PqsE protein, and more generally, for discovering binders to bacterial proteins revealed by genetic screening to have crucial in vivo activities but whose biological functions have not been well-defined.},
}
@article {pmid31877643,
year = {2019},
author = {Li, Q and Deng, J and Chen, C and Zeng, L and Lin, X and Cheng, Z and Qiao, G and Huang, X},
title = {DNA Barcoding Subtropical Aphids and Implications for Population Differentiation.},
journal = {Insects},
volume = {11},
number = {1},
pages = {},
pmid = {31877643},
issn = {2075-4450},
support = {31772504//National Natural Science Foundation of China/ ; 2016YFE0203100//National Key R&amp;D Program of China/ ; 2015J06005//Fujian Provincial Department of Science &amp; Technology/ ; },
abstract = {DNA barcoding has proven its worth in species identification, discovering cryptic diversity, and inferring genetic divergence. However, reliable DNA barcode reference libraries that these applications depend on are not available for many taxonomic groups and geographical regions. Aphids are a group of plant sap sucking insects, including many notorious pests in agriculture and forestry. The aphid fauna of the subtropical region has been understudied. In this study, based on extensive sampling effort across main subtropical areas, we sequenced 1581 aphid specimens of 143 morphospecies, representing 75 genera, and 13 subfamilies, to build the first comprehensive DNA barcode library for subtropical aphids. We examined the utility of DNA barcodes in identifying aphid species and population differentiation and evaluated the ability of different species delimitation methods (automatic barcode gap discovery (ABGD), generalized mixed Yule-coalescent (GMYC), and Bayesian Poisson tree processes (bPTP)). We found that most aphid species demonstrated barcode gaps and that a threshold value of 2% genetic distance is suitable for distinguishing most species. Our results indicated that ten morphospecies may have species divergence related to factors such as host plant or geography. By using two pest species Aphis spiraecola and A. gossypii as examples, we also discussed the effect of the sampling scale of host plants on the results and reliability of DNA barcoding of phytophagous insects. This DNA barcode library will be valuable for future studies and applications.},
}
@article {pmid31877364,
year = {2020},
author = {Veldman, S and Ju, Y and Otieno, JN and Abihudi, S and Posthouwer, C and Gravendeel, B and van Andel, TR and de Boer, HJ},
title = {DNA barcoding augments conventional methods for identification of medicinal plant species traded at Tanzanian markets.},
journal = {Journal of ethnopharmacology},
volume = {250},
number = {},
pages = {112495},
doi = {10.1016/j.jep.2019.112495},
pmid = {31877364},
issn = {1872-7573},
mesh = {*DNA Barcoding, Taxonomic ; *Medicine, African Traditional ; Plants, Medicinal/*classification/genetics ; Tanzania ; },
abstract = {ETHNOPHARMALOGICAL RELEVANCE: In Africa, traditional medicine is important for local healthcare and plants used for these purposes are commonly traded. Identifying medicinal plants sold on markets is challenging, as leaves, barks and roots are often fragmented or powdered. Vernacular names are often homonymic, and identification of material lacking sufficient morphological characters is time-consuming, season-dependent and might lead to incorrect assessments of commercialised species diversity.<br><br>AIM OF THE STUDY: In this study, we identified cases of vernacular heterogeneity of medicinal plants using a tiered approach of literature research, morphology and DNA barcoding.<br><br>MATERIAL AND METHODS: A total of 870 single ingredient medicinal plant samples corresponding to 452 local names were purchased from herbal markets in Dar-es-Salaam and Tanga, Tanzania, and identified using conventional methods as well as DNA barcoding using rbcL, matK and nrITS.<br><br>RESULTS: Using conventional methods, we could identify 70% of samples to at least family level, while 62% yielded a DNA barcode for at least one of the three markers. Combining conventional methods and DNA barcoding, 76% of the samples could be identified to species level, revealing a diversity of at least 175 species in 65 plant families. Analysis of the market samples revealed 80 cases of multilingualism and over- and under-differentiation. Afzelia quanzensis Welw., Zanthoxylum spp., Allophylus spp. and Albizia anthelmintica Brongn. were the most evident cases of multilingualism and over-differentiation, as they were traded under 8-12 vernacular names in up to five local languages. The most obvious case of under-differentiation was mwingajini (Swahili), which matched to eight scientific species in five different plant families.<br><br>CONCLUSIONS: Use of a tiered approach increases the identification success of medicinal plants sold in local market and corroborates findings that DNA barcoding can elucidate the identity of material that is unidentifiable based on morphology and literature as well as verify or disqualify these identifications. Results of this study can be used as a basis for quantitative market surveys of fragmented herbal medicine and to investigate conservation issues associated with this trade.},
}
@article {pmid31876057,
year = {2020},
author = {Tuma, J and Eggleton, P and Fayle, TM},
title = {Ant-termite interactions: an important but under-explored ecological linkage.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {95},
number = {3},
pages = {555-572},
doi = {10.1111/brv.12577},
pmid = {31876057},
issn = {1469-185X},
support = {156/2013/P//Grant agency of the University of South Bohemia/International ; 19-14620S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/International ; Bali consortium - NERC grant NE/L000016/1//Natural Environment Research Council/International ; },
mesh = {Animals ; Ants/genetics/*physiology ; DNA/analysis ; Ecology ; Isoptera/genetics/*physiology ; Predatory Behavior ; },
abstract = {Animal interactions play an important role in understanding ecological processes. The nature and intensity of these interactions can shape the impacts of organisms on their environment. Because ants and termites, with their high biomass and range of ecological functions, have considerable effects on their environment, the interaction between them is important for ecosystem processes. Although the manner in which ants and termites interact is becoming increasingly well studied, there has been no synthesis to date of the available literature. Here we review and synthesise all existing literature on ant-termite interactions. We infer that ant predation on termites is the most important, most widespread, and most studied type of interaction. Predatory ant species can regulate termite populations and subsequently slow down the decomposition of wood, litter and soil organic matter. As a consequence they also affect plant growth and distribution, nutrient cycling and nutrient availability. Although some ant species are specialised termite predators, there is probably a high level of opportunistic predation by generalist ant species, and hence their impact on ecosystem processes that termites are known to provide varies at the species level. The most fruitful future research direction will be to evaluate the impact of ant-termite predation on broader ecosystem processes. To do this it will be necessary to quantify the efficacy both of particular ant species and of ant communities as a whole in regulating termite populations in different biomes. We envisage that this work will require a combination of methods, including DNA barcoding of ant gut contents along with field observations and exclusion experiments. Such a combined approach is necessary for assessing how this interaction influences entire ecosystems.},
}
@article {pmid31875091,
year = {2019},
author = {Kurina, O and Kirik, H and Õunap, H and Õunap, E},
title = {The northernmost record of a blood-sucking ectoparasite, Lipoptena fortisetosa Maa (Diptera: Hippoboscidae), in Estonia.},
journal = {Biodiversity data journal},
volume = {7},
number = {},
pages = {e47857},
pmid = {31875091},
issn = {1314-2828},
abstract = {BACKGROUND: Deer keds are obligatory haematophagous parasites of large homeothermic animals, particularly cervids. Two of the five known species occurring in Europe-Lipoptena cervi (Linnaeus) and L. fortisetosa Maa-are known to have a relatively wide distribution. Lipoptena fortisetosa is considered to have been introduced into Europe with sika deer from the Eastern Palaearctic and is continuously expanding its range. Little is known about the medical importance of deer keds, but they can cause hair loss in cervids and are suspected to be vectors of several diseases.<br><br>NEW INFORMATION: Details of the distribution of Lipoptena fortisetosa in Europe, including its northernmost record, are provided. This species has been shown to have a viable population in Southern Estonia. Furthermore, the differences from allied L. cervi are discussed, based on morphological and molecular characters.},
}
@article {pmid31872629,
year = {2019},
author = {Meng, JQ and Li, HX and Luo, XM and Chen, XF and Liu, CS and Yang, YJ},
title = {[Diversity of fungi on surface of Pheretima].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {44},
number = {20},
pages = {4433-4438},
doi = {10.19540/j.cnki.cjcmm.20190729.101},
pmid = {31872629},
issn = {1001-5302},
mesh = {*Aflatoxins ; Alternaria ; Animals ; Aspergillus ; China ; *Drugs, Chinese Herbal ; *Fungi ; Penicillium ; },
abstract = {Traditional Chinese medicines(TCMs) are easily contaminated by fungi during planting,harvesting,processing,transportation and storage. The 2015 version of Chinese Pharmacopoeia stipulates the detection of aflatoxin in Dilong. After reviewing the literature,it has been found that there are no domestic and foreign scholars who have studied the surface fungi of Dilong. Pheretima,known as Dilong in China,is a commonly used TCMs in animal. In this experiment,8 batches of Dilong were collected from retail pharmacies in Beijing. The fungi on the surface of Dilong were cultured by traditional plate method and the single strain was obtained by the top purification method. The fungal colony morphology,microstructure characteristics and DNA barcode were used to isolate and identify the fungi. At the same time,based on Illumina Hi Seq 2500 high-throughput sequencing platform,the diversity of fungi on the surface of Dilong was analyzed. The results showed that 287 strains of 9 species of fungi were isolated and identified by plate method. Combined with 3 kinds of identification method,eight of nine fungi could be identified,respectively,Aspergillus niger,Penicillium,Alternaria nees,A. flavus,and Penicillium oxalicum,Humicola sp.,Talaromyces purpurogenus and A. insuetus,1 kind of fungi was not identified yet. Among them,Penicillium and Aspergillus were the dominant genus. The results of high-throughput sequencing belonged to 2 boundaries,6 gates,19 classes,44 orders,98 families,127 genus and 121 species in different classification levels. Wallemia,Aspergillus and Cordyceps were the dominant genus,and the relative abundances are 63. 33%,15. 28%,and 10. 28%,respectively. Through the diversity study on the surface fungi of Dilong in Beijing retail pharmacies,it can provide a reference for its safe storage and clinical use.},
}
@article {pmid31872627,
year = {2019},
author = {Lu, HS and Li, T and Jiang, D and Sun, YF and Chang, XX and Hu, XS and Liu, CS},
title = {[Identification and evaluation of Citrus grandis based on DNA barcode,UPLC and chromaticity method].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {44},
number = {20},
pages = {4419-4425},
doi = {10.19540/j.cnki.cjcmm.20190729.103},
pmid = {31872627},
issn = {1001-5302},
mesh = {Apigenin ; Citrus/classification/*genetics ; DNA Barcoding, Taxonomic ; Drugs, Chinese Herbal ; },
abstract = {In order to identify the source of Citrus grandis and evaluate its quality originate from two areas comprehensively,DNA barcode was used to identify 26 samples of C. grandis. The content of naringin,rhoifolin,naringenin and apigenin was determined by UPLC method,and the color difference was numerically studied by color difference analyzer,which was related to the effective components of C. grandis. The results showed that samples was the source of C. grandis in both regions. The ITS2 sequence length was about400-500 bp,and the sequence similarity reached 99. 82%. There was only one base deletion in the two groups. There was one base A in some medicinal materials of Guangdong at 330 bp,but no base in Chongqing. The contents of naringin and rhoifolin in Chongqing samples were higher than those in Guangdong samples,and there were statistical differences between naringenin and apigenin. The chroma value showed that L*value of Guangdong was larger,a*value was smaller,L*value of Chongqing was smaller,and a*value was larger,while the b*value of both was not significantly different; The results of correlation analysis showed that naringin,rhoifolin,naringenin were positively correlated with L*,b*value,negatively correlated with a*value,and apigenin had no correlation with L*,a*,b*value. In this study,the scientific identification and evaluation of C. grandis was carried out to provide a new idea for the further study of the rapid identification and evaluation of C. grandis.},
}
@article {pmid31872590,
year = {2019},
author = {Sun, SY and Fang, Y and Lai, MR and Ge, YQ and Zhang, GJ and Cheng, RB},
title = {[Morphological characteristics identification and molecular DNA barcoding analysis of Hippocampus spinosissimus].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {44},
number = {22},
pages = {4837-4843},
doi = {10.19540/j.cnki.cjcmm.20190829.109},
pmid = {31872590},
issn = {1001-5302},
mesh = {Animals ; Base Composition ; DNA ; *DNA Barcoding, Taxonomic ; Phylogeny ; Smegmamorpha/*genetics ; },
abstract = {The combination of morphological characteristics and DNA barcodes was used to a systematic study of Hippocampus spinosissimus,laying the foundation for rapid and accurate identification for the medical seahorse species. According to the reported literature and observation on seahorse samples,the typical characteristics of the H. spinosissimus include highly developed spiny,much short nose,single or double cheeks and strongly developed spines bordering pouch. Genomic DNAs of H. spinosissimus and other related seahorse species were extracted using the TIANamp Marine Animals DNA Kit. The COⅠ and ATP6 genes were amplified and sequenced in both directions. After the verification by Blast,the GC content,intraspecific and interspecific genetic distance,and the Neighbor joining(NJ) phylogenetic trees were analyzed by MEGA 7. The lengths of the COⅠ and ATP6 genes were 649 bp and 602-603 bp,respectively,with the average GC content of 39. 96% and 35. 37%. The maximum intraspecific genetic distances in H. spinosissimus based on COⅠ and ATP were both far less than the minimum interspecific genetic distance between H. spinosissimus and other seahorses,suggesting a significant barcoding gap. NJ analysis results of COⅠ and ATP6 exhibited that all H. spinosissimus species clustered together,indicating that the two DNA barcode could identify H. spinosissimus from other seahorses accurately and quickly. In addition,H. spinosissimus shared a close genetic relationship between H. kelloggi according to the NJ tree. Furthermore,there exits three stable subgroup structure of H. spinosissimus,indicating that COⅠ and ATP6 barcodes could be applied the indicator for the geographical ecology research of H. spinosissimus. The results obtained the typical morphological and molecular identification characteristics of H. spinosissimus,which played central roles for the development of species identification. This study provides an important basis data for expanding the medical seahorse resources and ensuring the safety of clinical medicine.},
}
@article {pmid31872587,
year = {2019},
author = {Chen, FR and Guo, QS and Yang, F and Zhu, ZB and Wang, T},
title = {[Application of ITS2 secondary structure phylogenetic information in DNA barcode identification of Chrysanthemum indicum and its related plants].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {44},
number = {22},
pages = {4813-4819},
doi = {10.19540/j.cnki.cjcmm.20190829.110},
pmid = {31872587},
issn = {1001-5302},
mesh = {*Chrysanthemum ; *DNA Barcoding, Taxonomic ; DNA, Plant ; DNA, Ribosomal Spacer ; Phylogeny ; Plants ; },
abstract = {By exploring additional phylogenetic information hidden in ITS2 secondary structure,the possibility of identifying Chrysanthemum indicum and its related species with DNA barcode of ITS2 nucleic acid sequence and its structure information were discussed.The genomic DNA was extracted from 12 samples. The ITS2 fragments were amplified by PCR and sequenced bidirectionally to obtain ITS2 sequence information. 28 sequences of related species for Ch. indicum were downloaded from Gen Bank. Until all 40 ITS2 sequences were aligned,ITS2 secondary structure prediction and structure comparison were finished. Then ITS2 secondary structure information was coded. After comparing ITS2 structure information and nucleic acid information,MP phylogenetic trees were built. The results showed that the secondary structures of ITS2 shared the same structure model--a four-fingered hand. They not only have the common characteristics of ITS2 secondary structures in plants,but also have many other conservative sequences,and their overall conservativeness is high. Among all species used in this study,their ITS2 secondary structures had obvious difference. In addition,the number of mutation sites in the joint matrix compared with the nucleic acid sequences increased by nearly 90%,which greatly enriched the number of mutation sites. This method of information analysis distinguished Ch. indicum from its related species. At the same time,the support rate of the branches of evolutionary trees and the identification rate of species were significantly improved. Although there was no distinction between Ch. zawadskii and Ch. morifolium,it effectively distinguished the three species,namely,Ch. hypargyrum,Ch.oreastrum,and Ch. dichrum. Therefore,the authors suggest that the ITS2 sequence combined with its structural data information should be applied to the identification of Ch. indicum and its related species,and be widely applied to DNA barcode research.},
}
@article {pmid31871665,
year = {2019},
author = {Adeniran, AA and Fernández-Santos, NA and Rodríguez-Rojas, JJ and Treviño-Garza, N and Huerta-Jiménez, H and Mis-Ávila, PC and Pérez-Pech, WA and Hernández-Triana, LM and Rodríguez-Pérez, MA},
title = {Identification of phlebotomine sand flies (Diptera: Psychodidae) from leishmaniasis endemic areas in southeastern Mexico using DNA barcoding.},
journal = {Ecology and evolution},
volume = {9},
number = {23},
pages = {13543-13554},
pmid = {31871665},
issn = {2045-7758},
abstract = {Leishmaniasis, a vector-borne disease transmitted to humans through the bite of phlebotomine sand flies, is of public health significance in southeastern Mexico. Active and continuous monitoring of vectors is an important aspect of disease control for the prediction of potential outbreaks. Thus, the correct identification of vectors is paramount in this regard. In this study, we employed DNA barcoding as a tool for identifying phlebotomine sand flies collected in localized cutaneous leishmaniasis endemic areas of Quintana Roo, Mexico. Specimens were collected using CDC light and Shannon traps as part of the Mexican Ministry of Health surveillance program. DNA extraction was carried out using a nondestructive protocol, and morphological identification based on taxonomic keys was conducted on slide-mounted specimens. Molecular taxonomic resolution using the 658-bp fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene was 100% congruent with the morphological identification. Seven species were identified: Lutzomyia cruciata (Coquillett 1907), Lutzomyia longipalpis (Lutz &amp; Neiva 1912), Psathyromyia shannoni (Dyar 1929), Dampfomyia deleoni (Fairchild &amp; Hertig 1947), Dampfomyia beltrani/steatopyga (Vargas &amp; Díaz-Nájera 1951), Bichromomyia olmeca olmeca (Vargas &amp; Díaz-Nájera, 1959), and Brumptomyia mesai (Sherlock 1962). Mean intraspecific divergence ranged from 0.12% to 1.22%, while interspecific distances ranged from 11.59% to 19.29%. Neighbor-joining (NJ) analysis using the Kimura 2-parameter model also showed specimens of the same species to be clustered together. The study provides the first cox1 sequences for three species of sand flies and indicates the utility of DNA barcoding for phlebotomine sand flies species identification in southeastern Mexico.},
}
@article {pmid31871662,
year = {2019},
author = {Everman, S and Wang, SY},
title = {Distinguishing Anuran species by high-resolution melting analysis of the COI barcode (COI-HRM).},
journal = {Ecology and evolution},
volume = {9},
number = {23},
pages = {13515-13520},
pmid = {31871662},
issn = {2045-7758},
abstract = {Taxonomic identification can be difficult when two or more species appear morphologically similar. DNA barcoding based on the sequence of the mitochondrial cytochrome c oxidase 1 gene (COI) is now widely used in identifying animal species. High-resolution melting analysis (HRM) provides an alternative method for detecting sequence variations among amplicons without having to perform DNA sequencing. The purpose of this study was to determine whether HRM of the COI barcode can be used to distinguish animal species. Using anurans as a model, we found distinct COI melting profiles among three congeners of both Lithobates spp. and Hyla spp. Sequence variations within species shifted the melting temperature of one or more melting domains slightly but do not affect the distinctness of the melting profiles for each species. An NMDS ordination plot comparing melting peak profiles among eight Anuran species showed overlapping profiles for Lithobates sphenocephala and Gastrophryne carolinensis. The COI amplicon for both species contained two melting domains with melting temperatures that were similar between the two species. The two species belong to two different families, highlighting the fact that COI melting profiles do not reveal phylogenetic relationships but simply reflect DNA sequence differences among stretches of DNA within amplicons. This study suggests that high-resolution melting analysis of COI barcodes (COI-HRM) may be useful as a simple and rapid method to distinguish animal species that appear morphologically similar.},
}
@article {pmid31871625,
year = {2019},
author = {Moura, CJ and Collins, AG and Santos, RS and Lessios, H},
title = {Predominant east to west colonizations across major oceanic barriers: Insights into the phylogeographic history of the hydroid superfamily Plumularioidea, suggested by a mitochondrial DNA barcoding marker.},
journal = {Ecology and evolution},
volume = {9},
number = {23},
pages = {13001-13016},
pmid = {31871625},
issn = {2045-7758},
abstract = {We provide preliminary insights into the global phylogeographic and evolutionary patterns across species of the hydrozoan superfamily Plumularioidea (Cnidaria: Hydrozoa). We analyzed 1,114 16S sequences of 198 putative species of Plumularioidea collected worldwide. We investigated genetic connections and divergence in relation to present-day and ancient biogeographic barriers, climate changes and oceanic circulation. Geographical distributions of most species are generally more constrained than previously assumed. Some species able to raft are dispersed widely. Human-mediated dispersal explains some wide geographical ranges. Trans-Atlantic genetic connections are presently unlikely for most of the tropical-temperate species, but were probably more frequent until the Miocene-Pliocene transition, before restriction of the Tethys Sea and the Central American Seaway. Trans-Atlantic colonizations were predominantly directed westwards through (sub)tropical waters. The Azores were colonized multiple times and through different routes, mainly from the east Atlantic, at least since the Pliocene. Extant geminate clades separated by the Isthmus of Panama have predominantly Atlantic origin. Various ancient colonizations mainly directed from the Indian Ocean to the Atlantic occurred through the Tethys Sea and around South Africa in periods of lower intensity of the Benguela upwelling. Thermal tolerance, population sizes, dispersal strategies, oceanic currents, substrate preference, and land barriers are important factors for dispersal and speciation of marine hydroids.},
}
@article {pmid31871399,
year = {2019},
author = {Han, HY and Ro, KE},
title = {DNA barcoding reveals a species group of the genus Campiglossa (Diptera, Tephritidae, Tephritinae) with recognition of a new species from East Asia and previously unknown females of Campiglossa coei (Hardy).},
journal = {ZooKeys},
volume = {899},
number = {},
pages = {1-36},
pmid = {31871399},
issn = {1313-2989},
abstract = {While analyzing DNA barcodes of all the Korean and some East Asian tephritid species in conjunction with the barcode sequences available from BOLD Systems (www.boldsystems.org), the large and taxonomically enigmatic genus Campiglossa was recovered as a monophyletic clade, together with the genera Dioxyna and Homoeotricha, which are here synonymized for that reason. Ten major lineages are also recognized within the Campiglossa clade: producta group, loewiana group, sororcula group, irrorata group, achyrophori group, difficilis group, luxorientis group, magniceps group, arisanica group, and misella group. Here, more detailed taxonomic accounts are provided for the misella group, including four DNA analysis-recovered members: C. coei, C. misella, C. paramelaena sp. nov., and C. melaena. A single morphological synapomorphy is proposed for this species group: the presence of a large mid-anterior dark wing marking in males with associated structural modification (more apically positioned crossvein R-M than in females). Based on the morphological characteristics, two presumptive members that are only known from male specimens are further recognized: C. pishanica and C. propria from China. A full description of C. paramelaena sp. nov., and a redescription of C. coei, for which only males were previously known, are provided. For all the included species, a taxonomic key, diagnoses, and photographs to aid their accurate identification are given. Finally, C. favillacea is synonymized with C. coei and C. roscida with C. misella, and C. coei and C. pishanica resurrected from the synonymy of C. misella.},
}
@article {pmid31870452,
year = {2019},
author = {Hanáková, K and Bernatík, O and Kravec, M and Micka, M and Kumar, J and Harnoš, J and Ovesná, P and Paclíková, P and Rádsetoulal, M and Potěšil, D and Tripsianes, K and Čajánek, L and Zdráhal, Z and Bryja, V},
title = {Comparative phosphorylation map of Dishevelled 3 links phospho-signatures to biological outputs.},
journal = {Cell communication and signaling : CCS},
volume = {17},
number = {1},
pages = {170},
pmid = {31870452},
issn = {1478-811X},
mesh = {Cells, Cultured ; Dishevelled Proteins/chemistry/*metabolism ; HEK293 Cells ; Humans ; Mass Spectrometry ; NIMA-Related Kinases/metabolism ; Phosphorylation ; Protein Conformation ; Signal Transduction ; },
abstract = {BACKGROUND: Dishevelled (DVL) is an essential component of the Wnt signaling cascades. Function of DVL is controlled by phosphorylation but the molecular details are missing. DVL3 contains 131 serines and threonines whose phosphorylation generates complex barcodes underlying diverse DVL3 functions. In order to dissect the role of DVL phosphorylation we analyzed the phosphorylation of human DVL3 induced by previously reported (CK1ε, NEK2, PLK1, CK2α, RIPK4, PKCδ) and newly identified (TTBK2, Aurora A) DVL kinases.<br><br>METHODS: Shotgun proteomics including TiO2 enrichment of phosphorylated peptides followed by liquid chromatography tandem mass spectrometry on immunoprecipitates from HEK293T cells was used to identify and quantify phosphorylation of DVL3 protein induced by 8 kinases. Functional characterization was performed by in-cell analysis of phospho-mimicking/non-phosphorylatable DVL3 mutants and supported by FRET assays and NMR spectroscopy.<br><br>RESULTS: We used quantitative mass spectrometry and calculated site occupancies and quantified phosphorylation of >&#x2009;80 residues. Functional validation demonstrated the importance of CK1&#x3b5;-induced phosphorylation of S268 and S311 for Wnt-3a-induced &#x3b2;-catenin activation. S630-643 cluster phosphorylation by CK1, NEK2 or TTBK2 is essential for even subcellular distribution of DVL3 when induced by CK1 and TTBK2 but not by NEK2. Further investigation showed that NEK2 utilizes a different mechanism to promote even localization of DVL3. NEK2 triggered phosphorylation of PDZ domain at S263 and S280 prevents binding of DVL C-terminus to PDZ and promotes an open conformation of DVL3 that is more prone to even subcellular localization.<br><br>CONCLUSIONS: We identify unique phosphorylation barcodes associated with DVL function. Our data provide an example of functional synergy between phosphorylation in structured domains and unstructured IDRs that together dictate the biological outcome. Video Abtract.},
}
@article {pmid31869382,
year = {2019},
author = {Shahhosseini, N and Kayedi, MH and Sedaghat, MM and Racine, T and Kobinger, GP and Moosa-Kazemi, SH},
title = {Correction: DNA barcodes corroborating identification of mosquito species and multiplex real-time PCR differentiating Culex pipiens complex and Culex torrentium in Iran.},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0227018},
pmid = {31869382},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0207308.].},
}
@article {pmid31869329,
year = {2019},
author = {Farrag, HMM and Huseein, EAM and Almatary, AM and Othman, RA},
title = {Morphological and initial molecular characterization of Clogmia albipunctatus larvae (Diptera: Psychodidae) causing urinary myiasis in Egypt.},
journal = {PLoS neglected tropical diseases},
volume = {13},
number = {12},
pages = {e0007887},
pmid = {31869329},
issn = {1935-2735},
mesh = {Adolescent ; Animals ; Child ; Child, Preschool ; Cluster Analysis ; Cytochromes b/genetics ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Egypt ; Female ; Humans ; Larva/*anatomy &amp; histology/classification/*genetics ; Male ; Microscopy ; Microscopy, Electron, Scanning ; Myiasis/*parasitology ; NADH Dehydrogenase/genetics ; Phylogeny ; Psychodidae/*anatomy &amp; histology/classification/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Urologic Diseases/*parasitology ; Young Adult ; },
abstract = {Myiasis is the infestation of human tissues by dipterous fly larvae of the class Insecta. Clogmia albipunctatus, family Psychodidae, is one of the most medically important insects that cause human myiasis. The aim of the present study is the morphological identification and the molecular characterization of moth flies causing many cases of urinary myiasis in Egypt, based on sequencing of the mitochondrial DNA of the larvae. Seven urinary samples of patients complaining of urinary symptoms and giving a history of low socioeconomic level were examined. Recovered larvae were identified using light microscopy and SEM. For molecular identification, the mitochondrial genes Cytochrome B (cytB), NADH1, NADH1, and 16S were sequenced and phylogenetically analyzed. The morphological and molecular characterization could accurately diagnose our patients to have C. albipunctatus infestation. Such results provided the initial set of data on the molecular identification and phylogenetic analysis of moth flies based on DNA barcoding in Egypt.},
}
@article {pmid31866739,
year = {2019},
author = {Ip, YCA and Tay, YC and Gan, SX and Ang, HP and Tun, K and Chou, LM and Huang, D and Meier, R},
title = {From marine park to future genomic observatory? Enhancing marine biodiversity assessments using a biocode approach.},
journal = {Biodiversity data journal},
volume = {7},
number = {},
pages = {e46833},
pmid = {31866739},
issn = {1314-2828},
abstract = {Few tropical marine sites have been thoroughly characterised for their animal species, even though they constitute the largest proportion of multicellular diversity. A number of focused biodiversity sampling programmes have amassed immense collections to address this shortfall, but obstacles remain due to the lack of identification tools and large proportion of undescribed species globally. These problems can be partially addressed with DNA barcodes ("biocodes"), which have the potential to facilitate the estimation of species diversity and identify animals to named species via barcode databases. Here, we present the first results of what is intended to be a sustained, systematic study of the marine fauna of Singapore's first marine park, reporting more than 365 animal species, determined based on DNA barcodes and/or morphology represented by 931 specimens (367 zooplankton, 564 macrofauna including 36 fish). Due to the lack of morphological and molecular identification tools, only a small proportion could be identified to species solely based on either morphology (24.5%) or barcodes (24.6%). Estimation of species numbers for some taxa was difficult because of the lack of sufficiently clear barcoding gaps. The specimens were imaged and added to "Biodiversity of Singapore" (http://singapore.biodiversity.online), which now contains images for > 13,000 species occurring in the country.},
}
@article {pmid31866734,
year = {2019},
author = {Likhitrakarn, N and Golovatch, SI and Semenyuk, I and Efeykin, BD and Panha, S},
title = {Review of the millipede genus Orthomorpha Bollman, 1893 (Diplopoda, Polydesmida, Paradoxosomatidae) in Vietnam, with several new records and descriptions of two new species.},
journal = {ZooKeys},
volume = {898},
number = {},
pages = {121-158},
pmid = {31866734},
issn = {1313-2989},
abstract = {The genus Orthomorpha is shown to currently be represented in Vietnam by ten species or varieties, including new records of O. arboricola (Attems, 1937), O. coarctata (de Saussure, 1860), O. rotundicollis (Attems, 1937) and O. scabra Jeekel, 1964, and two new species, O. caramel sp. nov. and O. vietnamica sp. nov. A key to all eight Orthomorpha species and two varieties known to occur in Vietnam is provided. Although the morphological characters that have been traditionally used for Orthomorpha taxonomy are here considered superior to molecular ones, molecular-based phylogenetic relationships and taxon assignments within the tribe Orthomorphini are provisionally analyzed using fragments of the cytochrome c oxidase subunit I (COI) mitochondrial gene. The preferred phylograms, both rooted and unrooted, demonstrate the monophyly of the tribe Orthomorphini, but due to the special, uncertain or even controversial position of O. coarctata, which occurs closer to the genera Antheromorpha and Hylomus, the genus Orthomorpha in current usage appears to be polyphyletic. However, if O. coarctata is to be treated within the monotypic genus Asiomorpha, the monophyly of Orthomorpha becomes manifest. On the other hand, a cautious approach is followed to avoid descriptions of suspicious new taxa/species. Thus, solely because the average genetic distance between O. rodundicollis subrotundicollis var. nov. and O. rodundicollis, as well as that between O. scabra grandis var. nov. and O. scabra, are both found to be negligibly small, the statuses of the sympatric and closest yet morphologically different varieties are treated only as such, i.e., infrasubspecific categories. The apparent discord observed between morphological and molecular data is obviously due to only partial and single-gene topologies used, possibly also to hybridization already known to occur in some closely related and sympatric paradoxosomatid species or even genera.},
}
@article {pmid31865924,
year = {2020},
author = {Taylor, GS and Martoni, F},
title = {Case of mistaken identity: resolving the taxonomy between Trioza eugeniae Froggatt and T. adventicia Tuthill (Psylloidea: Triozidae).},
journal = {Bulletin of entomological research},
volume = {110},
number = {3},
pages = {340-351},
doi = {10.1017/S0007485319000695},
pmid = {31865924},
issn = {1475-2670},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Female ; Hemiptera/*anatomy &amp; histology/*classification/genetics ; Male ; Species Specificity ; },
abstract = {The 'Eugenia psyllid' or 'Lilly pilly psyllid', widely recognized in Australia and in the USA as Trioza eugeniae Froggatt (Hemiptera: Triozidae), is not T. eugeniae, but rather T. adventicia Tuthill. In this study we assessed morphological comparisons of materials from throughout the native and introduced ranges and re-examined original descriptions of both taxa, together with Froggatt's type specimens of T. eugeniae. Furthermore, through DNA barcoding analyses, we confirmed the validity of both T. adventicia and T. eugeniae as separate species. We re-described both species to include additional characters not previously included and designated a lectotype for T. eugeniae. T. eugeniae has smaller fore wings that are slightly more elongate. These lack infuscation around veins R and R1, vein Rs is relatively longer, meeting the costa closer to the wing apex; with certain veins bearing long, fine divergent setae, a character not previously described. It has consistently three inner and one outer metatibial spurs. The male parameres appear narrowly pyriform with a weak dorsolateral lobe and weakly sclerotized apices. T. adventicia has larger fore wings that are slightly more ovate with dark infuscation around veins R and R1; vein Rs is relatively shorter, meeting the costa further from the wing apex, with veins lacking long, fine divergent setae. The usual configuration of two inner and one outer metatibial spurs, previously used to separate the two species, appears inconsistent. The male parameres appear a little more broadly pyriform with slightly more sclerotized apices. T. eugeniae refers to a distinct species which has a restricted distribution only in its native range in southern subcoastal New South Wales, Australia. T. adventicia refers to a separate species, with a natural distribution in eastern subcoastal Australia, but has been introduced widely in southern Australia, to New Zealand and the USA. This study elucidates a long history of misidentification of T. eugeniae in the nursery industry and in almost 30 years of literature on its biological control in the USA. Regardless, the biological control program, unknowingly, targeted the correct species of psyllid, T. adventicia, in its foreign exploration and importation of the appropriate parasitoid as a biocontrol agent in the USA. Despite being firmly entrenched in both the nursery trade and scientific literature, the name T. eugeniae is misapplied. While the acceptance of the valid name, T. adventicia, might be regarded as both problematic and protracted, this is the correct taxonomical attribution.},
}
@article {pmid31865184,
year = {2020},
author = {Chen, C and Tang, X and Masna, NVR and Bhunia, S and Mandal, S},
title = {Single-shot spatially-localized NQR using field-dependent relaxation rates.},
journal = {Journal of magnetic resonance (San Diego, Calif. : 1997)},
volume = {311},
number = {},
pages = {106660},
doi = {10.1016/j.jmr.2019.106660},
pmid = {31865184},
issn = {1096-0856},
abstract = {Nuclear quadrupole resonance (NQR) is commonly used to characterize solid materials containing quadrupolar nuclei. For example, NQR is a promising technique for detecting plastic explosives and other forbidden substances as well as for authenticating pharmaceutical products. Spatially-resolved NQR measurements are of particular interest for enabling automated sample positioning, evaluation of sample heterogeneity, and chemometric authentication of objects. This paper proposes a rapid "single-shot" method for spatially-resolved NQR with the potential to benefit such applications. The proposed method takes advantage of the fact that certain NQR relaxation rates are field-dependent: the observed field dependence is used to convert relaxation time distributions measured in a static field gradient (estimated via Laplace inversion of time-domain data) into spatial distributions. The method was validated using [35]Cl and [37]Cl NQR of sodium chlorate and other compounds. Effective spatial resolution was also improved by using machine learning (ML) to classify the measured spatial distributions. In particular, experimental results demonstrate accurate ML-based classification of 3D-printed objects containing arbitrary binary distributions of sodium chlorate. Such distributions can thus be used as NQR-based "embedded barcodes" for authenticating high-value objects.},
}
@article {pmid31862460,
year = {2020},
author = {García-Machado, E and Ponce de Léon, JL and Gutiérrez-Costa, MA and Michel-Salzat, A and Germon, I and Casane, D},
title = {Phylogeographic evidence that the distribution of cryptic euryhaline species in the Gambusia punctata species group in Cuba was shaped by the archipelago geological history.},
journal = {Molecular phylogenetics and evolution},
volume = {144},
number = {},
pages = {106712},
doi = {10.1016/j.ympev.2019.106712},
pmid = {31862460},
issn = {1095-9513},
mesh = {Animals ; Cuba ; Cyprinodontiformes/*classification/*genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/analysis/genetics ; *Ecosystem ; Genetic Speciation ; *Genetic Variation ; Geology ; Microsatellite Repeats/genetics ; Phylogeny ; Phylogeography ; Seawater ; Sequence Analysis, DNA ; },
abstract = {The main drivers of diversification of freshwater fishes in Cuba are not yet well understood. For example, salt tolerance was thought as the main factor involved in the diversification of Gambusia punctata species group in this archipelago. However, evidence from a recent DNA barcoding survey suggested the presence of cryptic species and no correlation between species delimitation and level of salinity. In this study, we analyzed the cryptic diversification of G. punctata species group in Cuba, based on a comprehensive sampling of its distribution and including habitats with different salinity levels. We evaluated the patterns of molecular divergence of the samples by sequencing a set of mitochondrial DNA (mtDNA) regions and genotyping nine nuclear microsatellite loci. We also used cytochrome b gene (cytb) partial sequences and these microsatellite loci to analyze population structure inside putative species. Five mtDNA well-differentiated haplogroups were found, four of them also identified by the analysis of the microsatellite polymorphism which corresponds to two already recognized species, G. punctata, and G. rhizophorae, and three putative new species. The extent of hybrid zones between these groups is also described. In each group, populations inhabiting environments with contrasting salinity levels were identified, indicating a generalized trait not specific to G. rhizophorae. The geographic distribution of the groups suggested a strong association with major relict territories of the Cuban Archipelago that was periodically joined or split-up by changes in seawater levels and land uplifts. Salinity tolerance might have facilitated sporadic and long-distance oversea dispersal but did not prevent speciation in the Cuban archipelago.},
}
@article {pmid31861293,
year = {2019},
author = {Samerjai, C and Sukontason, KL and Sontigun, N and Sukontason, K and Klong-Klaew, T and Chareonviriyaphap, T and Kurahashi, H and Klimpel, S and Kochmann, J and Saeung, A and Somboon, P and Wannasan, A},
title = {Mitochondrial DNA-Based Identification of Forensically Important Flesh Flies (Diptera: Sarcophagidae) in Thailand.},
journal = {Insects},
volume = {11},
number = {1},
pages = {},
pmid = {31861293},
issn = {2075-4450},
support = {IRN5803PHDW02//Thailand Research Fund/ ; 114/2560//Faculty of Medicine Endowment Fund/ ; 2562//Chiang Mai University/ ; },
abstract = {Flesh flies (Sarcophagidae) are necrophagous insects initially colonizing on a corpse. The species-specific developmental data of the flies collected from a death scene can be used to estimate the minimum postmortem interval (PMImin). Thus, the first crucial step is to correctly identify the fly species. Because of the high similarity among species of flesh flies, DNA-based identification is considered more favorable than morphology-based identification. In this study, we demonstrated the effectiveness of combined sequences (2216 to 2218 bp) of cytochrome c oxidase subunit I and II genes (COI and COII) for identification of the following 14 forensically important flesh fly species in Thailand: Boettcherisca nathani Lopes, Fengia ostindicae (Senior-White), Harpagophalla kempi (Senior-White), Liopygia ruficornis (Fabricius), Lioproctia pattoni (Senior-White), Lioproctia saprianovae (Pape &amp; Bänziger), Parasarcophaga albiceps (Meigen), Parasarcophaga brevicornis (Ho), Parasarcophaga dux (Thomson), Parasarcophaga misera (Walker), Sarcorohdendorfia antilope (Böttcher), Sarcorohdendorfia inextricata (Walker), Sarcorohdendorfia seniorwhitei (Ho) and Seniorwhitea princeps (Wiedemann). Nucleotide variations of Thai flesh flies were evenly distributed throughout the COI-COII genes. Mean intra- and interspecific variations ranged from 0.00 to 0.96% and 5.22% to 12.31%, respectively. Using Best Match (BM) and Best Close Match (BCM) criteria, identification success for the combined genes was 100%, while the All Species Barcodes (ASB) criterion showed 76.74% success. Maximum Likelihood (ML) and Bayesian Inference (BI) phylogenetic analyses yielded similar tree topologies of monophyletic clades between species with very strong support values. The achieved sequences covering 14 forensically important flesh fly species including newly submitted sequences for B. nathani, F. ostindicae and S. seniorwhitei, can serve as a reliable reference database for further forensic entomological research in Thailand and in other areas where those species occur.},
}
@article {pmid31858745,
year = {2020},
author = {Liu, X and Zimny, P and Zhang, Y and Rana, A and Nagel, R and Reisner, W and Dunbar, WB},
title = {Flossing DNA in a Dual Nanopore Device.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {16},
number = {3},
pages = {e1905379},
doi = {10.1002/smll.201905379},
pmid = {31858745},
issn = {1613-6829},
mesh = {Biosensing Techniques/methods ; DNA/*chemistry ; *Nanopores ; },
abstract = {Solid-state nanopores are a single-molecule technique that can provide access to biomolecular information that is otherwise masked by ensemble averaging. A promising application uses pores and barcoding chemistries to map molecular motifs along single DNA molecules. Despite recent research breakthroughs, however, it remains challenging to overcome molecular noise to fully exploit single-molecule data. Here, an active control technique termed "flossing" that uses a dual nanopore device is presented to trap a proteintagged DNA molecule and up to 100's of back-and-forth electrical scans of the molecule are performed in a few seconds. The protein motifs bound to 48.5 kb λ-DNA are used as detectable features for active triggering of the bidirectional control. Molecular noise is suppressed by averaging the multiscan data to produce averaged intertag distance estimates that are comparable to their known values. Since nanopore feature-mapping applications require DNA linearization when passing through the pore, a key advantage of flossing is that trans-pore linearization is increased to >98% by the second scan, compared to 35% for single nanopore passage of the same set of molecules. In concert with barcoding methods, the dual-pore flossing technique could enable genome mapping and structural variation applications, or mapping loci of epigenetic relevance.},
}
@article {pmid31857199,
year = {2020},
author = {Jardim de Queiroz, L and Cardoso, Y and Jacot-des-Combes, C and Bahechar, IA and Lucena, CA and Rapp Py-Daniel, L and Sarmento Soares, LM and Nylinder, S and Oliveira, C and Parente, TE and Torrente-Vilara, G and Covain, R and Buckup, P and Montoya-Burgos, JI},
title = {Evolutionary units delimitation and continental multilocus phylogeny of the hyperdiverse catfish genus Hypostomus.},
journal = {Molecular phylogenetics and evolution},
volume = {145},
number = {},
pages = {106711},
doi = {10.1016/j.ympev.2019.106711},
pmid = {31857199},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Catfishes/*classification/genetics ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Membrane Proteins/genetics ; Mitochondria/genetics ; Nerve Tissue Proteins/genetics ; Phylogeny ; Species Specificity ; },
abstract = {With 149 currently recognized species, Hypostomus is one of the most species-rich catfish genera in the world, widely distributed over most of the Neotropical region. To clarify the evolutionary history of this genus, we reconstructed a comprehensive phylogeny of Hypostomus based on four nuclear and two mitochondrial markers. A total of 206 specimens collected from the main Neotropical rivers were included in the present study. Combining morphology and a Bayesian multispecies coalescent (MSC) approach, we recovered 85 previously recognized species plus 23 putative new species, organized into 118 'clusters'. We presented the Cluster Credibility (CC) index that provides numerical support for every hypothesis of cluster delimitation, facilitating delimitation decisions. We then examined the correspondence between the morphologically identified species and their inter-specific COI barcode pairwise divergence. The mean COI barcode divergence between morphological sisters species was 1.3 ± 1.2%, and only in 11% of the comparisons the divergence was ≥2%. This indicates that the COI barcode threshold of 2% classically used to delimit fish species would seriously underestimate the number of species in Hypostomus, advocating for a taxon-specific COI-based inter-specific divergence threshold to be used only when approximations of species richness are needed. The phylogeny of the 108 Hypostomus species, together with 35 additional outgroup species, confirms the monophyly of the genus. Four well-supported main lineages were retrieved, hereinafter called super-groups: Hypostomus cochliodon, H. hemiurus, H. auroguttatus, and H. plecostomus super-groups. We present a compilation of diagnostic characters for each super-group. Our phylogeny lays the foundation for future studies on biogeography and on macroevolution to better understand the successful radiation of this Neotropical fish genus.},
}
@article {pmid31857178,
year = {2020},
author = {Zhao, W and Liu, M and Shen, C and Liu, H and Zhang, Z and Dai, W and Liu, X and Liu, J},
title = {Differentiation, chemical profiles and quality evaluation of five medicinal Stephania species (Menispermaceae) through integrated DNA barcoding, HPLC-QTOF-MS/MS and UHPLC-DAD.},
journal = {Fitoterapia},
volume = {141},
number = {},
pages = {104453},
doi = {10.1016/j.fitote.2019.104453},
pmid = {31857178},
issn = {1873-6971},
mesh = {Alkaloids/chemistry/metabolism ; Chromatography, Liquid/*methods ; *DNA Barcoding, Taxonomic ; DNA, Intergenic ; DNA, Plant/*genetics ; Genetic Variation ; Humans ; Plant Roots ; Plant Stems ; Species Specificity ; Stephania/*chemistry ; Tandem Mass Spectrometry/*methods ; },
abstract = {Stephania species is one of the alkaloid-rich genus of the family Menispermaceae. Most plants of the genus Stephania possess medicinal value, whose main components are alkaloids. However, the non-medical species are often mistakenly used as herbs because of the difficulty in identification of the species. A systematic method which involved the combination of DNA barcoding, HPLC-QTOF-MS/MS and UHPLC was established for differentiation, chemical profiles and quality evaluation of medicinal Stephania species. Firstly, twenty batches of Stephania species samples were classified into five Stephania species by DNA barcoding. Secondly, 114 alkaloids including 22 tetrahydroprotoberberines, 13 protoberberines, 27 aporphines, 13 benzylisoquinolines, 12 hasubanans, 3 morphines and 24 other alkaloids were clearly or tentatively identified. Thirdly, thirteen representative components were simultaneously detected by UHPLC-DAD to characterize the differences of chemical compositions among five Stephania species. In conclusion, this method was comprehensive and effective for identification, chemical profiles and quality evaluation of medicinal Stephania species. It will provide a basis for holistic quality evaluation of medicinal Stephania species.},
}
@article {pmid31856883,
year = {2019},
author = {Xu, J and Falconer, C and Nguyen, Q and Crawford, J and McKinnon, BD and Mortlock, S and Senabouth, A and Andersen, S and Chiu, HS and Jiang, L and Palpant, NJ and Yang, J and Mueller, MD and Hewitt, AW and Pébay, A and Montgomery, GW and Powell, JE and Coin, LJM},
title = {Genotype-free demultiplexing of pooled single-cell RNA-seq.},
journal = {Genome biology},
volume = {20},
number = {1},
pages = {290},
pmid = {31856883},
issn = {1474-760X},
mesh = {Humans ; *Sequence Analysis, RNA ; *Single-Cell Analysis ; *Software ; },
abstract = {A variety of methods have been developed to demultiplex pooled samples in a single cell RNA sequencing (scRNA-seq) experiment which either require hashtag barcodes or sample genotypes prior to pooling. We introduce scSplit which utilizes genetic differences inferred from scRNA-seq data alone to demultiplex pooled samples. scSplit also enables mapping clusters to original samples. Using simulated, merged, and pooled multi-individual datasets, we show that scSplit prediction is highly concordant with demuxlet predictions and is highly consistent with the known truth in cell-hashing dataset. scSplit is ideally suited to samples without external genotype information and is available at: https://github.com/jon-xu/scSplit.},
}
@article {pmid31856294,
year = {2020},
author = {Mukweze Mulelenu, C and Katemo Manda, B and Decru, E and Chocha Manda, A and Vreven, E},
title = {The Cyphomyrus Myers 1960 (Osteoglossiformes: Mormyridae) of the Lufira basin (Upper Lualaba: DR Congo): A generic reassignment and the description of a new species.},
journal = {Journal of fish biology},
volume = {96},
number = {5},
pages = {1123-1141},
doi = {10.1111/jfb.14237},
pmid = {31856294},
issn = {1095-8649},
support = {//This study was made possible by a DEA scholarship (2016-2018) to the first author (CMM) from the Mbisa Congo project (2013-2018), financed through a framework agreement project between the RMCA and the Belgian Development Cooperation./ ; 2016-2018//DEA scholarship/ ; 2013-2018//Mbisa Congo project/ ; //RMCA/ ; //Belgian Development Cooperation/ ; },
mesh = {Animals ; Congo ; Electric Fish/*anatomy &amp; histology/*classification ; Rivers ; Species Specificity ; },
abstract = {Within a comparative morphological framework, Hippopotamyrus aelsbroecki, only known from the holotype originating from Lubumbashi, most probably the Lubumbashi River, a left bank subaffluent of the Luapula River, is reallocated to the genus Cyphomyrus. This transfer is motivated by the fact that H. aelsbroecki possesses a rounded or vaulted predorsal profile, an insertion of the dorsal fin far anterior to the level of the insertion of the anal fin, and a compact, laterally compressed and deep body. In addition, a new species of Cyphomyrus is described from the Lufira basin, Cyphomyrus lufirae. Cyphomyrus lufirae was collected in large parts of the Middle Lufira, upstream of the Kyubo Falls and just downstream of these falls in the lower Lufira and its nearby left bank affluent, the Luvilombo River. The new species is distinguished from all its congeners, that is, firstly, from C. aelsbroecki, C. cubangoensis and C. discorhynchus, by a low number of dorsal fin rays, 27-32 (vs. higher, 36 (37), 34 (33-41) an 38 (38-40), respectively) and, secondly, from C. aelsbroecki, C. cubangoensis, and C. discorhynchus by a large prepelvic distance, 41.0-43.8% LS (vs. shorter, 39.7%, 38.9-39.1% and 37.0-41.0% LS , respectively). The description of yet another new species for the Upemba National Park and the Kundelungu National Park further highlights their importance for fish protection and conservation in the area. Hence, there is an urgent need for the full integration of fish into the management plans of these parks.},
}
@article {pmid31852987,
year = {2020},
author = {Jacobs, S and Ausema, A and Zwart, E and Weersing, E and Kingma, MJ and El Menshawi, YAS and de Haan, G and Bystrykh, LV and Belderbos, ME},
title = {Quantitative distribution of patient-derived leukemia clones in murine xenografts revealed by cellular barcodes.},
journal = {Leukemia},
volume = {34},
number = {6},
pages = {1669-1674},
pmid = {31852987},
issn = {1476-5551},
mesh = {Animals ; DNA Barcoding, Taxonomic/methods ; Heterografts ; Humans ; Mice ; Neoplastic Stem Cells/*pathology ; Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/genetics/*pathology ; },
}
@article {pmid31849682,
year = {2019},
author = {Zhang, Z and Zhang, Y and Song, M and Guan, Y and Ma, X},
title = {Species Identification of Dracaena Using the Complete Chloroplast Genome as a Super-Barcode.},
journal = {Frontiers in pharmacology},
volume = {10},
number = {},
pages = {1441},
pmid = {31849682},
issn = {1663-9812},
abstract = {The taxonomy and nomenclature of Dracaena plants are much disputed, particularly for several Dracaena species in Asia. However, neither morphological features nor common DNA regions are ideal for identification of Dracaena spp. Meanwhile, although multiple Dracaena spp. are sources of the rare traditional medicine dragon's blood, the Pharmacopoeia of the People's Republic of China has defined Dracaena cochinchinensis as the only source plant. The inaccurate identification of Dracaena spp. will inevitably affect the clinical efficacy of dragon's blood. It is therefore important to find a better method to distinguish these species. Here, we report the complete chloroplast (CP) genomes of six Dracaena spp., D. cochinchinensis, D. cambodiana, D. angustifolia, D. terniflora, D. hokouensis, and D. elliptica, obtained through high-throughput Illumina sequencing. These CP genomes exhibited typical circular tetramerous structure, and their sizes ranged from 155,055 (D. elliptica) to 155,449 bp (D. cochinchinensis). The GC content of each CP genome was 37.5%. Furthermore, each CP genome contained 130 genes, including 84 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. There were no potential coding or non-coding regions to distinguish these six species, but the maximum likelihood tree of the six Dracaena spp. and other related species revealed that the whole CP genome can be used as a super-barcode to identify these Dracaena spp. This study provides not only invaluable data for species identification and safe medical application of Dracaena but also an important reference and foundation for species identification and phylogeny of Liliaceae plants.},
}
@article {pmid31849560,
year = {2019},
author = {Urbaniak, J and Kwiatkowski, P},
title = {Taxonomic studies on the Chara section Hartmania in Poland based on morphological and molecular data.},
journal = {PhytoKeys},
volume = {135},
number = {},
pages = {71-90},
pmid = {31849560},
issn = {1314-2011},
abstract = {Charophytes are aquatic green macroalgae, which inhabit fresh and brackish water ecosystems. In this study, four species belonging to the genus Chara were examined to determine their taxonomic status. Morphological characteristics of the plant bodies as well as plastid psaB barcoding genes were applied to test the relations among Chara species. Plants were initially classified using morphological features into four species: C. baltica, C. hispida, C. polyacantha and C. rudis, and twelve quantitative characters were used in a principal component analysis and discriminant analysis to determine groupings among the species and to determine the morphological features that best separated the groups. In the component analysis and discriminant analysis, results showed that only C. polyacantha and partly C. baltica formed separate groups. The other species C. hispida and C. rudis were only partially distinguishable. All species from one molecular group, and no differentiation in the psaB variability between them has been found.},
}
@article {pmid31849210,
year = {2020},
author = {Shi, R and Hu, Z and Lu, H and Liu, L and Xu, L and Liu, Y and Wu, H and Huang, B and Zhang, GJ and Chen, S and Yang, F},
title = {Hierarchical Nanostructuring Array Enhances Mid-Hybridization for Accurate Herbal Identification via ITS2 DNA Barcode.},
journal = {Analytical chemistry},
volume = {92},
number = {2},
pages = {2136-2144},
doi = {10.1021/acs.analchem.9b04687},
pmid = {31849210},
issn = {1520-6882},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; Drugs, Chinese Herbal/*analysis ; Electrochemical Techniques ; Nanostructures/*chemistry ; Nucleic Acid Hybridization ; Plants, Medicinal/genetics ; },
abstract = {It remains a technical challenge to accurately identify close species of herbal medicines, especially from adulterants, because of their highly identical phenotypes and chemical compositions. Here, we report a direct, sequencing-free, high-curvature nanostructuring-based electrochemical herb sensor (nanoE-herb sensor) to identify herbal species quickly and accurately using ITS2 barcodes. We engineer a nano-roughened carbon-supported gold nanostructuring array by photolithograph-free, one-step electrodeposition. The 3D fractal nanostructures exhibit a high deflection angle that largely enhances DNA hybridization efficiency, particularly for the midcomplementary hybridization, as compared to the 2D planar surface. More importantly, such a trans-scale array biointerface (including macroscale carbon and nanoscale gold branches) can overcome the detection barrier of slow diffusion of a long genomic sequence and inaccessibility of the sequestered variations in ITS2 secondary structures through the out-protruded 3D functional nanostructures. Our nanoE-herb sensor achieves a detection limit of 0.18 fM for the 64-mer fragment of saffron ITS2 barcode with midhybridization and shows superior specificity against even single-base mismatch. The sensor also precisely differentiates saffron from six other adulterants by directly detecting unpurified asymmetric PCR amplicons (∼500 bp) with ITS2 sequences, suggesting its great potential in the field identification of herbal medicinal species and pathogenic bacteria with specific DNA barcodes.},
}
@article {pmid32214501,
year = {2019},
author = {Crous, PW and Wingfield, MJ and Lombard, L and Roets, F and Swart, WJ and Alvarado, P and Carnegie, AJ and Moreno, G and Luangsaard, J and Thangavel, R and Alexandrova, AV and Baseia, IG and Bellanger, JM and Bessette, AE and Bessette, AR and De la Peña-Lastra, S and García, D and Gené, J and Pham, THG and Heykoop, M and Malysheva, E and Malysheva, V and Martín, MP and Morozova, OV and Noisripoom, W and Overton, BE and Rea, AE and Sewall, BJ and Smith, ME and Smyth, CW and Tasanathai, K and Visagie, CM and Adamčík, S and Alves, A and Andrade, JP and Aninat, MJ and Araújo, RVB and Bordallo, JJ and Boufleur, T and Baroncelli, R and Barreto, RW and Bolin, J and Cabero, J and Caboň, M and Cafà, G and Caffot, MLH and Cai, L and Carlavilla, JR and Chávez, R and de Castro, RRL and Delgat, L and Deschuyteneer, D and Dios, MM and Domínguez, LS and Evans, HC and Eyssartier, G and Ferreira, BW and Figueiredo, CN and Liu, F and Fournier, J and Galli-Terasawa, LV and Gil-Durán, C and Glienke, C and Gonçalves, MFM and Gryta, H and Guarro, J and Himaman, W and Hywel-Jones, N and Iturrieta-González, I and Ivanushkina, NE and Jargeat, P and Khalid, AN and Khan, J and Kiran, M and Kiss, L and Kochkina, GA and Kolařík, M and Kubátová, A and Lodge, DJ and Loizides, M and Luque, D and Manjón, JL and Marbach, PAS and Massola, NS and Mata, M and Miller, AN and Mongkolsamrit, S and Moreau, PA and Morte, A and Mujic, A and Navarro-Ródenas, A and Németh, MZ and Nóbrega, TF and Nováková, A and Olariaga, I and Ozerskaya, SM and Palma, MA and Petters-Vandresen, DAL and Piontelli, E and Popov, ES and Rodríguez, A and Requejo, &#xd3; and Rodrigues, ACM and Rong, IH and Roux, J and Seifert, KA and Silva, BDB and Sklenář, F and Smith, JA and Sousa, JO and Souza, HG and De Souza, JT and Švec, K and Tanchaud, P and Tanney, JB and Terasawa, F and Thanakitpipattana, D and Torres-Garcia, D and Vaca, I and Vaghefi, N and van Iperen, AL and Vasilenko, OV and Verbeken, A and Yilmaz, N and Zamora, JC and Zapata, M and Jurjević, &#x17d; and Groenewald, JZ},
title = {Fungal Planet description sheets: 951-1041.},
journal = {Persoonia},
volume = {43},
number = {},
pages = {223-425},
pmid = {32214501},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Antarctica, Apenidiella antarctica from permafrost, Cladosporium fildesense from an unidentified marine sponge. Argentina, Geastrum wrightii on humus in mixed forest. Australia, Golovinomyces glandulariae on Glandularia aristigera, Neoanungitea eucalyptorum on leaves of Eucalyptus grandis, Teratosphaeria corymbiicola on leaves of Corymbia ficifolia, Xylaria eucalypti on leaves of Eucalyptus radiata. Brazil, Bovista psammophila on soil, Fusarium awaxy on rotten stalks of Zea mays, Geastrum lanuginosum on leaf litter covered soil, Hermetothecium mikaniae-micranthae (incl. Hermetothecium gen. nov.) on Mikania micrantha, Penicillium reconvexovelosoi in soil, Stagonosporopsis vannaccii from pod of Glycine max. British Virgin Isles, Lactifluus guanensis on soil. Canada, Sorocybe oblongispora on resin of Picea rubens. Chile, Colletotrichum roseum on leaves of Lapageria rosea. China, Setophoma caverna from carbonatite in Karst cave. Colombia, Lareunionomyces eucalypticola on leaves of Eucalyptus grandis. Costa Rica, Psathyrella pivae on wood. Cyprus, Clavulina iris on calcareous substrate. France, Chromosera ambigua and Clavulina iris var. occidentalis on soil. French West Indies, Helminthosphaeria hispidissima on dead wood. Guatemala, Talaromyces guatemalensis in soil. Malaysia, Neotracylla pini (incl. Tracyllales ord. nov. and Neotracylla gen. nov.) and Vermiculariopsiella pini on needles of Pinus tecunumanii. New Zealand, Neoconiothyrium viticola on stems of Vitis vinifera, Parafenestella pittospori on Pittosporum tenuifolium, Pilidium novae-zelandiae on Phoenix sp. Pakistan, Russula quercus-floribundae on forest floor. Portugal, Trichoderma aestuarinum from saline water. Russia, Pluteus liliputianus on fallen branch of deciduous tree, Pluteus spurius on decaying deciduous wood or soil. South Africa, Alloconiothyrium encephalarti, Phyllosticta encephalarticola and Neothyrostroma encephalarti (incl. Neothyrostroma gen. nov.) on leaves of Encephalartos sp., Chalara eucalypticola on leaf spots of Eucalyptus grandis × urophylla, Clypeosphaeria oleae on leaves of Olea capensis, Cylindrocladiella postalofficium on leaf litter of Sideroxylon inerme, Cylindromonium eugeniicola (incl. Cylindromonium gen. nov.) on leaf litter of Eugenia capensis, Cyphellophora goniomatis on leaves of Gonioma kamassi, Nothodactylaria nephrolepidis (incl. Nothodactylaria gen. nov. and Nothodactylariaceae fam. nov.) on leaves of Nephrolepis exaltata, Falcocladium eucalypti and Gyrothrix eucalypti on leaves of Eucalyptus sp., Gyrothrix oleae on leaves of Olea capensis subsp. macrocarpa, Harzia metrosideri on leaf litter of Metrosideros sp., Hippopotamyces phragmitis (incl. Hippopotamyces gen. nov.) on leaves of Phragmites australis, Lectera philenopterae on Philenoptera violacea, Leptosillia mayteni on leaves of Maytenus heterophylla, Lithohypha aloicola and Neoplatysporoides aloes on leaves of Aloe sp., Millesimomyces rhoicissi (incl. Millesimomyces gen. nov.) on leaves of Rhoicissus digitata, Neodevriesia strelitziicola on leaf litter of Strelitzia nicolai, Neokirramyces syzygii (incl. Neokirramyces gen. nov.) on leaf spots of Syzygium sp., Nothoramichloridium perseae (incl. Nothoramichloridium gen. nov. and Anungitiomycetaceae fam. nov.) on leaves of Persea americana, Paramycosphaerella watsoniae on leaf spots of Watsonia sp., Penicillium cuddlyae from dog food, Podocarpomyces knysnanus (incl. Podocarpomyces gen. nov.) on leaves of Podocarpus falcatus, Pseudocercospora heteropyxidicola on leaf spots of Heteropyxis natalensis, Pseudopenidiella podocarpi, Scolecobasidium podocarpi and Ceramothyrium podocarpicola on leaves of Podocarpus latifolius, Scolecobasidium blechni on leaves of Blechnum capense, Stomiopeltis syzygii on leaves of Syzygium chordatum, Strelitziomyces knysnanus (incl. Strelitziomyces gen. nov.) on leaves of Strelitzia alba, Talaromyces clemensii from rotting wood in goldmine, Verrucocladosporium visseri on Carpobrotus edulis. Spain, Boletopsis mediterraneensis on soil, Calycina cortegadensisi on a living twig of Castanea sativa, Emmonsiellopsis tuberculata in fluvial sediments, Mollisia cortegadensis on dead attached twig of Quercus robur, Psathyrella ovispora on soil, Pseudobeltrania lauri on leaf litter of Laurus azorica, Terfezia dunensis in soil, Tuber lucentum in soil, Venturia submersa on submerged plant debris. Thailand, Cordyceps jakajanicola on cicada nymph, Cordyceps kuiburiensis on spider, Distoseptispora caricis on leaves of Carex sp., Ophiocordyceps khonkaenensis on cicada nymph. USA, Cytosporella juncicola and Davidiellomyces juncicola on culms of Juncus effusus, Monochaetia massachusettsianum from air sample, Neohelicomyces melaleucae and Periconia neobrittanica on leaves of Melaleuca styphelioides × lanceolata, Pseudocamarosporium eucalypti on leaves of Eucalyptus sp., Pseudogymnoascus lindneri from sediment in a mine, Pseudogymnoascus turneri from sediment in a railroad tunnel, Pulchroboletus sclerotiorum on soil, Zygosporium pseudomasonii on leaf of Serenoa repens. Vietnam, Boletus candidissimus and Veloporphyrellus vulpinus on soil. Morphological and culture characteristics are supported by DNA barcodes.},
}
@article {pmid32625739,
year = {2018},
author = {, and Bragard, C and Dehnen-Schmutz, K and Di Serio, F and Gonthier, P and Jacques, MA and Jaques Miret, JA and Fejer Justesen, A and MacLeod, A and Magnusson, CS and Navas-Cortes, JA and Parnell, S and Potting, R and Reignault, PL and Thulke, HH and Van der Werf, W and Vicent Civera, A and Yuen, J and Zappalà, L and Grégoire, JC and Kertész, V and Milonas, P},
title = {Pest categorisation of non-EU Monochamus spp.},
journal = {EFSA journal. European Food Safety Authority},
volume = {16},
number = {11},
pages = {e05435},
pmid = {32625739},
issn = {1831-4732},
abstract = {The Panel on Plant Health performed a pest categorisation of non-EU Monochamus spp., a well-defined insect genus in the family Cerambycidae (Insecta: Coleoptera). Species can be identified using taxonomic keys at national and regional level, and DNA barcoding. Two online world catalogues exist for the genus. The genus includes about one hundred species and many subspecies colonising conifers and non-conifer trees in many areas in the world. The non-EU species are listed in Annex IAI of Council Directive 2000/29/EC. Although Monochamus spp. colonise weakened or dead trees and have therefore no direct impact, some species vector the pine wood nematode, Bursaphelenchus xylophilus, which they inoculate to healthy trees when they proceed to maturation feeding on twigs, causing high mortality among pines in Asia and the EU (Portugal). Sixteen species in Asia and America attack conifers. The main pathways for entry are raw untreated wood and wood products, wood packaging material, particle wood and waste wood, finished wood products and hitchhiking. Monochamus species were categorised in two groups. The first group includes 16 species colonising conifers and absent in the EU known or likely to vector the pine wood nematode. The species in this group satisfy all the criteria to be considered as Union quarantine pests. Measures are in place to prevent the introduction of Monochamus with coniferous wood. The second group gathers all the remaining species, all non-EU species colonising non-conifers. These do not satisfy all the criteria to be considered as Union quarantine pests. As plants for planting are not a pathway for Monochamus spp., and as most of the species within these groups are absent from the EU territory, the two groups do not meet the criteria to be considered as regulated non-quarantine pests.},
}
@article {pmid32715304,
year = {2018},
author = {Anderson, KL and Anderson, JS and Palande, S and Wang, B},
title = {Topological Data Analysis of Functional MRI Connectivity in Time and Space Domains.},
journal = {Connectomics in neuroImaging : second international workshop, CNI 2018, held in conjunction with MICCAI 2018, Granada, Spain, September 20, 2018 : proceedings. CNI (Workshop) (2nd : 2018 : Granada, Spain)},
volume = {11083},
number = {},
pages = {67-77},
pmid = {32715304},
support = {R01 EB022876/EB/NIBIB NIH HHS/United States ; R01 MH080826/MH/NIMH NIH HHS/United States ; },
abstract = {The functional architecture of the brain can be described as a dynamical system where components interact in flexible ways, constrained by physical connections between regions. Using correlation, either in time or in space, as an abstraction of functional connectivity, we analyzed resting state fMRI data from 1003 subjects. We compared several data preprocessing strategies and found that independent component-based nuisance regression outperformed other strategies, with the poorest reproducibility in strategies that include global signal regression. We also found that temporal vs. spatial functional connectivity can encode different aspects of cognition and personality. Topological analyses using persistent homology show that persistence barcodes are significantly correlated to individual differences in cognition and personality, with high reproducibility. Topological data analyses, including approaches to model connectivity in the time domain, are promising tools for representing high-level aspects of cognition, development, and neuropathology.},
}
@article {pmid32490366,
year = {2018},
author = {Crous, PW and Schumacher, RK and Wingfield, MJ and Akulov, A and Denman, S and Roux, J and Braun, U and Burgess, TI and Carnegie, AJ and Váczy, KZ and Guatimosim, E and Schwartsburd, PB and Barreto, RW and Hernández-Restrepo, M and Lombard, L and Groenewald, JZ},
title = {New and Interesting Fungi. 1.},
journal = {Fungal systematics and evolution},
volume = {1},
number = {},
pages = {169-216},
pmid = {32490366},
issn = {2589-3831},
abstract = {This study introduces two new families, one new genus, 22 new species, 10 new combinations, four epitypes, and 16 interesting new host and / or geographical records. Cylindriaceae (based on Cylindrium elongatum) is introduced as new family, with three new combinations. Xyladictyochaetaceae (based on Xyladictyochaeta lusitanica) is introduced to accommodate Xyladictyochaeta. Pseudoanungitea gen. nov. (based on P. syzygii) is described on stems of Vaccinium myrtillus (Germany). New species include: Exophiala eucalypticola on Eucalyptus obliqua leaf litter, Phyllosticta hakeicola on leaves of Hakea sp., Setophaeosphaeria citricola on leaves of Citrus australasica, and Sirastachys cyperacearum on leaves of Cyperaceae (Australia); Polyscytalum chilense on leaves of Eucalyptus urophylla (Chile); Pseudoanungitea vaccinii on Vaccinium myrtillus (Germany); Teichospora quercus on branch tissue of Quercus sp. (France); Fusiconidium lycopodiellae on stems of Lycopodiella inundata, Monochaetia junipericola on twig of Juniperus communis, Myrmecridium sorbicola on branch tissues of Sorbus aucuparia, Parathyridaria philadelphi on twigs of Philadelphus coronarius, and Wettsteinina philadelphi on twigs of Philadelphus coronarius (Germany); Zygosporium pseudogibbum on leaves of Eucalyptus pellita (Malaysia); Pseudoanungitea variabilis on dead wood (Spain); Alfaria acaciae on leaves of Acacia propinqua, Dictyochaeta mimusopis on leaves of Mimusops caffra, and Pseudocercospora breonadiae on leaves of Breonadia microcephala (South Africa); Colletotrichum kniphofiae on leaves of Kniphofia uvaria, Subplenodomus iridicola on Iris sp., and Trochila viburnicola on twig cankers on Viburnum sp. (UK); Polyscytalum neofecundissimum on Quercus robur leaf litter, and Roussoella euonymi on fallen branches of Euonymus europaeus (Ukraine). New combinations include: Cylindrium algarvense on leaves of Eucalyptus sp. (Portugal), Cylindrium purgamentum on leaf litter (USA), Cylindrium syzygii on leaves of Syzygium sp. (Australia), Microdochium musae on leaves of Musa sp. (Malaysia), Polyscytalum eucalyptigenum on Eucalyptus grandis × pellita (Malaysia), P. eucalyptorum on leaves of Eucalyptus (Australia), P. grevilleae on leaves of Grevillea (Australia), P. nullicananum on leaves of Eucalyptus (Australia), Pseudoanungitea syzygii on Syzygium cordatum leaf litter (South Africa), and Setophaeosphaeria sidae on leaves of Sida sp. (Brazil). New records include: Sphaerellopsis paraphysata on leaves of Phragmites sp., Vermiculariopsiella dichapetali on leaves of Melaleuca sp. and Eucalyptus regnans, and Xyladictyochaeta lusitanica on leaf litter of Eucalyptus sp. (Australia); Camarosporidiella mackenziei on twigs of Caragana sp. (Finland); Cyclothyriella rubronotata on twigs of Ailanthus altissima, Rhinocladiella quercus on Sorbus aucuparia branches (Germany); Cytospora viticola on stems of Vitis vinifera (Hungary); Echinocatena arthrinioides on leaves of Acacia crassicarpa (Malaysia); Varicosporellopsis aquatilis from garden soil (Netherlands); Pestalotiopsis hollandica on needles of Cupressus sempervirens (Spain), Pseudocamarosporium africanum on twigs of Erica sp. (South Africa), Pseudocamarosporium brabeji on branch of Platanus sp. (Switzerland); Neocucurbitaria cava on leaves of Quercus ilex (UK); Chaetosphaeria myriocarpa on decaying wood of Carpinus betulus, Haplograhium delicatum on decaying Carpinus betulus wood (Ukraine). Epitypes are designated for: Elsinoë mimosae on leaves of Mimosa diplotricha (Brazil), Neohendersonia kickxii on Fagus sylvatica twig bark (Italy), Caliciopsis maxima on fronds of Niphidium crassifolium (Brazil), Dictyochaeta septata on leaves of Eucalyptus grandis × urophylla (Chile), and Microdochium musae on leaves of Musa sp. (Malaysia).},
}
@article {pmid32704693,
year = {2018},
author = {Foster, TP and Schweihofer, JP and Grooms, DL and Clarke, RH and Buskirk, DD},
title = {Comparison of beef traceability in serial and parallel fabrication systems using RFID and two-dimensional barcodes.},
journal = {Translational animal science},
volume = {2},
number = {1},
pages = {101-110},
pmid = {32704693},
issn = {2573-2102},
abstract = {Traceability of beef attributes from small- and mid-sized farms through supply chains is a market barrier. The objective of this trial was to determine the influence of fabrication method on beef traceability system requirements. Individual identities of 54 animals were maintained through harvest, processing, packaging, and distribution. At harvest, each animal's unique radio frequency identification (RFID) animal identification number was transferred to a harvest label on each carcass quarter. Following transportation to a processor, nine carcasses were processed on alternating days by one of the two methods. Carcasses were fabricated, using a serial fabrication method (SFM), into wholesale cuts one at a time or fabricated using a parallel fabrication method (PFM), by processing multiple hindquarters or forequarters simultaneously into wholesale cuts. In-process labels were generated by scanning the two-dimensional (2D) barcode on the harvest label with a handheld mobile computer and printed from a wireless mobile printer. Tracking of SFM and PFM carcass quarters was accomplished by creating in-process labels for lugs and individual wholesale cuts, respectively. The process was recorded and the data was captured from video analysis. The mean number of in-process labels generated per carcass for SFM was 3.7 and for PFM was 30.9 (P < 0.01). The amount of time required for generating in-process labels for SFM (2 min 16 s) was less than PFM (8 min 45 s) (P = 0.01). The amount of time required to label each carcass was less (P < 0.01) for SFM (18 s) than for PFM (3 min 10 s) with in-process labels. Total cost of traceability, including fixed and consumable cost per carcass, was nearly twice as much for PFM ($17.98) than SFM ($9.02). Traceability, within both processing methods, was found to have 100% fidelity, as verified using DNA marker genotyping. Overall, the number of labels generated for traceability was less for SFM than that for PFM. The overall time spent on generating, applying, and removing labels was less for SFM than that for PFM. The total cost of traceability was approximately half for SFM compared with that for PFM; however both methods were able to track product accurately. Tracking of beef from individual animals, using RFID ear tags and 2D barcodes, appears to be feasible for the fabrication methods used in this study.},
}
@article {pmid32802939,
year = {2017},
author = {Kapoor, V and Elk, M and Toledo-Hernandez, C and Santo Domingo, JW},
title = {Analysis of human mitochondrial DNA sequences from fecally polluted environmental waters as a tool to study population diversity.},
journal = {AIMS environmental science},
volume = {4},
number = {3},
pages = {443-455},
pmid = {32802939},
issn = {2372-0344},
support = {EPA999999/ImEPA/Intramural EPA/United States ; },
abstract = {Mitochondrial signature sequences have frequently been used to study human population diversity around the world. Traditionally, this requires obtaining samples directly from individuals which is cumbersome, time consuming and limited to the number of individuals that participated in these types of surveys. Here, we used environmental DNA extracts to determine the presence and sequence variability of human mitochondrial sequences as a means to study the diversity of populations inhabiting in areas nearby a tropical watershed impacted with human fecal pollution. We used high-throughput sequencing (Illumina) and barcoding to obtain thousands of sequences from the mitochondrial hypervariable region 2 (HVR2) and determined the different haplotypes present in 10 different water samples. Sequence analyses indicated a total of 19 distinct variants with frequency greater than 5%. The HVR2 sequences were associated with haplogroups of West Eurasian (57.6%), Sub-Saharan African (23.9%), and American Indian (11%) ancestry. This was in relative accordance with population census data from the watershed sites. The results from this study demonstrates the potential value of mitochondrial sequence data retrieved from fecally impacted environmental waters to study the population diversity of local municipalities. This environmental DNA approach may also have other public health implications such as tracking background levels of human mitochondrial genes associated with diseases. It may be possible to expand this approach to other animal species inhabiting or using natural water systems.},
}
@article {pmid32704234,
year = {2017},
author = {Kolombia, YA and Karssen, G and Viaene, N and Kumar, PL and Joos, L and Coyne, DL and Bert, W},
title = {Morphological and molecular characterisation of Scutellonema species from yam (Dioscorea spp.) and a key to the species of the genus.},
journal = {Nematology : international journal of fundamental and applied nematological research},
volume = {19},
number = {7},
pages = {751-787},
pmid = {32704234},
issn = {1388-5545},
abstract = {The yam nematode, Scutellonema bradys, is a major threat to yam (Dioscorea spp.) production across yam-growing regions. In West Africa, this species cohabits with many morphologically similar congeners and, consequently, its accurate diagnosis is essential for control and for monitoring its movement. In the present study, 46 Scutellonema populations collected from yam rhizosphere and yam tubers in different agro-ecological zones in Ghana and Nigeria were characterised by their morphological features and by sequencing of the D2-D3 region of the 28S rDNA gene and the mitochondrial COI genes. Molecular phylogeny, molecular species delimitation and morphology revealed S. bradys, S. cavenessi, S. clathricaudatum and three undescribed species from yam rhizosphere. Only S. bradys was identified from yam tuber tissue, however. For barcoding and identifying Scutellonema spp., the most suitable marker used was the COI gene. Additionally, 99 new Scutellonema sequences were generated using populations obtained also from banana, carrot, maize and tomato, including the first for S. paralabiatum and S. clathricaudatum, enabling the development of a dichotomous key for identification of Scutellonema spp. The implications of these results are discussed.},
}
@article {pmid31966192,
year = {2016},
author = {Xiao, JG and Song, N and Han, ZQ and Gao, TX},
title = {Description and DNA Barcoding of a New Sillago Species, Sillago shaoi (Perciformes: Sillaginidae), in the Taiwan Strait.},
journal = {Zoological studies},
volume = {55},
number = {},
pages = {e47},
pmid = {31966192},
issn = {1810-522X},
abstract = {Jia-Guang Xiao, Na Song, Zhi-Qiang Han, and Tian-Xiang Gao (2016) Reliance only on morphology to identify fishes to the species level is challenging when the diagnostic characters are similar among related taxa. Within the genus Sillago, differences among some nominal species are generally small and restricted to a few characters. In this study, a new species of Sillago (Sillago shaoi sp. nov.) was described using morphology and genetic analysis of DNA barcoding. The morphological results differentiated S. shaoi sp. nov. from eight other Sillago spp. Genetic analysis verified both the validity of the current taxonomy and the relationships between the new species and other Sillago species. S. shaoi sp. nov. formed a monophyletic group as a distinct phylogenetic species and showed strong genetic divergence from others. The present study also revealed that the COI gene was an effective molecular marker for identifying Sillago species.},
}
@article {pmid31966180,
year = {2016},
author = {Rizman-Idid, M and Farrah-Azwa, AB and Chong, VC},
title = {Preliminary Taxonomic Survey and Molecular Documentation of Jellyfish Species (Cnidaria: Scyphozoa and Cubozoa) in Malaysia.},
journal = {Zoological studies},
volume = {55},
number = {},
pages = {e35},
pmid = {31966180},
issn = {1810-522X},
abstract = {Mohammed Rizman-Idid, Abu Bakar Farrah-Azwa, and Ving Ching Chong (2016) Scientific enquiries into jellyfish blooms and associated problems are often deterred by the lack of taxonomical and ecological studies worldwide. Taxonomic difficulty is attributed to the high degree of morphological variations among and within species. To date, only two scyphozoan jellyfish species have been documented from field surveys in Malaysian waters, whereas another four Malaysian scyphozoan and two cubozoan jellyfish species have been mentioned in toxicological studies. None of these species have; however, been verified. This study thus aimed to document and resolves the uncertainty of earlier identified species in the region using morphology and molecular DNA sequencing. Jellyfish specimens were collected from Malaysian waters in the Straits of Malacca, South-China Sea and the Sulu-Sulawesi Sea over two years (June 2008 to October 2010), and their DNA sequences were compared with those from the Atlantic and Pacific regions. Ten scyphozoan and two cubozoan species were recorded in Malaysian waters (South China Sea and Straits of Malacca). These jellyfish included eight species from the order Rhizostomeae (Rhizostomatidae, Lobonematidae, Mastigiidae, Catostylidae and Cepheidae), two species from Semaestomeae (Pelagiidae and Cyaneidae) and two species from class Cubozoa; one from order Carybdeida (family Carukiidae) and another from order Chirodropida (family Chiropsalmidae). Molecular identification of species using phylogenetic approaches was based on DNA sequences of partial cytochrome oxidase I (COI), 16S and internal transcribed spacer (ITS1) regions. The COI phylogenetic tree of Cubozoa and Scyphozoa species from the Atlantic and Pacific regions showed distinct clustering of six Malaysian jellyfish species. However, most of the deeper divergences and relationships between the families were unresolved, which were also observed in the 16S and ITS1 phylogenetic trees. The Malaysian edible species Lobonemoides robustus, Rhopilema hispidum and Rhopilema esculentum were grouped within Rhizostomeae, whereas other scyphozoans showed phylogenetic affinities to Semaestomeae and Kolpophorae. Chrysaora and Cyanea appeared non-monophyletic; however their paraphyly was not confirmed. This study has provided the much needed baseline information on the taxonomy of Malaysian jellyfish species which have been substantiated by partial COI, 16S and ITS1 sequences. A total of 12 putative species of jellyfish were identified, which encompassed 12 genera.},
}
@article {pmid31966176,
year = {2016},
author = {Lu, YT and Liu, MY and He, Y and Liao, TY},
title = {Smilosicyopus leprurus (Teleostei: Gobiidae) is a Fin-eater.},
journal = {Zoological studies},
volume = {55},
number = {},
pages = {e31},
pmid = {31966176},
issn = {1810-522X},
abstract = {Ying-Tzu Lu, Min-Yun Liu, You He, and Te-Yu Liao (2016) Smilosicyopus leprurus is a small goby distributed in the Ishigaki Island and Taiwan. Hobbyists found S. leprurus attacked on the caudal fin of fishes kept together. In this study we investigate whether this fin-eating behavior occurs in the field and whether S. leprurus can be considered a fin-eater. Behavior observation in a tank showed S. leprurus snapped off a piece of fins and swallowed. Among S. leprurus preserved immediately after capture, a fin fragment and a few scales were recovered in the gut of a specimen and DNA barcoding shows the fin fragment belonging to Sicyopterus japonicas. The fin-eating behavior of S. leprurus occurs in captivity and in the wild. In addition, the 3D renderings of oral jaws of S. leprurus were provided. Oral teeth are numerous and arranged in close proximity to each other all together like a bladed dentition, which may provide the capability to shear the fin of its prey. The present study shows S. leprurus a fin-eater despite not feeding exclusively on fins.},
}
@article {pmid31966168,
year = {2016},
author = {Tamburus, AF and Mantelatto, FL},
title = {Taxonomic and Biogeographical Status of Three Species of the Spider Crabs of the Genus Acanthonyx Latreille, 1828 (Majoidea: Epialtidae) as Determined by DNA Barcoding and Morphological Analyses Along the Western Atlantic.},
journal = {Zoological studies},
volume = {55},
number = {},
pages = {e23},
pmid = {31966168},
issn = {1810-522X},
abstract = {Ana Francisca Tamburus and Fernando Luis Mantelatto (2016) The genus Acanthonyx Latreille, 1828 contains 17 valid species, including A. dissimulatus Coelho, 1993, A. petiverii H. Milne Edwards, 1834 and A. scutiformis (Dana, 1851), which occur along the Brazilian coast. The high degree of intraspecific variation in the angle of hepatic region, size of the tubercles of the carapace and length of setae on the carapace and pereopods has resulted in difficulties with the taxonomy of this genus. Analysis of more consistent morphological and molecular characters are required to clarify the status of the three species that occurs in Brazil. For the molecular data, we used the barcode region of the mitochondrial gene COI as a marker, and we correlated this with morphological characters of adults and juveniles. The three species of Acanthonyx were morphologically similar and the matrix of genetic distances and maximum likelihood trees showed that A. dissimulatus and A. scutiformis belonged to the same group with A. petiverii. They could not be separated using the diagnosing characters proposed in the original description or genetically (present study), thus indicating that the taxonomic status of the first two species is questionable. The division into two distinct groups corresponding to A (Caribbean, Brazil, Venezuela) and B (USA, Mexico) was well supported and indicated that there are genetic differences between these populations. Present study suggests the existence of a single species in Brazil and Caribbean, assigned to A. petiverii (type locality in Antilles). The existence of a new species restricted to North America confirms the cryptic diversity within Acanthonyx.},
}
@article {pmid31966158,
year = {2016},
author = {Bossert, S and Gereben-Krenn, BA and Neumayer, J and Schneller, B and Krenn, HW},
title = {The Cryptic Bombus lucorum Complex (Hymenoptera: Apidae) in Austria: Phylogeny, Distribution, Habitat Usage and a Climatic Characterization Based on COI Sequence Data.},
journal = {Zoological studies},
volume = {55},
number = {},
pages = {e13},
pmid = {31966158},
issn = {1810-522X},
abstract = {Silas Bossert, Barbara-Amina Gereben-Krenn, Johann Neumayer, Bernhard Schneller, and Harald W. Krenn (2016) The Bombus lucorum complex represents a group of three distinct but cryptic bumblebee species in Europe. With the advent of DNA-based identification methods, their species status was confirmed and the use of COI barcoding proved to be an especially useful tool for species identification within the group. Meanwhile, the identification based on morphology remains difficult and recent studies challenged the general distinguishability by revealing an important character to be unreliable. This has consequences for our understanding of the distribution and ecology of the species in Europe and aggravates our patchy knowledge of the situation in Austria and the whole area of the European Alps. In this study, we investigate the exact species composition and distribution of the Bombus lucorum complex in Austria based on the reliable species identification with COI sequence data. The habitat usage is studied and the first extensive investigation of altitudinal and climatic differentiation is provided. The results support three distinct genotypic groups in the Bombus lucorum complex. B. lucorum and B. cryptarum co-occur in several areas across the country, with B. lucorum being the most common and most widespread species. The study provides no evidence for the presence of B. magnus in Austria. The less common species, B. cryptarum, mainly occurs in the high mountains and is the predominant species of the complex above altitudes of 2100 m a.s.l. Further, B. cryptarum is almost absent from woodlands and is relatively more abundant in habitats with colder climate than B. lucorum in Austria. Additionally, the results indicate a very low intraspecific genetic variation within B. lucorum and B. cryptarum. This study confirms previous findings of three distinct species within the species complex. Based on reliable COI identification, the first coherent overview of the species complex in Austria can be achieved. The climatic data allows us to explain the differences in the distribution patterns. Moreover, the low intraspecific variation may indicate past bottleneck conditions for B. lucorum and B. cryptarum.},
}
@article {pmid31966157,
year = {2016},
author = {Hong, Y and Csuzdi, C},
title = {New Data to the Earthworm Fauna of the Korean Peninsula with Redescription of Eisenia koreana (Zicsi) and Remarks on the Eisenia nordenskioldi Species Group (Oligochaeta, Lumbricidae).},
journal = {Zoological studies},
volume = {55},
number = {},
pages = {e12},
pmid = {31966157},
issn = {1810-522X},
abstract = {Yong Hong and Csaba Csuzdi (2016) The earthworm fauna of the Korean peninsula, especially the Northern part (Democratic People's Republic of Korea) is still poorly known. Altogether 148 earthworm taxa are reported from Korea of which 22, including some uncertain records, belong to the Holarctic family Lumbricidae. From these 22 lumbricid taxa only eight are thought to be autochthonous, including the widely distributed Eisenia nordenskioldi species group which consists of six highly diverged DNA lineages. Due to a lack of material, the phylogenetic affinities of the Korean E. nordenskioldi s.l. specimens have not been determined so far. Here we report on the first lumbricid records from the Northern part of the peninsula (DPRK) after the description of the endemic earthworm species Eisenia koreana (Zicsi, 1972) together with a redescription of its type specimens. The supposedly autochthonous Eisenia nordenskioldi species group is briefly reviewed and the specimens collected recently in South Korea (Republic of Korea) were DNA barcoded and compared to the published lineages from Siberia (Russia). The redescription of the type specimen of Eiseniella koreana confirmed its inclusion in the genus Eisenia. Barcoding of the unpigmented Korean E. nordenskioldi specimens revealed that they form an independent clade placed quite far from the previously published unpigmented E. nordenskioldi forms and might represent a distinct species.},
}
@article {pmid32355454,
year = {2016},
author = {Briski, E and Ghabooli, S and Bailey, SA and MacIsaac, HJ},
title = {Are genetic databases sufficiently populated to detect non-indigenous species?.},
journal = {Biological invasions},
volume = {18},
number = {7},
pages = {1911-1922},
pmid = {32355454},
issn = {1387-3547},
abstract = {Correct species identifications are of tremendous importance for invasion ecology, as mistakes could lead to misdirecting limited resources against harmless species or inaction against problematic ones. DNA barcoding is becoming a promising and reliable tool for species identifications, however the efficacy of such molecular taxonomy depends on gene region(s) that provide a unique sequence to differentiate among species and on availability of reference sequences in existing genetic databases. Here, we assembled a list of aquatic and terrestrial non-indigenous species (NIS) and checked two leading genetic databases for corresponding sequences of six genome regions used for DNA barcoding. The genetic databases were checked in 2010, 2012, and 2016. All four aquatic kingdoms (Animalia, Chromista, Plantae and Protozoa) were initially equally represented in the genetic databases, with 64, 65, 69, and 61 % of NIS included, respectively. Sequences for terrestrial NIS were present at rates of 58 and 78 % for Animalia and Plantae, respectively. Six years later, the number of sequences for aquatic NIS increased to 75, 75, 74, and 63 % respectively, while those for terrestrial NIS increased to 74 and 88 % respectively. Genetic databases are marginally better populated with sequences of terrestrial NIS of plants compared to aquatic NIS and terrestrial NIS of animals. The rate at which sequences are added to databases is not equal among taxa. Though some groups of NIS are not detectable at all based on available data-mostly aquatic ones-encouragingly, current availability of sequences of taxa with environmental and/or economic impact is relatively good and continues to increase with time.},
}
@article {pmid31966107,
year = {2015},
author = {de Almeida Castilho, MC and Dos Santos Wisniewski, MJ and de Abreu, CB and Orlando, TC},
title = {Life history and DNA barcode of Oxyurella longicaudis (Birgei, 1910) (Cladocera, Anomopoda, Chydoridae).},
journal = {Zoological studies},
volume = {54},
number = {},
pages = {e20},
pmid = {31966107},
issn = {1810-522X},
abstract = {BACKGROUND: Cladocera is an important group of freshwater zooplankton, and the species plays an important role in energy transfer and in aquatic food webs. Oxyurella longicaudis is a Chydoridae species that has been recorded in North and South America. The aim of this study is to investigate the life cycle aspects of parthenogenetic females of O. longicaudis cultured in laboratory under controlled conditions: temperature (23°C ± 05°C), photoperiod (12 h light/12 h dark), food supply, and reconstituted water.<br><br>RESULTS: Embryonic development duration (2.3 &#xb1; 0.5 days), post-embryonic development (5.2 &#xb1; 0.69 days), mean fecundity (two eggs female[-1] brood[-1]), total egg production (22.55 &#xb1; 3.98 eggs), average longevity (58 days), and body growth of the species were recorded. We also report the first DNA barcode for O. longicaudis isolated in Brazil, which will allow for easy identification in future zooplankton community studies. The analysis shows a genetic divergence of around 7% between our Brazilian isolate and O. longicaudisisolates from Mexico.<br><br>CONCLUSIONS: The time of embryonic and post-embryonic development of O. longicaudis was higher than that of the other species of the same family, which contributed to lower total egg production throughout its life cycle. The genetic divergence appears to be sufficient to classify the two isolates as different species.},
}
@article {pmid31966097,
year = {2015},
author = {Alfaya, JEF and Bigatti, G and Kajihara, H and Strand, M and Sundberg, P and Machordom, A},
title = {DNA barcoding supports identification of Malacobdella species (Nemertea: Hoplonemertea).},
journal = {Zoological studies},
volume = {54},
number = {},
pages = {e10},
pmid = {31966097},
issn = {1810-522X},
abstract = {BACKGROUND: Nemerteans of the genus Malacobdella live inside of the mantle cavity of marine bivalves. The genus currently contains only six species, five of which are host-specific and usually found in a single host species, while the sixth species, M. grossa, has a wide host range and has been found in 27 different bivalve species to date. The main challenge of Malacobdella species identification resides in the similarity of the external morphology between species (terminal sucker, gut undulations number, anus position and gonad colouration), and thus, the illustrations provided in the original descriptions do not allow reliable identification. In this article, we analyse the relationships amongthree species of Malacobdella:M.arrokeana,M.japonica andM.grossa,adding new data for the M.grossa and reporting the first for M. japonica, analysing 658 base pairs of the mitochondrial cytochrome c oxidase subunit I gene(COI).Based on these analyses, we present and discuss the potential of DNA barcoding for Malacobdellaspecies identification.<br><br>RESULTS: Sixty-four DNA barcoding fragments of the mitochondrial COI gene from three different Malacobdella species (M. arrokeana, M. japonica and M. grossa) are analysed (24 of them newly sequenced for this study, along with four outgroup specimens) and used to delineate species. Divergences, measured as uncorrected differences, between the three species were M.arrokeana-M. grossa11.73%,M.arrokeana-M.japonica 10.62%and M.grossa-M. japonica 10.97%. The mean intraspecific divergence within the ingroup species showed a patent gap with respect to the interspecific ones: 0.18% for M.arrokeana,0.13% for M.grossa and0.02% for M.japonica (rangesfrom 0 to 0.91%).<br><br>CONCLUSIONS: We conclude that there is a clear correspondence between the molecular data and distinguishing morphological characters. Our results thus indicate that some morphological characters are useful for species identification and support the potential of DNA barcoding for species identification in a taxonomic group with subtle morphological external differences.},
}
@article {pmid32262000,
year = {2014},
author = {Wang, G and Leng, Y and Guo, H and Song, S and Jiang, Z and Yuan, X and Wang, X and Sun, K and Sun, K and Dou, H},
title = {Efficient preparation of magnetic quantum dot barcodes.},
journal = {Journal of materials chemistry. B},
volume = {2},
number = {47},
pages = {8310-8313},
doi = {10.1039/c4tb01672f},
pmid = {32262000},
issn = {2050-7518},
abstract = {Quantum dot (QD)-encoded magnetic barcodes were prepared through a highly efficient membrane emulsification-solvent evaporation approach. Our study demonstrates the great potential of these QD-encoded magnetic barcodes for both magnetic separation and multiplex suspension assays.},
}
@article {pmid31849038,
year = {2020},
author = {Vieira, C and Henriques, F and D'hondt, S and Neto, A and Almada, CH and Kaufmann, M and Sansón, M and Sangil, C and Clerck, O},
title = {Lobophora (Dictyotales) Species Richness, Ecology and Biogeography Across the North-Eastern Atlantic Archipelagos and Description of Two New Species[1].},
journal = {Journal of phycology},
volume = {56},
number = {2},
pages = {346-357},
doi = {10.1111/jpy.12956},
pmid = {31849038},
issn = {1529-8817},
mesh = {Atlantic Ocean ; Caribbean Region ; Mediterranean Sea ; *Phaeophyceae ; Phylogeny ; },
abstract = {The brown alga Lobophora (Dictyotales, Phaeophyceae) is an important macroalga in the North-eastern Atlantic archipelagos (i.e., Macaronesia). Notably in the Canaries it can dominate benthic assemblages. While the genus has been the subject of several ecological studies in the Canaries, no study has yet been conducted to assess species-level diversity of Lobophora in Macaronesia. We reassessed the diversity of Lobophora in Macaronesia, reporting the presence of seven species (L. caboverdeana sp. nov., L. canariensis, L. dagamae sp. nov., L. delicata, L. dispersa, L. littlerorum, and L. schneideri). Lobophora spp. from Macaronesia are morphologically and ecologically distinguishable. In the Canaries, L. schneideri dominates the photophilic assemblages from the intertidal to 20-30 m depth. Lobophora dagamae sp. nov. grows in less illuminated shallow habitats, and replaces L. schneideri from 30 to ~80 m. Lobophora canariensis also has a wide vertical distribution, from the intertidal to deep waters, while L. delicata, L. dispersa and L. littlerorum grow in shallow waters. The dominance of species with an upright habit versus prostrate or crustose species may be mediated by the pressure of herbivores. Four species have an amphi-Atlantic distribution: L. littlerorum, L. canariensis, L. delicata, and L. schneideri. Lobophora schneideri and L. delicata are furthermore distributed in the Mediterranean Sea. By sampling a pivotal region in the Atlantic, this study significantly improves our knowledge of Lobophora biogeography in the Atlantic Ocean. Macaronesia constitutes a species-poor region for Lobophora where no diversification events occurred, and a region of overlap between the Greater Caribbean and the Indo-Pacific.},
}
@article {pmid31846969,
year = {2019},
author = {Mariotto, S and Centofante, L and Venere, PC and Ferreira, DC and Artoni, RF},
title = {New Comparative Cytogenetic Data on Three Genera of Armored Catfishes of Ancistrini (Loricariidae: Hypostominae).},
journal = {Cytogenetic and genome research},
volume = {159},
number = {4},
pages = {208-214},
doi = {10.1159/000504723},
pmid = {31846969},
issn = {1424-859X},
mesh = {Animals ; Catfishes/*genetics ; Chromosome Inversion/genetics ; Chromosomes/genetics ; Cytogenetics/methods ; DNA, Ribosomal/genetics ; Diploidy ; Female ; Heterochromatin/genetics ; Karyotype ; Male ; Phylogeny ; Telomere/genetics ; },
abstract = {The karyotypes and other chromosomal markers of 4 catfish species, namely Lasiancistrus schomburgkii, Lasiancistrus sp., Araichthysloro, and Megalancistrus sp., members of a taxonomically complex and speciose tribe of catfishes Ancistrini, Hypostominae, were examined using conventional (Giemsa staining, Ag-NOR, and C-banding) and molecular cytogenetic protocols (FISH) and DNA barcoding. In L. schomburgkii, Lasiancistrus sp., and A.loro a diploid number 2n = 54 was observed, with karyotypes composed of 28m + 16sm + 10st, 36m + 12sm + 6st chromosomes, while Megalancistrus sp. had 2n = 52, with the karyotype composed of 28m + 16sm + 8st chromosomes. The Ag-NOR phenotypes were simple in all 4 species, which was confirmed by FISH with an 18S rDNA probe. However, the positive 5S rDNA sites varied among species: 2 chromosome pairs in L. schomburgkii, Lasiancistrus sp., and A. loro, and only 1 pair in Megalancistrus sp. The blocks of constitutive heterochromatin were poorly visible in the pericentromeric and telomeric regions of most chromosomes of the examined species by C-banding. The genetic distance analysis, based on mtDNA COI gene sequences (DNA barcoding), confirmed the species as 4 taxonomic units. Ours and other published data indicate that karyotype differentiation among Ancistrini is complex and divergent and indicates the occurrence of common chromosomal rearrangements, such as pericentric inversions conserving the diploid number, and other rearrangements that are more frequent in some genera, such as centric fusions in Ancistrus.},
}
@article {pmid31846968,
year = {2020},
author = {Hagi, T and Kurokawa, Y and Takahashi, T and Saito, T and Yamashita, K and Tanaka, K and Makino, T and Yamasaki, M and Nakajima, K and Mori, M and Doki, Y},
title = {Molecular Barcode Sequencing for Highly Sensitive Detection of Circulating Tumor DNA in Patients with Esophageal Squamous Cell Carcinoma.},
journal = {Oncology},
volume = {98},
number = {4},
pages = {222-229},
doi = {10.1159/000504808},
pmid = {31846968},
issn = {1423-0232},
mesh = {Aged ; Circulating Tumor DNA/*blood ; DNA Barcoding, Taxonomic/*methods ; Esophageal Neoplasms/*genetics ; Esophageal Squamous Cell Carcinoma/*genetics ; Genes, p53 ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Male ; Middle Aged ; Mutation ; },
abstract = {INTRODUCTION: Next-generation sequencing (NGS) with molecular barcodes (MB) is a novel method that enables the highly sensitive detection of circulating tumor DNA (ctDNA) in a relatively wide range of genes.<br><br>OBJECTIVE: The aim of this study was to examine the utility of NGS with MB for detecting ctDNA in patients with esophageal squamous cell carcinoma (ESCC).<br><br>METHODS: Five patients with ESCC who underwent preoperative treatment followed by esophagectomy were examined. The frequency of TP53 mutations in DNA extracted from tumor tissue and plasma at each time point during the treatment course was analyzed using NGS without MB. In 1 patient, additional analysis using NGS with MB was conducted to compare the sensitivities and to evaluate the clinical utility of this novel method.<br><br>RESULTS: TP53 mutations in tumor tissue were identified in 3 of 5 patients with ESCC. In 1 patient, the mutational allele frequency in plasma was 1.97% before preoperative treatment, and decreased to 0.09% after preoperative treatment. As the maximum frequency of background errors were 3.22% using NGS without MB and 0.08% with MB, which indicated that the sensitivity of ctDNA detection using NGS with MB was much higher than without MB. In 1 patient who had recurrence half a year after surgery, only NGS with MB could detect ctDNA even at 4 weeks after surgery, at a frequency of 0.20%.<br><br>CONCLUSIONS: NGS with MB enabled comprehensive and highly sensitive detection of ctDNA in a patient with ESCC. This novel method may be useful for the clinical diagnosis of ESCC.},
}
@article {pmid31844413,
year = {2019},
author = {Cancian de Araujo, B and Tavares, MT and Brotto, TRA and Silva-Freitas, JM and Santos, MEV and Saguiah, PM and Schmidt, S},
title = {Accelerating the knowledge of Peruvian Chalcididae (Insecta, Hymenoptera, Chalcidoidea) with integrative taxonomy.},
journal = {Biodiversity data journal},
volume = {7},
number = {},
pages = {e35907},
pmid = {31844413},
issn = {1314-2828},
abstract = {We present the first regional inventory of the fauna of Chalcididae in the Peruvian Amazon, with a nearly 6-fold increase in the number of species recorded for the country. A total of 418 specimens of Chalcididae were collected between 2000 and 2017 at the Panguana Reserve, Peruvian Amazon, 400 of which were obtained using Malaise traps and the remaining 18 specimens by canopy fogging. The morphological analyses indicated that these specimens represent 183 species of Chalcididae in 10 different genera, with 173 new to Peru and 134 potentially new species. We submitted 268 specimens, representing 167 species, to DNA barcoding. Of these, 141 specimens yielded sequences, 136 of them with a minimum of 300 bp. Sixty specimens were assigned a BIN by the Barcode of Life Database System (BOLD), resulting in 50 BINs. A cluster analysis of 138 individuals that yielded DNA sequences longer than 100 bp revealed 118 MOTUs (molecular operative taxonomic units), all of them highly congruent with the morphological data. Prior to the present study, 37 species in 9 genera of Chalcididae were known from Peru. With our results, this number was increased to 210 species in 13 genera. The present study is the result of a joint effort between the SNSB - Zoologische Staatssammlung München, Germany (ZSM) and the Insect Biodiversity Laboratory of the Universidade Federal do Espírito Santo, Vitória, Brazil (LaBI-UFES), intending to apply an accelerated taxonomic treatment of the Chalcididae of the Panguana reserve using traditional morphological approaches in combination with DNA barcoding. The complete molecular dataset and associated voucher information is publicly available through BOLD. The new species that were discovered as part of the study are being formally described elsewhere as part of taxonomic treatments of Neotropical and world generic revisions at LaBI-UFES.},
}
@article {pmid31844412,
year = {2019},
author = {Reemer, M and Skevington, JH and Kelso, S},
title = {Revision of the Neotropical hoverfly genus Peradon Reemer (Diptera, Syrphidae, Microdontinae).},
journal = {ZooKeys},
volume = {896},
number = {},
pages = {1-93},
pmid = {31844412},
issn = {1313-2989},
abstract = {The species of the Neotropical hoverfly genus Peradon Reemer, 2013 are revised, based on morphological characters with aid of mitochondrial DNA barcodes. The resulting number of valid species is increased to 31, of which the following seven are described as new: P. ballux Reemer, sp. nov., P. brevis Reemer, sp. nov., P. costaricensis Reemer, sp. nov., P. notialus Reemer, sp. nov., P. palpator Reemer, sp. nov., P. pompiloides Reemer, sp. nov., and P. surinamensis Reemer, sp. nov. Two new synonymies are established: Microdon langi Curran, 1925, syn. nov. and Microdon flavomarginatum Curran, 1925, syn. nov. are both junior synonyms of Mulio bidens Fabricius, 1805. A neotype is designated for Microdon diaphanus Sack, 1921. This neotype, which has been reared from an ant nest, also represents the first case of a larval record for this genus. In some species, most notably in P. bidens (Fabricius) and P. normalis (Curran), discrete and distinct colour morphs are recognized, with strongly differing colouration of wings and abdomen.},
}
@article {pmid31844409,
year = {2019},
author = {Pentinsaari, M and Anderson, R and Borowiec, L and Bouchard, P and Brunke, A and Douglas, H and Smith, ABT and Hebert, PDN},
title = {DNA barcodes reveal 63 overlooked species of Canadian beetles (Insecta, Coleoptera).},
journal = {ZooKeys},
volume = {894},
number = {},
pages = {53-150},
pmid = {31844409},
issn = {1313-2989},
abstract = {This study demonstrates the power of DNA barcoding to detect overlooked and newly arrived taxa. Sixty-three species of Coleoptera representing 25 families are studied based on DNA barcode data and morphological analysis of the barcoded specimens. Three of the species involve synonymies or previous taxonomic confusion in North America, while the first Canadian records are published for 60 species. Forty-two species are adventive in North America, and 40 of these adventive species originate from the Palaearctic region. Three genera are recorded from the Nearctic region for the first time: Coelostoma Brullé, 1835 (Hydrophilidae), Scydmoraphes Reitter, 1891 (Staphylinidae), and Lythraria Bedel, 1897 (Chrysomelidae). Two new synonymies are established: Mycetoporus triangulatus Campbell, 1991 (Staphylinidae) is a junior synonym of Mycetoporus reichei Pandellé, 1869, syn. nov. while Bledius philadelphicus Fall, 1919 (Staphylinidae) is a junior synonym of Bledius gallicus (Gravenhorst, 1806), syn. nov. The previously suggested move of Ctenicera tigrina (Fall, 1901) to the genus Pseudanostirus Dolin, 1964 (Elateridae) is formalized, resulting in Pseudanostirus tigrinus (Fall, 1901), comb. nov.},
}
@article {pmid31844398,
year = {2019},
author = {Borrero-Pérez, GH and Vanegas-González, MJ},
title = {Holothuria (Mertensiothuria) viridiaurantia sp. nov. (Holothuriida, Holothuriidae), a new sea cucumber from the Eastern Pacific Ocean revealed by morphology and DNA barcoding.},
journal = {ZooKeys},
volume = {893},
number = {},
pages = {1-19},
pmid = {31844398},
issn = {1313-2989},
abstract = {Holothuria (Mertensiothuria) viridiaurantiasp. nov. is described based on specimens from rocky reefs of northern Chocó in the Colombian Pacific Ocean; however, it also occurs along the Eastern Pacific Ocean from Mexico and Panama. Although specimens from Mexico and Panama were previously identified as Holothuria (Mertensiothuria) hilla Lesson, 1830 the new species is easily distinguished morphologically and via mtDNA. In terms of morphology, the species can be identified by its olive-green background and white-orange papillae and tentacles, larger tentacles with deep indentations and also by larger buttons on the dorsal and ventral body wall, papillae and tube feet; large, thick and rough tentacle rods, and the absence of ossicles in the longitudinal muscles. The new species is included in the subgenus Mertensiothuria considering molecular evidence.},
}
@article {pmid31842348,
year = {2019},
author = {Zheng, L and Zhang, Y and Yang, W and Zeng, Y and Jiang, F and Qin, Y and Zhang, J and Jiang, Z and Hu, W and Guo, D and Wan, J and Zhao, Z and Liu, L and Li, Z},
title = {New Species-Specific Primers for Molecular Diagnosis of Bactrocera minax and Bactrocera tsuneonis (Diptera: Tephritidae) in China Based on DNA Barcodes.},
journal = {Insects},
volume = {10},
number = {12},
pages = {},
pmid = {31842348},
issn = {2075-4450},
support = {2016YFF0203200//National Key R&amp;D Program of China/ ; },
abstract = {Tephritidae fruit flies (Diptera: Tephritidae) are regarded as important damage-causing species due to their ability to cause great economic losses in fruit and vegetable crops. Bactrocera minax and Bactrocera tsuneonis are two sibling species of the subgenus Tetradacus of Bactrocera that are distributed across a limited area of China, but have caused serious impacts. They share similar morphological characteristics. These characteristics can only be observed in the female adult individuals. The differences between them cannot be observed in preimaginal stages. Thus, it is difficult to distinguish them in preimaginal stages morphologically. In this study, we used molecular diagnostic methods based on cytochrome c oxidase subunit I and species-specific markers to identify these two species and improve upon the false-positive results of previous species-detection primers. DNA barcode sequences were obtained from 900 individuals of B. minax and 63 individuals of B. tsuneonis. Based on these 658 bp DNA barcode sequences of the cytochrome c oxidase subunit I gene, we successfully designed the species-specific primers for B. minax and B. tsuneonis. The size of the B. minax specific fragment was 422 bp and the size of the B. tsuneonis specific fragment was 456 bp. A series of PCR trials ensured the specificity of these two pairs of primers. Sensitivity assay results demonstrated that the detection limit for the DNA template concentration was 0.1~1 ng/μL for these two species. In this study, we established a more reliable, rapid, and low-cost molecular identification method for all life stages of B. minax and B. tsuneonis. Species-specific PCR can be applied in plant quarantine, monitoring and control of B. minax and B. tsuneonis.},
}
@article {pmid31841262,
year = {2020},
author = {Kruger, DT and Jansen, MPHM and Konings, IRHM and Dercksen, WM and Jager, A and Oulad Hadj, J and Sleijfer, S and Martens, JWM and Boven, E},
title = {High ctDNA molecule numbers relate with poor outcome in advanced ER+, HER2- postmenopausal breast cancer patients treated with everolimus and exemestane.},
journal = {Molecular oncology},
volume = {14},
number = {3},
pages = {490-503},
pmid = {31841262},
issn = {1878-0261},
mesh = {Adult ; Aged ; Aged, 80 and over ; Androstadienes/*therapeutic use ; Antineoplastic Combined Chemotherapy Protocols ; Biomarkers, Tumor/genetics/metabolism ; Breast Neoplasms/blood/*drug therapy/mortality/pathology ; Circulating Tumor DNA/blood/*genetics ; Everolimus/*therapeutic use ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Middle Aged ; Mutation, Missense ; Neoplasm Metastasis ; Postmenopause ; Progression-Free Survival ; Receptor, ErbB-2/*metabolism ; Receptors, Estrogen/*metabolism ; Retrospective Studies ; },
abstract = {We determined whether progression-free survival (PFS) in metastatic breast cancer (MBC) patients receiving everolimus plus exemestane (EVE/EXE) varies depending on circulating tumour DNA (ctDNA) characteristics. Baseline plasma cell-free DNA (cfDNA) from 164 postmenopausal women with ER-positive, HER2-negative MBC refractory to a nonsteroidal aromatase inhibitor and treated with standard EVE/EXE (Everolimus Biomarker Study, Eudract 2013-004120-11) was characterised for 10 relevant breast cancer genes by next-generation sequencing with molecular barcoding. ctDNA molecule numbers, number of mutations and specific variants were related with PFS and overall survival (OS). Missense hotspot mutations in cfDNA were detected in 125 patients. The median of 54 ctDNA molecules per mL plasma distinguished patients with high and low/no ctDNA load. Patients with low/no ctDNA load (N = 102) showed longer median PFS of 5.7 months (P = 0.006) and OS of 124.8 months (P = 0.008) than patients with high ctDNA load (N = 62; 4.4 months and 107.7 months, respectively) in multivariate analyses. Patients with < 3 specific mutations (N = 135) had longer median PFS of 5.4 months compared to those with ≥ 3 mutations (3.4 months; P < 0.001). In conclusion, MBC patients with low/no ctDNA load or < 3 hotspot mutations experience longer PFS while treated with EVE/EXE.},
}
@article {pmid31837485,
year = {2020},
author = {Schlottau, K and Eggerbauer, E and Freuling, CM and Beer, M and Müller, T and Hoffmann, B},
title = {Rapid molecular species identification of indigenous bats from Germany for surveillance purposes.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {78},
number = {},
pages = {104140},
doi = {10.1016/j.meegid.2019.104140},
pmid = {31837485},
issn = {1567-7257},
mesh = {Animals ; Chiroptera/classification/*genetics ; Germany ; Polymerase Chain Reaction/*methods ; Species Specificity ; },
abstract = {Chiroptera form the second largest order of mammals and compromise >1200 species, of which only 51 species are abundant in Europe. As bats are important hosts involved in the emergence and spread of zoonotic infections, it is becoming more important to discriminate the different species of bats involved in the maintenance of causative agents. However, traditional taxonomic methods rely on morphological features and are challenging as they require long-lasting experience of an investigator and sometimes fail if the specimen is of poor condition. On the other hand, barcoding requires sequencing and is time consuming. Therefore, a versatile genetic approach for rapid species identification would be valuable. In this study, two mitochondrial loci, cytochrome b (cyt b) and cytochrome c oxidase subunit I (COI) were selected for the development of two multiplex qPCRs for differentiating four very abundant bat species in Germany using DNA extracted from the patagium or organ pools. Verification of the developed assays using a set of 1000 individual bat samples belonging to 20 different European species clearly showed that the multiplex qPCRs were able to determine the four most abundant species in this collection by a COI based qPCR. All other bat species which could not be covered by this approach could be easily identified by sequencing of the amplicon generated by broad-range qPCRs for cyt B and COI, respectively. Moreover, the double-check approach with cyt B and COI makes the identification of bats into species more reliable. The new multiplex PCRs allow a fast and easy genotyping of German bats and could be useful for screening approaches.},
}
@article {pmid31837483,
year = {2020},
author = {Rodrigues, CMF and Garcia, HA and Rodrigues, AC and Pereira, DL and Pereira, CL and Viola, LB and Neves, L and Camargo, EP and Gibson, W and Teixeira, MMG},
title = {Expanding our knowledge on African trypanosomes of the subgenus Pycnomonas: A novel Trypanosoma suis-like in tsetse flies, livestock and wild ruminants sympatric with Trypanosoma suis in Mozambique.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {78},
number = {},
pages = {104143},
doi = {10.1016/j.meegid.2019.104143},
pmid = {31837483},
issn = {1567-7257},
mesh = {Animals ; Animals, Wild ; Host-Parasite Interactions ; Livestock/parasitology ; Mozambique/epidemiology ; Phylogeny ; RNA, Ribosomal/genetics ; Ruminants/parasitology ; Swine ; Swine Diseases/parasitology ; Sympatry ; Trypanosoma/*genetics/pathogenicity ; Trypanosomiasis, African/epidemiology/*veterinary ; Tsetse Flies/*parasitology ; },
abstract = {Among the subgenera of African tsetse-transmitted trypanosomes pathogenic to livestock, the least known is the subgenus Pycnomonas, which contains a single species, Trypanosoma suis (TSU), a pathogen of domestic pigs first reported in 1905 and recently rediscovered in Tanzania and Mozambique. Analysis by Fluorescent Fragment Length Barcoding (FFLB) revealed an infection rate of 20.3% (108 out of 530 tsetse flies) in a recent study in the Gorongosa and Niassa wildlife reserves in Mozambique, and demonstrated two groups of Pycnomonas trypanosomes: one (14.1%, 75 flies) showing an FFLB profile identical to the reference TSU from Tanzania, and the other (6.2%, 33 flies) differing slightly from reference TSU and designated Trypanosoma suis-like (TSU-L). Phylogenetic analyses tightly clustered TSU and TSU-L from Mozambique with TSU from Tanzania forming the clade Pycnomonas positioned between the subgenera Trypanozoon and Nannomonas. Our preliminarily exploration of host ranges of Pycnomonas trypanosomes revealed TSU exclusively in warthogs while TSU-L was identified, for the first time for a member of the subgenus Pycnomonas, in ruminants (antelopes, Cape buffalo, and in domestic cattle and goats). The preferential blood meal sources of tsetse flies harbouring TSU and TSU-L were wild suids, and most of these flies concomitantly harboured the porcine trypanosomes T. simiae, T. simiae Tsavo, and T. godfreyi. Therefore, our findings support the link of TSU with suids while TSU-L remains to be comprehensively investigated in these hosts. Our results greatly expand our knowledge of the diversity, hosts, vectors, and epidemiology of Pycnomonas trypanosomes. Due to shortcomings of available molecular diagnostic methods, a relevant cohort of trypanosomes transmitted by tsetse flies to ungulates, especially suids, has been neglected or most likely misidentified. The method employed in the present study enables an accurate discrimination of trypanosome species and genotypes and, hence, a re-evaluation of the "lost" subgenus Pycnomonas and of porcine trypanosomes in general, the most neglected group of African trypanosomes pathogenic to ungulates.},
}
@article {pmid31837431,
year = {2020},
author = {Moore, RA and Zeng, T and Docking, TR and Bosdet, I and Butterfield, YS and Munro, S and Li, I and Swanson, L and Starks, ER and Tse, K and Mungall, AJ and Holt, RA and Karsan, A},
title = {Sample Tracking Using Unique Sequence Controls.},
journal = {The Journal of molecular diagnostics : JMD},
volume = {22},
number = {2},
pages = {141-146},
doi = {10.1016/j.jmoldx.2019.10.011},
pmid = {31837431},
issn = {1943-7811},
mesh = {Computational Biology ; DNA Contamination ; Databases, Nucleic Acid ; Gene Library ; High-Throughput Nucleotide Sequencing/*methods/*standards ; Humans ; Reference Standards ; Reproducibility of Results ; Sequence Analysis, DNA ; },
abstract = {Sample tracking and identity are essential when processing multiple samples in parallel. Sequencing applications often involve high sample numbers, and the data are frequently used in a clinical setting. As such, a simple and accurate intrinsic sample tracking process through a sequencing pipeline is essential. Various solutions have been implemented to verify sample identity, including variant detection at the start and end of the pipeline using arrays or genotyping, bioinformatic comparisons, and optical barcoding of samples. None of these approaches are optimal. To establish a more effective approach using genetic barcoding, we developed a panel of unique DNA sequences cloned into a common vector. A unique DNA sequence is added to the sample when it is first received and can be detected by PCR and/or sequencing at any stage of the process. The control sequences are approximately 200 bases long with low identity to any sequence in the National Center for Biotechnology Information nonredundant database (<30 bases) and contain no long homopolymer (>7) stretches. When a spiked next-generation sequencing library is sequenced, sequence reads derived from this control sequence are generated along with the standard sequencing run and are used to confirm sample identity and determine cross-contamination levels. This approach is used in our targeted clinical diagnostic whole-genome and RNA-sequencing pipelines and is an inexpensive, flexible, and platform-agnostic solution.},
}
@article {pmid31836767,
year = {2019},
author = {Di Muzio, G and Mussat Sartor, R and Nurra, N and Battuello, M and Pessani, D and Cervella, P and Cuesta, JA},
title = {Morphology of planktonic zoeal stages of Palicus caronii (Decapoda, Brachyura), identified by DNA barcoding, provides novelties to Palicoidea larval systematics.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {19132},
pmid = {31836767},
issn = {2045-2322},
mesh = {Animals ; Brachyura/anatomy &amp; histology/*genetics/*physiology ; *DNA Barcoding, Taxonomic ; Female ; Larva/physiology ; Mediterranean Sea ; Microscopy, Electron, Scanning ; Plankton ; },
abstract = {The zoeal development of the brachyuran crab, Palicus caronii, comprises two zoeal stages and the morphology is described and illustrated in detail. The zoeae were collected in plankton samples from the Southern Ligurian Sea (Western Mediterranean). Although the morphology of the larval stages of this species was unknown, a combination of characters allowed the zoeae to initially be assigned to the Palicidae, based on the previous unique known first zoeal description of one species of this family. Later, the identification of the larvae as Palicus caronii was confirmed through molecular analysis. The morphological features of the zoeae that characterize the Palicidae and separate them from the Crossotonotidae are confirmed. Also, the larval development comprising only two zoeal stages observed in Palicus caronii, the peculiar and uncommon carapace surface setation, and the presence of anterodorsal and posterodorsal sensory dorsal organs suggest that these characters could be common to the Palicoidea.},
}
@article {pmid31835363,
year = {2019},
author = {Kim, Y and Shin, J and Cho, SS and Hwang, YP and Choi, C},
title = {Development and Application of InDel Markers for Authentication of the Korean Herbs Zanthoxylum schinifolium and Zanthoxylum piperitum.},
journal = {Foods (Basel, Switzerland)},
volume = {8},
number = {12},
pages = {},
pmid = {31835363},
issn = {2304-8158},
abstract = {Zanthoxylum schinifolium and Zanthoxylum piperitum are the sources of the well-known traditional Korean herbal medicines "sancho" (prickly ash) and "chopi" (Korean pepper), respectively. Sancho and chopi are often indiscriminately mixed due to the similar appearance of the herbal materials when used as spices and herbal medicines. Moreover, commercial sancho and chopi products often contain adulterants, which is insufficient to ensure food efficacy and safety. In this study, we developed hypervariable insertion/deletion (InDel) markers to distinguish between sancho and chopi products by comparing the complete chloroplast genome sequences of four Zanthoxylum species deposited in the National Center for Biotechnology Information (NCBI) GenBank. Comparative analyses of the nucleotide diversity (Pi) of these Zanthoxylum genomes revealed four hypervariable divergent sites (trnH-psbA, psbZ-trnG, trnfM-rps14, and trnF-ndhK) with Pi > 0.025 among 520 windows. Of these four regions, including two genic and two intergenic regions, only psbZ-trnG yielded accurate PCR amplification results between commercial sancho and chopi products from the Korean herbal medicine market. We therefore selected psbZ-trnG, an InDel-variable locus with high discriminatory powers, as a candidate DNA barcode locus. This InDel marker could be used as a valuable, simple, and efficient tool for identifying these medicinal herbs, thereby increasing the safety of these spices and herbal materials in the food market.},
}
@article {pmid31834491,
year = {2020},
author = {Zittra, C and Schoener, ER and Wagner, R and Heddergott, M and Duscher, GG and Fuehrer, HP},
title = {Unnoticed arrival of two dipteran species in Austria: the synanthropic moth fly Clogmia albipunctata (Williston, 1893) and the parasitic bird louse fly Ornithoica turdi (Olivier in Latreille, 1811).},
journal = {Parasitology research},
volume = {119},
number = {2},
pages = {737-740},
pmid = {31834491},
issn = {1432-1955},
mesh = {Animals ; Austria ; Biodiversity ; DNA Barcoding, Taxonomic ; Diptera/genetics/*physiology ; Electron Transport Complex IV/genetics ; Psychodidae/genetics/*physiology ; },
abstract = {In the framework of a mosquito-monitoring program conducted from 2014 to 2018, non-culicid dipteran bycatch was identified to species-level with a focus on Diptera of medical and veterinary importance as part of a biodiversity initiative and barcoding project ("Austrian Barcode of Life"). Two species hitherto not known from Austria, the regularly sampled synanthropic moth fly Clogmia albipunctata (Psychodidae) and a single specimen of the louse fly Ornithoica turdi (Hippoboscidae), were collected in Vienna and Lower Austria. We confirmed identification results using a barcoding approach and provide the first reference sequence for O. turdi.},
}
@article {pmid31829619,
year = {2020},
author = {Salem, DP and Gong, X and Liu, AT and Akombi, K and Strano, MS},
title = {Immobilization and Function of nIR-Fluorescent Carbon Nanotube Sensors on Paper Substrates for Fluidic Manipulation.},
journal = {Analytical chemistry},
volume = {92},
number = {1},
pages = {916-923},
doi = {10.1021/acs.analchem.9b03756},
pmid = {31829619},
issn = {1520-6882},
abstract = {Nanoparticle-based optical sensors are capable of highly sensitive and selective chemical interactions and can form the basis of molecular recognition for various classes of analytes. However, their incorporation into standardized in vitro assays has been limited by their incompatibility with packaging or form factors necessary for specific applications. Here, we have developed a technique for immobilizing nIR-fluorescent single-walled carbon nanotube (SWCNT) sensors on seven different types of paper substrates including nitrocellulose, nylon, poly(vinylidene fluoride), and cellulose. Sensors remain functional upon immobilization and exhibit nIR fluorescence in nonaqueous solvent systems. We then extend this system to the Corona Phase Molecular Recognition (CoPhMoRe) approach of synthetic molecular recognition by screening ssDNA-wrapped SWCNTs with different sequences against a panel of fat-soluble vitamins in canola oil, identifying a sensor which responds to β-carotene with a dissociation constant of 2.2 μM. Moreover, we pattern hydrophobic regions onto nitrocellulose using the wax printing method and form one-dimensional sensor barcodes for rapid multiplexing. Using a sensor array of select ssDNA wrappings, we are able to distinguish between Cu(II), Cd(II), Hg(II), and Pb(II) at a concentration of 100 μM. Finally, we demonstrate that immobilized sensors remain fluorescent and responsive for nearly 60 days when stability is addressed. This work represents a significant step toward the deployment of fluorescent nanoparticle sensors for point-of-use applications.},
}
@article {pmid31828716,
year = {2020},
author = {Menolli, N and Sánchez-García, M},
title = {Brazilian fungal diversity represented by DNA markers generated over 20 years.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {51},
number = {2},
pages = {729-749},
pmid = {31828716},
issn = {1678-4405},
support = {88881.120176/2016-01//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 04/04319-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 09/53272-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2018/15677-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
mesh = {Biodiversity ; Brazil ; DNA, Fungal/*genetics ; Fungi/*classification ; Genetic Markers ; *Genetic Variation ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Molecular techniques using fungal DNA barcoding (ITS) and other markers have been key to identifying the biodiversity of different geographic areas, mainly in megadiverse countries. Here, we provide an overview of the fungal diversity in Brazil based on DNA markers of phylogenetic importance generated since 1996. We retrieved fungal sequences of ITS, LSU, SSU, tef1-α, β-tubulin, rpb1, rpb2, actin, chitin synthase, and ATP6 from GenBank using different field keywords that indicated their origin in Brazil. A total of 19,440 sequences were recovered. ITS is the most representative marker (11,209 sequences), with 70.1% belonging to Ascomycota, 18.6% Basidiomycota, 10.2% unidentified, 1.1% Mucoromycota, two sequences of Olpidium bornovanus (Fungi incertae sedis), one sequence of Blastocladiomycota (Allomyces arbusculus), and one sequence of Chytridiomycota (Batrachochytrium dendrobatidis). Considering the sequences of all selected markers, only the phyla Cryptomycota and Entorrhizomycota were not represented. Based on ITS, using a cutoff of 98%, all sequences comprise 3047 OTUs, with the majority being Ascomycota (2088 OTUs) and Basidiomycota (681 OTUs). Previous numbers based mainly on morphological and bibliographical data revealed 5264 fungal species from Brazil, with a predominance of Basidiomycota (2741 spp.) and Ascomycota (1881 spp.). The unidentified ITS sequences not assigned to a higher taxonomic level represent 1.61% of all ITS sequences sampled and correspond to 38 unknown class-level lineages (75% cutoff). A maximum likelihood phylogeny based on LSU illustrates the fungal classes occurring in Brazil.},
}
@article {pmid31828310,
year = {2020},
author = {Mokhtar, AS and Ling Lau, Y and Wilson, JJ and Abdul-Aziz, NM},
title = {Genetic Diversity of Pediculus humanus capitis (Phthiraptera: Pediculidae) in Peninsular Malaysia and Molecular Detection of Its Potential Associated Pathogens.},
journal = {Journal of medical entomology},
volume = {57},
number = {3},
pages = {915-926},
doi = {10.1093/jme/tjz234},
pmid = {31828310},
issn = {1938-2928},
mesh = {Animals ; Bacteria/*isolation &amp; purification ; DNA Barcoding, Taxonomic ; *Genetic Variation ; Housing ; Humans ; Lice Infestations/parasitology ; Malaysia ; Pediculus/*genetics/*microbiology ; Social Class ; },
abstract = {Pediculosis capitis caused by Pediculus humanus capitis (De Geer) is endemic all over the world, and children are mostly affected, particularly those living in overcrowded institutions. Several studies have shown that P. h. capitis carried human pathogenic bacteria, suggesting the potential role of head lice in the transmission of pathogens to humans. In this study, we determined the genetic diversity of head lice collected from welfare homes sheltering underprivileged children by using DNA barcoding and demonstrated the presence of Acinetobacter spp., Serratia marcescens, and Staphylococcus aureus in head lice, which have never been investigated before in Malaysia. Cox1 DNA barcoding identified the head lice, P. h. capitis collected from welfare homes across two geographical areas of Peninsular Malaysia as belonging to clades A, B, and D. Acinetobacter bacteria: Acinetobacter guillouiae, Acinetobacter junii, Acinetobacter baumannii, and Acinetobacter nosocomialis were detected in head lice belonging to clades A and also D. In addition, DNA from S. marcescens and S. aureus were also detected in both clades A and D. To our knowledge, this is the first report on the genetic diversity of head lice in Malaysia through DNA barcoding, as well as the first to provide molecular evidence on the type of bacteria occurring in head lice in Malaysia. It is anticipated that the DNA barcoding technique used in this study will be able to provide rapid and accurate identification of arthropods, in particular, medically important ectoparasites.},
}
@article {pmid31825988,
year = {2019},
author = {Alqahtani, FM and Arivett, BA and Taylor, ZE and Handy, ST and Farone, AL and Farone, MB},
title = {Chemogenomic profiling to understand the antifungal action of a bioactive aurone compound.},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0226068},
pmid = {31825988},
issn = {1932-6203},
mesh = {Actin Cytoskeleton/drug effects ; Antifungal Agents/chemistry/*pharmacology ; Benzofurans/chemistry/*pharmacology ; Candida albicans/*drug effects/genetics ; Cell Line, Tumor ; Cell Survival/drug effects ; Drug Design ; Drug Resistance, Fungal/genetics ; G1 Phase Cell Cycle Checkpoints/drug effects ; Gene Ontology ; Humans ; Microbial Sensitivity Tests ; Saccharomyces cerevisiae/drug effects/genetics/growth &amp; development ; },
abstract = {Every year, more than 250,000 invasive candidiasis infections are reported with 50,000 deaths worldwide. The limited number of antifungal agents necessitates the need for alternative antifungals with potential novel targets. The 2-benzylidenebenzofuran-3-(2H)-ones have become an attractive scaffold for antifungal drug design. This study aimed to determine the antifungal activity of a synthetic aurone compound and characterize its mode of action. Using the broth microdilution method, aurone SH1009 exhibited inhibition against C. albicans, including resistant isolates, as well as C. glabrata, and C. tropicalis with IC50 values of 4-29 μM. Cytotoxicity assays using human THP-1, HepG2, and A549 human cell lines showed selective toxicity toward fungal cells. The mode of action for SH1009 was characterized using chemical-genetic interaction via haploinsufficiency (HIP) and homozygous (HOP) profiling of a uniquely barcoded Saccharomyces cerevisiae mutant collection. Approximately 5300 mutants were competitively treated with SH1009 followed by DNA extraction, amplification of unique barcodes, and quantification of each mutant using multiplexed next-generation sequencing. Barcode post-sequencing analysis revealed 238 sensitive and resistant mutants that significantly (FDR P values ≤ 0.05) responded to aurone SH1009. The enrichment analysis of KEGG pathways and gene ontology demonstrated the cell cycle pathway as the most significantly enriched pathway along with DNA replication, cell division, actin cytoskeleton organization, and endocytosis. Phenotypic studies of these significantly enriched responses were validated in C. albicans. Flow cytometric analysis of SH1009-treated C. albicans revealed a significant accumulation of cells in G1 phase, indicating cell cycle arrest. Fluorescence microscopy detected abnormally interrupted actin dynamics, resulting in enlarged, unbudded cells. RT-qPCR confirmed the effects of SH1009 in differentially expressed cell cycle, actin polymerization, and signal transduction genes. These findings indicate the target of SH1009 as a cell cycle-dependent organization of the actin cytoskeleton, suggesting a novel mode of action of the aurone compound as an antifungal inhibitor.},
}
@article {pmid31824521,
year = {2019},
author = {Pirrello, C and Mizzotti, C and Tomazetti, TC and Colombo, M and Bettinelli, P and Prodorutti, D and Peressotti, E and Zulini, L and Stefanini, M and Angeli, G and Masiero, S and Welter, LJ and Hausmann, L and Vezzulli, S},
title = {Emergent Ascomycetes in Viticulture: An Interdisciplinary Overview.},
journal = {Frontiers in plant science},
volume = {10},
number = {},
pages = {1394},
pmid = {31824521},
issn = {1664-462X},
abstract = {The reduction of pesticide usage is a current imperative and the implementation of sustainable viticulture is an urgent necessity. A potential solution, which is being increasingly adopted, is offered by the use of grapevine cultivars resistant to its main pathogenic threats. This, however, has contributed to changes in defense strategies resulting in the occurrence of secondary diseases, which were previously controlled. Concomitantly, the ongoing climate crisis is contributing to destabilizing the increasingly dynamic viticultural context. In this review, we explore the available knowledge on three Ascomycetes which are considered emergent and causal agents of powdery mildew, black rot and anthracnose. We also aim to provide a survey on methods for phenotyping disease symptoms in fields, greenhouse and lab conditions, and for disease control underlying the insurgence of pathogen resistance to fungicide. Thus, we discuss fungal genetic variability, highlighting the usage and development of molecular markers and barcoding, coupled with genome sequencing. Moreover, we extensively report on the current knowledge available on grapevine-ascomycete interactions, as well as the mechanisms developed by the host to counteract the attack. Indeed, to better understand these resistance mechanisms, it is relevant to identify pathogen effectors which are involved in the infection process and how grapevine resistance genes function and impact the downstream cascade. Dealing with such a wealth of information on both pathogens and the host, the horizon is now represented by multidisciplinary approaches, combining traditional and innovative methods of cultivation. This will support the translation from theory to practice, in an attempt to understand biology very deeply and manage the spread of these Ascomycetes.},
}
@article {pmid31824488,
year = {2019},
author = {Navelsaker, S and Magadan, S and Jouneau, L and Quillet, E and Olesen, NJ and Munang'andu, HM and Boudinot, P and Evensen, &#xd8;},
title = {Sequential Immunization With Heterologous Viruses Does Not Result in Attrition of the B Cell Memory in Rainbow Trout.},
journal = {Frontiers in immunology},
volume = {10},
number = {},
pages = {2687},
pmid = {31824488},
issn = {1664-3224},
mesh = {Animals ; Antibodies, Neutralizing/blood ; Antibodies, Viral/blood ; B-Lymphocytes/*immunology ; Birnaviridae Infections/prevention &amp; control ; Immunization/*methods ; Immunologic Memory ; Infectious pancreatic necrosis virus/*immunology ; Novirhabdovirus/*immunology ; Oncorhynchus mykiss/blood/*immunology ; Rhabdoviridae Infections/prevention &amp; control ; Viral Vaccines/*administration &amp; dosage ; },
abstract = {Long-term immunity is of great importance for protection against pathogens and has been extensively studied in mammals. Successive heterologous infections can affect the maintenance of immune memory, inducing attrition of T memory cells and diminishing B cell mediated protection. In fish, the basis of immune memory and the mechanisms of immunization to heterologous pathogens remain poorly understood. We sequentially immunized isogenic rainbow trout with two immunologically distinct viruses, VHSV and IPNV, either with one virus only or in combination, and analyzed the antibody responses and repertoires. Neutralizing antibodies and ELISPOT did not reveal an effect of heterologous immunization. Using a consensus read sequencing approach that incorporates unique barcodes to each cDNA molecule, we focused on the diversity expressed by selected responding VH/C combinations. We identified both public and private responses against VHSV and/or IPNV in all groups of fish. In fish immunized with two viruses, we registered no significant reduction in the persistence of the response toward the primary immunization. Similarly, the response to the second immunization was not affected by a prior vaccination to the other virus. Our data suggest that heterologous immunization does not enforce attrition of pre-existing antibody producing cells, which may impair the protection afforded by multiple successive vaccinations. These observations are potentially important to improve vaccination strategies practiced in aquaculture.},
}
@article {pmid31824205,
year = {2019},
author = {Valdez-Mondragón, A and Navarro-Rodríguez, CI and Solís-Catalán, KP and Cortez-Roldán, MR and Juárez-Sánchez, AR},
title = {Under an integrative taxonomic approach: the description of a new species of the genus Loxosceles (Araneae, Sicariidae) from Mexico City.},
journal = {ZooKeys},
volume = {892},
number = {},
pages = {93-133},
pmid = {31824205},
issn = {1313-2989},
abstract = {A new species of the spider genus Loxosceles Heineken &amp; Lowe, 1832, Loxosceles tenochtitlan Valdez-Mondragón &amp; Navarro-Rodríguez, sp. nov., is described based on adult male and female specimens from the states of Mexico City, Estado de Mexico and Tlaxcala. Integrative taxonomy including traditional morphology, geometric and lineal morphology, and molecules (DNA barcodes of cytochrome c oxidase subunit 1 (CO1) and internal transcribed spacer 2 (ITS2)), were used as evidence to delimit the new species. Four methods were used for molecular analyses and species delimitation: 1) corrected p-distances under neighbor joining (NJ), 2) automatic barcode gap discovery (ABGD), 3) general mixed yule coalescent model (GMYC), and 4) poisson tree processes (bPTP). All molecular methods, traditional, geometric and lineal morphology were consistent in delimiting and recognizing the new species. Loxosceles tenochtitlan sp. nov. is closely related to L. misteca based on molecular data. Although both species are morphologically similar, the average p-distance from CO1 data was 13.8% and 4.2% for ITS2 data. The molecular species delimitation methods recovered well-supported monophyletic clusters for samples of L. tenochtitlan sp. nov. from Mexico City + Tlaxcala and for samples of L. misteca from Guerrero. Loxosceles tenochtitlan sp. nov. is considered a unique species for three reasons: (1) it can be distinguished by morphological characters (genitalic and somatic); (2) the four different molecular species delimitation methods were congruent to separate both species; and (3) there is variation in leg I length of males between both species, with the males of L. misteca having longer legs than males of L. tenochtitlan sp. nov., also morphometrically, the shape of tibiae of the palp between males of both species is different.},
}
@article {pmid31822991,
year = {2020},
author = {Taleb, M and Tail, G and Açıkgöz, HN},
title = {DNA barcoding of Stearibia nigriceps (Meigen) and Piophila casei (Linnaeus) (Diptera: Piophilidae) from Algeria and the first African report of Stearibia nigriceps.},
journal = {International journal of legal medicine},
volume = {134},
number = {3},
pages = {895-902},
pmid = {31822991},
issn = {1437-1596},
mesh = {Algeria ; Animals ; *DNA Barcoding, Taxonomic ; Diptera/*classification/*genetics ; Electron Transport Complex IV/*genetics ; *Forensic Entomology ; Genetic Markers ; Phylogeny ; },
abstract = {Stearibia (=Piophila) nigriceps (Meigen) occurs in the Palearctic Region from Europe and Far East Russia, and in the Nearctic, the Neotropical, and the Oriental regions. In this study, we report the first record of Stearibia nigriceps from Africa collected in Algeria. In addition, our results provide DNA sequences of Piophila casei (Linnaeus) and S. nigriceps that may serve as reference data for future identification. A region of the cytochrome c oxidase I (COI) gene marker of 473 bp was amplified and DNA was sequenced. Intra- and interspecific genetic distances were calculated. A phylogenetic tree was generated by the maximum likelihood (ML) method using 1000 bootstrap replicates based on the Tamura-Nei model. A total number of 9 adults of S. nigriceps were collected together with 72 adults of P. casei. The intraspecific variation of the species barcodes analysed in our study was < 3% and the interspecific nucleotide divergence of the same species was > 3%. The 473 bp COI region was sufficient to identify and distinguish unambiguously between the two species. P. casei and P. nigriceps individuals from Algeria clustered separately from each other. They were also separated from the individuals of the same species originating from other countries with a 100% high bootstrap value. There was no correlation between the clades and the geographic origins of the haplotypes. Our results contribute to update the knowledge of the distribution of Piophilidae family. They also contribute to the build-up of online DNA sequence databases.},
}
@article {pmid31822210,
year = {2019},
author = {Espinosa-Medina, I and Garcia-Marques, J and Cepko, C and Lee, T},
title = {High-throughput dense reconstruction of cell lineages.},
journal = {Open biology},
volume = {9},
number = {12},
pages = {190229},
pmid = {31822210},
issn = {2046-2441},
support = {/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; CRISPR-Cas Systems ; Cell Lineage/*genetics ; *Cell Tracking/methods ; Computational Biology ; DNA Barcoding, Taxonomic ; *Gene Expression Profiling/methods ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; *Molecular Imaging/methods ; Mutation ; Phylogeny ; Single-Cell Analysis/methods ; },
abstract = {The first meeting exclusively dedicated to the 'High-throughput dense reconstruction of cell lineages' took place at Janelia Research Campus (Howard Hughes Medical Institute) from 14 to 18 April 2019. Organized by Tzumin Lee, Connie Cepko, Jorge Garcia-Marques and Isabel Espinosa-Medina, this meeting echoed the recent eruption of new tools that allow the reconstruction of lineages based on the phylogenetic analysis of DNA mutations induced during development. Combined with single-cell RNA sequencing, these tools promise to solve the lineage of complex model organisms at single-cell resolution. Here, we compile the conference consensus on the technological and computational challenges emerging from the use of the new strategies, as well as potential solutions.},
}
@article {pmid31821347,
year = {2019},
author = {Naseem, MT and Ashfaq, M and Khan, AM and Rasool, A and Asif, M and Hebert, PDN},
title = {BIN overlap confirms transcontinental distribution of pest aphids (Hemiptera: Aphididae).},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0220426},
pmid = {31821347},
issn = {1932-6203},
mesh = {*Animal Distribution ; Animals ; Aphids/*genetics ; Crops, Agricultural/*parasitology ; *DNA Barcoding, Taxonomic ; Gene Library ; Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {DNA barcoding is highly effective for identifying specimens once a reference sequence library is available for the species assemblage targeted for analysis. Despite the great need for an improved capacity to identify the insect pests of crops, the use of DNA barcoding is constrained by the lack of a well-parameterized reference library. The current study begins to address this limitation by developing a DNA barcode reference library for the pest aphids of Pakistan. It also examines the affinities of these species with conspecific populations from other geographic regions based on both conventional taxonomy and Barcode Index Numbers (BINs). A total of 809 aphids were collected from a range of plant species at sites across Pakistan. Morphological study and DNA barcoding allowed 774 specimens to be identified to one of 42 species while the others were placed to a genus or subfamily. Sequences obtained from these specimens were assigned to 52 BINs whose monophyly were supported by neighbor-joining (NJ) clustering and Bayesian inference. The 42 species were assigned to 41 BINs with 38 showing BIN concordance. These species were represented on BOLD by 7,870 records from 69 countries. Combining these records with those from Pakistan produced 60 BINs with 12 species showing a BIN split and three a BIN merger. Geo-distance correlations showed that intraspecific divergence values for 49% of the species were not affected by the distance between populations. Forty four of the 52 BINs from Pakistan had counterparts in 73 countries across six continents, documenting the broad distributions of pest aphids.},
}
@article {pmid31818949,
year = {2019},
author = {Davidsson, M and Wang, G and Aldrin-Kirk, P and Cardoso, T and Nolbrant, S and Hartnor, M and Mudannayake, J and Parmar, M and Björklund, T},
title = {A systematic capsid evolution approach performed in vivo for the design of AAV vectors with tailored properties and tropism.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {52},
pages = {27053-27062},
pmid = {31818949},
issn = {1091-6490},
abstract = {Adeno-associated virus (AAV) capsid modification enables the generation of recombinant vectors with tailored properties and tropism. Most approaches to date depend on random screening, enrichment, and serendipity. The approach explored here, called BRAVE (barcoded rational AAV vector evolution), enables efficient selection of engineered capsid structures on a large scale using only a single screening round in vivo. The approach stands in contrast to previous methods that require multiple generations of enrichment. With the BRAVE approach, each virus particle displays a peptide, derived from a protein, of known function on the AAV capsid surface, and a unique molecular barcode in the packaged genome. The sequencing of RNA-expressed barcodes from a single-generation in vivo screen allows the mapping of putative binding sequences from hundreds of proteins simultaneously. Using the BRAVE approach and hidden Markov model-based clustering, we present 25 synthetic capsid variants with refined properties, such as retrograde axonal transport in specific subtypes of neurons, as shown for both rodent and human dopaminergic neurons.},
}
@article {pmid31818597,
year = {2020},
author = {Zadel, U and Nesme, J and Michalke, B and Vestergaard, G and Płaza, GA and Schröder, P and Radl, V and Schloter, M},
title = {Changes induced by heavy metals in the plant-associated microbiome of Miscanthus x giganteus.},
journal = {The Science of the total environment},
volume = {711},
number = {},
pages = {134433},
doi = {10.1016/j.scitotenv.2019.134433},
pmid = {31818597},
issn = {1879-1026},
mesh = {Biodegradation, Environmental ; Metals, Heavy ; *Microbiota ; Plant Roots ; RNA, Ribosomal, 16S ; Rhizosphere ; Soil ; Soil Pollutants ; },
abstract = {Miscanthus x giganteus is a high biomass producing plant with tolerance to heavy metals. This makes Miscanthus interesting to be used for phytoremediation of heavy metal contaminated areas coupled with energy production. Since plant performance in metal polluted areas is impaired, their growth and phytoremediation effect can be improved with bacterial assistance. To identify positive and negative responders of M. x giganteus associated microbiome influenced by Cd, Pb and Zn stress compared to non-contaminated controls, we designed a greenhouse experiment. Structure of the bacterial community in three rhizocompartments, namely rhizosphere, rhizoplane and root endosphere was analysed using an isolation independent molecular approach based on 16S rRNA gene barcoding. Furthermore, quantitative PCR (qPCR) was used for bacterial biomass estimation. Our results indicated that biomass and total bacterial diversity in rhizosphere, rhizoplane and root endosphere did not significantly change despite of substantial root uptake of heavy metals. Overall, we detected 6621 OTUs, from which 171 were affected by metal addition. Whereas Streptomyces and Amycolatopsis taxa were negatively affected by the heavy metal treatment in endosphere, taxa assigned to Luteolibacter in rhizosphere and rhizoplane (log2 fold change 1.9-4.1) and Micromonospora in endosphere (log2 fold change 10.2) were found to be significantly enriched and highly abundant (0.1-3.7% relative abundance) under heavy metal stress. Those taxa might be of key importance for M. x giganteus performance under heavy metal pollution and might be interesting candidates for the development of new bioinocula in the future to promote plant growth and phytoremediation in heavy metal contaminated soils.},
}
@article {pmid31816695,
year = {2020},
author = {Chen, R and Sun, Y and Huo, B and Yuan, S and Sun, X and Zhang, M and Yin, N and Fan, L and Yao, W and Wang, J and Han, D and Li, S and Peng, Y and Bai, J and Ning, B and Liang, J and Gao, Z},
title = {Highly sensitive detection of ochratoxin A based on bio-barcode immunoassay and catalytic hairpin assembly signal amplification.},
journal = {Talanta},
volume = {208},
number = {},
pages = {120405},
doi = {10.1016/j.talanta.2019.120405},
pmid = {31816695},
issn = {1873-3573},
mesh = {Antibodies/chemistry ; Antigens/chemistry ; Arachis/chemistry ; Catalysis ; DNA Barcoding, Taxonomic ; Food Contamination/*analysis ; Gold/chemistry ; Immunoassay ; Limit of Detection ; Magnetic Phenomena ; Metal Nanoparticles/chemistry ; Ochratoxins/*analysis/chemistry ; Triticum/chemistry ; Zea mays/chemistry ; },
abstract = {Herein, a highly sensitive ochratoxin A (OTA) detection strategy was developed based on a bio-barcode immunoassay with catalytic hairpin assembly (CHA). Two nanoprobes were designed for the assay: one was a gold nanoparticle (AuNP) harbouring numerous bio-barcode DNA and antibodies, and the other was an antigen-functionalized magnetic nanoparticle (MNP). In the presence of target OTA, the antigens of the MNPs competed with OTA for binding to the antibodies on the AuNPs. After magnetic separation, the unbound AuNPs and target OTA were washed away. Dithiothreitol (DTT) was then added to the MNP-bound AuNPs to elute the bio-barcode DNAs of AuNPs, which triggered the CHA reaction. Under optimal conditions, the proposed method could sensitively detect target OTA ranging from 0.001 to 10000 ng/mL. The limit of detection (LOD, 3 N/S) and limit of quantification (LOQ, 10 N/S) for OTA were 0.54 pg/mL and 1.80 pg/mL, respectively. The bio-barcode immunoassay was used to analyse food samples (corn, wheat, and peanut), and the recovery and relative standard deviations (RSD) ranged from 93.30% to 108.80% and from 3.2% to 6.9%, respectively. The total assay time was 6 h. Therefore, the proposed strategy will provide a new approach for the detection of mycotoxins and other small molecule analytes and can be applied for quality control to ensure food safety.},
}
@article {pmid31816016,
year = {2019},
author = {Takashima, M and Suh, SO and Bai, FY and Sugita, T},
title = {Takashi Nakase's last tweet: what is the current direction of microbial taxonomy research?.},
journal = {FEMS yeast research},
volume = {19},
number = {8},
pages = {},
doi = {10.1093/femsyr/foz066},
pmid = {31816016},
issn = {1567-1364},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Fungal/*genetics ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; Genome, Fungal ; Phenotype ; Phylogeny ; Phylogeography ; RNA, Fungal/genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; Yeasts/*classification/isolation &amp; purification ; },
abstract = {During the last few decades, type strains of most yeast species have been barcoded using the D1/D2 domain of their LSU rRNA gene and internal transcribed spacer (ITS) region. Species identification using DNA sequences regarding conspecificity in yeasts has also been studied. Most yeast species can be identified according to the sequence divergence of their ITS region or a combination of the D1/D2 and ITS regions. Studies that have examined intraspecific diversity have used multilocus sequence analyses, whereas the marker regions used in this analysis vary depending upon taxa. D1/D2 domain and ITS region sequences have been used as barcodes to develop primers suitable for the detection of the biological diversity of environmental DNA and the microbiome. Using these barcode sequences, it is possible to identify relative lineages and infer their gene products and function, and how they adapt to their environment. If barcode sequence was not variable enough to identify a described species, one could investigate the other biological traits of these yeasts, considering geological distance, environmental circumstances and isolation of reproduction. This article is dedicated to late Dr Takashi Nakase (1939-2018).},
}
@article {pmid31812823,
year = {2020},
author = {De Agostini, A and Caltagirone, C and Caredda, A and Cicatelli, A and Cogoni, A and Farci, D and Guarino, F and Garau, A and Labra, M and Lussu, M and Piano, D and Sanna, C and Tommasi, N and Vacca, A and Cortis, P},
title = {Heavy metal tolerance of orchid populations growing on abandoned mine tailings: A case study in Sardinia Island (Italy).},
journal = {Ecotoxicology and environmental safety},
volume = {189},
number = {},
pages = {110018},
doi = {10.1016/j.ecoenv.2019.110018},
pmid = {31812823},
issn = {1090-2414},
mesh = {Ascomycota/classification/isolation &amp; purification ; Biodegradation, Environmental ; Islands ; Italy ; Metals, Heavy/analysis/*metabolism ; Mining ; Orchidaceae/growth &amp; development/*metabolism/microbiology ; Plant Roots/growth &amp; development/microbiology ; Soil/chemistry ; Soil Pollutants/analysis/*metabolism ; },
abstract = {Understanding how environmental pollutants influence plant occurrence, growth, and development is key for effective management plans and potential bioremediation. Rare plants, such as orchids, may occur in modified habitats and on soils containing heavy metals, yet their ecological and physiological responses to heavy metals is poorly understood. We investigated the influence of heavy metal pollution on orchid growth rates and interactions with soil fungal mutualists by comparing a large population of the orchid Epipactis helleborine (L.) Crantz subsp. tremolsii (Pau) E. Klein that grows on mine tailings in south-west Sardinia (Italy) with a population that grows on non-contaminated soils in central Sardinia. Soils of the contaminated site had high levels of heavy metals and low organic matter and nutritive elements content. We performed a morphological analysis on twenty individuals that have been subjected to measurement of bioaccumulation and translocation of heavy metals. Fungi associated with the roots of plants from the contaminated and uncontaminated site were grown and identified by DNA barcoding approach. Plants from the contaminated site were smaller than the ones growing in the uncontaminated site and were found to be able to tolerate heavy metals from the soil and to accumulate and translocate them into their organs. Fungi belonging to the genus Ilyonectria (Ascomycota) were found both in contaminated and uncontaminated sites, while an unidentified fungus was isolated from roots in the contaminated site only. These results are discussed in terms of orchids' tolerance to heavy metals and its physiological and ecological mechanisms. The role of contaminated habitats in harbouring orchids and peculiar taxa is also discussed.},
}
@article {pmid31811161,
year = {2019},
author = {deWaard, JR and Ratnasingham, S and Zakharov, EV and Borisenko, AV and Steinke, D and Telfer, AC and Perez, KHJ and Sones, JE and Young, MR and Levesque-Beaudin, V and Sobel, CN and Abrahamyan, A and Bessonov, K and Blagoev, G and deWaard, SL and Ho, C and Ivanova, NV and Layton, KKS and Lu, L and Manjunath, R and McKeown, JTA and Milton, MA and Miskie, R and Monkhouse, N and Naik, S and Nikolova, N and Pentinsaari, M and Prosser, SWJ and Radulovici, AE and Steinke, C and Warne, CP and Hebert, PDN},
title = {A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples.},
journal = {Scientific data},
volume = {6},
number = {1},
pages = {308},
pmid = {31811161},
issn = {2052-4463},
mesh = {Animals ; Biodiversity ; Canada ; *DNA Barcoding, Taxonomic ; Invertebrates/*classification ; },
abstract = {The reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, a nation that comprises 7% of the planet's land surface. In total, 14 phyla, 43 classes, 163 orders, 1123 families, 6186 genera, and 64,264 Barcode Index Numbers (BINs; a proxy for species) are represented. Species-level taxonomy was available for 38% of the specimens, but higher proportions were assigned to a genus (69.5%) and a family (99.9%). Voucher specimens and DNA extracts are archived at the Centre for Biodiversity Genomics where they are available for further research. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, and the Global Genome Biodiversity Network Data Portal.},
}
@article {pmid31811119,
year = {2019},
author = {Fang, L and Kao, C and Gonzalez, MV and Mafra, FA and Pellegrino da Silva, R and Li, M and Wenzel, SS and Wimmer, K and Hakonarson, H and Wang, K},
title = {LinkedSV for detection of mosaic structural variants from linked-read exome and genome sequencing data.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {5585},
pmid = {31811119},
issn = {2041-1723},
support = {R01 GM132713/GM/NIGMS NIH HHS/United States ; U54 HD086984/HD/NICHD NIH HHS/United States ; },
mesh = {*Base Sequence ; Chromosome Breakpoints ; DNA Mutational Analysis/*methods ; *Exome ; Genome/genetics ; Genome, Human ; Genomic Structural Variation/*genetics ; Humans ; Models, Genetic ; Neurofibromin 1/genetics ; Sequence Analysis, DNA ; *Sequence Deletion ; Software ; },
abstract = {Linked-read sequencing provides long-range information on short-read sequencing data by barcoding reads originating from the same DNA molecule, and can improve detection and breakpoint identification for structural variants (SVs). Here we present LinkedSV for SV detection on linked-read sequencing data. LinkedSV considers barcode overlapping and enriched fragment endpoints as signals to detect large SVs, while it leverages read depth, paired-end signals and local assembly to detect small SVs. Benchmarking studies demonstrate that LinkedSV outperforms existing tools, especially on exome data and on somatic SVs with low variant allele frequencies. We demonstrate clinical cases where LinkedSV identifies disease-causal SVs from linked-read exome sequencing data missed by conventional exome sequencing, and show examples where LinkedSV identifies SVs missed by high-coverage long-read sequencing. In summary, LinkedSV can detect SVs missed by conventional short-read and long-read sequencing approaches, and may resolve negative cases from clinical genome/exome sequencing studies.},
}
@article {pmid31810454,
year = {2019},
author = {Wahlberg, E},
title = {FACEPAI: a script for fast and consistent environmental DNA processing and identification.},
journal = {BMC ecology},
volume = {19},
number = {1},
pages = {51},
pmid = {31810454},
issn = {1472-6785},
mesh = {*DNA, Environmental ; Ecology ; *High-Throughput Nucleotide Sequencing ; Software ; },
abstract = {BACKGROUND: The use of environmental DNA (eDNA) has become an increasing important tool in environmental surveys and taxonomic research. High throughput sequencing of samples from soil, water, sediment, trap alcohol or bulk samples generate large amount of barcode sequences that can be assigned to a known taxon with a reference sequence. This process can however be bioinformatic cumbersome and time consuming, especially for researchers without specialised bioinformatic training. A number of different software packages and pipelines are available, but require training in preparation of data, running of analysis and formatting results. Comparison of results produced by different packages are often difficult.<br><br>RESULTS: FACEPIE is an open source script dependant on a few open source applications that provides a pipeline for rapid analysis and taxonomic assignment of environmental DNA samples. It requires an initial formatting of a reference database, using the script CaPReSe, and a configuration file and can thereafter be run to process any number of samples in succession using the same settings and references. Both configuration and executing are designed to demand as little hands on work as possible, while assuring repeatable results.<br><br>CONCLUSION: The demonstration using example data from real environmental samples provides results in a time span ranging from less than 3&#xa0;min to just above 15&#xa0;min depending on the numbers of sequences to process. The memory usage is below 2&#xa0;GB on a desktop PC. FACEPAI and CaPReSe provides a pipeline for analysing a large number of eDNA samples on common equipment, with little bioinformatic skills necessary, for subsequent ecological and taxonomical studies.},
}
@article {pmid31809880,
year = {2020},
author = {Chel, HM and Nakao, R and Ohsawa, N and Oo, ZM and Nonaka, N and Katakura, K},
title = {First record and analysis of the COI gene of Cobboldia elephantis obtained from a captive Asian elephant from Myanmar.},
journal = {Parasitology international},
volume = {75},
number = {},
pages = {102035},
doi = {10.1016/j.parint.2019.102035},
pmid = {31809880},
issn = {1873-0329},
mesh = {Animals ; Diptera/genetics/growth &amp; development/*physiology ; Electron Transport Complex IV/analysis ; *Elephants ; Insect Proteins/analysis ; Japan ; Larva/genetics/growth &amp; development/physiology ; Myanmar ; Myiasis/parasitology/*veterinary ; },
abstract = {The stomach bot fly species in Asian elephants has long been known as Cobboldia elephantis. However, there is no genetic information available for this species to date. Here, we report that a third-instar fly larva was excreted from a captive Asian elephant four months after export from an elephant camp in Myanmar to a zoological garden in Japan. Morphological characteristics of the larva were coincident with published descriptions of C. elephantis. The mitochondrial cytochrome c oxidase subunit I (COI) gene was amplified from the larva by PCR using primers modified from those designed for DNA barcoding of insects and amphibians. The COI gene of C. elephantis showed 76.6 % and 83.6 % identity at the nucleotide and amino acid levels, respectively, to that of C. loxodontis, the stomach bot fly species in African elephants. Phylogenetic analysis of the COI genes of several stomach bot fly species revealed that the two Cobboldia species formed a clade separate from the stomach bot fly species found in rhinoceros and equids.},
}
@article {pmid31809676,
year = {2020},
author = {Xiong, X and Yuan, F and Huang, M and Xiong, X},
title = {Exploring the possible reasons for fish fraud in China based on results from monitoring sardine products sold on Chinese markets using DNA barcoding and real time PCR.},
journal = {Food additives &amp; contaminants. Part A, Chemistry, analysis, control, exposure &amp; risk assessment},
volume = {37},
number = {2},
pages = {193-204},
doi = {10.1080/19440049.2019.1694709},
pmid = {31809676},
issn = {1944-0057},
mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; Fish Products/*analysis ; Fishes/*classification ; *Food Labeling ; Fraud ; Phylogeny ; Species Specificity ; },
abstract = {Sardine is the common name for several small-sized pelagic species from Clupeiformes, representing a resource of great importance in the global fishery. Great efforts have been made to utilise these species as dried, smoked, and restructured fish products. However, in most of these products, it is quite challenging to identify the individual species as the external features are lost during processing, paving the way for species mislabelling. In this study, DNA barcoding (max, using about 650 bp, described as FDB; mini, of about 192 bp, described as MDB) was used for species identification of 139 specimens taken from 48 sardine products (canned and dried seasoning) randomly collected from local markets in Nanjing, China. Moreover, species specific primers were designed for Sardina pilchardus, with the aim to screen the species of S. pilchardus in mixed products. Results highlighted a success rate of amplification from 38.1% for FDB to 97.9% for MDB. Only one sample failed the Sanger-sequencing, and species-specific real time PCR confirmed the existence of S. pilchardus in the product. A maximum species identity in the range of 98-100% was obtained for all readable sequences and 11 species/genera were identified, belonging to 5 orders (Scorpaeniformes, Perciformes, Clupeiformes, Aulopiformes, Scombriformes). Significant legislative and managerial shortcomings and incentives to facilitate the market access of certain species, together with public indifference, represent the main reasons for fish fraud in China.},
}
@article {pmid31803173,
year = {2019},
author = {Zhou, JL and Xu, J and Jiao, AG and Yang, L and Chen, J and Callac, P and Liu, Y and Wang, SX},
title = {Patterns of PCR Amplification Artifacts of the Fungal Barcode Marker in a Hybrid Mushroom.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2686},
pmid = {31803173},
issn = {1664-302X},
abstract = {The polymerase chain reaction (PCR) is widely used in modern biology and medicine. However, PCR artifacts can complicate the interpretation of PCR-based results. The internal transcribed spacer (ITS) region of the ribosomal RNA gene cluster is the consensus fungal barcode marker and suspected PCR artifacts have been reported in many studies, especially for the analyses of environmental fungal samples. At present, the patterns of PCR artifacts in the whole fungal ITS region (ITS1+5.8S+ITS2) are not known. In this study, we analyzed the error rates of PCR at three template complexity levels using the divergent copies of ITS from the mushroom Agaricus subrufescens. Our results showed that PCR using the Phusion[®] High-Fidelity DNA Polymerase has a per nucleotide error rate of about 4 × 10[-6] per replication. Among the detected mutations, transitions were much more frequent than transversions, insertions, and deletions. When divergent alleles were mixed as templates in the same reaction, a significant proportion (∼30%) of recombinant molecules were detected. The in vitro mixed-template results were comparable to those obtained from using the genomic DNA of the original mushroom specimen as template. Our results indicate that caution should be in place when interpreting ITS sequences from individual fungal specimens, especially those containing divergent ITS copies. Similar results could also happen to PCR-based analyses of other multicopy DNA fragments as well as single-copy DNA sequences with divergent alleles in diploid organisms.},
}
@article {pmid31800740,
year = {2019},
author = {Laurito, M and Ontivero, IM and Almirón, WR},
title = {Increasing the digital repository of DNA barcoding sequences of sand flies (Psychodidae: Phlebotominae).},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {114},
number = {},
pages = {e190208},
pmid = {31800740},
issn = {1678-8060},
mesh = {Animals ; Argentina ; Base Sequence ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Female ; Genetic Variation ; Phylogeny ; Psychodidae/classification/*genetics ; Species Specificity ; },
abstract = {Sand fly identification is complex because it depends on the expertise of the taxonomist. The females show subtle morphological differences and the occurrence of the species complexes are usual in this taxon. Therefore, a fragment of the cytochrome c oxidase subunit I (COI) gene is used for taxon barcoding to resolve this kind of problem. This study incorporates barcode sequences, for the first time, for Evandromyia cortelezzii and Migonemyia migonei from Argentina. The nucleotide sequence divergences were estimated to generate a neighbour-joining (NJ) tree. The automatic barcode gap discovery (ABGD) approach was employed to find the barcode gaps and the operational taxonomic unit (OTU) delimitation. Other species of the subtribe were included. The frequency histogram of divergences showed a barcoding gap. The ABGD analysis identified 14 operational taxonomic units (OTUs) from 13 morphological species. Sequences of Ev. cortelezzii and Mg. migonei formed well supported clusters and were diagnosed as primary species. These sequences are useful tools for molecular identification of the sand flies of the New World.},
}
@article {pmid31796780,
year = {2019},
author = {Porter, TM and Morris, DM and Basiliko, N and Hajibabaei, M and Doucet, D and Bowman, S and Emilson, EJS and Emilson, CE and Chartrand, D and Wainio-Keizer, K and Séguin, A and Venier, L},
title = {Variations in terrestrial arthropod DNA metabarcoding methods recovers robust beta diversity but variable richness and site indicators.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {18218},
pmid = {31796780},
issn = {2045-2322},
mesh = {Animals ; Arthropods/*genetics ; *Biodiversity ; DNA/genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Forests ; Genetic Variation/*genetics ; Sequence Analysis, DNA/methods ; Soil ; },
abstract = {Terrestrial arthropod fauna have been suggested as a key indicator of ecological integrity in forest systems. Because phenotypic identification is expert-limited, a shift towards DNA metabarcoding could improve scalability and democratize the use of forest floor arthropods for biomonitoring applications. The objective of this study was to establish the level of field sampling and DNA extraction replication needed for arthropod biodiversity assessments from soil. Processing 15 individually collected soil samples recovered significantly higher median richness (488-614 sequence variants) than pooling the same number of samples (165-191 sequence variants) prior to DNA extraction, and we found no significant richness differences when using 1 or 3 pooled DNA extractions. Beta diversity was robust to changes in methodological regimes. Though our ability to identify taxa to species rank was limited, we were able to use arthropod COI metabarcodes from forest soil to assess richness, distinguish among sites, and recover site indicators based on unnamed exact sequence variants. Our results highlight the need to continue DNA barcoding local taxa during COI metabarcoding studies to help build reference databases. All together, these sampling considerations support the use of soil arthropod COI metabarcoding as a scalable method for biomonitoring.},
}
@article {pmid31793138,
year = {2020},
author = {Sordino, P and D'Aniello, S and Pelletier, E and Wincker, P and Nittoli, V and Stemmann, L and Mazzocchi, MG and Lombard, F and Iudicone, D and Caputi, L},
title = {Into the bloom: Molecular response of pelagic tunicates to fluctuating food availability.},
journal = {Molecular ecology},
volume = {29},
number = {2},
pages = {292-307},
doi = {10.1111/mec.15321},
pmid = {31793138},
issn = {1365-294X},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Ecology ; Ecosystem ; Transcriptome/genetics ; Urochordata/classification/*genetics ; },
abstract = {The planktonic tunicates appendicularians and thaliaceans are highly efficient filter feeders on a wide range of prey size including bacteria and have shorter generation times than any other marine grazers. These traits allow some tunicate species to reach high population densities and ensure their success in a favourable environment. However, there are still few studies focusing on which genes and gene pathways are associated with responses of pelagic tunicates to environmental variability. Herein, we present the effect of food availability increase on tunicate community and gene expression at the Marquesas Islands (South-East Pacific Ocean). By using data from the Tara Oceans expedition, we show that changes in phytoplankton density and composition trigger the success of a dominant larvacean species (an undescribed appendicularian). Transcriptional signature to the autotroph bloom suggests key functions in specific physiological processes, i.e., energy metabolism, muscle contraction, membrane trafficking, and proteostasis. The relative abundance of reverse transcription-related Pfams was lower at bloom conditions, suggesting a link with adaptive genetic diversity in tunicates in natural ecosystems. Downstream of the bloom, pelagic tunicates were outcompeted by copepods. Our work represents the first metaomics study of the biological effects of phytoplankton bloom on a key zooplankton taxon.},
}
@article {pmid31792271,
year = {2019},
author = {Redin, D and Frick, T and Aghelpasand, H and Käller, M and Borgström, E and Olsen, RA and Ahmadian, A},
title = {High throughput barcoding method for genome-scale phasing.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {18116},
pmid = {31792271},
issn = {2045-2322},
mesh = {DNA Barcoding, Taxonomic ; Data Visualization ; Gene Library ; Genome, Human ; Genomics/*methods ; Haplotypes ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; },
abstract = {The future of human genomics is one that seeks to resolve the entirety of genetic variation through sequencing. The prospect of utilizing genomics for medical purposes require cost-efficient and accurate base calling, long-range haplotyping capability, and reliable calling of structural variants. Short-read sequencing has lead the development towards such a future but has struggled to meet the latter two of these needs. To address this limitation, we developed a technology that preserves the molecular origin of short sequencing reads, with an insignificant increase to sequencing costs. We demonstrate a novel library preparation method for high throughput barcoding of short reads where millions of random barcodes can be used to reconstruct megabase-scale phase blocks.},
}
@article {pmid31792216,
year = {2019},
author = {Boone, PG and Rochelle, LK and Ginzel, JD and Lubkov, V and Roberts, WL and Nicholls, PJ and Bock, C and Flowers, ML and von Furstenberg, RJ and Stripp, BR and Agarwal, P and Borowsky, AD and Cardiff, RD and Barak, LS and Caron, MG and Lyerly, HK and Snyder, JC},
title = {A cancer rainbow mouse for visualizing the functional genomics of oncogenic clonal expansion.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {5490},
pmid = {31792216},
issn = {2041-1723},
support = {T32 HD040372/HD/NICHD NIH HHS/United States ; K22 CA212058/CA/NCI NIH HHS/United States ; U24 CA209923/CA/NCI NIH HHS/United States ; K12 CA100639/CA/NCI NIH HHS/United States ; R33 CA191198/CA/NCI NIH HHS/United States ; P30 CA014236/CA/NCI NIH HHS/United States ; R21 CA173245/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Carcinogenesis ; Cell Proliferation ; Colonic Neoplasms/*genetics/metabolism/physiopathology ; *Disease Models, Animal ; Humans ; Mice ; Mutation ; Neoplastic Stem Cells/*cytology/metabolism ; Oncogenes ; Thrombospondins/genetics/metabolism ; },
abstract = {Field cancerization is a premalignant process marked by clones of oncogenic mutations spreading through the epithelium. The timescales of intestinal field cancerization can be variable and the mechanisms driving the rapid spread of oncogenic clones are unknown. Here we use a Cancer rainbow (Crainbow) modelling system for fluorescently barcoding somatic mutations and directly visualizing the clonal expansion and spread of oncogenes. Crainbow shows that mutations of ß-catenin (Ctnnb1) within the intestinal stem cell results in widespread expansion of oncogenes during perinatal development but not in adults. In contrast, mutations that extrinsically disrupt the stem cell microenvironment can spread in adult intestine without delay. We observe the rapid spread of premalignant clones in Crainbow mice expressing oncogenic Rspondin-3 (RSPO3), which occurs by increasing crypt fission and inhibiting crypt fixation. Crainbow modelling provides insight into how somatic mutations rapidly spread and a plausible mechanism for predetermining the intratumor heterogeneity found in colon cancers.},
}
@article {pmid31792006,
year = {2020},
author = {Schmidt, SA and Kolouchova, R and Forgan, AH and Borneman, AR},
title = {Evaluation of Saccharomyces cerevisiae Wine Yeast Competitive Fitness in Enologically Relevant Environments by Barcode Sequencing.},
journal = {G3 (Bethesda, Md.)},
volume = {10},
number = {2},
pages = {591-603},
pmid = {31792006},
issn = {2160-1836},
mesh = {Australia ; *DNA Barcoding, Taxonomic ; *Environment ; *Fermentation ; Gene Expression Profiling ; *Genetic Fitness ; Saccharomyces cerevisiae/*genetics ; *Vitis ; *Wine ; },
abstract = {When a wine yeast is inoculated into grape juice the potential variation in juice composition that confronts it is huge. Assessing the performance characteristics of the many commercially available wine yeasts in the many possible grape juice compositions is a daunting task. To this end we have developed a barcoded Saccharomyces cerevisiae wine yeast collection to facilitate the task of performance assessment that will contribute to a broader understanding of genotype-phenotype relations. Barcode sequencing of mixed populations is used to monitor strain abundance in different grape juices and grape juice-like environments. Choice of DNA extraction method is shown to affect strain-specific barcode count in this highly related set of S. cerevisiae strains; however, the analytical approach is shown to be robust toward strain dependent variation in DNA extraction efficiency. Of the 38 unique compositional variables assessed, resistance to copper and SO2 are found to be dominant discriminatory factors in wine yeast performance. Finally, a comparison of competitive fitness profile with performance in single inoculum fermentations reveal strain dependent correspondence of yeast performance using these two different approaches.},
}
@article {pmid31790921,
year = {2020},
author = {Macumber, AL and Blandenier, Q and Todorov, M and Duckert, C and Lara, E and Lahr, DJG and Mitchell, EAD and Roe, HM},
title = {Phylogenetic divergence within the Arcellinida (Amoebozoa) is congruent with test size and metabolism type.},
journal = {European journal of protistology},
volume = {72},
number = {},
pages = {125645},
doi = {10.1016/j.ejop.2019.125645},
pmid = {31790921},
issn = {1618-0429},
mesh = {Amoebozoa/*classification/*cytology/metabolism ; Energy Metabolism ; *Phylogeny ; Protozoan Infections/genetics ; Species Specificity ; },
abstract = {Arcellinida (lobose testate amoebae) are abundant and diverse in many ecosystems, especially in moist to aquatic environments. Molecular phylogeny has shown that overall test morphology (e.g., spherical or elongate) is generally conserved in Arcellinida lineages, but the taxonomic value of other traits (e.g., size, ornamentation, mixotrophy/heterotrophy metabolism type) has not been systematically evaluated. Morphological and physiological traits that correspond to genetic differences likely represent adaptive traits of ecological significance. We combined high-resolution phylogenetics (NAD9-NAD7 genes) and advanced morphometrics to assess the phylogenetic signal of morphological traits of a group of elongate Difflugia species (Arcellinida). The phylogenetic analyses revealed two clades which could be reliably separated by test size and the presence/absence of mixotrophy. Differences in test size may reflect trophic level, with smaller organisms occupying lower trophic levels. In addition to having larger tests, elongate mixotrophic Difflugia are characterised by wide, flat bases and an inflation of the lower two thirds of their test. These morphological traits may provide additional volume for endosymbionts and/or increased surface area to aid light transmission. Our results showcase greater diversity within the elongate Difflugia and highlight morphological traits of ecological and evolutionary significance.},
}
@article {pmid31788226,
year = {2019},
author = {Ma, J and Liu, J and Shen, Y and Fan, Z and Yue, B and Zhang, X},
title = {Population genetic structure and intraspecific genetic distance of Periplaneta americana (Blattodea: Blattidae) based on mitochondrial and nuclear DNA markers.},
journal = {Ecology and evolution},
volume = {9},
number = {22},
pages = {12928-12939},
pmid = {31788226},
issn = {2045-7758},
abstract = {The American cockroach (Periplaneta americana) is a globally invasive pest that can cause significant economic loss and threaten human health. Although it is abundant and lives in close proximity to humans, few studies have investigated the genetic diversity of P. americana. Our study analyzed 1,053 P. americana and other Periplaneta species' samples from different locations in China and the United States. A traditional tree-based method using 17 unique mitochondrial COI haplotypes of P. americana and 20 haplotypes of the other Periplaneta species accurately identified P. americana with a barcoding threshold of 5.1%. To identify the population genetic structure of P. americana, we investigated wingless gene and pooled them with obtained mtDNA data for a combined analysis. Although the genetic diversity of the USA group was relatively higher than the China group, the number of haplotypes and alleles of both groups was small. The analysis of molecular variance (AMOVA), intraspecific phylogeny, and haplotype networks indicated that P. americana had very little global genetic differentiation. The weak geographic genetic structure might reflect the human-mediated dispersal of P. americana. Despite no apparent phylogeographic assignment of mtDNA and nuclear lineages was observed in both BI trees, the integrated COI sequence data identified four distinct P. americana haplotype groups, showing four ancient maternal lineages of P. americana in China and the United States.},
}
@article {pmid31787378,
year = {2019},
author = {Setliff, I and Shiakolas, AR and Pilewski, KA and Murji, AA and Mapengo, RE and Janowska, K and Richardson, S and Oosthuysen, C and Raju, N and Ronsard, L and Kanekiyo, M and Qin, JS and Kramer, KJ and Greenplate, AR and McDonnell, WJ and Graham, BS and Connors, M and Lingwood, D and Acharya, P and Morris, L and Georgiev, IS},
title = {High-Throughput Mapping of B Cell Receptor Sequences to Antigen Specificity.},
journal = {Cell},
volume = {179},
number = {7},
pages = {1636-1646.e15},
pmid = {31787378},
issn = {1097-4172},
support = {T32 GM008320/GM/NIGMS NIH HHS/United States ; P30 DK058404/DK/NIDDK NIH HHS/United States ; P30 EY008126/EY/NEI NIH HHS/United States ; DP2 DA042422/DA/NIDA NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; R01 AI145687/AI/NIAID NIH HHS/United States ; R01 AI137057/AI/NIAID NIH HHS/United States ; R01 AI131722/AI/NIAID NIH HHS/United States ; U01 AI136677/AI/NIAID NIH HHS/United States ; T32 AI112541/AI/NIAID NIH HHS/United States ; G20 RR030956/RR/NCRR NIH HHS/United States ; R01 AI124378/AI/NIAID NIH HHS/United States ; UL1 RR024975/RR/NCRR NIH HHS/United States ; },
mesh = {Antibodies, Neutralizing/chemistry/immunology ; Antigens/chemistry/immunology ; Cells, Cultured ; Epitope Mapping/*methods ; Epitopes/*chemistry/immunology ; HEK293 Cells ; HIV Antibodies/chemistry/immunology ; High-Throughput Nucleotide Sequencing/methods ; High-Throughput Screening Assays/methods ; Humans ; Receptors, Antigen, B-Cell/*chemistry/immunology ; Sequence Analysis, DNA/*methods ; Single-Cell Analysis/*methods ; THP-1 Cells ; },
abstract = {B cell receptor (BCR) sequencing is a powerful tool for interrogating immune responses to infection and vaccination, but it provides limited information about the antigen specificity of the sequenced BCRs. Here, we present LIBRA-seq (linking B cell receptor to antigen specificity through sequencing), a technology for high-throughput mapping of paired heavy- and light-chain BCR sequences to their cognate antigen specificities. B cells are mixed with a panel of DNA-barcoded antigens so that both the antigen barcode(s) and BCR sequence are recovered via single-cell next-generation sequencing. Using LIBRA-seq, we mapped the antigen specificity of thousands of B cells from two HIV-infected subjects. The predicted specificities were confirmed for a number of HIV- and influenza-specific antibodies, including known and novel broadly neutralizing antibodies. LIBRA-seq will be an integral tool for antibody discovery and vaccine development efforts against a wide range of antigen targets.},
}
@article {pmid31786687,
year = {2019},
author = {Liu, Q and Yuan, YM and Lai, Y and Wang, GQ and Xue, XF},
title = {Unravelling the phylogeny, cryptic diversity and morphological evolution of Diptilomiopus mites (Acari: Eriophyoidea).},
journal = {Experimental &amp; applied acarology},
volume = {79},
number = {3-4},
pages = {323-344},
pmid = {31786687},
issn = {1572-9702},
support = {31970437//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Biological Evolution ; Cell Nucleus/genetics ; Genes, Mitochondrial ; Mites/*anatomy &amp; histology/*classification ; *Phylogeny ; },
abstract = {The Eriophyoidea, notable for specific morphological characters (four-legged mites) and gall-formation in host plants (gall mites), is one of the most species-rich superfamilies of Acari. Monophyly of the superfamily Eriophyoidea is accepted by all acarologists; however, monophyly of most genera has not been evaluated in a molecular phylogenetic network. Furthermore, most eriophyoid mites, especially species in the genus Diptilomiopus, are morphologically similar, challenging their identification. Here we test the phylogeny and cryptic diversity of Diptilomiopus species using fragments of two mitochondrial (COI and 12S) and two nuclear (18S and 28S) genes. Our results revealed the monophyly of Diptilomiopus. Sequence distance, barcode gap, and species delimitation analyses of the COI gene allowed us to resolve cryptic diversity of Diptilomiopus species. Additionally, we supposed that characteristics of genu fused with femur on both legs and seta ft' absent on leg II evolved only once within Diptilomiopus, which are potential morphological synapomorphies. In contrast, characteristics of both setae ft' and ft″ divided into a short branch and a long branch were supposed evolving multiple times independently. Our findings contribute to the understanding of phylogeny and morphological evolution of Diptilomiopus species and provide a DNA-based approach for species delimitation of Diptilomiopus mites.},
}
@article {pmid31786239,
year = {2020},
author = {Vieira, WADS and Bezerra, PA and Silva, ACD and Veloso, JS and Câmara, MPS and Doyle, VP},
title = {Optimal markers for the identification of Colletotrichum species.},
journal = {Molecular phylogenetics and evolution},
volume = {143},
number = {},
pages = {106694},
doi = {10.1016/j.ympev.2019.106694},
pmid = {31786239},
issn = {1095-9513},
mesh = {Algal Proteins/*genetics ; Bayes Theorem ; Colletotrichum/classification/*genetics ; DNA Barcoding, Taxonomic ; DNA, Fungal/chemistry/genetics ; DNA-(Apurinic or Apyrimidinic Site) Lyase/genetics ; Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating)/genetics ; Histones/genetics ; Phylogeny ; Sequence Alignment ; },
abstract = {Colletotrichum is among the most important genera of fungal plant pathogens. Molecular phylogenetic studies over the last decade have resulted in a much better understanding of the evolutionary relationships and species boundaries within the genus. There are now approximately 200 species accepted, most of which are distributed among 13 species complexes. Given their prominence on agricultural crops around the world, rapid identification of a large collection of Colletotrichum isolates is routinely needed by plant pathologists, regulatory officials, and fungal biologists. However, there is no agreement on the best molecular markers to discriminate species in each species complex. Here we calculate the barcode gap distance and intra/inter-specific distance overlap to evaluate each of the most commonly applied molecular markers for their utility as a barcode for species identification. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone-3 (HIS3), DNA lyase (APN2), intergenic spacer between DNA lyase and the mating-type locus MAT1-2-1 (APN2/MAT-IGS), and intergenic spacer between GAPDH and a hypothetical protein (GAP2-IGS) have the properties of good barcodes, whereas sequences of actin (ACT), chitin synthase (CHS-1) and nuclear rDNA internal transcribed spacers (nrITS) are not able to distinguish most species. Finally, we assessed the utility of these markers for phylogenetic studies using phylogenetic informativeness profiling, the genealogical sorting index (GSI), and Bayesian concordance analyses (BCA). Although GAPDH, HIS3 and β-tubulin (TUB2) were frequently among the best markers, there was not a single set of markers that were best for all species complexes. Eliminating markers with low phylogenetic signal tends to decrease uncertainty in the topology, regardless of species complex, and leads to a larger proportion of markers that support each lineage in the Bayesian concordance analyses. Finally, we reconstruct the phylogeny of each species complex using a minimal set of phylogenetic markers with the strongest phylogenetic signal and find the majority of species are strongly supported as monophyletic.},
}
@article {pmid31783752,
year = {2019},
author = {Srivathsan, A and Hartop, E and Puniamoorthy, J and Lee, WT and Kutty, SN and Kurina, O and Meier, R},
title = {Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing.},
journal = {BMC biology},
volume = {17},
number = {1},
pages = {96},
pmid = {31783752},
issn = {1741-7007},
mesh = {Animals ; *Biodiversity ; Classification/*methods ; DNA Barcoding, Taxonomic/*methods ; Diptera/anatomy &amp; histology/*classification/genetics ; Uganda ; },
abstract = {BACKGROUND: More than 80% of all animal species remain unknown to science. Most of these species live in the tropics and belong to animal taxa that combine small body size with high specimen abundance and large species richness. For such clades, using morphology for species discovery is slow because large numbers of specimens must be sorted based on detailed microscopic investigations. Fortunately, species discovery could be greatly accelerated if DNA sequences could be used for sorting specimens to species. Morphological verification of such "molecular operational taxonomic units" (mOTUs) could then be based on dissection of a small subset of specimens. However, this approach requires cost-effective and low-tech DNA barcoding techniques because well-equipped, well-funded molecular laboratories are not readily available in many biodiverse countries.<br><br>RESULTS: We here document how MinION sequencing can be used for large-scale species discovery in a specimen- and species-rich taxon like the hyperdiverse fly family Phoridae (Diptera). We sequenced 7059 specimens collected in a single Malaise trap in Kibale National Park, Uganda, over the short period of 8&#xa0;weeks. We discovered >&#x2009;650 species which exceeds the number of phorid species currently described for the entire Afrotropical region. The barcodes were obtained using an improved low-cost MinION pipeline that increased the barcoding capacity sevenfold from 500 to 3500 barcodes per flowcell. This was achieved by adopting 1D sequencing, resequencing weak amplicons on a used flowcell, and improving demultiplexing. Comparison with Illumina data revealed that the MinION barcodes were very accurate (99.99% accuracy, 0.46% Ns) and thus yielded very similar species units (match ratio 0.991). Morphological examination of 100 mOTUs also confirmed good congruence with morphology (93% of mOTUs; >&#x2009;99% of specimens) and revealed that 90% of the putative species belong to the neglected, megadiverse genus Megaselia. We demonstrate for one Megaselia species how the molecular data can guide the description of a new species (Megaselia sepsioides sp. nov.).<br><br>CONCLUSIONS: We document that one field site in Africa can be home to an estimated 1000 species of phorids and speculate that the Afrotropical diversity could exceed 200,000 species. We furthermore conclude that low-cost MinION sequencers are very suitable for reliable, rapid, and large-scale species discovery in hyperdiverse taxa. MinION sequencing could quickly reveal the extent of the unknown diversity and is especially suitable for biodiverse countries with limited access to capital-intensive sequencing facilities.},
}
@article {pmid31782763,
year = {2020},
author = {Thielecke, L and Cornils, K and Glauche, I},
title = {genBaRcode: a comprehensive R-package for genetic barcode analysis.},
journal = {Bioinformatics (Oxford, England)},
volume = {36},
number = {7},
pages = {2189-2194},
doi = {10.1093/bioinformatics/btz872},
pmid = {31782763},
issn = {1367-4811},
mesh = {*Electronic Data Processing ; Genetic Testing ; High-Throughput Nucleotide Sequencing ; *Software ; },
abstract = {MOTIVATION: Genetic barcodes have been established as an efficient method to trace clonal progeny of uniquely labeled cells by introducing artificial genetic sequences into the corresponding genomes. The assessment of those sequences relies on next generation sequencing and the subsequent analysis aiming to identify sequences of interest and correctly quantifying their abundance.<br><br>RESULTS: We developed the genBaRcode package as a toolbox combining the flexibility of digesting next generation sequencing reads with or without a sophisticated barcode structure, with a variety of error-correction approaches and the availability of several types of visualization routines. Furthermore, a graphical user interface was incorporated to allow also less experienced R users package-based analyses. Finally, the provided tool is intended to bridge the gap between generating and analyzing barcode data and thereby supporting the establishment of standardized and reproducible analysis strategies.<br><br>The genBaRcode package is available at CRAN (https://cran.r-project.org/package=genBaRcode).},
}
@article {pmid31781058,
year = {2019},
author = {Oberhofer, M and Hess, J and Leutgeb, M and Gössnitzer, F and Rattei, T and Wawrosch, C and Zotchev, SB},
title = {Exploring Actinobacteria Associated With Rhizosphere and Endosphere of the Native Alpine Medicinal Plant Leontopodium nivale Subspecies alpinum.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2531},
pmid = {31781058},
issn = {1664-302X},
abstract = {The rhizosphere of plants is enriched in nutrients facilitating growth of microorganisms, some of which are recruited as endophytes. Endophytes, especially Actinobacteria, are known to produce a plethora of bioactive compounds. We hypothesized that Leontopodium nivale subsp. alpinum (Edelweiss), a rare alpine medicinal plant, may serve as yet untapped source for uncommon Actinobacteria associated with this plant. Rhizosphere soil of native Alpine plants was used, after physical and chemical pre-treatments, for isolating Actinobacteria. Isolates were selected based on morphology and identified by 16S rRNA gene-based barcoding. Resulting 77 Actinobacteria isolates represented the genera Actinokineospora, Kitasatospora, Asanoa, Microbacterium, Micromonospora, Micrococcus, Mycobacterium, Nocardia, and Streptomyces. In parallel, Edelweiss plants from the same location were surface-sterilized, separated into leaves, roots, rhizomes, and inflorescence and pooled within tissues before genomic DNA extraction. Metagenomic 16S rRNA gene amplicons confirmed large numbers of actinobacterial operational taxonomic units (OTUs) descending in diversity from roots to rhizomes, leaves and inflorescences. These metagenomic data, when queried with isolate sequences, revealed an overlap between the two datasets, suggesting recruitment of soil bacteria by the plant. Moreover, this study uncovered a profound diversity of uncultured Actinobacteria from Rubrobacteridae, Thermoleophilales, Acidimicrobiales and unclassified Actinobacteria specifically in belowground tissues, which may be exploited by a targeted isolation approach in the future.},
}
@article {pmid31779157,
year = {2019},
author = {Simon, JC and Mahéo, F and Mieuzet, L and Buchard, C and Gauthier, JP and Maurice, D and Bonhomme, J and Outreman, Y and Hullé, M},
title = {Life on the Edge: Ecological Genetics of a High Arctic Insect Species and Its Circumpolar Counterpart.},
journal = {Insects},
volume = {10},
number = {12},
pages = {},
pmid = {31779157},
issn = {2075-4450},
support = {426//Institut Polaire Fran&#xe7;ais Paul Emile Victor/ ; },
abstract = {Arctic ecosystems are subjected to strong environmental constraints that prevent both the colonization and development of many organisms. In Svalbard, few aphid species have established permanent populations. These high arctic aphid species have developed peculiar life-history traits such as shortened life cycles and reduced dispersal capacities. Here, we present data on the distribution and population genetics of Acyrthosiphon svalbardicum in Spitsbergen, the main island of the Svalbard archipelago, and compared its genetic structure with that of its close relative Acyrthosiphon brevicorne, sampled in the top of Scandinavian mainland. We found that A. svalbardicum is common but heterogeneously distributed along the west coast of Spitsbergen. We recorded this species up to 79°12', which constitutes the northernmost location for any aphid. Genetic structure examined using microsatellite markers showed more pronounced spatial differentiation in A. svalbardicum than in A. brevicorne populations, presumably due to reduced dispersal capacities in the former species. Although populations of A. brevicorne and A. svalbardicum were well-delineated at nuclear loci, they shared similar cytoplasmic DNA haplotypes as revealed by sequence analysis of two DNA barcodes. These results raise questions about whether these two taxa are different species, and the colonization sources and history of the Svalbard archipelago by A. svalbardicum.},
}
@article {pmid31779155,
year = {2019},
author = {Albo, JE and Marelli, JP and Puig, AS},
title = {Rapid Molecular Identification of Scolytinae (Coleoptera: Curculionidae).},
journal = {International journal of molecular sciences},
volume = {20},
number = {23},
pages = {},
pmid = {31779155},
issn = {1422-0067},
support = {58-6631-6-123//Mars/ ; },
mesh = {Animals ; DNA Barcoding, Taxonomic/*veterinary ; DNA Primers/genetics ; *Genetic Markers ; Insect Proteins/genetics ; Phylogeny ; Sample Size ; Sequence Analysis, DNA/veterinary ; Weevils/*classification/genetics ; },
abstract = {Routine identification of bark and ambrosia beetles is done using morphology. For people lacking the necessary taxonomic knowledge, proper identification of a novel specimen can be challenging and time consuming. This study compares the usefulness of four genetic markers (28S, EF-1a, ITS2, and COI) and five primer pairs (D2F1/D3R2, eflafor1/eflarev1, ets149/efa754, ITS2F/ITS2R, and LCO1490/HCO2198) to identify Scolytinae beetles, and outlines a molecular identification strategy, with results possible in two days. Markers COI and EF-1a were selected based on the ability of the respective primers to amplify DNA from multiple genera (Coptoborus, Xyleborus, Hypothenemus, Theoborus, and Araptus) and the ability of the resulting sequences to provide accurate and unambiguous matches in GenBank. BLASTn analysis of EF-1a sequences (both primer pairs) correctly identified four out of the five genera and COI sequences identified at least one sample of every genus tested and was the only primer pair to correctly identify Araptus specimens. Further, 28S sequences successfully identified Coptoborus, Xyleborus, and Theoborus but not Hypothenemus or Araptus. The low number of EF-1a (1), 28S (7), and ITS2 (0) sequences from Araptus individuals present in GenBank compared with COI (137) is likely the reason that only the latter marker was capable of identifying members of this genus. ITS2 sequences were insufficient to identify any of the samples tested. This study also determined the minimum quantity of DNA that could be used for molecular identification. Primers D2F1 and D3R2, which had the highest rate of amplification in all genera tested, could yield an informative sequence with as little as 0.00048 ng of DNA, however, at least 0.0024 ng was needed for reliable amplification.},
}
@article {pmid31779118,
year = {2019},
author = {Pang, X and Liu, H and Wu, S and Yuan, Y and Li, H and Dong, J and Liu, Z and An, C and Su, Z and Li, B},
title = {Species Identification of Oaks (Quercus L., Fagaceae) from Gene to Genome.},
journal = {International journal of molecular sciences},
volume = {20},
number = {23},
pages = {},
pmid = {31779118},
issn = {1422-0067},
support = {2017//national forest germplasm resources bank of Quercus mongolica and Quercus variabilis in Hongyashan of Hebei/ ; },
mesh = {Chloroplasts/*genetics ; DNA Barcoding, Taxonomic/*methods ; Evolution, Molecular ; Genetic Markers ; Genome, Chloroplast ; High-Throughput Nucleotide Sequencing ; Mutation ; Phylogeny ; Quercus/*classification/genetics ; Sequence Analysis, DNA ; },
abstract = {Species identification of oaks (Quercus) is always a challenge because many species exhibit variable phenotypes that overlap with other species. Oaks are notorious for interspecific hybridization and introgression, and complex speciation patterns involving incomplete lineage sorting. Therefore, accurately identifying Quercus species barcodes has been unsuccessful. In this study, we used chloroplast genome sequence data to identify molecular markers for oak species identification. Using next generation sequencing methods, we sequenced 14 chloroplast genomes of Quercus species in this study and added 10 additional chloroplast genome sequences from GenBank to develop a DNA barcode for oaks. Chloroplast genome sequence divergence was low. We identified four mutation hotspots as candidate Quercus DNA barcodes; two intergenic regions (matK-trnK-rps16 and trnR-atpA) were located in the large single copy region, and two coding regions (ndhF and ycf1b) were located in the small single copy region. The standard plant DNA barcode (rbcL and matK) had lower variability than that of the newly identified markers. Our data provide complete chloroplast genome sequences that improve the phylogenetic resolution and species level discrimination of Quercus. This study demonstrates that the complete chloroplast genome can substantially increase species discriminatory power and resolve phylogenetic relationships in plants.},
}
@article {pmid31775865,
year = {2019},
author = {Tumwebaze, I and Clewing, C and Dusabe, MC and Tumusiime, J and Kagoro-Rugunda, G and Hammoud, C and Albrecht, C},
title = {Molecular identification of Bulinus spp. intermediate host snails of Schistosoma spp. in crater lakes of western Uganda with implications for the transmission of the Schistosoma haematobium group parasites.},
journal = {Parasites &amp; vectors},
volume = {12},
number = {1},
pages = {565},
pmid = {31775865},
issn = {1756-3305},
mesh = {Animals ; Bulinus/*classification/*genetics/parasitology ; Epidemiological Monitoring/*veterinary ; Haplotypes ; Lakes/*parasitology ; Phylogeny ; Phylogeography ; Ruminants/parasitology ; Schistosoma haematobium ; Schistosomiasis haematobia/prevention &amp; control/*transmission ; Uganda ; },
abstract = {BACKGROUND: Human schistosomiasis is the second most important tropical disease and occurs in two forms in Africa (intestinal and urogenital) caused by the digenetic trematodes Schistosoma mansoni and Schistosoma haematobium, respectively. A proposed recent shift of schistosomiasis above a previously established altitudinal threshold of 1400 m above sea level in western Ugandan crater lakes has triggered more research interest there.<br><br>METHODS: Based on extensive field sampling in western Uganda and beyond and employing an approach using sequences of the mitochondrial barcoding gene cytochrome c oxidase subunit 1 (cox1) this study aims were: (i) identification and establishment of the phylogenetic affinities of Bulinus species as potential hosts for Schistosoma spp.; (ii) determining diversity, frequency and distribution patterns of Bulinus spp.; and (iii) establishing genetic variability and phylogeographical patterns using Bayesian inference and parsimony network analyses.<br><br>RESULTS: Out of the 58 crater lakes surveyed, three species of Bulinus snails were found in 34 crater lakes. Bulinus tropicus was dominating, Bulinus forskalii was found in two lakes and Bulinus truncatus in one. The latter two species are unconfirmed potential hosts for S. haematobium in this region. However, Bulinus tropicus is an important species for schistosomiasis transmission in ruminants. Bulinus tropicus comprised 31 haplotypes while both B. forskalii and B. truncatus exhibited only a single haplotype in the crater lakes. All species clustered with most of the haplotypes from surrounding lake systems forming source regions for the colonization of the crater lakes.<br><br>CONCLUSIONS: This first detailed malacological study of the crater lakes systems in western Uganda revealed presence of Bulinus species that are either not known or not regionally known to be hosts for S. haematobium, the causing agent of human urogenital schistosomiasis. Though this disease risk is almost negligible, the observed dominance of B. tropicus in the crater lakes shows that there is a likelihood of a high risk of infections with Schistosoma bovis. Thus, extra attention should be accorded to safeguard wild and domestic ruminants in this region as the population benefits from these animals.},
}
@article {pmid31774178,
year = {2020},
author = {Hasterok, R and Wang, K and Jenkins, G},
title = {Progressive refinement of the karyotyping of Brachypodium genomes.},
journal = {The New phytologist},
volume = {227},
number = {6},
pages = {1668-1675},
doi = {10.1111/nph.16342},
pmid = {31774178},
issn = {1469-8137},
mesh = {*Brachypodium/genetics ; Chromosomes, Plant/genetics ; Evolution, Molecular ; Genome, Plant/genetics ; In Situ Hybridization, Fluorescence ; Karyotyping ; Phylogeny ; },
abstract = {Brachypodium distachyon is a weedy grass species that is firmly established as a model for the comparative and functional genomics of temperate cereals and grasses. Its simple, nuclear genome of five chromosomes contrasts it with other relatives of the genus with different, and usually higher, basic chromosome numbers and ploidy levels. This variation in karyotypic structure affords the possibility of reconstructing evolutionary pathways that have shaped the genome structure of extant species. This Tansley insight documents how key refinements in molecular cytogenetic approaches, from simple fluorescence in situ hybridization to comparative chromosome barcoding, have enabled genome structure studies and yielded valuable information about the drivers of karyotypic reorganization and evolution in the model grass genus Brachypodium.},
}
@article {pmid31772837,
year = {2019},
author = {Kang, L and Xie, D and Xiao, Q and Peng, C and Yu, Y and He, X},
title = {Sequencing and analyses on chloroplast genomes of Tetrataenium candicans and two allies give new insights on structural variants, DNA barcoding and phylogeny in Apiaceae subfamily Apioideae.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e8063},
pmid = {31772837},
issn = {2167-8359},
abstract = {BACKGROUND: Tetrataenium candicans is a traditional Chinese folk herbal medicine used in the treatment of asthma and rheumatic arthritis. Alongside several Tordyliinae species with fleshy roots, it is also regarded as a substitute for a Chinese material medicine called 'Danggui'. However, a lack of sufficient sampling and genomic information has impeded species identification and the protection of wild resources.<br><br>METHODS: The complete chloroplast genomes of T. candicans from two populations, Tetrataenium yunnanense and Semenovia transilliensis, were assembled from two pipelines using data generated from next generation sequencing (NGS). Pseudogenes, inverted repeats (IRs) and hyper-variable regions were located by Geneious 11.1.5. Repeat motifs were searched using MISA and REPuter. DNA polymorphism and segment screening were processed by DNAsp5, and PCR product was sequenced with Sanger's sequencing method. Phylogeny was inferred by MEGA 7.0 and PhyML 3.0.<br><br>RESULTS: The complete chloroplast genomes of T. candicans from two populations, T. yunnanense and S. transilliensis, were 142,261 bp, 141,985 bp, 142,714 bp and 142,145 bp in length, respectively, indicating conservative genome structures and gene categories. We observed duplications of trnH and psbA caused by exceptional contractions and expansions of the IR regions when comparing the four chloroplast genomes with previously published data. Analyses on DNA polymorphism located 29 candidate cp DNA barcodes for the authentication of 'Danggui' counterfeits. Meanwhile, 34 hyper-variable markers were also located by the five Tordyliinae chloroplast genomes, and 11 of them were screened for population genetics of T. candicans based on plastome information from two individuals. The screening results indicated that populations of T.candicans may have expanded. Phylogeny inference on Apiaceae species by CDS sequences showed most lineages were well clustered, but the five Tordyliinae species failed to recover as a monophyletic group, and the phylogenetic relationship between tribe Coriandreae, tribe Selineae, subtribe Tordyliinae and Sinodielsia clade remains unclear.<br><br>DISCUSSION: The four chloroplast genomes offer valuable information for further research on species identification, cp genome structure, population demography and phylogeny in Apiaceae subfamily Apioideae.},
}
@article {pmid31769452,
year = {2020},
author = {Menezes, R and Dramé-Maigné, A and Taly, V and Rondelez, Y and Gines, G},
title = {Streamlined digital bioassays with a 3D printed sample changer.},
journal = {The Analyst},
volume = {145},
number = {2},
pages = {572-581},
doi = {10.1039/c9an01744e},
pmid = {31769452},
issn = {1364-5528},
mesh = {Biological Assay/methods ; DNA/analysis ; Deoxyribonucleases, Type II Site-Specific/genetics ; Emulsions/chemistry ; Equipment Design ; Humans ; MicroRNAs/analysis ; Microfluidic Analytical Techniques/*instrumentation/methods ; Polymerase Chain Reaction ; *Printing, Three-Dimensional ; },
abstract = {Droplet-based microfluidics has permeated many areas of life sciences including biochemistry, biology and medicine. Water-in-oil droplets act as independent femto- to nano-liter reservoirs, enabling the parallelization of (bio)chemical reactions with a minimum sample input. Among the range of applications spanned by droplet microfluidics, digital detection of biomolecules, using Poissonian isolation of single molecules in compartments, has gained considerable attention due to the high accuracy, sensitivity and robustness of these methods. However, while the droplet throughput can be very high, the sample throughput of these methods is poor in comparison to well plate-based assays. This limitation comes from the necessity to convert independently each sample into a monodisperse emulsion. In this paper, we report a versatile device that performs the quick sequential partitioning of up to 15 samples using a single microfluidic chip. A 3D printed sample rotor is loaded with all samples and connected to a pressure source. Simple magnetic actuation is then used to inject the samples in the microfluidic chip without pressure disruption. This procedure generates monodisperse droplets with high sample-to-sample consistency. We also describe a fluorescent barcoding strategy that allows all samples to be collected, incubated, imaged and analyzed simultaneously, thus decreasing significantly the time of the assay. As an example of application, we perform a droplet digital PCR assay for the quantification of a DNA amplicon from 8 samples in less than 2 hours. We further validate our approach demonstrating the parallel quantification of 11 microRNAs from a human sample using an isothermal nucleic acid amplification chemistry. As an off-chip device, the sample changer can be connected to a variety of microfluidic geometries and therefore, used for a wide range of applications.},
}
@article {pmid31768062,
year = {2020},
author = {Luro, S and Potvin-Trottier, L and Okumus, B and Paulsson, J},
title = {Isolating live cells after high-throughput, long-term, time-lapse microscopy.},
journal = {Nature methods},
volume = {17},
number = {1},
pages = {93-100},
pmid = {31768062},
issn = {1548-7105},
support = {R01 GM081563/GM/NIGMS NIH HHS/United States ; },
mesh = {Cell Separation/*methods ; Cell Tracking/methods ; Escherichia coli/genetics/*isolation &amp; purification/metabolism ; Escherichia coli Proteins/genetics/*metabolism ; Gene Library ; Genes, Synthetic ; High-Throughput Screening Assays/*methods ; Image Processing, Computer-Assisted ; Microfluidics/methods ; Single-Cell Analysis/*methods ; Time-Lapse Imaging/*instrumentation/*methods ; },
abstract = {Single-cell genetic screens can be incredibly powerful, but current high-throughput platforms do not track dynamic processes, and even for non-dynamic properties they struggle to separate mutants of interest from phenotypic outliers of the wild-type population. Here we introduce SIFT, single-cell isolation following time-lapse imaging, to address these limitations. After imaging and tracking individual bacteria for tens of consecutive generations under tightly controlled growth conditions, cells of interest are isolated and propagated for downstream analysis, free of contamination and without genetic or physiological perturbations. This platform can characterize tens of thousands of cell lineages per day, making it possible to accurately screen complex phenotypes without the need for barcoding or genetic modifications. We applied SIFT to identify a set of ultraprecise synthetic gene oscillators, with circuit variants spanning a 30-fold range of average periods. This revealed novel design principles in synthetic biology and demonstrated the power of SIFT to reliably screen diverse dynamic phenotypes.},
}
@article {pmid31765069,
year = {2020},
author = {Xiao, L and Wang, C and Dai, C and Littlepage, LE and Li, J and Schultz, ZD},
title = {Untargeted Tumor Metabolomics with Liquid Chromatography-Surface-Enhanced Raman Spectroscopy.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {59},
number = {9},
pages = {3439-3443},
pmid = {31765069},
issn = {1521-3773},
support = {P30 CA016058/CA/NCI NIH HHS/United States ; R33 CA206922/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Chromatography, High Pressure Liquid ; Disease Models, Animal ; *Metabolome ; Metabolomics/*methods ; Mice ; Neoplasms/*diagnosis/metabolism ; Spectrum Analysis, Raman ; Wnt1 Protein/metabolism ; },
abstract = {Metabolomics is a powerful systems biology approach that monitors changes in biomolecule concentrations to diagnose and monitor health and disease. However, leading metabolomics technologies, such as NMR and mass spectrometry (MS), access only a small portion of the metabolome. Now an approach is presented that uses the high sensitivity and chemical specificity of surface-enhanced Raman scattering (SERS) for online detection of metabolites from tumor lysates following liquid chromatography (LC). The results demonstrate that this LC-SERS approach has metabolite detection capabilities comparable to the state-of-art LC-MS but suggest a selectivity for the detection of a different subset of metabolites. Analysis of replicate LC-SERS experiments exhibit reproducible metabolite patterns that can be converted into barcodes, which can differentiate different tumor models. Our work demonstrates the potential of LC-SERS technology for metabolomics-based diagnosis and treatment of cancer.},
}
@article {pmid31763778,
year = {2019},
author = {Veeranagouda, Y and Remaury, A and Guillemot, JC and Didier, M},
title = {RNA Fragmentation and Sequencing (RF-Seq): Cost-Effective, Time-Efficient, and High-Throughput 3' mRNA Sequencing Library Construction in a Single Tube.},
journal = {Current protocols in molecular biology},
volume = {129},
number = {1},
pages = {e109},
doi = {10.1002/cpmb.109},
pmid = {31763778},
issn = {1934-3647},
mesh = {*Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Membrane Proteins/blood/genetics ; Polymerase Chain Reaction/*methods ; RNA, Messenger/*genetics ; Sequence Analysis, RNA/*methods ; Transcriptome ; },
abstract = {Over the past decade, transcriptomic studies using next-generation sequencing (NGS)-based RNA sequencing (RNA-Seq) have greatly contributed to characterizing biochemical and physiological changes in cells and tissues across organisms and experimental conditions. Critical steps in RNA-Seq include the preparation of the sequencing library from extracted RNA. Currently, a large panoply of RNA-Seq kits are commercially available. In these kits, conversion of RNA into a sequencing library involves multiple steps, which are labor-intensive, and cost per sample for library preparation may limit routine use of RNA-Seq. Here we describe a simple method for RNA-Seq library construction, referred to as RNA Fragmentation and Sequencing (RF-Seq). RF-Seq requires as little as 10 ng of total RNA and facilitates the sequencing of the 3' end of mRNAs. RF-Seq involves the fragmentation of total RNA followed by reverse transcription in presence of the oligo(dT) primer/template switch oligonucleotide and a sample barcoding/enrichment within a single PCR tube/well. The sample barcoding/enrichment step provides more flexibility for individual sample handling. The use of just twenty orthogonal Illumina TruSeq HT barcoding primers facilitates the preparation of 96 uniquely labeled RF-Seq libraries in a single 96-well PCR plate. Twelve RF-Seq libraries can be prepared within 4 hr, with an approximate cost of $10/sample. We provide an example of using RF-Seq to measure gene expression upon activation of an innate immune pathway using STING activator in human blood cells, highlighting the potential usefulness of the proposed method in routine transcriptomic applications such as high-throughput drug screening and/or preclinical toxicity assays. © 2019 by John Wiley &amp; Sons, Inc. Basic Protocol: RNA fragmentation and sequencing (RF-Seq): Cost-effective, time-efficient, and high-throughput 3' mRNA sequencing library construction in a single tube.},
}
@article {pmid31762958,
year = {2019},
author = {Bewicke-Copley, F and Arjun Kumar, E and Palladino, G and Korfi, K and Wang, J},
title = {Applications and analysis of targeted genomic sequencing in cancer studies.},
journal = {Computational and structural biotechnology journal},
volume = {17},
number = {},
pages = {1348-1359},
pmid = {31762958},
issn = {2001-0370},
abstract = {Next Generation Sequencing (NGS) has dramatically improved the flexibility and outcomes of cancer research and clinical trials, providing highly sensitive and accurate high-throughput platforms for large-scale genomic testing. In contrast to whole-genome (WGS) or whole-exome sequencing (WES), targeted genomic sequencing (TS) focuses on a panel of genes or targets known to have strong associations with pathogenesis of disease and/or clinical relevance, offering greater sequencing depth with reduced costs and data burden. This allows targeted sequencing to identify low frequency variants in targeted regions with high confidence, thus suitable for profiling low-quality and fragmented clinical DNA samples. As a result, TS has been widely used in clinical research and trials for patient stratification and the development of targeted therapeutics. However, its transition to routine clinical use has been slow. Many technical and analytical obstacles still remain and need to be discussed and addressed before large-scale and cross-centre implementation. Gold-standard and state-of-the-art procedures and pipelines are urgently needed to accelerate this transition. In this review we first present how TS is conducted in cancer research, including various target enrichment platforms, the construction of target panels, and selected research and clinical studies utilising TS to profile clinical samples. We then present a generalised analytical workflow for TS data discussing important parameters and filters in detail, aiming to provide the best practices of TS usage and analyses.},
}
@article {pmid31762946,
year = {2019},
author = {Lukhtanov, VA and Dantchenko, AV},
title = {Karyotype of Polyommatus (Agrodiaetus) eriwanensis Forster, 1960 and taxonomic position of P. (A.) interjectus de Lesse, 1960 (Lepidoptera, Lycaenidae).},
journal = {Comparative cytogenetics},
volume = {13},
number = {4},
pages = {359-366},
pmid = {31762946},
issn = {1993-0771},
abstract = {The karyotype of Polyommatus (Agrodiaetus) eriwanensis Forster, 1960 from the type locality ("Eriwan" [Yerevan, Armenia]) and other localities in Armenia was investigated. The number of chromosomal elements (bivalents+ multivalents) observed in male meiosis I was found to vary from 29 to 34. In individuals with n = 34, all observed elements were represented by bivalents. In other specimens, heterozygosity for different number of chromosomal fusions resulted in multivalent formation at MI stage and consequently in a lower number of recognizable chromosomal elements. We show that all karyotype peculiarities of P. (A.) interjectus de Lesse, 1960 (n = 29-32) from Turkey are similar to those in A. eriwanensis. The butterflies of these taxa have allopatric distribution and can be considered as conspecific.},
}
@article {pmid31760570,
year = {2020},
author = {Sugita, N and Ebihara, A and Hosoya, T and Jinbo, U and Kaneko, S and Kurosawa, T and Nakae, M and Yukawa, T},
title = {Non-destructive DNA extraction from herbarium specimens: a method particularly suitable for plants with small and fragile leaves.},
journal = {Journal of plant research},
volume = {133},
number = {1},
pages = {133-141},
pmid = {31760570},
issn = {1618-0860},
mesh = {DNA Barcoding, Taxonomic ; DNA, Plant ; *Plant Leaves ; *Plants ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {Protocols for DNA extraction from plants generally involve physical and chemical destruction of tissues. Use of these conventional methods precludes preservation of morphological information from herbarium specimens, especially for small plants with few leaves, and reduces the voucher value of specimens. Here, we developed a new, non-destructive DNA extraction protocol (Protocol 1) that only needs a small piece of leaf (< 25 mm[2]) to obtain DNA suitable for DNA sequencing from fragile herbarium specimens. The protocol was very simple and rapid; an extraction buffer was placed on the leaf surface of an intact specimen for 30 min at room temperature (20 °C). The quality of extracted DNA was checked by PCR amplification of two standard plant DNA barcode regions, the maturase K gene (matK, ca. 850 bp) and the ribulose-1,5-bisphosphatecarboxylase/oxygenase gene (rbcL, ca. 550 bp), for 14 vascular plant species encompassing various taxonomic groups. The protocol retrieved sequences from 80.0% of specimens for matK and 46.2% of specimens for rbcL. Placing of the extraction buffer onto specimens did not cause any tears or deformation, but caused discoloration in some plants. To improve DNA yield for specimens incompatible with Protocol 1, we developed an alternative protocol for DNA extraction with minimally invasive destruction of specimens (Protocol 2). In this protocol, a cut leaf was immersed in the extraction buffer for 30 min and stored subsequently in a fragment pocket on the specimen sheet. This alternative method retrieved matK sequences from 80.0% of specimens and rbcL sequences from 92.8% of specimens. The combination of Protocols 1 and 2 enabled us to obtain matK sequences from 90.0% of specimens and rbcL sequences form 92.8% of specimens. The new protocols facilitate the use of museum specimens for use of DNA of museum specimens while still preserving morphological information.},
}
@article {pmid31758080,
year = {2019},
author = {Osumi, H and Shinozaki, E and Yamaguchi, K and Zembutsu, H},
title = {Early change in circulating tumor DNA as a potential predictor of response to chemotherapy in patients with metastatic colorectal cancer.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {17358},
pmid = {31758080},
issn = {2045-2322},
mesh = {Adenocarcinoma/diagnosis/*drug therapy/mortality/pathology ; Adult ; Aged ; Antineoplastic Combined Chemotherapy Protocols/*therapeutic use ; Biomarkers, Pharmacological/analysis/blood ; *Biomarkers, Tumor/blood/genetics ; Circulating Tumor DNA/analysis/*blood ; Colorectal Neoplasms/diagnosis/*drug therapy/mortality/pathology ; DNA Mutational Analysis ; Early Diagnosis ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Liquid Biopsy ; Male ; Middle Aged ; Neoplasm Metastasis ; Predictive Value of Tests ; Prognosis ; },
abstract = {The impact of ctDNA changes after chemotherapy on the clinical outcomes of patients with metastatic colorectal cancer (mCRC) remains unclear. The present study evaluated the clinical implications of the early change in ctDNA levels as a predictor of objective response and clinical outcome in mCRC patients who received chemotherapy. We investigated the effects of after/before ratio of ctDNA levels 2 and 8 weeks after initiation of second-line chemotherapy, on objective response rate (ORR), progression-free survival (PFS), and overall survival (OS). ctDNA was detected using amplicon-based deep sequencing with a molecular barcode encompassing >240 hotspot mutations in 14 colon cancer-related genes. In multivariate analysis, as compared to baseline, patients with lower ctDNA level (≤50%) 8 weeks after initiation of chemotherapy showed significantly longer PFS and OS than the patients with higher (>50%) ctDNA level. In patients achieving a partial response or stable disease, the after/before ratio of ctDNA level 8 weeks after initiation of chemotherapy was significantly lower than those in patients with progressive disease. The present study suggests that an early change in the ctDNA level might serve as a biomarker to predict the chemotherapeutic efficacy and clinical outcomes in patients with mCRC.},
}
@article {pmid31754320,
year = {2019},
author = {Narakusumo, RP and Balke, M and Riedel, A},
title = {Seven new species of Trigonopterus Fauvel (Coleoptera, Curculionidae) from the Tanimbar Archipelago.},
journal = {ZooKeys},
volume = {888},
number = {},
pages = {75-93},
pmid = {31754320},
issn = {1313-2989},
abstract = {Based on recent fieldwork, the hyperdiverse weevil genus Trigonopterus Fauvel is recorded for the first time from the Indonesian Tanimbar Archipelago, halfway between Australia and Western New Guinea. All seven species discovered on Tanimbar are new to science, and described here: Trigonopterus atuf sp. nov., T. kumbang sp. nov., T. laratensis sp. nov., T. porg sp. nov., T. selaruensis sp. nov., T. tanimbarensis sp. nov., and T. triradiatus sp. nov. The new species are authored by the taxonomists-in-charge, Raden Pramesa Narakusumo and Alexander Riedel. This fauna appears discordant and established by relatively recent dispersal from New Guinea and other Moluccan islands.},
}
@article {pmid31754140,
year = {2019},
author = {Duan, H and Wang, W and Zeng, Y and Guo, M and Zhou, Y},
title = {The screening and identification of DNA barcode sequences for Rehmannia.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {17295},
pmid = {31754140},
issn = {2045-2322},
mesh = {China ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics/isolation &amp; purification ; Feasibility Studies ; Genes, Plant/*genetics ; Genetic Variation ; Mutation Rate ; Phylogeny ; Plants, Medicinal/classification/genetics ; Rehmannia/classification/*genetics ; Sequence Analysis, DNA ; *Species Specificity ; },
abstract = {In this study, ITS, ITS2, matK, rbcL and psbA-trnH in Rehmannia were successfully amplified and sequenced, but some ITS sequences need to be proofread according to ITS2 sequences. Compared with rbcL, matK and psbA-trnH, ITS and ITS2 had higher mutation rate and more information sites, and ITS2 had higher interspecific diversity and lower intraspecific variation in Rehmannia, but the interspecific genetic variation of rbcL and matK was lower. Furthermore, the obvious barcoding gap was found in psbA-trnH or ITS2 + psbA-trnH, and the overlap between interspecific and intraspecific variation of ITS, ITS2 or matK was less. In addition, the phylogenetic tree based on ITS or ITS2 indicated that R. glutinosa, R. chingii or R. henryi with obvious monophyly could be successfully identified, but R. piasezkii and R. elata were clustered into one branch, R. solanifolia could not be distinguished from R. glutinosa, and R. chingii was closer to R. henryi. In phylogenetic tree based on psbA-trnH or ITS2 + psbA-trnH, cultivars and wild varieties of R. glutinosa could be distinguished, were clearly separated from other Rehmannia species, and cultivars or wild varieties of R. glutinosa could be also distinguished by matK. Taken together, ITS2 has great potential in systematic study and species identification of Rehmannia, the combination of ITS2 and psbA-trnH might be the most suitable DNA barcode for Rehmannia species.},
}
@article {pmid31753001,
year = {2019},
author = {Bhowmick, B and Zhao, J and Øines, &#xd8; and Bi, T and Liao, C and Zhang, L and Han, Q},
title = {Molecular characterization and genetic diversity of Ornithonyssus sylviarum in chickens (Gallus gallus) from Hainan Island, China.},
journal = {Parasites &amp; vectors},
volume = {12},
number = {1},
pages = {553},
pmid = {31753001},
issn = {1756-3305},
support = {ZDYF2019073//Key Research and Development Project of Hainan Province (CN)/ ; hdkytg201702//Hainan University Research Fund/ ; },
mesh = {Acari/anatomy &amp; histology/*classification/*genetics ; Animals ; *Chickens ; China ; Disease Transmission, Infectious ; Electron Transport Complex IV/genetics ; Farms ; *Genetic Variation ; Microscopy, Electron ; Mite Infestations/parasitology/*veterinary ; Phylogeny ; Poultry Diseases/*parasitology ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The northern fowl mite (NFM), Ornithonyssus sylviarum, is an obligatory hematophagous ectoparasite of birds and one of the most important pests in the poultry industry on several continents. Although NFM poses a serious problem, it remains a neglected pest of poultry in China and other Asian countries. Therefore, a molecular analysis was conducted to provide baseline information on the occurrence, genetic diversity and emergence of NFM in poultry farms from China.<br><br>METHODS: This study focused on morphological description and identification of adults based on electron microscopy, molecular sequencing of the mitochondrial cox1 gene and phylogenetic analysis. We have also used the DNA sequences of the cox1 gene to study the genetic diversity, population structure and demographic history. The neutrality tests were used to analyze signatures of historical demographic events.<br><br>RESULTS: The mites collected were identified as the northern fowl mite Ornithonyssus sylviarum based on external morphological characterization using electron microscopy. Molecular analysis using a 756-bp long partial fragment of the cox1 gene revealed 99-100% sequence identity with NFM and phylogenetic inferences showed a bootstrap value of 99% indicating a well-supported monophyletic relationship. Molecular diversity indices showed high levels of haplotype diversity dominated by private haplotypes, but low nucleotide divergence between haplotypes. The Tajima's D test and Fu's Fs test showed negative value, indicating deviations from neutrality and both suggested recent population expansion of mite populations supported by a star-like topology of the isolates in the network analysis. Our genetic data are consistent with a single introduction of NFM infestations and the spread of NFM infestation in Hainan poultry farms and a private haplotype dominance, which suggest that infestations are recycled within the farms and transmission routes are limited between farms.<br><br>CONCLUSIONS: To our knowledge, this is the first time a molecular report of NFM in chicken from China including other Asian countries using DNA barcoding. The findings have potential implications with respect to understanding the transmission patterns, emergence and populations trends of parasitic infestations of poultry farms that will help for setting the parameters for integrated pest management (IPM) tactics against mite infestations.},
}
@article {pmid31752998,
year = {2019},
author = {Sweet, M and Burian, A and Fifer, J and Bulling, M and Elliott, D and Raymundo, L},
title = {Compositional homogeneity in the pathobiome of a new, slow-spreading coral disease.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {139},
pmid = {31752998},
issn = {2049-2618},
mesh = {Animals ; *Anthozoa/microbiology/physiology ; Bacteria/*pathogenicity ; *Coral Reefs ; Microbial Interactions/*physiology ; Microbiota/*physiology ; Micronesia ; Symbiosis/*physiology ; },
abstract = {BACKGROUND: Coral reefs face unprecedented declines in diversity and cover, a development largely attributed to climate change-induced bleaching and subsequent disease outbreaks. Coral-associated microbiomes may strongly influence the fitness of their hosts and alter heat tolerance and disease susceptibility of coral colonies. Here, we describe a new coral disease found in Micronesia and present a detailed assessment of infection-driven changes in the coral microbiome.<br><br>RESULTS: Combining field monitoring and histological, microscopic and next-generation barcoding assessments, we demonstrate that the outbreak of the disease, named 'grey-patch disease', is associated with the establishment of cyanobacterial biofilm overgrowing coral tissue. The disease is characterised by slow progression rates, with coral tissue sometimes growing back over the GPD biofilm. Network analysis of the corals' microbiome highlighted the clustering of specific microbes which appeared to benefit from the onset of disease, resulting in the formation of 'infection clusters' in the microbiomes of apparently healthy corals.<br><br>CONCLUSIONS: Our results appear to be in contrast to the recently proposed Anna-Karenina principle, which states that disturbances (such as disease) trigger chaotic dynamics in microbial communities and increase &#x3b2;-diversity. Here, we show significantly higher community similarity (compositional homogeneity) in the pathobiome of diseased corals, compared to the microbiome associated with apparently healthy tissue. A possible explanation for this pattern is strong competition between the pathogenic community and those associated with the 'healthy' coral holobiont, homogenising the composition of the pathobiome. Further, one of our key findings is that multiple agents appear to be involved in degrading the corals' defences causing the onset of this disease. This supports recent findings indicating a need for a shift from the one-pathogen-one-disease paradigm to exploring the importance of multiple pathogenic players in any given disease.},
}
@article {pmid31752677,
year = {2019},
author = {Han, CC and Hsu, KC and Fang, LS and Cheng, IM and Lin, HD},
title = {Geographical and temporal origins of Neocaridina species (Decapoda: Caridea: Atyidae) in Taiwan.},
journal = {BMC genetics},
volume = {20},
number = {1},
pages = {86},
pmid = {31752677},
issn = {1471-2156},
mesh = {Animals ; Arthropod Proteins/genetics ; China ; DNA Barcoding, Taxonomic/*veterinary ; Decapoda/*classification/genetics ; Electron Transport Complex IV/*genetics ; Japan ; Likelihood Functions ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/veterinary ; Taiwan ; },
abstract = {BACKGROUND: The freshwater species on Taiwan Island have been documented to have originated from mainland China and the Japanese islands from multiple events and by multiple colonization routes. Moreover, the sequences from the mitochondrial DNA cytochrome c oxidase subunit I (COI) have been used for DNA barcoding to identify the species. This study used the COI sequences to identify Neocaridina species in Taiwan and to examine their geographical and temporal origins.<br><br>RESULTS: In total, 479 specimens were collected from 35 localities, which covered almost all rivers in Taiwan. In addition, some sequences were downloaded from GenBank. The maximum likelihood (ML) tree displayed that all sequences were sorted into 13 taxa (clades), and all sequences in Taiwan were sorted into four clades. The Bayesian skyline plots revealed that these four Neocaridina species have declined recently in Taiwan.<br><br>CONCLUSIONS: All results support that (1) there are four Neocaridina species in Taiwan, which are N. davidi, N. saccam, N. ketagalan and an undescribed Neocaridina species (N. sp.); (2) these four species colonized Taiwan Island in four colonization events; (3) N. sp. colonized Taiwan first; (4) after the island reached its shape, N. ketagalan and N. saccam colonized Taiwan from the Japanese islands and mainland China, respectively; (5) N. davidi colonized northern Taiwan last; and (6) the cyclic glacial and landform changes in East Asia shaped the colonization events and population structures of the Neocaridina species.},
}
@article {pmid31752576,
year = {2019},
author = {Kunprom, C and Pramual, P},
title = {DNA barcoding of fruit flies (Diptera: Tephritidae) in Thailand: ambiguity, misidentification and cryptic diversity.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {8},
pages = {861-873},
doi = {10.1080/24701394.2019.1693550},
pmid = {31752576},
issn = {2470-1408},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Diptera/*genetics ; Electron Transport Complex IV/*genetics ; Genome, Mitochondrial/*genetics ; Species Specificity ; Thailand ; },
abstract = {Fruit flies (Diptera: Tephritidae) are significant insect pests of many commercially important fruits and vegetables. Therefore, rapid and accurate species identification methods are required for the regulation, management and quarantine of these pests. In this study, we examined the efficiency of mitochondrial cytochrome c oxidase I sequences for species identification of fruit flies in Thailand. Data analyses based on 42 fruit fly taxa revealed moderate performance of this genetic marker. There were 14 taxa that have no barcode gap and thus could not be identified unambiguously to species by this methodology. Taxonomic uncertainty, inadequate variation of the marker and misidentifications of specimens deposited in the public database are the most likely factors explaining unsuccessful identification. DNA barcodes also revealed cryptic diversity in five taxa (Bactrocera caudata, B. tuberculata, B. infesta, Zeugodacus isolatus, Carpomya vesuviana). These species require further taxonomic investigation of if they are different cryptic taxa or are indications of geographic structuring of within single species.},
}
@article {pmid31752298,
year = {2019},
author = {Doh, EJ and Kim, JH and Lee, G},
title = {Identification and Monitoring of Amomi Fructus and its Adulterants Based on DNA Barcoding Analysis and Designed DNA Markers.},
journal = {Molecules (Basel, Switzerland)},
volume = {24},
number = {22},
pages = {},
pmid = {31752298},
issn = {1420-3049},
support = {S2728663//Korea Ministry of SMEs and Startups/ ; },
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant ; DNA, Ribosomal Spacer ; Drugs, Chinese Herbal ; Fruit ; *Genetic Markers ; Phylogeny ; Zingiberaceae/*classification/*genetics ; },
abstract = {Amomi Fructus is one of the traditional medicines derived from the ripe fruits of the Zingiberaceae family of plants, which include Amomum villosum, A. villosum var. xanthioides, and A. longiligulare. Owing to their highly similar morphological traits, several kinds of adulterants of Amomi Fructus have been reported. Therefore, accurate and reliable methods of identification are necessary in order to ensure drug safety and quality. We performed DNA barcoding using five regions (ITS, matK, rbcL, rpoB, and trnL-F intergenic spacer) of 23 Amomi Fructus samples and 22 adulterants. We designed specific DNA markers for Amomi Fructus based on the single nucleotide polymorphisms (SNPs) in the ITS. Amomi Fructus was well separated from the adulterants and was classified with the species of origin based on the detected SNPs from the DNA barcoding results. The AVF1/ISR DNA marker for A. villosum produced a 270 bases amplified product, while the ALF1/ISF DNA marker produced a 350 bases product specific for A. longiligulare. Using these DNA markers, the monitoring of commercially distributed Amomi Fructus was performed, and the monitoring results were confirmed by ITS analysis. This method identified samples that were from incorrect origins, and a new species of adulterant was also identified. These results confirmed the accuracy and efficiency of the designed DNA markers; this method may be used as an efficient tool for the identification and verification of Amomi Fructus.},
}
@article {pmid31752022,
year = {2020},
author = {Yazaki, J and Kawashima, Y and Ogawa, T and Kobayashi, A and Okoshi, M and Watanabe, T and Yoshida, S and Kii, I and Egami, S and Amagai, M and Hosoya, T and Shiroguchi, K and Ohara, O},
title = {HaloTag-based conjugation of proteins to barcoding-oligonucleotides.},
journal = {Nucleic acids research},
volume = {48},
number = {2},
pages = {e8},
pmid = {31752022},
issn = {1362-4962},
mesh = {Antibodies, Anti-Idiotypic/genetics/immunology/*isolation &amp; purification ; Autoimmune Diseases/diagnosis/immunology ; Click Chemistry ; Cycloparaffins/chemistry ; Desmoglein 3/genetics/immunology/*isolation &amp; purification ; Enzyme-Linked Immunosorbent Assay ; Humans ; Immunoglobulin G/genetics/immunology ; Luciferases/chemistry ; Oligonucleotides ; Protein Interaction Domains and Motifs/*genetics ; Proteins/genetics/immunology/*isolation &amp; purification ; },
abstract = {Highly sensitive protein quantification enables the detection of a small number of protein molecules that serve as markers/triggers for various biological phenomena, such as cancer. Here, we describe the development of a highly sensitive protein quantification system called HaloTag protein barcoding. The method involves covalent linking of a target protein to a unique molecule counting oligonucleotide at a 1:1 conjugation ratio based on an azido-cycloalkyne click reaction. The sensitivity of the HaloTag-based barcoding was remarkably higher than that of a conventional luciferase assay. The HaloTag system was successfully validated by analyzing a set of protein-protein interactions, with the identification rate of 44% protein interactions between positive reference pairs reported in the literature. Desmoglein 3, the target antigen of pemphigus vulgaris, an IgG-mediated autoimmune blistering disease, was used in a HaloTag protein barcode assay to detect the anti-DSG3 antibody. The dynamic range of the assay was over 104-times wider than that of a conventional enzyme-linked immunosorbent assay (ELISA). The technology was used to detect anti-DSG3 antibody in patient samples with much higher sensitivity compared to conventional ELISA. Our detection system, with its superior sensitivity, enables earlier detection of diseases possibly allowing the initiation of care/treatment at an early disease stage.},
}
@article {pmid31750794,
year = {2020},
author = {Chimal-Sánchez, E and Senés-Guerrero, C and Varela, L and Montaño, NM and García-Sánchez, R and Pacheco, A and Montaño-Arias, SA and Camargo-Ricalde, SL},
title = {Septoglomus mexicanum, a new species of arbuscular mycorrhizal fungi from semiarid regions in Mexico.},
journal = {Mycologia},
volume = {112},
number = {1},
pages = {121-132},
doi = {10.1080/00275514.2019.1671147},
pmid = {31750794},
issn = {1557-2536},
mesh = {DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; *Desert Climate ; Fabaceae/microbiology ; Glomeromycota/*classification/cytology/genetics/growth &amp; development ; Hyphae/cytology/growth &amp; development ; Mexico ; Mycorrhizae/*classification/cytology/genetics/growth &amp; development ; RNA, Ribosomal/genetics ; Rhizosphere ; Sequence Analysis, DNA ; Spores, Fungal/classification/cytology/genetics/growth &amp; development ; },
abstract = {Septoglomus mexicanum is here described as a new species of arbuscular mycorrhizal fungi (AMF; Glomeromycota) based on morphological and phylogenetic analyses. It was isolated from rhizospheric soil of two endemic Mexican legumes: Prosopis laevigata and Mimosa luisana, which grow in semiarid regions of central Mexico. Septoglomus mexicanum is characterized by forming globose spores of (154.5-)202.8(-228.9) µm diam and a spore wall consisting of four layers (SWL1-SWL4): outer wall layer (SWL1) hyaline, evanescent, (1.7-)3.2(-4.3) µm thick; SWL2 laminate and smooth, orange to reddish orange, (3.1-)4.5(-6.1) µm thick; SWL3 laminate, smooth, reddish orange to reddish brown, (4.1-)5.1(-5.7) µm thick; and SWL4 hyaline, semiflexible, (0.93-)1.2(-1.4) µm thick. None of the spore wall layers stain with Melzer's reagent. The subtending hypha has a color from yellowish to golden and presents a septum on spore base. Septoglomus mexicanum can be distinguished from all other Septoglomus species by spore size and color, by spore wall structure (four layers), and by color change of the subtending hypha. Phylogenetic analysis based on the AMF extended DNA barcode covering a 1.5-kb fragment of the small subunit (SSU), internal transcribed spacer region (ITS1-5.8S-ITS2), and the large subunit (LSU) of rRNA genes places S. mexicanum in the genus Septoglomus, separated from other described Septoglomus species, especially S. turnauae, with whom it could be confused morphologically. All available sequences in public databases suggest that this new fungal species has not yet been previously detected. Thus, there are currently 149 Glomeromycota species registered in Mexico, representing 47.4% of the known species worldwide.},
}
@article {pmid31748867,
year = {2020},
author = {Kwak, ML and Lee, L and Okumura, C and Hsu, CD},
title = {First Report of Co-invasion by the Reptile Nematode Ozolaimus megatyphlon (Nematoda: Pharyngodonidae) with Invasive Green Iguanas (Iguana iguana) in the Asia-Pacific.},
journal = {Acta parasitologica},
volume = {65},
number = {1},
pages = {264-270},
pmid = {31748867},
issn = {1896-1851},
mesh = {Animals ; DNA Barcoding, Taxonomic ; *Ecosystem ; Electron Transport Complex IV/genetics ; Female ; Iguanas/*parasitology ; *Introduced Species ; Male ; Nematoda/anatomy &amp; histology/*classification/*isolation &amp; purification ; Singapore ; },
abstract = {PURPOSE: Co-invasion of naïve ecosystems by non-native parasites is a serious threat to global biodiversity, though such events are difficult to detect early in the invasion process. Green iguanas (Iguana iguana) are an emerging invasive species and have colonised several countries in the Asia-Pacific. A survey was undertaken to determine whether parasites of the green iguana had co-invaded naïve ecosystems with their introduced host.<br><br>METHODS: Over a 10-month period, wild green iguanas were trapped and euthanised in Singapore. All animals were necropsied and sampled for parasites. Parasites were then identified morphologically and subsequently characterised molecularly at the cytochrome c oxidase I (COI) locus.<br><br>RESULTS: The reptile nematode Ozolaimus megatyphlon was found in 38% of the sampled green iguanas, with burdens of 100&#x2009;+&#x2009;worms in all infected animals. This represents the first recorded co-invasion of this species with wild green iguanas in the Asia-Pacific. Based on the molecular characterisation of the cytochrome c oxidase I (COI) locus, the first DNA barcode is provided for O. megatyphlon.<br><br>CONCLUSION: For the first time, the reptile nematode Ozolaimus megatyphlon is shown to be invasive and to have colonised the Asia-Pacific region with its introduced host, the green iguana. The DNA barcode provided here will facilitate future monitoring programmes as O. megatyphlon invades new habitats and countries.},
}
@article {pmid31747540,
year = {2020},
author = {Anderson, K and Braoudakis, G and Kvist, S},
title = {Genetic variation, pseudocryptic diversity, and phylogeny of Erpobdella (Annelida: Hirudinida: Erpobdelliformes), with emphasis on Canadian species.},
journal = {Molecular phylogenetics and evolution},
volume = {143},
number = {},
pages = {106688},
doi = {10.1016/j.ympev.2019.106688},
pmid = {31747540},
issn = {1095-9513},
mesh = {Animals ; Annelida/classification/*genetics ; Biodiversity ; Canada ; Electron Transport Complex IV/classification/genetics ; *Genetic Variation ; Haplotypes ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal/classification/genetics ; },
abstract = {Leeches of the family Erpobdellidae are important members of benthic freshwater environments, where they are voracious predators of other invertebrates and an important source of nutrition for several species of vertebrates. Beset by a lack of reliable diagnostic morphological characters and destructive identification processes, molecular approaches have, in recent years, been employed to illuminate the relationships within this family, and DNA barcoding has been employed for identification purposes. However, an understanding of the levels of genetic variation across the geographic distributions of members of the genus is still lacking. Herein, we sequence the mitochondrial COI locus for 249 newly collected North American individuals, representing 5 species, as well as mitochondrial 12S rDNA, nuclear 18S rDNA, and nuclear 28S rDNA for a select subset of these. Our COI dataset was leveraged to detect potential cryptic species, and to calculate genetic distances as a proxy for the degree of gene flow between populations. Augmented by numerous sequences from GenBank, the multilocus dataset was used to reconstruct a phylogenetic hypothesis for worldwide members of the genus. Beyond corroborating previous overarching phylogenetic frameworks, our results show that an undescribed species that is morphologically and genetically similar to Erpobdella punctata exists in sympatry with this species - the new species has likely been overlooked in previous studies due to its morphological similarity with Erpobdella punctata. Erpobdella bucera is reported from Canada for the first time; and Erpobdella microstoma is newly reported from Saskatchewan and placed in a phylogeny for the first time. Finally, we find evidence for genetic structure in both E. cf. punctata and Erpobdella obscura that is correlated with major river drainage basin boundaries in North America.},
}
@article {pmid31744876,
year = {2019},
author = {Vassallo, CN and Wall, D},
title = {Self-identity barcodes encoded by six expansive polymorphic toxin families discriminate kin in myxobacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {49},
pages = {24808-24818},
pmid = {31744876},
issn = {1091-6490},
support = {R01 GM101449/GM/NIGMS NIH HHS/United States ; },
mesh = {Alleles ; Bacterial Outer Membrane Proteins/genetics/metabolism ; Bacterial Toxins/classification/*genetics/immunology/*isolation &amp; purification ; Cation Transport Proteins/genetics/metabolism ; Lipoproteins ; Myxococcales/*genetics/*metabolism ; Myxococcus xanthus/genetics/metabolism ; Phylogeny ; Receptors, Cell Surface/*metabolism ; Sequence Analysis ; },
abstract = {Myxobacteria are an example of how single-cell individuals can transition into multicellular life by an aggregation strategy. For these and all organisms that consist of social groups of cells, discrimination against, and exclusion of, nonself is critical. In myxobacteria, TraA is a polymorphic cell surface receptor that identifies kin by homotypic binding, and in so doing exchanges outer membrane (OM) proteins and lipids between cells with compatible receptors. However, TraA variability alone is not sufficient to discriminate against all cells, as traA allele diversity is not necessarily high among local strains. To increase discrimination ability, myxobacteria include polymorphic OM lipoprotein toxins called SitA in their delivered cargo, which poison recipient cells that lack the cognate, allele-specific SitI immunity protein. We previously characterized 3 SitAI toxin/immunity pairs that belong to 2 families. Here, we discover 4 additional SitA families. Each family is unique in sequence, but share the characteristic features of SitA: OM-associated toxins delivered by TraA. We demonstrate that, within a SitA family, C-terminal nuclease domains are polymorphic and often modular. Remarkably, sitA loci are strikingly numerous and diverse, with most genomes possessing >30 and up to 83 distinct sitAI loci. Interestingly, all SitA protein families are serially transferred between cells, allowing a SitA inhibitor cell to poison multiple targets, including cells that never made direct contact. The expansive suites of sitAI loci thus serve as identify barcodes to exquisitely discriminate against nonself to ensure populations are genetically homogenous to conduct cooperative behaviors.},
}
@article {pmid31743531,
year = {2020},
author = {Lokugamage, MP and Gan, Z and Zurla, C and Levin, J and Islam, FZ and Kalathoor, S and Sato, M and Sago, CD and Santangelo, PJ and Dahlman, JE},
title = {Mild Innate Immune Activation Overrides Efficient Nanoparticle-Mediated RNA Delivery.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {32},
number = {1},
pages = {e1904905},
pmid = {31743531},
issn = {1521-4095},
support = {T32 EB021962/EB/NIBIB NIH HHS/United States ; T32 GM105490/GM/NIGMS NIH HHS/United States ; PDF-JFA-1860//Parkinson's Disease Foundation/United States ; //Sangamo Therapeutics/ ; },
mesh = {Animals ; Endocytosis ; Endosomes/metabolism ; *Immunity, Innate/drug effects ; Lipids/chemistry ; Lipopolysaccharides/pharmacology ; Macrophages/cytology/drug effects/metabolism ; Mice ; Mice, Transgenic ; Nanoparticles/*chemistry ; RAW 264.7 Cells ; RNA, Messenger/chemistry/*metabolism ; Toll-Like Receptor 4/metabolism ; },
abstract = {Clinical mRNA delivery remains challenging, in large part because how physiology alters delivery in vivo remains underexplored. For example, mRNA delivered by lipid nanoparticles (LNPs) is being considered to treat inflammation, but whether inflammation itself changes delivery remains understudied. Relationships between immunity, endocytosis, and mRNA translation lead to hypothesize that toll-like receptor 4 (TLR4) activation reduced LNP-mediated mRNA delivery. Therefore, LNP uptake, endosomal escape, and mRNA translation with and without TLR4 activation are quantified. In vivo DNA barcoding is used to discover a novel LNP that delivers mRNA to Kupffer cells at clinical doses; unlike most LNPs, this LNP does not preferentially target hepatocytes. TLR4 activation blocks mRNA translation in all tested cell types, without reducing LNP uptake; inhibiting TLR4 or its downstream effector protein kinase R improved delivery. The discrepant effects of TLR4 on i) LNP uptake and ii) translation suggests TLR4 activation can "override" LNP targeting, even after mRNA is delivered into target cells. Given near-future clinical trials using mRNA to modulate inflammation, this highlights the need to understand inflammatory signaling in on- and off-target cells. More generally, this suggests an LNP which delivers mRNA to one inflammatory disease may not deliver mRNA to another.},
}
@article {pmid31741759,
year = {2019},
author = {Viborg, N and Ramskov, S and Andersen, RS and Sturm, T and Fugmann, T and Bentzen, AK and Rafa, VM and Straten, PT and Svane, IM and Met, &#xd6; and Hadrup, SR},
title = {T cell recognition of novel shared breast cancer antigens is frequently observed in peripheral blood of breast cancer patients.},
journal = {Oncoimmunology},
volume = {8},
number = {12},
pages = {e1663107},
pmid = {31741759},
issn = {2162-4011},
abstract = {Advances within cancer immunotherapy have fueled a paradigm shift in cancer treatment, resulting in increasing numbers of cancer types benefitting from novel treatment options. Despite originally being considered an immunologically silent malignancy, recent studies encourage the research of breast cancer immunogenicity to evaluate immunotherapy as a treatment strategy. However, the epitope landscape in breast cancer is minimally described, limiting the options for antigen-specific, targeted strategies. Aromatase, never in mitosis A-related kinase 3 (NEK3), protein inhibitor of activated STAT3 (PIAS3), and prolactin are known as upregulated proteins in breast cancer. In the present study, these four proteins are identified as novel T cell targets in breast cancer. From the four proteins, 147 peptides were determined to bind HLA-A*0201 and -B*0702 using a combined in silico/in vitro affinity screening. T cell recognition of all 147 peptide-HLA-A*0201/-B*0702 combinations was assessed through the use of a novel high-throughput method utilizing DNA barcode labeled multimers. T cell recognition of sequences within all four proteins was demonstrated in peripheral blood of patients, and significantly more T cell responses were detected in patients compared to healthy donors for both HLA-A*0201 and -B*0702. Notably, several of the identified responses were directed toward peptides, with a predicted low or intermediate binding affinity. This demonstrates the importance of including low-affinity binders in the search for epitopes within shared tumor associated antigens (TAAs), as these might be less subject to immune tolerance mechanisms. The study presents four novel TAAs containing multiple possible targets for immunotherapy of breast cancer.},
}
@article {pmid31740957,
year = {2020},
author = {Smirnov, A and Fishman, V and Yunusova, A and Korablev, A and Serova, I and Skryabin, BV and Rozhdestvensky, TS and Battulin, N},
title = {DNA barcoding reveals that injected transgenes are predominantly processed by homologous recombination in mouse zygote.},
journal = {Nucleic acids research},
volume = {48},
number = {2},
pages = {719-735},
pmid = {31740957},
issn = {1362-4962},
mesh = {Animals ; Animals, Genetically Modified ; DNA/*chemistry/genetics ; DNA Barcoding, Taxonomic ; *DNA Breaks, Double-Stranded ; DNA End-Joining Repair/genetics ; DNA Repair/genetics ; DNA, Cruciform/chemistry/genetics ; Homologous Recombination/*genetics ; Mice ; Transgenes/*genetics ; Zygote/growth &amp; development ; },
abstract = {Mechanisms that ensure repair of double-strand DNA breaks (DSBs) are instrumental in the integration of foreign DNA into the genome of transgenic organisms. After pronuclear microinjection, exogenous DNA is usually found as a concatemer comprising multiple co-integrated transgene copies. Here, we investigated the contribution of various DSB repair pathways to the concatemer formation. We injected mouse zygotes with a pool of linear DNA molecules carrying unique barcodes at both ends and obtained 10 transgenic embryos with 1-300 transgene copies. Sequencing the barcodes allowed us to assign relative positions to the copies in concatemers and detect recombination events that occurred during integration. Cumulative analysis of approximately 1,000 integrated copies reveals that over 80% of them underwent recombination when their linear ends were processed by synthesis-dependent strand annealing (SDSA) or double-strand break repair (DSBR). We also observed evidence of double Holliday junction (dHJ) formation and crossing over during the concatemer formations. Sequencing indels at the junctions between copies shows that at least 10% of DNA molecules introduced into the zygotes are ligated by non-homologous end joining (NHEJ). Our barcoding approach, verified with Pacific Biosciences Single Molecule Real-Time (SMRT) long-range sequencing, documents high activity of homologous recombination after DNA microinjection.},
}
@article {pmid31740838,
year = {2020},
author = {Askary, A and Sanchez-Guardado, L and Linton, JM and Chadly, DM and Budde, MW and Cai, L and Lois, C and Elowitz, MB},
title = {In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription.},
journal = {Nature biotechnology},
volume = {38},
number = {1},
pages = {66-75},
pmid = {31740838},
issn = {1546-1696},
support = {/HHMI_/Howard Hughes Medical Institute/United States ; R01 MH116508/MH/NIMH NIH HHS/United States ; T32 GM007616/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Base Pairing/*genetics ; Base Sequence ; Brain/metabolism ; Chick Embryo ; DNA Barcoding, Taxonomic/*methods ; DNA-Directed RNA Polymerases/metabolism ; *Gene Editing ; Gene Library ; HEK293 Cells ; Humans ; Lentivirus/genetics ; Mice ; Nucleotides/genetics ; Polymorphism, Single Nucleotide/genetics ; Promoter Regions, Genetic/genetics ; *Transcription, Genetic ; },
abstract = {Molecular barcoding technologies that uniquely identify single cells are hampered by limitations in barcode measurement. Readout by sequencing does not preserve the spatial organization of cells in tissues, whereas imaging methods preserve spatial structure but are less sensitive to barcode sequence. Here we introduce a system for image-based readout of short (20-base-pair) DNA barcodes. In this system, called Zombie, phage RNA polymerases transcribe engineered barcodes in fixed cells. The resulting RNA is subsequently detected by fluorescent in situ hybridization. Using competing match and mismatch probes, Zombie can accurately discriminate single-nucleotide differences in the barcodes. This method allows in situ readout of dense combinatorial barcode libraries and single-base mutations produced by CRISPR base editors without requiring barcode expression in live cells. Zombie functions across diverse contexts, including cell culture, chick embryos and adult mouse brain tissue. The ability to sensitively read out compact and diverse DNA barcodes by imaging will facilitate a broad range of barcoding and genomic recording strategies.},
}
@article {pmid31736630,
year = {2019},
author = {Canty, R and Ruzzier, E and Cronk, QC and Percy, DM},
title = {Salix transect of Europe: additional leaf beetle (Chrysomelidae) records and insights from chrysomelid DNA barcoding.},
journal = {Biodiversity data journal},
volume = {7},
number = {},
pages = {e46663},
pmid = {31736630},
issn = {1314-2828},
abstract = {Occurrence patterns of chrysomelid beetles (Coleoptera: Chrysomelidae), associated with willow (Salix spp.) at 42 sites across Europe, have previously been described. The sites form a transect from Greece (lat. 38.8 °N) to arctic Norway (lat. 69.7 °N). This paper reports additional records and the results of DNA sequencing in certain genera. Examination of further collections from the transect has added 13 species in the genera Aphthona, Chrysomela, Cryptocephalus, Epitrix, Galerucella (2 spp.), Gonioctena, Phyllotreta (2 spp.), Pachybrachis (3 spp.) and Syneta. We also report the sequencing of the DNA regions cytochrome oxidase 1 (CO1) and cytochrome B (cytB) for a number of samples in the genera Plagiodera, Chrysomela, Gonioctena, Phratora, Galerucella and Crepidodera. The cytB sequences are the first available for some of these taxa. The DNA barcoding largely confirmed previous identifications but allowed a small number of re-assignments between related species. Most notably, however, it was evident that the southernmost material (Greece and Bulgaria) of specimens, previously treated as Crepidodera aurata sens. lat., belonged to a distinctive molecular cluster. Morphological re-examination revealed these to be C. nigricoxis Allard, 1878. This is an example of how morphotaxonomy and DNA barcoding can work iteratively to refine identification. Our sequences for C. nigricoxis appear to be the first available for this taxon. Finally, there is little geographic structure evident, even in widely dispersed species.},
}
@article {pmid31736618,
year = {2019},
author = {Zlatkov, B and Huemer, P},
title = {Remarkable confusion in some Western Palearctic Clepsis leads to a revised taxonomic concept (Lepidoptera, Tortricidae).},
journal = {ZooKeys},
volume = {885},
number = {},
pages = {51-87},
pmid = {31736618},
issn = {1313-2989},
abstract = {The taxonomy of some Palearctic species of the genus Clepsis Guenée, 1845 (Lepidoptera, Tortricidae), in particular C. neglectana sensu auctt. and C. consimilana sensu auctt., is revised based on combined characters of external and internal adult morphology, including everted vesicae in male genitalia, and DNA barcodes. Clepsis striolana (Ragonot, 1879), stat. rev., C. acclivana (Zerny, 1933), C. trivia (Meyrick, 1913), stat rev., and C. xylotoma (Meyrick, 1891), stat. rev. are resurrected from synonymy with C. neglectana (Herrich-Schäffer, 1851), C. semiana (Chrétien, 1915), stat. nov. is considered as a valid species; C. eatoniana (Ragonot, 1881), stat. rev., is resurrected from synonymy with C. consimilana (Hübner, 1817), and C. razowskii Gastón, Vives &amp; Revilla, 2017, syn. nov. is synonymised with C. eatoniana.},
}
@article {pmid31736616,
year = {2019},
author = {Kolesnikova, AA and Baturina, MA and Shadrin, DM and Konakova, TN and Taskaeva, AA},
title = {New records of Lumbricidae and Collembola in anthropogenic soils of East European tundra.},
journal = {ZooKeys},
volume = {885},
number = {},
pages = {15-25},
pmid = {31736616},
issn = {1313-2989},
abstract = {The terrestrial environment of the East European tundra consists of a mosaic of habitat types. In addition to the natural habitat diversity, various human-influenced types may occur. In the town of Vorkuta, Komi Republic, Russia the manure-enriched soils near hydrogen sulfide springs were observed. This site represents an unusually nutrient-rich location with considerable development of organic soils, in contrast to the naturally forming soils in East European tundra which are typically thin and nutrient poor. In these organic soils, two species of Lumbricidae and two species of Collembola previously not recorded from the natural ecosystems in the study area of research territory were found. One earthworm species, Dendrodrilus rubidus tenuis, is likely to have been introduced. The presence of the three other species (Eiseniella tetraedra, Folsomia fimetaria, and Proisotoma minuta) is quite natural in East European tundra and such anthropogenic soils with high organic content may be a good habitat for them.},
}
@article {pmid31736615,
year = {2019},
author = {Sutcharit, C and Naggs, F and Ablett, J and Sang, PV and Luong Van Hao, and Panha, S},
title = {Notes on the sinistral helicoid snail Bertia cambojiensis (Reeve, 1860) from Vietnam (Eupulmonata, Dyakiidae).},
journal = {ZooKeys},
volume = {885},
number = {},
pages = {1-14},
pmid = {31736615},
issn = {1313-2989},
abstract = {Since the time of the original description there have been no precise locality records in Cambodia of Bertia cambojiensis (Reeve, 1860) and it was believed to be extinct. In 2012, a joint Natural History Museum survey with Vietnamese colleagues rediscovered living populations of this huge sinistral helicoid snail in a protected area of southern Vietnam. The genitalia and radula morphology are re-assessed and type specimens of all recognised congeners are figured herein. The unique morphological characters of this species are a small and simple penis, well-developed amatorial organ complex that incorporates four amatorial organ ducts, a short gametolytic organ complex and spiked papilla, and radula morphology with unicuspid teeth. The type locality of B. cambojiensis, which has been contentious, is determined here to be in the vicinity of 'Brelum', Vietnam, near the border with Cambodia. In addition, the nucleotide sequences of barcoding genes COI, 16SrRNA and 28S fragments were provided for further comparison.},
}
@article {pmid31735764,
year = {2020},
author = {Matsuo, H and Hirose, T and Mokudai, T and Nonaka, K and Niwano, Y and Sunazuka, T and Takahashi, Y and Ōmura, S and Nakashima, T},
title = {Absolute structure and anti-oxidative activity of chaetochiversin C isolated from fungal strain Neocosmospora sp. FKI-7792 by physicochemical screening.},
journal = {The Journal of general and applied microbiology},
volume = {66},
number = {3},
pages = {181-187},
doi = {10.2323/jgam.2019.06.001},
pmid = {31735764},
issn = {1349-8037},
mesh = {Antioxidants/*chemistry/isolation &amp; purification/*pharmacology ; Hypocreales/*chemistry ; Magnetic Resonance Spectroscopy ; Molecular Structure ; Reactive Oxygen Species/metabolism ; Singlet Oxygen/metabolism ; Stereoisomerism ; },
abstract = {A new chaetochiversin analog, designated chaetochiversin C (1), was discovered from a cultured broth of fungal strain FKI-7792 by physicochemical screening. This strain was identified as a member of genus Neocosmospora based on morphology and DNA barcoding. The partially relative configuration of 1 was determined by [13]C-NMR chemical shifts of the acetonide analog of 1. The absolute configuration was determined using an advanced Mosher's method. Compound 1 was assessed for anti-tumor, anti-microbial, and anti-malarial activities, and its ability to scavenge or quench reactive oxygen species (ROS), such as superoxide anion radicals, hydroxy radicals and singlet oxygen ([1]O2). Compound 1 showed a quenching effect on [1]O2.},
}
@article {pmid31732817,
year = {2019},
author = {Robin, A and Pradier, C and Sanguin, H and Mahé, F and Lambais, GR and de Araujo Pereira, AP and Germon, A and Santana, MC and Tisseyre, P and Pablo, AL and Heuillard, P and Sauvadet, M and Bouillet, JP and Andreote, FD and Plassard, C and de Moraes Gonçalves, JL and Cardoso, EJBN and Laclau, JP and Hinsinger, P and Jourdan, C},
title = {How deep can ectomycorrhizas go? A case study on Pisolithus down to 4 meters in a Brazilian eucalypt plantation.},
journal = {Mycorrhiza},
volume = {29},
number = {6},
pages = {637-648},
pmid = {31732817},
issn = {1432-1890},
mesh = {*Basidiomycota ; Brazil ; *Mycorrhizae ; Plant Roots ; Trees ; },
abstract = {Despite the strong ecological importance of ectomycorrhizal (ECM) fungi, their vertical distribution remains poorly understood. To our knowledge, ECM structures associated with trees have never been reported in depths below 2 meters. In this study, fine roots and ECM root tips were sampled down to 4-m depth during the digging of two independent pits differing by their water availability. A meta-barcoding approach based on Illumina sequencing of internal transcribed spacers (ITS1 and ITS2) was carried out on DNA extracted from root samples (fine roots and ECM root tips separately). ECM fungi dominated the root-associated fungal community, with more than 90% of sequences assigned to the genus Pisolithus. The morphological and barcoding results demonstrated, for the first time, the presence of ECM symbiosis down to 4-m. The molecular diversity of Pisolithus spp. was strongly dependent on depth, with soil pH and soil water content as primary drivers of the Pisolithus spp. structure. Altogether, our results highlight the importance to consider the ECM symbiosis in deep soil layers to improve our understanding of fine roots functioning in tropical soils.},
}
@article {pmid31730669,
year = {2019},
author = {Harvey, NR and Albury, CL and Stuart, S and Benton, MC and Eccles, DA and Connell, JR and Sutherland, HG and Allcock, RJN and Lea, RA and Haupt, LM and Griffiths, LR},
title = {Ion torrent high throughput mitochondrial genome sequencing (HTMGS).},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0224847},
pmid = {31730669},
issn = {1932-6203},
mesh = {DNA, Mitochondrial/genetics ; Genetic Variation ; *Genome, Mitochondrial ; *High-Throughput Nucleotide Sequencing ; Humans ; Quality Control ; },
abstract = {The implementation and popularity of next generation sequencing (NGS) has led to the development of various rapid whole mitochondrial genome sequencing techniques. We summarise an efficient and cost-effective NGS approach for mitochondrial genomic DNA in humans using the Ion Torrent platform, and further discuss our bioinformatics pipeline for streamlined variant calling. Ion 316 chips were utilised with the Ion Torrent semi-conductor platform Personal Genome Machine (PGM) to perform tandem sequencing of mitochondrial genomes from the core pedigree (n = 315) of the Norfolk Island Health Study. Key improvements from commercial methods focus on the initial PCR step, which currently requires extensive optimisation to ensure the accurate and reproducible elongation of each section of the complete mitochondrial genome. Dual-platform barcodes were incorporated into our protocol thereby extending its potential application onto Illumina-based systems. Our bioinformatics pipeline consists of a modified version of GATK best practices tailored for mitochondrial genomic data. When compared with current commercial methods, our method, termed high throughput mitochondrial genome sequencing (HTMGS), allows high multiplexing of samples and the use of alternate library preparation reagents at a lower cost per sample (~1.7 times) when compared to current commercial methodologies. Our HTMGS methodology also provides robust mitochondrial sequencing data (>450X average coverage) that can be applied and modified to suit various study designs. On average, we were able to identify ~30 variants per sample with 572 variants observed across 315 samples. We have developed a high throughput sequencing and analysis method targeting complete mitochondrial genomes; with the potential to be platform agnostic with analysis options that adhere to current best practices.},
}
@article {pmid31729573,
year = {2019},
author = {Locke, SA and Caffara, M and Barčák, D and Sonko, P and Tedesco, P and Fioravanti, ML and Li, W},
title = {A new species of Clinostomum Leidy, 1856 in East Asia based on genomic and morphological data.},
journal = {Parasitology research},
volume = {118},
number = {12},
pages = {3253-3265},
pmid = {31729573},
issn = {1432-1955},
mesh = {Animals ; Asia ; DNA, Ribosomal/genetics ; Fishes/parasitology ; Fresh Water/parasitology ; Genome, Mitochondrial/genetics ; Metacercariae/anatomy &amp; histology/classification/genetics ; *Phylogeny ; Species Specificity ; Trematoda/anatomy &amp; histology/*classification/genetics ; },
abstract = {Metacercariae of Clinostomum Leidy, 1856 are frequently encountered in freshwater fish. In 2015, a provisional species of Clinostomum in People's Republic of China (PRC) was distinguished from C. complanatum (Rudolphi, 1819) in Europe based on divergent cytochrome c oxidase I (CO1). However, in subsequent studies in East Asia, the same divergent CO1 genotype was identified as C. complanatum. These matching sequences suggest that either the provisional East Asian species was incorrectly distinguished from C. complanatum in 2015 or that C. complanatum in East Asia was misidentified in later studies. We tested these alternatives by sequencing the mitochondrial genome of C. complanatum in Italy, which was 5.7% divergent from a previously published sequence from Clinostomum in PRC, including differences in 80 of 3390 (2.4%) translated amino acids. Partial CO1 sequences of specimens from PRC and those from Italy, Romania, and Turkey also each formed reciprocally monophyletic clades. Partial CO1 from the East Asian clade varied by mean 3.6% (range 2.4-4.8%) from C. complanatum from Italy, Romania, and Turkey; mean intra-clade CO1 variation was 0.3% (range 0-1.9%). Metacercariae from Europe and East Asia display significant morphometric variation, and data from the literature suggest morphological differences in the genital complex of adults. Although sequences of nuclear rDNA did not differ between isolates from the west and East Asia, taken together, these results lead us to describe a new species of Clinostomum.},
}
@article {pmid31728967,
year = {2020},
author = {Goytain, A and Ng, T},
title = {NanoString nCounter Technology: High-Throughput RNA Validation.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2079},
number = {},
pages = {125-139},
doi = {10.1007/978-1-4939-9904-0_10},
pmid = {31728967},
issn = {1940-6029},
mesh = {Computational Biology/methods ; Databases, Genetic ; Gene Expression Profiling/*methods ; *High-Throughput Nucleotide Sequencing/methods ; Molecular Probes ; Nucleic Acid Hybridization/*methods ; *RNA/chemistry/genetics ; *Sequence Analysis, RNA/methods ; Web Browser ; },
abstract = {NanoString nCounter is a multiplex nucleic acid hybridization technology that enables reliable and reproducible assessment of the expression of up to 800 genes or 228 gene fusions in 12 samples in a single assay. The technique works well with a variety of starting materials from fresh or formalin-fixed tissues, cell lysates or biological fluid samples. As low as 1 ng RNA input per sample is needed. In addition to gene expression, copy number variation, single nucleotide variation and chimeric RNAs can be analyzed. In this chapter, we discuss the design, setup, and performance of a NanoString-based RNA assay for gene expression or fusion transcript assessment.},
}
@article {pmid31727682,
year = {2020},
author = {Li, S and Kendall, J and Park, S and Wang, Z and Alexander, J and Moffitt, A and Ranade, N and Danyko, C and Gegenhuber, B and Fischer, S and Robinson, BD and Lepor, H and Tollkuhn, J and Gillis, J and Brouzes, E and Krasnitz, A and Levy, D and Wigler, M},
title = {Copolymerization of single-cell nucleic acids into balls of acrylamide gel.},
journal = {Genome research},
volume = {30},
number = {1},
pages = {49-61},
pmid = {31727682},
issn = {1549-5469},
support = {R01 MH113005/MH/NIMH NIH HHS/United States ; R01 CA181595/CA/NCI NIH HHS/United States ; R01 LM012736/LM/NLM NIH HHS/United States ; T32 CA148056/CA/NCI NIH HHS/United States ; U01 MH105991/MH/NIMH NIH HHS/United States ; T32 GM065094/GM/NIGMS NIH HHS/United States ; P30 CA045508/CA/NCI NIH HHS/United States ; R01 MH113628/MH/NIMH NIH HHS/United States ; },
mesh = {*Acrylamide/chemistry ; DNA ; DNA Contamination ; DNA Copy Number Variations ; Gene Dosage ; Gene Expression Profiling/methods/standards ; Gene Library ; Humans ; Neoplasms/genetics/metabolism/pathology ; *Nucleic Acids/chemistry ; Oligonucleotide Array Sequence Analysis/methods/standards ; Polymerization ; RNA ; Single-Cell Analysis/*methods/standards ; },
abstract = {We show the use of 5'-Acrydite oligonucleotides to copolymerize single-cell DNA or RNA into balls of acrylamide gel (BAGs). Combining this step with split-and-pool techniques for creating barcodes yields a method with advantages in cost and scalability, depth of coverage, ease of operation, minimal cross-contamination, and efficient use of samples. We perform DNA copy number profiling on mixtures of cell lines, nuclei from frozen prostate tumors, and biopsy washes. As applied to RNA, the method has high capture efficiency of transcripts and sufficient consistency to clearly distinguish the expression patterns of cell lines and individual nuclei from neurons dissected from the mouse brain. By using varietal tags (UMIs) to achieve sequence error correction, we show extremely low levels of cross-contamination by tracking source-specific SNVs. The method is readily modifiable, and we will discuss its adaptability and diverse applications.},
}
@article {pmid31726053,
year = {2020},
author = {Tsai, WL and Vian, L and Giudice, V and Kieltyka, J and Liu, C and Fonseca, V and Gazaniga, N and Gao, S and Kajigaya, S and Young, NS and Biancotto, A and Gadina, M},
title = {High throughput pSTAT signaling profiling by fluorescent cell barcoding and computational analysis.},
journal = {Journal of immunological methods},
volume = {477},
number = {},
pages = {112667},
pmid = {31726053},
issn = {1872-7905},
support = {Z99 AR999999/ImNIH/Intramural NIH HHS/United States ; ZIA AR041132/ImNIH/Intramural NIH HHS/United States ; ZIC AR041181/ImNIH/Intramural NIH HHS/United States ; },
mesh = {B-Lymphocytes/metabolism ; Clinical Trials as Topic ; Computational Biology/methods ; Feasibility Studies ; Flow Cytometry/*methods ; Fluorescent Dyes/chemistry ; Healthy Volunteers ; High-Throughput Screening Assays/instrumentation/*methods ; Humans ; Immunophenotyping/*methods ; Monocytes/metabolism ; Phosphoproteins/metabolism ; Reproducibility of Results ; STAT Transcription Factors/*metabolism ; Signal Transduction/*immunology ; Software ; Staining and Labeling/methods ; T-Lymphocytes/metabolism ; },
abstract = {Fluorescent cell barcoding (FCB) is a multiplexing technique for high-throughput flow cytometry (FCM). Although powerful in minimizing staining variability, it remains a subjective FCM technique because of inter-operator variability and differences in data analysis. FCB was implemented by combining two-dye barcoding (DyLight 350 plus Pacific Orange) with five-color surface marker antibody and intracellular staining for phosphoprotein signaling analysis. We proposed a robust method to measure intra- and inter-assay variability of FCB in T/B cells and monocytes by combining range and ratio of variability to standard statistical analyses. Data analysis was carried out by conventional and semi-automated workflows and built with R software. Results obtained from both analyses were compared to assess feasibility and reproducibility of FCB data analysis by machine-learning methods. Our results showed efficient FCB using DyLight 350 and Pacific Orange at concentrations of 0, 15 or 30, and 250 μg/mL, and a high reproducibility of FCB in combination with surface marker and intracellular antibodies. Inter-operator variability was minimized by adding an internal control bridged across matrices used as rejection criterion if significant differences were present between runs. Computational workflows showed comparable results to conventional gating strategies. FCB can be used to study phosphoprotein signaling in T/B cells and monocytes with high reproducibility across operators, and the addition of bridge internal controls can further minimize inter-operator variability. This FCB protocol, which has high throughput analysis and low intra- and inter-assay variability, can be a powerful tool for clinical trial studies. Moreover, FCB data can be reliably analyzed using computational software.},
}
@article {pmid31723337,
year = {2019},
author = {Wang, XC and Liu, TZ and Chen, SL and Li, Y and Zhuang, WY},
title = {A four-locus phylogeny of rib-stiped cupulate species of Helvella (Helvellaceae, Pezizales) with discovery of three new species.},
journal = {MycoKeys},
volume = {60},
number = {},
pages = {45-67},
pmid = {31723337},
issn = {1314-4049},
abstract = {Helvella species are ascomycetous macrofungi with saddle-shaped or cupulate apothecia. They are distributed worldwide and play an important ecological role as ectomycorrhizal symbionts. A recent multi-locus phylogenetic study of the genus suggested that the cupulate group of Helvella was in need of comprehensive revision. In this study, all the specimens of cupulate Helvella sensu lato with ribbed stipes deposited in HMAS were examined morphologically and molecularly. A four-locus phylogeny was reconstructed using partial sequences of the heat shock protein 90, nuclear rDNA internal transcribed spacer region 2, nuclear large subunit ribosomal DNA and translation elongation factor 1-α genes. Three clades were revealed in Helvella sensu stricto. Twenty species were included in the analysis, of which 13 are distributed in China. Three new species, H. acetabuloides, H. sichuanensis and H. tianshanensis, are described and illustrated in detail. A neotype was designated for H. taiyuanensis. Helvella calycina is a new record for China, while Dissingia leucomelaena should be excluded from Chinese mycota. Hsp90 and ITS2 are recommended as useful supplementary barcodes for species identifications of the genus.},
}
@article {pmid31723263,
year = {2019},
author = {Nguyen Ba, AN and Cvijović, I and Rojas Echenique, JI and Lawrence, KR and Rego-Costa, A and Liu, X and Levy, SF and Desai, MM},
title = {High-resolution lineage tracking reveals travelling wave of adaptation in laboratory yeast.},
journal = {Nature},
volume = {575},
number = {7783},
pages = {494-499},
pmid = {31723263},
issn = {1476-4687},
support = {R01 HG008354/HG/NHGRI NIH HHS/United States ; HG008354/NH/NIH HHS/United States ; HL127522/NH/NIH HHS/United States ; R01 GM104239/GM/NIGMS NIH HHS/United States ; U01 HL127522/HL/NHLBI NIH HHS/United States ; GM104239/NH/NIH HHS/United States ; },
mesh = {Adaptation, Physiological/*genetics ; *Cell Lineage ; Clone Cells/cytology/metabolism ; DNA Barcoding, Taxonomic ; *Evolution, Molecular ; Genetic Fitness/genetics ; *Laboratories ; *Mutation ; Saccharomyces cerevisiae/*cytology/*genetics ; },
abstract = {In rapidly adapting asexual populations, including many microbial pathogens and viruses, numerous mutant lineages often compete for dominance within the population[1-5]. These complex evolutionary dynamics determine the outcomes of adaptation, but have been difficult to observe directly. Previous studies have used whole-genome sequencing to follow molecular adaptation[6-10]; however, these methods have limited resolution in microbial populations. Here we introduce a renewable barcoding system to observe evolutionary dynamics at high resolution in laboratory budding yeast. We find nested patterns of interference and hitchhiking even at low frequencies. These events are driven by the continuous appearance of new mutations that modify the fates of existing lineages before they reach substantial frequencies. We observe how the distribution of fitness within the population changes over time, and find a travelling wave of adaptation that has been predicted by theory[11-17]. We show that clonal competition creates a dynamical 'rich-get-richer' effect: fitness advantages that are acquired early in evolution drive clonal expansions, which increase the chances of acquiring future mutations. However, less-fit lineages also routinely leapfrog over strains of higher fitness. Our results demonstrate that this combination of factors, which is not accounted for in existing models of evolutionary dynamics, is critical in determining the rate, predictability and molecular basis of adaptation.},
}
@article {pmid31720100,
year = {2019},
author = {Windsor, AM and Moore, MK and Warner, KA and Stadig, SR and Deeds, JR},
title = {Evaluation of variation within the barcode region of Cytochrome c Oxidase I (COI) for the detection of commercial Callinectes sapidus Rathbun, 1896 (blue crab) products of non-US origin.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7827},
pmid = {31720100},
issn = {2167-8359},
abstract = {Callinectes sapidus Rathbun, 1896 is a western Atlantic species with a disjointed natural geographic range from Massachusetts, USA to Venezuela (distribution area 1) and from Alagoas, Brazil to northern Argentina (distribution area 2). It is the only species of portunid crab commercially harvested in the continental United States but is also imported into the US from several Latin American countries, Venezuela and Mexico in particular. In the United States, crab products labeled as "blue crab" and "Product of the USA" may not legally contain other species of crab or C. sapidus not harvested in the United States. The present study documents nucleotide variation within the barcode region of cytochrome c oxidase I (COI) in 417 reference specimens of C. sapidus collected from throughout its natural range. The goal of this study is to determine if this variation can be utilized to detect mislabeled C. sapidus products sold in interstate commerce by comparing genetic signatures in reference specimens to those observed in commercial crabmeat labeled as "Product of the USA" and "Product of Venezuela." In reference specimens, we observed high levels of genetic variation in the barcode region. However, three lineages were consistently observed with significant pairwise F st values between the lineages. Lineage 1 was observed throughout the natural geographic range but predominated in the continental US and was the only lineage observed in the major crabmeat-producing states (MD, LA, VA, NC). Lineage 2 primarily occurred in the Caribbean region of distribution area 1 but was also infrequently encountered in the South Atlantic Bight region of the US coast. Finally, Lineage 3 was only observed in Brazilian waters and had the lowest haplotype and nucleotide diversity values. Lineages 1 and 2 were separated by a mean pairwise distance (p-distance) of 3.15%, whereas Lineage 3 had a mean p-distance of 2.55% and 1.35% to Lineages 1 and 2, respectively. Within lineage mean p-distances were 0.45%, 0.19%, and 0.07% for Lineages 1, 2, and 3, respectively. Among all vouchered reference specimens collected from the continental United States, Mexico, Puerto Rico, and Venezuela, we identified 22 phylogenetically informative sites that drive observed lineage divergences. Haplotypes identified from barcode COI sequences from commercial C. sapidus products labeled as originating from the US all aligned with haplotypes from Lineage 1 reference specimens and haplotypes from commercial products labeled as originating from Venezuela all aligned with Lineage 2, suggesting that these lineages may be useful for indicating whether products originate from the continental US or are imported when package labeling is in question.},
}
@article {pmid31720096,
year = {2019},
author = {Aruge, S and Batool, H and Khan, FM and Fakhar-I-Abbas, and Janjua, S},
title = {A pilot study-genetic diversity and population structure of snow leopards of Gilgit-Baltistan, Pakistan, using molecular techniques.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7672},
pmid = {31720096},
issn = {2167-8359},
abstract = {BACKGROUND: The Hindu Kush and Karakoram mountain ranges in Pakistan's northern areas are a natural habitat of the snow leopard (Panthera uncia syn. Uncia uncia) but the ecological studies on this animal are scarce since it is human shy by nature and lives in difficult mountainous tracts. The pilot study is conducted to exploit the genetic diversity and population structure of the snow leopard in this selected natural habitat of the member of the wildcat family in Pakistan.<br><br>METHOD: About 50 putative scat samples of snow leopard from five localities of Gilgit-Baltistan (Pakistan) along with a control sample of zoo maintained male snow leopard were collected for comparison. Significant quality and quantity of genomic DNA was extracted from scat samples using combined Zhang-phenol-chloroform method and successful amplification of cytochrome c oxidase I gene (190 bp) using mini-barcode primers, seven simple sequence repeats (SSR) markers and Y-linked AMELY gene (200 bp) was done.<br><br>RESULTS: Cytochrome c oxidase I gene sequencing suggested that 33/50 (66%) scat samples were of snow leopard. AMELY primer suggested that out of 33 amplified samples, 21 (63.63%) scats were from male and 12 (36.36%) from female leopards. Through successful amplification of DNA of 25 out of 33 (75.75%) scat samples using SSR markers, a total of 68 alleles on seven SSR loci were identified, showing low heterozygosity, while high gene flow between population.<br><br>DISCUSSION: The low gene flow rate among the population results in low genetic diversity causing decreased diversification. This affects the adaptability to climatic changes, thus ultimately resulting in decreased population size of the species.},
}
@article {pmid31719502,
year = {2019},
author = {Orel, OV and Semenchenko, AA},
title = {Morphological description and DNA barcodes of adult males of Tanytarsus heliomesonyctios Langton, 1999 (Diptera, Chironomidae) in northeast of Russia.},
journal = {Zootaxa},
volume = {4686},
number = {1},
pages = {zootaxa.4686.1.6},
doi = {10.11646/zootaxa.4686.1.6},
pmid = {31719502},
issn = {1175-5334},
mesh = {Animals ; Bayes Theorem ; Canada ; *Chironomidae ; DNA Barcoding, Taxonomic ; Female ; Male ; Norway ; Russia ; Svalbard ; },
abstract = {An illustrated morphological description of the adult males of Tanytarsus heliomesonyctios Langton, 1999, is provided for the first time. The males were found in mountain lakes Bolshoi Darpir (Momsky District of the Republic of Sakha (Yakutia)) and Momontai (Susumansky District of the Magadan Region), located in the Kolyma River basin. Females, pupae and larvae of T. heliomesonyctios was previously described from Spitsbergen, Jan Mayen (Norway) and Ellesmere Island (Arctic Canada), and considered parthenogenetic. Tanytarsus heliomesonyctios is here for the first time noted for the fauna of Russia. Comparison of DNA barcodes shows high K2P nucleotide distances (1.7%) between the sexual populations (Norway and Russia) and the parthenogenetic populations (Svalbard and Canada). In the Bayesian tree, the COI- sequences from adult males group as sister to a strongly supported clade of sequences from parthenogenetic populations. This apparently indicates a single origin of parthenogeneticity, perhaps due to extreme environmental conditions.},
}
@article {pmid31719462,
year = {2019},
author = {Hickmann, F and Moraes, T and Bianchi, FM and Corrêa, AS and Schwertner, CF},
title = {Integrating data to redescribe Euschistus taurulus Berg (Hemiptera: Pentatomidae).},
journal = {Zootaxa},
volume = {4688},
number = {1},
pages = {zootaxa.4688.1.7},
doi = {10.11646/zootaxa.4688.1.7},
pmid = {31719462},
issn = {1175-5334},
mesh = {Agriculture ; Animals ; Female ; *Heteroptera ; Male ; Phylogeny ; South America ; },
abstract = {The genus Euschistus Dallas includes 67 species restricted to the New World, and several species are registered on cultivated plants in the Nearctic and Neotropical regions. In South America, most Euschistus species are completely overlooked due to the lack of information to allow accurate identification. Here, we redescribed Euschistus taurulus Berg, including for the first time, characterization of the internal and external genitalia of both sexes. We also report original information on bionomics, review and update information on geographical distribution and host plants records. Additionally, we provide DNA barcoding sequences for E. taurulus and three other morphologically similar key-agriculture pest species in South America: Euschistus heros (Fabricius), Dichelops melacanthus (Dallas), and Dichelops furcatus (Fabricius). We discuss means for correct identification of E. taurulus and its phylogenetic position within Euschistus and other similar stink bugs; the potential economic importance of the E. taurulus is also addressed.},
}
@article {pmid31719427,
year = {2019},
author = {Hendrixson, BE},
title = {A new species of Aphonopelma (Araneae: Mygalomorphae: Theraphosidae) from the Madrean pine-oak woodlands of northeastern Sonora, Mexico.},
journal = {Zootaxa},
volume = {4688},
number = {4},
pages = {zootaxa.4688.4.4},
doi = {10.11646/zootaxa.4688.4.4},
pmid = {31719427},
issn = {1175-5334},
mesh = {Animals ; Arizona ; Forests ; Islands ; Mexico ; New Mexico ; *Quercus ; *Spiders ; },
abstract = {The tarantula spider genus Aphonopelma Pocock, 1901 has received considerable attention in recent years but the group's diversity remains poorly understood in Mexico, particularly in the pine-oak woodlands of the Sierra Madre Occidental and associated Madrean "Sky Islands". A pair of tarantulas discovered from an unsampled region in the Sierra de Bacadéhuachi (the westernmost range of the Sierra Madre Occidental) in northeastern Sonora was found to be closely related to four species from the Madrean "Sky Islands" in Arizona and New Mexico. An integrative approach for delimiting species (incorporating data from molecular phylogenetics, morphology, distributions, and breeding periods) suggests that the specimens from Sierra de Bacadéhuachi belong to an undescribed species that is herein named Aphonopelma bacadehuachi sp. nov. This new species adds to our knowledge of an increasingly diverse assemblage of Aphonopelma from the Madrean Pine-Oak Woodlands Hotspot. Collaborations between Mexican and American researchers are needed to accelerate discovery and description of the group's remaining diversity, particularly in light of the many threats facing the ecoregion including habitat degradation and climate change.},
}
@article {pmid31719402,
year = {2019},
author = {Li, D and Liu, H and Xu, X},
title = {Three new species of the primitively segmented spiders from Mt Yuelu, Hunan, China (Mesothelae, Liphistiidae).},
journal = {Zootaxa},
volume = {4691},
number = {2},
pages = {zootaxa.4691.2.3},
doi = {10.11646/zootaxa.4691.2.3},
pmid = {31719402},
issn = {1175-5334},
mesh = {Animals ; China ; DNA ; Female ; Male ; *Spiders ; },
abstract = {We diagnose and describe two Songthela and one Vinathela species of the primitively segmented spiders, Liphistiidae, as new to science based on morphological characters and molecular data: Songthela pyriformis sp. nov. (male, female), Songthela shuyuan sp. nov. (male, female), Vinathela nenglianggu sp. nov. (male, female), which were collected at Mt Yuelu in Changsha, Hunan Province, China. To facilitate future identification of our species, we also provide the GenBank accession numbers of the DNA barcode gene, cytochrome c oxidase subunit I (COI) for all type specimens and the evidence of genetic distances based on COI for three new species.},
}
@article {pmid31719394,
year = {2019},
author = {Yu, T and Arita, Y and Kallies, A and Wang, M},
title = {Three new species of the genus Paradoxecia Hampson, 1919 (Lepidoptera: Sesiidae) from China.},
journal = {Zootaxa},
volume = {4691},
number = {3},
pages = {zootaxa.4691.3.6},
doi = {10.11646/zootaxa.4691.3.6},
pmid = {31719394},
issn = {1175-5334},
mesh = {Animals ; China ; *Lepidoptera ; Male ; *Moths ; },
abstract = {Three new species of the genus Paradoxecia Hampson, 1919 (Lepidoptera: Sesiidae) are described from China: Paradoxecia kishidai Yu Arita sp. nov., Paradoxecia polyzona Yu Kallies sp. nov. and Paradoxecia beibengensis Yu Kallies sp. nov. Illustrations of the holotypes and the male genitalia are provided along with a key to all currently known species of the genus. DNA barcodes of the new species are deposited in Genbank.},
}
@article {pmid31719389,
year = {2019},
author = {Feng, W and Zhuang, J and Yu, H},
title = {Sycacantha Diakonoff, 1959 from China, with the descriptions of three new species (Lepidoptera: Tortricidae: Olethreutinae).},
journal = {Zootaxa},
volume = {4691},
number = {3},
pages = {zootaxa.4691.3.1},
doi = {10.11646/zootaxa.4691.3.1},
pmid = {31719389},
issn = {1175-5334},
mesh = {Animals ; China ; Genitalia ; Genitalia, Male ; *Lepidoptera ; Male ; *Moths ; },
abstract = {Nine species of Sycacantha Diakonoff, 1959 are recorded from China. Among them, three are described as new: S. typicusivalva, sp. nov., S. camerata, sp. nov., and S. decursiva, sp. nov. Two new combinations are proposed based on DNA barcodes and characters of the male genitalia: S. diserta (Meyrick, 1909), comb. nov., and Phaecasiophora obtundana (Kuznetzov, 1988), comb. nov. Sycacantha complicitana (Walker, 1863) and S. catharia Diakonoff, 1973 are newly recorded from China. Photographs of adults and genitalia of the new species and new combinations are provided, and a key to the species based on genitalia is given.},
}
@article {pmid31719381,
year = {2019},
author = {Chávez, G and Pradel, R and Catenazzi, A},
title = {Integrative taxonomy reveals first country record of Hyalinobatrachium mondolfii Señaris and Ayarzagüena 2001, and distribution range extensions for Cochranella nola Harvey 1996, and Rulyrana spiculata Duellman 1976 (Anura: Centrolenidae) in Peru.},
journal = {Zootaxa},
volume = {4691},
number = {5},
pages = {zootaxa.4691.5.7},
doi = {10.11646/zootaxa.4691.5.7},
pmid = {31719381},
issn = {1175-5334},
mesh = {Animals ; *Anura ; Bolivia ; Peru ; Phylogeny ; RNA, Ribosomal, 16S ; },
abstract = {We used an integrative taxonomy approach to investigate the taxonomic identity of several populations of glassfrogs from Peru, which are notoriously challenging to identify due to their overall similarity in morphology and coloration. We relied on comparisons of morphology, bioacoustics, and partial fragments of 16S rRNA DNA sequences. We report for the first time the presence of Hyalinobatrachium mondolfii in Peru, being this the southernmost locality known for the species. Likewise, we update and extend the distribution ranges of Rulyrana spiculata and Cochranella nola in the Andes of Peru, provide a 16S sequence of a topotype of R. spiculata, and confirm its presence in Bolivia. For all three species, we increase the current knowledge on their geographic distribution and genetic and phenotypic variation.},
}
@article {pmid31719351,
year = {2019},
author = {Volponi, MAS},
title = {A new species of spectacular spider wasp mimic from Thailand is the first representative of the genus Melanosphecia Le Cerf 1916 (Lepidoptera: Sesiidae: Osminiini) to be filmed in the wild.},
journal = {Zootaxa},
volume = {4695},
number = {3},
pages = {zootaxa.4695.3.4},
doi = {10.11646/zootaxa.4695.3.4},
pmid = {31719351},
issn = {1175-5334},
mesh = {Animals ; Ecosystem ; *Moths ; Thailand ; *Wasps ; },
abstract = {A metallic blue, new species of clearwing moth from Thailand is described and shown on video. With its spectacular colouration, long hind legs and an incredible illusion of a wasp-waist, complemented by behavioural imitations, this sesiid is a striking spider wasp mimic. Notes on possible mimicry models, behaviour and conditions of occurrence are given. COI DNA barcode sequence is provided. This is the first country record of Melanosphecia Le Cerf 1916 for Thailand and the first representative of this genus to be filmed in its natural habitat.},
}
@article {pmid31719345,
year = {2019},
author = {Xue, G and Ikari, E and Inayoshi, Y and Li, M},
title = {Hasora mavis Evans, 1934 syn. n. is confirmed to be the female of H. leucospila leucospila (Mabille, 1891) (Hesperiidae, Coeliadinae) by DNA barcoding.},
journal = {Zootaxa},
volume = {4695},
number = {4},
pages = {zootaxa.4695.4.7},
doi = {10.11646/zootaxa.4695.4.7},
pmid = {31719345},
issn = {1175-5334},
mesh = {Animals ; *Butterflies/genetics ; *DNA Barcoding, Taxonomic ; Female ; },
abstract = {Based upon the comparison of the 649 bp COI gene sequences, Hasora mavis Evans, 1934 is proved to be the female of a sexually dimorphic species, H. leucospila leucospila (Mabille, 1891), and thus treated as a junior subjective synonym of the latter.},
}
@article {pmid31719336,
year = {2019},
author = {Čiampor, FJ and Linský, M and Čiamporová-Zaťovičová, Z},
title = {Ictelmis, a new riffle beetle genus from Ecuador (Coleoptera: Elmidae).},
journal = {Zootaxa},
volume = {4695},
number = {5},
pages = {zootaxa.4695.5.5},
doi = {10.11646/zootaxa.4695.5.5},
pmid = {31719336},
issn = {1175-5334},
mesh = {Animals ; *Coleoptera ; Ecuador ; },
abstract = {A new minute riffle beetle genus Ictelmis gen. nov. and the type species Ictelmis martae sp. nov. are described from Ecuador. The description is supported by characteristic morphological features and DNA barcoding data, drawings and habitus photographs are provided. Based on molecular data and morphology it is suggested that Ictelmis is closely related with Onychelmis Hinton, and Notelmis Hinton.},
}
@article {pmid31719322,
year = {2019},
author = {Piraonapicha, K and Sangpradub, N},
title = {Description of nymphs and female subimago of Sparsorythus multilabeculatus Sroka Soldán, 2008 (Ephemeroptera: Tricorythidae) associated with male imago based on DNA sequence data.},
journal = {Zootaxa},
volume = {4695},
number = {6},
pages = {zootaxa.4695.6.1},
doi = {10.11646/zootaxa.4695.6.1},
pmid = {31719322},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures ; Animals ; Base Sequence ; *Ephemeroptera ; Female ; Male ; Phylogeny ; Thailand ; Vietnam ; },
abstract = {Sparsorythus is a genus of Tricorythidae from the Oriental Region. Sparsorythus multilabeculatus Sroka Soldán, 2008 was described based on a male imago from Vietnam. Unknown nymphs and female subimagines of Sparsorythus and male imagines of S. multilabeculatus were collected from Thap Lan National Park, Khon Buri District, Nakhon Ratchasima Province, Thailand. Nymphs and female subimagines of Sparsorythus were associated with male imagines of S. multilabeculatus by analyzing sequences from the DNA barcoding region of the mitochrondrial gene cytochrome oxidase I. Phylogenetic analysis based on Maximum Likelihood indicated that all unknown specimens are conspecific with male imagines of S. multilabeculatus (bootstrap 100% and genetic distance 0-0.004). Male and female nymphs, female subimago and egg are described for the first time. Nymphs each bear a medial emargination on the hypopharynx, one bristle-like process at the base of the left prostheca, and a bifurcate rudimentary gill on abdominal segment VII. The male usually has smudges and light blotches on its forewings; the penis extends to the basal segment of the forceps and reaches to approximately 1/3 of the second segment of the forceps. Forewings of the female subimago have dark colour over more than half of the basal area, and the distal portion of each wing is translucent. The egg has a rounded pole; the polar cap covers approximately 1/4 of the surface; and the surface is covered with hexagonal structures.},
}
@article {pmid31717798,
year = {2019},
author = {Zhan, Z and Li, J and Xu, K},
title = {Ciliate Environmental Diversity Can Be Underestimated by the V4 Region of SSU rDNA: Insights from Species Delimitation and Multilocus Phylogeny of Pseudokeronopsis (Protist, Ciliophora).},
journal = {Microorganisms},
volume = {7},
number = {11},
pages = {},
pmid = {31717798},
issn = {2076-2607},
support = {41876171, 41476144 and 41406171//National Natural Science Foundation of China/ ; },
abstract = {Metabarcoding and high-throughput sequencing methods have greatly improved our understanding of protist diversity. Although the V4 region of small subunit ribosomal DNA (SSU-V4 rDNA) is the most widely used marker in DNA metabarcoding of eukaryotic microorganisms, doubts have recently been raised about its suitability. Here, using the widely distributed ciliate genus Pseudokeronopsis as an example, we assessed the potential of SSU-V4 rDNA and four other nuclear and mitochondrial markers for species delimitation and phylogenetic reconstruction. Our studies revealed that SSU-V4 rDNA is too conservative to distinguish species, and a threshold of 97% and 99% sequence similarity detected only one and three OTUs, respectively, from seven species. On the basis of the comparative analysis of the present and previously published data, we proposed the multilocus marker including the nuclear 5.8S rDNA combining the internal transcribed spacer regions (ITS1-5.8S-ITS2) and the hypervariable D2 region of large subunit rDNA (LSU-D2) as an ideal barcode rather than the mitochondrial cytochrome c oxidase subunit 1 gene, and the ITS1-5.8S-ITS2 as a candidate metabarcoding marker for ciliates. Furthermore, the compensating base change and tree-based criteria of ITS2 and LSU-D2 were useful in complementing the DNA barcoding and metabarcoding methods by giving second structure and phylogenetic evidence.},
}
@article {pmid31717238,
year = {2019},
author = {Wanke, D and Hausmann, A and Rajaei, H},
title = {An integrative taxonomic revision of the genus Triphosa Stephens, 1829 (Geometridae: Larentiinae) in the Middle East and Central Asia, with description of two new species.},
journal = {Zootaxa},
volume = {4603},
number = {1},
pages = {zootaxa.4603.1.2},
doi = {10.11646/zootaxa.4603.1.2},
pmid = {31717238},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Genitalia ; Middle East ; *Moths ; Wings, Animal ; },
abstract = {Western Palaearctic species of the genus Triphosa Stephens, 1829 are revised with focus on the Middle East and Central Asia. The analysis is based on the morphological examination (wing pattern and genitalia) of the type series of most species, as well as of large series of additional material. Additionally, DNA barcode data were used as an extra line of information. As result, Triphosa agnata Le Cerf, 1918 syn. n. is synonymized with T. sabaudiata (Duponchel, 1830), the taxonomy of the enigmatic Triphosa taochata Lederer, 1870 is clarified, and two species are described as new to science: T. silviae sp. n. and T. lecerfi sp. n.. Hydria ravulata (Staudinger, 1892) comb. rev., is transferred from Triphosa to the genus Hydria. Lectotypes are designated for Triphosa taochata and Hydria ravulata. Wing pattern, genitalia and diagnostic characters of all examined species are illustrated and the distribution data shown on the map.},
}
@article {pmid31717234,
year = {2019},
author = {Britz, R and Anoop, VK and Dahanukar, N and Raghavan, R},
title = {The subterranean Aenigmachanna gollum, a new genus and species of snakehead (Teleostei: Channidae) from Kerala, South India.},
journal = {Zootaxa},
volume = {4603},
number = {2},
pages = {zootaxa.4603.2.10},
doi = {10.11646/zootaxa.4603.2.10},
pmid = {31717234},
issn = {1175-5334},
mesh = {Animals ; *Elasmobranchii ; Eye ; *Fishes ; Head ; India ; },
abstract = {Aenigmachanna gollum, new genus and species, is described from Kerala, South India. It is the first subterranean species of the family Channidae. It has numerous derived and unique characters, separating it from both the Asian Channa Scopoli and the African Parachanna Teugels Daget. Uniquely among channids, A. gollum has a very slender (maximum body depth only 11.1-11.3% SL), eel-like body (head length 20.8-21.6% SL), large mouth (jaw length 60.4-61.1 % HL), 43-44 anal-fin rays, 83-85 scales in a lateral series, an unusual colour pattern and it lacks pored lateral-line scales on the body and body buoyancy. In addition, it is distinguished by its DNA barcode sequence, which is 15.8-24.2% divergent from other species of the family Channidae. Morphological modifications usually associated with a subterranean life, such as reduction of eyes and enhancement of non-visual senses (taste, smell, mechanosensory systems) are absent in A. gollum. However, it shares with subterranean fishes a slight reduction of its pigmentation in comparison to epigean channids.},
}
@article {pmid31717218,
year = {2019},
author = {Zhao, X and Yao, Z and Song, Y and Li, S},
title = {Two new species of the spider genus Belisana Thorell (Araneae: Pholcidae) from Xishuangbanna, Yunnan, China.},
journal = {Zootaxa},
volume = {4603},
number = {3},
pages = {zootaxa.4603.3.8},
doi = {10.11646/zootaxa.4603.3.8},
pmid = {31717218},
issn = {1175-5334},
mesh = {Animals ; China ; Female ; Male ; *Spiders ; },
abstract = {Two new species of the spider genus Belisana Thorell, 1898 are described based on material collected in Xishuangbanna, Yunnan, China: Belisana menghai Yao Li sp. nov. (male, female) and Belisana xishuangbanna Yao Li sp. nov. (male), bringing the total Chinese Belisana fauna to 41 species. The DNA barcode COI of B. menghai Yao Li sp. nov. is documented. All material studied is deposited in the Institute of Zoology, Chinese Academy of Sciences (IZCAS) in Beijing, China.},
}
@article {pmid31717204,
year = {2019},
author = {Pereira, CM and Arévalo-Maldonado, HA and Triberti, P and Brito, R and Isaias, RMS and Gonçalves, GL and Moreira, GRP},
title = {Vallissiana universitaria (Lepidoptera: Gracillariidae): a new genus and species of leaf-mining moth associated with Erythroxylum (Erythroxylaceae) in the Atlantic Forest of Brazil.},
journal = {Zootaxa},
volume = {4604},
number = {1},
pages = {zootaxa.4604.1.5},
doi = {10.11646/zootaxa.4604.1.5},
pmid = {31717204},
issn = {1175-5334},
mesh = {Animals ; Brazil ; *Erythroxylaceae ; Forests ; Larva ; *Lepidoptera ; *Moths ; },
abstract = {Vallissiana universitaria Pereira Arévalo, a new genus and species of leaf-miner moth (Gracillariidae: Gracillariinae) is described and illustrated with the aid of optical and scanning electron microscopy, including adults, larva, pupa and the mine. Its monophyletic status is confirmed within the subfamily based on a DNA barcode CoI tree. The immature stages are associated with Erythroxylum argentinum O. E. Schulz (Erythroxylaceae) and four larval instars are found, all forming a round blotch mine from the beginning of ontogeny. The first two instars are sap-feeders, using only the epidermal cells, whereas the last two are tissue-feeders, mining the parenchyma cells. Pupation occurs inside the leaf mine within a flimsy, silk-made cocoon. This is the third endemic genus of gracillariid moths described from the Atlantic Forest of Brazil and the first associated with Erythroxylum P. Browne. Characteristics found on the forewing and in the last abdominal segments of the adult were determinant for the proposition of the new genus. The CoI tree indicated that it is closely related to Aspilapteryx, while this genus was recovered as polyphyletic in the analyses. Morphological evidence supports this polyphyly. Consequently, Sabulopteryx Triberti, 1985, stat. nov. is considered a valid genus.},
}
@article {pmid31717182,
year = {2019},
author = {DA Silva, VCP and Kaydan, MB and DA Silva-Torres, CSA and Torres, JB},
title = {Mealybug species (Hemiptera: Coccomorpha: Pseudococcidae) on soursop and sugar apple (Annonaceae) in North-East Brazil, with description of a new species of Pseudococcus Westwood.},
journal = {Zootaxa},
volume = {4604},
number = {3},
pages = {zootaxa.4604.3.8},
doi = {10.11646/zootaxa.4604.3.8},
pmid = {31717182},
issn = {1175-5334},
mesh = {Animals ; *Annona ; *Annonaceae ; Brazil ; *Hemiptera ; *Malus ; Sugars ; },
abstract = {Several species of Annonaceae are economically important fruit-tree crops in North-East Brazil, including Pernambuco state. However, in several regions within the state, the fruits are commonly infested by mealybugs (Hemiptera: Coccomorpha: Pseudococcidae). There is a lack of information about the mealybug species damaging this produce, so a survey of mealybug species associated with commercial sugar apple (Annona squamosa L.) and soursop (A. muricata L.) was conducted in the main production areas. The species Ferrisia virgata (Cockerell), Maconellicoccus hirsutus (Green), Planococcus minor (Maskell), Phenacoccus solenopsis Tinsley and Pseudococcus jackbeardsleyi Gimpel Miller were found on both Annona species. Dysmicoccus brevipes (Cockerell), Ferrisia dayslirii Kaydan Gullan and Ferrisia malvastra (MacDaniel) were found only on soursop; and Ferrisia cristinae Kaydan Gullan, Planococcus citri (Risso), Pseudococcus annonae sp. n. Pacheco da Silva Kaydan and Pseudococcus sp. were found only on sugar apple. The species F. cristinae, F. dasylirii, F. malvastra and Ph. solenopsis are recorded infesting these hosts for the first time. The most abundant mealybug species found were F. virgata, Pl. minor, Ps. jackbeardsleyi and M. hirsutus, often forming heavy infestations and damaging the fruits. A new species, Pseudococcus annonae sp. n. Pacheco da Silva Kaydan, is described and illustrated, and an identification key to the mealybug genera occurring on annonaceous species in the Neotropical region is also provided.},
}
@article {pmid31717180,
year = {2019},
author = {Jackson, KJA and Meyer, HA},
title = {Morphological and genetic analysis of Milnesium cf. granulatum (Tardigrada: Milnesiidae) from Northeastern North America‡.},
journal = {Zootaxa},
volume = {4604},
number = {3},
pages = {zootaxa.4604.3.6},
doi = {10.11646/zootaxa.4604.3.6},
pmid = {31717180},
issn = {1175-5334},
mesh = {Animals ; *Bryophyta ; Canada ; Newfoundland and Labrador ; Parks, Recreational ; *Tardigrada ; },
abstract = {Specimens of a limnoterrestrial tardigrade collected from moss in New Hampshire, USA and Newfoundland, Canada were identified as belonging to the genus Milnesium. Morphometric data and genetic analysis of the COI gene demonstrated that animals collected from these sites represent the same species. Specimens most closely resemble Milnesium granulatum, a South American species that has been reported also from Great Smoky Mountains National Park (GSMNP), USA. New Hampshire and Newfoundland animals have the same adult claw configuration and cuticular granulation pattern as M. granulatum. Theira* (i.e., normalized to correct for allometric effects) pt values differ from GSMNP M. granulatum in having a more posterior stylet support insertion point. However, all their morphometric values overlap in range with GSMNP specimens. Unlike some other species in the genus, the claw configuration of New Hampshire Milnesium cf. granulatum shows no ontogenetic change in claw configuration. A short (269 bp on average) fragment of the internal transcribed spacer region 2 (ITS-2) was sequenced for 20 New Hampshire adults and from siblings hatched in the laboratory from 8 egg clutches. Genetic diversity among New Hampshire adults was 0.0-3.7%. Multiple haplotypes were found between siblings in a single clutch.},
}
@article {pmid31717147,
year = {2019},
author = {Köhler, G and Vargas, J},
title = {A new species of anole from Parque Nacional Volcán Arenal, Costa Rica (Reptilia, Squamata, Dactyloidae: Norops).},
journal = {Zootaxa},
volume = {4608},
number = {2},
pages = {zootaxa.4608.2.4},
doi = {10.11646/zootaxa.4608.2.4},
pmid = {31717147},
issn = {1175-5334},
mesh = {Animals ; Costa Rica ; Female ; *Lizards ; Male ; },
abstract = {We describe the new species Norops arenal sp. nov. from Parque Nacional Volcán Arenal, north-central Costa Rica. In external morphology and genetic similarity of the 16S DNA barcode, Norops arenal is most similar to N. altae, N. fortunensis, N. fuscoauratus, N. gruuo, N. kemptoni, N. monteverde, N. pseudokemptoni, and N. tenorioensis. In morphology it shares with these species the following characteristics: (1) short hind limbs; (2) a single elongate prenasal scale; (3) tiny, smooth, often juxtaposed body scales; and (4) a slender habitus, often delicate. Norops arenal differs from these species, among several scalation details, by having a blackish central area in the male dewlap in life and in preservative (vs. no suffusion of black pigment on male dewlap in the other species), and a small red female dewlap in life (vs. dirty white, cream colored, or orange); extremely short hind legs with the tip of fourth toe of the adpressed hind leg reaching only to level of shoulder (vs. usually at least to level of ear in the other species); a short tail with a tail length/SVL ratio of 1.53 in single specimen with complete tail (vs. this ratio >1.6 in the other species); and a tiny size with 41.5 mm in single known adult male and 38.5 mm in single known adult female (vs. SVL of adults usually >42.0 mm). It further differs from N. altae, N. fuscoauratus, N. gruuo, N. pseudokemptoni, and N. tenorioensis by having a unilobed hemipenis (vs. bilobed in these five species).},
}
@article {pmid31717104,
year = {2019},
author = {Taylor, CK and Murphy, MV and Hitchen, Y and Brothers, DJ},
title = {Four new species of Australian velvet ants (Hymenoptera: Mutillidae, Aglaotilla) reared from bee and wasp nests, with a review of Australian mutillid host records.},
journal = {Zootaxa},
volume = {4609},
number = {2},
pages = {zootaxa.4609.2.1},
doi = {10.11646/zootaxa.4609.2.1},
pmid = {31717104},
issn = {1175-5334},
mesh = {Animals ; *Ants ; Australia ; Bees ; Biology ; Female ; *Hymenoptera ; Male ; *Wasps ; },
abstract = {Four species of velvet ants (Mutillidae) were reared from nests of solitary bees and wasps collected using trap nests in southwest Australia and identified using morphological and DNA barcoding approaches. All four species, Aglaotilla micra sp. nov., A. lathronymphos sp. nov., A. chalcea sp. nov. and A. schadophaga sp. nov., are described as new, the last three from both sexes. A. micra, A. lathronymphos and A. chalcea are parasitoids of wasps in the genera Pison and Aulacophilinus (Crabronidae), with A. chalcea also recorded from Paralastor (Vespidae). Aglaotilla schadophaga is a parasitoid of bees in the genus Megachile (Megachilidae). The biologies and known hosts of Australian Mutillidae are reviewed. Photographs are also provided of type material for Ephutomorpha aeneidorsis Turner, 1914 (=Aglaotilla discolor Brothers, 2018), Mutilla metallica Smith, 1855 and Ephutomorpha subelegans Rayment, 1933. The lectotype of E. subelegans is formally designated.},
}
@article {pmid31717101,
year = {2019},
author = {Pellinen, MJ and Mutanen, M},
title = {Two new species of Ecpatia Turner, 1902, and the first records of Ecpatia sciachroa Hampson, 1926 and Ecpatia obscura Holloway, 2009 from Thailand (Lepidoptera: Noctuidae, Noctuinae).},
journal = {Zootaxa},
volume = {4609},
number = {3},
pages = {zootaxa.4609.3.11},
doi = {10.11646/zootaxa.4609.3.11},
pmid = {31717101},
issn = {1175-5334},
mesh = {Animals ; *Lepidoptera ; *Moths ; Thailand ; },
abstract = {Two new noctuid species, Ecpatia grisescens sp. n., E. spiculivalva sp. n. are described from Thailand based on a combination of morphological characters and DNA barcodes. Morphological structures and genetic distances are compared to those of related species. Ecpatia sciachroa Hampson, 1926 and Ecpatia obscura Holloway, 2009 are reporded from Thailand for the first time, and a checklist of 17 valid species of Ecpatia is provided.},
}
@article {pmid31717100,
year = {2019},
author = {Corley, M and Ferreira, S and Mata, VA},
title = {Ypsolopha rhinolophi sp. nov. (Lepidoptera: Ypsolophidae), a new species from Portugal and France unveiled by bats.},
journal = {Zootaxa},
volume = {4609},
number = {3},
pages = {zootaxa.4609.3.10},
doi = {10.11646/zootaxa.4609.3.10},
pmid = {31717100},
issn = {1175-5334},
mesh = {Animals ; *Chiroptera ; Female ; France ; Genitalia, Male ; *Lepidoptera ; Male ; *Moths ; Portugal ; },
abstract = {A new species Ypsolopha rhinolophi Corley is described from northern Portugal and south-east France. It resembles Y. alpella (Denis Schiffermüller, 1775) and Y. lucella (Fabricius, 1775) but shows clear differences from both species in DNA barcode and in male and female genitalia. Male genitalia of Y. lucella are illustrated for the first time. The new species has been collected at light, reared from larvae on Quercus pyrenaica Willd. and recognised from DNA barcode fragments obtained from droppings of horseshoe bats.},
}
@article {pmid31717094,
year = {2019},
author = {Oliver, PM and Richards, SJ and Donnellan, SC},
title = {Two new species of treefrog (Pelodrydidae: Litoria) from southern New Guinea elucidated by DNA barcoding.},
journal = {Zootaxa},
volume = {4609},
number = {3},
pages = {zootaxa.4609.3.4},
doi = {10.11646/zootaxa.4609.3.4},
pmid = {31717094},
issn = {1175-5334},
mesh = {Animals ; *Anura ; Color ; *DNA Barcoding, Taxonomic ; New Guinea ; Papua New Guinea ; },
abstract = {New Guinea is home to the world's most diverse insular frog biota, but only a small number of taxa have been included in genetically informed assessments of species diversity. Here we describe two new species of New Guinea treefrog in the genus Litoria that were first flagged during assessments of genetic diversity (DNA barcoding) and are currently only known from the holotypes. Litoria pterodactyla sp. nov. is a large green species in the Litoria graminea species complex from hill forests in Western Province, Papua New Guinea and is the third member of this group known from south of the Central Cordillera. Litoria vivissimia sp. nov. is a small, spike-nosed species from mid-montane forests on the Central Cordillera. It is morphologically very similar to Litoria pronimia, but occurs nearly 1000 m higher than any known locality for that species. More extensive genetically informed assessment of diversity in New Guinea frogs seems certain to reveal many more as-yet-unrecognised taxa in complexes of morphologically similar species.},
}
@article {pmid31717080,
year = {2019},
author = {Yang, X and Shi, K and Heller, K and Menzel, F and Huang, J and Wu, H},
title = {Morphology and DNA barcodes of two species of Bradysia Winnertz from China (Diptera, Sciaridae), with the description of Bradysia minorlobus Yang, Shi amp; Huang sp. n.},
journal = {Zootaxa},
volume = {4612},
number = {1},
pages = {zootaxa.4612.1.5},
doi = {10.11646/zootaxa.4612.1.5},
pmid = {31717080},
issn = {1175-5334},
mesh = {Animals ; China ; DNA Barcoding, Taxonomic ; *Diptera/genetics ; Nematocera ; },
abstract = {Two morphologically similar species of the fungicola species group of Bradysia Winnertz, 1867 were studied in China: Bradysia chenjinae Yang, Zhang Yang, 1993 and Bradysia minorlobus Yang, Shi Huang sp. n. The morphological species concepts were supported by the DNA barcodes of COI sequences. The genetic distances of 16 Bradysia fungicola group species were analyzed and a neighbor-joining tree was constructed. The morphological characters of both Chinese species were described and illustrated.},
}
@article {pmid31717067,
year = {2019},
author = {Makarchenko, EA and Makarchenko, MA and Semenchenko, AA},
title = {Towards the taxonomy of Corynoneura Winnertz (Diptera: Chironomidae: Orthocladiinae) from the Russian Far East and Eastern Siberia.},
journal = {Zootaxa},
volume = {4612},
number = {2},
pages = {zootaxa.4612.2.5},
doi = {10.11646/zootaxa.4612.2.5},
pmid = {31717067},
issn = {1175-5334},
mesh = {Animals ; *Chironomidae ; Asia, Eastern ; Larva ; Male ; Pupa ; Russia ; Siberia ; Sweden ; },
abstract = {The genus Corynoneura Winnertz is partly revised on the basis of materials from the Russian Far East and Eastern Siberia. Adult male of a new species, C. sikhotealinensis sp. nov., as well as pupa of C. schleei Makarchenko et Makarchenko and pupa with associated pharate male of Corynoneura sp. are described. Adult male of C. fujiundecima Sasa, earlier erroneously determined as C. lacustris Edwards, is briefly redescribed and annotated. DNA barcoding results of C. kadalinka Makarchenko et Makarchenko from Eastern Siberia (Baikal Lake basin) are also provided in comparison with closely related C. carriana Edwards from Sweden. As a result of the analysis, supported with sufficiently significant morphological differences between males of these two distant populations, the two species were combined into one, C. carriana, with two subspecies: C. carriana carriana Edwards (nominotypical) and C. carriana kadalinka Makarchenko et Makarchenko stat. nov. A morphological redescriptions of the adult male and pupa, as well as the 4th instar larva (here described for the first time) of C. carriana kadalinka in comparison with specimens of populations of the C. carriana carriana from Sweden and the Urals are presented. A key to adult males and pupae of the Corynoneura species from the Russian Far East and Eastern Siberia is also provided.},
}
@article {pmid31717064,
year = {2019},
author = {Shinohara, A and Kameda, Y},
title = {DNA barcodes and morphology revealed three species masquerading in Xiphydria camelus of authors (Hymenoptera, Xiphydriidae) in Northeast Asia: X. eborata sp. rev. and X. albopicta sp. nov.},
journal = {Zootaxa},
volume = {4612},
number = {2},
pages = {zootaxa.4612.2.2},
doi = {10.11646/zootaxa.4612.2.2},
pmid = {31717064},
issn = {1175-5334},
mesh = {Animals ; Asia ; Camelus ; China ; DNA Barcoding, Taxonomic ; Asia, Eastern ; *Hymenoptera ; Japan ; Russia ; },
abstract = {Taxonomic status of the widely spread xiphydriid woodwasp Xiphydria camelus (Linné, 1758) was revised by examining morphology of 964 specimens and by molecular analysis using COI barcode sequences. Both morphological and molecular approaches indicated existence of three separate species masquerading in X. camelus of authors in East Asia. The three species were finally determined as X. camelus, X. eborata Konow, 1899, and a new species, X. albopicta. Xiphydria eborata is revived from synonymy with X. camelus and X. albopicta is described as a new species from Russia (Primorskij Kraj), China (Heilongjiang) and Japan (Hokkaido). Collection records are given for all the specimens examined.},
}
@article {pmid31717035,
year = {2019},
author = {Sharifi, NM and Graham, L and Packer, L},
title = {Fifteen new species of Liphanthus Reed (Hymenoptera: Andrenidae) with two submarginal cells.},
journal = {Zootaxa},
volume = {4645},
number = {1},
pages = {zootaxa.4645.1.1},
doi = {10.11646/zootaxa.4645.1.1},
pmid = {31717035},
issn = {1175-5334},
mesh = {Animals ; Argentina ; Bees ; Bolivia ; Chile ; *Hymenoptera ; Male ; Peru ; },
abstract = {Hitherto, the panurgine genus Liphanthus Reed 1894 has been thought to have only a single species with two, as opposed to three, submarginal cells. Here we describe an additional fifteen species with two submarginal cells. These new species are: L. jenamro Mir Sharifi Packer, L. sapos Mir Sharifi Packer, L. domeykoi Packer, L. discolor Mir Sharifi Packer, L. centralis Mir Sharifi Packer, L. molavi Mir Sharifi Packer (all of the above are from Chile), L. abotorabi Mir Sharifi Packer, L. cochabambensis Mir Sharifi Packer (both from Bolivia), L. fritzi Mir Sharifi Packer, L. amblayensis Mir Sharifi Packer (both from Argentina), L. ancashensis Mir Sharifi Packer (from Peru), L. tregualemensis Packer (from Chile), L. yrigoyeni Packer, L. sparsipunctus Packer (both from Argentina) and L. aliavenus Packer (from Chile). Only L. tregualemensis readily fits within any of the previously described subgenera-Liphanthus (Leptophanthus) Ruz and Toro 1983. Liphanthus aliavenus is known from two specimens, one with three and one with two submarginal cells whereas L. molavi has one individual with two submarginal cells on one forewing and three on the other while all other specimens have two submarginal cells on each forewing. We verified that none of these new species are merely two submarginal celled variants of species with three submarginal cells (such intraspecific variation arises also in some other bees) by i) comparing each of the new species with all keys, figures and descriptions of all Liphanthus species, ii) comparisons with holotypes and/or paratypes of most of the described species and iii) surveys of the specimens of undescribed species with three submarginal cells in our collection. None of the new species seem closely related to L. (Neoliphanthis) bicellularis Ruz and Toro 1983, the only previously described Liphanthus species with two submarginal cells. It is the second submarginal crossvein that is lost in all species except L. aliavenus in which the first submarginal cross vein is lost. DNA barcode data are presented for some of the species. Some interesting morphological features associated with the penis valves are described and discussed. The genus is recorded from Bolivia for the first time.},
}
@article {pmid31716958,
year = {2019},
author = {Cruz, CAG and Caramaschi, U and Fusinatto, LA and Brasileiro, CA},
title = {Taxonomic review of Dendrophryniscus brevipollicatus Jiménez de la Espada, 1870, with revalidation of D. imitator (Miranda-Ribeiro, 1920) br /&gt;and D. lauroi Miranda-Ribeiro, 1926, and description of four new related species (Anura, Bufonidae).},
journal = {Zootaxa},
volume = {4648},
number = {1},
pages = {zootaxa.4648.1.2},
doi = {10.11646/zootaxa.4648.1.2},
pmid = {31716958},
issn = {1175-5334},
mesh = {Animals ; Brazil ; *Bufonidae ; Forests ; },
abstract = {Dendrophryniscus brevipollicatus Jiménez de la Espada is a Neotropical bufonid endemic to a small range of the Brazilian Coastal Atlantic Forest, with reduced body size for the family and bromeligenous habit. We reviewed the taxonomic status of populations of D. brevipollicatus from states of Rio de Janeiro and São Paulo, including some continental islands, based on external morphology. We tested our morphological species by a DNA-barcoding approach with sequences of 16S RNA ribosomal gene fragment. DNA-barcoding analysis included other recognized Dendrophryniscus species and was concordant with morphological species diagnosed in our review. Intraspecific genetic distances ranged from 0 to 2.72 % (± 0.91 %). Interspecific distances ranged from 3.35 % (± 0.90 %) to 20.15 (± 2.23 %). Optimal threshold values ranged from 2.8 % to 3.0 % and barcode gap analysis showed that for all individuals the furthest intraspecific distances was always lower than the closest non-conspecific individual. Seven distinct species were recognized. A neotype for D. brevipollicatus was designated and described; the type locality was determined for the Açude da Solidão (22º57'S, 43º17'W, Datum WGS 84; 410 m altitude), Parque Nacional da Tijuca, Municipality of Rio de Janeiro, State of Rio de Janeiro, Brazil. Two species were revalidated: D. imitator (Miranda-Ribeiro), with designation of a lectotype and descriptions of the lectotype and of a topotype from the restricted type locality, Alto da Serra (23o46'S, 46o19'W, Datum WGS 84, 800 m altitude), Municipality of Paranapiacaba, State of São Paulo, Brazil; and D. lauroi (Miranda-Ribeiro), with descriptions of the lectotype and of a topotype from the type locality, Municipality of Angra dos Reis (22o54'S, 44o20'W, Datum WGS 84; 25 m altitude), State of Rio de Janeiro, Brazil. Four new species were described: D. davori sp. nov., from Baixo Caledônia (22º21'S, 42º35'W, Datum WGS 84; 1600 m altitude), Municipality of Nova Friburgo, State of Rio de Janeiro, Brazil; D. haddadi sp. nov., from Parque Estadual da Serra do Mar, Núcleo Santa Virgínia (23o21'S, 45o08'W, Datum WGS 84; 970 m altitude), Municipality of São Luís do Paraitinga, State of São Paulo, Brazil; D. izecksohni sp. nov., from Campo de Fruticultura da Bocaina (currently Núcleo Senador Vergueiro), Municipality of São José do Barreiro (22º38'S, 44º34'W, Datum WGS 84, 540 m altitude), State of São Paulo, Brazil; and D. jureia sp. nov., from Estação Ecológica da Juréia-Itatins-Núcleo Rio Verde (24º22'S, 47º04'W, Datum WGS 84; 32 m altitude), Municipality of Iguape, State of São Paulo, Brazil. Geographical distributions of all species are provided.},
}
@article {pmid31716957,
year = {2019},
author = {Ditter, RE and Erdman, RB and Goebel, AM and Bracken-Grissom, HD},
title = {Widespread phenotypic hypervariation in the enigmatic anchialine shrimp Barbouria cubensis (Decapoda: Barbouriidae).},
journal = {Zootaxa},
volume = {4648},
number = {1},
pages = {zootaxa.4648.1.1},
doi = {10.11646/zootaxa.4648.1.1},
pmid = {31716957},
issn = {1175-5334},
mesh = {Animals ; Biological Evolution ; *Decapoda ; Genes, Mitochondrial ; Genetic Variation ; Islands ; Phenotype ; Phylogeny ; },
abstract = {Classification and evolutionary relationships among anchialine shrimp from the family Barbouriidae Christoffersen, 1987, has long been a topic of debate amongst crustacean taxonomists. To date, no study has examined morphological or molecular variation among populations of these enigmatic shrimp. The present study documents and analyzes patterns of widespread morphological variation within populations of Barbouria cubensis von Martens, 1872, from anchialine pools on three Bahamian islands. Such extensive morphological variation confounds identification using classic taxonomical methods. Phenotypic variation is by no means a new topic, but studies of decapods are typically limited to isolated individuals or few morphological characters. Moreover, past studies of B. cubensis do not report extensive morphological variation, however we find that upwards of 90% of individuals are affected. Anomalous phenotypes are described in 54 morphological characters with no detectable pattern associated with geographic distribution. The term phenotypic hypervariation (PhyV) is used to describe morphological variation that greatly deviates from any previous taxonomic descriptions. Analysis of partial sequences of the 16S and COI mitochondrial genes confirm the identity of morphologically variable specimens as B. cubensis without population structure across the tropical western Atlantic. A test for cryptic diversity within B. cubensis suggests PhyV is not correlated with cryptic diversity. Morphological variation at this scale likely depends on recent changes either to their environment or genetic diversity.},
}
@article {pmid31716944,
year = {2019},
author = {Marin, I},
title = {A new stygobiotic Xiphocaridinella (Crustacea: Decapoda: Atyidae) from the Motena Cave, Samegrelo-Zemo Svaneti region of Georgia, Caucasus.},
journal = {Zootaxa},
volume = {4648},
number = {3},
pages = {zootaxa.4648.3.12},
doi = {10.11646/zootaxa.4648.3.12},
pmid = {31716944},
issn = {1175-5334},
mesh = {Animals ; Caves ; *Decapoda ; Female ; Georgia (Republic) ; Male ; },
abstract = {A new stygobiotic atyid shrimp from the genus Xiphocaridinella Sadowsky, 1930 (Crustacea: Decapoda: Atyidae) is described based on morphology and DNA analysis from an underground lake inside the Motena Cave (Martvili Municipality, Samegrelo-Zemo Svaneti, Western Georgia, Caucasus). The new species is genetically well isolated from the West Georgian relatives and clearly differs from the other Caucasian congeners by specific lanceolate unarmed rostrum, turned forward, and by long fingers of pereiopod I and II in both males and females.},
}
@article {pmid31716938,
year = {2019},
author = {Darshan, A and Abujam, S and Kumar, R and Parhi, J and Singh, YS and Vishwanath, W and DAS, DN and Pandey, PK},
title = {Mystus prabini, a new species of catfish (Siluriformes: Bagridae) from Arunachal Pradesh, north-eastern, India.},
journal = {Zootaxa},
volume = {4648},
number = {3},
pages = {zootaxa.4648.3.6},
doi = {10.11646/zootaxa.4648.3.6},
pmid = {31716938},
issn = {1175-5334},
mesh = {Animals ; *Catfishes ; India ; Rivers ; },
abstract = {Mystus prabini, new species, is described from the Sinkin and the Dibang River in the Lower Dibang Valley District of Arunachal Pradesh, India. The new species differs from all South-Asian congeners except M. bleekeri, M. cavasius, M. zeylanicus, M. falcarius, M. seengtee, M. cineraceus, M. ngasep, M. rufescens and M. ankutta in having a long adipose fin that reaches anteriorly (vs. distinctly does not reach) the base of the last dorsal-fin ray. The new species can be distinguished from the named nine species in having (vs. lacking) a narrow black mid-lateral stripe extending from the anterior region of tympanic spot to the rounded black spot at the caudal-fin base. The analysis of mitochondrial cytochrome c oxidase subunit I (COI) gene sequence shows that the K2P value between Mystus prabini and all other Mystus species ranges from 8.6-22.1%. Mystus prabini is closest genetically to M. bleekeri and M. albolineatus, from which species it has a genetic distance of 8.6% and 13.9%, respectively. The genetic distance (K2P) between the new species and M. dibrugarensis is 21.1%.},
}
@article {pmid31716881,
year = {2019},
author = {Kirichenko, N and Triberti, P and Akulov, E and Ponomarenko, M and Gorokhova, S and Sheiko, V and Ohshima, I and Lopez-Vaamonde, C},
title = {Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding.},
journal = {Zootaxa},
volume = {4652},
number = {1},
pages = {zootaxa.4652.1.1},
doi = {10.11646/zootaxa.4652.1.1},
pmid = {31716881},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Europe ; Asia, Eastern ; Female ; *Lepidoptera ; Male ; Russia ; Siberia ; },
abstract = {The Russian Far East (RFE) is an important hotspot of biodiversity whose insect fauna remains understudied, particularly its Microlepidoptera. Here we explore the diversity of leaf-mining micromoths of the family Gracillariidae, their distribution and host plant associations in RFE using a combination of field observations and sampling, DNA barcoding, morphological analysis and literature review. We collected 91 gracillariid specimens (45 larvae, 9 pupae and 37 adults) in 12 localities across RFE and identified 34 species using a combination of DNA barcoding and morphology. We provide a genetic library of 57 DNA barcodes belonging to 37 Barcode Index Numbers (BINs), including four BINs that could potentially represent species new to science. Leaf mines and leaf shelters are described and illustrated for 32 studied species, male or female genitalia as well as forewing patterns of adults are shown, especially for those species identified based on morphology. Three species, Micrurapteryx caraganella (Hering), Callisto insperatella (Nickerl), and Phyllonorycter junoniella (Zeller) are newly recorded from RFE. Five species previously known from some regions of RFE, were found for the first time in Amurskaya Oblast: Phyllonorycter populifoliella (Treitschke), Primorskii Krai: Ph. sorbicola Kumata and Sahkalin Island: Caloptilia heringi Kumata, Ph. ermani (Kumata) and Ph. ulmifoliella (Hübner). Eight gracillariid-plant associations are novel to science: Caloptilia gloriosa Kumata on Acer pseudosieboldianum, Cameraria niphonica Kumata on A. caudatum subsp. ukurundense, Parornix ermolaevi Kuznetzov on Corylus sieboldiana, Phyllonorycter ermani (Kumata) on Betula platyphylla, Ph. nipponicella (Issiki) on Quercus mongolica, Ph. orientalis (Kumata) and Ph. pseudojezoniella Noreika on Acer saccharum, Ph. sorbicola on Prunus maakii. For the first time we documented the "green island" phenotype on Phyllonorycter cavella (Zeller) mines on Betula platyphylla. Two pestiferous species have been recorded during our surveys: Micrurapteryx caraganella on ornamental Caragana arborescens in urban plantations in Amurskaya Oblast, and the lime leafminer Phyllonorycter issikii (Kumata), a species known to be native to RFE and invasive elsewhere in Russia and in European countries. A revised checklist of RFE gracillariids has been compiled. It accounts for 135 species among which 17 species (13%) are only known to occur in RFE. The gracillariid fauna of RFE is more similar to the Japanese fauna (49%), than to the fauna of the rest of Russia (i.e European part and Siberia) (32%).},
}
@article {pmid31716854,
year = {2019},
author = {Porto-Hannes, I and Burlakova, LE and Karatayev, AY and Lasker, HR},
title = {Molecular phylogeny, biogeography, and conservation status of the Texas-endemic freshwater mussel Lampsilis bracteata (Bivalvia, Unionidae).},
journal = {Zootaxa},
volume = {4652},
number = {3},
pages = {zootaxa.4652.3.2},
doi = {10.11646/zootaxa.4652.3.2},
pmid = {31716854},
issn = {1175-5334},
mesh = {Animals ; *Bivalvia ; Fresh Water ; Phylogeny ; Texas ; *Unionidae ; },
abstract = {Lampsilis bracteata (Gould), the Texas Fatmucket, is a regional endemic species in the central Texas biogeographic province which is a candidate to be listed as threatened or endangered under the Endangered Species Act of 1973. Lampsilis bracteata is morphologically similar to the common species L. hydiana (Lea). Here, we examine the molecular taxonomic identification of L. bracteata, and compare its historical range with its current geographic distribution. Tests of genetic affinities based on two mitochondrial genes typically used for DNA barcoding (cytochrome oxidase subunit 1, COI and NADH dehydrogenase subunit 1, ND1) support recognition of L. bracteata as a full species. An unexpected spin-off result was that ND1 sequences of L. satura (Lea), a threatened species in Texas, formed a highly supported cluster within putative L. cardium Rafinesque. As an endemic species, the distribution of L. bracteata has been historically restricted; however, poor land and water management practices have further reduced its distribution from eighteen to just eight streams in the Colorado River drainage and to one stream in the Guadalupe River drainage. For L. bracteata, as for many other imperiled freshwater mussel species, effective conservation measures rely on correct species identification, definition of its geographic range and assessment of its changes in the recent past.},
}
@article {pmid31716836,
year = {2019},
author = {Vilkamaa, P and Halenius, P and Ševčík, J},
title = {Review of Pseudoaerumnosa Rudzinski (Diptera, Sciaridae), with the description of twenty-four new species.},
journal = {Zootaxa},
volume = {4656},
number = {1},
pages = {zootaxa.4656.1.1},
doi = {10.11646/zootaxa.4656.1.1},
pmid = {31716836},
issn = {1175-5334},
mesh = {Animals ; *Diptera ; Nematocera ; Phylogeny ; Taiwan ; },
abstract = {The genus Pseudoaerumnosa Rudzinski, 2006 is redefined. The genus includes the following species which are described, illustrated and keyed: Pseudoaerumnosa acinacea sp. n., P. ampliata sp. n., P. annae sp. n., P. awanensis sp. n., P. banari sp. n., P. clavidactyla sp. n., P. clivicola sp. n., P. collicola sp. n., P. consuota sp. n., P. cryptoloba sp. n., P. curvifalx sp. n., P. eminula sp. n., P. exacuta sp. n., P. filispicata sp. n., P. formosa sp. n., P. fragilis sp. n., P. impensa sp. n., P. inviolata Rudzinski, 2006, P. junciseta sp. n., P. obovata sp. n., P. pilicaudata sp. n., P. quadriquetra sp. n., P. saginata sp. n., P. tenuidens sp. n. and P. tkoci sp. n. Morphological characters and the phylogenetic position of Pseudoaerumnosa are discussed. For some species, the barcode (COI) sequence data were obtained. The genus is currently known from the Oriental (22 species), Malagasy (3 species) and Australasian regions (1 species).},
}
@article {pmid31716820,
year = {2019},
author = {Justine, JL and Théry, T and Gey, D and Winsor, L},
title = {First record of the invasive land flatworm Bipalium adventitium (Platyhelminthes, Geoplanidae) in Canada.},
journal = {Zootaxa},
volume = {4656},
number = {3},
pages = {zootaxa.4656.3.13},
doi = {10.11646/zootaxa.4656.3.13},
pmid = {31716820},
issn = {1175-5334},
mesh = {Animals ; Canada ; *Platyhelminths ; },
abstract = {Specimens of Bipalium adventitium (Platyhelminthes, Geoplanidae) were found in Montréal, Québec, Canada. The specimens showed the typical colour pattern of the species and barcoding (Cytochrome Oxidase I) demonstrated near-identity with a sequence of the same species from the USA. This is the first record of the species in Canada.},
}
@article {pmid31716817,
year = {2019},
author = {Laug, A and Hamerlík, L and Anslan, S and Engels, S and Turner, F and Wang, J and Schwalb, A},
title = {Acricotopus indet. morphotype incurvatus: Description and genetics of a new Orthocladiinae (Diptera: Chironomidae) larval morphotype from the Tibetan Plateau.},
journal = {Zootaxa},
volume = {4656},
number = {3},
pages = {zootaxa.4656.3.10},
doi = {10.11646/zootaxa.4656.3.10},
pmid = {31716817},
issn = {1175-5334},
mesh = {Animals ; *Chironomidae ; Ecosystem ; Larva ; Phylogeny ; Tibet ; },
abstract = {High mountain ranges such as the Tibetan Plateau with an average altitude above 4500 m are topographically complex formations. Elevational gradients, physiographic diversity and climatic heterogeneity have led to highly biodiverse ecosystems in these regions. Mountain ranges can be seen as cradles of evolution and harbour, due to their unique characteristics, a high number of highly adapted species. At the same time these areas are hard to access and therefore taxonomic information is limited. Here we describe a new Acricotopus (Diptera: Chironomidae: Orthocladiinae) larval morphotype occurring in lakes and ponds of differing salinity and water depths located on the Southern and Central Tibetan Plateau. The description is based on larvae and their genetics (ribosomal 18S, 28S and mitochondrial COI sequences) collected from a shallow pond in close proximity to the large saline lake Selin Co. Larvae of Acricotopus indet. morphotype incurvatus are characterized by a mentum with a cluster of lateral teeth, partially folded inwards, a mandible with a toothed lobe in addition to four inner teeth and a sclerotized plate positioned behind the mentum. Up to now, these morphological features have only been found in early instars of other Acricotopus species. The proposed morphotype name is inspired by the peculiar form of the mentum.},
}
@article {pmid31716801,
year = {2019},
author = {Lalramliana, L and Lalronunga, S and Singh, M},
title = {Cabdio crassus, a new species of cyprinid fish (Teleostei: Cyprinidae) from the Kaladan River of Mizoram, India.},
journal = {Zootaxa},
volume = {4657},
number = {1},
pages = {zootaxa.4657.1.7},
doi = {10.11646/zootaxa.4657.1.7},
pmid = {31716801},
issn = {1175-5334},
mesh = {Animals ; *Cyprinidae ; India ; Rivers ; },
abstract = {Cabdio crassus, a new fish species, is described from the Kaladan River in Mizoram, India. The new species is distinguished from all its congeners by having a ventral keel extending from the middle of the chest, between the posterior base of the pectoral fin and along the abdomen up to the anus (vs. more or less keeled median scales from mid-point of abdomen between posterior base of pelvic fin up to anus in all other Cabdio) and 11½-12½ branched anal-fin rays (vs. 7 in C. jaya and 9 in both C. morar and C. ukhrulensis). It is further distinguished from C. morar and C. ukhrulensis by possessing more lateral-line scales (45-51 vs. 38-42 in C. morar and 35-37 in C. ukhrulensis), more predorsal scales (20-23 vs. 17-18 in C. morar and 14 in C. ukhrulensis) and more lateral transverse scales (½7/1/3½ vs. 5/1/2 in both C. morar and C. ukhrulensis). It also differs from C. jaya in having fewer lateral-line scales (45-51 vs. 52-60), more lateral transverse scales (½7/1/3½ vs. 5/1/3) and more pharyngeal tooth-rows (3 vs. 2). Furthermore, the cytochrome c oxidase sub unit I (coi) gene sequence separates Cabdio crassus from all other Cabdio species (interspecies distance ranges from 7.8-12.3%). The anomalies observed among the GenBank sequences of the genus Cabdio are discussed and resolved.},
}
@article {pmid31716758,
year = {2019},
author = {Shen, HP and Chang, CH and Chih, WJ},
title = {Two new earthworm species of the genus Amynthas (Oligochaeta: Megascolecidae) from central Taiwan, with comments on some recent species assignments in Amynthas and Metaphire.},
journal = {Zootaxa},
volume = {4658},
number = {1},
pages = {zootaxa.4658.1.4},
doi = {10.11646/zootaxa.4658.1.4},
pmid = {31716758},
issn = {1175-5334},
mesh = {Animals ; *Asteraceae ; DNA ; Male ; *Oligochaeta ; Taiwan ; },
abstract = {This study describes two new species of earthworms belonging to the genus Amynthas (Oligochaeta: Megascolecidae) from central Taiwan. They are named Amynthas luridus sp. nov. and Amynthas ruiyenensis sp. nov. Both species are octothecal with the former found at elevations of 1500-2300 m and the latter at an elevation of 2200 m from the Central Mountain Range. In addition, DNA barcodes are made available for the first time for the following species: Amynthas catenus Tsai et al., 2001, Amynthas exiguus aquilonius Tsai et al., 2001, Amynthas proasacceus Tsai et al., 2001, Amynthas hohuanmontis Tsai et al., 2002, Amynthas tessellatus Shen et al., 2002, Amynthas fenestrus Shen et al., 2003, Amynthas tantulus Shen et al., 2003, and Amynthas uvaglandularis Shen et al., 2003. Furthermore, Amynthas exiguus ssp. aquilonius Tsai et al., 2001 distributed at elevations of 2200-3000 m in the Central Mountain Range is elevated to species level, as A. aquilonius Tsai et al., 2001. The highest altitude record so far for the exotic Eukerria saltensis (Beddard, 1895) in Taiwan, 2200 m above sea level, is documented. Moreover, some recent assignments of species to Amynthas and Metaphire and synonymies of names are critically discussed. It is argued that idiosyncratic genus concepts, inadequate species comparisons, and unexplained synonymies should be avoided. A hitherto undetected and possibly monophyletic species group of mainly Korean Amynthas species in the A. tokioensis-group is indicated, characterized by numerous genital papillae around each spermathecal pore and male porophore, large ampullae, long diverticula, large prostate glands, and manicate intestinal caeca. The names A. bimaculata, A. silvatica and A. surcata (Ishizuka, 1999), as well as A. odaesanensis, A. righii, A. fasciiformis, and A. sanchongensis Hong James, 2001, previously declared as junior synonyms of A. tappensis (Ohfuchi, 1935), are revalidated.},
}
@article {pmid31716728,
year = {2019},
author = {Whitworth, TL and Yusseff-Vanegas, S},
title = {A revision of the genera and species of the Neotropical family Mesembrinellidae (Diptera: Oestroidea).},
journal = {Zootaxa},
volume = {4659},
number = {1},
pages = {zootaxa.4659.1.1},
doi = {10.11646/zootaxa.4659.1.1},
pmid = {31716728},
issn = {1175-5334},
mesh = {Animals ; *Diptera ; Female ; South America ; },
abstract = {The Neotropical family Mesembrinellidae is revised. A total of 53 valid, extant species are included in the family, including 15 described as new and 38 redescribed based on study of type and non-type material and of the literature. A total of 18 primary types were examined. An additional ca. 2300 specimens, belonging to 47 species, were studied in detail, including dissection and photographic documentation of terminalia, with many females illustrated for the first time. Keys to subfamilies, genera, species-groups and species are provided. Type specimens of six species housed in South American institutions could not be obtained for study, i.e., M. bequaerti Séguy, 1925 and the five recently described species M. andina (Wolff et al., 2014), M. carvalhoi (Wolff et al., 2013b), M. cordillera (Wolff Ramos-Pastrana in Wolff et al., 2017), M. obscura (Wolff in Wolff et al., 2017) and Laneella patriciae (Wolff, 2013). We accept the synonymy, proposed by previous authors, of Eumesembrinella Townsend, 1931 with Mesembrinella Giglio-Tos, 1893. In addition, we synonymize the genera Albuquerquea Mello, 1967, Giovanella Bonatto in Bonatto Marinoni, 2005, Henriquella Bonatto in Bonatto Marinoni, 2005, Huascaromusca Townsend, 1918 and Thompsoniella Guimarães, 1977 with Mesembrinella Giglio-Tos, 1893, synn. nov., retaining three valid genera in the family: Laneella Mello, 1967, Mesembrinella and Souzalopesiella Guimarães, 1977. Laneella nigripes Guimarães, 1977 and Mesembrinella bellardiana Aldrich, 1922 are fixed as the type species of the genera Laneella Mello, 1967 and Mesembrinella Giglio-Tos, 1893, respectively, under Article 70.3 of the ICZN Code. We separate Mesembrinella into the following species-groups: M. latifrons (Mello, 1967), M. spicata Aldrich, 1925, M. bolivar (Bonatto in Bonatto Marinoni, 2005), M. aeneiventris (Wiedemann, 1830), M. bicolor (Fabricius, 1805), and M. anomala (Guimarães, 1977). The following 15 new species are described: Laneella fusconitida Whitworth, sp. nov. from Costa Rica, Ecuador and Venezuela, Laneella fuscosquamata Whitworth, sp. nov. from Guatemala and Mexico, Laneella purpurea Whitworth, sp. nov. from Costa Rica, Mesembrinella bullata Whitworth, sp. nov. from Bolivia, Mesembrinella chantryi Whitworth, sp. nov. from French Guiana and Brazil, Mesembrinella epandrioaurantia Whitworth, sp. nov. from Venezuela, Mesembrinella guaramacalensis Whitworth, sp. nov. from Venezuela, Mesembrinella longicercus Whitworth, sp. nov. from Bolivia, Mesembrinella mexicana Whitworth, sp. nov. from Mexico, Mesembrinella nigrocoerulea Whitworth, sp. nov. from Costa Rica, Ecuador and Venezuela, Mesembrinella serrata Whitworth, sp. nov. from Peru, Mesembrinella velasquezae Whitworth, sp. nov. from Venezuela, Mesembrinella violacea Whitworth, sp. nov. from Costa Rica, Mesembrinella woodorum Whitworth, sp. nov. from Ecuador, and Mesembrinella zurquiensis Whitworth, sp. nov. from Costa Rica. Mesembrinella abaca Hall, 1948 is proposed as a junior synonym of Mesembrinella socors (Walker, 1861), syn. nov. Lectotypes are designated for Dexia randa Walker, 1849 (now Mesembrinella) and Mesembrinella pictipennis Aldrich, 1922. We analyze the most extensive DNA-barcode dataset for Mesembrinellidae to date, encompassing the three genera considered valid and including 188 sequences (178 new) from 35 species, with data for 23 species provided for the first time. The topology of the resulting Neighbor-Joining tree is mostly congruent with morphology; however, some species show considerable genetic variation that is not reflected by morphology. Finally, we include a corrigendum to the recent Zootaxa paper on Nearctic Calliphora Robineau-Desvoidy (Diptera: Calliphoridae) by Tantawi et al.},
}
@article {pmid31716698,
year = {2019},
author = {Fochetti, R and Oliverio, M and Russini, V and Tapia, G and DE Figueroa, JMT},
title = {Molecular identity of Nemoura lacustris (Plecoptera: Nemouridae) throughout its distributional range.},
journal = {Zootaxa},
volume = {4661},
number = {3},
pages = {zootaxa.4661.3.4},
doi = {10.11646/zootaxa.4661.3.4},
pmid = {31716698},
issn = {1175-5334},
mesh = {Animals ; *DNA, Mitochondrial ; Europe ; France ; Genetic Variation ; *Neoptera/genetics ; Phylogeny ; United Kingdom ; },
abstract = {The recent report of Nemoura lacustris Pictet, 1865 in Great Britain has raised doubts on its identity, given the isolation with respect to the Mediterranean and continental populations of this species. Using molecular analyses, we tested if populations from the United Kingdom and the Iberian Peninsula were conspecific and tested the hypotheses of a recent colonization event versus a more ancient origin for the British populations. Phylogenetic analysis of the mitochondrial marker COI allowed us to conclude that the United Kingdom specimens morphologically ascribed to N. lacustris were conspecific with populations from France and the Iberian Peninsula. Based on the genetic divergence of the two reciprocally monophyletic clades from the Iberian Peninsula and Great Britain/France, respectively, the present distribution of N. lacustris can be postulated as a relatively recent dispersal or introduction into Great Britain from France. Finally, we note the isolated position displayed by N. lacustris in the phylogenetic tree of Nemoura species based on COI sequences, as the sister to all included species of the genus. This isolated position corresponds with the specific morphology of N. lacustris genitalia and requires additional studies to ascertain clearer generic boundaries within the Nemouridae.},
}
@article {pmid31716671,
year = {2019},
author = {Vega, R and Razzolini, E and Arbetman, M and Viozzi, G},
title = {Two new species of Gyrodactylus von Nordmann, 1832 (Monogenoidea: Gyrodactylidae) parasitizing introduced poeciliids in Patagonia.},
journal = {Zootaxa},
volume = {4664},
number = {3},
pages = {zootaxa.4664.3.9},
doi = {10.11646/zootaxa.4664.3.9},
pmid = {31716671},
issn = {1175-5334},
mesh = {Animals ; Argentina ; *Fish Diseases ; Species Specificity ; *Trematoda ; *Trematode Infections ; },
abstract = {Gyrodactylus superbus (Szidat, 1973) Popazoglo Boeger, 2000 was described from Corydoras paleatus (Jenyns) (Callichthyidae) and represents the only known viviparous gyrodactylid reported from the Parano-Platense basin of Argentina. We describe two new species of viviparous neotropical gyrodactylids parasitizing the introduced poeciliid, Cnesterodon decemmaculatus (Jenyns, 1842) (Poeciliidae), from southern Argentina: Gyrodactylus decemmaculati n. sp. and Gyrodactylus breviradix n. sp. The new species differ from other gyrodactylids parasitizing poeciliids in the morphology of superficial bars and hooklets. Gyrodactylus decemmaculati n. sp. has a superficial bar with two robust and rounded anterolateral projections (each with a ventral lobe), and a subtriangular shield, and has a slender hooklet with a delicate recurved point, a straight, elongate shaft, and a depressed, acute toe. Gyrodactylus breviradix n. sp. has a superficial bar with two robust, elongate anterolateral projections, folded inward, and a trapezoidal shield, and has a hooklet with a short point, angled at 90º, ending before level of toe tip, a straight, short shaft, a round, prominent heel, and a pointed, depressed toe. These identifications were supported by DNA analyses based on sequences of the ITS2 region and a barcoding gap analysis. Sequences of the Cytochrome oxidase II gene and fragments of the Internal Transcribed Spacers 1 for both species are also provided.},
}
@article {pmid31716602,
year = {2019},
author = {Sinclair, BJ and Vajda, &#xc9;A and Saigusa, T and Shamshev, IV and Wheeler, TA},
title = {Rhamphomyia Meigen of the Canadian Arctic Archipelago, Greenland and Iceland (Diptera: Empididae).},
journal = {Zootaxa},
volume = {4670},
number = {1},
pages = {zootaxa.4670.1.1},
doi = {10.11646/zootaxa.4670.1.1},
pmid = {31716602},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures ; Animals ; Canada ; *Diptera ; Female ; Greenland ; Iceland ; Male ; },
abstract = {Rhamphomyia of the Canadian Arctic Archipelago, Greenland and Iceland, comprising 23 species, including five new species, are revised: R. (Ctenempis) albopilosa Coquillett, R. (Dasyrhamphomyia) erinacioides Malloch, R. (Dasyrhamphomyia) hovgaardii Holmgren, R. (Dasyrhamphomyia) leptidiformis Frey, R. (Dasyrhamphomyia) nigrita Zetterstedt, R. (Eorhamphomyia) shewelli Sinclair, Vajda, Saigusa Shamshev sp. nov., R. (Pararhamphomyia) diversipennis Becker, R. (Pararhamphomyia) filicauda Henriksen Lundbeck, R. (Pararhamphomyia) frigida Sinclair, Vajda, Saigusa Shamshev sp. nov., R. (Pararhamphomyia) helleni Frey, R. (Pararhamphomyia) hilariformis Frey, R. (Pararhamphomyia) hoeli Frey, R. (Pararhamphomyia) kjellmanii Holmgren, R. (Pararhamphomyia) lymaniana Sinclair, Vajda, Saigusa Shamshev sp. nov., R. (Pararhamphomyia) omissinervis Becker, R. (Pararhamphomyia) petervajdai Sinclair, Vajda, Saigusa Shamshev sp. nov., R. (Pararhamphomyia) septentrionalis Sinclair, Vajda, Saigusa Shamshev sp. nov., R. (Pararhamphomyia) simplex Zetterstedt, R. (Pararhamphomyia) ursinella Melander, R. herschelli Malloch, R. hirtula Zetterstedt, R. laevigata Loew, R. setosa Coquillett. The following six new synonyms are proposed: R. calvimontis Cockerell, 1916 and R. wuorentausi Frey, 1922 = R. albopilosa Coquillett, 1900; R. fridolini Frey, 1950 = R. laevigata Loew, 1861; R. hirticula Collin, 1937 = R. setosa Coquillett, 1895; R. uralensis Becker, 1915 = R. kjellmanii Holmgren, 1880; R. zaitzevi Becker, 1915 = R. hovgaardii Holmgren, 1880. Lectotypes are designated for the following species: R. diversipennis Becker, R. filicauda Henriksen Lundbeck, R. helleni Frey, R. herschelli Malloch, R. hirticula Collin, R. hoeli Frey, R. leptidiformis Frey, R. omissinervis Becker, R. setosa Coquillett, R. uralensis Becker, R. wuorentausi Frey, R. zaitzevi Becker. A neotype is designated for R. laevigata Loew. Keys to male and female species of Rhamphomyia and distribution maps of this region are provided. DNA barcode data are presented for 16 species of arctic Rhamphomyia.},
}
@article {pmid31716597,
year = {2019},
author = {Saç, G and Özuluğ, M and Geiger, MF and Freyhof, J},
title = {Pseudophoxinus cilicicus, a new spring minnow from southern Anatolia (Teleostei: Leuciscidae).},
journal = {Zootaxa},
volume = {4671},
number = {1},
pages = {zootaxa.4671.1.8},
doi = {10.11646/zootaxa.4671.1.8},
pmid = {31716597},
issn = {1175-5334},
mesh = {Animals ; Color ; *Cyprinidae ; DNA, Mitochondrial ; Rivers ; Seasons ; },
abstract = {Pseudophoxinus cilicicus, new species, is described from the Arsuz, Ceyhan and Seyhan river drainages in the Gulf of İskenderun. It is distinguished from other members of the Pseudophoxinus zeregi species group by having a complete lateral line with 38-45 + 2-3 scales, the lower lip usually slightly projecting beyond the tip of the upper lip, a prominent black stripe along the flank, and no black pigments below the lateral line. Pseudophoxinus cilicicus is distinguished from P. zekayi by a minimum K2P distance of 3.8% based on the mitochondrial DNA barcode region. Pseudophoxinus atropatenus and P. sojuchbulagi are returned to the genus Rutilus.},
}
@article {pmid31716590,
year = {2019},
author = {Iwama, RE and Oceguera-Figueroa, A and DE Carle, D and Manglicmot, C and Erséus, C and Miles, NM and Siddall, ME and Kvist, S},
title = {Broad geographic sampling and DNA barcoding do not support the presence of Helobdella stagnalis (Linnaeus, 1758) (Clitellata: Glossiphoniidae) in North America.},
journal = {Zootaxa},
volume = {4671},
number = {1},
pages = {zootaxa.4671.1.1},
doi = {10.11646/zootaxa.4671.1.1},
pmid = {31716590},
issn = {1175-5334},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Leeches/genetics ; North America ; Phylogeny ; },
abstract = {The description of Helobdella stagnalis (Linnaeus, 1758) has emphasized the presence of a nuchal, chitinous scute located on the dorsal surface in the first third of the body as the diagnostic character for the species. Historically, identifications of species of Helobdella have relied heavily on this character and, as a result, Helobdella stagnalis has been reported from an inordinately broad geographic range, including Europe, Asia, Africa, North America, and South America. In addition to a few earlier investigations, a recent analysis showed that great genetic distances (orders of magnitude greater than previous estimations of intraspecific divergence in leeches) are present between scute-bearing specimens identified as H. stagnalis from Europe and North America, implying that H. stagnalis does not occur in North America. The present study expands the geographic boundaries of taxon sampling for both European and North American taxa, and re-examines the phylogenetic relationships and cytochrome c oxidase subunit I (COI) variation within scute-bearing species of the genus Helobdella. Our analyses include specimens putatively identified as "Helobdella stagnalis" from Sweden, Norway, Iceland, England, France, Italy, Slovenia, Turkey, Russia, and Iran, as well as numerous localities covering Canada and the USA. Our results corroborate previous studies in that European and west Asian specimens form a clade, including the neotype, which is separate from North American taxa. To alleviate future taxonomic confusion, we redescribe H. stagnalis and designate a neotype from the inferred type locality. The designation of a neotype stabilizes the taxonomy of scute-bearing leeches of the genus Helobdella and enables us to definitively correct erroneous identifications reported in previous studies. We also note that at least four lineages of scute-bearing, North American species of Helobdella lack formal descriptions.},
}
@article {pmid31716589,
year = {2019},
author = {Roh, SJ and Shin, YM and Byun, BK},
title = {A new species of Ceratosticha Meyrick, 1935 (Lepidoptera: Psychidae) from Korea.},
journal = {Zootaxa},
volume = {4560},
number = {2},
pages = {zootaxa.4560.2.12},
doi = {10.11646/zootaxa.4560.2.12},
pmid = {31716589},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Genitalia ; Larva ; *Moths ; Republic of Korea ; },
abstract = {Ceratosticha lineata Roh Byun, sp. n., is described from Korea. Adults, genitalia, and larvae of the species are described, and DNA barcodes are provided.},
}
@article {pmid31716588,
year = {2019},
author = {Zhang, XU and Hou, X and Li, G and Mu, RR and Zhang, HJ},
title = {With DNA barcoding revealing sexual dimorphism in a water mite: the first description of male Sperchon fuxiensis (Acari: Hydrachnidia: Sperchontidae).},
journal = {Zootaxa},
volume = {4560},
number = {2},
pages = {zootaxa.4560.2.11},
doi = {10.11646/zootaxa.4560.2.11},
pmid = {31716588},
issn = {1175-5334},
mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic ; Female ; Male ; *Mites/genetics ; Sex Characteristics ; Water ; },
abstract = {Sperchon fuxiensis Zhang, 2017 was published as a new species based on females alone. Two males of Sperchon were found in the same locality during our recent collection. The males resemble S. fuxiensis female in the integument pattern, excretory pore and the palps shape, but the chitinous plates of both dorsum and venter differ greatly. The males were paired with the female of S. fuxiensis using DNA barcoding, revealing unusual sexual dimorphism in the species. Descriptions and illustrations of the male of S. fuxiensis are given in the present study. Species identification based on the full-length DNA barcoding (658bp) of COI in water mites is also discussed.},
}
@article {pmid31716565,
year = {2019},
author = {Fagan-Jeffries, EP and Cooper, SJB and Austin, AD},
title = {New species of Australian microgastrine parasitoid wasps (Hymenoptera: Braconidae: Microgastrinae) documented through the 'Bush Blitz' surveys of national reserves.},
journal = {Zootaxa},
volume = {4560},
number = {3},
pages = {zootaxa.4560.3.1},
doi = {10.11646/zootaxa.4560.3.1},
pmid = {31716565},
issn = {1175-5334},
mesh = {Animals ; Australia ; *Hymenoptera ; South Australia ; Tasmania ; *Wasps ; },
abstract = {The braconid subfamily Microgastrinae are ecologically important parasitoids of larval lepidopterans, but are poorly studied in many regions of the world. In this study, we focus on describing new species of microgastrine wasps, in part from specimens collected on six different 'Bush Blitz' surveys of regional reserves in South Australia and Tasmania. Ten species of Microgastrinae are described as new and DNA barcodes of the genes COI and wingless are provided: three species in the genus Choeras Mason: C. bushblitz Fagan-Jeffries Austin sp. nov., C. parvoculus Fagan-Jeffries Austin sp. nov., and C. zygon Fagan-Jeffries Austin sp. nov.; six species in the genus Dolichogenidea Viereck: D. bonbonensis Fagan-Jeffries Austin sp. nov., D. brabyi Fagan-Jeffries Austin sp. nov., D. forrestae Fagan-Jeffries Austin sp. nov., D. garytaylori Fagan-Jeffries Austin sp. nov., D. kelleri Fagan-Jeffries Austin sp. nov., and D. lobesiae Fagan-Jeffries Austin sp. nov.; and one species from the genus Sathon Mason: S. oreo Fagan-Jeffries Austin sp. nov. These new species represent just a small fraction of the potential of 'Bush Blitz' surveys in regional Australia, which provide DNA-quality material allowing an integrative taxonomic approach and offer a window into the biodiversity of some of the least studied areas of the continent.},
}
@article {pmid31716562,
year = {2019},
author = {González-Vaquero, RA and Roig-Alsina, A},
title = {The bee Ruizanthedella mutabilis Spinola (Hymenoptera: Halictidae): a very common but poorly known species studied using integrative taxonomy.},
journal = {Zootaxa},
volume = {4563},
number = {1},
pages = {zootaxa.4563.1.12},
doi = {10.11646/zootaxa.4563.1.12},
pmid = {31716562},
issn = {1175-5334},
mesh = {Animals ; Argentina ; Bees ; Chile ; *Hymenoptera ; },
abstract = {Ruizanthedella mutabilis (Spinola) is a very abundant species in Chile and the northwest of Argentinean Patagonia. In this contribution, Halictus nigrocaeruleus Spinola 1851 is established as a junior synonym of R. mutabilis (Spinola 1851), after considering morphological data, DNA barcoding results, and biological observations. The variability in the colouration of the metasoma has been incorrectly used to distinguish these colour forms as valid species. New records enlarge the distribution of the species in Argentina, from the Andes to the Atlantic coast.},
}
@article {pmid31716539,
year = {2019},
author = {Wesener, T},
title = {First records of giant pill-millipedes from Laos (Diplopoda, Sphaerotheriida, Zephroniidae).},
journal = {Zootaxa},
volume = {4563},
number = {2},
pages = {zootaxa.4563.2.1},
doi = {10.11646/zootaxa.4563.2.1},
pmid = {31716539},
issn = {1175-5334},
mesh = {Animals ; *Arthropods ; Cambodia ; Female ; Laos ; Thailand ; },
abstract = {Before this study, giant pill-millipedes (order Sphaerotheriida) were unknown from Laos despite their presence in all surrounding countries. As by-catch from collections by arachnologists, 31 specimens of Sphaerotheriida from Laos became available for study. The sample included 14 species. Three species were only represented by females, which are described but cannot be named. Of the remaining 11 species, a single species belongs to the genus Zephronia Gray, 1832: Z. laotica n. sp.; and the other ten belong to the genus Sphaerobelum Verhoeff, 1924: S. bolavensis n. sp., S. phouloei n. sp., S. denticulatum n. sp., S. spinatum n. sp., S. lachneeis n. sp., S. peterjaegeri n. sp., S. nigrum n. sp., S. splendidum n. sp., S. laoticum n. sp., and S. schwendingeri n. sp. This more than doubles the known diversity of Sphaerobelum. Here, I integratively describe these species, combining morphology and DNA barcodes with a molecular analysis including all Zephroniidae species deposited on GenBank-including the only giant pill-millipede species known from Cambodia, Zephronia dawydoffi Attems, 1953. An updated determination key to the species of the genus is presented. Zephronia laotica n. sp. belongs to the monophyletic Zephronia sensu stricto group, which is confirmed by molecular barcoding. In contrast, most species of Sphaerobelum are in a weakly supported clade. Genetically, Sphaerobelum species differ greatly from one another, with most p-distances >15%. The lowest observed p-distance (9.8%) is between S. truncatum Wongthamwanich et al. 2012 from Thailand and S. peterjaegeri n. sp.},
}
@article {pmid31716511,
year = {2019},
author = {Nielsen, JG and Pogonoski, JJ and Appleyard, SA},
title = {Aphyonid-clade species of Australia (Teleostei, Bythitidae) with four species new to Australian waters and a new species of Barathronus.},
journal = {Zootaxa},
volume = {4564},
number = {2},
pages = {zootaxa.4564.2.12},
doi = {10.11646/zootaxa.4564.2.12},
pmid = {31716511},
issn = {1175-5334},
mesh = {Animals ; Atlantic Ocean ; Australia ; *Fishes ; Pacific Ocean ; },
abstract = {During voyages in 2017 off southern and southeastern Australia, the Australian Research Vessel Investigator deployed a series of demersal beam trawls to depths of around 5000 metres. Nineteen specimens of the rarely caught aphyonid-clade of the ophidiiform family Bythitidae, representing five species, were caught. Four of these are new to Australian waters: Barathronus pacificus Nielsen and Eagle, 1974 known from the northeastern and southwestern Pacific Ocean, Paraphyonus bolini (Nielsen, 1974) known from the western Indian and western Pacific Oceans, Paraphyonus rassi (Nielsen, 1975) known from the Atlantic Ocean and Sciadonus pedicellaris Garman, 1899, known from the northeastern Atlantic and northeastern and southwestern Pacific Oceans. Also included are Aphyonus gelatinosus Günther, 1878 known from all oceans including ten specimens from Australian waters, Barathronus maculatus Shcherbachev, 1976 known from South Africa to the westernmost Pacific including 13 specimens from Australian waters, Sciadonus longiventralis Nielsen, 2018 known from the holotype collected off New South Wales and finally Barathronus algrahami n. sp. known from the holotype caught off South Australia and four paratypes from off Taiwan and northern Philippines. Close examination of specimens collected during recent voyages combined with recent and ongoing studies by the first author and DNA COI barcoding analysis enabled an assessment of the aphyonid-clade species hitherto recorded from Australian waters. An identification key to the eight aphyonid clade species known from Australian waters is provided.},
}
@article {pmid31716391,
year = {2019},
author = {Litovkin, SV and Sazhnev, AS and Čiampor, FJ},
title = {Validation of Heterocerus heydeni Kuwert, 1890 based on morphology and DNA barcoding, with notes on the problems of classification of the Heteroceridae (Coleoptera).},
journal = {Zootaxa},
volume = {4614},
number = {1},
pages = {zootaxa.4614.1.7},
doi = {10.11646/zootaxa.4614.1.7},
pmid = {31716391},
issn = {1175-5334},
mesh = {Animals ; *Coleoptera/genetics ; DNA Barcoding, Taxonomic ; Russia ; },
abstract = {New taxonomic data on mud-loving beetles are provided based on morphological characters and DNA barcoding. Heterocerus heydeni Kuwert, 1890 was previously considered a junior synonym of H. flexuosus Stephens, 1828, but we support the validity of the species and restore the name. H. heydeni is redescribed, based on material from Central Asia and European part of Russia. Specimens of H. hauseri Kuwert, 1893 were also studied, suggesting it as a possible junior synonym of H. heydeni. We provide new DNA barcodes for H. flexuosus and Augyles cf. flavidus and comment on Heterocerus barcode data published in Barcode Of Life Data Systems (BOLD).},
}
@article {pmid31716389,
year = {2019},
author = {Levin, B and Thoni, R and Artaev, O and Bolotovskiy, A and Levina, M and Rasulov, A and Mirzoev, N and Simonov, E},
title = {Morphological and mtDNA data reveal broader distribution of Alburnoides holciki (Teleostei: Leuciscidae) in inland waters of Central Asia.},
journal = {Zootaxa},
volume = {4614},
number = {1},
pages = {zootaxa.4614.1.5},
doi = {10.11646/zootaxa.4614.1.5},
pmid = {31716389},
issn = {1175-5334},
mesh = {Animals ; Asia, Central ; *Cyprinidae ; *DNA, Mitochondrial ; Rivers ; Tajikistan ; },
abstract = {Alburnoides holciki was described from the Hari River basin, which was the only basin it was known from. Populations from the Amu Darya basin were previously recognized as A. eichwaldii or Alburnoides sp. Our study recognized specimens of Alburnoides from the Amu Darya basin as A. holciki based on morphological data and the COI barcode gene. The population from the Zeravshan basin showed some morphological differences compared to others but were similar in the COI gene and needs further investigation. New results extend the range of A. holciki for almost 1000 km -from the Hari River to the upper Amu Darya tributaries in Tajikistan. The intraspecific genetic similarity in the COI gene between populations in the Hari and Amu Darya rivers supports the geographical hypothesis of a recent connection of these rivers.},
}
@article {pmid31716353,
year = {2019},
author = {Liston, A and Prous, M and Vårdal, H},
title = {A review of West Palaearctic Hoplocampa species, focussing on Sweden (Hymenoptera, Tenthredinidae).},
journal = {Zootaxa},
volume = {4615},
number = {1},
pages = {zootaxa.4615.1.1},
doi = {10.11646/zootaxa.4615.1.1},
pmid = {31716353},
issn = {1175-5334},
mesh = {Animals ; *Hymenoptera ; Larva ; Sweden ; },
abstract = {Fourteen Hoplocampa species have been recorded in the West Palaearctic. We provide an illustrated key to these species, together with H. tadshikistanica, which is so far only known from Tadshikistan, but could occur in the West Palaearctic. The suitability of genetic sequencing for identification, particularly of larvae, is discussed. COI barcoding reliably distinguishes all European species which have been sampled (only H. phantoma lacks data), except for H. fulvicornis and H. minuta, which can be identified using nuclear sequences. Distributions in the Fennoscandian countries are outlined, with particular reference to Sweden. Hoplocampa chrysorrhoea is recorded for the first time in Scandinavia, from southern Sweden. Lectotypes are designated for twelve nominal taxa: Allantus ferrugineus Panzer, 1802, Hoplocampa chrysorrhoea var. nigrita Enslin, 1914, H. fabricii W. F. Kirby, 1882, H. oertzeni Konow, 1888, H. pectoralis Thomson, 1871, Hylotoma ferruginea Fabricius, 1804, Tenthredo alpina Zetterstedt, 1838, T. brevis Klug, 1816, T. chrysorrhoea Klug, 1816, T. crataegi Klug, 1816, T. plagiata Klug, 1816, and T. rutilicornis Klug, 1816. Hoplocampa minuta forma dudai Gregor, in Gregor Bata, 1942 is a new synonym of H. fulvicornis (Panzer, 1801).},
}
@article {pmid31716329,
year = {2019},
author = {Macià, R and Mally, R and Ylla, J and Gastón, J and Huertas, M},
title = {Integrative revision of the Iberian species of Coscinia Hübner, [1819] sensu lato and Spiris Hübner, [1819], (Lepidoptera: Erebidae, Arctiinae).},
journal = {Zootaxa},
volume = {4615},
number = {3},
pages = {zootaxa.4615.3.1},
doi = {10.11646/zootaxa.4615.3.1},
pmid = {31716329},
issn = {1175-5334},
mesh = {Animals ; Female ; Genitalia ; Male ; Mitochondria ; *Moths ; *Mustelidae ; Phylogeny ; },
abstract = {The Iberian species of the genera Coscinia Hübner, [1819] and Spiris Hübner, [1819], as well as three other species from the Mediterranean area, are revised based on morphological and molecular genetic data. Our results suggest the separation into four morphologically and phylogenetically different genera: Coscinia Hübner, [1819], Lerautia Kemal Koçak, 2006 stat. rev., Sagarriella Macià, Mally, Ylla, Gastón Huertas gen. nov. and Spiris Hübner, [1819]. We conclude that there are eight species of the Coscinia genus group present in the studied area: Coscinia cribraria (Linnaeus, 1758), Coscinia chrysocephala (Hübner, [1810]) stat. rev., Coscinia mariarosae Expósito, 1991, Sagarriella libyssa caligans (Turati, 1907) comb. nov., Sagarriella romei (Sagarra, 1924) (= romeii sensu auctorum) comb. nov., Spiris striata Hübner, [1819], Spiris slovenica (Daniel, 1939) and Lerautia bifasciata (Rambur, 1832) comb. rev. We consider Coscinia cribraria benderi (Marten, 1957) stat. nov., Coscinia c. rippertii (Boisduval, 1834) and Coscinia c. ibicenca Kobes, 1991 stat. rev. to be subspecies of C. cribraria. COI Barcodes of C. cribraria diverge by up to 7.99%, and the investigated specimens group into six different COI Barcode BINs. Both the phylogenetic analysis of mitochondrial and nuclear DNA and the morphological examination of different specimens corroborate the changes in taxonomic status and justify the proposed taxonomic categories. We present images of adults and genitalia of both sexes, the immature stages of some of the species and the subspecies studied, as well as phylogenetic results from the analysis of genetic data. We also include data on life history, foodplants and geographical distribution.},
}
@article {pmid31716328,
year = {2019},
author = {Normark, BB and Okusu, A and Morse, GE and Peterson, DA and Itioka, T and Schneider, SA},
title = {Phylogeny and classification of armored scale insects (Hemiptera: Coccomorpha: Diaspididae).},
journal = {Zootaxa},
volume = {4616},
number = {1},
pages = {zootaxa.4616.1.1},
doi = {10.11646/zootaxa.4616.1.1},
pmid = {31716328},
issn = {1175-5334},
mesh = {Animals ; Bayes Theorem ; *Hemiptera ; Phylogeny ; },
abstract = {Armored scale insects (Hemiptera: Coccomorpha: Diaspididae) are major economic pests and are among the world's most invasive species. Here we describe a system of specimen and identification management that establishes a basis for well-vouchered molecular identification. We also present an expanded Bayesian phylogenetic analysis based on concatenated fragments of 4 genetic loci: the large ribosomal subunit (28S), elongation factor-1 alpha (EF-1α), cytochrome oxidase I and II (COI‒II), and the small ribosomal subunit (16S) of the primary endosymbiont, Uzinura diaspidicola (Bacteroidetes: Flavobacteriales). Our sample includes 1,389 individuals, representing 11 outgroup species and at least 311 described and 61 undescribed diaspidid species. The results broadly support Takagi's 2002 classification but indicate that some revisions are needed. We propose a revised classification recognizing 4 subfamilies: Ancepaspidinae Borchsenius, new rank, Furcaspidinae Balachowsky, new rank, Diaspidinae Targioni Tozzetti, and Aspidiotinae Westwood. Within Aspidiotinae, in addition to the existing tribes Aspidiotini Westwood, Parlatoriini Leonardi, Odonaspidini Ferris, Leucaspidini Atkinson, and Smilacicolini Takagi, we recognize as tribes Gymnaspidini Balachowsky, new rank, and Aonidiini Balachowsky, new rank. Within Diaspidinae we recognize the 2 tribes Lepidosaphidini Shimer and Diaspidini Targioni Tozzetti, and within Diaspidini we recognize three subtribes: Diaspidina Targioni Tozzetti, Fioriniina Leonardi, and Chionaspidina Brues Melander. We regard Kuwanaspidina Borchsenius as a junior synonym of Fioriniina, Thysanaspidini Takagi as a junior synonym of Leucaspidini, and Protodiaspidina Takagi and Ulucoccinae Takagi as junior synonyms of Chionaspidina. To clarify the composition of the higher taxa we describe 2 new genera for Australian species heretofore misplaced in the genus Ancepaspis Ferris: Brimblecombia Normark (Aonidiini) and Hendersonaspis Normark (Leucaspidini). We also propose many additional minor modifications to the taxonomy of Diaspididae, including the following new combinations, revived combinations, and replacement names: Aonidia edgerleyi (Mamet), new combination (from Bigymnaspis Balachowsky); Aonidomytilus espinosai Porter, revived combination (from Porterinaspis González); Aspidiotus badius (Brain), new combination (this and the next 5 Aspidiotus species all from Aonidia Targioni Tozzetti); Aspidiotus biafrae (Lindinger), new combination; Aspidiotus chaetachmeae (Brain), new combination; Aspidiotus laticornis (Balachowsky), new combination; Aspidiotus rhusae (Brain), new combination; Aspidiotus sclerosus (Munting), new combination; Brimblecombia asperata (Brimblecombe), new combination (this and the next 5 Brimblecombia species all from Ancepaspis); Brimblecombia longicauda (Brimblecombe), new combination; Brimblecombia magnicauda (Brimblecombe), new combination; Brimblecombia reticulata (Brimblecombe), new combination; Brimblecombia rotundicauda (Brimblecombe), new combination; Brimblecombia striata (Brimblecombe), new combination; Cooleyaspis pseudomorpha (Leonardi), new combination (from Dinaspis Leonardi); Cupidaspis wilkeyi (Howell Tippins), new combination (from Paracupidaspis Howell Tippins); Cupressaspis isfarensis Borchsenius, revived combination (this species, the next 2 species in Cupressaspis Borchsenius, revived genus, and the next 9 species in Diaspidiotus Cockerell all from Aonidia); Cupressaspis mediterranea (Lindinger), revived combination; Cupressaspis relicta (Balachowsky), new combination; Diaspidiotus atlanticus (Ferris), new combination; Diaspidiotus marginalis (Brain), new combination; Diaspidiotus maroccanus (Balachowsky), new combination; Diaspidiotus mesembryanthemae (Brain), new combination; Diaspidiotus opertus (De Lotto), new combination; Diaspidiotus shastae (Coleman), new combination; Diaspidiotus simplex (Leonardi), new combination; Diaspidiotus visci (Hall), new combination; Diaspidiotus yomae (Munting), new combination; Diaspis arundinariae (Tippins Howell), new combination (from Geodiaspis Tippins Howell); Duplachionaspis arecibo (Howell), new combination (this and the next 10 Duplachionaspis MacGillivray species all from Haliaspis Takagi); Duplachionaspis asymmetrica Ferris, revived combination; Duplachionaspis distichlii (Ferris), revived combination; Duplachionaspis litoralis Ferris, revived combination; Duplachionaspis mackenziei McDaniel, revived combination; Duplachionaspis milleri (Howell), new combination; Duplachionaspis nakaharai (Howell), new combination; Duplachionaspis peninsularis (Howell), new combination; Duplachionaspis spartinae (Comstock), revived combination; Duplachionaspis texana (Liu Howell) new combination; Duplachionaspis uniolae (Takagi), new combination; Duplachionaspis mutica (Williams) (from Aloaspis Williams), new combination; Epidiaspis doumtsopi (Schneider), new combination (from Diaspis Costa); Fiorinia ficicola (Takahashi), new combination (from Ichthyaspis Takagi); Fiorinia macroprocta (Leonardi), revived combination (this and the next 2 species of Fiorinia Targioni Tozzetti all from Trullifiorinia Leonardi); Fiorinia rubrolineata Leonardi, revived combination; Fiorinia scrobicularum Green, revived combination; Genaparlatoria pseudaspidiotus (Lindinger), revived combination (from Parlatoria); Greeniella acaciae (Froggatt), new combination (this and the next 4 Greeniella Cockerell species all from Gymnaspis Newstead); Greeniella cassida (Hall Williams), new combination; Greeniella grandis (Green), new combination; Greeniella perpusilla (Maskell), new combination; Greeniella serrata (Froggatt), new combination; Hendersonaspis anomala (Green), new combination (from Ancepaspis); Hulaspis bulba (Munting), new combination (this and the next Hulaspis Hall species both from Andaspis MacGillivray); Hulaspis formicarum (Ben-Dov), new combination; Lepidosaphes antidesmae (Rao in Rao Ferris), new combination (this and the next 19 species all from Andaspis); Lepidosaphes arcana (Matile-Ferrero), new combination; Lepidosaphes betulae (Borchsenius), new combination; Lepidosaphes citricola (Young Hu), new combination; Lepidosaphes conocarpi (Takagi), new combination; Lepidosaphes crawi (Cockerell), revived combination; Lepidosaphes erythrinae Rutherford, revived combination; Lepidosaphes incisor Green, revived combination; Lepidosaphes indica (Borchsenius), new combination; Lepidosaphes kashicola Takahashi, revived combination; Lepidosaphes kazimiae (Williams), new combination; Lepidosaphes laurentina (Almeida), new combination; Lepidosaphes maai (Williams Watson), new combination; Lepidosaphes mackieana McKenzie, revived combination; Lepidosaphes micropori (Borchsenius), new combination; Lepidosaphes punicae Laing, revived combination; Lepidosaphes quercicola (Borchsenius), new combination; Lepidosaphes recurrens (Takagi Kawai), new combination; Lepidosaphes viticis (Takagi), new combination; Lepidosaphes xishuanbannae (Young Hu), new combination; Lepidosaphes giffardi (Adachi Fullaway), new combination (from Carulaspis MacGillivray); Lepidosaphes garciniae (Young Hu), new combination (this and the next 2 species all from Ductofrontaspis Young Hu); Lepidosaphes huangyangensis (Young Hu), new combination; Lepidosaphes jingdongensis (Young Hu), new combination; Lepidosaphes recurvata (Froggatt), revived combination (from Metandaspis Williams); Lepidosaphes ficicola Takahashi, revived combination (this and the next 2 species all from Ungulaspis MacGillivray); Lepidosaphes pinicolous Chen, revived combination; Lepidosaphes ungulata Green, revived combination; Lepidosaphes serrulata (Ganguli), new combination (from Velataspis Ferris); Lepidosaphes huyoung Normark, replacement name for Andaspis ficicola Young Hu; Lepidosaphes tangi Normark, replacement name for Andaspis schimae Tang; Lepidosaphes yuanfeng Normark, replacement name for Andaspis keteleeriae Yuan Feng; Leucaspis ilicitana (Gómez-Menor), new combination (from Aonidia); Lopholeucaspis spinomarginata (Green), new combination (from Gymnaspis); Melanaspis campylanthi (Lindinger), new combination (from Aonidia); Mohelnaspis bidens (Green), new combination (from Fiorinia); Parlatoria affinis (Ramakrishna Ayyar), new combination (this and the next 4 Parlatoria species all from Gymnaspis); Parlatoria ficus (Ramakrishna Ayyar), new combination; Parlatoria mangiferae (Ramakrishna Ayyar), new combination; Parlatoria ramakrishnai (Green), new combination; Parlatoria sclerosa (Munting), new combination; Parlatoria bullata (Green), new combination (from Bigymnaspis); Parlatoria leucaspis (Lindinger), new combination (this and the next species both from Cryptoparlatorea Lindinger); Parlatoria pini (Takahashi), new combination; Parlatoria tangi Normark, replacement name for Parlatoria pini Tang; Pseudoparlatoria bennetti (Williams), new combination (from Parlagena McKenzie); Pseudoparlatoria chinchonae (McKenzie), new combination (from Protodiaspis Cockerell); Pseudoparlatoria larreae (Leonardi), revived combination (from Protargionia Leonardi); Quernaspis lepineyi (Balachowsky), new combination (from Chionaspis); Rhizaspidiotus nullispinus (Munting), new combination (from Aonidia); Rolaspis marginalis (Leonardi), new combination (from Lepidosaphes); Salicicola lepelleyi (De Lotto), new combination (from Anotaspis Ferris); Tecaspis giffardi (Leonardi), new combination (from Dinaspis); Trullifiorinia geijeriae (Froggatt), new combination (from Fiorinia); Trullifiorinia nigra (Lindinger), new combination (from Crypthemichionaspis Lindinger); and Voraspis olivina (Leonardi), new combination (from Lepidosaphes).},
}
@article {pmid31716321,
year = {2019},
author = {Dumont, HJ and Vierstraete, A and Akbulut, N},
title = {Cornigerius lacustris of Lake Hazar, Turkey, a synonym of Cornigerius maeoticus (Pengo) of the Ponto-Caspian (Cladocera: Onychopoda).},
journal = {Zootaxa},
volume = {4619},
number = {1},
pages = {zootaxa.4619.1.9},
doi = {10.11646/zootaxa.4619.1.9},
pmid = {31716321},
issn = {1175-5334},
mesh = {Animals ; Black Sea ; *Cladocera ; Lakes ; Turkey ; },
abstract = {Cornigerius species are endemic to the Ponto-Caspian, with the exception of Cornigerius lacustris, which is endemic to freshwater Lake Hazar in the Euphrates basin. However, the barcoding fragment of the cytochrome c subunit I (COI) of animals from the type locality shows less than 1 % divergence with Black Sea and less than 2% with Caspian Lake C. maeoticus, the oldest and most widespread species of the genus. Black Sea and Caspian Lake animals show 1.5 % divergence. We therefore place the origin of the Hazar population in the Black Sea. Combined with a variable morphology, we also conclude that C. lacustris is a synonym of C. maeoticus, as already suspected by its describer. Dating the 'lacustris' population is difficult, but it has been there for at least a century.},
}
@article {pmid31716305,
year = {2019},
author = {Hsiao, Y and Tsai, CL},
title = {Cephalomalthinus simplicicornis (Wittmer, 1993) rev. stat. et comb. n.: a resurrected soldier beetle (Coleoptera, Cantharidae) from Taiwan based on morphological and molecular data.},
journal = {Zootaxa},
volume = {4619},
number = {2},
pages = {zootaxa.4619.2.6},
doi = {10.11646/zootaxa.4619.2.6},
pmid = {31716305},
issn = {1175-5334},
mesh = {Animals ; *Coleoptera ; Asia, Eastern ; Male ; Taiwan ; },
abstract = {The genus Cephalomalthinus Pic, 1921 is a diverse group of soldier beetles known from East Asia, with modifications on the male antennae, which are traditionally used for species delimitation. However, antennae are uniform in some Cephalomalthinus groups, thus making species identification difficult. In this study, both morphological and molecular data are applied to solve the generic classification and species status of Micropodabrus simplicicornis Wittmer, 1993, which was recently synonymized with Cephalomalthinus formosanus (Pic, 1910). We analyzed holotypes, multiple specimens and DNA barcodes to re-examine the validity of this synonymy. The results suggest that M. simplicicornis should be resurrected from the synonymy with C. formosanus, and a new combination, Cephalomalthinus simplicicornis (Wittmer, 1993) rev. stat. et comb. n., is proposed accordingly. The results highlight the value of multisource taxonomy and the discordance between molecular and morphological data.},
}
@article {pmid31716302,
year = {2019},
author = {Hsu, YF and Lu, CC and Lin, RJ and Huang, HC and Lu, CC and Liang, JY},
title = {On revised systematic status of Mycalesis suaveolens kagina Fruhstorfer, 1911, with notes on its immature biology and hostplant associations.},
journal = {Zootaxa},
volume = {4619},
number = {2},
pages = {zootaxa.4619.2.3},
doi = {10.11646/zootaxa.4619.2.3},
pmid = {31716302},
issn = {1175-5334},
mesh = {Animals ; Biology ; *Butterflies ; Female ; Genitalia ; Larva ; Male ; Taiwan ; },
abstract = {Mycalesis kagina Fruhstorfer, 1911 is separated from Mycalesis suaveolens Wood-Mason de Nicéville, 1883 to represent a species endemic to Taiwan based upon COI barcode divergence, morphological diagnosis of larva, and genitalia of both sexes. Both kagina and suaveolens are confirmed as members of the genus Mycalesis in Mycalesina. Immature morphology, biology, and hostplant associations for both species are given for the first time. Larvae of both species are recognized as specialists on Zingiberaceae, a plant family rarely used by satyrid butterflies.},
}
@article {pmid31716291,
year = {2019},
author = {Efetov, KA and Tarmann, GM and Parshkova, EV},
title = {"Ino Budensis var. Mollis" Grum-Grshimailo, 1893 (Lepidoptera: Zygaenidae) from Eastern Asia recognized as a valid species on the base of morphological and molecular analysis.},
journal = {Zootaxa},
volume = {4619},
number = {3},
pages = {zootaxa.4619.3.5},
doi = {10.11646/zootaxa.4619.3.5},
pmid = {31716291},
issn = {1175-5334},
mesh = {Animals ; China ; Asia, Eastern ; *Lepidoptera ; Republic of Korea ; Russia ; },
abstract = {Based on morphological and molecular data, Ino budensis var. mollis Grum-Grshimailo, 1893, from China, so far treated as a synonym of Jordanita (Roccia) paupera (Christoph, 1887), is here recognized as a good species, Jordanita (Roccia) mollis (Grum-Grshimailo, 1893), stat. nov. This species is recorded as new for the fauna of Russia and Korea. An identification key for this species is provided.},
}
@article {pmid31716277,
year = {2019},
author = {Mei, YU and Katoh, TK and Gao, JJ},
title = {The Hirtodrosophila melanderi species group (Diptera: Drosophilidae) from the Huanglong National Nature Reserve, Sichuan, China.},
journal = {Zootaxa},
volume = {4623},
number = {1},
pages = {zootaxa.4623.1.7},
doi = {10.11646/zootaxa.4623.1.7},
pmid = {31716277},
issn = {1175-5334},
mesh = {Animals ; China ; *Diptera ; *Drosophilidae ; Genes, Mitochondrial ; Phylogeny ; Tibet ; },
abstract = {The Hirtodrosophila melanderi species group is currently known for thirteen described species, most of which were thought to be fungivorous. More than half known species of this species group were recorded exclusively from high altitude zone to the southeast of the Qinghai-Tibet Plateau in China. In our recent field survey in the Huanglong National Nature Reserve (located to the east of the Qinghai-Tibet Plateau) in Sichuan Province, China, we collected dozens of specimens of the H. melanderi group there. In the present study, these specimens are subjected to species delimitation based on data of not only morphology, but also DNA barcodes (nucleotide sequences of a 658-bp fragment of the mitochondrial cytochrome c oxidase subunit I gene). The five new species thus recognized are described: Hirtodrosophila minshanensis sp. nov., H. lambda sp. nov., H. zhangae sp. nov., H. zouae sp. nov., and H. nigrispina sp. nov. In addition, an updated key to all species of the H. melanderi species group is provided.},
}
@article {pmid31716219,
year = {2019},
author = {Tabell, J and Mutanen, M and Sihvonen, P},
title = {Three morphologically and genetically confirmed new Pleurota species from Morocco (Lepidoptera: Gelechioidea: Oecophoridae: Pleurotinae).},
journal = {Zootaxa},
volume = {4624},
number = {3},
pages = {zootaxa.4624.3.12},
doi = {10.11646/zootaxa.4624.3.12},
pmid = {31716219},
issn = {1175-5334},
mesh = {Animals ; Female ; Genitalia ; Male ; Morocco ; *Moths ; },
abstract = {Three new Pleurota species (Oecophoridae: Pleurotinae) from Morocco, which form a species complex, are described: P. variocolor Tabell, sp. nov., P. azrouensis Tabell, sp. nov., and P. ternaria Tabell, sp. nov. Species are diagnosable by wing pattern and they have distinct genetic divergences in DNA barcodes, while genitalia structures are uniform and less informative. DNA barcodes of the new species are compared with those of all other Pleurotinae available in BOLD database. Each of the newly described species has a unique BIN (Barcode Index Number). Adult males and females, and their genitalia, are illustrated. Life histories of new species are unknown, but two of those were collected during daytime.},
}
@article {pmid31716209,
year = {2019},
author = {Liao, CQ and Yagi, S and Kobayashi, S and Huang, GH},
title = {Two new species of Bucculatrix Zeller (Lepidoptera: Bucculatricidae) from China.},
journal = {Zootaxa},
volume = {4624},
number = {3},
pages = {zootaxa.4624.3.2},
doi = {10.11646/zootaxa.4624.3.2},
pmid = {31716209},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; China ; Female ; Genitalia ; Genitalia, Male ; Male ; *Moths ; },
abstract = {Two new species of Bucculatrix are described from China: adults and male genitalia of B. yingjingensis Liao, Yagi Huang, sp. nov., are presented; and the adult female and genitalia of B. liubaensis Liao, Kobayashi Huang, sp. nov., are given, along with biological notes. DNA barcodes support the separation of two new species from each other and from related species.},
}
@article {pmid31716161,
year = {2019},
author = {Teslenko, VA and Palatov, DM and Semenchenko, AA},
title = {Description of new apterous winter species of Leuctra (Plecoptera: Leuctridae) based morphology and DNA barcoding and further records to stonefly fauna of the Caucasus, Georgia.},
journal = {Zootaxa},
volume = {4585},
number = {3},
pages = {zootaxa.4585.3.9},
doi = {10.11646/zootaxa.4585.3.9},
pmid = {31716161},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Female ; Georgia (Republic) ; *Insecta/genetics ; Male ; Turkey ; },
abstract = {Leuctra adjariae sp. n. and Leuctra georgiae sp. n. (Plecoptera: Leuctridae) are described as two new apterous stonefly species from the Meskheti Range (Lesser Caucasus) in southwestern Georgia. Descriptions and illustrations are provided for both sexes and diagnostic characters are discussed. Males and females of the two species are associated by DNA barcodes. Comparisons with corresponding regions of COI between L. adjariae sp. n. and L. georgiae sp. n. produced K2P genetic distances of 8.38%, values well associated with interspecific variation. The well-supported monophyly as well as results of an ABGD analysis confirms the validity of both new species. Capnioneura gouanerae Vinçon Sivec, 2011, previously described and known only from Turkey, is reported for the first time for the Caucasus.},
}
@article {pmid31716141,
year = {2019},
author = {Morek, W and Suzuki, AC and Schill, RO and Georgiev, D and Yankova, M and Marley, NJ and Michalczyk, &#x141;},
title = {Redescription of Milnesium alpigenum Ehrenberg, 1853 (Tardigrada: Apochela) and a description of Milnesium inceptum sp. nov., a tardigrade laboratory model.},
journal = {Zootaxa},
volume = {4586},
number = {1},
pages = {zootaxa.4586.1.2},
doi = {10.11646/zootaxa.4586.1.2},
pmid = {31716141},
issn = {1175-5334},
mesh = {Animals ; Base Sequence ; Microscopy, Electron, Scanning ; *Tardigrada ; },
abstract = {Intra- and interspecific variability, being at the very core of alpha taxonomy, has been a long-standing topic of debate among tardigrade taxonomists. Early studies tended to assume that tardigrades exhibit wide intraspecific variation. However, with more careful morphological studies, especially those incorporating molecular tools that allow for an independent verification of species identifications based on phenotypic traits, we now recognise that ranges of tardigrade intraspecific variability are narrower, and that differences between species may be more subtle than previously assumed. The taxonomic history of the genus Milnesium, and more specifically that of the nominal species, M. tardigradum described by Doyère in 1840, is a good illustration of the evolution of views on intraspecific variability in tardigrades. The assumption of wide intraspecific variability in claw morphology led Marcus (1928) to synonymise two species with different claw configurations, M. alpigenum and M. quadrifidum, with M. tardigradum. Currently claw configuration is recognised as one of the key diagnostic traits in the genus Milnesium, and the two species suppressed by Marcus have recently been suggested to be valid. In this study, we clarify the taxonomic status of M. alpigenum, a species that for nearly a century was considered invalid. We redescribe M. alpigenum, using a population collected from the locus typicus, by the means of integrative taxonomy, i.e. including light microscopy, scanning electron microscopy, ontogenetic observations, and genetic barcoding. Moreover, the redescription of M. alpigenum allowed us to verify the uncertain taxonomic status of two popular laboratory models that were originally considered to be M. tardigradum; though one was recently reidentified as M. cf. alpigenum. Our analysis showed that both laboratory strains, despite being morphologically and morphometrically nearly identical to M. alpigenum, in fact represent a new species, M. inceptum sp. nov. The two species, being disnguishable only by statistical morphometry and/or DNA sequences, are the first example of pseudocryptic species in tardigrades.},
}
@article {pmid31716133,
year = {2019},
author = {Kullander, S and Norén, M and Rahman, MM and Mollah, AR},
title = {Chameleonfishes in Bangladesh: hipshot taxonomy, sibling species, elusive species, and limits of species delimitation (Teleostei: Badidae).},
journal = {Zootaxa},
volume = {4586},
number = {2},
pages = {zootaxa.4586.2.7},
doi = {10.11646/zootaxa.4586.2.7},
pmid = {31716133},
issn = {1175-5334},
mesh = {Animals ; Bangladesh ; DNA Barcoding, Taxonomic ; *Fishes/genetics ; India ; Phylogeny ; Rivers ; },
abstract = {Five species of Badidae are reported from Bangladesh, with morphological diagnoses and mitochondrial DNA sequences (cytochrome b, cytb; and cytochrome c oxidase subunit I, coi). Dario kajal is recorded from Bangladesh for the first time with a precise locality. Badis badis is reported from several localities in central Bangladesh. Badis chittagongis is redescribed on the basis of samples from the region of Cox's Bazar, including Maheskhali Island. Badis pallidus, new species, is described from the Sangu and Karnafuli River drainages in Bangladesh. It is most similar to B. chittagongis, but differs slightly in colouration and meristics, and is separated by 3.8% uncorrected p-distance in coi from B. chittagongis. Badis chittagongis and B. pallidus are almost identical in morphology, colour pattern and meristics, but occupy different habitats and are reciprocally allopatric. Pronounced genetic difference but similar morphology in these two species may be due to strong stabilizing selection for cryptic colouration in Badis. Badis rhabdotus is a new species from northeastern Bangladesh and adjacent Meghalaya in India. It is distinguished from congeneric species by the colour pattern, including well-defined narrow vertical bars; posterior bars curved; and meristics. Species delimitation analysis of an alignment comprising all coi sequences available from GenBank longer than 600 bp and attributed to species of Badidae (21 June 2018) plus our coi sequences and outgroup sequences of Nandus nandus, using pairwise p-distance and the computer software GMYC, ABGD, and bPTP, produced similar results. Among 103 coi sequences of Badidae, unidentified or tagged with one of 18 valid species names, uncorrected p-distance suggests 27 OTUs at 2% difference threshold; ABGD found between 15 and 55 OTUs; GMYC with single evolutionary rate 33 OTUs, with multiple evolutionary rates 32 OTUs; PTP, mPTP and bPTP 27-28 OTUs. Phylogenetic analysis based on coi and cytb sequences support previous analyses and previously proposed species groups. Inadequate recent species descriptions and many misidentifications or provisional identifications of published DNA sequences hamper progress in species-level systematics in Badis. Based on published morphological data, Badis triocellus cannot be distinguished from B. singenensis; Badis dibruensis and B. pancharatnaensis cannot be distinguished from B. badis; Badis andrewraoi, B. autumnum, B. kyanos, and B. soraya are insufficiently well distinguished from each other.},
}
@article {pmid31716126,
year = {2019},
author = {Liao, C and Ohshima, I and Huang, G},
title = {A new leaf-mining moth, Caloptilia aesculi, sp. nov. (Lepidoptera: Gracillariidae: Gracillariinae) feeding on Aesculus chinensis Bunge (Hippocastanaceae) from China.},
journal = {Zootaxa},
volume = {4586},
number = {3},
pages = {zootaxa.4586.3.13},
doi = {10.11646/zootaxa.4586.3.13},
pmid = {31716126},
issn = {1175-5334},
mesh = {*Aesculus ; Animals ; China ; Female ; Hippocastanaceae ; *Lepidoptera ; Male ; *Moths ; Phylogeny ; },
abstract = {A new species of the genus Caloptilia associating with the Chinese horse chestnut, Aesculus chinensis Bunge (Hippocastanaceae) from China is described. The photographs of the adults, male and female genitalia, larva and pupa, the leaf mines and leaf shelters (rolls and stacks) are given. This is the first report of host association with Hippocastanaceae in the subfamily Gracillariinae. The sequence of mitochondrial COI barcoding region of this species is provided and its phylogenetic position is analyzed with other Caloptilia species.},
}
@article {pmid31716117,
year = {2019},
author = {Thaijarern, J and Wongpakam, K and Kangrang, A and Pramual, P},
title = {A new species of black fly (Diptera: Simuliidae) in the Simulium (Simulium) multistriatum species-group from Thailand.},
journal = {Zootaxa},
volume = {4586},
number = {3},
pages = {zootaxa.4586.3.4},
doi = {10.11646/zootaxa.4586.3.4},
pmid = {31716117},
issn = {1175-5334},
mesh = {Animals ; Indonesia ; Larva ; Phylogeny ; Pupa ; *Simuliidae ; Thailand ; Vietnam ; },
abstract = {A new black fly species of the Simulium multistriatum species-group of the subgenus Simulium Latreille is described from the mountainous area in northeastern Thailand, based on morphology and mitochondrial DNA sequences. The new species is morphologically similar to S. laui Takaoka and Sofian-Azirun and S. lacduongense Takaoka and Ya'cob originally described from Vietnam, S. fenestratum Edwards originally described from Indonesia and S. chaliowae Takaoka and Boonkemtong originally described from Thailand, but can be distinguished in the adult stage by the number of upper eye facets and globular shape of the spermatheca and in the pupal stage by the cocoon and shape of thoracic tubercles. Genetic distance and phylogenetic analyses of mitochondrial cytochrome c oxidase I sequences differentiated the new species from other members of S. multistriatum species-group. All specimens of the new species formed a monophyletic clade with strong support in all phylogenetic analyses. The minimum interspecific genetic distance of 4.9% is considerably greater than the new species maximum intraspecific genetic distance (2.7%).},
}
@article {pmid31716018,
year = {2019},
author = {Dorey, JB and Schwarz, MP and Stevens, MI},
title = {Review of the bee genus Homalictus Cockerell (Hymenoptera: Halictidae) from Fiji with description of nine new species.},
journal = {Zootaxa},
volume = {4674},
number = {1},
pages = {zootaxa.4674.1.1},
doi = {10.11646/zootaxa.4674.1.1},
pmid = {31716018},
issn = {1175-5334},
mesh = {Animals ; *Bees ; Fiji ; },
abstract = {The genus Homalictus Cockerell has not been taxonomically reviewed in the Fijian archipelago for 40 years. Here we redescribe the four known species and describe nine new ones, bringing the number of endemic Homalictus in Fiji to 13 species. We provide identifications keys to all species. Most of the species diversity (11 species) have their distributions over 800 m asl (meters above sea level; highlands), and with only two species under 800 m asl (lowlands). We highlight the vulnerability of the highland-restricted species to a warming climate, and document the potential extinction of one highland species. The new species described here are H. atritergus sp. nov., H. concavus sp. nov., H. groomi sp. nov., H. kaicolo sp. nov., H. nadarivatu sp. nov., H. ostridorsum sp. nov., H. taveuni sp. nov. H. terminalis sp. nov. and H. tuiwawae sp. nov.. [Zoobank URL: urn:lsid:zoobank.org:act:71318BEC-40CD-470F-A1E7-0E1FD18A6459].},
}
@article {pmid31716012,
year = {2019},
author = {Makarchenko, EA and Makarchenko, MA and Semenchenko, AA},
title = {Morphological description and DNA barcoding of Hydrobaenus laticaudus Sæther, 1976 (Diptera: Chironomidae: Orthocladiinae) from Amur River basin (Russian Far East).},
journal = {Zootaxa},
volume = {4674},
number = {2},
pages = {zootaxa.4674.2.4},
doi = {10.11646/zootaxa.4674.2.4},
pmid = {31716012},
issn = {1175-5334},
mesh = {Animals ; Bayes Theorem ; *Chironomidae/genetics ; DNA Barcoding, Taxonomic ; Asia, Eastern ; Male ; Phylogeny ; Rivers ; Russia ; },
abstract = {Illustrated redescription of adult male and description for the first time of pupa and fourth instar larva, as well as DNA barcoding, of Hydrobaenus laticaudus Sæther in comparison with close related known species of Hydrobaenus Fries, and an updated part of a key to species of Hydrobaenus from the Russian Far East are provided. A reference 658 bp barcode sequence from a fragment of the mitochondrial gene cytochrome oxidase I (COI) was used as a tool for species delimitation. For the estimation of interspecific distances and constructing detailed Bayesian tree within Hydrobaenus, we have obtained DNA barcoding for the two other species, H. distinctus and Hydrobaenus sp.1. The intraspecific sequence divergence of H. laticaudus based on the Kimura-2-parameter (K2P) distance ranged from 0.0-0.031, whereas the interspecific sequence divergence based on the K2P distance ranged from 0.106-0.197% between H. laticaudus and other species of genus Hydrobaenus. The well-supported monophyly as well as results of an ABGD analysis confirms the validity of H. laticaudus.},
}
@article {pmid31716006,
year = {2019},
author = {Gerstmeier, R and Morinière, J and Hendrich, L},
title = {High genetic variation within mitochondrial CO1 in Middle European Thanasimus formicarius (Linné, 1758) (Coleoptera: Cleridae).},
journal = {Zootaxa},
volume = {4674},
number = {3},
pages = {zootaxa.4674.3.7},
doi = {10.11646/zootaxa.4674.3.7},
pmid = {31716006},
issn = {1175-5334},
mesh = {Animals ; *Coleoptera/genetics ; *DNA, Mitochondrial ; England ; Europe ; France ; *Genetic Variation ; Haplotypes ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The aim of this study is to assess the species status of the Middle-European Thanasimus Latreille, 1806 species using mitochondrial CO1 sequence data. Molecular biological results clearly support the synonymy of T. pectoralis (Fuss, 1863) and T. rufipes (Brahm, 1797) with T. femoralis (Zetterstedt, 1828) as already proposed by Kolibáč (1992). Results of the present study indicate high genetic variation within T. formicarius (Linné, 1758) and emphasize the study of population dynamics of T. formicarius within Europe. Furthermore, preliminary screening of all available T. formicarius sequences on BOLD and Genbank (shorter than 500bp) indicates the presence of a "Continental" and a more "Atlantic" clade in T. formicarius. To support our hypothesis of a probably cryptic species among T. formicarius, more studies, with more specimens from different populations, especially from southern England, northern France and the northern part of the Iberian Peninsula, will be necessary.},
}
@article {pmid31716001,
year = {2019},
author = {Johnson, JW and Wilmer, JW},
title = {Epinephelus fuscomarginatus (Perciformes: Epinephelidae), a new species of grouper from off the Great Barrier Reef, Australia.},
journal = {Zootaxa},
volume = {4674},
number = {3},
pages = {zootaxa.4674.3.2},
doi = {10.11646/zootaxa.4674.3.2},
pmid = {31716001},
issn = {1175-5334},
mesh = {Animals ; Australia ; China ; Indian Ocean ; Japan ; *Perciformes ; },
abstract = {A new species of epinephelid fish from northeastern Australia is described based on five specimens 408-564 mm SL collected by deep water demersal dropline fishing. Epinephelus fuscomarginatus sp. nov. is known from the Capricorn Channel, off the southern end of the Swain Reefs, Qld, Australia, in depths of 220-230 m. It is distinguished by a combination of dorsal-fin rays XI, 14, pectoral-fin rays 17, anal-fin rays III, 8, caudal-fin rounded, lateral-line scales 60-67, gill rakers 9-10 + 16-19 = 25-28, body depth 3.0-3.4 in SL, angle of preopercle broadly rounded, bearing 4-9 small non-prominent serrae, midlateral part of lower jaw with 2 rows of teeth, tooth patches on vomer and palatines narrow, in 2-3 and 2-4 rows, respectively, and coloration including broad dark brown margins to the soft dorsal, anal and caudal fins. There are no dark spots on the head, body, or fins at any known size and in subadults there are two faint pale brown bars radiating from the eye to the posterior margin of the opercle, and diffuse irregular brown wavy bars and blotches on the sides of the body. Comparison of the mitochondrial cytochrome c oxidase subunit 1 (CO 1) genetic marker utilised in DNA barcoding produced modest but consistent genetic divergences of 1.10% and 2.70 % between E. fuscomarginatus sp. nov. and its closest sampled congeners, E. magniscuttis and E. epistictus, respectively. Further evidence is presented to indicate that populations of E. epistictus currently recognised from the Indian Ocean east to the Indo-Australian Archipelago may be distinct from those from the Sea of Japan to the East China Sea.},
}
@article {pmid31715992,
year = {2019},
author = {Cao, C and Huang, S and Xu, Y and Wu, H and Chen, T and Wang, M and DA, WA and Fan, X},
title = {New records and their associated DNA barcodes of the butterfly family Hesperiidae in Tibet, China.},
journal = {Zootaxa},
volume = {4674},
number = {4},
pages = {zootaxa.4674.4.2},
doi = {10.11646/zootaxa.4674.4.2},
pmid = {31715992},
issn = {1175-5334},
mesh = {Animals ; *Butterflies/genetics ; China ; DNA Barcoding, Taxonomic ; Phylogeny ; Tibet ; },
abstract = {The specimens of the family Hesperiidae collected from Tibet during 2016-2018 are identified using morphology. COI sequences of 76 individuals are newly obtained. The result of our morphological study is congruent with COI gene analyses. Maximum likehood (ML) and Bayesina inferences (BI) analyses reveal that individuals identified morphologically as the same species cluster cohesively. The minimum interspecific genetic distance is 1.7% between Halpe aucma and H. filda, and the genetic distance between conspecific individuals ranged from 0 to 0.2% for the genus Halpe. A total of 51 species are recognized, and six of them, Celaenorrhinus consanguineus Leech, 1891, Barca bicolor (Oberthür, 1896), Aeromachus propinquus Alphéraky, 1897, Pedesta bivitta (Oberthür, 1886), Baoris penicillata chapmani Evans, 1937, and Ochlodes brahma Moore, 1878, are reported from Tibet for the first time, and the last species is new to China.},
}
@article {pmid31715987,
year = {2019},
author = {García-Gómez, A and Palacios-Vargas, JG},
title = {Description of a new species of Willemia (Collembola: Hypogastruridae) from Panama with key to Willemia species occurring in the Americas.},
journal = {Zootaxa},
volume = {4674},
number = {5},
pages = {zootaxa.4674.5.5},
doi = {10.11646/zootaxa.4674.5.5},
pmid = {31715987},
issn = {1175-5334},
mesh = {Animals ; *Arthropods ; Panama ; },
abstract = {Willemia panamaensis sp. nov. from Panama is described and illustrated. It is characterised by the presence of sensilla I (S2) and i1 (S9) on antennal segment IV, nine vesicles in the postantennal organ, and having dorsal setae and sensilla on abdominal segments V and VI twice as long than on segments I and II. A dichotomous key to species recorded from the Americas is provided. Reference is given to the DNA barcoding sequences of the new species.},
}
@article {pmid31715979,
year = {2019},
author = {Huang, J and Gong, LU and Tsaur, SC and Zhu, L and An, K and Chen, H},
title = {Revision of the subgenus Phortica (sensu stricto) (Diptera, Drosophilidae) from East Asia, with assessment of species delimitation using DNA barcodes.},
journal = {Zootaxa},
volume = {4678},
number = {1},
pages = {zootaxa.4678.1.1},
doi = {10.11646/zootaxa.4678.1.1},
pmid = {31715979},
issn = {1175-5334},
mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; *Drosophilidae/genetics ; Asia, Eastern ; Phylogeny ; },
abstract = {A total of 50 (43 known and seven new) species in the subgenus Phortica (sensu stricto) were surveyed and (re)described from China: P. bicornuta (Chen Toda, 1997); P. bipartita (Toda Peng, 1992); P. biprotrusa (Chen Toda, 1998); P. cardua (Okada, 1977); P. chi (Toda Sidorenko, 1996); P. conifera (Okada, 1977); P. eparmata (Okada, 1977); P. eugamma (Toda Peng, 1990); P. excrescentiosa (Toda Peng, 1990); P. fangae (Máca, 1993); P. flexuosa (Zhang Gan, 1986); P. foliata (Chen Toda, 1997); P. gamma (Toda Peng, 1990); P. gigas (Okada, 1977); P. glabtabula Chen Gao, 2005; P. hainanensis (Chen Toda, 1998); P. hongae (Máca, 1993); P. huazhii Cheng Chen, 2008; P. iota (Toda Sidorenko, 1996); P. jadete Zhu, Cao Chen, 2018; P. kappa (Máca, 1977); P. lambda (Toda Peng, 1990); P. latifoliacea Chen Watabe, 2008; P. magna (Okada, 1960); P. okadai (Máca, 1977); P. omega (Okada, 1977); P. orientalis (Hendel, 1914); P. pangi Chen Wen, 2005; P. paramagna (Okada, 1971); P. perforcipata (Máca Lin, 1993); P. pi (Toda Peng, 1990); P. protrusa (Zhang Shi, 1997); P. pseudopi (Toda Peng, 1990); P. pseudotau (Toda Peng, 1990); P. psi (Zhang Gan, 1986); P. rhagolobos Chen Gao, 2008; P. saeta (Zhang Gan, 1986); P. setitabula Chen Gao, 2005; P. subradiata (Okada, 1977); P. tau (Toda Peng, 1990); P. uncinata Chen Gao, 2005; P. unipetala Chen Wen, 2005; P. allomega Gong Chen, sp. nov.; P. archikappa Gong Chen, sp. nov.; P. dianzangensis Gong Chen, sp. nov.; P. imbacilia Gong Chen, sp. nov.; P. liukuni Gong Chen, sp. nov.; P. tibeta Gong Chen, sp. nov.; and P. xianfui Gong Chen, sp. nov. In addition, seven new synonyms were recognized: P. acongruens (Zhang Shi, 1997), syn. nov.; P. antillaria (Chen Toda, 1997), syn. nov.; P. kukuanensis Máca, 2003, syn. nov.; P. linae (Máca Chen, 1993), syn. nov.; P. shillongensis (Singh Gupta, 1979), syn. nov.; P. takadai (Okada, 1977), syn. nov.; and P. watanabei (Máca Lin, 1993), syn. nov. A key to all Asian species (except for the eparmata species complex) of this subgenus was provided. All currently available DNA barcode (partial mitochondrial cytochrome c oxidase subunit I (COI) gene) sequences of this subgenus (217 sequences of 54 species) are employed in a molecular analysis using different species delimitation methods. The results indicate that approximately 68.5% (37 of 54 spp.) of Phortica (s. str.) species could be clearly distinguished from closely related morphospecies or cryptic species.},
}
@article {pmid31715962,
year = {2019},
author = {Tiunova, TM and Semenchenko, AA},
title = {Baetis pentaphyllus sp. nov., a new species of mayfly (Ephemeroptera: Baetidae) from the Russian Far East.},
journal = {Zootaxa},
volume = {4679},
number = {2},
pages = {zootaxa.4679.2.7},
doi = {10.11646/zootaxa.4679.2.7},
pmid = {31715962},
issn = {1175-5334},
mesh = {Animals ; Bayes Theorem ; *Ephemeroptera ; Asia, Eastern ; Larva ; Russia ; },
abstract = {A new species, Baetis pentaphyllus sp. nov., is described on the basis of larvae from the Far East of Russia (type locality Bolshoi Garmakan River). Larvae of Baetis pentaphyllus sp. nov. may be distinguished from other Baetis species by the presence of only five pairs of tergalii on segments III-VII. The mitochondrial COI sequence obtained from the described species was compared with the data present in GeneBank and BOLD. The DNA barcodes allowed discrimination of B. pentaphyllus sp. nov. from other species of Baetis with available sequence data. The average interspecific K2P distances were 10-15%, which are values well above those associated with intraspecific variation. COI sequences as well as 36 morphological larval characters were analysed using Bayesian inference to relate the described species to the recognized species-groups of the Baetis genus. B. pentaphyllus sp. nov formed a sister clade to B. vardarensis + B. lutheri which belong to the Baetis lutheri species-group.},
}
@article {pmid31715925,
year = {2019},
author = {Corley, M and Ferreira, S},
title = {A taxonomic revision of the Western Palaearctic genus Cacochroa Heinemann, 1870 (Lepidoptera, Depressariidae, Cryptolechiinae) with description of a new genus and a new species.},
journal = {Zootaxa},
volume = {4683},
number = {2},
pages = {zootaxa.4683.2.2},
doi = {10.11646/zootaxa.4683.2.2},
pmid = {31715925},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Female ; *Lepidoptera ; Male ; },
abstract = {Following the description of Cacochroa rosetella Corley, 2018 it soon became clear that there was considerable confusion regarding the identity of Cacochroa permixtella (Herrich-Schäffer, 1854). In this paper the genus Cacochroa is revised and this confusion is resolved, a neotype is chosen for C. permixtella and nearly all records verified. Male and female genitalia of C. permixtella are remarkably different from those of the remaining species, which are here placed in Rosetea Corley Ferreira, gen. nov. The distributions of the three species previously described in Cacochroa are clarified. Cacochroa permixtella has a distribution limited to Macedonia, Bulgaria, Greece and Turkey. Rosetea corfuella (Lvovsky, 2000), comb. nov., is recorded for the first time from Crete, Croatia, Macedonia, Turkey and Israel; the male of R. rosetella (Corley, 2018), comb. nov., is described for the first time and the species is recorded for the first time from Spain, France (mainland and Corsica), Italy (mainland and Sardinia), Greece (mainland and Crete), Croatia and Algeria. Rosetea sara sp. nov. is described from North Africa (Morocco and Tunisia). Male and female genitalia and DNA barcode data are presented for all four species.},
}
@article {pmid31715853,
year = {2019},
author = {Šumpich, J and Jaroš, J},
title = {Chrysoclista karsholti, sp. n., from Turkey, and a new record of C. germanica from central Europe (Lepidoptera: Elachistidae: Parametriotinae).},
journal = {Zootaxa},
volume = {4568},
number = {3},
pages = {zootaxa.4568.3.12},
doi = {10.11646/zootaxa.4568.3.12},
pmid = {31715853},
issn = {1175-5334},
mesh = {Animals ; Czech Republic ; Europe ; Genitalia, Male ; *Lepidoptera ; Male ; Turkey ; },
abstract = {Chrysoclista karsholti Šumpich, sp. n., is described from a single male collected in Turkey. This species most resembles C. germanica Šumpich Huemer, 2016, but differs in the colouration of the dorsum of the forewing and in the shape of the valva in the male genitalia. Differences in the DNA barcode region between these two species are rather low compared to differences between other species of the genus. Chrysoclista germanica, previously known only from the holotype, is recorded from the Czech Republic for the first time. An updated checklist of western Palaearctic Chrysoclista Stainton, 1854 is provided.},
}
@article {pmid31715818,
year = {2019},
author = {Lin, XL and Yu, HJ and Zhang, RL and Wang, XH},
title = {Polypedilum (Cerobregma) heberti sp. n. (Diptera: Chironomidae) from Gaoligong Mountains, Yunnan, China.},
journal = {Zootaxa},
volume = {4571},
number = {2},
pages = {zootaxa.4571.2.5},
doi = {10.11646/zootaxa.4571.2.5},
pmid = {31715818},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures ; Animals ; Body Size ; China ; *Chironomidae ; Male ; Organ Size ; },
abstract = {DNA barcodes and morphology recognize a new non-biting midge within the genus Polypedilum (Diptera: Chironomidae). Polypedilum (Cerobregma) heberti Lin et Wang sp. n. is described and illustrated based on an adult male from Gaoligong Mountains, Yunnan, China. Key to adult males of the subgenus Cerobregma is given.},
}
@article {pmid31715807,
year = {2019},
author = {Adamson, EAS and Britz, R and Lieng, S},
title = {Channa auroflammea, a new species of snakehead fish of the Marulius group from the Mekong River in Laos and Cambodia (Teleostei: Channidae).},
journal = {Zootaxa},
volume = {4571},
number = {3},
pages = {zootaxa.4571.3.7},
doi = {10.11646/zootaxa.4571.3.7},
pmid = {31715807},
issn = {1175-5334},
mesh = {Animals ; Cambodia ; China ; Laos ; *Perciformes ; Rivers ; },
abstract = {Channa auroflammea is a new freshwater fish species of the Marulius group from the Mekong River system. Previously reported as C. marulius, C. cf. marulius, or C. aff. marulius, C. auroflammea is readily distinguished from C. marulius and other members of the Marulius group by a different colour pattern, and a DNA barcode sequence at least 6.5% divergent from other members of the group. Comparison of counts of vertebrae, dorsal-fin rays, and lateral-line scales reveals that these counts are lower in the Mekong C. auroflammea than in C. aurolineata from the Salween and Irrawaddy-Chindwin, higher than in the Marulius group species C. pseudomarulius and C. marulioides, but similar to those in C. marulius. Channa auroflammea is known from the Mekong river and tributaries in Laos and Cambodia, where it forms a regular component of the wild fisheries catch from the rivers Tonle San and Tonle Srepok. Literature records of Channa marulius from China appear to be based on confusion originating with Cuvier's description of Ophiocephalus grandinosus.},
}
@article {pmid31715785,
year = {2019},
author = {DE Prins, J and Arévalo-Maldonado, HA and Davis, DR and Landry, B and Vargas, HA and Davis, MM and Brito, R and Fochezato, J and Ohshima, I and Moreira, GRP},
title = {An illustrated catalogue of the Neotropical Gracillariidae (Lepidoptera) with new data on primary types.},
journal = {Zootaxa},
volume = {4575},
number = {1},
pages = {zootaxa.4575.1.1},
doi = {10.11646/zootaxa.4575.1.1},
pmid = {31715785},
issn = {1175-5334},
mesh = {Animals ; *Lepidoptera ; },
abstract = {Gracillariidae leaf miners include 1987 species of poorly studied micromoths for which the majority of the diversity has been described from temperate regions. The Neotropics harbors one of the richest faunas of Gracillariidae, but the rate of taxon descriptions has been slow because of limited sampling and taxonomic activity. In this illustrated catalogue, we provide, for the first time, 476 high resolution illustrations for the 201 species of named gracillariids occurring in the region and revise their classification, newly considering the family-group names Oecophyllembiini stat. nov., Marmarini stat. nov., and Parornichini stat. nov. as tribes of Phyllocnistinae, in the first two cases and Gracillariinae in the last case respectively. Two species, Sauterina hexameris (Meyrick, 1921) comb. nov. and S. phiaropis (Meyrick, 1921) comb. nov., are transferred to Sauterina from Gracillaria. By making taxonomic, distributional, molecular and biological data available in a concise form, we aim to facilitate taxonomic work on Neotropical gracillariids, and in turn to enhance studies in general on poorly studied organisms such as parasitoids from this biogeographical region.},
}
@article {pmid31715775,
year = {2019},
author = {Li, B and Zhang, Y and Chen, H},
title = {Nine new species of the subgenus Stegana (Steganina) from China, with DNA barcoding information (Diptera: Drosophilidae).},
journal = {Zootaxa},
volume = {4576},
number = {1},
pages = {zootaxa.4576.1.4},
doi = {10.11646/zootaxa.4576.1.4},
pmid = {31715775},
issn = {1175-5334},
mesh = {Animals ; China ; DNA ; DNA Barcoding, Taxonomic ; *Drosophilidae/genetics ; Phylogeny ; },
abstract = {Eleven (two known and nine new) species of the subgenus Stegana (Steganina) from China are described or redescribed: S. (S.) longifibula Takada, 1968, S. (S.) toyaensis Okada Sidorenko, 1992, S. (S.) biflava sp. nov., S. (S.) flavivittata sp. nov., S. (S.) hirtifoliacea sp. nov., S. (S.) latitabula sp. nov., S. (S.) panda sp. nov., S. (S.) pinguifoliacea sp. nov., S. (S.) spatulata sp. nov., S. (S.) stachydifolia sp. nov. and S. (S.) unguiculata sp. nov.; they are assigned into the coleoptrata, ornatipes and undulata species groups, respectively. A total of 130 DNA sequences of partial mitochondrial cytochrome c oxidase subunit I (mtCOI) gene of 38 species (including the 11 species) of above-mentioned three groups are newly obtained in this study. These sequences and other available barcoding sequences of the three groups are involved in a molecular analysis using neighbor-joining (NJ) method, in order to assess the availability of DNA barcoding for delimiting the Steganina species. The result indicates that all the sampled Steganina morphospecies within the three groups are monophyletic.},
}
@article {pmid31715758,
year = {2019},
author = {Gyulai, P and Saldaitis, A and Truuverk, A and Vaitonis, G},
title = {A new Blepharosis species from China (Lepidoptera, Noctuidae).},
journal = {Zootaxa},
volume = {4576},
number = {3},
pages = {zootaxa.4576.3.13},
doi = {10.11646/zootaxa.4576.3.13},
pmid = {31715758},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; China ; *Lepidoptera ; Male ; *Moths ; },
abstract = {In 2017 the second author encountered a rather small Noctuidae species in western Sichuan (China) with unicolorous brown forewings and ochre reniform stigmata. Initially the six males collected resembled the taxa of the genus Cerapteryx Curtis, 1833, but the more gracile body, the finely serrate (and not bipectinated) male antennae and the late flight period indicated the need of further study. Dissection of the male genitalia revealed that the peculiar species belongs to the genus Blepharosis Boursin, 1964. The most recent review with descriptions of new Blepharosis taxa is available from Hreblay, Ronkay Plante (1998). Comparison of external and genitalia features of the newly found taxon with the known species confirmed that it represents an undescribed species, which is very different externally from all but one of the members of Blepharosis. Regarding the configuration of the male genitalia, the only similar species is Blepharosis anachoretoides (Alphéraky, 1892), displaying only surprisingly small differences between the two species. The large difference between their barcodes (13.5% difference in the COI sequences) indicate however their specific distinctness despite their similar male genitalia structures.},
}
@article {pmid31715716,
year = {2019},
author = {Winterbottom, R and Erdmann, MV},
title = {A new species of Trimma (Pisces; Gobiidae) from the Western Pacific Ocean.},
journal = {Zootaxa},
volume = {4577},
number = {3},
pages = {zootaxa.4577.3.10},
doi = {10.11646/zootaxa.4577.3.10},
pmid = {31715716},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Pacific Ocean ; Papua New Guinea ; *Perciformes ; Philippines ; Timor-Leste ; },
abstract = {A new species of Trimma, T. wangunui, is described from three localities in the western Pacific (Papua New Guinea, Timor-Leste and the Philippines). It belongs to a small group of species with scales in the predorsal midline, no scales on the cheek or the opercle, all pectoral fin rays unbranched, and a branched fifth pelvic fin ray. It differs from other species in this group in having an elongate second spine of the first dorsal fin which reaches to the bases of the 2nd-8th second dorsal-fin rays when adpressed, in having yellow bars on the head, and in the presence of vertically elongate yellow spots on a brown body when freshly collected.},
}
@article {pmid31712754,
year = {2019},
author = {Muñoz-Rodríguez, P and Carruthers, T and Wood, JRI and Williams, BRM and Weitemier, K and Kronmiller, B and Goodwin, Z and Sumadijaya, A and Anglin, NL and Filer, D and Harris, D and Rausher, MD and Kelly, S and Liston, A and Scotland, RW},
title = {A taxonomic monograph of Ipomoea integrated across phylogenetic scales.},
journal = {Nature plants},
volume = {5},
number = {11},
pages = {1136-1144},
pmid = {31712754},
issn = {2055-0278},
mesh = {Biological Specimen Banks ; DNA Barcoding, Taxonomic ; DNA, Plant ; Evolution, Molecular ; Ipomoea/*classification ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; },
abstract = {Taxonomic monographs have the potential to make a unique contribution to the understanding of global biodiversity. However, such studies, now rare, are often considered too daunting to undertake within a realistic time frame, especially as the world's collections have doubled in size in recent times. Here, we report a global-scale monographic study of morning glories (Ipomoea) that integrated DNA barcodes and high-throughput sequencing with the morphological study of herbarium specimens. Our approach overhauled the taxonomy of this megadiverse group, described 63 new species and uncovered significant increases in net diversification rates comparable to the most iconic evolutionary radiations in the plant kingdom. Finally, we show that more than 60 species of Ipomoea, including sweet potato, independently evolved storage roots in pre-human times, indicating that the storage root is not solely a product of human domestication but a trait that predisposed the species for cultivation. This study demonstrates how the world's natural history collections can contribute to global challenges in the Anthropocene.},
}
@article {pmid31712504,
year = {2019},
author = {Russell, BC and Hasan, ME and Durand, JD},
title = {Scolopsis igcarensis Mishra, Biswas, Russell, Satpathy amp; Selvanayagam, 2013, a junior synonym of S. vosmeri (Bloch, 1792) (Perciformes: Nemipteridae).},
journal = {Zootaxa},
volume = {4629},
number = {4},
pages = {zootaxa.4629.4.7},
doi = {10.11646/zootaxa.4629.4.7},
pmid = {31712504},
issn = {1175-5334},
mesh = {Animals ; Bangladesh ; India ; *Perciformes ; Phylogeny ; Sri Lanka ; },
abstract = {Scolopsis igcarensis Mishra, Biswas, Russell, Satpathy Selvanayagam, 2013 was described from specimens collected from coastal waters of southern India and Sri Lanka. A comparison of recently collected specimens from Bangladesh, initially identified as S. igcarensis, with Scolopsis vosmeri (Bloch, 1792) showed morphological differences between the two species are minor, and that specimens of S. igcarensis in fact represent juvenile and subadult colour forms of S. vosmeri. Underwater and aquarium observations, as well as molecular data based on the COI barcode region, support this conclusion. Accordingly, S. igcarensis is regarded as a junior synonym of S. vosmeri, which is redescribed herein. Phylogenetic analysis of COI barcodes of Scolopsis specimens produced in this study, together with those available from GenBank, indicate S. vosmeri is part of a species complex which includes two additional cryptic sister species that require further taxonomic investigation.},
}
@article {pmid31711827,
year = {2020},
author = {Bai, Y and Wang, Z and Liu, Z and Liang, G and Gu, W and Ge, Q},
title = {Technical progress in circulating tumor DNA analysis using next generation sequencing.},
journal = {Molecular and cellular probes},
volume = {49},
number = {},
pages = {101480},
doi = {10.1016/j.mcp.2019.101480},
pmid = {31711827},
issn = {1096-1194},
mesh = {Circulating Tumor DNA/*genetics ; Computational Biology ; DNA Mutational Analysis ; Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; },
abstract = {Circulating tumor DNA (ctDNA) is tumor-derived, fragmented DNA that circulates freely in body fluids, predominantly in the peripheral blood. Recently, ctDNA analysis has been suggested as a complement to tissue biopsy in the detection and treatment of cancer. Genetic and epigenetic information specific to tumor cells, including single nucleotide variations, copy number variations, and modified methylation patterns, can be detected in ctDNA. Importantly, mutations in heterogenous tumors that could impart therapeutic resistance could be identified in ctDNA, which would aid in cancer diagnosis, prognosis, and real-time monitoring, and inform treatment with targeted therapies. However, ctDNA is still not a routinely used method for this purpose, because its detection techniques lack adequate sensitivity for reliable use in scientific studies and clinical trials. This review provides an up-to-date summary of ctDNA mutation detection methods based on next generation sequencing, highlighting their advantages and limitations, and focusing in particular on several optimized library preparation methods for improved sensitivity and specificity of ctDNA detection.},
}
@article {pmid31711184,
year = {2020},
author = {Rosati, E and Pogorelyy, MV and Dowds, CM and Moller, FT and Sorensen, SB and Lebedev, YB and Frey, N and Schreiber, S and Spehlmann, ME and Andersen, V and Mamedov, IZ and Franke, A},
title = {Identification of Disease-associated Traits and Clonotypes in the T Cell Receptor Repertoire of Monozygotic Twins Affected by Inflammatory Bowel Diseases.},
journal = {Journal of Crohn's &amp; colitis},
volume = {14},
number = {6},
pages = {778-790},
pmid = {31711184},
issn = {1876-4479},
mesh = {Adult ; C-Reactive Protein/analysis ; *Colitis, Ulcerative/diagnosis/immunology/physiopathology ; *Crohn Disease/diagnosis/immunology/physiopathology ; Denmark ; Feces ; Female ; *Genes, T-Cell Receptor alpha ; *Genes, T-Cell Receptor beta ; Germany ; Humans ; Leukocyte L1 Antigen Complex/analysis ; Male ; Patient Acuity ; Receptors, Antigen, T-Cell, alpha-beta/*blood ; Sequence Analysis, DNA ; Smoking/immunology ; Twins, Monozygotic ; },
abstract = {BACKGROUND AND AIMS: Intestinal inflammation in inflammatory bowel diseases [IBD] is thought to be T cell mediated and therefore dependent on the interaction between the T cell receptor [TCR] and human leukocyte antigen [HLA] proteins expressed on antigen presenting cells. The collection of all TCRs in one individual, known as the TCR repertoire, is characterised by enormous diversity and inter-individual variability. It was shown that healthy monozygotic [MZ] twins are more similar in their TCR repertoire than unrelated individuals. Therefore MZ twins, concordant or discordant for IBD, may be useful to identify disease-related and non-genetic factors in the TCR repertoire which could potentially be used as disease biomarkers.<br><br>METHODS: Employing unique molecular barcoding that can distinguish between polymerase chain reaction [PCR] artefacts and true sequence variation, we performed deep TCR&#x3b1; and TCR&#x3b2; repertoire profiling of the peripheral blood of 28 MZ twin pairs from Denmark and Germany, 24 of whom were discordant and four concordant for IBD.<br><br>RESULTS: We observed disease- and smoking-associated traits such as sharing, diversity and abundance of specific clonotypes in the TCR repertoire of IBD patients, and particularly in patients with active disease, compared with their healthy twins.<br><br>CONCLUSIONS: Our findings identified TCR repertoire features specific for smokers and IBD patients, particularly when signs of disease activity were present. These findings are a first step towards the application of TCR repertoire analyses as a valuable tool to characterise inflammatory bowel diseases and to identify potential biomarkers and true disease causes.},
}
@article {pmid31710891,
year = {2019},
author = {Canzio, D and Maniatis, T},
title = {The generation of a protocadherin cell-surface recognition code for neural circuit assembly.},
journal = {Current opinion in neurobiology},
volume = {59},
number = {},
pages = {213-220},
pmid = {31710891},
issn = {1873-6882},
support = {R00 GM121815/GM/NIGMS NIH HHS/United States ; R01 MH108579/MH/NIMH NIH HHS/United States ; R01 NS088476/NS/NINDS NIH HHS/United States ; },
mesh = {Axons ; Cadherins ; Dendrites ; *Neurons ; Protein Isoforms ; },
abstract = {The assembly of functional neural circuits in vertebrate organisms requires complex mechanisms of self-recognition and self-avoidance. Neurites (axons and dendrites) from the same neuron recognize and avoid self, but engage in synaptic interactions with other neurons. Vertebrate neural self-avoidance requires the expression of distinct repertoires of clustered Protocadherin (Pcdh) cell-surface protein isoforms, which act as cell-surface molecular barcodes that mediate highly specific homophilic self-recognition, followed by repulsion. The generation of sufficiently diverse cell-surface barcodes is achieved by the stochastic and combinatorial activation of a subset of clustered Pcdh promoters in individual neurons. This remarkable mechanism leads to the generation of enormous molecular diversity at the cell surface. Here we review recent studies showing that stochastic expression of individual Pcdhα isoforms is accomplished through an extraordinary mechanism involving the activation of 'antisense strand' promoter within Pcdhα 'variable' exons, antisense transcription of a long non-coding RNA through the upstream 'sense strand' promoter, demethylation of this promoter, binding of the CTCF/cohesin complex and DNA looping to a distant enhancer through a mechanism of chromatin 'extrusion'.},
}
@article {pmid31706020,
year = {2020},
author = {Prous, M and Lee, KM and Mutanen, M},
title = {Cross-contamination and strong mitonuclear discordance in Empria sawflies (Hymenoptera, Tenthredinidae) in the light of phylogenomic data.},
journal = {Molecular phylogenetics and evolution},
volume = {143},
number = {},
pages = {106670},
doi = {10.1016/j.ympev.2019.106670},
pmid = {31706020},
issn = {1095-9513},
mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial ; Gene Flow ; Genes, Mitochondrial ; Genome, Mitochondrial ; Genomics ; Hymenoptera/*classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {In several sawfly taxa strong mitonuclear discordance has been observed, with nuclear genes supporting species assignments based on morphology, whereas the barcode region of the mitochondrial COI gene suggests different relationships. As previous studies were based on only a few nuclear genes, the causes and the degree of mitonuclear discordance remain ambiguous. Here, we obtained genomic-scale ddRAD data together with Sanger sequences of mitochondrial COI and two to three nuclear protein coding genes to investigate species limits and mitonuclear discordance in two closely related species groups of the sawfly genus Empria. As found previously based on nuclear ITS and mitochondrial COI sequences, species are in most cases supported as monophyletic based on new nuclear data reported here, but not based on mitochondrial COI. This mitonuclear discordance can be explained by occasional mitochondrial introgression with little or no nuclear gene flow, a pattern that might be common in haplodiploid taxa with slowly evolving mitochondrial genomes. Some species in the E. immersa group are not recovered as monophyletic according to either mitochondrial or nuclear data, but this could partly be because of unresolved taxonomy. Preliminary analyses of ddRAD data did not recover monophyly of E. japonica within the E. longicornis group (three Sanger sequenced nuclear genes strongly supported monophyly), but closer examination of the data and additional Sanger sequencing suggested that both specimens were substantially (possibly 10-20% of recovered loci) cross-contaminated. A reason could be specimen identification tag jumps during sequencing library preparation that in previous studies have been shown to affect up to 2.5% of the sequenced reads. We provide an R script to examine patterns of identical loci among the specimens and estimate that the cross-contamination rate is not unusually high for our ddRAD dataset as a whole (based on counting of identical sequences in the immersa and longicornis groups, which are well separated from each other and probably do not hybridise). The high rate of cross-contamination for both E. japonica specimens might be explained by the small number of recovered loci (~1000) compared to most other specimens (>10 000 in some cases) because of poor sequencing results. We caution against drawing unexpected biological conclusions when closely related specimens are pooled before sequencing and tagged only at one end of the molecule or at both ends using a unique combination of limited number of tags (less than the number of specimens).},
}
@article {pmid31704569,
year = {2020},
author = {Yang, J and Zhang, X},
title = {eDNA metabarcoding in zooplankton improves the ecological status assessment of aquatic ecosystems.},
journal = {Environment international},
volume = {134},
number = {},
pages = {105230},
doi = {10.1016/j.envint.2019.105230},
pmid = {31704569},
issn = {1873-6750},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic ; *Ecosystem ; Environmental Monitoring ; *Zooplankton ; },
abstract = {Aquatic ecosystems are monitored worldwide using a range of biological quality elements that are morphologically identified. The environmental DNA (eDNA)-based approach has unprecedented advantages (e.g., high throughput, high efficiency and low cost) for biodiversity surveys in both freshwater and marine ecosystems compared with traditional sampling and image recognition. The use of eDNA has been mostly limited to biodiversity estimation, how to apply the eDNA approach in assessing the ecological health status is largely unexplored. Here, using zooplankton as an example, we examined the application of eDNA monitoring for ecological status assessment in an aquatic ecosystem. The results showed that eDNA monitoring reflected the spatial and temporal variations in zooplankton structure. Both species composition and bio-interactions varied significantly between sampling seasons (dry, normal and wet). A total of 60 different zooplankton indices were calculated based on eDNA monitoring and most of these indices were highly correlated with the level of water pollution, which was indicated by the water quality index in one or all three seasons. Both qualitative and quantitative eDNA-based biological indices were correlated with water quality. The season-dependent eDNA zooplankton integrity index (IZI) reflected the ecological status, and this method improves the timeliness of bioassessment.},
}
@article {pmid31703754,
year = {2019},
author = {Hu, SJ and Hu, HY and Gao, H and Liu, X and Chen, SL},
title = {DNA barcoding and rapid identification of the precious herb Herba Anoectochili.},
journal = {Chinese journal of natural medicines},
volume = {17},
number = {10},
pages = {738-745},
doi = {10.1016/S1875-5364(19)30090-1},
pmid = {31703754},
issn = {1875-5364},
mesh = {DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Drugs, Chinese Herbal/*chemistry ; Phylogeny ; Plants, Medicinal/classification/*genetics ; Quality Control ; },
abstract = {Herba Anoectochili is a commonly used medicinal material. However, its adulteration is a serious concern. Due to the similar morphological characteristics of Herba Anoectochili and its adulterants, traditional identification techniques often fail to distinguish between them accurately, which is not conducive to the circulation management and safety of the medicinal materials. To improve the distinction between Herba Anoectochili and its adulterants accurately, this study identified 41 Herba Anoectochili and its adulterant samples based on the ITS2 sequence. Sequence characteristics, Basic Local Alignment Search Tool (BLAST) application, genetic distance, construction of phylogenetic tree, secondary structure prediction, and other methods showed the ITS2 sequence to accurately identify Herba Anoectochili from its adulterants. Furthermore, in this study, we designed a specific primer, based on the ITS2 sequence, and established a real-time PCR detection system for the rapid, sensitive, and specific identification of the original plant of Herba Anoectochili. Compared to DNA barcoding technology, this method has shorter detection time, stronger specificity, and higher sensitivity, which lays the foundation for the rapid identification of Herba Anoectochili.},
}
@article {pmid31703351,
year = {2019},
author = {Lusinska, J and Betekhtin, A and Lopez-Alvarez, D and Catalan, P and Jenkins, G and Wolny, E and Hasterok, R},
title = {Comparatively Barcoded Chromosomes of Brachypodium Perennials Tell the Story of Their Karyotype Structure and Evolution.},
journal = {International journal of molecular sciences},
volume = {20},
number = {22},
pages = {},
pmid = {31703351},
issn = {1422-0067},
support = {DEC-2012/04/A/NZ3/00572 and DEC-2014/14/M/NZ2/00519//National Science Centre Poland/ ; },
mesh = {Brachypodium/*genetics ; Chromosomes, Plant/*genetics ; *DNA Barcoding, Taxonomic ; *Evolution, Molecular ; *Karyotype ; *Polyploidy ; },
abstract = {The Brachypodium genus is an informative model system for studying grass karyotype organization. Previous studies of a limited number of species and reference chromosomes have not provided a comprehensive picture of the enigmatic phylogenetic relationships in the genus. Comparative chromosome barcoding, which enables the reconstruction of the evolutionary history of individual chromosomes and their segments, allowed us to infer the relationships between putative ancestral karyotypes of extinct species and extant karyotypes of current species. We used over 80 chromosome-specific BAC (bacterial artificial chromosome) clones derived from five reference chromosomes of B. distachyon as probes against the karyotypes of twelve accessions representing five diploid and polyploid Brachypodium perennials. The results showed that descending dysploidy is common in Brachypodium and occurs primarily via nested chromosome fusions. Brachypodium distachyon was rejected as a putative ancestor for allotetraploid perennials and B. stacei for B. mexicanum. We propose two alternative models of perennial polyploid evolution involving either the incorporation of a putative x = 5 ancestral karyotype with different descending dysploidy patterns compared to B. distachyon chromosomes or hybridization of two x = 9 ancestors followed by genome doubling and descending dysploidy. Details of the karyotype structure and evolution in several Brachypodium perennials are revealed for the first time.},
}
@article {pmid31696604,
year = {2020},
author = {Hsieh, CH and Huang, CG and Wu, WJ and Wang, HY},
title = {A rapid insect species identification system using mini-barcode pyrosequencing.},
journal = {Pest management science},
volume = {76},
number = {4},
pages = {1222-1227},
doi = {10.1002/ps.5674},
pmid = {31696604},
issn = {1526-4998},
support = {102AS-10.2.5-BQ-B1(3)//Bureau of Animal and Plant Health Inspection and Quarantine, Taiwan/ ; 108AS-8.4.1-BQ-B2//Bureau of Animal and Plant Health Inspection and Quarantine, Taiwan/ ; 105-2628-B-002 -015 -MY3//Ministry of Science of Technology, Taiwan/ ; 108-2313-B-034- 001//Ministry of Science of Technology, Taiwan/ ; },
mesh = {Animals ; Commerce ; DNA Barcoding, Taxonomic ; DNA Primers ; *High-Throughput Nucleotide Sequencing ; Insecta ; Internationality ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND: Rapid and accurate species identification is not only important for biodiversity studies and pest quarantine and management, but in some cases may also influence the results of international trade negotiations. In this study, we developed a rapid species identification system for insects.<br><br>RESULTS: A universal DNA mini-barcode primer pair was designed to target &#x223c;&#x2009;120&#x2009;bp of the mitochondrial 16S rDNA gene. This primer set can amplify the targeted region from all 300 species of 26 insect orders tested as well as other classes of Arthropoda. Although we found no within-species variation in this region, it provided enough information to separate closely related species or species complexes, in particular Thrips spp. and Bemisia spp. By combining a quick DNA extraction method with pyrosequencing, we were able to generate DNA sequences and complete species identification within 5&#xa0;h.<br><br>CONCLUSION: Mini-barcode pyrosequencing of 16S rDNA coupled with the GenBank database provides a rapid, accurate, and efficient species identification system. This system is therefore useful for biodiversity discovery, forensic identification, and quarantine control and management. &#xa9; 2019 Society of Chemical Industry.},
}
@article {pmid31695763,
year = {2019},
author = {Wu, W and Wang, X and Shen, M and Li, L and Yin, Y and Shen, L and Wang, W and Cui, D and Ni, J and Chen, X and Li, W},
title = {AIEgens Barcodes Combined with AIEgens Nanobeads for High-sensitivity Multiplexed Detection.},
journal = {Theranostics},
volume = {9},
number = {24},
pages = {7210-7221},
pmid = {31695763},
issn = {1838-7640},
mesh = {Allergens/analysis ; Animals ; Emulsions/chemistry ; Limit of Detection ; *Luminescence ; *Microspheres ; Nanoparticles/*chemistry ; Silicon Compounds/chemistry ; Spectrometry, Fluorescence ; Spectrophotometry, Ultraviolet ; },
abstract = {Suspension arrays based on optical encoded microspheres have attracted great attention for multiplexed detection in gene analysis, protein profiling, early disease diagnosis, treatment monitoring and so on. However, the fluorescence stability of barcodes and detection sensitivity require further improvement to meet the increasing demands of "precision diagnosis". Methods: This work reports a novel suspension array platform based on extremely stable AIEgens (AIE33 and AIE NIR800) microbeads as barcodes and AIEgens (1,1,2,3,4,5-Hexaphenyl-1H-silole, HPS) nanobeads as fluorescent signal reporter coupled with flow cytometry for multiplexed detection. Results: Due to the excellent fluorescent signal amplification effect of the HPS nanobeads, our multiplex assay showed enhanced detection sensitivity, compared to multiplex assay using QDs nanobeads (up to 3-fold improvement) and commercial organic dye of phycoerythrin (up to 5-fold improvement) as the fluorescent signal reporters. Conclusion: Furthermore, validating experiments showed similar detection performance to the clinical gold-standard method of ImmunoCAP for allergen detection in patient serum samples, demonstrating the suspension array platform based on AIEgens microbeads with excellent fluorescence stability and AIEgens nanobeads with strong signal amplification ability is promising for high-sensitivity multiplexed bioassay applications.},
}
@article {pmid31692070,
year = {2020},
author = {Tasneem, F and Shakoori, FR and Ilyas, M and Shahzad, N and Potekhin, A and Shakoori, AR},
title = {Genetic diversity of Paramecium species on the basis of multiple loci analysis and ITS secondary structure models.},
journal = {Journal of cellular biochemistry},
volume = {121},
number = {8-9},
pages = {3837-3853},
doi = {10.1002/jcb.29546},
pmid = {31692070},
issn = {1097-4644},
abstract = {Among ciliates, Paramecium has become a privileged model for the study of "species problem" particularly in the case of the "Paramecium aurelia complex" that has been intensely investigated. Despite extensive studies, the taxonomy of Paramecium is still challenging. The major problem is an uneven sampling of Paramecium with relatively few representatives of each species. To investigate species from the less discovered region (Pakistan), 10 isolates of Paramecium species including a standing-alone FT8 strain previously isolated by some of us were subjected to molecular characterization. Fragments of 18S recombinant DNA (rDNA), ITS1-5.8S-ITS2-5'LSU rDNA, cytochrome c oxidase subunit II, and hsp70 genes were used as molecular markers for phylogenetic analysis of particular isolates. The nucleotide sequences of polymerase chain reaction products of all markers were compared with the available sequences of relevant markers of other Paramecium species from GenBank. Phylogenetic trees based on all molecular markers showed that all the nine strains had a very close relationship with Paramecium primaurelia except for the FT8 strain. FT8 consistently showed its unique position in comparison to all other species in the phylogenetic trees. Available sequences of internal transcribed spacer 1 (ITS1) and ITS2 and some other ciliate sequences from GenBank were used for the construction of secondary models. Two highly conserved helices supported by compensatory base changes among all ciliates of ITS2 secondary structures were found similar to other eukaryotes. Therefore, the most conserved 120 to 180 base pairs regions were identified for their comparative studies. We found that out of the three helices in ITS1 structure, helix B was more conserved in Paramecium species. Despite various substitutions in the primary sequence, it was observed that secondary structures of ITS1 and ITS2 could be helpful in interpreting the phylogenetic relationships both at species as well as at generic level.},
}
@article {pmid31691003,
year = {2019},
author = {Mohammad Rahimi, H and Mirjalali, H and Niyyati, M and Haghighi, A and Asadzadeh Aghdaei, H and Zali, MR},
title = {Development and evaluation of high-resolution melting curve analysis for rapid detection and subtyping of Blastocystis and comparison the results with sequencing.},
journal = {Parasitology research},
volume = {118},
number = {12},
pages = {3469-3478},
pmid = {31691003},
issn = {1432-1955},
mesh = {Blastocystis/classification/genetics/*isolation &amp; purification ; Blastocystis Infections/diagnosis/*parasitology ; DNA Primers/chemistry/genetics ; DNA, Protozoan/chemistry/genetics ; Diagnostic Tests, Routine ; Feces/parasitology ; Humans ; Real-Time Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; },
abstract = {Blastocystis is a prevalent parasite that has a wide distribution. In order to design HRM real-time PCR, primers were selected from SSU rRNA gene to amplify specific fragment with different melting temperatures for each subtype of Blastocystis. Subsequently, HRM real-time PCR was performed and melting curve analysis was done by Rotor-Gene Q software. The results of HRM real-time PCR was then compared with sequence results of "barcoding region" of SSU rRNA gene of Blastocystis. To evaluate sensitivity of test, 10-fold serial dilutions of the parasite were prepared from ~ 10[6] to 1 parasite per mL of stool sample and were investigated by HRM real-time PCR. In order to determine specificity of method, HRM real-time PCR was done for some microorganisms and Blastocystis-negative stool samples. In silico analysis showed that all seventeen subtypes of Blastocystis were distinguish. In vitro analysis revealed that the test discriminated subtypes with specific melting temperatures.},
}
@article {pmid31690888,
year = {2019},
author = {Baron, CS and van Oudenaarden, A},
title = {Unravelling cellular relationships during development and regeneration using genetic lineage tracing.},
journal = {Nature reviews. Molecular cell biology},
volume = {20},
number = {12},
pages = {753-765},
doi = {10.1038/s41580-019-0186-3},
pmid = {31690888},
issn = {1471-0080},
mesh = {Animals ; *CRISPR-Cas Systems ; Cell Differentiation/*physiology ; Cell Lineage/*physiology ; Embryonic Development/*physiology ; Gene Expression Regulation, Developmental/*physiology ; High-Throughput Nucleotide Sequencing ; Humans ; Regeneration/*physiology ; },
abstract = {Tracking the progeny of single cells is necessary for building lineage trees that recapitulate processes such as embryonic development and stem cell differentiation. In classical lineage tracing experiments, cells are fluorescently labelled to allow identification by microscopy of a limited number of cell clones. To track a larger number of clones in complex tissues, fluorescent proteins are now replaced by heritable DNA barcodes that are read using next-generation sequencing. In prospective lineage tracing, unique DNA barcodes are introduced into single cells through genetic manipulation (using, for example, Cre-mediated recombination or CRISPR-Cas9-mediated editing) and tracked over time. Alternatively, in retrospective lineage tracing, naturally occurring somatic mutations can be used as endogenous DNA barcodes. Finally, single-cell mRNA-sequencing datasets that capture different cell states within a developmental or differentiation trajectory can be used to recapitulate lineages. In this Review, we discuss methods for prospective or retrospective lineage tracing and demonstrate how trajectory reconstruction algorithms can be applied to single-cell mRNA-sequencing datasets to infer developmental or differentiation tracks. We discuss how these approaches are used to understand cell fate during embryogenesis, cell differentiation and tissue regeneration.},
}
@article {pmid31690595,
year = {2019},
author = {Maixner, F},
title = {Molecular Reconstruction of the Diet in Human Stool Samples.},
journal = {mSystems},
volume = {4},
number = {6},
pages = {},
pmid = {31690595},
issn = {2379-5077},
abstract = {Understanding dietary effects on the gut microbial composition is one of the key questions in human microbiome research. It is highly important to have reliable dietary data on the stool samples to unambiguously link the microbiome composition to food intake. Often, however, self-reported diet surveys have low accuracy and can be misleading. Thereby, additional molecular biology-based methods could help to revise the diet composition. The article by Reese et al. [A. T. Reese, T. R. Kartzinel, B. L. Petrone, P. J. Turnbaugh, et al., mSystems 4(5):e00458-19, 2019, https://doi.org/10.1128/mSystems.00458-19] in a recent issue of mSystems describes a DNA metabarcoding strategy targeting chloroplast DNA markers in stool samples from 11 human subjects consuming both controlled and freely selected diets. The aim of this study was to evaluate the efficiency of this molecular method in detecting plant remains in the sample compared to the written dietary records. This study displays an important first step in implementing molecular dietary reconstructions in stool microbiome studies which will finally help to increase the accuracy of dietary metadata.},
}
@article {pmid31686955,
year = {2019},
author = {Özcan, T},
title = {Defining phylogenetic relationship of Nepeta x tmolea and its parents via DNA barcoding.},
journal = {PhytoKeys},
volume = {134},
number = {},
pages = {83-96},
pmid = {31686955},
issn = {1314-2011},
abstract = {Nepeta viscida and N. nuda subsp. nuda and N. × tmolea were examined in this study. Mainly fresh leaf pieces, dried with silica grains, were used for DNA extraction procedures via DNA isolation kits. Standard PCR techniques were executed using three different primer sets (one nuclear DNA region (nrITS) and two chloroplast DNA regions (rpl32-trnL and trnA(Leu)-trnA(Phe)-trnL-F). DNA sequences were analysed and evaluated using different molecular approaches and software. Consequently, the inconstant molecular structure and hybrid nature of N. × tmolea specimens were shown and interpreted in this study. According to our result, N. × tmolea have some intermediate characters compared to its parents. nrITS data give more information phylogenetically, and also the most polymorphic loci are seen in nrITS data. Morphological and molecular data contribute to define separation of N. × tmolea. Consequently, the inconstant molecular structure and hybrid nature of N. × tmolea specimens were shown and interpreted in this study.},
}
@article {pmid31686952,
year = {2019},
author = {Tujuba, TF and Sciarretta, A and Hausmann, A and Abate, GA},
title = {Lepidopteran biodiversity of Ethiopia: current knowledge and future perspectives.},
journal = {ZooKeys},
volume = {882},
number = {},
pages = {87-125},
pmid = {31686952},
issn = {1313-2989},
abstract = {Lepidoptera is the second largest order of insects. Encompassing moths and butterflies, it is regarded as one of the most important components of biodiversity. Here, an updated comprehensive overview of Lepidoptera recorded in Ethiopia is presented, composed of 2,438 taxa in 48 families, of which 664 are endemic. Records were compiled from various literature sources and website databases. Although still being far from complete, this review provides important baseline data for understanding zoogeographic patterns and thus for undertaking effective conservation action. Further research on Ethiopian Lepidoptera is encouraged.},
}
@article {pmid31683903,
year = {2019},
author = {Ferrito, V and Raffa, A and Rossitto, L and Federico, C and Saccone, S and Pappalardo, AM},
title = {Swordfish or Shark Slice? A Rapid Response by COIBar-RFLP.},
journal = {Foods (Basel, Switzerland)},
volume = {8},
number = {11},
pages = {},
pmid = {31683903},
issn = {2304-8158},
support = {22722132134//Universit&#xe0; di Catania/ ; },
abstract = {Market transparency is in strong demand by consumers, and the authentication of species is an important step for seafood traceability. In this study, a simple molecular strategy, COIBar-RFLP (cytochrome oxidase I barcode-restriction fragment length polymorphism), is proposed to unveil commercial fraud based on the practice of species substitution in the swordfish trade. In particular, COI barcoding allowed the identification of the species Prionace glauca, Mustelus mustelus, and Oxynotus centrina in slices labeled as Xiphias gladius. Furthermore, the enzymatic digestion of COI amplicons using the MboI restriction endonuclease allowed the simultaneous discrimination of the four species. Interestingly, an intraspecific differential MboI pattern was obtained for the swordfish samples. This pattern was useful to differentiate the two different clades revealed in this species by phylogenetic analyses using several molecular markers. These results indicate the need to strengthen regulations and define molecular tools for combating the occurrence of fraud along the seafood supply chain and show that COIBar-RFLP could become a standardized molecular tool to assess seafood authenticity.},
}
@article {pmid31683165,
year = {2020},
author = {Chiu, ES and Fox, K and Wolfe, L and Vandewoude, S},
title = {A novel test for determination of wild felid-domestic cat hybridization.},
journal = {Forensic science international. Genetics},
volume = {44},
number = {},
pages = {102160},
pmid = {31683165},
issn = {1878-0326},
support = {F30 OD023386/OD/NIH HHS/United States ; },
mesh = {Animals ; Animals, Domestic/*genetics ; Animals, Wild/*genetics ; Cat Diseases/genetics/*virology ; Cats ; Endogenous Retroviruses/*genetics ; *Hybridization, Genetic ; Leukemia Virus, Feline/*genetics ; Polymerase Chain Reaction ; },
abstract = {In October 2018, Colorado Parks and Wildlife seized an animal believed to be an illegally possessed bobcat. The owner claimed the animal was a bobcat/domestic cat hybrid, exempted from license requirements. Burden of proof lay with CPW to determine the lineage of the animal. Commercial microsatellite arrays and DNA barcoding have not been developed for identification of bobcat/domestic cat hybrids, and limited time and resources prevented development of such tests for this application. Instead, we targeted endogenous feline leukemia virus (enFeLV) to quickly and inexpensively demonstrate the absence of domestic cat DNA in the contested animal. Using this assay, we were able to confirm that the contested animal lacked enFeLV, and therefore was not a domestic cat hybrid.},
}
@article {pmid31682609,
year = {2019},
author = {Sabir, JSM and Rabah, S and Yacoub, H and Hajrah, NH and Atef, A and Al-Matary, M and Edris, S and Alharbi, MG and Ganash, M and Mahyoub, J and Al-Hindi, RR and Al-Ghamdi, KM and Hall, N and Bahieldin, A and Kamli, MR and Rather, IA},
title = {Molecular evolution of cytochrome C oxidase-I protein of insects living in Saudi Arabia.},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0224336},
pmid = {31682609},
issn = {1932-6203},
mesh = {Amino Acid Substitution ; Animals ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; *Evolution, Molecular ; Genetic Speciation ; Hymenoptera/*genetics ; Insect Proteins/*genetics ; Phylogeny ; Saudi Arabia ; },
abstract = {The study underpins barcode characterization of insect species collected from Saudi Arabia and explored functional constraints during evolution at the DNA and protein levels to expect the possible mechanisms of protein evolution in insects. Codon structure designated AT-biased insect barcode of the cytochrome C oxidase I (COI). In addition, the predicted 3D structure of COI protein indicated tyrosine in close proximity with the heme ligand, depicted substitution to phenylalanine in two Hymenopteran species. This change resulted in the loss of chemical bonding with the heme ligand. The estimated nucleotide substitution matrices in insect COI barcode generally showed a higher probability of transversion compared with the transition. Computations of codon-by-codon nonsynonymous substitutions in Hymenopteran and Hemipteran species indicated that almost half of the codons are under positive evolution. Nevertheless, codons of COI barcode of Coleoptera, Lepidoptera and Diptera are mostly under purifying selection. The results reinforce that codons in helices 2, 5 and 6 and those in loops 2-3 and 5-6 are mostly conserved and approach strong purifying selection. The overall results argue the possible evolutionary position of Hymenopteran species among those of other insects.},
}
@article {pmid31681275,
year = {2019},
author = {Schuyler, RP and Jackson, C and Garcia-Perez, JE and Baxter, RM and Ogolla, S and Rochford, R and Ghosh, D and Rudra, P and Hsieh, EWY},
title = {Minimizing Batch Effects in Mass Cytometry Data.},
journal = {Frontiers in immunology},
volume = {10},
number = {},
pages = {2367},
pmid = {31681275},
issn = {1664-3224},
support = {K23 AR070897/AR/NIAMS NIH HHS/United States ; },
mesh = {Flow Cytometry/instrumentation/*methods ; Humans ; },
abstract = {Cytometry by Time-Of-Flight (CyTOF) uses antibodies conjugated to isotopically pure metals to identify and quantify a large number of cellular features with single-cell resolution. A barcoding approach allows for 20 unique samples to be pooled and processed together in one tube, reducing the intra-barcode technical variability. However, with only 20 samples per barcode, multiple barcode sets (batches) are required to address questions in robustly powered study designs. A batch adjustment procedure is required to reduce variability across batches and to facilitate direct comparison of runs performed across multiple barcodes run over weeks, months, or years. We describe a method using technical replicates that are included in each run to determine and apply an appropriate adjustment per batch without manual intervention. The use of technical replicate samples (i.e., anchors or reference samples) avoids assumptions of sample homogeneity among batches, and allows direct estimation of batch effects and appropriate adjustment parameters applicable to all samples within a batch. Quantification of cell subpopulations and mean signal intensity pre- and post-adjustment using both manual gating and unsupervised clustering demonstrate substantial mitigation of batch effects in the anchor samples used for this adjustment calculation, and in a second validation set of technical replicates.},
}
@article {pmid31680728,
year = {2019},
author = {Ballin, NZ and Onaindia, JO and Jawad, H and Fernandez-Carazo, R and Maquet, A},
title = {High-resolution melting of multiple barcode amplicons for plant species authentication.},
journal = {Food control},
volume = {105},
number = {},
pages = {141-150},
pmid = {31680728},
issn = {0956-7135},
abstract = {In recent years, species identification in herbs has attracted considerable attention due to several cases of fraud; hence inexpensive high-throughput authentication methods are highly welcomed. Species authentication is often performed through DNA analysis and several specific regions (barcodes) are considered suitable. Each barcode (Bar) possesses different qualities in terms of universality and discrimination power. A multiplexed format where information can be extracted simultaneously from several barcode regions is seemingly appropriate to ensure the power of both universality and discrimination. In this approach, we amplified DNA from five different barcode regions in a multiplexed PCR format followed by high-resolution melting (HRM). This multiplexed Bar-HRM approach was first applied to plants spanning the plant kingdom and then gradually narrowing down the genetic variability within the Lamiaceae and the Solanaceae families to finally reach closely related cultivars. Universality was demonstrated through distinct melting profiles obtained for species originating from 29 different families spanning the angiosperms, gymnosperm, mosses, and liverwort (Marchantiophyta). Discrimination power was retained for species, sub-species, and a few cultivars through the application of multivariate statistics to the high-resolution melting profiles. This preliminary investigation has shown the potential to discriminate a vast amount of species within the whole plant kingdom. It requires no a priori knowledge of the species' DNA sequence and occurs in a closed system within 2.5 h at a reduced cost per sample compared to other DNA based approaches.},
}
@article {pmid31679243,
year = {2019},
author = {Mason, C and Erlick, B and La Belle, JT},
title = {Proof of Concept for a Universal Identification System for Medical Devices.},
journal = {Critical reviews in biomedical engineering},
volume = {47},
number = {2},
pages = {153-158},
doi = {10.1615/CritRevBiomedEng.2019026534},
pmid = {31679243},
issn = {1943-619X},
mesh = {Chromium/chemistry ; Electronic Data Processing/instrumentation ; Equipment and Supplies/*standards ; Humans ; Iron/chemistry ; Lead/chemistry ; Metals ; Optics and Photonics ; Patient Safety ; Photons ; Powders ; Proof of Concept Study ; *Prostheses and Implants ; Signal Processing, Computer-Assisted ; Software ; Spectrometry, Fluorescence ; Temperature ; Titanium/chemistry ; Water/chemistry ; X-Rays ; },
abstract = {Medical devices need a unified way of accessing information that uniquely identifies them. This can provide traceability to specifications, lot numbers, recalls, and the like. Such a system would have applications for devices both in and out of the body. Common barcodes, such as a UPC code, can only be read in plain sight, when nothing comes between the scanner and the code. UPC coding is not suitable for all medical devices because some are implanted in the body or are otherwise inaccessible without invasive techniques. This article demonstrates a proof of concept for XRF coding on devices. Material codes were made and read externally by an XRF reader. The reading showed trace amounts of the chemicals that compose the medical device in the background signal. The energy levels of the chemicals were assigned values to build a readable code correlated with information about the medical device it is attached to. Attachment can be made during material synthesis, part or product manufacture, or even after final assembly. The technique demonstrated here is a promising concept for the future of medical device detection.},
}
@article {pmid31678653,
year = {2019},
author = {Guimaraes, PPG and Zhang, R and Spektor, R and Tan, M and Chung, A and Billingsley, MM and El-Mayta, R and Riley, RS and Wang, L and Wilson, JM and Mitchell, MJ},
title = {Ionizable lipid nanoparticles encapsulating barcoded mRNA for accelerated in vivo delivery screening.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {316},
number = {},
pages = {404-417},
pmid = {31678653},
issn = {1873-4995},
support = {DP2 TR002776/TR/NCATS NIH HHS/United States ; P30 CA016520/CA/NCI NIH HHS/United States ; T32 HL007954/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Electronic Data Processing ; Female ; *Gene Transfer Techniques ; Genetic Therapy ; Lipids/*chemistry ; Mice ; Mice, Inbred C57BL ; Microfluidics ; *Nanoparticles ; RNA, Messenger/*administration &amp; dosage ; },
abstract = {Messenger RNA (mRNA) has recently emerged as a promising class of nucleic acid therapy, with the potential to induce protein production to treat and prevent a range of diseases. However, the widespread use of mRNA as a therapeutic requires safe and effective in vivo delivery technologies. Libraries of ionizable lipid nanoparticles (LNPs) have been designed to encapsulate mRNA, prevent its degradation, and mediate intracellular delivery. However, these LNPs are typically characterized and screened in an in vitro setting, which may not fully replicate the biological barriers that they encounter in vivo. Here, we designed and evaluated a library of engineered LNPs containing barcoded mRNA (b-mRNA) to accelerate the screening of mRNA delivery platforms in vivo. These b-mRNA are similar in structure and function to regular mRNA, and contain barcodes that enable their delivery to be quantified via deep sequencing. Using a mini-library of b-mRNA LNPs formulated via microfluidic mixing, we show that these different formulations can be pooled together, administered intravenously into mice as a single pool, and their delivery to multiple organs (liver, spleen, brain, lung, heart, kidney, pancreas, and muscle) can be quantified simultaneously using deep sequencing. In the context of liver and spleen delivery, LNPs that exhibited high b-mRNA delivery also yielded high luciferase expression, indicating that this platform can identify lead LNP candidates as well as optimal formulation parameters for in vivo mRNA delivery. Interestingly, LNPs with identical formulation parameters that encapsulated different types of nucleic acid barcodes (b-mRNA versus a DNA barcode) altered in vivo delivery, suggesting that the structure of the barcoded nucleic acid affects LNP in vivo delivery. This platform, which enables direct barcoding and subsequent quantification of a functional mRNA, can accelerate the in vivo screening and design of LNPs for mRNA therapeutic applications such as CRISPR-Cas9 gene editing, mRNA vaccination, and other mRNA-based regenerative medicine and protein replacement therapies.},
}
@article {pmid31677971,
year = {2019},
author = {Carter, JA and Preall, JB and Atwal, GS},
title = {Bayesian Inference of Allelic Inclusion Rates in the Human T Cell Receptor Repertoire.},
journal = {Cell systems},
volume = {9},
number = {5},
pages = {475-482.e4},
doi = {10.1016/j.cels.2019.09.006},
pmid = {31677971},
issn = {2405-4720},
support = {T32 GM008444/GM/NIGMS NIH HHS/United States ; },
mesh = {Alleles ; Bayes Theorem ; Databases, Genetic ; Gene Frequency/genetics ; Humans ; Receptors, Antigen, T-Cell/*genetics/physiology ; Receptors, Antigen, T-Cell, alpha-beta/*genetics/metabolism ; Single-Cell Analysis/methods ; T-Lymphocytes/metabolism ; },
abstract = {A small population of αβ T cells is characterized by the expression of more than one unique T cell receptor (TCR); this outcome is the result of "allelic inclusion," that is, inclusion of both α- or β-chain alleles during V(D)J recombination. Limitations in single-cell sequencing technology, however, have precluded comprehensive enumeration of these dual receptor T cells. Here, we develop and experimentally validate a fully Bayesian inference model capable of reliably estimating the true rate of α and β TCR allelic inclusion across two different emulsion-barcoding single-cell sequencing platforms. We provide a database composed of over 51,000 previously unpublished allelic inclusion TCR sequence sets drawn from eight healthy individuals and show that allelic inclusion contributes a distinct and functionally important set of sequences to the human TCR repertoire. This database and a Python implementation of our statistical inference model are freely available at our Github repository (https://github.com/JasonACarter/Allelic_inclusion).},
}
@article {pmid31676507,
year = {2020},
author = {Pallares, LF and Picard, S and Ayroles, JF},
title = {TM3'seq: A Tagmentation-Mediated 3' Sequencing Approach for Improving Scalability of RNAseq Experiments.},
journal = {G3 (Bethesda, Md.)},
volume = {10},
number = {1},
pages = {143-150},
pmid = {31676507},
issn = {2160-1836},
support = {R01 ES029929/ES/NIEHS NIH HHS/United States ; R35 GM124881/GM/NIGMS NIH HHS/United States ; },
mesh = {3' Untranslated Regions ; Animals ; Costs and Cost Analysis ; Drosophila melanogaster ; Female ; Humans ; RNA, Messenger/chemistry/genetics ; RNA-Seq/economics/*methods/standards ; Reproducibility of Results ; },
abstract = {RNA-seq has become the standard tool for collecting genome-wide expression data in diverse fields, from quantitative genetics and medical genomics to ecology and developmental biology. However, RNA-seq library preparation is still prohibitive for many laboratories. Recently, the field of single-cell transcriptomics has reduced costs and increased throughput by adopting early barcoding and pooling of individual samples -producing a single final library containing all samples. In contrast, RNA-seq protocols where each sample is processed individually are significantly more expensive and lower throughput than single-cell approaches. Yet, many projects depend on individual library generation to preserve important samples or for follow-up re-sequencing experiments. Improving on currently available RNA-seq methods we have developed TM3'seq, a 3'-enriched library preparation protocol that uses Tn5 transposase and preserves sample identity at each step. TM3'seq is designed for high-throughput processing of individual samples (96 samples in 6h, with only 3h hands-on time) at a fraction of the cost of commercial kits ($1.5 per sample). The protocol was tested in a range of human and Drosophila melanogaster RNA samples, recovering transcriptomes of the same quality and reliability than the commercial NEBNext kit. We expect that the cost- and time-efficient features of TM3'seq make large-scale RNA-seq experiments more permissive for the entire scientific community.},
}
@article {pmid31675177,
year = {2020},
author = {Spurgeon, BEJ and Naseem, KM},
title = {Phosphoflow cytometry and barcoding in blood platelets: Technical and analytical considerations.},
journal = {Cytometry. Part B, Clinical cytometry},
volume = {98},
number = {2},
pages = {123-130},
doi = {10.1002/cyto.b.21851},
pmid = {31675177},
issn = {1552-4957},
mesh = {Blood Platelets/chemistry/cytology/*metabolism ; Flow Cytometry/*methods/standards ; Metabolome ; Metabolomics/methods/standards ; Phosphoproteins/analysis/*metabolism ; Phosphorylation/physiology ; Phosphotransferases/metabolism ; Protein Processing, Post-Translational ; Proteomics/methods/standards ; Quality Control ; Staining and Labeling/methods/standards ; },
abstract = {Platelet function is regulated by finely tuned phosphoprotein signals. Subtle aberrations in signaling can cause platelet hyperactivity and severe cardiovascular events. Mapping phosphorylation profiles in health and disease could accelerate antiplatelet discovery and enhance cardiovascular management, but traditional assays are ill-suited to clinical application as they are laborious and low throughput. Recent advances in multiplex flow cytometry (barcoding) allow the rapid acquisition of highly batched samples with standard laboratory equipment. However, many assays have not been standardized, and success is largely dependent on protocol/reagent selection. Accordingly, we review the technical steps that are key to success with an emphasis on fixation, permeabilization, staining, controls, and data visualization.},
}
@article {pmid31674085,
year = {2019},
author = {Young, MR and Proctor, HC and deWaard, JR and Hebert, PDN},
title = {DNA barcodes expose unexpected diversity in Canadian mites.},
journal = {Molecular ecology},
volume = {28},
number = {24},
pages = {5347-5359},
doi = {10.1111/mec.15292},
pmid = {31674085},
issn = {1365-294X},
mesh = {Animals ; Arachnida/classification/genetics ; Canada ; DNA/genetics ; *DNA Barcoding, Taxonomic ; Ecosystem ; Genetic Variation/*genetics ; Mites/classification/*genetics ; },
abstract = {Mites (Arachnida: Acariformes, Parasitiformes) are the most abundant and species-rich group of arthropods in soil, but are also diverse in freshwater habitats, on plants, and as symbionts of larger animals. However, assessment of their diversity has been impeded by their small size and often cryptic morphology. As a consequence, published estimates of their species richness span more than two orders of magnitude (0.4-114 million). In this study we employ DNA barcoding and the Barcode Index Number (BIN) system to investigate mite diversity at over 1,800 sites across Canada, primarily from soil and litter habitats with smaller contributions from freshwater, plants, and animal hosts. Barcodes from 73,394 specimens revealed 7,077 BINs with representatives from all four orders (Ixodida, Mesostigmata, Sarcoptiformes, Trombidiformes) and 60% (186) of the known families. The BIN total is 2.4 times the number of species previously recorded from Canada (2,999), reflecting the unexpectedly high richness of several families. Richness projections suggest that more than 28,000 BINs occur at the sampled locations, indicating that the Canadian mite fauna almost certainly includes more than 30,000 species-a total similar to that for the most diverse insect order in Canada, Diptera. This unexpected diversity was partitioned into highly dissimilar, spatially-structured assemblages that likely reflect dispersal limitation and environmental heterogeneity. Further sampling of a greater diversity of habitats will refine understanding of mite diversity in Canada, but similar analyses in other geographic regions will be essential to ascertain their diversity at a global scale.},
}
@article {pmid31671920,
year = {2019},
author = {Lipps, C and Northe, P and Figueiredo, R and Rohde, M and Brahmer, A and Krämer-Albers, EM and Liebetrau, C and Wiedenroth, CB and Mayer, E and Kriechbaum, SD and Dörr, O and Nef, H and Hamm, CW and Keller, T and Troidl, C},
title = {Non-Invasive Approach for Evaluation of Pulmonary Hypertension Using Extracellular Vesicle-Associated Small Non-Coding RNA.},
journal = {Biomolecules},
volume = {9},
number = {11},
pages = {},
pmid = {31671920},
issn = {2218-273X},
mesh = {Aged ; Case-Control Studies ; Extracellular Vesicles/*metabolism ; Female ; Humans ; Hypertension, Pulmonary/*genetics/*pathology ; Male ; Middle Aged ; RNA, Small Untranslated/*genetics ; },
abstract = {Extracellular vesicles are released by numerous cell types of the human body under physiological but also under pathophysiological conditions. They are important for cell-cell communication and carry specific signatures of peptides and RNAs. In this study, we aimed to determine whether extracellular vesicles isolated from patients with pulmonary hypertension show a disease specific signature of small non-coding RNAs and thus have the potential to serve as diagnostic and prognostic biomarkers. Extracellular vesicles were isolated from the serum of 23 patients with chronic thromboembolic pulmonary hypertension (CTEPH) and 23 controls using two individual methods: a column-based method or by precipitation. Extracellular vesicle- associated RNAs were analyzed by next-generation sequencing applying molecular barcoding, and differentially expressed small non-coding RNAs were validated by quantitative real-time polymerase chain reaction (qRT-PCR). We identified 18 microRNAs and 21 P-element induced wimpy testis (PIWI)-interacting RNAs (piRNAs) or piRNA clusters that were differentially expressed in CTEPH patients compared with controls. Bioinformatic analysis predicted a contribution of these piRNAs to the progression of cardiac and vascular remodeling. Expression levels of DQ593039 correlated with clinically meaningful parameters such as mean pulmonary arterial pressure, pulmonary vascular resistance, right ventricular systolic pressure, and levels of N-terminal pro-brain natriuretic peptide. Thus, we identified the extracellular vesicle- derived piRNA, DQ593039, as a potential biomarker for pulmonary hypertension and right heart disease.},
}
@article {pmid31671909,
year = {2019},
author = {Krehenwinkel, H and Pomerantz, A and Prost, S},
title = {Genetic Biomonitoring and Biodiversity Assessment Using Portable Sequencing Technologies: Current Uses and Future Directions.},
journal = {Genes},
volume = {10},
number = {11},
pages = {},
pmid = {31671909},
issn = {2073-4425},
mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/instrumentation/*methods ; Ecological Parameter Monitoring/instrumentation/*methods ; Nanopore Sequencing/instrumentation/*methods ; },
abstract = {We live in an era of unprecedented biodiversity loss, affecting the taxonomic composition of ecosystems worldwide. The immense task of quantifying human imprints on global ecosystems has been greatly simplified by developments in high-throughput DNA sequencing technology (HTS). Approaches like DNA metabarcoding enable the study of biological communities at unparalleled detail. However, current protocols for HTS-based biodiversity exploration have several drawbacks. They are usually based on short sequences, with limited taxonomic and phylogenetic information content. Access to expensive HTS technology is often restricted in developing countries. Ecosystems of particular conservation priority are often remote and hard to access, requiring extensive time from field collection to laboratory processing of specimens. The advent of inexpensive mobile laboratory and DNA sequencing technologies show great promise to facilitate monitoring projects in biodiversity hot-spots around the world. Recent attention has been given to portable DNA sequencing studies related to infectious organisms, such as bacteria and viruses, yet relatively few studies have focused on applying these tools to Eukaryotes, such as plants and animals. Here, we outline the current state of genetic biodiversity monitoring of higher Eukaryotes using Oxford Nanopore Technology's MinION portable sequencing platform, as well as summarize areas of recent development.},
}
@article {pmid31671512,
year = {2019},
author = {Carneiro de Melo Moura, C and Brambach, F and Jair Hernandez Bado, K and Krutovsky, KV and Kreft, H and Tjitrosoedirdjo, SS and Siregar, IZ and Gailing, O},
title = {Integrating DNA Barcoding and Traditional Taxonomy for the Identification of Dipterocarps in Remnant Lowland Forests of Sumatra.},
journal = {Plants (Basel, Switzerland)},
volume = {8},
number = {11},
pages = {},
pmid = {31671512},
issn = {2223-7747},
support = {Collaborative Research Centre 990//Deutsche Forschungsgemeinschaft/ ; },
abstract = {DNA barcoding has been used as a universal tool for phylogenetic inferences and diversity assessments, especially in poorly studied species and regions. The aim of this study was to contrast morphological taxonomy and DNA barcoding, using the three frequently used markers matK, rbcL, and trnL-F, to assess the efficiency of DNA barcoding in the identification of dipterocarps in Sumatra, Indonesia. The chloroplast gene matK was the most polymorphic among these three markers with an average interspecific genetic distance of 0.020. The results of the molecular data were mostly in agreement with the morphological identification for the clades of Anthoshorea, Hopea, Richetia, Parashorea, and Anisoptera, nonetheless these markers were inefficient to resolve the relationships within the Rubroshorea group. The maximum likelihood and Bayesian inference phylogenies identified Shorea as a paraphyletic genus, Anthoshorea appeared as sister to Hopea, and Richetia was sister to Parashorea. A better discriminatory power among dipterocarp species provided by matK and observed in our study suggests that this marker has a higher evolutionary rate than the other two markers tested. However, a combination of several different barcoding markers is essential for reliable identification of the species at a lower taxonomic level.},
}
@article {pmid31671443,
year = {2019},
author = {Diallo, AO and Kiemtoré, T and Bicaba, BW and Medah, I and Tarbangdo, TF and Sanou, S and Soeters, HM and Novak, RT and Aké, HF},
title = {Development and Implementation of a Cloud-Based Meningitis Surveillance and Specimen Tracking System in Burkina Faso, 2018.},
journal = {The Journal of infectious diseases},
volume = {220},
number = {220 Suppl 4},
pages = {S198-S205},
pmid = {31671443},
issn = {1537-6613},
mesh = {Adolescent ; Adult ; *Biological Specimen Banks ; Burkina Faso/epidemiology ; Child ; Child, Preschool ; *Cloud Computing ; Geography, Medical ; History, 21st Century ; Humans ; Infant ; Meningitis, Meningococcal/*epidemiology/history/microbiology ; *Patient Identification Systems ; *Population Surveillance/methods ; Young Adult ; },
abstract = {Nationwide case-based meningitis surveillance was established in Burkina Faso following the introduction of meningococcal serogroup A conjugate vaccine in 2010. However, timely tracking and arrival of cerebrospinal fluid specimens for confirmation at national reference laboratories remained suboptimal. To better understand this gap and identify bottlenecks, the Burkina Faso Ministry of Health, along with key partners, developed and implemented a cloud-based System for Tracking Epidemiological Data and Laboratory Specimens (STELAB), allowing for timely nationwide data reporting and specimen tracking using barcodes. STELAB was adapted to Burkina Faso's infrastructure to ensure suitability, functionality, flexibility, and sustainability. We describe the design, development, and implementation of STELAB. In addition, we discuss strategies used to promote sustainability, lessons learned during the first year of implementation, and future directions. STELAB's novel design and country-driven approach has the potential to achieve sustainable real-time data reporting and specimen tracking for the first time in sub-Saharan Africa.},
}
@article {pmid31670953,
year = {2019},
author = {Cui, X and Jin, M and Zhang, C and Du, P and Chen, G and Qin, G and Jiang, Z and Zhang, Y and Li, M and Liao, Y and Wang, Y and Cao, Z and Yan, F and Abd El-Aty, AM and Wang, J},
title = {Enhancing the Sensitivity of the Bio-barcode Immunoassay for Triazophos Detection Based on Nanoparticles and Droplet Digital Polymerase Chain Reaction.},
journal = {Journal of agricultural and food chemistry},
volume = {67},
number = {46},
pages = {12936-12944},
doi = {10.1021/acs.jafc.9b05147},
pmid = {31670953},
issn = {1520-5118},
mesh = {DNA/genetics ; Gold/chemistry ; Immunoassay/instrumentation/*methods ; Insecticides/*analysis ; Limit of Detection ; Magnetics/methods ; Metal Nanoparticles/chemistry ; Organothiophosphates/*analysis ; Polymerase Chain Reaction/*methods ; Triazoles/*analysis ; },
abstract = {An ultrasensitive bio-barcode competitive immunoassay method based on droplet digital polymerase chain reaction (ddPCR) was developed for the determination of triazophos. Gold nanoparticles (AuNPs) were coated with monoclonal antibodies (mAbs) and complementary double-stranded DNA (dsDNA), which included bio-barcode DNA and thiol-capped DNA. Magnetic nanoparticle (MNP) probes were constructed by modifying the MNPs with ovalbumin-hapten conjugates (OVA-hapten). The target pesticide and OVA-hapten on the surface of the MNP probes competed with the AuNP probes simultaneously, and then the bio-barcode DNA was released for quantification by ddPCR. The concentration of released DNA was inversely proportional to the concentration of pesticide to be tested. Under the optimum conditions, the competitive immunoassay exhibited a wide linear range of 0.01-20 ng/mL and a low detection limit of 0.002 ng/mL. Spike recovery tests were carried out using apple, rice, cabbage, and cucumber samples to verify the feasibility of the method. The recovery and relative standard deviations (RSDs) of the technique ranged from 76.9 to 94.4% and from 10.8 to 19.9%, respectively. To further validate the results, a linear correlation analysis was performed between the proposed method and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Consequently, the bio-barcode immunoassay based on nanoparticles and ddPCR, an ultrasensitive method, showed great potential for the determination of target pesticides in real samples.},
}
@article {pmid31670116,
year = {2020},
author = {Xing, RR and Hu, RR and Han, JX and Deng, TT and Chen, Y},
title = {DNA barcoding and mini-barcoding in authenticating processed animal-derived food: A case study involving the Chinese market.},
journal = {Food chemistry},
volume = {309},
number = {},
pages = {125653},
doi = {10.1016/j.foodchem.2019.125653},
pmid = {31670116},
issn = {1873-7072},
mesh = {Animals ; China ; DNA/*analysis/isolation &amp; purification/metabolism ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/analysis/genetics/metabolism ; Fishes/*genetics ; Meat/analysis ; Poultry/*genetics ; RNA, Ribosomal, 16S/analysis/metabolism ; },
abstract = {This study used DNA barcoding and DNA mini-barcoding to test a variety of animal-derived food products sold in the Chinese market for potential mislabeling. Samples (52) including meat, poultry, and fish purchased from retail and online sources were examined. Regions of cytochrome C oxidase I (COI) gene (~650 bp) and 16S rRNA (~220 bp) were used as full- and mini-barcode markers, respectively. Approximately 94% (49 of 52) of the samples generated barcode sequences. The failure rate for full COI full-barcodes was 44%, but we obtained the 16S rRNA mini-barcode from 87% of the COI-failed cases. Overall, the survey revealed that 23% (12 of 52) of animal-derived products were mislabeled and, in most cases, contain undeclared species. Thus, regulatory measures and continuous monitoring for mislabeling of animal-derived products should be conducted.},
}
@article {pmid31667012,
year = {2019},
author = {Serdari, D and Kostaki, EG and Paraskevis, D and Stamatakis, A and Kapli, P},
title = {Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7754},
pmid = {31667012},
issn = {2167-8359},
abstract = {BACKGROUND: The classification of hepatitis viruses still predominantly relies on ad hoc criteria, i.e., phenotypic traits and arbitrary genetic distance thresholds. Given the subjectivity of such practices coupled with the constant sequencing of samples and discovery of new strains, this manual approach to virus classification becomes cumbersome and impossible to generalize.<br><br>METHODS: Using two well-studied hepatitis virus datasets, HBV and HCV, we assess if computational methods for molecular species delimitation that are typically applied to barcoding biodiversity studies can also be successfully deployed for hepatitis virus classification. For comparison, we also used ABGD, a tool that in contrast to other distance methods attempts to automatically identify the barcoding gap using pairwise genetic distances for a set of aligned input sequences.<br><br>RESULTS&#x2014;DISCUSSION: We found that the mPTP species delimitation tool identified even without adapting its default parameters taxonomic clusters that either correspond to the currently acknowledged genotypes or to known subdivision of genotypes (subtypes or subgenotypes). In the cases where the delimited cluster corresponded to subtype or subgenotype, there were previous concerns that their status may be underestimated. The clusters obtained from the ABGD analysis differed depending on the parameters used. However, under certain values the results were very similar to the taxonomy and mPTP which indicates the usefulness of distance based methods in virus taxonomy under appropriate parameter settings. The overlap of predicted clusters with taxonomically acknowledged genotypes implies that virus classification can be successfully automated.},
}
@article {pmid31666382,
year = {2020},
author = {McCune, BT and Lanahan, MR and tenOever, BR and Pfeiffer, JK},
title = {Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses.},
journal = {Journal of virology},
volume = {94},
number = {2},
pages = {},
pmid = {31666382},
issn = {1098-5514},
support = {R37 AI074668/AI/NIAID NIH HHS/United States ; F32 AI138392/AI/NIAID NIH HHS/United States ; R01 AI074668/AI/NIAID NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; T32 AI007520/AI/NIAID NIH HHS/United States ; T32 GM109776/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Enterovirus B, Human/*physiology ; *Enterovirus Infections/genetics/metabolism/pathology ; HeLa Cells ; Humans ; Mice ; Mice, Knockout ; *Virus Replication ; },
abstract = {The gastrointestinal tract presents a formidable barrier for pathogens to initiate infection. Despite this barrier, enteroviruses, including coxsackievirus B3 (CVB3), successfully penetrate the intestine to initiate infection and spread systemically prior to shedding in stool. However, the effect of the gastrointestinal barrier on CVB3 population dynamics is relatively unexplored, and the selective pressures acting on CVB3 in the intestine are not well characterized. To examine viral population dynamics in orally infected mice, we produced over 100 CVB3 clones harboring nine unique nucleotide "barcodes." Using this collection of barcoded viruses, we found diverse viral populations throughout each mouse within the first day postinfection, but by 48 h the viral populations were dominated by fewer than three barcoded viruses in intestinal and extraintestinal tissues. Using light-sensitive viruses to track replication status, we found that diverse viruses had replicated prior to loss of diversity. Sequencing whole viral genomes from samples later in infection did not reveal detectable viral adaptations. Surprisingly, orally inoculated CVB3 was detectable in pancreas and liver as soon as 20 min postinoculation, indicating rapid systemic dissemination. These results suggest rapid dissemination of diverse viral populations, followed by a major restriction in population diversity and monopolization in all examined tissues. These results underscore a complex dynamic between dissemination and clearance for an enteric virus.IMPORTANCE Enteric viruses initiate infection in the gastrointestinal tract but can disseminate to systemic sites. However, the dynamics of viral dissemination are unclear. In this study, we created a library of 135 barcoded coxsackieviruses to examine viral population diversity across time and space following oral inoculation of mice. Overall, we found that the broad population of viruses disseminates early, followed by monopolization of mouse tissues with three or fewer pool members at later time points. Interestingly, we detected virus in systemic tissues such as pancreas and liver just 20 min after oral inoculation. These results suggest rapid dissemination of diverse viral populations, followed by a major restriction in population diversity and monopolization in all examined tissues.},
}
@article {pmid31664164,
year = {2019},
author = {Worsaae, K and Kerbl, A and Vang, &#xc1; and Gonzalez, BC},
title = {Broad North Atlantic distribution of a meiobenthic annelid - against all odds.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {15497},
pmid = {31664164},
issn = {2045-2322},
mesh = {Animals ; Annelida/*classification/genetics ; Atlantic Ocean ; DNA Barcoding, Taxonomic ; Evolution, Molecular ; *Phylogeography ; },
abstract = {DNA barcoding and population genetic studies have revealed an unforeseen hidden diversity of cryptic species among microscopic marine benthos, otherwise exhibiting highly similar and simple morphologies. This has led to a paradigm shift, rejecting cosmopolitism of marine meiofauna until genetically proven and challenging the "Everything is Everywhere, but the environment selects" hypothesis that claims ubiquitous distribution of microscopic organisms. With phylogenetic and species delimitation analyses of worldwide genetic samples of the meiofaunal family Dinophilidae (Annelida) we here resolve three genera within the family and showcase an exceptionally broad, boreal, North Atlantic distribution of a single microscopic marine species with no obvious means of dispersal besides vicariance. With its endobenthic lifestyle, small size, limited migratory powers and lack of pelagic larvae, the broad distribution of Dinophilus vorticoides seems to constitute a "meiofaunal paradox". This species feasts in the biofilm among sand grains, but also on macroalgae and ice within which it can likely survive long-distance rafting dispersal due to its varying lifecycle stages; eggs encapsulated in cocoons and dormant encystment stages. Though often neglected and possibly underestimated among marine microscopic species, dormancy may be a highly significant factor for explaining wide distribution patterns and a key to solving this meiofaunal paradox.},
}
@article {pmid31661958,
year = {2019},
author = {Zhang, X and Cui, J and Zhang, K and Wu, J and Lee, Y},
title = {Machine Learning Prediction on Properties of Nanoporous Materials Utilizing Pore Geometry Barcodes.},
journal = {Journal of chemical information and modeling},
volume = {59},
number = {11},
pages = {4636-4644},
doi = {10.1021/acs.jcim.9b00623},
pmid = {31661958},
issn = {1549-960X},
mesh = {Machine Learning ; Metal-Organic Frameworks/chemistry ; *Models, Chemical ; Models, Molecular ; *Nanopores/ultrastructure ; Porosity ; Zeolites/chemistry ; },
abstract = {In this work, we propose a computational framework for machine learning prediction on structural and performance properties of nanoporous materials for methane storage application. For our machine learning prediction, two descriptors based on pore geometry barcodes were developed; one descriptor is a set of distances from a structure to the most diverse set in barcode space, and the second descriptor extracts and uses the most important features from the barcodes. First, to identify the optimal condition for machine learning prediction, the effects of training set preparation method, training set size, and machine learning models were investigated. Our analysis showed that kernel ridge regression provides the highest prediction accuracy, and randomly selected 5% structures of the entire set would work well as a training set. Our results showed that both descriptors accurately predicted performance and even structural properties of zeolites. Furthermore, we demonstrated that our approach predicts accurately properties of metal-organic frameworks, which might indicate the possibility of this approach to be easily applied to predict the properties of other types of nanoporous materials.},
}
@article {pmid31659691,
year = {2020},
author = {Cruz-Miranda, OL and Folch-Mallol, J and Martínez-Morales, F and Gesto-Borroto, R and Villarreal, ML and Taketa, AC},
title = {Identification of a Huperzine A-producing endophytic fungus from Phlegmariurus taxifolius.},
journal = {Molecular biology reports},
volume = {47},
number = {1},
pages = {489-495},
pmid = {31659691},
issn = {1573-4978},
support = {222714//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 156276//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; },
mesh = {*Alkaloids/analysis/chemistry/isolation &amp; purification ; Cholinesterase Inhibitors/analysis/isolation &amp; purification/metabolism ; DNA, Fungal/genetics ; Endophytes/*chemistry/isolation &amp; purification ; Fusarium/*chemistry/classification/genetics/isolation &amp; purification ; Lycopodiaceae/*microbiology ; *Sesquiterpenes/analysis/chemistry/isolation &amp; purification ; },
abstract = {Highly prized huperzine A (Hup A), a natural alkaloid formerly isolated from the Chinese medicinal plant Huperzia serrata, has been widely used for the treatment of Alzheimer disease, inspiring us to search for endophytic fungi that produce this compound. In this study, we obtained the C17 fungus isolate from the Mexican club moss Phlegmariurus taxifolius, which produced a yield of 3.2 μg/g Hup A in mycelial dry weight, when cultured in potato dextrose broth medium. The C17 isolate was identified as belonging to the genus Fusarium with reference to the colony´s morphological characteristics and the presence of macroconidia and microconidia structures; and this was confirmed by DNA-barcoding analysis, by amplifying and sequencing the ribosomal internal transcribed spacer (rITS).},
}
@article {pmid31659069,
year = {2019},
author = {Jensen, K and Haniff, R and Kamarinos, A and Rosenberg, A and Santiago, M and Laser, J},
title = {Improving Turnaround Times through a Process Improvement Initiative Involving Barcoding, Floorplans, Dual Measuring Cells, Chemistry Analyzers, and Staff Shifts.},
journal = {The journal of applied laboratory medicine},
volume = {4},
number = {3},
pages = {311-322},
doi = {10.1373/jalm.2018.028555},
pmid = {31659069},
issn = {2576-9456},
mesh = {Biomarkers ; *Chemistry, Analytic ; Diagnostic Tests, Routine ; *Efficiency, Organizational ; Emergency Service, Hospital/*organization &amp; administration/*standards ; Health Plan Implementation ; Humans ; Laboratories, Hospital ; *Quality Improvement ; *Shift Work Schedule ; Time Factors ; Workflow ; },
abstract = {BACKGROUND: Specimen turnaround time (TAT) is an important metric for laboratory safety and quality. Various methods to improve TAT have seen success using process improvement initiatives. However, there are limited data on barcoding, pneumatic receiving proximity to modular preanalytics, 1 vs 2 measuring cells, and upgrading to Cobas 8000. The example describes the complete execution of a process improvement initiative to improve TAT within these areas over a 20-month period. The study aimed to improve specimen timeliness by decreasing the TAT for preanalytic and analytic specimen processing through a systematic process improvement initiative and to empower staff to "own" their scientific method.<br><br>METHODS: The primary outcome TAT was reported from a prospective quality initiative beginning January 2017 for 2 analytes: troponin and potassium. TATs for albumins from the complete metabolic panels were added to the study design retrospectively during team rounds. Mean TAT was defined as time from arrival to verified times. Process improvement tools within the study design were borrowed from Lean management.<br><br>RESULTS: After implementation of the process improvement initiative, the number of steps medical laboratory assistants and technologists performed per specimen decreased from 8 to 5. Mean TATs decreased for all analytes. Preimplementation to postimplementation comparisons from 2017 to 2018 decreased for all 3 analytes and within 2017. The number of troponin specimens verified within 60 min improved from 70% in January 2017 to 95% in August 2018, with an improvement from 64% in January 2017 to 87% in August 2018 during peak hours.<br><br>CONCLUSIONS: A systematic process improvement initiative whereby employees "own" the scientific process within specimen preanalytic and analytic testing phases can significantly improve metrics for laboratory quality and safety.},
}
@article {pmid31652271,
year = {2019},
author = {Bryant, PJ and Arehart, TE},
title = {Diversity and life-cycle analysis of Pacific Ocean zooplankton by videomicroscopy and DNA barcoding: Hydrozoa.},
journal = {PloS one},
volume = {14},
number = {10},
pages = {e0218848},
pmid = {31652271},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; *Hydrozoa/classification/genetics/growth &amp; development ; Life Cycle Stages/*physiology ; Microscopy, Video ; Pacific Ocean ; *Zooplankton/genetics/growth &amp; development ; },
abstract = {Most, but not all cnidarian species in the class Hydrozoa have a life cycle in which a colonial, asexually reproducing hydroid phase alternates with a free-swimming, sexually reproducing medusa phase. They are not well known, in part because many of them are microscopic, at least in the medusa phase. Matching the two phases has previously required rearing of the organism from one phase to another, which has not often been possible. Here we show that DNA barcoding makes it possible to easily link life-cycle phases without the need for laboratory rearing. Hydrozoan medusae were collected by zooplankton tows in Newport Bay and the Pacific Ocean near Newport Beach, California, and hydroid colonies were collected from solid substrates in the same areas. Specimens were documented by videomicroscopy, preserved in ethanol, and sent to the Canadian Centre for DNA Barcoding at the University of Guelph, Ontario, Canada for sequencing of the COI DNA barcode. In the order Anthoathecata (athecate hydroids), DNA barcoding allowed for the discrimination between the medusae of eight putative species of Bougainvillia, and the hydroid stages were documented for two of these. The medusae of three putative species of Amphinema were identified, and the hydroid stages were identified for two of them. DNA barcodes were obtained from medusae of one species of Cladonema, one adult of the by-the wind Sailor, Velella velella, five putative species of Corymorpha with the matching hydroid phase for one; and Coryne eximia, Turritopsis dohrnii and Turritopsis nutricula with the corresponding hydroid phases. The actinula larvae and hydroid for the pink-hearted hydroid Ectopleura crocea were identified and linked by DNA barcoding. In the order Leptothecata (thecate hydroids) medusae were identified for Clytia elsaeoswaldae, Clytia gracilis and Clytia sp. 701 AC and matched with the hydroid phases for the latter two species. Medusae were matched with the hydroid phases for two species of Obelia (including O. dichotoma) and Eucheilota bakeri. Obelia geniculata was collected as a single hydroid. DNA barcodes were obtained for hydroids of Orthopyxis everta and three other species of Orthopyxis. One member of the family Solmarisidae, representing the order Narcomedusae, and one member (Liriope tetraphylla) of the order Trachymedusae were recognized as medusae. The results show the utility of DNA barcoding for matching life-cycle stages as well as for documenting the diversity of this class of organisms.},
}
@article {pmid31649688,
year = {2019},
author = {Li, QJ and Wang, X and Wang, JR and Su, N and Zhang, L and Ma, YP and Chang, ZY and Zhao, L and Potter, D},
title = {Efficient Identification of Pulsatilla (Ranunculaceae) Using DNA Barcodes and Micro-Morphological Characters.},
journal = {Frontiers in plant science},
volume = {10},
number = {},
pages = {1196},
pmid = {31649688},
issn = {1664-462X},
abstract = {Pulsatilla (Ranunculaceae) comprises about 40 species, many of which have horticultural and/or medicinal importance. However, the recognition and identification of wild Pulsatilla species is difficult due to the presence of complex morphological characters. DNA barcoding is a powerful molecular tool capable of rapidly and accurately distinguishing between species. Here, we assessed the effectiveness of four commonly used DNA barcoding loci-rbcL (R), trnH-psbA (T), matK (M), and ITS (I)-to identify species of Pulsatilla from a comprehensive sampling group. Among the four barcoding single loci, the nuclear ITS marker showed the highest interspecific distances and the highest rate of correct identification. Among the eleven combinations, the chloroplast multi-locus R+T and R+M+T combinations were found to have the best species discrimination rate, followed by R+M. Overall, we propose that the R+M+T combination and the ITS marker on its own are, respectively, the best multi- and single-locus barcodes for discriminating among species of Pulsatilla. The phylogenetic analysis was able to distinguish species of Pulsatilla to the subgenus level, but the analysis also showed relatively low species resolution. This may be caused by incomplete lineage sorting and/or hybridization events in the evolutionary history of the genus, or by the resolution limit of the candidate barcodes. We also investigated the leaf epidermis of eight representative species using scanning electronic microscopy. The resulting micro-morphological characters were valuable for identification of related species. Using additional genome fragments, or even whole chloroplast genomes combined with micro-morphological data may permit even higher resolution of species in Pulsatilla.},
}
@article {pmid31649681,
year = {2019},
author = {Truitt, LL and Yang, D and Espinoza, DA and Fan, X and Ram, DR and Moström, MJ and Tran, D and Sprehe, LM and Reeves, RK and Donahue, RE and Kaur, A and Dunbar, CE and Wu, C},
title = {Impact of CMV Infection on Natural Killer Cell Clonal Repertoire in CMV-Naïve Rhesus Macaques.},
journal = {Frontiers in immunology},
volume = {10},
number = {},
pages = {2381},
pmid = {31649681},
issn = {1664-3224},
support = {P51 OD011104/OD/NIH HHS/United States ; R01 DE026014/DE/NIDCR NIH HHS/United States ; T32 AI007387/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; CD56 Antigen/immunology ; *Cell Proliferation ; Cytomegalovirus/*immunology ; Cytomegalovirus Infections/*immunology/pathology ; Female ; *Immunity, Cellular ; Killer Cells, Natural/*immunology/pathology ; Macaca mulatta ; Male ; Receptors, IgG/immunology ; },
abstract = {Recent functional, gene expression, and epigenetic studies have suggested the presence of a subset of mature natural killer (NK) cells responsible for maintaining NK cell memory. The lack of endogenous clonal markers in NK cells impedes understanding the genesis of these cell populations. In humans, primates, and mice, this phenotype and memory or adaptive functions have been strongly linked to cytomegalovirus or related herpes virus infections. We have used transplantation of lentivirally-barcoded autologous hematopoietic stem and progenitor cells (HSPC) to track clonal hematopoiesis in rhesus macaques and previously reported striking oligoclonal expansions of NK-biased barcoded clones within the CD56[-]CD16[+] NK cell subpopulation, clonally distinct from ongoing output of myeloid, B cell, T cell, and CD56[+]16[-] NK cells from HSPC. These CD56[-]CD16[+] NK cell clones segregate by expression of specific KIR surface receptors, suggesting clonal expansion in reaction to specific environmental stimuli. We have now used this model to investigate the impact of rhesus CMV(RhCMV) infection on NK clonal dynamics. Following transplantation, RhCMV[neg] rhesus macaques display less dominant and oligoclonal CD16[+] NK cells biased clones compared to RhCMV[pos] animals, however these populations of cells are still clearly present. Upon RhCMV infection, CD16[+] NK cells proliferate, followed by appearance of new groups of expanded NK clones and disappearance of clones present prior to RhCMV infection. A second superinfection with RhCMV resulted in rapid viral clearance without major change in the mature NK cell clonal landscape. Our findings suggest that RhCMV is not the sole driver of clonal expansion and peripheral maintenance of mature NK cells; however, infection of macaques with this herpesvirus does result in selective expansion and persistence of specific NK cell clones, providing further information relevant to adaptive NK cells and the development of NK cell therapies.},
}
@article {pmid31649061,
year = {2019},
author = {Shi, D and Wu, J and Tang, H and Yin, H and Wang, H and Wang, R and Wang, R and Qian, M and Wu, J and Qi, K and Xie, Z and Wang, Z and Zhao, X and Zhang, S},
title = {Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants.},
journal = {Genome research},
volume = {29},
number = {11},
pages = {1889-1899},
pmid = {31649061},
issn = {1549-5469},
mesh = {Computational Biology ; DNA, Plant/genetics ; *Diploidy ; *Genome, Plant ; *Germ Cells, Plant ; Haplotypes ; High-Throughput Nucleotide Sequencing/methods ; Meiosis ; Pollen/*cytology ; },
abstract = {Genome assemblies from diploid organisms create mosaic sequences alternating between parental alleles, which can create erroneous gene models and other problems. In animals, a popular strategy to generate haploid genome-resolved assemblies has been the sampling of (haploid) gametes, and the advent of single-cell sequencing has further advanced such methods. However, several challenges for the isolation and amplification of DNA from plant gametes have limited such approaches in plants. Here, we combined a new approach for pollen protoplast isolation with a single-cell DNA amplification technique and then used a "barcoding" bioinformatics strategy to incorporate haploid-specific sequence data from 12 pollen cells, ultimately enabling the efficient and accurate phasing of the pear genome into its A and B haploid genomes. Beyond revealing that 8.12% of the genes in the pear reference genome feature mosaic assemblies and enabling a previously impossible analysis of allelic affects in pear gene expression, our new haploid genome assemblies provide high-resolution information about recombination during meiosis in pollen. Considering that outcrossing pear is an angiosperm species featuring very high heterozygosity, our method for rapidly phasing genome assemblies is potentially applicable to several yet-unsequenced outcrossing angiosperm species in nature.},
}
@article {pmid31644600,
year = {2019},
author = {Amaral, CRL and Chaves, ACS and Borges Júnior, VNT and Pereira, F and Silva, BM and Silva, DA and Amorim, A and Carvalho, EF and Rocha, CFD},
title = {Amphibians on the hotspot: Molecular biology and conservation in the South American Atlantic Rainforest.},
journal = {PloS one},
volume = {14},
number = {10},
pages = {e0224320},
pmid = {31644600},
issn = {1932-6203},
mesh = {Amphibians/*genetics ; Animals ; Atlantic Ocean ; *Conservation of Natural Resources ; Larva/genetics ; Molecular Biology ; RNA, Ribosomal, 16S/genetics ; *Rainforest ; South America ; },
abstract = {Amphibians are the focus of a recent debate and public attention owing to the global decline in their populations worldwide. Amphibians are one of the most threatened and poorly known groups of vertebrates in several geographic areas, even though they play a central role in their own ecosystems. At different levels, amphibians make their contribution to proper ecosystem functioning. They act as regulators of the food web and nutrient cycling, and they also provide several valuable ecosystem services, e.g., as a food source and as animal models for lab research. In this sense, it seems clear that the maintenance of amphibian diversity should be one of the major goals for the several countries where their population decline is observed. However, we are still struggling with the very first step of this process, i.e., the correct identification of the amphibian species diversity. Over the past few decades, research on molecular identification of amphibians using DNA barcoding has encountered some difficulties related to high variability in the mitochondrial genome of amphibians, and a research gap is noticeable in the literature. We herein evaluated both COI and 16S rRNA mitochondrial genes for the molecular identification of frogs and tadpoles in a large fragment of the South American Atlantic Rainforest in Rio de Janeiro, Brazil. Our results suggest that both COI and 16S rRNA are informative markers for the molecular identification of the amphibian specimens with all specimens unambiguously identified at the species level. We also made publicly available 12 new sequences of Atlantic Rainforest amphibian species for the first time, and we discussed some conservation issues related to amphibians within the Atlantic Rainforest domains in the state of Rio de Janeiro, Brazil.},
}
@article {pmid31644567,
year = {2019},
author = {von Oheimb, KCM and von Oheimb, PV and Hirano, T and Do, TV and Ablett, J and Luong, HV and Pham, SV and Naggs, F},
title = {Cryptic diversity of limestone karst inhabiting land snails (Cyclophorus spp.) in northern Vietnam, their evolutionary history and the description of four new species.},
journal = {PloS one},
volume = {14},
number = {10},
pages = {e0222163},
pmid = {31644567},
issn = {1932-6203},
mesh = {Animals ; Bayes Theorem ; *Biodiversity ; *Biological Evolution ; *Calcium Carbonate ; DNA Barcoding, Taxonomic ; Geography ; Phylogeny ; Snails/*physiology ; Species Specificity ; Vietnam ; },
abstract = {Limestone karsts can form terrestrial habitat islands for calcium-dependent organisms. In Vietnam, many karst habitats are threatened, while their rich biodiversity is still far from being thoroughly explored. Given that conservation of karst biota strongly relies on correct species identification, the presence of undetected cryptic species can pose severe problems. The present study focuses on cryptic diversity among karst-inhabiting land snails of the genus Cyclophorus in northern Vietnam, where specimens with a similar shell morphology have been reported from various regions. In order to examine the diversity and evolutionary history of this "widespread morphotype", we generated a Bayesian phylogeny based on DNA sequence data. Automatic Barcode Gap Discovery (ABGD) and the Bayesian implementation of the Poisson tree processes model (bPTP) contributed to species delimitation and analyses of shell shape and size aided the morphological characterisation of individual species. We found that the examined specimens of the widespread morphotype did not form a single monophyletic group in the phylogeny but clustered into several different clades. We delimited nine different species that develop the widespread morphotype and described four of them as new. Processes of convergent evolution were probably involved in the origin of the delimited species, while their generally allopatric distribution could result from interspecific competition. Our findings indicate ongoing processes of speciation and a potential case of morphological character displacement. The high degree of morphological overlap found among the species underlines the importance of DNA sequence data for species delimitation and description in the genus Cyclophorus. Given the findings of the present study and the high potential that as yet undiscovered cryptic taxa have also evolved in other groups of karst-inhabiting organisms, we argue for a systematic and efficient detection and description of Vietnam's karst biodiversity to provide a solid basis for future conservation planning.},
}
@article {pmid31641490,
year = {2019},
author = {Wang, Q and Bao, W and Zhang, Q and Fu, X and Yang, Y and Lu, Y},
title = {Host plant use of a polyphagous mirid, Apolygus lucorum: Molecular evidence from migratory individuals.},
journal = {Ecology and evolution},
volume = {9},
number = {19},
pages = {11518-11528},
pmid = {31641490},
issn = {2045-7758},
abstract = {While the host plant use of insect herbivores is important for understanding their interactions and coevolution, field evidence of these preferences is limited for generalist species. Molecular diet analysis provides an effective option for gaining such information, but data from field-sampled individuals are often greatly affected by the local composition of their host plants. The polyphagous mirid bug Apolygus lucorum (Meyer-Dür) seasonally migrates across the Bohai Sea, and molecular analysis of migrant bugs collected on crop-free islands can be used to estimate the host plant use of A. lucorum across the large area (northern China) from where these individuals come. In this study, the host plant use of A. lucorum adults was determined by identifying plant DNA using a three-locus DNA barcode (rbcL, trnH-psbA, and ITS) in the gut of migrant individuals collected on Beihuang Island. We successfully identified the host plant families of A. lucorum adults, and the results indicated that captured bugs fed on at least 17 plant families. In addition, gut analyses revealed that 35.9% of A. lucorum individuals fed on multiple host plants but that most individuals (64.1%) fed on only one plant species. Cotton, Gossypium hirsutum L., DNA was found in 35.8% of the A. lucorum bugs examined, which was much higher than the percentage of bugs in which other host plants were found. Our work provides a new understanding of multiple host plant use by A. lucorum under natural conditions, and these findings are available for developing effective management strategies against this polyphagous pest species.},
}
@article {pmid31641158,
year = {2019},
author = {Rimet, F and Gusev, E and Kahlert, M and Kelly, MG and Kulikovskiy, M and Maltsev, Y and Mann, DG and Pfannkuchen, M and Trobajo, R and Vasselon, V and Zimmermann, J and Bouchez, A},
title = {Diat.barcode, an open-access curated barcode library for diatoms.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {15116},
pmid = {31641158},
issn = {2045-2322},
mesh = {Base Sequence ; *DNA Barcoding, Taxonomic ; Data Curation ; Databases, Genetic ; Diatoms/*classification/*genetics ; *Gene Library ; Geography ; Ribulose-Bisphosphate Carboxylase/genetics ; },
abstract = {Diatoms (Bacillariophyta) are ubiquitous microalgae which produce a siliceous exoskeleton and which make a major contribution to the productivity of oceans and freshwaters. They display a huge diversity, which makes them excellent ecological indicators of aquatic ecosystems. Usually, diatoms are identified using characteristics of their exoskeleton morphology. DNA-barcoding is an alternative to this and the use of High-Throughput-Sequencing enables the rapid analysis of many environmental samples at a lower cost than analyses under microscope. However, to identify environmental sequences correctly, an expertly curated reference library is needed. Several curated libraries for protists exists; none, however are dedicated to diatoms. Diat.barcode is an open-access library dedicated to diatoms which has been maintained since 2012. Data come from two sources (1) the NCBI nucleotide database and (2) unpublished sequencing data of culture collections. Since 2017, several experts have collaborated to curate this library for rbcL, a chloroplast marker suitable for species-level identification of diatoms. For the latest version of the database (version 7), 605 of the 3482 taxonomical names originally assigned by the authors of the rbcL sequences were modified after curation. The database is accessible at https://www6.inra.fr/carrtel-collection_eng/Barcoding-database .},
}
@article {pmid31641155,
year = {2019},
author = {Mizuno, K and Akamatsu, S and Sumiyoshi, T and Wong, JH and Fujita, M and Maejima, K and Nakano, K and Ono, A and Aikata, H and Ueno, M and Hayami, S and Yamaue, H and Chayama, K and Inoue, T and Ogawa, O and Nakagawa, H and Fujimoto, A},
title = {eVIDENCE: a practical variant filtering for low-frequency variants detection in cell-free DNA.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {15017},
pmid = {31641155},
issn = {2045-2322},
mesh = {Biomarkers, Tumor/*genetics ; Carcinoma, Hepatocellular/diagnosis/*genetics ; Cell-Free Nucleic Acids/*genetics ; Humans ; Liver Neoplasms/diagnosis/*genetics ; *Mutation Rate ; Sequence Analysis, DNA/*methods ; *Software ; },
abstract = {Plasma cell-free DNA (cfDNA) testing plays an increasingly important role in precision medicine for cancer. However, circulating cell-free tumor DNA (ctDNA) is highly diluted by cfDNA from non-cancer cells, complicating ctDNA detection and analysis. To identify low-frequency variants, we developed a program, eVIDENCE, which is a workflow for filtering candidate variants detected by using the ThruPLEX tag-seq (Takara Bio), a commercially-available molecular barcoding kit. We analyzed 27 cfDNA samples from hepatocellular carcinoma patients. Sequencing libraries were constructed and hybridized to our custom panel targeting about 80 genes. An initial variant calling identified 36,500 single nucleotide variants (SNVs) and 9,300 insertions and deletions (indels) across the 27 samples, but the number was much greater than expected when compared with previous cancer genome studies. eVIDENCE was applied to the candidate variants and finally 70 SNVs and 7 indels remained. Of the 77 variants, 49 (63.6%) showed VAF of < 1% (0.20-0.98%). Twenty-five variants were selected in an unbiased manner and all were successfully validated, suggesting that eVIDENCE can identify variants with VAF of ≥ 0.2%. Additionally, this study is the first to detect hepatitis B virus integration sites and genomic rearrangements in the TERT region from cfDNA of HCC patients. We consider that our method can be applied in the examination of cfDNA from other types of malignancies using specific custom gene panels and will contribute to comprehensive ctDNA analysis.},
}
@article {pmid31639524,
year = {2020},
author = {Zaharias, P and Pante, E and Gey, D and Fedosov, AE and Puillandre, N},
title = {Data, time and money: evaluating the best compromise for inferring molecular phylogenies of non-model animal taxa.},
journal = {Molecular phylogenetics and evolution},
volume = {142},
number = {},
pages = {106660},
doi = {10.1016/j.ympev.2019.106660},
pmid = {31639524},
issn = {1095-9513},
mesh = {Animals ; Costs and Cost Analysis ; Gene Expression Profiling ; Genome ; High-Throughput Nucleotide Sequencing ; Mollusca/classification/genetics ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {For over a decade now, High Throughput sequencing (HTS) approaches have revolutionized phylogenetics, both in terms of data production and methodology. While transcriptomes and (reduced) genomes are increasingly used, generating and analyzing HTS datasets remain expensive, time consuming and complex for most non-model taxa. Indeed, a literature survey revealed that 74% of the molecular phylogenetics trees published in 2018 are based on data obtained through Sanger sequencing. In this context, our goal was to identify the strategy that would represent the best compromise among costs, time and robustness of the resulting tree. We sequenced and assembled 32 transcriptomes of the marine mollusk family Turridae, considered as a typical non-model animal taxon. From these data, we extracted the loci most commonly used in gastropod phylogenies (cox1, 12S, 16S, 28S, h3 and 18S), full mitogenomes, and a reduced nuclear transcriptome representation. With each dataset, we reconstructed phylogenies and compared their robustness and accuracy. We discuss the impact of missing data and the use of statistical tests, tree metrics, and supertree and supermatrix methods to further improve phylogenetic data acquisition pipelines. We evaluated the overall costs (time and money) in order to identify the best compromise for phylogenetic data sampling in non-model animal taxa. Although sequencing full mitogenomes seems to constitute the best compromise both in terms of costs and node support, they are known to induce biases in phylogenetic reconstructions. Rather, we recommend to systematically include loci commonly used for phylogenetics and taxonomy (i.e. DNA barcodes, rRNA genes, full mitogenomes, etc.) among the other loci when designing baits for capture.},
}
@article {pmid31639027,
year = {2019},
author = {Blattner, L and Gerecke, R and von Fumetti, S},
title = {Hidden biodiversity revealed by integrated morphology and genetic species delimitation of spring dwelling water mite species (Acari, Parasitengona: Hydrachnidia).},
journal = {Parasites &amp; vectors},
volume = {12},
number = {1},
pages = {492},
pmid = {31639027},
issn = {1756-3305},
support = {31003A_176234/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Animals ; Austria ; Bayes Theorem ; *Biodiversity ; Cyclooxygenase 1/genetics ; DNA/chemistry/isolation &amp; purification ; Fresh Water/parasitology ; Germany ; Likelihood Functions ; Mites/anatomy &amp; histology/*classification/genetics ; Natural Springs/*parasitology ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 28S/genetics ; Sequence Alignment ; Switzerland ; },
abstract = {BACKGROUND: Water mites are among the most diverse organisms inhabiting freshwater habitats and are considered as substantial part of the species communities in springs. As parasites, Hydrachnidia influence other invertebrates and play an important role in aquatic ecosystems. In Europe, 137 species are known to appear solely in or near springheads. New species are described frequently, especially with the help of molecular species identification and delimitation methods. The aim of this study was to verify the mainly morphology-based taxonomic knowledge of spring-inhabiting water mites of central Europe and to build a genetic species identification library.<br><br>METHODS: We sampled 65 crenobiontic species across the central Alps and tested the suitability of mitochondrial (cox1) and nuclear (28S) markers for species delimitation and identification purposes. To investigate both markers, distance- and phylogeny-based approaches were applied. The presence of a barcoding gap was tested by using the automated barcoding gap discovery tool and intra- and interspecific genetic distances were investigated. Furthermore, we analyzed phylogenetic relationships between different taxonomic levels.<br><br>RESULTS: A high degree of hidden diversity was observed. Seven taxa, morphologically identified as Bandakia concreta Thor, 1913, Hygrobates norvegicus (Thor, 1897), Ljania bipapillata Thor, 1898, Partnunia steinmanni Walter, 1906, Wandesia racovitzai Gledhill, 1970, Wandesia thori Schechtel, 1912 and Zschokkea oblonga Koenike, 1892, showed high intraspecific cox1 distances and each consisted of more than one phylogenetic clade. A clear intraspecific threshold between 5.6-6.0% K2P distance is suitable for species identification purposes. The monophyly of Hydrachnidia and the main superfamilies is evident with different species clearly separated into distinct clades. cox1 separates water mite species but is unsuitable for resolving higher taxonomic levels.<br><br>CONCLUSIONS: Water mite species richness in springs is higher than has been suggested based on morphological species identification alone and further research is needed to evaluate the true diversity. The standard molecular species identification marker cox1 can be used to identify species but should be complemented by a nuclear marker, e.g. 28S, to resolve taxonomic relationships. Our results contribute to the taxonomical knowledge on spring inhabiting Hydrachnida, which is indispensable for the development and implementation of modern environment assessment methods, e.g. metabarcoding, in spring ecology.},
}
@article {pmid31636728,
year = {2019},
author = {Marin-Felix, Y and Hernández-Restrepo, M and Iturrieta-González, I and García, D and Gené, J and Groenewald, JZ and Cai, L and Chen, Q and Quaedvlieg, W and Schumacher, RK and Taylor, PWJ and Ambers, C and Bonthond, G and Edwards, J and Krueger-Hadfield, SA and Luangsa-Ard, JJ and Morton, L and Moslemi, A and Sandoval-Denis, M and Tan, YP and Thangavel, R and Vaghefi, N and Cheewangkoon, R and Crous, PW},
title = {Genera of phytopathogenic fungi: GOPHY 3.},
journal = {Studies in mycology},
volume = {94},
number = {},
pages = {1-124},
pmid = {31636728},
issn = {0166-0616},
abstract = {This paper represents the third contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions, information about the pathology, distribution, hosts and disease symptoms for the treated genera, as well as primary and secondary DNA barcodes for the currently accepted species included in these. This third paper in the GOPHY series treats 21 genera of phytopathogenic fungi and their relatives including: Allophoma, Alternaria, Brunneosphaerella, Elsinoe, Exserohilum, Neosetophoma, Neostagonospora, Nothophoma, Parastagonospora, Phaeosphaeriopsis, Pleiocarpon, Pyrenophora, Ramichloridium, Seifertia, Seiridium, Septoriella, Setophoma, Stagonosporopsis, Stemphylium, Tubakia and Zasmidium. This study includes three new genera, 42 new species, 23 new combinations, four new names, and three typifications of older names.},
}
@article {pmid31636501,
year = {2019},
author = {Siddiqui, JA and Chen, Z and Li, Q and Deng, J and Lin, X and Huang, X},
title = {DNA barcoding of aphid-associated ants (Hymenoptera, Formicidae) in a subtropical area of southern China.},
journal = {ZooKeys},
volume = {879},
number = {},
pages = {117-136},
pmid = {31636501},
issn = {1313-2989},
abstract = {As one of the most abundant and complex groups of terrestrial insects, ants have associations with many other organismal groups, such as hemipteran insects producing honeydew. With the aim of expanding the knowledge base of ant species associated with aphids, this study analyzed mitochondrial COI barcodes of 301 ant samples for 37 aphid-associated ant species in a subtropical area of southern China. Sequence analyses revealed that the intraspecific and interspecific distances ranged from zero to 7.7%% and 0.2 to 31.7%, respectively. Three barcoding approaches - Automatic Barcode Gap Discovery, Bayesian Poisson Tree Processes and Generalized Mixed Yule-coalescent - were used to help delimit ant species based on COI sequences, and their results corresponded well with most of the morphospecies. All three approaches indicate cryptic diversity may exist within Tetramorium bicarinatum and Technomyrmex albipes, with intraspecific genetic distances of 7.7% and 6.24%, respectively. Our analyses also reported five species for the first time from Fujian Province of China, and the COI sequences of nine species are newly added into the GenBank. This study provides information about species diversity of aphid-associated ants in subtropical China and compiles a DNA barcode reference library for future ant barcoding work.},
}
@article {pmid31634725,
year = {2020},
author = {Ortega, A and Pastor-Palacios, G and Ortiz-Pastrana, N and Ávila-Cabezas, E and Toscano, RA and Joseph-Nathan, P and Morales-Jiménez, J and Bautista, E},
title = {Further galphimines from a new population of Galphimia glauca.},
journal = {Phytochemistry},
volume = {169},
number = {},
pages = {112180},
doi = {10.1016/j.phytochem.2019.112180},
pmid = {31634725},
issn = {1873-3700},
mesh = {Crystallography, X-Ray ; Galphimia/*chemistry ; Models, Molecular ; Molecular Conformation ; Triterpenes/*chemistry/isolation &amp; purification ; },
abstract = {Both DNA barcoding and phylogenetic data of the studied botanical material suggested the existence a new population of Galphimia glauca. Their leaves afforded three new nor-3,4-seco-friedelanes named galphimines M-O, together with known galphimines D, E, G, and I. Galphimines M and N possess bicyclic orthoacetates which are the first examples of orthoesters found in the Malpighiaceae family, while galphimine O has a 27,20-δ-lactone moiety. The structures elucidation followed from spectroscopic means and the absolute configuration followed from single crystal X-ray diffraction analyses. Tests for antibacterial and antifungal activities of galphimines N and M showed no promising effects.},
}
@article {pmid31634710,
year = {2020},
author = {Dong, F and Lin, J and You, J and Ji, J and Xu, X and Zhang, L and Jin, Y and Du, S},
title = {A chemometric modeling-free near infrared barcode strategy for smart authentication and geographical origin discrimination of Chinese ginseng.},
journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy},
volume = {226},
number = {},
pages = {117555},
doi = {10.1016/j.saa.2019.117555},
pmid = {31634710},
issn = {1873-3557},
mesh = {China ; Drugs, Chinese Herbal/chemistry/classification ; Feasibility Studies ; Models, Chemical ; Panax/*chemistry/*classification ; *Plants, Medicinal/chemistry/classification ; Quality Control ; Spectroscopy, Near-Infrared/methods/standards ; },
abstract = {With the growing interest in alternative medicine, handy identification and differentiation of herbal medicines are becoming increasingly important. Here we report a chemometric modeling-free near infrared (NIR) barcode strategy for the smart identification and geographical origin discrimination of Chinese ginseng. The novel strategy demands the transformation of Chinese ginseng (standard and sample) NIR spectra into a barcode representation through assigning zero intensity to every NIR peak except the peaks having intensities greater than average peak intensity. Meanwhile, for Chinese ginseng standard NIR barcode, barcoding condition such as padding size was carefully optimized. It has been demonstrated that the padding size for each bar in the barcode is 8 cm[-1]. By comparing the percentage of nonzero overlap between Chinese ginseng standard barcode and sample barcodes, eight batches of samples (including Chinese ginseng, American ginseng and counterfeit) were successfully identified with 100% accuracy, respectively. Interestingly, the discrimination of the origin of ginsengs from three provinces (Jilin, Liaoning and Heilongjiang) of Northeastern China was achieved utilizing NIR barcode method. Two characteristic bars at 7750 and 8250 cm[-1] were inspected in the ginseng sample from Jilin province, two specific bars at 6780 and 7015 cm[-1] were displayed in the ginseng sample from Liaoning province and three distinct bars at 6560, 6910 and 7995 cm[-1] were monitored in the ginseng sample from Heilongjiang province. The results indicate that the proposed method will be greatly expanded and applied as an inspecting platform for the on-site analysis and valid identification of Chinese ginseng in herbal markets by a handheld spectrometer or barcode scanner.},
}
@article {pmid31633883,
year = {2020},
author = {Van Gassen, S and Gaudilliere, B and Angst, MS and Saeys, Y and Aghaeepour, N},
title = {CytoNorm: A Normalization Algorithm for Cytometry Data.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {97},
number = {3},
pages = {268-278},
pmid = {31633883},
issn = {1552-4930},
support = {R21 DE027728/DE/NIDCR NIH HHS/United States ; },
mesh = {*Algorithms ; Cluster Analysis ; Flow Cytometry ; *Genomics ; Humans ; Proteomics ; },
abstract = {High-dimensional flow cytometry has matured to a level that enables deep phenotyping of cellular systems at a clinical scale. The resulting high-content data sets allow characterizing the human immune system at unprecedented single cell resolution. However, the results are highly dependent on sample preparation and measurements might drift over time. While various controls exist for assessment and improvement of data quality in a single sample, the challenges of cross-sample normalization attempts have been limited to aligning marker distributions across subjects. These approaches, inspired by bulk genomics and proteomics assays, ignore the single-cell nature of the data and risk the removal of biologically relevant signals. This work proposes CytoNorm, a normalization algorithm to ensure internal consistency between clinical samples based on shared controls across various study batches. Data from the shared controls is used to learn the appropriate transformations for each batch (e.g., each analysis day). Importantly, some sources of technical variation are strongly influenced by the amount of protein expressed on specific cell types, requiring several population-specific transformations to normalize cells from a heterogeneous sample. To address this, our approach first identifies the overall cellular distribution using a clustering step, and calculates subset-specific transformations on the control samples by computing their quantile distributions and aligning them with splines. These transformations are then applied to all other clinical samples in the batch to remove the batch-specific variations. We evaluated the algorithm on a customized data set with two shared controls across batches. One control sample was used for calculation of the normalization transformations and the second control was used as a blinded test set and evaluated with Earth Mover's distance. Additional results are provided using two real-world clinical data sets. Overall, our method compared favorably to standard normalization procedures. The algorithm is implemented in the R package "CytoNorm" and available via the following link: www.github.com/saeyslab/CytoNorm © 2019 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.},
}
@article {pmid31632856,
year = {2019},
author = {Leoro-Garzon, P and Gonedes, AJ and Olivera, IE and Tartar, A},
title = {Oomycete metabarcoding reveals the presence of Lagenidium spp. in phytotelmata.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7903},
pmid = {31632856},
issn = {2167-8359},
abstract = {The oomycete genus Lagenidium, which includes the mosquito biocontrol agent L. giganteum, is composed of animal pathogens, yet is phylogenetically closely related to the well characterized plant pathogens Phytophthora and Pythium spp. These phylogenetic affinities were further supported by the identification of canonical oomycete effectors in the L. giganteum transcriptome. In this study, culture-independent, metabarcoding analyses aimed at detecting L. giganteum in bromeliad phytotelmata (a proven mosquito breeding ground) microbiomes were performed. Two independent and complementary microbial detection strategies based on the amplification of cox1 DNA barcodes were used and produced globally concordant outcomes revealing that two distinct Lagenidium phylotypes are present in phytotelmata. A total of 23,869 high quality reads were generated from four phytotelmata, with 52%, and 11.5% of these reads taxonomically associated to oomycetes, and Lagenidium spp., respectively. Newly designed Lagenidium-specific cox1 primers combined with cloning/Sanger sequencing produced only Lagenidium spp. sequences, with a majority of variants clustering with L. giganteum. High throughput sequencing based on a Single Molecule Real Time (SMRT) approach combined with broad range cox1 oomycete primers confirmed the presence of L. giganteum in phytotelmata, but indicated that a potentially novel Lagenidium phylotype (closely related to L. humanum) may represent one of the most prevalent oomycetes in these environments (along with Pythium spp.). Phylogenetic analyses demonstrated that all detected Lagenidium phylotype cox1 sequences clustered in a strongly supported, monophyletic clade that included both L. giganteum and L. humanum. Therefore, Lagenidium spp. are present in phytotelmata microbiomes. This observation provides a basis to investigate potential relationships between Lagenidium spp. and phytotelma-forming plants, and reveals phytotelmata as sources for the identification of novel Lagenidium isolates with potential as biocontrol agents against vector mosquitoes.},
}
@article {pmid31631341,
year = {2020},
author = {Hashimoto, S and Py-Daniel, LHR and Batista, JS},
title = {A molecular assessment of species diversity in Tympanopleura and Ageneiosus catfishes (Auchenipteridae: Siluriformes).},
journal = {Journal of fish biology},
volume = {96},
number = {1},
pages = {14-22},
doi = {10.1111/jfb.14173},
pmid = {31631341},
issn = {1095-8649},
support = {NSF DEB-1257813//iXINGU Project and All Catfish Species Inventory/ ; NSF DEB-0315963//iXINGU Project and All Catfish Species Inventory/ ; FAPEAM/CNPq (563,348/2010-0)//SISBIOTA/UFAM net-BioPHAM/ ; CNPq (564,953/2010-5)//Br-BOL/INPA/ ; # 1199611//Shizuka Hashimoto/ ; //National Science Foundation/ ; //Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Amazonas/ ; //Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
mesh = {Animals ; Catfishes/classification/*genetics ; *DNA Barcoding, Taxonomic ; *Genetic Variation ; *Haplotypes ; Phylogeny ; Species Specificity ; },
abstract = {In order to test the congruence of genetic data to the morphologically defined Neotropical catfish genera Tympanopleura and Ageneiosus and explore species diversity, we generated 17 DNA barcodes from five of six species of Tympanopleura and 12 of 13 species of Ageneiosus. To discriminate limits between species, an automatic barcode gap discovery (ABGD), a generalised mixed yule-coalescent model (GYMC) and fixed distance thresholds Kimura two-parameter (K2P; 3%) were used to discriminate putative species limits from the DNA barcodes. The ABGD, GMYC and K2P methods agreed by each generating 13 clusters: six in Tympanopleura (five nominal plus one undescribed species) and seven in Ageneiosus. These clusters corresponded broadly to the described species, except in the case of the Ageneiosus ucayalensis group (A. akamai, A. dentatus, A. intrusus, A. ucayalensis, A. uranophthalmus and A. vittatus). Haplotype sharing and low divergences may have prevented molecular methods from distinguishing these species. We hypothesise that this is the result of a recent radiation of a sympatric species group distributed throughout the Amazon Basin. One putative new species of Tympanopleura was also supported by the molecular data. These results taken together highlight the utility of molecular methods such as DNA barcoding in understanding patterns of diversification across large geographic areas and in recognising overlooked diversity.},
}
@article {pmid31630951,
year = {2019},
author = {Christodoulou, M and O'Hara, TD and Hugall, AF and Arbizu, PM},
title = {Dark Ophiuroid Biodiversity in a Prospective Abyssal Mine Field.},
journal = {Current biology : CB},
volume = {29},
number = {22},
pages = {3909-3912.e3},
doi = {10.1016/j.cub.2019.09.012},
pmid = {31630951},
issn = {1879-0445},
mesh = {Animals ; *Biodiversity ; Echinodermata/metabolism ; Hydrothermal Vents/*analysis ; Invertebrates ; Pacific Ocean ; Phylogeny ; Prospective Studies ; Starfish/*metabolism ; },
abstract = {The seafloor contains valuable mineral resources, including polymetallic (or manganese) nodules that form on offshore abyssal plains. The largest and most commercially attractive deposits are located in the Clarion Clipperton Fracture Zone (CCZ), in the eastern Pacific Ocean (EP) between Hawaii and Mexico, where testing of a mineral collection system is set to start soon [1]. The requirement to establish pre-mining environmental management plans has prompted numerous recent biodiversity and DNA barcoding surveys across these remote regions. Here we map DNA sequences from sampled ophiuroids (brittle stars, including post-larvae) of the CCZ and Peru Basin onto a substantial tree of life to show unprecedented levels of abyssal ophiuroid phylogenetic diversity including at least three ancient (>70 Ma), previously unknown clades. While substantial dark (unobserved) biodiversity has been reported from various microbial meta-barcoding projects [2, 3], our data show that we have considerably under-estimated the biodiversity of even the most conspicuous mega-faunal invertebrates [4] of the EP abyssal plain.},
}
@article {pmid31629741,
year = {2020},
author = {Sakkestad, ST and Skavland, J and Hanevik, K},
title = {Whole blood preservation methods alter chemokine receptor detection in mass cytometry experiments.},
journal = {Journal of immunological methods},
volume = {476},
number = {},
pages = {112673},
doi = {10.1016/j.jim.2019.112673},
pmid = {31629741},
issn = {1872-7905},
mesh = {Adult ; Antigens, CD/*analysis ; Blood Preservation/*instrumentation ; Fixatives ; Flow Cytometry ; Humans ; *Leukocytes/immunology ; Receptors, Chemokine/analysis ; },
abstract = {A potential hurdle when applying mass cytometry to the field study setting is the streamlining of sample collection while at the same time protecting the integrity of important cell epitopes. Whole blood preservation kits applying fixation and/or permeabilization agents are increasingly used in clinical trials to preserve leukocytes needed for downstream analysis. We here present a structured overview of leukocyte surface marker detectability in samples processed with four commercially available whole blood preservation kits; 1) Proteomic Stabilizer, 2) Stable-Lyse V2 and Stable-Store V2, 3) Cytodelics and 4) Lyse/Fix Buffer, as well as in samples treated with buffers included in Mass-tag Cellular Barcoding kits. Isolated leukocytes were stained with a 28-marker panel (including 7 chemokine receptors) of metal-conjugated antibodies and analysed on a mass cytometer. Exploration of the data by manual gating and viSNE analysis showed that although many markers were similarly detected across all sample conditions, most of the chemokine receptors in our panel, particularly CXCR3, CCR4, CCR6 and CXCR5, were incorrectly detected in the preserved samples and thus incompatible with the fixation and permeabilization agents found in whole blood preservation kits and in buffers used prior to barcoding.},
}
@article {pmid31628304,
year = {2019},
author = {Zhang, X and Garnerone, S and Simonetti, M and Harbers, L and Nicoś, M and Mirzazadeh, R and Venesio, T and Sapino, A and Hartman, J and Marchiò, C and Bienko, M and Crosetto, N},
title = {CUTseq is a versatile method for preparing multiplexed DNA sequencing libraries from low-input samples.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {4732},
pmid = {31628304},
issn = {2041-1723},
mesh = {A549 Cells ; Cell Line, Tumor ; DNA/*genetics/isolation &amp; purification/metabolism ; DNA Restriction Enzymes/metabolism ; *Gene Library ; HeLa Cells ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; MCF-7 Cells ; Paraffin Embedding/*methods ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; },
abstract = {Current multiplexing strategies for massively parallel sequencing of genomic DNA mainly rely on library indexing in the final steps of library preparation. This procedure is costly and time-consuming, because a library must be generated separately for each sample. Furthermore, library preparation is challenging in the case of fixed samples, such as DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissues. Here we describe CUTseq, a method that uses restriction enzymes and in vitro transcription to barcode and amplify genomic DNA prior to library construction. We thoroughly assess the sensitivity and reproducibility of CUTseq in both cell lines and FFPE samples, and demonstrate an application of CUTseq for multi-region DNA copy number profiling within single FFPE tumor sections, to assess intratumor genetic heterogeneity at high spatial resolution. In conclusion, CUTseq is a versatile and cost-effective method for library preparation for reduced representation genome sequencing, which can find numerous applications in research and diagnostics.},
}
@article {pmid31626774,
year = {2019},
author = {Chen, X and Sun, YC and Zhan, H and Kebschull, JM and Fischer, S and Matho, K and Huang, ZJ and Gillis, J and Zador, AM},
title = {High-Throughput Mapping of Long-Range Neuronal Projection Using In Situ Sequencing.},
journal = {Cell},
volume = {179},
number = {3},
pages = {772-786.e19},
pmid = {31626774},
issn = {1097-4172},
support = {P30 CA045508/CA/NCI NIH HHS/United States ; R01 DA036913/DA/NIDA NIH HHS/United States ; R01 NS073129/NS/NINDS NIH HHS/United States ; U19 MH114821/MH/NIMH NIH HHS/United States ; },
mesh = {Animals ; Auditory Cortex/*metabolism ; Brain Mapping ; Humans ; Integrases/genetics ; Mice ; Nerve Net/*metabolism ; Neurites/metabolism ; Pyramidal Cells/metabolism ; Pyramidal Tracts/metabolism ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis/*methods ; },
abstract = {Understanding neural circuits requires deciphering interactions among myriad cell types defined by spatial organization, connectivity, gene expression, and other properties. Resolving these cell types requires both single-neuron resolution and high throughput, a challenging combination with conventional methods. Here, we introduce barcoded anatomy resolved by sequencing (BARseq), a multiplexed method based on RNA barcoding for mapping projections of thousands of spatially resolved neurons in a single brain and relating those projections to other properties such as gene or Cre expression. Mapping the projections to 11 areas of 3,579 neurons in mouse auditory cortex using BARseq confirmed the laminar organization of the three top classes (intratelencephalic [IT], pyramidal tract-like [PT-like], and corticothalamic [CT]) of projection neurons. In depth analysis uncovered a projection type restricted almost exclusively to transcriptionally defined subtypes of IT neurons. By bridging anatomical and transcriptomic approaches at cellular resolution with high throughput, BARseq can potentially uncover the organizing principles underlying the structure and formation of neural circuits.},
}
@article {pmid31624585,
year = {2019},
author = {Xia, W and Zhang, B and Xing, D and Li, Y and Wu, W and Xiao, Y and Sun, J and Dou, Y and Tang, W and Zhang, J and Huang, X and Xu, Y and Xie, J and Wang, J and Huang, D},
title = {Development of high-resolution DNA barcodes for Dioscorea species discrimination and phylogenetic analysis.},
journal = {Ecology and evolution},
volume = {9},
number = {18},
pages = {10843-10853},
pmid = {31624585},
issn = {2045-7758},
abstract = {The genus Dioscorea is widely distributed in tropical and subtropical regions, and is economically important in terms of food supply and pharmaceutical applications. However, DNA barcodes are relatively unsuccessful in discriminating between Dioscorea species, with the highest discrimination rate (23.26%) derived from matK sequences. In this study, we compared genic and intergenic regions of three Dioscorea chloroplast genomes and found that the density of SNPs and indels in intergenic sites was about twice and seven times higher than that of SNPs and indels in the genic regions, respectively. A total of 52 primer pairs covering highly variable regions were designed and seven pairs of primers had 80%-100% PCR success rate. PCR amplicons of 73 Dioscorea individuals and assembled sequences of 47 Dioscorea SRAs were used for estimating intraspecific and interspecific divergence for the seven loci: The rpoB-trnC locus had the highest interspecific divergence. Automatic barcoding gap discovery (ABGD), Poisson tree processes (PTP), and generalized mixed Yule coalescence (GMYC) analysis were applied for species delimitation based on the seven loci and successfully identified the majority of species, except for species in the Enantiophyllum section. Phylogenetic analysis of 51 Dioscorea individuals (28 species) showed that most individuals belonging to the same species tended to cluster in the same group. Our results suggest that the variable loci derived from comparative analysis of plastid genome sequences could be good DNA barcode candidates for taxonomic analysis and species delimitation.},
}
@article {pmid31624576,
year = {2019},
author = {Zhang, ZP and Wang, XY and Zhang, Z and Yao, H and Zhang, XM and Zhang, Y and Zhang, BG},
title = {The impact of genetic diversity on the accuracy of DNA barcoding to identify species: A study on the genus Phellodendron.},
journal = {Ecology and evolution},
volume = {9},
number = {18},
pages = {10723-10733},
pmid = {31624576},
issn = {2045-7758},
abstract = {DNA barcoding is widely used in species identification, but there is considerable controversy regarding the extent of sampling in research methods. Some scholars have proposed that this small sample size underestimates the intraspecific genetic diversity, which would impact on the accuracy of DNA barcoding to identify species. In study, we selected all Phellodendron species (including P. amurense Rupr., P. chinense Schneid., and P. chinense var. glabriusculum Schneid.) as the materials, collected 59 P. amurense samples from 35 populations greatly to represent the genetic diversity, and analyzed the haplotype, genetic distance, barcoding gap, and Neighbor-Joining (NJ) trees based on psbA-trnH and internal transcribed spacer gene sequences. Additionally, a sampling simulation was conducted to assess the correlation between genetic diversity and the number of populations. Finally, analysis of critical geographical populations was performed. Based on analysis of haplotype, genetic distance, barcoding gap, and NJ trees, we found that eight P. amurense samples impacted on the effectiveness of DNA barcoding, which genetic information were very important to identify Phellodendron species. Moreover, the result of the NJ tree analysis performed the small-scale P. amurense sample size did not completely match the objective phylogenetic relationship in Phellodendron. In simulation sampling analysis, the data showed the genetic diversity indexes at the same population level gradually decreased and stabilized as the number of simulation sampling populations increased. We found that 1-2 samples from over 24 populations based on uniform geographical distribution could represent 80% of the genetic diversity of P. amurense and ensure authenticity and reliability of DNA barcoding. Thus, we proposed it is particularly important adequately samples to cover infraspecific genetic diversity in order to ensure identification accuracy of DNA barcoding.},
}
@article {pmid31623720,
year = {2019},
author = {Song, Q and Li, J and Cao, Y and Liu, W and Huo, H and Wan, JB and Song, Y and Tu, P},
title = {Binary code, a flexible tool for diagnostic metabolite sequencing of medicinal plants.},
journal = {Analytica chimica acta},
volume = {1088},
number = {},
pages = {89-98},
doi = {10.1016/j.aca.2019.08.039},
pmid = {31623720},
issn = {1873-4324},
mesh = {Analytic Sample Preparation Methods ; Drug Compounding ; Drug Prescriptions ; Fraud/prevention &amp; control ; Limit of Detection ; Medicine, Chinese Traditional ; Metabolomics/*methods ; Plants, Medicinal/*chemistry/*metabolism ; },
abstract = {The principle of chromatographic fingerprint is that certain diagnostic metabolites should be always distributed in a given plant and currently, it has been widely accepted as a promising means for medicinal plant authentication. Moreover, the chemical profile is the only evidence to clarify the ingredients of those consumable plant products, e.g. traditional Chinese medicine (TCM) prescriptions. Herein, efforts were made to describe the diagnostic metabolome of medicinal plant or TCM prescription using a binary code sequence. Forty-five well-known medicinal plants along with six relevant prescriptions were employed for concept illustration and proof. Each plant was subjected to chemical characterization, and diagnostic metabolites of all plants were gathered into a chemical pool containing 595 compounds. A robust method enabling the detection of all 595 constituents was then developed using LC coupled to scheduled multiple reaction monitoring. Analyst™ software was responsible for automatically judging the presence (defined as "1") or absence (defined as "0") of each analyte with a defined signal-to-noise threshold (S/N > 100). After converting each medicinal plant to a binary sequence consisting of 595 codes, an in-house database was built by involving all sequences. The potentials of sequence library retrieval towards plant authentication, preliminary chemical characterization, and deformulation of TCM prescriptions were demonstrated after that the diagnostic metabolome of each test sample was translated to a binary code sequence. Above all, binary code is a flexible tool for diagnostic metabolite sequencing of medicinal plants, and it should be an alternative tool of DNA barcoding towards plant authentication.},
}
@article {pmid31620312,
year = {2019},
author = {Acosta-Rojas, DC and Jiménez-Franco, MV and Zapata-Pérez, VM and De la Rúa, P and Martínez-López, V},
title = {An integrative approach to discern the seed dispersal role of frugivorous guilds in a Mediterranean semiarid priority habitat.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7609},
pmid = {31620312},
issn = {2167-8359},
abstract = {Seed dispersal is an essential process to maintain the viability of plant populations, and understanding this ecological process allows management strategies to be developed to conserve ecosystems. European Union priority habitat 5220* is defined as "Mediterranean arborescent shrubland with Ziziphus lotus" and it represents a favorable microclimate within the severe climatic conditions typical of the semiarid south-eastern region of the Iberian Peninsula. Therefore, the study of seed dispersal in this priority habitat by different frugivorous guilds, is a challenge for its conservation. In this study, we have characterized a mutualistic network of seed dispersal that is mediated by vertebrates (mammals and birds) in the protected habitat 5220*. The aims of this study were to: (i) identify the seed disperser community; (ii) analyze the relative role of key species in the dispersal process; and (iii) compare the functional ecology of the seed dispersal process between mammals and birds. As such, we collected animal faeces to determine seed dispersers taxonomy, identifying the mammals through the visual aspect of the faeces and the birds by DNA barcoding. In the case of birds, we also collected regurgitated seeds in which the disperser species was also identified through molecular techniques. This allowed us to build-up a mutualistic network and to identify the relative role of these animals in seed dispersal. Our results showed that mammals and birds fulfilled complementary roles in seed dispersal, with birds representing the main dispersers of key plants within the 5220* habitat, and mammals the main dispersers of human-cultivated plants. Herein, we provide a useful approach with relevant information that can be used to propose management policies that focus on restoring the threatened 5220* habitat, promoting the role of birds to disperse key species that structure plant communities of this priority habitat.},
}
@article {pmid31620145,
year = {2019},
author = {Brewer, GE and Clarkson, JJ and Maurin, O and Zuntini, AR and Barber, V and Bellot, S and Biggs, N and Cowan, RS and Davies, NMJ and Dodsworth, S and Edwards, SL and Eiserhardt, WL and Epitawalage, N and Frisby, S and Grall, A and Kersey, PJ and Pokorny, L and Leitch, IJ and Forest, F and Baker, WJ},
title = {Factors Affecting Targeted Sequencing of 353 Nuclear Genes From Herbarium Specimens Spanning the Diversity of Angiosperms.},
journal = {Frontiers in plant science},
volume = {10},
number = {},
pages = {1102},
pmid = {31620145},
issn = {1664-462X},
abstract = {The world's herbaria collectively house millions of diverse plant specimens, including endangered or extinct species and type specimens. Unlocking genetic data from the typically highly degraded DNA obtained from herbarium specimens was difficult until the arrival of high-throughput sequencing approaches, which can be applied to low quantities of severely fragmented DNA. Target enrichment involves using short molecular probes that hybridise and capture genomic regions of interest for high-throughput sequencing. In this study on herbariomics, we used this targeted sequencing approach and the Angiosperms353 universal probe set to recover up to 351 nuclear genes from 435 herbarium specimens that are up to 204 years old and span the breadth of angiosperm diversity. We show that on average 207 genes were successfully retrieved from herbarium specimens, although the mean number of genes retrieved and target enrichment efficiency is significantly higher for silica gel-dried specimens. Forty-seven target nuclear genes were recovered from a herbarium specimen of the critically endangered St Helena boxwood, Mellissia begoniifolia, collected in 1815. Herbarium specimens yield significantly less high-molecular-weight DNA than silica gel-dried specimens, and genomic DNA quality declines with sample age, which is negatively correlated with target enrichment efficiency. Climate, taxon-specific traits, and collection strategies additionally impact target sequence recovery. We also detected taxonomic bias in targeted sequencing outcomes for the 10 most numerous angiosperm families that were investigated in depth. We recommend that (1) for species distributed in wet tropical climates, silica gel-dried specimens should be used preferentially; (2) for species distributed in seasonally dry tropical climates, herbarium and silica gel-dried specimens yield similar results, and either collection can be used; (3) taxon-specific traits should be explored and established for effective optimisation of taxon-specific studies using herbarium specimens; (4) all herbarium sheets should, in future, be annotated with details of the preservation method used; (5) long-term storage of herbarium specimens should be in stable, low-humidity, and low-temperature environments; and (6) targeted sequencing with universal probes, such as Angiosperms353, should be investigated closely as a new approach for DNA barcoding that will ensure better exploitation of herbarium specimens than traditional Sanger sequencing approaches.},
}
@article {pmid31618609,
year = {2020},
author = {Lozano-Sardaneta, YN and Paternina, LE and Sánchez-Montes, S and Quintero, A and Ibáñez-Bernal, S and Sánchez-Cordero, V and Bejarano, EE and Becker, I},
title = {DNA barcoding and fauna of phlebotomine sand flies (Diptera: Psychodidae: Phlebotominae) from Los Tuxtlas, Veracruz, Mexico.},
journal = {Acta tropica},
volume = {201},
number = {},
pages = {105220},
doi = {10.1016/j.actatropica.2019.105220},
pmid = {31618609},
issn = {1873-6254},
mesh = {Animals ; Brazil ; *DNA Barcoding, Taxonomic ; Disease Vectors/*classification ; Electron Transport Complex IV/*genetics ; Female ; Leishmaniasis/*genetics ; Mexico ; Phlebotomus/*classification/*genetics ; },
abstract = {Mexico has great diversity of phlebotomine sand flies related to cases of leishmaniasis, yet few studies have dressed the molecular taxonomy of these sand fly species. The use of the cytochrome oxidase subunit 1 (COI) gene, as a DNA Barcode has facilitated the molecular identification of sand flies species worldwide. We use the DNA barcode as a useful tool for the identification of phlebotomine sand flies of the natural reserve Los Tuxtlas from Veracruz, México. A fragment of 536 bp of the COI gene was obtained from 36 individuals belonging to eight species of five genera (Dampfomyia, Lutzomyia, Psathyromyia, Psychodopygus and Brumptomyia) with coverage between 92-100%, and found similarities ranging from 93-98% with other New World phlebotomine sand flies. The NJ dendogram grouped sand flies into eight clusters according to identified species, supported by bootstrap of 97%-100%. In conclusion, all phlebotomine sand flies were correctly identified and agree with the morphological identification, also could separate genetics the isomorphic females of the genus Brumptomyia.},
}
@article {pmid31616590,
year = {2019},
author = {Bustamante, K and Santos-Ordóñez, E and Miranda, M and Pacheco, R and Gutiérrez, Y and Scull, R},
title = {Morphological and molecular barcode analysis of the medicinal tree Mimusops coriacea (A.DC.) Miq. collected in Ecuador.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7789},
pmid = {31616590},
issn = {2167-8359},
abstract = {BACKGROUND: Mimusops coriacea (A.DC.) Miq., (Sapotaceae), originated from Africa, were introduced to coastal areas in Ecuador where it is not extensively used as a traditional medicine to treat various human diseases. Different therapeutically uses of the species include: analgesic, antimicrobial, hypoglycemic, inflammation and pain relieve associated with bone and articulation-related diseases. Furthermore, Mimusops coriacea could be used as anti-oxidant agent. However, botanical, chemical or molecular barcode information related to this much used species is not available from Ecuador. In this study, morphological characterization was performed from leaves, stem and seeds. Furthermore, genetic characterization was performed using molecular barcodes for rbcL, matk, ITS1 and ITS2 using DNA extracted from leaves.<br><br>METHODS: Macro-morphological description was performed on fresh leaves, stem and seeds. For anatomical evaluation, tissues were embedded in paraffin and transversal dissections were done following incubation with sodium hypochlorite and safranin for coloration and fixated later in glycerinated gelatin. DNA extraction was performed using a modified CTAB protocol from leaf tissues, while amplification by PCR was accomplished for the molecular barcodes rbcL, matK, ITS1 and ITS2. Sequence analysis was performed using blast in the GenBank. Phylogenetic analysis was performed with accessions queried in the GenBank belonging to the subfamily Sapotoideae.<br><br>RESULTS: Leaf size was 13.56 &#xb1; 1.46 &#xd7; 7.49 &#xb1; 0.65 cm; where is a macro-morphological description of the stem (see Methods). The peel of the seeds is dark brown. Sequence analysis revealed that amplicons were generated using the four barcodes selected. Phylogenetic analysis indicated that the barcodes rbcL and matK, were not discriminated between species within the same genus of the subfamily Sapotoideae. On the other hand, the ITS1 and ITS2 were discriminative at the level of genus and species of the Sapotoideae.},
}
@article {pmid31616583,
year = {2019},
author = {Bayona-Vásquez, NJ and Glenn, TC and Kieran, TJ and Pierson, TW and Hoffberg, SL and Scott, PA and Bentley, KE and Finger, JW and Louha, S and Troendle, N and Diaz-Jaimes, P and Mauricio, R and Faircloth, BC},
title = {Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD).},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7724},
pmid = {31616583},
issn = {2167-8359},
abstract = {Molecular ecologists frequently use genome reduction strategies that rely upon restriction enzyme digestion of genomic DNA to sample consistent portions of the genome from many individuals (e.g., RADseq, GBS). However, researchers often find the existing methods expensive to initiate and/or difficult to implement consistently, especially because it is difficult to multiplex sufficient numbers of samples to fill entire sequencing lanes. Here, we introduce a low-cost and highly robust approach for the construction of dual-digest RADseq libraries that build on adapters and primers designed in Adapterama I. Major features of our method include: (1) minimizing the number of processing steps; (2) focusing on a single strand of sample DNA for library construction, allowing the use of a non-phosphorylated adapter on one end; (3) ligating adapters in the presence of active restriction enzymes, thereby reducing chimeras; (4) including an optional third restriction enzyme to cut apart adapter-dimers formed by the phosphorylated adapter, thus increasing the efficiency of adapter ligation to sample DNA, which is particularly effective when only low quantity/quality DNA samples are available; (5) interchangeable adapter designs; (6) incorporating variable-length internal indexes within the adapters to increase the scope of sample indexing, facilitate pooling, and increase sequence diversity; (7) maintaining compatibility with universal dual-indexed primers and thus, Illumina sequencing reagents and libraries; and, (8) easy modification for the identification of PCR duplicates. We present eight adapter designs that work with 72 restriction enzyme combinations. We demonstrate the efficiency of our approach by comparing it with existing methods, and we validate its utility through the discovery of many variable loci in a variety of non-model organisms. Our 2RAD/3RAD method is easy to perform, has low startup costs, has increased utility with low-concentration input DNA, and produces libraries that can be highly-multiplexed and pooled with other Illumina libraries.},
}
@article {pmid31615997,
year = {2019},
author = {Ally, HM and Hamss, HE and Simiand, C and Maruthi, MN and Colvin, J and Omongo, CA and Delatte, H},
title = {What has changed in the outbreaking populations of the severe crop pest whitefly species in cassava in two decades?.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {14796},
pmid = {31615997},
issn = {2045-2322},
mesh = {Animal Distribution ; Animals ; Crop Protection ; DNA Barcoding, Taxonomic ; Disease Outbreaks/*statistics &amp; numerical data ; Disease Resistance/*genetics ; Electron Transport Complex IV/genetics ; Female ; Genetic Markers ; Genetic Variation ; Genotype ; Hemiptera/classification/*genetics/pathogenicity/virology ; Insect Proteins/genetics ; Insect Vectors/classification/*genetics/virology ; Male ; Manihot/genetics/*parasitology/virology ; Phylogeny ; Plant Diseases/parasitology/*statistics &amp; numerical data/virology ; Population Dynamics ; Uganda ; },
abstract = {High populations of African cassava whitefly (Bemisia tabaci) have been associated with epidemics of two viral diseases in Eastern Africa. We investigated population dynamics and genetic patterns by comparing whiteflies collected on cassava in 1997, during the first whitefly upsurges in Uganda, with collections made in 2017 from the same locations. Nuclear markers and mtCOI barcoding sequences were used on 662 samples. The composition of the SSA1 population changed significantly over the 20-year period with the SSA1-SG2 percentage increasing from 0.9 to 48.6%. SSA1-SG1 and SSA1-SG2 clearly interbreed, confirming that they are a single biological species called SSA1. The whitefly species composition changed: in 1997, SSA1, SSA2 and B. afer were present; in 2017, no SSA2 was found. These data and those of other publications do not support the 'invader' hypothesis. Our evidence shows that no new species or new population were found in 20 years, instead, the distribution of already present genetic clusters composing SSA1 species have changed over time and that this may be in response to several factors including the introduction of new cassava varieties or climate changes. The practical implications are that cassava genotypes possessing both whitefly and disease resistances are needed urgently.},
}
@article {pmid31614980,
year = {2019},
author = {Yu, X and Tan, W and Zhang, H and Gao, H and Wang, W and Tian, X},
title = {Complete Chloroplast Genomes of Ampelopsis humulifolia and Ampelopsis japonica: Molecular Structure, Comparative Analysis, and Phylogenetic Analysis.},
journal = {Plants (Basel, Switzerland)},
volume = {8},
number = {10},
pages = {},
pmid = {31614980},
issn = {2223-7747},
abstract = {Ampelopsis humulifolia (A. humulifolia) and Ampelopsis japonica (A. japonica), which belong to the family Vitaceae, are valuably used as medicinal plants. The chloroplast (cp) genomes have been recognized as a convincing data for marker selection and phylogenetic studies. Therefore, in this study we reported the complete cp genome sequences of two Ampelopsis species. Results showed that the cp genomes of A. humulifolia and A. japonica were 161,724 and 161,430 bp in length, respectively, with 37.3% guanine-cytosine (GC) content. A total of 114 unique genes were identified in each cp genome, comprising 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. We determined 95 and 99 small sequence repeats (SSRs) in A. humulifolia and A. japonica, respectively. The location and distribution of long repeats in the two cp genomes were identified. A highly divergent region of psbZ (Photosystem II reaction center protein Z) -trnG (tRNA-Glycine) was found and could be treated as a potential marker for Vitaceae, and then the corresponding primers were designed. Additionally, phylogenetic analysis showed that Vitis was closer to Tetrastigma than Ampelopsis. In general, this study provides valuable genetic resources for DNA barcoding marker identification and phylogenetic analyses of Ampelopsis.},
}
@article {pmid31613890,
year = {2019},
author = {Morandi, E and Cereda, M and Incarnato, D and Parlato, C and Basile, G and Anselmi, F and Lauria, A and Simon, LM and Laurence Polignano, I and Arruga, F and Deaglio, S and Tirtei, E and Fagioli, F and Oliviero, S},
title = {HaTSPiL: A modular pipeline for high-throughput sequencing data analysis.},
journal = {PloS one},
volume = {14},
number = {10},
pages = {e0222512},
pmid = {31613890},
issn = {1932-6203},
mesh = {DNA/*chemistry ; DNA Barcoding, Taxonomic/*methods ; Data Analysis ; *High-Throughput Nucleotide Sequencing ; Humans ; Reproducibility of Results ; Sequence Analysis, DNA/*statistics &amp; numerical data ; *Software ; Workflow ; },
abstract = {BACKGROUND: Next generation sequencing methods are widely adopted for a large amount of scientific purposes, from pure research to health-related studies. The decreasing costs per analysis led to big amounts of generated data and to the subsequent improvement of software for the respective analyses. As a consequence, many approaches have been developed to chain different software in order to obtain reliable and reproducible workflows. However, the large range of applications for NGS approaches entails the challenge to manage many different workflows without losing reliability.<br><br>METHODS: We here present a high-throughput sequencing pipeline (HaTSPiL), a Python-powered CLI tool designed to handle different approaches for data analysis with a high level of reliability. The software relies on the barcoding of filenames using a human readable naming convention that contains any information regarding the sample needed by the software to automatically choose different workflows and parameters. HaTSPiL is highly modular and customisable, allowing the users to extend its features for any specific need.<br><br>CONCLUSIONS: HaTSPiL is licensed as Free Software under the MIT license and it is available at https://github.com/dodomorandi/hatspil.},
}
@article {pmid31613670,
year = {2019},
author = {Shutt, JD and Burgess, MD and Phillimore, AB},
title = {A Spatial Perspective on the Phenological Distribution of the Spring Woodland Caterpillar Peak.},
journal = {The American naturalist},
volume = {194},
number = {5},
pages = {E109-E121},
doi = {10.1086/705241},
pmid = {31613670},
issn = {1537-5323},
mesh = {Altitude ; Animals ; DNA Barcoding, Taxonomic ; Food Chain ; Forests ; Larva/classification/growth &amp; development/physiology ; Lepidoptera/classification/*growth &amp; development/physiology ; Magnoliopsida/classification ; Scotland ; *Spatio-Temporal Analysis ; *Trees ; },
abstract = {A classic system for studying trophic mismatch focuses on the timing of the spring caterpillar peak in relation to the breeding time and productivity of woodland passerine birds. Most work has been conducted in single-site oak woodlands, and little is known about how insights generalize to other woodland types or across space. Here we present the results of a 3-year study on the species composition and temporal distribution of the spring caterpillar peak on different tree taxa across 40 woodland sites spanning 2° of latitude in Scotland. We used molecular barcoding to identify 62 caterpillar species, with winter moth (Operophtera brumata) being the most abundant, comprising one-third of the sample. Oak (Quercus sp.) and willow (Salix sp.) hosted significantly higher caterpillar abundances than other tree taxa, with winter moth exhibiting similar trends and invariantly proportionate across tree taxa. Caterpillar peak phenology was broadly similar between tree taxa. While latitude had little effect, increasing elevation increased the height of the caterpillar peak and retarded timing by 3.7 days per 100 m. These findings extend our understanding of how mismatch may play out spatially, with caterpillar peak date varying with elevation and tree taxa varying in the caterpillar resource that they host.},
}
@article {pmid31611697,
year = {2019},
author = {Chen, S and Lake, BB and Zhang, K},
title = {High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell.},
journal = {Nature biotechnology},
volume = {37},
number = {12},
pages = {1452-1457},
pmid = {31611697},
issn = {1546-1696},
support = {U01 MH114828/MH/NIMH NIH HHS/United States ; U01 MH098977/MH/NIMH NIH HHS/United States ; U54 HL145608/HL/NHLBI NIH HHS/United States ; U01 DK107350/DK/NIDDK NIH HHS/United States ; R01 HL123755/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Cells, Cultured ; Cerebral Cortex/cytology ; Chromatin/chemistry/*genetics ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Mice ; RNA, Messenger/chemistry/genetics ; Sequence Analysis, RNA/*methods ; Transcriptome/*genetics ; },
abstract = {Single-cell RNA sequencing can reveal the transcriptional state of cells, yet provides little insight into the upstream regulatory landscape associated with open or accessible chromatin regions. Joint profiling of accessible chromatin and RNA within the same cells would permit direct matching of transcriptional regulation to its outputs. Here, we describe droplet-based single-nucleus chromatin accessibility and mRNA expression sequencing (SNARE-seq), a method that can link a cell's transcriptome with its accessible chromatin for sequencing at scale. Specifically, accessible sites are captured by Tn5 transposase in permeabilized nuclei to permit, within many droplets in parallel, DNA barcode tagging together with the mRNA molecules from the same cells. To demonstrate the utility of SNARE-seq, we generated joint profiles of 5,081 and 10,309 cells from neonatal and adult mouse cerebral cortices, respectively. We reconstructed the transcriptome and epigenetic landscapes of major and rare cell types, uncovered lineage-specific accessible sites, especially for low-abundance cells, and connected the dynamics of promoter accessibility with transcription level during neurogenesis.},
}
@article {pmid31610807,
year = {2019},
author = {Díez-Fernández, A and Martínez-de la Puente, J and Ruiz, S and Gutiérrez-López, R and Soriguer, R and Figuerola, J},
title = {Correction to: Aedes vittatus in Spain: current distribution, barcoding characterization and potential role as vectors of human diseases.},
journal = {Parasites &amp; vectors},
volume = {12},
number = {1},
pages = {479},
pmid = {31610807},
issn = {1756-3305},
abstract = {Unfortunately, the original version of this article [1] contained an error. In the distribution map in Fig. 3, the presence of the mosquito Aedes vittatus was incorrectly indicated for Libya and Egypt.},
}
@article {pmid31610624,
year = {2019},
author = {Kim, DU and Lee, M and Han, S and Nam, M and Lee, S and Lee, J and Woo, J and Kim, D and Hoe, KL},
title = {Optimization of a microarray for fission yeast.},
journal = {Genomics &amp; informatics},
volume = {17},
number = {3},
pages = {e28},
pmid = {31610624},
issn = {1598-866X},
support = {//Chungnam National University/ ; },
abstract = {Bar-code (tag) microarrays of yeast gene-deletion collections facilitate the systematic identification of genes required for growth in any condition of interest. Anti-sense strands of amplified bar-codes hybridize with ~10,000 (5,000 each for up- and down-tags) different kinds of sense-strand probes on an array. In this study, we optimized the hybridization processes of an array for fission yeast. Compared to the first version of the array (11 µm, 100K) consisting of three sectors with probe pairs (perfect match and mismatch), the second version (11 µm, 48K) could represent ~10,000 up-/down-tags in quadruplicate along with 1,508 negative controls in quadruplicate and a single set of 1,000 unique negative controls at random dispersed positions without mismatch pairs. For PCR, the optimal annealing temperature (maximizing yield and minimizing extra bands) was 58°C for both tags. Intriguingly, up-tags required 3(?) higher amounts of blocking oligonucleotides than down-tags. A 1:1 mix ratio between up- and down-tags was satisfactory. A lower temperature (25°C) was optimal for cultivation instead of a normal temperature (30°C) because of extra temperature-sensitive mutants in a subset of the deletion library. Activation of frozen pooled cells for >1 day showed better resolution of intensity than no activation. A tag intensity analysis showed that tag(s) of 4,316 of the 4,526 strains tested were represented at least once; 3,706 strains were represented by both tags, 4,072 strains by up-tags only, and 3,950 strains by down-tags only. The results indicate that this microarray will be a powerful analytical platform for elucidating currently unknown gene functions.},
}
@article {pmid31609586,
year = {2019},
author = {Stiller, C and Aghelpasand, H and Frick, T and Westerlund, K and Ahmadian, A and Karlström, AE},
title = {Fast and Efficient Fc-Specific Photoaffinity Labeling To Produce Antibody-DNA Conjugates.},
journal = {Bioconjugate chemistry},
volume = {30},
number = {11},
pages = {2790-2798},
doi = {10.1021/acs.bioconjchem.9b00548},
pmid = {31609586},
issn = {1520-4812},
mesh = {Aminoacyltransferases/immunology/metabolism ; Antibodies, Monoclonal/*chemistry/immunology ; Antigen-Antibody Reactions/immunology ; Bacterial Proteins/immunology/metabolism ; Cysteine Endopeptidases/immunology/metabolism ; DNA/*chemistry/immunology ; Humans ; Immunoconjugates/*chemistry/immunology ; Immunoglobulin Fc Fragments/*chemistry/immunology ; Immunoglobulin G/*chemistry/immunology ; Phenylalanine/*analogs &amp; derivatives/chemistry ; Photoaffinity Labels/*chemistry ; },
abstract = {Antibody-DNA conjugates are powerful tools for DNA-assisted protein analysis. Growing usage of these methods demands efficient production of high-quality conjugates. We developed an easy and fast synthesis route yielding covalent antibody-DNA conjugates with a defined conjugation site and low batch-to-batch variability. We utilize the Z domain from protein A, containing the unnatural amino acid 4-benzoylphenylalanine (BPA) for photoaffinity labeling of the antibodies' Fc region. Z(xBPA) domains are C-terminally modified with triple-glycine (G3)-modified DNA-oligonucleotides via enzymatic Sortase A coupling. We show reliable modification of the most commonly used IgG's. To prove our conjugates' functionality, we detected antibody-antigen binding events in an assay called Droplet Barcode Sequencing for Protein analysis (DBS-Pro). It confirms not only retained functionality for both conjugate parts but also the potential of using DBS-Pro for quantifying protein abundances. As intermediates are easily storable and our approach is modular, it offers a convenient strategy for screening various antibody-DNA conjugates using the same starting material.},
}
@article {pmid31608180,
year = {2019},
author = {Pruski, S and Miglietta, MP},
title = {Fluctuation and diversity of Hydromedusae (Hydrozoa, Cnidaria) in a highly productive region of the Gulf of Mexico inferred from high frequency plankton sampling.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7848},
pmid = {31608180},
issn = {2167-8359},
abstract = {Hydrozoa medusae undergo blooms and seasonal fluctuations; however the drivers of such fluctuations are unknown. To understand how medusa populations fluctuate in response to seasonal factors such as temperature, salinity, dissolved oxygen, and chlorophyll a, and to enhance our taxonomic knowledge of Hydrozoa in Galveston Bay (TX), we performed frequent plankton sampling from September 2015 to September 2016. We collected 1,321 medusae in 190 sampling days. Using molecular barcoding and morphological analyses we identified 25 species, of which 21 are a first record for Galveston Bay and eight for the Gulf of Mexico. Daily medusa abundance is non-linearly related to temperature, with peak abundance estimated with multivariate regression analysis at approximately 21C. The role that temperature plays in driving medusa abundance has implications for future climate change scenarios, given that temperature in the Gulf of Mexico is expected to rise 4 °C by the end of the century. We also show that the biodiversity of the Galveston Bay and the Gulf of Mexico is underestimated and that molecular barcoding is an important and efficient tool to identify large number of medusae. We conclude that dense plankton sampling is necessary to capture both diversity and abundance of planktonic medusae.},
}
@article {pmid31607786,
year = {2019},
author = {Shi, W and Liu, PL and Wen, J and Feng, Y and Pan, B},
title = {New morphological and DNA evidence supports the existence of Calligonum jeminaicum Z. M. Mao (Calligoneae, Polygonaceae) in China.},
journal = {PhytoKeys},
volume = {132},
number = {},
pages = {53-73},
pmid = {31607786},
issn = {1314-2011},
abstract = {Calligonum jeminaicum Z. M. Mao, a species regarded as endemic to China, was thought to be nonexistent owing to a lack of scientific records. The similarity of C. jeminaicum to C. mongolicum Turcz. warranted an investigation into the taxonomical relationship between these species. In this study, a naturally occurring population of C. jeminaicum was discovered and the taxonomical relationships of this species with C. mongolicum were resolved. Morphological traits, including fruit and flower characteristics, as well as nuclear (ETS, ITS) and chloroplast (psbA-trnH, ycf6-psbM, rpl32-trnL, rbcL, and trnL-F) DNA sequence data were studied to confirm the taxonomic status of C. jeminaicum. The nrDNA data (ITS1-2 and ETS) from C. jeminaicum reflected variability from the whole C. mongolicum complex, showing distinctive haplotypes in the Calligonum sect. Medusa Sosk. &amp; Alexandr. The cpDNA data supplied similar evidence, showing unique branching in Bayesian and ML tree analyses. The specific status of C. jeminaicum is confirmed based on both morphological and molecular analyses. Here we present a revised description of C. jeminaicum along with its DNA barcode and discuss suggestions for the conservation of this species. Based on current evidence, this species was evaluated as Critically Endangered (CR) according to the IUCN criteria.},
}
@article {pmid31606085,
year = {2019},
author = {Kreuzer, J and Edwards, A and Haas, W},
title = {Multiplexed quantitative phosphoproteomics of cell line and tissue samples.},
journal = {Methods in enzymology},
volume = {626},
number = {},
pages = {41-65},
doi = {10.1016/bs.mie.2019.07.027},
pmid = {31606085},
issn = {1557-7988},
mesh = {Animals ; Cell Line ; Chromatography, Liquid/methods ; Humans ; Mass Spectrometry/*methods ; Phosphopeptides/*analysis/isolation &amp; purification ; Phosphorylation ; Protein Processing, Post-Translational ; Proteolysis ; Proteome/*analysis/isolation &amp; purification ; Proteomics/*methods ; Titanium/chemistry ; },
abstract = {Post-translational modifications (PTMs) of proteins increase a biological system's repertoire of regulatory tools to control cellular mechanisms. Protein phosphorylation is the most studied PTM and known to be dysregulated in many diseases, including cancer, and protein kinases are among the most important drug targets. Many proteins across the eukaryotic proteome are phosphorylated, and more than 50,000 unique protein phosphorylation sites have been identified in a single human cell line. Understanding the vast biological networks directed by protein phosphorylation requires deep quantitative mapping of the phosphoproteome across many samples. Multiplexed proteomics using isobaric labeling reagents to barcode proteome samples for simultaneous quantification has greatly increased the throughput of mass spectrometry-based proteomics and enabled the number of analyses required to understand complex biological systems. We are presenting a detailed protocol to use multiplexed proteomics for mapping phosphoproteomes in samples from cell culture experiments and in tissue samples. The protocol includes phosphopeptide enrichment with TiO2 and phosphotyrosine antibody technology. We are using tandem mass tag (TMT) reagents for barcoding the samples allowing parallel quantification of up to 11 samples. The mass spectrometry method is based on the MultiNotch MS3 method to generate quantitative data of high accuracy and reproducibility. Tandem mass spectrometry (MS2) based on regular collision-induced dissociation (CID) and higher-energy collisional dissociation (HCD) is used to maximize the number of quantified phosphopeptides. The protocol typically enables the quantification of more than 20,000 unique phosphoforms (unique patterns of peptide phosphorylations) from proteome samples of human origin requiring less than 8h of mass spectrometry time per sample.},
}
@article {pmid31603430,
year = {2019},
author = {Peine, A and Hallawa, A and Schöffski, O and Dartmann, G and Fazlic, LB and Schmeink, A and Marx, G and Martin, L},
title = {A Deep Learning Approach for Managing Medical Consumable Materials in Intensive Care Units via Convolutional Neural Networks: Technical Proof-of-Concept Study.},
journal = {JMIR medical informatics},
volume = {7},
number = {4},
pages = {e14806},
pmid = {31603430},
issn = {2291-9694},
abstract = {BACKGROUND: High numbers of consumable medical materials (eg, sterile needles and swabs) are used during the daily routine of intensive care units (ICUs) worldwide. Although medical consumables largely contribute to total ICU hospital expenditure, many hospitals do not track the individual use of materials. Current tracking solutions meeting the specific requirements of the medical environment, like barcodes or radio frequency identification, require specialized material preparation and high infrastructure investment. This impedes the accurate prediction of consumption, leads to high storage maintenance costs caused by large inventories, and hinders scientific work due to inaccurate documentation. Thus, new cost-effective and contactless methods for object detection are urgently needed.<br><br>OBJECTIVE: The goal of this work was to develop and evaluate a contactless visual recognition system for tracking medical consumable materials in ICUs using a deep learning approach on a distributed client-server architecture.<br><br>METHODS: We developed Consumabot, a novel client-server optical recognition system for medical consumables, based on the convolutional neural network model MobileNet implemented in Tensorflow. The software was designed to run on single-board computer platforms as a detection unit. The system was trained to recognize 20 different materials in the ICU, while 100 sample images of each consumable material were provided. We assessed the top-1 recognition rates in the context of different real-world ICU settings: materials presented to the system without visual obstruction, 50% covered materials, and scenarios of multiple items. We further performed an analysis of variance with repeated measures to quantify the effect of adverse real-world circumstances.<br><br>RESULTS: Consumabot reached a >99% reliability of recognition after about 60 steps of training and 150 steps of validation. A desirable low cross entropy of <0.03 was reached for the training set after about 100 iteration steps and after 170 steps for the validation set. The system showed a high top-1 mean recognition accuracy in a real-world scenario of 0.85 (SD 0.11) for objects presented to the system without visual obstruction. Recognition accuracy was lower, but still acceptable, in scenarios where the objects were 50% covered (P<.001; mean recognition accuracy 0.71; SD 0.13) or multiple objects of the target group were present (P=.01; mean recognition accuracy 0.78; SD 0.11), compared to a nonobstructed view. The approach met the criteria of absence of explicit labeling (eg, barcodes, radio frequency labeling) while maintaining a high standard for quality and hygiene with minimal consumption of resources (eg, cost, time, training, and computational power).<br><br>CONCLUSIONS: Using a convolutional neural network architecture, Consumabot consistently achieved good results in the classification of consumables and thus is a feasible way to recognize and register medical consumables directly to a hospital's electronic health record. The system shows limitations when the materials are partially covered, therefore identifying characteristics of the consumables are not presented to the system. Further development of the assessment in different medical circumstances is needed.},
}
@article {pmid31603254,
year = {2020},
author = {Hernández-Triana, LM and Brugman, VA and Pramual, P and Barrero, E and Nikolova, NI and Ruiz-Arrondo, I and Kaiser, A and Krüger, A and Lumley, S and Osório, HC and Ignjatović-Ćupina, A and Petrić, D and Laure Setier-Rio, M and Bødker, R and Johnson, N},
title = {Genetic diversity and population structure of Culex modestus across Europe: does recent appearance in the United Kingdom reveal a tendency for geographical spread?.},
journal = {Medical and veterinary entomology},
volume = {34},
number = {1},
pages = {86-96},
doi = {10.1111/mve.12412},
pmid = {31603254},
issn = {1365-2915},
mesh = {*Animal Distribution ; Animals ; Culex/genetics/*physiology ; Electron Transport Complex IV/analysis ; *Genetic Variation ; Insect Proteins/analysis ; United Kingdom ; },
abstract = {In mainland Europe, the mosquito species Culex modestus Ficalbi (1890) is a bridge vector for West Nile virus (WNV) from its natural bird-mosquito cycle to mammals. The present study assessed the genetic diversity of Cx. modestus, as well as related Culex species, using the mitochondrial COI DNA barcoding region and compared this with the population structure across Europe. A haplotype network was mapped to determine genealogical relationships among specimens. The intraspecific genetic diversity within individual Culex species was below 2%, whereas the interspecific genetic divergence varied from 2.99% to 13.74%. In total, 76 haplotypes were identified among 198 sequences. A median-joining network determined from 198 COI sequences identified two major lineages that were separated by at least four mutation steps. A high level of intraspecific genetic diversity was not detected in Cx. modestus in samples submitted from different European populations, which indicates that morphologically identified specimens represent a single species and not a species complex. Therefore, it is deduced that different populations of Cx. modestus will show a similar potential to transmit WNV, lending support to concerns that the population present in southeast England represents a risk of transmission to humans.},
}
@article {pmid31602606,
year = {2019},
author = {Poramba-Liyanage, DW and Korthout, T and van Leeuwen, F},
title = {Epi-ID: Systematic and Direct Screening for Chromatin Regulators in Yeast by Barcode-ChIP-Seq.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2049},
number = {},
pages = {87-103},
pmid = {31602606},
issn = {1940-6029},
mesh = {Chromatin/*genetics ; Chromatin Immunoprecipitation ; Chromatin Immunoprecipitation Sequencing ; DNA Barcoding, Taxonomic/methods ; Epigenesis, Genetic/*genetics ; Mutation/genetics ; Saccharomyces cerevisiae/*genetics ; },
abstract = {The assembly and regulation of chromatin requires coordinated activity of multiple mechanisms. Many factors feed into signaling networks that control the epigenome of a cell. It is this complexity that makes understanding the layers of epigenetic regulation a challenge. Genetic screens have been indispensable for studying chromatin processes. However, they can be laborious and the readout for chromatin changes is often indirect. Epi-ID is a screening strategy in yeast that enables the direct assessment of chromatin status in thousands of gene mutants in parallel. Epi-ID takes advantage of DNA sequences called DNA barcodes that are introduced into a library of yeast knockout mutants at a common chromosomal location in the genome. Chromatin immunoprecipitation on pools of barcoded mutant strains followed by barcode counting by high throughput sequencing will report on the abundance of the chromatin mark of interest in each mutant strain. Epi-ID is applicable to a wide range of chromatin proteins and modifications that are present and can be immunoprecipitated at or around the barcoded region.},
}
@article {pmid31601001,
year = {2019},
author = {Ali, NABM and Mac Aogáin, M and Morales, RF and Tiew, PY and Chotirmall, SH},
title = {Optimisation and Benchmarking of Targeted Amplicon Sequencing for Mycobiome Analysis of Respiratory Specimens.},
journal = {International journal of molecular sciences},
volume = {20},
number = {20},
pages = {},
pmid = {31601001},
issn = {1422-0067},
support = {Clinician-Scientist Individual Research Grant (MOH-000141)//Singapore Ministry of Health's National Medical Research Council/ ; Research Training Fellowship (NMRC/Fellowship/0049/2017)//Singapore Ministry of Health's National Medical Research Council/ ; Singapore Ministry of Education Academic Research Fund Tier 1 (2016-T1-001-050)//Singapore Ministry of Education/ ; NTU Integrated Medical, Biological and Environmental Life Sciences (NIMBELS) [NIM/03/2018]//Nanyang Technological University/ ; },
mesh = {Benchmarking ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Fungi/genetics ; Humans ; *Metagenome ; *Metagenomics/methods ; *Mycobiome ; Respiratory Mucosa/*microbiology ; },
abstract = {(1) Background: Firm consensus has yet to be established in relation to taxonomic classification and primer choice in targeted amplicon sequencing of the mycobiome. While the nuclear ribosomal internal transcribed spacer (ITS) region are recognized as the formal fungal taxonomic barcode, appraisal of different ITS sub-regions and the influence of DNA extraction methods have not been comprehensively undertaken using human respiratory specimens. (2) Methods: We performed ITS analysis of respiratory (sputum) samples by assessing (a) the effect of alternate DNA extraction techniques and (b) an evaluation of four different ITS primer pairs (ITS1F and ITS2; ITS1-30F and ITS1-217R; gITS7ngs and ITS4ng; and Fseq and Rseq) on the mycobiome profiles generated for mock fungal communities and their respective clinical (airway) specimens. (3) Results: Primer pairs varied in their resulting ITS mycobiome profiles, suggesting that particular pairs may be more relevant for analysis of respiratory samples compared to others. Assessment of DNA extraction methods highlighted lower final DNA concentrations achieved by mechanical disruption compared to enzymatic lysis. However, despite lower yields, DNA liberated by mechanical lysis more readily yielded ITS bands with highest success in combination with the Fseq and Rseq primers. (4) Conclusion: Choice of extraction method, primers used, and sequencing approach are all important considerations in sequencing the mycobiome and should be tailored to sample type. A standardization of approach to mycobiome studies using respiratory specimens will permit more reliable comparisons between studies and improve our understanding of the role of fungi in the human airway.},
}
@article {pmid31597830,
year = {2019},
author = {Tamura, T and Kurotaki, D},
title = {[Progress in single-cell analysis of hematopoiesis].},
journal = {[Rinsho ketsueki] The Japanese journal of clinical hematology},
volume = {60},
number = {9},
pages = {1075-1083},
doi = {10.11406/rinketsu.60.1075},
pmid = {31597830},
issn = {0485-1439},
mesh = {Cell Differentiation ; Cell Lineage ; Epigenomics ; *Hematopoiesis ; Hematopoietic Stem Cells/*cytology ; Humans ; *Single-Cell Analysis ; Transcriptome ; },
abstract = {The mechanism underlying production of various types of blood cells from hematopoietic stem and progenitor cells has been a central theme in hematology. Conventionally, hematopoietic cell populations are analyzed by cell surface markers to judge cell types and differentiation stages, and by transplantation assays to assess differentiation potential. Recently, however, next-generation sequencing technology has enabled single-cell transcriptome and epigenome analyses and cell barcoding-based lineage tracing during unperturbed hematopoiesis. These innovative assays revealed that each cell population is extensively heterogenous. Many cells within hematopoietic stem cell populations may not be multipotent, and conversely, hematopoietic progenitor cells often display self-renewal capacity. Moreover, cells tend to make their lineage choice much earlier than previously thought. Altogether, these results challenge the current hierarchical differentiation models and propose new continuous models. Single-cell analyses are expected to greatly contribute to our understanding of normal and abnormal hematopoiesis and to the development of new therapies for blood disorders.},
}
@article {pmid31597757,
year = {2019},
author = {Khanal, S and Fennessey, CM and O'Brien, SP and Thorpe, A and Reid, C and Immonen, TT and Smith, R and Bess, JW and Swanstrom, AE and Del Prete, GQ and Davenport, MP and Okoye, AA and Picker, LJ and Lifson, JD and Keele, BF},
title = {In Vivo Validation of the Viral Barcoding of Simian Immunodeficiency Virus SIVmac239 and the Development of New Barcoded SIV and Subtype B and C Simian-Human Immunodeficiency Viruses.},
journal = {Journal of virology},
volume = {94},
number = {1},
pages = {},
pmid = {31597757},
issn = {1098-5514},
support = {P51 OD011092/OD/NIH HHS/United States ; HHSN261200800001C/CA/NCI NIH HHS/United States ; UM1 AI126611/AI/NIAID NIH HHS/United States ; R37 AI054292/AI/NIAID NIH HHS/United States ; HHSN261200800001E/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Genetic Markers ; *Genome, Viral ; HIV Infections/immunology/virology ; HIV-1/classification/*genetics/immunology ; High-Throughput Nucleotide Sequencing ; Humans ; Macaca mulatta ; *Mutagenesis, Insertional ; Phylogeny ; RNA, Viral/classification/*genetics ; Reassortant Viruses/classification/*genetics/immunology ; Reproducibility of Results ; Simian Acquired Immunodeficiency Syndrome/immunology/virology ; Simian Immunodeficiency Virus/classification/*genetics/immunology ; Viral Load ; Virus Replication ; },
abstract = {Genetically barcoded viral populations are powerful tools for evaluating the overall viral population structure as well as assessing the dynamics and evolution of individual lineages in vivo over time. Barcoded viruses are generated by inserting a small, genetically unique tag into the viral genome, which is retained in progeny virus. We recently reported barcoding the well-characterized molecular clone simian immunodeficiency virus (SIV) SIVmac239, resulting in a synthetic swarm (SIVmac239M) containing approximately 10,000 distinct viral clonotypes for which all genetic differences were within a 34-base barcode that could be tracked using next-generation deep sequencing. Here, we assessed the population size, distribution, and authenticity of individual viral clonotypes within this synthetic swarm using samples from 120 rhesus macaques infected intravenously. The number of replicating barcodes in plasma correlated with the infectious inoculum dose, and the primary viral growth rate was similar in all infected animals regardless of the inoculum size. Overall, 97% of detectable clonotypes in the viral stock were identified in the plasma of at least one infected animal. Additionally, we prepared a second-generation barcoded SIVmac239 stock (SIVmac239M2) with over 16 times the number of barcoded variants of the original stock and an additional barcoded stock with suboptimal nucleotides corrected (SIVmac239Opt5M). We also generated four barcoded stocks from subtype B and C simian-human immunodeficiency virus (SHIV) clones. These new SHIV clones may be particularly valuable models to evaluate Env-targeting approaches to study viral transmission or viral reservoir clearance. Overall, this work further establishes the reliability of the barcoded virus approach and highlights the feasibility of adapting this technique to other viral clones.IMPORTANCE We recently developed and published a description of a barcoded simian immunodeficiency virus that has a short random sequence inserted directly into the viral genome. This allows for the tracking of individual viral lineages with high fidelity and ultradeep sensitivity. This virus was used to infect 120 rhesus macaques, and we report here the analysis of the barcodes of these animals during primary infection. We found that the vast majority of barcodes were functional in vivo We then expanded the barcoding approach in a second-generation SIVmac239 stock (SIVmac239M2) with over 16 times the number of barcoded variants of the original stock and a barcoded stock of SIVmac239Opt5M whose sequence had 5 changes from the wild-type SIVmac239 sequence. We also generated 4 barcoded stocks from subtype B and C SHIV clones each containing a human immunodeficiency virus (HIV) type 1 envelope. These virus models are functional and can be useful for studying viral transmission and HIV cure/reservoir research.},
}
@article {pmid31596992,
year = {2019},
author = {Peruzzi, JA and Jacobs, ML and Vu, TQ and Wang, KS and Kamat, NP},
title = {Barcoding Biological Reactions with DNA-Functionalized Vesicles.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {58},
number = {51},
pages = {18683-18690},
pmid = {31596992},
issn = {1521-3773},
support = {T32 GM008382/GM/NIGMS NIH HHS/United States ; T32GM008382/NH/NIH HHS/United States ; 1844336//National Science Foundation/International ; },
mesh = {DNA/*metabolism ; Humans ; },
abstract = {Targeted vesicle fusion is a promising approach to selectively control interactions between vesicle compartments and would enable the initiation of biological reactions in complex aqueous environments. Here, we explore how two features of vesicle membranes, DNA tethers and phase-segregated membranes, promote fusion between specific vesicle populations. Membrane phase-segregation provides an energetic driver for membrane fusion that increases the efficiency of DNA-mediated fusion events. The orthogonality provided by DNA tethers allows us to direct fusion and delivery of DNA cargo to specific vesicle populations. Vesicle fusion between DNA-tethered vesicles can be used to initiate in vitro protein expression to produce model soluble and membrane proteins. Engineering orthogonal fusion events between DNA-tethered vesicles provides a new strategy to control the spatiotemporal dynamics of cell-free reactions, expanding opportunities to engineer artificial cellular systems.},
}
@article {pmid31596175,
year = {2019},
author = {Alfeche, NKG and Binag, SDA and Medecilo, MMP and Alejandro, GJD},
title = {Standard reference material (SRM) DNA barcode library approach for authenticating Antidesma bunius (L.) Spreng. (bignay) derived herbal medicinal products.},
journal = {Food additives &amp; contaminants. Part A, Chemistry, analysis, control, exposure &amp; risk assessment},
volume = {36},
number = {12},
pages = {1777-1786},
doi = {10.1080/19440049.2019.1670868},
pmid = {31596175},
issn = {1944-0057},
mesh = {DNA Barcoding, Taxonomic/*standards ; Euphorbiaceae/*chemistry ; Food Contamination/*analysis ; Fruit/chemistry ; *Gene Library ; *Herbal Medicine ; Plants, Medicinal/*chemistry ; },
abstract = {In the Philippines, the herbal medicinal product (HMP) market is flourishing due to the abundance of pharmacologically important species, and the high level of ethnomedicinal knowledge still widely accepted by the public. As such, herbal products from Antidesma bunius (L.) Spreng., locally known as bignay, are popular as medicine for various ailments of the circulatory and digestive systems. Though efficacy is guaranteed, the authenticity of the marketed products is still in question as several other herbal plants can provide the said benefits. Similar morphology between wild species also hinders species identification and contributes confusion especially to the general consumer. The authenticity of the marketed HMPs was established by means of DNA barcoding techniques which offers quick and reliable species identification by means of (1) the Basic Local Alignment Search Tool (BLASTn) and (2) the establishment of the first Standard Reference Material (SRM) Herbal barcode library for Antidesma spp. A total of 56 gene accessions from matK-psbA-trnH-rbcL sequences of 9 wild Antidesma spp. comprised the SRM which was then used to confirm the identity of 11 randomly sampled bignay-derived HMPs. Following the BLASTn and the SRM (maximum likelihood tree reconstruction) criterion, the subjected sequences revealed that only three of the 11 HMPs were authentic A. bunius-derived products. The other eight HMPs contained substitutes that were either fillers or different herbal medicinal plant not indicated in the product labels. These results indicate that product safety should be reinforced with complete HMP authentication using traditional methods supported by molecular data.},
}
@article {pmid31590345,
year = {2019},
author = {Hager, FF and Sützl, L and Stefanović, C and Blaukopf, M and Schäffer, C},
title = {Pyruvate Substitutions on Glycoconjugates.},
journal = {International journal of molecular sciences},
volume = {20},
number = {19},
pages = {},
pmid = {31590345},
issn = {1422-0067},
support = {P31521-B22//Austrian Science Fund/ ; H-318348/2018//Hochschuljubil&#xe4;umsstiftung der Stadt Wien/ ; P27374-B22//Austrian Science Fund/ ; P 27374/FWF_/Austrian Science Fund FWF/Austria ; W 1224/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Acyltransferases/metabolism ; Bacteria/metabolism ; Bacterial Proteins/metabolism ; Glycoconjugates/chemistry/*metabolism ; Pyruvates/chemistry/*metabolism ; },
abstract = {Glycoconjugates are the most diverse biomolecules of life. Mostly located at the cell surface, they translate into cell-specific "barcodes" and offer a vast repertoire of functions, including support of cellular physiology, lifestyle, and pathogenicity. Functions can be fine-tuned by non-carbohydrate modifications on the constituting monosaccharides. Among these modifications is pyruvylation, which is present either in enol or ketal form. The most commonly best-understood example of pyruvylation is enol-pyruvylation of N-acetylglucosamine, which occurs at an early stage in the biosynthesis of the bacterial cell wall component peptidoglycan. Ketal-pyruvylation, in contrast, is present in diverse classes of glycoconjugates, from bacteria to algae to yeast-but not in humans. Mild purification strategies preventing the loss of the acid-labile ketal-pyruvyl group have led to a collection of elucidated pyruvylated glycan structures. However, knowledge of involved pyruvyltransferases creating a ring structure on various monosaccharides is scarce, mainly due to the lack of knowledge of fingerprint motifs of these enzymes and the unavailability of genome sequences of the organisms undergoing pyruvylation. This review compiles the current information on the widespread but under-investigated ketal-pyruvylation of monosaccharides, starting with different classes of pyruvylated glycoconjugates and associated functions, leading to pyruvyltransferases, their specificity and sequence space, and insight into pyruvate analytics.},
}
@article {pmid31587135,
year = {2020},
author = {Intharuksa, A and Sasaki, Y and Ando, H and Charoensup, W and Suksathan, R and Kertsawang, K and Sirisa-Ard, P and Mikage, M},
title = {The combination of ITS2 and psbA-trnH region is powerful DNA barcode markers for authentication of medicinal Terminalia plants from Thailand.},
journal = {Journal of natural medicines},
volume = {74},
number = {1},
pages = {282-293},
pmid = {31587135},
issn = {1861-0293},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic/*methods ; DNA, Intergenic/*genetics ; DNA, Plant/genetics ; Genetic Markers/genetics ; Photosystem II Protein Complex/*genetics ; Phytotherapy ; Plant Extracts/chemistry ; Plants, Medicinal/genetics ; Sequence Analysis, DNA ; Terminalia/*classification/*genetics ; Thailand ; },
abstract = {The dried fruits of Terminalia plant (Combretaceae) called "Samo" have been used as herbal medicine in Thai traditional medicine. Four "Samo" crude drugs, namely, Samo thai, Samo thed, Samo dee-ngu, and Samo phiphek, are used as the main ingredients in Triphala and Trisamo recipes. Their commercial products are available in processed and powdered form, but are difficult to authenticate by conventional methods. In this study, we aimed to discriminate species of genus Terminalia for the identification of their crude drugs by a DNA barcoding technique. A total of 208 closely related nucleotide sequences were obtained from nine Terminalia species collected from Thailand and the DDBJ/EMBL/GenBank database. An effective DNA barcode marker was selected from six DNA loci (matK, rbcL, psbA-trnH, ITS, ITS1, and ITS2) and their two-locus combination. All sequences were analyzed by three major methods: (1) BLAST search; (2) the genetic divergence method using Kimura 2-parameter (K2P) distance matrices; and (3) tree topology analysis based on the neighbor-joining method. Comparison of the six candidate DNA loci indicated that ITS identified Terminalia with 100% accuracy at the species and genus levels in the BLAST1 method. ITS2 showed the highest K2P variability. The data from the single markers and the two-locus combinations revealed that only the two-locus combinations, namely, the combinations of rbcL, ITS, ITS1, and ITS2 with psbA-trnH, clearly discriminated all the species. From the results of DNA sequence analysis and the three methods, ITS2 is recommended for the identification of Terminalia species to supplement psbA-trnH.},
}
@article {pmid31586669,
year = {2019},
author = {García-Martín, JM and Zamora, JC and Lado, C},
title = {Evidence of Intra-individual SSU Polymorphisms in Dark-spored Myxomycetes (Amoebozoa).},
journal = {Protist},
volume = {170},
number = {5},
pages = {125681},
doi = {10.1016/j.protis.2019.125681},
pmid = {31586669},
issn = {1618-0941},
mesh = {Genetic Variation ; Myxomycetes/*genetics ; Polymorphism, Genetic/*genetics ; RNA, Ribosomal, 18S/*genetics ; },
abstract = {The nuclear small subunit rRNA gene (SSU or 18S) is a marker frequently used in phylogenetic and barcoding studies in Amoebozoa, including Myxomycetes. Despite its common usage and the confirmed existence of divergent copies of ribosomal genes in other protists, the potential presence of intra-individual SSU variability in Myxomycetes has never been studied before. Here we investigated the pattern of nucleotide polymorphism in the 5' end fragment of SSU by cloning and sequencing a total of 238 variants from eight specimens, each representing a species of the dark-spored orders Stemonitidales and Physarales. After excluding singletons, a relatively low SSU intra-individual variability was found but our data indicate that this might be a widely distributed phenomenon in Myxomycetes as all samples analyzed possessed various ribotypes. To determine if the occurrence of multiple SSU variants within a single specimen has a negative effect on the circumscription of species boundaries, we conducted phylogenetic analyses that revealed that clone variation may be detrimental for inferring phylogenetic relationships among some of the specimens analyzed. Despite that intra-individual variability should be assessed in additional taxa, our results indicate that special care should be taken for species identification when working with closely related species.},
}
@article {pmid31585545,
year = {2019},
author = {Duan, YL and Bellis, G and Li, L and Li, HC and Miao, HS and Kou, ML and Liao, F and Wang, Z and Gao, L and Li, JZ},
title = {Potential vectors of bluetongue virus in high altitude areas of Yunnan Province, China.},
journal = {Parasites &amp; vectors},
volume = {12},
number = {1},
pages = {464},
pmid = {31585545},
issn = {1756-3305},
support = {2016FA005//The Key Project of Yunnan Science and Technique Department/ ; },
mesh = {Altitude ; Animals ; Base Sequence ; Bluetongue/epidemiology/*transmission ; Bluetongue virus/classification/genetics/isolation &amp; purification ; Cattle ; Cattle Diseases/epidemiology/*transmission/virology ; Ceratopogonidae/classification/*virology ; China/epidemiology ; DNA Barcoding, Taxonomic/veterinary ; DNA, Viral/chemistry/isolation &amp; purification ; Electron Transport Complex IV/genetics ; Goats ; Insect Vectors/classification/*virology ; Phylogeny ; RNA, Viral/isolation &amp; purification ; Real-Time Polymerase Chain Reaction/veterinary ; Reverse Transcription ; Ruminants ; Seroepidemiologic Studies ; },
abstract = {BACKGROUND: Bluetongue disease of ruminants is a typical insect-borne disease caused by bluetongue virus (BTV) of the genus Orbivirus (family Reoviridae) and transmitted by some species of Culicoides (Diptera: Ceratopogonidae). Recently, the detection of BTV in yaks in high altitude meadows of the Shangri-La district of Yunnan Province, China, prompted an investigation of the Culicoides fauna as potential vectors of BTV.<br><br>METHODS: A total of 806 Culicoides midges were collected by light trapping at three sites at altitudes ranging from 1800 to 3300 m. The species were identified based on morphology and the DNA sequences of cytochrome c oxidase subunit 1 (cox1). PCR and quantitative PCR following reverse transcription were used to test for the presence of BTV RNA in Culicoides spp. A phylogenetic analysis was used to analyze the cox1 sequences of some specimens.<br><br>RESULTS: Four species dominated these collections and cox1 barcoding revealed that at least two of these appear to belong to species new to science. Culicoides tainanus and a cryptic species morphologically similar to C. tainanus dominated low altitude valley collections while C. nielamensis was the most abundant species in the high-altitude meadow. A species related to C. obsoletus occurred at all altitudes but did not dominate any of the collections. BTV RT-qPCR analysis detected BTV RNA in two specimens of C. tainanus, in one specimen closely related to C. tainanus and in one specimen closely related to C. obsoletus by barcode sequencing.<br><br>CONCLUSIONS: This study suggests that BTV in high altitude areas of Yunnan is being transmitted by three species of Culicoides, two of which appear to be new to science. This research may be useful in improving understanding of the effects of global warming on arboviral disease epidemiology and further study is important in research into disease control and prevention.},
}
@article {pmid31584096,
year = {2019},
author = {Chen, F and Bai, M and Cao, X and Zhao, Y and Xue, J and Zhao, Y},
title = {Click-encoded rolling FISH for visualizing single-cell RNA polyadenylation and structures.},
journal = {Nucleic acids research},
volume = {47},
number = {22},
pages = {e145},
pmid = {31584096},
issn = {1362-4962},
mesh = {Cell Line, Tumor ; Click Chemistry/*methods ; DNA Barcoding, Taxonomic/methods ; Gene Expression Profiling/methods ; Humans ; In Situ Hybridization, Fluorescence/*methods ; MCF-7 Cells ; Mass Spectrometry ; Poly A/chemistry ; *Polyadenylation ; RNA, Messenger/*chemistry ; Sequence Analysis, RNA/methods ; Single-Cell Analysis/*methods ; Spatio-Temporal Analysis ; },
abstract = {Spatially resolved visualization of RNA processing and structures is important for better studying single-cell RNA function and landscape. However, currently available RNA imaging methods are limited to sequence analysis, and not capable of identifying RNA processing events and structures. Here, we developed click-encoded rolling FISH (ClickerFISH) for visualizing RNA polyadenylation and structures in single cells. In ClickerFISH, RNA 3' polyadenylation tails, single-stranded and duplex regions are chemically labeled with different clickable DNA barcodes. These barcodes then initiate DNA rolling amplification, generating repetitive templates for FISH to image their subcellular distributions. Combined with single-molecule FISH, the proposed strategy can also obtain quantitative information of RNA of interest. Finally, we found that RNA poly(A) tailing and higher-order structures are spatially organized in a cell type-specific style with cell-to-cell heterogeneity. We also explored their spatiotemporal patterns during cell cycle stages, and revealed the highly dynamic organization especially in S phase. This method will help clarify the spatiotemporal architecture of RNA polyadenylation and structures.},
}
@article {pmid31583491,
year = {2019},
author = {Garcia, HA and Rangel, CJ and Ortíz, PA and Calzadilla, CO and Coronado, RA and Silva, AJ and Pérez, AM and Lecuna, JC and García, ME and Aguirre, AM and Teixeira, MMG},
title = {Zoonotic Trypanosomes in Rats and Fleas of Venezuelan Slums.},
journal = {EcoHealth},
volume = {16},
number = {3},
pages = {523-533},
pmid = {31583491},
issn = {1612-9210},
support = {PNPD//CAPES/International ; 2016/03028-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/International ; 2012001268//FONACIT/International ; MCTI-PROSUL program//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/International ; },
mesh = {Animals ; Chagas Disease/veterinary ; DNA, Protozoan ; Disease Reservoirs/parasitology ; Insect Vectors/*parasitology ; Poverty Areas ; Rats ; Rodent Diseases/*epidemiology ; Siphonaptera/*parasitology ; Trypanosoma cruzi/genetics ; Trypanosoma lewisi/genetics ; Trypanosomiasis/*veterinary ; Venezuela/epidemiology ; Zoonoses/transmission ; },
abstract = {Rattus spp. are reservoirs of many human zoonoses, but their role in domestic transmission cycles of human trypanosomiasis is underestimated. In this study, we report trypanosome-infected Rattus norvegicus and Rattus rattus in human dwellings in slums neighboring Maracay, a large city near Caracas, the capital of Venezuela. Blood samples of R. norvegicus and R. rattus examined by PCR and FFLB (fluorescent fragment length barcoding) revealed a prevalence of 6.3% / 31.1% for Trypanosoma lewisi (agent of rat- and flea-borne human emergent zoonosis), and 10.5% / 24.6% for Trypanosoma cruzi (agent of Chagas disease). Detection in flea guts of T. lewisi (76%) and, unexpectedly, T. cruzi (21.3%) highlighted the role of fleas as carriers and vectors of these trypanosomes. A high prevalence of rats infected with T. lewisi and T. cruzi and respective flea and triatomine vectors poses a serious risk of human trypanosomiasis in Venezuelan slums. Anthropogenic activities responsible for growing rat and triatomine populations within human dwellings drastically increased human exposure to trypanosomes. This scenario has allowed for the reemergence of Chagas disease as an urban zoonosis in Venezuela and can propitiate the emergence of atypical T. lewisi infection in humans.},
}
@article {pmid31582555,
year = {2020},
author = {Fan, X and Wu, C and Truitt, LL and Espinoza, DA and Sellers, S and Bonifacino, A and Zhou, Y and Cordes, SF and Krouse, A and Metzger, M and Donahue, RE and Lu, R and Dunbar, CE},
title = {Clonal tracking of erythropoiesis in rhesus macaques.},
journal = {Haematologica},
volume = {105},
number = {7},
pages = {1813-1824},
pmid = {31582555},
issn = {1592-8721},
mesh = {Animals ; Cell Differentiation ; Cells, Cultured ; *Erythropoiesis ; Hematopoiesis ; *Hematopoietic Stem Cells ; Macaca mulatta ; Multipotent Stem Cells ; },
abstract = {The classical model of hematopoietic hierarchies is being reconsidered on the basis of data from in vitro assays and single cell expression profiling. Recent experiments suggested that the erythroid lineage might differentiate directly from multipotent hematopoietic stem cells / progenitors or from a highly biased subpopulation of stem cells, rather than transiting through common myeloid progenitors or megakaryocyte-erythrocyte progenitors. We genetically barcoded autologous rhesus macaque stem and progenitor cells, allowing quantitative tracking of the in vivo clonal output of thousands of individual cells over time following transplantation. CD34[+] cells were lentiviral-transduced with a high diversity barcode library, with the barcode in an expressed region of the provirus, allowing barcode retrieval from DNA or RNA, with each barcode representing an individual stem or progenitor cell clone. Barcode profiles from bone marrow CD45[-]CD71[+] maturing nucleated red blood cells were compared with other lineages purified from the same bone marrow sample. There was very high correlation of barcode contributions between marrow nucleated red blood cells and other lineages, with the highest correlation between nucleated red blood cells and myeloid lineages, whether at earlier or later time points post transplantation, without obvious clonal contributions from highly erythroid-biased or restricted clones. A similar profile occurred even under stressors such as aging or erythropoietin stimulation. RNA barcode analysis on circulating mature red blood cells followed over long time periods demonstrated stable erythroid clonal contributions. Overall, in this nonhuman primate model with great relevance to human hematopoiesis, we documented continuous production of erythroid cells from multipotent, non-biased hematopoietic stem cell clones at steady-state or under stress.},
}
@article {pmid31581700,
year = {2019},
author = {Mkenda, PA and Ndakidemi, PA and Stevenson, PC and Arnold, SEJ and Belmain, SR and Chidege, M and Gurr, GM and Woolley, VC},
title = {Characterization of Hymenopteran Parasitoids of Aphis fabae in an African Smallholder Bean Farming System through Sequencing of COI 'Mini-Barcodes'.},
journal = {Insects},
volume = {10},
number = {10},
pages = {},
pmid = {31581700},
issn = {2075-4450},
support = {13-335//McKnight Foundation/ ; 17-070//McKnight Foundation/ ; BB/R020361/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 22-021//Darwin Initiative/ ; },
abstract = {Parasitoids are among the most frequently reported natural enemies of insect pests, particularly aphids. The efficacy of parasitoids as biocontrol agents is influenced by biotic and abiotic factors. For example, hyperparasitoids can reduce the abundance of the primary parasitoids as well as modify their behavior. A field study was conducted at three contrasting elevations on Mount Kilimanjaro, Tanzania, to identify the parasitoids of aphids in smallholder bean farming agroecosystems. Sentinel aphids (Aphis fabae) on potted bean plants (Phaseolus vulgaris) were exposed in 15 bean fields at three elevations for 2 days. The sentinel aphids were then kept in cages in a greenhouse until emergence of the parasitoids, which were collected and preserved in 98% ethanol for identification. Of the 214 parasitoids that emerged from sentinel aphids, the greatest abundance (44.86%) were from those placed at intermediate elevations (1000-1500 m a.s.l), compared to 42.52% from the lowest elevations and only 12.62% from the highest elevation farms. Morphological identification of the parasitoids that emerged from parasitized aphids showed that 90% were Aphidius species (Hymenoptera: Braconidae: Aphidiinae). Further characterization by sequencing DNA 'mini-barcodes' identified parasitoids with ≥99% sequence similarity to Aphidius colemani, 94-95% sequence similarity to Pachyneuron aphidis and 90% similarity to a Charipinae sp. in the National Center for Biotechnology Information (NCBI) database. These results confidently identified A. colemani as the dominant primary aphid parasitoid of A. fabae in the study area. A Pachyneuron sp., which was most closely related to P. aphidis, and a Charipinae sp. occurred as hyperparasitoids. Thus, interventions to improve landscapes and farming practice should monitor specifically how to augment populations of A. colemani, to ensure any changes enhance the delivery of natural pest regulation. Further studies are needed for continuous monitoring of the hyperparasitism levels and the dynamics of aphids, primary parasitoids, and secondary parasitoids in different cropping seasons and their implications in aphid control.},
}
@article {pmid31581087,
year = {2020},
author = {Wang, B and Zhang, Q and Wei, X},
title = {Tabu Variable Neighborhood Search for Designing DNA Barcodes.},
journal = {IEEE transactions on nanobioscience},
volume = {19},
number = {1},
pages = {127-131},
doi = {10.1109/TNB.2019.2942036},
pmid = {31581087},
issn = {1558-2639},
mesh = {*Algorithms ; DNA/chemistry/genetics ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing ; },
abstract = {Massively parallel sequencing, a popular and efficient sequencing method, produces a tremendous number of sequences from multiple individual samples. Labeling sequences with barcodes (tags) prevents them from being unrecoverable or confused during sequencing, replication, and oligonucleotide synthesis. In view of DNA barcode set design, we propose a tabu variable neighborhood search (TVNS) to design DNA barcode sets. We propose using sequences with the maximum sum of edit distances as the basis for building the neighborhood structures of TVNS. We adopt an exhaustive search to complete local searches built from these structures. The algorithm switches between neighborhoods built from different seed data. Compared with previous designs, our proposed algorithm is effective for designing DNA barcode sets and improving the lower bound of DNA barcode sets.},
}
@article {pmid31579587,
year = {2019},
author = {Osathanunkul, M and Madesis, P},
title = {Bar-HRM: a reliable and fast method for species identification of ginseng (Panax ginseng, Panax notoginseng, Talinum paniculatum and Phytolacca Americana).},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7660},
pmid = {31579587},
issn = {2167-8359},
abstract = {BACKGROUND: Korean ginseng has long been famous and is one of the most well known forms of ginseng. The root of plants in the genus Panax is commonly recognized as ginseng. Different Panax species of ginseng root have been used as treatments. Although many other herbs are called ginseng, they do not contain the active compounds of ginsenosides. In Thailand, we have Thai ginseng which is of course not one of Panax species. Thai ginseng is the root from Talinum paniculatum and, due to its morphological root similarity, it is almost impossible to differentiate between them. Also, another plant species, Phytollacca americana, has significantly similar root morphology to real ginseng but its seeds and root are poisonous. Misunderstanding what true ginseng is compared to others could endanger lives and cause financial loss by buying inferior products.<br><br>METHODS: DNA barcoding combination with High Resolution Melting (called Bar-HRM) was used for species discrimination of the Panax ginseng and others. Five regions included ITS2, matK, psbA-trnH and rbcL were evaluated in the analyses.<br><br>RESULTS: The ITS2 region was found to be the most suitable primers for the analysis. The melting profile from the HRM analyses using the chosen ITS2 primers showed that Korean ginseng (Panax ginseng) could be discriminated from other Penax species. Also, other ginseng species with morphological similarity could be easily distinguished from the true ginseng. The developed Bar-HRM method poses a great potential in ginseng species discrimination and thus could be also useful in ginseng authentication.},
}
@article {pmid31576236,
year = {2019},
author = {Jaskuła, R and Sulikowska-Drozd, A and Jabłońska, A and Banaś, K and Rewicz, T},
title = {Undesirable immigrants: hobbyist vivaria as a potential source of alien invertebrate species.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7617},
pmid = {31576236},
issn = {2167-8359},
abstract = {BACKGROUND: Small size and large diversity of adaptations make invertebrates a group of animals which can be easily transported by different human activities. Many species can travel as "hitchhikers" with plant material (both on plant surfaces and in the soil), including plants used for decoration in vivaria. Vivaria are often tropical in nature environments, with high temperatures and humidity, suitable for invertebrates from tropical regions. Although many of such invertebrates cannot survive in temperate regions where harsh weather conditions are present, it is also known that some can successfully acclimatise. As a result, their negative impact on local flora and fauna cannot be excluded.<br><br>MATERIAL AND METHODS: Terrestrial invertebrates were collected in several cities of Poland from tropical vivaria where poison dart frogs (Dendrobatidae) and/or orchids (Orchidaceae) were kept by hobbyists. Collecting of the material was preceded by a simple questionnaire placed on the biggest Polish forum devoted to poison dart frogs. Moreover, we contacted some Polish wholesalers offering tropical invertebrates (Isopoda and Collembola), used as the food source for frogs, hoping to receive information about locations where those invertebrates were delivered, over the period of one year. We obtained mtDNA barcodes using the COI marker (cytochrome c oxidase subunit I gene) for seven potential morphospecies.<br><br>RESULTS: In total, 12 taxa classified as Turbellaria, Annelida, Gastropoda, Isopoda, Diplopoda, Chilopoda and Collembola were collected and preserved in pure ethanol. We collected material and/or information from 65 locations, including 56 cities to which exotic isopods and springtails were sold by wholesalers over the period of nine months (average number per month = 18 cities). We obtained 18 COI sequences which were assigned to seven BINs and thus confirmed identification of seven species. The results indicate that the number of species transported with exotic plants is not small and can be observed regularly. Species noted as "hitchhikers" on plant structures and/or as inhabitants of soil in plant pots, originally came from South and Central America, Africa, Asia and possibly from North America or Southern Europe. Three taxa were noted for the first time from Poland, including Rhynchodemus sylvaticus (Rhynchodemidae), Trichorhina sp.1 (Platharthridae), and Guppya gundlachi (Euconulidae).<br><br>DISCUSSION: The presented study clearly shows that an exotic hobby such as keeping tropical poison dart frogs and/or orchids may promote fast and uncontrolled dispersion of a high number of invertebrates classified in different taxonomical groups. Plant material (green elements of plants and the soil in which they are planted) used in vivaria can be an important source of such animals.},
}
@article {pmid31575965,
year = {2019},
author = {Tyagi, K and Kumar, V and Kundu, S and Pakrashi, A and Prasad, P and Caleb, JTD and Chandra, K},
title = {Identification of Indian Spiders through DNA barcoding: Cryptic species and species complex.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {14033},
pmid = {31575965},
issn = {2045-2322},
mesh = {Animals ; Classification ; DNA/genetics ; *DNA Barcoding, Taxonomic/methods ; Female ; Haplotypes ; India ; Male ; Phylogeny ; Polymerase Chain Reaction ; Spiders/anatomy &amp; histology/classification/*genetics ; },
abstract = {Spiders are mega diverse arthropods and play an important role in the ecosystem. Identification of this group is challenging due to their cryptic behavior, sexual dimorphism, and unavailability of taxonomic keys for juveniles. To overcome these obstacles, DNA barcoding plays a pivotal role in spider identification throughout the globe. This study is the first large scale attempt on DNA barcoding of spiders from India with 101 morphospecies of 72 genera under 21 families, including five endemic species and holotypes of three species. A total of 489 barcodes was generated and analyzed, among them 85 novel barcodes of 22 morphospecies were contributed to the global database. The estimated delimitation threshold of the Indian spiders was 2.6% to 3.7% K2P corrected pairwise distance. The multiple species delimitation methods (BIN, ABGD, GMYC and PTP) revealed a total of 107 molecular operational taxonomic units (MOTUs) for 101 morphospecies. We detected more than one MOTU in 11 morphospecies with discrepancies in genetic distances and tree topologies. Cryptic diversity was detected in Pardosa pusiola, Cyclosa spirifera, and Heteropoda venatoria. The intraspecies distances which were as large as our proposed delimitation threshold were observed in Pardosa sumatrana, Thiania bhamoensis, and Cheiracanthium triviale. Further, shallow genetic distances were detected in Cyrtophora cicatrosa, Hersilia savignyi, Argiope versicolor, Phintella vittata, and Oxyopes birmanicus. Two morphologically distinguished species (Plexippus paykulli and Plexippus petersi) showed intra-individual variation within their DNA barcode data. Additionally, we reinstate the original combination for Linyphia sikkimensis based on both morphology and DNA barcoding. These data show that DNA barcoding is a valuable tool for specimen identification and species discovery of Indian spiders.},
}
@article {pmid31575934,
year = {2019},
author = {Dell'Agnello, F and Natali, C and Bertolino, S and Fattorini, L and Fedele, E and Foggi, B and Martini, M and Pisani, C and Riga, F and Sgarlata, A and Ciofi, C and Zaccaroni, M},
title = {Assessment of seasonal variation of diet composition in rodents using DNA barcoding and Real-Time PCR.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {14124},
pmid = {31575934},
issn = {2045-2322},
mesh = {Animals ; Arvicolinae ; Climate ; DNA/*genetics ; DNA Barcoding, Taxonomic/methods ; Diet ; Ecosystem ; Feeding Behavior/physiology ; Food Preferences/physiology ; Gastrointestinal Contents ; Real-Time Polymerase Chain Reaction/methods ; Rodentia/*genetics ; Seasons ; },
abstract = {The study of animal diet and feeding behaviour is a fundamental tool for the illustration of the ecological role of species in the ecosystem. However, size and quality of food intake samples make it hard for researchers to describe the diet composition of many small species. In our study, we exploited genomic tools for the analysis of the diet composition of the Savi's pine vole (Microtus savii) using DNA barcoding and qPCR techniques for the identification of ingested plant species retrieved from stomach contents. In contrast with previous studies, we found that, despite being a fossorial species, the Savi's pine vole is a selective feeder that undergoes intense superficial activity in search for food. In addition, our study shows that with a a priori knowledge of the candidate plant species included in animal diet, qPCR is a powerful tool to assess presence/absence, frequency of occurrence and electivity of ingested species. We conclude that this approach offers new opportunities to implement the analysis of food selection in small animals, thereby revealing a detailed picture of plant-animal interactions.},
}
@article {pmid31572627,
year = {2019},
author = {Song, E and Park, S and Kim, S},
title = {Primers for complete chloroplast genome sequencing in Magnolia.},
journal = {Applications in plant sciences},
volume = {7},
number = {9},
pages = {e11286},
pmid = {31572627},
issn = {2168-0450},
abstract = {PREMISE: A new set of primers was developed for sequencing of whole chloroplast genomes of Magnolia species and gap-filling of unfinished genomes.<br><br>METHODS AND RESULTS: Two hundred and fifty primers were newly designed based on two previously reported chloroplast genomes from two different genera in Magnoliaceae. A total of 134 primer pairs, including the ones developed in this study and 18 previously reported ones, were enough to cover the entire chloroplast genome sequences in Magnoliaceae. Four species from different sections of Magnolia (M. dealbata, M. fraseri var. pyramidata, M. liliiflora, and M. odora) were used to show the general application of these primers to chloroplast genome sequencing in Magnolia.<br><br>CONCLUSIONS: Using the developed primers, four Magnolia chloroplast genomes were successfully assembled. These results show the utility of these primers across Magnolia and their potential use for phylogenetic studies, DNA barcoding, and population genetics in this group.},
}
@article {pmid31560817,
year = {2020},
author = {Melton, JT and Singla, M and Wood, FC and Collins, SJ and Tekle, YI},
title = {Three New Freshwater Cochliopodium Species (Himatismenida, Amoebozoa) from the Southeastern United States.},
journal = {The Journal of eukaryotic microbiology},
volume = {67},
number = {2},
pages = {154-166},
doi = {10.1111/jeu.12764},
pmid = {31560817},
issn = {1550-7408},
support = {R15 GM116103/GM/NIGMS NIH HHS/United States ; },
mesh = {Alabama ; Electron Transport Complex IV/analysis ; Georgia ; Immunohistochemistry ; Lobosea/*classification/cytology/enzymology ; Microscopy ; Protozoan Proteins/analysis ; },
abstract = {Cochliopodium is a lens-shaped genus of Amoebozoa characterized by a flexible layer of microscopic dorsal scales. Recent taxonomic and molecular studies reported cryptic diversity in this group and suggested that the often-used scale morphology is not a reliable character for species delineation in the genus. Here, we described three freshwater Cochliopodium spp. from the southeastern United States based on morphological, immunocytochemistry (ICC), and molecular data. A maximum-likelihood phylogenetic analysis and pairwise comparison of COI sequences of Cochliopodium species showed that each of these monoclonal cultures were genetically distinct from each other and any described species with molecular data. Two of the new isolates, "crystal UK-YT2" (Cochliopodium crystalli n. sp.) and "crystal-like UK-YT3" (C. jaguari n. sp.), formed a clade with C. larifeili, which all share a prominent microtubule organizing center (MTOC) and have cubical-shaped crystals. The "Marrs Spring UK-YT4" isolate, C. marrii n. sp., was 100% identical to "Cochliopodium sp. SG-2014 KJ569724." These sequences formed a clade with C. actinophorum and C. arabianum. While the new isolates can be separated morphologically, most of the taxonomic features used in the group show plasticity; therefore, Cochliopodium species can only be reliably identified with the help of molecular data.},
}
@article {pmid31560606,
year = {2019},
author = {Błaszkowski, J and Niezgoda, P and Piątek, M and Magurno, F and Malicka, M and Zubek, S and Mleczko, P and Yorou, NS and Jobim, K and Vista, XM and Lima, JLR and Goto, BT},
title = {Rhizoglomus dalpeae, R. maiae, and R. silesianum, new species.},
journal = {Mycologia},
volume = {111},
number = {6},
pages = {965-980},
doi = {10.1080/00275514.2019.1654637},
pmid = {31560606},
issn = {1557-2536},
mesh = {DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Glomeromycota/*classification/isolation &amp; purification ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; RNA, Ribosomal, 5.8S/genetics ; Rhizosphere ; Sequence Analysis, DNA ; Spores, Fungal/physiology ; },
abstract = {We examined three arbuscular mycorrhizal fungi (AMF; phylum Glomeromycota) producing glomoid spores. The mode of formation and morphology of these spores suggested that they represent undescribed species in the genus Rhizoglomus of the family Glomeraceae. Subsequent morphological studies of the spores and molecular phylogenetic analyses of sequences of the nuc rDNA small subunit (18S), internal transcribed spacer (ITS1-5.8S-ITS2 = ITS), and large subunit (28S) region (= 18S-ITS-28S) confirmed the suggestion and indicated that the fungi strongly differ from all previously described Rhizoglomus species with known DNA barcodes. Consequently, the fungi were described here as new species: R. dalpeae, R. maiae, and R. silesianum. Two of these species lived hypogeously in the field in habitats subjected to strong environmental stresses. Rhizoglomus dalpeae originated from an inselberg located within Guineo-Sudanian transition savanna zone in Benin, West Africa, where the temperature of the inselberg rock during a 5-mo drought ranges from 40 to 60 C. Rhizoglomus silesianum originated from a coal mine spoil heap in Poland, whose substrate is extremely poor in nutrients, has unfavorable texture, and may heat up to 50 C. By contrast, R. maiae was found in more favorable habitat conditions. It produced an epigeous cluster of spores among shrubs growing in a tropical humid reserve in Brazil. Moreover, the compatibility of phylogenies of species of the family Glomeraceae reconstructed from analyses of sequences of 18S-ITS-28S and the largest subunit of RNA polymerase II (RPB1) gene was discussed.},
}
@article {pmid31559946,
year = {2020},
author = {Lashkari, M and Burckhardt, D and Shamsi Gushki, R},
title = {Molecular and morphometric identification of pistachio psyllids with niche modeling of Agonoscena pistaciae (Hemiptera: Aphalaridae).},
journal = {Bulletin of entomological research},
volume = {110},
number = {2},
pages = {259-269},
doi = {10.1017/S0007485319000555},
pmid = {31559946},
issn = {1475-2670},
mesh = {*Animal Distribution ; Animals ; Climate Change ; *DNA Barcoding, Taxonomic ; Female ; Hemiptera/anatomy &amp; histology/*classification/*genetics ; Iran ; Male ; Models, Biological ; Pistacia ; Sex Characteristics ; Wings, Animal/*anatomy &amp; histology ; },
abstract = {Species of Agonoscena (Hemiptera: Aphalaridae) are key pests of pistachio in all of the most important pistachio producing countries in the Old World. The efficiency and accuracy of DNA barcoding for the identification of Agonoscena species were tested using mitochondrial cytochrome c oxidase subunit 1 (mtCO1) and cytochrome b (cytb) gene sequences. Moreover, morphometric sexual dimorphism was studied. Finally, the potential geographical distribution of Agonoscena pistaciae, the most important pistachio pest, was calculated using the MaxEnt model. Similar relationships of clustering were found in the morphometric analysis and the molecular analyses with mtCO1 and cytb genes, with A. bimaculata and A. pistaciae being closely related, and A. pegani constituting their sister group. Although the results showed that the cytb gene is a better marker for barcoding in this group, the mtCO1 gene clearly separates the three psyllid species making mtCO1 suitable for diagnostic purposes. A geometric morphometric analysis showed that the distance between landmark number 7 (bifurcation of vein M) to the fore margin of the forewing, and the distance between landmarks number 6 (apex of vein Cu1b) and 11 (wing base), are the most important geometric characters for diagnosing the studied species. Moreover, the forewing shape of males vs females is similar in A. pistaciae and A. bimaculata but differs significantly in A. pegani. In the ecological niche modeling of the distribution of A. pistaciae, the most important contribution was made by the variable 'minimum temperature of coldest period'. The most suitable areas for A. pistaciae are restricted to Eastern, Southern and some parts of Central Iran.},
}
@article {pmid31559943,
year = {2020},
author = {Rose, A and Ross, DW and Havill, NP and Motley, K and Wallin, KF},
title = {Coexistence of three specialist predators of the hemlock woolly adelgid in the Pacific Northwest USA.},
journal = {Bulletin of entomological research},
volume = {110},
number = {3},
pages = {303-308},
doi = {10.1017/S0007485319000622},
pmid = {31559943},
issn = {1475-2670},
mesh = {Animals ; Coleoptera/growth &amp; development/*physiology ; DNA Barcoding, Taxonomic ; Diptera/genetics/growth &amp; development/*physiology ; Hemiptera/growth &amp; development/*physiology ; Introduced Species ; Larva ; Life Cycle Stages ; Oregon ; *Pest Control, Biological ; *Predatory Behavior ; Tsuga/parasitology ; Washington ; },
abstract = {The hemlock woolly adelgid (Hemiptera: Adelgidae: Adelges tsugae Annand) is an invasive insect, introduced from Japan to eastern North America, where it causes decline and death of hemlock trees. There is a closely related lineage of A. tsugae native to western North America. To inform classical biological control of A. tsugae in the eastern USA, the density and phenology of three native western adelgid specialist predators, Leucopis argenticollis (Zetterstedt), Le. piniperda (Malloch) (Diptera: Chamaemyiidae), and Laricobius nigrinus Fender (Coleoptera: Derodontidae), were quantified in the Pacific Northwest. Infested branches were collected from western hemlock (Pinaceae: Tsuga heterophylla (Raf.) Sarg.) at four sites around the Puget Sound, Washington and three sites in Oregon. Immature Leucopis were identified to species using DNA barcodes. Leucopis argenticollis was roughly twice as abundant as Le. piniperda. Laricobius nigrinus larvae were more abundant than the two species of Leucopis during the egg stage of the first adelgid generation, but Leucopis were present as feeding larvae during the second adelgid generation when La. nigrinus was aestivating in the soil, resulting in Leucopis being more abundant than La. nigrinus across the entire sampling period. Adelges tsugae and La. nigrinus densities were not correlated, while A. tsugae and Leucopis spp. densities were positively correlated. Leucopis spp. and La. nigrinus densities were negatively correlated. These results support the complementary use of La. nigrinus and the two Leucopis species for biological control of A. tsugae in the eastern USA, and point to the need for further investigation of spatial and temporal niche partitioning among the three predator species.},
}
@article {pmid31559510,
year = {2019},
author = {Martello, A and Lambert, B and Johnston, C and Cutler, J and Stumpf, CF},
title = {Comparison of the novel dipstick DNA extraction technique with two established techniques for use in biological barcoding.},
journal = {Molecular biology reports},
volume = {46},
number = {6},
pages = {6625-6628},
pmid = {31559510},
issn = {1573-4978},
mesh = {Animals ; Astacoidea/*classification/genetics ; DNA Barcoding, Taxonomic/*veterinary ; DNA, Mitochondrial/*isolation &amp; purification ; Electron Transport Complex IV/genetics ; Phylogeny ; Polymerase Chain Reaction/veterinary ; Reproducibility of Results ; },
abstract = {The novel dipstick DNA extraction method was tested for its reliability and usability for biological barcoding in comparison to a commercial kit and to a simplified isopropanol precipitation method using crayfish gill tissue. Following DNA extraction, the mitochondrial COI-gene was amplified in a PCR-reaction using a standard set of universal invertebrate primers. All three extraction techniques resulted in successful amplifications. With the dipstick method, PCR immediately follows the very brief DNA extraction technique. We suggest that the dipstick method is an affordable, efficient, and reliable DNA extraction method uniquely suited for biological barcoding that results in reliable and reproducible amplification for downstream applications such as sequencing. Additional tests on crayfish with primers for different parts of the mitochondrial genome and on fish using specific fish COI-primers confirmed these findings. Due to the few steps involved in the DNA extraction procedure the dipstick technique is also highly recommended for high school and university biology courses.},
}
@article {pmid31555997,
year = {2020},
author = {Tanaka, S and Ito, M},
title = {Species identification of Indonesian agarwood using a DNA-barcoding method.},
journal = {Journal of natural medicines},
volume = {74},
number = {1},
pages = {323-330},
pmid = {31555997},
issn = {1861-0293},
mesh = {Commerce ; DNA ; DNA Barcoding, Taxonomic/*methods ; Endangered Species ; Indonesia ; Internationality ; Phytotherapy/methods ; Plants, Medicinal/*chemistry/classification ; Resins, Plant/*therapeutic use ; Thymelaeaceae/*chemistry/*classification ; },
abstract = {Agarwood is a type of resinous wood found in the trunks of Aquilaria and some other genera. It is widely used as an herbal medicine for sedation, detoxification, and treatment of stomachaches, as well as for incense sticks. However, the number of source plants is decreasing, and in 2005, they were added to Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). To identify source species of agarwood, we previously developed a DNA-barcoding method using resin deposition sites. In this study, to identify additional agarwood source species, the barcoding method was applied to source plants and commercial agarwood samples collected from Sumbawa, Lombok, Sulawesi, and Kalimantan in Indonesia, a major agarwood-producing country. In addition, the method was also applied to incense stick samples labeled as agarwood. As a result, several samples were identified as Gyrinops, which is not currently listed as an agarwood source plant in the Japanese standards for non-Pharmacopoeial crude drugs 2018 (Non-JPS 2018). From the viewpoint of securing future resources, these findings suggest that Gyrinops species should, therefore, be added to the list of agarwood source species.},
}
@article {pmid31555305,
year = {2019},
author = {Gao, Z and Liu, Y and Wang, X and Wei, X and Han, J},
title = {DNA Mini-Barcoding: A Derived Barcoding Method for Herbal Molecular Identification.},
journal = {Frontiers in plant science},
volume = {10},
number = {},
pages = {987},
pmid = {31555305},
issn = {1664-462X},
abstract = {In recent years, the demand for natural herbal products (NHP) has increased; however, the quality of these products is difficult to confirm due to the lack of a comprehensive quality control system. Traditional methods are not effective in detecting processed ingredients. DNA barcoding is an established technique that has been used for more than 10 years. This technique uses short standard sequences (generally 200-600 bp) to identify species. While a complete DNA barcode is difficult to obtain from NHP due to DNA degradation, mini-barcoding is a complementary tool to identify species in NHP. DNA mini-barcoding uses smaller DNA segments for polymerase chain reaction amplification and can be applied to identify species rapidly. The present review summarizes the development and application of DNA mini-barcodes over recent years and discusses the limitations of this technique. This review also compares mini-barcoding and meta-barcoding, a technique using universal polymerase chain reaction primers to simultaneously amplify multiple DNA barcodes and identify many species in a single environmental sample. Additionally, other detection methods that can be combined with mini-barcodes, such as nucleotide signatures, high-resolution DNA melting analysis, and gold nanoparticles, are discussed. DNA mini-barcoding can fill the gaps left by other methods in the field of herbal molecular identification.},
}
@article {pmid31554999,
year = {2019},
author = {Ide, T and Abe, Y},
title = {Heterogony in Cycloneuroterus (Hymenoptera: Cynipidae: Cynipini) From Rearing Experiments and DNA Barcoding.},
journal = {Annals of the Entomological Society of America},
volume = {112},
number = {5},
pages = {482-489},
pmid = {31554999},
issn = {0013-8746},
abstract = {Heterogony was confirmed in the cynipid genus Cycloneuroterus Melika and Tang in rearing experiments with DNA barcoding. These experiments involved Cycloneuroterus gilvus Tang and Melika, which was previously only described from the sexual generation adult. The first rearing experiment was conducted using unidentified asexual generation females collected from Quercus gilva Blume, and gall formation by the sexual generation offspring was confirmed on folded or unfolded young leaves of Q. gilva. The second experiment was conducted using sexual generation males and females reared from the leaf galls collected from Q. gilva, and gall formation by the asexual generation offspring was observed on leaves of Q. gilva. Based on the morphological features of the sexual generation adults and galls, this species was identified as C. gilvus. The species identity of wasp specimens of sexual and asexual generations used in the rearing experiments was cross-checked using DNA barcoding with the partial sequences of the cytochrome c oxidase subunit I (COI) region (658 bp). The asexual generation adult and gall of C. gilvus are described based on these results. The importance of 'closing the life cycle,' in this case a demonstration of heterogony, in oak gall wasps (Cynipini) is discussed.},
}
@article {pmid31551994,
year = {2019},
author = {Liao, YC and Cheng, HW and Wu, HC and Kuo, SC and Lauderdale, TY and Chen, FJ},
title = {Completing Circular Bacterial Genomes With Assembly Complexity by Using a Sampling Strategy From a Single MinION Run With Barcoding.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2068},
pmid = {31551994},
issn = {1664-302X},
abstract = {The Oxford Nanopore MinION is an affordable and portable DNA sequencer that can produce very long reads (tens of kilobase pairs), which enable de novo bacterial genome assembly. Although many algorithms and tools have been developed for base calling, read mapping, de novo assembly, and polishing, an automated pipeline is not available for one-stop analysis for circular bacterial genome reconstruction. In this paper, we present the pipeline CCBGpipe for completing circular bacterial genomes. Raw current signals are demultiplexed and base called to generate sequencing data. Sequencing reads are de novo assembled several times by using a sampling strategy to produce circular contigs that have a sequence in common between their start and end. The circular contigs are polished by using raw signals and sequencing reads; then, duplicated sequences are removed to form a linear representation of circular sequences. The circularized contigs are finally rearranged to start at the start position of dnaA/repA or a replication origin based on the GC skew. CCBGpipe implemented in Python is available at https://github.com/jade-nhri/CCBGpipe. Using sequencing data produced from a single MinION run, we obtained 48 circular sequences, comprising 12 chromosomes and 36 plasmids of 12 bacteria, including Acinetobacter nosocomialis, Acinetobacter pittii, and Staphylococcus aureus. With adequate quantities of sequencing reads (80×), CCBGpipe can provide a complete and automated assembly of circular bacterial genomes.},
}
@article {pmid31551622,
year = {2019},
author = {Crous, PW and Carnegie, AJ and Wingfield, MJ and Sharma, R and Mughini, G and Noordeloos, ME and Santini, A and Shouche, YS and Bezerra, JDP and Dima, B and Guarnaccia, V and Imrefi, I and Jurjević, &#x17d; and Knapp, DG and Kovács, GM and Magistà, D and Perrone, G and Rämä, T and Rebriev, YA and Shivas, RG and Singh, SM and Souza-Motta, CM and Thangavel, R and Adhapure, NN and Alexandrova, AV and Alfenas, AC and Alfenas, RF and Alvarado, P and Alves, AL and Andrade, DA and Andrade, JP and Barbosa, RN and Barili, A and Barnes, CW and Baseia, IG and Bellanger, JM and Berlanas, C and Bessette, AE and Bessette, AR and Biketova, AY and Bomfim, FS and Brandrud, TE and Bransgrove, K and Brito, ACQ and Cano-Lira, JF and Cantillo, T and Cavalcanti, AD and Cheewangkoon, R and Chikowski, RS and Conforto, C and Cordeiro, TRL and Craine, JD and Cruz, R and Damm, U and de Oliveira, RJV and de Souza, JT and de Souza, HG and Dearnaley, JDW and Dimitrov, RA and Dovana, F and Erhard, A and Esteve-Raventós, F and Félix, CR and Ferisin, G and Fernandes, RA and Ferreira, RJ and Ferro, LO and Figueiredo, CN and Frank, JL and Freire, KTLS and García, D and Gené, J and Gêsiorska, A and Gibertoni, TB and Gondra, RAG and Gouliamova, DE and Gramaje, D and Guard, F and Gusmão, LFP and Haitook, S and Hirooka, Y and Houbraken, J and Hubka, V and Inamdar, A and Iturriaga, T and Iturrieta-González, I and Jadan, M and Jiang, N and Justo, A and Kachalkin, AV and Kapitonov, VI and Karadelev, M and Karakehian, J and Kasuya, T and Kautmanová, I and Kruse, J and Kušan, I and Kuznetsova, TA and Landell, MF and Larsson, KH and Lee, HB and Lima, DX and Lira, CRS and Machado, AR and Madrid, H and Magalhães, OMC and Majerova, H and Malysheva, EF and Mapperson, RR and Marbach, PAS and Martín, MP and Martín-Sanz, A and Matočec, N and McTaggart, AR and Mello, JF and Melo, RFR and Mešić, A and Michereff, SJ and Miller, AN and Minoshima, A and Molinero-Ruiz, L and Morozova, OV and Mosoh, D and Nabe, M and Naik, R and Nara, K and Nascimento, SS and Neves, RP and Olariaga, I and Oliveira, RL and Oliveira, TGL and Ono, T and Ordoñez, ME and Ottoni, AM and Paiva, LM and Pancorbo, F and Pant, B and Pawłowska, J and Peterson, SW and Raudabaugh, DB and Rodríguez-Andrade, E and Rubio, E and Rusevska, K and Santiago, ALCMA and Santos, ACS and Santos, C and Sazanova, NA and Shah, S and Sharma, J and Silva, BDB and Siquier, JL and Sonawane, MS and Stchigel, AM and Svetasheva, T and Tamakeaw, N and Telleria, MT and Tiago, PV and Tian, CM and Tkalčec, Z and Tomashevskaya, MA and Truong, HH and Vecherskii, MV and Visagie, CM and Vizzini, A and Yilmaz, N and Zmitrovich, IV and Zvyagina, EA and Boekhout, T and Kehlet, T and Læssøe, T and Groenewald, JZ},
title = {Fungal Planet description sheets: 868-950.},
journal = {Persoonia},
volume = {42},
number = {},
pages = {291-473},
pmid = {31551622},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Chaetomella pseudocircinoseta and Coniella pseudodiospyri on Eucalyptus microcorys leaves, Cladophialophora eucalypti, Teratosphaeria dunnii and Vermiculariopsiella dunnii on Eucalyptus dunnii leaves, Cylindrium grande and Hypsotheca eucalyptorum on Eucalyptus grandis leaves, Elsinoe salignae on Eucalyptus saligna leaves, Marasmius lebeliae on litter of regenerating subtropical rainforest, Phialoseptomonium eucalypti (incl. Phialoseptomonium gen. nov.) on Eucalyptus grandis × camaldulensis leaves, Phlogicylindrium pawpawense on Eucalyptus tereticornis leaves, Phyllosticta longicauda as an endophyte from healthy Eustrephus latifolius leaves, Pseudosydowia eucalyptorum on Eucalyptus sp. leaves, Saitozyma wallum on Banksia aemula leaves, Teratosphaeria henryi on Corymbia henryi leaves. Brazil, Aspergillus bezerrae, Backusella azygospora, Mariannaea terricola and Talaromyces pernambucoensis from soil, Calonectria matogrossensis on Eucalyptus urophylla leaves, Calvatia brasiliensis on soil, Carcinomyces nordestinensis on Bromelia antiacantha leaves, Dendryphiella stromaticola on small branches of an unidentified plant, Nigrospora brasiliensis on Nopalea cochenillifera leaves, Penicillium alagoense as a leaf endophyte on a Miconia sp., Podosordaria nigrobrunnea on dung, Spegazzinia bromeliacearum as a leaf endophyte on Tilandsia catimbauensis, Xylobolus brasiliensis on decaying wood. Bulgaria, Kazachstania molopis from the gut of the beetle Molops piceus. Croatia, Mollisia endocrystallina from a fallen decorticated Picea abies tree trunk. Ecuador, Hygrocybe rodomaculata on soil. Hungary, Alfoldia vorosii (incl. Alfoldia gen. nov.) from Juniperus communis roots, Kiskunsagia ubrizsyi (incl. Kiskunsagia gen. nov.) from Fumana procumbens roots. India, Aureobasidium tremulum as laboratory contaminant, Leucosporidium himalayensis and Naganishia indica from windblown dust on glaciers. Italy, Neodevriesia cycadicola on Cycas sp. leaves, Pseudocercospora pseudomyrticola on Myrtus communis leaves, Ramularia pistaciae on Pistacia lentiscus leaves, Neognomoniopsis quercina (incl. Neognomoniopsis gen. nov.) on Quercus ilex leaves. Japan, Diaporthe fructicola on Passiflora edulis × P. edulis f. flavicarpa fruit, Entoloma nipponicum on leaf litter in a mixed Cryptomeria japonica and Acer spp. forest. Macedonia, Astraeus macedonicus on soil. Malaysia, Fusicladium eucalyptigenum on Eucalyptus sp. twigs, Neoacrodontiella eucalypti (incl. Neoacrodontiella gen. nov.) on Eucalyptus urophylla leaves. Mozambique, Meliola gorongosensis on dead Philenoptera violacea leaflets. Nepal, Coniochaeta dendrobiicola from Dendriobium lognicornu roots. New Zealand, Neodevriesia sexualis and Thozetella neonivea on Archontophoenix cunninghamiana leaves. Norway, Calophoma sandfjordenica from a piece of board on a rocky shoreline, Clavaria parvispora on soil, Didymella finnmarkica from a piece of Pinus sylvestris driftwood. Poland, Sugiyamaella trypani from soil. Portugal, Colletotrichum feijoicola from Acca sellowiana. Russia, Crepidotus tobolensis on Populus tremula debris, Entoloma ekaterinae, Entoloma erhardii and Suillus gastroflavus on soil, Nakazawaea ambrosiae from the galleries of Ips typographus under the bark of Picea abies. Slovenia, Pluteus ludwigii on twigs of broadleaved trees. South Africa, Anungitiomyces stellenboschiensis (incl. Anungitiomyces gen. nov.) and Niesslia stellenboschiana on Eucalyptus sp. leaves, Beltraniella pseudoportoricensis on Podocarpus falcatus leaf litter, Corynespora encephalarti on Encephalartos sp. leaves, Cytospora pavettae on Pavetta revoluta leaves, Helminthosporium erythrinicola on Erythrina humeana leaves, Helminthosporium syzygii on a Syzygium sp. bark canker, Libertasomyces aloeticus on Aloe sp. leaves, Penicillium lunae from Musa sp. fruit, Phyllosticta lauridiae on Lauridia tetragona leaves, Pseudotruncatella bolusanthi (incl. Pseudotruncatellaceae fam. nov.) and Dactylella bolusanthi on Bolusanthus speciosus leaves. Spain, Apenidiella foetida on submerged plant debris, Inocybe grammatoides on Quercus ilex subsp. ilex forest humus, Ossicaulis salomii on soil, Phialemonium guarroi from soil. Thailand, Pantospora chromolaenae on Chromolaena odorata leaves. Ukraine, Cadophora helianthi from Helianthus annuus stems. USA, Boletus pseudopinophilus on soil under slash pine, Botryotrichum foricae, Penicillium americanum and Penicillium minnesotense from air. Vietnam, Lycoperdon vietnamense on soil. Morphological and culture characteristics are supported by DNA barcodes.},
}
@article {pmid31550685,
year = {2020},
author = {Zhuang, QY and Wang, XH and Geng, ZX and Peng, HS},
title = {Facile synthesis of multifunctional nanoparticles encoded with quantum dots and magnetic nanoparticles: cell tagging and MRI.},
journal = {Nanotechnology},
volume = {31},
number = {6},
pages = {065101},
doi = {10.1088/1361-6528/ab4755},
pmid = {31550685},
issn = {1361-6528},
abstract = {In this study, fluorescence-encoded magnetic biocompatible nanoparticles (NPs) were constructed from CdSe@ZnS quantum dots (QDs) and Fe3O4 nanoparticles with a one-step reprecipitation-encapsulation method. The resultant hybrid NPs exhibit small size (∼130 nm in diameter), highly bright QDs, two-color emissions (green and red) under single-wavelength excitation, easy separation with a magnet and efficient cellular internalization. Energy transfer between the incorporated QDs was studied to better tailor the encoded fluorescence, and 11 barcodes were obtained by adjusting the ratio of green and red QDs. We used four sets of the barcodes to tag specific cancer cells (HepG2) as a proof-of-concept, and distinguished each set according to respective overlayed fluorescence images using laser confocal microscopy. Moreover, the incorporated Fe3O4 NPs endowed as-constructed optical barcode superparamagnetic property by T 2-enhanced magnetic resonance effect with an r 2 value of 145.25 s[-1] mM[-1] at 3 T. These results suggest that the multifunctional NPs are very promising for discriminating different cells and dual-modality imaging.},
}
@article {pmid31547865,
year = {2019},
author = {Selich, A and Zimmermann, K and Tenspolde, M and Dittrich-Breiholz, O and von Kaisenberg, C and Schambach, A and Rothe, M},
title = {Umbilical cord as a long-term source of activatable mesenchymal stromal cells for immunomodulation.},
journal = {Stem cell research &amp; therapy},
volume = {10},
number = {1},
pages = {285},
pmid = {31547865},
issn = {1757-6512},
mesh = {Animals ; Cells, Cultured ; Humans ; Immunomodulation ; Interferon-gamma/*genetics/metabolism ; Mesenchymal Stem Cells/immunology/*metabolism ; Mice ; Mice, Inbred NOD ; Transcriptome ; Tumor Necrosis Factor-alpha/*genetics/metabolism ; Umbilical Cord/*cytology ; },
abstract = {BACKGROUND: Mesenchymal stromal cells (MSCs) are used in over 800 clinical trials mainly due to their immune inhibitory activity. Umbilical cord (UC), the second leading source of clinically used MSCs, is usually cut in small tissue pieces. Subsequent cultivation leads to a continuous outgrowth of MSC explant monolayers (MSC-EMs) for months. Currently, the first MSC-EM culture takes approximately 2 weeks to grow out, which is then expanded and applied to patients. The initiating tissue pieces are then discarded. However, when UC pieces are transferred to new culture dishes, MSC-EMs continue to grow out. In case the functional integrity of these cells is maintained, later induced cultures could also be expanded and used for cell therapy. This would drastically increase the number of available cells for each patient. To test the functionality of MSC-EMs from early and late induction time points, we compared the first cultures to those initiated after 2 months by investigating their clonality and immunomodulatory capacity.<br><br>METHODS: We analyzed the clonal composition of MSC-EM cultures by umbilical cord piece transduction using integrating lentiviral vectors harboring genetic barcodes assessed by high-throughput sequencing. We investigated the transcriptome of these cultures by microarrays. Finally, the secretome was analyzed by multiplexed ELISAs, in vitro assays, and in vivo in mice.<br><br>RESULTS: DNA barcode analysis showed polyclonal MSC-EMs even after months of induction cycles. A transcriptome and secretome analyses of early and late MSC cultures showed only minor changes over time. However, upon activation with TNF-&#x3b1; and IFN-&#x3b3;, cells from both induction time points produced a multitude of immunomodulatory cytokines. Interestingly, the later induced MSC-EMs produced higher amounts of cytokines. To test whether the different cytokine levels were in a therapeutically relevant range, we used conditioned medium (CM) in an in vitro MLR and an in vivo killing assay. CM from late induced MSC-EMs was at least as immune inhibitory as CM from early induced MSC-EMs.<br><br>CONCLUSION: Human umbilical cord maintains a microenvironment for the long-term induction of polyclonal and immune inhibitory active MSCs for months. Thus, our results would offer the possibility to drastically increase the number of therapeutically applicable MSCs for a substantial amount of patients.},
}
@article {pmid31545949,
year = {2020},
author = {Lima-Oliveira, TM and Fontes, FVHM and Lilioso, M and Pires-Silva, D and Teixeira, MMG and Meza, JGV and Harry, M and Fileé, J and Costa, J and Valença-Barbosa, C and Folly-Ramos, E and Almeida, CE},
title = {Molecular eco-epidemiology on the sympatric Chagas disease vectors Triatoma brasiliensis and Triatoma petrocchiae: Ecotopes, genetic variation, natural infection prevalence by trypanosomatids and parasite genotyping.},
journal = {Acta tropica},
volume = {201},
number = {},
pages = {105188},
doi = {10.1016/j.actatropica.2019.105188},
pmid = {31545949},
issn = {1873-6254},
mesh = {Animals ; Brazil/epidemiology ; Chagas Disease/epidemiology/*transmission ; Ecosystem ; Genetic Variation ; Genotype ; Insect Vectors/*parasitology ; Molecular Epidemiology ; Prevalence ; *Sympatry ; Triatoma/*parasitology ; Trypanosoma cruzi/*genetics ; },
abstract = {Triatoma petrocchiae is the newly member of the Triatoma brasiliensis species complex. This species overlaps with T. brasiliensis in geographic and ecotypic occupation in the sylvatic habitat because both inhabit rocky outcrops in the semi-arid portion of Brazilian northeast. In this region T. brasiliensis is the most important Chagas disease vector because it constantly colonizes domiciles. In contrast, T. petrocchiae is rarely found in peri or intradomiciliary habitats - reason why little is known about this species. Therefore, Here, we present information for the first time on. the T. petrocchiae ecotopes, genetic diversity, Trypanosoma cruzi prevalence/genotyping in comparison to T. brasiliensis. We found T. brasilensis (N = 223) and T. petrocchiae (N = 69) in co-habitation in rocky outcrops in three Districts of Paraíba and Rio Grande do Norte states. Forty-tree T. petrocchiae insects of eleven sampling spots (composing three geographic populations) were genotyped for the mitochondrial Cyt B gene and little geographic structure was observed. Tajima's D test suggested that species is evolving toward a mutation-drift equilibrium in our collection range. Sylvatic T. petrocchiae had 4% (3/68) of infected insects by T. cruzi, whereas T. brasiliensis had 26% (59/223). Fluorescent Fragment Length Barcoding demonstrated that all three T. petrocchiae harbored TcI whereas T. brasiliensis had TcI, but also TcIII, TcII/TcVI and T. rangeli genotype A, sometimes under mixed infections. None of infected T. petrocchiae were carrying mixed infections. However, this result should be confirmed using a larger pool of infected bugs. We here presented the first documentation of T. rangeli infecting T. brasiliensis. The finding of infected T. petrocchiae calls for constant vector monitoring because the epidemiologic scenario is dynamic and sylvatic vectors are progressively found in adaptation to anthropic environments.},
}
@article {pmid31545363,
year = {2020},
author = {Balaban, M and Sarmashghi, S and Mirarab, S},
title = {APPLES: Scalable Distance-Based Phylogenetic Placement with or without Alignments.},
journal = {Systematic biology},
volume = {69},
number = {3},
pages = {566-578},
pmid = {31545363},
issn = {1076-836X},
support = {P30 AI027767/AI/NIAID NIH HHS/United States ; },
mesh = {Algorithms ; Base Sequence ; Classification/*methods ; *Phylogeny ; *Software ; },
abstract = {Placing a new species on an existing phylogeny has increasing relevance to several applications. Placement can be used to update phylogenies in a scalable fashion and can help identify unknown query samples using (meta-)barcoding, skimming, or metagenomic data. Maximum likelihood (ML) methods of phylogenetic placement exist, but these methods are not scalable to reference trees with many thousands of leaves, limiting their ability to enjoy benefits of dense taxon sampling in modern reference libraries. They also rely on assembled sequences for the reference set and aligned sequences for the query. Thus, ML methods cannot analyze data sets where the reference consists of unassembled reads, a scenario relevant to emerging applications of genome skimming for sample identification. We introduce APPLES, a distance-based method for phylogenetic placement. Compared to ML, APPLES is an order of magnitude faster and more memory efficient, and unlike ML, it is able to place on large backbone trees (tested for up to 200,000 leaves). We show that using dense references improves accuracy substantially so that APPLES on dense trees is more accurate than ML on sparser trees, where it can run. Finally, APPLES can accurately identify samples without assembled reference or aligned queries using kmer-based distances, a scenario that ML cannot handle. APPLES is available publically at github.com/balabanmetin/apples.},
}
@article {pmid31545107,
year = {2019},
author = {Luo, X and Li, H and Jiang, D and Meng, J and Zhang, F and Xu, Q and Chen, X and Liu, C and Yang, Y},
title = {Analysis of Fungi on Coix (Coix lacryma-jobi) Seed and the Effect of Its Aqueous Extract on the Growth of Aspergillus flavus.},
journal = {Journal of food protection},
volume = {82},
number = {10},
pages = {1775-1782},
doi = {10.4315/0362-028X.JFP-19-019},
pmid = {31545107},
issn = {1944-9097},
mesh = {Anti-Bacterial Agents/chemistry/pharmacology ; *Aspergillus flavus/drug effects ; *Coix/chemistry/microbiology ; *Fungi/chemistry/classification/isolation &amp; purification/metabolism ; *Seeds/chemistry ; Water/chemistry ; },
abstract = {Coix (Coix lacryma-jobi) seeds are susceptible to fungal infections, making their surface fungi complex and diverse. Some fungi can produce mycotoxins under suitable conditions, and fungal growth is closely related to the production of mycotoxins. In this study, the surface fungi of coix seed were identified by Illumina HiSeq high-throughput sequencing. Simultaneously, the fungi cultured by the plate method were identified by microscopy and DNA barcoding; finally, the species of fungi were identified accurately and reliably by combining three methods. The aqueous extract of coix seed was cocultured with Aspergillus flavus spores, and the relationship between the aqueous extract and the growth of A. flavus was studied with the dry weight of mycelium as an indicator. The results showed that there were 89 genera and 96 species of fungi on coix seed, which were mainly distributed in Ascomycota (81.48%) and Basidiomycota (4.08%), and Xeromyces (8.50%), Gibberella (7.25%), and Aspergillus (4.74%) were the predominant genera. Four fungi were isolated from coix seed by plate culture and identified as Aspergillus fumigatus, A. flavus, Aspergillus oryzae, and Rhizopus oryzae by microscopy and DNA barcoding. The aqueous extract of coix seed at low concentrations has a promoting effect on the growth of A. flavus. When the concentration is 3.125%, the promotion effect is the most pronounced, and the promotion rate is 29.17%. These results reveal the diversity of fungi on the coix seed, which can provide a reference for the prevention and control of harmful fungi on coix seed.},
}
@article {pmid31543695,
year = {2019},
author = {Skevington, JH and Young, AD and Locke, MM and Moran, KM},
title = {New Syrphidae (Diptera) of North-eastern North America.},
journal = {Biodiversity data journal},
volume = {7},
number = {},
pages = {e36673},
pmid = {31543695},
issn = {1314-2828},
abstract = {BACKGROUND: This paper describes 11 of 18 new species recognised in the recent book, "Field Guide to the Flower Flies of Northeastern North America". Four species are omitted as they need to be described in the context of a revision (three Cheilosia and a Palpada species) and three other species (one Neoascia and two Xylota) will be described by F. Christian Thompson in a planned publication. Six of the new species have been recognised for decades and were treated by J. Richard Vockeroth in unpublished notes or by Thompson in his unpublished but widely distributed "A conspectus of the flower flies (Diptera: Syrphidae) of the Nearctic Region". Five of the 11 species were discovered during the preparation of the Field Guide. Eight of the 11 have DNA barcodes available that support the morphology.<br><br>NEW INFORMATION: New species treated in this paper include: Anasimyia diffusa Locke, Skevington and Vockeroth (Smooth-legged Swamp Fly), Anasimyia matutina Locke, Skevington and Vockeroth (Small-spotted Swamp Fly), Brachyopa caesariata Moran and Skevington (Plain-winged Sapeater), Brachyopa cummingi Moran and Skevington (Somber Sapeater), Hammerschmidtia sedmani Vockeroth, Moran and Skevington (Pale-bristled Logsitter), Microdon (Microdon) scauros Skevington and Locke (Big-footed Ant Fly), Mixogaster fattigi Locke, Skevington and Greene (Fattig's Ant Fly), Neoascia guttata Skevington and Moran (Spotted Fen Fly), Orthonevra feei Moran and Skevington (Fee's Mucksucker), Psilota klymkoi Locke, Young and Skevington (Black Haireye) and Trichopsomyia litoralis Vockeroth and Young (Coastal Psyllid-killer). Common names follow the "Field Guide to the Flower Flies of Northeastern North America" (Skevington et al. 2019).},
}
@article {pmid31541152,
year = {2019},
author = {Cheng, CY and Chang, SL and Lin, IT and Yao, MC},
title = {Abundant and diverse Tetrahymena species living in the bladder traps of aquatic carnivorous Utricularia plants.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {13669},
pmid = {31541152},
issn = {2045-2322},
mesh = {Aquatic Organisms/parasitology ; Carnivory ; Cyclooxygenase 1/*genetics ; DNA Barcoding, Taxonomic ; Lamiales/*parasitology ; Phylogeny ; Phylogeography ; Protozoan Proteins/genetics ; Sequence Analysis, DNA/*methods ; Symbiosis ; Taiwan ; Tetrahymena/*classification/genetics/isolation &amp; purification ; },
abstract = {Ciliates are unicellular eukaryotes known for their cellular complexity and wide range of natural habitats. How they adapt to their niches and what roles they play in ecology remain largely unknown. The genus Tetrahymena is among the best-studied groups of ciliates and one particular species, Tetrahymena thermophila, is a well-known laboratory model organism in cell and molecular biology, making it an excellent candidate for study in protist ecology. Here, based on cytochrome c oxidase subunit I (COX1) gene barcoding, we identify a total of 19 different putative Tetrahymena species and two closely related Glaucoma lineages isolated from distinct natural habitats, of which 13 are new species. These latter include 11 Tetrahymena species found in the bladder traps of Utricularia plants, the most species-rich and widely distributed aquatic carnivorous plant, thus revealing a previously unknown but significant symbiosis of Tetrahymena species living among the microbial community of Utricularia bladder traps. Additional species were collected using an artificial trap method we have developed. We show that diverse Tetrahymena species may live even within the same habitat and that their populations are highly dynamic, suggesting that the diversity and biomass of species worldwide is far greater than currently appreciated.},
}
@article {pmid31538935,
year = {2019},
author = {Derouiche, I and Neifar, L and Gey, D and Justine, JL and Tazerouti, F},
title = {Holocephalocotyle monstrosae n. gen. n. sp. (Monogenea, Monocotylidae) from the olfactory rosette of the rabbit fish, Chimaera monstrosa (Holocephali, Chimaeridae) in deep waters off Algeria.},
journal = {Parasite (Paris, France)},
volume = {26},
number = {},
pages = {59},
pmid = {31538935},
issn = {1776-1042},
mesh = {Algeria ; Animals ; DNA, Ribosomal ; Female ; Fish Diseases/*parasitology ; Fishes/*parasitology ; Genitalia, Female ; Genitalia, Male ; Male ; Mediterranean Sea ; Phylogeny ; Seafood/parasitology ; Trematoda/anatomy &amp; histology/*classification ; Trematode Infections/*veterinary ; },
abstract = {Based on a molecular and morphological study, a new monocotylid genus, Holocephalocotyle n. gen. is proposed to accommodate Holocephalocotyle monstrosae n. sp., found on the olfactory rosette of the rabbit fish, Chimaera monstrosa Linnaeus (Chondrichthyes, Chimaeridae), from the Mediterranean Sea off Algeria. Identification of fish hosts was confirmed by molecular barcoding of the COI gene. A partial 28S rDNA sequence (D1-D2 domain) of Holocephalocotyle monstrosae was obtained; it was distinct from all known monocotylid sequences (p-distance: 15.5-23%). A phylogenetic tree constructed from available monocotylid sequences showed that Holocephalocotyle monstrosae was included, and basal, in a robust group including species of Merizocotyle, Mycteronastes and Empruthotrema, confirming that the species is a member of the Merizocotylinae. The new genus is unique among the Merizocotylinae in having a distinctive pattern of haptoral loculi with one central, five peripheral and seven "interperipheral loculi" partially inserted between peripheral loculi and a compartmentalised sclerotised male copulatory organ. The diagnosis of the Merizocotylinae is amended to include this new genus. The new genus represents the second monocotylid genus recorded from holocephalans.},
}
@article {pmid31536551,
year = {2019},
author = {Thu, PT and Huang, WC and Chou, TK and Van Quan, N and Van Chien, P and Li, F and Shao, KT and Liao, TY},
title = {DNA barcoding of coastal ray-finned fishes in Vietnam.},
journal = {PloS one},
volume = {14},
number = {9},
pages = {e0222631},
pmid = {31536551},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; DNA/*genetics ; DNA Barcoding, Taxonomic/methods ; Databases, Nucleic Acid ; Electron Transport Complex IV/genetics ; Phylogeny ; Skates, Fish/*genetics ; Vietnam ; },
abstract = {DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding database of coastal ray-finned fishes in Vietnam. A total of 3,638 specimens were collected from fish landing sites in northern, central and southern Vietnam. Seven hundred and sixty-five COI sequences of ray-finned fishes were generated, belonging to 458 species, 273 genera, 113 families and 43 orders. A total of 59 species were newly recorded in Vietnam and sequences of six species were new to the Genbank and BOLD online databases. Only 32 species cannot be annotated to species level because difficulty in morphological identifications and their Kimura-2-Parameter (K2P) genetic distances to most similar sequences were more than 2%. Moreover, intra-specific genetic distances in some species are also higher than 2%, implying the existence of putative cryptic species. The mean K2P genetic distances within species, genera, families, orders and classes were 0.34%, 12.14%, 17.39%, 21.42%, and 24.80, respectively. Species compositions are quite different with only 16 common species among northern, central and southern Vietnam. This may attribute to multiple habitats and environmental factors across the 3,260 km Vietnamese coastline. Our results confirmed that DNA barcoding is an efficient and reliable tool for coastal fish identification in Vietnam, and also established a reliable DNA barcode reference library for these fishes. DNA barcodes will contribute to future efforts to achieve better monitoring, conservation, and management of fisheries in Vietnam.},
}
@article {pmid31534400,
year = {2019},
author = {Liu, HM and Shen, JY and Liang, ZL and Peng, F and Wang, WZ and Yang, ZW and Wang, S and Parris, B and Harald Schneider, },
title = {Two out of one: revising the diversity of the epiphytic fern genus Scleroglossum (Polypodiaceae, Grammitidoideae) in southern China.},
journal = {PhytoKeys},
volume = {130},
number = {},
pages = {115-133},
pmid = {31534400},
issn = {1314-2011},
abstract = {Our understanding of the flora of China has greatly improved during the last 100 years but effective management of the rich biodiversity and unique natural resources requires resolving the taxonomic limitations of existing treatments. Here, we focus on the epiphytic genus Scleroglossum with special emphasis on the occurrences in Hainan and Yunnan of mainland China. By combining fieldwork, herbarium studies, and DNA barcoding we test the hypothesis that this genus is represented by more than one species in China. Our integrative results show the Yunnan accessions are distinct from those in Hainan in both phenotypic and genotypic variation. The Yunnan accessions belong to S. pusillum, whereas the Hainan accessions represent a distinct species displaying the morphological characteristics of S. sulcatum. Genotypic evidence suggests the occurrence of cryptic diversity among accessions with the morphology of S. sulcatum. In summary, the study contributes to the crucial assessment of the plant diversity in Yunnan and illustrates the importance of integrating collection efforts and DNA barcoding approaches to enable effective assessment of the epiphytic diversity of Yunnan.},
}
@article {pmid31534391,
year = {2019},
author = {Gao, LM and Tan, SL and Zhang, GL and Thomas, P},
title = {A new species of Amentotaxus (Taxaceae) from China, Vietnam, and Laos.},
journal = {PhytoKeys},
volume = {130},
number = {},
pages = {25-32},
pmid = {31534391},
issn = {1314-2011},
abstract = {A new species Amentotaxus hekouensis L.M. Gao is described as new to science from Hekou, Yunnan of China, Lao Cai of Vietnam and Xiang Khouang of Laos. The new species is similar to A. argotaenia (Hance) Pilg. in linear or linear-lanceolate leaves, stomatal bands white and microsporophylls 6-8, each with 4-6 pollen sacs, but differs from the latter by its larger leaf size with 8-12.5 cm × 0.9-1.4 cm (vs. 2-11 cm × 0.5-1.1 cm in A. argotaenia), long acuminate leaf apex (vs. rounded to sharply triangular in A. argotaenia), stomatal bands with 25-30 rows (vs. 15-25 rows in A. argotaenia), stomatal bands equal to or slightly narrower than marginal bands (vs. narrower than marginal bands in A. argotaenia); pollen-cone racemes borne 1-2 (vs. 2-4 (10) in A. argotaenia), cones in 12-16 pairs (vs. ca. 12 pairs in A. argotaenia). Its distinctive nature has also been confirmed through DNA barcoding analysis of this genus. The new species is provisionally assessed as endangered (EN) due to its restricted distribution, small population size and the prevalence of habitat destruction within its range.},
}
@article {pmid31534387,
year = {2019},
author = {Motamedinia, B and Skevington, JH and Kelso, S},
title = {Revision of Claraeola (Diptera, Pipunculidae) in the Middle East based on morphology and DNA barcodes.},
journal = {ZooKeys},
volume = {873},
number = {},
pages = {85-111},
pmid = {31534387},
issn = {1313-2989},
abstract = {The Middle East species of Claraeola Aczél (Diptera, Pipunculidae) are revised based on morphological characteristics and sequence data from the mitochondrial COI barcoding gene, using a novel COI mini-barcode protocol. Four new Claraeola species are described: C. bousynterga Motamedinia &amp; Skevington, sp. nov., C. heidiae Motamedinia &amp; Skevington, sp. nov., C. khuzestanensis Motamedinia &amp; Skevington, sp. nov., and C. mantisphalliga Motamedinia &amp; Skevington, sp. nov. Eudorylas thekkadiensis Kapoor, Grewal &amp; Sharma, 1987 is transferred to Claraeola, C. thekkadiensis (comb. nov.). Diagnoses, illustrations, an identification key, and a distributional map are given for the Middle East species.},
}
@article {pmid31534181,
year = {2019},
author = {Amambua-Ngwa, A and Jeffries, D and Mwesigwa, J and Seedy-Jawara, A and Okebe, J and Achan, J and Drakeley, C and Volkman, S and D'Alessandro, U},
title = {Long-distance transmission patterns modelled from SNP barcodes of Plasmodium falciparum infections in The Gambia.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {13515},
pmid = {31534181},
issn = {2045-2322},
support = {MC_EX_MR/K02440X/1/MRC_/Medical Research Council/United Kingdom ; MC_UP_A900_1119/MRC_/Medical Research Council/United Kingdom ; MC_EX_MR/J002364/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; DNA Barcoding, Taxonomic/methods ; Female ; Gambia/epidemiology ; Genotype ; Humans ; Malaria/*genetics/*transmission ; Malaria, Falciparum/parasitology ; Male ; Parasites ; Plasmodium falciparum/*genetics ; Polymorphism, Single Nucleotide/genetics ; Prevalence ; Seasons ; },
abstract = {Malaria has declined significantly in The Gambia and determining transmission dynamics of Plasmodium falciparum can help targeting control interventions towards elimination. This can be inferred from genetic similarity between parasite isolates from different sites and timepoints. Here, we imposed a P. falciparum life cycle time on a genetic distance likelihood model to determine transmission paths from a 54 SNP barcode of 355 isolates. Samples were collected monthly during the 2013 malaria season from six pairs of villages spanning 300 km from western to eastern Gambia. There was spatial and temporal hierarchy in pairwise genetic relatedness, with the most similar barcodes from isolates within the same households and village. Constrained by travel data, the model detected 60 directional transmission events, with 27% paths linking persons from different regions. We identified 13 infected individuals (4.2% of those genotyped) responsible for 2 to 8 subsequent infections within their communities. These super-infectors were mostly from high transmission villages. When considering paths between isolates from the most distant regions (west vs east) and travel history, there were 3 transmission paths from eastern to western Gambia, all at the peak (October) of the malaria transmission season. No paths with known travel originated from the extreme west to east. Although more than half of all paths were within-village, parasite flow from east to west may contribute to maintain transmission in western Gambia, where malaria transmission is already low. Therefore, interrupting malaria transmission in western Gambia would require targeting eastern Gambia, where malaria prevalence is substantially higher, with intensified malaria interventions.},
}
@article {pmid31531364,
year = {2019},
author = {Liu, H and Su, Z and Yu, S and Liu, J and Yin, X and Zhang, G and Liu, W and Li, B},
title = {Genome Comparison Reveals Mutation Hotspots in the Chloroplast Genome and Phylogenetic Relationships of Ormosia Species.},
journal = {BioMed research international},
volume = {2019},
number = {},
pages = {7265030},
pmid = {31531364},
issn = {2314-6141},
mesh = {Australia ; Chloroplasts/*genetics ; DNA, Chloroplast/genetics ; Evolution, Molecular ; Fabaceae/*genetics ; Asia, Eastern ; Genetics, Population/methods ; Genome, Chloroplast/*genetics ; Genomics/methods ; Microsatellite Repeats/genetics ; Mutation/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {The papilionoid legume genus Ormosia comprises approximately 130 species, which are distributed mostly in the Neotropics, with some species in eastern Asia and northeastern Australia. The taxonomy and evolutionary history remain unclear due to the lack of a robust species-level phylogeny. Chloroplast genomes can provide important information for phylogenetic and population genetic studies. In this study, we determined the complete chloroplast genome sequences of five Ormosia species by Illumina sequencing. The Ormosia chloroplast genomes displayed the typical quadripartite structure of angiosperms, which consisted of a pair of inverted regions separated by a large single-copy region and a small single-copy region. The location and distribution of repeat sequences and microsatellites were determined. Comparative analyses highlighted a wide spectrum of variation, with trnK-rbcL, atpE-trnS-rps4, trnC-petN, trnS-psbZ-trnG, trnP-psaJ-rpl33, and clpP intron being the most variable regions. Phylogenetic analysis revealed that Ormosia is in the Papilionoideae clade and is sister to the Lupinus clade. Overall, this study, which provides Ormosia chloroplast genomic resources and a comparative analysis of Ormosia chloroplast genomes, will be beneficial for the evolutionary study and phylogenetic reconstruction of the genus Ormosia and molecular barcoding in population genetics and will provide insight into the chloroplast genome evolution of legumes.},
}
@article {pmid31529041,
year = {2020},
author = {Qing, X and Wang, M and Karssen, G and Bucki, P and Bert, W and Braun-Miyara, S},
title = {PPNID: a reference database and molecular identification pipeline for plant-parasitic nematodes.},
journal = {Bioinformatics (Oxford, England)},
volume = {36},
number = {4},
pages = {1052-1056},
doi = {10.1093/bioinformatics/btz707},
pmid = {31529041},
issn = {1367-4811},
mesh = {Animals ; *Nematoda ; Phylogeny ; *Plants ; Software ; },
abstract = {MOTIVATION: The phylum Nematoda comprises the most cosmopolitan and abundant metazoans on Earth and plant-parasitic nematodes represent one of the most significant nematode groups, causing severe losses in agriculture. Practically, the demands for accurate nematode identification are high for ecological, agricultural, taxonomic and phylogenetic researches. Despite their importance, the morphological diagnosis is often a difficult task due to phenotypic plasticity and the absence of clear diagnostic characters while molecular identification is very difficult due to the problematic database and complex genetic background.<br><br>RESULTS: The present study attempts to make up for currently available databases by creating a manually-curated database including all up-to-date authentic barcoding sequences. To facilitate the laborious process associated with the interpretation and identification of a given query sequence, we developed an automatic software pipeline for rapid species identification. The incorporated alignment function facilitates the examination of mutation distribution and therefore also reveals nucleotide autapomorphies, which are important in species delimitation. The implementation of genetic distance, plot and maximum likelihood phylogeny analysis provides more powerful optimality criteria than similarity searching and facilitates species delimitation using evolutionary or phylogeny species concepts. The pipeline streamlines several functions to facilitate more precise data analyses, and the subsequent interpretation is easy and straightforward.<br><br>The pipeline was written in vb.net, developed on Microsoft Visual Studio 2017 and designed to work in any Windows environment. The PPNID is distributed under the GNU General Public License (GPL). The executable file along with tutorials is available at https://github.com/xueqing4083/PPNID.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid31528118,
year = {2019},
author = {Sroka, P and Bojková, J and Godunko, RJ and Soldán, T and Namin, JI and Nejat, F and Abdoli, A and Staniczek, AH},
title = {New Oligoneuriidae (Insecta, Ephemeroptera) from Iran.},
journal = {ZooKeys},
volume = {872},
number = {},
pages = {101-126},
pmid = {31528118},
issn = {1313-2989},
abstract = {Two new species of the mayfly family Oligoneuriidae are described based on larval specimens recently collected in Iran. The first new species, Oligoneuriella tuberculata Godunko &amp; Staniczek, sp. nov., can be distinguished from all its congeners by the presence of pronounced protuberances posteromedially on abdominal terga, highly reduced paracercus, large lamella of gill I, and setation on hind margin of middle and hind femora confined to their basal halves. The second species, Oligoneuriopsis villosus Bojková, Godunko, &amp; Staniczek, sp. nov., remarkably belongs to a mostly Afrotropical genus. The new species clearly differs from all its congeners in the shape of setae on the surface of gills and terga, pattern of body colouration, and the shape of posterolateral projections of abdominal segments. Except for the species description, the generic diagnosis of Oligoneuriopsis Crass, 1947 is briefly discussed. COI barcode sequences of both new species are provided and molecular species delimitation is tested using distance-based and likelihood-based approaches, with both new species unambiguously recognised as separate lineages. The analysis of COI also corroborates the respective affinities of both new species, estimated based on morphology. The two new species of Oligoneuriidae described herein highlight the importance of the Middle East as a centre of diversity of this mayfly family within the Palaearctic.},
}
@article {pmid31527883,
year = {2019},
author = {Madden, MJL and Young, RG and Brown, JW and Miller, SE and Frewin, AJ and Hanner, RH},
title = {Using DNA barcoding to improve invasive pest identification at U.S. ports-of-entry.},
journal = {PloS one},
volume = {14},
number = {9},
pages = {e0222291},
pmid = {31527883},
issn = {1932-6203},
mesh = {Animals ; Arthropods/*genetics ; DNA/genetics ; DNA Barcoding, Taxonomic/methods ; Humans ; Microcephaly/diagnosis/parasitology ; Pest Control/*methods ; Retrospective Studies ; },
abstract = {Interception of potential invasive species at ports-of-entry is essential for effective biosecurity and biosurveillance programs. However, taxonomic assessment of the immature stages of most arthropods is challenging; characters for identification are often dependent on adult morphology and reproductive structures. This study aims to strengthen the identification of such specimens through DNA barcoding, with a focus on microlepidoptera. A sample of 241 primarily immature microlepidoptera specimens intercepted at U.S. ports-of-entry from 2007 to 2011 were selected for analysis. From this sample, 201 COI-5P sequences were generated and analyzed for concordance between morphology-based and DNA-based identifications. The retrospective analysis of the data over 10 years (2009 to 2019) using the Barcode of Life Data (BOLD) system demonstrates the importance of establishing and growing DNA barcode reference libraries for use in specimen identification. Additionally, analysis of specimen identification using public data (43.3% specimens identified) vs. non-public data (78.6% specimens identified) highlights the need to encourage researchers to make data publicly accessible. DNA barcoding surpassed morphological identification with 42.3% (public) and 66.7% (non-public) of the sampled specimens achieving a species-level identification, compared to 38.3% species-level identification by morphology. Whilst DNA barcoding was not able to identify all specimens in our dataset, its incorporation into border security programs as an adjunct to morphological identification can provide secondary lines of evidence and lower taxonomic resolution in many cases. Furthermore, with increased globalization, database records need to be clearly annotated for suspected specimen origin versus interception location.},
}
@article {pmid31525221,
year = {2019},
author = {Bezeng, BS and van der Bank, HF},
title = {DNA barcoding of southern African crustaceans reveals a mix of invasive species and potential cryptic diversity.},
journal = {PloS one},
volume = {14},
number = {9},
pages = {e0222047},
pmid = {31525221},
issn = {1932-6203},
mesh = {Africa, Southern ; Animals ; Biodiversity ; Crustacea/classification/*genetics ; DNA Barcoding, Taxonomic/methods/*standards ; *Introduced Species ; *Phylogeny ; Reference Standards ; Reproducibility of Results ; },
abstract = {Globally, crustaceans represent one of the most taxonomically diverse and economically important invertebrate group. Notwithstanding, the diversity within this group is poorly known because most crustaceans are often associated with varied habits, forms, sizes and habitats; making species identification by conventional methods extremely challenging. In addition, progress towards understanding the diversity within this group especially in southern Africa has been severely hampered by the declining number of trained taxonomists, the presence of invasive alien species, over exploitation, etc. However, the advent of molecular techniques such as "DNA barcoding and Metabarcoding" can accelerate species identification and the discovery of new species. To contribute to the growing body of knowledge on crustacean diversity, we collected data from five southern African countries and used a DNA barcoding approach to build the first DNA barcode reference library for southern African crustaceans. We tested the reliability of this DNA barcode reference library to facilitate species identification using two approaches. We recovered high efficacy of specimen identification/discrimination; supported by both barcode gap and tree-base species identification methods. In addition, we identified alien invasive species and specimens with 'no ID" in our DNA barcode reference library. The later; highlighting specimens requiring (i) further investigation and/or (ii) the potential presence of cryptic diversity or (iii) misidentifications. This unique data set although with some sampling gaps presents many opportunities for exploring the effect and extent of invasive alien species, the role of the pet trade as a pathway for crustacean species introduction into novel environments, sea food authentication, phylogenetic relationships within the larger crustacean groupings and the discovery of new species.},
}
@article {pmid31523159,
year = {2019},
author = {Marthinsen, G and Rui, S and Timdal, E},
title = {OLICH: A reference library of DNA barcodes for Nordic lichens.},
journal = {Biodiversity data journal},
volume = {7},
number = {},
pages = {e36252},
pmid = {31523159},
issn = {1314-2828},
abstract = {BACKGROUND: DNA barcodes are increasingly being used for species identification amongst the lichenised fungi. This paper presents a dataset aiming to provide an authoritative DNA barcode sequence library for a wide array of Nordic lichens.<br><br>NEW INFORMATION: We present 1324 DNA barcode sequences (nrITS) for 507 species in 175 genera and 25 orders. Thirty-eight species are new to GenBank and, for 25 additional species, ITS sequences are here presented for the first time. The dataset covers 20-21% of the Nordic lichenised species. Barcode gap analyses are given and discussed for the three genera Cladonia, Ramalina and Umbilicaria. The new combination Bryobilimbia fissuriseda (Poelt) Timdal, Marthinsen &amp; Rui is proposed for Mycobilimbia fissuriseda and Nordic material of the species, currently referred to as Pseudocyphellaria crocata and Psoroma tenue ssp. boreale, are shown to belong in Pseudocyphellaria citrina and Psoroma cinnamomeum, respectively.},
}
@article {pmid31522412,
year = {2019},
author = {Giudice, V and Fantoni, G and Biancotto, A},
title = {Fluorescent Cell Barcoding for Immunophenotyping.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2032},
number = {},
pages = {53-68},
doi = {10.1007/978-1-4939-9650-6_3},
pmid = {31522412},
issn = {1940-6029},
mesh = {Antibodies/chemistry/immunology ; Flow Cytometry/*methods ; Fluorescence ; Fluorescent Dyes/chemistry ; Humans ; Immunophenotyping/*methods ; Mass Spectrometry/*methods ; Molecular Biology/*methods ; },
abstract = {Immunophenotyping using flow cytometry highly benefits from multiplexing samples for generation of more robust data, because of reduction of antibody consumption, batch effect and technical variations. One way to multiplex is via fluorescent cell barcoding (FCB) prior to staining procedure.FCB is a high-throughput multiplexed assay using various concentrations of different fluorescent dyes. Individual samples are uniquely labeled, then mixed together, stained and analyzed as a single sample, decreasing technical variations and increasing throughput and speed of acquisition. In addition, FCB simplifies implementation of normalization using a bridge control sample.In this chapter, we illustrate the protocol for FCB and recommendations for choosing barcoding dyes and concentrations among other technical considerations.},
}
@article {pmid31521765,
year = {2020},
author = {Waki, T and Sasaki, M and Mashino, K and Iwaki, T and Nakao, M},
title = {Brachylaima lignieuhadrae n. sp. (Trematoda: Brachylaimidae) from land snails of the genus Euhadra in Japan.},
journal = {Parasitology international},
volume = {74},
number = {},
pages = {101992},
doi = {10.1016/j.parint.2019.101992},
pmid = {31521765},
issn = {1873-0329},
mesh = {Animals ; Cercaria/classification/isolation &amp; purification ; DNA Barcoding, Taxonomic ; Japan ; Metacercariae/classification/isolation &amp; purification ; Mice ; Mice, Inbred ICR ; Phylogeny ; Sequence Analysis, DNA ; Snails/*parasitology ; Trematoda/*classification/isolation &amp; purification ; Trematode Infections/parasitology/*veterinary ; },
abstract = {Land snails of the genus Euhadra (Gastropoda: Bradybaenidae) are indigenous to the Japanese Archipelago. The larvae of an unknown species, tentatively named as Brachylaima sp. B (Trematoda: Brachylaimidae), have been found from Euhadra brandtii sapporo in Hokkaido, the northernmost island of Japan. In this study, a large-scale snail survey covering a wide area of Japan was conducted to confirm the larval parasite from members of Euhadra and related genera. Sporocysts with cercariae were found only from Eu. brandtii sapporo in Hokkaido and Euhadra callizona in central Honshu at low prevalence (1.0-9.6%). The metacercariae were detected widely from 6 species of Euhadra and the related genera at high prevalence (7.1-100%). A molecular identification by DNA barcoding demonstrated almost all of the larvae to be Brachylaima sp. B. Adult worms experimentally raised from the metacercariae were morphologically most similar to Brachylaima ezohelicis in Hokkaido, but could be differentiated by the microstructure of the tegumental surface. We propose Brachylaima lignieuhadrae n. sp. for the unknown species, based on the morphology, DNA profile, host specificity, and geographic distribution. Phylogeography of the new species suggests a possibility that migratory birds serve as the definitive hosts.},
}
@article {pmid31520569,
year = {2019},
author = {Tariel, J and Longo, G and Quiros, A and Crane, NL and Tenggardjaja, K and Jackson, A and Lyon, BE and Bernardi, G},
title = {Alloparental care in the sea: Brood parasitism and adoption within and between two species of coral reef Altrichthys damselfish?.},
journal = {Molecular ecology},
volume = {28},
number = {20},
pages = {4680-4691},
doi = {10.1111/mec.15243},
pmid = {31520569},
issn = {1365-294X},
mesh = {*Adoption ; Animals ; Coral Reefs ; Fishes/classification/*physiology ; Genotype ; Nesting Behavior/*physiology ; *Parenting ; },
abstract = {The evolution of parental care opens the door for the evolution of brood parasitic strategies that allow individuals to gain the benefits of parental care without paying the costs. Here we provide the first documentation for alloparental care in coral reef fish and we discuss why these patterns may reflect conspecific and interspecific brood parasitism. Species-specific barcodes revealed the existence of low levels (3.5% of all offspring) of mixed interspecific broods, mostly juvenile Amblyglyphidodon batunai and Pomacentrus smithi damselfish in Altrichthys broods. A separate analysis of conspecific parentage based on microsatellite markers revealed that mixed parentage broods are common in both species, and the genetic patterns are consistent with two different modes of conspecific brood parasitism, although further studies are required to determine the specific mechanisms responsible for these mixed parentage broods. While many broods had offspring from multiple parasites, in many cases a given brood contained only a single foreign offspring, perhaps a consequence of the movement of lone juveniles between nests. In other cases, broods contained large numbers of putative parasitic offspring from the same parents and we propose that these are more likely to be cases where parasitic adults laid a large number of eggs in the host nest than the result of movements of large numbers of offspring from a single brood after hatching. The evidence that these genetic patterns reflect adaptive brood parasitism, as well as possible costs and benefits of parasitism to hosts and parasites, are discussed.},
}
@article {pmid31518372,
year = {2019},
author = {Arabuli, T and Negm, MW and Matsuda, T and Kitashima, Y and Abramishvili, T and Akimov, IA and Zhovnerchuk, OV and Popov, SY and Gotoh, T},
title = {Morphological identification of Amphitetranychus species (Acari: Tetranychidae) with crossbreeding, esterase zymograms and DNA barcode data.},
journal = {PloS one},
volume = {14},
number = {9},
pages = {e0221951},
pmid = {31518372},
issn = {1932-6203},
mesh = {Animals ; DNA/genetics ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Esterases/metabolism ; Female ; Hybridization, Genetic ; Male ; Phenotype ; Phylogeny ; Species Specificity ; Tetranychidae/*anatomy &amp; histology/enzymology/genetics ; },
abstract = {The genus Amphitetranychus Oudemans (Tetranychidae) consists of only three species, A. quercivorus (Ehara &amp; Gotoh), A. savenkoae (Reck) and A. viennensis (Zacher). The original description of A. savenkoae was extremely simple and had no drawing of the aedeagus; however, a subsequent study described only the aedeagus. The present study investigated all three species in detail using a combination of morphological traits, crossbreeding experiments, esterase zymograms and the mitochondrial cytochrome c oxidase subunit I (COI) gene. Morphological differences in the peritremes and male aedeagi were observed among the three species. Complete reproductive isolation was confirmed in the reciprocal crosses between the morphologically similar A. savenkoae and A. quercivorus (no female offspring were produced). Esterase zymograms differed interspecifically, but not intraspecifically (among individuals in a given species). All three species formed clearly separate clades with 100% bootstrap values in the COI tree, and A. savenkoae was more closely related to A. quercivorus than to A. viennensis, which corresponded to the morphological similarity of their aedeagi and setal counts on tarsi IV. A key to Amphitetranychus species is provided.},
}
@article {pmid31515951,
year = {2020},
author = {Bian, F and Sun, L and Cai, L and Wang, Y and Wang, Y and Zhao, Y},
title = {Colloidal Crystals from Microfluidics.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {16},
number = {9},
pages = {e1903931},
doi = {10.1002/smll.201903931},
pmid = {31515951},
issn = {1613-6829},
mesh = {*Colloids/chemical synthesis/metabolism ; Drug Delivery Systems ; *Microfluidics/trends ; *Pharmaceutical Preparations ; },
abstract = {Colloidal crystals are of great interest to researchers because of their excellent optical properties and broad applications in barcodes, sensors, displays, drug delivery, and other fields. Therefore, the preparation of high quality colloidal crystals in large quantities with high speed is worth investigating. After decades of development, microfluidics have been developed that provide new choices for many fields, especially for the generation of functional materials in microscale. Through the design of microfluidic chips, colloidal crystals can be prepared controllably with the advantages of fast speed and low cost. In this Review, research progress on colloidal crystals from microfluidics is discussed. After summarizing the classifications, the generation of colloidal crystals from microfluidics is discussed, including basic colloidal particles preparation, and their assembly inside or outside of microfluidic devices. Then, applications of the achieved colloidal crystals from microfluidics are illustrated. Finally, the future development and prospects of microfluidic-based colloidal crystals are summarized.},
}
@article {pmid31515862,
year = {2019},
author = {Després, L},
title = {One, two or more species? Mitonuclear discordance and species delimitation.},
journal = {Molecular ecology},
volume = {28},
number = {17},
pages = {3845-3847},
doi = {10.1111/mec.15211},
pmid = {31515862},
issn = {1365-294X},
mesh = {Animals ; Butterflies/genetics ; Cell Nucleus/*genetics ; Climate ; DNA, Mitochondrial/genetics ; Gene Flow ; Geography ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; *Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Species Specificity ; },
abstract = {Delimiting species boundaries is central to understand ecological and evolutionary processes, and to monitor biodiversity patterns over time and space. Yet, most of our current knowledge on animal diversity and phylogeny relies on morphological and mitochondrial (mt) DNA variation, a popular molecular marker also used as a barcode to assign samples to species. For morphologically undistinguishable sympatric species (cryptic species), the congruence of several independent markers is necessary to define separate species. Nuclear markers are becoming more accessible, and have confirmed that cryptic species are widespread in all animal phyla (Fišer, Robinson, &amp; Malard, 2018). However, striking differences between the mitochondrial and nuclear variation patterns are also commonly found within single species. Mitonuclear discordance can result from incomplete lineage sorting, sex-biased dispersal, asymmetrical introgression, natural selection or Wolbachia-mediated genetic sweeps. But more generally, the distinct mode of transmission of these two types of markers (maternal vs. biparental) is sufficient to explain their distinct sensitivity to purely demographic events such as spatial range and population size fluctuations over time. In a From the Cover manuscript in this issue of Molecular Ecology, Hijonosa et al. (2019) show that highly divergent mtDNA lineages coexist in a widespread European butterfly (Figure 1). None of the hundreds of nuclear markers analyzed was associated with mt lineages, nor was Wolbachia variation. These findings rule out the presence of cryptic species but shed light on complex demographic history of lineage divergence/fusion during the Pleistocene climatic fluctuations, and pave the way to a better integration of both mt and nuclear information in demographic models.},
}
@article {pmid31514495,
year = {2019},
author = {Hlaváček, A and Křivánková, J and Přikryl, J and Foret, F},
title = {Photon-Upconversion Barcoding with Multiple Barcode Channels: Application for Droplet Microfluidics.},
journal = {Analytical chemistry},
volume = {91},
number = {20},
pages = {12630-12635},
doi = {10.1021/acs.analchem.9b03117},
pmid = {31514495},
issn = {1520-6882},
abstract = {Barcoding facilitates high-throughput analytical methods in complex matrixes with a reduced volume of sample, reagents, time, and cost. Because of orthogonality to fluorescence, photon-upconversion barcodes attracted considerable attention in recent years. We constructed an epiluminescence detector, which, for the first time, demonstrated the reading of photon-upconversion spectra from microdroplets in a microfluidic chip with frequency up to 10 Hz. Non-negative least-squares deconvolution enabled the reading of an unprecedented number of photon-upconversion barcode channels (six) from emission spectra (excitation 980 nm, emission 430-875 nm). The standard deviation of barcode reading from microdroplets was ∼1%. Described barcoding can be, for example, used for multiparameter titrations, multiplexed biological and chemical assays, optimizations on a microfluidic platform, and preparation of barcoded concentration gradients and libraries.},
}
@article {pmid31511069,
year = {2019},
author = {Fehlings, M and Jhunjhunwala, S and Kowanetz, M and O'Gorman, WE and Hegde, PS and Sumatoh, H and Lee, BH and Nardin, A and Becht, E and Flynn, S and Ballinger, M and Newell, EW and Yadav, M},
title = {Late-differentiated effector neoantigen-specific CD8+ T cells are enriched in peripheral blood of non-small cell lung carcinoma patients responding to atezolizumab treatment.},
journal = {Journal for immunotherapy of cancer},
volume = {7},
number = {1},
pages = {249},
pmid = {31511069},
issn = {2051-1426},
mesh = {Aged ; Antibodies, Monoclonal, Humanized/pharmacology/*therapeutic use ; Antigens, Neoplasm/genetics/isolation &amp; purification/metabolism ; Antineoplastic Agents, Immunological/pharmacology/*therapeutic use ; B7-H1 Antigen/antagonists &amp; inhibitors/immunology ; CD8-Positive T-Lymphocytes/*immunology/metabolism ; Carcinoma, Non-Small-Cell Lung/blood/*drug therapy/genetics/immunology ; Drug Monitoring/methods ; Female ; Humans ; Lung Neoplasms/blood/*drug therapy/genetics/immunology ; Male ; Middle Aged ; Mutation ; RNA-Seq ; Exome Sequencing ; },
abstract = {BACKGROUND: There is strong evidence that immunotherapy-mediated tumor rejection can be driven by tumor-specific CD8+ T cells reinvigorated to recognize neoantigens derived from tumor somatic mutations. Thus, the frequencies or characteristics of tumor-reactive, mutation-specific CD8+ T cells could be used as biomarkers of an anti-tumor response. However, such neoantigen-specific T cells are difficult to reliably identify due to their low frequency in peripheral blood and wide range of potential epitope specificities.<br><br>METHODS: Peripheral blood mononuclear cells (PBMC) from 14 non-small cell lung cancer (NSCLC) patients were collected pre- and post-treatment with the anti-PD-L1 antibody atezolizumab. Using whole exome sequencing and RNA sequencing we identified tumor neoantigens that are predicted to bind to major histocompatibility complex class I (MHC-I) and utilized mass cytometry, together with cellular 'barcoding', to profile immune cells from patients with objective response to therapy (n&#xa0;=&#x2009;8) and those with progressive disease (n&#xa0;=&#x2009;6). In parallel, a highly-multiplexed combinatorial tetramer staining was used to screen antigen-specific CD8+ T cells in peripheral blood for 782 candidate tumor neoantigens and 71 known viral-derived control peptide epitopes across all patient samples.<br><br>RESULTS: No significant treatment- or response associated phenotypic difference were measured in bulk CD8+ T cells. Multiplexed peptide-MHC multimer staining detected 20 different neoantigen-specific T cell populations, as well as T cells specific for viral control antigens. Not only were neoantigen-specific T cells more frequently detected in responding patients, their phenotypes were also almost entirely distinct. Neoantigen-specific T cells from responder patients typically showed a differentiated effector phenotype, most like Cytomegalovirus (CMV) and some types of Epstein-Barr virus (EBV)-specific CD8+ T cells. In contrast, more memory-like phenotypic profiles were observed for neoantigen-specific CD8+ T cells from patients with progressive disease.<br><br>CONCLUSION: This study demonstrates that neoantigen-specific T cells can be detected in peripheral blood in non-small cell lung cancer (NSCLC) patients during anti-PD-L1 therapy. Patients with an objective response had an enrichment of neoantigen-reactive T cells and these cells showed a phenotype that differed from patients without a response. These findings suggest the ex vivo identification, characterization, and longitudinal follow-up of rare tumor-specific differentiated effector neoantigen-specific T cells may be useful in predicting response to checkpoint blockade.<br><br>TRIAL REGISTRATION: POPLAR trial NCT01903993 .},
}
@article {pmid31510681,
year = {2019},
author = {Yang, X and Saito, Y and Rao, A and Kim, HJ and Singh, P and Scott, E and Larson, M and Pan, W and Desai, M and Hubbell, E},
title = {Alignment-free filtering for cfNA fusion fragments.},
journal = {Bioinformatics (Oxford, England)},
volume = {35},
number = {14},
pages = {i225-i232},
pmid = {31510681},
issn = {1367-4811},
mesh = {Alleles ; Cell-Free Nucleic Acids ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, RNA ; *Software ; },
abstract = {MOTIVATION: Cell-free nucleic acid (cfNA) sequencing data require improvements to existing fusion detection methods along multiple axes: high depth of sequencing, low allele fractions, short fragment lengths and specialized barcodes, such as unique molecular identifiers.<br><br>RESULTS: AF4 was developed to address these challenges. It uses a novel alignment-free kmer-based method to detect candidate fusion fragments with high sensitivity and orders of magnitude faster than existing tools. Candidate fragments are then filtered using a max-cover criterion that significantly reduces spurious matches while retaining authentic fusion fragments. This efficient first stage reduces the data sufficiently that commonly used criteria can process the remaining information, or sophisticated filtering policies that may not scale to the raw reads can be used. AF4 provides both targeted and de novo fusion detection modes. We demonstrate both modes in benchmark simulated and real RNA-seq data as well as clinical and cell-line cfNA data.<br><br>AF4 is open sourced, licensed under Apache License 2.0, and is available at: https://github.com/grailbio/bio/tree/master/fusion.},
}
@article {pmid31510649,
year = {2019},
author = {Sarkar, H and Srivastava, A and Patro, R},
title = {Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level.},
journal = {Bioinformatics (Oxford, England)},
volume = {35},
number = {14},
pages = {i136-i144},
pmid = {31510649},
issn = {1367-4811},
mesh = {Gene Expression Profiling ; *High-Throughput Nucleotide Sequencing ; Sequence Analysis, RNA ; *Single-Cell Analysis ; Software ; },
abstract = {SUMMARY: With the advancements of high-throughput single-cell RNA-sequencing protocols, there has been a rapid increase in the tools available to perform an array of analyses on the gene expression data that results from such studies. For example, there exist methods for pseudo-time series analysis, differential cell usage, cell-type detection RNA-velocity in single cells, etc. Most analysis pipelines validate their results using known marker genes (which are not widely available for all types of analysis) and by using simulated data from gene-count-level simulators. Typically, the impact of using different read-alignment or unique molecular identifier (UMI) deduplication methods has not been widely explored. Assessments based on simulation tend to start at the level of assuming a simulated count matrix, ignoring the effect that different approaches for resolving UMI counts from the raw read data may produce. Here, we present minnow, a comprehensive sequence-level droplet-based single-cell RNA-sequencing (dscRNA-seq) experiment simulation framework. Minnow accounts for important sequence-level characteristics of experimental scRNA-seq datasets and models effects such as polymerase chain reaction amplification, cellular barcodes (CB) and UMI selection and sequence fragmentation and sequencing. It also closely matches the gene-level ambiguity characteristics that are observed in real scRNA-seq experiments. Using minnow, we explore the performance of some common processing pipelines to produce gene-by-cell count matrices from droplet-bases scRNA-seq data, demonstrate the effect that realistic levels of gene-level sequence ambiguity can have on accurate quantification and show a typical use-case of minnow in assessing the output generated by different quantification pipelines on the simulated experiment.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid31510642,
year = {2019},
author = {Tolstoganov, I and Bankevich, A and Chen, Z and Pevzner, PA},
title = {cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs.},
journal = {Bioinformatics (Oxford, England)},
volume = {35},
number = {14},
pages = {i61-i70},
pmid = {31510642},
issn = {1367-4811},
mesh = {*Algorithms ; *Cloud Computing ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Sequence Analysis, DNA ; *Software ; },
abstract = {MOTIVATION: The recently developed barcoding-based synthetic long read (SLR) technologies have already found many applications in genome assembly and analysis. However, although some new barcoding protocols are emerging and the range of SLR applications is being expanded, the existing SLR assemblers are optimized for a narrow range of parameters and are not easily extendable to new barcoding technologies and new applications such as metagenomics or hybrid assembly.<br><br>RESULTS: We describe the algorithmic challenge of the SLR assembly and present a cloudSPAdes algorithm for SLR assembly that is based on analyzing the de Bruijn graph of SLRs. We benchmarked cloudSPAdes across various barcoding technologies/applications and demonstrated that it improves on the state-of-the-art SLR assemblers in accuracy and speed.<br><br>Source code and installation manual for cloudSPAdes are available at https://github.com/ablab/spades/releases/tag/cloudspades-paper.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid31509746,
year = {2019},
author = {Tang, YJ and Huang, J and Tsushima, H and Ban, GI and Zhang, H and Oristian, KM and Puviindran, V and Williams, N and Ding, X and Ou, J and Jung, SH and Lee, CL and Jiao, Y and Chen, BJ and Kirsch, DG and Alman, BA},
title = {Tracing Tumor Evolution in Sarcoma Reveals Clonal Origin of Advanced Metastasis.},
journal = {Cell reports},
volume = {28},
number = {11},
pages = {2837-2850.e5},
pmid = {31509746},
issn = {2211-1247},
support = {R01 CA183811/CA/NCI NIH HHS/United States ; },
mesh = {Aldehyde Dehydrogenase 1 Family/genetics/metabolism ; Animals ; Cell Lineage ; Clonal Evolution/*genetics ; Clone Cells/cytology/*metabolism ; GPI-Linked Proteins/genetics/metabolism ; Luminescent Proteins ; Mice ; Mice, Nude ; Neoplasm Recurrence, Local/genetics/*metabolism ; RNA-Seq ; Retinal Dehydrogenase/genetics/metabolism ; Sarcoma/genetics/*metabolism/pathology/*secondary ; Transcriptome/genetics ; ras Proteins/genetics/metabolism ; },
abstract = {Cellular heterogeneity is frequently observed in cancer, but the biological significance of heterogeneous tumor clones is not well defined. Using multicolor reporters and CRISPR-Cas9 barcoding, we trace clonal dynamics in a mouse model of sarcoma. We show that primary tumor growth is associated with a reduction in clonal heterogeneity. Local recurrence of tumors following surgery or radiation therapy is driven by multiple clones. In contrast, advanced metastasis to the lungs is driven by clonal selection of a single metastatic clone (MC). Using RNA sequencing (RNA-seq) and in vivo assays, we identify candidate suppressors of metastasis, namely, Rasd1, Reck, and Aldh1a2. These genes are downregulated in MCs of the primary tumors prior to the formation of metastases. Overexpression of these suppressors of metastasis impair the ability of sarcoma cells to colonize the lungs. Overall, this study reveals clonal dynamics during each step of tumor progression, from initiation to growth, recurrence, and distant metastasis.},
}
@article {pmid31507097,
year = {2020},
author = {Galen, SC and Borner, J and Williamson, JL and Witt, CC and Perkins, SL},
title = {Metatranscriptomics yields new genomic resources and sensitive detection of infections for diverse blood parasites.},
journal = {Molecular ecology resources},
volume = {20},
number = {1},
pages = {14-28},
pmid = {31507097},
issn = {1755-0998},
support = {//American Museum of Natural History/ ; //New Mexico Ornithological Society/ ; R03 AI117223/AI/NIAID NIH HHS/United States ; //Society of Systematic Biologists/ ; //Richard Gilder Graduate Scool/ ; 1R03AI117223-01A1/NH/NIH HHS/United States ; 1811806//Division of Biological Infrastructure/ ; //Explorers Club/ ; //Federal Bureau of Land Management Rio Puerco Field Office/ ; },
mesh = {Animals ; Bird Diseases/blood/*parasitology ; Blood/*parasitology ; Genomics/*methods ; Haemosporida/classification/genetics/*isolation &amp; purification ; Phylogeny ; Protozoan Infections, Animal/blood/*parasitology ; Songbirds/blood/parasitology ; Transcriptome ; },
abstract = {Metatranscriptomics is a powerful method for studying the composition and function of complex microbial communities. The application of metatranscriptomics to multispecies parasite infections is of particular interest, as research on parasite evolution and diversification has been hampered by technical challenges to genome-scale DNA sequencing. In particular, blood parasites of vertebrates are abundant and diverse although they often occur at low infection intensities and exist as multispecies infections, rendering the isolation of genomic sequence data challenging. Here, we use birds and their diverse haemosporidian parasites to illustrate the potential for metatranscriptome sequencing to generate large quantities of genome-wide sequence data from multiple blood parasite species simultaneously. We used RNA-sequencing of 24 blood samples from songbirds in North America to show that metatranscriptomes can yield large proportions of haemosporidian protein-coding gene repertoires even when infections are of low intensity (<0.1% red blood cells infected) and consist of multiple parasite taxa. By bioinformatically separating host and parasite transcripts and assigning them to the haemosporidian genus of origin, we found that transcriptomes detected ~23% more total parasite infections across all samples than were identified using microscopy and DNA barcoding. For single-species infections, we obtained data for >1,300 loci from samples with as low as 0.03% parasitaemia, with the number of loci increasing with infection intensity. In total, we provide data for 1,502 single-copy orthologous loci from a phylogenetically diverse set of 33 haemosporidian mitochondrial lineages. The metatranscriptomic approach described here has the potential to accelerate ecological and evolutionary research on haemosporidians and other diverse parasites.},
}
@article {pmid31506037,
year = {2019},
author = {Mitsi, K and Arroyo, AS and Ruiz-Trillo, I},
title = {A global metabarcoding analysis expands molecular diversity of Platyhelminthes and reveals novel early-branching clades.},
journal = {Biology letters},
volume = {15},
number = {9},
pages = {20190182},
pmid = {31506037},
issn = {1744-957X},
mesh = {Animals ; Biodiversity ; Biological Evolution ; Fresh Water ; Phylogeny ; *Platyhelminths ; },
abstract = {Understanding biological diversity is crucial for ecological and evolutionary studies. Even though a great part of animal diversity has already been documented, both morphological surveys and metabarcoding analyses have previously shown that some animal groups, such as Platyhelminthes, may harbour hidden diversity. To better understand the molecular diversity of Platyhelminthes, one of the most diverse and biomedically important animal phyla, we here combined data from six marine and two freshwater metabarcoding expeditions that cover a broad variety of aquatic habitats and analysed the data by phylogenetic placement. Our results show that a great part of the hidden diversity is located in early-branching clades such as Catenulida and Macrostomorpha, as well as in late-diverging clades such as Proseriata and Rhabdocoela. We also report the first freshwater record of Gnosonesimida, a group previously thought to be exclusively marine. Finally, we identified two putative novel freshwater Platyhelminthes clades that branch between well-defined orders of the phylum. Thus, our analyses of several environmental datasets confirm that a large part of the diversity of Platyhelminthes remains undiscovered, point to groups with more potential novel species and identify freshwater environments as potential reservoirs for novel species of flatworms.},
}
@article {pmid31505790,
year = {2019},
author = {Singh, G and Kukwa, M and Dal Grande, F and Łubek, A and Otte, J and Schmitt, I},
title = {A Glimpse into Genetic Diversity and Symbiont Interaction Patterns in Lichen Communities from Areas with Different Disturbance Histories in Białowieża Forest, Poland.},
journal = {Microorganisms},
volume = {7},
number = {9},
pages = {},
pmid = {31505790},
issn = {2076-2607},
support = {NA//Senckenberg Biodiversit&#xe4;t und Klima- Forschungszentrum/ ; NA//European Commission SYNTHESYS/ ; },
abstract = {Anthropogenic disturbances can have strong impacts on lichen communities, as well as on individual species of lichenized fungi. Traditionally, lichen monitoring studies are based on the presence and abundance of fungal morphospecies. However, the photobionts, as well photobiont mycobiont interactions also contribute to the structure, composition, and resilience of lichen communities. Here we assess the genetic diversity and interaction patterns of algal and fungal partners in lichen communities along an anthropogenic disturbance gradient in Białowieża Forest (Poland). We sampled a total of 224 lichen thalli in a protected, a managed, and a disturbed area of the forest, and sequenced internal transcribed spacer (ITS) ribosomal DNA (rDNA) of both, fungal and algal partners. Sequence clustering using a 97% similarity threshold resulted in 46 fungal and 23 green algal operational taxonomic units (OTUs). Most of the recovered photobiont OTUs (14 out of 23) had no similar hit in the NCBI-BLAST search, suggesting that even in well studied regions, such as central Europe, a lot of photobiont diversity is yet undiscovered. If a mycobiont was present at more than one site, it was typically associated with the same photobiont OTU(s). Generalist species, i.e., taxa that associate with multiple symbiont partners, occurred in all three disturbance regimes, suggesting that such taxa have few limitations in colonizing or persisting in disturbed areas. Trebouxia jamesii associated with 53% of the fungal OTUs, and was generally the most common photobiont OTU in all areas, implying that lichens that associate with this symbiont are not limited by the availability of compatible photobionts in Central European forests, regardless of land use intensity.},
}
@article {pmid31502567,
year = {2019},
author = {Nawkarkar, P and Singh, AK and Abdin, MZ and Kumar, S},
title = {Life cycle assessment of Chlorella species producing biodiesel and remediating wastewater.},
journal = {Journal of biosciences},
volume = {44},
number = {4},
pages = {},
pmid = {31502567},
issn = {0973-7138},
mesh = {*Biodegradation, Environmental ; Biofuels ; Biomass ; Chlorella/*genetics/growth &amp; development/metabolism ; Culture Media ; *Environmental Restoration and Remediation ; Fatty Acids/chemistry/genetics ; Humans ; Life Cycle Stages/*genetics ; Lipids/chemistry/genetics ; Microalgae ; Nitrogen/metabolism ; Wastewater/chemistry ; },
abstract = {Constantly rising energy demands, finite fossil fuel reserves and deteriorating environmental conditions have invoked worldwide interest to explore the sustainable sources of renewable biofuels. Locally adapted photosynthetic oleaginous microalgae with rapid growth on variable temperatures could be an ideal way for bioremediating the wastewater (WW) while producing the feedstock for biodiesel. To test this notion, an unknown strain was isolated from a sewage fed lake (Neela-Hauz). It was discerned as Chlorella sorokiniana-I using the 16S rDNA and 18S rDNA barcodes. The culture conditions such as pH, illumination, different temperature ranges and growth medium were cohesively optimized prior to the assessment of C. sorokiniana-I's efficacy to remediate the WWand biodiesel production. The strain has thrived well up to 40°C when continuously grown for 15 days. The highest lipid accumulation and biomass productivity were recorded in 100% WW. Fatty acid methyl ester (FAME) content was observed to be more than twice in WW (47%), compared to control synthetic media, TAP (20%) and BG11 (10%), which indicate the importance of this new isolate for producing economically viable biodiesel. Moreover, it is highly efficient in removing the total nitrogen (77%), total phosphorous (81%), iron (67%) and calcium (42%) from the WW. The quality of WW was considerably improved by reducing the overall chemical oxygen demand (48%), biological oxygen demand (47%) and alkalinity (15%). Thus, C. sorokiniana-I could be an ideal alga for the tropical countries in the remediation of WW while producing feedstock for biodiesel in a cost-effective manner.},
}
@article {pmid31502426,
year = {2019},
author = {Poyarkov, NA and Geissler, P and Gorin, VA and Dunayev, EA and Hartmann, T and Suwannapoom, C},
title = {Counting stripes: revision of the Lipinia vittigera complex (Reptilia, Squamata, Scincidae) with description of two new species from Indochina.},
journal = {Zoological research},
volume = {40},
number = {5},
pages = {358-393},
pmid = {31502426},
issn = {2095-8137},
support = {19-14-00050//the Russian Science Foundation/ ; UoE62005//University of Phayao/ ; },
mesh = {Animal Distribution ; Animals ; Indochina ; Lizards/*genetics/*physiology ; *Pigmentation ; Species Specificity ; },
abstract = {We provide an integrative taxonomic analysis of the Lipinia vittigera species complex from mainland Southeast Asia. Based on examination of external morphology, color pattern, and 681 base pairs of the cytochrome oxidase subunit I (COI) mitochondrial gene, we demonstrate the presence of four morphologically distinct lineages of Lipinia in Vietnam, Cambodia, Thailand, and Malaysia, showing a sequence divergence ranging 15.5%-20.4%. All discovered lineages are discretely diagnosable from one another by a combination of scalation traits and color patterns. A review of the published distribution data and a re-examination of available type material revealed the following results:(1) distribution of L. vittigera (Boulenger, 1894) sensu stricto is restricted to Sundaland and the Thai-Malay Peninsula south of the Isthmus of Kra; (2) L. microcercus (Boettger, 1901) stat. nov. is elevated to full species rank; the species has a wide distribution from central and southern Vietnam across Cambodia to eastern Thailand; we regard Lygosoma vittigerum kronfanum Smith, 1922 and Leiolopisma pranensis Cochran, 1930 as its junior synonyms; (3) Lipinia trivittata sp. nov. occurs in hilly areas of southern Vietnam, Cambodia, and eastern Thailand; and (4) Lipinia vassilievi sp. nov. is currently known only from a narrow area along the Vietnamese-Cambodian border in the foothills of the central Annamite Mountain Range. We further provide an identification key for Lipinia occurring in mainland Southeast Asia.},
}
@article {pmid31502169,
year = {2020},
author = {Beechem, JM},
title = {High-Plex Spatially Resolved RNA and Protein Detection Using Digital Spatial Profiling: A Technology Designed for Immuno-oncology Biomarker Discovery and Translational Research.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2055},
number = {},
pages = {563-583},
doi = {10.1007/978-1-4939-9773-2_25},
pmid = {31502169},
issn = {1940-6029},
mesh = {Biomarkers, Tumor/*genetics/*metabolism ; Gene Expression Profiling ; Humans ; Neoplasms/genetics/*immunology ; Paraffin Embedding ; Proteomics ; Software ; Spatial Analysis ; Tissue Fixation ; Translational Research, Biomedical ; Tumor Microenvironment ; },
abstract = {Digital spatial profiling (DSP) is a nondestructive method for high-plex spatial profiling of proteins and RNA from a wide variety of sample types, including formalin-fixed, paraffin-embedded (FFPE) tissue sections. This method uses small photocleavable oligonucleotide "barcodes" (PC-oligos) covalently attached to in-situ affinity reagents (antibodies and RNA-probes) to provide unlimited multiplexing capability. The photocleavage light is projected onto the tissue slice using two-digital micromirror devices (DMD), containing one-million semiconductor-based micromirrors allowing complete flexibility in the pattern of light utilized for high-plex digital profiling of the tissue. These spatial light-patterns can be automatically configured to profile (1) "tumor-only" cells plus "tumor-microenvironment-only" cells; (2) unique cell types and rare cell features (e.g., macrophages, CD8, CD3, CD45, PD-L1 on macrophages, PD-L1 on tumors, etc.); (3) spatial gradients around cell-features or tumor features (e.g., excluded boundaries); (4) hypothesis-free spatial grids; (5) simple hand-selected geometric areas (e.g., free-hand software-based "drawing" on tissue regions); and (6) or any combination of the above modalities. These DMDs can automatically configure themselves to "align" to the biology presented by each individual tissue section. Advanced validated high-plex panels of proteins (~100-plex) and RNA (up to 20,000-plex) specifically designed for immuno-oncology (IO) have been developed. Immuno-oncology clinical trial samples examined using DSP have already provided key insights into the mechanism of action of combination therapy in melanoma, appearing recently in back-to-back articles published in Nature Medicine. DSP has been developed with knowledge of key immuno-oncology terms (tumor, tumor microenvironment, stroma, etc.) and prevalidated high-plex panels of affinity markers (antibodies and in situ RNA probes) and has the potential to bring the full power of high-plex molecular profiling to spatially resolved studies.},
}
@article {pmid31502160,
year = {2020},
author = {Sahaf, B and Rahman, A and Maecker, HT and Bendall, SC},
title = {High-Parameter Immune Profiling with CyTOF.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2055},
number = {},
pages = {351-368},
pmid = {31502160},
issn = {1940-6029},
support = {UH3 CA246633/CA/NCI NIH HHS/United States ; U24 CA224309/CA/NCI NIH HHS/United States ; R01 AG056287/AG/NIA NIH HHS/United States ; R01 AG057915/AG/NIA NIH HHS/United States ; R00 GM104148/GM/NIGMS NIH HHS/United States ; DP2 EB024246/EB/NIBIB NIH HHS/United States ; },
mesh = {Antibodies/*immunology ; Blood Specimen Collection/instrumentation/*methods ; Cell Separation/*standards ; Flow Cytometry ; Freeze Drying ; Guidelines as Topic ; Humans ; Leukocytes, Mononuclear ; Mass Spectrometry ; Neoplasms/*immunology ; Proteomics ; Single-Cell Analysis ; },
abstract = {Mass cytometry, or CyTOF, is a useful technology for high-parameter single-cell phenotyping, especially from suspension cells such as blood or PBMC. It is particularly appealing to monitor the systemic immune changes that could accompany cancer immunotherapy. Here we present a reference panel for identification of all major immune cell populations, with flexibility for addition of trial-specific markers. We also describe best-practice measures for minimizing and tracking batch variability. These include: sample barcoding, use of spiked-in reference cells, and lyophilization of the antibody cocktail. Our protocol assumes the use of cryopreserved PBMC, both for convenience of batching samples and for maximum comparability across patients and time points. Finally, we show an option for automated analysis using the Astrolabe platform (Astrolabe Diagnostics, Inc.).},
}
@article {pmid31501547,
year = {2019},
author = {Vickovic, S and Eraslan, G and Salmén, F and Klughammer, J and Stenbeck, L and Schapiro, D and Äijö, T and Bonneau, R and Bergenstråhle, L and Navarro, JF and Gould, J and Griffin, GK and Borg, &#xc5; and Ronaghi, M and Frisén, J and Lundeberg, J and Regev, A and Ståhl, PL},
title = {High-definition spatial transcriptomics for in situ tissue profiling.},
journal = {Nature methods},
volume = {16},
number = {10},
pages = {987-990},
pmid = {31501547},
issn = {1548-7105},
support = {/HHMI/Howard Hughes Medical Institute/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; RM1 HG006193/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; Breast Neoplasms/pathology ; Female ; *Gene Expression Profiling ; Humans ; Mice ; Olfactory Bulb/cytology ; Sequence Analysis, RNA/methods ; Single-Cell Analysis/methods ; Tissue Array Analysis ; *Transcriptome ; },
abstract = {Spatial and molecular characteristics determine tissue function, yet high-resolution methods to capture both concurrently are lacking. Here, we developed high-definition spatial transcriptomics, which captures RNA from histological tissue sections on a dense, spatially barcoded bead array. Each experiment recovers several hundred thousand transcript-coupled spatial barcodes at 2-μm resolution, as demonstrated in mouse brain and primary breast cancer. This opens the way to high-resolution spatial analysis of cells and tissues.},
}
@article {pmid31500338,
year = {2019},
author = {Zhong, Y and Wang, H and Wei, Q and Cao, R and Zhang, H and He, Y and Wang, L},
title = {Combining DNA Barcoding and HPLC Fingerprints to Trace Species of an Important Traditional Chinese Medicine Fritillariae Bulbus.},
journal = {Molecules (Basel, Switzerland)},
volume = {24},
number = {18},
pages = {},
pmid = {31500338},
issn = {1420-3049},
support = {81603221//the National Natural Science Foundation of China/ ; },
mesh = {Chromatography, High Pressure Liquid ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; Drugs, Chinese Herbal/*chemistry ; Fritillaria/chemistry/*classification/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Fritillariae Bulbus is a precious Chinese herbal medicine that is grown at high elevation and used to relieve coughs, remove phlegm, and nourish the lungs. Historically, Fritillariae Bulbus has been divided into two odourless crude drugs: Fritillariae Cirrhosae Bulbus and Fritillariae Thunbergii Bulbus. However, now the Chinese Pharmacopoeia has described five Fritillariae Bulbus-the new additions include Fritillariae Pallidiflorae Bulbus, Fritillariae Ussuriensis Bulbus, and Fritillariae Hupehensis Bulbus. Because the morphology of dried Fritillariae Bulbus is similar, it is difficult to accurately identify the different types of Fritillariae Bulbus. In the current study, we develop a method combining DNA barcoding and high-performance liquid chromatography (HPLC) to help distinguish Fritillariae Cirrhosae Bulbus from other Fritillariae Bulbus and guarantee species traceability of the five types of Fritillariae Bulbus. We report on the validation of an integrated analysis method for plant species identification using DNA barcoding that is based on genetic distance, identification efficiency, inter- and intra-specific variation, calculated nearest distance, neighbour-joining tree and barcoding gap. Our results show that the DNA barcoding data successfully identified the five Fritillariae Bulbus by internal transcribed spacer region (ITS) and ITS2, with the ability to distinguish the species origin of these Fritillariae Bulbus. ITS2 can serve as a potentially useful DNA barcode for the Fritillaria species. Additionally, the effective chemical constituents are identified by HPLC combined with a chemical identification method to classify Fritillaria. The HPLC fingerprint data and HCA (hierarchical clustering analysis) show that Fritillariae Cirrhosae Bulbus is clearly different from Fritillariae Thunbergii Bulbus and Fritillariae Hupehensis Bulbus, but there is no difference between Fritillariae Cirrhosae Bulbus, Fritillariae Ussuriensis Bulbus, and Fritillariae Pallidiflorae Bulbus. These results show that DNA barcoding and HPLC fingerprinting can discriminate between the five Fritillariae Bulbus types and trace species to identify related species that are genetically similar.},
}
@article {pmid31499388,
year = {2019},
author = {Mohajeri, N and Imani, M and Mostafavi, E and Akbarzadeh, A and Sadighi, A and Zarghami, N},
title = {An update on advances in new developing DNA conjugation diagnostics and ultra-resolution imaging technologies: Possible applications in medical and biotechnological utilities.},
journal = {Biosensors &amp; bioelectronics},
volume = {144},
number = {},
pages = {111633},
doi = {10.1016/j.bios.2019.111633},
pmid = {31499388},
issn = {1873-4235},
mesh = {Biomedical Research/trends ; *Biosensing Techniques ; DNA/*chemistry ; Humans ; Molecular Imaging/*methods ; Nanostructures/chemistry ; *Nanotechnology ; },
abstract = {DNA molecule engineering has become an attractive discipline in various research scopes. The profound influence of selective and sensitive sensing of DNA molecules in disease diagnosis and molecular imaging is established. In this perspective, we try to shed light on the state-of-the-art technology of DNA bioconjugation assays in DNA biosensor, DNA barcode, DNA nanostructures, and DNA ultra-resolution fluorescence imaging. Non-invasive, simple, and swift biotechniques benefit molecular diagnosis, evaluation of disease stages, and also play a central role in fundamental researches. We discuss the limitations of traditional procedures and the eminence impacts of the advanced methods with clinical applications in timely detection and management of diseases like cancer, genetic disorders, and recognition of microbial pathogens. The predictable and programmable DNA strands have paved the way for cellular and molecular imaging with the ability of single-molecule switching nanoscopy. Consequently, the DNA conjugation tool as an identification paradigm of biological agents in interaction with bio-spesific components is at the heart of biological processes.},
}
@article {pmid31497840,
year = {2019},
author = {Samarasimhareddy, M and Mayer, D and Metanis, N and Veprintsev, D and Hurevich, M and Friedler, A},
title = {A targeted approach for the synthesis of multi-phosphorylated peptides: a tool for studying the role of phosphorylation patterns in proteins.},
journal = {Organic &amp; biomolecular chemistry},
volume = {17},
number = {42},
pages = {9284-9290},
doi = {10.1039/c9ob01874c},
pmid = {31497840},
issn = {1477-0539},
mesh = {Amino Acid Sequence ; Phosphorylation ; Protein Conformation ; Proteins/*chemical synthesis/*metabolism ; Rhodopsin/chemistry ; },
abstract = {Protein phosphorylation barcodes, clusters of several phosphorylation sites within a short unfolded region, control many cellular processes. Existing biochemical methods used to study the roles of these barcodes suffer from low selectivity and provide only qualitative data. Chemically synthesized multiphosphopeptide libraries are selective and specific, but their synthesis is extremely difficult using the current peptide synthesis methods. Here we describe a new microwave assisted approach for synthesizing a library of multiphosphopeptides, using the C-terminus of rhodopsin as a proof of concept. Our approach utilizes multiple protocols for synthesizing libraries of multiphosphopeptides instead of the inefficient single protocol methods currently used. Using our approach we demonstrated the synthesis with up to seven phosphorylated amino acids, sometimes next to each other, an accomplishment that was impractical before. Synthesizing the Rhodopsin derived multiphosphopeptide library enabled dissecting the precise phosphorylation barcode required for the recruitment, activation and modulation of the conformation of Arrestin. Since phosphorylation barcodes modulate the activity of hundreds of GPCRs, synthesizing libraries of multiphosphopeptides is the method of choice for studying their molecular mechanisms of action. Our approach provides an invaluable tool for evaluating how protein phosphorylation barcodes regulate their activity.},
}
@article {pmid31497670,
year = {2019},
author = {Avigliano, E and Rosso, JJ and Lijtmaer, D and Ondarza, P and Piacentini, L and Izquierdo, M and Cirigliano, A and Romano, G and Nuñez Bustos, E and Porta, A and Mabragaña, E and Grassi, E and Palermo, J and Bukowski, B and Tubaro, P and Schenone, N},
title = {Biodiversity and threats in non-protected areas: A multidisciplinary and multi-taxa approach focused on the Atlantic Forest.},
journal = {Heliyon},
volume = {5},
number = {8},
pages = {e02292},
pmid = {31497670},
issn = {2405-8440},
abstract = {Along many decades, protected environments were targeted by the scientific community for ecological research and for the collection of scientific information related to environmental aspects and biodiversity. However, most of the territory in hotspot regions with weak or even non legal protection has been left aside. These non-protected areas (NPA) could host high biodiversity values. This paper addresses how scientific effort on a NPA (CIAR) of 700 ha from the Atlantic Rain Forest, generates new information and tools for large-scale environmental and biodiversity management in NPAs. Information published during the last decade was summarized and complemented with subsequent novel data about biodiversity (new species, first records, DNA and chemical analyses, etc.). The results showed: 1 new genus (arachnid), 6 new species and several putative new species (fish and arthropod), 6 vulnerable species (bird and mammal) and 36 first records for Argentina (fish, arthropod, platyhelminth and fungi). When compared with protected natural areas of the same biome, the CIAR showed highly valuable aspects for fauna and environment conservation, positioning this NPA as a worldwide hotspot for some taxa. Indeed, when compared to international hotspots in a coordinated Malaise trap program, the CIAR showed 8,651 different barcode index numbers (∼species) of arthropods, 80% of which had not been previously barcoded. Molecules like Inoscavin A, with antifungal activity against phytopathogens, was isolated for the first time in Phellinus merrillii fungi. The study of major threats derived from anthropic activities measured 20 trace elements, 18 pesticides (i.e. endosulfans, chlorpyrifos, DDTs, HCHs) and 27 pharmaceuticals and drugs (i.e. benzoylecgonine and norfluoxetine) in different biotic and abiotic matrices (water, sediment, fish and air biomonitors). This integrated data analysis shows that biodiversity research in NPA is being undervalued and how multidisciplinary and multi-taxa surveys creates a new arena for research and a pathway towards sustainable development in emerging countries with biodiversity hotspots.},
}
@article {pmid31496886,
year = {2019},
author = {Darschnik, S and Leese, F and Weiss, M and Weigand, H},
title = {When barcoding fails: development of diagnostic nuclear markers for the sibling caddisfly species Sericostoma personatum (Spence in Kirby &amp; Spence, 1826) and Sericostoma flavicorne Schneider, 1845.},
journal = {ZooKeys},
volume = {872},
number = {},
pages = {57-68},
pmid = {31496886},
issn = {1313-2989},
abstract = {The larval stages of the central European sibling caddisfly species Sericostoma personatum (Spence in Kirby and Spence, 1826) and S. flavicorne Schneider, 1845 are morphologically similar and can only be distinguished by differences in coloration in late larval instars. Identification using the mitochondrial barcoding gene, i.e., the Cytochrome c Oxidase 1, is impossible, as both species share the same highly differentiated haplotypes due to introgression. Nuclear gene markers obtained through double digest restriction site associate sequencing (ddRAD seq), however, can reliably distinguish both species, yet the method is expensive as well as time-consuming and therefore not practicable for species determination. To facilitate accurate species identification without sequencing genome-wide markers, we developed nine diagnostic nuclear RFLP markers based on ddRAD seq data. The markers were successfully tested on geographically distinct populations of the two Sericostoma species in western Germany, on known hybrids, and on another sericostomatid caddisfly species, Oecismus monedula (Hagen, 1859) that sometimes shares the habitat and can be morphologically confounded with Sericostoma. We describe a simple and fast protocol for reliable species identification of S. personatum and S. flavicorne independent of the life cycle stage of the specimens.},
}
@article {pmid31494779,
year = {2019},
author = {Vafaizadeh, V and Peuhu, E and Mikkola, ML and Khaled, WT and Bentires-Alj, M and Koledova, Z},
title = {The Eleventh ENBDC Workshop: Advances in Technology Help to Unveil Mechanisms of Mammary Gland Development and Cancerogenesis.},
journal = {Journal of mammary gland biology and neoplasia},
volume = {24},
number = {3},
pages = {201-206},
pmid = {31494779},
issn = {1573-7039},
support = {17348/CRUK_/Cancer Research UK/United Kingdom ; 25850/CRUK_/Cancer Research UK/United Kingdom ; NC/N002369/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; },
mesh = {Animals ; Breast/metabolism/*pathology ; Breast Neoplasms/genetics/metabolism/*pathology ; Carcinogenesis/genetics/metabolism/*pathology ; Female ; Genomics ; Humans ; Proteomics ; Signal Transduction ; Societies, Scientific ; *Tumor Microenvironment ; },
abstract = {The eleventh annual workshop of the European Network for Breast Development and Cancer, Methods in mammary gland biology and breast cancer, took place on the 16th to 18th of May 2019 in Weggis, Switzerland. The main topics of the meeting were high resolution genomics and proteomics for the study of mammary gland development and cancer, breast cancer signaling, tumor microenvironment, preclinical models of breast cancer, and tissue morphogenesis. Exciting novel findings in, or highly relevant to, mammary gland biology and breast cancer field were presented, with insights into the methods used to obtain them. Among others, the discussed methods included single-cell RNA sequencing, genetic barcoding, lineage tracing, spatial transcriptomics, optogenetics, genetic mouse models and organoids.},
}
@article {pmid31494231,
year = {2020},
author = {Belderbos, ME and Jacobs, S and Koster, TK and Ausema, A and Weersing, E and Zwart, E and de Haan, G and Bystrykh, LV},
title = {Donor-to-Donor Heterogeneity in the Clonal Dynamics of Transplanted Human Cord Blood Stem Cells in Murine Xenografts.},
journal = {Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation},
volume = {26},
number = {1},
pages = {16-25},
doi = {10.1016/j.bbmt.2019.08.026},
pmid = {31494231},
issn = {1523-6536},
mesh = {Animals ; *Cord Blood Stem Cell Transplantation ; *Hematopoiesis ; Hematopoietic Stem Cells/*metabolism ; Heterografts ; Humans ; Mice ; Mice, Inbred NOD ; Mice, Knockout ; Mice, SCID ; },
abstract = {Umbilical cord blood (UCB) provides an alternative source of hematopoietic stem cells (HSCs) for allogeneic transplantation. Administration of sufficient donor HSCs is critical to restore recipient hematopoiesis and to maintain long-term polyclonal blood formation. However, due to lack of unique markers, the frequency of HSCs among UCB CD34[+] cells is the subject of ongoing debate, urging for reproducible strategies for their counting. Here, we used cellular barcoding to determine the frequency and clonal dynamics of human UCB HSCs and to determine how data analysis methods affect these parameters. We transplanted lentivirally barcoded CD34[+] cells from 20 UCB donors into Nod/Scid/IL2Ry[-/-] (NSG) mice (n = 30). Twelve recipients (of 8 UCB donors) engrafted with >1% GFP[+] cells, allowing for clonal analysis by multiplexed barcode deep sequencing. Using multiple definitions of clonal diversity and strategies for data filtering, we demonstrate that differences in data analysis can change clonal counts by several orders of magnitude and propose methods to improve their consistency. Using these methods, we show that the frequency of NSG-repopulating cells was low (median ∼1 HSC/10[4] CD34[+] UCB cells) and could vary up to 10-fold between donors. Clonal patterns in blood became increasingly consistent over time, likely reflecting initial output of transient progenitors, followed by long-term HSCs with stable hierarchies. The majority of long-term clones displayed multilineage output, yet clones with lymphoid- or myeloid-biased output were also observed. Altogether, this study uncovers substantial interdonor and analysis-induced variability in the frequency of UCB CD34[+] clones that contribute to post-transplant hematopoiesis. As clone tracing is increasingly relevant, we urge for universal and transparent methods to count HSC clones during normal aging and upon transplantation.},
}
@article {pmid31489263,
year = {2019},
author = {Jarquín-González, J and Carrera-Parra, LF},
title = {Redescription of Hargeria rapax (Harger, 1879) and description of H. chetumalensis a new species from the Mexican Caribbean (Crustacea, Peracarida, Tanaidacea, Leptocheliidae) based upon morphological and molecular evidence.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7472},
pmid = {31489263},
issn = {2167-8359},
abstract = {Until now, Hargeria was considered a monospecific leptocheliid genus, with the species Hargeria rapax considered a taxon with a wide distribution, from the Northwestern Atlantic to the Mexican Caribbean. Herein, after a detailed revision of type and topotype materials and specimens collected from the Mexican Caribbean, a new species H. chetumalensis sp. nov. is described, and the redescription of H. rapax is provided. Also, we found a significant genetic divergence between the two species based on the nucleotide sequences of cytochrome oxidase subunit I, which support the morphological data. The morphological features used to recognize both species are also adequate to link males, females, and juvenile stages, although these species have a high intraspecific polymorphism.},
}
@article {pmid31489261,
year = {2019},
author = {De Luca, D and Kooistra, WHCF and Sarno, D and Gaonkar, CC and Piredda, R},
title = {Global distribution and diversity of Chaetoceros (Bacillariophyta, Mediophyceae): integration of classical and novel strategies.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7410},
pmid = {31489261},
issn = {2167-8359},
abstract = {Information on taxa distribution is a prerequisite for many research fields, and biological records are a major source of data contributing to biogeographic studies. The Global Biodiversity Information Facility (GBIF) and the Ocean Biogeographic Information System (OBIS) are important infrastructures facilitating free and open access to classical biological data from several sources in both temporal and spatial scales. Over the last ten years, high throughput sequencing (HTS) metabarcoding data have become available, which constitute a great source of detailed occurrence data. Among the global sampling projects that have contributed to such data are Tara Oceans and the Ocean Sampling Day (OSD). Integration of classical and metabarcoding data may aid a more comprehensive assessment of the geographic range of species, especially of microscopic ones such as protists. Rare, small and cryptic species are often ignored in surveys or mis-assigned with the classical approaches. Here we show how integration of data from various sources can contribute to insight in the biogeography and diversity at the genus- and species-level using Chaetoceros as study system, one of the most diverse and abundant genera among marine planktonic diatoms. Chaetoceros records were extracted from GBIF and OBIS and literature data were collected by means of a Google Scholar search. Chaetoceros references barcodes where mapped against the metabarcode datasets of Tara Oceans (210 sites) and OSD (144 sites). We compared the resolution of different data sources in determining the global distribution of the genus and provided examples, at the species level, of detection of cryptic species, endemism and cosmopolitan or restricted distributions. Our results highlighted at genus level a comparable picture from the different sources but a more complete assessment when data were integrated. Both the importance of the integration but also the challenges related to it were illustrated. Chaetoceros data collected in this study are organised and available in the form of tables and maps, providing a powerful tool and a baseline for further research in e.g., ecology, conservation and evolutionary biology.},
}
@article {pmid31486977,
year = {2019},
author = {Shukla, MA and Joshi, BD and Kumar, VP and Mehta, AK and Goyal, SP},
title = {Investigating the genetic diversity and presence of forensically informative nucleotide sequences in Indian antelope (Antilope cervicapra) using multiple genes of the mitochondrial genome.},
journal = {Molecular biology reports},
volume = {46},
number = {6},
pages = {6187-6195},
pmid = {31486977},
issn = {1573-4978},
mesh = {Animals ; Antelopes/classification/*genetics ; Base Composition ; Evolution, Molecular ; Genes, Mitochondrial ; *Genetic Variation ; Genetics, Population ; *Genome, Mitochondrial ; *Genomics/methods ; India ; Phylogeny ; },
abstract = {Indian antelope or Blackbuck (Antilope cervicapra) is one of the widely distributed endemic species in India among wild bovids and a majority of preferred habitats are in human-dominated landscapes. Poaching threats and habitat degradation are major factors for the decline in Blackbuck population from its distribution range. Till date, there is no detailed study using molecular techniques in India on Blackbuck, except a few studies entailing phylogenetic scenario based on inadequate sampling and DNA sequences restricted over limited geographic areas. In view of this, the present study is aimed to screen the Blackbuck samples from a large part of its distribution range and to investigate the genetic diversity as well as to identify the forensically informative nucleotide sequences (FINS) for species identification. We relied on multi-genes approach using three genes of mtDNA genome viz. Cytochrome Oxidase I, Cytochrome b and 16S rRNA and identified the FINS in the Blackbuck population along with conspecific sequences divergence and genetic diversity indices. In all three genes, we observed 8 to 17 haplotypes with the intra-species sequence divergence of 0.004-0.016. Inter-species sequence divergence with the other closely related species of the Blackbuck was 0.0225-0.033. We report the presence of FINS across three genes from 12 to 18 and found more informative nucleotide sites using Cytochrome Oxidase I genes compared to Cytochrome b and 16S rRNA gene. We did not observe the presence of geographic-specific FINS amongst Blackbuck population that can be used to assign individuals to geographic origin. Besides, in the phylogenetic tree, samples from different locations did not cluster into geographic-specific clade and exhibited mixed homology for these sequences. We suggest exploring the feasibility of using nuclear markers for population assignment.},
}
@article {pmid31486741,
year = {2019},
author = {Consoli, E and Ruthes, AC and Reinhard, E and Dahlin, P},
title = {First Morphological and Molecular Report of Aphelenchoides blastophthorus on Strawberry Plants in Switzerland.},
journal = {Plant disease},
volume = {103},
number = {11},
pages = {2851-2856},
doi = {10.1094/PDIS-07-18-1241-RE},
pmid = {31486741},
issn = {0191-2917},
mesh = {Animals ; DNA Barcoding, Taxonomic ; *Fragaria/parasitology ; Genes, Helminth/genetics ; Phylogeny ; Switzerland ; *Tylenchida/anatomy &amp; histology/classification/genetics ; },
abstract = {Foliar nematodes represent a minor feeding group within the genus Aphelenchoides Fischer, 1894. The facultative plant parasitic species A. blastophthorus can cause crinkling of leaves, reduced vigor, and stunting of agricultural and ornamental plants. Here we report the first finding of A. blastophthorus in leaves, crowns, and roots of strawberry plants collected in Switzerland in 2018. Species identification was confirmed by morphological and morphometric characterization supported by molecular barcoding of 18S ribosomal RNA (18S), 28S ribosomal RNA (28S), and cytochrome c oxidase I (COI) gene fragment analyses. Phylogenetic analysis of 18S indicated that A. blastophthorus was grouped within close distance to A. fragariae, a well-known foliar nematode affecting strawberry plants. Furthermore, the newly generated molecular barcodes of the partial 28S and COI of A. blastophthorus will support species identification in the future.},
}
@article {pmid31485179,
year = {2019},
author = {Al Husnain, L and AlKahtani, M},
title = {Molecular heterogeneity in the 18s DNA gene of Alternaria sp. and Fusarium sp. producing mycotoxins in rice and maize grains.},
journal = {Saudi journal of biological sciences},
volume = {26},
number = {2},
pages = {368-372},
pmid = {31485179},
issn = {1319-562X},
abstract = {BACKGROUND: Food contaminated with fungi and their toxins is a problem that threatens many developing countries. Kingdom of Saudi Arabia depends on the exported grain and legume seeds.<br><br>MATERIALS AND METHODS: The study involved examination of 160 samples of rice and maize seeds collected from different locations in the Kingdom of Saudi Arabia. Heterogeneity in the 18s rRNA gene of toxigenic Alternaria sp. and Fusarium sp. was unraveled. The seeds were disinfected and cultured on Potato Dextrose Agar (PDA), Yeast Extract Sucrose (YES) media and incubated at 25&#x202f;&#xb0;C/7&#x202f;days. The isolated fungi were subjected to 18s rRNA gene sequencing. Five toxins were extracted from maize and rice grains infected with isolated fungi.<br><br>RESULTS: The isolated fungi were identified based on morphological and spores characters as Fusarium sp. and Alternaria sp. Molecular identification based on18s rDNA barcode' was performed due to its high degree of inter specific variability, conserved primer sites and multi-copy nature in the genome. Fusarium sp. produced the highest detected (2070&#x202f;&#x3bc;g/kg) fumonisin especially in cereal production season 2011. The collected grain from Dammam recorded the highest percentage (5485.2&#x202f;g/kg) of toxins.<br><br>CONCLUSION: This work highlights that 50% of samples were found contaminated with toxins in various concentrations which impose a threat for public health and necessitate rapid identification methods for toxigenic fungi such as 18s rDNA sequencing.},
}
@article {pmid31484777,
year = {2019},
author = {Hoffecker, IT and Yang, Y and Bernardinelli, G and Orponen, P and Högberg, B},
title = {A computational framework for DNA sequencing microscopy.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {39},
pages = {19282-19287},
pmid = {31484777},
issn = {1091-6490},
mesh = {Computational Biology/*methods ; Computer Simulation ; Genetic Code ; High-Throughput Nucleotide Sequencing ; Image Processing, Computer-Assisted ; *Microscopy ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {We describe a method whereby microscale spatial information such as the relative positions of biomolecules on a surface can be transferred to a sequence-based format and reconstructed into images without conventional optics. Barcoded DNA "polymerase colony" (polony) amplification techniques enable one to distinguish specific locations of a surface by their sequence. Image formation is based on pairwise fusion of uniquely tagged and spatially adjacent polonies. The network of polonies connected by shared borders forms a graph whose topology can be reconstructed from pairs of barcodes fused during a polony cross-linking phase, the sequences of which are determined by recovery from the surface and next-generation (next-gen) sequencing. We developed a mathematical and computational framework for this principle called polony adjacency reconstruction for spatial inference and topology and show that Euclidean spatial data may be stored and transmitted in the form of graph topology. Images are formed by transferring molecular information from a surface of interest, which we demonstrated in silico by reconstructing images formed from stochastic transfer of hypothetical molecular markers. The theory developed here could serve as a basis for an automated, multiplexable, and potentially superresolution imaging method based purely on molecular information.},
}
@article {pmid31483817,
year = {2019},
author = {Nakamura, A and Ohwada, C and Takeuchi, M and Takeda, Y and Tsukamoto, S and Mimura, N and Nagisa, OH and Sugita, Y and Tanaka, H and Wakita, H and Aotsuka, N and Matsue, K and Yokote, K and Ohara, O and Nakaseko, C and Sakaida, E},
title = {Detection of MYD88 L265P mutation by next-generation deep sequencing in peripheral blood mononuclear cells of Waldenström's macroglobulinemia and IgM monoclonal gammopathy of undetermined significance.},
journal = {PloS one},
volume = {14},
number = {9},
pages = {e0221941},
pmid = {31483817},
issn = {1932-6203},
mesh = {Aged ; Aged, 80 and over ; *DNA Mutational Analysis ; Female ; *High-Throughput Nucleotide Sequencing ; Humans ; Leukocytes, Mononuclear/*metabolism ; Male ; Middle Aged ; Monoclonal Gammopathy of Undetermined Significance/blood/*genetics ; Myeloid Differentiation Factor 88/*genetics ; Waldenstrom Macroglobulinemia/blood/*genetics ; },
abstract = {We investigated the feasibility of using next-generation sequencing (NGS) technique using molecular barcoding technology to detect MYD88 L265P mutation in unselected peripheral blood mononuclear cells (PBMCs) in 52 patients with Waldenström's macroglobulinemia [1] and 21 patients with IgM-monoclonal gammopathy of undetermined significance (MGUS). The NGS technique successfully detected the MYD88 L265P in unselected PBMCs at a sensitivity of 0.02%, which was ×5 higher than that of AS-PCR. All the results between paired BM and PB samples from 2 IgM MGUS and 4 untreated WM patients matched completely. MYD88 L265P mutation was detected in 14/21 (66.7%), 14/19 (73.7%), and 10/33 (30.3%) with the median mutant allele burden of 0.36% (range, 0.06-2.85%), 0.48% (range, 0.02-32.3%), and 0.16% (range, 0.02-33.8%), in IgM-MGUS, untreated WM, and previously treated WM, respectively. Multiple linear regression analysis identified an absolute peripheral lymphocyte count as the positive predictor of PB mutant allele burden (R2 = 0,72, P<0.0001). Our non-invasive, simple NGS method has the potential to detect MYD88 L265P mutations in PBMCs of IgM MGUS and WM patients, which may especially utilized for monitoring minimal residual tumor burden after treatment.},
}
@article {pmid31483102,
year = {2019},
author = {Luimstra, JJ and Franken, KLMC and Garstka, MA and Drijfhout, JW and Neefjes, J and Ovaa, H},
title = {Production and Thermal Exchange of Conditional Peptide-MHC I Multimers.},
journal = {Current protocols in immunology},
volume = {126},
number = {1},
pages = {e85},
pmid = {31483102},
issn = {1934-368X},
mesh = {Animals ; Antigens/*metabolism ; CD8-Positive T-Lymphocytes/*immunology ; Cell Culture Techniques ; Cell Separation/*methods ; Flow Cytometry ; Fluorescent Dyes ; Histocompatibility Antigens Class I/*metabolism ; Humans ; Mice ; Peptides/*metabolism ; Protein Binding ; Protein Multimerization ; Staining and Labeling/*methods ; T-Lymphocytes, Cytotoxic/*immunology ; },
abstract = {Cytotoxic CD8[+] T cells mediate cellular immunity through recognition of specific antigens presented by MHC class I on all nucleated cells. Studying T cell interactions and responses provides invaluable information on infection, autoimmunity and cancer. Fluorescently labeled multimers of MHC I can be used to quantify, characterize, and isolate specific CD8[+] T cells by flow cytometry. Here we describe the production and use of conditional MHC I multimers that can be loaded with peptides of choice by incubating them at a defined temperature. Multimers are folded with a template peptide that forms a stable complex at low temperature, but dissociates at a defined elevated temperature. Using this technology multiple MHC I multimers can be generated in parallel, to allow staining and isolation of large sets of antigen-specific CD8[+] T cells, especially when combined with barcoding technologies. © 2019 The Authors.},
}
@article {pmid31482739,
year = {2019},
author = {Kiran, VS and Asokan, R and Revannavar, R and Hanchipura Mallesh, MS and Ramasamy, E},
title = {Genetic characterization and DNA barcoding of coffee shot-hole borer, Xylosandrus compactus (Eichhoff) (Coleoptera: Curculionidae: Scolytinae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {7},
pages = {779-785},
doi = {10.1080/24701394.2019.1659249},
pmid = {31482739},
issn = {2470-1408},
mesh = {Animals ; Coleoptera/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Genome, Mitochondrial/*genetics ; Phylogeny ; Species Specificity ; },
abstract = {Beetles of the subfamily Scolytinae are the most damaging insects in the world. Among which the black twig borer, Xylosandrus compactus (Eichhoff) (Coleoptera: Curculionidae: Scolytinae), is one of the serious pests in coffee plantations. Their cryptic life cycle inside the host plant makes these insects difficult to control. For its effective management accurate, timely and rapid identification of species is critical. By cloning and sequencing the 5' mitochondrial cytochrome oxidase c subunit 1 (COI) gene, the beetle's molecular identification confirmed its identity as X. compactus. No pseudogenes and indels were found in analyzed nucleotide sequences; they match with high similarity in nucleotide NCBI Basic Local Alignment Search Tool search. The X. compactus COI genes sequences were deposited at NCBI GenBank with accession numbers of KY172634, KY172635 and the Barcode of Life (BOLD) with BIN ID: ACB4177. Furthermore, based on multiple sequence alignment of the X. compactus MtCOI gene, a phylogenetic tree with maximum probability was drawn. X. compactus species clustered together which agree with the species data collected from NCBI GenBank database from the different geographic regions. There were no morphological and molecular differences between space and time-collected coffee shot-hole borers, thus all the specimens described were X. compactus infesting both robusta and arabica coffee.},
}
@article {pmid31481742,
year = {2019},
author = {Gschwendtner, S and Kang, H and Thiering, E and Kublik, S and Fösel, B and Schulz, H and Krauss-Etschmann, S and Heinrich, J and Schöler, A and Schloter, M and Standl, M},
title = {Early life determinants induce sustainable changes in the gut microbiome of six-year-old children.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {12675},
pmid = {31481742},
issn = {2045-2322},
mesh = {Actinobacteria/genetics/isolation &amp; purification ; Adult ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/*isolation &amp; purification ; Breast Feeding ; Child ; Feces/microbiology ; Female ; Firmicutes/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome/drug effects ; Humans ; Male ; Pregnancy ; Principal Component Analysis ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; Sex Factors ; Smoking ; Social Class ; },
abstract = {While the association between early life determinants and the development of the gut microbiome composition in infancy has been widely investigated, a potential persistent influence of early life determinants on the gut microbial community after its stabilization at later childhood remains largely unknown. Therefore, we aimed to identify the association between several early life determinants and the gut microbiome composition in six-year-old children from the LISA birth cohort. A total number of 166 fecal samples were analyzed using 16S rRNA gene-based barcoding to assess bacterial diversity pattern. The bacterial profiles were investigated for their association with maternal smoking during pregnancy, mode of delivery, breastfeeding, antibiotic treatment between one and two years of age, gender and socioeconomic status (SES). While alpha and beta diversity of the infants' gut microbiome remained unaffected, amplicon sequence variants (ASVs) annotated to Firmicutes and Actinobacteria responded to early life determinants, mostly to feeding practice and antibiotics use. ASVs associated to Bacteriodetes remained unaffected. Our findings indicate that early life determinants could have a long-term sustainable effect on the gut microflora of six-year-old children, however, associations with early life determinates are weaker than reported for infants.},
}
@article {pmid31477010,
year = {2019},
author = {Bhagwate, AV and Liu, Y and Winham, SJ and McDonough, SJ and Stallings-Mann, ML and Heinzen, EP and Davila, JI and Vierkant, RA and Hoskin, TL and Frost, M and Carter, JM and Radisky, DC and Cunningham, JM and Degnim, AC and Wang, C},
title = {Bioinformatics and DNA-extraction strategies to reliably detect genetic variants from FFPE breast tissue samples.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {689},
pmid = {31477010},
issn = {1471-2164},
support = {P50 CA116201/CA/NCI NIH HHS/United States ; R01 CA187112/CA/NCI NIH HHS/United States ; CA187112-01//National Institute of Health/ ; CA116201//Mayo Clinic Breast SPORE Biospecimen Rersource for Breast Cancer Research/ ; },
mesh = {Breast/chemistry ; Breast Neoplasms/*genetics ; DNA Mutational Analysis/*methods ; DNA, Neoplasm/*isolation &amp; purification ; Female ; Fixatives ; Formaldehyde ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Humans ; Paraffin Embedding ; Tissue Fixation ; },
abstract = {BACKGROUND: Archived formalin fixed paraffin embedded (FFPE) samples are valuable clinical resources to examine clinically relevant morphology features and also to study genetic changes. However, DNA quality and quantity of FFPE samples are often sub-optimal, and resulting NGS-based genetics variant detections are prone to false positives. Evaluations of wet-lab and bioinformatics approaches are needed to optimize variant detection from FFPE samples.<br><br>RESULTS: As a pilot study, we designed within-subject triplicate samples of DNA derived from paired FFPE and fresh frozen breast tissues to highlight FFPE-specific artifacts. For FFPE samples, we tested two FFPE DNA extraction methods to determine impact of wet-lab procedures on variant calling: QIAGEN QIAamp DNA Mini Kit ("QA"), and QIAGEN GeneRead DNA FFPE Kit ("QGR"). We also used negative-control (NA12891) and positive control samples (Horizon Discovery Reference Standard FFPE). All DNA sample libraries were prepared for NGS according to the QIAseq Human Breast Cancer Targeted DNA Panel protocol and sequenced on the HiSeq 4000. Variant calling and filtering were performed using QIAGEN Gene Globe Data Portal. Detailed variant concordance comparisons and mutational signature analysis were performed to investigate effects of FFPE samples compared to paired fresh frozen samples, along with different DNA extraction methods. In this study, we found that five times or more variants were called with FFPE samples, compared to their paired fresh-frozen tissue samples even after applying molecular barcoding error-correction and default bioinformatics filtering recommended by the vendor. We also found that QGR as an optimized FFPE-DNA extraction approach leads to much fewer discordant variants between paired fresh frozen and FFPE samples. Approximately 92% of the uniquely called FFPE variants were of low allelic frequency range (<&#x2009;5%), and collectively shared a "C&#x2009;>&#x2009;T|G&#x2009;>&#x2009;A" mutational signature known to be representative of FFPE artifacts resulting from cytosine deamination. Based on control samples and FFPE-frozen replicates, we derived an effective filtering strategy with associated empirical false-discovery estimates.<br><br>CONCLUSIONS: Through this study, we demonstrated feasibility of calling and filtering genetic variants from FFPE tissue samples using a combined strategy with molecular barcodes, optimized DNA extraction, and bioinformatics methods incorporating genomics context such as mutational signature and variant allelic frequency.},
}
@article {pmid31475085,
year = {2019},
author = {Jamdade, RA and Mahmoud, T and Gairola, S},
title = {Prospects of genomic resources available at the global databases for the flora of United Arab Emirates.},
journal = {3 Biotech},
volume = {9},
number = {9},
pages = {333},
pmid = {31475085},
issn = {2190-572X},
abstract = {This article emphasizes available genomic resources at the global databases National Center for Biotechnology Information (NCBI) GenBank, Gramene and Phytozome for the selected 378 plant taxa of the United Arab Emirates (UAE). Germplasm of these species was collected and banked at the Sharjah Seed Bank and Herbarium (SSBH) along with their related information on habit, habitat and occurrence. The occurrence statistics exhibits almost 19.84% species under rare-to-very rare category, the GenBank search statistics for this category indicates 17.72% species as studied and 2.11% as not studied. Overall, from the global search statistics for 378 plant species, it seems that about 40 (10.58%) species remained unstudied. Most of the unstudied species were herbaceous plants belonging to the mountainous habitat. Moreover, full genomes were recorded for 7 species at NCBI GenBank, 2 species at Phytozome and 1 species at Gramene database. The local search statistics (for UAE) exhibits about 10.58% of the flora that still remained unstudied and only 11 (2.90%) of the recorded species were having genomic information at NCBI GenBank. It is necessary to prioritize studies on such species that could provide valuable insight on their genetic composition in order to understand their adaptation to the natural environment. At present, the SSBH is cataloguing UAE's flora using core barcode and assisted markers that could provide a robust DNA barcode library for native plants of UAE. Our study appeals researchers to recognize and prioritize the species that need attention to enrich their genomic resources at the global databases by supporting nucleotide libraries with their conspecifics. At present, genomic resources for UAE plant taxa are limited, but with the advent of low-cost sequencing technologies these resources would flourish in the near future. Nevertheless, the information generated through genomic studies could be utilized for conservation and management of threatened and endangered plant species, Crop Wild Relatives and medicinal plants. We hope this article will promote interest in conducting additional studies in genomics of desert plants by encouraging researchers to participate in this emerging field.},
}
@article {pmid31472895,
year = {2019},
author = {Liu, M and Li, XW and Liao, BS and Luo, L and Ren, YY},
title = {Species identification of poisonous medicinal plant using DNA barcoding.},
journal = {Chinese journal of natural medicines},
volume = {17},
number = {8},
pages = {585-590},
doi = {10.1016/S1875-5364(19)30060-3},
pmid = {31472895},
issn = {1875-5364},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Phylogeny ; Plant Proteins/genetics ; Plants, Medicinal/*classification/genetics ; Poisons/*classification ; Sequence Analysis, DNA ; },
abstract = {The aim is to select a universal DNA barcode for identifying all poisonous medicinal plants in Chinese pharmacopoeia and their poisonous related species or adulterants. We chose 4 commonly used regions as candidate DNA barcodes (ITS2, psbA-trnH, matK and rbcL) and compared their identification efficiency in 106 species from 27 families and 65 genera totally. Data analysis was performed including the information of sequence alignment, inter/intra-specific genetic distance and data distribution, identification efficiency and the situation of Neighbor-Joining (NJ) phylogenetic trees. We found ITS2 sequence region had high variation, stable genetic distance and identification efficiency relatively. The topological structure of NJ phylogenetic tree showed monophyletic. Our findings show that ITS2 can be applied as a universal barcode for identifying poisonous medicinal plants in Chinese pharmacopoeia and their poisonous related species or adulterants.},
}
@article {pmid31471188,
year = {2019},
author = {Wang, Q and Xiong, H and Ai, S and Yu, X and Liu, Y and Zhang, J and He, A},
title = {CoBATCH for High-Throughput Single-Cell Epigenomic Profiling.},
journal = {Molecular cell},
volume = {76},
number = {1},
pages = {206-216.e7},
doi = {10.1016/j.molcel.2019.07.015},
pmid = {31471188},
issn = {1097-4164},
mesh = {Acetylation ; Animals ; Cell Line ; Chromatin/*genetics/metabolism ; *Epigenome ; Epigenomics/*methods ; *High-Throughput Nucleotide Sequencing ; Histones/metabolism ; Methylation ; Mice ; Mice, Transgenic ; Mouse Embryonic Stem Cells/metabolism ; Protein Binding ; Protein Processing, Post-Translational ; *Single-Cell Analysis ; },
abstract = {An efficient, generalizable method for genome-wide mapping of single-cell histone modifications or chromatin-binding proteins is lacking. Here, we develop CoBATCH, combinatorial barcoding and targeted chromatin release, for single-cell profiling of genomic distribution of chromatin-binding proteins in cell culture and tissue. Protein A in fusion to Tn5 transposase is enriched through specific antibodies to genomic regions, and Tn5 generates indexed chromatin fragments ready for library preparation and sequencing. Importantly, this strategy enables not only low-input epigenomic profiling in intact tissues but also measures scalable up to tens of thousands of single cells per experiment under both native and cross-linked conditions. CoBATCH produces ∼12,000 reads/cell with extremely low background. Mapping of endothelial cell lineages from ten embryonic mouse organs through CoBATCH allows for efficient deciphering of epigenetic heterogeneity of cell populations and cis-regulatory mechanisms. Thus, obviating specialized devices, CoBATCH is broadly applicable and easily deployable for single-cell profiling of protein-DNA interactions.},
}
@article {pmid31470607,
year = {2019},
author = {Grädel, C and Terrazos Miani, MA and Barbani, MT and Leib, SL and Suter-Riniker, F and Ramette, A},
title = {Rapid and Cost-Efficient Enterovirus Genotyping from Clinical Samples Using Flongle Flow Cells.},
journal = {Genes},
volume = {10},
number = {9},
pages = {},
pmid = {31470607},
issn = {2073-4425},
mesh = {Consensus Sequence ; Enterovirus/*genetics ; Genotyping Techniques/economics/instrumentation/*methods ; Molecular Diagnostic Techniques/economics/instrumentation/*methods ; Nanopores ; Sequence Analysis, RNA/economics/instrumentation/*methods ; Viral Fusion Proteins/genetics ; },
abstract = {Enteroviruses affect millions of people worldwide and are of significant clinical importance. The standard method for enterovirus identification and genotyping still relies on Sanger sequencing of short diagnostic amplicons. In this study, we assessed the feasibility of nanopore sequencing using the new flow cell "Flongle" for fast, cost-effective, and accurate genotyping of human enteroviruses from clinical samples. PCR amplification of partial VP1 gene was performed from multiple patient samples, which were multiplexed together after barcoding PCR and sequenced multiple times on Flongle flow cells. The nanopore consensus sequences obtained from mapping reads to a reference database were compared to their Sanger sequence counterparts. Using clinical specimens sampled over different years, we were able to correctly identify enterovirus species and genotypes for all tested samples, even when doubling the number of barcoded samples on one flow cell. Average sequence identity across sequencing runs was >99.7%. Phylogenetic analysis showed that the consensus sequences achieved with Flongle delivered accurate genotyping. We conclude that the new Flongle-based assay with its fast turnover time, low cost investment, and low cost per sample represents an accurate, reproducible, and cost-effective platform for enterovirus identification and genotyping.},
}
@article {pmid31470170,
year = {2019},
author = {Zhang, D and Bian, F and Cai, L and Wang, T and Kong, T and Zhao, Y},
title = {Bioinspired photonic barcodes for multiplexed target cycling and hybridization chain reaction.},
journal = {Biosensors &amp; bioelectronics},
volume = {143},
number = {},
pages = {111629},
doi = {10.1016/j.bios.2019.111629},
pmid = {31470170},
issn = {1873-4235},
mesh = {*Biosensing Techniques ; Humans ; Indoles/chemistry ; Limit of Detection ; MicroRNAs/chemistry/*isolation &amp; purification ; Nucleic Acid Hybridization/*methods ; Photons ; Polymers/chemistry ; },
abstract = {Multiplexed detection of microRNA (miRNA) is of great value in clinical diagnosis. Here, a new type of polydopamine (PDA) encapsulated photonic crystal (PhC) barcodes are employed for target-triggering cycle amplification and hybridization chain reaction (HCR) to achieve multiplex miRNA quantification. The PDA-decorated PhC barcodes not only exhibit distinctive structural color for different encoding miRNAs, they also can immobilize biomolecules, allowing subsequent reaction with amino-modified hairpin probes (H1). When the PDA-decorated PhC barcodes are used in assays, target miRNAs can be circularly used to initiate HCR for cycle amplification. Therefore, by tuning the structural colors of the PDA-integrated PhC, the multiplexed miRNA quantification could be realized. We demonstrate that our strategy for multiplexed detection of miRNA is reasonably accurate, reliable and repeatable, with a detection limit as low as 8.0 fM. Our results show that PDA encapsulated PhC barcodes as a novel platform offer a pathway toward the multiplex analysis of low-abundance biomarkers for biomedical assays.},
}
@article {pmid31469430,
year = {2019},
author = {Rabaoui, L and Yacoubi, L and Sanna, D and Casu, M and Scarpa, F and Lin, YJ and Shen, KN and Clardy, TR and Arculeo, M and Qurban, MA},
title = {DNA barcoding of marine fishes from Saudi Arabian waters of the Gulf.},
journal = {Journal of fish biology},
volume = {95},
number = {5},
pages = {1286-1297},
doi = {10.1111/jfb.14130},
pmid = {31469430},
issn = {1095-8649},
support = {//Water, Research Institute, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia/ ; },
mesh = {Animals ; Bayes Theorem ; Biodiversity ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/chemistry/genetics ; Fishes/classification/*genetics ; Phylogeny ; Saudi Arabia ; Sequence Analysis, DNA ; },
abstract = {We used the cytochrome oxidase subunit I (coI) gene DNA to barcode 117 endemic Gulf and cosmopolitan Indo-West Pacific fish species belonging to 54 families and 13 orders. Novel DNA barcodes were provided for 18 fish species (Trachinocephalus sp., Nematalosa sp., Herklotsichthys lossei, Upeneus doriae, Trachurus indicus, Apogonichthyoides taeniatus, Verulux cypselurus, Favonigobius sp., Suezichthus gracilis, Sillago sp., Brachirus orientalis, Pegusa sp., Lepidotrigla bispinosa, Lepidotrigla sp., Grammoplites suppositus, Hippichthys sp., Paramonacanthus sp. and Triacanthus sp.). The species delimitation analysis, conducted with Poisson tree processes- Bayesian PTP (PTP-bPTP) and nucleotide-divergence-threshold (NDT) models), found 137 and 119 entities respectively. Overall, NDT method, neighbour-joining species tree and the prior taxonomic assessment provided similar results. Among the 54 families considered, only 10 (Ariommatidae, Ephippidae, Leiognathidae, Nemipteridae, Plotosidae, Pomacanthidae, Pomacentridae, Priacanthidae and Rachycentridae) showed the occurrence of molecular diagnostic pure characters. The DNA barcoding database developed during this study will help ichthyologists to identify and resolve the taxonomic ambiguities they may encounter with the fishes occurring in The Gulf and throughout the region.},
}
@article {pmid31467214,
year = {2019},
author = {Pinheiro, HT and Moreau, CS and Daly, M and Rocha, LA},
title = {Will DNA barcoding meet taxonomic needs?.},
journal = {Science (New York, N.Y.)},
volume = {365},
number = {6456},
pages = {873-874},
doi = {10.1126/science.aay7174},
pmid = {31467214},
issn = {1095-9203},
mesh = {Biodiversity ; *DNA ; *DNA Barcoding, Taxonomic ; },
}
@article {pmid31465460,
year = {2019},
author = {Chen, PH and Chuang, LY and Wu, KC and Wang, YH and Shieh, TY and Sheu, JJ and Chang, HW and Yang, CH},
title = {Application of simulation-based CYP26 SNP-environment barcodes for evaluating the occurrence of oral malignant disorders by odds ratio-based binary particle swarm optimization: A case-control study in the Taiwanese population.},
journal = {PloS one},
volume = {14},
number = {8},
pages = {e0220719},
pmid = {31465460},
issn = {1932-6203},
mesh = {Adult ; Case-Control Studies ; Computer Simulation ; Cytochrome P450 Family 26/*genetics ; Female ; *Gene-Environment Interaction ; Humans ; Male ; Middle Aged ; Mouth Neoplasms/epidemiology/*genetics ; Odds Ratio ; Pharyngeal Neoplasms/epidemiology/*genetics ; *Polymorphism, Single Nucleotide ; Risk Factors ; Taiwan/epidemiology ; },
abstract = {INTRODUCTION: Genetic polymorphisms and social factors (alcohol consumption, betel quid (BQ) usage, and cigarette consumption), both separately or jointly, play a crucial role in the occurrence of oral malignant disorders such as oral and pharyngeal cancers and oral potentially malignant disorders (OPMD).<br><br>MATERIAL AND METHODS: Simultaneous analyses of multiple single nucleotide polymorphisms (SNPs) and environmental effects on oral malignant disorders are essential to examine, albeit challenging. Thus, we conducted a case-control study (N = 576) to analyze the risk of occurrence of oral malignant disorders by using binary particle swarm optimization (BPSO) with an odds ratio (OR)-based method.<br><br>RESULTS: We demonstrated that a combination of SNPs (CYP26B1 rs887844 and CYP26C1 rs12256889) and socio-demographic factors (age, ethnicity, and BQ chewing), referred to as the combined effects of SNP-environment, correlated with maximal risk diversity of occurrence observed between the oral malignant disorder group and the control group. The risks were more prominent in the oral and pharyngeal cancers group (OR = 10.30; 95% confidence interval (CI) = 4.58-23.15) than in the OPMD group (OR = 5.42; 95% CI = 1.94-15.12).<br><br>CONCLUSIONS: Simulation-based "SNP-environment barcodes" may be used to predict the risk of occurrence of oral malignant disorders. Applying simulation-based "SNP-environment barcodes" may provide insight into the importance of screening tests in preventing oral and pharyngeal cancers and OPMD.},
}
@article {pmid31465135,
year = {2019},
author = {Lokugamage, MP and Sago, CD and Gan, Z and Krupczak, BR and Dahlman, JE},
title = {Constrained Nanoparticles Deliver siRNA and sgRNA to T Cells In Vivo without Targeting Ligands.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {31},
number = {41},
pages = {e1902251},
pmid = {31465135},
issn = {1521-4095},
support = {T32 EB021962/EB/NIBIB NIH HHS/United States ; T32 GM105490/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Drug Carriers/*chemistry ; Ligands ; Lipids/*chemistry ; Mice ; Nanoparticles/*chemistry ; RNA, Messenger/chemistry/genetics/metabolism ; RNA, Small Interfering/*chemistry/genetics/*metabolism ; T-Lymphocytes/*metabolism ; },
abstract = {T cells help regulate immunity, which makes them an important target for RNA therapies. While nanoparticles carrying RNA have been directed to T cells in vivo using protein- and aptamer-based targeting ligands, systemic delivery to T cells without targeting ligands remains challenging. Given that T cells endocytose lipoprotein particles and enveloped viruses, two natural systems with structures that can be similar to lipid nanoparticles (LNPs), it is hypothesized that LNPs devoid of targeting ligands can deliver RNA to T cells in vivo. To test this hypothesis, the delivery of siRNA to 9 cell types in vivo by 168 nanoparticles using a novel siGFP-based barcoding system and bioinformatics is quantified. It is found that nanomaterials containing conformationally constrained lipids form stable LNPs, herein named constrained lipid nanoparticles (cLNPs). cLNPs deliver siRNA and sgRNA to T cells at doses as low as 0.5 mg kg[-1] and, unlike previously reported LNPs, do not preferentially target hepatocytes. Delivery occurs via a chemical composition-dependent, size-independent mechanism. These data suggest that the degree to which lipids are constrained alters nanoparticle targeting, and also suggest that natural lipid trafficking pathways can promote T cell delivery, offering an alternative to active targeting approaches.},
}
@article {pmid31463161,
year = {2019},
author = {Galliano, GE},
title = {Process Variation Detection using Missing Data in a Multihospital Community Practice Anatomic Pathology Laboratory.},
journal = {Journal of pathology informatics},
volume = {10},
number = {},
pages = {25},
pmid = {31463161},
issn = {2229-5089},
abstract = {OBJECTIVES: Barcode-driven workflows reduce patient identification errors. Missing process timestamp data frequently confound our health system's pending lists and appear as actions left undone. Anecdotally, it was noted that missing data could be found when there is procedure noncompliance. This project was developed to determine if missing timestamp data in the histology barcode drive workflow correlated with other process variations, procedure noncompliance, or is an indicator of workflows needing focus for improvement projects.<br><br>MATERIALS AND METHODS: Data extracts of timestamp data from January 1, 2018, to December 15, 2018 for the major histology process steps were analyzed for missing data. Case level analysis to determine the presence or absence of expected barcoding events was performed on 1031 surgical pathology cases to determine the cause of the missing data and determine if additional data variations or procedure noncompliance events were present. The data variations were classified according to a scheme defined in the study.<br><br>RESULTS: Of 70,085, there were 7218 cases (10.3%) with missing process timestamp data. Missing histology process step data was associated with other additional data variations in case-level deep dives (P < 0.0001). Of the cases missing timestamp data in the initial review, 18.4% of the cases had no identifiable cause for the missing data (all expected events took place in the case-level deep dive).<br><br>CONCLUSIONS: Operationally, valuable information can be obtained by reviewing the types and causes of missing data in the anatomic pathology laboratory information system, but only in conjunction with user input and feedback.},
}
@article {pmid31453420,
year = {2019},
author = {Basak, S and Aadi Moolam, R and Parida, A and Mitra, S and Rangan, L},
title = {Evaluation of rapid molecular diagnostics for differentiating medicinal Kaempferia species from its adulterants.},
journal = {Plant diversity},
volume = {41},
number = {3},
pages = {206-211},
pmid = {31453420},
issn = {2468-2659},
abstract = {Accurate detection of unique herbs is crucial for herbal medicine preparation. Zingiberaceae species, which are important in Ayurvedic medicine of India, are often misidentified in Northeast (NE) Indian herbal markets. Kaempferia galanga (Zingiberaceae) is one of the major components of popular Ayurvedic drugs used for rheumatic diseases (i.e., "Gandha Thailam" and "Rasnairandadi Kashayam"), contusions, fractures, and sprains. In NE India, herbal healers often misidentify plants from the Marantaceae family (e.g., Calathea bachemiana and Maranta leuconeura) as Kaempferia, which leads to adulteration of the medicinal herb. This misidentification of herbs occurs in NE India because Zingiberaceae plant barcoding information is inadequate. As a consequence, herbal medicine is not only therapeutically less effective but may also cause adverse reactions that range from mild to life-threatening. In this study, we used eight barcoding loci to develop "fingerprints" for four Kaempferia species and two species frequently mistaken for Kaempferia. The PCR and sequencing success of the loci matK, rbcL and trnH-psbA were found to be 100%; the combination of matK, rbcL, and trnH-psbA proved to be the ideal locus for discriminating the Kaempferia species from their adulterants because the combined loci showed greater variability than individual loci. This reliable tool was therefore developed in the current study for accurate identification of Kaempferia plants which can effectively resolve identification issues for herbal healers.},
}
@article {pmid31452517,
year = {2019},
author = {Chou, SS and Chen, YJ and Shen, YT and Yen, HF and Kuo, SC},
title = {Implementation and Effectiveness of a Bar Code-Based Transfusion Management System for Transfusion Safety in a Tertiary Hospital: Retrospective Quality Improvement Study.},
journal = {JMIR medical informatics},
volume = {7},
number = {3},
pages = {e14192},
pmid = {31452517},
issn = {2291-9694},
abstract = {BACKGROUND: Large-scale and long-term studies are not sufficient to determine the efficiency that IT solutions can bring to transfusion safety.<br><br>OBJECTIVE: This quality-improvement report describes our continuous efforts to implement and upgrade a bar code-based transfusion management (BCTM) system since 2011 and examines its effectiveness and sustainability in reducing blood transfusion errors, in a 3000-bed tertiary hospital, where more than 60,000 prescriptions of blood transfusion are covered by 2500 nurses each year.<br><br>METHODS: The BCTM system uses barcodes for patient identification, onsite labeling, and blood product verification, through wireless connection to the hospital information systems. Plan-Do-Study-Act (PDSA) cycles were used to improve the process. Process maps before and after implementation of the BCTM system in 2011 were drawn to highlight the changes. The numbers of incorrect labeling or wrong blood in tube incidents that occurred quarterly were plotted on a run chart to monitor the quality changes of each intervention introduced. The annual occurrences of error events from 2011 to 2017 were compared with the mean occurrence of 2008-2010 to determine whether implementation of the BCTM system could effectively reduce the number of errors in 2016 and whether this reduction could persist in 2017.<br><br>RESULTS: The error rate decreased from 0.03% in 2008-2010 to 0.002% in 2016 (P<.001) and 0.001% in 2017 (P<.001) after implementation of the BTCM system. Only one incorrect labeling incident was noted among the 68,324 samples for blood typing, and no incorrect transfusions occurred among 67,423 transfusion orders in 2017.<br><br>CONCLUSIONS: This report demonstrates that continuous efforts to upgrade the existing process is critical to reduce errors in transfusion therapy, with support from information technology.},
}
@article {pmid31451692,
year = {2019},
author = {Wu, D and Yan, J and Shen, X and Sun, Y and Thulin, M and Cai, Y and Wik, L and Shen, Q and Oelrich, J and Qian, X and Dubois, KL and Ronquist, KG and Nilsson, M and Landegren, U and Kamali-Moghaddam, M},
title = {Profiling surface proteins on individual exosomes using a proximity barcoding assay.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {3854},
pmid = {31451692},
issn = {2041-1723},
mesh = {Body Fluids/cytology ; Cell Line, Tumor ; DNA, Single-Stranded/genetics/metabolism ; Exosomes/*metabolism ; Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Immunoconjugates/genetics/metabolism ; Membrane Proteins/genetics/*metabolism ; Molecular Probes/genetics/metabolism ; Oligonucleotides/genetics/metabolism ; Sequence Analysis, DNA/methods ; },
abstract = {Exosomes have been implicated in numerous biological processes, and they may serve as important disease markers. Surface proteins on exosomes carry information about their tissues of origin. Because of the heterogeneity of exosomes it is desirable to investigate them individually, but this has so far remained impractical. Here, we demonstrate a proximity-dependent barcoding assay to profile surface proteins of individual exosomes using antibody-DNA conjugates and next-generation sequencing. We first validate the method using artificial streptavidin-oligonucleotide complexes, followed by analysis of the variable composition of surface proteins on individual exosomes, derived from human body fluids or cell culture media. Exosomes from different sources are characterized by the presence of specific combinations of surface proteins and their abundance, allowing exosomes to be separately quantified in mixed samples to serve as markers for tissue-specific engagement in disease.},
}
@article {pmid31450860,
year = {2019},
author = {Arruda, PSS and Ferreira, DC and Oliveira, C and Venere, PC},
title = {DNA Barcoding Reveals High Levels of Divergence among Mitochondrial Lineages of Brycon (Characiformes, Bryconidae).},
journal = {Genes},
volume = {10},
number = {9},
pages = {},
pmid = {31450860},
issn = {2073-4425},
mesh = {Animals ; Characiformes/classification/*genetics ; DNA Barcoding, Taxonomic/*methods/standards ; Electron Transport Complex IV/genetics ; *Genetic Speciation ; *Genome, Mitochondrial ; Phylogeny ; *Polymorphism, Genetic ; },
abstract = {Brycon is an important group of Neotropical fish and the principal genus of the family Bryconidae, with 44 valid species that are found in some Central American rivers and practically all the major hydrographic basins of South America. These fish are medium to large in size, migratory, omnivorous, important seed dispersers for riparian forests, and bioindicators of environmental quality, given that they are found preferentially in rivers with clean, well oxygenated water. Many Brycon species are important fishery resources and some are farmed. Morphological and molecular studies have nevertheless indicated that the group is not monophyletic and has a number of unresolved taxonomic problems. Given this, the present study aimed to identify the Molecular Operational Taxonomic Units (MOTUs) of the genus using the mitochondrial cytochrome c oxidase I (COI) gene, with analyses of genetics distance (NJ), maximum likelihood (ML), and Bayesian Inference (BI), combined with two different species delimitation approaches (GMYC and ABGD). The results indicate that at least 31 MOTUs exist within the 18 species identified a priori based on their morphology. Many of these lineages require further investigation for a more definitive classification.},
}
@article {pmid31448451,
year = {2019},
author = {Suetsugu, K and Yamato, M and Matsubayashi, J and Tayasu, I},
title = {Comparative study of nutritional mode and mycorrhizal fungi in green and albino variants of Goodyera velutina, an orchid mainly utilizing saprotrophic rhizoctonia.},
journal = {Molecular ecology},
volume = {28},
number = {18},
pages = {4290-4299},
doi = {10.1111/mec.15213},
pmid = {31448451},
issn = {1365-294X},
mesh = {Carbon Isotopes ; DNA, Ribosomal Spacer/genetics ; Isotope Labeling ; Likelihood Functions ; Mycorrhizae/*physiology ; Nitrogen Isotopes ; *Nutritional Physiological Phenomena ; Orchidaceae/*microbiology ; Phylogeny ; Rhizoctonia/*physiology ; },
abstract = {The majority of chlorophyllous orchids form mycorrhizal associations with so-called rhizoctonia fungi, a phylogenetically heterogeneous assemblage of predominantly saprotrophic fungi in Ceratobasidiaceae, Tulasnellaceae, and Serendipitaceae. It is still a matter of debate whether adult orchids mainly associated with rhizoctonia species are partially mycoheterotrophic. Here, we investigated the nutritional modes of green and albino variants of Goodyera velutina, an orchid species considered to be mainly associated with Ceratobasidium spp., by measuring their [13] C and [15] N abundances, and by molecular barcoding of their mycorrhizal fungi. Molecular analysis revealed that both green and albino variants of G. velutina harbored a similar range of mycobionts, mainly saprotrophic Ceratobasidium spp., Tulasnella spp., and ectomycorrhizal Russula spp. In addition, stable isotope analysis revealed that albino variants were significantly enriched in [13] C but not so greatly in [15] N, suggesting that saprotrophic Ceratobasidium spp. and Tulasnella spp. are their main carbon source. However, in green variants, [13] C levels were depleted and those of [15] N were indistinguishable from the co-occurring autotrophic plants. Therefore, we concluded that the albino G. velutina variants are fully mycoheterotrophic plants whose C derives mainly from saprotrophic rhizoctonia, while the green G. velutina variants are mainly autotrophic plants, at least at our study site, in spite of their additional associations with ectomycorrhizal fungi. This is the first report demonstrating that adult nonphotosynthetic albino variants can obtain their nutrition mainly from nonectomycorrhizal rhizoctonia.},
}
@article {pmid31448375,
year = {2019},
author = {Paz-Neto, AA and Freitas, MTS and Gondim, MGC and Melo, JWS and Querino, RB and Balbino, VQ},
title = {Which Species of Coconut Moth Occurs in Brazil: Atheloca subrufella vs. Atheloca bondari (Lepidoptera: Pyralidae)?.},
journal = {Neotropical entomology},
volume = {48},
number = {6},
pages = {1039-1045},
pmid = {31448375},
issn = {1678-8052},
support = {88882.183145/2018-01//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
mesh = {Animal Distribution ; Animals ; Brazil ; *Cocos ; DNA Barcoding, Taxonomic ; *Genetic Variation ; Genitalia, Male/anatomy &amp; histology ; Male ; Moths/*anatomy &amp; histology/*classification ; },
abstract = {The moths, Atheloca subrufella (Hulst 1887) and A. bondari, (Heinrich 1956) are species known for their economic impact on coconut production, which Brazil is the fourth largest global producer. The first record of Atheloca in Brazil was reported by Bondar in 1940, where the author registered it being A. subrufella. The studies performed by C. Heinrich in 1956 related the existence of divergence in specimens of Brazilian Atheloca suggesting the presence of morphological differences between the males of A. bondari and A. subrufella. In this study, Atheloca specimens from the five states of northeastern Brazil were used. Samples from Pernambuco state were sent to taxonomist Dr. V. O. Becker (Uiraçu Institute-BA) for identification. Male individuals from the other states were mounted for photographic documentation, highlighting the characteristics that differentiate the two species. A fragment of the cytochrome c oxidase subunit 1 gene was sequenced and then compared with that of the Atheloca spp. deposited in GenBank. An analysis was conducted to evaluate the genetic distance between A. bondari and A. subrufella. The results indicate greater interspecific (0.030-0.034) than intraspecific (0.000-0.002) genetic variation between the groups, reinforcing the hypothesis of two distinct species. A geographic distribution map and a table with the host plants were constructed based on a literature review. This study concluded that the species occurring in Brazil is A. bondari, as suggested by C. Heinrich. Atheloca bondari and A. subrufella have only been reported in plants of the family Arecaceae, but only the coconut tree (Cocos nucifera L.) is shared by the two species.},
}
@article {pmid31446486,
year = {2019},
author = {Schüßler, A and Walker, C},
title = {Archaeospora ecuadoriana sp. nov. from a mountainous biodiversity hotspot area in Ecuador, and transfer of Palaeospora spainiae to Archaeospora, as A. spainiae comb. nov.},
journal = {Mycorrhiza},
volume = {29},
number = {5},
pages = {435-443},
pmid = {31446486},
issn = {1432-1890},
support = {SCHU1203/10//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Classification ; Ecuador ; Glomeromycota/*classification/genetics ; Peru ; RNA, Fungal/analysis ; RNA, Ribosomal/analysis ; Sequence Analysis, RNA ; },
abstract = {A new glomeromycotan fungus, Archaeospora ecuadoriana sp. nov., was found in the south Ecuadorian mountain rainforest region, a global plant biodiversity hotspot. It was cultivated as single spore isolate originating from nursery-grown native tree seedlings inoculated with mixed soil from pristine forest and agricultural fields. The new species is known from the Loja area, southern Ecuador, at about 2100 m above mean sea level (mamsl) and has been detected in potato roots from an Andean region in Peru at 2658 mamsl by previous molecular data. The fungus forms small, colourless to frosted white, mainly globose spores, averaging 61 × 60 μm, formed singly or very rarely in clusters. There is no reaction to Melzer's reagent, other than a slight unspecific overall yellow iodine staining. The spores are very similar to those of Archaeospora trappei and A. schenckii. However, molecular phylogenetic analysis shows the species to be clearly separate from all other described Archaeospora species. The analysis of the available Archaeospora sequence data shows that sequences of Palaeospora spainiae, of the monospecific genus Palaeospora, cluster within the genus Archaeospora. Palaeospora therefore is synonymised with Archaeospora and P. spainiae is transferred to Archaeospora, as A. spainiae comb. nov.},
}
@article {pmid31445898,
year = {2019},
author = {Swain, SN and Makunin, A and Dora, AS and Barik, TK},
title = {SNP barcoding based on decision tree algorithm: A new tool for identification of mosquito species with special reference to Anopheles.},
journal = {Acta tropica},
volume = {199},
number = {},
pages = {105152},
doi = {10.1016/j.actatropica.2019.105152},
pmid = {31445898},
issn = {1873-6254},
mesh = {Algorithms ; Animals ; Anopheles/*genetics ; Biological Evolution ; DNA Barcoding, Taxonomic/*methods ; *Decision Trees ; Electron Transport Complex IV/genetics ; Phylogeny ; *Polymorphism, Single Nucleotide ; Species Specificity ; },
abstract = {Molecular taxonomy based identification of species in the form of DNA barcodes are extensively used in evolutionary systematics. Almost all the DNA barcodes contain detailed information of the barcoding gene along with uninformative sequences of a particular species. Therefore, a technique is highly essential to remove or to reduce the number of uninformative sequences and ought to create species-specific barcodes for differentiation. The actual variation in genetic sequences, called single nucleotide polymorphism (SNP) genotyping, can be utilized to develop a new tool for rapid, reliable, and high-throughput assay to distinguish the known species. SNPs act as important hereditary markers for uncovering the evolutionary history and normal genetic polymorphisms. Keeping in mind, we propose a decision tree-based barcoding (DTB) algorithm for generating SNP barcodes from the DNA barcoding sequence of several evolutionarily related species to accurately identify a single species. To address this issue, we analyzed mitochondrial COI gene sequences of 64 species of Anopheles mosquitoes. After alignment and truncating, 32 SNPs were discovered in COI gene sequences of Anopheles mosquitoes and then computed to set up the decision rule for constructing the decision tree. The decision tree based barcoding algorithm generates 126 nodes and 32 loci for discriminating 64 Anopheles mosquito species. Finally, we concluded that the DTB method is useful and effective for generating sequence tags for Anopheles mosquito species identification.},
}
@article {pmid31444552,
year = {2019},
author = {Roman, MG and Gangitano, D and Houston, R},
title = {Characterization of new chloroplast markers to determine biogeographical origin and crop type of Cannabis sativa.},
journal = {International journal of legal medicine},
volume = {133},
number = {6},
pages = {1721-1732},
pmid = {31444552},
issn = {1437-1596},
mesh = {Cannabis/*genetics ; DNA, Chloroplast/*genetics ; Databases, Genetic ; Drug Trafficking ; *Genetic Variation ; Genome, Plant ; Genotype ; Haplotypes ; Humans ; Phylogeography ; Principal Component Analysis ; *Sequence Analysis, DNA ; },
abstract = {Marijuana (Cannabis sativa) is the most commonly used illicit drug in the USA. Despite its schedule I classification by the federal government, 33 states and the District of Columbia have legalized its use for medicinal or recreational purposes. This state-specific legalization has created a new problem for law enforcement: preventing and tracking the diversion of legally obtained Cannabis to states where it remains illegal. In addition, trafficking of the drug at the border with Mexico remains an issue for law enforcement agencies. C. sativa crops can be classified as marijuana (a drug containing the psychoactive chemical delta-9-tetrahydrocannabinol) or hemp (the non-drug form of the plant). Differentiation between crop types is important for forensic purposes. In addition, investigation of trafficking routes into and within the USA requires genetic association of samples from different seizures, and determining where the crop originated could provide important leads. This project seeks to exploit sequence variations in C. sativa chloroplast DNA (cpDNA) to allow genetic determination of biogeographic origin, discrimination between marijuana and hemp, and association between cases for C. sativa samples. Due to the limited discriminatory ability of common barcoding markers, the authors sought to discover more informative polymorphic regions. By comparing published whole genome cpDNA sequences, 58 polymorphisms and seven hotspot regions were identified. Hemp samples from the USA and Canada, marijuana samples from Mexico and Chile, and medical marijuana samples from Chile were evaluated using two cpDNA hotspot regions, rpl32-trnL and trnS-trnG. Principal component analysis supported some differences between the groups based on their crop type and biogeographic origin.},
}
@article {pmid31441477,
year = {2019},
author = {Zhukov, DV and Khorosheva, EM and Khazaei, T and Du, W and Selck, DA and Shishkin, AA and Ismagilov, RF},
title = {Microfluidic SlipChip device for multistep multiplexed biochemistry on a nanoliter scale.},
journal = {Lab on a chip},
volume = {19},
number = {19},
pages = {3200-3211},
pmid = {31441477},
issn = {1473-0189},
support = {DP5 OD012190/OD/NIH HHS/United States ; T32 GM007616/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Lab-On-A-Chip Devices ; *Microfluidic Analytical Techniques/instrumentation ; *Nanotechnology/instrumentation ; RNA/genetics ; *Single-Cell Analysis ; },
abstract = {We have developed a multistep microfluidic device that expands the current SlipChip capabilities by enabling multiple steps of droplet merging and multiplexing. Harnessing the interfacial energy between carrier and sample phases, this manually operated device accurately meters nanoliter volumes of reagents and transfers them into on-device reaction wells. Judiciously shaped microfeatures and surface-energy traps merge droplets in a parallel fashion. Wells can be tuned for different volumetric capacities and reagent types, including for pre-spotted reagents that allow for unique identification of original well contents even after their contents are pooled. We demonstrate the functionality of the multistep SlipChip by performing RNA transcript barcoding on-device for synthetic spiked-in standards and for biologically derived samples. This technology is a good candidate for a wide range of biological applications that require multiplexing of multistep reactions in nanoliter volumes, including single-cell analyses.},
}
@article {pmid31440866,
year = {2019},
author = {Gichira, AW and Avoga, S and Li, Z and Hu, G and Wang, Q and Chen, J},
title = {Comparative genomics of 11 complete chloroplast genomes of Senecioneae (Asteraceae) species: DNA barcodes and phylogenetics.},
journal = {Botanical studies},
volume = {60},
number = {1},
pages = {17},
pmid = {31440866},
issn = {1817-406X},
support = {Y323771W07//Sino Africa Joint Research Center/ ; SAJC201322//Sino Africa Joint Research Center/ ; },
abstract = {BACKGROUND: Majority of the species within Senecioneae are classified in Senecio, making it the tribe's largest genus. Certain intergeneric relationships within the tribe are vaguely defined, with the genus Senecio being partly linked to this ambiguity. Infrageneric relationships within Senecio remain largely unknown and consequently, the genus has undergone continuous expansion and contraction over the recent past due to addition and removal of taxa. Dendrosenecio, an endemic genus in Africa, is one of its segregate genera. To heighten the understanding of species divergence and phylogeny within the tribe, the complete chloroplast genomes of the first five Senecio and six Dendrosenecio species were sequenced and analyzed in this study.<br><br>RESULTS: The entire length of the complete chloroplast genomes was&#x2009;~&#x2009;150&#xa0;kb and&#x2009;~&#x2009;151&#xa0;kb in Dendrosenecio and Senecio respectively. Characterization of the 11 chloroplast genomes revealed a significant degree of similarity particularly in their organization, gene content, repetitive sequence composition and patterns of codon usage. The chloroplast genomes encoded an equal number of unique genes out of which 80 were protein-coding genes, 30 transfer ribonucleic acid, and four ribosomal ribonucleic acid genes. Based on comparative sequence analyses, the level of divergence was lower in Dendrosenecio. A total of 331 and 340 microsatellites were detected in Senecio and Dendrosenecio, respectively. Out of which, 25 and five chloroplast microsatellites (cpSSR) were identified as potentially valuable molecular markers. Also, through whole chloroplast genome comparisons and DNA polymorphism tests, ten divergent hotspots were identified. Potential primers were designed creating genomic tools to further molecular studies within the tribe. Intergeneric relationships within the tribe were firmly resolved using genome-scale dataset in partitioned and unpartitioned schemes. Two main clades, corresponding to two subtribes within the Senecioneae, were formed with the genus Ligularia forming a single clade while the other had Dendrosenecio, Pericallis, Senecio and Jacobaea. A sister relationship was revealed between Dendrosenecio and Pericallis whereas Senecio, and Jacobaea were closely placed in a different clade.<br><br>CONCLUSION: Besides emphasizing on the potential of chloroplast genome data in resolving intergeneric relationships within Senecioneae, this study provides genomic resources to facilitate species identification and phylogenetic reconstructions within the respective genera.},
}
@article {pmid31439012,
year = {2019},
author = {Erisoz Kasap, O and Linton, YM and Karakus, M and Ozbel, Y and Alten, B},
title = {Revision of the species composition and distribution of Turkish sand flies using DNA barcodes.},
journal = {Parasites &amp; vectors},
volume = {12},
number = {1},
pages = {410},
pmid = {31439012},
issn = {1756-3305},
support = {P0034_18_WR//Armed Forces Health Surveillance Board, Global Emerging Infections Surveillance and Response System (AFHSB-GEIS)/ ; SBAG: 114S999//The Scientific and Technological Research Council of Turkey/ ; 01001601001//Hacettepe University Scientific Research Unit/ ; },
mesh = {Animals ; Cyclooxygenase 1/genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Geography ; Insect Proteins/*genetics ; Insect Vectors/*classification/genetics ; Male ; Phlebotomus/*classification/genetics ; Turkey ; },
abstract = {BACKGROUND: Currently, knowledge regarding the phlebotomine sand fly (Diptera: Psychodidae) fauna of Turkey is restricted to regions with endemic leishmaniasis. However, rapidly changing environmental and social conditions highlight concerns on the possible future expansion of sand fly-borne diseases in Turkey, promoting risk assessment through biosurveillance activities in non-endemic regions. Traditional morphological approaches are complicated by extensive cryptic speciation in sand flies, thus integrated studies utilizing DNA markers are becoming increasingly important for correct sand fly identification. This study contributes to the knowledge of the sand fly fauna in understudied regions of Turkey, and provides an extensive DNA barcode reference library of expertly identified Turkish sand fly species for the first time.<br><br>METHODS: Fly sampling was conducted at 101 locations from 29 provinces, covering all three biogeographical regions of Turkey. Specimens were morphologically identified using available keys. Cytochrome c oxidase I (cox1) barcode sequences were analyzed both for morphologically distinct species and those specimens with cryptic identity. A taxon identity tree was obtained using Neighbor Joining (NJ) analysis. Species boundaries among closely related taxa evaluated using ABGD, Maximum Likelihood (ML) and haplotype network analyses. Sand fly richness of all three biogeographical regions were compared using nonparametric species richness estimators.<br><br>RESULTS: A total of 729 barcode sequences (including representatives of all previously reported subgenera) were obtained from a total of 9642 sand fly specimens collected in Turkey. Specimens belonging to the same species or species complex clustered together in the NJ tree, regardless of their geographical origin. The species delimitation methods revealed the existence of 33 MOTUs, increasing the previously reported 28 recorded sand fly species by 17.8%. The richest sand fly diversity was determined in Anatolia, followed by the Mediterranean, and then the Black Sea regions of the country.<br><br>CONCLUSIONS: A comprehensive cox1 reference library is provided for the sand fly species of Turkey, including the proposed novel taxa discovered herein. Our results have epidemiological significance exposing extensive distributions of proven and suspected sand fly vectors in Turkey, including those areas currently regarded as non-endemic for sand fly-borne disease.},
}
@article {pmid30815250,
year = {2018},
author = {Cuscó, A and Catozzi, C and Viñes, J and Sanchez, A and Francino, O},
title = {Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon.},
journal = {F1000Research},
volume = {7},
number = {},
pages = {1755},
pmid = {30815250},
issn = {2046-1402},
mesh = {Animals ; Dogs ; Metagenomics ; *Microbiota ; *Nanopores ; Operon ; RNA, Ribosomal, 16S ; },
abstract = {Background: Profiling the microbiome of low-biomass samples is challenging for metagenomics since these samples are prone to contain DNA from other sources (e.g. host or environment). The usual approach is sequencing short regions of the 16S rRNA gene, which fails to assign taxonomy to genus and species level. To achieve an increased taxonomic resolution, we aim to develop long-amplicon PCR-based approaches using Nanopore sequencing. We assessed two different genetic markers: the full-length 16S rRNA (~1,500 bp) and the 16S-ITS-23S region from the rrn operon (4,300 bp). Methods: We sequenced a clinical isolate of Staphylococcus pseudintermedius, two mock communities and two pools of low-biomass samples (dog skin). Nanopore sequencing was performed on MinION™ using the 1D PCR barcoding kit. Sequences were pre-processed, and data were analyzed using EPI2ME or Minimap2 with rrn database. Consensus sequences of the 16S-ITS-23S genetic marker were obtained using canu. Results: The full-length 16S rRNA and the 16S-ITS-23S region of the rrn operon were used to retrieve the microbiota composition of the samples at the genus and species level. For the Staphylococcus pseudintermedius isolate, the amplicons were assigned to the correct bacterial species in ~98% of the cases with the16S-ITS-23S genetic marker, and in ~68%, with the 16S rRNA gene when using EPI2ME. Using mock communities, we found that the full-length 16S rRNA gene represented better the abundances of a microbial community; whereas, 16S-ITS-23S obtained better resolution at the species level. Finally, we characterized low-biomass skin microbiota samples and detected species with an environmental origin. Conclusions: Both full-length 16S rRNA and the 16S-ITS-23S of the rrn operon retrieved the microbiota composition of simple and complex microbial communities, even from the low-biomass samples such as dog skin. For an increased resolution at the species level, targeting the 16S-ITS-23S of the rrn operon would be the best choice.},
}
@article {pmid31436852,
year = {2020},
author = {Jang, H and Shin, SE and Youm, KJ and Karagozlu, MZ and Kim, CB and Ko, KS and Park, SH},
title = {Molecular Identification of Necrophagous Dermestes Species in South Korea Using Cytochrome c Oxidase Subunit I Nucleotide Sequences (Genus Dermestes).},
journal = {Journal of forensic sciences},
volume = {65},
number = {1},
pages = {283-287},
doi = {10.1111/1556-4029.14170},
pmid = {31436852},
issn = {1556-4029},
support = {PA-G000001//Center for Research and Development of Police Science and Technology and the Korean National Police Agency/ ; },
mesh = {Animals ; Coleoptera/*genetics ; DNA Primers ; Electron Transport Complex IV/*genetics ; Forensic Entomology ; Larva ; Phylogeny ; Polymerase Chain Reaction ; Republic of Korea ; *Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Species identification of necrophagous insects found on a dead body is an essential key in applying medicolegal entomology to the estimation of postmortem interval (PMI). Due to limited morphological identification of insect evidence, several studies have identified species using molecular information such as DNA markers. While considerable cytochrome c oxidase subunit I (COI) gene sequence data of necrophagous fly species have been collected and annotated, those of necrophagous beetle species have not. Since necrophagous beetles such as Dermestes species have a larval period longer than that of flies, beetles are useful in even the late decomposition phase in estimating minimum PMI. To obtain the full-length COI gene sequences of six Dermestes species collected from South Korea, we designed primers for polymerase chain reaction amplification and sequencing. The obtained full COI nucleotide sequences were used for performing phylogenic analysis and comparison with previously reported sequences. The results demonstrated that the COI gene sequences could be used to identify forensically important Dermestes species in South Korea.},
}
@article {pmid31434161,
year = {2019},
author = {Berdot, S and Boussadi, A and Vilfaillot, A and Depoisson, M and Guihaire, C and Durieux, P and Le, LMM and Sabatier, B},
title = {Integration of a Commercial Barcode-Assisted Medication Dispensing System in a Teaching Hospital.},
journal = {Applied clinical informatics},
volume = {10},
number = {4},
pages = {615-624},
pmid = {31434161},
issn = {1869-0327},
mesh = {Adult ; Drug Prescriptions ; Electronic Data Processing ; Female ; Hospitals, Teaching/*statistics &amp; numerical data ; Humans ; Male ; *Medical Order Entry Systems ; Medication Errors/prevention &amp; control/statistics &amp; numerical data ; Pharmacy/statistics &amp; numerical data ; },
abstract = {OBJECTIVES: A commercial barcode-assisted medication administration (BCMA) system was integrated to secure the medication process and particularly the dispensing stage by technicians and the administration stage with nurses. We aimed to assess the impact of this system on medication dispensing errors and barriers encountered during integration process.<br><br>METHODS: We conducted a controlled randomized study in a teaching hospital, during dispensing process at the pharmacy department. Four wards were randomized in the experimental group and control group, with two wards using the system during 3 days with dedicated pharmacy technicians. The system was a closed loop system without information return to the computerized physician order entry system. The two dedicated technicians had a 1-week training session. Observations were performed by one observer among the four potential observers previously trained. The main outcomes assessed were dispensing error rates and the identification of barriers encountered to expose lessons learned from this study.<br><br>RESULTS: There was no difference between the dispensing error rate of the control and experimental groups (7.9% for both, p&#x2009;=&#x2009;0.927). We identified 10 barriers to pharmacy barcode-assisted system technology deployment. They concerned technical (problems with semantic interoperability interfaces, bad user interface, false errors generated, lack of barcodes), structural (poor integration with local information technology), work force (short staff training period, insufficient workforce), and strategic issues (system performance problems, insufficient budget).<br><br>CONCLUSION: This study highlights the difficulties encountered in integrating a commercial system in current hospital information systems. Several issues need to be taken into consideration before the integration of a commercial barcode-assisted system in a teaching hospital. In our experience, interoperability of this system with the electronic health record is the key for the success of this process with an entire closed loop system from prescription to administration. BCMA system at the dispensing process remains essential to purchase securing medication administration process.},
}
@article {pmid31433005,
year = {2019},
author = {Dutari, L and Loaiza, JR},
title = {Molecular validation of anthropophilic Phlebotominae sandflies (Diptera: Psychodidae) in Central Panama.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {114},
number = {},
pages = {e190034},
pmid = {31433005},
issn = {1678-8060},
mesh = {Animals ; *Biodiversity ; Insect Vectors/classification/*genetics ; Leishmaniasis, Cutaneous/transmission ; Panama ; Phylogeny ; Psychodidae/classification/*genetics ; },
abstract = {Six Phlebotominae sand fly species are incriminated as biological vectors of human pathogens in Panama, but molecular corroboration is still needed. We aim at confirming the identity of Phlebotominae species documented as anthropophilic in Panama. Adult sandflies were collected from August 2010 to February 2012 in Central Panama using CDC light traps. Species confirmation was accomplished through molecular barcodes and allied sequences from GenBank. A total of 53,366 sand fly specimens representing 18 species were collected. Five species were validated molecularly as single phylogenetic clusters, but Psychodopygus thula depicted two genetically divergent lineages, which may be indicative of cryptic speciation.},
}
@article {pmid31423084,
year = {2019},
author = {Huemer, P and Wieser, C and Stark, W and Hebert, PDN and Wiesmair, B},
title = {DNA barcode library of megadiverse Austrian Noctuoidea (Lepidoptera) - a nearly perfect match of Linnean taxonomy.},
journal = {Biodiversity data journal},
volume = {7},
number = {},
pages = {e37734},
pmid = {31423084},
issn = {1314-2828},
abstract = {The aim of the study was to establish a nationwide barcode library for the most diverse group of Austrian Lepidoptera, the Noctuoidea, with 5 families (Erebidae, Euteliidae, Noctuidae, Nolidae, Notodontidae) and around 690 species. Altogether, 3431 DNA barcode sequences from COI gene (cytochrome c oxidase 1) belonging to 671 species were gathered, with 3223 sequences >500 bp. The intraspecific divergence with a mean of only 0.17% is low in most species whereas interspecific distances to the Nearest Neighbour are significantly higher with an average of 4.95%. Diagnostic DNA barcodes were obtained for 658 species. Only 13 species (1.9% of the Austrian Noctuoidea) cannot be reliably identified from their DNA barcode (Setina aurita/Setina irrorella, Conisania leineri/Conisania poelli, Photedes captiuncula/Photedes minima, Euxoa obelisca/Euxoa vitta/Euxoa tritici, Mesapamaea secalella/Mesapamea secalis, Amphipoea fucosa/Amphipoea lucens). A similarly high identification performance was achieved by the Barcode Index (BIN) system. 671 species of Austrian Noctuoidea, representing 3202 records with BINs, are assigned to a total of 678 BINs. The vast majority of 649 species is placed into a single BIN, with only 13 species recognised as BIN-sharing (including the barcode sharing species above). Twenty-one species were assigned to more than one BIN and have to be checked for cryptic diversity in the future.},
}
@article {pmid31422094,
year = {2019},
author = {Onder, Z and Yildirim, A and Duzlu, O and Arslan, MO and Sari, B and Tasci, GT and Ciloglu, A and Aydin, NP and Inci, A and Adler, PH},
title = {Molecular characterization of black flies (Diptera: Simuliidae) in areas with pest outbreaks and simuliotoxicosis in Northeast Anatolia Region, Turkey.},
journal = {Acta tropica},
volume = {199},
number = {},
pages = {105149},
doi = {10.1016/j.actatropica.2019.105149},
pmid = {31422094},
issn = {1873-6254},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Disease Outbreaks ; Electron Transport Complex IV/*genetics ; Haplotypes ; Phylogeny ; Simuliidae/classification/*genetics ; Turkey ; },
abstract = {Accurate species identification provides the foundation for successful pest management and vector control of black flies. Accordingly, we examined the mitochondrial DNA cytochrome oxidase I (COI) gene sequences of four morphologically and chromosomally identified species of black flies (Simulium vernumgroup sp., S. bergi Rubtsov, S. bezzii (Corti), and S. kiritshenkoi Rubtsov) in Northeast Anatolia Region of Turkey where simuliid pest problems and simuliotoxicosis cases have been reported among cattle. COI gene sequences of these species and closely related species available in GenBank were used to provide species-level diagnoses and infer relationships. Both subgenera (Nevermannia and Simulium) were monophyletic, and subclades generally corresponded with species groups. Intraspecific genetic divergence was 0.2-1.6%, whereas the mean interspecific genetic divergence among the four species was 11.2-14.5%. The COI analysis produced results congruent with morphological concepts of the nominal species S. bergi and S. bezzii. Probable misidentifications in GenBank were revealed, especially for species in the S. ornatum and S. vernum groups, complicating identification capability. Sequence variation in the COI barcode region also might not be adequate for species delineation and identification among some species in these two species groups.},
}
@article {pmid31418605,
year = {2019},
author = {Flotte, TR},
title = {Getting Tough on Capsid Screening: Tough Decoys Enable Barcoding of Vectors Capable of both Entry and Expression.},
journal = {Human gene therapy},
volume = {30},
number = {8},
pages = {919-920},
doi = {10.1089/hum.2019.29090.trf},
pmid = {31418605},
issn = {1557-7422},
mesh = {Animals ; Capsid/*physiology ; Capsid Proteins/*genetics/*metabolism ; Dependovirus/*physiology ; *Gene Expression Regulation ; Genetic Engineering ; Genetic Variation ; Genetic Vectors/*genetics ; Humans ; Transgenes ; *Virus Internalization ; },
}
@article {pmid31418113,
year = {2019},
author = {Gazzonis, AL and Marangi, M and Zanzani, SA and Villa, L and Giangaspero, A and Manfredi, MT},
title = {Molecular epidemiology of Blastocystis sp. in dogs housed in Italian rescue shelters.},
journal = {Parasitology research},
volume = {118},
number = {10},
pages = {3011-3017},
pmid = {31418113},
issn = {1432-1955},
mesh = {Animals ; Blastocystis/classification/*genetics/isolation &amp; purification ; Blastocystis Infections/diagnosis/epidemiology/parasitology/*veterinary ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Dog Diseases/diagnosis/*epidemiology/parasitology ; Dogs ; Feces/parasitology ; Female ; Italy/epidemiology ; Male ; Molecular Epidemiology ; Phylogeny ; Prevalence ; Sequence Analysis, DNA ; },
abstract = {Blastocystis is a ubiquitous protozoan with a wide range of hosts. In humans, its presence has been associated with gastrointestinal disorders, although its role as a pathogen still needs to be elucidated. Until now, 17 Blastocystis subtypes (STs) have been identified, with ST1-ST4 the most commonly found in humans. Among domestic animals, the same STs reported in humans have been detected in dogs. An epidemiological survey on dog kennels was carried out to evaluate the prevalence of Blastocystis and the STs involved. Overall, 99 faecal samples were collected from the rescue shelters. Blastocystis detection was performed through conventional barcoding PCR targeting the 1800-bp SSU-rDNA, followed by sequencing and phylogenetic analysis. Blastocystis DNA was found in 21 faecal samples (21.2%), and all samples were successfully sequenced and identified as ST3 in a unique monophyletic group. The presence of Blastocystis was reported for the first time in dogs from Italy, with the identification of ST3, the subtype most commonly found in humans.},
}
@article {pmid31416630,
year = {2020},
author = {Boulgakov, AA and Ellington, AD and Marcotte, EM},
title = {Bringing Microscopy-By-Sequencing into View.},
journal = {Trends in biotechnology},
volume = {38},
number = {2},
pages = {154-162},
pmid = {31416630},
issn = {1879-3096},
support = {DP1 GM106408/GM/NIGMS NIH HHS/United States ; R35 GM122480/GM/NIGMS NIH HHS/United States ; },
mesh = {DNA Barcoding, Taxonomic/methods ; High-Throughput Nucleotide Sequencing/*methods ; Microscopy/*methods ; Molecular Imaging/methods ; },
abstract = {The spatial distribution of molecules and cells is fundamental to understanding biological systems. Traditionally, microscopies based on electromagnetic waves such as visible light have been used to localize cellular components by direct visualization. However, these techniques suffer from limitations of transmissibility and throughput. Complementary to optical approaches, biochemical techniques such as crosslinking can colocalize molecules without suffering the same limitations. However, biochemical approaches are often unable to combine individual colocalizations into a map across entire cells or tissues. Microscopy-by-sequencing techniques aim to biochemically colocalize DNA-barcoded molecules and, by tracking their thus unique identities, reconcile all colocalizations into a global spatial map. Here, we review this new field and discuss its enormous potential to answer a broad spectrum of questions.},
}
@article {pmid31414632,
year = {2019},
author = {Malatyalı, E and Ertabaklar, H and Ertuğ, S},
title = {[Subtype Distribution of Blastocystis spp. with DNA Barcoding and Evaluation of Diagnostic Methods].},
journal = {Mikrobiyoloji bulteni},
volume = {53},
number = {3},
pages = {308-318},
doi = {10.5578/mb.68344},
pmid = {31414632},
issn = {0374-9096},
mesh = {*Blastocystis/classification/genetics ; *Blastocystis Infections/diagnosis/parasitology ; *DNA Barcoding, Taxonomic ; DNA, Protozoan/genetics ; Diagnostic Techniques and Procedures/*standards ; Feces/parasitology ; *Genetic Variation ; Humans ; Parasitology/*methods/standards ; Phylogeny ; Retrospective Studies ; Turkey ; },
abstract = {Blastocystis spp. is one of the most common protozoa in Turkey and throughout the world; laboratory diagnosis, genetic diversity and clinical features are among the most controversial topics related to the parasite. The aims of the present study were to investigate the subtype distribution of Blastocystis spp. İsolates from Aydin, Turkey, to evaluate the efficiency of some diagnostic methods and to evaluate the relationship between Blastocystis spp. infection with demographic factors and clinical findings. According to the direct microscopy results, 100 stool samples with and without Blastocystis spp. were selected by simple random sampling method. All were directly subjected to DNA isolation and cultured in Jones medium. DNA isolation was also carried out in Blastocystis spp. positive cultures with a different kit. Genomic DNA samples were analysed by PCR targeting the Blastocystis spp. small subunit ribosomal RNA (SSU rRNA) gene and subtypes (ST) were determined according to the sequence analyses. Moreover, the samples with undetected ST were further studied with sequence tagged site-PCR (STS-PCR). In addition, the patients with and without Blastocystis spp. were compared in terms of demographic characteristics (gender, age, residence) and clinical findings (itching, diarrhoea, abdominal pain, dyspepsia, nausea, vomiting, constipation and weight loss)., Among 100 stool positive samples diagnosed with direct microscopic examination 81 (81%) and 86 (86%) were found as positive with culture and PCR, retrospectively. Additionally, among 100 Blastocystis spp. negative stool samples five (5%) and seven (7%) samples were found positive with the same methods, respectively. The results of the analysis of Blastocystis spp. with SSU rRNA gene sequencing and STS-PCR methods revealed the subtype distribution of 95 Blastocystis spp. isolates as follows: ST3 (n= 50, 52.6%), ST2 (n= 21, 22.1%), ST1 (n= 17, 17.9%), ST7 (n= 4, 4.2%), ST2 + ST3 (n= 2, 2.1%) and ST1 + ST3 (n= 1, 1.1%). In addition, a complete accordance was observed in subtype distribution between direct DNA isolation from stools and 35 randomly selected isolates from the culture. In our study, the comparison of 107 Blastocystis spp. positive (by any of the methods) cases and 93 negative cases showed that there was no correlation in terms of demographic characteristics and clinical findings. Similarly, there was no significant relationship between symptoms and subtypes. In conclusion, it is recommended that in addition to direct microscopic examination, the use of additional methods such as culture and PCR will be useful in routine laboratory diagnosis of Blastocystis spp. The distribution of Blastocystis subtype in Aydin is mainly in accordance with the global findings. Lack of a relationship between Blastocystis spp. İnfection and symptoms in our study was supported the idea that Blastocystis spp. infection is mostly asymptomatic in humans and it may be a member of healthy microbiota.},
}
@article {pmid31410262,
year = {2019},
author = {Muha, TP and Skukan, R and Borrell, YJ and Rico, JM and Garcia de Leaniz, C and Garcia-Vazquez, E and Consuegra, S},
title = {Contrasting seasonal and spatial distribution of native and invasive Codium seaweed revealed by targeting species-specific eDNA.},
journal = {Ecology and evolution},
volume = {9},
number = {15},
pages = {8567-8579},
pmid = {31410262},
issn = {2045-7758},
abstract = {AIM: Codium fragile, an invasive seaweed, has spread widely during the last century, impacting on local seaweed communities through competition and disturbance. Early detection of C. fragile can help on its control and management. Environmental DNA (eDNA) has proved successful for early detection of aquatic invasive species but its potential use for seaweed remains understudied. We used a species-specific eDNA qPCR approach to investigate the spatial distribution, abundance, and coexistence of the invasive C. fragile and three native Codium species (Codium vermilara, Codium tomentosum, and Codium decorticatum) in the Cantabrian Sea.<br><br>LOCATION: Bay of Biscay, Northern Atlantic Coast of the Iberian Peninsula; two ports, a beach and a rocky cliff.<br><br>METHODS: We designed species-specific primers in barcoding regions targeting short fragments of the rbcL gene for the invasive Codium species, and the elongation factor Tu (tufA) gene for the native species, to assess their spatial and seasonal distributions using quantitative real-time PCR in samples collected during summer, autumn, and winter.<br><br>RESULTS: We found seasonal differences in the presence of the invasive Codium fragile and two of the native Codium species, but did not detect C.&#xa0;decorticatum at any point. Species distribution patterns produced with qPCR targeting species-specific eDNA coincided with the known distribution based on previous conventional sampling, with a seasonal alternance of C.&#xa0;fragile and C.&#xa0;vermilara, and a marked dominance of invasive C.&#xa0;fragile in ports, which are known hotspots for invasive species.<br><br>MAIN CONCLUSIONS: Our results demonstrate the utility of using eDNA for early detection and monitoring of invasive seaweed. Native and invasive Codium spp. displayed significant seasonal and spatial differentiation that needs to be taken into account in risk management. Regular monitoring of ports and adjacent areas using eDNA should help to assess the potential expansion of invasive Codium and the need for management interventions to avoid the displacement of native seaweed.},
}
@article {pmid31409293,
year = {2019},
author = {Katayama, S and Skoog, T and Söderhäll, C and Einarsdottir, E and Krjutškov, K and Kere, J},
title = {Guide for library design and bias correction for large-scale transcriptome studies using highly multiplexed RNAseq methods.},
journal = {BMC bioinformatics},
volume = {20},
number = {1},
pages = {418},
pmid = {31409293},
issn = {1471-2105},
support = {2013fobi38282//Karolinska Institutet/ ; 2014fobi41753//Karolinska Institutet/ ; 2016fobi50455//Karolinska Institutet/ ; 309329//FP7/ ; KAW2015.0096//Knut och Alice Wallenbergs Stiftelse/ ; },
mesh = {Cell Line ; Cluster Analysis ; *Gene Library ; High-Throughput Nucleotide Sequencing ; Humans ; Principal Component Analysis ; RNA/chemistry/metabolism ; Sequence Analysis, RNA/*methods ; *Transcriptome ; User-Computer Interface ; },
abstract = {BACKGROUND: Standard RNAseq methods using bulk RNA and recent single-cell RNAseq methods use DNA barcodes to identify samples and cells, and the barcoded cDNAs are pooled into a library pool before high throughput sequencing. In cases of single-cell and low-input RNAseq methods, the library is further amplified by PCR after the pooling. Preparation of hundreds or more samples for a large study often requires multiple library pools. However, sometimes correlation between expression profiles among the libraries is low and batch effect biases make integration of data between library pools difficult.<br><br>RESULTS: We investigated 166 technical replicates in 14 RNAseq libraries made using the STRT method. The patterns of the library biases differed by genes, and uneven library yields were associated with library biases. The former bias was corrected using the NBGLM-LBC algorithm, which we present in the current study. The latter bias could not be corrected directly, but could be solved by omitting libraries with particularly low yields. A simulation experiment suggested that the library bias correction using NBGLM-LBC requires a consistent sample layout. The NBGLM-LBC correction method was applied to an expression profile for a cohort study of childhood acute respiratory illness, and the library biases were resolved.<br><br>CONCLUSIONS: The R source code for the library bias correction named NBGLM-LBC is available at https://shka.github.io/NBGLM-LBC and https://shka.bitbucket.io/NBGLM-LBC . This method is applicable to correct the library biases in various studies that use highly multiplexed sequencing-based profiling methods with a consistent sample layout with samples to be compared (e.g., "cases" and "controls") equally distributed in each library.},
}
@article {pmid31408638,
year = {2020},
author = {van Dijk, KSE and Parmentier, HK},
title = {Transfer of natural auto-antibodies via egg yolk in chickens divergently selected for natural antibodies binding keyhole limpet hemocyanin.},
journal = {Developmental and comparative immunology},
volume = {102},
number = {},
pages = {103466},
doi = {10.1016/j.dci.2019.103466},
pmid = {31408638},
issn = {1879-0089},
mesh = {Animals ; Antibody Diversity ; Autoantibodies/immunology/*metabolism ; Autoantigens/immunology ; *Breeding ; Chickens ; Egg Yolk/immunology/*metabolism ; Female ; Hemocyanins/*immunology ; Immunity, Maternally-Acquired ; Immunoglobulin G/immunology/metabolism ; Immunoglobulin Idiotypes/immunology/metabolism ; Immunoglobulin M/immunology/metabolism ; Male ; },
abstract = {Barcodes of natural auto-antibody (NAAb) profiles based on staining intensity of isotypes binding numbers of self-(tissue) antigen fragments were suggested as parameters for immune diversity, and related to genetic background and health status in man, rodents and poultry. Here, hens, eggs and hatchlings from chicken lines divergently selected and bred for high (H line) or low (L line) total natural antibodies (NAb) levels in plasma binding keyhole limpet hemocyanin (KLH) at 16 weeks of age were tested for their NAAb repertoire binding chicken liver homogenate (CLH) fragments using quantitative Western immunoblotting. The aims of this study were 1. to detect line differences between the H and L line adult hens, eggs and hatchlings for the IgM and IgG isotypes binding CLH fragments, 2. study the presence of NAAb of both isotypes in yolk and albumen, as well as in hatchlings to detect a maternal NAAb transfer route via the egg to the hatchling, and 3. study whether new self-antigen binding isotypes and idiotypes are present in the hatchling. NAAb binding CLH fragments were found in plasma of adult hens (both IgM and IgG), in yolk (IgG only), and hatchlings (mostly IgG, but low levels of IgM). Auto-profiles of IgM showed homogeneity, while IgG profiles were heterogenic between individual hens and individual hatchlings. Significant higher levels as indicated by staining intensity and number of stained CLH fragments were found in plasma of hens genetically selected for high levels of NAb binding KLH. Lines could be clustered based on their auto-profiles indicating that profiles of self-binding IgM and IgG antibodies are genetically based. Visual comparison, clustering and correlation of hens and their hatchlings showed similarities for the IgG, but not the IgM isotype, indicating maternal transfer of IgG NAAb via the yolk. The IgM profile in the hatchlings on the other hand might represent neonatal self-binding antibody formation. As a consequence, hatchlings initially depend for self-binding antibodies on maternal IgG provision during early life.},
}
@article {pmid31407894,
year = {2019},
author = {Teav, T and Gallart-Ayala, H and van der Velpen, V and Mehl, F and Henry, H and Ivanisevic, J},
title = {Merged Targeted Quantification and Untargeted Profiling for Comprehensive Assessment of Acylcarnitine and Amino Acid Metabolism.},
journal = {Analytical chemistry},
volume = {91},
number = {18},
pages = {11757-11769},
doi = {10.1021/acs.analchem.9b02373},
pmid = {31407894},
issn = {1520-6882},
mesh = {Amino Acids/*analysis/metabolism ; Brain/metabolism ; Brain Chemistry ; Calibration ; Carnitine/*analogs &amp; derivatives/analysis/metabolism ; Chromatography, Liquid/*methods ; Humans ; Hydrophobic and Hydrophilic Interactions ; Isotope Labeling ; Limit of Detection ; Mass Spectrometry/*methods ; Metabolome ; Reproducibility of Results ; },
abstract = {Acylcarnitines and amino acids are key players in energy metabolism; however, analytical methods for comprehensive and straightforward quantitative profiling of these metabolites, without derivatization or use of ion-pairing agents, are lacking. We therefore developed a hydrophilic interaction chromatography (HILIC)-based high-resolution mass spectrometry (HRMS) method for the simultaneous quantification of acylcarnitines and amino acids in a single run, while taking advantage of HRMS data acquired in full-scan mode to screen for additional derivatives and other polar metabolites. A single-step metabolite extraction with internal standard mixture (in methanol) warranted high-throughput sample preparation whose applicability was demonstrated on a panel of human biofluids (i.e., blood plasma, CSF, and urine) and brain tissue. Method accuracy was within 90-106% of validated NIST reference plasma concentrations for the panel of measured amino acids. Amino acid and acylcarnitine extraction recoveries were 87-100% on average, depending on the concentration range spiked. The coefficient of variation (CV) was 1-10% and 1-25% for intra- and interday measurements, respectively, with the highest CVs for the metabolites at the limit of quantification, depending on the biofluid. Acylcarnitine and amino acid signatures or chemical composition barcodes of the different biofluids and human brain tissue were acquired and biofluid- and tissue-associated differences were discussed in the context of their respective physiological roles. Significant differences were observed in the amino acid profiles, whereas acylcarnitine composition did not show biofluid-characteristic or brain region-specific pattern. The retrospective exploration of full-scan all-ion-fragmentation data allowed us to extract the information on unsaturated and hydroxylated acylcarnitine species, amines, and purine and pyrimidine metabolites. This merged targeted and untargeted approach provides an innovative strategy for simultaneous and comprehensive assessment of acylcarnitine and amino acid metabolism in clinical research studies using relevant biofluids and tissue extracts.},
}
@article {pmid31404610,
year = {2019},
author = {Kanduma, EG and Bishop, RP and Githaka, NW and Skilton, RA and Heyne, H and Mwacharo, JM},
title = {Mitochondrial and nuclear multilocus phylogeny of Rhipicephalus ticks from Kenya.},
journal = {Molecular phylogenetics and evolution},
volume = {140},
number = {},
pages = {106579},
doi = {10.1016/j.ympev.2019.106579},
pmid = {31404610},
issn = {1095-9513},
mesh = {Animals ; Base Sequence ; Cell Nucleus/*genetics ; DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; *Genetic Loci ; Haplotypes/genetics ; Kenya ; Mitochondria/*genetics ; *Phylogeny ; Rhipicephalus/anatomy &amp; histology/*classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {The morphological diversity of African ticks of the genus Rhipicephalus and subgenus Boophilus have been studied in detail. However, their taxonomy remains poorly resolved with limited molecular studies performed to improve inter-species discrimination. Herein, ribosomal cytochrome c oxidase I (COI), 12S ribosomal DNA (12S rDNA) and nuclear ribosomal DNA internal transcriber spacer 2 (ITS2) were analyzed in Rhipicephalus tick populations in Kenya. While the morphological and molecular criteria separated R. e. evertsi, R. pulchellus and R. appendiculatus from other members of the genus, except the morphologically similar sibling species R. zambeziensis, this was not the case for other tick populations. COI sequences of Rhipicephalus ticks from Ruma National Park (RNP) in Southwestern Kenya, that were morphologically similar to R. praetextatus/R. simus, a formed distinct clade and barcode gap group. 12S rDNA haplotypes of this population were 99% identical to a GenBank accession of R. muhsamae which is thought to be endemic in West and Central Africa. However, the ITS2 locus indicated that the RNP samples were genetically closest to ticks identified morphologically as R. praetextatus. The COI and 12S rDNA haplotype sequences of R. praetextatus clustered closely with R. simus reference sequences though the two species occurred in distinct barcode gap groups. Our results suggest that the R. simus/R. praetextatus/R. muhsamae comprise a closely related tick species complex found across sub-Saharan Africa and includes the yet to be described RNP population. More studies on the biology, ecology and genomics of all life stages of tick species in the complex may clarify their taxonomic status. A continent-wide study that combines morphology, DNA marker sequencing and emerging methods, such as mass spectrometry and whole-genome resequencing may reveal the diversity and distribution of taxa within the genus Rhipicephalus in sub-Saharan Africa.},
}
@article {pmid31404430,
year = {2019},
author = {Pardo-Diaz, C and Lopera Toro, A and Peña Tovar, SA and Sarmiento-Garcés, R and Sanchez Herrera, M and Salazar, C},
title = {Taxonomic reassessment of the genus Dichotomius (Coleoptera: Scarabaeinae) through integrative taxonomy.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7332},
pmid = {31404430},
issn = {2167-8359},
abstract = {Dung beetles of the subfamily Scarabaeinae are widely recognised as important providers of multiple ecosystem services and are currently experiencing revisions that have improved our understanding of higher-level relationships in the subfamily. However, the study of phylogenetic relationships at the level of genus or species is still lagging behind. In this study we investigated the New World beetle genus Dichotomius, one of the richest within the New World Scarabaeinae, using the most comprehensive molecular and morphological dataset for the genus to date (in terms of number of species and individuals). Besides evaluating phylogenetic relationships, we also assessed species delimitation through a novel Bayesian approach (iBPP) that enables morphological and molecular data to be combined. Our findings support the monophyly of the genus Dichotomius but not that of the subgenera Selenocopris and Dichotomius sensu stricto (s.s). Also, our results do not support the recent synonymy of Selenocopris with Luederwaldtinia. Some species-groups within the genus were recovered, and seem associated with elevational distribution. Our species delimitation analyses were largely congruent irrespective of the set of parameters applied, but the most robust results were obtained when molecular and morphological data were combined. Although our current sampling and analyses were not powerful enough to make definite interpretations on the validity of all species evaluated, we can confidently recognise D. nisus, D. belus and D. mamillatus as valid and well differentiated species. Overall, our study provides new insights into the phylogenetic relationships and classification of dung beetles and has broad implications for their systematics and evolutionary analyses.},
}
@article {pmid31404371,
year = {2019},
author = {Zhang, H and Zhang, Y and Duan, Y},
title = {DNA barcoding of Deltocephalus Burmeister leafhoppers (Cicadellidae, Deltocephalinae, Deltocephalini) in China.},
journal = {ZooKeys},
volume = {867},
number = {},
pages = {55-71},
pmid = {31404371},
issn = {1313-2989},
abstract = {We investigated the feasibility of using the DNA barcode region in identifying Deltocephalus from China. Sequences of the barcode region of the mitochondrial COI gene were obtained for 98 specimens (Deltocephalus vulgaris - 88, Deltocephalus pulicaris - 5, Deltocephalus uncinatus - 5). The average genetic distances among morphological and geographical groups of D. vulgaris ranged from 0.9% to 6.3% and among the three species of Deltocephalus ranged from 16.4% to 21.9% without overlap, which effectively reveals the existence of a "DNA barcoding gap". It is important to assess the status of these morphological variants and explore the genetic variation among Chinese populations of D. vulgaris because the status of this species has led to taxonomic confusion because specimens representing two distinct morphological variants based on the form of the aedeagus are often encountered at a single locality. Forty-five haplotypes (D. vulgaris - 36, D. pulicaris - 5, D. uncinatus - 4) were defined to perform the phylogenetic analyses; they revealed no distinct lineages corresponding either to the two morphotypes of D. vulgaris or to geographical populations. Thus, there is no evidence that these variants represent genetically distinct species.},
}
@article {pmid31404100,
year = {2019},
author = {Li, XY and Pape, T and Zhang, D},
title = {Gasterophilus flavipes (Oestridae: Gasterophilinae): A horse stomach bot fly brought back from oblivion with morphological and molecular evidence.},
journal = {PloS one},
volume = {14},
number = {8},
pages = {e0220820},
pmid = {31404100},
issn = {1932-6203},
mesh = {Animals ; China ; DNA/genetics ; Diptera/*anatomy &amp; histology/classification/genetics/physiology ; Female ; Horse Diseases/psychology ; Horses/parasitology ; Male ; Ovum ; Phylogeny ; Sequence Analysis, DNA ; Stomach/parasitology ; },
abstract = {Species of Gasterophilus Leach are obligate parasites in domestic and wild equids and responsible for cosmopolitan gasterophilosis. Although with only eight species known so far, they have received considerable attention because of their significant veterinary and economic importance. Surprisingly, we found that G. flavipes (Olivier) is a valid species based on morphological characters from male, female and the egg, after spending half a century as a synonym of G. haemorrhoidalis (Linnaeus). In the present study, G. flavipes, G. haemorrhoidalis and G. inermis (Brauer), which are the three closely related species possessing a remarkable mixture of shared morphological characters, are diagnosed and comparatively redescribed; the key to separate adults and eggs are provided, together with a series of high-resolution photographs from all the body parts. COI barcodes do not allow for a separation of G. flavipes, G. haemorrhoidalis and G. inermis, but showed a closer relationship between G. flavipes and G. haemorrhoidalis than the other two combinations, which is consistent with the morphological evidence. Geographically, G. flavipes seems to be common and widespread in the warmer parts of the Palaearctic region. Thus, the epidemiology of gasterophilosis where G. flavipes is known or supposed to occur calls for a more careful veterinarian re-assessment. A decline in the populations of Gasterophilus spp. has been noticed in Europe, but all seven Palaearctic species of Gasterophilus appear to maintain stable populations in Xinjiang (China), which may be explained by a higher biodiversity of equids and less use of anti-parasitic treatments in Xinjiang than in Europe. Our study shows that morphological characters still provide the solid backbone in classification of Gasterophilus at species-level, and updated diagnoses and a key is provided to distinguish G. flavipes, G. haemorrhoidalis and G. inermis, and to facilitate studies of epidemiology, phylogeny and host-parasite co-evolution.},
}
@article {pmid31401123,
year = {2019},
author = {Mallampati, S and Zalles, S and Duose, DY and Hu, PC and Medeiros, LJ and Wistuba, II and Kopetz, S and Luthra, R},
title = {Development and Application of Duplex Sequencing Strategy for Cell-Free DNA-Based Longitudinal Monitoring of Stage IV Colorectal Cancer.},
journal = {The Journal of molecular diagnostics : JMD},
volume = {21},
number = {6},
pages = {994-1009},
pmid = {31401123},
issn = {1943-7811},
support = {R01 CA184843/CA/NCI NIH HHS/United States ; },
mesh = {Adenocarcinoma/*genetics/pathology ; Artifacts ; Cell Line, Tumor ; Cell-Free Nucleic Acids/*genetics ; Colorectal Neoplasms/*genetics/pathology ; Computational Biology/*methods ; Gene Frequency ; Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; In Situ Hybridization ; Liquid Biopsy ; Mutation ; Reproducibility of Results ; },
abstract = {Potential applications of cell-free DNA (cfDNA)-based molecular profiling have used in patients with diverse malignant tumors. However, capturing all cfDNA that originates from tumor cells and identifying true variants present in this minute fraction remain challenges to the widespread application of cfDNA-based liquid biopsies in the clinical setting. In this study, we evaluate a systematic approach and identify key components of wet bench and bioinformatics strategies to address these challenges. We found that concentration of enrichment oligonucleotides, elements of the library preparation, and the structure of adaptors are critical for achieving high enrichment of target regions, retaining variant allele frequencies accurately throughout all involved steps of library preparation, and obtaining high variant coverage. We developed a dual molecular barcode-integrated error elimination strategy to remove sequencing artifacts and a background error correction strategy to distinguish true variants from abundant false-positive variants. We further describe a clinical application of this cfDNA-based duplex sequencing approach that can be used to monitor disease progression in patients with stage IV colorectal cancer. The findings also suggest that cfDNA-based molecular testing observations are highly concordant with observations obtained by traditional imaging methods. Overall, the findings presented in this study have potential implications for early detection of cancer, identification of minimal residual disease, and evaluation of therapeutic responses in patients with cancer.},
}
@article {pmid31400144,
year = {2019},
author = {Woodworth, KA and Frankovich, TA and Freshwater, DW},
title = {Melanothamnus maniticola sp. nov. (Ceramiales, Rhodophyta): an epizoic species evolved for living on the West Indian Manatee.},
journal = {Journal of phycology},
volume = {55},
number = {6},
pages = {1239-1245},
doi = {10.1111/jpy.12912},
pmid = {31400144},
issn = {1529-8817},
mesh = {Animals ; Florida ; *Rhodophyta ; *Seaweed ; *Trichechus manatus ; },
abstract = {Over 35 macroalgae have been documented growing epizoically on sea turtles, and macroalgae are also known to grow on the West Indian Manatee, but the number and identity of these latter species have not been determined. Analysis of DNA sequences of 12 samples collected from different manatees captured in three areas of Florida indicated that they represented a single undescribed species within the Rhodomelaceae genus Melanothamnus. Morphological analysis revealed Melanothamnus characteristics but also a previously undescribed combination of character states. These include eight to nine, but as many as 11, pericentral cells; heavy cortication restricted to the base of thalli, and a sharp transition between the corticated and ecorticate sections of the thallus; cells surrounding the ostiole being similar in size to the outer pericarp cells immediately below, and robust rhizoids that have no terminal lobes and develop from central axial cell filaments instead of pericentral cells. The unique characteristics of the rhizoids may be evolutionary adaptations for anchoring the thalli to manatee epidermis. This species is described as M. maniticola sp. nov.},
}
@article {pmid31397844,
year = {2020},
author = {Rodriguez, OL and Ritz, A and Sharp, AJ and Bashir, A},
title = {MsPAC: a tool for haplotype-phased structural variant detection.},
journal = {Bioinformatics (Oxford, England)},
volume = {36},
number = {3},
pages = {922-924},
pmid = {31397844},
issn = {1367-4811},
support = {F31 NS108797/NS/NINDS NIH HHS/United States ; R01 NS105781/NS/NINDS NIH HHS/United States ; R21 AI117407/AI/NIAID NIH HHS/United States ; S10 OD018522/OD/NIH HHS/United States ; },
mesh = {Genome ; *Genomics ; Haplotypes ; *High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; Software ; },
abstract = {SUMMARY: While next-generation sequencing (NGS) has dramatically increased the availability of genomic data, phased genome assembly and structural variant (SV) analyses are limited by NGS read lengths. Long-read sequencing from Pacific Biosciences and NGS barcoding from 10x Genomics hold the potential for far more comprehensive views of individual genomes. Here, we present MsPAC, a tool that combines both technologies to partition reads, assemble haplotypes (via existing software) and convert assemblies into high-quality, phased SV predictions. MsPAC represents a framework for haplotype-resolved SV calls that moves one step closer to fully resolved, diploid genomes.<br><br>https://github.com/oscarlr/MsPAC.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid31392819,
year = {2019},
author = {Xiao, M and Zou, K and Li, L and Wang, L and Tian, Y and Fan, C and Pei, H},
title = {Stochastic DNA Walkers in Droplets for Super-Multiplexed Bacterial Phenotype Detection.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {58},
number = {43},
pages = {15448-15454},
doi = {10.1002/anie.201906438},
pmid = {31392819},
issn = {1521-3773},
support = {21722502//National Science Foundation of China/International ; },
mesh = {Bacteria/genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic ; DNA Probes/chemistry/*metabolism ; DNA, Bacterial/chemistry/*metabolism ; Escherichia coli/genetics/isolation &amp; purification ; Exodeoxyribonucleases/metabolism ; Fluorescent Dyes/chemistry ; Gold/chemistry ; Metal Nanoparticles/chemistry ; Methicillin-Resistant Staphylococcus aureus/genetics/isolation &amp; purification ; Microscopy, Fluorescence ; Phenotype ; },
abstract = {Pathogen detection is growing in importance in the global health arena because of the high morbidity and mortality associated with bacterial blood stream infections. In this work, we present stochastic DNA walkers in droplets (SDwalker-Drop), a one-step, rapid, and super-multiplex method for ultrahigh-throughput bacterial detection. The SDwalkers, by exploiting cascade signal amplification, endow our analytical platform with fast analysis times and single-cell analysis ability. The autonomous and multiple-step walking behavior of the SDwalkers provides a super-multiplex droplet-encoding strategy by embedding intensity coded barcodes into a sequence of color-multiplexed barcodes. We realized a theoretical coding capacity of 8[3] -1=511 and achieved 20 distinct patterns for bacterial phenotype detection and identification. Moreover, our SDwalker-Drop platform could be readily integrated with a flow cytometer to afford a general approach for super-multiplexed, high-throughput biological assays and screening.},
}
@article {pmid31391880,
year = {2019},
author = {Potowski, M and Kunig, VBK and Losch, F and Brunschweiger, A},
title = {Synthesis of DNA-coupled isoquinolones and pyrrolidines by solid phase ytterbium- and silver-mediated imine chemistry.},
journal = {MedChemComm},
volume = {10},
number = {7},
pages = {1082-1093},
pmid = {31391880},
issn = {2040-2511},
abstract = {DNA-encoded libraries of chemically synthesized compounds are an important small molecule screening technology. The synthesis of encoded compounds in solution is currently restricted to a few DNA-compatible and water-tolerant reactions. Encoded compound synthesis of short DNA-barcodes covalently connected to solid supports benefits from a broad range of choices of organic solvents. Here, we show that this encoded chemistry approach allows for the synthesis of DNA-coupled isoquinolones by an Yb(iii)-mediated Castagnoli-Cushman reaction under anhydrous reaction conditions and for the synthesis of highly substituted pyrrolidines by Ag(i)-mediated 1,3-dipolar azomethine ylide cycloaddition. An encoding scheme for these DNA-barcoded compounds based on a DNA hairpin is demonstrated.},
}
@article {pmid31390056,
year = {2019},
author = {Adelir-Alves, J and Spier, D and Gerum, HLN and Machado, LF and Spach, HL and Boza, BR and Oliveira, C},
title = {Plectorhinchus macrolepis (Actinopterygii: Haemulidae) in the western Atlantic Ocean.},
journal = {Journal of fish biology},
volume = {95},
number = {4},
pages = {1156-1160},
doi = {10.1111/jfb.14117},
pmid = {31390056},
issn = {1095-8649},
support = {306054/2006-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 40001016008P4//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 2016/09204-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2014/26508-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
mesh = {*Animal Distribution ; Animals ; Atlantic Ocean ; Fishes/*genetics ; },
abstract = {Morphometric measurements, meristic counts and DNA barcoding identified the presence of a biglip grunt Plectorhinchus macrolepis in the western Atlantic Ocean. As the species is endemic to the tropical eastern Atlantic Ocean and has not previously been reported in the western Atlantic Ocean, we discuss the possible means by which it might have dispersed to the western Atlantic Ocean. Even though this species is not considered established in Paranaguá Bay, we advocate monitoring of possible new individuals and other exotic fish species.},
}
@article {pmid31387612,
year = {2019},
author = {Uzbas, F and Opperer, F and Sönmezer, C and Shaposhnikov, D and Sass, S and Krendl, C and Angerer, P and Theis, FJ and Mueller, NS and Drukker, M},
title = {BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis.},
journal = {Genome biology},
volume = {20},
number = {1},
pages = {155},
pmid = {31387612},
issn = {1474-760X},
mesh = {Breast Neoplasms/genetics ; Cost-Benefit Analysis ; Embryonic Stem Cells/metabolism ; Female ; Gene Expression Profiling/economics/*methods ; Genomics/economics/*methods ; High-Throughput Nucleotide Sequencing/economics/*methods ; Humans ; Pluripotent Stem Cells/metabolism ; Sequence Analysis, RNA/economics/*methods ; Single-Cell Analysis/economics/methods ; Wnt Signaling Pathway ; Workflow ; },
abstract = {We describe a highly sensitive, quantitative, and inexpensive technique for targeted sequencing of transcript cohorts or genomic regions from thousands of bulk samples or single cells in parallel. Multiplexing is based on a simple method that produces extensive matrices of diverse DNA barcodes attached to invariant primer sets, which are all pre-selected and optimized in silico. By applying the matrices in a novel workflow named Barcode Assembly foR Targeted Sequencing (BART-Seq), we analyze developmental states of thousands of single human pluripotent stem cells, either in different maintenance media or upon Wnt/β-catenin pathway activation, which identifies the mechanisms of differentiation induction. Moreover, we apply BART-Seq to the genetic screening of breast cancer patients and identify BRCA mutations with very high precision. The processing of thousands of samples and dynamic range measurements that outperform global transcriptomics techniques makes BART-Seq first targeted sequencing technique suitable for numerous research applications.},
}
@article {pmid31385271,
year = {2019},
author = {Jelocnik, M and Polkinghorne, A and Pannekoek, Y},
title = {Multilocus Sequence Typing (MLST) of Chlamydiales.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2042},
number = {},
pages = {69-86},
doi = {10.1007/978-1-4939-9694-0_7},
pmid = {31385271},
issn = {1940-6029},
mesh = {Bacterial Typing Techniques/*methods ; Chlamydia/classification/genetics ; Chlamydia Infections/microbiology ; Chlamydiales/classification/*genetics ; DNA, Bacterial/genetics ; Electrophoresis, Agar Gel/methods ; Genes, Essential ; Humans ; Multilocus Sequence Typing/*methods ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Developed two decades ago as a molecular method to provide definite characterization of a bacterial isolate, Multilocus Sequence Typing (MLST) is today globally adopted as a universal fine-detailed molecular typing tool and has been applied to numerous pathogenic and nonpathogenic bacterial as well eukaryotic organisms. MLST utilizes DNA sequence of several conserved housekeeping (HK) genes which are assigned an allelic number, which then collectively constitute an allelic profile or sequence type (ST), a "molecular barcode" of the interrogated bacterial strain or a eukaryotic organism. Here, we describe the principles and molecular approaches for generating MLST data for an analysis of a bacteria in the order Chlamydiales, using a Chlamydia pecorum-specific MLST scheme as an example.},
}
@article {pmid31379792,
year = {2019},
author = {Hoang, MTV and Irinyi, L and Chen, SCA and Sorrell, TC and , and Meyer, W},
title = {Dual DNA Barcoding for the Molecular Identification of the Agents of Invasive Fungal Infections.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1647},
pmid = {31379792},
issn = {1664-302X},
abstract = {Invasive fungal infections, such as aspergillosis, candidiasis, and cryptococcosis, have significantly increased among immunocompromised people. To tackle these infections the first and most decisive step is the accurate identification of the causal pathogen. Routine identification of invasive fungal infections has progressed away from culture-dependent methods toward molecular techniques, including DNA barcoding, a highly efficient and widely used diagnostic technique. Fungal DNA barcoding previously relied on a single barcoding region, the internal transcribed spacer (ITS) region. However, this allowed only for 75% of all fungi to be correctly identified. As such, the translational elongation factor 1α (TEF1α) was recently introduced as the secondary barcode region to close the gap. Both loci together form the dual fungal DNA barcoding scheme. As a result, the ISHAM Barcoding Database has been expanded to include sequences for both barcoding regions to enable practical implementation of the dual barcoding scheme into clinical practice. The present study investigates the impact of the secondary barcode on the identification of clinically important fungal taxa, that have been demonstrated to cause severe invasive disease. Analysis of the barcoding regions was performed using barcoding gap analysis based on the genetic distances generated with the Kimura 2-parameter model. The secondary barcode demonstrated an improvement in identification for all taxa that were unidentifiable with the primary barcode, and when combined with the primary barcode ensured accurate identification for all taxa analyzed, making DNA barcoding an important, efficient and reliable addition to the diagnostic toolset of invasive fungal infections.},
}
@article {pmid31379447,
year = {2019},
author = {Zúñiga-Centeno, A and Sandoval-Carvajal, I and Montero-Astúa, M and Villalobos-Muller, W and Quốc, NB and Hidalgo, NP},
title = {A molecular study of Neophyllaphisvaricolor (Hemiptera, Aphididae) in Costa Rica.},
journal = {ZooKeys},
volume = {865},
number = {},
pages = {123-135},
pmid = {31379447},
issn = {1313-2989},
abstract = {The genus Neophyllaphis (Takahashi) (Aphididae: Neophyllaphidinae) is composed of 18 species; however, in the Americas only nine species have been reported previously. A new species, Neophyllaphisvaricolor Miller &amp; Halbert, was described in 2014 in USA. Colonies resembling those of this new species have been observed in Costa Rica on Podocarpus spp. In order to determine if N.varicolor is also present in Costa Rica, we sampled Neophyllaphis colonies from Podocarpusfalcatus and P.chinensis. Additionally, we sampled individuals from Podocarpus sp. in Spain and Vietnam. DNA of each sample was extracted and used to amplify and sequence the cytochrome c oxidase subunit I (COI) and elongation factor I (EF-1α) partial regions. According to morphological characteristics, sequences comparisons done in GenBank and BOLD, and phylogenetic analyses, the colonies collected from Podocarpus spp. in Costa Rica and the colony from Vietnam corresponded to the species N.varicolor. To the best of our knowledge this is the first report of the presence of N.varicolor in Central America and Vietnam.},
}
@article {pmid31379444,
year = {2019},
author = {Lu, XQ and Wan, JP and Du, XC},
title = {Three new species of Herpetogramma Lederer (Lepidoptera, Crambidae) from China.},
journal = {ZooKeys},
volume = {865},
number = {},
pages = {67-85},
pmid = {31379444},
issn = {1313-2989},
abstract = {Five species of the genus Herpetogramma in China are studied with morphological and DNA barcode data. Herpetogrammabiconvexa Wan, Lu &amp; Du, sp. nov., H.longispina Wan, Lu &amp; Du, sp. nov., and H.brachyacantha Wan, Lu &amp; Du, sp. nov. are described as new. Herpetogrammarudis (Warren) and H.magna (Butler) are newly diagnosed. Photographs of the habitus and genitalia of these five species are provided.},
}
@article {pmid31378760,
year = {2019},
author = {Li, Y and Endo, H and Gotoh, Y and Watai, H and Ogawa, N and Blanc-Mathieu, R and Yoshida, T and Ogata, H},
title = {The Earth Is Small for "Leviathans": Long Distance Dispersal of Giant Viruses across Aquatic Environments.},
journal = {Microbes and environments},
volume = {34},
number = {3},
pages = {334-339},
pmid = {31378760},
issn = {1347-4405},
mesh = {DNA-Directed DNA Polymerase/genetics ; *Ecosystem ; Fresh Water/virology ; Geography ; Giant Viruses/classification/genetics/isolation &amp; purification/*physiology ; Metagenome ; Phylogeny ; Seawater/virology ; Viral Proteins/genetics ; *Water Microbiology ; },
abstract = {Giant viruses of 'Megaviridae' have the ability to widely disperse around the globe. We herein examined 'Megaviridae' communities in four distinct aquatic environments (coastal and offshore seawater, brackish water, and hot spring freshwater), which are distantly located from each other (between 74 and 1,765 km), using a meta-barcoding method. We identified between 593 and 3,627 OTUs in each sample. Some OTUs were detected in all five samples tested as well as in many of the Tara Oceans metagenomes, suggesting the existence of viruses of this family in a wide range of habitats and the ability to circulate on the planet.},
}
@article {pmid31376517,
year = {2019},
author = {Xu, M and Heidmarsson, S and de Boer, HJ and Kool, A and Olafsdottir, ES},
title = {Ethnopharmacology of the club moss subfamily Huperzioideae (Lycopodiaceae, Lycopodiophyta): A phylogenetic and chemosystematic perspective.},
journal = {Journal of ethnopharmacology},
volume = {245},
number = {},
pages = {112130},
doi = {10.1016/j.jep.2019.112130},
pmid = {31376517},
issn = {1872-7573},
mesh = {Ethnopharmacology ; *Lycopodiaceae/chemistry/genetics ; Phylogeny ; Phytochemicals/analysis ; },
abstract = {The most speciose subfamily Huperzioideae (Lycopodiaceae, Lycopodiophyta) contains about 276 species, and some (ca. 20 species) have traditionally been used for the treatment of e.g., dementia, rheumatism and traumatic injury. Ethnopharmacological studies have also contributed to the development of huperzine A as a drug lead, a compound first isolated from the club moss Huperzia serrata (Thunb. ex Murray) Trevis.<br><br>AIM OF THE REVIEW: This review, with a phylogenetic and chemosystematic perspective, intends to highlight plant identification challenges in these taxa with examples from club moss phytochemical and ethnopharmacological studies, as these lead to data inconsistency and confusion. We suggest that future studies should include more details on plant identification including for example plant specimen images and DNA barcoding data. An integrative approach combining DNA barcoding and chemical fingerprinting is also introduced.<br><br>MATERIALS AND METHODS: Literature concerning ethnopharmacology and chemosystematics of Huperzioideae club mosses was searched from databases, e.g. PubMed, Web of Science, SciFinder, etc. Plant names were retrieved from original publications, and compared with up-to-date taxonomic and phylogenetic status. Ethnobotanical uses and herbal preparations were summarized. Production of certain pharmaceutically interesting compounds, such as the alkaloid huperzine A, was explored in a phylogenetic context.<br><br>RESULTS: Most traditionally used club mosses are associated with psychoactivity, followed by medicinal uses against rheumatism and traumatic injury. Herbs are often prepared as infusions, decoctions or tinctures, and this implies importance of water- or aqueous-alcohol-soluble substances, such as alkaloids. Most ethnopharmacological papers on club mosses need to update or correct plant names according to recent taxonomic nomenclature, and there are still a number of unidentified species with traditional use. Advanced LC-MS chemical profiling techniques, enable distinction of genotypes of the same species as well as annotation of potential chemotaxonomic markers. In combination with DNA barcoding, chemosystematics could also help us select plant taxa with higher pharmaceutical potential. Caution should be taken when interpreting bioassay results, in terms of compounds or extract preparation and bioassay standardization.<br><br>CONCLUSION: Huperzioideae club mosses have interesting pharmaceutical potential supported by ethnopharmacological investigations. Bioprospecting of these plants should be preceded by careful plant identification to produce consistent and reproducible data. We expect that DNA barcoding and LC-MS-based chemical fingerprinting could facilitate and improve ethnopharmaceutical studies in selection of club moss taxa.},
}
@article {pmid31374987,
year = {2019},
author = {Herrojo, C and Paredes, F and Mata-Contreras, J and Martín, F},
title = {Chipless-RFID: A Review and Recent Developments.},
journal = {Sensors (Basel, Switzerland)},
volume = {19},
number = {15},
pages = {},
pmid = {31374987},
issn = {1424-8220},
support = {project TEC2016-75650-R//Ministerio de Econom&#xed;a y Competitividad/ ; project 2017SGR-1159//Generalitat de Catalunya/ ; ICREA//Instituci&#xf3; Catalana de Recerca i Estudis Avan&#xe7;ats/ ; },
abstract = {In this paper, a review of the state-of-the-art chipless radiofrequency identification (RFID) technology is carried out. This recent technology may provide low cost tags as long as these tags are not equipped with application specific integrated circuits (ASICs). Nevertheless, chipless-RFID presents a series of technological challenges that have been addressed by different research groups in the last decade. One of these challenges is to increase the data storage capacity of tags, in order to be competitive with optical barcodes, or even with chip-based RFID tags. Thus, the main aim of this paper is to properly clarify the advantages and disadvantages of chipless-RFID technology. Moreover, since the coding information is an important aspect in such technology, the different coding techniques, as well as the main figures of merit used to compare different chipless-RFID tags, will be analyzed.},
}
@article {pmid31366736,
year = {2019},
author = {Glowska, E and Broda, L and Dabert, M},
title = {Insight into the species diversity of the quill mite genus Betasyringophiloidus Skoracki, 2011 (Prostigmata: Syringophilidae) on the basis of the DNA barcodes.},
journal = {Folia parasitologica},
volume = {66},
number = {},
pages = {},
doi = {10.14411/fp.2019.009},
pmid = {31366736},
issn = {1803-6465},
mesh = {Animals ; Arthropod Proteins/analysis ; *Biodiversity ; Birds/*parasitology ; DNA Barcoding, Taxonomic/veterinary ; Electron Transport Complex IV/analysis ; Feathers/*parasitology ; Female ; *Host-Parasite Interactions ; Mites/anatomy &amp; histology/*classification ; *Phylogeny ; Sequence Analysis, DNA/veterinary ; },
abstract = {Betasyringophiloidus Skoracki, 2011 is a genus of quill mites (Prostigmata: Syringophilidae) that is believed to contain mono-, steno- and polyxenous parasites associated with a wide range of passerine birds (Passeriformes) across the world. In this work we applied the DNA-barcode marker (mitochondrial cytochrome c oxidase subunit I gene fragment, COI) to verify whether Betasyringophiloidus schoeniclus (Skoracki, 2002) and Betasyringophiloidus seiuri (Clark, 1964) are actual steno- and polyxenous species associated with the currently recognised host ranges, or their populations are highly host-specific, cryptic species. Our results revealed that a population living on the Tristram's bunting Emberiza tristrami Swinhoe (Emberizidae) in Russia, so far classified as B. schoeniclus, is a new cryptic species Betasyringophiloidus emberizae sp. nov. Both topologies of the neighbor-joining and maximum likelihood phylogenetic trees as well as genetic distance (11.9% Kimura 2-parameter distance) (K2P) support species status of the mite population from E. tristrami. The same data support previously established conspecific status of B. seiuri found on the ovenbird Seiurus aurocapilla (Linnaeus) (Parulidae) (type host) and the northern waterthrush Parkesia noveboracensis (Gmelin) (Parulidae) and expand its range with a population found on a new host species Icterus pustulatus (Wagler) (Icteridae) with intraspecific K2P distance up to 1.9% and interpopulation distances ranging from 1.3 to 3.1%.},
}
@article {pmid31365824,
year = {2019},
author = {Tan, H and Gong, G and Xie, S and Song, Y and Zhang, C and Li, N and Zhang, D and Xu, L and Xu, J and Zheng, J},
title = {Upconversion Nanoparticles@Carbon Dots@Meso-SiO2 Sandwiched Core-Shell Nanohybrids with Tunable Dual-Mode Luminescence for 3D Anti-Counterfeiting Barcodes.},
journal = {Langmuir : the ACS journal of surfaces and colloids},
volume = {35},
number = {35},
pages = {11503-11511},
doi = {10.1021/acs.langmuir.9b01919},
pmid = {31365824},
issn = {1520-5827},
abstract = {Development of advanced fluorescent materials for constructing a secure and unclonable encryption is urgently required; however, their application in anti-counterfeiting applications is a great challenge. In this work, we proposed and synthesized a new type of upconversion nanoparticles@carbon dots@meso-SiO2 nanohybrids by integrating two fluorescent materials of lanthanide-doped NaYF4 upconversion nanoparticles (UCNPs) and carbon dots (CDs) into mesoporous silica (mSiO2) to produce a novel sandwichlike core-shell structure and a dual-mode fluorescence from UCNPs and CDs. By tailoring the UCNP core of different upconversion luminescence, all three kinds of dual-mode luminescent UCNPs@CDs@mSiO2 nanohybrids exhibited typical RGB upconversion luminescence under a 980 nm laser and blue downconversion luminescence under a 365 nm UV light. Due to strong the hydrophilic nature of the nanohybrids, they can be further fabricated into environmentally benign luminescent inks for creating highly secured, fluorescent-based, three-dimensional anti-counterfeiting barcodes via inkjet printing. The resultant UCNPs@CDs@mSiO2 inks with a dual-mode and tunable luminescence nature endow the inkjet-printing barcodes with an extremely high encoding capacity and high security. Such dual-mode fluorescent inks and barcodes are simple to fabricate, easy to view, efficient for coding, and difficult to clone, thus making them promising nanomaterials for anti-counterfeiting applications.},
}
@article {pmid31361857,
year = {2019},
author = {Dunn, L and Anderson, J},
title = {Barcode medication administration implementation in the operating room.},
journal = {American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists},
volume = {76},
number = {10},
pages = {636-637},
doi = {10.1093/ajhp/zxz039},
pmid = {31361857},
issn = {1535-2900},
mesh = {Electronic Data Processing ; Medication Systems, Hospital ; *Operating Rooms ; *Pharmaceutical Preparations ; },
}
@article {pmid31361375,
year = {2019},
author = {Kitazono, S and Sakai, K and Yanagitani, N and Ariyasu, R and Yoshizawa, T and Dotsu, Y and Koyama, J and Saiki, M and Sonoda, T and Nishikawa, S and Uchibori, K and Horiike, A and Nishio, K and Nishio, M},
title = {Barcode sequencing identifies resistant mechanisms to epidermal growth factor receptor inhibitors in circulating tumor DNA of lung cancer patients.},
journal = {Cancer science},
volume = {110},
number = {10},
pages = {3350-3357},
pmid = {31361375},
issn = {1349-7006},
support = {14525177//Japan Agency for Medical Research and Development/ ; },
mesh = {Aged ; Carcinoma, Non-Small-Cell Lung/*genetics/pathology ; Circulating Tumor DNA/*genetics ; DNA Copy Number Variations ; *Drug Resistance, Neoplasm ; ErbB Receptors/genetics ; Female ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Lung Neoplasms/*genetics/pathology ; Male ; Middle Aged ; Neoplasm Staging ; Protein Kinase Inhibitors/pharmacology ; Proto-Oncogene Proteins c-met/genetics ; Sequence Analysis, DNA ; },
abstract = {Most patients with epidermal growth factor receptor (EGFR) mutation-positive non-small cell lung cancer (NSCLC) will inevitably develop acquired resistance induced by treatment with EGFR tyrosine kinase inhibitors (EGFR-TKI). The mechanisms of resistance to EGFR-TKI are multifactorial, and the detection of these mechanisms is critical for treatment choices in patients who have progressed after EGFR-TKI therapy. We evaluated the feasibility of a molecular barcode method using next-generation sequencing to detect multifactorial resistance mechanisms in circulating tumor DNA and compared the results with those obtained using other technologies. Plasma samples were collected from 25 EGFR mutation-positive NSCLC patients after the development of EGFR-TKI resistance. Somatic mutation profiles of these samples were assessed using two methods of next-generation sequencing and droplet digital PCR (ddPCR). The positive rate for EGFR-sensitizing mutations was 18/25 (72.0%) using ddPCR, 17/25 (68.0%) using amplicon sequencing, and 19/25 (76.0%) using molecular barcode sequencing. Rate of the EGFR T790M resistance mutation among patients with EGFR-sensitizing mutations was shown to be 7/18 (38.9%) using ddPCR, 6/17 (35.3%) using amplicon sequencing, and 8/19 (42.1%) using molecular barcode sequencing. Copy number gain in the MET gene was detected in three cases using ddPCR. PIK3CA, KRAS and TP53 mutations were detected using amplicon sequencing. Molecular barcode sequencing detected PIK3CA, TP53, KRAS, and MAP2K1 mutations. Results of the three assays were comparable; however, in cell-free DNA, molecular barcode sequencing detected mutations causing multifactorial resistance more sensitively than did the other assays.},
}
@article {pmid31358254,
year = {2019},
author = {Coyne, E and Northfield, S and Ash, K and Brown-West, L},
title = {Current evidence of education and safety requirements for the nursing administration of chemotherapy: An integrative review.},
journal = {European journal of oncology nursing : the official journal of European Oncology Nursing Society},
volume = {41},
number = {},
pages = {24-32},
doi = {10.1016/j.ejon.2019.05.001},
pmid = {31358254},
issn = {1532-2122},
mesh = {Adult ; Delivery of Health Care/*standards ; Drug Therapy/*standards ; Female ; Humans ; Male ; Middle Aged ; Nursing Staff, Hospital/*education ; Oncology Nursing/*education/*standards ; Patient Safety/*standards ; },
abstract = {PURPOSE: The administration of chemotherapy is a complex task which has many safety issues. Safe administration of chemotherapy by nurses should be evidence-based. The aim of this integrative review was to synthesise the evidence about education and practice requirements for safe administration of chemotherapy by nurses.<br><br>METHOD: A systematic search of four databases identified 17 studies for inclusion in this review. Key words: Nurse, chemotherapy, cytotoxic drug, administration, safety, education. Data extracted from the studies included author, year, aims, design, sample, outcome measures and findings. After screening the articles, extracting study data and completing a summary table, critical appraisal of the studies was completed using the Mixed Methods Appraisal Tool (MMAT).<br><br>RESULTS: All the studies focused on strategies to promote patient and nurse safety during nursing administration of chemotherapy. Content analysis identified five themes: governance, process safeguards, communication, interdisciplinary collaboration and education. Key strategies or interventions that increased patient and/or nurse safety identified were standardised computer-generated chemotherapy orders, barcodes, medication safety procedures, education and simulated learning.<br><br>CONCLUSIONS: This review found low-level evidence exists about the education and safety requirements for nursing administration of chemotherapy. High-level research is needed to assist healthcare services to select evidence-based educational and safety strategies and provide appropriately resourced work environments to support the safe nursing administration of chemotherapy and deliver the best possible patient outcomes.},
}
@article {pmid31357868,
year = {2020},
author = {Pei, Y and Zhang, Q and Wang, Y},
title = {Application of Authentication Evaluation Techniques of Ethnobotanical Medicinal Plant Genus Paris: A Review.},
journal = {Critical reviews in analytical chemistry},
volume = {50},
number = {5},
pages = {405-423},
doi = {10.1080/10408347.2019.1642734},
pmid = {31357868},
issn = {1547-6510},
mesh = {Liliaceae/*chemistry ; Medicine, Chinese Traditional ; Plants, Medicinal/*chemistry ; },
abstract = {Genus Paris mainly distributed in Asia and served as traditional ethnobotanical medicine in China, India, and Nepal. The main aim of this study was to review ethnic minorities medicinal records for Paris in China, the Chinese patent medicines based on Paris materials and the authentication and quality evaluation of Paris based on two parts of analytical technologies and data analysis. This article reviews approximately 100 articles from 1980 to 2019 published on the research of genus Paris materials and their Chinese patent medicines. Additionally, local books were also searched. Five major kinds of chemical techniques have been applied to authentication and quality assessment of Paris and among them, chromatography was the most widely used one, and DNA barcoding technique was the most worth further study. Additionally, more than 70% of the research studies were analyzed by unsupervised pattern-recognition techniques combined with analytical technologies such as spectroscopy. Meanwhile, the data fusion strategy with higher classification ability combined multiple supervised pattern-recognition techniques have been gradually applied to authentication assessment. The optimal analytical technologies and methods applied to Paris qualities for authentication and quality evaluation are greatly important, which could promote the development and utilization for ethnomedicines of Paris.},
}
@article {pmid31355980,
year = {2019},
author = {Wright, ES and Vetsigian, KH},
title = {Stochastic exits from dormancy give rise to heavy-tailed distributions of descendants in bacterial populations.},
journal = {Molecular ecology},
volume = {28},
number = {17},
pages = {3915-3928},
doi = {10.1111/mec.15200},
pmid = {31355980},
issn = {1365-294X},
mesh = {DNA Barcoding, Taxonomic ; Selection, Genetic ; Stochastic Processes ; Streptomyces/*genetics ; },
abstract = {Variance in reproductive success is a major determinant of the degree of genetic drift in a population. While many plants and animals exhibit high variance in their number of progeny, far less is known about these distributions for microorganisms. Here, we used a strain barcoding approach to quantify variability in offspring number among replicate bacterial populations and developed a Bayesian method to infer the distribution of descendants from this variability. We applied our approach to measure the offspring distributions for five strains of bacteria from the genus Streptomyces after germination and growth in a homogenous laboratory environment. The distributions of descendants were heavy-tailed, with a few cells effectively 'winning the jackpot' to become a disproportionately large fraction of the population. This extreme variability in reproductive success largely traced back to initial populations of spores stochastically exiting dormancy, which provided early-germinating spores with an exponential advantage. In simulations with multiple dormancy cycles, heavy-tailed distributions of descendants decreased the effective population size by many orders of magnitude and led to allele dynamics differing substantially from classical population genetics models with matching effective population size. Collectively, these results demonstrate that extreme variability in reproductive success can occur even in growth conditions that are far more homogeneous than the natural environment. Thus, extreme variability in reproductive success might be an important factor shaping microbial population dynamics with implications for predicting the fate of beneficial mutations, interpreting sequence variability within populations and explaining variability in infection outcomes across patients.},
}
@article {pmid31355548,
year = {2019},
author = {Su, YY and Li, WJ and Yang, L and Ding, DD and Xiang, L},
title = {[Rapid identification of Cordyceps and its products using DNA barcoding method].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {44},
number = {10},
pages = {1965-1973},
doi = {10.19540/j.cnki.cjcmm.20190131.002},
pmid = {31355548},
issn = {1001-5302},
mesh = {Cordyceps/*classification ; *DNA Barcoding, Taxonomic ; DNA Primers ; Mycelium ; Polymerase Chain Reaction ; },
abstract = {Cordyceps is one of the most valuable traditional Chinese medicines. There are various counterfeits in markets because of high price and limited output. In this study,116 Cordyceps,146 hosts and 29 related products were collected and detected by using normal DNA barcoding technology and specific PCR method. The results indicated that Cordyceps and its adulterants could be distinguished from each other through DNA barcoding technology based on ITS and COⅠsequences. Two pairs specific primers ITSSF1/ITSSR1 and ITSSF2/ITSSR2 were developed to amplify 297 bp and 136 bp ITS regions of Cordyceps sinensis,respectively. It could be used to identify C. sinensis specifically and rapidly. Furthermore,specific primers ITSSF1/ITSSR1 and ITSSF2/ITSSR2 combined with ITS and COⅠsequences could differentiate powder Cordyceps from fermentation mycelia and could identify related products. Therefore,the method developed from this study could be applied to identify the powder of Cordyceps from fermentation mycelia and related products efficiently.},
}
@article {pmid31348830,
year = {2019},
author = {Maher, GJ and Bernkopf, M and Koelling, N and Wilkie, AOM and Meistrich, ML and Goriely, A},
title = {The impact of chemo- and radiotherapy treatments on selfish de novo FGFR2 mutations in sperm of cancer survivors.},
journal = {Human reproduction (Oxford, England)},
volume = {34},
number = {8},
pages = {1404-1415},
pmid = {31348830},
issn = {1460-2350},
support = {102731/WT_/Wellcome Trust/United Kingdom ; 102731/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; 090532/WT_/Wellcome Trust/United Kingdom ; G0902418/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 091182/WT_/Wellcome Trust/United Kingdom ; MC_UU_12025/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Adult ; Antineoplastic Agents/*administration &amp; dosage/therapeutic use ; *Cancer Survivors ; DNA Damage/drug effects/radiation effects ; Humans ; Male ; Mutation/drug effects/radiation effects ; Neoplasms/drug therapy/radiotherapy/*therapy ; Radiotherapy ; Receptor, Fibroblast Growth Factor, Type 2/*genetics ; Semen Analysis ; Sperm Count ; Spermatogenesis/drug effects/radiation effects ; Spermatozoa/drug effects/metabolism/*radiation effects ; },
abstract = {STUDY QUESTION: What effect does cancer treatment have on levels of spontaneous selfish fibroblast growth factor receptor 2 (FGFR2) point mutations in human sperm?<br><br>SUMMARY ANSWER: Chemotherapy and radiotherapy do not increase levels of spontaneous FGFR2 mutations in sperm but, unexpectedly, highly-sterilizing treatments dramatically reduce the levels of the disease-associated c.755C&#x2009;>&#x2009;G (Apert syndrome) mutation in sperm.<br><br>WHAT IS KNOWN ALREADY: Cancer treatments lead to short-term increases in gross DNA damage (chromosomal abnormalities and DNA fragmentation) but the long-term effects, particularly at the single nucleotide resolution level, are poorly understood. We have exploited an ultra-sensitive assay to directly quantify point mutation levels at the FGFR2 locus.<br><br>STUDY DESIGN, SIZE, DURATION: 'Selfish' mutations are disease-associated mutations that occur spontaneously in the sperm of most men and their levels typically increase with age. Levels of mutations at c.752-755 of FGFR2 (including c.755C&#x2009;>&#x2009;G and c.755C&#x2009;>&#x2009;T associated with Apert and Crouzon syndromes, respectively) in semen post-cancer treatment from 18 men were compared to levels in pre-treatment samples from the same individuals (n&#x2009;=&#x2009;4) or levels in previously screened population controls (n&#x2009;=&#x2009;99).<br><br>Cancer patients were stratified into four different groups based on the treatments they received and the length of time for spermatogenesis recovery. DNA extracted from semen samples was analysed using a previously established highly sensitive assay to identify mutations at positions c.752-755 of FGFR2. Five to ten micrograms of semen genomic DNA was spiked with internal controls for quantification purposes, digested with MboI restriction enzyme and gel extracted. Following PCR amplification, further MboI digestion and a nested PCR with barcoding primers, samples were sequenced on Illumina MiSeq. Mutation levels were determined relative to the spiked internal control; in individuals heterozygous for a nearby common single nucleotide polymorphism (SNP), mutations were phased to their respective alleles.<br><br>Patients treated with moderately-sterilizing alkylating regimens and who recovered spermatogenesis within <3&#xa0;years after therapy (Group 3, n&#x2009;=&#x2009;4) or non&#x2009;-&#x2009;alkylating chemotherapy and/or low gonadal radiation doses (Group 1, n&#x2009;=&#x2009;4) had mutation levels similar to untreated controls. However, patients who had highly-sterilizing alkylating treatments (i.e. >5&#xa0;years to spermatogenesis recovery) (Group 2, n&#x2009;=&#x2009;7) or pelvic radiotherapy (Group 4, n&#x2009;=&#x2009;3) exhibited c.755C&#x2009;>&#x2009;G mutation levels at or below background. Two patients (A and B) treated with highly-sterilizing alkylating agents demonstrated a clear reduction from pre-treatment levels; however pre-treatment samples were not available for the other patients with low mutation levels. Therefore, although based on their age we would expect detectable levels of mutations, we cannot exclude the possibility that these patients also had low mutation levels pre-treatment. In three patients with low c.755C&#x2009;>&#x2009;G levels at the first timepoint post-treatment, we observed increasing mutation levels over time. For two such patients we could phase the mutation to a nearby polymorphism (SNP) and determine that the mutation counts likely originated from a single or a small number of mutational events.<br><br>This study was limited to 18 patients with different treatment regimens; for nine of the 18 patients, samples from only one timepoint were available. Only 12 different de novo substitutions at the FGFR2 c.752-755 locus were assessed, two of which are known to be disease associated.<br><br>Our data add to the body of evidence from epidemiological studies and experimental data in humans suggesting that male germline stem cells are resilient to the accumulation of spontaneous mutations. Collectively, these data should provide physicians and health-care professionals with reassuring experimental-based evidence for counselling of male cancer patients contemplating their reproductive options several years after treatment.<br><br>This work was primarily supported by grants from the Wellcome (grant 091182 to AG and AOMW; grant 102&#x2009;731 to AOMW), the University of Oxford Medical Sciences Division Internal Fund (grant 0005128 to GJM and AG), the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre Programme (to AG) and the US National Institutes of Health (to MLM). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. None of the authors has any conflicts of interest to declare.<br><br>TRIAL REGISTRATION NUMBER: NA.},
}
@article {pmid31347161,
year = {2020},
author = {Katemo Manda, B and Snoeks, J and Decru, E and Bills, R and Vreven, E},
title = {Enteromius thespesios (Teleostei: Cyprinidae): a new minnow species with a remarkable sexual dimorphism from the south-eastern part of the Upper Congo River.},
journal = {Journal of fish biology},
volume = {96},
number = {5},
pages = {1160-1175},
doi = {10.1111/jfb.14108},
pmid = {31347161},
issn = {1095-8649},
support = {//Mbisa Congo project (2013-2018)/ ; //RMCA/ ; //Belgian Development Cooperation/ ; },
mesh = {Animals ; Congo ; Cyprinidae/*anatomy &amp; histology/*classification ; Female ; Male ; Rivers ; Sex Characteristics ; Species Specificity ; },
abstract = {A new minnow species, Enteromius thespesios, is described from the south-eastern part of the upper Congo River; that is, the Kalule Nord, the Luvilombo and the Chambeshi Rivers. Enteromius thespesios belongs to the group of the soft-rayed species of Enteromius from the Congo Basin; that is, those with a weakly ossified, flexible last unbranched dorsal-fin ray that lacks serrations along its posterior edge. Within this group, E. thespesios is most similar to E. humeralis, from which it is distinguished by a higher number of circumpeduncular scales and shorter anterior and posterior barbels. Enteromius thespesios is a rheophilic and territorial species. It exhibits a marked sexual dimorphism, with males having: a red band towards the distal edge of dorsal, caudal and, to a lesser degree, anal fin; nuptial tubercles; a longer snout; longer pectoral fins; a shorter anal fin. This study gives extensive consideration to sexual shape differences for a species of Enteromius and also briefly reviews the current knowledge of sexual dimorphism in the species of Enteromius from the Congo Basin. Some conservation issues related to the new species are also highlighted.},
}
@article {pmid31346443,
year = {2019},
author = {Zhang, Z and Cheng, Q and Ge, Y},
title = {The complete mitochondrial genome of Rhynchocypris oxycephalus (Teleostei: Cyprinidae) and its phylogenetic implications.},
journal = {Ecology and evolution},
volume = {9},
number = {13},
pages = {7819-7837},
pmid = {31346443},
issn = {2045-7758},
abstract = {Rhynchocypris oxycephalus (Teleostei: Cyprinidae) is a typical small cold water fish, which is distributed widely and mainly inhabits in East Asia. Here, we sequenced and determined the complete mitochondrial genome of R. oxycephalus and studied its phylogenetic implication. R. oxycephalus mitogenome is 16,609 bp in length (GenBank accession no.: MH885043), and it contains 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and two noncoding regions (the control region and the putative origin of light-strand replication). 12 PCGs started with ATG, while COI used GTG as the start codon. The secondary structure of tRNA-Ser (AGN) lacks the dihydrouracil (DHU) arm. The control region is 943bp in length, with a termination-associated sequence, six conserved sequence blocks (CSB-1, CSB-2, CSB-3, CSB-D, CSB-E, CSB-F), and a repetitive sequence. Phylogenetic analysis was performed with maximum likelihood and Bayesian methods based on the concatenated nucleotide sequence of 13 PCGs and the complete sequence without control region, and the result revealed that the relationship between R. oxycephalus and R. percnurus is closest, while the relationship with R. kumgangensis is farthest. The genus Rhynchocypris is revealed as a polyphyletic group, and R. kumgangensis had distant relationship with other Rhynchocypris species. In addition, COI and ND2 genes are considered as the fittest DNA barcoding gene in genus Rhynchocypris. This work provides additional molecular information for studying R. oxycephalus conservation genetics and evolutionary relationships.},
}
@article {pmid31346417,
year = {2019},
author = {Li, J and Jin, Q and Zhu, GP and Jiang, C and Zhang, AB},
title = {Phylogeography of Dendrolimus punctatus (Lepidoptera: Lasiocampidae): Population differentiation and last glacial maximum survival.},
journal = {Ecology and evolution},
volume = {9},
number = {13},
pages = {7480-7496},
pmid = {31346417},
issn = {2045-7758},
abstract = {UNLABELLED: Although the Masson pine moth, Dendrolimus punctatus, is one of the most destructive forest pest insects and is an endemic condition in China, we still do not fully understand the patterns of how its distribution range varies in response to Quaternary climatic oscillations. Here, we sequenced one maternally inherited mitochondrial gene (COI) and biparentally inherited nuclear data (ITS1 and ITS2) among 23 natural populations across the entire range of the species in China. A total of 51 mitotypes and 38 ribotypes were separately obtained using mtDNA and ITS1 data. Furthermore, significant phylogeographical structure (N ST > G ST, p < 0.01) were detected. The spatial distribution of mitotypes implied that two distinct groups existed in the species: one in the southwest distribution, including 10 locations, and the other located in the northeast region of China. It is suggested, therefore, that each group was derived from ancestors that occupied different isolated refugia during previous periods, possibly last glacial maximum. Mismatch distribution and Bayesian population dynamics analysis suggested the population size underwent sudden expansion, which is consistent with the results of ecological niche modeling. As a typical phytophagous insect, the history of population expansion was in accordance with the host plants, providing abundant food resources and habitat. Intraspecific success rate of barcoding identification was lower than interspecific ones, indicating a level of difficulty in barcoding individuals from different populations. However, it still provides an early insight into the pattern of genetic diversity within a species.<br><br>OPEN RESEARCH BADGES: This article has been awarded an Open Data and Open Materials. All materials and data are publicly accessible via the Open Science Framework at https://doi.org/10.5061/dryad.2df87g2. Learn more about the Open Practices badges from the Center for Open Science: https://osf.io/tvyxz/wiki.},
}
@article {pmid31346415,
year = {2019},
author = {Anabalón, L and Encina-Montoya, F and Sánchez, P and Solano, J and Benavente, F and Guiñez, B and Olivares, F and Oberti, C and Vega, R},
title = {High-resolution melting of the cytochrome B gene in fecal DNA: A powerful approach for fox species identification of the Lycalopex genus in Chile.},
journal = {Ecology and evolution},
volume = {9},
number = {13},
pages = {7448-7454},
pmid = {31346415},
issn = {2045-7758},
abstract = {Easy, economic, precise species authentication is currently necessary in many areas of research and diagnosis in molecular biology applied to conservation studies of endangered species. Here, we present a new method for the identification of three fox species of the Lycalopex genus in Chile. We developed an assay based on high-resolution melt analysis of the mitochondrial cytochrome B gene, allowing a simple, low cost, fast, and accurate species determination. To validate the assay applicability for noninvasive samples, we collected fecal samples in the Atacama Desert, finding unexpectedly one species outside of its known distribution range. We conclude that the assay has a potential to become a valuable tool for a standardized genetic monitoring of the Lycalopex species in Chile.},
}
@article {pmid31346307,
year = {2019},
author = {Oya, Y and Kimura, T and Kajihara, H},
title = {Description of a new species of Paraplehnia (Polycladida, Stylochoidea) from Japan, with inference on the phylogenetic position of Plehniidae.},
journal = {ZooKeys},
volume = {864},
number = {},
pages = {1-13},
pmid = {31346307},
issn = {1313-2989},
abstract = {We describe a new species of polyclad flatworm, Paraplehniaseisuiae sp. nov., from 298-310 m depths in the Sea of Kumano, West Pacific, Japan. Paraplehniaseisuiae sp. nov. is characterized by i) a developed muscular wall proximally occupying about one-third of the prostatic vesicle, ii) no common duct between the spermiducal bulbs and the prostatic vesicle, and iii) a genital pit between the male and female gonopores. We provide a partial sequence (712 bp) of the mitochondrial cytochrome c oxidase subunit I gene as a DNA barcode for the species. Our phylogenetic analyses based on 603-bp 28S rDNA sequences indicate that P.seisuiae sp. nov. is nested in a clade consisting of stylochoid species along with unidentified species of Stylochus. It suggests that Plehniidae belongs to Stylochoidea, although this should be confirmed by future studies that contain Plehniaarctica (Plehn, 1896), the type species of the type genus of the family. The interfamily relationship among the superfamily Stylochoidea remains poorly resolved.},
}
@article {pmid31343800,
year = {2019},
author = {Yao, Y and Gao, Z and Lv, Y and Lin, X and Liu, Y and Du, Y and Hu, F and Zhao, YS},
title = {Heteroepitaxial Growth of Multiblock Ln-MOF Microrods for Photonic Barcodes.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {58},
number = {39},
pages = {13803-13807},
doi = {10.1002/anie.201907433},
pmid = {31343800},
issn = {1521-3773},
support = {2017YFA0204502//Ministry of Science and Technology of the People's Republic of China/ ; },
abstract = {Micro/nanoscale multicolor barcodes with unique identifiability and a small footprint play significant roles in applications such as multiplexed labeling and tracking systems. Now, a strategy is reported to design multicolor photonic barcodes based on 1D Ln-MOF multiblock heterostructures, where the domain-controlled emissive colors and different block lengths constitute the fingerprint of a corresponding heterostructure. The excellent heteroepitaxial growth characteristics of MOFs enable the effective modulation of the coding structures, thereby remarkably increasing the encoding capacity. The as-prepared multicolor barcodes enable an efficient authentication and exhibit great potential in fulfilling the functions of anti-counterfeiting, information security, and so on. The results will pave an avenue to novel hybrid MOFs for optical data recording and security labels.},
}
@article {pmid31341746,
year = {2019},
author = {Wang, S and Guo, H and Li, J and Li, W and Wang, Q and Yu, X},
title = {Evaluation of five regions as DNA barcodes for identification of Lepista species (Tricholomataceae, Basidiomycota) from China.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7307},
pmid = {31341746},
issn = {2167-8359},
abstract = {BACKGROUND: Distinguishing among species in the genus Lepista is difficult because of their similar morphologies.<br><br>METHODS: To identify a suitable DNA barcode for identification of Lepista species, we assessed the following five regions: internal transcribed spacer (ITS), the intergenic spacer (IGS), nuclear ribosomal RNA subunit, mitochondrial small subunit rDNA, and tef1. A total of 134 sequences from 34 samples belong to eight Lepista species were analyzed. The utility of each region as a DNA barcode was assessed based on the success rates of its PCR amplification and sequencing, and on its intra- and inter-specific variations.<br><br>RESULTS: The results indicated that the ITS region could distinguish all species tested. We therefore propose that the ITS region can be used as a DNA barcode for the genus Lepista. In addition, a phylogenetic tree based on the ITS region showed that the tested eight Lepista species, including two unrecognized species, formed eight separate and well-supported clades.},
}
@article {pmid31341290,
year = {2019},
author = {Li, S and Sun, J and Allesøe, R and Datta, K and Bao, Y and Oliveira, G and Forman, J and Jin, R and Olsen, LR and Keskin, DB and Shukla, SA and Wu, CJ and Livak, KJ},
title = {RNase H-dependent PCR-enabled T-cell receptor sequencing for highly specific and efficient targeted sequencing of T-cell receptor mRNA for single-cell and repertoire analysis.},
journal = {Nature protocols},
volume = {14},
number = {8},
pages = {2571-2594},
pmid = {31341290},
issn = {1750-2799},
support = {P01 CA229092/CA/NCI NIH HHS/United States ; P50 CA101942/CA/NCI NIH HHS/United States ; R21 CA216772/CA/NCI NIH HHS/United States ; R01 CA155010/CA/NCI NIH HHS/United States ; R01 CA279391/CA/NCI NIH HHS/United States ; U24 CA224331/CA/NCI NIH HHS/United States ; R50 CA211482/CA/NCI NIH HHS/United States ; },
mesh = {Cells, Cultured ; Cloning, Molecular ; Humans ; Polymerase Chain Reaction/*methods ; RNA, Messenger/*genetics/metabolism ; Receptors, Antigen, T-Cell/*genetics/metabolism ; Ribonuclease H/metabolism ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis/*methods ; T-Lymphocytes/chemistry/cytology ; },
abstract = {RNase H-dependent PCR-enabled T-cell receptor sequencing (rhTCRseq) can be used to determine paired alpha/beta T-cell receptor (TCR) clonotypes in single cells or perform alpha and beta TCR repertoire analysis in bulk RNA samples. With the enhanced specificity of RNase H-dependent PCR (rhPCR), it achieves TCR-specific amplification and addition of dual-index barcodes in a single PCR step. For single cells, the protocol includes sorting of single cells into plates, generation of cDNA libraries, a TCR-specific amplification step, a second PCR on pooled sample to generate a sequencing library, and sequencing. In the bulk method, sorting and cDNA library steps are replaced with a reverse-transcriptase (RT) reaction that adds a unique molecular identifier (UMI) to each cDNA molecule to improve the accuracy of repertoire-frequency measurements. Compared to other methods for TCR sequencing, rhTCRseq has a streamlined workflow and the ability to analyze single cells in 384-well plates. Compared to TCR reconstruction from single-cell transcriptome sequencing data, it improves the success rate for obtaining paired alpha/beta information and ensures recovery of complete complementarity-determining region 3 (CDR3) sequences, a prerequisite for cloning/expression of discovered TCRs. Although it has lower throughput than droplet-based methods, rhTCRseq is well-suited to analysis of small sorted populations, especially when analysis of 96 or 384 single cells is sufficient to identify predominant T-cell clones. For single cells, sorting typically requires 2-4 h and can be performed days, or even months, before library construction and data processing, which takes ~4 d; the bulk RNA protocol takes ~3 d.},
}
@article {pmid31341251,
year = {2019},
author = {Hernández, CM and Witting, J and Willis, C and Thorrold, SR and Llopiz, JK and Rotjan, RD},
title = {Evidence and patterns of tuna spawning inside a large no-take Marine Protected Area.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {10772},
pmid = {31341251},
issn = {2045-2322},
mesh = {Animals ; Chlorophyll A/analysis ; Conservation of Natural Resources ; Larva ; Pacific Ocean ; Reproduction ; Seawater/chemistry ; Temperature ; Tuna/*physiology ; },
abstract = {The Phoenix Islands Protected Area (PIPA), one of the world's largest marine protected areas, represents 11% of the exclusive economic zone of the Republic of Kiribati, which earns much of its GDP by selling tuna fishing licenses to foreign nations. We have determined that PIPA is a spawning area for skipjack (Katsuwonus pelamis), bigeye (Thunnus obesus), and yellowfin (Thunnus albacares) tunas. Our approach included sampling larvae on cruises in 2015-2017 and using a biological-physical model to estimate spawning locations for collected larvae. Temperature and chlorophyll conditions varied markedly due to observed ENSO states: El Niño (2015) and neutral (2016-2017). However, larval tuna distributions were similar amongst years. Generally, skipjack larvae were patchy and more abundant near PIPA's northeast corner, while Thunnus larvae exhibited lower and more even abundances. Genetic barcoding confirmed the presence of bigeye (Thunnus obesus) and yellowfin (Thunnus albacares) tuna larvae. Model simulations indicated that most of the larvae collected inside PIPA in 2015 were spawned inside, while stronger currents in 2016 moved more larvae across PIPA's boundaries. Larval distributions and relative spawning output simulations indicated that both focal taxa spawned inside PIPA in all 3 study years, demonstrating that PIPA is protecting viable tuna spawning habitat.},
}
@article {pmid31340637,
year = {2019},
author = {Weckman, NE and Ermann, N and Gutierrez, R and Chen, K and Graham, J and Tivony, R and Heron, A and Keyser, UF},
title = {Multiplexed DNA Identification Using Site Specific dCas9 Barcodes and Nanopore Sensing.},
journal = {ACS sensors},
volume = {4},
number = {8},
pages = {2065-2072},
doi = {10.1021/acssensors.9b00686},
pmid = {31340637},
issn = {2379-3694},
mesh = {*Biosensing Techniques ; DNA/*analysis ; *Electrochemical Techniques ; Fluorescent Dyes/*chemistry ; *Nanopores ; },
abstract = {Decorating double-stranded DNA with dCas9 barcodes to identify characteristic short sequences provides an alternative to fully sequencing DNA samples for rapid and highly specific analysis of a DNA sample. Solid state nanopore sensors are especially promising for this type of single-molecule sensing because of the ability to analyze patterns in the ionic current signatures of DNA molecules. Here, we systematically demonstrate the use of highly specific dCas9 probes to create unique barcodes on the DNA that can be read out using nanopore sensors. Single dCas9 probes are targeted to various positions on DNA strands up to 48 kbp long and are effectively measured in high salt conditions typical of nanopore sensing. Multiple probes bound to the same DNA strand at characteristic target sequences create distinct barcodes of double and triple peaks. Finally, double and triple barcodes are used to simultaneously identify two different DNA targets in a background mixture of bacterial DNA. Our method forms the basis of a fast and versatile assay for multiplexed DNA sensing applications in complex samples.},
}
@article {pmid31339181,
year = {2019},
author = {Rosińska, J and Piotrowicz, R and Celiński, K and Dabert, M and Rzymski, P and Klimaszyk, P},
title = {The Reappearance of An Extremely Rare and Critically Endangered Nitella translucens (Charophyceae) in Poland.},
journal = {Journal of phycology},
volume = {55},
number = {6},
pages = {1412-1415},
doi = {10.1111/jpy.12905},
pmid = {31339181},
issn = {1529-8817},
mesh = {*Charophyceae ; Europe ; Lakes ; *Nitella ; Phosphorus ; Poland ; },
abstract = {We report the reappearance of the rare charophyte Nitella translucens in Poland. It was identified in the soft-water lobelian Lake Jeleń (North Poland) during 2013 and 2018 phytolittoral surveys. This species is considered critically endangered in various European countries and was previously classified as extinct in Poland. Its occurrence was confirmed using morphological and molecular data (ITS1-18S, ITS2-28S, rDNA, and rbcL). The N. translucens occupied ~20% of the lake bottom, at depths of 1.5-6.5 m, water pH 7.5-8.6, conductivity of 59-66 μS · cm[-1] , and total nitrogen and phosphorus during growing season in the range of 1.1-1.4 mg · L[-1] and 0.07-0.1 mg · L[-1] , respectively. It co-occurred mainly with plant species typical for lobelia lakes: Isoetes lacustris, Littorella uniflora, and Myriophyllum alterniflorum, as well as Ceratophyllum demersum and Elodea canadensis, which are characteristic for eutrophicated waters. It appears that N. translucens may thrive in lobelia lakes during their transformation to more eutrophic states.},
}
@article {pmid31337759,
year = {2019},
author = {Ma, X and Liang, H and Cui, X and Liu, Y and Lu, H and Ning, W and Poon, NY and Ho, B and Zhou, K},
title = {A standard for near-scarless plasmid construction using reusable DNA parts.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {3294},
pmid = {31337759},
issn = {2041-1723},
mesh = {DNA/*chemistry ; Escherichia coli/genetics ; Genetic Engineering/*methods ; Metabolic Engineering/methods ; Plasmids/*chemistry ; Saccharomyces cerevisiae/genetics ; Synthetic Biology/*methods ; },
abstract = {Here we report GT (Guanin/Thymine) standard (GTS) for plasmid construction under which DNA sequences are defined as two types of standard, reusable parts (fragment and barcode). We develop a technology that can efficiently add any two barcodes to two ends of any fragment without leaving scars in most cases. We can assemble up to seven such barcoded fragments into one plasmid by using one of the existing DNA assembly methods, including CLIVA, Gibson assembly, In-fusion cloning, and restriction enzyme-based methods. Plasmids constructed under GTS can be easily edited, and/or be further assembled into more complex plasmids by using standard DNA oligonucleotides (oligos). Based on 436 plasmids we constructed under GTS, the averaged accuracy of the workflow was 85.9%. GTS can also construct a library of plasmids from a set of fragments and barcodes combinatorically, which has been demonstrated to be useful for optimizing metabolic pathways.},
}
@article {pmid31337110,
year = {2019},
author = {Huang, Y and Li, Z and Wang, C and Zou, C and Wen, W and Shao, J and Zhu, X},
title = {psbE-psbL and ndhA Intron, the Promising Plastid DNA Barcode of Fagopyrum.},
journal = {International journal of molecular sciences},
volume = {20},
number = {14},
pages = {},
pmid = {31337110},
issn = {1422-0067},
mesh = {*DNA Barcoding, Taxonomic ; *DNA, Plant ; Fagopyrum/*classification/*genetics ; *Genes, Plant ; Genetic Markers ; *Introns ; Phenotype ; Phylogeny ; Plastids/*genetics ; },
abstract = {Buckwheat is an important functional food material with high nutritional value. However, it is still a difficult task for the taxonomy studies of wild buckwheat that are only based on morphology. In order to demonstrate the most efficient DNA barcode in the phylogenetic research of buckwheat, promote the investigation of wild buckwheat, and also reveal the phylogenetic relationship between Fagopyrum species, psbE-psbL and ndhA intron were validated here, which previously have been proved to be promising DNA barcode candidates for phylogenetic studies in genera Fagopyrum. Meanwhile, ndhA intron + psbE-psbL and matK + psbE-psbL could distinguish the relationship between species clearly. Combining the results of morphology and molecular markers, we suggested the buckwheat species should be divided into two subgroups, one subgroup consisted of F. tataricum, F. esculentum, F. cymosum and its related wild species, and the other subgroup included other wild buckwheat species. Our results could fulfill molecular markers of taxonomy research in genera Fagopyrum, promote wild buckwheat species identification, and assist in the use of wild buckwheat resources in the future. Additionally, the phylogenetic relationship revealed here could provide valuable information for molecular breeding of buckwheat and provide reference for inter-species hybridization.},
}
@article {pmid31337082,
year = {2019},
author = {He, Q and Bao, M and Hass, K and Lin, W and Qin, P and Du, K},
title = {Perspective of Molecular Diagnosis in Healthcare: From Barcode to Pattern Recognition.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {9},
number = {3},
pages = {},
pmid = {31337082},
issn = {2075-4418},
abstract = {Barcode technology has a broad spectrum of applications including healthcare, food security, and environmental monitoring, due to its ability to encode large amounts of information. With the rapid development of modern molecular research, barcodes are utilized as a reporter with different molecular combinations to label many biomolecular targets, including genomic and metabolic elements, even with multiplex targeting. Along with the advancements in barcoded bioassay, the improvements of various designs of barcode components, encoding and decoding strategies, and their portable adoption are indispensable in satisfying multiple purposes, such as medical confirmation and point-of-care (POC) testing. This perspective briefly discusses the current direction and progress of barcodes development and provides a hypothesis for barcoded bioassay in the near future.},
}
@article {pmid31333328,
year = {2019},
author = {Du, J and Loh, KH and Then, AY and Zheng, X and Teguh Peristiwady, and Rizman-Idid, M and Alias, M},
title = {First record of the dotted grouper Epinephelusepistictus (Temminck &amp; Schlegel, 1843) (Perciformes, Serranidae) in Malaysia.},
journal = {ZooKeys},
volume = {861},
number = {},
pages = {107-118},
pmid = {31333328},
issn = {1313-2989},
abstract = {Five specimens of Epinephelusepistictus (Temminck &amp; Schlegel, 1843) were collected from a major landing site located on the west coast of Peninsula Malaysia during a fish faunal survey on 23 August 2017. The present study extends the distribution range of E.epistictus southwards from Andaman Sea to the Strait of Malacca. Species identification was confirmed by colour pattern and DNA barcoding (567 bp of cytochrome C oxidase I) of all E.epistictus specimens and nine closely related Epinephelus species. The interspecies genetic distance ranged from 0.002-0.245. This study also presents, for the first time for Malaysia, data on length-weight relationships and otolith measurements. It contributes to a better understanding of taxonomy, and phylogenetic and genetic diversity of E.epistictus.},
}
@article {pmid31332853,
year = {2019},
author = {Broman, E and Raymond, C and Sommer, C and Gunnarsson, JS and Creer, S and Nascimento, FJA},
title = {Salinity drives meiofaunal community structure dynamics across the Baltic ecosystem.},
journal = {Molecular ecology},
volume = {28},
number = {16},
pages = {3813-3829},
pmid = {31332853},
issn = {1365-294X},
mesh = {Animals ; *Biodiversity ; Computational Biology ; Finland ; Nematoda/*classification ; Oceans and Seas ; Population Dynamics ; Rivers ; *Salinity ; Sequence Analysis, DNA ; Sweden ; },
abstract = {Coastal benthic biodiversity is under increased pressure from climate change, eutrophication, hypoxia, and changes in salinity due to increase in river runoff. The Baltic Sea is a large brackish system characterized by steep environmental gradients that experiences all of the mentioned stressors. As such it provides an ideal model system for studying the impact of on-going and future climate change on biodiversity and function of benthic ecosystems. Meiofauna (animals < 1 mm) are abundant in sediment and are still largely unexplored even though they are known to regulate organic matter degradation and nutrient cycling. In this study, benthic meiofaunal community structure was analysed along a salinity gradient in the Baltic Sea proper using high-throughput sequencing. Our results demonstrate that areas with higher salinity have a higher biodiversity, and salinity is probably the main driver influencing meiofauna diversity and community composition. Furthermore, in the more diverse and saline environments a larger amount of nematode genera classified as predators prevailed, and meiofauna-macrofauna associations were more prominent. These findings show that in the Baltic Sea, a decrease in salinity resulting from accelerated climate change will probably lead to decreased benthic biodiversity, and cause profound changes in benthic communities, with potential consequences for ecosystem stability, functions and services.},
}
@article {pmid31329604,
year = {2019},
author = {Whitaker, MRL and Baker, CCM and Salzman, SM and Martins, DJ and Pierce, NE},
title = {Combining stable isotope analysis with DNA metabarcoding improves inferences of trophic ecology.},
journal = {PloS one},
volume = {14},
number = {7},
pages = {e0219070},
pmid = {31329604},
issn = {1932-6203},
mesh = {Animals ; Ants/physiology ; Butterflies/*physiology ; Carbon Isotopes ; DNA Barcoding, Taxonomic ; DNA, Chloroplast/genetics/isolation &amp; purification ; *Diet ; *Ecosystem ; Fabaceae/chemistry/genetics ; Gastrointestinal Microbiome/genetics ; Herbivory/genetics ; Larva/physiology ; Nitrogen Isotopes ; Symbiosis ; },
abstract = {Knowing what animals eat is fundamental to our ability to understand and manage biodiversity and ecosystems, but researchers often must rely on indirect methods to infer trophic position and food intake. Using an approach that combines evidence from stable isotope analysis and DNA metabarcoding, we assessed the diet and trophic position of Anthene usamba butterflies, for which there are no known direct observations of larval feeding. An earlier study that analyzed adults rather than caterpillars of A. usamba inferred that this butterfly was aphytophagous, but we found that the larval guts of A. usamba and two known herbivorous lycaenid species contain chloroplast 16S sequences. Moreover, chloroplast barcoding revealed high sequence similarity between chloroplasts found in A. usamba guts and the chloroplasts of the Vachellia drepanolobium trees on which the caterpillars live. Stable isotope analysis provided further evidence that A. usamba caterpillars feed on V. drepanolobium, and the possibilities of strict herbivory versus limited omnivory in this species are discussed. These results highlight the importance of combining multiple approaches and considering ontogeny when using stable isotopes to infer trophic ecology where direct observations are difficult or impossible.},
}
@article {pmid31325893,
year = {2019},
author = {Avila, E and Graebin, P and Chemale, G and Freitas, J and Kahmann, A and Alho, CS},
title = {Full mtDNA genome sequencing of Brazilian admixed populations: A forensic-focused evaluation of a MPS application as an alternative to Sanger sequencing methods.},
journal = {Forensic science international. Genetics},
volume = {42},
number = {},
pages = {154-164},
doi = {10.1016/j.fsigen.2019.07.004},
pmid = {31325893},
issn = {1878-0326},
mesh = {Brazil ; DNA, Mitochondrial/*genetics ; *Genetics, Population ; *Genome, Mitochondrial ; Haplotypes ; *High-Throughput Nucleotide Sequencing ; Humans ; Polymerase Chain Reaction ; *Sequence Analysis, DNA ; },
abstract = {The use of Massive Parallel Sequencing (MPS) techniques have been proposed by the forensic community as an alternative to Sanger sequencing methods in routine forensic casework analysis regarding mitochondrial DNA (mtDNA). Interesting features of MPS include high throughput, ability to simultaneously genotype a significant number of samples by barcoding techniques, processing automation, reduced time and costs, among others. Advantages include the capability of generating full mtDNA genome sequences versus usual techniques, usually limited to hypervariable or control regions exclusively. In this work, 96 reference single-source samples from three different Brazilian cities were subjected to full mtDNA genome sequencing by MPS techniques using an early-access version of Precision ID mtDNA Whole Genome Panel on an Ion Torrent PGM platform (Thermo Fisher Scientific, Waltham, MA, USA). Complete, high-quality sequences were obtained and sequencing performance was evaluated via four different metrics. As a subset of evaluated samples have been previously submitted for Sanger sequencing of the control region, a comparative analysis of both methods' results was conducted in order to compare technique adequacy within a forensic context. Even though this study is one of the first to report full mtDNA genome sequences for Brazilian admixed populations, the observed haplotypes exhibit a predominance of Native American and African maternal lineages in the studied sample set, reproducing results described in the literature for control regions only. Interpopulation analysis among Brazilian and 26 worldwide populations was also carried out. The results indicate that MPS-generated full mtDNA genome sequences may have great utility in forensic real casework applications, with a pronounced gain of genetic information and discrimination power provided by coding region evaluation and the enhanced capacity of heteroplasmies determination. Database construction and other relevant factors concerning implementation of such techniques in Brazilian forensic laboratories are also discussed.},
}
@article {pmid31325412,
year = {2019},
author = {Dapporto, L and Cini, A and Vodă, R and Dincă, V and Wiemers, M and Menchetti, M and Magini, G and Talavera, G and Shreeve, T and Bonelli, S and Casacci, LP and Balletto, E and Scalercio, S and Vila, R},
title = {Integrating three comprehensive data sets shows that mitochondrial DNA variation is linked to species traits and paleogeographic events in European butterflies.},
journal = {Molecular ecology resources},
volume = {19},
number = {6},
pages = {1623-1636},
doi = {10.1111/1755-0998.13059},
pmid = {31325412},
issn = {1755-0998},
support = {CGL2013-48277-P and CGL2016-76322-P//Ministerio de Econom&#xed;a y Competitividad/ ; 609402-2020//Marie Sk&#x142;odowska-Curie/ ; 625997//Marie Sk&#x142;odowska-Curie/ ; },
mesh = {Animals ; Biodiversity ; Butterflies/*genetics ; DNA, Mitochondrial/*genetics ; Ecosystem ; Europe ; Genetic Variation/*genetics ; Phenotype ; Phylogeny ; Phylogeography/methods ; },
abstract = {Understanding the dynamics of biodiversity, including the spatial distribution of genetic diversity, is critical for predicting responses to environmental changes, as well as for effective conservation measures. This task requires tracking changes in biodiversity at large spatial scales and correlating with species functional traits. We provide three comprehensive resources to understand the determinants for mitochondrial DNA differentiation represented by (a) 15,609 COI sequences and (b) 14 traits belonging to 307 butterfly species occurring in Western-Central Europe and (c) the first multi-locus phylogenetic tree of all European butterfly species. By applying phylogenetic regressions we show that mitochondrial DNA spatial differentiation (as measured with GST , G'ST , D and DST) is negatively correlated with species traits determining dispersal capability and colonization ability. Thanks to the high spatial resolution of the COI data, we also provide the first zoogeographic regionalization maps based on intraspecific genetic variation. The overall pattern obtained by averaging the spatial differentiation of all Western-Central European butterflies shows that the paradigm of long-term glacial isolation followed by rapid pulses of post-glacial expansion has been a pervasive phenomenon in European butterflies. The results and the extensive data sets we provide here constitute the basis for genetically-informed conservation plans for a charismatic group in a continent where flying insects are under alarming decline.},
}
@article {pmid31321434,
year = {2019},
author = {Coates, BS and Abel, CA},
title = {Differentiation of European Corn Borer (Lepidoptera: Crambidae) and American Lotus Borer (Lepidoptera: Crambidae), Ostrinia penitalis, from North American Field Collections.},
journal = {Journal of economic entomology},
volume = {112},
number = {4},
pages = {2007-2011},
doi = {10.1093/jee/toz078},
pmid = {31321434},
issn = {1938-291X},
mesh = {Animals ; *Bacillus thuringiensis ; Bacterial Proteins ; Endotoxins ; *Lepidoptera ; *Moths ; *Nelumbo ; North America ; Zea mays ; },
abstract = {The European corn borer, Ostrinia nubilalis (Lepidoptera: Crambidae), is a perennial insect pest of cultivated maize that was inadvertently introduced into North America in the early 1900s, but population densities have decreased since the widespread adoption of transgenic hybrids that express Bacillus thuringiensis (Bt) toxins. The native American lotus borer, Ostrinia penitalis (Lepidoptera: Crambidae), is among the most ancestral species described in the genus Ostrinia, and has a geographic range that coincides with that of O. nubilalis across major maize growing regions of North America. Due to the recent decrease in O. nubilalis populations, O. penitalis has become more pronounced in light trap samples intended to monitor O. nubilalis. A molecular tool based on variation in restriction endonuclease digestion pattern of a polymerase chain reaction amplified fragment of the mitochondrial cytochrome c oxidase subunit I (coxI) gene was developed and validated to differentiate these two species. This method was applied to light trap samples over a 2-yr period and achieved accurate quantification of species, and shows that O. penitalis can be prevalent in O. nubilalis first flight sampling. These methods are useful for contemporary O. nubilalis field research in North America.},
}
@article {pmid31312521,
year = {2019},
author = {Denissen, GAW and van Steenbergen, LN and Lollinga, WT and Verdonschot, NJJ and Schreurs, BW and Nelissen, RGHH},
title = {Generic implant classification enables comparison across implant designs: the Dutch Arthroplasty Register implant library.},
journal = {EFORT open reviews},
volume = {4},
number = {6},
pages = {344-350},
pmid = {31312521},
issn = {2058-5241},
abstract = {In the Dutch Arthroplasty Register (LROI), the product and batch number of prosthetic components and cement are registered for traceability. Registration of the product number provides opportunities to extend the information about a specific prosthesis. All product numbers used from the beginning of the registration in 2007 were characterized to develop and maintain an implant library.The Scientific Advisory Board developed a core-set that contains the most important characteristics needed to form an implant library. The final core-set contains the brand name, type, coating and material of the prosthesis. In total, 35 676 product numbers were classified, resulting in a complete implant library of all product numbers used in the LROI.To improve quality of the data and increase convenience of registration, the LROI implemented barcode scanning for data entry into the database. In 2017, 82% of prosthetic components and cement stickers had a GS1 barcode. The remaining product stickers used HIBCC barcodes and custom-made barcodes.With this implant library, implants can be grouped for analyses at group level, e.g. evaluation of the effect of a material of a prosthesis on survival of the implant. Apart from that, the implant library can be used for data quality control within the LROI database.The implant library reduces the registration burden and increases accuracy of the database. Such a system will facilitate new designs (learning from the past) and thus improve implant quality and ultimately patient safety. Cite this article: EFORT Open Rev 2019;4 DOI: 10.1302/2058-5241.4.180063.},
}
@article {pmid31312088,
year = {2019},
author = {Windsor, AM and Mendoza, JCE and Deeds, JR},
title = {Resolution of the Portunusgladiator species complex: taxonomic status and identity of Monomiagladiator (Fabricius, 1798) and Monomiahaanii (Stimpson, 1858) (Brachyura, Decapoda, Portunidae).},
journal = {ZooKeys},
volume = {858},
number = {},
pages = {11-43},
pmid = {31312088},
issn = {1313-2989},
abstract = {The United States Food and Drug Administration (FDA) has recently adopted DNA barcoding for the purpose of determining the species identity of commercial seafood products. This effort has revealed instances of incongruence between current scientifically accepted taxon names and those utilized by the seafood industry in product labelling. One such case is that of "Portunushaanii", a name utilized by the seafood industry to label commercial products under the market name "red swimming crab." However, carcinologists currently regard P.haanii as synonym of Portunusgladiator Fabricius, 1798, which itself is the subject of debate over whether it is a secondary homonym of Cancer gladiator Fabricius, 1793. Further complicating matters, DNA barcode sequences from commercial products match GenBank sequences identified as Portunuspseudoargentatus Stephenson, 1961. Here the complicated taxonomic history of the Portunusgladiator complex is reviewed and a resolution proposed based on combined morphological descriptions and molecular phylogenetic analyses. It is demonstrated that, given the provisions of the International Code of Zoological Nomenclature and the current elevation of Monomia Gistel, 1848, to full genus rank, its type species, Portunusgladiator Fabricius, 1798, should be treated as a valid and available taxon name. It is also shown, upon examination and comparison of types and topotypic material that Monomiahaanii (Stimpson, 1858) is a distinct taxon from M.gladiator, and Portunuspseudoargentatus Stephenson, 1961, is a junior subjective synonym of M.haanii (Stimpson, 1858). Furthermore, it is shown that crab meat sold in the US currently labeled as "Portunushaanii" and/or "red swimming crab" is in fact M.haanii using comparative analysis of DNA barcode sequences between museum-vouchered reference specimens, whole crabs provided directly by a seafood importer, and processed commercial products purchased at retail.},
}
@article {pmid31310229,
year = {2019},
author = {Prasad, YK and Dahal, S and Saikia, B and Bordoloi, B and Tandon, V and Ghatani, S},
title = {Artyfechinostomum sufrartyfex Trematode Infections in Children, Bihar, India.},
journal = {Emerging infectious diseases},
volume = {25},
number = {8},
pages = {1571-1573},
pmid = {31310229},
issn = {1080-6059},
mesh = {Adolescent ; Age Factors ; Animals ; Antiprotozoal Agents/therapeutic use ; Child ; Child, Preschool ; Female ; Geography, Medical ; Humans ; India/epidemiology ; Male ; Molecular Typing ; *Platyhelminths/classification/genetics/isolation &amp; purification ; Public Health Surveillance ; Symptom Assessment ; Treatment Outcome ; Trematode Infections/diagnosis/drug therapy/*epidemiology/*parasitology ; },
abstract = {Eating raw or insufficiently cooked mollusks is a known risk factor for human echinostomiasis. We confirmed identification of Artyfechinostomum sufrartyfex trematodes as the causative agent of disease among 170 children in northern Bihar, India. We also identified the snail Pila globosa as a potential source of infections in the study area.},
}
@article {pmid31309002,
year = {2019},
author = {Goodbody-Gringley, G and Strand, E and Pitt, JM},
title = {Molecular characterization of nearshore baitfish populations in Bermuda to inform management.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7244},
pmid = {31309002},
issn = {2167-8359},
abstract = {Small-bodied marine fishes play an important role in the food web, feeding both larger fishes and seabirds. Often referred to as baitfishes, they concentrate seasonally in coastal areas in large, often heterospecific assemblages that are targeted by both commercial and recreational fishers. Given apparent declines in at least some of Bermuda's baitfish species over the past 40 years, it is useful to determine the species composition of baitfish assemblages, and how it varies among sites, in order to inform management. Using genetic barcoding of the Cytochrome c oxidase 1 gene (COI), we confirm species identity, assess intraspecific genetic diversity locally, and determine rates of broader genetic connectivity for baitfish assemblages in Bermuda. Species analyzed included Hypoatherina harringtonensis, Anchoa choerostoma, Jenkinsia lamprotaenia, Harengula humeralis, Opisthonema oglinum and Sardinella aurita. Species identification based on molecular barcoding revealed some misidentification of individuals based solely on gross morphological characteristics, with an error rate of 11%, validating the usefulness of this approach. Interestingly, sequence results for the endemic Bermuda anchovy, A. choerostoma, were within 1% similarity to the more broadly distributed big-eye anchovy, A. lamprotaenia, and thus additional analyses are warranted to evaluate the genetic basis for endemism. Estimates of genetic diversity within and among baitfish assemblages in Bermuda were high, indicating high rates of local connectivity among sites for all species. As such, management should consider Bermuda's baitfish species as single, highly mixed populations. However, with the exception of H. humeralis and the endemic A. choerostoma, significant genetic differentiation and population structure were found when comparing Bermuda's baitfish populations with those from other regions, suggesting limited gene flow between other regions and Bermuda for these species. Limited regional connectivity has implications for management, as strong genetic divergence suggests that populations in Bermuda are predominantly self-seeding and thus not likely to be replenished from distant populations. These results therefore support precautionary management of baitfish species in Bermuda.},
}
@article {pmid31308971,
year = {2019},
author = {Bisschoff, C and Coulon, J and Isaacs, Z and van der Linde, L and Wilson, L and van Zyl, R and Joubert, G},
title = {HIV testing at birth: Are we getting it right?.},
journal = {Southern African journal of HIV medicine},
volume = {20},
number = {1},
pages = {951},
pmid = {31308971},
issn = {2078-6751},
abstract = {BACKGROUND: Birth polymerase chain reaction (PCR) testing improves early detection of HIV and allows for early treatment initiation. National guidelines exist, but it is unknown whether these are being implemented correctly.<br><br>OBJECTIVES: To determine whether HIV-exposed infants at the Mangaung University Community Partnership Programme Community Health Centre (MUCPP CHC) received PCR tests at birth, if HIV-positive infants were initiated on treatment, if follow-up dates were scheduled and the percentage of mothers or caregivers who returned to collect the results.<br><br>METHODS: The study was a retrospective descriptive file audit (1304 files) of births from 01 January to 31 December 2016 at MUCPP CHC. The study sample was 428 infants born to HIV-positive mothers. The birth register was used to collect the infants' HIV PCR test barcodes. The birth and 10-week PCR results were retrieved from an electronic database at the Virology Department, University of the Free State.<br><br>RESULTS: In total, 375 infants received a birth PCR test (87.6%) of which 4 (1.1%) tested HIV positive and 327 (87.2%) negative. Follow-up tests were not scheduled. However, 145 (44.3%) HIV-negative infants returned for a 10-week test. Irrespective of the PCR birth result, 157 (36.7%) infants were brought for a 10-week follow-up test at which time 3 (1.9%) tested positive and 151 (96.2%) negative.<br><br>CONCLUSION: The majority of HIV-exposed infants received a PCR test at birth; however, the clinic is below the national target (90%) for HIV testing. A record-keeping system of infants' visits does not exist at MUCPP CHC, making it impossible to determine whether HIV-positive infants were started on antiretroviral treatment.},
}
@article {pmid31306089,
year = {2019},
author = {Rush, TA and Golan, J and McTaggart, A and Kane, C and Schneider, RW and Aime, MC},
title = {Variation in the Internal Transcribed Spacer Region of Phakopsora pachyrhizi and Implications for Molecular Diagnostic Assays.},
journal = {Plant disease},
volume = {103},
number = {9},
pages = {2237-2245},
doi = {10.1094/PDIS-08-18-1426-RE},
pmid = {31306089},
issn = {0191-2917},
mesh = {DNA, Ribosomal Spacer/genetics ; *Genetic Variation ; Molecular Diagnostic Techniques/standards ; Pathology, Molecular ; *Phakopsora pachyrhizi/genetics ; *Plant Diseases/microbiology ; Glycine max/microbiology ; United States ; },
abstract = {Phakopsora pachyrhizi, the causal agent of soybean rust (SBR), is a global threat to soybean production. Since the discovery of SBR in the continental United States, quantitative polymerase chain reaction assays based on the internal transcribed spacer (ITS) ribosomal DNA locus were established for its rapid detection. However, insufficient data were initially available to test assays against factors that could give rise to misidentification. This study aimed to reevaluate current assays for (i) the potential for false-positive detection caused by nontarget Phakopsora species and (ii) the potential for false-negative detection caused by intraspecific variation within the ITS locus of P. pachyrhizi. A large amount of intraspecific and intragenomic variation in ITS was detected, including the presence of polymorphic ITS copies within single leaf samples and within single rust sori. The diagnostic assays were not affected by polymorphisms in the ITS region; however, current assays are at risk of false positives when screened against other species of Phakopsora. This study raises caveats to the use of multicopy genes (e.g., ITS) in single-gene detection assays and discusses the pitfalls of inferences concerning the aerobiological pathways of disease spread made in the absence of an evaluation of intragenomic ITS heterogeneity.},
}
@article {pmid31305956,
year = {2020},
author = {Heo, CC and Rahimi, R and Mengual, X and M Isa, MS and Zainal, S and Khofar, PN and Nazni, WA},
title = {Eristalinus arvorum (Fabricius, 1787) (Diptera: Syrphidae) in Human Skull: A New Fly Species of Forensic Importance.},
journal = {Journal of forensic sciences},
volume = {65},
number = {1},
pages = {276-282},
doi = {10.1111/1556-4029.14128},
pmid = {31305956},
issn = {1556-4029},
mesh = {Adult ; Animals ; Burial ; DNA Barcoding, Taxonomic ; Databases, Nucleic Acid ; Diptera/*genetics/*physiology ; Electron Transport Complex IV/genetics ; Feeding Behavior ; Female ; *Forensic Entomology ; Humans ; Larva/physiology ; Malaysia ; Postmortem Changes ; Skull/*pathology ; },
abstract = {A body of an unknown adult female was found within a shallow burial ground in Malaysia whereas the skull was exposed and visible on the ground. During autopsy examination, nine insect larvae were recovered from the interior of the human skull and subsequently preserved in 70% ethanol. The larvae were greyish in appearance, each with a posterior elongated breathing tube. A week after the autopsy, more larvae were collected at the burial site, and some of them were reared into adults. Adult specimens and larvae from the skull and from the burial site were sequenced to obtain DNA barcodes. Results showed all adult flies reared from the burial site, as well as the larvae collected from the skull were identified as Eristalinus arvorum (Fabricius, 1787) (Diptera: Syrphidae). Here, we report the colonization of E. arvorum larvae on a human corpse for the first time.},
}
@article {pmid31304599,
year = {2019},
author = {Bagley, JC and de Aquino, PPU and Breitman, MF and Langeani, F and Colli, GR},
title = {DNA barcode and minibarcode identification of freshwater fishes from Cerrado headwater streams in Central Brazil.},
journal = {Journal of fish biology},
volume = {95},
number = {4},
pages = {1046-1060},
doi = {10.1111/jfb.14098},
pmid = {31304599},
issn = {1095-8649},
support = {314724/2014-1//Brazilian Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 306566/2014//Brazilian Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; //Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; //Coordena&#xe7;&#xe3;o de Apoio &#xe0; Forma&#xe7;&#xe3;o de Pessoal de N&#xed;vel Superior (CAPES)/ ; //CNPq/ ; //Funda&#xe7;&#xe3;o de Apoio &#xe0; Pesquisa do Distrito Federal (FAPDF)/ ; AID-OAA-A-11-00012//USAID PEER programme/ ; },
mesh = {*Animal Distribution ; Animals ; Bayes Theorem ; Biodiversity ; Brazil ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Fishes/*genetics/physiology ; Gene Library ; Phylogeny ; Rivers ; Species Specificity ; },
abstract = {The extraordinary species diversity of the Neotropical freshwater fish fauna is world renown. Yet, despite rich species diversity, taxonomic and genetic resources for its Cerrado ichthyofauna remain poorly developed. We provide a reference library of 149 DNA barcodes for 39 species/lineages of Cerrado headwater stream fishes from the Brazilian Distrito Federal and nearby areas and test the utility of distance-based criteria, tree-based criteria and minibarcodes for specimen identification. Mean Kimura 2-parameter genetic distances within species to orders ranged 1·8-12·1%. However, mean intraspecific v. congeneric-interspecific distances (0·9-1·3%) overlapped extensively and distance-based barcoding failed to achieve correct identifications due to c. 4-12·1% error rates and 19·5% ambiguous identifications related to the presence of singletons. Overlap was reduced and best-match success rates improved drastically to 83·5% when Characidium barcodes representing potential misidentifications or undescribed species were removed. Tree-based monophyly criteria generally performed similarly to distance methods, correctly differentiating up to c. 85% of species/lineages despite neighbour-joining and Bayesian tree errors (random lineage-branching events, long-branch attraction). Five clusters (Ancistrus aguaboensis, Characidium spp., Eigenmannia trilineata, Hasemania hanseni and Hypostomus sp. 2) exhibited deep intraspecific divergences or para-/polyphyly and multiple Barcode Index Number assignments indicative of putative candidate species needing taxonomic re-examination. Sliding-window analyses also indicated that a 200 bp minibarcode region performed just as well at specimen identification as the entire barcode gene. Future DNA barcoding studies of Distrito Federal-Cerrado freshwater fishes will benefit from increased sampling coverage, as well as consideration of minibarcode targets for degraded samples and next-generation sequencing.},
}
@article {pmid31304059,
year = {2019},
author = {Hagerty, ML and Reyns, N and Pineda, J and Govindarajan, AF},
title = {Diversity and distribution of nearshore barnacle cyprids in southern California through the 2015-16 El Niño.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7186},
pmid = {31304059},
issn = {2167-8359},
abstract = {Abundance, species diversity, and horizontal distributions of barnacle cyprids offshore of La Jolla, southern California were described from May 2014 to August 2016 to determine how the nearshore barnacle larval assemblage changed before, during, and after the 2015-16 El Niño. The entire water column was sampled at five stations located within one km of shore with water depths of 4, 6, 8, 10, and 12 m during 33 cruises that encompassed the time when El Niño conditions impacted the area. Nearshore temperature and thermal stratification was concurrently measured using a CTD. Six identified cyprid species, including Chthamalus fissus, Pollicipes polymerus, Megabalanus rosa, Tetraclita rubescens, Balanus glandula, and B. trigonus, along with four unknown species, were collected in our samples. DNA barcoding was used to confirm identifications in a subset of the larvae. C. fissus was more than eight times more abundant than any other species, and while abundance varied by species, cyprid density was highest for all species except for M. rosa before and after the El Niño event, and lower during the environmental disturbance. There were significant differences in cross-shore distributions among cyprid species, with some located farther offshore than others, along with variability in cross-shore distributions by season. C. fissus cyprids were closest to shore during spring-summer cruises when waters were the most thermally stratified, which supports previous findings that C. fissus cyprids are constrained nearshore when thermal stratification is high. Relative species proportions varied throughout the study, but there was no obvious change in species assemblage or richness associated with El Niño. We speculate that barnacle cyprid species diversity did not increase at our study site during the 2015-16 El Niño, as it has in other areas during previous El Niño Southern Oscillation events, due to the lack of anomalous northward flow throughout the 2015-16 event.},
}
@article {pmid31303807,
year = {2019},
author = {Bidzilya, O and Huemer, P and Nupponen, K and Šumpich, J},
title = {A review of some new or little-known species of the genus Gnorimoschema (Lepidoptera, Gelechiidae) from the Palaearctic region.},
journal = {ZooKeys},
volume = {857},
number = {},
pages = {105-138},
pmid = {31303807},
issn = {1313-2989},
abstract = {Six new species of Gnorimoschema Busck, 1900 are described: G.pamira sp. nov. (Tadzhikistan), G.brachyptera sp. nov. (Russia: Buryatia), G.altaica sp. nov. (Russia: Altai), G.tabazhok sp. nov. (Russia, Altai, Tuva), G.yakovlevi sp. nov. (Russia: Altai, Buryatia), G.kozlovi sp. nov. (Mongolia). A new synonym is established: G.mikkolai Povolný, 1994 syn. nov. of G.radkevichi Piskunov, 1980. Gnorimoschemamontanum Povolný, 1966, sp. rev., stat. nov. is taken out from synonymy with G.soffneri (Riedl, 1965). An annotated check-list of the genus Gnorimoschema in the Palaearctic region is provided.},
}
@article {pmid31303506,
year = {2019},
author = {Selich, A and Ha, TC and Morgan, M and Falk, CS and von Kaisenberg, C and Schambach, A and Rothe, M},
title = {Cytokine Selection of MSC Clones with Different Functionality.},
journal = {Stem cell reports},
volume = {13},
number = {2},
pages = {262-273},
pmid = {31303506},
issn = {2213-6711},
mesh = {Animals ; Antigens, CD34/metabolism ; Cell Proliferation/*drug effects ; Cells, Cultured ; Culture Media, Conditioned/pharmacology ; Cytokines/*pharmacology ; Epidermal Growth Factor/pharmacology ; Fetal Blood/cytology ; Fibroblast Growth Factor 2/pharmacology ; Humans ; Mesenchymal Stem Cell Transplantation ; Mesenchymal Stem Cells/*cytology/metabolism ; Mice ; Principal Component Analysis ; Transforming Growth Factor beta1/pharmacology ; },
abstract = {Mesenchymal stromal cells (MSCs) are used in many clinical applications. However, ex vivo expansion is required to reach clinically relevant cell numbers, which might lead to selection of clones with different characteristics. To follow clonal selection, we transduced MSC progenitors in umbilical cord pieces (UCPs) with vectors encoding fluorescent proteins and genetic barcodes. After marked MSC cultures grew out from UCPs, we investigated the influence of cytokines on MSC functionality. Specific cytokine conditions selected for clones from common progenitors. MSC secretome analyses revealed differences dependent on the culture conditions used. Clones expanded in human serum containing culture medium secreted a plethora of growth factors. When expanded in the same medium containing TGF-β, MSCs secreted negligible amounts of cytokines but at the same time led to an increased human chimerism after hematopoietic stem cell transplantation into immunodeficient mice. Our results suggest a major influence of cytokine additives on MSC functionality.},
}
@article {pmid31300737,
year = {2019},
author = {Landinez-Torres, A and Panelli, S and Picco, AM and Comandatore, F and Tosi, S and Capelli, E},
title = {A meta-barcoding analysis of soil mycobiota of the upper Andean Colombian agro-environment.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {10085},
pmid = {31300737},
issn = {2045-2322},
mesh = {Biodiversity ; Colombia ; *DNA Barcoding, Taxonomic ; Fungi/*classification/*genetics/isolation &amp; purification ; Grassland ; Mycobiome/genetics ; Soil ; *Soil Microbiology ; },
abstract = {Colombia is a country for which one of the highest biodiversity rates is reported, and one of the first in the tropical areas where an effort was made to gather information on indigenous fungi. Nevertheless, mycological data are still scarce and discontinuous, above all on soil fungi. The present study wanted to contribute to unveil the large soil fungal biodiversity in the upper Andean Colombian agro-ecosystems. The studied area is located in the department of Boyacà, considered with a notable economical value, partly devoted to subsistence agriculture. More than 150 described species were revealed in this study, belonging to 5 phyla with Ascomycota representing the dominant taxon. Basidiomycota and Zygomycota are also well represented, dominated by species of the genus Sebacina and Mortierella respectively, mainly distributed in the semi-natural plots (woodland and grassland). Most of the species are reported as first records for Colombia. Some of them are particularly interesting for their conservation significance such as Geoglossum fallax, which is the dominant species in the unimproved grassland plot. The bootstrap-based clustering analysis showed a different distribution of the species in orchards and non-cultivated areas as a possible response of the fungal community to different use of soil in the agro-environment.},
}
@article {pmid31299548,
year = {2019},
author = {Sasaki, M and Katahira, H and Kobayashi, M and Kuramochi, T and Matsubara, H and Nakao, M},
title = {Infection status of commercial fish with cystacanth larvae of the genus Corynosoma (Acanthocephala: Polymorphidae) in Hokkaido, Japan.},
journal = {International journal of food microbiology},
volume = {305},
number = {},
pages = {108256},
doi = {10.1016/j.ijfoodmicro.2019.108256},
pmid = {31299548},
issn = {1879-3460},
mesh = {Acanthocephala/classification/genetics/*isolation &amp; purification/physiology ; Animals ; DNA Barcoding, Taxonomic ; Fishes/classification/*parasitology ; Helminthiasis, Animal ; Islands ; Japan ; Larva/genetics/physiology ; },
abstract = {Acanthocephalans of the genus Corynosoma are known as intestinal parasites, mainly of pinnipeds. Human corynosomiasis has been reported as an infrequent foodborne disease in Hokkaido, the northernmost island of Japan. Potential sources of the human infection are marine fish, because they are paratenic hosts of these parasites. In this study, the prevalence and intensity of larval Corynosoma in commercial fish from 17 fishing ports of Hokkaido were examined from April 2016 to January 2019. Out of a total of 1217 fish examined, 122 (10.0%) were infected with cystacanth larvae. The infected fish assemblage was composed of 7 families and 13 species from all the coastal seas of Hokkaido (the Pacific Ocean, Okhotsk Sea, and Japan Sea), showing that commercial fish can be source of human infection when eaten raw. Flatfish of the family Pleuronectidae showed the highest intensity of cystacanths, ranging from 1 to 56. A DNA barcoding system was developed in this study, based on the standard mitochondrial cox1 sequences of morphologically identified adults of Corynosoma spp. from pinnipeds in Hokkaido. By using the DNA barcoding, most of the fish-derived cystacanths were identified as either C. strumosum or C. villosum, and furthermore, a clinical isolate from human as C. villosum. Both of the species were commonly detected from various fish of Hokkaido, irrespective of the coastal seas. Flatfish frequently harbored C. villosum. Considering the wide range of commercial fish in Hokkaido and the advanced transportation system of fresh fish, there is a possibility that human corynosomiasis will occur everywhere in Japan.},
}
@article {pmid31295181,
year = {2019},
author = {Scalise, E and Piech, L},
title = {A Perfect Match: Barcoding Babies for ID Verification.},
journal = {Computers, informatics, nursing : CIN},
volume = {37},
number = {7},
pages = {331-336},
doi = {10.1097/CIN.0000000000000546},
pmid = {31295181},
issn = {1538-9774},
mesh = {Electronic Health Records/*standards ; Female ; Humans ; Infant, Newborn ; Medication Systems, Hospital/trends ; Mothers ; Nursing Staff, Hospital/*education ; *Patient Safety ; },
}
@article {pmid31295104,
year = {2021},
author = {Rioux, G and Scarvelis, C and Choksi, R and Hoheisel, T and Marechal, P},
title = {Blind Deblurring of Barcodes via Kullback-Leibler Divergence.},
journal = {IEEE transactions on pattern analysis and machine intelligence},
volume = {43},
number = {1},
pages = {77-88},
doi = {10.1109/TPAMI.2019.2927311},
pmid = {31295104},
issn = {1939-3539},
abstract = {Barcode encoding schemes impose symbolic constraints which fix certain segments of the image. We present, implement, and assess a method for blind deblurring and denoising based entirely on Kullback-Leibler divergence. The method is designed to incorporate and exploit the full strength of barcode symbologies. Via both standard barcode reading software and smartphone apps, we demonstrate the remarkable ability of our method to blindly recover simulated images of highly blurred and noisy barcodes. As proof of concept, we present one application on a real-life out of focus camera image.},
}
@article {pmid31294564,
year = {2019},
author = {Wolle, MM and Stadig, S and Conklin, SD},
title = {Market Basket Survey of Arsenic Species in the Top Ten Most Consumed Seafoods in the United States.},
journal = {Journal of agricultural and food chemistry},
volume = {67},
number = {29},
pages = {8253-8267},
doi = {10.1021/acs.jafc.9b02314},
pmid = {31294564},
issn = {1520-5118},
mesh = {Animals ; Arsenic/*chemistry ; Bivalvia/chemistry ; Brachyura/chemistry ; Consumer Product Safety ; Food Contamination/*analysis/economics/statistics &amp; numerical data ; Mass Spectrometry ; Seafood/*analysis/economics ; United States ; },
abstract = {The study focused on the determination of arsenic species in the top ten most consumed seafoods in the United States. Fifty-four samples were collected from local supermarkets, and their species identities were confirmed by DNA barcoding. The total arsenic in the samples varied greatly in the range of 8-22200 ng/g (wet mass). Speciation analysis based on extraction of water-soluble and nonpolar arsenic showed that inorganic arsenic (iAs) was found only in clams and crabs, while arsenobetaine (AsB) predominates in most samples. Among the other arsenicals, trimethylarsoniopropionate (TMAP) was found in most matrices with higher concentrations in crabs, and arsenosugars existed in most clams and crabs. Nonpolar arsenic accounted for 1-46% of the total arsenic in the samples. The accuracy of the analytical results was evaluated using standard reference materials and spike recovery tests. The survey showed that the iAs concentrations in America's most consumed seafood products are much lower than the tolerable intake set by the Joint FAO/WHO Expert Committee, even at the highest levels found in this study.},
}
@article {pmid31293086,
year = {2020},
author = {Ji, Y and Huotari, T and Roslin, T and Schmidt, NM and Wang, J and Yu, DW and Ovaskainen, O},
title = {SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes.},
journal = {Molecular ecology resources},
volume = {20},
number = {1},
pages = {256-267},
doi = {10.1111/1755-0998.13057},
pmid = {31293086},
issn = {1755-0998},
support = {31400470//National Natural Science Foundation of China/ ; 31500305//National Natural Science Foundation of China/ ; 31670536//National Natural Science Foundation of China/ ; 41661144002//National Natural Science Foundation of China/ ; 276909//Suomen Akatemia/ ; 284601//Suomen Akatemia/ ; 285803//Suomen Akatemia/ ; 309571//Suomen Akatemia/ ; //Jane and Aatos Erkko Foundation Grant/ ; 223257//Research Council of Norway through its Centres of Excellence Funding Scheme/ ; //Danish Environmental Protection Agency/ ; QYZDY-SSW-SMC024//Key Research Program of Frontier Sciences, CAS/ ; GJHZ1754//Bureau of International Cooperation/ ; XDA20050202//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2012FY110800//Ministry of Science and Technology of China/ ; GREKF18-04//State Key Laboratory of Genetic Resources and Evolution/ ; //Kunming Institute of Zoology/ ; //University of East Anglia/ ; //University of Chinese Academy of Sciences/ ; },
mesh = {Animals ; Biodiversity ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; Eukaryota/*classification/*genetics ; Metagenomics/instrumentation/*methods ; },
abstract = {The accurate quantification of eukaryotic species abundances from bulk samples remains a key challenge for community ecology and environmental biomonitoring. We resolve this challenge by combining shotgun sequencing, mapping to reference DNA barcodes or to mitogenomes, and three correction factors: (a) a percent-coverage threshold to filter out false positives, (b) an internal-standard DNA spike-in to correct for stochasticity during sequencing, and (c) technical replicates to correct for stochasticity across sequencing runs. The SPIKEPIPE pipeline achieves a strikingly high accuracy of intraspecific abundance estimates (in terms of DNA mass) from samples of known composition (mapping to barcodes R[2] = .93, mitogenomes R[2] = .95) and a high repeatability across environmental-sample replicates (barcodes R[2] = .94, mitogenomes R[2] = .93). As proof of concept, we sequence arthropod samples from the High Arctic, systematically collected over 17 years, detecting changes in species richness, species-specific abundances, and phenology. SPIKEPIPE provides cost-efficient and reliable quantification of eukaryotic communities.},
}
@article {pmid31291895,
year = {2019},
author = {Omelina, ES and Ivankin, AV and Letiagina, AE and Pindyurin, AV},
title = {Optimized PCR conditions minimizing the formation of chimeric DNA molecules from MPRA plasmid libraries.},
journal = {BMC genomics},
volume = {20},
number = {Suppl 7},
pages = {536},
pmid = {31291895},
issn = {1471-2164},
mesh = {DNA/*genetics ; DNA Primers ; *Gene Library ; High-Throughput Nucleotide Sequencing ; *Plasmids ; Polymerase Chain Reaction/*methods ; Templates, Genetic ; },
abstract = {BACKGROUND: Massively parallel reporter assays (MPRAs) enable high-throughput functional evaluation of various DNA regulatory elements and their mutant variants. The assays are based on construction of highly diverse plasmid libraries containing two variable fragments, a region of interest (a sequence under study; ROI) and a barcode (BC) used to uniquely tag each ROI, which are separated by a constant spacer sequence. The sequences of BC-ROI combinations present in the libraries may be either known a priori or not. In the latter case, it is necessary to identify these combinations before performing functional experiments. Typically, this is done by PCR amplification of the BC-ROI regions with flanking primers, followed by next-generation sequencing (NGS) of the products. However, chimeric DNA molecules formed on templates with identical spacer fragment during the amplification process may substantially hamper the identification of genuine BC-ROI combinations, and as a result lower the performance of the assays.<br><br>RESULTS: To identify settings that minimize formation of chimeric products we tested a number of PCR amplification parameters, such as conventional and emulsion types of PCR, one- or two-round amplification strategies, amount of DNA template, number of PCR cycles, and the duration of the extension step. Using specific MPRA libraries as templates, we found that the two-round amplification of the BC-ROI regions with a very low initial template amount, an elongated extension step, and a specific number of PCR cycles result in as low as 0.30 and 0.32% of chimeric products for emulsion and conventional PCR approaches, respectively.<br><br>CONCLUSIONS: We have identified PCR parameters that ensure synthesis of specific (non-chimeric) products from highly diverse MPRA plasmid libraries. In addition, we found that there is a negligible difference in performance of emulsion and conventional PCR approaches performed with the identified settings.},
}
@article {pmid31291259,
year = {2019},
author = {Zimmermann, HH and Harms, L and Epp, LS and Mewes, N and Bernhardt, N and Kruse, S and Stoof-Leichsenring, KR and Pestryakova, LA and Wieczorek, M and Trense, D and Herzschuh, U},
title = {Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly.},
journal = {PloS one},
volume = {14},
number = {7},
pages = {e0216966},
pmid = {31291259},
issn = {1932-6203},
mesh = {Chromosome Mapping ; DNA, Ancient ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; Genetic Variation ; Genetics, Population ; Genome, Chloroplast ; Genome, Mitochondrial ; Genome, Plant ; Haplotypes ; History, Ancient ; Larix/classification/*genetics ; Polymorphism, Single Nucleotide ; Siberia ; Taiga ; Tundra ; },
abstract = {Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are therefore largely unknown. We aim to generate organelle reference genomes for the detection of single nucleotide polymorphisms (SNPs) that can be used for paleogenetic studies. We present 19 complete chloroplast genomes and mitochondrial genomic sequences of larches from the southern lowlands of the Taymyr Peninsula (northernmost range of Larix gmelinii (Rupr.) Kuzen.), the lower Omoloy River, and the lower Kolyma River (both in the range of Larix cajanderi Mayr). The genomic data reveal 84 chloroplast SNPs and 213 putatively mitochondrial SNPs. Parsimony-based chloroplast haplotype networks show no spatial structure of individuals from different geographic origins, while the mitochondrial haplotype network shows at least a slight spatial structure with haplotypes from the Omoloy and Kolyma populations being more closely related to each other than to most of the haplotypes from the Taymyr populations. Whole genome alignments with publicly available complete chloroplast genomes of different Larix species show that among official plant barcodes only the rcbL gene contains sufficient polymorphisms, but has to be sequenced completely to distinguish the different provenances. We provide 8 novel mitochondrial SNPs that are putatively diagnostic for the separation of L. gmelinii and L. cajanderi, while 4 chloroplast SNPs have the potential to distinguish the L. gmelinii/L. cajanderi group from other Larix species. Our organelle references can be used for a targeted primer and probe design allowing the generation of short amplicons. This is particularly important with regard to future investigations of, for example, the biogeographic history of Larix by screening ancient sedimentary DNA of Larix.},
}
@article {pmid31290224,
year = {2020},
author = {Creedy, TJ and Norman, H and Tang, CQ and Qing Chin, K and Andujar, C and Arribas, P and O'Connor, RS and Carvell, C and Notton, DG and Vogler, AP},
title = {A validated workflow for rapid taxonomic assignment and monitoring of a national fauna of bees (Apiformes) using high throughput DNA barcoding.},
journal = {Molecular ecology resources},
volume = {20},
number = {1},
pages = {40-53},
doi = {10.1111/1755-0998.13056},
pmid = {31290224},
issn = {1755-0998},
support = {//Natural Environment Research Council/ ; 810729//H2020 European Research Council/ ; PH0521//Department for Environment, Food and Rural Affairs/ ; WC1101//Department for Environment, Food and Rural Affairs/ ; //European Commission/ ; //Defra/ ; WC1101//Scottish Government/ ; },
mesh = {Animals ; Bees/*classification/genetics ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Phylogeny ; United Kingdom ; Workflow ; },
abstract = {Improved taxonomic methods are needed to quantify declining populations of insect pollinators. This study devises a high-throughput DNA barcoding protocol for a regional fauna (United Kingdom) of bees (Apiformes), consisting of reference library construction, a proof-of-concept monitoring scheme, and the deep barcoding of individuals to assess potential artefacts and organismal associations. A reference database of cytochrome oxidase c subunit 1 (cox1) sequences including 92.4% of 278 bee species known from the UK showed high congruence with morphological taxon concepts, but molecular species delimitations resulted in numerous split and (fewer) lumped entities within the Linnaean species. Double tagging permitted deep Illumina sequencing of 762 separate individuals of bees from a UK-wide survey. Extracting the target barcode from the amplicon mix required a new protocol employing read abundance and phylogenetic position, which revealed 180 molecular entities of Apiformes identifiable to species. An additional 72 entities were ascribed to nuclear pseudogenes based on patterns of read abundance and phylogenetic relatedness to the reference set. Clustering of reads revealed a range of secondary operational taxonomic units (OTUs) in almost all samples, resulting from traces of insect species caught in the same traps, organisms associated with the insects including a known mite parasite of bees, and the common detection of human DNA, besides evidence for low-level cross-contamination in pan traps and laboratory procedures. Custom scripts were generated to conduct critical steps of the bioinformatics protocol. The resources built here will greatly aid DNA-based monitoring to inform management and conservation policies for the protection of pollinators.},
}
@article {pmid31289126,
year = {2019},
author = {Bykov, YS and Cohen, N and Gabrielli, N and Manenschijn, H and Welsch, S and Chlanda, P and Kukulski, W and Patil, KR and Schuldiner, M and Briggs, JAG},
title = {High-throughput ultrastructure screening using electron microscopy and fluorescent barcoding.},
journal = {The Journal of cell biology},
volume = {218},
number = {8},
pages = {2797-2811},
pmid = {31289126},
issn = {1540-8140},
support = {MC_UP_1201/16/MRC_/Medical Research Council/United Kingdom ; MC_UP_1201/8/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Cell Wall/metabolism/ultrastructure ; Fluorescent Dyes/metabolism ; Green Fluorescent Proteins/metabolism ; *High-Throughput Screening Assays ; *Microscopy, Electron ; Microscopy, Fluorescence ; Mitochondria/ultrastructure ; Osmotic Pressure ; Peroxisomes/metabolism ; Phenotype ; Saccharomyces cerevisiae/ultrastructure ; },
abstract = {Genetic screens using high-throughput fluorescent microscopes have generated large datasets, contributing many cell biological insights. Such approaches cannot tackle questions requiring knowledge of ultrastructure below the resolution limit of fluorescent microscopy. Electron microscopy (EM) reveals detailed cellular ultrastructure but requires time-consuming sample preparation, limiting throughput. Here we describe a robust method for screening by high-throughput EM. Our approach uses combinations of fluorophores as barcodes to uniquely mark each cell type in mixed populations and correlative light and EM (CLEM) to read the barcode of each cell before it is imaged by EM. Coupled with an easy-to-use software workflow for correlation, segmentation, and computer image analysis, our method, called "MultiCLEM," allows us to extract and analyze multiple cell populations from each EM sample preparation. We demonstrate several uses for MultiCLEM with 15 different yeast variants. The methodology is not restricted to yeast, can be scaled to higher throughput, and can be used in multiple ways to enable EM to become a powerful screening technique.},
}
@article {pmid31288682,
year = {2019},
author = {González-Varo, JP and Díaz-García, S and Arroyo, JM and Jordano, P},
title = {Seed dispersal by dispersing juvenile animals: a source of functional connectivity in fragmented landscapes.},
journal = {Biology letters},
volume = {15},
number = {7},
pages = {20190264},
pmid = {31288682},
issn = {1744-957X},
mesh = {Animals ; Ecosystem ; Forests ; *Seed Dispersal ; Seeds ; Trees ; },
abstract = {Juvenile animals generally disperse from their birthplace to their future breeding territories. In fragmented landscapes, habitat-specialist species must disperse through the anthropogenic matrix where remnant habitats are embedded. Here, we test the hypothesis that dispersing juvenile frugivores leave a footprint in the form of seed deposition through the matrix of fragmented landscapes. We focused on the Sardinian warbler (Sylvia melanocephala), a resident frugivorous passerine. We used data from field sampling of bird-dispersed seeds in the forest and matrix of a fragmented landscape, subsequent disperser identification through DNA-barcoding analysis, and data from a national bird-ringing programme. Seed dispersal by Sardinian warblers was confined to the forest most of the year, but warblers contributed a peak of seed-dispersal events in the matrix between July and October, mainly attributable to dispersing juveniles. Our study uniquely connects animal and plant dispersal, demonstrating that juveniles of habitat-specialist frugivores can provide mobile-link functions transiently, but in a seasonally predictable way.},
}
@article {pmid31288178,
year = {2019},
author = {Xiao, L},
title = {Designing and implementing a large-scale high-throughput Total Laboratory Automation (TLA) system for DNA database construction.},
journal = {Forensic science international},
volume = {302},
number = {},
pages = {109859},
doi = {10.1016/j.forsciint.2019.06.017},
pmid = {31288178},
issn = {1872-6283},
mesh = {Automation, Laboratory/*methods ; *DNA Fingerprinting ; *Databases, Nucleic Acid ; Electrophoresis, Capillary ; Forensic Genetics/*organization &amp; administration ; *High-Throughput Nucleotide Sequencing ; Humans ; Microsatellite Repeats ; Polymerase Chain Reaction ; Specimen Handling/instrumentation ; },
abstract = {This article describes a Total Laboratory Automation (TLA) system for DNA sample (FTA sample collection paper cwards or whole blood) processing, including barcoding, FTA card hole-punching or whole blood DNA extraction, PCR amplification, CE analysis and data acquisition process. This system designed to meet the needs of massive DNA database construction. Daily sample handling capacity for this TLA system is 800pcs (within 8h) to 2400pcs (within 24h). No such scaled system has previously used as STR analysis. Thus, it was important to find a suitable proportion numbers for different kind of components within the TLA system and to achieve the maximum efficiency as well as to make sure the system could achieve and maintain stable performance in continuously handling substantial DNA samples through performance test and stability test, in order to meet the needs of massive DNA database construction. In addition, the TLA system incorporates a novel track line system named RackRunner, a robotic access to all components in the pipeline, designed to transfer 96-well microplates whilst prevent all kinds of cross-contamination during STR tests. Experiments were undertaken to prove the performance of these factors in maintaining the STR test efficiency and prevent cross-contamination. This TLA system is also programmable for NGS (Next Generation Sequencing) tests in massive DNA Genome database construction without major changes.},
}
@article {pmid31285582,
year = {2019},
author = {Zhang, Y and Moss, A and Tan, K and Herr, AE},
title = {Barcodes for subcellular protein localization.},
journal = {Nature biomedical engineering},
volume = {3},
number = {9},
pages = {673-675},
pmid = {31285582},
issn = {2157-846X},
mesh = {Antibodies ; DNA/chemistry ; *Databases, Protein ; Humans ; Proteins/*metabolism ; },
}
@article {pmid31285580,
year = {2019},
author = {Sundah, NR and Ho, NRY and Lim, GS and Natalia, A and Ding, X and Liu, Y and Seet, JE and Chan, CW and Loh, TP and Shao, H},
title = {Barcoded DNA nanostructures for the multiplexed profiling of subcellular protein distribution.},
journal = {Nature biomedical engineering},
volume = {3},
number = {9},
pages = {684-694},
pmid = {31285580},
issn = {2157-846X},
mesh = {Antibodies/immunology/metabolism ; Base Sequence ; Cell Line, Tumor ; DNA/*chemistry/*classification ; DNA Barcoding, Taxonomic/instrumentation/*methods ; Gene Expression Profiling/*methods ; Humans ; Kinetics ; Lab-On-A-Chip Devices ; *Nanostructures ; Proteins ; Staining and Labeling ; },
abstract = {Massively parallel DNA sequencing is established, yet high-throughput protein profiling remains challenging. Here, we report a barcoding approach that leverages the combinatorial sequence content and the configurational programmability of DNA nanostructures for high-throughput multiplexed profiling of the subcellular expression and distribution of proteins in whole cells. The barcodes are formed by in situ hybridization of tetrahedral DNA nanostructures and short DNA sequences conjugated with protein-targeting antibodies, and by nanostructure-assisted ligation (either enzymatic or chemical) of the nanostructures and exogenous DNA sequences bound to nanoparticles of different sizes (which cause these localization sequences to differentially distribute across subcellular compartments). Compared with linear DNA barcoding, the nanostructured barcodes enhance the signal by more than 100-fold. By implementing the barcoding approach on a microfluidic device for the analysis of rare patient samples, we show that molecular subtypes of breast cancer can be accurately classified and that subcellular spatial markers of disease aggressiveness can be identified.},
}
@article {pmid31285351,
year = {2019},
author = {Hind, KR and Starko, S and Burt, JM and Lemay, MA and Salomon, AK and Martone, PT},
title = {Trophic control of cryptic coralline algal diversity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {30},
pages = {15080-15085},
pmid = {31285351},
issn = {1091-6490},
mesh = {Animals ; Anthozoa/physiology ; *Biodiversity ; Coral Reefs ; DNA Barcoding, Taxonomic ; DNA, Algal/genetics ; Ecosystem ; Food Chain ; Kelp/classification/genetics ; Otters/*physiology ; Pacific Ocean ; *Phylogeny ; Predatory Behavior/physiology ; Rhodophyta/*classification/genetics ; Sea Urchins/*physiology ; },
abstract = {Understanding how trophic dynamics drive variation in biodiversity is essential for predicting the outcomes of trophic downgrading across the world's ecosystems. However, assessing the biodiversity of morphologically cryptic lineages can be problematic, yet may be crucial to understanding ecological patterns. Shifts in keystone predation that favor increases in herbivore abundance tend to have negative consequences for the biodiversity of primary producers. However, in nearshore ecosystems, coralline algal cover increases when herbivory is intense, suggesting that corallines may uniquely benefit from trophic downgrading. Because many coralline algal species are morphologically cryptic and their diversity has been globally underestimated, increasing the resolution at which we distinguish species could dramatically alter our conclusions about the consequences of trophic dynamics for this group. In this study, we used DNA barcoding to compare the diversity and composition of cryptic coralline algal assemblages at sites that differ in urchin biomass and keystone predation by sea otters. We show that while coralline cover is greater in urchin-dominated sites (or "barrens"), which are subject to intense grazing, coralline assemblages in these urchin barrens are significantly less diverse than in kelp forests and are dominated by only 1 or 2 species. These findings clarify how food web structure relates to coralline community composition and reconcile patterns of total coralline cover with the widely documented pattern that keystone predation promotes biodiversity. Shifts in coralline diversity and distribution associated with transitions from kelp forests to urchin barrens could have ecosystem-level effects that would be missed by ignoring cryptic species' identities.},
}
@article {pmid31284589,
year = {2019},
author = {Song, JH and Kim, WJ and Cha, JM and Yang, S and Choi, G and Moon, BC},
title = {Comparative Morphological, Ultrastructural, and Molecular Studies of Four Cicadinae Species Using Exuvial Legs.},
journal = {Insects},
volume = {10},
number = {7},
pages = {},
pmid = {31284589},
issn = {2075-4450},
support = {KSN1812410//Korea Institute of Oriental Medicine/ ; },
abstract = {Previous studies have suggested that exuviae can be used for the identification of cicada species, but the precise characteristics that differ among species have not been determined. Thus, we performed the first comparative analyses of the leg morphology, ultrastructure, and mitochondrial DNA sequences of exuviae of four dominant cicada species in Korea, Hyalessa maculaticollis (Motschulsky, 1866), Meimuna opalifera (Walker, 1850), Platypleura kaempferi (Fabricius, 1794) and Cryptotympana atrata (Fabricius, 1775), the source of Cicadidae Periostracum, a well-known traditional medicine. A morphological analysis revealed that the profemur length, femoral tooth angle, and distance between the intermediate and last tooth of the femoral comb are useful characteristics for identification. We also evaluated the usefulness of the size, degree of reflex, and number of spines on the mid-legs and hind legs as diagnostic features. An ultrastructural study showed that Meimuna opalifera has a unique surface pattern on the legs. The sequences obtained using exuviae were identical to previously obtained sequences for adult tissues. Moreover, in a phylogenetic analysis using CO1 sequences, each species formed a monophyletic cluster with high bootstrap support. Accordingly, multiple methodological approaches using exuviae might provide highly reliable identification tools. The integrative data provide useful characteristics for the exuviae-based identification of closely related species and for further taxonomic and systematic studies of Cicadinae.},
}
@article {pmid31284383,
year = {2019},
author = {Pappalardo, AM and Petraccioli, A and Capriglione, T and Ferrito, V},
title = {From Fish Eggs to Fish Name: Caviar Species Discrimination by COIBar-RFLP, an Efficient Molecular Approach to Detect Fraud in the Caviar Trade.},
journal = {Molecules (Basel, Switzerland)},
volume = {24},
number = {13},
pages = {},
pmid = {31284383},
issn = {1420-3049},
mesh = {Animals ; Base Sequence ; Electron Transport Complex IV/*genetics ; *Fish Products ; Fishes/*genetics ; Ovum/*metabolism ; Polymorphism, Restriction Fragment Length/*genetics ; },
abstract = {The demand for caviar is growing as is its price on the market. Due to the decline of true caviar production from sturgeons, eggs from other fish species and other animals have been used as substitutes for caviar. The labels on these products should indicate the species from which the eggs were derived, but the label can be misleading in some cases. In this context, species identification using DNA analysis is crucial for traceability and authentication of caviar products. In this work, we applied the COIBar-RFLP procedure to obtain species-specific endonuclease restriction patterns useful to discriminate "caviar" species. The tested caviar products were identified as originating from eight species: Acipenser transmontanus, A. gueldenstaedtii, A. stellatus, A. baerii, Mallotus villosus, Huso huso, Cyclopterus lumpus and Eumicrotremus orbis. The results demonstrated that 14% of the caviar products examined have a label that does not indicate the species from which the eggs were originated. The MboI restriction enzyme produced specific profiles discriminating the eight species, confirming that the COIBar-RFLP is a useful approach for routine screening of seafood products due to its ease and rapid execution, as the results of screening can be obtained within 7 h, by-passing the need for sequencing.},
}
@article {pmid31280502,
year = {2019},
author = {Mihalca, AD and Păstrav, IR and Sándor, AD and Deak, G and Gherman, CM and Sarmaşi, A and Votýpka, J},
title = {First report of the dog louse fly Hippobosca longipennis in Romania.},
journal = {Medical and veterinary entomology},
volume = {33},
number = {4},
pages = {530-535},
doi = {10.1111/mve.12395},
pmid = {31280502},
issn = {1365-2915},
mesh = {*Animal Distribution ; Animals ; Diptera/*physiology ; Dog Diseases/*parasitology ; Dogs ; Ectoparasitic Infestations/parasitology/*veterinary ; },
abstract = {Hippobosca longipennis (Diptera: Hippoboscidae), the dog fly or dog louse fly, is an obligate blood-feeding ectoparasite of wild and domestic carnivores in Africa and the Middle East. Outside its typically known geographic range, H. longipennis has been reported occasionally on mainly domestic dogs in Asia and southern Europe, and infrequently in other areas (central Europe and the U.S.A.). This paper presents the first report of H. longipennis in Romania and the second record of Lipoptena fortisetosa (Diptera: Hippoboscidae), a potentially invasive species. Hippobosca longipennis was found on domestic dogs in two regions of the country (northern Romania in Maramures and southwestern Romania in Dobrogea) and on two road-killed wildcats in Maramures. Lipoptena fortisetosa was found on domestic dogs in Maramures. In both species identification was based on morphology and confirmed by barcoding of the cytochrome c oxidase subunit 1 gene. It is not clear for how long H. longipennis has been present in central Europe, nor if it was introduced (via the movement of domestic dogs or import of exotic carnivores) or present historically (Holocene remnants). This paper discusses the possible origins of H. longipennis in central Europe as its current distribution in the area is sparse and patchy.},
}
@article {pmid31279178,
year = {2019},
author = {Mohammadniaei, M and Go, A and Chavan, SG and Koyappayil, A and Kim, SE and Yoo, HJ and Min, J and Lee, MH},
title = {Relay-race RNA/barcode gold nanoflower hybrid for wide and sensitive detection of microRNA in total patient serum.},
journal = {Biosensors &amp; bioelectronics},
volume = {141},
number = {},
pages = {111468},
doi = {10.1016/j.bios.2019.111468},
pmid = {31279178},
issn = {1873-4235},
mesh = {Biosensing Techniques/*instrumentation ; Electrochemical Techniques/instrumentation ; Electrodes ; Equipment Design ; Gold/*chemistry ; Humans ; Limit of Detection ; Metal Nanoparticles/*chemistry ; MicroRNAs/*blood ; Nucleic Acid Hybridization ; },
abstract = {Development of a very sensitive biosensor is accompanied with an inevitable shrinkage in the linear detection range. Here, we developed an electrochemical biosensor with a novel methodology to detect microRNA-21 (miR21) at an ultralow level and broad linear detection range. A three-way junction RNA structure was designed harboring (i) a methylene blue (MB)-modified hairpin structure at its one leg to function as the sensing moiety and (ii) the other two legs to be further hybridized with barcode gold nanoparticles (MB/barG) as the signal amplifiers. Addition of target miR21 resulted in opening the hairpin moiety and subsequent hybridization with DNA-modified gold nanoflower/platinum electrode (GNF@Pt) to form the MB-3 sensor. Inspired by the relay-race run, to extend the dynamic detection range and increase the sensitivity of the biosensor, MB/barG was added to form the second detection modality (MBG-3). The combined sensor required very low sample volume (4 μL) and could identify 135 aM or 324 molecules of miR21 with the ability to operate within a wide linear range from 1 μM down to 500 aM. The fabricated GNF@Pt showed a remarkable conductivity compared with the gold nanoparticle-modified electrode. Addition of MB/barG boosted the electrochemical signal of the MB by almost 230 times. Moreover, a new protocol was introduced by the authors to increase the efficiency of microRNA extraction from the total serum. Possessing a sound selectivity and specificity towards single base-pair mutations, the developed biosensor could profile cancer development stages of two patient serums.},
}
@article {pmid31278475,
year = {2020},
author = {Kandemir, H and Dukik, K and Hagen, F and Ilkit, M and Gräser, Y and de Hoog, GS},
title = {Polyphasic Discrimination of Trichophyton tonsurans and T. equinum from Humans and Horses.},
journal = {Mycopathologia},
volume = {185},
number = {1},
pages = {113-122},
pmid = {31278475},
issn = {1573-0832},
support = {FEMS-RG-2016-0067//Federation of European Microbiological Societies (GB)/ ; },
mesh = {Amplified Fragment Length Polymorphism Analysis ; Animals ; Biodiversity ; DNA, Ribosomal/*genetics ; Genes, Mating Type, Fungal/genetics/physiology ; Horses ; Humans ; Mice ; Multilocus Sequence Typing ; Trichophyton/classification/*genetics ; },
abstract = {The anthropophilic dermatophyte Trichophyton tonsurans and its zoophilic counterpart T. equinum are phylogenetically closely related. The barcoding marker rDNA internal transcribed spacer (ITS) shows limited variation between these two species. In the current study, we combined molecular approaches with phenotypic data to determine the species boundaries between T. tonsurans (n = 52) and T. equinum (n = 15) strains originating from humans (n = 40), horses (n = 26), and a mouse (n = 1). Culture characteristics and physiology on Trichophyton agar media 1 and 5 were evaluated. Multi-locus sequencing involving ITS, partial large rDNA subunit (LSU), β-tubulin (TUB), 60S ribosomal protein (RPB), and translation elongation factor-3 (TEF3) genes, and the mating-type (MAT) locus was performed. Amplified fragment length polymorphism data were added. None of the test results showed complete mutual correspondence. With the exception of strains from New Zealand, strains of equine origin required niacin for growth, whereas most strains from human origin did not show this dependence. It is concluded that T. tonsurans and T. equinum incompletely diverged from a common lineage relatively recently. MAT1-1 and MAT1-2 are the main distinguishing genes between the two species.},
}
@article {pmid31276547,
year = {2019},
author = {Andriollo, T and Gillet, F and Michaux, JR and Ruedi, M},
title = {The menu varies with metabarcoding practices: A case study with the bat Plecotus auritus.},
journal = {PloS one},
volume = {14},
number = {7},
pages = {e0219135},
pmid = {31276547},
issn = {1932-6203},
mesh = {Animal Feed/*analysis ; Animals ; Chiroptera/*physiology ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; Feces/*chemistry ; Feeding Behavior ; High-Throughput Nucleotide Sequencing ; Predatory Behavior ; Sequence Analysis, DNA ; },
abstract = {Metabarcoding of feces has revolutionized the knowledge of animal diets by providing unprecedented resolution of consumed resources. However, it is still unclear how different methodological approaches influence the ecological conclusions that can be drawn from such data. Here, we propose a critical evaluation of several data treatments on the inferred diet of the bat Plecotus auritus using guano regularly collected from various colonies throughout the entire active season. First and unlike previous claims, our data indicates that DNA extracted from large amounts of fecal material issued from guano accumulates yield broader taxonomic diversity of prey than smaller numbers of pellets would do, provided that extraction buffer volumes are adapted to such increased amounts of material. Second, trophic niche analyses based on prey occurrence data uncover strong seasonality in the bat's diet and major differences among neighboring maternity colonies. Third, while the removal of rare prey items is not always warranted as it introduces biases affecting particularly samples with greater prey species richness. Fourth, examination of distinct taxonomic depths in diet analyses highlights different aspects of food consumption providing a better understanding of the consumer's diet. Finally, the biologically meaningful patterns recovered with presence-absence approaches are virtually lost when attempting to quantify prey consumed using relative read abundances. Even in an ideal situation where reference barcodes are available for most potential prey species, inferring realistic patterns of prey consumption remains relatively challenging. Although best practice in metabarcoding analyses will depend on the aims of the study, several previous methodological recommendations seem unwarranted for studying such diverse diets as that of brown long-eared bats.},
}
@article {pmid31275063,
year = {2019},
author = {Bagley, M and Pilgrim, E and Knapp, M and Yoder, C and Domingo, JS and Banerji, A},
title = {High-throughput environmental DNA analysis informs a biological assessment of an urban stream.},
journal = {Ecological indicators},
volume = {104},
number = {},
pages = {378-389},
pmid = {31275063},
issn = {1470-160X},
support = {EPA999999//Intramural EPA/United States ; },
abstract = {There is growing interest in the use of DNA barcoding and metabarcoding approaches to aid biological assessments and monitoring of waterbodies. While biodiversity measured by morphology and by DNA often has been found correlated, few studies have compared DNA data to established measures of impairment such as multimetric pollution tolerance indices used by many bioassessment programs. We incorporated environmental DNA (eDNA) metabarcoding of seston into a rigorous watershed-scale biological assessment of an urban stream to examine the extent to which eDNA richness and diversity patterns were correlated with multimetric indices and ecological impairment status designations. We also evaluated different filtering approaches and taxonomic classifications to identify best practices for environmental assessments. Seston eDNA revealed a wide diversity of eukaryotic taxa but was dominated by diatoms (36%). Differentiation among sites in alpha and beta diversity was greater when operational taxonomic units (OTUs) were classified taxonomically, but coarse resolution taxonomy (kingdom) was more informative than finer resolution taxonomy (family, genus). Correlations of DNA richness and diversity with multimetric indices for fish and macroinvertebrates were generally weak, possibly because Metazoa were not highly represented in our DNA dataset. Nonetheless, sites could be differentiated based on ecological impairment status, with more impaired sites having lower eDNA diversity as measured by the Shannon index, but higher taxonomic richness. Significant environmental drivers of community structure, as inferred from constrained ordination analyses, differed among kingdoms within the eDNA dataset, as well as from fish and macrobenthos, suggesting that eDNA provides novel environmental information. These results suggest that even a simple seston eDNA filtering protocol can provide biodiversity information of value to stream bioassessment programs. The approach bears further investigation as a potentially useful rapid assessment protocol to supplement more intensive field sampling efforts.},
}
@article {pmid31273217,
year = {2019},
author = {Delrieu-Trottin, E and Williams, JT and Pitassy, D and Driskell, A and Hubert, N and Viviani, J and Cribb, TH and Espiau, B and Galzin, R and Kulbicki, M and Lison de Loma, T and Meyer, C and Mourier, J and Mou-Tham, G and Parravicini, V and Plantard, P and Sasal, P and Siu, G and Tolou, N and Veuille, M and Weigt, L and Planes, S},
title = {A DNA barcode reference library of French Polynesian shore fishes.},
journal = {Scientific data},
volume = {6},
number = {1},
pages = {114},
pmid = {31273217},
issn = {2052-4463},
mesh = {Animals ; Biodiversity ; Coral Reefs ; *DNA Barcoding, Taxonomic ; Fishes/*classification/*genetics ; *Gene Library ; Polynesia ; },
abstract = {The emergence of DNA barcoding and metabarcoding opened new ways to study biological diversity, however, the completion of DNA barcode libraries is fundamental for such approaches to succeed. This dataset is a DNA barcode reference library (fragment of Cytochrome Oxydase I gene) for 2,190 specimens representing at least 540 species of shore fishes collected over 10 years at 154 sites across the four volcanic archipelagos of French Polynesia; the Austral, Gambier, Marquesas and Society Islands, a 5,000,000 km[2] area. At present, 65% of the known shore fish species of these archipelagoes possess a DNA barcode associated with preserved, photographed, tissue sampled and cataloged specimens, and extensive collection locality data. This dataset represents one of the most comprehensive DNA barcoding efforts for a vertebrate fauna to date. Considering the challenges associated with the conservation of coral reef fishes and the difficulties of accurately identifying species using morphological characters, this publicly available library is expected to be helpful for both authorities and academics in various fields.},
}
@article {pmid31271726,
year = {2019},
author = {Veldkornet, DA and Adams, JB and Boatwright, JS and Rajkaran, A},
title = {Barcoding of estuarine macrophytes and phylogenetic diversity of estuaries along the South African coastline.},
journal = {Genome},
volume = {62},
number = {9},
pages = {585-595},
doi = {10.1139/gen-2018-0067},
pmid = {31271726},
issn = {1480-3321},
mesh = {Aquatic Organisms/classification ; *Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Plant ; *Estuaries ; Phylogeny ; Plants/*classification/genetics ; South Africa ; },
abstract = {Plant DNA barcoding serves as an effective approach to building community phylogenies and increasing our understanding of the factors that determine plant community assemblages. The aims of the study were to (i) barcode macrophytes with high estuarine fidelity and (ii) to determine the phylogenetic diversity (PD) of selected South African estuaries for conservation prioritisation. Three DNA barcoding gene regions (rbcLa, matK, and trnH-psbA) were assessed, and community phylogenies were constructed for 270 estuaries. Generally, the matK barcode had the greatest discrimination success rate of 67.4% (parsimony informative sites = 418). Closely related species formed clades that also represent estuarine habitat types. Estuaries with high phylogenetic diversity along the southeast coast were associated with a combination of mangrove and salt marsh habitats. Species richness was strongly and significantly correlated with PD (r = 0.93; p < 0.000). Based on mean pairwise distance (MPD), more temperate estuaries (56) showed significant phylogenetic clustering compared to subtropical estuaries (24) (p < 0.05). Similarly, based on mean nearest taxon distance (MNTD), significant phylogenetic clustering was highest in temperate estuaries (50) compared to subtropical estuaries (12) (p < 0.05). This suggests that the coexistence of plant species in estuaries is structured by both biotic and abiotic interactions.},
}
@article {pmid31271485,
year = {2019},
author = {Zhang, X and Chen, G and Bian, F and Cai, L and Zhao, Y},
title = {Encoded Microneedle Arrays for Detection of Skin Interstitial Fluid Biomarkers.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {31},
number = {37},
pages = {e1902825},
doi = {10.1002/adma.201902825},
pmid = {31271485},
issn = {1521-4095},
support = {2017YFA0700404//National Key Research and Development Program of China/ ; 21473029//National Natural Science Foundation of China/ ; 51522302//National Natural Science Foundation of China/ ; U1530260//NSAF Joint Fund/ ; BK20180128//National Science Foundation of Jiangsu/ ; //Southeast University/ ; //Scientific Research Foundation of Graduate School of Southeast University/ ; U1530260//NSAF Foundation of China/ ; //Scientific Research Foundation of Southeast University/ ; },
mesh = {Biomarkers/*metabolism ; Body Fluids/*metabolism ; Humans ; Microarray Analysis/*instrumentation ; *Needles ; Skin/*metabolism ; },
abstract = {Skin interstitial fluid (ISF) is considered as an emerging source of biomarkers with physiological and medical significance. Microneedle arrays (MNs) provide a promising means for painless, noninvasive detection of these biomarkers. Here, novel MNs integrated with photonic crystal (PhC) barcodes are presented, and multiplex specific detection of ISF biomarkers is realized for the first time. The PhC barcodes-loaded flexible MNs are simply fabricated by replicating dynamic ferrofluid-cast micromoldings. When the prepared MNs are inserted into skin, they can enrich specific biomarkers to their probes-decorated PhC barcodes. Thus, by adding corresponding fluorescent probes to form sandwich immunocomplexes, the relative content of the biomarkers can be read out through the fluorescence intensity of the barcodes; meanwhile, the species of these biomarkers can be clearly distinguished by the reflection peaks of the PhC barcodes. Based on the encoded MNs, their sensitivity, flexibility, and versatility of capturing and detecting three inflammatory cytokines are demonstrated in a sepsis mice model. Compared with existing MNs for ISF detection, the encoded MNs not only possess equivalent detection effects with less post-processing and simplified procedures, but can also detect multiple biomarkers simultaneously, which makes them ideal in many clinical and biomedical detection areas.},
}
@article {pmid31269631,
year = {2019},
author = {Markotter, W and Geldenhuys, M and Jansen van Vuren, P and Kemp, A and Mortlock, M and Mudakikwa, A and Nel, L and Nziza, J and Paweska, J and Weyer, J},
title = {Paramyxo- and Coronaviruses in Rwandan Bats.},
journal = {Tropical medicine and infectious disease},
volume = {4},
number = {3},
pages = {},
pmid = {31269631},
issn = {2414-6366},
support = {98339//National Research Foundation/ ; },
abstract = {A high diversity of corona- and paramyxoviruses have been detected in different bat species at study sites worldwide, including Africa, however no biosurveillance studies from Rwanda have been reported. In this study, samples from bats collected from caves in Ruhengeri, Rwanda, were tested for the presence of corona- and paramyxoviral RNA using reverse transcription PCR assays. Positive results were further characterized by DNA sequencing and phylogenetic analysis. In addition to morphological identification of bat species, we also did molecular confirmation of species identities, contributing to the known genetic database available for African bat species. We detected a novel Betacoronavirus in two Geoffroy's horseshoe bats (Rhinolophus clivosus) bats. We also detected several different paramyxoviral species from various insectivorous bats. One of these viral species was found to be homologous to the genomes of viruses belonging to the Jeilongvirus genus. Additionally, a Henipavirus-related sequence was detected in an Egyptian rousette fruit bat (Rousettus aegyptiacus). These results expand on the known diversity of corona- and paramyxoviruses and their geographical distribution in Africa.},
}
@article {pmid31267103,
year = {2019},
author = {Morf, J and Wingett, SW and Farabella, I and Cairns, J and Furlan-Magaril, M and Jiménez-García, LF and Liu, X and Craig, FF and Walker, S and Segonds-Pichon, A and Andrews, S and Marti-Renom, MA and Fraser, P},
title = {RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus.},
journal = {Nature biotechnology},
volume = {37},
number = {7},
pages = {793-802},
pmid = {31267103},
issn = {1546-1696},
mesh = {Cell Line, Tumor ; Cell Nucleus ; DNA Barcoding, Taxonomic ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; },
abstract = {The global, three-dimensional organization of RNA molecules in the nucleus is difficult to determine using existing methods. Here we introduce Proximity RNA-seq, which identifies colocalization preferences for pairs or groups of nascent and fully transcribed RNAs in the nucleus. Proximity RNA-seq is based on massive-throughput RNA barcoding of subnuclear particles in water-in-oil emulsion droplets, followed by cDNA sequencing. Our results show RNAs of varying tissue-specificity of expression, speed of RNA polymerase elongation and extent of alternative splicing positioned at varying distances from nucleoli. The simultaneous detection of multiple RNAs in proximity to each other distinguishes RNA-dense from sparse compartments. Application of Proximity RNA-seq will facilitate study of the spatial organization of transcripts in the nucleus, including non-coding RNAs, and its functional relevance.},
}
@article {pmid31264503,
year = {2019},
author = {De Oliveira, EA and Penhacek, M and Guimarães, KLA and do Nascimento, GA and Rodrigues, LRR and Hernández-Ruz, EJ},
title = {Pristimantis in the Eastern Brazilian Amazon: DNA barcoding reveals underestimated diversity in a megadiverse genus.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {6},
pages = {731-738},
doi = {10.1080/24701394.2019.1634696},
pmid = {31264503},
issn = {2470-1408},
mesh = {Animals ; Anura/*genetics ; Brazil ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Genome, Mitochondrial/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Species Specificity ; },
abstract = {The genus Pristimantis has the highest species diversity among all terrestrial vertebrates, with most species observed in the Andean region and the Guiana Shield. Even with the recent description of a new species, only P. latro, P. dundeei and P. zimmermanae occur in the south of the Amazon River. The lack of taxonomists specialized in the field leads to the propagation of dubious terminologies (e.g. Pristimantis sp1, Pristimantis sp2, P. aff. Fenestratus and P. gr. conspicillatus) or even misidentification of species, resulting in erroneous species distributions. In this study, we applied the Automatic Barcode Gap Discovery (ABGD) algorithm for the delimitation of candidate species and values of genetic distances using the mitochondrial marker Cytochrome Oxidase Subunit I (COI), proposed in the barcode methodology, where values greater than 10% are considered as indicative of different species. We found large genetic distances between P. latro and Pristimantis sp1 Unconfirmed Candidate Species - UCS1 (21%), and between P. altamazonicus and Pristimantis sp2 UCS2 (14%). The ABGD method recognized UCS1 and UCS2 as distinct species. Pristimantis sp. UCS1 and UCS2 in the east of the Brazilian Amazon are indicated as candidate species. We suggest greater sampling of Pristimantis sp. UCS1 and UCS2, integrating morphology and bioacoustics to solve the taxonomic status in the east of the Brazilian Amazon.},
}
@article {pmid31259363,
year = {2019},
author = {Santos, EOD and Deon, GA and Almeida, RB and Oliveira, EA and Nogaroto, V and Silva, HPD and Pavanelli, CS and Cestari, MM and Bertollo, LAC and Moreira-Filho, O and Vicari, MR},
title = {Cytogenetics and DNA barcode reveal an undescribed Apareiodon species (Characiformes: Parodontidae).},
journal = {Genetics and molecular biology},
volume = {42},
number = {2},
pages = {365-373},
pmid = {31259363},
issn = {1415-4757},
abstract = {Parodontidae is a small group of fish and some species are particularly difficult to identify due to the lack of sufficiently consistent morphological traits. Cytogenetically, the species possess 2n = 54 chromosomes and are either sex-homomorphic or sex-heteromorphic (regarding its chromosomes). We evaluated data on color, tooth morphology, cytogenetics, and mitochondrial markers (COI) in Apareiodon specimens from the Aripuanã River (Amazon basin) and the results were compared to other congeneric taxa. Morphological results show an overlap of body color and tooth morphology to other known Apareiodon. The cytogenetics data showed that the 2n = 54 chromosomes, 50 m/sm + 4 st and, a ZZ/ZW sex chromosome system in Apareiodon sp. are common to other species of the genus. However, the number and chromosomal localization of the 45S ribosomal and pPh2004 satellite DNA sites, in addition to W chromosome localization of the pPh2004 appear to be exclusive cytogenetic features in Apareiodon sp. Our phylogenetic tree revealed well-supported clades and confirmed, by barcode species delimitation analysis, a new Molecular Operational Taxonomic Unit (MOTU) for Apareiodon sp. (Aripuanã River). As a whole, the above features support the occurrence of a new species of the Apareiodon, thus far unknown for the Parodontidae.},
}
@article {pmid31254926,
year = {2019},
author = {Katayama, K and Mitsunobu, H and Nishida, K},
title = {Mammalian synthetic biology by CRISPRs engineering and applications.},
journal = {Current opinion in chemical biology},
volume = {52},
number = {},
pages = {79-84},
doi = {10.1016/j.cbpa.2019.05.020},
pmid = {31254926},
issn = {1879-0402},
mesh = {Animals ; *Clustered Regularly Interspaced Short Palindromic Repeats ; DNA Barcoding, Taxonomic ; DNA Breaks, Double-Stranded ; Epigenesis, Genetic ; *Genetic Engineering ; Mammals ; RNA Editing ; *Synthetic Biology ; },
abstract = {Technologies harnessing CRISPR systems have been rapidly evolving and expanding the capacity of researchers for understanding of mammalian cell behavior and its underlying mechanisms through genome and epigenome manipulations. In this review, we summarized the recent developments of CRISPR-based technologies for genetic and epigenetic modifications that include engineering of Cas9 for PAM simplification, non-cleaving base editing tools and alteration of gene expression. Applications such as genome-wide screening methods or CRISPR-based DNA barcoding for cellular lineage tracking are highlighted. Anticipated and upcoming development for mammalian synthetic biology that includes organelle engineering is also discussed.},
}
@article {pmid31253861,
year = {2019},
author = {Rahman, MM and Norén, M and Mollah, AR and Kullander, SO},
title = {Building a DNA barcode library for the freshwater fishes of Bangladesh.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {9382},
pmid = {31253861},
issn = {2045-2322},
abstract = {We sequenced the standard DNA barcode gene fragment in 694 newly collected specimens, representing 243 species level Operational Barcode Units (OBUs) of freshwater fishes from Bangladesh. We produced coi sequences for 149 out of the 237 species already recorded from Bangladesh. Another 83 species sequenced were not previously recorded for the country, and include about 30 undescribed or potentially undescribed species. Several of the taxa that we could not sample represent erroneous records for the country, or sporadic occurrences. Species identifications were classified at confidence levels 1(best) to 3 (worst). We propose the new term Operational Barcode Unit (OBU) to simplify references to would-be DNA barcode sequences and sequence clusters. We found one case where there were two mitochondrial lineages present in the same species, several cases of cryptic species, one case of introgression, one species yielding a pseudogene to standard barcoding primers, and several cases of taxonomic uncertainty and need for taxonomic revision. Large scale national level DNA barcode prospecting in high diversity regions may suffer from lack of taxonomic expertise that cripples the result. Consequently, DNA barcoding should be performed in the context of taxonomic revision, and have a defined, competent end-user.},
}
@article {pmid31251609,
year = {2019},
author = {Chen, C and Corry, B and Huang, L and Hildebrandt, N},
title = {FRET-Modulated Multihybrid Nanoparticles for Brightness-Equalized Single-Wavelength Barcoding.},
journal = {Journal of the American Chemical Society},
volume = {141},
number = {28},
pages = {11123-11141},
doi = {10.1021/jacs.9b03383},
pmid = {31251609},
issn = {1520-5126},
mesh = {Carbocyanines/chemistry ; *Fluorescence Resonance Energy Transfer ; Fluorescent Dyes/*chemistry ; Nanoparticles/*chemistry ; Quantum Dots/chemistry ; Terbium/chemistry ; },
abstract = {Semiconductor quantum dots (QDs) are the most versatile fluorophores for Förster resonance energy transfer (FRET) because they can function as both donors and acceptors for a multitude of fluorophores. However, a complete understanding of multidonor-multiacceptor FRET networks on QDs and their full employment into advanced fluorescence sensing and imaging have not been accomplished. Here, we provide a holistic photophysical analysis of such multidonor-QD-multiacceptor FRET systems using time-resolved and steady-state photoluminescence (PL) spectroscopy and Monte Carlo simulations. Multiple terbium complex (Tb) donors (1-191 units) and Cy5.5 dye acceptors (1-60 units) were attached to a central QD, and the entire range of combinations of FRET pathways was investigated by Tb, QD, and Cy5.5 PL. Experimental and simulation results were in excellent agreement and could disentangle the distinct contributions of hetero-FRET, homo-FRET, and dye dimerization. The FRET efficiency was independent of the number of Tb donors and dependent on the number of Cy5.5 acceptors, which could be used to independently adapt the PL intensity by the number of Tb donors and the PL lifetime by the number of Cy5.5 acceptors. We used this unique tuning capability to prepare Tb-QD-Cy5.5 conjugates with distinct QD PL lifetimes but similar QD PL intensities. These brightness-equalized multihybrid FRET nanoparticles were applied to optical barcoding via three time-gated PL intensity detection windows, which resulted in simple RGB ratios. Direct applicability was demonstrated by an efficient RGB distinction of different nanoparticle-encoded microbeads within the same field of view with both single-wavelength excitation and detection on a standard fluorescence microscope.},
}
@article {pmid31250369,
year = {2020},
author = {Tanaka, S and Ito, M},
title = {DNA barcoding for identification of agarwood source species using trnL-trnF and matK DNA sequences.},
journal = {Journal of natural medicines},
volume = {74},
number = {1},
pages = {42-50},
pmid = {31250369},
issn = {1861-0293},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic/*methods ; Thymelaeaceae/*genetics ; Wood/chemistry/*classification/genetics ; },
abstract = {Agarwood is a type of resinous wood found in the trunks of Aquilaria, Gonystylus, and Gyrinops species [1]. High-quality agarwood is extraordinarily expensive and therefore its source plant species have become depleted due to exploitation. In 2005, these species were added to Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora [1]. Because these wild agarwood resources have become depleted, commercial production of agarwood has long been a desirable goal. In addition, inauthentic agarwood is sometimes produced from non-agarwood species. Few reports have attempted to identify source species in order to distinguish genuine from false agarwood. In this study, DNA was extracted from putative agarwood samples collected from Japanese, Indonesian, Thai, and Vietnamese markets. The trnL-trnF region and matK gene were amplified from each sample by PCR to serve as DNA barcodes for identifying the plant species to which each sample belonged. One of the wood samples did not originate from a genuine agarwood species. Although some species were identified, sequence data for agarwood source species currently available in GenBank is insufficient to identify the species to which all of these putative agarwood samples belonged. Thus, positive identification of remaining samples will require further exploration.},
}
@article {pmid31249062,
year = {2019},
author = {Patterson, K and Shavarebi, F and Magnan, C and Chang, I and Qi, X and Baldi, P and Bilanchone, V and Sandmeyer, SB},
title = {Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites.},
journal = {Genome research},
volume = {29},
number = {8},
pages = {1298-1309},
pmid = {31249062},
issn = {1549-5469},
support = {P30 CA062203/CA/NCI NIH HHS/United States ; R01 GM033281/GM/NIGMS NIH HHS/United States ; S10 OD010794/OD/NIH HHS/United States ; S10 RR025496/RR/NCRR NIH HHS/United States ; },
mesh = {*Genome, Fungal ; Integrases/*genetics/metabolism ; Mutagenesis, Insertional ; Nucleotide Motifs ; Plasmids/chemistry/metabolism ; RNA Polymerase III/*genetics/metabolism ; RNA, Transfer/genetics/metabolism ; *Retroelements ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Transcription Factor TFIIIB/genetics/metabolism ; Transcription Initiation Site ; *Transcription, Genetic ; },
abstract = {Retroelement integration into host genomes affects chromosome structure and function. A goal of a considerable number of investigations is to elucidate features influencing insertion site selection. The Saccharomyces cerevisiae Ty3 retrotransposon inserts proximal to the transcription start sites (TSS) of genes transcribed by RNA polymerase III (RNAP3). In this study, differential patterns of insertion were profiled genome-wide using a random barcode-tagged Ty3. Saturation transposition showed that tRNA genes (tDNAs) are targeted at widely different frequencies even within isoacceptor families. Ectopic expression of Ty3 integrase (IN) showed that it localized to targets independent of other Ty3 proteins and cDNA. IN, RNAP3, and transcription factor Brf1 were enriched at tDNA targets with high frequencies of transposition. To examine potential effects of cis-acting DNA features on transposition, targeting was tested on high-copy plasmids with restricted amounts of 5' flanking sequence plus tDNA. Relative activity of targets was reconstituted in these constructions. Weighting of genomic insertions according to frequency identified an A/T-rich sequence followed by C as the dominant site of strand transfer. This site lies immediately adjacent to the adenines previously implicated in the RNAP3 TSS motif (CAA). In silico DNA structural analysis upstream of this motif showed that targets with elevated DNA curvature coincide with reduced integration. We propose that integration mediated by the Ty3 intasome complex (IN and cDNA) is subject to inputs from a combination of host factor occupancy and insertion site architecture, and that this results in the wide range of Ty3 targeting frequencies.},
}
@article {pmid31249006,
year = {2019},
author = {Ludwig, CH and Bintu, L},
title = {Mapping chromatin modifications at the single cell level.},
journal = {Development (Cambridge, England)},
volume = {146},
number = {12},
pages = {},
pmid = {31249006},
issn = {1477-9129},
support = {R35 GM128947/GM/NIGMS NIH HHS/United States ; },
mesh = {Acetylation ; Animals ; Antibodies/chemistry ; Chromatin/*chemistry ; CpG Islands ; DNA/chemistry ; DNA Methylation ; DNA Repair ; Endonucleases/metabolism ; Epigenesis, Genetic ; Epigenome ; Gene Expression Profiling ; Gene Expression Regulation ; Genetic Engineering/methods ; Histones/chemistry ; Humans ; Mice ; Sequence Analysis, DNA ; Single-Cell Analysis/*methods ; },
abstract = {Understanding chromatin regulation holds enormous promise for controlling gene regulation, predicting cellular identity, and developing diagnostics and cellular therapies. However, the dynamic nature of chromatin, together with cell-to-cell heterogeneity in its structure, limits our ability to extract its governing principles. Single cell mapping of chromatin modifications, in conjunction with expression measurements, could help overcome these limitations. Here, we review recent advances in single cell-based measurements of chromatin modifications, including optimization to reduce DNA loss, improved DNA sequencing, barcoding, and antibody engineering. We also highlight several applications of these techniques that have provided insights into cell-type classification, mapping modification co-occurrence and heterogeneity, and monitoring chromatin dynamics.},
}
@article {pmid31247053,
year = {2019},
author = {Erlandson, MA and Mori, BA and Coutu, C and Holowachuk, J and Olfert, OO and Gariepy, TD and Hegedus, DD},
title = {Examining population structure of a bertha armyworm, Mamestra configurata (Lepidoptera: Noctuidae), outbreak in western North America: Implications for gene flow and dispersal.},
journal = {PloS one},
volume = {14},
number = {6},
pages = {e0218993},
pmid = {31247053},
issn = {1932-6203},
mesh = {Animal Distribution ; Animals ; Brassica napus/parasitology ; Brassica rapa/parasitology ; Electron Transport Complex IV/genetics ; Gene Flow ; Genetic Variation ; Genetics, Population ; Genome, Insect ; Haplotypes ; Insect Control ; Insect Proteins/genetics ; Male ; Moths/*genetics/pathogenicity ; North America ; Polymorphism, Single Nucleotide ; },
abstract = {The bertha armyworm (BAW), Mamestra configurata, is a significant pest of canola (Brassica napus L. and B. rapa L.) in western North America that undergoes cyclical outbreaks every 6-8 years. During peak outbreaks millions of dollars are spent on insecticidal control and, even with control efforts, subsequent damage can result in losses worth millions of dollars. Despite the importance of this pest insect, information is lacking on the dispersal ability of BAW and the genetic variation of populations from across its geographic range which may underlie potential differences in their susceptibility to insecticides or pathogens. Here, we examined the genetic diversity of BAW populations during an outbreak across its geographic range in western North America. First, mitochondrial cytochrome oxidase 1 (CO1) barcode sequences were used to confirm species identification of insects captured in a network of pheromone traps across the range, followed by haplotype analyses. We then sequenced the BAW genome and used double-digest restriction site associated DNA sequencing, mapped to the genome, to identify 1000s of single nucleotide polymorphisms (SNP) markers. CO1 haplotype analysis identified 9 haplotypes distributed across 28 sample locations and three laboratory-reared colonies. Analysis of genotypic data from both the CO1 and SNP markers revealed little population structure across BAW's vast range. The CO1 haplotype pattern showed a star-like phylogeny which is often associated with species whose population abundance and range has recently expanded and combined with pheromone trap data, indicates the outbreak may have originated from a single focal point in central Saskatchewan. The relatively recent introduction of canola and rapid expansion of the canola growing region across western North America, combined with the cyclical outbreaks of BAW caused by precipitous population crashes, has likely selected for a genetically homogenous BAW population adapted to this crop.},
}
@article {pmid31245647,
year = {2019},
author = {Ragupathy, S and Faller, AC and Shanmughanandhan, D and Kesanakurti, P and Shaanker, RU and Ravikanth, G and Sathishkumar, R and Mathivanan, N and Song, J and Han, J and Newmaster, S},
title = {Exploring DNA quantity and quality from raw materials to botanical extracts.},
journal = {Heliyon},
volume = {5},
number = {6},
pages = {e01935},
pmid = {31245647},
issn = {2405-8440},
abstract = {OBJECTIVES: The aim of this study was to explore the variability in DNA quality and quantity along a gradient of industrial processing of botanical ingredients from raw materials to extracts.<br><br>METHODS: A data matrix was assembled for 1242 botanical ingredient samples along a gradient of industrial processing commonly used in the Natural Health Product (NHP) industry. Multivariate statistics was used to explore dependant variables for quality and quantity. The success of attaining a positive DNA test result along a gradient of industrial processing was compared among four biotechnologies: DNA barcoding, NGS, Sanger sequencing and qPCR.<br><br>RESULTS: There was considerable variance in DNA quality and quantity among the samples, which could be interpreted along a gradient from raw materials with greater quantities (50-120 ng/&#x3bc;L) of DNA and longer DNA (400-500bp) sequences to extracts, which were characterized by lower quantities (0.1-10.0 ng/&#x3bc;L) and short fragments (50-150bp).<br><br>CONCLUSIONS: Targeted molecular diagnostic tests for species identity can be used in the NHP industry for raw and processed samples. Non-targeted tests or the use of NGS for any identity test needs considerable research and development and must be validated before it can be used in commercial operations as these methods are subject to considerable risk of false negative and positive results. Proper use of these tools can be used to ensure ingredient authenticity, and to avert adulteration, and contamination with plants that are a health concern. Lastly these tools can be used to prevent the exploitation of rare herbal species and the harvesting of native biodiversity for commercial purposes.},
}
@article {pmid31244854,
year = {2019},
author = {Amir, ED and Lee, B and Badoual, P and Gordon, M and Guo, XV and Merad, M and Rahman, AH},
title = {Development of a Comprehensive Antibody Staining Database Using a Standardized Analytics Pipeline.},
journal = {Frontiers in immunology},
volume = {10},
number = {},
pages = {1315},
pmid = {31244854},
issn = {1664-3224},
support = {S10 OD023547/OD/NIH HHS/United States ; U19 AI118610/AI/NIAID NIH HHS/United States ; U19 AI128949/AI/NIAID NIH HHS/United States ; },
mesh = {Algorithms ; Antibodies/*metabolism ; Biomarkers/blood ; Cloud Computing ; Computational Biology ; Databases, Factual ; Flow Cytometry ; Humans ; Leukocytes, Mononuclear/classification/cytology/immunology ; Monitoring, Immunologic/*methods/standards ; NK Cell Lectin-Like Receptor Subfamily B/blood ; Single-Cell Analysis/methods/standards ; Staining and Labeling ; Systems Biology ; Workflow ; },
abstract = {Large-scale immune monitoring experiments (such as clinical trials) are a promising direction for biomarker discovery and responder stratification in immunotherapy. Mass cytometry is one of the tools in the immune monitoring arsenal. We propose a standardized workflow for the acquisition and analysis of large-scale mass cytometry experiments. The workflow includes two-tiered barcoding, a broad lyophilized panel, and the incorporation of a fully automated, cloud-based analysis platform. We applied the workflow to a large antibody staining screen using the LEGENDScreen kit, resulting in single-cell data for 350 antibodies over 71 profiling subsets. The screen recapitulates many known trends in the immune system and reveals potential markers for delineating MAIT cells. Additionally, we examine the effect of fixation on staining intensity and identify several markers where fixation leads to either gain or loss of signal. The standardized workflow can be seamlessly integrated into existing trials. Finally, the antibody staining data set is available as an online resource for researchers who are designing mass cytometry experiments in suspension and tissue.},
}
@article {pmid31244538,
year = {2019},
author = {Zhang, X and Li, S},
title = {On three species of the spider genus Pimoa (Araneae, Pimoidae) from China.},
journal = {ZooKeys},
volume = {855},
number = {},
pages = {1-13},
pmid = {31244538},
issn = {1313-2989},
abstract = {Two new species of the spider genus Pimoa Chamberlin &amp; Ivie, 1943 are described from Hunan and Yunnan Provinces, China: P.binchuanensis sp. nov. (♂♀) and P.xinjianensis sp. nov. (♂♀). In addition, the male of P.lata Xu &amp; Li, 2009 is described for the first time. The DNA barcodes of the two new species are documented.},
}
@article {pmid31242865,
year = {2019},
author = {Gu, C and Ma, L and Wu, Z and Chen, K and Wang, Y},
title = {Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales.},
journal = {BMC plant biology},
volume = {19},
number = {1},
pages = {281},
pmid = {31242865},
issn = {1471-2229},
support = {LY17C160003//Zhejiang Provincial Natural Science Foundation of China/ ; (No. 31770681, 31370641)//National Natural Science Foundation of China/ ; },
mesh = {*Evolution, Molecular ; *Genome, Chloroplast ; *Genome, Plant ; Lythraceae/*genetics ; Phylogeny ; Sequence Alignment ; },
abstract = {BACKGROUND: Lythraceae belongs to the order Myrtales, which is part of Archichlamydeae. The family has 31 genera containing approximately 620 species of herbs, shrubs and trees. Of these 31 genera, five large genera each possess 35 or more species. They are Lythrum, with 35; Rotala, with 45; Nesaea, with 50; Lagerstroemia, with 56; and Cuphea, with 275 species.<br><br>RESULTS: We reported six newly sequenced chloroplast (cp) genomes (Duabanga grandiflora, Trapa natans, Lythrum salicaria, Lawsonia inermis, Woodfordia fruticosa and Rotala rotundifolia) and compared them with 16 other cp genomes of Lythraceae species. The cp genomes of the 22 Lythraceae species ranged in length from 152,049&#x2009;bp to 160,769&#x2009;bp. In each Lythraceae species, the cp genome contained 112 genes consisting of 78 protein coding genes, four ribosomal RNAs and 30 transfer RNAs. Furthermore, we detected 211-332 simple sequence repeats (SSRs) in six categories and 7-27 long repeats in four categories. We selected ten divergent hotspots (ndhF, matK, ycf1, rpl22, rpl32, trnK-rps16, trnR-atpA, rpl32-trnL, trnH-psbA and trnG-trnR) among the 22 Lythraceae species to be potential molecular markers. We constructed phylogenetic trees from 42 Myrtales plants with 8 Geraniales plants as out groups. The relationships among the Myrtales species were effectively distinguished by maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) trees constructed using 66 protein coding genes. Generally, the 22 Lythraceae species gathered into one clade, which was resolved as sister to the three Onagraceae species. Compared with Melastomataceae and Myrtaceae, Lythraceae and Onagraceae differentiated later within Myrtales.<br><br>CONCLUSIONS: The study provided ten potential molecular markers as candidate DNA barcodes and contributed cp genome resources within Myrtales for further study.},
}
@article {pmid31241702,
year = {2019},
author = {Li, J and Lin, X and Tang, G and Li, R and Wang, D and Ji, S},
title = {Pharmacognostical study of Desmodium caudatum.},
journal = {Anais da Academia Brasileira de Ciencias},
volume = {91},
number = {2},
pages = {e20180637},
doi = {10.1590/0001-3765201920180637},
pmid = {31241702},
issn = {1678-2690},
mesh = {DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; Fabaceae/*chemistry/classification/*genetics ; Pharmacognosy ; Sequence Analysis, DNA ; },
abstract = {Desmodium caudatum (Thunb.) DC, is an ever-green plant widely used in the central and southern China with great economic value for their medical values on fever, dysentery, gastroenteritis, rectal prolapse, snake bites, mastitis, and boils carbuncle. Despite its extensive uses as a traditional Chinese medicine, no systematic research on the identification of Desmodium caudatum has been reported. In this study, traditional pharmacognostical identification including the botanical origin and morphological characters, medicinal material characters, microscopic characters, physicochemical parameters determination and phytochemical screening, and DNA barcoding analysis were employed to establish an accurate and effective identification system of Desmodium caudatum. In addition, the molecular pharmacognosy study was adopted in order to identify the samples more accurately. The ITS loci of the nuclear genome and psbA-trnH loci of the chloroplast genome were selected and evaluated, which were the most variable loci. The study will be beneficial to the development of the quality standard and the identification of species.},
}
@article {pmid31240917,
year = {2019},
author = {Martinez-Farina, CF and Driscoll, S and Wicks, C and Burton, I and Wentzell, PD and Berrué, F},
title = {Chemical Barcoding: A Nuclear-Magnetic-Resonance-Based Approach To Ensure the Quality and Safety of Natural Ingredients.},
journal = {Journal of agricultural and food chemistry},
volume = {67},
number = {27},
pages = {7765-7774},
doi = {10.1021/acs.jafc.9b01066},
pmid = {31240917},
issn = {1520-5118},
mesh = {Drug Labeling/*methods ; Electronic Data Processing/*methods ; Food Handling ; Food Labeling/*methods/standards ; Food Quality ; Food Safety ; Functional Food/*analysis ; Magnetic Resonance Spectroscopy/*methods ; Multivariate Analysis ; Plant Preparations/*analysis ; Quality Control ; },
abstract = {One of the greatest challenges facing the functional food and natural health product (NHP) industries is sourcing high-quality, functional, natural ingredients for their finished products. Unfortunately, the lack of ingredient standards, modernized analytical methodologies, and industry oversight creates the potential for low quality and, in some cases, deliberate adulteration of ingredients. By exploring a diverse library of NHPs provided by the independent certification organization ISURA, we demonstrated that nuclear magnetic resonance (NMR) spectroscopy provides an innovative solution to authenticate botanicals and warrant the quality and safety of processed foods and manufactured functional ingredients. Two-dimensional NMR experiments were shown to be a robust and reproducible approach to capture the content of complex chemical mixtures, while a binary normalization step allows for emphasizing the chemical diversity in each sample, and unsupervised statistical methodologies provide key advantages to classify, authenticate, and highlight the potential presence of additives and adulterants.},
}
@article {pmid31239396,
year = {2019},
author = {Minich, JJ and Sanders, JG and Amir, A and Humphrey, G and Gilbert, JA and Knight, R},
title = {Quantifying and Understanding Well-to-Well Contamination in Microbiome Research.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
pmid = {31239396},
issn = {2379-5077},
abstract = {Microbial sequences inferred as belonging to one sample may not have originated from that sample. Such contamination may arise from laboratory or reagent sources or from physical exchange between samples. This study seeks to rigorously assess the behavior of this often-neglected between-sample contamination. Using unique bacteria, each assigned a particular well in a plate, we assess the frequency at which sequences from each source appear in other wells. We evaluate the effects of different DNA extraction methods performed in two laboratories using a consistent plate layout, including blanks and low-biomass and high-biomass samples. Well-to-well contamination occurred primarily during DNA extraction and, to a lesser extent, in library preparation, while barcode leakage was negligible. Laboratories differed in the levels of contamination. Extraction methods differed in their occurrences and levels of well-to-well contamination, with plate methods having more well-to-well contamination and single-tube methods having higher levels of background contaminants. Well-to-well contamination occurred primarily in neighboring samples, with rare events up to 10 wells apart. This effect was greatest in samples with lower biomass and negatively impacted metrics of alpha and beta diversity. Our work emphasizes that sample contamination is a combination of cross talk from nearby wells and background contaminants. To reduce well-to-well effects, samples should be randomized across plates, samples of similar biomasses should be processed together, and manual single-tube extractions or hybrid plate-based cleanups should be employed. Researchers should avoid simplistic removals of taxa or operational taxonomic units (OTUs) appearing in negative controls, as many will be microbes from other samples rather than reagent contaminants.IMPORTANCE Microbiome research has uncovered magnificent biological and chemical stories across nearly all areas of life science, at times creating controversy when findings reveal fantastic descriptions of microbes living and even thriving in what were once thought to be sterile environments. Scientists have refuted many of these claims because of contamination, which has led to robust requirements, including the use of controls, for validating accurate portrayals of microbial communities. In this study, we describe a previously undocumented form of contamination, well-to-well contamination, and show that this sort of contamination primarily occurs during DNA extraction rather than PCR, is highest with plate-based methods compared to single-tube extraction, and occurs at a higher frequency in low-biomass samples. This finding has profound importance in the field, as many current techniques to "decontaminate" a data set simply rely on an assumption that microbial reads found in blanks are contaminants from "outside," namely, the reagents or consumables.},
}
@article {pmid31237984,
year = {2019},
author = {Ji, Y and Liu, C and Yang, Z and Yang, L and He, Z and Wang, H and Yang, J and Yi, T},
title = {Testing and using complete plastomes and ribosomal DNA sequences as the next generation DNA barcodes in Panax (Araliaceae).},
journal = {Molecular ecology resources},
volume = {19},
number = {5},
pages = {1333-1345},
doi = {10.1111/1755-0998.13050},
pmid = {31237984},
issn = {1755-0998},
support = {31590820//Major Program of National Natural Science Foundation of China/ ; 31590823//Major Program of National Natural Science Foundation of China/ ; 31872673//National Natural Science Foundation of China/ ; 2017-LSF-GBOWS-02//Chinese Academy of Sciences the Large-scale Scientific Facilities/ ; U1802287//NSFC-Joint Foundation of Yunnan Province/ ; },
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; DNA, Ribosomal/*genetics ; Panax/*classification/*genetics ; Plastids/*genetics ; Sequence Analysis, DNA/methods ; },
abstract = {Complete plastid genome (plastome) sequences and nuclear ribosomal DNA (nrDNA) regions have been proposed as candidates for the next generation of DNA barcodes for plant species discrimination. However, the efficacy of this approach still lacks comprehensive evaluation. We carried out a case study in the economically important but phylogenetically and taxonomically difficult genus Panax (Araliaceae). We generated a large data set of plastomes and nrDNA sequences from multiple accessions per species. Our data improved the phylogenetic resolution and levels of species discrimination in Panax, compared to any previous studies using standard DNA barcodes. This provides new insights into the speciation, lineage diversification and biogeography of the genus. However, both plastome and nrDNA failed to completely resolve the phylogenetic relationships in the Panax bipinnatifidus species complex, and only half of the species within it were recovered as monophyletic units. The results suggest that complete plastome and ribosomal DNA sequences can substantially increase species discriminatory power in plants, but they are not powerful enough to fully resolve phylogenetic relationships and discriminate all species, particularly in evolutionarily young and complex plant groups. To gain further resolving power for closely related species, the addition of substantial numbers of nuclear markers is likely to be required.},
}
@article {pmid31237479,
year = {2019},
author = {Tschá, MK and Suzukawa, AA and Gräf, T and Piancini, LDS and da Silva, AM and Faoro, H and Riediger, IN and Medeiros, LC and Wowk, PF and Zanluca, C and Duarte Dos Santos, CN},
title = {Identification of a novel alphavirus related to the encephalitis complexes circulating in southern Brazil.},
journal = {Emerging microbes &amp; infections},
volume = {8},
number = {1},
pages = {920-933},
pmid = {31237479},
issn = {2222-1751},
mesh = {Adult ; Alphavirus/classification/genetics/*isolation &amp; purification/physiology ; Animals ; Brazil/epidemiology ; Culicidae/physiology/virology ; Encephalitis/epidemiology/*virology ; Female ; Humans ; Lymphocytes/virology ; Male ; Monocytes/virology ; Mosquito Vectors/physiology/virology ; Phylogeny ; Young Adult ; },
abstract = {In early 2017, an outbreak caused by an unknown and supposedly viral agent in the Marilena region of southern Brazil was investigated. Since the etiological agent causing the outbreak was not identified from human samples, mosquitoes from this region were collected. Three out of 121 mosquito pools collected from the region tested positive for alphavirus in molecular tests. Next generation sequencing results revealed the presence of a novel alphavirus, tentatively named here as Caainguá virus (CAAV). DNA barcoding analyses indicated that different species of Culex are hosts for CAAV. This new virus was basal to the New World encephalitic alphaviruses in a comprehensive and robust phylogenetic approach using complete genomes. Viral particles were observed in the cytosol and inside of intracellular compartments of cells in mosquito-derived cell cultures. Despite being noninfectious in vertebrate derived cell cultures, primary culturing of CAAV in human mononuclear cells suggests monocytes and lymphocytes as CAAV targets. However, the epidemiological link of CAAV on the human outbreak should be further explored.},
}
@article {pmid31235850,
year = {2019},
author = {Rossel, S and Martínez Arbizu, P},
title = {Revealing higher than expected diversity of Harpacticoida (Crustacea:Copepoda) in the North Sea using MALDI-TOF MS and molecular barcoding.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {9182},
pmid = {31235850},
issn = {2045-2322},
mesh = {Animals ; *Biodiversity ; Copepoda/*classification ; DNA Barcoding, Taxonomic ; North Sea ; *Phylogeny ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {The North Sea is one of the most extensively studied marine regions of the world. Hence, large amounts of molecular data for species identification are available in public repositories, and expectations to find numerous new species in this well-known region are rather low. However, molecular reference data for harpacticoid copepods from this area in particular but also for this group in general is scarce. By assessing COI barcodes and MALDI-TOF mass spectra for this group of small crustaceans, it was discovered that there is a huge unknown diversity in this area. In total, COI sequences for 548 specimens from 115 species of harpacticoid copepods are presented. Over 19% of these were new to science and ten MOTUs were found to be part of cryptic species complexes. MALDI-TOF mass spectra were assessed for 622 specimens from 75 species. Because results were in concordance with species delimitation by COI barcoding and also enabled recognition of possible cryptic species, the discriminative power of this technique for biodiversity assessments is highlighted. Findings imply, species diversity in this group may be largely underestimated and total species number can be expected to be much higher than previously assumed.},
}
@article {pmid31234905,
year = {2019},
author = {Hendrick, GC and Dolan, MC and McKay, T and Sikkel, PC},
title = {Host DNA integrity within blood meals of hematophagous larval gnathiid isopods (Crustacea, Isopoda, Gnathiidae).},
journal = {Parasites &amp; vectors},
volume = {12},
number = {1},
pages = {316},
pmid = {31234905},
issn = {1756-3305},
support = {OCR-1536794//National Science Foundation/ ; },
mesh = {Animals ; Blood ; DNA/*chemistry ; Feeding Behavior ; Fish Diseases/parasitology ; Fishes/*genetics/*parasitology ; Isopoda/*physiology ; Larva ; Male ; },
abstract = {BACKGROUND: Juvenile gnathiid isopods are common ectoparasites of marine fishes. Each of the three juvenile stages briefly attach to a host to obtain a blood meal but spend most of their time living in the substrate, thus making it difficult to determine patterns of host exploitation. Sequencing of host blood meals from wild-caught specimens is a promising tool to determine host identity. Although established protocols for this approach exist, certain challenges must be overcome when samples are subjected to typical field conditions that may contribute to DNA degradation. The goal of this study was to address a key methodological issue associated with molecular-based host identification from free-living, blood-engorged gnathiid isopods-the degradation of host DNA within blood meals. Here we have assessed the length of time host DNA within gnathiid blood meals can remain viable for positive host identification.<br><br>METHODS: Juvenile gnathiids were allowed to feed on fish of known species and subsets were preserved at 4-h intervals over 24&#xa0;h and then every 24&#xa0;h up to 5&#xa0;days post-feeding. Host DNA extracted from gnathiid blood meals was sequenced to validate the integrity of host DNA at each time interval. DNA was also extracted from blood meals of wild-fed gnathiids for comparison. Attempts were also made to extract host DNA from metamorphosed juveniles.<br><br>RESULTS: Using a cox1 universal fish primer set, known fish host DNA sequences were successfully identified for nearly 100% of third-stage juvenile gnathiid blood meals, digested for up to 5 days post-feeding. For second-stage juveniles, host identification was 100% successful when gnathiids were preserved within 24&#xa0;h of collection. Fish hosts were positively identified for 69% of sequences from wild-fed gnathiid isopods. Of the 31% of sequences not receiving a &#x2265;&#x2009;98 % match to a sequence in GenBank, 25 sequences were of possible invertebrate origin.<br><br>CONCLUSIONS: To our knowledge, this is the first study to examine the degradation rate of gnathiid isopod blood meals. Determining the rate at which gnathiids digest their blood meal is an important step in ensuring the successful host identification by DNA-based methods in large field studies.},
}
@article {pmid31233728,
year = {2019},
author = {Votýpka, J and Brzoňová, J and Ježek, J and Modrý, D},
title = {Horse flies (Diptera: Tabanidae) of three West African countries: A faunistic update, barcoding analysis and trypanosome occurrence.},
journal = {Acta tropica},
volume = {197},
number = {},
pages = {105069},
doi = {10.1016/j.actatropica.2019.105069},
pmid = {31233728},
issn = {1873-6254},
mesh = {Africa, Western ; Animals ; DNA Barcoding, Taxonomic ; Diptera/*classification/genetics/parasitology ; Phylogeny ; Trypanosoma/genetics/*isolation &amp; purification ; },
abstract = {Horse flies (Diptera: Tabanidae) are of medical and veterinary importance since they transmit a range of pathogens. The horse fly fauna of tropical Africa is still poorly known, and in some geographical areas has not been studied for decades. This study summarizes the results of tabanid collections performed in three West African countries where only sparse data were previously available, the Central African Republic (CAR), Gabon and Liberia. Of 1093 collected specimens, 28 morphospecies and 26 genospecies belonging to six genera were identified, including the first findings of eleven morphospecies in the countries where horse flies were collected: Philoliche (Subpangonia) gravoti Surcouf, 1908 and Tabanus ianthinus Surcouf, 1907 are new records for Liberia; Ancala fasciata f. mixta (Surcouf, 1914), Tabanus fraternus Macquart, 1846, and T. triquetrornatus Carter, 1915 for CAR; Chrysops longicornis Macquart, 1838, Haematopota albihirta Karsch, 1887, H. bowdeni Oldroyd, 1952, and H. brucei Austen, 1908 for Gabon; and Tabanus secedens f. regnaulti Surcouf, 1912 and T. thoracinus Palisot de Beauvois, 1807 for Gabon and Liberia. Species identification of all 28 morphospecies based on morphological features was further supplemented by barcoding of cytochrome oxidase I (COI). Based on the COI sequences of 115 specimens representing 74 haplotypes, a phylogenetic tree was constructed to illustrate the relationships among the tabanid species found and to demonstrate their intra- and interspecific divergences. Our study enriches the current number of barcoded tabanids with another 22 genospecies. Based on the analysis of molecular data we question the taxonomic relevance of the morphological forms Ancala fasciata f. mixta and Tabanus secedens f. regnaulti. A parasitological survey based on nested PCR of 18S rRNA revealed a high (˜25%) prevalence of Trypanosoma theileri in the studied horse flies, accompanied by two species of monoxenous trypanosomatids, Crithidia mellificae and Blastocrithidia sp.},
}
@article {pmid31233362,
year = {2019},
author = {Xiong, X and Yuan, F and Huang, M and Lu, L and Xiong, X and Wen, J},
title = {DNA Barcoding Revealed Mislabeling and Potential Health Concerns with Roasted Fish Products Sold across China.},
journal = {Journal of food protection},
volume = {82},
number = {7},
pages = {1200-1209},
doi = {10.4315/0362-028X.JFP-18-514},
pmid = {31233362},
issn = {1944-9097},
mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; *Fish Products/classification/standards/toxicity ; *Food Analysis/methods ; *Food Safety/methods ; Species Specificity ; },
abstract = {75.5% of products were identified as species outside the expected family. Six products were identified as containing multiple species from distinct families. Species from distinct families were verified in products of same brand for six groups. Identification of potentially toxic pufferfish species highlighted health concerns.},
}
@article {pmid31231598,
year = {2019},
author = {Mitchell, A and Rothbart, A and Frankham, G and Johnson, RN and Neaves, LE},
title = {Could do better! A high school market survey of fish labelling in Sydney, Australia, using DNA barcodes.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7138},
pmid = {31231598},
issn = {2167-8359},
abstract = {BACKGROUND: Processed seafood products are not readily identifiable based on physical characteristics, which leaves the industry vulnerable to high levels of product mislabelling (globally estimated at 5-30% mislabelled). This is both a food safety issue and a consumer protection issue as cheaper species could be substituted for more expensive species. DNA barcoding is proving to be a valuable tool for authentication of fish products. We worked with high school students to perform a market survey and subsequent species assessment via DNA barcoding to investigate the accuracy of fish product names used by retailers in Sydney, Australia.<br><br>METHODS: Sixty-eight fish samples, sold under 50 different common names, were purchased anonymously from two retailers in Sydney. Each product name was recorded and reconciled with the Australian Fish Names Standard (AFNS). Samples were DNA barcoded and resulting sequences were deposited in the online Barcode of Life Data system using the simplified Student Data Portal interface.<br><br>RESULTS: Forty percent of the fish names did not comply with the AFNS, however, half of these were either spelling errors or vendors supplied more information than the standard requires. The other half of the non-compliant samples were given common names not listed on the AFNS. Despite this lack of standardization, DNA barcode data confirmed the retailers' identifications for 93% of samples and 90% of species sampled.<br><br>DISCUSSION: The level of mislabelling we report for Sydney retailers (7% of samples or 10% of species) compares favorably with the global rates of 5-30%, but unfavorably with the only previous DNA barcode fish authentication study for Australia, which found no confirmed mislabelling in Hobart. Our study sampled mostly Australian produce, only two retailers and no restaurants. Results of our limited sample suggest that although many Sydney fish retailers attempt to implement the voluntary fish name standards, the standards are inadequate. As Australia imports 75% of its seafood, and in other countries restaurants generally show lower levels of compliance than retailers, broader surveys are needed before generalizing these results. DNA barcoding is a powerful yet simple method supported by accessible online analytical tools. Incorporation of fish barcoding into high school science classes provided students with valuable firsthand experience in scientific research and drew together different strands of the NSW curriculum relating to genetics and sustainability. Given the techniques, equipment, and reagents are now readily accessible, we expect to see greater uptake of DNA barcoding technology by high schools, citizen scientists and consumer groups in Australia in future. However, there remains much scope for further development of DNA barcode diagnostics (both data and analytical methods) for commercial fish species.},
}
@article {pmid31229118,
year = {2019},
author = {Shehata, HR and Naaum, AM and Chen, S and Murphy, T and Li, J and Shannon, K and Awmack, D and Locas, A and Hanner, RH},
title = {Re-visiting the occurrence of undeclared species in sausage products sold in Canada.},
journal = {Food research international (Ottawa, Ont.)},
volume = {122},
number = {},
pages = {593-598},
doi = {10.1016/j.foodres.2019.01.030},
pmid = {31229118},
issn = {1873-7145},
mesh = {Animals ; Bison ; Cattle ; Chickens ; DNA Barcoding, Taxonomic ; DNA Fragmentation ; DNA Primers/isolation &amp; purification ; *Food Analysis ; Food Contamination/*analysis ; Goats ; Horses ; Humans ; Meat Products/*analysis ; *Polymerase Chain Reaction ; Poultry ; Red Meat/analysis ; Sheep ; Swine ; Turkeys ; },
abstract = {Meat and poultry are major protein sources for humans worldwide. Undeclared ingredients in processed meat products, like sausage, continue to be identified in retail products all over the world. In collaboration with the Canadian Food Inspection Agency, a previous study of products purchased in Canada showed 20% mislabelling rate in sausage meats when tested for beef, pork, chicken, turkey and horse using DNA barcoding and digital PCR. In a follow-up to this study, an additional 100 "single species" sausage products were collected from Canadian retail markets, one year after our earlier study, to determine the prevalence of undeclared meat species in sausage. A new hierarchy of complementary molecular methods was applied in this study, including the testing of new target species (sheep and goat), in addition to beef, pork, chicken, turkey and horse. First, all samples were tested using DNA barcoding using universal primers, which revealed that 97% of the samples contained the declared species, presumably as the predominant species. Second, all samples were tested using ddPCR assays specifically targeting beef, pork, chicken, and turkey, which revealed that five beef samples, three chicken samples and two turkey samples contained undeclared species. Additionally, ddPCR revealed the presence of undeclared sheep in five samples. Overall, using complementary molecular methods, 14% of the samples contained additional undeclared species. It was encouraging to find a reduced rate of mislabelling compared to the previous study, though it remains clear that meat mislabelling is still an issue affecting Canadian consumers. The results from this study can be used to support decision-making processes for future inspection and monitoring activities in order to control species substitution or adulteration to protect consumers.},
}
@article {pmid31228251,
year = {2019},
author = {Lee, MR and Powell, JR and Oberle, B and Cornwell, WK and Lyons, M and Rigg, JL and Zanne, AE},
title = {Good neighbors aplenty: fungal endophytes rarely exhibit competitive exclusion patterns across a span of woody habitats.},
journal = {Ecology},
volume = {100},
number = {9},
pages = {e02790},
doi = {10.1002/ecy.2790},
pmid = {31228251},
issn = {1939-9170},
mesh = {Australia ; DNA, Fungal ; Ecosystem ; *Endophytes ; Fungi ; *Wood ; },
abstract = {Environmental forces and biotic interactions, both positive and negative, structure ecological communities, but their relative roles remain obscure despite strong theory. For instance, ecologically similar species, based on the principle of limiting similarity, are expected to be most competitive and show negative interactions. Specious communities that assemble along broad environmental gradients afford the most power to test theory, but the communities often are difficult to quantify. Microbes, specifically fungal endophytes of wood, are especially suited for testing community assembly theory because they are relatively easy to sample across a comprehensive range of environmental space with clear axes of variation. Moreover, endophytes mediate key forest carbon cycle processes, and although saprophytic fungi from dead wood typically compete, endophytic fungi in living wood may enhance success through cooperative symbioses. To classify interactions within endophyte communities, we analyzed fungal DNA barcode variation across 22 woody plant species growing in woodlands near Richmond, New South Wales, Australia. We estimated the response of endophytes to the measured wood environment (i.e., 11 anatomical and chemical wood traits) and each other using latent-variable models and identified recurrent communities across wood environments using model-based classification. We used this information to evaluate whether (1) co-occurrence patterns are consistent with strong competitive exclusion, and (2) a priori classifications by trophic mode and phylum distinguish taxa that are more likely to have positive vs. negative associations under the principle of limiting similarity. Fungal endophytes were diverse (mean = 140 taxa/sample), with differences in community composition structured by wood traits. Variation in wood water content and carbon concentration were associated with especially large community shifts. Surprisingly, after accounting for wood traits, fungal species were still more than three times more likely to have positive than negative co-occurrence patterns. That is, patterns consistent with strong competitive exclusion were rare, and positive interactions among fungal endophytes were more common than expected. Confirming the frequency of positive vs. negative interactions among fungal taxa requires experimental tests, and our findings establish clear paths for further study. Evidence to date intriguingly suggests that, across a wide range of wood traits, cooperation may outweigh combat for these fungi.},
}
@article {pmid31227427,
year = {2019},
author = {Crowson, AN and Harvey, M and Stout, S},
title = {Data warehouse strategies and the modern anatomic pathology laboratory: Quality management, patient safety, and pathology productivity issues and opportunities.},
journal = {Seminars in diagnostic pathology},
volume = {36},
number = {5},
pages = {294-302},
doi = {10.1053/j.semdp.2019.05.001},
pmid = {31227427},
issn = {0740-2570},
mesh = {Data Warehousing/*methods ; Humans ; Laboratories/*organization &amp; administration ; Pathology, Clinical/methods/*organization &amp; administration ; Patient Safety ; *Quality Assurance, Health Care ; *Workflow ; },
abstract = {Application of lean process management strategies to process improvement in clinical and anatomic pathology laboratories afford opportunities to enhance workflow process to lower costs and simultaneously to improve patient safety. Bar-codes are now employed in most modern anatomic pathology laboratories to track specimens from the clinicians' office or the operating room all through the continuum of service to specimen disposal. In order to enhance patient safety and workload optimization strategies, novel computer hardware and software assets are being developed to enable monitoring, analysis, and improvement of specimen workflow and diagnostic accuracy. More recently, data warehouse technologies from the retail industry have been optimized to permit high-throughput analysis of granular data in the laboratory arena. These optimize mass-data analysis in real time in the information technology space. In this review we describe the application of an in-house designed data warehouse to the anatomic pathology assets of a large regional reference laboratory.},
}
@article {pmid31226847,
year = {2019},
author = {Maestri, S and Cosentino, E and Paterno, M and Freitag, H and Garces, JM and Marcolungo, L and Alfano, M and Njunjić, I and Schilthuizen, M and Slik, F and Menegon, M and Rossato, M and Delledonne, M},
title = {A Rapid and Accurate MinION-Based Workflow for Tracking Species Biodiversity in the Field.},
journal = {Genes},
volume = {10},
number = {6},
pages = {},
pmid = {31226847},
issn = {2073-4425},
mesh = {*Biodiversity ; DNA Barcoding, Taxonomic/*instrumentation ; High-Throughput Nucleotide Sequencing/*instrumentation ; Nanopores ; Nanotechnology/*instrumentation ; Sequence Analysis, DNA/instrumentation ; Workflow ; },
abstract = {Genetic markers (DNA barcodes) are often used to support and confirm species identification. Barcode sequences can be generated in the field using portable systems based on the Oxford Nanopore Technologies (ONT) MinION sequencer. However, to achieve a broader application, current proof-of-principle workflows for on-site barcoding analysis must be standardized to ensure a reliable and robust performance under suboptimal field conditions without increasing costs. Here, we demonstrate the implementation of a new on-site workflow for DNA extraction, PCR-based barcoding, and the generation of consensus sequences. The portable laboratory features inexpensive instruments that can be carried as hand luggage and uses standard molecular biology protocols and reagents that tolerate adverse environmental conditions. Barcodes are sequenced using MinION technology and analyzed with ONTrack, an original de novo assembly pipeline that requires as few as 1000 reads per sample. ONTrack-derived consensus barcodes have a high accuracy, ranging from 99.8 to 100%, despite the presence of homopolymer runs. The ONTrack pipeline has a user-friendly interface and returns consensus sequences in minutes. The remarkable accuracy and low computational demand of the ONTrack pipeline, together with the inexpensive equipment and simple protocols, make the proposed workflow particularly suitable for tracking species under field conditions.},
}
@article {pmid31226765,
year = {2019},
author = {Maquia, I and Catarino, S and Pena, AR and Brito, DRA and Ribeiro, NS and Romeiras, MM and Ribeiro-Barros, AI},
title = {Diversification of African Tree Legumes in Miombo-Mopane Woodlands.},
journal = {Plants (Basel, Switzerland)},
volume = {8},
number = {6},
pages = {},
pmid = {31226765},
issn = {2223-7747},
support = {NA//Fundo para a Investiga&#xe7;&#xe3;o Aplicada e Multissectorial/ ; UID/GEO/04035/2013-Geobiotec, UID/AGR/04129/2013-LEAF, SFRH/BD/113951/2015, SFRH/BD/120054/2016//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; NA//Camoes, I.P./ ; },
abstract = {The southern African Miombo and Mopane ecoregions constitute a unique repository of plant diversity whose diversification and evolutionary history is still understudied. In this work, we assessed the diversity, distribution, and conservation status of Miombo and Mopane tree legumes within the Zambezian phytoregion. Data were retrieved from several plant and gene databases and phylogenetic analyses were performed based on genetic barcodes. Seventy-eight species (74 from Miombo and 23 from Mopane, 19 common to both ecoregions) have been scored. Species diversity was high within both ecoregions, but information about the actual conservation status is scarce and available only for ca. 15% of the species. Results of phylogenetic analyses were consistent with current legume classification but did not allow us to draw any conclusion regarding the evolutionary history of Miombo and Mopane tree legumes. Future studies are proposed to dissect the diversity and structure of key species in order to consolidate the network of conservation areas.},
}
@article {pmid31223230,
year = {2019},
author = {Biswas, R and Panja, AS and Bandopadhyay, R},
title = {In Silico Analyses of Burial Codon Bias Among the Species of Dipterocarpaceae Through Molecular and Phylogenetic Data.},
journal = {Evolutionary bioinformatics online},
volume = {15},
number = {},
pages = {1176934319834888},
pmid = {31223230},
issn = {1176-9343},
abstract = {INTRODUCTION: DNA barcode, a molecular marker, is used to distinguish among the closely related species, and it can be applied across a broad range of taxa to understand ecology and evolution. MaturaseK gene (matK) and rubisco bisphosphate carboxylase/oxygenase form I gene (rbcL) of the chloroplast are highly conserved in a plant system, which are used as core barcode. This present endeavor entails the comprehensive examination of the under threat plant species based on success of discrimination on DNA barcode under selection pressure.<br><br>RESULT: The family Dipterocarpaceae comprising of 15 genera is under threat due to some factors, namely, deforestation, habitat alteration, poor seed, pollen dispersal, etc. Species of this family was grouped into 6 clusters for matK and 5 clusters and 2 sub-clusters for rbcL in the phylogenetic tree by using neighbor-joining method. Cluster I to cluster VI of matK and cluster I to cluster V of rbcL genes were analyzed by various codon and substitution bias tools. Mutational pressure guided the codon bias which was favored by the avoidance of higher GC content and significant negative correlation between GC12 and GC3 (in sub-cluster I of cluster I [0.03&#x2009;<&#x2009;P], cluster I [0.00001&#x2009;<&#x2009;P], and cluster II [0.01&#x2009;<&#x2009;P] of rbcL, and cluster IV [0.013&#x2009;<&#x2009;P] of matK). After refining the results, it could be speculated that the lower null expectation values (R&#x2009;=&#x2009;0.5 or <0.5) were less divergent from the evolutionary perspective. Apart from that, the higher null expectation values (R&#x2009;=&#x2009;>0.85) also showed the same result, which possibly could be due to the negative impact of very high and low transition rate than transversion.<br><br>CONCLUSION: Through the analysis of inter-generic, inter/intra-specific variation and phylogenetic data, it was found that both selection and mutation played an important role in synonymous codon choice in these genes, but they acted inconsistently on the genes, both matK and rbcL. In vitro stable proteins of both matK and rbcL were selected through natural selection rather than mutational selection. matK gene had higher individual discrimination and barcode success compared with rbcL. These discriminatory approaches may describe the problem related to the extinction of plant species. Hence, it becomes very imperative to identify and detect the under threat plant species in advance.},
}
@article {pmid31222014,
year = {2019},
author = {Bell, CC and Fennell, KA and Chan, YC and Rambow, F and Yeung, MM and Vassiliadis, D and Lara, L and Yeh, P and Martelotto, LG and Rogiers, A and Kremer, BE and Barbash, O and Mohammad, HP and Johanson, TM and Burr, ML and Dhar, A and Karpinich, N and Tian, L and Tyler, DS and MacPherson, L and Shi, J and Pinnawala, N and Yew Fong, C and Papenfuss, AT and Grimmond, SM and Dawson, SJ and Allan, RS and Kruger, RG and Vakoc, CR and Goode, DL and Naik, SH and Gilan, O and Lam, EYN and Marine, JC and Prinjha, RK and Dawson, MA},
title = {Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {2723},
pmid = {31222014},
issn = {2041-1723},
support = {20097/CRUK_/Cancer Research UK/United Kingdom ; R01 CA174793/CA/NCI NIH HHS/United States ; P30 CA045508/CA/NCI NIH HHS/United States ; P01 CA013106/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Antineoplastic Agents/*pharmacology/therapeutic use ; Bone Marrow/pathology ; CRISPR-Cas Systems/genetics ; Cell Line, Tumor ; Drug Resistance, Neoplasm/*drug effects ; Epigenesis, Genetic/drug effects ; Female ; Gene Expression Regulation, Leukemic/*drug effects ; HEK293 Cells ; Humans ; Kaplan-Meier Estimate ; Leukemia, Myeloid, Acute/*drug therapy/genetics/mortality/pathology ; Mice ; Mice, Inbred C57BL ; Sequence Analysis, RNA ; Single-Cell Analysis ; Trans-Activators/*antagonists &amp; inhibitors/genetics/metabolism ; Transcription, Genetic/drug effects ; Treatment Outcome ; Xenograft Model Antitumor Assays ; },
abstract = {Non-genetic drug resistance is increasingly recognised in various cancers. Molecular insights into this process are lacking and it is unknown whether stable non-genetic resistance can be overcome. Using single cell RNA-sequencing of paired drug naïve and resistant AML patient samples and cellular barcoding in a unique mouse model of non-genetic resistance, here we demonstrate that transcriptional plasticity drives stable epigenetic resistance. With a CRISPR-Cas9 screen we identify regulators of enhancer function as important modulators of the resistant cell state. We show that inhibition of Lsd1 (Kdm1a) is able to overcome stable epigenetic resistance by facilitating the binding of the pioneer factor, Pu.1 and cofactor, Irf8, to nucleate new enhancers that regulate the expression of key survival genes. This enhancer switching results in the re-distribution of transcriptional co-activators, including Brd4, and provides the opportunity to disable their activity and overcome epigenetic resistance. Together these findings highlight key principles to help counteract non-genetic drug resistance.},
}
@article {pmid31221063,
year = {2019},
author = {Bigildeev, AE and Pilunov, AM and Sats, NV and Surin, VL and Shipounova, IN and Petinati, NA and Logacheva, MD and Fedotova, AV and Kasyanov, AS and Artyukhov, AS and Dashinimaev, EB and Drize, NJ},
title = {Clonal Composition of Human Multipotent Mesenchymal Stromal Cells: Application of Genetic Barcodes in Research.},
journal = {Biochemistry. Biokhimiia},
volume = {84},
number = {3},
pages = {250-262},
doi = {10.1134/S0006297919030076},
pmid = {31221063},
issn = {1608-3040},
mesh = {Cell Proliferation ; Cells, Cultured ; Clonal Evolution/*genetics ; Clone Cells/*metabolism ; *DNA Barcoding, Taxonomic ; Gene Library ; Humans ; Mesenchymal Stem Cells/*cytology/*metabolism ; },
abstract = {Clonal composition of human multipotent mesenchymal stromal cells (MMSCs) labeled with lentiviral vectors carrying genetic barcodes was studied. MMSCs were transduced with a cloned library of self-inactivating lentiviral vectors carrying 667 unique barcodes. At each cell culture passage, 120 cells were plated one cell per well in 96-well plates. The efficiency of cloning and labeling of the clonogenic cells was determined. DNA was extracted from the cell-derived colonies, and the barcodes were identified by Sanger sequencing. Also, DNA was extracted from the total MMSC population at each passage to analyze the diversity and representation of barcodes by deep sequencing using the Illumina platform. It was shown that the portion of MMSCs labeled with the lentiviral vectors remained stable in the passaged cells. Because of the high multiplicity of infection, the labeling procedure could decrease the proliferative potential of MMSCs. Identification of barcodes in individual cell clones confirmed the polyclonal character of the MMSC population. Clonal composition of MMSCs changed significantly with the passages due to the depletion of proliferative potential of most cells. Large clones were found at the first passage; at later passages, many small clones with a limited proliferative potential were detected in the population. The results of deep sequencing confirmed changes in the clonal composition of MMSCs. The polyclonal MMSC population contained only a small number of cells with a high proliferative potential, some of which could be stem cells. MMSCs with a high proliferative potential were detected more often in the earliest passages. In this regard, we would recommend to use MMSCs of early passages for regenerative medicine applications based on cell proliferation.},
}
@article {pmid31220292,
year = {2019},
author = {Đuknić, J and Jovanović, VM and Popović, N and Živić, I and Raković, M and Čerba, D and Paunović, M},
title = {Phylogeography of Simulium Subgenus Wilhelmia (Diptera: Simuliidae)-Insights From Balkan Populations.},
journal = {Journal of medical entomology},
volume = {56},
number = {4},
pages = {967-978},
pmid = {31220292},
issn = {1938-2928},
mesh = {Animals ; Balkan Peninsula ; Phylogeography ; Simuliidae/*genetics ; },
abstract = {Many morphologically similar species of the simuliid (Diptera: Simuliidae) subgenus Wilhelmia, Enderlein are difficult to distinguish. Thus, the revision of the subgenus using various morphological, cytogenetic, and genetic analyses has been attempted. Neglected until now, the Balkan Peninsula, a crossroad between Europe and Anatolia, provides insight which could resolve problematic interrelationships of the taxa within this subgenus. To uncover the status and relations within the subgenus Wilhelmia, mtDNA was extracted from 47 individuals of six morphospecies: Simulium balcanicum (Enderlein, 1924), Simulium turgaicum Rubtsov, 1940, Simulium lineatum (Meigen, 1804), Simulium pseudequinum Séguy, 1921, Simulium equinum (Linnaeus, 1758), and Simulium paraequinum Puri, 1933 from 21 sites throughout the Balkan Peninsula. Phylogenetic analysis of the Wilhelmia species using mitochondrial DNA barcoding (COI) gene showed two major branches, the lineatum branch, which includes the lineages sergenti, paraequinum, and lineatum, and the equinum branch. In the equinum branch, the mtDNA sequences formed six clades, with high genetic distances, suggesting the existence of different species. Historically, the clades of the equinum branch appeared at numerous islands, perhaps as a result of allopatric speciation. The paraequinum lineage (lineatum branch) is composed of two species. However, six clades of the lineatum lineage overlapped with intra- and interspecific genetic distances. Our results revealed that the species S. balcanicum, S. pseudequinum B, and S. equinum were omnipresent in the Balkans. The results point to not only the fair diversity of Wilhelmia species in the Balkans, but also indicate that most Wilhelmia species live in sympatry.},
}
@article {pmid31216285,
year = {2019},
author = {Meiklejohn, KA and Damaso, N and Robertson, JM},
title = {Assessment of BOLD and GenBank - Their accuracy and reliability for the identification of biological materials.},
journal = {PloS one},
volume = {14},
number = {6},
pages = {e0217084},
pmid = {31216285},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; *Databases, Nucleic Acid ; Fungi/classification/genetics ; Insecta/classification/genetics ; Plants/classification/genetics ; Reproducibility of Results ; },
abstract = {Taxonomic identification of biological materials can be achieved through DNA barcoding, where an unknown "barcode" sequence is compared to a reference database. In many disciplines, obtaining accurate taxonomic identifications can be imperative (e.g., evolutionary biology, food regulatory compliance, forensics). The Barcode of Life DataSystems (BOLD) and GenBank are the main public repositories of DNA barcode sequences. In this study, an assessment of the accuracy and reliability of sequences in these databases was performed. To achieve this, 1) curated reference materials for plants, macro-fungi and insects were obtained from national collections, 2) relevant barcode sequences (rbcL, matK, trnH-psbA, ITS and COI) from these reference samples were generated and used for searching against both databases, and 3) optimal search parameters were determined that ensure the best match to the known species in either database. While GenBank outperformed BOLD for species-level identification of insect taxa (53% and 35%, respectively), both databases performed comparably for plants and macro-fungi (~81% and ~57%, respectively). Results illustrated that using a multi-locus barcode approach increased identification success. This study outlines the utility of the BLAST search tool in GenBank and the BOLD identification engine for taxonomic identifications and identifies some precautions needed when using public sequence repositories in applied scientific disciplines.},
}
@article {pmid31212208,
year = {2019},
author = {Masuyama, N and Mori, H and Yachie, N},
title = {DNA barcodes evolve for high-resolution cell lineage tracing.},
journal = {Current opinion in chemical biology},
volume = {52},
number = {},
pages = {63-71},
doi = {10.1016/j.cbpa.2019.05.014},
pmid = {31212208},
issn = {1879-0402},
mesh = {Animals ; Biomarkers ; *Cell Lineage ; Clustered Regularly Interspaced Short Palindromic Repeats ; *DNA Barcoding, Taxonomic ; Evolution, Molecular ; Humans ; Mutation ; Single-Cell Analysis ; },
abstract = {Mammalian development involves continuous dynamic processes in which cells propagate, differentiate, orchestrate, and decease to produce high-order functions. Although accurate cell lineage information can provide a strong foundation to understand such complex processes, the cell lineages involved in development of the whole mammalian body remain largely unclear, except for in early embryogenesis, which is observable under a microscope. With CRISPR genome editing, the concept of 'evolving DNA barcodes' has rapidly emerged for large-scale, high-resolution cell lineage tracing, where cell-embedded DNA barcodes continuously accumulate random mutations that are inherited from mother to daughter cells. Similar to evolutionary tree reconstruction using species' DNA sequences, cell lineages can be reconstructed using shared mutation patterns in the DNA barcodes identified using massively parallel sequencing. The dramatic developments of single-cell and imaging technologies have enabled analyses of the molecular and spatial architecture of heterogeneous cells. The evolving DNA barcodes can also consolidate this information on a reconstructed cell lineage tree and accelerate our understanding of multicellular organisms.},
}
@article {pmid31210744,
year = {2019},
author = {Liao, S and Wang, Z and Che, Y},
title = {A new genus and a new species in the subfamily Polyzosteriinae (Blattodea, Blattidae) from China.},
journal = {ZooKeys},
volume = {852},
number = {},
pages = {85-100},
pmid = {31210744},
issn = {1313-2989},
abstract = {Laevifaciesquadrialata gen. et sp. nov. is described from Hainan Province, China based on morphological data. COI data (DNA barcodes) is utilized to confirm the sexual dimorphism occurring in Laevifaciesquadrialata gen. et sp. nov. Melanozosterianitida Brunner von Wattenwyl, 1865, is reported from Guangxi Province, China. A key to the Chinese Polyzosteriinae is provided.},
}
@article {pmid31209384,
year = {2019},
author = {McGinnis, CS and Patterson, DM and Winkler, J and Conrad, DN and Hein, MY and Srivastava, V and Hu, JL and Murrow, LM and Weissman, JS and Werb, Z and Chow, ED and Gartner, ZJ},
title = {MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices.},
journal = {Nature methods},
volume = {16},
number = {7},
pages = {619-626},
pmid = {31209384},
issn = {1548-7105},
support = {T32 GM007810/GM/NIGMS NIH HHS/United States ; UL1 TR001872/TR/NCATS NIH HHS/United States ; DP2 HD080351/HD/NICHD NIH HHS/United States ; F32 GM128366/GM/NIGMS NIH HHS/United States ; U01 CA199315/CA/NCI NIH HHS/United States ; S10 OD021822/OD/NIH HHS/United States ; },
mesh = {Animals ; Base Sequence ; HEK293 Cells ; High-Throughput Nucleotide Sequencing ; Humans ; Lipids/*chemistry ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis/*methods ; },
abstract = {Sample multiplexing facilitates scRNA-seq by reducing costs and identifying artifacts such as cell doublets. However, universal and scalable sample barcoding strategies have not been described. We therefore developed MULTI-seq: multiplexing using lipid-tagged indices for single-cell and single-nucleus RNA sequencing. MULTI-seq reagents can barcode any cell type or nucleus from any species with an accessible plasma membrane. The method involves minimal sample processing, thereby preserving cell viability and endogenous gene expression patterns. When cells are classified into sample groups using MULTI-seq barcode abundances, data quality is improved through doublet identification and recovery of cells with low RNA content that would otherwise be discarded by standard quality-control workflows. We use MULTI-seq to track the dynamics of T-cell activation, perform a 96-plex perturbation experiment with primary human mammary epithelial cells and multiplex cryopreserved tumors and metastatic sites isolated from a patient-derived xenograft mouse model of triple-negative breast cancer.},
}
@article {pmid31208245,
year = {2019},
author = {da Cruz, MOR and Weksler, M and Bonvicino, CR and Bezerra, AMR and Prosdocimi, F and Furtado, C and Geise, L and Catzeflis, F and de Thoisy, B and de Oliveira, LFB and Silva, C and de Oliveira, JA},
title = {DNA barcoding of the rodent genus Oligoryzomys (Cricetidae: Sigmodontinae): mitogenomic-anchored database and identification of nuclear mitochondrial translocations (Numts).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {5},
pages = {702-712},
doi = {10.1080/24701394.2019.1622692},
pmid = {31208245},
issn = {2470-1408},
mesh = {Animals ; Arvicolinae/*genetics ; Cell Nucleus/*genetics ; *DNA Barcoding, Taxonomic ; *Databases, Genetic ; Genome, Mitochondrial/*genetics ; Mitochondrial Dynamics/*genetics ; Species Specificity ; },
abstract = {DNA barcoding has become a standard method for species identification in taxonomically complex groups. An important step of the barcoding process is the construction of a library of voucher-based material that was properly identified by independent methods, free of inaccurate identification, and paralogs. We provide here a cytochrome oxidase I (mt-Co1) DNA barcode database for species of the genus Oligoryzomys, based on type material and karyotyped specimens, and anchored on the mitochondrial genome of one species of Oligoryzomys, O. stramineus. To evaluate the taxonomic determination of new COI sequences, we assessed species intra/interspecific genetic distances (barcode gap), performed the General Mixed Yule Coalescent method (GMYC) for lineages' delimitation, and identified diagnostic nucleotides for each species of Oligoryzomys. Phylogenetic analyses of Oligoryzomys were performed on 2 datasets including 14 of the 23 recognized species of this genus: a mt-Co1 only matrix, and a concatenated matrix including mt-Co1, cytochrome b (mt-Cytb), and intron 7 of the nuclear fibrinogen beta chain gene (i7Fgb). We recovered nuclear-mitochondrial translocated (Numts) pseudogenes on our samples and identified several published sequences that are cases of Numts. We analyzed the rate of non-synonymous and synonymous substitution, which were higher in Numts in comparison to mtDNA sequences. GMYC delimitations and DNA barcode gap results highlight the need for further work that integrate molecular, karyotypic, and morphological analyses, as well as additional sampling, to tackle persistent problems in the taxonomy of Oligoryzomys.},
}
@article {pmid31205446,
year = {2019},
author = {Gueidan, C and Elix, JA and McCarthy, PM and Roux, C and Mallen-Cooper, M and Kantvilas, G},
title = {PacBio amplicon sequencing for metabarcoding of mixed DNA samples from lichen herbarium specimens.},
journal = {MycoKeys},
volume = {53},
number = {},
pages = {73-91},
pmid = {31205446},
issn = {1314-4049},
abstract = {The detection and identification of species of fungi in the environment using molecular methods heavily depends on reliable reference sequence databases. However, these databases are largely incomplete in terms of taxon coverage, and a significant effort is required from herbaria and living fungal collections for the mass-barcoding of well-identified and well-curated fungal specimens or strains. Here, a PacBio amplicon sequencing approach is applied to recent lichen herbarium specimens for the sequencing of the fungal ITS barcode, allowing a higher throughput sample processing than Sanger sequencing, which often required the use of cloning. Out of 96 multiplexed samples, a full-length ITS sequence of the target lichenised fungal species was recovered for 85 specimens. In addition, sequences obtained for co-amplified fungi gave an interesting insight into the diversity of endolichenic fungi. Challenges encountered at both the laboratory and bioinformatic stages are discussed, and cost and quality are compared with Sanger sequencing. With increasing data output and reducing sequencing cost, PacBio amplicon sequencing is seen as a promising approach for the generation of reference sequences for lichenised fungi as well as the characterisation of lichen-associated fungal communities.},
}
@article {pmid31205309,
year = {2019},
author = {Mueller, A and Fischer, K and Suluku, R and Hoenen, T},
title = {Sequencing of mRNA from Whole Blood using Nanopore Sequencing.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {148},
pages = {},
doi = {10.3791/59377},
pmid = {31205309},
issn = {1940-087X},
mesh = {Animals ; Ebolavirus/genetics ; Gene Library ; High-Throughput Nucleotide Sequencing/methods ; *Nanopore Sequencing ; Nanopores ; RNA, Messenger/*blood/chemistry ; Sequence Analysis, RNA/*methods ; },
abstract = {Sequencing in remote locations and resource-poor settings presents unique challenges. Nanopore sequencing can be successfully used under such conditions, and was deployed to West Africa during the recent Ebola virus epidemic, highlighting this possibility. In addition to its practical advantages (low cost, ease of equipment transport and use), this technology also provides fundamental advantages over second-generation sequencing approaches, particularly the very long read length, ability to directly sequence RNA, and real-time availability of data. Raw read accuracy is lower than with other sequencing platforms, which represents the main limitation of this technology; however, this can be partially mitigated by the high read depth generated. Here, we present a field-compatible protocol for sequencing of the mRNAs encoding for Niemann-Pick C1, which is the cellular receptor for ebolaviruses. This protocol encompasses extraction of RNA from animal blood samples, followed by RT-PCR for target enrichment, barcoding, library preparation, and the sequencing run itself, and can be easily adapted for use with other DNA or RNA targets.},
}
@article {pmid31201544,
year = {2020},
author = {Zecca, G and Grassi, F and Tabidze, V and Pipia, I and Kotorashvili, A and Kotaria, N and Beridze, T},
title = {Dates and rates in grape's plastomes: evolution in slow motion.},
journal = {Current genetics},
volume = {66},
number = {1},
pages = {123-140},
pmid = {31201544},
issn = {1432-0983},
mesh = {Biological Evolution ; Computational Biology/methods ; Evolution, Molecular ; Genomic Library ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Plastids/*genetics ; Vitis/classification/*physiology ; },
abstract = {The family Vitaceae includes the domesticated grapevine (Vitis vinifera), one of the most economically important crops in the world. Despite the importance of Vitaceae, there is still considerable controversy surrounding their phylogenetic relationships and evolutionary timescales. Moreover, variation in rates of molecular evolution among Vitaceae remains mostly unexplored. The present research aims to fill these knowledge gaps through the analysis of plastome sequences. Thirteen newly sequenced grape plastomes are presented and their phylogenetic relationships examined. Divergence times and absolute substitution rates are inferred under different molecular clocks by the analysis of 95 non-coding plastid regions and 43 representative accessions of the major lineages of Vitaceae. Furthermore, the phylogenetic informativeness of non-coding plastid regions is investigated. We find strong evidence in favor of the random local clock model and rate heterogeneity within Vitaceae. Substitution rates decelerate in Ampelocissus, Ampelopsis, Nekemias, Parthenocissus, Rhoicissus, and Vitis, with genus Vitis showing the lowest values up to a minimum of ~ 4.65 × 10[-11] s/s/y. We suggest that liana-like species of Vitaceae evolve slower than erect growth habit plants and we invoke the "rate of mitosis hypothesis" to explain the observed pattern of the substitution rates. We identify a reduced set of 20 non-coding regions able to accurately reconstruct the phylogeny of Vitaceae and we provide a detailed description of all 152 non-coding regions identified in the plastomes of subg. Vitis. These polymorphic regions will find their applications in phylogenetics, phylogeography, and population genetics as well in grapes identification through DNA barcoding techniques.},
}
@article {pmid31200276,
year = {2019},
author = {Duncombe, TA and Dittrich, PS},
title = {Droplet barcoding: tracking mobile micro-reactors for high-throughput biology.},
journal = {Current opinion in biotechnology},
volume = {60},
number = {},
pages = {205-212},
doi = {10.1016/j.copbio.2019.05.004},
pmid = {31200276},
issn = {1879-0429},
mesh = {*Biological Assay ; Microfluidic Analytical Techniques ; Microfluidics ; },
abstract = {Droplet microfluidics has become a powerful analytical platform in biological research for conducting high-throughput screening in millions of discrete micro-reactors per hour. While the method facilitates faster and cheaper testing than conventional microtiter plates, the mobile nature of droplets makes micro-reaction tracking a notable challenge. To address this, researchers are developing a variety of tracking methods, ranging from organizing droplets into an index or labeling droplets with a barcode. The optimal tracking approach depends on the criteria for each specific application. Considerations include the requisite assay readout, throughput, droplet library size, reagent tracking and more. In this review, we summarize different strategies for droplet micro-reaction tracking and comment on promising future approaches in droplet barcoding. Topics range from indexing droplets by sequence or in an array, labeling droplets with barcodes, and reagent barcoding to track the input conditions in parametric screens.},
}
@article {pmid31199572,
year = {2020},
author = {Bernardo, A and St Amand, P and Le, HQ and Su, Z and Bai, G},
title = {Multiplex restriction amplicon sequencing: a novel next-generation sequencing-based marker platform for high-throughput genotyping.},
journal = {Plant biotechnology journal},
volume = {18},
number = {1},
pages = {254-265},
pmid = {31199572},
issn = {1467-7652},
mesh = {Chromosome Mapping ; Genetic Linkage ; *Genotyping Techniques ; *High-Throughput Nucleotide Sequencing ; Polymorphism, Single Nucleotide ; *Quantitative Trait Loci ; Triticum/*genetics ; },
abstract = {To enable rapid selection of traits in marker-assisted breeding, markers must be technically simple, low-cost, high-throughput and randomly distributed in a genome. We developed such a technology, designated as Multiplex Restriction Amplicon Sequencing (MRASeq), which reduces genome complexity by polymerase chain reaction (PCR) amplification of amplicons flanked by restriction sites. The first PCR primers contain restriction site sequences at 3'-ends, preceded by 6-10 bases of specific or degenerate nucleotide sequences and then by a unique M13-tail sequence which serves as a binding site for a second PCR that adds sequencing primers and barcodes to allow sample multiplexing for sequencing. The sequences of restriction sites and adjacent nucleotides can be altered to suit different species. Physical mapping of MRASeq SNPs from a biparental population of allohexaploid wheat (Triticum aestivum L.) showed a random distribution of SNPs across the genome. MRASeq generated thousands of SNPs from a wheat biparental population and natural populations of wheat and barley (Hordeum vulgare L.). This novel, next-generation sequencing-based genotyping platform can be used for linkage mapping to screen quantitative trait loci (QTL), background selection in breeding and many other genetics and breeding applications of various species.},
}
@article {pmid31198987,
year = {2020},
author = {Kasongo Ilunga, M and Abwe, E and Decru, E and Chocha Manda, A and Vreven, E},
title = {Description of a new small-sized Synodontis species (Siluriformes: Mochokidae) that is important for local subsistence fisheries in the middle Lufira (upper Congo River, DR Congo).},
journal = {Journal of fish biology},
volume = {96},
number = {5},
pages = {1142-1159},
doi = {10.1111/jfb.14076},
pmid = {31198987},
issn = {1095-8649},
support = {//DEA scholarship/ ; //Mbisa Congo project (2013-2018)/ ; //RMCA and the Belgian Development Cooperation/ ; (NN/3000769)//PRODEPAAK/ ; //CTB/ ; //BTC project (2008-2013)/ ; //Katanga Expedition 2012/ ; },
mesh = {Animals ; Catfishes/*anatomy &amp; histology/*classification/genetics ; Congo ; DNA, Mitochondrial/genetics ; *Fisheries ; Rivers ; Species Specificity ; },
abstract = {Synodontis denticulatus sp. nov. is an endemic from the middle Lufira Basin and its associated tributaries and lakes. The species shows close morphological resemblance to Synodontis greshoffi and Synodontis unicolor, which are widespread Congo Basin and Bangweulu-Mweru endemic species, respectively. However, it differs from both S. greshoffi and S. unicolor by its non-villous skin (v. villous skin), strong and numerous serrations on the posterior margin of the dorsal spine (v. weak and fewer serrations), weak and few serrations on the posterior margin of the pectoral spine (v. strong and numerous serrations), relatively short maxillary barbels (v. long) and its small maximum standard length (89.1 mm LS v. 148.0 and 190.7 mm LS respectively). A DNA barcoding study (coI, mtDNA) revealed that S. denticulatus forms a distinct genetic clade with a genetic distance of 2.18% with S. greshoffi and 0.84% with S. unicolor. Synodontis denticulatus is caught regularly and abundantly as a by-catch in the gillnet fisheries in the middle Lufira lakes. Owing to its small overall size and large bony head, the species has usually no real commercial value but is an important food fish for the fishermen's families.},
}
@article {pmid31198623,
year = {2019},
author = {Ginigini, J and Lecellier, GJ and Nicolas, M and Nour, M and Hnawia, E and Lebouvier, N and Herbette, G and Lockhart, P and Raharivelomanana, P},
title = {Chemodiversity of Calophyllum inophyllum L. oil bioactive components related to their specific geographical distribution in the South Pacific region.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6896},
pmid = {31198623},
issn = {2167-8359},
abstract = {BACKGROUND: Different parts of the tree Calophyllum inophyllum L. (nuts, leaves, roots, bark, fruits, nut oil and resin) are used as traditional medicines and cosmetics in most of the Pacific Islands. The oil efficiency as a natural cure and in traditional cosmetics has been largely described throughout the South Pacific, which led us to investigate C. inophyllum's chemical and genetic diversity. A correlative study of the nut resin and leaf DNA from three distinct archipelagos in the South Pacific was carried out in order to identify diversity patterns in C. inophyllum across the South Pacific.<br><br>METHODS: Calophyllum inophyllum plants were sampled from French Polynesia, New Caledonia and Fiji. We extracted tamanu oil (nut oil) resin for chemo-diversity studies and sampled leaf tissues for genetic studies. We applied an analysis method designed for small quantities (at a microscale level), and used High Performance Liquid Chromatography (HPLC) to establish the chemo-diversity of tamanu oil resin. In-house standards were co-eluted for qualitative determination. Genetic diversity was assessed using chloroplast barcoding markers (the Acetyl-CoA carboxylase (accD) gene and the psaA-ycf3 intergenic spacer region).<br><br>RESULTS: Our HPLC analysis revealed 11 previously known tamanu oil constituents, with variability among plant samples. We also isolated and characterized two new neoflavonoids from tamanu oil resin namely, tamanolide E1 and E2 which are diastereoisomers. Although genetic analysis revealed low genetic variation, our multivariate analysis (PCA) of the tamanu oil resin chemical profiles revealed differentiation among geographic regions.<br><br>CONCLUSION: We showed here that chromatographic analysis using formalized in-house standards of oil resin compounds for co-elution studies against oil resin samples could identify patterns of variation among samples of C. inophyllum, and discriminate samples from different geographical origins.},
}
@article {pmid31197716,
year = {2019},
author = {Yang, Y and Chandrashekar, R and Ricke, SC and Kwon, YM},
title = {Construction of DNA Barcode-Tagged Salmonella Strains.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2016},
number = {},
pages = {141-150},
doi = {10.1007/978-1-4939-9570-7_13},
pmid = {31197716},
issn = {1940-6029},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Polymerase Chain Reaction/methods ; Salmonella/classification/*genetics ; Salmonella Infections/*microbiology ; },
abstract = {This chapter provides a detailed protocol for construction of DNA barcode-tagged isogenic strains of Salmonella. The protocol is illustrated with S. Enteritidis in this chapter. However, this protocol should be widely applicable to other Salmonella serotypes. A series of the DNA barcode-tagged strains thus constructed can be used in combination with next generation sequencing or quantitative PCR to study the population dynamics of the bacterial pathogen during infection within the host or transmission within a population of the host in a quantitative manner.},
}
@article {pmid31197480,
year = {2019},
author = {Rumeu, B and Álvarez-Villanueva, M and Arroyo, JM and González-Varo, JP},
title = {Interspecific competition for frugivores: population-level seed dispersal in contrasting fruiting communities.},
journal = {Oecologia},
volume = {190},
number = {3},
pages = {605-617},
pmid = {31197480},
issn = {1432-1939},
mesh = {Animals ; Birds ; Feeding Behavior ; Fruit ; Herbivory ; *Seed Dispersal ; },
abstract = {Indirect interactions among plant species mediated by frugivorous animals can be central to population and community dynamics, since the successful seed dispersal of species may depend on facilitative or competitive interactions with heterospecific plants. Yet, empirical evidence on these interactions is very scarce and mostly available at small spatial scales, within populations. Because lipid-rich fruits are known to be preferred by migratory birds, here we test our prediction of competitive inferiority of a carbohydrate-rich fruited species (the hawthorn Crataegus monogyna) compared to lipid-rich co-fruiting species in a Mediterranean region where the bulk of seed dispersal relies on migratory birds. We assessed avian seed dispersal in both relative (fruit removal rate) and absolute terms (seed dispersal magnitude) in seven hawthorn populations distributed across an altitudinal gradient encompassing three contrasting fruiting contexts: hawthorn is scarce in the lowlands, common in the midlands, and the dominant fruit species in the highlands. We found evidence of seed dispersal reduction due to interspecific competition in the lowland populations, where lipid-rich fruits dominate. Besides, DNA barcoding analysis of bird-dispersed seeds revealed that only a small subset of the local frugivore assemblages consumed hawthorn fruits in the lowland communities. Instead, the consumers of hawthorn fruits resembled the local frugivore assemblages where hawthorn fruits were more dominant and frugivore choices more limited. Our study suggests mechanisms by which the rarity or dominance of plant species might be jointly influenced by environmental constraints (here, precipitation along the altitudinal gradient) and frugivore-mediated indirect interactions among plants hindering or facilitating seed dispersal.},
}
@article {pmid31196521,
year = {2019},
author = {Sundaresan, N and Sahu, AK and Jagan, EG and Pandi, M},
title = {Evaluation of ITS2 molecular morphometrics effectiveness in species delimitation of Ascomycota - A pilot study.},
journal = {Fungal biology},
volume = {123},
number = {7},
pages = {517-527},
doi = {10.1016/j.funbio.2019.05.002},
pmid = {31196521},
issn = {1878-6146},
mesh = {Ascomycota/*classification/*genetics ; Base Sequence ; DNA, Fungal/*chemistry/genetics ; DNA, Ribosomal Spacer/*chemistry/genetics ; Evolution, Molecular ; Genetic Variation ; Nucleic Acid Conformation ; *Phylogeny ; Pilot Projects ; Species Specificity ; },
abstract = {Exploring the secondary structure information of nuclear ribosomal internal transcribed spacer 2 (ITS2) has been a promising approach in species delimitation. However, Compensatory base changes (CBC) concept employed in this approach turns futile when CBC is absent. This prompted us to investigate the utility of insertion/deletion (INDELs) and substitutions in fungal delineation at species level. Upon this rationale, 116 strains representing 97 species, belonging to 6 genera (Colletotrichum, Boeremia, Leptosphaeria, Peyronellaea, Plenodomus and Stagonosporopsis) of Ascomycota were retrieved from Q-bank for molecular morphometric analysis. CBC, INDELs and substitutions between the species of their respective genus were recorded. Most species combinations lacked CBC. Among the substitution events, transitions were predominant. INDELs were less frequent than the substitutions. These evolutionary events were mapped upon the helices to discern species specific variation sites. In 68 species unique variation sites were recognised. The remaining 29 species shared absolute similarity with distinctly named species. The variation sites catalogued in them overlapped with other distinct species and resulted in the blurring of species boundaries. Species specific variation sites recognized in this study are the preliminary results and they could be discerned with absolute confidence when larger datasets encompassing all described species of genera were investigated. They could be of potential use in barcoding fungi at species level. This study also concludes that the ITS2 molecular morphometric analysis is an efficient third dimensional study of the fungal species delimitation. This may help to avoid the false positives in species delimitations and to alleviate the challenges in molecular characterization.},
}
@article {pmid31192977,
year = {2019},
author = {Smith, S and Govender, K and Moodley, P and La Russa, P and Kuhn, L and Archary, M},
title = {Impact of Shifts to Birth Testing on Early Infant Diagnosis Program Outcomes in KwaZulu-Natal, South Africa.},
journal = {The Pediatric infectious disease journal},
volume = {38},
number = {7},
pages = {e138-e142},
pmid = {31192977},
issn = {1532-0987},
support = {U01 HD080441/HD/NICHD NIH HHS/United States ; },
mesh = {Anti-Retroviral Agents/*therapeutic use ; Diagnostic Tests, Routine/*methods ; *Early Diagnosis ; Female ; HIV Infections/*diagnosis/*drug therapy ; Humans ; Infant ; Infant, Newborn ; Male ; Molecular Diagnostic Techniques/methods ; South Africa ; Treatment Outcome ; },
abstract = {BACKGROUND: South African early infant diagnosis guidelines shifted to recommending an initial HIV nucleic acid-based test (NAT) test at birth in 2015. Prior to this, initial NAT was recommended at 6 weeks of age. Here we examine parameters of early infant diagnosis performance in KwaZulu-Natal before and after this change.<br><br>METHODS: Data on all HIV diagnostic NAT conducted for the province between January 2013 and April 2016 were assembled and analyzed. Laboratory barcodes allowed identification of repeat tests on the same child. We evaluated coverage, positivity rates, age at testing and frequency of repeat tests across birth cohorts.<br><br>RESULTS: In birth cohorts 2013 and 2014, 62.1% and 61.8%, respectively, of tests <16 weeks were done in children who were 6-8 weeks of age. In birth cohort 2015, 41.3% of tests <16 weeks were done earlier at <2 weeks of age. The percentage of children with a positive result who had at least 1 follow-up test increased from 11.5% and 13.1% in birth cohorts 2013 and 2014, respectively, to 24.8% in 2015. The percentage of infants with an initial nonpositive result who received at least 1 follow-up test did not appreciably change from 15.0% and 14.4% in 2013 and 2014, respectively, to 14.7% in 2015.<br><br>CONCLUSIONS: Birth testing allows for earlier identification of HIV-infected infants who need urgent antiretroviral treatment initiation. Although follow-up testing rates may be underestimated in this data source, repeat testing rates remained low. More effort is needed to ensure infants tested at birth continue to be engaged in care and undergo follow-up testing.},
}
@article {pmid31190289,
year = {2019},
author = {Fang, T and Liao, S and Chen, X and Zhao, Y and Zhu, Q and Cao, Y and Wang, Q and Zhang, S and Gao, Z and Yang, Y and Wang, Y and Zhang, J},
title = {Forensic drowning site inference employing mixed pyrosequencing profile of DNA barcode gene (rbcL).},
journal = {International journal of legal medicine},
volume = {133},
number = {5},
pages = {1351-1360},
pmid = {31190289},
issn = {1437-1596},
support = {81571861//National Natural Science Foundation of China/ ; 81630054//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Diatoms/*classification ; Drowning/*pathology ; Forensic Genetics ; Forensic Pathology ; High-Throughput Nucleotide Sequencing/*methods ; Models, Animal ; Polymerase Chain Reaction ; Rabbits ; Ribulose-Bisphosphate Carboxylase/*genetics ; Sensitivity and Specificity ; },
abstract = {The development of DNA barcoding method has given rise to a promising way of studying genetic taxonomy. Our previous study showed that pyrosequencing profile of 18S rDNA V7 hypervariable region can be used for identifying water sources without resolving the exact components of diatom colonies in water samples. In this continued study, we aimed to improve the established analysis method and to provide scientific evidence for forensic practices. A drowning animal model was set up by injecting mimic drowning fluid into the respiratory tract of the rabbit. In order to minimize the interference of animal DNA, the hypervariable region of chloroplast ribulose-1,5-bisphosphate carboxylase large unit gene (rbcL) was used as the pyrosequencing target region for the consistency analysis of plankton populations in tissues and water samples. After decoding the pyrosequencing profile of the targeted rbcL gene with the AdvISER-M-PYRO algorithm, the plankton colony that was inhaled into drowning animal lung tissue could be successfully traced back to the source of drowning fluid. Our data suggest that this method could be a reliable tool assisting forensic drowning site inference.},
}
@article {pmid31189587,
year = {2019},
author = {Su, H and Packeu, A and Ahmed, SA and Al-Hatmi, AMS and Blechert, O and İlkit, M and Hagen, F and Gräser, Y and Liu, W and Deng, S and Hendrickx, M and Xu, J and Zhu, M and de Hoog, S},
title = {Species Distinction in the Trichophyton rubrum Complex.},
journal = {Journal of clinical microbiology},
volume = {57},
number = {9},
pages = {},
pmid = {31189587},
issn = {1098-660X},
mesh = {Amplified Fragment Length Polymorphism Analysis ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Humans ; Microbiological Techniques ; Microscopy ; Phylogeny ; Sequence Analysis, DNA ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Tinea/microbiology ; Trichophyton/*classification/genetics/isolation &amp; purification/physiology ; },
abstract = {The Trichophyton rubrum species complex comprises commonly encountered dermatophytic fungi with a worldwide distribution. The members of the complex usually have distinct phenotypes in culture and cause different clinical symptoms, despite high genome similarity. In order to better delimit the species within the complex, molecular, phenotypic, and physiological characteristics were combined to reestablish a natural species concept. Three groups, T. rubrum, T. soudanense, and T. violaceum, could be distinguished based on the sequence of the internal transcribed spacer (ITS) ribosomal DNA barcode gene. On average, strains within each group were similar by colony appearance, microscopy, and physiology, but strains between groups showed significant differences. Trichophyton rubrum strains had higher keratinase activity, whereas T. violaceum strains tended to be more lipophilic; however, none of the phenotypic features were diagnostic. The results of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and amplified fragment length polymorphism (AFLP) were partially consistent with the ITS data but failed to distinguish the species unambiguously. Despite their close similarity, T. violaceum, T. soudanense, and T. rubrum can be regarded as independent species with distinct geographical distributions and clinical predilections. Trichophyton soudanense is pheno- and genotypically intermediate between T. rubrum and T. violaceum For routine diagnostics, ITS sequencing is recommended.},
}
@article {pmid31188041,
year = {2019},
author = {Gomes, G and Correa, R and Veneza, I and da Silva, R and da Silva, D and Miranda, J and Sampaio, I},
title = {Forensic analysis reveals fraud in fillets from the "Gurijuba" Sciades parkeri (Ariidae - Siluriformes): a vulnerable fish in Brazilian Coastal Amazon.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {5},
pages = {721-729},
doi = {10.1080/24701394.2019.1622694},
pmid = {31188041},
issn = {2470-1408},
mesh = {Animals ; Brazil ; Catfishes/*classification/*genetics ; Cytochromes b/genetics/metabolism ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics/metabolism ; Genome, Mitochondrial/genetics ; Seafood/*analysis ; Species Specificity ; },
abstract = {The utilization of molecular tools for the certification of fishery products has been increasing over the last years. In general, economically important species are replaced by less valuable species, characterizing a commercial fraud. We evaluated the authenticity of 107 frozen fillets tagged as Gurijuba (Sciades parkeri) and Uritinga (Sciades proops) from local markets in northern amazon coast by sequencing two mitochondrial genes: Cytochrome oxidase subunit I and cytochrome b (Cyt b). About 16% of fillets putatively related to S. parkeri were replaced by S. proops. The Gurijuba faces high fishing pressure, being currently listed by the International Union for Conservation of Nature as vulnerable. Forensic analysis with DNA markers, proved to be highly efficient in the discrimination of the processed seafood products, providing unequivocal identification of species, revealing commercial fraud in the fillets of the Gurijuba, and revealing the utility of Cytb sequences as barcode in fishes.},
}
@article {pmid31185674,
year = {2019},
author = {Gosik, R and Mazur, MA and Sawka-Gądek, N},
title = {First Descriptions of Larva and Pupa of Bagous claudicans Boheman, 1845 (Curculionidae, Bagoinae) and Systematic Position of the Species Based on Molecular and Morphological Data.},
journal = {Insects},
volume = {10},
number = {6},
pages = {},
pmid = {31185674},
issn = {2075-4450},
abstract = {In this paper, the mature larva and pupa of Bagous claudicans are described and illustrated for the first time. Measurements of younger larval instars are also given. The biology of the species is discussed in association with larval morphology and feeding habits. Overall larval and pupal morphological characters of the genus Bagous are presented. Confirmation of the larva identification as Bagous claudicans species was conducted by cytochrome oxidase I (COI) sequencing. DNA barcoding was useful for specimen identification of larval stages. The systematic position of the species within the Bagous collignensis-group, based on morphological and molecular results, is also discussed.},
}
@article {pmid31185298,
year = {2019},
author = {Jirapatrasilp, P and Backeljau, T and Prasankok, P and Chanabun, R and Panha, S},
title = {Untangling a mess of worms: Species delimitations reveal morphological crypsis and variability in Southeast Asian semi-aquatic earthworms (Almidae, Glyphidrilus).},
journal = {Molecular phylogenetics and evolution},
volume = {139},
number = {},
pages = {106531},
doi = {10.1016/j.ympev.2019.106531},
pmid = {31185298},
issn = {1095-9513},
mesh = {Animals ; Aquatic Organisms/*classification/genetics ; Asia, Southeastern ; Base Sequence ; Bayes Theorem ; DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/chemistry/genetics ; Nucleic Acid Conformation ; Oligochaeta/*anatomy &amp; histology/*classification/genetics ; Phylogeny ; Polymorphism, Genetic ; Species Specificity ; },
abstract = {Semi-aquatic freshwater earthworms in the genus Glyphidrilus from Southeast Asia are characterized by both an extreme morphological crypsis among divergent phylogenetic lineages and a high morphological variability within the same phylogenetic lineages. The present study provides a new taxonomic framework for this problematic genus in SE Asia by integrating DNA sequence and morphological data. When single-locus and multilocus multispecies coalescent-based (MSC) species delimitation methods were applied to DNA sequence data, they usually yielded highly incongruent results compared to morphology-based species identifications. This suggested the presence of several cryptic species and high levels of intraspecific morphological variation. Applying reciprocal monophyly to the cytochrome c oxidase subunit 1 (COI) gene tree allowed us to propose the existence of 33 monophyletic species. Yet, often substantially more molecular operational taxonomic units (MOTUs) were obtained when species delimitation was based on COI and 16S rRNA sequences. In contrast, the ITS1 and ITS2 sequences suggested fewer MOTUs and did not recover most of the monophyletic species from the Mekong basin. However, several of these latter taxa were better supported when MSC species delimitation methods were applied to the combined mtDNA and ITS datasets. The ITS2 secondary structure retrieved one unnamed Mekong basin species that was not uncovered by the other methods when applied to ITS2 sequences. In conclusion, based on an integrative taxonomic workflow, 26 Glyphidrilus candidate species were retained and two remained to be confirmed. As such, this study provides evidence to suggest nine species new to science and to synonymize 12 nominal morphospecies. It also illustrates that the uncritical use of COI as a universal DNA barcode may overestimate species diversity because COI may be unable to distinguish between divergent conspecific lineages and different candidate species.},
}
@article {pmid31184885,
year = {2019},
author = {Gerry, CJ and Wawer, MJ and Clemons, PA and Schreiber, SL},
title = {DNA Barcoding a Complete Matrix of Stereoisomeric Small Molecules.},
journal = {Journal of the American Chemical Society},
volume = {141},
number = {26},
pages = {10225-10235},
pmid = {31184885},
issn = {1520-5126},
support = {R01 GM038627/GM/NIGMS NIH HHS/United States ; R35 GM127045/GM/NIGMS NIH HHS/United States ; },
mesh = {Carbonic Anhydrase IX/antagonists &amp; inhibitors/metabolism ; DNA/*chemistry ; *DNA Barcoding, Taxonomic ; Enzyme Inhibitors/chemical synthesis/*chemistry/pharmacology ; Horseradish Peroxidase/antagonists &amp; inhibitors/metabolism ; Molecular Structure ; Small Molecule Libraries/chemical synthesis/*chemistry/pharmacology ; Stereoisomerism ; },
abstract = {It is challenging to incorporate stereochemical diversity and topographic complexity into DNA-encoded libraries (DELs) because DEL syntheses cannot fully exploit the capabilities of modern synthetic organic chemistry. Here, we describe the design, construction, and validation of DOS-DEL-1, a library of 107 616 DNA-barcoded chiral 2,3-disubsituted azetidines and pyrrolidines. We used stereospecific C-H arylation chemistry to furnish complex scaffolds primed for DEL synthesis, and we developed an improved on-DNA Suzuki reaction to maximize library quality. We then studied both the structural diversity of the library and the physicochemical properties of individual compounds using Tanimoto multifusion similarity analysis, among other techniques. These analyses revealed not only that most DOS-DEL-1 members have "drug-like" properties, but also that the library more closely resembles compound collections derived from diversity synthesis than those from other sources (e.g., commercial vendors). Finally, we performed validation screens against horseradish peroxidase and carbonic anhydrase IX, and we developed a novel, Poisson-based statistical framework to analyze the results. A set of assay positives were successfully translated into potent carbonic anhydrase inhibitors (IC50 = 20.1-68.7 nM), which confirmed the success of the synthesis and screening procedures. These results establish a strategy to synthesize DELs with scaffold-based stereochemical diversity and complexity that does not require the development of novel DNA-compatible chemistry.},
}
@article {pmid31184247,
year = {2019},
author = {Lu, J and Xu, M and Cai, J and Yu, D and Meng, Y and Wang, H},
title = {Transcriptome-wide identification of microRNAs and functional insights inferred from microRNA-target pairs in Physalis angulata L.},
journal = {Plant signaling &amp; behavior},
volume = {14},
number = {8},
pages = {1629267},
pmid = {31184247},
issn = {1559-2324},
mesh = {Gene Expression Regulation, Plant/genetics ; MicroRNAs/*genetics ; Microsatellite Repeats/genetics ; Physalis/*genetics ; Transcriptome/*genetics ; },
abstract = {Physalis angulata L., a member of the family Solanaceae, is widely used as the folk medicine in various countries. Continuous research efforts are devoted to the discovery of the effective medicinal ingredients from Physalis angulata. However, due to the limited resources of genome and transcriptome sequencing data, only a few studies have been performed at the gene regulatory level. In this study, the transcriptomes of five organs (roots, stems, leaves, flowers and fruits) of Physalis angulata were reported. Based on the transcriptome assembly containing 196,117 unique transcripts, a total of 17,556 SSRs (simple sequence repeats) were identified, which could be useful RNA-based barcoding for discrimination of the plants closely relative to Physalis angulata. Additionally, 24 transcripts were discovered to be the potential microRNA (miRNA) precursors which encode a total of 31 distinct mature miRNAs. Some of these precursors showed organ-specific expression patterns. Target prediction revealed 116 miRNA-target pairs, involving 31 miRNAs and 83 target transcripts in Physalis angulata. Taken together, our results could serve as the data resource for in-depth studies on the molecular regulatory mechanisms related to the production of medicinal ingredients in Physalis angulata.},
}
@article {pmid31181977,
year = {2019},
author = {Karthika, P and Vadivalagan, C and Thirumurugan, D and Murugan, K},
title = {Intra-species variation and geographic differentiation among the populations of the quarantine agricultural pest leucinoides orbonalis (lepidoptera: Crambidae) in the global assemblage - a prospective of DNA barcoding.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {4},
pages = {682-693},
doi = {10.1080/24701394.2019.1622691},
pmid = {31181977},
issn = {2470-1408},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Genetic Variation/*genetics ; *Geographic Mapping ; Lepidoptera/*classification/*genetics ; *Pest Control ; *Quarantine ; Species Specificity ; },
abstract = {Leucinodes orbonalis Guenée is serious quarantine pest occurring globally, studies are needed to enlighten the genetic complexities associated with the species. India is considered to be the origin of the L. orbonalis, therefore availability of species records from this region enable to analyse the genetic differences and dispersal of the lineages. The results of the study reported 47 haplotypes in four clusters pertaining to their ancestral lineage. The transition/transversion bias (R) was observed to be higher with 1.238 and 1.312 in the first and third codon positions respectively. The overall intraspecies divergence was found to be 0.302. AMOVA revealed that the total variations were then as reported 67.15 among the south-east countries but our studies reported the total variation to be 77.25% (Germany, India, South east and Australia). FST and Mantel's test indicated that there was no correlation between the genetic variation and geographical distance. The overall haplotype diversity was 0.852, where the nucleotide diversity of H31 (0.00593) was highest and H1 (0.00087) was lowest. The genetic diversity indices Tajima D and Fu's Fs static for H1, H13 and H31 had negative values which possibly inferred for the bottle neck effect. The ML tree was constituted the branch length of 5.0157 with one out-group. The tree was formed with ten distinctive clades with the haplotypes congregated together based on similar genetic composition.},
}
@article {pmid31179548,
year = {2019},
author = {Celedon, JM and Bohlmann, J},
title = {Oleoresin defenses in conifers: chemical diversity, terpene synthases and limitations of oleoresin defense under climate change.},
journal = {The New phytologist},
volume = {224},
number = {4},
pages = {1444-1463},
doi = {10.1111/nph.15984},
pmid = {31179548},
issn = {1469-8137},
mesh = {Alkyl and Aryl Transferases/genetics/*metabolism ; Animals ; Climate Change ; Coleoptera ; Cytochrome P-450 Enzyme System/metabolism ; Gene Expression Regulation, Plant ; *Herbivory ; Phylogeny ; Plant Extracts/chemistry/*metabolism ; Terpenes/metabolism ; Tracheophyta/*chemistry/*physiology ; },
abstract = {Conifers have evolved complex oleoresin terpene defenses against herbivores and pathogens. In co-evolved bark beetles, conifer terpenes also serve chemo-ecological functions as pheromone precursors, chemical barcodes for host identification, or nutrients for insect-associated microbiomes. We highlight the genomic, molecular and biochemical underpinnings of the large chemical space of conifer oleoresin terpenes and volatiles. Conifer terpenes are predominantly the products of the conifer terpene synthase (TPS) gene family. Terpene diversity is increased by cytochromes P450 of the CYP720B class. Many conifer TPS are multiproduct enzymes. Multisubstrate CYP720B enzymes catalyse multistep oxidations. We summarise known terpenoid gene functions in various different conifer species with reference to the annotated terpenoid gene space in a spruce genome. Overall, biosynthesis of terpene diversity in conifers is achieved through a system of biochemical radiation and metabolic grids. Expression of TPS and CYP720B genes can be specific to individual cell types of constitutive or traumatic resin duct systems. Induced terpenoid transcriptomes in resin duct cells lead to dynamic changes of terpene composition and quantity to fend off herbivores and pathogens. While terpenoid defenses have contributed much to the evolutionary success of conifers, under new conditions of climate change, these defences may become inconsequential against range-expanding forest pests.},
}
@article {pmid31179213,
year = {2019},
author = {Yang, X and Zhou, Q and Zhou, W and Zhong, M and Guo, X and Wang, X and Fan, X and Yan, S and Li, L and Lai, Y and Wang, Y and Huang, J and Ye, Y and Zeng, H and Chuan, J and Du, Y and Ma, C and Li, P and Song, Z and Xu, X},
title = {A Cell-free DNA Barcode-Enabled Single-Molecule Test for Noninvasive Prenatal Diagnosis of Monogenic Disorders: Application to β-Thalassemia.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {6},
number = {11},
pages = {1802332},
pmid = {31179213},
issn = {2198-3844},
abstract = {Noninvasive prenatal testing of common aneuploidies has become routine over the past decade, but testing of monogenic disorders remains a challenge in clinical implementation. Most recent studies have inherent limitations, such as complicated procedures, a lack of versatility, and the need for prior knowledge of parental genotypes or haplotypes. To overcome these limitations, a robust and versatile next-generation sequencing-based cell-free DNA (cfDNA) allelic molecule counting system termed cfDNA barcode-enabled single-molecule test (cfBEST) is developed for the noninvasive prenatal diagnosis (NIPD) of monogenic disorders. The accuracy of cfBEST is found to be comparable to that of droplet digital polymerase chain reaction (ddPCR) in detecting low-abundance mutations in cfDNA. The analytical validity of cfBEST is evidenced by a β-thalassemia assay, in which a blind validation study of 143 at-risk pregnancies reveals a sensitivity of 99.19% and a specificity of 99.92% on allele detection. Because the validated cfBEST method can be used to detect maternal-fetal genotype combinations in cfDNA precisely and quantitatively, it holds the potential for the NIPD of human monogenic disorders.},
}
@article {pmid31179191,
year = {2019},
author = {Carbonara, P and Cannas, R and Donnaloia, M and Melis, R and Porcu, C and Spedicato, MT and Zupa, W and Follesa, MC},
title = {On the presence of Dipturus nidarosiensis (Storm, 1881) in the Central Mediterranean area.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7009},
pmid = {31179191},
issn = {2167-8359},
abstract = {The Norwegian skate Dipturus nidarosiensis (Storm, 1881) has only recently been recorded in the western Mediterranean Sea along the coast of southern Sardinia, off Algeria and the Alboran Sea. The present study confirmed the presence of the species in the Central Mediterranean Sea by identifying morphometric, morphological features and molecular markers. Biological sampling was conducted from 2010 to 2016 on eight specimens collected through commercial landings, offshore observer programmes and scientific surveys in Adriatic and Ionian waters at depths between 320 and 720 m. The total lengths of the specimens (juveniles and adults) ranged from 268 to 1,422 mm, and their body weights ranged from 44.5 to 12,540.0 g. They showed morphometric features that corresponded to those of Norwegian skates in the Northeast Atlantic and the Western Mediterranean. In previous analyses, molecular data were obtained by mitochondrial COI sequences. The haplotype network showed the occurrence of a common haplotype (Hap_1) shared by the individuals from areas in the North Atlantic, Sardinian, Algerian and Spanish Mediterranean Sea areas but not South Africa. The occurrence of individuals in different stages of life (i.e., juveniles, sub-adults and adults) and sexual development (immature and mature) suggested the presence of a species with a permanent reproductive allocation in the deep waters of the Mediterranean, which was exposed to a low level of fishing exploitation. Indeed, the deep depth distribution of the species could be the reason for the absence of information about this species in onshore or offshore fishery data collection programmes and scientific surveys.},
}
@article {pmid31175831,
year = {2019},
author = {Riddick, EW and Miller, GL and Owen, CL and Bauchan, GR and Schmidt, JM and Gariepy, T and Brown, RL and Grodowitz, MJ},
title = {Discovery of Aphis ruborum (Hemiptera: Aphididae) and Aphelinus varipes (Hymenoptera: Aphelinidae) on Cultivated Strawberry in Mississippi, USA.},
journal = {Journal of insect science (Online)},
volume = {19},
number = {3},
pages = {},
pmid = {31175831},
issn = {1536-2442},
mesh = {Animals ; Aphids/classification/*parasitology ; Female ; Fragaria ; *Host-Parasite Interactions ; Wasps/*physiology ; },
abstract = {An adventive aphid and novel host-parasitoid association from cultivated strawberry (Fragaria × ananessa Duch. cv. Chandler; Fragaria × ananessa Duch. cv. Camarosa) in Mississippi, USA are reported herein. The aphid, first detected in high tunnel cultivation, was found predominately on newly emerged, not fully developed leaflets of daughter plants in the Fall of 2016. By 2017, aphids and their associated mummies were observed on fully developed leaflets on mother plants of both cultivars. The aphid was identified as Aphis ruborum (Börner &amp; Schilder) using morphology and DNA barcoding studies. In addition, DNA barcoding identified parasitoid adults emerging from aphid mummies as two cryptic species, Aphelinus varipes (Foerster) and Aphelinus albipodus Hayat and Fatima. Occurrence of A. ruborum in Mississippi represents a new state record and the eastern-most established record in the United States. The A. ruborum - A. varipes or A. albipodus host-parasitoid association is reported for the first time anywhere in the world.},
}
@article {pmid31175441,
year = {2019},
author = {Pietras, M},
title = {First record of North American fungus Rhizopogon pseudoroseolus in Australia and prediction of its occurrence based on climatic niche and symbiotic partner preferences.},
journal = {Mycorrhiza},
volume = {29},
number = {4},
pages = {397-401},
pmid = {31175441},
issn = {1432-1890},
support = {DEC-2015/16/S/NZ9/00370//Narodowe Centrum Nauki/ ; },
mesh = {Australia ; Basidiomycota/classification/genetics/*isolation &amp; purification/*physiology ; Climate ; New Zealand ; North America ; Phylogeny ; Pinus/*microbiology/physiology ; *Symbiosis ; Tasmania ; },
abstract = {In 2017 a North American fungus, Rhizopogon pseudoroseolus (Boletales, Basidiomycota), formerly known in Oceania as only occurring in New Zealand, was found for the first time in South Australia. The morphological identification of collected specimens was confirmed using an internal transcribed spacer barcoding approach. In this study, the biogeography of R. pseudoroseolus is also presented, based on sporocarp and ectomycorrhiza records. Species distribution modeling implemented in MaxEnt was used to estimate the distribution of the potential range of R. pseudoroseolus in Australia and New Zealand. The obtained model illustrates, in the background of climatic variables and distribution of a symbiotic partner, its wide range of suitable habitats in New Zealand, South-East Australia, and Tasmania. Precipitation of the coldest quarters and annual mean temperature are important factors influencing the potential distribution of the fungus. The occurrence of Pinus radiata, the ectomycorrhizal partner of R. pseudoroseolus, is also an important factor limiting expansion of the fungus' invasion range.},
}
@article {pmid31174412,
year = {2019},
author = {Boggs, LM and Scheible, MKR and Machado, G and Meiklejohn, KA},
title = {Single Fragment or Bulk Soil DNA Metabarcoding: Which is Better for Characterizing Biological Taxa Found in Surface Soils for Sample Separation?.},
journal = {Genes},
volume = {10},
number = {6},
pages = {},
pmid = {31174412},
issn = {2073-4425},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA Fingerprinting ; Forensic Genetics/*methods ; High-Throughput Nucleotide Sequencing ; Insecta/chemistry/genetics ; Metagenome/*genetics ; Plants/chemistry/genetics ; Soil/*chemistry ; },
abstract = {In forensic geology casework, sample size typically limits routine characterization of material using bulk approaches. To address this, DNA-based characterization of biological taxa has received attention, as the taxa present can be useful for sample-to-sample comparisons and source attribution. In our initial work, low biodiversity was captured when DNA barcodes were Sanger-sequenced from plant and insect fragments isolated from 10 forensic-type surface soils. Considering some forensic laboratories now have access to massively parallel sequencing platforms, we assessed whether biological taxa present in the same surface soils could be better characterized using DNA metabarcoding. To achieve this, plant and animal barcodes were amplified and sequenced on an Illumina MiniSeq for three different DNA sample types (n = 50): individual fragments used in our initial study, and 250 and 100 mg of bulk soil (from the 10 sites used in the initial study). A total of 572 unique target barcode sequences passed quality filtering and were used in downstream statistical analyses: 54, 321, and 285 for individual fragments, 100 mg, and 250 mg bulk soil samples, respectively. Plant barcodes permitted some spatial separation of sample sites in non-metric multidimensional scaling plots; better separation was obtained for samples prepared from bulk soil. This study confirmed that bulk soil DNA metabarcoding is a better approach for characterizing biological taxa present in surface soils, which could supplement traditional geologic examinations.},
}
@article {pmid31173871,
year = {2019},
author = {Kebschull, JM},
title = {DNA sequencing in high-throughput neuroanatomy.},
journal = {Journal of chemical neuroanatomy},
volume = {100},
number = {},
pages = {101653},
doi = {10.1016/j.jchemneu.2019.101653},
pmid = {31173871},
issn = {1873-6300},
mesh = {Animals ; Connectome/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Neuroanatomy/*methods ; },
abstract = {Mapping brain connectivity at single cell resolution is critical for understanding brain structure. For decades, such mapping has been principally approached with microscopy techniques, aiming to visualize neurons and their connections. However, these techniques are often very labor intensive and do not scale well to the complexity of mammalian brains. We recently leveraged the speed and parallelization of DNA sequencing to map the projections of thousands of single neurons in single experiments, and to map cortical mesoscale connectivity in single mice. Here, I review the state of sequencing-based neuroanatomy, and discuss future directions in synaptic connectivity mapping and comparative connectomics.},
}
@article {pmid31173634,
year = {2019},
author = {Gemmellaro, MD and Hamilton, GC and Ware, JL},
title = {Review of Molecular Identification Techniques for Forensically Important Diptera.},
journal = {Journal of medical entomology},
volume = {56},
number = {4},
pages = {887-902},
doi = {10.1093/jme/tjz040},
pmid = {31173634},
issn = {1938-2928},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Diptera/*genetics ; Forensic Entomology/*methods ; },
abstract = {The medico-legal section of forensic entomology focuses on the analysis of insects associated with a corpse. Such insects are identified, and their life history characteristics are evaluated to provide information related to the corpse, such as postmortem interval and time of colonization. Forensically important insects are commonly identified using dichotomous keys, which rely on morphological characteristics. Morphological identifications can pose a challenge as local keys are not always available and can be difficult to use, especially when identifying juvenile stages. If a specimen is damaged, certain keys cannot be used for identification. In contrast, molecular identification can be a better instrument to identify forensically important insects, regardless of life stage or specimen completeness. Despite more than 20 yr since the first use of molecular data for the identification of forensic insects, there is little overlap in gene selection or phylogenetic methodology among studies, and this inconsistency reduces efficiency. Several methods such as genetic distance, reciprocal monophyly, or character-based methods have been implemented in forensic identification studies. It can be difficult to compare the results of studies that employ these different methods. Here we present a comprehensive review of the published results for the molecular identification of Diptera of forensic interest, with an emphasis on evaluating variation among studies in gene selection and phylogenetic methodology.},
}
@article {pmid31172374,
year = {2019},
author = {Vo, NTK and Everson, J and Moore, L and DeWitte-Orr, SJ},
title = {Class A scavenger receptor expression and function in eight novel tadpole cell lines from the green frog (Lithobates clamitans) and the wood frog (Lithobates sylvatica).},
journal = {Cytotechnology},
volume = {71},
number = {4},
pages = {757-768},
pmid = {31172374},
issn = {0920-9069},
support = {Discovery//Natural Sciences and Engineering Research Council of Canada/ ; ERA//Ontario Ministry of Research, Innovation and Science/ ; },
abstract = {A total of eight tadpole cell lines were established from green frogs (Lithobates clamitans) and wood frogs (Lithobates sylvatica). The five green frog cell lines were named GreenTad-HF1, GreenTad-HF2, GreenTad-HF3, GreenTad-HE4, and GreenTad-gill. The three wood frog cell lines were named WoodTad-HE1, WoodTad-Bone, and WoodTad-rpe. DNA barcoding confirmed the cell lines to be from the correct species and the growth characteristics (optimal temperature and FBS requirement) were elucidated. In order to begin studying the innate immune capacity for each cell line, class A scavenger receptor expression and function were next explored. All cell lines expressed genes for at least 3 of the 5 class A scavenger receptor (SR-A) family members, but the gene expression patterns varied between cell lines. MARCO was only expressed in GreenTad-HE4 and WoodTad-Bone, while only GreenTad-HF3 did not express SCARA5 and only WoodTad-rpe did not express SR-AI. Acetylated low density lipoprotein (AcLDL) is a well-defined ligand for SR-As and WoodTad-rpe was the only cell line to which it was unable to bind. In the other seven tadpole cell lines, the SR-A competitive ligands (dextran sulfate, fucoidan, polyinosinic acid) blocked AcLDL binding whereas the SR-A non-competitive ligand counterparts (chondroitin sulfate, fetuin, polycytidylic acid, respectively) did not. Overall, these new eight cell lines can become important tools in the study of innate immunity in general and SR-A functions in particular in green frogs and wood frogs.},
}
@article {pmid31171675,
year = {2019},
author = {Pennisi, E},
title = {DNA barcodes jump-start search for new species.},
journal = {Science (New York, N.Y.)},
volume = {364},
number = {6444},
pages = {920-921},
doi = {10.1126/science.364.6444.920},
pmid = {31171675},
issn = {1095-9203},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Sequence Analysis, DNA ; },
}
@article {pmid31170912,
year = {2019},
author = {Quattrini, AM and Wu, T and Soong, K and Jeng, MS and Benayahu, Y and McFadden, CS},
title = {A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals.},
journal = {BMC evolutionary biology},
volume = {19},
number = {1},
pages = {116},
pmid = {31170912},
issn = {1471-2148},
support = {52006301//Howard Hughes Medical Institute (US)/International ; },
mesh = {Animals ; Anthozoa/classification/*genetics ; DNA Barcoding, Taxonomic ; Discriminant Analysis ; *Hybridization, Genetic ; Likelihood Functions ; Phylogeny ; Principal Component Analysis ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND: Our ability to investigate processes shaping the evolutionary diversification of corals (Cnidaria: Anthozoa) is limited by a lack of understanding of species boundaries. Discerning species of corals has been challenging due to a multitude of factors, including homoplasious and plastic morphological characters and the use of molecular markers that are either not informative or have not completely sorted. Hybridization can also blur species boundaries by leading to incongruence between morphology and genetics. We used traditional DNA barcoding and restriction-site associated DNA sequencing combined with coalescence-based and allele-frequency methods to elucidate species boundaries and simultaneously examine the potential role of hybridization in a speciose genus of octocoral, Sinularia.<br><br>RESULTS: Species delimitations using two widely used DNA barcode markers, mtMutS and 28S rDNA, were incongruent with one another and with the morphospecies identifications. When mtMutS and 28S were concatenated, a 0.3% genetic distance threshold delimited the majority of morphospecies. In contrast, 12 of the 15 examined morphospecies formed well-supported monophyletic clades in both concatenated RAxML phylogenies and SNAPP species trees of >&#x2009;6000 RADSeq loci. DAPC and Structure analyses also supported morphospecies assignments, but indicated the potential for two additional cryptic species. Three morphologically distinct species pairs could not, however, be distinguished genetically. ABBA-BABA tests demonstrated significant admixture between some of those species, suggesting that hybridization may confound species delimitation in Sinularia.<br><br>CONCLUSIONS: A genomic approach can help to guide species delimitation while simultaneously elucidating the processes generating coral diversity. Results support the hypothesis that hybridization is an important mechanism in the evolution of Anthozoa, including octocorals, and future research should examine the contribution of this mechanism in generating diversity across the coral tree of life.},
}
@article {pmid31169834,
year = {2019},
author = {Feng, G and Guan, T and He, Q and Lu, B and Chen, X and Wang, B and Zhou, X and Ding, J and He, Y},
title = {Ion-chelation based digital barcodes for multiplexing of a suspension array.},
journal = {The Analyst},
volume = {144},
number = {13},
pages = {4093-4099},
doi = {10.1039/c9an00343f},
pmid = {31169834},
issn = {1364-5528},
abstract = {Ion-chelated microbeads (ICMs) for suspension arrays can be prepared by chelating metal ions (MIs), which are used as encoding materials. Stimulating the ICMs, laser induced breakdown spectra (LIBs) can be obtained and the atomic spectra of the chelated ions are chosen as the decoding signals. Our ICMs show digital characteristics with high stability due to the properties of LIBs. And, since there are many available coding materials and different kinds of coding materials can be easily combined, the coding capacity can be considerably enlarged. Further, the background interference in fluoroimmunoassay detection could be avoided, because the ICMs contain no fluorescence emission. In our studies, we achieved a total of 15 types of barcodes by taking full advantage of 4 kinds of ions, then a fluoroimmunoassay was performed to demonstrate the specificity and detection performance of our ICMs in multiplexing and the detection limit could reach 1.49 × 10[-10] M, showing promising potential in applications.},
}
@article {pmid31168752,
year = {2019},
author = {Jabin, G and Dewan, Y and Khatri, H and Singh, SK and Chandra, K and Thakur, M},
title = {Identifying the tick Amblyomma javanense (Acari: Ixodidae) from Chinese pangolin: generating species barcode, phylogenetic status and its implication in wildlife forensics.},
journal = {Experimental &amp; applied acarology},
volume = {78},
number = {3},
pages = {461-467},
pmid = {31168752},
issn = {1572-9702},
mesh = {Animals ; *Conservation of Natural Resources ; DNA Barcoding, Taxonomic ; Endangered Species ; *Forensic Sciences ; Ixodidae/classification/*genetics/physiology ; Mammals/parasitology ; Phylogeny ; Risk Assessment ; Tick-Borne Diseases/transmission ; },
abstract = {Zoonotic diseases transmitted through ticks and other ectoparasites often travel across the globe with illegally traded wildlife parts and products. In this study, we analyzed a confiscated case of pangolin scales and observed a few dead ticks attached. On genetic analysis, the pangolin scales were identified to be originated from Chinese pangolin (Manis pentadactyla), an IUCN listed Critically Endangered species, and ticks were identified as Amblyomma javanense. Here, we provide the first authentic physical record of A. javanense from India as a parasite of Chinese pangolin and also generated its species DNA barcode that may be useful for biologists working on ticks in species validation and constructing phylogenies across the globe.},
}
@article {pmid31166941,
year = {2019},
author = {García-Melo, JE and Oliveira, C and Da Costa Silva, GJ and Ochoa-Orrego, LE and Garcia Pereira, LH and Maldonado-Ocampo, JA},
title = {Species delimitation of neotropical Characins (Stevardiinae): Implications for taxonomy of complex groups.},
journal = {PloS one},
volume = {14},
number = {6},
pages = {e0216786},
pmid = {31166941},
issn = {1932-6203},
mesh = {Animals ; Characidae/*classification/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Accurate species delimitation is crucial for studies of phylogeny, phylogeography, ecology, conservation and biogeography. The limits of species and genera in the Characidae family are controversial due to its uncertain phylogenetic relationships, high level of morphological homoplasy and the use of ambiguous morphological characters for descriptions. Here we establish species boundaries for Bryconamericus, Hemibrycon, Knodus and Eretmobrycon (Stevardiinae: Characidae), previously diagnosed with morphology, using three different barcoding approaches (GMYC, PTP, ABGD). Results revealed that species delimitation was successful by the use of a single-gene approach and by following a workflow in the context of integrative taxonomy, making evident problems and mistakes in the cataloging of Characidae species. Hence, it was possible to infer boundaries at genus level for clusters in the trees (GMYC and PTP) and automatic partitions (ABGD) which were consistent with some of recent taxonomic changes proposed in Characidae. We found that discordance cases between methods were linked to limitations of the methods and associated to putative species cluster closely related, some historically problematic in their diagnosis and identification. Furthermore, we suggested taxonomic changes and possibly new species, revealing a high degree of hidden diversity. Finally, we propose a workflow as a fast, accurate and objective way to delimit species from mitochondrial DNA sequences and to help clarify the classification of this group.},
}
@article {pmid31166160,
year = {2019},
author = {Oulghazi, S and Pédron, J and Cigna, J and Lau, YY and Moumni, M and Van Gijsegem, F and Chan, KG and Faure, D},
title = {Dickeya undicola sp. nov., a novel species for pectinolytic isolates from surface waters in Europe and Asia.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {69},
number = {8},
pages = {2440-2444},
doi = {10.1099/ijsem.0.003497},
pmid = {31166160},
issn = {1466-5034},
mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Enterobacteriaceae/*classification/isolation &amp; purification ; France ; Fresh Water/*microbiology ; Genes, Bacterial ; Genomics ; Malaysia ; Multilocus Sequence Typing ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Strains 2B12[T], FVG1-MFV-O17 and FVG10-MFV-A16 were isolated from fresh water samples collected in Asia and Europe. The nucleotide sequences of the gapA barcodes revealed that all three strains belonged to the same cluster within the genus Dickeya. Using 13 housekeeping genes (fusA, rpoD, rpoS, glyA, purA, groEL, gapA, rplB, leuS, recA, gyrB, infB and secY), multilocus sequence analysis confirmed the existence of a new clade. When the genome sequences of these three isolates and other Dickeya species were compared, the in silico DNA-DNA hybridization and average nucleotide identity values were found to be no more than 45.50 and 91.22 %, respectively. The closest relative species was Dickeya fangzhongdai. Genome comparisons also highlighted genetic traits differentiating the new strains from D. fangzhongdai strains DSM 101947[T] (=CFBP 8607[T]) and B16. Phenotypical tests were performed to distinguish the three strains from D. fangzhongdai and other Dickeya species. The name Dickeya undicola sp. nov. is proposed with strain 2B12[T] (=CFBP 8650[T]=LMG 30903[T]) as the type strain.},
}
@article {pmid31164571,
year = {2018},
author = {Nussbaum, L and Telenius, JM and Hill, S and Hirschfeld, PP and Suciu, MC and , and Downes, DJ and Hughes, JR},
title = {High-Throughput Genotyping of CRISPR/Cas Edited Cells in 96-Well Plates.},
journal = {Methods and protocols},
volume = {1},
number = {3},
pages = {},
pmid = {31164571},
issn = {2409-9279},
support = {MC_UU_00016/14/MRC_/Medical Research Council/United Kingdom ; MC_UU_12009/15/MRC_/Medical Research Council/United Kingdom ; 106130/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; 4050189188/MRC_/Medical Research Council/United Kingdom ; },
abstract = {The emergence in recent years of DNA editing technologies-Zinc finger nucleases (ZFNs), transcription activator-like effector (TALE) guided nucleases (TALENs), clustered regularly interspaced short palindromic repeats (CRISPR)/Cas family enzymes, and Base-Editors-have greatly increased our ability to generate hundreds of edited cells carrying an array of alleles, including single-nucleotide substitutions. However, the infrequency of homology-dependent repair (HDR) in generating these substitutions in general requires the screening of large numbers of edited cells to isolate the sequence change of interest. Here we present a high-throughput method for the amplification and barcoding of edited loci in a 96-well plate format. After barcoding, plates are indexed as pools which permits multiplexed sequencing of hundreds of clones simultaneously. This protocol works at high success rate with more than 94% of clones successfully genotyped following analysis.},
}
@article {pmid31162600,
year = {2019},
author = {Park, JS and Husseneder, C and Schlub, RL},
title = {Morphological and Molecular Species Identification of Termites Attacking Ironwood Trees, Casuarina equisetifolia (Fagales: Casuarinaceae), in Guam.},
journal = {Journal of economic entomology},
volume = {112},
number = {4},
pages = {1902-1911},
doi = {10.1093/jee/toz097},
pmid = {31162600},
issn = {1938-291X},
mesh = {Animals ; *Cockroaches ; Fagales ; Guam ; *Isoptera ; Trees ; },
abstract = {Ironwood trees (Casuarina equisetifolia subsp. equisetifolia L.) are ecologically and economically important trees in tropical and subtropical regions of the Indo-Pacific. Ironwood is one of the dominant tree species in Guam, but since 2002, this tree has been declining dramatically. A previous study showed that numerous sick or dead trees were under termite attack. However, the species of termites were not identified. As a first step to investigate causal relationships between termites and ironwood tree death, we assigned termites collected from ironwood trees to species using a combination of morphological characters and DNA barcoding of the 12S, 16S, COI, COII, and ITS2 regions. Based on morphology and comparisons to reference sequences in NCBI GenBank, the most likely species assignments were Nasutitermes takasagoensis (Nawa) (Blattodea: Termitidae) found to infest 45 trees, followed by Coptotermes gestroi (Wasmann) (Blattodea: Rhinotermitidae) (2 trees), Microcerotermes crassus Snyder (Blattodea: Termitidae) (2 trees), and an additional unidentified Microcerotermes species (1 tree) with no close sequence match to identified species in NCBI GenBank. However, taxonomic revisions and broader representation of DNA markers of well-curated specimen in public databases are clearly needed, especially for the N. takasagoensis species complex.},
}
@article {pmid31160999,
year = {2019},
author = {Kolzenburg, R and Nicastro, KR and McCoy, SJ and Ford, AT and Zardi, GI and Ragazzola, F},
title = {Understanding the margin squeeze: Differentiation in fitness-related traits between central and trailing edge populations of Corallina officinalis.},
journal = {Ecology and evolution},
volume = {9},
number = {10},
pages = {5787-5801},
pmid = {31160999},
issn = {2045-7758},
abstract = {ABSTRACT: Assessing population responses to climate-related environmental change is key to understanding the adaptive potential of the species as a whole. Coralline algae are critical components of marine shallow water ecosystems where they function as important ecosystem engineers. Populations of the calcifying algae Corallina officinalis from the center (southern UK) and periphery (northern Spain) of the North Atlantic species natural distribution were selected to test for functional differentiation in thermal stress response. Physiological measurements of calcification, photosynthesis, respiration, growth rates, oxygen, and calcification evolution curves were performed using closed cell respirometry methods. Species identity was genetically confirmed via DNA barcoding. Through a common garden approach, we identified distinct vulnerability to thermal stress of central and peripheral populations. Southern populations showed a decrease in photosynthetic rate under environmental conditions of central locations, and central populations showed a decline in calcification rates under southern conditions. This shows that the two processes of calcification and photosynthesis are not as tightly coupled as previously assumed. How the species as whole will react to future climatic changes will be determined by the interplay of local environmental conditions and these distinct population adaptive traits.<br><br>OPEN RESEARCH BADGES: This article has earned an Open Materials Badge for making publicly available the components of the research methodology needed to reproduce the reported procedure and analysis. All materials are available at https://doi.pangaea.de/10.1594/PANGAEA.899568.},
}
@article {pmid31160883,
year = {2019},
author = {Guzow-Krzemińska, B and Jabłońska, A and Flakus, A and Pamela Rodriguez-Flakus, and Kosecka, M and Kukwa, M},
title = {Phylogenetic placement of Leprariacryptovouauxii sp. nov. (Lecanorales, Lecanoromycetes, Ascomycota) with notes on other Lepraria species from South America.},
journal = {MycoKeys},
volume = {53},
number = {},
pages = {1-22},
pmid = {31160883},
issn = {1314-4049},
abstract = {Leprariacryptovouauxii is described as a new semicryptic species similar to L.vouauxii, from which it differs geographically (South America) and phylogenetically; both species differ in nucleotide position characters in nucITS barcoding marker. Leprariaharrisiana is reported as new to South America and L.nothofagi as new to Antarctica, Bolivia, and Peru. Leprariaincana (South American records are referred to L.aff.hodkinsoniana) and L.vouauxii (most South American records are referred to L.cryptovouauxii) should be excluded at least temporarily from the lichen list of South America. All records previously referred to as L.alpina from Bolivia and Peru belong to L.nothofagi. Most of Bolivian records of L.pallida belong to L.harrisiana. Leprariaborealis and L.caesioalba should be included in L.neglecta. Leprariaachariana, L.impossibilis, and L.sipmaniana are sequenced for the first time.},
}
@article {pmid31160881,
year = {2019},
author = {Martin, MB and Chakona, A},
title = {Designation of a neotype for Enteromiuspallidus (Smith, 1841), an endemic cyprinid minnow from the Cape Fold Ecoregion, South Africa.},
journal = {ZooKeys},
volume = {848},
number = {},
pages = {103-118},
pmid = {31160881},
issn = {1313-2989},
abstract = {Enteromiuspallidus was described by Smith in 1841 without a designated type specimen for the species. Herein, we designate a specimen from the Baakens River system as a neotype for E.pallidus and provide a thorough description for this species to facilitate ongoing taxonomic revisions of southern African Enteromius. Enteromiuspallidus can be distinguished from the other minnows in the "goldie barb group" by having an incomplete lateral line, lack of distinct chevron or tubular markings around lateral line pores, absence of a distinct lateral stripe, absence of wavy parallel lines along scale rows and lack of black pigmentation around the borders of the scales. We provide mtDNA COI sequences for the neotype and an additional specimen from the Baakens River as DNA barcodes of types and topotypes are a fundamental requirement for further taxonomic studies.},
}
@article {pmid31160880,
year = {2019},
author = {Klimaszewski, J and Sikes, DS and Brunke, A and Bourdon, C},
title = {Species review of the genus Boreophilia Benick from North America (Coleoptera, Staphylinidae, Aleocharinae, Athetini): Systematics, habitat, and distribution.},
journal = {ZooKeys},
volume = {848},
number = {},
pages = {57-102},
pmid = {31160880},
issn = {1313-2989},
abstract = {Fourteen species of the genus Boreophilia Benick are now recognized in North America. Boreophiliainsecuta (Eppelsheim), reported by Lohse (1990) from North America, is a misidentification of a new species, which is described here as B.neoinsecuta Klimaszewski, sp. n., and the true B.insecuta (Epp.) does not occur in North America. An additional new species is found in Alaska, and described as B.beringi Klimaszewski &amp; Brunke, sp. n. The following three species are synonymized (second name being valid): Boreophiliaherschelensis Klimaszewski &amp; Godin, 2012, with Boreophiliavega (Fenyes, 1920); Boreophiliamanitobensis Lohse, 1990, with B.caseyi Lohse, 1990; and B.angusticornis (Bernahuer, 1907) with B.subplana (J Sahlberg, 1880), based on study of genital structures and external morphology. Athetagelida J Sahlberg, 1887, and Athetamunsteri Bernhauer, 1902, considered as Boreophilia in recent publications, are transferred to the genus Atheta Thomson, subgenus Dimetrota. Boreostibapiligera (J Sahlberg) is transferred to Boreophilia based on morphology and the results of our phylogenetic analysis. Boreophilianearctica is recorded from Alberta and B.nomensis is recorded from British Columbia for the first time. Each valid species is illustrated by color image of habitus, and black and white images of genitalia and tergite and sternite VIII. A new key to all Nearctic species of the genus is provided. DNA barcode data were available for nine of the 14 species, which we downloaded, analyzed, and used as additional evidence for the taxonomic conclusions reached herein.},
}
@article {pmid31160786,
year = {2019},
author = {Brummelman, J and Haftmann, C and Núñez, NG and Alvisi, G and Mazza, EMC and Becher, B and Lugli, E},
title = {Development, application and computational analysis of high-dimensional fluorescent antibody panels for single-cell flow cytometry.},
journal = {Nature protocols},
volume = {14},
number = {7},
pages = {1946-1969},
doi = {10.1038/s41596-019-0166-2},
pmid = {31160786},
issn = {1750-2799},
mesh = {Algorithms ; *Antibodies, Monoclonal ; Biomarkers ; Buffers ; Coloring Agents ; Computational Biology/methods ; Flow Cytometry/*methods ; Fluorescent Antibody Technique/*methods ; Forkhead Transcription Factors/immunology ; Humans ; Signaling Lymphocytic Activation Molecule Family/immunology ; Single-Cell Analysis/*methods ; T-Lymphocytes/cytology/immunology ; },
abstract = {The interrogation of single cells is revolutionizing biology, especially our understanding of the immune system. Flow cytometry is still one of the most versatile and high-throughput approaches for single-cell analysis, and its capability has been recently extended to detect up to 28 colors, thus approaching the utility of cytometry by time of flight (CyTOF). However, flow cytometry suffers from autofluorescence and spreading error (SE) generated by errors in the measurement of photons mainly at red and far-red wavelengths, which limit barcoding and the detection of dim markers. Consequently, development of 28-color fluorescent antibody panels for flow cytometry is laborious and time consuming. Here, we describe the steps that are required to successfully achieve 28-color measurement capability. To do this, we provide a reference map of the fluorescence spreading errors in the 28-color space to simplify panel design and predict the success of fluorescent antibody combinations. Finally, we provide detailed instructions for the computational analysis of such complex data by existing, popular algorithms (PhenoGraph and FlowSOM). We exemplify our approach by designing a high-dimensional panel to characterize the immune system, but we anticipate that our approach can be used to design any high-dimensional flow cytometry panel of choice. The full protocol takes a few days to complete, depending on the time spent on panel design and data analysis.},
}
@article {pmid31157099,
year = {2019},
author = {Moss, RJ and Süle, A and Kohl, S},
title = {eHealth and mHealth.},
journal = {European journal of hospital pharmacy : science and practice},
volume = {26},
number = {1},
pages = {57-58},
pmid = {31157099},
issn = {2047-9964},
abstract = {Both electronic health (eHealth) and mobile health (mHealth) are becoming prominent components of healthcare. In order for healthcare electronic services to be safe and effective and add genuine value to the system, the European Association of Hospital Pharmacists (EAHP) believes that these should be developed in close collaboration with healthcare professionals including hospital pharmacists, and patients. Consequently, the EAHP calls in its position paper upon national governments and health systems across Europe to work towards (1) systematic and European Union-wide achievement of electronic prescribing, administration and use of electronic medical records; (2) ensuring barcoding of medicines to the single units in primary packages to enable more widespread take-up of bedside scanning in European hospitals, thus improving patient safety; (3) appropriate regulatory oversight mechanisms for mHealth applications to ensure that they have a positive impact and adequately protect patient data; (4) provision of appropriate eHealth/mHealth training opportunities to healthcare professionals and promotion of digital health literacy; and (5) involvement of hospital pharmacists in the design, specification of parameters and evaluation of information and communication technology within the medicines processes.},
}
@article {pmid31153919,
year = {2019},
author = {Nakao, M and Sasaki, M and Waki, T and Iwaki, T and Morii, Y and Yanagida, K and Watanabe, M and Tsuchitani, Y and Saito, T and Asakawa, M},
title = {Distribution records of three species of Leucochloridium (Trematoda: Leucochloridiidae) in Japan, with comments on their microtaxonomy and ecology.},
journal = {Parasitology international},
volume = {72},
number = {},
pages = {101936},
doi = {10.1016/j.parint.2019.101936},
pmid = {31153919},
issn = {1873-0329},
mesh = {*Animal Distribution ; Animals ; Birds/parasitology ; DNA Barcoding, Taxonomic ; DNA, Helminth/genetics ; *Ecology ; Europe ; Japan ; Larva/physiology ; Oocysts ; Snails/*parasitology ; Trematoda/*classification/physiology ; },
abstract = {Insectivorous birds serve as definitive hosts for trematodes of the genus Leucochloridium. The parasites exclusively use amber snails of the family Succineidae as intermediate hosts. A pulsating and colorful display of the larval broodsac in the snail's eyestalk seems to be a caterpillar mimic for attracting birds. A colored design of the broodsac is very useful for parasite identification. In Japan, characteristic broodsacs from amber snails have been recorded from 1980's, but their taxonomic discrimination from Asian, European, and North American species has not been achieved. In this study, old scientific records, sighting information on broodsacs from the general public, and direct molecular evidence by DNA barcoding clearly showed that at least three species of Leucochloridium are distributed in Japan. A vertical-striped broodsac found from Succinea sp. in Okinawa, the subtropical island of Japan, were treated as Leucochloridium sp., but being almost identical to that of Leucochloridium passeri in neighboring Taiwan. The European species of Leucochloridium perturbatum and Leucochloridium paradoxum were frequently detected from Succinea lauta in Hokkaido, the northernmost island of Japan. The former species was common in inland areas of Hokkaido, whereas the latter species was frequently seen in the coastal areas. A possible explanation for the parasite distribution pattern is that principal definitive hosts (migratory or resident birds) differ in each parasite. The conspecificity of Leucochloridium variae in North America and L. perturbatum in Europe and the Far East is also discussed.},
}
@article {pmid31152352,
year = {2019},
author = {Lassance, JM and Svensson, GP and Kozlov, MV and Francke, W and Löfstedt, C},
title = {Pheromones and Barcoding Delimit Boundaries between Cryptic Species in the Primitive Moth Genus Eriocrania (Lepidoptera: Eriocraniidae).},
journal = {Journal of chemical ecology},
volume = {45},
number = {5-6},
pages = {429-439},
pmid = {31152352},
issn = {1573-1561},
mesh = {Animals ; DNA/isolation &amp; purification/metabolism ; Electron Transport Complex IV/classification/genetics ; Female ; Genetic Variation ; Glyceraldehyde 3-Phosphate Dehydrogenase (NADP+)/classification/genetics ; Male ; Mitochondria/genetics ; Moths/*genetics ; Phylogeny ; Sex Attractants/*chemistry/metabolism ; },
abstract = {Animal classification is primarily based on morphological characters, even though these may not be the first to diverge during speciation. In many cases, closely related taxa are actually difficult to distinguish based on morphological characters alone, especially when there is no substantial niche separation. As a consequence, the diversity of certain groups is likely to be underestimated. Lepidoptera -moths and butterflies- represent the largest group of herbivorous insects. The extensive diversification in the group is generally assumed to have its origin in the spectacular radiation of flowering plants and the resulting abundance of ecological niches. However, speciation can also occur without strong ecological divergence. For example, reproductive isolation can evolve as the result of divergence in mate preference and the associated pheromone communication system. We combined pheromone trapping and genetic analysis to elucidate the evolutionary relationships within a complex of primitive moth species (Lepidoptera: Eriocraniidae). Mitochondrial and nuclear DNA markers provided evidence that Eriocrania semipurpurella, as currently defined by morphological characters, includes three cryptic species in Northern and Western Europe. Male moths of these cryptic species, as well as of the closely related E. sangii, exhibited relative specificity in terms of their attraction to specific ratios of two major pheromone components, (2S,6Z)-nonen-2-ol and (2R,6Z)-nonen-2-ol. Our data suggest strong assortative mating in these species in the absence of apparent niche separation, indicating that Eriocrania moths may represent an example of non-ecological speciation. Finally, our study argues in favour of combining pheromone investigations and DNA barcoding as powerful tools for identifying and delimitating species boundaries.},
}
@article {pmid31150116,
year = {2019},
author = {Kotrba, M},
title = {Commentary on: Chimeno C, Morinière J, Podhorna J, Hardulak, L, Hausmann A, Reckel F, et al. DNA barcoding in forensic entomology-establishing a DNA reference library of potentially forensic relevant arthropod species. J Forensic Sci 2019;64(2):593-601.},
journal = {Journal of forensic sciences},
volume = {64},
number = {4},
pages = {1285-1286},
doi = {10.1111/1556-4029.14094},
pmid = {31150116},
issn = {1556-4029},
mesh = {Animals ; *Arthropods ; DNA ; DNA Barcoding, Taxonomic ; Entomology ; Forensic Sciences ; },
}
@article {pmid31148929,
year = {2019},
author = {Matson, TA and Wagner, DL and Miller, SE},
title = {A Revision of North American Lactura (Lepidoptera, Zygaenoidea, Lacturidae).},
journal = {ZooKeys},
volume = {846},
number = {},
pages = {75-116},
pmid = {31148929},
issn = {1313-2989},
abstract = {The Lactura Walker, 1854 fauna north of Mexico is revised. Six species are documented, one new species Lacturanalli Matson &amp; Wagner, sp. n. is described, and two new synonymies are proposed: Lacturapsammitis (Zeller, 1872), syn. n. and L.rhodocentra (Meyrick, 1913), syn. n. One new subspecies Lacturasubfervenssapeloensis Matson &amp; Wagner, ssp. n. is also described. Adult and larval stages, male and female genitalia, are illustrated, a preliminary phylogeny is presented based on nuclear and mitochondrial data, distribution records provided for verified specimens, and the biology and life history for each species is briefly characterized. Phylogenetic analyses, larval phenotypes, and life history information reveal that much of the historic taxonomic confusion rampant across this group in North America traces to the phenotypic variation in just one species, L.subfervens (Walker, 1854).},
}
@article {pmid31145032,
year = {2019},
author = {Huang, X and Rapševičius, P and Chapa-Vargas, L and Hellgren, O and Bensch, S},
title = {Within-Lineage Divergence of Avian Haemosporidians: A Case Study to Reveal the Origin of a Widespread Haemoproteus Parasite.},
journal = {The Journal of parasitology},
volume = {105},
number = {3},
pages = {414-422},
pmid = {31145032},
issn = {1937-2345},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Bayes Theorem ; Bird Diseases/*parasitology/transmission ; Cytochromes b/*genetics ; Diptera/parasitology ; Finches/parasitology ; Genome, Mitochondrial/*genetics ; Haemosporida/*classification/genetics/isolation &amp; purification ; Insect Vectors/parasitology ; Mexico ; Passeriformes/*parasitology ; Phylogeny ; Phylogeography ; Protozoan Infections, Animal/*parasitology/transmission ; Russia ; Sequence Alignment/veterinary ; Sweden ; },
abstract = {Avian haemosporidian parasites are particularly diverse and widespread. To date, more than 3,000 distinct cytochrome b lineages have been recorded, of which some present extremely wide geographical distributions, even including multiple continents. Whether these isolates represent one or several cryptic species remains unknown. Here we carried out a case study of SISKIN1, a common haemosporidian parasite lineage belonging to the morphologically described species Haemoproteus tartakovskyi. To shed light on its evolutionary origin, we investigated the divergence between SISKIN1 isolates obtained from siskins and redpolls in Europe (Russia and Sweden) and house finches in North America (Mexico). First, we used sequence capture of a small data set (2 Russian isolates and 1 Mexican isolate) to investigate the genetic structure based on the full-length mitochondrial genome and ∼1,000 genes. The mitochondrial genomes of Russian isolates were identical with each other but differed from the Mexican one at 6 positions. The nuclear divergence between Russian and Mexican isolates was on average 2.8%, close to what has been observed between 2 species of malaria parasites that respectively infect humans (Plasmodium falciparum) and gorillas (Plasmodium praefalciparum). Second, we used the expanded data set (15 samples in total) to investigate the genetic structure in 3 genes known to be involved in host invasion. The European isolates were identical across all sequenced genes, whereas the Mexican isolates were highly diverse. The lack of shared alleles between European and Mexican populations suggests that they might have diverged in isolation without gene flow. From the MalAvi database we examined the lineages most similar to the SISKIN1 barcode fragment (part of the cyt b gene) and found that most of them had been recorded in North and South America. This suggests that the lineage SISKIN1 originated in North America and subsequently spread to Europe. Our analyses support that the cyt b gene barcoding region is a useful marker for identification of avian haemosporidian lineages that can classify them into clusters of closely related parasites, but to further investigate species limits and evolutionary history, molecular data from multiple faster-evolving genes are required.},
}
@article {pmid31145030,
year = {2019},
author = {Morioka, T and Blyth, BJ and Imaoka, T and Nishimura, M and Takeshita, H and Shimomura, T and Ohtake, J and Ishida, A and Schofield, P and Grosche, B and Kulka, U and Shimada, Y and Yamada, Y and Kakinuma, S},
title = {Establishing the Japan-Store house of animal radiobiology experiments (J-SHARE), a large-scale necropsy and histopathology archive providing international access to important radiobiology data.},
journal = {International journal of radiation biology},
volume = {95},
number = {10},
pages = {1372-1377},
doi = {10.1080/09553002.2019.1625458},
pmid = {31145030},
issn = {1362-3095},
mesh = {*Access to Information ; Animal Experimentation ; Animals ; Archives ; Carcinogenesis ; Databases, Factual ; *Histology ; Humans ; Japan ; Medical Records ; Mice ; Neoplasms/epidemiology/genetics ; Neoplasms, Radiation-Induced/diagnosis/genetics ; Program Development ; Radiobiology/*methods/trends ; Research/trends ; Research Design ; Risk Assessment ; },
abstract = {Purpose: Projects evaluating the effects of radiation, within the National Institutes of Quantum and Radiological Science and Technology (QST), National Institute of Radiological Sciences (NIRS), have focused on risk analyses for life shortening and cancer prevalence using laboratory animals. Genetic and epigenetic alterations in radiation-induced tumors have been also analyzed with the aim of better understanding mechanisms of radiation carcinogenesis. As well as the economic and practical limitations of repeating such large-scale experiments, ethical considerations make it vital that we store and share the pathological data and samples of the animal experiments for future use. We are now constructing such an archive called the Japan-Storehouse of Animal Radiobiology Experiments (J-SHARE). Methods: J-SHARE records include information such as detailed experimental protocols, necropsy records and photographs of organs at necropsy. For each animal organs and tumor tissues are dissected, and parts are stored as frozen samples at -80 °C. Samples fixed with formalin are also embedded in paraffin blocks for histopathological analyses. Digital copies of stained tissues are being systematically saved using a virtual slide system linked to original records by barcodes. Embedded and frozen tissues are available for molecular analysis. Conclusion: Similar archive systems for radiation biology have also been under construction in the USA and Europe, the Northwestern University Radiation Archive (NURA), and STORE at the BfS, respectively. The J-SHARE will be linked with the sister-archives and made available for collaborative research to institutions and universities all over the world.},
}
@article {pmid31142396,
year = {2019},
author = {Selbach, C and Jorge, F and Dowle, E and Bennett, J and Chai, X and Doherty, JF and Eriksson, A and Filion, A and Hay, E and Herbison, R and Lindner, J and Park, E and Presswell, B and Ruehle, B and Sobrinho, PM and Wainwright, E and Poulin, R},
title = {Parasitological research in the molecular age.},
journal = {Parasitology},
volume = {146},
number = {11},
pages = {1361-1370},
doi = {10.1017/S0031182019000726},
pmid = {31142396},
issn = {1469-8161},
mesh = {Genetic Techniques/*instrumentation ; Molecular Biology/instrumentation/*methods ; Parasitology/instrumentation/*methods ; },
abstract = {New technological methods, such as rapidly developing molecular approaches, often provide new tools for scientific advances. However, these new tools are often not utilized equally across different research areas, possibly leading to disparities in progress between these areas. Here, we use empirical evidence from the scientific literature to test for potential discrepancies in the use of genetic tools to study parasitic vs non-parasitic organisms across three distinguishable molecular periods, the allozyme, nucleotide and genomics periods. Publications on parasites constitute only a fraction (<5%) of the total research output across all molecular periods and are dominated by medically relevant parasites (especially protists), particularly during the early phase of each period. Our analysis suggests an increasing complexity of topics and research questions being addressed with the development of more sophisticated molecular tools, with the research focus between the periods shifting from predominantly species discovery to broader theory-focused questions. We conclude that both new and older molecular methods offer powerful tools for research on parasites, including their diverse roles in ecosystems and their relevance as human pathogens. While older methods, such as barcoding approaches, will continue to feature in the molecular toolbox of parasitologists for years to come, we encourage parasitologists to be more responsive to new approaches that provide the tools to address broader questions.},
}
@article {pmid31141395,
year = {2019},
author = {Nooh, MM and Kale, A and Bahouth, SW},
title = {Involvement of PDZ-SAP97 interactions in regulating AQP2 translocation in response to vasopressin in LLC-PK1 cells.},
journal = {American journal of physiology. Renal physiology},
volume = {317},
number = {2},
pages = {F375-F387},
pmid = {31141395},
issn = {1522-1466},
support = {R01 HL085848/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Aquaporin 2/genetics/*metabolism ; Arginine Vasopressin/*pharmacology ; Cyclic AMP-Dependent Protein Kinases/metabolism ; Discs Large Homolog 1 Protein/genetics/*metabolism ; Epithelial Cells/*drug effects/metabolism ; Kidney Tubules, Proximal/*drug effects/metabolism ; LLC-PK1 Cells ; *PDZ Domains ; Phosphorylation ; Protein Binding ; Protein Processing, Post-Translational ; Protein Transport ; Serine ; Swine ; },
abstract = {Arginine-vasopressin (AVP)-mediated translocation of aquaporin-2 (AQP2) protein-forming water channels from storage vesicles to the membrane of renal collecting ducts is critical for the renal conservation of water. The type-1 PDZ-binding motif (PBM) in AQP2, "GTKA," is a critical barcode for its translocation, but its precise role and that of its interacting protein partners in this process remain obscure. We determined that synapse-associated protein-97 (SAP97), a membrane-associated guanylate kinase protein involved in establishing epithelial cell polarity, was an avid binding partner to the PBM of AQP2. The role of PBM and SAP97 on AQP2 redistribution in response to AVP was assessed in LLC-PK1 renal collecting cells by confocal microscopy and cell surface biotinylation techniques. These experiments indicated that distribution of AQP2 and SAP97 overlapped in the kidneys and LLC-PK1 cells and that knockdown of SAP97 inhibited the translocation of AQP2 in response to AVP. Binding between AQP2 and SAP97 was mediated by specific interactions between the second PDZ of SAP97 and PBM of AQP2. Mechanistically, inactivation of the PBM of AQP2, global delocalization of PKA, or knockdown of SAP97 inhibited AQP2 translocation as well as AVP- and forskolin-mediated phosphorylation of Ser[256] in AQP2, which serves as the major translocation barcode of AQP2. These results suggest that the targeting of PKA to the microdomain of AQP2 via SAP97-AQP2 interactions in association with cross-talk between two barcodes in AQP2, namely, the PBM and phospho-Ser[256], plays an important role in the translocation of AQP2 in the kidney.},
}
@article {pmid31139202,
year = {2019},
author = {Kreuzer, M and Howard, C and Adhikari, B and Pendry, CA and Hawkins, JA},
title = {Phylogenomic Approaches to DNA Barcoding of Herbal Medicines: Developing Clade-Specific Diagnostic Characters for Berberis.},
journal = {Frontiers in plant science},
volume = {10},
number = {},
pages = {586},
pmid = {31139202},
issn = {1664-462X},
abstract = {DNA barcoding of herbal medicines has been mainly concerned with authentication of products in trade and has raised awareness of species substitution and adulteration. More recently DNA barcodes have been included in pharmacopoeias, providing tools for regulatory purposes. The commonly used DNA barcoding regions in plants often fail to resolve identification to species level. This can be especially challenging in evolutionarily complex groups where incipient or reticulate speciation is ongoing. In this study, we take a phylogenomic approach, analyzing whole plastid sequences from the evolutionarily complex genus Berberis in order to develop DNA barcodes for the medicinally important species Berberis aristata. The phylogeny reconstructed from an alignment of ∼160 kbp of chloroplast DNA for 57 species reveals that the pharmacopoeial species in question is polyphyletic, complicating development of a species-specific DNA barcode. Instead we propose a DNA barcode that is clade specific, using our phylogeny to define Operational Phylogenetic Units (OPUs). The plastid alignment is then reduced to small, informative DNA regions including nucleotides diagnostic for these OPUs. These DNA barcodes were tested on commercial samples, and shown to discriminate plants in trade and therefore to meet the requirement of a pharmacopoeial standard. The proposed method provides an innovative approach for inferring DNA barcodes for evolutionarily complex groups for regulatory purposes and quality control.},
}
@article {pmid31138324,
year = {2019},
author = {Binetruy, F and Dupraz, M and Buysse, M and Duron, O},
title = {Surface sterilization methods impact measures of internal microbial diversity in ticks.},
journal = {Parasites &amp; vectors},
volume = {12},
number = {1},
pages = {268},
pmid = {31138324},
issn = {1756-3305},
mesh = {Animals ; Bacteria/classification/*isolation &amp; purification ; Biodiversity ; DNA Barcoding, Taxonomic ; Disinfectants/*pharmacology ; Ethanol/pharmacology ; Female ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Sodium Hypochlorite/pharmacology ; Specimen Handling/*methods ; Symbiosis ; Ticks/*microbiology ; },
abstract = {BACKGROUND: Ticks are obligate blood feeders transmitting major pathogens worldwide. Over the past few years, considerable research efforts have focused on the diversity, distribution and impact of gut and intracellular bacterial symbionts on tick development and tick-borne pathogen transmission. The study of this internal microbiome requires the use of a sterilization method to remove external (i.e. cuticular) microbes present on the tick's surface and to avoid any further contamination. Several sterilization methods exist, including ethanol- or bleach-based treatments that are both effective in killing microbes but with different potential effects on DNA denaturation.<br><br>METHODS: We examined how these different sterilization methods impact the measure of internal microbial diversity hosted by the Cayenne tick Amblyomma cajennense (sensu stricto). Bacterial barcoding investigations based on 16S rRNA gene sequences were conducted on two batches of 50 individuals each: Ticks of the first batch were sterilized with bleach diluted at 1% and the second batch with 70% ethanol. Tick external microbiome was also determined from cuticle smearing and water samples used for tick washing.<br><br>RESULTS: Bacterial barcoding investigations showed major differences between ethanol- and bleach-treated specimens. Both methods led to the detection of major intracellular bacteria associated with A. cajennense (s.s.) but ethanol-treated ticks always harbored a higher bacterial diversity than bleach-treated ticks. Further examinations of tick gut and tick external microbiome revealed that ethanol-based surface sterilization method is inefficient to eliminate the DNA of external bacteria.<br><br>CONCLUSIONS: We herein provide evidence that studies investigating the internal microbiome of ticks should consider bleach as the gold standard to efficiently remove cuticular bacterial DNA. Indeed, this method does not impact the internal bacterial diversity hosted by ticks and is thus a better method than the ethanol-based one for studying the internal microbiome.},
}
@article {pmid31136619,
year = {2019},
author = {Gesto-Borroto, R and Cardoso-Taketa, A and Yactayo-Chang, JP and Medina-Jiménez, K and Hornung-Leoni, C and Lorence, A and Villarreal, ML},
title = {DNA barcoding and TLC as tools to properly identify natural populations of the Mexican medicinal species Galphimia glauca Cav.},
journal = {PloS one},
volume = {14},
number = {5},
pages = {e0217313},
pmid = {31136619},
issn = {1932-6203},
mesh = {Animals ; Anti-Anxiety Agents/isolation &amp; purification ; Base Sequence ; Chromatography, Thin Layer ; DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Galphimia/chemistry/*classification/genetics ; Genes, Plant ; Humans ; Hypnotics and Sedatives/isolation &amp; purification ; Mexico ; Mice ; Phylogeny ; Plants, Medicinal/chemistry/*classification/genetics ; Species Specificity ; },
abstract = {Galphimia glauca is a plant that is endemic to Mexico and has been commonly used since pre-Hispanic times to treat various illnesses, including central nervous system disorders and inflammation. The first studies investigating a natural population of G. glauca in Mexico showed that the plant has anxiolytic and sedative activities in mice and humans. The plant's bioactive compounds were isolated and identified, and they belong to a family of nor-secofriedelanes called galphimines. The integration of DNA barcoding and thin-layer chromatography analysis was performed to clarify whether the botanical classification of the populations in the study, which were collected in different regions of Mexico, as G. glauca was correct or if the populations consist of more than one species of the genus Galphimia. We employed six DNA barcodes (matK, rbcL, rpoC1, psbA-trnH, ITS1 and ITS2) that were analyzed individually and in combination and then compared each other, to indicate differences among the studied populations. In the phylogenetic analysis, ITS1 and ITS2 markers as well as the combination of all DNA regions were the most efficient for discriminating the population studied. The thin-layer chromatography analysis exhibited four principal chemical profiles, one of which corresponded to the populations that produced galphimines. DNA barcoding was consistent and enabled us to differentiate the populations that produce galphimines from those that do not. The results of this investigation suggest that the studied populations belong to at least four different species of the genus Galphimia. The phylogenetic analysis and the thin-layer chromatography chemical profiles were convenient tools for establishing a strong relationship between the genotype and phenotype of the studied populations and could be used for quality control purposes to prepare herbal medicines from plants of the genus Galphimia.},
}
@article {pmid31136587,
year = {2019},
author = {Zakeri, Z and Otte, V and Sipman, H and Malíček, J and Cubas, P and Rico, VJ and Lenzová, V and Svoboda, D and Divakar, PK},
title = {Discovering cryptic species in the Aspiciliella intermutans complex (Megasporaceae, Ascomycota) - First results using gene concatenation and coalescent-based species tree approaches.},
journal = {PloS one},
volume = {14},
number = {5},
pages = {e0216675},
pmid = {31136587},
issn = {1932-6203},
mesh = {Ascomycota/*classification/*genetics ; Cell Nucleus/genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Fungal/genetics ; Lichens/classification/*genetics ; Mediterranean Region ; Phenotype ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Taxonomic identifications in some groups of lichen-forming fungi have been challenge largely due to the scarcity of taxonomically relevant features and limitations of morphological and chemical characters traditionally used to distinguish closely related taxa. Delineating species boundaries in closely related species or species complexes often requires a range of multisource data sets and comprehensive analytical methods. Here we aim to examine species boundaries in a group of saxicolous lichen forming fungi, the Aspiciliella intermutans complex (Megasporaceae), widespread mainly in the Mediterranean. We gathered DNA sequences of the nuclear ribosomal internal transcribed spacer (nuITS), the nuclear large subunit (nuLSU), the mitochondrial small subunit (mtSSU) ribosomal DNA, and the DNA replication licensing factor MCM7 from 80 samples mostly from Iran, Caucasia, Greece and eastern Europe. We used a combination of phylogenetic strategies and a variety of empirical, sequence-based species delimitation approaches to infer species boundaries in this group. The latter included: the automatic barcode gap discovery (ABGD), the multispecies coalescent approach *BEAST and Bayesian Phylogenetics and Phylogeography (BPP) program. Different species delimitation scenarios were compared using Bayes factors species delimitation analysis. Furthermore, morphological, chemical, ecological and geographical features of the sampled specimens were examined. Our study uncovered cryptic species diversity in A. intermutans and showed that morphology-based taxonomy may be unreliable, underestimating species diversity in this group of lichens. We identified a total of six species-level lineages in the A. intermutans complex using inferences from multiple empirical operational criteria. We found little corroboration between morphological and ecological features with our proposed candidate species, while secondary metabolite data do not corroborate tree topology. The present study on the A. intermutans species-complex indicates that the genus Aspiciliella, as currently circumscribed, is more diverse in Eurasia than previously expected.},
}
@article {pmid31133998,
year = {2019},
author = {Zhang, R and Neu, TR and Li, Q and Blanchard, V and Zhang, Y and Schippers, A and Sand, W},
title = {Insight Into Interactions of Thermoacidophilic Archaea With Elemental Sulfur: Biofilm Dynamics and EPS Analysis.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {896},
pmid = {31133998},
issn = {1664-302X},
abstract = {Biooxidation of reduced inorganic sulfur compounds (RISCs) by thermoacidophiles is of particular interest for the biomining industry and for environmental issues, e.g., formation of acid mine drainage (AMD). Up to now, interfacial interactions of acidophiles with elemental sulfur as well as the mechanisms of sulfur oxidation by acidophiles, especially thermoacidophiles, are not yet fully clear. This work focused on how a crenarchaeal isolate Acidianus sp. DSM 29099 interacts with elemental sulfur. Analysis by Confocal laser scanning microscopy (CLSM) and Atomic force microscopy (AFM) in combination with Epifluorescence microscopy (EFM) shows that biofilms on elemental sulfur are characterized by single colonies and a monolayer in first stage and later on 3-D structures with a diameter of up to 100 μm. The analysis of extracellular polymeric substances (EPS) by a non-destructive lectin approach (fluorescence lectin-barcoding analysis) using several fluorochromes shows that intial attachment was featured by footprints rich in biofilm cells that were embedded in an EPS matrix consisting of various glycoconjugates. Wet chemistry data indicate that carbohydrates, proteins, lipids and uronic acids are the main components. Attenuated reflectance (ATR)-Fourier transformation infrared spectroscopy (FTIR) and high-performance anion exchange chromatography with pulsed amperometric detection (HPAE-PAD) indicate glucose and mannose as the main monosaccharides in EPS polysaccharides. EPS composition as well as sugar types in EPS vary according to substrate (sulfur or tetrathionate) and lifestyle (biofilms and planktonic cells). This study provides information on the building blocks/make up as well as dynamics of biofilms of thermoacidophilic archaea in extremely acidic environments.},
}
@article {pmid31132072,
year = {2019},
author = {Shaw, JA and Bourret, TJ},
title = {Digital PCR-based Competitive Index for High-throughput Analysis of Fitness in Salmonella.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {147},
pages = {},
doi = {10.3791/59630},
pmid = {31132072},
issn = {1940-087X},
mesh = {Bacteriological Techniques ; Chromosomes, Bacterial ; Genetic Fitness ; Genetic Markers ; Polymerase Chain Reaction/*methods ; Salmonella/genetics/*physiology ; },
abstract = {A competitive index is a common method used to assess bacterial fitness and/or virulence. The utility of this approach is exemplified by its ease to perform and its ability to standardize the fitness of many strains to a wild-type organism. The technique is limited, however, by available phenotypic markers and the number of strains that can be assessed simultaneously, creating the need for a great number of replicate experiments. Concurrent with large numbers of experiments, the labor and material costs for quantifying bacteria based on phenotypic markers are not insignificant. To overcome these negative aspects while retaining the positive aspects, we have developed a molecular-based approach to directly quantify microorganisms after engineering genetic markers onto bacterial chromosomes. Unique, 25 base pair DNA barcodes were inserted at an innocuous locus on the chromosome of wild-type and mutant strains of Salmonella. In vitro competition experiments were performed using inocula consisting of pooled strains. Following the competition, the absolute numbers of each strain were quantified using digital PCR and the competitive indices for each strain were calculated from those values. Our data indicate that this approach to quantifying Salmonella is extremely sensitive, accurate, and precise for detecting both highly abundant (high fitness) and rare (low fitness) microorganisms. Additionally, this technique is easily adaptable to nearly any organism with chromosomes capable of modification, as well as to various experimental designs that require absolute quantification of microorganisms.},
}
@article {pmid31132040,
year = {2019},
author = {Fernandez, J and Torchia, EC},
title = {Isolation and Staining of Mouse Skin Keratinocytes for Cell Cycle Specific Analysis of Cellular Protein Expression by Mass Cytometry.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {147},
pages = {},
doi = {10.3791/59353},
pmid = {31132040},
issn = {1940-087X},
support = {P30 AR057212/AR/NIAMS NIH HHS/United States ; P30 CA046934/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Animals, Newborn ; *Cell Cycle ; Cell Separation/*methods ; Cell Survival ; Cells, Cultured ; Ear/anatomy &amp; histology ; Epidermal Cells/cytology ; Flow Cytometry/*methods ; Humans ; Keratinocytes/*cytology ; Mice, Inbred C57BL ; Skin/*cytology ; *Staining and Labeling ; Stem Cells/cytology ; },
abstract = {The goal of this protocol is to detect and quantify protein expression changes in a cell cycle-dependent manner using single cells isolated from the epidermis of mouse skin. There are seven important steps: separation of the epidermis from the dermis, digestion of the epidermis, staining of the epidermal cell populations with cisplatin, sample barcoding, staining with metal tagged antibodies for cell cycle markers and proteins of interest, detection of metal-tagged antibodies by mass cytometry, and the analysis of expression in the various cell cycle phases. The advantage of this approach over histological methods is the potential to assay the expression pattern of >40 different markers in a single cell at different phases of the cell cycle. This approach also allows for the multivariate correlation analysis of protein expression that is more quantifiable than histological/imaging methods. The disadvantage of this protocol is that a suspension of single cells is needed, which results in the loss of location information provided by the staining of tissue sections. This approach may also require the inclusion of additional markers to identify different cell types in crude cell suspensions. The application of this protocol is evident in the analysis of hyperplastic skin disease models. Moreover, this protocol can be adapted for the analysis of specific sub-type of cells (e.g., stem cells) by the addition of lineage-specific antibodies. This protocol can also be adapted for the analysis of skin cells in other experimental species.},
}
@article {pmid31129764,
year = {2019},
author = {Druciarek, T and Lewandowski, M and Tzanetakis, I},
title = {A new, sensitive and efficient method for taxonomic placement in the Eriophyoidea and virus detection in individual eriophyoids.},
journal = {Experimental &amp; applied acarology},
volume = {78},
number = {2},
pages = {247-261},
pmid = {31129764},
issn = {1572-9702},
support = {1002361//Hatch project/ ; USDA/APHIS/PPQ/14-8130-0404-CA//USDA-APHIS/ ; },
mesh = {Animals ; Arboviruses/*isolation &amp; purification ; Arthropod Vectors/anatomy &amp; histology/*classification/*virology ; Classification/*methods ; Female ; Mites/anatomy &amp; histology/*classification/*virology ; Reverse Transcriptase Polymerase Chain Reaction/methods/*veterinary ; Sensitivity and Specificity ; },
abstract = {Eriophyoids affect crops around the globe directly or indirectly as virus vectors. Eriophyoid systematics initiated over a century ago, yet more than 90% of their fauna remain undescribed. Morphological identification is challenging because of a limited number of traits, cryptic speciation and complex life cycle reported for many species in the group. Nucleic acids extraction for mite identification is challenging due to their microscopic size with researchers using pooled samples leading to polymorphisms and inconclusive results. Identification of mite virus vectors is a tiresome task that could be simplified with a protocol that allows for the detection of viruses in the individual specimen. This communication describes an innovative, highly efficient extraction and detection pipeline. Direct Reverse Transcriptase - Polymerase Chain Reaction (Drt-PCR) assays were implemented in the molecular identification of eriophyoids and detection of viruses present in their bodies. The reverse transcription step allows for amplification from a single mite or egg, as in addition to the genomic DNA, it incorporates the abundant transcripts of targeted genes, whereas it also allows for the amplification of viruses. This communication provides an efficient, sensitive and cost-effective alternative that can be implemented in pest identification and detection as well as biological and ecological studies.},
}
@article {pmid31124368,
year = {2019},
author = {Dey, P and Thurecht, KJ and Fredericks, PM and Blakey, I},
title = {Tagged Core-Satellite Nanoassemblies: Role of Assembling Sequence on Surface-Enhanced Raman Scattering (SERS) Performance.},
journal = {Applied spectroscopy},
volume = {73},
number = {12},
pages = {1428-1435},
doi = {10.1177/0003702819856666},
pmid = {31124368},
issn = {1943-3530},
abstract = {Plasmonic nanoassemblies with amplified optical responses are attractive as chemo/bio sensors and diagnostic tracking agents. For real-life implementation, such nanostructures require a well-designed and controlled formation for maximizing the optical amplification. Forming these nanoassemblies typically requires numerous steps; however, the importance of the sequence of the steps is typically not discussed. Thus, here we have investigated the role of the sequence of tagging (or labeling, barcoding) of such plasmonic nanoassemblies with Raman active molecules in a quest to maximize the surface-enhanced Raman scattering (SERS) enhancement that could be achieved from the nanoassemblies. We have chosen the core-satellite nanoassembly arrangement to study the role of tagging sequence because it allows us to keep structural parameters constant that would otherwise influence the SERS amplification. We demonstrate that incorporating the tag molecule at an assembly point before formation of the nanojunctions leads to more tag molecules being positioned at the core-satellite nanojunctions, thereby resulting in higher SERS signal enhancement. This will thus prove to be a useful tool in fully utilizing the nanoassembly morphology generated hot-spot and maximizing its SERS performance.},
}
@article {pmid31124243,
year = {2019},
author = {Muja-Bajraktari, N and Zhushi-Etemi, F and Dikolli-Velo, E and Kadriaj, P and Gunay, F},
title = {The composition, diversity, and distribution of mosquito fauna (Diptera: Culicidae) in Kosovo.},
journal = {Journal of vector ecology : journal of the Society for Vector Ecology},
volume = {44},
number = {1},
pages = {94-104},
doi = {10.1111/jvec.12333},
pmid = {31124243},
issn = {1948-7134},
mesh = {*Animal Distribution ; Animals ; *Biodiversity ; Culicidae/*classification/*physiology ; Kosovo ; Species Specificity ; },
abstract = {The aim of this study is to identify the mosquito species that currently exist and their distributions in Kosovo in order to determine current potential endemic zones and areas at a higher risk for future epidemics. These scientific data will be shared with public health authorities for implementing mosquito control programs. During a two-year period of monitoring in 48 localities in 23 provinces in Kosovo, a total of 1,604 mosquitoes representing 13 species and six genera were collected and morphologically identified. Members of species complexes were also classified to species using DNA barcoding. In total, 13 species were identified with Culex pipiens s.l., the predominant species with an abundance rate of 39%. The remaining 12 species identified were grouped into five genera: Anopheles, Aedes, Coquillettidia, Culiseta, Uranotaenia, including species that are vectors of arboviruses in other parts of the world.},
}
@article {pmid31124228,
year = {2019},
author = {Motoki, MT and Vongphayloth, K and Rueda, LM and Miot, EF and Hiscox, A and Hertz, JC and Brey, PT},
title = {New records and updated checklist of mosquitoes (Diptera: Culicidae) from Lao People's Democratic Republic, with special emphasis on adult and larval surveillance in Khammuane Province.},
journal = {Journal of vector ecology : journal of the Society for Vector Ecology},
volume = {44},
number = {1},
pages = {76-88},
doi = {10.1111/jvec.12331},
pmid = {31124228},
issn = {1948-7134},
mesh = {Animal Distribution ; Animals ; Culicidae/*classification/genetics ; Laos ; Larva/classification ; Phylogeny ; Species Specificity ; },
abstract = {A list of mosquitoes from the Nakai Nam Theun National Protected Area along the Nam Theun, Nam Mon, Nam Noy, and Nam On rivers, Nakai District, Khammuane Province, Lao People's Democratic Republic (Lao PDR) is presented. Fifty-four mosquito taxa were identified, including 15 new records in the Lao PDR. A fragment of the mtDNA cytochrome c oxidase subunit I (COI) gene, barcode region, was generated for 34 specimens, and together with four specimens already published, it represented 23 species in eight genera. In addition, an updated checklist of 170 mosquito taxa from Lao PDR is provided based on field collections from Khammuane Province, the literature, and specimens deposited in the Smithsonian Institution, National Museum of Natural History (SI-NMNH), Washington, DC, U.S.A. This paper provides additional information about the biodiversity of mosquito fauna in Lao PDR.},
}
@article {pmid31123639,
year = {2019},
author = {Wang, F and Wang, D and Guo, G and Hu, Y and Wei, J and Liu, J},
title = {Species delimitation of the Dermacentor ticks based on phylogenetic clustering and niche modeling.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6911},
pmid = {31123639},
issn = {2167-8359},
abstract = {Three species belonging to the genus Dermacentor (Acari: Ixodidae), D. marginatus, D. nuttalli and D. silvarum are well known as vectors for a great variety of infection pathogens. All three of them are host ticks, which are very similar in morphology characteristics, life cycle, seasonal variation and ecological conditions, making it difficult to distinguish the three species. In the present study, these three species were delimitated based on molecular data and ecological niche. The molecular analysis showed that the three species can be distinguished by COI and ITS2 sequences. We created future potential distribution maps for the three species under climate changes with MaxEnt, which highlighted the different levels of the suitable habitats for each tick species. In addition, niche comparisons among the three species in Dermacentor were conducted, and the analysis suggested that niche overlap was relatively high with D. nuttalli and D. silvarum compared to the other species pairs, which was consistent with the molecular data. Niche equivalency and similarity test confirmed that these Dermacentor species were closely related but distinct species. In conclusion, delimitation of these three species within Dermacentor was supported by molecular phylogeny and quantitative ecological space. This study will provide deep insights into the biology, ecology, and diversification processes within Dermacentor species, and for the development of effective control for ticks.},
}
@article {pmid31122184,
year = {2019},
author = {Ceballos-Garzón, A and Cortes, G and Morio, F and Zamora-Cruz, EL and Linares, MY and Ariza, BE and Valderrama, SL and Garzón, JR and Alvarez-Moreno, CA and Le Pape, P and Parra-Giraldo, CM},
title = {Comparison between MALDI-TOF MS and MicroScan in the identification of emerging and multidrug resistant yeasts in a fourth-level hospital in Bogotá, Colombia.},
journal = {BMC microbiology},
volume = {19},
number = {1},
pages = {106},
pmid = {31122184},
issn = {1471-2180},
mesh = {Antifungal Agents/pharmacology ; Colombia ; DNA, Fungal/genetics ; DNA, Ribosomal/*genetics ; *Drug Resistance, Multiple, Fungal ; Humans ; Microbial Sensitivity Tests ; Mycoses/*microbiology ; Phylogeny ; Sequence Analysis, DNA ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Tertiary Healthcare ; Yeasts/classification/drug effects/genetics/*isolation &amp; purification ; },
abstract = {BACKGROUND: The introduction of MALDI-TOF MS in the clinical microbiology laboratory has modified the approaches for the identification of fungi. Thanks to this tool, it is possible to identify cryptic species, which possess critical susceptibility patterns. Clinical strains were identified using the MicroScan and MALDI-TOF MS systems. Discrepant results from both methods were investigated using ITS rDNA barcoding. Finally, these isolates were also tested for in vitro susceptibility.<br><br>RESULTS: The percentage of agreement between both methods to 498 yeast isolates was of 93.6% (32 discrepant isolates). The concordance of ITS sequencing with MALDI-TOF MS was higher (99%) than that of MicroScan (94%). Several of these discordant yeasts displayed high MICs for antifungal agents.<br><br>CONCLUSIONS: Our study highlights the need of the MS and molecular approaches such as MALDI-TOF MS and ITS rDNA barcoding for the correct identification of emerging or cryptic yeast species; besides, some of these could be multidrug resistant. This work was the first experience in the implementation of the MALDI-TOF MS technology in Colombia. We found the first uncommon yeasts including Candida auris and we could identify Trichosporon faecalis. Our work highlights a clear necessity of an accurate yeast identification as a much more pertinent technique than the susceptibility profiles, because the most unusual yeasts exhibit resistance profiles to the few available antifungals.},
}
@article {pmid31121984,
year = {2019},
author = {Jiang, W and Ren, L and Guo, M and Mantri, N and Zhao, S and Pang, X},
title = {Detecting Schisandrae Chinensis Fructus and Its Chinese Patent Medicines with a Nucleotide Signature.},
journal = {Genes},
volume = {10},
number = {5},
pages = {},
pmid = {31121984},
issn = {2073-4425},
mesh = {Chromatography, High Pressure Liquid ; *DNA Barcoding, Taxonomic ; DNA, Intergenic/*genetics ; Drug Contamination ; Drugs, Chinese Herbal/chemistry/therapeutic use ; Fruit/chemistry ; Humans ; *Medicine, Chinese Traditional ; Nonprescription Drugs ; Nucleotide Motifs/genetics ; Schisandra/chemistry/*genetics ; },
abstract = {Schisandrae Chinensis Fructus (Wuweizi) is often adulterated with Schisandrae Sphenantherae Fructus (Nanwuweizi) in the herbal market. This adulteration is a threat to clinical treatment and safety. In this study, we aimed to develop a nucleotide signature for the identification of Wuweizi and its Chinese patent medicines based on the mini-DNA barcoding technique. We collected 49 samples to obtain internal transcribed spacer 2 (ITS2) sequences and developed a 26-bp nucleotide signature (5'-CGCTTTGCGACGCTCCCCTCCCTCCC-3') on the basis of a single nucleotide polymorphism (SNP) site within the ITS2 region that is unique to Wuweizi. Then, using the nucleotide signature, we investigated 27 batches of commercial crude drug samples labeled as Wuweizi and eight batches of Chinese patent medicines containing Wuweizi. Results showed that eight commercial crude drug samples were adulterants and one of the Chinese patent medicines contained adulterants. The nucleotide signature can serve as an effective tool for identifying Wuweizi and its Chinese patent medicines and can thus be used to ensure clinical drug safety.},
}
@article {pmid31121918,
year = {2019},
author = {Xu, Y and Zhang, S and Wang, H and Wang, M and Li, G},
title = {Mitochondrial Gene Sequence (COI) Reveals the Genetic Structure and Demographic History of Lymantria dispar (Lepidoptera: Erebidae: Lymantriinae) in and around China.},
journal = {Insects},
volume = {10},
number = {5},
pages = {},
pmid = {31121918},
issn = {2075-4450},
support = {CAFYBB2017ZE002//Chinese Academy of Forestry/ ; },
abstract = {The gypsy moth, Lymantria dispar, is among the most destructive quarantine pests of forests. Here, we reconstructed the genetic structure and determined the population differentiation of gypsy moths across its distribution range at different times. This information could be used to both improve the prevention and detection of gypsy moths in the field. Using 31 newly designed species-specific primers targeting fragments of 216-1102 bp, we identified 103 full-length cytochrome oxidase subunit I (COI) gene sequences from eight fresh samples and 95 L. dispar specimens collected between 1955 and 1996, mainly in China. Combining 103 full-length COI gene sequences with 146 COI gene sequences from Genbank or DNA barcode libraries, we analyzed the genetic differentiation, gene flow and haplotypes between gypsy moth populations in order to reflect the genetic structure and population dynamics of gypsy moths. We discovered 25 previously unknown haplotypes from old gypsy moth specimens. We found that the genetic diversity among gypsy moth populations (collected in the same region at different time points) was relatively high. Furthermore, the genetic structure of Chinese geographical populations (Heilongjiang, Liaoning, Beijing) in different years was distinct. Our results suggested that some gypsy moths in China showed the genetic affinity with European gypsy moths (a sub-species of gypsy moths found mainly in Europe).},
}
@article {pmid31120564,
year = {2019},
author = {Wu, Y and Yang, Y and Liu, M and Wang, B and Wang, Y and Wang, H},
title = {Applying COI Barcode to Identify Animal Origin of Food.},
journal = {Journal of food science},
volume = {84},
number = {6},
pages = {1256-1265},
doi = {10.1111/1750-3841.14627},
pmid = {31120564},
issn = {1750-3841},
support = {2016YFD0401203//Chinese Academy of Inspection and Quarantine (CAIQ) project/ ; 2018JK030//The National Key Research and Development Program of China/ ; },
mesh = {Amino Acid Sequence ; Animals ; DNA Barcoding, Taxonomic/*methods ; Discriminant Analysis ; Electron Transport Complex IV/*genetics ; Fishes/*genetics ; Food Contamination/*analysis ; Mammals/*genetics ; Meat/*analysis ; Poultry/*genetics ; Sequence Alignment ; },
abstract = {DNA barcoding possesses advantages of high resolution, high sensitivity, and capability in capturing as much identity information as possible. However, highly varying sources of food materials and a complicated supply chain bring about challenge to the application of barcoding methods. In this study, different barcode systems were compared to establish a robust method for tracing animal species in food. Experiments on food samples from mammal, poultry, and fish proved that a mini barcode system targeting a 192 bp COI gene fragment was able to accurately identify both raw and highly processed animal food. In order to distinguish species in a mixed food sample, cloning technique was used by which as low as 10% target animal ingredient could be detected. Testing of marketed food products verified the capability of the mini barcoding method in identifying illegally claimed product.},
}
@article {pmid31119972,
year = {2019},
author = {Nakagawa, T and Doi, M and Nishi, K and Sugahara, T and Nishimukai, H and Asano, M},
title = {A simple and versatile authenticity assay of coffee products by single-nucleotide polymorphism genotyping.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {83},
number = {10},
pages = {1829-1836},
doi = {10.1080/09168451.2019.1618697},
pmid = {31119972},
issn = {1347-6947},
mesh = {Coffea/classification/*genetics ; *Genotype ; *Polymorphism, Single Nucleotide ; Species Specificity ; },
abstract = {Interspecific single-nucleotide polymorphisms (SNPs) in the rbcL DNA barcode have been strictly validated and adopted as a designed SNP genotyping maker to discriminate between two major coffee species, Coffea arabica and C. canephora, and to estimate the mixing ratio of DNA from C. arabica/C. canephora in this study. The SNP genotyping is applicable to not only green (unroasted) coffee beans, but also processed coffee products (roasted coffee beans and instant coffee powder), in which genomic DNA is degraded, because the genotyping developed in this study requires only 10 copies of 63-bp-long DNA fragments of rbcL gene. The authenticity assay established in this study has several advantages: a high versatility to DNA sample conditions; simple and rapid procedures (only two steps; DNA extraction and SNP genotyping); the feasibility in coffee business for practical use to prevent false advertising and provide quality control. Abbreviations: SNP: single-nucleotide polymorphism; SBS: single base substitution; ISR: intergenic spacer region; INDEL: insertion-deletion.},
}
@article {pmid31118870,
year = {2019},
author = {Ranjith, AP and Fernandez-Triana, J and Veena, T and Priyadarsanan, DR and Nasser, M},
title = {Four new species of Philoplitis Nixon (Braconidae, Microgastrinae) with an updated key and illustrations of all described species.},
journal = {ZooKeys},
volume = {841},
number = {},
pages = {125-150},
pmid = {31118870},
issn = {1313-2989},
abstract = {The Microgastrinae genus Philoplitis Nixon is revised and four new species are described: P.keralensis sp. n. and P.trifoveatus sp. n. authored by Ranjith &amp; Fernandez-Triana, and P.dzangasangha sp. n. and P.margalla sp. n. authored by Fernandez-Triana &amp; Ranjith. A key to all nine known species is provided. Philoplitisadustipalpus Ahmad is redescribed and illustrated. Additional specimen records are presented, and the diagnostic value of some morphological characters previously used is discussed. Based on the very few specimens available for study in collections, Philoplitis seems to be restricted to the Old World tropics (Afrotropical and Oriental regions), with most known species found in the Oriental region. The first DNA barcodes for the genus are presented. No host data is currently available, but for one species a mass of five wasp cocoons was found and is illustrated for the first time.},
}
@article {pmid31116764,
year = {2019},
author = {Ashfaq, M and Blagoev, G and Tahir, HM and Khan, AM and Mukhtar, MK and Akhtar, S and Butt, A and Mansoor, S and Hebert, PDN},
title = {Assembling a DNA barcode reference library for the spiders (Arachnida: Araneae) of Pakistan.},
journal = {PloS one},
volume = {14},
number = {5},
pages = {e0217086},
pmid = {31116764},
issn = {1932-6203},
mesh = {Animals ; Bayes Theorem ; DNA Barcoding, Taxonomic/*methods/*standards ; *Gene Library ; Pakistan ; Phylogeny ; Reference Standards ; Spiders/*classification/*genetics ; },
abstract = {Morphological study of 1,795 spiders from sites across Pakistan placed these specimens in 27 families and 202 putative species. COI sequences >400 bp recovered from 1,782 specimens were analyzed using neighbor-joining trees, Bayesian inference, barcode gap, and Barcode Index Numbers (BINs). Specimens of 109 morphological species were assigned to 123 BINs with ten species showing BIN splits, while 93 interim species included representatives of 98 BINs. Maximum conspecific divergences ranged from 0-5.3% while congeneric distances varied from 2.8-23.2%. Excepting one species pair (Oxyopes azhari-Oxyopes oryzae), the maximum intraspecific distance was always less than the nearest-neighbor (NN) distance. Intraspecific divergence values were not significantly correlated with geographic distance. Most (75%) BINs detected in this study were new to science, while those shared with other nations mainly derived from India. The discovery of many new, potentially endemic species and the low level of BIN overlap with other nations highlight the importance of constructing regional DNA barcode reference libraries.},
}
@article {pmid31115839,
year = {2019},
author = {Gallou, A and Suaste-Dzul, AP and Moreno-Rodríguez, C and Sarmiento-Cordero, MA and Contreras-Bermúdez, Y and Arredondo-Bernal, HC and Palomares-Pérez, M},
title = {Haplotype characterization of Ceraeochrysa cubana (Hagen) and Ceraeochrysa valida (Banks) (Neuroptera: Chrysopidae) from the state of Colima, Mexico.},
journal = {Molecular biology reports},
volume = {46},
number = {4},
pages = {4313-4322},
pmid = {31115839},
issn = {1573-4978},
mesh = {Animals ; Citrus/parasitology ; Electron Transport Complex IV/genetics ; Genetic Variation ; Haplotypes ; Insecta/*genetics ; Larva ; Mexico ; Mitochondria/genetics ; Species Specificity ; },
abstract = {The larvae of Ceraeochrysa cubana and Ceraeochrysa valida, green lacewing species widely spread in Mexico, have been described as natural enemies of Diaphorina citri (Hemiptera: Liviidae), vector of the bacteria Candidatus Liberibacter spp. causing Huanglongbing disease. To develop an effective biological control program, the establishment of the genetic structure of the biocontrol agent species is mandatory. Consequently, the goal of this work was to obtain reliable DNA barcoding regions of the two species, and then by sequence analysis of the mitochondrial gene cytochrome c oxidase subunit I, evaluate the genetic structure of Mexican lime populations of C. cubana and C. valida from the state of Colima. This research produced the first barcode region of C. cubana and C. valida with morphological and molecular confirmation. The genetic parameters revealed the presence of 15 and 10 haplotypes, and haplotype diversity values of 0.889 and 0.838 for C. cubana and C. valida, respectively. The populations showed high diversity and gene flow, and AMOVA analysis demonstrated no genetic structure in the two populations. Consequently, these single populations of C. cubana and C. valida could be used as unique genetic source for mass production and release in the Mexican lime-producing state of Colima to control D. citri.},
}
@article {pmid31114909,
year = {2019},
author = {Molania, R and Gagnon-Bartsch, JA and Dobrovic, A and Speed, TP},
title = {A new normalization for Nanostring nCounter gene expression data.},
journal = {Nucleic acids research},
volume = {47},
number = {12},
pages = {6073-6083},
pmid = {31114909},
issn = {1362-4962},
mesh = {Adenocarcinoma of Lung/genetics/metabolism ; Dendritic Cells/metabolism ; Gene Expression Profiling/*methods ; Humans ; Inflammatory Bowel Diseases/genetics/metabolism ; Lung Neoplasms/genetics/metabolism ; Lymphocyte Activation/genetics ; Single Molecule Imaging ; },
abstract = {The Nanostring nCounter gene expression assay uses molecular barcodes and single molecule imaging to detect and count hundreds of unique transcripts in a single reaction. These counts need to be normalized to adjust for the amount of sample, variations in assay efficiency and other factors. Most users adopt the normalization approach described in the nSolver analysis software, which involves background correction based on the observed values of negative control probes, a within-sample normalization using the observed values of positive control probes and normalization across samples using reference (housekeeping) genes. Here we present a new normalization method, Removing Unwanted Variation-III (RUV-III), which makes vital use of technical replicates and suitable control genes. We also propose an approach using pseudo-replicates when technical replicates are not available. The effectiveness of RUV-III is illustrated on four different datasets. We also offer suggestions on the design and analysis of studies involving this technology.},
}
@article {pmid31113898,
year = {2019},
author = {Di Martino, ML and Ek, V and Hardt, WD and Eriksson, J and Sellin, ME},
title = {Barcoded Consortium Infections Resolve Cell Type-Dependent Salmonella enterica Serovar Typhimurium Entry Mechanisms.},
journal = {mBio},
volume = {10},
number = {3},
pages = {},
pmid = {31113898},
issn = {2150-7511},
mesh = {DNA Barcoding, Taxonomic ; *Endocytosis ; Epithelial Cells/*microbiology ; HeLa Cells ; Humans ; *Microbial Consortia ; Phagocytes/*microbiology ; Salmonella Infections/*physiopathology ; Salmonella typhimurium/*growth &amp; development ; Type III Secretion Systems/metabolism ; U937 Cells ; Virulence Factors/metabolism ; },
abstract = {Bacterial host cell invasion mechanisms depend on the bacterium's virulence factors and the properties of the target cell. The enteropathogen Salmonella enterica serovar Typhimurium (STm) invades epithelial cell types in the gut mucosa and a variety of immune cell types at later infection stages. The molecular mechanism(s) of host cell entry has, however, been studied predominantly in epithelial cell lines. STm uses a type three secretion system (TTSS-1) to translocate effectors into the host cell cytosol, thereby sparking actin ruffle-dependent entry. The ruffles also fuel cooperative invasion by bystander bacteria. In addition, several TTSS-1-independent entry mechanisms exist, involving alternative STm virulence factors, or the passive uptake of bacteria by phagocytosis. However, it remains ill-defined how STm invasion mechanisms vary between host cells. Here, we developed an internally controlled and scalable method to map STm invasion mechanisms across host cell types and conditions. The method relies on host cell infections with consortia of chromosomally tagged wild-type and mutant STm strains, where the abundance of each strain can be quantified by qPCR or amplicon sequencing. Using this methodology, we quantified cooccurring TTSS-1-dependent, cooperative, and TTSS-1-independent invasion events in epithelial, monocyte, and macrophage cells. We found STm invasion of epithelial cells and monocytes to proceed by a similar MOI-dependent mix of TTSS-1-dependent and cooperative mechanisms. TTSS-1-independent entry was more frequent in macrophages. Still, TTSS-1-dependent invasion dominated during the first minutes of interaction also with this cell type. Finally, the combined action of the SopB/SopE/SopE2 effectors was sufficient to explain TTSS-1-dependent invasion across both epithelial and phagocytic cells.IMPORTANCESalmonella enterica serovar Typhimurium (STm) is a widespread and broad-host-spectrum enteropathogen with the capacity to invade diverse cell types. Still, the molecular basis for the host cell invasion process has largely been inferred from studies of a few selected cell lines. Our work resolves the mechanisms that Salmonellae employ to invade prototypical host cell types, i.e., human epithelial, monocyte, and macrophage cells, at a previously unattainable level of temporal and quantitative precision. This highlights efficient bacterium-driven entry into innate immune cells and uncovers a type III secretion system effector module that dominates active bacterial invasion of not only epithelial cells but also monocytes and macrophages. The results are derived from a generalizable method, where we combine barcoding of the bacterial chromosome with mixed consortium infections of cultured host cells. The application of this methodology across bacterial species and infection models will provide a scalable means to address host-pathogen interactions in diverse contexts.},
}
@article {pmid31113529,
year = {2019},
author = {Faller, AC and Ragupathy, S and Shanmughanandhan, D and Zhang, Y and Lu, Z and Chang, P and Swanson, G and Newmaster, SG},
title = {DNA Quality and Quantity Analysis of Camellia sinensis Through Processing from Fresh Leaves to a Green Tea Extract.},
journal = {Journal of AOAC International},
volume = {102},
number = {6},
pages = {1798-1807},
doi = {10.5740/jaoacint.18-0318},
pmid = {31113529},
issn = {1944-7922},
mesh = {Camellia sinensis/*chemistry ; *DNA Damage ; DNA, Plant/*analysis/*genetics ; Food Handling ; Plant Extracts/*analysis ; Plant Leaves/*chemistry ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {Background: Although there has been some success using DNA barcoding to authenticate raw natural health product (NHP) botanical ingredients, there are many gaps in our understanding of DNA degradation, which may explain low PCR and sequencing success in processed NHPs. Objective: In this study, we measured multiple DNA variables after each step in the processing of a green tea extract in order to document DNA quality and quantity. Methods: We sampled plant material after each step of green tea extract processing: five steps at a Chinese tea farm (n = 10) and five at an NHP processing facility (n = 3). We hypothesized that processing treatments degrade and remove DNA from NHPs, reflected by decreasing quantities of extractable genomic DNA (gDNA), an increasing proportion of small DNA fragments in genomic extracts, and decreasing quantitative PCR (QPCR) efficiency [higher cycle threshold (Ct) values]. DNA from end-production green tea extract was sequenced in order to try to validate material as the botanical of interest. Results: We saw a 41.1% decrease in mean extractable gDNA through farm processing (P < 0.01) and a 99.7% decrease through facility processing (P < 0.05). There was a 26.3% decrease in mean DNA fragment size through farm processing (P < 0.001) and an 82.0% decrease through facility processing (P < 0.05). QPCR efficiency was reduced through processing, marked by significant increases in Ct values with 100 base pair (bp) and 200 bp PCR targets (P < 0.05), and an inability to amplify 300 bp targets when using DNA template from end-production green tea extract. Conclusions: Although there was significant degradation and removal of DNA through processing, sufficiently intact DNA was able to be recovered from highly processed green tea extract for further sequencing and identification. Highlights: This work addresses a key gap in the understanding of DNA degradation through processing and provides useful information to consider when designing molecular diagnostic techniques for NHP identification.},
}
@article {pmid31112297,
year = {2019},
author = {Drymon, JM and Feldheim, K and Fournier, AMV and Seubert, EA and Jefferson, AE and Kroetz, AM and Powers, SP},
title = {Tiger sharks eat songbirds: scavenging a windfall of nutrients from the sky.},
journal = {Ecology},
volume = {100},
number = {9},
pages = {e02728},
doi = {10.1002/ecy.2728},
pmid = {31112297},
issn = {1939-9170},
mesh = {Animals ; Nutrients ; Predatory Behavior ; *Sharks ; *Songbirds ; },
}
@article {pmid31110686,
year = {2019},
author = {Liu, J and Liu, J and Shan, YX and Ge, XJ and Burgess, KS},
title = {The use of DNA barcodes to estimate phylogenetic diversity in forest communities of southern China.},
journal = {Ecology and evolution},
volume = {9},
number = {9},
pages = {5372-5379},
pmid = {31110686},
issn = {2045-7758},
abstract = {To elucidate potential ecological and evolutionary processes associated with the assembly of plant communities, there is now widespread use of estimates of phylogenetic diversity that are based on a variety of DNA barcode regions and phylogenetic construction methods. However, relatively few studies consider how estimates of phylogenetic diversity may be influenced by single DNA barcodes incorporated into a sequence matrix (conservative regions vs. hypervariable regions) and the use of a backbone family-level phylogeny. Here, we use general linear mixed-effects models to examine the influence of different combinations of core DNA barcodes (rbcL, matK, ITS, and ITS2) and phylogeny construction methods on a series of estimates of community phylogenetic diversity for two subtropical forest plots in Guangdong, southern China. We ask: (a) What are the relative influences of single DNA barcodes on estimates phylogenetic diversity metrics? and (b) What is the effect of using a backbone family-level phylogeny to estimate topology-based phylogenetic diversity metrics? The combination of more than one barcode (i.e., rbcL + matK + ITS) and the use of a backbone family-level phylogeny provided the most parsimonious explanation of variation in estimates of phylogenetic diversity. The use of a backbone family-level phylogeny showed a stronger effect on phylogenetic diversity metrics that are based on tree topology compared to those that are based on branch lengths. In addition, the variation in the estimates of phylogenetic diversity that was explained by the top-rank models ranged from 0.1% to 31% and was dependent on the type of phylogenetic community structure metric. Our study underscores the importance of incorporating a multilocus DNA barcode and the use of a backbone family-level phylogeny to infer phylogenetic diversity, where the type of DNA barcode employed and the phylogenetic construction method used can serve as a significant source of variation in estimates of phylogenetic community structure.},
}
@article {pmid31110297,
year = {2019},
author = {Pei, W and Wang, X and Rössler, J and Feyerabend, TB and Höfer, T and Rodewald, HR},
title = {Using Cre-recombinase-driven Polylox barcoding for in vivo fate mapping in mice.},
journal = {Nature protocols},
volume = {14},
number = {6},
pages = {1820-1840},
pmid = {31110297},
issn = {1750-2799},
mesh = {Animals ; CRISPR-Cas Systems ; *Cell Lineage ; DNA/genetics/metabolism ; DNA Barcoding, Taxonomic/methods ; Female ; *Genes, Reporter ; Genotyping Techniques/methods ; Integrases/genetics ; Male ; Mice ; Mice, Transgenic ; Polymerase Chain Reaction/methods ; Recombination, Genetic ; Sequence Analysis, DNA/*methods ; },
abstract = {Fate mapping is a powerful genetic tool for linking stem or progenitor cells with their progeny, and hence for defining cell lineages in vivo. The resolution of fate mapping depends on the numbers of distinct markers that are introduced in the beginning into stem or progenitor cells; ideally, numbers should be sufficiently large to allow the tracing of output from individual cells. Highly diverse genetic barcodes can serve this purpose. We recently developed an endogenous genetic barcoding system, termed Polylox. In Polylox, random DNA recombination can be induced by transient activity of Cre recombinase in a 2.1-kb-long artificial recombination substrate that has been introduced into a defined locus in mice (Rosa26[Polylox] reporter mice). Here, we provide a step-by-step protocol for the use of Polylox, including barcode induction and estimation of induction efficiency, barcode retrieval with single-molecule real-time (SMRT) DNA sequencing followed by computational barcode identification, and the calculation of barcode-generation probabilities, which is key for estimations of single-cell labeling for a given number of stem cells. Thus, Polylox barcoding enables high-resolution fate mapping in essentially all tissues in mice for which inducible Cre driver lines are available. Alternative methods include ex vivo cell barcoding, inducible transposon insertion and CRISPR-Cas9-based barcoding; Polylox currently allows combining non-invasive and cell-type-specific labeling with high label diversity. The execution time of this protocol is ~2-3 weeks for experimental data generation and typically <2 d for computational Polylox decoding and downstream analysis.},
}
@article {pmid31109921,
year = {2019},
author = {Sakhanenko, NA and Cromie, GA and Dudley, AM and Galas, DJ},
title = {Computational Inference Software for Tetrad Assembly from Randomly Arrayed Yeast Colonies.},
journal = {G3 (Bethesda, Md.)},
volume = {9},
number = {7},
pages = {2071-2088},
pmid = {31109921},
issn = {2160-1836},
mesh = {Alleles ; Chromosome Segregation ; Computational Biology/*methods ; Gene Expression Regulation, Fungal ; Meiosis ; Recombination, Genetic ; Reproducibility of Results ; *Software ; Spores, Fungal ; Yeasts/*physiology ; },
abstract = {We describe an information-theory-based method and associated software for computationally identifying sister spores derived from the same meiotic tetrad. The method exploits specific DNA sequence features of tetrads that result from meiotic centromere and allele segregation patterns. Because the method uses only the genomic sequence, it alleviates the need for tetrad-specific barcodes or other genetic modifications to the strains. Using this method, strains derived from randomly arrayed spores can be efficiently grouped back into tetrads.},
}
@article {pmid31108801,
year = {2019},
author = {Shehata, HR and Bourque, D and Steinke, D and Chen, S and Hanner, R},
title = {Survey of mislabelling across finfish supply chain reveals mislabelling both outside and within Canada.},
journal = {Food research international (Ottawa, Ont.)},
volume = {121},
number = {},
pages = {723-729},
doi = {10.1016/j.foodres.2018.12.047},
pmid = {31108801},
issn = {1873-7145},
mesh = {Animals ; Consumer Product Safety/legislation &amp; jurisprudence/standards ; Cyclooxygenase 1/genetics/metabolism ; DNA Barcoding, Taxonomic ; Fish Products/*standards ; Fishes/*classification ; Food Labeling/*legislation &amp; jurisprudence/*standards ; Food Supply ; Nutrition Policy ; Ontario ; Sequence Analysis, DNA ; Species Specificity ; Surveys and Questionnaires ; United States ; United States Food and Drug Administration ; },
abstract = {Seafood has become one of the most heavily traded food commodities in the era of globalization. International seafood supply chains are complex and contend with many difficulties in bringing an enormous variety of products to market. A major challenge involves accurately labelling products such that they comply with a diverse set of regulatory frameworks, ranging from country-of-origin through to the final point of consumer sale. Thanks to DNA barcoding, seafood mislabelling is now recognized as a global problem, with potentially negative impacts on human health, economy and the environment. Mislabelling can result from species misidentification, use of inappropriate common names, incomplete and/or out-dated regulatory frameworks, or through market substitution. While prior studies have focused primarily on retail and food service establishments, this study used barcoding to assess rates of finfish mislabelling at multiple points in the supply chain within Ontario, Canada. A total of 203 specimens from 12 key targeted species were collected from varied importers, registered processing plants and retailers in Southern Ontario and identified using DNA barcoding. Species identity of samples was used to assess conformity of labelling against the Canadian Food Inspection Agency's (CFIA) Fish List, which revealed an overall mislabelling rate of 32.3% among targeted species. The mislabelling rate was significantly different between samples collected from importers and retailers. Among the mislabelled samples were seven samples that originated from US and were properly labelled according to US Food and Drug Administration (FDA) Seafood List. This study evaluated the integrity of chain of custody documents and identified discrepancies in 43 samples (21.4%). Implementing seafood traceability throughout the supply chain and harmonizing labelling regulations between countries can help to ensure industry compliance in a globalized market, while sampling at multiple points in the supply chain can help to reveal causes.},
}
@article {pmid31106407,
year = {2019},
author = {Kahlert, M and Kelly, MG and Mann, DG and Rimet, F and Sato, S and Bouchez, A and Keck, F},
title = {Connecting the morphological and molecular species concepts to facilitate species identification within the genus Fragilaria (Bacillariophyta).},
journal = {Journal of phycology},
volume = {55},
number = {4},
pages = {948-970},
doi = {10.1111/jpy.12886},
pmid = {31106407},
issn = {1529-8817},
mesh = {*Diatoms ; Genes, Chloroplast ; Genetic Markers ; Phylogeny ; },
abstract = {This paper explores the diversity and taxonomy of species within Fragilaria sensu stricto, an abundant and ecologically important diatom genus, taking advantage of cultured and DNA-barcoded material. The goal is to facilitate the identification of European taxa within this complex, providing a unified view on morphological and molecular diversity. There is a general agreement that the separation of species within the group of Fragilaria is difficult because morphological descriptions of species are not consistent between authorities, ongoing taxonomic revisions have resulted in species described with standards of the late 20th and 21st centuries alongside descriptions based on 19th century (light microscopical) criteria, and because not all diagnostic characters can be seen in all specimens encountered in routine analyses. Consequent confusion could blur potentially important ecological distinctions between species. Our study demonstrated that some species defined on morphological criteria could be confirmed using the rbcL chloroplast gene as a genetic marker, for example, Fragilaria gracilis, Fragilaria tenera, Fragilaria perminuta, and Fragilaria subconstricta. However, even for those species, preliminary identifications based on morphology often differed from identifications based on phylogenetic clustering combined with detailed morphological study. Clades were well-defined by rbcL, but based on morphology, the terminal taxa of these clades did not match the currently described Fragilaria species. To clarify recognition of these taxa, we describe three new species: Fragilaria agnesiae, Fragilaria heatherae, and Fragilaria joachimii.},
}
@article {pmid31106268,
year = {2019},
author = {Shin, D and Lee, W and Lee, JH and Bang, D},
title = {Multiplexed single-cell RNA-seq via transient barcoding for simultaneous expression profiling of various drug perturbations.},
journal = {Science advances},
volume = {5},
number = {5},
pages = {eaav2249},
pmid = {31106268},
issn = {2375-2548},
mesh = {Algorithms ; Animals ; Cell Line, Tumor ; Cluster Analysis ; *Gene Expression Profiling ; HEK293 Cells ; High-Throughput Nucleotide Sequencing ; Humans ; K562 Cells ; Mice ; NIH 3T3 Cells ; Oligonucleotides/*genetics ; RNA/*genetics ; RNA-Seq/*methods ; Single-Cell Analysis/*methods ; Stochastic Processes ; Transcriptome ; },
abstract = {The development of high-throughput single-cell RNA sequencing (scRNA-seq) has enabled access to information about gene expression in individual cells and insights into new biological areas. Although the interest in scRNA-seq has rapidly grown in recent years, the existing methods are plagued by many challenges when performing scRNA-seq on multiple samples. To simultaneously analyze multiple samples with scRNA-seq, we developed a universal sample barcoding method through transient transfection with short barcode oligonucleotides. By conducting a species-mixing experiment, we have validated the accuracy of our method and confirmed the ability to identify multiplets and negatives. Samples from a 48-plex drug treatment experiment were pooled and analyzed by a single run of Drop-Seq. This revealed unique transcriptome responses for each drug and target-specific gene expression signatures at the single-cell level. Our cost-effective method is widely applicable for the single-cell profiling of multiple experimental conditions, enabling the widespread adoption of scRNA-seq for various applications.},
}
@article {pmid31105367,
year = {2019},
author = {Kerber, M and Schreiber, H},
title = {Barcodes of Towers and a Streaming Algorithm for Persistent Homology.},
journal = {Discrete &amp; computational geometry},
volume = {61},
number = {4},
pages = {852-879},
pmid = {31105367},
issn = {0179-5376},
abstract = {A tower is a sequence of simplicial complexes connected by simplicial maps. We show how to compute a filtration, a sequence of nested simplicial complexes, with the same persistent barcode as the tower. Our approach is based on the coning strategy by Dey et al. (SoCG, 2014). We show that a variant of this approach yields a filtration that is asymptotically only marginally larger than the tower and can be efficiently computed by a streaming algorithm, both in theory and in practice. Furthermore, we show that our approach can be combined with a streaming algorithm to compute the barcode of the tower via matrix reduction. The space complexity of the algorithm does not depend on the length of the tower, but the maximal size of any subcomplex within the tower. Experimental evaluations show that our approach can efficiently handle towers with billions of complexes.},
}
@article {pmid31103380,
year = {2019},
author = {Grassmann, S and Pachmayr, LO and Leube, J and Mihatsch, L and Andrae, I and Flommersfeld, S and Oduro, J and Cicin-Sain, L and Schiemann, M and Flossdorf, M and Buchholz, VR},
title = {Distinct Surface Expression of Activating Receptor Ly49H Drives Differential Expansion of NK Cell Clones upon Murine Cytomegalovirus Infection.},
journal = {Immunity},
volume = {50},
number = {6},
pages = {1391-1400.e4},
doi = {10.1016/j.immuni.2019.04.015},
pmid = {31103380},
issn = {1097-4180},
mesh = {Animals ; *Cytomegalovirus Infections ; Killer Cells, Natural ; Mice ; Mice, Inbred C57BL ; *Muromegalovirus ; NK Cell Lectin-Like Receptor Subfamily A ; },
abstract = {Natural killer (NK) cells show some features of adaptive immunity but have not been studied at the clonal level. Here, we used retrogenic color-barcoding and single-cell adoptive transfers to track clonal immune responses to murine cytomegalovirus (MCMV) infection, derived from individual NK cells expressing activating receptor Ly49H. Clonal expansion of single NK cells varied substantially, and this variation could not be attributed to the additional presence or absence of inhibitory Ly49 receptors. Instead, single-cell-derived variability correlated with distinct surface expression levels of Ly49H itself. Ly49H[hi] NK cell clones maintained higher Ly49H expression and expanded more than their Ly49H[lo] counterparts in response to MCMV. Thus, akin to adaptive processes shaping an antigen-specific T cell receptor (TCR) repertoire, the Ly49H[+] NK cell population adapts to MCMV infection. This process relies on the clonal maintenance of distinct Ly49H expression levels, generating a repertoire of individual NK cells outfitted with distinct reactivity to MCMV.},
}
@article {pmid31101898,
year = {2019},
author = {Guimarães-Costa, AJ and Machado, FS and Oliveira, RRS and Silva-Costa, V and Andrade, MC and Giarrizzo, T and Saint-Paul, U and Sampaio, I and Schneider, H},
title = {Fish diversity of the largest deltaic formation in the Americas - a description of the fish fauna of the Parnaíba Delta using DNA Barcoding.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {7530},
pmid = {31101898},
issn = {2045-2322},
mesh = {Animals ; Biodiversity ; Brazil ; Catfishes/*classification/genetics ; DNA Barcoding, Taxonomic/methods ; Electron Transport Complex IV/genetics ; Fishes ; Flatfishes/*classification/genetics ; Geography ; Perciformes/*classification/genetics ; Rivers ; Wetlands ; },
abstract = {Deltas are dynamic and productive systems of enormous ecological significance, encompassing unique and biologically diverse wetland habitats. Here, we present the first data on the molecular diversity of the fish fauna of the Parnaíba Delta, the largest deltaic formation of the Americas. Partial sequences (626 bp) of the mitochondrial COI gene (Cytochrome c oxidase subunit I) were used to barcode 402 individuals, representing 128 species, belonging to 98 genera, 57 families, 17 orders and two classes. The most abundant orders were the Perciformes, Siluriformes, Gobiiformes, and Pleuronectiformes. The Neighbor-Joining (NJ), Bayesian Inference (BI), and BIN analyses produced 103 molecular clusters, while the Automatic Barcode Gap Discovery (ABGD) and Maximum Likelihood (ML) approaches revealed 102 clusters. The mean conspecific, congeneric and confamilial genetic distances were 0.33%, 14.37%, and 18.60%, respectively. Intraspecific divergence ranged from 0.0% to 1.4%, and all species presented barcode gaps, with the exception of two clusters of Cathorops spixii (OTU 96 and OTU 103), which were separated by a low interspecific distance (1.2%), which overlaps the maximum intraspecific genetic distance (1.4%). The barcode data provide new insights into the fish diversity of the Parnaíba Delta, which will be important for the development of further research on this fauna.},
}
@article {pmid31099728,
year = {2019},
author = {Launis, A and Malíček, J and Svensson, M and Tsurykau, A and Sérusiaux, E and Myllys, L},
title = {Sharpening species boundaries in the Micarea prasina group, with a new circumscription of the type species M. prasina.},
journal = {Mycologia},
volume = {111},
number = {4},
pages = {574-592},
doi = {10.1080/00275514.2019.1603044},
pmid = {31099728},
issn = {1557-2536},
mesh = {Ascomycota/*classification/cytology/genetics ; *Classification ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; Lichens/classification ; Phylogeny ; },
abstract = {Micarea is a lichenized genus in the family Pilocarpaceae (Ascomycota). We studied the phylogeny and reassessed the current taxonomy of the M. prasina group. We focused especially on the taxonomic questions concerning the type species M. prasina and, furthermore, challenges concerning type specimens that are too old for successful DNA barcoding and molecular studies. The phylogeny was reconstructed using nuc rDNA internal transcribed spacer region (ITS1-5.8S-ITS2 = ITS), mitochrondrial rDNA small subunit (mtSSU), and replication licensing factor MCM7 gene from 31 species. Fifty-six new sequences were generated. The data were analyzed using maximum parsimony and maximum likelihood methods. The results revealed four undescribed, well-supported lineages. Three lineages represent new species described here as M. fallax, M. flavoleprosa, and M. pusilla. In addition, our results support the recognition of M. melanobola as a distinct species. Micarea fallax is characterized by a vivid to olive green thallus composed of aggregated granules and whitish or brownish apothecia sometimes with grayish tinge (Sedifolia-gray pigment).Micarea flavoleprosa has a thick, wide-spreading yellowish green, whitish green to olive green sorediate thallus and lacks the Sedifolia-gray pigmentation. The species is mostly anamorphic, developing apothecia rarely. Micarea melanobola is characterized by a pale to dark vivid green granular thallus and darkly pigmented apothecia (Sedifolia-gray). Micarea pusilla is characterized by a whitish green to olive green thinly granular or membranous thallus, numerous and very small whitish apothecia lacking the Sedifolia-gray pigment, and by the production of methoxymicareic acid. Micarea fallax, M. flavoleprosa, and M. melanobola produce micareic acid. The reliability of crystalline granules as a character for species delimitation was investigated and was highly informative for linking the old type specimen of M. prasina to fresh material.},
}
@article {pmid31096658,
year = {2019},
author = {Mateussi, NTB and Melo, BF and Foresti, F and Oliveira, C},
title = {Molecular Data Reveal Multiple Lineages in Piranhas of the Genus Pygocentrus (Teleostei, Characiformes).},
journal = {Genes},
volume = {10},
number = {5},
pages = {},
pmid = {31096658},
issn = {2073-4425},
mesh = {Adaptation, Biological/genetics ; Animals ; Asia ; Bayes Theorem ; Biological Evolution ; Brazil ; Characiformes/*classification/*genetics ; Evolution, Molecular ; Haplotypes/genetics ; Phylogeny ; Phylogeography/methods ; },
abstract = {Carnivorous piranhas are distributed in four serrasalmid genera including Pygocentrus, which inhabit major river basins of South America. While P. cariba and P. piraya are endemics of the Orinoco and São Francisco basins, respectively, P. nattereri is widely distributed across the Amazonas, Essequibo, lower Paraná, Paraguay, and coastal rivers of northeastern Brazil, with recent records of introductions in Asia. Few studies have focused on the genetic diversity and systematics of Pygocentrus and the putative presence of additional species within P. nattereri has never been the subject of a detailed molecular study. Here we aimed to delimit species of Pygocentrus, test the phylogeographic structure of P. nattereri, and access the origin of introduced specimens of P. nattereri in Asia. Phylogenetic analyses based on a mitochondrial dataset involving maximum-likelihood tree reconstruction, genetic distances, Bayesian analysis, three delimitation approaches, and haplotype analysis corroborate the morphological hypothesis of the occurrence of three species of Pygocentrus. However, we provide here strong evidence that P. nattereri contains at least five phylogeographically-structured lineages in the Amazonas, Guaporé (type locality), Itapecuru, Paraná/Paraguay, and Tocantins/Araguaia river basins. We finally found that the introduced specimens in Asia consistently descend from the lineage of P. nattereri from the main Rio Amazonas. These results contribute to future research aimed to detect morphological variation that may occur in those genetic lineages of Pygocentrus.},
}
@article {pmid31096340,
year = {2019},
author = {Carolus, H and Muzarabani, KC and Hammoud, C and Schols, R and Volckaert, FAM and Barson, M and Huyse, T},
title = {A cascade of biological invasions and parasite spillback in man-made Lake Kariba.},
journal = {The Science of the total environment},
volume = {659},
number = {},
pages = {1283-1292},
doi = {10.1016/j.scitotenv.2018.12.307},
pmid = {31096340},
issn = {1879-1026},
mesh = {Animals ; Disease Vectors ; *Environmental Monitoring ; Fasciola hepatica ; Gastropoda/parasitology ; Host-Parasite Interactions ; Humans ; *Introduced Species ; Lakes/*parasitology ; Parasites/classification/growth &amp; development ; Phylogeny ; Ruminants ; Zimbabwe ; },
abstract = {Parasite spillback, the infection of a non-indigenous organism by a native parasite, is a highly important although understudied component of ecological invasion dynamics. Here, through the first analysis of the parasite fauna of lymnaeid gastropods of Lake Kariba (Zimbabwe). We illustrate how the creation of an artificial lake may lead to a cascade of biological invasions in which an invasive aquatic plant promotes the proliferation of invasive gastropods, which in turn alters the epidemiology of trematodiases of potential medical and veterinary importance. Using a new multiplex Rapid Diagnostic PCR assay, we assessed the prevalence of Fasciola sp. infections in the gastropod populations. Both gastropod hosts and trematode parasites were identified using DNA barcoding. We provide the first record of the invasive North-American gastropod Pseudosuccinea columella in Lake Kariba. This species was found at 14 out of 16 sampled sites and its abundance was strongly positively correlated with the abundance of the invasive South-American water hyacinth (Eichhornia crassipes). About 65% of the P. columella specimens analysed were infected with a hitherto unknown Fasciola species. Phylogenetic analyses indicate close affinity to Fasciola hepatica and F. gigantica, which cause fasciolosis, an important liver disease affecting both ruminants and humans. In addition, another non-native Lymnaeid species was found: a Radix sp. that clustered closely with a Vietnamese Radix species. Radix sp. hosted both amphistome and Fasciola trematodes. By linking an invasion cascade and parasite spillback, this study shows how both processes can act in combination to lead to potentially important epidemiological changes.},
}
@article {pmid31095566,
year = {2019},
author = {Nieder, C and Liao, CP and Chen, CA and Liu, SL},
title = {Filamentous calcareous alga provides substrate for coral-competitive macroalgae in the degraded lagoon of Dongsha Atoll, Taiwan.},
journal = {PloS one},
volume = {14},
number = {5},
pages = {e0200864},
pmid = {31095566},
issn = {1932-6203},
mesh = {Animals ; China ; Coral Reefs ; Ecology ; *Ecosystem ; Population Dynamics ; Seaweed ; Taiwan ; },
abstract = {BACKGROUND: The chemically-rich seaweed Galaxaura is not only highly competitive with corals, but also provides substrate for other macroalgae. Its ecology and associated epiphytes remain largely unexplored. To fill this knowledge gap, we undertook an ecological assessment to explore the spatial variation, temporal dynamics, and diversity of epiphytic macroalgae of Galaxaura divaricata on patch reefs in the lagoon of Dongsha Atoll, a shallow coral reef ecosystem in the northern South China Sea that has been repeatedly impacted by mass coral bleaching events.<br><br>METHODS: Twelve spatially independent patch reefs in the Dongsha lagoon were first surveyed to assess benthic composition in April 2016, and then revisited to determine G. divaricata cover in September 2017, with one additional Galaxaura-dominated reef (site 9). Four surveys over a period of 17 months were then carried out on a degraded patch reef site to assess the temporal variation in G. divaricata cover. Epiphytic macroalgae associated with G. divaricata were quantified and identified through the aid of DNA barcoding at this degraded site.<br><br>RESULTS: Patch reefs in the Dongsha lagoon were degraded, exhibiting relatively low coral cover (5-43%), but high proportions of macroalgae (13-58%) and other substrate (rubble and dead corals; 23-69%). The distribution of G. divaricata was heterogeneous across the lagoon, with highest abundance (16-41%) in the southeast area. Temporal surveys showed consistently high covers (mean &#xb1; SD = 16.9 &#xb1; 1.21%) of G. divaricata for 17 months. Additional photographic evidence suggested that overgrowth of G. divaricata can persist for 3.5 years. Yet, G. divaricata provides substrate to other macroalgae (e.g., Lobophora sp.) that also limit the growth of corals.<br><br>CONCLUSIONS: Our study demonstrates that an allelopathic seaweed, such as G. divaricata, can overgrow degraded coral reefs for extended periods of time. By providing habitat for other harmful macroalgae, a prolonged Galaxaura overgrowth could further enhance the spread of macroalgae, and strengthen negative feedback loops, decreasing the recovery potential of degraded reefs.},
}
@article {pmid31092822,
year = {2019},
author = {Cheng, YH and Chen, YC and Lin, E and Brien, R and Jung, S and Chen, YT and Lee, W and Hao, Z and Sahoo, S and Min Kang, H and Cong, J and Burness, M and Nagrath, S and S Wicha, M and Yoon, E},
title = {Hydro-Seq enables contamination-free high-throughput single-cell RNA-sequencing for circulating tumor cells.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {2163},
pmid = {31092822},
issn = {2041-1723},
support = {R35 CA 129765//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/International ; R01 CA 203810//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/International ; R01 CA203810/CA/NCI NIH HHS/United States ; 2017 Translational Research Partnership Program//University of Michigan (U-M)/International ; R21 CA 195016//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/International ; R35 CA197585/CA/NCI NIH HHS/United States ; R21 CA175857/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Biomarkers, Tumor/genetics/isolation &amp; purification ; Breast Neoplasms/blood/diagnosis/genetics/*pathology ; Cell Line ; Epithelial-Mesenchymal Transition ; Female ; Gene Expression Profiling/instrumentation/methods ; High-Throughput Nucleotide Sequencing/instrumentation/*methods ; High-Throughput Screening Assays/instrumentation/methods ; Humans ; Liquid Biopsy/instrumentation/methods ; Mice ; Neoplastic Cells, Circulating/*pathology ; Neoplastic Stem Cells/*pathology ; Sequence Analysis, RNA/instrumentation/methods ; Single-Cell Analysis/instrumentation/methods ; },
abstract = {Molecular analysis of circulating tumor cells (CTCs) at single-cell resolution offers great promise for cancer diagnostics and therapeutics from simple liquid biopsy. Recent development of massively parallel single-cell RNA-sequencing (scRNA-seq) provides a powerful method to resolve the cellular heterogeneity from gene expression and pathway regulation analysis. However, the scarcity of CTCs and the massive contamination of blood cells limit the utility of currently available technologies. Here, we present Hydro-Seq, a scalable hydrodynamic scRNA-seq barcoding technique, for high-throughput CTC analysis. High cell-capture efficiency and contamination removal capability of Hydro-Seq enables successful scRNA-seq of 666 CTCs from 21 breast cancer patient samples at high throughput. We identify breast cancer drug targets for hormone and targeted therapies and tracked individual cells that express markers of cancer stem cells (CSCs) as well as of epithelial/mesenchymal cell state transitions. Transcriptome analysis of these cells provides insights into monitoring target therapeutics and processes underlying tumor metastasis.},
}
@article {pmid31088028,
year = {2019},
author = {Powers, T and Skantar, A and Harris, T and Higgins, R and Mullin, P and Hafez, S and Handoo, Z and Todd, T and Powers, K},
title = {DNA barcoding evidence for the North American presence of alfalfa cyst nematode, Heterodera medicaginis.},
journal = {Journal of nematology},
volume = {51},
number = {},
pages = {1-17},
pmid = {31088028},
issn = {0022-300X},
abstract = {Specimens of Heterodera have been collected from alfalfa fields in Kearny County, Kansas &amp; Carbon County, Montana. DNA barcoding with the COI mitochondrial gene indicate that the species is not Heterodera glycines, soybean cyst nematode, H. schachtii, sugar beet cyst nematode, or H. trifolii, clover cyst nematode. Maximum likelihood phylogenetic trees show that the alfalfa specimens form a sister clade most closely related to H. glycines, with a 4.7% mean pairwise sequence divergence across the 862 nucleotides of the COI marker. Morphological analyses of juveniles and cysts conform to the measurements of H. medicaginis, the alfalfa cyst nematode originally described from the USSR in 1971. Initial host testing demonstrated that the nematode reproduced on alfalfa, but not on soybeans, tomato, or corn. Collectively, the evidence suggests that this finding represents the first record of H. medicaginis in North America. Definitive confirmation of this diagnosis would require COI sequence of eastern European isolates of this species. Specimens of Heterodera have been collected from alfalfa fields in Kearny County, Kansas &amp; Carbon County, Montana. DNA barcoding with the COI mitochondrial gene indicate that the species is not Heterodera glycines, soybean cyst nematode, H. schachtii, sugar beet cyst nematode, or H. trifolii, clover cyst nematode. Maximum likelihood phylogenetic trees show that the alfalfa specimens form a sister clade most closely related to H. glycines, with a 4.7% mean pairwise sequence divergence across the 862 nucleotides of the COI marker. Morphological analyses of juveniles and cysts conform to the measurements of H. medicaginis, the alfalfa cyst nematode originally described from the USSR in 1971. Initial host testing demonstrated that the nematode reproduced on alfalfa, but not on soybeans, tomato, or corn. Collectively, the evidence suggests that this finding represents the first record of H. medicaginis in North America. Definitive confirmation of this diagnosis would require COI sequence of eastern European isolates of this species.},
}
@article {pmid31085639,
year = {2019},
author = {Wang, C and Lu, T and Emanuel, G and Babcock, HP and Zhuang, X},
title = {Imaging-based pooled CRISPR screening reveals regulators of lncRNA localization.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {22},
pages = {10842-10851},
pmid = {31085639},
issn = {1091-6490},
support = {R01 MH113094/MH/NIMH NIH HHS/United States ; R35 GM122487/GM/NIGMS NIH HHS/United States ; U19 MH114830/MH/NIMH NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {CRISPR-Cas Systems/*genetics ; Cell Line, Tumor ; Cell Nucleus/chemistry/metabolism ; Gene Editing ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Image Processing, Computer-Assisted/*methods ; In Situ Hybridization, Fluorescence/*methods ; Molecular Probes/chemistry/genetics/metabolism ; RNA, Guide, CRISPR-Cas Systems/chemistry/genetics/metabolism ; *RNA, Long Noncoding/chemistry/genetics/metabolism ; RNA-Binding Proteins/chemistry/metabolism ; Single-Cell Analysis/*methods ; },
abstract = {Pooled-library CRISPR screening provides a powerful means to discover genetic factors involved in cellular processes in a high-throughput manner. However, the phenotypes accessible to pooled-library screening are limited. Complex phenotypes, such as cellular morphology and subcellular molecular organization, as well as their dynamics, require imaging-based readout and are currently beyond the reach of pooled-library CRISPR screening. Here we report an all imaging-based pooled-library CRISPR screening approach that combines high-content phenotype imaging with high-throughput single guide RNA (sgRNA) identification in individual cells. In this approach, sgRNAs are codelivered to cells with corresponding barcodes placed at the 3' untranslated region of a reporter gene using a lentiviral delivery system with reduced recombination-induced sgRNA-barcode mispairing. Multiplexed error-robust fluorescence in situ hybridization (MERFISH) is used to read out the barcodes and hence identify the sgRNAs with high accuracy. We used this approach to screen 162 sgRNAs targeting 54 RNA-binding proteins for their effects on RNA localization to nuclear compartments and uncovered previously unknown regulatory factors for nuclear RNA localization. Notably, our screen revealed both positive and negative regulators for the nuclear speckle localization of a long noncoding RNA, MALAT1, suggesting a dynamic regulation of lncRNA localization in subcellular compartments.},
}
@article {pmid31083669,
year = {2019},
author = {Van Nieuwenhove, AHM and Ratsimbazafy, HA and Kochzius, M},
title = {Cryptic diversity and limited connectivity in octopuses: Recommendations for fisheries management.},
journal = {PloS one},
volume = {14},
number = {5},
pages = {e0214748},
pmid = {31083669},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; DNA, Mitochondrial/chemistry/metabolism ; Electron Transport Complex IV/chemistry/genetics ; *Fisheries/economics ; Genetic Linkage ; *Genetic Variation ; Genetics, Population ; Haplotypes ; Octopodiformes/*genetics/growth &amp; development ; Sequence Analysis, DNA ; },
abstract = {The market demand for octopus grows each year, but landings are decreasing, and prices are rising. The present study investigated (1) diversity of Octopodidae in the Western Indian Ocean (WIO) and (2) connectivity and genetic structure of Octopus cyanea and O. vulgaris populations in order to obtain baseline data for management plans. A fragment of the cytochrome C oxidase subunit 1 (COI) gene was sequenced in 275 octopus individuals from Madagascar, Kenya and Tanzania. In addition, 41 sequences of O. vulgaris from South Africa, Brazil, Amsterdam Island, Tristan da Cunha, Senegal and Galicia were retrieved from databases and included in this study. Five different species were identified using DNA barcoding, with first records for O. oliveri and Callistoctopus luteus in the WIO. For O. cyanea (n = 229, 563 bp), 22 haplotypes were found, forming one haplogroup. AMOVA revealed shallow but significant genetic population structure among all sites (ϕST = 0.025, p = 0.02), with significant differentiation among: (1) Kanamai, (2) southern Kenya, Tanzania, North and West Madagascar, (3) Southwest Madagascar and (4) East Madagascar (ϕCT = 0.035, p = 0.017). For O. vulgaris (n = 71, 482 bp), 15 haplotypes were identified, forming three haplogroups. A significant genetic population structure was found among all sites (ϕST = 0.82, p ≤ 0.01). Based on pairwise ϕST-values and hierarchical AMOVAs, populations of O. vulgaris could be grouped as follows: (1) Brazil, (2) Madagascar and (3) all other sites. A significant increase in genetic distance with increasing geographic distance was found (Z = 232443, 81 r = 0.36, p = 0.039). These results indicate that for O. cyanea four regions should be considered as separate management units in the WIO. The very divergent haplogroups in O. vulgaris from Brazil and Madagascar might be evolving towards speciation and therefore should be considered as separate species in FAO statistics.},
}
@article {pmid31079561,
year = {2019},
author = {Tiknaik, A and Kalyankar, A and Shingare, M and Suryawanshi, R and Prakash, B and Sontakke, TA and Nalage, D and Sanil, R and Khedkar, G},
title = {Refutation of media reports on introduction of the red bellied piranha and potential impacts on aquatic biodiversity in India.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {4},
pages = {643-650},
doi = {10.1080/24701394.2019.1611798},
pmid = {31079561},
issn = {2470-1408},
mesh = {Animals ; *Biodiversity ; Characiformes/*classification/*genetics ; Genome, Mitochondrial/genetics ; India ; Lakes ; *Phylogeny ; Rivers ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The presence of a new, potentially deadly exotic fish resembling the Red Bellied Piranha, Pygocentrus nattereri was reported in India by print media from various aquatic resources. These reports raised dramatic concerns over public health issues and threats to the aquatic biodiversity of India. Considering the potential severity of the issue and concerns raised by the media, we undertook a study to evaluate the reliability of identification reports of the suspected fish, any relationships to other species of piranha and to address any possible threats to the aquatic biodiversity of India. For this study, samples were collected from most of the major river systems and lakes in India and evaluated for taxonomic identifications of the suspect fish and phylogenetic relationships to other fish species. Our results clearly show that the suspect fish is in fact Piaractus brachypomus, a species commonly referred as "Pacu", and not the red bellied piranha, P. nattereri. Comparisons of both fish do show striking similarities that may account for the misreporting in the media. Furthermore, P. brachypomusas is still an exotic fish, and as such may still have potentially harmful impacts on the native aquatic fauna of India. Quick attention to this issue and the imposition of control measures, including market bans, should be considered to prevent further loss of biodiversity.},
}
@article {pmid31077928,
year = {2019},
author = {Weigand, H and Beermann, AJ and Čiampor, F and Costa, FO and Csabai, Z and Duarte, S and Geiger, MF and Grabowski, M and Rimet, F and Rulik, B and Strand, M and Szucsich, N and Weigand, AM and Willassen, E and Wyler, SA and Bouchez, A and Borja, A and Čiamporová-Zaťovičová, Z and Ferreira, S and Dijkstra, KB and Eisendle, U and Freyhof, J and Gadawski, P and Graf, W and Haegerbaeumer, A and van der Hoorn, BB and Japoshvili, B and Keresztes, L and Keskin, E and Leese, F and Macher, JN and Mamos, T and Paz, G and Pešić, V and Pfannkuchen, DM and Pfannkuchen, MA and Price, BW and Rinkevich, B and Teixeira, MAL and Várbíró, G and Ekrem, T},
title = {DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work.},
journal = {The Science of the total environment},
volume = {678},
number = {},
pages = {499-524},
doi = {10.1016/j.scitotenv.2019.04.247},
pmid = {31077928},
issn = {1879-1026},
mesh = {*Aquatic Organisms ; *Biota ; *DNA Barcoding, Taxonomic/statistics &amp; numerical data ; *Environmental Monitoring ; Europe ; *Gene Library ; },
abstract = {Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly important if molecular identification tools are to be implemented in biomonitoring and reports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). We analysed gaps in the two most important reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses show that coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, caddisflies and vascular plants) are well represented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also found that species monitored in several countries often are represented by barcodes in reference libraries, while species monitored in a single country frequently lack sequence records. A large proportion of species (up to 50%) in several taxonomic groups are only represented by private data in BOLD. Our results have implications for the future strategy to fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species relevant to monitoring in multiple countries should be prioritized for future collaborative programs. We also discuss why a strategy for quality control and quality assurance of barcode reference libraries is needed and recommend future steps to ensure full utilisation of metabarcoding in aquatic biomonitoring.},
}
@article {pmid31077103,
year = {2019},
author = {Wagar, LE},
title = {Live Cell Barcoding for Efficient Analysis of Small Samples by Mass Cytometry.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1989},
number = {},
pages = {125-135},
doi = {10.1007/978-1-4939-9454-0_9},
pmid = {31077103},
issn = {1940-6029},
mesh = {Cell Separation ; Electronic Data Processing/*methods ; Flow Cytometry/*methods ; Humans ; Leukocytes, Mononuclear/*cytology ; Mass Spectrometry/*methods ; Metals/chemistry ; Single-Cell Analysis/*methods ; Specimen Handling ; Staining and Labeling/*methods ; },
abstract = {In mass cytometry, sample loss is of considerable concern due to the relative inefficiency of cell event collection compared to similar techniques such as flow cytometry. Cell stimulation and the harsh conditions required in the later stages of certain sample preparations also contribute to cell loss. Low starting cell numbers are especially susceptible to these effects, potentially limiting the ability to use mass cytometry. Here is presented a live cell barcoding scheme and additional efficiency methods to improve recovery and achieve consistent staining for small samples.},
}
@article {pmid31077101,
year = {2019},
author = {Schulz, AR and Mei, HE},
title = {Surface Barcoding of Live PBMC for Multiplexed Mass Cytometry.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1989},
number = {},
pages = {93-108},
doi = {10.1007/978-1-4939-9454-0_7},
pmid = {31077101},
issn = {1940-6029},
mesh = {Antibodies, Monoclonal/chemistry/immunology ; Chelating Agents/chemistry ; Flow Cytometry/*methods ; Humans ; Immunophenotyping/*methods ; Lanthanoid Series Elements/chemistry ; Leukocytes, Mononuclear/*cytology ; Mass Spectrometry/*methods ; Single-Cell Analysis/*methods ; beta 2-Microglobulin/*immunology ; },
abstract = {Sample barcoding is a powerful method for harmonizing mass cytometry data. By assigning a unique combination of barcode labels to each cell sample, a set of individual samples can be pooled and further processed and acquired as a large, single sample. For assays that require uncompromised profiling of cell-surface markers on live cells, barcoding by metal-labeled antibodies targeting cell-surface epitopes is the barcoding approach of choice. Here we provide an optimized and validated protocol for cell-surface barcoding of ten PBMC samples with palladium-labeled β2-microglobulin (B2M) antibodies used in a 5-choose-2 barcoding scheme, for subsequent immune phenotyping by mass cytometry. We further provide details on the generation of palladium-labeled antibodies utilizing amine-reactive isothiocyanobenzyl-EDTA (ITCB-EDTA) that permits the implementation of antibody-based barcoding not interfering with lanthanide channels typically used for analyte detection in mass cytometry assays.},
}
@article {pmid31077096,
year = {2019},
author = {Lee, BH and Rahman, AH},
title = {Acquisition, Processing, and Quality Control of Mass Cytometry Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1989},
number = {},
pages = {13-31},
doi = {10.1007/978-1-4939-9454-0_2},
pmid = {31077096},
issn = {1940-6029},
mesh = {Biomarkers/*analysis ; Cells/*cytology ; Flow Cytometry/*methods ; Humans ; Mass Spectrometry/*methods ; Quality Control ; Single-Cell Analysis/*methods ; Staining and Labeling/*methods ; },
abstract = {Mass cytometry uniquely combines the principles of mass spectrometry and flow cytometry for high dimensional profiling of immune cells at a single cell level. Using isotopically conjugated antibodies, mass cytometry overcomes the limitations of spectral overlap associated with flow cytometry and allows for deeper single cell characterization of complex biospecimens using more cellular markers. However, the nature of mass spectrometry-based single cell measurements requires specific considerations in acquiring and processing data. This chapter provides an overview of how to optimally acquire mass cytometry data and how to process this data for subsequent analysis and characterization of cell populations.},
}
@article {pmid31073796,
year = {2019},
author = {Chen, G and Jin, M and Yan, M and Cui, X and Wang, Y and Zheng, W and Qin, G and Zhang, Y and Li, M and Liao, Y and Zhang, X and Yan, F and Abd El-Aty, AM and Hacımüftüoğlu, A and Wang, J},
title = {Colorimetric bio-barcode immunoassay for parathion based on amplification by using platinum nanoparticles acting as a nanozyme.},
journal = {Mikrochimica acta},
volume = {186},
number = {6},
pages = {339},
pmid = {31073796},
issn = {1436-5073},
support = {2016YFD0401101//the projects of National Key Research Program of China/International ; 31671938//National Natural Science Foundation/International ; Y2017JC13//Special Fund for Agro-scientific Research in the Public Interest (CN)/International ; },
mesh = {Antibodies, Monoclonal/immunology ; Benzidines/chemistry ; Brassica/chemistry ; Catalysis ; Colorimetry/methods ; Gold/chemistry ; Hydrogen Peroxide/chemistry ; Immunoassay/*methods ; Limit of Detection ; Metal Nanoparticles/*chemistry ; Oryza/chemistry ; Parathion/*analysis/immunology ; Pesticide Residues/analysis/immunology ; Platinum/chemistry ; Pyrus/chemistry ; Water/analysis ; Water Pollutants, Chemical/analysis/immunology ; },
abstract = {A competitive bio-barcode immunoassay is described for the trace detection of parathion in water, pear, cabbage, and rice samples. It is based on amplification by platinum nanoparticle acting as a nanozyme. Gold nanoparticles (AuNPs) were modified with (a) monoclonal antibodies (mAbs) against parathion, and (b) thiolated single-stranded DNA (ssDNA) oligonucleotides. Magnetic nanoparticles (MNPs) were functionalized with ovalbumin coupled with parathion hapten. Parathion and its hapten compete with mAbs on the surface of the AuNPs. Subsequently, the platinum nanoparticles (PtNPs) probe, which was functionalized with the complementary thiolated ssDNA (C-ssDNA), was added to the reaction mixture for the detection of parathion. The signal was catalytically amplified by coupling with platinum nanozyme using teramethylbenzidine and H2O2 as the chromogenic system. The immunoassay has a linear range that extends from 0.01-50 μg·L[-1], and the limit of detection is 2.0 × 10[-3] μg·L[-1]. The recoveries and relative standard deviations (RSDs) ranged from 91.1-114.4% and 3.6-15.8%, respectively. The method correlates well with data obtained by gas chromatography-tandem mass spectrometry (GC-MS/MS). Graphical abstract The parathion and the magnetic nanoparticles (MNPs) labelled with hapten-OVA competitively reacted to AuNPs modified with mAbs and thiolated DNA for the detection of parathion. The signal was catalyzed by platinum nanozyme. The limit of detection for parathion is 2.0 ng·L[-1].},
}
@article {pmid31072405,
year = {2019},
author = {Guo, C and Kong, W and Kamimoto, K and Rivera-Gonzalez, GC and Yang, X and Kirita, Y and Morris, SA},
title = {CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics.},
journal = {Genome biology},
volume = {20},
number = {1},
pages = {90},
pmid = {31072405},
issn = {1474-760X},
support = {R21 HG009750/HG/NHGRI NIH HHS/United States ; T32 GM007200/GM/NIGMS NIH HHS/United States ; R01 GM126112/GM/NIGMS NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; },
mesh = {Cell Tracking/*methods ; Genomics/*methods ; Lentivirus ; *Single-Cell Analysis ; Transcriptome ; },
abstract = {High-throughput single-cell assays increasingly require special consideration in experimental design, sample multiplexing, batch effect removal, and data interpretation. Here, we describe a lentiviral barcode-based multiplexing approach, CellTag Indexing, which uses predefined genetic barcodes that are heritable, enabling cell populations to be tagged, pooled, and tracked over time in the same experimental replicate. We demonstrate the utility of CellTag Indexing by sequencing transcriptomes using a variety of cell types, including long-term tracking of cell engraftment and differentiation in vivo. Together, this presents CellTag Indexing as a broadly applicable genetic multiplexing tool that is complementary with existing single-cell technologies.},
}
@article {pmid31072187,
year = {2019},
author = {Jiménez-Armenta, J and Oceguera-Figueroa, A},
title = {Leeches from Mexico City, remnants of the ancient lake.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {4},
pages = {632-642},
doi = {10.1080/24701394.2019.1606217},
pmid = {31072187},
issn = {2470-1408},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Genome, Mitochondrial/genetics ; *Lakes ; Leeches/*genetics ; Mexico ; Species Specificity ; },
abstract = {Genetic barcodes (partial sequences of the mitochondrial cytochrome c oxidase subunit I) were generated for freshwater leeches that inhabit the Mexico Basin, upon which Mexico City and its metropolitan area have developed. Once a continuous lake, the basin has passed through continuous events of artificial desiccation in the last 500 years so that it is currently conformed by a few and highly modified and polluted isolated freshwater bodies. Six species of leeches from three families were collected in five localities. Current sequence databases were able to determine five of the six species collected for this study with the only exception of Haemopis caballeroi, for which no sequence data are available in public repositories. Taxonomic assignment of cocoons was possible via comparison of barcode sequences. We discuss the presence of a population of Erpobdella ochoterenai in Tecocomulco Lake that bares high genetic divergence from its conspecifics, which may indicate it is an undescribed species.},
}
@article {pmid31071268,
year = {2019},
author = {Boyd, M and Panoyan, MA and Michael, P and Nkongolo, KK},
title = {Development and characterization of species-diagnostic ISSR and SCAR DNA markers for differentiating red maple (Acer rubrum) and silver maple (A. saccharinum).},
journal = {Genome},
volume = {62},
number = {8},
pages = {527-535},
doi = {10.1139/gen-2019-0037},
pmid = {31071268},
issn = {1480-3321},
mesh = {Acer/*genetics ; Gene Amplification ; Genotyping Techniques/*methods/standards ; *Microsatellite Repeats ; *Polymorphism, Genetic ; Reference Standards ; },
abstract = {Red maple (Acer rubrum) and silver maple (A. saccharinum) are sister species that readily hybridize in nature. No genetic or barcoding markers have been tested in these species. The main objective of the present study is to develop and characterize molecular markers for distinguishing A. rubrum and A. saccharinum and to validate the hybridity of A. freemanii derived from their crossings using the ISSR marker system. Thirteen A. rubrum and seven A. saccharinum populations were used. Four ISSR primers including ISSR 5, ISSR 8, ISSR 10, and ISSR UBC 825 were selected to amplify genomic DNA from the two species and their hybrids. Each primer generated at least one species-diagnostic ISSR marker for a total of six. Analysis of A. freemanii collected from North Dakota (USA) confirmed that the genotypes screened were true hybrids between A. rubrum and A. saccharinum. These markers were cloned and sequenced. Successful sequences were converted to SCAR markers using specifically designed primers. Overall, the developed diagnostic and specific ISSR and SCAR markers are useful in the certification of these two maple species and their hybrids. They can be used in tracking the introgression of A. rubrum and A. saccharinum DNA in other hybrid trees or populations.},
}
@article {pmid31070984,
year = {2019},
author = {Sandhu, V and Labori, KJ and Borgida, A and Lungu, I and Bartlett, J and Hafezi-Bakhtiari, S and Denroche, RE and Jang, GH and Pasternack, D and Mbaabali, F and Watson, M and Wilson, J and Kure, EH and Gallinger, S and Haibe-Kains, B},
title = {Meta-Analysis of 1,200 Transcriptomic Profiles Identifies a Prognostic Model for Pancreatic Ductal Adenocarcinoma.},
journal = {JCO clinical cancer informatics},
volume = {3},
number = {},
pages = {1-16},
doi = {10.1200/CCI.18.00102},
pmid = {31070984},
issn = {2473-4276},
mesh = {Biomarkers, Tumor ; Carcinoma, Pancreatic Ductal/*genetics/*mortality/pathology ; Gene Expression Profiling ; Humans ; Kaplan-Meier Estimate ; Pancreatic Neoplasms/*genetics/*mortality/pathology ; Prognosis ; *Transcriptome ; },
abstract = {PURPOSE: With a dismal 8% median 5-year overall survival, pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy. Only 10% to 20% of patients are eligible for surgery, and more than 50% of these patients will die within 1 year of surgery. Building a molecular predictor of early death would enable the selection of patients with PDAC who are at high risk.<br><br>MATERIALS AND METHODS: We developed the Pancreatic Cancer Overall Survival Predictor (PCOSP), a prognostic model built from a unique set of 89 PDAC tumors in which gene expression was profiled using both microarray and sequencing platforms. We used a meta-analysis framework that was based on the binary gene pair method to create gene expression barcodes that were robust to biases arising from heterogeneous profiling platforms and batch effects. Leveraging the largest compendium of PDAC transcriptomic data sets to date, we show that PCOSP is a robust single-sample predictor of early death-1 year or less-after surgery in a subset of 823 samples with available transcriptomics and survival data.<br><br>RESULTS: The PCOSP model was strongly and significantly prognostic, with a meta-estimate of the area under the receiver operating curve of 0.70 (P = 2.6E-22) and d-index (robust hazard ratio) of 1.9 (range, 1.6 to 2.3; (= 1.4E-04) for binary and survival predictions, respectively. The prognostic value of PCOSP was independent of clinicopathologic parameters and molecular subtypes. Over-representation analysis of the PCOSP 2,619 gene pairs-1,070 unique genes-unveiled pathways associated with Hedgehog signaling, epithelial-mesenchymal transition, and extracellular matrix signaling.<br><br>CONCLUSION: PCOSP could improve treatment decisions by identifying patients who will not benefit from standard surgery/chemotherapy but who may benefit from a more aggressive treatment approach or enrollment in a clinical trial.},
}
@article {pmid31069611,
year = {2019},
author = {González-Castro, M and Rosso, JJ and Delpiani, SM and Mabragaña, E and Díaz de Astarloa, JM},
title = {Inferring boundaries among fish species of the new world silversides (Atherinopsidae; genus Odontesthes): new evidences of incipient speciation between marine and brackish populations of Odontesthes argentinensis.},
journal = {Genetica},
volume = {147},
number = {3-4},
pages = {217-229},
pmid = {31069611},
issn = {1573-6857},
support = {PIP No. 11220130100339//Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas/ ; PICT-2014-0665//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n Productiva/ ; },
mesh = {Animals ; Argentina ; Atlantic Ocean ; *DNA Barcoding, Taxonomic ; Fishes/*classification/genetics ; Fresh Water ; Genetic Speciation ; Genetic Variation ; Haplotypes ; Phylogeny ; Species Specificity ; },
abstract = {Species of new world silversides (Actinopterygii; Atherinopsidae; genus Odontesthes) possess economic relevance, biological interest and ecological importance. In the present paper we: (A) investigate the molecular diversity in marine species of Odontesthes from the South West Atlantic Ocean (SWAO), and analyse their interspecific relationships and divergence by means of DNA Barcoding, including its freshwater congeners, as well. (B) Explore the suitability of DNA Barcoding to analyse the diversity and distribution of haplotypes in Odontesthes argentinensis, the only well documented marine species from the SWAO that exhibit putative estuarine and marine populations. Molecular analysis revealed 100% of agreement between morphological identification and molecular identity. Odontesthes argentinensis, Odontesthes platensis, Odontesthes smitti, Odontesthes nigricans and Odontesthes incisa were assigned to five different barcode index numbers (BINs). Maximum-likelihood analysis showed that all marine species of Odontesthes clustered separately in a unique monophyletic phylogroup, comprising five well defined haplogroups, with genetic divergence between groups ranging from 2.75 to 7.11%. The genetic analysis including freshwater congeners showed that O. incisa clustered alone occupying a basal position. The Fst pairwise comparisons within O. argentinensis support the existence of three population groups: one conformed by Mar Chiquita Lagoon (MCh) specimens, and the others by Mar del Plata/Mar Chiquita coast and San Blas Bay coastal specimens, respectively. The AMOVA showed significant overall differentiation (Fst = 0.238; p = 0.00001) for the entire data set. The previous/present evidence is discussed, and strongly suggests that incipient speciation is occurring in O. argentinensis argentinean populations, and specimens from MCh would be considered at present as the leading candidate of a marine to freshwater incipient speciation event.},
}
@article {pmid31069120,
year = {2019},
author = {Li, GJ and Zhao, RL and Zhang, CL and Lin, FC},
title = {A preliminary DNA barcode selection for the genus Russula (Russulales, Basidiomycota).},
journal = {Mycology},
volume = {10},
number = {2},
pages = {61-74},
pmid = {31069120},
issn = {2150-1203},
abstract = {Russula is a worldwid genus which has a high species diversity . Aiming accurate and rapid species identification, candidate genes nLSU (28S), ITS, tef-1α, mtSSU, rpb1, and rpb2, were analysed as potential DNA barcodes. This analysis included 433 sequences from 38 well-circumscribed Russula species of eight subgenera. Two vital standards were analysed for success species identification using DNA barcodes, specifically inter- and intra-specific variations together with the success rates of PCR amplification and sequencing. Although the gap between inter- and intra-specific variations was narrow, ITS met the qualification standards for a target DNA barcode. Overlapping inter- and intra-specific pairwise distances were observed in nLSU, tef-1α, mtSSU, and rpb2. The success rates of PCR amplification and sequencing in mtSSU and rpb1 were lower than those of others. Gene combinations were also investigated for resolution of species recognition. ITS-rpb2 was suggested as the likely target DNA barcode for Russula, owing to the two viatal standards above. Since nLSU has the lowest minimum of inter-specific variation, and tef-1α has the highest overlap between intra- and inter-species variations among the candidate genes, they are disqualified from the selection for DNA barcode of Russula.},
}
@article {pmid31067783,
year = {2019},
author = {Zhang, P and Liu, C and Zheng, X and Wu, L and Liu, Z and Liao, B and Shi, Y and Li, X and Xu, J and Chen, S},
title = {Full-Length Multi-Barcoding: DNA Barcoding from Single Ingredient to Complex Mixtures.},
journal = {Genes},
volume = {10},
number = {5},
pages = {},
pmid = {31067783},
issn = {2073-4425},
mesh = {Chloroplast Proteins/genetics ; DNA, Intergenic/genetics ; DNA, Plant/*analysis ; DNA, Ribosomal/genetics ; Drug Combinations ; Drugs, Chinese Herbal/*analysis ; Sequence Analysis, DNA/*methods ; },
abstract = {DNA barcoding has been used for decades, although it has mostly been applied to somesingle-species. Traditional Chinese medicine (TCM), which is mainly used in the form ofcombination-one type of the multi-species, identification is crucial for clinical usage.Next-generation Sequencing (NGS) has been used to address this authentication issue for the pastfew years, but conventional NGS technology is hampered in application due to its short sequencingreads and systematic errors. Here, a novel method, Full-length multi-barcoding (FLMB) vialong-read sequencing, is employed for the identification of biological compositions in herbalcompound formulas in adequate and well controlled studies. By directly sequencing the full-lengthamplicons of ITS2 and psbA-trnH through single-molecule real-time (SMRT) technology, thebiological composition of a classical prescription Sheng-Mai-San (SMS) was analyzed. At the sametime, clone-dependent Sanger sequencing was carried out as a parallel control. Further, anotherformula-Sanwei-Jili-San (SJS)-was analyzed with genes of ITS2 and CO1. All the ingredients inthe samples of SMS and SJS were successfully authenticated at the species level, and 11 exogenousspecies were also checked, some of which were considered as common contaminations in theseproducts. Methodology analysis demonstrated that this method was sensitive, accurate andreliable. FLMB, a superior but feasible approach for the identification of biological complexmixture, was established and elucidated, which shows perfect interpretation for DNA barcodingthat could lead its application in multi-species mixtures.},
}
@article {pmid31065488,
year = {2019},
author = {Thakur, VV and Tiwari, S and Tripathi, N and Tiwari, G},
title = {Molecular identification of medicinal plants with amplicon length polymorphism using universal DNA barcodes of the atpF-atpH, trnL and trnH-psbA regions.},
journal = {3 Biotech},
volume = {9},
number = {5},
pages = {188},
pmid = {31065488},
issn = {2190-572X},
abstract = {Amplification success and species discrimination efficiency of universal DNA barcode primers (trnH-psbA, trnL, ycf1b, atpF-atpH, matK and rbcL) was evaluated in 46 representative medicinal plant species of 28 families on agarose gel. The results showed that amplicons length polymorphism revealed by the primers atpF-atpH, trnH-psbA and trnL can simultaneously discriminate all the 46 species under study precisely. Some of the plant species included in this study are used as potential adulterants to other plant species. We were able to successfully discriminate the plant species from their potential substitute. Vitex negundo is an adulterant of Ocimum sanctum which has been successfully discriminated by all these three markers. Another example of adulteration between Bacopa monnieri and Centella asiatica was successfully discriminated by atpF-atpH, trnL and trnH-psbA on the basis of variability in amplicon length of these two medicinal herbs. Further, Cassia tora and Cassia fistula are also adulterants for each other and variability in amplicon length between these two species was revealed by atpF-atpH and trnH-psbA markers. A colour code distance matrix based on amplicon length polymorphism was designed to select primers which can effectively discriminate plants species on the basis of their amplicon length. Discrimination of plant species with the universal markers on agarose gel is a noble and inexpensive approach as it does not require sequencing of amplicons. This procedure will provide a way for the development of diagnostic markers to identify adulteration not only in herbal drug formulations but also in food material.},
}
@article {pmid31065024,
year = {2019},
author = {Lee, TRC and Anderson, SJ and Tran-Nguyen, LTT and Sallam, N and Le Ru, BP and Conlong, D and Powell, K and Ward, A and Mitchell, A},
title = {Towards a global DNA barcode reference library for quarantine identifications of lepidopteran stemborers, with an emphasis on sugarcane pests.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {7039},
pmid = {31065024},
issn = {2045-2322},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Lepidoptera/classification/*genetics ; Moths/genetics ; *Pest Control ; Phylogeny ; Quarantine ; Saccharum ; },
abstract = {Lepidopteran stemborers are among the most damaging agricultural pests worldwide, able to reduce crop yields by up to 40%. Sugarcane is the world's most prolific crop, and several stemborer species from the families Noctuidae, Tortricidae, Crambidae and Pyralidae attack sugarcane. Australia is currently free of the most damaging stemborers, but biosecurity efforts are hampered by the difficulty in morphologically distinguishing stemborer species. Here we assess the utility of DNA barcoding in identifying stemborer pest species. We review the current state of the COI barcode sequence library for sugarcane stemborers, assembling a dataset of 1297 sequences from 64 species. Sequences were from specimens collected and identified in this study, downloaded from BOLD or requested from other authors. We performed species delimitation analyses to assess species diversity and the effectiveness of barcoding in this group. Seven species exhibited <0.03 K2P interspecific diversity, indicating that diagnostic barcoding will work well in most of the studied taxa. We identified 24 instances of identification errors in the online database, which has hampered unambiguous stemborer identification using barcodes. Instances of very high within-species diversity indicate that nuclear markers (e.g. 18S, 28S) and additional morphological data (genitalia dissection of all lineages) are needed to confirm species boundaries.},
}
@article {pmid31060231,
year = {2019},
author = {Lee, HO and Joh, HJ and Kim, K and Lee, SC and Kim, NH and Park, JY and Park, HS and Park, MS and Kim, S and Kwak, M and Kim, KY and Lee, WK and Yang, TJ},
title = {Dynamic Chloroplast Genome Rearrangement and DNA Barcoding for Three Apiaceae Species Known as the Medicinal Herb "Bang-Poong".},
journal = {International journal of molecular sciences},
volume = {20},
number = {9},
pages = {},
pmid = {31060231},
issn = {1422-0067},
support = {Project No. PJ13238//"The Genetic and Genomic Evaluation of Indigenous Biological Resources 2012" from the National Institute of Biological Resources under the Ministry of Environment and the "Cooperative Research Program for Agriculture Science &amp; Technology Development/ ; },
mesh = {Apiaceae/*classification/*genetics ; Chloroplasts/genetics ; *DNA Barcoding, Taxonomic ; DNA Copy Number Variations ; *Gene Rearrangement ; *Genome, Chloroplast ; Genomics/methods ; Mutation ; Open Reading Frames ; Phylogeny ; Plants, Medicinal/*classification/*genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; Tandem Repeat Sequences ; },
abstract = {Three Apiaceae species Ledebouriella seseloides, Peucedanum japonicum, and Glehnia littoralis are used as Asian herbal medicines, with the confusingly similar common name "Bang-poong". We characterized the complete chloroplast (cp) genomes and 45S nuclear ribosomal DNA (45S nrDNA) sequences of two accessions for each species. The complete cp genomes of G. littoralis, L. seseloides, and P. japonicum were 147,467, 147,830, and 164,633 bp, respectively. Compared to the other species, the P. japonicum cp genome had a huge inverted repeat expansion and a segmental inversion. The 45S nrDNA cistron sequences of the three species were almost identical in size and structure. Despite the structural variation in the P. japonicum cp genome, phylogenetic analysis revealed that G. littoralis diverged 5-6 million years ago (Mya), while P. japonicum diverged from L. seseloides only 2-3 Mya. Abundant copy number variations including tandem repeats, insertion/deletions, and single nucleotide polymorphisms, were found at the interspecies level. Intraspecies-level polymorphism was also found for L. seseloides and G. littoralis. We developed nine PCR barcode markers to authenticate all three species. This study characterizes the genomic differences between L. seseloides, P. japonicum, and G. littoralis; provides a method of species identification; and sheds light on the evolutionary history of these three species.},
}
@article {pmid31059708,
year = {2019},
author = {Jomkumsing, P and Tangkawanit, U and Wongpakam, K and Pramual, P},
title = {Who is biting you? DNA barcodes reveal cryptic diversity in human-biting black flies (Diptera: Simuliidae).},
journal = {Acta tropica},
volume = {196},
number = {},
pages = {22-29},
doi = {10.1016/j.actatropica.2019.05.001},
pmid = {31059708},
issn = {1873-6254},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Disease Vectors ; Haplotypes ; Humans ; *Insect Bites and Stings ; Phylogeny ; Simuliidae/classification/*genetics ; },
abstract = {Black flies (Simuliidae) are important biting insects and vectors of diseases agents of humans and livestock. Thus, understanding the taxonomy and biodiversity of these insects is crucial for control and management of these diseases. In this study, we used mitochondrial cytochrome c oxidase I sequences to examine genetic diversity of three human-biting and possible vector black fly taxa; the Simulium asakoae species-complex, S. chamlongi and S. nigrogilvum. High levels of genetic diversity (>3.5% intraspecific genetic divergence) were found in all three taxa. Phylogenetic analyses indicated that the S. asakoae complex can be divided into seven groups with the largest group consisting of specimens from Thailand, Malaysia and Myanmar. This group most likely represents true S. asakoae. The remaining haplotypes formed groups with conspecific haplotypes or with other closely related species. Among these groups, one including S. monglaense and another including S. myanmarense suggest that certain specimens identified as S. asakoae most likely belong to those species. Therefore, they constitute new locality records for Thailand and also represent new records of anthropophily. Members of S. chamlongi are not monophyletic as its clade also included S. hackeri. A median joining network revealed strong geographic associations of the haplotypes of S. nigrogilvum suggesting limitation of gene flow. Because this species occurs mainly in high elevation habitats, low land areas could present a barrier to gene flow.},
}
@article {pmid31058420,
year = {2019},
author = {Schulz, AR and Baumgart, S and Schulze, J and Urbicht, M and Grützkau, A and Mei, HE},
title = {Stabilizing Antibody Cocktails for Mass Cytometry.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {95},
number = {8},
pages = {910-916},
doi = {10.1002/cyto.a.23781},
pmid = {31058420},
issn = {1552-4930},
mesh = {Antibodies, Monoclonal/immunology/*pharmacology ; Flow Cytometry/*methods ; Humans ; Immunophenotyping/*methods ; Isotopes/pharmacology ; Lanthanoid Series Elements/pharmacology ; Leukocytes, Mononuclear/immunology ; Mass Spectrometry/*methods ; Palladium/pharmacology ; Single-Cell Analysis/methods ; },
abstract = {Mass cytometry is increasingly employed in larger immune profiling studies involving data acquisitions across several days and multiple sites. For gaining a maximum of information from respective data by computational analyses, several techniques have been developed to minimize noise in mass cytometric data sets, such as sample banking, standardized instrument setup, sample barcoding, and signal normalization. However, the repeated preparation of cocktails composed of isotope-tagged antibodies remained a significant source of error. We here show that premixed antibody cocktails fail to deliver expected staining patterns when stored at 4°C for 4 weeks. As a solution, we developed and tested a cryopreservation method for highly multiplexed antibody cocktails for mass cytometry including lanthanide, palladium, and platinum conjugates that yielded stable staining patterns for at least 9 months when stored at temperatures below -80°C. Using frozen aliquots of antibody cocktails is an economic and flexible approach to significantly improve data consistency in large mass cytometry studies with repetitive staining/measurement cycles spanning several days or involving multiple data acquisition sites. © 2019 International Society for Advancement of Cytometry.},
}
@article {pmid31050090,
year = {2019},
author = {Andersen, JC and Oboyski, P and Davies, N and Charlat, S and Ewing, C and Meyer, C and Krehenwinkel, H and Lim, JY and Noriyuki, S and Ramage, T and Gillespie, RG and Roderick, GK},
title = {Categorization of species as native or nonnative using DNA sequence signatures without a complete reference library.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {29},
number = {5},
pages = {e01914},
pmid = {31050090},
issn = {1939-5582},
support = {//Gordon and Betty Moore Foundation/International ; },
mesh = {Animals ; *Biodiversity ; DNA ; *DNA Barcoding, Taxonomic ; Gene Library ; Phylogeny ; },
abstract = {New genetic diagnostic approaches have greatly aided efforts to document global biodiversity and improve biosecurity. This is especially true for organismal groups in which species diversity has been underestimated historically due to difficulties associated with sampling, the lack of clear morphological characteristics, and/or limited availability of taxonomic expertise. Among these methods, DNA sequence barcoding (also known as "DNA barcoding") and by extension, meta-barcoding for biological communities, has emerged as one of the most frequently utilized methods for DNA-based species identifications. Unfortunately, the use of DNA barcoding is limited by the availability of complete reference libraries (i.e., a collection of DNA sequences from morphologically identified species), and by the fact that the vast majority of species do not have sequences present in reference databases. Such conditions are critical especially in tropical locations that are simultaneously biodiversity rich and suffer from a lack of exploration and DNA characterization by trained taxonomic specialists. To facilitate efforts to document biodiversity in regions lacking complete reference libraries, we developed a novel statistical approach that categorizes unidentified species as being either likely native or likely nonnative based solely on measures of nucleotide diversity. We demonstrate the utility of this approach by categorizing a large sample of specimens of terrestrial insects and spiders (collected as part of the Moorea BioCode project) using a generalized linear mixed model (GLMM). Using a training data set of known endemic (n = 45) and known introduced species (n = 102), we then estimated the likely native/nonnative status for 4,663 specimens representing an estimated 1,288 species (412 identified species), including both those specimens that were either unidentified or whose endemic/introduced status was uncertain. Using this approach, we were able to increase the number of categorized specimens by a factor of 4.4 (from 794 to 3,497), and the number of categorized species by a factor of 4.8 from (147 to 707) at a rate much greater than chance (77.6% accuracy). The study identifies phylogenetic signatures of both native and nonnative species and suggests several practical applications for this approach including monitoring biodiversity and facilitating biosecurity.},
}
@article {pmid31050080,
year = {2019},
author = {Hoenle, PO and Blüthgen, N and Brückner, A and Kronauer, DJC and Fiala, B and Donoso, DA and Smith, MA and Ospina Jara, B and von Beeren, C},
title = {Species-level predation network uncovers high prey specificity in a Neotropical army ant community.},
journal = {Molecular ecology},
volume = {28},
number = {9},
pages = {2423-2440},
doi = {10.1111/mec.15078},
pmid = {31050080},
issn = {1365-294X},
mesh = {Animals ; Ants/classification/*physiology ; Costa Rica ; DNA Barcoding, Taxonomic ; *Predatory Behavior ; Pupa ; Spatio-Temporal Analysis ; Sympatry ; Tropical Climate ; },
abstract = {Army ants are among the top arthropod predators and considered keystone species in tropical ecosystems. During daily mass raids with many thousand workers, army ants hunt live prey, likely exerting strong top-down control on prey species. Many tropical sites exhibit a high army ant species diversity (>20 species), suggesting that sympatric species partition the available prey niches. However, whether and to what extent this is achieved has not been intensively studied yet. We therefore conducted a large-scale diet survey of a community of surface-raiding army ants at La Selva Biological Station in Costa Rica. We systematically collected 3,262 prey items from eleven army ant species (genera Eciton, Nomamyrmex and Neivamyrmex). Prey items were classified as ant prey or non-ant prey. The prey nearly exclusively consisted of other ants (98%), and most booty was ant brood (87%). Using morphological characters and DNA barcoding, we identified a total of 1,103 ant prey specimens to the species level. One hundred twenty-nine ant species were detected among the army ant prey, representing about 30% of the known local ant diversity. Using weighted bipartite network analyses, we show that prey specialization in army ants is unexpectedly high and prey niche overlap very small. Besides food niche differentiation, we uncovered a spatiotemporal niche differentiation in army ant raid activity. We discuss competition-driven multidimensional niche differentiation and predator-prey arms races as possible mechanisms underlying prey specialization in army ants. By combining systematic prey sampling with species-level prey identification and network analyses, our integrative approach can guide future research by portraying how predator-prey interactions in complex communities can be reliably studied, even in cases where morphological prey identification is infeasible.},
}
@article {pmid31048970,
year = {2019},
author = {Linský, M and Čiamporová-Zaťovičová, Z and Čiampor, F},
title = {Four new species of Hexanchorus Sharp from Ecuador (Coleoptera, Elmidae) with DNA barcoding and notes on the distribution of the genus.},
journal = {ZooKeys},
volume = {838},
number = {},
pages = {85-109},
pmid = {31048970},
issn = {1313-2989},
abstract = {The riffle beetle genus Hexanchorus Sharp, 1882 is distributed from Mexico to Argentina, forming an important component of the freshwater invertebrate fauna of Latin America. With 21 described species, Hexanchorus represents one of the most speciose Larainae genera, but its real diversity is likely much higher. We analysed material from a relatively small area in Ecuador, resulting in the first record of H.cordillierae for Ecuador and discovery of four new species and one subspecies: Hexanchorusvirilis sp. n., Hexanchorusrostratus sp. n., Hexanchorusshepardi sp. n., Hexanchorusonorei sp. n. and Hexanchorusonoreisagittatus ssp. n. For delimiting and characterizing species, both morphological and molecular (mtCOI DNA barcodes) data were used. A distribution map of Hexanchorus species is provided based on published records.},
}
@article {pmid31048968,
year = {2019},
author = {Cryer, J and Wynne, F and Price, SJ and Puschendorf, R},
title = {Cryptic diversity in Lithobateswarszewitschii (Amphibia, Anura, Ranidae).},
journal = {ZooKeys},
volume = {838},
number = {},
pages = {49-69},
pmid = {31048968},
issn = {1313-2989},
abstract = {Lithobateswarszewitschii is a species of ranid frog distributed from southern Honduras to Panama. This species suffered severe population declines at higher elevations (above 500 m a.s.l.) from the 1980s to early 1990s, but there is more recent evidence of recovery in parts of its range. Here we advocate for the status of Lithobateswarszewitschii as a candidate cryptic species complex based on sequence data from mitochondrial genes CO1 and 16S. Using concatenated phylogenies, nucleotide diversity (K2P-π), net between group mean distance (NBGMD) (πnet) and species delimitation methods, we further elucidate cryptic diversity within this species. All phylogenies display polyphyletic lineages within Costa Rica and Panama. At both loci, observed genetic polymorphism (K2P-π) is also high within and between geographic populations, surpassing proposed species threshold values for amphibians. Additionally, patterns of phylogeographic structure are complicated for this species, and do not appear to be explained by geographic barriers or isolation by distance. These preliminary findings suggest L.warszewitschii is a wide-ranging species complex. Therefore, we propose further research within its wider range, and recommend integrative taxonomic assessment is merited to assess species status.},
}
@article {pmid31048958,
year = {2019},
author = {M Moran, K and H Skevington, J},
title = {Revision of world Sphecomyia Latreille (Diptera, Syrphidae).},
journal = {ZooKeys},
volume = {836},
number = {},
pages = {15-79},
pmid = {31048958},
issn = {1313-2989},
abstract = {The 16 world species of Sphecomyia Latreille are revised, including seven previously undescribed species (S.cryptica Moran, sp. n., S.hoguei Moran, sp. n., S.interrupta Moran, sp. n., S.oraria Moran, sp. n., S.pseudosphecomima Moran, sp. n., S.sexfasciata Moran, sp. n., and S.weismani Moran, sp. n.). Descriptions, redescriptions, male genitalia photographs, distribution maps, and an illustrated key for all Sphecomyia are presented. DNA barcode data are provided for all 16 species with a cytochrome oxidase subunit I gene tree presented and discussed. Sphecomyia stat. rev. is redefined to represent the monophyletic lineage of species within subtribe Criorhinina possessing a bare, medial vitta extending ventrally from the oral margin in both sexes, a bare gena, a bare katepimeron, a scutellum with at least anterior margin densely pruinose, an anterior ventral half of vein C before crossvein h without setae, and a narrow intersection of vein R1 with vein C. Three species groups of Sphecomyia are identified: the S.vittata group which possess pruinose scutellar vittae, the S.pattonii group which lack pruinose scutellar vittae, and S.metallica (Bigot), a hairy bee mimic with a completely pruinose scutum. Criorhinatsherepanovi Violovitsh is resurrected and transferred, along with Criorhinaaino Stackelberg, to the genus Sphecomyia: S.tsherepanovi (Violovitsh), comb. n. and S.aino (Stackelberg), comb. n. Criorhinametallica (Bigot) is designated as the senior synonym of C.lupina (Williston), not junior as improperly treated, and transferred to Sphecomyia: S.metallica (Bigot), comb. n. The species Sphecomyiafusca Weisman, S.nasica Osburn, and S.occidentalis Osburn are transferred to Criorhina Meigen: C.fusca (Weisman), comb. n., C.nasica (Osburn), comb. n., and C.occidentalis (Osburn), comb. n.},
}
@article {pmid31048956,
year = {2019},
author = {Liu, H and Xu, X and Zhang, Z and Liu, F and Li, D},
title = {Four new species of the trapdoor spider genus Conothele Thorell, 1878 (Araneae, Halonoproctidae) from China.},
journal = {ZooKeys},
volume = {833},
number = {},
pages = {133-150},
pmid = {31048956},
issn = {1313-2989},
abstract = {Herein four species of the trapdoor spider genus Conothele Thorell, 1878 collected from China are described as new to science based on the female genital morphology: C.baisha sp. n. (Hainan Province), C.baoting sp. n. (Hainan Province), C.linzhi sp. n. (Tibet), and C.jinggangshan sp. n. (Jiangxi Province). For two Hainan species, C.baisha sp. n. and C.baoting sp. n., between which it is difficult to distinguish solely based on female genital morphology, additional diagnoses derived from species-specific nucleotide substitution information and genetic distances using the mitochondrial gene, cytochrome c oxidase subunit I are provided.},
}
@article {pmid31048954,
year = {2019},
author = {Laurindo da Silva, F and Stur, E},
title = {Pentaneurellakatterjokki Fittkau &amp; Murray (Chironomidae, Tanypodinae): redescription and phylogenetic position.},
journal = {ZooKeys},
volume = {833},
number = {},
pages = {107-119},
pmid = {31048954},
issn = {1313-2989},
abstract = {The monotypic genus Pentaneurella Fittkau &amp; Murray was originally described based on larvae, pupal exuviae and pharate males. The latter prevented the observation of key features, such as wing dimensions, abdominal coloration pattern, and hypopygial apodemes (sternapodeme and phallapodeme), and the description of the adult male was considered incomplete by the authors. Herein, the adult female of Pentaneurellakatterjokki is described for the first time, and the adult male, pupa and larva are redescribed and figured based on specimens recently collected in Germany and Norway. We also discuss the phylogenetic position of Pentaneurella.},
}
@article {pmid31043850,
year = {2019},
author = {Fernandez-Triana, J and Boudreault, C and Dapkey, T and Alex Smith, M and Hallwachs, W and Janzen, D},
title = {A revision of Dolichogenidea (Hymenoptera, Braconidae, Microgastrinae) with the second mediotergite broadly rectangular from Area de Conservación Guanacaste, Costa Rica.},
journal = {ZooKeys},
volume = {835},
number = {},
pages = {87-123},
pmid = {31043850},
issn = {1313-2989},
abstract = {The first species of Dolichogenidea (Hymenoptera: Braconidae, Microgastrinae) with the second mediotergite broadly quadrate to rectangular are revised, and eight new species from Area de Conservación Guanacaste (ACG), Costa Rica are described, all authored by Fernandez-Triana &amp; Boudreault: alejandromasisi, angelagonzalezae, carlosmanuelrodriguezi, genuarnunezi, josealfredohernandezi, melaniamunozae, rogerblancoi, and yeimycedenoae. A new species group (carlosmanuelrodriguezi) within the genus is proposed to accommodate those species, as well as additional undescribed species from the Neotropical region found in collections. All new species are found in rainforests (120-900 m) and all are parasitoids of Depressariidae (except for one species parasitizing Choreutidae). The unique shape of the second mediotergite and long ovipositor are features shared with the alejandromorai species group in the genus Apanteles, an example of convergent evolution; both wasp groups also parasitize similar hosts in ACG.},
}
@article {pmid31043848,
year = {2019},
author = {Kirichenko, N and Triberti, P and Lopez-Vaamonde, C},
title = {New species of leaf-mining Phyllonorycter (LepidopteraGracillariidae) from Siberia feeding on Caragana (Fabaceae).},
journal = {ZooKeys},
volume = {835},
number = {},
pages = {17-41},
pmid = {31043848},
issn = {1313-2989},
abstract = {During a DNA barcoding campaign of leaf-mining Gracillariidae from the Asian part of Russia, a new species of Phyllonorycter Hübner, feeding on the Siberian pea shrub, Caraganaarborescens Lam. (Fabaceae) was discovered in Siberia. Here, this taxon is described as Phyllonorycterivani sp. n. Among Fabaceae-feeding Phyllonorycter, so far only P.caraganella (Ermolaev) has been known to develop on Caragana. Phyllonorycterivani and P.caraganella show a large divergence in morphology (external and male genitalia) and barcode region of the mtDNA-COI gene (8.6%). They feed on different host plants species and have different ranges in Russia. We show that DNA barcode data weakly supports the Fabaceae-feeding species groups. In addition, we show that morphologically (strongly) and genetically (weakly), P.ivani has affinity to the haasi species group, a West Palearctic group with asymmetrical male genitalia.},
}
@article {pmid31043484,
year = {2019},
author = {Wimmer, ME and Fant, B and Swinford-Jackson, SE and Testino, A and Van Nest, D and Abel, T and Pierce, RC},
title = {H3.3 Barcoding of Nucleus Accumbens Transcriptional Activity Identifies Novel Molecular Cascades Associated with Cocaine Self-administration in Mice.},
journal = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
volume = {39},
number = {27},
pages = {5247-5254},
pmid = {31043484},
issn = {1529-2401},
support = {R21 MH102679/MH/NIMH NIH HHS/United States ; K01 DA039308/DA/NIDA NIH HHS/United States ; R01 DA033641/DA/NIDA NIH HHS/United States ; R01 MH087463/MH/NIMH NIH HHS/United States ; T32 DA028874/DA/NIDA NIH HHS/United States ; R21 DA040837/DA/NIDA NIH HHS/United States ; },
mesh = {Animals ; Cocaine/*administration &amp; dosage ; Cocaine-Related Disorders/*genetics ; Drug-Seeking Behavior/*physiology ; *Epigenesis, Genetic ; Histones/*genetics ; Male ; Mice, Inbred C57BL ; Mice, Transgenic ; Neurons/*metabolism ; Nucleus Accumbens/*metabolism ; Signal Transduction ; },
abstract = {Although numerous epigenetic modifications have been associated with addiction, little work has explored the turnover of histone variants. Uniquely, the H3.3 variant incorporates stably and preferentially into chromatin independently of DNA replication at active sites of transcription and transcription factor binding. Thus, genomic regions associated with H3.3-containing nucleosomes are particularly likely to be involved in plasticity, such as following repeated cocaine exposure. A recently developed mouse line expressing a neuron-specific hemagglutinin (HA)-tagged H3.3 protein was used to track transcriptionally active sites cumulatively across 19 d of cocaine self-administration. RNA-seq and H3.3-HA ChIP-seq analyses were performed on NAcc tissue collected following cocaine or food self-administration in male mice. RNA sequencing revealed five genes upregulated in cocaine relative to food self-administering mice: Fosb, Npas4, Vgf, Nptx2, and Pmepa1, which reflect known and novel cocaine plasticity-associated genes. Subsequent ChIP-seq analysis confirmed increased H3.3 aggregation at four of these five loci, thus validating H3.3 insertion as a marker of enhanced cocaine-induced transcription. Further motif recognition analysis of the ChIP-seq data showed that cocaine-associated differential H3.3 accumulation correlated with the presence of several transcription factor binding motifs, including RBPJ1, EGR1, and SOX4, suggesting that these are potentially important regulators of molecular cascades associated with cocaine-induced neuronal plasticity. Additional ontological analysis revealed differential H3.3 accumulation mainly near genes involved in neuronal differentiation and dendrite formation. These results establish the H3.3-HA transgenic mouse line as a compelling molecular barcoding tool to identify the cumulative effects of long-term environmental perturbations, such as exposure to drugs of abuse.SIGNIFICANCE STATEMENT Histone H3.3 is a core histone variant that is stably incorporated at active sites of transcription. We used a tagged version of H3.3 expressed exclusively in neurons to delineate active transcription sites following extended cocaine self-administration in mice. This approach revealed the cumulative list of genes expressed in response to cocaine taking over the course of several weeks. We combined this technique with RNA sequencing of tissue collected from the same animals 24 h after the last cocaine exposure. Comparing these datasets provided a full picture of genes that respond to chronic cocaine exposure in NAcc neurons. These studies revealed novel transcription factors that are likely involved in cocaine-induced plasticity and addiction-like behaviors.},
}
@article {pmid31040429,
year = {2019},
author = {Rusk, N},
title = {Mitochondrial barcodes.},
journal = {Nature methods},
volume = {16},
number = {5},
pages = {361},
doi = {10.1038/s41592-019-0416-9},
pmid = {31040429},
issn = {1548-7105},
mesh = {DNA, Mitochondrial/*genetics ; Genomics ; Humans ; Mitochondria/*genetics ; Mutation ; },
}
@article {pmid31032503,
year = {2019},
author = {Cai, L and Bian, F and Sun, L and Wang, H and Zhao, Y},
title = {Condensing-enriched magnetic photonic barcodes on superhydrophobic surface for ultrasensitive multiple detection.},
journal = {Lab on a chip},
volume = {19},
number = {10},
pages = {1783-1789},
doi = {10.1039/c9lc00223e},
pmid = {31032503},
issn = {1473-0189},
mesh = {Hydrogels/*chemistry ; Hydrophobic and Hydrophilic Interactions ; Magnetite Nanoparticles/*chemistry ; MicroRNAs/*analysis ; Particle Size ; *Photons ; Surface Properties ; },
abstract = {The ultrasensitive detection of multiple nucleic acids has great significance in a broad range of medical fields since nucleic acid samples are usually of small volumes and highly diluted. Herein, we present a novel magnetic photonic crystal (PhC) barcode-integrated condensing-enriched superhydrophobic platform for the ultrasensitive multiple miRNA detection. Droplets containing targets could suck the hydrogel PhC barcodes without losing their targets due to the difference in wettability between the hydrophilic PhC barcodes and hydrophobic substrate. During the evaporation of water from the droplet microreactors, these targets could be effectively enriched in the barcodes for achieving higher sensitivities. As the encoding signals of the PhC barcodes are the characteristic reflection peaks generated by their ordered physical nanostructures, the barcodes are stable and free from any fluorescent background and photobleaching; thus, they are accurate for distinguishing different targets. In addition, with the integration of magnetic nanoparticles into the hydrogel PhC barcodes, they could be imparted with the features of immobilization during change of medium and flexible movement for controlling the reaction, both of which could facilitate the detection processes. Based on this platform, we have demonstrated that the detection limit of multiple miRNAs is improved by about three orders. Thus, our platform is an ideal alternative for the ultrasensitive simultaneous multiplex analysis in medical fields.},
}
@article {pmid31031952,
year = {2019},
author = {Caron, H and Molino, JF and Sabatier, D and Léger, P and Chaumeil, P and Scotti-Saintagne, C and Frigério, JM and Scotti, I and Franc, A and Petit, RJ},
title = {Chloroplast DNA variation in a hyperdiverse tropical tree community.},
journal = {Ecology and evolution},
volume = {9},
number = {8},
pages = {4897-4905},
pmid = {31031952},
issn = {2045-7758},
abstract = {We investigate chloroplast DNA variation in a hyperdiverse community of tropical rainforest trees in French Guiana, focusing on patterns of intraspecific and interspecific variation. We test whether a species genetic diversity is higher when it has congeners in the community with which it can exchange genes and if shared haplotypes are more frequent in genetically diverse species, as expected in the presence of introgression.We sampled a total of 1,681 individual trees from 472 species corresponding to 198 genera and sequenced them at a noncoding chloroplast DNA fragment.Polymorphism was more frequent in species that have congeneric species in the study site than in those without congeners (30% vs. 12%). Moreover, more chloroplast haplotypes were shared with congeners in polymorphic species than in monomorphic ones (44% vs. 28%).Despite large heterogeneities caused by genus-specific behaviors in patterns of hybridization, these results suggest that the higher polymorphism in the presence of congeners is caused by local introgression rather than by incomplete lineage sorting. Our findings suggest that introgression has the potential to drive intraspecific genetic diversity in species-rich tropical forests.},
}
@article {pmid31031936,
year = {2019},
author = {Chan-Chable, RJ and Martínez-Arce, A and Mis-Avila, PC and Ortega-Morales, AI},
title = {DNA barcodes and evidence of cryptic diversity of anthropophagous mosquitoes in Quintana Roo, Mexico.},
journal = {Ecology and evolution},
volume = {9},
number = {8},
pages = {4692-4705},
pmid = {31031936},
issn = {2045-7758},
abstract = {Culicidae mosquitoes are potential vectors of pathogens that affect human health. The correct species identification, as well as the discovery and description of cryptic species, is important in public health for the control and management of specific vectors. In the present study, the diversity of anthropophagous mosquitoes in Quintana Roo, at the border between Mexico and Belize, was evaluated using morphological and molecular data (COI-DNA Barcoding). A total of 1,413 adult female specimens were collected, belonging to eight genera and 31 morphospecies. Most species formed well-supported clades. Intraspecific Kimura 2 parameters (K2P) distance average was 0.75%, and a maximum distance of 4.40% was observed for Anopheles crucianss.l. ABGD method identified 28 entities, while 32 entities were identified with the BIN system. In Culex interrogator and Culex nigripalpus a low interspecific genetic distance of 0.1% was observed. One undescribed species belonging to the genus Aedes (Aedesn. sp.) was discovered, but no clear genetic divergence was found between this species and the closely related species Aedes angustivittatus. An intraspecific K2P distance greater than 2.7% was observed in Aedes serratus(3.9%), Anopheles crucianss.l. (4.4%), Culex taeniopus (3.7%), Haemagogus equinus (3.9%), Culex erraticus (5.0%), Psorophora ferox (4.5%), and in Anopheles apicimacula(8.10%); therefore, evidences of cryptic diversity are shown in these species. This study showed that DNA barcodes offer a reliable framework for mosquito species identification in Quintana Roo, except for some closely related species for which it is recommended to use additional nuclear genetic markers such as ITS2, in order to resolve these small discrepancies.},
}
@article {pmid31028653,
year = {2019},
author = {Baßler, K and Günther, P and Schulte-Schrepping, J and Becker, M and Biernat, P},
title = {A Bioinformatic Toolkit for Single-Cell mRNA Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1979},
number = {},
pages = {433-455},
doi = {10.1007/978-1-4939-9240-9_26},
pmid = {31028653},
issn = {1940-6029},
mesh = {Animals ; Cluster Analysis ; Gene Expression Profiling/*methods ; Genomics/*methods ; Humans ; Quality Control ; RNA, Messenger/*genetics ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis/*methods ; Software ; Transcriptome ; },
abstract = {The recent technological developments in the field of single-cell RNA-Seq enable us to assay the transcriptome of up to a million single cells in parallel. However, the analyses of such big datasets present a major challenge. During the last decade, a wide variety of strategies have been proposed covering different steps of the analysis. Here, we introduce a selection of computational tools to provide an overview of a generic analysis pipeline.The first step of every scRNA-Seq experiment is proper study design, which does not require sophisticated experimental or informatics skills but is nonetheless presumably the most important step. The quality of the resulting data strictly depends on the proper planning of the experiment, including the selection of the most suitable technology for the biological question of interest as well as an elaborated study design to minimize the influence of confounding factors. Once the experiment has been conducted, the raw sequencing data needs to be processed to extract the gene expression information for each cell. This task comprises quality assessment of the sequenced reads, alignment against a reference genome, demultiplexing of the cell barcodes, and quantification of the reads/transcripts per gene. As any other transcriptomics technology, single-cell mRNA-Seq requires data normalization to assure sample-to-sample, here cell-to-cell, comparability and the consideration of confounding factors.Once gene expression values have been extracted from the reads and normalized, the researcher has the agony of choosing between a plethora of analysis approaches to investigate diverse aspects of the single-cell transcriptomes, such as dimensionality reduction and clustering to explore cellular heterogeneity or trajectory analysis to model differentiation processes.In this chapter, we present a wrap-up of the abovementioned steps to conduct single-cell RNA-Seq analyses and present a selection of existing tools.},
}
@article {pmid31028640,
year = {2019},
author = {Li, S and Livak, KJ},
title = {Targeted TCR Amplification from Single-Cell cDNA Libraries.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1979},
number = {},
pages = {197-224},
doi = {10.1007/978-1-4939-9240-9_13},
pmid = {31028640},
issn = {1940-6029},
mesh = {*Alleles ; Base Sequence ; Complementarity Determining Regions/genetics ; DNA Primers/genetics ; *Gene Library ; Humans ; Polymerase Chain Reaction/methods ; Receptors, Antigen, T-Cell, alpha-beta/*genetics ; Single-Cell Analysis/*methods ; },
abstract = {Single-cell sequencing of TCR alleles enables determination of T cell specificity. Here we describe a sensitive protocol for targeted amplification of TCR CDR3 regions from single-cell full-length cDNA libraries. By exploiting the specificity of RNase H-dependent PCR (rhPCR), the protocol achieves amplification of TCR alleles and addition of cell barcodes in a single PCR step.},
}
@article {pmid31028635,
year = {2019},
author = {Aicher, TP and Carroll, S and Raddi, G and Gierahn, T and Wadsworth, MH and Hughes, TK and Love, C and Shalek, AK},
title = {Seq-Well: A Sample-Efficient, Portable Picowell Platform for Massively Parallel Single-Cell RNA Sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1979},
number = {},
pages = {111-132},
pmid = {31028635},
issn = {1940-6029},
support = {R01 HL095791/HL/NHLBI NIH HHS/United States ; Z01 AI000947/AI/NIAID NIH HHS/United States ; T32 GM008042/GM/NIGMS NIH HHS/United States ; P30 CA014051/CA/NCI NIH HHS/United States ; DP3 DK097681/DK/NIDDK NIH HHS/United States ; DP2 GM119419/GM/NIGMS NIH HHS/United States ; P01 AI039671/AI/NIAID NIH HHS/United States ; P01 AI045757/AI/NIAID NIH HHS/United States ; U19 AI089992/AI/NIAID NIH HHS/United States ; U24 AI118672/AI/NIAID NIH HHS/United States ; R56 HL126554/HL/NHLBI NIH HHS/United States ; Z01 AI000947/ImNIH/Intramural NIH HHS/United States ; R01 AI138546/AI/NIAID NIH HHS/United States ; R33 CA202820/CA/NCI NIH HHS/United States ; R21 AI106025/AI/NIAID NIH HHS/United States ; RM1 HG006193/HG/NHGRI NIH HHS/United States ; R56 AI104274/AI/NIAID NIH HHS/United States ; U54 CA217377/CA/NCI NIH HHS/United States ; R01 DA046277/DA/NIDA NIH HHS/United States ; },
mesh = {Animals ; Equipment Design ; Gene Expression Profiling/economics/instrumentation/methods ; Gene Library ; High-Throughput Nucleotide Sequencing/economics/instrumentation/*methods ; Humans ; Membranes, Artificial ; Polymerase Chain Reaction/economics/instrumentation/methods ; RNA, Messenger/*genetics ; Reverse Transcription ; Sequence Analysis, RNA/economics/instrumentation/methods ; Single-Cell Analysis/economics/instrumentation/*methods ; },
abstract = {Seq-Well is a low-cost picowell platform that can be used to simultaneously profile the transcriptomes of thousands of cells from diverse, low input clinical samples. In Seq-Well, uniquely barcoded mRNA capture beads and cells are co-confined in picowells that are sealed using a semipermeable membrane, enabling efficient cell lysis and mRNA capture. The beads are subsequently removed and processed in parallel for sequencing, with each transcript's cell of origin determined via the unique barcodes. Due to its simplicity and portability, Seq-Well can be performed almost anywhere.},
}
@article {pmid31028633,
year = {2019},
author = {Bageritz, J and Raddi, G},
title = {Single-Cell RNA Sequencing with Drop-Seq.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1979},
number = {},
pages = {73-85},
doi = {10.1007/978-1-4939-9240-9_6},
pmid = {31028633},
issn = {1940-6029},
support = {Z01 AI000947/AI/NIAID NIH HHS/United States ; T32 GM008042/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Equipment Design ; Gene Expression Profiling/economics/*instrumentation/methods ; Gene Library ; High-Throughput Nucleotide Sequencing/economics/*instrumentation/methods ; Humans ; *Lab-On-A-Chip Devices/economics ; Single-Cell Analysis/economics/*instrumentation/methods ; Transcriptome ; },
abstract = {Drop-Seq is a low-cost, high-throughput platform to profile thousands of cells by encapsualting them into individual droplets. Uniquely barcoded mRNA capture microparticles and cells are coconfined through a microfluidic device within the droplets where they undergo cell lysis and RNA hybridiztion. After breaking the droplets and pooling the hybridized particles, reverse transcription, PCR, and sequencing in single reactions allow to generate data from thousands of single-cell transcriptomes while maintaining information on the cellular origin of each transcript.},
}
@article {pmid31028631,
year = {2019},
author = {Yanai, I and Hashimshony, T},
title = {CEL-Seq2-Single-Cell RNA Sequencing by Multiplexed Linear Amplification.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1979},
number = {},
pages = {45-56},
doi = {10.1007/978-1-4939-9240-9_4},
pmid = {31028631},
issn = {1940-6029},
mesh = {Animals ; Base Sequence ; DNA, Complementary/genetics ; Flow Cytometry ; Gene Expression Profiling/economics/*methods ; Gene Library ; Humans ; Nucleic Acid Amplification Techniques/economics/methods ; RNA/*genetics ; Sequence Analysis, RNA/economics/*methods ; Single-Cell Analysis/economics/*methods ; },
abstract = {Single-cell RNA sequencing has revolutionized the way we look at cell populations. Of the methods available, CEL-Seq was the first to use linear RNA amplification. With early barcoding and 3' sequencing, it is sensitive, cost-effective and easy to perform. Here we describe a protocol for performing CEL-Seq2 on sorted cells, which can be performed without any special equipment.},
}
@article {pmid31028468,
year = {2019},
author = {Buddhachat, K and Chontananarth, T},
title = {Is species identification of Echinostoma revolutum using mitochondrial DNA barcoding feasible with high-resolution melting analysis?.},
journal = {Parasitology research},
volume = {118},
number = {6},
pages = {1799-1810},
pmid = {31028468},
issn = {1432-1955},
mesh = {Animals ; Asia, Southeastern ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*chemistry/*genetics ; Echinostoma/chemistry/*classification/genetics/*isolation &amp; purification ; Mitochondria/genetics ; Phylogeny ; Thailand ; Transition Temperature ; },
abstract = {The taxonomic evaluation of Echinostoma species is controversial. Echinostoma species are recognized as complex, leading to problems associated with accurate identification of these species. The aim of this study was to test the feasibility of using DNA barcoding of cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 1 (ND1) conjugated with high-resolution melting (HRM) analysis to identify Echinostoma revolutum. HRM using COI and ND1 was unable to differentiate between species in the "revolutum complex" but did distinguish between two isolates of 37-collar-spined echinostome species, including E. revolutum (Asian lineage) and Echinostoma sp. A from different genera, e.g., Hypoderaeum conoideum, Haplorchoides mehrai, Fasciola gigantica, and Thapariella anastomusa, based on the Tm values derived from HRM analysis. Through phylogenetic analysis, a new clade of the cryptic species known as Echinostoma sp. A was identified. In addition, we found that the E. revolutum clade of ND1 phylogeny obtained from the Thailand strain was from a different lineage than the Eurasian lineage. These findings reveal the complexity of the clade, which is composed of 37-collar-spined echinostome species found in Southeast Asia. Taken together, the systematic aspects of the complex revolutum group are in need of extensive investigation by integrating morphological, biological, and molecular features in order to clarify them, particularly in Southeast Asia.},
}
@article {pmid31027790,
year = {2019},
author = {Parlapani, FF and Michailidou, S and Anagnostopoulos, DA and Koromilas, S and Kios, K and Pasentsis, K and Psomopoulos, F and Argiriou, A and Haroutounian, SA and Boziaris, IS},
title = {Bacterial communities and potential spoilage markers of whole blue crab (Callinectes sapidus) stored under commercial simulated conditions.},
journal = {Food microbiology},
volume = {82},
number = {},
pages = {325-333},
doi = {10.1016/j.fm.2019.03.011},
pmid = {31027790},
issn = {1095-9998},
mesh = {Animals ; Bacteria/classification/growth &amp; development/isolation &amp; purification/metabolism ; Biodiversity ; Biomarkers/analysis ; Brachyura/*microbiology ; Colony Count, Microbial ; Food Microbiology/*methods ; Food Quality ; Food Storage ; Microbiota/*genetics ; Odorants/analysis ; RNA, Ribosomal, 16S/genetics ; Seafood/*microbiology ; Temperature ; Time Factors ; Volatile Organic Compounds/*analysis ; },
abstract = {Bacterial communities composition using 16S Next Generation Sequencing (NGS) and Volatile Organic Compounds (VOCs) profile of whole blue crabs (Callinectes sapidus) stored at 4 and 10 °C (proper and abuse temperature) simulating real storage conditions were performed. Conventional microbiological and chemical analyses (Total Volatile Base-Nitrogen/TVB-N and Trimethylamine-Nitrogen/TMA-N) were also carried out. The rejection time point was 10 and 6 days for the whole crabs stored at 4 and 10 °C, respectively, as determined by development of unpleasant odors, which coincided with crabs death. Initially, the Aerobic Plate Count (APC) was 4.87 log cfu/g and increased by 3 logs at the rejection time. The 16S NGS analysis of DNA extracted directly from the crab tissue (culture-independent method), showed that the initial microbiota of the blue crab mainly consisted of Candidatus Bacilloplasma, while potential pathogens e.g. Listeria monocytogenes, Pseudomonas aeruginosa and Acinetobacter baumannii, were also found. At the rejection point, bacteria of Rhodobacteraceae family (52%) and Vibrio spp. (40.2%) dominated at 4 and 10 °C, respectively. TVB-N and TMA-N also increased, reaching higher values at higher storage temperature. The relative concentrations of some VOCs such as 1-octen-3-ol, trans-2-octenal, trans,trans-2,4-heptadienal, 2-butanone, 3-butanone, 2-heptanone, ethyl isobutyrate, ethyl acetate, ethyl-2-methylbutyrate, ethyl isovalerate, hexanoic acid ethyl ester and indole, exhibited an increasing trend during crab storage, making them promising spoilage markers. The composition of microbial communities at different storage temperatures was examined by 16S amplicon meta-barcoding analysis. This kind of analysis in conjugation with the volatile profile can be used to explore the microbiological quality and further assist towards the application of the appropriate strategies to extend crab shelf-life and protect consumer's health.},
}
@article {pmid31026600,
year = {2019},
author = {Cheng, J and Cao, Y and MacLeay, A and Lennerz, JK and Baig, A and Frazier, RP and Lee, J and Hu, K and Pacula, M and Meneses, E and Robinson, H and Batten, JM and Brastianos, PK and Heist, RS and Bardia, A and Le, LP and Iafrate, AJ},
title = {Clinical Validation of a Cell-Free DNA Gene Panel.},
journal = {The Journal of molecular diagnostics : JMD},
volume = {21},
number = {4},
pages = {632-645},
doi = {10.1016/j.jmoldx.2019.02.008},
pmid = {31026600},
issn = {1943-7811},
mesh = {Adult ; Aged ; Aged, 80 and over ; *Biomarkers, Tumor ; *Cell-Free Nucleic Acids ; *Circulating Tumor DNA ; DNA Copy Number Variations ; Disease Progression ; Female ; *Genetic Testing/methods/standards ; Humans ; In Situ Hybridization, Fluorescence ; *Liquid Biopsy/methods/standards ; Male ; Middle Aged ; Neoplasm Staging ; Neoplasms/*diagnosis/*genetics ; Reproducibility of Results ; },
abstract = {The use of liquid biopsies to identify driver mutations in patients with solid tumors holds great promise for performing targeted therapy selection, monitoring disease progression, and detecting treatment resistance mechanisms. We describe herein the development and clinical validation of a 28-gene cell-free DNA panel that targets the most common genetic alterations in solid tumors. Bioinformatic and variant filtering solutions were developed to improve test sensitivity and specificity. The panel and these tools were used to analyze commercially available controls, allowing establishment of a limit of detection allele fraction cutoff of 0.25%, with 100% (95% CI, 81.5%-100%) specificity and 89.8% (95% CI, 81.0%-94.9%) sensitivity. In addition, we analyzed a total of 163 blood samples from patients with metastatic cancer (n = 123) and demonstrated a >90% sensitivity for detecting previously identified expected mutations. Longitudinal monitoring of patients revealed a strong correlation of variant allele frequency changes and clinical outcome. Additional clinically relevant information included identification of resistance mutations in patients receiving targeted treatment and detection of complex patterns of mutational heterogeneity. Achieving lower limits of detection will require additional improvements to molecular barcoding; however, these data strongly support clinical implementation of cell-free DNA panels in advanced cancer patients.},
}
@article {pmid31026598,
year = {2019},
author = {Yin, C and Liu, Y and Guo, X and Li, D and Fang, W and Yang, J and Zhou, F and Niu, W and Jia, Y and Yang, H and Xing, J},
title = {An Effective Strategy to Eliminate Inherent Cross-Contamination in mtDNA Next-Generation Sequencing of Multiple Samples.},
journal = {The Journal of molecular diagnostics : JMD},
volume = {21},
number = {4},
pages = {593-601},
doi = {10.1016/j.jmoldx.2019.02.006},
pmid = {31026598},
issn = {1943-7811},
mesh = {*DNA Contamination ; DNA, Mitochondrial/*genetics ; Haplotypes ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Mitochondrial Diseases/diagnosis/genetics ; Mutation ; Sensitivity and Specificity ; Sequence Analysis, DNA ; },
abstract = {Heteroplasmic mutations in mitochondrial DNA (mtDNA) play critical roles in mitochondrial disease, aging, and cancer. Recently, next-generation sequencing (NGS) has been widely used to detect mtDNA mutations for diagnosis and monitoring of the above-mentioned diseases. However, little attention is paid on inherent cross-contamination generated during mtDNA capture and sequencing of mixed samples, which may seriously reduce the detection accuracy of mtDNA heteroplasmic mutations. In this study, a novel sequencing strategy based on a unique double-barcode design was established. The results showed that when single barcode-based analysis strategy was used, cross-contamination level of 20 DNA samples ranged from 0.27% to 11.90% on HiSeq 2500 and from 0.93% to 17.70% on HiSeq X ten, whereas double barcode-based strategy could effectively eliminate cross-contamination. Moreover, the data indicated that cross-contamination was mainly derived from capture process and was significantly affected by different NGS platforms. In addition, contamination level was negatively related to sequencing depth. Moreover, cross-contamination significantly increased the false-positive calling of mtDNA heteroplasmic mutations and remarkably affected the heteroplasmy level of mtDNA mutations. In contrast, cross-contamination had no notable effect on classification of mtDNA haplogroup. Taken together, our novel double barcode-based sequencing strategy is effective in eliminating cross-contamination, enhancing the detection accuracy of mtDNA NGS, and improving its application in diagnosis or monitoring of diseases associated with mtDNA mutations.},
}
@article {pmid31024595,
year = {2019},
author = {Liu, ZW and Gao, YZ and Zhou, J},
title = {Molecular Authentication of the Medicinal Species of Ligusticum (Ligustici Rhizoma et Radix, "Gao-ben") by Integrating Non-coding Internal Transcribed Spacer 2 (ITS2) and Its Secondary Structure.},
journal = {Frontiers in plant science},
volume = {10},
number = {},
pages = {429},
pmid = {31024595},
issn = {1664-462X},
abstract = {Ligustici Rhizoma et Radix (LReR), an important Chinese medicine known as "Gao-ben," refers to Ligusticum sinense Oliv. or Ligusticum jeholense Nakai et Kitag. However, a number of other species are commonly sold as "Gao-ben" in the herbal medicine market, which may result in a series of quality control problems and inconsistent therapeutic effects. The "Gao-ben" is commonly sold sliced and dried, making traditional identification methods difficult. Here, the mini barcode ITS2 region was examined on 68 samples representing LReR and 7 potential adulterant or substitute species. The results showed 100% success rates of PCR and sequencing and the existence of a barcoding gap. The neighbor-joining (NJ) tree indicated that all the tested samples could be exactly identified. The ITS2 secondary structure revealed a clear difference between true "Gao-ben" and three adulterant species. We therefore recommend the use of ITS2 as a mini barcode for distinguishing between closely or distantly related plant species that may be used in Chinese medicine.},
}
@article {pmid31021738,
year = {2019},
author = {González-Solís, D and Elías-Gutiérrez, M and Prado-Bernal, JA and García-de la Cruz, MA},
title = {DNA Barcoding as a Diagnostic Tool of a Rare Human Parasitosis: The First Case of Lagochilascaris minor in Quintana Roo, Mexico.},
journal = {The Journal of parasitology},
volume = {105},
number = {2},
pages = {351-358},
pmid = {31021738},
issn = {1937-2345},
mesh = {Animals ; Ascaridida Infections/*diagnosis/diagnostic imaging/parasitology/surgery ; Ascaridoidea/*classification/enzymology/genetics/ultrastructure ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Female ; *Genes, Mitochondrial ; Humans ; Likelihood Functions ; Male ; Mexico ; Microscopy, Electron, Scanning ; Tomography, X-Ray Computed ; Young Adult ; },
abstract = {Recently, DNA barcoding based on the mitochondrial gene cytochrome c oxidase subunit 1 (COI) has become a widespread tool to identify animals. Its use with parasites of humans has been limited with some groups of nematodes where the amplification of this gene has been difficult. In this study, we present the first COI barcode sequence of a rare parasite from tropical regions, Lagochilascaris minor, which parasitized a human host from Quintana Roo, southern Yucatán Peninsula, Mexico. Destruction of the mastoid apophysis in the lateral sinus and cerebellar involvement were observed at the site of infection. After a radical mastoidectomy and a treatment with 200 mg oral albendazole for 63 days, the patient completely recovered. Lagochilascaris minor was identified based on the ratio between length of spicules and ejaculatory duct, shape of eggs, and host, as well as comparison with its congeners. The mode of infection is unknown, although it could be after direct exposure to eggs or consumption of uncooked wild meat. Morphology of adults is demonstrated using scanning electron microscopy, and high-quality sequences of COI barcode are presented from amplifications using semi-degenerate primers designed for micro-crustaceans. DNA barcoding proved to be a reliable identification method for L. minor. A comparison of the sequences for this species with 81 ascaridoids obtained from the Barcode of Life Database places it in a unique clade most closely related to Baylisascaris procyonis. Future diagnosis of larval and adult stages of L. minor using DNA barcoding will allow the recognition of its infection parameters, transmission, and precise epidemiology. Reports of lagochilascarosis in the Yucatán Peninsula have been occurred over the last decade, suggesting it is an emerging zoonotic disease in the region.},
}
@article {pmid31020752,
year = {2019},
author = {Ma, P and Xu, H and Li, J and Lu, F and Ma, F and Wang, S and Xiong, H and Wang, W and Buratto, D and Zonta, F and Wang, N and Liu, K and Hua, T and Liu, ZJ and Yang, G and Lerner, RA},
title = {Functionality-Independent DNA Encoding of Complex Natural Products.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {58},
number = {27},
pages = {9254-9261},
doi = {10.1002/anie.201901485},
pmid = {31020752},
issn = {1521-3773},
support = {21502114//National Natural Science Foundation of China/International ; 31770776//National Natural Science Foundation of China/International ; 31500632//National Natural Science Foundation of China/International ; 16DZ1910200//Science and Technology Commission of Shanghai Municipality/International ; },
mesh = {Biological Products/chemistry/*metabolism ; Click Chemistry ; DNA/*chemistry ; Enzyme Inhibitors/chemistry/metabolism ; HSP70 Heat-Shock Proteins/antagonists &amp; inhibitors/metabolism ; Humans ; Isomerism ; Luteolin/chemistry ; Medicine, Chinese Traditional ; Poly (ADP-Ribose) Polymerase-1/antagonists &amp; inhibitors/metabolism ; Small Molecule Libraries/chemistry/metabolism ; },
abstract = {DNA encoded chemical libraries (DELs) link the powers of genetics and chemical synthesis via combinatorial optimization. Through combinatorial chemistry, DELs can grow to the unprecedented size of billions to trillions. To take full advantage of the DEL approach, linking the power of genetics directly to chemical structures would offer even greater diversity in a finite chemical world. Natural products have evolved an incredible structural diversity along with their biological evolution. Herein, we used traditional Chinese medicines (TCMs) as examples in a late-stage modification toolbox approach to annotate these complex organic compounds with amplifiable DNA barcodes, which could be easily incorporated into a DEL. The method of end-products labeling also generates a cluster of isomers with a single DNA tag at different sites. These isomers provide an additional spatial diversity for multiple accessible pockets of targeted proteins. Notably, a novel PARP1 inhibitor from TCM has been identified from the natural products enriched DEL (nDEL).},
}
@article {pmid31019194,
year = {2019},
author = {Merino, D and Weber, TS and Serrano, A and Vaillant, F and Liu, K and Pal, B and Di Stefano, L and Schreuder, J and Lin, D and Chen, Y and Asselin-Labat, ML and Schumacher, TN and Cameron, D and Smyth, GK and Papenfuss, AT and Lindeman, GJ and Visvader, JE and Naik, SH},
title = {Publisher Correction: Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {1945},
doi = {10.1038/s41467-019-09916-1},
pmid = {31019194},
issn = {2041-1723},
abstract = {The original version of this Article contained an error in Fig. 4. In the left histogram of the right panel of Fig. 4d, several data points were inadvertently deleted from the histogram during the production process. This error has been corrected in both the PDF and HTML versions of the Article. The original, incorrect version of Fig. 4 is presented in the accompanying Publisher Correction.},
}
@article {pmid31019094,
year = {2019},
author = {Shuvaev, SA and Başerdem, B and Zador, AM and Koulakov, AA},
title = {Network cloning using DNA barcodes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {19},
pages = {9610-9615},
pmid = {31019094},
issn = {1091-6490},
support = {R01 DA036913/DA/NIDA NIH HHS/United States ; },
mesh = {Animals ; *Cloning, Molecular ; *DNA Barcoding, Taxonomic ; High-Throughput Nucleotide Sequencing ; Humans ; *Models, Genetic ; *Neurons ; Synapses/*genetics ; },
abstract = {The connections between neurons determine the computations performed by both artificial and biological neural networks. Recently, we have proposed SYNSeq, a method for converting the connectivity of a biological network into a form that can exploit the tremendous efficiencies of high-throughput DNA sequencing. In SYNSeq, each neuron is tagged with a random sequence of DNA-a "barcode"-and synapses are represented as barcode pairs. SYNSeq addresses the analysis problem, reducing a network into a suspension of barcode pairs. Here, we formulate a complementary synthesis problem: How can the suspension of barcode pairs be used to "clone" or copy the network back into an uninitialized tabula rasa network? Although this synthesis problem might be expected to be computationally intractable, we find that, surprisingly, this problem can be solved efficiently, using only neuron-local information. We present the "one-barcode-one-cell" (OBOC) algorithm, which forces all barcodes of a given sequence to coalesce into the same neuron, and show that it converges in a number of steps that is a power law of the network size. Rapid and reliable network cloning with single-synapse precision is thus theoretically possible.},
}
@article {pmid31018606,
year = {2019},
author = {Meng, Q and Fan, J and Liu, Z and Li, X and Zhang, F and Zhang, Y and Sun, Y and Li, L and Liu, X and Hua, E},
title = {Cytotoxic Withanolides from the Whole Herb of Physalis angulata L.},
journal = {Molecules (Basel, Switzerland)},
volume = {24},
number = {8},
pages = {},
pmid = {31018606},
issn = {1420-3049},
support = {81502968//National Natural Science Foundation of China/ ; },
mesh = {A549 Cells ; Animals ; Antineoplastic Agents, Phytogenic/chemistry/isolation &amp; purification/*pharmacology ; Apoptosis/*drug effects ; Cell Line, Tumor ; Cytotoxins/chemistry/isolation &amp; purification/*pharmacology ; HeLa Cells ; Humans ; Inhibitory Concentration 50 ; Lymphocytes/drug effects/pathology ; Mice ; Physalis/*chemistry ; Plant Extracts/chemistry ; Plants, Medicinal ; Structure-Activity Relationship ; Withanolides/chemistry/isolation &amp; purification/*pharmacology ; },
abstract = {Physalis angulata L. is a medicinal plant of the Solanaceae family, which is used to produce a variety of steroids. The present study reports on the cytotoxic withanolides of this plant. The species of Physalis angulata L. was identified by DNA barcoding techniques. Two new withanolides (1-2), together with six known analogues (3-8), were isolated from the whole plant of Physalis angulata L. The structures of these new compounds were determined on the basis of extensive spectroscopic data analyses and electronic circular dichroism (ECD) calculations. The withanolides exhibited strong cytotoxic activities against A549, Hela and p388 cell lines. Furthermore, compounds 1 and 2 induced typical apoptotic cell death in A549 cell line according to the evaluation of the apoptosis-inducing activity by flow cytometric analysis.},
}
@article {pmid31017948,
year = {2019},
author = {Lee, WK and Kim, SJ and Hou, BK and Van Dover, CL and Ju, SJ},
title = {Population genetic differentiation of the hydrothermal vent crab Austinograea alayseae (Crustacea: Bythograeidae) in the Southwest Pacific Ocean.},
journal = {PloS one},
volume = {14},
number = {4},
pages = {e0215829},
pmid = {31017948},
issn = {1932-6203},
mesh = {Animals ; Brachyura/*genetics ; Electron Transport Complex IV/genetics ; *Genetics, Population ; Geography ; Haplotypes/genetics ; *Hydrothermal Vents ; Pacific Ocean ; Phylogeny ; Species Specificity ; },
abstract = {To understand the origin, migration, and distribution of organisms across disjunct deep-sea vent habitats, previous studies have documented the population genetic structures of widely distributed fauna, such as gastropods, bivalves, barnacles, and squat lobsters. However, a limited number of investigations has been conducted in the Southwest Pacific Ocean, and many questions remain. In this study, we determined the population structure of the bythograeid crab Austinograea alayseae from three adjacent vent systems (Manus Basin, North Fiji Basin, and Tonga Arc) in the Southwest Pacific Ocean using the sequences of two mitochondrial genes (COI and 16S rDNA) and one nuclear gene (28S rDNA). Populations were divided into a Manus clade and a North Fiji-Tonga clade, with sequence divergence values in the middle of the barcoding gap for bythograeids. We inferred that hydrographic and/or physical barriers act on the gene flow of A. alayseae between the Manus and North Fiji basins. Austinograea alayseae individuals interact freely between the North Fiji Basin and the Lau Basin (Tonga Arc). Although further studies of genetic differentiation over a geological time scale, life-history attributes, and genome-based population genetics are needed to improve our understanding of the evolutionary history of A. alayseae, our results contribute to elucidating the phylogeny, evolution, and biogeography of bythograeids.},
}
@article {pmid31015776,
year = {2019},
author = {Li, Q and Yao, J and Zeng, L and Lin, X and Huang, X},
title = {Molecular and morphological evidence for the identity of two nominal species of Astegopteryx (Hemiptera, Aphididae, Hormaphidinae).},
journal = {ZooKeys},
volume = {833},
number = {},
pages = {59-74},
pmid = {31015776},
issn = {1313-2989},
abstract = {The morphology of many insect species is usually influenced by environmental factors and therefore high phenotypic variation exists even within a species. This causes difficulty and uncertainty in species taxonomy, which can be remedied by using molecular data and integrative taxonomy. Astegopteryxbambusae and A.bambucifoliae are currently regarded as two closely related aphid species with similar bamboo hosts and overlapping distributions in the oriental region. However, in practice it is hard to distinguish between them. By incorporating molecular data from four mitochondrial and nuclear genes as well as morphological information from an extensive collection of live specimens, the present study indicates that A.bambucifoliae is a junior synonym of A.bambusae. The data also indicate that large-scale geographic patterns of population differentiation may exist within this species.},
}
@article {pmid31013333,
year = {2019},
author = {Miyamoto, K and Aoki, W and Ohtani, Y and Miura, N and Aburaya, S and Matsuzaki, Y and Kajiwara, K and Kitagawa, Y and Ueda, M},
title = {Peptide barcoding for establishment of new types of genotype-phenotype linkages.},
journal = {PloS one},
volume = {14},
number = {4},
pages = {e0215993},
pmid = {31013333},
issn = {1932-6203},
mesh = {Antibodies/genetics/immunology/metabolism ; Antigens/genetics/immunology ; CD4 Antigens/genetics/immunology ; Genotype ; Humans ; *Nanotechnology ; Peptides/*chemistry/genetics/immunology ; Phenotype ; Pichia/chemistry/genetics ; Protein Binding/*genetics/immunology ; Single-Domain Antibodies/*chemistry/genetics/immunology ; Surface Plasmon Resonance ; },
abstract = {Measuring binding properties of binders (e.g., antibodies) is essential for developing useful experimental reagents, diagnostics, and pharmaceuticals. Display technologies can evaluate a large number of binders in a high-throughput manner, but the immobilization effect and the avidity effect prohibit the precise evaluation of binding properties. In this paper, we propose a novel methodology, peptide barcoding, to quantitatively measure the binding properties of multiple binders without immobilization. In the experimental scheme, unique peptide barcodes are fused with each binder, and they represent genotype information. These peptide barcodes are designed to have high detectability for mass spectrometry, leading to low identification bias and a high identification rate. A mixture of different peptide-barcoded nanobodies is reacted with antigen-coated magnetic beads in one pot. Peptide barcodes of functional nanobodies are cleaved on beads by a specific protease, and identified by selected reaction monitoring using triple quadrupole mass spectrometry. To demonstrate proof-of-principle for peptide barcoding, we generated peptide-barcoded anti-CD4 nanobody and anti-GFP nanobody, and determined whether we could simultaneously quantify their binding activities. We showed that peptide barcoding did not affect the properties of the nanobodies, and succeeded in measuring the binding activities of these nanobodies in one shot. The results demonstrate the advantages of peptide barcoding, new types of genotype-phenotype linkages.},
}
@article {pmid31012766,
year = {2019},
author = {Jamaluddin, JAF and Mohammed Akib, NA and Ahmad, SZ and Abdul Halim, SAA and Abdul Hamid, NK and Mohd Nor, SA},
title = {DNA barcoding of shrimps from a mangrove biodiversity hotspot.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {4},
pages = {618-625},
doi = {10.1080/24701394.2019.1597073},
pmid = {31012766},
issn = {2470-1408},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics/metabolism ; Penaeidae/*genetics ; Phylogeny ; Species Specificity ; },
abstract = {A total of 74 shrimp specimens were sequenced at a 584 bp segment of the cytochrome oxidase subunit I (COI) gene to examine patterns of DNA barcode variation in a mangrove biodiversity hotspot. The Maximum Likelihood tree, barcode gap analysis, Automatic Barcode Gap Discovery analysis and sequence comparisons with data available from Barcode of Life Data System and GenBank recovered 18 taxa of which 15 were identified to species level, 2 at genus level and a single taxon at order level. Two deep mitochondrial DNA lineage divergences were found in the giant tiger prawn, Penaeus monodon. It is suggested that one of the lineages is a consequence of an introduction from aquaculture activity. These results have provided a reliable barcode library for cataloguing shrimps in this area.},
}
@article {pmid31011184,
year = {2019},
author = {Egloff, P and Zimmermann, I and Arnold, FM and Hutter, CAJ and Morger, D and Opitz, L and Poveda, L and Keserue, HA and Panse, C and Roschitzki, B and Seeger, MA},
title = {Engineered peptide barcodes for in-depth analyses of binding protein libraries.},
journal = {Nature methods},
volume = {16},
number = {5},
pages = {421-428},
pmid = {31011184},
issn = {1548-7105},
support = {144823/SNSF_/Swiss National Science Foundation/Switzerland ; 170625/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Bacterial Outer Membrane Proteins/genetics ; Carrier Proteins/*genetics ; Chromatography, Liquid ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Legionella pneumophila/genetics ; Membrane Proteins/genetics ; *Peptide Library ; Tandem Mass Spectrometry ; },
abstract = {Binding protein generation typically relies on laborious screening cascades that process candidate molecules individually. We have developed NestLink, a binder selection and identification technology able to biophysically characterize thousands of library members at once without the need to handle individual clones at any stage of the process. NestLink uses genetically encoded barcoding peptides termed flycodes, which were designed for maximal detectability by mass spectrometry and support accurate deep sequencing. We demonstrate NestLink's capacity to overcome the current limitations of binder-generation methods in three applications. First, we show that hundreds of binder candidates can be simultaneously ranked according to kinetic parameters. Next, we demonstrate deep mining of a nanobody immune repertoire for membrane protein binders, carried out entirely in solution without target immobilization. Finally, we identify rare binders against an integral membrane protein directly in the cellular environment of a human pathogen. NestLink opens avenues for the selection of tailored binder characteristics directly in tissues or in living organisms.},
}
@article {pmid31009680,
year = {2019},
author = {Malvika, S and Ghosh, PR and Dhar, B and Devi, NN and Paul, R and Halder, A and Mazumder, A and Choudhury, Y and Ghosh, SK},
title = {Genetic status of indigenous poultry (red jungle fowl) from India.},
journal = {Gene},
volume = {705},
number = {},
pages = {77-81},
doi = {10.1016/j.gene.2019.04.051},
pmid = {31009680},
issn = {1879-0038},
mesh = {Animals ; Animals, Congenic ; Biodiversity ; Chickens/*classification/*genetics ; Cytochromes c1/genetics ; Evolution, Molecular ; Genetic Variation ; India ; Phylogeny ; Sequence Analysis, DNA/*veterinary ; },
abstract = {The global biodiversity of domesticated red jungle fowl (Gallus gallus) is gradually eroding by replacement with commercial poultry breeds and results loss of valuable genetic and physical traits like resistance to disease, extreme environment, etc. posing a threat to the poultry genetic resources. Very fewer reports exist on Indian poultry diversity, especially native chicken of India. Therefore, species identification and inventorying of the poultry genetic resource is indispensable. Thus, the present study aimed to characterize indigenous chicken from bio-diversity hotspot of Sunderban and Northeast India using DNA sequence based barcoding approach. A total of 15 CO1 (Cytochrome c Oxidase-I) DNA barcode of different indigenous chicken were newly sequenced along with 6 previously published sequences from our laboratory and compared with the available data of distinctive genera of Phasianidae as per the standard protocol and are identified as Gallus gallus. About 98.96% of the Phasianid birds were successfully delimitated into the respective species except for 12 congeneric pairs whose minimum interspecific K2P (Kimura 2-parameter) distance overlaps with the maximum intraspecific distance (3.9%). The least genetic divergence is observed between G. gallus and G. varius (0.013%) and highest between G. gallus and G. lafayettei (0.059%). The NJ tree showed a cohesive clustering of indigenous chicken with G. gallus and distinct with respect to all the different species under study, thereby revealing their taxonomic position except for few G. sonneratti that showed mixed clustering with G. gallus. This may be due to the genetic introgression between the species. Nevertheless, the study for the first time provided the molecular identification tag of indigenous poultry from biodiversity hotspot of East and Northeast India and will remain as a potential guide to recognize inimitable and valuable poultry genetic resources for future needs.},
}
@article {pmid31009252,
year = {2019},
author = {Fachiroh, J and Dwianingsih, EK and Wahdi, AE and Pramatasari, FLT and Hariyanto, S and Pastiwi, N and Yunus, J and Mendy, M and Scheerder, B and Lazuardi, L},
title = {Development of a Biobank from a Legacy Collection in Universitas Gadjah Mada, Indonesia: Proposed Approach for Centralized Biobank Development in Low-Resource Institutions.},
journal = {Biopreservation and biobanking},
volume = {17},
number = {5},
pages = {387-394},
doi = {10.1089/bio.2018.0125},
pmid = {31009252},
issn = {1947-5543},
support = {001/WHO_/World Health Organization/International ; },
mesh = {Biological Specimen Banks/*organization &amp; administration ; Cryopreservation ; Databases, Factual ; Economics ; Electronic Data Processing/*methods ; Humans ; Indonesia ; Specimen Handling/*methods ; },
abstract = {Introduction: The establishment of a biobank requires specific expertise along with relatively expensive infrastructure and appropriate technology. This causes certain challenges in biobank implementation for research in low-middle-income countries. Biobank development with established specimens and data collection (legacy collection) was an approach used in the Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada. This approach aimed to identify the resources available at present, while providing nontechnical information for further development of a centralized biobank. Materials and Methods: Retrospective modeling was done in 2015 by recruiting existing specimen collections and their associated data. The steps were as follows: (1) informing research stakeholders through discussion with experts and stakeholders; (2) identifying specimen collections to be used; (3) determining the system, infrastructure, and consumables needed; (4) determining inclusion criteria; (5) building an in-house database system; (6) organizing data and physical specimen collections; and (7) validating data and physical sample arrangement. All technical procedures were built into standard operating procedures. Results: The model included specimens from one -80°C freezer. The associated data included demographic, clinical diagnosis, and physical sample information. Samples came from six studies, collected between 2001 and 2014. A web-based database was built based on the MySQL programming system. Information on biospecimens from a total of 4196 subjects collected in 11,358 vials was entered into the database, following physical rearrangement of vials in the -80°C freezer with one-dimensional barcodes taped to vials, boxes, and racks. A validation test was done for data concordance between the database and physical arrangement in the -80°C freezer, showing no discrepancies. Conclusion: This report demonstrated current technical and nontechnical insights to further develop a centralized biobank for health research at an academic institution in Indonesia.},
}
@article {pmid31003471,
year = {2019},
author = {Ferrette, BLDS and Domingues, RR and Rotundo, MM and Miranda, MP and Bunholi, IV and De Biasi, JB and Oliveira, C and Foresti, F and Mendonça, FF},
title = {DNA Barcode Reveals the Bycatch of Endangered Batoids Species in the Southwest Atlantic: Implications for Sustainable Fisheries Management and Conservation Efforts.},
journal = {Genes},
volume = {10},
number = {4},
pages = {},
pmid = {31003471},
issn = {2073-4425},
mesh = {Animals ; Brazil ; Conservation of Natural Resources/*methods ; DNA Barcoding, Taxonomic/*veterinary ; Elasmobranchii/*classification/genetics/growth &amp; development ; Endangered Species ; Fisheries ; Phylogeny ; Sequence Analysis, DNA/veterinary ; },
abstract = {Today, elasmobranchs are one the most threatened vertebrate groups worldwide. In fact, at least 90% of elasmobranch species are listed in the International Union for Conservation of Nature (IUCN) Red List, while more than 40% are data-deficient. Although these vertebrates are mainly affected by unsustainable fishery activities, bycatch is also one of the major threats to sharks and batoids worldwide, and represents a challenge for both sustainable fishery management and for biodiversity and conservational efforts. Thus, in this study, DNA barcode methodology was used to identify the bycatch composition of batoid species from small-scale industrial fisheries in the southwest Atlantic and artisanal fisheries from southeast Brazil. A total of 228 individuals belonging to four Chondrichthyes orders, seven families, and at least 17 distinct batoid species were sequenced; among these individuals, 131 belonged to species protected in Brazil, 101 to globally threatened species, and some to species with trade restrictions provided by Appendix II of the Convention on International Trade in Endangered Species (CITES). These results highlight the impacts on marine biodiversity of bycatch by small-scale industrial and unmanaged artisanal fisheries from the southwest Atlantic, and support the implementation of DNA-based methodologies for species-specific identification in data-poor fisheries as a powerful tool for improving the quality of fisheries' catch statistics and for keeping precise bycatch records.},
}
@article {pmid31002692,
year = {2019},
author = {Ongchai, S and Chokchaitaweesuk, C and Kongdang, P and Chomdej, S and Buddhachat, K},
title = {In vitro chondroprotective potential of Senna alata and Senna tora in porcine cartilage explants and their species differentiation by DNA barcoding-high resolution melting (Bar-HRM) analysis.},
journal = {PloS one},
volume = {14},
number = {4},
pages = {e0215664},
pmid = {31002692},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Cartilage/*drug effects/metabolism/pathology ; Collagen Type II/metabolism ; DNA Barcoding, Taxonomic/methods ; DNA, Ribosomal Spacer/genetics ; Disease Models, Animal ; Ethanol/chemistry ; Osteoarthritis/metabolism/*prevention &amp; control ; Phytotherapy/methods ; Protective Agents/pharmacology ; Proteoglycans/metabolism ; Senna Extract/chemistry/*pharmacology ; Senna Plant/*chemistry/classification/genetics ; Sequence Homology, Nucleic Acid ; Species Specificity ; Swine ; },
abstract = {Senna species and anthraquinone derivatives generated by these organisms, rhein and aloe-emodin, exert anti-inflammatory effects. These species present a similar morphology but produce different ingredients when they are used as medicinal products. In this study, a DNA barcoding- (Bar-) high-resolution melting (HRM) technique was developed using internal transcribed sequence 2 (ITS2) to differentiate between Senna alata and Senna tora as a result of significant differences in their melting profiles. We used this approach for confirmation of S. alata and S. tora raw materials, and we examined the chondroprotective properties of the ethanolic extracts of S. alata and S. tora using a porcine model of cartilage degradation induced by a combination of interleukin-17A (IL-17A) and IL-1β. We found that both Senna ethanolic extracts, at a concentration of 25 μg/mL, effectively prevented cartilage degradation. Rhein and aloe-emodin were present in the extract of S. alata but not in that of S. tora. We observed a reduction in the release of sulfated glycosaminoglycans (S-GAGs) and hyaluronic acid (HA) into media in both treatments of Senna extracts, which indicated proteoglycan preservation in explant tissues. These results suggest that neither rhein nor aloe-emodin are the main factors responsible for cartilage-protecting properties. Taken together, results show that both S. alata and S. tora are promising for further development as anti-osteoarthritic agents and that Bar-HRM using ITS2 could be applied for species confirmation with Senna products.},
}
@article {pmid31001832,
year = {2019},
author = {Arroyave, J and Martinez, CM and Stiassny, MLJ},
title = {DNA barcoding uncovers extensive cryptic diversity in the African long-fin tetra Bryconalestes longipinnis (Alestidae: Characiformes).},
journal = {Journal of fish biology},
volume = {95},
number = {2},
pages = {379-392},
doi = {10.1111/jfb.13987},
pmid = {31001832},
issn = {1095-8649},
support = {//AMNH Axelrod Research Curatorship/ ; },
mesh = {Africa, Central ; Africa, Western ; Analysis of Variance ; Animals ; Characiformes/anatomy &amp; histology/classification/*genetics ; DNA/chemistry/isolation &amp; purification ; DNA Barcoding, Taxonomic/*veterinary ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Estuaries ; Female ; *Genetic Variation ; Male ; Multivariate Analysis ; Phenotype ; Phylogeny ; Phylogeography ; Rivers ; Sequence Analysis, DNA ; },
abstract = {To investigate the presence of cryptic diversity in the African longfin-tetra Bryconalestes longipinnis, we employed DNA barcoding in a phylogeographic context, as well as geometric morphometrics, documenting for the first time genetic and body shape variation in the species. Analysis of cytochrome oxidase I gene (coI) sequence variation exposed extremely high levels of genetic differentiation among samples from across the geographic range of the species (up to 18%), certainly much greater than the traditionally employed c. 3% sequence divergence heuristic threshold for conspecifics. Phylogeographic analyses of coI data revealed eight clusters/clades that diverge by >4% and up to 18% (p-distance), potentially representing cryptic members of a species complex. A clear biogeographic pattern was also uncovered, in which the two main coI lineages corresponded geographically with the upper Guinea (UG) and lower Guinea (LG) ichthyofaunal provinces of continental Africa, respectively. Within each of these main lineages, however, no apparent phylogeographic structuring was found. Despite strong genetic differentiation, there is considerable overlap in body shape variation between UG and LG populations. For the most part, morphological variation does not match the strength of the molecular phylogeographic signal. Therefore, the ability to reliably utilise external body shape for regional delimitation remains elusive. Further anatomical investigation appears necessary to establish whether compelling diagnostic morphological features do exist between the divergent lineages of the B. longipinnis complex uncovered in this study.},
}
@article {pmid31001317,
year = {2019},
author = {Yang, CH and Wu, KC and Chuang, LY and Chang, HW},
title = {Decision Theory-Based COI-SNP Tagging Approach for 126 Scombriformes Species Tagging.},
journal = {Frontiers in genetics},
volume = {10},
number = {},
pages = {259},
pmid = {31001317},
issn = {1664-8021},
abstract = {The mitochondrial gene cytochrome c oxidase I (COI) is commonly used for DNA barcoding in animals. However, most of the COI barcode nucleotides are conserved and sequences longer than about 650 base pairs increase the computational burden for species identification. To solve this problem, we propose a decision theory-based COI SNP tagging (DCST) approach that focuses on the discrimination of species using single nucleotide polymorphisms (SNPs) as the variable nucleotides of the sequences of a group of species. Using the example of 126 teleost mackerel fish species (order: Scombriformes), we identified 281 SNPs by alignment and trimming of their COI sequences. After decision rule making, 49 SNPs in 126 fish species were determined using the scoring system of the DCST approach. These COI-SNP barcodes were finally transformed into one-dimensional barcode images. Our proposed DCST approach simplifies the computational complexity and identifies the most effective and fewest SNPs to resolve or discriminate species for species tagging.},
}
@article {pmid30999927,
year = {2019},
author = {Alpern, D and Gardeux, V and Russeil, J and Mangeat, B and Meireles-Filho, ACA and Breysse, R and Hacker, D and Deplancke, B},
title = {BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing.},
journal = {Genome biology},
volume = {20},
number = {1},
pages = {71},
pmid = {30999927},
issn = {1474-760X},
mesh = {Gene Expression Profiling/*methods ; *Gene Library ; High-Throughput Nucleotide Sequencing ; *Sequence Analysis, RNA ; },
abstract = {Despite its widespread use, RNA-seq is still too laborious and expensive to replace RT-qPCR as the default gene expression analysis method. We present a novel approach, BRB-seq, which uses early multiplexing to produce 3' cDNA libraries for dozens of samples, requiring just 2 hours of hands-on time. BRB-seq has a comparable performance to the standard TruSeq approach while showing greater tolerance for lower RNA quality and being up to 25 times cheaper. We anticipate that BRB-seq will transform basic laboratory practice given its capacity to generate genome-wide transcriptomic data at a similar cost as profiling four genes using RT-qPCR.},
}
@article {pmid30998120,
year = {2019},
author = {},
title = {Trends in DNA Barcoding and Metabarcoding.},
journal = {Genome},
volume = {62},
number = {3},
pages = {iii},
doi = {10.1139/gen-2019-0060},
pmid = {30998120},
issn = {1480-3321},
}
@article {pmid30998119,
year = {2019},
author = {Adamowicz, SJ and Boatwright, JS and Chain, F and Fisher, BL and Hogg, ID and Leese, F and Lijtmaer, DA and Mwale, M and Naaum, AM and Pochon, X and Steinke, D and Wilson, JJ and Wood, S and Xu, J and Xu, S and Zhou, X and van der Bank, M},
title = {Trends in DNA barcoding and metabarcoding.},
journal = {Genome},
volume = {62},
number = {3},
pages = {v-viii},
doi = {10.1139/gen-2019-0054},
pmid = {30998119},
issn = {1480-3321},
mesh = {Africa ; *Biodiversity ; *Biota ; Conservation of Natural Resources ; DNA Barcoding, Taxonomic/*trends ; Databases, Nucleic Acid ; *Evolution, Molecular ; Phylogeny ; },
}
@article {pmid30998112,
year = {2019},
author = {Hu, L and Zhao, Y and Yang, Y and Niu, D and Yang, R},
title = {LSU rDNA D5 region: the DNA barcode for molecular classification and identification of Demodex.},
journal = {Genome},
volume = {62},
number = {5},
pages = {295-304},
doi = {10.1139/gen-2018-0168},
pmid = {30998112},
issn = {1480-3321},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Intergenic/genetics ; DNA, Ribosomal/genetics ; Mites/*classification/genetics ; Phylogeny ; },
abstract = {Whether ribosomal genes can be used as DNA barcodes for molecular identification of Demodex (Acariformes: Demodicidae) is unclear. To examine this, Demodex folliculorum, D. brevis, D. canis, and D. caprae were collected for DNA extraction, rDNA fragments amplification, sequencing, and analysis. The V2 and V4 regions of SSU rDNA; D5, D6, and D8 regions of LSU rDNA; and ITS region were obtained from the four morphospecies. BLAST analysis showed that the obtained sequences matched those of Demodex or Aplonobia (Acariformes: Tetranychidae) in Raphignathae. Phylogenetic trees derived from V2, V4, D5, D6, and D8 regions, but not from ITS region, showed that the four species of Demodex clustered independently. Sequence divergence analysis further demonstrated that D5, D6, and D8 regions had obvious barcoding gap between intraspecific and interspecific divergences, with the gap of D5 (16.91%) larger than that of D6 (11.82%) and D8 (4.66%). The V2 and V4 regions did not have a barcoding gap, as the intraspecific and interspecific divergences partially overlapped. For the ITS region, intraspecific and interspecific divergences completely overlapped. These results suggest that the D5, D6, and D8 regions of LSU rDNA, especially D5, are suitable DNA barcodes for Demodex.},
}
@article {pmid30994675,
year = {2019},
author = {Zou, D and Zhang, J and Cui, Y and Qian, G},
title = {Near-infrared-emissive metal-organic frameworks.},
journal = {Dalton transactions (Cambridge, England : 2003)},
volume = {48},
number = {20},
pages = {6669-6675},
doi = {10.1039/c9dt01197h},
pmid = {30994675},
issn = {1477-9234},
abstract = {Emerging as a promising novel material, near-infrared-emissive metal-organic frameworks (NIR-emissive MOFs) have drawn much attention for their unique properties. Here, we demonstrate recent advancements in enhancing the NIR emission performance of MOFs as well as their appealing applications in bio-imaging, sensing and barcoding. The present challenges are briefly concluded and the possible future prospects are discussed.},
}
@article {pmid30990927,
year = {2019},
author = {Gonzalez, E and Pitre, FE and Brereton, NJB},
title = {ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples.},
journal = {Environmental microbiology},
volume = {21},
number = {7},
pages = {2440-2468},
pmid = {30990927},
issn = {1462-2920},
support = {RGPIN-2017-05452//Natural Sciences and Engineering Research Council of Canada/International ; },
mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; DNA, Bacterial/*genetics ; Environmental Microbiology ; Exobiology/*methods ; Gastrointestinal Microbiome ; Humans ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spacecraft ; Species Specificity ; },
abstract = {Analysis of 16S ribosomal RNA (rRNA) gene amplification data for microbial barcoding can be inaccurate across complex environmental samples. A method, ANCHOR, is presented and designed for improved species-level microbial identification using paired-end sequences directly, multiple high-complexity samples and multiple reference databases. A standard operating procedure (SOP) is reported alongside benchmarking against artificial, single sample and replicated mock data sets. The method is then directly tested using a real-world data set from surface swabs of the International Space Station (ISS). Simple mock community analysis identified 100% of the expected species and 99% of expected gene copy variants (100% identical). A replicated mock community revealed similar or better numbers of expected species than MetaAmp, DADA2, Mothur and QIIME1. Analysis of the ISS microbiome identified 714 putative unique species/strains and differential abundance analysis distinguished significant differences between the Destiny module (U.S. laboratory) and Harmony module (sleeping quarters). Harmony was remarkably dominated by human gastrointestinal tract bacteria, similar to enclosed environments on earth; however, Destiny module bacteria also derived from nonhuman microbiome carriers present on the ISS, the laboratory's research animals. ANCHOR can help substantially improve sequence resolution of 16S rRNA gene amplification data within biologically replicated environmental experiments and integrated multidatabase annotation enhances interpretation of complex, nonreference microbiomes.},
}
@article {pmid30989947,
year = {2019},
author = {Cui, XY and Sun, W and Xiong, C and Meng, XX and Shi, YH and Wu, L and Cheng, LL and Li, WJ and Zheng, XL},
title = {[Identification of 23 unknown Li minority medicinal plants based on DNA barcoding].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {44},
number = {2},
pages = {283-292},
doi = {10.19540/j.cnki.cjcmm.20181106.002},
pmid = {30989947},
issn = {1001-5302},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Medicine, Chinese Traditional ; Plants, Medicinal/*classification ; Sequence Analysis, DNA ; },
abstract = {DNA barcode molecular biological technique is used to identify the species of 23 unknown Li minority medicinal plants.DNA was extracted from 23 unknown medicines using the Plant Genomic DNA Extraction kit. The ITS2 and psbA-trnH regions were amplified and sequenced bi-directionally. The Codon Code Aligner V 7. 0. 1 was used to proofread and assemble the contigs and generated consensus sequences. All the sequences were submitted to Traditional Chinese Medicine DNA Barcode Database and NCBI Gen Bank to get information of the species identifications. If the maximum similarity of the identification result is ≥ 97%,exact species can be known. If it is between 97% and 90%,samples' genus can be confirmed; If it is <90%,then we can only confirm its family. Finally there are 17 samples can be identified to species level,5 can be identified to genus level and 1 can be identified to family level. This shows that DNA barcoding used in medicinal plants molecular identification,can identify unknown species rapidly and accurately.},
}
@article {pmid30989942,
year = {2019},
author = {Gao, YZ and Wei, J and Liu, ZW and Zhou, J},
title = {[Application of DNA metabarcoding technology in identification of Chinese patent medicines].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {44},
number = {2},
pages = {261-264},
doi = {10.19540/j.cnki.cjcmm.20181106.006},
pmid = {30989942},
issn = {1001-5302},
mesh = {DNA ; *DNA Barcoding, Taxonomic ; Drugs, Chinese Herbal/*standards ; *Medicine, Chinese Traditional ; Nonprescription Drugs/*standards ; },
abstract = {Metabarcoding technology is a research method derived from the combination of traditional DNA barcodes and highthroughput sequencing technologies. It can quickly,easily and efficiently identify and restore biological samples from multiple species.Biological species are currently widely used in environmental biology research. In the market of traditional Chinese medicines,adulteration and quality instability have severely restricted the sustainable development of the related industries. This article introduced the background of the metabarcoding technology and its preliminary application in the identification of Chinese patent medicines. It also outlined the possible problems in the research process and prospected to the development of the DNA metabarcoding technology.},
}
@article {pmid30989877,
year = {2019},
author = {Chen, FR and Wang, T and Guo, QS and Zhu, ZB and Yang, F and Zou, QJ and Zhang, YJ},
title = {[Identification of Chrysanthemum indicum in different geographical populations and Ch. morifolium based on DNA barcodes of psbA-trnH,matK and trnL].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {44},
number = {4},
pages = {660-665},
doi = {10.19540/j.cnki.cjcmm.2019.0015},
pmid = {30989877},
issn = {1001-5302},
mesh = {*Chrysanthemum ; *DNA Barcoding, Taxonomic ; DNA, Plant ; Phylogeny ; Trees ; },
abstract = {DNA barcode technology was used to establish a rapid identification method of Chrysanthemum indicum and Ch. morifolium based on psbA-trn H,mat K and trn L sequences. The total DNA was extracted from 21 samples collected,and the psbA-trn H,mat K,trn L sequences were amplified by PCR and sequenced. The information of these sequences were obtained. We aligned all 63 sequences,calculated the intraspecific and interspecific distances,analysed the SNPs distribution of psbA-trn H+mat K+trn L combination sequences and constructed the Neighbor-joining(NJ) Tree,using MEGA 7. 0. The results showed that the genetic distances of Ch. indicum,Ch. indicum(Juhuanao)and Ch. morifolium were overlapped. The SNPs analysis of psbA-trn H+mat K+trn L combination sequences showed that there were 19 nucleotide polymorphism loci(SNPs) and nine parsim-informative sites in the combination sequences. In addition,Ch. indicum showed more obvious sequence polymorphism than those of Ch. indicum(Juhuanao) and Ch. morifolium. The psbA-trn H sequences showed obvious length variation.The NJ Tree showed that Ch. morifolium numbered C2-C5 were clustered into a single subbranch with a bootstrap value of 62%,and Ch.morifolium could be distinguished from Ch. indicum and Ch. indicum(Juhuanao). Moreover,Ch. indicum numbered Z9 and Z10 collected from Gansu province were singly clustered into one branch with a bootstrap value of 77%. It was also found that the changes of psbA-trn H and trn L sequences information of Ch. indicum samples from the northwest were obviously related to the geography and environment. Moreover,Ch.indicum and Ch. indicum(Juhuanao) had obvious differentiation,were also regarded as the evolutionary sources of Ch. morifolium. Therefore,psbA-trn H+mat K+trn L combination sequences as DNA barcode can identify Ch. indicum and Ch. morifolium accurately and rapidly,which provides an important basis for germplasm resources identification and species identification.},
}
@article {pmid30989876,
year = {2019},
author = {Chen, FR and Wang, T and Guo, QS and Zhu, ZB and Zou, QJ and Gui, SQ and Zhao, SY},
title = {[Identification of Chrysanthemum indicum and its adulterants based on ITS2 barcode].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {44},
number = {4},
pages = {654-659},
doi = {10.19540/j.cnki.cjcmm.20181204.010},
pmid = {30989876},
issn = {1001-5302},
mesh = {*Chrysanthemum ; DNA Barcoding, Taxonomic ; DNA, Plant ; DNA, Ribosomal Spacer ; *Drugs, Chinese Herbal ; Phylogeny ; Quality Control ; },
abstract = {DNA barcode technology was used to establish a rapid identification method of Chrysanthemum indicum based on ITS2 sequences. The total DNA was extracted from 22 collected samples,and the ITS2 sequence was amplified by PCR and sequenced,and the information of ITS2 sequence was obtained. Another 14 items of the same family or the same genus were downloaded from Gen Bank.We aligned all 36 sequences,calculated the intraspecific and interspecific distances,and constructed Neighbor Joining(NJ) phylogenetic tree,using MEGA 7. 0. The difference of the secondary structure between the ITS2 sequences was compared. The results showed that the genetic distance of Ch. indicum and Ch. morifolium was overlapped,but the maximum intraspecific distance was far less than the minimum interspecific distance between and among Ch. indicum and other species,with an obvious barcoding gap. The NJ tree showed that Ch. indicum and Ch. morifolium shared a clade,and most of Ch. morifolium with some Ch. indicum were shared a subclade,while Inula lineariifolia,Sinosenecio oldhamianus and Senecio scandens belonged to one clade separately. ITS2 secondary structures for I. lineariifolia,S. oldhamianus and S. scandens were significantly different enough to identify completely but Ch. indicum and Ch. morifolium shared two secondary structures of A and B. It was proved that Ch. indicum was one of the evolutionary sources of Ch.morifolium. Therefore ITS2 sequence as DNA barcode can identify Ch. indicum and its adulterants accurately and quickly. The study provides an important basis for Ch. indicum for the identification of germplasm resources and the safety of clinical medication.},
}
@article {pmid30986249,
year = {2019},
author = {Zhang, C and Liu, T and Yuan, X and Huang, H and Yao, G and Mo, X and Xue, X and Yan, H},
title = {The plastid genome and its implications in barcoding specific-chemotypes of the medicinal herb Pogostemon cablin in China.},
journal = {PloS one},
volume = {14},
number = {4},
pages = {e0215512},
pmid = {30986249},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic ; *Genome, Plastid ; Plants, Medicinal/*genetics ; Pogostemon/*genetics ; RNA, Plant/*genetics ; RNA, Ribosomal/*genetics ; RNA, Transfer/*genetics ; },
abstract = {Pogostemon cablin (Blanco) Benth. (Patchouli) is not only an important essential oil plant, but also a valuable medicinal plant in China. P. cablin in China can be divided into three cultivars (Shipai, Gaoyao, and Hainan) and two chemotypes (pogostone-type and patchoulol-type). The pogostone-type and patchoulol-type are, respectively, used for medicinals and perfumes. In this study, we sequenced and characterized the plastid genomes for all three Chinese cultivars and aimed to develop a chemotype-specific barcode for future quality control. The plastid genomes of P. cablin cultivars ranged from 152,461 to 152,462 bp in length and comprise 114 genes including 80 protein coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analyses suggested that P. cablin cultivars clustered with the other two Pogostemon species with strong support. Although extremely conserved in P. cablin plastid genomes, 58 cpSSRs were filtered out among the three cultivars. One single variable locus, cpSSR, was discovered. The cpSSR genotypes successfully matched the chemotypes of Chinese patchouli, which was further supported by PCR-based Sanger sequences in more Chinese patchouli samples. The barcode developed in this study is thought to be a simple and reliable quality control method for Chinese P. cablin on the market.},
}
@article {pmid30985109,
year = {2019},
author = {Ji, J and Lu, W and Zhu, Y and Jin, H and Yao, Y and Zhang, H and Zhao, Y},
title = {Porous Hydrogel-Encapsulated Photonic Barcodes for Multiplex Detection of Cardiovascular Biomarkers.},
journal = {ACS sensors},
volume = {4},
number = {5},
pages = {1384-1390},
doi = {10.1021/acssensors.9b00352},
pmid = {30985109},
issn = {2379-3694},
mesh = {Biomarkers/metabolism ; Capsules ; Gelatin/chemistry ; Humans ; Hydrogel, Polyethylene Glycol Dimethacrylate/chemistry ; Hydrogels/*chemistry ; Myocardium/*metabolism ; *Photons ; Porosity ; },
abstract = {Early detection of cardiac troponin I (cTnI), B-type natriuretic peptide (BNP), and myoglobin (Myo) is essential for the diagnosis of acute myocardial infarction (AMI) and heart failure (HF). We designed a porous hydrogel-encapsulated photonic crystal (PhC) barcode-based suspension array for multiple cardiovascular marker detection. The hybrid hydrogel was composed of polyethylene glycol diacrylate (PEGDA) and gelatin, resulting in a porous and hydrophilic scaffold which ensured stability of the PhC in aqueous solutions. The encapsulated PhC barcodes had stable diffraction peaks for the corresponding markers. Using a sandwich format, the proposed suspension array was used for simultaneous multiplex detection of cardiovascular biomarkers in a single tube. The immunoassay results we tested on cTnI, BNP, and Myo could be assayed in the ranges of 0.01 to 1000 ng/mL, 0.1 to 10 000 pg/mL, and 1 to 10 000 ng/mL with limits of detection of 0.009 ng/mL, 0.084 pg/mL, and 0.68 ng/mL at 3σ, respectively. This method also showed acceptable accuracy and repeated detection, and the results were consistent with the results of conventional clinical methods for detecting actual clinical samples. Therefore, suspension arrays based on hydrogel-encapsulated PhC barcodes are highly promising for AMI diagnosis.},
}
@article {pmid30984782,
year = {2019},
author = {Jang, H and Shin, SE and Ko, KS and Park, SH},
title = {SNP Typing Using Multiplex Real-Time PCR Assay for Species Identification of Forensically Important Blowflies and Fleshflies Collected in South Korea (Diptera: Calliphoridae and Sarcophagidae).},
journal = {BioMed research international},
volume = {2019},
number = {},
pages = {6762517},
pmid = {30984782},
issn = {2314-6141},
mesh = {Animals ; Autopsy ; Cadaver ; Classification/methods ; Cytochromes c/*genetics ; DNA, Mitochondrial/genetics ; Entomology ; *Forensic Genetics ; Humans ; Larva ; *Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Real-Time Polymerase Chain Reaction ; Republic of Korea ; Sarcophagidae/*genetics ; Species Specificity ; },
abstract = {Medicolegal entomology-a subfield of forensic entomology-is mainly used in medicolegal investigations to estimate the postmortem interval (PMI). The minimum PMI of a corpse invaded by necrophagous immature insects can be estimated because the PMI is near to or earlier than the oviposition time of the larvae that hatched and fed on the corpse. As the growth speeds of larvae differ depending on temperature and species, species-specific growth data are used to estimate the minimum PMI. While morphological identification of adult necrophagous flies can be done by a well-trained entomologist, identification of larvae is relatively difficult. Larvae can only be identified up to the family level and developmental stage by observing the posterior spiracles. For these reasons, the molecular biology method of DNA barcoding has been developed. DNA barcoding that targets the mitochondrial cytochrome c oxidase subunit I (COI) gene is commonly used. COI sequences are currently acquired using polymerase chain reaction (PCR) and Sanger sequencing, which are too time-consuming and complex for practical use in medicolegal investigations. To compensate for these limitations and facilitate the use of entomology for medicolegal investigation, we designed a multiplex real-time PCR system to identify nineteen forensically important species of Calliphoridae and Sarcophagidae flies collected in South Korea. In contrast to the Sanger nucleotide sequencing process, this technology only requires a one-step real-time PCR with melt curve analysis of amplicons generated by primers targeting species-specific single nucleotide polymorphisms (SNPs). Multiplex real-time PCR was performed for twelve species of Calliphoridae (four reactions) and for seven species of Sarcophagidae (three reactions). This assay is expected to make it easier and faster for investigating authorities to identify major species of necrophagous flies at beginning of investigation and to increase the utilization of entomological evidence in forensic investigations.},
}
@article {pmid30983442,
year = {2019},
author = {de Borba, RS and Mariotto, S and Centofante, L and Henrique Zawadzki, C and Pasquali Parise-Maltempi, P},
title = {Molecular discrimination of Ancistrus lineages (Siluriformes: Loricariidae) using barcode DNA tool.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {4},
pages = {602-608},
doi = {10.1080/24701394.2019.1597071},
pmid = {30983442},
issn = {2470-1408},
mesh = {Animals ; Brazil ; Catfishes/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics/metabolism ; Genome, Mitochondrial/genetics ; Species Specificity ; },
abstract = {Although several species of Ancistrus have been described from the Amazon and Paraguay river basins in the states of Amazonas and Mato Grosso, Brazil, the taxonomic status of most specimens from these regions remains doubtful. In the present work, cytogenetic and molecular data were used to discriminate and isolate unexpected Ancistrus lineages from the Amazon and Paraguay basins. For that, it was used DNA barcoding based on mitochondrial Cytochrome Oxidase Subunit I (COI) gene and cytogenic data to perform such molecular discrimination. The analyzed sequences had 669 bp, of which 171 bp were conserved and 491 bp were variable. The Neighbor-joining and Bayesian analysis revealed 21 distinct groups in topology. The genetic distances within each group was 0.4%, 21 times smaller than the mean distance observed among groups, which was 8.4%. These values showed seven distinct lineages of Ancistrus from the studied points of the Amazon basin and eight lineages from the Paraguay basin points. Our results illustrate the efficiency of this technique for the discrimination of the Ancistrus lineages once it indicates the occurrence of cryptic species in these regions, which cannot yet be identified either with just chromosomal or morphological analyzes.},
}
@article {pmid30981811,
year = {2019},
author = {Bribiesca-Contreras, G and Pineda-Enríquez, T and Márquez-Borrás, F and Solís-Marín, FA and Verbruggen, H and Hugall, AF and O'Hara, TD},
title = {Dark offshoot: Phylogenomic data sheds light on the evolutionary history of a new species of cave brittle star.},
journal = {Molecular phylogenetics and evolution},
volume = {136},
number = {},
pages = {151-163},
doi = {10.1016/j.ympev.2019.04.014},
pmid = {30981811},
issn = {1095-9513},
mesh = {Animals ; *Caves ; Echinodermata/*classification/*genetics ; Geography ; Mexico ; *Phylogeny ; Species Specificity ; },
abstract = {Caves are a useful system for testing evolutionary and biogeographic hypotheses, as they are isolated, and their environmental conditions have resulted in adaptive selection across different taxa. Although in recent years many more cave species have been discovered, cave-dwelling members of the class Ophiuroidea (brittle stars) remain scarce. Out of the more than two thousand species of brittle stars described to date, only three are regarded as true cave-dwellers. These occurrences represent rare colonising events, compared to other groups that are known to have successfully diversified in these systems. A third species from an anchihaline cave system in the Yucatan Peninsula, Mexico, has been previously identified from cytochrome oxidase I (COI) barcodes. In this study, we reassess the species boundaries of this putative cave species using a phylogenomic dataset (20 specimens in 13 species, 100 exons, 18.7 kbp). We perform species delimitation analyses using robust full-coalescent methods for discovery and validation of hypotheses on species boundaries, as well as infer its phylogenetic relationships with species distributed in adjacent marine regions, in order to investigate the origin of this cave-adapted species. We assess which hypotheses on the origin of subterranean taxa can be applied to this species by taking into account its placement within the genus Ophionereis and its demographic history. We provide a detailed description of Ophionereis commutabilis n. sp., and evaluate its morphological characters in the light of its successful adaptation to life in caves.},
}
@article {pmid30980716,
year = {2019},
author = {Rivers, CA and Rogers, MF and Stubbs, FE and Conway-Campbell, BL and Lightman, SL and Pooley, JR},
title = {Glucocorticoid Receptor-Tethered Mineralocorticoid Receptors Increase Glucocorticoid-Induced Transcriptional Responses.},
journal = {Endocrinology},
volume = {160},
number = {5},
pages = {1044-1056},
pmid = {30980716},
issn = {1945-7170},
support = {MR/R010919/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; Base Sequence ; Binding Sites/genetics ; Cell Line, Tumor ; Chromatin Immunoprecipitation ; DNA/genetics/metabolism ; Glucocorticoids/*pharmacology ; Mice ; Protein Binding ; RNA Interference ; Rats ; Receptors, Glucocorticoid/genetics/*metabolism ; Receptors, Mineralocorticoid/genetics/*metabolism ; Response Elements/genetics ; Transcription, Genetic/*drug effects ; },
abstract = {Mineralocorticoid and glucocorticoid receptors (MRs and GRs) constitute a functionally important dual receptor system detecting and transmitting circulating corticosteroid signals. High expression of MRs and GRs occurs in the same cells in the limbic system, the primary site of glucocorticoid action on cognition, behavior, and mood; however, modes of interaction between the receptors are poorly characterized. We used chromatin immunoprecipitation with nucleotide resolution using exonuclease digestion, unique barcode, and single ligation (ChIP-nexus) for high-resolution genome-wide characterization of MR and GR DNA binding profiles in neuroblastoma cells and demonstrate recruitment to highly similar DNA binding sites. Expressed MR or GR showed differential regulation of endogenous gene targets, including Syt2 and Ddc, whereas coexpression produced augmented transcriptional responses even when MRs were unable to bind DNA (MR-XDBD). ChIP confirmed that MR-XDBD could be tethered to chromatin by GR. Our data demonstrate that MR can interact at individual genomic DNA sites in multiple modes and suggest a role for MR in increasing the transcriptional response to glucocorticoids.},
}
@article {pmid30977972,
year = {2019},
author = {Morinière, J and Balke, M and Doczkal, D and Geiger, MF and Hardulak, LA and Haszprunar, G and Hausmann, A and Hendrich, L and Regalado, L and Rulik, B and Schmidt, S and Wägele, JW and Hebert, PDN},
title = {A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding-based biomonitoring.},
journal = {Molecular ecology resources},
volume = {19},
number = {4},
pages = {900-928},
pmid = {30977972},
issn = {1755-0998},
support = {//Bavarian State Ministry of Science and the Arts/ ; BMBF FKZ 01LI1101//German Federal Ministry of Education and Research/ ; BMBF FKZ 01LI1501//German Federal Ministry of Education and Research/ ; },
mesh = {Animals ; Ceratopogonidae/*classification/*genetics ; Chironomidae/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Diptera/*classification/*genetics ; Ecological Parameter Monitoring/methods ; Germany ; },
abstract = {This study summarizes results of a DNA barcoding campaign on German Diptera, involving analysis of 45,040 specimens. The resultant DNA barcode library includes records for 2,453 named species comprising a total of 5,200 barcode index numbers (BINs), including 2,700 COI haplotype clusters without species-level assignment, so called "dark taxa." Overall, 88 out of 117 families (75%) recorded from Germany were covered, representing more than 50% of the 9,544 known species of German Diptera. Until now, most of these families, especially the most diverse, have been taxonomically inaccessible. By contrast, within a few years this study provided an intermediate taxonomic system for half of the German Dipteran fauna, which will provide a useful foundation for subsequent detailed, integrative taxonomic studies. Using DNA extracts derived from bulk collections made by Malaise traps, we further demonstrate that species delineation using BINs and operational taxonomic units (OTUs) constitutes an effective method for biodiversity studies using DNA metabarcoding. As the reference libraries continue to grow, and gaps in the species catalogue are filled, BIN lists assembled by metabarcoding will provide greater taxonomic resolution. The present study has three main goals: (a) to provide a DNA barcode library for 5,200 BINs of Diptera; (b) to demonstrate, based on the example of bulk extractions from a Malaise trap experiment, that DNA barcode clusters, labelled with globally unique identifiers (such as OTUs and/or BINs), provide a pragmatic, accurate solution to the "taxonomic impediment"; and (c) to demonstrate that interim names based on BINs and OTUs obtained through metabarcoding provide an effective method for studies on species-rich groups that are usually neglected in biodiversity research projects because of their unresolved taxonomy.},
}
@article {pmid30977563,
year = {2019},
author = {Wan, A and Place, E and Pierce, EA and Comander, J},
title = {Characterizing variants of unknown significance in rhodopsin: A functional genomics approach.},
journal = {Human mutation},
volume = {40},
number = {8},
pages = {1127-1144},
pmid = {30977563},
issn = {1098-1004},
support = {K12 EY016335-10/EY/NEI NIH HHS/United States ; //Massachusetts Lions Eye Research Fund/International ; Career Development Award//Research to Prevent Blindness/International ; Enhanced Career Development Award/FFB/Foundation Fighting Blindness/United States ; P30 EY014104/EY/NEI NIH HHS/United States ; },
mesh = {Gene Expression Regulation ; Gene Library ; Genetic Predisposition to Disease ; *Genetic Variation ; Genomics ; HEK293 Cells ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Models, Biological ; Retinal Diseases/*genetics ; Rhodopsin/*genetics/metabolism ; Sequence Analysis, DNA ; },
abstract = {Characterizing the pathogenicity of DNA sequence variants of unknown significance (VUS) is a major bottleneck in human genetics, and is increasingly important in determining which patients with inherited retinal diseases could benefit from gene therapy. A library of 210 rhodopsin (RHO) variants from literature and in-house genetic diagnostic testing were created to efficiently detect pathogenic RHO variants that fail to express on the cell surface. This study, while focused on RHO, demonstrates a streamlined, generalizable method for detecting pathogenic VUS. A relatively simple next-generation sequencing-based readout was developed so that a flow cytometry-based assay could be performed simultaneously on all variants in a pooled format, without the need for barcodes or viral transduction. The resulting dataset characterized the surface expression of every RHO library variant with a high degree of reproducibility (r[2] = 0.92-0.95), recategorizing 37 variants. For example, three retinitis pigmentosa pedigrees were solved by identifying VUS which showed low expression levels (p.G18D, p.G101V, and p.P180T). Results were validated across multiple assays and correlated with clinical disease severity. This study presents a parallelized, higher-throughput cell-based assay for the functional characterization of VUS in RHO, and can be applied more broadly to other inherited retinal disease genes and other disorders.},
}
@article {pmid30976082,
year = {2019},
author = {de Luna Sales, JB and Haimovici, M and Ready, JS and Souza, RF and Ferreira, Y and de Cassia Silva Pinon, J and Costa, LFC and Asp, NE and Sampaio, I and Schneider, H},
title = {Surveying cephalopod diversity of the Amazon reef system using samples from red snapper stomachs and description of a new genus and species of octopus.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {5956},
pmid = {30976082},
issn = {2045-2322},
mesh = {Animals ; Biodiversity ; Data Collection/*methods ; Ecosystem ; Gastrointestinal Contents/*chemistry ; *Models, Biological ; Octopodiformes/*classification/*genetics ; *Phylogeny ; },
abstract = {The cephalopod fauna of the southwestern Atlantic is especially poorly-known because sampling is mostly limited to commercial net-fishing operations that are relatively inefficient at obtaining cephalopods associated with complex benthic substrates. Cephalopods have been identified in the diets of many large marine species but, as few hard structures survive digestion in most cases, the identification of ingested specimens to species level is often impossible. Samples can be identified by molecular techniques like barcoding and for cephalopods, mitochondrial 16S and COI genes have proven to be useful diagnostic markers for this purpose. The Amazon River estuary and continental shelf are known to encompass a range of different substrates with recent mapping highlighting the existence of an extensive reef system, a type of habitat known to support cephalopod diversity. The present study identified samples of the cephalopod fauna of this region obtained from the stomachs of red snappers, Lutjanus purpureus, a large, commercially-important fish harvested by fisheries using traps and hook-and-line gear that are capable of sampling habitats inaccessible to nets. A total of 98 samples were identified using molecular tools, revealing the presence of three squid species and eight MOTUs within the Octopodidae, representing five major clades. These include four known genera, Macrotritopus, Octopus, Scaeurgus and Amphioctopus, and one basal group distinct from all known octopodid genera described here as Lepidoctopus joaquini Haimovici and Sales, new genus and species. Molecular analysis of large predatory fish stomach contents was found to be an incredibly effective extended sampling method for biodiversity surveys where direct sampling is very difficult.},
}
@article {pmid30970623,
year = {2019},
author = {Howard, C and Hill, E and Kreuzer, M and Mali, P and Masiero, E and Slater, A and Sgamma, T},
title = {DNA Authentication of St John's Wort (Hypericum perforatum L.) Commercial Products Targeting the ITS Region.},
journal = {Genes},
volume = {10},
number = {4},
pages = {},
pmid = {30970623},
issn = {2073-4425},
mesh = {DNA/genetics ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/*genetics ; Hypericum/classification/*genetics ; Plant Extracts/classification/genetics ; Plants, Medicinal/classification/*genetics ; },
abstract = {There is considerable potential for the use of DNA barcoding methods to authenticate raw medicinal plant materials, but their application to testing commercial products has been controversial. A simple PCR test targeting species-specific sequences within the nuclear ribosomal internal transcribed spacer (ITS) region was adapted to screen commercial products for the presence of Hypericum perforatum L. material. DNA differing widely in amount and extent of fragmentation was detected in a number of product types. Two assays were designed to further analyse this DNA using a curated database of selected Hypericum ITS sequences: A qPCR assay based on a species-specific primer pair spanning the ITS1 and ITS2 regions, using synthetic DNA reference standards for DNA quantitation and a Next Generation Sequencing (NGS) assay separately targeting the ITS1 and ITS2 regions. The ability of the assays to detect H. perforatum DNA sequences in processed medicines was investigated. Out of twenty different matrices tested, both assays detected H. perforatum DNA in five samples with more than 10[3] ITS copies µL[-1] DNA extract, whilst the qPCR assay was also able to detect lower levels of DNA in two further samples. The NGS assay confirmed that H. perforatum was the major species in all five positive samples, though trace contaminants were also detected.},
}
@article {pmid30968784,
year = {2019},
author = {Francuski, L and Gojković, N and Krtinić, B and Milankov, V},
title = {The diagnostic utility of sequence-based assays for the molecular delimitation of the epidemiologically relevant Culex pipiens pipiens taxa (Diptera: Culicidae).},
journal = {Bulletin of entomological research},
volume = {109},
number = {6},
pages = {752-761},
doi = {10.1017/S0007485319000105},
pmid = {30968784},
issn = {1475-2670},
mesh = {Animals ; Culex/*classification/genetics ; DNA, Ribosomal Spacer/genetics ; *Ecotype ; Electron Transport Complex IV/genetics ; Gene Flow ; Genetic Markers ; Geography ; Mosquito Vectors ; Sequence Analysis, DNA ; Serbia ; },
abstract = {The northern house mosquito (Culex pipiens pipiens L.) is a vector of several important pathogens and comprises two epidemiologically distinct ecotypes (molestus Forskål and pipiens). The delimitation of its ecotypes is a crucial, yet controversial step in vector surveillance due to varying diagnostic values of different characters. Therefore, we reviewed the success of a diagnostic assay based on the mitochondrial cytochrome c oxidase subunit I locus (COI) by analyzing previously published sequences of molestus and pipiens sampled in different geographical areas. Next, by genotyping individuals from Northern Serbia at this locus, we additionally assessed whether genetic structure of urban and rural Cx. p. pipiens ecotypes corresponded to the admixture pattern. Finally, to account for the different susceptibility of genetic markers to introgression, we also analyzed genetic structuring based on the ribosomal internal transcribed spacer 2 (ITS2). No latitude-dependent differentiation of Cx. p. pipiens ecotypes was found at a global level, with the COI assay further failing to accurately identify molestus and pipiens ecotypes. Likewise, both individual- (BAPS) and population-based (analysis of molecular variance and FST estimates) methods showed no significant urban/rural genetic differentiation in Serbia, indicating unhindered gene flow between different Cx. p. pipiens habitat types. The findings challenge the previous instances of Cx. p. pipiens ecotype identification, while also spotlighting the vectorial capacity of their hybrid offspring.},
}
@article {pmid30968361,
year = {2019},
author = {Shum, EY and Walczak, EM and Chang, C and Christina Fan, H},
title = {Quantitation of mRNA Transcripts and Proteins Using the BD Rhapsody™ Single-Cell Analysis System.},
journal = {Advances in experimental medicine and biology},
volume = {1129},
number = {},
pages = {63-79},
doi = {10.1007/978-981-13-6037-4_5},
pmid = {30968361},
issn = {0065-2598},
mesh = {*Gene Expression Profiling ; *High-Throughput Nucleotide Sequencing ; RNA, Messenger/*analysis ; Sequence Analysis, RNA ; Single-Cell Analysis/*instrumentation/*methods ; Transcriptome ; },
abstract = {In this review, we describe the BD Rhapsody™ Single-Cell Analysis System, a platform that allows high-throughput capture of nucleic acids from single cells using a simple cartridge workflow and a multitier barcoding system. The resulting captured information can be used to generate various types of next-generation sequencing (NGS) libraries, including whole transcriptome analysis for discovery biology and targeted RNA analysis for high sensitivity transcript detection. The BD Rhapsody system can be used with emerging applications, such as BD™ AbSeq assays, to profile gene expression in both mRNA and protein level to provide ultra-high resolution analysis of single cells.},
}
@article {pmid30968360,
year = {2019},
author = {Hashimoto, S},
title = {Nx1-Seq (Well Based Single-Cell Analysis System).},
journal = {Advances in experimental medicine and biology},
volume = {1129},
number = {},
pages = {51-61},
doi = {10.1007/978-981-13-6037-4_4},
pmid = {30968360},
issn = {0065-2598},
mesh = {Cell Separation ; Gene Expression Profiling/*methods ; Sequence Analysis, RNA ; Single-Cell Analysis/*methods ; *Transcriptome ; },
abstract = {Research on the hierarchical nature of cell differentiation and heterogeneity in tissues has been performed by isolating and identifying cells by the use of monoclonal antibodies, cell sorting, microdissection, and functional assays. However, it is difficult to analyze continuous changes in cell differentiation and the identification of cells for which cell markers are unclear. Furthermore, cell populations considered identical were shown to be diverse. Recently, single cell gene expression analysis was performed to help understand the complexity of cell populations. Single-cell analysis can analyze the diversity of individual cell populations as well as the tissue microenvironment, and is extremely useful for research on intercellular interactions in diseases and identifying specific marker genes. Recent advances in technology have made it possible to analyze hundreds of single cells. In this paper, we introduce our newly developed well-based single-cell transcriptome method, which includes other methods.},
}
@article {pmid30964914,
year = {2019},
author = {Sundaresan, N and Jagan, EG and Kathamuthu, G and Pandi, M},
title = {Internal transcribed spacer 2 (ITS2) molecular morphometric analysis based species delimitation of foliar endophytic fungi from Aglaia elaeagnoidea, Flacourtia inermis and Premna serratifolia.},
journal = {PloS one},
volume = {14},
number = {4},
pages = {e0215024},
pmid = {30964914},
issn = {1932-6203},
mesh = {Aglaia/*genetics/microbiology ; Ascomycota/genetics/*physiology ; Biodiversity ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/*genetics ; Endophytes/*physiology ; Flacourtia/*genetics/microbiology ; Lamiaceae/*genetics/microbiology ; Phylogeny ; Species Specificity ; },
abstract = {Molecular morphometrics is an emerging third dimensional aspect of fungal species delimitation. They have been demonstrated to be more informative than conventional barcoding methods. Hence in this study, foliar endophytic fungal (FEF) assemblages in three Magnoliopsida plants were delimited using nuclear ribosomal internal transcribed spacer 2 (ITS2) sequence-secondary structural features based phylogenetic analysis, also known as molecular morphometrics. A total of 392 FEF isolates were obtained from the Aglaia elaeagnoidea, Flacourtia inermis, and Premna serratifolia leaves and grouped into 98 morphotypes. Among these host plants, P. serratifolia showed the maximum percentage of colonization frequency. Representatives of each morphotype was sequenced and subjected to further molecular characterization. The results revealed that morphotypes were belonged to the phylum of Ascomycota, distributed over two classes (Sordariomycetes (68.59%) and Dothideomycetes (31.41%)), 6 orders and 19 genera. Based on compensatory base changes (CBC) analysis and absolute identity of ITS2 structure, 21, 20 and 23 species were recognized from A. elaeagnoidea, F. inermis, and P. serratifolia respectively. Diversity indices were higher in A. elaeagnoidea, despite it accounted for a modest 16.8% of total isolates recorded in this study. The genus Colletotrichum was predominant in A. elaeagnoidea (39%) and P. serratifolia (48%). Similarly, Diaporthe (43%) was dominant in F. inermis. Several host-specific species were also observed. This study concludes that these plants host diverse species of Ascomycota. To the best of our knowledge, this is the first detailed report on FEF diversity from these plants. Also, the inclusion of ITS2 secondary structure information along with the sequence provides a further dimension to resolve the inherent problems in identification of fungal species.},
}
@article {pmid30962473,
year = {2019},
author = {Young, MR and Moraza, ML and Ueckermann, E and Heylen, D and Baardsen, LF and Lima-Barbero, JF and Gal, S and Gavish-Regev, E and Gottlieb, Y and Roy, L and Recht, E and El Adouzi, M and Palevsky, E},
title = {Linking morphological and molecular taxonomy for the identification of poultry house, soil, and nest dwelling mites in the Western Palearctic.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {5784},
pmid = {30962473},
issn = {2045-2322},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Ecosystem ; Genome, Insect ; Mites/*classification/genetics/pathogenicity ; *Phylogeny ; Poultry/parasitology ; },
abstract = {Because of its ability to expedite specimen identification and species delineation, the barcode index number (BIN) system presents a powerful tool to characterize hyperdiverse invertebrate groups such as the Acari (mites). However, the congruence between BINs and morphologically recognized species has seen limited testing in this taxon. We therefore apply this method towards the development of a barcode reference library for soil, poultry litter, and nest dwelling mites in the Western Palearctic. Through analysis of over 600 specimens, we provide DNA barcode coverage for 35 described species and 70 molecular taxonomic units (BINs). Nearly 80% of the species were accurately identified through this method, but just 60% perfectly matched (1:1) with BINs. High intraspecific divergences were found in 34% of the species examined and likely reflect cryptic diversity, highlighting the need for revision in these taxa. These findings provide a valuable resource for integrative pest management, but also highlight the importance of integrating morphological and molecular methods for fine-scale taxonomic resolution in poorly-known invertebrate lineages.},
}
@article {pmid30957604,
year = {2019},
author = {Velamala, GR and Naranji, MK and Kondamudi, RB and Netto-Ferreira, AL},
title = {DNA barcoding of commercially important snapper species (Lutjaniformes; Lutjanidae; Lutjanus) from Visakhapatnam, Central Eastern coast of India.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {4},
pages = {585-591},
doi = {10.1080/24701394.2018.1551387},
pmid = {30957604},
issn = {2470-1408},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics/metabolism ; Fishes/*genetics ; Genome, Mitochondrial/genetics ; India ; Phylogeny ; Species Specificity ; },
abstract = {Snappers are commercially important fishes in Indian waters, currently belonging to the order Lutjaniformes, family Lutjanidae. Generally, recognizing species of Lutjanus is a challenging task not only because of overlapping morphological characters, such as shapes, size groups, or colour patterns, but also based on the definition of the species concept or the definition of the threshold for speciation. In India there has not been any updated and accurate study of the genus so far. Besides, identification of the group based on ecological aspects and DNA barcoding tools were confined to limited laboratories. In the present study, ten species of snappers were identified from samples obtained from the major fish landing centres in the Visakhapatnam, Central Eastern coast of India. Snapper species were identified using COI (Cytochrome oxidase I) sequences for DNA barcoding. The validity of the conjecture species-level taxonomy based on COI is assisted with high equivalence search (98-100%) both in BOLD and BLAST, well-distributed genetic distance values.},
}
@article {pmid30956417,
year = {2019},
author = {Malik, S and Priya, A and Babbar, SB},
title = {Employing barcoding markers to authenticate selected endangered medicinal plants traded in Indian markets.},
journal = {Physiology and molecular biology of plants : an international journal of functional plant biology},
volume = {25},
number = {2},
pages = {327-337},
pmid = {30956417},
issn = {0971-5894},
abstract = {The high demand of medicinal plants and their unrestricted collection have rendered many of these as rare or endangered. The restrictions imposed on their collection and trade are difficult to implement because of the inability to identify them in fragmented form. The rarity of these plants in nature and lack of their cultivation raise doubt about the authenticity of the herbals sold in markets. Therefore, in the present investigation, ITS/ITS2, matK, rbcL and rpoC1 sequences of fourteen species of important medicinal plants, some of which are endangered, were generated and checked for their species-specificity (sequences having maximum similarity only with their own) by BLAST1 and/or BOLD identifications. ITS sequences of 12 species were species-specific. However, ITS2 of only 10 of these 12 species were species-specific. As for the chloroplast loci, rbcL and rpoC1 sequences of all 14 species could be obtained, while matK sequences of only 10 of these could be generated. Of the retrieved sequences, rbcL, rpoC1 and matK sequences of 7, 11 and 7 species, respectively, were species-specific. The sequences of the targeted loci from the herbal samples of these species were difficult to retrieve because of failure in the amplification or sequencing. Nevertheless, based on ITS2 and/or one or more of the chloroplast loci targeted, the botanical identities of 22 herbal market samples were checked by phylogenetic tree, BLAST1 and BOLD identification methods. Of these 22 samples, only one of each of Rauvolfia serpentina and Picrorhiza kurroa were found to be authentic.},
}
@article {pmid30954626,
year = {2019},
author = {da Silva, CF and Daneluz, CM and Camacho-Oliveira, RB and do Prado, FD and Foresti, F and Rodrigues, CE and Porto-Foresti, F},
title = {DNA Barcode reveals mislabelling in the identification of marine fish swimming bladders for commercialization.},
journal = {Forensic science international},
volume = {299},
number = {},
pages = {41-43},
doi = {10.1016/j.forsciint.2019.03.001},
pmid = {30954626},
issn = {1872-6283},
mesh = {Animals ; Brazil ; Commerce ; Conservation of Natural Resources ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Endangered Species ; Fishes/*genetics ; Polymerase Chain Reaction ; *Species Specificity ; },
abstract = {Sequences of the mitochondrial gene COI (DNA Barcode) wereused to identify marine fish swimming bladders commercialized in Brazil. The comparisons of the obtained sequences of the samples registered as catfish for the commerce with previously published data available in NCBI and BOLD showed that the fish products commercialized corresponded to two Perciform species, Pogonias cromis and Micropogonias furnieri. These results besides contradicting the formal identification of the species included in the fisheries control revealed an illegal trade of one of these species, M. furnieri that is threatened and consequently have its capture prohibited.},
}
@article {pmid30954477,
year = {2019},
author = {Liu, X and Liu, Z and Dziulko, AK and Li, F and Miller, D and Morabito, RD and Francois, D and Levy, SF},
title = {iSeq 2.0: A Modular and Interchangeable Toolkit for Interaction Screening in Yeast.},
journal = {Cell systems},
volume = {8},
number = {4},
pages = {338-344.e8},
pmid = {30954477},
issn = {2405-4720},
support = {R01 HG008354/HG/NHGRI NIH HHS/United States ; U01 HL127522/HL/NHLBI NIH HHS/United States ; },
mesh = {Fungal Proteins/chemistry/metabolism ; Gene Library ; Protein Interaction Mapping/*methods ; Recombinant Proteins/chemistry/metabolism ; Saccharomyces cerevisiae ; Sequence Analysis, DNA/*methods ; *Software ; },
abstract = {We developed a flexible toolkit for combinatorial screening in Saccharomyces cerevisiae, which generates large libraries of cells, each uniquely barcoded to mark a combination of DNA elements. This interaction sequencing platform (iSeq 2.0) includes genomic landing pads that assemble combinations through sequential integration of plasmids or yeast mating, 15 barcoded plasmid libraries containing split selectable markers (URA3AI, KanMXAI, HphMXAI, and NatMXAI), and an array of ∼24,000 "double-barcoder" strains that can make existing yeast libraries iSeq compatible. Various DNA elements are compatible with iSeq: DNA introduced on integrating plasmids, engineered genomic modifications, or entire genetic backgrounds. DNA element libraries are modular and interchangeable, and any two libraries can be combined, making iSeq capable of performing many new combinatorial screens by short-read sequencing.},
}
@article {pmid30952197,
year = {2019},
author = {Wang, T and Qi, D and Sun, S and Liu, Z and Du, Y and Guo, S and Ma, J},
title = {DNA barcodes and their characteristic diagnostic sites analysis of Schizothoracinae fishes in Qinghai province.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {4},
pages = {592-601},
doi = {10.1080/24701394.2019.1580273},
pmid = {30952197},
issn = {2470-1408},
mesh = {Animals ; China ; Cyprinidae/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Genome, Mitochondrial/genetics ; Phylogeny ; Species Specificity ; },
abstract = {The Qinghai-Tibetan Plateau (QTP), the source and upper reaches of many Asian rivers, are crisscrossed by rivers and dotted with lakes. Schizothoracinae fishes, species native to the QTP, are distributed widely through these rivers and lakes. Over the past decades, ecological protection has become increasingly intense. The rapid acquisition of the genetic information and accurate gene sequence database are assumed to play an important role in the conservation of species diversity and biodiversity. In this study, 153 COI sequences (648bp in length) covering 13 species in 8 genera of Schizothoracinae fishes in Qinghai Province were used to determine whether barcode could identify Schizothoracinae species accurately. The average Kimura two parameter (K2P) genetic distances within and among species were 0.35% and 8.83%, respectively. The maximum K2P distance within species was observed in Gymnocypris eckloni (1.36%) while minimum K2P distance among species was observed between Chuanchia labiosa and Schizopygopsis pylzovi (0.23%). Overlaps existed in K2P distance intra- and inter- species based on both the genes. Eleven groups with 9 single-species groups and 2 multi-species groups were identified through Automatic Barcode Gap Discovery System, which were consistent with the overlaps of K2P distance. 96.7% as the accurate ratio for COI barcode was calculated and high solution was observed in the phylogenetic trees based on COI gene and Cyt b gene. Except for the similar results based on two genes above, COI barcode was more economical than Cyt b gene. The SOM model successfully predicted characteristic-diagnostic sites at species level: 36 characteristic-diagnostic sites from eight species, in which 12 from Gmnodiptychus pachycgeilus, 2 from Platypharodon extremus, 7 from Ptychobarbus kaznakovi, 2 from Schizopygopsis anteroventris, 2 from Schizopygopsis malacanthus, 3 from Schizopygopsis malacanthus chengi, 3 from Schizothorax dolichonema and 5 from Schizothorax lantsangensis. Our results show that Schizothoracinae fishes can be identified validly by using COI DNA barcode. Thirty-six characteristic-diagnostic sites were proposed to be applied into works of species identification for the Schizothoracinae fishes in Qinghai Province.},
}
@article {pmid30951289,
year = {2019},
author = {Shah, S and Dubey, AK and Reif, J},
title = {Improved Optical Multiplexing with Temporal DNA Barcodes.},
journal = {ACS synthetic biology},
volume = {8},
number = {5},
pages = {1100-1111},
doi = {10.1021/acssynbio.9b00010},
pmid = {30951289},
issn = {2161-5063},
mesh = {DNA/chemistry/*metabolism ; DNA Barcoding, Taxonomic/*methods ; Fluorescent Dyes/chemistry ; Machine Learning ; Markov Chains ; Nanostructures/chemistry ; Nucleic Acid Hybridization ; },
abstract = {Many biochemical events of importance are complex and dynamic. Fluorescence microscopy offers a versatile solution to study the dynamics of biology at the mesoscale. An important challenge in the field is the simultaneous study of several objects of interest, referred to as optical multiplexing. For improved multiplexing, some prior techniques used repeated reporter washing or the geometry of nanostructures; however, these techniques require complex nanostructure assembly, multiple reporters, or advanced multistep drift correction. Here we propose a time-based approach, for improved optical multiplexing, that uses readily available inexpensive reporters and requires minimal preparation efforts. We program short DNA strands, referred hereby as DNA devices, such that they undergo unique conformation changes in the presence of the dye-labeled reporters. The universal fluorescent reporter transiently binds with the devices to report their activity. Since each device is programmed to exhibit different hybridization kinetics, their fluorescent time trace, referred to as the temporal barcode, will be unique. We model our devices using continuous-time Markov chains and use stochastic simulation algorithm to generate their temporal patterns. We first ran simulation experiments with a small number of DNA devices, demonstrating several distinct temporal barcodes, all of which use a single dye color. Later, using nanostructure-based devices, we designed a much larger pool of temporal barcodes and used machine learning for classification of these barcodes. Our simulation experiments and design principles can aid in the experimental demonstration of the DNA devices.},
}
@article {pmid30949588,
year = {2019},
author = {Ashford, P and Rydman, K and Sparks, A and Tilleman, K and Freire, M},
title = {Standard terminology for reproductive tissue and cell products for use in ART.},
journal = {Human reproduction open},
volume = {2019},
number = {2},
pages = {hoz005},
pmid = {30949588},
issn = {2399-3529},
abstract = {Medical products of human origin (MPHO) distributed for use in assisted reproduction are currently labelled and identified using national or local systems. Products may be distributed internationally with potentially confusing identification labelling due to inconsistent terminology and definitions. In other fields of MPHO activity terminology has previously been standardized through professional collaboration as a precursor to adoption of a global standard for identification, coding and labelling. The International Council for Commonality in Blood Bank Automation (ICCBBA), an international nongovernmental organization in official relations with the World Health Organization, brought together representatives from professional societies to develop a terminology using a well-established methodology. The terminology was reviewed by professional associations and released for public comment. Further refinements were made following the comment period. Representatives of the American Society for Reproductive Medicine (ASRM), ESHRE, the Reproductive Tissue Council of the American Association of Tissue Banks (AATB) and ICCBBA met by international conference call and interacted by email. The terminology was developed using a standard model previously used across many areas of MPHO. A terminology comprising six classes, and six attribute groups has been developed. The terminology design is such that additional classes, attribute groups and attribute values can be added to meet the developing needs of the ART community. The level of detail incorporated into the terminology is based on the consensus view of the experts. The objective has been to provide sufficient detail to satisfy clinical need in product identification but there is the possibility that the level of detail may need to be adjusted in the future. The terminology is designed in a way that can readily accommodate such adjustments. Adoption of a standard terminology provides the basis for standardization of identification, coding and labelling and the use of internationally standardized barcoding to improve the accuracy and efficiency of information transfer and to reduce the risks of harm due to manual transcriptions errors.},
}
@article {pmid30947330,
year = {2019},
author = {Jauffrais, T and LeKieffre, C and Schweizer, M and Jesus, B and Metzger, E and Geslin, E},
title = {Response of a kleptoplastidic foraminifer to heterotrophic starvation: photosynthesis and lipid droplet biogenesis.},
journal = {FEMS microbiology ecology},
volume = {95},
number = {5},
pages = {},
doi = {10.1093/femsec/fiz046},
pmid = {30947330},
issn = {1574-6941},
mesh = {Carbon/metabolism ; Diatoms/classification/genetics/metabolism ; Foraminifera/classification/*metabolism ; Heterotrophic Processes ; Lipid Droplets/*metabolism ; Oxygen/metabolism ; Photosynthesis ; Phylogeny ; },
abstract = {The aim of this work is to document the complex nutritional strategy developed by kleptoplastic intertidal foraminifera. We study the mixotrophic ability of a common intertidal foraminifer, Elphidium williamsoni, by (i) investigating the phylogenetic identity of the foraminiferal kleptoplasts, (ii) following their oxygenic photosynthetic capacity and (iii) observing the modification in cellular ultrastructural features in response to photoautotrophic conditions. This was achieved by coupling molecular phylogenetic analyses and TEM observations with non-destructive measurements of kleptoplast O2 production over a 15-day experimental study. Results show that the studied E. williamsoni actively selected kleptoplasts mainly from pennate diatoms and had the ability to produce oxygen, up to 13.4 nmol O2 cell-1 d-1, from low to relatively high irradiance over at least 15 days. Ultrastructural features and photophysiological data showed significant differences over time, the number of lipid droplets, residual bodies and the dark respiration increased; whereas, the number of kleptoplasts decreased accompanied by a minor decrease of the photosynthetic rate. These observations suggest that in E. williamsoni kleptoplasts might provide extra carbon storage through lipid droplets synthesis and highlight the complexity of E. williamsoni feeding strategy and the necessity of further dedicated studies regarding mechanisms developed by kleptoplastidic foraminifera for carbon partitioning and storage.},
}
@article {pmid30945667,
year = {2019},
author = {Purushothaman, P and Chakraborty, RD and Kuberan, G and Maheswarudu, G},
title = {Integrative taxonomy of commercially important deep water penaeoid shrimps from India.},
journal = {Journal of genetics},
volume = {98},
number = {},
pages = {},
pmid = {30945667},
issn = {0973-7731},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; Mitochondria/*genetics ; Penaeidae/*classification/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; },
abstract = {The deep water penaeoid shrimp is an important commercial crustacean resource along the Indian coast. The molecular and morphological information of this group from the Indian coast is scarcely known. In this study, we investigated the identification and phylogenetic relationships of the deep water penaeoid shrimps using three mitochondrial (cytochrome oxidase subunit I (COI), cytochrome b, 16S rRNA) genes, which were compared with 54 morphological characters and further used to evaluate character evolution. Our study revealed remarkable molecular divergence (3.3-33.0%) in nine species from three genera of Solenoceridae, four species from three genera of Penaeidae and one species from Aristeidae using COI. Phylogenetic analysis using maximum likelihood and Bayesian approaches revealed that all species from these families are monophyletic. The present analysis revealed the existence of subgroups in the genus Solenocera suggesting the slow reduction of postrostral carina which corresponds to the increase in distributional depth during the evolutionary process which further indicates the origin of the genus in the continental shelf and extending up to the continental slope. In addition, we generated the DNA barcode database involving these species which can help further to investigate the detailed evolution and biogeography of these valuable crustacean resources.},
}
@article {pmid30941670,
year = {2019},
author = {Chin, RI and Chen, K and Usmani, A and Chua, C and Harris, PK and Binkley, MS and Azad, TD and Dudley, JC and Chaudhuri, AA},
title = {Detection of Solid Tumor Molecular Residual Disease (MRD) Using Circulating Tumor DNA (ctDNA).},
journal = {Molecular diagnosis &amp; therapy},
volume = {23},
number = {3},
pages = {311-331},
pmid = {30941670},
issn = {1179-2000},
support = {Young Investigator Award//American Society of Clinical Oncology/International ; Young Investigator Award//Takeda Pharmaceuticals U.S.A./International ; SPORE in Pancreatic Cancer Career Enhancement Program//Washington University/International ; P50 CA196510/CA/NCI NIH HHS/United States ; K08 CA238711/CA/NCI NIH HHS/United States ; },
mesh = {*Biomarkers, Tumor ; *Circulating Tumor DNA ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Humans ; Liquid Biopsy ; Molecular Diagnostic Techniques ; Neoplasm, Residual/blood/*diagnosis/*genetics ; Neoplasms/blood/*diagnosis/*genetics ; },
abstract = {Circulating tumor DNA (ctDNA) is a component of cell-free DNA that is shed by malignant tumors into the bloodstream and other bodily fluids. Levels of ctDNA are typically low, particularly in patients with localized disease, requiring highly sophisticated methods for detection and quantification. Multiple liquid biopsy methods have been developed for ctDNA analysis in solid tumor malignancies and are now enabling detection and assessment of earlier stages of disease, post-treatment molecular residual disease (MRD), resistance to targeted systemic therapy, and tumor mutational burden. Understanding ctDNA biology, mechanisms of release, and clearance and size characteristics, in conjunction with the application of molecular barcoding and targeted error correction, have increased the sensitivity and specificity of ctDNA detection techniques. Combinatorial approaches including integration of ctDNA data with circulating protein biomarkers may further improve assay sensitivity and broaden the scope of ctDNA applications. Circulating viral DNA may be utilized to monitor disease in some virally induced malignancies. In spite of increasingly accurate methods of ctDNA detection, results need to be interpreted with caution given that somatic mosaicisms such as clonal hematopoiesis of indeterminate potential (CHIP) may give rise to genetic variants in the bloodstream unrelated to solid tumors, and the limited concordance observed between different commercial platforms. Overall, highly precise ctDNA detection and quantification methods have the potential to transform clinical practice via non-invasive monitoring of solid tumor malignancies, residual disease detection at earlier timepoints than standard clinical and/or imaging surveillance, and treatment personalization based on real-time assessment of the tumor genomic landscape.},
}
@article {pmid30941367,
year = {2019},
author = {Chen, X and Cui, Y and Nie, L and Hu, H and Xu, Z and Sun, W and Gao, T and Song, J and Yao, H},
title = {Identification and Phylogenetic Analysis of the Complete Chloroplast Genomes of Three Ephedra Herbs Containing Ephedrine.},
journal = {BioMed research international},
volume = {2019},
number = {},
pages = {5921725},
pmid = {30941367},
issn = {2314-6141},
mesh = {Chromosome Mapping ; Codon/genetics ; Ephedra/*classification/*genetics ; Ephedrine/*metabolism ; Gene Dosage ; *Genome, Chloroplast ; Inverted Repeat Sequences/genetics ; Likelihood Functions ; Microsatellite Repeats/genetics ; *Phylogeny ; Repetitive Sequences, Nucleic Acid/genetics ; Species Specificity ; },
abstract = {Ephedrae Herba and Ephedrae Radix et Rhizoma (Mahuang) have been used as Chinese herbal medicines. Ephedra plants mainly live in deserts and have good governance of desertification. Despite their important medicinal and environmental protection value, dietary supplements containing ephedrine from Ephedra species may threaten the health of people. Morphological resemblance amongst species causes difficulty in identifying the original species of Ephedra herbs. Chloroplast (CP) genome shows good prospects in identification and phylogenetic analysis. This study introduced the structures of the CP genomes of three Ephedra species and analysed their phylogenetic relationships. Three complete CP genomes of Ephedra showed four-part annular structures, namely, two single-copy regions and two inverted repeat regions. The entire CP genomes of three Ephedra species in terms of size were 109,550 bp (E. sinica), 109,667 bp (E. intermedia), and 109,558 bp (E. equisetina). Each CP genome of the three Ephedra species encoded 118 genes, including 73 protein-coding genes, 37 tRNA genes and 8 ribosomal RNA genes. Eleven high-variation regions were screened through mVISTA to be potential specific DNA barcodes for identifying Ephedra species. Maximum likelihood and maximum parsimony trees showed that CP genomes could be used to identify Ephedra species. The Ephedra species had a close phylogenetic relationship with Gnetum species and Welwitschia mirabilis. This research provided valuable information for the identification and phylogenetic analysis of gymnosperms and drug safety of Ephedra.},
}
@article {pmid30941138,
year = {2019},
author = {de Vries, TJ and El Bakkali, I and Kamradt, T and Schett, G and Jansen, IDC and D'Amelio, P},
title = {What Are the Peripheral Blood Determinants for Increased Osteoclast Formation in the Various Inflammatory Diseases Associated With Bone Loss?.},
journal = {Frontiers in immunology},
volume = {10},
number = {},
pages = {505},
pmid = {30941138},
issn = {1664-3224},
mesh = {Animals ; Bone Resorption/metabolism/*pathology ; Bone and Bones/metabolism/*pathology ; Cell Differentiation/physiology ; Humans ; Inflammation/metabolism/*pathology ; Osteoclasts/metabolism/*pathology ; Osteogenesis/physiology ; },
abstract = {Local priming of osteoclast precursors (OCp) has long been considered the main and obvious pathway that takes place in the human body, where local bone lining cells and RANKL-expressing osteocytes may facilitate the differentiation of OCp. However, priming of OCp away from bone, such as in inflammatory tissues, as revealed in peripheral blood, may represent a second pathway, particularly relevant in individuals who suffer from systemic bone loss such as prevalent in inflammatory diseases. In this review, we used a systematic approach to review the literature on osteoclast formation in peripheral blood in patients with inflammatory diseases associated with bone loss. Only studies that compared inflammatory (bone) disease with healthy controls in the same study were included. Using this core collection, it becomes clear that experimental osteoclastogenesis using peripheral blood from patients with bone loss diseases in prevalent diseases such as rheumatoid arthritis, osteoporosis, periodontitis, and cancer-related osteopenia unequivocally point toward an intrinsically increased osteoclast formation and activation. In particular, such increased osteoclastogenesis already takes place without the addition of the classical osteoclastogenesis cytokines M-CSF and RANKL in vitro. We show that T-cells and monocytes as OCp are the minimal demands for such unstimulated osteoclast formation. In search for common and disease-specific denominators of the diseases with inflammation-driven bone loss, we demonstrate that altered T-cell activity and a different composition-such as the CD14+CD16+ vs. CD14+CD16- monocytes-and priming of OCp with increased M-CSF, RANKL, and TNF- α levels in peripheral blood play a role in increased osteoclast formation and activity. Future research will likely uncover the barcodes of the OCp in the various inflammatory diseases associated with bone loss.},
}
@article {pmid30940991,
year = {2019},
author = {Riedel, A and Narakusumo, RP},
title = {One hundred and three new species of Trigonopterus weevils from Sulawesi.},
journal = {ZooKeys},
volume = {828},
number = {828},
pages = {1-153},
pmid = {30940991},
issn = {1313-2989},
abstract = {The genus Trigonopterus Fauvel, 1862 is highly diverse in Melanesia, the Moluccas, and the Sunda Islands. Only one species, Trigonopterusfulvicornis (Pascoe, 1885) was so far recorded from Sulawesi. Based on focused field-work the fauna from Sulawesi and nearby islands is here revised. We redescribe T.allotopus Riedel newly recorded for Sulawesi and describe an additional 103 new species: T.abnormis sp. n., T.adspersus sp. n., T.ambangensis sp. n., T.ampanensis sp. n., T.analis sp. n., T.arachnobas sp. n., T.armipes sp. n., T.artemis sp. n., T.asterix sp. n., T.barbipes sp. n., T.bonthainensis sp. n., T.carinirostris sp. n., T.castaneipennis sp. n., T.celebensis sp. n., T.cirripes sp. n., T.collaris sp. n., T.costatulus sp. n., T.curvipes sp. n., T.crenulatus sp. n., T.cricki sp. n., T.darwini sp. n., T.ejaculatorius sp. n., T.fuscipes sp. n., T.gracilipes sp. n., T.heberti sp. n., T.hirsutus sp. n., T.humilis sp. n., T.hypocrita sp. n., T.idefix sp. n., T.impressicollis sp. n., T.incendium sp. n., T.incognitus sp. n., T.indigenus sp. n., T.inhonestus sp. n., T.invalidus sp. n., T.jasminae sp. n., T.klabatensis sp. n., T.kolakensis sp. n., T.kotamobagensis sp. n., T.laevigatus sp. n., T.lampros sp. n., T.latipennis sp. n., T.lompobattangensis sp. n., T.luwukensis sp. n., T.mahawuensis sp. n., T.manadensis sp. n., T.mangkutanensis sp. n., T.matalibaruensis sp. n., T.mesai sp. n., T.minahassae sp. n., T.moatensis sp. n., T.modoindingensis sp. n., T.nanus sp. n., T.nitidulus sp. n., T.obelix sp. n., T.ovalipunctatus sp. n., T.ovatulus sp. n., T.pagaranganensis sp. n., T.palopensis sp. n., T.paracollaris sp. n., T.pauper sp. n., T.pendolensis sp. n., T.posoensis sp. n., T.prismae sp. n., T.procurtus sp. n., T.pseudallotopus sp. n., T.pseudanalis, sp. n., T.pseudovatulus sp. n., T.pseudovalipunctatus sp. n., T.pseudofulvicornis sp. n., T.pseudomanadensis sp. n., T.pseudosimulans sp. n., T.pumilus sp. n., T.rantepao sp. n., T.reticulatus sp. n., T.rhombiformis sp. n., T.rotundatus sp. n., T.rotundulus sp. n., T.rudis sp. n., T.rufipes sp. n., T.sampunensis sp. n., T.sampuragensis sp. n., T.satyrus sp. n., T.scabripes sp. n., T.scaphiformis sp. n., T.scitulus sp. n., T.selayarensis sp. n., T.serripes sp. n., T.seticnemis sp. n., T.silvicola sp. n., T.squalidulus sp. n., T.sulawesiensis sp. n., T.suturatus sp. n., T.tatorensis sp. n., T.tenuipes sp. n., T.tomohonensis sp. n., T.toraja sp. n., T.vicinus sp. n., T.viduus sp. n., T.volcanorum sp. n., T.wangiwangiensis sp. n., T.watsoni sp. n., and T.yoda sp. n. All new species are authored by the taxonomist-in-charge, Alexander Riedel.},
}
@article {pmid30940689,
year = {2019},
author = {Wang, O and Chin, R and Cheng, X and Wu, MKY and Mao, Q and Tang, J and Sun, Y and Anderson, E and Lam, HK and Chen, D and Zhou, Y and Wang, L and Fan, F and Zou, Y and Xie, Y and Zhang, RY and Drmanac, S and Nguyen, D and Xu, C and Villarosa, C and Gablenz, S and Barua, N and Nguyen, S and Tian, W and Liu, JS and Wang, J and Liu, X and Qi, X and Chen, A and Wang, H and Dong, Y and Zhang, W and Alexeev, A and Yang, H and Wang, J and Kristiansen, K and Xu, X and Drmanac, R and Peters, BA},
title = {Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly.},
journal = {Genome research},
volume = {29},
number = {5},
pages = {798-808},
pmid = {30940689},
issn = {1549-5469},
mesh = {Cost-Benefit Analysis ; Diploidy ; Gene Library ; Genome, Human ; Genomics ; Haplotypes/genetics ; High-Throughput Nucleotide Sequencing/economics/*methods ; Humans ; Whole Genome Sequencing/economics/*methods ; },
abstract = {Here, we describe single-tube long fragment read (stLFR), a technology that enables sequencing of data from long DNA molecules using economical second-generation sequencing technology. It is based on adding the same barcode sequence to subfragments of the original long DNA molecule (DNA cobarcoding). To achieve this efficiently, stLFR uses the surface of microbeads to create millions of miniaturized barcoding reactions in a single tube. Using a combinatorial process, up to 3.6 billion unique barcode sequences were generated on beads, enabling practically nonredundant cobarcoding with 50 million barcodes per sample. Using stLFR, we demonstrate efficient unique cobarcoding of more than 8 million 20- to 300-kb genomic DNA fragments. Analysis of the human genome NA12878 with stLFR demonstrated high-quality variant calling and phase block lengths up to N50 34 Mb. We also demonstrate detection of complex structural variants and complete diploid de novo assembly of NA12878. These analyses were all performed using single stLFR libraries, and their construction did not significantly add to the time or cost of whole-genome sequencing (WGS) library preparation. stLFR represents an easily automatable solution that enables high-quality sequencing, phasing, SV detection, scaffolding, cost-effective diploid de novo genome assembly, and other long DNA sequencing applications.},
}
@article {pmid30938289,
year = {2019},
author = {Chang, HH and Wesolowski, A and Sinha, I and Jacob, CG and Mahmud, A and Uddin, D and Zaman, SI and Hossain, MA and Faiz, MA and Ghose, A and Sayeed, AA and Rahman, MR and Islam, A and Karim, MJ and Rezwan, MK and Shamsuzzaman, AKM and Jhora, ST and Aktaruzzaman, MM and Drury, E and Gonçalves, S and Kekre, M and Dhorda, M and Vongpromek, R and Miotto, O and Engø-Monsen, K and Kwiatkowski, D and Maude, RJ and Buckee, C},
title = {Mapping imported malaria in Bangladesh using parasite genetic and human mobility data.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
pmid = {30938289},
issn = {2050-084X},
support = {DP2 LM013102/LM/NLM NIH HHS/United States ; G0600718/MRC_/Medical Research Council/United Kingdom ; CPT000390//Bill and Melinda Gates Foundation/International ; R35 GM124715/GM/NIGMS NIH HHS/United States ; U54GM088558/GM/NIGMS NIH HHS/United States ; 001/WHO_/World Health Organization/International ; R35GM124715-02/GM/NIGMS NIH HHS/United States ; U54 GM088558/GM/NIGMS NIH HHS/United States ; 204911/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; OPP1118166//Bill and Melinda Gates Foundation/International ; OPP1129596//Bill and Melinda Gates Foundation/International ; MR/M006212/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Bangladesh/epidemiology ; Communicable Diseases, Imported/*epidemiology ; Genotype ; *Human Migration ; Humans ; Incidence ; Malaria/*epidemiology ; Plasmodium/classification/genetics/*isolation &amp; purification ; *Topography, Medical ; },
abstract = {For countries aiming for malaria elimination, travel of infected individuals between endemic areas undermines local interventions. Quantifying parasite importation has therefore become a priority for national control programs. We analyzed epidemiological surveillance data, travel surveys, parasite genetic data, and anonymized mobile phone data to measure the spatial spread of malaria parasites in southeast Bangladesh. We developed a genetic mixing index to estimate the likelihood of samples being local or imported from parasite genetic data and inferred the direction and intensity of parasite flow between locations using an epidemiological model integrating the travel survey and mobile phone calling data. Our approach indicates that, contrary to dogma, frequent mixing occurs in low transmission regions in the southwest, and elimination will require interventions in addition to reducing imported infections from forested regions. Unlike risk maps generated from clinical case counts alone, therefore, our approach distinguishes areas of frequent importation as well as high transmission.},
}
@article {pmid30937457,
year = {2019},
author = {Li, R and Xie, M and Dong, N and Lin, D and Yang, X and Wong, MHY and Chan, EW and Chen, S},
title = {Erratum to: Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data.},
journal = {GigaScience},
volume = {8},
number = {3},
pages = {},
pmid = {30937457},
issn = {2047-217X},
}
@article {pmid30935148,
year = {2019},
author = {Viglietti, G and Galla, G and Porceddu, A and Barcaccia, G and Curk, F and Luro, F and Scarpa, GM},
title = {Karyological Analysis and DNA Barcoding of Pompia Citron: A First Step toward the Identification of Its Relatives.},
journal = {Plants (Basel, Switzerland)},
volume = {8},
number = {4},
pages = {},
pmid = {30935148},
issn = {2223-7747},
abstract = {Pompia is a citrus fruit endemic of Sardinia, Italy, with an essential oil profile showing outstanding anti-inflammatory and anti-microbic properties. Despite its remarkable pharmaceutical potential, little taxonomic and genetic information is available for this species. We applied flow cytometry and classical cytogenetic techniques to assess the DNA content and to reconstruct the karyotype of several Pompia accessions. Molecular data from plastid DNA barcoding and nuclear DNA sequencing were used to study the genetic distance between Pompia and other citrus species. Flow cytometric estimates of DNA content and somatic chromosome counts suggest that Pompia is a regular diploid Citrus species. DNA polymorphisms of nuclear and chloroplast markers allowed us to investigate the genetic relationships between Pompia accessions and other Citrus species. Based on DNA polymorphism data we propose that Pompia is a very recent interspecific hybrid generated by a cross between C. aurantium (as seed bearer) and C. medica (as pollen donor). Our findings pave the way for further and more specific investigations of local Pompia germplasm resources that may help the preservation and valorisation of this valuable citrus fruit tree.},
}
@article {pmid30934910,
year = {2019},
author = {Huang, W and Xie, X and Liang, X and Wang, X and Chen, X},
title = {Effects of Different Pretreatments of DNA Extraction from Dried Specimens of Ladybird Beetles (Coleoptera: Coccinellidae).},
journal = {Insects},
volume = {10},
number = {4},
pages = {},
pmid = {30934910},
issn = {2075-4450},
support = {31601878//National Natural Science Foundation of China/ ; 2017A030313212//Natural Science Foundation of Guangdong Province/ ; },
abstract = {Obtaining genetic information from museum specimens is a fundamental component of many fields of research, including DNA barcoding, population genetics, conservation genetics, and phylogenetic analysis. However, acquiring genetic information from museum specimens is challenging because of the difficulty in amplifying the target sequences due to DNA damage and degradation. Different pretreatments can significantly impact the purity and concentration of genomic DNA from museum specimens. Here, we assessed four pretreatment methods-use of 0.9% NaCl buffer, phosphate-buffered saline (PBS), Saline Tris-EDTA (STE) buffer, and sterile water-to determine which pretreatment is most suitable for DNA extraction from dried specimens of ladybird beetles. We completed a comprehensive phylogenetic analysis to test whether the sequences obtained from dried specimens enable proper phylogenetic inference. Our results showed that pretreatment can improve the quality of DNA from dried specimens. The pretreatment effects of 0.9% NaCl buffer and STE buffer were better than those of PBS buffer and sterile water. The phylogenetic analyses results showed that museum specimens can be used to generate cogent phylogenetic inferences. We report the optimum pretreatment methods for DNA extraction from dried ladybird beetles specimens as well as provide evidence for accurately determining phylogenetic relationships for museum specimens.},
}
@article {pmid30934734,
year = {2019},
author = {Wang, N and Lu, Y and Chen, Z and Fan, R},
title = {Multiplexed PCR-Free Detection of MicroRNAs in Single Cancer Cells Using a DNA-Barcoded Microtrough Array Chip.},
journal = {Micromachines},
volume = {10},
number = {4},
pages = {},
pmid = {30934734},
issn = {2072-666X},
abstract = {MicroRNAs are a class of small RNA molecules that regulate the expression of mRNAs in a wide range of biological processes and are implicated in human health and disease such as cancers. How to measure microRNA profiles in single cells with high throughput is essential to the development of cell-based assays for interrogating microRNA-mediated intratumor heterogeneity and the design of new lab tests for diagnosis and monitoring of cancers. Here, we report on an in situ hybridization barcoding workflow implemented in a sub-nanoliter microtrough array chip for high-throughput and multiplexed microRNA detection at the single cell level. The microtroughs are used to encapsulate single cells that are fixed, permeabilized, and pre-incubated with microRNA detection probes, each of which consists of a capture strand complementary to specific microRNA and a unique reporter strand that can be photocleaved in the microtroughs and subsequently detected by an array of DNA barcodes patterned on the bottom of the microtroughs. In this way, the measurement of reporter strands released from single cells is a surrogate for detecting single-cell microRNA profiles. This approach permits direct measurement of microRNAs without PCR amplification owing to the small volume (<1 nL) of microtroughs. It offers high throughput and high multiplexing capability for evaluating microRNA heterogeneity in single cells, representing a new approach toward microRNA-based diagnosis and monitoring of complex human diseases.},
}
@article {pmid30933711,
year = {2019},
author = {Bian, F and Sun, L and Cai, L and Wang, Y and Zhao, Y and Wang, S and Zhou, M},
title = {Molybdenum disulfide-integrated photonic barcodes for tumor markers screening.},
journal = {Biosensors &amp; bioelectronics},
volume = {133},
number = {},
pages = {199-204},
doi = {10.1016/j.bios.2019.02.066},
pmid = {30933711},
issn = {1873-4235},
mesh = {Biomarkers, Tumor/chemistry/*isolation &amp; purification ; *Biosensing Techniques ; Colloids/chemistry ; Disulfides/chemistry ; Humans ; Limit of Detection ; MicroRNAs/chemistry/*isolation &amp; purification ; Molybdenum/chemistry ; Neoplasms/*diagnosis ; Photons ; Quantum Dots/chemistry ; Silicon Dioxide/chemistry ; },
abstract = {As a new class of two-dimensional (2D) materials, molybdenum disulfide (MoS2) has huge potential in biomedical area; while its applications in multiplex bioassays are still a challenge. Here, we present novel MoS2-integrated silica colloidal crystal barcode (SCCB) for multiplex microRNA (miRNA) screening. MoS2 was adsorbed on SCCBs by electrostatic interaction, and quantum dots (QDs) decorated hairpin probes were coupled on MoS2 by covalent linkage. As the MoS2 could quench the QDs of the hairpin probes, they together formed a molecular beacon (MB) structure before the detection. When used in assays, target miRNA could form a double strand with the probe and made QDs keep away from MoS2 sheets to recovery their fluorescence. Because the released QDs were positively correlated with the concentration of the hybridized nucleic acid, the target miRNAs could be quantified by measuring the fluorescence signal of the QDs on the SCCBs. In addition, by utilizing different MoS2-integrated structural color encoded SCCBs, multiplexed miRNA quantification could also be realized. Based on this strategy, we have demonstrated that several pancreatic cancer-related miRNAs could be selectivity and sensitivity detected with a detection limit of 4.2 ± 0.3 nM. These features make the MoS2-integrated SCCB ideal for many potential applications.},
}
@article {pmid30931416,
year = {2018},
author = {Lokugamage, MP and Sago, CD and Dahlman, JE},
title = {Testing thousands of nanoparticles in vivo using DNA barcodes.},
journal = {Current opinion in biomedical engineering},
volume = {7},
number = {},
pages = {1-8},
pmid = {30931416},
issn = {2468-4511},
support = {T32 EB021962/EB/NIBIB NIH HHS/United States ; },
abstract = {Nanoparticles improve drug efficacy by delivering drugs to sites of disease. To effectively deliver a drug in vivo, a nanoparticle must overcome physical and physiological hurdles that are not present in cell culture, yet in vitro screens are used to predict nanoparticle delivery in vivo. An ideal nanoparticle discovery pipeline would enable scientists to study thousands of nanoparticles in vivo. Here, we discuss technologies that enable high throughput in vivo screens, focusing on DNA barcoded nanoparticles.},
}
@article {pmid30930645,
year = {2019},
author = {M Hernández-Triana, L and A Brugman, V and I Nikolova, N and Ignacio Ruiz-Arrondo, and Barrero, E and Thorne, L and Fernández de Marco, M and Krüger, A and Lumley, S and Johnson, N and R Fooks, A},
title = {DNA barcoding of British mosquitoes (Diptera, Culicidae) to support species identification, discovery of cryptic genetic diversity and monitoring invasive species.},
journal = {ZooKeys},
volume = {832},
number = {},
pages = {57-76},
pmid = {30930645},
issn = {1313-2989},
abstract = {Correct mosquito species identification is essential for mosquito and disease control programs. However, this is complicated by the difficulties in morphologically identifying some mosquito species. In this study, variation of a partial sequence of the cytochrome c oxidase unit I (COI) gene was used for the molecular identification of British mosquito species and to facilitate the discovery of cryptic diversity, and monitoring invasive species. Three DNA extraction methods were compared to obtain DNA barcodes from adult specimens. In total, we analyzed 42 species belonging to the genera Aedes Meigen, 1818 (21 species), Anopheles Meigen, 1818 (7 species), Coquillettidia Theobald, 1904 (1 species), Culex Linnaeus, 1758 (6 species), Culiseta Felt, 1904 (7 species), and Orthopodomyia Theobald, 1904 (1 species). Intraspecific genetic divergence ranged from 0% to 5.4%, while higher interspecific divergences were identified between Aedesgeminus Peus, 1971/Culisetalitorea (Shute, 1928) (24.6%) and Ae.geminus/An.plumbeus Stephens, 1828 (22.5%). Taxonomic discrepancy was shown between An.daciae Linton, Nicolescu &amp; Harbach, 2004 and An.messeae Falleroni, 1828 indicating the poor resolution of the COI DNA barcoding region in separating these taxa. Other species such as Ae.cantans (Meigen, 1818)/Ae.annulipes (Meigen, 1830) showed similar discrepancies indicating some limitation of this genetic marker to identify certain mosquito species. The combination of morphology and DNA barcoding is an effective approach for the identification of British mosquitoes, for invasive mosquitoes posing a threat to the UK, and for the detection of hidden diversity within species groups.},
}
@article {pmid30927061,
year = {2019},
author = {Garcia-Salguero, A and Delgado-Serra, S and Sola, J and Negre, N and Miranda, MA and Paredes-Esquivel, C},
title = {Combined morphology and DNA-barcoding to identify Plagiorhynchus cylindraceus cystacanths in Atelerix algirus.},
journal = {Parasitology research},
volume = {118},
number = {5},
pages = {1473-1478},
pmid = {30927061},
issn = {1432-1955},
mesh = {Acanthocephala/anatomy &amp; histology/*classification/*genetics ; Animals ; Birds/parasitology ; DNA/genetics ; *DNA Barcoding, Taxonomic ; Female ; Hedgehogs/*parasitology ; Helminthiasis, Animal/*epidemiology/parasitology ; Intestines/*pathology ; Larva/growth &amp; development ; Male ; Peritoneal Cavity/*parasitology ; Zoonoses/epidemiology ; },
abstract = {The acanthocephalan parasite Plagiorhynchus cylindraceus has a global distribution and utilizes isopods and birds as intermediate and definitive hosts, respectively. Occasionally, mammals of various orders can act as paratenic hosts. In hedgehogs, severe cases have been reported in juvenile specimens due to secondary infections, as a consequence of complete penetrations of the intestinal wall by cystacanths. In a 66-month study period, we found seven larvae of this parasite encysted in both, the peritoneal cavity and intestine of the Algerian hedgehog, Atelerix algirus in Majorca. Morphology alone was insufficient to identify the species, due to the lack of previous reports and taxonomy-informative characters. In the present report, we combined the use of morphology and the DNA-barcoding approach to confirm to identify cystacanths as P. cylindraceus. This is the first report of this parasite in this hedgehog species. The epidemiological implications will be discussed, including the risk of zoonosis and the importance of using modern approaches to identify immature acanthocephalan larvae in wildlife hosts.},
}
@article {pmid30923906,
year = {2019},
author = {Jiao, L and Lu, Y and He, T and Li, J and Yin, Y},
title = {A strategy for developing high-resolution DNA barcodes for species discrimination of wood specimens using the complete chloroplast genome of three Pterocarpus species.},
journal = {Planta},
volume = {250},
number = {1},
pages = {95-104},
pmid = {30923906},
issn = {1432-2048},
support = {CAFYBB2017MA013//Fundamental Research Funds of CAF/ ; 31600451//National Natural Science Foundation of China/ ; W02020331//National High-level Talents Special Support Plan (Ten-Thousand Talents Program) of China/ ; },
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Chloroplast/genetics ; DNA, Plant/genetics ; Genome, Chloroplast/*genetics ; Genome, Plant/*genetics ; Phylogeny ; Pterocarpus/*classification/genetics ; Species Specificity ; Wood/genetics ; },
abstract = {A method for extraction of wood DNA and a strategy for designing high-resolution barcodes for wood were developed. Ycf1b was the prioritized barcode to resolve the Pterocarpus wood species studied. DNA barcoding, an effective tool for wood species identification, mainly focuses on universal barcodes and often lacks high resolution to differentiate species, especially for closely related taxa within the same genus. Therefore, more highly informative DNA barcodes need to be identified. This study is the first to report a strategy for developing specific DNA barcodes of wood tissues. The complete chloroplast genomes of leaf samples of three Pterocarpus species, i.e., P. indicus, P. santalinus, and P. tinctorius, were sequenced, and thereafter, the most variable DNA regions were identified on the scale of the complete chloroplast genomes. Finally, wood DNA was extracted from 30 wood specimens of the three Pterocarpus species, and DNA recovery rates of the selected regions were tested for applicability to verification on the wood specimens studied. The seven regions with the most variation (rpl32-ccsA, rpl20-clpP, trnC-rpoB, ycf1b, accD-ycf4, ycf1a, and psbK-accD) were identified from the chloroplast genome by quantifying nucleotide diversity (Pi > 0.02), which was remarkably higher than that of the plant universal barcodes (rbcL, matK, and trnH-psbA) and the previously reported barcodes (ndhF-rpl32 and trnL-F) used for phylogenetic analysis in Pterocarpus. After comprehensive evaluation of species discrimination ability and applicability, the ycf1b region performed well in terms of the recovery success rate (76.7%) and species identification (100%) for wood specimens of the three Pterocarpus species, and was identified as the preferred high-resolution chloroplast barcode for selected Pterocarpus species. It will offer technical support for curbing illegal timber harvesting activities and for conserving endangered and valuable wood species.},
}
@article {pmid30923647,
year = {2019},
author = {Schiaparelli, S and Aliani, S},
title = {Oceanographic moorings as year-round laboratories for investigating growth performance and settlement dynamics in the Antarctic scallop Adamussium colbecki (E. A. Smith, 1902).},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6373},
pmid = {30923647},
issn = {2167-8359},
abstract = {BACKGROUND: Oceanographic moorings (OMs) are standard marine platforms composed of wires, buoys, weights and instruments, and are used as in situ observatories to record water column properties. However, OMs are also comprised of hard substrates on which a variety of invertebrates can settle when they encounter these structures along their dispersal routes. In this contribution, we studied the fouling communities found on two OMs deployed in the Ross Sea (Antarctica). Furthermore, a cage containing the Antarctic scallop Adamussium colbecki (E. A. Smith, 1902) was incorporated in the OM. The growth of the caged A. colbecki were evaluated after 1 year and their shells used as biological proxy for seawater temperature and salinity.<br><br>METHODS: A variety of settlers were collected from two different OMs deployed in the Ross Sea (Antarctica) and species identified using a combination of morphological and genetic (mainly through DNA barcoding) characteristics. Caged scallops were individually marked with permanent tags and their growth studied in terms of size-increment data (SID). Cages were specifically designed to prevent damage to individuals due to water drag during OM deployment and retrieval. Growth parameters from the caged individuals were applied to the A. colbecki juveniles that had settled on the mooring, to trace the likely settlement period.<br><br>RESULTS: The growth performance of caged A. colbecki was similar to that from previous growth studies of this species. The remarkable survival rate of caged specimens (96.6%) supports the feasibility of caging experiments, even for a species with a fragile shell such as the Antarctic scallop. Some of the new recruits found on the mooring were A. colbecki, the same species we put into special cages fixed to it. The settlement of the A. colbecki juveniles started during the Austral spring with a peak in summer months and, remarkably, coincided with seasonal changes in water temperature and flow direction, which were recorded by the mooring's instruments. Genetic data from other settlers provided new information about their larval ecology and connectivity.<br><br>DISCUSSION: Oceanographic moorings are expensive and complex experimental platforms that, at present, are strictly used for the acquisition of physical and biogeochemical data. Their use for in situ ecological experiments on model organisms suitable for caging and to study fouling species has yet to be fully explored. We present the outcomes of a study, which represents a baseline for the characterization of Antarctic fouling biodiversity. We hope that in the near future an internationally coordinated systematic study of settlers could be initiated around the Antarctic continent. This could utilize "new generation OMs" equipped with standardized settlement structures and agreed sampling protocols for the study of fouling communities.},
}
@article {pmid30920312,
year = {2019},
author = {Saravanan, M and Mohanapriya, G and Laha, R and Sathishkumar, R},
title = {DNA barcoding detects floral origin of Indian honey samples.},
journal = {Genome},
volume = {62},
number = {5},
pages = {341-348},
doi = {10.1139/gen-2018-0058},
pmid = {30920312},
issn = {1480-3321},
mesh = {Animals ; Bees/*physiology ; *DNA Barcoding, Taxonomic ; DNA, Intergenic/genetics ; DNA, Plant/chemistry/genetics ; Flowers/classification/genetics ; Honey/*analysis ; India ; Plants/*classification/genetics ; Pollen/*classification/genetics ; Polymerase Chain Reaction ; Ribulose-Bisphosphate Carboxylase/genetics ; },
abstract = {The unique medicinal and nutritional properties of honey are determined by its chemical composition. To evaluate the quality of honey, it is essential to study the surrounding vegetation where honeybees forage. In this study we used conventional melissopalynological and DNA barcoding techniques to determine the floral source of honey samples collected from different districts of the state of Mizoram, India. Pollen grains were isolated and genomic DNA was extracted from the honey samples. PCR amplification was carried out using universal barcode candidates ITS2 and rbcL to identify the plant species. Furthermore, TA cloning was carried out to screen the PCR amplicon libraries to identify the presence of multiple plant species. Results from both the melissopalynological and DNA barcoding analyses identified almost exactly the same 22 species, suggesting that both methods are suitable for analysis. However, DNA barcoding is easier and widely practiced. Hence, it can be concluded that DNA barcoding is a useful tool in determining the medicinal and commercial value of honey.},
}
@article {pmid30918973,
year = {2019},
author = {Medina-Hernández, D and Vargas-Salinas, M and Rueda-Puente, EO and Holguín-Peña, RJ},
title = {Seasonal Distribution of Bemisia tabaci (Hemiptera: Aleyrodidae) MEAM1 Species and Impact on Incidence of Begomoviral Diseases in Baja California Sur.},
journal = {Journal of economic entomology},
volume = {112},
number = {3},
pages = {1055-1061},
doi = {10.1093/jee/toz052},
pmid = {30918973},
issn = {1938-291X},
mesh = {Animals ; *Hemiptera ; Incidence ; *Solanum lycopersicum ; Mexico ; Seasons ; },
abstract = {For more than four decades, the presence of the whitefly Bemisia tabaci Gennadius complex as a pest and transmitter of begomoviral diseases has been one of the most important phytopathological events in cultivated species worldwide. In addition, the number of whitefly species, as well as the viruses they transmit, has been increasing over time. In the state of Baja California Sur (BCS), Mexico, the diversity of B. tabaci has been delimited to MEAM1 and NW species, affecting mainly tomato, pepper, and squash. However, the relationship of these species with the dispersion of the begomoviruses previously detected in the study area is still unknown. In a 5-yr study (2012-2016), these species of whiteflies and begomoviruses were identified. Moreover, the recurrence, seasonal distribution, and impact they have on the spread of the begomoviral diseases were assessed. The identification of whiteflies was done targeting the mtCOI by PCR-DNA barcoding assay. For begomoviruses identification, a set of degenerate and specific primers targeting the IR region and CP gene were used. To determine seasonal abundance, monitoring was performed every 15 d by means of yellow traps. The MEAM1 species in all localities was observed with the highest peak population (>10 whiteflies/trap) from March to April. The guidelines for naming begomovirus species for the International Committee on Taxonomy of Viruses (ICTV) establish that the names when they are preceded by the acronym the whole name is in lowercase, not italicized (e.g. bean golden mosaic virus (BGMV)); when the name goes alone without the acronym then its capitalizes the first letter (e.g. Bean golden mosaic virus) and when these are referred to in a taxonomic sense they are italicized and the first letter is capitalized (e.g. Bean golden mosaic virus). This study provides details of the distribution and occurrence of MEAM1 species and diversity of begomoviruses that could be useful in disease management in BCS and worldwide.},
}
@article {pmid30918971,
year = {2019},
author = {Wand, NO and Smith, DA and Wilkinson, AA and Rushton, AE and Busby, SJW and Styles, IB and Neely, RK},
title = {DNA barcodes for rapid, whole genome, single-molecule analyses.},
journal = {Nucleic acids research},
volume = {47},
number = {12},
pages = {e68},
pmid = {30918971},
issn = {1362-4962},
mesh = {Adenoviruses, Human/genetics/isolation &amp; purification ; Bacteriophage lambda/genetics ; Base Sequence ; CRISPR-Cas Systems ; Computer Simulation ; DNA/*chemistry ; DNA, Bacterial/chemistry ; DNA, Viral/chemistry ; Escherichia coli/genetics/isolation &amp; purification ; Fluorescent Dyes ; Genomics/*methods ; Humans ; Klebsiella pneumoniae/genetics ; },
abstract = {We report an approach for visualizing DNA sequence and using these 'DNA barcodes' to search complex mixtures of genomic material for DNA molecules of interest. We demonstrate three applications of this methodology; identifying specific molecules of interest from a dataset containing gigabasepairs of genome; identification of a bacterium from such a dataset and, finally, by locating infecting virus molecules in a background of human genomic material. As a result of the dense fluorescent labelling of the DNA, individual barcodes of the order 40 kb pairs in length can be reliably identified. This means DNA can be prepared for imaging using standard handling and purification techniques. The recorded dataset provides stable physical and electronic records of the total genomic content of a sample that can be readily searched for a molecule or region of interest.},
}
@article {pmid30916889,
year = {2019},
author = {Seifert, ME and Gaut, JP and Guo, B and Jain, S and Malone, AF and Geraghty, F and Della Manna, DL and Yang, ES and Yi, N and Brennan, DC and Mannon, RB},
title = {WNT pathway signaling is associated with microvascular injury and predicts kidney transplant failure.},
journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons},
volume = {19},
number = {10},
pages = {2833-2845},
pmid = {30916889},
issn = {1600-6143},
support = {K23 DK101690/DK/NIDDK NIH HHS/United States ; L40 DK099748/DK/NIDDK NIH HHS/United States ; },
mesh = {Biomarkers/metabolism ; Case-Control Studies ; Cross-Sectional Studies ; Female ; Follow-Up Studies ; Graft Rejection/*diagnosis/etiology/metabolism ; Graft Survival ; Humans ; Isoantibodies/*adverse effects ; Kidney Failure, Chronic/*surgery ; Kidney Transplantation/*adverse effects ; Longitudinal Studies ; Male ; Microvessels/injuries/metabolism/*pathology ; Middle Aged ; Postoperative Complications/*diagnosis/etiology/metabolism ; Prognosis ; Risk Factors ; *Wnt Signaling Pathway ; },
abstract = {Microvascular injury is associated with accelerated kidney transplant dysfunction and allograft failure. Molecular pathology can identify new mechanisms of microvascular injury while improving on the diagnostic and prognostic capabilities of traditional histology. We conducted a case-control study of archived kidney biopsy specimens stored up to 10 years with microvascular injury (n = 50) compared with biopsy specimens without histologic injury (n = 45) from patients of similar age, race, and sex. We measured WNT gene expression with a multiplex quantification platform by using digital barcoding, given the importance of WNT reactivation to the response to wounding in the kidney microvasculature and other compartments. Of 210 genes from a commercial WNT panel, 71 were associated with microvascular injury and 79 were associated with allograft failure, with considerable overlap of genes between each set. Molecular pathology identified 46 biopsy specimens with molecular evidence of microvascular injury; 18 (39%) were either C4d negative, donor-specific antibody negative, or had no microvascular injury by histology. The majority of cases with molecular evidence of microvascular injury had poor long-term outcomes. We identified novel WNT pathway genes associated with microvascular injury and allograft failure in residual clinical biopsy specimens obtained up to 10 years earlier. Further mechanistic studies may identify the WNT pathway as a new diagnostic and therapeutic target.},
}
@article {pmid30914659,
year = {2019},
author = {Singh, R and Iquebal, MA and Mishra, CN and Jaiswal, S and Kumar, D and Raghav, N and Paul, S and Sheoran, S and Sharma, P and Gupta, A and Tiwari, V and Angadi, UB and Kumar, N and Rai, A and Singh, GP and Kumar, D and Tiwari, R},
title = {Development of model web-server for crop variety identification using throughput SNP genotyping data.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {5122},
pmid = {30914659},
issn = {2045-2322},
mesh = {*Databases, Nucleic Acid ; *Genome, Plant ; *Genotype ; *Models, Genetic ; *Polymorphism, Single Nucleotide ; *Software ; Triticum/*genetics ; },
abstract = {Crop varieties or genotypes of a given species are pivotal for agricultural production and ownership, management and improvement of their germplasm is a great challenge. Its morphological identification requires time, cost and descriptors are often compromised statistically due to phenotypic plasticity. Development of DNA based signature of varieties can overcome these limitations. There is a global need to implement world trade organization (WTO) and intellectual property rights (IPR) guidelines of Plant Breeders Rights (PBR) where DUS (distinctness, uniformity and stability) testing can be supplemented by DNA profile. Universalization and minimization of SNP number without compromising identification accuracy is the major challenge in development of varietal profile by rapid genotype assay. Besides this, there is no server-based approach reducing computational skill with global accessibility of referral phenotypic and genotypic data. We report world's first model web server for crop variety identification using >350 Indian wheat varieties and Axiom 35 K SNP chip data. Standard filtering and linkage disequilibrium approach were used to develop varietal signature in Linux using HTML, Java, PHP and MySQL with provision of QR code generator to facilitate bar-coding. Phylogenetic tree constructed by selected SNPs confirms six major trait based clusters of varieties and their pedigree. Our user friendly server based tool, VISTa (Variety Identification System of Triticum aestivum) (http://webtom.cabgrid.res.in/vista) can be used in DUS testing having dispute resolution of sovereignty and access benefit sharing (ABS) issues. This model approach can be used in other crops with pan-global level management of crop germplasm in endeavour of crop productivity.},
}
@article {pmid30912868,
year = {2019},
author = {Gueuning, M and Ganser, D and Blaser, S and Albrecht, M and Knop, E and Praz, C and Frey, JE},
title = {Evaluating next-generation sequencing (NGS) methods for routine monitoring of wild bees: Metabarcoding, mitogenomics or NGS barcoding.},
journal = {Molecular ecology resources},
volume = {19},
number = {4},
pages = {847-862},
pmid = {30912868},
issn = {1755-0998},
support = {//Swiss Federal Office for Agriculture/ ; },
mesh = {Animals ; Bees/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/chemistry/*genetics ; Genetics, Population/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; },
abstract = {Implementing cost-effective monitoring programs for wild bees remains challenging due to the high costs of sampling and specimen identification. To reduce costs, next-generation sequencing (NGS)-based methods have lately been suggested as alternatives to morphology-based identifications. To provide a comprehensive presentation of the advantages and weaknesses of different NGS-based identification methods, we assessed three of the most promising ones, namely metabarcoding, mitogenomics and NGS barcoding. Using a regular monitoring data set (723 specimens identified using morphology), we found that NGS barcoding performed best for both species presence/absence and abundance data, producing only few false positives (3.4%) and no false negatives. In contrast, the proportion of false positives and false negatives was higher using metabarcoding and mitogenomics. Although strong correlations were found between biomass and read numbers, abundance estimates significantly skewed the communities' composition in these two techniques. NGS barcoding recovered the same ecological patterns as morphology. Ecological conclusions based on metabarcoding and mitogenomics were similar to those based on morphology when using presence/absence data, but different when using abundance data. In terms of workload and cost, we show that metabarcoding and NGS barcoding can compete with morphology, but not mitogenomics which was consistently more expensive. Based on these results, we advocate that NGS barcoding is currently the seemliest NGS method for monitoring of wild bees. Furthermore, this method has the advantage of potentially linking DNA sequences with preserved voucher specimens, which enable morphological re-examination and will thus produce verifiable records which can be fed into faunistic databases.},
}
@article {pmid30910665,
year = {2019},
author = {Chen, Y and Wu, X and Huang, Z and Lin, W and Li, Y and Yang, J and Li, J},
title = {Evaluation of a medication error monitoring system to reduce the incidence of medication errors in a clinical setting.},
journal = {Research in social &amp; administrative pharmacy : RSAP},
volume = {15},
number = {7},
pages = {883-888},
doi = {10.1016/j.sapharm.2019.02.006},
pmid = {30910665},
issn = {1934-8150},
mesh = {*Adverse Drug Reaction Reporting Systems ; China ; Humans ; Medication Errors/*statistics &amp; numerical data ; *Medication Systems, Hospital ; Pharmacy Service, Hospital/*statistics &amp; numerical data ; },
abstract = {BACKGROUND: Medication errors have significant health and economic consequences. Monitoring medication errors by implementing monitoring systems proved in the USA and European countries since 1990s to be an effective method for error detection, leading to improved safety at all levels of health care. Currently, China does not have a universal medication error monitoring system.<br><br>OBJECTIVE: To evaluate the effectiveness of the Medication Error Monitoring System for the reduction of medication errors in Xiamen Maternity and Child Care Hospital.<br><br>METHODS: Between January-June 2014, the Medication Error Monitoring System developed by Xiamen Maternity and Child Care Hospital was employed to monitor medication errors through error reporting by physicians and pharmacists. The errors collected by this system were then thoroughly assessed and addressed by specific improvements including more frequent training, introducing computerised prescribing systems and a bar-coding medicine dispensing system. Data collected from January-June 2015, was then compared with the data collected in 2014 to determine whether medication errors had been reduced.<br><br>RESULTS: Between 2014 and 2015, the total medication errors in prescribing and dispensing were reduced by approximately 27%. Compared with 2014, there was a marked reduction in the number of errors due to misdiagnoses and inappropriate usage/dosage in 2015, while the number of data entry errors increased and became the most common cause of medication error. The success rate of pharmacy interventions increased from 95.25% to 96.88%, albeit modest. However, across all medication errors in the stage of prescribing and dispensing, non-human-related errors significantly decreased from 44.25% in 2014 to 37.94% in 2015 with apvalue of 0.021.<br><br>CONCLUSION: The Medication Error Monitoring System is effective at monitoring medication error data, leading to a reduction in reported medication errors. Better training for hospital staff including doctors and pharmacists will be critical to reduce human-related medication errors in the hospital.},
}
@article {pmid30909941,
year = {2019},
author = {Jongejan, F and de Jong, S and Voskuilen, T and van den Heuvel, L and Bouman, R and Heesen, H and Ijzermans, C and Berger, L},
title = {"Tekenscanner": a novel smartphone application for companion animal owners and veterinarians to engage in tick and tick-borne pathogen surveillance in the Netherlands.},
journal = {Parasites &amp; vectors},
volume = {12},
number = {1},
pages = {116},
pmid = {30909941},
issn = {1756-3305},
support = {2017//Bayer (DE)/ ; },
mesh = {Animals ; Cat Diseases/diagnosis/*epidemiology/parasitology ; Cats ; Dog Diseases/diagnosis/*epidemiology/parasitology ; Dogs ; Epidemiological Monitoring/veterinary ; Female ; Male ; *Mobile Applications ; Molecular Typing/veterinary ; Netherlands/epidemiology ; Pets/*parasitology ; Phylogeography ; *Smartphone ; Tick Infestations/epidemiology/*veterinary ; Tick-Borne Diseases/diagnosis/*epidemiology ; Ticks/*parasitology ; },
abstract = {BACKGROUND: The engagement of companion animal owners into the process of collecting epidemiological data can be facilitated through smartphone applications. In April 2018, the "tekenscanner" (Dutch for tick scanner) app was launched with the aim of engaging pet owners and veterinarians to record ticks removed from their pets and submit these ticks for identification and pathogen testing. Tick-borne pathogens identified in ticks removed from dogs and cats during the first 6 months after the app was launched in the Netherlands are reported.<br><br>METHODS: The tekenscanner app was used to record the geographical coordinates of ticks removed from dogs or cats onto a map of the Netherlands. A barcode was assigned to each tick for the easy tracking of each submission to our laboratory for taxonomic identification. Thereafter, DNA extracted from the ticks was PCR amplified, subjected to reverse line blot hybridization (RLB) and screened for a broad range of tick-borne pathogens. Results were added to the same app, usually within 2&#xa0;weeks after the submission of each tick.<br><br>RESULTS: The app was downloaded 5591 times and resulted in the collection of 1273 georeferenced and barcoded ticks, with a peak submission in May and June of 2018. There were 1005 ticks collected from 406 dogs and 268 ticks collected from 111 cats. Ixodes ricinus was the predominant species (90.0%), with all stages found on dogs as well as on cats. Ixodes hexagonus (7.3%) female and nymphal ticks were also identified on both hosts, whereas adults of Dermacentor reticulatus (2.4%) and Rhipicephalus sanguineus (0.2%) were exclusively found on dogs. Nearly 15% of the ticks recovered from dogs carried one or more pathogens, whereas 13.8% of the ticks removed from cats were infected. Ixodes ricinus collected from dogs contained Borrelia spp. (1.9%), Babesia spp. (0.7%), Anaplasma phagocytophilum (1.3%), "Candidatus Neoehrlichia mikurensis" (2.9%) and Rickettsia helvetica (7.3%). Ixodes ricinus recovered from cats were infected with Borrelia spp. (1.9%), Babesia spp. (0.4%), A. phagocytophilum (1.9%), "Ca. Neoehrlichia mikurensis" (2.6%) and R. helvetica (6.7%). Ixodes hexagonus ticks (n&#x2009;=&#x2009;93) were not infected. Dermacentor reticulatus ticks, found only in autumn, were infected with Rickettsia raoultii (16 %) and A. phagocytophilum. Three R. sanguineus, on dogs from France and the USA imported into the Netherlands, were all negative.<br><br>CONCLUSIONS: The tekenscanner app is a versatile tool to use for submission of ticks and facilitated the fast feedback of test results. Community engagement through the app is suitable for identifying hotspots for ticks and tick-borne pathogens and provided an early warning system for exotic ticks invading the Netherlands.},
}
@article {pmid30908478,
year = {2019},
author = {Baniecki, ML and Moon, J and Sani, K and Lemieux, JE and Schaffner, SF and Sabeti, PC},
title = {Development of a SNP barcode to genotype Babesia microti infections.},
journal = {PLoS neglected tropical diseases},
volume = {13},
number = {3},
pages = {e0007194},
pmid = {30908478},
issn = {1935-2735},
mesh = {Babesia microti/*classification/genetics ; Babesiosis/epidemiology/*parasitology ; DNA Barcoding, Taxonomic/*methods ; Genetic Markers/genetics ; Genotype ; Humans ; Limit of Detection ; Polymorphism, Single Nucleotide/*genetics ; },
abstract = {Babesia microti is tick-borne disease that is an emerging threat to public health due to increasing prevalence and expanding geographic range. Detection and constant surveillance of babesiosis is imperative for predicting pathogen expansion. Leveraging our whole genome sequence (WGS) analyses of B. microti, we developed a single nucleotide polymorphism (SNP)-based high resolution melt (HRM) surveillance tool. We developed our HRM assay using available sequence data and identified 775 SNPs. From these candidate SNPs, we developed a 32-SNP barcode that is robust and differentiates geographically distinct populations; it contains SNPs that are putatively neutral, located in nuclear, mitochondrial, and apicoplastal regions. The assays are reproducible and robust, requiring a small quantity of DNA (limit of detection as low as 10 pg.). We analyzed the performance of our HRM assay using 26 B. microti clinical samples used in our WGS study from babesiosis endemic regions in the United States. We identified a minimal barcode consisting of 25 SNPs that differentiate geographically distinct populations across all clinical samples evaluated (average minor allele frequency > 0.22). Supporting our previous WGS findings, our 25-SNP barcode identified distinct barcode signatures that segregate B. microti into two lineages: Northeast and Midwest, with the Northeast having three subpopulations: Connecticut/Rhode Island, Nantucket, and the R1 reference group. Our 25-SNP HRM barcode provides a robust means genetic marker set that will aid in tracking the increasing incidence and expanding geographic range of B. microti infections.},
}
@article {pmid30908110,
year = {2019},
author = {Cortés-Pérez, A and Desjardin, DE and Perry, BA and Ramírez-Cruz, V and Ramírez-Guillén, F and Villalobos-Arámbula, AR and Rockefeller, A},
title = {New species and records of bioluminescent Mycena from Mexico.},
journal = {Mycologia},
volume = {111},
number = {2},
pages = {319-338},
doi = {10.1080/00275514.2018.1554172},
pmid = {30908110},
issn = {1557-2536},
mesh = {Agaricales/*classification/genetics/*isolation &amp; purification/physiology ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; *Luminescence ; Mexico ; *Phylogeny ; RNA, Ribosomal, 5.8S/genetics ; Sequence Analysis, DNA ; },
abstract = {Seven species of bioluminescent fungi are recorded from the cloud forests in Mexico. Six represent new species belonging to the genus Mycena, whereas Mycena globulispora is a new distribution record for the country. Descriptions, illustrations, photographs, and an identification key to bioluminescent fungi species from Mexico are provided. Sequences of nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) region were generated for barcoding purposes and comparisons with similar species.},
}
@article {pmid30906693,
year = {2019},
author = {Johansson, G and Andersson, D and Filges, S and Li, J and Muth, A and Godfrey, TE and Ståhlberg, A},
title = {Considerations and quality controls when analyzing cell-free tumor DNA.},
journal = {Biomolecular detection and quantification},
volume = {17},
number = {},
pages = {100078},
pmid = {30906693},
issn = {2214-7535},
support = {R01 CA208599/CA/NCI NIH HHS/United States ; },
abstract = {Circulating cell-free tumor DNA (ctDNA) is a promising biomarker in cancer. Ultrasensitive technologies enable detection of low (< 0.1%) mutant allele frequencies, a pre-requisite to fully utilize the potential of ctDNA in cancer diagnostics. In addition, the entire liquid biopsy workflow needs to be carefully optimized to enable reliable ctDNA analysis. Here, we discuss important considerations for ctDNA detection in plasma. We show how each experimental step can easily be evaluated using simple quantitative PCR assays, including detection of cellular DNA contamination and PCR inhibition. Furthermore, ctDNA assay performance is also demonstrated to be affected by both DNA fragmentation and target sequence. Finally, we show that quantitative PCR is useful to estimate the required sequencing depth and to monitor DNA losses throughout the workflow. The use of quality control assays enables the development of robust and standardized workflows that facilitate the implementation of ctDNA analysis into clinical routine.},
}
@article {pmid30903202,
year = {2019},
author = {Borg Dahl, M and Brejnrod, AD and Russel, J and Sørensen, SJ and Schnittler, M},
title = {Different Degrees of Niche Differentiation for Bacteria, Fungi, and Myxomycetes Within an Elevational Transect in the German Alps.},
journal = {Microbial ecology},
volume = {78},
number = {3},
pages = {764-780},
pmid = {30903202},
issn = {1432-184X},
support = {RTG2010//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; DNA, Protozoan/genetics ; Fungi/classification/genetics/*isolation &amp; purification ; Germany ; Myxomycetes/genetics/*isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Soil/*parasitology ; Soil Microbiology ; },
abstract = {We used direct DNA amplification from soil extracts to analyze microbial communities from an elevational transect in the German Alps by parallel metabarcoding of bacteria (16S rRNA), fungi (ITS2), and myxomycetes (18S rRNA). For the three microbial groups, 5710, 6133, and 261 operational taxonomic units (OTU) were found. For the latter group, we can relate OTUs to barcodes from fruit bodies sampled over a 4-year period. The alpha diversity of myxomycetes was positively correlated with that of bacteria. Vegetation type was found to be the main explanatory parameter for the community composition of all three groups and a substantial species turnover with elevation was observed. Bacteria and fungi display similar community responses, driven by symbiont species and plant substrate quality. Myxamoebae show a more patchy distribution, though still clearly stratified between taxa, which seems to be a response to both structural properties of the habitat and interaction with specific bacterial and fungal taxa. Finally, we report a high number of myxomycete OTUs not represented in a reference database from fructifications, which might represent novel species.},
}
@article {pmid30901215,
year = {2019},
author = {Böhme, K and Calo-Mata, P and Barros-Velázquez, J and Ortea, I},
title = {Review of Recent DNA-Based Methods for Main Food-Authentication Topics.},
journal = {Journal of agricultural and food chemistry},
volume = {67},
number = {14},
pages = {3854-3864},
doi = {10.1021/acs.jafc.8b07016},
pmid = {30901215},
issn = {1520-5118},
mesh = {Animals ; DNA/*genetics ; DNA Barcoding, Taxonomic/*methods ; Food ; Food Contamination/*analysis ; Meat/analysis ; Plants/chemistry/classification/*genetics ; },
abstract = {Adulteration and mislabeling of food products and the commercial fraud derived, either intentionally or not, is a global source of economic fraud to consumers but also to all stakeholders involved in food production and distribution. Legislation has been enforced all over the world aimed at guaranteeing the authenticity of the food products all along the distribution chain, thereby avoiding food fraud and adulteration. Accordingly, there is a growing need for new analytical methods able to verify that all the ingredients included in a foodstuff match the qualities claimed by the manufacturer or distributor. In this sense, the improved performance of most recent DNA-based tools in term of sensitivity, multiplexing ability, high-throughput, and relatively low-cost give them a game-changing role in food-authenticity-related topics. Here, we provide a thorough and updated vision on the recently reported approaches that are applying these DNA-based tools to assess the authenticity of food components and products.},
}
@article {pmid30901128,
year = {2019},
author = {Martins, FMS and Galhardo, M and Filipe, AF and Teixeira, A and Pinheiro, P and Paupério, J and Alves, PC and Beja, P},
title = {Have the cake and eat it: Optimizing nondestructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring.},
journal = {Molecular ecology resources},
volume = {19},
number = {4},
pages = {863-876},
pmid = {30901128},
issn = {1755-0998},
support = {PTDC/AAGMAA/2261/2014-POCI-1-145-FEDER-356016824//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BD/104703/2014//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 668981//Horizon 2020 Framework Programme/ ; //EDP-Biodiversity Chair/ ; },
mesh = {Animals ; DNA/*genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Ecological Parameter Monitoring/*methods ; Fresh Water/*chemistry ; Invertebrates/classification/genetics ; Metagenomics/*methods ; },
abstract = {DNA metabarcoding can contribute to improving cost-effectiveness and accuracy of biological assessments of aquatic ecosystems, but significant optimization and standardization efforts are still required to mainstream its application into biomonitoring programmes. In assessments based on freshwater macroinvertebrates, a key challenge is that DNA is often extracted from cleaned, sorted and homogenized bulk samples, which is time-consuming and may be incompatible with sample preservation requirements of regulatory agencies. Here, we optimize and evaluate metabarcoding procedures based on DNA recovered from 96% ethanol used to preserve field samples and thus including potential PCR inhibitors and nontarget organisms. We sampled macroinvertebrates at five sites and subsampled the preservative ethanol at 1 to 14 days thereafter. DNA was extracted using column-based enzymatic (TISSUE) or mechanic (SOIL) protocols, or with a new magnetic-based enzymatic protocol (BEAD), and a 313-bp COI fragment was amplified. Metabarcoding detected at least 200 macroinvertebrate taxa, including most taxa detected through morphology and for which there was a reference barcode. Better results were obtained with BEAD than SOIL or TISSUE, and with subsamples taken 7-14 than 1-7 days after sampling, in terms of DNA concentration and integrity, taxa diversity and matching between metabarcoding and morphology. Most variation in community composition was explained by differences among sites, with small but significant contributions of subsampling day and extraction method, and negligible contributions of extraction and PCR replication. Our methods enhance reliability of preservative ethanol as a potential source of DNA for macroinvertebrate metabarcoding, with a strong potential application in freshwater biomonitoring.},
}
@article {pmid30899595,
year = {2019},
author = {Velasco-Cuervo, SM and Aguirre-Ramirez, E and Gallo-Franco, JJ and González Obando, R and Carrejo, N and Toro-Perea, N},
title = {Saving DNA from museum specimens: The success of DNA mini-barcodes in haplotype reconstruction in the genus Anastrepha (Diptera: Tephritidae).},
journal = {Journal of advanced research},
volume = {16},
number = {},
pages = {123-134},
pmid = {30899595},
issn = {2090-1232},
abstract = {The fragmentation of DNA in historical specimens is very common, so obtaining sequences that allow molecular identification and the study of diversity is quite challenging. In this study, we used preserved and fresh specimens of the fruit fly genus Anastrepha, a genus of economic impact of fruit crops of the Neotropic. From these specimens, we evaluated: (1) the success PCR amplification rates of mini-barcodes fragments of the cytochrome c oxidase subunit I (COI) gene, and (2) the usefulness of mini-barcodes in the reconstruction of haplotypes for the identification of species and the diversity analysis. We used 93 specimens from 12 species, which had been preserved in 70% ethanol for more than 20 years. Internal primers were designed in the COI region and primers available in the literature were also evaluated. We obtained amplifications for 62.36% of the samples processed, and reconstructed haplotypes between 171 bp and 632 bp. Variable amplification rates between combinations of primers and between species were obtained, and molecular identification of some museum specimens was achieved. It was also possible to compare the haplotypes obtained in four species from which both fresh and museum samples were available. Our results also show the importance of the adjustment of the primers for the amplification, allowing to amplify fragments of up to 400 bp. The use available resources in biological collections is key to increasing knowledge of species of interest, and by means of the amplification of mini-barcodes, short sequences can be obtained that allow the molecular identification of specimens and the reconstruction of haplotypes with multiple purposes.},
}
@article {pmid30899320,
year = {2019},
author = {Marengo, A and Cagliero, C and Sgorbini, B and Anderson, JL and Emaus, MN and Bicchi, C and Bertea, CM and Rubiolo, P},
title = {Development of an innovative and sustainable one-step method for rapid plant DNA isolation for targeted PCR using magnetic ionic liquids.},
journal = {Plant methods},
volume = {15},
number = {},
pages = {23},
pmid = {30899320},
issn = {1746-4811},
abstract = {BACKGROUND: Nowadays, there is an increasing demand for fast and reliable plant biomolecular analyses. Conventional methods for the isolation of nucleic acids are time-consuming and require multiple and often non-automatable steps to remove cellular interferences, with consequence that sample preparation is the major bottleneck in the bioanalytical workflow. New opportunities have been created by the use of magnetic ionic liquids (MILs) thanks to their affinity for nucleic acids.<br><br>RESULTS: In the present study, a MIL-based magnet-assisted dispersive liquid-liquid microextraction (maDLLME) method was optimized for the extraction of genomic DNA from Arabidopsis thaliana (L.) Heynh leaves. MILs containing different metal centers were tested and the extraction method was optimized in terms of MIL volume and extraction time for purified DNA and crude lysates. The proposed approach yielded good extraction efficiency and is compatible with both quantitative analysis through fluorimetric-based detection and qualitative analysis as PCR amplification of multi and single locus genes. The protocol was successfully applied to a set of plant species and tissues.<br><br>CONCLUSIONS: The developed MIL-based maDLLME approach exhibits good enrichment of nucleic acids for extraction of template suitable for targeted PCR; it is very fast, sustainable and potentially automatable thereby representing a powerful tool for screening plants rapidly using DNA-based methods.},
}
@article {pmid30898844,
year = {2019},
author = {Shakiba, N and Fahmy, A and Jayakumaran, G and McGibbon, S and David, L and Trcka, D and Elbaz, J and Puri, MC and Nagy, A and van der Kooy, D and Goyal, S and Wrana, JL and Zandstra, PW},
title = {Cell competition during reprogramming gives rise to dominant clones.},
journal = {Science (New York, N.Y.)},
volume = {364},
number = {6438},
pages = {},
doi = {10.1126/science.aan0925},
pmid = {30898844},
issn = {1095-9203},
mesh = {Animals ; Cellular Reprogramming/genetics/*physiology ; Cellular Reprogramming Techniques ; *Clonal Evolution ; Clone Cells/cytology ; DNA/genetics ; Fibroblasts/cytology ; Induced Pluripotent Stem Cells/*cytology ; Mice ; Models, Theoretical ; },
abstract = {The ability to generate induced pluripotent stem cells from differentiated cell types has enabled researchers to engineer cell states. Although studies have identified molecular networks that reprogram cells to pluripotency, the cellular dynamics of these processes remain poorly understood. Here, by combining cellular barcoding, mathematical modeling, and lineage tracing approaches, we demonstrate that reprogramming dynamics in heterogeneous populations are driven by dominant "elite" clones. Clones arise a priori from a population of poised mouse embryonic fibroblasts derived from Wnt1-expressing cells that may represent a neural crest-derived population. This work highlights the importance of cellular dynamics in fate programming outcomes and uncovers cell competition as a mechanism by which cells with eliteness emerge to occupy and dominate the reprogramming niche.},
}
@article {pmid30898693,
year = {2019},
author = {Schäffer, S and Kerschbaumer, M and Koblmüller, S},
title = {Multiple new species: Cryptic diversity in the widespread mite species Cymbaeremaeus cymba (Oribatida, Cymbaeremaeidae).},
journal = {Molecular phylogenetics and evolution},
volume = {135},
number = {},
pages = {185-192},
doi = {10.1016/j.ympev.2019.03.008},
pmid = {30898693},
issn = {1095-9513},
support = {P 27843/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Animals ; *Biodiversity ; Ecosystem ; Europe ; Genetic Markers ; Geography ; Mites/*classification ; Phylogeny ; Species Specificity ; },
abstract = {The absence of obvious morphological differences between species impedes species identification in many groups of organisms. Such cryptic species appear to be particularly common in small-bodied animals, impacting species richness estimates. In this study we aimed at characterizing the molecular diversity of the Palearctic arboreal oribatid mite species Cymbaeremaeus cymba across large parts of Europe. Phylogenetic analyses of three molecular markers, including the COI barcoding region, identified eight well supported, fairly divergent clades within C. cymba, which we consider to represent distinct species based on molecular species delimitation methods. Intraspecific variation of the COI gene was extremely low in all putative species, contradicting previous assumptions of high intraspecific diversity in oribatid mites. The frequent co-occurrence of two species on a single tree suggests an ecological micro-niche differentiation. Contrary to previous studies on oribatid mites, we find that COI is a good marker for species delimitation and its further use for barcoding of oribatids is highly recommended. Furthermore, we provide descriptions of six new Cymbaeremaeus species and designate a neotype of C. cymba.},
}
@article {pmid30896178,
year = {2019},
author = {Shah, S and Dubey, AK and Reif, J},
title = {Programming Temporal DNA Barcodes for Single-Molecule Fingerprinting.},
journal = {Nano letters},
volume = {19},
number = {4},
pages = {2668-2673},
doi = {10.1021/acs.nanolett.9b00590},
pmid = {30896178},
issn = {1530-6992},
mesh = {DNA/chemistry/*isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Fluorescent Dyes/chemistry ; Microscopy, Fluorescence/methods ; Nanotechnology/methods ; Photobleaching ; },
abstract = {Fluorescence microscopy enables simultaneous observation of the dynamics of single molecules in a large region of interest. Most traditional techniques employ either the geometry or the color of single molecules to uniquely identify (or barcode) different species of interest. However, these techniques require complex sample preparation and multicolor hardware setup. In this work, we introduce a time-based amplification-free single-molecule barcoding technique using easy-to-design nucleic acid strands. A dye-labeled complementary reporter strand transiently binds to the programmed nucleic acid strands to emit temporal intensity signals. We program the DNA strands to emit uniquely identifiable temporal signals for molecular-scale fingerprinting. Since the reporters bind transiently to DNA devices, our method offers relative immunity to photobleaching. We use a single universal reporter strand for all DNA devices making our design extremely cost-effective. We show DNA strands can be programmed for generating a multitude of uniquely identifiable molecular barcodes. Our technique can be easily incorporated with the existing orthogonal methods that use wavelength or geometry to generate a large pool of distinguishable molecular barcodes thereby enhancing the overall multiplexing capabilities of single-molecule imaging.},
}
@article {pmid30894119,
year = {2019},
author = {Loontiens, S and Depestel, L and Vanhauwaert, S and Dewyn, G and Gistelinck, C and Verboom, K and Van Loocke, W and Matthijssens, F and Willaert, A and Vandesompele, J and Speleman, F and Durinck, K},
title = {Purification of high-quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {228},
pmid = {30894119},
issn = {1471-2164},
support = {G021415N &amp; G051516N//Fonds Wetenschappelijk Onderzoek/ ; BOF15/DOC/220//Bijzonder Onderzoeksfonds/ ; Methusalem Grant BOF08/01M01108//Bijzonder Onderzoeksfonds/ ; GOA//Bijzonder Onderzoeksfonds/ ; Emmanuel van der Schueren grant//Kom op tegen kanker/ ; },
mesh = {Animals ; Cell Count ; *Flow Cytometry ; Poly A/genetics ; Quality Control ; RNA/*genetics/*isolation &amp; purification ; *Sequence Analysis, RNA ; Zebrafish/*genetics ; },
abstract = {BACKGROUND: Transgenic zebrafish lines with the expression of a fluorescent reporter under the control of a cell-type specific promoter, enable transcriptome analysis of FACS sorted cell populations. RNA quality and yield are key determinant factors for accurate expression profiling. Limited cell number and FACS induced cellular stress make RNA isolation of sorted zebrafish cells a delicate process. We aimed to optimize a workflow to extract sufficient amounts of high-quality RNA from a limited number of FACS sorted cells from Tg(fli1a:GFP) zebrafish embryos, which can be used for accurate gene expression analysis.<br><br>RESULTS: We evaluated two suitable RNA isolation kits (the&#xa0;RNAqueous micro and the RNeasy plus micro kit) and determined that sorting cells directly into lysis buffer is a critical step for success. For low cell numbers, this ensures direct cell lysis, protects RNA from degradation and results in a higher RNA quality and yield. We showed that this works well up to 0.5&#xd7; dilution of the lysis buffer with sorted cells. In our sort settings, this corresponded to 30,000 and 75,000 cells for the RNAqueous micro kit and RNeasy plus micro kit respectively. Sorting more cells dilutes the lysis buffer too much and requires the use of a collection buffer. We also demonstrated that an additional genomic DNA removal step after RNA isolation is required to completely clear the RNA from any contaminating genomic DNA. For cDNA synthesis and library preparation, we combined SmartSeq v4 full length cDNA library amplification, Nextera XT tagmentation and sample barcoding. Using this workflow, we were able to generate highly reproducible RNA sequencing results.<br><br>CONCLUSIONS: The presented optimized workflow enables to generate high quality RNA and allows accurate transcriptome profiling of small populations of sorted zebrafish cells.},
}
@article {pmid30893940,
year = {2019},
author = {Frigerio, J and Pellesi, R and Mezzasalma, V and De Mattia, F and Galimberti, A and Lambertini, F and Suman, M and Zanardi, S and Leporati, A and Labra, M},
title = {Development of a DNA Barcoding-Like Approach to Detect Mustard Allergens in Wheat Flours.},
journal = {Genes},
volume = {10},
number = {3},
pages = {},
pmid = {30893940},
issn = {2073-4425},
mesh = {Allergens/*genetics ; DNA Barcoding, Taxonomic/*methods ; Edible Grain/standards ; Flour/*analysis ; Food Contamination/analysis ; Mustard Plant/*classification/genetics/immunology ; Plant Proteins/genetics ; Triticum ; },
abstract = {The spread of food allergens is a topic of global importance due to its impact on public health. National and International regulations ask food producers and manufacturers to declare product compositions on the label, especially in case of processed raw materials. Wheat flour (Triticum aestivum) can be contaminated by a wide range of species belonging to the Brassicaceae in the field or during grain harvests, storage, and processing. Among them, mustards (Brassica nigra, Brassica juncea and Sinapis alba) are well known allergenic species. Often, food quality laboratories adopt an ELISA approach to detect the presence of mustard species. However, this approach shows cross-reactivity with other non-allergenic species such as Brassica napus (rapeseed). In the last few years, DNA barcoding was proposed as a valid identification method, and it is now commonly used in the authentication of food products. This study aims to set up an easy and rapid DNA-based tool to detect mustard allergenic species. DNA barcoding (matK and ITS2) and chromosome markers (A6, B, C1 genome regions) were selected, and specific primers were validated on incurred reference food matrices. The developed test was proven to be able to distinguish mustard from rapeseed and wheat, overcoming cross-reactivity with Brassica napus.},
}
@article {pmid30892983,
year = {2019},
author = {Gangan, SS and Pavan-Kumar, A and K, JA},
title = {Multigene barcoding and phylogeny of selected Engraulidae species.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {3},
pages = {548-555},
doi = {10.1080/24701394.2019.1570175},
pmid = {30892983},
issn = {2470-1408},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Fishes/*genetics ; Multigene Family/*genetics ; *Phylogeny ; Species Specificity ; },
abstract = {Anchovies (Engraulidae) are one of the ecologically important groups and often difficult to identify due to their small size and overlapping morphological characters. In the present study, reference DNA barcodes were generated for 82 individuals representing 13 species of Engraulidae family using mitochondrial Cytochrome c oxidase subunit I (COI) and 16S rRNA genes. The average genetic distance value of COI gene for conspecific, congeneric and confamilial is 0.25, 20.45 and 22.28%, respectively. Mitochondrial 16S rRNA showed an average divergence value of 0.60, 10.28 and 14.37% for within species, between species and within families, respectively. Comparison of the present study reference barcodes with the reported sequences revealed high frequency of misidentification of species and possible occurrence of cryptic species in this family. Phylogenetic tree reconstructed using different methodologies revealed monophyletic nature of genus Stolephorus and the evolutionary relationship within genus Stolephorus is defined as ([S. insularis: S. tamilensis] S. dubiosus (S. waitei [S. commersonnii: S. indicus])).},
}
@article {pmid30891232,
year = {2019},
author = {Phillips, JD and Gillis, DJ and Hanner, RH},
title = {Incomplete estimates of genetic diversity within species: Implications for DNA barcoding.},
journal = {Ecology and evolution},
volume = {9},
number = {5},
pages = {2996-3010},
pmid = {30891232},
issn = {2045-7758},
abstract = {DNA barcoding has greatly accelerated the pace of specimen identification to the species level, as well as species delineation. Whereas the application of DNA barcoding to the matching of unknown specimens to known species is straightforward, its use for species delimitation is more controversial, as species discovery hinges critically on present levels of haplotype diversity, as well as patterning of standing genetic variation that exists within and between species. Typical sample sizes for molecular biodiversity assessment using DNA barcodes range from 5 to 10 individuals per species. However, required levels that are necessary to fully gauge haplotype variation at the species level are presumed to be strongly taxon-specific. Importantly, little attention has been paid to determining appropriate specimen sample sizes that are necessary to reveal the majority of intraspecific haplotype variation within any one species. In this paper, we present a brief outline of the current literature and methods on intraspecific sample size estimation for the assessment of COI DNA barcode haplotype sampling completeness. The importance of adequate sample sizes for studies of molecular biodiversity is stressed, with application to a variety of metazoan taxa, through reviewing foundational statistical and population genetic models, with specific application to ray-finned fishes (Chordata: Actinopterygii). Finally, promising avenues for further research in this area are highlighted.},
}
@article {pmid30891208,
year = {2019},
author = {Barbato, M and Kovacs, T and Coleman, MA and Broadhurst, MK and de Bruyn, M},
title = {Metabarcoding for stomach-content analyses of Pygmy devil ray (Mobula kuhlii cf. eregoodootenkee): Comparing tissue and ethanol preservative-derived DNA.},
journal = {Ecology and evolution},
volume = {9},
number = {5},
pages = {2678-2687},
pmid = {30891208},
issn = {2045-7758},
abstract = {The application of high-throughput sequencing to retrieve multi-taxon DNA from different substrates such as water, soil, and stomach contents has enabled species identification without prior knowledge of taxon compositions. Here we used three minibarcodes designed to target mitochondrial COI in plankton, 16S in fish, and 16S in crustaceans, to compare ethanol- and tissue-derived DNA extraction methodologies for metabarcoding. The stomach contents of pygmy devilrays (Mobula kuhlii cf. eregoodootenkee) were used to test whether ethanol-derived DNA would provide a suitable substrate for metabarcoding. The DNA barcoding assays indicated that tissue-derived operational taxonomic units (OTUs) were greater compared to those from extractions performed directly on the ethanol preservative. Tissue-derived DNA extraction is therefore recommended for broader taxonomic coverage. Metabarcoding applications should consider including the following: (i) multiple barcodes, both taxon specific (e.g., 12S or 16S) and more universal (e.g., COI or 18S) to overcome bias and taxon misidentification and (ii) PCR inhibitor removal steps that will likely enhance amplification yields. However, where tissue is limited or no longer available, but the ethanol-preservative medium is still available, metabarcoding directly from ethanol does recover the majority of common OTUs, suggesting the ethanol-retrieval method could be applicable for dietary studies. Metabarcoding directly from preservative ethanol may also be useful where tissue samples are limited or highly valued; bulk samples are collected, such as for rapid species inventories; or mixed-voucher sampling is conducted (e.g., for plankton, insects, and crustaceans).},
}
@article {pmid30891063,
year = {2019},
author = {Reed, E and Moses, E and Xiao, X and Liu, G and Campbell, J and Perdomo, C and Monti, S},
title = {Assessment of a Highly Multiplexed RNA Sequencing Platform and Comparison to Existing High-Throughput Gene Expression Profiling Techniques.},
journal = {Frontiers in genetics},
volume = {10},
number = {},
pages = {150},
pmid = {30891063},
issn = {1664-8021},
support = {P42 ES007381/ES/NIEHS NIH HHS/United States ; },
abstract = {The need to reduce per sample cost of RNA-seq profiling for scalable data generation has led to the emergence of highly multiplexed RNA-seq. These technologies utilize barcoding of cDNA sequences in order to combine multiple samples into a single sequencing lane to be separated during data processing. In this study, we report the performance of one such technique denoted as sparse full length sequencing (SFL), a ribosomal RNA depletion-based RNA sequencing approach that allows for the simultaneous sequencing of 96 samples and higher. We offer comparisons to well established single-sample techniques, including: full coverage Poly-A capture RNA-seq, microarrays, as well as another low-cost highly multiplexed technique known as 3' digital gene expression (3'DGE). Data was generated for a set of exposure experiments on immortalized human lung epithelial (AALE) cells in a two-by-two study design, in which samples received both genetic and chemical perturbations of known oncogenes/tumor suppressors and lung carcinogens. SFL demonstrated improved performance over 3'DGE in terms of coverage, power to detect differential gene expression, and biological recapitulation of patterns of differential gene expression from in vivo lung cancer mutation signatures.},
}
@article {pmid30889387,
year = {2019},
author = {Barendse, J and Roel, A and Longo, C and Andriessen, L and Webster, LMI and Ogden, R and Neat, F},
title = {DNA barcoding validates species labelling of certified seafood.},
journal = {Current biology : CB},
volume = {29},
number = {6},
pages = {R198-R199},
doi = {10.1016/j.cub.2019.02.014},
pmid = {30889387},
issn = {1879-0445},
mesh = {DNA Barcoding, Taxonomic/*statistics &amp; numerical data ; Food Handling ; Food-Processing Industry ; Seafood/*classification ; },
abstract = {Seafood is one of the most traded food commodities in the world with demand steadily increasing [1]. There is, however, a rising concern over the vulnerability of seafood supply chains to species mislabelling and fraud [1,2]. DNA methods have been widely used to detect species mislabelling and a recent meta-analysis of 4500 seafood product tests from 51 publications found an average of 30 percent were not the species stated on the label or menu [3]. This high rate poses a serious threat to consumer trust, reputations of seafood businesses and the sustainability of fishery resources. Seafood certification schemes may help reduce this problem. Here, we use DNA barcoding [4] to validate the species identity of 1402 certified seafood products derived from 27 species across 18 countries and find that in over 99% of cases species labelling was correct.},
}
@article {pmid30886872,
year = {2019},
author = {Poláková, I and Pelák, O and Thürner, D and Pokrývková, B and Tachezy, R and Kalina, T and Šmahel, M},
title = {Implementation of Mass Cytometry for Immunoprofiling of Patients with Solid Tumors.},
journal = {Journal of immunology research},
volume = {2019},
number = {},
pages = {6705949},
pmid = {30886872},
issn = {2314-7156},
mesh = {Antibodies, Monoclonal/metabolism ; Cell Separation ; Collagenases/metabolism ; DNA Barcoding, Taxonomic ; Deoxyribonuclease I/metabolism ; Flow Cytometry ; Humans ; Immunophenotyping/*methods ; Leukocyte Common Antigens/immunology ; Lymphocytes/*physiology ; Myeloid Cells/*physiology ; Neoplasms/diagnosis/*immunology ; Palladium/metabolism ; Single-Cell Analysis ; },
abstract = {Monitoring immune responses to solid cancers may be a better prognostic tool than conventional staging criteria, and it can also serve as an important criterion for the selection of individualized therapy. Multiparametric phenotyping by mass cytometry extended possibilities for immunoprofiling. However, careful optimization of each step of such method is necessary for obtaining reliable results. Also, with respect to procedure length and costs, sample preparation, staining, and storage should be optimized. Here, we designed a panel of 31 antibodies which allows for identification of several subpopulations of lymphoid and myeloid cells in a solid tumor and peripheral blood simultaneously. For sample preparation, disaggregation of tumor tissue with two different collagenases combined with DNase I was compared, and removal of dead or tumor cells by magnetic separation was evaluated. Two possible procedures of barcoding for single-tube staining of several samples were examined. While the palladium-based barcoding affected the stability of several antigens, the staining with two differently labeled CD45 antibodies was suitable for cells isolated from a patient's blood and tumor. The storage of samples in the intercalation solution for up to two weeks did not influence results of the analysis, which allowed the measurement of samples collected within this interval on the same day. This procedure optimized on samples from patients with head and neck squamous cell carcinoma enabled identification of various immune cells including rare subpopulations.},
}
@article {pmid30886426,
year = {2019},
author = {Li, X and Patena, W and Fauser, F and Jinkerson, RE and Saroussi, S and Meyer, MT and Ivanova, N and Robertson, JM and Yue, R and Zhang, R and Vilarrasa-Blasi, J and Wittkopp, TM and Ramundo, S and Blum, SR and Goh, A and Laudon, M and Srikumar, T and Lefebvre, PA and Grossman, AR and Jonikas, MC},
title = {A genome-wide algal mutant library and functional screen identifies genes required for eukaryotic photosynthesis.},
journal = {Nature genetics},
volume = {51},
number = {4},
pages = {627-635},
pmid = {30886426},
issn = {1546-1718},
support = {DP2 GM119137/GM/NIGMS NIH HHS/United States ; },
mesh = {Chlamydomonas reinhardtii/*genetics ; Chlorophyta/*genetics ; Eukaryota/*genetics ; Gene Library ; Genome/genetics ; Genome-Wide Association Study/methods ; Genomics/methods ; Mutation/*genetics ; Photosynthesis/*genetics ; Sequence Analysis, DNA/methods ; },
abstract = {Photosynthetic organisms provide food and energy for nearly all life on Earth, yet half of their protein-coding genes remain uncharacterized[1,2]. Characterization of these genes could be greatly accelerated by new genetic resources for unicellular organisms. Here we generated a genome-wide, indexed library of mapped insertion mutants for the unicellular alga Chlamydomonas reinhardtii. The 62,389 mutants in the library, covering 83% of nuclear protein-coding genes, are available to the community. Each mutant contains unique DNA barcodes, allowing the collection to be screened as a pool. We performed a genome-wide survey of genes required for photosynthesis, which identified 303 candidate genes. Characterization of one of these genes, the conserved predicted phosphatase-encoding gene CPL3, showed that it is important for accumulation of multiple photosynthetic protein complexes. Notably, 21 of the 43 higher-confidence genes are novel, opening new opportunities for advances in understanding of this biogeochemically fundamental process. This library will accelerate the characterization of thousands of genes in algae, plants, and animals.},
}
@article {pmid30885193,
year = {2019},
author = {Fulakeza, J and McNitt, S and Vareta, J and Saidi, A and Mvula, G and Taylor, T and Mathanga, DP and Small, DS and Skarbinski, J and Gutman, JR and Seydel, K},
title = {Comparison of msp genotyping and a 24 SNP molecular assay for differentiating Plasmodium falciparum recrudescence from reinfection.},
journal = {Malaria journal},
volume = {18},
number = {1},
pages = {84},
pmid = {30885193},
issn = {1475-2875},
support = {R01 AI034969/AI/NIAID NIH HHS/United States ; U01 CI000189/CI/NCPDCID CDC HHS/United States ; RO1AI34969//National Institutes of Health/ ; 5 U01 CI000189//Center for Global Health/ ; },
mesh = {Antigens, Protozoan/*genetics ; Child, Preschool ; Clinical Trials as Topic ; Female ; Genotype ; Genotyping Techniques/*methods ; Humans ; Infant ; Malaria, Falciparum/*diagnosis/*parasitology ; Malawi ; Male ; Merozoite Surface Protein 1/*genetics ; Plasmodium falciparum/*classification/genetics/isolation &amp; purification ; *Polymorphism, Single Nucleotide ; Protozoan Proteins/*genetics ; Recurrence ; Sensitivity and Specificity ; Time Factors ; },
abstract = {BACKGROUND: Current World Health Organization guidelines for conducting anti-malarial drug efficacy clinical trials recommend genotyping Plasmodium falciparum genes msp1 and msp2 to distinguish recrudescence from reinfection. A more recently developed potential alternative to this method is a molecular genotyping assay based on a panel of 24 single nucleotide polymorphism (SNP) markers.<br><br>METHODS: Performance parameters of these two genotyping methods were compared using data from two recently completed drug efficacy trials. Blood samples from two anti-malarial therapeutic trials were analysed by both msp genotyping and the 24 SNP assay. Additionally, to conserve time and resources, the statistical program R was used to select the most informative SNPs for a set of unrelated Malawian samples to develop a truncated SNP-based assay for the region surrounding Blantyre, Malawi. The ability of this truncated assay to distinguish reinfection from recrudescence when compared to the full 24 SNP assay was then analysed using data from the therapeutic trials.<br><br>RESULTS: A total of 360 samples were analysed; 66 for concordance of msp and SNP barcoding methodologies, and 294 for assessing the most informative of the 24 SNP markers. SNP genotyping performed comparably to msp genotyping, with only one case of disagreement among the 50 interpretable results, where the SNP assay identified the sample as reinfection and the msp typing as recrudescence. Furthermore, SNP typing was more robust; only 6% of samples were uninterpretable by SNP typing, compared to 19.7% when msp genotyping was used. For discriminating reinfection from recrudescence, a truncated 6 SNP assay was found to perform at 95.1% the accuracy of the full 24 SNP bar code.<br><br>CONCLUSIONS: The use of SNP analysis has similar sensitivity to the standard msp genotyping in determining recrudescence from reinfection. Although more expensive, SNP typing is faster and less work intensive. Limiting the assay to those SNPs most informative in the geographical region of interest may further decrease the workload and the cost, making this technique a feasible and affordable alternative in drug efficacy trials.},
}
@article {pmid30883559,
year = {2019},
author = {Amouroux, P and Crochard, D and Correa, M and Groussier, G and Kreiter, P and Roman, C and Guerrieri, E and Garonna, A and Malausa, T and Zaviezo, T},
title = {Natural enemies of armored scales (Hemiptera: Diaspididae) and soft scales (Hemiptera: Coccidae) in Chile: Molecular and morphological identification.},
journal = {PloS one},
volume = {14},
number = {3},
pages = {e0205475},
pmid = {30883559},
issn = {1932-6203},
mesh = {Anacardiaceae/parasitology ; Animals ; Bayes Theorem ; Chile ; *DNA Barcoding, Taxonomic ; Haplotypes ; Hemiptera/*anatomy &amp; histology/classification/*genetics ; *Host-Parasite Interactions ; Hymenoptera/*anatomy &amp; histology/*genetics ; Phylogeny ; },
abstract = {Scale insects (Hemiptera: Sternorrhyncha: Coccomorpha) are key pests of agricultural crops and ornamental plants worldwide. Their populations are difficult to control, even with insecticides, due to their cryptic habits. Moreover, there is growing concern over the use of synthetic pesticides for their control, due to deleterious environmental effects and the emergence of resistant populations of target pests. In this context, biological control may be an effective and sustainable approach. Hymenoptera Chalcidoidea includes natural enemies of scale insects that have been successfully used in many biological control programs. However, the correct identification of pest scale species and their natural enemies is particularly challenging because these insects are very small and highly specialized. Integrative taxonomy, coupling DNA barcoding and morphological analysis, has been successfully used to characterize pests and natural enemy species. In this study, we performed a survey of parasitoids and predators of armored and soft scales in Chile, based on 28S and COI barcodes. Fifty-three populations of Diaspididae and 79 populations of Coccidae were sampled over the entire length of the country, from Arica (18°S) to Frutillar (41°S), between January 2015 and February 2016. The phylogenetic relationships obtained by Bayesian inference from multilocus haplotypes revealed 41 putative species of Chalcidoidea, five Coccinellidae and three Neuroptera. Species delimitation was confirmed using ABGD, GMYC and PTP model. In Chalcidoidea, 23 species were identified morphologically, resulting in new COI barcodes for 12 species and new 28S barcodes for 14 species. Two predator species (Rhyzobius lophantae and Coccidophilus transandinus) were identified morphologically, and two parasitoid species, Chartocerus niger and Signiphora bifasciata, were recorded for the first time in Chile.},
}
@article {pmid30879469,
year = {2019},
author = {Amad, I and Hafeez, F and Khan, MA and Nahid, N and Javed, MR and Shaheen, S and Farooq, M and Khan, AZ and Hussain, K},
title = {Mitochondrial gene cytochrome c oxidase I (CO1) used for molecular identification of Bactrocera zonata in Pakistan.},
journal = {Cellular and molecular biology (Noisy-le-Grand, France)},
volume = {65},
number = {2},
pages = {82-84},
pmid = {30879469},
issn = {1165-158X},
mesh = {Algorithms ; Animals ; Electron Transport Complex IV/*genetics ; *Genes, Mitochondrial ; Pakistan ; Phylogeny ; Software ; Species Specificity ; Tephritidae/*enzymology/*genetics ; },
abstract = {Bactrocera zonata is fruit pest mostly attacked on peach and cause heavy destruction in production of peach fruits by sucking their juice. For their management, we start to detect them on basis of their molecular characterization. As mitochondrial genome encodes a gene COI used as biomarker for identification of eukaryotes including insects. In present study, we amplified COI gene and cloned into pTZ57R/T vector (Fermentas). Cloned gene was confirmed through restriction analysis and sequenced through its entirety on both strands from Macrogen (South Korea) by Sanger sequencing method. Different computational tools were utilized for comparative analysis of sequence with other related sequences retrieved from databases. Related species were identified through phylogenetic analysis using Mega 7 tool. Pairwise sequence alignment showed the sequence identity about 96% with Bactrocera zonata. By identifying the pests with more authentic molecular biomarker may help the research to control them more effectively in future.},
}
@article {pmid30875825,
year = {2019},
author = {Stuart, OP and Binns, M and Umina, PA and Holloway, J and Severtson, D and Nash, M and Heddle, T and van Helden, M and Hoffmann, AA},
title = {Morphological and Molecular Analysis of Australian Earwigs (Dermaptera) Points to Unique Species and Regional Endemism in the Anisolabididae Family.},
journal = {Insects},
volume = {10},
number = {3},
pages = {},
pmid = {30875825},
issn = {2075-4450},
support = {CSE00059//Grains Research and Development Corporation/ ; },
abstract = {Dermaptera (earwigs) from the Anisolabididae family may be important for pest control but their taxonomy and status in Australia is poorly studied. Here we used taxonomic information to assess the diversity of southern Australian Anisolabididae and then applied cox1 barcodes as well as additional gene fragments (mitochondrial and nuclear) to corroborate classification and assess the monophyly of the putative genera. Anisolabididae morphospecies fell into two genera, Anisolabis Fieber and Gonolabis Burr, based on paramere morphology. Combinations of paramere and forceps morphology distinguished seven morphospecies, which were further supported by morphometric analyses. The morphospecies were corroborated by barcode data; all showed within-species genetic distance < 4% and between-species genetic distance > 10%. Molecular phylogenies did not support monophyly of putative genera nor clades based on paramere shape, instead pointing to regional clades distinguishable by forceps morphology. This apparent endemism needs to be further tested by sampling of earwig diversity outside of agricultural production regions but points to a unique regional insect fauna potentially important in pest control.},
}
@article {pmid30875053,
year = {2019},
author = {Nichols, RV and Curd, E and Heintzman, PD and Shapiro, B},
title = {Targeted Amplification and Sequencing of Ancient Environmental and Sedimentary DNA.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1963},
number = {},
pages = {149-161},
doi = {10.1007/978-1-4939-9176-1_16},
pmid = {30875053},
issn = {1940-6029},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Ancient/*analysis ; Environmental Monitoring/*methods ; Geologic Sediments/*analysis ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Nucleic Acid Amplification Techniques/*methods ; Polymerase Chain Reaction/*methods ; },
abstract = {All organisms release their DNA into the environment through processes such as excretion and the senescence of tissues and limbs. This DNA, often referred to as environmental DNA (eDNA) or sedimentary ancient DNA (sedaDNA), can be recovered from both present-day and ancient soils, fecal samples, bodies of water and lake cores, and even air. While eDNA is a potentially useful record of past and present biodiversity, several challenges complicate data generation and interpretation of results. Most importantly, eDNA samples tend to be highly taxonomically mixed, and the target organism or group of organisms may be present at very low abundance within this mixture. To overcome this challenge, enrichment approaches are often used to target specific taxa of interest. Here, we describe a protocol to amplify metabarcodes or short, variable loci that identify lineages within broad taxonomic groups (e.g., plants, mammals), using the polymerase chain reaction (PCR) with established generic "barcode" primers. We also provide a catalog of animal and plant barcode primers that, because they target relatively short fragments of DNA, are potentially suitable for use with degraded DNA.},
}
@article {pmid30875052,
year = {2019},
author = {Wutke, S and Ludwig, A},
title = {Targeted PCR Amplification and Multiplex Sequencing of Ancient DNA for SNP Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1963},
number = {},
pages = {141-147},
doi = {10.1007/978-1-4939-9176-1_15},
pmid = {30875052},
issn = {1940-6029},
mesh = {DNA Fingerprinting/*methods ; DNA, Ancient/*analysis ; Forensic Genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Multiplex Polymerase Chain Reaction/*methods ; *Polymorphism, Single Nucleotide ; },
abstract = {The analysis of single-nucleotide polymorphisms (SNPs) has proven to be advantageous for addressing variation within samples of highly degraded or low-quality DNA samples. This is because only short fragments need to be amplified to analyze SNPs, and this can be achieved by multiplex PCR. Here, we present a sensitive method for the targeted sequencing of SNP loci that requires only small amounts of template DNA. The approach combines multiplex amplification of very short fragments covering SNP positions followed by sample barcoding and next-generation sequencing. This method allows generation of data from large sample sets of poorly preserved specimens, such as fossil remains, forensic samples, and museum specimens. The approach is cost-effective, rapid, and applicable to forensics, population genetics, and phylogenetic research questions.},
}
@article {pmid30874552,
year = {2019},
author = {Hwang, B and Lee, W and Yum, SY and Jeon, Y and Cho, N and Jang, G and Bang, D},
title = {Lineage tracing using a Cas9-deaminase barcoding system targeting endogenous L1 elements.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {1234},
pmid = {30874552},
issn = {2041-1723},
mesh = {CRISPR-Associated Protein 9/genetics ; Cell Differentiation/genetics ; Cell Lineage/*genetics ; Cytidine Deaminase/genetics ; DNA Barcoding, Taxonomic/*methods ; Gene Editing/*methods ; HEK293 Cells ; HeLa Cells ; Humans ; Long Interspersed Nucleotide Elements/*genetics ; Mutagenesis ; Single-Cell Analysis/methods ; Time-Lapse Imaging ; RNA, Guide, CRISPR-Cas Systems ; },
abstract = {Determining cell lineage and function is critical to understanding human physiology and pathology. Although advances in lineage tracing methods provide new insight into cell fate, defining cellular diversity at the mammalian level remains a challenge. Here, we develop a genome editing strategy using a cytidine deaminase fused with nickase Cas9 (nCas9) to specifically target endogenous interspersed repeat regions in mammalian cells. The resulting mutation patterns serve as a genetic barcode, which is induced by targeted mutagenesis with single-guide RNA (sgRNA), leveraging substitution events, and subsequent read out by a single primer pair. By analyzing interspersed mutation signatures, we show the accurate reconstruction of cell lineage using both bulk cell and single-cell data. We envision that our genetic barcode system will enable fine-resolution mapping of organismal development in healthy and diseased mammalian states.},
}
@article {pmid30872942,
year = {2019},
author = {Bubner, B and Buchheit, R and Friedrich, F and Kummer, V and Scholler, M},
title = {Species identification of European forest pathogens of the genus Milesina (Pucciniales) using urediniospore morphology and molecular barcoding including M.woodwardiana sp. nov.},
journal = {MycoKeys},
volume = {48},
number = {},
pages = {1-40},
pmid = {30872942},
issn = {1314-4049},
abstract = {Species of rust fungi of the genus Milesina (Pucciniastraceae, Pucciniales) are distributed mainly in northern temperate regions. They host-alternate between needles of fir (Abies spp.) and fronds of ferns (species of Polypodiales). Milesina species are distinguished based on host taxonomy and urediniospore morphology. In this study, 12 species of Milesina from Europe were revised. Specimens were examined by light and scanning electron microscopy for urediniospore morphology with a focus on visualising germ pores (number, size and position) and echinulation. In addition, barcode loci (ITS, nad6, 28S) were used for species delimitation and for molecular phylogenetic analyses. Barcodes of 72 Milesina specimens were provided, including 11 of the 12 species. Whereas urediniospore morphology features were sufficient to distinguish all 12 Milesina species except for 2 (M.blechni and M.kriegeriana), ITS sequences separated only 4 of 11 species. Sequencing with 28S and nad6 did not improve species resolution. Phylogenetic analysis, however, revealed four phylogenetic groups within Milesina that also correlate with specific urediniospore characters (germ pore number and position and echinulation). These groups are proposed as new sections within Milesina (sections Milesina, Vogesiacae M. Scholler &amp; Bubner, sect. nov., Scolopendriorum M. Scholler &amp; Bubner, sect. nov. and Carpaticae M. Scholler &amp; Bubner, sect. nov.). In addition, Milesinawoodwardiana Buchheit &amp; M. Scholler, sp. nov. on Woodwardiaradicans, a member of the type section Milesina, is newly described. An identification key for European Milesina species, based on urediniospore features, is provided.},
}
@article {pmid30872937,
year = {2018},
author = {Reip, HS and Wesener, T},
title = {Intraspecific variation and phylogeography of the millipede model organism, the Black Pill Millipede Glomerismarginata (Villers, 1789) (Diplopoda, Glomerida, Glomeridae).},
journal = {ZooKeys},
volume = {741},
number = {},
pages = {93-131},
pmid = {30872937},
issn = {1313-2989},
abstract = {The Black Pill Millipede, Glomerismarginata, is the best studied millipede species and a model organism for Diplopoda. Glomerismarginata is widespread, with numerous colour morphs occurring across its range, especially in the south. This study investigates whether colour morphs might represent cryptic species as well as the haplotype diversity and biogeography of G.marginata. The results of the COI barcoding fragment analysis include 97 G.marginata, as well as 21 specimens from seven potentially related species: G.intermedia Latzel, 1884, G.klugii Brandt, 1833 (G.undulata C.L. Koch, 1844), G.connexa Koch, 1847, G.hexasticha Brandt, 1833, G.maerens Attems, 1927, G.annulata Brandt, 1833 and G.apuana Verhoeff, 1911. The majority of the barcoding data was obtained through the German Barcode of Life project (GBOL). Interspecifically, G.marginata is separated from its congeners by a minimum uncorrected genetic distance of 12.9 %, confirming its monophyly. Uncorrected intraspecific distances of G.marginata are comparable to those of other widespread Glomeris species, varying between 0-4.7%, with the largest genetic distances (>2.5 %) found at the Mediterranean coast. 97 sampled specimens of G.marginata yielded 47 different haplotypes, with identical haplotypes occurring at large distances from one another, and different haplotypes being present in populations occurring in close proximity. The highest number of haplotypes was found in the best-sampled area, western Germany. The English haplotype is identical to northern Spain; specimens from southern Spain are closer to French Mediterranean specimens. Analyses (CHAO1) show that approximately 400 different haplotypes can be expected in G.marginata. To cover all haplotypes, it is projected that up to 6,000 specimens would need to be sequenced, highlighting the impossibility of covering the whole genetic diversity in barcoding attempts of immobile soil arthropod species.},
}
@article {pmid30872700,
year = {2019},
author = {Johri, S and Solanki, J and Cantu, VA and Fellows, SR and Edwards, RA and Moreno, I and Vyas, A and Dinsdale, EA},
title = {'Genome skimming' with the MinION hand-held sequencer identifies CITES-listed shark species in India's exports market.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {4476},
pmid = {30872700},
issn = {2045-2322},
mesh = {Animals ; Cell Nucleus/*genetics ; DNA/*genetics ; Endangered Species ; Fish Proteins/genetics ; Genome Size ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*instrumentation/veterinary ; India ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA/instrumentation/veterinary ; Sharks/*classification/genetics ; },
abstract = {Chondrichthyes - sharks, rays, skates, and chimeras, are among the most threatened and data deficient vertebrate species. Global demand for shark and ray derived products, drives unregulated and exploitative fishing practices, which are in turn facilitated by the lack of ecological data required for effective conservation of these species. Here, we describe a Next Generation Sequencing method (using the MinION, a hand-held portable sequencing device from Oxford Nanopore Technologies), and analyses pipeline for molecular ecological studies in Chondrichthyes. Using this method, the complete mitochondrial genome and nuclear intergenic and protein-coding sequences were obtained by direct sequencing of genomic DNA obtained from shark fin tissue. Recovered loci include mitochondrial barcode sequences- Cytochrome oxidase I, NADH2, 16S rRNA and 12S rRNA- and nuclear genetic loci such as 5.8S rRNA, Internal Transcribed Spacer 2, and 28S rRNA regions, which are commonly used for taxonomic identification. Other loci recovered were the nuclear protein-coding genes for antithrombin or SerpinC, Immunoglobulin lambda light chain, Preprogehrelin, selenium binding protein 1(SBP1), Interleukin-1 beta (IL-1β) and Recombination-Activating Gene 1 (RAG1). The median coverage across all genetic loci was 20x and sequence accuracy was ≥99.8% compared to reference sequences. Analyses of the nuclear ITS2 region and the mitochondrial protein-encoding loci allowed accurate taxonomic identification of the shark specimen as Carcharhinus falciformis, a CITES Appendix II species. MinION sequencing provided 1,152,211 bp of new shark genome, increasing the number of sequenced shark genomes to five. Phylogenetic analyses using both mitochondrial and nuclear loci provided evidence that Prionace glauca is nested within Carcharhinus, suggesting the need for taxonomic reassignment of P. glauca. We increased genomic information about a shark species for ecological and population genetic studies, enabled accurate identification of the shark tissue for biodiversity indexing and resolved phylogenetic relationships among multiple taxa. The method was independent of amplification bias, and adaptable for field assessments of other Chondrichthyes and wildlife species in the future.},
}
@article {pmid30871464,
year = {2019},
author = {Zhou, Z and Guo, H and Han, L and Chai, J and Che, X and Shi, F},
title = {Singleton molecular species delimitation based on COI-5P barcode sequences revealed high cryptic/undescribed diversity for Chinese katydids (Orthoptera: Tettigoniidae).},
journal = {BMC evolutionary biology},
volume = {19},
number = {1},
pages = {79},
pmid = {30871464},
issn = {1471-2148},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Genetic Variation ; Orthoptera/*classification/*genetics ; Phylogeny ; Species Specificity ; },
abstract = {BACKGROUND: DNA barcoding has been developed as a useful tool for species discrimination. Several sequence-based species delimitation methods, such as Barcode Index Number (BIN), REfined Single Linkage (RESL), Automatic Barcode Gap Discovery (ABGD), a Java program uses an explicit, determinate algorithm to define Molecular Operational Taxonomic Unit (jMOTU), Generalized Mixed Yule Coalescent (GMYC), and Bayesian implementation of the Poisson Tree Processes model (bPTP), were used. Our aim was to estimate Chinese katydid biodiversity using standard DNA barcode cytochrome c oxidase subunit I (COI-5P) sequences.<br><br>RESULTS: Detection of a barcoding gap by similarity-based analyses and clustering-base analyses indicated that 131 identified morphological species (morphospecies) were assigned to 196 BINs and were divided into four categories: (i) MATCH (83/131&#x2009;=&#x2009;64.89%), morphospecies were a perfect match between morphospecies and BINs (including 61 concordant BINs and 22 singleton BINs); (ii) MERGE (14/131&#x2009;=&#x2009;10.69%), morphospecies shared its unique BIN with other species; (iii) SPLIT (33/131&#x2009;=&#x2009;25.19%, when 22 singleton species were excluded, it rose to 33/109&#x2009;=&#x2009;30.28%), morphospecies were placed in more than one BIN; (iv) MIXTURE (4/131&#x2009;=&#x2009;5.34%), morphospecies showed a more complex partition involving both a merge and a split. Neighbor-joining (NJ) analyses showed that nearly all BINs and most morphospecies formed monophyletic cluster with little variation. The molecular operational taxonomic units (MOTUs) were defined considering only the more inclusive clades found by at least four of seven species delimitation methods. Our results robustly supported 61 of 109 (55.96%) morphospecies represented by more than one specimen, 159 of 213 (74.65%) concordant BINs, and 3 of 8 (37.5%) discordant BINs.<br><br>CONCLUSIONS: Molecular species delimitation analyses generated a larger number of MOTUs compared with morphospecies. If these MOTU splits are proven to be true, Chinese katydids probably contain a seemingly large proportion of cryptic/undescribed taxa. Future amplification of additional molecular markers, particularly from the nuclear DNA, may be especially useful for specimens that were identified here as problematic taxa.},
}
@article {pmid30867327,
year = {2019},
author = {Lombardi, L and Oliveira-Pacheco, J and Butler, G},
title = {Plasmid-Based CRISPR-Cas9 Gene Editing in Multiple Candida Species.},
journal = {mSphere},
volume = {4},
number = {2},
pages = {},
pmid = {30867327},
issn = {2379-5042},
mesh = {*CRISPR-Cas Systems ; Candida/*genetics ; Candida tropicalis/genetics ; DNA Barcoding, Taxonomic ; DNA End-Joining Repair ; Gene Editing/methods ; Genetic Vectors ; Genome, Fungal ; Mutation ; Plasmids/*genetics ; Streptothricins/pharmacology ; },
abstract = {Many Candida species that cause infection have diploid genomes and do not undergo classical meiosis. The application of clustered regularly interspaced short palindromic repeat-Cas9 (CRISPR-Cas9) gene editing systems has therefore greatly facilitated the generation of gene disruptions and the introduction of specific polymorphisms. However, CRISPR methods are not yet available for all Candida species. We describe here an adaption of a previously developed CRISPR system in Candida parapsilosis that uses an autonomously replicating plasmid. Guide RNAs can be introduced in a single cloning step and are released by cleavage between a tRNA and a ribozyme. The plasmid also contains CAS9 and a selectable nourseothricin SAT1 marker. It can be used for markerless editing in C. parapsilosis, C. orthopsilosis, and C. metapsilosis We also show that CRISPR can easily be used to introduce molecular barcodes and to reintroduce wild-type sequences into edited strains. Heterozygous mutations can be generated, either by careful selection of the distance between the polymorphism and the Cas9 cut site or by providing two different repair templates at the same time. In addition, we have constructed a different autonomously replicating plasmid for CRISPR-Cas9 editing in Candida tropicalis We show that editing can easily be carried out in multiple C. tropicalis isolates. Nonhomologous end joining (NHEJ) repair occurs at a high level in C. metapsilosis and C. tropicalisIMPORTANCECandida species are a major cause of infection worldwide. The species associated with infection vary with geographical location and with patient population. Infection with Candida tropicalis is particularly common in South America and Asia, and Candida parapsilosis infections are more common in the very young. Molecular methods for manipulating the genomes of these species are still lacking. We describe a simple and efficient CRISPR-based gene editing system that can be applied in the C. parapsilosis species group, including the sister species Candida orthopsilosis and Candida metapsilosis We have also constructed a separate system for gene editing in C. tropicalis.},
}
@article {pmid30865849,
year = {2019},
author = {Adeoba, M and Tesfamichael, SG and Yessoufou, K},
title = {Preserving the tree of life of the fish family Cyprinidae in Africa in the face of the ongoing extinction crisis [1].},
journal = {Genome},
volume = {62},
number = {3},
pages = {170-182},
doi = {10.1139/gen-2018-0023},
pmid = {30865849},
issn = {1480-3321},
mesh = {Africa ; Animals ; *Biological Evolution ; Cyprinidae/*classification/*genetics ; DNA/analysis/*genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Endangered Species/*statistics &amp; numerical data ; Extinction, Biological ; *Phylogeny ; Species Specificity ; },
abstract = {Our understanding of how the phylogenetic tree of fishes might be affected by the ongoing extinction risk is poor. This is due to the unavailability of comprehensive DNA data, especially for many African lineages. In addition, the ongoing taxonomic confusion within some lineages, e.g., Cyprinidae, makes it difficult to contribute to the debate on how the fish tree of life might be shaped by extinction. Here, we combine COI sequences and taxonomic information to assemble a fully sampled phylogeny of the African Cyprinidae and investigate whether we might lose more phylogenetic diversity (PD) than expected if currently threatened species go extinct. We found evidence for phylogenetic signal in extinction risk, suggesting that some lineages might be at higher risk than others. Based on simulated extinctions, we found that the loss of all threatened species, which approximates 37% of total PD, would lead to a greater loss of PD than expected, although highly evolutionarily distinct species are not particularly at risk. Pending the reconstruction of an improved multi-gene phylogeny, our results suggest that prioritizing high-EDGE species (evolutionary distinct and globally endangered species) in conservation programmes, particularly in some geographic regions, would contribute significantly to safeguarding the tree of life of the African Cyprinidae.},
}
@article {pmid30865559,
year = {2019},
author = {Hossain, MAM and Uddin, SMK and Chowdhury, ZZ and Sultana, S and Johan, MR and Rohman, A and Erwanto, Y and Ali, ME},
title = {Universal mitochondrial 16s rRNA biomarker for mini-barcode to identify fish species in Malaysian fish products.},
journal = {Food additives &amp; contaminants. Part A, Chemistry, analysis, control, exposure &amp; risk assessment},
volume = {36},
number = {4},
pages = {493-506},
doi = {10.1080/19440049.2019.1580389},
pmid = {30865559},
issn = {1944-0057},
mesh = {Animals ; Biomarkers/analysis ; *DNA Barcoding, Taxonomic ; Fish Products/*analysis ; Fishes/*classification/*genetics ; Malaysia ; Mitochondria/*genetics ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {Mislabelling in fish products is a highly significant emerging issue in world fish trade in terms of health and economic concerns. DNA barcoding is an efficient sequencing-based tool for detecting fish species substitution but due to DNA degradation, it is in many cases difficult to amplify PCR products of the full-length barcode marker (~650 bp), especially in severely processed products. In the present study, a pair of universal primers targeting a 198 bp sequence of the mitochondrial 16s rRNA gene was designed for identification of fish species in the processed fish products commonly consumed in Malaysia. The specificity of the universal primers was tested by both in-silico studies using bioinformatics software and through cross-reaction assessment by practical PCR experiments against the DNA from 38 fish species and 22 other non-target species (animals and plants) and found to be specific for all the tested fish species. To eliminate the possibility of any false-negative detection, eukaryotic endogenous control was used during specificity evaluation. The developed primer set was validated with various heat-treated (boiled, autoclaved and microwaved) fish samples and was found to show high stability under all processing conditions. The newly developed marker successfully identified 92% of the tested commercial fish products with 96-100% sequence similarities. This study reveals a considerable degree of species mislabelling (20.8%); 5 out of 24 fish products were found to be mislabelled. The new marker developed in this work is a reliable tool to identify fish species even in highly processed products and might be useful in detecting fish species substitution thus protecting consumers' health and economic interests.},
}
@article {pmid30864589,
year = {2019},
author = {Li, X and Zhao, C and Liu, Y and Li, Y and Lian, F and Wang, D and Zhang, Y and Wang, J and Song, X and Li, J and Yang, Y and Xu, K},
title = {Fluorescence signal amplification assay for the detection of B. melitensis 16M, based on peptide-mediated magnetic separation technology and a AuNP-mediated bio-barcode assembled by quantum dot technology.},
journal = {The Analyst},
volume = {144},
number = {8},
pages = {2704-2715},
doi = {10.1039/c9an00028c},
pmid = {30864589},
issn = {1364-5528},
mesh = {Animals ; Biotin/chemistry ; Brucella melitensis/immunology/*isolation &amp; purification ; Fluorescence ; Food Microbiology/*methods ; Gold/chemistry ; Hydrogen-Ion Concentration ; Immunoglobulin Isotypes/immunology ; Limit of Detection ; Magnetic Phenomena ; Metal Nanoparticles/*chemistry ; Milk/microbiology ; Nucleic Acid Hybridization ; Oligodeoxyribonucleotides/chemistry/genetics ; Peptides/*chemistry ; Quantum Dots/*chemistry ; Red Meat/microbiology ; Sheep ; Streptavidin/chemistry ; },
abstract = {Members of the Brucella spp. are facultative intracellular bacteria that can cause global brucellosis, a zoonotic disease. Herein, a novel fluorescence signal amplification (FSA) method for the rapid detection of B. melitensis 16M was developed based on peptide-mediated magnetic separation (PMS) technology and Au nanoparticle (AuNP)-mediated bio-barcode assay technology assembled by quantum dots (QDs). The PMS technology was used to specifically capture and isolate B. melitensis 16M from food. The immunomagnetic bead-B. melitensis 16M bioconjugates (IMBs-B. melitensis 16M) were then identified by IgY on the surface of AuNPs and the oligonucleotide chains on the surface of the gold nanoparticles were hybridized with bio-barcodes assembled by quantum dots (QD-probe2). The IMB/B. melitensis 16M/IgY-AuNP-probe1/QD-probe2 bioconjugates were concentrated by magnetic separation. Therefore, as the concentration of B. melitensis 16M in the sample increased, the unbound QD-probe2 in the supernatant reduced, and the B. melitensis 16M in the sample could be indirectly measured by detecting the fluorescence in the supernatant. This FSA method can detect B. melitensis 16M concentration in the range of 10 to 106 cfu ml-1 without pre-enrichment, and the limit of detection (LOD) is as low as 10 cfu ml-1 with high specificity. Furthermore, the proposed method for the detection of B. melitensis 16M has a LOD of 1.07 × 102 cfu ml-1 and a linear range from 102 to 107 cfu ml-1 in milk, and a LOD of 1.72 × 102 cfu ml-1, and a linear range from 102 to 106 cfu ml-1 in lamb leach. In addition, this method takes less than 3 h to perform. Thus, the assay that was developed in this study shows promise for rapid, sensitive, and specific detection of B. melitensis 16M.},
}
@article {pmid30864449,
year = {2019},
author = {Wade, OK and Woehrstein, JB and Nickels, PC and Strauss, S and Stehr, F and Stein, J and Schueder, F and Strauss, MT and Ganji, M and Schnitzbauer, J and Grabmayr, H and Yin, P and Schwille, P and Jungmann, R},
title = {124-Color Super-resolution Imaging by Engineering DNA-PAINT Blinking Kinetics.},
journal = {Nano letters},
volume = {19},
number = {4},
pages = {2641-2646},
pmid = {30864449},
issn = {1530-6992},
support = {R01 EB018659/EB/NIBIB NIH HHS/United States ; U01 MH106011/MH/NIMH NIH HHS/United States ; 1-U01-MH106011/NH/NIH HHS/United States ; R01EB018659/NH/NIH HHS/United States ; },
mesh = {Computer Simulation ; DNA/*chemistry ; Kinetics ; Microscopy, Fluorescence/*methods ; Nucleic Acid Conformation ; Oligonucleotides/chemistry ; Proteins/chemistry/*isolation &amp; purification ; RNA/chemistry/*isolation &amp; purification ; },
abstract = {Optical super-resolution techniques reach unprecedented spatial resolution down to a few nanometers. However, efficient multiplexing strategies for the simultaneous detection of hundreds of molecular species are still elusive. Here, we introduce an entirely new approach to multiplexed super-resolution microscopy by designing the blinking behavior of targets with engineered binding frequency and duration in DNA-PAINT. We assay this kinetic barcoding approach in silico and in vitro using DNA origami structures, show the applicability for multiplexed RNA and protein detection in cells, and finally experimentally demonstrate 124-plex super-resolution imaging within minutes.},
}
@article {pmid30863197,
year = {2019},
author = {Allan, EL and Livermore, L and Price, BW and Shchedrina, O and Smith, VS},
title = {A Novel Automated Mass Digitisation Workflow for Natural History Microscope Slides.},
journal = {Biodiversity data journal},
volume = {7},
number = {},
pages = {e32342},
pmid = {30863197},
issn = {1314-2828},
abstract = {The Natural History Museum, London (NHM) has embarked on an ambitious programme to digitise its collections. One aim of the programme has been to improve the workflows and infrastructure needed to support high-throughput digitisation and create comprehensive digital inventories of large scientific collections. This paper presents the workflow developed to digitise the entire Phthiraptera (parasitic lice) microscope slide collection (70,663 slides). Here we describe a novel process of semi-automated mass digitisation using both temporary and permanent barcode labels applied before and during slide imaging. By using a series of barcodes encoding information associated with each slide (i.e. unique identifier, location in the collection and taxonomic name), we can run a series of automated processes, including file renaming, image processing and bulk import into the NHM's collection management system. We provide data on the comparative efficiency of these processes, illustrating how simple activities, like automated file renaming, reduces image post-processing time, minimises human error and can be applied across multiple collection types.},
}
@article {pmid30862955,
year = {2019},
author = {Napolitani, G and Kurupati, P and Teng, KWW and Gibani, MM and Rei, M and Aulicino, A and Preciado-Llanes, L and Wong, MT and Becht, E and Howson, L and de Haas, P and Salio, M and Blohmke, CJ and Olsen, LR and Pinto, DMS and Scifo, L and Jones, C and Dobinson, H and Campbell, D and Juel, HB and Thomaides-Brears, H and Pickard, D and Bumann, D and Baker, S and Dougan, G and Simmons, A and Gordon, MA and Newell, EW and Pollard, AJ and Cerundolo, V},
title = {Publisher Correction: Clonal analysis of Salmonella-specific effector T cells reveals serovar-specific and cross-reactive T cell responses.},
journal = {Nature immunology},
volume = {20},
number = {4},
pages = {514},
doi = {10.1038/s41590-019-0357-6},
pmid = {30862955},
issn = {1529-2916},
support = {MC_PC_15002/MRC_/Medical Research Council/United Kingdom ; MC_U137884181/MRC_/Medical Research Council/United Kingdom ; G1000800/MRC_/Medical Research Council/United Kingdom ; 11331/CRUK_/Cancer Research UK/United Kingdom ; 17722/CRUK_/Cancer Research UK/United Kingdom ; G0800158/MRC_/Medical Research Council/United Kingdom ; MR/K021222/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_12010/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_00008/1/MRC_/Medical Research Council/United Kingdom ; MR/K01577X/1/MRC_/Medical Research Council/United Kingdom ; G0501975/MRC_/Medical Research Council/United Kingdom ; },
abstract = {In the version of this article initially published, the first affiliation lacked 'MRC'; the correct name of the institution is 'MRC Weatherall Institute of Molecular Medicine'. Two designations (SP110Y and ST110H) were incorrect in the legend to Fig. 6f,h,i. The correct text is as follows: for panel f, "...loaded with either the CdtB(105-125)SP110Y (DRB4*SP110Y) or the CdtB(105-125)ST110H (DRB4*ST110H) peptide variants..."; for panel h, "...decorated by the DRB4*SP110Y tetramer (lower-right quadrant), the DRB4*ST110H (upper-left quadrant)..."; and for panel i, "...stained ex vivo with DRB4*SP110Y, DRB4*ST110H...". In Fig. 8e, the final six residues (LTEAFF) of the sequence in the far right column of the third row of the table were missing; the correct sequence is 'CASSYRRTPPLTEAFF'. In the legend to Fig. 8d, a designation (HLyE) was incorrect; the correct text is as follows: "(HlyE?)." Portions of the Acknowledgements section were incorrect; the correct text is as follows: "This work was supported by the UK Medical Research Council (MRC) (MR/K021222/1) (G.N., M.A.G., A.S., V.C., A.J.P.),...the Oxford Biomedical Research Centre (A.J.P., V.C.),...and core funding from the Singapore Immunology Network (SIgN) (E.W.N.) and the SIgN immunomonitoring platform (E.W.N.)." Finally, a parenthetical element was phrased incorrectly in the final paragraph of the Methods subsection "T cell cloning and live fluorescence barcoding"; the correct phrasing is as follows: "...(which in all cases included HlyE, CdtB, Ty21a, Quailes, NVGH308, and LT2 strains and in volunteers T5 and T6 included PhoN)...". Also, in Figs. 3c and 4a, the right outlines of the plots were not visible; in the legend to Fig. 3, panel letter 'f' was not bold; and in Fig. 8f, 'ND' should be aligned directly beneath DRB4 in the key and 'ND' should be removed from the diagram at right, and the legend should be revised accordingly as follows: "...colors indicate the HLA class II restriction (gray indicates clones for which restriction was not determined (ND)). Clonotypes are grouped on the basis of pathogen selectivity (continuous line), protein specificity (dashed line) and epitope specificity; for ten HlyE-specific clones (pixilated squares), the epitope specificity was not determined...". The errors have been corrected in the HTML and PDF versions of the article.},
}
@article {pmid30862547,
year = {2019},
author = {Onozato, ML and Yapp, C and Richardson, D and Sundaresan, T and Chahal, V and Lee, J and Sullivan, JP and Madden, MW and Shim, HS and Liebers, M and Ho, Q and Maheswaran, S and Haber, DA and Zheng, Z and Clancy, B and Elliott, HL and Lennerz, JK and Iafrate, AJ},
title = {Highly Multiplexed Fluorescence in Situ Hybridization for in Situ Genomics.},
journal = {The Journal of molecular diagnostics : JMD},
volume = {21},
number = {3},
pages = {390-407},
pmid = {30862547},
issn = {1943-7811},
support = {R01 CA129933/CA/NCI NIH HHS/United States ; R21 CA183686/CA/NCI NIH HHS/United States ; S10 RR029237/RR/NCRR NIH HHS/United States ; UL1 TR001102/TR/NCATS NIH HHS/United States ; },
mesh = {Algorithms ; Cell Line, Tumor ; Chromosomes, Artificial, Bacterial/genetics ; Color ; Comparative Genomic Hybridization ; Fluorescent Dyes/chemistry ; *Genomics ; Humans ; In Situ Hybridization, Fluorescence/*methods ; Molecular Probes/chemistry ; Reproducibility of Results ; },
abstract = {The quantification of changes in gene copy number is critical to our understanding of tumor biology and for the clinical management of cancer patients. DNA fluorescence in situ hybridization is the gold standard method to detect copy number alterations, but it is limited by the number of genes one can quantify simultaneously. To increase the throughput of this informative technique, a fluorescent bar-code system for the unique labeling of dozens of genes and an automated image analysis algorithm that enabled their simultaneous hybridization for the quantification of gene copy numbers were devised. We demonstrate the reliability of this multiplex approach on normal human lymphocytes, metaphase spreads of transformed cell lines, and cultured circulating tumor cells. It also opens the door to the development of gene panels for more comprehensive analysis of copy number changes in tissue, including the study of heterogeneity and of high-throughput clinical assays that could provide rapid quantification of gene copy numbers in samples with limited cellularity, such as circulating tumor cells.},
}
@article {pmid30858327,
year = {2019},
author = {Ji, Y and Qi, D and Li, L and Su, H and Li, X and Luo, Y and Sun, B and Zhang, F and Lin, B and Liu, T and Lu, Y},
title = {Multiplexed profiling of single-cell extracellular vesicles secretion.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {13},
pages = {5979-5984},
pmid = {30858327},
issn = {1091-6490},
mesh = {Antigens, Surface/metabolism ; Cell Communication ; Cell Line, Tumor ; Cellular Microenvironment ; Extracellular Vesicles/*metabolism ; Humans ; Microchip Analytical Procedures ; },
abstract = {Extracellular vesicles (EVs) are important intercellular mediators regulating health and diseases. Conventional methods for EV surface marker profiling, which was based on population measurements, masked the cell-to-cell heterogeneity in the quantity and phenotypes of EV secretion. Herein, by using spatially patterned antibody barcodes, we realized multiplexed profiling of single-cell EV secretion from more than 1,000 single cells simultaneously. Applying this platform to profile human oral squamous cell carcinoma (OSCC) cell lines led to a deep understanding of previously undifferentiated single-cell heterogeneity underlying EV secretion. Notably, we observed that the decrement of certain EV phenotypes (e.g., [CD63+]EV) was associated with the invasive feature of both OSCC cell lines and primary OSCC cells. We also realized multiplexed detection of EV secretion and cytokines secretion simultaneously from the same single cells to investigate the multidimensional spectrum of cellular communications, from which we resolved tiered functional subgroups with distinct secretion profiles by visualized clustering and principal component analysis. In particular, we found that different cell subgroups dominated EV secretion and cytokine secretion. The technology introduced here enables a comprehensive evaluation of EV secretion heterogeneity at single-cell level, which may become an indispensable tool to complement current single-cell analysis and EV research.},
}
@article {pmid30858050,
year = {2019},
author = {Lawrence, AL and Webb, CE and Clark, NJ and Halajian, A and Mihalca, AD and Miret, J and D'Amico, G and Brown, G and Kumsa, B and Modrý, D and Šlapeta, J},
title = {Out-of-Africa, human-mediated dispersal of the common cat flea, Ctenocephalides felis: The hitchhiker's guide to world domination.},
journal = {International journal for parasitology},
volume = {49},
number = {5},
pages = {321-336},
doi = {10.1016/j.ijpara.2019.01.001},
pmid = {30858050},
issn = {1879-0135},
mesh = {Africa ; Animals ; Cat Diseases/*parasitology ; Cats ; Ctenocephalides/*classification/genetics/growth &amp; development ; Dog Diseases/*parasitology ; Dogs ; Female ; Flea Infestations/*parasitology/*veterinary ; Genetic Markers ; Humans ; Male ; Phylogeny ; },
abstract = {The cat flea (Ctenocephalides felis) is the most common parasite of domestic cats and dogs worldwide. Due to the morphological ambiguity of C. felis and a lack of - particularly largescale - phylogenetic data, we do not know whether global C. felis populations are morphologically and genetically conserved, or whether human-mediated migration of domestic cats and dogs has resulted in homogenous global populations. To determine the ancestral origin of the species and to understand the level of global pervasion of the cat flea and related taxa, our study aimed to document the distribution and phylogenetic relationships of Ctenocephalides fleas found on cats and dogs worldwide. We investigated the potential drivers behind the establishment of regional cat flea populations using a global collection of fleas from cats and dogs across six continents. We morphologically and molecularly evaluated six out of the 14 known taxa comprising genus Ctenocephalides, including the four original C. felis subspecies (Ctenocephalides felis felis, Ctenocephalides felis strongylus, Ctenocephalides felis orientis and Ctenocephalides felis damarensis), the cosmopolitan species Ctenocephalides canis and the African species Ctenocephalides connatus. We confirm the ubiquity of the cat flea, representing 85% of all fleas collected (4357/5123). Using a multigene approach combining two mitochondrial (cox1 and cox2) and two nuclear (Histone H3 and EF-1α) gene markers, as well as a cox1 survey of 516 fleas across 56 countries, we demonstrate out-of-Africa origins for the genus Ctenocephalides and high levels of genetic diversity within C. felis. We define four bioclimatically limited C. felis clusters (Temperate, Tropical I, Tropical II and African) using maximum entropy modelling. This study defines the global distribution, African origin and phylogenetic relationships of global Ctenocephalides fleas, whilst resolving the taxonomy of the C. felis subspecies and related taxa. We show that humans have inadvertently precipitated the expansion of C. felis throughout the world, promoting diverse population structure and bioclimatic plasticity. By demonstrating the link between the global cat flea communities and their affinity for specific bioclimatic niches, we reveal the drivers behind the establishment and success of the cat flea as a global parasite.},
}
@article {pmid30856358,
year = {2019},
author = {Meng, H and Warden, A and Zhang, L and Zhang, T and Li, Y and Tan, Z and Wang, B and Li, H and Jiang, H and Shen, G and Hong, Y and Ding, X},
title = {A Mass-Ratiometry-Based CD45 Barcoding Method for Mass Cytometry Detection.},
journal = {SLAS technology},
volume = {24},
number = {4},
pages = {408-419},
doi = {10.1177/2472630319834057},
pmid = {30856358},
issn = {2472-6311},
mesh = {*Calibration ; Flow Cytometry/*methods/standards ; Leukocyte Common Antigens/*analysis ; Proteomics/*methods/standards ; Sensitivity and Specificity ; Single-Cell Analysis/*methods/standards ; Staining and Labeling/*methods/standards ; },
abstract = {Mass cytometry (CyTOF) is a critical cell profiling tool in acquiring multiparameter proteome data at the single-cell level. A major challenge in CyTOF analysis is sample-to-sample variance arising from the pipetting process, staining variation, and instrument sensitivity. To reduce such variations, cell barcoding strategies that enable the combination of individual samples prior to antibody staining and data acquisition on CyTOF are often utilized. The most prevalent barcoding strategy is based on a binary scheme that cross-examines the existence or nonexistence of certain mass signals; however, it is limited by low barcoding efficiency and high cost, especially for large sample size. Herein, we present a novel barcoding method for CyTOF application based on mass ratiometry. Different mass tags with specific fixed ratios are used to label CD45 antibody to achieve sample barcoding. The presented method exponentially increases the number of possible barcoded samples with the same amount of mass tags compared with conventional methods. It also reduces the overall time for the labeling process to 40 min and avoids the need for expensive commercial barcoding buffer reagents. Moreover, unlike the conventional barcoding process, this strategy does not pre-permeabilize cells before the barcoding procedure, which offers additional benefits in preserving surface biomarker signals.},
}
@article {pmid30852321,
year = {2019},
author = {de Graaff, DR and Felz, S and Neu, TR and Pronk, M and van Loosdrecht, MCM and Lin, Y},
title = {Sialic acids in the extracellular polymeric substances of seawater-adapted aerobic granular sludge.},
journal = {Water research},
volume = {155},
number = {},
pages = {343-351},
doi = {10.1016/j.watres.2019.02.040},
pmid = {30852321},
issn = {1879-2448},
mesh = {Extracellular Polymeric Substance Matrix ; Seawater ; *Sewage ; *Sialic Acids ; Spectroscopy, Fourier Transform Infrared ; },
abstract = {Sialic acids have been discovered in the extracellular polymeric substances (EPS) of seawater-adapted aerobic granular sludge (AGS). Sialic acids are a group of monosaccharides with a nine-carbon backbone, commonly found in mammalian cells and pathogenic bacteria, and frequently described to protect EPS molecules and cells from attack by proteases or glycosidases. In order to further understand the role of these compounds in AGS, lectin staining, genome analysis of the dominant bacterial species, and shielding tests were done. Fluorescence lectin bar-coding (FLBC) analysis showed an overlap with protein staining, indicating presence of sialoglycoproteins in the EPS matrix. Genome analysis gives a positive indication for putative production of sialic acids by the dominant bacteria Candidatus Accumulibacter. FT-IR analysis shows upon selective removal of sialic acids a decrease in carbohydrates, extension of the protein side chain, and exposure of penultimate sugars. Enzymatic removal of sialic acids results in the removal of galactose residues from the EPS upon subsequent treatment with β-galactosidase, indicating a linkage between galactose and sialic acid at the terminus of glycan chains. This work indicates the importance of sialic acids in the protection of penultimate sugar residues of glycoproteins in EPS, and provides basis for future research in the composition of EPS from biofilms and granular sludge.},
}
@article {pmid30850720,
year = {2019},
author = {Miyake, T and Aihara, N and Maeda, K and Shinzato, C and Koyanagi, R and Kobayashi, H and Yamahira, K},
title = {Bloodmeal host identification with inferences to feeding habits of a fish-fed mosquito, Aedes baisasi.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {4002},
pmid = {30850720},
issn = {2045-2322},
mesh = {Aedes/physiology ; Animals ; Blood/*parasitology ; Culicidae/*physiology ; Feeding Behavior/*physiology ; Female ; Fishes/*parasitology ; Habits ; Host Specificity/physiology ; },
abstract = {The mosquito, Aedes baisasi, which inhabits brackish mangrove swamps, is known to feed on fish. However, its host assemblage has not been investigated at the species level. We amplified and sequenced the cytochrome oxidase subunit I barcoding regions as well as some other regions from blood-fed females to identify host assemblages in the natural populations from four islands in the Ryukyu Archipelago. Hosts were identified from 230 females. We identified 15 host fish species belonging to eight families and four orders. Contrary to expectations from previous observations, mudskippers were detected from only 3% of blood-engorged females. The dominant host was a four-eyed sleeper, Bostrychus sinensis (Butidae, Gobiiformes), in Iriomote-jima Island (61%), while it was a snake eel, Pisodonophis boro (Ophichthidae, Anguilliformes), in Amami-oshima and Okinawa-jima islands (78% and 79%, respectively). Most of the identified hosts were known as air-breathing or amphibious fishes that inhabit mangroves or lagoons. Our results suggest that A. baisasi females locate the bloodmeal hosts within the mangrove forests and sometimes in the adjacent lagoons and land on the surface of available amphibious or other air-breathing fishes exposed in the air to feed on their blood.},
}
@article {pmid30848092,
year = {2020},
author = {van der Valk, T and Vezzi, F and Ormestad, M and Dalén, L and Guschanski, K},
title = {Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies.},
journal = {Molecular ecology resources},
volume = {20},
number = {5},
pages = {1171-1181},
doi = {10.1111/1755-0998.13009},
pmid = {30848092},
issn = {1755-0998},
support = {//Jan L&#xf6;fqvist Endowments of the Royal Physiographic Society of Lund/ ; 2015-676//Svenska Forskningsr&#xe5;det Formas/ ; 2016-00835//Svenska Forskningsr&#xe5;det Formas/ ; //Science for Life Laboratory/ ; //Knut and Alice Wallenberg Foundation/ ; //National Genomics Infrastructure funded by the Swedish Research Council/ ; //Uppsala Multidisciplinary Center for Advanced Computational Science/ ; },
mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic ; *DNA, Ancient ; Gorilla gorilla/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Sequence Analysis, DNA/methods ; },
abstract = {The high-throughput capacities of the Illumina sequencing platforms and the possibility to label samples individually have encouraged wide use of sample multiplexing. However, this practice results in read misassignment (usually <1%) across samples sequenced on the same lane. Alarmingly high rates of read misassignment of up to 10% were reported for lllumina sequencing machines with exclusion amplification chemistry. This may make use of these platforms prohibitive, particularly in studies that rely on low-quantity and low-quality samples, such as historical and archaeological specimens. Here, we use barcodes, short sequences that are ligated to both ends of the DNA insert, to directly quantify the rate of index hopping in 100-year old museum-preserved gorilla (Gorilla beringei) samples. Correcting for multiple sources of noise, we identify on average 0.470% of reads containing a hopped index. We show that sample-specific quantity of misassigned reads depends on the number of reads that any given sample contributes to the total sequencing pool, so that samples with few sequenced reads receive the greatest proportion of misassigned reads. This particularly affects ancient DNA samples, as these frequently differ in their DNA quantity and endogenous content. Through simulations we show that even low rates of index hopping, as reported here, can lead to biases in ancient DNA studies when multiplexing samples with vastly different quantities of endogenous material.},
}
@article {pmid30847083,
year = {2019},
author = {Ren, FM and Wang, YW and Xu, ZC and Li, Y and Xin, TY and Zhou, JG and Qi, YD and Wei, XP and Yao, H and Song, JY},
title = {DNA barcoding of Corydalis, the most taxonomically complicated genus of Papaveraceae.},
journal = {Ecology and evolution},
volume = {9},
number = {4},
pages = {1934-1945},
pmid = {30847083},
issn = {2045-7758},
abstract = {The genus Corydalis is recognized as one of the most taxonomically challenging plant taxa. It is mainly distributed in the Himalaya-Hengduan Mountains, a global biodiversity hotspot. To date, no effective solution for species discrimination and taxonomic assignment in Corydalis has been developed. In this study, five nuclear and chloroplast DNA regions, ITS, ITS2, matK, rbcL, and psbA-trnH, were preliminarily assessed based on their ability to discriminate Corydalis to eliminate inefficient regions, and the three regions showing good performance (ITS, ITS2 and matK) were then evaluated in 131 samples representing 28 species of 11 sections of four subgenera in Corydalis using three analytical methods (NJ, ML, MP tree; K2P-distance and BLAST). The results showed that the various approaches exhibit different species identification power and that BLAST shows the best performance among the tested approaches. A comparison of different barcodes indicated that among the single barcodes, ITS (65.2%) exhibited the highest identification success rate and that the combination of ITS + matK (69.6%) provided the highest species resolution among all single barcodes and their combinations. Three Pharmacopoeia-recorded medicinal plants and their materia medica were identified successfully based on the ITS and ITS2 regions. In the phylogenetic analysis, the sections Thalictrifoliae, Sophorocapnos, Racemosae, Aulacostigma, and Corydalis formed well-supported separate lineages. We thus hypothesize that the five sections should be classified as an independent subgenus and that the genus should be divided into three subgenera. In this study, DNA barcoding provided relatively high species discrimination power, indicating that it can be used for species discrimination in this taxonomically complicated genus and as a potential tool for the authentication of materia medica belonging to Corydalis.},
}
@article {pmid30847077,
year = {2019},
author = {Amandita, FY and Rembold, K and Vornam, B and Rahayu, S and Siregar, IZ and Kreft, H and Finkeldey, R},
title = {DNA barcoding of flowering plants in Sumatra, Indonesia.},
journal = {Ecology and evolution},
volume = {9},
number = {4},
pages = {1858-1868},
pmid = {30847077},
issn = {2045-7758},
abstract = {The rapid conversion of Southeast Asian lowland rainforests into monocultures calls for the development of rapid methods for species identification to support ecological research and sustainable land-use management. Here, we investigated the utilization of DNA barcodes for identifying flowering plants from Sumatra, Indonesia. A total of 1,207 matK barcodes (441 species) and 2,376 rbcL barcodes (750 species) were successfully generated. The barcode effectiveness is assessed using four approaches: (a) comparison between morphological and molecular identification results, (b) best-close match analysis with TaxonDNA, (c) barcoding gap analysis, and (d) formation of monophyletic groups. Results show that rbcL has a much higher level of sequence recoverability than matK (95% and 66%). The comparison between morphological and molecular identifications revealed that matK and rbcL worked best assigning a plant specimen to the genus level. Estimates of identification success using best-close match analysis showed that >70% of the investigated species were correctly identified when using single barcode. The use of two-loci barcodes was able to increase the identification success up to 80%. The barcoding gap analysis revealed that neither matK nor rbcL succeeded to create a clear gap between the intraspecific and interspecific divergences. However, these two barcodes were able to discriminate at least 70% of the species from each other. Fifteen genera and twenty-one species were found to be nonmonophyletic with both markers. The two-loci barcodes were sufficient to reconstruct evolutionary relationships among the plant taxa in the study area that are congruent with the broadly accepted APG III phylogeny.},
}
@article {pmid30847071,
year = {2019},
author = {Zhu, C and Gravel, D and He, F},
title = {Seeing is believing? Comparing plant-herbivore networks constructed by field co-occurrence and DNA barcoding methods for gaining insights into network structures.},
journal = {Ecology and evolution},
volume = {9},
number = {4},
pages = {1764-1776},
pmid = {30847071},
issn = {2045-7758},
abstract = {Plant-herbivore interaction networks provide information about community organization. Two methods are currently used to document pairwise interactions among plants and insect herbivores. One is the traditional method that collects plant-herbivore interaction data by field observation of insect occurrence on host plants. The other is the increasing application of newly developed molecular techniques based on DNA barcodes to the analysis of gut contents. The second method is more appealing because it documents realized interactions. To construct complete interaction networks, each technique of network construction is urgent to be assessed. We addressed this question by comparing the effectiveness and reliability of the two methods in constructing plant-Lepidoptera larval network in a 50 ha subtropical forest in China. Our results showed that the accuracy of diet identification by observation method increased with the number of observed insect occurrences on food plants. In contrast, the molecular method using three plant DNA markers were able to identify food residues for 35.6% larvae and correctly resolved 77.3% plant (diet) species. Network analysis showed molecular networks had threefold more unique host plant species but fewer links than the traditional networks had. The molecular method detected plants that were not sampled by the traditional method, for example, bamboos, bryophytes and lianas in the diets of insect herbivores. The two networks also possessed significantly different structural properties. Our study indicates the traditional observation of co-occurrence is inadequate, while molecular method can provide higher species resolution of ecological interactions.},
}
@article {pmid30837972,
year = {2019},
author = {Pitsch, G and Bruni, EP and Forster, D and Qu, Z and Sonntag, B and Stoeck, T and Posch, T},
title = {Seasonality of Planktonic Freshwater Ciliates: Are Analyses Based on V9 Regions of the 18S rRNA Gene Correlated With Morphospecies Counts?.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {248},
pmid = {30837972},
issn = {1664-302X},
support = {I 2238/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Ciliates represent central nodes in freshwater planktonic food webs, and many species show pronounced seasonality, with short-lived maxima of a few dominant taxa while many being rare or ephemeral. These observations are primarily based on morphospecies counting methods, which, however, have limitations concerning the amount and volume of samples that can be processed. For high sampling frequencies at large scales, high throughput sequencing (HTS) of freshwater ciliates seems to be a promising tool. However, several studies reported large discrepancy between species abundance determinations by molecular compared to morphological means. Therefore, we compared ciliate DNA metabarcodes (V9 regions of the 18S rRNA gene) with morphospecies counts for a 3-year study (Lake Zurich, Switzerland; biweekly sampling, n = 74). In addition, we isolated, cultivated and sequenced the 18S rRNA gene of twelve selected ciliate species that served as seeds for HTS analyses. This workflow allowed for a detailed comparison of V9 data with microscopic analyses by quantitative protargol staining (QPS). The dynamics of V9 read abundances over the seasonal cycle corroborated well with morphospecies population patterns. Annual successions of rare and ephemeral species were more adequately characterized by V9 reads than by QPS. However, numbers of species specific sequence reads only partly reflected rank orders seen by counts. In contrast, biomass-based assemblage compositions showed higher similarity to V9 read numbers, probably indicating a relation between cell sizes and numbers / sizes of macronuclei (or 18S rRNA operons). Full-length 18S rRNA sequences of ciliates assigned to certain morphospecies are urgently needed for barcoding approaches as planktonic taxa are still poorly represented in public databases and the interpretation of HTS data depends on profound reference sequences. Through linking operational taxonomic units (OTUs) with known morphospecies, we can use the deep knowledge about the autecology of these species.},
}
@article {pmid30837525,
year = {2019},
author = {Filges, S and Yamada, E and Ståhlberg, A and Godfrey, TE},
title = {Impact of Polymerase Fidelity on Background Error Rates in Next-Generation Sequencing with Unique Molecular Identifiers/Barcodes.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {3503},
pmid = {30837525},
issn = {2045-2322},
support = {R01 CA208599/CA/NCI NIH HHS/United States ; },
mesh = {Circulating Tumor DNA/genetics ; DNA Barcoding, Taxonomic ; DNA-Directed DNA Polymerase/*metabolism ; Gene Frequency ; Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Liquid Biopsy ; Mutation ; Polymerase Chain Reaction ; Reproducibility of Results ; },
abstract = {Liquid biopsy and detection of tumor-associated mutations in cell-free circulating DNA often requires the ability to identify single nucleotide variants at allele frequencies below 0.1%. Standard sequencing protocols cannot achieve this level of sensitivity due to background noise from DNA damage and polymerase induced errors. Addition of unique molecular identifiers allows identification and removal of errors responsible for this background noise. Theoretically, high fidelity enzymes will also reduce error rates in barcoded NGS but this has not been thoroughly explored. We evaluated the impact of polymerase fidelity on the magnitude of error reduction at different steps of barcoded NGS library construction. We find that barcoding itself displays largest impact on error reduction, even with low fidelity polymerases. Use of high fidelity polymerases in the barcoding step of library construction further suppresses error in barcoded NGS, and allows detection of variant alleles below 0.1% allele frequency. However, the improvement in error correction is modest and is not directly proportional to polymerase fidelity. Depending on the specific application, other polymerase characteristics such as multiplexing capacity, PCR efficiency, buffer requirements and ability to amplify targets with high GC content may outweigh the relatively small additional decrease in error afforded by ultra-high fidelity polymerases.},
}
@article {pmid30835561,
year = {2019},
author = {Neiman, M and Hellström, C and Just, D and Mattsson, C and Fagerberg, L and Schuppe-Koistinen, I and Gummesson, A and Bergström, G and Kallioniemi, O and Achour, A and Sallinen, R and Uhlén, M and Nilsson, P},
title = {Individual and stable autoantibody repertoires in healthy individuals.},
journal = {Autoimmunity},
volume = {52},
number = {1},
pages = {1-11},
doi = {10.1080/08916934.2019.1581774},
pmid = {30835561},
issn = {1607-842X},
mesh = {Aged ; *Antibody Specificity ; *Autoantibodies/blood/immunology ; *Autoantigens/blood/immunology ; Female ; Humans ; *Immunoglobulin G/blood/immunology ; Male ; Middle Aged ; },
abstract = {In the era towards precision medicine, we here present the individual specific autoantibody signatures of 193 healthy individuals. The self-reactive IgG signatures are stable over time in a way that each individual profile is recognized in longitudinal sampling. The IgG autoantibody reactivity towards an antigen array comprising 335 protein fragments, representing 204 human proteins with potential relevance to autoimmune disorders, was measured in longitudinal plasma samples from 193 healthy individuals. This analysis resulted in unique autoantibody barcodes for each individual that were maintained over one year's time. The reactivity profiles, or signatures, are person specific in regards to the number of reactivities and antigen specificity. Two independent data sets were consistent in that each healthy individual displayed reactivity towards 0-16 antigens, with a median of six. Subsequently, four selected individuals were profiled on in-house produced high-density protein arrays containing 23,000 protein fragments representing 14,000 unique protein coding genes. Based on a unique, broad and deep longitudinal profiling of autoantibody reactivities, our results demonstrate a unique autoreactive profile in each analyzed healthy individual. The need and interest for broad-ranged and high-resolution molecular profiling of healthy individuals is rising. We have here generated and assessed an initial perspective on the global distribution of the self-reactive IgG repertoire in healthy individuals, by investigating 193 well-characterized healthy individuals. Highlights A unique longitudinal profiling of autoantibody repertoires in healthy individuals Autoantibody profiles are highly individual and stable over time All individuals display IgG binding to human protein fragments The specificity of disease associated autoantigens needs to be thoroughly characterized The identification of a small set of highly reactive autoantigens Importance of stringent antigen and sample specific cut-offs for defining reactivity.},
}
@article {pmid30832434,
year = {2019},
author = {Xie, Q and Zhang, H and Yan, F and Yan, C and Wei, S and Lai, J and Wang, Y and Zhang, B},
title = {Morphology and Molecular Identification of Twelve Commercial Varieties of Kiwifruit.},
journal = {Molecules (Basel, Switzerland)},
volume = {24},
number = {5},
pages = {},
pmid = {30832434},
issn = {1420-3049},
support = {31801870//National Natural Science Foundation of China/ ; 2016M590951//China Postdoctoral Science Foundation/ ; 2016JQ8018//Shaanxi Natural Science Foundation/ ; },
mesh = {Actinidia/anatomy &amp; histology/*genetics ; Chloroplasts/genetics ; DNA Barcoding, Taxonomic ; Food Safety ; Fruit/anatomy &amp; histology/*genetics ; Humans ; Plant Proteins/*genetics ; },
abstract = {The quality and safety of food are important guarantees for the health and legal rights of consumers. As an important special fruitcrop, there are frequently shoddy practices in the kiwifruit (Actinidia chinensis) market, which harms the interests of consumers. However, there is lack of rapid and accurate identification methods for commercial kiwifruit varieties. Here, twelve common commercial varieties of kiwifruit were morphologically discriminated. DNA barcodes of chloroplast regions psbA-trnH, rbcL, matK, rpoB, rpoC1, ycf1b, trnL and rpl32_trnL(UAG), the nuclear region At103 and intergenic region ITS2 were amplified. Divergences and phylogenetic trees were used to analyze the phylogenetic relationship of these twelve commercial kiwifruit varieties. The results showed that matK, ITS2 and rpl32_trnL(UAG) can be utilized as molecular markers to identify CuiYu, JinYan, HuangJinGuo, ChuanHuangJin, HuaYou, YaTe, XuXiang and HongYang. This provides experimental and practical basis to scientifically resolve kiwifruit-related judicial disputes and legal trials.},
}
@article {pmid30832272,
year = {2019},
author = {Chatterjee, S and Yadav, S},
title = {The Origin of Prebiotic Information System in the Peptide/RNA World: A Simulation Model of the Evolution of Translation and the Genetic Code.},
journal = {Life (Basel, Switzerland)},
volume = {9},
number = {1},
pages = {},
pmid = {30832272},
issn = {2075-1729},
abstract = {Information is the currency of life, but the origin of prebiotic information remains a mystery. We propose transitional pathways from the cosmic building blocks of life to the complex prebiotic organic chemistry that led to the origin of information systems. The prebiotic information system, specifically the genetic code, is segregated, linear, and digital, and it appeared before the emergence of DNA. In the peptide/RNA world, lipid membranes randomly encapsulated amino acids, RNA, and peptide molecules, which are drawn from the prebiotic soup, to initiate a molecular symbiosis inside the protocells. This endosymbiosis led to the hierarchical emergence of several requisite components of the translation machine: transfer RNAs (tRNAs), aminoacyl-tRNA synthetase (aaRS), messenger RNAs (mRNAs), ribosomes, and various enzymes. When assembled in the right order, the translation machine created proteins, a process that transferred information from mRNAs to assemble amino acids into polypeptide chains. This was the beginning of the prebiotic information age. The origin of the genetic code is enigmatic; herein, we propose an evolutionary explanation: the demand for a wide range of protein enzymes over peptides in the prebiotic reactions was the main selective pressure for the origin of information-directed protein synthesis. The molecular basis of the genetic code manifests itself in the interaction of aaRS and their cognate tRNAs. In the beginning, aminoacylated ribozymes used amino acids as a cofactor with the help of bridge peptides as a process for selection between amino acids and their cognate codons/anticodons. This process selects amino acids and RNA species for the next steps. The ribozymes would give rise to pre-tRNA and the bridge peptides to pre-aaRS. Later, variants would appear and evolution would produce different but specific aaRS-tRNA-amino acid combinations. Pre-tRNA designed and built pre-mRNA for the storage of information regarding its cognate amino acid. Each pre-mRNA strand became the storage device for the genetic information that encoded the amino acid sequences in triplet nucleotides. As information appeared in the digital languages of the codon within pre-mRNA and mRNA, and the genetic code for protein synthesis evolved, the prebiotic chemistry then became more organized and directional with the emergence of the translation and genetic code. The genetic code developed in three stages that are coincident with the refinement of the translation machines: the GNC code that was developed by the pre-tRNA/pre-aaRS /pre-mRNA machine, SNS code by the tRNA/aaRS/mRNA machine, and finally the universal genetic code by the tRNA/aaRS/mRNA/ribosome machine. We suggest the coevolution of translation machines and the genetic code. The emergence of the translation machines was the beginning of the Darwinian evolution, an interplay between information and its supporting structure. Our hypothesis provides the logical and incremental steps for the origin of the programmed protein synthesis. In order to better understand the prebiotic information system, we converted letter codons into numerical codons in the Universal Genetic Code Table. We have developed a software, called CATI (Codon-Amino Acid-Translator-Imitator), to translate randomly chosen numerical codons into corresponding amino acids and vice versa. This conversion has granted us insight into how the genetic code might have evolved in the peptide/RNA world. There is great potential in the application of numerical codons to bioinformatics, such as barcoding, DNA mining, or DNA fingerprinting. We constructed the likely biochemical pathways for the origin of translation and the genetic code using the Model-View-Controller (MVC) software framework, and the translation machinery step-by-step. While using AnyLogic software, we were able to simulate and visualize the entire evolution of the translation machines, amino acids, and the genetic code.},
}
@article {pmid30831270,
year = {2019},
author = {Belaiba, E and Marrone, F and Vecchioni, L and Bahri-Sfar, L and Arculeo, M},
title = {An exhaustive phylogeny of the combtooth blenny genus Salaria (Pisces, Blenniidae) shows introgressive hybridization and lack of reciprocal mtDNA monophyly between the marine species Salaria basilisca and Salaria pavo.},
journal = {Molecular phylogenetics and evolution},
volume = {135},
number = {},
pages = {210-221},
doi = {10.1016/j.ympev.2019.02.026},
pmid = {30831270},
issn = {1095-9513},
mesh = {Animals ; Aquatic Organisms/*genetics ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Geography ; Haplotypes/genetics ; *Hybridization, Genetic ; Mitochondria/genetics ; Perciformes/*genetics ; *Phylogeny ; Species Specificity ; },
abstract = {A comprehensive phylogeny of the genus Salaria based on mitochondrial and nuclear markers grouped the extant species of the genus in well-characterised marine and freshwater clades, thus rejecting the hypothesis of a polytypic origin of the freshwater Salaria populations and supporting the occurrence of a single invasion event of the inland waters by the genus. Based on both mitochondrial and nuclear DNA datasets, the Salaria species of the freshwater clade proved to be vicariant taxa originating from a common ancestor which could possibly spread throughout the circum-Mediterranean inland waters during the late Miocene Messinian salinity crisis, then experiencing a process of allopatric differentiation after the re-flooding of the Mediterranean basin. Within the marine clade, although the nuDNA datasets showed the existence of well-supported subclades in accordance to the morphological identification of the studied specimens, one of the two subclades obtained in the phylogenetic tree based on the mtDNA dataset included both S. basilisca and S. pavo specimens, thus failing to find the two species as reciprocally monophyletic. Such a mito-nuclear discordance is here ascribed to multiple mtDNA unidirectional introgression events from S. basilisca to S. pavo, and the molecular diversity pattern of the marine Salaria species is here ascribed to a Pleistocene speciation event nowadays partly concealed by the occurrence of introgressive hybridization phenomena between the two taxa. Our results urge for prudence when implementing DNA barcoding approaches since, in the presence of mito-nuclear discordance phenomena, single-marker mtDNA-only analyses might lead to significant misidentifications.},
}
@article {pmid30830463,
year = {2019},
author = {Quirós-Guerrero, L and Albertazzi, F and Araya-Valverde, E and Romero, RM and Villalobos, H and Poveda, L and Chavarría, M and Tamayo-Castillo, G},
title = {Phenolic variation among Chamaecrista nictitans subspecies and varieties revealed through UPLC-ESI(-)-MS/MS chemical fingerprinting.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {15},
number = {2},
pages = {14},
pmid = {30830463},
issn = {1573-3890},
mesh = {Chamaecrista/*chemistry/*metabolism ; Chromatography, High Pressure Liquid/methods ; Chromatography, Liquid/methods ; Cluster Analysis ; Discriminant Analysis ; Metabolomics/*methods ; Multivariate Analysis ; Phenols/chemistry ; Principal Component Analysis/methods ; Spectrometry, Mass, Electrospray Ionization/methods ; Tandem Mass Spectrometry/methods ; },
abstract = {INTRODUCTION: Comparative analysis of metabolic features of plants has a high potential for determination of quality control of active ingredients, ecological or chemotaxonomic purposes. Specifically, the development of efficient and rapid analytical tools that allow the differentiation among species, subspecies and varieties of plants is a relevant issue. Here we describe a multivariate model based on LC-MS/MS fingerprinting capable of discriminating between subspecies and varieties of the medicinal plant Chamaecrista nictitans, a rare distributed species in Costa Rica.<br><br>METHODS: Determination of the chemical fingerprint was carried out on a LC-MS (ESI-QTOF) in negative ionization mode, main detected and putatively identified compounds included proanthocyanidin oligomers, several flavonoid C- and O-glycosides, and flavonoid acetates. Principal component analysis (PCA), partial least square-discriminant analysis (PLS-DA) and cluster analysis of chemical profiles were performed.<br><br>RESULTS: Our method showed a clear discrimination between the subspecies and varieties of Chamaecrista nictitans, separating the samples into four fair differentiated groups: M1&#x2009;=&#x2009;C. nictitans ssp. patellaria; M2&#x2009;=&#x2009;C. nictitans ssp. disadena; M3&#x2009;=&#x2009;C. nictitans ssp. nictitans var. jaliscensis and M4&#x2009;=&#x2009;C. nictitans ssp. disadena var. pilosa. LC-MS/MS fingerprint data was validated using both morphological characters and DNA barcoding with ITS2 region. The comparison of the morphological characters against the chemical profiles and DNA barcoding shows a 63% coincidence, evidencing the morphological similarity in C. nictitans. On the other hand, genetic data and chemical profiles grouped all samples in a similar pattern, validating the functionality of our metabolomic approach.<br><br>CONCLUSION: The metabolomic method described in this study allows a reliably differentiation between subspecies and varieties of C. nictitans using a straightforward protocol that lacks extensive purification steps.},
}
@article {pmid30828983,
year = {2019},
author = {Wang, Y and Shang, L and Bian, F and Zhang, X and Wang, S and Zhou, M and Zhao, Y},
title = {Hollow Colloid Assembled Photonic Crystal Clusters as Suspension Barcodes for Multiplex Bioassays.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {15},
number = {13},
pages = {e1900056},
doi = {10.1002/smll.201900056},
pmid = {30828983},
issn = {1613-6829},
mesh = {Biological Assay/*methods ; Colloids/*chemistry ; Crystallization ; MicroRNAs/genetics ; Microfluidics ; *Photons ; Polystyrenes/chemistry ; Silicon Dioxide/chemistry ; },
abstract = {Barcode particles have a demonstrated value for multiplexed high-throughput bioassays. Here, a novel photonic crystal (PhC) barcode is presented that consists of hollow colloidal nanospheres assembled through microfluidic droplet templates. Due to their gas-filled core, the resultant barcode particles not only show increased refractive index contrast, but also remain in suspension by adjusting the overall density of the PhC to match that of a detection solution. In addition, magnetic nanoparticles can be integrated to give the barcodes a magnetically controllable motion ability. The encoding ability of the barcodes is demonstrated in microRNA detection with high specificity and sensitivity, and the excellent features of the barcodes make them potentially very useful for biomedical applications.},
}
@article {pmid30828253,
year = {2019},
author = {Morín, JG and Venera-Pontón, DE and Driskell, AC and Sánchez, JA and Lasker, HR and Collin, R},
title = {Reference DNA barcodes and other mitochondrial markers for identifying Caribbean Octocorals.},
journal = {Biodiversity data journal},
volume = {},
number = {7},
pages = {e30970},
pmid = {30828253},
issn = {1314-2828},
abstract = {DNA barcoding is a useful tool for documenting the diversity of metazoans. The most commonly used barcode markers, 16S and COI, are not considered suitable for species identification within some "basal" phyla of metazoans. Nevertheless metabarcoding studies of bulk mixed samples commonly use these markers and may obtain sequences for "basal" phyla. We sequenced mitochondrial DNA fragments of cytochrome oxidase c subunit I (COI), 16S ribosomal RNA (16S), NADH dehydrogenase subunits 2 (16S-ND2), 6 (ND6-ND3) and 4L (ND4L-MSH) for 27 species of Caribbean octocorals to create a reference barcode dataset and to compare the utility of COI and 16S to other markers more typically used for octocorals. The most common genera (Erythropodium, Ellisella, Briareum, Plexaurella, Muriceopsis and Pterogorgia) were effectively distinguished by small differences (5 or more substitutions or indels) in COI and 16S sequences. Gorgonia and Antillogorgia were effectively distinguished from each other by unique haplotypes, but the small genetic differences make distance approaches ineffective for these taxa. Plexaura, Pseudoplexaura and Eunicea were indistinguishable from each other but were generally effectively distinguished from other genera, further supporting the idea that these genera have undergone a rapid endemic radiation in the Caribbean.},
}
@article {pmid30828064,
year = {2019},
author = {Sato, Y and Matoba, R and Kato, K},
title = {Recent Advances in Liquid Biopsy in Precision Oncology Research.},
journal = {Biological &amp; pharmaceutical bulletin},
volume = {42},
number = {3},
pages = {337-342},
doi = {10.1248/bpb.b18-00804},
pmid = {30828064},
issn = {1347-5215},
mesh = {Animals ; Circulating Tumor DNA/*blood ; Gene Expression Regulation, Neoplastic/*physiology ; Humans ; Liquid Biopsy/methods/trends ; Neoplasms/blood/*diagnosis/*pathology ; },
abstract = {Liquid biopsy is a minimally invasive test for cancer genetic status based on circulating tumor DNA (ctDNA), circulating tumor cells, or other tumor-derived materials in blood plasma. Although the minimal invasiveness and time resolution are attractive features of liquid biopsy, the limited amount of ctDNA in plasma poses problems. Recent developments in digital PCR and next-generation sequencing (NGS)-based technology have improved the accuracy of liquid biopsy. In particular, molecular barcoding technology in NGS-based methods, i.e., tagging of molecular barcodes to cell-free DNA before amplification, reduces technical errors by validating the consensus of sequences originating from a single molecule, leading to marked improvement of the accuracy and detection limit. However, substitutions caused by DNA damage and somatic mutations originating from normal cells are still obstacles to the sensitive detection of mutations on ctDNA. Since there have been only a few clinical applications, a deeper understanding of ctDNA biology and more advanced analytical technology are needed for the practical application of liquid biopsy.},
}
@article {pmid30827679,
year = {2019},
author = {Ludwig, LS and Lareau, CA and Ulirsch, JC and Christian, E and Muus, C and Li, LH and Pelka, K and Ge, W and Oren, Y and Brack, A and Law, T and Rodman, C and Chen, JH and Boland, GM and Hacohen, N and Rozenblatt-Rosen, O and Aryee, MJ and Buenrostro, JD and Regev, A and Sankaran, VG},
title = {Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics.},
journal = {Cell},
volume = {176},
number = {6},
pages = {1325-1339.e22},
pmid = {30827679},
issn = {1097-4172},
support = {T32 GM007226/GM/NIGMS NIH HHS/United States ; F31 CA232670/CA/NCI NIH HHS/United States ; R33 HL120791/HL/NHLBI NIH HHS/United States ; R33 CA202820/CA/NCI NIH HHS/United States ; K99 HG012579/HG/NHGRI NIH HHS/United States ; U24 AI118672/AI/NIAID NIH HHS/United States ; T32 CA207021/CA/NCI NIH HHS/United States ; R01 CA208756/CA/NCI NIH HHS/United States ; R01 DK103794/DK/NIDDK NIH HHS/United States ; RM1 HG006193/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Base Sequence ; Cell Lineage ; Chromatin ; Colorectal Neoplasms/genetics/pathology ; DNA, Mitochondrial/*genetics ; Genomics/methods ; HEK293 Cells ; Hematopoietic Stem Cells/physiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Mitochondria/*genetics ; Mutation ; Single-Cell Analysis ; Transposases ; },
abstract = {Lineage tracing provides key insights into the fate of individual cells in complex organisms. Although effective genetic labeling approaches are available in model systems, in humans, most approaches require detection of nuclear somatic mutations, which have high error rates, limited scale, and do not capture cell state information. Here, we show that somatic mutations in mtDNA can be tracked by single-cell RNA or assay for transposase accessible chromatin (ATAC) sequencing. We leverage somatic mtDNA mutations as natural genetic barcodes and demonstrate their utility as highly accurate clonal markers to infer cellular relationships. We track native human cells both in vitro and in vivo and relate clonal dynamics to gene expression and chromatin accessibility. Our approach should allow clonal tracking at a 1,000-fold greater scale than with nuclear genome sequencing, with simultaneous information on cell state, opening the way to chart cellular dynamics in human health and disease.},
}
@article {pmid30825008,
year = {2019},
author = {He, T and Jiao, L and Wiedenhoeft, AC and Yin, Y},
title = {Machine learning approaches outperform distance- and tree-based methods for DNA barcoding of Pterocarpus wood.},
journal = {Planta},
volume = {249},
number = {5},
pages = {1617-1625},
pmid = {30825008},
issn = {1432-2048},
support = {31600451//Young Scientists Fund/ ; W02020331//National High-level Talent for Special Support Program of China/ ; 2017-3109//China Scholarship Council/ ; },
mesh = {DNA Barcoding, Taxonomic/*methods ; *Machine Learning ; Pterocarpus/*genetics ; Sequence Analysis, DNA ; Wood/*genetics ; },
abstract = {Machine-learning approaches (MLAs) for DNA barcoding outperform distance- and tree-based methods on identification accuracy and cost-effectiveness to arrive at species-level identification of wood. DNA barcoding is a promising tool to combat illegal logging and associated trade, and the development of reliable and efficient analytical methods is essential for its extensive application in the trade of wood and in the forensics of natural materials more broadly. In this study, 120 DNA sequences of four barcodes (ITS2, matK, ndhF-rpl32, and rbcL) generated in our previous study and 85 downloaded from National Center for Biotechnology Information (NCBI) were collected to establish a reference data set for six commercial Pterocarpus woods. MLAs (BLOG, BP-neural network, SMO and J48) were compared with distance- (TaxonDNA) and tree-based (NJ tree) methods based on identification accuracy and cost-effectiveness across these six species, and also were applied to discriminate the CITES-listed species Pterocarpus santalinus from its anatomically similar species P. tinctorius for forensic identification. MLAs provided higher identification accuracy (30.8-100%) than distance- (15.1-97.4%) and tree-based methods (11.1-87.5%), with SMO performing the best among the machine learning classifiers. The two-locus combination ITS2 + matK when using SMO classifier exhibited the highest resolution (100%) with the fewest barcodes for discriminating the six Pterocarpus species. The CITES-listed species P. santalinus was discriminated successfully from P. tinctorius using MLAs with a single barcode, ndhF-rpl32. This study shows that MLAs provided higher identification accuracy and cost-effectiveness for forensic application over other analytical methods in DNA barcoding of Pterocarpus wood.},
}
@article {pmid30824940,
year = {2019},
author = {Krehenwinkel, H and Pomerantz, A and Henderson, JB and Kennedy, SR and Lim, JY and Swamy, V and Shoobridge, JD and Graham, N and Patel, NH and Gillespie, RG and Prost, S},
title = {Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale.},
journal = {GigaScience},
volume = {8},
number = {5},
pages = {},
pmid = {30824940},
issn = {2047-217X},
mesh = {Animals ; *Biodiversity ; Classification ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal/*genetics ; Ecosystem ; High-Throughput Nucleotide Sequencing ; Nanopore Sequencing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: In light of the current biodiversity crisis, DNA barcoding is developing into an essential tool to quantify state shifts in global ecosystems. Current barcoding protocols often rely on short amplicon sequences, which yield accurate identification of biological entities in a community but provide limited phylogenetic resolution across broad taxonomic scales. However, the phylogenetic structure of communities is an essential component of biodiversity. Consequently, a barcoding approach is required that unites robust taxonomic assignment power and high phylogenetic utility. A possible solution is offered by sequencing long ribosomal DNA (rDNA) amplicons on the MinION platform (Oxford Nanopore Technologies).<br><br>FINDINGS: Using a dataset of various animal and plant species, with a focus on arthropods, we assemble a pipeline for long rDNA barcode analysis and introduce a new software (MiniBar) to demultiplex dual indexed Nanopore reads. We find excellent phylogenetic and taxonomic resolution offered by long rDNA sequences across broad taxonomic scales. We highlight the simplicity of our approach by field barcoding with a miniaturized, mobile laboratory in a remote rainforest. We also test the utility of long rDNA amplicons for analysis of community diversity through metabarcoding and find that they recover highly skewed diversity estimates.<br><br>CONCLUSIONS: Sequencing dual indexed, long rDNA amplicons on the MinION platform is a straightforward, cost-effective, portable, and universal approach for eukaryote DNA barcoding. Although bulk community analyses using long-amplicon approaches may introduce biases, the long rDNA amplicons approach signifies a powerful tool for enabling the accurate recovery of taxonomic and phylogenetic diversity across biological communities.},
}
@article {pmid30820628,
year = {2019},
author = {Wang, C and Yang, L and Wang, Z and He, J and Shi, Q},
title = {Highly multiplexed profiling of cell surface proteins on single circulating tumor cells based on antibody and cellular barcoding.},
journal = {Analytical and bioanalytical chemistry},
volume = {411},
number = {21},
pages = {5373-5382},
doi = {10.1007/s00216-019-01666-9},
pmid = {30820628},
issn = {1618-2650},
support = {81701852 (to L.Y.).//National Natural Science Foundation of China Grants/ ; 2016YFC0900200 (to Q.S.)//National Key Research and Development Program Grant/ ; },
mesh = {Antibodies/*immunology ; Antigens, Neoplasm/immunology ; Cell Line, Tumor ; *DNA Barcoding, Taxonomic ; High-Throughput Screening Assays ; Humans ; Membrane Proteins/genetics/immunology/*metabolism ; Neoplasm Proteins/genetics/*metabolism ; Neoplastic Cells, Circulating/immunology/*metabolism ; Reproducibility of Results ; Single-Cell Analysis/*methods ; },
abstract = {Circulating tumor cells (CTCs) are extraordinarily rare in blood samples and represent a real-time "liquid biopsy" of tumors. Although genetic and transcriptional sequencing of single CTCs has been reported, these methods fail to provide phenotypic and functional information of CTCs such as protein levels of surface proteins. Studies of single-cell proteomic assays of CTCs have been rare because of a lack of single-cell proteomic methods to handle and analyze rare cells in a high background of non-target cells with high sensitivity, throughput, and multiplexing capacity. Here, we develop a microchip-assisted single-cell proteomic method for profiling surface proteins of CTCs based on antibody and cellular DNA barcoding strategy. We combine DNA-encoded antibody tags and cell indexes to profile 15 proteins in ~ 100 single rare cells simultaneously, and use high-throughput sequencing as the readout to generate surface protein profiles of CTCs according to their cell indexes and antibody-derived protein barcodes. A 6400-well microchip and the automated puncher are used to rapidly retrieve single CTCs from enriched CTC population with minimal cell loss (~ 10%). This technological platform integrates reliable isolation and proteomic analysis of single CTCs and can be extendable to ~ 100 proteins in hundreds of rare cells with single-cell precision.},
}
@article {pmid30819903,
year = {2019},
author = {Chapellier, M and Peña-Martínez, P and Ramakrishnan, R and Eriksson, M and Talkhoncheh, MS and Orsmark-Pietras, C and Lilljebjörn, H and Högberg, C and Hagström-Andersson, A and Fioretos, T and Larsson, J and Järås, M},
title = {Arrayed molecular barcoding identifies TNFSF13 as a positive regulator of acute myeloid leukemia-initiating cells.},
journal = {Haematologica},
volume = {104},
number = {10},
pages = {2006-2016},
pmid = {30819903},
issn = {1592-8721},
mesh = {Animals ; B-Cell Maturation Antigen/genetics/metabolism ; Bone Marrow Cells/*metabolism/pathology ; Cell Line, Tumor ; Leukemia, Myeloid, Acute/genetics/*metabolism/pathology ; Mice ; Mice, Knockout ; Neoplasms, Experimental/genetics/*metabolism/pathology ; Neoplastic Stem Cells/*metabolism/pathology ; Oligonucleotide Array Sequence Analysis ; Oncogene Proteins, Fusion/genetics/metabolism ; *Tumor Microenvironment ; Tumor Necrosis Factor Ligand Superfamily Member 13/genetics/*metabolism ; },
abstract = {Dysregulation of cytokines in the bone marrow (BM) microenvironment promotes acute myeloid leukemia (AML) cell growth. Due to the complexity and low throughput of in vivo stem-cell based assays, studying the role of cytokines in the BM niche in a screening setting is challenging. Here, we developed an ex vivo cytokine screen using 11 arrayed molecular barcodes, allowing for a competitive in vivo readout of leukemia-initiating capacity. With this approach, we assessed the effect of 114 murine cytokines on MLL-AF9 AML mouse cells and identified the tumor necrosis factor ligand superfamily member 13 (TNFSF13) as a positive regulator of leukemia-initiating cells. By using Tnfsf13[-/-] recipient mice, we confirmed that TNFSF13 supports leukemia initiation also under physiological conditions. TNFSF13 was secreted by normal myeloid cells but not by leukemia mouse cells, suggesting that mature myeloid BM cells support leukemia cells by secreting TNFSF13. TNFSF13 supported leukemia cell proliferation in an NF-κB-dependent manner by binding TNFRSF17 and suppressed apoptosis. Moreover, TNFSF13 supported the growth and survival of several human myeloid leukemia cell lines, demonstrating that our findings translate to human disease. Taken together, using arrayed molecular barcoding, we identified a previously unrecognized role of TNFSF13 as a positive regulator of AML-initiating cells. The arrayed barcoded screening methodology is not limited to cytokines and leukemia, but can be extended to other types of ex vivo screens, where a multiplexed in vivo read-out of stem cell functionality is needed.},
}
@article {pmid30816920,
year = {2019},
author = {Ferlic, J and Shi, J and McDonald, TO and Michor, F},
title = {DIFFpop: a stochastic computational approach to simulate differentiation hierarchies with single cell barcoding.},
journal = {Bioinformatics (Oxford, England)},
volume = {35},
number = {19},
pages = {3849-3851},
pmid = {30816920},
issn = {1367-4811},
support = {T32 LM012411/LM/NLM NIH HHS/United States ; U54 CA193461/CA/NCI NIH HHS/United States ; },
mesh = {*Algorithms ; Cell Differentiation ; Clonal Evolution ; Computational Biology ; Single-Cell Analysis ; *Software ; Stochastic Processes ; },
abstract = {SUMMARY: DIFFpop is an R package designed to simulate cellular differentiation hierarchies using either exponentially-expanding or fixed population sizes. The software includes functionalities to simulate clonal evolution due to the emergence of driver mutations under the infinite-allele assumption as well as options for simulation and analysis of single cell barcoding and labeling data. The software uses the Gillespie Stochastic Simulation Algorithm and a modification of expanding or fixed-size stochastic process models expanded to a large number of cell types and scenarios.<br><br>DIFFpop is available as an R-package along with vignettes on Github (https://github.com/ferlicjl/diffpop).<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid30816181,
year = {2019},
author = {Guo, J and Cheng, T and Xu, H and Li, Y and Zeng, J},
title = {An efficient and cost-effective method for primer-induced nucleotide labeling for massive sequencing on next-generation sequencing platforms.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {3125},
pmid = {30816181},
issn = {2045-2322},
mesh = {DNA Barcoding, Taxonomic/economics/*methods ; DNA Primers/genetics ; DNA, Plant/genetics ; High-Throughput Nucleotide Sequencing/economics/*methods ; Nucleotides/genetics ; Plants/*genetics ; },
abstract = {Next generation sequencing (NGS) technologies play a powerful role in the preparation of large DNA databases such as DNA barcoding since it can produce a large number of sequence reads. Here we demonstrate a primer-induced sample labeling method aiming at sequencing a large number of samples simultaneously on NGS platforms. The strategy is to label samples with a unique oligo attached to the 5'-ends of primers. As a case study, 894 unique pentanucleotide oligoes were attached to the 5'-ends of three pairs of primers (for amplifying ITS, matK and rbcL) to label 894 samples. All PCR products of three barcodes of 894 samples were mixed together and sequenced on a high throughput sequencing platform. The results showed that 87.02%, 89.15% and 95.53% of the samples were successfully sequenced for rbcL, matK and ITS, respectively. The mean ratio of label mismatches for the three barcodes was 5.68%, and a sequencing depth of 30 ×to 40× was enough to obtain reliable sequences. It is flexible to label any number of samples simply by adjusting the length of oligoes. This easy, reliable and cost efficient method is useful in sequencing a large number of samples for construction of reference libraries for DNA barcoding, population biology and community phylogenetics.},
}
@article {pmid30816127,
year = {2019},
author = {Yeom, H and Lee, Y and Ryu, T and Noh, J and Lee, AC and Lee, HB and Kang, E and Song, SW and Kwon, S},
title = {Barcode-free next-generation sequencing error validation for ultra-rare variant detection.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {977},
pmid = {30816127},
issn = {2041-1723},
mesh = {Cloning, Molecular ; DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; Gene Library ; *Genetic Variation ; High-Throughput Nucleotide Sequencing/*methods/standards/statistics &amp; numerical data ; Polymerase Chain Reaction ; Quality Control ; Sequence Analysis, DNA/*methods/standards/statistics &amp; numerical data ; },
abstract = {The advent of next-generation sequencing (NGS) has accelerated biomedical research by enabling the high-throughput analysis of DNA sequences at a very low cost. However, NGS has limitations in detecting rare-frequency variants (< 1%) because of high sequencing errors (> 0.1~1%). NGS errors could be filtered out using molecular barcodes, by comparing read replicates among those with the same barcodes. Accordingly, these barcoding methods require redundant reads of non-target sequences, resulting in high sequencing cost. Here, we present a cost-effective NGS error validation method in a barcode-free manner. By physically extracting and individually amplifying the DNA clones of erroneous reads, we distinguish true variants of frequency > 0.003% from the systematic NGS error and selectively validate NGS error after NGS. We achieve a PCR-induced error rate of 2.5×10[-6] per base per doubling event, using 10 times less sequencing reads compared to those from previous studies.},
}
@article {pmid30811075,
year = {2019},
author = {Dopheide, A and Tooman, LK and Grosser, S and Agabiti, B and Rhode, B and Xie, D and Stevens, MI and Nelson, N and Buckley, TR and Drummond, AJ and Newcomb, RD},
title = {Estimating the biodiversity of terrestrial invertebrates on a forested island using DNA barcodes and metabarcoding data.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {29},
number = {4},
pages = {e01877},
doi = {10.1002/eap.1877},
pmid = {30811075},
issn = {1051-0761},
support = {//University of Auckland/International ; //New Zealand Tertiary Education Commission/International ; },
mesh = {Animals ; Biodiversity ; DNA ; *DNA Barcoding, Taxonomic ; *Ecosystem ; Invertebrates ; Islands ; New Zealand ; },
abstract = {Invertebrates are a major component of terrestrial ecosystems, however, estimating their biodiversity is challenging. We compiled an inventory of invertebrate biodiversity along an elevation gradient on the temperate forested island of Hauturu, New Zealand, by DNA barcoding of specimens obtained from leaf litter samples and pitfall traps. We compared the barcodes and biodiversity estimates from this data set with those from a parallel DNA metabarcoding analysis of soil from the same locations, and with pre-existing sequences in reference databases, before exploring the use of combined data sets as a basis for estimating total invertebrate biodiversity. We obtained 1,282 28S and 1,610 COI barcodes from a total of 1,947 invertebrate specimens, which were clustered into 247 (28S) and 366 (COI) OTUs, of which ≤ 10% were represented in GenBank. Coleoptera were most abundant (730 sequenced specimens), followed by Hymenoptera, Diptera, Lepidoptera, and Amphipoda. The most abundant OTU from both the 28S (153 sequences) and COI (140 sequences) data sets was an undescribed beetle from the family Salpingidae. Based on the occurrences of COI OTUs along the elevation gradient, we estimated there are ~1,000 arthropod species (excluding mites) on Hauturu, including 770 insects, of which 344 are beetles. A DNA metabarcoding analysis of soil DNA from the same sites resulted in the identification of similar numbers of OTUs in most invertebrate groups compared with the DNA barcoding, but less than 10% of the DNA barcoding COI OTUs were also detected by the metabarcoding analysis of soil DNA. A mark-recapture analysis based on the overlap between these data sets estimated the presence of approximately 6,800 arthropod species (excluding mites) on the island, including ~3,900 insects. Estimates of New Zealand-wide biodiversity for selected arthropod groups based on matching of the COI DNA barcodes with pre-existing reference sequences suggested over 13,200 insect species are present, including 4,000 Coleoptera, 2,200 Diptera, and 2,700 Hymenoptera species, and 1,000 arachnid species (excluding mites). These results confirm that metabarcoding analyses of soil DNA tends to recover different components of terrestrial invertebrate biodiversity compared to traditional invertebrate sampling, but the combined methods provide a novel basis for estimating invertebrate biodiversity.},
}
@article {pmid30809803,
year = {2019},
author = {Nauer, F and Deluqui Gurgel, CF and Ayres-Ostrock, LM and Plastino, EM and Oliveira, MC},
title = {Phylogeography of the Hypnea musciformis species complex (Gigartinales, Rhodophyta) with the recognition of cryptic species in the western Atlantic Ocean.},
journal = {Journal of phycology},
volume = {55},
number = {3},
pages = {676-687},
doi = {10.1111/jpy.12848},
pmid = {30809803},
issn = {1529-8817},
mesh = {Atlantic Ocean ; Brazil ; Caribbean Region ; DNA, Mitochondrial ; Genetic Variation ; Haplotypes ; Hawaii ; Mexico ; Pacific Ocean ; Phylogeny ; Phylogeography ; *Rhodophyta ; Sequence Analysis, DNA ; },
abstract = {Populations of the marine benthic red macroalgae Hypnea musciformis and Hypnea pseudomusciformis along the Atlantic and Pacific Oceans were tested for phylogeographic structure using the DNA barcode COI-5P combined with rbcL for the construction of the phylogenetic tree. Strong patterns of genetic structure were detected across 210 COI-5P DNA sequences, and 37 COI-5P haplotypes were found, using multiple statistical approaches. Hypnea musciformis was found in the Northeast and Northwest Atlantic, the Mediterrean Sea, Namibia, and along the Pacific coast of Mexico. Two new putative species were detected, Hypnea sp. 1 in the Caribbean Sea and Hypnea sp. 2 in the Dominican Republic. Three distinct marine phylogeographic provinces were recognized in the Southern Hemisphere for H. pseudomusciformis: Uruguay, South-Southeast Brazil, and Northeast Brazil. The degree of genetic isolation and distinctness among these provinces varied considerably. The Uruguay province was the most genetically distinct, as characterized by four unique haplotypes not shared with any of the Brazilian populations. Statistically significant results support both, isolation by distance and isolation by environment hypotheses, explaining the formation and mantainance of phylogeographic structuring along the Uruguay-Brazil coast. Geographic, taxonomic and molecular marker concordances were found between our H. pseudomusciformis results and published studies. Furthermore, our data indicate that the Hawaiian introduced populations of H. musciformis contain Hypnea sp. 1 haplotypes, the current known distribution of which is restricted to the Caribbean.},
}
@article {pmid30809427,
year = {2019},
author = {Potter, C and de Vere, N and Jones, LE and Ford, CR and Hegarty, MJ and Hodder, KH and Diaz, A and Franklin, EL},
title = {Pollen metabarcoding reveals broad and species-specific resource use by urban bees.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e5999},
pmid = {30809427},
issn = {2167-8359},
abstract = {Bee populations are currently undergoing severe global declines driven by the interactive effects of a number of factors. Ongoing urbanisation has the potential to exacerbate bee declines, unless steps are taken to ensure appropriate floral resources are available. Sown wildflower strips are one way in which floral resources can be provided to urban bees. However, the use of these strips by pollinators in urban environments remains little studied. Here, we employ pollen metabarcoding of the rbcL gene to compare the foraging patterns of different bee species observed using urban sown wildflower strips in July 2016, with a goal of identifying which plant species are most important for bees. We also demonstrate the use of a non-destructive method of pollen collection. Bees were found to forage on a wide variety of plant genera and families, including a diverse range of plants from outside the wildflower plots, suggesting that foragers visiting sown wildflower strips also utilize other urban habitats. Particular plants within the wildflower strips dominated metabarcoding data, particularly Papaver rhoeas and Phacelia tanacetifolia. Overall, we demonstrate that pollinators observed in sown wildflower strips use certain sown foodplants as part of a larger urban matrix.},
}
@article {pmid30808961,
year = {2019},
author = {Fu, CN and Wu, CS and Ye, LJ and Mo, ZQ and Liu, J and Chang, YW and Li, DZ and Chaw, SM and Gao, LM},
title = {Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {2773},
pmid = {30808961},
issn = {2045-2322},
abstract = {Taxus (yew) is both the most species-rich and taxonomically difficult genus in Taxaceae. To date, no study has elucidated the complexities of the plastid genome (plastome) or examined the possibility of whole plastomes as super-barcodes across yew species worldwide. In this study, we sequenced plastomes from two to three individuals for each of the 16 recognized yew species (including three potential cryptics) and Pseudotaxus chienii. Our comparative analyses uncovered several gene loss events that independently occurred in yews, resulting in a lower plastid gene number than other Taxaceous genera. In Pseudotaxus and Taxus, we found two isomeric arrangements that differ by the orientation of a 35 kb fragment flanked by "trnQ-IRs". These two arrangements exist in different ratios within each sampled individual, and intraspecific shifts in major isomeric arrangements are first reported here in Taxus. Moreover, we demonstrate that entire plastomes can be used to successfully discriminate all Taxus species with 100% support, suggesting that they are useful as super-barcodes for species identification. We also propose that accD and rrn16-rrn23 are promising special barcodes to discriminate yew species. Our newly developed Taxus plastomic sequences provide a resource for super-barcodes and conservation genetics of several endangered yews and serve as comprehensive data to improve models of plastome complexity in Taxaceae as a whole and authenticate Taxus species.},
}
@article {pmid30808329,
year = {2019},
author = {Namba, K and Tomida, S and Matsubara, T and Takahashi, Y and Kurihara, E and Ogoshi, Y and Yoshioka, T and Takeda, T and Torigoe, H and Sato, H and Shien, K and Yamamoto, H and Soh, J and Tsukuda, K and Toyooka, S},
title = {Application of amplicon-based targeted sequencing with the molecular barcoding system to detect uncommon minor EGFR mutations in patients with treatment-naïve lung adenocarcinoma.},
journal = {BMC cancer},
volume = {19},
number = {1},
pages = {175},
pmid = {30808329},
issn = {1471-2407},
support = {16H05431//Japan Society for the Promotion of Science/ ; 16H01574//Japan Society for the Promotion of Science/ ; },
mesh = {Adenocarcinoma/*diagnosis/genetics ; Aged ; Antineoplastic Agents/*therapeutic use ; Cohort Studies ; DNA Mutational Analysis ; ErbB Receptors/genetics ; Feasibility Studies ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Lung/pathology/*physiology ; Lung Neoplasms/*diagnosis/genetics ; Male ; Middle Aged ; Mutation/*genetics ; Nucleic Acid Amplification Techniques ; Protein Kinase Inhibitors/*therapeutic use ; Reproducibility of Results ; Retrospective Studies ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: In lung cancer, epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor sensitizing mutations co-existing with rare minor EGFR mutations are known as compound mutations. These minor EGFR mutations can lead to acquired resistance after EGFR tyrosine kinase inhibitor treatment, so determining the mutation status of patients is important. However, using amplicon-based targeted deep sequencing based on next-generation sequencing to characterize mutations is prone to sequencing error. We therefore assessed the benefit of incorporating molecular barcoding with high-throughput sequencing to investigate genomic heterogeneity in treatment-naïve patients who have undergone resection of their non-small cell lung cancer (NSCLC) EGFR mutations.<br><br>METHODS: We performed amplicon-based targeted sequencing with the molecular barcoding system (MBS) to detect major common EGFR mutations and uncommon minor mutations at a 0.5% allele frequency in fresh-frozen lung cancer samples.<br><br>RESULTS: Profiles of the common mutations of EGFR identified by MBS corresponded with the results of clinical testing in 63 (98.4%) out of 64 cases. Uncommon mutations of EGFR were detected in seven cases (10.9%). Among the three types of major EGFR mutations, patients with the G719X mutation had a significantly higher incidence of compound mutations than those with the L858R mutation or exon 19 deletion (p&#x2009;=&#x2009;0.0052). This was validated in an independent cohort from the Cancer Genome Atlas dataset (p&#x2009;=&#x2009;0.018).<br><br>CONCLUSIONS: Our findings demonstrate the feasibility of using the MBS to establish an accurate NSCLC patient genotype. This work will help understand the molecular basis of EGFR compound mutations in NSCLC, and could aid the development of new treatment modalities.},
}
@article {pmid30807749,
year = {2019},
author = {Ya'cob, Z and Takaoka, H and Low, VL and Tan, TK and Sofian-Azirun, M},
title = {Description of the female of Simulium (Gomphostilbia) aziruni (Diptera: Simuliidae) and its genetic relationships with members of the Simulium gombakense species-group.},
journal = {Acta tropica},
volume = {193},
number = {},
pages = {66-70},
doi = {10.1016/j.actatropica.2019.02.023},
pmid = {30807749},
issn = {1873-6254},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Female ; Genitalia, Female/*anatomy &amp; histology ; Malaysia ; Simuliidae/*anatomy &amp; histology/*genetics ; },
abstract = {Simulium (Gomphostilbia) aziruni Takaoka, Hashim &amp; Chen was described initially based only on a pupa and a mature larva collected from Peninsular Malaysia. Herein, we describe the morphological characters of the female of S. aziruni for the first time. It resembles those of the other members of the Simulium gombakense species-group by the genital fork with a distinct projection directed medioposteriorly from each arm and claw with a large basal tooth. Cytochrome c oxidase I (COI) barcoding analysis indicates that S. aziruni is the sister species of S. maleewongae, but both are distantly separated by a genetic distance of 4.9%.},
}
@article {pmid30807716,
year = {2019},
author = {Smit, JT and Miller, J},
title = {Bat Ectoparasites From Sint Eustatius, Lesser Antilles (Diptera: Hippoboscidae: Streblinae; Hemiptera: Polyctenidae).},
journal = {The Journal of parasitology},
volume = {105},
number = {1},
pages = {45-51},
pmid = {30807716},
issn = {1937-2345},
mesh = {Amino Acid Sequence ; Animals ; Chiroptera/*parasitology ; DNA Barcoding, Taxonomic/*veterinary ; Diptera/anatomy &amp; histology/*classification/genetics ; Ectoparasitic Infestations/parasitology/*veterinary ; Electron Transport Complex IV/genetics ; Female ; Hemiptera/anatomy &amp; histology/*classification/genetics ; Host-Parasite Interactions ; Male ; Sequence Alignment/veterinary ; West Indies ; },
abstract = {In this paper 4 species of bat ectoparasites are recorded from the island of Sint Eustatius, Dutch Caribbean. One species of true bug (Hemiptera: Polyctenidae) as well as 3 species of bat flies (Diptera: Hippoboscidae: Streblinae) are recorded. All species are photographed. The first DNA barcodes for 3 bat ectoparasite species (Trichobius frequens, Trichobius intermedius, and Hesperoctenes fumarius) have been posted to the BOLD database; DNA barcode sequences for a fourth species (Megistopoda aranea) are the first from a Caribbean island.},
}
@article {pmid30807707,
year = {2019},
author = {Dempsey, ZW and Burg, TM and Goater, CP},
title = {Spatiotemporal Patterns of Infection for Emerging Larval Liver Fluke (Dicrocoelium dendriticum) in Three Species of Land Snail in Southern Alberta, Canada.},
journal = {The Journal of parasitology},
volume = {105},
number = {1},
pages = {155-161},
pmid = {30807707},
issn = {1937-2345},
mesh = {Alberta ; Analysis of Variance ; Animals ; DNA Barcoding, Taxonomic ; Dicrocoelium/*physiology ; Ecosystem ; Electron Transport Complex IV/genetics ; Prevalence ; Seasons ; Snails/anatomy &amp; histology/classification/*parasitology ; Spatial Analysis ; Time Factors ; },
abstract = {The control of emerging parasites requires a fundamental knowledge of where and when rates of transmission are high. Data on spatiotemporal patterns of infection are challenging to obtain, particularly for complex life cycle parasites that involve transmission into multiple obligate hosts. The lancet liver fluke, Dicrocoelium dendriticum, has a long history of colonization outside its native host and geographical range in continental Europe. Infection patterns involving adult and metacercarial stages have been characterized for this trematode in a region of emergence in western Canada within co-grazing herbivores and ants, but infection patterns in snail intermediate hosts in this region are unknown. We combined spatiotemporal prevalence surveys with sequence analyses of the cytochrome c oxidase subunit 1 (COI) barcoding gene from samples of sporocyst tissue in infected snails to confirm that D. dendriticum utilizes 3 sympatric species of Oreohelid land snail (Oreohelix subrudis, Oreohelix sp., and Oreohelix cooperi) as first intermediate host. Mean prevalence within a total sample of 900 adult snails collected over 1 field season from 6 sites was 9.9 ± 2.4%. For each species of snail, prevalence ranged between 5-30% within monthly samples, with peaks in mid-summer followed by declines in fall. Between-site variation in prevalence was low and non-significant, implying that rates of transmission of D. dendriticum miracidia from domestic stock and wildlife into snails are similar within localized sites, despite high variation in local habitat characteristics and in the structure of the definitive host community.},
}
@article {pmid30805173,
year = {2019},
author = {Bourbour, RP and Martinico, BL and Crane, MM and Hull, AC and Hull, JM},
title = {Messy eaters: Swabbing prey DNA from the exterior of inconspicuous predators when foraging cannot be observed.},
journal = {Ecology and evolution},
volume = {9},
number = {3},
pages = {1452-1457},
pmid = {30805173},
issn = {2045-7758},
abstract = {Complex coevolutionary relationships among competitors, predators, and prey have shaped taxa diversity, life history strategies, and even the avian migratory patterns we see today. Consequently, accurate documentation of prey selection is often critical for understanding these ecological and evolutionary processes. Conventional diet study methods lack the ability to document the diet of inconspicuous or difficult-to-study predators, such as those with large home ranges and those that move vast distances over short amounts of time, leaving gaps in our knowledge of trophic interactions in many systems. Migratory raptors represent one such group of predators where detailed diet studies have been logistically challenging. To address knowledge gaps in the foraging ecology of migrant raptors and provide a broadly applicable tool for the study of enigmatic predators, we developed a minimally invasive method to collect dietary information by swabbing beaks and talons of raptors to collect trace prey DNA. Using previously published COI primers, we were able to isolate and reference gene sequences in an open-access barcode database to identify prey to species. This method creates a novel avenue to use trace molecular evidence to study prey selection of migrating raptors and will ultimately lead to a better understanding of raptor migration ecology. In addition, this technique has broad applicability and can be used with any wildlife species where even trace amounts of prey debris remain on the exterior of the predator after feeding.},
}
@article {pmid30805170,
year = {2019},
author = {Waraniak, JM and Marsh, TL and Scribner, KT},
title = {18S rRNA metabarcoding diet analysis of a predatory fish community across seasonal changes in prey availability.},
journal = {Ecology and evolution},
volume = {9},
number = {3},
pages = {1410-1430},
pmid = {30805170},
issn = {2045-7758},
abstract = {Predator-prey relationships are important ecological interactions, affecting biotic community composition and energy flow through a system, and are of interest to ecologists and managers. Morphological diet analysis has been the primary method used to quantify the diets of predators, but emerging molecular techniques using genetic data can provide more accurate estimates of relative diet composition. This study used sequences from the 18S V9 rRNA barcoding region to identify prey items in the gastrointestinal (GI) tracts of predatory fishes. Predator GI samples were taken from the Black River, Cheboygan Co., MI, USA (n = 367 samples, 12 predator species) during periods of high prey availability, including the larval stage of regionally threatened lake sturgeon (Acipenser fulvescens Rafinesque 1817) in late May/early June of 2015 and of relatively lower prey availability in early July of 2015. DNA was extracted and sequenced from 355 samples (96.7%), and prey DNA was identified in 286 of the 355 samples (80.6%). Prey were grouped into 33 ecologically significant taxonomic groups based on the lowest taxonomic level sequences that could be identified using sequences available on GenBank. Changes in the makeup of diet composition, dietary overlap, and predator preference were analyzed comparing the periods of high and low prey abundance. Some predator species exhibited significant seasonal changes in diet composition. Dietary overlap was slightly but significantly higher during the period of high prey abundance; however, there was little change in predator preference. This suggests that change in prey availability was the driving factor in changing predator diet composition and dietary overlap. This study demonstrates the utility of molecular diet analysis and how temporal variability in community composition adds complexity to predator-prey interactions.},
}
@article {pmid30805149,
year = {2019},
author = {Bozorov, TA and Luo, Z and Li, X and Zhang, D},
title = {Agrilus mali Matsumara (Coleoptera: Buprestidae), a new invasive pest of wild apple in western China: DNA barcoding and life cycle.},
journal = {Ecology and evolution},
volume = {9},
number = {3},
pages = {1160-1172},
pmid = {30805149},
issn = {2045-7758},
abstract = {Agrilus mali Matsumara (Coleoptera: Buprestidae) is a wood-boring beetle distributed to eastern China that occasionally injures apple species. However, this wood-boring beetle is new to the wild apple forests (Malus sieversii) of the Tianshan Mountains (western China) and has caused extensive tree mortality. The development of a biological control program for these wild apple forests is a high priority that requires exploration of the life cycle, DNA barcoding and taxonomic status of A. mali. In this study, to determine the diversity of invasive beetles, a fragment of the mitochondrial cytochrome oxidase gene was analyzed. Based on the results, beetles from Gongliu and Xinyuan counties of Xinjiang were identical but differed from those in the apple nursery of Gongliu by a single-nucleotide substitution. We summarize the taxonomic status, relationships, and genetic distances of A. mali among other Agrilus species using the Tajima-Nei model in maximum likelihood phylogeny. Analysis revealed that A. mali was closely related to Agrilus mendax and both belong to the Sinuatiagrulus subgenus. The life cycle of A. mali was investigated based on a monthly regular inspection in the wild apple forests of Tianshan. Similar to congeneric species, hosts are injured by larvae of A. mali feeding on phloem tissue, resulting in serpentine galleries constructed between bark and xylem that prevent nutrient transport and leading to tree mortality. Future studies will focus on plant physiological responses to the invasive beetles and include surveys of natural enemies for a potential classical biological control program.},
}
@article {pmid30804976,
year = {2019},
author = {Hofmann, EP and Nicholson, KE and Luque-Montes, IR and Köhler, G and Cerrato-Mendoza, CA and Medina-Flores, M and Wilson, LD and Townsend, JH},
title = {Cryptic Diversity, but to What Extent? Discordance Between Single-Locus Species Delimitation Methods Within Mainland Anoles (Squamata: Dactyloidae) of Northern Central America.},
journal = {Frontiers in genetics},
volume = {10},
number = {},
pages = {11},
pmid = {30804976},
issn = {1664-8021},
abstract = {Single-locus molecular barcoding is a useful method for identifying overlooked and undescribed biodiversity, providing the groundwork for further systematic study and taxonomic investigation. A variety of methods for delimiting species from barcoding libraries have been developed and applied, allowing for rapid estimates of species diversity in a broad range of taxa. However, tree-based and distance-based analyses can infer different group assignments, potentially over- or underestimating the number of putative species groups. Here, we explore diversity of mainland species of anole lizards from the Chortís Block biogeographical province of northern Central America using a DNA barcoding approach, generating and analyzing cytochrome oxidase subunit I (COI) sequences for over 400 samples assignable to 33 of 38 (86.8%) native and one introduced mainland species. We subsequently tested the effects different models of nucleotide substitution, different species-delimitation algorithms, and reducing our dataset had on species delimitation estimates. We performed of two distance-based (ABGD, RESL) and three tree-based (bPTP, mPTP, GMYC) analyses on both the full dataset and a dataset consisting only of unique halotypes. From 34 nominal taxa, analyses of the full dataset recovered between 34 and 64 operational taxonomic units (OTUs), while analyses of the reduced dataset inferred between 36 and 59. Reassigning individuals to either mPTP-inferred or ABGD clustered (7.2% threshold) groups improved the detection of a barcoding gap across three different models of nucleotide substitution, removing overlap between intra- and interspecific distances. Our results highlight the underestimated diversity of mainland Chortís Block anoles, but the lack of congruence between analyses demonstrates the importance of considering multiple analytical methods when dealing with single-locus datasets. We recommend future studies consider the effects of different models of nucleotide substitution on proposed barcoding gaps, as well as the effect reducing a dataset to unique haplotypes may have on proposed diversity estimates.},
}
@article {pmid30804961,
year = {2019},
author = {Seethapathy, GS and Raclariu-Manolica, AC and Anmarkrud, JA and Wangensteen, H and de Boer, HJ},
title = {DNA Metabarcoding Authentication of Ayurvedic Herbal Products on the European Market Raises Concerns of Quality and Fidelity.},
journal = {Frontiers in plant science},
volume = {10},
number = {},
pages = {68},
pmid = {30804961},
issn = {1664-462X},
abstract = {Ayurveda is one of the oldest systems of medicine in the world, but the growing commercial interest in Ayurveda based products has increased the incentive for adulteration and substitution within this herbal market. Fraudulent practices such as the use of undeclared fillers and use of other species of inferior quality is driven both by the increased as well as insufficient supply capacity of especially wild plant species. Developing novel strategies to exhaustively assess and monitor both the quality of raw materials and final marketed herbal products is a challenge in herbal pharmacovigilance. Seventy-nine Ayurvedic herbal products sold as tablets, capsules, powders, and extracts were randomly purchased via e-commerce and pharmacies across Europe, and DNA metabarcoding was used to assess the ability of this method to authenticate these products. Our analysis reveals that only two out of 12 single ingredient products contained only one species as labeled, eight out of 27 multiple ingredient products contained none of the species listed on the label, and the remaining 19 products contained 1 to 5 of the species listed on the label along with many other species not specified on the label. The fidelity for single ingredient products was 67%, the overall ingredient fidelity for multi ingredient products was 21%, and for all products 24%. The low level of fidelity raises concerns about the reliability of the products, and detection of threatened species raises further concerns about illegal plant trade. The study highlights the necessity for quality control of the marketed herbal products and shows that DNA metabarcoding is an effective analytical approach to authenticate complex multi ingredient herbal products. However, effort needs to be done to standardize the protocols for DNA metabarcoding before this approach can be implemented as routine analytical approaches for plant identification, and approved for use in regulated procedures.},
}
@article {pmid30799113,
year = {2019},
author = {Buehler, AJ and Evanowski, RL and Wiedmann, M and Martin, NH},
title = {Internal transcribed spacer (ITS) sequence-based characterization of fungal isolates from multiple yogurt facilities-A case study.},
journal = {Journal of dairy science},
volume = {102},
number = {4},
pages = {3646-3653},
doi = {10.3168/jds.2018-15636},
pmid = {30799113},
issn = {1525-3198},
mesh = {Alleles ; Animals ; Ascomycota/classification/genetics ; Base Sequence ; Basidiomycota/classification/genetics ; DNA, Fungal/*analysis/chemistry ; DNA, Intergenic/chemistry ; Dairy Products/microbiology ; *Food Handling ; Food Microbiology/*methods ; Fungi/classification/*genetics/*isolation &amp; purification ; Mucorales/classification/genetics ; Sorbic Acid ; Yogurt/*microbiology ; },
abstract = {Fungal spoilage remains a significant issue in dairy product quality, especially for cultured dairy products such as yogurt formulated without preservatives such as potassium sorbate. Fungal contamination can occur throughout the processing continuum, from the dairy farm environment to the finished product processing environment. As molecular characterization of fungal isolates is used more frequently, we obtained fungal isolates obtained in 2 yogurt processing facilities as part of routine fungal testing of raw materials (e.g., fruit preparations, added ingredients), in-process product samples, environmental samples (e.g., air plates, equipment surfaces such as valves, face plates, air nozzles), and finished product samples, to determine whether internal transcribed spacer (ITS) barcoding data would be helpful to support source tracking of fungal contamination issues. Internal transcribed spacer PCR amplification and sequencing allowed us to classify the 852 isolates from these 2 facilities into 200 unique ITS allelic types (AT), representing the phyla Ascomycota (743 isolates), Basidiomycota (97 isolates), and Mucoromycota (12 isolates). Thirty ITS AT were isolated from both facilities; 62 and 108 ITS AT were isolated from only facility A or only facility B, respectively. Nine ITS AT were each represented by more than 20 isolates; these AT comprised 53% of the 852 isolates. The considerable diversity of fungal isolates even within a single facility illustrates the challenge associated with controlling fungal contamination of dairy products. The ITS barcoding technique, however, did show promise for facilitating the source tracking of fungal contamination, particularly for ITS AT over-represented in a given facility. For example, we found evidence for equipment-specific reservoirs for 2 AT (14 and 219) in facility B. Our data suggest that despite its limited discriminatory power, ITS sequencing can provide initial information that can help trace fungal contamination along the processing continuum. However, development and implementation of discriminatory subtyping methods will be needed to further improve the ability to identify sources of fungal contamination in dairy facilities. Developing and implementing sampling plans that comprehensively capture yeast and mold diversity in a given processing facility remain a considerable challenge.},
}
@article {pmid30797461,
year = {2019},
author = {Li, SZ and Zeng, SL and Wu, Y and Zheng, GD and Chu, C and Yin, Q and Chen, BZ and Li, P and Lu, X and Liu, EH},
title = {Cultivar differentiation of Citri Reticulatae Pericarpium by a combination of hierarchical three-step filtering metabolomics analysis, DNA barcoding and electronic nose.},
journal = {Analytica chimica acta},
volume = {1056},
number = {},
pages = {62-69},
doi = {10.1016/j.aca.2019.01.004},
pmid = {30797461},
issn = {1873-4324},
mesh = {Citrus/*classification/genetics/growth &amp; development/metabolism ; *DNA Barcoding, Taxonomic ; DNA, Intergenic/genetics ; *Electronic Nose ; *Metabolomics ; },
abstract = {The traditional Chinese medicine Citri Reticulatae Pericarpium (CRP) was mainly originated from the dried pericarp of Citrus reticulata 'Chachi' (Crc), Citrus reticulata 'Dahongpao' (Crd), Citrus reticulata 'Unshiu' (Cru) and Citrus reticulata 'Tangerina' (Crt) in China. Since these four cultivars have great similarities in morphology, reliable methods to differentiate CRP cultivars have rarely been reported. To discriminate the differences of these CRP cultivars, herein an efficient and reliable method by combining metabolomics, DNA barcoding and electronic nose was first established. The hierarchical three-step filtering metabolomics analysis based on liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) indicated that 9 species-specific chemical markers including 6 flavanone glycosides and 3 polymethoxyflavones could be considered as marker metabolites for discrimination of the geoherb Crc from other cultivars. A total of 19 single nucleotide polymorphism (SNP) sites were found in nuclear internal transcribed spacer 2 (ITS2) of CRP, and three stable SNP sites (33, 128 and 174) in the ITS2 region can distinguish the four CRP cultivars. The electronic nose coupled with chemometrics could also be used to effectively distinguish Crc from other CRP cultivars. Therefore, our results indicated that the integrated method will be an effective strategy for discrimination of similar herbal medicines.},
}
@article {pmid30796652,
year = {2019},
author = {Leal, MF and Haynes, BP and MacNeill, FA and Dodson, A and Dowsett, M},
title = {Comparison of protein expression between formalin-fixed core-cut biopsies and surgical excision specimens using a novel multiplex approach.},
journal = {Breast cancer research and treatment},
volume = {175},
number = {2},
pages = {317-326},
pmid = {30796652},
issn = {1573-7217},
mesh = {AMP-Activated Protein Kinase Kinases ; Biomarkers, Tumor/*genetics ; Biopsy, Large-Core Needle ; Breast Neoplasms/*genetics/pathology/surgery ; Female ; Formaldehyde ; Gene Expression Regulation, Neoplastic/genetics ; Humans ; Immunohistochemistry ; Ki-67 Antigen/genetics ; Mastectomy ; Middle Aged ; Neoplasm Proteins/*genetics/isolation &amp; purification ; Paraffin Embedding ; Protein Kinases/genetics ; Proto-Oncogene Proteins c-raf/genetics ; Receptor, ErbB-2/genetics ; Receptors, Progesterone/genetics ; },
abstract = {PURPOSE: We evaluated whether multiplex protein quantification using antibody bar-coding with photocleavable oligonucleotides (NanoString) can be applied to evaluate protein expression in breast cancer FFPE specimens. We also assessed whether diagnostic core-cuts fixed immediately at time of procedures and surgical excision sections from routinely fixed breast cancers are affected by the same fixation related differences noted using immunohistochemistry (IHC).<br><br>METHODS: The expression of 26 proteins was analysed using NanoString technology in 16 pairs of FFPE breast cancer core-cuts and surgical excisions. The measurements yielded were compared with those by IHC on Ki67, PgR and HER2 biomarkers and pAKT and pERK1/2 phosphorylated proteins.<br><br>RESULTS: When considered irrespective of sample type, expression measured by the two methods was strongly correlated for all markers (p&#x2009;<&#x2009;0.001; &#x3c1;&#x2009;=&#x2009;0.69-0.88). When core-cuts and excisions were evaluated separately, the correlations between NanoString and IHC were weaker but significant except for pAKT in excisions. Surgical excisions showed lower levels of 8/12 phosphoproteins and higher levels of 4/13 non-phosphorylated proteins in comparison to core-cuts (p&#x2009;<&#x2009;0.01). Reduced p4EBP1, pAMPKa, pRPS6 and pRAF1 immunogenicity in excisions was correlated with tumour size and mastectomy specimens showed lower p4EBP1 and pRPS6 expression than lumpectomy (p&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: Our study supports the validity of the new multiplex approach to protein analysis but indicates that, as with IHC, caution is necessary for the analysis in excisions particularly of phosphoproteins. The specimen type, tumour size and surgery type may lead to biases in the quantitative analysis of many proteins of biologic and clinical interest in excision specimens.},
}
@article {pmid30794984,
year = {2019},
author = {Mallampati, S and Duose, DY and Harmon, MA and Mehrotra, M and Kanagal-Shamanna, R and Zalles, S and Wistuba, II and Sun, X and Luthra, R},
title = {Rational "Error Elimination" Approach to Evaluating Molecular Barcoded Next-Generation Sequencing Data Identifies Low-Frequency Mutations in Hematologic Malignancies.},
journal = {The Journal of molecular diagnostics : JMD},
volume = {21},
number = {3},
pages = {471-482},
pmid = {30794984},
issn = {1943-7811},
support = {P30 CA016672/CA/NCI NIH HHS/United States ; P50 CA100632/CA/NCI NIH HHS/United States ; R21 AI103652/AI/NIAID NIH HHS/United States ; },
mesh = {Cell Line, Tumor ; *DNA Barcoding, Taxonomic ; Hematologic Neoplasms/*genetics ; *High-Throughput Nucleotide Sequencing ; Humans ; Limit of Detection ; Multiplex Polymerase Chain Reaction ; Mutation/*genetics ; *Mutation Rate ; },
abstract = {The emergence of highly sensitive molecular diagnostic approaches, such as droplet digital PCR, has allowed the accurate identification of low-frequency variant alleles in clinical specimens; however, the multiplex capabilities of droplet digital PCR for variant detection are inadequate. The incorporation of molecular barcodes or unique IDs into next-generation sequencing libraries through PCR has enabled the detection of low-frequency variant alleles across multiple genomic regions. However, rational library preparation and sequencing data analytic strategies that integrate molecular barcodes have rarely been applied to clinical settings. In this study, we evaluated the parameters that are crucial in the use of molecular barcodes in next-generation sequencing for genotyping clinical specimens from patients with hematologic malignancies. The uniform incorporation of molecular barcodes into DNA templates through PCR was found to be crucial, and the extent of uniformity was governed by multiple interdependent variables. An error elimination strategy was developed for removing sequencing background errors by using molecular barcode sequence information as an alternative to the conventional error correction approach. This approach was successfully used to identify mutations with frequencies as low as 0.15%, and the clonal heterogeneity of hematologic malignancies was revealed. These findings have implications for elucidating heterogeneity and temporal and spatial clonal evolution, evaluating response to therapy, and monitoring relapse in patients with hematologic malignancies.},
}
@article {pmid30794582,
year = {2019},
author = {Siddall, ME and Barkdull, M and Tessler, M and Brugler, MR and Borda, E and Hekkala, E},
title = {Ideating iDNA: Lessons and limitations from leeches in legacy collections.},
journal = {PloS one},
volume = {14},
number = {2},
pages = {e0212226},
pmid = {30794582},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; DNA/*genetics/isolation &amp; purification ; *DNA Barcoding, Taxonomic ; *Databases, Nucleic Acid ; *Leeches ; *Vertebrates/classification/genetics ; },
abstract = {Indirect methods for conducting faunal inventories present great promise, and genomic inventories derived from environmental sources (eDNA) are improving. Invertebrate ingested DNA (iDNA) from terrestrial leeches in the family Haemadipsidae has shown potential for surveying vertebrates and biodiversity monitoring in protected areas. Here we present an initial, and critical, evaluation of the limitations and biases of current iDNA protocols for biodiversity monitoring using both standard and NGS barcoding approaches. Key findings include the need for taxon relevant multi-locus markers and reference databases. In particular, the limitations of available reference databases have profound potential to mislead and bias eDNA and iDNA results if not critically interpreted. Nevertheless, there is great potential for recovery of amplifiable DNA from gut contents of invertebrate museum specimens which may reveal both temporal patterns and cryptic diversity in protected areas with increased efficiency. Our analyses of ingested DNA (iDNA) from both freshly stored and previously collected (legacy) samples of terrestrial leeches successfully identified vertebrates from Myanmar, Australia and Madagascar and indicate the potential to characterize microbial communities, pathogen diversity and interactions at low cost.},
}
@article {pmid30790985,
year = {2019},
author = {Li, B and Zhao, Z and Zhang, C and Li, S},
title = {Troglocoelotes gen. n., a new genus of Coelotinae spiders (Araneae, Agelenidae) from caves in South China.},
journal = {Zootaxa},
volume = {4554},
number = {1},
pages = {219-238},
doi = {10.11646/zootaxa.4554.1.7},
pmid = {30790985},
issn = {1175-5334},
mesh = {Animals ; Caves ; China ; *Spiders ; },
abstract = {A new genus Troglocoelotes Z. Zhao S. Li gen. n. from South China is described with the type species T. yumiganensis Z. Zhao S. Li sp. n. (♂♀) and eight additional species: T. bailongensis Z. Zhao S. Li sp. n. (♀), T. banmenensis Z. Zhao S. Li sp. n. (♀), T. liangensis Z. Zhao S. Li sp. n. (♂♀), T. nongchiensis Z. Zhao S. Li sp. n. (♀), T. qixianensis Z. Zhao S. Li sp. n. (♂♀), T. proximus (Chen, Zhu Kim, 2008) comb. n. (♀), T. tortus (Chen, Zhu Kim, 2008) comb. n. (♂♀) and T. yosiianus (Nishikawa, 1999) comb. n (♀). All species are cave dwellers and not found outside of caves. New combinations are all ex-Draconarius Ovtchinnikov, 1999. DNA barcodes are provided for all species.},
}
@article {pmid30790946,
year = {2019},
author = {Hsu, YF and Xue, GX and Lin, RJ and Huang, L},
title = {Resurrection of Caltoris ranrunna (Sonan) from synonymy as a skipper endemic to Taiwan based on COI barcode and morphology.},
journal = {Zootaxa},
volume = {4555},
number = {1},
pages = {56-66},
doi = {10.11646/zootaxa.4555.1.4},
pmid = {30790946},
issn = {1175-5334},
mesh = {Animals ; Asia ; DNA Barcoding, Taxonomic ; Female ; Genitalia ; *Lepidoptera ; Male ; Taiwan ; },
abstract = {Caltoris ranrunna (Sonan, 1936) is resurrected from synonymy of Caltoris cahira austeni (Moore, 1883) to represent a Caltoris species endemic to Taiwan based upon COI barcode divergence and morphological diagnosis in genitalia of both sexes. This species distributes allopatrically from C. cahira of continental Asia and Andamans.},
}
@article {pmid30790927,
year = {2019},
author = {Liao, CQ and Wang, M and Huang, GH},
title = {A new genus Gnathospinosa (Lepidoptera: Tineidae: Euplocaminae) from China, with description of a new species and its taxonomic position.},
journal = {Zootaxa},
volume = {4555},
number = {3},
pages = {416-424},
doi = {10.11646/zootaxa.4555.3.10},
pmid = {30790927},
issn = {1175-5334},
mesh = {Animals ; China ; Genes, Mitochondrial ; Genitalia, Male ; *Lepidoptera ; Male ; Phylogeny ; },
abstract = {The genus Gnathospinosa Liao Huang, gen. nov., belonging to the subfamily Euplocaminae, is described with a new species G. qinlingensis Liao Huang, sp. nov. from China as its type species. The new species was illustrated with photographs of the adults and male genitalia. A preliminary phylogenetic study based on mitochondrial cytochrome c oxidase subunit I gene (co1) sequence data of the new species and Psecadioides cuneus are presented.},
}
@article {pmid30790893,
year = {2019},
author = {Wu, X and Liu, Z and Chen, Y and Wang, B},
title = {Description of larva of Euphaea superba Kimmins, 1936 (Odonata: Zygoptera: Euphaeidae) from China.},
journal = {Zootaxa},
volume = {4545},
number = {4},
pages = {585-592},
doi = {10.11646/zootaxa.4545.4.9},
pmid = {30790893},
issn = {1175-5334},
mesh = {Animal Structures ; Animals ; Body Size ; China ; Female ; Larva ; Male ; *Odonata ; },
abstract = {The final stadium larva of Euphaea superba Kimmins, 1936 is described and illustrated based on a male and a female specimens collected in Zhejiang province, China. The larvae were associated with the adults by mtCOI gene sequence. The larva of E. superba is diagnosed from other described members of the genus by the gena having 2-4 spines on outer side, the movable hook about 1.6 time as long as median cleft and female with primary genitalia extending to the posterior margin of abdominal segment 10.},
}
@article {pmid30790892,
year = {2019},
author = {Liu, T and Wang, H},
title = {Bucculatrix crataega sp. nov. (Lepidoptera: Bucculatricidae), a leaf miner on Crataegus, representing the first formally named species of the family from mainland China.},
journal = {Zootaxa},
volume = {4545},
number = {4},
pages = {578-584},
doi = {10.11646/zootaxa.4545.4.8},
pmid = {30790892},
issn = {1175-5334},
mesh = {Animals ; China ; *Crataegus ; Female ; Genitalia ; *Lepidoptera ; Male ; *Moths ; Plants ; },
abstract = {A new leaf-mining species of the genus Bucculatrix Zeller, 1839, B. crataega Liu, sp. nov., feeding on Crataegus pinnatifida Bunge is described herein, representing the first formally named species of Bucculatricidae from mainland China. Adult and genitalia of both sexes are described and illustrated. Host plant, leaf mine and cocoon are also illustrated. DNA barcode analysis supports the separation of B. crataega from related species.},
}
@article {pmid30790885,
year = {2019},
author = {Kaila, L and Mutanen, M and Sihvonen, P and Tyllinen, J and Tabell, J},
title = {Characterization of Pleurotinae, with review of Pleurota species close to P. aristella (Linnaeus) from Morocco (Lepidoptera: Gelechioidea: Oecophoridae).},
journal = {Zootaxa},
volume = {4545},
number = {4},
pages = {451-477},
doi = {10.11646/zootaxa.4545.4.1},
pmid = {30790885},
issn = {1175-5334},
mesh = {Animals ; Morocco ; *Moths ; },
abstract = {Morphological traits characterizing and delimiting Pleurotinae (Oecophoridae) are provided and discussed. The evidence supports the validity of the subfamily as suggested by recent molecular studies. The Pleurota aristella (Linnaeus, 1767) species group is characterized, and six new species belonging to the group from Morocco are described: Pleurota tricolor Tabell, sp. nov., P. pellicolor Tabell, sp. nov., P. lacteella Tabell, sp. nov., P. moroccoensis Tabell, sp. nov., P. ochreopalpella Tabell, sp. nov., and P. atlasensis Tabell, sp. nov. Habitus images and label data are provided for the types of P. goundafella Zerny, 1935; P. insignella Zerny, 1935; P. ochreostrigella Baker, 1885; P. macrosella Rebel, 1900; P. staintoniella Baker, 1888; P. mauretanica Baker, 1888; and P. algeriella Baker, 1885. DNA barcodes of the new species are compared with all available Pleurotinae sequences (BIN n = 117) in BOLD.},
}
@article {pmid30790876,
year = {2019},
author = {Hrivniak, &#x13d; and Sroka, P and TÜrkmen, G and Godunko, RJ and Kazanci, N},
title = {A new Epeorus (Caucasiron) (Ephemeroptera: Heptageniidae) species from Turkey based on molecular and morphological evidence.},
journal = {Zootaxa},
volume = {4550},
number = {1},
pages = {58-70},
doi = {10.11646/zootaxa.4550.1.2},
pmid = {30790876},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; *Ephemeroptera ; Larva ; Turkey ; },
abstract = {Epeorus (Caucasiron) turcicus sp. nov. is described based on larvae from NE Turkey. The new species can be distinguished from other Caucasiron by a unique combination of several diagnostic characters: the presence of a rounded hypodermal medial femur spot, colouration of abdominal terga and sterna, narrow gill plate VII, fine hair-like setae on the surface of abdominal terga, and absence of postero-lateral projections on tergum X. In addition to morphological analysis, two single-locus analytical approaches are employed for delimiting the new species using COI sequences (Automatic Barcode Gap Discovery, ABGD; and General Mixed Yule Coalescent Model, GMYC). Both approaches unambiguously recognized E. (C.) turcicus sp. nov. as a distinct species. Our molecular dataset contains all Caucasiron species occurring in the Caucasus and the delimitation of individual species mostly follows the morphologically defined species. This study confirms the suitability of the GMYC approach for species delimitation within Caucasiron.},
}
@article {pmid30790821,
year = {2019},
author = {Botero-Trujillo, R and Ott, R and Mattoni, CI and Nime, MF and Ojanguren-Affilastro, AA},
title = {Two new species of the sun-spider genus Gaucha from Argentina and Brazil (Solifugae, Mummuciidae).},
journal = {Zootaxa},
volume = {4551},
number = {2},
pages = {180-194},
doi = {10.11646/zootaxa.4551.2.3},
pmid = {30790821},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; *Arachnida ; Argentina ; Brazil ; *Spiders ; },
abstract = {Two new species in the South American sun-spider family Mummuciidae are herein described. Gaucha ramirezi sp. nov. is known from the Chancaní Provincial Park and Forest Reserve, Córdoba province, Argentina, and further reported for a single locality to the northeast, in Santiago del Estero province. The systematic position of this species is uncertain and it is not assigned to any species-group of Gaucha Mello-Leitão, 1924. The other species, Gaucha santana sp. nov., is only known from the Ibirapuitã Environmental Protection Area, in the southern Brazilian state of Rio Grande do Sul, and is a member of the fasciata species-group. With these descriptions, the number of known species of Gaucha is raised to eleven.},
}
@article {pmid30784950,
year = {2019},
author = {Li, Z and Liu, X and Yu, Y and Huang, H and Li, X and Ji, Q and Li, K and Yu, Y and Li, D and Mao, Z and Pu, Y and Chen, P and Chen, F},
title = {Barcoding for diatoms in the Yangtze River from the morphological observation and 18S rDNA polymorphic analysis.},
journal = {Forensic science international},
volume = {297},
number = {},
pages = {81-89},
doi = {10.1016/j.forsciint.2019.01.028},
pmid = {30784950},
issn = {1872-6283},
mesh = {China ; *DNA Barcoding, Taxonomic ; *DNA, Ribosomal ; Diatoms/*genetics ; Humans ; Microscopy ; Microscopy, Electron ; Phylogeny ; Polymerase Chain Reaction ; *RNA, Ribosomal, 18S ; Rivers ; Sequence Analysis, DNA ; },
abstract = {In forensic science, the determination of diatoms bears several goals, for example to estimate the post mortem interval (PMI), to determine the cause of death of a corpse found in water as well as to further locate the suspected drowning site. However, to identify diatoms using morphological method beyond the genus level is difficult and requires expert knowledge. During the last decade, a new concept of DNA barcode is becoming a promising approach to identify the taxa of diatoms. In the present study, we performed a diatom morphological analysis covering 10 different water areas in Nanjing section of the Yangtze River. The diatoms were classified to the 'genus' level by using optical microscope and electron microscope. According to the morphological study results, we further designed and analyzed the 18S rDNA sequences as barcodes at the 'species' level. Our study established the morphological and DNA barcoding profile for the diatoms in Nanjing section of the Yangtze River for the first time which will be of great significance for the using of diatoms in forensic application. The results indicated that detailed analysis of selected diatom DNA barcodes can be used as a useful tool for forensic applications.},
}
@article {pmid30784258,
year = {2019},
author = {Kaur, A and Sapkota, K and Dhakal, S},
title = {Multiplexed Nucleic Acid Sensing with Single-Molecule FRET.},
journal = {ACS sensors},
volume = {4},
number = {3},
pages = {623-633},
doi = {10.1021/acssensors.8b01373},
pmid = {30784258},
issn = {2379-3694},
mesh = {Biosensing Techniques/*methods ; DNA/*analysis/genetics ; DNA Probes/chemistry ; *Fluorescence Resonance Energy Transfer ; Inverted Repeat Sequences ; Polymorphism, Single Nucleotide ; },
abstract = {Multiplex detection of biomolecules is important in bionanotechnology and clinical diagnostics. Multiplexing using engineered solutions such as microarrays, synthetic nanopores, and DNA barcodes is promising, but they require sophisticated design/engineering and typically yield semiquantitative information. Single-molecule fluorescence resonance energy transfer (smFRET) is an attractive tool in this regard as it enables both sensitive and quantitative detection. However, multiplexing with smFRET remains a great challenge as it requires either multiple excitation sources, an antenna system created by multiple FRET pairs, or multiple acceptors of the donor fluorophore, which complicates not only the labeling schemes but also data analysis, due to overlapping of FRET efficiencies (EFRET). Here, we address these currently outstanding issues by designing interconvertible hairpin-based sensors (iHabSs) with nonoverlapping EFRET utilizing a single donor/acceptor pair and demonstrate a high-confidence multiplex detection of unlabeled nucleic acid sequences. We validated the reliability of our approach by systematically omitting one target at a time. Further, we demonstrate that these iHabSs are fully recyclable, sensitive with a limit of detection of ∼200 pM, and able to discriminate against single base mismatches. The multiplexed approach developed here has the potential to benefit the fields of biosensing and diagnostics by allowing simultaneous and quantitative detection of unlabeled nucleic acid biomarkers.},
}
@article {pmid30783180,
year = {2019},
author = {Belair, CD and Hu, T and Chu, B and Freimer, JW and Cooperberg, MR and Blelloch, RH},
title = {High-throughput, Efficient, and Unbiased Capture of Small RNAs from Low-input Samples for Sequencing.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {2262},
pmid = {30783180},
issn = {2045-2322},
support = {5F31CA200163//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/International ; U19CA179512//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/International ; R01 CA198145/CA/NCI NIH HHS/United States ; T32 HD007470/HD/NICHD NIH HHS/United States ; },
mesh = {*High-Throughput Nucleotide Sequencing ; Humans ; *MicroRNAs/chemistry/genetics/isolation &amp; purification/metabolism ; *Reverse Transcriptase Polymerase Chain Reaction ; *Sequence Analysis, RNA ; *Specimen Handling ; },
abstract = {MicroRNAs hold great promise as biomarkers of disease. However, there are few efficient and robust methods for measuring microRNAs from low input samples. Here, we develop a high-throughput sequencing protocol that efficiently captures small RNAs while minimizing inherent biases associated with library production. The protocol is based on early barcoding such that all downstream manipulations can be performed on a pool of many samples thereby reducing reagent usage and workload. We show that the optimization of adapter concentrations along with the addition of nucleotide modifications and random nucleotides increases the efficiency of small RNA capture. We further show, using unique molecular identifiers, that stochastic capture of low input RNA rather than PCR amplification influences the biased quantitation of intermediately and lowly expressed microRNAs. Our improved method allows the processing of tens to hundreds of samples simultaneously while retaining high efficiency quantitation of microRNAs in low input samples from tissues or bodily fluids.},
}
@article {pmid30783176,
year = {2019},
author = {Boutigny, AL and Barranger, A and De Boisséson, C and Blanchard, Y and Rolland, M},
title = {Targeted Next Generation Sequencing to study insert stability in genetically modified plants.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {2308},
pmid = {30783176},
issn = {2045-2322},
mesh = {High-Throughput Nucleotide Sequencing/*methods ; Humans ; Mutation/genetics ; Plants, Genetically Modified/*genetics ; },
abstract = {The EU directive 2001/18/EC requires any genetically modified (GM) event to be stable. In the present work, a targeted Next-Generation Sequencing (NGS) approach using barcodes to specifically tag each individual DNA molecules during library preparation was implemented to detect mutations taking into account the background noise due to amplification and sequencing errors. The method was first showed to be efficient in detecting the mutations in synthetic samples prepared with custom-synthesized mutated or non-mutated P35S sequences mixed in different proportions. The genetic stability of a portion of the P35S promoter targeted for GM detection was then analyzed in GM flour samples. Several low frequency mutations were detected in the P35S sequences. Some mutated nucleotides were located within the primers and probes used in the P35S diagnostic test. If present not as somatic mutations but as the consensus sequence of some individuals, these mutations could influence the efficiency of the P35S real time PCR diagnostic test. This methodology could be implemented in genetic stability studies of GM inserts but also to detect single nucleotide mutant GM plants produced using "new breeding techniques".},
}
@article {pmid30783092,
year = {2019},
author = {Pedersen, NW and Holm, A and Kristensen, NP and Bjerregaard, AM and Bentzen, AK and Marquard, AM and Tamhane, T and Burgdorf, KS and Ullum, H and Jennum, P and Knudsen, S and Hadrup, SR and Kornum, BR},
title = {CD8[+] T cells from patients with narcolepsy and healthy controls recognize hypocretin neuron-specific antigens.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {837},
pmid = {30783092},
issn = {2041-1723},
mesh = {Adolescent ; Adult ; CD8-Positive T-Lymphocytes/*immunology ; Case-Control Studies ; Child ; Female ; Genetic Predisposition to Disease ; HLA-DQ beta-Chains/*genetics ; Humans ; Male ; Middle Aged ; Narcolepsy/genetics/*immunology ; Neurons/metabolism ; Orexins/*immunology/metabolism ; Peptides/*immunology ; },
abstract = {Narcolepsy Type 1 (NT1) is a neurological sleep disorder, characterized by the loss of hypocretin/orexin signaling in the brain. Genetic, epidemiological and experimental data support the hypothesis that NT1 is a T-cell-mediated autoimmune disease targeting the hypocretin producing neurons. While autoreactive CD4[+] T cells have been detected in patients, CD8[+] T cells have only been examined to a minor extent. Here we detect CD8[+] T cells specific toward narcolepsy-relevant peptides presented primarily by NT1-associated HLA types in the blood of 20 patients with NT1 as well as in 52 healthy controls, using peptide-MHC-I multimers labeled with DNA barcodes. In healthy controls carrying the disease-predisposing HLA-DQB1*06:02 allele, the frequency of autoreactive CD8[+] T cells was lower as compared with both NT1 patients and HLA-DQB1*06:02-negative healthy individuals. These findings suggest that a certain level of CD8[+] T-cell reactivity combined with HLA-DQB1*06:02 expression is important for NT1 development.},
}
@article {pmid30779309,
year = {2019},
author = {Braukmann, TWA and Ivanova, NV and Prosser, SWJ and Elbrecht, V and Steinke, D and Ratnasingham, S and de Waard, JR and Sones, JE and Zakharov, EV and Hebert, PDN},
title = {Metabarcoding a diverse arthropod mock community.},
journal = {Molecular ecology resources},
volume = {19},
number = {3},
pages = {711-727},
pmid = {30779309},
issn = {1755-0998},
support = {//Ministry of Research, Innovation and Science/ ; },
mesh = {Animals ; Arthropods/*classification/*genetics ; DNA/chemistry/genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; *Metagenome ; Models, Theoretical ; Sequence Analysis, DNA ; },
abstract = {Although DNA metabarcoding is an attractive approach for monitoring biodiversity, it is often difficult to detect all the species present in a bulk sample. In particular, sequence recovery for a given species depends on its biomass and mitome copy number as well as the primer set employed for PCR. To examine these variables, we constructed a mock community of terrestrial arthropods comprised of 374 species. We used this community to examine how species recovery was impacted when amplicon pools were constructed in four ways. The first two protocols involved the construction of bulk DNA extracts from different body segments (Bulk Abdomen, Bulk Leg). The other protocols involved the production of DNA extracts from single legs which were then merged prior to PCR (Composite Leg) or PCR-amplified separately (Single Leg) and then pooled. The amplicons generated by these four treatments were then sequenced on three platforms (Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5). The choice of sequencing platform did not substantially influence species recovery, although the Miseq delivered the highest sequence quality. As expected, species recovery was most efficient from the Single Leg treatment because amplicon abundance varied little among taxa. Among the three treatments where PCR occurred after pooling, the Bulk Abdomen treatment produced a more uniform read abundance than the Bulk Leg or Composite Leg treatment. Primer choice also influenced species recovery and evenness. Our results reveal how variation in protocols can have substantial impacts on perceived diversity unless sequencing coverage is sufficient to reach an asymptote.},
}
@article {pmid30779047,
year = {2019},
author = {Alcaide, M and Rushton, C and Morin, RD},
title = {Ultrasensitive Detection of Circulating Tumor DNA in Lymphoma via Targeted Hybridization Capture and Deep Sequencing of Barcoded Libraries.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1956},
number = {},
pages = {383-435},
doi = {10.1007/978-1-4939-9151-8_20},
pmid = {30779047},
issn = {1940-6029},
mesh = {Blood Specimen Collection/methods ; Circulating Tumor DNA/blood/*genetics ; DNA Barcoding, Taxonomic/methods ; DNA Mutational Analysis/methods ; *Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Liquid Biopsy/*methods ; Lymphoma/blood/*genetics ; Nucleic Acid Hybridization/methods ; },
abstract = {Liquid biopsies are rapidly emerging as powerful tools for the early detection of cancer, noninvasive genomic profiling of localized or metastatic tumors, prompt detection of treatment resistance-associated mutations, and monitoring of therapeutic response and minimal residual disease in patients during clinical follow-up. Growing evidence strongly supports the utility of circulating tumor DNA (ctDNA) as a biomarker for the stratification and clinical management of lymphoma patients. However, ctDNA is diluted by variable amounts of cell-free DNA (cfDNA) shed by nonneoplastic cells causing a background signal of wild-type DNA that limits the sensitivity of methods that rely on DNA sequencing. Here, we describe an error suppression method for single-molecule counting that relies on targeted sequencing of cfDNA libraries constructed with semi-degenerate barcode adapters. Custom pools of biotinylated DNA baits for target enrichment can be designed to specifically track somatic mutations in one patient, survey mutation hotspots with diagnostic and prognostic value or be comprised of comprehensive gene panels with broad patient coverage in lymphoma. Such methods are amenable to track ctDNA levels during longitudinal liquid biopsy testing with high specificity and sensitivity and characterize, in real time, the genetic profiles of tumors without the need of standard invasive biopsies. The analysis of ultra-deep sequencing data according to the bioinformatics pipelines also described in this chapter affords to harness lower limits of detection for ctDNA below 0.1%.},
}
@article {pmid30779041,
year = {2019},
author = {Bagnoli, JW and Wange, LE and Janjic, A and Enard, W},
title = {Studying Cancer Heterogeneity by Single-Cell RNA Sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1956},
number = {},
pages = {305-319},
doi = {10.1007/978-1-4939-9151-8_14},
pmid = {30779041},
issn = {1940-6029},
mesh = {DNA, Complementary/genetics ; Flow Cytometry/methods ; Gene Library ; Humans ; Neoplasms/*genetics ; RNA/*genetics/isolation &amp; purification ; Reverse Transcription ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis/*methods ; Software ; *Transcriptome ; Workflow ; },
abstract = {A major hurdle for the treatment of cancer is the incomplete understanding of its evolution through the course of its emergence, dispersal, and relapse. Genetic and epigenetic changes in combination with external cues and selective forces are the driving factors behind tumor heterogeneity. Understanding this variability within and across patients may partly explain the unpredictable outcomes of cancer treatments. Measuring the variation of gene expression levels within cells of the same tumor is a crucial part of this endeavor. Hence, the recently developed single-cell RNA-sequencing (scRNA-seq) technologies have become a valuable tool for cancer research. In practice, however, this is still challenging, especially for clinical samples. Here, we describe mcSCRB-seq (molecular crowding single-cell RNA barcoding and sequencing), a highly sensitive and powerful plate-based scRNA-seq method, which shows great capability to generate transcriptome data for cancer cells. mcSCRB-seq is not only characterized by high sensitivity due to molecular crowding and the use of unique molecular identifiers (UMIs) but also features an easy workflow and a low per-cell cost and does not require specialized equipment.},
}
@article {pmid30773819,
year = {2019},
author = {Grealy, A and Bunce, M and Holleley, CE},
title = {Avian mitochondrial genomes retrieved from museum eggshell.},
journal = {Molecular ecology resources},
volume = {19},
number = {4},
pages = {1052-1062},
doi = {10.1111/1755-0998.13007},
pmid = {30773819},
issn = {1755-0998},
support = {DP160104473//Australian Research Council/ ; DP180100021//Australian Research Council/ ; //CSIRO Strategic Investment Funds (NCRA)/ ; },
mesh = {Animals ; Australia ; *Birds ; DNA, Mitochondrial/*genetics/*isolation &amp; purification ; Egg Shell/*chemistry ; *Genome, Mitochondrial ; Museums ; Sequence Analysis, DNA ; },
abstract = {Avian eggshell is a bio-ceramic material with exceptional properties for preserving DNA within its crystalline structure, presenting an opportunity to retrieve genomic information from extinct or historical populations of birds. However, intracrystalline DNA has only been recovered from the large, thick eggshell of palaeognaths; members of their more-diverse sister group (neognaths) lay smaller, thinner eggs that may not exhibit the same propensity for DNA preservation. Here, we use three 40-60-year-old museum eggshell specimens of Australian neognath birds to determine the minimum mass of eggshell from which intracrystalline DNA can be retrieved, and to characterize the yield and quality of such DNA. In doing so, we describe the first protocol for successful extraction of intracrystalline DNA from neognath eggshells, with the view to unlocking the potential of vast museum egg collections for genetic research. We were able to retrieve DNA fragments over 200 bp in length from 10 mg of eggshell powder from all three specimens, and demonstrate that expanding the existing blow-hole can allow sufficient material to be collected for DNA extraction while minimizing damage to the appearance and structural integrity of the egg. Furthermore, we were able to reconstruct near-complete mitochondrial genomes at a coverage of 40-83X through shotgun sequencing of these extracts on three NextSeq lanes. Given the current extinction and extirpation rates of many avian species world-wide, genetic data from eggshell could provide a rapid and cost-effective approach to examining temporal changes in avian diversity, which is not only becoming crucial for conservation management, but also serve to deepen our understanding of genome-wide evolutionary processes.},
}
@article {pmid30770823,
year = {2019},
author = {Merino, D and Weber, TS and Serrano, A and Vaillant, F and Liu, K and Pal, B and Di Stefano, L and Schreuder, J and Lin, D and Chen, Y and Asselin-Labat, ML and Schumacher, TN and Cameron, D and Smyth, GK and Papenfuss, AT and Lindeman, GJ and Visvader, JE and Naik, SH},
title = {Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {766},
pmid = {30770823},
issn = {2041-1723},
mesh = {Animals ; BRCA1 Protein/genetics ; Cell Line, Tumor ; Cisplatin/therapeutic use ; *Clone Cells ; Disease Models, Animal ; Female ; Gene Expression Regulation, Neoplastic/genetics ; Humans ; Mice ; Mutation/genetics ; Neoplasm Recurrence, Local/genetics ; Triple Negative Breast Neoplasms/drug therapy/*genetics ; Xenograft Model Antitumor Assays ; },
abstract = {Primary triple negative breast cancers (TNBC) are prone to dissemination but sub-clonal relationships between tumors and resulting metastases are poorly understood. Here we use cellular barcoding of two treatment-naïve TNBC patient-derived xenografts (PDXs) to track the spatio-temporal fate of thousands of barcoded clones in primary tumors, and their metastases. Tumor resection had a major impact on reducing clonal diversity in secondary sites, indicating that most disseminated tumor cells lacked the capacity to 'seed', hence originated from 'shedders' that did not persist. The few clones that continued to grow after resection i.e. 'seeders', did not correlate in frequency with their parental clones in primary tumors. Cisplatin treatment of one BRCA1-mutated PDX model to non-palpable levels had a surprisingly minor impact on clonal diversity in the relapsed tumor yet purged 50% of distal clones. Therefore, clonal features of shedding, seeding and drug resistance are important factors to consider for the design of therapeutic strategies.},
}
@article {pmid30764600,
year = {2019},
author = {Wu, SS and Lee, JH and Koo, BK},
title = {Lineage Tracing: Computational Reconstruction Goes Beyond the Limit of Imaging.},
journal = {Molecules and cells},
volume = {42},
number = {2},
pages = {104-112},
pmid = {30764600},
issn = {0219-1032},
mesh = {Animals ; *Cell Lineage/genetics ; *Computer Simulation ; Humans ; *Imaging, Three-Dimensional ; Mutation/genetics ; RNA/metabolism ; },
abstract = {Tracking the fate of individual cells and their progeny through lineage tracing has been widely used to investigate various biological processes including embryonic development, homeostatic tissue turnover, and stem cell function in regeneration and disease. Conventional lineage tracing involves the marking of cells either with dyes or nucleoside analogues or genetic marking with fluorescent and/or colorimetric protein reporters. Both are imaging-based approaches that have played a crucial role in the field of developmental biology as well as adult stem cell biology. However, imaging-based lineage tracing approaches are limited by their scalability and the lack of molecular information underlying fate transitions. Recently, computational biology approaches have been combined with diverse tracing methods to overcome these limitations and so provide high-order scalability and a wealth of molecular information. In this review, we will introduce such novel computational methods, starting from single-cell RNA sequencing-based lineage analysis to DNA barcoding or genetic scar analysis. These novel approaches are complementary to conventional imaging-based approaches and enable us to study the lineage relationships of numerous cell types during vertebrate, and in particular human, development and disease.},
}
@article {pmid30760303,
year = {2019},
author = {Sarmashghi, S and Bohmann, K and P Gilbert, MT and Bafna, V and Mirarab, S},
title = {Skmer: assembly-free and alignment-free sample identification using genome skims.},
journal = {Genome biology},
volume = {20},
number = {1},
pages = {34},
pmid = {30760303},
issn = {1474-760X},
support = {R01 GM114362/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Birds/genetics ; DNA Barcoding, Taxonomic/*methods ; *Genome, Insect ; Genomics/*methods ; *Models, Genetic ; Phylogeny ; },
abstract = {The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short markers by applying low-pass sequencing and recovering whole organelle genomes computationally. This approach discards the nuclear DNA, which constitutes the vast majority of the data. In contrast, we suggest using all unassembled reads. We introduce an assembly-free and alignment-free tool, Skmer, to compute genomic distances between the query and reference genome skims. Skmer shows excellent accuracy in estimating distances and identifying the closest match in reference datasets.},
}
@article {pmid30758899,
year = {2019},
author = {Thongjued, K and Chotigeat, W and Bumrungsri, S and Thanakiatkrai, P and Kitpipit, T},
title = {A new cost-effective and fast direct PCR protocol for insects based on PBS buffer.},
journal = {Molecular ecology resources},
volume = {19},
number = {3},
pages = {691-701},
doi = {10.1111/1755-0998.13005},
pmid = {30758899},
issn = {1755-0998},
support = {P//National Science and Technology Development Agency/ ; -//National Science and Technology Development Agency/ ; 14//National Science and Technology Development Agency/ ; -//National Science and Technology Development Agency/ ; 50620//National Science and Technology Development Agency/ ; },
mesh = {Animals ; *Buffers ; Costs and Cost Analysis ; DNA/genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic/economics/*methods ; Entomology/economics/*methods ; Insecta/*classification/*genetics ; Polymerase Chain Reaction/economics/*methods ; Workflow ; },
abstract = {Insect DNA barcoding is a species identification technique used in biodiversity assessment and ecological studies. However, DNA extraction can result in the loss of up to 70% of DNA. Recent research has reported that direct PCR can overcome this issue. However, the success rates could still be improved, and tissues used for direct PCR could not be reused for further genetic studies. Here, we developed a direct PCR workflow that incorporates a 2-min sample preparation in PBS-buffer step for fast and effective universal insect species identification. The developed protocol achieved 100% success rates for amplification in six orders: Mantodea, Phasmatodea, Neuroptera, Odonata, Blattodea and Orthoptera. High and moderate success rates were obtained for five other species: Lepidoptera (97.3%), Coleoptera (93.8%), Diptera (90.5%), Hemiptera (81.8%) and Hymenoptera (75.0%). High-quality sequencing data were also obtained from these amplifiable products, allowing confidence in species identification. The method was sensitive down to 1/4th of a 1-mm fragment of leg or body and its success rates with oven-dried, ethanol-preserved, food, bat guano and museum specimens were 100%, 98.6%, 90.0%, 84.0% and 30.0%, respectively. In addition, the pre-PCR solution (PBS with insect tissues) could be used for further DNA extraction if needed. The workflow will be beneficial in the fields of insect taxonomy and ecological studies due to its low cost, simplicity and applicability to highly degraded specimens.},
}
@article {pmid30758302,
year = {2019},
author = {Shahraki, AH and Chaganti, SR and Heath, D},
title = {Assessing high-throughput environmental DNA extraction methods for meta-barcode characterization of aquatic microbial communities.},
journal = {Journal of water and health},
volume = {17},
number = {1},
pages = {37-49},
doi = {10.2166/wh.2018.108},
pmid = {30758302},
issn = {1477-8920},
mesh = {*DNA ; Environmental Monitoring ; *Microbiota ; *Water Microbiology ; },
abstract = {The characterization of microbial community dynamics using genomic methods is rapidly expanding, impacting many fields including medical, ecological, and environmental research and applications. One of the biggest challenges for such studies is the isolation of environmental DNA (eDNA) from a variety of samples, diverse microbes, and widely variable community compositions. The current study developed environmentally friendly, user safe, economical, and high throughput eDNA extraction methods for mixed aquatic microbial communities and tested them using 16 s rRNA gene meta-barcoding. Five different lysis buffers including (1) cetyltrimethylammonium bromide (CTAB), (2) digestion buffer (DB), (3) guanidinium isothiocyanate (GITC), (4) sucrose lysis (SL), and (5) SL-CTAB, coupled with four different purification methods: (1) phenol-chloroform-isoamyl alcohol (PCI), (2) magnetic Bead-Robotic, (3) magnetic Bead-Manual, and (4) membrane-filtration were tested for their efficacy in extracting eDNA from recreational freshwater samples. Results indicated that the CTAB-PCI and SL-Bead-Robotic methods yielded the highest genomic eDNA concentrations and succeeded in detecting the core microbial community including the rare microbes. However, our study recommends the SL-Bead-Robotic eDNA extraction protocol because this method is safe, environmentally friendly, rapid, high-throughput and inexpensive.},
}
@article {pmid30758186,
year = {2019},
author = {Jin, Q and Fan, X and Chen, C and Huang, L and Wang, J and Tang, X},
title = {Multicolor Raman Beads for Multiplexed Tumor Cell and Tissue Imaging and in Vivo Tumor Spectral Detection.},
journal = {Analytical chemistry},
volume = {91},
number = {6},
pages = {3784-3789},
doi = {10.1021/acs.analchem.9b00028},
pmid = {30758186},
issn = {1520-6882},
mesh = {Animals ; Cell Line, Tumor ; Color ; Humans ; Mice ; *Microspheres ; Molecular Imaging/*methods ; Spectrum Analysis, Raman/*methods ; },
abstract = {Developing new nanomaterials with strong and distinctive Raman vibrations in the biological Raman-silent region (1800-2800 cm[-1]) were highly desirable for Raman hyperspectral detection and imaging in living cells and animals. Herein, polymeric nanoparticles with monomers containing alkyne, cyanide, azide, and carbon-deuterate were prepared as Raman-active nanomaterials (Raman beads) for bioimaging applications. Intense Raman signals were obtained due to the high density of alkyne, cyanide, azide, and carbon-deuterate in single nanoparticles, in absence of metal (such as Au or Ag) as Raman enhancers. We have developed a library of Raman beads for frequency multiplexing through the end-capping substitutions of monomers and demonstrated five-color SRS imaging of mixed nanoparticles with distinct Raman frequencies. In addition, with further surface functionalization of targeting moieties (such as nucleic acid aptamers and targeting peptides), targetable Raman beads were successfully used as probes for tumor targeting and Raman spectroscopic detection, including multicolor SRS imaging in living tumor cells and tissues with high specificity. Further in vivo studies indicated that Raman beads anchored with targeting moieties were successfully employed to target tumors in living mice after tail intravenous injection, and Raman spectral detection of tumor in live mice was achieved only through spontaneous Raman signal at the biological Raman-silent region without any signal enhancement due to a high density of Raman reporters in Raman beads. With further copolymerization of these monomers, Raman beads with supermultiplex barcoding could be readily achieved.},
}
@article {pmid30755235,
year = {2019},
author = {Kotowski, MA and Pietras, M and Łuczaj, &#x141;},
title = {Extreme levels of mycophilia documented in Mazovia, a region of Poland.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {15},
number = {1},
pages = {12},
pmid = {30755235},
issn = {1746-4269},
support = {Preludium no. 2015/17/N/NZ9/00963//Narodowe Centrum Nauki/ ; },
mesh = {Adolescent ; Adult ; Agaricales/*classification ; Aged ; Aged, 80 and over ; DNA Barcoding, Taxonomic ; *Diet ; Female ; *Food ; Humans ; Male ; Middle Aged ; Poland ; Young Adult ; },
abstract = {BACKGROUND: The paper presents documentation of the traditional use of wild edible mushrooms in Mazovia (33,900 km[2]), a region of Poland.<br><br>METHODS: A total of 695 semi-structured interviews were carried out among local informants in 38 localities proportionally distributed throughout the study area (one locality approximately every 30&#x2009;km), asking which mushrooms they collected and how. The species utilized were identified using visual props, morphological identification of voucher specimens, and DNA barcoding.<br><br>RESULTS: Altogether, 92 taxa identified to the species or genus level were recorded, among them 76 species used as food, 21 taxa known as toxic, and 11 taxa used for non-culinary purposes. Out of 76 identified edible fungi species, 47% (36 species) were identified using ITS DNA barcode method. Eleven of them were identified exclusively by molecular analysis. The mean number of edible taxa mentioned per interview was 9.5. Two species new to the mycobiota of Poland, Hydnum ellipsosporum and Paxillus cuprinus, were found. Frequent interaction with mushroom collectors enabled the transcription of local folk taxonomy into proper taxonomic classification and the definition of changes in local preferences concerning wild fungi collection.<br><br>CONCLUSIONS: The list of species utilized is the longest regional list of edible mushrooms ever recorded during ethnomycological field research, putting the inhabitants of the studied region at the top of the mycophilia spectrum.},
}
@article {pmid30748040,
year = {2019},
author = {Paunovska, K and Da Silva Sanchez, AJ and Sago, CD and Gan, Z and Lokugamage, MP and Islam, FZ and Kalathoor, S and Krupczak, BR and Dahlman, JE},
title = {Nanoparticles Containing Oxidized Cholesterol Deliver mRNA to the Liver Microenvironment at Clinically Relevant Doses.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {31},
number = {14},
pages = {e1807748},
pmid = {30748040},
issn = {1521-4095},
support = {T32 EB021962/EB/NIBIB NIH HHS/United States ; T32 GM008433/GM/NIGMS NIH HHS/United States ; T32 GM105490/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Cellular Microenvironment ; Cholesterol/*chemistry ; Drug Carriers/*chemistry ; Liver/*cytology ; Mice ; Nanoparticles/*chemistry ; Oxidation-Reduction ; RNA, Messenger/chemistry/metabolism ; },
abstract = {Using mRNA to produce therapeutic proteins is a promising approach to treat genetic diseases. However, systemically delivering mRNA to cell types besides hepatocytes remains challenging. Fast identification of nanoparticle delivery (FIND) is a DNA barcode-based system designed to measure how over 100 lipid nanoparticles (LNPs) deliver mRNA that functions in the cytoplasm of target cells in a single mouse. By using FIND to quantify how 75 chemically distinct LNPs delivered mRNA to 28 cell types in vivo, it is found that an LNP formulated with oxidized cholesterol and no targeting ligand delivers Cre mRNA, which edits DNA in hepatic endothelial cells and Kupffer cells at 0.05 mg kg[-1] . Notably, the LNP targets liver microenvironmental cells fivefold more potently than hepatocytes. The structure of the oxidized cholesterols added to the LNP is systematically varied to show that the position of the oxidative modification may be important; cholesterols modified on the hydrocarbon tail associated with sterol ring D tend to outperform cholesterols modified on sterol ring B. These data suggest that LNPs formulated with modified cholesterols can deliver gene-editing mRNA to the liver microenvironment at clinically relevant doses.},
}
@article {pmid30746727,
year = {2019},
author = {Bilbija, B and Auer, M and Široký, P},
title = {Long term persistence of introduced Amblyomma geoemydae tick population under indoor conditions in Austria.},
journal = {Medical and veterinary entomology},
volume = {33},
number = {2},
pages = {317-321},
doi = {10.1111/mve.12361},
pmid = {30746727},
issn = {1365-2915},
mesh = {Animals ; Animals, Zoo ; Austria ; DNA Barcoding, Taxonomic/veterinary ; Female ; Introduced Species ; Ixodidae/classification/genetics/growth &amp; development/*physiology ; Larva/classification/genetics/growth &amp; development/physiology ; Nymph/classification/genetics/growth &amp; development/physiology ; Seasons ; Tick Infestations/parasitology/prevention &amp; control/*veterinary ; *Turtles ; },
abstract = {An indoor terrarium population of Amblyomma geoemydae was established subsequent to the import of a single yellow-marginated box turtle Cuora flavomarginata. This indoor tick population revealed an unexpected resistance against de-ticking trials, with persistence between 2010 and 2015, when the ticks were successfully eliminated. Ticks were collected from the bodies and shells of turtles, as well as from terraria soil. Species diagnosis of ticks was carried out according to distinguishable morphological characters and supported by molecular analysis using DNA-barcoding. Introduced exotic ticks are potential vectors of pathogens and can have an impact on wildlife, domestic animals and the human population. This case emphasizes the need for sharp surveillance and control measures on imported reptiles.},
}
@article {pmid30746694,
year = {2019},
author = {Wu, J and Dai, W and Wu, L and Li, W and Xia, X and Wang, J},
title = {Decoding genetic and epigenetic information embedded in cell free DNA with adapted SALP-seq.},
journal = {International journal of cancer},
volume = {145},
number = {9},
pages = {2395-2406},
doi = {10.1002/ijc.32206},
pmid = {30746694},
issn = {1097-0215},
mesh = {Case-Control Studies ; Cell-Free Nucleic Acids/*genetics ; Epigenesis, Genetic ; Esophageal Neoplasms/*genetics ; Female ; Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Oligonucleotide Probes/genetics ; },
abstract = {Cell free DNA (cfDNA) in human plasma carries abundant information, which has therefore been the key sample for noninvasive prenatal testing (NIPT) and liquid biopsy. Especially by using the rapidly developed next-generation sequencing (NGS) techniques, the genetic and epigenetic information embedded in cfDNA has been effectively and extensively decoded. In this process, a key step is to construct the NGS library. Due to its high degradation, the single strand-based method was reported to be more qualified to construct the NGS library of cfDNA. In order to develop a new simple method for this application, this study adapted our recently developed single strand adaptor library preparation (SALP) method for constructing an NGS library of cfDNA. In the improved method, cfDNA was firstly denatured into single strands and then ligated with a single strand adaptor (SSA) that had a 3' overhang of 3 random bases by using T4 DNA ligase. The SSA-ligated DNA was converted into double-stranded DNA with an additional adenine at the other end by polymerizing with Taq polymerase. Next, a barcode T adaptor (BTA) was ligated to this end. Finally, the cfDNA ligated with two adaptors was amplified with the Illumina-compatible primers for NGS. Using the method, this study successfully sequenced 20 cfDNA samples from 16 esophageal cancer patients and 4 healthy people. By bioinformatics analysis, this study found the genetic and epigenetic difference between patients and healthy people and identified 23 epigenetic and 28 genetic altered esophageal cancer-specific genes.},
}
@article {pmid30745797,
year = {2019},
author = {Sudasinghe, H and Pethiyagoda, R and Maduwage, K and Madhava Meegaskumbura, },
title = {The identity of the Sri Lankan Amblypharyngodon (Teleostei, Cyprinidae).},
journal = {ZooKeys},
volume = {},
number = {820},
pages = {25-49},
pmid = {30745797},
issn = {1313-2989},
abstract = {Morphological and molecular analyses of specimens representative of the geographic range of the cyprinid genus Amblypharyngodon in Sri Lanka suggest the presence of only a single species in the island, for which the name Amblypharyngodongrandisquamis Jordan &amp; Starks, 1917, is available. Amblypharyngodongrandisquamis is a species endemic to Sri Lanka, distributed across the lowlands of both of the island's main climatic zones. It is distinguished from all other species of Amblypharyngodon, including the three species recorded from peninsular India (A.mola, A.microlepis, and A.melettinus), by a suite of characters that includes a body depth of 26.9-31.2% of the standard length (SL), 42-56 scales in the lateral series (of which usually 8-16 are pored), 20-24 circumpeduncular scales, 14-17 scale rows between the origins of the dorsal and pelvic fins, a dorsal-fin height of 21.1-27.6% SL, 18-19 caudal vertebrae and an eye diameter of 22.7-30.5% of the head length. Amblypharyngodongrandisquamis differs from A.melettinus and A.mola by uncorrected pairwise genetic distances of more than 9% and 6%, respectively, for the mitochondrial cytochrome oxidase subunit 1 (COI) gene.},
}
@article {pmid30744573,
year = {2019},
author = {Tizard, J and Patel, S and Waugh, J and Tavares, E and Bergmann, T and Gill, B and Norman, J and Christidis, L and Scofield, P and Haddrath, O and Baker, A and Lambert, D and Millar, C},
title = {DNA barcoding a unique avifauna: an important tool for evolution, systematics and conservation.},
journal = {BMC evolutionary biology},
volume = {19},
number = {1},
pages = {52},
pmid = {30744573},
issn = {1471-2148},
mesh = {Animals ; *Biological Evolution ; Birds/*classification/genetics ; *Conservation of Natural Resources ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Geography ; Islands ; New Zealand ; Phylogeny ; Species Specificity ; },
abstract = {BACKGROUND: DNA barcoding utilises a standardised region of the cytochrome c oxidase I (COI) gene to identify specimens to the species level. It has proven to be an effective tool for identification of avian samples. The unique island avifauna of New Zealand is taxonomically and evolutionarily distinct. We analysed COI sequence data in order to determine if DNA barcoding could accurately identify New Zealand birds.<br><br>RESULTS: We sequenced 928 specimens from 180 species. Additional Genbank sequences expanded the dataset to 1416 sequences from 211 of the estimated 236 New Zealand species. Furthermore, to improve the assessment of genetic variation in non-endemic species, and to assess the overall accuracy of our approach, sequences from 404 specimens collected outside of New Zealand were also included in our analyses. Of the 191 species represented by multiple sequences, 88.5% could be successfully identified by their DNA barcodes. This is likely a conservative estimate of the power of DNA barcoding in New Zealand, given our extensive geographic sampling. The majority of the 13 groups that could not be distinguished contain recently diverged taxa, indicating incomplete lineage sorting and in some cases hybridisation. In contrast, 16 species showed evidence of distinct intra-species lineages, some of these corresponding to recognised subspecies. For species identification purposes a character-based method was more successful than distance and phylogenetic tree-based methods.<br><br>CONCLUSIONS: DNA barcodes accurately identify most New Zealand bird species. However, low levels of COI sequence divergence in some recently diverged taxa limit the identification power of DNA barcoding. A small number of currently recognised species would benefit from further systematic investigations. The reference database and analysis presented will provide valuable insights into the evolution, systematics and conservation of New Zealand birds.},
}
@article {pmid30742542,
year = {2019},
author = {Chen, KC and Zakaria, D and Altarawneh, H and Andrews, GN and Ganesan, GS and John, KM and Khan, S and Ladumor, H},
title = {DNA barcoding of fish species reveals low rate of package mislabeling in Qatar.},
journal = {Genome},
volume = {62},
number = {2},
pages = {69-76},
doi = {10.1139/gen-2018-0101},
pmid = {30742542},
issn = {1480-3321},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Fish Products/*standards ; Fishes/*genetics ; Food Labeling/*standards ; Qatar ; },
abstract = {DNA barcoding technique has made it possible to authenticate various species used for food and medicinal purposes. In the identification of seafood species, studies are concentrated in North America, Europe, and Asia. Elsewhere, including countries in the Middle East and North Africa, studies of this sort are scarce. This study focuses on packaged fresh or minimally processed fish fillet available at eight major supermarket chains in Qatar. A cocktail of eight primers attached with M13 tails established for fish species identification was adopted to facilitate PCR and sequencing. Sequences were compared with those available in the Barcode of Life Databases (BOLD Systems) and BLAST in NCBI databases. Among the 62 unique fish packages with resolved sequences, only three are confirmed to be mislabeled, at a rate of about 5%. Two of the substituted species are high value items while the third species was replaced by another, equally low-cost species. The relatively low rate of mislabeling in the samples is perhaps a result of strict local food safety regulations, which may have led to high consistency between the package labels and their contents.},
}
@article {pmid30740824,
year = {2019},
author = {Gallon, R and Mühlegger, B and Wenzel, SS and Sheth, H and Hayes, C and Aretz, S and Dahan, K and Foulkes, W and Kratz, CP and Ripperger, T and Azizi, AA and Baris Feldman, H and Chong, AL and Demirsoy, U and Florkin, B and Imschweiler, T and Januszkiewicz-Lewandowska, D and Lobitz, S and Nathrath, M and Pander, HJ and Perez-Alonso, V and Perne, C and Ragab, I and Rosenbaum, T and Rueda, D and Seidel, MG and Suerink, M and Taeubner, J and Zimmermann, SY and Zschocke, J and Borthwick, GM and Burn, J and Jackson, MS and Santibanez-Koref, M and Wimmer, K},
title = {A sensitive and scalable microsatellite instability assay to diagnose constitutional mismatch repair deficiency by sequencing of peripheral blood leukocytes.},
journal = {Human mutation},
volume = {40},
number = {5},
pages = {649-655},
pmid = {30740824},
issn = {1098-1004},
support = {15934/CRUK_/Cancer Research UK/United Kingdom ; C569/A24991/CRUK_/Cancer Research UK/United Kingdom ; },
mesh = {Alleles ; Brain Neoplasms/*diagnosis/*genetics ; Colorectal Neoplasms/*diagnosis/*genetics ; *DNA Mismatch Repair ; *Genetic Association Studies/methods ; *Genetic Predisposition to Disease ; Germ-Line Mutation ; Humans ; Leukocytes/*metabolism ; *Microsatellite Instability ; Microsatellite Repeats ; Neoplastic Syndromes, Hereditary/*diagnosis/*genetics ; },
abstract = {Constitutional mismatch repair deficiency (CMMRD) is caused by germline pathogenic variants in both alleles of a mismatch repair gene. Patients have an exceptionally high risk of numerous pediatric malignancies and benefit from surveillance and adjusted treatment. The diversity of its manifestation, and ambiguous genotyping results, particularly from PMS2, can complicate diagnosis and preclude timely patient management. Assessment of low-level microsatellite instability in nonneoplastic tissues can detect CMMRD, but current techniques are laborious or of limited sensitivity. Here, we present a simple, scalable CMMRD diagnostic assay. It uses sequencing and molecular barcodes to detect low-frequency microsatellite variants in peripheral blood leukocytes and classifies samples using variant frequencies. We tested 30 samples from 26 genetically-confirmed CMMRD patients, and samples from 94 controls and 40 Lynch syndrome patients. All samples were correctly classified, except one from a CMMRD patient recovering from aplasia. However, additional samples from this same patient tested positive for CMMRD. The assay also confirmed CMMRD in six suspected patients. The assay is suitable for both rapid CMMRD diagnosis within clinical decision windows and scalable screening of at-risk populations. Its deployment will improve patient care, and better define the prevalence and phenotype of this likely underreported cancer syndrome.},
}
@article {pmid30740026,
year = {2019},
author = {Schilthuizen, M and Berenyi, AEA and Limin, A and Brahim, A and Cicuzza, D and Eales, AJ and Escoubas, P and Grafe, U and de Groot, MD and Hayden, WC and Paterno, M and Jambul, R and Slik, JWF and Ting Teck Wah, D and Tucker, A and Njunjić, I},
title = {A new species of Clavicornaltica (Coleoptera: Chrysomelidae), discovered and described on a field course to Kuala Belalong, Brunei.},
journal = {Biodiversity data journal},
volume = {},
number = {7},
pages = {e32555},
pmid = {30740026},
issn = {1314-2828},
abstract = {BACKGROUND: Clavicornaltica is a genus of very small flea beetles living in the leaf litter layer of Asian forests, easily sampled with Winkler extraction. The genus is presumably very rich in species, but their taxonomy is hampered by their small size and morphological uniformity.<br><br>NEW INFORMATION: On a 'taxon expedition'-style field course at Kuala Belalong Field Studies Centre in Brunei Darussalam (Borneo), a new species, Clavicornaltica belalongensis n. sp., was discovered and taxonomically treated by the course participants. We also present the first DNA barcodes for the genus.},
}
@article {pmid30740021,
year = {2019},
author = {Nakahara, S and Lamas, G and Tyler, S and Marín, MA and Huertas, B and Willmott, KR and Mielke, OHH and Espeland, M},
title = {A revision of the new genus Amiga Nakahara, Willmott &amp; Espeland, gen. n., described for Papilioarnaca Fabricius, 1776 (Lepidoptera, Nymphalidae, Satyrinae).},
journal = {ZooKeys},
volume = {},
number = {821},
pages = {85-152},
pmid = {30740021},
issn = {1313-2989},
abstract = {We here propose a new, monotypic genus, Amiga Nakahara, Willmott &amp; Espeland, gen. n., to harbor a common Neotropical butterfly, described as Papilioarnaca Fabricius, 1776, and hitherto placed in the genus Chloreuptychia Forster, 1964. Recent and ongoing molecular phylogenetic research has shown Chloreuptychia to be polyphyletic, with C.arnaca proving to be unrelated to remaining species and not readily placed in any other described genus. Amigaarnaca gen. n. et comb. n. as treated here is a widely distributed and very common species ranging from southern Mexico to southern Brazil. A neotype is designated for the names Papilioarnaca and its junior synonym, Papilioebusa Cramer, 1780, resulting in the treatment of the latter name as a junior objective synonym of the former. A lectotype is designated for Euptychiasericeella Bates, 1865, which is treated as a subspecies, Amigaarnacasericeella (Bates, 1865), comb. n. et stat. n., based on molecular and morphological evidence. We also describe two new taxa, Amigaarnacaadela Nakahara &amp; Espeland, ssp. n. and Amigaarnacaindianacristoi Nakahara &amp; Marín, ssp. n., new subspecies from the western Andes and eastern Central America, and northern Venezuela, respectively.},
}
@article {pmid30736952,
year = {2019},
author = {Fogt-Wyrwas, R and Dabert, M and Jarosz, W and Rząd, I and Pilarczyk, B and Mizgajska-Wiktor, H},
title = {Molecular data reveal cryptic speciation and host specificity in Toxascaris leonina (Nematoda: Ascarididae).},
journal = {Veterinary parasitology},
volume = {266},
number = {},
pages = {80-83},
doi = {10.1016/j.vetpar.2019.01.002},
pmid = {30736952},
issn = {1873-2550},
mesh = {Animals ; Cyclooxygenase 1/genetics ; DNA Barcoding, Taxonomic ; DNA, Intergenic/genetics ; Dogs/parasitology ; Felidae/parasitology ; Foxes/parasitology ; *Genetic Speciation ; Host Specificity/*genetics ; NADH Dehydrogenase/genetics ; Phylogeny ; Toxascariasis/parasitology/*veterinary ; Toxascaris/classification/*genetics ; Wolves/parasitology ; },
abstract = {Toxascaris leonina (Ascarididae) is a cosmopolitan and polyxenical parasite whose host are canids and felids. To date, molecular phylogenetic studies included toxascarid representatives collected only from dogs or felids, therefore the intra-species differences between T. leonina collected from different host species has not been noticed. In this paper, we test the hypothesis of cryptic speciation in the T. leonina complex based on extended sequence data (ITS1, nad1, cox1) and individuals collected from dogs, felids and foxes. Phylogenetic analysis clustered T. leonina representatives into three well-supported clades depending on their host species, i.e. dogs and wolves, wild felids and foxes. Both genetic distances and the barcoding-gap analysis strongly support the species status of populations inhabiting different hosts. The results suggest additional genetic separation in felids. However, to determine the actual size of the Toxascaris complex, it would be necessary to analyse individuals collected from other canid and felid Toxascaris leonina host species.},
}
@article {pmid30735035,
year = {2019},
author = {Zhou, W and Li, D and Yuan, R and Xiang, Y},
title = {Programmable DNA Ring/Hairpin-Constrained Structure Enables Ligation-Free Rolling Circle Amplification for Imaging mRNAs in Single Cells.},
journal = {Analytical chemistry},
volume = {91},
number = {5},
pages = {3628-3635},
doi = {10.1021/acs.analchem.8b05613},
pmid = {30735035},
issn = {1520-6882},
mesh = {Animals ; DNA/*chemistry ; Gene Expression Regulation ; Humans ; Nucleic Acid Amplification Techniques/*methods ; Nucleic Acid Conformation ; RNA, Messenger/*analysis ; Sequence Analysis, RNA ; Single-Cell Analysis/*methods ; },
abstract = {Self-assembled functional DNA structures have proven to be excellent materials for designing and implementing a variety of nanoscale devices. We demonstrate here that a rationally designed and programmable DNA ring/hairpin-constrained structure can achieve in situ ligation-free rolling circle amplification (RCA), which further leads to highly specific, sensitive, and multicolor imaging of mRNA molecules in single cells. Such a structure aims at addressing current challenges in terms of simplicity, sensitivity, and multiplexing capability related to the detection and imaging of intracellular mRNA sequences. With this new DNA ring/hairpin-RCA approach, we are able to detect the target mRNAs with high sensitivity at the subpicomolar levels in vitro. Besides, the multiplexing capability of the DNA structures can be readily realized by barcoding the DNA rings and hairpins with distinct sequences. Due to the excellent sequence recognition ability of the hairpins, the DNA structures exhibit single-base variation discrimination capability for the target mRNA and can be used to image trace amounts of down-expressed mRNAs in single cells. Moreover, drug-dependent mRNA expression variations can also be clearly differentiated by these DNA structures, highlighting the great potential of such structures for early disease diagnosis and for screening possible therapeutic drugs.},
}
@article {pmid30733766,
year = {2018},
author = {Hassan, AAM and Balabel, EA and Oraby, HAS and Darwish, SA},
title = {Buffalo species identification and delineation using genetic barcoding markers.},
journal = {Journal, genetic engineering &amp; biotechnology},
volume = {16},
number = {2},
pages = {499-505},
pmid = {30733766},
issn = {2090-5920},
abstract = {Enrichment of barcode databases with mitochondrial cytochrome c oxidase subunit I (COI) barcode sequences in different animal taxa has become important for identification of animal source in food samples to prevent commercial fraud. In this study, COI barcode sequence in seventy one river buffalo samples were determined, analyzed and deposited in Genbank barcode database and barcode of life database (BOLD) to contribute for construction of public reference library for COI barcode sequence in river buffalo. Moreover COI barcode sequence was used to identify the closely related buffalo groups: river buffalo, swamp buffalo, lowland anoa and African buffalo. Results indicated the success of the COI barcode in the identification of each of the tested groups. Whereas a suggested sequence of other mitochondrial segment representing two successive transfer RNA (tRNA) genes; tRNA-Threonine (MT-TT) and tRNA-Proline (MT-TP) was failed to be used as a barcode marker for differentiation between the tested buffalo groups.},
}
@article {pmid30732502,
year = {2019},
author = {Veeraragavan, S and Duraisamy, R and Mani, S},
title = {Mitochondrial cytochrome oxidase (COI) sequence-based identification of pod borer of Thylacoptila sp. AA isolated from Senna alata (L.) Roxb. for the first time in India.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {3},
pages = {407-413},
doi = {10.1080/24701394.2018.1532415},
pmid = {30732502},
issn = {2470-1408},
mesh = {Base Sequence ; DNA, Plant/*genetics/isolation &amp; purification ; Electron Transport Complex IV/*genetics ; Genes, Mitochondrial/*genetics ; India ; Seeds/genetics ; Senna Plant/*genetics ; },
abstract = {In the present study, two pod borer larvae were found to damage pods of the host plant Senna alata. As pods (seeds) are commercially important, it prompted the investigators to find out the adult of pod borer larvae by molecular sequencing and reported in this article for the first time from S. alata. Successful amplification was achieved for chloroplast DNA isolated from leaves of host plant S. alata and tissue DNA from unknown larvae and sequenced. The sequences were submitted to NCBI domain, and the taxonomic position of host plant of pod borer larvae was confirmed as S. alata (L.) Roxb. Of the two sequences belonging to pod borer larvae, specimen 1 (S1) matched with already available three sequences of Thylacoptila sp. AA. But, specimen 2 (S2) showed significant variation in its genetic distance in Neighborhood Joining tree and maximum likelihood tree; these factors imply that specimen 2 (S2) is distinct from Thylacoptila sp. AA. Therefore, it is reported that specimen 2 may be represented as Thylacoptila sp. BB where in BB indicates variant from other available sequences. Nonetheless, reporting species of Thylacoptila as insect pest in pods of S. alata is an important contribution to the annals of insect-pest-plant interaction more importantly in medicinally important plant species S. alata.},
}
@article {pmid30730769,
year = {2019},
author = {Jennings, WB and Ruschi, PA and Ferraro, G and Quijada, CC and Silva-Malanski, ACG and Prosdocimi, F and Buckup, PA},
title = {Barcoding the Neotropical freshwater fish fauna using a new pair of universal COI primers with a discussion of primer dimers and M13 primer tails.},
journal = {Genome},
volume = {62},
number = {2},
pages = {77-83},
doi = {10.1139/gen-2018-0145},
pmid = {30730769},
issn = {1480-3321},
mesh = {Animals ; Bacteriophage M13/genetics ; DNA Barcoding, Taxonomic/*methods/standards ; DNA Primers/*standards ; Electron Transport Complex IV/genetics ; Fish Proteins/genetics ; Fishes/classification/*genetics ; },
abstract = {Designing primers for DNA barcoding is a significant challenge for the rich Neotropical fish fauna, which is comprised of ∼6000 species. Previously, researchers required multiple pairs of PCR primers or primer cocktails to obtain standard COI (i.e., mitochondrial cytochrome c oxidase subunit I) barcode sequences from assemblages of freshwater fish in this region. To simplify DNA barcoding and metabarcoding studies of Neotropical freshwater fish, we present a new pair of COI primers, which have yielded high quality barcodes across six teleost orders-Characiformes, Cichliformes, Cyprinodontiformes, Gymnotiformes, Siluriformes, and Synbranchiformes-native to South America. Following previous fish barcoding studies, we also tailed our primers with M13 forward and reverse primers to facilitate the DNA sequencing process. Although this practice generates primer dimers, we obtained complete and high quality COI barcode sequences for all samples. We discuss the problem of primer dimers and suggest strategies for neutralizing their influence on data quality.},
}
@article {pmid30730721,
year = {2019},
author = {Wang, J and Suffren, Y and Daiguebonne, C and Freslon, S and Bernot, K and Calvez, G and Le Pollès, L and Roiland, C and Guillou, O},
title = {Multi-Emissive Lanthanide-Based Coordination Polymers for Potential Application as Luminescent Bar-Codes.},
journal = {Inorganic chemistry},
volume = {58},
number = {4},
pages = {2659-2668},
doi = {10.1021/acs.inorgchem.8b03277},
pmid = {30730721},
issn = {1520-510X},
abstract = {Isostructural lanthanide-based coordination polymers that are obtained by reactions in water of a lanthanide chloride and the sodium salt of 5-methoxyisophthalate (mip[2-]) have the general chemical formula [Ln2(mip)3(H2O)8·4H2O]∞ with Ln = Nd-Er except Pm plus Y (symbolized by [Ln2(mip)3]∞). Some of these homo-lanthanide compounds present very high luminescence brightness. The weak intermetallic energy transfer between lanthanide ions observed in these compounds allows the design of hetero-lanthanide coordination polymers with tunable luminescence properties. A molecular alloy that involved six different lanthanide ions (Nd[3+], Sm[3+], Eu[3+], Gd[3+], Tb[3+], Dy[3+]) has been prepared and its luminescent properties have been studied. This compound, under a unique irradiation wavelength (λexc = 325 nm), exhibits almost 20 emission peaks in both the visible and the NIR regions at room temperature. This unprecedented richness of the emission spectrum could be of great interest as far as luminescent bar-codes are targeted.},
}
@article {pmid30728607,
year = {2018},
author = {Crous, PW and Luangsa-Ard, JJ and Wingfield, MJ and Carnegie, AJ and Hernández-Restrepo, M and Lombard, L and Roux, J and Barreto, RW and Baseia, IG and Cano-Lira, JF and Martín, MP and Morozova, OV and Stchigel, AM and Summerell, BA and Brandrud, TE and Dima, B and García, D and Giraldo, A and Guarro, J and Gusmão, LFP and Khamsuntorn, P and Noordeloos, ME and Nuankaew, S and Pinruan, U and Rodríguez-Andrade, E and Souza-Motta, CM and Thangavel, R and van Iperen, AL and Abreu, VP and Accioly, T and Alves, JL and Andrade, JP and Bahram, M and Baral, HO and Barbier, E and Barnes, CW and Bendiksen, E and Bernard, E and Bezerra, JDP and Bezerra, JL and Bizio, E and Blair, JE and Bulyonkova, TM and Cabral, TS and Caiafa, MV and Cantillo, T and Colmán, AA and Conceição, LB and Cruz, S and Cunha, AOB and Darveaux, BA and da Silva, AL and da Silva, GA and da Silva, GM and da Silva, RMF and de Oliveira, RJV and Oliveira, RL and De Souza, JT and Dueñas, M and Evans, HC and Epifani, F and Felipe, MTC and Fernández-López, J and Ferreira, BW and Figueiredo, CN and Filippova, NV and Flores, JA and Gené, J and Ghorbani, G and Gibertoni, TB and Glushakova, AM and Healy, R and Huhndorf, SM and Iturrieta-González, I and Javan-Nikkhah, M and Juciano, RF and Jurjević, &#x17d; and Kachalkin, AV and Keochanpheng, K and Krisai-Greilhuber, I and Li, YC and Lima, AA and Machado, AR and Madrid, H and Magalhães, OMC and Marbach, PAS and Melanda, GCS and Miller, AN and Mongkolsamrit, S and Nascimento, RP and Oliveira, TGL and Ordoñez, ME and Orzes, R and Palma, MA and Pearce, CJ and Pereira, OL and Perrone, G and Peterson, SW and Pham, THG and Piontelli, E and Pordel, A and Quijada, L and Raja, HA and Rosas de Paz, E and Ryvarden, L and Saitta, A and Salcedo, SS and Sandoval-Denis, M and Santos, TAB and Seifert, KA and Silva, BDB and Smith, ME and Soares, AM and Sommai, S and Sousa, JO and Suetrong, S and Susca, A and Tedersoo, L and Telleria, MT and Thanakitpipattana, D and Valenzuela-Lopez, N and Visagie, CM and Zapata, M and Groenewald, JZ},
title = {Fungal Planet description sheets: 785-867.},
journal = {Persoonia},
volume = {41},
number = {},
pages = {238-417},
pmid = {30728607},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Angola, Gnomoniopsis angolensis and Pseudopithomyces angolensis on unknown host plants. Australia, Dothiora corymbiae on Corymbia citriodora, Neoeucasphaeria eucalypti (incl. Neoeucasphaeria gen. nov.) on Eucalyptus sp., Fumagopsis stellae on Eucalyptus sp., Fusculina eucalyptorum (incl. Fusculinaceae fam. nov.) on Eucalyptus socialis, Harknessia corymbiicola on Corymbia maculata, Neocelosporium eucalypti (incl. Neocelosporium gen. nov., Neocelosporiaceae fam. nov. and Neocelosporiales ord. nov.) on Eucalyptus cyanophylla, Neophaeomoniella corymbiae on Corymbia citriodora, Neophaeomoniella eucalyptigena on Eucalyptus pilularis, Pseudoplagiostoma corymbiicola on Corymbia citriodora, Teratosphaeria gracilis on Eucalyptus gracilis, Zasmidium corymbiae on Corymbia citriodora. Brazil, Calonectria hemileiae on pustules of Hemileia vastatrix formed on leaves of Coffea arabica, Calvatia caatinguensis on soil, Cercospora solani-betacei on Solanum betaceum, Clathrus natalensis on soil, Diaporthe poincianellae on Poincianella pyramidalis, Geastrum piquiriunense on soil, Geosmithia carolliae on wing of Carollia perspicillata, Henningsia resupinata on wood, Penicillium guaibinense from soil, Periconia caespitosa from leaf litter, Pseudocercospora styracina on Styrax sp., Simplicillium filiforme as endophyte from Citrullus lanatus, Thozetella pindobacuensis on leaf litter, Xenosonderhenia coussapoae on Coussapoa floccosa. Canary Islands (Spain), Orbilia amarilla on Euphorbia canariensis. Cape Verde Islands, Xylodon jacobaeus on Eucalyptus camaldulensis. Chile, Colletotrichum arboricola on Fuchsia magellanica. Costa Rica, Lasiosphaeria miniovina on tree branch. Ecuador, Ganoderma chocoense on tree trunk. France, Neofitzroyomyces nerii (incl. Neofitzroyomyces gen. nov.) on Nerium oleander. Ghana, Castanediella tereticornis on Eucalyptus tereticornis, Falcocladium africanum on Eucalyptus brassiana, Rachicladosporium corymbiae on Corymbia citriodora. Hungary, Entoloma silvae-frondosae in Carpinus betulus-Pinus sylvestris mixed forest. Iran, Pseudopyricularia persiana on Cyperus sp. Italy, Inocybe roseascens on soil in mixed forest. Laos, Ophiocordyceps houaynhangensis on Coleoptera larva. Malaysia, Monilochaetes melastomae on Melastoma sp. Mexico, Absidia terrestris from soil. Netherlands, Acaulium pannemaniae, Conioscypha boutwelliae, Fusicolla septimanifiniscientiae, Gibellulopsis simonii, Lasionectria hilhorstii, Lectera nordwiniana, Leptodiscella rintelii, Parasarocladium debruynii and Sarocladium dejongiae (incl. Sarocladiaceae fam. nov.) from soil. New Zealand, Gnomoniopsis rosae on Rosa sp. and Neodevriesia metrosideri on Metrosideros sp. Puerto Rico, Neodevriesia coccolobae on Coccoloba uvifera, Neodevriesia tabebuiae and Alfaria tabebuiae on Tabebuia chrysantha. Russia, Amanita paludosa on bogged soil in mixed deciduous forest, Entoloma tiliae in forest of Tilia × europaea, Kwoniella endophytica on Pyrus communis. South Africa, Coniella diospyri on Diospyros mespiliformis, Neomelanconiella combreti (incl. Neomelanconiellaceae fam. nov. and Neomelanconiella gen. nov.) on Combretum sp., Polyphialoseptoria natalensis on unidentified plant host, Pseudorobillarda bolusanthi on Bolusanthus speciosus, Thelonectria pelargonii on Pelargonium sp. Spain, Vermiculariopsiella lauracearum and Anungitopsis lauri on Laurus novocanariensis, Geosmithia xerotolerans from a darkened wall of a house, Pseudopenidiella gallaica on leaf litter. Thailand, Corynespora thailandica on wood, Lareunionomyces loeiensis on leaf litter, Neocochlearomyces chromolaenae (incl. Neocochlearomyces gen. nov.) on Chromolaena odorata, Neomyrmecridium septatum (incl. Neomyrmecridium gen. nov.), Pararamichloridium caricicola on Carex sp., Xenodactylaria thailandica (incl. Xenodactylariaceae fam. nov. and Xenodactylaria gen. nov.), Neomyrmecridium asiaticum and Cymostachys thailandica from unidentified vine. USA, Carolinigaster bonitoi (incl. Carolinigaster gen. nov.) from soil, Penicillium fortuitum from house dust, Phaeotheca shathenatiana (incl. Phaeothecaceae fam. nov.) from twig and cone litter, Pythium wohlseniorum from stream water, Superstratomyces tardicrescens from human eye, Talaromyces iowaense from office air. Vietnam, Fistulinella olivaceoalba on soil. Morphological and culture characteristics along with DNA barcodes are provided.},
}
@article {pmid30728605,
year = {2018},
author = {Consiglio, G and Setti, L and Thorn, RG},
title = {New species of Hohenbuehelia, with comments on the Hohenbuehelia atrocoerulea - Nematoctonus robustus species complex.},
journal = {Persoonia},
volume = {41},
number = {},
pages = {202-212},
pmid = {30728605},
issn = {0031-5850},
abstract = {Four new species of Hohenbuehelia (Fungi: Pleurotaceae) are described in the group of Hohenbuehelia atrocoerulea and Hohenbuehelia grisea. Hohenbuehelia algonquinensis, found on Pinus in Ontario, Canada, may be distinguished macroscopically from bluish collections of H. atrocoerulea and watery grey-brown collections of H. grisea by its coal-black pileus. Hohenbuehelia canadensis, on or associated with Pinus in both Ontario and Alberta, Canada, and Hohenbuehelia nimueae, on Salix in Ontario and Abies in Wyoming, USA, have similarly dark fruiting bodies and were previously misidentified as H. approximans (which we treat as a synonym of H. grisea), H. atrocoerulea, H. mustialensis or H. nigra. The latter species is shown to be a member of Resupinatus, despite the presence of prominent metuloid cystidia in its hymenium. Hohenbuehelia carlothornii has been found in Costa Rica; collections of the sexual fruiting bodies were previously identified as H. grisea and isolates from soil nematodes were identified by the anamorph name Nematoctonus robustus. That name has been treated as a synonym of H. atrocoerulea but, given the genetic and geographic variation within this complex, we transfer it to Hohenbuehelia as a distinct species. Sequences of the nuclear ribosomal DNA internal transcribed spacer region (ITS), the D1/D2 variable region of the large subunit gene, and a portion of the translation elongation factor (TEF1) gene provide good separation and support for these new species. A key to the dimidiate species of Hohenbuehelia of North America and Europe is provided.},
}
@article {pmid30727954,
year = {2019},
author = {Boettcher, M and Covarrubias, S and Biton, A and Blau, J and Wang, H and Zaitlen, N and McManus, MT},
title = {Tracing cellular heterogeneity in pooled genetic screens via multi-level barcoding.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {107},
pmid = {30727954},
issn = {1471-2164},
support = {K25 HL121295/HL/NHLBI NIH HHS/United States ; 1U01MH105028/NH/NIH HHS/United States ; U01CA168370/NH/NIH HHS/United States ; },
mesh = {*CRISPR-Cas Systems ; *Gene Editing ; Genetic Testing/*methods ; Humans ; Jurkat Cells ; Molecular Typing/*methods ; *RNA, Guide, CRISPR-Cas Systems ; },
abstract = {BACKGROUND: While pooled loss- and gain-of-function CRISPR screening approaches have become increasingly popular to systematically investigate mammalian gene function, the large majority of them have thus far not investigated the influence of cellular heterogeneity on screen results. Instead most screens are analyzed by averaging the abundance of perturbed cells from a bulk population of cells.<br><br>RESULTS: Here we developed multi-level barcoded sgRNA libraries to trace multiple clonal Cas9 cell lines exposed to the same environment. The first level of barcoding allows monitoring growth kinetics and treatment responses of multiplexed clonal cell lines under identical conditions while the second level enables in-sample replication and tracing of sub-clonal lineages of cells expressing the same sgRNA.<br><br>CONCLUSION: Using our approach, we illustrate how heterogeneity in growth kinetics and treatment response of clonal cell lines impairs the results of pooled genetic screens.},
}
@article {pmid30723628,
year = {2019},
author = {Chen, J and Zhao, YB and Wang, YJ and Li, XG},
title = {Identification of species and materia medica within Saussurea subg. Amphilaena based on DNA barcodes.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6357},
pmid = {30723628},
issn = {2167-8359},
abstract = {Saussurea is one of the most species-rich genera in the family Asteraceae, where some have a complex evolutionary history, including radiation and convergent evolution, and the identification of these species is notoriously difficult. This genus contains many plants with medical uses, and thus an objective identification method is urgently needed. Saussurea subg. Amphilaena is one of the four subgenera of Saussurea and it is particularly rich in medical resources, where 15/39 species are used in medicine. To test the application of DNA barcodes in this subgenus, five candidates were sequenced and analyzed using 131 individuals representing 15 medical plants and four additional species from this subgenus. Our results suggested that internal transcribed spacer (ITS) + rbcL or ITS + rbcL + psbA-trnH could distinguish all of the species, while the ITS alone could identify all of the 15 medical plants. However, the species identification rates based on plastid barcodes were low, i.e., 0% to 36% when analyzed individually, and 63% when all four loci were combined. Thus, we recommend using ITS + rbcL as the DNA barcode for S. subg. Amphilaena or the ITS alone for medical plants. Possible taxonomic problems and substitutes for medicinal plant materials are also discussed.},
}
@article {pmid30722917,
year = {2019},
author = {Sousa, AI and Ferreira, IMPLVO and Faria, MA},
title = {Sensitive detection of Piper nigrum L. adulterants by a novel screening approach based on qPCR.},
journal = {Food chemistry},
volume = {283},
number = {},
pages = {596-603},
doi = {10.1016/j.foodchem.2019.01.062},
pmid = {30722917},
issn = {1873-7072},
mesh = {Capsicum/genetics ; Carica/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/metabolism ; DNA, Plant/*analysis/genetics/metabolism ; Fruit/genetics ; Limit of Detection ; Nucleic Acid Hybridization ; Piper nigrum/*genetics ; Plant Proteins/genetics ; Real-Time Polymerase Chain Reaction ; Zea mays/genetics ; },
abstract = {The spice made from the fruits of Piper nigrum L. (Piperaceae) has high economic value since the beginnings of international trade. Because its price has been increasing, adulterations with papaya seeds, cayenne pepper and maize flour were reported. These have been screened by methodologies dedicated to the detection of single adulterants lacking sensitivity and specificity. Herein we propose a specific, highly-sensitive, high-throughput and affordable qPCR-based methodology for the detection of P. nigrum contaminants (Carica papaya, Zea mays and Capsicum annuum) using plant DNA barcodes trnL and psbA-trnH. The method enables the specific detection of contaminants in a short time with low limits of detection (LOD6 values of 1, 2 and 10 Haploid Genome Equivalents). A market survey (29 samples) revealed 41% of samples contaminated, though about ¾ at very low levels indicating accidental contamination. The proposed tool will contribute to the improvement of quality of this much traded spice.},
}
@article {pmid30722881,
year = {2019},
author = {Xu, Y and Huo, B and Li, C and Peng, Y and Tian, S and Fan, L and Bai, J and Ning, B and Gao, Z},
title = {Ultrasensitive detection of staphylococcal enterotoxin B in foodstuff through dual signal amplification by bio-barcode and real-time PCR.},
journal = {Food chemistry},
volume = {283},
number = {},
pages = {338-344},
doi = {10.1016/j.foodchem.2018.12.128},
pmid = {30722881},
issn = {1873-7072},
mesh = {Antibodies, Monoclonal/chemistry/immunology ; Benzothiazoles ; DNA/chemistry/metabolism ; DNA Barcoding, Taxonomic/*methods ; Diamines ; Enterotoxins/*analysis/immunology ; Gold/chemistry ; Immunoassay ; Limit of Detection ; Magnetics ; Metal Nanoparticles/chemistry ; Organic Chemicals/chemistry ; Quinolines ; Real-Time Polymerase Chain Reaction/*methods ; },
abstract = {This study developed an ultrasensitive method involving (1) gold nanoparticles encoded with a double-stranded DNA as the first signal amplification and goat anti-staphylococcal enterotoxin B (SEB) polyclonal antibody and (2) magnetic microparticles coated with anti-SEB monoclonal antibody to detect SEB. Both functionalized nanoparticles can capture SEB in a sandwich system. The released DNA barcodes were then characterized through SYBR Green real-time polymerase chain reaction and resulted in the second signal amplification. Under optimized experimental conditions, an ultrasensitive bio-barcode for SEB detection was established, and its detection limit could reach 0.269 pg mL[-1], which was 1000-fold lower than that of conventional enzyme-linked/immunosorbent assay. The proposed method shows great potential in food security.},
}
@article {pmid30719028,
year = {2018},
author = {Mosa, KA and Gairola, S and Jamdade, R and El-Keblawy, A and Al Shaer, KI and Al Harthi, EK and Shabana, HA and Mahmoud, T},
title = {The Promise of Molecular and Genomic Techniques for Biodiversity Research and DNA Barcoding of the Arabian Peninsula Flora.},
journal = {Frontiers in plant science},
volume = {9},
number = {},
pages = {1929},
pmid = {30719028},
issn = {1664-462X},
abstract = {The Arabian Peninsula is known to have a comprehensive and rich endowment of unique and genetically diverse plant genetic resources. Analysis and conservation of biological diversity is a crucial issue to the whole Arabian Peninsula. The rapid and accurate delimitation and identification of a species is crucial to genetic diversity analysis and the first critical step in the assessment of distribution, population abundance and threats related to a particular target species. During the last two decades, classical strategies of evaluating genetic variability, such as morphology and physiology, have been greatly complemented by phylogenetic, taxonomic, genetic diversity and breeding research molecular studies. At present, initiatives are taking place around the world to generate DNA barcode libraries for vascular plant flora and to make these data available in order to better understand, conserve and utilize biodiversity. The number of herbarium collection-based plant evolutionary genetics and genomics studies being conducted has been increasing worldwide. The herbaria provide a rich resource of already preserved and identified material, and these as well as freshly collected samples from the wild can be used for creating a reference DNA barcode library for the vascular plant flora of a region. This review discusses the main molecular and genomic techniques used in plant identification and biodiversity analysis. Hence, we highlight studies emphasizing various molecular techniques undertaken during the last 10 years to study the plant biodiversity of the Arabian Peninsula. Special emphasis on the role of DNA barcoding as a powerful tool for plant biodiversity analysis is provided, along with the crucial role of herbaria in creating a DNA barcode library.},
}
@article {pmid30717821,
year = {2019},
author = {Lu, Z and Thompson, CM and Chua, T and Babajanian, S and Zhang, Y and Gao, Q and Chang, P and Swanson, G},
title = {Single-Laboratory Validation of a Two-Tiered DNA Barcoding Method for Raw Botanical Identification.},
journal = {Journal of AOAC International},
volume = {102},
number = {5},
pages = {1435-1447},
doi = {10.5740/jaoacint.18-0130},
pmid = {30717821},
issn = {1944-7922},
mesh = {DNA Barcoding, Taxonomic/*methods ; Plants, Medicinal/*classification/genetics ; },
abstract = {Background: The applications of deoxyribonucleic acid (DNA) barcoding methods have been extended from authenticating taxonomic provenance of animal products to identifying botanicals used as herbal medicine and in botanical dietary supplements. DNA barcoding methods for botanical identification must be adequately validated to meet regulatory compliance. Objective: The goal of this study is to provide a validation protocol for a two-tiered DNA barcoding method that aims to identify raw botanicals. Methods: A barcode database was computationally validated to define the barcode combinations that can unambiguously identify botanicals in the database. A maximum variation sampling technique was used to capture a wide range of perspectives relating to DNA barcode-based botanical identification, including plant parts and species distance, for the experimental validation. Twenty-two authenticated botanicals were purposively sampled from different plant parts-covering both closely related and distantly related species-to validate the two-tiered DNA barcoding method. The performance of the method was assessed on accuracy, precision, ruggedness, and uncertainty. Results: High accuracy (100%) and precision (1.0) were obtained from the validation samples. The method was also found to be rugged and have acceptable uncertainty. Conclusions: The method was validated and suitable for DNA-based identification of botanical raw materials listed in the current database. Highlights: This work will provide support guidance for manufacturers and regulatory policy makers to implement equivalent validated and compliant DNA-based testing in quality control processes to improve botanical raw material identification and authentication.},
}
@article {pmid30717546,
year = {2018},
author = {Jing, L and Su, H and Sui, BW and Zhang, H and Pan, DA and Qi, B},
title = {[Research progress about molecular identification of DNA barcoding in medicinal animal].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {43},
number = {23},
pages = {4587-4591},
doi = {10.19540/j.cnki.cjcmm.20181025.008},
pmid = {30717546},
issn = {1001-5302},
mesh = {Animals ; China ; DNA ; *DNA Barcoding, Taxonomic ; Research ; },
abstract = {The use of animal medicine has a long history in China, it has the characteristics of high curative effect,strong activity, wide application and great potential. However,the circulation of animal medicine in current market mixed counterfeit variety and complex. Molecular identification technology of DNA barcoding is an emerging molecular biotechnology in recent years, it is a powerful supplement to traditional identification methods. This method can well identify animal species at the molecular level and has high accuracy, it can identify animal medicines quickly and monitor the medicine market effectively. This article summarizes the research process of molecular identification of DNA barcoding, the application of DNA barcoding in medicinal animals identification in recent years, and the limitations of DNA barcoding technology.},
}
@article {pmid30717544,
year = {2018},
author = {Zhang, QF and Liu, YY and Tan, QQ and Jiang, XX and Chen, XY and Ge, FC and Bu, X and Zhang, YQ},
title = {[A real-time fluorescence quantitative PCR method for source identification of Crocus sativus and Carthamus tinctorius].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {43},
number = {23},
pages = {4575-4581},
doi = {10.19540/j.cnki.cjcmm.20181025.005},
pmid = {30717544},
issn = {1001-5302},
mesh = {*Carthamus tinctorius ; *Crocus ; Real-Time Polymerase Chain Reaction ; },
abstract = {The specific PCR primer was designed base on ITS2 sequence in GenBank, and we developed a SYBRGreen real-time fluorescence quantitative PCR system for identification of Crocus sativus and Carthamus tinctorius source. Compared with Chinese herbal medicine DNA barcode technique, this method showed characteristics of shorter time, higher specificity and sensitivity. Using this method to detect 15 samples, 4 were C. sativus, 8 were C. tinctorius, and the other 3 samples were none of them. The result was in accordance with Chinese herbal medicine DNA barcode. This study lays the foundation for identification of related Chinese medical materials.},
}
@article {pmid30714424,
year = {2019},
author = {Felix, T and Jordan, JB and Akers, C and Patel, B and Drago, D},
title = {Current state of biologic pharmacovigilance in the European Union: improvements are needed.},
journal = {Expert opinion on drug safety},
volume = {18},
number = {3},
pages = {231-240},
doi = {10.1080/14740338.2019.1577818},
pmid = {30714424},
issn = {1744-764X},
mesh = {Adverse Drug Reaction Reporting Systems ; Biological Products/*adverse effects ; Biosimilar Pharmaceuticals/*adverse effects ; Drug-Related Side Effects and Adverse Reactions/epidemiology ; European Union ; Humans ; *Pharmacovigilance ; },
abstract = {INTRODUCTION: Pharmacovigilance is essential to monitoring the safety profiles of authorized medicines. Compared with small-molecule drugs, biological drugs are more complex, more susceptible to structural variability due to manufacturing processes, and have the potential to induce immune-related reactions, underscoring the importance of safety monitoring for these products. Although highly similar to reference products, biosimilars are not expected to be structurally identical. For these reasons, proper reporting of potential adverse drug reactions (ADRs) using distinguishable names and batch numbers is essential for accurate tracing of all biological drugs. To address the need for robust pharmacovigilance, the European Parliament and Council of the European Union provided legislation regarding pharmacovigilance of biologics in 2010.<br><br>AREAS COVERED: This narrative review examines the current state of pharmacovigilance for biologics in the European Union (EU) and discusses relevant information on pharmacovigilance of biosimilars, the current EU pharmacovigilance system, and areas that could be improved.<br><br>EXPERT OPINION: Although steps have been taken to improve pharmacovigilance of biologics in the EU, several enhancements can still be made, including additional training for healthcare professionals on ADR reporting, the use of 2D barcodes that enhance traceability, and an open discussion of potentially missed opportunities in the pharmacovigilance of biosimilars.},
}
@article {pmid30713460,
year = {2019},
author = {Sheffield, CS and deWaard, JR and Morse, JC and Rasmussen, AK},
title = {Trichoptera of Canada.},
journal = {ZooKeys},
volume = {},
number = {819},
pages = {507-520},
pmid = {30713460},
issn = {1313-2989},
abstract = {Trichoptera, or caddisflies, are common members of freshwater ecosystems as larvae and are important indicators of aquatic system health. As such, the species are relatively well studied, with keys available for larvae and adults of many of the taxa occurring in Canada. The number of species recorded from Canada since 1979 (Wiggins 1979) has increased from 546 to 636, an increase of 16.4%. Of those species newly recorded, 17 represent newly described taxa since 1979. Taking into consideration the species likely to be subsequently found in Canada based on records in adjacent parts of the United States and results from DNA barcoding, an estimated 129-181 species remain to be documented in Canada.},
}
@article {pmid30713459,
year = {2019},
author = {Pohl, GR and Andry, JF and Schmidt, BC and deWaard, JR},
title = {Lepidoptera of Canada.},
journal = {ZooKeys},
volume = {},
number = {819},
pages = {463-505},
pmid = {30713459},
issn = {1313-2989},
abstract = {The known Lepidoptera (moths and butterflies) of the provinces and territories of Canada are summarised, and current knowledge is compared to the state of knowledge in 1979. A total of 5405 species are known to occur in Canada in 81 families, and a further 50 species have been reported but are unconfirmed. This represents an increase of 1348 species since 1979. The DNA barcodes available for Canadian Lepidoptera are also tabulated, based on a dataset of 148,314 specimens corresponding to 5842 distinct clusters. A further yet-undiscovered 1400 species of Lepidoptera are estimated to occur in Canada. The Gelechioidea are the most poorly known major lineage of Lepidoptera in Canada. Nunavut, Prince Edward Island, and British Columbia are thought to show the greatest deficit in our knowledge of Lepidoptera. The unglaciated portions of the Yukon (Beringia), and the Pacific Maritime, Montane Cordillera, and Western Interior Basin ecozones of British Columbia are also identified as hotbeds of undescribed biodiversity.},
}
@article {pmid30713457,
year = {2019},
author = {Blades, DCA},
title = {Mecoptera of Canada.},
journal = {ZooKeys},
volume = {},
number = {819},
pages = {451-453},
pmid = {30713457},
issn = {1313-2989},
abstract = {The Mecoptera are represented in Canada by 25 extant species in four families, an increase of three species since the prior assessment in 1979. An additional 18 or more species and one family are expected to occur in Canada based on distributional records, recent collections and DNA analyses. The Barcode of Life Data System currently lists 24 Barcode Index Numbers for Canadian Mecoptera. There are nine species of fossil Mecoptera known from Canada.},
}
@article {pmid30713454,
year = {2019},
author = {Blades, DCA},
title = {Neuroptera of Canada.},
journal = {ZooKeys},
volume = {},
number = {819},
pages = {387-392},
pmid = {30713454},
issn = {1313-2989},
abstract = {The Neuroptera of Canada consists of 101 extant species, an increase of 26 (35%) since the previous assessment of the fauna in 1979. More than 48 additional species are believed to occur in Canada based largely on recent DNA evidence and new distribution records. The Barcode Of Life Data System (BOLD) currently includes 141 Barcode Index Numbers (BINs) for Canadian Neuroptera. Canadian fossils have thus far yielded 15 species in three families of Neuroptera.},
}
@article {pmid30713453,
year = {2019},
author = {Blades, DCA},
title = {Raphidioptera of Canada.},
journal = {ZooKeys},
volume = {},
number = {819},
pages = {383-386},
pmid = {30713453},
issn = {1313-2989},
abstract = {There are eight species in two families of Raphidioptera known from Canada, an increase of one species since the prior assessment in 1979. Another four species are likely to occur in Canada based on DNA evidence and distributional records. The Barcode of Life Data System currently lists ten Barcode Index Numbers for Canadian Raphidioptera.},
}
@article {pmid30713452,
year = {2019},
author = {Straka, J},
title = {Strepsiptera of Canada.},
journal = {ZooKeys},
volume = {},
number = {819},
pages = {377-382},
pmid = {30713452},
issn = {1313-2989},
abstract = {In Canada, the order Strepsiptera consists of 27 known species representing five families: Corioxenidae (1 species), Elenchidae (1 species), Halictophagidae (5 species), Stylopidae (15 species), and Xenidae (5 species). These totals represent an increase of 21 species since the 1979 assessment. Half of these species represent unpublished records recently discovered by study of stylopized hosts in museum collections and DNA barcoded species. It is estimated that as many as 19 more species will eventually be discovered in Canada. DNA barcode sequences are available for 4 Canadian species. The fauna of Canada is poorly surveyed and there is a need to fill knowledge gaps with increased examination of museum specimens for stylopized hosts, broader field surveys (including use of pheromone-baited traps), and more effort to obtain DNA samples.},
}
@article {pmid30713450,
year = {2019},
author = {Bennett, AMR and Sheffield, CS and deWaard, JR},
title = {Hymenoptera of Canada.},
journal = {ZooKeys},
volume = {},
number = {819},
pages = {311-360},
pmid = {30713450},
issn = {1313-2989},
abstract = {A summary of the numbers of species of the 83 families of Hymenoptera recorded in Canada is provided. In total, 8757 described species are recorded compared to approximately 6000 in 1979, which is a 46% increase. Of the families recognized in 1979, three have been newly recorded to Canada since the previous survey: Anaxyelidae (Anaxyleoidea), Liopteridae (Cynipoidea), and Mymarommatidae (Mymarommatoidea). More than 18,400 BINs of Canadian Hymenoptera are available in the Barcode of Life Data Systems (Ratnasingham and Hebert 2007) implying that nearly 9650 undescribed or unrecorded species of Hymenoptera may be present in Canada (and more than 10,300 when taking into account additional species that have not been DNA barcoded). The estimated number of unrecorded species is very similar to that of 1979 (10,637 species), but the percentage of the fauna described/recorded has increased from 36% in 1979 to approximately 45% in 2018. Summaries of the state of knowledge of the major groups of Hymenoptera are presented, including brief comments on numbers of species, biology, changes in classification since 1979, and relevant taxonomic references.},
}
@article {pmid30713447,
year = {2019},
author = {Foottit, RG and Maw, HEL},
title = {Thysanoptera of Canada.},
journal = {ZooKeys},
volume = {},
number = {819},
pages = {291-294},
pmid = {30713447},
issn = {1313-2989},
abstract = {The known Canadian Thysanoptera fauna currently consists of 147 species, including 28 non-native species, and there are five additional species found only indoors. DNA barcoding data, presence of species in adjacent regions, and preliminary evidence of the presence of host-associated cryptic species suggest that there may be as many as 255 additional species awaiting discovery or description in Canada.},
}
@article {pmid30713446,
year = {2019},
author = {Foottit, RG and Maw, HEL and Kits, JH and Scudder, GGE},
title = {Hemiptera of Canada.},
journal = {ZooKeys},
volume = {},
number = {819},
pages = {277-290},
pmid = {30713446},
issn = {1313-2989},
abstract = {The Canadian Hemiptera (Sternorrhyncha, Auchenorrhyncha, and Heteroptera) fauna is reviewed, which currently comprises 4011 species, including 405 non-native species. DNA barcodes available for Canadian specimens are represented by 3275 BINs. The analysis was based on the most recent checklist of Hemiptera in Canada (Maw et al. 2000) and subsequent collection records, literature records and compilation of DNA barcode data. It is estimated that almost 600 additional species remain to be discovered among Canadian Hemiptera.},
}
@article {pmid30713444,
year = {2019},
author = {Miskelly, J and Paiero, SM},
title = {Mantodea, Blattodea, Orthoptera, Dermaptera, and Phasmida of Canada.},
journal = {ZooKeys},
volume = {},
number = {819},
pages = {255-269},
pmid = {30713444},
issn = {1313-2989},
abstract = {In the last 40 years, the number of species in the orthopteroid orders has increased by ~10% from that known in 1979. The largest order, the Orthoptera, has increased from 205 to 235 species known in Canada. The number of Blattodea has increased from 14 to 18 species, while Dermaptera has increased from 5 to 6 species. The number of species of Mantodea (3) and Phasmida (1) known in Canada have remained unchanged. Most new species records reported in Canada since 1979 have resulted from new collections along the periphery of the range of more widespread species. Some species reported since 1979 are recent introductions to Canada, including species restricted to homes or other heated buildings. The taxonomy of these orders has also changed, with only the Dermaptera having maintained its order definition since the 1979 treatment. Additional orthopteroid species are likely to occur in Canada, particularly in the orders Orthoptera and Blattodea. DNA barcodes are available for more than 60% of the species known to occur in Canada.},
}
@article {pmid30713442,
year = {2019},
author = {Cannings, RA},
title = {Odonata of Canada.},
journal = {ZooKeys},
volume = {},
number = {819},
pages = {227-241},
pmid = {30713442},
issn = {1313-2989},
abstract = {Since Corbet's thorough 1979 overview of Canadian Odonata, hundreds of regional works on taxonomy, faunistics, distribution, life history, ecology and behaviour have been written. Canada records 214 species of Odonata, an increase of 20 since the 1979 assessment. Estimates of unrecorded species are small; this reflects the well-known nature of the fauna. A major impetus for surveys and analyses of the status of species is the work of the Committee on the Status of Endangered Wildlife in Canada which provides a scientifically sound classification of wildlife species potentially at risk. As of 2017, six species have been designated "Endangered" and two "Special Concern" (only five of which are officially listed under the Federal Species at Risk Act (SARA)). The Order provides a good example of molecular barcoding effort in insects, as many well-accepted morphological species in Canada have been barcoded to some degree. However, more barcoding of accurately identified specimens of many species is still required, especially in most of the larger families, which have less than 70% of their species barcoded. Corbet noted that the larvae of 15 Canadian species were unknown, but almost all larvae are now well, or cursorily, described. Extensive surveys have greatly improved our understanding of species' geographical distributions, habitat requirements and conservation status but more research is required to better define occurrence, abundance and biological details for almost all species.},
}
@article {pmid30713441,
year = {2019},
author = {Jacobus, LM},
title = {Ephemeroptera of Canada.},
journal = {ZooKeys},
volume = {},
number = {819},
pages = {211-225},
pmid = {30713441},
issn = {1313-2989},
abstract = {Thus far, 335 currently valid species in 82 genera and 21 families of mayflies (Ephemeroptera) have been documented from Canada, remarkably representing a little more than half of the combined species richness of Canada, Mexico and the USA. The current known species richness for Canada represents an increase of 11.3% as compared to that reported in 1979. Species richness is greatest in the families Heptageniidae (83), Baetidae (76) and Ephemerellidae (45). A total of 328 DNA Barcode Index Numbers (BINs) are available for Canadian mayfly species. The greatest net gains anticipated for future species tallies are for Baetidae (25), Heptageniidae (10) and Leptophlebiidae (10). A total of 66 more species overall is anticipated for Canada, with greatest gains potentially coming from lentic habitats across Canada and from far eastern and far western areas in general. However, even metropolitan areas should not be overlooked for the potential of discovery.},
}
@article {pmid30713438,
year = {2019},
author = {Turnbull, MS and Stebaeva, S},
title = {Collembola of Canada.},
journal = {ZooKeys},
volume = {},
number = {819},
pages = {187-195},
pmid = {30713438},
issn = {1313-2989},
abstract = {The state of knowledge of diversity of Collembola in Canada was assessed by examination of literature and DNA barcode data. There are 474 described extant Collembola species known from Canada, a significant change compared to the 520 species estimated to occur in Canada in 1979 (Richards 1979) and the 341 reported in the most recent national checklist (Skidmore 1993). Given the number of indeterminate or cryptic species records, the dearth of sampling in many regions, and the growing use of genetic biodiversity assessment methods such as Barcode Index Numbers, we estimate the total diversity of Collembola in Canada to be approximately 675 species. Advances in Collembola systematics and Canadian research are discussed.},
}
@article {pmid30713437,
year = {2019},
author = {Langor, DW and deWaard, JR and Snyder, BA},
title = {Myriapoda of Canada.},
journal = {ZooKeys},
volume = {},
number = {819},
pages = {169-186},
pmid = {30713437},
issn = {1313-2989},
abstract = {The currently documented fauna of described species of myriapods in Canada includes 54 Chilopoda, 66 Diplopoda, 23 Pauropoda, and two Symphyla, representing increases of 24, 23, 23, and one species, respectively, since 1979. Of the 145 myriapod species currently documented, 40 species are not native to Canada. The myriapods have not been well documented with DNA barcodes and no barcodes are available for Pauropoda. It is conservatively estimated that at least 93 additional myriapods species will be discovered in Canada: Chilopoda (40), Diplopoda (29), Pauropoda (17), and Symphyla (seven). In general, there is a serious dearth of knowledge about myriapods in Canada, and systematics research and surveys continue to be needed to help document the diversity and distribution of these groups in the country.},
}
@article {pmid30713436,
year = {2019},
author = {Baulieu, F and Knee, W and Nowell, V and Schwarzfeld, M and Lindo, Z and Behan-Pelletier, VM and Lumley, L and Young, MR and Smith, I and Proctor, HC and Mironov, SV and Galloway, TD and Walter, DE and Lindquist, EE},
title = {Acari of Canada.},
journal = {ZooKeys},
volume = {},
number = {819},
pages = {77-168},
pmid = {30713436},
issn = {1313-2989},
abstract = {Summaries of taxonomic knowledge are provided for all acarine groups in Canada, accompanied by references to relevant publications, changes in classification at the family level since 1979, and notes on biology relevant to estimating their diversity. Nearly 3000 described species from 269 families are recorded in the country, representing a 56% increase from the 1917 species reported by Lindquist et al. (1979). An additional 42 families are known from Canada only from material identified to family- or genus-level. Of the total 311 families known in Canada, 69 are newly recorded since 1979, excluding apparent new records due solely to classification changes. This substantial progress is most evident in Oribatida and Hydrachnidia, for which many regional checklists and family-level revisions have been published. Except for recent taxonomic leaps in a few other groups, particularly of symbiotic mites (Astigmata: feather mites; Mesostigmata: Rhinonyssidae), knowledge remains limited for most other taxa, for which most species records are unpublished and may require verification. Taxonomic revisions are greatly needed for a large majority of families in Canada. Based in part on species recorded in adjacent areas of the USA and on hosts known to be present here, we conservatively estimate that nearly 10,000 species of mites occur in Canada, but the actual number could be 15,000 or more. This means that at least 70% of Canada's mite fauna is yet unrecorded. Much work also remains to match existing molecular data with species names, as less than 10% of the ~7500 Barcode Index Numbers for Canadian mites in the Barcode of Life Database are associated with named species. Understudied hosts and terrestrial and aquatic habitats require investigation across Canada to uncover new species and to clarify geographic and ecological distributions of known species.},
}
@article {pmid30713433,
year = {2019},
author = {Shultz, JW},
title = {Opiliones of Canada.},
journal = {ZooKeys},
volume = {},
number = {819},
pages = {57-65},
pmid = {30713433},
issn = {1313-2989},
abstract = {The taxonomic diversity of the Opiliones fauna of Canada is reviewed and summarised. At present, 36 native and seven non-native species have been documented in Canada using traditional morphological taxonomy, although more than 20 species may remain undiscovered based on species diversity in the adjacent United States and evidence from DNA barcoding. Consequently, the native fauna is yet to be fully explored and the number, distribution and ecological effects of non-native species remain unclear. Until the 1960s, work on the Canadian Opiliones fauna was largely conducted by researchers based outside the country. From that time on, several Canadian workers became active. However, these taxonomists have now retired and no one has assumed their role. Thus, there is a need to invigorate taxonomic research on the harvestmen of Canada and for the production of easy-to-use identification tools for use by non-taxonomists.},
}
@article {pmid30713432,
year = {2019},
author = {Bennett, R and Blagoev, G and Copley, C},
title = {Araneae of Canada.},
journal = {ZooKeys},
volume = {},
number = {819},
pages = {41-56},
pmid = {30713432},
issn = {1313-2989},
abstract = {In 1979 nearly 1400 spider species in 32 families either had been recorded (1249) or were believed to occur (~140) in Canada. Twenty years later, although significant progress had been made in survey efforts in some regions, Canada's spider inventory had only increased by approximately 7% to roughly 1500 species known or expected to occur. The family count had increased to 38 but only two additions were truly novel (five family additions and one family deletion were the result of advances in family-level systematics). The first comprehensive taxonomic checklist of Canadian spider species was published in 2010 documenting the regional distributions of 1376 species representing 42 families (three novel since 1999). From 2010 through 2017 new national records steadily accumulated resulting in the current (2018) Canadian inventory of 1477 species classified in 45 families (one novel since 2010). Although there has been close to a 20% increase in the number of spider species recorded in Canada since 1979, much greater increases have occurred in some of the regional species checklists, indicating increasing knowledge of the regional distribution of species previously recorded elsewhere in Canada. For example the regional checklists for Newfoundland, British Columbia, and Prince Edward Island have increased by 69%, 339%, and 520%, respectively. The national and regional increases reflect significant advances in the first two decades of the 21[st] Century in spider faunistics research in previously under-sampled habitats and regions and the development of molecular techniques and consequent barcoding of spiders. Of the 1477 species recorded in Canada, 92% have been successfully DNA barcoded resulting in 1623 unique Barcode Index Numbers (BINs). At least 25 of the BINs are associated with relatively easily distinguished but undescribed morpho-species. The majority, however, appear to indicate the existence of many cryptic species within Canada's known spider fauna. These data, coupled with the fact that novel Canadian or even Nearctic spider species records (including of undescribed species) continue to accumulate annually (especially in habitat-diverse regions such as British Columbia), suggest that Canada's tally of spider species may approach or even exceed 1800.},
}
@article {pmid30713431,
year = {2019},
author = {Langor, DW},
title = {The diversity of terrestrial arthropods in Canada.},
journal = {ZooKeys},
volume = {819},
number = {819},
pages = {9-40},
pmid = {30713431},
issn = {1313-2989},
abstract = {Based on data presented in 29 papers published in the Biota of Canada Special Issue of ZooKeys and data provided herein about Zygentoma, more than 44,100 described species of terrestrial arthropods (Arachnida, Myriapoda, Insecta, Entognatha) are now known from Canada. This represents more than a 34% increase in the number of described species reported 40 years ago (Danks 1979a). The most speciose groups are Diptera (9620 spp.), Hymenoptera (8757), and Coleoptera (8302). Less than 5% of the fauna has a natural Holarctic distribution and an additional 5.1% are non-native species. A conservatively estimated 27,000-42,600 additional species are expected to be eventually discovered in Canada, meaning that the total national species richness is ca. 71,100-86,700 and that currently 51-62% of the fauna is known. Of the most diverse groups, those that are least known, in terms of percent of the Canadian fauna that is documented, are Acari (31%), Thysanoptera (37%), Hymenoptera (46%), and Diptera (32-65%). All groups but Pauropoda have DNA barcodes based on Canadian material. More than 75,600 Barcode Index Numbers have been assigned to Canadian terrestrial arthropods, 63.5% of which are Diptera and Hymenoptera. Much work remains before the Canadian fauna is fully documented, and this will require decades to achieve. In particular, greater and more strategic investment in surveys and taxonomy (including DNA barcoding) is needed to adequately document the fauna.},
}
@article {pmid30710531,
year = {2019},
author = {Laidemitt, MR and Brant, SV and Mutuku, MW and Mkoji, GM and Loker, ES},
title = {The diverse echinostomes from East Africa: With a focus on species that use Biomphalaria and Bulinus as intermediate hosts.},
journal = {Acta tropica},
volume = {193},
number = {},
pages = {38-49},
pmid = {30710531},
issn = {1873-6254},
support = {D43 TW010543/TW/FIC NIH HHS/United States ; P30 GM110907/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Biodiversity ; *Biomphalaria ; *Bulinus ; *Echinostoma ; *Host-Parasite Interactions ; Kenya ; Phylogeny ; Uganda ; },
abstract = {Echinostomes are a diverse group of digenetic trematodes that are globally distributed. The diversity of echinostomes in Africa remains largely unknown, particularly in analyses using molecular markers. Therefore, we were interested in the composition and host usage patterns of African echinostomes, especially those that also use schistosome transmitting snails as intermediate hosts. We collected adults and larval stages of echinostomes from 19 different localities in East Africa (1 locality in Uganda and 18 in Kenya). In this study we provide locality information, host use, museum vouchers, and genetic data for two loci (28S and nad1) from 98 samples of echinostomes from East Africa. Combining morphological features, host use information, and phylogenetic analyses we found 17 clades of echinostomes in East Africa. Four clades were found to use more than one genus of freshwater snails as their first intermediate hosts. We also determined at least partial life cycles (2 of the 3) of four clades using molecular markers. Of the 17 clades, 13 use Biomphalaria or Bulinus as a first intermediate host. The overlap in host usage creates opportunities for competition, including against human schistosomes. Thus, our study can be used as a foundation for future studies to ascertain the interactions between schistosomes and echinostomes in their respective intermediate hosts.},
}
@article {pmid30707854,
year = {2019},
author = {Binan, L and Drobetsky, EA and Costantino, S},
title = {Exploiting Molecular Barcodes in High-Throughput Cellular Assays.},
journal = {SLAS technology},
volume = {24},
number = {3},
pages = {298-307},
doi = {10.1177/2472630318824337},
pmid = {30707854},
issn = {2472-6311},
mesh = {Automation, Laboratory/methods ; Cytological Techniques/*methods ; Flow Cytometry ; High-Throughput Screening Assays/methods ; Microscopy ; *Molecular Probe Techniques ; Staining and Labeling/*methods ; },
abstract = {Multiplexing strategies, which greatly increase the number of simultaneously measured parameters in single experiments, are now being widely implemented by both the pharmaceutical industry and academic researchers. Color has long been used to identify biological signals and, when combined with molecular barcodes, has substantially enhanced the depth of multiplexed sample characterization. Moreover, the recent advent of DNA barcodes has led to an explosion of innovative cell sequencing approaches. Novel barcoding strategies also show great promise for encoding spatial information in transcriptomic studies, and for precise assessment of molecular abundance. Both color- and DNA-based barcodes can be conveniently analyzed with either a microscope or a cytometer, or via DNA sequencing. Here we review the basic principles of several technologies used to create barcodes and detail the type of samples that can be identified with such tags.},
}
@article {pmid30707055,
year = {2019},
author = {Paranaiba, RTF and Carvalho, CBV and Freitas, JM and Fassio, LH and Botelho, &#xc9;D and Neves, DBJ and Silva, RC and Aguiar, SM},
title = {Forensic botany and forensic chemistry working together: application of plant DNA barcoding as a complement to forensic chemistry-a case study in Brazil.},
journal = {Genome},
volume = {62},
number = {1},
pages = {11-18},
doi = {10.1139/gen-2018-0066},
pmid = {30707055},
issn = {1480-3321},
mesh = {Artemisia/chemistry/genetics ; Bicyclic Monoterpenes ; Brazil ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; Forensic Genetics/*methods ; Illicit Drugs/chemistry ; Monoterpenes/analysis ; },
abstract = {Recently, Brazilian Federal Police used forensic chemistry and forensic botany techniques on a case. Two packets containing fragmented plant matter were seized and sent for forensic analysis. Forensic chemistry, the gold standard for evaluating plant material suspected to contain illicit substances, did not find illicit materials. Gas chromatography coupled mass spectrometry (GC-MS) identified thujone in the botanical material. Thujone is a chemical compound naturally found in many plant species, notably Artemisia absinthium. Because doubt remained, we next used plant DNA barcoding methods. Total DNA from plant tissue fragments was extracted and five different DNA regions were amplified, sequenced, and analyzed using plant DNA barcoding methods. Genetic analysis yielded 30 good quality sequences representing five taxa. Most specimens were identified as A. absinthium. Few studies focus on practical forensic applications of plant DNA barcoding methods using a case solved in a forensic laboratory with its difficulties and limitations. To the best of our knowledge, this is the first study to report an effective joint effort of forensic chemistry and botany techniques to assess plant material in Brazil. The availability of a new technical approach for the genetic sequencing of plant species will enhance many forensic investigations and inspire similar initiatives.},
}
@article {pmid30705397,
year = {2019},
author = {Hobbs, CAD and Potts, RWA and Bjerregaard Walsh, M and Usher, J and Griffiths, AM},
title = {Using DNA Barcoding to Investigate Patterns of Species Utilisation in UK Shark Products Reveals Threatened Species on Sale.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {1028},
pmid = {30705397},
issn = {2045-2322},
support = {MR/N006364/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animal Fins ; Animals ; *Commerce ; DNA Barcoding, Taxonomic/*methods ; Endangered Species/*economics ; Geography ; Meat/*economics ; Sharks/*genetics ; Species Specificity ; United Kingdom ; },
abstract = {Many shark populations are in decline, primarily due to overexploitation. In response, conservation measures have been applied at differing scales, often severely restricting sales of declining species. Therefore, DNA barcoding was used to investigate sales of shark products in fishmongers and fish and chip takeaways in England. The majority of samples were identified as Spiny Dogfish (Squalus acanthias), which is critically endangered in the Northeast Atlantic and landings have been prohibited (although there is evidence of importation of this species). Significant differences in the species sold between retailer types were also identified, suggesting differing supply chains. The results underline issues surrounding the use of 'umbrella' sales terms where many species are labelled with the same designation. This denies consumer choice as purchasers cannot easily avoid declining species or those associated with high levels of toxicants. For the first time in Europe, minibarcodes are also used to identify species from dried shark fins. Despite a small sample size, analysis of UK wholesaler fins identified threatened sharks, including the endangered and CITES listed Scalloped Hammerhead (Sphyrna lewini). This highlights the global nature of the damaging trade in endangered shark species, in which Europe and the UK have a continuing role.},
}
@article {pmid30703281,
year = {2019},
author = {Gill, BA and Musili, PM and Kurukura, S and Hassan, AA and Goheen, JR and Kress, WJ and Kuzmina, M and Pringle, RM and Kartzinel, TR},
title = {Plant DNA-barcode library and community phylogeny for a semi-arid East African savanna.},
journal = {Molecular ecology resources},
volume = {19},
number = {4},
pages = {838-846},
doi = {10.1111/1755-0998.13001},
pmid = {30703281},
issn = {1755-0998},
support = {//The Nature Conservancy/ ; DEB-1355122//National Science Foundation/ ; DEB-1457679//National Science Foundation/ ; DEB-1556728//National Science Foundation/ ; IOS-1656527//National Science Foundation/ ; Natural Sciences and Engineering Council Research&#xa0;Tools and Instruments Grant//National Science Foundation/ ; },
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/chemistry/*genetics ; DNA, Ribosomal Spacer ; *Databases, Genetic ; Grassland ; Kenya ; *Phylogeny ; Plant Proteins/genetics ; Plants/*classification/*genetics ; },
abstract = {Applications of DNA barcoding include identifying species, inferring ecological and evolutionary relationships between species, and DNA metabarcoding. These applications require reference libraries that are not yet available for many taxa and geographic regions. We collected, identified, and vouchered plant specimens from Mpala Research Center in Laikipia, Kenya, to develop an extensive DNA-barcode library for a savanna ecosystem in equatorial East Africa. We amassed up to five DNA barcode markers (rbcL, matK, trnL-F, trnH-psbA, and ITS) for 1,781 specimens representing up to 460 species (~92% of the known flora), increasing the number of plant DNA barcode records for Africa by ~9%. We evaluated the ability of these markers, singly and in combination, to delimit species by calculating intra- and interspecific genetic distances. We further estimated a plant community phylogeny and demonstrated its utility by testing if evolutionary relatedness could predict the tendency of members of the Mpala plant community to have or lack "barcode gaps", defined as disparities between the maximum intra- and minimum interspecific genetic distances. We found barcode gaps for 72%-89% of taxa depending on the marker or markers used. With the exception of the markers rbcL and ITS, we found that evolutionary relatedness was an important predictor of barcode-gap presence or absence for all of the markers in combination and for matK, trnL-F, and trnH-psbA individually. This plant DNA barcode library and community phylogeny will be a valuable resource for future investigations.},
}
@article {pmid30702138,
year = {2019},
author = {Domingues, RR and Garrone-Neto, D and Hilsdorf, AWS and Gadig, OBF},
title = {Use of mucus as a non-invasive sampling method for DNA barcoding of stingrays and skates (batoid elasmobranchs).},
journal = {Journal of fish biology},
volume = {94},
number = {3},
pages = {512-516},
doi = {10.1111/jfb.13919},
pmid = {30702138},
issn = {1095-8649},
support = {#2011/18513-9//The S&#xe3;o Paulo Research Foundation (FAPESP)/ ; #2013/08675-7//The S&#xe3;o Paulo Research Foundation (FAPESP)/ ; #2017/02420-8//The S&#xe3;o Paulo Research Foundation (FAPESP)/ ; #308430/2015-8//The National Council for Scientific and Technological Development (CNPq)/ ; },
mesh = {Animals ; Base Sequence ; DNA/*analysis ; DNA Barcoding, Taxonomic/*methods ; Elasmobranchii ; Electron Transport Complex IV/genetics ; Mucus/*chemistry ; *Phylogeny ; Skates, Fish/*genetics ; },
abstract = {In this study we tested the use of mucus from five species of Neotropical marine batoid elasmobranchs to extract genomic DNA for barcoding and phylogenetic analysis. The DNA from all individuals sampled was successfully amplified and sequenced for molecular barcode, allowing 99-100% accuracy to the species level. This method proved to provide reliable and good-quality DNA for barcoding and phylogenetic analysis of Neotropical elasmobranchs, through rapid handling and with low disturbance to animals.},
}
@article {pmid30701382,
year = {2019},
author = {Bouguerche, C and Gey, D and Justine, JL and Tazerouti, F},
title = {Microcotyle visa n. sp. (Monogenea: Microcotylidae), a gill parasite of Pagrus caeruleostictus (Valenciennes) (Teleostei: Sparidae) off the Algerian coast, Western Mediterranean.},
journal = {Systematic parasitology},
volume = {96},
number = {2},
pages = {131-147},
pmid = {30701382},
issn = {1573-5192},
mesh = {Animals ; Cyclooxygenase 1/genetics ; Gills/*parasitology ; Mediterranean Sea ; Perciformes/*parasitology ; Species Specificity ; Trematoda/anatomy &amp; histology/*classification/genetics/*physiology ; },
abstract = {Parasite biodiversity of fish of the southern part of the Mediterranean sea is still incompletely explored. We describe here Microcotyle visa n. sp. from the gill filaments of the bluespotted seabream Pagrus caeruleostictus (Valenciennes) (Sparidae) collected off the Algerian coast. The identity of fish hosts was confirmed by barcoding. Microcotyle visa n. sp. is herein described and illustrated. Analysis of the cox1 gene of the monogeneans revealed minor intraspecific variation (1.4%), an order of magnitude lower than the distance between this species and other Microcotyle species (10-15 %). Microcotyle visa n. sp. is distinguished from Microcotyle erythrini van Beneden &amp; Hesse, 1863, a congener infesting sparids, on the basis of morphological (size of clamps, number of testes) and molecular (cox1) differences. This is the fourth member of the genus known to parasitise a sparid host. A species of Paramicrocotyle sp. included in the molecular analysis was nested within a robust Microcotyle + Paramicrocotyle clade; in the absence of demonstrated molecular and morphological differences, we consider that Paramicrocotyle Caballero &amp; Bravo-Hollis, 1972 is a junior synonym of Microcotyle van Beneden &amp; Hesse, 1863 and transfer two species of Paramicrocotyle as Microcotyle danielcarrioni (Martinez &amp; Barrantes, 1977) n. comb. and Microcotyle moyanoi (Villalba &amp; Fernandes, 1986) n. comb.},
}
@article {pmid30701138,
year = {2019},
author = {Yang, Z and Wang, G and Ma, Q and Ma, W and Liang, L and Zhao, T},
title = {The complete chloroplast genomes of three Betulaceae species: implications for molecular phylogeny and historical biogeography.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6320},
pmid = {30701138},
issn = {2167-8359},
abstract = {BACKGROUND: Previous phylogenetic conclusions on the family Betulaceae were based on either morphological characters or traditional single loci, which may indicate some limitations. The chloroplast genome contains rich polymorphism information, which is very suitable for phylogenetic studies. Thus, we sequenced the chloroplast genome sequences of three Betulaceae species and performed multiple analyses to investigate the genome variation, resolve the phylogenetic relationships, and clarify the divergence history.<br><br>METHODS: Chloroplast genomes were sequenced using the high-throughput sequencing. A comparative genomic analysis was conducted to examine the global genome variation and screen the hotspots. Three chloroplast partitions were used to reconstruct the phylogenetic relationships using Maximum Likelihood and Bayesian Inference approaches. Then, molecular dating and biogeographic inferences were conducted based on the whole chloroplast genome data.<br><br>RESULTS: Betulaceae chloroplast genomes consisted of a small single-copy region and a large single copy region, and two copies of inverted repeat regions. Nine hotspots can be used as potential DNA barcodes for species delimitation. Phylogenies strongly supported the division of Betulaceae into two subfamilies: Coryloideae and Betuloideae. The phylogenetic position of Ostryopsis davidiana was controversial among different datasets. The divergence time between subfamily Coryloideae and Betuloideae was about 70.49 Mya, and all six extant genera were inferred to have diverged fully by the middle Oligocene. Betulaceae ancestors were probably originated from the ancient Laurasia.<br><br>DISCUSSIONS: This research elucidates the potential of chloroplast genome sequences in the application of developing molecular markers, studying evolutionary relationships and historical dynamic of Betulaceae.It also reveals the advantages of using chloroplast genome data to illuminate those phylogenies that have not been well solved yet by traditional approaches in other plants.},
}
@article {pmid30698997,
year = {2019},
author = {Baillargeon, P and Coss-Flores, K and Singhera, F and Shumate, J and Williams, H and DeLuca, L and Spicer, TP and Scampavia, L},
title = {Design of Microplate-Compatible Illumination Panels for a Semiautomated Benchtop Pipetting System.},
journal = {SLAS technology},
volume = {24},
number = {4},
pages = {399-407},
doi = {10.1177/2472630318822476},
pmid = {30698997},
issn = {2472-6311},
mesh = {Automation, Laboratory/instrumentation/*methods ; Lighting/instrumentation/*methods ; Specimen Handling/instrumentation/*methods ; User-Computer Interface ; },
abstract = {Microplates are an essential tool used in laboratories for storing research materials and performing assays. Many types of laboratory automation exist that greatly reduce the effort needed to utilize microplates; however, there are cases where the use of such automation is not feasible or practical. In these instances, researchers must work in an environment where liquid handling operations are performed manually with handheld pipetting devices. This type of work is tedious and error-prone as it relies on researchers to manually track a significant amount of metadata, including transfer volumes, plate barcodes, well contents, and well locations. To address this challenge, we have developed an open-source, semiautomated benchtop system that facilitates manual pipetting using visual indicators. This device streamlines the process of identifying the location of wells so that the researcher can perform manual transfers in a more efficient, reliable, and accurate manner. This system utilizes a graphical user interface that allows the user to load worklists and then issues commands to illuminate wells of interest, providing a visual indicator for users to follow in real time. The software and hardware tools utilized for development, along with the implementation techniques used to produce this system, are described within.},
}
@article {pmid30697333,
year = {2019},
author = {Gous, A and Swanevelder, DZH and Eardley, CD and Willows-Munro, S},
title = {Plant-pollinator interactions over time: Pollen metabarcoding from bees in a historic collection.},
journal = {Evolutionary applications},
volume = {12},
number = {2},
pages = {187-197},
pmid = {30697333},
issn = {1752-4571},
abstract = {Pollination is a key component in agricultural food production and ecosystem maintenance, with plant-pollinator interactions an important research theme in ecological and evolutionary studies. Natural history collections provide unique access to samples collected at different spatial and temporal scales. Identification of the plant origins of pollen trapped on the bodies of pollinators in these collections provides insight into historic plant communities and pollinators' preferred floral taxa. In this study, pollen was sampled from Megachile venusta Smith bees from the National Collection of Insects, South Africa, spanning 93 years. Three barcode regions, the internal transcribed spacer 1 and 2 (ITS1 and ITS2) and ribulose-1,5-biphosphate carboxylase (rbcL), were sequenced from mixed pollen samples using a next-generation sequencing approach (MiSeq, Illumina). Sequenced reads were compared to sequence reference databases that were generated by extracting sequence and taxonomic data from GenBank. ITS1 and ITS2 were amplified successfully across all (or most) samples, while rbcL performed inconsistently. Age of sample had no impact on sequencing success. Plant classification was more informative using ITS2 than ITS1 barcode data. This study also highlights the need for comprehensive reference databases as limited local plant sequence representation in reference databases resulted in higher-level taxon classifications being more confidently interpreted. The results showed that small, insect-carried pollen samples from historic bee specimens collected from as early as 1914 can be used to obtain pollen metabarcodes. DNA metabarcoding of mixed origin pollen samples provided a faster, more accurate method of determining pollen provenance, without the need for expert palynologists. The use of historic collections to sample pollen directly from pollinators provided additional value to these collections. Sampling pollen from historic collections can potentially provide the spatial and temporal scales for investigations into changes in plant community structure or pollinator floral choice in the face of global climate change.},
}
@article {pmid30693970,
year = {2020},
author = {Phelps, MP and Seeb, LW and Seeb, JE},
title = {Transforming ecology and conservation biology through genome editing.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {34},
number = {1},
pages = {54-65},
doi = {10.1111/cobi.13292},
pmid = {30693970},
issn = {1523-1739},
mesh = {*CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats ; Conservation of Natural Resources ; Ecosystem ; *Gene Editing ; },
abstract = {As the conservation challenges increase, new approaches are needed to help combat losses in biodiversity and slow or reverse the decline of threatened species. Genome-editing technology is changing the face of modern biology, facilitating applications that were unimaginable only a decade ago. The technology has the potential to make significant contributions to the fields of evolutionary biology, ecology, and conservation, yet the fear of unintended consequences from designer ecosystems containing engineered organisms has stifled innovation. To overcome this gap in the understanding of what genome editing is and what its capabilities are, more research is needed to translate genome-editing discoveries into tools for ecological research. Emerging and future genome-editing technologies include new clustered regularly interspaced short palindromic repeats (CRISPR) targeted sequencing and nucleic acid detection approaches as well as species genetic barcoding and somatic genome-editing technologies. These genome-editing tools have the potential to transform the environmental sciences by providing new noninvasive methods for monitoring threatened species or for enhancing critical adaptive traits. A pioneering effort by the conservation community is required to apply these technologies to real-world conservation problems.},
}
@article {pmid30691682,
year = {2019},
author = {Aalam, SMM and Beer, PA and Kannan, N},
title = {Assays for functionally defined normal and malignant mammary stem cells.},
journal = {Advances in cancer research},
volume = {141},
number = {},
pages = {129-174},
doi = {10.1016/bs.acr.2018.12.004},
pmid = {30691682},
issn = {2162-5557},
mesh = {Animals ; Biological Assay ; Breast Neoplasms/*pathology ; Cell Differentiation/physiology ; Cell Lineage ; Female ; Humans ; Mammary Glands, Animal/*cytology/pathology ; Mammary Glands, Human/*cytology/pathology ; Multipotent Stem Cells/*cytology/pathology ; Neoplastic Stem Cells/*pathology ; },
abstract = {The discovery of rare, heterogeneous self-renewing stem cells with shared developmental and molecular features within epithelial components of mammary gland and breast cancers has provided a conceptual framework to understand cellular composition of these tissues and mechanisms that control their number. These normal mammary epithelial stem cells (MaSCs) and breast cancer stem cells (BCSCs) were identified and analyzed using transplant assays (namely mammary repopulating unit (MRU) assay, mammary tumor-initiating cell (TIC) assay), which reveal their latent ability to regenerate respective normal and malignant epithelial tissues with self-renewing units displaying hierarchical cellular differentiation over multiple generations in recipient mice. "Next-generation" methods using "barcoded" normal and malignant mammary cells, with the help of next-generation sequencing (NGS) technology, have revealed hidden complexity and heterogeneous growth potential of MaSCs and BCSCs. Several single markers or combinations of markers have been reported to prospectively enrich MaSCs and BCSCs. Such markers and the extent to which they enrich for MaSCs and BCSCs activity require a critical appraisal. Also, knowledge of the functional assays and their limitations and harmonious reporting of results is a prerequisite to improve our understanding of MaSCs and BCSCs. This chapter describes evolution of the concept of MaSCs and BCSCs, and specific methodologies to investigate them.},
}
@article {pmid30688305,
year = {2019},
author = {Stratton, JA and Sinha, S and Shin, W and Labit, E and Chu, TH and Shah, PT and Midha, R and Biernaskie, J},
title = {Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {143},
pages = {},
doi = {10.3791/58709},
pmid = {30688305},
issn = {1940-087X},
support = {//CIHR/Canada ; },
mesh = {Animals ; Computational Biology ; High-Throughput Nucleotide Sequencing ; Mammals/*genetics ; Mice ; Organ Specificity/*genetics ; Quality Control ; Sequence Analysis, RNA ; Single-Cell Analysis/*methods ; Transcriptome/*genetics ; },
abstract = {The analysis of single cell gene expression across thousands of individual cells within a tissue or microenvironment is a valuable tool for identifying cell composition, discrimination of functional states, and molecular pathways underlying observed tissue functions and animal behaviors. However, the isolation of intact, healthy single cells from adult mammalian tissues for subsequent downstream single cell molecular analysis can be challenging. This protocol describes the general processes and quality control checks necessary to obtain high-quality adult single cell preparations from the nervous system or skin that enabled subsequent unbiased single cell RNA sequencing and analysis. Guidelines for downstream bioinformatic analysis are also provided.},
}
@article {pmid30688015,
year = {2019},
author = {Li, H and Kong, L and Wang, K and Zhang, S and Motokawa, M and Wu, Y and Wang, W and Li, Y},
title = {Molecular phylogeographic analyses and species delimitations reveal that Leopoldamys edwardsi (Rodentia: Muridae) is a species complex.},
journal = {Integrative zoology},
volume = {14},
number = {5},
pages = {494-505},
doi = {10.1111/1749-4877.12378},
pmid = {30688015},
issn = {1749-4877},
mesh = {Animal Distribution ; Animals ; China ; DNA, Mitochondrial/genetics ; Genetic Variation ; Muridae/*genetics/physiology ; *Phylogeny ; Phylogeography ; Species Specificity ; },
abstract = {Leopoldamys edwardsi is a species with wide distribution ranges in southern China but is not discussed in studies on geographic variation and species differentiation. We used 2 mitochondrial (Cytb, CO1) and 3 nuclear (GHR, IRBP and RAG1) genes to clarify species phylogeography and geographical differentiation. Maximum likelihood (ML) and Bayesian phylogenetic inference (BI) trees consistently indicated that L. edwardsi is a species complex containing 3 main lineages with high Kimura-2-parameter (K2P) divergences (i.e. lineages LN , LS and LHN) found in the northern and southern China and Hainan Island, respectively. The 3 species delimitation methods, automated barcoding gap discovery, Bayesian poisson tree process analysis and Bayesian phylogenetics and phylogeography, consistently supported the existence of cryptic species. Divergence times among the main lineages were inferred to be during the Pleistocene, with LHN /LS split at 1.33 Ma and LN /(LHN +LS) at 2.61 Ma; the diversifications of L. edwardsi complex might be caused by the rapid uplifts of Tibetan Plateau, paleoclimate change and complex topography. The divergence between LHN and LS was probably related to the separation of Hainan Island from the mainland via the formation of the Qiongzhou Strait. Lineages LN and (LS +LHN) likely diverged due to the Wuyi-Nanling mountain range forming a dispersal barrier. Our results suggested that L. edwardsi complex contains at least 3 distinct species: LHN represents L. hainanensis, endemic to Hainan Island and previously considered as a subspecies L. e. hainanensis; LS represents a cryptic species distributed throughout the southern Chinese continent; and LN represents the nominotypical species L. edwardsi.},
}
@article {pmid30687457,
year = {2019},
author = {Lukhtanov, VA},
title = {Two types of highly ordered micro- and macrochromosome arrangement in metaphase plates of butterflies (Lepidoptera).},
journal = {Comparative cytogenetics},
volume = {13},
number = {1},
pages = {19-25},
pmid = {30687457},
issn = {1993-0771},
abstract = {In karyotype of many organisms, chromosomes form two distinct size groups: macrochromosomes and microchromosomes. During cell divisions, the position of the macro- and microchromosomes is often ordered within metaphase plate. In many reptiles, amphibians, birds, insects of the orthopteran family Tettigoniidae and in some plants, a so called "reptilian" type organization is found, with microchromosomes situated in the center of metaphase plate and with macrochromosomes situated at the periphery. An opposite, "lepidopteran" type is known in butterflies and moths (i.e. in the order Lepidoptera) and is characterized by macrochromosomes situated in the center and by microchromosomes situated at the periphery. The anomalous arrangement found in Lepidoptera was previously explained by holocentric organization of their chromosomes. Here I analyse the structure of meiotic metaphase I plates in ithomiine butterfly, Forbestraolivencia (H. Bates, 1862) (Nymphalidae, Danainae, Ithomiini) which has a clear "reptilian" organization, contrary to previous observations in Lepidoptera. In this species large bivalents (i.e. macrochromosomes) form a regular peripheral circle, whereas the minute bivalents (i.e. microchromosomes) occupy the center of this circle. The reasons and possible mechanisms resulting in two drastically different spatial chromosome organization in butterflies are discussed.},
}
@article {pmid30686928,
year = {2019},
author = {Cancian de Araujo, B and Schmidt, S and Schmidt, O and von Rintelen, T and von Rintelen, K and Floren, A and Ubaidillah, R and Peggie, D and Balke, M},
title = {DNA barcoding data release for Coleoptera from the Gunung Halimun canopy fogging workpackage of the Indonesian Biodiversity Information System (IndoBioSys) project.},
journal = {Biodiversity data journal},
volume = {},
number = {7},
pages = {e31432},
pmid = {30686928},
issn = {1314-2828},
abstract = {We present the results of a DNA barcoding pipeline that was established as part of the German-Indonesian IndobioSys project - Indonesian Biodiversity Information System. Our data release provides the first large-scale diversity assessment of Indonesian coleoptera obtained by canopy fogging. The project combined extensive fieldwork with databasing, DNA barcode based species delineation and the release of results in collaboration with Indonesian counterparts, aimed at supporting further analyses of the data. Canopy fogging on 28 trees was undertaken at two different sites, Cikaniki and Gunung Botol, in the south-eastern area of the Gunung Halimun-Salak National Park in West Java, Indonesia. In total, 7,447 specimens of Coleoptera were processed, of which 3,836 specimens produced DNA barcode sequences that were longer than 300 bp. A total of 3,750 specimens were assigned a Barcode Index Number (BIN), including 2,013 specimens from Cikaniki and 1,737 specimens from Gunung Botol. The 747 BINs, that were obtained, represented 39 families of Coleoptera. The distribution of specimens with BINs per tree was quite heterogeneous in both sites even in terms of the abundance of specimens or diversity of BINs. The specimen distribution per taxon was heterogeneous as well. Some 416 specimens could not be identified to family level, corresponding to 72 BINs that lack a family level identification. The data have shown a large heterogeneity in terms of abundance and distribution of BINs between sites, trees and families of Coleoptera. From the total of 747 BINs that were recovered, 421 (56%) are exclusive from a single tree. Although the two study sites were in close proximity and separated by a distance of only about five kilometres, the number of shared BINs between sites is low, with 81 of the 747 BINs. With this data release, we expect to shed some light on the largely hidden diversity in the canopy of tropical forests in Indonesia and elsewhere.},
}
@article {pmid30686322,
year = {2019},
author = {Bowdle, A and Jelacic, S and Nair, B and Jense, R and Webster, CS and Merry, AF},
title = {Why we scan the barcodes of anaesthetic medications.},
journal = {British journal of anaesthesia},
volume = {122},
number = {2},
pages = {e24-e26},
doi = {10.1016/j.bja.2018.11.014},
pmid = {30686322},
issn = {1471-6771},
mesh = {*Anesthetics ; Humans ; Medication Errors ; *Self Report ; },
}
@article {pmid30686100,
year = {2019},
author = {Yanqing, C and Bo, W and Ping, W and Bisheng, H and Hegang, L and Chao, X and Mingli, W and Nili, W and Di, L and Zhigang, H and Shilin, C},
title = {Rapid identification of common medicinal snakes and their adulterants using the Bar-HRM analysis method.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {2},
pages = {367-374},
doi = {10.1080/24701394.2018.1532417},
pmid = {30686100},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Snakes/classification/*genetics ; },
abstract = {Effective identification methods for snake species are lacking, exacerbating the extermination of medicinal and commercially valuable snake species. Hence, it is imperative to find fast and reliable methods to distinguish snake samples available on the market. Seventy-three samples from four families belonging to 13 genera were collected in China and found to contain common medicinal snakes and their adulterants. Cytochrome oxidase I (COI) was utilized as a DNA barcode to analyse these common snakes, and a DNA mini-barcode was employed for fast detection. Then, the DNA mini-barcode assays were coupled with a high-resolution melting (HRM) analysis (Bar-HRM) to realize the rapid discrimination of these snake species. The results showed the power of DNA barcoding with COI, which was capable of distinguishing all collected snake samples, and the combined Bar-HRM method can successfully identify the adulterants and different snake species. In particular, Bar-HRM revealed Bungarus fasciatus adulterants in B. multicinctus at concentrations as low as 1.6%. Moreover, the results of the study confirmed the effectiveness of the technique in terms of the rapid identification of snakes, which has great potential for ensuring the safety of commercially valuable snake species.},
}
@article {pmid30683922,
year = {2019},
author = {Fiévet, A and Bernard, V and Tenreiro, H and Dehainault, C and Girard, E and Deshaies, V and Hupe, P and Delattre, O and Stern, MH and Stoppa-Lyonnet, D and Golmard, L and Houdayer, C},
title = {ART-DeCo: easy tool for detection and characterization of cross-contamination of DNA samples in diagnostic next-generation sequencing analysis.},
journal = {European journal of human genetics : EJHG},
volume = {27},
number = {5},
pages = {792-800},
pmid = {30683922},
issn = {1476-5438},
support = {ANR-10-EQPX-03//Agence Nationale de la Recherche (French National Research Agency)/International ; },
mesh = {Alleles ; DNA/*analysis ; *DNA Contamination ; Genotype ; *High-Throughput Nucleotide Sequencing ; Humans ; *Molecular Diagnostic Techniques ; Polymorphism, Single Nucleotide/genetics ; },
abstract = {Next-generation sequencing (NGS) is routinely used for constitutional genetic analysis. However, cross-contamination between samples constitutes a major risk that could impact the results of the analysis. We have developed ART-DeCo, a tool using the allelic ratio (AR) of the Single Nucleotide Polymorphisms sequenced with regions of interest. When a sample is contaminated by DNA with a different genotype, unexpected ARs are obtained, which are in turn used for detection of contamination with a screening test, followed by identification and quantification of the contaminant. Following optimization, ART-DeCo was applied to 2222 constitutional DNA samples. The screening test was positive for 191 samples. In 33 cases (contamination percentages: 1.3% to 29.2%), the contaminant was identified and was mostly located in adjacent wells. Three other positive cases were due to barcoding errors or mixture of two DNA samples. Interestingly, the last contaminated sample corresponded to a bone marrow transplant recipient. Lastly, no contaminant was identified in 154 weakly positive (< 4%) samples that were considered to be irrelevant to constitutional genetic analysis. ART-DeCo lends itself to mandatory quality control procedures, also highlighting the delicate steps of library preparation, resulting in practice improvement. Importantly, ART-DeCo can be implemented in any NGS workflow, from gene panel to genome-wide analyses. https://sourceforge.net/projects/ngs-art-deco/ .},
}
@article {pmid30680143,
year = {2019},
author = {Rytkönen, S and Vesterinen, EJ and Westerduin, C and Leviäkangas, T and Vatka, E and Mutanen, M and Välimäki, P and Hukkanen, M and Suokas, M and Orell, M},
title = {From feces to data: A metabarcoding method for analyzing consumed and available prey in a bird-insect food web.},
journal = {Ecology and evolution},
volume = {9},
number = {1},
pages = {631-639},
pmid = {30680143},
issn = {2045-7758},
abstract = {Diets play a key role in understanding trophic interactions. Knowing the actual structure of food webs contributes greatly to our understanding of biodiversity and ecosystem functioning. The research of prey preferences of different predators requires knowledge not only of the prey consumed, but also of what is available. In this study, we applied DNA metabarcoding to analyze the diet of 4 bird species (willow tits Poecile montanus, Siberian tits Poecile cinctus, great tits Parus major and blue tits Cyanistes caeruleus) by using the feces of nestlings. The availability of their assumed prey (Lepidoptera) was determined from feces of larvae (frass) collected from the main foraging habitat, birch (Betula spp.) canopy. We identified 53 prey species from the nestling feces, of which 11 (21%) were also detected from the frass samples (eight lepidopterans). Approximately 80% of identified prey species in the nestling feces represented lepidopterans, which is in line with the earlier studies on the parids' diet. A subsequent laboratory experiment showed a threshold for fecal sample size and the barcoding success, suggesting that the smallest frass samples do not contain enough larval DNA to be detected by high-throughput sequencing. To summarize, we apply metabarcoding for the first time in a combined approach to identify available prey (through frass) and consumed prey (via nestling feces), expanding the scope and precision for future dietary studies on insectivorous birds.},
}
@article {pmid30680104,
year = {2019},
author = {Tapolczai, K and Vasselon, V and Bouchez, A and Stenger-Kovács, C and Padisák, J and Rimet, F},
title = {The impact of OTU sequence similarity threshold on diatom-based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean).},
journal = {Ecology and evolution},
volume = {9},
number = {1},
pages = {166-179},
pmid = {30680104},
issn = {2045-7758},
abstract = {Extensive studies on the taxonomic resolution required for bioassessment purposes have determined that resolution above species level (genus, family) is sufficient for their use as indicators of relevant environmental pressures. The high-throughput sequencing (HTS) and meta-barcoding methods now used for bioassessment traditionally employ an arbitrary sequence similarity threshold (SST) around 95% or 97% to cluster sequences into operational taxonomic units, which is considered descriptive of species-level resolution. In this study, we analyzed the effect of the SST on the resulting diatom-based ecological quality index, which is based on OTU abundance distribution along a defined environmental gradient, ideally avoiding taxonomic assignments that could result in high rates of unclassified OTUs and biased final values. A total of 90 biofilm samples were collected in 2014 and 2015 from 51 stream sites on Mayotte Island in parallel with measures of relevant physical and chemical parameters. HTS sequencing was performed on the biofilms using the rbcL region as the genetic marker and diatom-specific primers. Hierarchical clustering was used to group sequences into OTUs using 20 experimental SST levels (80%-99%). An OTU-based quality index (IdxOTU) was developed based on a weighted average equation using the abundance profiles of the OTUs. The developed IdxOTU revealed significant correlations between the IdxOTU values and the reference pressure gradient, which reached maximal performance using an SST of 90% (well above species level delimitation). We observed an interesting and important trade-off with the power to discriminate between sampling sites and index stability that will greatly inform future applications of the index. Taken together, the results from this study detail a thoroughly optimized and validated approach to generating robust, reproducible, and complete indexes that will greatly facilitate effective and efficient environmental monitoring.},
}
@article {pmid30680092,
year = {2019},
author = {Davis, MJ and Andersen, JC and Elkinton, J},
title = {Identification of the parasitoid community associated with an outbreaking gall wasp, Zapatella davisae, and their relative abundances in New England and Long Island, New York.},
journal = {Ecology and evolution},
volume = {9},
number = {1},
pages = {19-25},
pmid = {30680092},
issn = {2045-7758},
abstract = {Gall wasps (Hymenoptera: Cynipidae) are phytophagous insects that often go unnoticed; however, when they are introduced to a new area or released from their natural enemies, they have the capacity to outbreak and cause extensive foliar damage. One such outbreaking pest, Zapatella davisae (Cynipidae: Cynipini), causes significant damage and mortality to black oak, Quercus velutina, in the northeastern United States. In this study, we aimed to identify the parasitoid community associated with Z. davisae, compare differences in percent parasitism of Z. davisae in Cape Cod and Long Island, and determine which parasitoid species contribute most to parasitism in each region. From both locations, we reared parasitoids, identified morphological groups, analyzed percent parasitism rates for each group, and used DNA barcoding to provide species-level identifications. On Long Island, there was nearly 100% parasitism in 2015 followed by a near total collapse of the population in 2016. In contrast, parasitism rates were lower and remained consistent on Cape Cod between 2015 and 2016, which may explain the greater canopy damage observed in that region. Species of Sycophila were the dominant parasitoids, with one species Sycophila nr. novascotiae representing ~65% of reared parasitoids from Long Island, and two species of Sycophila (S. nr. novascotiae and S. foliatae) with near equal representations on Cape Cod. In order to manage an insect pest, it is important to understand factors that influence its mortality and survival. An understanding of how these infestations progress overtime can help predict the impact that newer infestations in Nantucket, MA, and coastal Rhode Island will have on black oak populations and will aid in the management of this rapidly spreading gall wasp pest.},
}
@article {pmid30679638,
year = {2019},
author = {Mauvisseau, Q and Burian, A and Gibson, C and Brys, R and Ramsey, A and Sweet, M},
title = {Influence of accuracy, repeatability and detection probability in the reliability of species-specific eDNA based approaches.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {580},
pmid = {30679638},
issn = {2045-2322},
mesh = {Aquatic Organisms/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Environmental/*analysis ; Electron Transport Complex IV/genetics ; Metagenomics/*methods ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sensitivity and Specificity ; },
abstract = {Environmental DNA (eDNA) barcoding has a high potential to increase the cost-efficiency of species detection and monitoring in aquatic habitats. However, despite vast developments in the field, many published assays often lack detailed validation and there is little to no commonly (agreed upon) standardization of protocols. In this study, we evaluated the reliability of eDNA detection and quantification using published primers and assays targeting the Freshwater Pearl Mussel as a model organism. We first assessed limits of detection for two different target genes (COI and 16S) following the MIQE guidelines, and then tested the reliability of quantification in a double-blind mesocosm experiment. Our results reveal that different methodological indicators, namely accuracy, repeatability and detection probability affected the reliability of eDNA measurement at the different levels tested. The selection of the optimal analytical method was mainly determined by detection probability. Both the COI and 16S assays were highly specific for the targeted organism and showed similar accuracy and repeatability, whilst the limit of detection was clearly lower for the COI based approach. In contrast, the reliability of eDNA quantification hinged on repeatability, reflected by the scattering (r[2] = 0.87) around the relationship between eDNA and mussel density in mesocosms. A bootstrapping approach, which allowed for the assignment of measures associated with repeatability of samples, revealed that variability between natural replicates (i.e. accuracy) strongly influenced the number of replicates required for a reliable species detection and quantification in the field.},
}
@article {pmid30679622,
year = {2019},
author = {Anglès d'Auriac, MB and Le Gall, L and Peña, V and Hall-Spencer, JM and Steneck, RS and Fredriksen, S and Gitmark, J and Christie, H and Husa, V and Grefsrud, ES and Rinde, E},
title = {Efficient coralline algal psbA mini barcoding and High Resolution Melt (HRM) analysis using a simple custom DNA preparation.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {578},
pmid = {30679622},
issn = {2045-2322},
mesh = {Animals ; Anthozoa/*microbiology ; DNA Barcoding, Taxonomic/*methods ; DNA, Algal/chemistry/genetics/*isolation &amp; purification ; *Nucleic Acid Denaturation ; Photosystem II Protein Complex/*genetics ; Rhodophyta/*classification/enzymology/*genetics ; },
abstract = {Coralline algae form extensive maerl and rhodolith habitats that support a rich biodiversity. Calcium carbonate harvesting as well as trawling activities threatens this ecosystem. Eleven species were recorded so far as maerl-forming in NE Atlantic, but identification based on morphological characters is unreliable. As for most red algae, we now use molecular characters to resolve identification of these taxa. However, obtaining DNA sequences requires time and resource demanding methods. The purpose of our study was to improve methods for achieving simple DNA extraction, amplification, sequencing and sequence analysis to allow robust identification of maerl species and other coralline algae. Our novel and easy DNA preparation method for coralline algae was of sufficient quality for qPCR amplification and sequencing of all 47 tested samples. The new psbA qPCR assay successfully amplified a 350 bp fragment identifying six species and uncovering two new Operational Taxonomic Units. Molecular results were corroborated with anatomical examination using i.e. scanning electron microscopy. Finally, the qPCR assay was coupled with High Resolution Melt analysis that successfully differentiated the closely related species Lithothamnion erinaceum and L. cf. glaciale. This DNA preparation and qPCR technique should vitalize coralline research by reducing time and cost associated with molecular systematics.},
}
@article {pmid30678712,
year = {2019},
author = {Djuikwo-Teukeng, FF and Kouam Simo, A and Allienne, JF and Rey, O and Njayou Ngapagna, A and Tchuem-Tchuente, LA and Boissier, J},
title = {Population genetic structure of Schistosoma bovis in Cameroon.},
journal = {Parasites &amp; vectors},
volume = {12},
number = {1},
pages = {56},
pmid = {30678712},
issn = {1756-3305},
mesh = {Abattoirs ; Animals ; Cameroon/epidemiology ; Cattle ; Cattle Diseases/*parasitology ; Female ; Genetic Variation ; Genetics, Population ; Genotyping Techniques ; Male ; Schistosoma/*genetics ; Schistosomiasis/parasitology/*veterinary ; },
abstract = {BACKGROUND: Schistosomiasis is neglected tropical parasitic disease affecting both humans and animals. Due to the human health impact, population genetic studies have focused on the three main human-infecting schistosome species: Schistosoma mansoni, S. haematobium and S. japonicum. Here we present novel data on the population genetic structure of Schistosoma bovis, a highly widespread and prevalent schistosome infecting ruminants, and therefore of veterinary importance.<br><br>METHODS: Adult S. bovis were sampled in the two main abattoirs of Cameroon (Yaound&#xe9; and Douala). Twenty-two cows originating from four distinct localities were sampled and a total of 218 parasites were recovered. All parasites were genotyped using a panel of 14 microsatellite markers and a sub-sample of 91 parasites were sequenced and characterized with the mitochondrial (cox1) and nuclear (ITS) genetic markers.<br><br>RESULTS: No significant difference in allelic richness, heterozygosity, nucleotide diversity and haplotype diversity was observed between the populations. Additionally, no strong genetic structure was observed at the country scale. Our data also show that S. bovis is more polymorphic than its sister species, S. haematobium, and that the haplotype diversity is similar to that of S. mansoni while the nucleotide diversity does not significantly differ from that of S. haematobium. The resulting negative Tajima's D* and Fu and Li's D* indices could be a signature of population demographic expansion. No S. haematobium/S. bovis hybrids were observed in our populations, thus all samples were considered as pure S. bovis.<br><br>CONCLUSIONS: This study provides novel insights into genetic diversity and population genetic structure of S. bovis. No strong genetic structure was observed at the country scale but some genetic indices could be associated as a signature of population demographic expansion.},
}
@article {pmid30678704,
year = {2019},
author = {Zhu, S and Cao, Z and Liu, Z and He, Y and Wang, Y and Yuan, P and Li, W and Tian, F and Bao, Y and Wei, W},
title = {Guide RNAs with embedded barcodes boost CRISPR-pooled screens.},
journal = {Genome biology},
volume = {20},
number = {1},
pages = {20},
pmid = {30678704},
issn = {1474-760X},
mesh = {Bacterial Proteins ; Bacterial Toxins ; *CRISPR-Cas Systems ; Gene Targeting ; Genomics/*methods ; HEK293 Cells ; HeLa Cells ; Humans ; *RNA, Guide, CRISPR-Cas Systems ; },
abstract = {We report a new method using re-designed guide RNAs with internal barcodes (iBARs) embedded in their loop regions. Our iBAR approach outperforms the conventional method by producing screening results with much lower false-positive and false-negative rates especially with a high multiplicity of infection (MOI). Importantly, the iBAR approach reduces the starting cells at high MOI significantly with greatly improved efficiency and accuracy compared with the canonical CRISPR screens at a low MOI. This new system is particularly useful when the source of cells is limited or when it is difficult to control viral infection for in vivo screening.},
}
@article {pmid30677051,
year = {2019},
author = {Govender, A and Groeneveld, J and Singh, S and Willows-Munro, S},
title = {The design and testing of mini-barcode markers in marine lobsters.},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0210492},
pmid = {30677051},
issn = {1932-6203},
mesh = {Animals ; Biomarkers/*analysis ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Electron Transport Complex IV/*genetics ; Mitochondrial Proteins/*genetics ; Nephropidae/classification/*genetics ; Protein Subunits ; Reproducibility of Results ; Seafood ; Species Specificity ; },
abstract = {Full-length mitochondrial cytochrome c oxidase I (COI) sequence information from lobster phyllosoma larvae can be difficult to obtain when DNA is degraded or fragmented. Primers that amplify smaller fragments are also more useful in metabarcoding studies. In this study, we developed and tested a method to design a taxon-specific mini-barcode primer set for marine lobsters. The shortest, most informative portion of the COI gene region was identified in silico, and a DNA barcode gap analysis was performed to assess its reliability as species diagnostic marker. Primers were designed, and cross-species amplification success was tested on DNA extracted from a taxonomic range of spiny-, clawed-, slipper- and blind lobsters. The mini-barcode primers successfully amplified both adult and phyllosoma COI fragments, and were able to successfully delimit all species analyzed. Previously published universal primer sets were also tested and sometimes failed to amplify COI from phyllosoma samples. The newly designed taxon-specific mini-barcode primers will increase the success rate of species identification in bulk environmental samples and add to the growing DNA metabarcoding toolkit.},
}
@article {pmid30672692,
year = {2019},
author = {Faver, JC and Riehle, K and Lancia, DR and Milbank, JBJ and Kollmann, CS and Simmons, N and Yu, Z and Matzuk, MM},
title = {Quantitative Comparison of Enrichment from DNA-Encoded Chemical Library Selections.},
journal = {ACS combinatorial science},
volume = {21},
number = {2},
pages = {75-82},
pmid = {30672692},
issn = {2156-8944},
support = {P01 HD087157/HD/NICHD NIH HHS/United States ; P20 CA221729/CA/NCI NIH HHS/United States ; P20 CA221731/CA/NCI NIH HHS/United States ; },
mesh = {Amines/chemistry ; Amino Acids/chemistry ; Base Sequence ; Combinatorial Chemistry Techniques/methods ; DNA/*chemistry ; Drug Discovery ; Epoxide Hydrolases/chemistry ; Small Molecule Libraries/*chemistry ; Triazines/*chemistry ; },
abstract = {DNA-encoded chemical libraries (DELs) provide a high-throughput and cost-effective route for screening billions of unique molecules for binding affinity for diverse protein targets. Identifying candidate compounds from these libraries involves affinity selection, DNA sequencing, and measuring enrichment in a sample pool of DNA barcodes. Successful detection of potent binders is affected by many factors, including selection parameters, chemical yields, library amplification, sequencing depth, sequencing errors, library sizes, and the chosen enrichment metric. To date, there has not been a clear consensus about how enrichment from DEL selections should be measured or reported. We propose a normalized z-score enrichment metric using a binomial distribution model that satisfies important criteria that are relevant for analysis of DEL selection data. The introduced metric is robust with respect to library diversity and sampling and allows for quantitative comparisons of enrichment of n-synthons from parallel DEL selections. These features enable a comparative enrichment analysis strategy that can provide valuable information about hit compounds in early stage drug discovery.},
}
@article {pmid30670720,
year = {2019},
author = {Carroll, EL and Gallego, R and Sewell, MA and Zeldis, J and Ranjard, L and Ross, HA and Tooman, LK and O'Rorke, R and Newcomb, RD and Constantine, R},
title = {Multi-locus DNA metabarcoding of zooplankton communities and scat reveal trophic interactions of a generalist predator.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {281},
pmid = {30670720},
issn = {2045-2322},
mesh = {Animals ; Balaenoptera ; DNA Barcoding, Taxonomic/*methods ; *Diet ; Ecosystem ; *Food Chain ; New Zealand ; Seasons ; Zooplankton/*genetics ; },
abstract = {To understand the ecosystem dynamics that underpin the year-round presence of a large generalist consumer, the Bryde's whale (Balaenoptera edeni brydei), we use a DNA metabarcoding approach and systematic zooplankton surveys to investigate seasonal and regional changes in zooplankton communities and if whale diet reflects such changes. Twenty-four zooplankton community samples were collected from three regions throughout the Hauraki Gulf, New Zealand, over two temperature regimes (warm and cool seasons), as well as 20 samples of opportunistically collected Bryde's whale scat. Multi-locus DNA barcode libraries were constructed from 18S and COI gene fragments, representing a trade-off between identification and resolution of metazoan taxa. Zooplankton community OTU occurrence and relative read abundance showed regional and seasonal differences based on permutational analyses of variance in both DNA barcodes, with significant changes in biodiversity indices linked to season in COI only. In contrast, we did not find evidence that Bryde's whale diet shows seasonal or regional trends, but instead indicated clear prey preferences for krill-like crustaceans, copepods, salps and ray-finned fishes independent of prey availability. The year-round presence of Bryde's whales in the Hauraki Gulf is likely associated with the patterns of distribution and abundance of these key prey items.},
}
@article {pmid30663383,
year = {2020},
author = {Yang, Y and Zheng, Y and Lu, B and Jiao, Z and Chen, L and Gblinwon, RT and Jia, X and Shen, Y and Yang, H},
title = {Rapid identification of cervus antlers by species-specific PCR assay.},
journal = {Natural product research},
volume = {34},
number = {9},
pages = {1315-1319},
doi = {10.1080/14786419.2018.1560285},
pmid = {30663383},
issn = {1478-6427},
mesh = {Animals ; Antlers/*physiology ; DNA Primers ; Deer/*genetics ; Drug Contamination ; Genome, Mitochondrial ; Medicine, Chinese Traditional ; Polymerase Chain Reaction/*methods ; Time Factors ; },
abstract = {A rapid PCR technology was developed to differentiate Cervus antlers species and adulteration based on the difference in mitochondrial genome. Three specifically designed primer sets were confirmed to have high inter-species specificity and good intra-species stability. Limits of detection were estimated to be 1 ng of genomes for reindeer and 10 ng for the other species. Especially, when the mixture of Cervus antlers and reindeer or sambar was assayed, these primer sets still exhibited strong capability of differentiation but not the conventional COI barcoding. By using the newly developed approach, five batches out of fourteen commercial Cervus antler products were identified to be fake products made from reindeer antlers. It has shown its good potential to be extensively applied in the identification of counterfeits or adulterates of Cornu Chinese medicines for their pulverized and processed form, and even the traditional Chinese patent medicines composed of these species.},
}
@article {pmid30659179,
year = {2019},
author = {Mutalik, VK and Novichkov, PS and Price, MN and Owens, TK and Callaghan, M and Carim, S and Deutschbauer, AM and Arkin, AP},
title = {Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {308},
pmid = {30659179},
issn = {2041-1723},
mesh = {DNA Barcoding, Taxonomic ; DNA, Bacterial/*genetics ; Escherichia coli/*genetics ; Gene Library ; Genetic Fitness ; *Genome, Bacterial ; Reproducibility of Results ; },
abstract = {A major challenge in genomics is the knowledge gap between sequence and its encoded function. Gain-of-function methods based on gene overexpression are attractive avenues for phenotype-based functional screens, but are not easily applied in high-throughput across many experimental conditions. Here, we present Dual Barcoded Shotgun Expression Library Sequencing (Dub-seq), a method that uses random DNA barcodes to greatly increase experimental throughput. As a demonstration of this approach, we construct a Dub-seq library with Escherichia coli genomic DNA, performed 155 genome-wide fitness assays in 52 experimental conditions, and identified overexpression phenotypes for 813 genes. We show that Dub-seq data is reproducible, accurately recapitulates known biology, and identifies hundreds of novel gain-of-function phenotypes for E. coli genes, a subset of which we verified with assays of individual strains. Dub-seq provides complementary information to loss-of-function approaches and will facilitate rapid and systematic functional characterization of microbial genomes.},
}
@article {pmid30656991,
year = {2019},
author = {Batta-Lona, PG and Galindo-Sánchez, CE and Arteaga, MC and Robles-Flores, J and Jiménez-Rosenberg, SPA},
title = {DNA barcoding and morphological taxonomy: identification of lanternfish (Myctophidae) larvae in the Gulf of Mexico.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {2},
pages = {375-383},
doi = {10.1080/24701394.2018.1538364},
pmid = {30656991},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Fishes/classification/*genetics/growth &amp; development ; },
abstract = {Accurate identification of fish larval stages is complicated and time-consuming due to the lack of diagnostic morphological characters, especially during early developmental stages. The distribution of lanternfish (Myctophidae) has been described based on the morphological identification of adult stages. Larvae of only a few species of Myctophidae have been described, and the description is not always precise. In this study, larvae were collected and morphologically identified as Diaphus mollis, Hygophum hygomii, H. reinhardtii, H. taaningi, Myctophum obtusirostre and M. selenops. The DNA barcode region of the mitochondrial cytochrome oxidase I gene (COI) was determined for all larvae. The COI sequences matched reference barcodes available in GenBank for 14 of the identified larvae. The remaining COI sequences matched reference barcodes for different species of Myctophidae including Centrobranchus nigroocellatus, Diogenichthys atlanticus and Lepidophanes guentheri. This effort demonstrated the importance of integrated morphological and molecular analysis of species diversity and distribution of the Myctophidae in the Gulf of México.},
}
@article {pmid30656990,
year = {2019},
author = {Abhyankar, S and Khobragade, K and Khanwelkar, G and Tiknaik, A and Khedkar, G},
title = {Evidence for a species complex in Indialona ganapati (Chydoridae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {3},
pages = {457-465},
doi = {10.1080/24701394.2018.1546299},
pmid = {30656990},
issn = {2470-1408},
mesh = {Animals ; Cladocera/*classification/*genetics ; DNA/genetics/isolation &amp; purification ; Electron Transport Complex IV/genetics ; India ; *Molecular Typing ; Species Specificity ; },
abstract = {Indialona ganapati (Petkovski 1966), is one of the three known cladoceran endemic species from India. It is also the only one of these species that is monotypic and endemic to central India. In this study we report on habitat shifts for this species as well as presence of parthenogenetic and ephippial females throughout the year, phenomena that are uncommon in most species of the family Chydoridae. These factors prompted us to undertake a study evaluating the taxonomic status of this species in collections from India using morphological and molecular methods. This included recognition of some degree of morphometric diversity based on sexual differentiation and reproductive patterns which were not correlated with speciation events. Analysis of our data does, however, suggest that I. ganapati can be split into two recent clades. Also, phylogenetic as well as haplotype network analysis of our data suggests the presence of a sibling species complex of I. ganapati in the river Godavari. This suggests that reconsideration of taxonomic status of this species may be appropriate. In addition, this study underscores the potential utility of using COI gene based 'barcode' DNA sequences for recognizing the existence of cryptic species among the cladocera.},
}
@article {pmid30656939,
year = {2019},
author = {Dahotre, SN and Chang, YM and Romanov, AM and Kwong, GA},
title = {DNA-Barcoded pMHC Tetramers for Detection of Single Antigen-Specific T Cells by Digital PCR.},
journal = {Analytical chemistry},
volume = {91},
number = {4},
pages = {2695-2700},
pmid = {30656939},
issn = {1520-6882},
support = {DP2 HD091793/HD/NICHD NIH HHS/United States ; T32 GM008169/GM/NIGMS NIH HHS/United States ; UL1 TR000454/TR/NCATS NIH HHS/United States ; UL1 TR002378/TR/NCATS NIH HHS/United States ; },
mesh = {Animals ; Antigens, Viral/immunology ; Carbocyanines/chemistry ; Cell Separation/*methods ; DNA/*analysis/chemistry/radiation effects ; Female ; Fluorescent Dyes/chemistry ; HLA-A2 Antigen/*chemistry ; Lymphocytic choriomeningitis virus/chemistry ; Mice, Inbred C57BL ; Mice, Transgenic ; Peptides/*chemistry ; Polymerase Chain Reaction/methods ; Staining and Labeling/methods ; T-Lymphocytes/*chemistry/immunology ; Ultraviolet Rays ; },
abstract = {Antigen-specific T cells are found at low frequencies in circulation but carry important diagnostic information as liquid biomarkers in numerous biomedical settings, such as monitoring the efficacy of vaccines and cancer immunotherapies. To enable detection of antigen-specific T cells with high sensitivity, we develop peptide-MHC (pMHC) tetramers labeled with DNA barcodes to detect single T cells by droplet digital PCR (ddPCR). We show that site-specific conjugation of DNA via photocleavable linkers allows barcoded tetramers to stain T cells with similar avidity compared to conventional fluorescent tetramers and efficient recovery of barcodes by light with no loss in cell viability. We design an orthogonal panel of DNA-barcoded tetramers to simultaneously detect multiple antigen-specific T cell populations, including from a mouse model of viral infection, and discriminate single cancer-specific T cells with high diagnostic sensitivity and specificity. This approach of DNA-barcoding can be broadened to encompass additional rare cells for monitoring immunological health at the single cell level.},
}
@article {pmid30654831,
year = {2019},
author = {Torrontegi, O and Alvarez, V and Acevedo, P and Gerrikagoitia, X and Höfle, U and Barral, M},
title = {Long-term avian influenza virus epidemiology in a small Spanish wetland ecosystem is driven by the breeding Anseriformes community.},
journal = {Veterinary research},
volume = {50},
number = {1},
pages = {4},
pmid = {30654831},
issn = {1297-9716},
support = {RTA2011-00111-C03 grant//Instituto Nacional de Investigaci&#xf3;n y Tecnolog&#xed;a Agraria y Alimentaria/ ; Predoctoral grant//Instituto Nacional de Investigaci&#xf3;n y Tecnolog&#xed;a Agraria y Alimentaria/ ; Ramon y Cajal contract (RYC-2012-11970)//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; Ramon y Cajal contract (RYC-2012-11970)//Universidad de Castilla-La Mancha (ES)/ ; },
mesh = {Animals ; Anseriformes ; Avian Proteins/analysis ; *Birds ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/analysis ; Influenza A virus/*isolation &amp; purification ; Influenza in Birds/*epidemiology/virology ; Longitudinal Studies ; Mitochondrial Proteins/analysis ; Prevalence ; Spain/epidemiology ; Wetlands ; },
abstract = {During 2007-2009 and 2012-2014, avian influenza virus (AIV) was studied in a wild avian community of a northern Spanish wetland using non-invasive sampling methods and host identification by COI barcoding. The aim of this longitudinal study was to evaluate AIV dynamics in a natural wetland ecosystem, taking into account both virological aspects and ecological traits of hosts. Global AIV prevalence decreased significantly during the second sampling period (0.3%) compared to the first (6.6%). Circulating subtype distributions were also different between periods, with a noteworthy H5 and H7 subtype richness during the first sampling period. Mallard Anas platyrhynchos was identified as the main AIV host, although not all positive samples could be ascribed to the host. We modelled AIV prevalence with regard to the avian host community composition and meteorological data from the wetland. Statistical analysis revealed seasonal differences in AIV detection, with higher prevalence during the breeding season compared to other phenological events. The model also shows that the lower AIV prevalence during the second study period was associated with a significant reduction of breeding Anseriformes in the wetland, revealing a long-term fluctuation of AIV prevalence driven by the breeding Anseriformes community. This longitudinal study on AIV epidemiology in a natural ecosystem reveals that although prevalence follows seasonal and annual patterns, long-term prevalence fluctuation is linked to the breeding community composition and size. These results are relevant to understanding the influence of host ecology on pathogen transmission for preventing and managing influenza emergence.},
}
@article {pmid30654736,
year = {2019},
author = {Tambe, A and Pachter, L},
title = {Barcode identification for single cell genomics.},
journal = {BMC bioinformatics},
volume = {20},
number = {1},
pages = {32},
pmid = {30654736},
issn = {1471-2105},
mesh = {DNA/*genetics ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: Single-cell sequencing experiments use short DNA barcode 'tags' to identify reads that originate from the same cell. In order to recover single-cell information from such experiments, reads must be grouped based on their barcode tag, a crucial processing step that precedes other computations. However, this step can be difficult due to high rates of mismatch and deletion errors that can afflict barcodes.<br><br>RESULTS: Here we present an approach to identify and error-correct barcodes by traversing the de Bruijn graph of circularized barcode k-mers. Our approach is based on the observation that circularizing a barcode sequence can yield error-free k-mers even when the size of k is large relative to the length of the barcode sequence, a regime which is typical single-cell barcoding applications. This allows for assignment of reads to consensus fingerprints constructed from k-mers.<br><br>CONCLUSION: We show that for single-cell RNA-Seq circularization improves the recovery of accurate single-cell transcriptome estimates, especially when there are a high number of errors per read. This approach is robust to the type of error (mismatch, insertion, deletion), as well as to the relative abundances of the cells. Sircel, a software package that implements this approach is described and publically available.},
}
@article {pmid30654506,
year = {2019},
author = {Korb, J and Kasseney, BD and Cakpo, YT and Casalla Daza, RH and Gbenyedji, JNKB and Ilboudo, ME and Josens, G and Koné, NA and Meusemann, K and Ndiaye, AB and Okweche, SI and Poulsen, M and Roisin, Y and Sankara, F},
title = {Termite Taxonomy, Challenges and Prospects: West Africa, A Case Example.},
journal = {Insects},
volume = {10},
number = {1},
pages = {},
pmid = {30654506},
issn = {2075-4450},
support = {KO1895/24-1//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Termites are important ecosystem engineers. Yet they are often difficult to identify due to the lack of reliable species-specific morphological traits for many species, which hampers ecological research. Recently, termitologists working with West African termites (West African Termite Taxonomy Initiative) convened for a workshop with the aim of beginning to address this problem. Repeated determination of the same termite samples by the most renowned taxonomists for West African termites identified the huge scale of the problem, as less than 10% of all species could be unambiguously determined to the species level. Intensive discussions and comparisons increased the identification success to around 25% at the end of the workshop. Yet many groups remained problematic and molecular markers and barcoding techniques combined with species delimitation approaches will be needed to help resolve these existing taxonomic problems. Based on the outcome of this workshop, we propose concerted initiatives to address termite taxonomy on a global scale. We are convinced that dedicated workshops on regional taxonomy that follow a similar structured approach, with repeated determination of the same sample, will help overcome the difficulties that termite taxonomy faces. This initiative can also serve as a blueprint for other taxonomical groups that are difficult to identify.},
}
@article {pmid30654133,
year = {2019},
author = {Becarelli, S and Chicca, I and Siracusa, G and La China, S and Gentini, A and Lorenzi, R and Munz, G and Petroni, G and Levin, DB and Di Gregorio, S},
title = {Hydrocarbonoclastic Ascomycetes to enhance co-composting of total petroleum hydrocarbon (TPH) contaminated dredged sediments and lignocellulosic matrices.},
journal = {New biotechnology},
volume = {50},
number = {},
pages = {27-36},
doi = {10.1016/j.nbt.2019.01.006},
pmid = {30654133},
issn = {1876-4347},
mesh = {Ascomycota/isolation &amp; purification/*metabolism ; Composting ; Geologic Sediments/*chemistry ; Hydrocarbons/*metabolism ; Petroleum/*metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; },
abstract = {Four new Ascomycete fungi capable of degrading diesel oil were isolated from sediments of a river estuary mainly contaminated by shipyard fuels or diesel oil. The isolates were identified as species of Lambertella, Penicillium, Clonostachys, and Mucor. The fungal candidates degraded and adsorbed the diesel oil in suspension cultures. The Lambertella sp. isolate displayed the highest percentages of oxidation of diesel oil and was characterised by the capacity to utilise the latter as a sole carbon source. This isolate showed extracellular laccase and Mn-peroxidase activities in the presence of diesel oil. It was tested for capacity to accelerate the process of decontamination of total petroleum hydrocarbon contaminated sediments, co-composted with lignocellulosic residues and was able to promote the degradation of 47.6% of the TPH contamination (54,074 ± 321 mg TPH/Kg of sediment) after two months of incubation. The response of the bacterial community during the degradation process was analysed by 16S rRNA gene meta-barcoding.},
}
@article {pmid30651512,
year = {2018},
author = {Colpani, D and Benetti, CJ and Hamada, N and Andrade-Souza, V and Michat, MC},
title = {Gyretes Brullé (Coleoptera: Gyrinidae) from Brazil: Morphology of eggs and early instars.},
journal = {Zootaxa},
volume = {4526},
number = {3},
pages = {331-346},
doi = {10.11646/zootaxa.4526.3.3},
pmid = {30651512},
issn = {1175-5334},
mesh = {Animals ; Brazil ; *Coleoptera ; Ecosystem ; Larva ; Ovum ; },
abstract = {Taxonomic information regarding Gyrinidae is mostly based on adults, especially due to the difficulty in collecting immatures and assigning them to a particular species. Association between immatures and adults is sometimes difficult because closely related species can be found in the same habitat. To solve this problem a feasible technique is rearing under laboratory conditions. However, this method is challenging because larval survival rate is usually low, and emulation of natural conditions is difficult. Molecular techniques, especially the use of the COI gene, have been applied to identify species and to associate different life stages. However, in some species groups this marker has not been successful in distinguishing closely related species. The objectives of this study are to describe the egg and the first two instars of Gyretes nubilus Ochs, 1965 and the egg of G. minax Ochs, 1967 and to evaluate the utility of COI to associate immatures and adults. The association of these immature stages with adults was done either rearing adults under laboratory conditions or by using DNA sequence data (COI), corroborating the utility of this molecular marker to associate immature and adults in Gyretes. These immature stages are described, including chaetotaxic analysis of larvae for the first time for the genus Gyretes Brullé, 1835. The eggs are described based on scanning electron microscopy. The eggs are similar to those of other Gyrinidae genera in having a micropylar region in the anterior pole and a longitudinal fissure, and by the absence of an aeropyle, but they differ mainly in characters related to chorionic structure and reticulation. Larvae of Gyretes can be distinguished from those of the other Neotropical Gyrinidae genera by a combination of several characters, including the frontoclypeal seta FR3 short, presence of three conspicuous additional setae on lateral region of parietal (contiguous to stemmata), and posterior margin of lacinia smooth, with apex not indented.},
}
@article {pmid30651464,
year = {2018},
author = {Sepahvand, V and Komai, T and Momtazi, F and Shahabi, S},
title = {A new species of the ghost shrimp genus Neocallichirus Sakai, 1988 from Iran, and new record of N. manningi Kazmi Kazmi, 1992 (Decapoda: Axiidea: Callianassidae).},
journal = {Zootaxa},
volume = {4527},
number = {2},
pages = {239-254},
doi = {10.11646/zootaxa.4527.2.5},
pmid = {30651464},
issn = {1175-5334},
mesh = {*Animal Distribution ; Animal Structures ; Animals ; Body Size ; *Decapoda ; Iran ; Organ Size ; Pakistan ; },
abstract = {Two species of the callianassid ghost shrimp genus Neocallichirus Sakai, 1988 are newly recorded from Iran. Neocallichirus darvishi n. sp. appears close to N. jousseaumei (Nobili, 1904), but combined morphological and genetic analyses provide evidence for recognition of the new taxon. Neocallichirus manningi Kazmi Kazmi, 1992, originally described from Pakistan, is reported for the first time since its original description. A supplemental description and figures are given for N. manningi.},
}
@article {pmid30649718,
year = {2019},
author = {Thorson, JA and Murray, SS},
title = {Library Preparation Using FFPE-Derived Tumor DNA for High-Throughput Hybridization-Based Targeted or Exome Sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1908},
number = {},
pages = {19-36},
doi = {10.1007/978-1-4939-9004-7_2},
pmid = {30649718},
issn = {1940-6029},
mesh = {DNA, Neoplasm ; Formaldehyde ; *Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Neoplasms/*genetics ; Nucleic Acid Hybridization/methods ; *Paraffin Embedding ; RNA, Neoplasm ; *Tissue Fixation ; Exome Sequencing/*methods ; },
abstract = {The use of next generation sequencing (NGS) to profile tumor genomes for the presence of diagnostic, prognostic, or therapeutically targetable variants is revolutionizing the practice of oncology and is increasingly utilized in clinical laboratory settings. Beginning with the isolation of DNA of sufficient quality and quantity from a tumor specimen, the creation of a library of genomic fragments representing the portion of the genome of interest, ranging from a few genes to the entire exome, is the first step required in the sequencing process. Fixed tumor tissue in the form of a tissue block is the most commonly encountered specimen for analysis in a clinical setting. Special precautions must be employed to ensure that material isolated from these specimens is suitable for use. Once DNA is obtained, one of the most commonly used methods for library preparation involves fluid phase hybridization-based capture of the genomic regions to be interrogated. This multistep process involves fragmentation of the DNA to a uniform size distribution, ligating adapter molecules which are labeled with specific barcodes to enable downstream sequencing and sample identification, and the use of a multiplexed pool of biotinylated single stranded RNA or DNA hybridization probes to recognize and capture the targeted genomic regions. Fragments which are not specifically captured during the hybridization process are removed via a series of wash steps, and a final low cycle amplification is used to prepare the library of captured fragments for sequencing. In this chapter, we provide a step-by-step guide to the preparation of fixed tissue-derived DNA libraries for sequencing via the Illumina process and highlight some of the precautions necessary when working with these types of specimens.},
}
@article {pmid30649283,
year = {2019},
author = {Sickel, W and Van de Weyer, AL and Bemm, F and Schultz, J and Keller, A},
title = {Venus flytrap microbiotas withstand harsh conditions during prey digestion.},
journal = {FEMS microbiology ecology},
volume = {95},
number = {3},
pages = {},
doi = {10.1093/femsec/fiz010},
pmid = {30649283},
issn = {1574-6941},
mesh = {Amino Acids/pharmacology ; Animals ; Droseraceae/*microbiology ; Host Microbial Interactions ; Indenes/pharmacology ; Metagenomics ; *Microbiota/drug effects/genetics ; Plant Leaves/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The carnivorous Venus flytrap (Dionaea muscipula) overcomes environmental nutrient limitation by capturing small animals. Such prey is digested with an acidic enzyme-containing mucilage that is secreted into the closed trap. However, surprisingly little is known about associations with microorganisms. Therefore, we assessed microbiotas of traps and petioles for the Venus flytrap by 16S amplicon meta-barcoding. We also performed time-series assessments of dynamics during digestion in traps and experimental acidification of petioles. We found that the traps hosted distinct microbiotas that differed from adjacent petioles. Further, they showed a significant taxonomic turnover during digestion. Following successful catches, prey-associated bacteria had strong effects on overall composition. With proceeding digestion, however, microbiotas were restored to compositions resembling pre-digestion stages. A comparable, yet less extensive shift was found when stimulating digestion with coronatine. Artificial acidification of petioles did not induce changes towards trap-like communities. Our results show that trap microbiota were maintained during digestion despite harsh conditions and recovered after short-term disturbances through prey microbiota. This indicates trap-specific and resilient associations. By mapping to known genomes, we predicted putative adaptations and functional implications for the system, yet direct mechanisms and quantification of host benefits, like the involvement in digestion, remain to be addressed.},
}
@article {pmid30647399,
year = {2018},
author = {Sigwart, JD and Chen, C},
title = {A new deep water chiton (Mollusca: Polyplacophora) from hydrothermal vent ecosystems in the Okinawa Trough, Japan.},
journal = {Zootaxa},
volume = {4531},
number = {3},
pages = {430-436},
doi = {10.11646/zootaxa.4531.3.7},
pmid = {30647399},
issn = {1175-5334},
mesh = {Animals ; China ; Ecosystem ; *Hydrothermal Vents ; Japan ; Mollusca ; Phylogeny ; *Polyplacophora ; Water ; },
abstract = {Recent expeditions exploring deep-sea hydrothermal vent ecosystems in the Okinawa Trough, East China Sea resulted in the collection of a hitherto undescribed species of polyplacophoran mollusc found living at three different vent fields at depths of 950-1178 m. This new chiton is a member of the small lepidopleuran family Protochitonidae and is morphologically similar to Hanleyella japonica Saito, 1997. The two species differ in small morphological differences of the valve shape and elevation, are divergent in the standard molecular barcoding mitochondrial gene cytochrome oxidase I (COI), and furthermore the known distribution range of H. japonica is considerably more northern and also shallower. The new species is described herein as Hanleyella henrici n. sp. Additional in situ observations taken in the course of collecting material for this study indicates that chitons are more abundant in the vicinity of hydrothermal vents than was previously appreciated, and perhaps more speciose.},
}
@article {pmid30647386,
year = {2018},
author = {Modak, N and Korn, M and Padhye, SM},
title = {Molecular phylogenetic investigations of Triops granarius (Lucas, 1864 (Branchiopoda: Notostraca) from the type locality of the former Apus orientalis Tiwari, 1952 and three other localities in the Western Ghats of India.},
journal = {Zootaxa},
volume = {4531},
number = {4},
pages = {541-553},
doi = {10.11646/zootaxa.4531.4.5},
pmid = {30647386},
issn = {1175-5334},
mesh = {Animals ; *Crustacea/genetics ; *DNA Barcoding, Taxonomic ; India ; *Phylogeny ; RNA, Ribosomal, 16S ; },
abstract = {We investigated the phylogenetic position of Triops granarius populations from four localities in the Western Ghats using partial sequences of three mitochondrial genes (COI, 12S rRNA and 16S rRNA) publicly available on the GenBank database. One of these localities, Panchgani, is particularly important since it is the type locality of the former Apus orientalis which is currently treated as a junior synonym of T. granarius. Phylogenetic analyses reveal that populations from all the four localities (Kolhapur, Chalkewadi, Panchgani, and Dighi) form a single lineage, which is here named 'Maharashtra lineage'. One of the two previously published samples from India, treated as lineage 'Triops granarius 4' is nested within this clade. The 'Maharashtra lineage' is separated from other lineages by mean maximum likelihood distance ≥ 11.9% in the COI gene. This distance is suggestive of a separation on species level from other lineages of T. granarius. This interpretation is further supported by a conservative genus-wide species delimitation analysis performed in the present study upon application of the Automatic Barcode Gap Discovery method. The 'Maharashtra lineage' branches out in two sub-lineages of Panchgani+Kolhapur and Dighi+L4+Chalkewadi samples, separated by 5.9% mean ML distance (uncorrected p-distance = 5.4%) in COI. The application of a 5% threshold to the COI dataset would thus even suggest a possible differentiation of both sub-lineages on species level. Comparative morphological data is presently not available because most vouchers associated with the sequences were depleted for DNA extraction. Further studies are needed in order to prepare a sound taxonomic revision. Thus, in the current study we refrain from re-instating Apus orientalis to full species status (likewise, for other names of Asian taxa in this morphogroup, including Apus sinensis Uéno, we retain the status as junior synonym of T. granarius). Nonetheless, our study highlights the fact that still there may be undescribed cryptic species associated with the specific name in this part of Western Ghats (Linnean Shortfall) and paves the way for future taxonomic investigations and conservation strategies for the genus Triops in India.},
}
@article {pmid30647364,
year = {2018},
author = {Boonstra, H and Rinne, A and Kubiak, M and Wiberg-Larsen, P},
title = {Description of the larva of Holocentropus insignis Martynov 1924 (Trichoptera: Polycentropodidae) with notes on biology and distribution.},
journal = {Zootaxa},
volume = {4532},
number = {2},
pages = {231-247},
doi = {10.11646/zootaxa.4532.2.3},
pmid = {30647364},
issn = {1175-5334},
mesh = {Animals ; Europe ; *Insecta ; Larva ; },
abstract = {The hitherto undescribed larva of Holocentropus insignis Martynov 1924 was collected in Denmark, the Netherlands, and Finland. Based on larval morphology and DNA association with adults, we were able to distinguish the larva of H. insignis from other Holocentropus species known to occur in Europe and confirm its identification. We provide morphological features to separate H. insignis from the other known species within the genus and give an updated key to all known European larvae of Holocentropus. Extensive notes on the life cycle, biology, and distribution of H. insignis are given.},
}
@article {pmid30647363,
year = {2018},
author = {SimÕes, PI and Costa, JCL and Rojas-Runjaic, FJM and Gagliardi-Urrutia, G and Sturaro, MJ and Peloso, PLV and Castroviejo-Fisher, S},
title = {A new species of Phyzelaphryne Heyer, 1977 (Anura: Eleutherodactylidae) from the Japurá River basin, with a discussion of the diversity and distribution of the genus.},
journal = {Zootaxa},
volume = {4532},
number = {2},
pages = {203-230},
doi = {10.11646/zootaxa.4532.2.2},
pmid = {30647363},
issn = {1175-5334},
mesh = {Animals ; *Anura/genetics ; Brazil ; Phylogeny ; RNA, Ribosomal, 16S ; *Rivers ; },
abstract = {We describe and name the second species of Phyzelaphryne (Brachycephaloidea, Eleutherodactylidae), from northwestern Brazilian Amazonia. Phyzelaphryne nimio sp. nov. is distinguished from its only congener, Phyzelaphryne miriamae, by its smaller body size and the anatomy of the carpal and metacarpal regions, with relatively larger (sometimes fused) supernumerary carpal and metacarpal tubercles. Molecular phylogenetic analyses based on fragments of the mitochondrial genes 16S rRNA and COI suggest that the currently known distribution of the species is restricted to its type locality and other areas within Estação Ecológica Juami-Japurá, state of Amazonas, Brazil. Based on molecular, morphological and bioacoustic evidence, we assigned other specimens recently collected in Parque Nacional do Jaú, state of Amazonas, Brazil, to P. miriamae, extending the species' known geographic distribution north of the Amazon River.},
}
@article {pmid30647352,
year = {2018},
author = {Wang, WY and Yong, GWJ and Jaitrong, W},
title = {The ant genus Rhopalomastix (Hymenoptera: Formicidae: Myrmicinae) in Southeast Asia, with descriptions of four new species from Singapore based on morphology and DNA barcoding.},
journal = {Zootaxa},
volume = {4532},
number = {3},
pages = {301-340},
doi = {10.11646/zootaxa.4532.3.1},
pmid = {30647352},
issn = {1175-5334},
mesh = {Animals ; *Ants/genetics ; DNA ; *DNA Barcoding, Taxonomic ; Male ; Singapore ; },
abstract = {The true diversity of the Asian ant genus Rhopalomastix Forel is poorly understood. We use an integrated approach to review the known species and subspecies of Rhopalomastix in Southeast Asia. Based on morphology and supporting DNA evidence, we recognize six species. We raise two subspecies of R. rothneyi Forel to species rank (R. johorensis Wheeler stat. n, R. javana Wheeler stat. n.), synonymize R. janeti Donisthorpe (syn. nov.) with R. johorensis, and describe four new species from Singapore: R. glabricephala sp. n., R. murphyi sp. n., R. striata sp. n., and R. tenebra sp. n. All six species found in Southeast Asia are distinct from each other based on morphology; morphological delimitation of these species is further supported by and congruent with mOTUs generated from objective clustering of short fragment COI barcodes using the best close match criteria. Different castes and sexes of most species are described, including redescriptions of the queen of R. javana and male of R. johorensis. A key to the Southeast Asian species based on the worker caste is also provided. Variation among sympatric and also geographically distant populations, and the possibilities of cryptic species, are discussed.},
}
@article {pmid30647351,
year = {2018},
author = {Kuberan, G and Chakraborty, RD and Purushothaman, P and Maheswarudu, G},
title = {Record of the deep sea shrimp Pasiphaea alcocki (Wood-Mason Alcock, 1891) (Crustacea: Decapoda: Pasiphaeidae) from the southwestern coast of India.},
journal = {Zootaxa},
volume = {4532},
number = {4},
pages = {597-600},
doi = {10.11646/zootaxa.4532.4.10},
pmid = {30647351},
issn = {1175-5334},
mesh = {Animals ; DNA ; *Decapoda/genetics ; Ecosystem ; India ; },
abstract = {The present study provides a report on the rare occurrence of the deep sea caridean shrimp Pasiphaea alcocki (Wood-Mason Alcock, 1891) from the southwest coast of India after three decades. Earlier this species was recorded from Indian waters at a depth range between 335 and 1732 m while the present specimens were obtained in the depth range of 200-300m from the commercial bottom trawlers operated off Sakthikulangara fishing harbour (8°56'60.78"N /76°32'34.27"E) off (8°56'60.78"N /76°32'34.27"E), Kerala from the southern region of Arabian Sea, India. The level of interspecies genetic divergence using COI and 16S DNA sequences of Pasiphaea sp from the United States, National Center for Biotechnology Information (NCBI) were observed. The present study reports the record of Pasiphaea alcocki with a morphological description along with DNA barcoding and supplements the existing knowledge on this deep sea shrimp from the southwest coast of India, which is mandatory to understand the role of this species in ecosystem functioning.},
}
@article {pmid30647339,
year = {2018},
author = {Freyhof, J and BayÇelebİ, E and Geiger, M},
title = {Review of the genus Cobitis in the Middle East, with the description of eight new species (Teleostei: Cobitidae).},
journal = {Zootaxa},
volume = {4535},
number = {1},
pages = {1-75},
doi = {10.11646/zootaxa.4535.1.1},
pmid = {30647339},
issn = {1175-5334},
mesh = {Animals ; Black Sea ; *Cypriniformes ; Male ; Middle East ; *Perciformes ; },
abstract = {The diversity of Cobitis in the Middle East is reviewed, resulting in the recognition of 30 species, of which eight are described herein as new. Two species, C. amphilekta and C. kellei, seem to be extinct. Hypotheses on species-level diversity derived from distance and Poisson tree process analyses of DNA barcode data are tested against morphometric and morphological characters including colour patterns. For species pairs separated by small K2P distances in COI sequence data we follow a practitioner-oriented diagnostic species concept, in which we recognise species only if differentiated morphologically (including by colour pattern). For all 30 species we provide diagnoses and identification keys. Cobitis afifeae, new species, from the Büyük Menderes River drainage in the Aegean Sea basin, is distinguished by having two laminae circularis in the male, a row of blotches below Z4, a small, roundish or comma-shaped black spot at the upper caudal-fin base, and elevated mental lobes. Cobitis aliyeae, new species, from the lower Seyhan and Ceyhan River drainages, is distinguished by having two laminae circularis in the male, the blotches in Z2 and Z4 anterior to the dorsal-fin origin usually well separated from each other, and the pigmentation in Z1 well distinguished from the pigmentation in Z2. Cobitis anabelae, new species, from the lower Orontes River drainage, is distinguished by having two laminae circularis in the male, the pigmentation in Z2 formed by small, brown spots, always much smaller than blotches in Z3, much smaller than the pupil diameter, Z2 and Z3 well separated, and no pigmentation below Z4. Cobitis erkakanae, new species, from the Gölbasi Lakes, adjacent to the Ceyhan River drainage, is distinguished by having two laminae circularis in the male, no blotches below Z4, the blotches in Z2 and Z4 being horizontally elongated and often fused with adjacent ones, and the caudal fin with 4-6 wide, regularly-shaped, brown bands. Cobitis emrei, new species, from the Lake Sapanca basin is distinguished by having one lamina circularis in the male, a large black spot at the upper caudal-fin base, and Z3 fully covered by very small spots forming a sand-like pattern. Cobitis joergbohleni, new species, from the Sultan marshes in Central Anatolia is distinguished by having two laminae circularis in the male, and the flank colour pattern being completely disorganised, not following the Gambetta zones. Cobitis pirii, new species, from the endorheic Lake Eğirdir basin and the Mediterranean Aksu and Köprü Rivers, is distinguished by having two laminae circularis in the male, a simple external part of the suborbital spine and two distinct rows of small blotches in Z4, one along the lateral midline and one distinctly below. Cobitis troasensis, new species, from the Tuzla River drainage, is distinguished by having one lamina circularis in the male and 25-36 small, comma-shaped brown blotches in Z4. A lectotype is designated for Cobitis battalgilae. As First Revisers, priority is given to Cobitis fahireae over C. kurui. Cobitis damlae and C. kurui are treated as synonyms of C. fahireae. Cobitis strumicae and C. taenia are recorded for the first time from Anatolia and C. saniae is newly documented from the Black Sea basin in Georgia. The Poisson tree process analysis of COI data proposed 31 groups, most of which could be distinguished by morphological characters. Cobitis troasensis is described based on morphological data alone.},
}
@article {pmid30647304,
year = {2019},
author = {Tanaka, H and Wakabayashi, K and Fujita, T},
title = {A new species of Fibularia from Japanese waters with a redescription of F. japonica and F. ovulum (Echinodermata: Echinoidea: Clypeasteroida).},
journal = {Zootaxa},
volume = {4543},
number = {2},
pages = {241-260},
doi = {10.11646/zootaxa.4543.2.4},
pmid = {30647304},
issn = {1175-5334},
mesh = {Animals ; Base Sequence ; *Echinodermata/genetics ; Japan ; *Sea Urchins ; },
abstract = {A new species, Fibularia coffea sp. nov., occurs from shallow waters in Japan. This new species is distinguished from the other species of Fibularia by the following characters: test height is low, oral surface is slightly depressed toward the peristome, number of pores of petal III continues to increase with the test growth, reaching over 30 at TL > 7.5 mm, and black pigments form symmetric pentaradial on aboral surface in living animals. Two further Japanese species, Fibularia japonica and F. ovulum, are redescribed based on the type specimens (F. japonica) and additional specimens (F. ovulum), respectively. A tabular key to the extant species of Fibularia is also provided. A partial fragment of the mitochondrial gene cytochrome oxidase subunit I (COI) of the type specimens of F. coffea sp. nov. and the additional specimen of F. japonica was sequenced for barcoding in future works.},
}
@article {pmid30647256,
year = {2019},
author = {Bochkov, AV and Klimov, PB and Kim, DH and Skoracki, M},
title = {Validation of the status of a species with high CO1 and low nuclear genetic divergences: the scab mite Caparinia ictonyctis stat. res. (Acariformes: Psoroptidae) parasitizing the African hedgehog Atelerix albiventris.},
journal = {Zootaxa},
volume = {4544},
number = {4},
pages = {523-547},
doi = {10.11646/zootaxa.4544.4.4},
pmid = {30647256},
issn = {1175-5334},
mesh = {Animals ; Europe ; *Hedgehogs/parasitology ; *Mite Infestations/veterinary ; *Mites ; Psoroptidae ; },
abstract = {We report two host-specific lineages of scab mites of the genus Caparinia, parasitizing European and African hedgehogs. Based on morphology, these mite lineages are closely related sister groups. The morphological differences, however, are subtle and do not provide clear-cut evidence for the existence of separate species. CO1 divergence between these lineages was 7.4-7.8%, well above the CO1 barcoding gaps or thresholds commonly used to separate species, whereas divergence of five nuclear genes was very low, 0.06-0.53%, suggesting that these lineages could belong to a single species with gene flow between them. Thus, there is a conflict between the mitochondrial (CO1) gene and nuclear genes (i.e mito-nuclear discordance). We attribute this conflict to the 'gray zone' where species delimitation is ambiguous due to substantial gene flow. We also report another 'gray zone' species, Psoroptes ovis (a species of veterinary importance), whose within-species CO1 distances reached 6.0%. We provide a detailed morphological description and figures of C. ictonyctis stat. res. from the African hedgehog, using light and SEM microscopy and give morphometric data for this species and its sister species, Caparinia tripilis from Europe. For all known species of Caparinia, we document their host associations and give a key to species of the world based on results of our morphological and molecular analyses and a nearly exhaustive study of museum specimens.},
}
@article {pmid30647239,
year = {2019},
author = {James, SW and Bartz, MLC and Stanton, DWG and Conrado, AC and Dupont, L and Taheri, S and Silva, ED and Cunha, L and Brown, GG},
title = {A neotype for Pontoscolex corethrurus (Müller, 1857) (Clitellata).},
journal = {Zootaxa},
volume = {4545},
number = {1},
pages = {124-132},
doi = {10.11646/zootaxa.4545.1.7},
pmid = {30647239},
issn = {1175-5334},
mesh = {Animals ; Ecology ; *Oligochaeta ; },
abstract = {Following many decades of work on the taxonomy, biology and ecology of the globally-distributed tropical earthworm Pontoscolex corethrurus (Müller, 1857), morphological and molecular data have shown that the stability and effectiveness of nomenclature depends on the designation of a neotype from the type locality. We do that, with all the required justifications, and provide sufficient information to permit the correct identification of this species.},
}
@article {pmid30644063,
year = {2019},
author = {Kundu, S and Kumar, V and Tyagi, K and Pakrashi, A and Laskar, BA and Chandra, K},
title = {DNA Barcoding Reveals Association of Glossiphoniidae Species on Endangered Freshwater Turtles in Northeast India.},
journal = {Acta parasitologica},
volume = {64},
number = {1},
pages = {213-217},
doi = {10.2478/s11686-018-00023-7},
pmid = {30644063},
issn = {1896-1851},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Fresh Water ; India ; Leeches/*classification/*genetics ; Turtles/*parasitology ; },
abstract = {BACKGROUND: The identification of Glossiphoniidae species is often confusing due to the lack of both morphological and molecular data worldwide.<br><br>PURPOSE: The study aimed to identify the collected leech specimens from two endangered freshwater turtles, Chitra indica and Pangshura sylhetensis from northeast India.<br><br>METHODS: We generated DNA barcode sequences and estimated the genetic distances and phylogenetic relationship of the studied taxa with another 14 Glossiphoniidae genera (114 barcode sequences).<br><br>RESULTS: The high genetic distinctiveness (17.9 to 26.3%) and distinct clustering in Neighbor-Joining (NJ) phylogeny, we identified the studied specimens as Glossiphoniidae sp. We assumed that the studied specimens might be a new member of Glossiphoniidae or an extant species without DNA information.<br><br>CONCLUSION: Hence, the study recommends further sampling of leeches from the similar host as well as from same and various localities and also generates the molecular data to perceive the exact diversity. The aimed study is also helpful to encourage the awareness and conservation management of freshwater turtles and other threatened animals.},
}
@article {pmid30639766,
year = {2019},
author = {Yang, J and Feng, L and Yue, M and He, YL and Zhao, GF and Li, ZH},
title = {Species delimitation and interspecific relationships of the endangered herb genus Notopterygium inferred from multilocus variations.},
journal = {Molecular phylogenetics and evolution},
volume = {133},
number = {},
pages = {142-151},
doi = {10.1016/j.ympev.2019.01.002},
pmid = {30639766},
issn = {1095-9513},
mesh = {Apiaceae/*genetics ; DNA, Chloroplast/genetics ; DNA, Plant/genetics ; *Endangered Species ; *Genetic Loci ; Genetic Markers ; *Genetic Variation ; Genome, Chloroplast ; Phylogeny ; Species Specificity ; Time Factors ; },
abstract = {Species identification and discrimination is the basis of biodiversity research. In general, it is considered that numerous nucleotide variations (e.g., whole chloroplast genomes) can identify species with higher resolution than a few loci, e.g., partial chloroplast or nuclear gene fragments. In this study, we tested this hypothesis by sampling population genetics samples of the endangered herb genus Notopterygium. We sequenced the complete plastomes, five nuclear gene regions, three chloroplast DNA fragments, and a nuclear internal transcribed spacer (nrITS) region for 18 populations sampled throughout most of the geographic ranges of all six Notopterygium species. Species identification analysis showed that four DNA barcodes (matK, rbcL, trnS-trnG, and nrITS) and/or combinations of these markers achieved Notopterygium species discrimination at higher resolution than the general plastomes and nuclear gene sequences. In particular, nrITS had the highest discriminatory power among all of the individual markers. Molecular data sets and morphological evidence indicated that all six Notopterygium species could be reclassified unambiguously to four putative species clades. N. oviforme and N. franchetii had the closest relationship. Molecular dating showed that the origin and divergence of Notopterygium species was significantly associated with geological and climatic fluctuations during the middle of the Pliocene. In conclusion, our results suggest that a few nucleotide variations can achieve species discrimination with higher resolution than numerous plastomes and general nuclear gene fragments when discerning related Notopterygium species.},
}
@article {pmid30639545,
year = {2019},
author = {Rodrigues, CMF and Garcia, HA and Sheferaw, D and Rodrigues, AC and Pereira, CL and Camargo, EP and Teixeira, MMG},
title = {Genetic diversity of trypanosomes pathogenic to livestock in tsetse flies from the Nech Sar National Park in Ethiopia: A concern for tsetse suppressed area in Southern Rift Valley?.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {69},
number = {},
pages = {38-47},
doi = {10.1016/j.meegid.2019.01.010},
pmid = {30639545},
issn = {1567-7257},
mesh = {Animals ; Ethiopia/epidemiology ; Genes, Protozoan ; *Genetic Variation ; Genotype ; Geography, Medical ; Haplotypes ; Humans ; Livestock/*parasitology ; Molecular Typing ; Parks, Recreational ; Protozoan Infections, Animal/*epidemiology/*parasitology/transmission ; Public Health Surveillance ; Sequence Analysis, DNA ; Trypanosoma/classification/*genetics ; Trypanosomiasis/*veterinary ; Trypanosomiasis, African/epidemiology/parasitology/transmission ; Tsetse Flies/*parasitology ; },
abstract = {In Ethiopia, home to the largest African herd of cattle, animal trypanosomiasis is a major constraint to the efforts made for food self-sufficiency. We searched for trypanosomes in tsetse flies caught in the Nech Sar National Park (NSNP), Southern Rifty Valley, Ethiopia, at the district of Arba Minch where intensive tsetse control is successfully improving cattle productivity. Despite narrow geographical and temporal scales of our survey, we found a remarkable diversity of trypanosomes using the sensitive and discriminative method of fluorescent fragment length barcoding. We also found a high density of Glossina pallidipes (47.8 flies/trap/day) showing relevant cytochrome oxidase I gene variability. The identification of blood meal sources through cytochrome b gene sequences revealed cattle and warthog as preferential ungulate hosts of tsetse flies in the study area. Our survey identified trypanosomes in 38% of the 287 flies examined (42% of proboscises and 32% of guts), and the following infection rates for each species: Trypanosoma vivax 23%, T. simiae 23%, T. congolense 22%, T. theileri 19.9%, T. (Trypanozoon) spp. 10.5%, T. godfreyi 9.4%, T. simiae Tsavo 6.3%, and mixed infections in proboscises (30%) and guts (61%). Phylogenetic analysis revealed T. vivax of the "West African-South American" genotype, T. congolense of Savannah (16.7%), Kilifi (3.5%) and Forest (2.1%) lineages, and new genotypes of T. simiae. To our knowledge, this is the first survey of trypanosomes in the NSNP, and the most comprehensive molecular characterisation of trypanosomes in tsetse flies of Ethiopia, including the comparison with samples from West and other East African countries. Our results support the diversification of T. vivax in East Africa, and the dispersion of the genotype herein identified in Ethiopia across West Africa and then in South America. Altogether, tsetse density and infection rate, repertoire of trypanosomes and feeding behavior indicate a high risk of transmission of trypanosomes pathogenic to ungulates by tsetse flies from the NSNP, a hotspot of tsetse infestation and trypanosome diversity. Our findings reinforce the need for constant surveillance, and the reliance on community efforts to prevent reinvasion of tsetse and animal trypanosomiasis in suppressed areas of Southern Rift Valley.},
}
@article {pmid30638172,
year = {2019},
author = {Caffara, M and Locke, SA and Halajian, A and Luus-Powell, WJ and Benini, D and Tedesco, P and Kasembele, GK and Fioravanti, ML},
title = {Molecular data show Clinostomoides Dollfus, 1950 is a junior synonym of Clinostomum Leidy, 1856, with redescription of metacercariae of Clinostomum brieni n. comb.},
journal = {Parasitology},
volume = {146},
number = {6},
pages = {805-813},
doi = {10.1017/S0031182018002172},
pmid = {30638172},
issn = {1469-8161},
mesh = {Animals ; Catfishes/parasitology ; Cluster Analysis ; DNA, Helminth/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Democratic Republic of the Congo ; Electron Transport Complex IV/genetics ; Fish Diseases/parasitology ; Metacercariae/*classification/*genetics/isolation &amp; purification ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; South Africa ; Trematoda/*classification/*genetics/isolation &amp; purification ; Trematode Infections/parasitology/veterinary ; },
abstract = {The genus Clinostomoides Dollfus, 1950 was erected to accommodate a single worm from Ardea goliath sampled in the Belgian Congo. The specimen was distinguished from other clinostomids by its large size and posterior genitalia. In the following years, metacercariae of Clinostomoides brieni, have been described in Clarias spp. in southern and western Africa. A few authors have referred to Clinostomum brieni, but all such usages appear to be lapsus calami, and the validity of Clinostomoides remains widely accepted. In this study our aim was: position C. brieni among the growing clinostomids molecular database, and redescribe the species with emphasis on characters that have emerged as important in recent work. We sequenced two nuclear (partial 18S and ITS) and one mitochondrial marker (partial cytochrome c oxidase I) and studied morphology in metacercariae from hosts and localities likely to harbour the type species (Clarias spp., Democratic Republic of the Congo, South Africa). Phylogenetic analysis shows C. brieni belongs within Clinostomum Leidy, 1856. We therefore transfer C. brieni to Clinostomum, amend the diagnosis for the genus Clinostomum and provide a critical analysis of other species in Clinostomoides, all of which we consider species inquirendae, as they rest on comparisons of different developmental stages.},
}
@article {pmid30637150,
year = {2018},
author = {Choi, YJ and Park, JH and Lee, J and Shin, HD},
title = {Bremia itoana (Oomycota, Peronosporales), a Specialized Downy Mildew Pathogen on an East Asian Plant, Crepidiastrum sonchifolium (Asteraceae).},
journal = {Mycobiology},
volume = {46},
number = {4},
pages = {416-420},
pmid = {30637150},
issn = {1229-8093},
abstract = {Crepidiastrum sonchifolium, a flowering plant in the daisy family (Asteraceae), is native to East Asia. In Korea, this plant is a locally cultivated vegetable, and its market size is gradually growing. Since the plants with downy mildew infection were initially found at a private farm of Chuncheon city, the occurrences have continued in commercial farms of other regions, highlighting that this disease is spreading throughout Korea. The pathogen was attributed to a member of the genus Bremia that contains many specialized species, each of which displays a narrow host spectrum on Asteraceae. Based on morphological and molecular phylogenetic analyses, along with the high host specificity recently proven for Bremia species, the identity of the causal agent was confirmed as a so far undescribed species of Bremia. Here, we introduce Bremia itoana sp. nov., specific to C. sonchifolium.},
}
@article {pmid30633772,
year = {2019},
author = {Fotedar, S and Lukehurst, S and Jackson, G and Snow, M},
title = {Molecular tools for identification of shark species involved in depredation incidents in Western Australian fisheries.},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0210500},
pmid = {30633772},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Bites and Stings/epidemiology/physiopathology ; Conservation of Natural Resources/*methods ; Cytochromes b/genetics ; DNA/*analysis/genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Fish Proteins/genetics ; *Fisheries ; Incidence ; Sequence Homology, Nucleic Acid ; Sharks/classification/*genetics/physiology ; Species Specificity ; Western Australia/epidemiology ; },
abstract = {Shark depredation is an issue of concern in some Western Australian recreational and commercial fisheries where it can have economic, social and ecological consequences. Knowledge of the shark species involved is fundamental to developing effective management strategies to mitigate the impacts of depredation. Identification of the species responsible is difficult as direct observation of depredation events is uncommon and evaluating bite marks on fish has a high degree of uncertainty. The use of trace DNA techniques has provided an alternative method for species identification. We demonstrate proof of concept for a targeted DNA barcoding approach to identify shark species using trace DNA found at bite marks on recovered remains of hooked fish. Following laboratory validation, forensic analysis of swabs collected from samples of bitten demersal fish, led to the definitive identification of shark species involved in 100% of the incidences of depredation (n = 16).},
}
@article {pmid30633651,
year = {2019},
author = {Paracchini, V and Petrillo, M and Lievens, A and Kagkli, DM and Angers-Loustau, A},
title = {Nuclear DNA barcodes for cod identification in mildly-treated and processed food products.},
journal = {Food additives &amp; contaminants. Part A, Chemistry, analysis, control, exposure &amp; risk assessment},
volume = {36},
number = {1},
pages = {1-14},
doi = {10.1080/19440049.2018.1556402},
pmid = {30633651},
issn = {1944-0057},
mesh = {Animals ; Cell Nucleus/*genetics ; *DNA Barcoding, Taxonomic ; Food Analysis/*methods ; Gadus morhua/*genetics ; },
abstract = {Gadoids are a group of fish with historical importance in the fishing industry. The high demand for cod is one of the reasons why cod products are often mislabelled, and numerous observations have been made on the replacement of Atlantic cod (Gadus morhua) by cheaper species or its illegal capture in contravention of fish quotas. Fish species identification is traditionally based on morphological features, but this may be difficult in case of heat-treated or processed products, or where the species look similar, as in the Gadoid group. DNA-based approaches (using either nuclear or mitochondrial DNA) are most commonly used in this case, due to their high specificity and to the high resilience of the target molecules to food processing techniques. In this article, we identified, using an automated screening approach, novel barcode regions and their associated primers in the nuclear genome, to be used for the efficient identification of Gadoids. The barcode regions were tested on official and commercial samples, raw or mildly treated products, like frozen, or salted, as well as pre-cooked complex mixtures and processed samples, using next-generation sequencing (NGS) technique. The method proposed could complement existing fish identification strategies in establishing an efficient framework to detect and prevent frauds along the food chain.},
}
@article {pmid30633607,
year = {2019},
author = {Lanner, J and Curto, M and Pachinger, B and Neumüller, U and Meimberg, H},
title = {Illumina midi-barcodes: quality proof and applications.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {3},
pages = {490-499},
doi = {10.1080/24701394.2018.1551386},
pmid = {30633607},
issn = {2470-1408},
mesh = {Animals ; Bees/genetics ; DNA/*genetics ; DNA Barcoding, Taxonomic/*methods/*standards ; High-Throughput Nucleotide Sequencing/*methods ; Polymerase Chain Reaction ; Reproducibility of Results ; },
abstract = {DNA barcoding constitutes a supplemental genetically based characterization tool for the identification of species. Traditionally, the barcodes are generated with a length of 650 bp using standardized Sanger sequencing, but with the introduction of high-throughput sequencing (HTS) methods new opportunities for sequencing are available. To use HTS for barcode collection and identification, the amplification of shorter fragments is preferred. Reference DNA midi-barcodes of wild bees were produced using the Illumina MiSeq as well as the Sanger method. Although DNA midi-barcodes derived from Illumina were comparatively shorter (418 bp), their sequences were coherent to the morphological assignment of species. The Illumina barcodes proved to be effective and dealt better with some general limitations of DNA barcoding.},
}
@article {pmid30632223,
year = {2019},
author = {Fagan-Jeffries, EP and Cooper, SJB and Bradford, TM and Austin, AD},
title = {Intragenomic internal transcribed spacer 2 variation in a genus of parasitoid wasps (Hymenoptera: Braconidae): implications for accurate species delimitation and phylogenetic analysis.},
journal = {Insect molecular biology},
volume = {28},
number = {4},
pages = {485-498},
doi = {10.1111/imb.12564},
pmid = {30632223},
issn = {1365-2583},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/*analysis ; Insect Proteins/analysis ; *Phylogeny ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Wasps/*classification/genetics ; },
abstract = {A recent DNA barcoding study of Australian microgastrines (Hymenoptera: Braconidae) sought to use next-generation sequencing of the cytochrome c oxidase subunit 1 (COI) barcoding gene region, the wingless (WG) gene and the internal transcribed spacer 2 (ITS2) to delimit molecular species in a highly diverse group of parasitic wasps. Large intragenomic distances between ITS2 variants, often larger than the average interspecific variation, caused difficulties in using ITS2 for species delimitation in both threshold and tree-based approaches, and the gene was not included in the reported results of the previous DNA barcoding study. We here report on the intragenomic, and the intra- and interspecies, variation in ITS2in the microgastrine genus Diolcogasterto further investigate the value of ITS2as a marker for species delimitation and phylogenetics of the Microgastrinae. Distinctive intragenomic variant patterns were found in different species of Diolcogaster, with some species possessing a single major variant, and others possessing many divergent variants. Characterizing intragenomic variation of ITS2is critical as it is a widely used marker in hymenopteran phylogenetics and species delimitation, and large intragenomic distances such as those found in this study may obscure phylogenetic signal.},
}
@article {pmid30631651,
year = {2019},
author = {Gardner, PP and Watson, RJ and Morgan, XC and Draper, JL and Finn, RD and Morales, SE and Stott, MB},
title = {Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6160},
pmid = {30631651},
issn = {2167-8359},
abstract = {Metagenomic and meta-barcode DNA sequencing has rapidly become a widely-used technique for investigating a range of questions, particularly related to health and environmental monitoring. There has also been a proliferation of bioinformatic tools for analysing metagenomic and amplicon datasets, which makes selecting adequate tools a significant challenge. A number of benchmark studies have been undertaken; however, these can present conflicting results. In order to address this issue we have applied a robust Z-score ranking procedure and a network meta-analysis method to identify software tools that are consistently accurate for mapping DNA sequences to taxonomic hierarchies. Based upon these results we have identified some tools and computational strategies that produce robust predictions.},
}
@article {pmid30630407,
year = {2019},
author = {Ceballos, SG and Roesti, M and Matschiner, M and Fernández, DA and Damerau, M and Hanel, R and Salzburger, W},
title = {Phylogenomics of an extra-Antarctic notothenioid radiation reveals a previously unrecognized lineage and diffuse species boundaries.},
journal = {BMC evolutionary biology},
volume = {19},
number = {1},
pages = {13},
pmid = {30630407},
issn = {1471-2148},
mesh = {Animals ; Antarctic Regions ; Base Sequence ; Calibration ; Fishes/*classification ; Genetic Loci ; Genetic Markers ; Genetic Variation ; Genome ; Haplotypes/genetics ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Phylogeography ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA ; Species Specificity ; Time Factors ; },
abstract = {BACKGROUND: The impressive adaptive radiation of notothenioid fishes in Antarctic waters is generally thought to have been facilitated by an evolutionary key innovation, antifreeze glycoproteins, permitting the rapid evolution of more than 120 species subsequent to the Antarctic glaciation. By way of contrast, the second-most species-rich notothenioid genus, Patagonotothen, which is nested within the Antarctic clade of Notothenioidei, is almost exclusively found in the non-Antarctic waters of Patagonia. While the drivers of the diversification of Patagonotothen are currently unknown, they are unlikely to be related to antifreeze glycoproteins, given that water temperatures in Patagonia are well above freezing point. Here we performed a phylogenetic analysis based on genome-wide single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (RADseq) in a total of twelve Patagonotothen species.<br><br>RESULTS: We present a well-supported, time-calibrated phylogenetic hypothesis including closely and distantly related outgroups, confirming the monophyly of the genus Patagonotothen with an origin approximately 3 million years ago and the paraphyly of both the sister genus Lepidonotothen and the family Notothenidae. Our phylogenomic and population genetic analyses highlight a previously unrecognized linage and provide evidence for shared genetic variation between some closely related species. We also provide a mitochondrial phylogeny showing mitonuclear discordance.<br><br>CONCLUSIONS: Based on a combination of phylogenomic and population genomic approaches, we provide evidence for the existence of a new, potentially cryptic, Patagonotothen species, and demonstrate that genetic boundaries between some closely related species are diffuse, likely due to recent introgression and/or incomplete linage sorting. The detected mitonuclear discordance highlights the limitations of relying on a single locus for species barcoding. In addition, our time-calibrated phylogenetic hypothesis shows that the early burst of diversification roughly coincides with the onset of the intensification of Quaternary glacial cycles and that the rate of species accumulation may have been stepwise rather than constant. Our phylogenetic framework not only advances our understanding of the origin of a high-latitude marine radiation, but also provides the basis for the study of the ecology and life history of the genus Patagonotothen, as well as for their conservation and commercial management.},
}
@article {pmid30629718,
year = {2019},
author = {Gruenstaeudl, M and Hartmaring, Y},
title = {EMBL2checklists: A Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA.},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0210347},
pmid = {30629718},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Fungal ; DNA, Plant ; *Databases, Genetic ; Fungi/*genetics ; Information Dissemination/methods ; Plants/*genetics ; *Software ; },
abstract = {BACKGROUND: The submission of DNA sequences to public sequence databases is an essential, but insufficiently automated step in the process of generating and disseminating novel DNA sequence data. Despite the centrality of database submissions to biological research, the range of available software tools that facilitate the preparation of sequence data for database submissions is low, especially for sequences generated via plant and fungal DNA barcoding. Current submission procedures can be complex and prohibitively time expensive for any but a small number of input sequences. A user-friendly software tool is needed that streamlines the file preparation for database submissions of DNA sequences that are commonly generated in plant and fungal DNA barcoding.<br><br>METHODS: A Python package was developed that converts DNA sequences from the common EMBL and GenBank flat file formats to submission-ready, tab-delimited spreadsheets (so-called 'checklists') for a subsequent upload to the annotated sequence section of the European Nucleotide Archive (ENA). The software tool, titled 'EMBL2checklists', automatically converts DNA sequences, their annotation features, and associated metadata into the idiosyncratic format of marker-specific ENA checklists and, thus, generates files that can be uploaded via the interactive Webin submission system of ENA.<br><br>RESULTS: EMBL2checklists provides a simple, platform-independent tool that automates the conversion of common DNA barcoding sequences into easily editable spreadsheets that require no further processing but their upload to ENA via the interactive Webin submission system. The software is equipped with an intuitive graphical as well as an efficient command-line interface for its operation. The utility of the software is illustrated by its application in four recent investigations, including plant phylogenetic and fungal metagenomic studies.<br><br>DISCUSSION: EMBL2checklists bridges the gap between common software suites for DNA sequence assembly and annotation and the interactive data submission process of ENA. It represents an easy-to-use solution for plant and fungal biologists without bioinformatics expertise to generate submission-ready checklists from common DNA sequence data. It allows the post-processing of checklists as well as work-sharing during the submission process and solves a critical bottleneck in the effort to increase participation in public data sharing.},
}
@article {pmid30629584,
year = {2019},
author = {Chiovitti, A and Thorpe, F and Gorman, C and Cuxson, JL and Robevska, G and Szwed, C and Duncan, JC and Vanyai, HK and Cross, J and Siemering, KR and Sumner, J},
title = {A citizen science model for implementing statewide educational DNA barcoding.},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0208604},
pmid = {30629584},
issn = {1932-6203},
mesh = {Animals ; Australia ; Base Sequence ; *DNA Barcoding, Taxonomic ; Feedback ; Genetic Variation ; Mitochondria/genetics ; *Models, Educational ; Phylogeny ; Reptiles/classification/genetics ; *Science ; Species Specificity ; Students ; },
abstract = {Our aim was to develop a widely available educational program in which students conducted authentic research that met the expectations of both the scientific and educational communities. This paper describes the development and implementation of a citizen science project based on DNA barcoding of reptile specimens obtained from the Museums Victoria frozen tissue collection. The student program was run by the Gene Technology Access Centre (GTAC) and was delivered as a "one day plus one lesson" format incorporating a one-day wet laboratory workshop followed by a single lesson at school utilising online bioinformatics tools. The project leveraged the complementary resources and expertise of the research and educational partners to generate robust scientific data that could be analysed with confidence, meet the requirements of the Victorian state education curriculum, and provide participating students with an enhanced learning experience. During two 1-week stints in 2013 and 2014, 406 students mentored by 44 postgraduate university students participated in the project. Students worked mainly in pairs to process ~200 tissue samples cut from 53 curated reptile specimens representing 17 species. A total of 27 novel Cytochrome Oxidase subunit 1 (CO1) sequences were ultimately generated for 8 south-east Australian reptile species of the families Scincidae and Agamidae.},
}
@article {pmid30628589,
year = {2019},
author = {Austin, MJ and Rosales, AM},
title = {Tunable biomaterials from synthetic, sequence-controlled polymers.},
journal = {Biomaterials science},
volume = {7},
number = {2},
pages = {490-505},
doi = {10.1039/c8bm01215f},
pmid = {30628589},
issn = {2047-4849},
mesh = {Biocompatible Materials/*chemistry ; Biomimetic Materials/chemistry ; Humans ; Polymerization ; Polymers/*chemistry ; Proteins/metabolism ; },
abstract = {Polymeric biomaterials have many applications including therapeutic delivery vehicles, medical implants and devices, and tissue engineering scaffolds. Both naturally-derived and synthetic materials have successfully been used for these applications in the clinic. However, the increasing complexity of these applications requires materials with advanced properties, especially customizable or tunable materials with bioactivity. To address this issue, there have been recent efforts to better recapitulate the properties of natural materials using synthetic biomaterials composed of sequence-controlled polymers. Sequence control mimics the primary structure found in biopolymers, and in many cases, provides an extra handle for functionality in synthetic polymers. Here, we first review the advances in synthetic methods that have enabled sequence-controlled biomaterials on a relevant scale, and discuss strategies for choosing functional sequences from a biomaterials engineering context. Then, we highlight several recent studies that show strong impact of sequence control on biomaterial properties, including in vitro and in vivo behavior, in the areas of hydrogels, therapeutic materials, and novel applications such as molecular barcodes for medical devices. The role of sequence control in biomaterials properties is an emerging research area, and there remain many opportunities for investigation. Further study of this topic may significantly advance our understanding of bioactive or smart materials, as well as contribute design rules to guide the development of synthetic biomaterials for future applications in tissue engineering and regenerative medicine.},
}
@article {pmid30627682,
year = {2018},
author = {Sheir, SK and Galal-Khallaf, A and Mohamed, AH and Mohammed-Geba, K},
title = {Morphological and molecular clues for recording the first appearance of Artemia franciscana () in Egypt.},
journal = {Heliyon},
volume = {4},
number = {12},
pages = {e01110},
pmid = {30627682},
issn = {2405-8440},
abstract = {Artemia franciscana is a native species to the New World, and became an exotic species to most parts of the world. The Egyptian hypersaline, continental Qaroun Lake (Fayoum Governorate, Middle of Egypt) is subjected to a gradually increasing salinity rates that approximate or exceed these of seawater. Artemia populations there are known to be parthenogenetic. Yet, these populations started to exhibit abnormal morphologies. Therefore, Qaroun Lake samples of Artemia were subjected to several morphological, biometric, and molecular phylogenetic analyses for accurate species identification and phylogeographic origin approximation. These analyses revealed the existence of the alien sexual species of brine shrimp A. franciscana in Qaroun Lake. The characteristics of the subspherical frontal knob with several spines on the top, ovisac lateral triangular lobe on both sides and its projection together with the biometrics confirmed this species morphotype. DNA barcoding and other molecular analyses based on PCR-based amplification and sequencing of the barcode region of the cytochrome oxidase subunit I gene (COI) exhibited that all the collected samples belong to five haplotypes. Egyptian A. franciscana COI sequences phylogeny and pairwise distances analysis exhibited closer proximity to Latin American strains than to the Northern American ones. A. franciscana presence may be ascribed to the migratory birds present in Qaroun Lake protectorate, since no marine aquaculture activity in Qaroun Lake is known. Therefore, and for the best of our knowledge, this is the first record of the invasive A. franciscana in Egypt.},
}
@article {pmid30624727,
year = {2019},
author = {Ng, JCF and Quist, J and Grigoriadis, A and Malim, MH and Fraternali, F},
title = {Pan-cancer transcriptomic analysis dissects immune and proliferative functions of APOBEC3 cytidine deaminases.},
journal = {Nucleic acids research},
volume = {47},
number = {3},
pages = {1178-1194},
pmid = {30624727},
issn = {1362-4962},
support = {MR/L01257X/1/MRC_/Medical Research Council/United Kingdom ; MR/L01257X/2/MRC_/Medical Research Council/United Kingdom ; },
mesh = {APOBEC Deaminases ; Cell Line, Tumor ; Cell Proliferation ; Cytidine Deaminase/genetics/metabolism ; Cytosine Deaminase/*genetics/metabolism ; Gene Expression Profiling ; Humans ; Immune System/metabolism ; Minor Histocompatibility Antigens/genetics/metabolism ; Mutation ; Neoplasms/*enzymology/genetics/immunology/metabolism ; Software ; Transcriptome ; },
abstract = {APOBEC3 cytidine deaminases are largely known for their innate immune protection from viral infections. Recently, members of the family have been associated with a distinct mutational activity in some cancer types. We report a pan-tissue, pan-cancer analysis of RNA-seq data specific to the APOBEC3 genes in 8,951 tumours, 786 cancer cell lines and 6,119 normal tissues. By deconvolution of levels of different cell types in tumour admixtures, we demonstrate that APOBEC3B (A3B), the primary candidate as a cancer mutagen, shows little association with immune cell types compared to its paralogues. We present a pipeline called RESPECTEx (REconstituting SPecific Cell-Type Expression) and use it to deconvolute cell-type specific expression levels in a given cohort of tumour samples. We functionally annotate APOBEC3 co-expressing genes, and create an interactive visualization tool which 'barcodes' the functional enrichment (http://fraternalilab.kcl.ac.uk/apobec-barcodes/). These analyses reveal that A3B expression correlates with cell cycle and DNA repair genes, whereas the other APOBEC3 members display specificity for immune processes and immune cell populations. We offer molecular insights into the functions of individual APOBEC3 proteins in antiviral and proliferative contexts, and demonstrate the diversification this family of enzymes displays at the transcriptomic level, despite their high similarity in protein sequences and structures.},
}
@article {pmid30624408,
year = {2019},
author = {Roberts, DS and Maurya, R and Takemon, Y and Vitte, J and Gong, L and Zhao, J and Wong, CH and Slattery, W and Peng, KA and Lekovic, G and Schwartz, MS and Bulsara, K and Ngan, CY and Giovannini, M and Wei, CL},
title = {Linked-read Sequencing Analysis Reveals Tumor-specific Genome Variation Landscapes in Neurofibromatosis Type 2 (NF2) Patients.},
journal = {Otology &amp; neurotology : official publication of the American Otological Society, American Neurotology Society [and] European Academy of Otology and Neurotology},
volume = {40},
number = {2},
pages = {e150-e159},
doi = {10.1097/MAO.0000000000002096},
pmid = {30624408},
issn = {1537-4505},
support = {P30 CA034196/CA/NCI NIH HHS/United States ; },
mesh = {Genetic Variation ; Genome-Wide Association Study ; Humans ; Male ; Mutation ; Neurofibromatosis 2/*genetics ; Neuroma, Acoustic/*genetics ; },
abstract = {HYPOTHESIS: We hypothesize that genomic variants including deletions, insertions, inversions, and tandem duplications beyond the changes in tumor suppressor NF2 gene affect gene expression of tumor-specific pathways in vestibular schwannomas (VS) patients with Neurofibromatosis type 2 (NF2), thus contributing to their clinical behavior.<br><br>BACKGROUND: Genomic variation could reconfigure transcription in NF2 transformation process. Therefore, genome-wide high-resolution characterization of structural variants (SV) landscapes in NF2 tumors can expand our understanding of the genes regulating the clinical phenotypes in NF2-associated VS.<br><br>METHODS: We performed whole-genome haplotype-specific structural variation analysis using synthetic linked reads generated through microfluidics-based barcoding of high molecular weight DNA followed by high-coverage Illumina paired-end whole-genome sequencing from 10 patients' tumors of different growth rates and their matching blood samples.<br><br>RESULTS: NF2 tumor-specific deletions and large SVs were detected and can be classified based on their association with tumor growth rates. Through detailed annotation of these mutations, we uncover common alleles affected by these deletions and large SVs that can be associated with signaling pathways implicated in cell proliferation and tumorigenesis.<br><br>CONCLUSION: The genomic variation landscape of NF2-related VS was investigated through whole-genome linked-read sequencing. Large SVs, in addition to deletions, were identified and may serve as modulators of clinical behavior.},
}
@article {pmid30624143,
year = {2019},
author = {Salgado-Salazar, C and Crouch, JA},
title = {Genome resources for the stem and bark canker pathogens Corinectria fuckeliana, Neonectria hederae and N. punicea.},
journal = {Plant disease},
volume = {103},
number = {3},
pages = {389-391},
doi = {10.1094/PDIS-05-18-0904-A},
pmid = {30624143},
issn = {0191-2917},
mesh = {*Genome, Fungal/genetics ; *Hypocreales/genetics ; Plant Bark/microbiology ; Plant Diseases/microbiology ; Plant Stems/microbiology ; *Trees/microbiology ; Wood/microbiology ; },
abstract = {Corinectria fuckeliana, Neonectria hederae, and N. punicea are fungi in the family Nectriaceae that cause canker diseases of numerous hardwood trees, conifers, and woody perennials, often leading to plant mortality. Here, we report draft genome sequences for these three phytopathogenic fungal species. The genome sizes are consistent with those reported for other members of the Nectriaceae (28 to 43 Mb). These are the first genome resources available for C. fuckeliana, N. hederae, and N. punicea. These genome sequences may provide insights into the mechanisms of virulence and pathogenicity employed by these three destructive plant pathogens, and are resources suitable for the development of molecular markers that could be used for species identification, diagnostic tools and barcodes, and population studies.},
}
@article {pmid30622885,
year = {2018},
author = {Bakhshi, M and Arzanlou, M and Babai-Ahari, A and Groenewald, JZ and Crous, PW},
title = {Novel primers improve species delimitation in Cercospora.},
journal = {IMA fungus},
volume = {9},
number = {},
pages = {299-332},
pmid = {30622885},
issn = {2210-6340},
abstract = {The genus Cercospora includes many important plant pathogens that are commonly associated with leaf spot diseases on a wide range of cultivated and wild plant species. Due to the lack of useful morphological features and high levels of intraspecific variation, host plant association has long been a decisive criterion for species delimitation in Cercospora. Because several taxa have broader host ranges, reliance on host data in Cercospora taxonomy has proven problematic. Recent studies have revealed multi-gene DNA sequence data to be highly informative for species identification in Cercospora, especially when used in a concatenated alignment. In spite of this approach, however, several species complexes remained unresolved as no single gene proved informative enough to act as DNA barcoding locus for the genus. Therefore, the aims of the present study were firstly to improve species delimitation in the genus Cercospora by testing additional genes and primers on a broad set of species, and secondly to find the best DNA barcoding gene(s) for species delimitation. Novel primers were developed for tub2 and rpb2 to supplement previously published primers for these loci. To this end, 145 Cercospora isolates from the Iranian mycobiota together with 25 additional reference isolates preserved in the Westerdijk Fungal Biodiversity Institute were subjected to an eight-gene (ITS, tef1, actA, cmdA, his3, tub2, rpb2 and gapdh) analysis. Results from this study provided new insights into DNA barcoding in Cercospora, and revealed gapdh to be a promising gene for species delimitation when supplemented with cmdA, tef1 and tub2. The robust eight-gene phylogeny revealed several novel clades within the existing Cercospora species complexes, such as C. apii, C. armoraciae, C. beticola, C. cf. flagellaris and Cercospora sp. G. The C. apii s. lat. isolates are distributed over three clades, namely C. apii s. str., C. plantaginis and C. uwebrauniana sp. nov. The C. armoraciae s. lat. isolates are distributed over two clades, C. armoraciae s. str. and C. bizzozeriana. The C. beticola s. lat. isolates are distributed over two clades, namely C. beticola s. str. and C. gamsiana, which is newly described.},
}
@article {pmid30622883,
year = {2018},
author = {Scambler, R and Niskanen, T and Assyov, B and Ainsworth, AM and Bellanger, JM and Loizides, M and Moreau, PA and Kirk, PM and Liimatainen, K},
title = {Diversity of Chroogomphus (Gomphidiaceae, Boletales) in Europe, and typification of C. rutilus.},
journal = {IMA fungus},
volume = {9},
number = {},
pages = {271-290},
pmid = {30622883},
issn = {2210-6340},
abstract = {In this study, eight species of Chroogomphus are recognized from Europe: C. britannicus, C. aff. filiformis 1, C. fulmineus, C. cf. helveticus, C. mediterraneus, C. cf. purpurascens, C. rutilus, and C. subfulmineus. Different candidates for the application of the name C. rutilus are evaluated and the best fit to the description is selected; lecto- and epitypes are chosen to fix the name. Chroogomphus fulmineus and C. mediterraneus are also epitypified and a new species, C. subfulmineus, is described. The infrageneric classification is revised and a new subgenus Siccigomphus and three new sections, Confusi, Filiformes, and Fulminei are introduced. The former sections Chroogomphus and Floccigomphus are elevated to subgeneric level. Comparison of the ITS regions (nuc rDNA ITS1-5.8S-ITS2) of all species studied shows that there is a minimum interspecific difference of 1.5 %, with the exception of the two species belonging to sect. Fulminei which differ by a minimum of 0.9 %. Ecological specimen data indicate that species of Chroogomphus form basidiomes under members of Pinaceae, with a general preference for species of Pinus. Five European species have been recorded under Picea, while Abies and Larix have also been recorded as tree associates, although the detailed nutritional relationships of the genus, involving other suilloid fungi in particular, have yet to be fully clarified.},
}
@article {pmid30622422,
year = {2019},
author = {Zhong, W and Tan, Z and Wang, B and Yan, H},
title = {Next-generation sequencing analysis of Pardosa pseudoannulata's diet composition in different habitats.},
journal = {Saudi journal of biological sciences},
volume = {26},
number = {1},
pages = {165-172},
pmid = {30622422},
issn = {1319-562X},
abstract = {Spiders are the most common and predominant predators in terrestrial ecosystems. The predatory behavior of spiders affects the energy flow across the food web within an ecosystem. Traditiaonal methods for analyzing spider diets such as field observation, anatomy and faeces analysis are not suitable for spider experiments due to spiders' special dietary behavior. The molecular method based on the specific primers of prey DNA seems to be inefficient either in spite of its wide application in diet analysis. As the next-generation sequencing (NGS) technology becomes prevalent in many different areas, several cases of the NGS-based analysis of mammal diets have been published. This study analyzed the diet differences of Pardosa pseudoannulata (Araneae: Lycosidae) in four habitats (a wetland, a tea plantation, an alpine meadow and a paddy field) by using the NGS technology, combined with the DNA barcode method. The results suggested that the Pardosa pseudoannulata feed on a broad range of prey, and 7 orders and 24 families of insects were detected in the four investigated habitats. Moreover, it is found that the diet diversity of Pardosa pseudoannulata is greatly influenced by their living environments and seasons. In a nutshell, this study established an NGS-based methodology for spider diets analysis, and the results provided some basic materials to inform the protection and utilization of the Pardosa pseudoannulata as a potential eco-friendly predator against pests.},
}
@article {pmid30622399,
year = {2018},
author = {Kirichenko, N and Triberti, P and Kobayashi, S and Hirowatari, T and Doorenweerd, C and Ohshima, I and Huang, GH and Wang, M and Magnoux, E and Lopez-Vaamonde, C},
title = {Systematics of Phyllocnistis leaf-mining moths (Lepidoptera, Gracillariidae) feeding on dogwood (Cornus spp.) in Northeast Asia, with the description of three new species.},
journal = {ZooKeys},
volume = {},
number = {736},
pages = {79-118},
pmid = {30622399},
issn = {1313-2989},
abstract = {During an ongoing DNA-barcoding campaign of the leaf-mining moths that feed on woody plants in Northeast Asia, four lineages of the genus Phyllocnistis (Gracillariidae, Phyllocnistinae) were discovered on dogwood (Cornus spp): P. cornella Ermolaev, 1987 on C. controversa Hemsl. (Japan: Hokkaido) and three new species - one feeding on C. controversa, C. florida L. and C. macrophylla Wall. in Japan (Honshu, Shikoku, Kyushu), a second species on C. macrophylla in China (Yunnan) and a third on Siberian dogwood Cornus alba L. in Russia (Siberia). All these species showed differences in morphology, in the barcode region of the cytochrome c oxidase I gene and in two nuclear genes (histone H3 and 28S ribosomal RNA). No correlation was found between the deep mitochondrial splits observed and the Wolbachia infection pattern. Based on both morphological and molecular evidence, the three recently discovered lineages are described here as new species: P. indistincta Kobayashi &amp; Triberti, sp. n. (Japan), P. saepta Kirichenko, Ohshima &amp; Huang, sp. n. (China) and P. verae Kirichenko, Triberti &amp; Lopez-Vaamonde, sp. n. (Russia). In addition, the authors re-describe the adult morphology of P. cornella, provide the first record of this species from Japan and highlight the diagnostic characters that allow these Cornus-feeding Phyllocnistis species to be distinguished.},
}
@article {pmid30621230,
year = {2019},
author = {Wei, S and Luo, Z and Cui, S and Qiao, J and Zhang, Z and Zhang, L and Fu, J and Ma, X},
title = {Molecular Identification and Targeted Quantitative Analysis of Medicinal Materials from Uncaria Species by DNA Barcoding and LC-MS/MS.},
journal = {Molecules (Basel, Switzerland)},
volume = {24},
number = {1},
pages = {},
pmid = {30621230},
issn = {1420-3049},
mesh = {Alkaloids/chemistry/*genetics ; Chromatography, Liquid ; *DNA Barcoding, Taxonomic ; DNA, Plant/chemistry/*genetics ; Indole Alkaloids/chemistry ; Medicine, Chinese Traditional ; Tandem Mass Spectrometry ; Uncaria/chemistry/*genetics ; },
abstract = {The genus Uncaria is an important source of traditional Chinese medicines with multiple therapeutic effects. The identification of the correct species and accurate determination of the contents of bioactive constituents are important for quality control of Uncaria medicinal materials. Here, an integrated evaluation system based on DNA barcoding for species identification and quantitative analysis by LC-MS/MS has been established. DNA barcoding based on the ITS2 barcode region showed sufficient discriminatory power to precisely identify 24 samples from seven Uncaria species. The length of the 24 ITS2 sequences of Uncaria samples is 227 bp, and 17 variation sites were detected. Additionally, the results of qualitative and quantitative chemical analyses by LC-MS/MS indicated that the chemical compositions of all Uncaria samples were similar; while their contents of targeted alkaloids in samples from different species and origin areas were different. The contents of rhynchophylline (RC) and isorhynchophylline (IRC) were 2.9[-]1612 mg/kg and 2.60[-]1299 mg/kg in all tested samples, respectively. This study concludes that DNA barcoding should be used as the first screening step for Uncaria medicinal materials. Then, integration of DNA barcoding with chemical analyses should be applied in quality control of Uncaria medicinal materials in the medicinal industry.},
}
@article {pmid30620135,
year = {2019},
author = {Asmus, N and Papale, LA and Madrid, A and Alisch, RS},
title = {Simultaneous Targeted Methylation Sequencing (sTM-Seq).},
journal = {Current protocols in human genetics},
volume = {101},
number = {1},
pages = {e81},
doi = {10.1002/cphg.81},
pmid = {30620135},
issn = {1934-8258},
mesh = {5-Methylcytosine/analogs &amp; derivatives/chemistry/metabolism ; DNA/genetics ; DNA Methylation/*genetics ; DNA Primers/chemistry/genetics ; Epigenesis, Genetic ; Genome/*genetics ; Genomics/trends ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Sequence Analysis, DNA/*methods ; Software ; },
abstract = {Mapping patterns of DNA methylation throughout the epigenome are critical to our understanding of several important biological and regulatory functions, such as transcriptional regulation, genomic imprinting, and embryonic development. The development and rapid advancement of next-generation sequencing (NGS) technologies have provided clinicians and researchers with accurate and reliable read-outs of genomic and epigenomic information at the nucleotide level. Such improvements have significantly lowered the cost required for genome-wide sequencing, facilitating the vast acquisition of data that has led to many improvements in patient care. However, the torrid rate of NGS data generation has left targeted validation approaches behind, including the confirmation of epigenetic marks such as DNA methylation. To overcome these shortcomings, we present a rapid and robust protocol for the parallel examination of multiple methylated sequences that we have termed simultaneous targeted methylation sequencing (sTM-Seq). Key features of this technique include the elimination of the need for large amounts of high-molecular weight DNA and the nucleotide specific distinction of both 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Moreover, sTM-Seq is scalable and can be used to investigate multiple loci in dozens of samples within a single sequencing run. By utilizing freely available web-based software and universal primers for multipurpose barcoding, library preparation, and customized sequencing, sTM-Seq is affordable, efficient, and widely applicable. Together, these features enable sTM-Seq to have wide-reaching clinical applications that will greatly improve turnaround rates for same-day procedures and allow clinicians to collect high-resolution data that can be used in a variety of patient settings. © 2019 by John Wiley &amp; Sons, Inc.},
}
@article {pmid30619587,
year = {2018},
author = {Andriollo, T and Ashrafi, S and Arlettaz, R and Ruedi, M},
title = {Porous barriers? Assessment of gene flow within and among sympatric long-eared bat species.},
journal = {Ecology and evolution},
volume = {8},
number = {24},
pages = {12841-12854},
pmid = {30619587},
issn = {2045-7758},
abstract = {Species are the basic units for measuring biodiversity and for comprehending biological interactions. Yet, their delineation is often contentious, especially in groups that are both diverse and phenotypically conservative. Three cryptic species of long-eared bats, Plecotus auritus, P. austriacus, and P. macrobullaris, co-occur over extensive areas of Western Europe. The latter is a fairly recent discovery, questioning the overall diversity of the entire Plecotus complex. Yet, high morphological and acoustic similarities compromise the reliable identification of long-eared bats in the field. We postulate that such extensive phenotypic overlap, along with the recurrent observation of morphologically intermediate individuals, may hide rampant interspecific hybridization. Based on a geographic sampling centered on areas of sympatry in the Alps and Corsica, we assessed the level of reproductive isolation of these three Plecotus species with mitochondrial and nuclear markers, looking at both inter- and intraspecific genetic population structuring. No sign of hybridization was detected between these three species that appear well separated biologically. Genetic structuring of populations, however, reflected different species-specific responses to environmental connectivity, that is, to the presence of orographic or sea barriers. While the Alpine range and the Ligurian Sea coincided with sharp genetic discontinuities in P. macrobullaris and P. austriacus, the more ubiquitous P. auritus showed no significant population structuration. There were clear phylogeographic discrepancies between microsatellite and mitochondrial markers at the intraspecific level, however, which challenges the reliance on simple barcoding approaches for the delineation of sound conservation units.},
}
@article {pmid30619549,
year = {2018},
author = {Rennstam Rubbmark, O and Sint, D and Horngacher, N and Traugott, M},
title = {A broadly applicable COI primer pair and an efficient single-tube amplicon library preparation protocol for metabarcoding.},
journal = {Ecology and evolution},
volume = {8},
number = {24},
pages = {12335-12350},
pmid = {30619549},
issn = {2045-7758},
abstract = {The nucleotide variation in the cytochrome c oxidase subunit I (COI) gene makes it ideal for assigning sequences to species. However, this variability also makes it difficult to design truly universal primers. Here, we present the forward primer "Sauron-S878," specifically designed to facilitate library preparation for metabarcoding. This primer is modified to improve the coverage of terrestrial species compared to the primer mCOIintF, optimized for aquatic systems, which raised the in silico coverage from 74.4% to 98.3% of available NCBI sequences (perfect match in 3' region, up to three mismatches in remaining primer). When paired with the reverse primer "jgHCO2198" (fragment length ~313 bp), these primers amplified 98.4% of 255 tested DNA extracts from various taxa, which are better than many other common COI barcoding primers. Furthermore, a single-tube protocol was developed, wherein these primers amplify the target gene, and attach MIDs and Illumina sequencing adapters in one reaction. This eliminates the need for re-amplification or enzymatic ligation during library preparation while keeping the flexibility to modularly combine primers and MIDs. Using the single-tube approach, three replicates of three mock samples were sequenced on a MiSeq platform with no adverse effects compared to commercial Nextera indexing kits. From this run, 75% of all included taxa could be recovered, with no considerable bias among taxonomic groups. Despite the fact that 98.4% of the extracts were confirmed to amplify in vitro, this number was lower than expected. A reason for this discrepancy was a clear link between the relative concentration of a specific DNA type in the template and the number of returned reads for this DNA. We would argue that such a bias may be especially problematic in metabarcoding where samples usually contain trace DNA in unknown amounts. However, how this affects the completeness of metabarcoding results has yet been poorly investigated.},
}
@article {pmid30619422,
year = {2018},
author = {Wetters, S and Horn, T and Nick, P},
title = {Goji Who? Morphological and DNA Based Authentication of a "Superfood".},
journal = {Frontiers in plant science},
volume = {9},
number = {},
pages = {1859},
pmid = {30619422},
issn = {1664-462X},
abstract = {"Goji" (Lycium barbarum and Lycium chinense) is a generic name for medical plants with a long historical background in the traditional Chinese medicine. With the emerging trend of "Superfoods" several years ago, Goji berries soon became an established product in European countries and not only are the most popular product of traditional Chinese medicine outside of China but to this day one of the symbols of the entire "Superfood" trend. However, since Goji is an umbrella term for different plant species that are closely related, mislabeling and adulterations (unconsciously or purposely) are possible. We carefully verified the identity of Goji reference plant material based on morphological traits, mainly floral structures of several inflorescences of each individual, in order to create a robust background for the downstream applications that were used on those reference plants and additionally on commercial Goji products. We report morphological and molecular based strategies for the differentiation of Lycium barbarum and Lycium chinense. The two different Goji species vary significantly in seed size, with an almost double average seed area in Lycium chinense compared to Lycium barbarum. Differences could be traced on the molecular level as well; using the psbA-trnH barcoding marker, we detected a single nucleotide substitution that was used to develop an easy one-step differentiation tool based on ARMS (amplification refractory mutation system). Two diagnostic primers used in distinct multiplex PCRs yield a second diagnostic band in a subsequent gel electrophoresis for Lycium barbarum or Lycium chinense, respectively. Our ARMS approach is a strong but simple tool to trace either of the two different Goji species. Both the morphological and the molecular analysis showed that all of the tested commercial Goji products contained fruits of the species Lycium barbarum var. barbarum, leading to the assumption that consumer protection is satisfactory.},
}
@article {pmid30619401,
year = {2018},
author = {Sgamma, T and Masiero, E and Mali, P and Mahat, M and Slater, A},
title = {Sequence-Specific Detection of Aristolochia DNA - A Simple Test for Contamination of Herbal Products.},
journal = {Frontiers in plant science},
volume = {9},
number = {},
pages = {1828},
pmid = {30619401},
issn = {1664-462X},
abstract = {Herbal medicines are used globally for their health benefits as an alternative therapy method to modern medicines. The market for herbal products has increased rapidly over the last few decades, but this has in turn increased the opportunities for malpractices such as contamination or substitution of products with alternative plant species. In the 1990s, a series of severe renal disease cases were reported in Belgium associated with weight loss treatment, in which the active species Stephania tetrandra was found to be substituted with Aristolochia fangchi. A. fangchi contains toxic aristolochic acids, which have been linked to kidney failure, as well as cancers of the urinary tract. Because of these known toxicities, herbal medicines containing these compounds, or potentially contaminated by these plants, have been restricted or banned in some countries, but they are still available via the internet and in alternate formulations. In this study, a DNA based method based on quantitative real-time PCR (qPCR) was tested to detect and distinguish Aristolochia subg. Siphisia (Duch.) O.C.Schmidt species from a range of medicinal plants that could potentially be contaminated with Aristolochia material. Specific primers were designed to confirm that Aristolochia subg. Siphisia can be detected, even in small amounts, if it is present in the products, fulfilling the aim of offering a simple, cheaper and faster solution than the chemical methods. A synthetic gBlock template containing the primer sequences was used as a reference standard to calibrate the qPCR assay and to estimate the copy number of a target gene per sample. Generic primers covering the conserved 5.8S rRNA coding region were used as internal control to verify DNA quality and also as a reference gene for relative quantitation. To cope with potentially degraded DNA, all qPCR primer sets were designed to generate PCR products of under 100 bp allowing detection and quantification of A. fangchi gBlock even when mixed with S. tetrandra gBlock in different ratios. All proportions of Aristolochia, from 100 to 2%, were detected. Using standards, associating the copy number to each start quantity, the detection limit was calculated and set to about 50 copies.},
}
@article {pmid30616524,
year = {2019},
author = {Meher, PK and Sahu, TK and Gahoi, S and Tomar, R and Rao, AR},
title = {funbarRF: DNA barcode-based fungal species prediction using multiclass Random Forest supervised learning model.},
journal = {BMC genetics},
volume = {20},
number = {1},
pages = {2},
pmid = {30616524},
issn = {1471-2156},
mesh = {Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/genetics ; Fungi/*classification/*genetics ; Software ; *Supervised Machine Learning ; },
abstract = {BACKGROUND: Identification of unknown fungal species aids to the conservation of fungal diversity. As many fungal species cannot be cultured, morphological identification of those species is almost impossible. But, DNA barcoding technique can be employed for identification of such species. For fungal taxonomy prediction, the ITS (internal transcribed spacer) region of rDNA (ribosomal DNA) is used as barcode. Though the computational prediction of fungal species has become feasible with the availability of huge volume of barcode sequences in public domain, prediction of fungal species is challenging due to high degree of variability among ITS regions within species.<br><br>RESULTS: A Random Forest (RF)-based predictor was built for identification of unknown fungal species. The reference and query sequences were mapped onto numeric features based on gapped base pair compositions, and then used as training and test sets respectively for prediction of fungal species using RF. More than 85% accuracy was found when 4 sequences per species in the reference set were utilized; whereas it was seen to be stabilized at ~88% if &#x2265;7 sequence per species in the reference set were used for training of the model. The proposed model achieved comparable accuracy, while evaluated against existing methods through cross-validation procedure. The proposed model also outperformed several existing models used for identification of different species other than fungi.<br><br>CONCLUSIONS: An online prediction server "funbarRF" is established at http://cabgrid.res.in:8080/funbarrf/ for fungal species identification. Besides, an R-package funbarRF (https://cran.r-project.org/web/packages/funbarRF/) is also available for prediction using high throughput sequence data. The effort put in this work will certainly supplement the future endeavors in the direction of fungal taxonomy assignments based on DNA barcode.},
}
@article {pmid30615158,
year = {2019},
author = {Gilligan, TM and Goldstein, PZ and Timm, AE and Farris, R and Ledezma, L and Cunningham, AP},
title = {Identification of Heliothine (Lepidoptera: Noctuidae) Larvae Intercepted at U.S. Ports of Entry From the New World.},
journal = {Journal of economic entomology},
volume = {112},
number = {2},
pages = {603-615},
doi = {10.1093/jee/toy402},
pmid = {30615158},
issn = {1938-291X},
mesh = {Animals ; Guatemala ; Larva ; *Lepidoptera ; Mexico ; *Moths ; Peru ; Reproducibility of Results ; },
abstract = {Heliothine larvae, especially early instars, are difficult to identify, and determinations sometimes rely on indirect information such as origin and host data. The introduction of Helicoverpa armigera (Hübner) into the New World has undermined the reliability of host and origin data to identify intercepted Helicoverpa larvae, and suspect Heliothinae/Helicoverpa larvae intercepted at U.S. ports of entry are now screened for H. armigera and Helicoverpa zea (Boddie) using molecular methods. Here, we analyze heliothine larvae intercepted during 2014-2106 to identify nontargets and evaluate morphological characters traditionally used to separate taxa. In total, nine species were identified, with Chloridea virescens (Fabricius) making up the bulk of interception records. The majority of heliothine suspects originate from Mexico and Peru on pigeon pea, chickpea, tomatillo, pea, and corn. Helicoverpa armigera is commonly intercepted from Peru on pea. Chloridea virescens is recorded from every country where interceptions were identified for this study except Guatemala and is found on multiple hosts. Identification issues and specific host/origin associations are discussed in detail.},
}
@article {pmid30611872,
year = {2019},
author = {Bentley, J and Moore, JP and Farrant, JM},
title = {Metabolomics as a complement to phylogenetics for assessing intraspecific boundaries in the desiccation-tolerant medicinal shrub Myrothamnus flabellifolia (Myrothamnaceae).},
journal = {Phytochemistry},
volume = {159},
number = {},
pages = {127-136},
doi = {10.1016/j.phytochem.2018.12.016},
pmid = {30611872},
issn = {1873-3700},
mesh = {*Adaptation, Physiological ; Africa, Southern ; Bayes Theorem ; Chromatography, Liquid ; *Desiccation ; Likelihood Functions ; Magnoliopsida/*classification/*metabolism ; *Metabolomics ; *Phylogeny ; Phytochemicals/metabolism ; Tandem Mass Spectrometry ; },
abstract = {The desiccation-tolerant shrub Myrothamnus flabellifolia has colonised a unique and harsh niche that provides little protection from the elements. It has a wide distribution range in southern Africa, occurring across an environmental gradient that is exceptionally arid in the southwest and highly mesic in the northeast. It is also harvested for use in medicinal preparations, both traditionally and commercially. However, the phytochemical variability of plants from different rainfall regions has not been assessed, nor have the intraspecific relationships been evaluated by means of a rigorously tested phylogeny. The aims of the present study were thus (1) to test a phylogenetic hypothesis for intraspecific relationships in M. flabellifolia; (2) to assess, based on the global metabolomic profiles, whether accessions collected from the three different geographic locations in southern Africa across a rainfall gradient can be differentiated, and if this corroborates the phylogenetic signature; and (3) with the aid of multivariate statistical analysis, identify and evaluate the most significant discriminatory metabolites between the three sampled regions that could act as potential barcodes. The results show that the phylogenetic and metabolomic signatures were congruent, and the metabolomic data were better able to discriminate the different populations collected from the three regions. Several potential barcodes for discriminating the material from the three regions are proposed. Quercetin-rhamnoside and 3-O-methylquercetin, both significant antioxidants, were present at significantly higher quantities in the material from the driest region in the west than from the more mesic regions in the south and east, whereas quercetin-3-O-glucuronide was significantly higher in the latter. A naringenin-like compound or arbutin derivative could discriminate the southern samples from the eastern samples, whereas digalloylglucose differentiated the eastern samples from the southern samples. In summary, the findings of this study imply that the origin of the material should be considered when used in medicinal and cosmetic preparations.},
}
@article {pmid30611284,
year = {2019},
author = {Klimov, PB and Skoracki, M and Bochkov, AV},
title = {Cox1 barcoding versus multilocus species delimitation: validation of two mite species with contrasting effective population sizes.},
journal = {Parasites &amp; vectors},
volume = {12},
number = {1},
pages = {8},
pmid = {30611284},
issn = {1756-3305},
support = {NCN 2014/15/B/NZ8/00208//Narodowe Centrum Nauki/ ; 15-29-02533//Russian Foundation for Basic Research/ ; 18-04-01092A//Russian Foundation for Basic Research/ ; 16-14-10109//Russian Science Foundation/ ; },
mesh = {Animals ; DNA Barcoding, Taxonomic/*veterinary ; Electron Transport Complex IV/genetics ; Female ; Male ; Mites/anatomy &amp; histology/*classification/genetics ; Multilocus Sequence Typing/veterinary ; Phylogeny ; Population Density ; },
abstract = {BACKGROUND: The cox1-barcoding approach is currently extensively used for high-throughput species delimitation and discovery. However, this method has several limitations, particularly when organisms have large effective population sizes. Paradoxically, most common, abundant, and widely distributed species may be misclassified by this technique.<br><br>RESULTS: We conducted species delimitation analyses for two host-specific lineages of scab mites of the genus Caparinia, having small population sizes. Cox1 divergence between these lineages was high (7.4-7.8%) while that of nuclear genes was low (0.06-0.53%). This system was contrasted with the medically important American house dust mite, Dermatophagoides farinae, a globally distributed species with very large population size. This species has two distinct, sympatric cox1 lineages with 4.2% divergence. We tested several species delimitation algorithms PTP, GMYC, ABGD, BPP, STACEY and PHRAPL, which inferred different species boundaries for these entities. Notably, STACEY recovered the Caparinia lineages as two species and D. farinae as a single species. BPP agreed with these results when the prior on ancestral effective population sizes was set to expected values, although delimitation of Caparinia was still equivocal. No other cox1 species delimitation algorithms inferred D. farinae as a single species, despite the fact that the nuclear CPW2 gene shows some evidence for introgression between the cox1 groups. This indicates that the cox1-barcoding approach may result in excessive species splitting.<br><br>CONCLUSIONS: Our research highlights the importance of using nuclear genes and demographic characteristics to infer species boundaries rather than relying on a single-gene barcoding approach, particularly for putative species having large effective population sizes.},
}
@article {pmid30610042,
year = {2018},
author = {Song, YE and Kang, H and Park, H},
title = {Algorithm to Estimate the Extended Turnaround Time Including Outpatient Waiting Time for Blood Specimen Collection when a Stand-alone Queue Ticket System not Connectable to Laboratory Information System Is Used.},
journal = {Annals of clinical and laboratory science},
volume = {48},
number = {6},
pages = {726-735},
pmid = {30610042},
issn = {1550-8080},
mesh = {*Algorithms ; Blood Specimen Collection/*methods ; *Clinical Laboratory Information Systems ; Delivery of Health Care ; Female ; Humans ; Laboratories, Hospital ; Male ; Outpatients ; Time Factors ; *Waiting Lists ; },
abstract = {BACKGROUND: A queue ticket system (QTS) used in an outpatient phlebotomy clinic was unable to be directly integrated with the laboratory information system (LIS). To monitor patient's waiting time and extended turnaround time (TAT) as patient-centered quality indicators for outpatient laboratory services, we developed an algorithm to integrate data between the QTS and the LIS.<br><br>METHODS: Between June 1 to September 30, 2017, data files were exported from a QSYS-8000 (HION Tech, Seoul, Korea). Each calling event from the QTS data was matched to a barcode of test requests from the LIS if the following conditions were met: (1) time interval between "call time" from QTS and "barcode printing time" from LIS <90 s; (2) "Counter Number" from LIS="Counter Number" from QTS. Extended TAT was estimated as the interval between pulling the queue ticket and the reporting of the test result.<br><br>RESULTS: 82.66%&#xb1;3.14% of the barcodes from the LIS were matched to issued tickets. Median waiting time (mean&#xb1;SD) was 6.5&#xb1;5.3 min. Median extended TAT was 84.7&#xb1;11.2 min for non-STAT and 53.0&#xb1;6.4 min for STAT.<br><br>CONCLUSION: When a stand-alone QTS was used in the outpatient phlebotomy clinic, data from the QTS and the LIS were integrated using a novel algorithm we developed.},
}
@article {pmid30609873,
year = {2019},
author = {Jeon, JH and Kim, SC},
title = {Comparative Analysis of the Complete Chloroplast Genome Sequences of Three Closely Related East-Asian Wild Roses (Rosa sect. Synstylae; Rosaceae).},
journal = {Genes},
volume = {10},
number = {1},
pages = {},
pmid = {30609873},
issn = {2073-4425},
mesh = {DNA Barcoding, Taxonomic/methods ; *Genome, Chloroplast ; Microsatellite Repeats ; *Phylogeny ; Plant Proteins/genetics ; Rosaceae/classification/*genetics ; },
abstract = {Species belonging to Rosa section Synstylae (Rosaceae) are mainly distributed in East Asia, and represent recently diverged lineages within the genus. Over decades, inferring phylogenetic relationships within section Synstylae have been exceptional challenges, due to short branch lengths and low support values. Of approximately 36 species in the section Synstylae, Rosa multiflora, Rosa luciae and Rosa maximowicziana are widely distributed in the Sino-Japanese floristic region. In this study, we assembled chloroplast genomes of these three species to compare the genomic features within section Synstylae, and to compare with other infrageneric groups. We found that three Rosa sect. Synstylae species had lost infA genes with pseudogenization, and they were almost identical to each other. Two protein-coding gene regions (ndhF and ycf1) and five non-coding regions (5'matK-trnK, psbI-trnS-trnG, rps16-trnG, rpoB-trnC, and rps4-trnT) were identified as being highly informative markers. Within three section Synstylae chloroplast genomes, 85 simple sequence repeat (SSR) motifs were detected, of which at least 13 motifs were identified to be effective markers. The phylogenetic relationships of R. multiflora, R. luciae and R. maximowicziana could not be resolved, even with chloroplast genome-wide data. This study reveals the chloroplast genomic data of Rosa sect. Synstylae, and it provides valuable markers for DNA barcoding and phylogenetic analyses for further studies.},
}
@article {pmid30604410,
year = {2019},
author = {Vecchioni, L and Marrone, F and Belaiba, E and Tiralongo, F and Bahri-Sfar, L and Arculeo, M},
title = {The DNA barcoding of Mediterranean combtooth blennies suggests the paraphyly of some taxa (Perciformes, Blenniidae).},
journal = {Journal of fish biology},
volume = {94},
number = {2},
pages = {339-344},
doi = {10.1111/jfb.13897},
pmid = {30604410},
issn = {1095-8649},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Mediterranean Sea ; Perciformes/*genetics ; *Phylogeny ; },
abstract = {A dataset including novel and publicly available mtDNA COI sequences of 14 Mediterranean combtooth blenny species belonging to nine genera was assembled in order to provide a reference dataset for DNA barcoding studies. Some inconsistencies in the current taxonomy of some genera were observed. In particular, the monophyly of the genera Parablennius and Salaria is not supported by the present dataset and the absence of reciprocal monophyly between the morphospecies Salaria basilisca and S. pavo questions their status and stresses the need of a revision of the genus Salaria.},
}
@article {pmid30602774,
year = {2019},
author = {Liu, K and Pan, C and Kuhn, A and Nievergelt, AP and Fantner, GE and Milenkovic, O and Radenovic, A},
title = {Detecting topological variations of DNA at single-molecule level.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {3},
pmid = {30602774},
issn = {2041-1723},
mesh = {DNA/*chemistry ; DNA Barcoding, Taxonomic/*methods ; Disulfides ; Molybdenum ; Nanopores ; },
abstract = {In addition to their use in DNA sequencing, ultrathin nanopore membranes have potential applications in detecting topological variations in deoxyribonucleic acid (DNA). This is due to the fact that when topologically edited DNA molecules, driven by electrophoretic forces, translocate through a narrow orifice, transient residings of edited segments inside the orifice modulate the ionic flow. Here we utilize two programmable barcoding methods based on base-pairing, namely forming a gap in dsDNA and creating protrusion sites in ssDNA for generating a hybrid DNA complex. We integrate a discriminative noise analysis for ds and ss DNA topologies into the threshold detection, resulting in improved multi-level signal detection and consequent extraction of reliable information about topological variations. Moreover, the positional information of the barcode along the template sequence can be determined unambiguously. All methods may be further modified to detect nicks in DNA, and thereby detect DNA damage and repair sites.},
}
@article {pmid30602765,
year = {2019},
author = {Jacobsen, SEW and Nerlov, C},
title = {Haematopoiesis in the era of advanced single-cell technologies.},
journal = {Nature cell biology},
volume = {21},
number = {1},
pages = {2-8},
pmid = {30602765},
issn = {1476-4679},
support = {G0900892/MRC_/Medical Research Council/United Kingdom ; MC_UU_00016/7/MRC_/Medical Research Council/United Kingdom ; MC_UU_12009/5/MRC_/Medical Research Council/United Kingdom ; G0701761/MRC_/Medical Research Council/United Kingdom ; MC_PC_12020/MRC_/Medical Research Council/United Kingdom ; MC_UU_12009/7/MRC_/Medical Research Council/United Kingdom ; G0501838/MRC_/Medical Research Council/United Kingdom ; MC_UU_00016/5/MRC_/Medical Research Council/United Kingdom ; G0801073/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; Cell Differentiation/genetics ; Cell Lineage/genetics ; Gene Expression Profiling/*methods ; *Hematopoiesis ; Hematopoietic Stem Cells/cytology/*metabolism ; Humans ; Reproducibility of Results ; Single-Cell Analysis/*methods ; },
abstract = {The molecular and functional characterization of single cells at scale has emerged as a key driver to unravel tissue biology. Thus, it is important to understand the strengths and limitations of transcriptomic approaches, molecular barcoding and functional assays used to study cellular properties at the single-cell level. Here, we review recent relevant work from the haematopoietic system and discuss how to interpret and integrate data obtained with different technologies.},
}
@article {pmid30599919,
year = {2019},
author = {Campanaro, A and Tommasi, N and Guzzetti, L and Galimberti, A and Bruni, I and Labra, M},
title = {DNA barcoding to promote social awareness and identity of neglected, underutilized plant species having valuable nutritional properties.},
journal = {Food research international (Ottawa, Ont.)},
volume = {115},
number = {},
pages = {1-9},
doi = {10.1016/j.foodres.2018.07.031},
pmid = {30599919},
issn = {1873-7145},
mesh = {Biodiversity ; Conservation of Natural Resources ; *DNA Barcoding, Taxonomic ; Food Supply ; Fruit/chemistry ; Micronutrients/analysis ; Nutritional Status ; *Nutritive Value ; Plant Leaves/chemistry ; Plants/*chemistry ; Seeds/chemistry ; },
abstract = {It is estimated that about 7000 plant species and a large number of cultivars and varieties have been cultivated for consumption in human history. However, <0.5% of these currently provide the majority of human food energy needs worldwide (e.g., rice, wheat, maize, and potato). Global issues such as climate change, diffusion of pests, and resistance to agrochemical treatments are posing great concern about the sustainable cultivation of these major staples, especially in equatorial and tropical countries, such as Sub Saharan Africa. In addition, most of these regions contain malnutrition and micronutrient deficiencies, and the sum of such problems create serious implications at social, political, and economic levels. A possible solution relies on the exploitation of plant biodiversity and particularly on the so-called NUS (Neglected and Underutilized Species). These plants are traditionally grown in their centres of origin and continue to be maintained by sociocultural preferences, however they remain inadequately documented and neglected by formal research and conservation programs. Although they are important in terms of micronutrients and the ability to grow in harsh conditions, these species are falling into disuse due to agronomic, genetic, economic, and cultural reasons. To promote and spread their cultivation at the global scale, along with knowledge on their suitability for human nutrition, reliable identification systems are necessary to guarantee adequate authenticity along the entire supply chain and distribution network. A precise identification of the different species and their varieties is fundamental both to retrieve information on their origin and authenticate the raw materials (i.e., seeds, leaves and fruit) and related processed products that can be distributed at the local or global scale. DNA-based techniques can help achieve this mission. In particular, the DNA barcoding approach has gained a role of primary importance due to its universality and versatility. Here, we discuss the advantages in using DNA barcoding for the identification of some of the most representative NUS species, as well as their traceability and conservation of cultural practices around them.},
}
@article {pmid30598619,
year = {2018},
author = {Cancian de Araujo, B and Schmidt, S and Schmidt, O and von Rintelen, T and Ubaidillah, R and Balke, M},
title = {The Mt Halimun-Salak Malaise Trap project - releasing the most species rich DNA Barcode library for Indonesia.},
journal = {Biodiversity data journal},
volume = {},
number = {6},
pages = {e29927},
pmid = {30598619},
issn = {1314-2828},
abstract = {The Indonesian archipelago features an extraordinarily rich biota. However, the actual taxonomic inventory of the archipelago remains highly incomplete and there is hardly any significant taxonomic activity that utilises recent technological advances. The IndoBioSys project was established as a biodiversity information system aiming at, amongst other goals, creating inventories of the Indonesian entomofauna using DNA barcoding. Here, we release the first large scale assessment of the megadiverse insect groups that occur in the Mount Halimun-Salak National Park, one of the largest tropical rain-forest ecosystem in West Java, with a focus on Hymenoptera, Coleoptera, Diptera and Lepidoptera collected with Malaise traps. From September 2015 until April 2016, 34 Malaise traps were placed in different localities in the south-eastern part of the Halimun-Salak National Park. A total of 4,531 specimens were processed for DNA barcoding and in total, 2,382 individuals produced barcode compliant records, representing 1,195 exclusive BINs or putative species in 98 insect families. A total of 1,149 BINs were new to BOLD. Of 1,195 BINs detected, 804 BINs were singletons and more than 90% of the BINs incorporated less than five specimens. The astonishing heterogeneity of BINs, as high as 1.1 exclusive BIN per specimen of Diptera successfully processed, shows that the cost/benefit relationship of the discovery of new species in those areas is very low. In four genera of Chalcidoidea, a superfamily of the Hymenoptera, the number of discovered species was higher than the number of species known from Indonesia, suggesting that our samples contain many species that are new to science. Those numbers shows how fast molecular pipelines contribute substantially to the objective inventorying of the fauna giving us a good picture of how potentially diverse tropical areas might be.},
}
@article {pmid30598607,
year = {2018},
author = {Skuhrovec, J and Gosik, R and Caldara, R and Toševski, I and Łętowski, J and Szwaj, E},
title = {Morphological characters of immature stages of Palaearctic species of Cleopomiarus and Miarus and their systematic value in Mecinini (Coleoptera, Curculionidae, Curculioninae).},
journal = {ZooKeys},
volume = {},
number = {808},
pages = {23-92},
pmid = {30598607},
issn = {1313-2989},
abstract = {The relationship between the genera Cleopomiarus and Miarus of Mecinini (Curculionidae, Curculioninae) was tested on the basis of morphological characters from the immature stages. The mature larvae of five Cleopomiarus species (C.distinctus (Boheman, 1845), C.graminis (Gyllenhal, 1813), C.longirostris (Gyllenhal, 1838), C.medius (Desbrochers des Loges, 1893), and C.meridionalis (H. Brisout de Barneville, 1863)), three Miarus species (M.abnormis Solari, 1947, M.ajugae (Herbst, 1795), and M.campanulae (Linnaeus, 1767)), and the pupae of four Cleopomiarus species (C.distinctus, C.graminis, C.longirostris, and C.medius) and two Miarus species (M.abnormis and M.ajugae) are described in detail for the first time. To confirm the taxonomic identification of some larvae, DNA COI barcode was obtained and compared with those of adults. The immature stages of the species herein studied were compared with those known from other genera in tribe Mecinini. It is suggested that Miarus and Cleopomiarus may be monophyletic based on several shared distinctive characters. Larvae of Miarus have a characteristic maxillary mala with six finger-like dms of two sizes (one or two dms very long and the rest of medium length), this feature being apparently unique among weevils. Other genus-specific character states are observed in the pupae, such as the length of setae on the head, rostrum and pronotum, including the number of rs on the rostrum, ds on pronotum, and finally the shape of the urogomphi. A key to the described larvae and pupae were respectively presented. New biological and distributional data on some species are reported.},
}
@article {pmid30597735,
year = {2019},
author = {Lagarde, A and Millot, M and Pinon, A and Liagre, B and Girardot, M and Imbert, C and Ouk, TS and Jargeat, P and Mambu, L},
title = {Antiproliferative and antibiofilm potentials of endolichenic fungi associated with the lichen Nephroma laevigatum.},
journal = {Journal of applied microbiology},
volume = {126},
number = {4},
pages = {1044-1058},
doi = {10.1111/jam.14188},
pmid = {30597735},
issn = {1365-2672},
support = {//European Regional Development Fund/ ; //State-Region Planning Contracts (CPER)/ ; Doctoral fellowship grant to Aur&#xe9;lie Lagarde//The Limousin region/ ; //Centre National de la Recherche Scientifique/ ; },
mesh = {Antifungal Agents/*pharmacology ; Antineoplastic Agents/*pharmacology ; Apoptosis/drug effects ; Ascomycota/*chemistry/classification/genetics ; Biofilms/*drug effects/growth &amp; development ; Candida albicans/drug effects ; Cell Line, Tumor ; Humans ; Lichens/*chemistry/microbiology ; Plant Extracts/pharmacology ; },
abstract = {AIMS: The objective of this study was to explore the diversity of endolichenic fungi from Nephroma laevigatum and to investigate their antiproliferative and antibiofilm potential.<br><br>METHODS AND RESULTS: Forty-six isolates were obtained and identified by DNA barcoding. They belonged to genera Nemania, Daldinia, Peziza and Coniochaeta. Six strains belonging to the most represented species were selected and tested for their antiproliferative and antibiofilm activities. Extracts were analysed by reversed-phase HPLC. Activities against fungal and bacterial biofilm were evaluated using tetrazolium salt (XTT) assay and crystal violet assay respectively. Antiproliferative responses of extracts were determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Apoptosis induction by two extracts was observed in two cell lines (HT-29 and PC-3) via morphological changes, pro-apoptotic and anti-apoptotic proteins analysis (Western blotting) and DNA fragmentation. Four extracts displayed activities against Candida albicans biofilm with IC50 values ranging from 25 to 200&#xa0;&#x3bc;g&#xa0;ml[-1] . All extracts were inactive against Staphylococcus aureus and Pseudomonas aeruginosa biofilms. The most active isolates against human colorectal (HT-29 and HCT116) and prostate (PC-3 and DU145) cancer cell lines were Nemania serpens (NL08) and Nemania aenea var. aureolatum (NL38) with IC50 values ranging from 13 to 39&#xa0;&#x3bc;g&#xa0;ml[-1] . These extracts induced an apoptotic process through activation of caspases 8 and 3, poly(ADP-ribose) polymerase cleavage and DNA fragmentation.<br><br>CONCLUSIONS: Selected crude fungal extracts have antiproliferative and antibiofilm activities. Data suggest that this antipoliferative effect is due to apoptosis process. This is the first report showing the effects of endolichenic fungi from N. laevigatum.<br><br>This study highlights the therapeutic potential of endolichenic fungi metabolites as sources for drug discovery programmes.},
}
@article {pmid30597034,
year = {2019},
author = {Takaoka, H and Low, VL and Tan, TK and Ya'cob, Z and Sofian-Azirun, M and Dhang Chen, C and Lau, KW and Da Pham, X},
title = {A New Black Fly Species of the Simulium (Gomphostilbia) duolongum Subgroup (Diptera: Simuliidae) From Vietnam, and Molecular Comparisons With Related Species Using the COI Barcoding Gene.},
journal = {Journal of medical entomology},
volume = {56},
number = {2},
pages = {432-440},
doi = {10.1093/jme/tjy222},
pmid = {30597034},
issn = {1938-2928},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Larva/anatomy &amp; histology ; Male ; Phylogeny ; Pupa/anatomy &amp; histology ; Simuliidae/anatomy &amp; histology/*classification/genetics ; Species Specificity ; },
abstract = {Simulium (Gomphostilbia) yvonneae sp. nov. is described based on adults, pupae, and mature larvae from Vietnam. This new species belongs to the Simulium duolongum subgroup in the S. batoense species-group of the subgenus Gomphostilbia Enderlein. It is distinguished by having a relatively larger number of male upper-eye facets in 16 vertical columns and 16 horizontal rows and a pupal gill with eight filaments arranged as 3+(1+2)+2 from dorsal to ventral, of which two filaments of the ventral pair are 1.8 times as long as the longest filament of the middle and dorsal triplets. Morphological comparisons are made to distinguish this new species from all 22 related species. The genetic distinctiveness of this new species in the S. duolongum subgroup is also presented based on the DNA barcoding COI gene.},
}
@article {pmid30595656,
year = {2018},
author = {Singh, G and Ptroot, A and Ico, VJ and Tte, J and Pradeep K Divakar, and Crespo, A and Cáceres, MEDS and H Thorsten Lumbsch, and Schmitt, I},
title = {Neoprotoparmelia gen. nov. and Maronina (Lecanorales, Protoparmelioideae): species description and generic delimitation using DNA barcodes and phenotypical characters.},
journal = {MycoKeys},
volume = {},
number = {44},
pages = {19-50},
pmid = {30595656},
issn = {1314-4049},
abstract = {Multilocus phylogenetic studies revealed a high level of cryptic diversity within the lichen-forming fungal genus Maronina (Protoparmelioideae, Parmeliaceae). Coalescent-based species delimitation suggested that most of the cryptic molecular lineages warranted recognition as separate species. Here we study the morphology and chemistry of these taxa and formally describe eight new species based on phenotypical and molecular characters. Further, we evaluate the use of ITS rDNA as a DNA barcode for identifying species in this genus. For the first time, we obtained an ITS sequence of Maroninaaustraliensis, the type species of the genus and showed that it is phylogenetically not closely related to species currently placed in Maronina or Protoparmelia. We assembled a dataset of 66 ITS sequences to assess the interspecies genetic distances amongst the twelve Maronina species using ITS as DNA barcode. We found that Maronina and Protoparmelia form a supported monophyletic group whereas M.australiensis is sister to both. We therefore propose a new genus Neoprotoparmelia to accommodate the tropical-subtropical species within Protoparmelioideae, with Neoprotoparmeliacorallifera as the type, N.amerisidiata, N.australisidiata, N.brasilisidiata, N.capensis, N.crassa, N.pauli, N.plurisporibadia and N.siamisidiata as new species and N.capitata, N.isidiata, N.multifera, N.orientalis and N.pulchra as new proposed combinations. We provide a key to Neoprotoparmelia and confirm the use of ITS for accurately identifying species in this group.},
}
@article {pmid30595654,
year = {2018},
author = {Yi, P and Yu, P and Liu, J and Xu, H and Liu, X},
title = {A DNA barcode reference library of Neuroptera (Insecta, Neuropterida) from Beijing.},
journal = {ZooKeys},
volume = {},
number = {807},
pages = {127-147},
pmid = {30595654},
issn = {1313-2989},
abstract = {Neuroptera (lacewings) is one of the ancient holometabolous insect groups, but some extant species stand as important natural enemies for biological control. As the capital city of China, Beijing has a rich fauna of Neuroptera, previously with 47 species recorded and sorted in 32 genera of seven families. In this study, DNA barcoding based on sequences of COI gene fragments is used to discriminate lacewing species from Beijing. 217 DNA barcode sequences belonging to 49 species were successfully obtained. The COI barcode data worked well for identification of almost all lacewing species herein examined except Pseudomalladaprasinus (Burmeister), in which cryptic species may exist. Twenty species of Neuroptera are newly recorded from Beijing. Besides, Nothochrysinae is first recorded from Beijing. Chrysopidiaciliata (Wesmael) and Drepanepteryxalgida (Erichson) are first recorded from China.},
}
@article {pmid30594583,
year = {2019},
author = {Ma, ZS and Li, L and Ye, C and Peng, M and Zhang, YP},
title = {Hybrid assembly of ultra-long Nanopore reads augmented with 10x-Genomics contigs: Demonstrated with a human genome.},
journal = {Genomics},
volume = {111},
number = {6},
pages = {1896-1901},
doi = {10.1016/j.ygeno.2018.12.013},
pmid = {30594583},
issn = {1089-8646},
mesh = {Contig Mapping/methods ; *Genome, Human ; Genomics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Software ; },
abstract = {The 3rd generation of sequencing (3GS) technologies generate ultra-long reads (up to 1 Mb), which makes it possible to eliminate gaps and effectively resolve repeats in genome assembly. However, the 3GS technologies suffer from the high base-level error rates (15%-40%) and high sequencing costs. To address these issues, the hybrid assembly strategy, which utilizes both 3GS reads and inexpensive NGS (next generation sequencing) short reads, was invented. Here, we use 10×-Genomics® technology, which integrates a novel bar-coding strategy with Illumina® NGS with an advantage of revealing long-range sequence information, to replace common NGS short reads for hybrid assembly of long erroneous 3GS reads. We demonstrate the feasibility of integrating the 3GS with 10×-Genomics technologies for a new strategy of hybrid de novo genome assembly by utilizing DBG2OLC and Sparc software packages, previously developed by the authors for regular hybrid assembly. Using a human genome as an example, we show that with only 7× coverage of ultra-long Nanopore® reads, augmented with 10× reads, our approach achieved nearly the same level of quality, compared with non-hybrid assembly with 35× coverage of Nanopore reads. Compared with the assembly with 10×-Genomics reads alone, our assembly is gapless with slightly high cost. These results suggest that our new hybrid assembly with ultra-long 3GS reads augmented with 10×-Genomics reads offers a low-cost (less than ¼ the cost of the non-hybrid assembly) and computationally light-weighted (only took 109 calendar hours with peak memory-usage = 61GB on a dual-CPU office workstation) solution for extending the wide applications of the 3GS technologies.},
}
@article {pmid30591790,
year = {2018},
author = {Zahra, A and Hussain, B and Jamil, A and Ahmed, Z and Mahboob, S},
title = {Forensic STR profiling based smart barcode, a highly efficient and cost effective human identification system.},
journal = {Saudi journal of biological sciences},
volume = {25},
number = {8},
pages = {1720-1723},
pmid = {30591790},
issn = {1319-562X},
abstract = {In forensic science, the human identification is the major goal in criminal cases and in paternity dispute, based on DNA profiling of individual. Analysis of short tandem repeat (STRs) markers used as a reliable technique for this purpose. In this study the main objective was to develop a human identification based on DNA fingerprinting using Human Identification Barcode System (HIBS). HIBS may be used to provide a unique molecular signature of human in the form of a barcode. DNA was isolated from blood by using PCR technique to detect bands to design human barcode using self-designed system. HIBS is a web based application that can be accessed via www.hibs.com.pk. HIBS can be accessed with internet access and may be introduced on security checkpoints to identify an individual based on his own DNA instead of conventional procedures of identification. The barcode generated through DNA fingerprinting will be stored in a HIBS, and may also be a part of CNIC. It may be successfully used against suicide bombers, target killers, etc., as even a single blood spot, a few skin cells, root of the hair etc., to identify such culprits. It may also be effectively used to relieve the individuals with false accusations.},
}
@article {pmid30587194,
year = {2018},
author = {Shahhosseini, N and Friedrich, J and Moosa-Kazemi, SH and Sedaghat, MM and Kayedi, MH and Tannich, E and Schmidt-Chanasit, J and Lühken, R},
title = {Host-feeding patterns of Culex mosquitoes in Iran.},
journal = {Parasites &amp; vectors},
volume = {11},
number = {1},
pages = {669},
pmid = {30587194},
issn = {1756-3305},
support = {SAW-2014-SGN-3//Leibniz-Gemeinschaft/ ; 200/97308//Lorestan University of Medical Sciences, Iran/ ; },
mesh = {Animals ; Birds ; Culex/classification/genetics/*physiology ; Feeding Behavior ; Female ; Humans ; Insect Bites and Stings/blood/parasitology ; Iran ; Mammals ; Mosquito Vectors/classification/genetics/*physiology ; Reptiles ; },
abstract = {BACKGROUND: Different mosquito-borne pathogens are circulating in Iran including Sindbis virus, West Nile virus, filarioid worms and malaria parasites. However, the local transmission cycles of these pathogenic agents are poorly understood, especially because ecological data on vector species are scarce and there is limited knowledge about the host range; this understanding could help to direct species-specific vector control measurements or to prioritize research.<br><br>METHODS: In the summers of 2015 and 2016, blood-fed mosquitoes were collected at 13 trapping sites on the coast of the Caspian Sea in northern Iran and at an additional trapping site in western Iran. Mosquitoes were generally collected with either a Biogents Sentinel trap or a Heavy Duty Encephalitis Vector Survey trap installed outside. A handheld aspirator was used at the trapping site in western Iran, in addition to a few samplings around the other trapping sites. On average, eight trapping periods were conducted per trapping site. The sources of blood meals were identified using a DNA barcoding approach targeting the cytochrome b or 16S rRNA gene fragment.<br><br>RESULTS: The source of blood meals for 580 blood-fed mosquito specimens of 20 different taxa were determined, resulting in the identification of 13 different host species (9 mammals including humans, 3 birds and 1 reptile), whereby no mixed blood meals were detected. Five mosquito species represented more than 85.8% of all collected blood-fed specimens: Culex pipiens pipiens form pipiens (305 specimens, 55.7% of all mosquito specimens), Cx. theileri (60, 10.9%), Cx. sitiens (51, 9.3%), Cx. perexiguus (29, 5.3%) and Anopheles superpictus (25, 4.6%). The most commonly detected hosts of the four most abundant mosquito species were humans (Homo sapiens; 224 mosquito specimens, 40.9% of all mosquito specimens), cattle (Bos taurus; 171, 31.2%) and ducks (Anas spp.; 75, 13.7%). These four mosquito species had similar host-feeding patterns. The only exceptions were a relatively high proportion of birds for Cx. pipiens pipiens f. pipiens (23.2% of detected blood meal sources) and a high proportion of non-human mammals for Cx. theileri (73.4%). Trapping month, surrounding area, or trapping method had no statistically significant impact on the observed host-feeding patterns of Cx. pipiens pipiens f. pipiens.<br><br>CONCLUSIONS: Due to the diverse and overlapping host-feeding patterns, several mosquito species must be considered as potential enzootic and bridge vectors for diverse mosquito-borne pathogens in Iran. Most species can potentially transmit pathogens between mammals as well as between mammals and birds, which might be the result of a similar host selection or a high dependence on the host availability.},
}
@article {pmid30587116,
year = {2018},
author = {Zhao, X and Tian, K and Yau, SS},
title = {A new efficient method for analyzing fungi species using correlations between nucleotides.},
journal = {BMC evolutionary biology},
volume = {18},
number = {1},
pages = {200},
pmid = {30587116},
issn = {1471-2148},
mesh = {Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Fungi/*classification/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: In recent years, DNA barcoding has become an important tool for biologists to identify species and understand their natural biodiversity. The complexity of barcode data makes it difficult to analyze quickly and effectively. Manual classification of this data cannot keep up to the rate of increase of available data.<br><br>RESULTS: In this study, we propose a new method for DNA barcode classification based on the distribution of nucleotides within the sequence. By adding the covariance of nucleotides to the original natural vector, this augmented 18-dimensional natural vector makes good use of the available information in the DNA sequence. The accurate classification results we obtained demonstrate that this new 18-dimensional natural vector method, together with the random forest classifier algorthm, can serve as a computationally efficient identification tool for DNA barcodes. We performed phylogenetic analysis on the genus Megacollybia to validate our method. We also studied how effective our method was in determining the genetic distance within and between species in our barcoding dataset.<br><br>CONCLUSIONS: The classification performs well on the fungi barcode dataset with high and robust accuracy. The reasonable phylogenetic trees we obtained further validate our methods. This method is alignment-free and does not depend on any model assumption, and it will become a powerful tool for classification and evolutionary analysis.},
}
@article {pmid30586452,
year = {2018},
author = {Gaonkar, CC and Piredda, R and Minucci, C and Mann, DG and Montresor, M and Sarno, D and Kooistra, WHCF},
title = {Annotated 18S and 28S rDNA reference sequences of taxa in the planktonic diatom family Chaetocerotaceae.},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0208929},
pmid = {30586452},
issn = {1932-6203},
mesh = {Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Ribosomal/genetics ; Diatoms/classification/*genetics ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; *Phylogeny ; Plankton/classification/genetics ; RNA, Ribosomal, 18S/*genetics ; RNA, Ribosomal, 28S/*genetics ; },
abstract = {The species-rich diatom family Chaetocerotaceae is common in the coastal marine phytoplankton worldwide where it is responsible for a substantial part of the primary production. Despite its relevance for the global cycling of carbon and silica, many species are still described only morphologically, and numerous specimens do not fit any described taxa. Nowadays, studies to assess plankton biodiversity deploy high throughput sequencing metabarcoding of the 18S rDNA V4 region, but to translate the gathered metabarcodes into biologically meaningful taxa, there is a need for reference barcodes. However, 18S reference barcodes for this important family are still relatively scarce. We provide 18S rDNA and partial 28S rDNA reference sequences of 443 morphologically characterized chaetocerotacean strains. We gathered 164 of the 216 18S sequences and 244 of the 413 28S sequences of strains from the Gulf of Naples, Atlantic France, and Chile. Inferred phylogenies showed 84 terminal taxa in seven principal clades. Two of these clades included terminal taxa whose rDNA sequences contained spliceosomal and Group IC1 introns. Regarding the commonly used metabarcode markers in planktonic diversity studies, all terminal taxa can be discriminated with the 18S V4 hypervariable region; its primers fit their targets in all but two species, and the V4-tree topology is similar to that of the 18S. Hence V4-metabarcodes of unknown Chaetocerotaceae are assignable to the family. Regarding the V9 hypervariable region, most terminal taxa can be discriminated, but several contain introns in their primer targets. Moreover, poor phylogenetic resolution of the V9 region affects placement of metabarcodes of putative but unknown chaetocerotacean taxa, and hence, uncertainty in taxonomic assignment, even of higher taxa.},
}
@article {pmid30586404,
year = {2018},
author = {Moskowitz, NA and Roland, AB and Fischer, EK and Ranaivorazo, N and Vidoudez, C and Aguilar, MT and Caldera, SM and Chea, J and Cristus, MG and Crowdis, JP and DeMessie, B and desJardins-Park, CR and Effenberger, AH and Flores, F and Giles, M and He, EY and Izmaylov, NS and Lee, CC and Pagel, NA and Phu, KK and Rosen, LU and Seda, DA and Shen, Y and Vargas, S and Murray, AW and Abebe, E and Trauger, SA and Donoso, DA and Vences, M and O'Connell, LA},
title = {Seasonal changes in diet and chemical defense in the Climbing Mantella frog (Mantella laevigata).},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0207940},
pmid = {30586404},
issn = {1932-6203},
support = {520008146/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Alkaloids/*analysis/metabolism ; Animals ; Animals, Poisonous/*physiology ; Anura/*physiology ; Arthropods ; Feeding Behavior/*physiology ; Female ; Gas Chromatography-Mass Spectrometry ; Humidity ; Madagascar ; Poisons/*analysis/metabolism ; Predatory Behavior/physiology ; Seasons ; Skin/chemistry/metabolism ; Temperature ; },
abstract = {Poison frogs acquire chemical defenses from the environment for protection against potential predators. These defensive chemicals are lipophilic alkaloids that are sequestered by poison frogs from dietary arthropods and stored in skin glands. Despite decades of research focusing on identifying poison frog alkaloids, we know relatively little about how environmental variation and subsequent arthropod availability impacts alkaloid loads in poison frogs. We investigated how seasonal environmental variation influences poison frog chemical profiles through changes in the diet of the Climbing Mantella (Mantella laevigata). We collected M. laevigata females on the Nosy Mangabe island reserve in Madagascar during the wet and dry seasons and tested the hypothesis that seasonal differences in rainfall is associated with changes in diet composition and skin alkaloid profiles of M. laevigata. The arthropod diet of each frog was characterized into five groups (i.e. ants, termites, mites, insect larvae, or 'other') using visual identification and cytochrome oxidase 1 DNA barcoding. We found that frog diet differed between the wet and dry seasons, where frogs had a more diverse diet in the wet season and consumed a higher percentage of ants in the dry season. To determine if seasonality was associated with variation in frog defensive chemical composition, we used gas chromatography / mass spectrometry to quantify alkaloids from individual skin samples. Although the assortment of identified alkaloids was similar across seasons, we detected significant differences in the abundance of certain alkaloids, which we hypothesize reflects seasonal variation in the diet of M. laevigata. We suggest that these variations could originate from seasonal changes in either arthropod leaf litter composition or changes in frog behavioral patterns. Although additional studies are needed to understand the consequences of long-term environmental shifts, this work suggests that alkaloid profiles are relatively robust against short-term environmental perturbations.},
}
@article {pmid30582760,
year = {2019},
author = {Darienko, T and Pröschold, T},
title = {Reevaluation and discovery of new species of the rare genus Watanabea and establishment of Massjukichlorella gen. nov. (Trebouxiophyceae, Chlorophyta) using an integrative approach.},
journal = {Journal of phycology},
volume = {55},
number = {2},
pages = {493-499},
doi = {10.1111/jpy.12830},
pmid = {30582760},
issn = {1529-8817},
mesh = {Biodiversity ; *Chlorella ; Chlorophyceae ; DNA, Ribosomal ; Phylogeny ; },
abstract = {Chlorella-like coccoid green algae are widely distributed in almost all terrestrial habitats and belong to different lineages of the Chlorophyceae and Trebouxiophyceae. The Watanabea clade of the Trebouxiophyceae shows a high genetic biodiversity. Re-investigation of the authentic strain of the rarely found W. reniformis showed several morphological differences compared to the original description. To clarify the taxonomic status of Watanabea, we compared several new isolates with similar morphology. Phylogenetic analyses of the SSU and SSU+ITS rDNA sequences revealed that all new isolates were distinct from W. reniformis. The ITS-2/CBC approach clearly demonstrated that the strains belonging to Watanabea represented species. We emended the generic diagnosis of Watanabea, and proposed four new species. One strain, SAG 2552, represented a separate lineage that we propose as a new genus Massjukichlorella with one species M. epiphytica.},
}
@article {pmid30576403,
year = {2019},
author = {Trébeau, C and Boutet de Monvel, J and Wong Jun Tai, F and Petit, C and Etournay, R},
title = {DNABarcodeCompatibility: an R-package for optimizing DNA-barcode combinations in multiplex sequencing experiments.},
journal = {Bioinformatics (Oxford, England)},
volume = {35},
number = {15},
pages = {2690-2691},
pmid = {30576403},
issn = {1367-4811},
mesh = {Base Sequence ; DNA ; Gene Library ; Sequence Analysis ; *Software ; },
abstract = {SUMMARY: Using adequate DNA barcodes is essential to unambiguously identify each DNA library within a multiplexed set of libraries sequenced using next-generation sequencers. We introduce DNABarcodeCompatibility, an R-package that allows one to design single or dual-barcoding multiplex experiments by imposing desired constraints on the barcodes (including sequencer chemistry, barcode pairwise minimal distance and nucleotide content), while optimizing barcode frequency usage, thereby allowing one to both facilitate the demultiplexing step and spare expensive library-preparation kits. The package comes with a user-friendly interface and a web app developed in Java and Shiny (https://dnabarcodecompatibility.pasteur.fr), respectively, with the aim to help bridge the expertise of core facilities with the experimental needs of non-experienced users.<br><br>DNABarcodeCompatibility can be easily extended to fulfil specific project needs. The source codes of the R-package and its user interfaces are publicly available along with documentation at [https://github.com/comoto-pasteur-fr] under the GPL-2 licence.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid30576366,
year = {2018},
author = {Guimarães, KLA and de Sousa, MPA and Ribeiro, FRV and Porto, JIR and Rodrigues, LRR},
title = {DNA barcoding of fish fauna from low order streams of Tapajós River basin.},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0209430},
pmid = {30576366},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; Brazil ; Conservation of Natural Resources ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Fish Proteins/genetics ; Fishes/*genetics ; Phylogeny ; Rivers ; },
abstract = {The Amazon basin harbors a megadiverse fish fauna spread in an intricate network of big rivers and small streams. The Amazonian streams are home of many small sized fishes that remains poorly documented. In order to accelerate the scientific knowledge on these important aquatic systems we adopted a modern integrative approach joining morphology and molecular tools to investigate the ichthyofauna assemblages from low order streams situated on the lower Tapajós River Basin. Cytochrome c Oxidase I (COI) DNA barcodes from 252 specimens collected from 10 stream sites were obtained. The combined analysis revealed 29 species, 21 genera and 11 families. Cryptic diversity was evidenced in Knodus sp.1, Aequidens epae and Copella callolepis, in which deep genetic divergence were detected (intraspecific distances: 20.48%, 7.99% and 3.77%, respectively). The putative new species showed closer relationships with their counterparts occurring in the Tapajós-Xingu water drainages.},
}
@article {pmid30576327,
year = {2018},
author = {Litman, J and Chittaro, Y and Birrer, S and Praz, C and Wermeille, E and Fluri, M and Stalling, T and Schmid, S and Wyler, S and Gonseth, Y},
title = {A DNA barcode reference library for Swiss butterflies and forester moths as a tool for species identification, systematics and conservation.},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0208639},
pmid = {30576327},
issn = {1932-6203},
mesh = {Animals ; Butterflies/classification/*genetics ; DNA/chemistry/isolation &amp; purification/metabolism ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/classification/genetics ; Female ; Gene Library ; Insect Proteins/classification/genetics ; Male ; Moths/classification/*genetics ; Switzerland ; },
abstract = {Butterfly monitoring and Red List programs in Switzerland rely on a combination of observations and collection records to document changes in species distributions through time. While most butterflies can be identified using morphology, some taxa remain challenging, making it difficult to accurately map their distributions and develop appropriate conservation measures. In this paper, we explore the use of the DNA barcode (a fragment of the mitochondrial gene COI) as a tool for the identification of Swiss butterflies and forester moths (Rhopalocera and Zygaenidae). We present a national DNA barcode reference library including 868 sequences representing 217 out of 224 resident species, or 96.9% of Swiss fauna. DNA barcodes were diagnostic for nearly 90% of Swiss species. The remaining 10% represent cases of para- and polyphyly likely involving introgression or incomplete lineage sorting among closely related taxa. We demonstrate that integrative taxonomic methods incorporating a combination of morphological and genetic techniques result in a rate of species identification of over 96% in females and over 98% in males, higher than either morphology or DNA barcodes alone. We explore the use of the DNA barcode for exploring boundaries among taxa, understanding the geographical distribution of cryptic diversity and evaluating the status of purportedly endemic taxa. Finally, we discuss how DNA barcodes may be used to improve field practices and ultimately enhance conservation strategies.},
}
@article {pmid30576073,
year = {2019},
author = {Sonet, G and Snoeks, J and Nagy, ZT and Vreven, E and Boden, G and Breman, FC and Decru, E and Hanssens, M and Ibala Zamba, A and Jordaens, K and Mamonekene, V and Musschoot, T and Van Houdt, J and Van Steenberge, M and Lunkayilakio Wamuini, S and Verheyen, E},
title = {DNA barcoding fishes from the Congo and the Lower Guinean provinces: Assembling a reference library for poorly inventoried fauna.},
journal = {Molecular ecology resources},
volume = {19},
number = {3},
pages = {728-743},
doi = {10.1111/1755-0998.12983},
pmid = {30576073},
issn = {1755-0998},
support = {//FishBase/ ; JEMU; Actie 1 project 'Multidisciplinair onderzo//Belgisch Ontwikkelingsagentschap/ ; project RA04F11//Federaal Wetenschapsbeleid/ ; },
mesh = {Animals ; *Biodiversity ; Congo ; *DNA Barcoding, Taxonomic ; Fishes/*classification/*genetics ; Guinea ; *Rivers ; },
abstract = {The Congolese and Lower Guinean ichthyological provinces are understudied hotspots of the global fish diversity. Here, we barcoded 741 specimens from the Lower and Middle Congo River and from three major drainage basins of the Lower Guinean ichthyological province, Kouilou-Niari, Nyanga and Ogowe. We identified 194 morphospecies belonging to 82 genera and 25 families. Most morphospecies (92.8%) corresponded to distinct clusters of DNA barcodes. Of the four morphospecies present in both neighbouring ichthyological provinces, only one showed DNA barcode divergence <2.5%. A small fraction of the fishes barcoded here (12.9% of the morphospecies and 16.1% of the barcode clusters representing putative species) were also barcoded in a previous large-scale DNA analysis of freshwater fishes of the Lower Congo published in 2011 (191 specimens, 102 morphospecies). We compared species assignments before and after taxonomic updates and across studies performed by independent research teams and observed that most cases of inconsistent species assignments were due to unknown diversity (undescribed species and unknown intraspecific variation). Our results report more than 17 putative new species and show that DNA barcode data provide a measure of genetic variability that facilitates the inventory of underexplored ichthyofaunae. However, taxonomic scrutiny, associated with revisions and new species descriptions, is indispensable to delimit species and build a coherent reference library.},
}
@article {pmid30573739,
year = {2018},
author = {Moura, CJ and Lessios, H and Cortés, J and Nizinski, MS and Reed, J and Santos, RS and Collins, AG},
title = {Hundreds of genetic barcodes of the species-rich hydroid superfamily Plumularioidea (Cnidaria, Medusozoa) provide a guide toward more reliable taxonomy.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {17986},
pmid = {30573739},
issn = {2045-2322},
support = {SFRH/BPD/84582/2012//Minist&#x00E9;rio da Ci&#x00EA;ncia, Tecnologia e Ensino Superior (MCTES)/International ; },
mesh = {Animals ; Aquatic Organisms ; Classification/*methods ; Cnidaria/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Phylogeny ; Reproducibility of Results ; Species Specificity ; },
abstract = {Marine hydroids are important benthic components of shallow and deep waters worldwide, but their taxonomy is controversial because diagnostic morphological characters to categorize taxa are limited. Their genetic relationships are also little investigated. We tested taxonomic hypotheses within the highly speciose superfamily Plumularioidea by integrating a classical morphological approach with DNA barcoding of the 16S and COI mitochondrial markers for 659 and 196 specimens of Plumularioidea, respectively. Adding Genbank sequences, we inferred systematic relationships among 1,114 plumularioids, corresponding to 123 nominal species and 17 novel morphospecies in five families of Plumularioidea. We found considerable inconsistencies in the systematics of nominal families, genera and species. The families Kirchenpaueriidae and Plumulariidae were polyphyletic and the Halopterididae paraphyletic. Most genera of Plumularioidea are not monophyletic. Species diversity is considerably underestimated. Within our study, at least 10% of the morphologically-distinctive morphospecies are undescribed, and about 40% of the overall species richness is represented by cryptic species. Convergent evolution and morphological plasticity therefore blur systematic relationships. Additionally, cryptic taxa occur frequently in sympatry or parapatry, complicating correspondence with type material of described species. Sometimes conspecificity of different morphotypes was found. The taxonomy of hydroids requires continued comprehensive revision.},
}
@article {pmid30572096,
year = {2019},
author = {Galal-Khallaf, A and Osman, AGM and El-Ganainy, A and Farrag, MM and Mohammed-AbdAllah, E and Moustafa, MA and Mohammed-Geba, K},
title = {Mitochondrial genetic markers for authentication of major Red Sea grouper species (Perciformes: Serranidae) in Egypt: A tool for enhancing fisheries management and species conservation.},
journal = {Gene},
volume = {689},
number = {},
pages = {235-245},
doi = {10.1016/j.gene.2018.12.021},
pmid = {30572096},
issn = {1879-0038},
mesh = {Animals ; Bass/*classification/*genetics ; *Conservation of Natural Resources/methods ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Egypt ; *Fisheries/organization &amp; administration/standards ; *Genetic Markers ; Genetic Speciation ; Indian Ocean ; Molecular Typing ; Phylogeny ; },
abstract = {Groupers are coral fish species of prime ecological and economic significance. The interactions among them and other coral reefs organisms aid the healthiness and species balance in this fundamental marine niches. Also, groupers are among the top priced fisheries species. The Egyptian habitats of the Red Sea are lacking genetic studies that assess species diversity for the final goal of conservation and fisheries management. Moreover, morphological similarities among these organisms sometimes hinder a proper species identification. Hence, more accurate groupers authentication methods are crucially required. Sixteen grouper species belonging to the genera Epinephelus, Anyperodon, Cephaolopholes, Aethaloperca, Variola, and Plectropomus, present in the Red Sea in Egypt, were investigated for species authentication through mitochondrial DNA variations, applying cytochrome oxidase subunit I (COI) and 12srRNA genes sequencing. GenBank comparisons, phylogenetic analyses and comparisons of pairwise distances were carried out. All these analyses aimed to species authentication and identifying their relations at the international scale. The results exhibited >98% identity with E. fasciatus, A. rogaa, C. oligosticta, E. areolatus, V. louti, P. areolatus, E. malabaricus, C. sexmaculata, E. summana, E. chlorostigma, E. polyphekadion, C. miniataus, A. leucogrammicus, E. tauvina, C. argus, C. hemistiktos. Pairwise distances showed a clear increase upon raising comparison level from among species to among-genera. Combined 12srRNA and COI genes sequencing resulted in an accurate tool for Egyptian Red Sea grouper species unambiguous discrimination. This can provide vital aid to the active efforts for these species conservation and fisheries management in Egypt and the world.},
}
@article {pmid30570141,
year = {2019},
author = {Decalf, J and Albert, ML and Ziai, J},
title = {New tools for pathology: a user's review of a highly multiplexed method for in situ analysis of protein and RNA expression in tissue.},
journal = {The Journal of pathology},
volume = {247},
number = {5},
pages = {650-661},
doi = {10.1002/path.5223},
pmid = {30570141},
issn = {1096-9896},
mesh = {Biomarkers, Tumor/*metabolism ; Data Analysis ; Disease Progression ; Electronic Data Processing ; Humans ; In Situ Hybridization ; Neoplasms/*pathology ; RNA, Neoplasm/*metabolism ; },
abstract = {Tumor cell heterogeneity and tumor cell-stromal interactions are being explored as determinants of disease progression and treatment resistance in solid tumor and hematological malignancies. As such, tools simultaneously capable of highly multiplexed profiling of tissues' protein and RNA content, as well as interrogation of rare or single cells, are required to precisely characterize constituent tumor cell populations, infiltrating lymphocytes and stromal elements. Access to spatial relationships will enable more precise characterization of tumors, support patient stratification and may help to identify novel drug targets. Multiple platforms are being developed to address these critical unmet needs. The NanoString digital spatial profiling (DSP) platform enables highly multiplexed, spatial assessment of protein and/or RNA targets in tissues by detecting oligonucleotide barcodes conjugated via a photocleavable linker to primary antibodies or nucleic acid probes. Although this platform enables high-dimensional spatial interrogation of tissue protein and RNA expression, a detailed understanding of its composition, function and chemistry is advisable to guide experimental design and data interpretation. The purpose of this review is to provide an independent, comprehensive description of the DSP technology, including an overview of NanoString's capture and antibody barcode conjugation chemistries, experimental workflow, data output and analysis methods. The DSP technology will be discussed in the context of other highly multiplexed immunohistochemistry methods, including imaging mass cytometry and multiplexed ion beam imaging, to inform potential users of the advantages and limitations of each. Additional issues such as preanalytical variability, sampling and specimen adequacy will be considered with respect to the platforms to inform potential experimental design. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley &amp; Sons, Ltd.},
}
@article {pmid30569485,
year = {2019},
author = {Bleuven, C and Dubé, AK and Nguyen, GQ and Gagnon-Arsenault, I and Martin, H and Landry, CR},
title = {A collection of barcoded natural isolates of Saccharomyces paradoxus to study microbial evolutionary ecology.},
journal = {MicrobiologyOpen},
volume = {8},
number = {7},
pages = {e00773},
pmid = {30569485},
issn = {2045-8827},
support = {//Universit&#xe9; Laval/ ; //PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications/ ; //Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {While the use of barcoded collections of laboratory microorganisms and the development of barcode-based cell tracking are rapidly developing in genetics and genomics research, tools to track natural populations are still lacking. The yeast Saccharomyces paradoxus is an emergent microbial model in ecology and evolution. More than five allopatric and sympatric lineages have been identified and hundreds of strains have been isolated for this species, allowing to assess the impact of natural diversity on complex traits. We constructed a collection of 550 barcoded and traceable strains of S. paradoxus, including all three North American lineages SpB, SpC, and SpC*. These strains are diploid, many have their genome fully sequenced and are barcoded with a unique 20 bp sequence that allows their identification and quantification. This yeast collection is functional for competitive experiments in pools as the barcodes allow to measure each lineage's and individual strains' fitness in common conditions. We used this tool to demonstrate that in the tested conditions, there are extensive genotype-by-environment interactions for fitness among S. paradoxus strains, which reveals complex evolutionary potential in variable environments. This barcoded collection provides a valuable resource for ecological genomics studies that will allow gaining a better understanding of S. paradoxus evolution and fitness-related traits.},
}
@article {pmid30568859,
year = {2018},
author = {Vivien, R and Werner, I and Ferrari, BJD},
title = {Simultaneous preservation of the DNA quality, the community composition and the density of freshwater oligochaetes for the development of genetically based biological indices.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e6050},
pmid = {30568859},
issn = {2167-8359},
abstract = {INTRODUCTION: Oligochaetes are recognized as valuable bioindicators of sediment quality in streams and lakes. The development of an oligochaete index based on the identification of specimens using DNA barcodes requires a method for simultaneously preserving the DNA quality and information on the specimen density and oligochaete community composition. Absolute ethanol optimally preserves DNA but fixation of freshwater oligochaetes with this medium can cause disintegration and fragmentation of specimens. Here, we investigated the possibility to preserve oligochaete specimens in low-pH formalin and in neutral buffered formalin for up to four weeks before genetic analyses and tested if the addition of absolute ethanol to formalin-fixed oligochaetes resulted in a loss of specimens and/or species.<br><br>METHODS: We performed guanidine extraction and polymerase chain reaction (PCR) amplification/sequencing of a fragment of the cytochrome c oxidase I (COI) gene on tissue fragments preserved in low-pH formalin for up to 3 weeks and in neutral buffered formalin for up to 4 weeks. In addition, we compared the density and taxonomic composition of formalin-fixed oligochaetes of several sieved sediment samples before and after the addition of absolute ethanol.<br><br>RESULTS: The COI fragment of all oligochaete specimens preserved in neutral buffered formalin for up to 28 days was successfully amplified by PCR and obtained sequences were complete and of high quality. The amplification success rate for low-pH formalin fixed specimens declined after 7 days of storage. The addition of absolute ethanol to formalin-fixed oligochaete communities did not alter density or diversity estimates.<br><br>DISCUSSION: Our results indicate that sediment samples can be stored in neutral buffered formalin for up to 4 weeks and the sieved material can then be transferred to absolute ethanol, without affecting DNA quality, density and community composition of oligochaetes. Based on these results, a protocol for preserving freshwater oligochaetes, describing all the steps from collection of sediments to preservation of the biological material in absolute ethanol, is proposed. This method of fixation/preservation is of relevance for establishing DNA barcode reference databases, inventories of genetic diversity and developing genetically based biological indices.},
}
@article {pmid30568527,
year = {2018},
author = {Li, B and Zhao, Z and Chen, H and Wu, Z and Zhang, C and Li, S},
title = {Guilotes, a new genus of Coelotinae spiders from Guangxi Zhuang Autonomous Region, China (Araneae, Agelenidae).},
journal = {ZooKeys},
volume = {},
number = {802},
pages = {1-17},
pmid = {30568527},
issn = {1313-2989},
abstract = {A new genus of the subfamily Coelotinae F.O. Pickard-Cambridge, 1893, Guilotes Z. Zhao &amp; S. Li, gen. n. from China is described, as well as four new species: G.ludiensis Z. Zhao &amp; S. Li, sp. n. (♂♀, type species), G.qingshitanensis Z. Zhao &amp; S. Li, sp. n. (♂♀), G.xingpingensis Z. Zhao &amp; S. Li, sp. n. (♂♀) and G.yandongensis Z. Zhao &amp; S. Li, sp. n. (♀). The DNA barcodes of all species are documented for future use.},
}
@article {pmid30565609,
year = {2019},
author = {Yang, M and Liu, Y and Jiang, X},
title = {Barcoded point-of-care bioassays.},
journal = {Chemical Society reviews},
volume = {48},
number = {3},
pages = {850-884},
doi = {10.1039/c8cs00303c},
pmid = {30565609},
issn = {1460-4744},
mesh = {Animals ; Biological Assay/*instrumentation/*methods ; Biosensing Techniques/*instrumentation/*methods ; Fluorescent Dyes/chemistry ; Humans ; Mobile Applications/trends ; Optical Imaging/methods ; Point-of-Care Systems/*trends ; Precision Medicine/methods ; Theranostic Nanomedicine/methods ; },
abstract = {Barcode technology can deliver batched information for patient healthcare. For clinical examinations, barcodes serve as reporters for labeling multiple targets, and meanwhile, facilitate improved sensitivity and specificity, thus enabling barcode as a promising alternative to traditional labels for biomarker identification and signal amplification. However, faced with the stringent claims of point-of-care (POC) bioassays, efforts are needed to advance current technologies toward rapidity, robustness, affordability, and user-friendliness. In the past decades, chemists have succeeded in delicate fabrication of the barcode libraries for encoding. Nevertheless, the decoding technologies remain poorly discussed, especially simplified decoding strategies for POC bioassays. Recent emergence of portable cartridges and miniaturized signal-recording devices has brought a promise to merge barcodes-assisted bioassay with POC testing (POCT). This review provides a comprehensive summary on barcode encoding and decoding, with emphasis on their potential use in POCT, facilitated by improved manufacturing and portable devices. Future directions of barcoded bioassays for POCT and current challenges are also presented. We anticipate that this review will be beneficial to promoting barcodes toward broad applications.},
}
@article {pmid30564515,
year = {2018},
author = {Hakala, SM and Seppä, P and Heikkilä, M and Punttila, P and Sorvari, J and Helanterä, H},
title = {Genetic analysis reveals Finnish Formica fennica populations do not form a separate genetic entity from F. exsecta.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e6013},
pmid = {30564515},
issn = {2167-8359},
abstract = {Coptoformica Müller, 1923 is a subgenus of Formica Linnaeus, 1758 that consists of c. a dozen species of ants that typically inhabit open grassy habitats and build small nest mounds. The most recent addition to the group is Formica fennica Seifert, 2000. The description was based on morphological characters, but the species status has not been confirmed by molecular methods. In this study, we use thirteen DNA microsatellite markers and a partial mitochondrial COI gene sequence to assess the species status of F. fennica, by comparing the genetic variation among samples identified as F. fennica and six other boreal Formica (Coptoformica) species. Most of the species studied form separate, discontinuous clusters in phylogenetic and spatial analyses with only little intraspecific genetic variation. However, both nuclear and mitochondrial markers fail to separate the species pair F. exsecta Nylander, 1846 and F. fennica despite established morphological differences. The genetic variation within the F. exsecta/fennica group is extensive, but reflects spatial rather than morphological differences. Finnish F. fennica populations studied so far should not be considered a separate species, but merely a morph of F. exsecta.},
}
@article {pmid30563583,
year = {2019},
author = {Bayley, A},
title = {A Summary of Current DNA Methods for Herb and Spice Identification.},
journal = {Journal of AOAC International},
volume = {102},
number = {2},
pages = {386-389},
doi = {10.5740/jaoacint.18-0388},
pmid = {30563583},
issn = {1944-7922},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/*genetics/isolation &amp; purification ; Databases, Genetic ; Plants, Medicinal/*genetics ; *Polymerase Chain Reaction ; *Spices ; },
abstract = {Appropriate use of genetic methods for botanical identification is based on the type of sequencing used as well as testing region selection. Although Sanger sequencing is useful for single-target species identification, targeted next generation sequencing is ideal for testing blended products or those that contain unexpected species. Unknown, fresh, or lightly processed materials are best tested through the use of long, universal deoxyribonucleic acid (DNA) regions (e.g., DNA barcodes). For highly processed products, using shorter and more specific regions helps to prevent false negatives and positives. All approaches must use DNA extraction techniques that address the presence of inhibitory compounds, which often occur in abundance within herbs and spices. The accuracy of identifications is improved when comparing genetic data of any type with a reference database that contains expertly determined vouchered materials, a variety of closely related species, and multiple specimens of the same species.},
}
@article {pmid30563109,
year = {2018},
author = {Giorgio, A and De Bonis, S and Balestrieri, R and Rossi, G and Guida, M},
title = {The Isolation and Identification of Bacteria on Feathers of Migratory Bird Species.},
journal = {Microorganisms},
volume = {6},
number = {4},
pages = {},
pmid = {30563109},
issn = {2076-2607},
abstract = {Worldwide, bacteria are the most ubiquitous microorganisms, and it has been extensively demonstrated that migratory wild birds can increase bacterial global scale dispersion through long-distance migration and dispersal. The microbial community hosted by wild birds can be highly diverse, including pathogenic strains that can contribute to infections and disease spread. This study focused on feather and plumage bacteria within bird microbial communities. Samples were collected during ornithological activities in a bird ringing station. Bacterial identification was carried out via DNA barcoding of the partial 16S rRNA gene. Thirty-seven isolates of bacteria were identified on the chest feathers of 60 migratory birds belonging to three trans-Saharan species: Muscicapa striata, Hippolais icterina, and Sylvia borin. Our results demonstrate the possibility of bacterial transfer, including pathogens, through bird migration between very distant countries. The data from the analysis of plumage bacteria can aid in the explanation of phenomena such as migratory birds' fitness or the development of secondary sexual traits. Moreover, these results have deep hygienic[-]sanitary implications, since many bird species have synanthropic behaviors during their migration that increase the probability of disease spread.},
}
@article {pmid30563021,
year = {2018},
author = {Guo, M and Xu, Y and Ren, L and He, S and Pang, AX},
title = {A Systematic Study on DNA Barcoding of Medicinally Important Genus Epimedium L. (Berberidaceae).},
journal = {Genes},
volume = {9},
number = {12},
pages = {},
pmid = {30563021},
issn = {2073-4425},
support = {81573541//National Natural Science Foundation of China/ ; 2017-I2M-1-013//CAMS Innovation Fund for Medical Sciences&#xff08;CIFMS&#xff09;/ ; },
abstract = {Genus Epimedium consists of approximately 50 species in China, and more than half of them possess medicinal properties. The high similarity of species' morphological characteristics complicates the identification accuracy, leading to potential risks in herbal efficacy and medical safety. In this study, we tested the applicability of four single loci, namely, rbcL, psbA-trnH, internal transcribed spacer (ITS), and ITS2, and their combinations as DNA barcodes to identify 37 Epimedium species on the basis of the analyses, including the success rates of PCR amplifications and sequencing, specific genetic divergence, distance-based method, and character-based method. Among them, character-based method showed the best applicability for identifying Epimedium species. As for the DNA barcodes, psbA-trnH showed the best performance among the four single loci with nine species being correctly differentiated. Moreover, psbA-trnH + ITS and psbA-trnH + ITS + rbcL exhibited the highest identification ability among all the multilocus combinations, and 17 species, of which 12 are medicinally used, could be efficiently discriminated. The DNA barcode data set developed in our study contributes valuable information to Chinese resources of Epimedium. It provides a new means for discrimination of the species within this medicinally important genus, thus guaranteeing correct and safe usage of Herba Epimedii.},
}
@article {pmid30561532,
year = {2019},
author = {Chen, H and Alvarez, JJS and Ng, SH and Nielsen, R and Zhai, W},
title = {Passage Adaptation Correlates With the Reduced Efficacy of the Influenza Vaccine.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {69},
number = {7},
pages = {1198-1204},
doi = {10.1093/cid/ciy1065},
pmid = {30561532},
issn = {1537-6591},
mesh = {Adaptation, Biological/*immunology ; Animals ; Antibodies, Viral/immunology ; Chick Embryo ; Evolution, Molecular ; Hemagglutinin Glycoproteins, Influenza Virus/genetics/immunology ; Humans ; Influenza A Virus, H3N2 Subtype/classification/genetics/*immunology ; Influenza Vaccines/*immunology ; Influenza, Human/*immunology/prevention &amp; control/*virology ; Mutation ; Patient Outcome Assessment ; Sequence Analysis, DNA ; *Vaccine Potency ; Virus Replication/immunology ; },
abstract = {BACKGROUND: As a dominant seasonal influenza virus, H3N2 virus rapidly evolves in humans and is a constant threat to public health. Despite sustained research efforts, the efficacy of H3N2 vaccine has decreased rapidly. Even though antigenic drift and passage adaptation (substitutions accumulated during vaccine production in embryonated eggs) have been implicated in reduced vaccine efficacy (VE), their respective contributions to the phenomenon remain controversial.<br><br>METHODS: We utilized mutational mapping, a powerful probabilistic method for studying sequence evolution, to analyze patterns of substitutions in different passage conditions for an unprecedented amount of H3N2 hemagglutinin sequences (n = 32 278).<br><br>RESULTS: We found that passage adaptation in embryonated eggs is driven by repeated convergent evolution over 12 codons. Based on substitution patterns at these sites, we developed a metric, adaptive distance (AD), to quantify the strength of passage adaptation and subsequently identified a strong negative correlation between AD and VE.<br><br>CONCLUSIONS: The high correlation between AD and VE implies that passage adaptation in embryonated eggs may be a strong contributor to the recent reduction in H3N2 VE. We developed a computational package called MADE (Measuring Adaptive Distance and vaccine Efficacy based on allelic barcodes) to measure the strength of passage adaptation and predict the efficacy of a candidate vaccine strain. Our findings shed light on strategies for reducing Darwinian evolution within the passaging medium in order to potentially restore an effective vaccine program in the future.},
}
@article {pmid30560153,
year = {2019},
author = {Sweatt, JD},
title = {The Epigenetic Basis of Individuality.},
journal = {Current opinion in behavioral sciences},
volume = {25},
number = {},
pages = {51-56},
pmid = {30560153},
issn = {2352-1546},
support = {R01 MH057014/MH/NIMH NIH HHS/United States ; U54 HD083211/HD/NICHD NIH HHS/United States ; },
abstract = {This commentary reviews the concept of experience-dependent epigenetic modifications in the CNS as a core mechanism underlying individuality and individuation at the behavioral level. I use the term individuation to refer to the underlying neurobiological processes that result in individuality, with the discussion focusing on individuality of cognitive, emotional, and behavioral repertoire. The review describes recent work supporting the concept of neuroepigenetic mechanisms underlying individuation, possible roles of transgenerational effects, and implications for precision medicine.},
}
@article {pmid30558508,
year = {2019},
author = {More, SN and Hernandez, O and Castleman, WL},
title = {Mycotic Rhinitis and Sinusitis in Florida Horses.},
journal = {Veterinary pathology},
volume = {56},
number = {4},
pages = {586-598},
doi = {10.1177/0300985818817046},
pmid = {30558508},
issn = {1544-2217},
mesh = {Animals ; Ascomycota/genetics/*isolation &amp; purification ; Aspergillus/genetics/*isolation &amp; purification ; Basidiomycota/genetics/*isolation &amp; purification ; DNA Primers/genetics ; Horse Diseases/*diagnosis/microbiology/pathology ; Horses ; Mycoses/diagnosis/microbiology/pathology/*veterinary ; Phaeohyphomycosis/diagnosis/microbiology/pathology/veterinary ; Polymerase Chain Reaction/veterinary ; Rhinitis/diagnosis/microbiology/pathology/*veterinary ; Sequence Analysis, DNA/veterinary ; Sinusitis/diagnosis/microbiology/pathology/*veterinary ; },
abstract = {Rhinitis and sinusitis caused by fungal pathogens were studied in biopsy samples submitted from 52 horses distributed throughout subtropical and tropical regions of Florida. Methods included routine histopathology as well as polymerase chain reaction (PCR) with panfungal/panoomycete primers and DNA sequencing on extracted DNA (DNA barcoding). Granulomatous, pyogranulomatous, and fibrinopurulent lesions in nasal and sinus mucosa were associated with signs of upper airway obstruction and noise as well as nasal discharge. Morphologic and histochemical assessment of cases identified 31 cases of zygomycosis/pythiosis plus 1 mixed infection case, 16 cases of phaeohyphomycosis with 2 additional mixed infection cases, and 3 cases caused by other fungi. Morphologic evidence of Aspergillus sp. infection as a superficial copathogen was found in 2 of the mixed fungal infection cases. PCR and DNA sequencing facilitated identification of fungal pathogens in 11 of 52 cases (21%). No evidence of oomycete infection was found. Histomorphologic features of previously unrecognized forms of equine rhinitis/sinusitis were described, including those caused by Flavodon flavus, Curvularia lunata, Exserohilum rostrata, Alternaria alternata, Alternaria sp., Cladophialophora bantiana, Fusarium solani, and Toxicocladosporium irritans. PCR and DNA sequencing using panfungal and oomycete primers with DNA from formalin-fixed and paraffin-embedded specimens successfully identified the pathogen in phaeohyphomycosis (7/18 cases, 39%), zygomycosis/pythiosis (1/32 cases, 3%), and other nonpigmented fungal infections (3/3 cases, 100%). Zygomycosis and phaeohyphomycosis were the most common forms of fungal rhinitis found in Florida horses.},
}
@article {pmid30557098,
year = {2019},
author = {Erpenbeck, D and Steiner, M and Schuster, A and Genner, MJ and Manconi, R and Pronzato, R and Ruthensteiner, B and van den Spiegel, D and van Soest, RWM and Wörheide, G},
title = {Minimalist barcodes for sponges: a case study classifying African freshwater Spongillida.},
journal = {Genome},
volume = {62},
number = {1},
pages = {1-10},
doi = {10.1139/gen-2018-0098},
pmid = {30557098},
issn = {1480-3321},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods/standards ; *Phylogeny ; Porifera/classification/*genetics ; },
abstract = {African sponges, particularly freshwater sponges, are understudied relative to demosponges in most other geographical regions. Freshwater sponges (Spongillida) likely share a common ancestor; however, their evolutionary history, particularly during their radiation into endemic and allegedly cosmopolitan groups, is unclear. Freshwater sponges of at least 58 species of 17 genera and four families are described from Central and Eastern Africa, but the diversity is underestimated due to limited distinguishable morphological features. The discovery of additional cryptic species is very likely with the use of molecular techniques such as DNA barcoding. The Royal Museum of Central Africa (MRAC, Tervuren, Belgium) hosts one of the largest collections of (Central) African freshwater sponge type material. Type specimens in theory constitute ideal targets for molecular taxonomy; however, the success is frequently hampered by DNA degradation and deamination, which are a consequence of suboptimal preservation techniques. Therefore, we genotyped African demosponge holotype material of the MRAC with specific short primers suitable for degenerated tissue and compare the results with the current, morphology-based classification. Our results demonstrate the utility of minimalistic barcodes for identification of sponges, potentially enabling efficient identification of individuals in taxonomic or metabarcoding studies, and highlight inconsistencies in the current freshwater sponge classification.},
}
@article {pmid30555697,
year = {2018},
author = {Sago, CD and Kalathoor, S and Fitzgerald, JP and Lando, GN and Djeddar, N and Bryksin, AV and Dahlman, JE},
title = {Barcoding chemical modifications into nucleic acids improves drug stability in vivo.},
journal = {Journal of materials chemistry. B},
volume = {6},
number = {44},
pages = {7197-7203},
pmid = {30555697},
issn = {2050-750X},
support = {R01 DE026941/DE/NIDCR NIH HHS/United States ; T32 EB021962/EB/NIBIB NIH HHS/United States ; },
abstract = {The efficacy of nucleic acid therapies can be limited by unwanted degradation. Chemical modifications are known to improve nucleic acid stability, but the (i) types, (ii) positions, and (iii) numbers of modifications all matter, making chemically optimizing nucleic acids a combinatorial problem. As a result, in vivo studies of nucleic acid stability are time consuming and expensive. We reasoned that DNA barcodes could simultaneously study how chemical modification patterns affect nucleic acid stability, saving time and resources. We confirmed that rationally designed DNA barcodes can elucidate the role of specific chemical modifications in serum, in vitro and in vivo; we also identified a modification pattern that enhanced stability. This approach to screening chemical modifications in vivo can efficiently optimize nucleic acid structure, which will improve biomaterial-based nucleic acid drugs.},
}
@article {pmid30554480,
year = {2019},
author = {Barrow, LN and Allen, JM and Huang, X and Bensch, S and Witt, CC},
title = {Genomic sequence capture of haemosporidian parasites: Methods and prospects for enhanced study of host-parasite evolution.},
journal = {Molecular ecology resources},
volume = {19},
number = {2},
pages = {400-410},
doi = {10.1111/1755-0998.12977},
pmid = {30554480},
issn = {1755-0998},
support = {DEB-1146491//National Science Foundation/ ; PRFB-1611710//National Science Foundation/ ; //New Mexico Ornithological Society/ ; },
mesh = {Animals ; Bird Diseases/*parasitology ; Birds/*parasitology ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/chemistry/genetics ; DNA, Protozoan/chemistry/genetics ; *Genome, Protozoan ; Haemosporida/*genetics/isolation &amp; purification ; New Mexico ; Parasitemia/parasitology/*veterinary ; Peru ; Protozoan Infections/*parasitology ; Sequence Analysis, DNA/*methods ; },
abstract = {Avian malaria and related haemosporidians (Plasmodium, [Para]Haemoproteus and Leucocytoozoon) represent an exciting multihost, multiparasite system in ecology and evolution. Global research in this field accelerated after the publication in 2000 of PCR protocols to sequence a haemosporidian mitochondrial (mtDNA) barcode and the development in 2009 of an open-access database to document the geographic and host ranges of parasite mtDNA haplotypes. Isolating haemosporidian nuclear DNA from bird hosts, however, has been technically challenging, slowing the transition to genomic-scale sequencing techniques. We extend a recently developed sequence capture method to obtain hundreds of haemosporidian nuclear loci from wild bird samples, which typically have low levels of infection, or parasitemia. We tested 51 infected birds from Peru and New Mexico and evaluated locus recovery in light of variation in parasitemia, divergence from reference sequences and pooling strategies. Our method was successful for samples with parasitemia as low as ~0.02% (2 of 10,000 blood cells infected) and mtDNA divergence as high as 15.9% (one Leucocytozoonsample), and using the most cost-effective pooling strategy tested. Phylogenetic relationships estimated with >300 nuclear loci were well resolved, providing substantial improvement over the mtDNA barcode. We provide protocols for sample preparation and sequence capture including custom probe sequences and describe our bioinformatics pipeline using atram 2.0, phyluce and custom Perl/Python scripts. This approach can be applied to thousands of avian samples that have already been found to have haemosporidian infections of at least moderate intensity, greatly improving our understanding of parasite speciation, biogeography and evolutionary dynamics.},
}
@article {pmid30550548,
year = {2018},
author = {Esnaola, A and Arrizabalaga-Escudero, A and González-Esteban, J and Elosegi, A and Aihartza, J},
title = {Determining diet from faeces: Selection of metabarcoding primers for the insectivore Pyrenean desman (Galemys pyrenaicus).},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0208986},
pmid = {30550548},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA Primers/*genetics ; *Diet ; Endangered Species ; Eulipotyphla/*classification/genetics ; *Feces ; },
abstract = {Molecular techniques allow non-invasive dietary studies from faeces, providing an invaluable tool to unveil ecological requirements of endangered or elusive species. They contribute to progress on important issues such as genomics, population genetics, dietary studies or reproductive analyses, essential knowledge for conservation biology. Nevertheless, these techniques require general methods to be tailored to the specific research objectives, as well as to substrate- and species-specific constraints. In this pilot study we test a range of available primers to optimise diet analysis from metabarcoding of faeces of a generalist aquatic insectivore, the endangered Pyrenean desman (Galemys pyrenaicus, É. Geoffroy Saint-Hilaire, 1811, Talpidae), as a step to improve the knowledge of the conservation biology of this species. Twenty-four faeces were collected in the field, DNA was extracted from them, and fragments of the standard barcode region (COI) were PCR amplified by using five primer sets (Brandon-Mong, Gillet, Leray, Meusnier and Zeale). PCR outputs were sequenced on the Illumina MiSeq platform, sequences were processed, clustered into OTUs (Operational Taxonomic Units) using UPARSE algorithm and BLASTed against the NCBI database. Although all primer sets successfully amplified their target fragments, they differed considerably in the amounts of sequence reads, rough OTUs, and taxonomically assigned OTUs. Primer sets consistently identified a few abundant prey taxa, probably representing the staple food of the Pyrenean desman. However, they differed in the less common prey groups. Overall, the combination of Gillet and Zeale primer sets were most cost-effective to identify the widest taxonomic range of prey as well as the desman itself, which could be further improved stepwise by adding sequentially the outputs of Leray, Brandon-Mong and Meusnier primers. These results are relevant for the conservation biology of this endangered species as they allow a better characterization of its food and habitat requirements.},
}
@article {pmid30549365,
year = {2019},
author = {Richardson, RT and Curtis, HR and Matcham, EG and Lin, CH and Suresh, S and Sponsler, DB and Hearon, LE and Johnson, RM},
title = {Quantitative multi-locus metabarcoding and waggle dance interpretation reveal honey bee spring foraging patterns in Midwest agroecosystems.},
journal = {Molecular ecology},
volume = {28},
number = {3},
pages = {686-697},
doi = {10.1111/mec.14975},
pmid = {30549365},
issn = {1365-294X},
support = {//Project Apis m.-Costco Honey Bee Biology Fellowship/International ; //Pollinator Partnership Corn Dust Research Consortium grant/International ; OHO01277//state and federal funds appropriated to The Ohio State University, Ohio Agricultural Research and Development Center/International ; },
mesh = {Animals ; *Appetitive Behavior ; Bees/*physiology ; *Behavior, Animal ; DNA Barcoding, Taxonomic ; Databases, Nucleic Acid ; Ohio ; Pollen/*genetics ; Seasons ; },
abstract = {We explored the pollen foraging behaviour of honey bee colonies situated in the corn and soybean dominated agroecosystems of central Ohio over a month-long period using both pollen metabarcoding and waggle dance inference of spatial foraging patterns. For molecular pollen analysis, we developed simple and cost-effective laboratory and bioinformatics methods. Targeting four plant barcode loci (ITS2, rbcL, trnL and trnH), we implemented metabarcoding library preparation and dual-indexing protocols designed to minimize amplification biases and index mistagging events. We constructed comprehensive, curated reference databases for hierarchical taxonomic classification of metabarcoding data and used these databases to train the metaxa2 DNA sequence classifier. Comparisons between morphological and molecular palynology provide strong support for the quantitative potential of multi-locus metabarcoding. Results revealed consistent foraging habits between locations and show clear trends in the phenological progression of honey bee spring foraging in these agricultural areas. Our data suggest that three key taxa, woody Rosaceae such as pome fruits and hawthorns, Salix, and Trifolium provided the majority of pollen nutrition during the study. Spatially, these foraging patterns were associated with a significant preference for forests and tree lines relative to herbaceous land cover and nonflowering crop fields.},
}
@article {pmid30547835,
year = {2018},
author = {Joyce, AL and Torres, MM and Torres, R and Moreno, M},
title = {Genetic variability of the Aedes aegypti (Diptera: Culicidae) mosquito in El Salvador, vector of dengue, yellow fever, chikungunya and Zika.},
journal = {Parasites &amp; vectors},
volume = {11},
number = {1},
pages = {637},
pmid = {30547835},
issn = {1756-3305},
mesh = {Aedes/*genetics/virology ; Amplified Fragment Length Polymorphism Analysis ; Animals ; Chikungunya Fever/*transmission ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Dengue/*transmission ; El Salvador/epidemiology ; Electron Transport Complex IV/genetics ; Female ; Genetic Variation ; Genetics, Population ; Haplotypes ; Humans ; Larva ; Male ; Mosquito Vectors/*genetics/virology ; Yellow Fever/*transmission ; Zika Virus Infection/*transmission ; },
abstract = {BACKGROUND: Aedes aegypti is associated with dengue, yellow fever, chikungunya and Zika viruses. This vector is widespread in tropical and subtropical areas, and can also occur in temperate areas at higher latitudes. The geographical distribution of Ae. aegypti continues to spread due to human activities. This is the first study to examine the population genetic structure of this insect in El Salvador, Central America.<br><br>METHODS: Aedes aegypti larvae were collected from six geographical regions of El Salvador: Sonsonate, San Salvador, Chalatenango, Usulut&#xe1;n, San Miguel and Moraz&#xe1;n. Larvae were raised into adults, identified and preserved. Two molecular markers, amplified fragment length polymorphism (AFLP) genotyping and mitochondrial DNA (mtDNA) cytochrome c&#xa0;oxidase subunit 1&#xa0;(cox1) sequencing, were used to investigate population genetic structure.<br><br>RESULTS: Structure analysis found two genetically distinct populations; one occurs predominantly in the north and west, and a mix of two populations occurs in the southeast of the country. Genetic distances ranged from 0.028 (2.8%) to 0.091 (9%), and an AMOVA analysis found 11% variation between populations. Mitochondrial DNA&#xa0;cox1 sequences produced a haplotype network which consisted of 3 haplogroups and 10 haplotypes. Haplogroup 1 had low haplotype and nucleotide diversity and was found in all six regions. Haplogroups 2 and 3 had higher haplotype and nucleotide diversity, and were less abundant; haplogroup 3 was found in only 3 of the six regions studied. Bottleneck tests were significant, suggesting that populations had undergone a recent bottleneck. A maximum likelihood tree, which combined samples from this study with available sequences in GenBank, suggested that two genetically divergent lineages had been introduced.<br><br>CONCLUSIONS: Relatively high genetic diversity was found in Ae. aegypti in El Salvador. The mtDNA sequences clustered into two lineages, as found in previous studies. Samples in El Salvador may be introduced from regions in North and South America where past eradication was not complete. Future study of genotypes in surrounding countries would provide a more complete picture of the movement and potential source of introductions of this vector. The distribution of the lineages and haplogroups may further our understanding of the epidemiology of Ae. aegypti associated vector borne diseases.},
}
@article {pmid31435510,
year = {2018},
author = {Marcus, JM},
title = {Our love-hate relationship with DNA barcodes, the Y2K problem, and the search for next generation barcodes.},
journal = {AIMS genetics},
volume = {5},
number = {1},
pages = {1-23},
pmid = {31435510},
issn = {2377-1143},
abstract = {DNA barcodes are very useful for species identification especially when identification by traditional morphological characters is difficult. However, the short mitochondrial and chloroplast barcodes currently in use often fail to distinguish between closely related species, are prone to lateral transfer, and provide inadequate phylogenetic resolution, particularly at deeper nodes. The deficiencies of short barcode identifiers are similar to the deficiencies of the short year identifiers that caused the Y2K problem in computer science. The resolution of the Y2K problem was to increase the size of the year identifiers. The performance of conventional mitochondrial COI barcodes for phylogenetics was compared with the performance of complete mitochondrial genomes and nuclear ribosomal RNA repeats obtained by genome skimming for a set of caddisfly taxa (Insect Order Trichoptera). The analysis focused on Trichoptera Family Hydropsychidae, the net-spinning caddisflies, which demonstrates many of the frustrating limitations of current barcodes. To conduct phylogenetic comparisons, complete mitochondrial genomes (15 kb each) and nuclear ribosomal repeats (9 kb each) from six caddisfly species were sequenced, assembled, and are reported for the first time. These sequences were analyzed in comparison with eight previously published trichopteran mitochondrial genomes and two triochopteran rRNA repeats, plus outgroup sequences from sister clade Lepidoptera (butterflies and moths). COI trees were not well-resolved, had low bootstrap support, and differed in topology from prior phylogenetic analyses of the Trichoptera. Phylogenetic trees based on mitochondrial genomes or rRNA repeats were well-resolved with high bootstrap support and were largely congruent with each other. Because they are easily sequenced by genome skimming, provide robust phylogenetic resolution at various phylogenetic depths, can better distinguish between closely related species, and (in the case of mitochondrial genomes), are backwards compatible with existing mitochondrial barcodes, it is proposed that mitochondrial genomes and rRNA repeats be used as next generation DNA barcodes.},
}
@article {pmid31015655,
year = {2018},
author = {Hadrup, SR and Newell, EW},
title = {Publisher Correction: Determining T-cell specificity to understand and treat disease.},
journal = {Nature biomedical engineering},
volume = {2},
number = {1},
pages = {51},
doi = {10.1038/s41551-017-0176-8},
pmid = {31015655},
issn = {2157-846X},
abstract = {In the version of this Perspective originally published, in Fig. 4, in the schematic for the DNA barcoded multimers, the barcodes were missing; they have now been included and the figure updated in all versions of the Perspective.},
}
@article {pmid30740526,
year = {2017},
author = {Zhang, J and Cong, Q and Shen, J and Grishin, NV},
title = {Mitogenomes of the four Agathymus holotypes collected 55 years ago.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {2},
number = {2},
pages = {598-600},
pmid = {30740526},
issn = {2380-2359},
support = {R01 GM094575/GM/NIGMS NIH HHS/United States ; },
abstract = {Giant-Skipper butterflies from the genus Agathymus (family Hesperiidae) are unusual as their caterpillars feed inside Agave leaves. Relationships among Agathymus taxa and their names (i.e., if they are species, subspecies, or synonyms) are poorly understood due to phenotypic similarity. DNA sequences are promising to clarify the taxonomic questions, but it is challenging to sequence name-bearing types that are usually old specimens with poorly preserved DNA. Using next generation sequencing, we assembled mitochondrial genomes of four Agathymus mariae group holotype specimens collected more than 55 years ago and housed pinned and dry in the American Museum of Natural History (New York, NY). We compared the holotype mitogenomes to those we obtained from fresh A. mariae specimens and the sister species Agathymus micheneri. All but A. micheneri mitogenomes were highly similar to each other (more than 99% identity), suggesting that the four names chinatiensis, lajitaensis, rindgei and gilberti proposed by H. A. Freeman in 1964 may not refer to species-level taxa. The mitogenomes grouped eastern populations (rindgei and gilberti) together and apart from the western populations (nominal mariae, chinatiensis and lajitaensis). Mexican A. micheneri differs by about 2.5% (about 5% in the COI barcode region) from A. mariae, and is likely to be a distinct species.},
}
@article {pmid31014497,
year = {2016},
author = {Šlapeta, &#x160; and Šlapeta, J},
title = {Molecular identity of cat fleas (Ctenocephalides felis) from cats in Georgia, USA carrying Bartonella clarridgeiae, Bartonella henselae and Rickettsia sp. RF2125.},
journal = {Veterinary parasitology, regional studies and reports},
volume = {3-4},
number = {},
pages = {36-40},
doi = {10.1016/j.vprsr.2016.06.005},
pmid = {31014497},
issn = {2405-9390},
abstract = {The cat flea (Ctenocephalides felis) is the most common ectoparasite of dogs and cats. Close association of humans with cats and dogs enables flea-borne disease transmission either directly, via flea bites, or indirectly, via pathogens excreted in flea faeces. The aim of this study was to evaluate molecular identity of C. felis from cats in Georgia, USA based on a molecular barcode marker gene (cox1) and the frequency at which the fleas were carriers of the vector-borne bacteria, Bartonella and Rickettsia. The multiplexed Bartonella and Rickettsia real-time PCR assay (targeting ssrA and gltA, respectively) adopted in this study, together with sequencing of the ssrA enabled rapid identification of Bartonella spp. in cat fleas. Eighteen out of 20 fleas examined were positive for Bartonella spp. and all fleas were positive for Rickettsia spp. DNA sequencing of the ssrA confirmed presence B. clarridgeiae and B. henselae. Amplification and DNA sequencing of gltA and ompA confirmed presence of Rickettsia sp. RF2125 (Rickettsia felis-like organism). All fleas from 21 cats in Georgia, USA were morphologically identical with C. felis. Sequencing of the flea cox1 revealed identity with C. felis from Seychelles, Africa recognised as a subspecies C. felis strongylus, the African cat flea. Analysis of the cox1 sequences of fleas improves understanding of global distribution of cat flea cox1 clades (C. felis) when compared with sequences from Ctenocephalides spp. from Asia, Africa, Europe, Asia and Australia. Coupling flea barcoding approach with the multiplexed real-time PCR assay followed by Bartonella sequencing represents a rational approach for screening and elucidation of fleas' capacity to vector infectious agents.},
}
@article {pmid30703957,
year = {2014},
author = {Montecchio, L and Fanchin, G and Simonato, M and Faccoli, M},
title = {First Record of Thousand Cankers Disease Fungal Pathogen Geosmithia morbida and Walnut Twig Beetle Pityophthorus juglandis on Juglans regia in Europe.},
journal = {Plant disease},
volume = {98},
number = {10},
pages = {1445},
doi = {10.1094/PDIS-07-14-0719-PDN},
pmid = {30703957},
issn = {0191-2917},
abstract = {Thousand cankers disease (TCD) is a disease complex caused by the fungus Geosmithia morbida Kolařik (Ascomycota, Hypocreales) and its vector Pityophthorus juglandis Blackman 1928 (Coleoptera, Scolytinae; walnut twig beetle, WTB). Since the mid-1990s, the disease was responsible for widespread mortality of many walnut species in the United States (4). After the first detection of TCD on black walnut (Juglans nigra L.) in Italy (3), an extensive survey was activated in cooperation with the Regional Phytosanitary Service. In May 2014, early TCD symptoms (4) were observed on English walnuts (J. regia L.). Canopies showed yellowing, wilting, and dieback of the youngest twigs, and a number of small brown cankers. Longitudinal and radial sections sampled through the cankers revealed gray to brown discoloration of both phloem and bark, and the presence of bark beetle galleries. Xylem discoloration was never observed. From one ~20-year-old European walnut growing in a garden neighboring an infected black walnut plantation (Santorso, Vicenza, 45°72' N, 11°40' E), a number of 1- to 2.5-cm-diameter twigs showing cankers up to 2 cm long surrounding bark beetle holes were collected. Whitish mycelium producing verticillate conidiophores was detected inside the insect galleries. From the necrotic margin of eight cankers previously surface-sterilized with 3% sodium hypochlorite, two 4-mm-wide chips per canker were placed on potato dextrose agar and incubated at 28 ± 1°C in the dark. Slow growing lobate, plane, yellowish-ocher colonies with hyaline mycelium appeared in 5 days. After subculturing to the same medium, growth features, mycelium, conidiophores, and conidia with morphological characteristics matching Kolarik's description of G. morbida (2) were observed. The ITS region of rDNA from the fungus strain LM14GM001-JR was amplified by using ITS1F and ITS4 primers and sequenced obtaining a 387-bp gene fragment. BLAST analysis showed 99% identity to the G. morbida strain U19 (GenBank Accession No. KF808301.1) for 384 bp, and 99% identity to the G. morbida strain LM13GM001-JN previously isolated from J. nigra in Italy (3). From the same samples, two emerging beetles were collected and identified as P. juglandis both morphologically (5) and genetically by DNA extraction following a standard salting out protocol. The barcode region of the mitochondrial gene cytochrome oxidase I was then amplified by using universal primers (1) and sequenced to obtain a 614-bp fragment of the gene. BLAST analysis showed 100% identity to P. juglandis based on comparison with KJ451422. A few other English walnuts with both the fungus and WTB were also found close to other infected black walnut plantations. To our knowledge, this is the first record of G. morbida and P. juglandis on J. regia in Europe, where the tree is cultivated for both fruit and timber production, as well as a traditional landscape tree. Voucher specimens are stored in the TeSAF herbarium and in the DAFNAE insect collection. References: (1) O. Folmer et al. Mol. Marine Biol. Biotechnol. 3:294, 1994. (2) M. Kolarik et al. Mycologia 103:325, 2011. (3) L. Montecchio and M. Faccoli. Plant Dis. 98:696, 2014. (4) S. J. Seybold et al. USDA Forest Service, NA-PR-02-10, 2013. (5) S. L. Wood. Great Basin Naturalist Memoirs 6:1123, 1982.},
}
@article {pmid30708556,
year = {2014},
author = {Montecchio, L and Faccoli, M},
title = {First Record of Thousand Cankers Disease Geosmithia morbida and Walnut Twig Beetle Pityophthorus juglandis on Juglans nigra in Europe.},
journal = {Plant disease},
volume = {98},
number = {5},
pages = {696},
doi = {10.1094/PDIS-10-13-1027-PDN},
pmid = {30708556},
issn = {0191-2917},
abstract = {Thousand cankers disease (TCD) of walnut is responsible for widespread mortality of black walnut (Juglans nigra L.) in the United States since the mid-1990s (2). The disease is caused by the fungus Geosmithia morbida Kolařik (Ascomycota, Hypocreales), vectored by the walnut twig beetle Pityophthorus juglandis Blackman 1928 (Coleoptera, Scolytinae). In September 2013, TDC was observed in northeastern Italy (Bressanvido, Vicenza, 45°39' N, 11°38' E) in black walnuts of different ages: ~80-year-old plants growing in a garden and 17-year-old trees belonging to a nearby walnut plantation for timber production. Main symptoms were yellowing, wilting, twig and branch dieback, and a high number of small bark cankers (3). Longitudinal and radial sections collected through the cankers revealed gray to brown discoloration of both phloem and outer bark, and the presence of bark beetle galleries radiating from the mating chamber and developing horizontally (across the wood grain), and vertical (along the grain) larval galleries. Occasionally, discoloration involved the outward xylematic tissues. Fungal fruiting bodies were not found on or near the cankers. Whitish mycelium, sometimes producing verticillate conidiophores, was frequently detected inside galleries. A number of 1- to 3-cm diameter twigs showing cankers up to 2 cm long surrounding bark beetle penetration holes were randomly collected. From samples, emerging beetles were identified as P. juglandis both morphologically (4) and genetically. DNA extraction was carried following a standard salting out protocol. The barcode region of the mitochondrial gene cytochrome oxydase I was then amplified using universal primers (1) and sequenced, obtaining 627 bp. BLAST analysis showed 100% identity to P. juglandis. Sequences were finally deposited in the BoldSystem database (GenBank Accession No. KF725084). From the necrotic margin of six cankers previously surface-sterilized with 3% sodium hypochlorite, two 3-mm-wide chips per canker were placed on potato dextrose agar and incubated at 23 ± 1°C in the dark. Among a variety of microorganisms, slow growing lobate, plane, yellowish-ochre colonies with hyaline mycelium appeared in 6 days. After subculturing to the same medium, growing features, mycelium, conidiophores, and conidia with morphological characteristics matching Kolařik's description of G. morbida (2) were observed. Same result was obtained culturing the mycelium growing inside the galleries. The ITS region of rDNA was amplified using ITS1F and ITS4 primers and sequenced, obtaining 597 bp. BLAST analysis showed 100% identity to G. morbida strain U173 (HF546283.1) for 558 bp. To our knowledge, this is the first record of TCD and P. juglandis to Europe, where walnut species (mainly J. regia, J. nigra, and their hybrids) are intensively cultivated for timber production. This finding is therefore of particular importance. An intensive survey of the disease is suggested, both to assess fungus/beetle presence and to verify possible pathways of introduction, likely associated to importation of infested/infected timber from native Nearctic regions. Voucher specimens are stored in the TeSAF herbarium (fungus) and in the DAFNAE insect collection. References: (1) O. Folmer et al. Mol. Marine Biol. Biotechnol. 3:294, 1994. (2) M. Kolařik et al. Mycologia 103:325, 2011. (3) C. Nischwitz and M. Murray, Utah Pests Fact Sheet, PRP-015pr, 2011. (4) S. L. Wood. Great Basin Naturalist Memoirs 6:1123, 1982.},
}
@article {pmid30727351,
year = {2012},
author = {Ristaino, JB},
title = {A Lucid Key to the Common Species of Phytophthora.},
journal = {Plant disease},
volume = {96},
number = {6},
pages = {897-903},
doi = {10.1094/PDIS-08-11-0636},
pmid = {30727351},
issn = {0191-2917},
abstract = {The Key to the Common Phytophthora species (Lucid v 3.4) is a matrix-based computerized identification key and includes important morphological and molecular characters that are useful for identification of 55 common species of Phytophthora. A set of 20 features are used to make a correct species identification. Once a culture is obtained, the user enters responses to known character state options into Lucid Player, and the correct species is identified. Illustrations of each character state for a feature are included in the key. The main morphological features included in the key are: asexual structures, sexual structures, and chlamydospore, hyphae, and cultural characteristics. The user can read an illustrated "Fact Sheet" on each species that includes pictures of morphological characters, disease symptoms, host range, and relevant references. A cross-linked glossary of terminology is included in each fact sheet. In addition, a DNA search function that contains a simple search of internal transcribed spacer (ITS) and Barcode of Life (BOL, 5' end of the cox 1 gene) sequences for each species can be queried. The key was created to provide teachers, diagnosticians, and regulatory personnel with easily accessible tools to distinguish common species in the genus Phytophthora based on a number of important morphological and molecular characteristics. The key is available for purchase from APS Press and should provide another useful tool for the identification of members of this destructive group of Oomycete plant pathogens.},
}
@article {pmid30764276,
year = {2009},
author = {Wilson, AD and Schiff, NM and Haugen, DA and Hoebeke, ER},
title = {First Report of Amylostereum areolatum in Pines in the United States.},
journal = {Plant disease},
volume = {93},
number = {1},
pages = {108},
doi = {10.1094/PDIS-93-1-0108A},
pmid = {30764276},
issn = {0191-2917},
abstract = {The wood decay fungus Amylostereum areolatum (Fr.) Boidin, native to Eurasia and North Africa (4), is the mycosymbiont of several siricid woodwasps including Sirex noctilio Fabricius, a major pest of pines in New Zealand, Australia, South America, and South Africa where it has been introduced. Adult females of S. noctilio are effective vectors of arthrospores (hyphal fragments) of the fungus, stored internally within mycangia in the abdomen, which are injected with the eggs and a phytotoxic mucus into the outer sapwood of coniferous tree hosts during oviposition. The toxin is translocated upward into the foliage causing needle wilting, necrosis, and crown dieback. The fungus decays the wood (white rot) and provides food for hatching larvae that form borer galleries. Extensive damage to the host via wood decay, galleries, and toxin effects cause mortality in heavily infested trees. S. noctilio adults have been intercepted from several locations in North America prior to 2003, but there has been no evidence of an established population in any native forests until recently. In September 2004, a single adult female was collected from a funnel-trap at the edge of a forest stand in Fulton, NY (Oswego County) and identified in February 2005 (3). A local survey in May 2005 revealed red pines and Scotch pines infested with siricid larvae on the SUNY Oswego campus and in Rice Creek Nature Preserve, 3 km from campus. All larvae from infested trees were identified as S. noctilio using the DNA barcode method (2). Bole sections of infested red pines were sent to the USDA-ARS quarantine facility in Stoneville, MS. Wood samples, taken from areas of incipient decay adjacent to larval galleries, were plated onto 4.5% potato dextrose agar. Fungal colonies in pure cultures arising from wood pieces were appressed and exhibited microscopic characters typical of A. areolatum. Molecular confirmation of identifications for nine isolates was achieved by PCR amplification and sequencing of the rDNA internal transcribed spacer (ITS) region using ITS1 and ITS4 universal primer pairs. BLAST program analyses of these sequences compared against the NCBI GenBank database revealed the isolates were identical (GenBank Accession No. FJ040860) and had 98.8 to 99.8% sequence homology with five A. areolatum GenBank sequences (AF454428, AY781245, AF218389, EU249343, and EU249344) from Germany, Sweden, Japan, and Canada. To our knowledge, this represents the first confirmed isolation of A. areolatum from a native pine stand in the United States and confirms the first incidence of infections of North American pines, 16 months prior to isolations in Ontario (1). This insect vector-decay fungus complex, native to Eurasia, has a very high-risk rating and threatens many pine (Pinus) species in North America, particularly southern U.S. species that have been severely attacked and killed where introduced in the Southern Hemisphere. The lack of complete sequence homology between New York and Ontario, Canada strains of A. areolatum suggests that these recent incidences probably resulted from multiple woodwasp introductions rather than from vector (S. noctilio female) movement after one introduction. References: (1) M. J. Bergeron et al. Plant Dis. 92:1138, 2008. (2) P. D. N. Hebert et al. Proc. R. Soc. Lond. B 270:313, 2003. (3) E. R. Hoebeke et al. Newsl. Mich. Entomol. Soc. 50:24, 2005. (4) J. P. Spradbery and A. A. Kirk. Bull. Entomol. Res. 68:341, 1978.},
}
@article {pmid30547744,
year = {2018},
author = {Finch, JTD and Power, SA and Welbergen, JA and Cook, JM},
title = {Two's company, three's a crowd: co-occurring pollinators and parasite species in Breynia oblongifolia (Phyllanthaceae).},
journal = {BMC evolutionary biology},
volume = {18},
number = {1},
pages = {193},
pmid = {30547744},
issn = {1471-2148},
mesh = {Animals ; Bayes Theorem ; DNA Barcoding, Taxonomic ; Female ; Geography ; Male ; Malpighiaceae/*parasitology ; Moths/anatomy &amp; histology/physiology/ultrastructure ; New South Wales ; Ovary/cytology ; Oviposition ; Ovule/cytology ; Parasites/anatomy &amp; histology/*physiology/ultrastructure ; Phylogeny ; Pollination/*physiology ; Species Specificity ; },
abstract = {BACKGROUND: Obligate pollination mutualisms (OPMs) are specialized interactions in which female pollinators transport pollen between the male and female flowers of a single plant species and then lay eggs into those same flowers. The pollinator offspring hatch and feed upon some or all of the developing ovules pollinated by their mothers. Strong trait matching between plants and their pollinators in OPMs is expected to result in reciprocal partner specificity i.e., a single pollinator species using a single plant species and vice versa, and strict co-speciation. These issues have been studied extensively in figs and fig wasps, but little in the more recently discovered co-diversification of Epicephala moths and their Phyllanthaceae hosts. OPMs involving Epicephala moths are believed occur in approximately 500 species of Phyllanthaceae, making it the second largest OPM group after the Ficus radiation (> 750 species). In this study, we used a mixture of DNA barcoding, genital morphology and behavioral observations to determine the number of Epicephala moth species inhabiting the fruits of Breynia oblongifolia, their geographic distribution, pollinating behavior and phylogenetic relationships.<br><br>RESULTS: We found that B. oblongifolia hosts two species of pollinator that co-occurred at all study sites, violating the assumption of reciprocal specificity. Male and female genital morphologies both differed considerably between the two moth species. In particular, females differed in the shape of their ovipositors, eggs and oviposition sites. Phylogenetic analyses indicated that the two Epicephala spp. on B. oblongifolia likely co-exist due to a host switch. In addition, we discovered that Breynia fruits are also often inhabited by a third moth, an undescribed species of Herpystis, which is a non-pollinating seed parasite.<br><br>CONCLUSIONS: Our study reveals new complexity in interactions between Phyllantheae and Epicephala pollinators and highlights that host switching, co-speciation and non-pollinating seed parasites can shape species interactions in OPMs. Our finding that co-occurring Epicephala species have contrasting oviposition modes parallels other studies and suggests that such traits are important in Epicephala species coexistence.},
}
@article {pmid30547048,
year = {2018},
author = {Yabe, IM and Truitt, LL and Espinoza, DA and Wu, C and Koelle, S and Panch, S and Corat, MAF and Winkler, T and Yu, KR and Hong, SG and Bonifacino, A and Krouse, A and Metzger, M and Donahue, RE and Dunbar, CE},
title = {Barcoding of Macaque Hematopoietic Stem and Progenitor Cells: A Robust Platform to Assess Vector Genotoxicity.},
journal = {Molecular therapy. Methods &amp; clinical development},
volume = {11},
number = {},
pages = {143-154},
pmid = {30547048},
issn = {2329-0501},
abstract = {Gene therapies using integrating retrovirus vectors to modify hematopoietic stem and progenitor cells have shown great promise for the treatment of immune system and hematologic diseases. However, activation of proto-oncogenes via insertional mutagenesis has resulted in the development of leukemia. We have utilized cellular bar coding to investigate the impact of different vector designs on the clonal behavior of hematopoietic stem and progenitor cells (HSPCs) during in vivo expansion, as a quantitative surrogate assay for genotoxicity in a non-human primate model with high relevance for human biology. We transplanted two rhesus macaques with autologous CD34+ HSPCs transduced with three lentiviral vectors containing different promoters and/or enhancers of a predicted range of genotoxicities, each containing a high-diversity barcode library that uniquely tags each individual transduced HSPC. Analysis of clonal output from thousands of individual HSPCs transduced with these barcoded vectors revealed sustained clonal diversity, with no progressive dominance of clones containing any of the three vectors for up to almost 3 years post-transplantation. Our data support a low genotoxic risk for lentivirus vectors in HSPCs, even those containing strong promoters and/or enhancers. Additionally, this flexible system can be used for the testing of future vector designs.},
}
@article {pmid30545104,
year = {2018},
author = {Kooij, PW and Dentinger, BM and Donoso, DA and Shik, JZ and Gaya, E},
title = {Cryptic Diversity in Colombian Edible Leaf-Cutting Ants (Hymenoptera: Formicidae).},
journal = {Insects},
volume = {9},
number = {4},
pages = {},
pmid = {30545104},
issn = {2075-4450},
abstract = {Leaf-cutting ants are often considered agricultural pests, but they can also benefit local people and serve important roles in ecosystems. Throughout their distribution, winged reproductive queens of leaf-cutting ants in the genus Atta Fabricius, 1804 are consumed as a protein-rich food source and sometimes used for medical purposes. Little is known, however, about the species identity of collected ants and the accuracy of identification when ants are sold, ambiguities that may impact the conservation status of Atta species as well as the nutritional value that they provide to consumers. Here, 21 samples of fried ants bought in San Gil, Colombia, were identified to species level using Cytochrome Oxidase I (COI) barcoding sequences. DNA was extracted from these fried samples using standard Chelex extraction methods, followed by phylogenetic analyses with an additional 52 new sequences from wild ant colonies collected in Panama and 251 publicly available sequences. Most analysed samples corresponded to Atta laevigata (Smith, 1858), even though one sample was identified as Atta colombica Guérin-Méneville, 1844 and another one formed a distinct branch on its own, more closely related to Atta texana (Buckley, 1860) and Atta mexicana (Smith, 1858). Analyses further confirm paraphyly within Atta sexdens (Linnaeus, 1758) and A. laevigata clades. Further research is needed to assess the nutritional value of the different species.},
}
@article {pmid30545022,
year = {2018},
author = {Wang, J and Gao, Y and Chen, Y and Chen, Y and Zhang, Y and Xiang, L and Pan, Z},
title = {Lamiophlomis rotata Identification via ITS2 Barcode and Quality Evaluation by UPLC-QTOF-MS Couple with Multivariate Analyses.},
journal = {Molecules (Basel, Switzerland)},
volume = {23},
number = {12},
pages = {},
pmid = {30545022},
issn = {1420-3049},
support = {CSTC2016jcyj A0288//Chong Qing Science Foundation Project/ ; KJ1702030//Chongqing Municipal Education Commission/ ; zy201602066//Chongqing Health and Family Planning Commission/ ; 2017-ZJ-Y10//Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources/ ; },
mesh = {Chromatography, High Pressure Liquid/methods ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer ; Lamiaceae/*chemistry/*genetics ; Least-Squares Analysis ; Mass Spectrometry/*methods/statistics &amp; numerical data ; Multivariate Analysis ; },
abstract = {Lamiophlomis rotata (L. rotata), is known as "Daba" in the Tibetan region, Ajuga ovalifolia and Oreosolen wartii have also been utilized as substitutes for "Daba", however, only L. rotata has been officially listed in the Chinese Pharmacopoeia for hemostasis preparations. To safely apply the traditional uses of the herb, internal transcribed spacer 2 (ITS2) DNA barcodes were employed to discriminate L. rotata from its adulterants. For further evaluation of the quality of different originating habitats, the chemical profiles of 25 samples were determined by ultra-high-performance liquid chromatography coupled with time-of-flight mass spectrometry (UPLC-QTOF-MS) coupled with multivariate analyses. ITS2 DNA barcodes differentiated L. rotata from O. wartii and A. ovalifolia accurately. A neighbor-joining (NJ) tree showed that three origins clustered into three clades. Forty-nine compounds were identified in the total ion current (TIC) profile of L. rotata. Additionally, two pairs of isomers were identified for the first time by using mass spectrometry fragmentation. The differences between the variable habitats were determined by multivariate statistical analysis of the UPLC-QTOF-MS data from 25 specimens. Ten compounds were identified as the characteristic markers distinguishing the sample from four geographical origins. The results also suggest that samples from Qinghai and Sichuan province would be the most suitable choice for traditional prescriptions and preparations.},
}
@article {pmid30523036,
year = {2019},
author = {Danko, DC and Meleshko, D and Bezdan, D and Mason, C and Hajirasouliha, I},
title = {Minerva: an alignment- and reference-free approach to deconvolve Linked-Reads for metagenomics.},
journal = {Genome research},
volume = {29},
number = {1},
pages = {116-124},
pmid = {30523036},
issn = {1549-5469},
support = {T32 GM083937/GM/NIGMS NIH HHS/United States ; },
mesh = {*Algorithms ; *Metagenome ; Metagenomics/*methods ; Sequence Analysis, DNA/*methods ; *Software ; },
abstract = {Emerging Linked-Read technologies (aka read cloud or barcoded short-reads) have revived interest in short-read technology as a viable approach to understand large-scale structures in genomes and metagenomes. Linked-Read technologies, such as the 10x Chromium system, use a microfluidic system and a specialized set of 3' barcodes (aka UIDs) to tag short DNA reads sourced from the same long fragment of DNA; subsequently, the tagged reads are sequenced on standard short-read platforms. This approach results in interesting compromises. Each long fragment of DNA is only sparsely covered by reads, no information about the ordering of reads from the same fragment is preserved, and 3' barcodes match reads from roughly 2-20 long fragments of DNA. However, compared to long-read technologies, the cost per base to sequence is far lower, far less input DNA is required, and the per base error rate is that of Illumina short-reads. In this paper, we formally describe a particular algorithmic issue common to Linked-Read technology: the deconvolution of reads with a single 3' barcode into clusters that represent single long fragments of DNA. We introduce Minerva, a graph-based algorithm that approximately solves the barcode deconvolution problem for metagenomic data (where reference genomes may be incomplete or unavailable). Additionally, we develop two demonstrations where the deconvolution of barcoded reads improves downstream results, improving the specificity of taxonomic assignments and of k-mer-based clustering. To the best of our knowledge, we are the first to address the problem of barcode deconvolution in metagenomics.},
}
@article {pmid30522381,
year = {2019},
author = {Shukla, M and Joshi, BD and Kumar, VP and Thakur, M and Mehta, AK and Sathyakumar, S and Goyal, SP},
title = {Species dilemma of musk deer (Moschus spp) in India: molecular data on cytochrome c oxidase I suggests distinct genetic lineage in Uttarakhand compared to other Moschus species.},
journal = {Animal biotechnology},
volume = {30},
number = {3},
pages = {193-201},
doi = {10.1080/10495398.2018.1521822},
pmid = {30522381},
issn = {1532-2378},
mesh = {Animals ; Bayes Theorem ; Electron Transport Complex IV/*genetics ; Endangered Species ; *Genetic Variation ; Geography ; Haplotypes ; India ; Phylogeny ; Ruminants/classification/*genetics ; },
abstract = {Musk deer are of high conservation priority owing to poaching pressure because of its musk pod. Representation of musk deer status using genetics is poorly documented in India, and it is not confirmed as to how many species of musk deer are present. We characterize for the first time, the genetic diversity of musk deer from Uttarakhand using Cytochrome Oxidase sub-unit (COI) gene (486 bp) and compared with the data available for other species. Results revealed the presence of six haplotypes in the Uttarakhand population amongst 17 sequences. Of these, 12 sequences shared the single haplotype. The intra-species sequences divergence was 0.003-0.017, whereas divergence with other species of musk deer was 0.071-0.081. Bayesian phylogenetic tree revealed that samples from Uttarakhand formed a separate clade with respect to other species of musk deer, whereas three species distributed in China clustered in the same clade and showed low sequences divergence, i.e., 0.002-0.061. Because of different ecomorph reported, we suggest using the barcoding based approach for inter and intra-species distinction and delineating species boundaries across the range for effective conservation. Besides, systematic classification, DNA barcoding would also help in dealing wildlife offence cases for disposal of the legal report in court.},
}
@article {pmid30534606,
year = {2018},
author = {Arrigoni, L and Al-Hasani, H and Ramírez, F and Panzeri, I and Ryan, DP and Santacruz, D and Kress, N and Pospisilik, JA and Bönisch, U and Manke, T},
title = {RELACS nuclei barcoding enables high-throughput ChIP-seq.},
journal = {Communications biology},
volume = {1},
number = {},
pages = {214},
pmid = {30534606},
issn = {2399-3642},
abstract = {Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is an invaluable tool for mapping chromatin-associated proteins. Current barcoding strategies aim to improve assay throughput and scalability but intense sample handling and lack of standardization over cell types, cell numbers and epitopes hinder wide-spread use in the field. Here, we present a barcoding method to enable high-throughput ChIP-seq using common molecular biology techniques. The method, called RELACS (restriction enzyme-based labeling of chromatin in situ) relies on standardized nuclei extraction from any source and employs chromatin cutting and barcoding within intact nuclei. Barcoded nuclei are pooled and processed within the same ChIP reaction, for maximal comparability and workload reduction. The innovative barcoding concept is particularly user-friendly and suitable for implementation to standardized large-scale clinical studies and scarce samples. Aiming to maximize universality and scalability, RELACS can generate ChIP-seq libraries for transcription factors and histone modifications from hundreds of samples within three days.},
}
@article {pmid30533322,
year = {2018},
author = {Kim, J and Jung, S},
title = {COI barcoding of plant bugs (Insecta: Hemiptera: Miridae).},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e6070},
pmid = {30533322},
issn = {2167-8359},
abstract = {The family Miridae is the most diverse and one of the most economically important groups in Heteroptera. However, identification of mirid species on the basis of morphology is difficult and time-consuming. In the present study, we evaluated the effectiveness of COI barcoding for 123 species of plant bugs in seven subfamilies. With the exception of three Apolygus species-A. lucorum, A. spinolae, and A. watajii (subfamily Mirinae)-each of the investigated species possessed a unique COI sequence. The average minimum interspecific genetic distance of congeners was approximately 37 times higher than the average maximum intraspecific genetic distance, indicating a significant barcoding gap. Despite having distinct morphological characters, A. lucorum, A. spinolae, and A. watajii mixed and clustered together, suggesting taxonomic revision. Our findings indicate that COI barcoding represents a valuable identification tool for Miridae and can be economically viable in a variety of scientific research fields.},
}
@article {pmid30532624,
year = {2018},
author = {Crespo, LC and Domènech, M and Enguídanos, A and Malumbres-Olarte, J and Cardoso, P and Moya-Laraño, J and Frías-López, C and Macías-Hernández, N and De Mas, E and Mazzuca, P and Mora, E and Opatova, V and Planas, E and Ribera, C and Roca-Cusachs, M and Ruiz, D and Sousa, P and Tonzo, V and Arnedo, MA},
title = {A DNA barcode-assisted annotated checklist of the spider (Arachnida, Araneae) communities associated to white oak woodlands in Spanish National Parks.},
journal = {Biodiversity data journal},
volume = {},
number = {6},
pages = {e29443},
pmid = {30532624},
issn = {1314-2828},
abstract = {BACKGROUND: A large scale semi-quantitative biodiversity assessment was conducted in white oak woodlands in areas included in the Spanish Network of National Parks, as part of a project aimed at revealing biogeographic patterns and identify biodiversity drivers. The semi-quantitative COBRA sampling protocol was conducted in sixteen 1-ha plots across six national parks using a nested design. All adult specimens were identified to species level based on morphology. Uncertain delimitations and identifications due to either limited information of diagnostic characters or conflicting taxonomy were further investigated using DNA barcode information.<br><br>NEW INFORMATION: We identified 376 species belonging to 190 genera in 39 families, from the 8,521 adults found amongst the 20,539 collected specimens. Faunistic results include the discovery of 7 new species to the Iberian Peninsula, 3 new species to Spain and 11 putative new species to science. As largely expected by environmental features, the southern parks showed a higher proportion of Iberian and Mediterranean species than the northern parks, where the Palearctic elements were largely dominant. The analysis of approximately 3,200 DNA barcodes generated in the present study, corroborated and provided finer resolution to the morphologically based delimitation and identification of specimens in some taxonomically challenging families. Specifically, molecular data confirmed putative new species with diagnosable morphology, identified overlooked lineages that may constitute new species, confirmed assignment of specimens of unknown sexes to species and identified cases of misidentifications and phenotypic polymorphisms.},
}
@article {pmid30532622,
year = {2018},
author = {Morigengaowa, and Luo, JJ and Knapp, R and Wei, HJ and Liu, BD and Yan, YH and Shang, H},
title = {The identity of Hypolepis robusta, as a new synonym of Hypolepis alpina (Dennstaedtiaceae), based on morphology and DNA barcoding and the new distribution.},
journal = {PhytoKeys},
volume = {},
number = {96},
pages = {35-45},
pmid = {30532622},
issn = {1314-2011},
abstract = {Based on field observations and examinations of herbarium specimens (including type material), consulting the original literature and molecular phylogenetic analysis of the rbcL and trnL-F sequences, it is concluded that Hypolepis robusta is conspecific with Hypolepis alpina and is here formally treated as a synonym of it. Additionally H. alpina is reported with new distribution records in Guangdong, Guangxi and the Hainan Island of China, respectively.},
}
@article {pmid30532621,
year = {2018},
author = {Huemer, P and Karsholt, O},
title = {Revision of the genus Megacraspedus Zeller, 1839, a challenging taxonomic tightrope of species delimitation (Lepidoptera, Gelechiidae).},
journal = {ZooKeys},
volume = {},
number = {800},
pages = {1-278},
pmid = {30532621},
issn = {1313-2989},
abstract = {The taxonomy of the Palearctic genus Megacraspedus Zeller, 1839 (Lepidoptera, Gelechiidae) is revised, based on external morphology, genitalia and DNA barcodes. An integrative taxonomic approach supports the existence of 85 species which are arranged in 24 species groups (disputed taxa from other faunal regions are discussed). Morphology of all species is described and figured in detail. For 35 species both sexes are described; for 46 species only the male sex is reported, in one species the male is unknown, whereas in three species the female adult and/or genitalia morphology could not be analysed due to lack of material. DNA barcode sequences of the COI barcode fragment with > 500 bp were obtained from 264 specimens representing 62 species or about three-quarters of the species. Species delimitation is particularly difficult in a few widely distributed species with high and allegedly intraspecific DNA barcode divergence of nearly 14%, and with up to 23 BINs in a single species. Deep intraspecific or geographical splits in DNA barcode are frequently not supported by morphology, thus indicating a complex phylogeographic history or other unresolved molecular problems. The following 44 new species (22 of them from Europe) are described: Megacraspedusbengtssoni sp. n. (Spain), M.junnilaineni sp. n. (Turkey), M.similellus sp. n. (Bulgaria, Romania, Turkey), M.golestanicus sp. n. (Iran), M.tokari sp. n. (Croatia), M.neli sp. n. (France, Italy), M.faunierensis sp. n. (Italy), M.gredosensis sp. n. (Spain), M.bidentatus sp. n. (Spain), M.fuscus sp. n. (Spain), M.trineae sp. n. (Portugal, Spain), M.skoui sp. n. (Spain), M.spinophallus sp. n. (Spain), M.occidentellus sp. n. (Portugal), M.granadensis sp. n. (Spain), M.heckfordi sp. n. (Spain), M.tenuiuncus sp. n. (France, Spain), M.devorator sp. n. (Bulgaria, Romania), M.brachypteris sp. n. (Albania, Greece, Macedonia, Montenegro), M.barcodiellus sp. n. (Macedonia), M.sumpichi sp. n. (Spain), M.tabelli sp. n. (Morocco), M.gallicus sp. n. (France, Spain), M.libycus sp. n. (Libya, Morocco), M.latiuncus sp. n. (Kazahkstan), M.kazakhstanicus sp. n. (Kazahkstan), M.knudlarseni sp. n. (Spain), M.tenuignathos sp. n. (Morocco), M.glaberipalpus sp. n. (Morocco), M.nupponeni sp. n. (Russia), M.pototskii sp. n. (Kyrgyzstan), M.feminensis sp. n. (Kazakhstan), M.kirgizicus sp. n. (Afghanistan, Kazakhstan, Kyrgyzstan), M.ibericus sp. n. (Portugal, Spain), M.steineri sp. n. (Morocco), M.gibeauxi sp. n. (Algeria, Tunisia), M.multipunctellus sp. n. (Turkey), M.teriolensis sp. n. (Croatia, Greece, Italy, Slovenia), M.korabicus sp. n. (Macedonia), M.skulei sp. n. (Spain), M.longivalvellus sp. n. (Morocco), M.peslieri sp. n. (France, Spain), M.pacificus sp. n. (Afghanistan), and M.armatophallus sp. n. (Afghanistan). Nevadia Caradja, 1920, syn. n. (homonym), Cauloecista Dumont, 1928, syn. n., Reichardtiella Filipjev, 1931, syn. n., and Vadenia Caradja, 1933, syn. n. are treated as junior synonyms of Megacraspedus. Furthermore the following species are synonymised: M.subdolellus Staudinger, 1859, syn. n., M.tutti Walsingham, 1897, syn. n., and M.grossisquammellus Chrétien, 1925, syn. n. of M.lanceolellus (Zeller, 1850); M.culminicola Le Cerf, 1932, syn. n. of M.homochroa Le Cerf, 1932; M.separatellus (Fischer von Röslerstamm, 1843), syn. n. and M.incertellus Rebel, 1930, syn. n. of M.dolosellus (Zeller, 1839); M.mareotidellus Turati, 1924, syn. n. of M.numidellus (Chrétien, 1915); M.litovalvellus Junnilainen, 2010, syn. n. of M.imparellus (Fischer von Röslerstamm, 1843); M.kaszabianus Povolný, 1982, syn. n. of M.leuca (Filipjev, 1929); M.chretienella (Dumont, 1928), syn. n., M.halfella (Dumont, 1928), syn. n., and M.arnaldi (Turati &amp; Krüger, 1936), syn. n. of M.violacellum (Chrétien, 1915); M.escalerellus Schmidt, 1941, syn. n. of M.squalida Meyrick, 1926. Megacraspedusribbeella (Caradja, 1920), comb. n., M.numidellus (Chrétien, 1915), comb. n., M.albella (Amsel, 1935), comb. n., M.violacellum (Chrétien, 1915), comb. n., and M.grisea (Filipjev, 1931), comb. n. are newly combined in Megacraspedus.},
}
@article {pmid30530312,
year = {2020},
author = {Chevyrev, I and Nanda, V and Oberhauser, H},
title = {Persistence Paths and Signature Features in Topological Data Analysis.},
journal = {IEEE transactions on pattern analysis and machine intelligence},
volume = {42},
number = {1},
pages = {192-202},
doi = {10.1109/TPAMI.2018.2885516},
pmid = {30530312},
issn = {1939-3539},
abstract = {We introduce a new feature map for barcodes as they arise in persistent homology computation. The main idea is to first realize each barcode as a path in a convenient vector space, and to then compute its path signature which takes values in the tensor algebra of that vector space. The composition of these two operations-barcode to path, path to tensor series-results in a feature map that has several desirable properties for statistical learning, such as universality and characteristicness, and achieves state-of-the-art results on common classification benchmarks.},
}
@article {pmid30522008,
year = {2019},
author = {Thomsen, HA and Østergaard, JB},
title = {Loricate choanoflagellates (Acanthoecida) from warm water seas. I. Conioeca gen. nov. and Nannoeca Thomsen.},
journal = {European journal of protistology},
volume = {67},
number = {},
pages = {77-88},
doi = {10.1016/j.ejop.2018.11.001},
pmid = {30522008},
issn = {1618-0429},
mesh = {Animal Distribution ; Aquatic Organisms/*classification/*cytology ; Choanoflagellata/*classification/*cytology ; Seawater/parasitology ; Species Specificity ; Temperature ; },
abstract = {The main outcome of this and subsequent papers is to provide a baseline survey of heterotrophic protist diversity from warm water marine ecosystems, exemplified by loricate choanoflagellates (Acanthoecida). Loricate choanoflagellates are heterotrophic, nano-sized protists that are ubiquitous in marine and brackish water habitats. They dwell in a lorica formed by silicified costal strips organized in species specific patterns. The single anteriorly directed flagellum is surrounded by a collar formed by microvilli which together constitute the feeding apparatus. Keystone benefits from this warm water survey, which covers all three major oceans, is an improved understanding of global biogeographical patterns, and a further consolidation of the morphospecies matrix, that constitutes a highly essential reference framework for the current efforts to provide barcodes for as many species of loricate choanoflagellates as possible, based on e.g. single cell pipetting techniques. We describe here Conioeca gen. et sp. nov., which is so far distributionally confined to warm water habitats, and elaborate on the morphological variability encountered within the N. minuta complex. This leads to both the circumscription of a new N. minuta form A as well as the description of N. mexicana sp. nov.},
}
@article {pmid30520467,
year = {2019},
author = {Tortajada-Genaro, LA and Niñoles, R and Mena, S and Maquieira, &#xc1;},
title = {Digital versatile discs as platforms for multiplexed genotyping based on selective ligation and universal microarray detection.},
journal = {The Analyst},
volume = {144},
number = {2},
pages = {707-715},
doi = {10.1039/c8an01830h},
pmid = {30520467},
issn = {1364-5528},
mesh = {Genomics ; Genotyping Techniques/*instrumentation ; *Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide ; },
abstract = {The development of a high-performance assay readout using integrated detectors is a current challenge in the implementation of DNA tests in diagnostic laboratories, particularly for supporting pharmacogenetic tests. A method for allelic discrimination, associated with single nucleotide polymorphisms (SNPs), is presented. Genomic DNA is extracted from blood and buccal swab samples. The procedure comprises fast multiplex ligation-dependent probe amplification, PCR amplification using universal primers and subsequent barcode hybridization. In this last step, each product is recognized by the specific probes immobilized on the surface of an optical disc. Assay results can be obtained with a disc reader. The optical sensing method in a DNA microarray format was optimized and evaluated for the simultaneous identification of 28 polymorphisms associated with psychiatric pharmacogenomics. The target biomarkers were located in the genes related to drug-metabolizing enzymes and drug transporters. The multiplexing capability and assay selectivity strongly depended on correct design (ligation probes, tails and barcodes). The discriminant analysis of reader outputs (spot intensities) led to patients being classified into different allelic populations. The obtained assignations correlated properly with the results provided by the reference technique (bead arrays), and the assay ended in an 8-fold shorter time using affordable equipment. The combination of a highly selective genotyping reaction as array-MLPA and the compact disc technology provides a reliable point-of-care approach. This genotyping tool is useful for the selection of personalized drug therapies in decentralized clinical laboratories.},
}
@article {pmid30519651,
year = {2018},
author = {Kaya, S and Çıplak, B},
title = {Possibility of numt co-amplification from gigantic genome of Orthoptera: testing efficiency of standard PCR protocol in producing orthologous COI sequences.},
journal = {Heliyon},
volume = {4},
number = {11},
pages = {e00929},
pmid = {30519651},
issn = {2405-8440},
abstract = {Mitochondrial DNA has been the preferential genome biodiversity studies. However, several factors contribute to its inadequacy. Numts constitute one of the main complications that prevent obtaining orthologous mitochondrial sequences. Orthoptera have been a model group in numt studies because of their huge genome size. In this study we aimed to; (i) test efficiency of standard PCR protocol in producing orthologous sequences of cytochrome C oxidase, (ii) study presence/absence of numts in several unstudied Orthoptera species, (iii) test if there is a threshold between the length of mtDNA targeted for amplification and possibility of encountering numts, and (iv) estimate reliability of the sequences in databases in light of these findings. For these aims we studied 38 species of Orthoptera representing different sublineages and genome sizes. DNA extracted from each sample was used to amplify five different fragments of COI region by standard PCR protocol. Sequenced PCR amplicons were checked for numt possibility by several different numt criteria. No sequences without numt signs were obtained for the first fragment. The number of samples with numt signs for the other four fragments differed between the suborders Ensifera and Caelifera. The percentage of samples with numt signs was higher in Caelifera than Ensifera for all fragments. The numt percentage considerably decreased for the longest two fragments. Numts are more prevalent in families with larger genome size. We arrived at the following conclusions: (i) numts are common in all members of Orthoptera, but, their prevalence differs among intra-lineages, especially more prevalent in Caelifera, (ii) there seems a correlation between numt rate and genome size, (iii) there is no threshold to avoid numt co-amplification, but, a 1,000 bp length may be a threshold for Ensifera, (iv) Folmer region of COI doesn't seem an appropriate marker for animal barcoding. Additionally, a phylogenetic tree produced from the numt sequences of fragment four detected in genus Anterastes suggested a paleonumt gained in generic ancestor a 3.5-4 times slower divergence rate for numt sequences.},
}
@article {pmid30519409,
year = {2018},
author = {Šarhanová, P and Pfanzelt, S and Brandt, R and Himmelbach, A and Blattner, FR},
title = {SSR-seq: Genotyping of microsatellites using next-generation sequencing reveals higher level of polymorphism as compared to traditional fragment size scoring.},
journal = {Ecology and evolution},
volume = {8},
number = {22},
pages = {10817-10833},
pmid = {30519409},
issn = {2045-7758},
abstract = {Microsatellites (or simple sequence repeats, SSR) are widely used markers in population genetics. Traditionally, genotyping was and still is carried out through recording fragment length. Now, next-generation sequencing (NGS) makes it easy to obtain also sequence information for the loci of interest. This avoids misinterpretations that otherwise could arise due to size homoplasy. Here, an NGS strategy is described that allows to genotype hundreds of individuals at many custom-designed SSR loci simultaneously, combining multiplex PCR, barcoding, and Illumina sequencing. We created three different datasets for which alleles were coded according to (a) length of the repetitive region, (b) total fragment length, and (c) sequence identity, in order to evaluate the eventual benefits from having sequence data at hand, not only fragment length data. For each dataset, genetic diversity statistics, as well as F ST and R ST values, were calculated. The number of alleles per locus, as well as observed and expected heterozygosity, was highest in the sequence identity dataset, because of single-nucleotide polymorphisms and insertions/deletions in the flanking regions of the SSR motif. Size homoplasy was found to be very common, amounting to 44.7%-63.5% (mean over all loci) in the three study species. Thus, the information obtained by next-generation sequencing offers a better resolution than the traditional way of SSR genotyping and allows for more accurate evolutionary interpretations.},
}
@article {pmid30507127,
year = {2018},
author = {Preiss, J and Kage, D and Hoffmann, K and Martínez, TJ and Resch-Genger, U and Presselt, M},
title = {Ab Initio Prediction of Fluorescence Lifetimes Involving Solvent Environments by Means of COSMO and Vibrational Broadening.},
journal = {The journal of physical chemistry. A},
volume = {122},
number = {51},
pages = {9813-9820},
doi = {10.1021/acs.jpca.8b08886},
pmid = {30507127},
issn = {1520-5215},
abstract = {The fluorescence lifetime is a key property of fluorophores that can be utilized for microenvironment probing, analyte sensing, and multiplexing as well as barcoding applications. For the rational design of lifetime probes and barcodes, theoretical methods have been developed to enable the ab initio prediction of this parameter, which depends strongly on interactions with solvent molecules and other chemical species in the emitteŕs immediate environment. In this work, we investigate how a conductor-like screening model (COSMO) can account for variations in fluorescence lifetimes that are caused by such fluorophore-solvent interactions. Therefore, we calculate vibrationally broadened fluorescence spectra using the nuclear ensemble method to obtain distorted molecular geometries to sample the electronic transitions with time-dependent density functional theory (TDDFT). The influence of the solvent on fluorescence lifetimes is accounted for with COSMO. For example, for 4-hydroxythiazole fluorophore containing different heteroatoms and acidic and basic moieties in aprotic and protic solvents of varying polarity, this approach was compared to experimentally determined lifetimes in the same solvents. Our results demonstrate a good correlation between theoretically predicted and experimentally measured fluorescence lifetimes except for the polar solvents ethanol and acetonitrile that can specifically interact with the heteroatoms and the carboxylic acid of the thiazole derivative.},
}
@article {pmid30506979,
year = {2019},
author = {Rennstam Rubbmark, O and Sint, D and Cupic, S and Traugott, M},
title = {When to use next generation sequencing or diagnostic PCR in diet analyses.},
journal = {Molecular ecology resources},
volume = {19},
number = {2},
pages = {388-399},
pmid = {30506979},
issn = {1755-0998},
support = {P26144//Austrian Science Fund/ ; //(FWF)/ ; },
mesh = {Animals ; *Feeding Behavior ; High-Throughput Nucleotide Sequencing/*methods ; Polymerase Chain Reaction/*methods ; },
abstract = {Next-generation sequencing (NGS) is increasingly used for diet analyses; however, it may not always describe diet samples well. A reason for this is that diet samples contain mixtures of food DNA in different amounts as well as consumer DNA which can reduce the food DNA characterized. Because of this, detections will depend on the relative amount and identity of each type of DNA. For such samples, diagnostic PCR will most likely give more reliable results, as detection probability is only marginally dependent on other copresent DNA. We investigated the reliability of each method to test (a) whether predatory beetle regurgitates, supposed to be low in consumer DNA, allow to retrieve prey sequences using general barcoding primers that co-amplify the consumer DNA, and (b) to assess the sequencing depth or replication needed for NGS and diagnostic PCR to give stable results. When consumer DNA is co-amplified, NGS is better suited to discover the range of possible prey, than for comparing co-occurrences of diet species between samples, as retested samples were repeatedly different in prey detections with this approach. This shows that samples were incompletely described, as prey detected by diagnostic PCR frequently were missed by NGS. As the sequencing depth needed to reliably describe the diet in such samples becomes very high, the cost-efficiency and reliability of diagnostic PCR make diagnostic PCR better suited for testing large sample-sets. Especially if the targeted prey taxa are thought to be of ecological importance, as diagnostic PCR gave more nested and consistent results in repeated testing of the same sample.},
}
@article {pmid30505003,
year = {2018},
author = {Crous, PW and Wingfield, MJ and Burgess, TI and Hardy, GESJ and Gené, J and Guarro, J and Baseia, IG and García, D and Gusmão, LFP and Souza-Motta, CM and Thangavel, R and Adamčík, S and Barili, A and Barnes, CW and Bezerra, JDP and Bordallo, JJ and Cano-Lira, JF and de Oliveira, RJV and Ercole, E and Hubka, V and Iturrieta-González, I and Kubátová, A and Martín, MP and Moreau, PA and Morte, A and Ordoñez, ME and Rodríguez, A and Stchigel, AM and Vizzini, A and Abdollahzadeh, J and Abreu, VP and Adamčíková, K and Albuquerque, GMR and Alexandrova, AV and Álvarez Duarte, E and Armstrong-Cho, C and Banniza, S and Barbosa, RN and Bellanger, JM and Bezerra, JL and Cabral, TS and Caboň, M and Caicedo, E and Cantillo, T and Carnegie, AJ and Carmo, LT and Castañeda-Ruiz, RF and Clement, CR and Čmoková, A and Conceição, LB and Cruz, RHSF and Damm, U and da Silva, BDB and da Silva, GA and da Silva, RMF and de A Santiago, ALCM and de Oliveira, LF and de Souza, CAF and Déniel, F and Dima, B and Dong, G and Edwards, J and Félix, CR and Fournier, J and Gibertoni, TB and Hosaka, K and Iturriaga, T and Jadan, M and Jany, JL and Jurjević, &#x17d; and Kolařík, M and Kušan, I and Landell, MF and Leite Cordeiro, TR and Lima, DX and Loizides, M and Luo, S and Machado, AR and Madrid, H and Magalhães, OMC and Marinho, P and Matočec, N and Mešić, A and Miller, AN and Morozova, OV and Neves, RP and Nonaka, K and Nováková, A and Oberlies, NH and Oliveira-Filho, JRC and Oliveira, TGL and Papp, V and Pereira, OL and Perrone, G and Peterson, SW and Pham, THG and Raja, HA and Raudabaugh, DB and Řehulka, J and Rodríguez-Andrade, E and Saba, M and Schauflerová, A and Shivas, RG and Simonini, G and Siqueira, JPZ and Sousa, JO and Stajsic, V and Svetasheva, T and Tan, YP and Tkalčec, Z and Ullah, S and Valente, P and Valenzuela-Lopez, N and Abrinbana, M and Viana Marques, DA and Wong, PTW and Xavier de Lima, V and Groenewald, JZ},
title = {Fungal Planet description sheets: 716-784.},
journal = {Persoonia},
volume = {40},
number = {},
pages = {240-393},
pmid = {30505003},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Chaetopsina eucalypti on Eucalyptus leaf litter, Colletotrichum cobbittiense from Cordyline stricta × C. australis hybrid, Cyanodermella banksiae on Banksia ericifolia subsp. macrantha, Discosia macrozamiae on Macrozamia miquelii, Elsinoë banksiigena on Banksia marginata, Elsinoë elaeocarpi on Elaeocarpus sp., Elsinoë leucopogonis on Leucopogon sp., Helminthosporium livistonae on Livistona australis, Idriellomyces eucalypti (incl. Idriellomyces gen. nov.) on Eucalyptus obliqua, Lareunionomyces eucalypti on Eucalyptus sp., Myrotheciomyces corymbiae (incl. Myrotheciomyces gen. nov., Myrotheciomycetaceae fam. nov.), Neolauriomyces eucalypti (incl. Neolauriomyces gen. nov., Neolauriomycetaceae fam. nov.) on Eucalyptus sp., Nullicamyces eucalypti (incl. Nullicamyces gen. nov.) on Eucalyptus leaf litter, Oidiodendron eucalypti on Eucalyptus maidenii, Paracladophialophora cyperacearum (incl. Paracladophialophoraceae fam. nov.) and Periconia cyperacearum on leaves of Cyperaceae, Porodiplodia livistonae (incl. Porodiplodia gen. nov., Porodiplodiaceae fam. nov.) on Livistona australis, Sporidesmium melaleucae (incl. Sporidesmiales ord. nov.) on Melaleuca sp., Teratosphaeria sieberi on Eucalyptus sieberi, Thecaphora australiensis in capsules of a variant of Oxalis exilis. Brazil, Aspergillus serratalhadensis from soil, Diaporthe pseudoinconspicua from Poincianella pyramidalis, Fomitiporella pertenuis on dead wood, Geastrum magnosporum on soil, Marquesius aquaticus (incl. Marquesius gen. nov.) from submerged decaying twig and leaves of unidentified plant, Mastigosporella pigmentata from leaves of Qualea parviflorae, Mucor souzae from soil, Mycocalia aquaphila on decaying wood from tidal detritus, Preussia citrullina as endophyte from leaves of Citrullus lanatus, Queiroziella brasiliensis (incl. Queiroziella gen. nov.) as epiphytic yeast on leaves of Portea leptantha, Quixadomyces cearensis (incl. Quixadomyces gen. nov.) on decaying bark, Xylophallus clavatus on rotten wood. Canada, Didymella cari on Carum carvi and Coriandrum sativum. Chile, Araucasphaeria foliorum (incl. Araucasphaeria gen. nov.) on Araucaria araucana, Aspergillus tumidus from soil, Lomentospora valparaisensis from soil. Colombia, Corynespora pseudocassiicola on Byrsonima sp., Eucalyptostroma eucalyptorum on Eucalyptus pellita, Neometulocladosporiella eucalypti (incl. Neometulocladosporiella gen. nov.) on Eucalyptus grandis × urophylla, Tracylla eucalypti (incl. Tracyllaceae fam. nov., Tracyllalales ord. nov.) on Eucalyptus urophylla. Cyprus, Gyromitra anthracobia (incl. Gyromitra subg. Pseudoverpa) on burned soil. Czech Republic, Lecanicillium restrictum from the surface of the wooden barrel, Lecanicillium testudineum from scales of Trachemys scripta elegans. Ecuador, Entoloma yanacolor and Saproamanita quitensis on soil. France, Lentithecium carbonneanum from submerged decorticated Populus branch. Hungary, Pleuromyces hungaricus (incl. Pleuromyces gen. nov.) from a large Fagus sylvatica log. Iran, Zymoseptoria crescenta on Aegilops triuncialis. Malaysia, Ochroconis musicola on Musa sp. Mexico, Cladosporium michoacanense from soil. New Zealand , Acrodontium metrosideri on Metrosideros excelsa, Polynema podocarpi on Podocarpus totara, Pseudoarthrographis phlogis (incl. Pseudoarthrographis gen. nov.) on Phlox subulata. Nigeria, Coprinopsis afrocinerea on soil. Pakistan, Russula mansehraensis on soil under Pinus roxburghii. Russia, Baorangia alexandri on soil in deciduous forests with Quercus mongolica. South Africa, Didymocyrtis brachylaenae on Brachylaena discolor. Spain, Alfaria dactylis from fruit of Phoenix dactylifera, Dothiora infuscans from a blackened wall, Exophiala nidicola from the nest of an unidentified bird, Matsushimaea monilioides from soil, Terfezia morenoi on soil. United Arab Emirates, Tirmania honrubiae on soil. USA, Arxotrichum wyomingense (incl. Arxotrichum gen. nov.) from soil, Hongkongmyces snookiorum from submerged detritus from a fresh water fen, Leratiomyces tesquorum from soil, Talaromyces tabacinus on leaves of Nicotiana tabacum. Vietnam, Afroboletus vietnamensis on soil in an evergreen tropical forest, Colletotrichum condaoense from Ipomoea pes-caprae. Morphological and culture characteristics along with DNA barcodes are provided.},
}
@article {pmid30505000,
year = {2018},
author = {Barnes, I and Fourie, A and Wingfield, MJ and Harrington, TC and McNew, DL and Sugiyama, LS and Luiz, BC and Heller, WP and Keith, LM},
title = {New Ceratocystis species associated with rapid death of Metrosideros polymorpha in Hawai'i.},
journal = {Persoonia},
volume = {40},
number = {},
pages = {154-181},
pmid = {30505000},
issn = {0031-5850},
abstract = {The native 'ōhi'a lehua (Metrosideros polymorpha) has cultural, biological and ecological significance to Hawai'i, but it is seriously threatened by a disease commonly referred to as rapid 'ōhi'a death (ROD). Preliminary investigations showed that a Ceratocystis species similar to C. fimbriata s.lat. was the cause of the disease. In this study, we used a combination of the phylogenetic, morphological and biological species concepts, as well as pathogenicity tests and microsatellite analyses, to characterise isolates collected from diseased 'ōhi'a trees across Hawai'i Island. Two distinct lineages, representing new species of Ceratocystis, were evident based on multigene phylogenetic analyses. These are described here as C. lukuohia and C. huliohia. Ceratocystis lukuohia forms part of the Latin American clade (LAC) and was most closely associated with isolates from Syngonium and Xanthosoma from the Caribbean and elsewhere, including Hawai'i, and C. platani, which is native to eastern USA. Ceratocystis huliohia resides in the Asian-Australian clade (AAC) and is most closely related to C. uchidae, C. changhui and C. cercfabiensis, which are thought to be native to Asia. Morphology and interfertility tests support the delineation of these two new species and pathogenicity tests show that both species are aggressive pathogens on seedlings of M. polymorpha. Characterisation of isolates using microsatellite markers suggest that both species are clonal and likely represent recently-introduced strains. Intensive research is underway to develop rapid screening protocols for early detection of the pathogens and management strategies in an attempt to prevent the spread of the pathogens to the other islands of Hawai'i, which are currently disease free.},
}
@article {pmid30504877,
year = {2018},
author = {Nawy, T},
title = {Protein-based cell barcodes.},
journal = {Nature methods},
volume = {15},
number = {12},
pages = {1002},
doi = {10.1038/s41592-018-0250-5},
pmid = {30504877},
issn = {1548-7105},
mesh = {*Clustered Regularly Interspaced Short Palindromic Repeats ; *DNA Barcoding, Taxonomic ; },
}
@article {pmid30502138,
year = {2019},
author = {Zhao, J and Xu, Z and You, X and Zhao, Y and He, W and Zhao, L and Chen, A and Yang, S},
title = {Genetic traceability practices in a large-size beef company in China.},
journal = {Food chemistry},
volume = {277},
number = {},
pages = {222-228},
doi = {10.1016/j.foodchem.2018.10.007},
pmid = {30502138},
issn = {1873-7072},
mesh = {Animals ; Cattle/*genetics ; China ; DNA/genetics ; *Food Safety ; *Food Supply ; Genetic Loci/genetics ; Genotype ; Polymorphism, Single Nucleotide ; *Red Meat ; },
abstract = {An effective and trustworthy traceability system is important for food safety and quality; however, traditional traceability systems that only rely on the recording method do not completely prevent food fraud. DNA-based traceability techniques facilitate seamless connectivity within the entire food supply chain. A convenient and low-cost ear tag device was invented for collecting animal blood samples as an identity control, and a panel including 12 single nucleotide polymorphic (SNP) loci was selected to distinguish individuals with a matching probability of 1.70 × 10[-5]. The exact animal individual was identified by comparing the SNP genotype barcodes between the meat and blood samples derived from the recording system to further validate authenticity of the recording system. These results illustrate that a combination of the genetic traceability method and a traditional recording system can provide trustworthy traceability for consumers.},
}
@article {pmid30517131,
year = {2018},
author = {Litchfield, CA and Lowry, R and Dorrian, J},
title = {Recycling 115,369 mobile phones for gorilla conservation over a six-year period (2009-2014) at Zoos Victoria: A case study of 'points of influence' and mobile phone donations.},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0206890},
pmid = {30517131},
issn = {1932-6203},
mesh = {Animals ; Cell Phone/economics/instrumentation ; Conservation of Natural Resources ; Data Collection ; Equipment Reuse/*economics ; Gorilla gorilla ; Humans ; Recycling/*methods ; Victoria ; },
abstract = {More than seven billion mobile phones are estimated to be in service globally, with more than a billion older phones likely to be retired. A major barrier to a sustainable circular economy for mobile phones is people's hoarding of their retired phones. Old mobile phones may be refurbished for re-use or ultimately dismantled for possible extraction of elements, including 'conflict' metals such as coltan (containing elements tantalum and niobium), mined in eastern Democratic Republic of Congo and threatening wild populations of eastern Grauer's gorillas (Gorilla beringei graueri). Zoos Victoria cares for western gorillas (Gorilla gorilla gorilla) who served as ambassadors for their Grauer's gorilla counterparts in this community-based social marketing initiative. Through tracking of barcodes on satchels of recycled mobile phones, efficiency of ten different points of influence could be calculated for the 'They're Calling on You' mobile phone recycling community campaign at Zoos Victoria in Australia. Over a six-year period (2009-2014), a total of 115,369 mobile phones were donated. The Courier Collect initiative resulted in 50,883 mobile phone donations (44% of total), followed by the Static Display at Melbourne Zoo, resulting in 29,778 mobile phone donations (26% of total). The number of phones collected for Keeper Talks (at Melbourne Zoo and Werribee Open Range Zoo) was 12,684 (11% of total), and in terms of fostering close connections between visitors and the conservation campaign, keeper talks were effective as one phone was donated for every four people attending a keeper talk at Werribee Open Range Zoo and one phone was donated for every 28 people who attended a keeper talk at Melbourne Zoo. We provide suggestions for future campaigns, so that accurate data capture can allow cost-benefit analyses to be conducted. Our results demonstrate that a conservation-based organisation, in partnership with corporate sponsors and community groups can effectively influenced people's mobile phone recycling behavior, paving the way for international collaborations to maximize scale and impact.},
}
@article {pmid30514408,
year = {2019},
author = {Torres-Vila, LM and Bonal, R},
title = {DNA barcoding of large oak-living cerambycids: diagnostic tool, phylogenetic insights and natural hybridization between Cerambyx cerdo and Cerambyx welensii (Coleoptera: Cerambycidae).},
journal = {Bulletin of entomological research},
volume = {109},
number = {5},
pages = {583-594},
doi = {10.1017/S0007485318000925},
pmid = {30514408},
issn = {1475-2670},
mesh = {Animals ; Coleoptera/*classification/*genetics ; DNA Barcoding, Taxonomic/methods ; Electron Transport Complex IV/genetics ; Genes, Insect ; Genotype ; Hybridization, Genetic ; Life Cycle Stages/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; Spain ; Species Specificity ; },
abstract = {Three large saproxylic cerambycids with different pest/legal status co-occur in the Iberian oak woodlands, Cerambyx welensii (Cw), Cerambyx cerdo (Cc) and Prinobius myardi (Pm): Cw is an emerging pest, Cc is a protected but sometimes harmful species and Pm is a secondary/minor pest. A precise taxonomic diagnosis is necessary for research, management or protection purposes, but may be problematic mainly because Cw and Cc larvae are morphologically indistinguishable. To resolve this constraint, we genotyped adults, larvae and eggs collected over a wide geographical range using the mitochondrial barcoding of the cytochrome c oxidase subunit I (COI). A Neighbour-Joining tree phylogram revealed three distinct clusters corresponding to Cw, Cc and Pm. We further first sequenced for Cw and Cc two mitochondrial (12S rRNA and 16S rRNA) and one nuclear (28S rRNA) gene fragments. For the first two genes, interspecific divergence was lower than in COI, and for the 28S (lower mutation rate), the two species shared identical haplotypes. Two approaches for species delimitation (General Mixed Yule Coalescent (GMYC), Barcode Index Number (BIN)) confirmed the species distinctiveness of Cc and Cw. The Bayesian COI gene tree showed a remarkable genetic divergence between Cc populations from Iberia and the rest of Europe. Such divergence has relevant taxonomic connotations and stresses the importance of a wide geographical scale sampling for accurate DNA barcoding species identification. Incongruities between morphology/lineage and COI barcodes in some individuals revealed natural hybridization between Cw and Cc. Natural hybridization is important from a phylogenetic/evolutionary perspective in these cerambycids, but the prevalence of (and the behavioural/ecological factors involved in) interspecific cross-breeding remain to be investigated.},
}
@article {pmid30513666,
year = {2018},
author = {Veldman, S and Kim, SJ and van Andel, TR and Bello Font, M and Bone, RE and Bytebier, B and Chuba, D and Gravendeel, B and Martos, F and Mpatwa, G and Ngugi, G and Vinya, R and Wightman, N and Yokoya, K and de Boer, HJ},
title = {Trade in Zambian Edible Orchids-DNA Barcoding Reveals the Use of Unexpected Orchid Taxa for Chikanda.},
journal = {Genes},
volume = {9},
number = {12},
pages = {},
pmid = {30513666},
issn = {2073-4425},
support = {23034//Darwin Initiative (UK Government)/ ; W 02.29.102//NWO-SIDA-COSTECH/ ; },
abstract = {In Zambia, wild edible terrestrial orchids are used to produce a local delicacy called chikanda, which has become increasingly popular throughout the country. Commercialization puts orchid populations in Zambia and neighbouring countries at risk of overharvesting. Hitherto, no study has documented which orchid species are traded on local markets, as orchid tubers are difficult to identify morphologically. In this study, the core land-plant DNA barcoding markers rbcL and matK were used in combination with nrITS to determine which species were sold in Zambian markets. Eighty-two interviews were conducted to determine harvesting areas, as well as possible sustainability concerns. By using nrITS DNA barcoding, a total of 16 orchid species in six different genera could be identified. Both rbcL and matK proved suitable to identify the tubers up to the genus or family level. Disa robusta, Platycoryne crocea and Satyrium buchananii were identified most frequently and three previously undocumented species were encountered on the market. Few orchid species are currently listed on the global International Union for the Conservation of Nature (IUCN) Red List. Local orchid populations and endemic species could be at risk of overharvesting due to the intensive and indiscriminate harvesting of chikanda orchids, and we therefore encourage increased conservation assessment of terrestrial African orchids.},
}
@article {pmid30513195,
year = {2019},
author = {Herrmann, AK and Bender, C and Kienle, E and Grosse, S and El Andari, J and Botta, J and Schürmann, N and Wiedtke, E and Niopek, D and Grimm, D},
title = {A Robust and All-Inclusive Pipeline for Shuffling of Adeno-Associated Viruses.},
journal = {ACS synthetic biology},
volume = {8},
number = {1},
pages = {194-206},
doi = {10.1021/acssynbio.8b00373},
pmid = {30513195},
issn = {2161-5063},
mesh = {Dependovirus/*genetics ; Evolution, Molecular ; Gene Transfer Techniques ; Genetic Vectors/*genetics ; },
abstract = {Adeno-associated viruses (AAV) are attractive templates for engineering of synthetic gene delivery vectors. A particularly powerful technology for breeding of novel vectors with improved properties is DNA family shuffling, i.e., generation of chimeric capsids by homology-driven DNA recombination. Here, to make AAV DNA shuffling available to a wider community, we present a robust experimental and bioinformatical pipeline comprising: (i) standardized and partially codon-optimized plasmids carrying 12 different AAV capsid genes; (ii) a scalable protocol including troubleshooting guide for viral library production; and (iii) the freely available software SALANTO for comprehensive analysis of chimeric AAV DNA and protein sequences. Moreover, we describe a set of 12 premade and ready-to-use AAV libraries. Finally, we demonstrate the usefulness of DNA barcoding technology to trace AAV capsid libraries within a complex mixture. Our protocols and resources facilitate the implementation and tailoring of AAV evolution technology in any laboratory interested in customized viral gene transfer.},
}
@article {pmid30510468,
year = {2018},
author = {Daly-Engel, TS and Koch, A and Anderson, JM and Cotton, CF and Rubbs, RD},
title = {Description of a new deep-water dogfish shark from Hawaii, with comments on the Squalusmitsukurii species complex in the West Pacific.},
journal = {ZooKeys},
volume = {},
number = {798},
pages = {135-157},
pmid = {30510468},
issn = {1313-2989},
support = {K12 GM000708/GM/NIGMS NIH HHS/United States ; },
abstract = {Dogfish sharks of the genus Squalus are small, deep-water sharks with a slow rate of molecular evolution that has led to their designation as a series of species complexes, with low between-species diversity relative to other taxa. The largest of these complexes is named for the Shortspine spurdog (Squalusmitsukurii Jordan &amp; Snyder), a medium-sized dogfish shark common to warm upper slope and seamount habitats, with a putative circumglobal distribution that has come under investigation recently due to geographic variation in morphology and genetic diversity. The Hawaiian population of Squalusmitsukurii was examined using both morphological and molecular analyses, putting this group in an evolutionary context with animals from the type population in Japan and closely-related congeners. External morphology differs significantly between the Hawaiian and Japanese S.mitsukurii, especially in dorsal fin size and relative interdorsal length, and molecular analysis of 1,311 base pairs of the mitochondrial genes ND2 and COI show significant, species-level divergence on par with other taxonomic studies of this genus. The dogfish shark in Hawaii represents a new species in the genus, and the name Squalushawaiiensis, the Hawaiian spurdog, is designated after the type location.},
}
@article {pmid30510466,
year = {2018},
author = {Tang, C and Yang, D and Grootaert, P},
title = {Revision of the genus Lichtwardtia Enderlein in Southeast Asia, a tale of highly diverse male terminalia (Diptera, Dolichopodidae).},
journal = {ZooKeys},
volume = {},
number = {798},
pages = {63-107},
pmid = {30510466},
issn = {1313-2989},
abstract = {In the present paper the Oriental species of the genus Lichtwardtia Enderlein, 1912 are revised based on the type material of known species and new material from Singapore and Cambodia. A re-description and illustration of the holotype female of Lichtwardtiaziczac (Wiedemann, 1824) is given but since it has been described on the basis of a female only and its provenance India Orientalis is only a vague indication of its type locality, it is considered as a nomen dubium. All the species put as junior synonyms by Becker (1922) of L.ziczac are re-established to their original status with diagnosis: Lichtwardtiapolychroma (Loew, 1864) and Lichtwardtiaformosana Enderlein, 1912. However, L.coxalis is now also considered as a nomen dubium since the original description is too short to distinguish it from other species and the holotype female is lost. In addition a re-description and illustrations of L.hirsutiseta (de Meijere, 1916) are provided. Eight new species for science are described and illustrated: Lichtwardtiacambodiensis Tang &amp; Grootaert, sp. n. (Cambodia), Lichtwardtiaconspicabilis Tang &amp; Grootaert, sp. n. (Cambodia), Lichtwardtiainfuscata Tang &amp; Grootaert, sp. n. (Cambodia), Lichtwardtiamonstruosa Tang &amp; Grootaert, sp. n. (Cambodia), Lichtwardtianodulata Grootaert &amp; Tang, sp. n. (Singapore), Lichtwardtiasemakau Grootaert &amp; Tang, sp. n. (Singapore) and Lichtwardtiasingaporensis Grootaert &amp; Tang, sp. n. (Singapore). Lichtwardtiazhangae Tang &amp; Grootaert, sp. n. (Bali, Indonesia) is a new name for the species described by Zhang, Masunaga &amp; Yang, 2009, as Lichtwardtiaziczac (Wiedemann, 1824). There are only a few good diagnostic non-genitalic characters for the species, but the male terminalia are distinctive, from simple to very complicated and armed structures. A key is given to the species of the Oriental region. Barcodes are provided for the Singaporean species. Although Lichtwardtia is a common genus in Southeast Asia it is generally not abundant locally. It is often found in anthropogenic disturbed habitats only. Four species are recorded from Singapore while eight species are sympatric and very abundant at the locality of Siem Reap in Cambodia.},
}
@article {pmid30509304,
year = {2018},
author = {Bakhoum, MT and Sarr, M and Fall, AG and Huber, K and Fall, M and Sembène, M and Seck, MT and Labuschagne, K and Gardès, L and Ciss, M and Gimonneau, G and Bouyer, J and Baldet, T and Garros, C},
title = {DNA barcoding and molecular identification of field-collected Culicoides larvae in the Niayes area of Senegal.},
journal = {Parasites &amp; vectors},
volume = {11},
number = {1},
pages = {615},
pmid = {30509304},
issn = {1756-3305},
mesh = {Animals ; Biodiversity ; Ceratopogonidae/*classification/genetics ; Cyclooxygenase 1/genetics ; *DNA Barcoding, Taxonomic ; Insect Proteins/genetics ; Insect Vectors/*classification/genetics ; Larva/*classification/genetics ; Senegal ; },
abstract = {BACKGROUND: Biting midge species of the genus Culicoides Latreille (Diptera: Ceratopogonidae) comprise more than 1300 species distributed worldwide. Several species of Culicoides are vectors of various viruses that can affect animals, like the African horse sickness virus (AHSV), known to be endemic in sub-Saharan Africa. The ecological and veterinary interest of Culicoides emphasizes the need for rapid and reliable identification of vector species. However, morphology-based identification has limitations and warrants integration of molecular data. DNA barcoding based on the mitochondrial gene cytochrome c oxidase subunit 1 (cox1) is used as a rapid and authentic tool for species identification in a wide variety of animal taxa across the globe. In this study, our objectives were as follows: (i) establish a reference DNA barcode for Afrotropical Culicoides species; (ii) assess the accuracy of cox1 in identifying Afrotropical Culicoides species; and (iii) test the applicability of DNA barcoding for species identification on a large number of samples of Culicoides larvae from the Niayes area of Senegal, West Africa.<br><br>RESULTS: A database of 230 cox1 sequences belonging to 42 Afrotropical Culicoides species was found to be reliable for species-level assignments, which enabled us to identify cox1 sequences of Culicoides larvae from the Niayes area of Senegal. Of the 933 cox1 sequences of Culicoides larvae analyzed, 906 were correctly identified by their barcode sequences corresponding to eight species of Culicoides. A total of 1131 cox1 sequences of adult and larval Culicoides were analyzed, and a hierarchical increase in mean divergence was observed according to two taxonomic levels: within species (mean = 1.92%, SE = 0.00), and within genus (mean = 17.82%, SE = 0.00).<br><br>CONCLUSIONS: Our study proves the efficiency of DNA barcoding for studying Culicoides larval diversity in field samples. Such a diagnostic tool offers great opportunities for investigating Culicoides immature stages ecology and biology, a prerequisite for the implementation of eco-epidemiological studies to better control AHSV in the Niayes region of Senegal, and more generally in sub-Saharan Africa.},
}
@article {pmid30496721,
year = {2019},
author = {Takaoka, H and Low, VL and Tan, TK and Sofian-Azirun, M and Chen, CD and Lau, KW and Pham, XD},
title = {A new black fly species of Simulium (Nevermannia) (Diptera: Simuliidae) from Vietnam.},
journal = {Acta tropica},
volume = {190},
number = {},
pages = {320-328},
doi = {10.1016/j.actatropica.2018.11.025},
pmid = {30496721},
issn = {1873-6254},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Eye/*anatomy &amp; histology ; Female ; Male ; Simuliidae/*classification/genetics ; Tooth/*anatomy &amp; histology ; Vietnam ; },
abstract = {Simulium pumatense sp. nov. is described from Vietnam, and is placed in the Simulium feuerborni species-group of the subgenus Simulium (Nevermannia) Enderlein. Its morphological characteristics include the relatively smaller numbers of the following three numerical features: inner teeth of the female mandible (15-18), minute conical processes (16) on the female cibarium, and male upper-eye facets (in 15 vertical columns and 16 horizontal rows). Keys are constructed to distinguish this species from four species of the same group in Vietnam. Our molecular analysis of the DNA barcoding COI gene shows that this species is most closely related to cytoform A of the S. feuerborni complex from Thailand.},
}
@article {pmid30489223,
year = {2018},
author = {San-Fabian, B and Niskanen, T and Liimatainen, K and Kooij, PW and Mujic, AB and Truong, C and Peintner, U and Dresch, P and Nouhra, E and Matheny, PB and Smith, ME},
title = {New species of Cortinarius sect. Austroamericani, sect. nov., from South American Nothofagaceae forests.},
journal = {Mycologia},
volume = {110},
number = {6},
pages = {1127-1144},
doi = {10.1080/00275514.2018.1515449},
pmid = {30489223},
issn = {1557-2536},
mesh = {Chile ; Cortinarius/*classification/isolation &amp; purification ; DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Fagales ; *Forests ; Genetic Variation ; Mycological Typing Techniques ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {In this study, we document and describe the new Cortinarius section Austroamericani. Our results reveal high species diversity within this clade, with a total of 12 recognized species. Of these, only C. rufus was previously documented. Seven species are described as new based on basidiomata collections. The four remaining species are only known from environmental sequences. All examined species form ectomycorrhizal associations with species of Nothofagaceae and are currently only known from Argentinean and Chilean Patagonia. The phylogenetic analysis based on the nuc rDNA internal transcriber spacer (ITS1-5.8S-ITS2 = ITS) and partial 28S gene (28S) sequences shows that this section is related to other taxa from the Southern Hemisphere. Species in this group do not belong to subg. Telamonia, where C. rufus was initially placed. Cortinarius rufus and the newly described C. subrufus form a basal clade within sect. Austroamericani that has a weakly supported relationship with the core clade. Because the two species are morphologically similar to species from the core clade and share their distribution and Nothofagaceae associations, we include them here as part of sect. Austroamericani sensu lato (s.l.) until more material is available to refine the delimitation.},
}
@article {pmid30486530,
year = {2018},
author = {Wang, H and Shi, LL and Zhou, J and Zhu, GP},
title = {[DNA barcoding identification of Dendrobium huoshanense and its adulterants].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {43},
number = {20},
pages = {4055-4061},
doi = {10.19540/j.cnki.cjcmm.2018.0107},
pmid = {30486530},
issn = {1001-5302},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Dendrobium/*classification ; *Drug Contamination ; Plant Preparations/*standards ; Plants, Medicinal/classification ; Reproducibility of Results ; },
abstract = {This research preliminarily discusses the relations of Dendrobium system growth through chloroplast gene rbcL, matK and the nuclear genome ITS2. The DNA barcoding universal sequence for authentication of the Dendrobium medical plants was slected and the possibility concerning utilizing the DNA barcoding to distinguish the D. huoshanenseand its adulterants was analyzed. Using the universal primer pair of ITS2, rbcL and matK, series of extended sequencing in the Dendrobium were conducted. Meanwhile, considering the different index about amplification and sequencing success rate of each sequence, the intraspecific and interspecific aberrance, the employment of BioEdit and MEGA 5.0 software were applied to establish the systematic tree of the NJ molecular and evaluate the diversified authentication capability of various sequences. The consequence demonstrates that the sequence of ITS2 is not only the largest one both in the intraspecific and interspecific aberrance of the Dendrobium but also has obvious barcoding gap. Considering the few overlap between the intraspecific and interspecific aberrance and the highest percentage regarding the formation of unilateral branch in diverse Dendrobium which have different ITS2 sequences, it can differentiate the species of Dendrobium. Furthermore, due to the inferior success rate of the rbcL and thematK and the lower reliability of NJ systematic tree, the percentage of the unilateral species which are generated by the systematic tree of rbcL and matK sequences is deficient. Therefore, the sequence of ITS2 can serves as DNA barcoding to distinguish the D. huoshanense, the D. moniliform and the D. officinale.},
}
@article {pmid30486194,
year = {2018},
author = {Adamson, EAS and Britz, R},
title = {The snakehead fish Channa aurolineata is a valid species (Teleostei: Channidae) distinct from Channa marulius.},
journal = {Zootaxa},
volume = {4514},
number = {4},
pages = {542-552},
doi = {10.11646/zootaxa.4514.4.7},
pmid = {30486194},
issn = {1175-5334},
mesh = {Animals ; *Fishes ; Geography ; Myanmar ; Rivers ; },
abstract = {Channa aurolineata is a valid species of the Marulius group. Previously treated as a synonym of C. marulius, C. aurolineata is readily distinguished from C. marulius by a different colour pattern, in which a conspicuous white posterior margin is present on the black scales that form the dark lateral blotches in larger juveniles and adults (vs. scales without white margin but with white spots in C. marulius). Channa aurolineata also differs from C. marulius by having more lateral line scales (65-71 vs 62-65), more dorsal-fin rays (55-58 vs 52-56) and more vertebrae (63-66 vs 59-63). In addition to these morphological differences, C. aurolineata is genetically more than 8% different (uncorrected p-distance) from C. marulius at the COI barcoding gene, a difference consistent with levels of genetic divergence observed among different species. The same characters that distinguish C. aurolineata from C. marulius also distinguish it from C. pseudomarulius, the other Indian member of the Marulius group. Channa aurolineata has a widespread distribution in larger rivers in Myanmar, including the Chindwin, Ayeyarwaddy, Sittaung and Thanlwin river basins. The Indo-Burman ranges appear to delineate the western geographical limit of this species, with C. marulius restricted to the western side of this mountain chain.},
}
@article {pmid30486184,
year = {2018},
author = {Harrison, SE and Rix, MG and Harvey, MS and Austin, AD},
title = {Systematics of the Australian spiny trapdoor spiders of the genus Blakistonia Hogg (Araneae: Idiopidae).},
journal = {Zootaxa},
volume = {4518},
number = {1},
pages = {1-76},
doi = {10.11646/zootaxa.4518.1.1},
pmid = {30486184},
issn = {1175-5334},
mesh = {Animals ; *Bayes Theorem ; Queensland ; *Spiders ; Victoria ; Western Australia ; },
abstract = {A combined molecular and morphological approach was used to revise the Australian spiny trapdoor spiders of the genus Blakistonia Hogg. Where possible, our molecular approach used sequence data from the COI barcoding gene, which were analysed using Bayesian, RAxML and neighbour-joining approaches. These molecular data were combined with morphology to describe and diagnose the genus, to redescribe the type (and only previously valid) species, B. aurea Hogg, 1902, and to diagnose, describe and map 19 new species: B. bassi sp. n., B. bella sp. n., B. birksi sp. n., B. carnarvon sp. n., B. emmottiorum sp. n., B. gemmelli sp. n., B. hortoni sp. n., B. mainae sp. n., B. maryae sp. n., B. newtoni sp. n., B. nullarborensis sp. n., B. olea sp. n., B. parva sp. n., B. pidax sp. n., B. plata sp. n., B. raveni sp. n., B. tariae sp. n., B. tunstilli sp. n., and B. wingellina sp. n. The genus Blakistonia is found to be distributed throughout the Australian arid and semi-arid zones, from the Wheatbelt region of Western Australia to central Queensland and western Victoria.},
}
@article {pmid30486156,
year = {2018},
author = {Martinsson, S and Klinth, M and ErsÉus, C},
title = {A new Scandinavian Chamaedrilus species (Clitellata: Enchytraeidae), with additional notes on others.},
journal = {Zootaxa},
volume = {4521},
number = {3},
pages = {417-429},
doi = {10.11646/zootaxa.4521.3.7},
pmid = {30486156},
issn = {1175-5334},
mesh = {Animals ; Denmark ; Forests ; Norway ; *Oligochaeta ; Phylogeny ; Sweden ; },
abstract = {Chamaedrilus (earlier referred to as Cognettia) is a well-known genus of terrestrial and limnic enchytraeids, currently with 19 known species in the world. Some of its species are morphologically cryptic and can only be identified using genetic (DNA) information. Many of them reproduce asexually, and the prevalence of sexual mature individuals is generally low in the populations. Chamaedrilus asloae sp. nov. (Clitellata: Enchytraeidae) is described based on material from two rivers in Norway, one in Sweden, and from a wet deciduous forest in Denmark. With the material at hand, no morphological characters completely separate C. asloae from C. chalupskyi; none of the available specimens of the new species are sexually mature. However, four molecular markers (two mitochondrial, two nuclear) support that C. asloae is a distinct, separately evolved lineage, which is sister to a clade consisting of C. glandulosus and C. varisetosus. In this study, too, the fully developed sexual organs of C. chalupskyi and C. varisetosus are described and illustrated.},
}
@article {pmid30486151,
year = {2018},
author = {Yamasaki, T and Hashimoto, Y and Endo, T and Hyodo, F and Itioka, T and Meleng, P},
title = {New species of the ant-mimicking genus Myrmarachne MacLeay, 1839 (Araneae: Salticidae) from Sarawak, Borneo.},
journal = {Zootaxa},
volume = {4521},
number = {3},
pages = {335-356},
doi = {10.11646/zootaxa.4521.3.2},
pmid = {30486151},
issn = {1175-5334},
mesh = {Animals ; Asia, Southeastern ; Borneo ; Female ; Malaysia ; Male ; *Spiders ; },
abstract = {The genus Myrmarachne MacLeay, 1839 (Araneae: Salticidae) is one of the most diversified salticid groups in Southeast Asia, with 23 species previously recorded from Borneo. Based on the collections accumulated from 2004 to 2014 in the Lambir Hills National Park, we herein describe six new species: M. amabilis sp. nov., M. hashimotoi sp. nov., M. lagarosoma sp. nov., M. leptosoma sp. nov., M. salaputium sp. nov. and M. tintinnabulum sp. nov. In addition, we describe the female of M. endoi Yamasaki Ahmad, 2013 for the first time. The male-female combination in M. amabilis sp. nov., M. tintinnabulum sp. nov. and M. endoi were confirmed by DNA barcoding.},
}
@article {pmid30486147,
year = {2018},
author = {Smit, J and Raemakers, I and Beentjes, K},
title = {First host record of Myopa pellucida Robineau-Desvoidy (Diptera: Conopidae) identified using DNA barcoding.},
journal = {Zootaxa},
volume = {4521},
number = {4},
pages = {593-596},
doi = {10.11646/zootaxa.4521.4.8},
pmid = {30486147},
issn = {1175-5334},
mesh = {Animals ; Bees ; *DNA Barcoding, Taxonomic ; *Diptera ; Europe ; Female ; Larva ; Seasons ; },
abstract = {Thick-headed flies of the genus Myopa Fabricius are a common sight in early spring in Europe. Several species can be found flying among Salix catkins together with their supposed Andrena Fabricius hosts (Hymenoptera: Apidae) (John Smit observations). Despite the fact that some of these Myopa species are very common, little is known about their actual host-parasitoid associations. Only a few scattered host records can be found in the literature, most of which refer to M. testacea s.l.. Whether or not these records actually concern M. testacea (Linnaeus) is uncertain due to the confusion over the identity of several species within the M. testacea species group (Stuke Clements 2008). Stuke (2017), in his World Catalogue of Conopids, provides all recorded host associations and distinguishes between unambiguously accepted host records and doubtful records based on three criteria: 1) the conopid has been reared from the host or a larva has been identified by DNA barcoding; 2) there is no doubt concerning the identity of the conopid species concerned, and 3) there is no doubt concerning the identity of the host species. Because the vast majority of the host records in the literature do not fulfil one or more of these criteria they are regarded as doubtful (Stuke 2017). Thus, only three host associations for the genus Myopa can be regarded as confirmed: Andrena vaga Panzer, for both M. hirsuta Stuke Clements (Jentzsch 2009) and M. testacea (Erteld 1998, Fellendorf et al. 2004, De Meijere 1912), and the Nearctic Andrena regularis Malloch, for the Holarctic M. vicaria Walker (Miliczky Osgood 1995). Here we report on a fourth host association for the genus Myopa, since a second instar larva of M. pellucida Robineau-Desvoidy was found in the abdomen of an Andrena nitida (Müller) female and identified using DNA barcoding.},
}
@article {pmid30486144,
year = {2018},
author = {Cross, I and Wood, TJ},
title = {New data on the Iberian endemic bee genus Flavipanurgus Warncke Hymenoptera: Apoidea: Andrenidae): Ecological and genomic data reveal a hidden species.},
journal = {Zootaxa},
volume = {4521},
number = {4},
pages = {563-572},
doi = {10.11646/zootaxa.4521.4.5},
pmid = {30486144},
issn = {1175-5334},
mesh = {Animals ; Bees ; Europe ; Female ; *Genomics ; *Hymenoptera ; Male ; Portugal ; Spain ; },
abstract = {Flavipanurgus is a small genus of panurgine bees known only from the Iberian Peninsula. Despite its status as one of the few bee genera endemic to Europe, Flavipanurgus are poorly represented in collections and until recently, their ecology had been almost unknown. Flavipanurgus ibericus (Warncke, 1972) was described from southern Iberia, with a northern subspecies F. i. kastiliensis (Warncke, 1987) later described from the north. Recent collections in Portugal have revealed clear differences in the pollen collecting patterns of the two taxa, with southern females collecting exclusively from Jasione montana and northern females from Sedum species. In combination with this ecological difference, COI and 28S barcode data indicate that Flavipanurgus kastiliensis stat. nov. should be raised to full species status. The male of Flavipanurgus ibericus s. str. is described for the first time, and updated keys to Flavipanurgus species are provided. Flavipanurgus fuzetus Patiny, 1999 is recorded for the first time from Spain. Further significant records and new floral associations for Flavipanurgus are also presented.},
}
@article {pmid30486076,
year = {2018},
author = {Setiawan, E and Erpenbeck, D and WÖrheide, G and De Voogd, NJ},
title = {Bearing the wrong identity: A case study of an Indo-Pacific common shallow water sponge of the genus Neopetrosia (Haplosclerida; Petrosiidae).},
journal = {Zootaxa},
volume = {4500},
number = {1},
pages = {43-58},
doi = {10.11646/zootaxa.4500.1.2},
pmid = {30486076},
issn = {1175-5334},
mesh = {Animals ; *Coral Reefs ; Indonesia ; *Phylogeny ; Porifera ; Water ; },
abstract = {Sponges of the order Haplosclerida are often abundant and characteristic components of Indo-Pacific reefs, but are often misidentified, because of the lack of clear distinctive morphological characters. Neopetrosia exigua is an example of a haplosclerid sponge that is very common in Indonesian shallow coral reef environments but bears several different names. In the present study we investigated type material of several Indo-Pacific Neopetrosia species with a similar morphology and examined freshly collected specimen materials including specimens that are deposited at several institutions. In addition, we used molecular phylogenetic methods for assisting the morphological examinations. We conclude that the true identity of Neopetrosia exigua should be Neopetrosia chaliniformis. Likewise, N. exigua and N. pacifica should be considered as junior synonyms of N. chaliniformis. In conclusion, we advocate that molecular barcoding could significantly aid on sponge species' delimitation that possess limited morphological characters.},
}
@article {pmid30486069,
year = {2018},
author = {Grebennikov, VV},
title = {Dryophthorinae weevils (Coleoptera: Curculionidae) of the forest floor in Southeast Asia: DNA analysis of two new Nephius from Vietnam and Taiwan suggests non-monophyly of Stromboscerini.},
journal = {Zootaxa},
volume = {4500},
number = {3},
pages = {381-387},
doi = {10.11646/zootaxa.4500.3.5},
pmid = {30486069},
issn = {1175-5334},
mesh = {Animals ; *Coleoptera ; DNA ; Forests ; Phylogeny ; Taiwan ; Vietnam ; *Weevils ; },
abstract = {The weevil genus Nephius Pascoe is for the first time reported from Vietnam (N. argus sp. nov.) and Taiwan (N. acastus sp. nov.). Until now the genus was attributed to the tribe Stromboscerini and contained nine nominal species and two subspecies known only from the type series. Phylogenetic analysis of one mitochondrial (COI) and two nuclear (ITS2 and 28S) markers strongly rejected monophyly of the tribe by placing the monophyletic Nephius as sister to a clade consisting of reciprocally monophyletic Dryophthorus and the rest of Stromboscerini. All herein used data (localities, DNA sequences, specimen images) are available online in public datasets dx.doi.org/10.5883/DS-NEPHIUS1 and dx.doi.org/10.5883/DS-NEPHIUS2.},
}
@article {pmid30486068,
year = {2018},
author = {Grebennikov, VV},
title = {Discovery of Lymantini weevils (Coleoptera: Curculionidae: Molytinae) outside the Americas: Devernodes, a new genus for five new species from Southeast Asia.},
journal = {Zootaxa},
volume = {4500},
number = {3},
pages = {363-380},
doi = {10.11646/zootaxa.4500.3.4},
pmid = {30486068},
issn = {1175-5334},
mesh = {Americas ; Animal Distribution ; Animals ; Asia ; China ; *Coleoptera ; Female ; Malaysia ; Phylogeny ; Vietnam ; *Weevils ; },
abstract = {This paper reports a new weevil genus Devernodes gen. n. established for five new species from Southeast Asia: D. alkippe sp. n. (China: Mt. Emei), D. asteria sp. n. (Vietnam: Tam Dao), D. chthonia sp. n. (Vietnam: Tam Dao; the type species), D. drimo sp. n. (Malaysia: Pasoh Forest Reserve) and D. methone sp. n. (Malaysia: Tanah Rata). All Devernodes are wingless and inhabit the forest leaf litter. Adult Devernodes share a combination of two head characters unique among weevils in Asia: antenna with apparently unsegmented club and 6-segmented antennal funicle, as well as strong constriction separating the eye-bearing rostrum from the head capsule. To test monophyly and investigate phylogenetic relationships of Devernodes, Maximum Likelihood phylogenetic analysis was undertaken using parts of mitochondrial (COI) and nuclear ribosomal (28S) genes, as well as the nuclear internal transcribed spacer (ITS2) from 14 Devernodes and 55 outgroup Curculionidae specimens. Results strongly corroborated monophyly of Devernodes and did not suggest its realistic sister-group. The new genus is assigned to the molytine tribe Lymantini (not represented in the DNA analysis) based on two potential synapomorphies: head markedly constricted behind eyes and presence of undivided female hemisternites IX (= "merged coxite and stylus"). Thus interpreted, Devernodes is the twelfth nominal genus of Lymantini and the first record of the tribe outside of the Americas. All original data (localities, DNA sequences, specimen images) are available online in public datasets dx.doi.org/10.5883/DS-DEVERNO1 and dx.doi.org/10.5883/DS-DEVERNO2.},
}
@article {pmid30486043,
year = {2018},
author = {Huang, J and Wang, Y and O'grady, PM and Su, Y and Chen, H},
title = {The genus Leucophenga (Diptera, Drosophilidae), part VIII: twenty-one species from the Oriental region, with morphological and molecular evidence.},
journal = {Zootaxa},
volume = {4503},
number = {1},
pages = {1-70},
doi = {10.11646/zootaxa.4503.1.1},
pmid = {30486043},
issn = {1175-5334},
mesh = {Animals ; *Diptera ; *Drosophilidae ; Gastropoda ; Genes, Mitochondrial ; Male ; Phylogeny ; },
abstract = {Twenty-one (six known and 15 new) species of the genus Leucophenga from the Oriental region are described or redescribed: L. jacobsoni Duda, 1926; L. kurahashii Okada, 1987; L. setipalpis Duda, 1923; L. sorii Kang, Lee Bhang, 1965; L. spinifera Okada, 1987; L. varinervis Duda, 1923; L. acantha Huang Chen, sp. nov.; L. alafumosa Huang Chen, sp. nov.; L. brevipenis Huang Chen, sp. nov.; L. brevitabulata Huang Chen, sp. nov.; L. delta Huang Chen, sp. nov.; L. forcipula Huang Chen, sp. nov.; L. fuscipalpula Huang Chen, sp. nov.; L. glabtabulata Huang Chen, sp. nov.; L. helvipecta Huang Chen, sp. nov.; L. hyaloptera Huang Chen, sp. nov.; L. oxyptera Huang Chen, sp. nov.; L. platypyga Huang Chen, sp. nov.; L. serrateiceps Huang Chen, sp. nov.; L. valvata Huang Chen, sp. nov.; L. zebrina Huang Chen, sp. nov. A key and a morphological summary table to all these Leucophenga species are provided. Phylogenetic relationships among these 21 Leucophenga species, another 14 congeneric, known species from seven groups, and two representative outgroup taxa are reconstructed using 169 DNA sequences of the partial mitochondrial cytochrome c oxidase subunit I (mtCOI) gene. In sum, 13 of the 21 Leucophenga species, which possess the only diagnostic character of the proxima species group (abdominal third tergite shortened, anteriorly discolored in males), are not monophyletic. Therefore, all the Leucophenga species described or redescribed in this study are temporarily classified as unplaced species (except for L. sorii, which has been assigned to the sorii species group) to avoid further confusion.},
}
@article {pmid30486037,
year = {2018},
author = {Rahman, MM and NorÉn, M and Mollah, AR and Kullander, S},
title = {The identity of Osteobrama cotio, and the status of "Osteobrama serrata" (Teleostei: Cyprinidae: Cyprininae).},
journal = {Zootaxa},
volume = {4504},
number = {1},
pages = {105-118},
doi = {10.11646/zootaxa.4504.1.5},
pmid = {30486037},
issn = {1175-5334},
mesh = {Animals ; Bangladesh ; *Cyprinidae ; India ; *RNA, Ribosomal, 16S ; Rivers ; },
abstract = {Osteobrama cotio is considered to be a widespread species in India and Bangladesh. Mitochondrial DNA (COI, 16S rRNA) shows that populations from the Meghna River, Karnafuli and Sangu Rivers, Narmada River, and Godavari River are genetically distinct from each other. No morphological differences were found to separate Meghna and Karnafuli+Sangu populations, however. A putative new species, "Osteobrama serrata" has been described from the Barak River basin, stated to be distinguished from O. cotio by the presence of a serrated third dorsal-fin ray. The description of "O. serrata" does not fulfil requirements of the International Code of Zoological Nomenclature, (International Commission on Zoological Nomenclature 1999) and the name is thus unavailable. Published DNA sequences of "Osteobrama serrata" are identical to sequences of O. cotio from Bangladesh. As mentioned already in the original description, O. cotio has a serrated third dorsal-fin ray.},
}
@article {pmid30485999,
year = {2018},
author = {Lin, YP and Kondo, T and Kondo, T and Gullan, PJ and Cook, LG},
title = {A newly recognised species of Cryptes Maskell 1892 (Hemiptera: Coccidae) from Western Australia.},
journal = {Zootaxa},
volume = {4508},
number = {1},
pages = {101-114},
doi = {10.11646/zootaxa.4508.1.6},
pmid = {30485999},
issn = {1175-5334},
mesh = {Animals ; Australia ; Fabaceae ; Female ; *Hemiptera ; *Phylogeny ; Western Australia ; },
abstract = {Cryptes utzoni Lin, Kondo Cook sp. n. (Hemiptera: Coccidae) is described based on adult female morphology and DNA sequences from mitochondrial and nuclear loci. This Australian endemic species was found on the stem of Acacia aneura (Fabaceae) in Western Australia. All phylogenetic analyses of three independent DNA loci show that C. utzoni is closely related to C. baccatus (Maskell), the type and only species of Cryptes Maskell, 1892. The adult female of C. utzoni is described and illustrated and a table is provided of the characters that differ among adult females of the two species of Cryptes now recognised (C. baccatus and C. utzoni) and a morphologically similar Western Australian species, Austrolichtensia hakearum (Fuller). There is deep genetic divergence in COI among samples of C. baccatus, suggesting the possibility of a species complex in this taxon.},
}
@article {pmid30485979,
year = {2018},
author = {Haran, J},
title = {A review of the genus Smicronyx Schoenherr (Coleoptera, Curculionidae, Curculioninae) in tropical Africa.},
journal = {Zootaxa},
volume = {4508},
number = {2},
pages = {267-287},
doi = {10.11646/zootaxa.4508.2.9},
pmid = {30485979},
issn = {1175-5334},
mesh = {Africa ; Animals ; *Coleoptera ; Crops, Agricultural ; Genitalia, Male ; Male ; *Weevils ; },
abstract = {The genus Smicronyx Schoenherr (Curculionidae, Curculioninae, Smicronychini) contains several species considered as potential biocontrol agents of parasitic and hemi-parasitic plants of crops (Striga spp. (Orobanchaceae) and Cuscuta spp. (Convolvulaceae)). However, the diversity of species occurring in Africa has not been explored in detail. This study reviews the species of Smicronyx occurring in continental tropical Africa. In total, 16 species are recorded for this region: 6 species previously described (S. bisignatus Hoffmann, S. gossypii Marshall, S. guineanus Voss, S. kiboanus Voss, S. pauperculus Wollaston and S. remaudierei Hoffmann), 2 newly recorded for the area (S. albosquamosus Wollaston, S. syriacus Faust), and 8 species are described as new (S. adjamati sp. n., S. crassithorax sp. n., S. kenyanus sp. n., S. namibicus sp. n., S. rufus sp. n., S. buchnerae sp. n., S. zambianus sp. n., S. zonatus sp. n.). A key to the species and photographs of the habitus and male genitalia are provided.},
}
@article {pmid30485977,
year = {2018},
author = {Van den Broek, R and Smit, JT and Bree, E and Beentjes, K},
title = {Tolmerus calceatus (Meigen) confirmed as a valid species separate from Tolmerus atricapillus (Fallén) (Diptera: Asilidae).},
journal = {Zootaxa},
volume = {4508},
number = {2},
pages = {249-258},
doi = {10.11646/zootaxa.4508.2.7},
pmid = {30485977},
issn = {1175-5334},
mesh = {Animals ; *Diptera ; Ecology ; Europe ; },
abstract = {The status of Tolmerus atricapillus calceatus (Meigen) is discussed. Based on morphological, ecological as well as genetic information it is concluded that Tolmerus calceatus stat. rev. should be treated as a valid species separate from T. atricapillus (Fallén). Characters to separate both are provided as well as a key to all Tolmerus species of northwestern Europe.},
}
@article {pmid30485960,
year = {2018},
author = {Cruz, INBD and NuÑeza, OM and Lin, CP},
title = {A new record of Neoperla obliqua Banks, 1930 (Plecoptera: Perlidae) from Mt. Malindang, Mindanao, Philippines and association of life stages using DNA barcodes.},
journal = {Zootaxa},
volume = {4514},
number = {1},
pages = {145-150},
doi = {10.11646/zootaxa.4514.1.12},
pmid = {30485960},
issn = {1175-5334},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Female ; *Lepidoptera ; Male ; Nymph ; Philippines ; },
abstract = {The nymph of the perlid Neoperla obliqua Banks, 1913 from Mt. Malindang, Mindanao Island, the Philippines is described and associated with the male and female adults using DNA barcodes. Using pairwise CO1, the nymph was associated with 99.9 ± 0.14% interspecific similarity, while comparison between sexes generated a 0.2% intraspecific divergence between males and females of putative conspecifics. Additionally, the mature ova from female adults are described using scanning electron microscopy (SEM). The distinctive chorionic surface is rugose with longitudinal ridge-like pattern with a bare and flat collar.},
}
@article {pmid30477329,
year = {2018},
author = {Smith, CF and McGlaughlin, ME and Mackessy, SP},
title = {DNA barcodes from snake venom: a broadly applicable method for extraction of DNA from snake venoms.},
journal = {BioTechniques},
volume = {65},
number = {6},
pages = {339-345},
doi = {10.2144/btn-2018-0096},
pmid = {30477329},
issn = {1940-9818},
mesh = {Alethinophidia/classification/*genetics ; Animals ; Cell Nucleus/genetics ; DNA/*genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Mitochondria/genetics ; Phylogeny ; Snake Venoms/classification/*genetics ; },
abstract = {DNA barcoding is a simple technique used to develop a large-scale system of classification that is broadly applicable across a wide variety of taxa. DNA-based analysis of snake venoms can provide a system of classification independent of currently accepted taxonomic relationships by generating DNA barcodes specific to each venom sample. DNA purification from dried snake venoms has previously required large amounts of starting material, has resulted in low yields and inconsistent amplification, and was possible with front-fanged snakes only. Here, we present a modified DNA extraction protocol applied to venoms of both front- and rear-fanged snakes that requires significantly less starting material (1 mg) and yields sufficient amounts of DNA for successful PCR amplification of regions commonly used for DNA barcoding. [Formula: see text].},
}
@article {pmid30476129,
year = {2019},
author = {Kinyanjui, G and Khamis, FM and Ombura, FLO and Kenya, EU and Ekesi, S and Mohamed, SA},
title = {Infestation Levels and Molecular Identification Based on Mitochondrial COI Barcode Region of Five Invasive Gelechiidae Pest Species in Kenya.},
journal = {Journal of economic entomology},
volume = {112},
number = {2},
pages = {872-882},
doi = {10.1093/jee/toy357},
pmid = {30476129},
issn = {1938-291X},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Introduced Species ; Kenya ; *Solanum lycopersicum ; *Moths ; Phylogeny ; },
abstract = {Invasive Gelechiidae pest species, namely Tuta absoluta, Phthorimaea operculella, Aproaerema simplixella, Sitotroga cerealella, and Pectinophora gossypiella are among the major constraints hampering agricultural economy in Kenya. Infestation levels were determined on respective host crops sampled from different localities and P. operculella recorded the highest infestation of 68.00 ± 4.92% on stored potato. Aproaerema simplixella and T. absoluta accounted for 61.33 ± 5.35% and 51.56 ± 5.22% maximal infestation on groundnuts and tomato leaves, respectively. Stored maize was significantly infested by S. cerealella (54.33 ± 5.31%) while no infestation was observed on the freshly harvested grains. Infestation on open bolls by P. gossypiella was relatively low (6.11 ± 3.46%) compared to Anatrachyntis simplex (45.67 ± 7.84%) that emerged as the key pest of cotton. The species were discriminated based on sequence similarities, evolutionary divergences, and phylogenetic analyses. A 658-bp fragment of mitochondrial cytochrome c oxidase subunit I (COI) gene was obtained from 302 specimens. Generally, genetic variations were low within and between Gelechiid populations, with an average of 0.02% and all intraspecific divergences were less than 2% except for S. cerealella. The Gelechiids data set generated eight Barcode Index Numbers (BINs), five of which were concordant and three belonging to S. cerealella were singleton. All species were separated into distinct clusters on a maximum likelihood tree. Data on infestation levels will be useful in defining the pest status of these Gelechiids in Kenya. DNA barcoding is also presented as a valuable tool to complement traditional taxonomy for rapid and accurate identification of these species of agronomic interest.},
}
@article {pmid30475948,
year = {2019},
author = {Liu, J and Chen, X and Wang, J and Zhou, S and Wang, CL and Ye, MZ and Wang, XY and Song, Y and Wang, YQ and Zhang, LT and Wu, RH and Yang, HM and Zhu, SD and Zhou, MZ and Zhang, XC and Zhu, HM and Qian, ZY},
title = {Biological background of the genomic variations of cf-DNA in healthy individuals.},
journal = {Annals of oncology : official journal of the European Society for Medical Oncology},
volume = {30},
number = {3},
pages = {464-470},
doi = {10.1093/annonc/mdy513},
pmid = {30475948},
issn = {1569-8041},
mesh = {Aged ; Cell-Free Nucleic Acids/*blood/genetics ; Clonal Evolution/*genetics ; DNA (Cytosine-5-)-Methyltransferases/genetics ; DNA Methyltransferase 3A ; DNA-Binding Proteins/genetics ; Dioxygenases ; Gene Frequency/genetics ; Genome, Human/genetics ; Genomics ; Healthy Volunteers ; Hematologic Neoplasms/*blood/genetics/pathology ; Hematopoiesis/genetics ; Humans ; Janus Kinase 2/genetics ; Middle Aged ; Mutation/genetics ; *Prognosis ; Proto-Oncogene Proteins/genetics ; },
abstract = {BACKGROUND: Cell-free DNA (cf-DNA)-based liquid biopsy is emerging as a revolutionary new method in individualized cancer treatment and prognosis monitoring, although detecting early-stage cancers using cf-DNA remains challenging, partially because of the undefined biological background of cf-DNA.<br><br>MATERIALS AND METHODS: We investigated somatic mutations in the cf-DNA of 259 cancer-free individuals with a median age of 47&#x2009;years using an endogenous barcoding duplex method with an ultralow base error rate (2&#x2009;&#xd7;&#x2009;10-7) and compared the variant allele frequencies (VAFs) of these mutations between the cf-DNA and the corresponding blood cell DNA.<br><br>RESULTS: Sixty percent (155/259) of the samples showed at least one nonsynonymous mutation on either of two similar target panels covering 508 and 559 cancer-related genes. For individuals older than 50&#x2009;years of age, the positive rate increased to 76%. Most cf-DNA mutations were also present at similar VAFs in the paired blood cell DNA. The most frequently mutated genes were driver genes of hematologic malignancies, including DNMT3A, TET2, AXSL1, and JAK2. However, the other 58.4% (192/329) of the mutations were likely 'passenger mutations' of clonal hematopoiesis, including mutations in NOTCH2, FAT3, EXT2, ERBB4, and ARID2, which are driver genes of solid tumors.<br><br>CONCLUSION: Hematopoietic clone-derived mutations, including 'driver mutations' and 'passenger mutations', are prevalent in the cf-DNA of both healthy individuals and cancer patients and may be a potential source of false positives in the liquid biopsy. Our results also suggest the ineffectiveness for distinguishing clonal hematopoietic mutations of low VAF (&#x2264;0.1%) from tumor-derived mutations using conventional next-generation sequencing of blood cell DNA. However, an error correction model with an ultralow error rate and high coverage depth is required for blood cell DNA sequencing, which is difficult and costly to achieve with current technologies.},
}
@article {pmid30475878,
year = {2018},
author = {Jürges, G and Sahi, V and Rios Rodriguez, D and Reich, E and Bhamra, S and Howard, C and Slater, A and Nick, P},
title = {Product authenticity versus globalisation-The Tulsi case.},
journal = {PloS one},
volume = {13},
number = {11},
pages = {e0207763},
pmid = {30475878},
issn = {1932-6203},
mesh = {DNA Barcoding, Taxonomic ; Fraud/*prevention &amp; control ; *Internationality ; Ocimum sanctum/*classification/genetics ; Plastids/genetics ; },
abstract = {Using the Indian medicinal plant Tulsi (Holy Basil) as a case study, we have tested to what extent the discrepancy between vernacular and scientific nomenclature can be resolved, whether the presumed chemical diversity underlying the medicinal use of Tulsi has a genetic component, and whether it is possible to detect this genetic component using genetic barcoding markers. Based on four plastidic markers, we can define several haplotypes within Ocimum that are consistent across these markers. Haplotype II is congruent with O. tenuiflorum, while haplotype I extends over several members of the genus and cannot be resolved into genetically separate subclades. The vernacular subdivision of Tulsi into three types (Rama, Krishna, Vana) can only be partially linked with genetic differences-whereby Rama and Krishna Tulsi can be assigned to O. tenuiflorum, while Vana Tulsi belongs to haplotype I. This genetic difference is mirrored by differences in the profiles of secondary compounds. While developmental state and light quality modulate the amplitude to which the chemical profile is expressed, the profile itself seems to be linked with genetic differences. We finally develop an authentication assay that makes use of a characteristic single nucleotide polymorphism in one of the barcoding markers, establishing a differential restriction pattern that can be used to discriminate Vana Tulsi.},
}
@article {pmid30473614,
year = {2018},
author = {Kim, YI and Cho, SH and Lee, JH and Kang, DH and Jin Hee Park, and Kim, YD},
title = {Chrysospleniumramosissimum Y.I.Kim &amp; Y.D.Kim (Saxifragaceae), a new species from Korea.},
journal = {PhytoKeys},
volume = {},
number = {111},
pages = {1-10},
pmid = {30473614},
issn = {1314-2011},
abstract = {This study describes and illustrates Chrysospleniumramosissimum, a new plant species from Mt. Seonjaryeong, located in the central region of the Korean Peninsula. The species is most similar to C.valdepilosum but is readily distinguishable by the presence of yellowish-green bracteal leaves during flowering, highly branched sterile branches, shiny silvery dots on sterile branch leaves and larger tubercles on the seed coat.},
}
@article {pmid30472020,
year = {2018},
author = {Hinohara, K and Wu, HJ and Vigneau, S and McDonald, TO and Igarashi, KJ and Yamamoto, KN and Madsen, T and Fassl, A and Egri, SB and Papanastasiou, M and Ding, L and Peluffo, G and Cohen, O and Kales, SC and Lal-Nag, M and Rai, G and Maloney, DJ and Jadhav, A and Simeonov, A and Wagle, N and Brown, M and Meissner, A and Sicinski, P and Jaffe, JD and Jeselsohn, R and Gimelbrant, AA and Michor, F and Polyak, K},
title = {KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance.},
journal = {Cancer cell},
volume = {34},
number = {6},
pages = {939-953.e9},
pmid = {30472020},
issn = {1878-3686},
support = {R35 CA197623/CA/NCI NIH HHS/United States ; P01 CA080111/CA/NCI NIH HHS/United States ; R01 CA202634/CA/NCI NIH HHS/United States ; U54 HG008097/HG/NHGRI NIH HHS/United States ; U54 CA193461/CA/NCI NIH HHS/United States ; },
mesh = {Breast Neoplasms/drug therapy/*genetics/metabolism ; Cell Line, Tumor ; Drug Resistance, Neoplasm/drug effects/*genetics ; Estradiol/pharmacology ; Estrogen Receptor Modulators/pharmacology ; Female ; Fulvestrant/pharmacology ; Genetic Heterogeneity ; Humans ; Jumonji Domain-Containing Histone Demethylases/*genetics/metabolism ; MCF-7 Cells ; Nuclear Proteins/*genetics/metabolism ; Repressor Proteins/*genetics/metabolism ; Retinoblastoma-Binding Protein 2/*genetics/metabolism ; Transcriptome/drug effects/*genetics ; Exome Sequencing/methods ; },
abstract = {Members of the KDM5 histone H3 lysine 4 demethylase family are associated with therapeutic resistance, including endocrine resistance in breast cancer, but the underlying mechanism is poorly defined. Here we show that genetic deletion of KDM5A/B or inhibition of KDM5 activity increases sensitivity to anti-estrogens by modulating estrogen receptor (ER) signaling and by decreasing cellular transcriptomic heterogeneity. Higher KDM5B expression levels are associated with higher transcriptomic heterogeneity and poor prognosis in ER[+] breast tumors. Single-cell RNA sequencing, cellular barcoding, and mathematical modeling demonstrate that endocrine resistance is due to selection for pre-existing genetically distinct cells, while KDM5 inhibitor resistance is acquired. Our findings highlight the importance of cellular phenotypic heterogeneity in therapeutic resistance and identify KDM5A/B as key regulators of this process.},
}
@article {pmid30470696,
year = {2018},
author = {Milo, I and Bedora-Faure, M and Garcia, Z and Thibaut, R and Périé, L and Shakhar, G and Deriano, L and Bousso, P},
title = {The immune system profoundly restricts intratumor genetic heterogeneity.},
journal = {Science immunology},
volume = {3},
number = {29},
pages = {},
doi = {10.1126/sciimmunol.aat1435},
pmid = {30470696},
issn = {2470-9468},
support = {310917/ERC_/European Research Council/International ; },
mesh = {Animals ; Female ; Genetic Heterogeneity ; Lymphoma, B-Cell/*genetics/*immunology/pathology ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Neoplasms, Experimental/genetics/immunology/pathology ; },
abstract = {Tumors develop under the selective pressure of the immune system. However, it remains critical to establish how the immune system affects the clonal heterogeneity of tumors that often display cell-to-cell variation in genetic alterations and antigenic expression. To address these questions, we introduced a multicolor barcoding strategy to study the growth of a MYC-driven B cell lymphoma harboring a large degree of intratumor genetic diversity. Using intravital imaging, we visualized that lymphoma subclones grow as patches of sessile cells in the bone marrow, creating a spatially compartmentalized architecture for tumor diversity. Using multicolor barcoding and whole-exome sequencing, we demonstrated that immune responses strongly restrict intratumor genomic diversity and favor clonal dominance, a process mediated by the selective elimination of more immunogenic cells and amplified by epitope spreading. Anti-PD-1 treatment also narrowed intratumor diversity. Our results provide direct evidence that immune pressure shapes the level of intratumor genetic heterogeneity and have important implications for the design of therapeutic strategies.},
}
@article {pmid30468939,
year = {2019},
author = {Weber, AA and Stöhr, S and Chenuil, A},
title = {Species delimitation in the presence of strong incomplete lineage sorting and hybridization: Lessons from Ophioderma (Ophiuroidea: Echinodermata).},
journal = {Molecular phylogenetics and evolution},
volume = {131},
number = {},
pages = {138-148},
doi = {10.1016/j.ympev.2018.11.014},
pmid = {30468939},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial ; Discriminant Analysis ; Echinodermata/*classification/*genetics ; Geography ; *Hybridization, Genetic ; Mitochondria/genetics ; Multigene Family ; *Phylogeny ; Principal Component Analysis ; Species Specificity ; Time Factors ; },
abstract = {Accurate species delimitation is essential to properly assess biodiversity, but also for management and conservation purposes. Yet, it is not always trivial to accurately define species boundaries in closely related species due to incomplete lineage sorting. Additional difficulties may be caused by hybridization, now evidenced as a frequent phenomenon. The brittle star cryptic species complex Ophioderma longicauda encompasses six mitochondrial lineages, including broadcast spawners and internal brooders, yet the actual species boundaries are unknown. Here, we combined three methods to delimit species in the Ophioderma longicauda complex and to infer its divergence history: (i) unsupervised species discovery based on multilocus genotypes; (ii) divergence time estimation using the multi-species coalescent; (iii) divergence scenario testing (including gene flow) using Approximate Bayesian Computation (ABC) methods. 30 sequence markers (transcriptome-based, mitochondrial or non-coding) for 89 O. longicauda and outgroup individuals were used. First, multivariate analyses revealed six genetic clusters, which globally corresponded to the mitochondrial lineages, yet with many exceptions, suggesting ancient hybridization events and challenging traditional mitochondrial barcoding approaches. Second, multi-species coalescent-based analyses confirmed the occurrence of six species and provided divergence time estimates, but the sole use of this method failed to accurately delimit species, highlighting the power of multilocus genotype clustering to delimit recently diverged species. Finally, Approximate Bayesian Computation showed that the most likely scenario involves hybridization between brooders and broadcasters. Our study shows that despite strong incomplete lineage sorting and past hybridization, accurate species delimitation in Ophioderma was possible using a combination of complementary methods. We propose that these methods, especially multilocus genotype clustering, may be useful to resolve other complex speciation histories.},
}
@article {pmid30466976,
year = {2018},
author = {Bansal, S and Thakur, S and Mangal, M and Mangal, AK and Gupta, RK},
title = {DNA barcoding for specific and sensitive detection of Cuminum cyminum adulteration in Bunium persicum.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {50},
number = {},
pages = {178-183},
doi = {10.1016/j.phymed.2018.04.023},
pmid = {30466976},
issn = {1618-095X},
mesh = {Apiaceae/*genetics ; Base Sequence ; Cuminum/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; *Drug Contamination ; Genetic Markers ; Plants, Medicinal/genetics ; Reproducibility of Results ; },
abstract = {BACKGROUND: Bunium persicum commonly called as Kala zeera, a very high value herbaceous spice used for medicinal purposes is often adulterated with Cuminum cyminum or Safed zeera, a closely related species. Lack of distinctive morphological features makes the identification of genuine kala zeera from its adulterant difficult, the problem is even exaggerated in case of powdered material.<br><br>METHODOLOGY: Genomic DNA was extracted from all the plant materials by using CTAB-SDS method (M&#xf6;ller et&#xa0;al., 1992) with slight modifications. On the basis of reproducibility and high amplification ability, four universal barcoding loci viz. ITS2, rbcL-a, mat K and psbA-trnH and a specific locus Cum were used in the present study. The amplified PCR products were sequenced bidirectionally and assembled to obtain contigs. The sequences thus obtained were aligned using MUSCLE algorithm (Edgar, 2004) and information pertaining to conserved/ variable/ parsimony informative sites, number of transitions, transversions and Indels was obtained after analyzing the sequences.<br><br>RESULTS AND CONCLUSION: Among the tested barcoding loci, psbA-trnH has proven to be best barcode in authentication of kala zeera as its amplification and sequencing success was high and it showed the presence of polymorphic sites to detect interspecific variation. This barcode could differentiate between safed zeera and kala zeera in a single reaction, simultaneously.},
}
@article {pmid30465911,
year = {2019},
author = {Polat, C and Ergünay, K and Irmak, S and Erdin, M and Brinkmann, A and Çetintaş, O and Çoğal, M and Sözen, M and Matur, F and Nitsche, A and Öktem, &#x130;MA},
title = {A novel genetic lineage of Tula orthohantavirus in Altai voles (Microtus obscurus) from Turkey.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {67},
number = {},
pages = {150-158},
doi = {10.1016/j.meegid.2018.11.015},
pmid = {30465911},
issn = {1567-7257},
mesh = {Animal Diseases/*epidemiology/*virology ; Animals ; Arvicolinae/*virology ; DNA Barcoding, Taxonomic ; Genome, Viral ; Genomics/methods ; Geography, Medical ; Orthohantavirus/*classification/*genetics ; High-Throughput Nucleotide Sequencing ; Phylogeny ; RNA, Viral ; Turkey/epidemiology ; },
abstract = {Orthohantaviruses (family Hantaviridae order Bunyavirales) are emerging pathogens with a significant impact on human health. They are transmitted via aerosolized excreta of rodents which also act as reservoir hosts, constituting a unique route for dispersion. Dobrava-Belgrade and Puumala orthohantaviruses have been previously reported from Anatolia, in rodents, case reports and occasional outbreaks. We have collected rodents at several locations during a surveillance study in eastern Anatolia. The specimens were morphologically-identified and various tissues were screened via a generic orthohantavirus reverse transcription polymerase chain reaction assay. DNA barcoding via mitochondrial cytochrome b sequencing was performed in rodents with detectable orthohantavirus sequences. High throughput sequencing was performed for viral genome characterization. Fifty rodents were collected and identified morphologically as Microtus spp. (96%) and Apodemus spp. (4%). Orthohantavirus sequences were detected in lung and spleen or liver tissues of 4 voles (8%), barcoded as Microtus obscurus. The virus sequences were identified as Tula orthohantavirus (TULV) and near-complete genomic segments of the prototype viral genome, tentatively named as the Tula orthohantavirus-Turkey (TULV-T), could be characterized. Putative open reading frames for viral nucleocapsid and a nonstructural protein on the S segment, glycoproteins G1 and G2 on the M segment and viral replicase on the L segment were identified on the TULV-T. Several minor sequence variants were further characterized. No evidence of recombination could be detected and pairwise comparisons displayed over 95% amino acid sequence identities to various Eurasian TULV strains. Phylogenetic analyses revealed distinct clustering of all genome segments from previously-characterized TULV strains via various approaches and models. Here, TULV-T constituted a novel lineage, forming an intermediate among Asian and European TULV lineages. This report describes the initial documentation of TULV circulation and its potential reservoir in Anatolia. The extent of virus dispersion, alternate hosts or outcomes of human exposure require elucidation.},
}
@article {pmid30465691,
year = {2019},
author = {Meyer, W and Irinyi, L and Hoang, MTV and Robert, V and Garcia-Hermoso, D and Desnos-Ollivier, M and Yurayart, C and Tsang, CC and Lee, CY and Woo, PCY and Pchelin, IM and Uhrlaß, S and Nenoff, P and Chindamporn, A and Chen, S and Hebert, PDN and Sorrell, TC and , },
title = {Database establishment for the secondary fungal DNA barcode translational elongation factor 1α (TEF1α) [1].},
journal = {Genome},
volume = {62},
number = {3},
pages = {160-169},
doi = {10.1139/gen-2018-0083},
pmid = {30465691},
issn = {1480-3321},
mesh = {*Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/analysis/*genetics ; DNA, Ribosomal Spacer/genetics ; *Databases, Factual ; Fungi/*classification/*genetics ; Peptide Elongation Factor 1/*genetics ; },
abstract = {With new or emerging fungal infections, human and animal fungal pathogens are a growing threat worldwide. Current diagnostic tools are slow, non-specific at the species and subspecies levels, and require specific morphological expertise to accurately identify pathogens from pure cultures. DNA barcodes are easily amplified, universal, short species-specific DNA sequences, which enable rapid identification by comparison with a well-curated reference sequence collection. The primary fungal DNA barcode, ITS region, was introduced in 2012 and is now routinely used in diagnostic laboratories. However, the ITS region only accurately identifies around 75% of all medically relevant fungal species, which has prompted the development of a secondary barcode to increase the resolution power and suitability of DNA barcoding for fungal disease diagnostics. The translational elongation factor 1α (TEF1α) was selected in 2015 as a secondary fungal DNA barcode, but it has not been implemented into practice, due to the absence of a reference database. Here, we have established a quality-controlled reference database for the secondary barcode that together with the ISHAM-ITS database, forms the ISHAM barcode database, available online at http://its.mycologylab.org/ . We encourage the mycology community for active contributions.},
}
@article {pmid30465068,
year = {2019},
author = {Hubert, J and Nesvorna, M and Kopecky, J and Erban, T and Klimov, P},
title = {Population and Culture Age Influence the Microbiome Profiles of House Dust Mites.},
journal = {Microbial ecology},
volume = {77},
number = {4},
pages = {1048-1066},
pmid = {30465068},
issn = {1432-184X},
support = {17-12068S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; (No. 6.1933.2014/K Project Code 1933//Ministry of Education and Science of the Russian Federation/ ; No. 15-04-0s5185-a//the Russian Foundation for Basic Research/ ; },
mesh = {Animals ; *Bacteria/classification ; DNA Barcoding, Taxonomic ; *Fungi/classification ; *Microbiota ; Population Dynamics ; Pyroglyphidae/*microbiology/*physiology ; RNA, Bacterial/analysis ; RNA, Fungal/analysis ; RNA, Ribosomal, 16S/analysis ; RNA, Ribosomal, 18S/analysis ; Real-Time Polymerase Chain Reaction ; Species Specificity ; },
abstract = {Interactions with microorganisms might enable house dust mites (HDMs) to derive nutrients from difficult-to-digest structural proteins and to flourish in human houses. We tested this hypothesis by investigating the effects of changes in the mite culture growth and population of two HDM species on HDM microbiome composition and fitness. Growing cultures of laboratory and industrial allergen-producing populations of Dermatophagoides farinae (DFL and DFT, respectively) and Dermatophagoides pteronyssinus (DPL and DPT, respectively) were sampled at four time points. The symbiotic microorganisms of the mites were characterized by DNA barcode sequencing and quantified by qPCR using universal/specific primers. The population growth of mites and nutrient contents of mite bodies were measured and correlated with the changes in bacteria in the HDM microbiome. The results showed that both the population and culture age significantly influenced the microbiome profiles. Cardinium formed 93% and 32% of the total sequences of the DFL and DFT bacterial microbiomes, respectively, but this bacterial species was less abundant in the DPL and DPT microbiomes. Staphylococcus abundance was positively correlated with increased glycogen contents in the bodies of mites, and increased abundances of Aspergillus, Candida, and Kocuria were correlated with increased lipid contents in the bodies of mites. The xerophilic fungus Wallemia accounted for 39% of the fungal sequences in the DPL microbiome, but its abundance was low in the DPT, DFL, and DFT microbiomes. With respect to the mite culture age, we made three important observations: the mite population growth from young cultures was 5-8-fold higher than that from old cultures; specimens from old cultures had greater abundances of fungi and bacteria in their bodies; and yeasts predominated in the gut contents of specimens from young cultures, whereas filamentous mycelium prevailed in specimens from old cultures. Our results are consistent with the hypothesis that mites derive nutrients through associations with microorganisms.},
}
@article {pmid30464830,
year = {2018},
author = {Li, S and Qian, X and Zheng, Z and Shi, M and Chang, X and Li, X and Liu, J and Tu, T and Zhang, D},
title = {DNA barcoding the flowering plants from the tropical coral islands of Xisha (China).},
journal = {Ecology and evolution},
volume = {8},
number = {21},
pages = {10587-10593},
pmid = {30464830},
issn = {2045-7758},
abstract = {AIM: DNA barcoding has been widely applied to species diversity assessment in various ecosystems, including temperate forests, subtropical forests, and tropical rain forests. However, tropical coral islands have never been barcoded before due to the difficulties in field exploring. This study aims at barcoding the flowering plants from a unique ecosystem of the tropical coral islands in the Pacific Ocean and supplying valuable evolutionary information for better understanding plant community assembly of those particular islands in the future.<br><br>LOCATION: Xisha Islands, China.<br><br>METHODS: This study built a DNA barcode database for 155 plant species from the Xisha Islands using three DNA markers (ITS, rbcL, and matK). We applied the sequence similarity method and a phylogenetic-based method to assess the barcoding resolution.<br><br>RESULTS: All the three DNA barcodes showed high levels of PCR success (96%-99%) and sequencing success (98%-100%). ITS performed the highest rate of species resolution (>95%) among the three markers, while plastid markers delivered a relatively poor species resolution (85%-90%). Our analyses obtained a marginal increase in species resolution when combining the three DNA barcodes.<br><br>MAIN CONCLUSIONS: This study provides the first plant DNA barcode data for the unique ecosystem of tropical coral islands and considerably supplements the DNA barcode library for the flowering plants on the oceanic islands. Based on the PCR and sequencing success rates, and the discriminatory power of the three DNA regions, we recommend ITS as the most successful DNA barcode to identify the flowering plants from Xisha Islands. Due to its high sequence variation and low fungal contamination, ITS could be a preferable candidate of DNA barcode for plants from other tropical coral islands as well. Our results also shed lights on the importance of biodiversity conservation of tropical coral islands.},
}
@article {pmid30463016,
year = {2018},
author = {Roh, V and Abramowski, P and Hiou-Feige, A and Cornils, K and Rivals, JP and Zougman, A and Aranyossy, T and Thielecke, L and Truan, Z and Mermod, M and Monnier, Y and Prassolov, V and Glauche, I and Nowrouzi, A and Abdollahi, A and Fehse, B and Simon, C and Tolstonog, GV},
title = {Cellular Barcoding Identifies Clonal Substitution as a Hallmark of Local Recurrence in a Surgical Model of Head and Neck Squamous Cell Carcinoma.},
journal = {Cell reports},
volume = {25},
number = {8},
pages = {2208-2222.e7},
doi = {10.1016/j.celrep.2018.10.090},
pmid = {30463016},
issn = {2211-1247},
mesh = {Animals ; Biomarkers, Tumor/metabolism ; Carcinogenesis/pathology ; Cell Line, Tumor ; Cell Lineage ; Cell Proliferation ; Clone Cells ; Disease Models, Animal ; Epithelial-Mesenchymal Transition ; Female ; Humans ; Male ; Mice, Nude ; *Models, Anatomic ; Models, Statistical ; Neoplasm Recurrence, Local/*pathology ; Neoplastic Stem Cells/pathology ; Neprilysin/metabolism ; Phenotype ; Squamous Cell Carcinoma of Head and Neck/genetics/*pathology/*surgery ; Xenograft Model Antitumor Assays ; },
abstract = {Local recurrence after surgery for head and neck squamous cell carcinoma (HNSCC) remains a common event associated with a dismal prognosis. Improving this outcome requires a better understanding of cancer cell populations that expand from postsurgical minimal residual disease (MRD). Therefore, we assessed clonal dynamics in a surgical model of barcoded HNSCC growing in the submental region of immunodeficient mice. Clonal substitution and massive reduction of clonal heterogeneity emerged as hallmarks of local recurrence, as the clones dominating in less heterogeneous recurrences were scarce in their matched primary tumors. These lineages were selected by their ability to persist after surgery and competitively expand from MRD. Clones enriched in recurrences exhibited both private and shared genetic features and likely originated from ancestors shared with clones dominating in primary tumors. They demonstrated high invasiveness and epithelial-to-mesenchymal transition, eventually providing an attractive target for obtaining better local control for these tumors.},
}
@article {pmid30462308,
year = {2019},
author = {Broadwater, DWB and Altman, RB and Blanchard, SC and Kim, HD},
title = {ERASE: a novel surface reconditioning strategy for single-molecule experiments.},
journal = {Nucleic acids research},
volume = {47},
number = {3},
pages = {e14},
pmid = {30462308},
issn = {1362-4962},
support = {R01 GM112882/GM/NIGMS NIH HHS/United States ; },
mesh = {Carbocyanines ; Fluorescent Dyes ; Nucleic Acid Hybridization ; Oligodeoxyribonucleotides/*chemistry ; Single Molecule Imaging ; },
abstract = {While surface-based single-molecule experiments have revolutionized our understanding of biology and biomolecules, the workflow in preparing for such experiments, especially surface cleaning and functionalization, remains labor-intensive and time-consuming. Even worse, meticulously assembled flow channels can be used only once for most experiments. A reusable surface would thus dramatically increase productivity and efficiency of single-molecule experiments. In this paper, we report a novel surface reconditioning strategy termed ERASE (Epitaxial Removal Aided by Strand Exchange) that allows a single flow cell to be used for vast repetition of single-molecule experiments. In this method, biomolecules immobilized to the surface through a nucleic acid duplex are liberated when a competing DNA strand disrupts the duplex via toehold-mediated strand displacement. We demonstrate the wide-range applicability of this method with various common surface preparation techniques, fluorescent dyes, and biomolecules including the bacterial ribosome. Beyond time and cost savings, we also show ERASE can assort molecules based on a nucleic acid barcode sequence, thus allowing experiments on different molecules in parallel. Our method increases the utility of prepared surfaces and is a significant improvement to the current single-use paradigm.},
}
@article {pmid30462277,
year = {2019},
author = {Dura, B and Choi, JY and Zhang, K and Damsky, W and Thakral, D and Bosenberg, M and Craft, J and Fan, R},
title = {scFTD-seq: freeze-thaw lysis based, portable approach toward highly distributed single-cell 3' mRNA profiling.},
journal = {Nucleic acids research},
volume = {47},
number = {3},
pages = {e16},
pmid = {30462277},
issn = {1362-4962},
support = {P50 CA121974/CA/NCI NIH HHS/United States ; R37 AR040072/AR/NIAMS NIH HHS/United States ; T32 GM007205/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Cell Line ; Freezing ; Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Human Umbilical Vein Endothelial Cells ; Humans ; Lupus Erythematosus, Systemic/genetics/immunology ; Male ; Melanoma, Experimental/genetics/metabolism ; Mice ; Oligonucleotide Array Sequence Analysis ; RNA, Messenger/*chemistry/metabolism ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis/methods ; T-Lymphocytes ; Workflow ; },
abstract = {Cellular barcoding of 3' mRNAs enabled massively parallel profiling of single-cell gene expression and has been implemented in droplet and microwell based platforms. The latter further adds the value for compatibility with low input samples, optical imaging, scalability, and portability. However, cell lysis in microwells remains challenging despite the recently developed sophisticated solutions. Here, we present scFTD-seq, a microchip platform for performing single-cell freeze-thaw lysis directly toward 3' mRNA sequencing. It offers format flexibility with a simplified, widely adoptable workflow that reduces the number of preparation steps and hands-on time, with the quality of data and cost per sample matching that of the state-of-the-art scRNA-seq platforms. Freeze-thaw, known as an unfavorable lysis method resulting in possible RNA fragmentation, turns out to be fully compatible with 3' scRNA-seq. We applied it to the profiling of circulating follicular helper T cells implicated in systemic lupus erythematosus pathogenesis. Our results delineate the heterogeneity in the transcriptional programs and effector functions of these rare pathogenic T cells. As scFTD-seq decouples on-chip cell isolation and library preparation, we envision it to allow sampling at the distributed sites including point-of-care settings and downstream processing at centralized facilities, which should enable wide-spread adoption beyond academic laboratories.},
}
@article {pmid30461375,
year = {2018},
author = {Ring, N and Abrahams, JS and Jain, M and Olsen, H and Preston, A and Bagby, S},
title = {Resolving the complex Bordetella pertussis genome using barcoded nanopore sequencing.},
journal = {Microbial genomics},
volume = {4},
number = {11},
pages = {},
pmid = {30461375},
issn = {2057-5858},
support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Bordetella pertussis/*genetics ; *Genome, Bacterial ; Molecular Sequence Annotation ; Nanopores ; Sequence Analysis, DNA/*methods ; },
abstract = {The genome of Bordetella pertussis is complex, with high G+C content and many repeats, each longer than 1000 bp. Long-read sequencing offers the opportunity to produce single-contig B. pertussis assemblies using sequencing reads which are longer than the repetitive sections, with the potential to reveal genomic features which were previously unobservable in multi-contig assemblies produced by short-read sequencing alone. We used an R9.4 MinION flow cell and barcoding to sequence five B. pertussis strains in a single sequencing run. We then trialled combinations of the many nanopore user community-built long-read analysis tools to establish the current optimal assembly pipeline for B. pertussis genome sequences. This pipeline produced closed genome sequences for four strains, allowing visualization of inter-strain genomic rearrangement. Read mapping to the Tohama I reference genome suggests that the remaining strain contains an ultra-long duplicated region (almost 200 kbp), which was not resolved by our pipeline; further investigation also revealed that a second strain that was seemingly resolved by our pipeline may contain an even longer duplication, albeit in a small subset of cells. We have therefore demonstrated the ability to resolve the structure of several B. pertussis strains per single barcoded nanopore flow cell, but the genomes with highest complexity (e.g. very large duplicated regions) remain only partially resolved using the standard library preparation and will require an alternative library preparation method. For full strain characterization, we recommend hybrid assembly of long and short reads together; for comparison of genome arrangement, assembly using long reads alone is sufficient.},
}
@article {pmid30461309,
year = {2019},
author = {Loeza-Quintana, T and Carr, CM and Khan, T and Bhatt, YA and Lyon, SP and Hebert, PDN and Adamowicz, SJ},
title = {Recalibrating the molecular clock for Arctic marine invertebrates based on DNA barcodes [1].},
journal = {Genome},
volume = {62},
number = {3},
pages = {200-216},
doi = {10.1139/gen-2018-0107},
pmid = {30461309},
issn = {1480-3321},
mesh = {Animals ; Arthropods/*genetics ; DNA/analysis/*genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; *Genetic Variation ; Mollusca/*genetics ; Phylogeny ; Polychaeta/*genetics ; },
abstract = {Divergence times for species assemblages of Arctic marine invertebrates have often been estimated using a standard rate (1.4%/MY) of molecular evolution calibrated using a single sister pair of tropical crustaceans. Because rates of molecular evolution vary among taxa and environments, it is essential to obtain clock calibrations from northern lineages. The recurrent opening and closure of the Bering Strait provide an exceptional opportunity for clock calibration. Here, we apply the iterative calibration approach to investigate patterns of molecular divergence among lineages of northern marine molluscs and arthropods using publicly available sequences of the cytochrome c oxidase subunit I (COI) gene and compare these results with previous estimates of trans-Bering divergences for echinoderms and polychaetes. The wide range of Kimura two-parameter (K2P) divergences among 73 trans-Bering sister pairs (0.12%-16.89%) supports multiple pulses of migration through the Strait. Overall, the results indicate a rate of K2P divergence of 3.2%/MY in molluscs, 5%-5.2%/MY in arthropods, and 3.5%-4.7%/MY in polychaetes. While these rates are considerably higher than the often-adopted 1.4%/MY rate, they are similar to calibrations (3%-5%/MY) in several other studies of marine invertebrates. This upward revision in rates means there is a need both to reevaluate the evolutionary history of marine lineages and to reexamine the impact of prior climatic changes upon the diversification of marine life.},
}
@article {pmid30461199,
year = {2018},
author = {Bian, F and Wu, J and Wang, H and Sun, L and Shao, C and Wang, Y and Li, Z and Wang, X and Zhao, Y},
title = {Bioinspired Photonic Barcodes with Graphene Oxide Encapsulation for Multiplexed MicroRNA Quantification.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {14},
number = {52},
pages = {e1803551},
doi = {10.1002/smll.201803551},
pmid = {30461199},
issn = {1613-6829},
mesh = {Graphite/*chemistry ; MicroRNAs/*chemistry ; },
abstract = {Multiplexed microRNA (miRNA) quantification has a demonstrated value in clinical diagnosis. In this paper, novel mussel-inspired photonic crystal (PhC) barcodes with graphene oxide (GO) encapsulation for multiplexed miRNA detection are presented. Using the excellent adhesion capability of polydopamine, the dispersed GO particles can be immobilized on the surfaces of the PhC barcodes to form an additional functional layer. The GO-decorated PhC barcodes have constant characteristic reflection peaks because the GO immobilization process not only maintains their periodic microstructure but also enhances their stability and anti-incoherent light-scattering capability. The immobilized GO particles are shown to enable high-sensitivity miRNA screening on the surface of the PhC barcodes by integration with a hybridization chain reaction amplification strategy. Because the PhC barcodes have stable encoding reflection peaks, multiplexed low-abundance miRNA quantification can also be achieved rapidly, accurately, and reproducibly by employing different GO-decorated PhC barcodes. These features should make GO-encapsulated PhC barcodes ideal for many practical applications.},
}
@article {pmid30459837,
year = {2018},
author = {Zhang, GK and Chain, FJJ and Abbott, CL and Cristescu, ME},
title = {Metabarcoding using multiplexed markers increases species detection in complex zooplankton communities.},
journal = {Evolutionary applications},
volume = {11},
number = {10},
pages = {1901-1914},
pmid = {30459837},
issn = {1752-4571},
abstract = {Metabarcoding combines DNA barcoding with high-throughput sequencing, often using one genetic marker to understand complex and taxonomically diverse samples. However, species-level identification depends heavily on the choice of marker and the selected primer pair, often with a trade-off between successful species amplification and taxonomic resolution. We present a versatile metabarcoding protocol for biomonitoring that involves the use of two barcode markers (COI and 18S) and four primer pairs in a single high-throughput sequencing run, via sample multiplexing. We validate the protocol using a series of 24 mock zooplanktonic communities incorporating various levels of genetic variation. With the use of a single marker and single primer pair, the highest species recovery was 77%. With all three COI fragments, we detected 62%-83% of species across the mock communities, while the use of the 18S fragment alone resulted in the detection of 73%-75% of species. The species detection level was significantly improved to 89%-93% when both markers were used. Furthermore, multiplexing did not have a negative impact on the proportion of reads assigned to each species and the total number of species detected was similar to when markers were sequenced alone. Overall, our metabarcoding approach utilizing two barcode markers and multiple primer pairs per barcode improved species detection rates over a single marker/primer pair by 14% to 35%, making it an attractive and relatively cost-effective method for biomonitoring natural zooplankton communities. We strongly recommend combining evolutionary independent markers and, when necessary, multiple primer pairs per marker to increase species detection (i.e., reduce false negatives) in metabarcoding studies.},
}
@article {pmid30459313,
year = {2018},
author = {Forin-Wiart, MA and Poulle, ML and Piry, S and Cosson, JF and Larose, C and Galan, M},
title = {Evaluating metabarcoding to analyse diet composition of species foraging in anthropogenic landscapes using Ion Torrent and Illumina sequencing.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {17091},
pmid = {30459313},
issn = {2045-2322},
support = {D201011937//Conseil R&#x00E9;gional Champagne Ardenne (Champage Ardenne Regional Council)/International ; },
mesh = {Animal Feed/*analysis ; Animals ; Cats ; Computational Biology ; DNA Barcoding, Taxonomic/*methods ; Diet/*veterinary ; Feces/*chemistry ; Feeding Behavior ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; },
abstract = {DNA metabarcoding of faecal samples is being successfully used to study the foraging niche of species. We assessed the ability of two benchtop high-throughput sequencing (HTS) platforms, to identify a large taxonomic array of food items from domestic cats Felis silvestris catus, including prey and human-related food taxa (pet food and leftovers leaving undetectable solid remains in faeces). Scats from a captive feeding trial (n = 41) and from free-ranging individuals (n = 326) were collected and analysed using a cytb mini-barcode in independent PCR replicates on the Ion PGM and the MiSeq platforms. Outputs from MiSeq were more sensitive and reproducible than those from Ion PGM due to a higher sequencing depth and sequence quality on MiSeq. DNA from intact prey taxa was detected more often (82% of the expected occurrences) than DNA from pet food (54%) and raw fish and meat (31%). We assumed that this variability was linked to different degree of DNA degradation: The Ion PGM detected significantly less human-linked food, birds, field voles, murids and shrews in the field-collected samples than the MiSeq platform. Pooling the replicates from both platforms and filtering the data allowed identification of at least one food item in 87.4% of the field-collected samples. Our DNA metabarcoding approach identified 29 prey taxa, of which 25 to species level (90% of items) including 9 rodents, 3 insectivores, 12 birds and 1 reptile and 33 human-related food taxa of which 23 were identified to genus level (75% of items). Our results demonstrate that using HTS platforms such as MiSeq, which provide reads of sufficiently high quantity and quality, with sufficient numbers of technical replicates, is a robust and non-invasive approach for further dietary studies on animals foraging on a wide range of food items in anthropogenic landscapes.},
}
@article {pmid30458005,
year = {2018},
author = {Wick, RR and Judd, LM and Holt, KE},
title = {Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks.},
journal = {PLoS computational biology},
volume = {14},
number = {11},
pages = {e1006583},
pmid = {30458005},
issn = {1553-7358},
mesh = {Algorithms ; Bacteria/genetics ; Computational Biology/*methods ; DNA/analysis ; *DNA Barcoding, Taxonomic ; Electronic Data Processing ; Gene Library ; Genome ; High-Throughput Nucleotide Sequencing ; Nanopores ; Nanotechnology/*methods ; *Neural Networks, Computer ; Reproducibility of Results ; Software ; },
abstract = {Multiplexing, the simultaneous sequencing of multiple barcoded DNA samples on a single flow cell, has made Oxford Nanopore sequencing cost-effective for small genomes. However, it depends on the ability to sort the resulting sequencing reads by barcode, and current demultiplexing tools fail to classify many reads. Here we present Deepbinner, a tool for Oxford Nanopore demultiplexing that uses a deep neural network to classify reads based on the raw electrical read signal. This 'signal-space' approach allows for greater accuracy than existing 'base-space' tools (Albacore and Porechop) for which signals must first be converted to DNA base calls, itself a complex problem that can introduce noise into the barcode sequence. To assess Deepbinner and existing tools, we performed multiplex sequencing on 12 amplicons chosen for their distinguishability. This allowed us to establish a ground truth classification for each read based on internal sequence alone. Deepbinner had the lowest rate of unclassified reads (7.8%) and the highest demultiplexing precision (98.5% of classified reads were correctly assigned). It can be used alone (to maximise the number of classified reads) or in conjunction with other demultiplexers (to maximise precision and minimise false positive classifications). We also found cross-sample chimeric reads (0.3%) and evidence of barcode switching (0.3%) in our dataset, which likely arise during library preparation and may be detrimental for quantitative studies that use multiplexing. Deepbinner is open source (GPLv3) and available at https://github.com/rrwick/Deepbinner.},
}
@article {pmid30455081,
year = {2019},
author = {Caron, DA and Hu, SK},
title = {Are We Overestimating Protistan Diversity in Nature?.},
journal = {Trends in microbiology},
volume = {27},
number = {3},
pages = {197-205},
doi = {10.1016/j.tim.2018.10.009},
pmid = {30455081},
issn = {1878-4380},
mesh = {*Biodiversity ; *Ecosystem ; Eukaryota/*classification/*physiology ; *Genetic Variation ; High-Throughput Nucleotide Sequencing ; Phylogeny ; },
abstract = {Documenting the immense diversity of single-celled, eukaryotic organisms (protists) has been a formidable challenge for ecologists. These species were originally defined by morphological criteria, but shortcomings of the morphospecies concept, and a bewildering array of sizes and cellular attributes, has made constructing a taxonomy that is useful for ecologists nearly impossible. Consequently, physiological and genetic information has been integrated to address these shortcomings, and to develop the framework of a unifying taxonomy. DNA sequence information, in particular, has revolutionized studies of protistan diversity. However, the exponential increase in sequence-based protistan species richness published from field surveys in recent years raises the question of whether we have moved beyond characterizing species-level diversity and begun to reveal intraspecies diversity. The answer to that question appears to be 'yes', at least for some protistan lineages. The need to document such microdiversity may be justified, but it is important for protistologists to recognize and acknowledge that possibility, and its consequences.},
}
@article {pmid30453710,
year = {2018},
author = {Xing, YP and Chen, SY and Xu, L and Liang, YM and Wang, JH and Wang, B and Liu, T and Kang, TG},
title = {[Study on high throughput sequencing identification of Fructus Arctii and five counterfeit species mix power].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {43},
number = {19},
pages = {3862-3866},
doi = {10.19540/j.cnki.cjcmm.20180703.012},
pmid = {30453710},
issn = {1001-5302},
mesh = {Arctium/*chemistry/classification ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; *Drug Contamination ; Drugs, Chinese Herbal/*standards ; Fabaceae ; Fruit ; *High-Throughput Nucleotide Sequencing ; Silybum marianum ; Onopordum ; Phylogeny ; Saussurea ; },
abstract = {Fructus Arctii is a traditional Chinese medicine. The main counterfeit species are the seeds of Arctium tomentosum, Onopordum acanthium, Silybum marianum, Saussurea costus, Amorpha fruticosa. Traditional identification methods or molecular barcoding techniques can identify Fructus Arctii and its counterfeit species. However, the identification of the mixture of it and its spurious species is rarely reported. In this paper, we sequenced the ITS2 sequences of Fructus Arctii and 5 kinds of spurious species mix powder by high-throughput sequencing to identify the mixed powder species and providing new ideas for the identification of Fructus Arctii mix powder. The total DNA in mixed powder was extracted, and the ITS2 sequences in total DNA was amplified. Paired-end sequencing was performed on the DNA fragment of the community using the Illumina MiSeq platform. The sequence was analyzed by the software FLASH, QIIME and GraPhlAn etc. The results showed that the high quality ITS2 sequences of 39910 mix samples were obtained from the mixed samples, of which the total ITS2 sequence of the samples genus was 34 935. Phylogenetic analysis showed that the samples contained Fructus Arctii, A. tomentosum, O. acanthium, S. marianum, S. costus and A. fruticosa. Using ITS2 sequences as DNA barcodes, high-throughput sequencing technology can be used to detect the Fructus Arctii and its spurious specie in mixed powder, which can provide reference for the quality control, safe use of medicinal materials of Fructus Arctii and the identification of mixed powder of traditional Chinese medicine.},
}
@article {pmid30451423,
year = {2018},
author = {Powers, T and Harris, T and Higgins, R and Mullin, P and Powers, K},
title = {Discovery and Identification of Meloidogyne Species Using COI DNA Barcoding.},
journal = {Journal of nematology},
volume = {50},
number = {3},
pages = {399-412},
pmid = {30451423},
issn = {0022-300X},
abstract = {DNA barcoding with a new cytochrome oxidase c subunit 1 primer set generated a 721 to 724 bp fragment used for the identification of 322 Meloidogyne specimens, including 205 new sequences combined with 117 from GenBank. A maximum likelihood analysis grouped the specimens into 19 well-supported clades and four single-specimen lineages. The "major" tropical apomictic species (Meloidogyne arenaria , Meloidogyne incognita , Meloidogyne javanica) were not discriminated by this barcode although some closely related species such as Meloidogyne konaensis were characterized by fixed diagnostic nucleotides. Species that were collected from multiple localities and strongly characterized as discrete lineages or species include Meloidogyne enterolobii , Meloidogyne partityla , Meloidogyne hapla , Meloidogyne graminicola , Meloidogyne naasi , Meloidogyne chitwoodi , and Meloidogyne fallax . Seven unnamed groups illustrate the limitations of DNA barcoding without the benefit of a well-populated reference library. The addition of these DNA sequences to GenBank and the Barcode of Life Database (BOLD) should stimulate and facilitate root-knot nematode identification and provide a first step in new species discovery.},
}
@article {pmid30448259,
year = {2018},
author = {Lyne, AM and Kent, DG and Laurenti, E and Cornils, K and Glauche, I and Perié, L},
title = {A track of the clones: new developments in cellular barcoding.},
journal = {Experimental hematology},
volume = {68},
number = {},
pages = {15-20},
doi = {10.1016/j.exphem.2018.11.005},
pmid = {30448259},
issn = {1873-2399},
support = {MC_PC_12009/MRC_/Medical Research Council/United Kingdom ; MC_PC_16040/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; BB/R021465/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Cell Lineage ; Cell Separation/methods ; Cell Tracking/*methods ; Clinical Trials as Topic ; Clone Cells/*cytology ; *DNA Barcoding, Taxonomic/methods/standards ; DNA Transposable Elements ; Data Display/standards ; Forecasting ; Genetic Markers ; Genetic Therapy ; Guidelines as Topic ; Hematopoiesis ; Models, Biological ; Mosaicism ; Reproducibility of Results ; Research Design ; Stem Cells/cytology ; Virus Integration/genetics ; },
abstract = {International experts from multiple disciplines gathered at Homerton College in Cambridge, UK from September 12-14, 2018 to consider recent advances and emerging opportunities in the clonal tracking of hematopoiesis in one of a series of StemCellMathLab workshops. The group included 35 participants with experience in the fields of theoretical and experimental aspects of clonal tracking, and ranged from doctoral students to senior professors. Data from a variety of model systems and from clinical gene therapy trials were discussed, along with strategies for data analysis and sharing and challenges arising due to underlying assumptions in data interpretation and communication. Recognizing the power of this technology underpinned a group consensus of a need for improved mechanisms for sharing data and analytical protocols to maintain reproducibility and rigor in its application to complex tissues.},
}
@article {pmid30446870,
year = {2019},
author = {Liu, Q and Wang, C and Jiao, X and Zhang, H and Song, L and Li, Y and Gao, C and Wang, K},
title = {Hi-TOM: a platform for high-throughput tracking of mutations induced by CRISPR/Cas systems.},
journal = {Science China. Life sciences},
volume = {62},
number = {1},
pages = {1-7},
doi = {10.1007/s11427-018-9402-9},
pmid = {30446870},
issn = {1869-1889},
mesh = {Base Sequence ; *CRISPR-Cas Systems ; Computational Biology/*methods ; Gene Editing/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Mutation ; Reproducibility of Results ; },
abstract = {The CRISPR/Cas system has been extensively applied to make precise genetic modifications in various organisms. Despite its importance and widespread use, large-scale mutation screening remains time-consuming, labour-intensive and costly. Here, we developed Hi-TOM (available at https://doi.org/www.hi-tom.net/hi-tom/), an online tool to track the mutations with precise percentage for multiple samples and multiple target sites. We also described a corresponding next-generation sequencing (NGS) library construction strategy by fixing the bridge sequences and barcoding primers. Analysis of the samples from rice, hexaploid wheat and human cells reveals that the Hi-TOM tool has high reliability and sensitivity in tracking various mutations, especially complex chimeric mutations frequently induced by genome editing. Hi-TOM does not require special design of barcode primers, cumbersome parameter configuration or additional data analysis. Thus, the streamlined NGS library construction and comprehensive result output make Hi-TOM particularly suitable for high-throughput identification of all types of mutations induced by CRISPR/Cas systems.},
}
@article {pmid30445905,
year = {2018},
author = {Tekle, YI and Wood, FC},
title = {A practical implementation of large transcriptomic data analysis to resolve cryptic species diversity problems in microbial eukaryotes.},
journal = {BMC evolutionary biology},
volume = {18},
number = {1},
pages = {170},
pmid = {30445905},
issn = {1471-2148},
support = {R15 GM116103/GM/NIGMS NIH HHS/United States ; 1R15GM116103-01/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Base Sequence ; Biological Evolution ; DNA Barcoding, Taxonomic ; *Data Analysis ; Eukaryota/*genetics ; *Gene Expression Profiling ; Genetic Markers ; *Genetic Variation ; Genome ; Phylogeny ; Species Specificity ; Transcriptome/genetics ; },
abstract = {BACKGROUND: Transcriptome sequencing has become a method of choice for evolutionary studies in microbial eukaryotes due to low cost and minimal sample requirements. Transcriptome data has been extensively used in phylogenomic studies to infer ancient evolutionary histories. However, its utility in studying cryptic species diversity is not well explored. An empirical investigation was conducted to test the applicability of transcriptome data in resolving two major types of discordances at lower taxonomic levels. These include cases where species have the same morphology but different genetics (cryptic species) and species of different morphologies but have the same genetics. We built a species comparison bioinformatic pipeline that takes into account the nature of transcriptome data in amoeboid microbes exemplifying such discordances.<br><br>RESULT: Our analyses of known or suspected cryptic species yielded consistent results regardless of the methods of culturing, RNA collection or sequencing. Over 95% of the single copy genes analyzed in samples of the same species sequenced using different methods and cryptic species had intra- and interspecific divergences below 2%. Only a minority of groups (2.91-4.87%) had high distances exceeding 2% in these taxa, which was likely caused by low data quality. This pattern was also observed in suspected genetically similar species with different morphologies. Transcriptome data consistently delineated all taxa above species level, including cryptically diverse species. Using our approach we were able to resolve cryptic species problems, uncover misidentification and discover new species. We also identified several potential barcode markers with varying evolutionary rates that can be used in lineages with different evolutionary histories.<br><br>CONCLUSION: Our findings demonstrate that transcriptome data is appropriate for understanding cryptic species diversity in microbial eukaryotes.},
}
@article {pmid30445082,
year = {2019},
author = {Amini, A and Kamali, M and Amini, B and Najafi, A and Narmani, A and Hasani, L and Rashidiani, J and Kooshki, H and Elahi, N},
title = {Bio-barcode technology for detection of Staphylococcus aureus protein A based on gold and iron nanoparticles.},
journal = {International journal of biological macromolecules},
volume = {124},
number = {},
pages = {1256-1263},
doi = {10.1016/j.ijbiomac.2018.11.123},
pmid = {30445082},
issn = {1879-0003},
mesh = {*Bacterial Typing Techniques ; *Biosensing Techniques ; DNA Barcoding, Taxonomic/*methods ; DNA Probes/chemical synthesis/chemistry ; DNA, Bacterial/*chemistry/metabolism ; Gold/chemistry ; Humans ; Iron/chemistry ; Limit of Detection ; Magnets ; Metal Nanoparticles/*chemistry ; Spectrometry, Fluorescence ; Staphylococcal Protein A/*analysis ; Staphylococcus aureus/classification/*genetics/isolation &amp; purification ; },
abstract = {S. aureus is one of important causes of disease, food poisoning in humans and animals. The generally methods for detection of S. aureus is time consuming. Therefore, a new method is necessary for rapid, sensitive and specific diagnosis of S. aureus. In the present study, two probes and a Bio-barcode DNA were designed for detection of S. aureus (Protein A). Firstly, magnetic nanoparticle (MNPs) and gold nanoparticle (AuNPs) were synthesized at 80 °C and 100 °C, respectively. The AuNPs and the MNPs were functionalized with probe1, Bio-barcode DNA and probe2, respectively. Target DNA was added into the nanomaterial's system containing bio-barcode DNA-AuNPs-probe1 and probe2-MNPs to formed bio-barcode DNA-AuNPs-probe1-target DNA-probe2-MNPs complex. The bio-barcode DNA-AuNPs-probe1-target DNA-probe2-MNPs complex was separated with magnetic field. Finally, the bio-barcode DNA was released from surface of complex using DTT (0.8 M) and there was isolated of nanoparticles by magnetic field and centrifuge. The fluorescence intensity of bio-barcode DNA was measured in different concentrations of S. aureus (10[1] to 10[8] CFU mL[-1]) by fluorescence spectrophotometry. The results showed that standard curve was linearly from 10[2] to 10[7] CFU mL[-1]. Limit of detection of bio-barcode assay for both PBS and real samples was 86 CFU mL[-1].},
}
@article {pmid30444869,
year = {2018},
author = {Marín, A and Serna, J and Robles, C and Ramírez, B and Reyes-Flores, LE and Zelada-Mázmela, E and Sotil, G and Alfaro, R},
title = {A glimpse into the genetic diversity of the Peruvian seafood sector: Unveiling species substitution, mislabeling and trade of threatened species.},
journal = {PloS one},
volume = {13},
number = {11},
pages = {e0206596},
pmid = {30444869},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; Conservation of Natural Resources ; DNA Barcoding, Taxonomic ; Humans ; Oceans and Seas ; Peru ; Phylogeny ; Restaurants ; *Seafood ; },
abstract = {Peru is one of the world's leading fishing nations and its seafood industry relies on the trade of a vast variety of aquatic resources, playing a key role in the country's socio-economic development. DNA barcoding has become of paramount importance for systematics, conservation, and seafood traceability, complementing or even surpassing conventional identification methods when target organisms show similar morphology during the early life stages, have recently diverged, or have undergone processing. Aiming to increase our knowledge of the species diversity available across the Peruvian supply chain (from fish landing sites to markets and restaurants), we applied full and mini-barcoding approaches targeting three mitochondrial genes (COI, 16S, and 12S) and the control region to identify samples purchased at retailers from six departments along the north-central Peruvian coast. DNA barcodes from 131 samples were assigned to 55 species (plus five genus-level taxa) comprising 47 families, 24 orders, and six classes including Actinopterygii (45.03%), Chondrichthyes (36.64%), Bivalvia (6.87%), Cephalopoda (6.11%), Malacostraca (3.82%), and Gastropoda (1.53%). The identified samples included commercially important pelagic (anchovy, bonito, dolphinfish) and demersal (hake, smooth-hound, Peruvian rock seabass, croaker) fish species. Our results unveiled the marketing of protected and threatened species such as whale shark, Atlantic white marlin, smooth hammerhead (some specimens collected during closed season), shortfin mako, and pelagic thresher sharks. A total of 35 samples (26.72%) were mislabeled, including tilapia labeled as wild marine fish, dolphinfish and hake labeled as grouper, and different shark species sold as "smooth-hounds". The present study highlights the necessity of implementing traceability and monitoring programs along the entire seafood supply chain using molecular tools to enhance sustainability efforts and ensure consumer choice.},
}
@article {pmid30443805,
year = {2019},
author = {Urcelay, C and Longo, S and Geml, J and Tecco, PA},
title = {Can arbuscular mycorrhizal fungi from non-invaded montane ecosystems facilitate the growth of alien trees?.},
journal = {Mycorrhiza},
volume = {29},
number = {1},
pages = {39-49},
pmid = {30443805},
issn = {1432-1890},
support = {30720150101048CB//Secretaria de Ciencia y Tecnica, Universidad de Buenos Aires (AR)/ ; -//Naturalis Research Initiative grant/ ; },
mesh = {Anacardiaceae/growth &amp; development/microbiology ; Argentina ; *Ecosystem ; Gleditsia/growth &amp; development/microbiology ; Introduced Species ; Ligustrum/growth &amp; development/microbiology ; Mycorrhizae/*physiology ; Pyracantha/growth &amp; development/microbiology ; Trees/*growth &amp; development/*microbiology ; },
abstract = {It is generally assumed that recruitment and expansion of alien species along elevation gradients are constrained by climate. But, if plants are not fully constrained by climate, their expansion could be facilitated or hindered by other factors such as biotic interactions. Here, we assessed the composition of arbuscular mycorrhizal fungi (AMF) in soils along an elevation gradient (i.e. 900 m, 1600 m, 2200 m and 2700 m a.s.l.) through a fungal DNA meta-barcoding approach. In addition, we studied in the greenhouse the effects of AMF on growth and phosphorous (P) nutrition of seedlings of the alien trees Gleditsia triacanthos, Ligustrum lucidum and Pyracantha angustifolia cultivated in soils from those elevations, spanning the elevation at which they already form monospecific stands (below 1450 m a.s.l.) and higher elevations, above their current range of distribution in montane ecosystems of Central Argentina. For comparison, we also included in the experiment the dominant native tree Lithraea molleoides that historically occurs below 1300 m a.s.l. Arbuscular mycorrhizal fungal community composition showed strong community turnover with increasing elevation. The effects of these AMF communities on plant growth and nutrition differed among native and alien trees. While P nutrition in alien species' seedlings was generally enhanced by AMF along the whole gradient, the native species benefited only from AMF that occur in soils from the elevation corresponding to its current altitudinal range of distribution. These results suggest that AMF might foster upper range expansion of these invasive trees over non-invaded higher elevations.},
}
@article {pmid30431229,
year = {2019},
author = {Schmid-Egger, C and Straka, J and Ljubomirov, T and Blagoev, GA and Morinière, J and Schmidt, S},
title = {DNA barcodes identify 99 per cent of apoid wasp species (Hymenoptera: Ampulicidae, Crabronidae, Sphecidae) from the Western Palearctic.},
journal = {Molecular ecology resources},
volume = {19},
number = {2},
pages = {476-484},
doi = {10.1111/1755-0998.12963},
pmid = {30431229},
issn = {1755-0998},
support = {//Bayerisches Staatsministerium f&#xfc;r Wissenschaft und Kunst, Science and Art/ ; //German Federal Ministry of Education and Research/ ; //Ontario Ministry of Research and Innovation/ ; },
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Europe ; Wasps/*classification/*genetics ; },
abstract = {The apoid wasps have traditionally been regarded as a paraphyletic assemblage of four families (Ampulicidae, Crabronidae, Heterogynaidae and Sphecidae) that are closely related to the bees (Anthophila). The present study covers the three families of apoid wasps known to occur in Europe, that is, the Ampulicidae, Crabronidae and Sphecidae. DNA barcode sequences of 3,695 specimens of apoid wasps were analysed for the present study, including 21 specimens of Ampulicidae, 3,398 Crabronidae and 276 Sphecidae. The sequences of the dataset represent 661 species of apoid wasps, including two species of Ampulicidae, 613 of Crabronidae and 46 species of Sphecidae. The dataset includes DNA barcodes of 240 species of German apoid wasps, representing 88% of the German fauna, and 578 European species, representing 65% of the European apoid wasp fauna. The study demonstrates that virtually all species of the three examined families can be reliably identified by DNA barcodes. The implications of highly congruent results between traditional taxonomy and DNA barcoding for the reliable application of DNA-based identifications are discussed.},
}
@article {pmid30429654,
year = {2018},
author = {Garces, JM and Bauernfeind, E and Freitag, H},
title = {Sparsorythussescarorum, new species from Mindoro, Philippines (Ephemeroptera, Tricorythidae).},
journal = {ZooKeys},
volume = {},
number = {795},
pages = {13-30},
pmid = {30429654},
issn = {1313-2989},
abstract = {A new mayfly species, Sparsorythussescarorum sp. n. (Tricorythidae) is described from Mindoro Island, Philippines. Nymphs are characterized by the combination of the following characters: compound eyes of approximately equal size in both sexes, shape and setation of legs, presence of rudimentary gills on abdominal segment VII, and some details of mouthparts. Male imagines are characterized by the coloration pattern of wings and details of genitalia. The developmental stages are matched by DNA barcodes.},
}
@article {pmid30429653,
year = {2018},
author = {Jochum, A and Ruthensteiner, B and Kampschulte, M and Martels, G and Kneubühler, J and Favre, A},
title = {Fulfilling the taxonomic consequence after DNA Barcoding: Carychiumpanamaense sp. n. (Eupulmonata, Ellobioidea, Carychiidae) from Panama is described using computed tomographic (CT) imaging.},
journal = {ZooKeys},
volume = {},
number = {795},
pages = {1-12},
pmid = {30429653},
issn = {1313-2989},
abstract = {Five years ago, the Panamanian evolutionary lineage (EL) C12 was uncovered along with four other ELs in an integrative phylogenetic investigation of worldwide Carychiidae. Since EL C12 lacked shell material post-molecular analysis to serve as a museum voucher, it remained undescribed. Now, after recent collection efforts of C12 and the congener, Carychiumzarzaae Jochum &amp; Weigand, 2017 at their original Panamanian sites, C12 is morphologically described and formally assigned the name, Carychiumpanamaense Jochum, sp. n. In sync with recent taxonomic treatment of the genus, computed tomography (CT) is used in this work to differentiate shells of C.panamaense sp. n. from geographically-proximal, Caribbean, North and Central American congeners. Recent material of topotypic Carychiumjardineanum (Chitty, 1853) and undamaged C.zarzaae were additionally CT-scanned and assessed in the comparative analyses.},
}
@article {pmid30427929,
year = {2018},
author = {Shahhosseini, N and Kayedi, MH and Sedaghat, MM and Racine, T and P Kobinger, G and Moosa-Kazemi, SH},
title = {DNA barcodes corroborating identification of mosquito species and multiplex real-time PCR differentiating Culex pipiens complex and Culex torrentium in Iran.},
journal = {PloS one},
volume = {13},
number = {11},
pages = {e0207308},
pmid = {30427929},
issn = {1932-6203},
mesh = {Animals ; Culex/*classification/genetics ; Culicidae/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; Female ; Iran ; Multiplex Polymerase Chain Reaction/methods ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {Identifying mosquito species is a fundamental step in risk assessment and implementation of preventative strategies. Moreover, Culex pipiens is the most widespread mosquito vector in several regions of Iran and is the main vector for transmission of West Nile virus (WNV). Mosquitoes were collected at 14 sites in northern regions of Iran in 2015 and 2016. A subset of mosquito specimens was selected for identification confirmation using a DNA-barcoding technique. Construction of a phylogenetic tree showed clustering of mosquito sequences into three main genera: Aedes, Anopheles and Culex with individuals of a single species clustered closely together, regardless of where and when they were collected. Cx. pipiens complex and Cx. torrentium were identified and differentiated using multiplex real-time PCR targeting the gene locus for acetylcholinesterase 2 (ace2) to discriminate between Cx. pipiens pipiens and Cx. torrentium. The CQ11 microsatellite locus was used for discrimination between Cpp. biotypes. The predominant mosquito species in investigated regions were Cx. pipiens pipiens biotype pipiens, but we also detected Culex pipiens pipiens biotype molestus and hybrids of the two pipiens biotypes, as well as Cx. torrentium. The results of this study represent the first certain evidence of the presence of Cx. pipiens pipiens biotype molestus and hybrids between pipiens and molestus forms, and Cx. torrentium in Iran through a molecular identification approach. This report of a potentially important bridge vector for WNV might have key influence in the risk projections for WNV in Iran.},
}
@article {pmid30427082,
year = {2019},
author = {Clare, EL and Fazekas, AJ and Ivanova, NV and Floyd, RM and Hebert, PDN and Adams, AM and Nagel, J and Girton, R and Newmaster, SG and Fenton, MB},
title = {Approaches to integrating genetic data into ecological networks.},
journal = {Molecular ecology},
volume = {28},
number = {2},
pages = {503-519},
doi = {10.1111/mec.14941},
pmid = {30427082},
issn = {1365-294X},
mesh = {Animals ; Costa Rica ; *DNA Barcoding, Taxonomic ; *Ecology ; Food Chain ; Insecta/*genetics/physiology ; Plants/*genetics ; Symbiosis/genetics ; },
abstract = {As molecular tools for assessing trophic interactions become common, research is increasingly focused on the construction of interaction networks. Here, we demonstrate three key methods for incorporating DNA data into network ecology and discuss analytical considerations using a model consisting of plants, insects, bats and their parasites from the Costa Rica dry forest. The simplest method involves the use of Sanger sequencing to acquire long sequences to validate or refine field identifications, for example of bats and their parasites, where one specimen yields one sequence and one identification. This method can be fully quantified and resolved and these data resemble traditional ecological networks. For more complex taxonomic identifications, we target multiple DNA loci, for example from a seed or fruit pulp sample in faeces. These networks are also well resolved but gene targets vary in resolution and quantification is difficult. Finally, for mixed templates such as faecal contents of insectivorous bats, we use DNA metabarcoding targeting two sequence lengths (157 and 407 bp) of one gene region and a MOTU, BLAST and BIN association approach to resolve nodes. This network type is complex to generate and analyse, and we discuss the implications of this type of resolution on network analysis. Using these data, we construct the first molecular-based network of networks containing 3,304 interactions between 762 nodes of eight trophic functions and involving parasitic, mutualistic and predatory interactions. We provide a comparison of the relative strengths and weaknesses of these data types in network ecology.},
}
@article {pmid30426225,
year = {2019},
author = {Kambayashi, C and Kurabayashi, A and Nakano, T},
title = {Evaluating the ontogenetic external morphology of an ectoparasitic Torix tukubana (Hirudinida: Glossiphoniidae), with records of its new host amphibian species.},
journal = {Parasitology research},
volume = {118},
number = {2},
pages = {663-666},
pmid = {30426225},
issn = {1432-1955},
support = {JP15J00720//Japan Society for the Promotion of Science/ ; JP17K20064//Japan Society for the Promotion of Science/ ; JP26291080//Japan Society for the Promotion of Science/ ; JP18H02497//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; Cyclooxygenase 1/genetics ; Fresh Water/parasitology ; Host Specificity/*physiology ; Japan ; Leeches/classification/*genetics ; Phylogeny ; Ranidae/*parasitology ; Caudata/*parasitology ; },
abstract = {Torix is a leech genus containing freshwater proboscidate species, and several members of this taxon are ectoparasites specific to amphibians. Torix tukubana inhabits mountain streams in Japan, and only two frog species are known to be hosts. We collected this leech from two other amphibians, Onychodactylus japonicus (Japanese clawed salamander) and Rana ornativentris (montane brown frog), for the first time. This finding suggests that the host specificity of T. tukubana is low. The immature individuals of T. tukubana were also collected and identified based on DNA data. This is the first juvenile record of this species confirmed by its DNA barcode sequences. Several morphological characters known from large individuals and used as diagnostic characteristics in taxonomic keys were not observed in the juveniles, suggesting that these are ontogenetic traits.},
}
@article {pmid30426073,
year = {2018},
author = {McPartland, JM},
title = {Cannabis Systematics at the Levels of Family, Genus, and Species.},
journal = {Cannabis and cannabinoid research},
volume = {3},
number = {1},
pages = {203-212},
pmid = {30426073},
issn = {2578-5125},
abstract = {New concepts are reviewed in Cannabis systematics, including phylogenetics and nomenclature. The family Cannabaceae now includes Cannabis, Humulus, and eight genera formerly in the Celtidaceae. Grouping Cannabis, Humulus, and Celtis actually goes back 250 years. Print fossil of the extinct genus Dorofeevia (=Humularia) reveals that Cannabis lost a sibling perhaps 20 million years ago (mya). Cannabis print fossils are rare (n=3 worldwide), making it difficult to determine when and where she evolved. A molecular clock analysis with chloroplast DNA (cpDNA) suggests Cannabis and Humulus diverged 27.8 mya. Microfossil (fossil pollen) data point to a center of origin in the northeastern Tibetan Plateau. Fossil pollen indicates that Cannabis dispersed to Europe by 1.8-1.2 mya. Mapping pollen distribution over time suggests that European Cannabis went through repeated genetic bottlenecks, when the population shrank during range contractions. Genetic drift in this population likely initiated allopatric differences between European Cannabis sativa (cannabidiol [CBD]>Δ[9]-tetrahydrocannabinol [THC]) and Asian Cannabis indica (THC>CBD). DNA barcode analysis supports the separation of these taxa at a subspecies level, and recognizing the formal nomenclature of C. sativa subsp. sativa and C. sativa subsp. indica. Herbarium specimens reveal that field botanists during the 18th-20th centuries applied these names to their collections rather capriciously. This may have skewed taxonomic determinations by Vavilov and Schultes, ultimately giving rise to today's vernacular taxonomy of "Sativa" and "Indica," which totally misaligns with formal C. sativa and C. indica. Ubiquitous interbreeding and hybridization of "Sativa" and "Indica" has rendered their distinctions almost meaningless.},
}
@article {pmid30420949,
year = {2018},
author = {Appenroth, KJ and Sree, KS and Bog, M and Ecker, J and Seeliger, C and Böhm, V and Lorkowski, S and Sommer, K and Vetter, W and Tolzin-Banasch, K and Kirmse, R and Leiterer, M and Dawczynski, C and Liebisch, G and Jahreis, G},
title = {Nutritional Value of the Duckweed Species of the Genus Wolffia (Lemnaceae) as Human Food.},
journal = {Frontiers in chemistry},
volume = {6},
number = {},
pages = {483},
pmid = {30420949},
issn = {2296-2646},
abstract = {Species of the genus Wolffia are traditionally used as human food in some of the Asian countries. Therefore, all 11 species of this genus, identified by molecular barcoding, were investigated for ingredients relevant to human nutrition. The total protein content varied between 20 and 30% of the freeze-dry weight, the starch content between 10 and 20%, the fat content between 1 and 5%, and the fiber content was ~25%. The essential amino acid content was higher or close to the requirements of preschool-aged children according to standards of the World Health Organization. The fat content was low, but the fraction of polyunsaturated fatty acids was above 60% of total fat and the content of n-3 polyunsaturated fatty acids was higher than that of n-6 polyunsaturated fatty acids in most species. The content of macro- and microelements (minerals) not only depended on the cultivation conditions but also on the genetic background of the species. This holds true also for the content of tocopherols, several carotenoids and phytosterols in different species and even intraspecific, clonal differences were detected in Wolffia globosa and Wolffia arrhiza. Thus, the selection of suitable clones for further applications is important. Due to the very fast growth and the highest yield in most of the nutrients, Wolffia microscopica has a high potential for practical applications in human nutrition.},
}
@article {pmid30418699,
year = {2019},
author = {Tiusanen, M and Huotari, T and Hebert, PDN and Andersson, T and Asmus, A and Bêty, J and Davis, E and Gale, J and Hardwick, B and Hik, D and Körner, C and Lanctot, RB and Loonen, MJJE and Partanen, R and Reischke, K and Saalfeld, ST and Senez-Gagnon, F and Smith, PA and Šulavík, J and Syvänperä, I and Urbanowicz, C and Williams, S and Woodard, P and Zaika, Y and Roslin, T},
title = {Flower-visitor communities of an arcto-alpine plant-Global patterns in species richness, phylogenetic diversity and ecological functioning.},
journal = {Molecular ecology},
volume = {28},
number = {2},
pages = {318-335},
pmid = {30418699},
issn = {1365-294X},
support = {276909//Suomen Akatemia/International ; //Societas entomologica helsingforsiensis/International ; //FP7 Ideas: European Research Council/International ; //Ella ja Georg Ehrnroothin S&#xe4;&#xe4;ti&#xf6;/International ; //Ella &amp; Georg Ehrnrooth Foundation/International ; //International Network for Terrestrial Research and Monitoring in the Arctic under the European Community's Seventh Framework Programme/International ; },
mesh = {Animals ; Arctic Regions ; Arthropods/genetics/*physiology ; DNA Barcoding, Taxonomic ; *Ecosystem ; Flowers/genetics/growth &amp; development ; Models, Biological ; Phylogeny ; Pollination/*physiology ; Reproduction ; Rosaceae/growth &amp; development/physiology/*poisoning ; Seeds/genetics/growth &amp; development ; },
abstract = {Pollination is an ecosystem function of global importance. Yet, who visits the flower of specific plants, how the composition of these visitors varies in space and time and how such variation translates into pollination services are hard to establish. The use of DNA barcodes allows us to address ecological patterns involving thousands of taxa that are difficult to identify. To clarify the regional variation in the visitor community of a widespread flower resource, we compared the composition of the arthropod community visiting species in the genus Dryas (mountain avens, family Rosaceae), throughout Arctic and high-alpine areas. At each of 15 sites, we sampled Dryas visitors with 100 sticky flower mimics and identified specimens to Barcode Index Numbers (BINs) using a partial sequence of the mitochondrial COI gene. As a measure of ecosystem functioning, we quantified variation in the seed set of Dryas. To test for an association between phylogenetic and functional diversity, we characterized the structure of local visitor communities with both taxonomic and phylogenetic descriptors. In total, we detected 1,360 different BINs, dominated by Diptera and Hymenoptera. The richness of visitors at each site appeared to be driven by local temperature and precipitation. Phylogeographic structure seemed reflective of geological history and mirrored trans-Arctic patterns detected in plants. Seed set success varied widely among sites, with little variation attributable to pollinator species richness. This pattern suggests idiosyncratic associations, with function dominated by few and potentially different taxa at each site. Taken together, our findings illustrate the role of post-glacial history in the assembly of flower-visitor communities in the Arctic and offer insights for understanding how diversity translates into ecosystem functioning.},
}
@article {pmid30415443,
year = {2019},
author = {Basak, S and Chakrabartty, I and Hedaoo, V and Shelke, RG and Rangan, L},
title = {Assessment of genetic variation among wild Alpinia nigra (Zingiberaceae) population: an approach based on molecular phylogeny.},
journal = {Molecular biology reports},
volume = {46},
number = {1},
pages = {177-189},
pmid = {30415443},
issn = {1573-4978},
support = {DBT Twinning Programme for NE (BT/33/NE/TBP/2010)//Department of Biotechnology, Government of India/ ; },
mesh = {China ; DNA Barcoding, Taxonomic/*methods ; Gene Flow ; Genetic Variation/genetics ; Genetics, Population/*methods ; Microsatellite Repeats ; Phylogeny ; Random Amplified Polymorphic DNA Technique ; Zingiberaceae/*genetics ; },
abstract = {Genetic structure was evaluated among wild Alpinia nigra (Gaertn.) B.L. Burtt, populations. The information of genetic relatedness was developed using random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR) and barcoding loci (plastid and mitochondrial). The order (high to low) of Shannon's information index (I) and Nei's gene diversity (h) from the populations was: "IIT Guwahati" > "Amingaon" > "Saraighat". Genetic diversity decreased and genetic differentiation increased among the three populations. We observed no isolation by distance thus lower amount of gene flow was observed. Narrow range of genetic distance among the three populations and appearance of two distinct clusters strengthened the geographical isolation in dendrogram and principal component analysis. No mutation among the three populations was observed for seven plastid loci and two mitochondrial tested suggesting the taxonomic homogeneity. The phylogeny based on nine barcoding loci supported our observation that individuals of IIT Guwahati were partially isolated from the outside populations. Our study will provide a backbone for developing strategies to resist habitat fragmentation of Zingiberaceous plants.},
}
@article {pmid30413082,
year = {2018},
author = {Sontigun, N and Sukontason, KL and Amendt, J and Zajac, BK and Zehner, R and Sukontason, K and Chareonviriyaphap, T and Wannasan, A},
title = {Molecular Analysis of Forensically Important Blow Flies in Thailand.},
journal = {Insects},
volume = {9},
number = {4},
pages = {},
pmid = {30413082},
issn = {2075-4450},
support = {PHD/0118/2556//Thailand Research Fund through the Royal Golden Jubilee Ph.D. Program/ ; IRN58W0003//International Research Network/ ; PAR-2560-04663//Faculty of Medicine Research Fund and Diamond Research Grant of the Faculty of Medicine, Chiang Mai University/ ; },
abstract = {Blow flies are the first insect group to colonize on a dead body and thus correct species identification is a crucial step in forensic investigations for estimating the minimum postmortem interval, as developmental times are species-specific. Due to the difficulty of traditional morphology-based identification such as the morphological similarity of closely related species and uncovered taxonomic keys for all developmental stages, DNA-based identification has been increasing in interest, especially in high biodiversity areas such as Thailand. In this study, the effectiveness of long mitochondrial cytochrome c oxidase subunit I and II (COI and COII) sequences (1247 and 635 bp, respectively) in identifying 16 species of forensically relevant blow flies in Thailand (Chrysomya bezziana, Chrysomya chani, Chrysomya megacephala, Chrysomya nigripes, Chrysomya pinguis, Chrysomya rufifacies, Chrysomya thanomthini, Chrysomya villeneuvi, Lucilia cuprina, Lucilia papuensis, Lucilia porphyrina, Lucilia sinensis, Hemipyrellia ligurriens, Hemipyrellia pulchra, Hypopygiopsis infumata, and Hypopygiopsis tumrasvini) was assessed using distance-based (Kimura two-parameter distances based on Best Match, Best Close Match, and All Species Barcodes criteria) and tree-based (grouping taxa by sequence similarity in the neighbor-joining tree) methods. Analyses of the obtained sequence data demonstrated that COI and COII genes were effective markers for accurate species identification of the Thai blow flies. This study has not only demonstrated the genetic diversity of Thai blow flies, but also provided a reliable DNA reference database for further use in forensic entomology within the country and other regions where these species exist.},
}
@article {pmid30405561,
year = {2018},
author = {Zhang, P and Cui, S and Ren, X and Kang, S and Wei, F and Ma, S and Liu, B},
title = {Discriminatory Power Evaluation of Nuclear Ribosomal RNA Barcoding Sequences Through Ophiocordyceps sinensis Related Samples.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2498},
pmid = {30405561},
issn = {1664-302X},
abstract = {Since the cost of Ophiocordyceps sinensis has increased dramatically and the counterfeits may have adverse effect to health, a rapid and precise species-level DNA barcoding identification system could be a potent approach and significantly enhance the regulatory capacity. The discrimination power of three subunits sequences from nuclear ribosomal RNA gene cluster were determined by Simpson's index of discrimination using 43 wild O. sinensis fruiting bodies, pure cultures, commercial mycelium fermented powder and counterfeits. The internal transcribed spacer (ITS) sequences showed the highest variance and discrimination power among 43 samples, as determined by Simpson's index of discrimination (D = 0.972), followed by large subunit (LSU; D = 0.963) and small subunit (SSU; D = 0.921). ITS-2 sequences showed the highest discrimination power for 43 samples among ITS-1, ITS-2, and 5.8S region of ITS sequences. All O. sinensis samples were grouped into a unique ITS sequence cluster under 95% similarity and two O. sinensis samples and six non-O. sinensis samples showed false claims. Our data showed that the ITS region could provide accurate species identification for O. sinensis samples, especially when macroscopic and microscopic method could not be applied in the highly processed commercial products. Since the authentication of O. sinensis related products is essential to ensure its safety and efficacy, identification of O. sinensis through ITS sequence comparison or unique PCR amplification of the species specific target, such as the ITS region, should be considered in the next revision of Chinese pharmacopeia.},
}
@article {pmid30398899,
year = {2018},
author = {Liu, L and Guo, Z and Zhong, C and Shi, S},
title = {DNA barcoding reveals insect diversity in the mangrove ecosystems of Hainan Island, China.},
journal = {Genome},
volume = {61},
number = {11},
pages = {797-806},
doi = {10.1139/gen-2018-0062},
pmid = {30398899},
issn = {1480-3321},
mesh = {Animals ; *Biodiversity ; China ; *DNA Barcoding, Taxonomic ; Genetic Variation ; Insecta/*classification/*genetics ; Islands ; Phylogeography ; Population Dynamics ; Wetlands ; },
abstract = {Insect diversity is an indicator of environmental conditions. Frequent outbreaks of mangrove pests have threatened the fragile mangrove ecosystem in China and the sustainable utilization of mangrove resources. The understanding of mangrove pests, as well as a fundamental knowledge of insect diversity, in mangrove forests in China has been hindered by the difficulty of morphological species delimitation because captured insect specimens are either larvae or incompletely preserved adults. DNA barcoding technology uses only a small amount of DNA to conduct species identification. Taking advantage of this, we investigated the entomofauna of mangrove forests on Hainan Island by using a barcode combining cytochrome c oxidase subunit I (COI) and cytochrome-b (Cytb). We collected 627 specimens at six localities around the island, which were identified as 219 insect species belonging to 11 orders and 72 families. Lepidoptera, Coleoptera, and Hymenoptera are the most species-rich and abundant taxa. We also identified 13 mangrove pests, 5 parasitoids, and 12 species of predators.},
}
@article {pmid30396893,
year = {2019},
author = {Baker, SP and Nulton, TJ and Kitten, T},
title = {Genomic, Phenotypic, and Virulence Analysis of Streptococcus sanguinis Oral and Infective-Endocarditis Isolates.},
journal = {Infection and immunity},
volume = {87},
number = {1},
pages = {},
pmid = {30396893},
issn = {1098-5522},
support = {R01 AI114926/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Blood/microbiology ; Carrier State/*microbiology ; Disease Models, Animal ; Endocarditis/*microbiology ; *Genetic Variation ; *Genomics ; Humans ; Mouth/microbiology ; Phylogeny ; Rabbits ; Sequence Analysis, DNA ; Streptococcal Infections/*microbiology ; Streptococcus sanguis/classification/genetics/*isolation &amp; purification/physiology ; Virulence ; Virulence Factors/*genetics ; },
abstract = {Streptococcus sanguinis, an abundant and benign inhabitant of the oral cavity, is an important etiologic agent of infective endocarditis (IE), particularly in people with predisposing cardiac valvular damage. Although commonly isolated from patients with IE, little is known about the factors that make any particular S. sanguinis isolate more virulent than another or, indeed, whether significant differences in virulence exist among isolates. In this study, we compared the genomes of a collection of S. sanguinis strains comprised of both oral isolates and bloodstream isolates from patients diagnosed with IE. Oral and IE isolates could not be distinguished by phylogenetic analyses, and we did not succeed in identifying virulence genes unique to the IE strains. We then investigated the virulence of these strains in a rabbit model of IE using a variation of the Bar-seq (barcode sequencing) method wherein we pooled the strains and used Illumina sequencing to count unique barcodes that had been inserted into each isolate at a conserved intergenic region. After we determined that several of the genome sequences were misidentified in GenBank, our virulence results were used to inform our bioinformatic analyses, identifying genes that may explain the heterogeneity in virulence. We further characterized these strains by assaying for phenotypes potentially contributing to virulence. Neither strain competition via bacteriocin production nor biofilm formation showed any apparent relationship with virulence. Increased cell-associated manganese was, however, correlated with blood isolates. These results, combined with additional phenotypic assays, suggest that S. sanguinis virulence is highly variable and results from multiple genetic factors.},
}
@article {pmid30394729,
year = {2018},
author = {Sago, CD and Lokugamage, MP and Islam, FZ and Krupczak, BR and Sato, M and Dahlman, JE},
title = {Nanoparticles That Deliver RNA to Bone Marrow Identified by in Vivo Directed Evolution.},
journal = {Journal of the American Chemical Society},
volume = {140},
number = {49},
pages = {17095-17105},
pmid = {30394729},
issn = {1520-5126},
support = {R01 DE026941/DE/NIDCR NIH HHS/United States ; T32 EB021962/EB/NIBIB NIH HHS/United States ; },
mesh = {Animals ; Antigens, CD/genetics ; Bone Marrow/*metabolism ; Cell Adhesion Molecules/genetics ; Computational Biology ; Directed Molecular Evolution ; Drug Carriers/*chemistry/metabolism ; Endothelial Cells/metabolism ; Gene Silencing ; Mice ; Nanoparticles/*chemistry/metabolism ; Phosphatidylcholines/chemistry/metabolism ; Polyethylene Glycols/chemistry/metabolism ; RNA, Guide, CRISPR-Cas Systems/genetics/*pharmacology ; RNA, Small Interfering/genetics/*pharmacology ; },
abstract = {Bone marrow endothelial cells (BMECs) regulate their microenvironment, which includes hematopoietic stem cells. This makes BMECs an important target cell type for siRNA or gene editing (e.g., CRISPR) therapies. However, siRNA and sgRNA have not been delivered to BMECs using systemically administered nanoparticles. Given that in vitro nanoparticle screens have not identified nanoparticles with BMEC tropism, we developed a system to quantify how >100 different nanoparticles deliver siRNA in a single mouse. This is the first barcoding system capable of quantifying functional cytosolic siRNA delivery (where the siRNA drug is active), distinguishing it from in vivo screens that quantify biodistribution (where the siRNA drug went). Combining this approach with bioinformatics, we performed in vivo directed evolution, and identified BM1, a lipid nanoparticle (LNP) that delivers siRNA and sgRNA to BMECs. Interestingly, chemical analysis revealed BMEC tropism was not related to LNP size; tropism changed with the structure of poly(ethylene glycol), as well as the presence of cholesterol. These results suggest that significant changes to vascular targeting can be imparted to a LNP by making simple changes to its chemical composition, rather than using active targeting ligands. BM1 is the first nanoparticle to efficiently deliver siRNA and sgRNA to BMECs in vivo, demonstrating that this functional in vivo screen can identify nanoparticles with novel tropism in vivo. More generally, in vivo screening may help reveal the complex relationship between nanoparticle structure and tropism, thereby helping scientists understand how simple chemical changes control nanoparticle targeting.},
}
@article {pmid30393862,
year = {2019},
author = {Eischeid, AC},
title = {A method to detect allergenic fish, specifically cod and pollock, using quantitative real-time PCR and COI DNA barcoding sequences.},
journal = {Journal of the science of food and agriculture},
volume = {99},
number = {5},
pages = {2641-2645},
doi = {10.1002/jsfa.9466},
pmid = {30393862},
issn = {1097-0010},
mesh = {Allergens/genetics/immunology ; Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics/immunology ; Fish Proteins/*genetics/immunology ; Food Hypersensitivity/diagnosis ; Gadiformes/*genetics/immunology ; Gadus morhua/*genetics/immunology ; Humans ; Real-Time Polymerase Chain Reaction/*methods ; },
abstract = {BACKGROUND: Fish are one of eight major allergens defined in the US Food Allergen Labeling and Consumer Protection Act, and cod and pollock are two of the major fish allergens. This paper describes development and validation of a method to detect cod and pollock in complex food matrices using real-time polymerase chain reaction (PCR). Mitochondrial cytochrome oxidase I (COI) sequences obtained through DNA barcoding were used to design a single set of primers and probe which detected three species in the genus Gadus: Atlantic cod, Pacific cod, and walleye pollock.<br><br>RESULTS: Cod spiked into three different food matrices (cooking oil, clam chowder, and hushpuppy mix) yielded high linearity, dynamic range spanning six orders of magnitude, and lower limits of detection at 1-10&#xa0;ppm (ppm; mg&#x2009;kg[-1]). Frying had an adverse effect on the lower limit of detection, but not on linearity.<br><br>CONCLUSIONS: This work shows that COI DNA barcoding sequences can be used to effectively design real-time PCR assays for detection of food allergens in complex matrices. While full-length DNA barcodes distinguish individual species, the PCR assay designed here detected three different species. This is likely because real-time PCR assays are tolerant to basepair mismatches and do not utilize the full length of the DNA barcode. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.},
}
@article {pmid30393148,
year = {2019},
author = {Hansen, S and Dill, V and Shalaby, MA and Eschbaumer, M and Böhlken-Fascher, S and Hoffmann, B and Czerny, CP and Abd El Wahed, A},
title = {Serotyping of foot-and-mouth disease virus using oxford nanopore sequencing.},
journal = {Journal of virological methods},
volume = {263},
number = {},
pages = {50-53},
doi = {10.1016/j.jviromet.2018.10.020},
pmid = {30393148},
issn = {1879-0984},
mesh = {Animals ; Cell Line ; Diagnostic Tests, Routine/*veterinary ; Foot-and-Mouth Disease/*virology ; Foot-and-Mouth Disease Virus/classification/genetics/*isolation &amp; purification ; Molecular Diagnostic Techniques/*veterinary ; *Nanopores ; RNA, Viral/genetics ; Sensitivity and Specificity ; Serogroup ; Serotyping/*methods ; Time Factors ; },
abstract = {Foot-and-mouth disease virus (FMDV), belonging to the family of Picornaviridae, infects mostly cloven-hoofed animals and leads to huge economic losses. Since there is no cross-protection between the seven serotypes of FMDV, effective vaccination relies on the knowledge of the serotype causing the outbreak. The most common methods of serotyping are antigen ELISAs and amplification-based sequencing. Serotype-specific PCR methods exist but have limitations due to emerging mutants within serotypes. Sequencing is a promising technology, but currently suffers from cumbersome procedures and long turnaround times. In this study, we have established a novel sequencing protocol relying on nanopore sequencing and offline BLAST search. The procedure was completed in 5 h including RNA extraction, reverse transcription, second-strand synthesis, barcoding, sequencing and data analysis, which did not require a bioinformatician. In total, 12,193 sequence files were obtained. The offline BLAST search to the P1 region revealed the most successful categorization of the seven FMDV serotypes (specificity: 98.3%) over whole genome (24.8%), P2 (23.6%) and P3 (21.4%). In conclusion, our protocol enables rapid and reliable FMDV serotyping. The whole procedure can be conducted with a mobile suitcase laboratory, which is easy to use at the point of need in endemic countries.},
}
@article {pmid30392838,
year = {2019},
author = {Wang, L and Koppitch, K and Cutting, A and Dong, P and Kudtarkar, P and Zeng, J and Cameron, RA and Davidson, EH},
title = {Developmental effector gene regulation: Multiplexed strategies for functional analysis.},
journal = {Developmental biology},
volume = {445},
number = {1},
pages = {68-79},
pmid = {30392838},
issn = {1095-564X},
support = {P01 HD037105/HD/NICHD NIH HHS/United States ; P40 OD010959/OD/NIH HHS/United States ; P41 HD095831/HD/NICHD NIH HHS/United States ; R24 OD023046/OD/NIH HHS/United States ; P41 HD071837/HD/NICHD NIH HHS/United States ; },
mesh = {Animals ; Chromosomes, Artificial, Bacterial/genetics ; Gene Expression Regulation, Developmental/genetics/*physiology ; Gene Regulatory Networks/genetics/physiology ; Genes, Reporter/genetics ; Genetic Engineering/*methods ; High-Throughput Nucleotide Sequencing/methods ; Models, Biological ; Sea Urchins/embryology/genetics ; Sequence Analysis, DNA/*methods ; Transcription Factors/metabolism ; },
abstract = {The staggering complexity of the genome controls for developmental processes is revealed through massively parallel cis-regulatory analysis using new methods of perturbation and readout. The choice of combinations of these new methods is tailored to the system, question and resources at hand. Our focus is on issues that include the necessity or sufficiency of given cis-regulatory modules, cis-regulatory function in the normal spatial genomic context, and easily accessible high throughput and multiplexed analysis methods. In the sea urchin embryonic model, recombineered BACs offer new opportunities for consecutive modes of cis-regulatory analyses that answer these requirements, as we here demonstrate on a diverse suite of previously unstudied sea urchin effector genes expressed in skeletogenic cells. Positively active cis-regulatory modules were located in single Nanostring experiments per BAC containing the gene of interest, by application of our previously reported "barcode" tag vectors of which> 100 can be analyzed at one time. Computational analysis of DNA sequences that drive expression, based on the known skeletogenic regulatory state, then permitted effective identification of functional target site clusters. Deletion of these sub-regions from the parent BACs revealed module necessity, as simultaneous tests of the same regions in short constructs revealed sufficiency. Predicted functional inputs were then confirmed by site mutations, all generated and tested in multiplex formats. There emerged the simple conclusion that each effector gene utilizes a small subset of inputs from the skeletogenic GRN. These inputs may function to only adjust expression levels or in some cases necessary for expression. Since we know the GRN architecture upstream of the effector genes, we could then conceptually isolate and compare the wiring of the effector gene driver sub-circuits and identify the inputs whose removal abolish expression.},
}
@article {pmid30392674,
year = {2018},
author = {Zhang, M and Huo, B and Yuan, S and Ning, B and Bai, J and Peng, Y and Liu, B and Gao, Z},
title = {Ultrasensitive detection of T-2 toxin in food based on bio-barcode and rolling circle amplification.},
journal = {Analytica chimica acta},
volume = {1043},
number = {},
pages = {98-106},
doi = {10.1016/j.aca.2018.09.007},
pmid = {30392674},
issn = {1873-4324},
mesh = {Antibodies, Immobilized/chemistry/immunology ; Antibodies, Monoclonal/chemistry/immunology ; Benzothiazoles ; DNA, Single-Stranded/*chemistry/metabolism ; Diamines ; Food Contamination/*analysis ; Gold/chemistry ; Immobilized Nucleic Acids/chemistry/metabolism ; Limit of Detection ; Magnetics ; Metal Nanoparticles/chemistry ; Nucleic Acid Amplification Techniques/*methods ; Organic Chemicals/chemistry ; Quinolines ; *Spectrometry, Fluorescence ; T-2 Toxin/*analysis/immunology ; },
abstract = {A novel and highly sensitive method based on bio-barcode with rolling circle amplification (RCA) was developed for the detection of T-2 toxin. Gold nanoparticles (AuNPs) were modified with anti-T-2 monoclonal antibody and single-stranded thiol-oligonucleotides (SH-ssDNAs) and magnetic microparticles (MMPs) coated with T-2 antigen. The T-2 toxin competes with the antigen on MMPs for the anti-T-2 antibody on AuNPs. Then, the isolating complex system was separated by a magnetic field, and the DNA of the probes was released after washing in dithiothreitol solution. The barcode DNA via RCA and products were stained by SYBR Green I and then detected by fluorescence spectrophotometry. The optimized method was performed on oats, millet, flour, and other substances. This method exhibits a low limit of detection (0.26 pg mL[-1]) and linear range of 0.002-200 ng mL[-1]. Moreover, the approach offers good recovery and relative standard deviations ranging from 88.65% to 10.04% and 0.6%-13.1%, respectively. In conclusion, this method exhibits potential for use as an ultrasensitive assay for the detection of a variety of small molecules in complex matrices.},
}
@article {pmid30392423,
year = {2018},
author = {Zhu, S and Li, Q and Chen, S and Wang, Y and Zhou, L and Zeng, C and Dong, J},
title = {Phylogenetic analysis of Uncaria species based on internal transcribed spacer (ITS) region and ITS2 secondary structure.},
journal = {Pharmaceutical biology},
volume = {56},
number = {1},
pages = {548-558},
pmid = {30392423},
issn = {1744-5116},
mesh = {DNA Barcoding, Taxonomic/methods ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/*genetics ; *Genes, rRNA ; Nucleic Acid Conformation ; Phylogeny ; Plants, Medicinal/classification/genetics ; Polymerase Chain Reaction ; Uncaria/*classification/*genetics ; },
abstract = {CONTEXT: The plant genus Uncaria (Rubiaceae), also known as Gouteng, is the source of an important traditional Chinese medicine. Misidentification and adulteration of Gouteng affect the safety and efficacy of the medication. Phylogenetic relationships among the species of this genus are unknown.<br><br>OBJECTIVE: The present study sought to detect the phylogenetic relationships based on internal transcribed spacer (ITS) region of all 12 species of Uncaria recorded in the Flora of China.<br><br>MATERIALS AND METHODS: Accession of seven species of Uncaria served as reference samples. ITS region was used for polymerase chain reaction (PCR) amplification of the reference samples representing 39 specimens. Distance analysis, species discrimination, and secondary structure of ITS2 were used to assess the ability of ITS sequence in authenticating. The phylogenetic relationships were detected using three methods: Bayesian inference (BI), maximum likelihood (ML), and neighbor joining (NJ).<br><br>RESULTS: Five species of traditional Chinese medicine Gouteng were well resolved in molecular phylogenetic tree. Besides, Uncaria lancifolia Hutch. was closer to U. rhynchophylloides F.C. How and U. sessilifructus Roxb. was closer to U. laevigata Wall. within the tree. Further, we also found that ITS2 secondary structure can be a candidate tool in distinguishing two closely related species U. yunnanensis K.C.Hsia and U. lanosa Wall. For accurate identification of different species of Uncaria based on species-specific nucleotide sites, a consensus sequences database with all 12 species is established.<br><br>DISCUSSIONS AND CONCLUSIONS: The results are able to discriminate Uncaria species and illustrate the phylogenetic relationships, which are essential for the investigation of adulterants and misidentifications of Uncaria.},
}
@article {pmid30391400,
year = {2019},
author = {Doysabas, KCC and Oba, M and Furuta, M and Iida, K and Omatsu, T and Furuya, T and Okada, T and Sutummaporn, K and Shimoda, H and Wong, ML and Wu, CH and Ohmori, Y and Kobayashi, R and Hengjan, Y and Yonemitsu, K and Kuwata, R and Kim, YK and Han, SH and Sohn, JH and Han, SH and Suzuki, K and Kimura, J and Maeda, K and Oh, HS and Endoh, D and Mizutani, T and Hondo, E},
title = {Encephalomyocarditis virus is potentially derived from eastern bent-wing bats living in East Asian countries.},
journal = {Virus research},
volume = {259},
number = {},
pages = {62-67},
pmid = {30391400},
issn = {1872-7492},
mesh = {Animal Diseases/*virology ; Animals ; Cardiovirus Infections/*veterinary ; Chiroptera/*virology ; Disease Reservoirs/*virology ; Encephalomyocarditis virus/*classification/*genetics ; Asia, Eastern ; Genetic Variation ; Genome, Viral ; Sequence Analysis, DNA ; },
abstract = {Bats are reservoir hosts of many zoonotic viruses and identification of viruses that they carry is important. This study aimed to use high throughput screening to identify the viruses in fecal guano of Taiwanese insectivorous bats caves in order to obtain more information on bat-derived pathogenic viruses in East Asia. Guano samples were collected from two caves in Taiwan, pooled, and then subjected to Multiplex PCR-based next generation sequencing for viral identification. Subsequently, encephalomyocarditis virus (EMCV) sequence was detected and confirmed by reverse transcription PCR. EMCV is considered as rodent virus and thus, animal species identification through cytochrome oxidase I (COI) barcoding was further done to identify the viral source. Finally, determination of distribution and verification of the presence of EMCV in guano obtained from Japanese and South Korean caves was also done. We concluded that the guano collected was not contaminated with the excrement of rodents which were reported and presumed to live in Taiwan. Also, EMCV genome fragments were found in guanos of Japanese and South Korean caves. It is possible that the eastern bent-wing bat (Miniopterus fuliginosus) is one of the natural hosts of EMCV in East Asia.},
}
@article {pmid30389926,
year = {2018},
author = {Chen, X and Litzenburger, UM and Wei, Y and Schep, AN and LaGory, EL and Choudhry, H and Giaccia, AJ and Greenleaf, WJ and Chang, HY},
title = {Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {4590},
pmid = {30389926},
issn = {2041-1723},
support = {P50 HG007735/HG/NHGRI NIH HHS/United States ; R35 CA209919/CA/NCI NIH HHS/United States ; S10 OD018220/OD/NIH HHS/United States ; },
mesh = {Animals ; Breast Neoplasms/genetics/pathology ; Cell Hypoxia/genetics ; Cell Line, Tumor ; Chromatin/metabolism ; DNA/*genetics ; *Environment ; Epigenesis, Genetic ; *Epigenomics ; Epithelial Cell Adhesion Molecule/metabolism ; Epitopes/*metabolism ; Lymphocytes/metabolism ; Mice ; Nucleotide Motifs/genetics ; Proteins/*metabolism ; Reproducibility of Results ; Sequence Analysis, DNA ; *Single-Cell Analysis ; Transcription Factors/metabolism ; Transposases/metabolism ; },
abstract = {Here we introduce Protein-indexed Assay of Transposase Accessible Chromatin with sequencing (Pi-ATAC) that combines single-cell chromatin and proteomic profiling. In conjunction with DNA transposition, the levels of multiple cell surface or intracellular protein epitopes are recorded by index flow cytometry and positions in arrayed microwells, and then subject to molecular barcoding for subsequent pooled analysis. Pi-ATAC simultaneously identifies the epigenomic and proteomic heterogeneity in individual cells. Pi-ATAC reveals a casual link between transcription factor abundance and DNA motif access, and deconvolute cell types and states in the tumor microenvironment in vivo. We identify a dominant role for hypoxia, marked by HIF1α protein, in the tumor microvenvironment for shaping the regulome in a subset of epithelial tumor cells.},
}
@article {pmid30389013,
year = {2018},
author = {Li, XY and Chen, YO and Wang, QK and Li, K and Pape, T and Zhang, D},
title = {Molecular and morphological characterization of third instar Palaearctic horse stomach bot fly larvae (Oestridae: Gasterophilinae, Gasterophilus).},
journal = {Veterinary parasitology},
volume = {262},
number = {},
pages = {56-74},
doi = {10.1016/j.vetpar.2018.09.011},
pmid = {30389013},
issn = {1873-2550},
mesh = {Animals ; DNA Barcoding, Taxonomic/veterinary ; Diptera/*classification/genetics/ultrastructure ; Female ; Horse Diseases/*parasitology ; Horses ; Larva ; Male ; Myiasis/parasitology/*veterinary ; Phylogeny ; Stomach/parasitology ; },
abstract = {Species of Gasterophilus are obligate parasites of equids and may induce severe, even lethal myiasis. However, identification of the third instar Gasterophilus larva at the species level is still problematic predominantly due to a shortage of diagnostic morphological features and incomplete molecular libraries. Testing the suitability of three different molecular markers showed that the traditional 650 bp barcode region near the 5' terminus of the cytochrome c oxidase subunit I (COI) served as a better tool for species-level identification than a 663 bp region near the 3' terminus of COI and a 554 bp region near the 5' terminus of the large subunit ribosomal RNA. We found that barcoding discriminates G. intestinalis, G. nasalis, G. nigricornis and G. pecorum but not G. haemorrhoidalis and G. inermis. A comparative morphological study using scanning electron microscopy was conducted to promote the identification of the third instar larvae. Photographs of fresh mature third instar larvae are provided for all species, and the remarkable green body colour of third instar G. nigricornis is fully documented for the first time. Two morphological keys are provided, one is suitable for quick identification, and the other based on ultrastructural details is provided for further comparative morphological investigation. A new term 'oral plate' instead of 'mandible' was proposed for a pair of sclerites of uncertain homology emerging from the secondary mouth opening. Our data shows that DNA barcodes cannot replace morphology for identification of third instars of Gasterophilus species, and a scaffold is provided for an integrated taxonomic reference system, which will contribute to monitoring gasterophilosis for equid welfare and protection, and also facilitate further studies in functional anatomy, phylogenetic analyses and host-parasite co-evolutionary investigations of Gasterophilus.},
}
@article {pmid30388379,
year = {2018},
author = {Tungphatthong, C and Somnuek, J and Phadungcharoen, T and Ingkaninan, K and Denduangboripant, J and Sukrong, S},
title = {DNA barcoding of species of Bacopa coupled with high-resolution melting analysis.},
journal = {Genome},
volume = {61},
number = {12},
pages = {867-877},
doi = {10.1139/gen-2018-0059},
pmid = {30388379},
issn = {1480-3321},
mesh = {Bacopa/*classification/genetics ; DNA Barcoding, Taxonomic ; Nucleic Acid Denaturation ; Thailand ; },
abstract = {In Thailand, there are three species of Bacopa, namely, B. monnieri, B. caroliniana, and B. floribunda. Among these species of Bacopa, B. monnieri is the only medicinal species, used for the treatment of cognitive impairment and improvement of cognitive abilities because of its bioactive constituents, bacoside A and B. However, because of the similar characteristics of these species, it is difficult to differentiate among related species, resulting in confusion during identification. For this reason, and to ensure therapeutic quality for consumers, authentication is important. In this study, the three abovementioned species of Bacopa were evaluated using barcoding coupled with high-resolution melting (Bar-HRM) analysis based on primers designed for the trnL-F sequences of the three species. The melting profiles of the trnL-F amplicons of B. caroliniana and B. floribunda were clearly different from the melting profile of the trnL-F amplicon from B. monnieri; thus, the species could be discriminated by Bar-HRM analysis. Bar-HRM was then used to authenticate commercial products in various forms. The melting curves of the six commercial samples indicated that all the tested products contained genuine B. monnieri species. This method provides an efficient and reliable authentication system for future commercial herbal products and offers a reference system for quality control.},
}
@article {pmid30388147,
year = {2018},
author = {Huemer, P and Hebert, PDN and Mutanen, M and Wieser, C and Wiesmair, B and Hausmann, A and Yakovlev, R and Möst, M and Gottsberger, B and Strutzenberger, P and Fiedler, K},
title = {Large geographic distance versus small DNA barcode divergence: Insights from a comparison of European to South Siberian Lepidoptera.},
journal = {PloS one},
volume = {13},
number = {11},
pages = {e0206668},
pmid = {30388147},
issn = {1932-6203},
mesh = {*Animal Distribution ; Animals ; DNA ; DNA Barcoding, Taxonomic ; Europe ; *Genetic Variation ; Lepidoptera/*genetics ; Siberia ; Spatial Analysis ; Species Specificity ; },
abstract = {Spanning nearly 13,000 km, the Palearctic region provides an opportunity to examine the level of geographic coverage required for a DNA barcode reference library to be effective in identifying species with broad ranges. This study examines barcode divergences between populations of 102 species of Lepidoptera from Europe and South Siberia, sites roughly 6,000 km apart. While three-quarters of these species showed divergence between their Asian and European populations, these divergence values ranged between 0-1%, distinctly less than the distance to the Nearest-Neighbor species in all but a few cases. Our results suggest that further taxonomic studies may be required for 16 species that showed either extremely low interspecific or high intraspecific variation. For example, seven species pairs showed low or no barcode divergence, but four of these cases are likely to reflect taxonomic over-splitting while the others involve species pairs that are either young or show evidence for introgression. Conversely, some of the nine species with deep intraspecific divergence at varied spatial levels may include overlooked species. Although these 16 cases require further investigation, our overall results indicate that barcode reference libraries based on records from one locality can be very effective in identifying specimens across an extensive geographic area.},
}
@article {pmid30387157,
year = {2019},
author = {Poulsen, JY},
title = {New observations and ontogenetic transformation of photogenic tissues in the tubeshoulder Sagamichthys schnakenbecki (Platytroctidae, Alepocephaliformes).},
journal = {Journal of fish biology},
volume = {94},
number = {1},
pages = {62-76},
doi = {10.1111/jfb.13857},
pmid = {30387157},
issn = {1095-8649},
mesh = {Animals ; Atlantic Ocean ; DNA Barcoding, Taxonomic ; Fishes/anatomy &amp; histology/genetics/*growth &amp; development ; Greenland ; Larva/growth &amp; development ; *Luminescence ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Several species of the luminescent tubeshoulder fish (family Platytroctidae) show extensive ontogenetic transformations in the development of bioluminescent structures from larvae to adults. Several types of luminescent tissues are present in platytroctids, although these tissues are poorly known for most species because specimens are rarely observed. The present study describes the ontogenetic transformation of photogenic structures in Sagamichthys schnakenbecki, a species that is found in meso and bathy-pelagic depths of the Atlantic Ocean. Five newly described luminous structures are included in addition to a review of all known bioluminescent tissues described in the family. The newly discovered photogenic tissues were observed at the pectoral-fin base in early juveniles, as a pair of large globule-like tissues inside the caudal peduncle of early juveniles, at the pelvic girdle of late juveniles and early adults and as photogenic tissue observed as pigment over the cleithral bone in adults. A peculiar skin-slit structure, which was observed only in S. schnakenbecki, is described and discussed. Skin slits were associated with certain bioluminescent structures during the transformation into adulthood. In addition, coI sequence data from nine of 13 recognized platytroctid genera were used to construct the first molecular phylogenetic tree for the family. Finally, the first photographic evidence of the rarely observed luminous discharge of a tubeshoulder shoulder organ is presented from observations off south-east Greenland.},
}
@article {pmid30386703,
year = {2018},
author = {Yeong, KC and Takizawa, H and Liew, TS},
title = {Investigating leaf beetles (Coleoptera, Chrysomelidae) on the west coast islands of Sabah via checklist-taking and DNA barcoding.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5811},
pmid = {30386703},
issn = {2167-8359},
abstract = {Sabah is a province of Malaysia located on the northern part of the island of Borneo. Most of the leaf beetle fauna studies from this region conducted over the past 15 years have focussed on the mainland habitats while the leaf beetle fauna from island habitats (ca. 500 islands) have largely been overlooked. This study looks into the leaf beetle fauna of 13 small satellite islands off the west coast of Sabah. All specimens were first sorted into morpho-species operational taxonomic unit (OTU) before being identified to species rank where possible based on morphological characters and species names assigned when the specimens fitted the description of species in the literature. We collected 75 OTUs from 35 genera and five subfamilies according to morphology, 12 of which were identifiable to species level. In addition, the DNA barcode for each OTU was cross checked with records in GenBank and Barcoding of Life Data system (BOLD) to verify their identity. The number of species recorded was reduced from 12 species and 63 OTUs (total 75 OTUs) to 12 species and 56 OTUs (total 68 OTUs) after removal of the colour polymorphic species based on DNA barcode analyses. Pulau Gaya has the highest species richness and Pulau Sulug has the lowest species richness. A total of 64 Barcode Index Numbers consisting of 101 DNA barcodes were obtained from the 12 leaf beetle species and 48 OTUs. Based on the DNA barcode analyses, it was possible to confirm several polymorphic OTUs and cryptic species. The mean intraspecific and interspecific genetic divergence were determined as 0.77% and 16.11%, respectively. DNA barcodes of this study show a low similarity with records in GenBank and BOLD, highlighting the lack of representation and the urgency of studying leaf beetles from this region. The study provides the first documentation of leaf beetle fauna from island habitats of Sabah and the first DNA barcoding data for leaf beetles from this part of the world, with the next steps being larger scale sampling over a wider geographical scale for a better understanding of tropical arthropod diversity.},
}
@article {pmid30385812,
year = {2018},
author = {Miralles, L and Ardura, A and Clusa, L and Garcia-Vazquez, E},
title = {DNA barcodes of Antipode marine invertebrates in Bay of Biscay and Gulf of Lion ports suggest new biofouling challenges.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {16214},
pmid = {30385812},
issn = {2045-2322},
mesh = {Animals ; Aquatic Organisms/*classification/*genetics ; Atlantic Ocean ; Bays ; Biodiversity ; *Biofouling ; *DNA Barcoding, Taxonomic ; Introduced Species ; Invertebrates/*classification/*genetics ; Mediterranean Sea ; Oceanography ; Phylogeny ; },
abstract = {Marine biological invasions threaten global biodiversity nowadays. In this article, we have studied fouling communities from 10 port areas of south Bay of Biscay (Atlantic Ocean) and Gulf of Lion (Mediterranean Sea). A total of 834 individuals were genetically barcoded and corresponded to 95 different species. A total of 76 native species 8 genera and 1 family were identified, 58 from the Bay of Biscay and 23 from the Gulf of Lion. Furthermore, 19 species were identified as non-indigenous or cryptogenic (18 from the Bay of Biscay and 4 from the Gulf of Lion). We found a high proportion of Antipode non-indigenous species (NIS) that represented the 19.3% of all sampled individuals and the 54.21% of NIS specimens of this study. A framework for inference of donor regions based on a phylogenetic screening of genetic sequences was proposed as a proof of concept and tested, as well as models for the relationship between NIS introductions, maritime imports and distance to NIS native range and inferred donor areas. Consistent generalized linear models (GLM) with positive association between NIS genetic diversity and distance, not with maritime growth weight imports, strongly suggest that distant NIS could pose higher invasion risk than closer species. Selection for wider tolerance ranges during the long travel -direct or stepwise, as well as environmental similarity between donor and receiving regions, may explain these results.},
}
@article {pmid30385746,
year = {2018},
author = {Jo, Y and Kwon, J and Kim, M and Choi, W and Choi, M},
title = {Microsphere-based interferometric optical probe.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {4577},
pmid = {30385746},
issn = {2041-1723},
mesh = {Animals ; Bacterial Proteins/genetics ; *Fluorescent Dyes ; HeLa Cells ; Humans ; Luminescent Agents ; Luminescent Proteins/genetics ; Melanoma, Experimental ; Mice ; Mice, Transgenic ; Microscopy, Electron, Scanning ; *Microspheres ; NIH 3T3 Cells ; Optical Imaging/*methods ; Thy-1 Antigens ; },
abstract = {Fluorescent optical probes have rapidly transformed our understanding of complex biological systems by providing specific information on biological targets in the natural living state. However, their utility is often limited by insufficient brightness, photostability, and multiplexing capacity. Here, we report a conceptually new optical probe, termed 'reflectophore', which is based on the spectral interference from a dielectric microsphere. Reflectophores are orders-of-magnitudes brighter than conventional fluorophores and are free from photobleaching, enabling practically unlimited readout at high fidelity. They also offer high-degree multiplexing, encoded in their optical size, which can be readily decoded through interferometric detection with nanoscale accuracy, even in turbid biological media. Furthermore, we showcase their biological applications in cellular barcoding and microenvironmental sensing of a target protein and local electric field.},
}
@article {pmid30382095,
year = {2018},
author = {Giedt, RJ and Pathania, D and Carlson, JCT and McFarland, PJ and Del Castillo, AF and Juric, D and Weissleder, R},
title = {Single-cell barcode analysis provides a rapid readout of cellular signaling pathways in clinical specimens.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {4550},
pmid = {30382095},
issn = {2041-1723},
support = {R33 CA202064/CA/NCI NIH HHS/United States ; },
mesh = {Antibodies/metabolism ; Biomarkers, Tumor/metabolism ; Cell Line, Tumor ; DNA Barcoding, Taxonomic/*methods ; Humans ; Phosphoproteins/metabolism ; Phosphorylation ; *Signal Transduction ; Single-Cell Analysis/*methods ; Treatment Outcome ; },
abstract = {Serial tissue sampling has become essential in guiding modern targeted and personalized cancer treatments. An alternative to image guided core biopsies are fine needle aspirates (FNA) that yield cells rather than tissues but are much better tolerated and have lower complication rates. The efficient pathway analysis of such cells in the clinic has been difficult, time consuming and costly. Here we develop an antibody-DNA barcoding approach where harvested cells can be rapidly re-stained through the use of custom designed oligonucleotide-fluorophore conjugates. We show that this approach can be used to interrogate drug-relevant pathways in scant clinical samples. Using the PI3K/PTEN/CDK4/6 pathways in breast cancer as an example, we demonstrate how analysis can be performed in tandem with trial enrollment and can evaluate downstream signaling following therapeutic inhibition. This approach should allow more widespread use of scant single cell material in clinical samples.},
}
@article {pmid30381482,
year = {2019},
author = {Goldhill, DH and Langat, P and Xie, H and Galiano, M and Miah, S and Kellam, P and Zambon, M and Lackenby, A and Barclay, WS},
title = {Determining the Mutation Bias of Favipiravir in Influenza Virus Using Next-Generation Sequencing.},
journal = {Journal of virology},
volume = {93},
number = {2},
pages = {},
pmid = {30381482},
issn = {1098-5514},
support = {//Wellcome Trust/United Kingdom ; 200187/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Amides/*pharmacology ; Animals ; Bias ; DNA Primers/genetics ; Dogs ; HEK293 Cells ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Influenza A virus/drug effects/*genetics ; Madin Darby Canine Kidney Cells ; *Mutation ; Pyrazines/*pharmacology ; Sequence Analysis, RNA ; Whole Genome Sequencing ; },
abstract = {Favipiravir is a broad-spectrum antiviral drug that may be used to treat influenza. Previous research has identified that favipiravir likely acts as a mutagen, but the precise mutation bias that favipiravir induces in influenza virus RNAs has not been described. Here, we use next-generation sequencing (NGS) with barcoding of individual RNA molecules to accurately and quantitatively detect favipiravir-induced mutations and to sample orders of magnitude more mutations than would be possible through Sanger sequencing. We demonstrate that favipiravir causes mutations and show that favipiravir primarily acts as a guanine analogue and secondarily as an adenine analogue resulting in the accumulation of transition mutations. We also use a standard NGS pipeline to show that the mutagenic effect of favipiravir can be measured by whole-genome sequencing of virus.IMPORTANCE New antiviral drugs are needed as a first line of defense in the event of a novel influenza pandemic. Favipiravir is a broad-spectrum antiviral which is effective against influenza. The exact mechanism of how favipiravir works to inhibit influenza is still unclear. We used next-generation sequencing (NGS) to demonstrate that favipiravir causes mutations in influenza RNA. The greater depth of NGS sequence information over traditional sequencing methods allowed us to precisely determine the bias of particular mutations caused by favipiravir. NGS can also be used in a standard diagnostic pipeline to show that favipiravir is acting on the virus by revealing the mutation bias pattern typical to the drug. Our work will aid in testing whether viruses are resistant to favipiravir and may help demonstrate the effect of favipiravir on viruses in a clinical setting. This will be important if favipiravir is used during a future influenza pandemic.},
}
@article {pmid30381339,
year = {2018},
author = {Zheng, C and Dos Santos, PC},
title = {Metallocluster transactions: dynamic protein interactions guide the biosynthesis of Fe-S clusters in bacteria.},
journal = {Biochemical Society transactions},
volume = {46},
number = {6},
pages = {1593-1603},
doi = {10.1042/BST20180365},
pmid = {30381339},
issn = {1470-8752},
mesh = {Bacterial Proteins/chemistry/*metabolism ; Carbon-Sulfur Lyases/chemistry/*metabolism ; Iron-Sulfur Proteins/chemistry/*metabolism ; Protein Binding ; },
abstract = {Iron-sulfur (Fe-S) clusters are ubiquitous cofactors present in all domains of life. The chemistries catalyzed by these inorganic cofactors are diverse and their associated enzymes are involved in many cellular processes. Despite the wide range of structures reported for Fe-S clusters inserted into proteins, the biological synthesis of all Fe-S clusters starts with the assembly of simple units of 2Fe-2S and 4Fe-4S clusters. Several systems have been associated with the formation of Fe-S clusters in bacteria with varying phylogenetic origins and number of biosynthetic and regulatory components. All systems, however, construct Fe-S clusters through a similar biosynthetic scheme involving three main steps: (1) sulfur activation by a cysteine desulfurase, (2) cluster assembly by a scaffold protein, and (3) guided delivery of Fe-S units to either final acceptors or biosynthetic enzymes involved in the formation of complex metalloclusters. Another unifying feature on the biological formation of Fe-S clusters in bacteria is that these systems are tightly regulated by a network of protein interactions. Thus, the formation of transient protein complexes among biosynthetic components allows for the direct transfer of reactive sulfur and Fe-S intermediates preventing oxygen damage and reactions with non-physiological targets. Recent studies revealed the importance of reciprocal signature sequence motifs that enable specific protein-protein interactions and consequently guide the transactions between physiological donors and acceptors. Such findings provide insights into strategies used by bacteria to regulate the flow of reactive intermediates and provide protein barcodes to uncover yet-unidentified cellular components involved in Fe-S metabolism.},
}
@article {pmid30380708,
year = {2018},
author = {Zhou, Y and Nie, J and Xiao, L and Hu, Z and Wang, B},
title = {Comparative Chloroplast Genome Analysis of Rhubarb Botanical Origins and the Development of Specific Identification Markers.},
journal = {Molecules (Basel, Switzerland)},
volume = {23},
number = {11},
pages = {},
pmid = {30380708},
issn = {1420-3049},
support = {81603246//the National Science Foundation of China/ ; 81603246//National Science Foundation of China/ ; },
mesh = {Chloroplasts/genetics ; DNA Barcoding, Taxonomic ; DNA, Chloroplast/*genetics ; Genome, Chloroplast/*genetics ; *Phylogeny ; Plants, Medicinal/classification/genetics ; Rheum/classification/*genetics ; },
abstract = {Rhubarb is an important ingredient in traditional Chinese medicine known as Rhei radix et rhizome. However, this common name refers to three different botanical species with different pharmacological effects. To facilitate the genetic identification of these three species for their more precise application in Chinese medicine we here want to provide chloroplast sequences with specific identification sites that are easy to amplify. We therefore sequenced the complete chloroplast genomes of all three species and then screened those for suitable sequences describing the three species. The length of the three chloroplast genomes ranged from 161,053 bp to 161,541 bp, with a total of 131 encoded genes including 31 tRNA, eight rRNA and 92 protein-coding sequences. The simple repeat sequence analysis indicated the differences existed in these species, phylogenetic analyses showed the chloroplast genome can be used as an ultra-barcode to distinguish the three botanical species of rhubarb, the variation of the non-coding regions is higher than that of the protein coding regions, and the variations in single-copy region are higher than that in inverted repeat. Twenty-one specific primer pairs were designed and eight specific identification sites were experimentally confirmed that can be used as special DNA barcodes for the identification of the three species based on the highly variable regions. This study provides a molecular basis for precise medicinal plant selection, and supplies the groundwork for the next investigation of the closely related Rheum species comparing and correctly identification on these important medicinal species.},
}
@article {pmid30379813,
year = {2018},
author = {Chakraborty, R and Tyagi, K and Kundu, S and Rahaman, I and Singha, D and Chandra, K and Patnaik, S and Kumar, V},
title = {The complete mitochondrial genome of Melon thrips, Thrips palmi (Thripinae): Comparative analysis.},
journal = {PloS one},
volume = {13},
number = {10},
pages = {e0199404},
pmid = {30379813},
issn = {1932-6203},
mesh = {Animals ; Base Composition ; Bayes Theorem ; Codon ; Codon, Initiator ; Comparative Genomic Hybridization ; DNA, Intergenic ; Gene Order ; Gene Rearrangement ; *Genome, Mitochondrial ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Thysanoptera/*genetics ; },
abstract = {The melon thrips, Thrips palmi is a serious pest and vector for plant viruses on a wide range of economically important crops. DNA barcoding evidenced the presence of cryptic diversity in T. palmi and that warrants exhaustive molecular studies. Our present study is on decoding the first complete mitochondrial genome of T. palmi (15,333 bp) through next-generation sequencing (NGS). The T. palmi mt genome contains 37 genes, including 13 Protein coding genes (PCGs), two ribosomal RNA (rRNAs), 22 transfer RNA (tRNAs), and two control regions (CRs). The majority strand of T. palmi revealed 78.29% A+T content, and 21.72% G+C content with positive AT skew (0.09) and negative GC skew (-0.06). The ATN initiation codons were observed in 12 PCGs except for cox1 which have unique start codon (TTG). The relative synonymous codon usage (RSCU) analysis revealed Phe, Leu, Ile, Tyr, Asn, Lys and Met were the most frequently used amino acids in all PCGs. The codon (CGG) which is assigned to Arginine in most insects but absent in T. palmi. The Ka/Ks ratio ranges from 0.078 in cox1 to 0.913 in atp8. We observed the typical cloverleaf secondary structure in most of the tRNA genes with a few exceptions; absence of DHU stem and loop in trnV and trnS, absence of DHU loop in trnE, lack of T-arm and loop in trnN. The T. palmi gene order (GO) was compared with ancestral GO and observed an extensive gene arrangement in PCGs, tRNAs and rRNAs. The cox2 gene was separated from the gene block 'cox2-trnL2' in T. palmi as compared with the other thrips mt genomes, including ancestor GO. Further, the nad1, trnQ, trnC, trnL1, trnV, trnF, rrnS, and rrnL were inversely transpositioned in T. palmi GO. The gene blocks 'trnQ-trnS2-trnD' and 'trnN-trnE-trnS1-trnL1' seems to be genus specific. The T. palmi mt genome contained 24 intergenic spacer regions and 12 overlapping regions. The 62 bp of CR2 shows the similarity with CR1 indicating a possible duplication. The occurrence of multiple CRs in thrips mt genomes seems to be a derived trait which needs further investigation. Although, the study depicted extensive gene rearrangements in T. palmi mt genome, but the negative GC skew reflects only strand asymmetry. Both the ML and BI phylogenetic trees revealed the close relationships of Thrips with Scirtothrips as compared to Frankliniella. Thus, more mt genomes of the diverse thrips species are required to understand the in-depth phylogenetic and evolutionary relationships.},
}
@article {pmid30377352,
year = {2018},
author = {Kebschull, JM and Zador, AM},
title = {Cellular barcoding: lineage tracing, screening and beyond.},
journal = {Nature methods},
volume = {15},
number = {11},
pages = {871-879},
doi = {10.1038/s41592-018-0185-x},
pmid = {30377352},
issn = {1548-7105},
mesh = {Cell Lineage/*genetics ; *Cell Physiological Phenomena ; Cell Tracking/*methods ; *DNA Barcoding, Taxonomic ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Sequence Analysis, DNA/*methods ; },
abstract = {Cellular barcoding is a technique in which individual cells are labeled with unique nucleic acid sequences, termed barcodes, so that they can be tracked through space and time. Cellular barcoding can be used to track millions of cells in parallel, and thus is an efficient approach for investigating heterogeneous populations of cells. Over the past 25 years, cellular barcoding has been used for fate mapping, lineage tracing and high-throughput screening, and has led to important insights into developmental biology and gene function. Driven by plummeting sequencing costs and the power of synthetic biology, barcoding is now expanding beyond traditional applications and into diverse fields such as neuroanatomy and the recording of cellular activity. In this review, we discuss the fundamental principles of cellular barcoding, including the underlying mathematics, and its applications in both new and established fields.},
}
@article {pmid30376898,
year = {2018},
author = {Leiby, JS and McCormick, K and Sherrill-Mix, S and Clarke, EL and Kessler, LR and Taylor, LJ and Hofstaedter, CE and Roche, AM and Mattei, LM and Bittinger, K and Elovitz, MA and Leite, R and Parry, S and Bushman, FD},
title = {Lack of detection of a human placenta microbiome in samples from preterm and term deliveries.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {196},
pmid = {30376898},
issn = {2049-2618},
support = {P30 AI045008/AI/NIAID NIH HHS/United States ; T32 AI007324/AI/NIAID NIH HHS/United States ; T32 AI007632/AI/NIAID NIH HHS/United States ; },
mesh = {Adult ; Bacteria/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Female ; Humans ; Microbiota/*genetics ; Placenta/*microbiology ; Pregnancy ; Premature Birth ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Term Birth ; Uterus/*microbiology ; },
abstract = {BACKGROUND: Historically, the human womb has been thought to be sterile in healthy pregnancies, but this idea has been challenged by recent studies using DNA sequence-based methods, which have suggested that the womb is colonized with bacteria. For example, analysis of DNA from placenta samples yielded small proportions of microbial sequences which were proposed to represent normal bacterial colonization. However, an analysis by our group showed no distinction between background negative controls and placenta samples. Also supporting the idea that the womb is sterile is the observation that germ-free mammals can be generated by sterile delivery of neonates into a sterile isolator, after which neonates remain germ-free, which would seem to provide strong data in support of sterility of the womb.<br><br>RESULTS: To probe this further and to investigate possible placental colonization associated with spontaneous preterm birth, we carried out another study comparing microbiota in placenta samples from 20 term and 20 spontaneous preterm deliveries. Both 16S rRNA marker gene sequencing and shotgun metagenomic sequencing were used to characterize placenta and control samples. We first quantified absolute amounts of bacterial 16S rRNA gene sequences using 16S rRNA gene quantitative PCR (qPCR). As in our previous study, levels were found to be low in the placenta samples and indistinguishable from negative controls. Analysis by DNA sequencing did not yield a placenta microbiome distinct from negative controls, either using marker gene sequencing as in our previous work, or with shotgun metagenomic sequencing. Several types of artifacts, including erroneous read classifications and barcode misattribution, needed to be identified and removed from the data to clarify this point.<br><br>CONCLUSIONS: Our findings do not support the existence of a consistent placental microbiome, in either placenta from term deliveries or spontaneous preterm births.},
}
@article {pmid30375755,
year = {2019},
author = {Shen, Y and Hubert, N and Huang, Y and Wang, X and Gan, X and Peng, Z and He, S},
title = {DNA barcoding the ichthyofauna of the Yangtze River: Insights from the molecular inventory of a mega-diverse temperate fauna.},
journal = {Molecular ecology resources},
volume = {19},
number = {5},
pages = {1278-1291},
doi = {10.1111/1755-0998.12961},
pmid = {30375755},
issn = {1755-0998},
support = {XDB13020100//Chinese Academy of Sciences/ ; 2018-175//Chinese Academy of Sciences/ ; },
mesh = {Animals ; *Biota ; China ; *DNA Barcoding, Taxonomic ; Fishes/*classification/*genetics ; Phylogeography ; *Rivers ; },
abstract = {Intensification of inland fisheries and aquatic landscape conversion led to a drastic decline of fish populations in the Yangtze River (YR) during the last decades. This situation urges for the development of a large-scale molecular assessment of YR ichthyofauna to further develop standardized methods of molecular identification for conservation and fisheries management purposes. We present here the results of a large-scale campaign to DNA barcode YR freshwater fishes that succeeded in producing 1,424 new DNA barcodes for 123 species. Together with 1,406 sequences mined from BOLD and GenBank, a reference library including 2,830 DNA barcodes for 238 species was compiled. By using four DNA-based species delimitation methods, RESL, ABGD, mPTP and mGMYC, 230 operational taxonomic units (OTUs) were identified and 195 species displayed OTUs that tightly match species boundaries. No barcoding gap was observed; however, and conflicting cases of species and OTU delimitation were identified. A total of 23 species with maximum intraspecific distances above 2% were detected and null genetic distances to the nearest phylogenetic relatives were detected in 11 species. Among those 23 species, 16 were represented by multiple OTUs amounting to 40 OTUs delineated. Several cases of multiple OTUs confined to species boundaries were detected suggesting the presence of overlooked species. A total of 18 OTUs, however, were shared by several species and particularly so for the Qinghai-Tibet plateau endemic species. These results are discussed with reference to previous large-scale DNA barcoding campaign and compared to previous phylogeographic studies in the YR.},
}
@article {pmid30375609,
year = {2018},
author = {Postek, W and Gargulinski, P and Scheler, O and Kaminski, TS and Garstecki, P},
title = {Microfluidic screening of antibiotic susceptibility at a single-cell level shows the inoculum effect of cefotaxime on E. coli.},
journal = {Lab on a chip},
volume = {18},
number = {23},
pages = {3668-3677},
doi = {10.1039/c8lc00916c},
pmid = {30375609},
issn = {1473-0189},
mesh = {Anti-Bacterial Agents/*pharmacology ; Cefotaxime/*pharmacology ; Escherichia coli/*cytology/*drug effects ; *Lab-On-A-Chip Devices ; Microbial Sensitivity Tests/*instrumentation ; Single-Cell Analysis/*instrumentation ; },
abstract = {Measurement of antibiotic susceptibility at the level of single cells is important as it reveals the concentration of an antibiotic that leads to drug resistance in bacterial strains. To date, no solution for large-scale studies of antibiotic susceptibility at the single-cell level has been shown. Here, we present a method for production and separation of emulsions consisting of subnanoliter droplets that allows us to identify each emulsion by their spatial position in the train of emulsions without chemical barcoding. The emulsions of droplets are separated by a third immiscible phase, thus forming large compartments-tankers-each filled with an emulsion of droplet reactors. Each tanker in a train can be set under different reaction conditions for hundreds or thousands of replications of the same reaction. The tankers allow for long term incubation - needed to check for growth of bacteria under a screen of conditions. We use microfluidic tankers to analyze susceptibility to cefotaxime in ca. 1900 replications for each concentration of the antibiotic in one experiment. We test cefotaxime susceptibility for different initial concentrations of bacteria, showing the inoculum effect down to the level of single cells for more than a hundred single-cell events per tanker. Lastly, we use tankers to observe the formation of aggregates of bacteria in the presence of cefotaxime in the increasing concentration of the antibiotic. The microfluidic tankers allow for facile studies of the inoculum effect and antibiotic susceptibility, and constitute an attractive, label-free screening method for a variety of other experiments in chemistry and biology.},
}
@article {pmid30371906,
year = {2019},
author = {Voulgari-Kokota, A and Grimmer, G and Steffan-Dewenter, I and Keller, A},
title = {Bacterial community structure and succession in nests of two megachilid bee genera.},
journal = {FEMS microbiology ecology},
volume = {95},
number = {1},
pages = {},
doi = {10.1093/femsec/fiy218},
pmid = {30371906},
issn = {1574-6941},
mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bees/classification/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Ecology ; Larva/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Studies on honeybees have revealed bacterial taxa which adopt key functions in the hive, in terms of nutrient uptake and immune responses. Despite solitary bees providing invaluable ecological services, the contribution of their microbial communities to larval health and the development and fitness of adults is mainly unknown. To address this gap, we conducted a 16S rDNA meta-barcoding study including larvae and stored pollen in nest chambers from two different megachilid solitary bee genera. We tested how host taxonomy, environmental context and the developmental stage of larvae determined richness and composition of associated bacterial communities. A total of 198 specimens from Osmia bicornis, Osmia caerulescens, Megachile rotundataandMegachile versicolor nests were investigated. Solitary bee bacterial microbiota in the nesting environment were mostly homogeneous within species, and not significantly affected by landscape. For each bee species, we identified bacterial taxa that showed consistent occurrence in the larvae and stored pollen. For the pollen provision, we also described a community shift with progressing larval development, suggesting a reduction of imported floral bacteria.},
}
@article {pmid30369813,
year = {2018},
author = {Li, C and Chen, B and Xu, X and Li, D and Dong, J},
title = {Simple sequence repeat markers associated/linked with agronomic traits, as core primers, are eminently suitable for DNA fingerprinting in Upland cotton.},
journal = {Breeding science},
volume = {68},
number = {4},
pages = {393-403},
pmid = {30369813},
issn = {1344-7610},
abstract = {Analyzing the genetic differences among crop germplasm resources scientifically and accurately is very important for the selection of core accessions, the identification of new cultivars, and the determination of seed purity. However, phenotypic selection per se is not sufficient to identify genetically distinct accessions. In this study, 26 out of 83 simple sequence repeat markers associated/linked with cotton important agronomic traits derived from our previous and other published research, corresponding to the 26 chromosomes of Upland cotton (Gossypium hirsutum L.), were selected as core primers for DNA fingerprinting construction. The 26 markers showed clear band patterns, good repeatability and high polymorphism. The average alleles, gene diversity index and polymorphism information content were 3.12, 0.4312 and 0.3830, respectively. Using TM-1, a genetic standard line for Upland cotton, as the control, DNA fingerprinting pattern and DNA barcodes were obtained based on the core primers. There was a significant positive correlation between genetic distance matrix determined using 26 core primers and that determined using more primers (335) derived from previous research, further suggesting that the core primers were eminently suitable for DNA fingerprinting in Upland cotton. This study provides a molecular basis for assessing identification, authenticity and seed purity of cotton cultivars.},
}
@article {pmid30368064,
year = {2019},
author = {Leonavicius, K and Nainys, J and Kuciauskas, D and Mazutis, L},
title = {Multi-omics at single-cell resolution: comparison of experimental and data fusion approaches.},
journal = {Current opinion in biotechnology},
volume = {55},
number = {},
pages = {159-166},
doi = {10.1016/j.copbio.2018.09.012},
pmid = {30368064},
issn = {1879-0429},
mesh = {Animals ; *Data Analysis ; Databases as Topic ; Epigenesis, Genetic ; Genomics/*methods ; Humans ; Single-Cell Analysis/*methods ; Transcriptome/genetics ; },
abstract = {Biological samples are inherently heterogeneous and complex. Tackling this complexity requires innovative technological and analytical solutions. Recent advances in high-throughput single-cell isolation and nucleic acid barcoding methods are rapidly changing the technological landscape of biological sciences and now make it possible to measure the (epi)genomic, transcriptomic, or proteomic state of individual cells. In addition, few experimental approaches enable multi-omics measurements of the same cell. However, merging-omics data collected from different experiments remains a considerable challenge. Although several strategies for merging transcriptomics datasets have recently been introduced, cell-to-cell variability and heterogeneity remains one of the confounding factors limiting data fusion and integration. Here, we focus our discussion on the latest single-cell technological and analytical solutions to achieve high data dimensionality and resolution. Obtaining datasets with a wealth of multi-omics information will undoubtedly provide new avenues for researchers to unravel the complexity of biological samples encountered in modern biological research and molecular diagnostics.},
}
@article {pmid30367754,
year = {2018},
author = {Glowska, E and Laniecka, I and Romanowska, K and Dabert, M},
title = {A new quill mite Torotrogla emberizae sp. nov. (Acariformes: Syringophilidae) from the Chestnut-eared Bunting (Passeriformes: Emberizidae) in Japan (morphology and DNA barcode data).},
journal = {Acta parasitologica},
volume = {63},
number = {4},
pages = {791-794},
doi = {10.1515/ap-2018-0095},
pmid = {30367754},
issn = {1896-1851},
mesh = {Animals ; Bird Diseases/*parasitology ; DNA Barcoding, Taxonomic/veterinary ; DNA, Mitochondrial/chemistry ; Electron Transport Complex IV/genetics ; Feathers/*parasitology ; Female ; Genome, Mitochondrial/genetics ; Japan ; Microscopy, Interference/veterinary ; Mite Infestations/parasitology/*veterinary ; Mites/anatomy &amp; histology/*classification/genetics ; Passeriformes/*parasitology ; Polymerase Chain Reaction/veterinary ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA/veterinary ; },
abstract = {A new quill mite Torotrogla emberizae sp. nov. (Acariformes: Syringophilidae) parasitizing the Chestnut-eared Bunting Emberiza fucata Pallas, 1776 (Passeriformes: Emberizidae) in Japan is described based on the external morphology and DNA barcode data (mitochondrial cytochrome c oxidase subunit I sequences, COI). Females of T. emberizae sp. nov. differ from T. volgini Skoracki and Mironov, 2013 by having the short, wide and blunt-ended hypostomal protuberances (vs long, thin and sharp-ended), setae h1 ca. twice shorter than f1 (vs h1 longer than f1), the fan-like setae p' and p" of legs III-IV provided with ca. 10 tines (vs 7-8 tines) and lengths of setae vi 70-105 (vs 55-65), ve 105-135 (vs 85-90) and h1 55-60 (vs 95-120).},
}
@article {pmid30366198,
year = {2018},
author = {Duckert, C and Blandenier, Q and Kupferschmid, FAL and Kosakyan, A and Mitchell, EAD and Lara, E and Singer, D},
title = {En garde! Redefinition of Nebela militaris (Arcellinida, Hyalospheniidae) and erection of Alabasta gen. nov.},
journal = {European journal of protistology},
volume = {66},
number = {},
pages = {156-165},
doi = {10.1016/j.ejop.2018.08.005},
pmid = {30366198},
issn = {1618-0429},
mesh = {DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; Lobosea/*classification/genetics ; *Phylogeny ; Species Specificity ; },
abstract = {Molecular data have considerably contributed to building the taxonomy of protists. Recently, the systematics of Hyalospheniidae (Amoebozoa; Tubulinea; Arcellinida) has been widely revised, with implications extending to ecological, biogeographical and evolutionary investigations. Certain taxa, however, still have an uncertain phylogenetic position, including the common and conspicuous species Nebela militaris. A phylogenetic reconstruction of the Hyalospheniidae using partial sequences of the mitochondrial Cytochrome Oxidase Subunit 1 (COI) gene shows that N. militaris does not belong to genus Nebela, but should be placed in its own genus. The morphological singularities (strongly curved pseudostome and a marked notch in lateral view) and phylogenetic placement of our isolates motivated the creation of a new genus: Alabasta gen. nov. Based on their morphology, we include in this genus Nebela kivuense and Nebela longicollis. We discuss the position of genus Alabasta within Hyalospheniidae, and the species that could integrate this new genus based on their morphological characteristics.},
}
@article {pmid30366085,
year = {2019},
author = {Engelbrecht, HM and Branch, WR and Greenbaum, E and Alexander, GJ and Jackson, K and Burger, M and Conradie, W and Kusamba, C and Zassi-Boulou, AG and Tolley, KA},
title = {Diversifying into the branches: Species boundaries in African green and bush snakes, Philothamnus (Serpentes: Colubridae).},
journal = {Molecular phylogenetics and evolution},
volume = {130},
number = {},
pages = {357-365},
doi = {10.1016/j.ympev.2018.10.023},
pmid = {30366085},
issn = {1095-9513},
mesh = {Africa, Western ; Animals ; Bayes Theorem ; Colubridae/*genetics ; *Genetic Variation ; Geography ; Likelihood Functions ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The African green and bush snakes of the genus Philothamnus currently comprises 21 species and three subspecies and occurs throughout sub-Saharan Africa. The genus has been the subject of previous taxonomic revisions based on traditional morphological characters and limited genetic assessment, and may not reflect their evolutionary history. Indeed, previous findings based on phylogenetics show discordant results of interspecific relationships and question the monophyly of the genus, although taxon sampling has been limited to date. We investigated phylogenetic affinities within Philothamnus with more inclusive genetic and geographical sampling, with the aim of better understanding their evolutionary history, so that future taxonomic revision of Philothamnus can be better informed. Species relationships were examined within a phylogenetic context and sampling included 133 ingroup samples from 16 taxa. Phylogenies were constructed in Bayesian and likelihood frameworks using three mitochondrial (16S, cyt b and ND4) and two nuclear (c-mos and RAG1) markers. Competing hypotheses relating to the monophyly of the genus were tested with a Shimodaira-Hasegawa test. To examine species boundaries, Bayesian General Mixed Yule-Coalescent Model and multi-rate Poisson Tree Processes analyses were conducted. In addition, a barcoding approach was used to further clarify species-level relationships by comparing frequency distributions between intra- and interspecific sequence divergence. The genus was recovered as monophyletic; however, species-delimitation results suggest that the current taxonomy does not reflect the evolutionary history of this group. For example, Philothamnus s. semivariegatus is paraphyletic, with at least four distinct clades. Philothamnus carinatus consists of two cryptic (sister) lineages from Central and West Africa that are deeply divergent, suggesting a long history of isolation between those regions. Furthermore, the subspecies P. n. natalensis and P. n. occidentalis show strong support for species-level divergence, which reflects their morphological and ecological differences. Accordingly, we elevate P. occidentalisnov. comb. to a full species. A fully informed taxonomic revision of these taxa will require additional morphological and ecological data for corroboration, but it seems that the morphological characters (e.g. scalation, dentition) used to describe these species to date are labile within and between species. This most likely has clouded our understanding of the species boundaries within the genus. Our phylogeny and species-delimitation analyses should provide a sounder framework for taxonomy, but may also prove useful toward understanding the morphological adaptations of these species to their respective habitats.},
}
@article {pmid30365918,
year = {2019},
author = {Powell, C and Caleca, V and Sinno, M and van Staden, M and van Noort, S and Rhode, C and Allsopp, E and van Asch, B},
title = {Barcoding of parasitoid wasps (Braconidae and Chalcidoidea) associated with wild and cultivated olives in the Western Cape of South Africa [1].},
journal = {Genome},
volume = {62},
number = {3},
pages = {183-199},
doi = {10.1139/gen-2018-0068},
pmid = {30365918},
issn = {1480-3321},
mesh = {Animals ; *Biodiversity ; DNA/analysis/*genetics ; DNA Barcoding, Taxonomic/*methods ; Olea/genetics/*parasitology ; Phylogeny ; South Africa ; Wasps/*classification/*genetics ; },
abstract = {Wild and cultivated olives harbor and share a diversity of insects, some of which are considered agricultural pests, such as the olive fruit fly. The assemblage of olive-associated parasitoids and seed wasps is rich and specialized in sub-Saharan Africa, with native species possibly coevolving with their hosts. Although historical entomological surveys reported on the diversity of olive wasp species in the Western Cape Province of South Africa, no comprehensive study has been performed in the region in the molecular era. In this study, a dual approach combining morphological and DNA-based methods was used for the identification of adult specimens reared from olive fruits. Four species of Braconidae and six species of Chalcidoidea were identified, and DNA barcoding methodologies were used to investigate conspecificity among individuals, based on randomly selected representative specimens. Morphological identifications were congruent with DNA data, as NJ and ML trees correctly placed the sequences for each species either at the genus or species level, depending on the available taxa coverage, and genetic distances strongly supported conspecificity. No clear evidence of cryptic diversity was found. Overall seed infestation and parasitism rates were higher in wild olives compared to cultivated olives, and highest for Eupelmus spermophilus and Utetes africanus. These results can be used for early DNA-based detection of wasp larvae in olives and to further investigate the biology and ecology of these species.},
}
@article {pmid30365909,
year = {2018},
author = {Ekrem, T and Stur, E and Orton, MG and Adamowicz, SJ},
title = {DNA barcode data reveal biogeographic trends in Arctic non-biting midges.},
journal = {Genome},
volume = {61},
number = {11},
pages = {787-796},
doi = {10.1139/gen-2018-0100},
pmid = {30365909},
issn = {1480-3321},
mesh = {Animals ; Arctic Regions ; Biodiversity ; Chironomidae/*classification/genetics ; *DNA Barcoding, Taxonomic ; Female ; Male ; Phylogeography ; },
abstract = {Chironomid flies (non-biting midges) are among the most abundant and diverse animals in Arctic regions, but detailed analyses of species distributions and biogeographical patterns are hampered by challenging taxonomy and reliance on morphology for species-level identification. Here we take advantage of available DNA barcode data of Arctic Chironomidae in BOLD to analyse similarities in species distributions across a northern Nearctic - West Palearctic gradient. Using more than 260 000 barcodes representing 4666 BINs (Barcode Index Numbers) and 826 named species (some with interim names) from a combination of public and novel data, we show that the Greenland chironomid fauna shows affinities to both the Nearctic and the West Palearctic regions. While raw taxon counts indicate a strong Greenland - North American affinity, comparisons using Chao's dissimilarity metric support a slightly higher similarity between Greenland and West Palearctic chironomid communities. Results were relatively consistent across different definitions of species taxonomic units, including morphologically determined species, BINs, and superBINs based on a ∼4.5% threshold. While most taxa found in Greenland are shared with at least one other region, reflecting circum-Arctic dispersal, our results also reveal that Greenland harbours a small endemic biodiversity. Our exploratory study showcases how DNA barcoding efforts using standardized gene regions contribute to an understanding of broad-scale patterns in biogeography by enabling joint analysis of public DNA sequence data derived from diverse prior studies.},
}
@article {pmid30365901,
year = {2018},
author = {Cong, Q and Grishin, NV},
title = {Comparative analysis of swallowtail transcriptomes suggests molecular determinants for speciation and adaptation.},
journal = {Genome},
volume = {61},
number = {12},
pages = {843-855},
pmid = {30365901},
issn = {1480-3321},
support = {R01 GM094575/GM/NIGMS NIH HHS/United States ; R35 GM127390/GM/NIGMS NIH HHS/United States ; },
mesh = {Acclimatization/genetics ; Animals ; Butterflies/classification/*genetics ; Genes, Insect ; *Genetic Speciation ; Transcriptome ; },
abstract = {Genetic determinants of speciation in closely related species are poorly understood. We sequenced and analyzed transcriptomes of swallowtail butterflies Heraclides cresphontes (northeastern species) and Heraclides rumiko (southwestern species), a pair of mostly allopatric sister species whose distribution ranges overlap narrowly in central Texas. We found that the two swallowtails confidently differ (FST > 0.5 for both species) in about 5% of genes, similarly to the divergence in another pair of swallowtail species Pterourus glaucus (southern species) and Pterourus canadensis (northern species). The same genes tend to diverge in both species pairs, suggesting similar speciation paths in Heraclides and Pterourus. The most significant differences for both species pairs were found in the circadian clock genes that were conserved within each species and diverged strongly between species (P-value < 0.01 and FST > 0.7). This divergence implied that adaptations to different climates and photoperiod at different latitudes or differences in mating behavior, including mating time and copulation duration, may be possible factors in ecological or behavioral-based speciation. Finally, we suggest several nuclear DNA regions that consistently and prominently differ between the sister swallowtail species as nuclear barcodes for swallowtail identification, with the best barcode being an exon from the protein TIMELESS.},
}
@article {pmid30364647,
year = {2018},
author = {Zheng, Y and Hou, Z and Li, S},
title = {Bogidiellapingxiangensis, a new species of subterranean Amphipoda from southern China (Bogidiellidae).},
journal = {ZooKeys},
volume = {},
number = {790},
pages = {63-75},
pmid = {30364647},
issn = {1313-2989},
abstract = {A new species of subterranean amphipod, Bogidiellapingxiangensis Hou &amp; Li, sp. n., is described from Xiongshizilong Cave in Pingxiang City, China. The new species is characterized by having the bases of pereopods III and V expanded; the inner ramus of pleopods I-III with one segment; the telson longer than wide and with the apical margin with a shallow U-shaped excavation. DNA barcode of the new species is documented as support of molecular differences between related species.},
}
@article {pmid30361962,
year = {2018},
author = {Jacobina, UP and Lima, SMQ and Maia, DG and Souza, G and Batalha-Filho, H and Torres, RA},
title = {DNA barcode sheds light on systematics and evolution of neotropical freshwater trahiras.},
journal = {Genetica},
volume = {146},
number = {6},
pages = {505-515},
pmid = {30361962},
issn = {1573-6857},
support = {425080/2016-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (BR)/ ; BCT-0125-2.04/15//Funda&#xe7;&#xe3;o de Amparo &#xe0; Ci&#xea;ncia e Tecnologia do Estado de Pernambuco/ ; 443249/2014-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 552086/2011-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 483878/2013-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; RED0045/2014//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado da Bahia/ ; JCB0026/2016//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado da Bahia/ ; },
mesh = {Animals ; Characiformes/classification/*genetics ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Fish Proteins/genetics ; Haplotypes ; Karyotype ; *Phylogeny ; Phylogeography ; },
abstract = {We assessed the presence of independent evolving lineages of the trahira, Hoplias malabaricus, one of the few freshwater fish species having wide distribution in the Neotropics which is the region with the highest global diversity of freshwater fish. To achieve that goal, 58 mitochondrial sequences of cytochrome c oxidase subunit I (COI; DNA barcoding) were generated from collected samples and 85 obtained from public databases, which were analyzed in comparison to chromosomal and geological data. The magnitude of genetic diversity found among different sampling sites was greater than 2%. Molecular species delimitation methods indicated the existence of a least four distinct lineages. The recognised cytotypes did not form monophyletic groups, suggesting that the karyotypic macrostructure could be a homoplastic character. The haplotype relationships suggested secondary contacts between the ecoregions of Northern and Northeastern Brazil that were shaped by coastal routes between adjacent watersheds during the Pleistocene epoch and probable exchanges of their ichthyofaunas. Our results indicated that multiple factors have driven the diversification of H. malabaricus, from ancient geological events linked to the reactivation of tectonic faults to more recent occurrences related to eustatic changes in ocean levels. Ultimately, the magnitude of its genetic diversity suggests the necessity of revising its taxonomic status.},
}
@article {pmid30360419,
year = {2018},
author = {Han, K and Wang, M and Zhang, L and Wang, C},
title = {Application of Molecular Methods in the Identification of Ingredients in Chinese Herbal Medicines.},
journal = {Molecules (Basel, Switzerland)},
volume = {23},
number = {10},
pages = {},
pmid = {30360419},
issn = {1420-3049},
support = {2015RQQXJ082//Harbin Science and Technology Bureau/ ; },
mesh = {Computational Biology/methods ; *DNA Barcoding, Taxonomic ; Drugs, Chinese Herbal/analysis/*chemistry/*classification ; Medicine, Chinese Traditional/methods/standards ; Microarray Analysis/methods/standards ; },
abstract = {There are several kinds of Chinese herbal medicines originating from diverse sources. However, the rapid taxonomic identification of large quantities of Chinese herbal medicines is difficult using traditional methods, and the process of identification itself is prone to error. Therefore, the traditional methods of Chinese herbal medicine identification must meet higher standards of accuracy. With the rapid development of bioinformatics, methods relying on bioinformatics strategies offer advantages with respect to the speed and accuracy of the identification of Chinese herbal medicine ingredients. This article reviews the applicability and limitations of biochip and DNA barcoding technology in the identification of Chinese herbal medicines. Furthermore, the future development of the two technologies of interest is discussed.},
}
@article {pmid30359742,
year = {2019},
author = {Ahmed, MS and Chowdhury, MMK and Nahar, L},
title = {Molecular characterization of small indigenous fish species (SIS) of Bangladesh through DNA barcodes.},
journal = {Gene},
volume = {684},
number = {},
pages = {53-57},
doi = {10.1016/j.gene.2018.10.048},
pmid = {30359742},
issn = {1879-0038},
mesh = {Animals ; Bangladesh ; Base Composition/genetics ; Base Sequence/genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial ; Databases, Genetic ; Electron Transport Complex IV/*genetics ; Fishes/classification/*genetics ; Fresh Water ; Genes, Mitochondrial/genetics ; Genetic Speciation ; Genetic Variation ; Phylogeny ; },
abstract = {The mitochondrial DNA gene cytochrome oxidase subunit I (COI) has been adopted as a global bioidentification system for animals. This study represents the comprehensive molecular identification of small indigenous fish species (SIS) of Bangladesh assessed by DNA barcoding. DNA barcodes were generated from 81 SIS species belongs to the orders Clupeiformes, Cypriniforms, Siluriformes, Perciformes, Synbranchiformes, Beloniformes and Tetraodontiformes representing 55 genera and 24 families. For all the samples, %G were significantly lowered compared to other nucleotides and %GC compared to %AT. Also, a significantly lowered GC content was observed in second and third codon position compared to the first codon position in all samples. The average Kimura two-parameter (K2P) distances within genera, families, and orders were 15.83%, 19.14%, and 25.07%, respectively. The minimum and maximum K2P distance based genetic divergences were 0.19% and 57.14% respectively. Members of Cypriniformes, Siluriformes, and Perciformes were clustered separately in the neighbour-joining (NJ) tree. Nucleotide composition, GC distribution across codon positions, K2P distance, genetic divergence, and phylogenetic analyses reveal that these freshwater SIS fishes are genetically very diverse. Along with morphological data, we have confirmed the existence of seven new records of SIS fishes in Bangladesh using such barcode approach. These findings suggest that fishes can be discriminated using these barcode data without any confusion.},
}
@article {pmid30353175,
year = {2018},
author = {Raj, B and Gagnon, JA and Schier, AF},
title = {Large-scale reconstruction of cell lineages using single-cell readout of transcriptomes and CRISPR-Cas9 barcodes by scGESTALT.},
journal = {Nature protocols},
volume = {13},
number = {11},
pages = {2685-2713},
pmid = {30353175},
issn = {1750-2799},
support = {DP1 HD094764/HD/NICHD NIH HHS/United States ; R01 HD085905/HD/NICHD NIH HHS/United States ; U01 MH105960/MH/NIMH NIH HHS/United States ; },
mesh = {Animals ; Animals, Genetically Modified ; Brain/growth &amp; development/metabolism ; CRISPR-Associated Protein 9/*genetics/metabolism ; *CRISPR-Cas Systems ; Cell Lineage/*genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; Embryo, Nonmammalian ; Gene Editing/*methods ; Gene Library ; Organ Specificity ; RNA, Guide, CRISPR-Cas Systems/genetics/metabolism ; Single-Cell Analysis/methods ; *Transcriptome ; Zebrafish/*genetics/growth &amp; development/metabolism ; },
abstract = {Lineage relationships among the large number of heterogeneous cell types generated during development are difficult to reconstruct in a high-throughput manner. We recently established a method, scGESTALT, that combines cumulative editing of a lineage barcode array by CRISPR-Cas9 with large-scale transcriptional profiling using droplet-based single-cell RNA sequencing (scRNA-seq). The technique generates edits in the barcode array over multiple timepoints using Cas9 and pools of single-guide RNAs (sgRNAs) introduced during early and late zebrafish embryonic development, which distinguishes it from similar Cas9 lineage-tracing methods. The recorded lineages are captured, along with thousands of cellular transcriptomes, to build lineage trees with hundreds of branches representing relationships among profiled cell types. Here, we provide details for (i) generating transgenic zebrafish; (ii) performing multi-timepoint barcode editing; (iii) building scRNA-seq libraries from brain tissue; and (iv) concurrently amplifying lineage barcodes from captured single cells. Generating transgenic lines takes 6 months, and performing barcode editing and generating single-cell libraries involve 7 d of hands-on time. scGESTALT provides a scalable platform to map lineage relationships between cell types in any system that permits genome editing during development, regeneration, or disease.},
}
@article {pmid30351359,
year = {2019},
author = {Orabi, B and Erhan, E and McConeghy, B and Volik, SV and Le Bihan, S and Bell, R and Collins, CC and Chauve, C and Hach, F},
title = {Alignment-free clustering of UMI tagged DNA molecules.},
journal = {Bioinformatics (Oxford, England)},
volume = {35},
number = {11},
pages = {1829-1836},
doi = {10.1093/bioinformatics/bty888},
pmid = {30351359},
issn = {1367-4811},
mesh = {Algorithms ; Cluster Analysis ; DNA ; *High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; *Software ; },
abstract = {MOTIVATION: Next-Generation Sequencing has led to the availability of massive genomic datasets whose processing raises many challenges, including the handling of sequencing errors. This is especially pertinent in cancer genomics, e.g. for detecting low allele frequency variations from circulating tumor DNA. Barcode tagging of DNA molecules with unique molecular identifiers (UMI) attempts to mitigate sequencing errors; UMI tagged molecules are polymerase chain reaction (PCR) amplified, and the PCR copies of UMI tagged molecules are sequenced independently. However, the PCR and sequencing steps can generate errors in the sequenced reads that can be located in the barcode and/or the DNA sequence. Analyzing UMI tagged sequencing data requires an initial clustering step, with the aim of grouping reads sequenced from PCR duplicates of the same UMI tagged molecule into a single cluster, and the size of the current datasets requires this clustering process to be resource-efficient.<br><br>RESULTS: We introduce Calib, a computational tool that clusters paired-end reads from UMI tagged sequencing experiments generated by substitution-error-dominant sequencing platforms such as Illumina. Calib clusters are defined as connected components of a graph whose edges are defined in terms of both barcode similarity and read sequence similarity. The graph is constructed efficiently using locality sensitive hashing and MinHashing techniques. Calib's default clustering parameters are optimized empirically, for different UMI and read lengths, using a simulation module that is packaged with Calib. Compared to other tools, Calib has the best accuracy on simulated data, while maintaining reasonable runtime and memory footprint. On a real dataset, Calib runs with far less resources than alignment-based methods, and its clusters reduce the number of tentative false positive in downstream variation calling.<br><br>Calib is implemented in C++ and its simulation module is implemented in Python. Calib is available at https://github.com/vpc-ccg/calib.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid30350554,
year = {2018},
author = {Gomes, S and Breia, R and Carvalho, T and Carnide, V and Martins-Lopes, P},
title = {Microsatellite High-Resolution Melting (SSR-HRM) to Track Olive Genotypes: From Field to Olive Oil.},
journal = {Journal of food science},
volume = {83},
number = {10},
pages = {2415-2423},
doi = {10.1111/1750-3841.14333},
pmid = {30350554},
issn = {1750-3841},
support = {NORTE-07-0124-FEDER-0000029//Portuguese Foundation for Science and Technology (FCT) in the project INNOFOOD - INNOvation in the FOOD/ ; BI/INNOFOOD/UTAD/256/2014//Portuguese Foundation for Science and Technology (FCT)/ ; SFRH/BPD/70378/2010//Portuguese Foundation for Science and Technology (FCT)/ ; },
mesh = {DNA, Plant/*genetics ; Food Analysis ; Food Contamination/analysis ; Food Labeling ; Genetic Markers ; *Genotype ; *Microsatellite Repeats ; Olea/*genetics ; Olive Oil/*analysis ; Polymerase Chain Reaction ; Reproducibility of Results ; },
abstract = {The need to support food labelling has driven to the development of PCR-based techniques suitable for food analysis. DNA-based markers have been successfully employed for varietal tracing in Protected Designation of Origin (PDO) olive oils. In this study, we report a fast, sensitive, and easy-to-use strategy for PDO olive varietal identification. To achieve this aim four different DNA extraction methods were tested and compared, based on initial volume, extraction time, the gDNA concentration, and quality ratios. The optimized DNA extraction protocol from extra virgin olive oils, based on CTAB-hexane-chloroform extraction, proved to be the most effective. High-resolution melting (HRM) DNA assay was developed based on nuclear microsatellites (gSSR) and plastid DNA (cpDNA) aiming an accurate identification of the olive varieties present in the olive oil samples. After PCR reproducibility evaluation, six molecular markers: three SSRs and three cpDNA loci were chosen based on their discrimination power. The SSR-HRM strategy assays were designed to target UDO99-011, UDO99-039, UDO99-024, and ssrOeUA-DCA16 loci. All SSR-PCR products generated from these primers were analyzed by capillary electrophoresis (CE) for HRM data validation. The SSR coupled with HRM melting curve analysis generated 14 HRM profiles sufficient to genotype all varieties, highlighting their potential use for varietal discrimination. The locus ssrOeUA-DCA16 generated a specific melting curve that allow a high-throughput discrimination of the Picual and Cobrançosa varieties in olive oil samples. Further, the UDO99-024 was also tested by SSR-HRM assay in commercial olive oil samples with promising results. Considering time, cost, and performance SSR-HRM proved to be a reliable method suitable for varietal tracing of olive oils. PRACTICAL APPLICATION: Olive oil authenticity is a form of protecting producers and consumers against fraudulent practices. Herein, we present a DNA barcode suitable for the identification of olive varieties, allowing an accurate identification of the olive varieties in olive oil samples using SSR-HRM assay. Its applicability in commercial olive oil samples is viable. This methodology can be used as a tool for Extra Virgin Olive Oil (EVOO) adulterations detection.},
}
@article {pmid30349088,
year = {2018},
author = {Ando, H and Fujii, C and Kawanabe, M and Ao, Y and Inoue, T and Takenaka, A},
title = {Evaluation of plant contamination in metabarcoding diet analysis of a herbivore.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {15563},
pmid = {30349088},
issn = {2045-2322},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/analysis/genetics ; DNA, Plant/*analysis/genetics ; Feces/*chemistry ; *Feeding Behavior ; *Food Contamination ; Geese ; Herbivory/*physiology ; *Metagenomics ; },
abstract = {Fecal DNA metabarcoding is currently used in various fields of ecology to determine animal diets. Contamination of non-food DNA from complex field environments is a considerable challenge to the reliability of this method but has rarely been quantified. We evaluated plant DNA contamination by sequencing the chloroplast trnL P6 loop region from food-controlled geese feces. The average percentage of contaminant sequences per sample was 1.86%. According to the results of generalized linear models, the probability of contamination was highest in samples placed in wet soil. The proportion of contaminant sequences was lowest at the earliest sampling point and was slightly higher in samples placed in open conditions. Exclusion of rare OTUs (operational taxonomic units) was effective for obtaining reliable dietary data from the obtained sequences, and a 1% cutoff reduced the percentage of contaminated samples to less than 30%. However, appropriate interpretation of the barcoding results considering inevitable contamination is an important issue to address. We suggest the following procedures for fecal sampling and sequence data treatment to increase the reliability of DNA metabarcoding diet analyses: (i) Collect samples as soon as possible after deposition, (ii) avoid samples from deposits on wet soil, and (iii) exclude rare OTUs from diet composition estimations.},
}
@article {pmid30348075,
year = {2018},
author = {Wong, TKF and Ranjard, L and Lin, Y and Rodrigo, AG},
title = {HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations.},
journal = {BMC bioinformatics},
volume = {19},
number = {1},
pages = {389},
pmid = {30348075},
issn = {1471-2105},
support = {DP160103474//Australian Research Council (AU)/ ; },
mesh = {*Algorithms ; Base Sequence ; Computer Simulation ; Databases, Genetic ; Haplotypes/*genetics ; Humans ; },
abstract = {BACKGROUND: Pooling techniques, where multiple sub-samples are mixed in a single sample, are widely used to take full advantage of high-throughput DNA sequencing. Recently, Ranjard et al. (PLoS ONE 13:0195090, 2018) proposed a pooling strategy without the use of barcodes. Three sub-samples were mixed in different known proportions (i.e. 62.5%, 25% and 12.5%), and a method was developed to use these proportions to reconstruct the three haplotypes effectively.<br><br>RESULTS: HaploJuice provides an alternative haplotype reconstruction algorithm for Ranjard et al.'s pooling strategy. HaploJuice significantly increases the accuracy by first identifying the empirical proportions of the three mixed sub-samples and then assembling the haplotypes using a dynamic programming approach. HaploJuice was evaluated against five different assembly algorithms, Hmmfreq (Ranjard et al., PLoS ONE 13:0195090, 2018), ShoRAH (Zagordi et al., BMC Bioinformatics 12:119, 2011), SAVAGE (Baaijens et al., Genome Res 27:835-848, 2017), PredictHaplo (Prabhakaran et al., IEEE/ACM Trans Comput Biol Bioinform 11:182-91, 2014) and QuRe (Prosperi and Salemi, Bioinformatics 28:132-3, 2012). Using simulated and real data sets, HaploJuice reconstructed the true sequences with the highest coverage and the lowest error rate.<br><br>CONCLUSION: HaploJuice provides high accuracy in haplotype reconstruction, making Ranjard et al.'s pooling strategy more efficient, feasible, and applicable, with the benefit of reducing the sequencing cost.},
}
@article {pmid30346411,
year = {2018},
author = {Skånland, SS},
title = {Phospho Flow Cytometry with Fluorescent Cell Barcoding for Single Cell Signaling Analysis and Biomarker Discovery.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {140},
pages = {},
pmid = {30346411},
issn = {1940-087X},
mesh = {Biomarkers/*analysis/metabolism ; *Flow Cytometry ; Fluorescent Dyes/chemistry ; Humans ; Leukocytes, Mononuclear/cytology/metabolism ; Phosphoproteins/analysis/metabolism ; Phosphorylation ; *Signal Transduction ; Single-Cell Analysis/*methods ; Tumor Cells, Cultured ; },
abstract = {Aberrant cell signaling plays a central role in cancer development and progression. Most novel targeted therapies are indeed directed at proteins and protein functions, and cell signaling aberrations may therefore serve as biomarkers to indicate personalized treatment options. As opposed to DNA and RNA analyses, changes in protein activity can more efficiently evaluate the mechanisms underlying drug sensitivity and resistance. Phospho flow cytometry is a powerful technique that measures protein phosphorylation events at the cellular level, an important feature that distinguishes this method from other antibody-based approaches. The method allows for simultaneous analysis of multiple signaling proteins. In combination with fluorescent cell barcoding, larger medium- to high-throughput data-sets can be acquired by standard cytometer hardware in short time. Phospho flow cytometry has applications both in studies of basic biology and in clinical research, including signaling analysis, biomarker discovery and assessment of pharmacodynamics. Here, a detailed experimental protocol is provided for phospho flow analysis of purified peripheral blood mononuclear cells, using chronic lymphocytic leukemia cells as an example.},
}
@article {pmid30346097,
year = {2018},
author = {Derocles, SAP and Lunt, DH and Berthe, SCF and Nichols, PC and Moss, ED and Evans, DM},
title = {Climate warming alters the structure of farmland tritrophic ecological networks and reduces crop yield.},
journal = {Molecular ecology},
volume = {27},
number = {23},
pages = {4931-4946},
doi = {10.1111/mec.14903},
pmid = {30346097},
issn = {1365-294X},
mesh = {Animals ; Aphids/parasitology ; *Climate Change ; Crops, Agricultural/*growth &amp; development ; *Ecosystem ; Farms ; Herbivory ; *Temperature ; Triticum/growth &amp; development ; Wasps ; },
abstract = {It is unclear how sustained increases in temperature and changes in precipitation, as a result of climate change, will affect crops and their interactions with agricultural weeds, insect pests and predators, due to the difficulties in quantifying changes in such complex relationships. We simulated the combined effects of increasing temperature (by an average of 1.4°C over a growing season) and applying additional rainwater (10% of the monthly mean added weekly, 40% total) using a replicated, randomized block experiment within a wheat crop. We examined how this affected the structure of 24 quantitative replicate plant-aphid-parasitoid networks constructed using DNA-based methods. Simulated climate warming affected species richness, significantly altered consumer-resource asymmetries and reduced network complexity. Increased temperature induced an aphid outbreak, but the parasitism rates of aphids by parasitoid wasps remained unchanged. It also drove changes in the crop, altering in particular the phenology of the wheat as well as its quality (i.e., fewer, lighter seeds). We discuss the importance of considering the wider impacts of climate change on interacting species across trophic levels in agroecosystems.},
}
@article {pmid30344443,
year = {2018},
author = {Kruse, J and Kummer, V and Shivas, RG and Thines, M},
title = {The first smut fungus, Thecaphoraanthemidis sp. nov. (Glomosporiaceae), described from Anthemis (Asteraceae).},
journal = {MycoKeys},
volume = {},
number = {41},
pages = {39-50},
pmid = {30344443},
issn = {1314-4049},
abstract = {There are 63 known species of Thecaphora (Glomosporiaceae, Ustilaginomycotina), a third of which occur on Asteraceae. These smut fungi produce yellowish-brown to reddish-brown masses of spore balls in specific, mostly regenerative, plant organs. A species of Thecaphora was collected in the flower heads of Anthemischia (Anthemideae, Asteraceae) on Rhodes Island, Greece, in 2015 and 2017, which represents the first smut record of a smut fungus on a host plant species in this tribe. Based on its distinctive morphology, host species and genetic divergence, this species is described as Thecaphoraanthemidis sp. nov. Molecular barcodes of the ITS region are provided for this and several other species of Thecaphora. A phylogenetic and morphological comparison to closely related species showed that Th.anthemidis differed from other species of Thecaphora. Thecaphoraanthemidis produced loose spore balls in the flower heads and peduncles of Anthemischia unlike other flower-infecting species.},
}
@article {pmid30344433,
year = {2018},
author = {Constantinescu, IC and Popa, OP and Popa, LO and Cobzaru, I and B, MDK and Adam, C},
title = {A new feather mite species of the genus Trouessartia Canestrini, 1899 (Acarina, Trouessartiidae) - an integrative description (morphology and DNA barcoding data).},
journal = {ZooKeys},
volume = {},
number = {789},
pages = {19-35},
pmid = {30344433},
issn = {1313-2989},
abstract = {A new species of the feather mite genus Trouessartia (Trouessartiidae) is described from the Large NiltavaNiltavagrandis (Blyth) (Passeriformes, Muscicapidae) in Northeast India (Meghalaya, Jaintia Hills, Shnongrim village). Trouessartianiltavae Constantinescu, sp. n. is morphologically closely related (no phylogenetic meaning) to T.bulligera Gaud, 1968 from Clytorhynchushamlini (Mayr) (Passeriformes: Monarchidae), sharing in males a unique character within the genus, by having setae e on legs IV hemispheroid, with spine-shaped apex. Males of the new species have the prodorsal shield without ornamentation, the prohysteronotal shield and lobar shield connected, and the terminal cleft parallel sided. Females have the posterior half of the hysteronotal shield ornamented with large ovate lacunae in central area and small elliptical lacunae marginally. To the morphological description of this new feather mite species we added sequence data on the mitochondrial cytochrome c oxidase subunit I gene fragment (COI). The phylogenetic relationships between Trouessartia species are briefly discussed.},
}
@article {pmid30344010,
year = {2018},
author = {Philipp, F and Selich, A and Rothe, M and Hoffmann, D and Rittinghausen, S and Morgan, MA and Klatt, D and Glage, S and Lienenklaus, S and Neuhaus, V and Sewald, K and Braun, A and Schambach, A},
title = {Human Teratoma-Derived Hematopoiesis Is a Highly Polyclonal Process Supported by Human Umbilical Vein Endothelial Cells.},
journal = {Stem cell reports},
volume = {11},
number = {5},
pages = {1051-1060},
pmid = {30344010},
issn = {2213-6711},
mesh = {Animals ; Cytokines/administration &amp; dosage/pharmacology ; *Hematopoiesis/drug effects ; Hematopoietic Stem Cells/cytology/drug effects/metabolism ; Human Umbilical Vein Endothelial Cells/drug effects/*metabolism ; Humans ; Induced Pluripotent Stem Cells/drug effects/metabolism ; Ligands ; Mice ; Receptors, Notch/metabolism ; Teratoma/*pathology ; },
abstract = {Hematopoietic stem cells (HSCs) ensure a life-long regeneration of the blood system and are therefore an important source for transplantation and gene therapy. The teratoma environment supports the complex development of functional HSCs from human pluripotent stem cells, which is difficult to recapitulate in culture. This model mimics various aspects of early hematopoiesis, but is restricted by the low spontaneous hematopoiesis rate. In this study, a feasible protocol for robust hematopoiesis has been elaborated. We achieved a significant increase of the teratoma-derived hematopoietic population when teratomas were generated in the NSGS mouse, which provides human cytokines, together with co-injection of human umbilical vein endothelial cells. Since little is known about hematopoiesis in teratomas, we addressed localization and clonality of the hematopoietic lineage. Our results indicate that early human hematopoiesis is closely reflected in teratoma formation, and thus highlight the value of this model.},
}
@article {pmid30343902,
year = {2018},
author = {Wroblewska, A and Dhainaut, M and Ben-Zvi, B and Rose, SA and Park, ES and Amir, ED and Bektesevic, A and Baccarini, A and Merad, M and Rahman, AH and Brown, BD},
title = {Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens.},
journal = {Cell},
volume = {175},
number = {4},
pages = {1141-1155.e16},
pmid = {30343902},
issn = {1097-4172},
support = {U19 AI128949/AI/NIAID NIH HHS/United States ; R01 AI113221/AI/NIAID NIH HHS/United States ; R01 CA190400/CA/NCI NIH HHS/United States ; R33 CA182377/CA/NCI NIH HHS/United States ; U24 AI118644/AI/NIAID NIH HHS/United States ; S10 OD023547/OD/NIH HHS/United States ; R01 CA154947/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; *CRISPR-Cas Systems ; Epitopes/chemistry/classification/genetics ; Flow Cytometry/*methods ; Genomics/*methods ; HEK293 Cells ; Humans ; Immunophenotyping/methods ; Jurkat Cells ; Mass Spectrometry/*methods ; Mice, Inbred BALB C ; Proteome/chemistry/classification/genetics ; Single-Cell Analysis/*methods ; THP-1 Cells ; },
abstract = {CRISPR pools are being widely employed to identify gene functions. However, current technology, which utilizes DNA as barcodes, permits limited phenotyping and bulk-cell resolution. To enable novel screening capabilities, we developed a barcoding system operating at the protein level. We synthesized modules encoding triplet combinations of linear epitopes to generate >100 unique protein barcodes (Pro-Codes). Pro-Code-expressing vectors were introduced into cells and analyzed by CyTOF mass cytometry. Using just 14 antibodies, we detected 364 Pro-Code populations; establishing the largest set of protein-based reporters. By pairing each Pro-Code with a different CRISPR, we simultaneously analyzed multiple phenotypic markers, including phospho-signaling, on dozens of knockouts. Pro-Code/CRISPR screens found two interferon-stimulated genes, the immunoproteasome component Psmb8 and a chaperone Rtp4, are important for antigen-dependent immune editing of cancer cells and identified Socs1 as a negative regulator of Pd-l1. The Pro-Code technology enables simultaneous high-dimensional protein-level phenotyping of 100s of genes with single-cell resolution.},
}
@article {pmid30337830,
year = {2018},
author = {Crabo, LG and Hammond, PC and Mustelin, T and Wikle, DL},
title = {Six new species and one new subspecies of noctuid moths from western United States of America and Mexico (Lepidoptera, Noctuidae).},
journal = {ZooKeys},
volume = {},
number = {788},
pages = {201-239},
pmid = {30337830},
issn = {1313-2989},
abstract = {Six new species and one new subspecies of Noctuidae are described from western United States of America and Baja California, Mexico: Dolocuculliapoolei Crabo &amp; Hammond, sp. n. (Cuculliinae), Plagiomimicusyakama Crabo &amp; Wikle, sp. n., Plagiomimicusyakamamojave Wikle &amp; Crabo, ssp. n., Plagiomimicusincomitatus Mustelin, sp. n. (Amphipyrinae), Sympistisferrirena Crabo, sp. n. (Oncocnemidinae), Aseptisharpi Crabo &amp; Mustelin, sp. n., and Hypotrixlactomellis Wikle &amp; Crabo, sp. n. (Noctuinae). The adults and genitalia of these species are described, illustrated, and compared to similar related moths. The larvae of the Plagiomimicustepperi species group, unknown previously, are reported to feed on several species of Brickellia Ell. (Asteraceae). The early stages of Plagiomimicusyakamamojave are described and late instars are illustrated.},
}
@article {pmid30337829,
year = {2018},
author = {Crabo, LG},
title = {A new genus and three new species of noctuid moths from western United States of America and Mexico (Lepidoptera, Noctuidae, Noctuinae, Eriopygini).},
journal = {ZooKeys},
volume = {},
number = {788},
pages = {183-199},
pmid = {30337829},
issn = {1313-2989},
abstract = {The genus Rhabdorthodes gen. n. is described for three previously unnamed noctuid moths from the mountains of south-western United States and Mexico. It is assigned to subfamily Noctuinae, tribe Eriopygini. Rhabdorthodespattersoni sp. n. from the United States and Rhabdorthodesdurango sp. n. and Rhabdorthodespetersoni sp. n. from Mexico are described. These moths are small, dull gray brown, and lack highly diagnostic wing markings, but are distinctive structurally. The adults and genitalia of both sexes are illustrated and distribution maps are presented. Two species eponyms honor persons who have facilitated the study and enjoyment of moths in North America by creating moth-specific websites.},
}
@article {pmid30337828,
year = {2018},
author = {Crabo, LG and Schmidt, BC},
title = {A revision of Admetovis Grote, with the description of a new species from western North America (Noctuidae, Noctuinae, Hadenini).},
journal = {ZooKeys},
volume = {},
number = {788},
pages = {167-181},
pmid = {30337828},
issn = {1313-2989},
abstract = {The genus Admetovis Grote is revised. Admetovisicarus sp. n. is described from the mountains of western North America. A lectotype of Admetovisoxymorus Grote is designated. Illustrations of the adults, male and female genitalia, and distribution maps are presented, together with an identification key. The classification of the genus is reviewed resulting in its reassignment to the tribe Hadenini from Orthosiini.},
}
@article {pmid30337827,
year = {2018},
author = {Goldstein, PZ and Janzen, DH and Proshek, B and Dapkey, T and Hallwachs, W},
title = {Review of Lophomyra Schaus, 1911 (Lepidoptera, Noctuidae): a new combination and re-descriptions of species newly associated with ferns (Polypodiaceae).},
journal = {ZooKeys},
volume = {},
number = {788},
pages = {135-165},
pmid = {30337827},
issn = {1313-2989},
abstract = {Lophomyra Schaus, 1911 (Noctuidae) is the smaller of two noctuid genera originally described by Schaus that include species recently associated with ferns (Pteridophyta), in this case Polypodiaceae, as larval food plants. Following an examination of type material and reared specimens accompanied by DNA barcode data, Lophomyra is revised to include L.tacita Schaus, 1911, L.santista (Jones, 1914), and L.commixta (Schaus, 1914), comb. n., the last of which is transferred from Chytonidia Schaus, 1914 (= Leucosigma Druce, 1908). Lophomyra is characterized based on adult and larval morphology, especially that of the male genitalia. Structures associated with the valvae are discussed with reference to dissected and in situ images. Larvae of L.commixta and L.tacita are described from images, and the recorded food plants of both species are discussed in the context of known New World noctuid pteridivores.},
}
@article {pmid30337826,
year = {2018},
author = {Goldstein, PZ and Janzen, DH and Proshek, B and Dapkey, T and Hallwachs, W},
title = {A review of Leucosigma Druce, 1908: a newly discovered case of fern-feeding and descriptions of three new species (Lepidoptera, Noctuidae).},
journal = {ZooKeys},
volume = {},
number = {788},
pages = {87-133},
pmid = {30337826},
issn = {1313-2989},
abstract = {Chytonidia Schaus, 1914, is one of two noctuine genera originally described by Schaus that includes species recently found to feed on fern foliage (Pteridophyta) as larvae. By examining museum specimens, including type material and reared specimens accompanied by DNA barcode data, Chytonidia Schaus, 1914, syn. n. is synonymized with Leucosigma Druce, 1908, all currently recognized species are re-described, including males of three species described from female holotypes, and three new species are described: Leucosigmasolisae Goldstein, sp. n., Leucosigmapoolei Goldstein, sp. n., and L.schausi Goldstein, sp. n. Images of adults and, where available, larvae as well as dissected genitalia are presented, with a key to adults.},
}
@article {pmid30335763,
year = {2018},
author = {Orantes, LC and Monroy, C and Dorn, PL and Stevens, L and Rizzo, DM and Morrissey, L and Hanley, JP and Rodas, AG and Richards, B and Wallin, KF and Helms Cahan, S},
title = {Uncovering vector, parasite, blood meal and microbiome patterns from mixed-DNA specimens of the Chagas disease vector Triatoma dimidiata.},
journal = {PLoS neglected tropical diseases},
volume = {12},
number = {10},
pages = {e0006730},
pmid = {30335763},
issn = {1935-2735},
mesh = {Animals ; Archaea/genetics/isolation &amp; purification ; Bacteria/genetics/isolation &amp; purification ; Central America ; Cluster Analysis ; Computational Biology ; DNA/*genetics/*isolation &amp; purification ; *Feeding Behavior ; Fungi/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Nematoda/genetics/isolation &amp; purification ; Phylogeny ; Sequence Analysis, DNA ; Triatoma/*genetics/microbiology/parasitology/physiology ; Trypanosoma cruzi/genetics/*isolation &amp; purification ; Viruses/genetics/isolation &amp; purification ; },
abstract = {Chagas disease, considered a neglected disease by the World Health Organization, is caused by the protozoan parasite Trypanosoma cruzi, and transmitted by >140 triatomine species across the Americas. In Central America, the main vector is Triatoma dimidiata, an opportunistic blood meal feeder inhabiting both domestic and sylvatic ecotopes. Given the diversity of interacting biological agents involved in the epidemiology of Chagas disease, having simultaneous information on the dynamics of the parasite, vector, the gut microbiome of the vector, and the blood meal source would facilitate identifying key biotic factors associated with the risk of T. cruzi transmission. In this study, we developed a RADseq-based analysis pipeline to study mixed-species DNA extracted from T. dimidiata abdomens. To evaluate the efficacy of the method across spatial scales, we used a nested spatial sampling design that spanned from individual villages within Guatemala to major biogeographic regions of Central America. Information from each biotic source was distinguished with bioinformatics tools and used to evaluate the prevalence of T. cruzi infection and predominant Discrete Typing Units (DTUs) in the region, the population genetic structure of T. dimidiata, gut microbial diversity, and the blood meal history. An average of 3.25 million reads per specimen were obtained, with approximately 1% assigned to the parasite, 20% to the vector, 11% to bacteria, and 4% to putative blood meals. Using a total of 6,405 T. cruzi SNPs, we detected nine infected vectors harboring two distinct DTUs: TcI and a second unidentified strain, possibly TcIV. Vector specimens were sufficiently variable for population genomic analyses, with a total of 25,710 T. dimidiata SNPs across all samples that were sufficient to detect geographic genetic structure at both local and regional scales. We observed a diverse microbiotic community, with significantly higher bacterial species richness in infected T. dimidiata abdomens than those that were not infected. Unifrac analysis suggests a common assemblage of bacteria associated with infection, which co-occurs with the typical gut microbial community derived from the local environment. We identified vertebrate blood meals from five T. dimidiata abdomens, including chicken, dog, duck and human; however, additional detection methods would be necessary to confidently identify blood meal sources from most specimens. Overall, our study shows this method is effective for simultaneously generating genetic data on vectors and their associated parasites, along with ecological information on feeding patterns and microbial interactions that may be followed up with complementary approaches such as PCR-based parasite detection, 18S eukaryotic and 16S bacterial barcoding.},
}
@article {pmid30335153,
year = {2018},
author = {Wong, TH and But, GW and Wu, HY and Tsang, SS and Lau, DT and Shaw, PC},
title = {Medicinal Materials DNA Barcode Database (MMDBD) version 1.5-one-stop solution for storage, BLAST, alignment and primer design.},
journal = {Database : the journal of biological databases and curation},
volume = {2018},
number = {},
pages = {},
pmid = {30335153},
issn = {1758-0463},
mesh = {Base Sequence ; *DNA Barcoding, Taxonomic ; DNA Primers/*metabolism ; DNA, Plant/genetics ; *Databases, Nucleic Acid ; Plants, Medicinal/*genetics ; Sequence Alignment/*methods ; },
abstract = {Authentication of medicinal materials by deoxyribonucleic acid (DNA) technology is gaining popularity. In 2010, our team has created Medicinal Materials DNA Barcode Database (MMDBD) version 1.0 to provide an interactive database for documenting DNA barcode sequences of medicinal materials. This database now contains DNA barcode sequences of medicinal materials listed in the Chinese Pharmacopoeia, Dietary Supplements Compendium and Herbal Medicine Compendium of the US Pharmacopoeia and selected adulterants. The data archive is regularly updated and currently it stores 62 011 DNA sequences of 2111 medicinal materials. Our team has recently completed the major improvement on the interfaces and incorporated essential bioinformatics tools to facilitate the authentication work. MMDBD version 1.5 contains detailed information of each medicinal material including their material names, medical part, pharmacopeia information, biological classification in rank of family and status on the Convention on International Trade in Endangered Species of Wild Fauna and Flora and the International Union for Conservation of Nature's Red List of Threatened Species, if any. DNA sequences can be retrieved by search in Latin scientific name, Chinese name, family name, material name, medical part and simplified Chinese character stroke. A `BLAST'-based engine for searching DNA sequences is included in the MMDBD version 1.5. Since primer design is a key step in DNA barcoding authentication, we have integrated the `Clustal Omega alignment tool' and `Primer3' in the form of web interface. These new tools facilitate multiple sequence comparison and the design of primers for amplification of a target DNA barcode region, allowing DNA barcoding authentication.},
}
@article {pmid30329222,
year = {2019},
author = {Hoff, SNK and Baalsrud, HT and Tooming-Klunderud, A and Skage, M and Richmond, T and Obernosterer, G and Shirzadi, R and Tørresen, OK and Jakobsen, KS and Jentoft, S},
title = {Long-read sequence capture of the haemoglobin gene clusters across codfish species.},
journal = {Molecular ecology resources},
volume = {19},
number = {1},
pages = {245-259},
pmid = {30329222},
issn = {1755-0998},
support = {222378//Norges Forskningsr&#xe5;d/ ; },
mesh = {Animals ; Computational Biology ; Evolution, Molecular ; Gadiformes/*classification/*genetics ; Gadus morhua ; Gene Order ; *Genetic Loci ; Genetic Variation ; Genomics/*methods ; Hemoglobins/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; *Multigene Family ; Synteny ; },
abstract = {Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long-read sequencing technology for comparative genomic analyses of the haemoglobin (Hb) gene clusters across eight species separated by up to 70 million years. Guided by the reference genome assembly of the Atlantic cod (Gadus morhua) together with genome information from draft assemblies of selected codfishes, we designed probes covering the two Hb gene clusters. Use of custom-made barcodes combined with PacBio RSII sequencing led to highly continuous assemblies of the LA (~100 kb) and MN (~200 kb) clusters, which include syntenic regions of coding and intergenic sequences. Our results revealed an overall conserved genomic organization of the Hb genes within this lineage, yet with several, lineage-specific gene duplications. Moreover, for some of the species examined, we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. This study highlights the use of targeted long-read capture as a versatile approach for comparative genomic studies by generation of a cross-species genomic resource elucidating the evolutionary history of the Hb gene family across the highly divergent group of codfishes.},
}
@article {pmid30324686,
year = {2019},
author = {Yang, Q and Liu, S and He, C and Cowie, RH and Yu, X and Hayes, KA},
title = {Invisible apple snail invasions: importance of continued vigilance and rigorous taxonomic assessments.},
journal = {Pest management science},
volume = {75},
number = {5},
pages = {1277-1286},
doi = {10.1002/ps.5241},
pmid = {30324686},
issn = {1526-4998},
support = {2017YFF0210200, 2018YFC0809200//China National Key Research and Development Program/ ; 31800462//The National Natural Science Foundation of China/ ; DEB 0949061//US National Science Foundation/ ; OISE-1130694//US National Science Foundation/ ; 2017YCGC006//Yucai Project of the Zhejiang Association for Science and Technology Foundation/ ; },
mesh = {Animals ; DNA Barcoding, Taxonomic ; *Introduced Species ; *Malus ; Phylogeny ; Snails/*classification/genetics ; Species Specificity ; },
abstract = {BACKGROUND: Due to the similarities of overall shell morphology among apple snail species and considerable variability within species, substantial taxonomic confusion has plagued the accurate identification of Pomacea species. Many invasive apple snails have been mistakenly identified as P. canaliculata since their introduction to Asia around 1980. In 2008, three other introduced species in addition to P. canaliculata were recognized. In 2013, a fifth, previously unrecognized lineage was reported from China, indicating that despite the taxonomic clarity brought by previous work, continued surveys and taxonomic research are necessary to prevent additional introductions and continued spread, as well as to develop effective management strategies.<br><br>RESULTS: Phylogenetic analysis of mitochondrial COI sequences confirmed the presence of a widespread unidentified Pomacea lineage in China. All sequences from samples of this newly documented lineage were recovered in a monophyletic clade delineated from closely related species; however, different DNA barcoding methods yielded inconsistent species boundaries. Additionally, nuclear EF1&#x3b1; sequences indicated incomplete lineage sorting or recent hybridization of the unidentified lineage with the other two established species.<br><br>CONCLUSION: Barcoding is a valuable tool for species discovery, and a powerful approach for delineating introduced species. However, determining the identity of the newly discovered invasive lineage in China will require an integrated taxonomic approach incorporating individuals from the native range, and examination of natural history collections at museums around the world. To manage and prevent additional spread of already established species, and to stop the introduction of new taxa, continued monitoring and rigorous taxonomic assessments must be undertaken. &#xa9; 2018 Society of Chemical Industry.},
}
@article {pmid30322608,
year = {2018},
author = {Cheng, QQ and Cheng, CS and Ouyang, Y and Lao, CC and Cui, H and Xian, Y and Jiang, ZH and Li, WJ and Zhou, H},
title = {Discovery of differential sequences for improving breeding and yield of cultivated Ophiocordyceps sinensis through ITS sequencing and phylogenetic analysis.},
journal = {Chinese journal of natural medicines},
volume = {16},
number = {10},
pages = {749-755},
doi = {10.1016/S1875-5364(18)30114-6},
pmid = {30322608},
issn = {1875-5364},
mesh = {Breeding ; DNA, Fungal/*genetics ; DNA, Intergenic/*genetics ; Genes, Mating Type, Fungal ; Hypocreales/chemistry/classification/*genetics/*growth &amp; development ; *Phylogeny ; },
abstract = {To accelerate the breeding process of cultivated Ophiocordyceps sinensis and increase its yield, it is important to identify molecular fingerprint of dominant O. sinensis. In the present study, we collected 3 batches of industrially cultivated O. sinensis product with higher yield than the others and compared their internal transcribed spacer (ITS) sequences with the wild and the reported. The ITS sequence was obtained by bidirectional sequencing and analyzed with molecular systematics as a DNA barcode for rapid and accurate identification of wild and cultivated O. sinensis collected. The ITS sequences of O. sinensis with detailed collection loci on NCBI were downloaded to construct a phylogenetic tree together with the sequences obtained from the present study by using neighbor-joining method based on their evolution relationship. The information on collection loci was analyzed with ArcGIS 10.2 to demonstrate the geographic distribution of these samples and thus to determine the origin of the dominant samples. The results showed that all wild and cultivated samples were identified as O. sinensis and all sequences were divided into seven phylogenetic groups in the tree. Those groups were precisely distributed on the map and the process of their system evolution was clearly presented. The three cultivated samples were clustered into two dominant groups, showing the correlation between the industrially cultivated samples and the dominant wild samples, which can provide references for its optimized breeding in the future.},
}
@article {pmid30322067,
year = {2018},
author = {Budel, JM and Wang, M and Raman, V and Zhao, J and Khan, SI and Rehman, JU and Techen, N and Tekwani, B and Monteiro, LM and Heiden, G and Takeda, IJM and Farago, PV and Khan, IA},
title = {Essential Oils of Five Baccharis Species: Investigations on the Chemical Composition and Biological Activities.},
journal = {Molecules (Basel, Switzerland)},
volume = {23},
number = {10},
pages = {},
pmid = {30322067},
issn = {1420-3049},
support = {88881.119611/2016-01//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 58-6066-6-043//U.S. Department of Agriculture/ ; },
mesh = {Animals ; Antimalarials/*chemistry/pharmacology ; Baccharis/chemistry/*classification/genetics ; Bedbugs/drug effects ; Bicyclic Monoterpenes ; Bridged Bicyclo Compounds/chemistry/pharmacology ; DNA Barcoding, Taxonomic ; Gas Chromatography-Mass Spectrometry ; Insecticides/*chemistry/pharmacology ; Limonene/chemistry/pharmacology ; Monocyclic Sesquiterpenes ; Monoterpenes/chemistry/pharmacology ; Oils, Volatile/*chemistry/pharmacology ; Plant Leaves/chemistry ; Plant Oils/chemistry/pharmacology ; Plant Stems/chemistry ; Sesquiterpenes/chemistry/pharmacology ; Trypanocidal Agents/*chemistry/pharmacology ; },
abstract = {This paper provides a comparative account of the essential oil chemical composition and biological activities of five Brazilian species of Baccharis (Asteraceae), namely B. microdonta, B. pauciflosculosa, B. punctulata, B. reticularioides, and B. sphenophylla. The chemical compositions of three species (B. pauciflosculosa, B. reticularioides, and B. sphenophylla) are reported for the first time. Analyses by GC/MS showed notable differences in the essential oil compositions of the five species. α-Pinene was observed in the highest concentration (24.50%) in B. reticularioides. Other major compounds included α-bisabolol (23.63%) in B. punctulata, spathulenol (24.74%) and kongol (22.22%) in B. microdonta, β-pinene (18.33%) and limonene (18.77%) in B. pauciflosculosa, and β-pinene (15.24%), limonene (14.33%), and spathulenol (13.15%) in B. sphenophylla. In vitro analyses for antimalarial, antitrypanosomal, and insecticidal activities were conducted for all of the species. B. microdonta and B. reticularioides showed good antitrypanosomal activities; B. sphenophylla showed insecticidal activities in fumigation bioassay against bed bugs; and B. pauciflosculosa, B. reticularioides, and B. sphenophylla exhibited moderate antimalarial activities. B. microdonta and B. punctulata showed cytotoxicity. The leaves and stems of all five species showed glandular trichomes and ducts as secretory structures. DNA barcoding successfully determined the main DNA sequences of the investigated species and enabled authenticating them.},
}
@article {pmid30321370,
year = {2019},
author = {Antwi, J and Rondon, SI},
title = {Molecular and Morphological Identifications Reveal Species Composition of Lygus (Hemiptera: Miridae) Bugs in Potatoes Fields in the Lower Columbia Basin of the United States.},
journal = {Journal of economic entomology},
volume = {112},
number = {1},
pages = {364-370},
doi = {10.1093/jee/toy314},
pmid = {30321370},
issn = {1938-291X},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Hemiptera/anatomy &amp; histology/*classification/genetics ; Oregon ; Solanum tuberosum ; },
abstract = {Lygus bugs are highly polyphagous insect pests. In recent years, Lygus bugs have become more conspicuous on potato, Solanum tuberosum L., fields in the Pacific Northwest, particularly in the Lower Columbia Basin. There are concerns that direct feeding damage or potential pathogen transmission can reduce yield. Lygus species on potatoes in the region are collectively identified as 'Lygus bugs'. Overlapping physical traits and the fact that the same species exhibit morphological variations across a geographic range makes it difficult to identify Lygus to species level. Thus, in this study we used DNA barcodes in combination with morphological characters to identify Lygus species on potatoes. Three species were identified in the Lower Columbia Basin: Lygus hesperus (Knight) and Lygus elisus L. were the most common, whereas Lygus keltoni L. was the least common. Interspecific genetic distances among Lygus species were relatively low, ranging from 0.013 to 0.004. Neighbor-joining (NJ) tree clustered L. hesperus and L. elisus into two major clades, with L. keltoni forming a subclade within L. hesperus clade. Statistical parsimony analysis corroborated findings from phylogenetic analysis with L. keltoni and L. hesperus sharing one haplotype. Our study demonstrates the utility of integrating morphology and molecular markers in identifying morphologically similar species such as Lygus bugs. The study also serves as a fundamental step in contributing to developing suitable management strategies against Lygus bugs on potato.},
}
@article {pmid30320650,
year = {2019},
author = {Bowdle, TA and Jelacic, S and Nair, B and Zucker, F and Bussey, LS and Togashi, K and Yang, JT and Lang, J},
title = {Electronic Audit and Feedback With Positive Rewards Improve Anesthesia Provider Compliance With a Barcode-Based Drug Safety System.},
journal = {Anesthesia and analgesia},
volume = {129},
number = {2},
pages = {418-425},
doi = {10.1213/ANE.0000000000003861},
pmid = {30320650},
issn = {1526-7598},
mesh = {Anesthesia Department, Hospital/standards ; Anesthesiologists/education/psychology/*standards ; Anesthetics/*administration &amp; dosage/adverse effects ; Attitude of Health Personnel ; Drug Labeling/*standards ; *Formative Feedback ; Guideline Adherence/*standards ; Health Knowledge, Attitudes, Practice ; Humans ; Internship and Residency ; Medical Audit ; Medication Systems, Hospital/*standards ; Nurse Anesthetists/psychology/*standards ; Practice Patterns, Nurses'/*standards ; Practice Patterns, Physicians'/*standards ; Prospective Studies ; Quality Improvement/standards ; Quality Indicators, Health Care/standards ; *Reward ; },
abstract = {BACKGROUND: We implemented a previously described barcode-based drug safety system in all of our anesthetizing locations. Providers were instructed to scan the barcode on syringes using our Anesthesia Information Management System before drug administration, but the rate of provider adherence was low. We studied an implementation intervention intended to increase the rate of scanning.<br><br>METHODS: Using our Anesthesia Information Management System and Smart Anesthesia Manager software, we quantified syringe drug administrations by anesthesia providers with and without barcode scanning. We use an anesthesia team model in which an attending anesthesiologist is paired with a certified registered nurse anesthetist (CRNA) or a resident. Our system identified the pair of providers associated with a particular drug administration, but did not distinguish which providers actually administered the drug. Therefore, the rate of barcode scanning for a particular case was assigned to both providers equally. A baseline rate of scanning was established over a period of 17 months. An audit and feedback intervention was then performed that consisted of monthly performance reports sent by email to individual providers along with coffee gift card awards for top performers. The coffee gift cards were awarded in only the first 2 months of the intervention, while the email performance reports continued on a monthly basis. The coffee card awards were made public. The monthly emails reported the individual provider's rank order of performance relative to other providers, but was otherwise anonymous. The baseline rate of scanning was compared to the rate of scanning after the intervention for a period of 7 months.<br><br>RESULTS: From November 2014 to March 2017, we accumulated 60,197 cases performed by 88 attending anesthesiologists, 65 CRNAs, and 148 residents. The total number of syringe drug administrations was 653,355. Average scanning performance improved from 8.7% of syringe barcodes scanned during the baseline period from November 2014 to February 2016 to 64.4% scanned during the period September 2016 to March 2017 (P < .001). Variation in performance among individuals was marked, ranging from 0% to 100% of syringes scanned. The performance of some individuals showed marked oscillation over time. There was greater variation in performance attributable to residents than in performance attributable to CRNAs.<br><br>CONCLUSIONS: Feedback of individual provider performance data from the anesthesia information system to providers can be used in conjunction with other measures to improve performance. Despite improved average performance, there was marked variation in performance between individuals, and some individuals had marked oscillation of their performance over time.},
}
@article {pmid30316947,
year = {2019},
author = {Galaska, MP and Li, Y and Kocot, KM and Mahon, AR and Halanych, KM},
title = {Conservation of mitochondrial genome arrangements in brittle stars (Echinodermata, Ophiuroidea).},
journal = {Molecular phylogenetics and evolution},
volume = {130},
number = {},
pages = {115-120},
doi = {10.1016/j.ympev.2018.10.002},
pmid = {30316947},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Cell Nucleus/genetics ; Echinodermata/*classification/*genetics ; Gene Order/*genetics ; Genome, Mitochondrial/*genetics ; *Phylogeny ; RNA, Transfer/genetics ; },
abstract = {Brittle stars are conspicuous members of benthic ecosystems, fill many ecological niches and are the most speciose of all classes of echinoderms. With high levels of biodiversity, elucidating the evolutionary history of this group is important. Understanding of higher-level relationships within Ophiuroidea has been aided by multilocus nuclear data and DNA barcoding. However, the degree of consistency between mitochondrial and nuclear data within ophiuroids remains unclear and deserves further assessment. In this study, 17 mitochondrial genomes spanning the taxonomic breadth of Ophiuroidea were utilized to explore evolutionary relationships through maximum likelihood analyses, Bayesian inference and comparative assessment of gene order. Our phylogenetic analyses, based on both nucleotide and amino acid residues, support recent findings based on multilocus nuclear data and morphology, in that the brittle star clades Ophintegrida and Euryophiurida were recovered as monophyletic with the latter comprising Euyalida, Ophiuridae and Ophiopyrgidae. Only three different arrangements of the 13 protein coding and 2 ribosomal RNA genes were observed. As expected, tRNA genes were more likely to have undergone rearrangement but the order of all 37 genes was found to be conserved in all sampled Euryalida and Ophiuridae. Both Euryalida and the clade comprised of Ophiuridae and Ophiopyrgidae, each had their own conserved rearrangement of protein coding genes and ribosomal genes, after divergence from their last common ancestor. Euryalida has a rearrangement of the two ribosomal RNA genes, rrnS and rrnL, in contrast to Ophiuridae and Ophiopyrgidae, which had an inversion of the genes nad1, nad2, and cob relative to Ophintegrida. Further, our data support the gene order found in all sampled Euryalida as the most likely ancestral order for all Ophiuroidea.},
}
@article {pmid30314252,
year = {2018},
author = {Roszkowska, M and Stec, D and Gawlak, M and Kaczmarek, &#x141;},
title = {An integrative description of a new tardigrade species Mesobiotus romani sp. nov. (Macrobiotidae: harmsworthi group) from the Ecuadorian Pacific coast.},
journal = {Zootaxa},
volume = {4450},
number = {5},
pages = {550-564},
doi = {10.11646/zootaxa.4450.5.2},
pmid = {30314252},
issn = {1175-5334},
mesh = {Animals ; Ecuador ; *Ovum ; RNA, Ribosomal, 28S ; *Tardigrada ; },
abstract = {In a mixed moss and lichen sample collected in Esmeraldas Province in north-western Ecuador, 20 tardigrades and 11 eggs, belonging to a new species of the genus Mesobiotus, were found. In addition to the traditional taxonomic description with morphometrics, light and scanning microscopy imaging, we also provide nucleotide sequences of three nuclear (18S rRNA, 28S rRNA, ITS-2) and one mitochondrial (COI) DNA fragments of the new species. Based on the egg chorion morphology, Mesobiotus romani sp. nov. is the most similar to: M. binieki, M. coronatus, M. dimentmani, M. patiens, M. perfidus, M. philippinicusi, M. pseudoblocki, M. pseudocoronatus, M. pseudopatiens, M. radiatus, M. rigidus, M. simulans and M. wuzhishanensis, but differs mainly by some specific characters of both egg and adult morphology, and morphometrics.},
}
@article {pmid30314225,
year = {2018},
author = {Zhao, Q and Wei, J and Bu, W and Liu, G and Zhang, H},
title = {Synonymize Arma chinensis as Arma custos based on morphological, molecular and geographical data.},
journal = {Zootaxa},
volume = {4455},
number = {1},
pages = {161-176},
doi = {10.11646/zootaxa.4455.1.7},
pmid = {30314225},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Geography ; *Heteroptera ; Phylogeny ; },
abstract = {Arma custos and A. chinensis have a very conspicuous difference in the shape of the pronotal humeral angle, but the genitalic morphological characters are ambiguous and difficult to recognize. The aim of this study was to analyze the taxonomic status of A. chinensis and A. custos based on morphological, molecular, and geographical evidence, and to determine whether DNA barcoding could be a useful additional tool for differentiating similar species. The results clearly demonstrate that A. custos and A. chinensis have not diverged into separate species. So, the following new synonym is proposed: Arma chinensis Fallou, 1881 = Arma custos (Fabricius, 1794) syn. nov.. The results also showed that DNA barcoding using the marker COI can resolve insect taxonomic problems.},
}
@article {pmid30314181,
year = {2018},
author = {Nazarov, RA and Melnikov, DA and Radjabizadeh, M and Poyarkov, NA},
title = {A new species of short-fingered geckos Stenodactylus (Squamata, Geckonidae) from South Iran with taxonomic notes on validity of the genus Trigonodactylus Hass, 1957.},
journal = {Zootaxa},
volume = {4457},
number = {1},
pages = {93-113},
doi = {10.11646/zootaxa.4457.1.4},
pmid = {30314181},
issn = {1175-5334},
mesh = {Animal Structures ; Animals ; Body Size ; Ecosystem ; Environment ; Iran ; *Lizards ; },
abstract = {In the present study we provide evidence for the validity of the genus Trigonodactylus Hass, 1957, improve the diagnosis for this genus and describe a new species that belongs to it-Trigonodactylus persicus sp. nov., from the sand dunes in Khuzestan Province, southwestern Iran. The new species is closely related to Trigonodactylus [Stenodactylus] arabicus sensu Hass, and can be distinguished by the following morphological characteristics: small size, maximum SVL 34 mm; SVL/TailL-approximately 1:1; ventral scales roundish, weakly keeled, 54-61 longitudinal rows at midbody and 190-25 along midbody. No enlarged postmentals. Fingers and toes slightly flattened dorso-ventrally. Lateral edge of digits fringed by series of projecting triangular scales. No web between digits. No preanal and femoral pores. Dorsal color pattern formed by thin, dark, irregular vermicular patches and spots. Sometimes these dark dorsal patterns blend with each other and form transverse bands. There is a narrow, dark, longitudinal line between forelimbs and hindlimbs on lateral sides. Dark, well developed ʌ-shaped marking on snout, which continues behind orbit on tympanum region, approaches the upper ear opening and ends on the pectoral arch. Labial scales white, in some cases with grey-brown dots. Dorsal surfaces of limbs and digits with irregular dark bands. Dorsal surface of tail with 8-10 wide, dark brown bands with irregular margins, same size as alternating light bands. Ventral surface of body and limbs white, tail with dark spots that become more distinct posteriorly.},
}
@article {pmid30314168,
year = {2018},
author = {Li, B and Zhao, Z and Zhang, C and Li, S},
title = {Nuconarius gen. n. and Hengconarius gen. n., two new genera of Coelotinae (Araneae, Agelenidae) spiders from Southwest China.},
journal = {Zootaxa},
volume = {4457},
number = {2},
pages = {237-263},
doi = {10.11646/zootaxa.4457.2.2},
pmid = {30314168},
issn = {1175-5334},
mesh = {Animals ; China ; Male ; *Spiders ; },
abstract = {Two new genera of Coelotinae F.O.Pickard-Cambridge, 1893 from Southwest China are described: Nuconarius Z. Zhao S. Li gen. n. and Hengconarius Z. Zhao S. Li gen. n. The type species of Nuconarius Z. Zhao S. Li gen. n. is N. brevipatellatus Z. Zhao S. Li sp. n. and two additional species also belong here: N. capitulatus (Wang, 2003) comb. n. and N. pseudocapitulatus (Wang, 2003) comb. n. The type species of Hengconarius Z. Zhao S. Li gen. n. is H. exilis (Zhang, Zhu Wang, 2005) comb. n. and this genus includes seven additional species: H. dedaensis Z. Zhao S. Li sp. n., H. falcatus (Xu Li, 2006) comb. n., H. incertus (Wang, 2003) comb. n., H. latusincertus (Wang, Griswold Miller, 2010) comb. n., H. longipalpus Z. Zhao S. Li sp. n., H. longpuensis Z. Zhao S. Li sp. n. and H. pseudobrunneus (Wang, 2003) comb. n. All species are from Southwest China and their distributions are mapped. New combinations are all ex-Draconarius Ovtchinnikov, 1999. The male of N. capitulatus is matched correctly for the first time and the DNA barcodes of all species are documented.},
}
@article {pmid30314120,
year = {2018},
author = {KovaČiĆ, M and Bogorodsky, SV and Mal, AO and Alpermann, TJ},
title = {Redescription of the genus Koumansetta (Teleostei: Gobiidae), with description of a new species from the Red Sea.},
journal = {Zootaxa},
volume = {4459},
number = {3},
pages = {453-481},
doi = {10.11646/zootaxa.4459.3.3},
pmid = {30314120},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Fiji ; Indian Ocean ; Micronesia ; Pacific Ocean ; *Perciformes ; *Phylogeny ; Yemen ; },
abstract = {The gobiid genus Koumansetta Whitley, placed in synonymy by some authors with the similar genus Amblygobius Bleeker, is redescribed and its validity based on an integrated morphological and molecular assessment is confirmed. The following characters have been found that distinguish Koumansetta from any of 15 recognized valid species of Amblygobius: oculoscapular transverse rows trp and tra long, extending dorsally well above level of rows x1 and x2; snout pointed, prominent, longer than eye diameter, with gently sloping dorsal profile, overhanging mouth; mouth subterminal; the upper limb of first gill arch with 1-2 slender, weak and soft gill rakers anteriorly, followed by 1-5 short, also soft, broad structures; first two dorsal-fin spines elongate, remaining spines progressively shorter; pelvic frenum absent; body brown to brown-green in upper and lateral sides with narrow yellow or orange longitudinal stripes on body and head, black ocellated spot on the second dorsal fin, and another black spot dorsoposteriorly on caudal peduncle. The following three species are assigned to Koumansetta: K. rainfordi Whitley, the type species of the genus, known from the western Pacific Ocean; K. hectori (Smith), the most widespread species, known from islands of the western Indian Ocean to Micronesia and Fiji; and a new species, restricted to the Red Sea and the inner Gulf of Aden. Koumansetta hoesei sp. nov. has formerly been confused with similar K. hectori, but differs in various details of coloration, and in some morphological characters. Moreover, K. hoesei sp. nov. is evolutionary well divergent from K. rainfordi and K. hectori, its closest relative, as shown by phylogenetic analysis of the mitochondrial COI barcoding region. In addition to the description of the new species, brief species accounts are provided for K. hectori and K. rainfordi, and a key to the three species.},
}
@article {pmid30314066,
year = {2018},
author = {Turan, D and Kaya, C and Geiger, M and Freyhof, J},
title = {Barbus anatolicus, a new barbel from the Kızılırmak and Yeşilırmak River drainages in northern Anatolia (Teleostei: Cyprinidae).},
journal = {Zootaxa},
volume = {4461},
number = {4},
pages = {539-557},
doi = {10.11646/zootaxa.4461.4.5},
pmid = {30314066},
issn = {1175-5334},
mesh = {Animals ; Black Sea ; Bulgaria ; *Cyprinidae ; *Rivers ; Turkey ; },
abstract = {Barbus anatolicus, new species, is described from the Kızılırmak and Yeşilırmak River drainages in the southern Black Sea basin. It is distinguished from other Barbus species in the Middle East by having 58-71 total lateral line scales, a moderately ossified last simple dorsal-fin ray, serrated along about 70-80% of its posterior margin, many small irregular shaped black or brown spots, smaller or as large as scales, often forming large, dark-brown blotches on the head, back and flank in adults and juveniles, and a concave posterior dorsal-fin margin. In addition, DNA barcode data reject the hypothesis that it belongs to one of the other species of the B. barbus species group. Barbus bergi from Bulgaria and adjacent Turkey is treated as synonym of B. tauricus. Barbus tauricus was previously believed to be restricted to the Crimean Peninsula but is found to be widespread in the Black Sea basin.},
}
@article {pmid30314006,
year = {2018},
author = {Marin, I},
title = {Cryptic diversity of stygobiotic shrimp genus Xiphocaridinella Sadowsky, 1930 (Crustacea: Decapoda: Atyidae): the first case of species co-occurrence in the same cave system in the Western Caucasus.},
journal = {Zootaxa},
volume = {4441},
number = {2},
pages = {201-224},
doi = {10.11646/zootaxa.4441.2.1},
pmid = {30314006},
issn = {1175-5334},
mesh = {Animals ; *Caves ; DNA, Mitochondrial ; *Decapoda ; },
abstract = {DNA barcoding of stygobiotic shrimps of the genus Xiphocaridinella Sadowsky, 1930 (Crustacea: Decapoda: Atyidae) collected in underground streams flowing inside two neighboring large karst caves (Otap and Abrskil сaves) revealed the presence of two distinct genetic lineages representing the first case of species co-occurrence in the Western Caucasus. The paper presents the complete morphological re-description of stygobiotic atyid shrimp Xiphocaridinella ablaskiri (Birštein, 1939) and the description of a new species using genetic and morphological analysis. Other known cases of co-occurrence of several stygobiotic shrimp species in the same cave system as well as new genetic data (COI mtDNA) on Western Caucasian species of the genus Xiphocaridinella are discussed in the paper.},
}
@article {pmid30313974,
year = {2018},
author = {Borges, LMS and Merckelbach, LM},
title = {Lyrodus mersinensis sp. nov. (Bivalvia: Teredinidae) another cryptic species in the Lyrodus pedicellatus (Quatrefages, 1849) complex.},
journal = {Zootaxa},
volume = {4442},
number = {3},
pages = {441-457},
doi = {10.11646/zootaxa.4442.3.6},
pmid = {30313974},
issn = {1175-5334},
mesh = {Animals ; *Bivalvia ; *Phylogeny ; RNA, Ribosomal, 18S ; RNA, Ribosomal, 28S ; },
abstract = {New data from barcode index numbers (BINs) and 28S rRNA gene sequences confirm a cryptic species pair in Lyrodus pedicellatus from the eastern Mediterranean and European Atlantic coasts. Therefore, it is paramount to associate the new species to a scientific name for a reliable reference system of biological information. To this end, we describe Lyrodus mersinensis sp. nov., another cryptic species in the L. pedicellatus complex, and redescribe the `true´ L. pedicellatus. Both the description and redescription are based on molecular diagnostic characters obtained from sequences of the mitochondrial cytochrome c oxidase subunit I (COI) and nuclear 28S rRNA genes. The 18S rRNA gene sequences did not yield diagnostic characters to distinguish these species. A morphological diagnosis of pedicellatus-like Lyrodus species is also provided.},
}
@article {pmid30313916,
year = {2018},
author = {Sidorov, D and Hou, Z and Sket, B},
title = {Three new remarkable amphipod species (Crustacea: Gammaridae) from springs and subterranean waters of Central Asia.},
journal = {Zootaxa},
volume = {4444},
number = {4},
pages = {437-461},
doi = {10.11646/zootaxa.4444.4.5},
pmid = {30313916},
issn = {1175-5334},
mesh = {*Amphipoda ; Animals ; Kyrgyzstan ; Natural Springs ; *Phylogeny ; Turkmenistan ; },
abstract = {Three new species of the family Gammaridae-Gammarus troglomorphus, sp. n., G. parvioculatus, sp. n. from Lebap Province of Turkmenistan and Tadzocrangonyx alaicus, sp. n. from Batken Region of Kyrgyzstan are described and illustrated. Morphological studies of a closely related Turkmenistan population of G. cf. subaequalis-Garlyk, probably conspecific with Gammarus subaequalis Martynov, 1935 was provided. The affinity of new species to concerned taxa is discussed. To define phylogenetic position of mentioned species DNA barcode data are obtained. Gammarus troglomorphus and G. parvioculatus are close neighbors but exceedingly different morphologically. Gammarus troglomorphus is a troglobiont; G. parvioculatus is an eutroglophile, but with exception of slightly smaller eyes, not troglomorph. Both found only within small areas in the extreme East of Turkmenistan. Gammarus cf. subaequalis-Garlyk seems to extend from the same region far into the eastern Kyrgyzstan.},
}
@article {pmid30313898,
year = {2018},
author = {Royals, HR and Landry, JF and Gilligan, TM},
title = {The myth of monophagy in Paralobesia (Lepidoptera: Tortricidae)? A new species feeding on Cypripedium reginae (Orchidaceae).},
journal = {Zootaxa},
volume = {4446},
number = {1},
pages = {81-96},
doi = {10.11646/zootaxa.4446.1.6},
pmid = {30313898},
issn = {1175-5334},
mesh = {Animals ; Manitoba ; *Moths ; Ontario ; *Orchidaceae ; },
abstract = {The genus Paralobesia Obraztsov, 1953 is found primarily in eastern North America and consists of 18 described and several undescribed species. Prior to 1900, all North American Paralobesia were assumed to be P. viteana (Clemens). However, rearing experiments by William Kearfott in the early 1900s suggested that species of Paralobesia were monophagous and could be separated by host. Recently, a species of Paralobesia was reared from showy lady's slipper, Cypripedium reginae Walter (Orchidaceae), during a study of two populations of this orchid in eastern Ontario and southwestern Québec. Although originally assumed to be P. cypripediana (Forbes), which was described from specimens reared from Cypripedium in Manitoba, DNA barcode data and genital morphology confirmed that this was a new species similar to P. cypripediana and P. monotropana (Heinrich). Herein, we describe P. marilynae, sp. n., and provide specifics of its discovery and life history. Rearing records indicate that Paralobesia can span the range from strictly monophagous to polyphagous, even for very similar species with similar feeding habits, and that host records should be combined with morphological and molecular data when circumscribing species in this genus. This work is part of a complete systematic revision of Paralobesia currently in progress.},
}
@article {pmid30313854,
year = {2018},
author = {Ivshin, N and Krutov, V and Romanov, D},
title = {Three new taxa of the genus Cechetra Zolotuhin Ryabov, 2012 (Lepidoptera, Sphingidae) from South-East Asia with notes on other species of the genus.},
journal = {Zootaxa},
volume = {4450},
number = {1},
pages = {1-25},
doi = {10.11646/zootaxa.4450.1.1},
pmid = {30313854},
issn = {1175-5334},
mesh = {*Animal Distribution ; Animals ; Asia, Southeastern ; *Lepidoptera ; Male ; },
abstract = {Two new species and one subspecies of the genus Cechetra Zolotuhin Ryabov, 2012 are described from South-East Asia. Cechetra bryki sp.n. is described from Nepal, Myanmar (Burma), southwestern China and northern Vietnam. This species is most closely related in habitus, male genitalia morphology and COI mtDNA to the sympatric species, C. lineosa (Walker, 1856) and C. scotti (Rothschild, 1920) in habitus, male genitalia morphology and COI mtDNA. Cechetra inconspicua sp.n. is described from Peninsular Malaysia, Borneo and Sumatra. In habitus, it is closest to C. lineosa and C.subangustata (Rothschild, 1920), but its COI mtDNA (COI-5P "barcode region") is very different from all other species in the genus. Cechetra subangustata continentalis ssp.n. is described from continental Indochina and Taiwan. It differs from the nominotypical subspecies in habitus. Cechetra scotti comb. nov. is transferred to Cechetra from Cechenena Rothschild Jordan, 1903.},
}
@article {pmid30313839,
year = {2018},
author = {Almeida, AO and Terossi, M and Buranelli, RC and Castilho, AL and Costa, RC and Zara, FJ and Mantelatto, FL},
title = {Checklist of decapods (Crustacea) from the coast of São Paulo State (Brazil) supported by integrative molecular and morphological data: II. Infraorder Caridea: family Alpheidae.},
journal = {Zootaxa},
volume = {4450},
number = {3},
pages = {331-358},
doi = {10.11646/zootaxa.4450.3.2},
pmid = {30313839},
issn = {1175-5334},
mesh = {Animals ; Biodiversity ; Brazil ; *Decapoda ; Estuaries ; *Phylogeny ; },
abstract = {This study is part of a series of checklists resulting from a long-term multidisciplinary project on the biodiversity of decapod crustaceans from the marine and coastal environments (including estuaries) of São Paulo State (Brazil). For that, we integrated molecular techniques (mitochondrial DNA markers) and morphological analyses of adult specimens for an accurate and detailed identification. The DNA markers were used when the morphological identification was doubtful, particularly in the recognition of cryptic species. This second manuscript presents a checklist of the Alpheidae caridean shrimps from the coast of São Paulo. We report the occurrence of Alpheus cf. paracrinitus and Synalpheus townsendi for the first time in the region. Based on our survey, 39 species of Alpheidae are known for this region: Alpheus (21 spp.), Athanas (2 spp.), Automate (2 spp.), Leptalpheus (1 spp.), Salmoneus (3 spp.), and Synalpheus (10 spp.). We collected 28 species and obtained cytochrome oxidase subunit I (barcode region) and/or 16S partial sequences of 26 of them. These sequences may be used for phylogenetic and populational analyses in further studies.},
}
@article {pmid30313838,
year = {2018},
author = {Salgueiro-sepÚlveda, FJ and Álvarez-Padilla, F},
title = {New species of the orb-weaving spider genus Chrysometa (Araneae, Tetragnathidae) from oak forests near of the Pico de Orizaba National Park (Veracruz, Mexico).},
journal = {Zootaxa},
volume = {4450},
number = {3},
pages = {301-330},
doi = {10.11646/zootaxa.4450.3.1},
pmid = {30313838},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Female ; Forests ; Male ; Mexico ; Parks, Recreational ; *Quercus ; *Spiders ; },
abstract = {Seven new species of the genus Chrysometa Simon are described: C. citlaltepetl n. sp., C. triangulosa n. sp., C. rosarium n. sp., C. atotonilco n. sp., C. xamaticpac n. sp. C. puya n. sp. and C. sagicuta n. sp. Species identities were evaluated and sexes for each species matched with a fragment of the cytochrome c oxidase subunit I. These data were analyzed with maximum likelihood and the resulting cladograms separated all species with high support values (95-100) and an average distance of 0.093 %. The genetic signal also agreed with the diagnostic morphological features used to separate these taxa. The sex matching results discovered that the female of C. chipinque Levi actually belongs to C. puya n. sp.; the correct female of C. chipinque is here described for the first time. A redescription of the male of C. chipinque and the female of C. puya is also provided. All species were collected as part of a faunistic inventory from two oak forests near Pico de Orizaba Volcano National Park. A total of 399 adult specimens, 209 females and 195 males, were sorted and identified. Most individuals were collected from medium height vegetation by beating trays and from high vegetation by direct collecting at night. High resolution images for all species are available at www.unamfcaracnolab.com. Finally, the functional anatomy of the epigynum for the species described here is discussed.},
}
@article {pmid30313813,
year = {2018},
author = {KÓbor, P and TÓbiÁs, I and Roca-Cusachs, M and Kondorosy, E},
title = {The subspecies concept in Geocorinae: an integrated taxonomic case study on Geocoris (Piocoris) erythrocephalus (Lepeletier Serville, 1825) (Hemiptera: Heteroptera: Geocoridae).},
journal = {Zootaxa},
volume = {4482},
number = {3},
pages = {541-550},
doi = {10.11646/zootaxa.4482.3.6},
pmid = {30313813},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; *Heteroptera ; *Phylogeny ; },
abstract = {The validity and necessity of subspecies as a taxonomic category and the implications of the subspecies concept in various taxa of animals is subject of debates since its very existence. In case of the species of the lygaeoid subfamily Geocorinae there are multiple examples of species consisting of up to nine subspecies which were mostly described as varieties or forms before the middle of 20th century, but upgraded to valid subspecies subsequently, usually without providing any arguments. As part of an integrated taxonomic study on the Palaearctic representatives of Geocorinae, the status of the subspecies of Geocoris (Piocoris) erythrocephalus (Lepeletier Serville, 1825) was revisited. A critical review of the literature available and our studies, involving analysis of COI sequences, morphological examination and distribution data processing with the use of Geographic Information System, concluded that two of the three subspecies, G. e. erythrocephalus and G. e. marginellus Horváth, 1907, can be considered valid, while G. e. litoreus Horváth, 1895, is merely a phenotypically manifested infrasubspecific genetic variety of G. e. erythrocephalus, with no taxonomic value as it was suggested by earlier study of another author. Besides the interpretation of evidence, the applicability of the subspecies concept in Geocorinae is discussed as well.},
}
@article {pmid30313775,
year = {2018},
author = {DomÉnech, C and Barbera, VM and Larriba, E},
title = {A phylogenetic approach to the Philippines endemic centipedes of the genus Scolopendra Linnaeus, 1758 (Scolopendromorpha, Scolopendridae), with the description of a new species.},
journal = {Zootaxa},
volume = {4483},
number = {3},
pages = {401-427},
doi = {10.11646/zootaxa.4483.3.1},
pmid = {30313775},
issn = {1175-5334},
mesh = {Animals ; *Arthropods ; DNA, Mitochondrial ; Male ; Philippines ; *Phylogeny ; },
abstract = {The genus Scolopendra Linnaeus, 1758 is represented in the Philippines' fauna by five species, two of which are endemic. Mitochondrial DNA sequences of gene cytochrome c oxidase subunit I (COI) were obtained from six Scolopendra specimens belonging to two endemic species and a new one, described here as Scolopendra paradoxa Doménech sp. nov. These sequences were analyzed together with another forty-one sequences from GenBank, including additional species of Scolopendra and a few representatives of other Scolopendridae genera. Phylogenetic trees inferred from the COI analysis using maximum likelihood and neighbor joining showed the three Philippines Scolopendra endemic species as a polyphyletic group coherent with their respective morphologies, although the position of S. spinosissima Kraepelin, 1903 varied within the obtained trees. Species delimitation based on standard external morphological characters was also concordant with the observed genetic distances, monophyly and node support, confirming S. subcrustalis Kronmüller, 2009 and S. paradoxa sp. nov. as separate species also at the molecular level, while only the position of S. spinosissima could not be properly established with any of the statistical methods used. In addition, the male genitalia of the three studied species were found to lack gonopods and a penis. Remarks on the ultimate legs prefemoral spinous formula of S. spinosissima plus a key to the species of the genus Scolopendra in the Philippines are provided.},
}
@article {pmid30313767,
year = {2018},
author = {Kvifte, GM and IvkoviĆ, M},
title = {New species and records of the Pericoma trifasciata group from Croatia (Diptera: Psychodidae).},
journal = {Zootaxa},
volume = {4486},
number = {1},
pages = {76-82},
doi = {10.11646/zootaxa.4486.1.5},
pmid = {30313767},
issn = {1175-5334},
mesh = {Animals ; Croatia ; Germany ; Male ; *Psychodidae ; },
abstract = {Pericoma miljenkoi sp. nov. is described based on adult males from the Plitvička jezera National Park, Croatia. Pericoma trifasciata is recorded from Croatia for the first time, and COI DNA barcodes are given from specimens collected in Germany. An emended key to adult Pericoma of the trifasciata group is presented. The Croatian Psychodidae fauna now stands at 35 species.},
}
@article {pmid30313744,
year = {2018},
author = {Sudasinghe, H and Ranasinghe, RHT and Goonatilake, SA and Meegaskumbura, M},
title = {A review of the genus Labeo (Teleostei: Cyprinidae) in Sri Lanka.},
journal = {Zootaxa},
volume = {4486},
number = {3},
pages = {201-235},
doi = {10.11646/zootaxa.4486.3.1},
pmid = {30313744},
issn = {1175-5334},
mesh = {Animals ; *Cyprinidae ; Genes, Mitochondrial ; India ; Rivers ; Sri Lanka ; },
abstract = {The taxonomy of the three native taxa assigned to the genus Labeo (L. dussumieri, L. fisheri and L. porcellus lankae) in Sri Lanka is reviewed. The population hitherto identified as L. dussumieri in Sri Lanka is shown to be a distinct species, here named L. heladiva. Labeo heladiva, new species, has a wide distribution in the low and mid-elevations of the island and is distinguished from its Indian congeners by the combination of having two pairs of barbels; 12-13 branched dorsal-fin rays; lateral line with 44-51 scales; ½8-½9+1+6-7 scales in transverse series; and 19-22 circumpeduncular scales. It differs from its closest relative, L. dussumieri, principally by having 44-51 vs. 50-60 lateral-line scales, 19-22 vs. 22-27 circumpeduncular scales, and by uncorrected pairwise genetic distances of 1.27-2.22% and 1.88-2.91% for the two mitochondrial genes COI and cytb, respectively. Labeo fisheri, which is endemic to the upper reaches of the Mahaweli River basin in the Knuckles mountain range and the central hills in the vicinity of Kandy, is distinguished from Indian congeners by having (in combination) only a single pair of barbels; dorsal fin with 10-12 branched rays; lateral line with 37-39 scales; 7+1+4½-6 scales in transverse series; and 17-20 circumpeduncular scales. Labeo lankae is recognized as a valid species endemic to Sri Lanka. Long suspected to have become extinct, or known only from spurious records, an extant population is reported from the northern dry zone of the island. Labeo lankae is the sister species of L. porcellus of peninsular India; it can be distinguished from its congeners by having, in combination, 10-12 branched dorsal-fin rays; 36-39 lateral-line scales; ½8+1+5-6½ scales in transverse series; and 21-24 circumpeduncular scales. It differs from L. porcellus principally by having ½8 (vs. ½6-½7) scales between the origin of the dorsal fin and the lateral line, 21-24 (vs. 20-21) circumpeduncular scales and uncorrected pairwise genetic distances of 1.27% and 1.41% for the mitochondrial genes COI and cytb, respectively. The three species of Labeo in Sri Lanka do not form a monophyletic group.},
}
@article {pmid30313705,
year = {2018},
author = {Shen, HP and Chang, CH and Chih, WJ},
title = {Two new earthworm species of the genus Drawida (Oligochaeta: Moniligastridae) from southwestern Taiwan.},
journal = {Zootaxa},
volume = {4496},
number = {1},
pages = {302-312},
doi = {10.11646/zootaxa.4496.1.25},
pmid = {30313705},
issn = {1175-5334},
mesh = {Animals ; China ; *Oligochaeta ; Republic of Korea ; Taiwan ; },
abstract = {This study describes two new species of earthworms belonging to the genus Drawida (Oligochaeta: Moniligastridae) from southwestern Taiwan. They are Drawida alishanensis sp. nov. and Drawida fenqihuensis sp. nov. The two species were found at elevations of 1407-1661 m in the Alishan area, Chiayi County. DNA barcodes from type specimens of the new species are reported. This is the first time that new species of Drawida are discovered from the island of Taiwan. In addition, Drawida keikiensis Kobayashi, 1938 from Korea is found to be synonymous with Drawida syringa Chen, 1933 from central China. The synonymy of Drawida glabella Chen, 1938 with Drawida barwelli (Beddard, 1886) is rejected.},
}
@article {pmid30313704,
year = {2018},
author = {Sun, J and Jiang, JB and Bartlam, S and Qiu, JP and Hu, F},
title = {Four new Amynthas and Metaphire earthworm species from nine provinces in southern China.},
journal = {Zootaxa},
volume = {4496},
number = {1},
pages = {287-301},
doi = {10.11646/zootaxa.4496.1.24},
pmid = {30313704},
issn = {1175-5334},
mesh = {Animals ; China ; DNA ; Male ; *Oligochaeta ; },
abstract = {Four new species belonging to genera Amyntha and Metaphire were discovered from an extensive area in southern China, covering the provinces Sichuan, Yunnan, Guizhou, Guangdong, Guangxi, Fujian, Hunan, Jiangxi and Anhui. The species are named Amynthas dispersus Sun Qiu, sp. nov., Amynthas shanghangensis Sun Qiu, sp. nov., Amynthas dentiformis Sun Jiang, sp. nov. and Metaphire sanmingensis Sun Jiang, sp. nov. The first two new species have four pairs of intersegmental spermathecal pores in 5/6-8/9. A. dispersus has elliptical and glandular male pore porophores raised on a low pad-like area surrounded by two to three shallow skin folds, the genital papillae are variable in the spermathecal pore and male pore regions, and prostate glands are vestigial or rudimentary. Amynthas shanghangensis has male porophores surrounded by three papillae, each prostate gland accompanied by an accessory gland, and the distal ½-⅓ of the spermathecal diverticulum dilated into a rod-shaped seminal chamber. Amynthas dentiformis has two pairs of spermathecal pores in 7/8-8/9, male pores always surrounded by two papillae, and small sacs on the dorsal and ventral margins of the intestinal caecae; the prostate gland occasionally has stalked accessory glands. M. sanmingensis is in the Metaphire houlleti-group, and has secondary male pores opening to copulatory pouches, rod-shaped spermathecal seminal chamber, as well as variable genital papillae in spermathecal and male pores regions. The GenBank accession numbers of DNA barcode data are attached under the description of each species.},
}
@article {pmid30313700,
year = {2018},
author = {Nguyen, TT and Nguyen, NQ and Nguyen, AD},
title = {First record of the earthworm genus Pheretima Kinberg, 1867 sensu stricto in Vietnam, with description of a new species (Annelida: Clitellata: Megascolecidae).},
journal = {Zootaxa},
volume = {4496},
number = {1},
pages = {251-258},
doi = {10.11646/zootaxa.4496.1.20},
pmid = {30313700},
issn = {1175-5334},
mesh = {Animals ; *DNA ; Male ; *Oligochaeta ; Thailand ; Vietnam ; },
abstract = {The earthworm genus Pheretima Kinberg, 1867 sensu stricto is recorded in Vietnam for the first time with a new species, P. vungtauensis sp. nov. The new species is characterized by three pairs of spermathecal pores in intersegments 6/7/8/9, spermathecal ducts with dense micronephridia, no genital markings in spermathecal and male regions, male pores located inside copulatory pouches, intestinal origin at xv, caeca simple from xxvii, and holandry. DNA-COI barcode sequences of the holotype are most similar to those of Metaphire houlleti (Perrier, 1872) from Thailand and not to other species of Pheretima.},
}
@article {pmid30313698,
year = {2018},
author = {Seesamut, T and Sutcharit, C and Jirapatrasilp, P and Chanabun, R and Panha, S},
title = {Morphological and molecular evidence reveal a new species of the earthworm genus Pontodrilus Perrier, 1874 (Clitellata, Megascolecidae) from Thailand and Peninsular Malaysia.},
journal = {Zootaxa},
volume = {4496},
number = {1},
pages = {218-237},
doi = {10.11646/zootaxa.4496.1.18},
pmid = {30313698},
issn = {1175-5334},
mesh = {Animals ; Ecosystem ; Malaysia ; *Oligochaeta ; Thailand ; },
abstract = {A new species of the megascolecid earthworm genus Pontodrilus Perrier, 1874, Pontodrilus longissimus sp. n., is described from seashores of Thailand and Peninsular Malaysia. The new species differs from congeners, especially the cosmopolitan P. litoralis (Grube, 1855) in the size of the body, number of segments and the shape of the spermathecae. P. litoralis is redescribed, based on specimens collected from the same region and the same type of habitat. DNA fragments of the mitochondrial cytochrome oxidase subunit I of both species were sequenced. Morphological as well as DNA sequence-based comparisons confirm that P. longissimus sp. n. is a lineage distinct from P. litoralis and in fact a new species. The illustrated descriptions are accompanied by a key to species of Pontodrilus.},
}
@article {pmid30313693,
year = {2018},
author = {Rota, E and Martinsson, S and ErsÉus, C and Petushkov, VN and Rodionova, NS and Omodeo, P},
title = {Green light to an integrative view of Microscolex phosphoreus (Dugès, 1837) (Annelida: Clitellata: Acanthodrilidae).},
journal = {Zootaxa},
volume = {4496},
number = {1},
pages = {175-189},
doi = {10.11646/zootaxa.4496.1.13},
pmid = {30313693},
issn = {1175-5334},
mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic ; *Oligochaeta ; *Phylogeny ; Siberia ; },
abstract = {The small synanthropic and peregrine earthworm Microscolex phosphoreus (Dugès, 1837) is reported for the first time from Siberia. Morphological and DNA barcode (COI) analyses of this and widely separate samples worldwide demonstrate that, as currently identified, M. phosphoreus is a heterogeneous taxon, with divergent lineages occurring often in the same locality and hardly providing geographically structured genetic signals. The combined morphological and genetic evidence suggests that at least four of the found clades should be reclassified as separate species, both morphologically and genetically distinct from each other. However, as the specimen number was limited and only the COI gene was studied for the genetic work, we hesitate in formally describing new species. There would also be the problem of assigning the available names to specific lineages. Our findings encourage careful external and anatomical examination and using reliable characters such as the interchaetal distances and spermathecal morphology for correct identification and for deeper evaluation of cryptic diversity in this interesting bioluminescent worm.},
}
@article {pmid30313685,
year = {2018},
author = {Csuzdi, C and Szederjesi, T and MarchÁn, DF and Sosa, I and Gavinelli, F and Dorigo, L and Pamio, A and Dreon, AL and Fusaro, S and Moretto, E and Paoletti, MG},
title = {DNA barcoding of the Italian anecic Octodrilus species in rural (vineyard) and forested areas with description of Octodrilus zicsiniello sp. nov. (Clitellata, Megadrili).},
journal = {Zootaxa},
volume = {4496},
number = {1},
pages = {43-64},
doi = {10.11646/zootaxa.4496.1.5},
pmid = {30313685},
issn = {1175-5334},
mesh = {Animals ; Bayes Theorem ; Croatia ; *DNA Barcoding, Taxonomic ; Farms ; Forests ; Italy ; *Oligochaeta ; *Phylogeny ; },
abstract = {DNA barcoding of 172 anecic Octodrilus specimens collected in NE Italy and bordering Croatia has been carried out. The Bayesian phylogenetic tree showed high support for almost all currently recognized species, however, some unexpected results also appeared. The clade representing Oc. pseudocomplanatus contains a highly advanced subclade, which morphologically resembles Oc. slovenicus. The highly supported Oc. tergestinus clade consists of four unresolved divergent lineages of which the first corresponds to Oc. istrianus and the second resembles Oc. mimus morphologically; the third and fourth clades show typical tergestinus characters. The widely distributed Oc. complanatus consists of three highly divergent subclades which are sister to a new species, Oc. zicsiniello sp. nov., hereunder described.},
}
@article {pmid30313675,
year = {2018},
author = {Grados, J and Laguerre, M and BopprÉ, M},
title = {Gloora gen. nov. (Lepidoptera: Erebidae: Arctiinae: Arctiini: Ctenuchina) for several Agylla-like Arctiinae.},
journal = {Zootaxa},
volume = {4497},
number = {2},
pages = {226-240},
doi = {10.11646/zootaxa.4497.2.4},
pmid = {30313675},
issn = {1175-5334},
mesh = {Animals ; Male ; *Moths ; },
abstract = {Gloora gen. nov. is established for Eucereon alba (Druce, 1894), Hyaleucerea mundula (Berg, 1882), Agaraea sericeum (Zerny, 1931), and Gloora canae sp. nov. These species are (re‑)described considering male genitalia in particular and, in case, barcodes. Further species which might fit into Gloora gen. nov. are discussed.},
}
@article {pmid30313672,
year = {2018},
author = {Lindt, A and Hausmann, A and Viidalepp, J},
title = {Review of some species groups of the genus Oospila Warren, with descriptions of nine new species (Lepidoptera: Geometridae: Geometrinae).},
journal = {Zootaxa},
volume = {4497},
number = {2},
pages = {151-194},
doi = {10.11646/zootaxa.4497.2.1},
pmid = {30313672},
issn = {1175-5334},
mesh = {Animals ; Bolivia ; Brazil ; Costa Rica ; Ecuador ; Female ; French Guiana ; Male ; *Moths ; },
abstract = {The Neotropical geometrine genus Oospila Warren, 1897 includes seventy-nine species and was revised by Cook Scoble (1995). The genus is distinctive in having a row of raised abdominal crests, which are composed of specialized, erect, metallic shining scales. This paper focuses on the integrative morphological and molecular delimitation of the smallest Oospila species. The wing patterns and genitalia structures of males and females are illustrated. Cook Scoble (1995) distinguished 13 species groups within Oospila. We discuss the species of the Oospila flavilimes species group, the O. stigma species group and O. miccularia species group below, and separate the O. arpata species complex into a group of its own. Nine new species and two new subspecies are described in this paper: O. cristae sp. n. from Ecuador, O. falcata sp. n. from French Guiana, O. pallidaria boliviensis subsp. n. from Bolivia, and O. loreenae sp. n. from Bolivia (flavilimes species group), O. ehakernae sp. n. from Costa Rica, O. similiplaga bolarpata subsp. n. from Bolivia (arpata species group), O. brehmi sp. n. and O. bifida sp. n. both from Bolivia, O. moseri sp. n. from Brazil, O. absaloni sp. n. and O. pipa sp. n. both from Ecuador (miccularia species group). Oospila similiplaga (Warren) (stat. nov.) is raised here from synonymy with O. arpata (Schaus) and O. imula (Dognin) from synonymy with O. miccularia (Guenée), respectively. Oospila agnetaforslundae nom. nov. is proposed as a replacement name for Oospila marginata Schaus, 1912 (nec Oospila marginata Warren, 1897), raising it to species rank from synonymy of Oospila permagna (Warren, 1909). With this paper, the number of Neotropical Oospila species is raised to 88.},
}
@article {pmid30313667,
year = {2018},
author = {Chen, LP and Chang, YG and Li, J and Wang, JM and Liu, JL and Zhi, YC and Li, XJ},
title = {Application of DNA Barcoding in the Classification of Grasshoppers (Orthoptera: Acridoidea)-A Case Study of grasshoppers from Hebei Province, China.},
journal = {Zootaxa},
volume = {4497},
number = {1},
pages = {99-110},
doi = {10.11646/zootaxa.4497.1.6},
pmid = {30313667},
issn = {1175-5334},
mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; *Grasshoppers ; Phylogeny ; },
abstract = {Grasshoppers (Orthoptera: Acridoidea) are the main pests in agriculture, animal husbandry and forestry, and some species of grasshoppers can cause serious disaster. Taxonomy is the basis of pest control. Traditional morphological identification is time-consuming and laborious. It may be due to the existence of cryptic species or the limited number of morphologists, making the identification extremely unstable. In recent years, with the development of molecular systematics, DNA barcoding technology has been applied to environment, ecology, quarantine and so on. This study focuses on testing the feasibility of DNA barcoding in the species identification for superfamily Acridoidea. Sequences of the cox1 gene were obtained from 245 individuals of 43 species of Acridoidea and one species of Tetrigoidea as outgroup from Hebei Province. Phylogenetic, genetic distance and sequence difference threshold analyses using the Maximum Likelihood (ML), Automatic Barcode Gap Discovery (ABGD) and Molecular Defined Operational Taxonomic Units (MOTU) methods, respectively, were performed for obtained sequences and the 139 additional sequences of 21 species downloaded from GenBank. The results have shown that 40, 33, and 35 species among the 48 species are consistent with the traditional morphological classification based on the phylogenetic tree, ABGD and MOTU results, respectively and the DNA barcoding technology is very efficient and helpful for identifying the species of the superfamily Acridoidea; however, the morphological approach is still playing a key role in the species identifications. It also indicates that the cox1 gene is suitable for the phylogeny of genera and species level, but it is not suitable for the phylogenetic relationship of the advanced taxa such as families.},
}
@article {pmid30313649,
year = {2018},
author = {Knihinicki, DK and PetanoviĆ, R and CvrkoviĆ, T and Varia, S},
title = {A new species of Aculus mite (Acari: Eriophyidae), a potential biocontrol agent for Australian swamp stonecrop, Crassula helmsii (Crassulaceae).},
journal = {Zootaxa},
volume = {4497},
number = {4},
pages = {573-585},
doi = {10.11646/zootaxa.4497.4.7},
pmid = {30313649},
issn = {1175-5334},
mesh = {Animal Structures ; Animals ; Australia ; Body Size ; *Crassulaceae ; Europe ; *Mites ; New Zealand ; Organ Size ; United Kingdom ; Wetlands ; },
abstract = {A new, gall-forming eriophyoid mite species is described from Australia. Aculus crassulae sp. nov. was found causing significant leaf deformation in Crassula helmsii (Kirk) Cockayne (Crassulaceae), a semi-aquatic, succulent plant. Native to Australia and New Zealand, this plant is now a highly invasive weed in the United Kingdom and Western Europe. The host specificity of the new mite species, and damage caused to the host plant, infer its potential to be a valuable biological control agent in countries where Australian swamp stonecrop is threatening native flora. The species description provided here, which also includes a revised diagnosis for the genus Aculus, incorporates line drawings and scanning electron micrographs (SEM). This is supplemented by a partial mitochondrial gene sequence of cytochrome c oxidase subunit I (mtCOI) and the sequence was compared with Aculus amygdali Xue Hong and Aculus ichnocarpi (Ghosh Chakrabarati) available in the NCBI database. Pairwise comparison of mtCOI sequences between A. crassulae sp. nov. and two congeneric species revealed 22.6% and 23.1% genetic divergence, respectively.},
}
@article {pmid30313642,
year = {2018},
author = {Lee, GE and Li, H and Han, T and Park, H},
title = {A taxonomic review of the genus Palumbina Rondani, 1876 (Lepidoptera, Gelechiidae, Thiotrichinae) from China, with descriptions of twelve new species.},
journal = {Zootaxa},
volume = {4414},
number = {1},
pages = {1-73},
doi = {10.11646/zootaxa.4414.1.1},
pmid = {30313642},
issn = {1175-5334},
mesh = {*Animal Distribution ; Animal Structures ; Animals ; China ; *Moths ; Organ Size ; },
abstract = {Palumbina is a small genus of Gelechiidae that includes species distributed only in the Old World. It was recently assigned to the subfamily Thiotrichinae, but the morphological and molecular studies at the species level have not been extensively conducted. In this study, we focused on the taxonomy of the Chinese Palumbina using morphology and DNA barcoding analysis to confirm the species identification and the relationship among closely related species. In China, three species of this genus were recorded previously. A total of 19 were finally recognized in the present study, including 12 new species: P. magnisigna sp. nov., P. grandiunca sp. nov., P. melanotricha sp. nov., P. atricha sp. nov., P. sigmoides sp. nov., P. acuticula sp. nov., P. rugosa sp. nov., P. sineloba sp. nov., P. spinevalva sp. nov., P. acerosa sp. nov., P. triangularis sp. nov. and P. acinacea sp. nov., and five species that are new records for China: P. chelophora (Meyrick, 1918), P. diplobathra (Meyrick, 1918), P. macrodelta (Meyrick, 1918), P. nesoclera (Meyrick, 1929) and P. operaria (Meyrick, 1918). Three new combinations are proposed: P. operaria (Meyrick, 1918) comb. nov., P. albilustra (Walia et Wadhawan, 2005) comb. nov. and P. shivai (Walia et Wadhawan, 2005) comb. nov., and one new synonymy is established: Thyrsostoma albilustra (Walia et Wadhawan, 2005), syn. nov. of P. oxyprora (Meyrick, 1922). Based on the neighbor-joining analysis of COI gene sequences of 67 exemplar specimens, four clades were well supported with high bootstrap values resulting in four species-groups: the guerinii-group, the grandiunca-group, the macrodelta-group and the nesoclera-group. However, seven species were grouped together in an additional clade with weak support and P. diplobathra and P. chelophora were not clustered with any other species due to the high genetic divergences. Palumbina chelophora showed typical characteristics of the genus morphologically, but it was not embedded within Palumbina as monophyletic from the tree, assuming that the sole use of mitochondrial fragments could not resolve the deeper relationship. Therefore, further investigation is needed to clarify those issues. In this study, the generic diagnosis was reviewed based on previous studies and morphological examination.},
}
@article {pmid30313545,
year = {2018},
author = {Hosseini, R and Madahi, K},
title = {A multiplex PCR method for identification of two common true cutworm species (Lepidoptera: Noctuidae) tested in the central plain of Guilan province, Iran.},
journal = {Zootaxa},
volume = {4420},
number = {2},
pages = {243-250},
doi = {10.11646/zootaxa.4420.2.6},
pmid = {30313545},
issn = {1175-5334},
mesh = {Animals ; DNA Primers ; Iran ; *Lepidoptera ; Moths ; Multiplex Polymerase Chain Reaction ; },
abstract = {Many species of cutworms (Lepidoptera: Noctuidae) are important agricultural pest. They feed on roots and foliage of their host plants. Traditionally these species are identified based on morphological characteristics of adults. Hence identification of specimens in poor condition, immature stages and also closely related species or cryptic species is a difficult task. The basics of biological and ecological studies largely rely on an accurate species identification; consequently these investigations are impacted by potential misidentifications. In this study, we amplified 5' region of mitochondrial c cytochrome oxidase subunit I (COI) gene (DNA barcode region) of various common true cutworm species including Agrotis ipsilon (Hufnagel, 1766), Agrotis exclamationis (Linnaeus, 1758), Peridroma saucia (Hübner, 1808) and Xestia c-nigrum (Linnaeus, 1758) from agricultural fields of Guilan province (North of Iran). We were able to detect 66 conservative Single Nucleotide Polymorphisms (SNPs) among the targeted pest species and eventually design specific primers and develop a multiplex polymerase chain reaction assay as a molecular diagnostic tool for immature stages of two the most common and abundant species including A. ipsilon and X. c-nigrum in Guilan province.},
}
@article {pmid30313544,
year = {2018},
author = {PreradoviĆ, J and AndriĆ, A and RadenkoviĆ, S and ZoriĆ, L&#x160; and PÉrez-baÑÓn, C and Campoy, A and VujiĆ, A},
title = {Pupal stages of three species of the phytophagous genus Merodon Meigen (Diptera: Syrphidae).},
journal = {Zootaxa},
volume = {4420},
number = {2},
pages = {229-242},
doi = {10.11646/zootaxa.4420.2.5},
pmid = {30313544},
issn = {1175-5334},
mesh = {Animals ; *Diptera ; Germany ; Larva ; Microscopy, Electron, Scanning ; *Pupa ; Serbia ; },
abstract = {plants, are mostly unknown. All known immature stages of Merodon feed on underground storage organs (bulbs, rhizomes and corms) of geophytes of the families Asparagaceae, Iridaceae and Amaryllidaceae. Of 160 known Merodon species, to date, the pupal stages have been described for only four: M. equestris (Fabricius), M. bombiformis Hull, M. luteihumerus Marcos-García, Vujić Mengual, and M. geniculatus Strobl. During field investigations in Đerdap National Park, Serbia, Merodon puparia were found in the ground near the bulbs of Ornithogalum umbellatum L. (Asparagaceae). DNA barcoding revealed that they belonged to the species M. aureus Fabricius and M. avidus (Rossi). Analysis of museum material from the Bavarian State Collection of Zoology in Germany revealed the puparium of an additional species, M. rufus Meigen. In our study we provide for the first time descriptions of the puparia of these three Merodon species. The main diagnostic morphological characters of the pupal spiracles and posterior respiratory processes are described using scanning electron microscopy, and cephalopharyngeal skeletons using binocular microscopy. In addition, puparium morphology of M. aureus, M. avidus and M. rufus is compared with known puparia of four other Merodon species and with the third larval stage of M. hurkmansi Marcos-García, Vujić Mengual.},
}
@article {pmid30313502,
year = {2018},
author = {Pyrcz, TW and Lorenc-Brudecka, J and Boyer, P and Zubek, A},
title = {Subspecies-level systematics and affinities of Cheimas Thieme-an endemic genus of the subparamo of the Venezuelan Cordillera de Mérida (Lepidoptera: Nymphalidae, Satyrinae).},
journal = {Zootaxa},
volume = {4422},
number = {2},
pages = {219-243},
doi = {10.11646/zootaxa.4422.2.4},
pmid = {30313502},
issn = {1175-5334},
mesh = {Animals ; *Butterflies ; *Forests ; Nevada ; },
abstract = {The validity of the monobasic neotropical butterfly genus Cheimas Thieme (Nymphalidae, Satyrinae, Satyrini, Pronophilina) is discussed, and confirmed based on morphological and molecular data. Cheimas opalinus (Staudinger), endemic to the Venezuelan Cordillera de Mérida, and considered prior to this study to be monotypic and restricted to the central part of the range, is demonstrated to be polytypic and more widely distributed. Five subspecies are recognised, differing mostly in their dorsal patterns, in particular the shape and colour of hindwing greenish-blue patch. Mitochondrial DNA sequences (COI) were obtained for three of them. The nominate subspecies is found in the central part of the range, in the Sierra Nevada and La Culata. The other subspecies are found as follows: C. opalinus dominici n. ssp.; in the Santo Domingo valley in the centre-north; C. opalinus cristalinus n. ssp. in the north; C. opalinus iosephi n. ssp. on the eastern slopes, and C. opalinus rosalinus n. ssp. in the southern Páramo El Batallón massif. A hybrid zone between the latter two subspecies was detected in the northern part of the Batallón massif based on unusual individual variation and intermediate phenotypes. All the populations of Cheimas opalinus occur in the forest-paramo ecotone at 2800-3400 m a.s.l., with the notable exception of C. opalinus cristalinus n. ssp. found also in mid-elevation forests down to 2300 m a.s.l.},
}
@article {pmid30313490,
year = {2018},
author = {Katoh, TK and Zhang, G and Zhou, CJ and Gao, JJ},
title = {Taxonomy of the Hirtodrosophila melanderi species group (Diptera: Drosophilidae), with descriptions of four new species from southwestern China.},
journal = {Zootaxa},
volume = {4422},
number = {3},
pages = {345-365},
doi = {10.11646/zootaxa.4422.3.2},
pmid = {30313490},
issn = {1175-5334},
mesh = {Animals ; China ; *Diptera ; *Drosophilidae ; Mitochondria ; Phylogeny ; Tibet ; },
abstract = {The Hirtodrosophila melanderi species group contains nine known species recorded from either the Old or the New World. All these species were thought to be strict fungivorous drosophilids. In the present study, we give supplementary descriptions for three of these known species, all recorded from Yunnan, southwestern China, H. furcapenis, H. furcapenisoides, and H. longifurcapenis, by examining respective type specimen(s). We then describe four new species of the same group, H. seticlasper Katoh Gao, sp. nov., H. spinicerca Katoh Gao, sp. nov., H. serratifurcapenis Katoh Gao, sp. nov., and H. truncifurca Katoh Gao, sp. nov., all discovered recently from high altitudes (ca. 3,500 to 3,800 m a.s.l.) in Tibet (Xizang), southwestern China. The delimitation of these new species is firstly performed in light of morphology and further with the aid of DNA sequences of the mitochondrial COI (cytochrome c oxydase, subunits I) gene. In addition, a key to all the species of the species group is provided.},
}
@article {pmid30313487,
year = {2018},
author = {Kodama, A and Kawai, K and Saito, H},
title = {A new species of Tanytarsus van der Wulp, 1874 (Diptera: Chironomidae) and the first Japanese record of Tanytarsus ovatus Johannsen, 1932 with DNA barcodes.},
journal = {Zootaxa},
volume = {4422},
number = {4},
pages = {591-599},
doi = {10.11646/zootaxa.4422.4.9},
pmid = {30313487},
issn = {1175-5334},
mesh = {Animals ; *Chironomidae ; *DNA Barcoding, Taxonomic ; Japan ; Male ; },
abstract = {A new species of the genus Tanytarsus van der Wulp, 1874 was described and illustrated based on an adult male. Tanytarsus trichovalis sp. nov. belongs to the eminulus species group, and is closely related to T. tamaundecimus Sasa, 1980, T. okuboi Sasa, 1986, and T. tonebeceus Sasa Tanaka, 2000. However, the species is distinguished from these species by the morphology of the hypopygium. We also present the first record of T. ovatus Johannsen, 1932 in Japan. In addition, DNA barcoding of 5 species including T. trichovalis sp. nov., T. ovatus, and other morphologically related species was undertaken. A new key of the eleven Japanese eminulus species group was compiled.},
}
@article {pmid30313484,
year = {2018},
author = {Liu, T and Sun, J and Cai, B and Wu, Y},
title = {Phyllocnistis podocarpa sp. nov. (Lepidoptera, Gracillariidae), a buddhist pine leaf-miner from Japan: taxonomy, DNA barcodes, damage and parasitoids.},
journal = {Zootaxa},
volume = {4422},
number = {4},
pages = {558-568},
doi = {10.11646/zootaxa.4422.4.6},
pmid = {30313484},
issn = {1175-5334},
mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; Japan ; *Lepidoptera ; Pupa ; },
abstract = {Phyllocnistis podocarpa sp. nov., is described from mines in Podocarpus macrophyllus (Family Podocarpaceae). The host plant P. macrophyllus, also known as buddhist pine on the IUCN Red List, is a noticeable garden plant and thus of high economic value. Buddhist pine has been introduced to many other countries from its native habitat in southern Japan. Special attention has been paid for it during the overseas import in China. The morphology of the pupae of P. podocarpa, particularly the frontal process of the head and the spine clusters on terga, ones of the most useful diagnostic characters for species identification of Phyllocnistis on morphology, is demonstrated using SEM. Two parasitoid species of Eulophidae (Hymenoptera) are identified and illustrated. COI barcode sequences are provided along with a Neighbor Joining Tree covering related species for aiding identification.},
}
@article {pmid30313483,
year = {2018},
author = {Barbosa, EP and Siewert, RR and Mielke, OHH and Lamas, G and Willmott, KR and Freitas, AVL},
title = {Redescription of Yphthimoides patricia (Hayward, 1957), with taxonomic notes on the names Euptychia saltuensis Hayward, 1962 and Yphthimoides manasses (C. Felder R. Felder, 1867) (Nymphalidae: Satyrinae).},
journal = {Zootaxa},
volume = {4422},
number = {4},
pages = {537-557},
doi = {10.11646/zootaxa.4422.4.5},
pmid = {30313483},
issn = {1175-5334},
mesh = {Animals ; *Butterflies ; *Ecosystem ; Genitalia, Male ; Male ; },
abstract = {Euptychia saltuensis Hayward, 1962, new synonym, currently regarded as a nomen dubium and possibly a junior subjective synonym of Yphthimoides manasses (C. Felder R. Felder, 1867), is here treated as a junior subjective synonym of Yphthimoides patricia (Hayward, 1957), based on morphological characters of the male genitalia and the DNA barcode. The taxonomic status of Y. patricia is re-examined, and a detailed redescription of the adult morphology, including the male genitalia, is presented. Information on the distribution, habitat and immature stages of Y. patricia is also provided. Yphthimoides patricia is clearly a distinct species from Y. manasses based on the analysis of DNA barcode sequences and the morphology of the male genitalia.},
}
@article {pmid30313465,
year = {2018},
author = {ÖzuluĞ, M and Geiger, MF and Freyhof, J},
title = {Alburnus goekhani, a new species of bleak from the Anatolian Black Sea basin (Teleostei: Leuciscidae).},
journal = {Zootaxa},
volume = {4425},
number = {1},
pages = {29-40},
doi = {10.11646/zootaxa.4425.1.2},
pmid = {30313465},
issn = {1175-5334},
mesh = {Animals ; Black Sea ; *Cyprinidae ; Gills ; Rivers ; },
abstract = {Alburnus goekhani, new species, is described from the Yeşilırmak and Kızılırmak River drainages. It belongs to the A. alburnus species group and is distinguished from other species in this group in Anatolia by having 48-56 + 2-3 scales in the lateral-line, 12-15 gill rakers, a distinct dark lateral stripe along the flank on live and preserved specimens and the anal-fin origin situated below the branched dorsal-fin ray 6-8. Alburnus goekhani is also well distinguished from other Alburnus species by its DNA barcode sequence.},
}
@article {pmid30313457,
year = {2018},
author = {Qian, CY and Bu, Y and Luan, YX},
title = {DNA barcoding and an updated key to the genus Hesperentomon (Protura: Acerentomata: Hesperentomidae), with a new species from Northwest China.},
journal = {Zootaxa},
volume = {4462},
number = {4},
pages = {523-534},
doi = {10.11646/zootaxa.4462.4.5},
pmid = {30313457},
issn = {1175-5334},
mesh = {Animals ; *Arthropods ; China ; DNA ; *DNA Barcoding, Taxonomic ; Genetic Drift ; },
abstract = {Hesperentomon bolense sp. n., described from Northwest China, is distinguished from other Hesperentomon spp. by having foretarsal sensillum b clearly shorter than c, a robust sensillum c broader than the other foretarsal sensilla, 18 posterior setae on the mesonotum and 16 posterior setae on the metanotum, 12 posterior setae on urotergites II-VI (P1a and P2a absent), 8 posterior setae on urosternites IV-VI (Pc absent), and absence of seta P2a on urotergite VII. The morphological characters of all described species of Hesperentomon are compared, and an updated identification key to species is given. The DNA barcodes of H. bolense sp. n. were compared to similar species of the genus; the K2P genetic divergences were 0-5.1% between individuals of H. bolense sp. n., but 21.4%-27.3% between H. bolense sp. n. and other congeneric species. The molecular data further confirmed H. bolense as a distinct species.},
}
@article {pmid30313397,
year = {2018},
author = {GiŁka, W and Paasivirta, L and Gadawski, P and Grabowski, M},
title = {Morphology and molecules say: Tanytarsus latens, sp. nov. from Finland (Diptera: Chironomidae).},
journal = {Zootaxa},
volume = {4471},
number = {3},
pages = {569-579},
doi = {10.11646/zootaxa.4471.3.8},
pmid = {30313397},
issn = {1175-5334},
mesh = {Animals ; *Chironomidae ; Electron Transport Complex IV ; Finland ; Male ; },
abstract = {Tanytarsus latens sp. nov. is described from Finland (Ostrobothnia borealis, Satakunta). Both morphological and molecular analyses indicate that T. latens belongs to the mendax species group. The adult male hypopygium of the new species resembles that of Tanytarsus occultus Brundin and of T. desertor Giłka et Paasivirta, while the molecular analysis based on the mitochondrial cytochrome oxidase (COI) gene fragment evidences that T. latens is a sister species to most of European Tanytarsus of the mendax group's core, for which the COI barcodes are known. Notes on biology of T. latens are also provided.},
}
@article {pmid30313373,
year = {2018},
author = {Bartlett, CR and Passos, EMD and Da Silva, FG and Diniz, LEC and Dollet, M},
title = {A new species of Oecleus Stål (Hemiptera: Fulgoroidea: Cixiidae) from coconut in Brazil.},
journal = {Zootaxa},
volume = {4472},
number = {2},
pages = {358-364},
doi = {10.11646/zootaxa.4472.2.8},
pmid = {30313373},
issn = {1175-5334},
mesh = {Animals ; Brazil ; *Cocos ; Databases, Nucleic Acid ; *Hemiptera ; Mitochondria ; },
abstract = {A new species of cixiid planthopper (Hemiptera: Fulgoroidea) in the genus Oecleus Stål, Oecleus sergipensis n. sp., is described from Sergipe State, Brazil. This new taxon is associated with coconut (Cocos nucifera L.) and date palm (Phoenix L). The species was detected in Auchenorrhyncha surveys to find potential vectors of lethal yellowing type syndrome. This is the first report of the genus Oecleus in Brazil. Sequence data from the mitochondrial cytochrome c oxidase subunit I (COI) barcoding region was obtained and accessioned into GenBank.},
}
@article {pmid30313293,
year = {2018},
author = {Van Soest, RWM and De Voogd, NJ},
title = {Calcareous sponges of the Western Indian Ocean and Red Sea.},
journal = {Zootaxa},
volume = {4426},
number = {1},
pages = {1-160},
doi = {10.11646/zootaxa.4426.1.1},
pmid = {30313293},
issn = {1175-5334},
mesh = {Animals ; Indian Ocean ; Indian Ocean Islands ; Middle East ; *Phylogeny ; *Porifera ; },
abstract = {Past taxonomic studies of Western Indian Ocean and Red Sea Calcarea have been few and sporadic (e.g. Schuffner 1877, Jenkin 1908, Row 1909, Dendy 1913, 1916, Voigt et al. 2017, 2018). Nevertheless, approximately 70 species are known from these studies for the considered region, but the descriptions of the older records often lack sufficient details for reliable identification. We studied the Western Indian Ocean Calcarea collection kept in the Naturalis Biodiversity Center. Available specimens numbered 145, collected in the Red Sea, Seychelles, Maldives, Mayotte and Rodrigues, in addition to incidental samples from Oman, the Lakshadweep Islands, the Mozambique Channel, and Eastern South Africa. Using a combination of techniques (in situ and 'on deck' photography, detailed field notes, light microscopic studies and measurements, SEM microscopy, and selected DNA sequencing) we identified 45 species, divided over the two main classes Calcinea (24 spp.) and Calcaronea (21 spp.). Not all species could be definitely assigned to an already described or a new species, as seven remained qualified as 'spec.' or 'aff.' for reasons of insufficient material or lack of details of in situ habitus. Sixteen species appeared to be new to science: Borojevia voigti sp.nov., Borojevia tubulata sp.nov., Borojevia pirella sp.nov., Clathrina rodriguesensis sp.nov., Clathrina maremeccae sp.nov., Clathrina repens sp.nov., Leucascus schleyeri sp.nov., Leucetta sulcata sp.nov., Ute insulagemmae sp.nov., Leucandra pilula sp.nov., Leucandra mozambiquensis sp.nov., Grantessa woerheidei sp.nov., Sycettusa hirsutissima sp.nov., Vosmaeropsis glebula sp.nov., Paraleucilla erpenbecki sp.nov., and Kebira tetractinifera sp.nov. For a selection of the identified species from the Western Indian Ocean and the Red Sea (30 spp.), as well as from Indonesian material (22 spp.) published previously (see Van Soest De Voogd 2015) we obtained sequences of the partial 28S gene of nuclear rDNA (C2-D2 region, cf. Voigt Wörheide 2016). The sequences of the Western Indian Ocean and Red Sea species were used to assign these to genera and families based on a phylogenetic analysis using MEGA pack vs. 06.6 for Mac of the available dataset. The Indonesian sequences supplemented by partial 28S sequences taken from the Sponge Barcode Project website and the NCBI website were included in the phylogenetic analysis to confirm the assignments. The results were compared and discussed with additional information on regional Calcarea not represented in our material. The latter chapter yielded the discovery of a preoccupied name leading to Sycon oscari nom.nov. for a species described from Mauritius.},
}
@article {pmid30313272,
year = {2018},
author = {Tabell, J and Mutanen, M and Sihvonen, P},
title = {Descriptions of five morphologically and genetically confirmed new species of the Coleophora poecilella Walsingham, 1907 species group (Lepidoptera, Coleophoridae) from the Palearctic Region.},
journal = {Zootaxa},
volume = {4429},
number = {2},
pages = {331-347},
doi = {10.11646/zootaxa.4429.2.8},
pmid = {30313272},
issn = {1175-5334},
mesh = {Animals ; Female ; *Lepidoptera ; Male ; },
abstract = {Five new Coleophora species belonging to the C. poecilella species group are described: C. mirleftensis Tabell, sp. nov. from Morocco, C. embaensis Tabell, sp. nov. and C. charynensis Tabell, sp. nov. from Kazakhstan, C. nupponeni Tabell, sp. nov. from Kazakhstan and Tajikistan, and C. tugaicola Tabell, sp. nov. from Tajikistan. The male genitalia of C. hypomona (Falkovitsh, 1979) and the female genitalia of C. trichopterella Baldizzone, 1985 are illustrated for the first time. DNA barcodes are provided for each species, with a comparison to the genetically most similar species.},
}
@article {pmid30313271,
year = {2018},
author = {Fei, Y and Zhao, J and Liu, K},
title = {First record of Hiroshiinoueana Kawabe, 1978 from China (Lepidoptera: Tortricidae: Olethreutinae), with descriptions of two new species.},
journal = {Zootaxa},
volume = {4429},
number = {2},
pages = {324-330},
doi = {10.11646/zootaxa.4429.2.7},
pmid = {30313271},
issn = {1175-5334},
mesh = {Animals ; China ; *Moths ; },
abstract = {The genus Hiroshiinoueana Kawabe, 1978 is recorded from China for the first time. Two new species, H. wuzhishanica sp. nov. and H. inequivalva sp. nov., are described and illustrated. A key to the species of Hiroshiinoueana is provided. Cytochrome oxidase subunit I (COI) sequences of the new species are deposited in GenBank.},
}
@article {pmid30313232,
year = {2018},
author = {Cumming, RT and Leong, JV and Lohman, DJ},
title = {Addendum to "Leaf insects from Luzon, Philippines, with descriptions of four new species, the new genus Pseudomicrophyllium, and redescription of Phyllium (Phyllium) geryon Gray, 1843, (Phasmida: Phylliidae)".},
journal = {Zootaxa},
volume = {4433},
number = {2},
pages = {389},
doi = {10.11646/zootaxa.4433.2.10},
pmid = {30313232},
issn = {1175-5334},
mesh = {Animals ; Color ; DNA Barcoding, Taxonomic ; *Insecta ; Philippines ; *Phylogeny ; Specimen Handling ; },
abstract = {At the time Cumming et al. (2017) was published, the GenBank accession numbers for partial cytochrome c oxidase subunit I (COI) DNA barcode sequences from Microphyllium specimens sampled in the phylogenetic analysis were not yet available. This information is provided in Table 1.},
}
@article {pmid30313198,
year = {2018},
author = {Grados, J},
title = {Four new species and one new subspecies of Arctiinae (Lepidoptera: Erebidae) from the Tambopata river, Madre de Dios, Peru.},
journal = {Zootaxa},
volume = {4434},
number = {1},
pages = {29-48},
doi = {10.11646/zootaxa.4434.1.2},
pmid = {30313198},
issn = {1175-5334},
mesh = {Animals ; Expeditions ; Male ; *Moths ; Peru ; Rainforest ; Rivers ; },
abstract = {Four new species and one new subspecies of Arctiinae (Lepidoptera: Erebidae) are described. Aphyle niedmandi sp. nov., Evius ocassus sp. nov., Paranerita maculata sandeepani ssp. nov., Paranerita kotolnuki sp. nov. and Baritius flexuosus sp. nov. were collected in the Tambopata River region, Madre de Dios (Peru), as part of a Citizen Science Project, in mutual collaboration between the Natural History Museum (Lima-Peru) and Rainforest Expeditions. External morphological descriptions, morphology of male genitalia, and geographic distributions in Peru are given for all taxa as well as their barcoding.},
}
@article {pmid30313157,
year = {2018},
author = {Motta, J and Menin, M and Almeida, AP and Hrbek, T and Farias, IP},
title = {When the unknown lives next door: a study of central Amazonian anurofauna.},
journal = {Zootaxa},
volume = {4438},
number = {1},
pages = {79-104},
doi = {10.11646/zootaxa.4438.1.3},
pmid = {30313157},
issn = {1175-5334},
mesh = {Animals ; *Anura ; Biodiversity ; Databases, Nucleic Acid ; Ecosystem ; Phylogeny ; *RNA, Ribosomal, 16S ; },
abstract = {The number of species of anurans in the Amazon is highly underestimated with new studies reporting the discovery of a large number of species every year. This advance in the discovery of biodiversity is due to the use of molecular tools, especially 16S rRNA gene barcoding, which is used to identify species and discover cryptic lineages. Few anurans of the central Amazon have molecular sequence data available in public databases, which contrasts with the considerable species richness of this biome. The aim of the present study was to test for the presence of cryptic species using the mPTP delimitation algorism. We morphologically identified 26 species, of which 23 were confirmed molecularly with the remaining three species identified as other congeneric species, since sequences with the same epithet do not exist in GenBank. Of these 23 species, nine contained one lineage restricted to central Amazon. This represents an underestimate of 39% in the taxonomic diversity in our sample. This is particularly surprising given that our sampling sites are among the best-studied regions of the central Amazon.},
}
@article {pmid30313133,
year = {2018},
author = {PopoviĆ, M and Verovnik, R},
title = {Revised checklist of the butterflies of Serbia (Lepidoptera: Papilionoidea).},
journal = {Zootaxa},
volume = {4438},
number = {3},
pages = {501-527},
doi = {10.11646/zootaxa.4438.3.5},
pmid = {30313133},
issn = {1175-5334},
mesh = {Animals ; *Butterflies ; Genitalia ; Museums ; Serbia ; },
abstract = {With studies spanning almost two centuries, butterflies are one of the best known insect groups in Serbia. However, there are still several inconsistencies regarding the number and selection of species included in national checklists published in the last decades. In order to overcome the confusing situation we provide a taxonomically up-to-date checklist of the butterflies for the country, including Kosovo, based on a comprehensive survey of the literature, inspection of available museum collections and from intensive field surveys over the last twenty years. Our aim is also to resolve some long standing problems with species potentially occurring in the country. For this purpose genitalia dissections and DNA barcoding have been used for identification where necessary. The annotated checklist includes 199 species of which Carcharodus orientalis is new for the country and the recently discovered white Anthocharis damone is listed for the first time. We also provide conclusive evidence of the presence of Melitaea ornata in Serbia. Among species listed in the previous species lists we excluded eight species due to inconclusive evidence, and provide a detailed explanation for their exclusion. We hope this publication will stimulate further studies of this important bioindicator group of insects and provide the basis for their conservation in the country.},
}
@article {pmid30309592,
year = {2019},
author = {Khilare, V and Tiknaik, A and Prakash, B and Ughade, B and Korhale, G and Nalage, D and Ahmed, N and Khedkar, C and Khedkar, G},
title = {Multiple tests on saffron find new adulterant materials and reveal that Ist grade saffron is rare in the market.},
journal = {Food chemistry},
volume = {272},
number = {},
pages = {635-642},
doi = {10.1016/j.foodchem.2018.08.089},
pmid = {30309592},
issn = {1873-7072},
mesh = {Crocus/*chemistry/classification/genetics ; DNA Barcoding, Taxonomic ; DNA, Plant/chemistry/isolation &amp; purification/metabolism ; *Food Quality ; Microscopy ; Phylogeny ; Spectrophotometry ; },
abstract = {Among spices, Saffron is among the most extensively interrogated for purity and authenticity. Numerous methods have been recommended for authentication of Saffron samples and for detection of adulterants for codex compliance. However, none of these methods can fulfill both of these important quality criteria. This study describes a three step approach to achieving this goal by including the established ISO3632 method and two additional methods based on microscopic examination and DNA barcoding. We provide results showing the utility of these methods both independently and in combination for quality evaluation of 36 commercial saffron samples. Our results show that use of the ISO3632 approach alone can reveal the color and aroma but not the genetic origin of the material or distinguish between synthetic components versus natural ingredients. Also, the microscopic observation method can give a preliminary indication of saffron authenticity, but used alone it is unable to quantify purity. Finally, a relatively new method based on the use of DNA barcodes can authenticate the biological origin of the saffron, but here results may be misleading if auto-adulterating materials are present. Overall, our study reveals that through the combined use of all three methods, saffron authentication can substantially improved.},
}
@article {pmid30308279,
year = {2019},
author = {Vakati, V and Eyun, SI and Lee, W},
title = {Unraveling the intricate biodiversity of the benthic harpacticoid genus Nannopus (Copepoda, Harpacticoida, Nannopodidae) in Korean waters.},
journal = {Molecular phylogenetics and evolution},
volume = {130},
number = {},
pages = {366-379},
doi = {10.1016/j.ympev.2018.10.004},
pmid = {30308279},
issn = {1095-9513},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; *Biodiversity ; Copepoda/*classification ; DNA Barcoding, Taxonomic ; Databases, Genetic ; Geography ; Phylogeny ; Republic of Korea ; *Seawater ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Nannopus (Harpacticoida, Nannopodidae) species are abundant and widely distributed throughout the world across a variety of habitats. Nannopus is well known for high frequencies of misidentifications and thus may comprise several cryptic complexes and morphologically distinct species. Cryptic taxa are common in meiofauna communities. In this study, we aimed to identify Nannopus species using an integrative approach including molecular taxonomy. We adopted a non-destructive DNA extraction method so that morphological and molecular data could be obtained from the same specimen. We analyzed the molecular diversity and distributions of Nannopus using a total of 190 individuals. We sequenced the 190 mtCOI, 53 mtCYTB, 25 18SrDNA, and 43 28SrDNA genes from 190 individuals. Several species delimitation approaches were applied, including uncorrected p-distances for mtCOI, mtCYTB, 18SrDNA, and 28SrDNA, and Automatic Barcode Gap Discovery and Bayesian implemented Poisson tree processes for mtCOI and mtCYTB data. The maximum likelihood and Bayesian approaches were used to examine the phylogenetic relationships among individuals using the combined set of all four genes. Our species delimitation and phylogenetic analyses indicated the presence of three cryptic and six morphologically distinct species. All species are sympatric and widely distributed across mudflats ranging from the Yellow Sea to the South Sea in Korea. The divergence patterns of the four genes were not congruent. A phylogenetic tree based on the concatenated dataset was the most robust, was congruent with morphology, and suggested two major clades. We considered the validity of reinstating the genus Ilyophilus (Lilljeborg, 1902) and ultimately concluded that including all congeners in Nannopus until the type species (N. palustris Brady, 1880) is re-described was the most prudent approach.},
}
@article {pmid30308278,
year = {2019},
author = {Huang, XC and Su, JH and Ouyang, JX and Ouyang, S and Zhou, CH and Wu, XP},
title = {Towards a global phylogeny of freshwater mussels (Bivalvia: Unionida): Species delimitation of Chinese taxa, mitochondrial phylogenomics, and diversification patterns.},
journal = {Molecular phylogenetics and evolution},
volume = {130},
number = {},
pages = {45-59},
doi = {10.1016/j.ympev.2018.09.019},
pmid = {30308278},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Bivalvia/*classification/genetics ; China ; Electron Transport Complex IV/genetics ; Fresh Water ; Genetic Variation ; Genome, Mitochondrial/genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; Species Specificity ; },
abstract = {The Yangtze River Basin in China is one of the global hotspots of freshwater mussel (order Unionida) diversity with 68 nominal species. Few studies have tested the validity of these nominal species. Some taxa from the Yangtze unionid fauna have not been adequately examined using molecular data and well-positioned phylogenetically with respect to the global Unionida. We evaluated species boundaries of Chinese freshwater mussels, and disentangled their phylogenetic relationships within the context of the global freshwater mussels based on the multi-locus data and complete mitochondrial genomes. Moreover, we produced the time-calibrated phylogeny of Unionida and explored patterns of diversification. COI barcode data suggested the existence of 41 phylogenetic distinct species from our sampled 40 nominal taxa inhabiting the middle and lower reaches of the Yangtze River. Maximum likelihood and Bayesian inference analyses on three loci (COI, 16S, and 28S) and complete mitochondrial genomes showed that the subfamily Unioninae sensu stricto was paraphyletic, and the subfamily Anodontinae should be subsumed under Unioninae. In addition, we described two new tribes (Aculamprotulini tribe nov. and Lepidodesmini tribe nov.) in the subfamily Unioninae and one new genus (Parvasolenaiagen. nov.) in the subfamily Gonideinae. Molecular dating analysis suggested freshwater mussels diversified at 346.1 Mya (HPD = 286.6-409.9). The global diversification rate for Unionida was estimated to be 0.025 species/Myr. Our study found only a single well-supported rate shift in Unionida diversification, occurring at the base of the subfamily Ambleminae. The evolution of active host-attraction may have triggered the burst of speciation in Ambleminae, and the environment and geography of the Mississippi River Basin likely sustained this radiation.},
}
@article {pmid30307925,
year = {2018},
author = {Elsner, M},
title = {Barcodes galore for developmental biology.},
journal = {Nature biotechnology},
volume = {36},
number = {10},
pages = {936},
pmid = {30307925},
issn = {1546-1696},
mesh = {Animals ; Biotechnology ; Cell Lineage/genetics ; *DNA Barcoding, Taxonomic ; *Developmental Biology ; Embryonic Development/genetics ; Mice ; RNA, Guide, CRISPR-Cas Systems ; },
}
@article {pmid30306564,
year = {2018},
author = {Barreto, SB and Silva, AT and Batalha-Filho, H and Affonso, PRAM and Zanata, AM},
title = {Integrative approach reveals a new species of Nematocharax (Teleostei: Characidae).},
journal = {Journal of fish biology},
volume = {93},
number = {6},
pages = {1151-1162},
doi = {10.1111/jfb.13834},
pmid = {30306564},
issn = {1095-8649},
support = {RED0045/2014//FAPESB/ ; JCB0026/2016//FAPESB/ ; RED0009/2013//FAPESB/ ; 2012/58050-0//FAPESP/ ; //IBAMA/ ; 443249/2014-8//CNPq/ ; //CAPES Foundation/ ; },
mesh = {Animals ; Biological Evolution ; Brazil ; Characidae/anatomy &amp; histology/*classification/genetics ; Classification/methods ; *Genetic Variation ; Male ; Phylogeny ; Rivers ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {An integrative approach based on morphological and multilocus genetic data was used to describe a new species of Nematocharax from the headwaters of the upper Contas River on the Diamantina Plateau, north-eastern Brazil and to infer the relationships among evolutionary lineages within this fish genus. Multispecies coalescent inference using three mitochondrial and five nuclear loci strongly supports a basal split between Nematocharax venustus and the new species, whose distinctive morphological characters include absence of filamentous rays on pelvic fins of maturing and mature males, reduced anal-fin lobe length and lower body depth. The unique morphological and genetic traits of the population from the upper Contas River were supported by previous reports based on cytogenetics, DNA barcode and geometric morphometrics, reinforcing the validation of the new species. The conservation status of this new species is discussed.},
}
@article {pmid30304922,
year = {2018},
author = {Lee, M and Choi, SJ and Han, S and Nam, M and Kim, D and Kim, DU and Hoe, KL},
title = {Mutation Analysis of Synthetic DNA Barcodes in a Fission Yeast Gene Deletion Library by Sanger Sequencing.},
journal = {Genomics &amp; informatics},
volume = {16},
number = {2},
pages = {22-29},
pmid = {30304922},
issn = {1598-866X},
support = {//Chungnam National University/ ; },
abstract = {Incorporation of unique barcodes into fission yeast gene deletion collections has enabled the identification of gene functions by growth fitness analysis. For fine tuning, it is important to examine barcode sequences, because mutations arise during strain construction. Out of 8,708 barcodes (4,354 strains) covering 88.5% of all 4,919 open reading frames, 7,734 barcodes (88.8%) were validated as high-fidelity to be inserted at the correct positions by Sanger sequencing. Sequence examination of the 7,734 high-fidelity barcodes revealed that 1,039 barcodes (13.4%) deviated from the original design. In total, 1,284 mutations (mutation rate of 16.6%) exist within the 1,039 mutated barcodes, which is comparable to budding yeast (18%). When the type of mutation was considered, substitutions accounted for 845 mutations (10.9%), deletions accounted for 319 mutations (4.1%), and insertions accounted for 121 mutations (1.6%). Peculiarly, the frequency of substitutions (67.6%) was unexpectedly higher than in budding yeast (∼28%) and well above the predicted error of Sanger sequencing (∼2%), which might have arisen during the solid-phase oligonucleotide synthesis and PCR amplification of the barcodes during strain construction. When the mutation rate was analyzed by position within 20-mer barcodes using the 1,284 mutations from the 7,734 sequenced barcodes, there was no significant difference between up-tags and down-tags at a given position. The mutation frequency at a given position was similar at most positions, ranging from 0.4% (32/7,734) to 1.1% (82/7,734), except at position 1, which was highest (3.1%), as in budding yeast. Together, well-defined barcode sequences, combined with the next-generation sequencing platform, promise to make the fission yeast gene deletion library a powerful tool for understanding gene function.},
}
@article {pmid30301497,
year = {2018},
author = {Paydar, S and Ucar, E and Yari, P and Safavi, SM and Kahrizi, D and Nateqi, M and Mirmoayedi, A and Yari, K},
title = {A simplified and optimized protocol for total DNA extraction from insect species: applicable for studying genetic diversity and PCR-based specimen identification via partial amplification of cytochrome oxidase I (COI) gene.},
journal = {Cellular and molecular biology (Noisy-le-Grand, France)},
volume = {64},
number = {12},
pages = {22-25},
pmid = {30301497},
issn = {1165-158X},
mesh = {Animals ; DNA/*isolation &amp; purification ; Electron Transport Complex IV/*genetics ; Genetic Variation/genetics ; Insecta/*genetics ; Polymerase Chain Reaction ; },
abstract = {The efficient DNA extraction from insects has been suggested as a critical and main step affecting molecular entomology for taxonomic identification, the establishment of DNA barcoding library and analysis of genetic diversity relationship between insect populations. For successfully apply these molecular techniques, high-quantity and high-quality of the extracted DNA are required. Several protocols for efficient genomic DNA extraction from insects have been developed. In this research, we represent a rapid, reliable and cost-effective method that it is not reliant on poisonous and enzymatic reagents for DNA extraction from insect tissues. Results showed that high quantity and high-quality of the isolated DNA by this method is suitable and can be used directly for PCR, also is enough to do hundreds of molecular reactions. In conclusion, we described a fast, cost-effective, non-toxic and enzyme-free protocol for high yield genomic DNA extraction from green Lacewings (Chrysoperla carnea) tissues in basic equipment laboratories.},
}
@article {pmid30300110,
year = {2019},
author = {Lwande, OW and Näslund, J and Lundmark, E and Ahlm, K and Ahlm, C and Bucht, G and Evander, M},
title = {Experimental Infection and Transmission Competence of Sindbis Virus in Culex torrentium and Culex pipiens Mosquitoes from Northern Sweden.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {19},
number = {2},
pages = {128-133},
pmid = {30300110},
issn = {1557-7759},
mesh = {Animals ; Culex/*virology ; Female ; Mosquito Vectors/*virology ; Sindbis Virus/*physiology ; Species Specificity ; Sweden ; },
abstract = {INTRODUCTION: Sindbis virus (SINV) is a mosquito-borne Alphavirus known to infect birds and cause intermittent outbreaks among humans in Fenno-Scandia. In Sweden, the endemic area has mainly been in central Sweden. Recently, SINV infections have emerged to northern Sweden, but the vectorial efficiency for SINV of mosquito species in this northern region has not yet been ascertained.<br><br>OBJECTIVE: Mosquito larvae were sampled from the Ume&#xe5; region in northern Sweden and propagated in a laboratory to adult stage to investigate the infection, dissemination, and transmission efficiency of SINV in mosquitoes.<br><br>MATERIALS AND METHODS: The mosquito species were identified by DNA barcoding of the cytochrome oxidase I gene. Culex torrentium was the most abundant (82.2%) followed by Culex pipiens (14.4%), Aedes annulipes (1.1%), Anopheles claviger (1.1%), Culiseta bergrothi (1.1%), or other unidentified species (1.1%). Mosquitoes were fed with SINV-infected blood and monitored for 29 days to determine the viral extrinsic incubation period. Infection and dissemination were determined by RT-qPCR screening of dissected body parts of individual mosquitoes. Viral transmission was determined from saliva collected from individual mosquitoes at 7, 14, and 29 days. SINV was detected by cell culture using BHK-21 cells, RT-qPCR, and sequencing.<br><br>RESULTS: Cx. torrentium was the only mosquito species in our study that was able to transmit SINV. The overall transmission efficiency of SINV in Cx. torrentium was 6.8%. The rates of SINV infection, dissemination, and transmission in Cx. torrentium were 11%, 75%, and 83%, respectively.<br><br>CONCLUSIONS: Cx. torrentium may be the key vector involved in SINV transmission in northern Sweden.},
}
@article {pmid30298786,
year = {2018},
author = {Maruoka, N and Ohtsuki, H and Makino, W and Urabe, J},
title = {Rediscovery after Almost 120 Years: Morphological and Genetic Evidence Supporting the Validity of Daphnia mitsukuri (Crustacea: Cladocera).},
journal = {Zoological science},
volume = {35},
number = {5},
pages = {468-475},
doi = {10.2108/zs170081},
pmid = {30298786},
issn = {0289-0003},
mesh = {Animals ; Daphnia/*anatomy &amp; histology/classification/*genetics ; Female ; Phylogeny ; Species Specificity ; },
abstract = {We examined the morphology of Daphnia individuals maintained in our laboratory for several years, originally collected in Lake Inbanuma, Chiba, Japan. We determined partial sequences of the mitochondrial cytochrome c oxidase subunit I and 12S rRNA genes from specimens in the cultured material. These animals are morphologically similar to D. obtusa Kurz, 1874 , but genetically distinct from this species. Our detailed observation shows that the morphological characteristics in the female and male individuals of our material are highly congruent with those of D. mitsukuri Ishikawa, 1896 , which has not been identified positively for more than 120 years since its original description, with its taxonomic identity having been questioned for almost 90 years. Based on our morphological and genetic data, we conclude that D. mitsukuri should be regarded as a taxonomically valid species. A search among public DNA sequence databases suggests D. mitsukuri is also distributed in China, although these Chinese sequences have been labeled as 'Daphnia pulex', representing misidentification.},
}
@article {pmid30291070,
year = {2018},
author = {Schmocker, KS and Zwahlen, FS and Denecke, K},
title = {Mobile App for Simplifying Life With Diabetes: Technical Description and Usability Study of GlucoMan.},
journal = {JMIR diabetes},
volume = {3},
number = {1},
pages = {e6},
pmid = {30291070},
issn = {2371-4379},
abstract = {BACKGROUND: Patients with diabetes can be affected by several comorbidities that require immediate action when occurring as they may otherwise cause fatal or consequential damage. For this reason, patients must closely monitor their metabolism and inject insulin when necessary. The documentation of glucose values and other relevant measurements is often still on paper in a diabetes diary.<br><br>OBJECTIVE: The goal of this work is to develop and implement a novel mobile health system for the secure collection of relevant data referring to a person's metabolis and to digitize the diabetes diary to enable continuous monitoring for both patients and treating physicians. One specific subgoal is to enable data transmission of health parameters to secure data storage.<br><br>METHODS: The process of implementing the system consists of (1) requirements analysis with patients and physicians to identify patient needs and specify relevant functionalities, (2) design and development of the app and the data transmission, and (3) usability study.<br><br>RESULTS: We developed and implemented the mobile app GlucoMan to support data collection pertaining to a person's metabolism. An automated transfer of measured values from a glucometer was implemented. Medication and nutrition data could be entered using product barcodes. Relevant background knowledge such as information on carbohydrates was collected from existing databases. The recorded data was transmitted using international interoperability standards to the MIDATA.coop storage platform. The usability study revealed some design issues that needs to be solved, but in principle, the study results show that the app is easy to use and provides useful features.<br><br>CONCLUSIONS: Data collection on a patient's metabolism can be supported with a multifunctional app such as GlucoMan. Besides monitoring, continuous data can be documented and made available to the treating physician. GlucoMan allows patients to monitor disease-relevant parameters and decide who accesses their health data. In this way, patients are empowered not only to manage diabetes but also manage their health data.},
}
@article {pmid30288248,
year = {2018},
author = {Yang, J and Meng, Z and Liu, Q and Shimada, Y and Olsthoorn, RCL and Spaink, HP and Herrmann, A and Kros, A},
title = {Performing DNA nanotechnology operations on a zebrafish.},
journal = {Chemical science},
volume = {9},
number = {36},
pages = {7271-7276},
pmid = {30288248},
issn = {2041-6520},
abstract = {Nanoscale engineering of surfaces is becoming an indispensable technique to modify membranes and, thus cellular behaviour. Here, such membrane engineering related was explored on the surface of a living animal using DNA nanotechnology. We demonstrate the immobilization of oligonucleotides functionalized with a membrane anchor on 2 day old zebrafish. The protruding single-stranded DNA on the skin of zebrafish served as a handle for complementary DNAs, which allowed the attachment of small molecule cargo, liposomes and dynamic relabeling by DNA hybridization protocols. Robust anchoring of the oligonucleotides was proven as DNA-based amplification processes were successfully performed on the outer membrane of the zebrafish enabling the multiplication of surface functionalities from a single DNA-anchoring unit and the dramatic improvement of fluorescent labeling of these animals. As zebrafish are becoming an alternative to animal models in drug development, toxicology and nanoparticles characterization, we believe the platform presented here allows amalgamation of DNA nanotechnology tools with live animals and this opens up yet unexplored avenues like efficient bio-barcoding as well as in vivo tracking.},
}
@article {pmid30287908,
year = {2018},
author = {Günther, B and Knebelsberger, T and Neumann, H and Laakmann, S and Martínez Arbizu, P},
title = {Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {14822},
pmid = {30287908},
issn = {2045-2322},
mesh = {Aquatic Organisms/classification/genetics ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*genetics/*isolation &amp; purification ; DNA, Ribosomal/*genetics/*isolation &amp; purification ; Electron Transport Complex IV/genetics ; Metagenomics/*methods ; North Sea ; RNA, Ribosomal, 18S/genetics ; Seawater/*chemistry ; },
abstract = {We establish the new approach of environmental DNA (eDNA) analyses for the North Sea. Our study uses a multigene approach, including the mitochondrial cytochrome-c-oxidase subunit I (COI) gene for analyzing species composition and the nuclear hypervariable region V8 of 18S rDNA for analyzing supraspecific biodiversity. A new minibarcode primer (124 bp) was created on the basis of a metazoan COI barcode library with 506 species and tested in silico, in vitro, and in situ. We applied high throughput sequencing to filtrates of 23 near-bottom water samples taken at three seasons from 14 stations. The set of COI primers allowed amplification of mitochondrial minibarcodes for diverse metazoan phyla and the differentiation at the species level for more than 99% of the specimens in the dataset. Our results revealed that the number of sequences is not consistent with proportions in the given DNA mixture. Altogether, environmental sequences could be assigned to 114 species and to 12 metazoan phyla. A spatial distribution of taxa recovered by eDNA was congruent with known distributions. Finally, the successful detection of species and biodiversity depends on a comprehensive sequence reference database. Our study offers a powerful tool for future biodiversity research, including the detection of nonnative species.},
}
@article {pmid30287276,
year = {2019},
author = {Kaito, S and Sasaki, M and Goto, K and Matsusue, R and Koyama, H and Nakao, M and Hasegawa, H},
title = {A case of small bowel obstruction due to infection with Bolbosoma sp. (Acanthocephala: Polymorphidae).},
journal = {Parasitology international},
volume = {68},
number = {1},
pages = {14-16},
doi = {10.1016/j.parint.2018.09.007},
pmid = {30287276},
issn = {1873-0329},
mesh = {Abdominal Pain ; Acanthocephala/genetics/*isolation &amp; purification ; Adult ; Animals ; DNA Barcoding, Taxonomic ; Female ; Helminthiasis/*complications/diagnosis/epidemiology/parasitology ; Humans ; Intestinal Obstruction/*etiology/*parasitology ; Intestine, Small/parasitology ; Japan/epidemiology ; Jejunum/parasitology/surgery ; Sequence Analysis, DNA ; },
abstract = {A case of small bowel obstruction caused by Bolbosoma sp. infection is reported. A 27-year-old woman admitted with abdominal pain was diagnosed as small bowel obstruction. Laparoscopic surgery revealed induration in jejunum at ca. 120 cm distal to the ligament of Treiz, attributed to a band connecting the serosa to the ascending mesocolon. Resected band contained an acanthocephalan accompanying foreign body reaction with abscess formation. The parasite belonged to the genus Bolbosoma, of which identification was made by DNA sequence analysis. This is the eighth case of Bolbosoma infection in humans, and the first one causing an ileus.},
}
@article {pmid30284935,
year = {2018},
author = {Mäki, A and Tiirola, M},
title = {Directional high-throughput sequencing of RNAs without gene-specific primers.},
journal = {BioTechniques},
volume = {65},
number = {4},
pages = {219-223},
doi = {10.2144/btn-2018-0082},
pmid = {30284935},
issn = {1940-9818},
mesh = {DNA Primers/genetics ; DNA, Complementary/genetics ; *Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Phytoplankton/genetics ; RNA, Ribosomal/*genetics ; Workflow ; },
abstract = {Ribosomal RNA analysis is a useful tool for characterization of microbial communities. However, the lack of broad-range primers has hampered the simultaneous analysis of eukaryotic and prokaryotic members by amplicon sequencing. We present a complete workflow for directional, primer-independent sequencing of size-selected small subunit ribosomal RNA fragments. The library preparation protocol includes gel extraction of the target RNA, ligation of an RNA oligo to the 5'-end of the target, and cDNA synthesis with a tailed random-hexamer primer and further barcoding. The sequencing results of a phytoplankton mock community showed a highly similar profile to the biomass indicators. This method has universal potential for microbiome studies, and is compatible for the 5'-end sequencing of other RNA types with minimum library preparation costs.},
}
@article {pmid30283430,
year = {2018},
author = {Xu, Y and Lewandowski, K and Lumley, S and Pullan, S and Vipond, R and Carroll, M and Foster, D and Matthews, PC and Peto, T and Crook, D},
title = {Detection of Viral Pathogens With Multiplex Nanopore MinION Sequencing: Be Careful With Cross-Talk.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2225},
pmid = {30283430},
issn = {1664-302X},
abstract = {Metagenomic sequencing with the Oxford Nanopore MinION sequencer offers potential for point-of-care testing of infectious diseases in clinical settings. To improve cost-effectiveness, multiplexing of several, barcoded samples upon a single flow cell will be required during sequencing. We generated a unique sequencing dataset to assess the extent and source of cross barcode contamination caused by multiplex MinION sequencing. Sequencing libraries for three different viruses, including influenza A, dengue, and chikungunya, were prepared separately and sequenced on individual flow cells. We also pooled the respective libraries and performed multiplex sequencing. We identified 0.056% of total reads in the multiplex sequencing data that were assigned to incorrect barcodes. Chimeric reads were the predominant source of this error. Our findings highlight the need for careful filtering of multiplex sequencing data before downstream analysis, and the trade-off between sensitivity and specificity that applies to the barcode demultiplexing methods.},
}
@article {pmid30280041,
year = {2018},
author = {Ogura, T and Watanabe, HK and Chen, C and Sasaki, T and Kojima, S and Ishibashi, JI and Fujikura, K},
title = {Population history of deep-sea vent and seep Provanna snails (Mollusca: Abyssochrysoidea) in the northwestern Pacific.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5673},
pmid = {30280041},
issn = {2167-8359},
abstract = {BACKGROUND: Gastropods of the genus Provanna are abundant and widely distributed in deep-sea chemosynthetic environments with seven extant species described in the northwestern Pacific.<br><br>METHODS: We investigated the population history and connectivity of five Provanna species in the northwestern Pacific through population genetic analyses using partial sequences of the cytochrome c oxidase subunit I gene.<br><br>RESULTS: We found that P. subglabra, the most abundant and genetically diverse species, is genetically segregated by depth. Among the five species, the three comparatively shallower species (P. lucida, P. kuroshimensis, P. glabra) had a more constant demographic history compared to the deeper species (P. subglabra, P.&#xa0; clathrata).<br><br>DISCUSSION: Environmental differences, especially depth, appears to have a role in the segregation of Provanna snails. The population of P. clathrata in the Irabu Knoll appears to have expanded after P. subglabra population. The remaining three species, P. lucida, P. kuroshimensis, and P. glabra, are only known from a single site each, all of which were shallower than 1,000 m. These data indicate that Provanna gastropods are vertically segregated, and that their population characteristics likely depend on hydrothermal activities.},
}
@article {pmid30279632,
year = {2018},
author = {van Nieukerken, EJ and Gilrein, DO and Eiseman, CS},
title = {Stigmellamultispicata Rociene. &amp; Stonis, an Asian leafminer on Siberian elm, now widespread in eastern North America (Lepidoptera, Nepticulidae).},
journal = {ZooKeys},
volume = {},
number = {784},
pages = {95-125},
pmid = {30279632},
issn = {1313-2989},
abstract = {Stigmellamultispicata Rocienė &amp; Stonis, 2014, previously known from the single male holotype from Primorye, Russia, is reported as a new invasive species mining leaves of Siberian elm, Ulmuspumila L., in eastern North America. Both adults and leafmines have been reported from many sites as unidentified Nepticulidae since 2010. Crucial for the identification was a match of the DNA barcode of a single larva collected on Ulmuspumila in Beijing with adults from North America. The single larva constitutes a new record for China. Stigmellamultispicata is closely related to the European S.ulmivora (Fologne, 1860), feeding likewise on Ulmus, but differs in details of external morphology and genitalia, particularly in the female, where S.multispicata has a remarkable elongated narrow ovipositor, suitable for oviposition in underside hairy leaf vein axils, where all mines start. In North America S.multispicata is the only Ulmus-feeding nepticulid with green larvae. Currently the species is known from USA: Illinois, Indiana, Iowa, Maryland, Massachusetts, Minnesota, New York, Ohio, Tennessee, Wisconsin, and Canada: Ontario and Québec. In Sagaponack, on Long Island, New York, larvae have been reported to occur en masse on Siberian elms from at least two sites. The current distribution could be reconstructed thanks also to many online photographs from observation websites. The species is redescribed, with the first descriptions of female, larva, and leafmine, and compared with S.ulmivora, which is fully redescribed. The two native North American nepticulid Ulmus leafminers, S.apicialbella (Chambers, 1873) and Ectoedemiaulmella (Braun, 1912), are diagnosed and new provincial and state records are provided. A key to linear mines on Ulmus in North America is provided. We suspect that trade of live plants through nurseries played a role in the sudden spread of this invasive species.},
}
@article {pmid30278147,
year = {2019},
author = {Delabye, S and Rougerie, R and Bayendi, S and Andeime-Eyene, M and Zakharov, EV and deWaard, JR and Hebert, PDN and Kamgang, R and Le Gall, P and Lopez-Vaamonde, C and Mavoungou, JF and Moussavou, G and Moulin, N and Oslisly, R and Rahola, N and Sebag, D and Decaëns, T},
title = {Characterization and comparison of poorly known moth communities through DNA barcoding in two Afrotropical environments in Gabon [1].},
journal = {Genome},
volume = {62},
number = {3},
pages = {96-107},
doi = {10.1139/gen-2018-0063},
pmid = {30278147},
issn = {1480-3321},
mesh = {Animals ; *Biodiversity ; DNA/analysis/*genetics ; DNA Barcoding, Taxonomic/*methods ; Ecosystem ; Gabon ; Moths/*classification/*genetics ; *Tropical Climate ; },
abstract = {Biodiversity research in tropical ecosystems-popularized as the most biodiverse habitats on Earth-often neglects invertebrates, yet invertebrates represent the bulk of local species richness. Insect communities in particular remain strongly impeded by both Linnaean and Wallacean shortfalls, and identifying species often remains a formidable challenge inhibiting the use of these organisms as indicators for ecological and conservation studies. Here we use DNA barcoding as an alternative to the traditional taxonomic approach for characterizing and comparing the diversity of moth communities in two different ecosystems in Gabon. Though sampling remains very incomplete, as evidenced by the high proportion (59%) of species represented by singletons, our results reveal an outstanding diversity. With about 3500 specimens sequenced and representing 1385 BINs (Barcode Index Numbers, used as a proxy to species) in 23 families, the diversity of moths in the two sites sampled is higher than the current number of species listed for the entire country, highlighting the huge gap in biodiversity knowledge for this country. Both seasonal and spatial turnovers are strikingly high (18.3% of BINs shared between seasons, and 13.3% between sites) and draw attention to the need to account for these when running regional surveys. Our results also highlight the richness and singularity of savannah environments and emphasize the status of Central African ecosystems as hotspots of biodiversity.},
}
@article {pmid30278145,
year = {2018},
author = {Cooke, T and Kulenkampff, K and Heyns, M and Heathfield, LJ},
title = {DNA barcoding of forensically important flies in the Western Cape, South Africa.},
journal = {Genome},
volume = {61},
number = {12},
pages = {823-828},
doi = {10.1139/gen-2018-0054},
pmid = {30278145},
issn = {1480-3321},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Diptera/*classification/genetics ; *Forensic Genetics ; South Africa ; },
abstract = {Forensic entomology aids the determination of post mortem interval based on arthropods associated with a deceased body. This relies on the accurate identification of insects that visit the body, particularly first colonisers such as Calliphoridae (Diptera). Traditional species identification though morphological keys can be challenging as immature or closely related specimens can look similar. Some of these challenges have been overcome through "DNA barcoding", which involves the sequencing of informative regions within a species' DNA and comparison to a database of reference sequences. However, reference DNA sequences of blow fly species in South Africa is currently limited. In this study, adult blow flies representing four species common to the Western Cape, South Africa (Chrysomya chloropyga, Chrysomya albiceps, Chrysomya marginalis, Lucilia sericata) were examined using morphological keys and DNA barcoding of two regions: COI and ITS2. These DNA sequences were then used as references for the successful identification of seven unknown immature specimens. Intraspecific divergence showed a maximum of 0.36% and 2.25% for COI and ITS2, respectively; interspecific divergence showed a minimum of 6.14% and 64.6% for COI and ITS2, respectively. According to these results, COI and ITS2 have sufficient discriminatory power for species-level identification for the four species studied.},
}
@article {pmid30278055,
year = {2018},
author = {Pel, J and Choi, WWY and Leung, A and Shibahara, G and Gelinas, L and Despotovic, M and Ung, WL and Marziali, A},
title = {Duplex Proximity Sequencing (Pro-Seq): A method to improve DNA sequencing accuracy without the cost of molecular barcoding redundancy.},
journal = {PloS one},
volume = {13},
number = {10},
pages = {e0204265},
pmid = {30278055},
issn = {1932-6203},
mesh = {Cell Line, Tumor ; Circulating Tumor DNA/*analysis ; High-Throughput Nucleotide Sequencing/*economics ; Humans ; Liquid Biopsy/economics ; Neoplasms/*diagnosis/genetics ; Sensitivity and Specificity ; Sequence Analysis, DNA/economics ; },
abstract = {A challenge in the clinical adoption of cell-free DNA (cfDNA) liquid biopsies for cancer care is their high cost compared to potential reimbursement. The most common approach used in liquid biopsies to achieve high specificity detection of circulating tumor DNA (ctDNA) among a large background of normal cfDNA is to attach molecular barcodes to each DNA template, amplify it, and then sequence it many times to reach a low-error consensus. In applications where the highest possible specificity is required, error rate can be lowered further by independently detecting the sequences of both strands of the starting cfDNA. While effective in error reduction, the additional sequencing redundancy required by such barcoding methods can increase the cost of sequencing up to 100-fold over standard next-generation sequencing (NGS) of equivalent depth. We present a novel library construction and analysis method for NGS that achieves comparable performance to the best barcoding methods, but without the increase in sequencing and subsequent sequencing cost. Named Proximity-Sequencing (Pro-Seq), the method merges multiple copies of each template into a single sequencing read by physically linking the molecular copies so they seed a single sequencing cluster. Since multiple DNA copies of the same template are compared for consensus within the same cluster, sequencing accuracy is improved without the use of redundant reads. Additionally, it is possible to represent both senses of the starting duplex in a single cluster. The resulting workflow is simple, and can be completed by a single technician in a work day with minimal hands on time. Using both cfDNA and cell line DNA, we report the average per-mutation detection threshold and per-base analytical specificity to be 0.003% and >99.9997% respectively, demonstrating that Pro-Seq is among the highest performing liquid biopsy technologies in terms of both sensitivity and specificity, but with greatly reduced sequencing costs compared to existing methods of comparable accuracy.},
}
@article {pmid30277662,
year = {2019},
author = {Manohar, S and Shah, P and Biswas, S and Mukadam, A and Joshi, M and Viswanathan, G},
title = {Combining fluorescent cell barcoding and flow cytometry-based phospho-ERK1/2 detection at short time scales in adherent cells.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {95},
number = {2},
pages = {192-200},
doi = {10.1002/cyto.a.23602},
pmid = {30277662},
issn = {1552-4930},
mesh = {A549 Cells ; Antibodies/chemistry ; Cell Line, Tumor ; Epidermal Growth Factor/chemistry ; Flow Cytometry/methods ; Fluorescent Dyes/*chemistry ; HeLa Cells ; Humans ; MAP Kinase Signaling System/physiology ; MCF-7 Cells ; Phosphoproteins/*chemistry ; Phosphorylation/physiology ; Signal Transduction/physiology ; Staining and Labeling/methods ; },
abstract = {Detection of levels of intracellular phospho-proteins is key to analyzing the dynamics of signal transduction in cellular systems. Cell-to-cell variability in the form of differences in protein level in each cell affects signaling and is implicated in prognosis of many diseases. Quantitative analysis of such variability necessitate measuring the protein levels at single-cell resolution. Single-cell intracellular protein abundance detection in statistically significant number of adherent cells for short time sampling points post stimulation using classical flow cytometry (FCM) technique has thus far been a challenge due to the detrimental effects of cell detachment methods on the cellular machinery. We systematically show that cell suspension obtained by noninvasive temperature-sensitive detachment of adherent cells is amenable to high-throughput phospho-ERK1/2 protein detection at single-cell level using FCM in these short time sampling points. We demonstrate this on three adherent cell lines, viz., HeLa, A549, and MCF7, from distinct lineages having characteristically different elasticity at 37 °C. In particular, we use a right combination of multiplexing via fluorescent cell barcoding (FCB) and intracellular antibody staining for simultaneous detection of phospho-ERK1/2 (pERK) stimulated by epidermal growth factor (EGF) in multiple samples. Based on systematic characterization using Alexa 350 dye, we arrive at two conditions that must be satisfied for correct implementation of FCB. Our study reveals that the temperature-sensitive detachment of HeLa cells correctly captures the expected pronounced bimodal pERK distribution as an early response to EGF, which the enzymatic treatment methods fail to detect. © 2018 International Society for Advancement of Cytometry.},
}
@article {pmid30277305,
year = {2019},
author = {Jauffrais, T and LeKieffre, C and Schweizer, M and Geslin, E and Metzger, E and Bernhard, JM and Jesus, B and Filipsson, HL and Maire, O and Meibom, A},
title = {Kleptoplastidic benthic foraminifera from aphotic habitats: insights into assimilation of inorganic C, N and S studied with sub-cellular resolution.},
journal = {Environmental microbiology},
volume = {21},
number = {1},
pages = {125-141},
doi = {10.1111/1462-2920.14433},
pmid = {30277305},
issn = {1462-2920},
support = {EC2CO/LEFE project "ForChlo"//Centre National de la Recherche Scientifique/International ; //Region Pays de Loire/International ; 200021_149333/SNSF_/Swiss National Science Foundation/Switzerland ; //Universit&#xe9; d'Angers/International ; //Woods Hole Oceanographic Institution/International ; },
mesh = {Carbon/*metabolism ; Cytoplasm/metabolism ; *Ecosystem ; Foraminifera/classification/genetics/*metabolism/radiation effects ; Light ; Nitrogen/*metabolism ; Photosynthesis ; Phylogeny ; Sulfur/*metabolism ; },
abstract = {The assimilation of inorganic compounds in foraminiferal metabolism compared to predation or organic matter assimilation is unknown. Here, we investigate possible inorganic-compound assimilation in Nonionellina labradorica, a common kleptoplastidic benthic foraminifer from Arctic and North Atlantic sublittoral regions. The objectives were to identify the source of the foraminiferal kleptoplasts, assess their photosynthetic functionality in light and darkness and investigate inorganic nitrogen and sulfate assimilation. We used DNA barcoding of a ~ 830 bp fragment from the SSU rDNA to identify the kleptoplasts and correlated transmission electron microscopy and nanometre-scale secondary ion mass spectrometry (TEM-NanoSIMS) isotopic imaging to study [13] C-bicarbonate, [15] N-ammonium and [34] S-sulfate uptake. In addition, respiration rate measurements were determined to assess the response of N. labradorica to light. The DNA sequences established that over 80% of the kleptoplasts belonged to Thalassiosira (with 96%-99% identity), a cosmopolitan planktonic diatom. TEM-NanoSIMS imaging revealed degraded cytoplasm and an absence of [13] C assimilation in foraminifera exposed to light. Oxygen measurements showed higher respiration rates under light than dark conditions, and no O2 production was detected. These results indicate that the photosynthetic pathways in N. labradorica are not functional. Furthermore, N. labradorica assimilated both [15] N-ammonium and [34] S-sulfate into its cytoplasm, which suggests that foraminifera might have several ammonium or sulfate assimilation pathways, involving either the kleptoplasts or bona fide foraminiferal pathway(s) not yet identified.},
}
@article {pmid30276228,
year = {2018},
author = {Rengaiyan, P and Ingole, B},
title = {18S rDNA sequencing data of benthic polychaetes from the Eastern Arabian Sea.},
journal = {Data in brief},
volume = {20},
number = {},
pages = {1749-1752},
pmid = {30276228},
issn = {2352-3409},
abstract = {The limited DNA sequence data of the polychaetes species are available from the Eastern Arabian Sea. We have sequenced 18S rDNA gene from 54 polychaetes species and 37 species identified up to the species level. The DNA bar-coding data provides for molecular identification of benthic polychaetes that will provide imminent into drivers of species diversity in the Eastern Arabian Sea. The 18S rDNA sequence data set is made publicly available to enable critical or extended analyzes of DNA bar-coding.},
}
@article {pmid30275735,
year = {2018},
author = {Zhang, L and Wang, M and Ma, T and Liu, J},
title = {Taxonomic status of Populuswulianensis and P.ningshanica (Salicaceae).},
journal = {PhytoKeys},
volume = {},
number = {108},
pages = {117-129},
pmid = {30275735},
issn = {1314-2011},
abstract = {Species delimitation in the genus Populus is particularly challenging due to high levels of intraspecific polymorphism as well as frequent interspecific hybridisation and introgression. In this study, we aimed to examine the taxonomic status of Populusningshanica and P.wulianensis using an integrative taxonomy that considers multiple operational criteria. We carried out morphometric analyses of leaf traits and genetic examinations (including sequence variations at five barcoding DNAs and polymorphisms at 14 nuclear microsatellite SSR primers) at the population level between them and two closely related species P.adenopoda and P.davidiana. Results suggest that P.wulianensis belongs to the polymorphic species, P.adenopoda and should be considered as a synonym of the latter. P.ningshanica may have arisen as a result on the hybridisation between P.adenopoda and P.davidiana and therefore should be treated as P.×ningshanica. This study highlights the importance of the integrated evidence in taxonomic decisions of the disputed species.},
}
@article {pmid30275721,
year = {2018},
author = {Boulaassafer, K and Ghamizi, M and Delicado, D},
title = {The genus Mercuria Boeters, 1971 in Morocco: first molecular phylogeny of the genus and description of two new species (Caenogastropoda, Truncatelloidea, Hydrobiidae).},
journal = {ZooKeys},
volume = {},
number = {782},
pages = {95-128},
pmid = {30275721},
issn = {1313-2989},
abstract = {The western Palearctic freshwater snail genus Mercuria (Caenogastropoda: Hydrobiidae) comprises 26 species primarily distributed in lowland localities of Western Europe and North Africa. Although this genus in North Africa has received considerable attention in terms of species discoveries through morphological descriptions, its distribution and phylogenetic patterns remain unknown. Based on morphological and mitochondrial DNA (mtCOI) evidence, this study examines the three Mercuria species (M.bakeri, M.tingitana, and M.targouasensis) from Morocco identified so far. Besides expanding on information regarding the anatomy of these species, two new species (M.midarensis sp. n. and M.tensiftensis sp. n.) are described for this region and phylogenetic relationships inferred between these species and the European M.emiliana and M.similis. All Moroccan and European species were recovered as independent entities according to these phylogenetic inferences (uncorrected p-distances 2.8-8.5%) and DNA barcode data. Moroccan Mercuria species clustered with M.emiliana from Spain, although basal relationships within this clade were not well supported. Given that factors such as the season when specimens are collected, habitat type, and parasites could be responsible for the remarkable intraspecific variation observed in shell and penis morphology, it is proposed that the most efficient approach to delimit and identify Mercuria species is to combine morphological descriptions with genetic data.},
}
@article {pmid30271992,
year = {2018},
author = {Leasi, F and Sevigny, JL and Laflamme, EM and Artois, T and Curini-Galletti, M and de Jesus Navarrete, A and Di Domenico, M and Goetz, F and Hall, JA and Hochberg, R and Jörger, KM and Jondelius, U and Todaro, MA and Wirshing, HH and Norenburg, JL and Thomas, WK},
title = {Biodiversity estimates and ecological interpretations of meiofaunal communities are biased by the taxonomic approach.},
journal = {Communications biology},
volume = {1},
number = {},
pages = {112},
pmid = {30271992},
issn = {2399-3642},
abstract = {Accurate assessments of biodiversity are crucial to advising ecosystem-monitoring programs and understanding ecosystem function. Nevertheless, a standard operating procedure to assess biodiversity accurately and consistently has not been established. This is especially true for meiofauna, a diverse community (>20 phyla) of small benthic invertebrates that have fundamental ecological roles. Recent studies show that metabarcoding is a cost-effective and time-effective method to estimate meiofauna biodiversity, in contrast to morphological-based taxonomy. Here, we compare biodiversity assessments of a diverse meiofaunal community derived by applying multiple taxonomic methods based on comparative morphology, molecular phylogenetic analysis, DNA barcoding of individual specimens, and metabarcoding of environmental DNA. We show that biodiversity estimates are strongly biased across taxonomic methods and phyla. Such biases affect understanding of community structures and ecological interpretations. This study supports the urgency of improving aspects of environmental high-throughput sequencing and the value of taxonomists in correctly understanding biodiversity estimates.},
}
@article {pmid30271538,
year = {2018},
author = {Bylemans, J and Gleeson, DM and Hardy, CM and Furlan, E},
title = {Toward an ecoregion scale evaluation of eDNA metabarcoding primers: A case study for the freshwater fish biodiversity of the Murray-Darling Basin (Australia).},
journal = {Ecology and evolution},
volume = {8},
number = {17},
pages = {8697-8712},
pmid = {30271538},
issn = {2045-7758},
abstract = {High-throughput sequencing of environmental DNA (i.e., eDNA metabarcoding) has become an increasingly popular method for monitoring aquatic biodiversity. At present, such analyses require target-specific primers to amplify DNA barcodes from co-occurring species, and this initial amplification can introduce biases. Understanding the performance of different primers is thus recommended prior to undertaking any metabarcoding initiative. While multiple software programs are available to evaluate metabarcoding primers, all programs have their own strengths and weaknesses. Therefore, a robust in silico workflow for the evaluation of metabarcoding primers will benefit from the use of multiple programs. Furthermore, geographic differences in species biodiversity are likely to influence the performance of metabarcoding primers and further complicate the evaluation process. Here, an in silico workflow is presented that can be used to evaluate the performance of metabarcoding primers on an ecoregion scale. This workflow was used to evaluate the performance of published and newly developed eDNA metabarcoding primers for the freshwater fish biodiversity of the Murray-Darling Basin (Australia). To validate the in silico workflow, a subset of the primers, including one newly designed primer pair, were used in metabarcoding analyses of an artificial DNA community and eDNA samples. The results show that the in silico workflow allows for a robust evaluation of metabarcoding primers and can reveal important trade-offs that need to be considered when selecting the most suitable primer. Additionally, a new primer pair was described and validated that allows for more robust taxonomic assignments and is less influenced by primer biases compared to commonly used fish metabarcoding primers.},
}
@article {pmid30271241,
year = {2018},
author = {Qiao, P and Qin, W and Ma, H and Zhang, T and Su, J and Lin, G},
title = {Two new species of Lithobius on Qinghai-Tibetan plateau identified from morphology and COI sequences (Lithobiomorpha: Lithobiidae).},
journal = {ZooKeys},
volume = {},
number = {785},
pages = {11-28},
pmid = {30271241},
issn = {1313-2989},
abstract = {Lithobius (Ezembius) longibasitarsussp. n. and Lithobius (Ezembius) datongensissp. n. (Lithobiomorpha: Lithobiidae), recently discovered from Qinghai-Tibet Plateau, China, are described. A key to the species of the subgenus Ezembius in China is presented. The partial mitochondrial cytochrome c oxidase subunit I barcoding gene was amplified and sequenced for eight individuals of the two new species and the dataset was used for molecular phylogenetic analysis and genetic distance determination. Both morphology and molecular data show that the specimens examined should be referred to Lithobius (Ezembius).},
}
@article {pmid30271232,
year = {2018},
author = {Katoh, TK and Zhang, G and Toda, MJ and Suwito, A and Gao, JJ},
title = {A revision of the subgenus Dudaica Strand of the genus Drosophila Fallén, with descriptions of six new species (Diptera, Drosophilidae).},
journal = {ZooKeys},
volume = {},
number = {781},
pages = {19-50},
pmid = {30271232},
issn = {1313-2989},
abstract = {The subgenus Dudaica Strand of the genus Drosophila Fallén has been known to comprise only two species: Drosophila (Dudaica) senilis Duda, 1926 (recorded from Indonesia, Philippines, Vietnam, Bhutan, and India) and D.malayana (Takada, 1976) (recorded from Malaysia). In the present study, this subgenus is revised, with D.malayana redescribed and six new species discovered and described from China, Malaysia, and Indonesia: gracilipalpis Katoh &amp; Gao, sp. n., puberula Katoh &amp; Gao, sp. n., albipalpis Katoh, Toda &amp; Gao, sp. n., qiongzhouensis Katoh &amp; Gao, sp. n., orthophallata Katoh, Toda &amp; Gao, sp. n., and dissimilis Katoh &amp; Gao, sp. n. Both morphological and molecular data (DNA barcodes) are used to distinguish the above species. A key to species of this subgenus is provided.},
}
@article {pmid30270233,
year = {2018},
author = {Fujito, NT and Satta, Y and Hayakawa, T and Takahata, N},
title = {A new inference method for detecting an ongoing selective sweep.},
journal = {Genes &amp; genetic systems},
volume = {93},
number = {4},
pages = {149-161},
doi = {10.1266/ggs.18-00008},
pmid = {30270233},
issn = {1880-5779},
mesh = {Genome, Human ; Genome-Wide Association Study/*methods/standards ; Humans ; Linkage Disequilibrium ; *Models, Genetic ; Polymorphism, Single Nucleotide ; *Selection, Genetic ; Sensitivity and Specificity ; Sialyltransferases/genetics ; },
abstract = {A simple method was developed to detect signatures of ongoing selective sweeps in single nucleotide polymorphism (SNP) data. Based largely on the traditional site frequency spectrum (SFS), the method additionally incorporates linkage disequilibrium (LD) between pairs of SNP sites and uniquely represents both SFS and LD information as hierarchical "barcodes." This barcode representation allows the identification of a hitchhiking genomic region surrounding a putative target site of positive selection, or a core site. Sweep signals at linked neutral sites are then measured by the proportion (Fc) of derived alleles within the hitchhiking region that are linked in the derived allele group defined at the core site. In measuring Fc or intra-allelic variability in an informative way, certain conditions for derived allele frequencies are required, as illustrated with the human ST8SIA2 locus. Coalescent simulators with and without positive selection are used to assess the false-positive and false-negative rates of the Fc statistic. To demonstrate its power, the method was further applied to the LCT, OCA2, EDAR, SLC24A5 and ASPM loci, which are known to have undergone positive selection in human populations. Overall, the method is powerful and can be used to identify core sites responsible for ongoing selective sweeps.},
}
@article {pmid30269696,
year = {2019},
author = {Lawrence, AL and Batovska, J and Webb, CE and Lynch, SE and Blacket, MJ and Šlapeta, J and Parola, P and Laroche, M},
title = {Accurate identification of Australian mosquitoes using protein profiling.},
journal = {Parasitology},
volume = {146},
number = {4},
pages = {462-471},
doi = {10.1017/S0031182018001658},
pmid = {30269696},
issn = {1469-8161},
mesh = {Animals ; Australia ; Culicidae/classification/*genetics ; Electron Transport Complex IV/*analysis ; Insect Proteins/*analysis ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; },
abstract = {Australian mosquito species significantly impact human health through nuisance biting and the transmission of endemic and exotic pathogens. Surveillance programmes designed to provide an early warning of mosquito-borne disease risk require reliable identification of mosquitoes. This study aimed to investigate the viability of Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) as a rapid and inexpensive approach to the identification of Australian mosquitoes and was validated using a three-step taxonomic approach. A total of 300 mosquitoes representing 21 species were collected from south-eastern New South Wales and morphologically identified. The legs from the mosquitoes were removed and subjected to MALDI-TOF MS analysis. Fifty-eight mosquitoes were sequenced at the cytochrome c oxidase subunit I (cox1) gene region and genetic relationships were analysed. We create the first MALDI-TOF MS spectra database of Australian mosquito species including 19 species. We clearly demonstrate the accuracy of MALDI-TOF MS for identification of Australian mosquitoes. It is especially useful for assessing gaps in the effectiveness of DNA barcoding by differentiating closely related taxa. Indeed, cox1 DNA barcoding was not able to differentiate members of the Culex pipiens group, Cx. quinquefasciatus and Cx. pipiens molestus, but these specimens were correctly identified using MALDI-TOF MS.},
}
@article {pmid30268455,
year = {2018},
author = {Sim, WC and Loh, CH and Toh, GL and Lim, CW and Chopra, A and Chang, AYC and Goh, LL},
title = {Non-invasive detection of actionable mutations in advanced non-small-cell lung cancer using targeted sequencing of circulating tumor DNA.},
journal = {Lung cancer (Amsterdam, Netherlands)},
volume = {124},
number = {},
pages = {154-159},
doi = {10.1016/j.lungcan.2018.08.007},
pmid = {30268455},
issn = {1872-8332},
mesh = {Aged ; Aged, 80 and over ; Antineoplastic Agents/*therapeutic use ; Carcinoma, Non-Small-Cell Lung/*diagnosis/drug therapy/genetics ; Circulating Tumor DNA/*analysis ; Drug Resistance, Neoplasm/genetics ; ErbB Receptors/genetics ; Feasibility Studies ; Female ; Humans ; Lung Neoplasms/*diagnosis/drug therapy/*genetics ; Male ; Middle Aged ; Mutation/genetics ; Pathology, Molecular ; Practice Guidelines as Topic ; Protein Kinase Inhibitors/*therapeutic use ; Proto-Oncogene Proteins B-raf/genetics ; Receptor, ErbB-2/genetics ; Sequence Analysis, DNA ; },
abstract = {OBJECTIVE: To evaluate the feasibility of detecting actionable gene mutations in circulating tumor DNA (ctDNA) in patients with advanced non-small-cell lung cancer (NSCLC) using targeted next-generation sequencing (NGS).<br><br>MATERIALS AND METHODS: In total 50 plasma samples from patients newly diagnosed with advanced NSCLC or resistant to first-line tyrosine kinase inhibitors (TKIs) were subjected to deep sequencing on a seven-gene panel (BRAF, EGFR, ERBB2, KRAS, NRAS, PIK3CA, PTEN) incorporated with molecular barcodes to improve accuracy in variant detection. When possible, results were compared with those from matched tissue samples.<br><br>RESULTS: At least one alteration in the ctDNA was detected in 44 out of 50 patients (88%); EGFR was the most frequently mutated gene. Half the total number of patients (50%, 25 of 50) had at least one actionable genetic alteration with targeted therapies available for treatment. Our results showed a high concordance rate of 81% in detection of EGFR mutation between 26 matched tissue and plasma samples. For progressive patients, from whom tissue is mostly unavailable, the resistant EGFR T790&#x2009;M mutation was validated using the droplet digital polymerase chain reaction (ddPCR), yielding a concordance of 92% between alternative platforms.<br><br>CONCLUSION: Our study demonstrated that therapeutically actionable mutations can be detected with high accuracy in ctDNA using NGS. This promising approach offers alternative and non-invasive diagnostic methods for treatment guidance and clinical monitoring.},
}
@article {pmid30266791,
year = {2018},
author = {Cira, NJ and Pearce, MT and Quake, SR},
title = {Neutral and selective dynamics in a synthetic microbial community.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {42},
pages = {E9842-E9848},
pmid = {30266791},
issn = {1091-6490},
mesh = {*Biodiversity ; *Ecosystem ; Microbial Consortia/*physiology ; *Models, Theoretical ; *Population Dynamics ; Species Specificity ; },
abstract = {Ecologists debate the relative importance of selective vs. neutral processes in understanding biodiversity. This debate is especially pertinent to microbial communities, which play crucial roles in areas such as health, disease, industry, and the environment. Here, we created a synthetic microbial community using heritable genetic barcodes and tracked community composition over repeated rounds of subculture with immigration. Consistent with theory, we find a transition exists between neutral and selective regimes, and the crossover point depends on the fraction of immigrants and the magnitude of fitness differences. Neutral models predict an increase in diversity with increased carrying capacity, while our selective model predicts a decrease in diversity. The community here lost diversity with an increase in carrying capacity, highlighting that using the correct model is essential for predicting community response to change. Together, these results emphasize the importance of including selection to obtain realistic models of even simple systems.},
}
@article {pmid30264284,
year = {2019},
author = {Azevedo Portilho, N and Kobayashi, M and Yoshimoto, M},
title = {What do the lineage tracing studies tell us? Consideration for hematopoietic stem cell origin, dynamics, and leukemia-initiating cells.},
journal = {International journal of hematology},
volume = {109},
number = {1},
pages = {35-40},
pmid = {30264284},
issn = {1865-3774},
support = {R01 AI121197/AI/NIAID NIH HHS/United States ; R01AI121197//National Institute of Allergy and Infectious Diseases/ ; },
mesh = {Animals ; Carcinogenesis/*pathology ; *Cell Lineage ; Embryo, Mammalian/cytology/embryology ; Hematopoiesis ; Hematopoietic Stem Cells/*cytology ; Humans ; Leukemia/pathology ; Mice/embryology ; },
abstract = {The recent advance of technologies enables us to trace the cell fate in vivo by marking the cells that express the gene of interest or by barcoding them at a single cell level. Various tamoxifen-inducible Cre-recombinase mice combined with Rosa-floxed lines are utilized. In this review, with the results revealed by lineage tracing assays, we re-visit the long-standing debate for the origin of hematopoietic stem cells in the mouse embryo, and introduce the view of native hematopoiesis, and possible leukemic-initiating cells emerged during fetal stages.},
}
@article {pmid30261656,
year = {2018},
author = {Gong, S and Ding, Y and Wang, Y and Jiang, G and Zhu, C},
title = {Advances in DNA Barcoding of Toxic Marine Organisms.},
journal = {International journal of molecular sciences},
volume = {19},
number = {10},
pages = {},
pmid = {30261656},
issn = {1422-0067},
mesh = {Animals ; Aquatic Organisms/classification/*genetics ; Cnidaria/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; Diatoms/classification/genetics ; Dinoflagellida/classification/*genetics ; Mollusca/classification/genetics ; Reproducibility of Results ; Species Specificity ; Tetraodontiformes/classification/*genetics ; },
abstract = {There are more than 200,000 marine species worldwide. These include many important economic species, such as large yellow croaker, ribbonfish, tuna, and salmon, but also many potentially toxic species, such as blue-green algae, diatoms, cnidarians, ctenophores, Nassarius spp., and pufferfish. However, some edible and toxic species may look similar, and the correct identification of marine species is thus a major issue. The failure of traditional classification methods in certain species has promoted the use of DNA barcoding, which uses short, standard DNA fragments to assist with species identification. In this review, we summarize recent advances in DNA barcoding of toxic marine species such as jellyfish and pufferfish, using genes including cytochrome oxidase I gene (COI), cytochrome b gene (cytb), 16S rDNA, internal transcribed spacer (ITS), and Ribulose-1,5-bisphosphate carboxylase oxygenase gene (rbcL). We also discuss the application of this technique for improving the identification of marine species. The use of DNA barcoding can benefit the studies of biological diversity, biogeography, food safety, and the detection of both invasive and new species. However, the technique has limitations, particularly for the analysis of complex objects and the selection of standard DNA barcodes. The development of high-throughput methods may offer solutions to some of these issues.},
}
@article {pmid30258563,
year = {2018},
author = {Jamieson, LE and Wetherill, C and Faulds, K and Graham, D},
title = {Ratiometric Raman imaging reveals the new anti-cancer potential of lipid targeting drugs.},
journal = {Chemical science},
volume = {9},
number = {34},
pages = {6935-6943},
pmid = {30258563},
issn = {2041-6520},
abstract = {De novo lipid synthesis is upregulated in cancer cells and inhibiting these pathways has displayed anti-tumour activity. Here we use Raman spectroscopy, focusing solely on high wavenumber spectra, to detect changes in lipid composition in single cells in response to drugs targeting de novo lipid synthesis. Unexpectedly, the beta-blocker propranolol showed selectively towards cancerous PC3 compared to non-cancerous PNT2 prostate cells, demonstrating the potential of this approach to identify new anti-cancer drug leads. A unique and simple ratiometric approach for intracellular lipid investigation is reported using statistical analysis to create phenotypic 'barcodes', a globally applicable strategy for Raman drug-cell studies. High wavenumber spectral analysis is compatible with low cost glass substrates, easily translatable into the cytological work stream. The analytical strength of this technique could have a significant impact on cancer treatment through vastly improved understanding of cancer cell metabolism, and thus guide drug design and enhance personalised medicine strategies.},
}
@article {pmid30258176,
year = {2018},
author = {Han, G and Spitzer, MH and Bendall, SC and Fantl, WJ and Nolan, GP},
title = {Metal-isotope-tagged monoclonal antibodies for high-dimensional mass cytometry.},
journal = {Nature protocols},
volume = {13},
number = {10},
pages = {2121-2148},
pmid = {30258176},
issn = {1750-2799},
support = {1U19AI100627/NH/NIH HHS/United States ; R33 CA183654/CA/NCI NIH HHS/United States ; R33 CA183654/NH/NIH HHS/United States ; N01-HV-00242/NH/NIH HHS/United States ; U19 AI057229/AI/NIAID NIH HHS/United States ; U19 AI100627/AI/NIAID NIH HHS/United States ; R01CA184968/NH/NIH HHS/United States ; U19 AI057229/NH/NIH HHS/United States ; R33 CA183692/CA/NCI NIH HHS/United States ; R01 CA184968/CA/NCI NIH HHS/United States ; R33 CA183692/NH/NIH HHS/United States ; },
mesh = {Animals ; Antibodies, Monoclonal/*chemistry ; Antigens, CD/analysis ; Bismuth/chemistry ; Chelating Agents/chemistry ; Flow Cytometry/*methods ; Heterocyclic Compounds, 1-Ring/*chemistry ; Humans ; Immunoassay/methods ; Immunoconjugates/*chemistry ; Immunoglobulin G/chemistry ; Indium/chemistry ; Isotopes/chemistry ; Jurkat Cells ; Metals/*chemistry ; Mice, Inbred C57BL ; Palladium/chemistry ; Yttrium/chemistry ; },
abstract = {Advances in single-cell mass cytometry have increasingly improved highly multidimensional characterization of immune cell heterogeneity. The immunoassay multiplexing capacity relies on monoclonal antibodies labeled with stable heavy-metal isotopes. To date, a variety of rare-earth elements and noble and post-transition metal isotopes have been used in mass cytometry; nevertheless, the methods used for antibody conjugation differ because of the individual metal coordination chemistries and distinct stabilities of various metal cations. Herein, we provide three optimized protocols for conjugating monoclonal IgG antibodies with 48 high-purity heavy-metal isotopes: (i) 38 isotopes of lanthanides, 2 isotopes of indium, and 1 isotope of yttrium; (ii) 6 isotopes of palladium; and (iii) 1 isotope of bismuth. Bifunctional chelating agents containing coordinative ligands of monomeric DOTA (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) or polymeric pentetic acid (DTPA) were used to stably sequester isotopic cations in aqueous solutions and were subsequently coupled to IgG antibodies using site-specific biorthogonal reactions. Furthermore, quantification methods based on antibody inherent absorption at 280 nm and on extrinsic absorption at 562 nm after staining with bicinchoninic acid (BCA) are reported to determine metal-isotope-tagged antibodies. In addition, a freeze-drying procedure to prepare palladium isotopic mass tags is described. To demonstrate the utility, experiments using six palladium-tagged CD45 antibodies for barcoding assays of live immune cells in cytometry by time-of-flight (CyTOF) are described. Conjugation of pure isotopes of lanthanides, indium, or yttrium takes ~3.5 h. Conjugation of bismuth takes ~4 h. Preparation of palladium mass tags takes ~8 h. Conjugation of pure isotopes of palladium takes ~2.5 h. Antibody titration takes ~4 h.},
}
@article {pmid30257096,
year = {2019},
author = {deWaard, JR and Levesque-Beaudin, V and deWaard, SL and Ivanova, NV and McKeown, JTA and Miskie, R and Naik, S and Perez, KHJ and Ratnasingham, S and Sobel, CN and Sones, JE and Steinke, C and Telfer, AC and Young, AD and Young, MR and Zakharov, EV and Hebert, PDN},
title = {Expedited assessment of terrestrial arthropod diversity by coupling Malaise traps with DNA barcoding [1].},
journal = {Genome},
volume = {62},
number = {3},
pages = {85-95},
doi = {10.1139/gen-2018-0093},
pmid = {30257096},
issn = {1480-3321},
mesh = {Animals ; Arthropods/*classification/*genetics ; *Biodiversity ; DNA/analysis/*genetics ; DNA Barcoding, Taxonomic/*methods ; Entomology/*instrumentation ; Phylogeny ; Species Specificity ; },
abstract = {Monitoring changes in terrestrial arthropod communities over space and time requires a dramatic increase in the speed and accuracy of processing samples that cannot be achieved with morphological approaches. The combination of DNA barcoding and Malaise traps allows expedited, comprehensive inventories of species abundance whose cost will rapidly decline as high-throughput sequencing technologies advance. Aside from detailing protocols from specimen sorting to data release, this paper describes their use in a survey of arthropod diversity in a national park that examined 21 194 specimens representing 2255 species. These protocols can support arthropod monitoring programs at regional, national, and continental scales.},
}
@article {pmid30256981,
year = {2019},
author = {Ranu, N and Villani, AC and Hacohen, N and Blainey, PC},
title = {Targeting individual cells by barcode in pooled sequence libraries.},
journal = {Nucleic acids research},
volume = {47},
number = {1},
pages = {e4},
pmid = {30256981},
issn = {1362-4962},
support = {RM1 HG006193/HG/NHGRI NIH HHS/United States ; U24 AI118668/AI/NIAID NIH HHS/United States ; },
mesh = {Blood Cells/classification ; Cell Lineage/genetics ; DNA/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Leukocytes, Mononuclear/cytology ; Multiplex Polymerase Chain Reaction/*methods ; Single-Cell Analysis/methods ; },
abstract = {Transcriptional profiling of thousands of single cells in parallel by RNA-seq is now routine. However, due to reliance on pooled library preparation, targeting analysis to particular cells of interest is difficult. Here, we present a multiplexed PCR method for targeted sequencing of select cells from pooled single-cell sequence libraries. We demonstrated this molecular enrichment method on multiple cell types within pooled single-cell RNA-seq libraries produced from primary human blood cells. We show how molecular enrichment can be combined with FACS to efficiently target ultra-rare cell types, such as the recently identified AXL+SIGLEC6+ dendritic cell (AS DC) subset, in order to reduce the required sequencing effort to profile single cells by 100-fold. Our results demonstrate that DNA barcodes identifying cells within pooled sequencing libraries can be used as targets to enrich for specific molecules of interest, for example reads from a set of target cells.},
}
@article {pmid30256803,
year = {2018},
author = {Landschoff, J and Komai, T and du Plessis, A and Gouws, G and Griffiths, CL},
title = {MicroCT imaging applied to description of a new species of Pagurus Fabricius, 1775 (Crustacea: Decapoda: Anomura: Paguridae), with selection of three-dimensional type data.},
journal = {PloS one},
volume = {13},
number = {9},
pages = {e0203107},
pmid = {30256803},
issn = {1932-6203},
mesh = {Animals ; Anomura/*anatomy &amp; histology/*classification/genetics ; DNA Barcoding, Taxonomic ; Databases, Factual ; Female ; Imaging, Three-Dimensional/methods ; Internet ; Male ; Photography ; South Africa ; Species Specificity ; *X-Ray Microtomography/methods ; },
abstract = {A new species of hermit crab, Pagurus fraserorum n. sp. (family Paguridae) is described from rocky subtidal reefs off KwaZulu-Natal, South Africa, and illustrated using both conventional drawings and colour photographs, and via three-dimensional (3D) X-ray micro-computed tomography (μCT). Because of the limitation μCT has in detecting very fine and soft structures, a novel approach of manually drawing setation and spinulation onto the two-dimensional images of the 3D visualizations was used to illustrate the pereopods. In addition, an interactive figure and rotation movie clips in the supplement section complement the species description, and the 3D raw data of the 3D type data are downloadable from the Gigascience Database repository. The new species is the sixth species of Pagurus Fabricius, 1775 reported from South Africa and is closely allied to the Indo-Pacific P. boriaustraliensis Morgen, 1990 and P. pitagsaleei McLaughlin, 2002, from which it differs by its shorter ocular peduncles, by the armature of the carpus of the right cheliped, and also in colouration. This study presents the first description of a hermit crab in which a majority of taxonomic details are illustrated through 3D volume-rendered illustrations. In addition, colour photographs and COI molecular barcodes are provided, and the latter compared to COI sequences of specimens from Western Australia previously identified as P. boriaustraliensis and of specimens of P. pitagsaleei from Taiwan, as well as to three additional South African members of the genus. The South African taxon was confirmed to be genetically distinct from all species tested.},
}
@article {pmid30254661,
year = {2018},
author = {Wang, A and Wu, H and Zhu, X and Lin, J},
title = {Species Identification of Conyza bonariensis Assisted by Chloroplast Genome Sequencing.},
journal = {Frontiers in genetics},
volume = {9},
number = {},
pages = {374},
pmid = {30254661},
issn = {1664-8021},
abstract = {Flaxleaf fleabane (Conyza bonariensis [L.] Cronquist) is one of the most difficult weeds to control worldwide. There are more than 150 Conyza species in the world and eight species in Australia. Correct identification of these species can be problematic due to their morphological similarities especially at seedling stage. Developing a robust genetics - based species identification method to distinguish C. bonariensis from other closely related species is important for early control of weeds. We thus examined the chloroplast (cp) genome of C. bonariensis, aiming to identify novel DNA barcodes from the genome sequences, and use the entire cp genome as a super-barcode for molecular identification. The C. bonariensis chloroplast genome is 152,076 bp in size, encodes 133 genes including 88 protein-coding genes, 37 tRNA genes and 8 ribosomal RNA genes. A total of 151 intergenic regions and 19 simple sequence repeats were identified in the cp genome of C. bonariensis, which provides a useful genetic resource to develop robust markers for the genetic diversity studies of Conyza species. The sequence information was used to design a robust DNA barcode rps16 and trnQ-UUG which successfully separated three predominant Conyza species (C. bonariensis, C. canadensis, and C. sumatrensis). Phylogenetic analyses based on the cp genomes of C. bonariensis, C. canadensis and 18 other Asteraceae species revealed the potential of using entire cp genome as a plant super-barcode to distinguish closely-related weed species.},
}
@article {pmid30253789,
year = {2018},
author = {Gaj, T and Perez-Pinera, P},
title = {The continuously evolving CRISPR barcoding toolbox.},
journal = {Genome biology},
volume = {19},
number = {1},
pages = {143},
pmid = {30253789},
issn = {1474-760X},
mesh = {Animals ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; },
abstract = {Two articles recently described the development of CRISPR technologies that have the potential to fundamentally transform the barcoding and tracing of mammalian cells.},
}
@article {pmid30252979,
year = {2018},
author = {Abdelkrim, J and Aznar-Cormano, L and Buge, B and Fedosov, A and Kantor, Y and Zaharias, P and Puillandre, N},
title = {Delimiting species of marine gastropods (Turridae, Conoidea) using RAD sequencing in an integrative taxonomy framework.},
journal = {Molecular ecology},
volume = {27},
number = {22},
pages = {4591-4611},
doi = {10.1111/mec.14882},
pmid = {30252979},
issn = {1365-294X},
mesh = {Animal Shells ; Animals ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Gastropoda/*classification ; *Genetic Speciation ; Indian Ocean ; Likelihood Functions ; Pacific Ocean ; *Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {Species delimitation in poorly known and diverse taxa is usually performed based on monolocus, DNA-barcoding-like approaches, while multilocus data are often used to test alternative species hypotheses in well-studied groups. We combined both approaches to delimit species in the Xenuroturris/Iotyrris complex, a group of venomous marine gastropods from the Indo-Pacific. First, COI sequences were analysed using three methods of species delimitation to propose primary species hypotheses. Second, RAD sequencing data were also obtained and a maximum-likelihood phylogenetic tree produced. We tested the impact of the level of missing data on the robustness of the phylogenetic tree obtained with the RAD-seq data. Alternative species partitions revealed with the COI data set were also tested using the RAD-seq data and the Bayes factor species delimitation method. The congruence between the species hypotheses proposed with the mitochondrial nuclear data sets, together with the morphological variability of the shell and the radula and the distribution pattern, was used to turn the primary species hypotheses into secondary species hypotheses. Allopatric primary species hypotheses defined with the COI gene were interpreted to correspond to intraspecific structure. Most of the species are found sympatrically in the Philippines, and only one is confidently identified as a new species and described as Iotyrris conotaxis n. sp. The results obtained demonstrate the efficiency of the combined monolocus/multilocus approach to delimit species.},
}
@article {pmid30250036,
year = {2018},
author = {Jin, Q and Hu, XM and Han, HL and Chen, F and Cai, WJ and Ruan, QQ and Liu, B and Luo, GJ and Wang, H and Liu, X and Ward, RD and Wu, CS and Wilson, JJ and Zhang, AB},
title = {A two-step DNA barcoding approach for delimiting moth species: moths of Dongling Mountain (Beijing, China) as a case study.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {14256},
pmid = {30250036},
issn = {2045-2322},
mesh = {Animals ; Bayes Theorem ; *Biodiversity ; China ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*genetics ; Moths/*genetics ; Phylogeography ; Species Specificity ; },
abstract = {DNA barcoding, based on a fragment of cytochrome c oxidase I (COI) mtDNA, is as an effective molecular tool for identification, discovery, and biodiversity assessment for most animals. However, multiple gene markers coupled with more sophisticated analytical approaches may be necessary to clarify species boundaries in cases of cryptic diversity or morphological plasticity. Using 339 moths collected from mountains surrounding Beijing, China, we tested a pipeline consisting of two steps: (1) rapid morphospecies sorting and screening of the investigated fauna with standard COI barcoding approaches; (2) additional analyses with multiple molecular markers for those specimens whose morphospecies and COI barcode grouping were incongruent. In step 1, 124 morphospecies were delimited into 116 barcode units, with 90% of the conflicts being associated with specimens identified to the genus Hypena. In step 2, 55 individuals representing all 12 Hypena morphospecies were analysed using COI, COII, 28S, EF-1a, Wgl sequences or their combinations with the BPP (Bayesian Phylogenetics and Phylogeography) multigene species delimitation method. The multigene analyses supported the delimitation of 5 species, consistent with the COI analysis. We conclude that a two-step barcoding analysis pipeline is able to rapidly characterize insect biodiversity and help to elucidate species boundaries for taxonomic complexes without jeopardizing overall project efficiency by substantially increasing analytical costs.},
}
@article {pmid30240145,
year = {2019},
author = {Wurzbacher, C and Larsson, E and Bengtsson-Palme, J and Van den Wyngaert, S and Svantesson, S and Kristiansson, E and Kagami, M and Nilsson, RH},
title = {Introducing ribosomal tandem repeat barcoding for fungi.},
journal = {Molecular ecology resources},
volume = {19},
number = {1},
pages = {118-127},
doi = {10.1111/1755-0998.12944},
pmid = {30240145},
issn = {1755-0998},
support = {//Stiftelsen Lars Hiertas Minne/ ; //Stiftelsen Olle Engkvist Byggm&#xe4;stare/ ; //Kapten Carl Stenholms Donationsfond/ ; //Birgit och Birger W&#xe5;lhstr&#xf6;ms Minnesfond/ ; //The Swedish Taxonomy Initiative/ ; //Deutsche Forschungsgemeinschaft/ ; //Japan Society for the Promotion of Science/ ; },
mesh = {Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/*genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Fungi/*classification/*genetics ; *Genes, rRNA ; High-Throughput Nucleotide Sequencing ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 5.8S/genetics ; Sequence Analysis, DNA ; *Tandem Repeat Sequences ; },
abstract = {Sequence comparison and analysis of the various ribosomal genetic markers are the dominant molecular methods for identification and description of fungi. However, new environmental fungal lineages known only from DNA data reveal significant gaps in our sampling of the fungal kingdom in terms of both taxonomy and marker coverage in the reference sequence databases. To facilitate the integration of reference data from all of the ribosomal markers, we present three sets of general primers that allow for amplification of the complete ribosomal operon from the ribosomal tandem repeats. The primers cover all ribosomal markers: ETS, SSU, ITS1, 5.8S, ITS2, LSU and IGS. We coupled these primers successfully with third-generation sequencing (PacBio and Nanopore sequencing) to showcase our approach on authentic fungal herbarium specimens (Basidiomycota), aquatic chytrids (Chytridiomycota) and a poorly understood lineage of early diverging fungi (Nephridiophagidae). In particular, we were able to generate high-quality reference data with Nanopore sequencing in a high-throughput manner, showing that the generation of reference data can be achieved on a regular desktop computer without the involvement of any large-scale sequencing facility. The quality of the Nanopore generated sequences was 99.85%, which is comparable with the 99.78% accuracy described for Sanger sequencing. With this work, we hope to stimulate the generation of a new comprehensive standard of ribosomal reference data with the ultimate aim to close the huge gaps in our reference datasets.},
}
@article {pmid30239330,
year = {2018},
author = {Sarfraz, S and Riaz, K and Oulghazi, S and Cigna, J and Sahi, ST and Khan, SH and Faure, D},
title = {Pectobacterium punjabense sp. nov., isolated from blackleg symptoms of potato plants in Pakistan.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {68},
number = {11},
pages = {3551-3556},
doi = {10.1099/ijsem.0.003029},
pmid = {30239330},
issn = {1466-5034},
mesh = {Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Genes, Bacterial ; Multilocus Sequence Typing ; Nucleic Acid Hybridization ; Pakistan ; Pectobacterium/*classification/genetics/isolation &amp; purification ; *Phylogeny ; Plant Diseases/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Solanum tuberosum/*microbiology ; },
abstract = {Pectobacterium isolates SS95[T], SS54 and SS56 were collected from a potato field in the Chiniot district in the plains of the Punjab province, Pakistan. Sequencing of the gapA barcode revealed that these strains belong to a novel phylogenetic group separated from P.ectobacterium wasabiae and Pectobacterium parmentieri species. Furthermore, multilocus sequence analyses of 13 housekeeping genes (fusA, rpoD, acnA, purA, gyrB, recA, mdh, mtlD, groEL, secY, glyA, gapA and rplB) clearly distinguished the type strain, SS95[T], from its closest relatives, i.e. P. parmentieri RNS 08-42-1A[T] and P. wasabiae CFBP3304[T], as well as from all the other known Pectobacteriumspecies. In silico DNA-DNA hybridization (<44.1 %) and average nucleotide identity (<90.75 %) values of strain SS95[T] compared with other Pectobacterium type strains supported the delineation of a new species. Genomic and phenotypic comparisons permitted the identification of additional traits that distinguished the Pakistani isolates from all other known Pectobacterium type strains. The name Pectobacterium punjabense sp. nov. is proposed for this taxon with the type strain SS95[T] (=CFBP 8604[T]=LMG 30622[T]).},
}
@article {pmid30235400,
year = {2018},
author = {Lima, RAF and Oliveira, AA and Colletta, GD and Flores, TB and Coelho, RLG and Dias, P and Frey, GP and Iribar, A and Rodrigues, RR and Souza, VC and Chave, J},
title = {Can plant DNA barcoding be implemented in species-rich tropical regions? A perspective from São Paulo State, Brazil.},
journal = {Genetics and molecular biology},
volume = {41},
number = {3},
pages = {661-670},
pmid = {30235400},
issn = {1415-4757},
abstract = {DNA barcoding helps to identify species, especially when identification is based on parts of organisms or life stages such as seeds, pollen, wood, roots or juveniles. However, the implementation of this approach strongly depends on the existence of complete reference libraries of DNA sequences. If such a library is incomplete, DNA-based identification will be inefficient. Here, we assess if DNA barcoding can already be implemented in species-rich tropical regions. We focus on the tree flora of São Paulo state, Brazil, which contains more than 2000 tree species. Using new DNA sequence data and carefully assembled GenBank accessions, we assembled 12,113 sequences from ten different regions. The ITS, rbcL, psbA-trnH, matK and trnL regions were better represented within the available sequences for São Paulo tree flora. Currently, only 58% of the São Paulo tree flora currently have at least one barcoding sequence available. However, these species represent on average 89% of the trees in São Paulo state forests. Therefore, conservation-oriented and ecological studies can already benefit from DNA barcoding to obtain more accurate species identifications. We present which taxa remain underrepresented for the São Paulo tree flora and discuss the implications of this result for other species-rich tropical regions.},
}
@article {pmid30233373,
year = {2018},
author = {Rasheed, H and Höllein, L and Holzgrabe, U},
title = {Future Information Technology Tools for Fighting Substandard and Falsified Medicines in Low- and Middle-Income Countries.},
journal = {Frontiers in pharmacology},
volume = {9},
number = {},
pages = {995},
pmid = {30233373},
issn = {1663-9812},
abstract = {Substandard and falsified (SF) medicines have emerged as a global public health issue within the last two decades especially in low- and middle-income countries (LMICs). Serious consequences of this problem include a loss of trust and increased financial costs due to less disease control and more frequent complications during therapy. Of note, antimicrobial resistance is an additional long-term implication of poor-quality antimicrobials. This review covers information technology tools including medicines authentication tools (MAT) as mobile apps and messaging service, 2D barcoding approaches with drug safety alert systems, web based drug safety alerts, radiofrequency identification tags, databases to support visual inspection, digital aids to enhance the performance of quality evaluation kits, reference libraries for identification of falsified and substandard medicines, and quality evaluation kits based on machine learning for field testing. While being easy to access and simple to use, these initiatives are gaining acceptance in LMICs. Implementing 2D barcoding based on end-to-end verification and "Track and Trace" systems has emerged as a step toward global security in the supply chain. A breakthrough in web-based drug safety alert systems and data bases was the establishment of the Global Surveillance and Monitoring System by the World Health Organization in 2013. Future applications include concepts including "lab on a chip" and "paper analytical devices" and are claimed to be convenient and simple to use as well as affordable. The principles discussed herein are making profound impact in the fight against substandard and falsified medicines, offering cheap and accessible solutions.},
}
@article {pmid30232720,
year = {2018},
author = {Glowska, E and Romanowska, K and Schmidt, BK and Dabert, M},
title = {Combined description (morphology with DNA barcode data) of a new quill mite Torotrogla paenae n. sp. (Acariformes: Syringophilidae) parasitising the Kalahari scrub-robin Cercotrichas paena (Smith) (Passeriformes: Muscicapidae) in Namibia.},
journal = {Systematic parasitology},
volume = {95},
number = {8-9},
pages = {863-869},
pmid = {30232720},
issn = {1573-5192},
support = {2014/15/B/NZ8/00208//National Science Centre of Poland/International ; 2015/19/D/NZ8/00191//National Science Centre of Poland/International ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Mites/anatomy &amp; histology/*classification/genetics ; Namibia ; Passeriformes/*parasitology ; Species Specificity ; },
abstract = {A new quill mite species Torotrogla paenae n. sp. (Acariformes: Syringophilidae) parasitising the Kalahari scrub-robin Cercotrichas paena (Smith) (Passeriformes: Muscicapidae) in Namibia is described based on the external morphology and DNA barcode data (the mitochondrial cytochrome c oxidase subunit 1 sequences, cox1). Females of T. paenae n. sp. morphologically differ from the most similar species T. lusciniae Skoracki, 2004 by the total body length (780-830 vs 645-715 µm in T. lusciniae) and the presence of hysteronotal shields (vs absence), apunctate propodonotal and pygidial shields (vs punctate), apunctate coxal fields (vs punctate), the fan-like setae p' and p" of legs III-IV provided with c.10 tines (vs 14-15) and the length of setae si (140-180 vs 190-210 µm) and se (160-185 vs 210-225 µm). The male of T. paenae n. sp. morphologically differs from T. lusciniae by the lateral branch of peritremes composed of 4 chambers (vs 7-8 chambers) and lengths of setae ve (45 vs 70-75 µm) and se (120 vs 165 µm).},
}
@article {pmid30230969,
year = {2018},
author = {Salas-Lizana, R and Oono, R},
title = {A comparative analysis of Lophodermium fissuratum, sp. nov., found in haploxylon pine needles in the Pacific Northwest, and other Lophodermium endophytes.},
journal = {Mycologia},
volume = {110},
number = {5},
pages = {797-810},
doi = {10.1080/00275514.2018.1499991},
pmid = {30230969},
issn = {1557-2536},
mesh = {Ascomycota/*classification/cytology/genetics/*isolation &amp; purification ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Endophytes/*classification/cytology/genetics/*isolation &amp; purification ; Microscopy ; Northwestern United States ; *Phylogeny ; Pinus/*microbiology ; Plant Leaves/microbiology ; RNA, Ribosomal, 28S/genetics ; RNA, Ribosomal, 5.8S/genetics ; Sequence Analysis, DNA ; Spores, Fungal/cytology/growth &amp; development ; },
abstract = {Lophodermium is a large fungal genus consisting of over 100 named species, with ca. 38 of these commonly found as endophytes of pine needles. In this study, we use both morphological and sequencing data to describe a new Lophodermium species associated with haploxylon pines from the Pacific Northwest. This new species resembled the morphology of L. nitens, another commonly occurring species from the same geographic regions and host species. They both present dark subcuticular ascocarps without lips. However, the upper walls of their ascocarps are different, as the new species forms an inward V-shaped folding, not present in L. nitens. Phylogenies using nuc rDNA internal transcribed spacer barcodes (ITS1-5.8S-ITS2 = ITS), partial D1-D2 domains of nuc rDNA 28S, and partial sequences of the nuc actin gene confirmed that this species represents a unique lineage not closely related to L. nitens. We discuss the current state of the phylogeny in light of all currently available sequences from pine-associated Lophodermium species.},
}
@article {pmid30227932,
year = {2018},
author = {Seena, S and Marvanová, L and Letourneau, A and Bärlocher, F},
title = {Articulospora - Phylogeny vs morphology.},
journal = {Fungal biology},
volume = {122},
number = {10},
pages = {965-976},
doi = {10.1016/j.funbio.2018.06.001},
pmid = {30227932},
issn = {1878-6146},
mesh = {Ascomycota/*classification/*cytology/genetics ; DNA, Fungal ; DNA, Ribosomal Spacer/genetics ; Phylogeny ; Sequence Analysis, DNA ; Spores, Fungal/classification/cytology ; },
abstract = {The taxonomy of the aquatic hyphomycete genus Articulospora (Ascomycota, Pezizomycotima, Leotiales, Helotiaceae) is based on the morphology of the generative phase of its lifecycle. The type species is Articulospora tetracladia, which is distributed worldwide. Its most frequent populations in nature have dimorphic conidia, differing by the extent of conidial branching (i.e., one or two levels of branching). Some strains, stable in culture, produce exclusively conidia of one type. With the molecular analyses employed here and the relatively low number of available isolates (20), separation based on branching of conidia has not been fully supported. Therefore we propose to retain the broad concept of A. tetracladia with dimorphic conidia. Among the three gene sequences tested as potential barcodes, the internal transcribed spacer (ITS) gene was the most promising region. All strains yielded amplifiable DNA which provided adequate resolution, according to accepted ranges in inter/intraspecific differences, to differentiate among the three Articulospora and two Fontanospora species that were tested (Articulospora atra, Articulospora proliferata, A. tetracladia, Fontanospora eccentrica, Fontanospora fusiramosa). D1/D2 primers also permitted amplification in all strains, however without much resolution. Amplification of the COX1 gene sequence was least consistent.},
}
@article {pmid30227086,
year = {2019},
author = {Usso, MC and Santos, ARD and Gouveia, JG and Frantine-Silva, W and Araya-Jaime, C and Oliveira, MLM and Foresti, F and Giuliano-Caetano, L and Dias, AL},
title = {Genetic and Chromosomal Differentiation of Rhamdia quelen (Siluriformes, Heptapteridae) Revealed by Repetitive Molecular Markers and DNA Barcoding.},
journal = {Zebrafish},
volume = {16},
number = {1},
pages = {87-97},
doi = {10.1089/zeb.2018.1576},
pmid = {30227086},
issn = {1557-8542},
mesh = {Animals ; Brazil ; Catfishes/*genetics ; *Chromosome Mapping ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/analysis ; Female ; Fish Proteins/analysis ; Genes, rRNA ; *Genetic Variation ; Male ; },
abstract = {Rhamdia quelen, a species of Heptapteridae, is considered to be a complex because of taxonomic and phylogenetic inconsistencies. Determining the physical location of repetitive DNA sequences on the chromosomes and the DNA barcode might increase our understanding of these inconsistencies within different groups of fish. To this end, we analyzed R. quelen populations from two river basins in Brazil, Paraguay and Parana, using DNA barcoding and different chromosomal markers, including U2 snDNA, which has never been analyzed for any Rhamdia species. Cytochrome c oxidase I gene sequence analysis revealed a significant differentiation among populations from the Miranda and Quexada rivers, with genetic distances compatible to those found among different species in neotropical fishes. Our results, in general, revealed a conservative chromosomal evolution in R. quelen and a differential distribution of some markers, such as 5S rDNA and U2 snDNA, in different populations. We suggest that R. quelen must undergo a major revision in its morphological, genetic, and cytogenetic molecular and taxonomic structure to elucidate possible operational taxonomic units.},
}
@article {pmid30226333,
year = {2018},
author = {Gong, H and Liu, Z and Chen, Y and Zhang, J and Cheng, R and Huang, Z},
title = {[Microscopic and molecular identification of pine needles].},
journal = {Zhejiang da xue xue bao. Yi xue ban = Journal of Zhejiang University. Medical sciences},
volume = {47},
number = {3},
pages = {300-306},
pmid = {30226333},
issn = {1008-9292},
mesh = {Animals ; DNA, Ribosomal Spacer/genetics ; *Phylogeny ; *Pinus/classification/cytology/genetics ; Plant Leaves/cytology ; Polymerase Chain Reaction ; },
abstract = {OBJECTIVE: To identify pine needles from different plant origins by microscopic and molecular approaches.<br><br>METHODS: The characteristics of pine needles of Pinus massoniana Lamb., Pinus thunbergii Parl. and Pinus armandii Franch. were investigated via plant morphology and microscopic characteristics. ITS2 and rbcL were analyzed with PCR amplification and bi-directional sequencing. MEGA 6.0 was used to calculate the intra-and inter-specific Kimura-2-Parameter (K2P) distances, and the phylogenetic tree was constructed by using the neighbor-joining (NJ) method.<br><br>RESULTS: There were significant differences in the number and length of pine needles, number of vascular bundles, distribution of stomatal lines, number and distribution of resin channels among three kinds of pine needles. The lengths of ITS2 sequences of Pinus massoniana Lamb., Pinus thunbergii Parl. and Pinus armandii Franch. were 470, 469 and 470 bp, respectively. The lengths of rbcL sequences in three kinds of pine needles were 553 bp. The intraspecific variation rates of ITS2 sequences in Pinus massoniana Lamb., Pinus thunbergii Parl. and Pinus armandii Franch. were 0%, 0.2%, and 2.8%, respectively; and the intraspecific variation rates of rbcL sequences were 0%, 2.4%, and 1.1%, respectively. There was no significant barcoding gap in intraspecific and interspecific genetic distances of ITS2 sequences. The intraspecific and interspecific distances of rbcL sequences were clearly separated in the barcoding gap test. The NJ tree based on rbcL showed that the three pine needles clustered into three separate groups, indicating that rbcL DNA marker could distinguish the Pinus massoniana Lamb., Pinus thunbergii Parl., Pinus armandii Franch. and its close relative species.<br><br>CONCLUSIONS: s The three types of pine needles can be distinguished accurately and rapidly by microscopic and molecular identification. The study provides methodology and experimental basis for the quality evaluation and classification of pine needles.},
}
@article {pmid30226026,
year = {2019},
author = {Marquina, D and Andersson, AF and Ronquist, F},
title = {New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods.},
journal = {Molecular ecology resources},
volume = {19},
number = {1},
pages = {90-104},
pmid = {30226026},
issn = {1755-0998},
support = {642241//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; 642241//Horizon 2020/ ; BIG4//Horizon 2020/ ; 2014-05901//Horizon 2020/ ; //Swedish Research Council/ ; },
mesh = {Animals ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/*genetics ; DNA, Ribosomal/chemistry/genetics ; Electron Transport Complex IV/genetics ; Insecta/*classification/*genetics ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Insect metabarcoding has been mainly based on PCR amplification of short fragments within the "barcoding region" of the gene cytochrome oxidase I (COI). However, because of the variability of this gene, it has been difficult to design good universal PCR primers. Most primers used today are associated with gaps in the taxonomic coverage or amplification biases that make the results less reliable and impede the detection of species that are present in the sample. We identify new primers for insect metabarcoding using computational approaches (ecoprimers and degeprime) applied to the most comprehensive reference databases of mitochondrial genomes of Hexapoda assembled to date. New primers are evaluated in silico against previously published primers in terms of taxonomic coverage and resolution of the corresponding amplicons. For the latter criterion, we propose a new index, exclusive taxonomic resolution, which is a more biologically meaningful measure than the standard index used today. Our results show that the best markers are found in the ribosomal RNA genes (12S and 16S); they resolve about 90% of the genetically distinct species in the reference database. Some markers in protein-coding genes provide similar performance but only at much higher levels of primer degeneracy. Combining two of the best individual markers improves the effective taxonomic resolution with up to 10%. The resolution is strongly dependent on insect taxon: COI primers detect 40% of Hymenoptera, while 12S primers detect 12% of Collembola. Our results indicate that amplicon-based metabarcoding of insect samples can be improved by choosing other primers than those commonly used today.},
}
@article {pmid30225943,
year = {2019},
author = {Gariepy, TD and Bruin, A and Konopka, J and Scott-Dupree, C and Fraser, H and Bon, MC and Talamas, E},
title = {A modified DNA barcode approach to define trophic interactions between native and exotic pentatomids and their parasitoids.},
journal = {Molecular ecology},
volume = {28},
number = {2},
pages = {456-470},
doi = {10.1111/mec.14868},
pmid = {30225943},
issn = {1365-294X},
support = {//Agriculture and Agri-Food Canada/International ; //OMAFRA/University of Guelph Partnership-Emergency Management and Production Systems/International ; },
mesh = {Animals ; Canada ; *DNA Barcoding, Taxonomic ; Ecosystem ; Food Chain ; Host-Parasite Interactions/*genetics ; Pest Control, Biological ; Species Specificity ; Wasps/genetics/*parasitology ; },
abstract = {The establishment of invasive Halyomorpha halys (Stål) outside of its native range may impact native species assemblages, including other pentatomids and their scelionid parasitoids. This has generated interest in defining species diversity and host-parasitoid associations in this system to better understand the impact of invasive alien species on trophic interactions in invaded regions. Information on scelionid-pentatomid associations in natural habitats is lacking, and species-level identification of these associations can be tenuous using rearing and dissection techniques. Naturally occurring pentatomid eggs were collected in areas where H. halys has established in Canada and were analysed using a modified DNA barcoding approach to define species-level trophic interactions. Identification was possible for >90% of egg masses. Eleven pentatomid and five scelionid species were identified, and trophic links were established. Approximately 70% of egg masses were parasitized; parasitism and parasitoid species composition were described for each species. Telenomus podisi Ashmead was the dominant parasitoid and was detected in all host species. Trissolcus euschisti Ashmead was detected in several host species, but was significantly more prevalent in Chinavia hilaris (Say) and Brochymena quadripustulata (Fabricius). Trissolcus brochymenae Ashmead and Tr. thyantae Ashmead were recorded sporadically. Parasitism of H. halys was 55%, and this species was significantly less likely to be parasitized than native pentatomids. The scelionid species composition of H. halys consisted of Te. podisi, Tr. euschisti and Tr. thyantae. Although these species cannot develop in fresh H. halys eggs, we demonstrate that parasitoids attempt to exploit this host under field conditions.},
}
@article {pmid30224310,
year = {2019},
author = {Binetruy, F and Chevillon, C and de Thoisy, B and Garnier, S and Duron, O},
title = {Survey of ticks in French Guiana.},
journal = {Ticks and tick-borne diseases},
volume = {10},
number = {1},
pages = {77-85},
doi = {10.1016/j.ttbdis.2018.09.003},
pmid = {30224310},
issn = {1877-9603},
mesh = {*Animal Distribution ; Animals ; Animals, Domestic ; Animals, Wild ; Arthropod Proteins/analysis ; *Biodiversity ; Electron Transport Complex IV/analysis ; Female ; French Guiana ; *Host-Parasite Interactions ; Humans ; Ixodidae/growth &amp; development/*physiology ; Larva/growth &amp; development/physiology ; Male ; Nymph/growth &amp; development/physiology ; Ornithodoros/growth &amp; development/*physiology ; RNA, Ribosomal, 16S/analysis ; Tick Infestations/epidemiology/parasitology/*veterinary ; },
abstract = {In this study, we examine the current pattern of tick diversity and host use in French Guiana, South America, from 97 sampling localities encompassing peri-urban, rural and natural habitats. We collected 3395 ticks, including 1485 specimens from 45 vertebrate species (humans, domestic and wild animals) and 1910 questing specimens from vegetation. Morphological examinations identified 22 species belonging to six genera: Amblyomma (16 species), Rhipicephalus (two species), Ixodes (one species), Dermacentor (one species), Haemaphysalis (one species), Ornithodoros (one species). To facilitate future identification, we produced a bank of pictures of different stages for all these species. Taxonomic identification was then confirmed by molecular characterization of two mitochondrial genes, cytochrome c oxidase CO1 and 16S rDNA. Eleven of the 22 reported species were collected on humans, six on domestic animals and 12 on wild animals. The most widespread tick species collected were A. cajennense sensu stricto and, to a lesser extent, A. oblongoguttatum; both of these species were frequently found on humans. We used these results to discuss the tick-associated risks for human and animal health in French Guiana.},
}
@article {pmid30217970,
year = {2018},
author = {Yang, JS and Garriga-Canut, M and Link, N and Carolis, C and Broadbent, K and Beltran-Sastre, V and Serrano, L and Maurer, SP},
title = {rec-YnH enables simultaneous many-by-many detection of direct protein-protein and protein-RNA interactions.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {3747},
pmid = {30217970},
issn = {2041-1723},
support = {IJCI-2014-22070//Ministry of Economy and Competitiveness | Consejo Superior de Investigaciones Cient&#xed;ficas (Spanish National Research Council)/International ; BFU2015-63571-P//Ministry of Economy and Competitiveness | Consejo Superior de Investigaciones Cient&#xed;ficas (Spanish National Research Council)/International ; PE 2013-2016//Ministry of Economy and Competitiveness | Consejo Superior de Investigaciones Cient&#xed;ficas (Spanish National Research Council)/International ; BFU2014-54278-P//Ministry of Economy and Competitiveness | Consejo Superior de Investigaciones Cient&#xed;ficas (Spanish National Research Council)/International ; BFU2015-62550-ERC//Ministry of Economy and Competitiveness | Consejo Superior de Investigaciones Cient&#xed;ficas (Spanish National Research Council)/International ; },
mesh = {Cloning, Molecular ; High-Throughput Nucleotide Sequencing ; High-Throughput Screening Assays ; *Protein Interaction Maps ; RNA/*metabolism ; RNA-Binding Proteins/*metabolism ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/*metabolism ; *Two-Hybrid System Techniques ; },
abstract = {Knowing which proteins and RNAs directly interact is essential for understanding cellular mechanisms. Unfortunately, discovering such interactions is costly and often unreliable. To overcome these limitations, we developed rec-YnH, a new yeast two and three-hybrid-based screening pipeline capable of detecting interactions within protein libraries or between protein libraries and RNA fragment pools. rec-YnH combines batch cloning and transformation with intracellular homologous recombination to generate bait-prey fusion libraries. By developing interaction selection in liquid-gels and using an ORF sequence-based readout of interactions via next-generation sequencing, we eliminate laborious plating and barcoding steps required by existing methods. We use rec-Y2H to simultaneously map interactions of protein domains and reveal novel putative interactors of PAR proteins. We further employ rec-Y2H to predict the architecture of published coprecipitated complexes. Finally, we use rec-Y3H to map interactions between multiple RNA-binding proteins and RNAs-the first time interactions between protein and RNA pools are simultaneously detected.},
}
@article {pmid30217841,
year = {2018},
author = {Cecil, JH and Garcia, DC and Giannone, RJ and Michener, JK},
title = {Rapid, Parallel Identification of Catabolism Pathways of Lignin-Derived Aromatic Compounds in Novosphingobium aromaticivorans.},
journal = {Applied and environmental microbiology},
volume = {84},
number = {22},
pages = {},
pmid = {30217841},
issn = {1098-5336},
mesh = {Bacterial Proteins/genetics/metabolism ; Coumaric Acids/*metabolism ; DNA Transposable Elements ; Esterases/genetics/metabolism ; Lignin/*metabolism ; Metabolic Engineering ; *Metabolic Networks and Pathways ; Mutagenesis, Insertional/*methods ; Sphingomonadaceae/genetics/*metabolism ; },
abstract = {Transposon mutagenesis is a powerful technique in microbial genetics for the identification of genes in uncharacterized pathways. Recently, the throughput of transposon mutagenesis techniques has been dramatically increased through the combination of DNA barcoding and high-throughput sequencing. Here, we show that when applied to catabolic pathways, barcoded transposon libraries can be used to distinguish redundant pathways, decompose complex pathways into substituent modules, discriminate between enzyme homologs, and rapidly identify previously hypothetical enzymes in an unbiased genome-scale search. We used this technique to identify two genes, desC and desD, which are involved in the degradation of the lignin-derived aromatic compound sinapic acid in the nonmodel bacterium Novosphingobium aromaticivorans We show that DesC is a methyl esterase acting on an intermediate formed during sinapic acid catabolism, providing the last enzyme in a proposed catabolic pathway. This approach will be particularly useful in the identification of complete pathways suitable for heterologous expression in metabolic engineering.IMPORTANCE The identification of the genes involved in specific biochemical transformations is a key step in predicting microbial function from nucleic acid sequences and in engineering microbes to endow them with new functions. We have shown that new techniques for transposon mutagenesis can dramatically simplify this process and enable the rapid identification of genes in uncharacterized pathways. These techniques provide the necessary scale to fully elucidate complex biological networks such as those used to degrade mixtures of lignin-derived aromatic compounds.},
}
@article {pmid30217175,
year = {2018},
author = {Wu, W and Ng, WL and Yang, JX and Li, WM and Ge, XJ},
title = {High cryptic species diversity is revealed by genome-wide polymorphisms in a wild relative of banana, Musa itinerans, and implications for its conservation in subtropical China.},
journal = {BMC plant biology},
volume = {18},
number = {1},
pages = {194},
pmid = {30217175},
issn = {1471-2229},
support = {31261140366//National Natural Science Foundation of China/ ; },
mesh = {Bayes Theorem ; China ; Genetic Variation ; Genome, Plant ; Musa/classification/*genetics ; Phylogeography ; *Polymorphism, Single Nucleotide ; },
abstract = {BACKGROUND: Species delimitation is a challenging but essential task in conservation biology. Morphologically similar species are sometimes difficult to recognize even after examination by experienced taxonomists. With the advent of molecular approaches in species delimitation, this hidden diversity has received much recent attention. In addition to DNA barcoding approaches, analytical tools based on the multi-species coalescence model (MSC) have been developed for species delimitation. Musa itinerans is widely distributed in subtropical Asia, and at least six varieties have been documented. However, the number of evolutionarily distinct lineages remains unknown.<br><br>RESULTS: Using genome resequencing data of five populations (making up four varieties), we examined genome-wide variation and found four varieties that were evolutionary significant units. A Bayesian Phylogenetics and Phylogeography (BP&amp;P) analysis using 123 single copy nuclear genes support three speciation events of M. itinerans varieties with robust posterior speciation probabilities; However, a Bayes factor delimitation of species with genomic data (BFD*) analysis using 1201 unlinked single nucleotide polymorphisms gave decisive support for a five-lineage model. When reconciling divergence time estimates with a speciation time scale, a modified three-lineage model was consistent with that of BP&amp;P, in which the speciation time of two varieties (M. itinerans var. itinerans and M. itinerans var. lechangensis) were dated to 26.2 kya and 10.7 kya, respectively. In contrast, other two varieties (M. itinerans var. chinensis and M. itinerans var. guangdongensis) diverged only 3.8 kya in the Anthropocene; this may be a consequence of genetic drift rather than a speciation event.<br><br>CONCLUSION: Our results showed that the M. itinerans species complex harbours high cryptic species diversity. We recommend that M. itinerans var. itinerans and M. itinerans var. lechangensis be elevated to subspecies status, and the extremely rare latter subspecies be given priority for conservation. We also recommend that the very recently diverged M. itinerans var. chinensis and M. itinerans var. guangdongensis should be merged under the subspecies M. itinerans var. chinensis. Finally, we speculate that species delimitation of recently diverged lineages may be more effective using genome-wide bi-allelic SNP markers with BFD* than by using unlinked loci and BP&amp;P.},
}
@article {pmid30217078,
year = {2018},
author = {Li, Y and Hingamp, P and Watai, H and Endo, H and Yoshida, T and Ogata, H},
title = {Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters.},
journal = {Viruses},
volume = {10},
number = {9},
pages = {},
pmid = {30217078},
issn = {1999-4915},
support = {203143100025//Canon Foundation for Scientific Research/International ; 16KT0020//Japan Society for the Promotion of Science/International ; 17H03850//Japan Society for the Promotion of Science/International ; 26430184//Japan Society for the Promotion of Science/International ; 2016-28//Institute for Chemical Research, Kyoto University/International ; 2017-25//Institute for Chemical Research, Kyoto University/International ; ANR-11-BTBR-0008//French Investments for the Future program/International ; },
mesh = {*Biodiversity ; Computational Biology/methods ; Genome, Viral ; Giant Viruses/*classification/*genetics ; Metagenome ; Metagenomics/methods ; Phylogeny ; *Polymerase Chain Reaction/methods ; Seawater/*virology ; *Water Microbiology ; },
abstract = {"Megaviridae" is a proposed family of giant viruses infecting unicellular eukaryotes. These viruses are ubiquitous in the sea and have impact on marine microbial community structure and dynamics through their lytic infection cycle. However, their diversity and biogeography have been poorly characterized due to the scarce detection of Megaviridae sequences in metagenomes, as well as the limitation of reference sequences used to design specific primers for this viral group. Here, we propose a set of 82 degenerated primers (referred to as MEGAPRIMER), targeting DNA polymerase genes (polBs) of Megaviridae. MEGAPRIMER was designed based on 921 Megaviridae polBs from sequenced genomes and metagenomes. By applying this primer set to environmental DNA meta-barcoding of a coastal seawater sample, we report 5595 non-singleton operational taxonomic units (OTUs) of Megaviridae at 97% nucleotide sequence identity. The majority of the OTUs were found to form diverse clades, which were phylogenetically distantly phylogenetically related to known viruses such as Mimivirus. The Megaviridae OTUs detected in this study outnumber the giant virus OTUs identified in previous individual studies by more than an order of magnitude. Hence, MEGAPRIMER represents a useful tool to study the diversity of Megaviridae at the population level in natural environments.},
}
@article {pmid30216729,
year = {2018},
author = {Sago, CD and Lokugamage, MP and Lando, GN and Djeddar, N and Shah, NN and Syed, C and Bryksin, AV and Dahlman, JE},
title = {Modifying a Commonly Expressed Endocytic Receptor Retargets Nanoparticles in Vivo.},
journal = {Nano letters},
volume = {18},
number = {12},
pages = {7590-7600},
pmid = {30216729},
issn = {1530-6992},
support = {T32 EB021962/EB/NIBIB NIH HHS/United States ; },
mesh = {Animals ; Caveolin 1/genetics/*metabolism ; Cell Line ; Cells, Cultured ; Drug Carriers/chemistry/*metabolism ; Drug Delivery Systems ; Endocytosis ; Kupffer Cells/metabolism ; Lipid Metabolism ; Lipids/chemistry ; Macrophages/metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Nanoparticles/chemistry/*metabolism ; Nucleic Acids/*administration &amp; dosage/pharmacokinetics ; Tissue Distribution ; },
abstract = {Nanoparticles are often targeted to receptors expressed on specific cells, but few receptors are (i) highly expressed on one cell type and (ii) involved in endocytosis. One unexplored alternative is manipulating an endocytic gene expressed on multiple cell types; an ideal gene would inhibit delivery to cell type A more than cell type B, promoting delivery to cell type B. This would require a commonly expressed endocytic gene to alter nanoparticle delivery in a cell type-dependent manner in vivo; whether this can occur is unknown. Based on its microenvironmental regulation, we hypothesized Caveolin 1 (Cav1) would exert cell type-specific effects on nanoparticle delivery. Fluorescence was not sensitive enough to investigate this question, and as a result, we designed a platform named QUANT to study nanoparticle biodistribution. QUANT is 10[8]× more sensitive than fluorescence and can be multiplexed. By measuring how 226 lipid nanoparticles (LNPs) delivered nucleic acids to multiple cell types in vivo in wild-type and Cav1 knockout mice, we found Cav1 altered delivery in a cell-type specific manner. Cav1 knockout did not alter LNP delivery to lung and kidney macrophages but substantially reduced LNP delivery to Kupffer cells, which are liver-resident macrophages. These data suggest caveolin-mediated endocytosis of nanomedicines by macrophages varies with tissue type. These results suggest manipulating receptors expressed on multiple cell types can tune drug delivery.},
}
@article {pmid30215679,
year = {2019},
author = {Holec, PV and Berleant, J and Bathe, M and Birnbaum, ME},
title = {A Bayesian framework for high-throughput T cell receptor pairing.},
journal = {Bioinformatics (Oxford, England)},
volume = {35},
number = {8},
pages = {1318-1325},
pmid = {30215679},
issn = {1367-4811},
support = {P30 CA014051/CA/NCI NIH HHS/United States ; T32 GM087237/GM/NIGMS NIH HHS/United States ; },
mesh = {Algorithms ; Bayes Theorem ; Immunotherapy ; Receptors, Antigen, T-Cell ; *T-Lymphocytes ; },
abstract = {MOTIVATION: The study of T cell receptor (TCR) repertoires has generated new insights into immune system recognition. However, the ability to robustly characterize these populations has been limited by technical barriers and an inability to reliably infer heterodimeric chain pairings for TCRs.<br><br>RESULTS: Here, we describe a novel analytical approach to an emerging immune repertoire sequencing method, improving the resolving power of this low-cost technology. This method relies upon the distribution of a T cell population across a 96-well plate, followed by barcoding and sequencing of the relevant transcripts from each T cell. Multicell Analytical Deconvolution for High Yield Paired-chain Evaluation (MAD-HYPE) uses Bayesian inference to more accurately extract TCR information, improving our ability to study and characterize T cell populations for immunology and immunotherapy applications.<br><br>The MAD-HYPE algorithm is released as an open-source project under the Apache License and is available from https://github.com/birnbaumlab/MAD-HYPE.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid30215579,
year = {2018},
author = {Niskanen, T and Liimatainen, K and Nuytinck, J and Kirk, P and Ibarguren, IO and Garibay-Orijel, R and Norvell, L and Huhtinen, S and Kytövuori, I and Ruotsalainen, J and Niemelä, T and Ammirati, JF and Tedersoo, L},
title = {Identifying and naming the currently known diversity of the genus Hydnum, with an emphasis on European and North American taxa.},
journal = {Mycologia},
volume = {110},
number = {5},
pages = {890-918},
doi = {10.1080/00275514.2018.1477004},
pmid = {30215579},
issn = {1557-2536},
mesh = {Basidiomycota/*classification/cytology/growth &amp; development/*isolation &amp; purification ; Biometry ; DNA Barcoding, Taxonomic ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Europe ; Fruiting Bodies, Fungal/*growth &amp; development ; Microscopy ; North America ; Sequence Analysis, DNA ; Spores, Fungal/cytology ; Terminology as Topic ; },
abstract = {In this study, 49 species of Hydnum are recognized worldwide. Twenty-two of them are described here as new species. Epitypes are proposed for H. repandum and H. rufescens. The majority of the species are currently known only from a single continent. The barcodes produced in this study are deposited in the RefSeq database and used as a basis to name species hypotheses in UNITE. Eleven infrageneric clades recovered in a phylogenetic analysis are supported by morphological characteristics and formally recognized: subgenera Alba, Hydnum, Pallida, and Rufescentia; sections Hydnum, Olympica, Magnorufescentia, and Rufescentia; and subsections Mulsicoloria, Rufescentia, and Tenuiformia.},
}
@article {pmid30214837,
year = {2018},
author = {Yodphaka, S and Boonpragob, K and Lumbsch, HT and Kraichak, E},
title = {Evaluation of six regions for their potential as DNA barcodes in epiphyllous liverworts from Thailand.},
journal = {Applications in plant sciences},
volume = {6},
number = {8},
pages = {e01174},
pmid = {30214837},
issn = {2168-0450},
abstract = {PREMISE OF THE STUDY: Studies on the diversity of epiphyllous bryophytes have been limited because of minute and incomplete specimens and a lack of taxonomic expertise. The recent development of the DNA barcoding approach has allowed taxon identification and species discovery of many obscure groups of organisms.<br><br>METHODS: With DNA extractions from 99 samples of 16 species, we compared the efficiencies of six DNA markers (rbcL, matK, trnL-F, psbA, ITS1, and ITS2) in their ability to amplify, using a standard set of primers, as well as their discriminatory power, using distance-based and tree-based approaches with nucleotide data.<br><br>RESULTS: The amplification success was relatively high (70-90%) with all of the markers, except for matK, which yielded no success. The barcoding gap, as calculated from the difference between inter- and intraspecific genetic distances, was the highest in ITS2, whereas the highest numbers of monophyletic groups were found with ITS2 and rbcL.<br><br>DISCUSSION: rbcL should be used as a main barcoding marker with the addition of ITS2 for epiphyllous species. The development of DNA barcoding as a tool for quantifying species diversity will provide a rapid and reliable identification tool for epiphyllous bryophytes.},
}
@article {pmid30209224,
year = {2018},
author = {Schär, S and Eastwood, R and Arnaldi, KG and Talavera, G and Kaliszewska, ZA and Boyle, JH and Espeland, M and Nash, DR and Vila, R and Pierce, NE},
title = {Ecological specialization is associated with genetic structure in the ant-associated butterfly family Lycaenidae.},
journal = {Proceedings. Biological sciences},
volume = {285},
number = {1886},
pages = {},
pmid = {30209224},
issn = {1471-2954},
mesh = {Animals ; Ants/*physiology ; Butterflies/genetics/*physiology ; Electron Transport Complex IV/analysis ; Genes, Mitochondrial ; Insect Proteins/analysis ; Phylogeny ; *Symbiosis ; },
abstract = {The role of specialization in diversification can be explored along two geological axes in the butterfly family Lycaenidae. In addition to variation in host-plant specialization normally exhibited by butterflies, the caterpillars of most Lycaenidae have symbioses with ants ranging from no interactions through to obligate and specific associations, increasing niche dimensionality in ant-associated taxa. Based on mitochondrial sequences from 8282 specimens from 967 species and 249 genera, we show that the degree of ecological specialization of lycaenid species is positively correlated with genetic divergence, haplotype diversity and an increase in isolation by distance. Nucleotide substitution rate is higher in carnivorous than phytophagous lycaenids. The effects documented here for both micro- and macroevolutionary processes could result from increased spatial segregation as a consequence of reduced connectivity in specialists, niche-based divergence or a combination of both. They could also provide an explanation for the extraordinary diversity of the Lycaenidae and, more generally, for diversity in groups of organisms with similar multi-dimensional ecological specialization.},
}
@article {pmid30206100,
year = {2018},
author = {Grootens, J and Ungerstedt, JS and Nilsson, G and Dahlin, JS},
title = {Deciphering the differentiation trajectory from hematopoietic stem cells to mast cells.},
journal = {Blood advances},
volume = {2},
number = {17},
pages = {2273-2281},
pmid = {30206100},
issn = {2473-9537},
mesh = {*Cell Differentiation ; Hematopoiesis ; Hematopoietic Stem Cells/*cytology ; Humans ; Mast Cells/*cytology ; Mastocytosis, Systemic/genetics/pathology ; },
abstract = {Hematopoietic stem cells differentiate into all types of blood cells, including peripheral tissue-resident mast cells. The early mast cell differentiation takes place in the bone marrow, after which the progenitor cells enter the circulation and mature once reaching their target organ. Early results from single-cell culture experiments and colony-forming assays have produced the classic hierarchical tree model of hematopoiesis. The introduction of high-throughput, single-cell RNA sequencing is now revolutionizing our understanding of the differentiation process, questioning the classic tree-based models. By integrating the results from early cell culture experiments with single-cell transcriptomics, we present a differentiation landscape model of hematopoiesis and discuss it with focus on mast cells. The review also describes how the hematologic neoplasm systemic mastocytosis can be used to model human hematopoiesis using naturally occurring cell barcoding by means of the common KIT D816V mutation.},
}
@article {pmid30203730,
year = {2019},
author = {Virgilio, M and Daneel, JH and Manrakhan, A and Delatte, H and Meganck, K and De Meyer, M},
title = {An integrated diagnostic setup for the morphological and molecular identification of the Ceratitis FAR complex (C. anonae, C. fasciventris, C. rosa, C. quilicii, Diptera, Tephritidae).},
journal = {Bulletin of entomological research},
volume = {109},
number = {3},
pages = {376-382},
doi = {10.1017/S0007485318000615},
pmid = {30203730},
issn = {1475-2670},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Female ; Genotype ; Larva/classification/genetics ; Male ; Microsatellite Repeats ; Species Specificity ; Tephritidae/anatomy &amp; histology/*classification/*genetics ; },
abstract = {The Ceratitis FAR complex (Diptera, Tephritidae) includes four economically important frugivorous flies (Ceratitis anonae, Ceratitis fasciventris, Ceratitis quilicii, Ceratitis rosa) whose immature stages and adult females cannot be properly resolved through morphological identification. In order to develop a simplified molecular tool for the identification of two of these species (C. rosa, C. quilicii), we selected a subset of six microsatellite markers out of a panel of 16 loci that were previously developed for the molecular differentiation of the taxa within the complex. These six markers were first tested in silico and then used for the actual genotyping of C. quilicii and C. rosa, resulting in the correct identification of all male reference specimens. Here, we propose an integrated morphological and molecular setup for the identification of the four species of the FAR complex. The decision map relies on preliminary DNA barcoding or morphological identification (when possible) to exclude species not belonging to the complex followed by (a) morphological identification of all adult male specimens and female C. anonae, (b) molecular identification via a panel of 16 microsatellite markers for immature stages, damaged vouchers and samples potentially including adult female C. fasciventris/C. quilicii/C. rosa and (c) molecular identification via a reduced panel of six microsatellite markers for samples including only C. quilicii and C. rosa. This simplified diagnostic setup was profitably implemented in the framework of the ERAfrica fruit fly project and will help correctly identify species within the FAR complex for their early detection and monitoring.},
}
@article {pmid30202640,
year = {2018},
author = {Lu, J and Zhang, Y and Chen, H},
title = {Integrative taxonomy of the genus Pseudostegana (Diptera, Drosophilidae) from China, with descriptions of eleven new species.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5160},
pmid = {30202640},
issn = {2167-8359},
abstract = {The genus Pseudostegana (Okada, 1978) currently contains thirty-nine described species. A number of Pseudostegana were collected from the fieldwork in southwestern China from 2010 to 2017. Eleven new species were discovered and are described from southwestern China: Pseudostegana alpina Zhang &amp; Chen, sp. nov.; Pseudostegana amnicola Zhang &amp; Chen, sp. nov.; Pseudostegana amoena Zhang &amp; Chen, sp. nov.; Pseudostegana mailangang Zhang &amp; Chen, sp. nov.; Pseudostegana meiduo Zhang &amp; Chen, sp. nov.; Pseudostegana meiji Zhang &amp; Chen, sp. nov.; Pseudostegana mystica Zhang &amp; Chen, sp. nov.; Pseudostegana stictiptrata Zhang &amp; Chen, sp. nov.; Pseudostegana stigmatptera Zhang &amp; Chen, sp. nov.; Pseudostegana ximalaya Zhang &amp; Chen, sp. nov. and Pseudostegana zhuoma Zhang &amp; Chen, sp. nov. A key to all Chinese Pseudostegana species based on morphological characters is provided. Two mitochondrial loci (COI and ND2) and one nuclear locus (28S rRNA) were sequenced for the Pseudostegana specimens, and Bayesian and RAxML concatenated analyses were run. Molecular species delimitation is performed using the distance-based automatic barcode gap discovery (ABGD) method. Molecular data support the morphological characteristics observed among these Chinese species and confirm the new species as being distinctly different.},
}
@article {pmid30202084,
year = {2019},
author = {Orton, MG and May, JA and Ly, W and Lee, DJ and Adamowicz, SJ},
title = {Is molecular evolution faster in the tropics?.},
journal = {Heredity},
volume = {122},
number = {5},
pages = {513-524},
pmid = {30202084},
issn = {1365-2540},
support = {2016-06199//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en G&#xe9;nie du Canada)/International ; },
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Databases, Genetic ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Geography ; Invertebrates/classification/genetics ; Linear Models ; Phylogeny ; *Tropical Climate ; },
abstract = {The evolutionary speed hypothesis (ESH) suggests that molecular evolutionary rates are higher among species inhabiting warmer environments. Previously, the ESH has been investigated using small numbers of latitudinally-separated sister lineages; in animals, these studies typically focused on subsets of Chordata and yielded mixed support for the ESH. This study analyzed public DNA barcode sequences from the cytochrome c oxidase subunit I (COI) gene for six of the largest animal phyla (Arthropoda, Chordata, Mollusca, Annelida, Echinodermata, and Cnidaria) and paired latitudinally-separated taxa together informatically. Of 8037 lineage pairs, just over half (51.6%) displayed a higher molecular rate in the lineage inhabiting latitudes closer to the equator, while the remainder (48.4%) displayed a higher rate in the higher-latitude lineage. To date, this study represents the most comprehensive analysis of latitude-related molecular rate differences across animals. While a statistically-significant pattern was detected from our large sample size, our findings suggest that the EHS may not serve as a strong universal mechanism underlying the latitudinal diversity gradient and that COI molecular clocks may generally be applied across latitudes. This study also highlights the merits of using automation to analyze large DNA barcode datasets.},
}
@article {pmid30200705,
year = {2018},
author = {Duan, YP and Luo, JY and Dou, XW and He, L and Li, KL and Yang, SH and Yang, MH},
title = {[Identification and quality evaluation of Tripterygium wilfordii].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {43},
number = {15},
pages = {3105-3114},
doi = {10.19540/j.cnki.cjcmm.20180510.005},
pmid = {30200705},
issn = {1001-5302},
mesh = {Chromatography, Liquid ; DNA Barcoding, Taxonomic ; Drugs, Chinese Herbal/*standards ; Phylogeny ; Plants, Medicinal/chemistry/*classification ; Quality Control ; Tandem Mass Spectrometry ; Tripterygium/chemistry/*classification ; },
abstract = {With the extensive clinical application of Tripterygium wilfordii, there are many counterfeit products on the market. Traditional technology can not effectively identify the authenticity of the traditional Chinese medicine. Therefore, a strategy of accurate identification and quality evaluation of Tripterygium based on DNA barcode and chemical fingerprint spectrum was established. Based on DNA barcode technology, HMMer annotation method of hidden Markov model and K2P model were used to analyze genetic distance.BLAST1, nearest distance and phylogenetic tree (NJ-tree) methods were used to assess the identification efficiency of the ITS2 barcode. The fingerprint of 27 T. wilfordii was established by UPLC-PDA method, and the similarity of the fingerprint of different sources was evaluated. The main components of T. wilfordii were determined by LC-MS/MS. The results revealed that the intraspecific genetic distances of T. wilfordii were lower than the interspecific genetic distances between T. wilfordii and its adulterants. The results of similarity search showed that ITS2 sequence was used to identify T. wilfordii and its adulterants. The clustering of T. wilfordii and its adulterants was clear in the tree of NJ cluster, and 12 of 27 samples were identified as true T. wilfordii.The chemical fingerprint spectrum research indicates that the feature one region can distinguish the false product of tripterygium glycosides more intuitively. The cluster analysis of HCA-thermal map showed that the contents of six active components of T. wilfordii from different habitats were significantly different, which could be used to evaluate the quality of T. wilfordii. This paper is of guiding significance for the accurate identification and quality evaluation of Tripterygium medicinal plants.},
}
@article {pmid30200312,
year = {2018},
author = {Jeske, H},
title = {Barcoding of Plant Viruses with Circular Single-Stranded DNA Based on Rolling Circle Amplification.},
journal = {Viruses},
volume = {10},
number = {9},
pages = {},
pmid = {30200312},
issn = {1999-4915},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA Viruses/*classification/*genetics/isolation &amp; purification ; DNA, Circular/genetics ; DNA, Single-Stranded/genetics ; Nucleic Acid Amplification Techniques/methods ; Plant Diseases/*virology ; Plant Viruses/*classification/*genetics/isolation &amp; purification ; },
abstract = {The experience with a diagnostic technology based on rolling circle amplification (RCA), restriction fragment length polymorphism (RFLP) analyses, and direct or deep sequencing (Circomics) over the past 15 years is surveyed for the plant infecting geminiviruses, nanoviruses and associated satellite DNAs, which have had increasing impact on agricultural and horticultural losses due to global transportation and recombination-aided diversification. Current state methods for quarantine measures are described to identify individual DNA components with great accuracy and to recognize the crucial role of the molecular viral population structure as an important factor for sustainable plant protection.},
}
@article {pmid30199026,
year = {2018},
author = {Couper, L and Swei, A},
title = {Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {138},
pages = {},
pmid = {30199026},
issn = {1940-087X},
mesh = {Animals ; High-Throughput Nucleotide Sequencing/*methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; Ticks/*genetics ; },
abstract = {In recent decades, vector-borne diseases have re-emerged and expanded at alarming rates, causing considerable morbidity and mortality worldwide. Effective and widely available vaccines are lacking for a majority of these diseases, necessitating the development of novel disease mitigation strategies. To this end, a promising avenue of disease control involves targeting the vector microbiome, the community of microbes inhabiting the vector. The vector microbiome plays a pivotal role in pathogen dynamics, and manipulations of the microbiome have led to reduced vector abundance or pathogen transmission for a handful of vector-borne diseases. However, translating these findings into disease control applications requires a thorough understanding of vector microbial ecology, historically limited by insufficient technology in this field. The advent of next-generation sequencing approaches has enabled rapid, highly parallel sequencing of diverse microbial communities. Targeting the highly-conserved 16S rRNA gene has facilitated characterizations of microbes present within vectors under varying ecological and experimental conditions. This technique involves amplification of the 16S rRNA gene, sample barcoding via PCR, loading samples onto a flow cell for sequencing, and bioinformatics approaches to match sequence data with phylogenetic information. Species or genus-level identification for a high number of replicates can typically be achieved through this approach, thus circumventing challenges of low detection, resolution, and output from traditional culturing, microscopy, or histological staining techniques. Therefore, this method is well-suited for characterizing vector microbes under diverse conditions but cannot currently provide information on microbial function, location within the vector, or response to antibiotic treatment. Overall, 16S next-generation sequencing is a powerful technique for better understanding the identity and role of vector microbes in disease dynamics.},
}
@article {pmid30198261,
year = {2018},
author = {Guo, Y and Zhang, H and Chen, W and Zhang, Y},
title = {Herbivore-Diet Analysis Based on Illumina MiSeq Sequencing: The Potential Use of an ITS2-Barcoding Approach to Establish Qualitative and Quantitative Predictions of Diet Composition of Mongolian Sheep.},
journal = {Journal of agricultural and food chemistry},
volume = {66},
number = {37},
pages = {9858-9867},
doi = {10.1021/acs.jafc.8b02814},
pmid = {30198261},
issn = {1520-5118},
mesh = {Animal Feed/*analysis ; Animals ; China ; DNA Barcoding, Taxonomic ; DNA, Intergenic/*genetics ; DNA, Plant/*genetics ; Feces/chemistry ; Herbivory ; Phylogeny ; Plants/*classification/genetics/*metabolism ; Sheep/*metabolism ; },
abstract = {DNA-barcoding approaches to estimate the diet compositions of grazing animals have received significant attention, and particularly when combined with next-generation sequencing, these techniques have substantially improved in recent years. In this study, the identity and species composition of plant material ingested by Mongolian sheep were estimated through the use of 350 bp ITS2 gene sequences of the vegetation found in fecal samples. Four diets were formulated using varying amounts of eight plant species that are common in the grasslands of northern China. Sixteen Mongolian sheep were taken from pastures and randomly assigned to four groups, and each group received one of four diets. Each sheep was randomly assigned to one of 16 confinement pens and fed its respective diet for 12 consecutive days. Fecal samples were removed from each pen from days 7-12, preserved, and composited for each pen. All herbage species included in the daily diets were detected in each fecal sample, with the exception of Phragmites australis. Moreover, 12 additional different plant species were retrieved from feces of the experimental sheep. The obtained data provided preliminary support for the use of the ITS2 barcode to determine which plants were consumed. Moreover, the proportions of the herbage DNA sequences recovered from sheep feces and those of the herbage masses in the daily diets did not completely match. These results indicate that the non-Gramineae DNA sequences amplified with ITS2 primers (including those of Chenopodium album, Artemisia scoparia, Artemisia tanacetifolia, and Medicago sativa) far exceeded those of the Gramineae species (including Leymus chinensis and Puccinellia distans), which constitute the largest share of the experimental diets. A significant positive correlation (Spearman's ρ = 0.376, P = 0.003) between the actual herbage mass proportions in the experimental diets and the herbage-DNA-sequence proportions provided sufficiently favorable support for the further investigation of DNA barcoding for the quantification of plants in feces. A significant regression coefficient was found between the relative DNA-sequence proportions of L. chinensis (R[2] = 0.82, P < 0.0001), P. distans (R[2] = 0.64, P = 0.0017), and C. album (R[2] = 0.98, P < 0.0001) and their respective herbage mass proportions. The quantitative relationship can be expressed by the linear-regression equations y = 0.90 x - 0.22, y = 0.98 x - 0.03, and y = 5.00 x - 0.25, respectively. Thus, these results demonstrate that dietary-DNA-barcoding methods exhibited potential in providing valuable quantitative information regarding food-item components. However, it should be noted that this explorative data needs to be further improved by using additional genes and by creating a sophisticated reference database, thus enhancing both quality and accuracy of the obtained results.},
}
@article {pmid30196122,
year = {2018},
author = {Cheon, SH and Lee, YN and Kang, SI and Kye, SJ and Lee, EK and Heo, GB and Lee, MH and Kim, JW and Lee, KN and Son, HM and Lee, YJ},
title = {Genetic evidence for the intercontinental movement of avian influenza viruses possessing North American-origin nonstructural gene allele B into South Korea.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {66},
number = {},
pages = {18-25},
doi = {10.1016/j.meegid.2018.09.001},
pmid = {30196122},
issn = {1567-7257},
mesh = {*Alleles ; Animal Migration ; Animals ; Animals, Wild ; Birds/virology ; Geese/virology ; *Genetic Variation ; Geographic Information Systems ; Influenza A virus/*classification/*genetics/isolation &amp; purification ; Influenza in Birds/*epidemiology/transmission/*virology ; North America/epidemiology ; Phylogeny ; Republic of Korea/epidemiology ; Viral Nonstructural Proteins/*genetics ; },
abstract = {Avian influenza viruses (AIVs) are genetically separated by geographical barriers, resulting in the independent evolution of North American and Eurasian lineages. In the present study, to determine whether AIVs possessing the North American-origin nonstructural (NS) gene were previously introduced into South Korea, we performed a genetic analysis of AIVs isolated from fecal samples of migratory birds. We detected seven viruses possessing the North American-origin NS allele B among 413 AIV-positive samples obtained during AI surveillance between 2012 and 2017. We found evidence for the intercontinental transmission of at least three genetically distinct clusters of the B allele of the North American-origin NS gene into Eurasia at a low frequency. The host species of three viruses were identified as the greater white-fronted goose (Anser albifrons) using a DNA barcoding technique. Moreover, we used GPS-CDMA-based telemetry to determine the migration route of the greater white-fronted goose between the Far East of Russia and South Korea and found that this species may play an important role as an intermediate vector in the intercontinental transmission of AIVs. To improve our understanding of the role of wild birds in the ecology of AIVs, advanced AIV surveillance is required in the Far East of Russia as well as in Alaska region of Beringia accompanied by host identification and wild bird tracking.},
}
@article {pmid30195940,
year = {2018},
author = {Severins, I and Szczepaniak, M and Joo, C},
title = {Multiplex Single-Molecule DNA Barcoding Using an Oligonucleotide Ligation Assay.},
journal = {Biophysical journal},
volume = {115},
number = {6},
pages = {957-967},
pmid = {30195940},
issn = {1542-0086},
support = {309509/ERC_/European Research Council/International ; },
mesh = {Base Sequence ; Biosensing Techniques/instrumentation/*methods ; DNA Probes/genetics ; Fluorescence ; Lab-On-A-Chip Devices ; Nucleic Acid Amplification Techniques ; Oligonucleotides/*genetics ; Polymorphism, Single Nucleotide ; },
abstract = {Detection of specific nucleic acid sequences is invaluable in biological studies such as genetic disease diagnostics and genome profiling. Here, we developed a highly sensitive and specific detection method that combines an advanced oligonucleotide ligation assay with multicolor single-molecule fluorescence. We demonstrated that under our experimental conditions, 7-nucleotide long DNA barcodes have the optimal short length to ascertain specificity while being long enough for sufficient ligation. Using four spectrally separated fluorophores to label DNA barcodes, we simultaneously distinguished four DNA target sequences differing by only a single nucleotide. Our single-molecule approach will allow for accurate identification of low-abundance molecules without the need for target DNA preamplification.},
}
@article {pmid30194432,
year = {2018},
author = {Magoga, G and Sahin, DC and Fontaneto, D and Montagna, M},
title = {Barcoding of Chrysomelidae of Euro-Mediterranean area: efficiency and problematic species.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {13398},
pmid = {30194432},
issn = {2045-2322},
mesh = {Animals ; Coleoptera/classification/*genetics ; DNA Barcoding, Taxonomic/methods/*standards ; Electron Transport Complex IV/genetics ; Insect Proteins/genetics ; *Phylogeny ; },
abstract = {Leaf beetles (Coleoptera: Chrysomelidae), with more than 37,000 species worldwide and about 2,300 in the Euro-Mediterranean region, are an ecological and economical relevant family, making their molecular identification of interest also in agriculture. This study, part of the Mediterranean Chrysomelidae Barcoding project (www.c-bar.org), aims to: (i) develop a reference Cytochrome c oxidase I (COI) library for the molecular identification of the Euro-Mediterranean Chrysomelidae; (ii) test the efficiency of DNA barcoding for leaf beetles identification; (iii) develop and compare optimal thresholds for distance-based identifications estimated at family and subfamily level, minimizing false positives and false negatives. Within this study, 889 COI nucleotide sequences of 261 species were provided; after the inclusion of information from other sources, a dataset of 7,237 sequences (542 species) was analysed. The average intra-interspecific distances were in the range of those recorded for Coleoptera: 1.6-24%. The estimated barcoding efficiency (~94%) confirmed the usefulness of this tool for Chrysomelidae identification. The few cases of failure were recorded for closely related species (e.g., Cryptocephalus marginellus superspecies, Cryptocephalus violaceus - Cryptocephalus duplicatus and some Altica species), even with morphologically different species sharing the same COI haplotype. Different optimal thresholds were achieved for the tested taxonomic levels, confirming that group-specific thresholds significantly improve molecular identifications.},
}
@article {pmid30192752,
year = {2018},
author = {Porter, TM and Hajibabaei, M},
title = {Over 2.5 million COI sequences in GenBank and growing.},
journal = {PloS one},
volume = {13},
number = {9},
pages = {e0200177},
pmid = {30192752},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic ; *Databases, Nucleic Acid ; Electron Transport Complex IV/*genetics ; Humans ; },
abstract = {The increasing popularity of cytochrome c oxidase subunit 1 (COI) DNA metabarcoding warrants a careful look at the underlying reference databases used to make high-throughput taxonomic assignments. The objectives of this study are to document trends and assess the future usability of COI records for metabarcode identification. The number of COI records deposited to the NCBI nucleotide database has increased by a geometric average of 51% per year, from 8,137 records deposited in 2003 to a cumulative total of ~ 2.5 million by the end of 2017. About half of these records are fully identified to the species rank, 92% are at least 500 bp in length, 74% have a country annotation, and 51% have latitude-longitude annotations. To ensure the future usability of COI records in GenBank we suggest: 1) Improving the geographic representation of COI records, 2) Improving the cross-referencing of COI records in the Barcode of Life Data System and GenBank to facilitate consolidation and incorporation into existing bioinformatic pipelines, 3) Adherence to the minimum information about a marker gene sequence guidelines, and 4) Integrating metabarcodes from eDNA and mixed community studies with existing reference sequences. The growth of COI reference records over the past 15 years has been substantial and is likely to be a resource across many fields for years to come.},
}
@article {pmid30191440,
year = {2018},
author = {Chu, P and Wilson, GM and Michael, TP and Vaiciunas, J and Honig, J and Lam, E},
title = {Sequence-guided approach to genotyping plant clones and species using polymorphic NB-ARC-related genes.},
journal = {Plant molecular biology},
volume = {98},
number = {3},
pages = {219-231},
pmid = {30191440},
issn = {1573-5028},
support = {DGE-0903675//Directorate for Biological Sciences/ ; 12116//New Jersey Agricultural Experiment Station/ ; },
mesh = {Araceae/*genetics ; *Cloning, Organism ; DNA Fingerprinting ; DNA, Plant/genetics ; Gene Expression Regulation, Plant/*physiology ; *Genotype ; Nucleic Acid Amplification Techniques ; Plant Proteins/genetics/*metabolism ; *Polymorphism, Single Nucleotide ; },
abstract = {Leveraging the heightened levels of polymorphism in NB-ARC-related protein encoding genes in higher plants, a bioinformatic pipeline was created to identify regions in this gene family from sequenced plant genomes that exhibit fragment length or single nucleotide differences in different accessions of the same species. Testing this approach with the aquatic plant Spirodela polyrhiza demonstrated its superior performance in comparison with currently available genotyping technologies based on PCR amplification. Rapid and economical genotyping tools that can reliably distinguish species and intraspecific variations in plants can be powerful tools for biogeographical and ecological studies. Clones of the cosmopolitan duckweed species, Spirodela polyrhiza, are difficult to distinguish morphologically due to their highly abbreviated architecture and inherently low levels of sequence variation. The use of plastidic markers and generic Amplification Fragment Length Polymorphism approaches have met with limited success in resolving clones of S. polyrhiza from diverse geographical locales. Using whole genome sequencing data from nine S. polyrhiza clones as a training set, we created an informatic pipeline to identify and rank polymorphic regions from nuclear-encoded NB-ARC-related genes to design markers for PCR, Sanger sequencing (barcoding), and fragment length analysis. With seven primer sets, we found 21 unique fingerprints from a set of 23 S. polyrhiza clones. However, three of these clones share the same fingerprint and are indistinguishable by these markers. These primer sets can also be used as interspecific barcoding tools to rapidly resolve S. polyrhiza from the closely related S. intermedia species without the need for DNA sequencing. Our work demonstrates a general approach of using hyper-polymorphic loci within genomes as a resource to produce facile tools that can have high resolving power for genotyping applications.},
}
@article {pmid30184444,
year = {2019},
author = {Lopez-Vaamonde, C and Sire, L and Rasmussen, B and Rougerie, R and Wieser, C and Allaoui, AA and Minet, J and deWaard, JR and Decaëns, T and Lees, DC},
title = {DNA barcodes reveal deeply neglected diversity and numerous invasions of micromoths in Madagascar [1].},
journal = {Genome},
volume = {62},
number = {3},
pages = {108-121},
doi = {10.1139/gen-2018-0065},
pmid = {30184444},
issn = {1480-3321},
mesh = {Animals ; *Biodiversity ; DNA/analysis/*genetics ; DNA Barcoding, Taxonomic/*methods ; *Ecosystem ; Introduced Species/*statistics &amp; numerical data ; Madagascar ; Moths/*classification/*genetics ; },
abstract = {Madagascar is a prime evolutionary hotspot globally, but its unique biodiversity is under threat, essentially from anthropogenic disturbance. There is a race against time to describe and protect the Madagascan endangered biota. Here we present a first molecular characterization of the micromoth fauna of Madagascar. We collected 1572 micromoths mainly using light traps in both natural and anthropogenically disturbed habitats in 24 localities across eastern and northwest Madagascar. We also collected 1384 specimens using a Malaise trap in a primary rain forest at Andasibe, eastern Madagascar. In total, we DNA barcoded 2956 specimens belonging to 1537 Barcode Index Numbers (BINs), 88.4% of which are new to BOLD. Only 1.7% of new BINs were assigned to species. Of 47 different families found, Dryadaulidae, Bucculatricidae, Bedelliidae, Batrachedridae, and Blastobasidae are newly reported for Madagascar and the recently recognized Tonzidae is confirmed. For test faunas of Canada and Australia, 98.9%-99.4% of Macroheterocera BINs exhibited the molecular synapomorphy of a phenylalanine in the 177th complete DNA barcode codon. Non-macroheteroceran BINs could thus be sifted out efficiently in the Malaise sample. The Madagascar micromoth fauna shows highest affinity with the Afrotropics (146 BINs also occur in the African continent). We found 22 recognised pests or invasive species, mostly occurring in disturbed habitats. Malaise trap samples show high temporal turnover and alpha diversity with as many as 507 BINs collected; of these, astonishingly, 499 (98.4%) were novel to BOLD and 292 (57.6%) were singletons. Our results provide a baseline for future surveys across the island.},
}
@article {pmid30184372,
year = {2018},
author = {Atencia, M and Toro-Cantillo, A and Hoyos-López, R},
title = {Genetic diversity and population structure of Anopheles triannulatus s. l. in the department of Córdoba, Colombia, using DNA barcoding.},
journal = {Biomedica : revista del Instituto Nacional de Salud},
volume = {38},
number = {0},
pages = {117-126},
doi = {10.7705/biomedica.v38i0.4055},
pmid = {30184372},
issn = {2590-7379},
mesh = {Animal Distribution ; Animals ; Anopheles/classification/enzymology/*genetics ; Cities ; Colombia ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Genes, Insect ; Genetic Variation ; Haplotypes/genetics ; Incidence ; Insect Proteins/genetics ; Malaria/epidemiology/transmission ; Mosquito Vectors/classification/enzymology/*genetics ; Phylogeny ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; },
abstract = {Introduction: Anopheles triannulatus is not incriminated as a vector of malaria transmission in Colombia despite recent reports of infection with Plasmodium spp. in populations related to the northwestern and southeastern lineages. Genetic diversity can delimit information about gene flow and population differentiation in localities with malaria. Objective: To estimate the genetic diversity of An. triannulatus in five municipalities with high and low incidence of malaria in the department of Córdoba. Materials and methods: The entomological collections were done between August and November, 2016, in Tierralta, Puerto Libertador, Montelíbano, Sahagún, and Planeta Rica. We used the COI barcoding fragment as molecular marker. The genetic analysis included the estimation of genetic parameters such as the diversity haplotype, the genetic structure, the gene flow, the Tajima’s D test, the haplotype network, and the phylogenetic relationship. Results: We obtained 148 sequences with a length of 655 nucleotides of the COI gene, from which we derived 44 haplotypes. The H2 and H21 haplotypes were the most frequent in the populations. The values of the Tajima’s D test were negative and not significant (p>0.10). The genetic structure index (FST=0.01427) and the gene flow (Nm=17.27) evidenced no differentiation between sampled populations due to the high exchange of migrants. Using phylogenetic inferences and the haplotype network, we identified one single species without geographic differentiation or lineages in the geographic range studied. Conclusions: The genetic diversity calculated for An. triannulatus in this context indicated stable populations in constant exchange.},
}
@article {pmid30183729,
year = {2018},
author = {Bakar, AA and Adamson, EAS and Juliana, LH and Nor Mohd, SA and Wei-Jen, C and Man, A and Md, DN},
title = {DNA barcoding of Malaysian commercial snapper reveals an unrecognized species of the yellow-lined Lutjanus (Pisces:Lutjanidae).},
journal = {PloS one},
volume = {13},
number = {9},
pages = {e0202945},
pmid = {30183729},
issn = {1932-6203},
mesh = {Animal Distribution ; Animals ; Biodiversity ; Coral Reefs ; DNA Barcoding, Taxonomic ; Industry ; Malaysia ; Oceans and Seas ; Perciformes/*classification/*genetics/growth &amp; development ; Seafood ; Species Specificity ; },
abstract = {Management of wild fisheries resources requires accurate knowledge on which species are being routinely exploited, but it can be hard to identify fishes to species level, especially in speciose fish groups where colour patterns vary with age. Snappers of the genus Lutjanus represent one such group, where fishes can be hard to identify and as a result fisheries statistics fail to capture species-level taxonomic information. This study employs traditional morphological and DNA barcoding approaches to identify adult and juvenile Lutjanus species harvested in Malaysian waters. Our results reveal a suite of species that differs markedly from those that have previously been considered important in the Malaysian wild-capture fishery and show that official fisheries statistics do not relate to exploitation at the species level. Furthermore, DNA barcoding uncovered two divergent groups of bigeye snapper ('Lutjanus lutjanus') distributed on either side of the Malay Peninsula, displaying a biogeographical pattern similar to distributions observed for many co-occurring reef-distributed fish groups. One of these bigeye snapper groups almost certainly represents an unrecognized species in need of taxonomic description. The study demonstrates the utility of DNA barcoding in uncovering overlooked diversity and for assessing species catch composition in a complicated but economically important taxonomic group.},
}
@article {pmid30183632,
year = {2018},
author = {Zhang, L and Chen, C and Mow, WH},
title = {Accurate Modelling and Efficient Estimation of the Print-Capture Channel with Application in Barcoding.},
journal = {IEEE transactions on image processing : a publication of the IEEE Signal Processing Society},
volume = {},
number = {},
pages = {},
doi = {10.1109/TIP.2018.2868383},
pmid = {30183632},
issn = {1941-0042},
abstract = {With the rapid advancement of sensing capability and computational power in consumer electronic devices, the use of mobile cameras for communications has attracted significant attention from both academia and industry. The design of a reliable communication system over the print-capture channel is a key challenge in some important applications, such as barcoding and document authentication. However, the real-world printcapture channel is spatially non-linear and non-stationary, and lacks a standard parametric model. As a consequence, advanced channel coding techniques developed for common channel models are not applicable in the existing systems without costly and device-dependent pre-training. In this work, an accurate parametric print-capture channel model and an efficient channel estimation scheme requiring low training overhead are proposed. With the estimated parameters, the proposed print-capture channel model can be linearized to the (possibly input-dependent) additive white Gaussian noise (AWGN) channel model. This allows the use of state-of-the-art channel coding schemes, such as low-density parity-check (LDPC) codes with iterative soft decoding, to improve the reliability of the communication system under challenging conditions, e.g., at a low signal-to-noise ratio. As an example application of the proposed print-capture channel model, a demonstrative multilevel 2D barcode using an LDPC code with iterative soft decoding, is designed to enhance the reliability over the conventional QR code which is based on the Reed-Solomon code with hard decoding. At a printing resolution of 600dpi, the 8-level 2D barcode achieves data capacity gains of about 10% and 56% over the QR code in the in-focus and blurlimited scenarios, respectively. It is noteworthy that the enhanced data capacity of the multilevel barcode is made possible by the proposed channel estimation scheme, which incurs an additional training overhead of about 3.3% only.},
}
@article {pmid30183560,
year = {2018},
author = {LaCoursiere, CM and Ullmann, JFP and Poduri, A},
title = {An Open-Source Husbandry Repository.},
journal = {Zebrafish},
volume = {15},
number = {6},
pages = {656-658},
pmid = {30183560},
issn = {1557-8542},
support = {R01 NS100766/NS/NINDS NIH HHS/United States ; },
mesh = {Animal Husbandry/*methods ; Animals ; *Databases, Factual ; *Information Management ; Internet ; Search Engine ; Smartphone ; *Zebrafish ; },
abstract = {Electronic databases provide effective and efficient management of zebrafish colony operations, but commercially available options are expensive. In this study we have developed a free zebrafish management repository alternative using free Google applications. Husbandry information is logged into a Google Sheets-based catalog through Google Form (GF) entries. Form autopopulation can be streamlined by barcodes, which can be generated and deciphered through free smartphone applications. The repository is capable of calculating pertinent husbandry dates from GF input and sending e-mail reminders to users for specified tasks. A Google application-based repository allows for a free simple zebrafish husbandry management solution.},
}
@article {pmid30182521,
year = {2018},
author = {Xu, W and Yin, P and Dai, M},
title = {Super-resolution Geometric Barcoding for Multiplexed miRNA Profiling.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {57},
number = {43},
pages = {14075-14079},
pmid = {30182521},
issn = {1521-3773},
support = {1DP2OD007292/NH/NIH HHS/United States ; 1R01EB018659/NH/NIH HHS/United States ; DP2 OD007292/OD/NIH HHS/United States ; R21 HD072481/HD/NICHD NIH HHS/United States ; 5R21HD072481/NH/NIH HHS/United States ; R01 EB018659/EB/NIBIB NIH HHS/United States ; },
mesh = {HeLa Cells ; Humans ; MicroRNAs/*analysis/chemistry ; *Molecular Typing ; Optical Imaging ; RNA Probes/chemistry ; },
abstract = {MicroRNA (miRNA) expression profiles hold promise as biomarkers for diagnostics and prognosis of complex diseases. Herein, we report a super-resolution fluorescence imaging-based digital profiling method for specific, sensitive, and multiplexed detection of miRNAs. In particular, we applied the DNA-PAINT (point accumulation for imaging in nanoscale topography) method to implement a super-resolution geometric barcoding scheme for multiplexed single-molecule miRNA capture and digital counting. Using synthetic DNA nanostructures as a programmable miRNA capture nano-array, we demonstrated high-specificity (single nucleotide mismatch discrimination), multiplexed (8-plex, 2 panels), and sensitive measurements on synthetic miRNA samples, as well as applied one 8-plex panel to measure endogenous miRNAs levels in total RNA extract from HeLa cells.},
}
@article {pmid30181603,
year = {2018},
author = {Bisconti, R and Porretta, D and Arduino, P and Nascetti, G and Canestrelli, D},
title = {Hybridization and extensive mitochondrial introgression among fire salamanders in peninsular Italy.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {13187},
pmid = {30181603},
issn = {2045-2322},
mesh = {Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Female ; Gene Flow ; Gene Frequency ; Genetics, Population ; Genomic Imprinting ; *Hybridization, Genetic ; Italy ; Male ; Mitochondria/*genetics ; Phylogeny ; Salamandra/*genetics ; },
abstract = {Discordance between mitochondrial and nuclear patterns of population genetic structure is providing key insights into the eco-evolutionary dynamics between and within species, and their assessment is highly relevant to biodiversity monitoring practices based on DNA barcoding approaches. Here, we investigate the population genetic structure of the fire salamander Salamandra salamandra in peninsular Italy. Both mitochondrial and nuclear markers clearly identified two main population groups. However, nuclear and mitochondrial zones of geographic transition between groups were located 600 km from one another. Recent population declines in central Italy partially erased the genetic imprints of past hybridization dynamics. However, the overall pattern of genetic variation, together with morphological and fossil data, suggest that a rampant mitochondrial introgression triggered the observed mitonuclear discordance, following a post-glacial secondary contact between lineages. Our results clearly show the major role played by reticulate evolution in shaping the structure of Salamandra salamandra populations and, together with similar findings in other regions of the species' range, contribute to identify the fire salamander as a particularly intriguing case to investigate the complexity of mechanisms triggering patterns of mitonuclear discordance in animals.},
}
@article {pmid30180802,
year = {2018},
author = {Ott, A and Schnable, JC and Yeh, CT and Wu, L and Liu, C and Hu, HC and Dalgard, CL and Sarkar, S and Schnable, PS},
title = {Linked read technology for assembling large complex and polyploid genomes.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {651},
pmid = {30180802},
issn = {1471-2164},
support = {Not applicable//Office of Biotechnology, Iowa State University/ ; Not applicable//Plant Sciences Institute, Iowa State University (US)/ ; DGE1247194//National Science Foundation/ ; },
mesh = {*Genome, Plant ; High-Throughput Nucleotide Sequencing/*methods ; Plant Leaves/*genetics ; *Polyploidy ; Sequence Analysis, DNA/*methods ; Zea mays/*genetics ; },
abstract = {BACKGROUND: Short read DNA sequencing technologies have revolutionized genome assembly by providing high accuracy and throughput data at low cost. But it remains challenging to assemble short read data, particularly for large, complex and polyploid genomes. The linked read strategy has the potential to enhance the value of short reads for genome assembly because all reads originating from a single long molecule of DNA share a common barcode. However, the majority of studies to date that have employed linked reads were focused on human haplotype phasing and genome assembly.<br><br>RESULTS: Here we describe a de novo maize B73 genome assembly generated via linked read technology which contains ~&#x2009;172,000 scaffolds with an N50 of 89&#xa0;kb that cover 50% of the genome. Based on comparisons to the B73 reference genome, 91% of linked read contigs are accurately assembled. Because it was possible to identify errors with >&#x2009;76% accuracy using machine learning, it may be possible to identify and potentially correct systematic errors. Complex polyploids represent one of the last grand challenges in genome assembly. Linked read technology was able to successfully resolve the two subgenomes of the recent allopolyploid, proso millet (Panicum miliaceum). Our assembly covers ~&#x2009;83% of the 1 Gb genome and consists of 30,819 scaffolds with an N50 of 912&#xa0;kb.<br><br>CONCLUSIONS: Our analysis provides a framework for future de novo genome assemblies using linked reads, and we suggest computational strategies that if implemented have the potential to further improve linked read assemblies, particularly for repetitive genomes.},
}
@article {pmid30178802,
year = {2018},
author = {Xu, AM and Liu, Q and Takata, KL and Jeoung, S and Su, Y and Antoshechkin, I and Chen, S and Thomson, M and Heath, JR},
title = {Integrated measurement of intracellular proteins and transcripts in single cells.},
journal = {Lab on a chip},
volume = {18},
number = {21},
pages = {3251-3262},
pmid = {30178802},
issn = {1473-0189},
support = {F32 CA213966/CA/NCI NIH HHS/United States ; U54 CA199090/CA/NCI NIH HHS/United States ; DP5 OD012194/OD/NIH HHS/United States ; },
mesh = {Equipment Design ; *Gene Expression Profiling ; Intracellular Space/*metabolism ; *Lab-On-A-Chip Devices ; Proteomics ; RNA, Messenger/genetics ; Single-Cell Analysis/*instrumentation ; },
abstract = {Biological function arises from the interplay of proteins, transcripts, and metabolites. An ongoing revolution in miniaturization technologies has created tools to analyze any one of these species in single cells, thus resolving the heterogeneity of tissues previously invisible to bulk measurements. An emerging frontier is single cell multi-omics, which is the measurement of multiple classes of analytes from single cells. Here, we combine bead-based transcriptomics with microchip-based proteomics to measure intracellular proteins and transcripts from single cells and defined small numbers of cells. The transcripts and proteins are independently measured by sequencing and fluorescent immunoassays respectively, to preserve their optimal measurement modes, and linked by encoding the physical address locations of the cells into digital sequencing space using spatially patterned DNA barcodes. We resolve cell-type-specific protein and transcript signatures and present a path forward to scaling the platform to high-throughput.},
}
@article {pmid30174334,
year = {2018},
author = {Cichocka, JM and Bielecki, A and Kulikowski, M and Jabłońska-Barna, I and Najda, K},
title = {New record of the fish leech Piscicola pojmanskae (Annelida: Hirudinida: Piscicolidae) - DNA barcoding and phylogeny.},
journal = {Biologia},
volume = {73},
number = {7},
pages = {693-701},
pmid = {30174334},
issn = {0006-3088},
abstract = {The aim of this study was to confirm the taxonomic status of Piscicola pojmanskae Bielecki, 1994 found on Salmonidae fish. The fish leech was identified based on a diligent morphological analysis as well as COI gene sequence (DNA barcoding). The phylogenetic relationship with other piscicolid leeches was analyzed as well. Piscicola pojmanskae was found on various fins of both graylings and the resident form of trouts. The prevalence of infection was 1.63%. In this paper, probable causes of the lack of relation between the number of leeches on the fins and the fish body length as well as the host-searching strategy used by P. pojmanskae are discussed.},
}
@article {pmid30171837,
year = {2018},
author = {Chan-Chable, RJ and Martinez-Arce, A and Mis-Avila, PC and Ortega-Morales, AI},
title = {Confirmation of occurrence of Anopheles (Anopheles) veruslanei Vargas in Quintana Roo, Mexico using morphology and DNA barcodes.},
journal = {Acta tropica},
volume = {188},
number = {},
pages = {138-141},
doi = {10.1016/j.actatropica.2018.08.036},
pmid = {30171837},
issn = {1873-6254},
mesh = {Animals ; Anopheles/anatomy &amp; histology/*classification/genetics ; *DNA Barcoding, Taxonomic ; Female ; Mexico ; },
abstract = {In Mexico, genus Anopheles includes 27 species divided into three subgenera: Anopheles, Kerteszia, and Nyssorhynchus. Some species occur in the Nearctic region (northern Mexico), whereas other species occur in the Neotropical region (south and southeast Mexico) and only a few species occur in both regions. In Quintana Roo State (southeast Mexico) 11 species have been recorded: An. apicimacula, An. atropos, An. bradleyi, An. crucians, An. franciscanus, An. neomaculipalpus, An. pseudopunctipennis, An. punctimacula, An. veruslanei, An. vestitipennis and An. albimanus. However, the occurrence and identity of An. veruslanei has been questioned in recent years, since its description 39 years ago, it has not been reported in recent studies. In October 2015, five females of An. veruslanei were collected and identified. To corroborate their occurrence and identity in Quintana Roo State, we used morphological and molecular evidence that confirms it, and the type material of this species was studied to compare with the specimens of our collections.},
}
@article {pmid30171574,
year = {2018},
author = {Spurgeon, BEJ and Naseem, KM},
title = {High-Throughput Signaling Profiling in Blood Platelets by Multiplexed Phosphoflow Cytometry.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1812},
number = {},
pages = {95-111},
doi = {10.1007/978-1-4939-8585-2_6},
pmid = {30171574},
issn = {1940-6029},
mesh = {Blood Platelets/*cytology/physiology ; Flow Cytometry/*methods ; Humans ; Plasma/cytology ; Staining and Labeling ; },
abstract = {Multiplexed phosphoflow cytometry is a novel method that provides rapid and quantitative readouts on intracellular phosphoprotein signaling. In this approach, flow cytometry is combined with fluorescent cell barcoding (FCB) to facilitate high-throughput analyses of signaling events. After stimulation, fixed and permeabilized platelets are labeled with distinct dye intensities to create unique fluorescent signatures for individual samples. These uniquely labeled samples can be combined for simultaneous antibody staining and acquisition. During software analysis, multiplexed samples can be differentiated by their distinct fluorescence intensities and analyzed as if they had been acquired individually. Multiplexing eliminates intersample variation, increases statistical robustness, and allows 4-96 samples to be processed with no appreciable increase in antibody consumption or runtime. The method can be performed on washed platelets, platelet-rich plasma (PRP), and whole blood. Its inherent versatility can fulfil wide-ranging experimental requirements from simple dose titrations to complex pharmacologic screens.},
}
@article {pmid30171478,
year = {2018},
author = {Laska, A and Majer, A and Szydło, W and Karpicka-Ignatowska, K and Hornyák, M and Labrzycka, A and Skoracka, A},
title = {Cryptic diversity within grass-associated Abacarus species complex (Acariformes: Eriophyidae), with the description of a new species, Abacarus plumiger n. sp.},
journal = {Experimental &amp; applied acarology},
volume = {76},
number = {1},
pages = {1-28},
pmid = {30171478},
issn = {1572-9702},
support = {Grant No. 6 P04 C0 5418//Polish Scientific Research Committee/ ; Grant No. 2011/03/B/NZ8/00129//Narodowe Centrum Nauki/ ; },
mesh = {Animals ; Arthropod Proteins/genetics ; *Biodiversity ; Biological Coevolution ; Female ; Male ; Mites/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Nymph/anatomy &amp; histology/classification/genetics/growth &amp; development ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Accurate estimation of species richness is often complex as genetic divergence is not always accompanied by appreciable morphological differentiation. In consequence, cryptic lineages or species evolve. Cryptic speciation is common especially in taxa characterized by small and simplified bodies, what makes their proper identification challenging. The cereal rust mite, Abacarus hystrix, was regarded for a long time as a species associated with a wide range of grass hosts, whereas wide host ranges are rather rare in eriophyoid mites. Therefore, the generalist status of A. hystrix was questioned. In this paper we demonstrate that the diversity within Abacarus species associated with grasses is more complex than it was previously thought. The 78 Abacarus mtDNA COI sequences used in this study formed 10 highly supported clades (bootstrap value 99%) and four more distinct genetic lineages were represented by unique sequences. The genetic distances between them ranged from 6.6 to 26.5%. Moreover, morphological study and genetic approach based on the combination of the Poisson Tree Processes model for species delimitation (PTP) and a Bayesian implementation of PTP (bPTP), and Neighbour Joining analyses led to delimitation of a new species within the Abacarus complex: Abacarus plumiger, specialized on smooth brome (Bromus inermis). Furthermore, our analyses demonstrated a pattern of host-associated differentiation within the complex. Overall, our study indicates that cryptic speciation occurs in the grass-associated Abacarus genus, and suggests the need for more extensive sampling using integrative methods.},
}
@article {pmid30171254,
year = {2019},
author = {Gao, C and Montoya, L and Xu, L and Madera, M and Hollingsworth, J and Purdom, E and Hutmacher, RB and Dahlberg, JA and Coleman-Derr, D and Lemaux, PG and Taylor, JW},
title = {Strong succession in arbuscular mycorrhizal fungal communities.},
journal = {The ISME journal},
volume = {13},
number = {1},
pages = {214-226},
pmid = {30171254},
issn = {1751-7370},
mesh = {Agriculture ; DNA, Fungal/genetics ; Ecology ; Mycobiome ; Mycorrhizae/classification/*genetics/*physiology ; Plant Roots/microbiology ; Rhizosphere ; Soil ; *Soil Microbiology ; Sorghum/microbiology ; Symbiosis ; },
abstract = {The ecology of fungi lags behind that of plants and animals because most fungi are microscopic and hidden in their substrates. Here, we address the basic ecological process of fungal succession in nature using the microscopic, arbuscular mycorrhizal fungi (AMF) that form essential mutualisms with 70-90% of plants. We find a signal for temporal change in AMF community similarity that is 40-fold stronger than seen in the most recent studies, likely due to weekly samplings of roots, rhizosphere and soil throughout the 17 weeks from seedling to fruit maturity and the use of the fungal DNA barcode to recognize species in a simple, agricultural environment. We demonstrate the patterns of nestedness and turnover and the microbial equivalents of the processes of immigration and extinction, that is, appearance and disappearance. We also provide the first evidence that AMF species co-exist rather than simply co-occur by demonstrating negative, density-dependent population growth for multiple species. Our study shows the advantages of using fungi to test basic ecological hypotheses (e.g., nestedness v. turnover, immigration v. extinction, and coexistence theory) over periods as short as one season.},
}
@article {pmid30169961,
year = {2018},
author = {Al'Khafaji, AM and Deatherage, D and Brock, A},
title = {Control of Lineage-Specific Gene Expression by Functionalized gRNA Barcodes.},
journal = {ACS synthetic biology},
volume = {7},
number = {10},
pages = {2468-2474},
pmid = {30169961},
issn = {2161-5063},
support = {R21 CA212928/CA/NCI NIH HHS/United States ; },
mesh = {Base Sequence ; CRISPR-Associated Protein 9/genetics ; Cell Line, Tumor ; Cell Lineage ; Gene Expression ; HEK293 Cells ; Humans ; Lentivirus/physiology ; },
abstract = {Lineage tracking delivers essential quantitative insight into dynamic, probabilistic cellular processes, such as somatic tumor evolution and differentiation. Methods for high diversity lineage quantitation rely on sequencing a population of DNA barcodes. However, manipulation of specific individual lineages is not possible with this approach. To address this challenge, we developed a functionalized lineage tracing tool, Control of Lineages by Barcode Enabled Recombinant Transcription (COLBERT), that enables high diversity lineage tracing and lineage-specific manipulation of gene expression. This modular platform utilizes expressed barcode gRNAs to both track cell lineages and direct lineage-specific gene expression.},
}
@article {pmid30166107,
year = {2018},
author = {Xin, T and Su, C and Lin, Y and Wang, S and Xu, Z and Song, J},
title = {Precise species detection of traditional Chinese patent medicine by shotgun metagenomic sequencing.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {47},
number = {},
pages = {40-47},
doi = {10.1016/j.phymed.2018.04.048},
pmid = {30166107},
issn = {1618-095X},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; Drugs, Chinese Herbal/*analysis ; Medicine, Chinese Traditional ; Plants, Medicinal/*classification ; Quality Control ; },
abstract = {BACKGROUND: Current quality control methods for traditional Chinese patent medicines (TCPMs), e.g., microscopy, thin-layer chromatography (TLC), and high-performance liquid chromatography (HPLC), cannot detect herbal species composition with adequate precision. To address this issue, more effective detection methods should be explored.<br><br>HYPOTHESIS/PURPOSE: We hypothesized that shotgun metagenomic sequencing can fulfill the requirements for the species detection of multi-ingredient TCPMs.<br><br>METHODS: Longdan Xiegan Wan (LDXGW), once thought to be the chief culprit in aristolochic acid nephropathy (AAN), was selected to establish the method. It was used for both reference and commercial LDXGW samples. The precision authentication of herbal species contained in multi-ingredient TCPM is based on the shotgun metagenomic sequencing of genomic DNA without PCR amplification. Chemical analyses were also conducted as a contrast test.<br><br>RESULTS: Over 100&#x202f;G of raw data was obtained, and this value represented more than 0.75 billion reads. After assembling and filtering all the reads, a total of 261 contigs were obtained, which belonged to the ITS2, psbA-trnH, and matK regions of the reference and commercial samples. Because the homology of the rbcL region was high, it was not analyzed in the HTS data. Bioinformatics analysis indicated that the ITS2 region, as a DNA barcode, showed the highest identification efficiency. It could successfully detect all prescribed species, including four processed herbal ingredients, in the lab-made reference samples. The commercial samples all met the requirements of the Chinese Pharmacopoeia according to the TLC and HPLC tests. However, the shotgun metagenomic sequencing detected the substitution of Akebiae Caulis (Mutong) in the commercial samples, while the chemical analyses could not distinguish.<br><br>CONCLUSION: The results highlight that shotgun metagenomic sequencing is a complementary method for the precise species detection of TCPMs.},
}
@article {pmid30165908,
year = {2018},
author = {Guérillot, R and Li, L and Baines, S and Howden, B and Schultz, MB and Seemann, T and Monk, I and Pidot, SJ and Gao, W and Giulieri, S and Gonçalves da Silva, A and D'Agata, A and Tomita, T and Peleg, AY and Stinear, TP and Howden, BP},
title = {Comprehensive antibiotic-linked mutation assessment by resistance mutation sequencing (RM-seq).},
journal = {Genome medicine},
volume = {10},
number = {1},
pages = {63},
pmid = {30165908},
issn = {1756-994X},
support = {GNT1066791//National Health and Medical Research Council/International ; GNT1008549//National Health and Medical Research Council/International ; GNT1105905//National Health and Medical Research Council/International ; },
mesh = {Anti-Bacterial Agents/pharmacology ; Daptomycin/pharmacology ; Drug Resistance, Bacterial/*genetics ; Genetic Pleiotropy ; *Mutation ; Mycobacterium tuberculosis/drug effects/genetics ; Rifampin/pharmacology ; Staphylococcus aureus/drug effects/genetics ; },
abstract = {Mutation acquisition is a major mechanism of bacterial antibiotic resistance that remains insufficiently characterised. Here we present RM-seq, a new amplicon-based deep sequencing workflow based on a molecular barcoding technique adapted from Low Error Amplicon sequencing (LEA-seq). RM-seq allows detection and functional assessment of mutational resistance at high throughput from mixed bacterial populations. The sensitive detection of very low-frequency resistant sub-populations permits characterisation of antibiotic-linked mutational repertoires in vitro and detection of rare resistant populations during infections. Accurate quantification of resistance mutations enables phenotypic screening of mutations conferring pleiotropic phenotypes such as in vivo persistence, collateral sensitivity or cross-resistance. RM-seq will facilitate comprehensive detection, characterisation and surveillance of resistant bacterial populations (https://github.com/rguerillot/RM-seq).},
}
@article {pmid30165813,
year = {2018},
author = {Rotimi, AM and Pierneef, R and Reva, ON},
title = {Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools.},
journal = {BMC bioinformatics},
volume = {19},
number = {1},
pages = {309},
pmid = {30165813},
issn = {1471-2105},
support = {93664//National Research Foundation/ ; },
mesh = {Algorithms ; Bacteria/*genetics ; Base Sequence ; DNA Barcoding, Taxonomic/*methods ; *Genes, Bacterial ; Genetic Markers ; Humans ; Metagenome/genetics ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeny ; ROC Curve ; Reproducibility of Results ; Sample Size ; *Software ; Species Specificity ; Whole Genome Sequencing ; },
abstract = {BACKGROUND: Metagenomic approaches have revealed the complexity of environmental microbiomes with the advancement in whole genome sequencing displaying a significant level of genetic heterogeneity on the species level. It has become apparent that patterns of superior bioactivity of bacteria applicable in biotechnology as well as the enhanced virulence of pathogens often requires distinguishing between closely related species or sub-species. Current methods for binning of metagenomic reads usually do not allow for identification below the genus level and generally stops at the family level.<br><br>RESULTS: In this work, an attempt was made to improve metagenomic binning resolution by creating genome specific barcodes based on the core and accessory genomes. This protocol was implemented in novel software tools available for use and download from http://bargene.bi.up.ac.za /. The most abundant barcode genes from the core genomes were found to encode for ribosomal proteins, certain central metabolic genes and ABC transporters. Performance of metabarcode sequences created by this package was evaluated using artificially generated and publically available metagenomic datasets. Furthermore, a program (Barcoding 2.0) was developed to align reads against barcode sequences and thereafter calculate various parameters to score the alignments and the individual barcodes. Taxonomic units were identified in metagenomic samples by comparison of the calculated barcode scores to set cut-off values. In this study, it was found that varying sample sizes, i.e. number of reads in a metagenome and metabarcode lengths, had no significant effect on the sensitivity and specificity of the algorithm. Receiver operating characteristics (ROC) curves were calculated for different taxonomic groups based on the results of identification of the corresponding genomes in artificial metagenomic datasets. The reliability of distinguishing between species of the same genus or family by the program was nearly perfect.<br><br>CONCLUSIONS: The results showed that the novel online tool BarcodeGenerator (http://bargene.bi.up.ac.za /) is an efficient approach for generating barcode sequences from a set of complete genomes provided by users. Another program, Barcoder 2.0 is available from the same resource to enable an efficient and practical use of metabarcodes for visualization of the distribution of organisms of interest in environmental and clinical samples.},
}
@article {pmid30165810,
year = {2018},
author = {Galen, SC and Nunes, R and Sweet, PR and Perkins, SL},
title = {Integrating coalescent species delimitation with analysis of host specificity reveals extensive cryptic diversity despite minimal mitochondrial divergence in the malaria parasite genus Leucocytozoon.},
journal = {BMC evolutionary biology},
volume = {18},
number = {1},
pages = {128},
pmid = {30165810},
issn = {1471-2148},
support = {1358465//National Science Foundation/International ; },
mesh = {Animals ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Genetic Loci ; *Genetic Variation ; Haemosporida/*genetics ; Haplotypes/genetics ; *Host Specificity ; Malaria/*parasitology ; Mitochondria/*genetics ; Parasites/*genetics ; Phylogeny ; Songbirds/parasitology ; Species Specificity ; },
abstract = {BACKGROUND: Coalescent methods that use multi-locus sequence data are powerful tools for identifying putatively reproductively isolated lineages, though this approach has rarely been used for the study of microbial groups that are likely to harbor many unrecognized species. Among microbial symbionts, integrating genetic species delimitation methods with trait data that could indicate reproductive isolation, such as host specificity data, has rarely been used despite its potential to inform species limits. Here we test the ability of an integrative approach combining genetic and host specificity data to delimit species within the avian malaria parasite genus Leucocytozoon in central Alaska.<br><br>RESULTS: We sequenced seven nuclear loci for 69 Leucocytozoon samples and used multiple species delimitation methods (GMYC and BPP models), tested for differences in host infection patterns among putative species based on 406 individual infections, and characterized parasite morphology. We found that cryptic morphology has masked a highly diverse Leucocytozoon assemblage, with most species delimitation methods recovering support for at least 21 separate species that occur sympatrically and have divergent host infection patterns. Reproductive isolation among putative species appears to have evolved despite low mtDNA divergence, and in one instance two Leucocytozoon cytb haplotypes that differed by a single base pair (~&#x2009;0.2% divergence) were supported as separate species. However, there was no consistent association between mtDNA divergence and species limits. Among cytb haplotypes that differed by one to three base pairs we observed idiosyncratic patterns of nuclear and ecological divergence, with cytb haplotype pairs found to be either conspecific, reproductively isolated with no divergence in host specificity, or reproductively isolated with divergent patterns of host specialization.<br><br>CONCLUSION: Integrating multi-locus genetic species delimitation methods and non-traditional ecological data types such as host specificity provide a novel view of the diversity of avian malaria parasites that has been missed previously using morphology and mtDNA barcodes. Species delimitation methods show that Leucocytozoon is highly species-rich in Alaska, and the genus is likely to harbor extraordinary species-level diversity worldwide. Integrating genetic and ecological data will be an important approach for understanding the diversity and evolutionary history of microbial symbionts moving forward.},
}
@article {pmid30165585,
year = {2019},
author = {Varet, H and Coppée, JY},
title = {checkMyIndex: a web-based R/Shiny interface for choosing compatible sequencing indexes.},
journal = {Bioinformatics (Oxford, England)},
volume = {35},
number = {5},
pages = {901-902},
pmid = {30165585},
issn = {1367-4811},
mesh = {*Internet ; Sequence Analysis ; *Software ; },
abstract = {SUMMARY: When sequencing several libraries simultaneously, the selection of compatible combinations of indexes is critical for ensuring that the sequencer will be able to decipher the short, sample-specific barcodes added to each fragment. However, researchers have few tools to help them choose optimal indexes. Here, we present checkMyIndex, an online R/Shiny application that facilitates the selection of the right indexes as a function of the experimental constraints.<br><br>checkMyIndex is available free of charge at https://checkmyindex.pasteur.fr as an online, web-based R/Shiny application. The source code is available on GitHub at https://github.com/PF2-pasteur-fr/checkMyIndex.},
}
@article {pmid30165073,
year = {2018},
author = {Lawton, SP and Allan, F and Hayes, PM and Smit, NJ},
title = {DNA barcoding of the medically important freshwater snail Physa acuta reveals multiple invasion events into Africa.},
journal = {Acta tropica},
volume = {188},
number = {},
pages = {86-92},
doi = {10.1016/j.actatropica.2018.08.027},
pmid = {30165073},
issn = {1873-6254},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Fresh Water ; Haplotypes ; Phylogeny ; Snails/*genetics ; South Africa ; },
abstract = {The medically important freshwater snail Physa acuta is highly invasive and has been reported in several freshwater environments across Africa. To identify species and provide initial insights into the origins of P. acuta into African freshwater environments standard molecular barcoding analyses, using the mitochondrial cytochrome c oxidase subunit I gene (COI), was performed on P. acuta isolates from Angola, Burundi and South Africa. Phylogenetic analyses of isolates from Africa could not be distinguished from P. acuta populations from other countries. Comparisons of COI sequences between isolates of P. acuta showed there to be no geographically specific clusters and the African isolates were distributed across four distinct unrelated clades suggesting several independent invasion events. Haplotype analyses indicated that there were a high number of haplotypes with low variation between them, which led to significant differences in AMOVA analyses between countries. This was further evidence of multiple invasion events suggesting multiple novel haplotypes being continually and independently introduced to each country. This approach not only provides initial insight into the invasion of Africa by P. acuta but a molecular method to monitor and manage the use of an agent of biological control.},
}
@article {pmid30161128,
year = {2018},
author = {Reeves, LE and Gillett-Kaufman, JL and Kawahara, AY and Kaufman, PE},
title = {Barcoding blood meals: New vertebrate-specific primer sets for assigning taxonomic identities to host DNA from mosquito blood meals.},
journal = {PLoS neglected tropical diseases},
volume = {12},
number = {8},
pages = {e0006767},
pmid = {30161128},
issn = {1935-2735},
mesh = {Animals ; Culicidae/*physiology ; DNA/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA Replication ; Feeding Behavior ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Vertebrates/*blood/*genetics ; },
abstract = {The transmission dynamics of mosquito-vectored pathogens are, in part, mediated by mosquito host-feeding patterns. These patterns are elucidated using blood meal analysis, a collection of serological and molecular techniques that determine the taxonomic identities of the host animals from which blood meals are derived. Modern blood meal analyses rely on polymerase chain reaction (PCR), DNA sequencing, and bioinformatic comparisons of blood meal DNA sequences to reference databases. Ideally, primers used in blood meal analysis PCRs amplify templates from a taxonomically diverse range of vertebrates, produce a short amplicon, and avoid co-amplification of non-target templates. Few primer sets that fit these requirements are available for the cytochrome c oxidase subunit I (COI) gene, the species identification marker with the highest taxonomic coverage in reference databases. Here, we present new primer sets designed to amplify fragments of the DNA barcoding region of the vertebrate COI gene, while avoiding co-amplification of mosquito templates, without multiplexed or nested PCR. Primers were validated using host vertebrate DNA templates from mosquito blood meals of known origin, representing all terrestrial vertebrate classes, and field-collected mosquito blood meals of unknown origin. We found that the primers were generally effective in amplifying vertebrate host, but not mosquito DNA templates. Applied to the sample of unknown mosquito blood meals, > 98% (60/61) of blood meals samples were reliably identified, demonstrating the feasibility of identifying mosquito hosts with the new primers. These primers are beneficial in that they can be used to amplify COI templates from a diverse range of vertebrate hosts using standard PCR, thereby streamlining the process of identifying the hosts of mosquitoes, and could be applied to next generation DNA sequencing and metabarcoding approaches.},
}
@article {pmid30156177,
year = {2018},
author = {Cheng, VCC and Wong, SC and Wong, SCY and Sridhar, S and Yip, CCY and Chen, JHK and Fung, J and Chiu, KHY and Ho, PL and Chen, S and Cheng, BWC and Ho, CL and Lo, CM and Yuen, KY},
title = {Nosocomial transmission of hepatitis C virus in a liver transplant center in Hong Kong: implication of reusable blood collection tube holder as the vehicle for transmission.},
journal = {Infection control and hospital epidemiology},
volume = {39},
number = {10},
pages = {1170-1177},
doi = {10.1017/ice.2018.175},
pmid = {30156177},
issn = {1559-6834},
mesh = {*Contact Tracing ; Cross Infection/*transmission/virology ; *Equipment Contamination ; Female ; Genotype ; Hepacivirus/*genetics ; Hepatitis C/*transmission/virology ; Hong Kong ; Humans ; Liver Transplantation/*adverse effects ; Male ; Medical Records ; Middle Aged ; Phylogeny ; RNA, Viral/genetics ; },
abstract = {BACKGROUND: A liver transplant recipient developed hospital-acquired symptomatic hepatitis C virus (HCV) genotype 6a infection 14 months post transplant.<br><br>OBJECTIVE: Standard outbreak investigation.<br><br>METHODS: Patient chart review, interviews of patients and staff, observational study of patient care practices, environmental surveillance, blood collection simulation experiments, and phylogenetic study of HCV strains using partial envelope gene sequences (E1-E2) of HCV genotype 6a strains from the suspected source patient, the environment, and the index patient were performed.<br><br>RESULTS: Investigations and data review revealed no further cases of HCV genotype 6a infection in the transplant unit. However, a suspected source with a high HCV load was identified. HCV genotype 6a was found in a contaminated reusable blood-collection tube holder with barely visible blood and was identified as the only shared item posing risk of transmission to the index case patient. Also, 14 episodes of sequential blood collection from the source patient and the index case patient were noted on the computerized time log of the laboratory barcoding system during their 13 days of cohospitalization in the liver transplant ward. Disinfection of the tube holders was not performed after use between patients. Blood collection simulation experiments showed that HCV and technetium isotope contaminating the tip of the sleeve capping the sleeved-needle can reflux back from the vacuum-specimen tube side to the patient side.<br><br>CONCLUSIONS: A reusable blood-collection tube holder without disinfection between patients can cause a nosocomial HCV infection. Single-use disposable tube holders should be used according to the recommendations by Occupational Safety and Health Administration and World Health Organization.},
}
@article {pmid30154353,
year = {2018},
author = {Zhang, X and Zhou, T and Yang, J and Sun, J and Ju, M and Zhao, Y and Zhao, G},
title = {Comparative Analyses of Chloroplast Genomes of Cucurbitaceae Species: Lights into Selective Pressures and Phylogenetic Relationships.},
journal = {Molecules (Basel, Switzerland)},
volume = {23},
number = {9},
pages = {},
pmid = {30154353},
issn = {1420-3049},
support = {31270364//National Natural Science Foundation of China/ ; 31770229//National Natural Science Foundation of China/ ; IRT1174//Program for Changjiang Scholars and Innovative Research Team in University (PCSIRT)/ ; },
mesh = {Codon ; Computational Biology/methods ; Cucurbitaceae/classification/*genetics ; Evolution, Molecular ; Genetic Variation ; *Genome, Chloroplast ; Genomics/methods ; Microsatellite Repeats ; Molecular Sequence Annotation ; Phylogeny ; Selection, Genetic ; },
abstract = {Cucurbitaceae is the fourth most important economic plant family with creeping herbaceous species mainly distributed in tropical and subtropical regions. Here, we described and compared the complete chloroplast genome sequences of ten representative species from Cucurbitaceae. The lengths of the ten complete chloroplast genomes ranged from 155,293 bp (C. sativus) to 158,844 bp (M. charantia), and they shared the most common genomic features. 618 repeats of three categories and 813 microsatellites were found. Sequence divergence analysis showed that the coding and IR regions were highly conserved. Three protein-coding genes (accD, clpP, and matK) were under selection and their coding proteins often have functions in chloroplast protein synthesis, gene transcription, energy transformation, and plant development. An unconventional translation initiation codon of psbL gene was found and provided evidence for RNA editing. Applying BI and ML methods, phylogenetic analysis strongly supported the position of Gomphogyne, Hemsleya, and Gynostemma as the relatively original lineage in Cucurbitaceae. This study suggested that the complete chloroplast genome sequences were useful for phylogenetic studies. It would also determine potential molecular markers and candidate DNA barcodes for coming studies and enrich the valuable complete chloroplast genome resources of Cucurbitaceae.},
}
@article {pmid30154183,
year = {2019},
author = {Kahn, S and Abramson, EL},
title = {What is new in paediatric medication safety?.},
journal = {Archives of disease in childhood},
volume = {104},
number = {6},
pages = {596-599},
doi = {10.1136/archdischild-2018-315175},
pmid = {30154183},
issn = {1468-2044},
mesh = {Child ; Decision Support Systems, Clinical ; Drug Prescriptions/standards ; Electronic Prescribing/standards ; Humans ; Medical Order Entry Systems ; Medication Errors/*prevention &amp; control/statistics &amp; numerical data ; Medication Systems/organization &amp; administration/*standards ; Mobile Applications ; Patient Safety ; Pediatrics/organization &amp; administration/*standards ; Pharmacy Service, Hospital/organization &amp; administration/standards ; Quality Improvement ; },
abstract = {Medication-related errors are among the most common medical errors, and studies have shown that the paediatric population is particularly vulnerable. Errors can occur during any step in the medication process. This review article seeks to highlight new advancements in the field of paediatric medication safety at each stage of the medication process, from ordering and transcribing to medication dispensing and administration. We will focus on interventions that are increasingly widely used, such as computerised provider order entry with clinical decision support, barcoding technologies and safe medication administration through technologies pumps (SMART pumps), as well as innovative mobile application devices and workflow management systems that are being piloted at single institutions. By highlighting what is new in paediatric medication safety, as well as the gaps that remain, we hope to continue to foster focus on this critically important area in order to create the safest possible environment for children.},
}
@article {pmid30153374,
year = {2019},
author = {Liszczak, G and Muir, TW},
title = {Nucleic Acid-Barcoding Technologies: Converting DNA Sequencing into a Broad-Spectrum Molecular Counter.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {58},
number = {13},
pages = {4144-4162},
pmid = {30153374},
issn = {1521-3773},
support = {F32 GM110880/GM/NIGMS NIH HHS/United States ; P01 CA196539/CA/NCI NIH HHS/United States ; R01 GM086868/GM/NIGMS NIH HHS/United States ; R01 GM107047/GM/NIGMS NIH HHS/United States ; R37 GM086868/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Computational Biology ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Nucleic Acids/*analysis ; Proteins/genetics/*metabolism ; },
abstract = {The emergence of high-throughput DNA sequencing technologies sparked a revolution in the field of genomics that has rippled into many branches of the life and physical sciences. The remarkable sensitivity, specificity, throughput, and multiplexing capacity that are inherent to parallel DNA sequencing have since motivated its use as a broad-spectrum molecular counter. A key aspect of extrapolating DNA sequencing to non-traditional applications is the need to append nucleic-acid barcodes to entities of interest. In this review, we describe the chemical and biochemical approaches that have enabled nucleic-acid barcoding of proteinaceous and non-proteinaceous materials and provide examples of downstream technologies that have been made possible by DNA-encoded molecules. As commercially available high-throughput sequencers were first released less than 15 years ago, we believe related applications will continue to mature and close by proposing new frontiers to support this assertion.},
}
@article {pmid30151871,
year = {2019},
author = {González-Varo, JP and Arroyo, JM and Jordano, P},
title = {The timing of frugivore-mediated seed dispersal effectiveness.},
journal = {Molecular ecology},
volume = {28},
number = {2},
pages = {219-231},
pmid = {30151871},
issn = {1365-294X},
support = {CGL2017-82847-P//Spanish MINECO/International ; RNM-5731//Junta de Andaluc&#xed;a Excellence Projects/International ; SEV-2012-0262//Severo Ochoa Award for Centres of Excellence in R+D+I/International ; H2020-MSCA-IF-2014-656572//Individual Fellowship from the Marie Sklodowska-Curie Actions/International ; },
mesh = {Animals ; Birds/classification/physiology ; *Ecosystem ; Feeding Behavior ; Forests ; Herbivory/physiology ; *Plant Physiological Phenomena ; Seed Dispersal/*physiology ; Seeds/growth &amp; development ; Symbiosis/*physiology ; },
abstract = {The seed dispersal effectiveness framework allows assessing mutualistic services from frugivorous animals in terms of quantity and quality. Quantity accounts for the number of seeds dispersed and quality for the probability of recruitment of dispersed seeds. Research on this topic has largely focused on the spatial patterns of seed deposition because seed fates often vary between microhabitats due to differences in biotic and abiotic factors. However, the temporal dimension has remained completely overlooked despite these factors-and even local disperser assemblages-can change dramatically during long fruiting periods. Here, we test timing effects on seed dispersal effectiveness, using as study case a keystone shrub species dispersed by frugivorous birds and with a fruiting period of 9 months. We evaluated quantity and quality in different microhabitats of a Mediterranean forest and different periods of the fruiting phenophase. We identified the bird species responsible for seed deposition through DNA barcoding and evaluated the probability of seedling recruitment through a series of field experiments on sequential demographic processes. We found that timing matters: The disperser assemblage was temporally structured, seed viability decreased markedly during the plant's fruiting phenophase, and germination was lower for viable seeds dispersed in the fruiting peak. We show how small contributions to seed deposition by transient migratory species can result in a relevant effectiveness if they disperse seeds in a high-quality period for seedling recruitment. This study expands our understanding of seed dispersal effectiveness, highlighting the importance of timing and infrequent interactions for population and community dynamics.},
}
@article {pmid30151767,
year = {2018},
author = {Gupta, M and Sonnett, M and Ryazanova, L and Presler, M and Wühr, M},
title = {Quantitative Proteomics of Xenopus Embryos I, Sample Preparation.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1865},
number = {},
pages = {175-194},
pmid = {30151767},
issn = {1940-6029},
support = {F31 GM116451/GM/NIGMS NIH HHS/United States ; R01 GM103785/GM/NIGMS NIH HHS/United States ; R35 GM128813/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Chemical Precipitation ; Chromatography, Liquid ; Cysteine/metabolism ; Egg Yolk/metabolism ; Embryo, Nonmammalian/*metabolism ; Hydrogen-Ion Concentration ; Mass Spectrometry ; Peptides/metabolism ; Proteomics/*methods ; Quality Control ; Solid Phase Extraction ; Xenopus/*embryology ; Xenopus Proteins/metabolism ; },
abstract = {Xenopus oocytes and embryos are model systems optimally suited for quantitative proteomics. This is due to the availability of large amount of protein material and the ease of physical manipulation. Furthermore, facile in vitro fertilization provides superbly synchronized embryos for cell cycle and developmental stages. Here, we detail protocols developed over the last few years for sample preparation of multiplexed proteomics with TMT-tags followed by quantitative mass spectrometry analysis using the MultiNotch MS3 approach. In this approach, each condition is barcoded with an isobaric tag at the peptide level. After barcoding, samples are combined and the relative abundance of ~100,000 peptides is quantified on a mass spectrometer. High reproducibility of the sample preparation process prior to peptides being tagged and combined is of upmost importance for obtaining unbiased data. Otherwise, differences in sample handling can inadvertently appear as biological changes. We detail and exemplify the application of our sample workflow on an embryonic time-series of ten developmental stages of Xenopus laevis embryos ranging from the egg to stage 35 (just before hatching). Our accompanying paper (Chapter 14) details a bioinformatics pipeline to analyze the quality of the given sample preparation and strategies to convert spectra of X. laevis peptides into biologically interpretable data.},
}
@article {pmid30150316,
year = {2018},
author = {Mansukhani, S and Barber, LJ and Kleftogiannis, D and Moorcraft, SY and Davidson, M and Woolston, A and Proszek, PZ and Griffiths, B and Fenwick, K and Herman, B and Matthews, N and O'Leary, B and Hulkki, S and Gonzalez De Castro, D and Patel, A and Wotherspoon, A and Okachi, A and Rana, I and Begum, R and Davies, MN and Powles, T and von Loga, K and Hubank, M and Turner, N and Watkins, D and Chau, I and Cunningham, D and Lise, S and Starling, N and Gerlinger, M},
title = {Ultra-Sensitive Mutation Detection and Genome-Wide DNA Copy Number Reconstruction by Error-Corrected Circulating Tumor DNA Sequencing.},
journal = {Clinical chemistry},
volume = {64},
number = {11},
pages = {1626-1635},
pmid = {30150316},
issn = {1530-8561},
support = {/DH_/Department of Health/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 18377/CRUK_/Cancer Research UK/United Kingdom ; 105104/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; MR/N002121/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Biomarkers, Tumor/*blood/genetics ; Circulating Tumor DNA/*blood/genetics ; Colorectal Neoplasms/blood/genetics/pathology ; DNA Copy Number Variations/*genetics ; DNA Mutational Analysis/*methods ; Genome-Wide Association Study ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Mutation ; Neoplasm Metastasis ; Sensitivity and Specificity ; },
abstract = {BACKGROUND: Circulating free DNA sequencing (cfDNA-Seq) can portray cancer genome landscapes, but highly sensitive and specific technologies are necessary to accurately detect mutations with often low variant frequencies.<br><br>METHODS: We developed a customizable hybrid-capture cfDNA-Seq technology using off-the-shelf molecular barcodes and a novel duplex DNA molecule identification tool for enhanced error correction.<br><br>RESULTS: Modeling based on cfDNA yields from 58 patients showed that this technology, requiring 25 ng of cfDNA, could be applied to >95% of patients with metastatic colorectal cancer (mCRC). cfDNA-Seq of a 32-gene, 163.3-kbp target region detected 100% of single-nucleotide variants, with 0.15% variant frequency in spike-in experiments. Molecular barcode error correction reduced false-positive mutation calls by 97.5%. In 28 consecutively analyzed patients with mCRC, 80 out of 91 mutations previously detected by tumor tissue sequencing were called in the cfDNA. Call rates were similar for point mutations and indels. cfDNA-Seq identified typical mCRC driver mutations in patients in whom biopsy sequencing had failed or did not include key mCRC driver genes. Mutations only called in cfDNA but undetectable in matched biopsies included a subclonal resistance driver mutation to anti-EGFR antibodies in KRAS, parallel evolution of multiple PIK3CA mutations in 2 cases, and TP53 mutations originating from clonal hematopoiesis. Furthermore, cfDNA-Seq off-target read analysis allowed simultaneous genome-wide copy number profile reconstruction in 20 of 28 cases. Copy number profiles were validated by low-coverage whole-genome sequencing.<br><br>CONCLUSIONS: This error-corrected, ultradeep cfDNA-Seq technology with a customizable target region and publicly available bioinformatics tools enables broad insights into cancer genomes and evolution.<br><br>CLINICALTRIALSGOV IDENTIFIER: NCT02112357.},
}
@article {pmid30149558,
year = {2018},
author = {Noh, P and Kim, WJ and Yang, S and Park, I and Moon, BC},
title = {Authentication of the Herbal Medicine Angelicae Dahuricae Radix Using an ITS Sequence-Based Multiplex SCAR Assay.},
journal = {Molecules (Basel, Switzerland)},
volume = {23},
number = {9},
pages = {},
pmid = {30149558},
issn = {1420-3049},
mesh = {Angelica/*chemistry/classification ; Base Sequence ; *DNA, Intergenic ; Herbal Medicine/*standards ; *Nucleic Acid Amplification Techniques ; Phylogeny ; Plants, Medicinal/*genetics ; Species Specificity ; },
abstract = {The accurate identification of plant species is of great concern for the quality control of herbal medicines. The Korean Pharmacopoeia and the Pharmacopoeia of the People's Republic of China define Angelicae Dahuricae Radix (Baek-Ji in Korean and Bai-zhi in Chinese) as the dried roots of Angelica dahurica or A. dahurica var. formosana belonging to the family Apiaceae. Discrimination among Angelica species on the basis of morphological characteristics is difficult due to their extremely polymorphic traits and controversial taxonomic history. Furthermore, dried roots processed for medicinal applications are indistinguishable using conventional methods. DNA barcoding is a useful and reliable method for the identification of species. In this study, we sequenced the internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes in A. dahurica, A. dahurica var. formosana, and the related species A. anomala and A. japonica. Using these sequences, we designed species-specific primers, and developed and optimized a multiplex sequence-characterized amplified region (SCAR) assay that can simply and rapidly identify respective species, and verify the contamination of adulterant depending on the polymerase chain reaction (PCR) amplification without sequencing analysis in a single PCR reaction. This assay successfully identified commercial samples of Angelicae Dahuricae Radix collected from Korean and Chinese herbal markets, and distinguished them from adulterants. This multiplex SCAR assay shows a great potential in reducing the time and cost involved in the identification of genuine Angelicae Dahuricae Radix and adulterant contamination.},
}
@article {pmid30144131,
year = {2018},
author = {Tabssum, F and Ahmad, QU and Qazi, JI},
title = {DNA sequenced based bacterial taxonomy should entail decisive phenotypic remarks: Towards a balanced approach.},
journal = {Journal of basic microbiology},
volume = {58},
number = {11},
pages = {918-927},
doi = {10.1002/jobm.201800319},
pmid = {30144131},
issn = {1521-4028},
mesh = {Bacteria/chemistry/*classification/*genetics/isolation &amp; purification ; Bacterial Typing Techniques/*standards ; DNA Barcoding, Taxonomic/standards ; DNA, Bacterial/genetics ; Genome, Bacterial/genetics ; Genotype ; Metagenomics/standards ; Phenotype ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*standards ; },
abstract = {Phenotypic characteristics while complimenting 16S rRNA gene sequencing in identifying bacteria become decisive in solving conflicts of equal % similarity of a given DNA sequence to more than one classified microorganisms. "Phenotypic light" may also indicate right direction when a new species' 16S rDNA sequence is under consideration. In fact 16S rRNA gene sequences give indication that either a novel species has been isolated or the test organism is identified. In each case additional tests are required for resolving different issues. Predictions of microbial phenotypes from metagenomic data depend heavily on our knowledge of expressed genes. Thus renaissance of microbial phenotypic characterization is likely to emerge at par with genotypic signatures. Interplay of these and other complimentary levels of analyses are likely to lead DNA barcoding for microorganisms as it has provided efficient methods for species-level identifications of animals and plants. In this review, an attempt has been made to realize the reader(s) importance of interplay of genotypic and phenotypic characteristics of bacteria for development of comprehensive and more stable classification schemes. It is expected that future valid classification schemes will be based on the phenetic relationships of microorganisms.},
}
@article {pmid30143746,
year = {2018},
author = {Osathanunkul, M and Osathanunkul, K and Wongwanakul, S and Osathanunkul, R and Madesis, P},
title = {Multiuse of Bar-HRM for Ophiocordyceps sinensis identification and authentication.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {12770},
pmid = {30143746},
issn = {2045-2322},
mesh = {DNA Barcoding, Taxonomic/*methods ; Hypocreales/*classification/*genetics ; Nucleic Acid Denaturation ; Species Specificity ; Transition Temperature ; },
abstract = {Bar-HRM is a hybrid method which combines DNA barcoding and High Resolution Melting analysis. It has proven to be a fast, cost-effective and reliable molecular approach for species identification and authentication. Here, three aspects of the use of Bar-HRM are focused on. First, Bar-HRM is used to discriminate between closely related Ophiocordyceps species. Second, identification of an unknown powder that is claimed to be Ophiocordyceps species using Bar-HRM. Third, authenticating the O. sinensis products sold on the market by the Bar-HRM. Results from HRM analyses with ITS primers shows that the two Ophiocordyceps species (Ophiocordyceps sinensis and Ophiocordyceps militaris) were easily differentiated. Also, an unknown sample was able to be identified in less time compared with using DNA barcoding alone. In addition, the substitution or adulteration of O. sinensis products sold on market was detected via Bar-HRM. The substitution or adulteration of inferior Ophiocordyceps species, particularly O. militaris in high price O. sinensis products has been a concern throughout Asia. Based on our results, the Bar-HRM was again proved to be a promising tool for species identification and authentication.},
}
@article {pmid30139965,
year = {2018},
author = {Osathanunkul, M},
title = {Bar-HRM for authenticating soursop (Annona muricata) tea.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {12666},
pmid = {30139965},
issn = {2045-2322},
mesh = {Annona/classification/*genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Plant/genetics ; Plants, Medicinal/classification/*genetics ; },
abstract = {Drinking soursop (Annona muricata) tea has become popular in Thailand due to recent findings about the medicinal properties of soursop tea regarding anti-cancer in particular. Consequently, numerous A. muricata tea products were found to be sold on markets and relatively expensive. It is almost impossible to identify the plant species component in the tea bag or powder products using traditional methods which are based on morphological characters. Therefore, a main objective of this study is to develop a molecular method called Bar-HRM (DNA barcoding coupled with High Resolution Melting) for authenticating A. muricata products. Three chloroplast regions including matK, rbcL and trnL were selected for in silico analyses. The findings show that rbcL is the most suitable region to be used for species identification in HRM analysis. Eleven A. muricata herbal products were purchased and tested with rbcL primers. Results from melting profile indicated that three out of eleven tested products were adulterated with other Annona species. It is believed that the Annona products are adulterated to increase the quantity and to make more profit. Notably, all of the tested products purchased from local producers were found to contain herbal species that differ from the species indicated by the seller.},
}
@article {pmid30139253,
year = {2018},
author = {Wu, X and DeGottardi, Q and Wu, IC and Wu, L and Yu, J and Kwok, WW and Chiu, DT},
title = {Ratiometric Barcoding for Mass Cytometry.},
journal = {Analytical chemistry},
volume = {90},
number = {18},
pages = {10688-10694},
pmid = {30139253},
issn = {1520-6882},
support = {DP3 DK097653/DK/NIDDK NIH HHS/United States ; R01 MH115767/MH/NIMH NIH HHS/United States ; },
mesh = {Cell Separation ; Endocytosis ; Flow Cytometry/*methods ; Fluorescent Dyes/chemistry ; *High-Throughput Screening Assays ; Humans ; Leukocyte Common Antigens/immunology ; Leukocytes, Mononuclear/cytology/immunology ; MCF-7 Cells ; Radiometry/methods ; Semiconductors ; },
abstract = {Barcoding is of importance for high-throughput cellular and molecular analysis. A ratiometric barcoding strategy using lanthanide-coordinated polymer dots (Ln-Pdots) was developed for mass cytometric analysis. By using 3 metal isotopes and 4 ratio intensity levels, 16 barcodes were generated to code, and later decode, cell samples in mass cytometry. The ratiometric Ln-Pdot barcodes not only provided high-mass-signal intensities but also eliminated the bias caused by different concentrations of the labeling reagents/barcodes and run-to-run differences in cell labeling efficiency. The ability to distinguish clearly the 16 sets of labeled MCF-7 cells with mass cytometry demonstrated the excellent resolving power of the ratiometric Ln-Pdot barcodes. Furthermore, the results from barcoding PBMC samples via CD45-specific cellular targeting indicated that the ratiometric Ln-Pdot barcodes could facilitate mass cytometry in high-throughput and multiplexed analysis, especially with precious human samples.},
}
@article {pmid30131909,
year = {2018},
author = {Dean, GH and Asmarayani, R and Ardiyani, M and Santika, Y and Triono, T and Mathews, S and Webb, CO},
title = {Generating DNA sequence data with limited resources for molecular biology: Lessons from a barcoding project in Indonesia.},
journal = {Applications in plant sciences},
volume = {6},
number = {7},
pages = {e01167},
pmid = {30131909},
issn = {2168-0450},
abstract = {The advent of the DNA sequencing age has led to a revolution in biology. The rapid and cost-effective generation of high-quality sequence data has transformed many fields, including those focused on discovering species and surveying biodiversity, monitoring movement of biological materials, forensic biology, and disease diagnostics. There is a need to build capacity to generate useful sequence data in countries with limited historical access to laboratory resources, so that researchers can benefit from the advantages offered by these data. Commonly used molecular techniques such as DNA extraction, PCR, and DNA sequencing are within the reach of small laboratories in many countries, with the main obstacles to successful implementation being lack of funding and limited practical experience. Here we describe a successful approach that we developed to obtain DNA sequence data during a small DNA barcoding project in Indonesia.},
}
@article {pmid30131899,
year = {2018},
author = {Zhao, LL and Feng, SJ and Tian, JY and Wei, AZ and Yang, TX},
title = {Internal transcribed spacer 2 (ITS2) barcodes: A useful tool for identifying Chinese Zanthoxylum.},
journal = {Applications in plant sciences},
volume = {6},
number = {6},
pages = {e01157},
pmid = {30131899},
issn = {2168-0450},
abstract = {PREMISE OF THE STUDY: The genus Zanthoxylum in the Rutaceae family of trees and shrubs has a long history of domestication and cultivation in Asia for both economic and medicinal purposes. However, many Zanthoxylum species are morphologically similar and are easily confused. This often leads to false authentication of source materials and confusion in herbal markets, hindering their safe utilization and genetic resource conservation. DNA barcoding is a promising tool for identifying plant taxa.<br><br>METHODS: We used three candidate DNA barcoding regions (ITS2, ETS, and trnH-psbA) to identify 69 accessions representing 13 Chinese Zanthoxylum species. The discriminatory capabilities of these regions were evaluated in terms of PCR amplification success, intra- and interspecific divergence, DNA barcoding gaps, and identification efficiency using the BLAST and tree-building methods.<br><br>RESULTS: ITS2 proved the most useful for discriminating Chinese Zanthoxylum species, with a correct identification rate of 100%, and this region also exhibited significantly higher intra- and interspecific divergence.<br><br>DISCUSSION: Phylogenetic analysis confirmed that ITS2 has a powerful discriminatory ability both at and below the species level. We confirmed that ITS2 is a powerful barcoding region for identifying Chinese Zanthoxylum species, and will be useful for analyzing and managing Chinese Zanthoxylum germplasm collections.},
}
@article {pmid30131893,
year = {2018},
author = {Thomson, AM and Vargas, OM and Dick, CW},
title = {Complete plastome sequences from Bertholletia excelsa and 23 related species yield informative markers for Lecythidaceae.},
journal = {Applications in plant sciences},
volume = {6},
number = {5},
pages = {e01151},
pmid = {30131893},
issn = {2168-0450},
abstract = {PREMISE OF THE STUDY: The tropical tree family Lecythidaceae has enormous ecological and economic importance in the Amazon basin. Lecythidaceae species can be difficult to identify without molecular data, however, and phylogenetic relationships within and among the most diverse genera are poorly resolved.<br><br>METHODS: To develop informative genetic markers for Lecythidaceae, we used genome skimming to de novo assemble the full plastome of the Brazil nut tree (Bertholletia excelsa) and 23 other Lecythidaceae species. Indices of nucleotide diversity and phylogenetic signal were used to identify regions suitable for genetic marker development.<br><br>RESULTS: The B. excelsa plastome contained 160,472 bp and was arranged in a quadripartite structure. Using the 24 plastome alignments, we developed primers for 10 coding and non-coding DNA regions containing exceptional nucleotide diversity and phylogenetic signal. We also developed 19 chloroplast simple sequence repeats for population-level studies.<br><br>DISCUSSION: The coding region ycf1 and the spacer rpl16-rps3 outperformed plastid DNA markers previously used for barcoding and phylogenetics. Used in a phylogenetic analysis, the matrix of 24 plastomes showed with 100% bootstrap support that Lecythis and Eschweilera are polyphyletic. The plastomes and primers presented in this study will facilitate a broad array of ecological and evolutionary studies in Lecythidaceae.},
}
@article {pmid30130188,
year = {2019},
author = {Chen, C and Huang, W and Zhang, L and Mow, WH},
title = {Robust and Unobtrusive Display-to-Camera Communications via Blue Channel Embedding.},
journal = {IEEE transactions on image processing : a publication of the IEEE Signal Processing Society},
volume = {28},
number = {1},
pages = {156-169},
doi = {10.1109/TIP.2018.2865681},
pmid = {30130188},
issn = {1941-0042},
abstract = {Due to the rapid advancement in processing power and camera quality of mobile devices, research on the display-to-camera (D2C) communication channel has recently received increasing attention. Unlike the traditional QR Code, the unobtrusive D2C communication scheme normally serves both the human eyes and the mobile camera in commercial advertisements. Thus, attention should be paid to both unobtrusiveness and reliability of the design of a D2C communication scheme. In this paper, 2D barcodes with unobtrusive embedding in the blue channel are proposed in image and video formats to yield the robust and unobtrusive (RU) code and video-based RU (vRU) code, respectively. The proposed RU code is featured with a modulation scheme in blue channel that leverages several important properties of the human visual system; such as insensitivity toward the yellow-blue chrominance component, the proximity principle, and the oblique effect. Both RU code and vRU code employ a low-density-parity-check code for intra-frame channel coding. In addition, vRU code adopts an erasure-correcting Reed-Solomon code for inter-frame channel coding. Under a high perceptual quality constraint (multiscale structural similarity (MS-SSIM) ≈ 0.95), RU code achieves a demodulation bit error probability of 3.84%, which is an order of magnitude smaller than that of the existing picture-embedding 2D barcodes. Meanwhile, under a similar perceptual quality requirement (MS-SSIM ≈ 0.95 for each video frame), the goodput of vRU code is reported to be as high as 34.33 kbps under practical settings, e.g., a display frame rate of 30 fps and a capture frame rate of 42 fps.},
}
@article {pmid30130099,
year = {2018},
author = {Pan, M and Liao, WM and Yin, SY and Sun, SS and Su, CY},
title = {Single-Phase White-Light-Emitting and Photoluminescent Color-Tuning Coordination Assemblies.},
journal = {Chemical reviews},
volume = {118},
number = {18},
pages = {8889-8935},
doi = {10.1021/acs.chemrev.8b00222},
pmid = {30130099},
issn = {1520-6890},
abstract = {Metal-organic complexes assembled from coordinative interactions are known to be able to display a wide range of photoluminescent behaviors benefiting from an extensive number of metal ions, organic linkers, and inclusion guests, depending on the multifaceted nature of their chemical structures and photophysical properties. In the past two decades, the white-light-emitting (WLE) and photoluminescent color-tuning (PLCT) materials based on the single-phase metal-organic coordination assemblies have merited particular attention and gained substantial advances. In this review, we give an overview of recent progress in this field, placing emphasis on the WLE and PLCT properties realized in the single-phase materials, which covers the origin, generation, and manipulation of different types of photoluminescence (PL) derived from ligand-centered (LC), metal/cluster-centered (MC or CC), excimer/exciplex-based (EX), metal-to-ligand or ligand-to-metal charge-transfer-based (MLCT or LMCT), or guest-included emissions. The coordination assemblies in this topic can be generally classified into three categories [(1) mono/homometallic coordination assemblies based on main group (s,p-block), transition (d-block), or lanthanide (f-block) metal centers, (2) s/p-f-, d-f-, or f-f-type heterometallic coordination assemblies, and (3) guest-included coordination assemblies] for which WLE and PLCT properties can be achieved by virtue of either a wide-band/overlapped emission covering the whole visible spectrum from a single emitting center or a combination of complementary color emissions from multiple emitting centers/origins. Some state-of-the-art assembly methods and successful design models relevant to the above three categories are elaborated to demonstrate how to achieve efficient and controllable white-light emission in a single-phase material through a tunable PL approach. Potential applications in the fields of lighting and displaying, sensing and detecting, and barcoding and patterning are surveyed, and at the end, possible prospects and challenges for future development along this line are proposed.},
}
@article {pmid30129071,
year = {2018},
author = {Andújar, C and Arribas, P and Yu, DW and Vogler, AP and Emerson, BC},
title = {Why the COI barcode should be the community DNA metabarcode for the metazoa.},
journal = {Molecular ecology},
volume = {27},
number = {20},
pages = {3968-3975},
doi = {10.1111/mec.14844},
pmid = {30129071},
issn = {1365-294X},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; },
abstract = {Metabarcoding of complex metazoan communities is increasingly being used to measure biodiversity in terrestrial, freshwater and marine ecosystems, revolutionizing our ability to observe patterns and infer processes regarding the origin and conservation of biodiversity. A fundamentally important question is which genetic marker to amplify, and although the mitochondrial cytochrome oxidase subunit I (COI) gene is one of the more widely used markers in metabarcoding for the Metazoa, doubts have recently been raised about its suitability. We argue that (a) the extensive coverage of reference sequence databases for COI; (b) the variation it presents; (c) the comparative advantages for denoising protein-coding genes; and (d) recent advances in DNA sequencing protocols argue in favour of standardizing for the use of COI for metazoan community samples. We also highlight where research efforts should focus to maximize the utility of metabarcoding.},
}
@article {pmid30128603,
year = {2018},
author = {De Castro, O and Avino, M and Di Maio, A and Menale, B and Guida, M},
title = {Sanger and next generation sequencing in the characterisation of arbuscular mycorrhizal fungi (AMF) in Pancratium maritimum L. (Amaryllidaceae), a representative plant species of Mediterranean sand dunes.},
journal = {Planta},
volume = {248},
number = {6},
pages = {1443-1453},
pmid = {30128603},
issn = {1432-2048},
support = {2012-83//Nando and Elsa Peretti Foundation/ ; },
mesh = {Amaryllidaceae/*microbiology ; DNA Barcoding, Taxonomic ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fungi/*genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Mycorrhizae/*genetics/isolation &amp; purification ; Plant Roots/microbiology ; Sequence Analysis, DNA ; },
abstract = {An interesting AMF colonization microcosm has been detected in the roots of Pancratium maritimum (sea daffodil). Both sequencing techniques (Sanger and NGS) have been used for AMF characterisation, showing a balanced trade-off between pros and cons. By Sanger and next generation sequencing of rRNA nuclear molecular markers (SSU-ITS-LSU and ITS2, respectively), the presence of AMF communities in the roots of P. maritimum was evaluated. Our results shed light on the presence of AMF in sea daffodil and the diversity of assemblages of AMF detected after Sanger sequencing of the SSU-ITS-LSU marker is much higher than that determined following NGS sequencing of ITS2 alone.},
}
@article {pmid30127839,
year = {2018},
author = {Baloğlu, B and Clews, E and Meier, R},
title = {NGS barcoding reveals high resistance of a hyperdiverse chironomid (Diptera) swamp fauna against invasion from adjacent freshwater reservoirs.},
journal = {Frontiers in zoology},
volume = {15},
number = {},
pages = {31},
pmid = {30127839},
issn = {1742-9994},
abstract = {BACKGROUND: Macroinvertebrates such as non-biting midges (Chironomidae: Diptera) are important components of freshwater ecosystems. However, they are often neglected in biodiversity and conservation research because invertebrate species richness is difficult and expensive to quantify with traditional methods. We here demonstrate that Next Generation Sequencing barcodes ("NGS barcodes") can provide relief because they allow for fast and large-scale species-level sorting of large samples at low cost.<br><br>RESULTS: We used NGS barcoding to investigate the midge fauna of Singapore's swamp forest remnant (Nee Soon Swamp Forest). Based on >&#x2009;14.000 barcoded specimens, we find that the swamp forest maintains an exceptionally rich fauna composed of an observed number of 289 species (estimated 336 species) in a very small area (90&#xa0;ha). We furthermore barcoded the chironomids from three surrounding reservoirs that are located in close proximity. Although the swamp forest remnant is much smaller than the combined size of the freshwater reservoirs in the study (90&#xa0;ha vs. >&#x2009;450&#xa0;ha), the latter only contains 33 (estimated 61) species. We show that the resistance of the swamp forest species assemblage is high because only 8 of the 314 species are shared despite the close proximity. Moreover, shared species are not very abundant (3% of all specimens). A redundancy analysis revealed that ~&#x2009;21% of the compositional variance of midge communities within the swamp forest was explained by a range of variables with conductivity, stream order, stream width, temperature, latitude&#xa0;(flow direction), and year being significant factors influencing community structure. An LME analysis demonstrates that the total species richness decreased with increasing&#xa0;conductivity.<br><br>CONCLUSION: Our study demonstrates that midge diversity of a swamp forest can be so high that it questions global species diversity estimates for Chironomidae, which are an important component of many freshwater ecosystems. We furthermore demonstrate that small and natural habitat remnants can have high species turnover and can be very resistant to the invasion of species from neighboring reservoirs. Lastly, the study shows how NGS barcodes can be used to integrate specimen- and species-rich invertebrate taxa in biodiversity and conservation research.},
}
@article {pmid30125304,
year = {2018},
author = {Dechbumroong, P and Aumnouypol, S and Denduangboripant, J and Sukrong, S},
title = {DNA barcoding of Aristolochia plants and development of species-specific multiplex PCR to aid HPTLC in ascertainment of Aristolochia herbal materials.},
journal = {PloS one},
volume = {13},
number = {8},
pages = {e0202625},
pmid = {30125304},
issn = {1932-6203},
mesh = {Aristolochia/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; DNA, Ribosomal Spacer/classification/genetics ; Europe ; Multiplex Polymerase Chain Reaction/*methods ; Plant Preparations ; Species Specificity ; Thailand ; },
abstract = {The anecdotal evidence is outstanding on the uses of Aristolochia plants as traditional medicines and dietary supplements in many regions of the world. However, herbal materials derived from Aristolochia species have been identified as potent human carcinogens since the first case of severe renal disease after ingesting these herbal preparations. Any products containing Aristolochia species have thus been banned on many continents, including Europe, America and Asia. Therefore, the development of a method to identify these herbs is critically needed for customer safety. The present study evaluated DNA barcoding of the rbcL, matK, ITS2 and trnH-psbA regions among eleven Aristolochia species collected in Thailand. Polymorphic sites were observed in all four DNA loci. Among those eleven Aristolochia species, three species (A. pierrei, A. tagala and A. pothieri) are used as herbal materials in Thai folk medicine, namely, in Thai "Krai-Krue". "Krai-Krue" herbs are interchangeably used as an admixture in Thai traditional remedies without specific knowledge of their identities. A species-specific multiplex PCR based on nucleotide polymorphisms in the ITS2 region was developed as an identification tool to differentiate these three Aristolochia species and to supplement the HPTLC pattern in clarifying the origins of herbal materials. The combination of multiplex PCR and HPTLC profiling achieves accurate herbal identification with the goal of protecting consumers from the health risks associated with product substitution and contamination.},
}
@article {pmid30123709,
year = {2018},
author = {Moore, CS and Ruocchio, MJ and Blakeslee, AMH},
title = {Distribution and population structure in the naked goby Gobiosoma bosc (Perciformes: Gobiidae) along a salinity gradient in two western Atlantic estuaries.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5380},
pmid = {30123709},
issn = {2167-8359},
abstract = {Many species of fish produce larvae that undergo a prolonged dispersal phase. However, evidence from a number of recent studies on demersal fishes suggests that the dispersal of propagules may not be strongly correlated with gene flow. Instead, other factors like larval behavior and the availability of preferred settlement habitat may be more important to maintaining population structure. We used an ecologically important benthic fish species, Gobiosoma bosc (naked goby), to investigate local and regional scale population structure and gene flow along a salinity gradient (∼3 ppt to ∼18 ppt) in two North Carolina estuaries. G. bosc is an abundant and geographically widespread species that requires complex but patchy microhabitat (e.g. oyster reefs, rubble, woody debris) for reproduction and refuge. We sequenced 155 fish from 10 sites, using a common barcoding gene (COI). We also included recent sequence data from GenBank to determine how North Carolina populations fit into the larger biogeographic understanding of this species. In North Carolina, we found a significant amount of gene flow within and between estuaries. Our analysis also showed high predicted genetic diversity based upon a large number of rare haplotypes found within many of our sampled populations. Moreover, we detected a number of new haplotypes in North Carolina that had not yet been observed in prior work. Sampling along a salinity gradient did not reveal any significant positive or negative correlations between salinity and genetic diversity, nor the proportion of singleton haplotypes, with the exception of a positive correlation between salinity standard deviation and genetic diversity. We also found evidence that an introduced European population of naked gobies may have originated from an Atlantic source population. Altogether, this system offers a compelling way to evaluate whether factors other than dispersal per se mediate recruitment in an estuarine-dependent species of fish with a larval dispersal phase. It also demonstrates the importance of exploring both smaller and larger scale population structure in marine organisms to better understand local and regional patterns of population connectivity and gene flow.},
}
@article {pmid30123658,
year = {2018},
author = {Hosoya, T and Hosaka, K and Nam, KO},
title = {A check list of non-lichenised fungi occurring on Fagus crenata, a tree endemic to Japan.},
journal = {Mycology},
volume = {9},
number = {1},
pages = {29-34},
pmid = {30123658},
issn = {2150-1203},
abstract = {Non-lichenised fungi from Fagus crenata, an endemic and major temperate tree species, were enumerated based on three approaches: fungarium specimens at the National Museum of Nature and Science; isolates obtained mainly from leaves and roots, and their molecular identification by barcoding region; and literature. In total, 209, 49, and 232 taxa were recognised from the fungarium specimens, isolates, and literature, respectively. Only three taxa were commonly observed using all three approaches. Moreover, the results demonstrate the diversity of fungi occurring on a single host plant species, and provide the basis for comparisons between fungi from Fagus spp. in other regions of the world.},
}
@article {pmid30123025,
year = {2018},
author = {Morano, E and Bonal, R},
title = {Araneusbonali sp. n., a novel lichen-patterned species found on oak trunks (Araneae, Araneidae).},
journal = {ZooKeys},
volume = {},
number = {779},
pages = {119-145},
pmid = {30123025},
issn = {1313-2989},
abstract = {The new species Araneusbonali Morano, sp. n. (Araneae, Araneidae) collected in central and western Spain is described and illustrated. Its novel status is confirmed after a thorough revision of the literature and museum material from the Mediterranean Basin. The taxonomy of Araneus is complicated, but both morphological and molecular data supported the genus membership of Araneusbonali Morano, sp. n. Additionally, the species uniqueness was confirmed by sequencing the barcode gene cytochrome oxidase I from the new species and comparing it with the barcodes available for species of Araneus. A molecular phylogeny, based on nuclear and mitochondrial genes, retrieved a clade with a moderate support that grouped Araneusdiadematus Clerck, 1757 with another eleven species, but neither included Araneusbonali sp. n. nor Araneusangulatus Clerck, 1757, although definitive conclusions about the relationships among Araneus species need more markers examined and a broader taxonomic coverage. The new species was collected on isolated holm oaks and forest patches within agricultural landscapes. Adults were mostly trapped on tree trunks, where their lichen-like colours favour mimicry, while juveniles were collected on tree branches. Specimens were never found either in ground traps or grass samples. This species overwinters as egg, juveniles appear in early spring, but reproduction does not take place until late summer-early autumn. Araneusbonali Morano, sp. n. was found in the same locality from where another new spider species was described. Nature management policies should thus preserve isolated trees as key refuges for forest arthropods in agricultural landscapes, as they may be hosting more unnoticed new species. After including Araneusbonali Morano, sp. n. and removing doubtful records and synonymies, the list of Araneus species in the Iberian Peninsula numbers eight.},
}
@article {pmid30118872,
year = {2018},
author = {Yowang, A and Tsaousis, AD and Chumphonsuk, T and Thongsin, N and Kullawong, N and Popluechai, S and Gentekaki, E},
title = {High diversity of Blastocystis subtypes isolated from asymptomatic adults living in Chiang Rai, Thailand.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {65},
number = {},
pages = {270-275},
doi = {10.1016/j.meegid.2018.08.010},
pmid = {30118872},
issn = {1567-7257},
support = {BB/M009971/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Asymptomatic Diseases ; Blastocystis/*genetics ; Blastocystis Infections/*epidemiology/etiology/*parasitology ; Feces/parasitology ; Genetic Variation ; Humans ; *Phylogeny ; Prevalence ; Thailand/epidemiology ; },
abstract = {Blastocystis is a common and broadly distributed microbial eukaryote inhabiting the gut of humans and other animals. The genetic diversity of Blastocystis is extremely high comprising no less than 17 subtypes in mammals and birds. Nonetheless, little is known about the prevalence and distribution of Blastocystis subtypes colonising humans in Thailand. Molecular surveys of Blastocystis remain extremely limited and usually focus on the central, urban part of the country. To address this knowledge gap, we collected stool samples from a population of Thai adults (n = 178) residing in Chiang Rai Province. The barcoding region of the small subunit ribosomal RNA was employed to screen for Blastocystis and identify the subtype. Forty-one stool samples (23%) were identified as Blastocystis positive. Six of the nine subtypes that colonise humans were detected with subtype (ST) three being the most common (68%), followed by ST1 (17%) and ST7 (7%). Comparison of subtype prevalence across Thailand using all publicly available sequences showed that subtype distribution differs among geographic regions in the country. ST1 was most commonly encountered in the central region of Thailand, while ST3 dominated in the more rural north and northeast regions. ST2 was absent in the northeast, while ST7 was not found in the center. Thus, this study shows that ST prevalence and distribution differs not only among countries, but also among geographic regions within a country. Potential explanations for these observations are discussed herewith.},
}
@article {pmid30118180,
year = {2019},
author = {Bell, KL and Burgess, KS and Botsch, JC and Dobbs, EK and Read, TD and Brosi, BJ},
title = {Quantitative and qualitative assessment of pollen DNA metabarcoding using constructed species mixtures.},
journal = {Molecular ecology},
volume = {28},
number = {2},
pages = {431-455},
doi = {10.1111/mec.14840},
pmid = {30118180},
issn = {1365-294X},
support = {W911NF-13-1-0100//Army Research Office/International ; W911NF-13-1-0247//Army Research Office/International ; W911NF-17-1-0382//Army Research Office/International ; },
mesh = {Computational Biology ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/classification/*genetics ; Pollen/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Pollen DNA metabarcoding-marker-based genetic identification of potentially mixed-species pollen samples-has applications across a variety of fields. While basic species-level pollen identification using standard DNA barcode markers is established, the extent to which metabarcoding (a) correctly assigns species identities to mixes (qualitative matching) and (b) generates sequence reads proportionally to their relative abundance in a sample (quantitative matching) is unclear, as these have not been assessed relative to known standards. We tested the quantitative and qualitative robustness of metabarcoding in constructed pollen mixtures varying in species richness (1-9 species), taxonomic relatedness (within genera to across class) and rarity (5%-100% of grains), using Illumina MiSeq with the markers rbcL and ITS2. Qualitatively, species composition determinations were largely correct, but false positives and negatives occurred. False negatives were typically driven by lack of a barcode gap or rarity in a sample. Species richness and taxonomic relatedness, however, did not strongly impact correct determinations. False positives were likely driven by contamination, chimeric sequences and/or misidentification by the bioinformatics pipeline. Quantitatively, the proportion of reads for each species was only weakly correlated with its relative abundance, in contrast to suggestions from some other studies. Quantitative mismatches are not correctable by consistent scaling factors, but instead are context-dependent on the other species present in a sample. Together, our results show that metabarcoding is largely robust for determining pollen presence/absence but that sequence reads should not be used to infer relative abundance of pollen grains.},
}
@article {pmid30117780,
year = {2018},
author = {Waki, T and Nakao, M and Hayashi, K and Ikezawa, H and Tsutumi, N},
title = {MOLECULAR AND MORPHOLOGICAL DISCRIMINATION OF DICROCOELIID LARVAE (TREMATODA: DIGENEA) FROM TERRESTRIAL MOLLUSKS IN JAPAN.},
journal = {The Journal of parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1645/18-24},
pmid = {30117780},
issn = {1937-2345},
abstract = {Trematodes of the family Dicrocoeliidae commonly use terrestrial mollusks as the first intermediate host. Despite the abundant studies on the adult worms in birds and mammals, few reports exist on their larval stage in snail intermediate hosts. A present survey of mollusks in Japan led us to the discovery of dicrocoeliid sporocysts with cercariae in 16 out of 303 individuals, encompassing eight snail species and one slug species. A DNA barcoding based on sequencing of mitochondrial cytochrome c oxidase subunit 1 showed that the larvae consisted of five species. Phylogenetic trees of nuclear 18S and 28S ribosomal DNAs confirmed the five species to be members of the Dicrocoeliidae. These were temporarily termed dicrocoeliid spp. 1 to 5, since conclusive identification was impossible without adult worms. These unknown species were phylogenetically related to each other, except sp. 5. The phylogenetic trees demonstrated close genetic relationships between sp. 3 and the genus Lutztrema, and between sp. 5 and the genus Lyperosomum. The phylogenetic analysis also suggested that a division into the subfamilies Dicrocoeliinae and Leipertrematinae is a wrong classification due to the paraphyly of the Dicrocoeliinae. Morphological characterization of the cercariae and their DNA barcodes provide a primary platform for differentiating dicrocoeliids from various mollusks in Japan. The DNA barcodes, in particular, will enable tracing the parasite life cycles, in case of finding metacercariae and adults from presently unknown hosts.},
}
@article {pmid30117742,
year = {2019},
author = {Ta, M and Yin, C and Smith, GL and Xu, W},
title = {A Workflow to Improve Variant Calling Accuracy in Molecular Barcoded Sequencing Reads.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {26},
number = {1},
pages = {96-103},
doi = {10.1089/cmb.2018.0110},
pmid = {30117742},
issn = {1557-8666},
mesh = {DNA Barcoding, Taxonomic/*methods ; Data Accuracy ; Databases, Genetic ; Gene Library ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Sequence Analysis, DNA ; Workflow ; },
abstract = {Multiplexed molecular barcoded amplicon sequencing has been previously demonstrated to improve the sensitivity of low-frequency variant detection. Molecular barcoded reads can be used to identify and correct amplification biases introduced during library preparation and sequencing errors. We propose a generic workflow to improve variant calling accuracy that takes advantage of molecular barcoded sequencing reads by applying a base score correction method to duplicate or overlapping read pairs across the targeted panel. The workflow is able to reduce the false-positive rate of variant calls in homopolymer and repetitive regions where the sequencer commonly encounters phasing errors interfering with base calling. The analysis was focused on three specific regions within a custom QIAseq targeted DNA (Qiagen, USA) of 220 genes observed to have a high false-positive rate in a clinical validation study. Uncorrected and corrected datasets were compared at targeted regions to reference calls from NIST and exome data from a reference laboratory (Macrogen, USA). Base correction removed all false positives identified without the correction method and retained the true positive call in the dataset. We have shown that our workflow incorporating base correction of molecular barcoded sequencing data can be applied to germline sequencing to improve variant calling accuracy in genomic regions with certain repetitive sequence motifs.},
}
@article {pmid30108428,
year = {2018},
author = {Kaspi, R and Kontsedalov, S and Ghanim, M},
title = {First report of Trichogrammadanausicida and Trichogrammacacaeciae reared from Thaumatotibialeucotreta eggs in Israel.},
journal = {ZooKeys},
volume = {},
number = {779},
pages = {19-25},
pmid = {30108428},
issn = {1313-2989},
abstract = {The egg parasitpoids Trichogrammadanausicida (Nagaraja) and Trichogrammacacaeciae (Marchal) (Hymenoptera: Trichogrammatidae), are reported for the first time in Israel. Moreover, our discovery of T.danausicida is the first report of this parasitoid species outside of India. The occurrence of those trichogrammatids was first discovered and documented in May 2016 during a survey of egg parasitoids of the False codling moth Thaumatotibialeucotreta (Lepidoptera: Tortricidae). The field survey was conducted on castor bean fruits (Ricinuscommunis) in the Israeli central coastal plain. The identity of the parasitoids was revealed by means of sequencing a portion of the cytochrome oxidase I gene (COI) of the studied parasitoids.},
}
@article {pmid30106556,
year = {2018},
author = {Chen, XC and Huang, WP and Ren, KF and Ji, J},
title = {Self-Healing Label Materials Based on Photo-Cross-Linkable Polymeric Films with Dynamic Surface Structures.},
journal = {ACS nano},
volume = {12},
number = {8},
pages = {8686-8696},
doi = {10.1021/acsnano.8b04656},
pmid = {30106556},
issn = {1936-086X},
abstract = {Spatially controlling the evolution of surface structures may provide an effective strategy for patterning surface roughness and facilitating the construction of various functional surfaces. In this study, we report a photo-cross-linkable polymeric film with dynamic surface micro/nanostructures. The surface structures of the un-cross-linked regions can be eliminated under saturated humidity, which can be utilized to create patterned roughness on the film. One potential application of this patternable platform is as a "smart" label material for graphical symbols. Various graphical symbols can be programmed onto this film by partially erasing its surface roughness, enabling visibility due to the difference in light scattering between different areas of the film. When a thus-prepared label was blurred by mechanical scratches, it could be healed under saturated humidity, and its original readability could be fully restored. Furthermore, the patterned rough surface created using our approach can also be very useful in many other research fields, such as surface wettability and cell behavior manipulation.},
}
@article {pmid30104213,
year = {2018},
author = {Morrison, HA and Lowe, D and Robbins, JR and Bakardjiev, AI},
title = {In Vivo Virulence Characterization of Pregnancy-Associated Listeria monocytogenes Infections.},
journal = {Infection and immunity},
volume = {86},
number = {11},
pages = {},
pmid = {30104213},
issn = {1098-5522},
support = {F32 AI102491/AI/NIAID NIH HHS/United States ; F32 AI120676/AI/NIAID NIH HHS/United States ; R01 AI084928/AI/NIAID NIH HHS/United States ; },
mesh = {Animal Structures/microbiology ; Animals ; Disease Models, Animal ; Female ; Guinea Pigs ; Humans ; Listeria monocytogenes/genetics/growth &amp; development/isolation &amp; purification/*pathogenicity ; Listeriosis/*microbiology/*pathology ; Mice ; Placenta/microbiology ; Pregnancy ; Pregnancy Complications, Infectious/*microbiology/*pathology ; Virulence ; Virulence Factors/*analysis/genetics ; },
abstract = {Listeria monocytogenes is a foodborne pathogen that infects the placenta and can cause pregnancy complications. Listeriosis usually occurs as a sporadic infection, but large outbreaks are also reported. Virulence from clinical isolates is rarely analyzed due to the large number of animals required, but this knowledge could help guide the response to an outbreak. We implemented a DNA barcode system using signature tags that allowed us to efficiently assay variations in virulence across a large number of isolates. We tested 77 signature-tagged clones of clinical L. monocytogenes strains from 72 infected human placentas and 5 immunocompromised patients, all of which were isolated since 2000. These strains were tested for virulence in a modified competition assay in comparison to that of the laboratory strain 10403S. We used two in vivo models of listeriosis: the nonpregnant mouse and the pregnant guinea pig. Strains that were frequently found at a high abundance within infected organs were considered hypervirulent, while strains frequently found at a low abundance were considered hypovirulent. Virulence split relatively evenly among hypovirulent strains, hypervirulent strains, and strains as virulent as 10403S. The laboratory strain was found to have an intermediate virulence phenotype, supporting its suitability for use in pathogenesis studies. Further, we found that splenic virulence and placental virulence are closely linked in both the guinea pig and mouse models. This suggests that outbreak and sporadic pregnancy-associated L. monocytogenes strains are not generally more virulent than lab reference strains. However, some strains did show consistent and reproducible virulence differences, suggesting that their further study may reveal deeper insights into the biological underpinnings of listeriosis.},
}
@article {pmid30103795,
year = {2018},
author = {Ruiz-Arrondo, I and Hernández-Triana, LM and Ignjatović-Ćupina, A and Nikolova, N and Garza-Hernández, JA and Rodríguez-Pérez, MA and Oteo, JA and Fooks, AR and Lucientes Curdi, J},
title = {DNA barcoding of blackflies (Diptera: Simuliidae) as a tool for species identification and detection of hidden diversity in the eastern regions of Spain.},
journal = {Parasites &amp; vectors},
volume = {11},
number = {1},
pages = {463},
pmid = {30103795},
issn = {1756-3305},
support = {SV3045, SE4113//Department for Environment, Food and Rural Affairs/ ; III43007, TR31084//Ministry of Education, Science and Technology Development of the Republic of Serbia/ ; 271108//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; },
mesh = {Animal Distribution ; Animals ; Biodiversity ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Insect Proteins/genetics ; Phylogeny ; Simuliidae/*genetics ; Spain ; Species Specificity ; },
abstract = {BACKGROUND: Blackflies have negative impact on public and animal health due to the haematophagous habit of females. In recent times, in some regions in Spain, blackfly outbreaks are becoming more and more frequent, threatening the public health. However, there is still a paucity of data concerning the Spanish blackfly fauna. Correct identification of species is of paramount importance in order to provide correct information on species distribution, biology and behaviour, so that control measures could be implemented appropriately.<br><br>METHODS: Blackflies specimens (larvae, pupae, reared adults and biting females) were collected in the period 2015-2017 in and near rivers and streams from different regions in Spain. A modified Hotshot technique was used for the DNA extraction and the cox1 DNA barcoding region of the cytochrome c oxidase subunit 1 was sequenced from the specimens collected.<br><br>RESULTS: In total, we collected 239 specimens representing 22 species. Of these, six species are new records for the Arag&#xf3;n region: P. tomosvaryi, S. bertrandi, S. galloprovinciale, S. lineatum, S. rubzovianum and S. xanthinum. Cox1 DNA barcode sequences for 21 species were recovered, including four species of the genus Prosimulium and 17 species of the genus Simulium [Boophthora (1 species), Eusimulium (1 species), Nevermannia (4 species), Simulium (s.s.) (6 species), Trichodagmia (1 species) and Wilhelmia (4 species)]. For the first time the complete DNA barcodes for five species (P. tomosvaryi, S. carthusiense, S. brevidens, S. monticola and S. sergenti) were registered. Most of the specimens belonging to the same recognized species were clustered together in the neighbour-joining tree, except for S. argyreatum, S. monticola and S. variegatum. The overall genetic distance in the dataset was 0.14%. The average of the intraspecific genetic divergence within the different taxa was 1.47% (0.05-3.96%). In contrast, the interspecific divergence varied between 2.50-22.0%.<br><br>CONCLUSIONS: In this study we assessed the use of the cox1 DNA barcoding region for the identification of species of blackflies in Spain. Our results showed that combining DNA barcoding with morphology enhanced our taxonomic rationale in identifying the blackflies in the country.},
}
@article {pmid30103683,
year = {2018},
author = {Oyebola, KM and Aina, OO and Idowu, ET and Olukosi, YA and Ajibaye, OS and Otubanjo, OA and Awolola, TS and Awandare, GA and Amambua-Ngwa, A},
title = {A barcode of multilocus nuclear DNA identifies genetic relatedness in pre- and post-Artemether/Lumefantrine treated Plasmodium falciparum in Nigeria.},
journal = {BMC infectious diseases},
volume = {18},
number = {1},
pages = {392},
pmid = {30103683},
issn = {1471-2334},
support = {/WT_/Wellcome Trust/United Kingdom ; MC_EX_MR/K02440X/1/MRC_/Medical Research Council/United Kingdom ; DEL-15-007: Awandare//DELTAS Africa grant/International ; 107755/Z/15/ZZ: Awandare/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Adolescent ; Adult ; Aged ; Alleles ; Antimalarials/*therapeutic use ; Artemether/*therapeutic use ; Child ; Child, Preschool ; *DNA Barcoding, Taxonomic ; DNA, Protozoan/classification/isolation &amp; purification ; Dihydropteroate Synthase/genetics ; Drug Combinations ; Drug Resistance/*genetics ; Female ; Genotype ; Humans ; Infant ; Lumefantrine/*therapeutic use ; Malaria, Falciparum/drug therapy/*parasitology ; Male ; Middle Aged ; Mutation ; Nigeria ; Plasmodium falciparum/classification/*genetics/isolation &amp; purification ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Young Adult ; },
abstract = {BACKGROUND: The decline in the efficacy of artemisinin-based combination treatment (ACT) in some endemic regions threatens the progress towards global elimination of malaria. Molecular surveillance of drug resistance in malaria-endemic regions is vital to detect the emergence and spread of mutant strains.<br><br>METHODS: We observed 89 malaria patients for the efficacy of artemether-lumefantrine for the treatment of uncomplicated Plasmodium falciparum infections in Lagos, Nigeria and determined the prevalence of drug resistant strains in the population. Parasite clearance rates were determined by microscopy and the highly sensitive var gene acidic terminal sequence (varATS) polymerase chain reaction for 65 patients with samples on days 0, 1, 3, 7, 14, 21 and 28 after commencement of treatment. The genomic finger print of parasite DNA from pre- and post-treatment samples were determined using 24 nuclear single nucleotide polymorphisms (SNP) barcode for P. falciparum. Drug resistance associated alleles in chloroquine resistance transporter gene (crt-76), multidrug resistance genes (mdr1-86 and mdr1-184), dihydropteroate synthase (dhps-540), dihydrofolate reductase (dhfr-108) and kelch domain (K-13580) were genotyped by high resolution melt analysis of polymerase chain reaction (PCR) fragments.<br><br>RESULTS: By varATS qPCR, 12 (18.5%) of the participants had detectable parasite DNA in their blood three days after treatment, while eight (12.3%) individuals presented with genotypable day 28 parasitaemia. Complexity of infection (CoI) was 1.30 on day 0 and 1.34 on day 28, the mean expected heterozygosity (HE) values across all barcodes were 0.50&#x2009;&#xb1;&#x2009;0.05 and 0.56&#x2009;&#xb1;&#x2009;0.05 on days 0 and 28 respectively. Barcode (&#x3c0;) pairwise comparisons showed high genetic relatedness of day 0 and day 28 parasite isolates in three (37.5%) of the eight individuals who presented with re-appearing infections. Crt-76 mutant allele was present in 38 (58.5%) isolates. The mdr1-86 mutant allele was found in 56 (86.2%) isolates. No mutation in the K-13580 was observed.<br><br>CONCLUSIONS: Persistence of DNA-detectable parasitaemia in more than 18% of cases after treatment and indications of genetic relatedness between pre- and post-treatment infections warrants further investigation of a larger population for signs of reduced ACT efficacy in Nigeria.},
}
@article {pmid30103564,
year = {2018},
author = {Fadzil, NF and Wagiran, A and Mohd Salleh, F and Abdullah, S and Mohd Izham, NH},
title = {Authenticity Testing and Detection of Eurycoma longifolia in Commercial Herbal Products Using Bar-High Resolution Melting Analysis.},
journal = {Genes},
volume = {9},
number = {8},
pages = {},
pmid = {30103564},
issn = {2073-4425},
abstract = {The present study demonstrated High Resolution Melting (HRM) analysis combined with DNA barcode (Bar-HRM) as a fast and highly sensitive technique for detecting adulterants in Eurycoma longifolia commercial herbal products. Targeting the DNA barcoding of the chloroplastic region-ribulose biphosphate carboxylase large chain (rbcL) and the nuclear ribosomal region- internal transcribed spacer 2 (ITS2), PCR amplification and HRM analysis using saturated Eva green dye as the source of fluorescence signals, was accomplished by employing a real-time cycler. The results were further validated by sequencing to identify unknown sequence from Genbank database and to generate phylogenetic tree using neighbour joint (NJ) analysis. Both of the DNA markers exhibited a distinguishable melting temperature and shape of the normalised curve between the reference and the adulterants. In the case of species identification, ITS2 was more successful in differentiating between species. Additionally, detection of admixture sample containing small traces of targeted E. longifolia DNA (w/v) can be detected as low as 5% for rbcL and less than 1% for ITS2, proving the sensitivity and versatility of the HRM analysis. In conclusion, the Bar-HRM analysis is a fast and reliable technique that can effectively detect adulterants in herbal products. Therefore, this will be beneficial for regulatory agencies in order to regulate food safety issues.},
}
@article {pmid30102742,
year = {2018},
author = {Cardoso, YP and Rosso, JJ and Mabragaña, E and González-Castro, M and Delpiani, M and Avigliano, E and Bogan, S and Covain, R and Schenone, NF and Díaz de Astarloa, JM},
title = {A continental-wide molecular approach unraveling mtDNA diversity and geographic distribution of the Neotropical genus Hoplias.},
journal = {PloS one},
volume = {13},
number = {8},
pages = {e0202024},
pmid = {30102742},
issn = {1932-6203},
mesh = {Animals ; Argentina ; *Biodiversity ; DNA Barcoding, Taxonomic ; *DNA, Mitochondrial ; Fishes/*classification/*genetics ; Fresh Water ; *Genetic Variation ; Phylogeny ; Phylogeography ; Tropical Climate ; },
abstract = {With an estimate of around 9,000 species, the Neotropical region hosts the greatest diversity of freshwater fishes of the world. Genetic surveys have the potential to unravel isolated and unique lineages and may result in the identification of undescribed species, accelerating the cataloguing of extant biodiversity. In this paper, molecular diversity within the valuable and widespread Neotropical genus Hoplias was assessed by means of DNA Barcoding. The geographic coverage spanned 40 degrees of latitude from French Guiana to Argentina. Our analyses revealed 22 mitochondrial lineages fully supported by means of Barcode Index Number, Automatic Barcode Gap Discovery and phylogenetic analyses. This mtDNA survey revealed the existence of 15 fully supported mitochondrial lineages within the once considered to be the continentally distributed H. malabaricus. Only four of them are currently described as valid species however, leaving 11 mitochondrial lineages currently "masked" within this species complex. Mean genetic divergence was 13.1%. Barcoding gap analysis discriminated 20 out of the 22 lineages tested. Phylogenetic analyses showed that all taxonomically recognized species form monophyletic groups. Hoplias malabaricus sensu stricto clustered within a large clade, excluding the representatives of the La Plata River Basin. In the H. lacerdae group, all species but H. curupira showed a cohesive match between taxonomic and molecular identification. Two different genetic lineages were recovered for H. aimara. Given the unexpected hidden mitochondrial diversity within H. malabaricus, the COI sequence composition of specimens from Suriname (the type locality), identified as H. malabaricus sensu stricto, is of major importance.},
}
@article {pmid30100985,
year = {2018},
author = {Bürckert, JP and Faison, WJ and Mustin, DE and Dubois, ARSX and Sinner, R and Hunewald, O and Wienecke-Baldacchino, A and Brieger, A and Muller, CP},
title = {High-throughput sequencing of murine immunoglobulin heavy chain repertoires using single side unique molecular identifiers on an Ion Torrent PGM.},
journal = {Oncotarget},
volume = {9},
number = {54},
pages = {30225-30239},
pmid = {30100985},
issn = {1949-2553},
abstract = {With the advent of high-throughput sequencing (HTS), profiling immunoglobulin (IG) repertoires has become an essential part of immunological research. Advances in sequencing technology enable the IonTorrent Personal Genome Machine (PGM) to cover the full-length of IG mRNA transcripts. Nucleotide insertions and deletions (indels) are the dominant errors of the PGM sequencing platform and can critically influence IG repertoire assessments. Here, we present a PGM-tailored IG repertoire sequencing approach combining error correction through unique molecular identifier (UID) barcoding and indel detection through ImMunoGeneTics (IMGT), the most commonly used sequence alignment database for IG sequences. Using artificially falsified sequences for benchmarking, we found that IMGT's underlying algorithms efficiently detect 98% of the introduced indels. Undetected indels are either located at the end of the sequences or produce masked frameshifts with an insertion and deletion in close proximity. The complementary determining regions 3 (CDR3s) are returned correct for up to 3 insertions or 3 deletions through conservative culling. We further show, that our PGM-tailored unique molecular identifiers result in highly accurate HTS data if combined with the presented processing strategy. In this regard, considering sequences with at least two copies from datasets with UID families of minimum 3 reads result in correct sequences with over 99% confidence. Finally, we show that the protocol can readily be used to generate homogenous datasets for bulk sequencing of murine bone marrow samples. Taken together, this approach will help to establish benchtop-scale sequencing of IG heavy chain transcripts in the field of IG repertoire research.},
}
@article {pmid30100617,
year = {2018},
author = {Kamo, T and Kusumoto, Y and Tokuoka, Y and Okubo, S and Hayakawa, H and Yoshiyama, M and Kimura, K and Konuma, A},
title = {A DNA barcoding method for identifying and quantifying the composition of pollen species collected by European honeybees, Apis mellifera (Hymenoptera: Apidae).},
journal = {Applied entomology and zoology},
volume = {53},
number = {3},
pages = {353-361},
pmid = {30100617},
issn = {0003-6862},
abstract = {The European honeybee, Apis mellifera L. (Hymenoptera: Apidae), is the most important crop pollinator, and there is an urgent need for a sustained supply of honeybee colonies. Understanding the availability of pollen resources around apiaries throughout the brood-rearing season is crucial to increasing the number of colonies. However, detailed information on the floral resources used by honeybees is limited due to a scarcity of efficient methods for identifying pollen species composition. Therefore, we developed a DNA barcoding method for identifying the species of each pollen pellet and for quantifying the species composition by summing the weights of the pellets for each species. To establish the molecular biological protocol, we analyzed 1008 pellets collected between late July and early September 2016 from five hives placed in a forest/agricultural landscape of Hokkaido, northern Japan. Pollen was classified into 31 plant taxa, of which 29 were identified with satisfactory discrimination (25 species and 4 genera) using trnL-trnF and ITS2 as DNA barcoding regions together with available floral and phenological information. The remaining two taxa were classified to the species level using other DNA barcoding regions. Of the 1008 pollen pellets tested, 1005 (99.7%) were successfully identified. As an example of the use of this method, we demonstrated the change in species composition of pollen pellets collected each week for 9 weeks from the same hive.},
}
@article {pmid30098396,
year = {2018},
author = {Maetzig, T and Morgan, M and Schambach, A},
title = {Fluorescent genetic barcoding for cellular multiplex analyses.},
journal = {Experimental hematology},
volume = {67},
number = {},
pages = {10-17},
doi = {10.1016/j.exphem.2018.08.001},
pmid = {30098396},
issn = {1873-2399},
mesh = {Animals ; Animals, Genetically Modified ; Cell Line ; Cell Lineage ; Cell Separation/*methods ; Cell Tracking/*methods ; Clone Cells ; Computer Systems ; Flow Cytometry/*methods ; *Genes, Reporter ; Genetic Vectors ; Glioblastoma/pathology ; Hematopoiesis ; Humans ; Lentivirus/genetics ; Luminescent Proteins/*analysis/genetics ; Mice ; Microscopy, Fluorescence ; },
abstract = {Hematopoiesis depends on the controlled differentiation of hematopoietic stem cells to mature cells with defined functions. Although each cell population within the hematopoietic hierarchy can be described by phenotypic markers, isolation of marker pure populations does not necessarily result in cells with homogeneous functionality. However, techniques that enable the efficient characterization of cell behavior with high resolution are limited. Although single-cell transplantation assays demand high mouse numbers and workload, sequencing-based fate tracking techniques require the destruction of the host cell, substantial financial resources, and bioinformatics expertise and suffer from a delay between sample acquisition and data interpretation. To make analyses more efficient, several laboratories recently developed flow cytometry-driven, fluorescence-based multiplexing approaches that enable parallel analysis of longitudinal behavior from multiple clonally derived cells or polyclonal populations. Although these fluorescent genetic barcoding systems are still in their infancy, their power lies in the use of retroviral vectors for gene marking of multiple populations with unique fluorescent color codes. Tracing of color-coded cells by flow cytometry guarantees the accessibility of information on population behavior in real time and at low cost, supports the prospective isolation of cells for downstream analyses, and can be applied to cell line models as well as to human- and animal-derived primary cells. Here, we discuss recent progress in the emerging field of fluorescent genetic barcoding for longitudinal multiplex cell tracking in biomedical research and how this technique will help to uncover mechanisms regulating cell behavior with clonal resolution in a reduced number of experimental samples.},
}
@article {pmid30096152,
year = {2018},
author = {Tian, L and Su, S and Dong, X and Amann-Zalcenstein, D and Biben, C and Seidi, A and Hilton, DJ and Naik, SH and Ritchie, ME},
title = {scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data.},
journal = {PLoS computational biology},
volume = {14},
number = {8},
pages = {e1006361},
pmid = {30096152},
issn = {1553-7358},
mesh = {Animals ; Base Sequence ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; RNA/genetics ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis/*methods ; Software ; },
abstract = {Single-cell RNA sequencing (scRNA-seq) technology allows researchers to profile the transcriptomes of thousands of cells simultaneously. Protocols that incorporate both designed and random barcodes have greatly increased the throughput of scRNA-seq, but give rise to a more complex data structure. There is a need for new tools that can handle the various barcoding strategies used by different protocols and exploit this information for quality assessment at the sample-level and provide effective visualization of these results in preparation for higher-level analyses. To this end, we developed scPipe, an R/Bioconductor package that integrates barcode demultiplexing, read alignment, UMI-aware gene-level quantification and quality control of raw sequencing data generated by multiple protocols that include CEL-seq, MARS-seq, Chromium 10X, Drop-seq and Smart-seq. scPipe produces a count matrix that is essential for downstream analysis along with an HTML report that summarises data quality. These results can be used as input for downstream analyses including normalization, visualization and statistical testing. scPipe performs this processing in a few simple R commands, promoting reproducible analysis of single-cell data that is compatible with the emerging suite of open-source scRNA-seq analysis tools available in R/Bioconductor and beyond. The scPipe R package is available for download from https://www.bioconductor.org/packages/scPipe.},
}
@article {pmid30093604,
year = {2018},
author = {Kalhor, R and Kalhor, K and Mejia, L and Leeper, K and Graveline, A and Mali, P and Church, GM},
title = {Developmental barcoding of whole mouse via homing CRISPR.},
journal = {Science (New York, N.Y.)},
volume = {361},
number = {6405},
pages = {},
pmid = {30093604},
issn = {1095-9203},
support = {P50 HG005550/HG/NHGRI NIH HHS/United States ; R01 GM123313/GM/NIGMS NIH HHS/United States ; R01 MH103910/MH/NIMH NIH HHS/United States ; R01 CA222826/CA/NCI NIH HHS/United States ; R01 HG009285/HG/NHGRI NIH HHS/United States ; },
mesh = {Alleles ; Animals ; *CRISPR-Cas Systems ; Cell Lineage ; Embryonic Development/*genetics ; Embryonic Stem Cells ; Gene Expression Profiling/*methods ; Mice ; Mutation ; RNA, Guide, CRISPR-Cas Systems/genetics ; },
abstract = {In vivo barcoding using nuclease-induced mutations is a powerful approach for recording biological information, including developmental lineages; however, its application in mammalian systems has been limited. We present in vivo barcoding in the mouse with multiple homing guide RNAs that each generate hundreds of mutant alleles and combine to produce an exponential diversity of barcodes. Activation upon conception and continued mutagenesis through gestation resulted in developmentally barcoded mice wherein information is recorded in lineage-specific mutations. We used these recordings for reliable post hoc reconstruction of the earliest lineages and investigation of axis development in the brain. Our results provide an enabling and versatile platform for in vivo barcoding and lineage tracing in a mammalian model system.},
}
@article {pmid30092617,
year = {2018},
author = {Perichet, C and Philippe, F and Dupouyet, A and Marteaux, B and Schnaebele, N and Dubrulle, N and Lavoine-Hanneguelle, S and Giraud, N},
title = {Study of Some Zanthoxylum Species by Chemical and DNA Analysis Approaches.},
journal = {Chemistry &amp; biodiversity},
volume = {15},
number = {10},
pages = {e1800251},
doi = {10.1002/cbdv.201800251},
pmid = {30092617},
issn = {1612-1880},
mesh = {DNA, Plant/analysis/classification/*genetics ; Fruit/chemistry/classification/genetics ; Gas Chromatography-Mass Spectrometry ; *Phylogeny ; Plant Extracts/chemistry/classification/genetics ; Rutaceae/chemistry/classification/genetics ; Zanthoxylum/*chemistry/classification/*genetics ; },
abstract = {The authentication and traceability of spices is a major concern for industrials and consumers. We focused on species from Zanthoxylum genera which are used for many different applications by local populations and also for trading as spices (dried pericarps or whole fruits). In this case, literature gives contradictory data about botanical names, and commercial labelling is often confusing. We studied commercial fruits pericarps extracts obtained by supercritical CO2 and analyzed them by GC/MS. The very complex volatile and semi volatile fractions composition of each extract is described. The barcoding method including molecular biology and phylogenetic analyses was also developed in order to check the commercial botanical identification of the raw material. This is a robust method to identify species in berries samples. We used one genetic marker to identify two Rutaceae clusters, including several species of Zanthoxylum genus. These results indicate that Fagara and Zanthoxylum groups could be considered as two different genera. Combination of chemical analysis and DNA analysis provides an original approach to increase chemical and botanical Zanthoxylum genus knowledge.},
}
@article {pmid30089904,
year = {2018},
author = {Ben-David, U and Siranosian, B and Ha, G and Tang, H and Oren, Y and Hinohara, K and Strathdee, CA and Dempster, J and Lyons, NJ and Burns, R and Nag, A and Kugener, G and Cimini, B and Tsvetkov, P and Maruvka, YE and O'Rourke, R and Garrity, A and Tubelli, AA and Bandopadhayay, P and Tsherniak, A and Vazquez, F and Wong, B and Birger, C and Ghandi, M and Thorner, AR and Bittker, JA and Meyerson, M and Getz, G and Beroukhim, R and Golub, TR},
title = {Genetic and transcriptional evolution alters cancer cell line drug response.},
journal = {Nature},
volume = {560},
number = {7718},
pages = {325-330},
pmid = {30089904},
issn = {1476-4687},
support = {R01 CA188228/CA/NCI NIH HHS/United States ; R01 CA219943/CA/NCI NIH HHS/United States ; U54 HG008097/HG/NHGRI NIH HHS/United States ; U54 HL127366/HL/NHLBI NIH HHS/United States ; },
mesh = {Breast Neoplasms/*drug therapy/*genetics/pathology ; Cell Proliferation ; Cell Shape ; Clone Cells/cytology/drug effects/metabolism ; *Evolution, Molecular ; Genetic Variation/drug effects/*genetics ; Genomic Instability/drug effects/*genetics ; Humans ; MCF-7 Cells ; Reproducibility of Results ; Transcription, Genetic/*genetics ; },
abstract = {Human cancer cell lines are the workhorse of cancer research. Although cell lines are known to evolve in culture, the extent of the resultant genetic and transcriptional heterogeneity and its functional consequences remain understudied. Here we use genomic analyses of 106 human cell lines grown in two laboratories to show extensive clonal diversity. Further comprehensive genomic characterization of 27 strains of the common breast cancer cell line MCF7 uncovered rapid genetic diversification. Similar results were obtained with multiple strains of 13 additional cell lines. Notably, genetic changes were associated with differential activation of gene expression programs and marked differences in cell morphology and proliferation. Barcoding experiments showed that cell line evolution occurs as a result of positive clonal selection that is highly sensitive to culture conditions. Analyses of single-cell-derived clones demonstrated that continuous instability quickly translates into heterogeneity of the cell line. When the 27 MCF7 strains were tested against 321 anti-cancer compounds, we uncovered considerably different drug responses: at least 75% of compounds that strongly inhibited some strains were completely inactive in others. This study documents the extent, origins and consequences of genetic variation within cell lines, and provides a framework for researchers to measure such variation in efforts to support maximally reproducible cancer research.},
}
@article {pmid30089465,
year = {2018},
author = {Oliveira, RRM and Nunes, GL and de Lima, TGL and Oliveira, G and Alves, R},
title = {PIPEBAR and OverlapPER: tools for a fast and accurate DNA barcoding analysis and paired-end assembly.},
journal = {BMC bioinformatics},
volume = {19},
number = {1},
pages = {297},
pmid = {30089465},
issn = {1471-2105},
support = {443270/2015-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/International ; 440880/2013-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (BR)/International ; 307479/2016-1)//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (BR)/International ; 20/2016//Conselho de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior - CAPES - BR/International ; 22298//Funda&#xe7;&#xe3;o de Desenvolvimento da Pesquisa (BR)/International ; },
mesh = {Base Sequence ; Codon, Terminator/genetics ; Consensus Sequence ; DNA Barcoding, Taxonomic/*methods ; Frameshift Mutation/genetics ; *Software ; },
abstract = {BACKGROUND: Taxonomic identification of plants and insects is a hard process that demands expert taxonomists and time, and it's often difficult to distinguish on morphology only. DNA barcodes allow a rapid species discovery and identification and have been widely used for taxonomic identification by targeting known gene regions that permit to discriminate these species. DNA barcode sequence analysis is usually carried out with processes and tools that still demand a high interaction with the user or researcher. To reduce at most such interaction, we proposed PIPEBAR, a pipeline for DNA chromatograms analysis of Sanger platform sequencing, ensuring high quality consensus sequences along with efficient running time. We also proposed a paired-end reads assembly tool, OverlapPER, which is used in sequence or independently of PIPEBAR.<br><br>RESULTS: PIPEBAR is a command line tool to automatize the processing of large number of trace files. It is accurate as the proprietary Geneious tool and faster than most popular software for barcoding analysis. It is 7 times faster than Geneious and 14 times faster than SeqTrace for processing hundreds of barcoding sequences. OverlapPER is a novel tool for overlapping paired-end reads accurately that accepts both substitution and indel errors and returns both overlapped and non-overlapped regions between a pair of reads. OverlapPER obtained the best results compared to currently used tools when merging 1,000,000 simulated paired-end reads.<br><br>CONCLUSIONS: PIPEBAR and OverlapPER run on most operating systems and are freely available, along with supporting code and documentation, at https://sourceforge.net/projects/PIPEBAR / and https://sourceforge.net/projects/overlapper-reads /.},
}
@article {pmid30089144,
year = {2018},
author = {Nunes, GL and Oliveira, RRM and Guimarães, JTF and Giulietti, AM and Caldeira, C and Vasconcelos, S and Pires, E and Dias, M and Watanabe, M and Pereira, J and Jaffé, R and Bandeira, CHMM and Carvalho-Filho, N and da Silva, EF and Rodrigues, TM and Dos Santos, FMG and Fernandes, T and Castilho, A and Souza-Filho, PWM and Imperatriz-Fonseca, V and Siqueira, JO and Alves, R and Oliveira, G},
title = {Quillworts from the Amazon: A multidisciplinary populational study on Isoetes serracarajensis and Isoetes cangae.},
journal = {PloS one},
volume = {13},
number = {8},
pages = {e0201417},
pmid = {30089144},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic ; *Genome, Chloroplast ; *Lycopodiaceae/classification/genetics/growth &amp; development ; South America ; },
abstract = {Isoetes are ancient quillworts members of the only genus of the order Isoetales. The genus is slow evolving but is resilient, and widespread worldwide. Two recently described species occur in the Eastern Brazilian Amazon, Isoetes serracarajensis and Isoetes cangae. They are found in the ironstone grasslands known as Canga. While I. serracarajensis is present mostly in seasonal water bodies, I. cangae is known to occur in a single permanent lake at the South mountain range. In this work, we undertake an extensive morphological, physiological and genetic characterization of both species to establish species boundaries and better understand the morphological and genetic features of these two species. Our results indicate that the morphological differentiation of the species is subtle and requires a quantitative assessment of morphological elements of the megaspore for diagnosis. We did not detect differences in microspore output, but morphological peculiarities may establish a reproductive barrier. Additionally, genetic analysis using DNA barcodes and whole chloroplast genomes indicate that although the plants are genetically very similar both approaches provide diagnostic characters. There was no indication of population structuring I. serracarajensis. These results set the basis for a deeper understanding of the evolution of the Isoetes genus.},
}
@article {pmid30089124,
year = {2018},
author = {Wu, RW and Liu, YT and Wang, S and Liu, XJ and Zanatta, DT and Roe, KJ and Song, XL and An, CT and Wu, XP},
title = {Testing the utility of DNA barcodes and a preliminary phylogenetic framework for Chinese freshwater mussels (Bivalvia: Unionidae) from the middle and lower Yangtze River.},
journal = {PloS one},
volume = {13},
number = {8},
pages = {e0200956},
pmid = {30089124},
issn = {1932-6203},
mesh = {Animals ; Bivalvia/*genetics ; China ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Fresh Water ; Genes, Mitochondrial ; Genetic Speciation ; Genome, Mitochondrial ; NADH Dehydrogenase/genetics ; Phylogeny ; Rivers ; Unionidae/genetics ; },
abstract = {The middle and lower portions of the Yangtze River basin is the most species-rich region for freshwater mussels in Asia. The management and conservation of the taxa in this region has been greatly hampered by the lack of a well-developed phylogeny and species-level taxonomic framework. In this study, we tested the utility of two mitochondrial genes commonly used as DNA barcodes: the first subunit of the cytochrome oxidase c gene (COI) and the first subunit of the NADH dehydrogenase gene (ND1) for 34 putative species representing 15 genera, and also generated phylogenetic hypotheses for Chinese unionids based on the combined dataset of the two mitochondrial genes. The results showed that both loci performed well as barcodes for species identification, but the ND1 sequences provided better resolution when compared to COI. Based on the two-locus dataset, Bayesian Inference (BI) and Maximum Likelihood (ML) phylogenetic analyses indicated 3 of the 15 genera of Chinese freshwater mussels examined were polyphyletic. Additionally, the analyses placed the 15 genera into 3 subfamilies: Unioninae (Aculamprotula, Cuneopsis, Nodularia and Schistodesmus), Gonideninae (Lamprotula, Solenaia and Ptychorhychus) and Anodontinae (Cristaria, Arconaia, Acuticosta, Lanceolaria, Anemina and Sinoanodonta). Our results contradict previous taxonomic classification that placed the genera Arconaia, Acuticosta and Lanceolaria in the Unioninae. This study represents one of the first attempts to develop a molecular phylogenetic framework for the Chinese members of the Unionidae and will provide a basis for future research on the evolution, ecology, and conservation of Chinese freshwater mussels.},
}
@article {pmid30087693,
year = {2018},
author = {Sales, NG and Mariani, S and Salvador, GN and Pessali, TC and Carvalho, DC},
title = {Hidden Diversity Hampers Conservation Efforts in a Highly Impacted Neotropical River System.},
journal = {Frontiers in genetics},
volume = {9},
number = {},
pages = {271},
pmid = {30087693},
issn = {1664-8021},
abstract = {Neotropical Rivers host a highly diverse ichthyofauna, but taxonomic uncertainty prevents appropriate conservation measures. The Doce River Basin (DRB), lying within two Brazilian threatened hotspots (Atlantic Forest and Brazilian Savanna) in south-east Brazil, faced the worst ever environmental accident reported for South American catchments, due to a dam collapse that spread toxic mining tailings along the course of its main river. Its ichthyofauna was known to comprise 71 native freshwater fish species, of which 13 endemic. Here, we build a DNA barcode library for the DRB ichthyofauna, using samples obtained before the 2015 mining disaster, in order to provide a more robust biodiversity record for this basin, as a baseline for future management actions. Throughout the whole DRB, we obtained a total of 306 barcodes, assigned to 69 putative species (with a mean of 4.54 barcodes per species), belonging to 45 genera, 18 families, and 5 orders. Average genetic distances within species, genus, and families were 2.59, 11.4, and 20.5%, respectively. The 69 species identified represent over 76% of the known DRB ichthyofauna, comprising 43 native (five endemic, of which three threatened by extinction), 13 already known introduced species, and 13 unknown species (such as Characidium sp., Neoplecostomus sp., and specimens identified only at the sub-family level Neoplecostominae, according to morphological identification provided by the museum collections). Over one fifth of all analyzed species (N = 16) had a mean intraspecific genetic divergence higher than 2%. An integrative approach, combining NND (nearest neighbor distance), BIN (barcode index number), ABGD (automatic barcode gap discovery), and bPTP (Bayesian Poisson Tree Processes model) analyses, suggested the occurrence of potential cryptic species, species complex, or historical errors in morphological identification. The evidence presented calls for a more robust, DNA-assisted cataloging of biodiversity-rich ecosystems, in order to enable effective monitoring and informed actions to preserve and restore these delicate habitats.},
}
@article {pmid30087684,
year = {2018},
author = {Ramalho, AJ and Zappi, DC and Nunes, GL and Watanabe, MTC and Vasconcelos, S and Dias, MC and Jaffé, R and Prous, X and Giannini, TC and Oliveira, G and Giulietti, AM},
title = {Blind Testing: DNA Barcoding Sheds Light Upon the Identity of Plant Fragments as a Subsidy for Cave Conservation.},
journal = {Frontiers in plant science},
volume = {9},
number = {},
pages = {1052},
pmid = {30087684},
issn = {1664-462X},
abstract = {Plants living above and around caves represent an important, albeit poorly studied, resource within cave ecosystems. The presence of plant material (root-like structures or rhizothemes, saplings, seeds, and seedlings) correlates positively with the biodiversity of the cave dwelling animals as shown for iron-ore caves in Carajás, Pará, Brazil. Plant material collected in caves has proven to be difficult to identify by traditional botanical methods, thus this research aims to provide a qualitative insight into the taxonomy and morphology of rhizothemes and other plant fragments found in the caves. The identification process used a combination of different molecular markers (ITS2, rbcL, and trnH-psbA) followed by a comparison of the sequences obtained against publicly available databases. The rhizothemes were submitted to micromorphological analysis to ascertain their putative root or stem origin and to compare their anatomy with known patterns found in the plant families or genera recovered through molecular matches. All studied samples were Angiosperms, mostly belonging to subclass Rosideae, within four orders: Malpighiales (Euphorbiaceae, Hypericaceae), Sapindales (Anacardiaceae and Sapindaceae), Myrtales (Myrtaceae), Fabales (Fabaceae), and only two belonging to subclass Asteridae, order Gentianales (Apocynaceae). Some of the samples were matched to generic level, with ITS2 being the best marker to identify the fragments because it shows high degree of sequence variation even at specific level and result reliability. All rhizothemes turned out to be roots, and correspondence was found between the existing literature and the individual anatomical patterns for the families and genera retrieved. DNA barcode has proved to be a useful tool to identify plant fragments found in this challenging environment. However, the existence of well curated, authoritatively named collections with ample biological information has proven to be essential to achieve a reliable identification.},
}
@article {pmid30087104,
year = {2018},
author = {Pellegrino, M and Sciambi, A and Treusch, S and Durruthy-Durruthy, R and Gokhale, K and Jacob, J and Chen, TX and Geis, JA and Oldham, W and Matthews, J and Kantarjian, H and Futreal, PA and Patel, K and Jones, KW and Takahashi, K and Eastburn, DJ},
title = {High-throughput single-cell DNA sequencing of acute myeloid leukemia tumors with droplet microfluidics.},
journal = {Genome research},
volume = {28},
number = {9},
pages = {1345-1352},
pmid = {30087104},
issn = {1549-5469},
support = {R44 HG009465/HG/NHGRI NIH HHS/United States ; },
mesh = {Aged ; Cells, Cultured ; Clonal Evolution ; Humans ; Leukemia, Myeloid, Acute/*genetics/pathology ; Male ; Microfluidics/*methods ; Mutation ; Sequence Analysis, DNA/*methods ; Single-Cell Analysis/*methods ; },
abstract = {To enable the characterization of genetic heterogeneity in tumor cell populations, we developed a novel microfluidic approach that barcodes amplified genomic DNA from thousands of individual cancer cells confined to droplets. The barcodes are then used to reassemble the genetic profiles of cells from next-generation sequencing data. By using this approach, we sequenced longitudinally collected acute myeloid leukemia (AML) tumor populations from two patients and genotyped up to 62 disease relevant loci across more than 16,000 individual cells. Targeted single-cell sequencing was able to sensitively identify cells harboring pathogenic mutations during complete remission and uncovered complex clonal evolution within AML tumors that was not observable with bulk sequencing. We anticipate that this approach will make feasible the routine analysis of AML heterogeneity, leading to improved stratification and therapy selection for the disease.},
}
@article {pmid30084847,
year = {2018},
author = {Heller, P and Casaletto, J and Ruiz, G and Geller, J},
title = {A database of metazoan cytochrome c oxidase subunit I gene sequences derived from GenBank with CO-ARBitrator.},
journal = {Scientific data},
volume = {5},
number = {},
pages = {180156},
pmid = {30084847},
issn = {2052-4463},
mesh = {Algorithms ; Animals ; Biological Evolution ; Databases, Nucleic Acid ; Electron Transport Complex IV/*genetics ; Sequence Analysis, DNA/methods ; },
abstract = {The Cytochrome C Oxidase subunit I gene ("COI") is the de facto standard for animal DNA barcoding. Organism identification based on COI requires an accurate and extensive annotated database of COI sequences. Such a database can also be of value in reconstructing evolutionary history and in diversity studies. Two COI databases are currently available: BOLD and Midori. BOLD's submissions conform to stringent sequence and metadata requirements; BOLD is specific to COI but makes no attempt to be comprehensive. Midori, derived from GenBank, has more sequences but less stringent standards than BOLD, resulting in higher error rates. To address the need for a comprehensive and accurate COI database, we adapted the ARBitrator algorithm, which classifies based only on sequence properties and has successfully auto-curated bacterial genes mined from GenBank. The adapted algorithm, which we call CO-ARBitrator, built a database of over a million metazoan COI sequences. Sensitivity and specificity are significantly higher than Midori. Specificity is comparable to what BOLD achieves with data quality prerequisites. Results and software are publicly available.},
}
@article {pmid30084526,
year = {2018},
author = {Chen, C and Ao, L and Wu, YT and Cifliku, V and Cardoso Dos Santos, M and Bourrier, E and Delbianco, M and Parker, D and Zwier, JM and Huang, L and Hildebrandt, N},
title = {Single-Nanoparticle Cell Barcoding by Tunable FRET from Lanthanides to Quantum Dots.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {57},
number = {41},
pages = {13686-13690},
pmid = {30084526},
issn = {1521-3773},
mesh = {Europium/*chemistry ; Fluorescence Resonance Energy Transfer/*methods ; *Nanoparticles ; *Quantum Dots ; Terbium/*chemistry ; },
abstract = {Fluorescence barcoding based on nanoparticles provides many advantages for multiparameter imaging. However, creating different concentration-independent codes without mixing various nanoparticles and by using single-wavelength excitation and emission for multiplexed cellular imaging is extremely challenging. Herein, we report the development of quantum dots (QDs) with two different SiO2 shell thicknesses (6 and 12 nm) that are coated with two different lanthanide complexes (Tb and Eu). FRET from the Tb or Eu donors to the QD acceptors resulted in four distinct photoluminescence (PL) decays, which were encoded by simple time-gated (TG) PL intensity detection in three individual temporal detection windows. The well-defined single-nanoparticle codes were used for live cell imaging and a one-measurement distinction of four different cells in a single field of view. This single-color barcoding strategy opens new opportunities for multiplexed labeling and tracking of cells.},
}
@article {pmid30078711,
year = {2018},
author = {Goltsev, Y and Samusik, N and Kennedy-Darling, J and Bhate, S and Hale, M and Vazquez, G and Black, S and Nolan, GP},
title = {Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging.},
journal = {Cell},
volume = {174},
number = {4},
pages = {968-981.e15},
pmid = {30078711},
issn = {1097-4172},
support = {R33 CA183654/CA/NCI NIH HHS/United States ; U19 AI057229/AI/NIAID NIH HHS/United States ; U19 AI100627/AI/NIAID NIH HHS/United States ; R01 HL120724/HL/NHLBI NIH HHS/United States ; U54 CA209971/CA/NCI NIH HHS/United States ; R21 CA183660/CA/NCI NIH HHS/United States ; R01 HL128173/HL/NHLBI NIH HHS/United States ; R33 CA183692/CA/NCI NIH HHS/United States ; R01 CA184968/CA/NCI NIH HHS/United States ; UH2 AR067676/AR/NIAMS NIH HHS/United States ; },
mesh = {Animals ; Antibodies/*chemistry ; *Disease Models, Animal ; Female ; Image Processing, Computer-Assisted/*methods ; Lupus Erythematosus, Systemic/*pathology ; Male ; Mass Spectrometry ; Mice ; Mice, Inbred MRL lpr ; Oligonucleotide Probes/*chemistry ; Spleen/*pathology ; },
abstract = {A highly multiplexed cytometric imaging approach, termed co-detection by indexing (CODEX), is used here to create multiplexed datasets of normal and lupus (MRL/lpr) murine spleens. CODEX iteratively visualizes antibody binding events using DNA barcodes, fluorescent dNTP analogs, and an in situ polymerization-based indexing procedure. An algorithmic pipeline for single-cell antigen quantification in tightly packed tissues was developed and used to overlay well-known morphological features with de novo characterization of lymphoid tissue architecture at a single-cell and cellular neighborhood levels. We observed an unexpected, profound impact of the cellular neighborhood on the expression of protein receptors on immune cells. By comparing normal murine spleen to spleens from animals with systemic autoimmune disease (MRL/lpr), extensive and previously uncharacterized splenic cell-interaction dynamics in the healthy versus diseased state was observed. The fidelity of multiplexed spatial cytometry demonstrated here allows for quantitative systemic characterization of tissue architecture in normal and clinically aberrant samples.},
}
@article {pmid30075753,
year = {2018},
author = {Gogoi, B and Bhau, BS},
title = {DNA barcoding of the genus Nepenthes (Pitcher plant): a preliminary assessment towards its identification.},
journal = {BMC plant biology},
volume = {18},
number = {1},
pages = {153},
pmid = {30075753},
issn = {1471-2229},
mesh = {Caryophyllales/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/genetics ; Genes, Plant/genetics ; Genetic Loci/genetics ; Phylogeny ; Species Specificity ; },
abstract = {BACKGROUND: DNA barcoding is impending towards the generation of universal standards for species discrimination with a standard gene region that can be sequenced accurately and within short span of time. In this study, we were successful in developing efficient barcode locus in the Nepenthes genus. A total of 317 accessions were retrieved from GenBank of NCBI which represent 140 different species Nepenthes and evaluated the efficacy of ITS, rbcl and matK barcode candidates using barcode gap, applied distance similarity, and tree-based methods.<br><br>RESULT: Our result indicates that single-locus ITS or combined with plastid regions (matK) showed the best species discrimination with distinctive barcoding gaps. Therefore, we tentatively proposed the combination of ITS+matK as a core barcode for Nepenthes genus.<br><br>CONCLUSION: This study provides a report on DNA barcoding for unique insectivores' Nepenthes genus. As the different species of Nepenthes are higly endemic and endangered, it would be a useful study to understand the evolutionary relationship, sketched in emigration, mislabeling and can be a probable assessment for its biodiversity.},
}
@article {pmid30075091,
year = {2018},
author = {Powell, RF and Magee, AR and Boatwright, JS},
title = {Decoding ice plants: challenges associated with barcoding and phylogenetics in the diverse succulent family Aizoaceae.},
journal = {Genome},
volume = {61},
number = {11},
pages = {815-821},
doi = {10.1139/gen-2018-0055},
pmid = {30075091},
issn = {1480-3321},
mesh = {Aizoaceae/classification/*genetics ; Biodiversity ; *DNA Barcoding, Taxonomic ; *DNA, Plant ; Genes, Plant ; Phylogeography ; Plastids/genetics ; },
abstract = {Aizoaceae is the largest succulent plant family in the world, including in excess of 1800 species. Despite its richness, a large proportion of its taxa are listed as data deficient and as such, has been identified as the top priority for taxonomic research in South Africa. Limitations to accurate taxonomic identification of taxa in the family may be partly attributed to the degree of technical knowledge required to identify taxa in the Aizoaceae. DNA barcoding may provide an alternative method of identification; however, the suitability of commonly used gene regions has not been tested in the family. Here, we analyse variable and parsimony informative characters (PIC), as well as the barcoding gap, in commonly used plastid regions (atpB-rbcL, matK, psbA-trnH, psbJ-petA, rpl16, rps16, trnD-trnT, trnL-trnF, trnQ-rps16, and trnS-trnG) and the nuclear region ITS (for Aizooideae only) across two subfamilies and two expanded clades within the Aizoaceae. The relative percentage of PIC was much greater in subfamilies Aizooideae and Mesembryanthemoideae than in Ruschioideae. Although nrITS had the highest percentage of PIC, barcoding gap analyses identified neither ITS nor any chloroplast region as suitable for barcoding of the family. From the results, it is evident that novel barcoding regions need to be explored within the Aizoaceae.},
}
@article {pmid30073397,
year = {2018},
author = {Beatrice-Lindner, P and Garrido-Cardenas, JA and Sepulveda, C and Acien-Fernandez, FG},
title = {A new approach for detection and quantification of microalgae in industrial-scale microalgal cultures.},
journal = {Applied microbiology and biotechnology},
volume = {102},
number = {19},
pages = {8429-8436},
doi = {10.1007/s00253-018-9268-y},
pmid = {30073397},
issn = {1432-0614},
support = {727874 SABANA//Horizon 2020/ ; },
mesh = {Biomass ; DNA Barcoding, Taxonomic/methods ; Industry/methods ; Microalgae/genetics/*growth &amp; development ; Scenedesmus/genetics/growth &amp; development ; },
abstract = {In industrial-scale microalgal cultures, non-target microalgae compete with the desired species for nutrients and CO2, thus reducing the growth rate of the target species and the quality of the produced biomass. Microalgae identification is generally considered a complicated issue; although, in the last few years, new molecular methods have helped to rectify this problem. Among the different techniques available, DNA barcoding has proven very useful in providing rapid, accurate, and automatable species identification; in this work, it is used to assess the genomic identity of the microalga species Scenedesmus sp. 'almeriensis', a common strain in industrial-scale cultures. Barcode markers rbcL and ITS1-5.8S-ITS2 were sequenced and the obtained genomic information was used to design a quantitative PCR assay to precisely quantify the S. almeriensis concentration in microalgal cultures of industrial interest. TaqMan chemistry was used to quantify down to 1 μg/L dry weight of S. almeriensis cells, including in the presence of concentrated mixed cultures of other microalgae. A simple direct qPCR approach was also investigated to avoid classic DNA extraction and to reduce total assay time to approximately 2 h. The objective was to design strain-specific tools able to confirm and quantify the presence of different strains in whatever microalgae culture so as to achieve maximal productivity and quality of the produced biomass.},
}
@article {pmid30073078,
year = {2018},
author = {Tan, SL and Luo, YH and Hollingsworth, PM and Burgess, KS and Xu, K and Li, DZ and Gao, LM},
title = {DNA barcoding herbaceous and woody plant species at a subalpine forest dynamics plot in Southwest China.},
journal = {Ecology and evolution},
volume = {8},
number = {14},
pages = {7195-7205},
pmid = {30073078},
issn = {2045-7758},
abstract = {Although DNA barcoding has been widely used to identify plant species composition in temperate and tropical ecosystems, relatively few studies have used DNA barcodes to document both herbaceous and woody components of forest plot. A total of 201 species (72 woody species and 129 herbaceous species) representing 135 genera distributed across 64 families of seed plants were collected in a 25 ha CForBio subalpine forest dynamics plot. In total, 491 specimens were screened for three DNA regions of the chloroplast genome (rbcL, matK, and trnH-psbA) as well as the internal transcribed spacers (ITS) of nuclear ribosomal DNA. We quantified species resolution for each barcode separately or in combination using a ML tree-based method. Amplification and sequencing success were highest for rbcL, followed by trnH-psbA, which performed better than ITS and matK. The rbcL + ITS barcode had slightly higher species resolution rates (88.60%) compared with rbcL + matK (86.60%) and rbcL + trnH-psbA (86.01%). The addition of trnH-psbA or ITS to the rbcL + matK barcode only marginally increased species resolution rates, although in combination the four barcodes had the highest discriminatory power (90.21%). The situations where DNA barcodes did not discriminate among species were typically associated with higher numbers of co-occurring con-generic species. In addition, herbaceous species were much better resolved than woody species. Our study represents one of the first applications of DNA barcodes in a subalpine forest dynamics plot and contributes to our understanding of patterns of genetic divergence among woody and herbaceous plant species.},
}
@article {pmid30073057,
year = {2018},
author = {Iyiola, OA and Nneji, LM and Mustapha, MK and Nzeh, CG and Oladipo, SO and Nneji, IC and Okeyoyin, AO and Nwani, CD and Ugwumba, OA and Ugwumba, AAA and Faturoti, EO and Wang, YY and Chen, J and Wang, WZ and Adeola, AC},
title = {DNA barcoding of economically important freshwater fish species from north-central Nigeria uncovers cryptic diversity.},
journal = {Ecology and evolution},
volume = {8},
number = {14},
pages = {6932-6951},
pmid = {30073057},
issn = {2045-7758},
abstract = {This study examines the utility of morphology and DNA barcoding in species identification of freshwater fishes from north-central Nigeria. We compared molecular data (mitochondrial cytochrome c oxidase subunit I (COI) sequences) of 136 de novo samples from 53 morphologically identified species alongside others in GenBank and BOLD databases. Using DNA sequence similarity-based (≥97% cutoff) identification technique, 50 (94.30%) and 24 (45.30%) species were identified to species level using GenBank and BOLD databases, respectively. Furthermore, we identified cases of taxonomic problems in 26 (49.00%) morphologically identified species. There were also four (7.10%) cases of mismatch in DNA barcoding in which our query sequence in GenBank and BOLD showed a sequence match with different species names. Using DNA barcode reference data, we also identified four unknown fish samples collected from fishermen to species level. Our Neighbor-joining (NJ) tree analysis recovers several intraspecific species clusters with strong bootstrap support (≥95%). Analysis uncovers two well-supported lineages within Schilbe intermedius. The Bayesian phylogenetic analyses of Nigerian S. intermedius with others from GenBank recover four lineages. Evidence of genetic structuring is consistent with geographic regions of sub-Saharan Africa. Thus, cryptic lineage diversity may illustrate species' adaptive responses to local environmental conditions. Finally, our study underscores the importance of incorporating morphology and DNA barcoding in species identification. Although developing a complete DNA barcode reference library for Nigerian ichthyofauna will facilitate species identification and diversity studies, taxonomic revisions of DNA sequences submitted in databases alongside voucher specimens are necessary for a reliable taxonomic and diversity inventory.},
}
@article {pmid30072640,
year = {2018},
author = {Moon, BC and Kim, WJ and Park, I and Sung, GH and Noh, P},
title = {Establishment of a PCR Assay for the Detection and Discrimination of Authentic Cordyceps and Adulterant Species in Food and Herbal Medicines.},
journal = {Molecules (Basel, Switzerland)},
volume = {23},
number = {8},
pages = {},
pmid = {30072640},
issn = {1420-3049},
mesh = {Cordyceps/*genetics ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; Food Contamination/*analysis ; Genetic Markers ; *Herbal Medicine ; Limit of Detection ; Real-Time Polymerase Chain Reaction/*methods ; Reproducibility of Results ; Sensitivity and Specificity ; },
abstract = {Accurate detection and differentiation of adulterants in food ingredients and herbal medicines are crucial for the safety and basic quality control of these products. Ophiocordyceps sinensis is described as the only fungal source for the authentic medicinal ingredient used in the herbal medicine "Cordyceps", and two other fungal species, Cordyceps militaris and Isaria tenuipes, are the authentic fungal sources for food ingredients in Korea. However, substitution of these three species, and adulteration of herbal material and dietary supplements originating from Cordyceps pruinosa or Isaria cicadae, seriously affects the safety and reduces the therapeutic efficacy of these products. Distinguishing between these species based on their morphological features is very difficult, especially in commercially processed products. In this study, we employed DNA barcode-based species-specific sequence characterized amplified region (SCAR) markers to discriminate authentic herbal Cordyceps medicines and Cordyceps-derived dietary supplements from related but inauthentic species. The reliable authentication tool exploited the internal transcribed spacer (ITS) region of a nuclear ribosomal RNA gene (nrDNA). We used comparative nrDNA-ITS sequence analysis of the five fungal species to design two sets of SCAR markers. Furthermore, we used a set of species-specific SCAR markers to establish a real-time polymerase chain reaction (PCR) assay for the detection of species, contamination, and degree of adulteration. We confirmed the discriminability and reproducibility of the SCAR marker analysis and the real-time PCR assay using commercially processed food ingredients and herbal medicines. The developed SCAR markers may be used to efficiently differentiate authentic material from their related adulterants on a species level. The ITS-based SCAR markers and the real-time PCR assay constitute a useful genetic tool for preventing the adulteration of Cordyceps and Cordyceps-related dietary supplements.},
}
@article {pmid30071090,
year = {2018},
author = {Li, Y and Geng, L and Liu, Y and Chen, M and Mu, Q and Zhang, X and Zhang, Z and Ren, G and Liu, C},
title = {Identification of three Daphne species by DNA barcoding and HPLC fingerprint analysis.},
journal = {PloS one},
volume = {13},
number = {8},
pages = {e0201711},
pmid = {30071090},
issn = {1932-6203},
mesh = {Chromatography, High Pressure Liquid ; *DNA Barcoding, Taxonomic ; Daphne/*chemistry/*classification/genetics ; Ecosystem ; },
abstract = {In order to well identify the 93 wild Cortex Daphnes samples from different species and habitats in western China and develop a standard operating procedure (SOP) for the authentication and quality of them in the future, a comprehensive and efficient identification system based on DNA barcoding and HPLC fingerprint technologies has been developed. The result showed that only 17 samples (18%) were Daphne giraldii Nitsche (DG), which is recorded in Chinese Pharmacopeia, while the others (82%) might have safety hazards. Additionally, the result of HPLC fingerprint analysis indicated that samples in the same species origins and wild distributions could be clustered together, which was consistent with DNA barcoding analysis. The study can provide a significant system for the authentication and quality of commercial Cortex Daphnes herbs. Undoubtedly, this study undoubtedly confirmed that the chemical compositions of Cortex Daphnes herbs were affected by both species origins and ecological environments, which is required more in-depth research.},
}
@article {pmid30069054,
year = {2018},
author = {Halperin, SO and Tou, CJ and Wong, EB and Modavi, C and Schaffer, DV and Dueber, JE},
title = {CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window.},
journal = {Nature},
volume = {560},
number = {7717},
pages = {248-252},
doi = {10.1038/s41586-018-0384-8},
pmid = {30069054},
issn = {1476-4687},
mesh = {CRISPR-Cas Systems/*genetics ; DNA-Directed DNA Polymerase/genetics/*metabolism ; Directed Molecular Evolution/*methods ; Drug Resistance, Microbial/drug effects/genetics ; Escherichia coli/drug effects/genetics ; Escherichia coli Proteins/genetics ; Gene Editing/*methods ; Mutagenesis, Site-Directed/*methods ; Mutation ; Mutation Rate ; Nucleotides/*genetics/metabolism ; Ribosomal Proteins/genetics ; Spectinomycin/pharmacology ; },
abstract = {The capacity to diversify genetic codes advances our ability to understand and engineer biological systems[1,2]. A method for continuously diversifying user-defined regions of a genome would enable forward genetic approaches in systems that are not amenable to efficient homology-directed oligonucleotide integration. It would also facilitate the rapid evolution of biotechnologically useful phenotypes through accelerated and parallelized rounds of mutagenesis and selection, as well as cell-lineage tracking through barcode mutagenesis. Here we present EvolvR, a system that can continuously diversify all nucleotides within a tunable window length at user-defined loci. This is achieved by directly generating mutations using engineered DNA polymerases targeted to loci via CRISPR-guided nickases. We identified nickase and polymerase variants that offer a range of targeted mutation rates that are up to 7,770,000-fold greater than rates seen in wild-type cells, and editing windows with lengths of up to 350 nucleotides. We used EvolvR to identify novel ribosomal mutations that confer resistance to the antibiotic spectinomycin. Our results demonstrate that CRISPR-guided DNA polymerases enable multiplexed and continuous diversification of user-defined genomic loci, which will be useful for a broad range of basic and biotechnological applications.},
}
@article {pmid30068321,
year = {2018},
author = {Dörler, D and Kropf, M and Laaha, G and Zaller, JG},
title = {Occurrence of the invasive Spanish slug in gardens: can a citizen science approach help deciphering underlying factors?.},
journal = {BMC ecology},
volume = {18},
number = {1},
pages = {23},
pmid = {30068321},
issn = {1472-6785},
support = {100994//Bundesministerium f&#xfc;r Land- und Forstwirtschaft, Umwelt und Wasserwirtschaft/International ; },
mesh = {*Animal Distribution ; Animals ; Austria ; DNA Barcoding, Taxonomic ; *Environment ; Gardens ; Gastropoda/genetics/*physiology ; *Introduced Species ; Phylogeny ; Sequence Analysis, DNA ; *Weather ; },
abstract = {BACKGROUND: The Spanish slug (Arion vulgaris, also known as A. lusitanicus) is considered one of the most invasive species in agriculture, horticulture and private gardens all over Europe. Although this slug has been problematic for decades, there is still not much known about its occurrence across private gardens and the underlying meteorological and ecological factors. One reason for this knowledge gap is the limited access of researchers to private gardens. Here we used a citizen science approach to overcome this obstacle and examined whether the occurrence of Arionidae in Austrian gardens was associated with meteorological (air temperature, precipitation, global solar radiation, relative humidity) or ecological factors (plant diversity, earthworm activity). Occurrence of the invasive A. vulgaris versus the similar-looking native A. rufus was compared using a DNA-barcoding approach.<br><br>RESULTS: Slugs were collected from 1061 gardens from the dry Pannonian lowland to the wet alpine climate (altitudinal range 742&#xa0;m). Slug abundance in gardens was best explained and negatively associated with the parameters "sum of the mean air temperature in spring", "number of frost days in the previous winter" and "mean daily global solar radiation on the day of data collection". Precipitation, plant diversity and earthworm activity were also related to slug abundance, but positively. Out of our genetic sampling of collected slugs, 92% belonged to A. vulgaris.<br><br>CONCLUSIONS: Our study showed that citizen science (i) is a feasible approach to record species occurrence in restricted areas across a wide geographical range and (ii) could be more widely employed in order to identify underlying environmental factors of species occurrence.},
}
@article {pmid30067814,
year = {2018},
author = {Emenyeonu, LC and Croxford, AE and Wilkinson, MJ},
title = {The potential of aerosol eDNA sampling for the characterisation of commercial seed lots.},
journal = {PloS one},
volume = {13},
number = {8},
pages = {e0201617},
pmid = {30067814},
issn = {1932-6203},
support = {BBS/E/0012843C//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Aerosols/*analysis ; Crops, Agricultural ; DNA, Plant/genetics ; Dust/*analysis ; High-Throughput Nucleotide Sequencing ; Real-Time Polymerase Chain Reaction ; Seeds/*classification/genetics ; Sequence Analysis, DNA ; Specimen Handling ; Transition Temperature ; Vigna/classification/*genetics ; Zea mays/classification/*genetics ; },
abstract = {Seed shipments, silos and storage houses often contain weed seeds or seeds of restricted crops such as undeclared genetically modified (GM) varieties. Random sub-sampling is the favoured approach to detect unwanted biological materials in seed lots but is prohibitively expensive or else ineffective for the huge volumes of seeds moved in commercial operations. This study uses maize and cowpea seed admixtures as an exemplar to evaluate the feasibility of using aerosol sampling of "seed dust" as an alternative to seed sub-sampling. In an initial calibration phase, qPCR of the rbcL barcode followed by high-resolution melting (HRM) of a DNA titration series revealed a strong linear relationship between mix composition and HRM profiles. However, the relationship became skewed when flour mixes were used to build the titration, implying a DNA extraction bias favouring cowpea. Aerosol samples of seed dust above a titration of mixed seed samples were then collected along vertical and lateral axes. Aerosols were characterised by light microscopy, qPCR-HRM and next-generation DNA sequencing (Illumina MiSeq). Both molecular approaches again showed bias but this time in a reverse direction to flour samples. Microscopic examination of the aerosol sample suggested this divergence could be attributed to differences in abundance of airborne starch particles. Despite the bias, it was nevertheless possible to estimate relative abundance of each species using the abundance of minibarcodes. In light of these results we explore the feasibility of aerosol sampling for commercial seed lot characterisation.},
}
@article {pmid30066033,
year = {2018},
author = {Salles-Loustau, G and Le, T and Najafizadeh, L and Zonouz, S and Javanmard, M},
title = {Cytocoded passwords: BioMEMS based barcoding of biological samples for user authentication in microfluidic diagnostic devices.},
journal = {Biomedical microdevices},
volume = {20},
number = {3},
pages = {63},
doi = {10.1007/s10544-018-0306-4},
pmid = {30066033},
issn = {1572-8781},
mesh = {Biological Products ; *Biometric Identification ; Confidentiality ; Flow Cytometry ; Hematologic Tests ; Humans ; *Lab-On-A-Chip Devices ; *Micro-Electrical-Mechanical Systems ; },
abstract = {Smart and connected point-of-care (POC) medical devices are becoming ever more ubiquitous and have the potential to radically improve disease diagnosis and health monitoring. This emerging connectivity can potentially create serious security issues where patient privacy can be easily compromised. Protection of patient data from malicious cyber-physical attackers requires radical solutions at the BioMEMS level. Ideally, the information exchange between the patient and practitioner is an automated and transparent process for the patient. In practice, this exchange requires both the patient and the test results to be authenticated and validated respectively on the storage service to ensure that the medical diagnostic results are properly stored and their access is protected. This secure authentication phase is particularly critical for medical diagnostics: patient data exposure could lead to negative social effects. This work focuses on providing a transparent authentication mechanism for patient blood tests performed using impedance flow cytometry. The goal is twofold: first, to alleviate the user from security procedures, precisely an authentication step, while using the medical device; second, to provide a unique identifier for the test results when stored in a remote server. This paper describes a domain specific authentication method for impedance flow cytometry devices. We spike into the blood samples synthetic micro-beads of different sizes, at determined concentrations, to generate a unique authentication string that uniquely identify a test result on the remote storage service. These authentication strings are embedded in the test devices and can be used as a convenient alternative to generic authentication methods, such as logins and passwords. This alternative method removes the authentication burden from the user and protects patient's privacy further by preventing them from linking their personal information to their test results.},
}
@article {pmid30064144,
year = {2019},
author = {Parveen, I and Techen, N and Khan, IA},
title = {Identification of Species in the Aromatic Spice Family Apiaceae Using DNA Mini-barcodes.},
journal = {Planta medica},
volume = {85},
number = {2},
pages = {139-144},
doi = {10.1055/a-0664-0947},
pmid = {30064144},
issn = {1439-0221},
support = {U01 FD004246/FD/FDA HHS/United States ; },
mesh = {Apiaceae/*genetics ; Conium/genetics ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Ligusticum/genetics ; Oligonucleotides/genetics ; Polymerase Chain Reaction ; },
abstract = {The species of the aromatic plant family Apiaceae are mainly used as spices and foods, but the family also includes medicinal and some poisonous plant species. Due to the similar chemical compounds or aroma and morphology, the poisonous species are often mistaken for the edible aromatic species. It is therefore imperative to correctly identify the species present at the initial raw stage samples to ensure product safety and efficacy. At the molecular level, plant species can be identified using DNA loci either from nuclear or plastid genome with easily available universal oligonucleotides, a technique called DNA barcoding. However, this is possible when single-species plant material is present but may not work on a mixture of plants species. Another disadvantage is that using universal oligonucleotides is of limited help, especially if the adulterating material is present in low quantities. On the other hand, if using the species-specific oligonucleotides, only single specific adulterating plant material could be detected and, consequently, the unexpected adulterants may go undetected. Therefore, in the current work, four degenerated oligonucleotides from ITS1 and ITS2 regions of the nuclear genome were designed that can bind to a variety of Apiaceae genera only and not to other genera belonging to different plant families. These family-specific oligonucleotides were able to amplify a diagnostic PCR product from 16 Apiaceae species that, upon sequencing, revealed the identity of the plant it was derived from. The size of these products is around 140 bp for ITS1 and approximately 80 bp for the ITS2 region. The size range of the amplified products falls in the category of a desired mini-barcode size to be used for damaged/fragmented DNA and next generation sequencing.},
}
@article {pmid30062908,
year = {2018},
author = {Zealley, B and de Grey, ADNJ},
title = {Commentary on Some Recent Theses Relevant to Combating Aging: August 2018.},
journal = {Rejuvenation research},
volume = {21},
number = {4},
pages = {374-379},
doi = {10.1089/rej.2018.2112},
pmid = {30062908},
issn = {1557-8577},
abstract = {Theses reviewed in this issue include "Bowties, Barcodes, and DNA Origami: A Novel Approach for Paired-Chain Immune Receptor Repertoire Analysis," "Development of Canine Chimeric Antigen Receptor T Cell Therapy for Treatment &amp; Translation," "Endocytic Vesicle Rupture in the Pathogenesis and Propagation of Neurodegenerative Proteinopathies," "Exploring Mechanisms of Metastasis Suppression in Metastatic Melanoma," "Polymer and Nucleic Acid Self-Assemblies: Properties and Applications at the Biological Interface," and "Towards a Scalable, Biomimetic, Antibacterial Coating."},
}
@article {pmid30061659,
year = {2018},
author = {Dagher, M and Kleinman, M and Ng, A and Juncker, D},
title = {Ensemble multicolour FRET model enables barcoding at extreme FRET levels.},
journal = {Nature nanotechnology},
volume = {13},
number = {10},
pages = {925-932},
doi = {10.1038/s41565-018-0205-0},
pmid = {30061659},
issn = {1748-3395},
abstract = {Quantitative models of Förster resonance energy transfer (FRET)-pioneered by Förster-define our understanding of FRET and underpin its widespread use. However, multicolour FRET (mFRET), which arises between multiple, stochastically distributed fluorophores, lacks a mechanistic model and remains intractable. mFRET notably arises in fluorescently barcoded microparticles, resulting in a complex, non-orthogonal fluorescence response that impedes their encoding and decoding. Here, we introduce an ensemble mFRET (emFRET) model, and apply it to guide barcoding into regimes with extreme FRET. We further introduce a facile, proportional multicolour labelling method using oligonucleotides as homogeneous linkers. A total of 580 barcodes were rapidly designed and validated using four dyes-with FRET efficiencies reaching 76%-and used for multiplexed immunoassays with cytometric readout and fully automated decoding. The emFRET model helps to expand the barcoding capacity of barcoded microparticles using common organic dyes and will benefit other applications subject to stochastic mFRET.},
}
@article {pmid30060026,
year = {2018},
author = {Wang, YS and Zhou, P and Tian, H and Wan, FH and Zhang, GF},
title = {First Record of the Invasive Pest Pseudococcus jackbeardsleyi (Hemiptera: Pseudococcidae) on the Chinese Mainland and Its Rapid Identification Based on Species-Specific Polymerase Chain Reaction.},
journal = {Journal of economic entomology},
volume = {111},
number = {5},
pages = {2120-2128},
doi = {10.1093/jee/toy223},
pmid = {30060026},
issn = {1938-291X},
mesh = {Animals ; China ; DNA Barcoding, Taxonomic ; Female ; Hemiptera/anatomy &amp; histology/*classification/genetics ; *Introduced Species ; Polymerase Chain Reaction ; },
abstract = {The Jack Beardsley mealybug, Pseudococcus jackbeardsleyi Gimpel &amp; Miller (Hemiptera: Pseudococcidae), a globally devastating, invasive polyphagous insect, causes great damage to many fruits, ornamentals, vegetables, and food crops worldwide. It is of Neotropical origin and has invaded throughout America and in parts of Asia, Africa and Oceania, and is still expanding its invasion ranges. Therefore, a method for quick and correct identification of this invasive species is crucial for quarantine and spreading interruption of it. In present study, we report the first record of P. jackbeardsleyi on the Chinese mainland, which would cause great damage to many crops. The identification of P. jackbeardsleyi was verified via morphological characters and DNA barcoding. One pair of species-specific polymerase chain reaction (SS-PCR) primers was designed based on variations in the sequences of the mitochondrial cytochromecoxidasesubunitI gene among P. jackbeardsleyi and 28 other mealybug species. No cross-reaction was detected among 21 closely related species using this SS-PCR assay, demonstrating the specificity of this marker. Furthermore, this method was successfully applied to detect individuals from different developmental stages and adult debris across four geographic populations of P. jackbeardsleyi, showing the high stability of the assay. Additionally, the detection limit of the marker was 55.94 ± 5.05 pg/µl of P. jackbeardsleyi DNA, illustrating the high sensitivity of the assay. The SS-PCR assay developed in this study provides a rapid, simple and reliable method for the identification of P. jackbeardsleyi, which should be crucial in the plant quarantine, early detection and sustainable management of this globally invasive pest.},
}
@article {pmid30058427,
year = {2018},
author = {Abubakar, BM and Salleh, FM and Shamsir Omar, MS and Wagiran, A},
title = {Assessing product adulteration of Eurycoma longifolia (Tongkat Ali) herbal medicinal product using DNA barcoding and HPLC analysis.},
journal = {Pharmaceutical biology},
volume = {56},
number = {1},
pages = {368-377},
pmid = {30058427},
issn = {1744-5116},
mesh = {Chromatography, High Pressure Liquid/methods ; DNA Barcoding, Taxonomic/*methods ; *Drug Contamination ; Eurycoma/*genetics ; Plant Extracts/*genetics/*isolation &amp; purification ; Plant Roots ; Plants, Medicinal/*genetics ; },
abstract = {CONTEXT: Eurycoma longifolia Jack (Simaroubaceae) commonly known as Tongkat Ali is one of the most important plants in Malaysia. The plant extracts (particularly roots) are widely used for the treatment of cough and fever besides having antimalarial, antidiabetic, anticancer and aphrodisiac activities.<br><br>OBJECTIVES: This study assesses the extent of adulteration of E. longifolia herbal medicinal products (HMPs) using DNA barcoding validated by HPLC analysis.<br><br>MATERIALS AND METHODS: Chloroplastic rbcL and nuclear ITS2 barcode regions were used in the present study. The sequences generated from E. longifolia HMPs were compared to sequences in the GenBank using MEGABLAST to verify their taxonomic identity. These results were verified by neighbor-joining tree analysis in which branches of unknown specimen are compared to the reference sequences established from this study and other retrieved from the GenBank. The HMPs were also analysed using HPLC analysis for the presence of eurycomanone bioactive marker.<br><br>RESULTS: Identification using DNA barcoding revealed that 37% of the tested HMPs were authentic while 27% were adulterated with the ITS2 barcode region proven to be the ideal marker. The validation of the authenticity using HPLC analysis showed a situation in which a species which was identified as authentic was found not to contain the expected chemical compound.<br><br>DISCUSSION AND CONCLUSIONS: DNA barcoding should be used as the first screening step for testing of HMPs raw materials. However, integration of DNA barcoding with HPLC analysis will help to provide detailed knowledge about the safety and efficacy of the HMPs.},
}
@article {pmid30056981,
year = {2018},
author = {Changbunjong, T and Bhusri, B and Sedwisai, P and Weluwanarak, T and Nitiyamatawat, E and Chareonviriyaphap, T and Ruangsittichai, J},
title = {Species identification of horse flies (Diptera: Tabanidae) in Thailand using DNA barcoding.},
journal = {Veterinary parasitology},
volume = {259},
number = {},
pages = {35-43},
doi = {10.1016/j.vetpar.2018.07.002},
pmid = {30056981},
issn = {1873-2550},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Diptera/classification/*genetics ; Electron Transport Complex IV/genetics ; Genetic Variation ; Horses ; Insect Vectors/classification/genetics ; Phylogeny ; Sequence Analysis, DNA ; Thailand ; },
abstract = {Horse flies (Diptera: Tabanidae) are of medical and veterinary importance because they are known to transmit pathogens. Approximately 80 species of horse flies have been reported in Thailand. Monitoring the distribution of horse fly species is important to control the spread of diseases transmitted by them. Currently, the species identification of horse flies is based on their morphology; this requires considerable skills and taxonomic expertise, and it may be difficult to identify morphologically similar species. DNA-based identification methods are increasingly being developed for rapid and accurate identification of various insect species. In this study, we used mitochondrial cytochrome oxidase subunit I (COI) for species identification of horse flies in Thailand. A 658 bp fragment of COI was amplified from 145 adult horse flies belonging to 48 morphologically distinct species and sequenced. Sequence analysis revealed an intraspecific divergence of 0.0%-4.4% and an interspecific divergence of 0.0%-16.2%. Our results showed that COI barcodes were effective in discriminating a majority of horse flies in Thailand on the basis of the barcoding gap and phylogenetic analyses. However, COI barcodes were unable to distinguish among members of the Tabanus striatus complex and some species within the T. ceylonicus group.},
}
@article {pmid30056284,
year = {2018},
author = {Chen, W and Shang, Y and Ren, L and Xie, K and Zhang, X and Zhang, C and Sun, S and Wang, Y and Zha, L and Guo, Y},
title = {Developing a MtSNP-based genotyping system for genetic identification of forensically important flesh flies (Diptera: Sarcophagidae).},
journal = {Forensic science international},
volume = {290},
number = {},
pages = {178-188},
doi = {10.1016/j.forsciint.2018.07.012},
pmid = {30056284},
issn = {1872-6283},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Genotype ; Polymerase Chain Reaction ; *Polymorphism, Single Nucleotide ; Sarcophagidae/*genetics ; *Sequence Analysis, DNA ; },
abstract = {Some representatives of flesh flies visiting/colonizing the decomposed remains demonstrated their values in estimating the minimal postmortem interval (PMImin) since death. However, the utility of sarcophagid flies has been seriously hampered by limited ecological, biological and taxonomic knowledge of them. Although mitochondrial genes have been proposed as a potential DNA barcode for the species-level identification of sarcophagids, some defects still remain such as the substantial memory and processing time taken for homologous comparisons online. Moreover, species identification is mainly achieved by Sanger sequencing based on PCR with genus-specific primers. In the present study we characterized 24 single nucleotide polymorphisms (SNPs) as robust markers of genetic variation for identifying different sarcophagids based on available cytochrome c oxidase I (COI) data and verified them through pyrosequencing (PSQ) technology to establish a SNP-based genotyping system. The system provides a preliminary foundation for developing a rapid, reliable, and high-throughput assay so as to efficiently and accurately identify the sarcophgid flies. Furthermore, the PSQ approach is proved to be faster, more cost-effective as well as more sensitive and specific than custom Sanger sequencing.},
}
@article {pmid30054474,
year = {2018},
author = {Tycko, J and Barrera, LA and Huston, NC and Friedland, AE and Wu, X and Gootenberg, JS and Abudayyeh, OO and Myer, VE and Wilson, CJ and Hsu, PD},
title = {Pairwise library screen systematically interrogates Staphylococcus aureus Cas9 specificity in human cells.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {2962},
pmid = {30054474},
issn = {2041-1723},
support = {P30 CA014195/CA/NCI NIH HHS/United States ; },
mesh = {Bacterial Proteins/genetics ; Base Sequence ; CRISPR-Associated Protein 9/*genetics ; CRISPR-Cas Systems ; Cloning, Molecular ; Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Editing/*methods ; *Gene Library ; Genes, Bacterial/genetics ; HEK293 Cells ; Humans ; RNA, Guide, CRISPR-Cas Systems/genetics ; Staphylococcus aureus/*genetics ; },
abstract = {Therapeutic genome editing with Staphylococcus aureus Cas9 (SaCas9) requires a rigorous understanding of its potential off-target activity in the human genome. Here we report a high-throughput screening approach to measure SaCas9 genome editing variation in human cells across a large repertoire of 88,692 single guide RNAs (sgRNAs) paired with matched or mismatched target sites in a synthetic cassette. We incorporate randomized barcodes that enable whitelisting of correctly synthesized molecules for further downstream analysis, in order to circumvent the limitation of oligonucleotide synthesis errors. We find SaCas9 sgRNAs with 21-mer or 22-mer spacer sequences are generally more active, although high efficiency 20-mer spacers are markedly less tolerant of mismatches. Using this dataset, we developed an SaCas9 specificity model that performs robustly in ranking off-target sites. The barcoded pairwise library screen enabled high-fidelity recovery of guide-target relationships, providing a scalable framework for the investigation of CRISPR enzyme properties and general nucleic acid interactions.},
}
@article {pmid30053343,
year = {2018},
author = {Willis, LM and Park, H and Watson, MWL and Majonis, D and Watson, JL and Nitz, M},
title = {Tellurium-based mass cytometry barcode for live and fixed cells.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {93},
number = {7},
pages = {685-694},
doi = {10.1002/cyto.a.23495},
pmid = {30053343},
issn = {1552-4930},
support = {//Natural Sciences and Engineering Research Council of Canada/International ; //Ontario Centres of Excellence and Fluidigm Inc./International ; },
mesh = {Antibodies/chemistry ; Biomarkers/chemistry ; Flow Cytometry/*methods ; Humans ; Single-Cell Analysis/*methods ; Staining and Labeling/*methods ; Tellurium/*chemistry ; },
abstract = {Mass cytometry is a revolutionary technology that allows for the simultaneous quantification of >40 different biomarkers with cellular resolution. The biomarkers are detected using metal-labeled antibodies as well as small-molecule probes of cell size, viability, and biochemical status. Barcoding is an important component of sample preparation because it reduces processing time, eliminates sample-to-sample variation, discriminates cell doublets, reduces the amount of antibody needed, and conserves sample. We developed a thiol-reactive tellurium-based barcode, TeMal. TeMal is nontoxic at working concentrations, compatible with metal-labeled antibodies, and can readily be applied to live or fixed cells, making it advantageous and complementary compared to existing barcoding reagents. We have demonstrated the utility of TeMal by barcoding microscale samples in situ to facilitate analysis of cells from an automated cell culture system using mass cytometry.},
}
@article {pmid30053016,
year = {2018},
author = {Sigwart, JD and Garbett, A},
title = {Biodiversity Assessment, DNA Barcoding, and the Minority Majority.},
journal = {Integrative and comparative biology},
volume = {58},
number = {6},
pages = {1146-1156},
doi = {10.1093/icb/icy076},
pmid = {30053016},
issn = {1557-7023},
mesh = {Animals ; *Biodiversity ; Biological Evolution ; Birds/*classification/genetics ; Bivalvia/*classification/genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/analysis/genetics ; Electron Transport Complex IV/analysis/genetics ; Sequence Analysis, DNA ; },
abstract = {The majority of species on Earth are in "under-studied" groups, and indeed probably the majority of species remain undiscovered and undescribed. Species are natural units of evolution, and they are formed from branching phylogenetic processes that have a mathematical structure. So it follows that we should be able to develop a set of general principles that describe global patterns of species groups, like genera. Understanding such patterns would lend considerable power to the approach of "taxonomic surrogacy." In environmental assessments, ecology, and paleontology, it is common to substitute genus-level or family-level identification where definitive species identification is impractical. Clarity and confidence in fundamental patterns, based on a robust null model for species and genus level diversity, can accelerate species discovery: there are more species in the tropics, species-poor genera are very common, large genera are rare. Much hope has been placed in DNA barcoding as an effective tool to increase the pace of species discovery, but it is abundantly clear that certain mitochondrial DNA (mtDNA) markers are more or less variable in different clades and universal threshold values are impractical to delimit species. This study further examines the patterns of divergence in one common mtDNA barcode fragment, cytochrome c oxidase subunit 1at the genus level. We compared pairwise divergence in this fragment between two animal clades that have similar species richness but different evolutionary histories: birds and bivalves. We analyzed quality controlled alignments of over 39,000 published sequences in 1223 genera. Median pairwise differences at the genus level are positively correlated with the species richness of a genus, and this is not dependent of the number of sequences sampled. Unsurprisingly, sequence divergence in vertebrates was far more constrained than in evolutionarily more ancient non-vertebrate clades. Differences among the groups examined highlight the need for DNA barcode approaches to be considered in the context of specific biological groups. Vertebrates are better studied, but not necessarily representative of the majority of biodiversity. A technique that provides powerful insights for vertebrate species may be ineffective for the majority of organisms.},
}
@article {pmid30051821,
year = {2018},
author = {Rodrigues, ASL and Charpentier, A and Bernal-Casasola, D and Gardeisen, A and Nores, C and Pis Millán, JA and McGrath, K and Speller, CF},
title = {Forgotten Mediterranean calving grounds of grey and North Atlantic right whales: evidence from Roman archaeological records.},
journal = {Proceedings. Biological sciences},
volume = {285},
number = {1882},
pages = {},
pmid = {30051821},
issn = {1471-2954},
mesh = {Animals ; Archaeology ; DNA Barcoding, Taxonomic ; Homing Behavior ; Mediterranean Sea ; *Sexual Behavior, Animal ; Whales/genetics/*physiology ; },
abstract = {Right whales (Eubalaena glacialis) were extirpated from the eastern North Atlantic by commercial whaling. Grey whales (Eschrichtius robustus) disappeared from the entire North Atlantic in still-mysterious circumstances. Here, we test the hypotheses that both species previously occurred in the Mediterranean Sea, an area not currently considered part of their historical range. We used ancient DNA barcoding and collagen fingerprinting methods to taxonomically identify a rare set of 10 presumed whale bones from Roman and pre-Roman archaeological sites in the Strait of Gibraltar region, plus an additional bone from the Asturian coast. We identified three right whales, and three grey whales, demonstrating that the ranges of both of these species historically encompassed the Gibraltar region, probably including the Mediterranean Sea as calving grounds. Our results significantly extend the known range of the Atlantic grey whale, and suggest that 2000 years ago, right and grey whales were common when compared with other whale species. The disappearance of right and grey whales from the Mediterranean region is likely to have been accompanied by broader ecosystem impacts, including the disappearance of their predators (killer whales) and a reduction in marine primary productivity. The evidence that these two coastal and highly accessible species were present along the shores of the Roman Empire raises the hypothesis that they may have formed the basis of a forgotten whaling industry.},
}
@article {pmid30051566,
year = {2018},
author = {Bañón, R and Alonso-Fernández, A and Barros-García, D and Rios, MB and de Carlos, A},
title = {Geographic range expansion of Ephippion guttifer (Tetraodontidae) in the north-eastern Atlantic.},
journal = {Journal of fish biology},
volume = {93},
number = {4},
pages = {733-737},
doi = {10.1111/jfb.13761},
pmid = {30051566},
issn = {1095-8649},
support = {070401150009//CSIC and Xunta de Galicia to analyse fisheries-dependent data from the monitoring program of small-scale fisheries in Galicia/ ; },
mesh = {*Animal Distribution ; Animals ; Atlantic Ocean ; Male ; Reproduction ; Spain ; Testis/anatomy &amp; histology ; Tetraodontiformes/*anatomy &amp; histology ; },
abstract = {The first record of the prickly puffer Ephippion guttifer (Tetraodontidae) from Galician waters (north-west Spain) is reported based on a male specimen of 570 mm total length (LT) caught in the Ría de Vigo. Morphometric, meristic and DNA barcode data confirmed the identification. Histological examination of reproductive tissue was carried out in this species for the first time, showing a mature male in an actively spawning phase. A historical revision invalidates a previous record and establishes this as the northernmost confirmed capture ever reported in the north-eastern Atlantic Ocean.},
}
@article {pmid30050112,
year = {2018},
author = {Bagnoli, JW and Ziegenhain, C and Janjic, A and Wange, LE and Vieth, B and Parekh, S and Geuder, J and Hellmann, I and Enard, W},
title = {Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {2937},
pmid = {30050112},
issn = {2041-1723},
support = {SFB1243/A14//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; SFB1243/A15//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; },
mesh = {Base Sequence ; High-Throughput Nucleotide Sequencing/methods ; RNA/*genetics ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis ; Software ; },
abstract = {Single-cell RNA sequencing (scRNA-seq) has emerged as a central genome-wide method to characterize cellular identities and processes. Consequently, improving its sensitivity, flexibility, and cost-efficiency can advance many research questions. Among the flexible plate-based methods, single-cell RNA barcoding and sequencing (SCRB-seq) is highly sensitive and efficient. Here, we systematically evaluate experimental conditions of this protocol and find that adding polyethylene glycol considerably increases sensitivity by enhancing cDNA synthesis. Furthermore, using Terra polymerase increases efficiency due to a more even cDNA amplification that requires less sequencing of libraries. We combined these and other improvements to develop a scRNA-seq library protocol we call molecular crowding SCRB-seq (mcSCRB-seq), which we show to be one of the most sensitive, efficient, and flexible scRNA-seq methods to date.},
}
@article {pmid30047136,
year = {2018},
author = {Berbel-Filho, WM and Ramos, TPA and Jacobina, UP and Maia, DJG and Torres, RA and Lima, SMQ},
title = {Updated checklist and DNA barcode-based species delimitations reveal taxonomic uncertainties among freshwater fishes from the mid-north-eastern Caatinga ecoregion, north-eastern Brazil.},
journal = {Journal of fish biology},
volume = {93},
number = {2},
pages = {311-323},
doi = {10.1111/jfb.13758},
pmid = {30047136},
issn = {1095-8649},
support = {233161/2014-7//Cnpq/ ; 306290/2015-4//Cnpq/ ; 350674/2012-4//CNPq/FAPERN/ ; 552086/2011-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/Minist&#xe9;rio de Ci&#xea;ncias e Tecnologia/ ; BCT-0125-2.04/15//FACEPE/ ; 1273846//PNPD-CAPES/ ; //Universidade Federal do Rio Grande do Norte/ ; },
mesh = {Animals ; *Biodiversity ; Brazil ; *Checklist ; DNA ; DNA Barcoding, Taxonomic ; Fishes/*classification ; Fresh Water ; Rivers ; },
abstract = {The mid-north-eastern Caatinga is a semiarid freshwater ecoregion in North-eastern Brazil that is dominated by temporary rivers and is currently classified as one of the least ichthyologically-known ecoregions in the world. The present study aimed to provide an updated checklist of mid-north-eastern Caatinga ecoregion (MNCE) freshwater fish species and evaluate their taxonomic identity using morphology, DNA barcoding and multiple species delimitation approaches. After reviewing published studies and ichthyological collections, 119 species were identified. Among these were 94 putatively valid native and 14 non-native species, five undescribed native species, four new records for the MNCE, 11 potential cases of misidentification and 14 species listed as inquirenda. Additionally, 252 individuals from 49 species were barcoded, revealing three potential taxonomic synonyms. The combined molecular approaches estimated a total of 91 native species, although a finalized species list for the MNCE awaits additional taxonomic revisions and field surveys. This study provides the most up-to-date species checklist for the MNCE and a molecular reference database for identifying MNCE fishes with DNA barcodes. Results highlight the need to integrate traditional taxonomy with molecular approaches to correctly identify species, especially in taxonomically problematic ecoregions such as the MNCE.},
}
@article {pmid30046552,
year = {2018},
author = {Tinacci, L and Guidi, A and Toto, A and Guardone, L and Giusti, A and D'Amico, P and Armani, A},
title = {DNA barcoding for the verification of supplier's compliance in the seafood chain: How the lab can support companies in ensuring traceability.},
journal = {Italian journal of food safety},
volume = {7},
number = {2},
pages = {6894},
pmid = {30046552},
issn = {2239-7132},
abstract = {Food Business Operators (FBOs) rely on laboratory analysis to ensure seafood traceability. DNA barcoding and Forensically Informative Nucleotide Sequencing may represent a support within self-checking programs finalized to suppliers' qualification and products identity certification. The present study aimed at verifying the usefulness of a decisional procedure (decision tree) set up at the FishLab (Department of Veterinary Sciences, University of Pisa, Italy) for seafood species identification by DNA analysis, to cope with FBOs' needs. The decision tree was applied to the analysis of 182 seafood (fish and molluscs) products, conferred to the FishLab by different FBOs between 2014 and 2015 as result of their self-checking activities. The analysis relied on a standard COI gene fragment eventually integrated by the analysis of alternative or supportive molecular targets (cytb and 16S rRNA). It also included a mini-DNA barcoding approach for processed products. Overall, 96.2% of the samples were unambiguously identified at species level using the elective target alone (92.4%) or a multi-target approach (3.8%). The lack of species identification (3.8%) was attributable to the absence of reference sequences or to the low resolution of the molecular targets. Nonetheless, all the molecular results were deemed adequate to evaluate the sample's compliance to the label information. Non-compliances were highlighted in 18.1% of the products. The protocol was proven as an effective supportive tool for the seafood identity verification within the supply chain self-checking activities. In addition, a considerable fraud rate was confirmed and the species most frequently involved in substitution were pointed out.},
}
@article {pmid30046044,
year = {2018},
author = {Aksenova, OV and Bolotov, IN and Gofarov, MY and Kondakov, AV and Vinarski, MV and Bespalaya, YV and Kolosova, YS and Palatov, DM and Sokolova, SE and Spitsyn, VM and Tomilova, AA and Travina, OV and Vikhrev, IV},
title = {Species Richness, Molecular Taxonomy and Biogeography of the Radicine Pond Snails (Gastropoda: Lymnaeidae) in the Old World.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {11199},
pmid = {30046044},
issn = {2045-2322},
support = {L60 MD002394/MD/NIMHD NIH HHS/United States ; },
mesh = {Africa ; Animals ; *Biological Evolution ; Classification/methods ; DNA, Mitochondrial/genetics ; Lakes ; *Phylogeography ; Ponds ; Snails/classification/*genetics/*physiology ; Species Specificity ; },
abstract = {The radicine pond snails represent a species-rich and widely distributed group, many species of which are key vectors of human and animal trematodoses. Here we clarify the taxonomy, distribution and evolutionary biogeography of the radicine lymnaeids in the Old World based on the most comprehensive multi-locus molecular dataset sampled to date. We show that the subfamily Amphipepleinae is monophyletic and contains at least ten genus-level clades: Radix Montfort, 1810, Ampullaceana Servain, 1881, Peregriana Servain, 1881, Tibetoradix Bolotov, Vinarski &amp; Aksenova gen. nov., Kamtschaticana Kruglov &amp; Starobogatov, 1984, Orientogalba Kruglov &amp; Starobogatov, 1985, Cerasina Kobelt, 1881, Myxas G. B. Sowerby I, 1822, Bullastra Bergh, 1901, and Austropeplea Cotton, 1942. With respect to our phylogeny, species-delimitation model and morphological data, the Old World fauna includes 35 biological species of radicines. Tibet and Eastern Europe harbor the richest faunas, while East Asia and Africa appear to be the most species-poor areas. The radicine clade could have originated near the Cretaceous - Paleocene boundary. The Miocene great lakes in Eurasia seems to be the most important evolutionary hotspots shaping spatial patterns of recent species richness. Finally, we present the first DNA barcode reference library for the reliable molecular identification of species within this group.},
}
@article {pmid30045782,
year = {2018},
author = {Wennmann, JT and Keilwagen, J and Jehle, JA},
title = {Baculovirus Kimura two-parameter species demarcation criterion is confirmed by the distances of 38 core gene nucleotide sequences.},
journal = {The Journal of general virology},
volume = {99},
number = {9},
pages = {1307-1320},
doi = {10.1099/jgv.0.001100},
pmid = {30045782},
issn = {1465-2099},
mesh = {Baculoviridae/classification/*genetics ; Base Sequence ; DNA, Viral/genetics ; *Genome, Viral ; Phylogeny ; Sequence Alignment ; Species Specificity ; },
abstract = {Kimura two-parameter nucleotide distance comparisons based on polyhedrin/granulin (polh/gran), late expression factor 8 (lef-8) and late expression factor 9 (lef-9) are a widely applied method for species demarcation for lepidopteran-specific baculoviruses. Baculoviruses are considered to belong to the same species when a pairwise distance threshold of 0.015 is not exceeded and are considered as possibly belonging to the same species with a distance of up to 0.050. In the present work this method was revised and extended for 172 entirely sequenced lepidopteran, hymenopteran and dipteran baculovirus genomes by applying the nucleotide sequences of all 38 known baculovirus core genes for pairwise distance calculations. On the basis of this large dataset, the previously established standard thresholds for baculovirus species demarcation were adjusted for pairwise nucleotide distances estimated from the alignments of all 38 core genes. With the newly applied thresholds for the 38 core-gene dataset, a more sophisticated Kimura two-parameter method was established, avoiding the possible influence of the chimerical polh gene of the Autographa californica multiple nucleopolyhedrovirus. Based on the new dataset, the present classification of baculovirus species was confirmed. Thereby the Kimura two-parameter method for baculovirus demarcation was extended to include the information from all 38 Baculoviridae core genes, which represent the established standard information for baculovirus phylogeny to date.},
}
@article {pmid30044868,
year = {2018},
author = {Gong, L and Qiu, XH and Huang, J and Xu, W and Bai, JQ and Zhang, J and Su, H and Xu, CM and Huang, ZH},
title = {Constructing a DNA barcode reference library for southern herbs in China: A resource for authentication of southern Chinese medicine.},
journal = {PloS one},
volume = {13},
number = {7},
pages = {e0201240},
pmid = {30044868},
issn = {1932-6203},
mesh = {China ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; Drugs, Chinese Herbal/metabolism ; *Gene Library ; Genetic Variation ; Medicine, Chinese Traditional ; Plants, Medicinal/*genetics ; Quality Control ; },
abstract = {Southern Chinese Medicine (SCM) is an important sect of Traditional Chinese Medicine (TCM) with its own special cultural style. Species identification is essential for TCM quality control because authentic herbs are possibly substituted with adulterants that would threaten the health of the public or even cause death. Here, we provided the first local reference DNA barcode library based on the second internal transcribed spacer (ITS2) for the molecular identification of SCM. A total of 1512 specimens of southern herbs representing 359 species were collected under the instructions and identification of taxonomic experts. Genomic DNA was extracted, and the PCR reaction proceeded according to standard procedures. After Sanger sequencing, sequence assembling and annotation, a reliable ITS2 barcode library with 1276 sequences from 309 species of Southern herbs was constructed. The PCR efficiency of the whole samples was 84.39%. Characteristics of the ITS2 barcode were analyzed, including sequence lengths and GC contents in different taxa. Neighbor-joining trees based on Kimura 2-Parameter (K2P) genetic distances showed a 67.56% successful rate of species identification with ITS2 barcode. In addition, 96.57% of species could be successfully identified at the genus level by the BLAST method. Eleven plant species were discovered to be cryptic. In addition, we found that there is an incorrect sequence existing in the public database, making a reliable local DNA barcode reference more meaningful. ITS2 barcodes exhibit advantages in TCM identification. This DNA barcode reference library could be used in Southern Chinese Medicine quality control, thus contributing to protecting public health.},
}
@article {pmid30042153,
year = {2018},
author = {Binenbaum, Y and Fridman, E and Yaari, Z and Milman, N and Schroeder, A and Ben David, G and Shlomi, T and Gil, Z},
title = {Transfer of miRNA in Macrophage-Derived Exosomes Induces Drug Resistance in Pancreatic Adenocarcinoma.},
journal = {Cancer research},
volume = {78},
number = {18},
pages = {5287-5299},
doi = {10.1158/0008-5472.CAN-18-0124},
pmid = {30042153},
issn = {1538-7445},
mesh = {Adenocarcinoma/metabolism/*therapy ; Animals ; Carcinoma, Pancreatic Ductal/*drug therapy/metabolism ; Cell Line, Tumor ; Deoxycytidine/analogs &amp; derivatives/pharmacology ; Disease Models, Animal ; *Drug Resistance, Neoplasm ; Exosomes/*metabolism ; Gene Transfer Techniques ; Macrophages, Peritoneal/metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; MicroRNAs/*metabolism ; Pancreatic Neoplasms/metabolism/*therapy ; Tumor Microenvironment ; Up-Regulation ; rab27 GTP-Binding Proteins/genetics ; Gemcitabine ; },
abstract = {Pancreatic ductal adenocarcinoma (PDAC) is known for its resistance to gemcitabine, which acts to inhibit cell growth by termination of DNA replication. Tumor-associated macrophages (TAM) were recently shown to contribute to gemcitabine resistance; however, the exact mechanism of this process is still unclear. Using a genetic mouse model of PDAC and electron microscopy analysis, we show that TAM communicate with the tumor microenvironment via secretion of approximately 90 nm vesicles, which are selectively internalized by cancer cells. Transfection of artificial dsDNA (barcode fragment) to murine peritoneal macrophages and injection to mice bearing PDAC tumors revealed a 4-log higher concentration of the barcode fragment in primary tumors and in liver metastasis than in normal tissue. These macrophage-derived exosomes (MDE) significantly decreased the sensitivity of PDAC cells to gemcitabine, in vitro and in vivo This effect was mediated by the transfer of miR-365 in MDE. miR-365 impaired activation of gemcitabine by upregulation of the triphospho-nucleotide pool in cancer cells and the induction of the enzyme cytidine deaminase; the latter inactivates gemcitabine. Adoptive transfer of miR-365 in TAM induced gemcitabine resistance in PDAC-bearing mice, whereas immune transfer of the miR-365 antagonist recovered the sensitivity to gemcitabine. Mice deficient of Rab27 a/b genes, which lack exosomal secretion, responded significantly better to gemcitabine than did wildtype. These results identify MDE as key regulators of gemcitabine resistance in PDAC and demonstrate that blocking miR-365 can potentiate gemcitabine response.Significance: Harnessing macrophage-derived exosomes as conveyers of antagomiRs augments the effect of chemotherapy against cancer, opening new therapeutic options against malignancies where resistance to nucleotide analogs remains an obstacle to overcome. Cancer Res; 78(18); 5287-99. ©2018 AACR.},
}
@article {pmid30042097,
year = {2018},
author = {Höfer, T and Rodewald, HR},
title = {Differentiation-based model of hematopoietic stem cell functions and lineage pathways.},
journal = {Blood},
volume = {132},
number = {11},
pages = {1106-1113},
pmid = {30042097},
issn = {1528-0020},
mesh = {Animals ; Cell Differentiation/*physiology ; Gene Expression Regulation/*physiology ; Hematopoiesis/*physiology ; Hematopoietic Stem Cells/cytology/*metabolism ; Humans ; *Models, Biological ; },
abstract = {Advances in genetic labeling and barcoding of hematopoietic stem cells (HSCs) in situ now allow direct measurements of physiological HSC output, both quantitatively and qualitatively. Turning on a heritable label in HSCs and measuring the kinetics of label emergence in downstream compartments reveal rates of differentiation and self-renewal of HSCs and progenitor cells, whereas endogenous HSC barcoding probes physiological precursor-product relationships. Labels have been inserted at different stages of the hematopoietic differentiation hierarchy. Recent genetic and functional evidence suggests a phenotype (Tie2[+]) for tip HSCs. Fate mapping shows that many tip HSCs regularly feed into downstream stages, with individual cells contributing infrequently. Stem and progenitor cells downstream of tip HSCs serve as a major, nearly self-renewing source of day-to-day hematopoiesis, rendering the blood and immune system HSC-independent for extended periods of time. HSCs realize multilineage output, yet, fates restricted to several lineages or even a single lineage have also been observed. Single HSCs within a clone in the bone marrow that develop from a fetal HSC precursor have been observed to express clone-specific fates. Thus, the new tools probing HSC differentiation in situ are progressing beyond assays for HSC activity based on proliferation measurements and fates of transplanted stem cells, and the data challenge lineage interpretations of single-cell gene expression snapshots. Linking in vivo fate analyses to gene expression and other molecular determinants of cell fate will aid in unraveling the mechanisms of lineage commitment and the architecture of physiological hematopoiesis.},
}
@article {pmid30041026,
year = {2018},
author = {Bogarín, D and Pérez-Escobar, OA and Groenenberg, D and Holland, SD and Karremans, AP and Lemmon, EM and Lemmon, AR and Pupulin, F and Smets, E and Gravendeel, B},
title = {Anchored hybrid enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex.},
journal = {Molecular phylogenetics and evolution},
volume = {129},
number = {},
pages = {27-47},
doi = {10.1016/j.ympev.2018.07.014},
pmid = {30041026},
issn = {1095-9513},
mesh = {Cell Nucleus/*genetics ; Cluster Analysis ; Databases, Genetic ; Flowers/anatomy &amp; histology ; Genetic Loci ; Genetic Markers ; *Hybridization, Genetic ; Likelihood Functions ; Mitochondria/*genetics ; Orchidaceae/*genetics ; Phylogeny ; Plastids/*genetics ; Species Specificity ; },
abstract = {Phylogenetic relationships in species complexes and lineages derived from rapid diversifications are often challenging to resolve using morphology or standard DNA barcoding markers. The hyper-diverse genus Lepanthes from Neotropical cloud forest includes over 1200 species and many recent, explosive diversifications that have resulted in poorly supported nodes and morphological convergence across clades. Here, we assess the performance of 446 nuclear-plastid-mitochondrial markers derived from an anchored hybrid enrichment approach (AHE) coupled with coalescence- and species network-based inferences to resolve phylogenetic relationships and improve species recognition in the Lepanthes horrida species group. In addition to using orchid-specific probes to increase enrichment efficiency, we improved gene tree resolution by extending standard angiosperm targets into adjacent exons. We found high topological discordance among individual gene trees, suggesting that hybridization/polyploidy may have promoted speciation in the lineage via formation of new hybrid taxa. In addition, we identified ten loci with the highest phylogenetic informativeness values from these genomes. Most previous phylogenetic sampling in the Pleurothallidinae relies on two regions (ITS and matK), therefore, the evaluation of other markers such as those shown here may be useful in future phylogenetic studies in the orchid family. Coalescent-based species tree estimation methods resolved the phylogenetic relationships of the L. horrida species group. The resolution of the phylogenetic estimations was improved with the inclusion of extended anchor targets. This approach produced longer loci with higher discriminative power. These analyses also disclosed two undescribed species, L. amicitiae and L. genetoapophantica, formally described here, which are also supported by morphology. Our study demonstrates the utility of combined genomic evidence to disentangle phylogenetic relationships at very shallow levels of the tree of life, and in clades showing convergent trait evolution. With a fully resolved phylogeny, is it possible to disentangle traits evolving in parallel or convergently across these orchid lineages such as flower color and size from diagnostic traits such as the shape and orientation of the lobes of the petals and lip.},
}
@article {pmid30039365,
year = {2018},
author = {Wiedenhoeft, J and Schliep, A},
title = {Using HaMMLET for Bayesian Segmentation of WGS Read-Depth Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1833},
number = {},
pages = {83-93},
doi = {10.1007/978-1-4939-8666-8_6},
pmid = {30039365},
issn = {1940-6029},
support = {U01 CA198952/CA/NCI NIH HHS/United States ; },
mesh = {DNA Barcoding, Taxonomic/*methods ; *High-Throughput Nucleotide Sequencing ; Markov Chains ; Sequence Analysis, DNA/*methods ; },
abstract = {CNV detection requires a high-quality segmentation of genomic data. In many WGS experiments, sample and control are sequenced together in a multiplexed fashion using DNA barcoding for economic reasons. Using the differential read depth of these two conditions cancels out systematic additive errors. Due to this detrending, the resulting data is appropriate for inference using a hidden Markov model (HMM), arguably one of the principal models for labeled segmentation. However, while the usual frequentist approaches such as Baum-Welch are problematic for several reasons, they are often preferred to Bayesian HMM inference, which normally requires prohibitively long running times and exceeds a typical user's computational resources on a genome scale data. HaMMLET solves this problem using a dynamic wavelet compression scheme, which makes Bayesian segmentation of WGS data feasible on standard consumer hardware.},
}
@article {pmid30038233,
year = {2020},
author = {Lago, SG and Tomasik, J and van Rees, GF and Ramsey, JM and Haenisch, F and Cooper, JD and Broek, JA and Suarez-Pinilla, P and Ruland, T and Auyeug, B and Mikova, O and Kabacs, N and Arolt, V and Baron-Cohen, S and Crespo-Facorro, B and Bahn, S},
title = {Exploring the neuropsychiatric spectrum using high-content functional analysis of single-cell signaling networks.},
journal = {Molecular psychiatry},
volume = {25},
number = {10},
pages = {2355-2372},
pmid = {30038233},
issn = {1476-5578},
mesh = {*Autism Spectrum Disorder/metabolism ; *Bipolar Disorder/metabolism ; *Depressive Disorder, Major/metabolism ; Female ; Humans ; Male ; *Schizophrenia/metabolism ; *Signal Transduction ; *Single-Cell Analysis ; },
abstract = {Neuropsychiatric disorders overlap in symptoms and share genetic risk factors, challenging their current classification into distinct diagnostic categories. Novel cross-disorder approaches are needed to improve our understanding of the heterogeneous nature of neuropsychiatric diseases and overcome existing bottlenecks in their diagnosis and treatment. Here we employ high-content multi-parameter phospho-specific flow cytometry, fluorescent cell barcoding and automated sample preparation to characterize ex vivo signaling network responses (n = 1764) measured at the single-cell level in B and T lymphocytes across patients diagnosed with four major neuropsychiatric disorders: autism spectrum condition (ASC), bipolar disorder (BD), major depressive disorder (MDD), and schizophrenia (SCZ; n = 25 each), alongside matched healthy controls (n = 100). We identified 25 nodes (individual cell subtype-epitope-ligand combinations) significantly altered relative to the control group, with variable overlap between different neuropsychiatric diseases and heterogeneously expressed at the level of each individual patient. Reconstruction of the diagnostic categories from the altered nodes revealed an overlapping neuropsychiatric spectrum extending from MDD on one end, through BD and SCZ, to ASC on the other end. Network analysis showed that although the pathway structure of the epitopes was broadly preserved across the clinical groups, there were multiple discrete alterations in network connectivity, such as disconnections within the antigen/integrin receptor pathway and increased negative regulation within the Akt1 pathway in CD4[+] T cells from ASC and SCZ patients, in addition to increased correlation of Stat1 (pY701) and Stat5 (pY694) responses in B cells from BD and MDD patients. Our results support the "dimensional" approach to neuropsychiatric disease classification and suggest potential novel drug targets along the neuropsychiatric spectrum.},
}
@article {pmid30034337,
year = {2018},
author = {Chen, X and Zhou, J and Cui, Y and Wang, Y and Duan, B and Yao, H},
title = {Identification of Ligularia Herbs Using the Complete Chloroplast Genome as a Super-Barcode.},
journal = {Frontiers in pharmacology},
volume = {9},
number = {},
pages = {695},
pmid = {30034337},
issn = {1663-9812},
abstract = {More than 30 Ligularia Cass. (Asteraceae) species have long been used in folk medicine in China. Morphological features and common DNA regions are both not ideal to identify Ligularia species. As some Ligularia species contain pyrrolizidine alkaloids, which are hazardous to human and animal health and are involved in metabolic toxification in the liver, it is important to find a better way to distinguish these species. Here, we report complete chloroplast (CP) genomes of six Ligularia species, L. intermedia, L. jaluensis, L. mongolica, L. hodgsonii, L. veitchiana, and L. fischeri, obtained through high-throughput Illumina sequencing technology. These CP genomes showed typical circular tetramerous structure and their sizes range from 151,118 to 151,253 bp. The GC content of each CP genome is 37.5%. Every CP genome contains 134 genes, including 87 protein-coding genes, 37 tRNA genes, eight rRNA genes, and two pseudogenes (ycf1 and rps19). From the mVISTA, there were no potential coding or non-coding regions to distinguish these six Ligularia species, but the maximum likelihood tree of the six Ligularia species and other related species showed that the whole CP genome can be used as a super-barcode to identify these six Ligularia species. This study provides invaluable data for species identification, allowing for future studies on phylogenetic evolution and safe medical applications of Ligularia.},
}
@article {pmid30032765,
year = {2018},
author = {Kwon, SJ and Kim, D and Lee, I and Nam, J and Kim, J and Dordick, JS},
title = {Sensitive multiplex detection of whole bacteria using self-assembled cell binding domain complexes.},
journal = {Analytica chimica acta},
volume = {1030},
number = {},
pages = {156-165},
doi = {10.1016/j.aca.2018.05.008},
pmid = {30032765},
issn = {1873-4324},
mesh = {Bacillus anthracis/cytology/*isolation &amp; purification ; Binding Sites ; Cell Wall/chemistry/metabolism ; DNA, Bacterial/chemistry ; Glucose Oxidase/metabolism ; Listeria/cytology/*isolation &amp; purification ; Spectrophotometry ; Staphylococcus aureus/cytology/*isolation &amp; purification ; Streptavidin/chemistry ; },
abstract = {Detecting bacterial cells at low levels is critical in public health, the food industry and first response. Current processes typically involve laborious cell lysis and genomic DNA extraction to achieve 100-1000 CFU mL[-1] levels for detecting gram-positive bacteria. As an alternative to DNA-based methods, cell wall binding domains (CBDs) derived from lysins having a modular structure with an N-terminal catalytic domain and a C-terminal CBD, can be used to detect bacterial pathogens as a result of their exceptionally specific binding to target bacteria with great avidity. We have developed a highly sensitive method for multiplex detection of whole bacterial cells using self-assembled CBD complexes. Self-assembled CBD-SA-reporter complexes were generated using streptavidin (SA), biotin-CBDs, and biotinylated reporters, such as glucose oxidase (GOx) and specific DNA sequences. The simultaneous detection of three test bacteria, Staphylococcus aureus, Bacillus anthracis-Sterne, and Listeria innocua cells in PBS could be accomplished with a 96-well plate-based sandwich method using CBD-SA-GOx complex-coupled spectrophotometric assay to achieve a detection limit of >100 CFU mL[-1]. To achieve greater detection sensitivity, we used CBD-SA-DNA complexes and qPCR of specific DNA barcodes selectively bound to the surface of target bacterial cells, which resulted in a detection sensitivity as low as 1-10 CFU mL[-1] without cross-reactivity. This sensitive multiplex detection of bacterial pathogens using both CBD-SA-GOx and CBD-SA-DNA complexes has the potential to be quickly combined with point-of-care compatible diagnostics for the rapid detection of pathogens in test samples.},
}
@article {pmid30032613,
year = {2018},
author = {Gentile, SD and Griebel, ME and Anderson, EW and Underhill, GH},
title = {Click Chemistry-Based DNA Labeling of Cells for Barcoding Applications.},
journal = {Bioconjugate chemistry},
volume = {29},
number = {8},
pages = {2846-2854},
doi = {10.1021/acs.bioconjchem.8b00435},
pmid = {30032613},
issn = {1520-4812},
mesh = {A549 Cells ; Cell Separation ; *Click Chemistry ; DNA/*chemistry ; *DNA Barcoding, Taxonomic ; Flow Cytometry ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Polymerase Chain Reaction ; },
abstract = {Cell labeling and tracking methodologies can play an important role in experiments aimed at understanding biological systems. However, many current cell labeling and tracking techniques have limitations that preclude their use in a variety of multiplexed and high-throughput applications that could best represent the heterogeneity and combinatorial complexity present in physiologic contexts. Here, we demonstrate an approach for labeling, tracking, and quantifying cells using double-stranded DNA barcodes. These barcodes are introduced to the outside of the cell membrane, giving the labeled cells a unique identifier. This approach is compatible with flow cytometric and PCR-based identification and relative quantification of the presence of barcode-labeled cells. Further, utilizing this strategy, we demonstrate the capacity for sorting and enrichment of barcoded cells from a bulk population. In addition, we illustrate the design and utility of a range of orthogonal barcode sequences, which can enable the use of multiple independent barcodes to track, sort, and enrich multiple cell types and/or cells receiving distinct treatments from a pooled sample. Overall, this method of labeling cells has the potential to track multiple populations of cells in both high-throughput in vitro and physiologic in vivo settings.},
}
@article {pmid30028648,
year = {2018},
author = {Sultana, S and Hossain, MAM and Naquiah, NNA and Ali, ME},
title = {Novel multiplex PCR-RFLP assay discriminates bovine, porcine and fish gelatin substitution in Asian pharmaceuticals capsule shells.},
journal = {Food additives &amp; contaminants. Part A, Chemistry, analysis, control, exposure &amp; risk assessment},
volume = {35},
number = {9},
pages = {1662-1673},
doi = {10.1080/19440049.2018.1500719},
pmid = {30028648},
issn = {1944-0057},
mesh = {Animals ; Capsules/chemistry ; Cattle ; Chemistry, Pharmaceutical ; DNA/chemistry/*genetics ; Fishes ; Gelatin/chemistry/*genetics ; Malaysia ; Multiplex Polymerase Chain Reaction/*methods ; Pharmaceutical Preparations/*chemistry ; Polymorphism, Restriction Fragment Length/*genetics ; Swine ; },
abstract = {Gelatin is widely used in pharmaceuticals as a protective coating, such as soft and hard capsule shells. However, the animal source of gelatin is a sensitive issue because certain gelatins such as porcine and bovine gelatins are not welcome in Halal, Kosher and Hindus' consumer goods. Recently, we have documented DNA barcoding and multiplex PCR platforms for discriminating porcine, bovine and fish gelatins in various fish and confectionary products; but those assays were not self-authenticating and also not tested in highly refined pharmaceutical products. To address this knowledge gap, here we report a self-authenticating multiplex PCR-restriction fragment length polymorphism (RFLP) assay to identify animal sources of various gelatin in pharmaceutical capsules. Three different restriction enzymes, BsaAI, Hpy188I and BcoDI were used to yield distinctive RFLP patterns for gelatin-based bovine (26, 94 bp), fish (97, 198 bp) and porcine (17, 70 bp) DNA in control experiments. The specificity was cross-tested against 16 non-target species and the optimised assay was used to screen gelatin sources in 30 halal-branded pharmaceuticals capsule shells. Bovine and porcine DNA was found in 27 and 3 of the 30 different capsules products. The assay was suitable for detecting 0.1 to 0.01 ng total DNA extracted from pure and mixed gelatins. The study might be useful to authenticate and monitor halal, kosher, vegetarian and Hindu compliant pharmaceuticals, foods and cosmetics.},
}
@article {pmid30026801,
year = {2018},
author = {Swift, JF and Lance, RF and Guan, X and Britzke, ER and Lindsay, DL and Edwards, CE},
title = {Multifaceted DNA metabarcoding: Validation of a noninvasive, next-generation approach to studying bat populations.},
journal = {Evolutionary applications},
volume = {11},
number = {7},
pages = {1120-1138},
pmid = {30026801},
issn = {1752-4571},
abstract = {As multiple species of bats are currently experiencing dramatic declines in populations due to white-nose syndrome (WNS) and other factors, conservation managers have an urgent need for data on the ecology and overall status of populations of once-common bat species. Standard approaches to obtain data on bat populations often involve capture and handling, requiring extensive expertise and unavoidably resulting in stress to the bats. New methods to rapidly obtain critical data are needed that minimize both the stress on bats and the spread of WNS. Guano provides a noninvasive source of DNA that includes information from the bat, but also dietary items, parasites, and pathogens. DNA metabarcoding is a high-throughput, DNA-based identification technique to assess the biodiversity of environmental or fecal samples. We investigated the use of multifaceted DNA metabarcoding (MDM), a technique combining next-generation DNA sequencing (NGS), DNA barcodes, and bioinformatic analysis, to simultaneously collect data on multiple parameters of interest (bat species composition, individual genotype, sex ratios, diet, parasites, and presence of WNS) from fecal samples using a single NGS run. We tested the accuracy of each MDM assay using samples in which these parameters were previously determined using conventional approaches. We found that assays for bat species identification, insect diet, parasite diversity, and genotype were both sensitive and accurate, the assay to detect WNS was highly sensitive but requires careful sample processing steps to ensure the reliability of results, while assays for nectivorous diet and sex showed lower sensitivity. MDM was able to quantify multiple data classes from fecal samples simultaneously, and results were consistent whether we included assays for a single data class or multiple data classes. Overall, MDM is a useful approach that employs noninvasive sampling and a customizable suite of assays to gain important and largely accurate information on bat ecology and population dynamics.},
}
@article {pmid30026663,
year = {2018},
author = {Kobayashi, S and Johns, CA and Lopez-Vaamonde, C and Camiel Doorenweerd, and Kawakita, A and Ohshima, I and Lees, DC and Hanabergh, S and Kawahara, AY},
title = {Hawaiian Philodoria (Lepidoptera, Gracillariidae, Ornixolinae) leaf mining moths on Myrsine (Primulaceae): two new species and biological data.},
journal = {ZooKeys},
volume = {},
number = {773},
pages = {109-141},
pmid = {30026663},
issn = {1313-2989},
abstract = {This paper provides new taxonomic and biological data on a complex of gracillariid moths in the endemic genus Philodoria Walsingham, 1907 that are associated with Myrsine (Primulaceae) in the Hawaiian Islands, United States. Two new species, Philodoria kauaulaensis Kobayashi, Johns &amp; Kawahara, sp. n. (host: Myrsine lanaiensis, M. lessertiana, and M. sandwicensis) and P. kolea Kobayashi, Johns &amp; Kawahara, sp. n. (host: M. lessertiana) are described. Biological data are provided for two previously described species that also feed on Myrsine: P. auromagnifica Walsingham, 1907 and P. succedanea Walsingham, 1907. For the first time we detail and illustrate genital structures, immature stages, biology, and host plants of P. auromagnifica and P. succedanea. Philodoria kolea, P. auromagnifica, and P. succedanea occur in sympatry on the island of Hawaii (Big Island), but each species differs in behavioral characters: P. kolea utilizes leaves of seedlings and forms a serpentine mine, whereas the latter two utilize leaves of larger plants, and form linear or serpentine to blotch mines. More broadly, leaf mine forms and diagnostic characteristics of the Myrsine-feeding species complex of Philodoria (as currently known) are reviewed and illustrated.},
}
@article {pmid30026559,
year = {2018},
author = {Tyler, AD and Mataseje, L and Urfano, CJ and Schmidt, L and Antonation, KS and Mulvey, MR and Corbett, CR},
title = {Evaluation of Oxford Nanopore's MinION Sequencing Device for Microbial Whole Genome Sequencing Applications.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {10931},
pmid = {30026559},
issn = {2045-2322},
mesh = {Bacillus anthracis/*genetics ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing/instrumentation ; Metagenomics ; Nanopores ; Whole Genome Sequencing/*instrumentation ; },
abstract = {The MinION sequencer (Oxford Nanopore Technologies) is a paradigm shifting device allowing rapid, real time long read sequencing of nucleic acids. Yet external benchmarking of this technologies' capabilities has not been extensively reported, nor has thorough evaluation of its utility for field-based analysis with sub-optimal sample types been described. The aim of this study was to evaluate the capability of the MinION sequencer for bacterial genomic and metagenomic applications, with specific emphasis placed on the quality, yield, and accuracy of generated sequence data. Two independent laboratories at the National Microbiology Laboratory (Public Health Agency of Canada), sequenced a set of microbes in replicate, using the currently available flowcells, sequencing chemistries, and software available at the time of the experiment. Overall sequencing yield and quality improved through the course of this set of experiments. Sequencing alignment accuracy was high reaching 97% for all 2D experiments, though was slightly lower for 1D sequencing (94%). 1D sequencing provided much longer sequences than 2D. Both sequencing chemistries performed equally well in constructing genomic assemblies. There was evidence of barcode cross-over using both the native and PCR barcoding methods. Despite the sub-optimal nature of samples sequenced in the field, sequences attributable to B. anthracis the target organism used in this scenario, could none-the-less be detected. Together, this report showcases the rapid advancement in this technology and its utility in the context of genomic sequencing of microbial isolates of importance to public health.},
}
@article {pmid30025666,
year = {2018},
author = {Cvijović, I and Nguyen Ba, AN and Desai, MM},
title = {Experimental Studies of Evolutionary Dynamics in Microbes.},
journal = {Trends in genetics : TIG},
volume = {34},
number = {9},
pages = {693-703},
pmid = {30025666},
issn = {0168-9525},
support = {R01 GM104239/GM/NIGMS NIH HHS/United States ; },
mesh = {Adaptation, Physiological/*genetics ; Bacteria/*genetics/growth &amp; development ; *Directed Molecular Evolution ; Genetic Fitness/*genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {Evolutionary dynamics in laboratory microbial evolution experiments can be surprisingly complex. In the past two decades, observations of these dynamics have challenged simple models of adaptation and have shown that clonal interference, hitchhiking, ecological diversification, and contingency are widespread. In recent years, advances in high-throughput strain maintenance and phenotypic assays, the dramatically reduced cost of genome sequencing, and emerging methods for lineage barcoding have made it possible to observe evolutionary dynamics at unprecedented resolution. These new methods can now begin to provide detailed measurements of key aspects of fitness landscapes and of evolutionary outcomes across a range of systems. These measurements can highlight challenges to existing theoretical models and guide new theoretical work towards the complications that are most widely important.},
}
@article {pmid30022040,
year = {2018},
author = {Vyskočilová, S and Tay, WT and van Brunschot, S and Seal, S and Colvin, J},
title = {An integrative approach to discovering cryptic species within the Bemisia tabaci whitefly species complex.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {10886},
pmid = {30022040},
issn = {2045-2322},
support = {R-8681-1//Commonwealth Scientific and Industrial Research Organisation (CSIRO)/International ; OPP1058938//Bill and Melinda Gates Foundation/International ; OPP1058938//Bill and Melinda Gates Foundation/International ; OPP1058938//Bill and Melinda Gates Foundation/International ; UQ1305//Cotton Research and Development Corporation (CRDC)/International ; },
mesh = {Animals ; Crosses, Genetic ; Cucurbita/metabolism ; Female ; *Genome, Mitochondrial ; Hemiptera/*classification/*genetics ; High-Throughput Nucleotide Sequencing ; Insect Proteins/*genetics ; Male ; Mitochondrial Proteins/*genetics ; Phylogeny ; *Polymorphism, Genetic ; Pseudogenes ; },
abstract = {Bemisia tabaci is a cryptic whitefly-species complex that includes some of the most damaging pests and plant-virus vectors of a diverse range of food and fibre crops worldwide. We combine experimental evidence of: (i) differences in reproductive compatibility, (ii) hybrid verification using a specific nuclear DNA marker and hybrid fertility confirmation and (iii) high-throughput sequencing-derived mitogenomes, to show that the "Mediterranean" (MED) B. tabaci comprises at least two distinct biological species; the globally invasive MED from the Mediterranean Basin and the "African silver-leafing" (ASL) from sub-Saharan Africa, which has no associated invasion records. We demonstrate that, contrary to its common name, the "ASL" does not induce squash silver-leafing symptoms and show that species delimitation based on the widely applied 3.5% partial mtCOI gene sequence divergence threshold produces discordant results, depending on the mtCOI region selected. Of the 292 published mtCOI sequences from MED/ASL groups, 158 (54%) are low quality and/or potential pseudogenes. We demonstrate fundamental deficiencies in delimiting cryptic B. tabaci species, based solely on partial sequences of a mitochondrial barcoding gene. We advocate an integrative approach to reveal the true species richness within cryptic species complexes, which is integral to the deployment of effective pest and disease management strategies.},
}
@article {pmid30021015,
year = {2018},
author = {Jiao, J and Huang, W and Bai, Z and Liu, F and Ma, C and Liang, Z},
title = {DNA barcoding for the efficient and accurate identification of medicinal polygonati rhizoma in China.},
journal = {PloS one},
volume = {13},
number = {7},
pages = {e0201015},
pmid = {30021015},
issn = {1932-6203},
mesh = {China ; *DNA Barcoding, Taxonomic ; Phylogeny ; Polygonatum/*classification/*genetics ; Rhizome/*genetics ; },
abstract = {Polygonati rhizoma (PR), a traditional medicinal and edible product with various bioactive components (Polygonatum polysaccharides, saponins, phenols, and flavonoids), is widely consumed in China. However, other species with morphological characteristics similar to those of the actual components are being used to replace or adulterate PR, causing issues with quality control and product safety. The morphological similarity of PR and its substitutes makes classic morphological identification challenging. To address this issue, DNA barcoding-based identification using ITS2 and psbA-trnH sequences was applied in this study to evaluate the efficiency and accuracy of this approach in identifying PR samples collected from 39 different regions in China. The identification of PR by this method was confirmed by other methods (phylogeny-based and character-based methods), and all the samples were clearly and accurately distinguished. This study highlights the efficient and accurate nature of DNA barcoding in PR identification. Applying this technique will provide a means to differentiate PR from other altered formulations, thus improving product quality and safety for consumers of PR and its products.},
}
@article {pmid30020927,
year = {2018},
author = {Marizzi, C and Florio, A and Lee, M and Khalfan, M and Ghiban, C and Nash, B and Dorey, J and McKenzie, S and Mazza, C and Cellini, F and Baria, C and Bepat, R and Cosentino, L and Dvorak, A and Gacevic, A and Guzman-Moumtzis, C and Heller, F and Holt, NA and Horenstein, J and Joralemon, V and Kaur, M and Kaur, T and Khan, A and Kuppan, J and Laverty, S and Lock, C and Pena, M and Petrychyn, I and Puthenkalam, I and Ram, D and Ramos, A and Scoca, N and Sin, R and Gonzalez, I and Thakur, A and Usmanov, H and Han, K and Wu, A and Zhu, T and Micklos, DA},
title = {DNA barcoding Brooklyn (New York): A first assessment of biodiversity in Marine Park by citizen scientists.},
journal = {PloS one},
volume = {13},
number = {7},
pages = {e0199015},
pmid = {30020927},
issn = {1932-6203},
mesh = {Academies and Institutes ; *Biodiversity ; DNA/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; Databases, Nucleic Acid ; Diagnostic Tests, Routine ; Leukocytes ; New York City ; Plants/classification/*genetics ; Students ; },
abstract = {DNA barcoding is both an important research and science education tool. The technique allows for quick and accurate species identification using only minimal amounts of tissue samples taken from any organism at any developmental phase. DNA barcoding has many practical applications including furthering the study of taxonomy and monitoring biodiversity. In addition to these uses, DNA barcoding is a powerful tool to empower, engage, and educate students in the scientific method while conducting productive and creative research. The study presented here provides the first assessment of Marine Park (Brooklyn, New York, USA) biodiversity using DNA barcoding. New York City citizen scientists (high school students and their teachers) were trained to identify species using DNA barcoding during a two-week long institute. By performing NCBI GenBank BLAST searches, students taxonomically identified 187 samples (1 fungus, 70 animals and 116 plants) and also published 12 novel DNA barcodes on GenBank. Students also identified 7 ant species and demonstrated the potential of DNA barcoding for identification of this especially diverse group when coupled with traditional taxonomy using morphology. Here we outline how DNA barcoding allows citizen scientists to make preliminary taxonomic identifications and contribute to modern biodiversity research.},
}
@article {pmid30020505,
year = {2018},
author = {Mashaly, AM and Al-Ajmi, RA and Al-Johani, HA},
title = {Molecular Identification of the Carrion Beetles (Coleoptera) in Selected Regions of Saudi Arabia.},
journal = {Journal of medical entomology},
volume = {55},
number = {6},
pages = {1423-1430},
doi = {10.1093/jme/tjy116},
pmid = {30020505},
issn = {1938-2928},
mesh = {Animals ; *Coleoptera ; Environment ; Forensic Sciences ; Saudi Arabia ; Sheep ; },
abstract = {Geographical regions have a major effect on the arrival times of different insect species on carrion. This means that data generated in one region should not be used to determine time of death in a different region. In the present study, we demonstrate the effect of geographical location on the diversity of carrion beetles in Saudi Arabia, whereas the mitochondrial cytochrome c oxidase subunit I (mtCOI) barcodes were used as a marker for molecular identification of the carrion beetles at a dry stage on sheep carrion. We analyzed 819 adult beetles belonging to nine species originating from Riyadh (609 beetles), Jazan (157 beetles), and Arar (53 beetles). In Riyadh, results showed the presence of six species belonging to three different families. On the other hand, in Jazan five species belonging to four families were collected. From Arar, five species belonging to three families were collected. By comparing between individuals of the same species from different regions, individuals of Necrobia rufipes DeGeer (Coleoptera: Cleridae) showed the highest intraspecific variations 0-20%, while individuals of Saprinus splendens Paykull and Saprinus semistriatus Scriba (Coleoptera: Histeridae) showed the lowest intraspecific variations 0-1%. Interspecific variability was also measured between collected and identified species, with differences revealed to be in the range of 3.8-29.8%. The results are important from an ecological point of view and for Medico-Legal Forensic Entomology.},
}
@article {pmid30018879,
year = {2018},
author = {Lücking, R and Kirk, PM and Hawksworth, DL},
title = {Sequence-based nomenclature: a reply to Thines et al. and Zamora et al. and provisions for an amended proposal "from the floor" to allow DNA sequences as types of names.},
journal = {IMA fungus},
volume = {9},
number = {1},
pages = {185-198},
pmid = {30018879},
issn = {2210-6340},
abstract = {We reply to two recently published, multi-authored opinion papers by opponents of sequence-based nomenclature, namely Zamora et al. (IMA Fungus9: 167-175,2018) and Thines et al. (IMA Fungus9: 177-183, 2018). While we agree with some of the principal arguments brought forward by these authors, we address misconceptions and demonstrate that some of the presumed evidence presented in these papers has been wrongly interpreted. We disagree that allowing sequences as types would fundamentally alter the nature of types, since a similar nature of abstracted features as type is already allowed in the Code (Art. 40.5), namely an illustration. We also disagree that there is a high risk of introducing artifactual taxa, as this risk can be quantified at well below 5 %, considering the various types of high-throughput sequencing errors. Contrary to apparently widespread misconceptions, sequence-based nomenclature cannot be based on similarity-derived OTUs and their consensus sequences, but must be derived from rigorous, multiple alignment-based phylogenetic methods and quantitative, single-marker species recognition algorithms, using original sequence reads; it is therefore identical in its approach to single-marker studies based on physical types, an approach allowed by the Code. We recognize the limitations of the ITS as a single fungal barcoding marker, but point out that these result in a conservative approach, with "false negatives" surpassing "false positives"; a desirable feature of sequence-based nomenclature. Sequence-based nomenclature does not aim at accurately resolving species, but at naming sequences that represent unknown fungal lineages so that these can serve as a means of communication, so ending the untenable situation of an exponentially growing number of unlabeled fungal sequences that fill online repositories. The risks are outweighed by the gains obtained by a reference library of named sequences spanning the full array of fungal diversity. Finally, we elaborate provisions in addition to our original proposal to amend the Code that would take care of the issues brought forward by opponents to this approach. In particular, taking up the idea of the Candidatus status of invalid, provisional names in prokaryote nomenclature, we propose a compromise that would allow valid publication of voucherless, sequence-based names in a consistent manner, but with the obligate designation as "nom. seq." (nomen sequentiae). Such names would not have priority over specimen- or culture-based names unless either epitypified with a physical type or adopted for protection on the recommendation of a committee of the International Commission on the Taxonomy of Fungi following evaluation based on strict quality control of the underlying studies based on established rules or recommendations.},
}
@article {pmid30018876,
year = {2018},
author = {Lücking, R and Hawksworth, DL},
title = {Formal description of sequence-based voucherless Fungi: promises and pitfalls, and how to resolve them.},
journal = {IMA fungus},
volume = {9},
number = {1},
pages = {143-166},
pmid = {30018876},
issn = {2210-6340},
abstract = {There is urgent need for a formal nomenclature of sequence-based, voucherless Fungi, given that environmental sequencing has accumulated more than one billion fungal ITS reads in the Sequence Read Archive, about 1,000 times as many as fungal ITS sequences in GenBank. These unnamed Fungi could help to bridge the gap between 115,000 to 140,000 currently accepted and 2.2 to 3.8 million predicted species, a gap that cannot realistically be filled using specimen or culture-based inventories. The Code never aimed at placing restrictions on the nature of characters chosen for taxonomy, and the requirement for physical types is now becoming a constraint on the advancement of science. We elaborate on the promises and pitfalls of sequence-based nomenclature and provide potential solutions to major concerns of the mycological community. Types of sequence-based taxa, which by default lack a physical specimen or culture, could be designated in four alternative ways: (1) the underlying sample ('bag' type), (2) the DNA extract, (3) fluorescent in situ hybridization (FISH), or (4) the type sequence itself. Only (4) would require changes to the Code and the latter would be the most straightforward approach, complying with three of the five principal functions of types better than physical specimens. A fifth way, representation of the sequence in an illustration, has been ruled as unacceptable in the Code. Potential flaws in sequence data are analogous to flaws in physical types, and artifacts are manageable if a stringent analytical approach is applied. Conceptual errors such as homoplasy, intragenomic variation, gene duplication, hybridization, and horizontal gene transfer, apply to all molecular approaches and cannot be used as a specific argument against sequence-based nomenclature. The potential impact of these phenomena is manageable, as phylogenetic species delimitation has worked satisfactorily in Fungi. The most serious shortcoming of sequence-based nomenclature is the likelihood of parallel classifications, either by describing taxa that already have names based on physical types, or by using different markers to delimit species within the same lineage. The probability of inadvertently establishing sequence-based species that have names available is between 20.4 % and 1.5 % depending on the number of globally predicted fungal species. This compares favourably to a historical error rate of about 30 % based on physical types, and this rate could be reduced to practically zero by adding specific provisions to this approach in the Code. To avoid parallel classifications based on different markers, sequence-based nomenclature should be limited to a single marker, preferably the fungal ITS barcoding marker; this is possible since sequence-based nomenclature does not aim at accurate species delimitation but at naming lineages to generate a reference database, independent of whether these lineages represent species, closely related species complexes, or infraspecies. We argue that clustering methods are inappropriate for sequence-based nomenclature; this approach must instead use phylogenetic methods based on multiple alignments, combined with quantitative species recognition methods. We outline strategies to obtain higher-level phylogenies for ITS-based, voucherless species, including phylogenetic binning, 'hijacking' species delimitation methods, and temporal banding. We conclude that voucherless, sequence-based nomenclature is not a threat to specimen and culture-based fungal taxonomy, but a complementary approach capable of substantially closing the gap between known and predicted fungal diversity, an approach that requires careful work and high skill levels.},
}
@article {pmid30018874,
year = {2018},
author = {Colabella, C and Corte, L and Roscini, L and Bassetti, M and Tascini, C and Mellor, JC and Meyer, W and Robert, V and Vu, D and Cardinali, G},
title = {NGS barcode sequencing in taxonomy and diagnostics, an application in "Candida" pathogenic yeasts with a metagenomic perspective.},
journal = {IMA fungus},
volume = {9},
number = {1},
pages = {91-105},
pmid = {30018874},
issn = {2210-6340},
abstract = {Species identification of yeasts and other Fungi is currently carried out with Sanger sequences of selected molecular markers, mainly from the ribosomal DNA operon, characterized by hundreds of tandem repeats of the 18S, ITS1, 5.8S, ITS2 and LSU loci. The ITS region has been recently proposed as a primary barcode marker making this region the most used one in taxonomy, phylogeny and diagnostics. The introduction of NGS is providing tools of high efficacy and relatively low cost to amplify two or more markers simultaneously with great sequencing depth. However, the presence of intra-genomic variability between the repeats requires specific analytical procedures and pipelines. In this study, 286 strains belonging to 11 pathogenic yeasts species were analysed with NGS of the region spanning from ITS1 to the D1/D2 domain of the LSU encoding ribosomal DNA. Results showed that relatively high heterogeneity can hamper the use of these sequences for the identification of single strains and even more of complex microbial mixtures. These observations point out that the metagenomics studies could be affected by species inflection at levels higher than currently expected.},
}
@article {pmid30018858,
year = {2018},
author = {Velez, P and Ojeda, M and Espinosa-Asuar, L and Pérez, TM and Eguiarte, LE and Souza, V},
title = {Experimental and molecular approximation to microbial niche: trophic interactions between oribatid mites and microfungi in an oligotrophic freshwater system.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5200},
pmid = {30018858},
issn = {2167-8359},
abstract = {Mite-fungal interactions play a key role in structuring core ecosystem processes such as nutrient dynamics. Despite their ecological relevance, these cross-kingdom interactions remain poorly understood particularly in extreme environments. Herein, we investigated feeding preferences of a novel genetic lineage of aquatic oribatids obtained from an oligotrophic freshwater system in the Cuatro Ciénegas Basin (CCB) within the Chihuahuan Desert, Mexico. During in vitro diet preference bioassays, transient aquatic microfungi (Aspergillus niger, Talaromyces sp., and Pleosporales sp.) recovered from the same mesocosm samples were offered individually and simultaneously to mites. Gut content was analyzed using classic plating and culture-independent direct PCR (focusing on the fungal barcoding region) methods. Our results indicated that oribatids fed on all tested fungal isolates, yet the profusely developing A. niger was preferentially consumed with all fungal components being digested. This feeding habit is particularly interesting since A. niger has been reported as an unsuitable dietary element for population growth, being consistently avoided by mites in previous laboratory experiments. It is possible that our mites from the CCB have adapted to exploit available resources within this oligotrophic site. This work confirms the trophic relationship between microfungi and mites, two rarely investigated major components of the microbial community, shedding light on the niche dynamics under low-nutrient conditions.},
}
@article {pmid30018552,
year = {2018},
author = {Xiong, C and Sun, W and Li, J and Yao, H and Shi, Y and Wang, P and Huang, B and Shi, L and Liu, D and Hu, Z and Chen, S},
title = {Identifying the Species of Seeds in Traditional Chinese Medicine Using DNA Barcoding.},
journal = {Frontiers in pharmacology},
volume = {9},
number = {},
pages = {701},
pmid = {30018552},
issn = {1663-9812},
abstract = {Seed is not only the main reproductive organ of most of herbal plants but also an important part of Traditional Chinese Medicine (TCM). Seed TCMs possess important medicinal properties and have been widely used as components of pharmaceutical products. In parallel with the increasing popularity and accessibility of seeds as medicinal products in recent years, numerous substitutes and adulterants have also appeared on the market. Due to the small volume and similar appearances of many seed TCMs, they are very difficult to accurately identify the constituent plant species through organoleptic methods. Usage of the wrong herb may be ineffective or may worsen the condition and even cause death. Correct identification of seed herbal medicines is therefore essential for their safe use. Here, we acquired 177 ITS2 sequences and 15 psbA-trnH sequences from 51 kinds of seed TCMs belonging to 64 species that have been described in the Chinese Pharmacopoeia. Tree-building analysis showed that the ITS2 sequences of 48 seed TCMs can be differentiated from each other, and they formed distinct, non-overlapping groups in the maximum-likelihood tree. Furthermore, all of the sequences acquired in this study have been submitted to the public DNA barcoding system for herbal medicine, and this integrated database was used to identify 400 seed TCM samples purchased from medicinal markets, drug stores, and the Internet, enabling the identification of 7.5% of the samples as containing non-declared species. This study provides a brief operating procedure for the identification of seed TCMs found in herbal medicine. In the future, researchers and traditional herbal medicine enterprises can use this system to test their herbal materials.},
}
@article {pmid30018357,
year = {2018},
author = {Nurul Farhana, S and Muchlisin, ZA and Duong, TY and Tanyaros, S and Page, LM and Zhao, Y and Adamson, EAS and Khaironizam, MZ and de Bruyn, M and Siti Azizah, MN},
title = {Exploring hidden diversity in Southeast Asia's Dermogenys spp. (Beloniformes: Zenarchopteridae) through DNA barcoding.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {10787},
pmid = {30018357},
issn = {2045-2322},
support = {1002/PBIOLOGI/910403//Universiti Sains Malaysia (USM)/International ; },
mesh = {Animals ; Beloniformes/*genetics ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry ; Genetic Variation ; Indonesia ; Malaysia ; Phylogeny ; Sequence Analysis, DNA ; Thailand ; Vietnam ; },
abstract = {Members of the freshwater halfbeak genus Dermogenys are hard to identify to the species level, despite several previous attempts to isolate fixed meristic, morphometric and colour pattern differences. This has led to ongoing confusion in scientific literature, records of species occurrence, and entries in museum collections. Here, a DNA barcoding study was conducted on the genus to gain further understanding of its taxonomic status across the Southeast Asian region. Fish were collected from 33 localities, spanning freshwater and brackish habitats in Malaysia, Western Indonesia, Thailand and Vietnam. In total, 290 samples of Dermogenys spp. were amplified for a 651 base pair fragment of the mitochondrial cytochrome oxidase c subunit I (COI) gene. Analysis was able to successfully differentiate the three species: D. collettei, D. siamensis, D. sumatrana; reveal the presence of a new putative species, Dermogenys sp., that was sampled in sympatry with D. collettei at three locations; as well as uncovering two genetic lineages of a fifth species, D. bispina, that display non-overlapping geographical distributions in drainages of northern Borneo; Kudat and Sandakan. This study expands the barcode library for Zenarchopteridae, demonstrates the efficacy of DNA barcoding techniques for differentiating Dermogenys species, and the potential thereof in species discovery.},
}
@article {pmid30018331,
year = {2018},
author = {Hartmann, FJ and Simonds, EF and Bendall, SC},
title = {A Universal Live Cell Barcoding-Platform for Multiplexed Human Single Cell Analysis.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {10770},
pmid = {30018331},
issn = {2045-2322},
support = {U19 AI104209/AI/NIAID NIH HHS/United States ; U24 CA224331/CA/NCI NIH HHS/United States ; K99 GM104148/GM/NIGMS NIH HHS/United States ; U19 AI116484/AI/NIAID NIH HHS/United States ; U24 CA224309/CA/NCI NIH HHS/United States ; R01 AG056287/AG/NIA NIH HHS/United States ; R01 AG057915/AG/NIA NIH HHS/United States ; R00 GM104148/GM/NIGMS NIH HHS/United States ; DP2 EB024246/EB/NIBIB NIH HHS/United States ; },
mesh = {Cell Line ; Cells, Cultured ; Cisplatin ; Histocompatibility Antigens Class I/genetics ; Humans ; Jurkat Cells ; Single-Cell Analysis/*methods ; },
abstract = {Single-cell barcoding enables the combined processing and acquisition of multiple individual samples as one. This maximizes assay efficiency and eliminates technical variability in both sample preparation and analysis. Remaining challenges are the barcoding of live, unprocessed cells to increase downstream assay performance combined with the flexibility of the approach towards a broad range of cell types. To that end, we developed a novel antibody-based platform that allows the robust barcoding of live human cells for mass cytometry (CyTOF). By targeting both the MHC class I complex (beta-2-microglobulin) and a broadly expressed sodium-potassium ATPase-subunit (CD298) with platinum-conjugated antibodies, human immune cells, stem cells as well as tumor cells could be multiplexed in the same single-cell assay. In addition, we present a novel palladium-based covalent viability reagent compatible with this barcoding strategy. Altogether, this platform enables mass cytometry-based, live-cell barcoding across a multitude of human sample types and provides a scheme for multiplexed barcoding of human single-cell assays in general.},
}
@article {pmid30018232,
year = {2018},
author = {Park, I and Yang, S and Kim, WJ and Noh, P and Lee, HO and Moon, BC},
title = {Authentication of Herbal Medicines Dipsacus asper and Phlomoides umbrosa Using DNA Barcodes, Chloroplast Genome, and Sequence Characterized Amplified Region (SCAR) Marker.},
journal = {Molecules (Basel, Switzerland)},
volume = {23},
number = {7},
pages = {},
pmid = {30018232},
issn = {1420-3049},
mesh = {*DNA Barcoding, Taxonomic ; Dipsacaceae/*genetics ; *Drugs, Chinese Herbal ; Genetic Markers ; *Genome, Chloroplast ; Lamiaceae/*genetics ; },
abstract = {Dried roots of Dipsacus asper (Caprifoliaceae) are used as important traditional herbal medicines in Korea. However, the roots are often used as a mixture or contaminated with Dipsacus japonicus in Korean herbal markets. Furthermore, the dried roots of Phlomoides umbrosa (Lamiaceae) are used indiscriminately with those of D. asper, with the confusing Korean names of Sok-Dan and Han-Sok-Dan for D. asper and P. umbrosa, respectively. Although D. asper and P. umbrosa are important herbal medicines, the molecular marker and genomic information available for these species are limited. In this study, we analysed DNA barcodes to distinguish among D. asper, D. japonicus, and P. umbrosa and sequenced the chloroplast (CP) genomes of D. asper and D. japonicus. The CP genomes of D. asper and D. japonicus were 160,530 and 160,371 bp in length, respectively, and were highly divergent from those of the other Caprifoliaceae species. Phylogenetic analysis revealed a monophyletic group within Caprifoliaceae. We also developed a novel sequence characterised amplified region (SCAR) markers to distinguish among D. asper, D. japonicus, and P. umbrosa. Our results provide important taxonomic, phylogenetic, and evolutionary information on the Dipsacus species. The SCAR markers developed here will be useful for the authentication of herbal medicines.},
}
@article {pmid30017001,
year = {2019},
author = {Petrović, A and Mitrović, M and Ghaliow, ME and Ivanović, A and Kavallieratos, NG and Starý, P and Tomanović, &#x17d;},
title = {Resolving the taxonomic status of biocontrol agents belonging to the Aphidius eadyi species group (Hymenoptera: Braconidae: Aphidiinae): an integrative approach.},
journal = {Bulletin of entomological research},
volume = {109},
number = {3},
pages = {342-355},
doi = {10.1017/S000748531800055X},
pmid = {30017001},
issn = {1475-2670},
mesh = {Animals ; Aphids/parasitology ; Biological Control Agents/*classification ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; Female ; Male ; Species Specificity ; Wasps/anatomy &amp; histology/*classification/genetics ; Wings, Animal/anatomy &amp; histology ; },
abstract = {Species that belong to the Aphidius eadyi group have been used as biocontrol agents against Acyrthosiphon pisum worldwide. However, despite their extensive use, there are still gaps in our knowledge about their taxonomy and distribution. In this study, we employed an integrative taxonomic approach by combining genetic analyses (mtDNA COI barcoding) with standard morphological analyses and geometric morphometrics of forewing shape. We identified three species within the A. eadyi species group, viz., A. smithi, A. eadyi and A. banksae. Genetic separation of all three species was confirmed, with mean genetic distances between species ranging from 5 to 7.4%. The following morphological characters were determined as the most important for separating species of the A. eadyi group: number and shape of costulae on the anterolateral part of the petiole, shape of the central areola on the propodeum, and shape and venation of the forewings. The differences in wing shape of all three species were statistically significant, but with some overlapping. We identified A. banksae as a widely distributed pea aphid parasitoid, whose known range covers most of the western Palaearctic (from the UK to Israel). Aphidius banksae is diagnosed and redescribed.},
}
@article {pmid30016980,
year = {2018},
author = {Shin, T and Fujikawa, K and Moe, AZ and Uchiyama, H},
title = {Traditional knowledge of wild edible plants with special emphasis on medicinal uses in Southern Shan State, Myanmar.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {14},
number = {1},
pages = {48},
pmid = {30016980},
issn = {1746-4269},
mesh = {Adult ; Biodiversity ; Conservation of Natural Resources ; Ethnobotany ; Humans ; *Knowledge ; Middle Aged ; Myanmar ; *Phytotherapy ; *Plants, Edible ; *Plants, Medicinal ; },
abstract = {BACKGROUND: Myanmar is one of the hotspots of biodiversity and is a rapidly developing country. Performing floristic research in Myanmar is an urgent issue, and ethnobotanical studies of wild edible plants (WEPs) will provide new information on natural plant resources.<br><br>METHOD: Ethnobotanical data were collected in three villages with different historical backgrounds in Southern Shan State, Myanmar. A total of 19 key informants were interviewed, and specimens were collected in the fields with the participation of key informants in June-July 2015. Group discussions were organized during 2016 and 2017 to reinforce the information on use of WEPs. DNA barcoding was used to facilitate species identification.<br><br>RESULTS: A total of 83 species from 44 families of angiosperms were recorded as WEPs. Most of the species were used as wild vegetables (47 species), followed by fruits and nuts (31 species). Eighteen WEPs were consumed as medicinal foods. Differences in use of WEPs between the communities of the villages were observed. The age class of 30-39&#xa0;years was more familiar with the environments where they could collect WEPs and had more knowledge of WEPs than did the older groups. The use of Elaeocarpus floribundus as an edible oil is a very interesting tradition.<br><br>CONCLUSION: WEPs play an important role in the livelihood of local communities. The indigenous society has maintained traditional knowledge of the WEPs. Historical background, land use system and surrounding vegetation could have effects on the variation in the traditional uses of WEPs. Increasing awareness of the importance of WEPs will encourage the conservation of traditional knowledge of indigenous populations.},
}
@article {pmid30016131,
year = {2018},
author = {Neil, W and Zipp, G and Nemeth, G and Russo, MF and Nirschl, DS},
title = {End-to-End Sample Tracking in the Laboratory Using a Custom Internet of Things Device.},
journal = {SLAS technology},
volume = {23},
number = {5},
pages = {412-422},
doi = {10.1177/2472630318783979},
pmid = {30016131},
issn = {2472-6311},
mesh = {Automation, Laboratory/*instrumentation ; Chemistry Techniques, Analytical/*instrumentation ; High-Throughput Screening Assays/*instrumentation ; Internet/*instrumentation ; },
abstract = {We describe a custom Internet of Things (IoT) device used for tracking barcoded containers end to end in a high-throughput analysis and purification laboratory. Our IoT device fills an important gap that previously prevented us from fully tracking barcoded sample containers through manual steps in a multistep workflow, such as when samples are "parked" for temporary storage, or when using instrumentation not otherwise equipped with barcode scanners, a common occurrence found with specific centrifugal evaporation instruments. The custom device reads container barcodes and sends a small amount of data to our back-end data systems. Once data have been received and processed, users are alerted to any system responses via aural and visual feedback. Components of the IoT system include a low-cost headless IoT computer, a barcode reader, and a multicolor LED strip. We believe that the model for our device will facilitate simple and rapid deployment of IoT to the broader laboratory community. All source code and device configurations will be released into the public domain and made freely available.},
}
@article {pmid30016076,
year = {2018},
author = {Paunovska, K and Gil, CJ and Lokugamage, MP and Sago, CD and Sato, M and Lando, GN and Gamboa Castro, M and Bryksin, AV and Dahlman, JE},
title = {Analyzing 2000 in Vivo Drug Delivery Data Points Reveals Cholesterol Structure Impacts Nanoparticle Delivery.},
journal = {ACS nano},
volume = {12},
number = {8},
pages = {8341-8349},
pmid = {30016076},
issn = {1936-086X},
support = {T32 EB006343/EB/NIBIB NIH HHS/United States ; T32 EB021962/EB/NIBIB NIH HHS/United States ; T32 GM008433/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Cholesterol/*chemistry/metabolism ; Drug Carriers/chemistry/metabolism ; *Drug Delivery Systems ; Endothelial Cells/chemistry/metabolism ; Female ; Liver/chemistry/metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Nanoparticles/*chemistry/metabolism ; RNA, Small Interfering/*chemistry/metabolism ; RNA, Guide, CRISPR-Cas Systems ; },
abstract = {Lipid nanoparticles (LNPs) are formulated using unmodified cholesterol. However, cholesterol is naturally esterified and oxidized in vivo, and these cholesterol variants are differentially trafficked in vivo via lipoproteins including LDL and VLDL. We hypothesized that incorporating the same cholesterol variants into LNPs-which can be structurally similar to LDL and VLDL-would alter nanoparticle targeting in vivo. To test this hypothesis, we quantified how >100 LNPs made with six cholesterol variants delivered DNA barcodes to 18 cell types in wild-type, LDLR[-/-], and VLDLR[-/-] mice that were both age-matched and female. By analyzing ∼2000 in vivo drug delivery data points, we found that LNPs formulated with esterified cholesterol delivered nucleic acids more efficiently than LNPs formulated with regular or oxidized cholesterol when compared across all tested cell types in the mouse. We also identified an LNP containing cholesteryl oleate that efficiently delivered siRNA and sgRNA to liver endothelial cells in vivo. Delivery was as-or more-efficient as the same LNP made with unmodified cholesterol. Moreover, delivery to liver endothelial cells was 3 times more efficient than delivery to hepatocytes, distinguishing this oleate LNP from hepatocyte-targeting LNPs. RNA delivery can be improved by rationally selecting cholesterol variants, allowing optimization of nanoparticle targeting.},
}
@article {pmid30011183,
year = {2018},
author = {Lee, SH and Ahn, G and Kim, MS and Jeong, OC and Lee, JH and Kwon, HG and Kim, YH and Ahn, JY},
title = {Poly-adenine-Coupled LAMP Barcoding to Detect Apple Scar Skin Viroid.},
journal = {ACS combinatorial science},
volume = {20},
number = {8},
pages = {472-481},
doi = {10.1021/acscombsci.8b00022},
pmid = {30011183},
issn = {2156-8944},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Viral/*analysis ; Gold/chemistry ; Limit of Detection ; Malus/*virology ; Metal Nanoparticles/chemistry ; Nucleic Acid Amplification Techniques/methods ; Plant Diseases/*virology ; Plant Leaves/virology ; Plant Viruses/*isolation &amp; purification ; Poly A/*chemistry ; Sensitivity and Specificity ; Time Factors ; },
abstract = {Apple Scar Skin Viroid (ASSVd), a nonprotein coding, circular RNA pathogen is relatively difficult to detect by immunoassay. We report here a one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to improve selectivity for diagnostic use in detecting ASSVd in plants. ASSVd RT-LAMP was accelerated using loop primers and was found to be highly sensitive with a detection limit of 10[4] copies of cDNA-ASSVd within 30 min. Real-time LAMP and melting curve analysis could differentiate between the true-positive LAMP amplicons and false-positive nonspecific primer amplification products. The optimized RT-LAMP was then followed by the addition of nonthiolated AuNP:poly-adenine (A10)-ASSVd LAMP barcodes, showing a high authentication capacity with colorimetric changes. This type of barcoding assay is a potential alternative for rapid and multiple viroid diagnosis, providing for visible sensing in the field that can be applied to viroid-free planting.},
}
@article {pmid30009719,
year = {2019},
author = {Ellis, VA and Sari, EHR and Rubenstein, DR and Dickerson, RC and Bensch, S and Ricklefs, RE},
title = {The global biogeography of avian haemosporidian parasites is characterized by local diversification and intercontinental dispersal.},
journal = {Parasitology},
volume = {146},
number = {2},
pages = {213-219},
doi = {10.1017/S0031182018001130},
pmid = {30009719},
issn = {1469-8161},
mesh = {Analysis of Variance ; Animal Migration ; Animals ; Bird Diseases/*epidemiology/parasitology/transmission ; Birds ; Communicable Diseases, Emerging/*epidemiology/parasitology/transmission/veterinary ; DNA Barcoding, Taxonomic/veterinary ; Diptera/classification/parasitology ; Genetic Variation ; *Global Health ; Haemosporida/classification/*physiology ; Insect Vectors/classification/parasitology ; Likelihood Functions ; Phylogeny ; Phylogeography ; Protozoan Infections, Animal/*epidemiology/parasitology/transmission ; },
abstract = {The biogeographic histories of parasites and pathogens are infrequently compared with those of free-living species, including their hosts. Documenting the frequency with which parasites and pathogens disperse across geographic regions contributes to understanding not only their evolution, but also the likelihood that they may become emerging infectious diseases. Haemosporidian parasites of birds (parasite genera Plasmodium, Haemoproteus and Leucocytozoon) are globally distributed, dipteran-vectored parasites. To date, over 2000 avian haemosporidian lineages have been designated by molecular barcoding methods. To achieve their current distributions, some lineages must have dispersed long distances, often over water. Here we quantify such events using the global avian haemosporidian database MalAvi and additional records primarily from the Americas. We scored lineages as belonging to one or more global biogeographic regions based on infection records. Most lineages were restricted to a single region but some were globally distributed. We also used part of the cytochrome b gene to create genus-level parasite phylogenies and scored well-supported nodes as having descendant lineages in regional sympatry or allopatry. Descendant sister lineages of Plasmodium, Haemoproteus and Leucocytozoon were distributed in allopatry in 11, 16 and 15% of investigated nodes, respectively. Although a small but significant fraction of the molecular variance in cytochrome b of all three genera could be explained by biogeographic region, global parasite dispersal likely contributed to the majority of the unexplained variance. Our results suggest that avian haemosporidian parasites have faced few geographic barriers to dispersal over their evolutionary history.},
}
@article {pmid30008702,
year = {2018},
author = {Coleine, C and Stajich, JE and Zucconi, L and Onofri, S and Pombubpa, N and Egidi, E and Franks, A and Buzzini, P and Selbmann, L},
title = {Antarctic Cryptoendolithic Fungal Communities Are Highly Adapted and Dominated by Lecanoromycetes and Dothideomycetes.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {1392},
pmid = {30008702},
issn = {1664-302X},
support = {S10 OD016290/OD/NIH HHS/United States ; },
abstract = {Endolithic growth is one of the most spectacular microbial adaptations to extreme environmental constraints and the predominant life-form in the ice-free areas of Continental Antarctica. Although Antarctic endolithic microbial communities are known to host among the most resistant and extreme-adapted organisms, our knowledge on microbial diversity and composition in this peculiar niche is still limited. In this study, we investigated the diversity and structure of the fungal assemblage in the cryptoendolithic communities inhabiting sandstone using a meta-barcoding approach targeting the fungal Internal Transcribed Sequence region 1 (ITS1). Samples were collected from 14 sites in the Victoria Land, along an altitudinal gradient ranging from 1,000 to 3,300 m a.s.l. and from 29 to 96 km distance to coast. Our study revealed a clear dominance of a 'core' group of fungal taxa consistently present across all the samples, mainly composed of lichen-forming and Dothideomycetous fungi. Pareto-Lorenz curves indicated a very high degree of specialization (F0 approximately 95%), suggesting these communities are highly adapted but have limited ability to recover after perturbations. Overall, both fungal community biodiversity and composition did not show any correlation with the considered abiotic parameters, potentially due to strong fluctuations of environmental conditions at local scales.},
}
@article {pmid30007430,
year = {2018},
author = {McTaggart, AR and Aime, MC},
title = {The species of Coleosporium (Pucciniales) on Solidago in North America.},
journal = {Fungal biology},
volume = {122},
number = {8},
pages = {800-809},
doi = {10.1016/j.funbio.2018.04.007},
pmid = {30007430},
issn = {1878-6146},
mesh = {Basidiomycota/*classification/genetics/growth &amp; development/*isolation &amp; purification ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Microscopy ; North America ; Phylogeny ; Sequence Analysis, DNA ; Solidago/*microbiology ; },
abstract = {Species of Coleosporium (Pucciniales) are rust fungi that typically alternate between pines and angiosperms. In North America, species of Coleosporium often infect Solidago (goldenrods), although their taxonomy on these hosts is unresolved. Joseph. C. Arthur and George B. Cummins regarded these as a single species, Coleosporium solidaginis (fide Arthur) or C. asterum (fide Cummins), but later inoculation studies demonstrated the presence of more than one species, distinguishable by their aecial hosts. A more recent taxonomic study of Coleosporium found that specimens on Solidago identified as C. asterum in North America were not conspecific with the type, which is from Japan, prompting the present study. Herein, we conducted a systematic study on ca. 60 collections of Coleosporium infecting species of Asteraceae from North America using regions of ribosomal DNA and morphology of teliospores and basidia. Our data indicate at least three species of Coleosporium occur on Solidago in North America, C. solidaginis, C. montanum comb. nov., which is proposed for the taxon that has commonly been identified as C. asterum in North America, and C. delicatulum, all of which can be differentiated by morphology of their basidia. In addition, the challenges of marker selection for molecular barcoding of rust fungi is discussed.},
}
@article {pmid30006809,
year = {2018},
author = {Low, VL and Takaoka, H and Adler, PH and Tan, TK and Weng, FC and Chen, CY and Lim, YAL and Ya'cob, Z and Chen, CD and Sofian-Azirun, M and Wang, D},
title = {A novel molecular and chromosomal lineage of the anthropophilic Simulium (Simulium) rufibasis subgroup (Diptera: Simuliidae) in Taiwan.},
journal = {Parasitology research},
volume = {117},
number = {10},
pages = {3137-3143},
pmid = {30006809},
issn = {1432-1955},
support = {RP021C-16SUS//Universiti Malaya/ ; RU005-201//Universiti Malaya/ ; SC-1700527//NIFA/USDA/ ; },
mesh = {Animals ; Chromosomes, Insect/*genetics ; Electron Transport Complex IV/genetics/metabolism ; Female ; Insect Proteins/genetics/metabolism ; Larva/classification/genetics ; Male ; Phylogeny ; Simuliidae/classification/*genetics ; Taiwan ; Thailand ; Vietnam ; },
abstract = {The Simulium rufibasis subgroup is one of three subgroups of the Simulium (Simulium) tuberosum species-group; it is characterized by a pair of clustered stout hairs on the ventral surface of female abdominal segment 7. A member of the S. rufibasis subgroup in Taiwan was investigated morphologically and genetically using the universal cytochrome c oxidase subunit I (COI) barcoding gene and polytene chromosomal banding pattern. The Taiwanese material is morphologically similar to S. rosliramlii Takaoka &amp; Chen from Vietnam and represents the second species of the S. rufibasis subgroup known from Taiwan. It also represents a novel molecular lineage that is distinct from three other primary lineages identified as S. doipuiense, S. doipuiense/S. rufibasis, and S. weji previously reported from Thailand. The mitochondrial evidence for a distinct lineage in Taiwan is supported by chromosomal analysis, which revealed unique sex chromosomes. For nomenclatural stability, we associate the name S. arisanum Shiraki with the Taiwanese entity. Originally described from females from Taiwan, S. arisanum until now has remained an enigmatic species.},
}
@article {pmid30005073,
year = {2018},
author = {Korthout, T and Poramba-Liyanage, DW and van Kruijsbergen, I and Verzijlbergen, KF and van Gemert, FPA and van Welsem, T and van Leeuwen, F},
title = {Decoding the chromatin proteome of a single genomic locus by DNA sequencing.},
journal = {PLoS biology},
volume = {16},
number = {7},
pages = {e2005542},
pmid = {30005073},
issn = {1545-7885},
mesh = {Chromatin/*metabolism ; DNA Barcoding, Taxonomic ; *Genetic Loci ; *Genome, Fungal ; Hydroxyurea/pharmacology ; Promoter Regions, Genetic/genetics ; Protein Binding ; Proteome/*metabolism ; Saccharomyces cerevisiae/drug effects/*genetics ; *Sequence Analysis, DNA ; Terminator Regions, Genetic ; },
abstract = {Transcription, replication, and repair involve interactions of specific genomic loci with many different proteins. How these interactions are orchestrated at any given location and under changing cellular conditions is largely unknown because systematically measuring protein-DNA interactions at a specific locus in the genome is challenging. To address this problem, we developed Epi-Decoder, a Tag-chromatin immunoprecipitation-Barcode-Sequencing (TAG-ChIP-Barcode-Seq) technology in budding yeast. Epi-Decoder is orthogonal to proteomics approaches because it does not rely on mass spectrometry (MS) but instead takes advantage of DNA sequencing. Analysis of the proteome of a transcribed locus proximal to an origin of replication revealed more than 400 interacting proteins. Moreover, replication stress induced changes in local chromatin proteome composition prior to local origin firing, affecting replication proteins as well as transcription proteins. Finally, we show that native genomic loci can be decoded by efficient construction of barcode libraries assisted by clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9). Thus, Epi-Decoder is an effective strategy to identify and quantify in an unbiased and systematic manner the proteome of an individual genomic locus by DNA sequencing.},
}
@article {pmid30003088,
year = {2018},
author = {Fang, Y and Zhang, J and Wu, R and Xue, B and Qian, Q and Gao, B},
title = {Genetic Polymorphism Study on Aedes albopictus of Different Geographical Regions Based on DNA Barcoding.},
journal = {BioMed research international},
volume = {2018},
number = {},
pages = {1501430},
pmid = {30003088},
issn = {2314-6141},
mesh = {Aedes/*genetics ; Animals ; China ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV ; *Genetic Variation ; Mosquito Vectors ; *Polymorphism, Genetic ; Taiwan ; },
abstract = {Aedes albopictus is a very important vector for pathogens of many infectious diseases including dengue fever. In this study, we explored the genetic polymorphism of Aedes albopictus strains in different geographical regions using DNA barcoding of mitochondrial COI (MT-COI) gene. We collected MT-COI sequence of 106 Aedes albopictus mosquitos from 6 provinces in China including Fujian, Guangdong, Hainan, Yunnan, and Taiwan. The length of the sequences is 709bp with the content of A+T (67.7%) greater than that of G+C (32.3%). We identified mutations in 90 (13.68%) loci, of which 57 (63.33%) are transitions, 28 (31.11%) are transversions, and 5 (5.56%) are hypervariable loci. In addition, we obtained 42 haplotypes, 4 (9.52%) of which are shared among different populations. The haplotype diversity of Aedes albopictus is 0.882 and nucleotide diversity is 0.01017. Moreover, the pedigree network diagram shows that most haplotypes are under parallel evolution, suggesting a local expansion of Aedes albopictus in history. Finally, the Neighbor-Joining tree of MT-COI haplotypes reveals a certain correlation between haplotype clusters and geographical distribution, and there are differences among Aedes albopictus in different geographical regions. In conclusion, DNA barcoding of MT-COI gene is an effective method to study the genetic structure of Aedes albopictus.},
}
@article {pmid30002984,
year = {2018},
author = {Borstein, SR and O'Meara, BC},
title = {AnnotationBustR: an R package to extract subsequences from GenBank annotations.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5179},
pmid = {30002984},
issn = {2167-8359},
abstract = {BACKGROUND: DNA sequences are pivotal for a wide array of research in biology. Large sequence databases, like GenBank, provide an amazing resource to utilize DNA sequences for large scale analyses. However, many sequence records on GenBank contain more than one gene or are portions of genomes. Inconsistencies in the way genes are annotated and the numerous synonyms a single gene may be listed under provide major challenges for extracting large numbers of subsequences for comparative analysis across taxa. At present, there is no easy way to extract portions from many GenBank accessions based on annotations where gene names may vary extensively.<br><br>RESULTS: The R package AnnotationBustR allows users to extract sequences based on GenBank annotations through the ACNUC retrieval system given search terms of gene synonyms and accession numbers. AnnotationBustR extracts subsequences of interest and then writes them to a FASTA file for users to employ in their research endeavors.<br><br>CONCLUSION: FASTA files of extracted subsequences and accession tables generated by AnnotationBustR allow users to quickly find and extract subsequences from GenBank accessions. These sequences can then be incorporated in various analyses, like the construction of phylogenies to test a wide range of ecological and evolutionary hypotheses.},
}
@article {pmid30002592,
year = {2018},
author = {Li, B and Zhao, Z and Zhang, C and Li, S},
title = {Sinodraconarius gen. n., a new genus of Coelotinae spiders from Southwest China (Araneae, Agelenidae).},
journal = {ZooKeys},
volume = {},
number = {770},
pages = {117-135},
pmid = {30002592},
issn = {1313-2989},
abstract = {A new genus of the subfamily Coelotinae F.O. Pickard-Cambridge, 1893, Sinodraconariusgen. n., with four new species, S. cawarongensissp. n. (♂♀), S. muruoensissp. n. (♂♀), S. sangjiuensissp. n. (♂♀, type species), S. yuisp. n. (♂♀) and S. patellabifidus (Wang, 2003) comb. n., ex. Draconarius Ovtchinnikov, 1999 is described. The genus is restricted to Southwest China. Sinodraconariusgen. n. is most similar to Draconarius but can be distinguished by the shape of the copulatory organs. The DNA barcodes of all species were documented for future use.},
}
@article {pmid30002410,
year = {2018},
author = {Seethapathy, GS and Tadesse, M and Urumarudappa, SKJ and V Gunaga, S and Vasudeva, R and Malterud, KE and Shaanker, RU and de Boer, HJ and Ravikanth, G and Wangensteen, H},
title = {Authentication of Garcinia fruits and food supplements using DNA barcoding and NMR spectroscopy.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {10561},
pmid = {30002410},
issn = {2045-2322},
mesh = {Anti-Obesity Agents/*analysis/chemistry ; Chromatography, High Pressure Liquid ; Citrates/analysis ; DNA Barcoding, Taxonomic ; Dietary Supplements/*analysis ; Drug Contamination/*prevention &amp; control ; Food Contamination/*analysis/prevention &amp; control ; Fruit/chemistry ; Garcinia/*chemistry/genetics ; India ; Magnetic Resonance Spectroscopy ; },
abstract = {Garcinia L. (Clusiaceae) fruits are a rich source of (-)-hydroxycitric acid, and this has gained considerable attention as an anti-obesity agent and a popular weight loss food supplement. In this study, we assessed adulteration of morphologically similar samples of Garcinia using DNA barcoding, and used NMR to quantify the content of (-)-hydroxycitric acid and (-)-hydroxycitric acid lactone in raw herbal drugs and Garcinia food supplements. DNA barcoding revealed that mostly G. gummi-gutta (previously known as G. cambogia) and G. indica were traded in Indian herbal markets, and there was no adulteration. The content of (-)-hydroxycitric acid and (-)-hydroxycitric acid lactone in the two species varied from 1.7% to 16.3%, and 3.5% to 20.7% respectively. Analysis of ten Garcinia food supplements revealed a large variation in the content of (-)-hydroxycitric acid, from 29 mg (4.6%) to 289 mg (50.6%) content per capsule or tablet. Only one product contained quantifiable amounts of (-)-hydroxycitric acid lactone. Furthermore the study demonstrates that DNA barcoding and NMR could be effectively used as a regulatory tool to authenticate Garcinia fruit rinds and food supplements.},
}
@article {pmid30002235,
year = {2018},
author = {Pennisi, E and Price, M},
title = {Molecular 'barcodes' reveal lost whale hunts.},
journal = {Science (New York, N.Y.)},
volume = {361},
number = {6398},
pages = {119},
doi = {10.1126/science.361.6398.119},
pmid = {30002235},
issn = {1095-9203},
mesh = {Animals ; *Biodiversity ; Bone and Bones ; *DNA Barcoding, Taxonomic ; DNA, Ancient ; Phylogeny ; Whales/*classification/*genetics ; },
}
@article {pmid29997447,
year = {2018},
author = {Ordynets, A and Scherf, D and Pansegrau, F and Denecke, J and Lysenko, L and Larsson, KH and Langer, E},
title = {Short-spored Subulicystidium (Trechisporales, Basidiomycota): high morphological diversity and only partly clear species boundaries.},
journal = {MycoKeys},
volume = {},
number = {35},
pages = {41-99},
pmid = {29997447},
issn = {1314-4049},
abstract = {Diversity of corticioid fungi (resupinate Basidiomycota), especially outside the northern temperate climatic zone, remains poorly explored. Furthermore, most of the known species are delimited by morphological concepts only and, not rarely, these concepts are too broad and need to be tested by molecular tools. For many decades, the delimitation of species in the genus Subulicystidium (Hydnodontaceae, Trechisporales) was a challenge for mycologists. The presence of numerous transitional forms as to basidiospore size and shape hindered species delimitation and almost no data on molecular diversity have been available. In this study, an extensive set of 144 Subulicystidium specimens from Paleo- and Neotropics was examined. Forty-nine sequences of ITS nuclear ribosomal DNA region and 51 sequences of 28S nuclear ribosomal DNA region from fruit bodies of Subulicystidium were obtained and analysed within the barcoding gap framework and with phylogenetic Bayesian and Maximum likelihood approaches. Eleven new species of Subulicystidium are described based on morphology and molecular analyses: Subulicystidium boidinii, S. fusisporum, S. grandisporum, S. harpagum, S. inornatum, S. oberwinkleri, S. parvisporum, S. rarocrystallinum, S. robustius, S. ryvardenii and S. tedersooi. Morphological and DNA-evidenced borders were revised for the five previously known species: S. naviculatum, S. nikau, S. obtusisporum, S. brachysporum and S. meridense. Species-level variation in basidiospore size and shape was estimated based on systematic measurements of 2840 spores from 67 sequenced specimens. An updated identification key to all known species of Subulicystidium is provided.},
}
@article {pmid29997401,
year = {2019},
author = {Marin-Felix, Y and Hernández-Restrepo, M and Wingfield, MJ and Akulov, A and Carnegie, AJ and Cheewangkoon, R and Gramaje, D and Groenewald, JZ and Guarnaccia, V and Halleen, F and Lombard, L and Luangsa-Ard, J and Marincowitz, S and Moslemi, A and Mostert, L and Quaedvlieg, W and Schumacher, RK and Spies, CFJ and Thangavel, R and Taylor, PWJ and Wilson, AM and Wingfield, BD and Wood, AR and Crous, PW},
title = {Genera of phytopathogenic fungi: GOPHY 2.},
journal = {Studies in mycology},
volume = {92},
number = {},
pages = {47-133},
pmid = {29997401},
issn = {0166-0616},
abstract = {This paper represents the second contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions and information regarding the pathology, distribution, hosts and disease symptoms for the treated genera. In addition, primary and secondary DNA barcodes for the currently accepted species are included. This second paper in the GOPHY series treats 20 genera of phytopathogenic fungi and their relatives including: Allantophomopsiella, Apoharknessia, Cylindrocladiella, Diaporthe, Dichotomophthora, Gaeumannomyces, Harknessia, Huntiella, Macgarvieomyces, Metulocladosporiella, Microdochium, Oculimacula, Paraphoma, Phaeoacremonium, Phyllosticta, Proxypiricularia, Pyricularia, Stenocarpella, Utrechtiana and Wojnowiciella. This study includes the new genus Pyriculariomyces, 20 new species, five new combinations, and six typifications for older names.},
}
@article {pmid29995972,
year = {2019},
author = {Chimeno, C and Morinière, J and Podhorna, J and Hardulak, L and Hausmann, A and Reckel, F and Grunwald, JE and Penning, R and Haszprunar, G},
title = {DNA Barcoding in Forensic Entomology - Establishing a DNA Reference Library of Potentially Forensic Relevant Arthropod Species.},
journal = {Journal of forensic sciences},
volume = {64},
number = {2},
pages = {593-601},
doi = {10.1111/1556-4029.13869},
pmid = {29995972},
issn = {1556-4029},
support = {FKZ 01LI1101 and 01LI1501//German Federal Ministry of Education and Research/ ; },
mesh = {Animals ; Arthropods/*genetics ; *DNA Barcoding, Taxonomic ; *Databases, Nucleic Acid ; Electron Transport Complex IV/genetics ; Entomology ; *Forensic Sciences ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {Throughout the years, DNA barcoding has gained in importance in forensic entomology as it leads to fast and reliable species determination. High-quality results, however, can only be achieved with a comprehensive DNA barcode reference database at hand. In collaboration with the Bavarian State Criminal Police Office, we have initiated at the Bavarian State Collection of Zoology the establishment of a reference library containing arthropods of potential forensic relevance to be used for DNA barcoding applications. CO1-5P' DNA barcode sequences of hundreds of arthropods were obtained via DNA extraction, PCR and Sanger Sequencing, leading to the establishment of a database containing 502 high-quality sequences which provide coverage for 88 arthropod species. Furthermore, we demonstrate an application example of this library using it as a backbone to a high throughput sequencing analysis of arthropod bulk samples collected from human corpses, which enabled the identification of 31 different arthropod Barcode Index Numbers.},
}
@article {pmid29990742,
year = {2018},
author = {Wachowska, U and Irzykowski, W and Jędryczka, M},
title = {Agrochemicals: Effect on genetic resistance in yeasts colonizing winter wheat kernels.},
journal = {Ecotoxicology and environmental safety},
volume = {162},
number = {},
pages = {77-84},
doi = {10.1016/j.ecoenv.2018.06.042},
pmid = {29990742},
issn = {1090-2414},
mesh = {Agaricales/drug effects/genetics ; Agrochemicals/*pharmacology ; Ascomycota/drug effects/genetics ; Benzimidazoles/pharmacology ; Candida albicans/drug effects/genetics ; Carbamates/pharmacology ; Drug Resistance, Fungal/*genetics ; Epoxy Compounds/pharmacology ; Fungicides, Industrial/*pharmacology ; Microbial Sensitivity Tests ; Pesticide Residues/analysis ; Plant Diseases/microbiology ; Pyrimidines/pharmacology ; Seasons ; Silanes/pharmacology ; Strobilurins/pharmacology ; Triazoles/pharmacology ; Triticum/*microbiology ; Xenobiotics/pharmacology ; Yeasts/classification/*drug effects/*genetics ; },
abstract = {Crop protection agents are widely used in modern agriculture and exert direct effects on non-target microorganisms such as yeasts. Yeasts abundantly colonize wheat grain and affect its chemical composition. They can also limit pathogen growth. This study evaluated the sensitivity of yeast communities colonizing winter wheat kernels to benzimidazole, strobilurin, triazole and morpholine fungicides, trinexapac-ethyl, a commercial mixture of o-nitrophenol+p-nitrophenol+5-nitroguaiacol, and chitosan applied during the growing season of winter wheat and in vitro in a diffusion test. A molecular identification analysis of yeasts isolated from winter wheat kernels was performed, and nucleotide polymorphisms in the CYTb gene (G143A) conferring resistance to strobilurin fungicides in yeast cells were identified. The size of yeast communities increased during grain storage, and the total counts of endophytic yeasts were significantly (85%) reduced following intensive fungicide treatment (fenpropimorph, a commercial mixture of pyraclostrobin, epoxiconazole and thiophanate-methyl). This study demonstrated that agrochemical residues in wheat grain can drive selection of yeast communities for reduced sensitivity to xenobiotics. A mutation in the CYTb gene (G143A) was observed in all analyzed isolates of the following azoxystrobin-resistant species: Aureobasidium pullulans, Debaryomyces hansenii, Candida albicans and C. sake. Agrochemicals tested in vitro were divided into four classes of toxicity to yeasts: (1) tebuconazole and a commercial mixture of flusilazole and carbendazim - most toxic to yeasts; (2) fenpropimorph and a commercial mixture of pyraclostrobin and epoxyconazole; (3) propiconazole, chitosan, thiophanate-methyl and a commercial mixture of o-nitrophenol, p-nitrophenol and 5-nitroguaiacol; (4) trinexapac-ethyl and azoxystrobin - least toxic to yeasts. It was found that agrochemicals can have an adverse effect on yeast abundance and the composition of yeast communities, mostly due to differences in fungicide resistance between yeast species, including the clinically significant C. albicans.},
}
@article {pmid29985924,
year = {2018},
author = {Ashfaq, M and Sabir, JSM and El-Ansary, HO and Perez, K and Levesque-Beaudin, V and Khan, AM and Rasool, A and Gallant, C and Addesi, J and Hebert, PDN},
title = {Insect diversity in the Saharo-Arabian region: Revealing a little-studied fauna by DNA barcoding.},
journal = {PloS one},
volume = {13},
number = {7},
pages = {e0199965},
pmid = {29985924},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Egypt ; Insecta/*classification/genetics ; Pakistan ; Saudi Arabia ; },
abstract = {Although insects dominate the terrestrial fauna, sampling constraints and the poor taxonomic knowledge of many groups have limited assessments of their diversity. Passive sampling techniques and DNA-based species assignments now make it possible to overcome these barriers. For example, Malaise traps collect specimens with minimal intervention while the Barcode Index Number (BIN) system automates taxonomic assignments. The present study employs Malaise traps and DNA barcoding to extend understanding of insect diversity in one of the least known zoogeographic regions, the Saharo-Arabian. Insects were collected at four sites in three countries (Egypt, Pakistan, Saudi Arabia) by deploying Malaise traps. The collected specimens were analyzed by sequencing 658 bp of cytochrome oxidase I (DNA barcode) and assigning BINs on the Barcode of Life Data Systems. The year-long deployment of a Malaise trap in Pakistan and briefer placements at two Egyptian sites and at one in Saudi Arabia collected 53,092 specimens. They belonged to 17 insect orders with Diptera and Hymenoptera dominating the catch. Barcode sequences were recovered from 44,432 (84%) of the specimens, revealing the occurrence of 3,682 BINs belonging to 254 families. Many of these taxa were uncommon as 25% of the families and 50% of the BINs from Pakistan were only present in one sample. Family and BIN counts varied significantly through the year, but diversity indices did not. Although more than 10,000 specimens were analyzed from each nation, just 2% of BINs were shared by Pakistan and Saudi Arabia, 4% by Egypt and Pakistan, and 7% by Egypt and Saudi Arabia. The present study demonstrates how the BIN system can circumvent the barriers imposed by limited access to taxonomic specialists and by the fact that many insect species in the Saharo-Arabian region are undescribed.},
}
@article {pmid29979783,
year = {2018},
author = {Ramünke, S and de Almeida Borges, F and von Son-de Fernex, E and von Samson-Himmelstjerna, G and Krücken, J},
title = {Molecular marker sequences of cattle Cooperia species identify Cooperia spatulata as a morphotype of Cooperia punctata.},
journal = {PloS one},
volume = {13},
number = {7},
pages = {e0200390},
pmid = {29979783},
issn = {1932-6203},
mesh = {Animals ; Cattle ; Cattle Diseases/diagnosis/parasitology ; *Genetic Markers ; Male ; Phylogeny ; Trichostrongyloidea/anatomy &amp; histology/*classification/*genetics/isolation &amp; purification ; Trichostrongyloidiasis/diagnosis/parasitology/veterinary ; },
abstract = {The genus Cooperia includes important parasites of ruminants and currently contains 34 accepted species. However, even for those species infecting livestock, there is a considerable lack of molecular information and many species are only identifiable using subtle morphological traits. The present study aimed to provide molecular data to allow diagnosis of Cooperia species infecting cattle. Partial sequences of two mitochondrial (cytochrome oxidase 2, 12S rRNA gene) and two nuclear genes (isotype 1 β tubulin gene including two introns, internal transcribed spacers (ITS) were obtained from morphologically identified specimens of Cooperia pectinata, Cooperia punctata and Cooperia spatulata as well as from larvae of pure Cooperia oncophora and C. punctata laboratory isolates. Pairwise identity of ITS-2 sequences was very high and it was the only region able to identify a specimen as Cooperia sp. However, the ITS-2 was unreliable for diagnosis at the species level. All other marker sequences could not unequivocally be allocated to the genus Cooperia but allowed clear species identification with the exception of the pair C. punctata/C. spatulata for which no significant differences were found for any marker sequence. Maximum-likelihood phylogenetic analyses of individual genes as well as a multi-locus analysis covering all four sequences confirmed that specimen identified as C. spatulata were randomly distributed throughout the C. punctata cluster and formed no group of their own. In contrast, the other Cooperia species formed clearly separated and statistically supported clusters. These data indicate that C. spatulata is most likely only a morphotype of C. punctata and the name should be considered a synonym. Combinations of nuclear and mitochondrial markers should be used to identify morphotypes or cryptic species to benefit from excellent barcoding properties of the latter but allowing proper phylogenetic analyses and controlling for lineage sorting that might occur for mitochondrial genotypes within a species.},
}
@article {pmid29976857,
year = {2018},
author = {Zhou, T and Wang, J and Jia, Y and Li, W and Xu, F and Wang, X},
title = {Comparative Chloroplast Genome Analyses of Species in Gentiana section Cruciata (Gentianaceae) and the Development of Authentication Markers.},
journal = {International journal of molecular sciences},
volume = {19},
number = {7},
pages = {},
pmid = {29976857},
issn = {1422-0067},
mesh = {Chloroplasts/*genetics ; Gene Library ; Gene Order ; Genetic Loci ; Genetic Markers ; *Genome, Plant ; Gentiana/*classification/*genetics ; INDEL Mutation ; Phylogeny ; Rubiaceae/*classification/*genetics ; Whole Genome Sequencing ; },
abstract = {Gentiana section Cruciata is widely distributed across Eurasia at high altitudes, and some species in this section are used as traditional Chinese medicine. Accurate identification of these species is important for their utilization and conservation. Due to similar morphological and chemical characteristics, correct discrimination of these species still remains problematic. Here, we sequenced three complete chloroplast (cp) genomes (G. dahurica, G. siphonantha and G. officinalis). We further compared them with the previously published plastomes from sect. Cruciata and developed highly polymorphic molecular markers for species authentication. The eight cp genomes shared the highly conserved structure and contained 112 unique genes arranged in the same order, including 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. We found that four genes (accD, clpP, matK and ycf1) were subject to positive selection, and sixteen InDel-variable loci with high discriminatory powers were selected as candidate barcodes. Our phylogenetic analyses based on plastomes further confirmed the monophyly of sect. Cruciata and primarily elucidated the phylogeny of Gentianales. This study indicated that cp genomes can provide more integrated information for better elucidating the phylogenetic pattern and improving discriminatory power during species authentication.},
}
@article {pmid29976145,
year = {2018},
author = {Somervuo, P and Koskinen, P and Mei, P and Holm, L and Auvinen, P and Paulin, L},
title = {BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing.},
journal = {BMC bioinformatics},
volume = {19},
number = {1},
pages = {257},
pmid = {29976145},
issn = {1471-2105},
mesh = {DNA Barcoding, Taxonomic/*methods ; High-Throughput Screening Assays/*methods ; Humans ; },
abstract = {BACKGROUND: Current high-throughput sequencing platforms provide capacity to sequence multiple samples in parallel. Different samples are labeled by attaching a short sample specific nucleotide sequence, barcode, to each DNA molecule prior pooling them into a mix containing a number of libraries to be sequenced simultaneously. After sequencing, the samples are binned by identifying the barcode sequence within each sequence read. In order to tolerate sequencing errors, barcodes should be sufficiently apart from each other in sequence space. An additional constraint due to both nucleotide usage and basecalling accuracy is that the proportion of different nucleotides should be in balance in each barcode position. The number of samples to be mixed in each sequencing run may vary and this introduces a problem how to select the best subset of available barcodes at sequencing core facility for each sequencing run. There are plenty of tools available for de novo barcode design, but they are not suitable for subset selection.<br><br>RESULTS: We have developed a tool which can be used for three different tasks: 1) selecting an optimal barcode set from a larger set of candidates, 2) checking the compatibility of user-defined set of barcodes, e.g. whether two or more libraries with existing barcodes can be combined in a single sequencing pool, and 3) augmenting an existing set of barcodes. In our approach the selection process is formulated as a minimization problem. We define the cost function and a set of constraints and use integer programming to solve the resulting combinatorial problem. Based on the desired number of barcodes to be selected and the set of candidate sequences given by user, the necessary constraints are automatically generated and the optimal solution can be found. The method is implemented in C programming language and web interface is available at http://ekhidna2.biocenter.helsinki.fi/barcosel .<br><br>CONCLUSIONS: Increasing capacity of sequencing platforms raises the challenge of mixing barcodes. Our method allows the user to select a given number of barcodes among the larger existing barcode set so that both sequencing errors are tolerated and the nucleotide balance is optimized. The tool is easy to access via web browser.},
}
@article {pmid29974525,
year = {2018},
author = {Pansare, AV and Khairkar, SR and Shedge, AA and Chhatre, SY and Patil, VR and Nagarkar, AA},
title = {In Situ Nanoparticle Embedding for Authentication of Epoxy Composites.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e1801523},
doi = {10.1002/adma.201801523},
pmid = {29974525},
issn = {1521-4095},
abstract = {In situ reduction of chloroauric acid inside an amine-cured epoxy matrix leads to formation of gold nanoparticles which are embedded inside the part. This phenomenon is leveraged to design an authentication system for composites wherein the particles are embedded spatially and are invisible to the naked eye. Under UV light, the particles diffract light and create an easily visible path. The particles penetrate inside the part and create a permanent, cost-effective, tamper-proof code. The advantage of this technique is that this authentication system can be built in composite parts after fabrication of the composite structure. As very small amount (nanograms) of particles are present in the part, negligible change in the thermal characteristics of the parent matrix is observed. The particles can be embedded easily in carbon fiber as well as glass fiber reinforced epoxy structures.},
}
@article {pmid29967752,
year = {2018},
author = {Richardson, RT and Bengtsson-Palme, J and Gardiner, MM and Johnson, RM},
title = {A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding data.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5126},
pmid = {29967752},
issn = {2167-8359},
abstract = {Metabarcoding is a popular application which warrants continued methods optimization. To maximize barcoding inferences, hierarchy-based sequence classification methods are increasingly common. We present methods for the construction and curation of a database designed for hierarchical classification of a 157 bp barcoding region of the arthropod cytochrome c oxidase subunit I (COI) locus. We produced a comprehensive arthropod COI amplicon dataset including annotated arthropod COI sequences and COI sequences extracted from arthropod whole mitochondrion genomes, the latter of which provided the only source of representation for Zoraptera, Callipodida and Holothyrida. The database contains extracted sequences of the target amplicon from all major arthropod clades, including all insect orders, all arthropod classes and Onychophora, Tardigrada and Mollusca outgroups. During curation, we extracted the COI region of interest from approximately 81 percent of the input sequences, corresponding to 73 percent of the genus-level diversity found in the input data. Further, our analysis revealed a high degree of sequence redundancy within the NCBI nucleotide database, with a mean of approximately 11 sequence entries per species in the input data. The curated, low-redundancy database is included in the Metaxa2 sequence classification software (http://microbiology.se/software/metaxa2/). Using this database with the Metaxa2 classifier, we performed a cross-validation analysis to characterize the relationship between the Metaxa2 reliability score, an estimate of classification confidence, and classification error probability. We used this analysis to select a reliability score threshold which minimized error. We then estimated classification sensitivity, false discovery rate and overclassification, the propensity to classify sequences from taxa not represented in the reference database. Our work will help researchers design and evaluate classification databases and conduct metabarcoding on arthropods and alternate taxa.},
}
@article {pmid29967722,
year = {2018},
author = {Wang, L and Wu, Z and Liu, M and Liu, W and Zhao, W and Liu, H and You, F},
title = {DNA barcoding of marine fish species from Rongcheng Bay, China.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5013},
pmid = {29967722},
issn = {2167-8359},
abstract = {Rongcheng Bay is a coastal bay of the Northern Yellow Sea, China. To investigate and monitor the fish resources in Rongcheng Bay, 187 specimens from 41 different species belonging to 28 families in nine orders were DNA-barcoded using the mitochondrial cytochrome c oxidase subunit I gene (COI). Most of the fish species could be discriminated using this COI sequence with the exception of Cynoglossus joyneri and Cynoglossus lighti. The average GC% content of the 41 fish species was 47.3%. The average Kimura 2-parameter genetic distances within the species, genera, families, and orders were 0.21%, 5.28%, 21.30%, and 23.63%, respectively. Our results confirmed that the use of combined morphological and DNA barcoding identification methods facilitated fish species identification in Rongcheng Bay, and also established a reliable DNA barcode reference library for these fish. DNA barcodes will contribute to future efforts to achieve better monitoring, conservation, and management of fisheries in this area.},
}
@article {pmid29962361,
year = {2019},
author = {Maringer, M and Wisse-Voorwinden, N and Veer, PV' and Geelen, A},
title = {Food identification by barcode scanning in the Netherlands: a quality assessment of labelled food product databases underlying popular nutrition applications.},
journal = {Public health nutrition},
volume = {22},
number = {7},
pages = {1215-1222},
pmid = {29962361},
issn = {1475-2727},
mesh = {*Databases, Factual ; *Food Labeling ; Humans ; *Mobile Applications ; Netherlands ; *Nutritive Value ; },
abstract = {OBJECTIVE: The quality of labelled food product databases underlying popular diet applications (apps) with barcode scanners was investigated.<br><br>DESIGN: Product identification rates for the scanned products and the availability and accuracy of nutrient values were calculated.<br><br>SETTING: One hundred food products were selected from the two largest supermarket chains in the Netherlands. Using the barcode scanners of the selected apps, the products were scanned and the results recorded as food diary entries. The collected data were exported.<br><br>SUBJECTS: Seven diet apps with barcode scanner and food recording feature were selected from the Google Play and Apple app stores.<br><br>RESULTS: Energy values were available for 99 % of the scanned products, of which on average 79 % deviated not more than 5 % from the true value. MyFitnessPal provided values for sixteen nutrients, while Virtuagym Food and Yazio provided values for only four nutrients. MyFitnessPal also showed the largest percentage of correctly identified products (i.e. 96 %) and SparkPeople the smallest (i.e. 5 %). The accuracy of the provided nutrient values varied greatly between apps and nutrients.<br><br>CONCLUSIONS: While energy was the most consistently and accurately reported value, the availability and accuracy of other values varied greatly between apps. Whereas popular diet apps with barcode scanners might be valuable tools for dietary assessments on the product and energy level, they appear less suitable for assessments on the nutrient level. The presence of user-generated database entries implies that the availability of food products might vary depending on the size and diversity of an app's user base.},
}
@article {pmid29959484,
year = {2018},
author = {Lai, Y and Schlücker, S and Wang, Y},
title = {Rapid and sensitive SERS detection of the cytokine tumor necrosis factor alpha (tnf-α) in a magnetic bead pull-down assay with purified and highly Raman-active gold nanoparticle clusters.},
journal = {Analytical and bioanalytical chemistry},
volume = {410},
number = {23},
pages = {5993-6000},
doi = {10.1007/s00216-018-1218-0},
pmid = {29959484},
issn = {1618-2650},
support = {WA 3369/1-1//German Research Foundation/ ; },
mesh = {Dimerization ; Gold/*chemistry ; Humans ; Limit of Detection ; Metal Nanoparticles/*chemistry/ultrastructure ; Silicon Dioxide/chemistry ; Spectrum Analysis, Raman/*methods ; Tumor Necrosis Factor-alpha/*analysis ; },
abstract = {Tumor necrosis factor alpha (TNF-α) is a cytokine with significance in early diagnosis of cardiovascular diseases, obesity and insulin resistance. We demonstrate the proof of concept for a rapid and sensitive detection of TNF-α using a magnetic bead pull-down assay in combination with surface-enhanced Raman scattering (SERS). The use of purified and highly SERS-active small clusters of gold nanoparticles (AuNP) provides the high sensitivity of the assay with a limit of detection of ca. 1 pg/mL. Continuous density gradient centrifugation was employed for separating the very bright silica-encapsulated AuNP dimers and trimers from the significantly weaker AuNP monomers. Negative control experiments with other cytokines (IL-6, IL-8) and bovine serum albumin (BSA) confirm the high specificity of the assay, but indicate also space for future improvements by further reducing non-specific binding between proteins and the SERS nanotags. The multiplexing potential of this SERS-based detection scheme is exemplarily demonstrated by using a set of three spectrally distinct and highly SERS-active AuNP clusters with unique spectral barcodes. Graphical abstract ᅟ.},
}
@article {pmid29956319,
year = {2018},
author = {Waraniak, JM and Baker, EA and Scribner, KT},
title = {Molecular diet analysis reveals predator-prey community dynamics and environmental factors affecting predation of larval lake sturgeon Acipenser fulvescens in a natural system.},
journal = {Journal of fish biology},
volume = {93},
number = {4},
pages = {616-629},
doi = {10.1111/jfb.13726},
pmid = {29956319},
issn = {1095-8649},
support = {//Michigan Department of Natural Resources/ ; //Great Lakes Fisheries Trust/ ; //U.S. Fish and Wildlife Coastal Program/ ; },
mesh = {Animals ; Biomass ; DNA Barcoding, Taxonomic ; *Diet ; *Ecosystem ; Fishes/classification/growth &amp; development/*physiology ; Lakes ; Larva/physiology ; Life Cycle Stages ; *Predatory Behavior ; Rivers ; Sequence Analysis, DNA ; },
abstract = {This study utilized molecular tools to quantify the prevalence of predation during the vulnerable drifting larval life-history stage of lake sturgeon Acipenser fulvescens. How predators, the co-distributed prey community and abiotic environmental conditions (e.g., stream substrata) affected predation levels was quantified. Nightly D-frame drift net surveys were used to estimate the biomass of A. fulvescens and co-distributed prey. Gastrointestinal diet samples (n = 1,140) from 28 species of potential fish predators were collected during electrofishing surveys. Sampling was conducted for 17 days across 2015 and 2016. Based on DNA barcode analysis using sturgeon-specific mtDNA cytochrome oxidase I primers, A. fulvescens DNA was detected in 73 of 1,140 diet samples (6.40%) from 16 of the 28 predator species examined. A logistic regression model was used to analyse the effects of biotic and abiotic variables associated with the likelihood a predator had consumed larval A. fulvescens. Increasing lunar illumination and biomass of larval A. fulvescens increased predation rates on larval A. fulvescens. Higher discharge and greater biomass and proportions of alternative prey decreased predation rates of larval A. fulvescens. Predation rates were slightly higher in habitats with sand substrata. Most predator species preyed upon larval A. fulvescens at similar rates. The study revealed considerably higher incidence of predation on larval A. fulvescens than previous studies had documented using traditional morphological diet analysis. Co-distributed prey and abiotic environmental variables that affected the predation rates of a species of regional conservation concern can inform future management actions.},
}
@article {pmid29956164,
year = {2018},
author = {Tang, MS and Bowcutt, R and Loke, P},
title = {Assessing the Mouse Intestinal Microbiota in Settings of Type-2 Immune Responses.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1799},
number = {},
pages = {359-370},
doi = {10.1007/978-1-4939-7896-0_26},
pmid = {29956164},
issn = {1940-6029},
mesh = {Animals ; Gastrointestinal Microbiome/*immunology ; Helminthiasis/diagnosis/immunology/parasitology ; Helminths/immunology ; Host-Pathogen Interactions ; *Immunity ; Metagenome ; Metagenomics/methods ; Mice ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {The microbial communities that reside within the mammalian host play important roles in the development of a robust host immune system. With the advent of sequencing technology and barcoding strategy of the bacterial 16S ribosomal RNA (rRNA) gene, microbiota studies are becoming more economical but also more important in many immunology studies. Here, we described a representative study protocol to characterize how the microbiota changes during an intestinal helminth infection, with emphasis on subtle aspects of the experimental design that are critical for data interpretation.},
}
@article {pmid29955212,
year = {2018},
author = {Chakona, A and Kadye, WT and Bere, T and Mazungula, DN and Vreven, E},
title = {Evidence of hidden diversity and taxonomic conflicts in five stream fishes from the Eastern Zimbabwe Highlands freshwater ecoregion.},
journal = {ZooKeys},
volume = {},
number = {768},
pages = {69-95},
pmid = {29955212},
issn = {1313-2989},
abstract = {Stream fishes of the Eastern Afromontane region are among the least studied vertebrates in this region, despite the potential for harbouring cryptic diversity. The present study examined mitochondrial cytochrome oxidase subunit I (COI) sequence divergence in 153 specimens of stream fishes belonging to four genera and three families, [(Amphilius and Zaireichthys (Amphiliidae); Chiloglanis (Mochokidae); and Hippopotamyrus (Mormyridae)], in the Eastern Zimbabwe Highlands (EZH) freshwater ecoregion to explore the extent to which the current taxonomy conceals the ichthyofaunal diversity in the region. The General Mixed Yule Coalescent (GMYC) species delineation method identified 14 clusters within five currently recognised 'species' from the EZH ecoregion. Only one of these clusters represents a named species, while 13 of them represent candidate or undescribed species. Our results revealed that effective conservation of this region's unique biota is limited by the incomplete knowledge of taxonomic diversity and inaccurate mapping of species distribution ranges.},
}
@article {pmid29955203,
year = {2019},
author = {Vu, D and Groenewald, M and de Vries, M and Gehrmann, T and Stielow, B and Eberhardt, U and Al-Hatmi, A and Groenewald, JZ and Cardinali, G and Houbraken, J and Boekhout, T and Crous, PW and Robert, V and Verkley, GJM},
title = {Large-scale generation and analysis of filamentous fungal DNA barcodes boosts coverage for kingdom fungi and reveals thresholds for fungal species and higher taxon delimitation.},
journal = {Studies in mycology},
volume = {92},
number = {},
pages = {135-154},
pmid = {29955203},
issn = {0166-0616},
abstract = {Species identification lies at the heart of biodiversity studies that has in recent years favoured DNA-based approaches. Microbial Biological Resource Centres are a rich source for diverse and high-quality reference materials in microbiology, and yet the strains preserved in these biobanks have been exploited only on a limited scale to generate DNA barcodes. As part of a project funded in the Netherlands to barcode specimens of major national biobanks, sequences of two nuclear ribosomal genetic markers, the Internal Transcribed Spaces and 5.8S gene (ITS) and the D1/D2 domain of the 26S Large Subunit (LSU), were generated as DNA barcode data for ca. 100 000 fungal strains originally assigned to ca. 17 000 species in the CBS fungal biobank maintained at the Westerdijk Fungal Biodiversity Institute, Utrecht. Using more than 24 000 DNA barcode sequences of 12 000 ex-type and manually validated filamentous fungal strains of 7 300 accepted species, the optimal identity thresholds to discriminate filamentous fungal species were predicted as 99.6 % for ITS and 99.8 % for LSU. We showed that 17 % and 18 % of the species could not be discriminated by the ITS and LSU genetic markers, respectively. Among them, ∼8 % were indistinguishable using both genetic markers. ITS has been shown to outperform LSU in filamentous fungal species discrimination with a probability of correct identification of 82 % vs. 77.6 %, and a clustering quality value of 84 % vs. 77.7 %. At higher taxonomic classifications, LSU has been shown to have a better discriminatory power than ITS. With a clustering quality value of 80 %, LSU outperformed ITS in identifying filamentous fungi at the ordinal level. At the generic level, the clustering quality values produced by both genetic markers were low, indicating the necessity for taxonomic revisions at genus level and, likely, for applying more conserved genetic markers or even whole genomes. The taxonomic thresholds predicted for filamentous fungal identification at the genus, family, order and class levels were 94.3 %, 88.5 %, 81.2 % and 80.9 % based on ITS barcodes, and 98.2 %, 96.2 %, 94.7 % and 92.7 % based on LSU barcodes. The DNA barcodes used in this study have been deposited to GenBank and will also be publicly available at the Westerdijk Institute's website as reference sequences for fungal identification, marking an unprecedented data release event in global fungal barcoding efforts to date.},
}
@article {pmid29955026,
year = {2018},
author = {Liu, SY and He, K and Chen, SD and Jin, W and Murphy, RW and Tang, MK and Liao, R and Li, FJ},
title = {How many species of Apodemus and Rattus occur in China? A survey based on mitochondrial cyt b and morphological analyses.},
journal = {Zoological research},
volume = {39},
number = {5},
pages = {309-320},
pmid = {29955026},
issn = {2095-8137},
mesh = {Animals ; China ; Cytochromes b/*genetics ; Mitochondria/*genetics ; Murinae/anatomy &amp; histology/*genetics ; Phylogeny ; Rats/anatomy &amp; histology/*genetics ; Skull/anatomy &amp; histology ; Surveys and Questionnaires ; Tooth/anatomy &amp; histology ; },
abstract = {Apodemus (mice) and Rattus (rats) are the top rodent reservoirs for zoonoses in China, yet little is known about their diversity. We reexamined the alpha diversity of these two genera based on a new collection of specimens from China and their cyt b sequences in GenBank. We also tested whether species could be identified using external and craniodental measurements exclusively. Measurements from 147 specimens of Apodemus and 236 specimens of Rattus were used for morphological comparisons. We analysed 74 cyt b sequences of Apodemus and 100 cyt b sequences of Rattus to facilitate phylogenetic estimations. Results demonstrated that nine species of Apodemus and seven species of Rattus, plus a new subspecies of Rattus nitidus, are distributed in China. Principal component analysis using external and craniodental measurements revealed that measurements alone could not separate the recognized species. The occurrence of Rattus pyctoris in China remains uncertain.},
}
@article {pmid29953855,
year = {2018},
author = {Zaman, S and Chobrutskiy, BI and Patel, JS and Callahan, BM and Tong, WL and Blanck, G},
title = {Mutant cytoskeletal and ECM peptides sensitive to the ST14 protease are associated with a worse outcome for glioblastoma multiforme.},
journal = {Biochemical and biophysical research communications},
volume = {503},
number = {4},
pages = {2218-2225},
doi = {10.1016/j.bbrc.2018.06.141},
pmid = {29953855},
issn = {1090-2104},
mesh = {Amino Acid Substitution ; Computational Biology ; Cytoskeletal Proteins/*metabolism ; Extracellular Matrix Proteins/*metabolism ; Genes, T-Cell Receptor ; Glioblastoma/*diagnosis/genetics/mortality ; Humans ; Mutant Proteins/metabolism ; Prognosis ; Protein Binding ; Serine Endopeptidases/genetics/*metabolism ; Survival Analysis ; V(D)J Recombination/genetics ; },
abstract = {We previously identified a set of the most frequently mutated cytoskeleton- and extracellular matrix-related proteins (CECMPs) in numerous cancer datasets. In this report, we used a bioinformatics approach to assess the impact of amino acid (AA) substitutions on the sensitivity of CECMPs to the ST14 protease (matriptase I), a transmembrane serine protease previously implicated in cancer development. Results indicated that AA substitutions in glioblastoma multiforme (GBM) CECMPs are skewed toward increased resistance to the ST14 protease, in comparison to the wild-type peptide sequence. Furthermore, the protease resistant AA substitutions represent relatively high binding affinities to HLA class I proteins, when assessing the binding specificities using HLA class I alleles matched to the source of the mutant AA. Moreover, samples representing AA substitutions that increased protease sensitivity also represented reduced overall and disease-free survival periods for patients with glioblastoma. To assess tumor specimen immunogenicity, we identified T-cell receptor (TCR) V(D)J recombinations in GBM exome files. The overlap between ST14 protease sensitive mutant barcodes and the TCR V(D)J recombination read positive barcodes represented significantly reduced survival.},
}
@article {pmid29953352,
year = {2018},
author = {Mukhin, VA and Zhuykova, EV and Badalyan, SM},
title = {Genetic Variability of the Medicinal Tinder Bracket Polypore, Fomes fomentarius (Agaricomycetes), from the Asian Part of Russia.},
journal = {International journal of medicinal mushrooms},
volume = {20},
number = {6},
pages = {561-568},
doi = {10.1615/IntJMedMushrooms.2018026278},
pmid = {29953352},
issn = {1940-4344},
mesh = {Asia ; China ; Coriolaceae/*genetics ; DNA Barcoding, Taxonomic ; DNA, Fungal/chemistry/genetics/isolation &amp; purification ; DNA, Ribosomal Spacer/genetics ; Europe ; *Genetic Variation ; Genotype ; Iran ; *Phylogeny ; Polymorphism, Genetic ; Russia ; Sequence Alignment ; },
abstract = {We analyzed intraspecies genetic variability of the medicinal tinder bracket polypore, Fomes fomentarius, from the Asian part of Russia, including the Ural, Altai, Western Sayan, and Baikal regions. We used nuclear ribosomal DNA internal transcribed spacer (ITS) sequence data as a standard marker for fungal DNA barcoding. In the Asian part of Russia, lineage A occurs as sublineage A2, which differs from sublineage A1 by a single nucleotide insertion at ITS2.3. Sublineage A2 is distributed up to Lake Baikal in the Ural, Altai, and Western Sayan regions. It can be characterized as a Eurasian sublineage of F. fomentarius. Lineage B is also represented by 2 sublineages (B1 and B2), which differ from each other by nucleotide sequences at ITS2.1. Sublineage B1 is represented by a small group of isolates from Asia (Iran, China, Nepal, South Korea), whereas sublineage B2 mainly includes isolates from Europe (Great Britain, Italy, Latvia, Slovakia, Slovenia) and 2 separate samples from Asia (Iran, China); these locales compose the distribution area of F. fomentarius. In the Asian part of Russia, lineage B is represented by sublineage B2 found in the Southern Urals (at the border between Europe and Asia), which is the only area where sublineages A2 and B2 are present. These sublineages are characterized by different substrate spectra: sublineage A2 is predominantly associated with Betula spp. and rarely with Alnus and Larix trees, whereas sublineage B2 does not have a pronounced substrate preference and is found in basidiomes collected from Acer, Duschekia, Prunus, and Salix trees, but not Betula trees. In general, the spectrum of substrates for F. fomentarius lineages A and B in the Asian part of Russia corresponds to that in other parts of this polypore's distribution area. Data are needed on genetic intraspecies variability (polymorphism) in relation to pharmacological properties for further biotechnological cultivation and use of the medicinal fungus F. fomentarius.},
}
@article {pmid29946303,
year = {2018},
author = {Sipiczki, M and Horvath, E and Pfliegler, WP},
title = {Birth-and-Death Evolution and Reticulation of ITS Segments of Metschnikowia andauensis and Metschnikowia fructicola rDNA Repeats.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {1193},
pmid = {29946303},
issn = {1664-302X},
abstract = {The internal transcribed spacer (ITS) region (ITS1, 5.8S rDNA, and ITS2) separates the genes coding for the SSU 18S and the LSU 26S genes in the rDNA units which are organized into long tandem arrays in the overwhelming majority of fungi. As members of a multigenic family, these units are subject of concerted evolution, which homogenizes their sequences. Exceptions have been observed in certain groups of plants and in a few fungal species. In our previous study we described exceptionally high degree of sequence diversity in the D1/D2 domains of two pulcherrimin-producing Metschnikowia (Saccharomycotina) species which appeared to evolve by reticulation. The major goals of this study were the examination of the diversity of the ITS segments and their evolution. We show that the ITS sequences of these species are not homogenized either, differ from each other by up to 38 substitutions and indels which have dramatic effects on the predicted secondary structures of the transcripts. The high intragenomic diversity makes the D1/D2 domains and the ITS spacers unsuitable for barcoding of these species and therefore the taxonomic position of strains previously assigned to them needs revision. By analyzing the genome sequence of the M. fructicola type strain, we also show that the rDNA of this species is fragmented, contains pseudogenes and thus evolves by the birth-and-death mechanism rather than by homogenisation, which is unusual in yeasts. The results of the network analysis of the sequences further indicate that the ITS regions are also involved in reticulation. M. andauensis and M. fructicola can form interspecies hybrids and their hybrids segregate, providing thus possibilities for reticulation of the rDNA repeats.},
}
@article {pmid29944686,
year = {2018},
author = {Mallott, EK and Garber, PA and Malhi, RS},
title = {trnL outperforms rbcL as a DNA metabarcoding marker when compared with the observed plant component of the diet of wild white-faced capuchins (Cebus capucinus, Primates).},
journal = {PloS one},
volume = {13},
number = {6},
pages = {e0199556},
pmid = {29944686},
issn = {1932-6203},
mesh = {Animals ; Animals, Wild ; *Cebus ; DNA Barcoding, Taxonomic/*methods ; *DNA, Plant ; *Diet ; Feces ; Feeding Behavior ; Female ; *Fruit/genetics ; *Genetic Markers ; Male ; Plants/genetics ; },
abstract = {DNA metabarcoding is a powerful tool for assessing the diets of wild animals, but there is no clear consensus on which proposed plant barcoding marker is most suitable for dietary analysis. This study compares two DNA plant barcoding markers that are commonly used for dietary analyses from degraded DNA, rbcL and trnL, to detailed dietary observations of wild white-faced capuchins (Cebus capucinus). Observational dietary data and fecal samples (n = 170) were collected for one year from a group of individually recognizable monkeys at La Suerte Biological Field Station, Costa Rica. DNA was extracted and portions of the rbcL and trnL chloroplast were amplified and sequenced on the Illumina MiSeq platform. Sequences were analyzed using obitools. Of the two barcoding markers tested, trnL yielded greater numbers of sequences with equal sequencing effort, higher resolution taxonomic identifications (albeit with a larger reference database), and identified a greater number of families also found in the observed diet. There was no relationship between observed capuchin feeding behavior and dietary composition based on either sequence occurrence or relative abundance of sequences using rbcL as a marker. However, dietary composition based on the relative abundance of trnL sequences was significantly positively associated with the observed percentage of feeding and foraging time capuchins' spent on each plant species. Additionally, in 35% of cases, the relative abundance of trnL sequences assigned to particular plant families in fecal samples was highly positively correlated with time spent consuming plants from those same families. Our results indicate that trnL is a more robust DNA metabarcoding marker for plant dietary analysis and may potentially be used to quantitatively assess differences in diet within or between species.},
}
@article {pmid29942045,
year = {2018},
author = {Li, D and Waite, DW and Fan, QH and George, S and Semeraro, L and Blacket, MJ},
title = {Molecular detection of small hive beetle Aethina tumida Murray (Coleoptera: Nitidulidae): DNA barcoding and development of a real-time PCR assay.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {9623},
pmid = {29942045},
issn = {2045-2322},
mesh = {Animals ; *Bees ; Coleoptera/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Mitochondria/enzymology ; Phylogeny ; *Real-Time Polymerase Chain Reaction ; },
abstract = {Small hive beetle (SHB), Aethina tumida can feed on honey, pollen and brood in honey bee colonies. It was endemic to Africa, but since 1996 has been detected in a number of countries worldwide, including Australia, Brazil, Canada, Italy, Mexico, South Korea, Philippines and the USA where it has had economic effects on local apiculture. To improve SHB identification, we obtained the first reference sequences from the DNA barcoding 5' COI gene region for SHB and some species of the family Nitidulidae associated with beehives. Phylogenetic analysis of SHB COI sequences (3' COI) revealed two divergent lineages, with those from Australia and USA being genetically different from the recent detection in Italy. Many countries, including New Zealand, are currently free from SHB, and require a rapid detection method for biosecurity. Here we present the development and validation of a real-time PCR assay for detection of SHB. The assay showed high specificity and sensitivity for detecting SHB, with no cross-reaction observed with closely related species, such as A. concolor. The real-time PCR is sensitive, detecting the target sequences up to 100 copies/µL. This assay should prove a useful biosecurity tool for rapid detection of SHB worldwide.},
}
@article {pmid29938135,
year = {2018},
author = {Sun, X and Bedos, A and Deharveng, L},
title = {Unusually low genetic divergence at COI barcode locus between two species of intertidal Thalassaphorura (Collembola: Onychiuridae).},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5021},
pmid = {29938135},
issn = {2167-8359},
abstract = {Species classification is challenging when taxa display limited morphological differences. In this paper, we combined morphology and DNA barcode data to investigate the complicated taxonomy of two Onychiurid Collembolan species. Thalassaphorura thalassophila and Thalassaphorura debilis are among the most common arthropod species in intertidal ecosystems and are often considered to be synonymous. Based on morphological and barcode analyses of fresh material collected in their type localities, we redescribed and compared the two species. However, their morphological distinctiveness was supported by a molecular divergence much smaller than previously reported at the interspecific level among Collembola. This divergence was even smaller than inter-population divergences recognized in the related edaphic species T. zschokkei, as well as those known between MOTUs within many Collembolan species. Our results may indicate a link between low genetic interspecific divergence and intertidal habitat, as the only biological peculiarity of the two species of interest compared to other Collembolan species analyzed to date is their strict intertidal life.},
}
@article {pmid29938133,
year = {2018},
author = {Troyer, EM and Coker, DJ and Berumen, ML},
title = {Comparison of cryptobenthic reef fish communities among microhabitats in the Red Sea.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5014},
pmid = {29938133},
issn = {2167-8359},
abstract = {Knowledge of community structure within an ecosystem is essential when trying to understand the function and importance of the system and when making related management decisions. Within the larger ecosystem, microhabitats play an important role by providing inhabitants with a subset of available resources. On coral reefs, cryptobenthic fishes encompass many groups and make up an important proportion of the biodiversity. However, these fishes are relatively small, exhibit extreme visual or behavioral camouflage, and, therefore, are often overlooked. We examined the differences in fish community structure between three common reef microhabitats (live hard coral, dead coral rubble, and sand) using ichthyocide stations in the central Red Sea. Using a combination of morphological and genetic (cytochrome oxidase I (COI) barcoding) techniques, we identified 326 individuals representing 73 species spread across 17 families, from fifteen 1 m[2] quadrats. Fish assemblages in the three microhabitats were significantly different from each other. Rubble microhabitats yielded the highest levels of fish abundance, richness, and diversity, followed by hard coral, and then sand. The results show that benthic composition, even at a small scale, influences cryptobenthic communities. This study also provides new COI sequence data to public databases, in order to further the research of cryptobenthic fishes in the Red Sea region.},
}
@article {pmid29938097,
year = {2018},
author = {Fitzek, E and Delcamp, A and Guichoux, E and Hahn, M and Lobdell, M and Hipp, AL},
title = {A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting.},
journal = {Ecology and evolution},
volume = {8},
number = {11},
pages = {5837-5851},
pmid = {29938097},
issn = {2045-7758},
abstract = {DNA barcoding has proved difficult in a number of woody plant genera, including the ecologically important oak genus Quercus. In this study, we utilized restrictionsite-associated DNA sequencing (RAD-seq) to develop an economical single nucleotide polymorphism (SNP) DNA barcoding system that suffices to distinguish eight common, sympatric eastern North American white oak species. Two de novo clustering pipelines, PyRAD and Stacks, were used in combination with postclustering bioinformatic tools to generate a list of 291 potential SNPs, 80 of which were included in a barcoding toolkit that is easily implemented using MassARRAY mass spectrometry technology. As a proof-of-concept, we used the genotyping toolkit to infer potential hybridization between North American white oaks transplanted outside of their native range (Q. michauxii, Q. montana, Q muehlenbergii/Q. prinoides, and Q. stellata) into a horticultural collection surrounded by natural forests of locally native trees (Q. alba and Q. macrocarpa) in the living collection at The Morton Arboretum (Lisle, IL, USA). Phylogenetic and clustering analyses suggested low rates of hybridization between cultivated and native species, with the exception of one Q. michauxii mother tree, the acorns of which exhibited high admixture from either Q. alba or Q. stellata and Q. macrocarpa, and a hybrid between Q. stellata that appears to have backcrossed almost exclusively to Q. alba. Together, RAD-seq and MassARRAY technologies allow for efficient development and implementation of a multispecies barcode for one of the more challenging forest tree genera.},
}
@article {pmid29936291,
year = {2018},
author = {Venter, PC and Nitsche, F and Scherwass, A and Arndt, H},
title = {Discrepancies Between Molecular and Morphological Databases of Soil Ciliates Studied for Temperate Grasslands of Central Europe.},
journal = {Protist},
volume = {169},
number = {4},
pages = {521-538},
doi = {10.1016/j.protis.2018.04.001},
pmid = {29936291},
issn = {1618-0941},
mesh = {Ciliophora/*classification ; *Databases, Factual/standards ; Databases, Genetic ; Europe ; *Grassland ; High-Throughput Nucleotide Sequencing ; Molecular Typing ; *Soil Microbiology ; },
abstract = {By measuring the change in soil protist communities, the effect of human land use on grasslands can be monitored to promote sustainable ecosystem functioning. Protists form the active link in the rhizosphere between the plant roots and higher trophic organisms; however, only few morphological species and their ecological values have yet been described in this context. To investigate the communicability between morphological and molecular databases used in the molecular barcoding of protists and in the biomonitoring of grassland soil, the present high-throughput sequencing (HTS) study (N=150) covered the area of central Europe (mesoscale) known to be well studied for ciliated protists. HTS delivered 2,404 unique reads identifying taxa in all major ciliophoran classes but exact reference matches were few. The study identified clear discrepancies between databases for well-studied taxa, where molecular databases contained multiple gene variants for single morphospecies of dominant taxa. Gene variants presented own biogeography - the eukaryotic microdiversity along gradients (e.g., land-use intensity, soil water). It is possible that many of the so called novel phylogenetic lineages and hidden diversity pointed out in environmental surveys could be evidence for the severe lack of molecular data for already known and morphologically described species, present in morphological databases.},
}
@article {pmid29936259,
year = {2018},
author = {Clark, TA and Chung, JH and Kennedy, M and Hughes, JD and Chennagiri, N and Lieber, DS and Fendler, B and Young, L and Zhao, M and Coyne, M and Breese, V and Young, G and Donahue, A and Pavlick, D and Tsiros, A and Brennan, T and Zhong, S and Mughal, T and Bailey, M and He, J and Roels, S and Frampton, GM and Spoerke, JM and Gendreau, S and Lackner, M and Schleifman, E and Peters, E and Ross, JS and Ali, SM and Miller, VA and Gregg, JP and Stephens, PJ and Welsh, A and Otto, GA and Lipson, D},
title = {Analytical Validation of a Hybrid Capture-Based Next-Generation Sequencing Clinical Assay for Genomic Profiling of Cell-Free Circulating Tumor DNA.},
journal = {The Journal of molecular diagnostics : JMD},
volume = {20},
number = {5},
pages = {686-702},
pmid = {29936259},
issn = {1943-7811},
support = {P30 CA093373/CA/NCI NIH HHS/United States ; },
mesh = {Circulating Tumor DNA/blood/*genetics ; Gene Amplification ; Gene Dosage ; Gene Rearrangement ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; INDEL Mutation/genetics ; },
abstract = {Genomic profiling of circulating tumor DNA derived from cell-free DNA (cfDNA) in blood can provide a noninvasive method for detecting genomic biomarkers to guide clinical decision making for cancer patients. We developed a hybrid capture-based next-generation sequencing assay for genomic profiling of circulating tumor DNA from blood (FoundationACT). High-sequencing coverage and molecular barcode-based error detection enabled accurate detection of genomic alterations, including short variants (base substitutions, short insertions/deletions) and genomic re-arrangements at low allele frequencies (AFs), and copy number amplifications. Analytical validation was performed on 2666 reference alterations. The assay achieved >99% overall sensitivity (95% CI, 99.1%-99.4%) for short variants at AF >0.5%, >95% sensitivity (95% CI, 94.2%-95.7%) for AF 0.25% to 0.5%, and 70% sensitivity (95% CI, 68.2%-71.5%) for AF 0.125% to 0.25%. No false positives were detected in 62 samples from healthy volunteers. Genomic alterations detected by FoundationACT demonstrated high concordance with orthogonal assays run on the same clinical cfDNA samples. In 860 routine clinical FoundationACT cases, genomic alterations were detected in cfDNA at comparable frequencies to tissue; for the subset of cases with temporally matched tissue and blood samples, 75% of genomic alterations and 83% of short variant mutations detected in tissue were also detected in cfDNA. On the basis of analytical validation results, FoundationACT has been approved for use in our Clinical Laboratory Improvement Amendments-certified/College of American Pathologists-accredited/New York State-approved laboratory.},
}
@article {pmid29935423,
year = {2018},
author = {Weger-Lucarelli, J and Garcia, SM and Rückert, C and Byas, A and O'Connor, SL and Aliota, MT and Friedrich, TC and O'Connor, DH and Ebel, GD},
title = {Using barcoded Zika virus to assess virus population structure in vitro and in Aedes aegypti mosquitoes.},
journal = {Virology},
volume = {521},
number = {},
pages = {138-148},
pmid = {29935423},
issn = {1096-0341},
support = {R56 AI132563/AI/NIAID NIH HHS/United States ; R01 AI067380/AI/NIAID NIH HHS/United States ; R01 AI132563/AI/NIAID NIH HHS/United States ; R21 AI125996/AI/NIAID NIH HHS/United States ; R01 AI125392/AI/NIAID NIH HHS/United States ; R21 AI131454/AI/NIAID NIH HHS/United States ; P51 OD011106/OD/NIH HHS/United States ; },
mesh = {Aedes/*virology ; Animals ; Cell Line ; *Genetic Variation ; Haplorhini/*virology ; Zika Virus/*classification/genetics/*growth &amp; development ; },
abstract = {Arboviruses such as Zika virus (ZIKV, Flaviviridae; Flavivirus) must replicate in both mammalian and insect hosts possessing strong immune defenses. Accordingly, transmission between and replication within hosts involves genetic bottlenecks, during which viral population size and genetic diversity may be significantly reduced. To help quantify these bottlenecks and their effects, we constructed 4 "barcoded" ZIKV populations that theoretically contain thousands of barcodes each. After identifying the most diverse barcoded virus, we passaged this virus 3 times in 2 mammalian and mosquito cell lines and characterized the population using deep sequencing of the barcoded region of the genome. C6/36 maintain higher barcode diversity, even after 3 passages, than Vero. Additionally, field-caught mosquitoes exposed to the virus to assess bottlenecks in a natural host. A progressive reduction in barcode diversity occurred throughout systemic infection of these mosquitoes. Differences in bottlenecks during systemic spread were observed between different populations of Aedes aegypti.},
}
@article {pmid29933389,
year = {2018},
author = {Mioduchowska, M and Czyż, MJ and Gołdyn, B and Kur, J and Sell, J},
title = {Instances of erroneous DNA barcoding of metazoan invertebrates: Are universal cox1 gene primers too "universal"?.},
journal = {PloS one},
volume = {13},
number = {6},
pages = {e0199609},
pmid = {29933389},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *DNA Primers ; *DNA, Mitochondrial ; Databases, Nucleic Acid ; Electron Transport Complex IV/*genetics ; Invertebrates/*genetics ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {The cytochrome c oxidase subunit I (cox1) gene is the main mitochondrial molecular marker playing a pivotal role in phylogenetic research and is a crucial barcode sequence. Folmer's "universal" primers designed to amplify this gene in metazoan invertebrates allowed quick and easy barcode and phylogenetic analysis. On the other hand, the increase in the number of studies on barcoding leads to more frequent publishing of incorrect sequences, due to amplification of non-target taxa, and insufficient analysis of the obtained sequences. Consequently, some sequences deposited in genetic databases are incorrectly described as obtained from invertebrates, while being in fact bacterial sequences. In our study, in which we used Folmer's primers to amplify COI sequences of the crustacean fairy shrimp Branchipus schaefferi (Fischer 1834), we also obtained COI sequences of microbial contaminants from Aeromonas sp. However, when we searched the GenBank database for sequences closely matching these contaminations we found entries described as representatives of Gastrotricha and Mollusca. When these entries were compared with other sequences bearing the same names in the database, the genetic distance between the incorrect and correct sequences amplified from the same species was c.a. 65%. Although the responsibility for the correct molecular identification of species rests on researchers, the errors found in already published sequences data have not been re-evaluated so far. On the basis of the standard sampling technique we have estimated with 95% probability that the chances of finding incorrectly described metazoan sequences in the GenBank depend on the systematic group, and variety from less than 1% (Mollusca and Arthropoda) up to 6.9% (Gastrotricha). Consequently, the increasing popularity of DNA barcoding and metabarcoding analysis may lead to overestimation of species diversity. Finally, the study also discusses the sources of the problems with amplification of non-target sequences.},
}
@article {pmid29932153,
year = {2018},
author = {Kasambala Donga, T and Meadow, R},
title = {Determination of Genetic Diversity in Chilo partellus, Busseola fusca, and Spodoptera frugiperda Infesting Sugarcane in Southern Malawi Using DNA Barcodes.},
journal = {Insects},
volume = {9},
number = {3},
pages = {},
pmid = {29932153},
issn = {2075-4450},
abstract = {Sugarcane is one of the most valuable crops in the world. Native and exotic Lepidopteran stemborers significantly limit sugarcane production. However, the identity and genetic diversity of stemborers infesting sugarcane in Malawi is unknown. The main objectives for this study were to identify and determine genetic diversity in stemborers infesting sugarcane in Malawi. We conducted field surveys between June 2016 and March 2017 in the Lower Shire Valley district of Chikwawa and Nsanje, southern Malawi. Molecular identification was based amplification the partial cytochrome oxidase subunit I (COI) gene region. Phylogenetic trees for sequences were generated and published GenBank accessions for each species were constructed. We found that Malawi Busseola fusca (Lepidoptera: Noctuidae) specimens belonged to clade II, Spodoptera frugiperda sp. 1 (Lepidoptera: Noctuidae) and Chilo partellus (Lepidoptera: Crambidae) were infesting sugarcane. Interspecific divergence ranged from 8.7% to 15.3%. Intraspecific divergence was highest for B. fusca, 3.6%. There were eight haplotypes for B. fusca, three for S. frugiperda and three for C. partellus. The importance of accurate species identification and genetic diversity on stemborer management is presented.},
}
@article {pmid29929208,
year = {2018},
author = {Inglis, PW and Mata, LR and da Silva, MJ and Vieira, RF and Alves, RBN and Silva, DB and Azevedo, VCR},
title = {DNA Barcoding for the Identification of Phyllanthus Taxa Used Medicinally in Brazil.},
journal = {Planta medica},
volume = {84},
number = {17},
pages = {1300-1310},
doi = {10.1055/a-0644-2688},
pmid = {29929208},
issn = {1439-0221},
mesh = {Brazil ; *DNA Barcoding, Taxonomic/methods ; DNA, Plant/genetics ; Phyllanthus/*genetics ; Plants, Medicinal/genetics ; Polymerase Chain Reaction ; },
abstract = {Plants of the genus Phyllanthus, principally Phyllanthus amarus, Phyllanthus urinaria, Phyllanthus niruri, and Phyllanthus tenellus, are used in Brazilian folk medicine to treat kidney stones as well as other ailments, where the latter two species are listed in the Brazilian Pharmacopeia as quebra-pedra (stone-breaker). However, only P. niruri has been shown to be effective in a clinical setting. Nuclear ribosomal internal transcribed spacer (ITS1 - 5.8S rRNA-ITS2), internal transcribed spacer 2, and chloroplasts rbcL, matK, psbA-trnH, trnL, and trnL-trnF were screened for their potential as DNA barcodes for the identification of 48 Phyllanthus taxa in Brazilian medicinal plant germplasm banks and in "living pharmacies". The markers were also tested for their ability to validate four commercial herbal teas labelled as quebra-pedra. Using the criterion of high clade posterior probability in Bayesian phylogenetic analysis, the internal transcribed spacer, internal transcribed spacer 2, and chloroplast matK, psbA-trnH, trnL, and trnL-trnF markers all reliably differentiated the four Phyllanthus species, with the internal transcribed spacer and matK possessing the additional advantage that the genus is well represented for these markers in the Genbank database. However, in the case of rbcL, posterior probability for some clades was low and while P. amarus and P. tenellus formed monophyletic groups, P. niruri and P. urinaria accessions could not be reliably distinguished with this marker. Packaged dried quebra-pedra herb from three Brazilian commercial suppliers comprised P. tenellus, but one sample was also found to be mixed with alfalfa (Medicago sativa). An herb marketed as quebra-pedra from a fourth supplier was found to be composed of a mixture of Desmodium barbatum and P. niruri.},
}
@article {pmid29928291,
year = {2018},
author = {Zeng, CX and Hollingsworth, PM and Yang, J and He, ZS and Zhang, ZR and Li, DZ and Yang, JB},
title = {Genome skimming herbarium specimens for DNA barcoding and phylogenomics.},
journal = {Plant methods},
volume = {14},
number = {},
pages = {43},
pmid = {29928291},
issn = {1746-4811},
abstract = {BACKGROUND: The world's herbaria contain millions of specimens, collected and named by thousands of researchers, over hundreds of years. However, this treasure has remained largely inaccessible to genetic studies, because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates.<br><br>RESULTS: As a practical test of routine recovery of rDNA and plastid genome sequences from herbarium specimens, we sequenced 25 herbarium specimens up to 80&#xa0;years old from 16 different Angiosperm families. Paired-end reads were generated, yielding successful plastid genome assemblies for 23 species and nuclear rDNAs for 24 species, respectively. These data showed that genome skimming can be used to generate genomic information from herbarium specimens as old as 80&#xa0;years and using as little as 500&#xa0;pg of degraded starting DNA.<br><br>CONCLUSIONS: The routine plastome sequencing from herbarium specimens is feasible and cost-effective (compare with Sanger sequencing or plastome-enrichment approaches), and can be performed with limited sample destruction.},
}
@article {pmid29927104,
year = {2018},
author = {Elliott, SE and Kongpachith, S and Lingampalli, N and Adamska, JZ and Cannon, BJ and Mao, R and Blum, LK and Robinson, WH},
title = {Affinity Maturation Drives Epitope Spreading and Generation of Proinflammatory Anti-Citrullinated Protein Antibodies in Rheumatoid Arthritis.},
journal = {Arthritis &amp; rheumatology (Hoboken, N.J.)},
volume = {70},
number = {12},
pages = {1946-1958},
pmid = {29927104},
issn = {2326-5205},
support = {R01 AR063676/AR/NIAMS NIH HHS/United States ; U01 AI101981/AI/NIAID NIH HHS/United States ; U19 AI110491/AI/NIAID NIH HHS/United States ; T32 AR050942/AR/NIAMS NIH HHS/United States ; U19-AI-11049103/AI/NIAID NIH HHS/United States ; R01-AR-063676/AR/NIAMS NIH HHS/United States ; U01-AI-101981/AI/NIAID NIH HHS/United States ; U19-AI-110491/AI/NIAID NIH HHS/United States ; UH2 AR067676/AR/NIAMS NIH HHS/United States ; 5T32-AI-07290-30/AI/NIAID NIH HHS/United States ; AI007290/AI/NIAID NIH HHS/United States ; },
mesh = {Aged ; Aged, 80 and over ; Anti-Citrullinated Protein Antibodies/*immunology ; Antibody Affinity/*physiology ; Arthritis, Rheumatoid/blood/*immunology ; Autoantibodies/*immunology ; B-Lymphocytes/immunology ; Computational Biology ; Epitopes/*immunology ; Female ; Humans ; Male ; Middle Aged ; Plasma Cells/immunology ; },
abstract = {OBJECTIVE: Rheumatoid arthritis (RA) is characterized by the presence of anti-citrullinated protein antibodies (ACPAs); nevertheless, the origin, specificity, and functional properties of ACPAs remain poorly understood. The aim of this study was to characterize the evolution of ACPAs by sequencing the plasmablast antibody repertoire at serial time points in patients with established RA.<br><br>METHODS: Blood samples were obtained at up to 4 serial time points from 8 individuals with established RA who were positive for ACPAs by the anti-cyclic citrullinated peptide test. CD19+CD3-IgD-CD14-CD20-CD27+CD38++ plasmablasts were isolated by single-cell sorting and costained with citrullinated peptide tetramers to identify ACPA-expressing plasmablasts. Cell-specific oligonucleotide barcodes were utilized, followed by large-scale sequencing and bioinformatics analysis, to obtain error-corrected, paired heavy- and light-chain antibody gene sequences for each B cell.<br><br>RESULTS: Bioinformatics analysis revealed 170 persistent plasmablast lineages in the RA blood, of which 19% included multiple isotypes. Among IgG- and IgA-expressing plasmablasts, significantly more IgA-expressing than IgG-expressing persistent lineages were observed (P < 0.01). Shared complementarity-determining region 3 sequence motifs were identified across subjects. A subset of the plasmablast lineages included members derived from later time points with divergent somatic hypermutations that encoded antibodies that bind an expanded set of citrullinated antigens. Furthermore, these recombinant, differentially mutated plasmablast antibodies formed immune complexes that stimulated higher macrophage production of tumor necrosis factor (TNF) compared to antibodies representing earlier time point-derived lineage members that were less mutated.<br><br>CONCLUSION: These findings demonstrate that established RA is characterized by a persistent IgA ACPA response that exhibits ongoing affinity maturation. This observation suggests the presence of a persistent mucosal antigen that continually promotes the production of IgA plasmablasts and their affinity maturation and epitope spreading, thus leading to the generation of ACPAs that bind additional citrullinated antigens and more potently stimulate macrophage production of TNF.},
}
@article {pmid29926869,
year = {2018},
author = {Zhang, DS and Jiang, Y and Wei, D and Wei, X and Xu, H and Gu, H},
title = {Polymers mediate a one-pot route for functionalized quantum dot barcodes with a large encoding capacity.},
journal = {Nanoscale},
volume = {10},
number = {26},
pages = {12461-12471},
doi = {10.1039/c8nr01888j},
pmid = {29926869},
issn = {2040-3372},
abstract = {With the increasing demands for high-throughput multiplexed bioassays, quantum dot (QD)-encoded microbeads as biocarriers for various bioreactions have attracted considerable attention. However, three key requirements for these biocarriers are still longstanding issues: a stable fluorescence intensity, a large encoding capacity and abundant surface functional groups. Here, a novel one-pot strategy is developed, generating functionalized QD-encoded microspheres with a strong fluorescence intensity and optical stability. With poly(styrene-co-maleic anhydride) (PSMA) molecules as mediators, the encapsulation of QDs and carboxylation of the bead surface are integrated together, greatly improving the preparation efficiency and guaranteeing their potential application in biodetection. Moreover, the mechanism for preparing QD-doped beads is further proposed, which helps to precisely manipulate the preparation process and accurately encode the beads. Through this approach, a single- and dual-color barcode library of QD-encoded microspheres has been successfully established, which demonstrates their great potential in suspension arrays.},
}
@article {pmid29925993,
year = {2018},
author = {Napolitani, G and Kurupati, P and Teng, KWW and Gibani, MM and Rei, M and Aulicino, A and Preciado-Llanes, L and Wong, MT and Becht, E and Howson, L and de Haas, P and Salio, M and Blohmke, CJ and Olsen, LR and Pinto, DMS and Scifo, L and Jones, C and Dobinson, H and Campbell, D and Juel, HB and Thomaides-Brears, H and Pickard, D and Bumann, D and Baker, S and Dougan, G and Simmons, A and Gordon, MA and Newell, EW and Pollard, AJ and Cerundolo, V},
title = {Clonal analysis of Salmonella-specific effector T cells reveals serovar-specific and cross-reactive T cell responses.},
journal = {Nature immunology},
volume = {19},
number = {7},
pages = {742-754},
doi = {10.1038/s41590-018-0133-z},
pmid = {29925993},
issn = {1529-2916},
support = {MC_UU_00008/1/MRC_/Medical Research Council/United Kingdom ; MR/K021222/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_00008/7/MRC_/Medical Research Council/United Kingdom ; MC_UU_12010/7/MRC_/Medical Research Council/United Kingdom ; NIHR-RP-R3-12-026/DH_/Department of Health/United Kingdom ; },
mesh = {ADP-ribosyl Cyclase 1/analysis ; Adult ; Antigens, Bacterial/immunology/metabolism ; CD4-Positive T-Lymphocytes/chemistry/*immunology ; Clone Cells ; Humans ; Phenotype ; Receptors, CCR7/analysis ; Salmonella paratyphi A/*immunology ; Salmonella typhi/*immunology ; Typhoid Fever/immunology ; },
abstract = {To tackle the complexity of cross-reactive and pathogen-specific T cell responses against related Salmonella serovars, we used mass cytometry, unbiased single-cell cloning, live fluorescence barcoding, and T cell-receptor sequencing to reconstruct the Salmonella-specific repertoire of circulating effector CD4[+] T cells, isolated from volunteers challenged with Salmonella enterica serovar Typhi (S. Typhi) or Salmonella Paratyphi A (S. Paratyphi). We describe the expansion of cross-reactive responses against distantly related Salmonella serovars and of clonotypes recognizing immunodominant antigens uniquely expressed by S. Typhi or S. Paratyphi A. In addition, single-amino acid variations in two immunodominant proteins, CdtB and PhoN, lead to the accumulation of T cells that do not cross-react against the different serovars, thus demonstrating how minor sequence variations in a complex microorganism shape the pathogen-specific T cell repertoire. Our results identify immune-dominant, serovar-specific, and cross-reactive T cell antigens, which should aid in the design of T cell-vaccination strategies against Salmonella.},
}
@article {pmid29925596,
year = {2018},
author = {Hawkins, JA and Jones, SK and Finkelstein, IJ and Press, WH},
title = {Indel-correcting DNA barcodes for high-throughput sequencing.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {27},
pages = {E6217-E6226},
pmid = {29925596},
issn = {1091-6490},
support = {F32 AG053051/AG/NIA NIH HHS/United States ; R01 GM120554/GM/NIGMS NIH HHS/United States ; R01 GM124141/GM/NIGMS NIH HHS/United States ; },
mesh = {*Base Sequence ; *DNA Barcoding, Taxonomic ; *High-Throughput Nucleotide Sequencing ; *INDEL Mutation ; },
abstract = {Many large-scale, high-throughput experiments use DNA barcodes, short DNA sequences prepended to DNA libraries, for identification of individuals in pooled biomolecule populations. However, DNA synthesis and sequencing errors confound the correct interpretation of observed barcodes and can lead to significant data loss or spurious results. Widely used error-correcting codes borrowed from computer science (e.g., Hamming, Levenshtein codes) do not properly account for insertions and deletions (indels) in DNA barcodes, even though deletions are the most common type of synthesis error. Here, we present and experimentally validate filled/truncated right end edit (FREE) barcodes, which correct substitution, insertion, and deletion errors, even when these errors alter the barcode length. FREE barcodes are designed with experimental considerations in mind, including balanced guanine-cytosine (GC) content, minimal homopolymer runs, and reduced internal hairpin propensity. We generate and include lists of barcodes with different lengths and error correction levels that may be useful in diverse high-throughput applications, including >10[6] single-error-correcting 16-mers that strike a balance between decoding accuracy, barcode length, and library size. Moreover, concatenating two or more FREE codes into a single barcode increases the available barcode space combinatorially, generating lists with >10[15] error-correcting barcodes. The included software for creating barcode libraries and decoding sequenced barcodes is efficient and designed to be user-friendly for the general biology community.},
}
@article {pmid29925315,
year = {2018},
author = {Coombe, L and Zhang, J and Vandervalk, BP and Chu, J and Jackman, SD and Birol, I and Warren, RL},
title = {ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.},
journal = {BMC bioinformatics},
volume = {19},
number = {1},
pages = {234},
pmid = {29925315},
issn = {1471-2105},
support = {R01 HG007182/HG/NHGRI NIH HHS/United States ; },
mesh = {Chromosomes, Human/*genetics ; *Genome, Human ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Sequence Analysis, DNA/*methods ; *Software ; },
abstract = {BACKGROUND: The long-range sequencing information captured by linked reads, such as those available from 10× Genomics (10xG), helps resolve genome sequence repeats, and yields accurate and contiguous draft genome assemblies. We introduce ARKS, an alignment-free linked read genome scaffolding methodology that uses linked reads to organize genome assemblies further into contiguous drafts. Our approach departs from other read alignment-dependent linked read scaffolders, including our own (ARCS), and uses a kmer-based mapping approach. The kmer mapping strategy has several advantages over read alignment methods, including better usability and faster processing, as it precludes the need for input sequence formatting and draft sequence assembly indexing. The reliance on kmers instead of read alignments for pairing sequences relaxes the workflow requirements, and drastically reduces the run time.<br><br>RESULTS: Here, we show how linked reads, when used in conjunction with Hi-C data for scaffolding, improve a draft human genome assembly of PacBio long-read data five-fold (baseline vs. ARKS NG50&#x2009;=&#x2009;4.6 vs. 23.1 Mbp, respectively). We also demonstrate how the method provides further improvements of a megabase-scale Supernova human genome assembly (NG50&#x2009;=&#x2009;14.74 Mbp vs. 25.94 Mbp before and after ARKS), which itself exclusively uses linked read data for assembly, with an execution speed six to nine times faster than competitive linked read scaffolders (~&#x2009;10.5&#xa0;h compared to 75.7&#xa0;h, on average). Following ARKS scaffolding of a human genome 10xG Supernova assembly (of cell line NA12878), fewer than 9 scaffolds cover each chromosome, except the largest (chromosome 1, n&#x2009;=&#x2009;13).<br><br>CONCLUSIONS: ARKS uses a kmer mapping strategy instead of linked read alignments to record and associate the barcode information needed to order and orient draft assembly sequences. The simplified workflow, when compared to that of our initial implementation, ARCS, markedly improves run time performances on experimental human genome datasets. Furthermore, the novel distance estimator in ARKS utilizes barcoding information from linked reads to estimate gap sizes. It accomplishes this by modeling the relationship between known distances of a region within contigs and calculating associated Jaccard indices. ARKS has the potential to provide correct, chromosome-scale genome assemblies, promptly. We expect ARKS to have broad utility in helping refine draft genomes.},
}
@article {pmid29923321,
year = {2018},
author = {Keck, F and Vasselon, V and Rimet, F and Bouchez, A and Kahlert, M},
title = {Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units' ecological profiles.},
journal = {Molecular ecology resources},
volume = {18},
number = {6},
pages = {1299-1309},
doi = {10.1111/1755-0998.12919},
pmid = {29923321},
issn = {1755-0998},
mesh = {Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; Diatoms/classification/genetics ; Environmental Monitoring/*methods ; Metagenomics/*methods ; Microscopy ; Phylogeny ; Rivers/microbiology ; Sensitivity and Specificity ; },
abstract = {DNA metabarcoding has been introduced as a revolutionary way to identify organisms and monitor ecosystems. However, the potential of this approach for biomonitoring remains partially unfulfilled because a significant part of the sampled DNA cannot be affiliated to species due to incomplete reference libraries. Thus, biotic indices, which are based on the estimated abundances of species in a community and their ecological profiles, can be inaccurate. We propose to compute biotic indices using phylogenetic imputation of operational taxonomic units (OTUs') ecological profiles (OTU-PITI approach). First, OTUs sequences are inserted within a reference phylogeny. Second, OTUs' ecological profiles are estimated on the basis of their phylogenetic relationships with reference species whose ecology is known. Based on these ecological profiles, biotic indices can be computed using all available OTUs. Using freshwater diatoms as a case study, we show that short DNA barcodes can be placed accurately within a phylogeny and their ecological preferences estimated with a satisfactory level of precision. In the light of these results, we tested the approach with a data set of 139 environmental samples of benthic river diatoms for which the same biotic index (specific sensitivity index) was calculated using (a) traditional microscopy, (b) OTUs with taxonomic assignment approach, (c) OTUs with phylogenetic estimation of ecological profiles (OTU-PITI) and (d) OTU with taxonomic assignment completed by the phylogenetic approach (OTU-PITI) for unclassified OTUs. Using traditional microscopy as a reference, we found that the combination of the OTUs' taxonomic assignment completed by the phylogenetic method performed satisfactorily and substantially better than the other methods tested.},
}
@article {pmid29922486,
year = {2018},
author = {Zhao, L and Yu, X and Shen, J and Xu, X},
title = {Identification of three kinds of Plumeria flowers by DNA barcoding and HPLC specific chromatogram.},
journal = {Journal of pharmaceutical analysis},
volume = {8},
number = {3},
pages = {176-180},
pmid = {29922486},
issn = {2214-0883},
abstract = {DNA barcoding and HPLC specific chromatogram were used to identify three kinds of Plumeria flowers respectively. DNAs extracted from the three Plumeria species were amplified by PCR with universal primers, and the psbA-trnH region was selected. All the amplified products were sequenced and the results were analyzed by MEGA 5.0. Chemometric methods including principal components analysis and hierarchical clustering analysis were conducted on the SAS 9.0 software to demonstrate the variability among samples. In conclusion, the psbA-trnH of all samples were successfully amplified from total DNA and sequenced. These three varieties of Plumeria can be differentiated by the psbA-trnH region and clustered into three groups respectively through building neighbor joining tree, which conformed to their germplasm origins. However, it was hard to distinguish them by HPLC specific chromatograms combined with chemometrics analysis. These indicated that DNA barcoding was a promising and reliable tool for the identification of three kinds of Plumeria flowers compared to HPLC specific chromatogram generally used. It could be treated as a powerful complementary method for traditional authentication, especially for those varieties which are difficult to be identified by conventional chromatography.},
}
@article {pmid29921301,
year = {2018},
author = {Petukhov, V and Guo, J and Baryawno, N and Severe, N and Scadden, DT and Samsonova, MG and Kharchenko, PV},
title = {dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments.},
journal = {Genome biology},
volume = {19},
number = {1},
pages = {78},
pmid = {29921301},
issn = {1474-760X},
support = {R01DK107784/DK/NIDDK NIH HHS/United States ; R01 HL131768/HL/NHLBI NIH HHS/United States ; R01 DK107784/DK/NIDDK NIH HHS/United States ; NSF-14-532//National Science Foundation/International ; P01 HL131477/HL/NHLBI NIH HHS/United States ; R01HL131768/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Cell Line, Tumor ; DNA Barcoding, Taxonomic/*methods ; Gene Expression Profiling/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; K562 Cells ; Male ; Mice ; Mice, Inbred C57BL ; Microfluidics/methods ; RNA/*genetics ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis/*methods ; Software ; Transcriptome/genetics ; },
abstract = {Recent single-cell RNA-seq protocols based on droplet microfluidics use massively multiplexed barcoding to enable simultaneous measurements of transcriptomes for thousands of individual cells. The increasing complexity of such data creates challenges for subsequent computational processing and troubleshooting of these experiments, with few software options currently available. Here, we describe a flexible pipeline for processing droplet-based transcriptome data that implements barcode corrections, classification of cell quality, and diagnostic information about the droplet libraries. We introduce advanced methods for correcting composition bias and sequencing errors affecting cellular and molecular barcodes to provide more accurate estimates of molecular counts in individual cells.},
}
@article {pmid29916730,
year = {2018},
author = {Chang, CH and Dai, WY and Chen, TY and Lee, AH and Hou, HY and Liu, SH and Jang-Liaw, NH},
title = {DNA barcoding reveals CITES-listed species among Taiwanese government-seized chelonian specimens.},
journal = {Genome},
volume = {61},
number = {8},
pages = {615-624},
doi = {10.1139/gen-2017-0264},
pmid = {29916730},
issn = {1480-3321},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Genetic Markers ; Government ; Mitochondria/*genetics ; Phylogeny ; Species Specificity ; Taiwan ; Turtles/classification/*genetics ; },
abstract = {Compared to traditional morphological identification, DNA barcoding-molecular identification based on sequencing of a segment of mitochondrial cytochrome c oxidase subunit I (COI)-provides a shortcut to authenticating chelonian identifications. Here, we selected 63 government-seized chelonian specimens deposited at Taipei Zoo for DNA barcoding analysis. DNA barcoding and subsequent phylogenetic analysis successfully authenticated 36 chelonian species, including five that are listed in CITES Appendix I. Approximately 90% (57/63) of the specimens were successfully authenticated by our molecular approach, but lack or error of BOLD reference sequences, biological processes such as hybridization, and uncertain species delimitation all reduced the accuracy of DNA barcoding. To increase the accuracy of DNA barcoding, Taipei Zoo will continue to enrich the BOLD database and also establish a genetic database, to include additional genetic markers, by using government-seized chelonian specimens. A fast and accurate method to authenticate seized samples could assist law enforcement agencies to prosecute criminals and restrict illegal exploitation of wild chelonian resources.},
}
@article {pmid29916451,
year = {2018},
author = {Toro-Cantillo, A and Hoyos-López, R},
title = {Molecular identification of Deinocerites atlanticus (Adames, 1971) (Diptera: Culicidae) using cytochrome oxidase I.},
journal = {Journal of vector borne diseases},
volume = {55},
number = {1},
pages = {63-65},
doi = {10.4103/0972-9062.234629},
pmid = {29916451},
issn = {0972-9062},
mesh = {Animals ; Colombia ; Culicidae/*classification/*genetics ; DNA/chemistry/isolation &amp; purification ; Electron Transport Complex IV/*genetics ; Female ; Haplotypes ; Phylogeny ; Sequence Analysis, DNA ; },
}
@article {pmid29915706,
year = {2018},
author = {Robicheau, BM and Chase, EE and Hoeh, WR and Harris, JL and Stewart, DT and Breton, S},
title = {Evaluating the utility of the female-specific mitochondrial f-orf gene for population genetic, phylogeographic and systematic studies in freshwater mussels (Bivalvia: Unionida).},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5007},
pmid = {29915706},
issn = {2167-8359},
abstract = {Freshwater mussels (order: Unionida) represent one of the most critically imperilled groups of animals; consequently, there exists a need to establish a variety of molecular markers for population genetics and systematic studies in this group. Recently, two novel mitochondrial protein-coding genes were described in unionoids with doubly uniparental inheritance of mtDNA. These genes are the f-orf in female-transmitted mtDNA and the m-orf in male-transmitted mtDNA. In this study, whole F-type mitochondrial genome sequences of two morphologically similar Lampsilis spp. were compared to identify the most divergent protein-coding regions, including the f-orf gene, and evaluate its utility for population genetic and phylogeographic studies in the subfamily Ambleminae. We also tested whether the f-orf gene is phylogenetically informative at the species level. Our preliminary results indicated that the f-orf gene could represent a viable molecular marker for population- and species-level studies in freshwater mussels.},
}
@article {pmid29915700,
year = {2018},
author = {Carew, ME and Coleman, RA and Hoffmann, AA},
title = {Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding?.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e4980},
pmid = {29915700},
issn = {2167-8359},
abstract = {BACKGROUND: High throughput DNA sequencing of bulk invertebrate samples or metabarcoding is becoming increasingly used to provide profiles of biological communities for environmental monitoring. As metabarcoding becomes more widely applied, new reference DNA barcodes linked to individual specimens identified by taxonomists are needed. This can be achieved through using DNA extraction methods that are not only suitable for metabarcoding but also for building reference DNA barcode libraries.<br><br>METHODS: In this study, we test the suitability of a rapid non-destructive DNA extraction method for metabarcoding of freshwater invertebrate samples.<br><br>RESULTS: This method resulted in detection of taxa from many taxonomic groups, comparable to results obtained with two other tissue-based extraction methods. Most taxa could also be successfully used for subsequent individual-based DNA barcoding and taxonomic identification. The method was successfully applied to field-collected invertebrate samples stored for taxonomic studies in 70% ethanol at room temperature, a commonly used storage method for freshwater samples.<br><br>DISCUSSION: With further refinement and testing, non-destructive extraction has the potential to rapidly characterise species biodiversity in invertebrate samples, while preserving specimens for taxonomic investigation.},
}
@article {pmid29915686,
year = {2018},
author = {Balech, B and Sandionigi, A and Manzari, C and Trucchi, E and Tullo, A and Licciulli, F and Grillo, G and Sbisà, E and De Felici, S and Saccone, C and D'Erchia, AM and Cesaroni, D and Casiraghi, M and Vicario, S},
title = {Tackling critical parameters in metazoan meta-barcoding experiments: a preliminary study based on coxI DNA barcode.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e4845},
pmid = {29915686},
issn = {2167-8359},
abstract = {Nowadays DNA meta-barcoding is a powerful instrument capable of quickly discovering the biodiversity of an environmental sample by integrating the DNA barcoding approach with High Throughput Sequencing technologies. It mainly consists of the parallel reading of informative genomic fragment/s able to discriminate living entities. Although this approach has been widely studied, it still needs optimization in some necessary steps requested in its advanced accomplishment. A fundamental element concerns the standardization of bioinformatic analyses pipelines. The aim of the present study was to underline a number of critical parameters of laboratory material preparation and taxonomic assignment pipelines in DNA meta-barcoding experiments using the cytochrome oxidase subunit-I (coxI) barcode region, known as a suitable molecular marker for animal species identification. We compared nine taxonomic assignment pipelines, including a custom in-house method, based on Hidden Markov Models. Moreover, we evaluated the potential influence of universal primers amplification bias in qPCR, as well as the correlation between GC content with taxonomic assignment results. The pipelines were tested on a community of known terrestrial invertebrates collected by pitfall traps from a chestnut forest in Italy. Although the present analysis was not exhaustive and needs additional investigation, our results suggest some potential improvements in laboratory material preparation and the introduction of additional parameters in taxonomic assignment pipelines. These include the correct setup of OTU clustering threshold, the calibration of GC content affecting sequencing quality and taxonomic classification, as well as the evaluation of PCR primers amplification bias on the final biodiversity pattern. Thus, careful attention and further validation/optimization of the above-mentioned variables would be required in a DNA meta-barcoding experimental routine.},
}
@article {pmid29912410,
year = {2018},
author = {Wang, R and Zhang, Z and Hu, X and Wu, S and Wang, J and Zhang, F},
title = {Molecular Detection and Genetic Diversity of Casuarina Moth, Lymantria xylina (Lepidoptera: Erebidae).},
journal = {Journal of insect science (Online)},
volume = {18},
number = {3},
pages = {},
pmid = {29912410},
issn = {1536-2442},
mesh = {Animals ; Base Sequence ; *DNA Barcoding, Taxonomic ; DNA Primers ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Moths/classification/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {The casuarina moth, Lymantria xylina Swinhoe (Lepidoptera: Erebidae), is an important pest in the Australian pine tree, Casuarina equisetifolia, forest in the coastal area of South China. At the same time, as a closely related species of Lymantria dispar L. (Lepidoptera: Erebidae), it is also a potential quarantine pest. In the present study, specific primers were designed for identification of L. xylina based on the COI barcoding sequence between L. xylina and four other common forest pests. A 569-bp fragment was successfully amplified from 40 L. xylina from five geographical populations in four Chinese provinces. In addition, even through the analysis came from five highly diverse populations of L. xylina, the genetic distances ranged from 0.001 to 0.031. The neighbor-joining tree showed that the species from Hubei and Chongqing were clustered within a distinct group.},
}
@article {pmid29912385,
year = {2018},
author = {Bengtsson-Palme, J and Richardson, RT and Meola, M and Wurzbacher, C and Tremblay, &#xc9;D and Thorell, K and Kanger, K and Eriksson, KM and Bilodeau, GJ and Johnson, RM and Hartmann, M and Nilsson, RH},
title = {Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {23},
pages = {4027-4033},
pmid = {29912385},
issn = {1367-4811},
mesh = {Computational Biology ; *DNA Barcoding, Taxonomic ; *Genetic Markers ; *Metagenomics ; *Phylogeny ; *Software ; },
abstract = {MOTIVATION: Correct taxonomic identification of DNA sequences is central to studies of biodiversity using both shotgun metagenomic and metabarcoding approaches. However, no genetic marker gives sufficient performance across all the biological kingdoms, hampering studies of taxonomic diversity in many groups of organisms. This has led to the adoption of a range of genetic markers for DNA metabarcoding. While many taxonomic classification software tools can be re-trained on these genetic markers, they are often designed with assumptions that impair their utility on genes other than the SSU and LSU rRNA. Here, we present an update to Metaxa2 that enables the use of any genetic marker for taxonomic classification of metagenome and amplicon sequence data.<br><br>RESULTS: We evaluated the Metaxa2 Database Builder on 11 commonly used barcoding regions and found that while there are wide differences in performance between different genetic markers, our software performs satisfactorily provided that the input taxonomy and sequence data are of high quality.<br><br>Freely available on the web as part of the Metaxa2 package at http://microbiology.se/software/metaxa2/.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid29910663,
year = {2018},
author = {Guimarães, EC and Brito, PS and Feitosa, LM and Carvalho-Costa, LF and Ottoni, FP},
title = {A new species of Hyphessobrycon Durbin from northeastern Brazil: evidence from morphological data and DNA barcoding (Characiformes, Characidae).},
journal = {ZooKeys},
volume = {},
number = {765},
pages = {79-101},
pmid = {29910663},
issn = {1313-2989},
abstract = {A new species of Hyphessobrycon is described for the upper Munim and Preguiças river basins, northeastern Brazil, supported by morphological and molecular species delimitation methods. This new species belongs to the Hyphessobryconsensu stricto group, as it has the three main diagnostic character states of this assemblage: presence of a dark brown or black blotch on the dorsal fin, absence of a black midlateral stripe on its flank and the position of Weberian apparatus upward horizontal through dorsal margin of operculum. Our phylogenetic analysis also supported the allocation of the new species in this group; however, it was not possible to recover the species sister-group. Pristella maxillaris and Moenkhausia hemigrammoides were recovered as the sister-clade of the Hyphessobryconsensu stricto group.},
}
@article {pmid29908074,
year = {2018},
author = {Gómez, F and Wang, L and Lin, S},
title = {Morphology and molecular phylogeny of epizoic araphid diatoms on marine zooplankton, including Pseudofalcula hyalina gen. &amp; comb. nov. (Fragilariophyceae, Bacillariophyta).},
journal = {Journal of phycology},
volume = {54},
number = {4},
pages = {557-570},
doi = {10.1111/jpy.12760},
pmid = {29908074},
issn = {1529-8817},
mesh = {Animals ; DNA, Ribosomal/analysis ; Diatoms/*classification/cytology/genetics/ultrastructure ; Microscopy, Electron, Scanning ; Phylogeny ; Phytoplankton/classification/cytology/genetics/ultrastructure ; Ribulose-Bisphosphate Carboxylase/analysis ; Zooplankton/*classification/cytology/genetics/ultrastructure ; },
abstract = {Some diatoms are able to colonize as epibionts on their potential zooplankton predators. Here, we report Pseudohimantidium pacificum living on the copepod Corycaeus giesbrechti and as a new finding on Oithona nana, Protoraphis atlantica living on the copepod Pontellopsis brevis, Protoraphis hustedtiana on the cypris larvae of barnacles, and Falcula hyalina on the copepod Acartia lilljeborgii. The epizoic diatoms were able to grow as free-living forms under culture conditions. Pseudohimantidium pacificum and P. atlantica appeared as the most derived species from their benthic diatom ancestors. The mucilage pad or stalk of the strains of these species showed important morphological distinction when compared with their epizoic forms. Barnacle larvae explore benthic habitats before settlement, and epibiosis on them is an example where P. hustedtiana profits from the host behavior for dispersal of its benthic populations. Molecular phylogenies based on the SSU rRNA and RuBisCO large subunit (rbcL) gene sequences revealed F. hyalina as an independent lineage within the Fragilariales (Tabularia, Catacombas, and others), consistent with its morphological distinction in the low number of rows (≤6) in the ocellulimbus, among other features. We propose the transfer of F. hyalina to the genus Pseudofalcula gen. nov. Molecular phylogeny suggests a single order for the members of the Cyclophorales and the Protoraphidales, and that the epibioses of araphid diatoms on marine zooplankton have been independently acquired several times. These clades are constituted of both epizoic and epiphytic/epilithic forms that evidence a recent acquisition of the epizoic modus vivendi.},
}
@article {pmid29906795,
year = {2018},
author = {Greenberg, RG and Smith, PB and Bose, C and Clark, RH and Cotten, CM and DeRienzo, C},
title = {National Survey of Neonatal Intensive Care Unit Medication Safety Practices.},
journal = {American journal of perinatology},
volume = {35},
number = {14},
pages = {1419-1422},
doi = {10.1055/s-0038-1660837},
pmid = {29906795},
issn = {1098-8785},
support = {R21 HD080606/HD/NICHD NIH HHS/United States ; },
mesh = {Adverse Drug Reaction Reporting Systems/organization &amp; administration ; Drug-Related Side Effects and Adverse Reactions/*prevention &amp; control/*therapy ; Humans ; Infant, Newborn ; Intensive Care Units, Neonatal/*organization &amp; administration ; Medication Errors/*prevention &amp; control ; Quality Assurance, Health Care ; Safety Management/*standards ; Surveys and Questionnaires ; United States ; },
abstract = {OBJECTIVE: We conducted a detailed survey to identify medication safety practices among a large network of United States neonatal intensive care units (NICUs).<br><br>METHODS: We created a 53-question survey to assess 300 U.S. NICU's demographics, medication safety practices, adverse drug event (ADE) reporting, and ADE response plans.<br><br>RESULTS: Among the 164 (55%) NICUs that responded to the survey, more than 85% adhered to practices including use of electronic health records, computerized physician order entry, and clinical decision support; fewer reported adopting barcoding, formal safety surveys, and formal culture training; 137 of 164 (84%) developed at least one NICU-specific order-set with a median of 10 order-sets.<br><br>CONCLUSION: Among our survey of 164 NICUs, we found that many safety practices remain unused. Understanding safety practice variation is critical to prevent ADEs and other negative infant outcomes. Future efforts should focus on linking safety practices identified from our survey with ADEs and infant outcomes.},
}
@article {pmid29906604,
year = {2018},
author = {Sun, Y and Wong, E and Ahyong, ST and Williamson, JE and Hutchings, PA and Kupriyanova, EK},
title = {Barcoding and multi-locus phylogeography of the globally distributed calcareous tubeworm genus Hydroides Gunnerus, 1768 (Annelida, Polychaeta, Serpulidae).},
journal = {Molecular phylogenetics and evolution},
volume = {127},
number = {},
pages = {732-745},
doi = {10.1016/j.ympev.2018.06.021},
pmid = {29906604},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; *Genetic Loci ; Genetic Variation ; Geography ; *Internationality ; Phylogeny ; *Phylogeography ; Polychaeta/anatomy &amp; histology/*classification/*genetics ; Time Factors ; },
abstract = {Hydroides is a large and diverse group of calcareous tubeworms (Serpulidae, Annelida) recognised by a distinctive but variable two-tiered operculum. Despite considerable research using several species of Hydroides as models in ecological and biofouling studies, phylogenetic and biogeographic relationships within the genus are still poorly understood. Using combined mitochondrial (COI, cytochrome b) and nuclear (18S, 28S and ITS) gene markers for 284 individuals of 45 morphospecies of Hydroides, we investigated the global phylogenetic and biogeographic relationships within the genus. Phylogenetic topologies were well supported and indicated high genetic diversity within Hydroides, revealing potential cryptic species. Present results also include the first COI barcoding data enabling rapid and effective species identification of Hydroides on a global scale. Phylogenetic relationships within Hydroides were more concordant with geographical distributions than morphological similarity of their opercula. Molecular divergence estimates suggested the origin and subsequent diversification in the western Tethys Sea followed by a shift of the historical centre of diversity from the Indo-Mediterranean region to the central Indo-Pacific during the last 50 million years. Further studies on population genetics of species consisting of multiple lineages would provide a better understanding on the status of potential cryptic species. Furthermore, paleogeographic studies based on fossil Hydroides tubes would provide evidence to test this biogeographic hypothesis.},
}
@article {pmid29904663,
year = {2018},
author = {Loureiro, LO and Lim, BK and Engstrom, MD},
title = {Molecular data on the CO1 and beta fibrinogen gene in the evolutionary relationships of the mastiff bat (Chiroptera, Molossidae, Molossus).},
journal = {Data in brief},
volume = {18},
number = {},
pages = {1609-1613},
pmid = {29904663},
issn = {2352-3409},
abstract = {Molossus is one of the most diverse genera of free-tailed bats in the pantropical family Molossidae and occurs though all the Neotropics. Nevertheless, the taxonomy and phylogeny of this group is poorly understood. Here, we present the data on evolutionary relationships of Molossus based on DNA barcodes of COI gene from 346 specimens of Molossus and its sister genus Promops and another New World molossid Eumops. Of these specimens, 50 are new sequences and 296 were obtained from GenBank. In addition, the nuclear gene beta fibrinogen was sequenced from a subset of 35 specimens. These data provide the basis for further exploration and understanding of the phylogenetic relationships of the genus Molossus (Loureiro et al., 2018) [1].},
}
@article {pmid29900810,
year = {2018},
author = {Morand, S},
title = {Advances and challenges in barcoding of microbes, parasites, and their vectors and reservoirs.},
journal = {Parasitology},
volume = {145},
number = {5},
pages = {537-542},
doi = {10.1017/S0031182018000884},
pmid = {29900810},
issn = {1469-8161},
mesh = {Animals ; Bacteria/*genetics ; DNA Barcoding, Taxonomic/*methods ; Disease Reservoirs ; Disease Vectors ; High-Throughput Nucleotide Sequencing ; Parasites/*genetics ; },
abstract = {DNA barcoding is now a common tool in parasitology and epidemiology, which require good methods for identification not only of parasites and pathogens but vectors and reservoirs. This special issue presents some advances and challenges in barcoding of microbes, parasites, and their vectors and reservoirs. DNA barcoding found new applications in disease ecology, conservation parasitology, environmental parasitology and in paleoparasitology. New technologies such as next-generation sequencing and matrix-assisted laser desorption-ionization time-of-flight have made it now possible to investigate large samples of specimens. By allowing the investigation of parasites at the interface between environment, biodiversity, animal and human health, barcoding and biobanking have important policy outcomes as well as ethics and legal implications. The special issue 'Advances and challenges in the barcoding of parasites, vectors and reservoirs' illustrates some recent advances and proposes new avenues for research in barcoding in parasitology.},
}
@article {pmid29899678,
year = {2018},
author = {Cancian de Araujo, B and Schmidt, S and Schmidt, O and von Rintelen, T and Kilmaskossu, A and Panjaitan, R and Balke, M},
title = {From field courses to DNA barcoding data release for West Papua - making specimens and identifications from university courses more sustainable.},
journal = {Biodiversity data journal},
volume = {},
number = {6},
pages = {e25237},
pmid = {29899678},
issn = {1314-2828},
}
@article {pmid29899659,
year = {2018},
author = {Vu, HT and Huynh, P and Tran, HD and Le, L},
title = {In Silico Study on Molecular Sequences for Identification of Paphiopedilum Species.},
journal = {Evolutionary bioinformatics online},
volume = {14},
number = {},
pages = {1176934318774542},
pmid = {29899659},
issn = {1176-9343},
abstract = {Our study searched all available sequences of Paphiopedilum from NCBI (National Center for Biotechnology Information) and tested for their species resolution capability in single as well as in combination forms. A total of 28 loci were applied for analyses in the study. From the nuclear genome, the highest resolution was of LFY, followed by ACO, DEF4, and RAD51. These 4 loci were found to be even better than the popular region ITS for Paphiopedilum identification. Among the chloroplast regions, the intergenic spacer atpB-rbcL gave the highest species resolution (76.7%), followed by matK, trnL, rpoC2, and ycf1. The divergence of CHS, XDH, 18S, Nad1, ccsA, rbcL, and ycf2 was very low and should not be used as identifying markers for Paphiopedilum. In addition, 2-locus combinations could improve significantly the resolving capability for the genus, in which 14/36 data sets could be resolved completely (100%) with interspecies relationships. The indel information was also effective supporting data for molecular discrimination of species.},
}
@article {pmid29899599,
year = {2018},
author = {Kulczycka, A and Łukomska-Kowalczyk, M and Zakryś, B and Milanowski, R},
title = {PCR identification of toxic euglenid species Euglena sanguinea.},
journal = {Journal of applied phycology},
volume = {30},
number = {3},
pages = {1759-1763},
pmid = {29899599},
issn = {0921-8971},
abstract = {Euglena sanguinea Ehrenberg is the only known species of euglenids which forms toxic blooms causing tangible losses to fish farms. Euglena sanguinea produces euglenophycin, a toxin similar in structure to solenopsin, an alkaloid found in fire ant venom. It was proved that euglenophycin exhibits not only ichthyotoxic but also herbicidal and anticancer activity. Recently, a specific mass spectrometric method of identification and quantitation of euglenophycin was developed to facilitate monitoring of that toxin in freshwater ponds. Despite the recent taxonomic verifications, proper identification of E. sanguinea is still difficult, especially for less experienced researchers. Herein, we describe a simple method based on nested PCR amplification of the nSSU rDNA fragments to identify a single E. sanguinea cell and its detection in a sample of water. The method will further facilitate monitoring of water reservoirs, especially estimating the risk of toxic blooms.},
}
@article {pmid29899412,
year = {2018},
author = {Kanturski, M and Lee, Y and Choi, J and Lee, S},
title = {DNA barcoding and a precise morphological comparison revealed a cryptic species in the Nippolachnus piri complex (Hemiptera: Aphididae: Lachninae).},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {8998},
pmid = {29899412},
issn = {2045-2322},
mesh = {Animals ; Aphids/anatomy &amp; histology/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Haplotypes ; Host-Parasite Interactions ; Insect Proteins/genetics ; Microscopy, Electron, Scanning ; Phylogeny ; Plants/classification/*parasitology ; Species Specificity ; },
abstract = {Nippolachnus is a small Palaearctic-Oriental genus of very characteristic aphids that live on the leaves of woody Rosaceae. One species, N. piri, has hitherto been regarded to be widely distributed and relatively polyphagous. Members of this genus are considered to be easy to recognize due to the absence of the ocular tubercle and triommatidia on the head. We conducted research on the morphology and generic characters of Nippolachnus piri complex using scanning electron microscopy (for the first time) and DNA barcoding. We analyzed N. piri populations on Pyrus and other plants (Eriobotrya, Rhaphiolepis and Sorbus) in Japan and the Republic of Korea. Specifically, a high genetic divergence value was found between the N. piri populations associated with different host plants. SEM investigation of the head capsule revealed that a triommatidium is present under the compound eye, despite their lack of an ocular tubercle. We propose Nippolachnus micromeli Shinji, 1924 stat. nov. as a cryptic species in the N. piri complex based on a morphological comparison, DNA barcoding and different host-plant associations. Illustrations and descriptions of studied species are given. Morphological keys to the apterae and alatae of all known species of the genus Nippolachnus are also provided.},
}
@article {pmid29896045,
year = {2018},
author = {Goulding, TC and Khalil, M and Tan, SH and Dayrat, B},
title = {Integrative taxonomy of a new and highly-diverse genus of onchidiid slugs from the Coral Triangle (Gastropoda, Pulmonata, Onchidiidae).},
journal = {ZooKeys},
volume = {},
number = {763},
pages = {1-111},
pmid = {29896045},
issn = {1313-2989},
abstract = {A new genus of onchidiid slugs, Wallaconchis Goulding &amp; Dayrat, gen. n., is described, including ten species. Five species were previously described but known only from the type material: Wallaconchis ater (Lesson, 1830), W. graniferum (Semper, 1880), W. nangkauriense (Plate, 1893), W. buetschlii (Stantschinsky, 1907), and W. gracile (Stantschinsky, 1907), all of which were originally classified in Onchidium Buchannan, 1800. Many new records are provided for these five species, which greatly expand their known geographic distributions. Five species are new: Wallaconchis achleitneri Goulding, sp. n., W. comendadori Goulding &amp; Dayrat, sp. n., W. melanesiensis Goulding &amp; Dayrat, sp. n., W. sinanui Goulding &amp; Dayrat, sp. n., and W. uncinus Goulding &amp; Dayrat, sp. n. Nine of the ten Wallaconchis species are found in the Coral Triangle (eastern Indonesia and the Philippines). Sympatry is high, with up to six species found on the island of Bohol (Philippines) and eight species overlapping in northern Sulawesi (Indonesia). Wallaconchis is distinguished from other onchidiids by its bright dorsal colors (red, yellow, orange) but those are extremely variable and not useful for specific identification. Internally, the reproductive system can be used to identify all Wallaconchis species. The copulatory organs of Wallaconchis species are especially diverse compared to other onchidiid genera, and the possible role of reproductive incompatibility in species diversification is discussed. All specimens examined were freshly collected for the purpose of a worldwide revision of the Onchidiidae Rafinesque, 1815. The species are well delineated using DNA sequences and comparative anatomy. Mitochondrial DNA analysis yields thirteen molecular units separated by a large barcode gap, while nuclear DNA yields nine units. By integrating nuclear DNA and mitochondrial DNA with morphology, ten species are recognized. The natural history of each species (e.g., the microhabitat where they are found) is also documented. Nomenclature is addressed thoroughly (the types of all onchidiid species were examined, lectotypes were designated when needed, nomina dubia are discussed). Morphological characters, transitions to new microhabitats, and diversification processes are discussed in the context of a robust molecular phylogeny.},
}
@article {pmid29893795,
year = {2018},
author = {Lusinska, J and Majka, J and Betekhtin, A and Susek, K and Wolny, E and Hasterok, R},
title = {Chromosome identification and reconstruction of evolutionary rearrangements in Brachypodium distachyon, B. stacei and B. hybridum.},
journal = {Annals of botany},
volume = {122},
number = {3},
pages = {445-459},
pmid = {29893795},
issn = {1095-8290},
mesh = {Brachypodium/*genetics ; Chromosomes, Plant/*genetics ; DNA, Ribosomal/genetics ; Diploidy ; *Gene Rearrangement ; Genome, Plant/*genetics ; In Situ Hybridization, Fluorescence ; Karyotype ; Karyotyping ; Phylogeny ; Physical Chromosome Mapping ; },
abstract = {BACKGROUND AND AIMS: The Brachypodium genus represents a useful model system to study grass genome organization. Palaeogenomic analyses (e.g. Murat F, Armero A, Pont C, Klopp C, Salse J. 2017. Reconstructing the genome of the most recent common ancestor of flowering plants. Nature Genetics49: 490-496) have identified polyploidization and dysploidy as the prime mechanisms driving the diversity of plant karyotypes and nested chromosome fusions (NCFs) crucial for shaping grass chromosomes. This study compares the karyotype structure and evolution in B. distachyon (genome Bd), B. stacei (genome Bs) and in their putative allotetraploid B. hybridum (genomes BdBs).<br><br>METHODS: Brachypodium chromosomes were measured and identified using multicolour fluorescence in situ hybridization (mcFISH). For higher resolution, comparative chromosome barcoding was developed using sets of low-repeat, physically mapped B. distachyon-derived bacterial artificial chromosome (BAC) clones.<br><br>KEY RESULTS: All species had rather small chromosomes, and essentially all in the Bs genome were morphometrically indistinguishable. Seven BACs combined with two rDNA-based probes provided unambiguous and reproducible chromosome discrimination. Comparative chromosome barcoding revealed NCFs that contributed to the reduction in the x = 12 chromosome number that has been suggested for the intermediate ancestral grass karyotype. Chromosome Bd3 derives from two NCFs of three ancestral chromosomes (Os2, Os8, Os10). Chromosome Bs6 shows an ancient Os8/Os10 NCF, whilst Bs4 represents Os2 only. Chromosome Bd4 originated from a descending dysploidy that involves two NCFs of Os12, Os9 and Os11. The specific distribution of BACs along Bs9 and Bs5, in both B. stacei and B. hybridum, suggests a Bs genome-specific Robertsonian rearrangement.<br><br>CONCLUSIONS: mcFISH-based karyotyping identifies all chromosomes in Brachypodium annuals. Comparative chromosome barcoding reveals rearrangements responsible for the diverse organization of Bd and Bs genomes and provides new data regarding karyotype evolution since the split of the two diploids. The fact that no chromosome rearrangements were observed in B. hybridum compared with the karyotypes of its phylogenetic ancestors suggests prolonged genome stasis after the formation of the allotetraploid.},
}
@article {pmid29891996,
year = {2018},
author = {Zhao, ML and Song, Y and Ni, J and Yao, X and Tan, YH and Xu, ZF},
title = {Comparative chloroplast genomics and phylogenetics of nine Lindera species (Lauraceae).},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {8844},
pmid = {29891996},
issn = {2045-2322},
mesh = {China ; Chloroplasts/*genetics ; DNA, Chloroplast/chemistry/genetics ; Genes, Chloroplast ; Genetic Variation ; *Genome, Chloroplast ; Genomics ; Lindera/*classification/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Lindera, a core genus of the Lauraceae family, has important economic uses in eastern Asia and North America. However, its historical diversification has not been clarified. In this study, we report nine newly sequenced Lindera plastomes. The plastomes of these nine Lindera species range from 152,211 (L. nacusua) to 152,968 bp (L. metcalfiana) in length, similar to that of another Lauraceae species, Litsea glutinosa (152,618 bp). The length variation of these plastomes derived from the length variation in the loci ycf1, ycf2, ψycf1, and ndhF-ψycf1. Comparing our sequences with other available plastomes in the Lauraceae indicated that eight hypervariable loci, ihbA-trnG, ndhA, ndhF-rpl32, petA-psbJ, psbK-psbI, rps16, trnS-trnG, and ycf1, could serve as DNA barcodes for species delineation, and that the inverted repeats (IRs) showed contraction/expansion. Further phylogenetic analyses were performed using 32 complete plastomes of Lauraceae and seven barcodes from 14 additional species of Lindera and related species in the core Lauraceae. The results showed that these Lindera species grouped into two or four sub-clades, and that two Litsea species and Laurus nobilis were located in the same sub-clade as five Lindera species. These data support a close relationship between the genera Laurus, Lindera, and Litsea, and suggest that Lindera is polyphyletic.},
}
@article {pmid29890665,
year = {2018},
author = {Jiang, L and Li, M and Zhao, F and Chu, S and Zha, L and Xu, T and Peng, H and Zhang, W},
title = {Molecular Identification and Taxonomic Implication of Herbal Species in Genus Corydalis (Papaveraceae).},
journal = {Molecules (Basel, Switzerland)},
volume = {23},
number = {6},
pages = {},
pmid = {29890665},
issn = {1420-3049},
mesh = {DNA Barcoding, Taxonomic ; Genes, Plant ; Medicine, Chinese Traditional ; Papaveraceae/*classification ; Phylogeny ; Species Specificity ; },
abstract = {Many species of Corydalis (Papaveraceae) have been used as medicinal plants in East Asia, and the most well-known species are Corydalis yanhusuo and C. decumbens in the Pharmacopoeia of China. However, authentication of these species remains problematic because of their high morphological variation. Here, we selected 14 closely related species and five genomic regions (chloroplast: matK, trnG, rbcL, psbA-trnH; nuclear: ITS) to explore the utility of DNA barcoding for authenticating these herbs. In addition, the Poisson tree process (PTP) and automatic barcode gap discovery (ABGD) were also used and compared with DNA barcoding. Our results showed that the ITS region was not suitable for molecular analysis because of its heterogeneous nature in Corydalis. In contrast, matK was an ideal region for species identification because all species could be resolved when matK was used along with the other three chloroplast regions. We found that at least five traditional identified species were lumped into one genetic species by ABGD and PTP methods; thus, highlighting the overestimation of species diversity using the morphological approach. In conclusion, our first attempt of molecular analysis of Corydalis herbs presented here successfully resolved the identification of medicinal species and encouraged their taxonomic re-assessment.},
}
@article {pmid29890621,
year = {2018},
author = {Jensen-Vargas, E and Marizzi, C},
title = {DNA Barcoding for Identification of Consumer-Relevant Fungi Sold in New York: A Powerful Tool for Citizen Scientists?.},
journal = {Foods (Basel, Switzerland)},
volume = {7},
number = {6},
pages = {},
pmid = {29890621},
issn = {2304-8158},
abstract = {Although significant progress has been made in our understanding of fungal diversity, identification based on phenotype can be difficult, even for trained experts. Fungi typically have a cryptic nature and can have a similar appearance to distantly related species. Moreover, the appearance of industrially processed mushrooms complicates species identification, as they are often sold sliced and dried. Here we present a small-scale citizen science project, wherein the participants generated and analyzed DNA sequences from fruiting bodies of dried and fresh fungi that were sold for commercial use in New York City supermarkets. We report positive outcomes and the limitations of a youth citizen scientist, aiming to identify dried mushrooms, using established DNA barcoding protocols and exclusively open-access data analysis tools for species identification. Our results indicate that the single-locus nuclear ribosomal internal transcribed spacer (ITS) DNA barcoding approach allowed for identification of only a subset of all of the samples at the species level, although the generated high-quality DNA barcodes were submitted to three different databases. Our results highlight the need for a curated, centralized, and open access ITS reference database that allows rapid third-party annotations for the benefit of both traditional research as well as the emerging citizen science community.},
}
@article {pmid29889211,
year = {2018},
author = {Demaree, B and Weisgerber, D and Lan, F and Abate, AR},
title = {An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {135},
pages = {},
pmid = {29889211},
issn = {1940-087X},
support = {DP2 AR068129/AR/NIAMS NIH HHS/United States ; R01 EB019453/EB/NIBIB NIH HHS/United States ; R01 HG008978/HG/NHGRI NIH HHS/United States ; R21 HG007233/HG/NHGRI NIH HHS/United States ; },
mesh = {Genomics/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Microfluidics/*methods ; },
abstract = {Sequencing technologies have undergone a paradigm shift from bulk to single-cell resolution in response to an evolving understanding of the role of cellular heterogeneity in biological systems. However, single-cell sequencing of large populations has been hampered by limitations in processing genomes for sequencing. In this paper, we describe a method for single-cell genome sequencing (SiC-seq) which uses droplet microfluidics to isolate, amplify, and barcode the genomes of single cells. Cell encapsulation in microgels allows the compartmentalized purification and tagmentation of DNA, while a microfluidic merger efficiently pairs each genome with a unique single-cell oligonucleotide barcode, allowing >50,000 single cells to be sequenced per run. The sequencing data is demultiplexed by barcode, generating groups of reads originating from single cells. As a high-throughput and low-bias method of single-cell sequencing, SiC-seq will enable a broader range of genomic studies targeted at diverse cell populations.},
}
@article {pmid29887737,
year = {2018},
author = {Li, F and Xu, X and Zhang, Z and Liu, F and Zhang, H and Li, D},
title = {Two new species of the purse-web spider genus Atypus Latreille, 1804 from Hainan Island, China (Araneae, Atypidae).},
journal = {ZooKeys},
volume = {},
number = {762},
pages = {47-57},
pmid = {29887737},
issn = {1313-2989},
abstract = {Two species of the purse-web spider genus Atypus Latreille, 1804 collected from Hainan Island, China, are diagnosed and described as new to science based on genital morphology, A. baotingensissp. n. (♂♀) and A. jianfengensissp. n. (♀). The DNA barcodes of the two species are also provided for future use.},
}
@article {pmid29885808,
year = {2018},
author = {Porwollik, S and Genovese, K and Chu, W and Loneragan, GH and Edrington, T and McClelland, M},
title = {Neutral barcoding of genomes reveals the dynamics of Salmonella colonization in cattle and their peripheral lymph nodes.},
journal = {Veterinary microbiology},
volume = {220},
number = {},
pages = {97-106},
doi = {10.1016/j.vetmic.2018.05.007},
pmid = {29885808},
issn = {1873-2542},
support = {P30 CA062203/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Bacterial Load/genetics ; Cattle/*microbiology ; Cattle Diseases/microbiology ; Colony Count, Microbial ; *Expressed Sequence Tags ; Feces/microbiology ; Gastrointestinal Tract/microbiology ; Genome, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing ; Lymph Nodes/*microbiology ; Salmonella/*genetics/physiology ; Salmonella Infections, Animal/epidemiology/*microbiology ; },
abstract = {Feedlot cattle often contain Salmonella. The number of bacteria that initiate colonization of different cattle organs and the bacterial migration within these large animals are poorly understood. To investigate these questions, we constructed wild-type isogenic tagged strains (WITS) of Salmonella by inserting 21-base barcodes flanked by Illumina sequencing primers into a neutral genome location. We then delivered several different pools of uniquely barcoded clones orally and into multiple intradermal sites, in individual Holstein steers, and subsequently performed Salmonella-directed sequence tag-based analysis of microbial populations (STAMP). Using high-throughput sequencing of the barcodes of Salmonella grown from steer lymph nodes, organs and feces, we monitored how individual barcoded clones travel from different entry sites within animals. Data showed that gastrointestinal colonization was established by up to hundreds of Salmonella founder cells, whereas peripheral lymph nodes were usually colonized by very low numbers of founding bacteria, often originating from the nearest draining intradermal delivery site. Transmission of Salmonella from the gastrointestinal tract to the lymphatic system was frequently observed, whereas entry of intradermally delivered bacteria into the gut was rare. Bacteria undergo limited extraintestinal proliferation within or prior to arrival at peripheral lymph nodes. Overall, the application of the STAMP technique facilitated characterization of the migration routes and founder population size of Salmonella within feedlot cattle and their organs and lymph nodes in unprecedented detail.},
}
@article {pmid29885050,
year = {2019},
author = {Doerder, FP},
title = {Barcodes Reveal 48 New Species of Tetrahymena, Dexiostoma, and Glaucoma: Phylogeny, Ecology, and Biogeography of New and Established Species.},
journal = {The Journal of eukaryotic microbiology},
volume = {66},
number = {1},
pages = {182-208},
doi = {10.1111/jeu.12642},
pmid = {29885050},
issn = {1550-7408},
mesh = {Hymenostomatida/*classification/genetics/*physiology ; *Life History Traits ; *Phylogeny ; Tetrahymena/classification/genetics/physiology ; Tetrahymenina/classification/genetics/physiology ; },
abstract = {Tetrahymena mitochondrial cox1 barcodes and nuclear SSUrRNA sequences are particularly effective at distinguishing among its many cryptic species. In a project to learn more about Tetrahymena natural history, the majority of >1,000 Tetrahymena-like fresh water isolates were assigned to established Tetrahymena species with the remaining assigned to 37 new species of Tetrahymena, nine new species of Dexiostoma and 12 new species of Glaucoma. Phylogenetically, all but three Tetrahymena species belong to the well-established "australis" or "borealis" clades; the minority forms a divergent "paravorax" clade. Most Tetrahymena species are micronucleate, but others are exclusively amicronucleate. The self-splicing intron of the LSUrRNA precursor is absent in Dexiostoma and Glaucoma and was likely acquired subsequent to the "australis/borealis" split; in some instances, its sequence is diagnostic of species. Tetrahymena americanis, T. elliotti, T. gruchyi n. sp., and T. borealis, together accounted for >50% of isolates, consistent with previous findings for established species. The biogeographic range of species found previously in Austria, China, and Pakistan was extended to the Nearctic; some species show evidence of population structure consistent with endemism. Most species were most frequently collected from ponds or lakes, while others, particularly Dexiostoma species, were collected most often from streams or rivers. The results suggest that perhaps hundreds of species remain to be discovered, particularly if collecting is global and includes hosts of parasitic forms.},
}
@article {pmid29884089,
year = {2018},
author = {Zhao, Z and Henowitz, L and Zweifach, A},
title = {A Multiplexed Assay That Monitors Effects of Multiple Compound Treatment Times Reveals Candidate Immune-Enhancing Compounds.},
journal = {SLAS discovery : advancing life sciences R &amp; D},
volume = {23},
number = {7},
pages = {646-655},
pmid = {29884089},
issn = {2472-5560},
support = {R01 AI121069/AI/NIAID NIH HHS/United States ; },
mesh = {*Biological Assay/methods ; Dose-Response Relationship, Drug ; Drug Discovery/*methods ; Drug Evaluation, Preclinical ; Flow Cytometry ; *High-Throughput Screening Assays ; Humans ; Immunologic Factors/*pharmacology ; Immunomodulation/*drug effects ; Small Molecule Libraries ; T-Lymphocytes, Cytotoxic/drug effects/immunology/metabolism ; },
abstract = {We previously developed a flow cytometry assay that monitored lytic granule exocytosis in cytotoxic T lymphocytes stimulated by contacting beads coated with activating anti-CD3 antibodies. That assay was multiplexed in that responses of cells that did or did not receive the activating stimulus were distinguished via changes in light scatter accompanying binding of cells to beads, allowing us to discriminate compounds that activate responses on their own from compounds that enhance responses in cells that received the activating stimulus, all within a single sample. Here we add a second dimension of multiplexing by developing means to assess in a single sample the effects of treating cells with test compounds for different times. Bar-coding cells before adding them to test wells lets us determine compound treatment time while also monitoring activation status and response amplitude at the point of interrogation. This multiplexed assay is suitable for screening 96-well plates. We used it to screen compounds from the National Cancer Institute, identifying several compounds that enhance anti-LAMP1 responses. Multiple-treatment-time (MTT) screening enabled by bar-coding and read via high-throughput flow cytometry may be a generally useful method for facilitating the discovery of compounds of interest.},
}
@article {pmid29882805,
year = {2018},
author = {De Luca, A and Sibilio, G and De Luca, P and Del Guacchio, E},
title = {DNA Barcoding to Confirm the Morphological Identification of the Coral Trees (Erythrina spp., Fabaceae) in the Ancient Gardens of Naples (Campania, Italy).},
journal = {Plants (Basel, Switzerland)},
volume = {7},
number = {2},
pages = {},
pmid = {29882805},
issn = {2223-7747},
abstract = {The coral trees (genus Erythrina) have been fostering great interest among the botanists and gardeners of Naples, since their arrival in Europe in the second half of the 18th century. Numerous species were present in the royal and private botanical gardens of the region, but their number has decreased today. The purpose of this work was to verify which species occur nowadays in the public areas of Naples and associate them with the historical information about their introduction. The identification was carried out also by molecular methods, by means of sequencing nuclear and chloroplast DNA markers. The comparison of the sequences obtained for the specimens present in Naples with those present in the literature, together with a morphological examination, allowed us to identify with accuracy the species anciently introduced or nowadays cultivated in Naples.},
}
@article {pmid29882648,
year = {2018},
author = {Luan, C and Wang, H and Han, Q and Ma, X and Zhang, D and Xu, Y and Chen, B and Li, M and Zhao, Y},
title = {Folic Acid-Functionalized Hybrid Photonic Barcodes for Capture and Release of Circulating Tumor Cells.},
journal = {ACS applied materials &amp; interfaces},
volume = {10},
number = {25},
pages = {21206-21212},
doi = {10.1021/acsami.8b06882},
pmid = {29882648},
issn = {1944-8252},
mesh = {Cell Count ; Cell Line, Tumor ; Folic Acid ; Humans ; *Neoplastic Cells, Circulating ; Reproducibility of Results ; },
abstract = {Recovery of circulating tumor cells (CTCs) from cancer patients by an efficient CTCs capture and release method can greatly increase their application in diagnostics and treatment of cancers. In this paper, we presented a folic acid (FA)-functionalized hybrid photonic barcode for capture and release of CTCs. The hybrid photonic barcodes were formed by two nano-ordered parts, poly(ethylene glycol) diacrylate (PEGDA) inverse opal structure for sustaining integrity and methacrylated gelatin (GelMA) gel filler for conjugating FA molecules to mediate cell capture. The nano-ordered structures of the hybrid photonic barcodes not only increased contact area, but also decreased steric hindrance among FA molecules. Thus, the topographic interaction between the barcodes and CTCs was greatly enhanced. In addition, GelMA gel was soft and extracellular matrix (ECM) alike, which was beneficial to decrease impairment to CTCs during the CTCs-barcode interaction as well as preserving their viability. Demonstrated by four CTCs types, Hela (epithelial tissue, folate receptor positive, FR+), A02 (bone marrow, FR+), Raji (lymphoid tissue, FR+), and A549 (epithelial tissue, folate receptor negative, FR-), FR+ CTCs could be captured efficiently with reliability and specificity. The captured cells could be controllably released with high viability just by quick trypsinization. The whole processes were simple and efficient. These features indicated that the FA-functionalized hybrid photonic barcodes were promising for full recovery of CTCs from cancer patients, which was important for diagnosis and treatment of cancer.},
}
@article {pmid29882402,
year = {2018},
author = {Li, F and Lin, Y and Lau, A and Tang, Y and Chen, J and Le, XC},
title = {Binding-Induced Molecular Amplifier as a Universal Detection Platform for Biomolecules and Biomolecular Interaction.},
journal = {Analytical chemistry},
volume = {90},
number = {14},
pages = {8651-8657},
doi = {10.1021/acs.analchem.8b01985},
pmid = {29882402},
issn = {1520-6882},
mesh = {Animals ; Biosensing Techniques/instrumentation/*methods ; Cattle ; DNA/*chemistry ; Humans ; Protein Interaction Mapping/instrumentation/*methods ; Protein Interaction Maps ; },
abstract = {Techniques that detect multiple classes of biomolecules and biomolecular interactions from biological or patient samples are highly desirable for applications ranging from accurate disease diagnosis to deciphering comprehensive biological processes. Because of the large variations in target recognition, signal transduction, and instrumentation, it is technically challenging to generalize a single detection method to a diverse range of analytical targets. Herein, we introduce a binding-induced molecular amplifier (BIMA) strategy that translates a variety of biomolecules and biomolecular interactions into unified predesigned DNA barcode in homogeneous solutions. On the basis of a three-dimensional DNA-walking mechanism, BIMA not only translates various targets into a unified barcode but also amplifies the translation by generating multiple barcode molecules in response to a single input target molecule. Using this strategy, we have successfully expanded the uses of a simple toehold-mediated strand displacement beacon for the sensitive detection of multiple classes of targets, including nucleic acids, proteins, and protein-protein interactions.},
}
@article {pmid29881688,
year = {2018},
author = {Xin, T and Xu, Z and Jia, J and Leon, C and Hu, S and Lin, Y and Ragupathy, S and Song, J and Newmaster, SG},
title = {Biomonitoring for traditional herbal medicinal products using DNA metabarcoding and single molecule, real-time sequencing.},
journal = {Acta pharmaceutica Sinica. B},
volume = {8},
number = {3},
pages = {488-497},
pmid = {29881688},
issn = {2211-3835},
abstract = {Global concerns have been paid to the potential hazard of traditional herbal medicinal products (THMPs). Substandard and counterfeit THMPs, including traditional Chinese patent medicine, health foods, dietary supplements, etc. are potential threats to public health. Recent marketplace studies using DNA barcoding have determined that the current quality control methods are not sufficient for ensuring the presence of authentic herbal ingredients and detection of contaminants/adulterants. An efficient biomonitoring method for THMPs is of great needed. Herein, metabarcoding and single-molecule, real-time (SMRT) sequencing were used to detect the multiple ingredients in Jiuwei Qianghuo Wan (JWQHW), a classical herbal prescription widely used in China for the last 800 years. Reference experimental mixtures and commercial JWQHW products from the marketplace were used to confirm the method. Successful SMRT sequencing results recovered 5416 and 4342 circular-consensus sequencing (CCS) reads belonging to the ITS2 and psbA-trnH regions. The results suggest that with the combination of metabarcoding and SMRT sequencing, it is repeatable, reliable, and sensitive enough to detect species in the THMPs, and the error in SMRT sequencing did not affect the ability to identify multiple prescribed species and several adulterants/contaminants. It has the potential for becoming a valuable tool for the biomonitoring of multi-ingredient THMPs.},
}
@article {pmid29880685,
year = {2018},
author = {Tittl, A and Leitis, A and Liu, M and Yesilkoy, F and Choi, DY and Neshev, DN and Kivshar, YS and Altug, H},
title = {Imaging-based molecular barcoding with pixelated dielectric metasurfaces.},
journal = {Science (New York, N.Y.)},
volume = {360},
number = {6393},
pages = {1105-1109},
doi = {10.1126/science.aas9768},
pmid = {29880685},
issn = {1095-9203},
support = {//European Research Council/International ; },
abstract = {Metasurfaces provide opportunities for wavefront control, flat optics, and subwavelength light focusing. We developed an imaging-based nanophotonic method for detecting mid-infrared molecular fingerprints and implemented it for the chemical identification and compositional analysis of surface-bound analytes. Our technique features a two-dimensional pixelated dielectric metasurface with a range of ultrasharp resonances, each tuned to a discrete frequency; this enables molecular absorption signatures to be read out at multiple spectral points, and the resulting information is then translated into a barcode-like spatial absorption map for imaging. The signatures of biological, polymer, and pesticide molecules can be detected with high sensitivity, covering applications such as biosensing and environmental monitoring. Our chemically specific technique can resolve absorption fingerprints without the need for spectrometry, frequency scanning, or moving mechanical parts, thereby paving the way toward sensitive and versatile miniaturized mid-infrared spectroscopy devices.},
}
@article {pmid29879621,
year = {2018},
author = {Bruger, EL and Marx, CJ},
title = {A decade of genome sequencing has revolutionized studies of experimental evolution.},
journal = {Current opinion in microbiology},
volume = {45},
number = {},
pages = {149-155},
doi = {10.1016/j.mib.2018.03.002},
pmid = {29879621},
issn = {1879-0364},
mesh = {Bacteria/*genetics/metabolism ; *Evolution, Molecular ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Whole Genome Sequencing ; },
abstract = {Genome sequencing has revolutionized studies using experimental evolution of microbes because it readily provides comprehensive insight into the genetic bases of adaptation. In this perspective we discuss applications of sequencing-based technologies used to study evolution in microbes, including genomic sequencing of isolated evolved clones and mixed evolved populations, and also the use of sequencing methods to follow the fate of introduced variations, whether neutral barcodes or variants introduced by genome editing. Collectively, these sequencing-based approaches have vastly advanced the examination of evolution in the lab, as well as begun to synthesize this work with examination of the genetic bases of adaptation and evolutionary dynamics within natural populations.},
}
@article {pmid29877542,
year = {2018},
author = {Guo, S and Lin, WN and Hu, Y and Sun, G and Phan, DT and Chen, CH},
title = {Ultrahigh-throughput droplet microfluidic device for single-cell miRNA detection with isothermal amplification.},
journal = {Lab on a chip},
volume = {18},
number = {13},
pages = {1914-1920},
doi = {10.1039/c8lc00390d},
pmid = {29877542},
issn = {1473-0189},
mesh = {Cell Line, Tumor ; DNA/analysis ; Equipment Design ; Humans ; Microfluidic Analytical Techniques/instrumentation/*methods ; Polymerase Chain Reaction/instrumentation/*methods ; Single-Cell Analysis/instrumentation/*methods ; },
abstract = {Analysis of microRNA (miRNA), a pivotal primary regulator of fundamental cellular processes, at the single-cell level is essential to elucidate regulated gene expression precisely. Most single-cell gene sequencing methods use the polymerase chain reaction (PCR) to increase the concentration of the target gene for detection, thus requiring a barcoding process for cell identification and creating a challenge for real-time, large-scale screening of sequences in cells to rapidly profile physiological samples. In this study, a rapid, PCR-free, single-cell miRNA assay is developed from a continuous-flow microfluidic process employing a DNA hybridization chain reaction to amplify the target miRNA signal. Individual cells are encapsulated with DNA amplifiers in water-in-oil droplets and then lysed. The released target miRNA interacts with the DNA amplifiers to trigger hybridization reactions, producing fluorescence signals. Afterward, the target sequences are recycled to trigger a cyclic cascade reaction and significantly amplify the fluorescence signals without using PCR thermal cycling. Multiple DNA amplifiers with distinct fluorescence signals can be encapsulated simultaneously in a droplet to measure multiple miRNAs from a single cell simultaneously. Moreover, this process converts the lab bench PCR assay to a real-time droplet assay with the post-reaction fluorescence signal as a readout to allow flow cytometry-like continuous-flow measurement of sequences in a single cell with an ultrahigh throughput (300-500 cells per minute) for rapid biomedical identification.},
}
@article {pmid29876760,
year = {2018},
author = {de Rojas, M and Doña, J and Jovani, R and Dimov, I and Zurita, A and Callejón, R and Rodríguez-Plá, M},
title = {Evidence of cryptic species in the genus Tinaminyssus (Acari: Rhinonyssidae) based on morphometrical and molecular data.},
journal = {Experimental &amp; applied acarology},
volume = {75},
number = {3},
pages = {355-368},
pmid = {29876760},
issn = {1572-9702},
mesh = {Animals ; Arthropod Proteins/analysis ; Columbidae/*parasitology ; DNA, Ribosomal Spacer/analysis ; Electron Transport Complex IV/analysis ; Mites/anatomy &amp; histology/*classification/genetics ; Mitochondrial Proteins/analysis ; Phylogeny ; },
abstract = {The study of cryptic species allows to describe and to understand biodiversity, and the evolutionary processes shaping it. Mites of the family Rhinonyssidae are permanent parasites of the nasal cavities of birds, currently including about 500 described species and 12 genera. Here, we tested the hypothesis that mites from five populations of the genus Tinaminyssus-three isolated from European turtle doves (Streptopelia turtur), and two from Eurasian collared doves (Streptopelia decaocto; Aves: Columbiformes)-are, in fact, two cryptic species inhabiting different hosts. First, we performed a morphometrical study on 16 traits. Then, we used the ITS1-5.8S rDNA-ITS2 nuclear region (ITS region), and a fragment of the mitochondrial cytochrome c-oxidase 1 (COI) to carry out phylogenetic and species delimitation analyses on Tinaminyssus species. Morphological analyses revealed a lack of biometric differentiation among Tinaminyssus populations from the two host species. However, molecular analyses indicated a high degree of genetic differentiation between populations of Tinaminyssus sp. from S. turtur and S. decaocto. Overall, results show that they can be considered as different cryptic species, suggesting a case of evolutionary stasis, likely because of the anatomical similarity between closely-related bird host species.},
}
@article {pmid29876082,
year = {2018},
author = {Xu, L and Lin, Q and Xu, S and Gu, Y and Hou, J and Liu, Y and Dumont, HJ and Han, BP},
title = {Daphnia diversity on the Tibetan Plateau measured by DNA taxonomy.},
journal = {Ecology and evolution},
volume = {8},
number = {10},
pages = {5069-5078},
pmid = {29876082},
issn = {2045-7758},
abstract = {Daphnia on the Tibetan Plateau has been little studied, and information on species diversity and biogeography is lacking. Here, we conducted a 4-year survey using the barcoding fragment of the mitochondrial COI gene to determine the distribution and diversity of Daphnia species found across the Plateau. Our results show that species richness is higher than previously thought, with total described and provisional species number doubling from 5 to 10. Six of the taxonomic units recovered by DNA taxonomy agreed well with morphology, but DNA barcoding distinguished three clades each for the D. longispina (D. galeata, D. dentifera, and D. longispina) and D. pulex (D. pulex, D. cf. tenebrosa, and D. pulicaria) complexes. The sequence divergence between congeneric species varied within a large range, from 9.25% to 30.71%. The endemic D. tibetana was the most common and widespread species, occurring in 12 hyposaline to mesosaline lakes. The lineage of D. longispina is the first confirmed occurrence in west Tibet.},
}
@article {pmid29874832,
year = {2018},
author = {Liu, X and Zhou, B and Yang, H and Li, Y and Yang, Q and Lu, Y and Gao, Y},
title = {Sequencing and Analysis of Chrysanthemum carinatum Schousb and Kalimeris indica. The Complete Chloroplast Genomes Reveal Two Inversions and rbcL as Barcoding of the Vegetable.},
journal = {Molecules (Basel, Switzerland)},
volume = {23},
number = {6},
pages = {},
pmid = {29874832},
issn = {1420-3049},
mesh = {Asteraceae/*genetics ; Chrysanthemum/classification/*genetics ; Codon ; Codon, Terminator ; *DNA Barcoding, Taxonomic ; *Genome, Chloroplast ; Phylogeny ; Plants, Edible/*genetics ; Repetitive Sequences, Nucleic Acid ; Ribulose-Bisphosphate Carboxylase/*genetics ; *Sequence Analysis, DNA ; },
abstract = {Chrysanthemum carinatum Schousb and Kalimeris indica are widely distributed edible vegetables and the sources of the Chinese medicine Asteraceae. The complete chloroplast (cp) genome of Asteraceae usually occurs in the inversions of two regions. Hence, the cp genome sequences and structures of Asteraceae species are crucial for the cp genome genetic diversity and evolutionary studies. Hence, in this paper, we have sequenced and analyzed for the first time the cp genome size of C. carinatum Schousb and K. indica, which are 149,752 bp and 152,885 bp, with a pair of inverted repeats (IRs) (24,523 bp and 25,003) separated by a large single copy (LSC) region (82,290 bp and 84,610) and a small single copy (SSC) region (18,416 bp and 18,269), respectively. In total, 79 protein-coding genes, 30 distinct transfer RNA (tRNA) genes, four distinct rRNA genes and two pseudogenes were found not only in C. carinatum Schousb but also in the K. indica cp genome. Fifty-two (52) and fifty-nine (59) repeats, and seventy (70) and ninety (90) simple sequence repeats (SSRs) were found in the C. carinatum Schousb and K. indica cp genomes, respectively. Codon usage analysis showed that leucine, isoleucine, and serine are the most frequent amino acids and that the UAA stop codon was the significantly favorite stop codon in both cp genomes. The two inversions, the LSC region ranging from trnC-GCA to trnG-UCC and the whole SSC region were found in both of them. The complete cp genome comparison with other Asteraceae species showed that the coding area is more conservative than the non-coding area. The phylogenetic analysis revealed that the rbcL gene is a good barcoding marker for identifying different vegetables. These results give an insight into the identification, the barcoding, and the understanding of the evolutionary model of the Asteraceae cp genome.},
}
@article {pmid29874289,
year = {2018},
author = {Xie, S and Cooley, A and Armendariz, D and Zhou, P and Hon, GC},
title = {Frequent sgRNA-barcode recombination in single-cell perturbation assays.},
journal = {PloS one},
volume = {13},
number = {6},
pages = {e0198635},
pmid = {29874289},
issn = {1932-6203},
support = {DP2 GM128203/GM/NIGMS NIH HHS/United States ; },
mesh = {CRISPR-Cas Systems/genetics ; Genetic Vectors/genetics ; HEK293 Cells ; Humans ; K562 Cells ; Lentivirus/genetics ; RNA, Guide, CRISPR-Cas Systems/*genetics ; Sequence Analysis, RNA ; Single-Cell Analysis/*methods ; Transfection/*methods ; },
abstract = {Simultaneously detecting CRISPR-based perturbations and induced transcriptional changes in the same cell is a powerful approach to unraveling genome function. Several lentiviral approaches have been developed, some of which rely on the detection of distally located genetic barcodes as an indirect proxy of sgRNA identity. Since barcodes are often several kilobases from their corresponding sgRNAs, viral recombination-mediated swapping of barcodes and sgRNAs is feasible. Using a self-circularization-based sgRNA-barcode library preparation protocol, we estimate the recombination rate to be ~50% and we trace this phenomenon to the pooled viral packaging step. Recombination is random, and decreases the signal-to-noise ratio of the assay. Our results suggest that alternative approaches can increase the throughput and sensitivity of single-cell perturbation assays.},
}
@article {pmid29873880,
year = {2020},
author = {Krosch, MN and Strutt, F and Blacket, MJ and Batovska, J and Starkie, M and Clarke, AR and Cameron, SL and Schutze, MK},
title = {Development of internal COI primers to improve and extend barcoding of fruit flies (Diptera: Tephritidae: Dacini).},
journal = {Insect science},
volume = {27},
number = {1},
pages = {143-158},
doi = {10.1111/1744-7917.12612},
pmid = {29873880},
issn = {1744-7917},
support = {PBCRC2147//Plant Biosecurity CRC/ ; //Science and Engineering Faculty (QUT)/ ; //Australian Research Council's Industrial Transformation Training Centre Program (ARC ITTC)/ ; },
mesh = {Animals ; Asia, Southeastern ; Australia ; Base Sequence ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/*analysis ; Electron Transport Complex IV/analysis ; Insect Proteins/analysis ; Male ; Pacific Islands ; Phylogeny ; Tephritidae/*classification/genetics ; },
abstract = {Accurate species-level identifications underpin many aspects of basic and applied biology; however, identifications can be hampered by a lack of discriminating morphological characters, taxonomic expertise or time. Molecular approaches, such as DNA "barcoding" of the cytochrome c oxidase (COI) gene, are argued to overcome these issues. However, nuclear encoding of mitochondrial genes (numts) and poor amplification success of suboptimally preserved specimens can lead to erroneous identifications. One insect group for which these molecular and morphological problems are significant are the dacine fruit flies (Diptera: Tephritidae: Dacini). We addressed these issues associated with COI barcoding in the dacines by first assessing several "universal" COI primers against public mitochondrial genome and numt sequences for dacine taxa. We then modified a set of four primers that more closely matched true dacine COI sequence and amplified two overlapping portions of the COI barcode region. Our new primers were tested alongside universal primers on a selection of dacine species, including both fresh preserved and decades-old dry specimens. Additionally, Bactrocera tryoni mitochondrial and nuclear genomes were compared to identify putative numts. Four numt clades were identified, three of which were amplified using existing universal primers. In contrast, our new primers preferentially amplified the "true" mitochondrial COI barcode in all dacine species tested. The new primers also successfully amplified partial barcodes from dry specimens for which full length barcodes were unobtainable. Thus we recommend these new primers be incorporated into the suites of primers used by diagnosticians and quarantine labs for the accurate identification of dacine species.},
}
@article {pmid29872708,
year = {2017},
author = {Lyons, YA and Wu, SY and Overwijk, WW and Baggerly, KA and Sood, AK},
title = {Immune cell profiling in cancer: molecular approaches to cell-specific identification.},
journal = {NPJ precision oncology},
volume = {1},
number = {1},
pages = {26},
pmid = {29872708},
issn = {2397-768X},
support = {P30 CA016672/CA/NCI NIH HHS/United States ; R01 CA177909/CA/NCI NIH HHS/United States ; UH3 TR000943/TR/NCATS NIH HHS/United States ; R01 CA109298/CA/NCI NIH HHS/United States ; P50 CA098258/CA/NCI NIH HHS/United States ; P50 CA083639/CA/NCI NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; },
abstract = {The immune system has many important regulatory roles in cancer development and progression. Given the emergence of effective immune therapies against many cancers, reliable predictors of response are needed. One method of determining response is by evaluating immune cell populations from treated and untreated tumor samples. The amount of material obtained from tumor biopsies can be limited; therefore, gene-based or protein-based analyses may be attractive because they require minimal tissue. Cell-specific signatures are being analyzed with use of the latest technologies, including NanoString's nCounter technology, intracellular staining flow cytometry, cytometry by time-of-flight, RNA-Seq, and barcoding antibody-based protein arrays. These signatures provide information about the contributions of specific types of immune cells to bulk tumor samples. To date, both tumor tissue and immune cells have been analyzed for molecular expression profiles that can assess genes and proteins that are specific to immune cells, yielding results of varying specificity. Here, we discuss the importance of profiling tumor tissue and immune cells to identify immune-cell-associated genes and proteins and specific gene profiles of immune cells. We also discuss the use of these signatures in cancer treatment and the challenges faced in molecular expression profiling of immune cell populations.},
}
@article {pmid29872366,
year = {2018},
author = {Fišer, C and Alther, R and Zakšek, V and Borko, &#x160; and Fuchs, A and Altermatt, F},
title = {Translating Niphargus barcodes from Switzerland into taxonomy with a description of two new species (Amphipoda, Niphargidae).},
journal = {ZooKeys},
volume = {},
number = {760},
pages = {113-141},
pmid = {29872366},
issn = {1313-2989},
abstract = {The amphipod genus Niphargus (Amphipoda: Niphargidae Bousfield, 1977) is the most species-rich genus of freshwater amphipods in the World. Species of this genus, which live almost exclusively in subterranean water, offer an interesting model system for basic and applied biodiversity science. Their use, however, is often limited due to the hitherto unresolved taxonomy within the whole genus. As a comprehensive taxonomic revision of the currently >425 Niphargus species is too demanding, it has been suggested that the taxonomy of the genus could be advanced in smaller steps, by reviewing regional faunas, that would eventually integrate into a global revision. In this study, we provide such a revision of Niphargus in Switzerland. First, we molecularly delimited, morphologically diagnosed, and formally described two new species, namely Niphargus luchoffmannisp. n. and Niphargus tonywhittenisp. n. Second, we updated and revised a checklist of Niphargus in Switzerland with new findings, and prepared a list of reference sequences for routine molecular identification, available at BOLD and GenBank. All available specimens of 22 known species from the area were morphologically examined, and their morphological variation was compiled in a data file of DEscription Language for TAxonomy, which can be used for automated generation of dichotomous or interactive keys. The data file is freely available at the World Amphipoda Database. Together, the checklist, the library of reference sequences, the DELTA file, but also a list of hitherto unresolved aspects are an important step towards a complete revision of the genus within a well-defined and biogeographically interesting area in Central Europe.},
}
@article {pmid29872224,
year = {2018},
author = {Barman, AS and Singh, M and Singh, SK and Saha, H and Singh, YJ and Laishram, M and Pandey, PK},
title = {DNA Barcoding of Freshwater Fishes of Indo-Myanmar Biodiversity Hotspot.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {8579},
pmid = {29872224},
issn = {2045-2322},
mesh = {Animals ; Bayes Theorem ; *Biodiversity ; Conservation of Natural Resources/methods ; DNA Barcoding, Taxonomic/*methods ; Ecosystem ; Electron Transport Complex IV/classification/genetics ; Fishes/classification/*genetics ; Fresh Water ; *Genetic Variation ; Geography ; India ; Myanmar ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {To develop an effective conservation and management strategy, it is required to assess the biodiversity status of an ecosystem, especially when we deal with Indo-Myanmar biodiversity hotspot. Importance of this reaches to an entirely different level as the hotspot represents the area of high endemism which is under continuous threat. Therefore, the need of the present study was conceptualized, dealing with molecular assessment of the fish fauna of Indo-Myanmar region, which covers the Indian states namely, Manipur, Meghalaya, Mizoram, and Nagaland. A total of 363 specimens, representing 109 species were collected and barcoded from the different rivers and their tributaries of the region. The analyses performed in the present study, i.e. Kimura 2-Parameter genetic divergence, Neighbor-Joining, Automated Barcode Gap Discovery and Bayesian Poisson Tree Processes suggest that DNA barcoding is an efficient and reliable tool for species identification. Most of the species were clearly delineated. However, presence of intra-specific and inter-specific genetic distance overlap in few species, revealed the existence of putative cryptic species. A reliable DNA barcode reference library, established in our study provides an adequate knowledge base to the groups of non-taxonomists, researchers, biodiversity managers and policy makers in sketching effective conservation measures for this ecosystem.},
}
@article {pmid29872173,
year = {2018},
author = {Surridge, C},
title = {Batshit barcoding.},
journal = {Nature plants},
volume = {4},
number = {6},
pages = {317},
doi = {10.1038/s41477-018-0182-1},
pmid = {29872173},
issn = {2055-0278},
}
@article {pmid29870882,
year = {2018},
author = {Santos, C and Pereira, F},
title = {Identification of plant species using variable length chloroplast DNA sequences.},
journal = {Forensic science international. Genetics},
volume = {36},
number = {},
pages = {1-12},
doi = {10.1016/j.fsigen.2018.05.009},
pmid = {29870882},
issn = {1878-0326},
mesh = {*DNA, Chloroplast ; *Genetic Variation ; Genome, Plant ; INDEL Mutation ; Plants/classification/*genetics ; *Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The correct identification of species in the highly divergent group of plants is crucial for several forensic investigations. Previous works had difficulties in the establishment of a rapid and robust method for the identification of plants. For instance, DNA barcoding requires the analysis of two or three different genomic regions to attain reasonable levels of discrimination. Therefore, new methods for the molecular identification of plants are clearly needed. Here we tested the utility of variable-length sequences in the chloroplast DNA (cpDNA) as a way to identify plant species. The SPInDel (Species Identification by Insertions/Deletions) approach targets hypervariable genomic regions that contain multiple insertions/deletions (indels) and length variability, which are found interspersed with highly conserved regions. The combination of fragment lengths defines a unique numeric profile for each species, allowing its identification. We analysed more than 44,000 sequences retrieved from public databases belonging to 206 different plant families. Four target regions were identified as suitable for the SPInDel concept: atpF-atpH, psbA-trnH, trnL CD and trnL GH. When considered alone, the discrimination power of each region was low, varying from 5.18% (trnL GH) to 42.54% (trnL CD). However, the discrimination power reached more than 90% when the length of some of these regions is combined. We also observed low diversity in intraspecific data sets for all target regions, suggesting they can be used for identification purposes. Our results demonstrate the utility of the SPInDel concept for the identification of plants.},
}
@article {pmid29870859,
year = {2018},
author = {Bolstad, KSR and Braid, HE and Strugnell, JM and Lindgren, AR and Lischka, A and Kubodera, T and Laptikhovsky, VL and Roura Labiaga, A},
title = {A mitochondrial phylogeny of the family Onychoteuthidae (Cephalopoda: Oegopsida).},
journal = {Molecular phylogenetics and evolution},
volume = {128},
number = {},
pages = {88-97},
doi = {10.1016/j.ympev.2018.05.032},
pmid = {29870859},
issn = {1095-9513},
mesh = {Animals ; Cephalopoda/*classification/genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Mitochondria/*genetics ; *Phylogeny ; Species Specificity ; },
abstract = {The oegopsid squid family Onychoteuthidae was recently revised based on morphology, but sufficient material for a complementary molecular analysis has not been available until now. In the present study, over 250 sequences of cytochrome c oxidase subunit I (COI) and 16S rRNA for 222 individuals were analysed to create a combined phylogeny for the family. Results support monophyly for the family and all seven onychoteuthid genera (including Moroteuthopsis, established herein as the senior genus name for species formerly attributed to Kondakovia); 29 genetically distinct species were recovered, with the BIN (Barcode Index Number) analysis for COI showing good congruence overall with morphological species groupings. No sequences were available for five additional known species, making the total family diversity likely to exceed 34 species. Seven of the BINs formed in this study appear to represent undescribed taxa, suggesting that even in this relatively well-studied family, much additional work remains before a comprehensive understanding of the diversity and evolutionary relationships for the Onychoteuthidae can be achieved.},
}
@article {pmid29870316,
year = {2018},
author = {Benabdelkrim Filali, O and Kabine, M and El Hamouchi, A and Lemrani, M and Debboun, M and Sarih, M},
title = {First Molecular Identification and Phylogeny of Moroccan Anopheles sergentii (Diptera: Culicidae) Based on Second Internal Transcribed Spencer (ITS2) and Cytochrome c Oxidase I (COI) Sequences.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {18},
number = {9},
pages = {479-484},
doi = {10.1089/vbz.2018.2269},
pmid = {29870316},
issn = {1557-7759},
mesh = {Animals ; Anopheles/*genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/*genetics ; Electron Transport Complex IV/*genetics ; Haplotypes ; *Phylogeny ; },
abstract = {Anopheles sergentii known as the "oasis vector" or the "desert malaria vector" is considered the main vector of malaria in the southern parts of Morocco. Its presence in Morocco is confirmed for the first time through sequencing of mitochondrial DNA (mDNA) cytochrome c oxidase subunit I (COI) barcodes and nuclear ribosomal DNA (rDNA) second internal transcribed spacer (ITS2) sequences and direct comparison with specimens of A. sergentii of other countries. The DNA barcodes (n = 39) obtained from A. sergentii collected in 2015 and 2016 showed more diversity with 10 haplotypes, compared with 3 haplotypes obtained from ITS2 sequences (n = 59). Moreover, the comparison using the ITS2 sequences showed closer evolutionary relationship between the Moroccan and Egyptian strains than the Iranian strain. Nevertheless, genetic differences due to geographical segregation were also observed. This study provides the first report on the sequence of rDNA-ITS2 and mtDNA COI, which could be used to better understand the biodiversity of A. sergentii.},
}
@article {pmid29868793,
year = {2019},
author = {Pfeiler, E},
title = {Genetic Diversity and Demographic History in the Cactophilic Drosophila repleta Species Group (Diptera: Drosophilidae) in North America Inferred from Mitochondrial DNA Barcodes.},
journal = {The Journal of heredity},
volume = {110},
number = {1},
pages = {34-45},
doi = {10.1093/jhered/esy023},
pmid = {29868793},
issn = {1465-7333},
mesh = {Animals ; Cactaceae ; DNA Barcoding, Taxonomic ; *DNA, Mitochondrial ; Demography ; Drosophila/enzymology/*genetics ; Electron Transport Complex IV/genetics ; Female ; *Genetic Variation ; Male ; North America ; Species Specificity ; },
abstract = {Genetic diversity in mitochondrial DNA barcodes, comprising a segment of the cytochrome c oxidase subunit I (COI) gene, was used to infer demographic histories in selected taxa of the cactophilic Drosophila repleta species group in North America. Haplotype and nucleotide diversities were determined in 16 taxa based on both previously published and new sequences. Haplotype diversity (h) differed dramatically in different taxa, varying from h = 0 in Drosophila eremophila, Drosophila hexastigma, and Drosophila bifurca to h = 0.99 in Drosophila hamatofila. Genetic diversity indices and sample sizes were sufficient to infer demographic histories from mismatch distribution analysis and Bayesian skyline plots for 9 taxa: Drosophila mojavensis baja, Drosophila mojavensis sonorensis, Drosophila arizonae, Drosophila aldrichi, D. hamatofila, Drosophila spenceri, Drosophila mainlandi, Drosophila mettleri, and Drosophila nigrospiracula. Evidence was found for both population expansions and relatively stable populations in these species. Demographic history varied dramatically in subspecies of D. mojavensis, showing a relatively stable population size over time in D. m. sonorensis from the mainland Sonoran Desert whereas a large population expansion was evident in D. m. baja from the Baja California Peninsula, providing support for the hypothesis that the split of sister species D. mojavensis and D. arizonae from a common ancestor occurred on the mainland rather than the peninsula as proposed by others. No evidence was found for a causal relationship between a stable or expanding population and host plant shifts from prickly-pear cactus to columnar cacti, which has occurred independently in many taxa of the repleta group.},
}
@article {pmid29868621,
year = {2018},
author = {Yang, Y and Tellez, G and Latorre, JD and Ray, PM and Hernandez, X and Hargis, BM and Ricke, SC and Kwon, YM},
title = {Salmonella Excludes Salmonella in Poultry: Confirming an Old Paradigm Using Conventional and Barcode-Tagging Approaches.},
journal = {Frontiers in veterinary science},
volume = {5},
number = {},
pages = {101},
pmid = {29868621},
issn = {2297-1769},
abstract = {Salmonella is one of the major foodborne bacterial pathogens, and the consumption of contaminated chicken meats isa primary route of Salmonella transmission into human food chains. However, the mechanism of Salmonella transmission within the chicken flock is not fully understood, including competition among Salmonella strains during chicken infection. The purpose of the present study was to evaluate the competitive exclusion (CE) between different or same Salmonella species consecutively challenged through the oral route. Two different approaches were used to evaluate the CE effect, including tracking Salmonella colonization by wild-type strains with difference in natural antibiotic resistance or DNA barcode-tagged isogenic strains. When day-of-hatch chicks were administered by wild-type S. Typhimurium (ST) on day 1, followed by infection on day 2 by S. Enteritidis (SE) or vice versa, most of the birds were colonized only by the first strains administered (82% by ST or 83% by SE). When similar experiments were performed using two different isogenic barcode-tagged SE strains, Illumina sequencing analysis of the barcode region showed that the first barcode-tagged strains administered were dominant strains, ranging from 92 to 99% of the Salmonella recovered from ceca. These results provide quantitative evidence supporting the CE theory that oral administration of Salmonella will produce predominant inhibition over the subsequent colonization of ceca by the following administration one day later by different or same Salmonella species. We also showed that the use of barcode-tagged isogenic strains in combination with deep profiling of barcodes by Illumina sequencing can serve as a quantitative method for studying complex dynamics of Salmonella infection, transmission and colonization in poultry.},
}
@article {pmid29868290,
year = {2018},
author = {Pereira, EA and Rocha, LCL and Folly, H and da Silva, HR and Santana, DJ},
title = {A new species of spotted leaf frog, genus Phasmahyla (Amphibia, Phyllomedusidae) from Southeast Brazil.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e4900},
pmid = {29868290},
issn = {2167-8359},
abstract = {Based on concordant differences in male advertisement call, tadpole morphology, and absence of haplotype sharing in the barcoding 16S mitochondrial DNA, we describe here a new species of spotted leaf frog of the genus Phasmahyla from Atlantic Forest, State of Rio de Janeiro, Southeast Brazil. The new species is most similar to P. cochranae (type locality) and P. spectabilis (type locality). It differs from these species by the size of the calcar, moderate-sized body (snout-vent length 30.4-34.4 mm in adult eight males), and in the advertisement call. The tadpoles of Phasmahyla lisbella sp. nov. differ from P. exilis, P. spectabilis, P. timbo, P. guttata and P. jandaia because they do not have row of teeth in the anterior part; differ from P. cruzi by the shape of the anterior end of the oral disc. Through genetic data (phylogenetic distance and haplotype genealogy) we diagnosed the new species where the genetic divergences among its congeners is about 3-6% in a fragment of the 16S rRNA gene, which is above the threshold typically characterizing distinct species of anurans. However, the new species can be distinguished from other congeneric species based on an integrative approach (molecular, bioacoustics, larval, and adult morphology).},
}
@article {pmid29868047,
year = {2018},
author = {Yan, M and Xiong, Y and Liu, R and Deng, M and Song, J},
title = {The Application and Limitation of Universal Chloroplast Markers in Discriminating East Asian Evergreen Oaks.},
journal = {Frontiers in plant science},
volume = {9},
number = {},
pages = {569},
pmid = {29868047},
issn = {1664-462X},
abstract = {The East Asian subtropics mostly occupied by evergreen broad-leaved forests (EBLFs), is one of the global diversity centers for evergreen oaks. Evergreen oaks are keystone canopy trees in EBLFs with important ecosystem function and crucial significance for regional biodiversity conservation. However, the species composition and diversity of Asian evergreen oaks are poorly understood. Here, we test whether the four chloroplast markers atpI-atpH, matK, psbA-trnH, and ycf1, can discriminate the two evergreen oak sections in Asia - Cyclobalanopsis and Ilex. Two hundred and seventy-two individuals representing 57 species were scanned and 17 species from other oaks sections were included for phylogenetic reconstruction. The genetic diversity of the Quercus sections was also compared. Overall, we found that universal chloroplast DNA (cpDNA) barcoding markers could resolve two clades in Quercus, i.e., subgenus Cerris (Old World Clade) and subgenus Quercus (New World Clade). The chloroplast markers distinguished the main sections, with few exceptions. Each cpDNA region showed no barcoding gap and none of them provided good resolution at the species level. The best species resolution (27.78%) was obtained when three or four markers were combined and analyzed using BLAST. The high conservation of the cpDNA and complicated evolutionary patterns, due to incomplete lineage sorting, interspecific hybridization and introgressions may hinder the ability of cpDNA markers to discriminate different species. When comparing diversification pattern across Quercus sections (Cyclobalanopsis, Ilex, Cerris, Quercus, and Protobalanus), we found that section Ilex was the most genetically diverse, and section Cyclobalanopsis was lower genetically diverse. This diversification pattern may have resulted from the interplay of the Eurasia Cenozoic tectonic movements, climate changes and different niches of their ancestral lineages.},
}
@article {pmid29867115,
year = {2018},
author = {Moorhouse-Gann, RJ and Dunn, JC and de Vere, N and Goder, M and Cole, N and Hipperson, H and Symondson, WOC},
title = {New universal ITS2 primers for high-resolution herbivory analyses using DNA metabarcoding in both tropical and temperate zones.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {8542},
pmid = {29867115},
issn = {2045-2322},
mesh = {Animals ; *Birds ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/*genetics ; DNA, Plant/*genetics ; DNA, Ribosomal Spacer/*genetics ; *Herbivory ; Polymerase Chain Reaction/*methods ; *Reptiles ; },
abstract = {DNA metabarcoding is a rapidly growing technique for obtaining detailed dietary information. Current metabarcoding methods for herbivory, using a single locus, can lack taxonomic resolution for some applications. We present novel primers for the second internal transcribed spacer of nuclear ribosomal DNA (ITS2) designed for dietary studies in Mauritius and the UK, which have the potential to give unrivalled taxonomic coverage and resolution from a short-amplicon barcode. In silico testing used three databases of plant ITS2 sequences from UK and Mauritian floras (native and introduced) totalling 6561 sequences from 1790 species across 174 families. Our primers were well-matched in silico to 88% of species, providing taxonomic resolution of 86.1%, 99.4% and 99.9% at the species, genus and family levels, respectively. In vitro, the primers amplified 99% of Mauritian (n = 169) and 100% of UK (n = 33) species, and co-amplified multiple plant species from degraded faecal DNA from reptiles and birds in two case studies. For the ITS2 region, we advocate taxonomic assignment based on best sequence match instead of a clustering approach. With short amplicons of 187-387 bp, these primers are suitable for metabarcoding plant DNA from faecal samples, across a broad geographic range, whilst delivering unparalleled taxonomic resolution.},
}
@article {pmid29864000,
year = {2018},
author = {Hughes, KW and Tulloss, RH and Petersen, RH},
title = {Intragenomic nuclear RNA variation in a cryptic Amanita taxon.},
journal = {Mycologia},
volume = {110},
number = {1},
pages = {93-103},
doi = {10.1080/00275514.2018.1427402},
pmid = {29864000},
issn = {1557-2536},
mesh = {Amanita/*classification/*genetics ; Cluster Analysis ; Costa Rica ; DNA, Fungal/chemistry/genetics ; DNA, Mitochondrial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; *Genetic Variation ; Mexico ; North America ; Phylogeny ; RNA Polymerase II/genetics ; RNA, Fungal/*genetics ; RNA, Nuclear/*genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; },
abstract = {Amanita cf. lavendula collections in eastern North America, Mexico, and Costa Rica were found to consist of four cryptic taxa, one of which exhibited consistently unreadable nuclear rDNA ITS1-5.8S-ITS2 (fungal barcode) sequences after ITS1 base 130. This taxon is designated here as Amanita cf. lavendula taxon 1. ITS sequences from dikaryotic basidiomata were cloned, but sequences recovered from cloning did not segregate into distinct haplotypes. Rather, there was a mix of haplotypes that varied among themselves predominantly at 28 ITS positions. Analysis of each of these 28 variable bases showed predominantly two alternate bases at each position. Based on these findings and additional sequence data from the nuclear rDNA 28S, RNA polymerase II subunit 2 (RPB2) and mitochondrial rDNA small subunit (SSU) and 23S genes, we speculate that taxon 1 represents an initial hybridization event between two divergent taxa followed by failure of the ribosomal repeat to homogenize. Homogenization failure may be a result of repeated hybridization between divergent internal transcribed spacer (ITS) types with inadequate time for concerted evolution of the ribosomal repeat or, alternately, a complete failure of the ribosomal homogenization process. To our knowledge, this finding represents the first report of a geographically widespread taxon (Canada, eastern USA, Costa Rica) with apparent homogenization failure across all collections. Findings such as these have implications for fungal barcoding efforts and the application of fungal barcodes in identifying environmental sequences.},
}
@article {pmid29863086,
year = {2018},
author = {Li, Q and Yan, H and Lin, D and Wang, Y and He, M and Zhang, W and Gao, X and Zhu, S},
title = {Molecular Identification of Three Aquilaria (Thymelaeaceae) Species through DNA Barcoding.},
journal = {Biological &amp; pharmaceutical bulletin},
volume = {41},
number = {6},
pages = {967-971},
doi = {10.1248/bpb.b18-00050},
pmid = {29863086},
issn = {1347-5215},
mesh = {DNA Barcoding, Taxonomic ; DNA, Intergenic ; DNA, Plant ; Endoribonucleases/genetics ; Genes, Plant ; Nucleotidyltransferases/genetics ; Phylogeny ; Thymelaeaceae/*genetics ; },
abstract = {Aquilaria LAM. is an endangered tropical tree that produces agarwood, a common ingredient in medicine, perfumes and incense. The species endemic to China, Aquilaria yunnanensis, is often misidentified as the two valuable species, Aquilaria sinensis and Aquilaria crassna. In present study, three DNA barcodes (internal transcribed spacer (ITS), maturase K gene (matK) and trnL-trnF) were used to evaluate whether these genes can be used to discriminate the three species, and evaluate the phylogenetic relationship between the three Aquilaria species. For accurate identification of the three Aquilaria species, a total of 26 nucleotide variations were detected when comparing the three DNA barcodes. We found that A. sinensis is closely related to A. crassna based on combination of nuclear and chloroplast DNA barcodes, and is closely related to A. yunnanensis based on chloroplast DNA barcodes. Taken together, we suggest that the combination of ITS+matK and ITS+trnL-trnF are suitable for identifying these three Aquilaria species.},
}
@article {pmid29861452,
year = {2018},
author = {Liu, HY and Yu, Y and Deng, YQ and Li, J and Huang, ZX and Zhou, SD},
title = {The Chloroplast Genome of Lilium henrici: Genome Structure and Comparative Analysis.},
journal = {Molecules (Basel, Switzerland)},
volume = {23},
number = {6},
pages = {},
pmid = {29861452},
issn = {1420-3049},
mesh = {Codon ; Computational Biology/methods ; *Genome, Chloroplast ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Lilium/classification/*genetics ; Microsatellite Repeats ; Molecular Sequence Annotation ; Phylogeny ; },
abstract = {Lilium henrici Franchet, which belongs to the family Liliaceae, is an endangered plant native to China. The wild populations of L. henrici have been largely reduced by habitat degradation or loss. In our study, we determined the whole chloroplast genome sequence for L. henrici and compared its structure with other Lilium (including Nomocharis) species. The chloroplast genome of L. henrici is a circular structure and 152,784 bp in length. The large single copy and small single copy is 82,429 bp and 17,533 bp in size, respectively, and the inverted repeats are 26,411 bp in size. The L. henrici chloroplast genome contains 116 different genes, including 78 protein coding genes, 30 tRNA genes, 4 rRNA genes, and 4 pseudogenes. There were 51 SSRs detected in the L. henrici chloroplast genome sequence. Genic comparison among L. henrici with other Lilium (including Nomocharis) chloroplast genomes shows that the sequence lengths and gene contents show little variation, the only differences being in three pseudogenes. Phylogenetic analysis revealed that N. pardanthina was a sister species to L. henrici. Overall, this study, providing L. henrici genomic resources and the comparative analysis of Lilium chloroplast genomes, will be beneficial for the evolutionary study and phylogenetic reconstruction of the genus Lilium, molecular barcoding in population genetics.},
}
@article {pmid29856794,
year = {2018},
author = {Bingpeng, X and Heshan, L and Zhilan, Z and Chunguang, W and Yanguo, W and Jianjun, W},
title = {DNA barcoding for identification of fish species in the Taiwan Strait.},
journal = {PloS one},
volume = {13},
number = {6},
pages = {e0198109},
pmid = {29856794},
issn = {1932-6203},
mesh = {Animals ; Base Composition ; Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Fishes/*classification/genetics ; Genetic Markers ; Oceans and Seas ; },
abstract = {DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene in the mitochondrial genome is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding reference database of fishes in the Taiwan Strait and evaluate the applicability of using the COI gene for the identification of fish at the species level. A total of 284 mitochondrial COI barcode sequences were obtained from 85 genera, 38 families and 12 orders of fishes. The mean length of the sequences was 655 base pairs. The average Kimura two parameter (K2P) distances within species, genera, families, orders and classes were 0.21%, 6.50%, 23.70% and 25.60%, respectively. The mean interspecific distance was 31-fold higher than the mean intraspecific distance. The K2P neighbor-joining trees based on the sequence generally clustered species in accordance with their taxonomic classifications. High efficiency of species identification was demonstrated in the present study by DNA barcoding, and we conclude that COI sequencing can be used to identify fish species.},
}
@article {pmid29856506,
year = {2018},
author = {Bacon, CW and Hinton, DM and Mitchell, TR and Palencia, ER},
title = {In situ ergot alkaloid detection in three Balansia epichloe-infected grass species.},
journal = {Journal of applied microbiology},
volume = {125},
number = {4},
pages = {976-985},
doi = {10.1111/jam.13941},
pmid = {29856506},
issn = {1365-2672},
mesh = {Endophytes/chemistry/genetics/isolation &amp; purification/*metabolism ; Ergot Alkaloids/*chemistry/metabolism ; Hypocreales/chemistry/genetics/isolation &amp; purification/*metabolism ; Mass Spectrometry ; Molecular Structure ; Phylogeny ; Poaceae/*chemistry/*microbiology ; Symbiosis ; },
abstract = {AIMS: The objectives of this work were to characterize molecularly the morphologically described endophyte Balansia epichloe symbiotic on three grass species, and to determine the in situ production of ergot alkaloids on these three symbiota.<br><br>METHODS AND RESULTS: Balansia epichloe symbiotic with smut grass (Sporobolus poiretii), love grass (Eragrostis hirsuta) and lace grass (Eragrostis capillaries, a new host) were characterized using DNA barcoding. Laser ablation electro spray ionization (LAESI)-mass spectrometry was used to detect ergot alkaloids in&#xa0;situ for each symbiotum.<br><br>CONCLUSIONS: The three morphologically described symbionts on the three host grasses were indicated as belonging to the species B. epichloe, DNA barcoding suggested they were related although a cryptic species was suggested. LAESI-mass spectrometry showed that ergot alkaloids were produced in&#xa0;vivo in two hosts but not the third although this same symbiotum was related to one of the ergot alkaloid producing symbiota as revealed by the DNA-barcoding procedure.<br><br>These results established the accumulation of ergot alkaloids in pot culture by a morpho species although there were variations with each species of grass. Barcoding described divergence among species, but considering its limitation, the suggested existence of cryptic species among this morphospecies requires substantiation by studies that are more rigorous.},
}
@article {pmid29853775,
year = {2018},
author = {Raupach, MJ and Hannig, K and Moriniére, J and Hendrich, L},
title = {A DNA barcode library for ground beetles of Germany: the genus Amara Bonelli, 1810 (Insecta, Coleoptera, Carabidae).},
journal = {ZooKeys},
volume = {},
number = {759},
pages = {57-80},
pmid = {29853775},
issn = {1313-2989},
abstract = {The genus Amara Bonelli, 1810 is a very speciose and taxonomically difficult genus of the Carabidae. The identification of many of the species is accomplished with considerable difficulty, in particular for females and immature stages. In this study the effectiveness of DNA barcoding, the most popular method for molecular species identification, was examined to discriminate various species of this genus from Central Europe. DNA barcodes from 690 individuals and 47 species were analysed, including sequences from previous studies and more than 350 newly generated DNA barcodes. Our analysis revealed unique BINs for 38 species (81%). Interspecific K2P distances below 2.2% were found for three species pairs and one species trio, including haplotype sharing between Amara alpina/Amara torrida and Amara communis/Amara convexior/Amara makolskii. This study represents another step in generating an extensive reference library of DNA barcodes for carabids, highly valuable bioindicators for characterizing disturbances in various habitats.},
}
@article {pmid29851299,
year = {2018},
author = {Chen, HC and Zorita, E and Filion, GJ},
title = {Using Barcoded HIV Ensembles (B-HIVE) for Single Provirus Transcriptomics.},
journal = {Current protocols in molecular biology},
volume = {122},
number = {1},
pages = {e56},
doi = {10.1002/cpmb.56},
pmid = {29851299},
issn = {1934-3647},
mesh = {Computer Simulation ; DNA Barcoding, Taxonomic/*methods ; HEK293 Cells ; HIV-1/*genetics ; Humans ; Jurkat Cells ; Polymerase Chain Reaction ; Proviruses/*genetics ; RNA, Messenger/genetics/metabolism ; Recombination, Genetic/genetics ; Reproducibility of Results ; Transcriptome/*genetics ; Virus Latency/genetics ; },
abstract = {The latent HIV reservoir is the main barrier to curing AIDS, because infected cells escape the immune system and antiretroviral therapies. Developing new treatment strategies requires technologies to trace latent proviruses. Here, we describe a genome-wide technique called Barcoded HIV Ensembles (B-HIVE) to measure HIV expression at the single provirus level. The principle of B-HIVE is to tag the genome of HIV with DNA barcodes to trace viral transcripts produced by single proviruses in an infected cell population. This in turn reveals which proviruses are active and which are latent or expressed at low level. B-HIVE is a high-throughput method to identify and quantify thousands of individual viral transcripts per round of infection. It can be applied in different conditions, characterizing the response of single proviruses to different treatments. Overall, B-HIVE gives unprecedented insight into the expression of single proviruses in populations of HIV-infected cells. © 2018 by John Wiley &amp; Sons, Inc.},
}
@article {pmid29849709,
year = {2018},
author = {Yang, F and Ding, F and Chen, H and He, M and Zhu, S and Ma, X and Jiang, L and Li, H},
title = {DNA Barcoding for the Identification and Authentication of Animal Species in Traditional Medicine.},
journal = {Evidence-based complementary and alternative medicine : eCAM},
volume = {2018},
number = {},
pages = {5160254},
pmid = {29849709},
issn = {1741-427X},
abstract = {Animal-based traditional medicine not only plays a significant role in therapeutic practices worldwide but also provides a potential compound library for drug discovery. However, persistent hunting and illegal trade markedly threaten numerous medicinal animal species, and increasing demand further provokes the emergence of various adulterants. As the conventional methods are difficult and time-consuming to detect processed products or identify animal species with similar morphology, developing novel authentication methods for animal-based traditional medicine represents an urgent need. During the last decade, DNA barcoding offers an accurate and efficient strategy that can identify existing species and discover unknown species via analysis of sequence variation in a standardized region of DNA. Recent studies have shown that DNA barcoding as well as minibarcoding and metabarcoding is capable of identifying animal species and discriminating the authentics from the adulterants in various types of traditional medicines, including raw materials, processed products, and complex preparations. These techniques can also be used to detect the unlabelled and threatened animal species in traditional medicine. Here, we review the recent progress of DNA barcoding for the identification and authentication of animal species used in traditional medicine, which provides a reference for quality control and trade supervision of animal-based traditional medicine.},
}
@article {pmid29849152,
year = {2018},
author = {Machado, VN and Collins, RA and Ota, RP and Andrade, MC and Farias, IP and Hrbek, T},
title = {One thousand DNA barcodes of piranhas and pacus reveal geographic structure and unrecognised diversity in the Amazon.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {8387},
pmid = {29849152},
issn = {2045-2322},
mesh = {Animals ; *Biodiversity ; Characiformes/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Genetic Loci/genetics ; *Geography ; Phylogeny ; },
abstract = {Piranhas and pacus (Characiformes: Serrasalmidae) are a charismatic but understudied family of Neotropical fishes. Here, we analyse a DNA barcode dataset comprising 1,122 specimens, 69 species, 16 genera, 208 localities, and 34 major river drainages in order to make an inventory of diversity and to highlight taxa and biogeographic areas worthy of further sampling effort and conservation protection. Using four methods of species discovery-incorporating both tree and distance based techniques-we report between 76 and 99 species-like clusters, i.e. between 20% and 33% of a priori identified taxonomic species were represented by more than one mtDNA lineage. There was a high degree of congruence between clusters, with 60% supported by three or four methods. Pacus of the genus Myloplus exhibited the most intraspecific variation, with six of the 13 species sampled found to have multiple lineages. Conversely, piranhas of the Serrasalmus rhombeus group proved difficult to delimit with these methods due to genetic similarity and polyphyly. Overall, our results recognise substantially underestimated diversity in the serrasalmids, and emphasise the Guiana and Brazilian Shield rivers as biogeographically important areas with multiple cases of across-shield and within-shield diversifications. We additionally highlight the distinctiveness and complex phylogeographic history of rheophilic taxa in particular, and suggest multiple colonisations of these habitats by different serrasalmid lineages.},
}
@article {pmid29848777,
year = {2018},
author = {Nooh, MM and Mancarella, S and Bahouth, SW},
title = {Novel Paradigms Governing β1-Adrenergic Receptor Trafficking in Primary Adult Rat Cardiac Myocytes.},
journal = {Molecular pharmacology},
volume = {94},
number = {2},
pages = {862-875},
pmid = {29848777},
issn = {1521-0111},
support = {R01 HL085848/HL/NHLBI NIH HHS/United States ; },
mesh = {Adrenergic beta-1 Receptor Agonists/*pharmacology ; Adrenergic beta-1 Receptor Antagonists/*pharmacology ; Alprenolol/pharmacology ; Animals ; Cell Membrane/metabolism ; Cells, Cultured ; Humans ; Isoproterenol/pharmacology ; Myocytes, Cardiac/*cytology/metabolism ; Protein Transport/drug effects ; Rats ; Receptors, Adrenergic, beta-1/chemistry/genetics/*metabolism ; },
abstract = {The β1-adrenergic receptor (β1-AR) is a major cardiac G protein-coupled receptor, which mediates cardiac actions of catecholamines and is involved in genesis and treatment of numerous cardiovascular disorders. In mammalian cells, catecholamines induce the internalization of the β1-AR into endosomes and their removal promotes the recycling of the endosomal β1-AR back to the plasma membrane; however, whether these redistributive processes occur in terminally differentiated cells is unknown. Compartmentalization of the β1-AR in response to β-agonists and antagonists was determined by confocal microscopy in primary adult rat ventricular myocytes (ARVMs), which are terminally differentiated myocytes with unique structures such as transverse tubules (T-tubules) and contractile sarcomeres. In unstimulated ARVMs, the fluorescently labeled β1-AR was expressed on the external membrane (the sarcolemma) of cardiomyocytes. Exposing ARVMs to isoproterenol redistributed surface β1-ARs into small (∼225-250 nm) regularly spaced internal punctate structures that overlapped with puncta stained by Di-8 ANEPPS, a membrane-impermeant T-tubule-specific dye. Replacing the β-agonist with the β-blocker alprenolol, induced the translocation of the wild-type β1-AR from these punctate structures back to the plasma membrane. This step was dependent on two barcodes, namely, the type-1 PDZ binding motif and serine at position 312 of the β1-AR, which is phosphorylated by a pool of cAMP-dependent protein kinases anchored at the type-1 PDZ of the β1-AR. These data show that redistribution of the β1-AR in ARVMs from internal structures back to the plasma membrane was mediated by a novel sorting mechanism, which might explain unique aspects of cardiac β1-AR signaling under normal or pathologic conditions.},
}
@article {pmid29844951,
year = {2018},
author = {Justine, JL and Winsor, L and Gey, D and Gros, P and Thévenot, J},
title = {Giant worms chez moi! Hammerhead flatworms (Platyhelminthes, Geoplanidae, Bipalium spp., Diversibipalium spp.) in metropolitan France and overseas French territories.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e4672},
pmid = {29844951},
issn = {2167-8359},
abstract = {BACKGROUND: Species of the genera Bipalium and Diversibipalium, or bipaliines, are giants among land planarians (family Geoplanidae), reaching length of 1 m; they are also easily distinguished from other land flatworms by the characteristic hammer shape of their head. Bipaliines, which have their origin in warm parts of Asia, are invasive species, now widespread worldwide. However, the scientific literature is very scarce about the widespread repartition of these species, and their invasion in European countries has not been studied.<br><br>METHODS: In this paper, on the basis of a four year survey based on citizen science, which yielded observations from 1999 to 2017 and a total of 111 records, we provide information about the five species present in Metropolitan France and French overseas territories. We also investigated the molecular variability of cytochrome-oxidase 1 (COI) sequences of specimens.<br><br>RESULTS: Three species are reported from Metropolitan France: Bipalium kewense, Diversibipalium multilineatum, and an unnamed Diversibipalium 'black' species. We also report the presence of B. kewense from overseas territories, such as French Polynesia (Oceania), French Guiana (South America), the Caribbean French islands of Martinique, Guadeloupe, Saint Martin and Saint Barth&#xe9;lemy, and Montserrat (Central America), and La R&#xe9;union island (off South-East Africa). For B. vagum, observations include French Guiana, Guadeloupe, Martinique, Saint Barth&#xe9;lemy, Saint Martin, Montserrat, La R&#xe9;union, and Florida (USA). A probable new species, Diversibipalium sp. 'blue,' is reported from Mayotte Island (off South-East Africa). B. kewense, B. vagum and D. multilineatum each showed 0% variability in their COI sequences, whatever their origin, suggesting that the specimens are clonal, and that sexual reproduction is probably absent. COI barcoding was efficient in identifying species, with differences over 10% between species; this suggests that barcoding can be used in the future for identifying these invasive species. In Metropolitan south-west France, a small area located in the Department of Pyr&#xe9;n&#xe9;es-Atlantiques was found to be a hot-spot of bipaliine biodiversity and abundance for more than 20 years, probably because of the local mild weather.<br><br>DISCUSSION: The present findings strongly suggest that the species present in Metropolitan France and overseas territories should be considered invasive alien species. Our numerous records in the open in Metropolitan France raise questions: as scientists, we were amazed that these long and brightly coloured worms could escape the attention of scientists and authorities in a European developed country for such a long time; improved awareness about land planarians is certainly necessary.},
}
@article {pmid29844713,
year = {2018},
author = {Percy, DM},
title = {Revision of the Hawaiian psyllid genus Swezeyana, with descriptions of seven new species (Hemiptera, Psylloidea, Triozidae).},
journal = {ZooKeys},
volume = {},
number = {758},
pages = {75-113},
pmid = {29844713},
issn = {1313-2989},
abstract = {The endemic Hawaiian genus Swezeyana Caldwell, 1940 is highly distinctive due to the extremely long genal processes. In addition, some of the immatures are ornamented with extraordinary tubercles and tentacles. Two Swezeyana species are redescribed, and seven new species are described, bringing the total number of species in the genus to nine. All species are hosted by a single, endemic host plant, Planchonella sandwicensis (Sapotaceae), which is distributed across all major islands in the archipelago. The majority of Swezeyana species are single island endemics. A sister taxon pair is found sympatrically on the same individual plants on Kauai, and putative sister or at least closely related species are also found sympatrically on Oahu and Hawaii, suggesting these taxa may have diversified in sympatry. However, there is no observed ecological niche partitioning, despite some striking morphological diversity, as all Swezeyana species have free-living immatures that are found on the leaf surface, and therefore no apparent biological shifts are coincident with occupying the same host plant. Two species groups are represented by strikingly different female terminalia structure and endoskeletal development, although ovipositor structure is very similar between the two groups. Mitochondrial DNA barcodes (COI and cytB) are provided for eight of the nine species. A phylogenetic analysis of the mitochondrial barcode regions indicates species relationships within Swezeyana and provides a comparison of genetic divergence with other Hawaiian endemic genera.},
}
@article {pmid29844337,
year = {2018},
author = {Li, Q and Sun, Y and Guo, H and Sang, F and Ma, H and Peng, H and Zheng, N and Xu, L},
title = {Quality control of the traditional Chinese medicine Ruyi jinhuang powder based on high-throughput sequencing and real-time PCR.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {8261},
pmid = {29844337},
issn = {2045-2322},
mesh = {Arisaema ; Chemistry Techniques, Analytical ; Complex Mixtures/*chemistry ; Counterfeit Drugs ; DNA Barcoding, Taxonomic ; Drugs, Chinese Herbal/*chemistry ; High-Throughput Nucleotide Sequencing ; *Medicine, Chinese Traditional ; Pinellia ; *Quality Control ; Real-Time Polymerase Chain Reaction ; },
abstract = {Traditional Chinese medicine (TCM) has been practiced for thousands of years, although concerns about the efficacy, legality, and safety of TCM continue to be raised. Chromatographic studies have detected the presence of heavy metals and plant toxins within some TCM preparations. However, chromatography is not able to identify all of the compounds of TCM, particularly those items that are not clearly labeled on the packaging. The present study aimed to establish a supplemental method that better assesses the ingredient components of TCM preparations.We established an effective approach to screen the biological and toxical composition of TCM based on high-throughput sequencing (HTS), as well as fast detection and validation of the toxical species by real-time PCR, based on ITS2 DNA barcoding. Ruyi jinhuang powder (RHP), a classical herbal prescription containing the toxical herb Arisaematis rhizoma, was chosen to test the method. This method could determine whether the Arisaematis Rhizoma had been replaced by Pinellia pedatisecta in the RHP. The results were validated by real-time PCR. 90% compositions of RHP were identified by ITS2 DNA barcoding, suggesting that more DNA barcoding markers are needed for TCM identification. The strategy of high-throughput sequencing has the potential for comprehensive ingredient profiling for TCM preparations. Real-time PCR provides a expeditious metehod for monitoring the safety and legality of TCM preparations.},
}
@article {pmid29843817,
year = {2018},
author = {Boukouvalas, A and Hensman, J and Rattray, M},
title = {BGP: identifying gene-specific branching dynamics from single-cell data with a branching Gaussian process.},
journal = {Genome biology},
volume = {19},
number = {1},
pages = {65},
pmid = {29843817},
issn = {1474-760X},
support = {MR/K022016/2/MRC_/Medical Research Council/United Kingdom ; MR/M008908/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; Embryonic Stem Cells/metabolism ; Gene Expression Profiling/*methods ; Hematopoiesis/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Mice ; Normal Distribution ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis ; },
abstract = {High-throughput single-cell gene expression experiments can be used to uncover branching dynamics in cell populations undergoing differentiation through pseudotime methods. We develop the branching Gaussian process (BGP), a non-parametric model that is able to identify branching dynamics for individual genes and provide an estimate of branching times for each gene with an associated credible region. We demonstrate the effectiveness of our method on simulated data, a single-cell RNA-seq haematopoiesis study and mouse embryonic stem cells generated using droplet barcoding. The method is robust to high levels of technical variation and dropout, which are common in single-cell data.},
}
@article {pmid29808909,
year = {2018},
author = {Wu, Y and Li, M and Yang, Y and Jiang, L and Liu, M and Wang, B and Wang, Y},
title = {Authentication of Small Berry Fruit in Fruit Products by DNA Barcoding Method.},
journal = {Journal of food science},
volume = {83},
number = {6},
pages = {1494-1504},
doi = {10.1111/1750-3841.14177},
pmid = {29808909},
issn = {1750-3841},
mesh = {Cloning, Molecular ; *DNA Barcoding, Taxonomic ; DNA, Plant/*analysis ; Food Analysis/methods ; *Food Labeling ; *Fruit ; Fruit and Vegetable Juices/*analysis ; Genes, Plant ; Humans ; Magnoliopsida/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Small berry fruit products are gaining an expanded market due to their high nutrition value. However, the authenticity of products is challenged by adulteration and mislabeling. To establish an accurate and robust method for identifying both known and unknown fruit species in small berry fruit products, DNA barcoding technology based on Sanger sequencing was adopted. To overcome the influence of processing conditions on DNA recovery, mini-barcodes of rbcL and ITS and a medium-barcode of psbA-trnH were applied. To identify ingredients in products containing mixed species, plasmid cloning was applied to separate mixed barcodes. The method established in this paper could detect 1% to 10% target species in mixed fruit juice.},
}
@article {pmid29807908,
year = {2018},
author = {Díaz-Mejía, JJ and Celaj, A and Mellor, JC and Coté, A and Balint, A and Ho, B and Bansal, P and Shaeri, F and Gebbia, M and Weile, J and Verby, M and Karkhanina, A and Zhang, Y and Wong, C and Rich, J and Prendergast, D and Gupta, G and Öztürk, S and Durocher, D and Brown, GW and Roth, FP},
title = {Mapping DNA damage-dependent genetic interactions in yeast via party mating and barcode fusion genetics.},
journal = {Molecular systems biology},
volume = {14},
number = {5},
pages = {e7985},
pmid = {29807908},
issn = {1744-4292},
support = {R21 HG004756/HG/NHGRI NIH HHS/United States ; F32 HG004825/HG/NHGRI NIH HHS/United States ; R01 HG001715/HG/NHGRI NIH HHS/United States ; U01 HG001715/HG/NHGRI NIH HHS/United States ; P50 HG004233/HG/NHGRI NIH HHS/United States ; U41 HG001715/HG/NHGRI NIH HHS/United States ; MOP-79368//CIHR/Canada ; FDN143343//CIHR/Canada ; },
mesh = {*Chromosome Mapping ; *DNA Barcoding, Taxonomic ; *DNA Damage ; DNA Repair ; Epistasis, Genetic ; Gene Deletion ; Genetic Loci ; High-Throughput Nucleotide Sequencing ; Methyl Methanesulfonate ; Models, Theoretical ; Promoter Regions, Genetic ; Reproducibility of Results ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/*genetics ; },
abstract = {Condition-dependent genetic interactions can reveal functional relationships between genes that are not evident under standard culture conditions. State-of-the-art yeast genetic interaction mapping, which relies on robotic manipulation of arrays of double-mutant strains, does not scale readily to multi-condition studies. Here, we describe barcode fusion genetics to map genetic interactions (BFG-GI), by which double-mutant strains generated via en masse "party" mating can also be monitored en masse for growth to detect genetic interactions. By using site-specific recombination to fuse two DNA barcodes, each representing a specific gene deletion, BFG-GI enables multiplexed quantitative tracking of double mutants via next-generation sequencing. We applied BFG-GI to a matrix of DNA repair genes under nine different conditions, including methyl methanesulfonate (MMS), 4-nitroquinoline 1-oxide (4NQO), bleomycin, zeocin, and three other DNA-damaging environments. BFG-GI recapitulated known genetic interactions and yielded new condition-dependent genetic interactions. We validated and further explored a subnetwork of condition-dependent genetic interactions involving MAG1, SLX4, and genes encoding the Shu complex, and inferred that loss of the Shu complex leads to an increase in the activation of the checkpoint protein kinase Rad53.},
}
@article {pmid29806572,
year = {2020},
author = {Beebe, NW},
title = {DNA barcoding mosquitoes: advice for potential prospectors - CORRIGENDUM.},
journal = {Parasitology},
volume = {147},
number = {1},
pages = {126},
pmid = {29806572},
issn = {1469-8161},
}
@article {pmid29806008,
year = {2018},
author = {Kim, KL and Park, KM and Murray, J and Kim, K and Ryu, SH},
title = {Direct Profiling the Post-Translational Modification Codes of a Single Protein Immobilized on a Surface Using Cu-free Click Chemistry.},
journal = {ACS central science},
volume = {4},
number = {5},
pages = {614-623},
pmid = {29806008},
issn = {2374-7943},
abstract = {Combinatorial post-translational modifications (PTMs), which can serve as dynamic "molecular barcodes", have been proposed to regulate distinct protein functions. However, studies of combinatorial PTMs on single protein molecules have been hindered by a lack of suitable analytical methods. Here, we describe erasable single-molecule blotting (eSiMBlot) for combinatorial PTM profiling. This assay is performed in a highly multiplexed manner and leverages the benefits of covalent protein immobilization, cyclic probing with different antibodies, and single molecule fluorescence imaging. Especially, facile and efficient covalent immobilization on a surface using Cu-free click chemistry permits multiple rounds (>10) of antibody erasing/reprobing without loss of antigenicity. Moreover, cumulative detection of coregistered multiple data sets for immobilized single-epitope molecules, such as HA peptide, can be used to increase the antibody detection rate. Finally, eSiMBlot enables direct visualization and quantitative profiling of combinatorial PTM codes at the single-molecule level, as we demonstrate by revealing the novel phospho-codes of ligand-induced epidermal growth factor receptor. Thus, eSiMBlot provides an unprecedentedly simple, rapid, and versatile platform for analyzing the vast number of combinatorial PTMs in biological pathways.},
}
@article {pmid29801222,
year = {2018},
author = {Pawlowski, J and Kelly-Quinn, M and Altermatt, F and Apothéloz-Perret-Gentil, L and Beja, P and Boggero, A and Borja, A and Bouchez, A and Cordier, T and Domaizon, I and Feio, MJ and Filipe, AF and Fornaroli, R and Graf, W and Herder, J and van der Hoorn, B and Iwan Jones, J and Sagova-Mareckova, M and Moritz, C and Barquín, J and Piggott, JJ and Pinna, M and Rimet, F and Rinkevich, B and Sousa-Santos, C and Specchia, V and Trobajo, R and Vasselon, V and Vitecek, S and Zimmerman, J and Weigand, A and Leese, F and Kahlert, M},
title = {The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems.},
journal = {The Science of the total environment},
volume = {637-638},
number = {},
pages = {1295-1310},
doi = {10.1016/j.scitotenv.2018.05.002},
pmid = {29801222},
issn = {1879-1026},
mesh = {*Biodiversity ; *DNA Barcoding, Taxonomic ; Ecosystem ; Environmental Monitoring/*methods ; },
abstract = {The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.},
}
@article {pmid29799876,
year = {2018},
author = {Hegde, M and Strand, C and Hanna, RE and Doench, JG},
title = {Uncoupling of sgRNAs from their associated barcodes during PCR amplification of combinatorial CRISPR screens.},
journal = {PloS one},
volume = {13},
number = {5},
pages = {e0197547},
pmid = {29799876},
issn = {1932-6203},
mesh = {*CRISPR-Cas Systems ; Cell Line, Tumor ; DNA Barcoding, Taxonomic/*methods ; Genetic Vectors ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Lentivirus/genetics ; Polymerase Chain Reaction/*methods ; RNA, Guide, CRISPR-Cas Systems/*genetics ; Recombination, Genetic ; },
abstract = {Many implementations of pooled screens in mammalian cells rely on linking an element of interest to a barcode, with the latter subsequently quantitated by next generation sequencing. However, substantial uncoupling between these paired elements during lentiviral production has been reported, especially as the distance between elements increases. We detail that PCR amplification is another major source of uncoupling, and becomes more pronounced with increased amounts of DNA template molecules and PCR cycles. To lessen uncoupling in systems that use paired elements for detection, we recommend minimizing the distance between elements, using low and equal template DNA inputs for plasmid and genomic DNA during PCR, and minimizing the number of PCR cycles. We also present a vector design for conducting combinatorial CRISPR screens that enables accurate barcode-based detection with a single short sequencing read and minimal uncoupling.},
}
@article {pmid29797549,
year = {2018},
author = {Nichols, RV and Vollmers, C and Newsom, LA and Wang, Y and Heintzman, PD and Leighton, M and Green, RE and Shapiro, B},
title = {Minimizing polymerase biases in metabarcoding.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.12895},
pmid = {29797549},
issn = {1755-0998},
abstract = {DNA metabarcoding is an increasingly popular method to characterize and quantify biodiversity in environmental samples. Metabarcoding approaches simultaneously amplify a short, variable genomic region, or "barcode," from a broad taxonomic group via the polymerase chain reaction (PCR), using universal primers that anneal to flanking conserved regions. Results of these experiments are reported as occurrence data, which provide a list of taxa amplified from the sample, or relative abundance data, which measure the relative contribution of each taxon to the overall composition of amplified product. The accuracy of both occurrence and relative abundance estimates can be affected by a variety of biological and technical biases. For example, taxa with larger biomass may be better represented in environmental samples than those with smaller biomass. Here, we explore how polymerase choice, a potential source of technical bias, might influence results in metabarcoding experiments. We compared potential biases of six commercially available polymerases using a combination of mixtures of amplifiable synthetic sequences and real sedimentary DNA extracts. We find that polymerase choice can affect both occurrence and relative abundance estimates and that the main source of this bias appears to be polymerase preference for sequences with specific GC contents. We further recommend an experimental approach for metabarcoding based on results of our synthetic experiments.},
}
@article {pmid29797251,
year = {2018},
author = {Smets, T and Stevenaert, F and Adams, HC and Vanhoof, G},
title = {Deep Profiling of the Immune System of Multiple Myeloma Patients Using Cytometry by Time-of-Flight (CyTOF).},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1792},
number = {},
pages = {47-54},
doi = {10.1007/978-1-4939-7865-6_4},
pmid = {29797251},
issn = {1940-6029},
mesh = {*Biomarkers ; Blood Cells ; Bone Marrow Cells/immunology/metabolism ; *Flow Cytometry/methods ; Humans ; Immune System/*immunology/*metabolism ; Immunophenotyping ; Multiple Myeloma/*immunology/*metabolism ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; },
abstract = {Mass cytometry has emerged as a new state-of-the-art technology that enables in-depth characterization of cellular populations and functions at a single cell resolution. We describe the application of this technology to deeply phenotype the blood and bone marrow components of multiple myeloma patients in a clinical setting. This technology allows for simultaneous quantification of more than 40 markers, overcoming the challenges of traditional fluorescence-based flow cytometry.},
}
@article {pmid29796039,
year = {2018},
author = {Najafi, S and Vasheghani Farahani, A and Keshavarz-Bahaghighat, H},
title = {Initial Results of a Prospective Study and Identification of New Strategies to Increase Traceability of Plasma-derived Medicines.},
journal = {Iranian journal of pharmaceutical research : IJPR},
volume = {17},
number = {Suppl},
pages = {145-150},
pmid = {29796039},
issn = {1735-0328},
abstract = {Plasma medicine is an innovative and emerging field used in a broad range of medical conditions. The present study focused on consumption and documentation pattern of plasma-derived medicines in a teaching hospital. A two-step study was conducted from October to December 2015. During the first phase, the patient records receiving plasma-derived medicines including Coagulation Factor VIII, IX, Prothrombin Complex Concentrate, Factor VIII/Von Wilberand Complex, Anti-Hepatitis B Immunoglobulin, Intravenous Immunoglobulin, Anti-Tetanus Immunoglobulin, and Albumin were checked to assess recording details of these medications at the time of administration. Adverse events reported with the mentioned products were examined from traceability viewpoint. The second step concentrated on practical strategies to improve documentation status of plasma-derived medicines in the hospital. We proposed national guideline as the first strategy and a new barcoding system to track and identify drug information of plasma medicines. Of the expected drug information, only generic name, dosage from, and strength were recorded after administration. Post-marketing safety surveillance of the plasma products was poor similarly. Unavailability of suitable instructions was the main reason for documentation deficiency. A guideline was designed and implemented to inform healthcare professionals about essentials of appropriate documentation for plasma-derived medicines. Updated results of the ongoing phase will be submitted soon. Our survey highlights the importance of documentation as a key component of plasma-derived medicines surveillance within the hospitals.},
}
@article {pmid29793045,
year = {2018},
author = {Fries, FN and Pattmöller, M and Seitz, B and Berger, F and Kampen, H and Szentmáry, N and Becker, SL},
title = {Ophthalmomyiasis externa due to Oestrus ovis in a traveller returning from Greece.},
journal = {Travel medicine and infectious disease},
volume = {23},
number = {},
pages = {101-102},
doi = {10.1016/j.tmaid.2018.05.007},
pmid = {29793045},
issn = {1873-0442},
mesh = {Animals ; *Diptera ; Greece ; Humans ; Larva ; *Myiasis ; Sheep ; },
}
@article {pmid29791787,
year = {2018},
author = {Fagan-Jeffries, EP and Cooper, SJB and Bertozzi, T and Bradford, TM and Austin, AD},
title = {DNA barcoding of microgastrine parasitoid wasps (Hymenoptera: Braconidae) using high-throughput methods more than doubles the number of species known for Australia.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.12904},
pmid = {29791787},
issn = {1755-0998},
abstract = {The Microgastrinae are a hugely diverse subfamily of endoparasitoid wasps of lepidopteran caterpillars. They are important in agriculture as biological control agents and play a significant ecological role in the regulation of caterpillar populations. Whilst the group has been the focus of intensive rearing and DNA barcoding studies in the Northern Hemisphere, the Australian fauna has received little attention. In total, 99 species have been described from or have been introduced into Australia, but the real species diversity for the region is clearly much larger than this. In this study, museum ethanol samples and recent field collections were mined for hundreds of specimens of microgastrine wasps, which were then barcoded for the COI region, ITS2 ribosomal spacer and the wingless nuclear genes, using a pooled sequencing approach on an Illumina Miseq system. Full COI sequences were obtained for 525 individuals which, when combined with 162 publicly available sequences, represented 417 haplotypes, and a total of 236 species were delimited using a consensus approach. By more than doubling the number of known microgastrine wasp species in Australia, our study highlights the value of DNA barcoding in the context of employing high-throughput sequencing methods of bulk ethanol museum collections for biodiversity assessment.},
}
@article {pmid29791719,
year = {2018},
author = {Molins, A and Moya, P and García-Breijo, FJ and Reig-Armiñana, J and Barreno, E},
title = {Molecular and morphological diversity of Trebouxia microalgae in sphaerothallioid Circinaria spp. lichens[1].},
journal = {Journal of phycology},
volume = {54},
number = {4},
pages = {494-504},
doi = {10.1111/jpy.12751},
pmid = {29791719},
issn = {1529-8817},
mesh = {Ascomycota/*physiology ; Biodiversity ; Chlorophyta/classification/genetics/*physiology/ultrastructure ; Genetic Variation ; Lichens/classification/genetics/*physiology/ultrastructure ; Microalgae/classification/genetics/*physiology/ultrastructure ; Microscopy, Electron, Transmission ; Phylogeny ; Sequence Analysis, DNA ; Spain ; *Symbiosis ; },
abstract = {Three vagrant (Circinaria hispida, Circinaria gyrosa, and Circinaria sp. 'paramerae') and one crustose (semi-vagrant, Circinaria sp. 'oromediterranea') lichens growing in very continental areas in the Iberian Peninsula were selected to study the phycobiont diversity. Mycobiont identification was checked using nrITS DNA barcoding: Circinaria sp. 'oromediterranea' and Circinaria sp. 'paramerae' formed a new clade. Phycobiont diversity was analyzed in 50 thalli of Circinaria spp. using nrITS DNA and LSU rDNA, with microalgae coexistence being found in all the species analyzed by Sanger sequencing. The survey of phycobiont diversity showed up to four different Trebouxia spp. as the primary phycobiont in 20 thalli of C. hispida, in comparison with the remaining Circinaria spp., where only one Trebouxia was the primary microalga. In lichen species showing coexistence, some complementary approaches are needed (454 pyrosequencing and/or ultrastructural analyses). Five specimens were selected for high-throughput screening (HTS) analyses: 22 Trebouxia OTUs were detected, 10 of them not previously known. TEM analyses showed three different cell morphotypes (Trebouxia sp. OTU A12, OTU S51, and T. cretacea) whose ultrastructure is described here in detail for the first time. HTS revealed a different microalgae pool in each species studied, and we cannot assume a specific pattern between these pools and the ecological and/or morphological characteristics. The mechanisms involved in the selection of the primary phycobiont and the other microalgae by the mycobiont are unknown, and require complex experimental designs. The systematics of the genus Circinaria is not yet well resolved, and more analyses are needed to establish a precise delimitation of the species.},
}
@article {pmid29791459,
year = {2018},
author = {Tempestini, A and Rysgaard, S and Dufresne, F},
title = {Species identification and connectivity of marine amphipods in Canada's three oceans.},
journal = {PloS one},
volume = {13},
number = {5},
pages = {e0197174},
pmid = {29791459},
issn = {1932-6203},
mesh = {Amphipoda/classification/*genetics ; Animals ; Arctic Regions ; Biodiversity ; Canada ; Molecular Typing ; Oceans and Seas ; Phylogeny ; },
abstract = {Monitoring the distribution of marine biodiversity is a crucial step to better assess the impacts of global changes. Arctic marine fauna is dominated by amphipods in terms of abundance and biomass. These peracarids are an important marine order of crustaceans but the number of species found in the different Canadian oceans is currently unknown. Furthermore, most species are difficult to identify due to poor taxonomic descriptions and morphological convergence. The aim of this study was to assess the species diversity of marine amphipods in the three Canadian oceans using DNA barcoding. To do so, we produced a database of DNA barcodes of amphipods from the three Canadian Oceans publicly available from the BOLD website to which we added 310 new sequences from the Canadian Arctic Archipelago. We first delimited amphipod species based on barcode gap detection techniques and tree based method (bPTP) and then compared the composition of amphipods among the three oceans in order to assess the influence of past transarctic exchanges on Arctic diversity. Our analysis of 2309 sequences which represent more than 250 provisional species revealed a high connectivity between the Atlantic and Arctic Oceans. Our results also suggest that a single threshold to delimitate species is not suitable for amphipods. This study highlights the challenges involved in species delimitation and the need to obtain complete barcoding inventories in marine invertebrates.},
}
@article {pmid29788324,
year = {2018},
author = {Ren, L and Chen, W and Shang, Y and Meng, F and Zha, L and Wang, Y and Guo, Y},
title = {The Application of COI Gene for Species Identification of Forensically Important Muscid Flies (Diptera: Muscidae).},
journal = {Journal of medical entomology},
volume = {55},
number = {5},
pages = {1150-1159},
doi = {10.1093/jme/tjy076},
pmid = {29788324},
issn = {1938-2928},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Forensic Sciences ; Muscidae/*classification/genetics ; },
abstract = {Muscid Flies (Diptera: Muscidae) are of great forensic importance due to their wide distribution, ubiquitous and synanthropic nature. They are frequently neglected as they tend to arrive at the corpses later than the flesh flies and blow flies. Moreover, the lack of species-level identification also hinders investigation of medicolegal purposes. To overcome the difficulty of morphological identification, molecular method has gained relevance. Cytochrome c oxidase subunit I (COI) gene has been widely utilized. Nonetheless, to achieve correct identification of an unknown sample, it is important to survey certain muscid taxa from its geographic distribution range. Accordingly, the aim of this study is to contribute more geographically specific. We sequenced the COI gene of 51 muscid specimens of 12 species, and added all correct sequences available in GenBank to yield a total data set of 125 COI sequences from 33 muscid species to evaluate the COI gene as a molecular diagnostic tool. The interspecific distances were extremely high (4.7-19.8%) in either the standard barcoding fragment (658 bp) or the long COI sequence (1,019-1,535 bp), demonstrating that these two genetic markers were nearly identical in the species identification. However, the intraspecific distances of the long COI sequences were significantly higher than the barcoding region for the conspecific species that geographical locations vary greatly. Therefore, genetic diversity presented in this study provides a reference for species identification of muscid flies. Nevertheless, further investigation and data from more muscid species are required to enhance the efficacy of species-level identification using COI gene as a genetic marker.},
}
@article {pmid29786943,
year = {2018},
author = {Liu, J and Milne, RI and Möller, M and Zhu, GF and Ye, LJ and Luo, YH and Yang, JB and Wambulwa, MC and Wang, CN and Li, DZ and Gao, LM},
title = {Integrating a comprehensive DNA barcode reference library with a global map of yews (Taxus L.) for forensic identification.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.12903},
pmid = {29786943},
issn = {1755-0998},
abstract = {Rapid and accurate identification of endangered species is a critical component of biosurveillance and conservation management, and potentially policing illegal trades. However, this is often not possible using traditional taxonomy, especially where only small or preprocessed parts of plants are available. Reliable identification can be achieved via a comprehensive DNA barcode reference library, accompanied by precise distribution data. However, these require extensive sampling at spatial and taxonomic scales, which has rarely been achieved for cosmopolitan taxa. Here, we construct a comprehensive DNA barcode reference library and generate distribution maps using species distribution modelling (SDM), for all 15 Taxus species worldwide. We find that trnL-trnF is the ideal barcode for Taxus: It can distinguish all Taxus species and in combination with ITS identify hybrids. Among five analysis methods tested, NJ was the most effective. Among 4,151 individuals screened for trnL-trnF, 73 haplotypes were detected, all species-specific and some population private. Taxonomical, geographical and genetic dimensions of sampling strategy were all found to affect the comprehensiveness of the resulting DNA barcode library. Maps from SDM showed that most species had allopatric distributions, except T. mairei in the Sino-Himalayan region. Using the barcode library and distribution map data, two unknown forensic samples were identified to species (and in one case, population) level and another was determined as a putative interspecific hybrid. This integrated species identification system for Taxus can be used for biosurveillance, conservation management and to monitor and prosecute illegal trade. Similar identification systems are recommended for other IUCN- and CITES-listed taxa.},
}
@article {pmid29785925,
year = {2018},
author = {Fulakeza, JRM and Banda, RL and Lipenga, TR and Terlouw, DJ and Nkhoma, SC and Hodel, EM},
title = {Comparison of Two Genotyping Methods for Distinguishing Recrudescence from Reinfection in Antimalarial Drug Efficacy/Effectiveness Trials.},
journal = {The American journal of tropical medicine and hygiene},
volume = {99},
number = {1},
pages = {84-86},
pmid = {29785925},
issn = {1476-1645},
mesh = {Antigens, Protozoan/*genetics ; Antimalarials/*therapeutic use ; Artemether, Lumefantrine Drug Combination/therapeutic use ; Artemisinins/therapeutic use ; Child ; Cluster Analysis ; Drug Combinations ; Female ; Gene Expression ; Genotype ; Genotyping Techniques ; Humans ; Malaria, Falciparum/diagnosis/*drug therapy/parasitology ; Malawi ; Male ; Merozoite Surface Protein 1/*genetics ; Merozoites/drug effects/*genetics/growth &amp; development ; Plasmodium falciparum/*drug effects/genetics/growth &amp; development ; Polymorphism, Single Nucleotide ; Protozoan Proteins/*genetics ; Quinolines/therapeutic use ; Recurrence ; Treatment Outcome ; },
abstract = {Genotyping of allelic variants of Plasmodium falciparum merozoite surface proteins 1 and 2 (msp-1 and msp-2), and the glutamate-rich protein is the gold standard for distinguishing reinfections from recrudescences in antimalarial drug trials. We compared performance of the recently developed 24-single-nucleotide polymorphism (SNP) Barcoding Assay against msp-1 and msp-2 genotyping in a cluster-randomized effectiveness trial of artemether-lumefantrine and dihydroartemisinin-piperaquine in Malawi. Rates of recrudescence and reinfection estimated by the two methods did not differ significantly (Fisher's exact test; P = 0.887 and P = 0.768, respectively). There was a strong agreement between the two methods in predicting treatment outcomes and resolving the genetic complexity of malaria infections in this setting. These results support the use of this SNP assay as an alternative method for correcting antimalarial efficacy/effectiveness data.},
}
@article {pmid29784414,
year = {2018},
author = {Jansson, D and Wolterink, A and Bergwerff, L and Hough, P and Geukens, K and Åstot, C},
title = {Source attribution profiling of five species of Amanita mushrooms from four European countries by high resolution liquid chromatography-mass spectrometry combined with multivariate statistical analysis and DNA-barcoding.},
journal = {Talanta},
volume = {186},
number = {},
pages = {636-644},
doi = {10.1016/j.talanta.2018.03.069},
pmid = {29784414},
issn = {1873-3573},
mesh = {Agaricales/*chemistry ; Amanita/*chemistry ; Chromatography, Liquid ; DNA/*analysis ; Europe ; Mass Spectrometry ; Multivariate Analysis ; Species Specificity ; },
abstract = {Source attribution profiling of five species of Amanita mushrooms from four European countries was performed using Liquid Chromatography-High Resolution Mass Spectrometry (LC-HRMS) combined with multivariate statistical analysis. Initially, species determination was carried out morphologically and was verified by DNA-analysis. This data was then combined with chemical profiling, generated from LC-HRMS full scan analysis. The untargeted data was processed and the 720 most abundant peaks in the LC-HRMS chromatogram were used to build a multivariate PLS-DA model. The two independent methods for species determination showed 100% correlation, indicating the potential use of chemical profiling as a supporting technique to genetic methods. When specimens of one species were studied, significant variation related to the region of growth was found. The potential of the geo-positioning was shown for A. phalloides from Sweden, Denmark and UK and A. virosa from Sweden and Denmark. Additionally, A. virosa specimens could be attributed to three geographically different regions of Sweden.},
}
@article {pmid29784069,
year = {2019},
author = {Kelnarova, I and Jendek, E and Grebennikov, VV and Bocak, L},
title = {First molecular phylogeny of Agrilus (Coleoptera: Buprestidae), the largest genus on Earth, with DNA barcode database for forestry pest diagnostics.},
journal = {Bulletin of entomological research},
volume = {109},
number = {2},
pages = {200-211},
doi = {10.1017/S0007485318000330},
pmid = {29784069},
issn = {1475-2670},
mesh = {Animals ; Coleoptera/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; Forestry ; *Phylogeny ; },
abstract = {All more than 3000 species of Agrilus beetles are phytophagous and some cause economically significant damage to trees and shrubs. Facilitated by international trade, Agrilus species regularly invade new countries and continents. This necessitates a rapid identification of Agrilus species, as the first step for subsequent protective measures. This study provides the first DNA reference library for ~100 Agrilus species from the Northern Hemisphere based on three mitochondrial markers: cox1-5' (DNA barcode fragment), cox1-3', and rrnL. All 329 Agrilus records available in the Barcode of Life Database format, including specimen images and geo data, are released through a public dataset 'Agrilus1 329' available at: dx.doi.org/10.5883/DS-AGRILUS1. All Agrilus species were identified using adult morphology and by using molecular phylogenetic trees, as well as distance- and tree-based algorithms. Most DNA-based species limits agree well with the morphology-based identification. Our results include cases of high intraspecific variability and multiple species para- and polyphyly. DNA barcoding is a powerful species identification tool in Agrilus, although it frequently fails to recover morphologically-delimited Agrilus species-group. Even though the current three-gene database covers only ~3% of the known Agrilus diversity, it contains representatives of all principal lineages from the Northern Hemisphere and represents the most extensive dataset built for DNA-delimited species identification within this genus so far. Molecular data analyses can rapidly and cost-effectively identify an unknown sample, including immature stages and/or non-native taxa, or species not yet formally named.},
}
@article {pmid29783865,
year = {2018},
author = {Chan, BM and Badh, A and Berry, KA and Grauer, SA and King, CT},
title = {Flow Cytometry-Based Epitope Binning Using Competitive Binding Profiles for the Characterization of Monoclonal Antibodies against Cellular and Soluble Protein Targets.},
journal = {SLAS discovery : advancing life sciences R &amp; D},
volume = {23},
number = {7},
pages = {613-623},
doi = {10.1177/2472555218774334},
pmid = {29783865},
issn = {2472-5560},
mesh = {Antibodies, Monoclonal/*immunology ; Antigens/*immunology ; Binding, Competitive ; Biotinylation ; Cell Line ; Drug Discovery/methods ; Epitope Mapping/*methods ; *Flow Cytometry/methods ; High-Throughput Screening Assays ; Humans ; Protein Binding ; },
abstract = {A key step in the therapeutic antibody drug discovery process is early identification of diverse candidate molecules. Information comparing antibody binding epitopes can be used to classify antibodies within a large panel, guiding rational lead molecule selection. We describe a novel epitope binning method utilizing high-throughput flow cytometry (HTFC) that leverages cellular barcoding or spectrally distinct beads to multiplex samples to characterize antibodies raised against cell membrane receptor or soluble protein targets. With no requirement for sample purification or direct labeling, the method is suited for early characterization of antibody candidates. This method generates competitive binding profiles of each antibody against a defined set of known or unknown reference antibodies for binding to epitopes of an antigen. Antibodies with closely related competitive binding profiles indicate similar epitopes and are classified in the same bin. These large, high-throughput, multiplexed experiments can yield epitope bins or clusters for the entire antibody panel, from which a conceptual map of the epitope space for each antibody can be created. Combining this valuable epitope information with other data, such as functional activity, sequence, and selectivity of binding to orthologs and paralogs, enables us to advance the best epitope-diverse candidates for further development.},
}
@article {pmid29783021,
year = {2018},
author = {Pinacho-Pinacho, CD and García-Varela, M and Sereno-Uribe, AL and Pérez-Ponce de León, G},
title = {A hyper-diverse genus of acanthocephalans revealed by tree-based and non-tree-based species delimitation methods: Ten cryptic species of Neoechinorhynchus in Middle American freshwater fishes.},
journal = {Molecular phylogenetics and evolution},
volume = {127},
number = {},
pages = {30-45},
doi = {10.1016/j.ympev.2018.05.023},
pmid = {29783021},
issn = {1095-9513},
mesh = {Acanthocephala/*classification/genetics ; Animals ; Bayes Theorem ; Electron Transport Complex IV/genetics ; Female ; Fishes/*parasitology ; *Fresh Water ; Genetic Variation ; Geography ; Male ; Phenotype ; Phylogeny ; Reproducibility of Results ; Species Specificity ; United States ; },
abstract = {The genus Neoechinorhynchus represents a hyper-diverse group of acanthocephalans, parasites of fresh and brackish water fish and freshwater turtles, with approximately 116 species described worldwide. Forty-nine species have been recorded in the Americas, nine of them in Middle America. Even though species delimitation methods using DNA sequences have been rarely used for parasitic helminths, the genetic library for species of Neoechinorhynchus has grown in the past few years, enhancing the possibility of using these methods for inferring evolutionary relationships and for establishing more robust species boundaries. In this study, we used non-tree-based and tree-based methods through a coalescent approach to explore the species limits of specimens of Neoechinorhynchus collected in 57 localities across Middle America. We sequenced a large number of individuals to build a comprehensive dataset for three genes: the mitochondrial cytochrome c oxidase subunit I (352 individuals), the internal transcribed spacers (330 individuals), and the D2 + D3 domains of the large subunit (278 individuals). Several species delimitation methods were implemented, i.e., Automatic Barcode Gap Discovery (ABGD), General Mixed Yule-Coalescent Model (GMYC), Bayesian species delimitation (BPP) and species tree (∗BEAST). Additionally, we conducted a detailed morphological study of the diagnostic traits associated with the proboscis of 184 males and 169 females. Overall, our analyses allowed us to validate nine nominal species of Neoechinorhynchus and to identify 10 additional genetic lineages herein regarded as candidate species. This unexpected genetic diversity and the lack of reliable morphological traits show that the genus Neoechinorhynchus includes a group of cryptic species, at least in Middle America.},
}
@article {pmid29782489,
year = {2018},
author = {Miller, D and Brandt, N and Gresham, D},
title = {Systematic identification of factors mediating accelerated mRNA degradation in response to changes in environmental nitrogen.},
journal = {PLoS genetics},
volume = {14},
number = {5},
pages = {e1007406},
pmid = {29782489},
issn = {1553-7404},
support = {R01 GM107466/GM/NIGMS NIH HHS/United States ; 5R01GM107466/NH/NIH HHS/United States ; },
mesh = {Amino Acid Transport Systems/genetics ; Gene Expression Regulation, Fungal ; In Situ Hybridization, Fluorescence ; Mutation ; Nitrogen/*metabolism ; RNA Stability/*genetics ; RNA, Messenger/*genetics ; Ribonucleoproteins/genetics ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/genetics ; Transcriptome/genetics ; },
abstract = {Cellular responses to changing environments frequently involve rapid reprogramming of the transcriptome. Regulated changes in mRNA degradation rates can accelerate reprogramming by clearing or stabilizing extant transcripts. Here, we measured mRNA stability using 4-thiouracil labeling in the budding yeast Saccharomyces cerevisiae during a nitrogen upshift and found that 78 mRNAs are subject to destabilization. These transcripts include Nitrogen Catabolite Repression (NCR) and carbon metabolism mRNAs, suggesting that mRNA destabilization is a mechanism for targeted reprogramming of the transcriptome. To explore the molecular basis of destabilization we implemented a SortSeq approach to screen the pooled deletion collection library for trans factors that mediate rapid GAP1 mRNA repression. We combined low-input multiplexed Barcode sequencing with branched-DNA single-molecule mRNA FISH and Fluorescence-activated cell sorting (BFF) to identify the Lsm1-7p/Pat1p complex and general mRNA decay machinery as important for GAP1 mRNA clearance. We also find that the decapping modulators EDC3 and SCD6, translation factor eIF4G2, and the 5' UTR of GAP1 are factors that mediate rapid repression of GAP1 mRNA, suggesting that translational control may impact the post-transcriptional fate of mRNAs in response to environmental changes.},
}
@article {pmid29780268,
year = {2018},
author = {Mulcahy, DG and Lee, JL and Miller, AH and Chand, M and Thura, MK and Zug, GR},
title = {Filling the BINs of life: Report of an amphibian and reptile survey of the Tanintharyi (Tenasserim) Region of Myanmar, with DNA barcode data.},
journal = {ZooKeys},
volume = {},
number = {757},
pages = {85-152},
pmid = {29780268},
issn = {1313-2989},
abstract = {Despite threats of species extinctions, taxonomic crises, and technological advances in genomics and natural history database informatics, we are still distant from cataloguing all of the species of life on earth. Amphibians and reptiles are no exceptions; in fact new species are described nearly every day and many species face possible extinction. The number of described species continues to climb as new areas of the world are explored and as species complexes are examined more thoroughly. The use of DNA barcoding provides a mechanism for rapidly estimating the number of species at a given site and has the potential to record all of the species of life on Earth. Though DNA barcoding has its caveats, it can be useful to estimate the number of species in a more systematic and efficient manner, to be followed in combination with more traditional, morphology-based identifications and species descriptions. Herein, we report the results of a voucher-based herpetological expedition to the Tanintharyi (Tenasserim) Region of Myanmar, enhanced with DNA barcode data. Our main surveys took place in the currently proposed Tanintharyi National Park. We combine our results with photographs and observational data from the Chaung-nauk-pyan forest reserve. Additionally, we provide the first checklist of amphibians and reptiles of the region, with species based on the literature and museum. Amphibians, anurans in particular, are one of the most poorly known groups of vertebrates in terms of taxonomy and the number of known species, particularly in Southeast Asia. Our rapid-assessment program combined with DNA barcoding and use of Barcode Index Numbers (BINs) of voucher specimens reveals the depth of taxonomic diversity in the southern Tanintharyi herpetofauna even though only a third of the potential amphibians and reptiles were seen. A total of 51 putative species (one caecilian, 25 frogs, 13 lizards, 10 snakes, and two turtles) were detected, several of which represent potentially undescribed species. Several of these species were detected by DNA barcode data alone. Furthermore, five species were recorded for the first time in Myanmar, two amphibians (Ichthyophis cf. kohtaoensis and Chalcorana eschatia) and three snakes (Ahaetulla mycterizans, Boiga dendrophila, and Boiga drapiezii).},
}
@article {pmid29774898,
year = {2018},
author = {Górecki, M and Carpita, L and Arrico, L and Zinna, F and Di Bari, L},
title = {Chiroptical methods in a wide wavelength range for obtaining Ln[3+] complexes with circularly polarized luminescence of practical interest.},
journal = {Dalton transactions (Cambridge, England : 2003)},
volume = {47},
number = {21},
pages = {7166-7177},
doi = {10.1039/c8dt00865e},
pmid = {29774898},
issn = {1477-9234},
abstract = {We studied enantiopure chiral trivalent lanthanide (Ln3+ = La3+, Sm3+, Eu3+, Gd3+, Tm3+, and Yb3+) complexes with two fluorinated achiral tris(β-diketonate) ligands (HFA = hexafluoroacetylacetonate and TTA = 2-thenoyltrifluoroacetonate), incorporating a chiral bis(oxazolinyl)pyridine (PyBox) unit as a neutral ancillary ligand, by the combined use of optical and chiroptical methods, ranging from UV to IR both in absorption and circular dichroism (CD), and including circularly polarized luminescence (CPL). Ultimately, all the spectroscopic information is integrated into a total and a chiroptical super-spectrum, which allows one to characterize a multidimensional chemical space, spanned by the different Ln3+ ions, the acidity and steric demand of the diketone and the chirality of the PyBox ligand. In all cases, the Ln3+ ions endow the systems with peculiar chiroptical properties, either allied to f-f transitions or induced by the metal onto the ligand. In more detail, we found that Sm3+ complexes display interesting CPL features, which partly superimpose and partly integrate the more common Eu3+ properties. Especially, in the context of security tags, the pair Sm/Eu may be a winning choice for chiroptical barcoding.},
}
@article {pmid29774786,
year = {2019},
author = {Panprommin, D and Soontornprasit, K and Pangeson, T},
title = {Comparison of three molecular methods for species identification of the family Cichlidae in Kwan Phayao, Thailand.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {1},
pages = {184-190},
doi = {10.1080/24701394.2018.1472248},
pmid = {29774786},
issn = {2470-1408},
mesh = {Animals ; Cichlids/classification/*genetics ; DNA Barcoding, Taxonomic/*methods/standards ; Electron Transport Complex IV/genetics ; Fish Proteins/genetics ; *Phylogeny ; Polymorphism, Genetic ; Sensitivity and Specificity ; },
abstract = {The species diversity of cichlids was investigated in Kwan Phayao from August 2016 to May 2017. Four cichlid species were found, including Oreochromis niloticus, Oreochromis mossambicus, Coptodon rendalli and Coptodon zillii. Due to similar characterizations, it is very difficult to identify each species. Three molecular methods were used to distinguish these four species. DNA barcodes or partial cytochrome c oxidase I (COI) gene sequences were amplified by PCR and sequenced. In Oreochromis sp. and Coptodon sp., 707- and 704-bp fragments were amplified, respectively. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis showed clear differences between the four cichlid species after digestion with three restriction enzymes, ScaI, HindIII and PdiI. ScaI and HindIII separated Oreochromis sp. from Coptodon sp. due to different fragment sizes. PdiI distinguished each cichlid species in the same genus. Finally, high resolution melting (HRM) analysis showed the sensitivity of the primers for discriminating these species with small amplicons and melting curves. From the comparison, HRM analysis was the most efficient method because the primer was shown to be sensitive for discriminating the four cichlids. In addition, it was inexpensive and required a short time to detect large samples. However, direct sequencing or DNA barcodes were still necessary in the case of the COI sequences of organisms of interest, which have not been reported in any databases. These four cichlids are alien species in Thailand; thus, species identification is very important for fishery management.},
}
@article {pmid29773077,
year = {2018},
author = {Díez-Fernández, A and Martínez-de la Puente, J and Ruiz, S and Gutiérrez-López, R and Soriguer, R and Figuerola, J},
title = {Aedes vittatus in Spain: current distribution, barcoding characterization and potential role as a vector of human diseases.},
journal = {Parasites &amp; vectors},
volume = {11},
number = {1},
pages = {297},
pmid = {29773077},
issn = {1756-3305},
support = {CGL2015-65055-P//Ministerio de Econom&#xed;a y Competitividad/International ; Severo-Ochoa grant SVP-2014-068571//Ministerio de Econom&#xed;a y Competitividad/International ; BES-2013-065274//Ministerio de Econom&#xed;a y Competitividad/International ; 2017 Leonardo Grant for Researchers and Cultural Creators//Fundaci&#xf3;n BBVA/International ; CSIC Open Access Publication Support Initiative//Consejo Superior de Investigaciones Cient&#xed;ficas/International ; },
mesh = {Aedes/*genetics/physiology/*virology ; *Animal Distribution ; Animals ; DNA Barcoding, Taxonomic/*methods ; *Disease Vectors ; Electron Transport Complex IV/genetics ; Europe ; Humans ; India ; Larva/genetics ; Mosquito Vectors/genetics/physiology/virology ; Spain/epidemiology ; Virus Diseases/epidemiology/prevention &amp; control/transmission/virology ; },
abstract = {BACKGROUND: Aedes vittatus is currently found in Africa, Asia and Europe, where it acts as a vector of pathogens causing animal and human diseases (e.g. chikungunya, Zika and dengue). Like other Aedes species, Ae. vittatus is able to breed in artificial containers. The ECDC has recently highlighted the need for molecular tools (i.e. barcoding characterization) that enable Aedes species to be identified in entomological surveys.<br><br>RESULTS: We sampled mosquito larvae and adults in southern Spain and used a molecular approach to amplify and sequence a fragment of the cytochrome c oxidase subunit 1 gene (barcoding region) of the mosquitoes. The blast comparison of the mosquito sequences isolated from Spain with those deposited in public databases provided a &#x2265; 99% similarity with sequences for two Aedes mosquitoes, Ae. vittatus and Ae. cogilli, while similarities with other Aedes species were &#x2264; 94%. Aedes cogilli is only present in India and there are no records of this species from Europe.<br><br>CONCLUSIONS: Due to the low genetic differences between Ae. vittatus and Ae. cogilli, the barcoding region should not be used as the only method for identifying Ae. vittatus, especially in areas where both of these Aedes species are present. This type of analysis should thus be combined with morphological identification using available keys and/or the characterization of other molecular markers. In addition, further entomological surveys should be conducted in order to identify the fine-scale distribution of this mosquito species in Europe.},
}
@article {pmid29769836,
year = {2018},
author = {Onuferko, TM},
title = {A revision of the cleptoparasitic bee genus Epeolus Latreille for Nearctic species, north of Mexico (Hymenoptera, Apidae).},
journal = {ZooKeys},
volume = {},
number = {755},
pages = {1-185},
pmid = {29769836},
issn = {1313-2989},
abstract = {Herein, the cleptoparasitic (cuckoo) bee genus Epeolus (Hymenoptera: Apidae) is revised for species occurring in North America, north of Mexico, and an updated checklist of all species known to occur in Canada and the United States of America is provided with comprehensive descriptions, diagnoses, and a single dichotomous key (using the same couplets for both sexes) to aid in their identification. To increase their recognition among North American naturalists, English common names are also proposed for all North American Epeolus. A total of 43 species is confirmed as present in the region, 15 of which are newly recognized. The following new species are proposed based on unique morphological (and in most cases also molecular) attributes: E. andriyisp. n., E. attenboroughisp. n., E. axillarissp. n., E. basilisp. n., E. brumleyisp. n., E. chamaesarachaesp. n., E. deyrupisp. n., E. diadematussp. n., E. ferrariisp. n., E. gibbsisp. n., E. inornatussp. n., E. nebulosussp. n., E. packerisp. n., E. splendidussp. n., and E. tessierissp. n. Of the 15, six (E. axillaris, E. brumleyi, E. chamaesarachae, E. diadematus, E. splendidus, and E. tessieris) were identified as new species under different names (nomina nuda) in an M.Sc. thesis by Richard L. Brumley in 1965, but until now they have not been formally described. Detailed morphological comparisons with some evidence from DNA barcoding support the following synonymies, one of which C was first proposed by Brumley (1965): a) E. melectimimus Cockerell and Sandhouse, syn. n., under E. asperatus Cockerell; b) E. crucis Cockerell, syn. n., under E. compactus Cresson; c) E. mesillae palmarum Linsley, syn. n., under E. mesillae (Cockerell); and d) E. weemsi Mitchell, syn. n., and e) E. vernalis Mitchell, syn. n., under E. ilicis Mitchell. Only one member of the almost entirely Neotropical "Trophocleptria group" (Epeolus bifasciatus Cresson) is confirmed as occurring north of Mexico, and is widespread East of the Rocky Mountains. Known floral associations are indicated for each species, as are suspected or known host species of Colletes Latreille. Evidence is presented that suggests further investigation into the possible synonymy of Colletes wickhami Timberlake under C. scopiventer Swenk is warranted.},
}
@article {pmid29769698,
year = {2018},
author = {Cucco, F and Clipson, A and Kennedy, H and Sneath Thompson, J and Wang, M and Barrans, S and van Hoppe, M and Ochoa Ruiz, E and Caddy, J and Hamid, D and Cummin, T and Burton, C and Davies, AJ and Johnson, P and Du, MQ},
title = {Mutation screening using formalin-fixed paraffin-embedded tissues: a stratified approach according to DNA quality.},
journal = {Laboratory investigation; a journal of technical methods and pathology},
volume = {98},
number = {8},
pages = {1084-1092},
doi = {10.1038/s41374-018-0066-z},
pmid = {29769698},
issn = {1530-0307},
support = {13006/LLR_/Blood Cancer UK/United Kingdom ; 15002/LLR_/Blood Cancer UK/United Kingdom ; 15019/LLR_/Blood Cancer UK/United Kingdom ; },
mesh = {DNA/chemistry/genetics/metabolism ; DNA Mutational Analysis/*methods ; Formaldehyde ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Mutation ; Paraffin Embedding/*methods ; Polymerase Chain Reaction/methods ; Reproducibility of Results ; Tissue Fixation/*methods ; },
abstract = {DNA samples from formalin-fixed paraffin-embedded tissues are highly degraded with variable quality, and this imposes a big challenge for targeted sequencing due to false positives, largely caused by PCR errors and cytosine deamination. To eliminate false positives, a common practice is to validate the detected variants by Sanger sequencing or perform targeted sequencing in duplicate. Technically, PCR errors could be removed by molecular barcoding of template DNA prior to amplification as in the HaloPlexHS design. Nonetheless, it is uncertain to what extent variants detected using this approach should be further validated. Here, we addressed this question by correlating variant reproducibility with DNA quality using HaloPlexHS target enrichment and Illumina HiSeq4000, together with an in-house validated variant calling algorithm. The overall sequencing coverage, as shown by analyses of 70 genes in 266 cases of large B-cell lymphoma, was excellent (98%) in DNA samples amenable for PCR of ≥400 bp, but suboptimal (92%) and poor (80%) in those amenable for PCR of 300 bp and 200 bp respectively. By mutation analysis in duplicate in 93 cases, we demonstrated that 20 alternative allele depth (AAD) was an optimal cut-off value for separating reproducible from non-reproducible variants in DNA samples amenable for PCR of ≥300 bp, with 97% sensitivity and 100% specificity. By cross validation with a previously established targeted sequencing protocol by Fluidigm-PCR and Illumina MiSeq, the HaloPlexHS protocol was shown to be highly sensitive and specific in mutation screening. To conclude, we proposed a stratified approach for mutation screening by HaloplexHS and Illumina HiSeq4000 according to DNA quality. DNA samples with good quality (≥400 bp) are amenable for mutation analysis with a single replicate, with only variants at 15-20 AAD requiring for further validation, while those with suboptimal quality (300 bp) are better analysed in duplicate with reproducible variants at >15 AAD regarded as true genetic changes.},
}
@article {pmid29767359,
year = {2018},
author = {Warren, S},
title = {Simultaneous, Multiplexed Detection of RNA and Protein on the NanoString[®] nCounter[®] Platform.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1783},
number = {},
pages = {105-120},
doi = {10.1007/978-1-4939-7834-2_5},
pmid = {29767359},
issn = {1940-6029},
mesh = {Gene Expression Profiling/*methods ; Humans ; Molecular Diagnostic Techniques/*methods ; Nanotechnology/*methods ; Neoplasm Proteins/*analysis ; Neoplasms/*genetics/*metabolism ; Nucleic Acid Hybridization ; RNA, Messenger/*analysis ; Specimen Handling ; },
abstract = {The NanoString nCounter Analysis System uses a digital fluorescent barcode technology that allows for direct multiplexed measurement of gene expression (mRNA), DNA, and protein. The technology uses molecular barcodes and single-molecule imaging to detect and count unique mRNA and protein targets in a single reaction. nCounter-based detection is enzyme-free (no amplification of mRNA is required), fully automated, and allows simultaneous detection of up to 770 mRNA and 30 protein targets from multiple sample types. Target counting is fully digital with quantitative data output. Here we describe preparation of solid tumor lysate samples for use in the nCounter Analysis System.},
}
@article {pmid29765686,
year = {2018},
author = {Watanabe, HK and Chen, C and Marie, DP and Takai, K and Fujikura, K and Chan, BKK},
title = {Phylogeography of hydrothermal vent stalked barnacles: a new species fills a gap in the Indian Ocean 'dispersal corridor' hypothesis.},
journal = {Royal Society open science},
volume = {5},
number = {4},
pages = {172408},
pmid = {29765686},
issn = {2054-5703},
abstract = {Phylogeography of animals provides clues to processes governing their evolution and diversification. The Indian Ocean has been hypothesized as a 'dispersal corridor' connecting hydrothermal vent fauna of Atlantic and Pacific oceans. Stalked barnacles of the family Eolepadidae are common associates of deep-sea vents in Southern, Pacific and Indian oceans, and the family is an ideal group for testing this hypothesis. Here, we describe Neolepas marisindica sp. nov. from the Indian Ocean, distinguished from N. zevinae and N. rapanuii by having a tridentoid mandible in which the second tooth lacks small elongated teeth. Morphological variations suggest that environmental differences result in phenotypic plasticity in the capitulum and scales on the peduncle in eolepadids. We suggest that diagnostic characters in Eolepadidae should be based mainly on more reliable arthropodal characters and DNA barcoding, while the plate arrangement should be used carefully with their intraspecific variation in mind. We show morphologically that Neolepas specimens collected from the South West Indian Ridge, the South East Indian Ridge and the Central Indian Ridge belong to the new species. Molecular phylogeny and fossil evidence indicated that Neolepas migrated from the southern Pacific to the Indian Ocean through the Southern Ocean, providing key evidence against the 'dispersal corridor' hypothesis. Exploration of the South East Indian Ridge is urgently required to understand vent biogeography in the Indian Ocean.},
}
@article {pmid29765667,
year = {2018},
author = {Yang, H and Yu, P and Lu, Y and Jiao, Z and Chen, L and Zhou, Y and Shen, Y and Jia, X},
title = {A novel non-sequencing approach for rapid authentication of Testudinis Carapax et Plastrum and Trionycis Carapax by species-specific primers.},
journal = {Royal Society open science},
volume = {5},
number = {4},
pages = {172140},
pmid = {29765667},
issn = {2054-5703},
abstract = {A novel non-sequencing approach was developed to detect short DNA fragments (ca 100 bp) for rapid authentication of two natural products, namely Testudinis Carapax et Plastrum and Trionycis Carapax, based on the difference in mitochondrial genome. Five specifically designed primer reactions were established to target species for reliable identification of their commercial products. They were confirmed to have a high level of inter-species-specificity and good intra-species stability. The limit of detection was estimated to be 1 ng of genomes for all of five assays. Also, the validation results demonstrated that the raw materials and processed products in addition to some of the highly processed products can be conveniently authenticated with good sensitivity and precision by this newly proposed approach. Especially, when reference sample mixtures were assayed, these primer sets have still performed well but not the prevailing COI barcoding technology. These could assist in the discrimination and identification of other animal-derived medicines for their form of raw material, the pulverized and the complex.},
}
@article {pmid29765588,
year = {2018},
author = {Wang, X and Gussarova, G and Ruhsam, M and de Vere, N and Metherell, C and Hollingsworth, PM and Twyford, AD},
title = {DNA barcoding a taxonomically complex hemiparasitic genus reveals deep divergence between ploidy levels but lack of species-level resolution.},
journal = {AoB PLANTS},
volume = {10},
number = {3},
pages = {ply026},
pmid = {29765588},
issn = {2041-2851},
abstract = {DNA barcoding is emerging as a useful tool not only for species identification but also for studying evolutionary and ecological processes. Although plant DNA barcodes do not always provide species-level resolution, the generation of large DNA barcode data sets can provide insights into the mechanisms underlying the generation of species diversity. Here, we study evolutionary processes in taxonomically complex British Euphrasia (Orobanchaceae), a group with multiple ploidy levels, frequent self-fertilization, young species divergence and widespread hybridization. We use a phylogenetic approach to investigate the colonization history of British Euphrasia, followed by a DNA barcoding survey and population genetic analyses to reveal the causes of shared sequence variation. Phylogenetic analysis shows Euphrasia have colonized Britain from mainland Europe on multiple occasions. DNA barcoding reveals that no British Euphrasia species has a consistent diagnostic sequence profile, and instead, plastid haplotypes are either widespread across species, or are population specific. The partitioning of nuclear genetic variation suggests differences in ploidy act as a barrier to gene exchange, while the divergence between diploid and tetraploid ITS sequences supports the polyploids being allotetraploid in origin. Overall, these results show that even when lacking species-level resolution, analyses of DNA barcoding data can reveal evolutionary patterns in taxonomically complex genera.},
}
@article {pmid29765262,
year = {2018},
author = {Jeong, MK and Soh, HY and Wi, JH and Suh, HL},
title = {A new Notomastus (Annelida, Capitellidae) species from Korean waters, with genetic comparison based on three gene markers.},
journal = {ZooKeys},
volume = {},
number = {754},
pages = {141-155},
pmid = {29765262},
issn = {1313-2989},
abstract = {Notomastus koreanussp. n., collected from the sublittoral muddy bottom of Korean waters, is described as a new species. The Korean new species closely resembles N. torquatus Hutchings &amp; Rainer, 1979 in the chaetal arrangement and the details of abdominal segments, but differs in the position of genital pores and the absence of eyes. DNA sequences (mtCOI, 16S rRNA, and histone H3) of the new species were compared with all the available sequences of Notomastus species in the GenBank database. Three genes showed significant genetic differences between the new species and its congeners (COI: 51.2%, 16S: 38.1-47.3%, H3: 3.7-9.3%). This study also includes a comprehensive comparison of the new Korean Notomastus species with its most closely similar species, based on the morphological and genetic results.},
}
@article {pmid29763782,
year = {2018},
author = {Wawrzyniak, R and Wasiak, W and Jasiewicz, B and Ludwiczuk, A and Bączkiewicz, A and Buczkowska, K},
title = {High correlation of chemical composition with genotype in cryptic species of the liverwort Aneura pinguis.},
journal = {Phytochemistry},
volume = {152},
number = {},
pages = {134-147},
doi = {10.1016/j.phytochem.2018.05.004},
pmid = {29763782},
issn = {1873-3700},
mesh = {Genotype ; Hepatophyta/*chemistry/*genetics ; Multivariate Analysis ; Solid Phase Microextraction ; Species Specificity ; Volatile Organic Compounds/*chemistry/isolation &amp; purification ; },
abstract = {Chemical constituents of cryptic species detected within the liverwort Aneura pinguis were identified using headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS). Fibre coating with divinylbenzene/carboxen/polydimethylsiloxane (DVB/CAR/PDMS) was used. A total of 48 samples of A. pinguis were analysed. The studied plants were identified genetically based on barcode DNA sequences and represented three cryptic species (A, B and F) of A. pinguis. Cryptic species A and B are genetically diverse; both represent three evolutionary lineages: A1, A2, A3 and B1, B2, B3, respectively. The cryptic species F that was recently detected is not diverse. The most characteristic compounds in analysed samples were sesquiterpene hydrocarbons (up to 17.7% for A1; 15.7% for A2; 20.6% for A3; 7.7% for B1; 2.0% for B2; 3.7% for B3; 10.2% for F), oxygenated sesquiterpenoids (up to 68.0% for A1; 54.7% for A2; 52.6% for A3; 63.5% for B1; 88.7% for B2; 82.7% for B3; 78.8% for F), and linear aliphatic hydrocarbons (up to 14.8% for A1; 1.1% for A2; 12.1% for A3; 6.9 for B1; 5.2% for B2; 1.1% for B3; 7.0% for F). The dominant compound in the studied samples was pinguisone. The second dominant compound present in the tested plant material was deoxopinguisone, except for lineage B2, where only a small relative concentration of this compound was found. A high content of deoxopinguisone in cryptic species A (lineages A1, A2 and A3) was accompanied by the presence of isopinguisone and methyl norpinguisonate, whereas these two compounds were not detected in cryptic species B (lineages B1 and B3) and F. The chemical compounds detected in the studied samples of A. pinguis were subjected to multivariate statistical analysis. The results showed that the chemical composition depends mainly on the genotype of the plant and slightly on the habitat. However, there was no clear correlation between the volatile compounds and the date of collection of the studied plants.},
}
@article {pmid29762744,
year = {2018},
author = {Shayya, S and Debruyne, R and Nel, A and Azar, D},
title = {Forensically Relevant Blow Flies in Lebanon Survey and Identification Using Molecular Markers (Diptera: Calliphoridae).},
journal = {Journal of medical entomology},
volume = {55},
number = {5},
pages = {1113-1123},
doi = {10.1093/jme/tjy068},
pmid = {29762744},
issn = {1938-2928},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Diptera ; Electron Transport Complex IV/genetics ; *Forensic Sciences ; Lebanon ; Phylogeny ; },
abstract = {Calliphoridae are among the first insects associated to decomposing animal remains. We have collected 1,841 specimens of three calliphorid genera: Calliphora, Lucilia, and Chrysomya, from different Lebanese localities as a first step in implementing a database of insects of forensic relevance for the country. Blow-flies are crucial for the estimation of the postmortem interval. DNA-based identification is a rapid and accurate method, often used for morphologically similar species, especially for immatures or incomplete specimens. In this study, we test the suitability of three genetic markers to identify adults and immature stages of calliphorids, viz., mitochondrial cytochrome c oxidase subunit I (COI) barcode, a region including partial sequences of mitochondrial Cyt-b-tRNAser-ND1, and second internal transcribed spacer (ITS2) region of nuclear ribosomal DNA. Forty Lebanese specimens of various developmental stages (egg, larva, wandering third instar, pupa, newly emerged adult, and mature adult) were identified among the three calliphorid genera: Calliphora, Lucilia, and Chrysomya, and compared with published sequences to confirm their specific assignation. Phylogenetic analyses showed the robustness of ITS2 and COI to identify calliphorids at species level. Nevertheless, ITS2 failed to discriminate Lucilia caesar (Linnaeus) (Diptera, Calliphoridae) from Lucilia illustris (Meigen) (Diptera, Calliphoridae), and COI had a similar issue with Lucilia sericata (Meigen) (Diptera, Calliphoridae) and Lucilia cuprina (Wiedemann) (Diptera, Calliphoridae). Thus, these two markers are complementary. This work contributes new nucleotide sequences for Lebanon. It is a first step in implementing a molecular database of forensic relevant insects for the country.},
}
@article {pmid29761363,
year = {2018},
author = {Zwart, H},
title = {Scientific iconoclasm and active imagination: synthetic cells as techno-scientific mandalas.},
journal = {Life sciences, society and policy},
volume = {14},
number = {1},
pages = {10},
pmid = {29761363},
issn = {2195-7819},
support = {BaSyC 024.003.019//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
mesh = {*Artificial Cells ; Biomedical Research/*ethics/*methods ; Humans ; Synthetic Biology/*ethics/*methods ; },
abstract = {Metaphors allow us to come to terms with abstract and complex information, by comparing it to something which is structured, familiar and concrete. Although modern science is "iconoclastic", as Gaston Bachelard phrases it (i.e. bent on replacing living entities by symbolic data: e.g. biochemical and mathematical symbols and codes), scientists are at the same time prolific producers of metaphoric images themselves. Synthetic biology is an outstanding example of a technoscientific discourse replete with metaphors, including textual metaphors such as the "Morse code" of life, the "barcode" of life and the "book" of life. This paper focuses on a different type of metaphor, however, namely on the archetypal metaphor of the mandala as a symbol of restored unity and wholeness. Notably, mandala images emerge in textual materials (papers, posters, PowerPoints, etc.) related to one of the new "frontiers" of contemporary technoscience, namely the building of a synthetic cell: a laboratory artefact that functions like a cell and is even able to replicate itself. The mandala symbol suggests that, after living systems have been successfully reduced to the elementary building blocks and barcodes of life, the time has now come to put these fragments together again. We can only claim to understand life, synthetic cell experts argue, if we are able to technically reproduce a fully functioning cell. This holistic turn towards the cell as a meaningful whole (a total work of techno-art) also requires convergence at the "subject pole": the building of a synthetic cell as a practice of the self, representing a turn towards integration, of multiple perspectives and various forms of expertise.},
}
@article {pmid29757342,
year = {2018},
author = {Guerin, S and Syed, TAM and Thompson, D},
title = {Deconstructing collagen piezoelectricity using alanine-hydroxyproline-glycine building blocks.},
journal = {Nanoscale},
volume = {10},
number = {20},
pages = {9653-9663},
doi = {10.1039/c8nr01634h},
pmid = {29757342},
issn = {2040-3372},
abstract = {Collagen piezoelectricity has been the focus of a large number of experimental and theoretical studies for over fifty years. Less is known about the piezoelectric properties of its building blocks, in particular but not limited to, proline and hydroxyproline. Spurred by the recent upsurge of interest in piezoelectricity in organic crystals including our own report of unprecedentedly high piezoelectricity in amino acid glycine, we predict and measure the piezoelectric properties of collagen subcomponents in single crystalline forms and the collagen-like alanine-hydroxyproline-glycine trimer peptide. We map the modulation of piezoelectric charge constants in collagen building blocks as the crystal symmetry is lowered and the molecule size increases, finding strong evidence for amino acid-level barcoding of collagen piezoelectricity that can in turn be tuned using very simple chemistry. The simple addition of an -OH group can increase piezoelectric constants by up to two orders of magnitude (d25 = 25 ± 5 pC N-1) as measured in Y-cut hydroxyproline crystals. The value is similar to that obtained from thermoelectrically poled commercial polyvinylidene di fluoride (PVDF) films. Overall, our findings support a simple block by block approach in which first principles calculations can guide the understanding and re-engineering of piezoelectric biomolecules.},
}
@article {pmid29755504,
year = {2018},
author = {Almerón-Souza, F and Sperb, C and Castilho, CL and Figueiredo, PICC and Gonçalves, LT and Machado, R and Oliveira, LR and Valiati, VH and Fagundes, NJR},
title = {Molecular Identification of Shark Meat From Local Markets in Southern Brazil Based on DNA Barcoding: Evidence for Mislabeling and Trade of Endangered Species.},
journal = {Frontiers in genetics},
volume = {9},
number = {},
pages = {138},
pmid = {29755504},
issn = {1664-8021},
abstract = {Elasmobranchs, the group of cartilaginous fishes that include sharks and rays, are especially vulnerable to overfishing due to low fecundity and late sexual maturation. A significant number of elasmobranch species are currently overexploited or threatened by fisheries activities. Additionally, several recent reports have indicated that there has been a reduction in regional elasmobranch population sizes. Brazil is an important player in elasmobranch fisheries and one of the largest importers of shark meat. However, carcasses entering the shark meat market have usually had their fins and head removed, which poses a challenge to reliable species identification based on the morphology of captured individuals. This is further complicated by the fact that the internal Brazilian market trades several different elasmobranch species under a common popular name: "cação." The use of such imprecise nomenclature, even among governmental agencies, is problematic for both controlling the negative effects of shark consumption and informing the consumer about the origins of the product. In this study, we used DNA barcoding (mtDNA, COI gene) to identify, at the species level, "cação" samples available in local markets from Southern Brazil. We collected 63 samples traded as "cação," which we found to correspond to 20 different species. These included two teleost species: Xiphias gladius (n = 1) and Genidens barbus (n = 6), and 18 species from seven elasmobranch orders (Carcharhiniformes, n = 42; Squaliformes, n = 3; Squatiniformes, n = 2; Rhinopristiformes, n = 4; Myliobatiformes, n = 3; Rajiformes, n = 1; and Torpediniformes, n = 1). The most common species in our sample were Prionace glauca (n = 15) and Sphyrna lewini (n = 14), while all other species were represented by four samples or less. Considering IUCN criteria, 47% of the elasmobranch species found are threatened at the global level, while 53% are threatened and 47% are critically endangered in Brazil. These results underline that labeling the meat of any shark species as "cação" is problematic for monitoring catch allocations from the fishing industry and discourages consumer engagement in conservationist practices through informed decision-making.},
}
@article {pmid29750998,
year = {2018},
author = {Barbosa, VC},
title = {Information-theoretic signatures of biodiversity in the barcoding gene.},
journal = {Journal of theoretical biology},
volume = {451},
number = {},
pages = {111-116},
doi = {10.1016/j.jtbi.2018.05.008},
pmid = {29750998},
issn = {1095-8541},
mesh = {Animals ; *Biodiversity ; Biological Evolution ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Phylogeny ; Principal Component Analysis ; },
abstract = {Analyzing the information content of DNA, though holding the promise to help quantify how the processes of evolution have led to information gain throughout the ages, has remained an elusive goal. Paradoxically, one of the main reasons for this has been precisely the great diversity of life on the planet: if on the one hand this diversity is a rich source of data for information-content analysis, on the other hand there is so much variation as to make the task unmanageable. During the past decade or so, however, succinct fragments of the COI mitochondrial gene, which is present in all animal phyla and in a few others, have been shown to be useful for species identification through DNA barcoding. A few million such fragments are now publicly available through the BOLD systems initiative, thus providing an unprecedented opportunity for relatively comprehensive information-theoretic analyses of DNA to be attempted. Here we show how a generalized form of total correlation can yield distinctive information-theoretic descriptors of the phyla represented in those fragments. In order to illustrate the potential of this analysis to provide new insight into the evolution of species, we performed principal component analysis on standardized versions of the said descriptors for 23 phyla. Surprisingly, we found that, though based solely on the species represented in the data, the first principal component correlates strongly with the natural logarithm of the number of all known living species for those phyla. The new descriptors thus constitute clear information-theoretic signatures of the processes whereby evolution has given rise to current biodiversity, which suggests their potential usefulness in further related studies.},
}
@article {pmid29748725,
year = {2018},
author = {Yang, W and Li, T and Shu, C and Ji, S and Wang, L and Wang, Y and Li, D and Mtalimanja, M and Sun, L and Ding, L},
title = {Non-enzymolytic adenosine barcode-mediated dual signal amplification strategy for ultrasensitive protein detection using LC-MS/MS.},
journal = {Mikrochimica acta},
volume = {185},
number = {6},
pages = {293},
pmid = {29748725},
issn = {1436-5073},
support = {81573387//National Natural Science Foundation of China/International ; 81703472//National Natural Science Foundation of China/International ; 81603072//National Natural Science Foundation of China/International ; 81560695//National Natural Science Foundation of China/International ; KYCX17_0683//the Postgraduate Research &amp; Practice Innovation Program of Jiangsu Province/International ; },
mesh = {Adenosine/*chemistry ; Aptamers, Nucleotide/metabolism ; Biosensing Techniques/*methods ; Chromatography, Liquid/*methods ; Gold/chemistry ; Humans ; Hydrogen-Ion Concentration ; *Limit of Detection ; Metal Nanoparticles/chemistry ; Models, Molecular ; Molecular Conformation ; Proteins/*analysis/chemistry/metabolism ; Surface Properties ; Tandem Mass Spectrometry/*methods ; },
abstract = {A method is described for the determination of proteins with LC-MS/MS enabled by a small molecule (adenosine) barcode and based on a double-recognition sandwich structure. The coagulation protein thrombin was chosen as the model analyte. Magnetic nanoparticles were functionalized with aptamer29 (MNP/apt29) and used to capture thrombin from the samples. MNP/apt29 forms a sandwich with functionalized gold nanoparticles modified with (a) aptamer15 acting as thrombin-recognizing element and (b) a large number of adenosine as mass barcodes. The sandwich formed (MNP/apt29-thrombin-apt15/AuNP/adenosine) can ben magnetically separated from the sample. Mass barcodes are subsequently released from the sandwiched structure for further analysis by adding 11-mercaptoundecanoic acid. Adenosine is then detected by LC-MS/MS as it reflects the level of thrombin with impressively amplified signal. Numerous adenosines introduced into the sandwich proportional to the target concentration further amplify the signal. Under optimized conditions, the response is linearly proportional to the thrombin concentration in the range of 0.02 nM to 10 nM, with a detection limit of 9 fM. The application of this method to the determination of thrombin in spiked plasma samples gave recoveries that ranged from 92.3% to 104.7%. Graphical abstract Schematic representation of a method for the determination of thrombin with LC-MS/MS. The method is based on a double-recognition sandwiched structure. With LC-MS/MS, mass barcodes (adenosine) are detected to quantify thrombin, which amplifies the detection signal impressively.},
}
@article {pmid29747755,
year = {2018},
author = {Doganay-Knapp, K and Orland, A and König, GM and Knöss, W},
title = {The potential of three different PCR-related approaches for the authentication of mixtures of herbal substances and finished herbal medicinal products.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {43},
number = {},
pages = {60-67},
doi = {10.1016/j.phymed.2018.03.062},
pmid = {29747755},
issn = {1618-095X},
mesh = {Aristolochiaceae/genetics ; Cloning, Molecular ; Herbal Medicine/standards ; Matricaria/genetics ; Multiplex Polymerase Chain Reaction ; Plant Preparations/*standards ; Plants, Medicinal/*genetics ; Polymerase Chain Reaction/*methods ; Quercus/genetics ; Salvia/genetics ; },
abstract = {BACKGROUND: Herbal substances and preparations thereof play an important role in healthcare systems worldwide. Due to the variety of these products regarding origin, composition and processing procedures, appropriate methodologies for quality assessment need to be considered. A majority of herbal substances is administered as multicomponent mixtures, especially in the field of Traditional Chinese Medicine and ayurvedic medicine, but also in finished medicinal products. Quality assessment of complex mixtures of herbal substances with conventional methods is challenging. Thus, emphasis of the present work was directed on the development of complementary methods to elucidate the composition of mixtures of herbal substances and finished herbal medicinal products.<br><br>HYPOTHESIS/PURPOSE: An indispensable prerequisite for the safe and effective use of herbal medicines is the unequivocal authentication of the medicinal plants used therein. In this context, we investigated the potential of three different PCR-related methods in the characterization and authentication of herbal substances.<br><br>METHODS: A multiplex PCR assay and a quantitative PCR (qPCR) assay were established to analyze defined mixtures of the herbal substances Quercus cortex, Juglandis folium, Aristolochiae herba, Matricariae flos and Salviae miltiorrhizae radix et rhizoma and a finished herbal medicinal product. Furthermore, a standard cloning approach using universal primers targeting the ITS region was established in order to allow the investigation of herbal mixtures with unknown content.<br><br>RESULTS: The cloning approach had some limitations regarding the detection/recovery of the components in defined mixtures of herbal substances, but the complementary use of two sets of universal primer pairs increased the detection of components out of the mixture. While the multiplex PCR did not retrace all components in the defined mixtures of herbal substances, the established qPCR resulted in simultaneous and specific detection of the five target sequences in all defined mixtures.<br><br>CONCLUSION: These data indicate that for authentication purposes, complementary PCR-related methods are highly recommendable for the analysis of herbal mixtures in parallel.},
}
@article {pmid29742801,
year = {2018},
author = {Okuzaki, Y and Sota, T},
title = {Predator size divergence depends on community context.},
journal = {Ecology letters},
volume = {21},
number = {7},
pages = {1097-1107},
doi = {10.1111/ele.12976},
pmid = {29742801},
issn = {1461-0248},
mesh = {Animals ; *Body Size ; *Coleoptera ; Ecosystem ; Female ; Food Chain ; Larva ; *Phylogeny ; Predatory Behavior ; },
abstract = {Body size is a multi-functional trait related to various fitness components, but the relative importance of different selection pressures is seldom resolved. In Carabus japonicus beetles, of which the larvae exclusively prey on earthworms, adult body size is related to the presence/absence of a larger congener and habitat temperature. In sympatry, C. japonicus consistently exhibits smaller body size which is effective for avoiding interspecific mating, but in allopatry, it shows size variation unrelated to temperature. Here, we show that this predator-size variation is attributed to prey-size variation, associated with high phylogenetic diversity in earthworm communities. In allopatry, the predator size was larger where larger prey occurred. Larger adult size may have been selected because larger females produce larger larvae, which can subdue larger prey. Thus, in the absence of a larger congener, variation in prey body size had a pronounced effect on geographic body size divergence in C. japonicus.},
}
@article {pmid29740326,
year = {2018},
author = {Li, J and Xiong, C and He, X and Lu, Z and Zhang, X and Chen, X and Sun, W},
title = {Using SSR-HRM to Identify Closely Related Species in Herbal Medicine Products: A Case Study on Licorice.},
journal = {Frontiers in pharmacology},
volume = {9},
number = {},
pages = {407},
pmid = {29740326},
issn = {1663-9812},
abstract = {Traditional herbal medicines have played important roles in the ways of life of people around the world since ancient times. Despite the advanced medical technology of the modern world, herbal medicines are still used as popular alternatives to synthetic drugs. Due to the increasing demand for herbal medicines, plant species identification has become an important tool to prevent substitution and adulteration. Here we propose a method for biological assessment of the quality of prescribed species in the Chinese Pharmacopoeia by use of high resolution melting (HRM) analysis of microsatellite loci. We tested this method on licorice, a traditional herbal medicine with a long history. Results showed that nine simple sequence repeat (SSR) markers produced distinct melting curve profiles for the five licorice species investigated using HRM analysis. These results were validated by capillary electrophoresis. We applied this protocol to commercially available licorice products, thus enabling the consistent identification of 11 labels with non-declared Glycyrrhiza species. This novel strategy may thus facilitate DNA barcoding as a method of identification of closely related species in herbal medicine products. Based on this study, a brief operating procedure for using the SSR-HRM protocol for herbal authentication is provided.},
}
@article {pmid29739332,
year = {2018},
author = {Costello, M and Fleharty, M and Abreu, J and Farjoun, Y and Ferriera, S and Holmes, L and Granger, B and Green, L and Howd, T and Mason, T and Vicente, G and Dasilva, M and Brodeur, W and DeSmet, T and Dodge, S and Lennon, NJ and Gabriel, S},
title = {Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {332},
pmid = {29739332},
issn = {1471-2164},
support = {UM1 HG008895/HG/NHGRI NIH HHS/United States ; UM1HG008895//Center for Common Disease/ ; },
mesh = {DNA/chemistry/isolation &amp; purification/metabolism ; Gene Library ; Genome, Human ; *High-Throughput Nucleotide Sequencing ; Humans ; Sequence Analysis/*methods ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Here we present an in-depth characterization of the mechanism of sequencer-induced sample contamination due to the phenomenon of index swapping that impacts Illumina sequencers employing patterned flow cells with Exclusion Amplification (ExAmp) chemistry (HiSeqX, HiSeq4000, and NovaSeq). We also present a remediation method that minimizes the impact of such swaps.<br><br>RESULTS: Leveraging data collected over a two-year period, we demonstrate the widespread prevalence of index swapping in patterned flow cell data. We calculate mean swap rates across multiple sample preparation methods and sequencer models, demonstrating that different library methods can have vastly different swapping rates and that even non-ExAmp chemistry instruments display trace levels of index swapping. We provide methods for eliminating sample data cross contamination by utilizing non-redundant dual indexing for complete filtering of index swapped reads, and share the sequences for 96 non-combinatorial dual indexes we have validated across various library preparation methods and sequencer models. Finally, using computational methods we provide a greater insight into the mechanism of index swapping.<br><br>CONCLUSIONS: Index swapping in pooled libraries is a prevalent phenomenon that we observe at a rate of 0.2 to 6% in all sequencing runs on HiSeqX, HiSeq 4000/3000, and NovaSeq. Utilizing non-redundant dual indexing allows for the removal (flagging/filtering) of these swapped reads and eliminates swapping induced sample contamination, which is critical for sensitive applications such as RNA-seq, single cell, blood biopsy using circulating tumor DNA, or clinical sequencing.},
}
@article {pmid29737162,
year = {2018},
author = {Zhou, Z and Luo, G and Wulf, V and Willner, I},
title = {Application of DNA Machineries for the Barcode Patterned Detection of Genes or Proteins.},
journal = {Analytical chemistry},
volume = {90},
number = {11},
pages = {6468-6476},
doi = {10.1021/acs.analchem.7b04916},
pmid = {29737162},
issn = {1520-6882},
mesh = {Aptamers, Nucleotide/analysis/genetics ; Base Sequence ; Biosensing Techniques/*methods ; DNA/analysis/*genetics ; Electrophoresis/methods ; Genes ; Humans ; Optical Imaging/methods ; Pattern Recognition, Automated/*methods ; Proteins/analysis/*genetics ; },
abstract = {The study introduces an analytical platform for the detection of genes or aptamer-ligand complexes by nucleic acid barcode patterns generated by DNA machineries. The DNA machineries consist of nucleic acid scaffolds that include specific recognition sites for the different genes or aptamer-ligand analytes. The binding of the analytes to the scaffolds initiate, in the presence of the nucleotide mixture, a cyclic polymerization/nicking machinery that yields displaced strands of variable lengths. The electrophoretic separation of the resulting strands provides barcode patterns for the specific detection of the different analytes. Mixtures of DNA machineries that yield, upon sensing of different genes (or aptamer ligands), one-, two-, or three-band barcode patterns are described. The combination of nucleic acid scaffolds acting, in the presence of polymerase/nicking enzyme and nucleotide mixture, as DNA machineries, that generate multiband barcode patterns provide an analytical platform for the detection of an individual gene out of many possible genes. The diversity of genes (or other analytes) that can be analyzed by the DNA machineries and the barcode patterned imaging is given by the Pascal's triangle. As a proof-of-concept, the detection of one of six genes, that is, TP53, Werner syndrome, Tay-Sachs normal gene, BRCA1, Tay-Sachs mutant gene, and cystic fibrosis disorder gene by six two-band barcode patterns is demonstrated. The advantages and limitations of the detection of analytes by polymerase/nicking DNA machineries that yield barcode patterns as imaging readout signals are discussed.},
}
@article {pmid29736329,
year = {2018},
author = {Havemann, N and Gossner, MM and Hendrich, L and Morinière, J and Niedringhaus, R and Schäfer, P and Raupach, MJ},
title = {From water striders to water bugs: the molecular diversity of aquatic Heteroptera (Gerromorpha, Nepomorpha) of Germany based on DNA barcodes.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e4577},
pmid = {29736329},
issn = {2167-8359},
abstract = {With about 5,000 species worldwide, the Heteroptera or true bugs are the most diverse taxon among the hemimetabolous insects in aquatic and semi-aquatic ecosystems. Species may be found in almost every freshwater environment and have very specific habitat requirements, making them excellent bioindicator organisms for water quality. However, a correct determination by morphology is challenging in many species groups due to high morphological variability and polymorphisms within, but low variability between species. Furthermore, it is very difficult or even impossible to identify the immature life stages or females of some species, e.g., of the corixid genus Sigara. In this study we tested the effectiveness of a DNA barcode library to discriminate species of the Gerromorpha and Nepomorpha of Germany. We analyzed about 700 specimens of 67 species, with 63 species sampled in Germany, covering more than 90% of all recorded species. Our library included various morphological similar taxa, e.g., species within the genera Sigara and Notonecta as well as water striders of the genus Gerris. Fifty-five species (82%) were unambiguously assigned to a single Barcode Index Number (BIN) by their barcode sequences, whereas BIN sharing was observed for 10 species. Furthermore, we found monophyletic lineages for 52 analyzed species. Our data revealed interspecific K2P distances with below 2.2% for 18 species. Intraspecific distances above 2.2% were shown for 11 species. We found evidence for hybridization between various corixid species (Sigara, Callicorixa), but our molecular data also revealed exceptionally high intraspecific distances as a consequence of distinct mitochondrial lineages for Cymatia coleoptrata and the pygmy backswimmer Plea minutissima. Our study clearly demonstrates the usefulness of DNA barcodes for the identification of the aquatic Heteroptera of Germany and adjacent regions. In this context, our data set represents an essential baseline for a reference library for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future. The existing data also opens new questions regarding the causes of observed low inter- and high intraspecific genetic variation and furthermore highlight the necessity of taxonomic revisions for various taxa, combining both molecular and morphological data.},
}
@article {pmid29736197,
year = {2018},
author = {Übleis, SS and Cuk, C and Nawratil, M and Butter, J and Schoener, E and Obwaller, AG and Zechmeister, T and Duscher, GG and Rubel, F and Lebl, K and Zittra, C and Fuehrer, HP},
title = {Xenomonitoring of Mosquitoes (Diptera: Culicidae) for the Presence of Filarioid Helminths in Eastern Austria.},
journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale},
volume = {2018},
number = {},
pages = {9754695},
pmid = {29736197},
issn = {1712-9532},
abstract = {Information on mosquito-borne filarioid helminths in Austria is scarce, but recent discoveries of Dirofilaria repens indicate autochthonous distribution of this parasite in Eastern Austria. In the current xenomonitoring study, more than 48,000 mosquitoes were collected in Eastern Austria between 2013 and 2015, using different sampling techniques and storage conditions, and were analysed in pools with molecular tools for the presence of filarioid helminth DNA. Overall, DNA of D. repens, Setaria tundra, and two unknown filarioid helminths were documented in twenty mosquito pools within the mitochondrial cox1 gene (barcode region). These results indicate that S. tundra, with roe deer as definite hosts, is common in Eastern Austria, with most occurrences in floodplain mosquitoes (e.g., Aedes vexans). Moreover, DNA of D. repens was found in an Anopheles plumbeus mosquito close to the Slovakian border, indicating that D. repens is endemic in low prevalence in Eastern Austria. This study shows that xenomonitoring is an adequate tool to analyse the presence of filarioid helminths, but results are influenced by mosquito sampling techniques, storage conditions, and molecular protocols.},
}
@article {pmid29734387,
year = {2018},
author = {Komura, R and Aoki, W and Motone, K and Satomura, A and Ueda, M},
title = {High-throughput evaluation of T7 promoter variants using biased randomization and DNA barcoding.},
journal = {PloS one},
volume = {13},
number = {5},
pages = {e0196905},
pmid = {29734387},
issn = {1932-6203},
mesh = {Bacteriophage T7/genetics ; DNA Barcoding, Taxonomic/methods ; DNA-Directed RNA Polymerases/genetics ; Gene Expression Regulation/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Mutation ; *Promoter Regions, Genetic ; Regulatory Sequences, Nucleic Acid/*genetics ; *Transcription, Genetic ; },
abstract = {Cis-regulatory elements (CREs) are one of the important factors in controlling gene expression and elucidation of their roles has been attracting great interest. We have developed an improved method for analyzing a large variety of mutant CRE sequences in a simple and high-throughput manner. In our approach, mutant CREs with unique barcode sequences were obtained by biased randomization in a single PCR amplification. The original T7 promoter sequence was randomized by biased randomization, and the target number of base substitutions was set to be within the range of 0 to 5. The DNA library and subsequent transcribed RNA library were sequenced by next generation sequencers (NGS) to quantify transcriptional activity of each mutant. We succeeded in producing a randomized T7 promoter library with high coverage rate at each target number of base substitutions. In a single NGS analysis, we quantified the transcriptional activity of 7847 T7 promoter variants. We confirmed that the bases from -9 to -7 play an important role in the transcriptional activity of the T7 promoter. This information coincides with the previous researches and demonstrated the validity of our methodology. Furthermore, using an in vitro transcription/translation system, we found that transcriptional activities of these T7 variants were well correlated with the resultant protein abundance. We demonstrate that our method enables simple and high-throughput analysis of the effects of various CRE mutations on transcriptional regulation.},
}
@article {pmid29734294,
year = {2018},
author = {Roy, KR and Smith, JD and Vonesch, SC and Lin, G and Tu, CS and Lederer, AR and Chu, A and Suresh, S and Nguyen, M and Horecka, J and Tripathi, A and Burnett, WT and Morgan, MA and Schulz, J and Orsley, KM and Wei, W and Aiyar, RS and Davis, RW and Bankaitis, VA and Haber, JE and Salit, ML and St Onge, RP and Steinmetz, LM},
title = {Multiplexed precision genome editing with trackable genomic barcodes in yeast.},
journal = {Nature biotechnology},
volume = {36},
number = {6},
pages = {512-520},
pmid = {29734294},
issn = {1546-1696},
support = {294542/ERC_/European Research Council/International ; P01 HG000205/HG/NHGRI NIH HHS/United States ; R01 GM044530/GM/NIGMS NIH HHS/United States ; U01 GM110706/GM/NIGMS NIH HHS/United States ; R01 GM121932/GM/NIGMS NIH HHS/United States ; R01 GM061766/GM/NIGMS NIH HHS/United States ; R37 GM020056/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Substitution ; Biotechnology ; CRISPR-Cas Systems ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/genetics ; Gene Editing/*methods ; Genome, Fungal ; Homologous Recombination ; Phospholipid Transfer Proteins/genetics ; Plasmids/genetics ; RNA, Fungal/genetics ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/genetics ; },
abstract = {Our understanding of how genotype controls phenotype is limited by the scale at which we can precisely alter the genome and assess the phenotypic consequences of each perturbation. Here we describe a CRISPR-Cas9-based method for multiplexed accurate genome editing with short, trackable, integrated cellular barcodes (MAGESTIC) in Saccharomyces cerevisiae. MAGESTIC uses array-synthesized guide-donor oligos for plasmid-based high-throughput editing and features genomic barcode integration to prevent plasmid barcode loss and to enable robust phenotyping. We demonstrate that editing efficiency can be increased more than fivefold by recruiting donor DNA to the site of breaks using the LexA-Fkh1p fusion protein. We performed saturation editing of the essential gene SEC14 and identified amino acids critical for chemical inhibition of lipid signaling. We also constructed thousands of natural genetic variants, characterized guide mismatch tolerance at the genome scale, and ascertained that cryptic Pol III termination elements substantially reduce guide efficacy. MAGESTIC will be broadly useful to uncover the genetic basis of phenotypes in yeast.},
}
@article {pmid29732463,
year = {2018},
author = {Zhao, Y and Chen, X and Yang, Y and Zhao, X and Zhang, S and Gao, Z and Fang, T and Wang, Y and Zhang, J},
title = {Potential forensic biogeographic application of diatom colony consistency analysis employing pyrosequencing profiles of the 18S rDNA V7 region.},
journal = {International journal of legal medicine},
volume = {132},
number = {6},
pages = {1611-1620},
pmid = {29732463},
issn = {1437-1596},
support = {81571861//National Natural Science Foundation of China/ ; 81630054//National Natural Science Foundation of China/ ; },
mesh = {*DNA Barcoding, Taxonomic ; DNA, Ribosomal/*genetics ; Diatoms ; Drowning/diagnosis ; Humans ; *Sequence Analysis, DNA ; },
abstract = {Diatom examination has always been used for the diagnosis of drowning in forensic practice. However, traditional examination of the microscopic features of diatom frustules is time-consuming and requires taxonomic expertise. In this study, we demonstrate a potential DNA-based method of inferring suspected drowning site using pyrosequencing (PSQ) of the V7 region of 18S ribosome DNA (18S rDNA) as a diatom DNA barcode. By employing a sparse representation-based AdvISER-M-PYRO algorithm, the original PSQ signals of diatom DNA mixtures were deciphered to determine the corresponding taxa of the composite diatoms. Additionally, we evaluated the possibility of correlating water samples to collection sites by analyzing the PSQ signal profiles of diatom mixtures contained in the water samples via multidimensional scaling. The results suggest that diatomaceous PSQ profile analysis could be used as a cost-effective method to deduce the geographical origin of an environmental bio-sample.},
}
@article {pmid29732322,
year = {2018},
author = {Piras, P and Sardu, F and Meloni, D and Riina, MV and Beltramo, C and Acutis, PL},
title = {A case study on the labeling of bottarga produced in Sardinia from ovaries of grey mullets (Mugil cephalus and Mugil capurrii) caught in Eastern Central Atlantic coasts.},
journal = {Italian journal of food safety},
volume = {7},
number = {1},
pages = {6893},
pmid = {29732322},
issn = {2239-7132},
abstract = {The aim of this case study is to show how traditional and molecular methods can be employed to identify the Mugilidae species currently used in Sardinia (Italy) to produce the traditional bottarga for the processing of their ovaries. A total of six specimens of Mugil cephalus (n=3) and Mugil capurrii (n=3) were subjected to external morphology and meristic measurements. Subsequently, tissue samples of white muscle and ovaries from three individuals per species were underwent PCR-sequencing assay of mitochondrial DNA cytochrome oxidase subunit I (COI). The external morphology and meristic characters showed a sufficient level of reliability in the identification between the two species. At the same time, the molecular techniques showed the discriminatory power and confirmed the correct species identification in all the sampling units. DNA barcoding may be an effective aid to traditional taxonomy and can facilitate accurate species identification among the Mugilidae.},
}
@article {pmid29729674,
year = {2019},
author = {Li, D and Waite, DW and Gunawardana, DN and McCarthy, B and Anderson, D and Flynn, A and George, S},
title = {DNA barcoding and real-time PCR detection of Bactrocera xanthodes (Tephritidae: Diptera) complex.},
journal = {Bulletin of entomological research},
volume = {109},
number = {1},
pages = {102-110},
doi = {10.1017/S0007485318000251},
pmid = {29729674},
issn = {1475-2670},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Real-Time Polymerase Chain Reaction ; Tephritidae/*genetics ; },
abstract = {Immature fruit fly stages of the family Tephritidae are commonly intercepted on breadfruit from Pacific countries at the New Zealand border but are unable to be identified to the species level using morphological characters. Subsequent molecular identification showed that they belong to Bactrocera xanthodes, which is part of a species complex that includes Bactrocera paraxanthodes, Bactrocera neoxanthodes and an undescribed species. To establish a more reliable molecular identification system for B. xanthodes, a reference database of DNA barcode sequences for the 5'-fragment of COI gene region was constructed for B. xanthodes from Fiji, Samoa and Tonga. To better understand the species complex, B. neoxanthodes from Vanuatu and B. paraxanthodes from New Caledonia were also barcoded. Using the results of this analysis, real-time TaqMan polymerase chain reaction (PCR) assays for the detection of B. xanthodes complex and for the three individual species of the complex were developed and validated. The assay showed high specificity for the target species, with no cross-reaction observed for closely related organisms. Each of the real-time PCR assays is sensitive, detecting the target sequences at concentrations as low as ten copies µl-1 and can be used as either singleplex or multiplex formats. This real-time PCR assay for B. xanthodes has been successfully applied at the borders in New Zealand, leading to the rapid identification of intercepted Tephritidae eggs and larvae. The developed assays will be useful biosecurity tools for rapid detection of species in the B. xanthodes complex worldwide.},
}
@article {pmid29725068,
year = {2018},
author = {Jahn, LJ and Porse, A and Munck, C and Simon, D and Volkova, S and Sommer, MOA},
title = {Chromosomal barcoding as a tool for multiplexed phenotypic characterization of laboratory evolved lineages.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {6961},
pmid = {29725068},
issn = {2045-2322},
mesh = {Anti-Bacterial Agents/pharmacology ; Directed Molecular Evolution ; Drug Resistance, Bacterial ; Escherichia coli/drug effects/*genetics ; Gene Library ; Genetic Fitness ; Genome, Bacterial ; Phenotype ; Selection, Genetic ; },
abstract = {Adaptive laboratory evolution is an important tool to evolve organisms to increased tolerance towards different physical and chemical stress. It is applied to study the evolution of antibiotic resistance as well as genetic mechanisms underlying improvements in production strains. Adaptive evolution experiments can be automated in a high-throughput fashion. However, the characterization of the resulting lineages can become a time consuming task, when the performance of each lineage is evaluated individually. Here, we present a novel method for the markerless insertion of randomized genetic barcodes into the genome of Escherichia coli using a novel dual-auxotrophic selection approach. The barcoded E. coli library allows multiplexed phenotyping of evolved strains in pooled competition experiments. We use the barcoded library in an adaptive evolution experiment; evolving resistance towards three common antibiotics. Comparing this multiplexed phenotyping with conventional susceptibility testing and growth-rate measurements we can show a significant positive correlation between the two approaches. Use of barcoded bacterial strain libraries for individual adaptive evolution experiments drastically reduces the workload of characterizing the resulting phenotypes and enables prioritization of lineages for in-depth characterization. In addition, barcoded clones open up new ways to profile community dynamics or to track lineages in vivo or situ.},
}
@article {pmid29722246,
year = {2018},
author = {Yang, QQ and Liu, SW and Yu, XP},
title = {[Research progress on DNA barcoding analysis methods].},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {29},
number = {3},
pages = {1006-1014},
doi = {10.13287/j.1001-9332.201803.032},
pmid = {29722246},
issn = {1001-9332},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Fungi ; Phylogeny ; Plants ; Sequence Analysis, DNA ; },
abstract = {DNA barcode is a fragment of short DNA sequence from a standard part of the genome. DNA barcoding is an effective taxonomic method for species identification through analyzing the DNA barcodes. With the dramatic increasing of DNA barcode sequences, the analysis methods have developed rapidly, which promoted their applications in molecular identification for organisms. Since 2003, DNA barcoding has been widely used in species identification for animals, plants, fungi, etc. It has also robustly promoted the development of scientific disciplines, such as taxonomy, biodiversity science, and ecology. Based on review of DNA barcoding techniques, we summarized five main analysis methods on DNA barcodes, i.e. the genetic distance-, genetic similarity-, phylogenetic tree-, sequence characters-, and statistical classification-based methods. Moreover, we proposed a prospect for research and applications of DNA barcoding in the future.},
}
@article {pmid29720606,
year = {2018},
author = {Beermann, J and Westbury, MV and Hofreiter, M and Hilgers, L and Deister, F and Neumann, H and Raupach, MJ},
title = {Cryptic species in a well-known habitat: applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida).},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {6893},
pmid = {29720606},
issn = {2045-2322},
mesh = {Amphipoda/anatomy &amp; histology/*classification/*genetics ; Animals ; Biodiversity ; DNA Barcoding, Taxonomic ; *Ecosystem ; Genome, Mitochondrial ; Genomics/methods ; RNA, Ribosomal, 18S ; RNA, Transfer ; },
abstract = {Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of 'taxonomics'. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research.},
}
@article {pmid29719478,
year = {2018},
author = {Li, Y and Zhang, L and Zhao, L and Feng, J and Loh, K and Zheng, X and Lin, L},
title = {New identification of the moray eel Gymnothorax minor (Temminck &amp; Schlegel, 1846) in China (Anguilliformes, Muraenidae).},
journal = {ZooKeys},
volume = {},
number = {752},
pages = {149-161},
pmid = {29719478},
issn = {1313-2989},
abstract = {A new identification of Gymnothorax minor (Temminck &amp; Schlegel, 1846) is documented based on morphological characteristics and DNA barcoding. Sixty-one individuals of G. minor were collected from the East China Sea and the South China Sea. This species was previously reported as Gymnothorax reticularis Bloch, 1795 in China because of the similarity in external shape and color. Gymnothorax minor can be easily distinguished from G. reticularis by its color pattern of 18-20 irregular dark brown vertical bars and the body having scattered small brown spots. Additionally, the teeth are uniserial on both jaws, and the vertebrae number 137-139. By combining congener sequences of the cytochrome oxidase I (COI) gene from GenBank, two groups were detected among all the COI sequences of the currently named G. minor, which further indicated that two valid species were present based on genetic distance. A divergence also occurred on the number of vertebrae between the northern and southern populations. The phylogenetic and morphological analysis strongly supports that the northern and southern populations of G. minor are two different species. Furthermore, the distribution area of the northern G. minor has expanded southward to 5°15'N in the South China Sea. More specimens of G. minor and G. reticularis are crucial in order to define their geographical distribution boundaries and provide the correct DNA barcoding.},
}
@article {pmid29718976,
year = {2018},
author = {Kishor, R and Sharma, GJ},
title = {The use of the hypervariable P8 region of trnL(UAA) intron for identification of orchid species: Evidence from restriction site polymorphism analysis.},
journal = {PloS one},
volume = {13},
number = {5},
pages = {e0196680},
pmid = {29718976},
issn = {1932-6203},
mesh = {Genome, Plant/genetics ; Introns/*genetics ; Orchidaceae/*genetics ; Phylogeny ; Polymorphism, Genetic/*genetics ; Restriction Mapping/methods ; Sequence Alignment ; },
abstract = {The P8 stem-loop region of the trnL intron, which is known to be hypervariable in size with multiple repeat motifs and created difficulties in alignment, is always excluded in phylogenetic as well as barcode analyses. This region was investigated for species discrimination in 98 taxa of orchids belonging to the tribe Vandeae using in silico mapping of restriction site polymorphism. The length of the P8 regions varied from 200 nucleotides in Aerides rosea to 669 nucleotides in Dendrophylax sallei. Forty two taxa had unique lengths, while as many as eight shared a common length of 521 nucleotides. Of the 35 restriction endonucleases producing digestions in the P8 regions, three, viz., AgsI, ApoI and TspDTI turned out to have recognition sites across all the 98 taxa being studied. When their restriction data were combined, 92 taxa could be discriminated leaving three taxon pairs. However, Acampe papillosa and Aeranthes arachnites despite having similar restriction sites differed in their P8 lengths. This is the first report on thorough investigation of the P8 region of trnL intron for search of species specific restriction sites and hence its use as a potential plant DNA barcode.},
}
@article {pmid29715264,
year = {2018},
author = {Chan, BKK and Xu, G and Kim, HK and Park, JH and Kim, W},
title = {Living with marginal coral communities: Diversity and host-specificity in coral-associated barnacles in the northern coral distribution limit of the East China Sea.},
journal = {PloS one},
volume = {13},
number = {5},
pages = {e0196309},
pmid = {29715264},
issn = {1932-6203},
mesh = {Animals ; *Anthozoa ; *Biodiversity ; China ; *Host Specificity ; *Oceans and Seas ; Thoracica/*physiology ; },
abstract = {Corals and their associated fauna are extremely diverse in tropical waters and form major reefs. In the high-latitude temperate zone, corals living near their distribution limit are considered marginal communities because they are particularly extremely sensitive to environmental and climatic changes. In this study, we examined the diversity and host usage of coral-associated barnacles on Jeju Island, Korea, the northern coral distribution limit in the East China Sea. In this study, only three coral-associated barnacles-from two genera in two subfamilies-were collected. The Pyrgomatinid barnacles Cantellius arcuatus and Cantellius cf. euspinulosum were found only on the corals Montipora millepora and Alveopora japonica, respectively. The Megatrematinid barnacle Pyrgomina oulastreae, relatively a generalist, was found on Psammocora spp. (both profundacella and albopicta) and Oulastrea crispata corals. The host usage of these three barnacles does not overlap. DNA barcode sequences of the C. arcuatus specimens collected in the present study matched those collected in Kochi in Japan, Taiwan, Malaysia and Papua New Guinea, suggesting that this species has a wide geographical distribution. C. arcuatus covers a wider host range in Taiwan waters, inhabiting Montipora spp. and Porites spp., which suggests that the host specificity of coral-associated barnacles varies with host availability. C. cf. euspinulosum probably has a very narrow distribution and host usage. The sequences of C. cf. euspinulosum on Jeju Island do not match those of any known sequences of Cantellius barnacles in the Indo-Pacific region. P. oulastreae probably prefers cold water because it has been reported in temperate regions. Coral-associated barnacles in marginal communities have considerably lower diversity than their subtropical and tropical counterparts. When host availability is limited, marginal coral-associated barnacles exhibit higher host specificity than those in subtropical and tropical reef systems.},
}
@article {pmid29709632,
year = {2018},
author = {Ya'cob, Z and Takaoka, H and Low, VL and Sofian-Azirun, M},
title = {Characterization of Simulium (Simulium) hackeri Edwards (Diptera: Simuliidae) from Malaysia: Morphological description of the pupa and larva, and DNA barcoding.},
journal = {Acta tropica},
volume = {185},
number = {},
pages = {110-114},
doi = {10.1016/j.actatropica.2018.04.029},
pmid = {29709632},
issn = {1873-6254},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Female ; Larva/*anatomy &amp; histology ; Malaysia ; Male ; Pupa/*anatomy &amp; histology ; Simuliidae/*anatomy &amp; histology ; },
abstract = {Simulium (Simulium) hackeri Edwards, 1928 of the Simulium variegatum species-group from Malaysia was described initially based on the female specimen from Cameron Highlands, Pahang. In the present study, the pupa and larva of this species are described for the first time. Their morphological characters resemble those of the Simulium variegatum species-group by having six gill filaments per side, abdomen with dorsal spine-combs at least on segments 7 and 8, cocoon with wall-pocket shaped and with or without an anterodorsal projection. Postgenal cleft of the larva medium-sized, rarely small, ventral papillae small or absent. The DNA barcode of this species is also reported herein.},
}
@article {pmid29705206,
year = {2018},
author = {Arrigoni, E and Antonielli, L and Pindo, M and Pertot, I and Perazzolli, M},
title = {Tissue age and plant genotype affect the microbiota of apple and pear bark.},
journal = {Microbiological research},
volume = {211},
number = {},
pages = {57-68},
doi = {10.1016/j.micres.2018.04.002},
pmid = {29705206},
issn = {1618-0623},
mesh = {Bacteria/classification/genetics ; Bacterial Physiological Phenomena ; Biodiversity ; DNA, Bacterial ; DNA, Fungal ; DNA, Plant ; Fruit ; Fungi/classification/genetics/physiology ; *Genotype ; Malus/*genetics/*microbiology/physiology ; Microbial Consortia ; *Microbiota/genetics ; Phylogeny ; Plant Development ; Plant Diseases/genetics/microbiology ; Plant Shoots ; Pyrus/*genetics/*microbiology/physiology ; },
abstract = {Plant tissues host complex fungal and bacterial communities, and their composition is determined by host traits such as tissue age, plant genotype and environmental conditions. Despite the importance of bark as a possible reservoir of plant pathogenic microorganisms, little is known about the associated microbial communities. In this work, we evaluated the composition of fungal and bacterial communities in the pear (Abate and Williams cultivars) and apple (Golden Delicious and Gala cultivars) bark of three/four-year-old shoots (old bark) or one-year-old shoots (young bark), using a meta-barcoding approach. The results showed that both fungal and bacterial communities are dominated by genera with ubiquitous attitudes, such as Aureobasidium, Cryptococcus, Deinococcus and Hymenobacter, indicating intense microbial migration to surrounding environments. The shoot age, plant species and plant cultivar influenced the composition of bark fungal and bacterial communities. In particular, bark communities included potential biocontrol agents that could maintain an equilibrium with potential plant pathogens. The abundance of fungal (e.g. Alternaria, Penicillium, Rosellinia, Stemphylium and Taphrina) and bacterial (e.g. Curtobacterium and Pseudomonas) plant pathogens was affected by bark age and host genotype, as well as those of fungal genera (e.g. Arthrinium, Aureobasidium, Rhodotorula, Sporobolomyces) and bacterial genera (e.g. Bacillus, Brevibacillus, Methylobacterium, Sphingomonas and Stenotrophomonas) with possible biocontrol and plant growth promotion properties.},
}
@article {pmid29705201,
year = {2018},
author = {Lagarde, A and Jargeat, P and Roy, M and Girardot, M and Imbert, C and Millot, M and Mambu, L},
title = {Fungal communities associated with Evernia prunastri, Ramalina fastigiata and Pleurosticta acetabulum: Three epiphytic lichens potentially active against Candida biofilms.},
journal = {Microbiological research},
volume = {211},
number = {},
pages = {1-12},
doi = {10.1016/j.micres.2018.03.006},
pmid = {29705201},
issn = {1618-0623},
mesh = {Ascomycota/classification/enzymology/genetics/isolation &amp; purification ; Biofilms/*drug effects ; Candida/*physiology ; DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; France ; Lichens/*microbiology ; Parmeliaceae/*classification/*enzymology/genetics/*isolation &amp; purification ; Peptide Synthases/genetics/metabolism ; Phylogeny ; Polyketide Synthases/genetics/metabolism ; Secondary Metabolism/genetics ; Symbiosis ; },
abstract = {Fungal communities associated to three epiphytic lichens active against Candida, were investigated using culture-based methods We hypothetized that associated fungi would contribute to lichens activities. The ability of specific fungi to grow inside or outside lichens was investigated. To detect biogenesis pathways involved in the production of secondary metabolites, genes coding for nonribosomal peptide synthetase (NRPS) and polyketide synthase I (PKS I) were screened by PCR from fungal DNA extracts. Both endo and epilichenic communities were isolated from two fructicose (Evernia prunastri and Ramalina fastigiata) and one foliose (Pleurosticta acetabulum) lichens. A total of 86 endolichenic and 114 epilichenic isolates were obtained, corresponding to 18 and 24 phylogenetic groups respectively suggesting a wide diversity of fungi. The communities and the species richness were distinct between the three lichens which hosted potentially new fungal species. Additionally, the endo- and epilichenic communities differed in their composition: Sordariomycetes were particularly abundant among endolichenic fungi and Dothideomycetes among epilichenic fungi. Only a few fungi colonized both habitats, such as S. fimicola, Cladosporium sp1 and Botrytis cinerea. Interestingly, Nemania serpens (with several genotypes) was the most abundant endolichenic fungus (53% of isolates) and was shared by the three lichens. Finally, 12 out of 36 phylogenetic groups revealed the presence of genes coding for nonribosomal peptide synthetase (NRPs) and polyketide synthase I (PKS I). This study shows that common lichens are reservoirs of diverse fungal communities, which could potentially contribute to global activity of the lichen and, therefore, deserve to be isolated for further chemical studies.},
}
@article {pmid29705144,
year = {2018},
author = {Nakao, M and Sasaki, M and Waki, T and Anders, JL and Katahira, H},
title = {Brachylaima asakawai sp. nov. (Trematoda: Brachylaimidae), a rodent intestinal fluke in Hokkaido, Japan, with a finding of the first and second intermediate hosts.},
journal = {Parasitology international},
volume = {67},
number = {5},
pages = {565-574},
doi = {10.1016/j.parint.2018.04.010},
pmid = {29705144},
issn = {1873-0329},
mesh = {Animals ; Cercaria ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Female ; Genetic Variation ; Intestines/*parasitology ; Japan ; Metacercariae ; Murinae/parasitology ; Rats/parasitology ; Rodentia/*parasitology ; Snails/*parasitology ; Trematoda/*genetics/isolation &amp; purification ; Trematode Infections/*parasitology ; },
abstract = {In the 1970's and 1980's, an unknown species of the genus Brachylaima (Trematoda: Brachylaimidae) had been recorded from the intestines of Rattus norvegicus and Apodemus speciosus in Hokkaido, Japan. The rodent fluke was characteristic in extending a bilateral vitellarium till the level of posterior margin of anterior testis and in keeping almost the same-sized spherical ovary and testes. In this study, the rodent fluke was rediscovered from A. speciosus, Apodemus argenteus, and Myodes rufocanus in Hokkaido. The resultant parasite collection enabled us to make a mitochondrial DNA (mtDNA) barcode for tracking its intermediate hosts. The metacercaria of the rodent fluke was detected frequently from the kidney of three species of land snails (Discus pauper, Succinea lauta, and Ainohelix editha). However, its sporocyst with cercariae was found only from the hepatopancreas of D. pauper, a fairly small snail. The wide-spectrum of the second intermediate host seems to increase the chance of transmitting the parasite to various mammals and birds. The use of indigenous land snails as the first and second intermediate hosts, the distinctiveness of the mtDNA sequence, and the characteristic morphology of all the developmental stages prompted us to propose Brachylaima asakawai sp. nov. for the rodent intestinal fluke in Hokkaido. The present field survey suggests that the life cycle of the new species is primarily dependent on a predator-prey relationship between rodents and D. pauper.},
}
@article {pmid29703988,
year = {2018},
author = {Appleyard, SA and White, WT and Vieira, S and Sabub, B},
title = {Artisanal shark fishing in Milne Bay Province, Papua New Guinea: biomass estimation from genetically identified shark and ray fins.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {6693},
pmid = {29703988},
issn = {2045-2322},
mesh = {*Animal Fins ; Animals ; Bays ; *Biomass ; DNA Barcoding, Taxonomic ; *Endangered Species ; *Fisheries ; Human Activities ; Papua New Guinea ; Sharks/classification/*genetics ; Skates, Fish/classification/*genetics ; },
abstract = {Our study is the first detailed examination of species composition using DNA COI barcoding of elasmobranchs from an artisanal fishery of Papua New Guinea. The study is the first in the region to provide biomass estimates based on species confirmation following examination of dried fins. Over 20 species of elasmobranchs were identified from 623 fins from the artisanal fishery in Milne Bay Province of PNG, with Carcharhinus amblyrhynchos and Carcharhinus melanopterus the most abundant species in the catches. Of concern, 21% of fins examined were from IUCN listed threatened species (Vulnerable or Endangered) with 8% of fins from the Endangered scalloped hammerhead (Sphyrna lewini). Following species identifications and use of species-specific length and weight extrapolations, we estimated over 9 t of elasmobranchs contributed to the fin batch. Importantly, the vast majority of the elasmobranchs in this batch were from immature animals. Genetic identification has an important role to play in the ongoing sustainable management of elasmobranchs in artisanal fisheries in PNG and more widely. However in the absence of ongoing genetic testing, recording the species (if known) at the time of catch is more achievable and would provide more robust data for fisheries managers in PNG over the longer term.},
}
@article {pmid29701675,
year = {2018},
author = {Meng, J and Li, X and Li, H and Yang, J and Wang, H and He, J},
title = {Comparative Analysis of the Complete Chloroplast Genomes of Four Aconitum Medicinal Species.},
journal = {Molecules (Basel, Switzerland)},
volume = {23},
number = {5},
pages = {},
pmid = {29701675},
issn = {1420-3049},
mesh = {Aconitum/*classification/genetics ; China ; Chloroplasts/*genetics ; Evolution, Molecular ; Genome Size ; Genome, Chloroplast ; High-Throughput Nucleotide Sequencing/*methods ; Microsatellite Repeats ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {Aconitum (Ranunculaceae) consists of approximately 400 species distributed in the temperate regions of the northern hemisphere. Many species are well-known herbs, mainly used for analgesia and anti-inflammatory purposes. This genus is well represented in China and has gained widespread attention for its toxicity and detoxification properties. In southwestern China, several Aconitum species, called ‘Dula’ in the Yi Nationality, were often used to control the poisonous effects of other Aconitum plants. In this study, the complete chloroplast (cp) genomes of these species were determined for the first time through Illumina paired-end sequencing. Our results indicate that their cp genomes ranged from 151,214 bp (A. episcopale) to 155,769 bp (A. delavayi) in length. A total of 111[-]112 unique genes were identified, including 85 protein-coding genes, 36[-]37 tRNA genes and eight ribosomal RNA genes (rRNA). We also analyzed codon usage, IR expansion or contraction and simple sequence repeats in the cp genomes. Eight variable regions were identified and these may potentially be useful as specific DNA barcodes for species identification of Aconitum. Phylogenetic analysis revealed that all five studied species formed a new clade and were resolved with 100% bootstrap support. This study will provide genomic resources and potential plastid markers for DNA barcoding, further taxonomy and germplasm exploration of Aconitum.},
}
@article {pmid29701079,
year = {2019},
author = {Park, MH and Jung, JH and Jo, E and Park, KM and Baek, YS and Kim, SJ and Min, GS},
title = {Utility of mitochondrial CO1 sequences for species discrimination of Spirotrichea ciliates (Protozoa, Ciliophora).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {1},
pages = {148-155},
doi = {10.1080/24701394.2018.1464563},
pmid = {29701079},
issn = {2470-1408},
mesh = {Ciliophora/classification/*genetics ; DNA Barcoding, Taxonomic/methods/*standards ; Electron Transport Complex IV/*genetics ; High-Throughput Nucleotide Sequencing/methods/standards ; Oligonucleotide Probes/standards ; Phylogeny ; Protozoan Proteins/*genetics ; Reference Standards ; },
abstract = {Ciliates are a diverse species group of the Protozoa, and nuclear and mitochondrial genes have been utilized to discover new species and discriminate closely related species. The mitochondrial cytochrome c oxidase subunit 1 (CO1) gene has been used to discriminate metazoan species and has also been applied for some groups in the phylum Ciliophora. However, it is difficult to produce a universal primer as a standard barcode, because unlike metazoans, mitochondrial DNA sequences of ciliates are long and highly variable. Therefore, to design the new primer set, we sequenced the mitochondrial genomes of two pseudokeronopsids in the class Spirotrichea using next-generation sequencing technology (HiSeq™ 2000). Based on putative CO1 gene fragments of the pseudokeronopsids, we designed the new primer set and successfully sequenced the CO1 of 69 populations representing 47 species (five orders, 14 families, and 27 genera). We found that CO1 showed higher resolution for separating congeneric species than did nuclear SSU rRNA gene sequences, and we identified some putative cryptic species.},
}
@article {pmid29701068,
year = {2018},
author = {Feng, S and Jiao, K and Zhu, Y and Wang, H and Jiang, M and Wang, H},
title = {Corrigendum: Molecular identification of species of Physalis (Solanaceae) using a candidate DNA barcode: the chloroplast psbA-trnH intergenic region.},
journal = {Genome},
volume = {61},
number = {6},
pages = {467},
doi = {10.1139/gen-2018-0074},
pmid = {29701068},
issn = {1480-3321},
}
@article {pmid29700678,
year = {2018},
author = {Murillo, P and Klimov, P and Hubert, J and OConnor, B},
title = {Investigating species boundaries using DNA and morphology in the mite Tyrophagus curvipenis (Acari: Acaridae), an emerging invasive pest, with a molecular phylogeny of the genus Tyrophagus.},
journal = {Experimental &amp; applied acarology},
volume = {75},
number = {2},
pages = {167-189},
pmid = {29700678},
issn = {1572-9702},
support = {University of Michigan//by Block grants from the Department of Ecology and Evolutionary Biology and a Rackham Graduate Student Research Grant/ ; OAICE-08-CAB-147-2013//Universidad de Costa Rica (CR)/ ; FI-0161-13//CONICIT- Costa Rica/ ; No 15-04-05185-a//Russian Foundation for Basic Research/ ; PVE 88881.064989/2014-01//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES) Ci&#xea;ncia sem Fronteiras/ ; 16-14-10109//Russian Science Foundation/ ; 6.1933.2014/K project code 1933//Ministry of Education and Science of the Russian Federation/ ; RO0417//Ministry of Agriculture of the Czech Republic/ ; },
mesh = {Acaridae/anatomy &amp; histology/*classification/enzymology/genetics ; Animal Distribution ; Animals ; Arthropod Proteins/*genetics ; *Biological Evolution ; Electron Transport Complex IV/genetics ; Mitochondrial Proteins/genetics ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Mites of the genus Tyrophagus (Acari: Acaridae) are among the most widespread and common mites, inhabiting diverse natural and anthropogenic habitats. Some species are pests of agricultural products and stored food and/or live in house dust, causing allergies to humans. We sequenced 1.2 kb of the mitochondrial COI gene for 38 individuals belonging to seven species of Tyrophagus, including T. curvipenis, T. putrescentiae, T. fanetzhangorum, T. longior, T. perniciosus, and T. cf. similis. Molecular phylogenetic analyses (1) recovered two major clades corresponding to the presence or absence of eyespots, and (2) separated all included morphological species. Tyrophagus curvipenis and T. putrescentiae had the lowest between-species genetic distances (range, mean ± SD): 14.20-16.30, 15.17 ± 0.40 (K2P). The highest within-species variation was found in T. putrescentiae 0.00-4.33, 1.78 ± 1.44 (K2P). In this species, we recovered two distinct groups; however, no geographical or ecological dissimilarities were observed between them. Based on our analyses, we document important morphological differences between T. curvipenis and T. putrescentiae. For the first time, we record the occurrence of T. curvipenis in the New World and suggest that it may be an emerging pest as it is currently spreading in agricultural produce.},
}
@article {pmid29700229,
year = {2018},
author = {Wagner, DE and Weinreb, C and Collins, ZM and Briggs, JA and Megason, SG and Klein, AM},
title = {Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo.},
journal = {Science (New York, N.Y.)},
volume = {360},
number = {6392},
pages = {981-987},
pmid = {29700229},
issn = {1095-9203},
support = {R01 GM107733/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 DC015478/DC/NIDCD NIH HHS/United States ; T32 GM080177/GM/NIGMS NIH HHS/United States ; K99 GM121852/GM/NIGMS NIH HHS/United States ; //Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Clonal Evolution/*genetics ; Gene Expression ; *Gene Expression Regulation, Developmental ; Glycoproteins/genetics ; Intercellular Signaling Peptides and Proteins/genetics ; Sequence Analysis, RNA/methods ; Single-Cell Analysis/methods ; Zebrafish/*embryology/*genetics ; Zebrafish Proteins/*genetics ; },
abstract = {High-throughput mapping of cellular differentiation hierarchies from single-cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single-cell RNA sequencing to >92,000 cells from zebrafish embryos during the first day of development. Using a graph-based approach, we mapped a cell-state landscape that describes axis patterning, germ layer formation, and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon-based barcoding approach (TracerSeq) for reconstructing single-cell lineage histories. Clonally related cells were often restricted by the state landscape, including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in embryos lacking the chordin gene. We provide web-based resources for further analysis of the single-cell data.},
}
@article {pmid29698856,
year = {2018},
author = {Parlapani, FF and Michailidou, S and Pasentsis, K and Argiriou, A and Krey, G and Boziaris, IS},
title = {A meta-barcoding approach to assess and compare the storage temperature-dependent bacterial diversity of gilt-head sea bream (Sparus aurata) originating from fish farms from two geographically distinct areas of Greece.},
journal = {International journal of food microbiology},
volume = {278},
number = {},
pages = {36-43},
doi = {10.1016/j.ijfoodmicro.2018.04.027},
pmid = {29698856},
issn = {1879-3460},
mesh = {Animals ; Aquaculture ; Female ; Fisheries ; *Food Microbiology ; Food Preservation/methods ; Greece ; Microbiota/genetics ; Oceans and Seas ; Pseudomonas/genetics/*isolation &amp; purification ; Psychrobacter/genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sea Bream/*microbiology ; Shewanella/genetics/*isolation &amp; purification ; Temperature ; },
abstract = {Bacterial diversity of whole gilt-head sea bream (Sparus aurata L. 1758) originating from Ionian and Aegean Sea aquaculture farms and stored at 0 (ice), 4 and 8 °C was determined by 16S rRNA gene amplicon sequencing method using the Illumina's MiSeq platform. The composition of Aerobic Plate Counts (APC) was also monitored by 16S rRNA gene sequencing. The rejection time point of sea bream from either area, as determined by sensory evaluation, was about 14, 6 and 3 days at 0, 4 and 8 °C, respectively. APC was approximately 4.5 log cfu/g at day 0 and ranged from 7.5 to 8.5 log cfu/g at sensory rejection. Culture-depended analysis showed that Pseudomonas and Shewanella were the most abundant microorganisms grown on plates for both seas. Moreover, culture-independent analysis of DNA extracted directly from fish flesh showed that sea bream originating from different geographical areas exhibited different bacterial diversity. Pseudomonas and Psychrobacter were the dominant microorganisms of chill-stored fish from Ionian (apart from 8 °C, where Carnobacterium dominated) and Aegean Sea, respectively. In addition, small changes of storage temperature greatly affected bacterial microbiota of stored fish. Various bacterial species, not detected by conventional microbiological methods, were also revealed through 16S amplicon sequencing. In conclusion, the use of NGS approach is a promising methodology for assessing bacterial diversity of sea bream originating from different geographical areas and stored at various temperatures.},
}
@article {pmid29697902,
year = {2018},
author = {Liu, L and Li, T and Zhang, S and Song, P and Guo, B and Zhao, Y and Wu, HC},
title = {Simultaneous Quantification of Multiple Cancer Biomarkers in Blood Samples through DNA-Assisted Nanopore Sensing.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {57},
number = {37},
pages = {11882-11887},
doi = {10.1002/anie.201803324},
pmid = {29697902},
issn = {1521-3773},
mesh = {Biomarkers, Tumor/*blood ; Biosensing Techniques/*methods ; Carcinoembryonic Antigen/blood ; DNA/*chemistry ; Gold/chemistry ; Humans ; *Nanopores ; Neoplasms/blood/diagnosis ; Prostate-Specific Antigen/blood ; },
abstract = {Protein biomarkers in blood have been widely used in the early diagnosis of disease. However, simultaneous detection of many biomarkers in a single sample remains challenging. Herein, we show that the combination of a sandwich assay and DNA-assisted nanopore sensing could unambiguously identify and quantify several antigens in a mixture. We use five barcode DNAs to label different gold nanoparticles that can selectively bind specific antigens. After the completion of the sandwich assay, barcode DNAs are released and subject to nanopore translocation tests. The distinct current signatures generated by each barcode DNA allow simultaneous quantification of biomarkers at picomolar level in clinical samples. This approach would be very useful for accurate and multiplexed quantification of cancer-associated biomarkers within a very small sample volume, which is critical for non-invasive early diagnosis of cancer.},
}
@article {pmid29697299,
year = {2019},
author = {Lalramliana, and Lalronunga, S and Kumar, S and Singh, M},
title = {DNA barcoding revealed a new species of Neolissochilus Rainboth, 1985 from the Kaladan River of Mizoram, North East India.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {1},
pages = {52-59},
doi = {10.1080/24701394.2018.1450398},
pmid = {29697299},
issn = {2470-1408},
mesh = {Animals ; Cyprinidae/classification/*genetics ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Fish Proteins/genetics ; India ; *Phylogeny ; },
abstract = {Neolissochilus kaladanensis sp. nov., a new cyprinid species, is described from the Kaladan River drainage of Mizoram. It differs from all other valid Neolissochilus species in having higher number of gill rakers on the lower arm of the first gill arch (13-14 vs. 12 or below in all the species). The analysis of mitochondrial gene cytochrome c oxidase subunit I (COI) sequences separated N. kaladanensis sp. nov. from all other Neolissochilus and Tor species with an average genetic distance of 6.0%. It is further separated from the morphologically most similar species N. hendersoni and N. soroides by a genetic distance of 6.7% and 6.8%, respectively. Based on the lowest BIC and AICc scores, best fit model for COI dataset was TN93 + G + I, out of 24 different nucleotide substitution models tested. The maximum-likelihood (ML) phylogenetic tree was constructed using the COI sequences of representative Neolissochilus and Tor species. The anomalies observed among the GenBank sequences of the genera Tor and Neolissochilus are also discussed.},
}
@article {pmid29695263,
year = {2018},
author = {Weeraratne, TC and Surendran, SN and Parakrama Karunaratne, SHP},
title = {DNA barcoding of morphologically characterized mosquitoes belonging to the subfamily Culicinae from Sri Lanka.},
journal = {Parasites &amp; vectors},
volume = {11},
number = {1},
pages = {266},
pmid = {29695263},
issn = {1756-3305},
support = {Grant No. InRC/RG/13/21//International Research Center (InRC), University of Peradeniya, Sri Lanka/International ; },
mesh = {Animals ; Cluster Analysis ; Culicidae/anatomy &amp; histology/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/chemistry/genetics ; Electron Transport Complex IV/genetics ; Entomology/*methods ; Mosquito Vectors/anatomy &amp; histology/*classification/genetics ; *Phylogeny ; Sri Lanka ; },
abstract = {BACKGROUND: Vectors of mosquito-borne diseases in Sri Lanka, except for malaria, belong to the subfamily Culicinae, which includes nearly 84% of the mosquito fauna of the country. Hence, accurate and precise species identification of culicine mosquitoes is a crucial factor in implementing effective vector control strategies. During the present study, a combined effort using morphology and DNA barcoding was made to characterize mosquitoes of the subfamily Culicinae for the first time from nine districts of Sri Lanka. Cytochrome c oxidase subunit 1 (cox1) gene from the mitochondrial genome and the internal transcribed spacer 2 (ITS2) region from the nuclear ribosomal DNA were used for molecular characterization.<br><br>RESULTS: According to morphological identification, the field collected adult mosquitoes belonged to 5 genera and 14 species, i.e. Aedes aegypti, Ae. albopictus, Ae. pallidostriatus, Aedes sp. 1, Armigeres sp. 1, Culex bitaeniorhynchus, Cx. fuscocephala, Cx. gelidus, Cx. pseudovishnui, Cx. quinquefasciatus, Cx. tritaeniorhynchus, Cx. whitmorei, Mansonia uniformis and Mimomyia chamberlaini. Molecular analyses of 62 cox1 and 36 ITS2 sequences were exclusively comparable with the morphological identifications of all the species except for Ae. pallidostriatus and Aedes sp. 1. Although the species identification of Armigeres sp. 1 specimens using morphological features was not possible during this study, DNA barcodes of the specimens matched 100% with the publicly available Ar. subalbatus sequences, giving their species status. Analysis of all the cox1 sequences (14 clades supported by strong bootstrap value in the Neighbor-Joining tree and interspecific distances of > 3%) showed the presence of 14 different species. This is the first available DNA sequence in the GenBank records for morphologically identified Ae. pallidostriatus. Aedes sp. 1 could not be identified morphologically or by publicly available sequences. Aedes aegypti, Ae. albopictus and all Culex species reported during the current study are vectors of human diseases. All these vector species showed comparatively high diversity.<br><br>CONCLUSIONS: The current study reflects the significance of integrated systematic approach and use of cox1 and ITS genetic markers in mosquito taxonomy. Results of DNA barcoding were comparable with morphological identifications and, more importantly, DNA barcoding could accurately identify the species in the instances where the traditional morphological identification failed due to indistinguishable characters of damaged specimens and the presence of subspecies.},
}
@article {pmid29690531,
year = {2018},
author = {Osório, HC and Zé-Zé, L and Neto, M and Silva, S and Marques, F and Silva, AS and Alves, MJ},
title = {Detection of the Invasive Mosquito Species Aedes (Stegomyia) albopictus (Diptera: Culicidae) in Portugal.},
journal = {International journal of environmental research and public health},
volume = {15},
number = {4},
pages = {},
pmid = {29690531},
issn = {1660-4601},
mesh = {Aedes/*genetics/physiology/*virology ; Animals ; Arboviruses/*isolation &amp; purification ; Disease Vectors ; Introduced Species/*statistics &amp; numerical data ; Mosquito Vectors/*genetics/physiology/*virology ; Phylogeny ; Portugal ; Zika Virus/*isolation &amp; purification ; },
abstract = {The Asian tiger mosquito Aedes albopictus is an invasive mosquito originating from the Asia-Pacific region. This species is of major concern to public and veterinary health because of its vector role in the transmission of several pathogens, such as chikungunya, dengue, and Zika viruses. In Portugal, a National Vector Surveillance Network (REde de VIgil&amp;acirc;ncia de VEctores&amp;mdash;REVIVE) is responsible for the surveillance of autochthonous, but also invasive, mosquito species at points of entry, such as airports, ports, storage areas, and specific border regions with Spain. At these locations, networks of mosquito traps are set and maintained under surveillance throughout the year. In September 2017, Ae. albopictus was detected for the first time in a tyre company located in the North of Portugal. Molecular typing was performed, and a preliminary phylogenetic analysis indicated a high similarity with sequences of Ae. albopictus collected in Europe. A prompt surveillance response was locally implemented to determine its dispersal and abundance, and adult mosquitoes were screened for the presence of arboviral RNA. A total of 103 specimens, 52 immatures and 51 adults, were collected. No pathogenic viruses were detected. Despite the obtained results suggest low abundance of the population locally introduced, the risk of dispersal and potential establishment of Ae. albopictus in Portugal has raised concern for autochthonous mosquito-borne disease outbreaks.},
}
@article {pmid29690494,
year = {2018},
author = {Zhang, J and Hu, X and Wang, P and Huang, B and Sun, W and Xiong, C and Hu, Z and Chen, S},
title = {Investigation on Species Authenticity for Herbal Products of Celastrus Orbiculatus and Tripterygum Wilfordii from Markets Using ITS2 Barcoding.},
journal = {Molecules (Basel, Switzerland)},
volume = {23},
number = {4},
pages = {},
pmid = {29690494},
issn = {1420-3049},
mesh = {Celastrus/*classification/*genetics ; *DNA Barcoding, Taxonomic ; *DNA, Intergenic ; Drugs, Chinese Herbal/*classification/standards ; Phylogeny ; Polymorphism, Single Nucleotide ; Tripterygium/*classification/*genetics ; },
abstract = {Herbal material is both a medicine and a commodity. Accurate identification of herbal materials is necessary to ensure the safety and effectiveness of medication. With this work, we initiated an identification method to investigate the species authenticity for herbal products of Celastrus orbiculatus and Tripterygum wilfordii utilizing DNA barcoding technology. An ITS2 (internal transcribed spacer two) barcode database including 59 sequences was successfully established to estimate the reliability of species-level identification for Celastrus and Tripterygium. Our findings showed that ITS2 can effectively and clearly distinguish C. orbiculatus, T. wilfordii and its congeners. Then, we investigated the proportions and varieties of adulterant species in the herbal markets. The data from ITS2 region indicated that 13 (62%) of the 21 samples labeled as “Nan-she-teng” and eight (31%) of the 26 samples labeled as “Lei-gong-teng” were authentic; the remaining were adulterants. Of the 47 herbal products, approximately 55% of the product identity were not in accordance with the label. In summary, we support the efficacy of the ITS2 barcode for the traceability of C. orbiculatus and T. wilfordii, and the present study provides one method and reference for the identification of the herbal materials and adulterants in the medicinal markets.},
}
@article {pmid29690468,
year = {2018},
author = {Tangkawanit, U and Wongpakam, K and Pramual, P},
title = {A new black fly (Diptera: Simuliidae) species of the subgenus Asiosimulium Takaoka Choochote from Thailand.},
journal = {Zootaxa},
volume = {4388},
number = {1},
pages = {111-122},
doi = {10.11646/zootaxa.4388.1.8},
pmid = {29690468},
issn = {1175-5334},
mesh = {Animals ; Ecology ; Larva ; Phylogeny ; *Simuliidae ; Thailand ; },
abstract = {A new black fly species of the subgenus Asiosimulium Takaoka Choochote of the genus Simulium was recognized from northeastern Thailand based on morphology, mitochondrial DNA and ecology. This black fly species has similar morphological characteristics to Simulium oblongum Takaoka and Choochote that was also described from the same geographic region in all life stages. However, this new species could be distinguished at the adult stage by coloration of the maxillary palp and in the larval stage by the presence of a pigmented subesophageal ganglion that is lacking in S. oblongum. Genetic distance and phylogenetic analyses based on mitochondrial cytochrome c oxidase I sequences clearly differentiated the two species with minimum genetic distance of 3.51%. These species are also ecologically isolated as S. oblongum is found only at low elevation (<650 m above sea level) but the new species occurs only at high elevation (>1,100 m above sea level).},
}
@article {pmid29690460,
year = {2018},
author = {Ruiz-garcÍa, A and Zamora-muÑoz, C and GarzÓn, A and Ferreras-Romero, M},
title = {Description of the last instar larva of Stenophylax espanioli Schmid 1957 (Trichoptera: Limnephilidae) from southern Iberian Peninsula with the barcode of the species and synoptic key for identification of the known Stenophylax larvae from the Iberian Peninsula.},
journal = {Zootaxa},
volume = {4388},
number = {2},
pages = {292-300},
doi = {10.11646/zootaxa.4388.2.11},
pmid = {29690460},
issn = {1175-5334},
mesh = {Animals ; Europe ; Holometabola ; *Insecta ; Larva ; },
abstract = {The larva of Stenophylax espanioli Schmid 1957 is described, illustrated, and compared with morphologically similar Limnephilidae larvae from the Iberian Peninsula. In addition, the sequence of fragments of the mtCOI gene in the barcode region of two individuals are reported and registered in the GenBank Database. Finally, a synoptic key of the known larvae of Stenophylax species from the Iberian Peninsula is given.},
}
@article {pmid29690450,
year = {2018},
author = {Johnson, JW and Wilmer, JW},
title = {Three new species of Parapercis (Perciformes: Pinguipedidae) and first records of P. muronis (Tanaka, 1918) and P. rubromaculata Ho, Chang Shao, 2012 from Australia.},
journal = {Zootaxa},
volume = {4388},
number = {2},
pages = {151-181},
doi = {10.11646/zootaxa.4388.2.1},
pmid = {29690450},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Australia ; Japan ; *Perciformes ; Philippines ; Taiwan ; Western Australia ; },
abstract = {Three new species of pinguipedid fishes from northern Australia are described based on specimens collected by deep water demersal trawling. Parapercis algrahami sp. nov. is recorded from off Dunk Island, Qld, south to Newcastle, NSW, in 67-333 m. It is distinct in having five narrow transverse dark bars across the upper body and a dark spot dorsally on the caudal-fin base, 6 canine teeth in outer row at front of lower jaw, palatines with 1-2 rows of teeth, and predorsal scales extending far forward on the nape to the posterior portion of the interorbital region. Parapercis imamurai sp. nov. is recorded from off Saumarez Reef, Qld, south to off Coffs Harbour, NSW, in 256-405 m. It is unique in having colouration that includes a broad dusky bar from lower margin of eye across the suborbital region and three broad dusky bands crossing the body between the middle of the soft dorsal-fin and the caudal-fin base, 10 canine teeth in outer row at front of lower jaw, and the fifth dorsal-fin spine longest. Parapercis pogonoskii sp. nov. is unique in having a combination of three reddish-brown vertical bars on the upper body between the anterior and posterior portions of the soft dorsal fin, the soft dorsal fin with two large dusky blotches and caudal-fin base with a dusky blotch in the upper corner, 8-10 canine teeth in outer row at front of lower jaw, fifth dorsal-fin spine longest, angle of subopercle with a single broad spine, and angle of preopercle with 4-5 large widely-separated spines. Comparison of the mitochondrial cytochrome c oxidase subunit 1 (CO 1) genetic marker utilised in DNA barcoding produced significant genetic divergences of at least 8.1% and 14.1% between P. algrahami sp. nov. and P. pogonoskii sp. nov. respectively and their closest sampled congeners. The geographic range of Parapercis rubromaculata Ho, Chang Shao, 2012 is extended from Taiwan to the southern hemisphere waters off Western Australia, based on specimens collected from Shark Bay, north to Ashmore Terrace, in depths of 56-107 m. A revised diagnosis for the species is presented, meristic, morphometric and DNA barcoding data for the two populations are compared, and a detailed description of the colouration of fresh and preserved specimens from Australia is provided. Previous records of Parapercis macrophthalma (Pietschmann, 1911) from Western Australia are established as misidentifications of Parapercis muronis (Tanaka, 1918) and the latter is thereby confirmed from the southern hemisphere and Australian waters for the first time. Comparative meristic, morphometric and DNA barcoding data is provided for populations of P. muronis from Japan, Philippines and Western Australia.},
}
@article {pmid29690359,
year = {2018},
author = {Potapov, M and Porco, D and Deharveng, L},
title = {A new member of the genus Isotomurus from the Kuril Islands (Collembola: Isotomidae): returning to the problem of "colour pattern species".},
journal = {Zootaxa},
volume = {4394},
number = {3},
pages = {383-394},
doi = {10.11646/zootaxa.4394.3.4},
pmid = {29690359},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures ; Animals ; *Arthropods ; Color ; Asia, Eastern ; Islands ; Russia ; },
abstract = {Colour pattern is the most common character to identify species in several large genera of Collembola. Its use often raises problems due to various and poorly investigated extent of chromatic variability among species. Isotomurus festus sp. nov. is here described from Kunashir Isl. (the Kuriles, the Far East of Russia). The species, a member of the 'antennalis' group, is characterized by the lack of trichobothria and slender claws, but is greatly variable in coloration. DNA barcoding (COI) results supports that all the colour forms encountered belong to the same species. While colour pattern has been shown to be the most reliable character for species identification in several Entomobryidae genera, it might not be the case in Isotomurus Börner, 1903, the sole large Isotomidae genus where colour pattern is routinely used for taxonomy.},
}
@article {pmid29690328,
year = {2018},
author = {Schmidt, BC},
title = {Cryptic species among bumblebee mimics: an unrecognized Hemaris hawkmoth (Lepidoptera: Sphingidae) in eastern North America.},
journal = {Zootaxa},
volume = {4399},
number = {1},
pages = {32-48},
doi = {10.11646/zootaxa.4399.1.2},
pmid = {29690328},
issn = {1175-5334},
mesh = {Animals ; *Bees ; Manitoba ; Moths ; North America ; Ontario ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Through integrating molecular, morphological and natural history evidence, nominal Hemaris diffinis (Boisduval) of eastern North America is shown to include a second, cryptic species, Hemaris aethra (Strecker) stat. rev. Despite highly divergent mtDNA sequences and differing larval phenotypes, genitalic morphology, habitat and larval host plants, adults of H. aethra and sympatric H. diffinis are externally so similar that H. aethra has remained unrecognized for over a century. With a more northerly distribution than H. diffinis, H. aethra occurs from Manitoba to Nova Scotia and adjacent parts of the United States, the two species occurring in strict sympatry in eastern Ontario and likely other regions. Co-mimicry of Bombus Latreille bumblebee models has likely resulted in phenotypic convergence of H. diffinis and H. aethra, as the two do not appear to be sister taxa, the latter instead being more closely related to the western species H. thetis (Boisduval). The larvae of H. aethra are illustrated for the first time, together with diagnostic images and comparisons of adults. Lectotypes are designated for Hemaris tenuis Grote and Hemaris marginalis Grote.},
}
@article {pmid29690278,
year = {2018},
author = {Borkent, A and Brown, BV and Adler, PH and Amorim, DS and Barber, K and Bickel, D and Boucher, S and Brooks, SE and Burger, J and Burington, ZL and Capellari, RS and Costa, DNR and Cumming, JM and Curler, G and Dick, CW and Epler, JH and Fisher, E and Gaimari, SD and Gelhaus, J and Grimaldi, DA and Hash, J and Hauser, M and Hippa, H and IbÁÑez-Bernal, S and Jaschhof, M and Kameneva, EP and Kerr, PH and Korneyev, V and Korytkowski, CA and Kung, GA and Kvifte, GM and Lonsdale, O and Marshall, SA and Mathis, WN and Michelsen, V and Naglis, S and Norrbom, AL and Paiero, S and Pape, T and Pereira-Colavite, A and Pollet, M and Rochefort, S and Rung, A and Runyon, JB and Savage, J and Silva, VC and Sinclair, BJ and Skevington, JH and Stireman, JOI and Swann, J and Vilkamaa, P and Wheeler, T and Whitworth, T and Wong, M and Wood, DM and Woodley, N and Yau, T and Zavortink, TJ and Zumbado, MA},
title = {Remarkable fly (Diptera) diversity in a patch of Costa Rican cloud forest: Why inventory is a vital science.},
journal = {Zootaxa},
volume = {4402},
number = {1},
pages = {53-90},
doi = {10.11646/zootaxa.4402.1.3},
pmid = {29690278},
issn = {1175-5334},
mesh = {Animals ; Biodiversity ; Central America ; Colombia ; Costa Rica ; *Diptera ; Forests ; },
abstract = {Study of all flies (Diptera) collected for one year from a four-hectare (150 x 266 meter) patch of cloud forest at 1,600 meters above sea level at Zurquí de Moravia, San José Province, Costa Rica (hereafter referred to as Zurquí), revealed an astounding 4,332 species. This amounts to more than half the number of named species of flies for all of Central America. Specimens were collected with two Malaise traps running continuously and with a wide array of supplementary collecting methods for three days of each month. All morphospecies from all 73 families recorded were fully curated by technicians before submission to an international team of 59 taxonomic experts for identification. Overall, a Malaise trap on the forest edge captured 1,988 species or 51% of all collected dipteran taxa (other than of Phoridae, subsampled only from this and one other Malaise trap). A Malaise trap in the forest sampled 906 species. Of other sampling methods, the combination of four other Malaise traps and an intercept trap, aerial/hand collecting, 10 emergence traps, and four CDC light traps added the greatest number of species to our inventory. This complement of sampling methods was an effective combination for retrieving substantial numbers of species of Diptera. Comparison of select sampling methods (considering 3,487 species of non-phorid Diptera) provided further details regarding how many species were sampled by various methods. Comparison of species numbers from each of two permanent Malaise traps from Zurquí with those of single Malaise traps at each of Tapantí and Las Alturas, 40 and 180 km distant from Zurquí respectively, suggested significant species turnover. Comparison of the greater number of species collected in all traps from Zurquí did not markedly change the degree of similarity between the three sites, although the actual number of species shared did increase. Comparisons of the total number of named and unnamed species of Diptera from four hectares at Zurquí is equivalent to 51% of all flies named from Central America, greater than all the named fly fauna of Colombia, equivalent to 14% of named Neotropical species and equal to about 2.7% of all named Diptera worldwide. Clearly the number of species of Diptera in tropical regions has been severely underestimated and the actual number may surpass the number of species of Coleoptera. Various published extrapolations from limited data to estimate total numbers of species of larger taxonomic categories (e.g., Hexapoda, Arthropoda, Eukaryota, etc.) are highly questionable, and certainly will remain uncertain until we have more exhaustive surveys of all and diverse taxa (like Diptera) from multiple tropical sites. Morphological characterization of species in inventories provides identifications placed in the context of taxonomy, phylogeny, form, and ecology. DNA barcoding species is a valuable tool to estimate species numbers but used alone fails to provide a broader context for the species identified.},
}
@article {pmid29690248,
year = {2018},
author = {Shinohara, A and Kakuda, T and Wei, M and Kameda, Y},
title = {DNA Barcodes Identify the Larvae and Unassociated Male of Three Onycholyda Sawflies (Hymenoptera, Pamphiliidae) from China.},
journal = {Zootaxa},
volume = {4403},
number = {1},
pages = {123-132},
doi = {10.11646/zootaxa.4403.1.7},
pmid = {29690248},
issn = {1175-5334},
mesh = {Animals ; China ; DNA Barcoding, Taxonomic ; *Hymenoptera ; Larva ; Male ; Rosaceae ; },
abstract = {A molecular analysis based on mitochondrial cytochrome oxidase subunit 1 (COI) gene sequences has indicated that larvae collected in Sichuan and Zhejiang Provinces, China, belong to Onycholyda xanthogaster Shinohara, 1999, and O. fulvicornis Shinohara, in Shinohara Wei, 2016 (Hymenoptera, Pamphiliidae), and that a male Onycholyda specimen from Mt. Tianmushan, Zhejiang Province is the hitherto unknown male of O. tianmushana Shinohara Xiao, 2006. The first host plant records are Rubus inopertus (Focke) Focke (Rosaceae) for O. xanthogaster and Rubus hirsutus Thunb. for O. fulvicornis. The larvae of O. xanthogaster and O. fulvicornis are briefly described and O. xanthogaster is newly recorded from Sichuan Province. The male of O. tianmushana is described for the first time.},
}
@article {pmid29690239,
year = {2018},
author = {Makarchenko, EA and Makarchenko, MA and Semenchenko, AA and Palatov, DM},
title = {Morphological description and DNA barcoding of Chaetocladius (Chaetocladius) elisabethae sp. nov. (Diptera: Chironomidae: Orthocladiinae) from the Moscow Region.},
journal = {Zootaxa},
volume = {4403},
number = {2},
pages = {378-388},
doi = {10.11646/zootaxa.4403.2.9},
pmid = {29690239},
issn = {1175-5334},
mesh = {Animals ; *Chironomidae ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV ; Male ; Moscow ; Phylogeny ; Pupa ; },
abstract = {Illustrated descriptions of the adult male, pupa and fourth instar larva, as well as DNA barcoding results of Chaetocladius (Chaetocladius) elisabethae sp. nov. in comparison with closely related species of Chaetocladius s. str. from the Moscow Region are provided. A reference 658 bp barcode sequence from a fragment of the mitochondrial gene cytochrome oxidase I (COI) was used as a tool for species delimitation. Comparisons with corresponding regions of COI between C. (s. str.) elisabethae sp. nov. and other species of the subgenus produced K2P genetic distances of 0.11-0.16, values well associated with interspecific variation. The barcodes of the new species were identical to the Chaetocladius sp. 2ES in BOLD systems. Molecular data were also used for the reconstruction of the phylogenetic relationships within the subgenus Chaetocladius s. str.},
}
@article {pmid29690236,
year = {2018},
author = {Friedrich, T and Wiesner, C and Zangl, L and Daill, D and Freyhof, J and KoblmÜller, S},
title = {Romanogobio skywalkeri, a new gudgeon (Teleostei: Gobionidae) from the upper Mur River, Austria.},
journal = {Zootaxa},
volume = {4403},
number = {2},
pages = {336-350},
doi = {10.11646/zootaxa.4403.2.6},
pmid = {29690236},
issn = {1175-5334},
mesh = {Animals ; Austria ; *Cyprinidae ; Rivers ; },
abstract = {Romanogobio skywalkeri, new species, is described from the upper Mur River in the Austrian Danube drainage. It is related to R. banarescui from the Mediterranean basin. Romanogobio skywalkeri is distinguished from R. banarescui by lacking epithelial crests on the predorsal back, having 12-14 total pectoral-fin rays (vs. 10-11) and usually 8½ branched dorsal-fin rays (vs. 7½). It is distinguished from other Romanogobio species in the Danube drainage by having a very slender body; a moderately long barbel, extending slightly beyond the posterior eye margin; and no epithelial crests on the predorsal back. Romanogobio skywalkeri is distinguished by a minimum net divergence of 6.3% (uncorrected p-distance against R. banarescui) in the COI barcoding region from other European Romanogobio species. A key to the Romanogobio species of the Danube drainage is provided. Romanogobio banarescui from the Vardar drainage and R. carpathorossicus from the Danube drainage are treated as valid species.},
}
@article {pmid29690209,
year = {2018},
author = {Chan, BKK and Chang, YW},
title = {A new deep-sea scalpelliform barnacle, Vulcanolepas buckeridgei sp. nov. (Eolepadidae: Neolepadinae) from hydrothermal vents in the Lau Basin.},
journal = {Zootaxa},
volume = {4407},
number = {1},
pages = {117-129},
doi = {10.11646/zootaxa.4407.1.8},
pmid = {29690209},
issn = {1175-5334},
mesh = {Animals ; Hydrothermal Vents ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; *Thoracica ; },
abstract = {The present study describes a new species of Vulcanolepas from the Lau Basin in the South Pacific. The basal angle of the tergum of Vulcanolepas buckeridgei sp. nov. is elevated from the capitular-peduncular margin at ~1/6 of the capitular height. The mandibles of V. buckeridgei sp. nov. are tridentoid; the cutting margins of the second and third teeth are long and each tooth possesses 18-20 sharp spines. The proximal segments of the anterior and posterior rami of cirrus I are protuberant and with dense, simple setae. DNA barcode sequences of Vulcanolepas buckeridgei sp. nov. are similar to Vulcanolepas sp. 1 collected from the Lau Basin (Herrera et al. 2015). Vulcanolepas buckeridgei is morphologically similar to Vulcanolepas 'Lau A' collected in the Lau Basin (Southward Newman 1998). This suggests that Vulcanolepas buckeridgei sp. nov. is widespread in the Lau Basin.},
}
@article {pmid29690208,
year = {2018},
author = {Parslow, BA and Stevens, MI and Schwarz, MP},
title = {First record of Gasteruption Latreille (Hymenoptera: Evanioidea: Gasteruptiidae) from Fiji with the description of a new species.},
journal = {Zootaxa},
volume = {4407},
number = {1},
pages = {111-116},
doi = {10.11646/zootaxa.4407.1.7},
pmid = {29690208},
issn = {1175-5334},
mesh = {Animals ; DNA, Mitochondrial ; Fiji ; *Hymenoptera ; },
abstract = {A new Gasteruption Latreille species, G. tomanivi, is described from Viti Levu, Fiji. The new species is the first record of the genus for Fiji and can be distinguished from other Oceanian Gasteruption species by the length of the mesosoma and the large malar space compared with the length of the pedicel. DNA Barcode (mtDNA-COI) sequence is provided.},
}
@article {pmid29690179,
year = {2018},
author = {Magnussen, T and KjÆrandsen, J and Johnsen, A and SØli, GEE},
title = {Six new species of Afrotropical Allodia (Diptera: Mycetophilidae): DNA barcodes indicate recent diversification with a single origin.},
journal = {Zootaxa},
volume = {4407},
number = {3},
pages = {301-320},
doi = {10.11646/zootaxa.4407.3.1},
pmid = {29690179},
issn = {1175-5334},
mesh = {Africa, Eastern ; Animal Distribution ; Animal Structures ; Animals ; DNA Barcoding, Taxonomic ; *Diptera ; Male ; },
abstract = {Only one species of the genus Allodia has been previously recorded from the Afrotropical region, Allodia (Brachycampta) flavorufa Matile, 1978. Six new species are described here, all representing the nominotypical subgenus, Allodia s.s. The new species are described from material collected in different mountainous areas in south and east Africa; A. jaschhofi sp. nov., A. karkloofensis sp. nov., A. drakensbergensis sp. nov., A. nyeriensis sp. nov., A. mazumbaiensis sp. nov. and A. keurbosensis sp. nov. The species are morphologically very similar, and can only be separated based on minor differences in wing venation and characters of the male terminalia. The genetic differences between the species in the DNA barcode region (CO1), however, support delimitation. The origin and distribution of these Afrotropical taxa, in relation to each other and to their Holarctic relatives, is discussed.},
}
@article {pmid29690173,
year = {2018},
author = {Xia, JH and Wu, HL and Li, CH and Wu, YQ and Liu, SH},
title = {A new species of Rhinogobius (Pisces: Gobiidae), with analyses of its DNA barcode.},
journal = {Zootaxa},
volume = {4407},
number = {4},
pages = {553-562},
doi = {10.11646/zootaxa.4407.4.7},
pmid = {29690173},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Asia ; China ; DNA Barcoding, Taxonomic ; Male ; *Perciformes ; },
abstract = {The genus Rhinogobius Gill 1859 is widely distributed in fresh waters along the Western Pacific coast of tropical and temperate Asia. A new species, Rhinogobius maxillivirgatus, is described from Anhui Province in Eastern China. This species can be differentiated from all congeners by a combination of the following characters: up to 6 longitudinal brown to black stripes along the side of the body; pectoral-fin rays modally 14; predorsal scale series 5-9; lateral scale series 28-30; transverse scale series 6-7; branchiostegal membrane with about 20 red round spots in males; and 2 black oblique stripes parallel along the upper jaw on the anterior portion of the cheek. Analyzing sequences of cytochrome c oxidase subunit I revealed that the new species is closely related to, but distinct, from Rhinogobius wuyanlingensis.},
}
@article {pmid29690172,
year = {2018},
author = {Baldizzone, G and Huemer, P and Nel, J},
title = {Coleophora meridiogallica Baldizzone, Huemer Nel, sp. n. from France (Lepidoptera, Coleophoridae).},
journal = {Zootaxa},
volume = {4407},
number = {4},
pages = {543-552},
doi = {10.11646/zootaxa.4407.4.6},
pmid = {29690172},
issn = {1175-5334},
mesh = {Animals ; France ; Larva ; *Lepidoptera ; },
abstract = {Coleophora meridiogallica sp. n., a new species detected as a result of a DNA study, is described and compared with C. meridionella Rebel, 1912 with which it was confused. The new species whose larvae feed on Silene saxifraga is known only from a few departments of southeastern France.},
}
@article {pmid29690158,
year = {2018},
author = {Komai, T and Chen, C and Watanabe, HK},
title = {Two new species of the crangonid genus Metacrangon Zarenkov, 1965 (Crustacea: Decapoda: Caridea) from the Okinawa Trough, Japan.},
journal = {Zootaxa},
volume = {4410},
number = {1},
pages = {97-112},
doi = {10.11646/zootaxa.4410.1.5},
pmid = {29690158},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Crangonidae ; *Decapoda ; Islands ; Japan ; },
abstract = {Two new species of the crangonid shrimp genus Metacrangon Zarenkov, 1965, are described and illustrated on the basis of materials collected from the Okinawa Trough, Ryukyu Islands, southern Japan, during diving operations of remotely operated vehicles (ROVs): M. ryukyu n. sp. from off Iheya Island, at depth of 986 m; and Metacrangon kaiko n. sp. from NE of Yonaguni Island, at depth of 2205 m. The two new species resemble members of the M. munita (Dana, 1852) species group, but are both characteristic in having setose dactyli on pereopods 4 and 5. Some minor differences in morphology and genetic analysis using partial sequences of the barcoding mitochondrial COI gene support the recognition of the two new species. Holotypes of the two new species were collected from hydrothermally influenced areas, representing a previously unknown habitat for species of Metacrangon.},
}
@article {pmid29690059,
year = {2018},
author = {Aguilera-Uribe, M and MartÍnez, JJ and ZaldÍvar-riverÓn, A},
title = {Three new species of Pambolus (Braconidae: Pambolinae) from Mexico, with comments on the variation of P. oblongispina Papp.},
journal = {Zootaxa},
volume = {4377},
number = {1},
pages = {125-137},
doi = {10.11646/zootaxa.4377.1.8},
pmid = {29690059},
issn = {1175-5334},
mesh = {Animals ; Female ; Honduras ; Male ; Mexico ; Phylogeny ; *Wasps ; },
abstract = {Three species of the braconid genus Pambolus (Braconidae) are described from Mexico: P. jarocho sp. n., P. chinanteco sp. n. and P. bizelab sp. n. The external morphological variation in males and females of P. oblongispina Papp, previously known only by two females from Honduras and northern Mexico, is described based on material from Jalisco and Oaxaca in central and southeast Mexico. Molecular characterisation of the examined species was carried out based on the 28S nuclear ribosomal and the COI mitochondrial DNA gene markers.},
}
@article {pmid29690028,
year = {2018},
author = {Pawson, DL},
title = {A new species of the remarkable brittle star genus Astrophiura (Echinodermata: Ophiuroidea) from the western Atlantic Ocean.},
journal = {Zootaxa},
volume = {4378},
number = {2},
pages = {257-264},
doi = {10.11646/zootaxa.4378.2.4},
pmid = {29690028},
issn = {1175-5334},
mesh = {Animals ; Atlantic Ocean ; Caribbean Region ; Curacao ; *Echinodermata ; Female ; Gulf of Mexico ; Ovum ; West Indies ; },
abstract = {Astrophiura caroleae, new species, is described from off Curacao in the southern Caribbean, and from the western Gulf of Mexico, in depths of 244 to 434 meters. This new species, the first in the genus Astrophiura to be described from the Atlantic Ocean, has a distinctive combination of characters, including regularly arranged primary plates, large radial shields whose radial edges are in contact for their entire visible length, and prominent tubercles on central and radial plates. The mottled reddish coloration of the dorsal surface of this species usually contrasts with the color of the substratum, rendering it readily visible in situ, despite its disc diameter of less than 10 mm. Like its congeners, A. caroleae is gonochoric, the gonads of females containing conspicuous masses of bright orange eggs that are approximately 165 µm in diameter. DNA Barcoding data are provided for this new species, these are the first for Astrophiura.},
}
@article {pmid29690007,
year = {2018},
author = {Vences, M and Rasoloariniaina, JR and Riemann, JC},
title = {A preliminary assessment of genetic divergence and distribution of Malagasy cave fish in the genus Typhleotris (Teleostei: Milyeringidae).},
journal = {Zootaxa},
volume = {4378},
number = {3},
pages = {367-376},
doi = {10.11646/zootaxa.4378.3.5},
pmid = {29690007},
issn = {1175-5334},
mesh = {Animals ; Caves ; DNA, Mitochondrial ; Fishes/*genetics ; Genetic Variation ; Haplotypes ; Madagascar ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; },
abstract = {The genus Typhleotris contains three poorly known blind fish species, inhabiting aquifers in the limestone plateau of south-western Madagascar. Until recently these species were known from only few localities, and their pattern of genetic differentiation remains poorly studied. In this study we analyse 122 Typhleotris tissue samples collected from 12 localities, spanning the entire known range of the genus, and use DNA sequences to assign these samples to the three species known. The phylogeny based on the mitochondrial marker cox1 revealed three main clades corresponding to the three species: Typhleotris madagascariensis, T. mararybe and T. pauliani, differing by uncorrected pairwise sequence divergences of 6.3-9.8%. The distribution ranges of the three species overlapped widely: T. mararybe was collected only in a southern group of localities, T. madagascariensis was found in both the southern and the central group of localities, and T. pauliani occurred from the northernmost site to the southern group of localities; yet the three species did not share haplotypes in two nuclear genes, except for three individuals that we hypothesize are hybrids of T. pauliani with T. madagascariensis and T. mararybe. This pattern of concordant mitochondrial and nuclear divergence despite sympatry strongly supports the status of all three taxa as separate species. Phylogeographic structure was obvious in T. madagascariensis, with two separate shallow mitochondrial clades occupying (1) the central vs. (2) the southern group of populations, and in T. pauliani, with separate mitochondrial clades for (1) the northern vs. (2) the central/southern populations. The widespread occurrence of these three cave fish species suggests that the aquifers in south-western Madagascar have at least in the past allowed episodic dispersal and gene flow of subterraneous organisms, whereas the phylogeographic pattern of T. madagascariensis and T. pauliani provides evidence for isolation and loss of connectivity in the more recent past.},
}
@article {pmid29689996,
year = {2018},
author = {Cruz-lÓpez, JA},
title = {A new leaf-litter harvestman species of the genus Karos (Opiliones: Stygnopsidae: Karosinae), with a reanalysis of the morphological phylogeny of the genus.},
journal = {Zootaxa},
volume = {4378},
number = {4},
pages = {533-548},
doi = {10.11646/zootaxa.4378.4.5},
pmid = {29689996},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; *Arachnida ; Female ; Likelihood Functions ; Male ; Mexico ; Phylogeny ; },
abstract = {Karos Goodnight Goodnight, 1944 is the most diverse genus of the family Stygnopsidae. It contains seven micro-endemic species from the Huasteca region in eastern Mexico. In this paper, the new species Karos morronei sp. nov. is described based on the morphology of adults of both sexes. The new species is from Zacualtipán de Ángeles, Hidalgo State, which represents the southernmost record for the genus. Additionally, a reanalysis of the previous morphological phylogeny of the genus using both parsimony and maximum likelihood methods is provided. According to the morphological reanalysis, K. morronei sp. nov. exhibits an autapomorphy (males with femur IV thicker than females) and is the sister group of the clade that includes K. barbarikos, K. hexasetosus, K. monjarazi, K. parvus and K. singularis. Finally, information of barcoding (CO1) is provided for this new species.},
}
@article {pmid29689905,
year = {2018},
author = {Mateussi, NTB and Oliveira, C and Pavanelli, CS},
title = {Taxonomic revision of the Cis-Andean species of Mylossoma Eigenmann Kennedy, 1903 (Teleostei: Characiformes: Serrasalmidae).},
journal = {Zootaxa},
volume = {4387},
number = {2},
pages = {275-309},
doi = {10.11646/zootaxa.4387.2.3},
pmid = {29689905},
issn = {1175-5334},
mesh = {Animals ; Brazil ; *Characiformes ; },
abstract = {A revision of the cis-Andean species of Mylossoma is presented. Four species were recognized: M. albiscopum and M. aureum from the rio Amazonas and rio Orinoco basins; M. duriventre, from the rio Paraguai, lower rio Paraná and rio Uruguai basins; and M. unimaculatum, an endemic species from the Tocantins-Araguaia system. Both Mylossoma albiscopum and M. unimaculatum were removed from the synonymy of Mylossoma duriventre, which had its occurrence range restricted to the La Plata basin. The recognition of these four valid species corroborates the results of a previous DNA barcode study. Redescriptions of each species, and an identification key for the genus are provided.},
}
@article {pmid29689891,
year = {2018},
author = {Gibbs, S and Hundt, PJ and Nelson, A and Egan, JP and Tongnunui, P and Simons, AM},
title = {Systematics of the combtooth blenny clade Omobranchus (Blenniidae: Omobranchini), with notes on early life history stages.},
journal = {Zootaxa},
volume = {4369},
number = {2},
pages = {270-280},
doi = {10.11646/zootaxa.4369.2.7},
pmid = {29689891},
issn = {1175-5334},
mesh = {Animals ; DNA, Mitochondrial ; Evolution, Molecular ; Fishes ; Malaysia ; *Perciformes ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; },
abstract = {The combtooth blenny (Blenniidae) genus Omobranchus contains small, cryptobenthic fishes common to nearshore habitats throughout the Indo-West Pacific. Recent molecular systematic studies have resolved Omobranchus as monophyletic but little research has been done to resolve species-level relationships. Herein, phylogenetic analyses of one mitochondrial (CO1) and four nuclear (ENC1, myh6, sreb2, and tbr1) genes provide evidence for the monophyly of Omobranchus and support for the elongatus and banditus species group. Sampling of multiple individuals from widespread species (O. ferox, O. punctatus, and O. elongatus) suggested that the Thai-Malay Peninsula is a phylogeographic break that may be a historic barrier to gene flow. Additionally, common meristics and other morphological characters are used to describe an early life history stage of O. ferox and O. punctatus.},
}
@article {pmid29689889,
year = {2018},
author = {Infusino, M and Hausmann, A and Scalercio, S},
title = {Ptilophora variabilis Hartig, 1968, bona species, and description of Ptilophora nebrodensis sp. n. from Sicily (Lepidoptera, Notodontidae).},
journal = {Zootaxa},
volume = {4369},
number = {2},
pages = {237-252},
doi = {10.11646/zootaxa.4369.2.5},
pmid = {29689889},
issn = {1175-5334},
mesh = {Animals ; Forests ; Genitalia ; *Lepidoptera ; Sicily ; Trees ; },
abstract = {In this paper, we redescribe Ptilophora plumigera variabilis Hartig, 1968 and raise it to species rank. Furthermore we describe Ptilophora nebrodensis sp. n. from Sicily, as the third European species belonging to the genus Ptilophora Stephens, 1828. These two species are allopatric vicariants of Ptilophora plumigera (Denis Schiffermüller, 1775) respectively in Apennine Italy and Sicily. We present the differential features mainly concerning the morphology of genitalia and molecular data. Ptilophora variabilis shows a scattered distribution, generally very localized, whereas P. nebrodensis sp. n. is restricted to a few localities in the mountainous areas of North Sicily, being very rare. Both species predominantly inhabit forests in mountain areas, with occurrence of broadleaved trees, especially Acer spp. (Fam. Aceraceae).},
}
@article {pmid29689857,
year = {2018},
author = {Terossi, M and Almeida, AO and Buranelli, RC and Castilho, AL and Costa, RC and Zara, FJ and Mantelatto, FL},
title = {Checklist of decapods (Crustacea) from the coast of the São Paulo state (Brazil) supported by integrative molecular and morphological data: I. Infraorder Caridea: families Hippolytidae, Lysmatidae, Ogyrididae, Processidae and Thoridae.},
journal = {Zootaxa},
volume = {4370},
number = {1},
pages = {76-94},
doi = {10.11646/zootaxa.4370.1.6},
pmid = {29689857},
issn = {1175-5334},
mesh = {Animals ; Atlantic Ocean ; Biodiversity ; Brazil ; *Decapoda ; Estuaries ; },
abstract = {The current checklist is the result of a long-term multidisciplinary project which combined molecular techniques (mitochondrial DNA markers) and morphological analyses of adult specimens for an accurate and detailed identification of the total biodiversity of decapod crustaceans from marine and coastal (including estuaries) environments of São Paulo State (Brazil). This is the first of a series of reports and providing a checklist of caridean shrimps of the families Hippolytidae (5 spp.), Lysmatidae (6 spp.), Ogyrididae (2 spp.), Processidae (5 spp.) and Thoridae (1 sp.). We collected material of 13 species out of 19 recorded, with sequences of cytochrome oxidase subunit I - barcode region and 16S generated from 10 species. The previous record of Lysmata cf. intermedia for São Paulo is actually L. jundalini, as the first record in São Paulo/South Atlantic waters. The molecular data were helpful to confirm the identification of some species, as the occurrence of L. wurdemanni which is confirmed in the South Atlantic Ocean based on morphological, color pattern and molecular data.},
}
@article {pmid29689854,
year = {2018},
author = {Thiel, R and Knebelsberger, T and Eidus, I},
title = {Description and DNA barcoding of Lycenchelys lenzeni, a new species of eelpout (Perciformes: Zoarcidae) from the deep sea off the Kuril Archipelago.},
journal = {Zootaxa},
volume = {4370},
number = {1},
pages = {45-56},
doi = {10.11646/zootaxa.4370.1.3},
pmid = {29689854},
issn = {1175-5334},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Mitochondria ; Perciformes/*genetics ; },
abstract = {A new species of eelpout genus Lycenchelys Gill, 1884 is described based on seven specimens caught at a depth of about 2350 m in the Bussol Strait, southwest of the Kuril Island Simushir. The species differs from its congeners in the following combination of characters: vertebrae 26-28 + 100-102 = 126-130; interorbital and occipital pores absent; postorbital pores 3-4; suborbital pores 7 (rarely 6); preoperculomandibular pores 4 + 4; gill rakers 11-16; dorsal fin rays 118-122; anal fin rays 105-108; pelvic fin rays 2; middle and lower ray tips of pectoral fin very slightly exserted; lateral line double with mediolateral and ventral branches; pyloric caeca not developed. The new species is morphologically most similar to Lycenchelys micropora and Lycenchelys jordani, which differ from the new species in having three pelvic-fin rays (vs. two pelvic-fin rays in the new species). L. micropora has the pectoral-fin origin below body midline, whereas the new species has the pectoral-fin origin at body midline. Middle and lower ray tips of pectoral fin are very slightly exserted in L. lenzeni sp. nov., whereas they are well exserted in L. jordani and L. micropora. Mitochondrial COI sequences were analyzed from four paratype specimens and all show the same haplotype sequence. The DNA barcodes allowed discrimination of L. lenzeni sp. nov. from other species of Lycenchelys where sequence data were available. The nearest match with already published sequences was Lycenchelys antarctica, with a sequence similarity of 98.25%, followed by Lycenchelys aratrirostris (sequence similarities 97.95-97.96%) and L. jordani (sequence similarity of 97.81%).},
}
@article {pmid29689827,
year = {2018},
author = {Galil, BS and Douek, J and Gevili, R and Goren, M and Yudkovsky, Y and Paz, G and Rinekvich, B},
title = {The resurrection of Charybdis (Gonioinfradens) giardi (Nobili, 1905), newly recorded from the SE Mediterranean Sea.},
journal = {Zootaxa},
volume = {4370},
number = {5},
pages = {580-590},
doi = {10.11646/zootaxa.4370.5.9},
pmid = {29689827},
issn = {1175-5334},
mesh = {Animals ; *Brachyura ; Indian Ocean ; Mediterranean Sea ; Oman ; },
abstract = {A single adult specimen of Gonioinfradens giardi, a portunid crab known from the Red Sea, Gulf of Oman and Arabian Gulf, was recently collected off the southern Israeli coast, in the southeastern Mediterranean Sea. Morphological characters, as well as molecular analyses based on the mitochondrial barcoding gene cytochrome oxidase sub unit I (COI), support its distinction from the widely distributed G. paucidentata. Therefore, G. giardi is reinstated as a valid species, and withdrawn from its synonymy with G. paucidentata. Previous Mediterranean records of the latter species are misidentifications and should be referred to G. giardi. The species is described, illustrated, and differentiated from its cogener.},
}
@article {pmid29689826,
year = {2018},
author = {Vargas-Ortiz, M and Vargas, HA},
title = {A new species of Strepsicrates Meyrick (Lepidoptera: Tortricidae) from the Atacama Desert of northern Chile previously misidentified as S. smithiana Walsingham.},
journal = {Zootaxa},
volume = {4370},
number = {5},
pages = {569-579},
doi = {10.11646/zootaxa.4370.5.8},
pmid = {29689826},
issn = {1175-5334},
mesh = {Animals ; Bayes Theorem ; Chile ; Larva ; *Lepidoptera ; Pupa ; },
abstract = {The adult, larva, and pupa of Strepsicrates gattii Vargas-Ortiz Vargas, sp. n. (Lepidoptera: Tortricidae: Olethreutinae: Eucosmini), are described and illustrated from the Atacama Desert of northern Chile. The larvae are leaf-tiers on the vulnerable native tree Morella pavonis (Myricaceae). As S. gattii was previously misidentified as S. smithiana Walsingham, morphological differences that enable the separation of the two species are highlighted. Sequences of the DNA barcode fragment of the cytochrome oxidase subunit I mitochondrial gene of the new species are provided and used in a Bayesian analysis with congeneric representatives to assess their relationships preliminarily. The divergence (K2P) with S. smithiana was 6.4-7.4%, providing additional support for separating the two species.},
}
@article {pmid29689811,
year = {2018},
author = {Xu, JH and Sun, CH and Wang, BX},
title = {Descriptions of larvae of three species of Hydropsyche (Trichoptera, Hydropsychidae) from China.},
journal = {Zootaxa},
volume = {4374},
number = {1},
pages = {1-24},
doi = {10.11646/zootaxa.4374.1.1},
pmid = {29689811},
issn = {1175-5334},
mesh = {Animals ; China ; *Insecta ; Larva ; Male ; },
abstract = {Twenty-one individuals of Hydropsyche from An-hui and Zhe-jiang Provinces, China, were examined and their DNA barcode sequences were generated and analyzed. The larvae and males of H. arion, H. columnata, H. simulata, and H. trifora were associated by mtCOI gene sequences. The larvae of H. arion, H. columnata, and H. trifora are described in detail and their diagnostic photographs are provided. Character photographs of the H. simulata larva are also presented. A key to 5th instar larvae of 15 species of Chinese Hydropsyche is provided.},
}
@article {pmid29689797,
year = {2018},
author = {Shashank, PR and Kammar, V and Mally, R and Chakravarthy, AK},
title = {A new Indian species of shoot and capsule borer of the genus Conogethes (Lepidoptera: Crambidae), feeding on cardamom.},
journal = {Zootaxa},
volume = {4374},
number = {2},
pages = {215-234},
doi = {10.11646/zootaxa.4374.2.3},
pmid = {29689797},
issn = {1175-5334},
mesh = {Animals ; Elettaria ; India ; *Lepidoptera ; Phylogeny ; },
abstract = {A new species, Conogethes sahyadriensis sp. nov. (Lepidoptera: Crambidae), feeding on cardamom, is described from India. The species status is supported by diagnostic morphology as well as by genetic data. A phylogenetic analysis based on the publicly available Conogethes COI barcode sequences finds C. sahyadriensis as sister to C. pluto, and it further reveals a number of clades that potentially represent additional undescribed species.The new species is delineated from closely related and superficially similar species of Conogethes.},
}
@article {pmid29687751,
year = {2018},
author = {Sarmiento-Camacho, S and Valdez-Moreno, M},
title = {DNA barcode identification of commercial fish sold in Mexican markets.},
journal = {Genome},
volume = {61},
number = {6},
pages = {457-466},
doi = {10.1139/gen-2017-0222},
pmid = {29687751},
issn = {1480-3321},
mesh = {Animals ; DNA Barcoding, Taxonomic/methods/*standards ; Endangered Species ; Fish Products/*standards ; Fishes/classification/*genetics ; Mexico ; },
abstract = {The substitution of high-value fish species for those of lower value is common practice. Although numerous studies have addressed this issue, few have been conducted in Mexico. In this study, we sought to identify fresh fillets of fish, sharks, and rays using DNA barcodes. We analyzed material from "La Viga" in Mexico City, and other markets located on the Gulf and Caribbean coasts of Mexico. From 134 samples, we obtained sequences from 129, identified to 9 orders, 28 families, 38 genera, and 44 species. The most common species were Seriola dumerili, Pangasianodon hypophthalmus, Carcharhinus falciformis, Carcharhinus brevipinna, and Hypanus americanus. Pangasianodon hypophthalmus was most commonly used as a substitute for higher-value species. The substitution rate was 18% of the total. A review of the conservation status of the specimens identified against the IUNC list enabled us to establish that some species marketed in Mexico are threatened: Makaira nigricans, Lachnolaimus maximus, Hyporthodus flavolimbatus, and Isurus oxyrinchus are classified as vulnerable; Lopholatilus chamaeleonticeps and Sphyrna lewini are endangered; and the status of Hyporthodus nigritus is critical. These results will demonstrate to the Mexican authorities that DNA barcoding is a reliable tool for species identification, even when morphological identification is difficult or impossible.},
}
@article {pmid29686213,
year = {2017},
author = {Cumming, RT and Leong, JV and Lohman, DJ},
title = {Leaf insects from Luzon, Philippines, with descriptions of four new species, the new genus Pseudomicrophyllium, and redescription of Phyllium (Phyllium) geryon Gray, 1843, (Phasmida: Phylliidae).},
journal = {Zootaxa},
volume = {4365},
number = {2},
pages = {101-131},
doi = {10.11646/zootaxa.4365.2.1},
pmid = {29686213},
issn = {1175-5334},
mesh = {Animals ; *Insecta ; Neoptera ; Philippines ; },
abstract = {Examination of unidentified Phylliidae specimens revealed a number of undescribed species from the island of Luzon, Philippines. Morphological and molecular study of specimens from the obscure phasmid genus Microphyllium Zompro, 2001, revealed a new species, which we describe as Microphyllium haskelli Cumming sp. nov.. It is here described and differentiated from the two other species in the genus, both currently only known from adults of a single sex. Pseudomicrophyllium Cumming gen. nov. is described as a new genus within Phylliidae with the type species Pseudomicrophyllium faulkneri Cumming gen. et sp. nov. as the sole known species in the genus. As is unfortunately often the case in the leaf-mimicking family Phylliidae, this new genus and species is only known from a single specimen. In addition to the new genus, two new Phyllium (Phyllium) species from the siccifolium species-group are named and described as Ph. (Ph.) antonkozlovi Cumming sp. nov. and Ph. (Ph.) bourquei Cumming Le Tirant sp. nov.. In addition to the newly described species, Phyllium (Phyllium) geryon Gray, 1843 is redescribed from a nearly perfect specimen, completing some of the morphological knowledge gaps currently missing because of the severely damaged holotype specimen. A key to all known species of Phylliidae from Luzon is included. Holotype specimens for all four new species will be deposited in the National Museum of the Philippines type collection and paratype specimens will be deposited into the San Diego Natural History Museum collection or retained within the first author's collection.},
}
@article {pmid29686202,
year = {2017},
author = {Watson, JE and Govindarajan, AF},
title = {A new species of Gonionemus (Hydrozoa: Limnomedusae) from southern Australia.},
journal = {Zootaxa},
volume = {4365},
number = {4},
pages = {487-494},
doi = {10.11646/zootaxa.4365.4.8},
pmid = {29686202},
issn = {1175-5334},
mesh = {Animals ; Australia ; *Hydrozoa ; Phylogeny ; RNA, Ribosomal, 16S ; South Australia ; Victoria ; },
abstract = {A new species of a crawling limnomedusa belonging to the genus Gonionemus (Hydrozoa: Limnomedusae: Olindiidae) was collected from the brown alga Cystophora monilifera in an intertidal rock pool in Western Port, Victoria, Australia. The new species is described and compared with the three known species of Gonionemus. The mitochondrial DNA barcode markers cytochrome oxidase I and 16S rRNA were sequenced and compared to sequences from other olindiid species. The sequencing results corroborate the morphological findings.},
}
@article {pmid29686200,
year = {2017},
author = {Khosravani, A and Rastegar-Pouyani, E and Rastegar-Pouyani, N and Oraie, H and Papenfuss, TJ},
title = {Resolving species delimitation within the genus Bunopus Blanford, 1874 (Squamata: Gekkonidae) in Iran using DNA barcoding approach.},
journal = {Zootaxa},
volume = {4365},
number = {4},
pages = {467-479},
doi = {10.11646/zootaxa.4365.4.6},
pmid = {29686200},
issn = {1175-5334},
mesh = {Animals ; DNA ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; Iran ; *Lizards ; Phylogeny ; },
abstract = {Mitochondrial COI sequences were used to investigate species delimitation within the genus Bunopus in Iran. A dataset with a final sequence length of 633 nucleotides including 100 specimens from 31 geographically distant localities across Iran were generated. The result demonstrated that two major clades with strong support can be identified within the genus Bunopus in Iran. Clade A includes Bunopus crassicaudus and two new entities, eastern populations (subclade A2,1) and Shahdad populations (subclade A2,2). The second clade comprises western and southwestern populations (subclade B1,1), Arabian populations (subclade B1,2) and south and southeast populations in Iran, to which Bunopus tuberculatus (subclade B2) is assigned. In addition to Bunopus crassicaudus and B. tuberculatus, three new candidate species in Iran can easily be identified based on the DNA barcoding approach.},
}
@article {pmid29684023,
year = {2018},
author = {Uhse, S and Pflug, FG and Stirnberg, A and Ehrlinger, K and von Haeseler, A and Djamei, A},
title = {In vivo insertion pool sequencing identifies virulence factors in a complex fungal-host interaction.},
journal = {PLoS biology},
volume = {16},
number = {4},
pages = {e2005129},
pmid = {29684023},
issn = {1545-7885},
support = {I 3033/FWF_/Austrian Science Fund FWF/Austria ; P 27429/FWF_/Austrian Science Fund FWF/Austria ; P 27818/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {DNA Transposable Elements ; Expressed Sequence Tags ; Gene Library ; *Genome, Fungal ; High-Throughput Nucleotide Sequencing/*methods ; Host-Pathogen Interactions ; Mutagenesis, Insertional/*methods ; Mutation ; Plant Diseases/microbiology ; Ustilago/*genetics/metabolism/pathogenicity ; Virulence ; Virulence Factors/*genetics/metabolism ; Zea mays/*microbiology ; },
abstract = {Large-scale insertional mutagenesis screens can be powerful genome-wide tools if they are streamlined with efficient downstream analysis, which is a serious bottleneck in complex biological systems. A major impediment to the success of next-generation sequencing (NGS)-based screens for virulence factors is that the genetic material of pathogens is often underrepresented within the eukaryotic host, making detection extremely challenging. We therefore established insertion Pool-Sequencing (iPool-Seq) on maize infected with the biotrophic fungus U. maydis. iPool-Seq features tagmentation, unique molecular barcodes, and affinity purification of pathogen insertion mutant DNA from in vivo-infected tissues. In a proof of concept using iPool-Seq, we identified 28 virulence factors, including 23 that were previously uncharacterized, from an initial pool of 195 candidate effector mutants. Because of its sensitivity and quantitative nature, iPool-Seq can be applied to any insertional mutagenesis library and is especially suitable for genetically complex setups like pooled infections of eukaryotic hosts.},
}
@article {pmid29683493,
year = {2018},
author = {Favalli, N and Bassi, G and Scheuermann, J and Neri, D},
title = {DNA-encoded chemical libraries - achievements and remaining challenges.},
journal = {FEBS letters},
volume = {592},
number = {12},
pages = {2168-2180},
pmid = {29683493},
issn = {1873-3468},
support = {163479/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Combinatorial Chemistry Techniques ; DNA/*chemistry ; Drug Discovery ; Drug Evaluation, Preclinical/*methods ; Humans ; *Small Molecule Libraries ; Structure-Activity Relationship ; },
abstract = {DNA-encoded chemical libraries (DECLs) are collections of compounds, individually coupled to DNA tags serving as amplifiable identification barcodes. Since individual compounds can be identified by the associated DNA tag, they can be stored as a mixture, allowing the synthesis and screening of combinatorial libraries of unprecedented size, facilitated by the implementation of split-and-pool synthetic procedures or other experimental methodologies. In this review, we briefly present relevant concepts and technologies, which are required for the implementation and interpretation of screening procedures with DNA-encoded chemical libraries. Moreover, we illustrate some success stories, detailing how novel ligands were discovered from encoded libraries. Finally, we critically review what can realistically be achieved with the technology at the present time, highlighting challenges and opportunities for the future.},
}
@article {pmid29683355,
year = {2019},
author = {Yang, H and Zhou, Y and Yu, P and Yang, Y and Jiao, Z and Tam, JP and Shen, Y and Jia, X},
title = {A novel PCR-based technology for rapid and non-sequencing authentication of Bombyx batryticatus using species-specific primers.},
journal = {Natural product research},
volume = {33},
number = {9},
pages = {1251-1256},
doi = {10.1080/14786419.2018.1466127},
pmid = {29683355},
issn = {1478-6427},
mesh = {Animals ; Beauveria/*genetics ; Bombyx/*genetics ; DNA Primers ; Drug Contamination ; *Medicine, Chinese Traditional ; Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; Species Specificity ; },
abstract = {A novel PCR technology was developed to detect short DNA fragments using species-specific primers for rapid and non-sequencing authentication of Bombyx batryticatus based on differences in the mitochondrial genome. Three specifically designed primer reactions were established to target species for the reliable identification of their commercial products. They were confirmed to have a high inter-species specificity and intra-species stability. The limit of detection was estimated as 1 ng of genomes for Beauveria bassiana and 100 pg for Bombyx mori and Metarhizium anisopliae. Furthermore, validation results demonstrated that raw materials and their processed products can be conveniently authenticated with good sensitivity and precision using this newly proposed approach. In particular, when counterfeits were assayed, these primer sets performed well, whereas COI barcoding technology did not. These could also assist in the discrimination and identification of adulterates of other animal-derived medicines in their pulverized and processed forms and even in complexes.},
}
@article {pmid29683108,
year = {2018},
author = {Neang, T and Chan, S and Poyarkov, NA},
title = {A new species of smooth skink (Squamata: Scincidae: Scincella) from Cambodia.},
journal = {Zoological research},
volume = {39},
number = {3},
pages = {220-240},
pmid = {29683108},
issn = {2095-8137},
mesh = {Animals ; Cambodia ; DNA, Mitochondrial/genetics ; Lizards/*anatomy &amp; histology/classification/genetics ; Phylogeny ; },
abstract = {Based on morphological and genetic evidence we evaluated the taxonomic status of a newly discovered forest-dwelling population of skink (genus Scincella) from the Keo Seima Wildlife Sanctuary, Mondulkiri Province, Cambodia. From phylogenetic analysis of a 668-bp fragment of the mtDNA COI and diagnostic morphological characters we allocate the newly discovered population to the Scincella reevesii-S. rufocaudata species complex and describe it as Scincella nigrofasciata sp. nov. The new skink species can be distinguished from all other Southeast Asian congeners by the following combination of morphological characters: snout-vent length (SVL) 40.0-52.6 mm; relative tail length (TaL/SVL ratio) 1.25-1.94; prefrontals in broad contact; infralabials 6; primary temporals 2; relative forelimb length (FIL/SVL ratio) 0.20-0.22; relative hindlimb length (HIL/SVL ratio) 0.30-0.33; relative forearm length (FoL/SVL ratio) 0.14-0.16; adpressed forelimbs and hind limbs either overlapping (0.4-2.2 mm) or separated (1.9-2.3 mm); midbody scale rows 32-33, paravertebral scales 69-74, vertebral scales 65-69; dorsal scales between dorsolateral stripes 8; comparatively slender fingers and toes, subdigital lamellae under fourth toe 15-17; dark discontinuous regular dorsal stripes 5-7; distinct black dorsolateral stripes, narrowing to lateral sides and extending to 52%-86% of total tail length. We provide additional information on the holotype of Scincella rufocaudata (Darevsky &amp; Nguyen, 1983), and provide evidence for the species status of Scincella rupicola. Our discovery brings the number of Scincella species in Cambodia to five and emphasizes the incompleteness of knowledge on the herpetofaunal diversity of this country.},
}
@article {pmid29682531,
year = {2018},
author = {Park, JH and Shin, SE and Ko, KS and Park, SH},
title = {Identification of Forensically Important Calliphoridae and Sarcophagidae Species Collected in Korea Using SNaPshot Multiplex System Targeting the Cytochrome c Oxidase Subunit I Gene.},
journal = {BioMed research international},
volume = {2018},
number = {},
pages = {2953892},
pmid = {29682531},
issn = {2314-6141},
mesh = {Animals ; Base Sequence/genetics ; DNA/genetics ; Diptera/*genetics ; Electron Transport Complex IV/*genetics ; Larva/genetics ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Postmortem Changes ; Pupa/genetics ; Republic of Korea ; Sarcophagidae/*genetics ; Sequence Analysis, DNA/methods ; Species Specificity ; },
abstract = {Estimation of postmortem interval (PMI) is paramount in modern forensic investigation. After the disappearance of the early postmortem phenomena conventionally used to estimate PMI, entomologic evidence provides important indicators for PMI estimation. The age of the oldest fly larvae or pupae can be estimated to pinpoint the time of oviposition, which is considered the minimum PMI (PMImin). The development rate of insects is usually temperature dependent and species specific. Therefore, species identification is mandatory for PMImin estimation using entomological evidence. The classical morphological identification method cannot be applied when specimens are damaged or have not yet matured. To overcome this limitation, some investigators employ molecular identification using mitochondrial cytochrome c oxidase subunit I (COI) nucleotide sequences. The molecular identification method commonly uses Sanger's nucleotide sequencing and molecular phylogeny, which are complex and time consuming and constitute another obstacle for forensic investigators. In this study, instead of using conventional Sanger's nucleotide sequencing, single-nucleotide polymorphisms (SNPs) in the COI gene region, which are unique between fly species, were selected and targeted for single-base extension (SBE) technology. These SNPs were genotyped using a SNaPshot® kit. Eleven Calliphoridae and seven Sarcophagidae species were covered. To validate this genotyping, fly DNA samples (103 adults, 84 larvae, and 4 pupae) previously confirmed by DNA barcoding were used. This method worked quickly with minimal DNA, providing a potential alternative to conventional DNA barcoding. Consisting of only a few simple electropherogram peaks, the results were more straightforward compared with those of the conventional DNA barcoding produced by Sanger's nucleotide sequencing.},
}
@article {pmid29682427,
year = {2018},
author = {Holmes, I and Davis Rabosky, AR},
title = {Natural history bycatch: a pipeline for identifying metagenomic sequences in RADseq data.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e4662},
pmid = {29682427},
issn = {2167-8359},
abstract = {BACKGROUND: Reduced representation genomic datasets are increasingly becoming available from a variety of organisms. These datasets do not target specific genes, and so may contain sequences from parasites and other organisms present in the target tissue sample. In this paper, we demonstrate that (1) RADseq datasets can be used for exploratory analysis of tissue-specific metagenomes, and (2) tissue collections house complete metagenomic communities, which can be investigated and quantified by a variety of techniques.<br><br>METHODS: We present an exploratory method for mining metagenomic "bycatch" sequences from a range of host tissue types. We use a combination of the pyRAD assembly pipeline, NCBI's blastn software, and custom R scripts to isolate metagenomic sequences from RADseq type datasets.<br><br>RESULTS: When we focus on sequences that align with existing references in NCBI's GenBank, we find that between three and five percent of identifiable double-digest restriction site associated DNA (ddRAD) sequences from host tissue samples are from phyla to contain known blood parasites. In addition to tissue samples, we examine ddRAD sequences from metagenomic DNA extracted snake and lizard hind-gut samples. We find that the sequences recovered from these samples match with expected bacterial and eukaryotic gut microbiome phyla.<br><br>DISCUSSION: Our results suggest that (1) museum tissue banks originally collected for host DNA archiving are also preserving valuable parasite and microbiome communities, (2) that publicly available RADseq datasets may include metagenomic sequences that could be explored, and (3) that restriction site approaches are a useful exploratory technique to identify microbiome lineages that could be missed by primer-based approaches.},
}
@article {pmid29679524,
year = {2018},
author = {Rath, S and Kumar, V and Kundu, S and Tyagi, K and Singha, D and Chakraborty, R and Chatterjee, S},
title = {DNA testing of edible crabs from seafood shops on the Odisha coast, India.},
journal = {Biomolecular concepts},
volume = {9},
number = {1},
pages = {12-16},
doi = {10.1515/bmc-2018-0002},
pmid = {29679524},
issn = {1868-503X},
mesh = {Animals ; Brachyura/classification/*genetics ; *DNA Barcoding, Taxonomic ; India ; Phylogeny ; Seafood/analysis ; *Shellfish ; },
abstract = {Seafood consumption is highly demanding due to the important source of protein it contains, as well as being rich in omega-3 fatty acids. However, the adulteration of seafood is an alarming issue worldwide, including India. This study deals with edible crabs from seafood shops on the Odisha state coast in eastern India. The generated DNA barcode sequences successfully identified most of the studied brachyuran crab species by similarity search results in global databases. The species were also delimited by significant genetic divergence and Neighbour-Joining phylogeny. Additionally, the study detected the contamination of unknown organisms in the commercialized crab recipes from seafood shops. The DNA based species detection of brachyuran crab may be useful to resolve many ambiguities in species identification and monitoring of commercialized seafood concerning food safety.},
}
@article {pmid29678013,
year = {2018},
author = {Daus, MY and Maydana, TG and Rizzato Lede, DA and Luna, DR},
title = {Implementation of a New Traceability Process for Breast Milk Feeding.},
journal = {Studies in health technology and informatics},
volume = {247},
number = {},
pages = {511-515},
pmid = {29678013},
issn = {1879-8365},
mesh = {*Breast Feeding ; *Enteral Nutrition ; Female ; Humans ; Infant, Newborn ; Intensive Care Units, Neonatal ; *Milk, Human ; Mothers ; Physicians ; },
abstract = {Many newborns at the neonatal intensive care unit are unable to feed themselves, and receive human milk through enteric nutrition devices such as orogastric or nasogastric probes. The mothers extract their milk, and the nursing staff is responsible for the fractionation, storage and administration when prescribed by physicians. It is very important to remind that it is a bodily fluid that carries the risk of disease transmission if misused. Health information technologies can enhance patient safety by avoiding preventable adverse events. Barcoding technology could track every step of the milk manipulation. Many processes must be addressed to implement it. Our goal is to explain our planning and implementation process in an academic tertiary hospital.},
}
@article {pmid29676091,
year = {2018},
author = {Zhao, R and Shao, F and Yin, HB and Kang, TG},
title = {[Identification of Dioscorea nipponica and its sects based on psbA-trnH barcode].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {43},
number = {5},
pages = {938-944},
doi = {10.19540/j.cnki.cjcmm.20180109.007},
pmid = {29676091},
issn = {1001-5302},
mesh = {China ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Dioscorea/*classification ; Genes, Plant ; Sequence Analysis, DNA ; },
abstract = {A rapid and accurate method was established by psbA-trnH sequence to distinguish Dioscorea nipponica from other species belonging to the same genus.In this study, we collected 144 samples of D. nipponica from 17 different producing areas in China, the psbA-trnH sequenced of 23 nucleotide sequences were downloaded from GenBank, the sequences from Dioscorea genus. DNAMAN 8.0 software was used to show splicing, MEGA 6.0 software was applied for sequence analysis and comparison. The results showed that the genetic relationship between D. nipponica and D. subcalva was the closest, and the genetic relationship with D. zingiberensis was the furthest. It is indicated that the psbA-trnH sequence as a DNA barcode can effectively distinguish between D. nipponica and other plants in the genus of Dioscorea.},
}
@article {pmid29676034,
year = {2018},
author = {D'Souza, ML and Hebert, PDN},
title = {Stable baselines of temporal turnover underlie high beta diversity in tropical arthropod communities.},
journal = {Molecular ecology},
volume = {27},
number = {10},
pages = {2447-2460},
doi = {10.1111/mec.14693},
pmid = {29676034},
issn = {1365-294X},
mesh = {Animals ; Arthropods/*genetics ; DNA Barcoding, Taxonomic/ethics ; *Environment ; *Genetic Variation ; Honduras ; Linear Models ; Tropical Climate ; },
abstract = {While the high species diversity of tropical arthropod communities has often been linked to marked spatial heterogeneity, their temporal dynamics have received little attention. This study addresses this gap by examining spatio-temporal variation in the arthropod communities of a tropical montane forest in Honduras. By employing DNA barcode analysis and Malaise trap sampling across 4 years and five sites, 51,596 specimens were assigned to 8,193 presumptive species. High beta diversity was linked more strongly to elevation than geographic distance, decreasing by 12% when only the dominant species were considered. When sampling effort was increased by deploying more traps at a site, beta diversity only decreased by 2%, but extending sampling across years decreased beta diversity by 27%. Species inconsistently detected among years, likely transients from other settings, drove the low similarity in species composition among traps only a few metres apart. The dominant, temporally persistent species substantially influenced the cyclic pattern of change in community composition among years. This pattern likely results from divergence-convergence dynamics, suggesting a stable baseline of temporal turnover in each community. The overall results establish that large sample sizes are necessary to reveal species richness, but are not essential for quantifying beta diversity. This study further highlights the need for standardized methods of sampling and species identification to generate the comparative data required to evaluate biodiversity change in space and time.},
}
@article {pmid29674926,
year = {2018},
author = {Binh, HT and Ngoc, NV and Tagane, S and Toyama, H and Mase, K and Mitsuyuki, C and Strijk, JS and Suyama, Y and Yahara, T},
title = {A taxonomic study of Quercus langbianensis complex based on morphology and DNA barcodes of classic and next generation sequences.},
journal = {PhytoKeys},
volume = {},
number = {95},
pages = {37-70},
pmid = {29674926},
issn = {1314-2011},
abstract = {The taxonomy of Quercus langbianensis and its relatives in Vietnam and Cambodia have been revised based on evidence obtained from field observations, morphological comparison of herbarium specimens and molecular analyses using both classic and next generation DNA markers. Based on Bayesian inference using rbcL, matK and ITS regions and Neighbour-joining tree using genome-wide sequences amplified with multiplexed inter-simple sequence repeat (ISSR) primers (MIG-seq), the authors recognised ten species in the complex in Vietnam and Cambodia, three of which are newly described in this paper: Q. baolamensissp. nov., Q. bidoupensissp. nov. and Q. honbaensissp. nov. These new species are all phenotypically similar to Q. langbianensiss. str. in having lanceolate to oblanceolate leaf shape, upper 4-5/6-serrated leaf margin, acute or acuminate leaf apex and bracts of cupule arranged in 5-9 rings but distinguished both morphologically and phylogenetically. In molecular phylogenetic reconstructions, Q. bidoupensis is not close to any other species. In the Bayesian tree, Q. honbaensis is sister to both Q. blaoensis and Q. camusiae that are found in the same locality but morphologically distinct and those three species are sister to Q. langbianensiss. str., while Quercus baolamensis is not sister to Q. langbianensiss. str. in both the Bayesian tree and MIG-seq tree. In addition, Q. cambodiensis and Q. baniensis previously reduced to Q. langbianensiss. lat. have been recognised as distinct species. Six species were in need of lectotypification and that is undertaken herein.},
}
@article {pmid29674920,
year = {2018},
author = {Hou, Z and Zhao, S and Li, S},
title = {Seven new freshwater species of Gammarus from southern China (Crustacea, Amphipoda, Gammaridae).},
journal = {ZooKeys},
volume = {},
number = {749},
pages = {1-79},
pmid = {29674920},
issn = {1313-2989},
abstract = {Seven new species of the genus Gammarus are described and illustrated from southern China. The new species Gammarus vallecula Hou &amp; Li, sp. n., G. qinling Hou &amp; Li, sp. n., G. zhigangi Hou &amp; Li, sp. n. and G. jidutanxian Hou &amp; Li, sp. n. are characterized by inner ramus of uropod III half the length of outer ramus. Gammarus longdong Hou &amp; Li, sp. n. is characterized by inner ramus of uropod III 0.9 times as long as outer ramus. Gammarus mosuo Hou &amp; Li, sp. n. is characterized by pereopods V-VII with long setae on anterior margins and both rami of uropod III armed with simple setae. Gammarus caecigenus Hou &amp; Li, sp. n. can be distinguished from other species by eyes absent. DNA barcodes of the new species are documented as proof of molecular differences between species. A key to the new species and a map of their distributions are provided.},
}
@article {pmid29674916,
year = {2018},
author = {Schmidt, RE and Shoobs, NF and McMullin, ER},
title = {Occurrence of the large ostracod, Chlamydotheca unispinosa (Baird, 1862), in temporary waters of Montserrat, Lesser Antilles.},
journal = {ZooKeys},
volume = {},
number = {748},
pages = {89-95},
pmid = {29674916},
issn = {1313-2989},
abstract = {Four populations of the large freshwater ostracod, Chlamydotheca unispinosa (Baird, 1862), were discovered on the Caribbean island of Montserrat. These are the first records of the species on Montserrat and extend its known distribution approximately 113 km northwest and 63 km southeast of the closest known populations on Îles des Saintes (Guadeloupe) and Nevis, respectively. We provide the first DNA barcode for C. unispinosa, a 686 bp fragment of the COI gene which may be used for future comparative studies of this widely distributed species.},
}
@article {pmid29674898,
year = {2018},
author = {Adeoba, MI and Kabongo, R and der Bank, HV and Yessoufou, K},
title = {Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae).},
journal = {ZooKeys},
volume = {},
number = {746},
pages = {105-121},
pmid = {29674898},
issn = {1313-2989},
abstract = {Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for phylogenetic comparative analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.},
}
@article {pmid29674896,
year = {2018},
author = {Mally, R and Huemer, P and Nuss, M},
title = {Deep intraspecific DNA barcode splits and hybridisation in the Udea alpinalis group (Insecta, Lepidoptera, Crambidae) - an integrative revision.},
journal = {ZooKeys},
volume = {},
number = {746},
pages = {51-90},
pmid = {29674896},
issn = {1313-2989},
abstract = {The analysis of mitochondrial COI data for the European-Centroasian montane Udea alpinalis species group finds deep intraspecific splits. Specimens of U. austriacalis and U. rhododendronalis separate into several biogeographical groups. These allopatric groups are not recovered in the analyses of the two nuclear markers wingless and Elongation factor 1-alpha, except for U. austriacalis from the Pyrenees and the French Massif Central. The latter populations are also morphologically distinct and conspecific with Scopula donzelalis Guenée, 1854, which is removed from synonymy and reinstated as Udea donzelalis (Guenée, 1854) stat. rev. Furthermore, Udea altaica (Zerny, 1914), stat. n. from the Mongolian central Altai mountains, U. juldusalis (Zerny, 1914), stat. n. from the Tian Shan mountains of Kazakhstan, Kyrgyzstan and NW China, and U. plumbalis (Zerny, 1914), stat. n. from the Sayan Mountains of Northern Mongolia are raised to species level, and lectotypes are designated. Evidence of introgression of U. alpinalis into U. uliginosalis at three localities in the Central Alps is presented. A screening for Wolbachia using the markers wsp, gatB and ftsZ was negative for the U. alpinalis species group, but Wolbachia was found in single specimens of U. fulvalis and U. olivalis (both in the U. numeralis species group). We do not find evidence for the conjecture of several authors of additional subspecies in U. rhododendronalis, and synonymise U. rhododendronalis luquetalis Leraut, 1996, syn. n. and U. r. ventosalis Leraut, 1996, syn. n. with the nominal U. rhododendronalis (Duponchel, 1834).},
}
@article {pmid29674869,
year = {2018},
author = {Liu, YQ and Chen, HW},
title = {The genus Scaptodrosophila Duda part II: the coracina species group from East Asia, with morphological and molecular evidence (Diptera, Drosophilidae).},
journal = {ZooKeys},
volume = {},
number = {736},
pages = {119-148},
pmid = {29674869},
issn = {1313-2989},
abstract = {Eight new species of the Scaptodrosophila coracina species group are described from China: S. fuscilimbasp. n., S. fusciventriculasp. n., S. helvpectasp. n., S. longispinatasp. n., S. nigrolimbatasp. n., S. trivittatasp. n., S. ventriobscuratasp. n., and S. zebrinasp. n. One known species S. coracina (Kikkawa &amp; Peng) is redescribed. A key to all the examined species in the coracina group is provided. Species delimitations have been improved by integrating the DNA sequences with morphological information. The intra- and interspecific pairwise p-distances (proportional distance) are summarized. Some nucleotide sites with fixed status in the alignment of the COI sequences (662 nucleotide sites in length) are used as "pure" molecular diagnostic characters to delineate species in the coracina group.},
}
@article {pmid29674866,
year = {2018},
author = {Arriaga-Varela, E and Tomaszewska, W and Huo, L and Seidel, M},
title = {On Neotropical Merophysiinae with descriptions of a new genus and new species (Coleoptera, Endomychidae).},
journal = {ZooKeys},
volume = {},
number = {736},
pages = {1-41},
pmid = {29674866},
issn = {1313-2989},
abstract = {Intensive survey of museum collections and new field collecting resulted in discovery of six new, closely related species of the Neotropical Merophysiinae. A new species of the genus Lycoperdinella Champion, L. boliviensissp. n., from Bolivia and Brazil, and five new species from Mexico for which a new genus is proposed here as Rueckeriagen. n.: R. inecol (type species), R. nigrileonis, R. ocelotl, R. puma, R. skelleyispp. n., have been discovered. Lycoperdinella, Rueckeriagen. n., L. subcaeca Champion and all new species are diagnosed, described, and illustrated. Keys to the species of Lycoperdinella and Rueckeria and a distribution map are provided. A lectotype of Lycoperdinella subcaeca Champion, 1913 is designated. Molecular barcodes of three new species of Rueckeria are provided in order to help with the identification of these taxa.},
}
@article {pmid29674862,
year = {2018},
author = {Qiao, P and Qin, W and Ma, H and Su, J and Zhang, T},
title = {Two new species of the genus Hessebius Verhoeff, 1941 from China (Lithobiomorpha, Lithobiidae).},
journal = {ZooKeys},
volume = {},
number = {735},
pages = {65-82},
pmid = {29674862},
issn = {1313-2989},
abstract = {Two new species, Hessebius luquensissp. n. and Hessebius ruoergaiensissp. n., are described based on material from Qinghai-Tibet Plateau. A key to the Chinese species of Hessebius is presented. The partial mitochondrial cytochrome c oxidase subunit I (COI) barcoding gene was amplified and sequenced for nine individuals of both species and the dataset was used for molecular phylogenetic analysis and genetic distance determination.},
}
@article {pmid29674859,
year = {2018},
author = {Angyal, D and Solís, EC and Magaña, B and Balázs, G and Simoes, N},
title = {Mayaweckelia troglomorpha, a new subterranean amphipod species from Yucatán state, México (Amphipoda, Hadziidae).},
journal = {ZooKeys},
volume = {},
number = {735},
pages = {1-25},
pmid = {29674859},
issn = {1313-2989},
abstract = {A detailed description of a new stygobiont species of the amphipod family Hadziidae, Mayaweckelia troglomorpha Angyal, sp. n. is given, based on material collected in four cenotes of Yucatán federal state, México. Morphology was studied under light microscopy and with scanning electron microscopy. Morphological description is complemented with mitochondrial cytochrome c oxidase subunit I (COI) sequences as barcodes, with affinities to the related taxa and with notes on the species' ecology. Using COI Bayesian inference and genetic distance analyses, we show that the closest relative of the new species is M. cenoticola, forming a monophyletic group referring to the genus Mayaweckelia. Based on the available sequences, we also revealed that Mayaweckelia and Tuluweckelia are sister genera, standing close to the third Yucatán subterranean genus, Bahadzia. The data gathered on the habitat, distribution, abundance, and ecology will contribute to the conservation planning for M. troglomorpha Angyal, sp. n.},
}
@article {pmid29673447,
year = {2018},
author = {An, CH and Chen, BB and Fan, SP and Sun, YX and Lyu, W and She, JJ},
title = {The Taxonomic Status of Spermophilus in the Plague Area of Dingbian County, Shaanxi Province, China.},
journal = {Biomedical and environmental sciences : BES},
volume = {31},
number = {3},
pages = {238-241},
doi = {10.3967/bes2018.030},
pmid = {29673447},
issn = {0895-3988},
mesh = {Animals ; China ; Cytochromes b/analysis ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/analysis ; *Karyotype ; Plague/microbiology ; Sciuridae/*anatomy &amp; histology/classification/*genetics ; },
abstract = {This study was conducted to define the taxonomic status of Spermophilus in the plague area of Dingbian County in Shaanxi Province, China, through the two-factor variance analysis of morphological characteristics, DNA barcoding, and chromosome karyotype analysis. The Spermophilus samples collected from Dingbian and Zhengxiang Baiqi Counties exhibited significant differences in their morphological measurements. All Spermophilus samples form two distinct branches in neighbor-joining (NJ) tree. One branch included the Spermophilus samples collected from Inner Mongolia, and the other branch included samples collected from the plague foci of Shaanxi Province and the Ningxia Region. The Spermophilus samples collected from Dingbian County had a chromosome number of 2n = 38 in 84.40% of all their cells. The Spermophilus species collected from the plague area of Dingbian County was categorized as Spermophilus alashanicus (S.alashamicus). The findings reported in this study are epidemiologically significant for monitoring plague in this region of west-central China.},
}
@article {pmid29673390,
year = {2018},
author = {Chan, Y and Chan, YK and Goodman, DB and Guo, X and Chavez, A and Lim, ET and Church, GM},
title = {Enabling multiplexed testing of pooled donor cells through whole-genome sequencing.},
journal = {Genome medicine},
volume = {10},
number = {1},
pages = {31},
pmid = {29673390},
issn = {1756-994X},
support = {P50 HG005550/HG/NHGRI NIH HHS/United States ; RM1 HG008525/HG/NHGRI NIH HHS/United States ; RM1HG008525//National Human Genome Research Institute (US)/International ; 74178//Robert Wood Johnson Foundation/International ; },
mesh = {Algorithms ; B-Lymphocytes/*metabolism ; Computer Simulation ; Genome, Human ; *High-Throughput Nucleotide Sequencing ; Humans ; Polymorphism, Single Nucleotide/genetics ; Sample Size ; *Tissue Donors ; *Whole Genome Sequencing ; },
abstract = {We describe a method that enables the multiplex screening of a pool of many different donor cell lines. Our method accurately predicts each donor proportion from the pool without requiring the use of unique DNA barcodes as markers of donor identity. Instead, we take advantage of common single nucleotide polymorphisms, whole-genome sequencing, and an algorithm to calculate the proportions from the sequencing data. By testing using simulated and real data, we showed that our method robustly predicts the individual proportions from a mixed-pool of numerous donors, thus enabling the multiplexed testing of diverse donor cells en masse.More information is available at https://pgpresearch.med.harvard.edu/poolseq/.},
}
@article {pmid29673082,
year = {2018},
author = {Srivathsan, A and Baloğlu, B and Wang, W and Tan, WX and Bertrand, D and Ng, AHQ and Boey, EJH and Koh, JJY and Nagarajan, N and Meier, R},
title = {A MinION™-based pipeline for fast and cost-effective DNA barcoding.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.12890},
pmid = {29673082},
issn = {1755-0998},
abstract = {DNA barcodes are useful for species discovery and species identification, but obtaining barcodes currently requires a well-equipped molecular laboratory and is time-consuming, and/or expensive. We here address these issues by developing a barcoding pipeline for Oxford Nanopore MinION™ and demonstrating that one flow cell can generate barcodes for ~500 specimens despite the high basecall error rates of MinION™ reads. The pipeline overcomes these errors by first summarizing all reads for the same tagged amplicon as a consensus barcode. Consensus barcodes are overall mismatch-free but retain indel errors that are concentrated in homopolymeric regions. They are addressed with an optional error correction pipeline that is based on conserved amino acid motifs from publicly available barcodes. The effectiveness of this pipeline is documented by analysing reads from three MinION™ runs that represent three different stages of MinION™ development. They generated data for (i) 511 specimens of a mixed Diptera sample, (ii) 575 specimens of ants and (iii) 50 specimens of Chironomidae. The run based on the latest chemistry yielded MinION™ barcodes for 490 of the 511 specimens which were assessed against reference Sanger barcodes (N = 471). Overall, the MinION™ barcodes have an accuracy of 99.3%-100% with the number of ambiguous bases after correction ranging from <0.01% to 1.5% depending on which correction pipeline is used. We demonstrate that it requires ~2 hr of sequencing to gather all information needed for obtaining reliable barcodes for most specimens (>90%). We estimate that up to 1,000 barcodes can be generated in one flow cell and that the cost per barcode can be <USD 2.},
}
@article {pmid29671657,
year = {2019},
author = {Prieto, C and Nuñez, R and Hausmann, A},
title = {Molecular species delimitation in the genus Rhamma Johnson, 1992 (Lepidoptera: Lycaenidae, Theclinae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {1},
pages = {101-117},
doi = {10.1080/24701394.2018.1462348},
pmid = {29671657},
issn = {2470-1408},
mesh = {Animals ; Butterflies/classification/*genetics ; DNA Barcoding, Taxonomic/*methods/standards ; Electron Transport Complex IV/genetics ; Genome, Mitochondrial ; Insect Proteins/genetics ; *Phylogeny ; Polymorphism, Genetic ; },
abstract = {In this work, we used mtDNA data as a tool to delimit species and we compared the resulting molecular operational taxonomic units (barcode index number, BIN) with morphology-based identifications in the Colombian species of Rhamma Johnson, 1992 exploring the usefulness of DNA barcodes for taxonomy, species identification and delimitation. We obtained cytochrome oxidase I (COI) sequences for 134 morphologically identified specimens, representing 12 species of Rhamma from Colombia. Ten of these species have not been previously barcoded. DNA barcodes suggested the potential for eight additional cryptic species in Colombia but we were readily able to morphologically diagnose just one of these linages as a new species which recently was described in a separate paper as Rhamma dawkinsi Prieto &amp; Lorenc-Brudecka, 2017. The morphological species were separated into three categories: species showing a perfect match between morphological species and BINs (33%, four species); species sharing a BIN completely or partly (single specimens) with another morphological species (42%, five species placed in three BINs); and morphological species splitting up into more than one BIN (25%, three species placed in 10 BINs). The high percentages of incongruence between morphology-based identification and species delineation through BINs, could be explained as a consequence of high rates of introgressive hybridization. However, DNA barcodes can be considered diagnostic even in cases where specimens of a species were assigned to two or more distinct BINs and in species showing a low but constant divergence causing their assignment to a single BIN, which is often the case in young, allopatric species. We retain 10 of the 12 species (83%) to be diagnostic in molecular identification.},
}
@article {pmid29670644,
year = {2018},
author = {Melo, BF and Dorini, BF and Foresti, F and Oliveira, C},
title = {Little Divergence Among Mitochondrial Lineages of Prochilodus (Teleostei, Characiformes).},
journal = {Frontiers in genetics},
volume = {9},
number = {},
pages = {107},
pmid = {29670644},
issn = {1664-8021},
abstract = {Evidence that migration prevents population structure among Neotropical characiform fishes has been reported recently but the effects upon species diversification remain unclear. Migratory species of Prochilodus have complex species boundaries and intrincate taxonomy representing a good model to address such questions. Here, we analyzed 147 specimens through barcode sequences covering all species of Prochilodus across a broad geographic area of South America. Species delimitation and population genetic methods revealed very little genetic divergence among mitochondrial lineages suggesting that extensive gene flow resulted likely from the highly migratory behavior, natural hybridization or recent radiation prevent accumulation of genetic disparity among lineages. Our results clearly delimit eight genetic lineages in which four of them contain a single species and four contain more than one morphologically problematic taxon including a trans-Andean species pair and species of the P. nigricans group. Information about biogeographic distribution of haplotypes presented here might contribute to further research on the population genetics and taxonomy of Prochilodus.},
}
@article {pmid29670444,
year = {2018},
author = {Wang, N and Liu, T and Xu, J and Jiang, B},
title = {The leaf-mining genus Antispila Hübner, 1825 feeding on Vitaceae in Shandong Peninsula, China with one new species (Lepidoptera, Heliozelidae).},
journal = {ZooKeys},
volume = {},
number = {744},
pages = {49-65},
pmid = {29670444},
issn = {1313-2989},
abstract = {The Antispila species feeding on Vitaceae from Shandong Peninsula, China are treated. Antispila kunyuensis Liu, sp. n., feeding on Ampelopsis humulifolia, is described as new to science, and A. uenoi Kuroko, 1987, feeding on Vitis amurensis, is recorded as new for China. Vitis amurensis is documented as a new host plant for A. uenoi. The adult male and female, host plant and typical patterns of leaf-mines of both species are illustrated, as are male and female genitalia and venation. The venation and the paired tufts of scales on the 7[th] abdominal segment in male are illustrated for A. uenoi for the first time. DNA barcodes of both species are also provided, together with a neighbor-joining tree for facilitating species delimitation.},
}
@article {pmid29670433,
year = {2018},
author = {Kullander, SO and Rahman, MM and Norén, M and Mollah, AR},
title = {Laubuka tenella, a new species of cyprinid fish from southeastern Bangladesh and southwestern Myanmar (Teleostei, Cyprinidae, Danioninae).},
journal = {ZooKeys},
volume = {},
number = {742},
pages = {105-126},
pmid = {29670433},
issn = {1313-2989},
abstract = {Laubuka tenella is a new species characterized by the colour pattern, consisting of short dark vertical bars anteriorly on the side, and a dark lateral band posteriorly on the side, combined with a relatively short pelvic fin and 29-30 lateral-line scales. It is separated from other Laubuka analysed by minimum 9 % uncorrected p-distance in the mitochondrial COI gene. The type series is composed of specimens from small streams in the Cox's Bazar District in Bangladesh (the type locality), and the Thandwe River drainage in western Myanmar. Laubuka brahmaputraensis is strongly indicated to be a junior synonym of L. laubuca, the second known species of Laubuka in Bangladesh. Eustira ceylonensis, currently in the synonymy of Devario malabaricus, is a valid species of Laubuka.},
}
@article {pmid29670192,
year = {2018},
author = {Crainey, JL and Marín, MA and Silva, TRRD and de Medeiros, JF and Pessoa, FAC and Santos, YV and Vicente, ACP and Luz, SLB},
title = {Mansonella ozzardi mitogenome and pseudogene characterisation provides new perspectives on filarial parasite systematics and CO-1 barcoding.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {6158},
pmid = {29670192},
issn = {2045-2322},
mesh = {Animals ; Electron Transport Complex IV/*genetics ; *Genome, Mitochondrial ; Genomics/methods ; Humans ; Mansonella/*classification/*genetics ; Mansonelliasis/*parasitology ; Phylogeny ; *Pseudogenes ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 5S/genetics ; },
abstract = {Despite the broad distribution of M. ozzardi in Latin America and the Caribbean, there is still very little DNA sequence data available to study this neglected parasite's epidemiology. Mitochondrial DNA (mtDNA) sequences, especially the cytochrome oxidase (CO1) gene's barcoding region, have been targeted successfully for filarial diagnostics and for epidemiological, ecological and evolutionary studies. MtDNA-based studies can, however, be compromised by unrecognised mitochondrial pseudogenes, such as Numts. Here, we have used shot-gun Illumina-HiSeq sequencing to recover the first complete Mansonella genus mitogenome and to identify several mitochondrial-origin pseudogenes. Mitogenome phylogenetic analysis placed M. ozzardi in the Onchocercidae "ONC5" clade and suggested that Mansonella parasites are more closely related to Wuchereria and Brugia genera parasites than they are to Loa genus parasites. DNA sequence alignments, BLAST searches and conceptual translations have been used to compliment phylogenetic analysis showing that M. ozzardi from the Amazon and Caribbean regions are near-identical and that previously reported Peruvian M. ozzardi CO1 reference sequences are probably of pseudogene origin. In addition to adding a much-needed resource to the Mansonella genus's molecular tool-kit and providing evidence that some M. ozzardi CO1 sequence deposits are pseudogenes, our results suggest that all Neotropical M. ozzardi parasites are closely related.},
}
@article {pmid29669453,
year = {2019},
author = {Laskar, BA and Kumar, V and Kundu, S and Darshan, A and Tyagi, K and Chandra, K},
title = {DNA barcoding of fishes from River Diphlu within Kaziranga National Park in northeast India.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {1},
pages = {126-134},
doi = {10.1080/24701394.2018.1463373},
pmid = {29669453},
issn = {2470-1408},
mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/methods/standards ; Electron Transport Complex IV/genetics ; Fish Proteins/genetics ; Fishes/classification/*genetics ; India ; *Phylogeny ; },
abstract = {DNA barcoding technique has been gaining importance in biodiversity research for its easy and rapid ability of delineating organisms' partial DNA sequences into molecular operational taxonomic units (MOTUs), and identification based on referral sequences from expert identified species. We generated mtCOI barcode sequences from morphologically identified fishes from River Diphlu in northeast India. A portion of this river falls within an important rhinoceros and tiger conservation site, the Kaziranga National Park. Partial mtCOI sequences for 103 fish specimens belonging to six orders, 19 families, 37 genera and 47 a priori identified species, were delineated into 48 MOTUs based on reciprocal monophyly criteria in maximum likelihood and Bayesian tree, and 49 groups by automatic barcode gap discovery (ABGD). Morphological and molecular basis of species identification was congruent for around 80% straightforward cases. We contributed barcodes for eight species which either had no barcodes in databases or are having ambiguous barcodes. We detected four 'near threatened' and two data deficient species as per the IUCN Red List status, besides a few 'least concerned' species. We also observed a wide scope of barcoding studies on fishes from northeast India to cover the endemic species and to resolve the prevailing taxonomic problems.},
}
@article {pmid29667570,
year = {2018},
author = {Boon, NAM and Van Den Broeck, F and Faye, D and Volckaert, FAM and Mboup, S and Polman, K and Huyse, T},
title = {Barcoding hybrids: heterogeneous distribution of Schistosoma haematobium × Schistosoma bovis hybrids across the Senegal River Basin.},
journal = {Parasitology},
volume = {145},
number = {5},
pages = {634-645},
doi = {10.1017/S0031182018000525},
pmid = {29667570},
issn = {1469-8161},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics ; Genotype ; Genotyping Techniques ; Humans ; *Hybridization, Genetic ; Prevalence ; Schistosoma/classification/*genetics ; Schistosoma haematobium/classification/*genetics ; Schistosomiasis/parasitology/urine ; Senegal ; },
abstract = {Hybridization events between Schistosoma species (Digenea, Platyhelminthes) are reported with increasing frequency, largely due to improved access to molecular tools. Nevertheless, little is known about the distribution and frequency of hybrid schistosomes in nature. Screening for hybrids on a large scale is complicated by the need for nuclear and mitochondrial sequence information, precluding a 'simple' barcoding approach. Here we aimed to determine and understand the spatiotemporal distribution of Schistosoma haematobium × Schistosoma bovis hybrids in the Senegal River Basin. From ten villages, distributed over the four main water basins, we genotyped a total of 1236 schistosome larvae collected from human urine samples using a partial mitochondrial cox1 fragment; a subset of 268 parasites was also genotyped using ITS rDNA. Hybrid schistosomes were unevenly distributed, with substantially higher numbers in villages bordering Lac de Guiers than in villages from the Lampsar River and the Middle Valley of the Senegal River. The frequency of hybrids per village was not linked with the prevalence of urinary schistosomiasis in that village. However, we did find a significant positive association between the frequency of hybrids per village and the prevalence of Schistosoma mansoni. We discuss the potential consequences of adopting a barcoding approach when studying hybrids in nature.},
}
@article {pmid29667329,
year = {2018},
author = {Bista, I and Carvalho, GR and Tang, M and Walsh, K and Zhou, X and Hajibabaei, M and Shokralla, S and Seymour, M and Bradley, D and Liu, S and Christmas, M and Creer, S},
title = {Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.12888},
pmid = {29667329},
issn = {1755-0998},
abstract = {New applications of DNA and RNA sequencing are expanding the field of biodiversity discovery and ecological monitoring, yet questions remain regarding precision and efficiency. Due to primer bias, the ability of metabarcoding to accurately depict biomass of different taxa from bulk communities remains unclear, while PCR-free whole mitochondrial genome (mitogenome) sequencing may provide a more reliable alternative. Here, we used a set of documented mock communities comprising 13 species of freshwater macroinvertebrates of estimated individual biomass, to compare the detection efficiency of COI metabarcoding (three different amplicons) and shotgun mitogenome sequencing. Additionally, we used individual COI barcoding and de novo mitochondrial genome sequencing, to provide reference sequences for OTU assignment and metagenome mapping (mitogenome skimming), respectively. We found that, even though both methods occasionally failed to recover very low abundance species, metabarcoding was less consistent, by failing to recover some species with higher abundances, probably due to primer bias. Shotgun sequencing results provided highly significant correlations between read number and biomass in all but one species. Conversely, the read-biomass relationships obtained from metabarcoding varied across amplicons. Specifically, we found significant relationships for eight of 13 (amplicons B1FR-450 bp, FF130R-130 bp) or four of 13 (amplicon FFFR, 658 bp) species. Combining the results of all three COI amplicons (multiamplicon approach) improved the read-biomass correlations for some of the species. Overall, mitogenomic sequencing yielded more informative predictions of biomass content from bulk macroinvertebrate communities than metabarcoding. However, for large-scale ecological studies, metabarcoding currently remains the most commonly used approach for diversity assessment.},
}
@article {pmid29659610,
year = {2018},
author = {Rivera, SF and Vasselon, V and Ballorain, K and Carpentier, A and Wetzel, CE and Ector, L and Bouchez, A and Rimet, F},
title = {DNA metabarcoding and microscopic analyses of sea turtles biofilms: Complementary to understand turtle behavior.},
journal = {PloS one},
volume = {13},
number = {4},
pages = {e0195770},
pmid = {29659610},
issn = {1932-6203},
mesh = {Animals ; Behavior, Animal ; *Biofilms ; Comoros ; *DNA Barcoding, Taxonomic ; Indian Ocean Islands ; *Metagenome ; *Metagenomics/methods ; Microscopy ; Phylogeny ; Turtles/*microbiology ; },
abstract = {Sea turtles are distributed in tropical and subtropical seas worldwide. They play several ecological roles and are considered important indicators of the health of marine ecosystems. Studying epibiotic diatoms living on turtle shells suggestively has great potential in the study of turtle behavior because diatoms are always there. However, diatom identification at the species level is time consuming, requires well-trained specialists, and there is a high probability of finding new taxa growing on turtle shells, which makes identification tricky. An alternative approach based on DNA barcoding and high throughput sequencing (HTS), metabarcoding, has been developed in recent years to identify species at the community level by using a DNA reference library. The suitabilities of morphological and molecular approaches were compared. Diatom assemblages were sampled from seven juvenile green turtles (Chelonia mydas) from Mayotte Island, France. The structures of the epibiotic diatom assemblages differed between both approaches. This resulted in different clustering of the turtles based on their diatom communities. Metabarcoding allowed better discrimination between turtles based on their epibiotic diatom assemblages and put into evidence the presence of a cryptic diatom diversity. Microscopy, for its part, provided more ecological information of sea turtles based on historical bibliographical data and the abundances of ecological guilds of the diatom species present in the samples. This study shows the complementary nature of these two methods for studying turtle behavior.},
}
@article {pmid29658115,
year = {2018},
author = {Lucas, A and Bodger, O and Brosi, BJ and Ford, CR and Forman, DW and Greig, C and Hegarty, M and Neyland, PJ and de Vere, N},
title = {Generalisation and specialisation in hoverfly (Syrphidae) grassland pollen transport networks revealed by DNA metabarcoding.},
journal = {The Journal of animal ecology},
volume = {87},
number = {4},
pages = {1008-1021},
pmid = {29658115},
issn = {1365-2656},
support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA, Plant/analysis ; Diptera/*physiology ; Grassland ; Magnoliopsida/classification/*physiology ; *Pollen ; *Pollination ; Species Specificity ; Wales ; },
abstract = {Pollination by insects is a key ecosystem service and important to wider ecosystem function. Most species-level pollination networks studied have a generalised structure, with plants having several potential pollinators, and pollinators in turn visiting a number of different plant species. This is in apparent contrast to a plant's need for efficient conspecific pollen transfer. The aim of this study was to investigate the structure of pollen transport networks at three levels of biological hierarchy: community, species and individual. We did this using hoverflies in the genus Eristalis, a key group of non-Hymenopteran pollinators. We constructed pollen transport networks using DNA metabarcoding to identify pollen. We captured hoverflies in conservation grasslands in west Wales, UK, removed external pollen loads, sequenced the pollen DNA on the Illumina MiSeq platform using the standard plant barcode rbcL, and matched sequences using a pre-existing plant DNA barcode reference library. We found that Eristalis hoverflies transport pollen from 65 plant taxa, more than previously appreciated. Networks were generalised at the site and species level, suggesting some degree of functional redundancy, and were more generalised in late summer compared to early summer. In contrast, pollen transport at the individual level showed some degree of specialisation. Hoverflies defined as "single-plant visitors" varied from 40% of those captured in early summer to 24% in late summer. Individual hoverflies became more generalised in late summer, possibly in response to an increase in floral resources. Rubus fruticosus agg. and Succisa pratensis were key plant species for hoverflies at our sites Our results contribute to resolving the apparent paradox of how generalised pollinator networks can provide efficient pollination to plant species. Generalised hoverfly pollen transport networks may result from a varied range of short-term specialised feeding bouts by individual insects. The generalisation and functional redundancy of Eristalis pollen transport networks may increase the stability of the pollination service they deliver.},
}
@article {pmid29657011,
year = {2018},
author = {Liu, Y and Tao, H and Yu, Y and Yue, L and Xia, W and Zheng, W and Ma, H and Liu, X and Chen, H},
title = {Molecular differentiation and species composition of genus Culicoides biting midges (Diptera: Ceratopogonidae) in different habitats in southern China.},
journal = {Veterinary parasitology},
volume = {254},
number = {},
pages = {49-57},
doi = {10.1016/j.vetpar.2018.02.035},
pmid = {29657011},
issn = {1873-2550},
mesh = {Animals ; *Biodiversity ; Bluetongue virus/physiology ; Ceratopogonidae/anatomy &amp; histology/*classification/*genetics ; China ; DNA Barcoding, Taxonomic ; *Ecosystem ; Electron Transport Complex IV/genetics ; Female ; Insect Proteins/*genetics ; Insect Vectors/anatomy &amp; histology/*classification/*genetics ; Male ; Mitochondrial Proteins/genetics ; Phylogeny ; Species Specificity ; },
abstract = {Culicoides biting midges (Diptera:Ceratopogonidae) cause a significant biting nuisance to humans, livestock, which are the biological vectors of a range of risky pathogens. Accurate illustration of vector play a key role in arthropod borne diseases surveillance. However, few studies have focused on the Culicoides, which caused bluetongue disease in 29 provinces of China since 1979. In this study, we assessed cytochrome oxidase subunit I (COI) mtDNA molecular marker for identification of ten major vector species and analyzed the Culicoides species community and diversity in different habitats. A total of 20,795 Culicoides samples collected from 11 sample sites were identified as 23 species belonging to 7 subgenera. Sequences of COI gene worked well as barcodes for identifying all the determined specimen in this study and were comparable with the existing sequence data from GenBank. We first reported COI barcode sequences of C. morisitai, C. insignipennis and C. homotomus. Morphological identification of Culicoides spp. samples within southern China appears relatively robust and some unidentified species were required further study. Our study shows that the COI sequence data can be used as a tool to identify species of Culicoides in Jiangxi Province. In our sampled area, the most abundant species was C. arakawae (61.89%), followed by C. oxystoma (13.77%), C. punctatus (10.10%), C. nipponensis (8.82%), C. homotomus (3.19%) and C.morisitai (1.17%) in this study. C. punctatus was the dominant species of Park habitat (62.22%), C. arakawae was the predominant species of Chicken habitat (96.66%), Vegetable plot habitat (92.0%), and Peasant household habitat (83.21%), respectively. C. oxystoma was the abundant species of Residential area habitat (40.11%), Hospital habitat (56.65%), and Pig &amp; Cow habitat (48.77%), respectively. Results also show that the potential Bluetongue virus vectors belong to the Obsoletus and Pulicaris groups, are also included and relatively abundant, notably: Culicoides punctatus. These findings expand the current knowledge of Culicoides population composition in the southern part of China.},
}
@article {pmid29644996,
year = {2018},
author = {Spanjaard, B and Hu, B and Mitic, N and Olivares-Chauvet, P and Janjuha, S and Ninov, N and Junker, JP},
title = {Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars.},
journal = {Nature biotechnology},
volume = {36},
number = {5},
pages = {469-473},
pmid = {29644996},
issn = {1546-1696},
support = {715361/ERC_/European Research Council/International ; },
mesh = {Animals ; CRISPR-Cas Systems/*genetics ; Cell Lineage/genetics ; Cell Tracking/methods ; Computational Biology/methods ; *Gene Editing ; Genetic Engineering ; Heart/growth &amp; development ; High-Throughput Nucleotide Sequencing/methods ; Liver/growth &amp; development/metabolism ; Pancreas/growth &amp; development/metabolism ; Single-Cell Analysis/methods ; Telencephalon/growth &amp; development/metabolism ; Transcriptome/*genetics ; Zebrafish/*genetics/growth &amp; development/metabolism ; },
abstract = {A key goal of developmental biology is to understand how a single cell is transformed into a full-grown organism comprising many different cell types. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ. However, organizing the resulting taxonomy of cell types into lineage trees to understand the developmental origin of cells remains challenging. Here we present LINNAEUS (lineage tracing by nuclease-activated editing of ubiquitous sequences)-a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes, generated by genome editing of transgenic reporter genes, we reconstruct developmental lineage trees in zebrafish larvae, and in heart, liver, pancreas, and telencephalon of adult fish. LINNAEUS provides a systematic approach for tracing the origin of novel cell types, or known cell types under different conditions.},
}
@article {pmid29644017,
year = {2018},
author = {Othman, MNA and Hassan, R and Harith, MN and Sah, ASRM},
title = {Morphological Characteristics and Habitats of Red Seaweed Gracilaria spp. (Gracilariaceae, Rhodophyta) in Santubong and Asajaya, Sarawak, Malaysia.},
journal = {Tropical life sciences research},
volume = {29},
number = {1},
pages = {87-101},
pmid = {29644017},
issn = {1985-3718},
abstract = {Red seaweed Gracilaria, one of the largest genus in Division Rhodophyta inhabits Sarawak coastal water. This study was designed to identify the species of Gracilaria using morphological approach and to assess selected water quality parameters in Gracilaria habitats. Three field samplings were carried out in Santubong and Asajaya, Sarawak from November 2013 to December 2014. Overall, three species were identified namely Gracilaria changii, G. blodgettii and G. coronopifolia, attached to net of cage culture in Santubong and root of mangrove trees in Asajaya. In addition, three different taxa of aquatic macroinvertebrates (polychaete, small crab, bivalve) and single species of red seaweed (Acanthophora sp.) were observed in Gracilaria assemblages. An estimate of 37% to 40% of the upper part of the cage net in Santubong was covered by seaweeds and only 16% to 20% in Asajaya's mangrove. The study had provided better information on identification of Gracilaria and their habitat in Sarawak. Future work involving DNA barcoding of each species is in progress.},
}
@article {pmid29643280,
year = {2018},
author = {Omatsu, T and Omura, M and Katayama, Y and Kimura, T and Okumura, M and Okumura, A and Murata, Y and Mizutani, T},
title = {Molecular diversity of the faecal microbiota of Toy Poodles in Japan.},
journal = {The Journal of veterinary medical science},
volume = {80},
number = {5},
pages = {749-754},
pmid = {29643280},
issn = {1347-7439},
mesh = {Animals ; Dog Diseases/microbiology ; *Dogs ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; Japan ; Male ; Molecular Typing/veterinary ; Protein-Losing Enteropathies/microbiology/veterinary ; RNA, Ribosomal, 16S ; Sequence Analysis, RNA ; Species Specificity ; },
abstract = {The intestinal microbiota was revealed with the recent advances in molecular techniques, such as high-throughput sequencing analysis. As a result, the microbial changes are thought to influence the health of humans and animals and such changes are affected by several factors including diet, genetics, age, sex, and diseases. Similar studies are being conducted in dogs, and the knowledge of intestinal microbiota in dogs is expanding. Nonetheless, basic information on intestinal microbiota in dogs is less than that of humans. Our aim was to study toy poodles (n=21), a popular companion dog, in terms of basic characteristics of the faecal microbiota by 16S rRNA gene barcoding analysis. In the faecal microbiota, Firmicutes, Bacteroidetes, Proteobacteria, and Fusobacteria were the dominant phyla (over 93.4% of faecal microbiota) regardless of the attributes of the dogs. In family level, Enterobacteriaceae, Bacteroidaceae, and Lachnospiraceae were most prevalent. In case of a dog with protein-losing enteropathy, the diversity of faecal microbiota was different between before and after treatment. This study provides basic information for studying on faecal microbiota in toy poodles.},
}
@article {pmid29642684,
year = {2018},
author = {Tu, Y and Shu, J and Ji, G and Zhang, M and Zou, J},
title = {Monitoring conservation effects on a Chinese indigenous chicken breed using major histocompatibility complex B-G gene and DNA Barcodes.},
journal = {Asian-Australasian journal of animal sciences},
volume = {31},
number = {10},
pages = {1558-1564},
pmid = {29642684},
issn = {1011-2367},
support = {31402032//National Natural Science Foundation of China/ ; 31572358//National Natural Science Foundation of China/ ; 2014-NY-004//Sixth talent peaks project in Jiangsu Province/ ; CARS-41//China agriculture research system/ ; SXGC[2017]254//Jiangsu Provincial Agricultural three new Project/ ; PZCZ201728//Jiangsu Province major agricultural new varieties creation project/ ; BE2015344//Jiangsu Province, key research and development plan/ ; CX [15] 1009//Jiangsu Province, Agricultural Science and Technology Independent Innovation Funds/ ; BK20161322//Jiangsu Natural Science Foundation/ ; YZ2016221//Yangzhou City Science and Technology Public Service Platform Construction/ ; YZ2017171//Yangzhou City Science and Technology Public Service Platform Construction/ ; },
abstract = {OBJECTIVE: We report monitoring conservation effect for a Chinese indigenous chicken (Langshan) breed using major histocompatibility complex (MHC) and DNA barcords.<br><br>METHODS: The full length of MHC B-G gene and mitochondrial cytochrome oxidase I (COI) gene in generations 0, 5, 10, 15, 16, and 17 was measured using re-sequencing and sequencing procedures, respectively.<br><br>RESULTS: There were 292 single nucleotide polymorphisms of MHC B-G gene identified in six generations. Heterozygosity (He) and polymorphic information content (PIC) of MHC B-G gene in generations 10, 15, 16, and 17 remained stable. He and PIC of MHC B-G gene were different in six generations, with G10, G15, G16, G17 >G5>G0 (p<0.05). For the COI gene, there were five haplotypes in generations 0, 5, 10, 15, 16, and 17. Where Hap2 and Hap4 were the shared haplotypes, 164 individuals shared Hap2 haplotypes, while Hap1 and Hap3 were the shared haplotypes in generations 0 and 5 and Hap5 was a shared haplotype in generations 10, 15, 16, and 17. The sequence of COI gene in 6 generations was tested by Tajima's and D value, and the results were not significant, which were consistent with neutral mutation. There were no differences in generations 10, 15, 16, and 17for measured phenotypic traits. In other generations, for annual egg production, with G5, G10, G15, G16, G17>G0 (p<0.05). For age at the first egg and age at sexual maturity, with G10, G15, G16, G17>G5>G0 (p<0.05).<br><br>CONCLUSION: Combined with the results of COI gene DNA barcodes, MHC B-G gene, and phenotypic traits we can see that genetic diversity remained stable from generations 10 to 17 and the equimultiple random matching pedigrees conservation population conservation effect of Langshan chicken was effective as measured by these criteria.},
}
@article {pmid29642545,
year = {2018},
author = {Liu, X and Li, Y and Yang, H and Zhou, B},
title = {Chloroplast Genome of the Folk Medicine and Vegetable Plant Talinum paniculatum (Jacq.) Gaertn.: Gene Organization, Comparative and Phylogenetic Analysis.},
journal = {Molecules (Basel, Switzerland)},
volume = {23},
number = {4},
pages = {},
pmid = {29642545},
issn = {1420-3049},
mesh = {Base Sequence ; Biological Evolution ; Caryophyllales/classification/*genetics ; Databases, Genetic ; Genome Size ; *Genome, Chloroplast ; *Genome, Plant ; Introns ; Medicine, Traditional ; Microsatellite Repeats ; Phylogeny ; RNA, Transfer/genetics ; Vegetables/classification/genetics ; },
abstract = {The complete chloroplast (cp) genome of Talinum paniculatum (Caryophyllale), a source of pharmaceutical efficacy similar to ginseng, and a widely distributed and planted edible vegetable, were sequenced and analyzed. The cp genome size of T. paniculatum is 156,929 bp, with a pair of inverted repeats (IRs) of 25,751 bp separated by a large single copy (LSC) region of 86,898 bp and a small single copy (SSC) region of 18,529 bp. The genome contains 83 protein-coding genes, 37 transfer RNA (tRNA) genes, eight ribosomal RNA (rRNA) genes and four pseudogenes. Fifty one (51) repeat units and ninety two (92) simple sequence repeats (SSRs) were found in the genome. The pseudogene rpl23 (Ribosomal protein L23) was insert AATT than other Caryophyllale species by sequence alignment, which located in IRs region. The gene of trnK-UUU (tRNA-Lys) and rpl16 (Ribosomal protein L16) have larger introns in T. paniculatum, and the existence of matK (maturase K) genes, which usually located in the introns of trnK-UUU, rich sequence divergence in Caryophyllale. Complete cp genome comparison with other eight Caryophyllales species indicated that the differences between T. paniculatum and P. oleracea were very slight, and the most highly divergent regions occurred in intergenic spacers. Comparisons of IR boundaries among nine Caryophyllales species showed that T. paniculatum have larger IRs region and the contraction is relatively slight. The phylogenetic analysis among 35 Caryophyllales species and two outgroup species revealed that T. paniculatum and P. oleracea do not belong to the same family. All these results give good opportunities for future identification, barcoding of Talinum species, understanding the evolutionary mode of Caryophyllale cp genome and molecular breeding of T. paniculatum with high pharmaceutical efficacy.},
}
@article {pmid29636477,
year = {2018},
author = {Chen, L and Yang, L and Yao, L and Kuang, XY and Zuo, WJ and Li, S and Qiao, F and Liu, YR and Cao, ZG and Zhou, SL and Zhou, XY and Yang, WT and Shi, JX and Huang, W and Hu, X and Shao, ZM},
title = {Characterization of PIK3CA and PIK3R1 somatic mutations in Chinese breast cancer patients.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {1357},
pmid = {29636477},
issn = {2041-1723},
mesh = {Antineoplastic Agents/pharmacology ; Binding Sites ; Breast Neoplasms/*genetics/metabolism/pathology ; Cell Line, Tumor ; Class I Phosphatidylinositol 3-Kinases/chemistry/*genetics/metabolism ; Class Ia Phosphatidylinositol 3-Kinase ; Doxorubicin/pharmacology ; Female ; *Gene Expression Regulation, Neoplastic ; Genetic Predisposition to Disease ; Humans ; Models, Molecular ; *Mutation ; PTEN Phosphohydrolase/genetics/metabolism ; Phosphatidylinositol 3-Kinases/chemistry/*genetics/metabolism ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Proto-Oncogene Proteins c-akt/genetics/metabolism ; Receptor, ErbB-2/genetics/metabolism ; Receptors, Estrogen/genetics/metabolism ; Receptors, Progesterone/genetics/metabolism ; Recombinant Proteins/chemistry/genetics/metabolism ; Retrospective Studies ; Signal Transduction ; },
abstract = {Deregulation of the phosphoinositide 3-kinase (PI3K) pathway contributes to the development and progression of tumors. Here, we determine that somatic mutations in PIK3CA (44%), PIK3R1 (17%), AKT3 (15%), and PTEN (12%) are prevalent and diverse in Chinese breast cancer patients, with 60 novel mutations identified. A high proportion of tumors harbors multiple mutations, especially PIK3CA plus PIK3R1 mutations (9.0%). Next, we develop a recombination-based mutation barcoding (ReMB) library for impactful mutations conferring clonal advantage in proliferation and drug responses. The highest-ranking PIK3CA and PIK3R1 mutations include previously reported deleterious mutations, as well as mutations with unknown significance. These PIK3CA and PIK3R1 impactful mutations exhibit a mutually exclusive pattern, leading to oncogenesis and hyperactivity of PI3K pathway. The PIK3CA impactful mutations are tightly associated with hormone receptor positivity. Collectively, these findings advance our understanding of PI3K impactful mutations in breast cancer and have important implications for PI3K-targeted therapy in precision oncology.},
}
@article {pmid29635368,
year = {2018},
author = {Koroiva, R and de Souza, MS and Roque, FO and Pepinelli, M},
title = {DNA Barcodes for Forensically Important Fly Species in Brazil.},
journal = {Journal of medical entomology},
volume = {55},
number = {4},
pages = {1055-1061},
doi = {10.1093/jme/tjy045},
pmid = {29635368},
issn = {1938-2928},
mesh = {Animals ; Brazil ; *DNA Barcoding, Taxonomic ; Diptera/*classification/genetics ; Electron Transport Complex IV/analysis ; *Forensic Sciences ; Insect Proteins/analysis ; },
abstract = {Here, we analyze 248 DNA barcode sequences of 35 fly species of forensic importance in Brazil. DNA barcoding can be effectively used for specimen identification of these species, allowing the unambiguous identification of 31 species, an overall success rate of 88%. Our results show a high rate of success for molecular identification using DNA barcoding sequences and open new perspectives for immature species identification, a subject on which limited forensic investigations exist in Tropical regions. We also address the implications of building a robust forensic DNA barcode database. A geographic bias is recognized for the COI dataset available for forensically important fly species in Brazil, with concentration of sequences from specimens collected mainly in sites located in the Cerrado, Mata Atlântica, and Pampa biomes.},
}
@article {pmid29631807,
year = {2018},
author = {Liu, C and Guo, DA and Liu, L},
title = {Quality transitivity and traceability system of herbal medicine products based on quality markers.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {44},
number = {},
pages = {247-257},
doi = {10.1016/j.phymed.2018.03.006},
pmid = {29631807},
issn = {1618-095X},
mesh = {Biomarkers/*analysis ; DNA Barcoding, Taxonomic ; Herbal Medicine/*standards ; Humans ; Medicine, Chinese Traditional/standards ; Phytotherapy/standards ; Plants, Medicinal ; *Quality Control ; },
abstract = {BACKGROUND: Due to a variety of factors to affect the herb quality, the existing quality management model is unable to evaluate the process control. The development of the concept of "quality marker" (Q-marker) lays basis for establishing an independent process quality control system for herbal products.<br><br>HYPOTHESIS/PURPOSE: To ensure the highest degree of safety, effectiveness and quality process control of herbal products, it is aimed to establish a quality transitivity and traceability system of quality and process control from raw materials to finished herbal products.<br><br>STUDY DESIGN: Based on the key issues and challenges of quality assessment, the current status of quality and process controls from raw materials to herbal medicinal products listed in Pharmacopoeia were analyzed and the research models including discovery and identification of Q-markers, analysis and quality management of risk evaluation were designed.<br><br>METHODS: Authors introduced a few new technologies and methodologies, such as DNA barcoding, chromatographic technologies, fingerprint analysis, chemical markers, bio-responses, risk management and solution for quality process control.<br><br>RESULTS: The quality and process control models for herbal medicinal products were proposed and the transitivity and traceability system from raw materials to the finished products was constructed to improve the herbal quality from the entire supply and production chain.<br><br>CONCLUSION: The transitivity and traceability system has been established based on quality markers, especially on how to control the production process under Good Engineering Practices, as well as to implement the risk management for quality and process control in herbal medicine production.},
}
@article {pmid29630678,
year = {2018},
author = {Kamps-Hughes, N and McUsic, A and Kurihara, L and Harkins, TT and Pal, P and Ray, C and Ionescu-Zanetti, C},
title = {ERASE-Seq: Leveraging replicate measurements to enhance ultralow frequency variant detection in NGS data.},
journal = {PloS one},
volume = {13},
number = {4},
pages = {e0195272},
pmid = {29630678},
issn = {1932-6203},
mesh = {Cell Line ; Computational Biology ; DNA Barcoding, Taxonomic/statistics &amp; numerical data ; Gene Frequency ; Gene Library ; Genetic Variation ; High-Throughput Nucleotide Sequencing/*statistics &amp; numerical data ; Humans ; INDEL Mutation ; Sequence Analysis, DNA/*statistics &amp; numerical data ; },
abstract = {The accurate detection of ultralow allele frequency variants in DNA samples is of interest in both research and medical settings, particularly in liquid biopsies where cancer mutational status is monitored from circulating DNA. Next-generation sequencing (NGS) technologies employing molecular barcoding have shown promise but significant sensitivity and specificity improvements are still needed to detect mutations in a majority of patients before the metastatic stage. To address this we present analytical validation data for ERASE-Seq (Elimination of Recurrent Artifacts and Stochastic Errors), a method for accurate and sensitive detection of ultralow frequency DNA variants in NGS data. ERASE-Seq differs from previous methods by creating a robust statistical framework to utilize technical replicates in conjunction with background error modeling, providing a 10 to 100-fold reduction in false positive rates compared to published molecular barcoding methods. ERASE-Seq was tested using spiked human DNA mixtures with clinically realistic DNA input quantities to detect SNVs and indels between 0.05% and 1% allele frequency, the range commonly found in liquid biopsy samples. Variants were detected with greater than 90% sensitivity and a false positive rate below 0.1 calls per 10,000 possible variants. The approach represents a significant performance improvement compared to molecular barcoding methods and does not require changing molecular reagents.},
}
@article {pmid29630670,
year = {2018},
author = {Komura, T and Ando, H and Horikoshi, K and Suzuki, H and Isagi, Y},
title = {DNA barcoding reveals seasonal shifts in diet and consumption of deep-sea fishes in wedge-tailed shearwaters.},
journal = {PloS one},
volume = {13},
number = {4},
pages = {e0195385},
pmid = {29630670},
issn = {1932-6203},
mesh = {Animals ; Aquatic Organisms/genetics ; Birds/*physiology ; Breeding ; *DNA Barcoding, Taxonomic ; *Diet ; Ecosystem ; Feeding Behavior ; Female ; Fishes/*genetics ; Food Chain ; Japan ; Male ; Mollusca/genetics ; Predatory Behavior ; Seasons ; },
abstract = {The foraging ecology of pelagic seabirds is difficult to characterize because of their large foraging areas. In the face of this difficulty, DNA metabarcoding may be a useful approach to analyze diet compositions and foraging behaviors. Using this approach, we investigated the diet composition and its seasonal variation of a common seabird species on the Ogasawara Islands, Japan: the wedge-tailed shearwater Ardenna pacifica. We collected fecal samples during the prebreeding (N = 73) and rearing (N = 96) periods. The diet composition of wedge-tailed shearwater was analyzed by Ion Torrent sequencing using two universal polymerase chain reaction primers for the 12S and 16S mitochondrial DNA regions that targeted vertebrates and mollusks, respectively. The results of a BLAST search of obtained sequences detected 31 and 1 vertebrate and mollusk taxa, respectively. The results of the diet composition analysis showed that wedge-tailed shearwaters frequently consumed deep-sea fishes throughout the sampling season, indicating the importance of these fishes as a stable food resource. However, there was a marked seasonal shift in diet, which may reflect seasonal changes in food resource availability and wedge-tailed shearwater foraging behavior. The collected data regarding the shearwater diet may be useful for in situ conservation efforts. Future research that combines DNA metabarcoding with other tools, such as data logging, may provide further insight into the foraging ecology of pelagic seabirds.},
}
@article {pmid29629668,
year = {2018},
author = {Mosa, KA and Soliman, S and El-Keblawy, A and Ali, MA and Hassan, HA and Tamim, AAB and Al-Ali, MM},
title = {Using DNA Barcoding to Detect Adulteration in Different Herbal Plant- Based Products in the United Arab Emirates: Proof of Concept and Validation.},
journal = {Recent patents on food, nutrition &amp; agriculture},
volume = {9},
number = {1},
pages = {55-64},
doi = {10.2174/2212798410666180409101714},
pmid = {29629668},
issn = {1876-1429},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant ; *Drug Contamination ; Humans ; Patents as Topic ; Plants, Medicinal/*genetics ; Quality Control ; Reproducibility of Results ; United Arab Emirates ; },
abstract = {BACKGROUND: Commercially available herbal and medicinal plants-based products are susceptible to substitution or contamination with other unlabeled or undesired materials. This will reduce the quality of the product, and may lead to intoxication and allergy.<br><br>METHODS: DNA barcoding is a molecular technology that allows the identification of plant materials at the species level, by sequencing short stretches of standardized gene sequences from nuclear or organelle genome in an easy, rapid, accurate and cost-effective manner. The aim of this research is to apply DNA barcoding to investigate the authenticity of commercially available herbal and medicinal plant-based products within the UAE markets. A total of 30 samples were analyzed, covering six different herbal products (thyme, cardamom, anise, basil, turmeric, and ginger), obtained in fresh and dried forms. DNA was extracted and three barcode loci including (rbcL), (matK) and (ITS) were amplified, sequenced and analyzed by BLAST.<br><br>RESULTS: In terms of amplification efficiency, the results suggest that rbcL is the most suitable marker for species identification giving 75% of successful amplification, followed by ITS with 66.67%, whereas matK had the lowest with 18.52%. Adulteration was detected in two samples, ginger powder and dry thyme leave samples. The adulterants were from Triticum and Oryza genera.<br><br>CONCLUSION: Clearly, the results from this report provide evidence that DNA barcoding technique is efficient in the recognition of commercial plant products. Thus, it can be considered as a fast, effective, and reliable method to detect adulteration in plant-based products in the UAE market.},
}
@article {pmid29625979,
year = {2018},
author = {Rossmann, S and Dees, MW and Perminow, J and Meadow, R and Brurberg, MB},
title = {Soft Rot Enterobacteriaceae Are Carried by a Large Range of Insect Species in Potato Fields.},
journal = {Applied and environmental microbiology},
volume = {84},
number = {12},
pages = {},
pmid = {29625979},
issn = {1098-5336},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Enterobacteriaceae/genetics/*isolation &amp; purification/pathogenicity ; Insecta/classification/*microbiology ; Microbiota ; Norway ; Pectobacterium/genetics/isolation &amp; purification/pathogenicity ; Pest Control ; Plant Diseases/microbiology ; Plant Tubers/*microbiology ; Real-Time Polymerase Chain Reaction ; Solanum tuberosum/*microbiology ; },
abstract = {Pathogenic soft rot Enterobacteriaceae (SRE) belonging to the genera Pectobacterium and Dickeya cause diseases in potato and numerous other crops. Seed potatoes are the most important source of infection, but how pathogen-free tubers initially become infected remains an enigma. Since the 1920s, insects have been hypothesized to contribute to SRE transmission. To validate this hypothesis and to map the insect species potentially involved in SRE dispersal, we have analyzed the occurrence of SRE in insects recovered from potato fields over a period of 2 years. Twenty-eight yellow sticky traps were set up in 10 potato fields throughout Norway to attract and trap insects. Total DNA recovered from over 2,000 randomly chosen trapped insects was tested for SRE, using a specific quantitative PCR (qPCR) TaqMan assay, and insects that tested positive were identified by DNA barcoding. Although the occurrence of SRE-carrying insects varied, they were found in all the tested fields. While Delia species were dominant among the insects that carried the largest amount of SRE, more than 80 other SRE-carrying insect species were identified, and they had different levels of abundance. Additionally, the occurrence of SRE in three laboratory-reared insect species was analyzed, and this suggested that SRE are natural members of some insect microbiomes, with herbivorous Delia floralis carrying more SRE than the cabbage moth (Plutella xylostella) and carnivorous green lacewing larvae (Chrysoperla carnea). In summary, the high proportion, variety, and ubiquity of insects that carried SRE show the need to address this source of the pathogens to reduce the initial infection of seed material.IMPORTANCE Soft rot Enterobacteriaceae are among the most important pathogens of a wide range of vegetables and fruits. The bacteria cause severe rots in the field and in storage, leading to considerable harvest losses. In potato, efforts to understand how soft rot bacteria infect and spread between healthy plants have been made for over a century. Early on, fly larvae were implicated in the transmission of these bacteria. This work aimed at investigating the occurrence of soft rot bacteria in insects present in potato fields and at identifying the species of these insects to better understand the potential of this suspected source of transmission. In all tested potato fields, a large proportion of insects were found to carry soft rot bacteria. This suggests a need to give more weight to the role of insects in soft rot ecology and epidemiology to design more effective pest management strategies that integrate this factor.},
}
@article {pmid29625090,
year = {2018},
author = {Karthika, P and Vadivalagan, C and Thirumurugan, D and Kumar, RR and Murugan, K and Canale, A and Benelli, G},
title = {DNA barcoding of five Japanese encephalitis mosquito vectors (Culex fuscocephala, Culex gelidus, Culex tritaeniorhynchus, Culex pseudovishnui and Culex vishnui).},
journal = {Acta tropica},
volume = {183},
number = {},
pages = {84-91},
doi = {10.1016/j.actatropica.2018.04.006},
pmid = {29625090},
issn = {1873-6254},
mesh = {Animals ; Asia ; Culex/*genetics/physiology ; *DNA Barcoding, Taxonomic ; Ecology ; Encephalitis, Japanese/*transmission ; Genetic Variation ; Haplotypes ; Humans ; Mosquito Vectors/*genetics/physiology ; },
abstract = {Culex mosquitoes can act as vectors of several important diseases, including Japanese encephalitis, West Nile virus, St. Louis encephalitis and equine encephalitis. Besides the neurological sequelae caused in humans, Japanese encephalitis can lead to abortion in sows and encephalitis in horses. Effective vector control and early diagnosis, along with continuous serosurveillance in animals, are crucial to fight this arboviral disease. However, the success of vector control operations is linked with the fast and reliable identification of targeted species, and knowledge about their biology and ecology. Since the DNA barcoding of Culex vectors of Japanese encephalitis is scarcely explored, here we evaluated the efficacy of this tool to identify and analyze the variations among five overlooked Culex vectors of Japanese encephalitis, Culex fuscocephala, Culex gelidus, Culex tritaeniorhynchus, Culex pseudovishnui and Culex vishnui, relying to the analysis of mitochondrial CO1 gene. Variations in their base pair range were elucidated by the entropy Hx plot. The differences among individual conspecifics and on base pair range across the same were studied. The C (501-750 bp) region showed a moderate variation among all the selected species. C. tritaeniorhynchus exhibited the highest variation in all the ranges. The observed genetic divergence was partially non-discriminatory. i.e., the overall intra- and inter nucleotide divergence was 0.0920 (0.92%) and 0.125 (1.25%), respectively. However, 10X rule fits accurately intraspecies divergence <3% for the five selected Culex species. The analysis of individual scatter plots showed threshold values (10X) of 0.008 (0.08%), 0.005 (0.05%), 0.123 (1.23%), 0.033 (0.33%) and 0.019 (0.19%) for C. fuscocephala, C. gelidus, C. tritaeniorhynchus, C. pseudovishnui and C. vishnui, respectively. The C. tritaeniorhynchus haplotypes KU497604, KU497603, AB690847 and AB690854 exhibited the highest divergence range, i.e., from 0.465 -0.546. Comparatively, the intra-divergence among the other haplotypes of C. tritaeniorhynchus ranged from 0-0.056. The maximum parsimony tree was formed by distinctive conspecific clusters with appreciable branch values illustrating their close congruence and extensive genetic deviations. Overall, this study adds valuable knowledge to the molecular biology and systematics of five overlooked mosquito species acting as major vectors of Japanese encephalitis in Asian countries.},
}
@article {pmid29624609,
year = {2018},
author = {Yu, N and Wei, YL and Zhu, Y and Zhu, N and Wang, YL and Zhang, HP and Sun, AD},
title = {Integrated approach for identifying and evaluating the quality of Marsdenia tenacissima in the medicine market.},
journal = {PloS one},
volume = {13},
number = {4},
pages = {e0195240},
pmid = {29624609},
issn = {1932-6203},
mesh = {China ; Chromatography, High Pressure Liquid ; Chromatography, Thin Layer ; DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Drug Contamination ; Drugs, Chinese Herbal/*chemistry/*standards ; Humans ; Marsdenia/*chemistry/genetics ; Plants, Medicinal/*chemistry/genetics ; Quality Control ; },
abstract = {The accurate identification and quality evaluation of herbal medical plants is highly necessary to ensure their safety and efficacy. In present study, a new strategy combining DNA barcoding techniques with thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC) was proposed to facilitate the identification and quality control of M. tenacissima. In present work, the internal transcribed spacer 2 (ITS2) barcode was successfully used to identify 58 M. tenacissima samples and its adulterants. TLC successfully identified the other three M. tenacissima samples that failed to produce ITS2 regions. An adulterant was found in all the 62 samples. Moreover, the content of active medicinal ingredients is important for herbal plants quality. The content of tenacissoside H (TS-H) of M. tenacissima samples was determined by HPLC to range from 0.39% to 1.09%, which meets the criterion of the Chinese Pharmacopoeia. Thus, DNA barcoding coupled with TLC and HPLC is very promising to identify and evaluate the quality of M. tenacissima in the medicine market.},
}
@article {pmid29621260,
year = {2018},
author = {Ranjard, L and Wong, TKF and Rodrigo, AG},
title = {Reassembling haplotypes in a mixture of pooled amplicons when the relative concentrations are known: A proof-of-concept study on the efficient design of next-generation sequencing strategies.},
journal = {PloS one},
volume = {13},
number = {4},
pages = {e0195090},
pmid = {29621260},
issn = {1932-6203},
mesh = {Animals ; Chromosome Mapping ; Computational Biology/methods ; DNA, Mitochondrial ; Genome, Mitochondrial ; *Haplotypes ; *High-Throughput Nucleotide Sequencing/economics/methods/standards ; Macropodidae/genetics ; Markov Chains ; Sequence Analysis, DNA ; },
abstract = {Next-generation sequencing can be costly and labour intensive. Usually, the sequencing cost per sample is reduced by pooling amplified DNA = amplicons) derived from different individuals on the same sequencing lane. Barcodes unique to each amplicon permit short-read sequences to be assigned appropriately. However, the cost of the library preparation increases with the number of barcodes used. We propose an alternative to barcoding: by using different known proportions of individually-derived amplicons in a pooled sample, each is characterised a priori by an expected depth of coverage. We have developed a Hidden Markov Model that uses these expected proportions to reconstruct the input sequences. We apply this method to pools of mitochondrial DNA amplicons extracted from kangaroo meat, genus Macropus. Our experiments indicate that the sequence coverage can be efficiently used to index the short-reads and that we can reassemble the input haplotypes when secondary factors impacting the coverage are controlled. We therefore demonstrate that, by combining our approach with standard barcoding, the cost of the library preparation is reduced to a third.},
}
@article {pmid29619212,
year = {2018},
author = {Carter, ED and Ndhlovu, M and Munos, M and Nkhama, E and Katz, J and Eisele, TP},
title = {Validity of maternal report of care-seeking for childhood illness.},
journal = {Journal of global health},
volume = {8},
number = {1},
pages = {010602},
pmid = {29619212},
issn = {2047-2986},
mesh = {Acute Disease ; Adolescent ; Adult ; Child Health Services/*statistics &amp; numerical data ; Child, Preschool ; Diarrhea/*therapy ; Female ; Fever/*therapy ; *Health Care Surveys ; Humans ; Infant ; Infant, Newborn ; Male ; Mothers/*psychology/statistics &amp; numerical data ; Patient Acceptance of Health Care/*statistics &amp; numerical data ; Public Sector/statistics &amp; numerical data ; Reproducibility of Results ; Respiratory Tract Infections/*therapy ; Young Adult ; Zambia ; },
abstract = {BACKGROUND: Accurate data on care-seeking for child illness are needed to improve public health programs and reduce child mortality. The accuracy of maternal report of care-seeking for child illness as collected through household surveys has not been validated.<br><br>METHODS: A 2016 survey compared reported care-seeking against a gold-standard of health care provider documented care-seeking events among a random sample of mothers of children <5 years in Southern Province, Zambia. Enrolled children were assigned cards with unique barcodes. Seventy-five health care providers were given smartphones with a barcode reader and instructed to scan the cards of participating children seeking care at the source, generating an electronic record of the care-seeking event. Additionally, providers gave all caregivers accessing care for a child <5 years provider-specific tokens used to verify the point of care during the household survey. Reported care-seeking events were ascertained in each household using a questionnaire modeled off the Zambia Demographic and Health Survey (DHS) / Multiple Indicator Cluster Survey (MICS). The accuracy of maternal report of care-seeking behavior was estimated by comparing care-seeking events reported by mothers against provider-documented events.<br><br>RESULTS: Data were collected on 384 children with fever, diarrhea, and/or symptoms of ARI in the preceding 2 weeks. Most children sought care from government facilities or community-based agents (CBAs). We found high sensitivity (Rural: 0.91, 95% confidence interval CI 0.84-0.95; Urban: 0.98, 95% CI 0.92-0.99) and reasonable specificity (Rural: 0.71, 95% CI 0.57-0.82; Urban: 0.76, 95% CI 0.62-0.85) of maternal report of care-seeking for child illness by type of provider. Maternal report of any care-seeking and seeking care from a skilled provider had slightly higher sensitivity and specificity. Seeking care from a traditional practitioner was associated with lower odds of accurately reporting the event, while seeking care from a government provider was associated with greater odds of accurate report. The measure resulted in a slight overestimation of true care-seeking behavior in the study population.<br><br>CONCLUSIONS: Maternal report is a valid measure of care-seeking for child illness in settings with high utilization of public sector providers. The study findings were limited by the low diversity in care-seeking practices for child illness and the exclusion of shops.},
}
@article {pmid29618379,
year = {2018},
author = {Guo, Y and Song, Z and Luo, L and Wang, Q and Zhou, G and Yang, D and Zhong, D and Zheng, X},
title = {Molecular evidence for new sympatric cryptic species of Aedes albopictus (Diptera: Culicidae) in China: A new threat from Aedes albopictus subgroup?.},
journal = {Parasites &amp; vectors},
volume = {11},
number = {1},
pages = {228},
pmid = {29618379},
issn = {1756-3305},
support = {31630011//National Natural Science Foundation of China (CN)/International ; 2013B021800042//Science and Technology Plan Project of Guangdong Province (CN)/International ; 2015A030313784//Natural Science Foundation of Guangdong Province (CN)/International ; },
mesh = {Aedes/*classification/genetics/*growth &amp; development/microbiology ; Animals ; China ; Cluster Analysis ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; *Genotype ; Mosquito Vectors/*classification/genetics/*growth &amp; development ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Wolbachia/genetics/isolation &amp; purification ; },
abstract = {BACKGROUND: Aedes (Stegomyia) albopictus (Skuse) is an indigenous species and the predominant vector of dengue fever in China. Understanding of genetic diversity and structure of the mosquito would facilitate dengue prevention and vector control. Sympatric cryptic species have been identified in the Ae. albopictus subgroup in Southeast Asia; however, little is known about the presence and distribution of cryptic species in China. This study aimed to examine the genetic diversity, evaluate potential new cryptic sibling species, and assess the prevalence of Wolbachia infections in field populations.<br><br>METHODS: Aedes adult female specimens were collected from five provinces in southern and central China during 2015-2016. Morphological identification was performed under dissection microscope. The mitochondrial DNA cytochrome c oxidase subunit 1 (cox1, DNA barcoding) locus and the ribosomal DNA internal transcribed spacer region 2 (ITS2) marker were used to examine the genetic variation, evaluate cryptic sibling species, and population structure in the field populations. Screening for the presence of Wolbachia was performed using multiplex PCR.<br><br>RESULTS: A total of 140 individual specimens with morphological characteristics similar to Ae. albopictus were sequenced for DNA barcoding. Among these, 129 specimens (92.1%) were confirmed and identified as Ae. albopictus. The remaining 11 specimens, from 2 provinces, were identified as 2 distinct sequence groups, which were confirmed by ITS2 marker sequencing, suggesting the existence of potential cryptic species of Ae. albopictus. In Ae. albopictus, we found significant genetic differentiation and population structure between populations collected from different climate zones. Medium to high frequencies of Wolbachia infections were observed in natural Ae. albopictus populations, whereas Wolbachia was infrequent or absent in cryptic species populations.<br><br>CONCLUSIONS: Our findings highlight the population differentiation by climate zone and the presence of novel, cryptic Aedes species in China. The low prevalence of Wolbachia infections in cryptic species populations could reflect either a recent invasion of Wolbachia in Ae. albopictus or different host immune responses to this symbiont in the cryptic species. The study provides useful information for vector control and host-symbiont coevolution. Further study is needed to investigate the potential for arbovirus infection and disease transmission in the emerged cryptic species.},
}
@article {pmid29617771,
year = {2018},
author = {Pomerantz, A and Peñafiel, N and Arteaga, A and Bustamante, L and Pichardo, F and Coloma, LA and Barrio-Amorós, CL and Salazar-Valenzuela, D and Prost, S},
title = {Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building.},
journal = {GigaScience},
volume = {7},
number = {4},
pages = {},
pmid = {29617771},
issn = {2047-217X},
mesh = {Animals ; Biodiversity ; Ecuador ; Nanopores ; Rainforest ; Reptiles/*genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: Advancements in portable scientific instruments provide promising avenues to expedite field work in order to understand the diverse array of organisms that inhabit our planet. Here, we tested the feasibility for in situ molecular analyses of endemic fauna using a portable laboratory fitting within a single backpack in one of the world's most imperiled biodiversity hotspots, the Ecuadorian Chocó rainforest. We used portable equipment, including the MinION nanopore sequencer (Oxford Nanopore Technologies) and the miniPCR (miniPCR), to perform DNA extraction, polymerase chain reaction amplification, and real-time DNA barcoding of reptile specimens in the field.<br><br>FINDINGS: We demonstrate that nanopore sequencing can be implemented in a remote tropical forest to quickly and accurately identify species using DNA barcoding, as we generated consensus sequences for species resolution with an accuracy of >99% in less than 24 hours after collecting specimens. The flexibility of our mobile laboratory further allowed us to generate sequence information at the Universidad Tecnol&#xf3;gica Indoam&#xe9;rica in Quito for rare, endangered, and undescribed species. This includes the recently rediscovered Jambato toad, which was thought to be extinct for 28 years. Sequences generated on the MinION required as few as 30 reads to achieve high accuracy relative to Sanger sequencing, and with further multiplexing of samples, nanopore sequencing can become a cost-effective approach for rapid and portable DNA barcoding.<br><br>CONCLUSIONS: Overall, we establish how mobile laboratories and nanopore sequencing can help to accelerate species identification in remote areas to aid in conservation efforts and be applied to research facilities in developing countries. This opens up possibilities for biodiversity studies by promoting local research capacity building, teaching nonspecialists and students about the environment, tackling wildlife crime, and promoting conservation via research-focused ecotourism.},
}
@article {pmid29617397,
year = {2018},
author = {Spitsyn, VM and Kondakov, AV and Bolotov, NI and Thi Pham, N and Gofarov, MY and Bolotov, IN},
title = {DNA barcoding unravels contrasting evolutionary history of two widespread Asian tiger moth species during the Late Pleistocene.},
journal = {PloS one},
volume = {13},
number = {4},
pages = {e0194200},
pmid = {29617397},
issn = {1932-6203},
mesh = {Animal Migration ; Animals ; Arabia ; Asia ; Australia ; Bayes Theorem ; Biological Evolution ; *DNA Barcoding, Taxonomic ; Genetic Variation ; Moths/*genetics ; Phylogeography ; },
abstract = {Populations of widespread pest insects in tropical areas are characterized by a complex evolutionary history, with overlapping natural and human-mediated dispersal events, sudden expansions, and bottlenecks. Here, we provide biogeographic reconstructions for two widespread pest species in the tiger moth genus Creatonotos (Lepidoptera: Erebidae: Arctiinae) based on the mitochondrial cytochrome c oxidase subunit I (COI) gene. The Asian Creatonotos transiens reveals shallow genetic divergence between distant populations that does not support its current intraspecific systematics with several local subspecies. In contrast, the more widespread Creatonotos gangis comprises at least three divergent subclades corresponding to certain geographic areas, i.e. Australia, Arabia + South Asia and Southeast Asia. With respect to our approximate Bayesian computation (ABC) model, the expansion of Creatonotos gangis into Australia is placed in the Late Pleistocene (~65-63 ka). This dating coincide with an approximate time of the earliest human migration into the continent (~65-54 ka) and the period of intervisibility between Timor and Australia (~65-62 ka). Our findings highlight that the drying Sunda and Sahul shelf areas likely support successful migrations of Asian taxa into Australia during the Pleistocene. The phylogeographic patterns discovered in this study can be used to improve the effectiveness of integrated pest control programs that is a task of substantial practical importance to a broad range of agricultural stakeholders.},
}
@article {pmid29616077,
year = {2018},
author = {Cardoso, AL and Pieczarka, JC and Crampton, WGR and Ready, JS and de Figueiredo Ready, WMB and Waddell, JC and de Oliveira, JA and Nagamachi, CY},
title = {Karyotypic Diversity and Evolution in a Sympatric Assemblage of Neotropical Electric Knifefish.},
journal = {Frontiers in genetics},
volume = {9},
number = {},
pages = {81},
pmid = {29616077},
issn = {1664-8021},
abstract = {Chromosome changes can perform an important role in speciation by acting as post-zygotic reproductive barriers. The Neotropical electric fish genus Brachyhypopomus (Gymnotiformes, Hypopomidae) has 28 described species, but cytogenetic data are hitherto available only for four of them. To understand karyotype evolution and investigate the possible role of chromosome changes in the diversification of this genus, we describe here the karyotype of eight species of Brachyhypopomus from a sympatric assemblage in the central Amazon basin. We analyzed cytogenetic data in the context of a phylogenetic reconstruction of the genus and known patterns of geographical distribution. We found a strong phylogenetic signal for chromosome number and noted that sympatric species have exclusive karyotypes. Additional insights into the role of chromosome changes in the diversification of Brachyhypopomus are discussed.},
}
@article {pmid29615023,
year = {2018},
author = {Darwell, CT and Segar, ST and Cook, JM},
title = {Conserved community structure and simultaneous divergence events in the fig wasps associated with Ficus benjamina in Australia and China.},
journal = {BMC ecology},
volume = {18},
number = {1},
pages = {13},
pmid = {29615023},
issn = {1472-6785},
support = {(#NE/G523912/1)//Natural Environment Research Council/International ; 15-24571S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/International ; },
mesh = {Animals ; Australia ; *Biological Evolution ; *Biota ; China ; DNA, Ribosomal Spacer/analysis ; Electron Transport Complex IV/analysis ; Ficus/growth &amp; development ; *Food Chain ; Insect Proteins/analysis ; Phylogeny ; Sequence Analysis, DNA ; Wasps/genetics/*physiology ; },
abstract = {BACKGROUND: Localised patterns of species diversity can be influenced by many factors, including regional species pools, biogeographic features and interspecific interactions. Despite recognition of these issues, we still know surprisingly little about how invertebrate biodiversity is structured across geographic scales. In particular, there have been few studies of how insect communities vary geographically while using the same plant host. We compared the composition (species, genera) and functional structure (guilds) of the chalcid wasp communities associated with the widespread fig tree, Ficus benjamina, towards the northern (Hainan province, China) and southern (Queensland, Australia) edges of its natural range. Sequence data were generated for nuclear and mtDNA markers and used to delimit species, and Bayesian divergence analyses were used to test patterns of community cohesion through evolutionary time.<br><br>RESULTS: Both communities host at least 14 fig wasp species, but no species are shared across continents. Community composition is similar at the genus level, with six genera shared although some differ in species diversity between China and Australia; a further three genera occur in only China or Australia. Community functional structure remains very similar in terms of numbers of species in each ecological guild despite community composition differing a little (genera) or a lot (species), depending on taxonomic level. Bayesian clustering analyses favour a single community divergence event&#xa0;across continents over multiple events for different ecological guilds. Molecular dating estimates of lineage splits between nearest inter-continental species pairs are broadly consistent with a scenario of synchronous community divergence from a shared "ancestral community".<br><br>CONCLUSIONS: Fig wasp community structure and genus-level composition are largely conserved in a wide geographic comparison between China and Australia. Moreover, dating analyses suggest that the functional community structure has remained stable for long periods during historic range expansions. This suggests that ecological interactions between species may play a persistent role in shaping these communities, in contrast to findings in some comparable temperate systems.},
}
@article {pmid29614961,
year = {2018},
author = {Manzanilla, V and Kool, A and Nguyen Nhat, L and Nong Van, H and Le Thi Thu, H and de Boer, HJ},
title = {Phylogenomics and barcoding of Panax: toward the identification of ginseng species.},
journal = {BMC evolutionary biology},
volume = {18},
number = {1},
pages = {44},
pmid = {29614961},
issn = {1471-2148},
support = {VAST02.01/16-17//Vietnam Academy of Science/International ; 606895//Marie-Curie ITN/International ; },
mesh = {Base Sequence ; Bayes Theorem ; DNA Barcoding, Taxonomic/*methods ; DNA Methylation/genetics ; Genome, Mitochondrial ; *Genome, Plastid ; *Genomics ; High-Throughput Nucleotide Sequencing ; Microbiota ; Panax/*genetics ; *Phylogeny ; Species Specificity ; },
abstract = {BACKGROUND: The economic value of ginseng in the global medicinal plant trade is estimated to be in excess of US$2.1 billion. At the same time, the evolutionary placement of ginseng (Panax ginseng) and the complex evolutionary history of the genus is poorly understood despite several molecular phylogenetic studies. In this study, we use a full plastome phylogenomic framework to resolve relationships in Panax and to identify molecular markers for species discrimination.<br><br>RESULTS: We used high-throughput sequencing of MBD2-Fc fractionated Panax DNA to supplement publicly available plastid genomes to create a phylogeny based on fully assembled and annotated plastid genomes from 60 accessions of 8 species. The plastome phylogeny based on a 163 kbp matrix resolves the sister relationship of Panax ginseng with P. quinquefolius. The closely related species P. vietnamensis is supported as sister of P. japonicus. The plastome matrix also shows that the markers trnC-rps16, trnS-trnG, and trnE-trnM could be used for unambiguous molecular identification of all the represented species in the genus.<br><br>CONCLUSIONS: MBD2 depletion reduces the cost of plastome sequencing, which makes it a cost-effective alternative to Sanger sequencing based DNA barcoding for molecular identification. The plastome phylogeny provides a robust framework that can be used to study the evolution of morphological characters and biosynthesis pathways of ginsengosides for phylogenetic bioprospecting. Molecular identification of ginseng species is essential for authenticating ginseng in international trade and it provides an incentive for manufacturers to create authentic products with verified ingredients.},
}
@article {pmid29610476,
year = {2018},
author = {Rogers, ZN and McFarland, CD and Winters, IP and Seoane, JA and Brady, JJ and Yoon, S and Curtis, C and Petrov, DA and Winslow, MM},
title = {Mapping the in vivo fitness landscape of lung adenocarcinoma tumor suppression in mice.},
journal = {Nature genetics},
volume = {50},
number = {4},
pages = {483-486},
pmid = {29610476},
issn = {1546-1718},
support = {R25 CA180993/CA/NCI NIH HHS/United States ; R01 CA207133/CA/NCI NIH HHS/United States ; F31 CA210627/CA/NCI NIH HHS/United States ; R35 GM118165/GM/NIGMS NIH HHS/United States ; K22 HG000044/HG/NHGRI NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; F32 CA189659/CA/NCI NIH HHS/United States ; R01 CA175336/CA/NCI NIH HHS/United States ; },
mesh = {Adenocarcinoma of Lung/*genetics ; Animals ; CRISPR-Cas Systems ; DNA Barcoding, Taxonomic ; Gene Deletion ; Gene Editing ; *Genes, Tumor Suppressor ; Genes, p53 ; Genetic Fitness ; High-Throughput Nucleotide Sequencing ; Humans ; Lung Neoplasms/*genetics ; Mice ; Mice, Transgenic ; Retinoblastoma Protein/genetics ; Sequence Analysis, DNA ; },
abstract = {The functional impact of most genomic alterations found in cancer, alone or in combination, remains largely unknown. Here we integrate tumor barcoding, CRISPR/Cas9-mediated genome editing and ultra-deep barcode sequencing to interrogate pairwise combinations of tumor suppressor alterations in autochthonous mouse models of human lung adenocarcinoma. We map the tumor suppressive effects of 31 common lung adenocarcinoma genotypes and identify a landscape of context dependence and differential effect strengths.},
}
@article {pmid29608961,
year = {2018},
author = {Rezaei Riabi, T and Mirjalali, H and Haghighi, A and Rostami Nejad, M and Pourhoseingholi, MA and Poirier, P and Delbac, F and Wawrzyniak, I and Zali, MR},
title = {Genetic diversity analysis of Blastocystis subtypes from both symptomatic and asymptomatic subjects using a barcoding region from the 18S rRNA gene.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {61},
number = {},
pages = {119-126},
doi = {10.1016/j.meegid.2018.03.026},
pmid = {29608961},
issn = {1567-7257},
mesh = {Asymptomatic Infections ; Blastocystis/classification/*genetics ; Blastocystis Infections/*parasitology ; DNA, Protozoan/genetics ; Feces/parasitology ; Female ; Gene Frequency/genetics ; Genetic Markers/genetics ; Genetic Variation/genetics ; Humans ; Male ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; },
abstract = {Blastocystis is the most prevalent protozoa found in human stool samples. This study aimed to evaluate genetic diversity among Blastocystis subtypes isolated from both symptomatic and asymptomatic subjects as well as the potential correlation between subtypes and symptoms. A total of 55 Blastocystis-positive isolates were included in this study. A barcoding region of the small subunit rDNA was amplified and genetically assessed using MEGA6 and DnaSP regarding the presence of symptoms. BLAST analyses revealed the presence of 5 different subtypes (ST1, ST2, ST3, ST6 and ST7) among the samples. ST3 was the most prevalent subtype (25/55, 45%) while only one ST7 isolate was detected. Moreover, alleles 4 and 86 for ST1; alleles 9, 11 and 12 for ST2; alleles 31, 34, 36, 37 and 52 for ST3; allele 122 for ST6 and allele 137 for ST7 were detected. No statistically significant association was found between gender and symptoms with certain subtypes. Analysis of the intra-subtype variability in both symptomatic and asymptomatic subjects revealed highest similarity among ST1 isolates while lowest similarity was seen among ST3 isolates. Neutrality indices, Tajima's D and Fu's Fs, were negative but only statistically significant for ST3. Furthermore, highest values of Hd, π and S were observed among ST1, ST2 and ST3 isolated from symptomatic patients indicating high level of diversity among isolates obtained from these subjects. In addition, inter-subtype analysis showed the highest similarity between ST1 and ST2 isolates and the lowest similarity between ST2 and ST7 isolates. This is the first study revealing the presence of both ST6 and ST7 isolates in human from Iran. Phylogenetic analysis did not suggest any significant correlation between clinical manifestations and certain subtypes although genetic analysis showed highest value of diversity and significant neutrality indices among ST3 isolates obtained from symptomatic patients.},
}
@article {pmid29608392,
year = {2018},
author = {Khan, FM and William, K and Aruge, S and Janjua, S and Shah, SA},
title = {Illegal product manufacturing and exportation from Pakistan: Revealing the factuality of highly processed wildlife skin samples via DNA mini-barcoding.},
journal = {Nucleosides, nucleotides &amp; nucleic acids},
volume = {37},
number = {3},
pages = {179-185},
doi = {10.1080/15257770.2018.1450507},
pmid = {29608392},
issn = {1532-2335},
mesh = {Animals ; Animals, Wild/*genetics ; Base Sequence ; *Crime ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Pakistan ; Ruminants/genetics ; *Skin ; },
abstract = {Illegal trade is a major threat to the biodiversity and the efforts initiated for the conservation of wildlife. The shortcomings of the traditional taxonomic identification methods have been coped by a revolutionary and emerging technique, the "DNA (Deoxyribonucleic Acid) barcoding". Here we report a case of trader who was allegedly making footwear for a famous international celebrity from wild animal cutis. The samples confiscated during a raid on a footwear manufacturing industry by KP Wildlife department in August, 2016, were received by Bioresource Research Centre (BRC) for molecular identification on 1[st] September, 2016. The study costed about USD 88 from processing to the identification of the samples. The samples identified via DNA mini-barcoding by targeting cytochrome oxidase I (COI) gene belong to Gazella bennettii and Bos taurus. Such studies are helpful for credible investigations that only lead to effective prosecution and control of illegal wildlife trade ultimately helping in conservation of wild animals.},
}
@article {pmid29608178,
year = {2018},
author = {Raj, B and Wagner, DE and McKenna, A and Pandey, S and Klein, AM and Shendure, J and Gagnon, JA and Schier, AF},
title = {Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain.},
journal = {Nature biotechnology},
volume = {36},
number = {5},
pages = {442-450},
pmid = {29608178},
issn = {1546-1696},
support = {T32 HL007312/HL/NHLBI NIH HHS/United States ; DP1 HD094764/HD/NICHD NIH HHS/United States ; U01 MH105960/MH/NIMH NIH HHS/United States ; R01 HD085905/HD/NICHD NIH HHS/United States ; K99 GM121852/GM/NIGMS NIH HHS/United States ; //Wellcome Trust/United Kingdom ; T32 GM007266/GM/NIGMS NIH HHS/United States ; DP1 HG007811/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; Brain/cytology/growth &amp; development ; CRISPR-Cas Systems/*genetics ; Cell Lineage/genetics ; Gene Editing/methods ; Humans ; Mice ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis/*methods ; Transcriptome/*genetics ; Zebrafish ; },
abstract = {The lineage relationships among the hundreds of cell types generated during development are difficult to reconstruct. A recent method, GESTALT, used CRISPR-Cas9 barcode editing for large-scale lineage tracing, but was restricted to early development and did not identify cell types. Here we present scGESTALT, which combines the lineage recording capabilities of GESTALT with cell-type identification by single-cell RNA sequencing. The method relies on an inducible system that enables barcodes to be edited at multiple time points, capturing lineage information from later stages of development. Sequencing of ∼60,000 transcriptomes from the juvenile zebrafish brain identified >100 cell types and marker genes. Using these data, we generate lineage trees with hundreds of branches that help uncover restrictions at the level of cell types, brain regions, and gene expression cascades during differentiation. scGESTALT can be applied to other multicellular organisms to simultaneously characterize molecular identities and lineage histories of thousands of cells during development and disease.},
}
@article {pmid29603526,
year = {2018},
author = {Soares, DA and de Oliveira, DP and Dos Santos, TT and Marson, PG and Pimenta, RS},
title = {Multiloci identification of Diaporthe fungi isolated from the medicinal plant Costus spiralis (Jacq.) Roscoe (Costaceae).},
journal = {Journal of applied microbiology},
volume = {125},
number = {1},
pages = {172-180},
doi = {10.1111/jam.13769},
pmid = {29603526},
issn = {1365-2672},
mesh = {*Ascomycota/classification/genetics ; Costus/*microbiology ; DNA, Fungal/genetics ; Phylogeny ; Plants, Medicinal/*microbiology ; },
abstract = {AIMS: The purpose of this study is to identify species from genus Diaporthe associated with a medicinal plant Costus spiralis by ITS, EF 1-α, TUB and CAL gens.<br><br>METHODS AND RESULTS: The 30 isolates from the genus Diaporthe associated with the medicinal plant Costus spiralis were characterized based on morphological characters and the microculture technique and grouped by DNA fingerprinting with the ISSP gene. Afterwards, a total of 12 isolates were selected for the identification of the species based on the comparative research on the blast through the sequences of the ITS gene. Phylogenetic Tree of Maximum Likelihood were generated with the ITS gene individually and with the genes ITS, TUB, CAL and EF1-&#x3b1; combined with the Diaporthe species recognized and with the additional sequences obtained from GenBank for these species.<br><br>CONCLUSIONS: It was not possible to characterize the 30 isolates microscopically and macromorphologically through the microculture technique and the macromorphological characteristics. The 12 isolates selected based on the DNA fingerprinting profile identified phylogenetically, revealed five distinct species of Diaporthe which are present in C. spiralis.<br><br>The molecular analyses used in this study are excellent alternatives for species-level identification of Diaporthe associated with medicinal plants.},
}
@article {pmid29602313,
year = {2018},
author = {Cai, QG and Han, XM and Yang, YH and Zhang, XY and Ma, LQ and Karanis, P and Hu, YH},
title = {Lasiopodomys fuscus as an important intermediate host for Echinococcus multilocularis: isolation and phylogenetic identification of the parasite.},
journal = {Infectious diseases of poverty},
volume = {7},
number = {1},
pages = {27},
pmid = {29602313},
issn = {2049-9957},
support = {2016-ZJ-791//Basic research project of Qinghai Science and Technology Department/ ; 2015-HZ-809//International cooperation project of Qinghai Science and Technology Department/ ; },
mesh = {Animals ; *Arvicolinae/classification/genetics ; China/epidemiology ; Disease Reservoirs/parasitology/*veterinary ; Echinococcosis/epidemiology/parasitology/transmission/*veterinary ; Echinococcus multilocularis/genetics/*isolation &amp; purification ; Electron Transport Complex IV/genetics ; Helminth Proteins/genetics ; Male ; Phylogeny ; Polymerase Chain Reaction/veterinary ; Prevalence ; Rodent Diseases/*epidemiology/parasitology/transmission ; },
abstract = {BACKGROUND: Echinococcus multilocularis causes alveolar echinococcosis (AE) and is widely prevalent in Qinghai Province, China, where a number of different species have been identified as hosts. However, limited information is available on the Qinghai vole (Lasiopodomys fuscus), which is hyper endemic to Qinghai Province and may represent a potential intermediate host of E. multilocularis. Thus, L. fuscus could contribute to the endemicity of AE in the area.<br><br>METHODS: Fifty Qinghai voles were captured from Jigzhi County in Qinghai Province for the clinical identification of E. multilocularis infection via anatomical examination. Hydatid fluid was collected from vesicles of the livers in suspected voles and subjected to a microscopic examination and PCR assay based on the barcoding gene of cox 1. PCR-amplified segments were sequenced for a phylogenetic analysis. E. multilocularis-infected Qinghai voles were morphologically identified and subjected to a phylogenetic analysis to confirm their identities.<br><br>RESULTS: Seventeen of the 50 Qinghai voles had E. multilocularis-infection-like vesicles in their livers. Eleven out of the 17 Qinghai voles presented E. multilocularis infection, which was detected by PCR and sequencing. The phylogenetic analysis showed that all 11 positive samples belonged to the E. multilocularis Asian genotype. A morphological identification and phylogenetic analysis of the E. multilocularis-infected Qinghai voles confirmed that all captured animals were L. fuscus.<br><br>CONCLUSIONS: L. fuscus can be infected with E. multilocularis and plays a potential role in the life cycle and epidemiology of E. multilocularis in the Qinghai-Tibetan Plateau of China.},
}
@article {pmid29602086,
year = {2018},
author = {Hering, D and Borja, A and Jones, JI and Pont, D and Boets, P and Bouchez, A and Bruce, K and Drakare, S and Hänfling, B and Kahlert, M and Leese, F and Meissner, K and Mergen, P and Reyjol, Y and Segurado, P and Vogler, A and Kelly, M},
title = {Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive.},
journal = {Water research},
volume = {138},
number = {},
pages = {192-205},
doi = {10.1016/j.watres.2018.03.003},
pmid = {29602086},
issn = {1879-2448},
mesh = {Animals ; DNA/*analysis ; *DNA Barcoding, Taxonomic ; Ecosystem ; Environmental Monitoring/*methods ; Fishes ; Invertebrates ; Lakes ; Phytoplankton ; Rivers ; Seawater ; },
abstract = {Assessment of ecological status for the European Water Framework Directive (WFD) is based on "Biological Quality Elements" (BQEs), namely phytoplankton, benthic flora, benthic invertebrates and fish. Morphological identification of these organisms is a time-consuming and expensive procedure. Here, we assess the options for complementing and, perhaps, replacing morphological identification with procedures using eDNA, metabarcoding or similar approaches. We rate the applicability of DNA-based identification for the individual BQEs and water categories (rivers, lakes, transitional and coastal waters) against eleven criteria, summarised under the headlines representativeness (for example suitability of current sampling methods for DNA-based identification, errors from DNA-based species detection), sensitivity (for example capability to detect sensitive taxa, unassigned reads), precision of DNA-based identification (knowledge about uncertainty), comparability with conventional approaches (for example sensitivity of metrics to differences in DNA-based identification), cost effectiveness and environmental impact. Overall, suitability of DNA-based identification is particularly high for fish, as eDNA is a well-suited sampling approach which can replace expensive and potentially harmful methods such as gill-netting, trawling or electrofishing. Furthermore, there are attempts to replace absolute by relative abundance in metric calculations. For invertebrates and phytobenthos, the main challenges include the modification of indices and completing barcode libraries. For phytoplankton, the barcode libraries are even more problematic, due to the high taxonomic diversity in plankton samples. If current assessment concepts are kept, DNA-based identification is least appropriate for macrophytes (rivers, lakes) and angiosperms/macroalgae (transitional and coastal waters), which are surveyed rather than sampled. We discuss general implications of implementing DNA-based identification into standard ecological assessment, in particular considering any adaptations to the WFD that may be required to facilitate the transition to molecular data.},
}
@article {pmid29600642,
year = {2018},
author = {Hu, L and Xiao, H},
title = {[Development and research advance of pharmacognosy field based on CNKI].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {43},
number = {4},
pages = {689-695},
doi = {10.19540/j.cnki.cjcmm.20171208.004},
pmid = {29600642},
issn = {1001-5302},
mesh = {*Bibliometrics ; China ; DNA Barcoding, Taxonomic ; Data Mining ; *Pharmacognosy ; Random Amplified Polymorphic DNA Technique ; Research ; },
abstract = {Based on the literature data in CNKI, data mining and analysis technologies were used in this paper to describe the scientific research and development direction of Pharmacognosy in the last decade from the perspective of bibliometrics. The analysis of measured data revealed the core research institutions, excellent research teams, leading scholars, major research aspects and research progress in the field. Results showed that most of the scholars in the field were from colleges and institutions, accounting for 74.6% of the total research findings and forming a group of core scholars. In terms of frequency and timeliness of citation, pharmacognosy is a discipline in sustained growth and development since it mainly cites the literature in the other disciplines, absorbs and utilizes knowledge of the other disciplines. Over the last few years, molecular identification and genetic diversity have become the research hotspots in pharmacognosy, and the techniques and methods such as ISSR, RAPD, DNA barcoding and DNA molecular marker have been widely used.},
}
@article {pmid29600635,
year = {2018},
author = {Xu, YC and Xiong, C and Jiang, CL and Duan, YB and Sun, W and Liu, SY and Xue, DS and Xue, JP},
title = {[Identification of bear bile powder and its adulterants by using DNA barcoding technology].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {43},
number = {4},
pages = {645-650},
doi = {10.19540/j.cnki.cjcmm.2018.0014},
pmid = {29600635},
issn = {1001-5302},
mesh = {Animals ; Bile/*chemistry ; *DNA Barcoding, Taxonomic ; *Medicine, Chinese Traditional ; Phylogeny ; Quality Control ; *Ursidae ; },
abstract = {To identify the precious bile powder and its adulterants by DNA barcoding, and establish its standard experimental process to ensure the safe and effective utilization. Total twelve sequences from samples of bear bile powder which come from Ursus thibetanus for DNA extraction, PCR(polymerase chain reaction) and sequence, then using CodonCode Aligner V 7.0.1 shear primer region to obtain COI sequence. The COI sequences of U. arctos and their adulterants were obtained from GenBank. MEGA7.0 software was applied for analyzing mutation, calculating intraspecific and interspecific K2P(Kimura 2-Parameter) genetic distance and constructing the Neighbor-joining tree(NJ). The results showed that the maximum K2P genetic distance of bear bile powder of U. thibetanus and U. arctos are far less than minimum K2P genetic distance within its adulterants species, and the results of NJ tree demonstrated that each species could be distinguished from the counterfeits obviously. DNA barcoding is a safe, convenient and reliable technique for species identification, and it is important to establish the standard sequence of COI sequences for animal medicines.},
}
@article {pmid29593777,
year = {2018},
author = {Pimentel, JSM and Carmo, AO and Rosse, IC and Martins, APV and Ludwig, S and Facchin, S and Pereira, AH and Brandão-Dias, PFP and Abreu, NL and Kalapothakis, E},
title = {High-Throughput Sequencing Strategy for Microsatellite Genotyping Using Neotropical Fish as a Model.},
journal = {Frontiers in genetics},
volume = {9},
number = {},
pages = {73},
pmid = {29593777},
issn = {1664-8021},
abstract = {Genetic diversity and population studies are essential for conservation and wildlife management programs. However, monitoring requires the analysis of multiple loci from many samples. These processes can be laborious and expensive. The choice of microsatellites and PCR calibration for genotyping are particularly daunting. Here we optimized a low-cost genotyping method using multiple microsatellite loci for simultaneous genotyping of up to 384 samples using next-generation sequencing (NGS). We designed primers with adapters to the combinatorial barcoding amplicon library and sequenced samples by MiSeq. Next, we adapted a bioinformatics pipeline for genotyping microsatellites based on read-length and sequence content. Using primer pairs for eight microsatellite loci from the fish Prochilodus costatus, we amplified, sequenced, and analyzed the DNA of 96, 288, or 384 individuals for allele detection. The most cost-effective methodology was a pseudo-multiplex reaction using a low-throughput kit of 1 M reads (Nano) for 384 DNA samples. We observed an average of 325 reads per individual per locus when genotyping eight loci. Assuming a minimum requirement of 10 reads per loci, two to four times more loci could be tested in each run, depending on the quality of the PCR reaction of each locus. In conclusion, we present a novel method for microsatellite genotyping using Illumina combinatorial barcoding that dispenses exhaustive PCR calibrations, since non-specific amplicons can be eliminated by bioinformatics analyses. This methodology rapidly provides genotyping data and is therefore a promising development for large-scale conservation-genetics studies.},
}
@article {pmid29593755,
year = {2018},
author = {Mishra, P and Shukla, AK and Sundaresan, V},
title = {Candidate DNA Barcode Tags Combined With High Resolution Melting (Bar-HRM) Curve Analysis for Authentication of Senna alexandrina Mill. With Validation in Crude Drugs.},
journal = {Frontiers in plant science},
volume = {9},
number = {},
pages = {283},
pmid = {29593755},
issn = {1664-462X},
abstract = {Senna alexandrina (Fabaceae) is a globally recognized medicinal plant for its laxative properties as well as the only source of sennosides, and is highly exported bulk herb from India. Its major procurement is exclusively from limited cultivation, which leads to risks of deliberate or unintended adulteration. The market raw materials are in powdered or finished product form, which lead to difficulties in authentication. Here, DNA barcode tags based on chloroplast genes (rbcL and matK) and intergenic spacers (psbA-trnH and ITS) were developed for S. alexandrina along with the allied species. The ability and performance of the ITS1 region to discriminate among the Senna species resulted in the present proposal of the ITS1 tags as successful barcode. Further, these tags were coupled with high-resolution melting (HRM) curve analysis in a real-time PCR genotyping method to derive Bar-HRM (Barcoding-HRM) assays. Suitable HRM primer sets were designed through SNP detection and mutation scanning in genomic signatures of Senna species. The melting profiles of S. alexandrina and S. italica subsp. micrantha were almost identical and the remaining five species were clearly separated so that they can be differentiated by HRM method. The sensitivity of the method was utilized to authenticate market samples [Herbal Sample Assays (HSAs)]. HSA01 (S. alexandrina crude drug sample from Bangalore) and HSA06 (S. alexandrina crude drug sample from Tuticorin, Tamil Nadu, India) were found to be highly contaminated with S. italica subsp. micrantha. Species admixture samples mixed in varying percentage was identified sensitively with detection of contamination as low as 1%. The melting profiles of PCR amplicons are clearly distinct, which enables the authentic differentiation of species by the HRM method. This study reveals that DNA barcoding coupled with HRM is an efficient molecular tool to authenticate Senna herbal products in the market for quality control in the drug supply chain. CIMAP Communication Number: CIMAP/PUB/2017/31.},
}
@article {pmid29591722,
year = {2019},
author = {Wilson, JJ and Brandon-Mong, GJ and Gan, HM and Sing, KW},
title = {High-throughput terrestrial biodiversity assessments: mitochondrial metabarcoding, metagenomics or metatranscriptomics?.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {1},
pages = {60-67},
doi = {10.1080/24701394.2018.1455189},
pmid = {29591722},
issn = {2470-1408},
mesh = {Animals ; Arthropods/genetics ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods/standards ; Electron Transport Complex IV/genetics ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/methods/standards ; Insect Proteins/genetics ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Reference Standards ; *Transcriptome ; },
abstract = {Consensus on the optimal high-throughput sequencing (HTS) approach to examine biodiversity in mixed terrestrial arthropod samples has not been reached. Metatranscriptomics could increase the proportion of taxonomically informative mitochondrial reads in HTS outputs but has not been investigated for terrestrial arthropod samples. We compared the efficiency of 16S rRNA metabarcoding, metagenomics and metatranscriptomics for detecting species in a mixed terrestrial arthropod sample (pooled DNA/RNA from 38 taxa). 16S rRNA metabarcoding and nuclear rRNA-depleted metatranscriptomics had the highest detection rate with 97% of input species detected. Based on cytochrome c oxidase I, metagenomics had the highest detection rate with 82% of input species detected, but metatranscriptomics produced a larger proportion of reads matching (Sanger) reference sequences. Metatranscriptomics with nuclear rRNA depletion may offer advantages over metabarcoding through reducing the number of spurious operational taxonomic units while retaining high detection rates, and offers natural enrichment of mitochondrial sequences which may enable increased species detection rates compared with metagenomics.},
}
@article {pmid29590202,
year = {2018},
author = {Aliota, MT and Dudley, DM and Newman, CM and Weger-Lucarelli, J and Stewart, LM and Koenig, MR and Breitbach, ME and Weiler, AM and Semler, MR and Barry, GL and Zarbock, KR and Haj, AK and Moriarty, RV and Mohns, MS and Mohr, EL and Venturi, V and Schultz-Darken, N and Peterson, E and Newton, W and Schotzko, ML and Simmons, HA and Mejia, A and Hayes, JM and Capuano, S and Davenport, MP and Friedrich, TC and Ebel, GD and O'Connor, SL and O'Connor, DH},
title = {Molecularly barcoded Zika virus libraries to probe in vivo evolutionary dynamics.},
journal = {PLoS pathogens},
volume = {14},
number = {3},
pages = {e1006964},
pmid = {29590202},
issn = {1553-7374},
support = {R56 AI132563/AI/NIAID NIH HHS/United States ; R01 AI067380/AI/NIAID NIH HHS/United States ; T32 GM008692/GM/NIGMS NIH HHS/United States ; R01 AI132563/AI/NIAID NIH HHS/United States ; R21 AI125996/AI/NIAID NIH HHS/United States ; R01 AI125392/AI/NIAID NIH HHS/United States ; R21 AI131454/AI/NIAID NIH HHS/United States ; P51 OD011106/OD/NIH HHS/United States ; C06 RR020141/RR/NCRR NIH HHS/United States ; C06 RR015459/RR/NCRR NIH HHS/United States ; R01 AI116382/AI/NIAID NIH HHS/United States ; R24 OD017850/OD/NIH HHS/United States ; },
mesh = {Animals ; *Biological Evolution ; Female ; *Gene Library ; High-Throughput Nucleotide Sequencing ; *Infectious Disease Transmission, Vertical ; Macaca mulatta/*genetics/virology ; Male ; *Mosquito Vectors ; Viremia ; Zika Virus/*classification/genetics/pathogenicity ; Zika Virus Infection/*complications/transmission/virology ; },
abstract = {Defining the complex dynamics of Zika virus (ZIKV) infection in pregnancy and during transmission between vertebrate hosts and mosquito vectors is critical for a thorough understanding of viral transmission, pathogenesis, immune evasion, and potential reservoir establishment. Within-host viral diversity in ZIKV infection is low, which makes it difficult to evaluate infection dynamics. To overcome this biological hurdle, we constructed a molecularly barcoded ZIKV. This virus stock consists of a "synthetic swarm" whose members are genetically identical except for a run of eight consecutive degenerate codons, which creates approximately 64,000 theoretical nucleotide combinations that all encode the same amino acids. Deep sequencing this region of the ZIKV genome enables counting of individual barcodes to quantify the number and relative proportions of viral lineages present within a host. Here we used these molecularly barcoded ZIKV variants to study the dynamics of ZIKV infection in pregnant and non-pregnant macaques as well as during mosquito infection/transmission. The barcoded virus had no discernible fitness defects in vivo, and the proportions of individual barcoded virus templates remained stable throughout the duration of acute plasma viremia. ZIKV RNA also was detected in maternal plasma from a pregnant animal infected with barcoded virus for 67 days. The complexity of the virus population declined precipitously 8 days following infection of the dam, consistent with the timing of typical resolution of ZIKV in non-pregnant macaques and remained low for the subsequent duration of viremia. Our approach showed that synthetic swarm viruses can be used to probe the composition of ZIKV populations over time in vivo to understand vertical transmission, persistent reservoirs, bottlenecks, and evolutionary dynamics.},
}
@article {pmid29590089,
year = {2018},
author = {Alemany, A and Florescu, M and Baron, CS and Peterson-Maduro, J and van Oudenaarden, A},
title = {Whole-organism clone tracing using single-cell sequencing.},
journal = {Nature},
volume = {556},
number = {7699},
pages = {108-112},
pmid = {29590089},
issn = {1476-4687},
mesh = {Animal Fins/cytology ; Animals ; Brain/cytology ; CRISPR-Cas Systems/genetics ; *Cell Lineage/genetics ; Cell Tracking/*methods ; Clone Cells/*cytology/*metabolism ; Embryonic Stem Cells/cytology/metabolism ; Eye/cytology ; Female ; Genes, Reporter/genetics ; Hematopoietic Stem Cells/cytology/metabolism ; Male ; Multipotent Stem Cells/cytology/metabolism ; Organ Specificity ; Regeneration ; Sequence Analysis/*methods ; *Single-Cell Analysis ; Transcriptome ; Whole Body Imaging ; Zebrafish/*anatomy &amp; histology/embryology/genetics ; },
abstract = {Embryonic development is a crucial period in the life of a multicellular organism, during which limited sets of embryonic progenitors produce all cells in the adult body. Determining which fate these progenitors acquire in adult tissues requires the simultaneous measurement of clonal history and cell identity at single-cell resolution, which has been a major challenge. Clonal history has traditionally been investigated by microscopically tracking cells during development, monitoring the heritable expression of genetically encoded fluorescent proteins and, more recently, using next-generation sequencing technologies that exploit somatic mutations, microsatellite instability, transposon tagging, viral barcoding, CRISPR-Cas9 genome editing and Cre-loxP recombination. Single-cell transcriptomics provides a powerful platform for unbiased cell-type classification. Here we present ScarTrace, a single-cell sequencing strategy that enables the simultaneous quantification of clonal history and cell type for thousands of cells obtained from different organs of the adult zebrafish. Using ScarTrace, we show that a small set of multipotent embryonic progenitors generate all haematopoietic cells in the kidney marrow, and that many progenitors produce specific cell types in the eyes and brain. In addition, we study when embryonic progenitors commit to the left or right eye. ScarTrace reveals that epidermal and mesenchymal cells in the caudal fin arise from the same progenitors, and that osteoblast-restricted precursors can produce mesenchymal cells during regeneration. Furthermore, we identify resident immune cells in the fin with a distinct clonal origin from other blood cell types. We envision that similar approaches will have major applications in other experimental systems, in which the matching of embryonic clonal origin to adult cell type will ultimately allow reconstruction of how the adult body is built from a single cell.},
}
@article {pmid29587839,
year = {2018},
author = {Osathanunkul, M and Osathanunkul, R and Madesis, P},
title = {Species identification approach for both raw materials and end products of herbal supplements from Tinospora species.},
journal = {BMC complementary and alternative medicine},
volume = {18},
number = {1},
pages = {111},
pmid = {29587839},
issn = {1472-6882},
support = {DBG6080012//Thailand Research Fund/ ; },
mesh = {DNA Barcoding, Taxonomic ; *DNA, Plant/analysis/classification/genetics ; *Dietary Supplements/analysis/classification/standards ; *Plant Extracts/classification/genetics/standards ; Tinospora/*genetics ; },
abstract = {BACKGROUND: Nowadays herbal products used in traditional medicine are sold in processed forms and thus morphological authentication is almost impossible. With herbal industry rapidly growing size, consumer safety becomes an important issue that requires special attention. Identification of herbal species in the products is therefore needed.<br><br>METHODS: Sequences from the selected regions (matK, rbcL, trnL and ITS1) were retrieved and analysed. Then the most suitable barcode was assessed for discrimination of T. crispa from closely related species by HRM analysis and used in authentication of commercial products.<br><br>RESULTS: The ITS1 barcode was found to be the suitable primer as melting data from the HRM assay proved to be capable of distinguishing T. crispa from its related species. The developed protocol was then employed to authenticate medicinal products in powdered form. HRM analysis of all tested samples here revealed that five out of eight products contained not only the indicated species T. crispa but also other Tinospora, that have a high level of morphological similarity.<br><br>CONCLUSION: Misrepresentation, poor packaging and inappropriate labeling of the tested medicinal herbal products are thought to be the reason of the results here. Using Bar-HRM with the ITS marker lead to success in authenticating the tested herbal products.},
}
@article {pmid29580219,
year = {2018},
author = {Hebert, PDN and Braukmann, TWA and Prosser, SWJ and Ratnasingham, S and deWaard, JR and Ivanova, NV and Janzen, DH and Hallwachs, W and Naik, S and Sones, JE and Zakharov, EV},
title = {A Sequel to Sanger: amplicon sequencing that scales.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {219},
pmid = {29580219},
issn = {1471-2164},
mesh = {Animals ; Arthropods/classification/*genetics ; Genetic Variation ; High-Throughput Nucleotide Sequencing/*methods ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: Although high-throughput sequencers (HTS) have largely displaced their Sanger counterparts, the short read lengths and high error rates of most platforms constrain their utility for amplicon sequencing. The present study tests the capacity of single molecule, real-time (SMRT) sequencing implemented on the SEQUEL platform to overcome these limitations, employing 658 bp amplicons of the mitochondrial cytochrome c oxidase I gene as a model system.<br><br>RESULTS: By examining templates from more than 5000 species and 20,000 specimens, the performance of SMRT sequencing was tested with amplicons showing wide variation in GC composition and varied sequence attributes. SMRT and Sanger sequences were very similar, but SMRT sequencing provided more complete coverage, especially for amplicons with homopolymer tracts. Because it can characterize amplicon pools from 10,000 DNA extracts in a single run, the SEQUEL can reduce greatly reduce sequencing costs in comparison to first (Sanger) and second generation platforms (Illumina, Ion).<br><br>CONCLUSIONS: SMRT analysis generates high-fidelity sequences from amplicons with varying GC content and is resilient to homopolymer tracts. Analytical costs are low, substantially less than those for first or second generation sequencers. When implemented on the SEQUEL platform, SMRT analysis enables massive amplicon characterization because each instrument can recover sequences from more than 5 million DNA extracts a year.},
}
@article {pmid29576968,
year = {2018},
author = {Tahir, A and Hussain, F and Ahmed, N and Ghorbani, A and Jamil, A},
title = {Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e4499},
pmid = {29576968},
issn = {2167-8359},
abstract = {In pursuit of developing fast and accurate species-level molecular identification methods, we tested six DNA barcodes, namely ITS2, matK, rbcLa, ITS2+matK, ITS2+rbcLa, matK+rbcLa and ITS2+matK+rbcLa, for their capacity to identify frequently consumed but geographically isolated medicinal species of Fabaceae and Poaceae indigenous to the desert of Cholistan. Data were analysed by BLASTn sequence similarity, pairwise sequence divergence in TAXONDNA, and phylogenetic (neighbour-joining and maximum-likelihood trees) methods. Comparison of six barcode regions showed that ITS2 has the highest number of variable sites (209/360) for tested Fabaceae and (106/365) Poaceae species, the highest species-level identification (40%) in BLASTn procedure, distinct DNA barcoding gap, 100% correct species identification in BM and BCM functions of TAXONDNA, and clear cladding pattern with high nodal support in phylogenetic trees in both families. ITS2+matK+rbcLa followed ITS2 in its species-level identification capacity. The study was concluded with advocating the DNA barcoding as an effective tool for species identification and ITS2 as the best barcode region in identifying medicinal species of Fabaceae and Poaceae. Current research has practical implementation potential in the fields of pharmaco-vigilance, trade of medicinal plants and biodiversity conservation.},
}
@article {pmid29576956,
year = {2018},
author = {Lait, LA and Hebert, PDN},
title = {Phylogeographic structure in three North American tent caterpillar species (Lepidoptera: Lasiocampidae): Malacosoma americana, M. californica, and M. disstria.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e4479},
pmid = {29576956},
issn = {2167-8359},
abstract = {While phylogeographic structure has been examined in many North American vertebrate species, insects have received much less attention despite their central ecological roles. The moth genus Malacosoma (Hübner, 1820), is an important group of forestry pests responsible for large-scale defoliation across much of the Nearctic and Palearctic. The present study uses sequence variation in the mitochondrial cytochrome c oxidase 1 (COI) gene to examine the population genetic structure of the three widespread Malacosoma species (M. americana, M. californica, and M. disstria). Populations of all three species showed highest diversity in the south, suggesting that modern populations derived from southern refugia with loss of variation as these lineages dispersed northwards. However, despite similar life histories and dispersal abilities, the extent of regional variation varied among the taxa. M. americana, a species restricted to eastern North America, showed much less genetic structure than the western M. californica or the widespread M. disstria. The regional differentiation in the latter reflects the likely derivation of modern lineages from several refugia, as well as taxonomic uncertainty in M. californica. In these respects, the three species of Malacosoma share phylogeographic patterns similar to those detected in vertebrates which are characterised by greater phylogeographic breaks in the western half of the continent and limited structure in the east.},
}
@article {pmid29576703,
year = {2018},
author = {Yu, X and Zhang, Y and Wang, D and Jiang, L and Xu, X},
title = {Identification of Three Kinds of Citri Reticulatae Pericarpium Based on Deoxyribonucleic Acid Barcoding and High-performance Liquid Chromatography-diode Array Detection-electrospray Ionization/Mass Spectrometry/Mass Spectrometry Combined with Chemometric Analysis.},
journal = {Pharmacognosy magazine},
volume = {14},
number = {53},
pages = {64-69},
pmid = {29576703},
issn = {0973-1296},
abstract = {BACKGROUND: Citri Reticulatae Pericarpium is the dried mature pericarp of Citrus reticulata Blanco which can be divided into "Chenpi" and "Guangchenpi." "Guangchenpi" is the genuine Chinese medicinal material in Xinhui, Guangdong province; based on the greatest quality and least amount, it is most expensive among others. Hesperidin is used as the marker to identify Citri Reticulatae Pericarpium described in the Chinese Pharmacopoeia 2010. However, both "Chenpi" and "Guangchenpi" contain hesperidin so that it is impossible to differentiate them by measuring hesperidin.<br><br>OBJECTIVE: Our study aims to develop an efficient and accurate method to separate and identify "Guangchenpi" from other Citri Reticulatae Pericarpium.<br><br>MATERIALS AND METHODS: The genomic deoxyribonucleic acid (DNA) of all the materials was extracted and then the internal transcribed spacer 2 was amplified, sequenced, aligned, and analyzed. The secondary structures were created in terms of the database and website established by J&#xf6;rg Schultz et al. High-performance liquid chromatography-diode array detection-electrospray Ionization/mass spectrometry (HPLC-DAD-ESI-MS)/MS coupled with chemometric analysis was applied to compare the differences in chemical profiles of the three kinds of Citri Reticulatae Pericarpium.<br><br>RESULTS: A total of 22 samples were classified into three groups. The results of DNA barcoding were in accordance with principal component analysis and hierarchical cluster analysis. Eight compounds were deduced from HPLC-DAD-ESI-MS/MS.<br><br>CONCLUSIONS: This method is a reliable and effective tool to differentiate the three Citri Reticulatae Pericarpium.<br><br>SUMMARY: The internal transcribed spacer 2 regions and the secondary structure among three kinds of Citri Reticulatae Pericarpium varied considerablyAll the 22 samples were analyzed by high-performance liquid chromatography (HPLC) to obtain the chemical profilesPrincipal component analysis and hierarchical cluster analysis were used in the chemometric analysisdeoxyribonucleic acid barcoding and HPLC-diode array detection-electrospray ionization/mass spectrometry/MS coupled with chemometric analysis provided an accurate and strong proof to identify these three herbs. Abbreviations used: CTAB: Hexadecyltrimethylammonium bromide, DNA: Deoxyribonucleic acid, ITS2: Internal transcribed spacer 2, PCR: Polymerase chain reaction.},
}
@article {pmid29575567,
year = {2018},
author = {Pichler, M and Coskun, &#xd6;K and Ortega-Arbulú, AS and Conci, N and Wörheide, G and Vargas, S and Orsi, WD},
title = {A 16S rRNA gene sequencing and analysis protocol for the Illumina MiniSeq platform.},
journal = {MicrobiologyOpen},
volume = {7},
number = {6},
pages = {e00611},
pmid = {29575567},
issn = {2045-8827},
mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; DNA Primers/genetics ; DNA, Bacterial/*genetics ; Environmental Microbiology ; High-Throughput Nucleotide Sequencing/economics/instrumentation/*methods ; Microbiota ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {High-throughput sequencing of the 16S rRNA gene on the Illumina platform is commonly used to assess microbial diversity in environmental samples. The MiniSeq, Illumina's latest benchtop sequencer, enables more cost-efficient DNA sequencing relative to larger Illumina sequencing platforms (e.g., MiSeq). Here we used a modified custom primer sequencing approach to test the fidelity of the MiniSeq for high-throughput sequencing of the V4 hypervariable region of 16S rRNA genes from complex communities in environmental samples. To this end, we designed additional sequencing primers that enabled application of a dual-index barcoding method on the MiniSeq. A mock community was sequenced alongside the environmental samples in four different sequencing runs as a quality control benchmark. We were able to recapture a realistic richness of the mock community in all sequencing runs, and identify meaningful differences in alpha and beta diversity in the environmental samples. Furthermore, rarefaction analysis indicated diversity in many environmental samples was close to saturation. These results show that the MiniSeq can produce similar quantities of high-quality V4 reads compared to the MiSeq, yet is a cost-effective option for any laboratory interested in performing high-throughput 16S rRNA gene sequencing.},
}
@article {pmid29575366,
year = {2018},
author = {Ivanov, V and Lee, KM and Mutanen, M},
title = {Mitonuclear discordance in wolf spiders: Genomic evidence for species integrity and introgression.},
journal = {Molecular ecology},
volume = {27},
number = {7},
pages = {1681-1695},
doi = {10.1111/mec.14564},
pmid = {29575366},
issn = {1365-294X},
mesh = {Animals ; Cell Nucleus/*genetics ; Electron Transport Complex IV/genetics ; Genetic Loci ; *Genome, Mitochondrial ; *Genomics ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; Species Specificity ; Spiders/*genetics ; },
abstract = {Systematists and taxonomists have benefited greatly from the emergence of molecular methods. Species identification has become straightforward through DNA barcoding and the rapid build-up of massive DNA barcode reference libraries. In animals, mitonuclear discordance can significantly complicate the process of species identification and delimitation. The causes of mitonuclear discordance are either biological (e.g., introgression, incomplete lineage sorting, horizontal gene transfer androgenesis) or induced by operational factors (e.g., human error with specimen misidentification or incorrect species delimitation). Moreover, endosymbionts may play an important role in promoting fixation of mitochondrial genomes. Here, we study the mitonuclear discordance of wolf spiders species (Lycosidae) (independent cases from Alopecosa aculeata and Pardosa pullata groups) that share identical COI DNA barcodes. We approached the case utilizing double-digest restriction site-associated DNA sequencing (ddRADseq) to obtain and analyse genomic-scale data. Our results suggest that the observed cases of mitonuclear discordance are not due to operational reasons but result from biological processes. Further analysis indicated introgression and that incomplete lineage sorting is unlikely to have been responsible for the observed discrepancy. Additional survey of endosymbionts provided ideas on further research and their role in shaping mitochondrial DNA distribution patterns. Thus, ddRADseq grants an efficient way to study the taxonomy of problematic groups with insight into underlying evolutionary processes.},
}
@article {pmid29572213,
year = {2018},
author = {Aguayo, J and Fourrier-Jeandel, C and Husson, C and Ioos, R},
title = {Assessment of Passive Traps Combined with High-Throughput Sequencing To Study Airborne Fungal Communities.},
journal = {Applied and environmental microbiology},
volume = {84},
number = {11},
pages = {},
pmid = {29572213},
issn = {1098-5336},
mesh = {*Air Microbiology ; DNA Barcoding, Taxonomic ; DNA Primers/genetics ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Fungi/*classification/*isolation &amp; purification ; *Genetic Variation ; High-Throughput Nucleotide Sequencing ; *Mycobiome ; Real-Time Polymerase Chain Reaction ; },
abstract = {Techniques based on high-throughput sequencing (HTS) of environmental DNA have provided a new way of studying fungal diversity. However, these techniques suffer from a number of methodological biases which may appear at any of the steps involved in a metabarcoding study. Air is one of the most important environments where fungi can be found, because it is the primary medium of dispersal for many species. Looking ahead to future developments, it was decided to test 20 protocols, including different passive spore traps, spore recovery procedures, DNA extraction kits, and barcode loci. HTS was performed with the Illumina MiSeq platform targeting two subloci of the fungal internal transcribed spacer. Multivariate analysis and generalized linear models showed that the type of passive spore trap, the spore recovery procedure, and the barcode all impact the description of fungal communities in terms of richness and diversity when assessed by HTS metabarcoding. In contrast, DNA extraction kits did not significantly impact these results. Although passive traps may be used to describe airborne fungal communities, a study using specific real-time PCR and a mock community showed that these kinds of traps are affected by environmental conditions that may induce losses of biological material, impacting diversity and community composition results.IMPORTANCE The advent of high-throughput sequencing (HTS) methods, such as those offered by next-generation sequencing (NGS) techniques, has opened a new era in the study of fungal diversity in different environmental substrates. In this study, we show that an assessment of the diversity of airborne fungal communities can reliably be achieved by the use of simple and robust passive spore traps. However, a comparison of sample processing protocols showed that several methodological biases may impact the results of fungal diversity when assessed by metabarcoding. Our data suggest that identifying these biases is of paramount importance to enable a correct identification and relative quantification of community members.},
}
@article {pmid29571411,
year = {2018},
author = {Shinde, VL and Meena, RM and Shenoy, BD},
title = {Phylogenetic characterization of culturable bacteria and fungi associated with tarballs from Betul beach, Goa, India.},
journal = {Marine pollution bulletin},
volume = {128},
number = {},
pages = {593-600},
doi = {10.1016/j.marpolbul.2018.01.064},
pmid = {29571411},
issn = {1879-3363},
mesh = {Ascomycota/classification/*isolation &amp; purification ; Bacteria/classification/*isolation &amp; purification ; Bathing Beaches/*standards ; Biodegradation, Environmental ; DNA Barcoding, Taxonomic ; India ; Petroleum/metabolism/*microbiology ; *Petroleum Pollution ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Tarballs are semisolid blobs of crude oil, normally formed due to weathering of crude-oil in the sea after any kind of oil spills. Microorganisms are believed to thrive on hydrocarbon-rich tarballs and possibly assist in biodegradation. The taxonomy of ecologically and economically important tarball-associated microbes, however, needs improvement as DNA-based identification and phylogenetic characterization have been scarcely incorporated into it. In this study, bacteria and fungi associated with tarballs from touristic Betul beach in Goa, India were isolated, followed by phylogenetic analyses of 16S rRNA gene and the ITS sequence-data to decipher their clustering patterns with closely-related taxa. The gene-sequence analyses identified phylogenetically diverse 20 bacterial genera belonging to the phyla Proteobacteria (14), Actinobacteria (3), Firmicutes (2) and Bacteroidetes (1), and 8 fungal genera belonging to the classes Eurotiomycetes (6), Sordariomycetes (1) and Leotiomycetes (1) associated with the Betul tarball samples. Future studies employing a polyphasic approach, including multigene sequence-data, are needed for species-level identification of culturable tarball-associated microbes. This paper also discusses potentials of tarball-associated microbes to degrade hydrocarbons.},
}
@article {pmid29568476,
year = {2017},
author = {Zhuo, Z and Liu, Y and Liu, D and Huang, P and Jiang, F and Chen, X and Hong, M},
title = {Manipulating energy transfer in lanthanide-doped single nanoparticles for highly enhanced upconverting luminescence.},
journal = {Chemical science},
volume = {8},
number = {7},
pages = {5050-5056},
pmid = {29568476},
issn = {2041-6520},
abstract = {Energy transfer (ET) is of fundamental importance in tuning the optical performance of lanthanide-doped upconversion nanoparticles (UCNPs). However, the fine control and manipulation of the ETs particularly for deleterious cross-relaxation type ETs (CR-ETs) in lanthanide-doped UCNPs remains a formidable challenge to date. Herein, we demonstrate a rational design strategy to manipulate the deleterious CR-ETs in lanthanide-doped UCNPs, by fine-tuning the distances at an extremely large length scale (>20 nm) among multiple lanthanide dopants that are simultaneously embedded into one single nanoparticle with specially designed multilayer nanostructures. The successful inhibition of the CR-ETs leads to a significantly enhanced upconversion luminescence signal with an intensity ∼70 times higher than that of co-doped conventional UCNPs. This finding paves a new way for the better control of the ETs in lanthanide-doped nanoparticles, and offers the possibility of constructing a series of promising single-nanocrystal-based anti-counterfeiting barcodes with well-identified UC emission color and lifetime outputs.},
}
@article {pmid29568316,
year = {2018},
author = {von Beeren, C and Brückner, A and Maruyama, M and Burke, G and Wieschollek, J and Kronauer, DJC},
title = {Chemical and behavioral integration of army ant-associated rove beetles - a comparison between specialists and generalists.},
journal = {Frontiers in zoology},
volume = {15},
number = {},
pages = {8},
pmid = {29568316},
issn = {1742-9994},
abstract = {Host-symbiont interactions are embedded in ecological communities and range from unspecific to highly specific relationships. Army ants and their arthropod guests represent a fascinating example of species-rich host-symbiont associations where host specificity ranges across the entire generalist - specialist continuum. In the present study, we compared the behavioral and chemical integration mechanisms of two extremes of the generalist - specialist continuum: generalist ant-predators in the genus Tetradonia (Staphylinidae: Aleocharinae: Athetini), and specialist ant-mimics in the genera Ecitomorpha and Ecitophya (Staphylinidae: Aleocharinae: Ecitocharini). Similar to a previous study of Tetradonia beetles, we combined DNA barcoding with morphological studies to define species boundaries in ant-mimicking beetles. This approach found four ant-mimicking species at our study site at La Selva Biological Station in Costa Rica. Community sampling of Eciton army ant parasites revealed that ant-mimicking beetles were perfect host specialists, each beetle species being associated with a single Eciton species. These specialists were seamlessly integrated into the host colony, while generalists avoided physical contact to host ants in behavioral assays. Analysis of the ants' nestmate recognition cues, i.e. cuticular hydrocarbons (CHCs), showed close similarity in CHC composition and CHC concentration between specialists and Eciton burchellii foreli host ants. On the contrary, the chemical profiles of generalists matched host profiles less well, indicating that high accuracy in chemical host resemblance is only accomplished by socially integrated species. Considering the interplay between behavior, morphology, and cuticular chemistry, specialists but not generalists have cracked the ants' social code with respect to various sensory modalities. Our results support the long-standing idea that the evolution of host-specialization in parasites is a trade-off between the range of potential host species and the level of specialization on any particular host.},
}
@article {pmid29566047,
year = {2018},
author = {Dzangué-Tchoupou, G and Corneau, A and Blanc, C and Benveniste, O and Allenbach, Y},
title = {Analysis of cell surface and intranuclear markers on non-stimulated human PBMC using mass cytometry.},
journal = {PloS one},
volume = {13},
number = {3},
pages = {e0194593},
pmid = {29566047},
issn = {1932-6203},
mesh = {Antigens, Surface/*analysis/metabolism ; Biomarkers/analysis ; Cell Membrane/drug effects/*immunology/metabolism ; Cell Membrane Permeability/drug effects ; Cell Nucleus/drug effects/*immunology/metabolism ; Cell Separation/methods ; Epitopes/analysis/metabolism ; Fixatives/adverse effects ; Flow Cytometry/methods ; Humans ; Isotopes/chemistry ; Leukocytes, Mononuclear ; Molecular Typing/methods ; Palladium/chemistry ; Staining and Labeling/*methods ; Tissue Fixation/methods ; },
abstract = {Mass cytometry is a powerful tool that allows simultaneous analysis of more than 37 markers at the single cell level. Mass cytometry is of particular interest in the identification of a wide variety of cell phenotypes in autoimmune diseases. Moreover, cells can be labelled with palladium isotopes and pooled before staining (barcoding). Nevertheless, immunologists often face an important problem concerning the choice of markers to be included in a panel. This problem arises due to the incompatibility of different buffers used for the fixation and permeabilization of cells with various cell surface epitopes. In this study, we used a panel of 27 markers (19 surface markers and 8 intranuclear markers) to demonstrate disparities in the detection of cell surface antigens when comparing different buffers to stain unstimulated peripheral blood mononuclear cells. These disparities range from mild differences to very important differences in population frequencies depending on the buffers. Finally, we demonstrate the harmful effects of permeabilization prior to barcoding on the detection of some cell surface antigens. Here, we optimize a protocol that is suitable to use when targeting a large panel including both cell surface and intranuclear markers on unstimulated human peripheral blood mononuclear cells.},
}
@article {pmid29565982,
year = {2018},
author = {Kamaludin, H and Mahdin, H and Abawajy, JH},
title = {Clone tag detection in distributed RFID systems.},
journal = {PloS one},
volume = {13},
number = {3},
pages = {e0193951},
pmid = {29565982},
issn = {1932-6203},
mesh = {Computer Security ; Confidentiality ; Electronic Data Processing/methods ; Humans ; Radio Frequency Identification Device/*methods ; },
abstract = {Although Radio Frequency Identification (RFID) is poised to displace barcodes, security vulnerabilities pose serious challenges for global adoption of the RFID technology. Specifically, RFID tags are prone to basic cloning and counterfeiting security attacks. A successful cloning of the RFID tags in many commercial applications can lead to many serious problems such as financial losses, brand damage, safety and health of the public. With many industries such as pharmaceutical and businesses deploying RFID technology with a variety of products, it is important to tackle RFID tag cloning problem and improve the resistance of the RFID systems. To this end, we propose an approach for detecting cloned RFID tags in RFID systems with high detection accuracy and minimal overhead thus overcoming practical challenges in existing approaches. The proposed approach is based on consistency of dual hash collisions and modified count-min sketch vector. We evaluated the proposed approach through extensive experiments and compared it with existing baseline approaches in terms of execution time and detection accuracy under varying RFID tag cloning ratio. The results of the experiments show that the proposed approach outperforms the baseline approaches in cloned RFID tag detection accuracy.},
}
@article {pmid29564995,
year = {2018},
author = {Beebe, NW},
title = {DNA barcoding mosquitoes: advice for potential prospectors.},
journal = {Parasitology},
volume = {145},
number = {5},
pages = {622-633},
doi = {10.1017/S0031182018000343},
pmid = {29564995},
issn = {1469-8161},
mesh = {Animals ; Culicidae/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/*genetics ; Genome, Mitochondrial ; },
abstract = {Mosquitoes' importance as vectors of pathogens that drive disease underscores the importance of precise and comparable methods of taxa identification among their species. While several molecular targets have been used to study mosquitoes since the initiation of PCR in the 1980s, its application to mosquito identification took off in the early 1990s. This review follows the research's recent journey into the use of mitochondrial DNA (mtDNA) cytochrome oxidase 1 (COI or COX1) as a DNA barcode target for mosquito species identification - a target whose utility for discriminating mosquitoes is now escalating. The pros and cons of using a mitochondrial genome target are discussed with a broad sweep of the mosquito literature suggesting that nuclear introgressions of mtDNA sequences appear to be uncommon and that the COI works well for distantly related taxa and shows encouraging utility in discriminating more closely related species such as cryptic/sibling species groups. However, the utility of COI in discriminating some closely related groups can be problematic and investigators are advised to proceed with caution as problems with incomplete lineage sorting and introgression events can result in indistinguishable COI sequences appearing in reproductively independent populations. In these - if not all - cases, it is advisable to run a nuclear marker alongside the mtDNA and thus the utility of the ribosomal DNA - and in particular the internal transcribed spacer 2 - is also briefly discussed as a useful counterpoint to the COI.},
}
@article {pmid29563060,
year = {2018},
author = {Raju, SC and Lagström, S and Ellonen, P and de Vos, WM and Eriksson, JG and Weiderpass, E and Rounge, TB},
title = {Reproducibility and repeatability of six high-throughput 16S rDNA sequencing protocols for microbiota profiling.},
journal = {Journal of microbiological methods},
volume = {147},
number = {},
pages = {76-86},
doi = {10.1016/j.mimet.2018.03.003},
pmid = {29563060},
issn = {1872-8359},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic/methods ; DNA Primers ; Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; Reproducibility of Results ; Saliva/microbiology ; },
abstract = {Culture-independent molecular techniques and advances in next generation sequencing (NGS) technologies make large-scale epidemiological studies on microbiota feasible. A challenge using NGS is to obtain high reproducibility and repeatability, which is mostly attained through robust amplification. We aimed to assess the reproducibility of saliva microbiota by comparing triplicate samples. The microbiota was produced with simplified in-house 16S amplicon assays taking advantage of large number of barcodes. The assays included primers with Truseq (TS-tailed) or Nextera (NX-tailed) adapters and either with dual index or dual index plus a 6-nt internal index. All amplification protocols produced consistent microbial profiles for the same samples. Although, in our study, reproducibility was highest for the TS-tailed method. Five replicates of a single sample, prepared with the TS-tailed 1-step protocol without internal index sequenced on the HiSeq platform provided high alpha-diversity and low standard deviation (mean Shannon and Inverse Simpson diversity was 3.19 ± 0.097 and 13.56 ± 1.634 respectively). Large-scale profiling of microbiota can consistently be produced by all 16S amplicon assays. The TS-tailed-1S dual index protocol is preferred since it provides repeatable profiles on the HiSeq platform and are less labour intensive.},
}
@article {pmid29562268,
year = {2018},
author = {Rodrigues, BL and Carvalho-Costa, LF and Pinto, IS and Rebêlo, JMM},
title = {DNA Barcoding Reveals Hidden Diversity of Sand Flies (Diptera: Psychodidae) at Fine and Broad Spatial Scales in Brazilian Endemic Regions for Leishmaniasis.},
journal = {Journal of medical entomology},
volume = {55},
number = {4},
pages = {893-901},
doi = {10.1093/jme/tjy032},
pmid = {29562268},
issn = {1938-2928},
mesh = {Animals ; *Biodiversity ; Brazil ; *DNA Barcoding, Taxonomic ; Female ; Male ; Psychodidae/*classification/*genetics ; },
abstract = {Sand fly (Diptera: Psychodidae) taxonomy is complex and time-consuming, which hampers epidemiological efforts directed toward controlling leishmaniasis in endemic regions such as northeastern Brazil. Here, we used a fragment of the mitochondrial cytochrome c oxidase I (COI) gene to identify sand fly species in Maranhão State (northeastern Brazil) and to assess cryptic diversity occurring at different spatial scales. For this, we obtained 148 COI sequences of 15 sand fly species (10 genera) from Maranhão (fine spatial scale), and joined them to COI sequences from other Brazilian localities (distant about 2,000 km from Maranhão, broad spatial scale) available in GenBank. We revealed cases of cryptic diversity in sand flies both at fine (Lutzomyia longipalpis (Lutz and Neiva) and Evandromyia termitophila (Martins, Falcão and Silva)) and broad spatial scales (Migonemyia migonei (França), Pressatia choti (Floch and Abonnenc), Psychodopygus davisi (Root), Sciopemyia sordellii (Shannon and Del Ponte), and Bichromomyia flaviscutellata (Mangabeira)). We argue that in the case of Bi. flaviscutellata, the cryptic diversity is associated with a putative new species. Cases in which DNA taxonomy was not as effective as morphological identification possibly involved recent speciation and/or introgressive hybridization, highlighting the need for integrative approaches to identify some sand fly species. Finally, we provide the first barcode sequences for four species (Brumptomyia avellari (Costa Lima), Evandromyia infraspinosa (Mangabeira), Evandromyia evandroi (Costa Lima and Antunes), and Psychodopygus complexus (Mangabeira)), which will be useful for further molecular identification of neotropical species.},
}
@article {pmid29561604,
year = {2018},
author = {Tang, S and Zhang, Y and Dhakal, P and Ravelo, L and Anderson, CL and Collins, KM and Raymo, FM},
title = {Photochemical Barcodes.},
journal = {Journal of the American Chemical Society},
volume = {140},
number = {13},
pages = {4485-4488},
pmid = {29561604},
issn = {1520-5126},
support = {R01 NS086932/NS/NINDS NIH HHS/United States ; },
mesh = {Boron Compounds/*chemistry ; *DNA Barcoding, Taxonomic ; *Light ; Oxyquinoline/chemistry ; },
abstract = {A photochemical strategy to encode fluorescence signals in vivo with spatial control was designed around the unique properties of a photoactivatable borondipyrromethene (BODIPY). The photoinduced disconnection of two oxazines, flanking a single BODIPY, in two consecutive steps produces a mixture of three emissive molecules with resolved fluorescence inside polymer beads. The relative amounts and emission intensities of the three fluorophores can be regulated precisely in each bead by adjusting the dose of activating photons to mark individual particles with distinct codes of fluorescence signals. The visible wavelengths and mild illumination sufficient to induce these transformations permit the photochemical barcoding of beads also in living nematodes. Different regions of the same animal can be labeled with distinct barcodes to allow the monitoring of their dynamics for long times with no toxic effects. Thus, our photochemical strategy for the generation of fluorescence barcodes can produce multiple and distinguishable labels in the same biological sample to enable the spatiotemporal tracking of, otherwise indistinguishable, targets.},
}
@article {pmid29559822,
year = {2018},
author = {Nilsson, RH and Taylor, AFS and Adams, RI and Baschien, C and Johan Bengtsson-Palme, and Cangren, P and Coleine, C and Heide-Marie Daniel, and Glassman, SI and Hirooka, Y and Irinyi, L and Reda Iršėnaitė, and Pedro M Martin-Sanchez, and Meyer, W and Seung-Yoon Oh, and Jose Paulo Sampaio, and Seifert, KA and Sklenář, F and Dirk Stubbe, and Suh, SO and Summerbell, R and Svantesson, S and Martin Unterseher, and Cobus M Visagie, and Weiss, M and Woudenberg, JH and Christian Wurzbacher, and den Wyngaert, SV and Yilmaz, N and Andrey Yurkov, and Kõljalg, U and Abarenkov, K},
title = {Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK).},
journal = {MycoKeys},
volume = {},
number = {28},
pages = {65-82},
pmid = {29559822},
issn = {1314-4057},
abstract = {Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi - whether transient visitors or more persistent residents - may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions - such as country and host/substrate of collection - are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10-11, 2017) organized at the James Hutton Institute/University of Aberdeen (UK) to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS barcode sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes - including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences - were implemented in the UNITE database for molecular identification of fungi (https://unite.ut.ee/) and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were Penicillium, Talaromyces, Cladosporium, Acremonium, and Alternaria, all of them of significant importance in both culture-based and culture-independent surveys of the built environment.},
}
@article {pmid29558527,
year = {2018},
author = {Banchi, E and Ametrano, CG and Stanković, D and Verardo, P and Moretti, O and Gabrielli, F and Lazzarin, S and Borney, MF and Tassan, F and Tretiach, M and Pallavicini, A and Muggia, L},
title = {DNA metabarcoding uncovers fungal diversity of mixed airborne samples in Italy.},
journal = {PloS one},
volume = {13},
number = {3},
pages = {e0194489},
pmid = {29558527},
issn = {1932-6203},
mesh = {*Air Microbiology ; Allergens/immunology ; Cell Nucleus/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/chemistry/*genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Fungi/classification/*genetics ; Genetic Variation ; Geography ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Italy ; Species Specificity ; Spores, Fungal/genetics/immunology ; },
abstract = {Fungal spores and mycelium fragments are particles which become and remain airborne and have been subjects of aerobiological studies. The presence and the abundance of taxa in aerobiological samples can be very variable and impaired by changeable climatic conditions. Because many fungi produce mycotoxins and both their mycelium fragments and spores are potential allergens, monitoring the presence of these taxa is of key importance. So far data on exposure and sensitization to fungal allergens are mainly based on the assessment of few, easily identifiable taxa and focused only on certain environments. The microscopic method used to analyze aerobiological samples and the inconspicuous fungal characters do not allow a in depth taxonomical identification. Here, we present a first assessment of fungal diversity from airborne samples using a DNA metabarcoding analysis. The nuclear ITS2 region was selected as barcode to catch fungal diversity in mixed airborne samples gathered during two weeks in four sites of North-Eastern and Central Italy. We assessed the taxonomic composition and diversity within and among the sampled sites and compared the molecular data with those obtained by traditional microscopy. The molecular analyses provide a tenfold more comprehensive determination of the taxa than the traditional morphological inspections. Our results prove that the metabarcoding analysis is a promising approach to increases quality and sensitivity of the aerobiological monitoring. The laboratory and bioinformatic workflow implemented here is now suitable for routine, high-throughput, regional analyses of airborne fungi.},
}
@article {pmid29557324,
year = {2018},
author = {Wood, JR},
title = {DNA barcoding of ancient parasites.},
journal = {Parasitology},
volume = {145},
number = {5},
pages = {646-655},
doi = {10.1017/S0031182018000380},
pmid = {29557324},
issn = {1469-8161},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Ancient/analysis/*isolation &amp; purification ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Parasites/*genetics ; Parasitic Diseases/parasitology ; },
abstract = {Ancient samples present a number of technical challenges for DNA barcoding, including damaged DNA with low endogenous copy number and short fragment lengths. Nevertheless, techniques are available to overcome these issues, and DNA barcoding has now been used to successfully recover parasite DNA from a wide variety of ancient substrates, including coprolites, cesspit sediment, mummified tissues, burial sediments and permafrost soils. The study of parasite DNA from ancient samples can provide a number of unique scientific insights, for example: (1) into the parasite communities and health of prehistoric human populations; (2) the ability to reconstruct the natural parasite faunas of rare or extinct host species, which has implications for conservation management and de-extinction; and (3) the ability to view in 'real-time' processes that may operate over century- or millenial-timescales, such as how parasites responded to past climate change events or how they co-evolved alongside their hosts. The application of DNA metabarcoding and high-throughput sequencing to ancient specimens has so far been limited, but in future promises great potential for gaining empirical data on poorly understood processes such as parasite co-extinction.},
}
@article {pmid29557238,
year = {2019},
author = {Han, T and Kim, SH and Yoon, HJ and Park, IG and Park, H},
title = {Genetic variations of DNA barcoding region of bumble bees (Hymenoptera: Apidae) from South Korea.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {1},
pages = {30-42},
doi = {10.1080/24701394.2018.1450396},
pmid = {29557238},
issn = {2470-1408},
mesh = {Animals ; Bees/classification/*genetics ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Insect Proteins/genetics ; Phylogeny ; *Polymorphism, Genetic ; Republic of Korea ; },
abstract = {We reassessed species diversity and genetic structure in Korean bumble bees using DNA barcode analyses of 484 cytochrome c oxidase subunit I (COI) sequences from 24 morphospecies. Based on COI, all of the Korean species formed distinct clades in the phylogenetic trees, except for Bombus (Megabombus) koreanus in the maximum likelihood tree. Five species exhibited low interspecific genetic distances (range: 1.2-2.7%), indicating that they are recently diverged species. COI data could not be used to identify bumble bees at the subspecies level. For the dominant species, most local populations in Korea were panmictic and were more closely related to continental populations than to allopatric populations. Furthermore, sympatric haplotypes within Korea could be distinguished. We detected B. (Megabombus) diversus in South Korea for the first time. Our results demonstrate that DNA barcoding is a useful technique for species recognition and for allopatric and sympatric haplotype detection in bumble bees.},
}
@article {pmid29556741,
year = {2018},
author = {Viljoen, E and Odeny, DA and Coetzee, MPA and Berger, DK and Rees, DJG},
title = {Application of Chloroplast Phylogenomics to Resolve Species Relationships Within the Plant Genus Amaranthus.},
journal = {Journal of molecular evolution},
volume = {86},
number = {3-4},
pages = {216-239},
pmid = {29556741},
issn = {1432-1432},
mesh = {Amaranthus/*classification ; DNA Barcoding, Taxonomic ; *Genome, Chloroplast ; *Genome, Plant ; Genomics ; *Phylogeny ; },
abstract = {Amaranthus species are an emerging and promising nutritious traditional vegetable food source. Morphological plasticity and poorly resolved dendrograms have led to the need for well resolved species phylogenies. We hypothesized that whole chloroplast phylogenomics would result in more reliable differentiation between closely related amaranth species. The aims of the study were therefore: to construct a fully assembled, annotated chloroplast genome sequence of Amaranthus tricolor; to characterize Amaranthus accessions phylogenetically by comparing barcoding genes (matK, rbcL, ITS) with whole chloroplast sequencing; and to use whole chloroplast phylogenomics to resolve deeper phylogenetic relationships. We generated a complete A. tricolor chloroplast sequence of 150,027 bp. The three barcoding genes revealed poor inter- and intra-species resolution with low bootstrap support. Whole chloroplast phylogenomics of 59 Amaranthus accessions increased the number of parsimoniously informative sites from 92 to 481 compared to the barcoding genes, allowing improved separation of amaranth species. Our results support previous findings that two geographically independent domestication events of Amaranthus hybridus likely gave rise to several species within the Hybridus complex, namely Amaranthus dubius, Amaranthus quitensis, Amaranthus caudatus, Amaranthus cruentus and Amaranthus hypochondriacus. Poor resolution of species within the Hybridus complex supports the recent and ongoing domestication within the complex, and highlights the limitation of chloroplast data for resolving recent evolution. The weedy Amaranthus retroflexus and Amaranthus powellii was found to share a common ancestor with the Hybridus complex. Leafy amaranth, Amaranthus tricolor, Amaranthus blitum, Amaranthus viridis and Amaranthus graecizans formed a stable sister lineage to the aforementioned species across the phylogenetic trees. This study demonstrates the power of next-generation sequencing data and reference-based assemblies to resolve phylogenies, and also facilitated the identification of unknown Amaranthus accessions from a local genebank. The informative phylogeny of the Amaranthus genus will aid in selecting accessions for breeding advanced genotypes to satisfy global food demand.},
}
@article {pmid29555914,
year = {2018},
author = {Wang, G and Moffitt, JR and Zhuang, X},
title = {Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {4847},
pmid = {29555914},
issn = {2045-2322},
support = {R01 MH113094/MH/NIMH NIH HHS/United States ; },
mesh = {*Gene Expression Profiling ; *In Situ Hybridization, Fluorescence ; *Microscopy ; Proteomics ; RNA/*genetics ; Single-Cell Analysis ; },
abstract = {As an image-based single-cell transcriptomics approach, multiplexed error-robust fluorescence in situ hybridization (MERFISH) allows hundreds to thousands of RNA species to be identified, counted and localized in individual cells while preserving the native spatial context of RNAs. In MERFISH, RNAs are identified via a combinatorial labeling approach that encodes RNA species with error-robust barcodes followed by sequential rounds of single-molecule FISH (smFISH) to read out these barcodes. The accuracy of RNA identification relies on spatially separated signals from individual RNA molecules, which limits the density of RNAs that can be measured and makes the multiplexed imaging of a large number of high-abundance RNAs challenging. Here we report an approach that combines MERFISH and expansion microscopy to substantially increase the total density of RNAs that can be measured. Using this approach, we demonstrate accurate identification and counting of RNAs, with a near 100% detection efficiency, in a ~130-RNA library composed of many high-abundance RNAs, the total density of which is more than 10 fold higher than previously reported. In parallel, we demonstrate the combination of MERFISH with immunofluorescence in expanded samples. These advances increase the versatility of MERFISH and will facilitate its application to a wide range of biological problems.},
}
@article {pmid29552015,
year = {2018},
author = {Lu, MY and Lu, SS and Chang, SL and Liao, F},
title = {The Phosphorylation of CCR6 on Distinct Ser/Thr Residues in the Carboxyl Terminus Differentially Regulates Biological Function.},
journal = {Frontiers in immunology},
volume = {9},
number = {},
pages = {415},
pmid = {29552015},
issn = {1664-3224},
mesh = {Actins/*metabolism ; Humans ; Jurkat Cells ; Mutagenesis, Site-Directed ; Mutation/genetics ; Phosphorylation ; Protein Domains/genetics ; Receptor Aggregation/genetics ; Receptors, CCR6/genetics/*metabolism ; Serine/genetics/metabolism ; Signal Transduction/*genetics ; Threonine/genetics/metabolism ; beta-Arrestin 1/metabolism ; beta-Arrestin 2/metabolism ; },
abstract = {CCR6 is a G protein-coupled receptor (GPCR) that recognizes a single chemokine ligand, CCL20 and is primarily expressed by leukocytes. Upon ligand binding, CCR6 activates Gαi heterotrimeric G proteins to induce various potential cellular outcomes through context-specific cell signaling. It is well known that differential phosphorylation of Ser and Thr residues in the C-terminal domains or intracellular loops of GPCRs can generate barcodes that regulate GPCR function by regulating the recruitment of β-arrestins. In this study, we demonstrate that ligand binding to CCR6 induces receptor phosphorylation at Ser/Thr residues in the C-terminal tail, rather than intracellular loops. Using mutagenesis experiments, we determined that distinct clusters of Ser/Thr residues in the C-terminal domain differentially regulate CCL20-induced signaling and cellular response. Substituting the Thr360/Ser361/Thr363 cluster or the Ser370/Ser371 cluster with Ala residues modulated cellular response upon CCL20 stimulation. Notably, receptor internalization, chemotaxis, F-actin distribution, transient ERK1/2 activation, and β-arrestin 2 recruitment were oppositely affected by mutating the two clusters, suggesting that phosphorylation of CCR6 C-terminal Ser/Thr residues directs the cell signaling response upon receptor activation. Moreover, activated CCR6 weakly recruited β-arrestin 1 in comparison with β-arrestin 2, and the two arrestin proteins seemed to play overlapping but distinct roles in mediating CCL20/CCR6-induced cellular responses. Taken together, the effects of site-specific Ser/Thr phosphorylation on CCR6 demonstrate the existence of barcodes on the protein that dictate the activation of different cell signaling profiles and lead to distinct biological outcomes.},
}
@article {pmid29551885,
year = {2018},
author = {Yang, CH and Wu, KC and Chuang, LY and Chang, HW},
title = {Decision Tree Algorithm-Generated Single-Nucleotide Polymorphism Barcodes of rbcL Genes for 38 Brassicaceae Species Tagging.},
journal = {Evolutionary bioinformatics online},
volume = {14},
number = {},
pages = {1176934318760856},
pmid = {29551885},
issn = {1176-9343},
abstract = {DNA barcode sequences are accumulating in large data sets. A barcode is generally a sequence larger than 1000 base pairs and generates a computational burden. Although the DNA barcode was originally envisioned as straightforward species tags, the identification usage of barcode sequences is rarely emphasized currently. Single-nucleotide polymorphism (SNP) association studies provide us an idea that the SNPs may be the ideal target of feature selection to discriminate between different species. We hypothesize that SNP-based barcodes may be more effective than the full length of DNA barcode sequences for species discrimination. To address this issue, we tested a ribulose diphosphate carboxylase (rbcL) SNP barcoding (RSB) strategy using a decision tree algorithm. After alignment and trimming, 31 SNPs were discovered in the rbcL sequences from 38 Brassicaceae plant species. In the decision tree construction, these SNPs were computed to set up the decision rule to assign the sequences into 2 groups level by level. After algorithm processing, 37 nodes and 31 loci were required for discriminating 38 species. Finally, the sequence tags consisting of 31 rbcL SNP barcodes were identified for discriminating 38 Brassicaceae species based on the decision tree-selected SNP pattern using RSB method. Taken together, this study provides the rational that the SNP aspect of DNA barcode for rbcL gene is a useful and effective sequence for tagging 38 Brassicaceae species.},
}
@article {pmid29551197,
year = {2018},
author = {Urbina, H and Breed, MF and Zhao, W and Lakshmi Gurrala, K and Andersson, SGE and Ågren, J and Baldauf, S and Rosling, A},
title = {Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere.},
journal = {Fungal biology},
volume = {122},
number = {4},
pages = {231-240},
doi = {10.1016/j.funbio.2017.12.013},
pmid = {29551197},
issn = {1878-6146},
mesh = {Arabidopsis/*microbiology ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Fungi/*classification/*genetics ; Italy ; *Mycobiome ; Phylogeny ; Plant Roots/*microbiology ; Rhizosphere ; Sequence Analysis, DNA ; Soil Microbiology ; Sweden ; },
abstract = {Biotic and abiotic conditions in soil pose major constraints on growth and reproductive success of plants. Fungi are important agents in plant soil interactions but the belowground mycobiota associated with plants remains poorly understood. We grew one genotype each from Sweden and Italy of the widely-studied plant model Arabidopsis thaliana. Plants were grown under controlled conditions in organic topsoil local to the Swedish genotype, and harvested after ten weeks. Total DNA was extracted from three belowground compartments: endosphere (sonicated roots), rhizosphere and bulk soil, and fungal communities were characterized from each by amplification and sequencing of the fungal barcode region ITS2. Fungal species diversity was found to decrease from bulk soil to rhizosphere to endosphere. A significant effect of plant genotype on fungal community composition was detected only in the endosphere compartment. Despite A. thaliana being a non-mycorrhizal plant, it hosts a number of known mycorrhiza fungi in its endosphere compartment, which is also colonized by endophytic, pathogenic and saprotrophic fungi. Species in the Archaeorhizomycetes were most abundant in rhizosphere samples suggesting an adaptation to environments with high nutrient turnover for some of these species. We conclude that A. thaliana endosphere fungal communities represent a selected subset of fungi recruited from soil and that plant genotype has small but significant quantitative and qualitative effects on these communities.},
}
@article {pmid29545511,
year = {2018},
author = {Rosenberg, AB and Roco, CM and Muscat, RA and Kuchina, A and Sample, P and Yao, Z and Graybuck, LT and Peeler, DJ and Mukherjee, S and Chen, W and Pun, SH and Sellers, DL and Tasic, B and Seelig, G},
title = {Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding.},
journal = {Science (New York, N.Y.)},
volume = {360},
number = {6385},
pages = {176-182},
pmid = {29545511},
issn = {1095-9203},
support = {R01 CA207029/CA/NCI NIH HHS/United States ; R01 NS064404/NS/NINDS NIH HHS/United States ; R21 NS086500/NS/NINDS NIH HHS/United States ; TL1 TR002318/TR/NCATS NIH HHS/United States ; },
mesh = {Animals ; Brain/*growth &amp; development ; Cell Nucleus/genetics ; Gene Expression Profiling/*methods ; *Gene Expression Regulation, Developmental ; HEK293 Cells ; Humans ; Mice ; NIH 3T3 Cells ; Neurons/metabolism ; Sequence Analysis, RNA ; Single-Cell Analysis/*methods ; Spinal Cord/*growth &amp; development ; *Transcriptome ; },
abstract = {To facilitate scalable profiling of single cells, we developed split-pool ligation-based transcriptome sequencing (SPLiT-seq), a single-cell RNA-seq (scRNA-seq) method that labels the cellular origin of RNA through combinatorial barcoding. SPLiT-seq is compatible with fixed cells or nuclei, allows efficient sample multiplexing, and requires no customized equipment. We used SPLiT-seq to analyze 156,049 single-nucleus transcriptomes from postnatal day 2 and 11 mouse brains and spinal cords. More than 100 cell types were identified, with gene expression patterns corresponding to cellular function, regional specificity, and stage of differentiation. Pseudotime analysis revealed transcriptional programs driving four developmental lineages, providing a snapshot of early postnatal development in the murine central nervous system. SPLiT-seq provides a path toward comprehensive single-cell transcriptomic analysis of other similarly complex multicellular systems.},
}
@article {pmid29544703,
year = {2018},
author = {Espinosa-Álvarez, O and Ortiz, PA and Lima, L and Costa-Martins, AG and Serrano, MG and Herder, S and Buck, GA and Camargo, EP and Hamilton, PB and Stevens, JR and Teixeira, MMG},
title = {Trypanosoma rangeli is phylogenetically closer to Old World trypanosomes than to Trypanosoma cruzi.},
journal = {International journal for parasitology},
volume = {48},
number = {7},
pages = {569-584},
doi = {10.1016/j.ijpara.2017.12.008},
pmid = {29544703},
issn = {1879-0135},
mesh = {Animals ; Chiroptera/*parasitology ; Genome, Protozoan ; Guinea-Bissau/epidemiology ; *Phylogeny ; Trypanosoma cruzi/*genetics ; Trypanosoma rangeli/*genetics ; Trypanosomiasis/epidemiology/parasitology/*veterinary ; },
abstract = {Trypanosoma rangeli and Trypanosoma cruzi are generalist trypanosomes sharing a wide range of mammalian hosts; they are transmitted by triatomine bugs, and are the only trypanosomes infecting humans in the Neotropics. Their origins, phylogenetic relationships, and emergence as human parasites have long been subjects of interest. In the present study, taxon-rich analyses (20 trypanosome species from bats and terrestrial mammals) using ssrRNA, glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH), heat shock protein-70 (HSP70) and Spliced Leader RNA sequences, and multilocus phylogenetic analyses using 11 single copy genes from 15 selected trypanosomes, provide increased resolution of relationships between species and clades, strongly supporting two main sister lineages: lineage Schizotrypanum, comprising T. cruzi and bat-restricted trypanosomes, and Tra[Tve-Tco] formed by T. rangeli, Trypanosoma vespertilionis and Trypanosoma conorhini clades. Tve comprises European T. vespertilionis and African T. vespertilionis-like of bats and bat cimicids characterised in the present study and Trypanosoma sp. Hoch reported in monkeys and herein detected in bats. Tco included the triatomine-transmitted tropicopolitan T. conorhini from rats and the African NanDoum1 trypanosome of civet (carnivore). Consistent with their very close relationships, Tra[Tve-Tco] species shared highly similar Spliced Leader RNA structures that were highly divergent from those of Schizotrypanum. In a plausible evolutionary scenario, a bat trypanosome transmitted by cimicids gave origin to the deeply rooted Tra[Tve-Tco] and Schizotrypanum lineages, and bat trypanosomes of diverse genetic backgrounds jumped to new hosts. A long and independent evolutionary history of T. rangeli more related to Old World trypanosomes from bats, rats, monkeys and civets than to Schizotrypanum spp., and the adaptation of these distantly related trypanosomes to different niches of shared mammals and vectors, is consistent with the marked differences in transmission routes, life-cycles and host-parasite interactions, resulting in T. cruzi (but not T. rangeli) being pathogenic to humans.},
}
@article {pmid29543431,
year = {2018},
author = {Chen, H and Yao, J and Fu, Y and Pang, Y and Wang, J and Huang, Y},
title = {Tagmentation on Microbeads: Restore Long-Range DNA Sequence Information Using Next Generation Sequencing with Library Prepared by Surface-Immobilized Transposomes.},
journal = {ACS applied materials &amp; interfaces},
volume = {10},
number = {14},
pages = {11539-11545},
doi = {10.1021/acsami.8b01560},
pmid = {29543431},
issn = {1944-8252},
mesh = {Base Sequence ; DNA Copy Number Variations ; *High-Throughput Nucleotide Sequencing ; Microspheres ; Sequence Analysis, DNA ; },
abstract = {The next generation sequencing (NGS) technologies have been rapidly evolved and applied to various research fields, but they often suffer from losing long-range information due to short library size and read length. Here, we develop a simple, cost-efficient, and versatile NGS library preparation method, called tagmentation on microbeads (TOM). This method is capable of recovering long-range information through tagmentation mediated by microbead-immobilized transposomes. Using transposomes with DNA barcodes to identically label adjacent sequences during tagmentation, we can restore inter-read connection of each fragment from original DNA molecule by fragment-barcode linkage after sequencing. In our proof-of-principle experiment, more than 4.5% of the reads are linked with their adjacent reads, and the longest linkage is over 1112 bp. We demonstrate TOM with eight barcodes, but the number of barcodes can be scaled up by an ultrahigh complexity construction. We also show this method has low amplification bias and effectively fits the applications to identify copy number variations.},
}
@article {pmid29536450,
year = {2018},
author = {Fan, B and Wang, J and Xu, Y and Chen, J},
title = {Single-Cell Protein Assays: A Review.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1754},
number = {},
pages = {293-309},
doi = {10.1007/978-1-4939-7717-8_17},
pmid = {29536450},
issn = {1940-6029},
mesh = {Flow Cytometry/instrumentation/methods ; Humans ; Mass Spectrometry/instrumentation/methods ; Microfluidic Analytical Techniques/instrumentation/methods ; Microtechnology/instrumentation/methods ; Protein Array Analysis/instrumentation/methods ; Proteins/*analysis/metabolism ; Proteomics/instrumentation/*methods/trends ; Single-Cell Analysis/instrumentation/*methods ; },
abstract = {Quantification of single-cell proteomics provides key insights in the field of cellular heterogeneity. This chapter discusses the emerging techniques that are being used to measure the protein copy numbers at the single-cell level, which includes flow cytometry, mass cytometry, droplet cytometry, microengraving, and single-cell barcoding microchip. The advantages and limitations of each technique are compared, and future research opportunities are highlighted.},
}
@article {pmid29535364,
year = {2018},
author = {Séne, S and Selosse, MA and Forget, M and Lambourdière, J and Cissé, K and Diédhiou, AG and Rivera-Ocasio, E and Kodja, H and Kameyama, N and Nara, K and Vincenot, L and Mansot, JL and Weber, J and Roy, M and Sylla, SN and Bâ, A},
title = {A pantropically introduced tree is followed by specific ectomycorrhizal symbionts due to pseudo-vertical transmission.},
journal = {The ISME journal},
volume = {12},
number = {7},
pages = {1806-1816},
pmid = {29535364},
issn = {1751-7370},
mesh = {Basidiomycota/classification/genetics/isolation &amp; purification/*physiology ; Brazil ; Caribbean Region ; Japan ; Mycorrhizae/genetics/growth &amp; development/isolation &amp; purification/*physiology ; Polygonaceae/*microbiology ; Seedlings/microbiology/physiology ; Soil ; Spores, Fungal/classification/genetics/isolation &amp; purification/physiology ; *Symbiosis ; Trees/*microbiology/physiology ; },
abstract = {Global trade increases plant introductions, but joint introduction of associated microbes is overlooked. We analyzed the ectomycorrhizal fungi of a Caribbean beach tree, seagrape (Coccoloba uvifera, Polygonacaeae), introduced pantropically to stabilize coastal soils and produce edible fruits. Seagrape displays a limited symbiont diversity in the Caribbean. In five regions of introduction (Brazil, Japan, Malaysia, Réunion and Senegal), molecular barcoding showed that seagrape mostly or exclusively associates with Scleroderma species (Basidiomycota) that were hitherto only known from Caribbean seagrape stands. An unknown Scleroderma species dominates in Brazil, Japan and Malaysia, while Scleroderma bermudense exclusively occurs in Réunion and Senegal. Population genetics analysis of S. bermudense did not detect any demographic bottleneck associated with a possible founder effect, but fungal populations from regions where seagrape is introduced are little differentiated from the Caribbean ones, separated by thousands of kilometers, consistently with relatively recent introduction. Moreover, dry seagrape fruits carry Scleroderma spores, probably because, when drying on beach sand, they aggregate spores from the spore bank accumulated by semi-hypogeous Scleroderma sporocarps. Aggregated spores inoculate seedlings, and their abundance may limit the founder effect after seagrape introduction. This rare pseudo-vertical transmission of mycorrhizal fungi likely contributed to efficient and repeated seagrape/Scleroderma co-introductions.},
}
@article {pmid29533208,
year = {2018},
author = {Federico, C and Lombardo, D and La Porta, N and Pappalardo, AM and Ferrito, V and Lombardo, F and Saccone, S},
title = {Rapid molecular identification of necrophagous diptera by means of variable-length intron sequences in the wingless gene.},
journal = {Journal of forensic and legal medicine},
volume = {56},
number = {},
pages = {66-72},
doi = {10.1016/j.jflm.2018.03.003},
pmid = {29533208},
issn = {1878-7487},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Diptera/*genetics ; Electron Transport Complex IV/genetics ; Entomology ; Forensic Sciences ; *Introns ; Larva ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Wnt1 Protein/*genetics ; },
abstract = {The arrival of arthropods at a corpse exhibits specific temporal patterns, and Diptera play a key role in the initial stages of the decomposition process. Thus, the correct species assignment of the insect larvae found on a decomposing body is an important step in forensic investigations. Here, we describe a molecular procedure to define the species at larval age found on a corpse more quickly and easily than current systems. Our method involves a unique PCR amplification of a DNA segment within the evolutionarily conserved wingless gene, involved in embryo development. The amplified DNA segment contains the fourth intron of wingless, which we found to be variable in length, from about 800 to 3000 bp, among species of necrophagous Diptera. The identification of the amplified segment size in species from Lucilia, Calliphora and Sarcophaga genera, allowed us to determine the species at larval age collected in the early stages of a decomposing body, with a simple PCR amplification and subsequent electrophoresis. This procedure may help in forensic investigations to estimate the minimum Post Mortem Interval (PMI-min) of a body colonized by these larvae, avoiding the use of time-consuming and/or more expensive procedures.},
}
@article {pmid29532636,
year = {2018},
author = {Summa, M and Henttonen, H and Maunula, L},
title = {Human noroviruses in the faeces of wild birds and rodents-new potential transmission routes.},
journal = {Zoonoses and public health},
volume = {65},
number = {5},
pages = {512-518},
doi = {10.1111/zph.12461},
pmid = {29532636},
issn = {1863-2378},
mesh = {Animals ; Animals, Wild ; Birds/*virology ; Caliciviridae Infections/*transmission/virology ; Feces/*virology ; Humans ; Mice ; Norovirus/genetics/*isolation &amp; purification ; Phylogeny ; Rats ; Rodentia/*virology ; Seasons ; },
abstract = {Human noroviruses (HuNoVs) are one of the leading global causes of diarrhoeal diseases and are transmitted mainly from person to person but also through contaminated food, water and fomites. The possible zoonotic nature of NoVs has occasionally been discussed, although the viruses are generally considered to be host-species-specific. We investigated whether wild birds and rodents could serve as carriers of HuNoVs, thereby transmitting the virus to humans directly or indirectly by contaminating foods. All samples, 115 avian and 100 rat faeces collected in springs 2009-2013 from dump sites, and 85 faeces from yellow-necked mice trapped in late autumn 2008 and 2009 after the rodents entered human settlements due to the first night frosts, were screened for HuNoV using real-time reverse transcription PCR. HuNoVs were detected in 31 (27%) faecal samples of wild birds, in two (2%) faecal samples of rats and in no samples of mice. Most (25) of the positive bird samples and both rat samples contained genogroup II, and six positive bird samples contained genogroup I HuNoV. The avian species shedding faeces containing HuNoVs were identified as gulls and crows using DNA barcoding. Our results show that wildlife, birds and rats in particular, is capable of spreading HuNoVs in the environment.},
}
@article {pmid29531713,
year = {2018},
author = {Elías-Gutiérrez, M and Valdez-Moreno, M and Topan, J and Young, MR and Cohuo-Colli, JA},
title = {Improved protocols to accelerate the assembly of DNA barcode reference libraries for freshwater zooplankton.},
journal = {Ecology and evolution},
volume = {8},
number = {5},
pages = {3002-3018},
pmid = {29531713},
issn = {2045-7758},
abstract = {Currently, freshwater zooplankton sampling and identification methodologies have remained virtually unchanged since they were first established in the beginning of the XX century. One major contributing factor to this slow progress is the limited success of modern genetic methodologies, such as DNA barcoding, in several of the main groups. This study demonstrates improved protocols which enable the rapid assessment of most animal taxa inhabiting any freshwater system by combining the use of light traps, careful fixation at low temperatures using ethanol, and zooplankton-specific primers. We DNA-barcoded 2,136 specimens from a diverse array of taxonomic assemblages (rotifers, mollusks, mites, crustaceans, insects, and fishes) from several Canadian and Mexican lakes with an average sequence success rate of 85.3%. In total, 325 Barcode Index Numbers (BINs) were detected with only three BINs (two cladocerans and one copepod) shared between Canada and Mexico, suggesting a much narrower distribution range of freshwater zooplankton than previously thought. This study is the first to broadly explore the metazoan biodiversity of freshwater systems with DNA barcodes to construct a reference library that represents the first step for future programs which aim to monitor ecosystem health, track invasive species, or improve knowledge of the ecology and distribution of freshwater zooplankton.},
}
@article {pmid29527965,
year = {2019},
author = {Pogoda, CS and Keepers, KG and Hamsher, SE and Stepanek, JG and Kane, NC and Kociolek, JP},
title = {Comparative analysis of the mitochondrial genomes of six newly sequenced diatoms reveals group II introns in the barcoding region of cox1.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {1},
pages = {43-51},
doi = {10.1080/24701394.2018.1450397},
pmid = {29527965},
issn = {2470-1408},
mesh = {Diatoms/classification/*genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; *Genome, Mitochondrial ; *Introns ; Phylogeny ; *Polymorphism, Genetic ; Retroelements ; Sequence Alignment ; },
abstract = {Diatoms are the most diverse lineage of algae and at the base of most aquatic food webs, but only 11 of their mitochondrial genomes have been described. Herein, we present the mitochondrial genomes of six diatom species, including: Melosira undulata, Nitzschia alba, Surirella sp., Entomoneis sp., Halamphora coffeaeformis, and Halamphora calidilacuna. Comparison of these six genomes to the 11 currently published diatom mitochondrial genomes revealed a novel ubiquitous feature block consisting of tatC-orf157-rps11. The presence of intronic retrotransposable elements in the barcoding region of cox1 in the Halamphora genomes may explain historic difficulty (especially PCR) with cox1 as a universal barcode for diatoms. Our analysis suggests that high rates of variability in number and position of introns, in many commonly used coding sequences, prevent these from being universally viable as barcodes for diatoms. Therefore, we suggest researchers examine the chloroplast and/or nuclear genomes for universal barcoding markers.},
}
@article {pmid29527448,
year = {2018},
author = {Hegde, S and Saini, A and Hegde, HV and Kholkute, SD and Roy, S},
title = {Molecular identification of Saraca asoca from its substituents and adulterants.},
journal = {3 Biotech},
volume = {8},
number = {3},
pages = {161},
pmid = {29527448},
issn = {2190-572X},
abstract = {ABSTRACT: Saraca asoca (Roxb.) De Wilde is an important medicinal plant from the Western Ghats of India, traditionally used in treatment of various gynecological disorders. Increasing commercial demand and decreasing numbers has resulted in this plant becoming endangered with crude drug materials being extensively substituted/adulterated with other plant species. The present study was undertaken with the objective of development and evaluation of multivariate cluster analysis of ISSR fingerprints against rbcL-based DNA barcodes as tool to understand the relationships and to differentiate common adulterants and substituents from S. asoca. ISSR-based Hierarchical Cluster Analysis was carried out on 41 samples of S. asoca and 5 each of the 5 common substituent/adulterant plants and the clustering patterns were evaluated against DNA-sequence-based barcoding of rbcL region of their plastids. Factorial analysis and Principal Coordinate Analysis revealed distinct groups of genetic pools of respective taxa thereby confirming the utility of ISSR fingerprinting as a useful tool for differentiation between the genuine and the adulterants/substituents. NCBI-BLAST search on DNA barcode rbcL region confirmed the results of ISSR assays. Therefore, our study demonstrated the utility of simple, cost-effective method of ISSR fingerprinting coupled with rbcL barcoding in differentiating this important medicinal plant from its common adulterants/substituents.},
}
@article {pmid29524146,
year = {2018},
author = {Bashtrykov, P and Jeltsch, A},
title = {DNA Methylation Analysis by Bisulfite Conversion Coupled to Double Multiplexed Amplicon-Based Next-Generation Sequencing (NGS).},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1767},
number = {},
pages = {367-382},
doi = {10.1007/978-1-4939-7774-1_20},
pmid = {29524146},
issn = {1940-6029},
mesh = {Base Sequence ; DNA/analysis/genetics ; *DNA Methylation ; Genomics/methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Polymerase Chain Reaction/methods ; Sulfites/chemistry ; },
abstract = {Methylation of cytosine bases in DNA is one of the main epigenetic signals regulating gene expression and chromatin structure. The distribution of DNA methylation in the genome has a cell-type-specific pattern and can be modulated by internal or external stimuli. One of the most powerful approaches to investigate DNA methylation patterns is bisulfite conversion of the DNA followed by DNA sequencing, which allows to determine methylation patterns at a single-cytosine resolution. Here, we present a protocol for bisulfite DNA methylation analysis of targeted genomic regions using amplicon-based next-generation sequencing (NGS) on an Illumina sequencing system. We use a PCR-free library generation approach and implement a nested strategy for double molecular barcoding of samples (combining indexing of adapters and in-line barcoding of individual amplicons) which allows highly multiplexed sequencing. Also, we discuss the main limitations of this technology in particular in relation to clonal DNA amplification and other PCR artifacts.},
}
@article {pmid29523951,
year = {2018},
author = {Thormann, B and Ahrens, D and Espinosa, CI and Armijos, DM and Wagner, T and Wägele, JW and Peters, MK},
title = {Small-scale topography modulates elevational α-, β- and γ-diversity of Andean leaf beetles.},
journal = {Oecologia},
volume = {187},
number = {1},
pages = {181-189},
pmid = {29523951},
issn = {1432-1939},
support = {WA 530/46-1//Deutsche Forschungsgemeinschaft (DE)/International ; },
mesh = {Altitude ; Animals ; Biodiversity ; *Coleoptera ; Ecuador ; Forests ; },
abstract = {Elevational diversity gradients are typically studied without considering the complex small-scale topography of large mountains, which generates habitats of strongly different environmental conditions within the same elevational zones. Here we analyzed the importance of small-scale topography for elevational diversity patterns of hyperdiverse tropical leaf beetles (Coleoptera: Chrysomelidae). We compared patterns of elevational diversity and species composition of beetles in two types of forests (on mountain ridges and in valleys) and analyzed whether differences in the rate of species turnover among forest habitats lead to shifts in patterns of elevational diversity when scaling up from the local study site to the elevational belt level. We sampled beetle assemblages at 36 sites in the Podocarpus National Park, Ecuador, which were equally distributed over two forest habitats and three elevational levels. DNA barcoding and Poisson tree processes modelling were used to delimitate putative species. On average, local leaf beetle diversity showed a clear hump-shaped pattern. However, only diversity in forests on mountain ridges peaked at mid-elevation, while beetle diversity in valleys was similarly high at low- and mid-elevation and only declined at highest elevations. A higher turnover of species assemblages at lower than at mid-elevations caused a shift from a hump-shaped diversity pattern found at the local level to a low-elevation plateau pattern (with similar species numbers at low and mid-elevation) at the elevational belt level. Our study reveals an important role of small-scale topography and spatial scale for the inference on gradients of elevational species diversity.},
}
@article {pmid29523803,
year = {2018},
author = {Porter, TM and Hajibabaei, M},
title = {Automated high throughput animal CO1 metabarcode classification.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {4226},
pmid = {29523803},
issn = {2045-2322},
mesh = {Automation ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Environmental Monitoring ; },
abstract = {We introduce a method for assigning names to CO1 metabarcode sequences with confidence scores in a rapid, high-throughput manner. We compiled nearly 1 million CO1 barcode sequences appropriate for classifying arthropods and chordates. Compared to our previous Insecta classifier, the current classifier has more than three times the taxonomic coverage, including outgroups, and is based on almost five times as many reference sequences. Unlike other popular rDNA metabarcoding markers, we show that classification performance is similar across the length of the CO1 barcoding region. We show that the RDP classifier can make taxonomic assignments about 19 times faster than the popular top BLAST hit method and reduce the false positive rate from nearly 100% to 34%. This is especially important in large-scale biodiversity and biomonitoring studies where datasets can become very large and the taxonomic assignment problem is not trivial. We also show that reference databases are becoming more representative of current species diversity but that gaps still exist. We suggest that it would benefit the field as a whole if all investigators involved in metabarocoding studies, through collaborations with taxonomic experts, also planned to barcode representatives of their local biota as a part of their projects.},
}
@article {pmid29522539,
year = {2018},
author = {Dvirnas, A and Pichler, C and Stewart, CL and Quaderi, S and Nyberg, LK and Müller, V and Kumar Bikkarolla, S and Kristiansson, E and Sandegren, L and Westerlund, F and Ambjörnsson, T},
title = {Facilitated sequence assembly using densely labeled optical DNA barcodes: A combinatorial auction approach.},
journal = {PloS one},
volume = {13},
number = {3},
pages = {e0193900},
pmid = {29522539},
issn = {1932-6203},
mesh = {*Algorithms ; Benzoxazoles/metabolism ; Binding, Competitive ; Chromosomes/chemistry ; Computer Simulation ; Contig Mapping/*methods ; *DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Models, Genetic ; Netropsin/metabolism ; Plasmids/genetics ; Proof of Concept Study ; Quinolinium Compounds/metabolism ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Alignment ; },
abstract = {The output from whole genome sequencing is a set of contigs, i.e. short non-overlapping DNA sequences (sizes 1-100 kilobasepairs). Piecing the contigs together is an especially difficult task for previously unsequenced DNA, and may not be feasible due to factors such as the lack of sufficient coverage or larger repetitive regions which generate gaps in the final sequence. Here we propose a new method for scaffolding such contigs. The proposed method uses densely labeled optical DNA barcodes from competitive binding experiments as scaffolds. On these scaffolds we position theoretical barcodes which are calculated from the contig sequences. This allows us to construct longer DNA sequences from the contig sequences. This proof-of-principle study extends previous studies which use sparsely labeled DNA barcodes for scaffolding purposes. Our method applies a probabilistic approach that allows us to discard "foreign" contigs from mixed samples with contigs from different types of DNA. We satisfy the contig non-overlap constraint by formulating the contig placement challenge as a combinatorial auction problem. Our exact algorithm for solving this problem reduces computational costs compared to previous methods in the combinatorial auction field. We demonstrate the usefulness of the proposed scaffolding method both for synthetic contigs and for contigs obtained using Illumina sequencing for a mixed sample with plasmid and chromosomal DNA.},
}
@article {pmid29521145,
year = {2019},
author = {Robert, R and Rodrigues, KF and Waheed, Z and Kumar, SV},
title = {Extensive sharing of mitochondrial COI and CYB haplotypes among reef-building staghorn corals (Acropora spp.) in Sabah, North Borneo.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {1},
pages = {16-23},
doi = {10.1080/24701394.2018.1448080},
pmid = {29521145},
issn = {2470-1408},
mesh = {Animals ; Anthozoa/*genetics ; Borneo ; Cytochromes b/*genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; *Haplotypes ; Selection, Genetic ; },
abstract = {This study is aimed at establishing a baseline on the genetic diversity of the Acropora corals of Sabah, North Borneo based on variations in the partial COI and CYB nucleotide sequences. Comparison across 50 shallow-water Acropora morphospecies indicated that the low substitution rates in the two genes were due to negative selection and that rate heterogeneity between them was asymmetric. CYB appeared to have evolved faster than COI in the Acropora as indicated by differences in the rate of pairwise genetic distance, degrees of transition bias (Ts/Tv), synonymous-to-nonsynonymous rate ratio (dN/dS), and substitution patterns at the three codon positions. Despite the relatively high haplotype diversity (Hd), nucleotide diversity (π) of the haplotype datasets was low due to stringent purifying selection operating on the genes. Subsequently, we identified individual COI and CYB haplotypes that were each extensively shared across sympatrically and allopatrically distributed Indo-Pacific Acropora. These reciprocally common mtDNA types were suspected to be ancestral forms of the genes whereas other haplotypes have mostly evolved from autoapomorphic mutations which have not been fixed within the species even though they are selectively neutral. To our knowledge, this is the first report on DNA barcodes of Acropora species in North Borneo and this understanding will play an important role in the management and conservation of these important reef-building corals.},
}
@article {pmid29520295,
year = {2018},
author = {Paixão, RV and Ribolli, J and Zaniboni-Filho, E},
title = {Genetic Variation of the Endangered Neotropical Catfish Steindachneridion scriptum (Siluriformes: Pimelodidae).},
journal = {Frontiers in genetics},
volume = {9},
number = {},
pages = {48},
pmid = {29520295},
issn = {1664-8021},
abstract = {Steindachneridion scriptum is an important species as a resource for fisheries and aquaculture; it is currently threatened and has a reduced occurrence in South America. The damming of rivers, overfishing, and contamination of freshwater environments are the main impacts on the maintenance of this species. We accessed the genetic diversity and structure of S. scriptum using the DNA barcode and control region (D-loop) sequences of 43 individuals from the Upper Uruguay River Basin (UUR) and 10 sequences from the Upper Paraná River Basin (UPR), which were obtained from GenBank. S. scriptum from the UUR and the UPR were assigned in two distinct molecular operational taxonomic units (MOTUs) with higher inter-specific K2P distance than the optimum threshold (OT = 0.0079). The COI Intra-MOTU distances of S. scriptum specimens from the UUR ranged from 0.0000 to 0.0100. The control region indicated a high number of haplotypes and low nucleotide diversity, compatible with a new population in recent expansion process. Genetic structure was observed, with high differentiation between UUR and UPR basins, identified by BAPS, haplotype network, AMOVA (FST = 0.78, p < 0.05) and Mantel test. S. scriptum from the UUR showed a slight differentiation (FST = 0.068, p < 0.05), but not isolation-by-distance. Negative values of Tajima's D and Fu's Fs suggest recent demographic oscillations. The Bayesian skyline plot analysis indicated possible population expansion from beginning 2,500 years ago and a recent reduction in the population size. Low nucleotide diversity, spatial population structure, and the reduction of effective population size should be considered for the planning of strategies aimed at the conservation and rehabilitation of this important fisheries resource.},
}
@article {pmid29514522,
year = {2019},
author = {Wang, ZL and Wang, TZ and Zhu, HF and Wang, ZY and Yu, XP},
title = {DNA barcoding evaluation and implications for phylogenetic relationships in ladybird beetles (Coleoptera: Coccinellidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {30},
number = {1},
pages = {1-8},
doi = {10.1080/24701394.2018.1446950},
pmid = {29514522},
issn = {2470-1408},
mesh = {Animals ; Coleoptera/classification/*genetics ; DNA Barcoding, Taxonomic/methods/standards ; Electron Transport Complex IV/genetics ; Insect Proteins/genetics ; *Phylogeny ; },
abstract = {Ladybird beetles (Coleoptera: Coccinellidae), with broad morphological diversity, wide geographic distribution and substantial agricultural significance, are a challenging group for taxonomists and phylogenetics. As a promising tool to identify and discover new species, DNA barcoding might offer significant potential for identification, taxonomy and phylogeny of ladybird beetles. In the present study, a total of 1364 COI (cytochrome C oxidase subunit I) sequences representing 128 species from 52 genera of ladybird beetles were screened for barcoding evaluation and phylogenetic analysis. Our results from the barcoding analysis revealed that COI displays a similar level of species identification efficiency (nearly 90%) either based on Kimura two-parameter (K2P) distances calculation or on simplified neighbour-joining (NJ) tree construction. The phylogenetic relationships within the family Coccinellidae was analyzed by Bayesian-inference (BI) method. The phylogenetic results confirmed the monophyly of the subfamilies Microweisinae and Coccinellinae sensu Ślipiński (2007), and suggested that the subfamilies Coccidulinae, Chilocorinae and Scymninae are paraphyletic. However, the phylogenetic relationships among different subfamilies are not clearly defined and thus remain to be thoroughly studied. Overall, our study confirmed the usefulness of DNA barcoding for coccinellid species identification and phylogenetic inference.},
}
@article {pmid29514085,
year = {2018},
author = {Lin, DS and Kan, A and Gao, J and Crampin, EJ and Hodgkin, PD and Naik, SH},
title = {DiSNE Movie Visualization and Assessment of Clonal Kinetics Reveal Multiple Trajectories of Dendritic Cell Development.},
journal = {Cell reports},
volume = {22},
number = {10},
pages = {2557-2566},
doi = {10.1016/j.celrep.2018.02.046},
pmid = {29514085},
issn = {2211-1247},
mesh = {Animals ; Clone Cells ; Dendritic Cells/*cytology ; Kinetics ; Male ; Mice, Inbred C57BL ; Stochastic Processes ; *Time-Lapse Imaging ; },
abstract = {A thorough understanding of cellular development is incumbent on assessing the complexities of fate and kinetics of individual clones within a population. Here, we develop a system for robust periodical assessment of lineage outputs of thousands of transient clones and establishment of bona fide cellular trajectories. We appraise the development of dendritic cells (DCs) in fms-like tyrosine kinase 3 ligand culture from barcode-labeled hematopoietic stem and progenitor cells (HSPCs) by serially measuring barcode signatures and visualize these multidimensional data using developmental interpolated t-distributed stochastic neighborhood embedding (DiSNE) time-lapse movies. We identify multiple cellular trajectories of DC development that are characterized by distinct fate bias and expansion kinetics and determine that these are intrinsically programmed. We demonstrate that conventional DC and plasmacytoid DC trajectories are largely separated already at the HSPC stage. This framework allows systematic evaluation of clonal dynamics and can be applied to other steady-state or perturbed developmental systems.},
}
@article {pmid29511234,
year = {2018},
author = {Lavagi, I and Krebs, S and Simmet, K and Beck, A and Zakhartchenko, V and Wolf, E and Blum, H},
title = {Single-cell RNA sequencing reveals developmental heterogeneity of blastomeres during major genome activation in bovine embryos.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {4071},
pmid = {29511234},
issn = {2045-2322},
mesh = {Animals ; Blastomeres/*cytology ; Cattle ; *Embryonic Development ; *Gene Expression Regulation ; Gene Library ; Genetic Variation ; Sequence Analysis, DNA ; *Sequence Analysis, RNA ; *Single-Cell Analysis ; Time Factors ; *Transcriptional Activation ; },
abstract = {Embryonic development is initially controlled by maternal RNAs and proteins stored in the oocyte, until gene products gradually generated by the embryo itself take over. Major embryonic genome activation (EGA) in bovine embryos occurs at the eight- to 16-cell stage. Morphological observations, such as size of blastomeres and distribution of microvilli, suggested heterogeneity among individual cells already at this developmental stage. To address cell heterogeneity on the transcriptome level, we performed single-cell RNA sequencing of 161 blastomeres from 14 in vitro produced bovine embryos at Day 2 (n = 6) and Day 3 (n = 8) post fertilization. Complementary DNA libraries were prepared using the Single-Cell RNA-Barcoding and Sequencing protocol and sequenced. Non-supervised clustering of single-cell transcriptome profiles identified six clusters with specific sets of genes. Most embryos were comprised of cells from at least two different clusters. Sorting cells according to their transcriptome profiles resulted in a non-branched pseudo-time line, arguing against major lineage inclination events at this developmental stage. In summary, our study revealed heterogeneity of transcriptome profiles among single cells in bovine Day 2 and Day 3 embryos, suggesting asynchronous blastomere development during the phase of major EGA.},
}
@article {pmid29506565,
year = {2018},
author = {Sauvage, T and Plouviez, S and Schmidt, WE and Fredericq, S},
title = {TREE2FASTA: a flexible Perl script for batch extraction of FASTA sequences from exploratory phylogenetic trees.},
journal = {BMC research notes},
volume = {11},
number = {1},
pages = {164},
pmid = {29506565},
issn = {1756-0500},
support = {1455569//NSF DEB/ ; },
mesh = {*Biodiversity ; *Databases, Nucleic Acid ; *Phylogeny ; *Sequence Analysis, DNA ; *Software ; },
abstract = {OBJECTIVE: The body of DNA sequence data lacking taxonomically informative sequence headers is rapidly growing in user and public databases (e.g. sequences lacking identification and contaminants). In the context of systematics studies, sorting such sequence data for taxonomic curation and/or molecular diversity characterization (e.g. crypticism) often requires the building of exploratory phylogenetic trees with reference taxa. The subsequent step of segregating DNA sequences of interest based on observed topological relationships can represent a challenging task, especially for large datasets.<br><br>RESULTS: We have written TREE2FASTA, a Perl script that enables and expedites the sorting of FASTA-formatted sequence data from exploratory phylogenetic trees. TREE2FASTA takes advantage of the interactive, rapid point-and-click color selection and/or annotations of tree leaves in the popular Java tree-viewer FigTree to segregate groups of FASTA sequences of interest to separate files. TREE2FASTA allows for both simple and nested segregation designs to facilitate the simultaneous preparation of multiple data sets that may overlap in sequence content.},
}
@article {pmid29506533,
year = {2018},
author = {Simion, P and Belkhir, K and François, C and Veyssier, J and Rink, JC and Manuel, M and Philippe, H and Telford, MJ},
title = {A software tool 'CroCo' detects pervasive cross-species contamination in next generation sequencing data.},
journal = {BMC biology},
volume = {16},
number = {1},
pages = {28},
pmid = {29506533},
issn = {1741-7007},
support = {322790/ERC_/European Research Council/International ; BB/H006966/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Computational Biology/methods/*standards ; Databases, Genetic/*standards ; Gene Expression Profiling/methods/standards ; High-Throughput Nucleotide Sequencing/methods/*standards ; Hydrozoa ; *Phylogeny ; RNA, Messenger/analysis/*genetics ; Software/*standards ; Species Specificity ; },
abstract = {BACKGROUND: Multiple RNA samples are frequently processed together and often mixed before multiplex sequencing in the same sequencing run. While different samples can be separated post sequencing using sample barcodes, the possibility of cross contamination between biological samples from different species that have been processed or sequenced in parallel has the potential to be extremely deleterious for downstream analyses.<br><br>RESULTS: We present CroCo, a software package for identifying and removing such cross contaminants from assembled transcriptomes. Using multiple, recently published sequence datasets, we show that cross contamination is consistently present at varying levels in real data. Using real and simulated data, we demonstrate that CroCo detects contaminants efficiently and correctly. Using a real example from a molecular phylogenetic dataset, we show that contaminants, if not eliminated, can have a decisive, deleterious impact on downstream comparative analyses.<br><br>CONCLUSIONS: Cross contamination is pervasive in new and published datasets and, if undetected, can have serious deleterious effects on downstream analyses. CroCo is a database-independent, multi-platform tool, designed for ease of use, that efficiently and accurately detects and removes cross contamination in assembled transcriptomes to avoid these problems. We suggest that the use of CroCo should become a standard cleaning step when processing multiple samples for transcriptome sequencing.},
}
@article {pmid29505595,
year = {2018},
author = {Saraiva, JF and Souto, RNP and Scarpassa, VM},
title = {Molecular taxonomy and evolutionary relationships in the Oswaldoi-Konderi complex (Anophelinae: Anopheles: Nyssorhynchus) from the Brazilian Amazon region.},
journal = {PloS one},
volume = {13},
number = {3},
pages = {e0193591},
pmid = {29505595},
issn = {1932-6203},
mesh = {Animals ; Anopheles/*classification/*genetics ; Brazil ; DNA Barcoding, Taxonomic ; DNA, Intergenic/genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; *Evolution, Molecular ; Phylogeny ; },
abstract = {Recent studies have shown that Anopheles oswaldoi sensu lato comprises a cryptic species complex in South America. Anopheles konderi, which was previously raised to synonymy with An. oswaldoi, has also been suggested to form a species complex. An. oswaldoi has been incriminated as a malaria vector in some areas of the Brazilian Amazon, Colombia, Peru and Venezuela, but was not recognized as a vector in the remaining regions in its geographic distribution. The role of An. konderi as a malaria vector is unknown or has been misattributed to An. oswaldoi. The focus of this study was molecular identification to infer the evolutionary relationships and preliminarily delimit the geographic distribution of the members of these complexes in the Brazilian Amazon region. The specimens were sampled from 18 localities belonging to five states in the Brazilian Amazon and sequenced for two molecular markers: the DNA barcode region (COI gene of mitochondrial DNA) and Internal Transcribed Spacer 2 (ITS2 ribosomal DNA). COI (83 sequences) and ITS2 (27 sequences) datasets generated 43 and 10 haplotypes, respectively. Haplotype networks and phylogenetic analyses generated with the barcode region (COI gene) recovered five groups corresponding to An. oswaldoi s.s., An. oswaldoi B, An. oswaldoi A, An. konderi and An. sp. nr. konderi; all pairwise genetic distances were greater than 3%. The group represented by An. oswaldoi A exhibited three strongly supported lineages. The molecular dating indicated that the diversification process in these complexes started approximately 2.8 Mya, in the Pliocene. These findings confirm five very closely related species and present new records for these species in the Brazilian Amazon region. The paraphyly observed for the An. oswaldoi complex suggests that An. oswaldoi and An. konderi complexes may comprise a unique species complex named Oswaldoi-Konderi. Anopheles oswaldoi B may be a potential malaria vector in the extreme north of the Brazilian Amazon, whereas evidence of sympatry for the remaining species in other parts of the Brazilian Amazon (Acre, Amazonas, Pará and Rondônia) precluded identification of probable vectors in those areas.},
}
@article {pmid29505116,
year = {2018},
author = {Garganese, F and Ippolito, A and di Rienzo, V and Lotti, C and Montemurro, C and Sanzani, SM},
title = {A new high-resolution melting assay for genotyping Alternaria species causing citrus brown spot.},
journal = {Journal of the science of food and agriculture},
volume = {98},
number = {12},
pages = {4578-4583},
doi = {10.1002/jsfa.8986},
pmid = {29505116},
issn = {1097-0010},
mesh = {Alternaria/*chemistry/classification/*genetics/isolation &amp; purification ; Citrus/*microbiology ; DNA, Fungal/*chemistry/genetics ; Genotype ; Genotyping Techniques/*methods ; Plant Diseases/*microbiology ; Plant Leaves/microbiology ; Transition Temperature ; },
abstract = {BACKGROUND: Alternaria brown spot is one of the most important diseases of tangerines and their hybrids worldwide. To set up effective control strategy, the accurate detection and identification of the species responsible for the diseases is crucial. However, characterization based on morphology and/or multilocus genetic approaches is time consuming, requires great expertise and sometimes is not conclusive. Therefore, the set-up of a rapid and efficient DNA-based assay might be of paramount importance. High-resolution melting (HRM) analysis represents an interesting tool for the uncovering of nucleotide variations as small as one base difference and, as such, relevant to species characterization.<br><br>RESULTS: In the present investigation, an HRM assay based on the Alternaria barcoding region OPA1-3 was set up. Specimen strains of the main citrus-associated Alternaria species and morphotypes generated distinct and normalized profiles, allowing their differentiation when HRM-tested. Moreover, when the assay was used to screen an Alternaria collection from citrus fruit and leaves, it distributed the 180 isolates in three independent clusters, readily and consistently resolved. Isolates were identified as belonging to the species Alternaria alternata and the species complex A. arborescens. Within A. alternata, the morphotypes alternata (77% of the collection) and limoniasperae (17% of the collection) were present.<br><br>CONCLUSIONS: Although further validation experiments will be performed to optimize the assay for a diagnostic use, this HRM approach might represent a rapid, sensitive and specific method for the detection and identification of Alternaria spp. responsible for citrus brown spot disease. &#xa9; 2018 Society of Chemical Industry.},
}
@article {pmid29503478,
year = {2017},
author = {Crous, PW and Wingfield, MJ and Burgess, TI and Carnegie, AJ and Hardy, GESJ and Smith, D and Summerell, BA and Cano-Lira, JF and Guarro, J and Houbraken, J and Lombard, L and Martín, MP and Sandoval-Denis, M and Alexandrova, AV and Barnes, CW and Baseia, IG and Bezerra, JDP and Guarnaccia, V and May, TW and Hernández-Restrepo, M and Stchigel, AM and Miller, AN and Ordoñez, ME and Abreu, VP and Accioly, T and Agnello, C and Agustin Colmán, A and Albuquerque, CC and Alfredo, DS and Alvarado, P and Araújo-Magalhães, GR and Arauzo, S and Atkinson, T and Barili, A and Barreto, RW and Bezerra, JL and Cabral, TS and Camello Rodríguez, F and Cruz, RHSF and Daniëls, PP and da Silva, BDB and de Almeida, DAC and de Carvalho Júnior, AA and Decock, CA and Delgat, L and Denman, S and Dimitrov, RA and Edwards, J and Fedosova, AG and Ferreira, RJ and Firmino, AL and Flores, JA and García, D and Gené, J and Giraldo, A and Góis, JS and Gomes, AAM and Gonçalves, CM and Gouliamova, DE and Groenewald, M and Guéorguiev, BV and Guevara-Suarez, M and Gusmão, LFP and Hosaka, K and Hubka, V and Huhndorf, SM and Jadan, M and Jurjević, &#x17d; and Kraak, B and Kučera, V and Kumar, TKA and Kušan, I and Lacerda, SR and Lamlertthon, S and Lisboa, WS and Loizides, M and Luangsa-Ard, JJ and Lysková, P and Mac Cormack, WP and Macedo, DM and Machado, AR and Malysheva, EF and Marinho, P and Matočec, N and Meijer, M and Mešić, A and Mongkolsamrit, S and Moreira, KA and Morozova, OV and Nair, KU and Nakamura, N and Noisripoom, W and Olariaga, I and Oliveira, RJV and Paiva, LM and Pawar, P and Pereira, OL and Peterson, SW and Prieto, M and Rodríguez-Andrade, E and Rojo De Blas, C and Roy, M and Santos, ES and Sharma, R and Silva, GA and Souza-Motta, CM and Takeuchi-Kaneko, Y and Tanaka, C and Thakur, A and Smith, MT and Tkalčec, Z and Valenzuela-Lopez, N and van der Kleij, P and Verbeken, A and Viana, MG and Wang, XW and Groenewald, JZ},
title = {Fungal Planet description sheets: 625-715.},
journal = {Persoonia},
volume = {39},
number = {},
pages = {270-467},
pmid = {29503478},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Antarctica: Cadophora antarctica from soil. Australia: Alfaria dandenongensis on Cyperaceae, Amphosoma persooniae on Persoonia sp., Anungitea nullicana on Eucalyptus sp., Bagadiella eucalypti on Eucalyptus globulus, Castanediella eucalyptigena on Eucalyptus sp., Cercospora dianellicola on Dianella sp., Cladoriella kinglakensis on Eucalyptus regnans, Cladoriella xanthorrhoeae (incl. Cladoriellaceae fam. nov. and Cladoriellales ord. nov.) on Xanthorrhoea sp., Cochlearomyces eucalypti (incl. Cochlearomyces gen. nov. and Cochlearomycetaceae fam. nov.) on Eucalyptus obliqua, Codinaea lambertiae on Lambertia formosa, Diaporthe obtusifoliae on Acacia obtusifolia, Didymella acaciae on Acacia melanoxylon, Dothidea eucalypti on Eucalyptus dalrympleana, Fitzroyomyces cyperi (incl. Fitzroyomyces gen. nov.) on Cyperaceae, Murramarangomyces corymbiae (incl. Murramarangomyces gen. nov., Murramarangomycetaceae fam. nov. and Murramarangomycetales ord. nov.) on Corymbia maculata, Neoanungitea eucalypti (incl. Neoanungitea gen. nov.) on Eucalyptus obliqua, Neoconiothyrium persooniae (incl. Neoconiothyrium gen. nov.) on Persoonia laurina subsp. laurina, Neocrinula lambertiae (incl. Neocrinulaceae fam. nov.) on Lambertia sp., Ochroconis podocarpi on Podocarpus grayae, Paraphysalospora eucalypti (incl. Paraphysalospora gen. nov.) on Eucalyptus sieberi, Pararamichloridium livistonae (incl. Pararamichloridium gen. nov., Pararamichloridiaceae fam. nov. and Pararamichloridiales ord. nov.) on Livistona sp., Pestalotiopsis dianellae on Dianella sp., Phaeosphaeria gahniae on Gahnia aspera, Phlogicylindrium tereticornis on Eucalyptus tereticornis, Pleopassalora acaciae on Acacia obliquinervia, Pseudodactylaria xanthorrhoeae (incl. Pseudodactylaria gen. nov., Pseudodactylariaceae fam. nov. and Pseudodactylariales ord. nov.) on Xanthorrhoea sp., Pseudosporidesmium lambertiae (incl. Pseudosporidesmiaceae fam. nov.) on Lambertia formosa, Saccharata acaciae on Acacia sp., Saccharata epacridis on Epacris sp., Saccharata hakeigena on Hakea sericea, Seiridium persooniae on Persoonia sp., Semifissispora tooloomensis on Eucalyptus dunnii, Stagonospora lomandrae on Lomandra longifolia, Stagonospora victoriana on Poaceae, Subramaniomyces podocarpi on Podocarpus elatus, Sympoventuria melaleucae on Melaleuca sp., Sympoventuria regnans on Eucalyptus regnans, Trichomerium eucalypti on Eucalyptus tereticornis, Vermiculariopsiella eucalypticola on Eucalyptus dalrympleana, Verrucoconiothyrium acaciae on Acacia falciformis, Xenopassalora petrophiles (incl. Xenopassalora gen. nov.) on Petrophile sp., Zasmidium dasypogonis on Dasypogon sp., Zasmidium gahniicola on Gahnia sieberiana.Brazil: Achaetomium lippiae on Lippia gracilis, Cyathus isometricus on decaying wood, Geastrum caririense on soil, Lycoperdon demoulinii (incl. Lycoperdon subg. Arenicola) on soil, Megatomentella cristata (incl. Megatomentella gen. nov.) on unidentified plant, Mutinus verrucosus on soil, Paraopeba schefflerae (incl. Paraopeba gen. nov.) on Schefflera morototoni, Phyllosticta catimbauensis on Mandevilla catimbauensis, Pseudocercospora angularis on Prunus persica, Pseudophialophora sorghi on Sorghum bicolor, Spumula piptadeniae on Piptadenia paniculata.Bulgaria: Yarrowia parophonii from gut of Parophonus hirsutulus. Croatia: Pyrenopeziza velebitica on Lonicera borbasiana.Cyprus: Peziza halophila on coastal dunes. Czech Republic: Aspergillus contaminans from human fingernail. Ecuador: Cuphophyllus yacurensis on forest soil, Ganoderma podocarpense on fallen tree trunk. England: Pilidium anglicum (incl. Chaetomellales ord. nov.) on Eucalyptus sp. France: Planamyces parisiensis (incl. Planamyces gen. nov.) on wood inside a house. French Guiana: Lactifluus ceraceus on soil. Germany: Talaromyces musae on Musa sp. India: Hyalocladosporiella cannae on Canna indica, Nothophoma raii from soil. Italy: Setophaeosphaeria citri on Citrus reticulata, Yuccamyces citri on Citrus limon.Japan: Glutinomyces brunneus (incl. Glutinomyces gen. nov.) from roots of Quercus sp. Netherlands (all from soil): Collariella hilkhuijsenii, Fusarium petersiae, Gamsia kooimaniorum, Paracremonium binnewijzendii, Phaeoisaria annesophieae, Plectosphaerella niemeijerarum, Striaticonidium deklijnearum, Talaromyces annesophieae, Umbelopsis wiegerinckiae, Vandijckella johannae (incl. Vandijckella gen. nov. and Vandijckellaceae fam. nov.), Verhulstia trisororum (incl. Verhulstia gen. nov.). New Zealand: Lasiosphaeria similisorbina on decorticated wood. Papua New Guinea: Pseudosubramaniomyces gen. nov. (based on Pseudosubramaniomyces fusisaprophyticus comb. nov.). Slovakia: Hemileucoglossum pusillum on soil. South Africa: Tygervalleyomyces podocarpi (incl. Tygervalleyomyces gen. nov.) on Podocarpus falcatus.Spain: Coniella heterospora from herbivorous dung, Hymenochaete macrochloae on Macrochloa tenacissima, Ramaria cistophila on shrubland of Cistus ladanifer.Thailand: Polycephalomyces phaothaiensis on Coleoptera larvae, buried in soil. Uruguay: Penicillium uruguayense from soil. Vietnam: Entoloma nigrovelutinum on forest soil, Volvariella morozovae on wood of unknown tree. Morphological and culture characteristics along with DNA barcodes are provided.},
}
@article {pmid29503476,
year = {2017},
author = {Skrede, I and Carlsen, T and Schumacher, T},
title = {A synopsis of the saddle fungi (Helvella: Ascomycota) in Europe - species delimitation, taxonomy and typification.},
journal = {Persoonia},
volume = {39},
number = {},
pages = {201-253},
pmid = {29503476},
issn = {0031-5850},
abstract = {Helvella is a widespread, speciose genus of large apothecial ascomycetes (Pezizomycete: Pezizales) that are found in terrestrial biomes of the Northern and Southern Hemispheres. This study represents a beginning on assessing species limits and applying correct names for Helvella species based on type material and specimens in the university herbaria (fungaria) of Copenhagen (C), Harvard (FH) and Oslo (O). We use morphology and phylogenetic evidence from four loci - heat shock protein 90 (hsp), translation elongation factor alpha (tef), RNA polymerase II (rpb2) and the nuclear large subunit ribosomal DNA (LSU) - to assess species boundaries in an expanded sample of Helvella specimens from Europe. We combine the morphological and phylogenetic information from 55 Helvella species from Europe with a small sample of Helvella species from other regions of the world. Little intraspecific variation was detected within the species using these molecular markers; hsp and rpb2 markers provided useful barcodes for species delimitation in this genus, while LSU provided more variable resolution among the pertinent species. We discuss typification issues and identify molecular characteristics for 55 European Helvella species, designate neo- and epitypes for 30 species, and describe seven Helvella species new to science, i.e., H. alpicola, H. alpina, H. carnosa, H. danica, H. nannfeldtii, H. pubescens and H. scyphoides.},
}
@article {pmid29503468,
year = {2017},
author = {Zhang, ZF and Liu, F and Zhou, X and Liu, XZ and Liu, SJ and Cai, L},
title = {Culturable mycobiota from Karst caves in China, with descriptions of 20 new species.},
journal = {Persoonia},
volume = {39},
number = {},
pages = {1-31},
pmid = {29503468},
issn = {0031-5850},
abstract = {Karst caves are distinctly characterised by darkness, low to moderate temperatures, high humidity, and scarcity of organic matter. During the years of 2014-2015, we explored the mycobiota in two unnamed Karst caves in Guizhou province, China, and obtained 563 fungal strains via the dilution plate method. Preliminary ITS analyses of these strains suggested that they belonged to 246 species in 116 genera, while 23.5 % were not identified to species level. Among these species, 85.8 % (211 species) belonged to Ascomycota; 7.3 % (18 species) belonged to Basidiomycota; 6.9 % (17 species) belonged to Mucoromycotina. The majority of these species have been previously known from other environments, mostly from plants or animals as pathogens, endophytes or via a mycorrhizal association. We also found that 59 % of these species were discovered for the first time from Karst caves, including 20 new species that are described in this paper. The phylogenetic tree based on LSU sequences revealed 20 new species were distributed in six different orders. In addition, ITS or multi-locus sequences were employed to infer the phylogenetic relationships of new taxa with closely related allies. We conclude that Karst caves encompass a high fungal diversity, including a number of previously unknown species. Novel species described include: Amphichorda guana, Auxarthronopsis guizhouensis, Biscogniauxia petrensis, Cladorrhinum globisporum, Collariella quadrum, Gymnoascus exasperatus, Humicola limonisporum, Metapochonia variabilis, Microascus anfractus, Microascus globulosus, Microdochium chrysanthemoides, Paracremonium variiforme, Pectinotrichum chinense, Phaeosphaeria fusispora, Ramophialophora globispora, Ramophialophora petraea, Scopulariopsis crassa, Simplicillium calcicola, Volutella aeria, and Wardomycopsis longicatenata.},
}
@article {pmid29492973,
year = {2018},
author = {Violi, B and Gaither, MR and Burns, F and Rus Hoelzel, A and Neat, F},
title = {Assessing ecological and molecular divergence between the closely related species Hydrolagus pallidus and H. affinis (Chimaeridae).},
journal = {Journal of fish biology},
volume = {92},
number = {4},
pages = {1211-1217},
doi = {10.1111/jfb.13572},
pmid = {29492973},
issn = {1095-8649},
mesh = {Animals ; Atlantic Ocean ; Bayes Theorem ; *DNA Barcoding, Taxonomic ; Ecology ; Electron Transport Complex IV/genetics ; Fishes/*classification ; Likelihood Functions ; Male ; *Phylogeny ; Scotland ; },
abstract = {This study investigated taxonomic validity of the pale ghost shark Hydrolagus pallidus Hardy &amp; Stehmann, 1990, which was described as a species distinct from the smalleyed rabbitfish H. affinis (de Brito Capello 1868). While few morphological characters distinguish the two taxa, a striking difference in sex ratio and fixed differences (1·1-1·6% divergence) in the cytochrome oxidase subunit I barcoding gene support the recognition of both species.},
}
@article {pmid29491019,
year = {2018},
author = {Normand, AC and Packeu, A and Cassagne, C and Hendrickx, M and Ranque, S and Piarroux, R},
title = {Nucleotide Sequence Database Comparison for Routine Dermatophyte Identification by Internal Transcribed Spacer 2 Genetic Region DNA Barcoding.},
journal = {Journal of clinical microbiology},
volume = {56},
number = {5},
pages = {},
pmid = {29491019},
issn = {1098-660X},
mesh = {Arthrodermataceae/*classification/*genetics/isolation &amp; purification ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Dermatomycoses/diagnosis/*microbiology ; Humans ; Phylogeny ; Prospective Studies ; Sequence Analysis, DNA ; },
abstract = {Conventional dermatophyte identification is based on morphological features. However, recent studies have proposed to use the nucleotide sequences of the rRNA internal transcribed spacer (ITS) region as an identification barcode of all fungi, including dermatophytes. Several nucleotide databases are available to compare sequences and thus identify isolates; however, these databases often contain mislabeled sequences that impair sequence-based identification. We evaluated five of these databases on a clinical isolate panel. We selected 292 clinical dermatophyte strains that were prospectively subjected to an ITS2 nucleotide sequence analysis. Sequences were analyzed against the databases, and the results were compared to clusters obtained via DNA alignment of sequence segments. The DNA tree served as the identification standard throughout the study. According to the ITS2 sequence identification, the majority of strains (255/292) belonged to the genus Trichophyton, mainly T. rubrum complex (n = 184), T. interdigitale (n = 40), T. tonsurans (n = 26), and T. benhamiae (n = 5). Other genera included Microsporum (e.g., M. canis [n = 21], M. audouinii [n = 10], Nannizzia gypsea [n = 3], and Epidermophyton [n = 3]). Species-level identification of T. rubrum complex isolates was an issue. Overall, ITS DNA sequencing is a reliable tool to identify dermatophyte species given that a comprehensive and correctly labeled database is consulted. Since many inaccurate identification results exist in the DNA databases used for this study, reference databases must be verified frequently and amended in line with the current revisions of fungal taxonomy. Before describing a new species or adding a new DNA reference to the available databases, its position in the phylogenetic tree must be verified.},
}
@article {pmid29489381,
year = {2018},
author = {Paunovska, K and Sago, CD and Monaco, CM and Hudson, WH and Castro, MG and Rudoltz, TG and Kalathoor, S and Vanover, DA and Santangelo, PJ and Ahmed, R and Bryksin, AV and Dahlman, JE},
title = {A Direct Comparison of in Vitro and in Vivo Nucleic Acid Delivery Mediated by Hundreds of Nanoparticles Reveals a Weak Correlation.},
journal = {Nano letters},
volume = {18},
number = {3},
pages = {2148-2157},
pmid = {29489381},
issn = {1530-6992},
support = {T32 EB006343/EB/NIBIB NIH HHS/United States ; T32 EB021962/EB/NIBIB NIH HHS/United States ; T32 GM008433/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Cell Line ; Cells, Cultured ; *Drug Delivery Systems ; Endothelial Cells/metabolism ; Female ; Humans ; Lipids/*chemistry ; Macrophages/metabolism ; Mice ; Mice, Inbred C57BL ; Nanoparticles/*chemistry ; Nanotechnology ; Nucleic Acids/*administration &amp; dosage/pharmacokinetics ; },
abstract = {Endothelial cells and macrophages play active roles in disease and as a result are important targets for nucleic acid therapies. While thousands of chemically distinct lipid nanoparticles (LNPs) can be synthesized to deliver nucleic acids, studying more than a few LNPs in vivo is challenging. As a result, it is difficult to understand how nanoparticles target these cells in vivo. Using high throughput LNP barcoding, we quantified how well LNPs delivered DNA barcodes to endothelial cells and macrophages in vitro, as well as endothelial cells and macrophages isolated from the lung, heart, and bone marrow in vivo. We focused on two fundamental questions in drug delivery. First, does in vitro LNP delivery predict in vivo LNP delivery? By comparing how 281 LNPs delivered barcodes to endothelial cells and macrophages in vitro and in vivo, we found in vitro delivery did not predict in vivo delivery. Second, does LNP delivery change within the microenvironment of a tissue? We quantified how 85 LNPs delivered barcodes to eight splenic cell populations, and found that cell types derived from myeloid progenitors tended to be targeted by similar LNPs, relative to cell types derived from lymphoid progenitors. These data demonstrate that barcoded LNPs can elucidate fundamental questions about in vivo nanoparticle delivery.},
}
@article {pmid29486789,
year = {2018},
author = {Barber, J and Harrup, LE and Silk, R and Veronesi, E and Gubbins, S and Bachanek-Bankowska, K and Carpenter, S},
title = {Blood-feeding, susceptibility to infection with Schmallenberg virus and phylogenetics of Culicoides (Diptera: Ceratopogonidae) from the United Kingdom.},
journal = {Parasites &amp; vectors},
volume = {11},
number = {1},
pages = {116},
pmid = {29486789},
issn = {1756-3305},
support = {BBS/E/I/00001701/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/I/00007036/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 261504 (EDENext number -)//European Union FP7/International ; BBS/E/I/00007033/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/I/00007038/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Arboviruses/physiology ; Bunyaviridae Infections/epidemiology/transmission/*veterinary/virology ; Ceratopogonidae/classification/*genetics/physiology/*virology ; DNA Barcoding, Taxonomic ; Europe/epidemiology ; Feeding Behavior ; Female ; Genes, Mitochondrial/genetics ; Insect Vectors/genetics/physiology/virology ; Orthobunyavirus/*physiology ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Ruminants/parasitology/virology ; United Kingdom/epidemiology ; },
abstract = {BACKGROUND: Culicoides biting midges (Diptera: Ceratopogonidae) are responsible for the biological transmission of internationally important arboviruses of livestock. In 2011, a novel Orthobunyavirus was discovered in northern Europe causing congenital malformations and abortions in ruminants. From field studies, Culicoides were implicated in the transmission of this virus which was subsequently named Schmallenberg virus (SBV), but to date no assessment of susceptibility to infection of field populations under standardised laboratory conditions has been carried out. We assessed the influence of membrane type (chick skin, collagen, Parafilm M®) when offered in conjunction with an artificial blood-feeding system (Hemotek, UK) on field-collected Culicoides blood-feeding rates. Susceptibility to infection with SBV following blood-feeding on an SBV-blood suspension provided via either (i) the Hemotek system or via (ii) a saturated cotton wool pledglet was then compared. Schmallenberg virus susceptibility was defined by RT-qPCR of RNA extractions of head homogenates and related to Culicoides species and haplotype identifications based on the DNA barcode region of the mitochondrial cytochrome c oxidase 1 (cox1) gene.<br><br>RESULTS: Culicoides blood-feeding rates were low across all membrane types tested (7.5% chick skin, 0.0% for collagen, 4.4% Parafilm M&#xae;, with 6029 female Culicoides being offered a blood meal in total). Susceptibility to infection with SBV through membrane blood-feeding (8 of 109 individuals tested) and pledglet blood-feeding (1 of 94 individuals tested) was demonstrated for the Obsoletus complex, with both C. obsoletus (Meigen) and C. scoticus Downes &amp; Kettle susceptible to infection with SBV through oral feeding. Potential evidence of cryptic species within UK populations was found for the Obsoletus complex in phylogenetic analyses of cox1 DNA barcodes of 74 individuals assessed from a single field-site.<br><br>CONCLUSIONS: Methods described in this study provide the means to blood-feed Palaearctic Culicoides for vector competence studies and colonisation attempts. Susceptibility to SBV infection was 7.3% for membrane-fed members of the subgenus Avaritia and 1.1% for pledglet-fed. Both C. obsoletus and C. scoticus were confirmed as being susceptible to infection with SBV, with potential evidence of cryptic species within UK Obsoletus complex specimens, however the implications of cryptic diversity in the Obsoletus complex on arbovirus transmission remains unknown.},
}
@article {pmid29479511,
year = {2018},
author = {Santhosh Kumar, JU and Krishna, V and Seethapathy, GS and Ganesan, R and Ravikanth, G and Shaanker, RU},
title = {Assessment of adulteration in raw herbal trade of important medicinal plants of India using DNA barcoding.},
journal = {3 Biotech},
volume = {8},
number = {3},
pages = {135},
pmid = {29479511},
issn = {2190-572X},
abstract = {A number of studies have shown that there could be widespread substitution and/or adulteration (hereafter referred to as substitution) in raw herbal trade of medicinal plants. Substitution could potentially endanger the health and safety of the consumers. In this study, the extent of adulteration in raw herbal trade of 30 important medicinal plants in South India was analyzed. Biological reference material (BRM) consisting of taxonomically authenticated samples of each of the 30 species along with 14 other co-occurring and congeneric allied species that are likely to be used in adulteration was established. DNA barcode signatures of 124 BRM using two candidate regions, nr-ITS and psbA-trnH were identified. A total of 203 herbal trade samples representing the 30 medicinal plant species were collected from 34 locations in South India. Using the DNA barcode sequences of the BRM as reference, the analysis indicated that the substitution ranged from 20 to 100%. Overall, approximately 12% of the market samples were adulterated. Considering the potential health hazard that such adulteration can cause, the need for a national regulatory framework that can authenticate and regulate raw herbal trade in the country is discussed.},
}
@article {pmid29479121,
year = {2018},
author = {Wall-Palmer, D and Burridge, AK and Goetze, E and Stokvis, FR and Janssen, AW and Mekkes, L and Moreno-Alcántara, M and Bednaršek, N and Schiøtte, T and Sørensen, MV and Smart, CW and T C A Peijnenburg, K},
title = {Biogeography and genetic diversity of the atlantid heteropods.},
journal = {Progress in oceanography},
volume = {160},
number = {},
pages = {1-25},
pmid = {29479121},
issn = {0079-6611},
abstract = {The atlantid heteropods are regularly encountered, but rarely studied marine planktonic gastropods. Relying on a small (<14 mm), delicate aragonite shell and living in the upper ocean means that, in common with pteropods, atlantids are likely to be affected by imminent ocean changes. Variable shell morphology and widespread distributions indicate that the family is more diverse than the 23 currently known species. Uncovering this diversity is fundamental to determining the distribution of atlantids and to understanding their environmental tolerances. Here we present phylogenetic analyses of all described species of the family Atlantidae using 437 new and 52 previously published cytochrome c oxidase subunit 1 mitochondrial DNA (mtCO1) sequences. Specimens and published sequences were gathered from 32 Atlantic Ocean stations, 14 Indian Ocean stations and 21 Pacific Ocean stations between 35°N and 43°S. DNA barcoding and Automatic Barcode Gap Discovery (ABGD) proved to be valuable tools for the identification of described atlantid species, and also revealed ten additional distinct clades, suggesting that the diversity within this family has been underestimated. Only two of these clades displayed obvious morphological characteristics, demonstrating that much of the newly discovered diversity is hidden from morphology-based identification techniques. Investigation of six large atlantid collections demonstrated that 61% of previously described (morpho) species have a circumglobal distribution. Of the remaining 39%, two species were restricted to the Atlantic Ocean, five occurred in the Indian and Pacific oceans, one species was only found in the northeast Pacific Ocean, and one occurred only in the Southern Subtropical Convergence Zone. Molecular analysis showed that seven of the species with wide distributions were comprised of two or more clades that occupied distinct oceanographic regions. These distributions may suggest narrower environmental tolerances than the described morphospecies. Results provide an updated biogeography and mtCO1 reference dataset of the Atlantidae that may be used to identify atlantid species and provide a first step in understanding their evolutionary history and accurate distribution, encouraging the inclusion of this family in future plankton research.},
}
@article {pmid29476344,
year = {2018},
author = {Skelton, J and Jusino, MA and Li, Y and Bateman, C and Thai, PH and Wu, C and Lindner, DL and Hulcr, J},
title = {Detecting Symbioses in Complex Communities: the Fungal Symbionts of Bark and Ambrosia Beetles Within Asian Pines.},
journal = {Microbial ecology},
volume = {76},
number = {3},
pages = {839-850},
pmid = {29476344},
issn = {1432-184X},
support = {12-CA-11420004-042//U.S. Forest Service/ ; 14-8130-0377-CA//USDA Farm Bill Agreement/ ; DEB 1556283//Division of Environmental Biology/ ; },
mesh = {Animals ; Biodiversity ; China ; Coleoptera/classification/*microbiology/physiology ; Fungi/classification/genetics/*isolation &amp; purification/physiology ; Host Specificity ; Phylogeny ; Pinus/*parasitology ; *Symbiosis ; Vietnam ; },
abstract = {Separating symbioses from incidental associations is a major obstacle in symbiosis research. In this survey of fungi associated with Asian bark and ambrosia beetles, we used quantitative culture and DNA barcode identification to characterize fungal communities associated with co-infesting beetle species in pines (Pinus) of China and Vietnam. To quantitatively discern likely symbioses from coincidental associations, we used multivariate analysis and multilevel pattern analysis (a type of indicator species analysis). Nearly half of the variation in fungal community composition in beetle galleries and on beetle bodies was explained by beetle species. We inferred a spectrum of ecological strategies among beetle-associated fungi: from generalist multispecies associates to highly specialized single-host symbionts that were consistently dominant within the mycangia of their hosts. Statistically significant fungal associates of ambrosia beetles were typically only found with one beetle species. In contrast, bark beetle-associated fungi were often associated with multiple beetle species. Ambrosia beetles and their galleries were frequently colonized by low-prevalence ambrosia fungi, suggesting that facultative ambrosial associations are commonplace, and ecological mechanisms such as specialization and competition may be important in these dynamic associations. The approach used here could effectively delimit symbiotic interactions in any system where symbioses are obscured by frequent incidental associations. It has multiple advantages including (1) powerful statistical tests for non-random associations among potential symbionts, (2) simultaneous evaluation of multiple co-occurring host and symbiont associations, and (3) identifying symbionts that are significantly associated with multiple host species.},
}
@article {pmid29475862,
year = {2018},
author = {Chen, W and Hambleton, S and Seifert, KA and Carisse, O and Diarra, MS and Peters, RD and Lowe, C and Chapados, JT and Lévesque, CA},
title = {Assessing Performance of Spore Samplers in Monitoring Aeromycobiota and Fungal Plant Pathogen Diversity in Canada.},
journal = {Applied and environmental microbiology},
volume = {84},
number = {9},
pages = {},
pmid = {29475862},
issn = {1098-5336},
mesh = {*Air Microbiology ; Ascomycota/isolation &amp; purification ; Basidiomycota/isolation &amp; purification ; British Columbia ; Environmental Monitoring/instrumentation/methods ; Fungi/*isolation &amp; purification ; *Mycobiome ; Pilot Projects ; Prince Edward Island ; Quebec ; Rain ; Specimen Handling/instrumentation/*methods ; Spores, Fungal/*isolation &amp; purification ; },
abstract = {Spore samplers are widely used in pathogen surveillance but not so much for monitoring the composition of aeromycobiota. In Canada, a nationwide spore-sampling network (AeroNet) was established as a pilot project to assess fungal community composition in air and rain samples collected using three different spore samplers in the summers of 2010 and 2011. Metabarcodes of the internal transcribed spacer (ITS) were exhaustively characterized for three of the network sites, in British Columbia (BC), Québec (QC), and Prince Edward Island (PEI), to compare performance of the samplers. Sampler type accounted for ca. 20% of the total explainable variance in aeromycobiota compositional heterogeneity, with air samplers recovering more Ascomycota and rain samplers recovering more Basidiomycota. Spore samplers showed different abilities to collect 27 fungal genera that are plant pathogens. For instance, Cladosporium spp., Drechslera spp., and Entyloma spp. were collected mainly by air samplers, while Fusarium spp., Microdochium spp., and Ustilago spp. were recovered more frequently with rain samplers. The diversity and abundance of some fungi were significantly affected by sampling location and time (e.g., Alternaria and Bipolaris) and weather conditions (e.g., Mycocentrospora and Leptosphaeria), and depended on using ITS1 or ITS2 as the barcoding region (e.g., Epicoccum and Botrytis). The observation that Canada's aeromycobiota diversity correlates with cooler, wetter conditions and northward wind requires support from more long-term data sets. Our vision of the AeroNet network, combined with high-throughput sequencing (HTS) and well-designed sampling strategies, may contribute significantly to a national biovigilance network for protecting plants of agricultural and economic importance in Canada.IMPORTANCE The current study compared the performance of spore samplers for collecting broad-spectrum air- and rain-borne fungal pathogens using a metabarcoding approach. The results provided a thorough characterization of the aeromycobiota in the coastal regions of Canada in relation to the influence of climatic factors. This study lays the methodological basis to eventually develop knowledge-based guidance on pest surveillance by assisting in the selection of appropriate spore samplers.},
}
@article {pmid29474560,
year = {2018},
author = {MacKenzie, TDB and Arju, I and Poirier, R and Singh, M},
title = {A Genetic Survey of Pyrethroid Insecticide Resistance in Aphids in New Brunswick, Canada, with Particular Emphasis on Aphids as Vectors of Potato virus Y.},
journal = {Journal of economic entomology},
volume = {111},
number = {3},
pages = {1361-1368},
doi = {10.1093/jee/toy035},
pmid = {29474560},
issn = {1938-291X},
mesh = {Animals ; Aphids/drug effects/*genetics ; Insect Proteins/*genetics ; Insecticide Resistance/*genetics ; Insecticides/*pharmacology ; *Mutation/drug effects ; New Brunswick ; Plant Diseases/microbiology ; Potyvirus/physiology ; Pyrethrins/*pharmacology ; Solanum tuberosum/microbiology ; },
abstract = {Aphids are viral vectors in potatoes, most importantly of Potato virus Y (PVY), and insecticides are frequently used to reduce viral spread during the crop season. Aphids collected from the potato belt of New Brunswick, Canada, in 2015 and 2016 were surveyed for known and novel mutations in the Na-channel (para) gene, coding for the target of synthetic pyrethroid insecticides. Specific genetic mutations known to confer resistance (kdr and skdr) were found in great abundance in Myzus persicae (Sulzer) (Hemiptera: Aphididae), which rose from 76% in 2015 to 96% in 2016. Aphids other than M. persicae showed lower frequency of resistance. In 2015, 3% of individuals contained the resistance mutation skdr, rising to 13% in 2016 (of 45 species). Several novel resistance mutations or mutations not before reported in aphids were identified in this gene target. One of these mutations, I936V, is known to confer pyrethroid resistance in another unrelated insect, and three others occur immediately adjacent and prompt similar chemical shifts in the primary protein structure, to previously characterized mutations associated with pyrethroid resistance. Most novel mutations were found in species other than M. persicae or others currently tracked individually by the provincial aphid monitoring program, which were determined by cytochrome C oxidase I (cox1) sequencing. Through our cox1 DNA barcoding survey, at least 45 species of aphids were discovered in NB potato fields in 2015 and 2016, many of which are known carriers of PVY.},
}
@article {pmid29472762,
year = {2018},
author = {Jażdżewska, AM and Corbari, L and Driskell, A and Frutos, I and Havermans, C and Hendrycks, E and Hughes, L and Lörz, AN and Bente Stransky, and Tandberg, AHS and Vader, W and Brix, S},
title = {A genetic fingerprint of Amphipoda from Icelandic waters - the baseline for further biodiversity and biogeography studies.},
journal = {ZooKeys},
volume = {},
number = {731},
pages = {55-73},
pmid = {29472762},
issn = {1313-2989},
abstract = {Amphipods constitute an abundant part of Icelandic deep-sea zoobenthos yet knowledge of the diversity of this fauna, particularly at the molecular level, is scarce. The present work aims to use molecular methods to investigate genetic variation of the Amphipoda sampled during two IceAGE collecting expeditions. The mitochondrial cytochrome oxidase subunit 1 (COI) of 167 individuals originally assigned to 75 morphospecies was analysed. These targeted morhospecies were readily identifiable by experts using light microscopy and representative of families where there is current ongoing taxonomic research. The study resulted in 81 Barcode Identity Numbers (BINs) (of which >90% were published for the first time), while Automatic Barcode Gap Discovery revealed the existence of 78 to 83 Molecular Operational Taxonomic Units (MOTUs). Six nominal species (Rhachotropis helleri, Arrhis phyllonyx, Deflexilodes tenuirostratus, Paroediceros propinquus, Metopa boeckii, Astyra abyssi) appeared to have a molecular variation higher than the 0.03 threshold of both p-distance and K2P usually used for amphipod species delineation. Conversely, two Oedicerotidae regarded as separate morphospecies clustered together with divergences in the order of intraspecific variation. The incongruence between the BINs associated with presently identified species and the publicly available data of the same taxa was observed in case of Paramphithoe hystrix and Amphilochus manudens. The findings from this research project highlight the necessity of supporting molecular studies with thorough morphology species analyses.},
}
@article {pmid29472512,
year = {2018},
author = {Hamm, MW and Calabrese, SV and Knoer, SJ and Duty, AM},
title = {Developing an electronic system to manage and track emergency medications.},
journal = {American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists},
volume = {75},
number = {5},
pages = {304-308},
doi = {10.2146/ajhp160956},
pmid = {29472512},
issn = {1535-2900},
mesh = {Academic Medical Centers/methods/trends ; Drug Therapy, Computer-Assisted/methods/*trends ; *Electronic Prescribing ; Emergency Medical Services/methods/*trends ; Humans ; Medical Order Entry Systems/*trends ; Pharmacy Service, Hospital/methods/*trends ; *Program Development/methods ; },
abstract = {PURPOSE: The development of a Web-based program to track and manage emergency medications with radio frequency identification (RFID) is described.<br><br>SUMMARY: At the Cleveland Clinic, medication kit restocking records and dispense locations were historically documented using a paper record-keeping system. The Cleveland Clinic investigated options to replace the paper-based tracking logs with a Web-based program that could track the real-time location and inventory of emergency medication kits. Vendor collaboration with a board of pharmacy (BOP) compliance inspector and pharmacy personnel resulted in the creation of a dual barcoding system using medication and pocket labels. The Web-based program was integrated with a Cleveland Clinic-developed asset tracking system using active RFID tags to give the real-time location of the medication kit. The Web-based program and the asset tracking system allowed identification of kits nearing expiration or containing recalled medications. Conversion from a paper-based system to a Web-based program began in October 2013. After 119 days, data were evaluated to assess the success of the conversion. Pharmacists spent an average of 27 minutes per day approving medication kits during the postimplementation period versus 102 minutes daily using the paper-based system, representing a 74% decrease in pharmacist time spent on this task. Prospective reports are generated monthly to allow the manager to assess the expected workload and adjust staffing for the next month.<br><br>CONCLUSION: Implementation of a BOP-approved Web-based system for managing and tracking emergency medications with RFID integration decreased pharmacist review time, minimized compliance risk, and increased access to real-time data.},
}
@article {pmid29468086,
year = {2018},
author = {Toju, H and Baba, YG},
title = {DNA metabarcoding of spiders, insects, and springtails for exploring potential linkage between above- and below-ground food webs.},
journal = {Zoological letters},
volume = {4},
number = {},
pages = {4},
pmid = {29468086},
issn = {2056-306X},
abstract = {BACKGROUND: Understanding feedback between above- and below-ground processes of biological communities is a key to the effective management of natural and agricultural ecosystems. However, as above- and below-ground food webs are often studied separately, our knowledge of material flow and community dynamics in terrestrial ecosystems remains limited.<br><br>RESULTS: We developed a high-throughput sequencing method for examining how spiders link above- and below-ground food webs as generalist predators. To overcome problems related to DNA-barcoding-based analyses of arthropod-arthropod interactions, we designed spider-specific blocking primers and Hexapoda-specific primers for the selective PCR amplification of Hexapoda prey sequences from spider samples. By applying the new DNA metabarcoding framework to spider samples collected in a temperate secondary forest in Japan, we explored the structure of a food web involving 15 spider species and various taxonomic groups of Hexapoda prey. These results support the hypothesis that multiple spider species in a community can prey on both above- and below-ground prey species, potentially coupling above- and below-ground food-web dynamics.<br><br>CONCLUSIONS: The PCR primers and metabarcoding pipeline described in this study are expected to accelerate nuclear marker-based analyses of food webs, illuminating poorly understood trophic interactions in ecosystems.},
}
@article {pmid29468035,
year = {2018},
author = {Healey, AJE and McKeown, NJ and Taylor, AL and Provan, J and Sauer, W and Gouws, G and Shaw, PW},
title = {Cryptic species and parallel genetic structuring in Lethrinid fish: Implications for conservation and management in the southwest Indian Ocean.},
journal = {Ecology and evolution},
volume = {8},
number = {4},
pages = {2182-2195},
pmid = {29468035},
issn = {2045-7758},
abstract = {Analysis of genetic variation can provide insights into ecological and evolutionary diversification which, for commercially harvested species, can also be relevant to the implementation of spatial management strategies and sustainability. In comparison with other marine biodiversity hot spots, there has been less genetic research on the fauna of the southwest Indian Ocean (SWIO). This is epitomized by the lack of information for lethrinid fish, which support socioeconomically important fisheries in the region. This study combines comparative phylogeographic and population genetic analyses with ecological niche modeling to investigate historical and contemporary population dynamics of two species of emperor fish (Lethrinus mahsena and Lethrinus harak) across the SWIO. Both species shared similarly shallow phylogeographic patterns and modeled historical (LGM) habitat occupancies. For both species, allele frequency and kinship analyses of microsatellite variation revealed highly significant structure with no clear geographical pattern and nonrandom genetic relatedness among individuals within samples. The genetic patterns for both species indicate recurrent processes within the region that prevent genetic mixing, at least on timescales of interest to fishery managers, and the potential roles of recruitment variability and population isolation are discussed in light of biological and environmental information. This consistency in both historical and recurrent population processes indicates that the use of model species may be valuable in management initiatives with finite resources to predict population structure, at least in cases wherein biogeographic and ecological differences between taxa are minimized. Paradoxically, mtDNA sequencing and microsatellite analysis of samples from the Seychelles revealed a potential cryptic species occurring in sympatry with, and seemingly morphologically identical to, L. mahsena. BLAST results point to the likely misidentification of species and incongruence between voucher specimens, DNA barcodes, and taxonomy within the group, which highlights the utility and necessity of genetic approaches to characterize baseline biodiversity in the region before such model-based methods are employed.},
}
@article {pmid29467794,
year = {2018},
author = {Li, X and Shen, X and Chen, X and Xiang, D and Murphy, RW and Shen, Y},
title = {Detection of Potential Problematic Cytb Gene Sequences of Fishes in GenBank.},
journal = {Frontiers in genetics},
volume = {9},
number = {},
pages = {30},
pmid = {29467794},
issn = {1664-8021},
abstract = {Fishes are, by far, the most diverse group of vertebrates. Their classification relies heavily on morphology. In practice, the correct morphological identification of species often depends on personal experience because many species vary in their body shape, color and other external characters. Thus, the identification of a species may be prone to errors. Due to the rapid development of molecular biology, the number of sequences of fishes deposited in GenBank has grown explosively. These published data likely contain errors owing to invalid or incorrectly identified species. The erroneous data can lead to downstream problems. Thus, it is critical that such errors get identified and corrected. A strategy based on DNA barcoding can detect potentially erroneous data, especially when intraspecific K2P variation exceeds interspecific K2P divergence. Analyses of the most used DNA marker for fishes (mitochondrial Cytb) discovers that intraspecific differences of fishes are generally less than 1%, while interspecific differences are generally higher than 10%. Based on this ruler, our analyses identify 1,303 potential problematic Cytb sequences of fishes in GenBank and point to taxonomic problems, errors in identification, genetic introgression and other concerns. Care must be taken to avoid the perpetuation of errors when using these available data.},
}
@article {pmid29467742,
year = {2018},
author = {Borghesan, TC and Campaner, M and Matsumoto, TE and Espinosa, OA and Razafindranaivo, V and Paiva, F and Carranza, JC and Añez, N and Neves, L and Teixeira, MMG and Camargo, EP},
title = {Genetic Diversity and Phylogenetic Relationships of Coevolving Symbiont-Harboring Insect Trypanosomatids, and Their Neotropical Dispersal by Invader African Blowflies (Calliphoridae).},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {131},
pmid = {29467742},
issn = {1664-302X},
abstract = {This study is about the inter- and intra-specific genetic diversity of trypanosomatids of the genus Angomonas, and their association with Calliphoridae (blowflies) in Neotropical and Afrotropical regions. Microscopic examination of 3,900 flies of various families, mostly Calliphoridae, revealed that 31% of them harbored trypanosomatids. Small subunit rRNA (SSU rRNA) barcoding showed that Angomonas predominated (46%) over the other common trypanosomatids of blowflies of genera Herpetomonas and Wallacemonas. Among Angomonas spp., A. deanei was much more common than the two-other species, A. desouzai and A. ambiguus. Phylogenetic analyses based on SSU rRNA, glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH) and internal transcribed spacer rDNA (ITS rDNA) sequences revealed a marked genetic diversity within A. deanei, which comprised four infraspecific genotypes (Dea1-Dea4), and four corresponding symbiont genotypes (Kcr1-Kcr4). Host and symbiont phylogenies were highly congruent corroborating their co-divergence, consistent with host-symbiont interdependent metabolism and symbiont reduced genomes shaped by a long coevolutionary history. We compared the diversity of Angomonas/symbionts from three genera of blowflies, Lucilia, Chrysomya and Cochliomyia. A. deanei, A. desouzai, and A. ambiguus were found in the three genera of blowflies in South America. In Africa, A. deanei and A. ambiguus were identified in Chrysomya. The absence of A. desouzai in Africa and its presence in Neotropical Cochliomyia and Lucilia suggests parasite spillback of A. desouzai into Chrysomya, which was most likely introduced four decades ago from Africa into the Neotropic. The absence of correlation between parasite diversity and geographic and genetic distances, with identical genotypes of A. deanei found in the Neotropic and Afrotropic, is consistent with disjunct distribution due to the recent human-mediated transoceanic dispersal of Angomonas by Chrysomya. This study provides the most comprehensive data gathered so far on the genetic repertoires of a genus of trypanosomatids found in flies from a wide geographical range.},
}
@article {pmid29462921,
year = {2018},
author = {Zhou, J and Cui, Y and Chen, X and Li, Y and Xu, Z and Duan, B and Li, Y and Song, J and Yao, H},
title = {Complete Chloroplast Genomes of Papaver rhoeas and Papaver orientale: Molecular Structures, Comparative Analysis, and Phylogenetic Analysis.},
journal = {Molecules (Basel, Switzerland)},
volume = {23},
number = {2},
pages = {},
pmid = {29462921},
issn = {1420-3049},
mesh = {Chloroplasts/*genetics ; Genome, Chloroplast/*genetics ; Molecular Structure ; Papaver/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; Whole Genome Sequencing ; },
abstract = {Papaver rhoeas L. and P. orientale L., which belong to the family Papaveraceae, are used as ornamental and medicinal plants. The chloroplast genome has been used for molecular markers, evolutionary biology, and barcoding identification. In this study, the complete chloroplast genome sequences of P. rhoeas and P. orientale are reported. Results show that the complete chloroplast genomes of P. rhoeas and P. orientale have typical quadripartite structures, which are comprised of circular 152,905 and 152,799-bp-long molecules, respectively. A total of 130 genes were identified in each genome, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Sequence divergence analysis of four species from Papaveraceae indicated that the most divergent regions are found in the non-coding spacers with minimal differences among three Papaver species. These differences include the ycf1 gene and intergenic regions, such as rpoB-trnC, trnD-trnT, petA-psbJ, psbE-petL, and ccsA-ndhD. These regions are hypervariable regions, which can be used as specific DNA barcodes. This finding suggested that the chloroplast genome could be used as a powerful tool to resolve the phylogenetic positions and relationships of Papaveraceae. These results offer valuable information for future research in the identification of Papaver species and will benefit further investigations of these species.},
}
@article {pmid29455845,
year = {2018},
author = {Buchholz, VR and Flossdorf, M},
title = {Single-Cell Resolution of T Cell Immune Responses.},
journal = {Advances in immunology},
volume = {137},
number = {},
pages = {1-41},
doi = {10.1016/bs.ai.2017.12.001},
pmid = {29455845},
issn = {1557-8445},
mesh = {Adaptive Immunity ; Animals ; *Computational Biology ; Humans ; Immune Tolerance ; *Immunity, Cellular ; Immunologic Techniques/*methods ; Lymphocyte Activation ; Models, Immunological ; Single-Cell Analysis/*methods ; T-Lymphocytes/*immunology ; },
abstract = {Single antigen-specific B or T lymphocytes are the smallest functional units, into which an adaptive immune response can be dissected. Today, novel high-throughput technologies are providing researches with increasingly complex information on the diverse phenotypic signatures of individual lymphocytes. With a focus on T cells, we summarize here, how computational approaches are becoming increasingly important to identify the relevant developmental boundaries and connections between these high-dimensional lymphocyte states. We then describe how these insights may be further expanded by novel experimental approaches that allow to map the fate of individual T cells and their progeny in vivo and in vitro. Finally, we highlight how these experiments have uncovered a probabilistic regulatory structure of T cell immune responses and briefly discuss, how two distinct theoretical frameworks used to describe this structure may be merged to best capture single T cell behavior in computational terms.},
}
@article {pmid29455678,
year = {2018},
author = {Zittel, M and Grabner, D and Wlecklik, A and Sures, B and Leese, F and Taraschewski, H and Weigand, AM},
title = {Cryptic species and their utilization of indigenous and non-indigenous intermediate hosts in the acanthocephalan Polymorphus minutus sensu lato (Polymorphidae).},
journal = {Parasitology},
volume = {145},
number = {11},
pages = {1421-1429},
doi = {10.1017/S0031182018000173},
pmid = {29455678},
issn = {1469-8161},
mesh = {Acanthocephala/classification/*genetics ; Amphipoda/*parasitology ; Animals ; DNA Barcoding, Taxonomic ; Ecology ; France ; *Genetic Variation ; Germany ; *Host-Parasite Interactions ; },
abstract = {The bird-infecting acanthocephalan Polymorphus minutus has been suggested to comprise different lineages or even cryptic species using different intermediate hosts. To clarify this open question, we investigated Polymorphus cf. minutus cystacanths originating from amphipod intermediate hosts from 27 sites in Germany and France. Parasites and hosts were identified using integrated datasets (COI and/or morphology for hosts and COI + ITS1-5.8S-ITS2 for parasites).Mitochondrial and nuclear data (ITS1) strongly support the existence of three cryptic species in Polymorphus cf. minutus (type 1-3). These three types reveal a high degree of intermediate host specificity, with Polymorphus type 1 only encountered in Gammarus fossarum type B, Polymorphus type 2 in Echinogammarus sp. and Echinogammarus berilloni, and Polymorphus type 3 in Gammarus pulex and Gammarus roeselii. Our results point to a so far neglected cryptic diversity of the genus Polymorphus in Central Europe. Furthermore, Polymorphus type 2 is most likely a non-native parasite in Germany that co-invaded with E. berilloni from the Mediterranean area. Potentially, type 3 originates from South-East Europe and migrated to Germany by G. roeselii, where it might have captured G. pulex as an intermediate host. Therefore, our findings can be seen in the context of ecological globalization in terms of the anthropogenic displacement of intermediate hosts and its impact on the genetic divergence of the parasites.},
}
@article {pmid29454363,
year = {2018},
author = {Dokianakis, E and Tsirigotakis, N and Christodoulou, V and Poulakakis, N and Antoniou, M},
title = {Identification of wild-caught phlebotomine sand flies from Crete and Cyprus using DNA barcoding.},
journal = {Parasites &amp; vectors},
volume = {11},
number = {1},
pages = {94},
pmid = {29454363},
issn = {1756-3305},
support = {261504//EU FP7 EDENext program/International ; ELKE code 3768//The study was partly funded by the University of Crete Research Account/International ; },
mesh = {Animals ; Cyclooxygenase 1/genetics ; Cyprus ; DNA/genetics ; DNA Barcoding, Taxonomic ; Female ; Greece ; Insect Vectors/*classification/genetics/parasitology ; Leishmaniasis/transmission ; Male ; Molecular Sequence Data ; *Phylogeny ; Psychodidae/*classification/genetics/parasitology ; },
abstract = {BACKGROUND: Phlebotomine sand flies (Diptera: Psychodidae) are vectors of Leishmania spp., protozoan parasites responsible for a group of neglected diseases called leishmaniases. Two sand fly genera, Phlebotomus and Sergentomyia, contain species that are present in the Mediterranean islands of Crete and Cyprus where the visceral (VL), cutaneous (CL) and canine (CanLei) leishmaniases are a public health concern. The risk of transmission of different Leishmania species can be studied in an area by monitoring their vectors. Sand fly species are traditionally identified using morphological characteristics but minute differences between individuals or populations could be overlooked leading to wrong epidemiological predictions. Molecular identification of these important vectors has become, therefore, an essential tool for research tasks concerning their geographical distribution which directly relates to leishmaniasis control efforts. DNA barcoding is a widely used molecular identification method for cataloguing animal species by sequencing a fragment of the mitochondrial gene encoding cytochrome oxidase I.<br><br>RESULTS: DNA barcoding was used to identify individuals of five sand fly species (Phlebotomus papatasi, P. similis, P. killicki, Sergentomyia minuta, S. dentata) circulating in the islands of Crete and Cyprus during the years 2011-2014. Phlebotomus papatasi is a known vector of zoonotic CL in the Middle East and it is found in both islands. Phlebotomus similis is the suspected vector of Leishmania tropica in Greece causing anthroponotic CL. Phlebotomus killicki was collected in Cyprus for the first time. Sergentomyia minuta, found to present intraspecific diversity, is discussed for its potential as a Leishmania vector. Molecular identification was consistent with the morphological identification. It successfully identified males and females, which is difficult when using only morphological characters. A phylogenetic tree was constructed based on the barcodes acquired, representing their genetic relationships along with other species from the area studied. All individuals identified were clustered according to their species and subgenus.<br><br>CONCLUSIONS: Molecular identification of sand flies via DNA barcoding can accurately identify these medically important insects assisting traditional morphological tools, thus helping to assess their implication in Leishmania transmission.},
}
@article {pmid29451897,
year = {2018},
author = {Kukita, Y and Ohkawa, K and Takada, R and Uehara, H and Katayama, K and Kato, K},
title = {Selective identification of somatic mutations in pancreatic cancer cells through a combination of next-generation sequencing of plasma DNA using molecular barcodes and a bioinformatic variant filter.},
journal = {PloS one},
volume = {13},
number = {2},
pages = {e0192611},
pmid = {29451897},
issn = {1932-6203},
mesh = {Computational Biology ; DNA, Neoplasm/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Mutation ; Pancreatic Neoplasms/*genetics ; },
abstract = {The accuracy of next-generation sequencing (NGS) for detecting tumor-specific mutations in plasma DNA is hindered by errors introduced during PCR/sequencing, base substitutions caused by DNA damage, and pre-existing mutations in normal cells that are present at a low frequency. Here, we performed NGS of genes related to pancreatic cancer (comprising 2.8 kb of genomic DNA) in plasma DNA (average 4.5 ng) using molecular barcodes. The average number of sequenced molecules was 900, and the sequencing depth per molecule was 100 or more. We also developed a bioinformatic variant filter, called CV78, to remove variants that were not considered to be tumor-specific, i.e., those that are either absent or occur at low frequencies in the Catalogue of Somatic Mutations in Cancer database. In a cohort comprising 57 pancreatic cancer patients and 12 healthy individuals, sequencing initially identified variants in 31 (54%) and 5 (42%), respectively, whereas after applying the CV78 filter, 19 (33%) and zero were variant-positive. In a validation cohort consisting of 86 patients with pancreatic cancer and 20 patients with intraductal papillary mucinous neoplasm (IPMN), 62 (72%) with pancreatic cancer patients and 10 (50%) IPMN patients were initially variant positive. After CV78 filtering, these values were reduced to 32 (37%) and 1 (5%), respectively. The variant allele frequency of filtered variants in plasma ranged from 0.25% to 76.1%. Therefore, combining NGS and molecular barcodes with subsequent filtering is likely to eliminate most non-tumor-specific mutations.},
}
@article {pmid29451846,
year = {2018},
author = {Briosio-Aguilar, R and Pinto, HA and Rodríguez-Santiago, MA and López-García, K and García-Varela, M and de León, GP},
title = {Link Between the Adult and the Metacercaria of Clinostomum heluans Braun, 1899 (Trematoda: Clinostomidae) Through DNA Sequences, and its Phylogenetic Position Within the Genus Clinostomum Leidy, 1856.},
journal = {The Journal of parasitology},
volume = {104},
number = {3},
pages = {292-296},
doi = {10.1645/17-183},
pmid = {29451846},
issn = {1937-2345},
mesh = {Animals ; Base Sequence ; Bird Diseases/*parasitology ; Birds ; Brazil ; Cichlids/parasitology ; DNA Barcoding, Taxonomic/veterinary ; DNA, Helminth/*chemistry/genetics ; Electron Transport Complex IV/chemistry/genetics ; Fish Diseases/*parasitology ; Metacercariae/classification/genetics ; Mexico ; Mitochondria/enzymology/genetics ; *Phylogeny ; Trematoda/*classification/genetics/growth &amp; development ; Trematode Infections/parasitology/*veterinary ; },
abstract = {The phylogenetic position of Clinostomum heluans Braun, 1899 within the genus Clinostomum Leidy, 1856 is reported in this study based on sequences of the barcoding region of the mitochondrial cytochrome c oxidase subunit 1 gene (COX1). Additionally, molecular data are used to link the adult and the metacercariae of the species. The metacercariae of C. heluans were found encysted infecting the cichlid fish Australoheros sp. in Minas Gerais, Brazil, whereas the adults were obtained from the mouth cavity of the Great White Egret, Ardea alba, in Campeche, Mexico. The COX1 sequences obtained for the Mexican clinostomes and the Brazilian metacercaria were almost identical (0.2% molecular divergence), indicating conspecificity. Similar molecular divergence (0.2-0.4%) was found between sequences of C. heluans reported here and Clinostomum sp. 6 previously obtained from a metacercaria recovered from the cichlid Cichlasoma boliviense in Santa Cruz, Bolivia. Both maximum likelihood and Bayesian inference analyses unequivocally showed the conspecificity between C. heluans and Clinostomum sp. 6, which form a monophyletic clade with high nodal support and very low genetic divergence. Moreover, tree topology reveals that C. heluans occupies a basal position with respect to New World species of Clinostomum, although a denser taxon sampling of species within the genus is further required. The metacercaria of C. heluans seems to be specific to cichlid fish because both samples from South America were recovered from species of this fish family, although not closely related.},
}
@article {pmid29449876,
year = {2018},
author = {Duan, BZ and Wang, YP and Fang, HL and Xiong, C and Li, XW and Wang, P and Chen, SL},
title = {Authenticity analyses of Rhizoma Paridis using barcoding coupled with high resolution melting (Bar-HRM) analysis to control its quality for medicinal plant product.},
journal = {Chinese medicine},
volume = {13},
number = {},
pages = {8},
pmid = {29449876},
issn = {1749-8546},
abstract = {BACKGROUND: Rhizoma Paridis (Chonglou) is a commonly used and precious traditional Chinese medicine. Paris polyphylla Smith var. yunnanensis (Franch.) Hand. -Mazz. and Paris polyphylla Smith var. chinensis (Franch.) Hara are the two main sources of Chonglou under the monograph of Rhizoma Paridis in Chinese Pharmacopoeia. In the local marketplace, however, this medicine is prone to be accidentally contaminated, deliberately substituted or admixed with other species that are similar to Rhizoma Paridis in shape and color. Consequently, these adulterations might compromise quality control and result in considerable health concerns for consumers. This study aims to develop a rapid and sensitive method for accurate identification of Rhizoma Paridis and its common adulterants.<br><br>METHODS: DNA barcoding coupled with high resolution melting analysis was applied in this research to distinguish Rhizoma Paridis from its adulteration. The internal transcribed spacer 2 (ITS2) barcode was selected for HRM analysis to produce standard melting profile of the selected species. DNA of the tested herbal medicines was isolated and their melting profiles were generated and compared with the standard melting profile of P. polyphylla var. chinensis.<br><br>RESULTS: The results indicate that the ITS2 molecular regions coupled with HRM analysis can effectively differentiate nine herbal species, including two authentic origins of Chonglou and their seven common adulterants. Ten herbal medicines labeled "Chonglou" obtained from a local market were collected and identified with our methods, and their sequence information was analyzed to validate the accuracy of HRM analysis.<br><br>CONCLUSIONS: DNA barcoding coupled with HRM analysis is a accurate, reliable, rapid, cost-effective and robust tool, which could contribute to the quality control of Rhizoma Paridis in the supply chain of the natural health product industry (NHP).},
}
@article {pmid29447904,
year = {2018},
author = {Schaffrath, S and Prendini, L and Predel, R},
title = {Intraspecific venom variation in southern African scorpion species of the genera Parabuthus, Uroplectes and Opistophthalmus (Scorpiones: Buthidae, Scorpionidae).},
journal = {Toxicon : official journal of the International Society on Toxinology},
volume = {144},
number = {},
pages = {83-90},
doi = {10.1016/j.toxicon.2018.02.004},
pmid = {29447904},
issn = {1879-3150},
mesh = {Africa, Southern ; Animals ; Cluster Analysis ; Female ; Male ; Molecular Weight ; Scorpion Venoms/*chemistry ; Scorpions/*chemistry/classification ; Species Specificity ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {Scorpion venoms comprise cocktails of proteins, peptides, and other molecules used for immobilizing prey and deterring predators. The composition and efficacy of scorpion venoms appears to be taxon-specific due to a coevolutionary arms race with prey and predators that adapt at the molecular level. The taxon-specific components of scorpion venoms can be used as barcodes for species identification if the amount of intraspecific variation is low and the analytical method is fast, inexpensive and reliable. The present study assessed the extent of intraspecific variation in newly regenerated venom collected in the field from geographically separated populations of four southern African scorpion species: three buthids, Parabuthus granulatus (Ehrenberg, 1831), Uroplectes otjimbinguensis (Karsch, 1879), and Uroplectes planimanus (Karsch, 1879), and one scorpionid, Opistophthalmus carinatus (Peters, 1861). Although ion signal patterns were generally similar among venom samples of conspecific individuals from different populations, MALDI-TOF mass spectra in the mass range m/z 700-10,000 revealed only a few ion signals that were identical suggesting that species identification based on simple venom mass fingerprints (MFPs) will be more reliable if databases contain data from multiple populations. In general, hierarchical cluster analysis (HCA) of the ion signals in mass spectra was more reliable for species identification than counts of mass-identical substances in MFPs. The statistical approach revealed conclusive information about intraspecific diversity. In combination with a comprehensive database of MALDI-TOF mass spectra in reflectron mode, HCA may offer a method for rapid species identification based on venom MFPs.},
}
@article {pmid29441235,
year = {2018},
author = {Robertson, DR and Dominguez-Dominguez, O and Victor, B and Simoes, N},
title = {An Indo-Pacific damselfish (Neopomacentrus cyanomos) in the Gulf of Mexico: origin and mode of introduction.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e4328},
pmid = {29441235},
issn = {2167-8359},
abstract = {The Indo-West Pacific (IWP) coral-reef damselfish Neopomacentrus cyanomos is well established across the south-west Gulf of Mexico (SwGoMx). Comparisons of mtDNA sequences of the SwGoMx population with those from conspecifics from 16 sites scattered across its native geographic range show that the SwGoMx population is derived from two of four native lineages: one from the north-west Pacific Ocean, the other from the northern Indian Ocean. Three hypotheses address how this species was introduced to the SwGoMX: (1) aquarium release; (2) borne by cargo-ship; and (3) carried by offshore petroleum platform (petro-platform). The first is unlikely because this species rarely features in the aquarium trade, and "N. cyanomos" traded to the USA from the sole IWP source we are aware of are a misidentified congener, N. taeniurus. The second hypothesis is unlikely because shipping has not been associated with the introduction of alien damselfishes, there is little international shipping between the IWP and the SwGoMx, and voyages between those areas would be lengthy and along environmentally unfavorable routes. Various lines of evidence support the third hypothesis: (i) bio-fouled petro-platforms represent artificial reefs that can sustain large and diverse populations of tropical reef-fishes, including N. cyanomos in the SwGoMx; (ii) relocation of such platforms has been implicated in trans-oceanic introductions leading to establishment of non-native populations of such fishes; and (iii) genetic characteristics of the SwGoMx population indicate that it was established by a large and diverse group of founders drawn from the IWP regions where many petro-platforms currently in the SwGoMx and other Atlantic offshore oilfields originated.},
}
@article {pmid29440965,
year = {2018},
author = {Nguyen Van, N and Nguyen Viet, H and Hoang Thi, B and Tagane, S and Toyama, H and Son, HT and Tran Viet, H and Yahara, T},
title = {Lithocarpus vuquangensis (Fagaceae), a new species from Vu Quang National Park, Vietnam.},
journal = {PhytoKeys},
volume = {},
number = {95},
pages = {15-25},
pmid = {29440965},
issn = {1314-2011},
abstract = {Lithocarpus vuquangensis Ngoc &amp; Hung is described from Vu Quang National Park, North Central Vietnam. The morphological comparison and phylogenetic analysis based on rbcL, matK and ITS provided evidence that the new species was not assignable to any of the previously known taxa in Vietnam and its surrounding countries. The description, photographs, preliminary conservation status and DNA barcode sequences are also provided for the new species.},
}
@article {pmid29440575,
year = {2018},
author = {Haig, SJ and Kotlarz, N and LiPuma, JJ and Raskin, L},
title = {A High-Throughput Approach for Identification of Nontuberculous Mycobacteria in Drinking Water Reveals Relationship between Water Age and Mycobacterium avium.},
journal = {mBio},
volume = {9},
number = {1},
pages = {},
pmid = {29440575},
issn = {2150-7511},
mesh = {Bacterial Load ; DNA, Bacterial/analysis/isolation &amp; purification ; DNA-Directed RNA Polymerases/genetics ; Drinking Water/*microbiology ; *High-Throughput Screening Assays ; Microbiological Techniques/*methods ; Molecular Diagnostic Techniques/methods ; Mycobacterium Infections, Nontuberculous/*prevention &amp; control ; Nontuberculous Mycobacteria/*classification/genetics/*isolation &amp; purification ; Sequence Analysis, DNA ; Time Factors ; },
abstract = {Nontuberculous mycobacteria (NTM) frequently detected in drinking water (DW) include species associated with human infections, as well as species rarely linked to disease. Methods for improved the recovery of NTM DNA and high-throughput identification of NTM are needed for risk assessment of NTM infection through DW exposure. In this study, different methods of recovering bacterial DNA from DW were compared, revealing that a phenol-chloroform DNA extraction method yielded two to four times as much total DNA and eight times as much NTM DNA as two commercial DNA extraction kits. This method, combined with high-throughput, single-molecule real-time sequencing of NTM rpoB genes, allowed the identification of NTM to the species, subspecies, and (in some cases) strain levels. This approach was applied to DW samples collected from 15 households serviced by a chloraminated distribution system, with homes located in areas representing short (<24 h) and long (>24 h) distribution system residence times. Multivariate statistical analysis revealed that greater water age (i.e., combined distribution system residence time and home plumbing stagnation time) was associated with a greater relative abundance of Mycobacterium avium subsp. avium, one of the most prevalent NTM causing infections in humans. DW from homes closer to the treatment plant (with a shorter water age) contained more diverse NTM species, including Mycobacterium abscessus and Mycobacterium chelonae Overall, our approach allows NTM identification to the species and subspecies levels and can be used in future studies to assess the risk of waterborne infection by providing insight into the similarity between environmental and infection-associated NTM.IMPORTANCE An extraction method for improved recovery of DNA from nontuberculous mycobacteria (NTM), combined with single-molecule real-time sequencing (PacBio) of NTM rpoB genes, was used for high-throughput characterization of NTM species and in some cases strains in drinking water (DW). The extraction procedure recovered, on average, eight times as much NTM DNA and three times as much total DNA from DW as two widely used commercial DNA extraction kits. The combined DNA extraction and sequencing approach allowed high-throughput screening of DW samples to identify NTM, revealing that the relative abundance of Mycobacterium avium subsp. avium increased with water age. Furthermore, the two-step barcoding approach developed as part of the PacBio sequencing method makes this procedure highly adaptable, allowing it to be used for other target genes and species.},
}
@article {pmid29438348,
year = {2018},
author = {Chang, H and Guo, J and Fu, X and Liu, Y and Wyckhuys, KAG and Hou, Y and Wu, K},
title = {Molecular-Assisted Pollen Grain Analysis Reveals Spatiotemporal Origin of Long-Distance Migrants of a Noctuid Moth.},
journal = {International journal of molecular sciences},
volume = {19},
number = {2},
pages = {},
pmid = {29438348},
issn = {1422-0067},
mesh = {*Animal Distribution ; Animals ; *Feeding Behavior ; Magnoliopsida/genetics/physiology ; Moths/*physiology ; Pollen/classification/*genetics/ultrastructure ; Pollination ; },
abstract = {Pollen grains are regularly used as markers to determine an insect's movement patterns or host (plant) feeding behavior, yet conventional morphology-based pollen grain analysis (or palynology) encounters a number of important limitations. In the present study, we combine conventional analytical approaches with DNA meta-barcoding to identify pollen grains attached to migrating adults of the turnip moth, Agrotis segetum (Lepidoptera: Noctuidae) in Northeast China. More specifically, pollen grains were dislodged from 2566 A. segetum long-distance migrants captured on Beihuang Island (Bohai Sea) and identified to many (plant) species level. Pollen belonged to 26 families of plants, including Fagaceae, Oleaceae, Leguminosae, Asteraceae, Pinaceae and Rosaceae, including common species such as Citrus sinensis, Olea europaea, Ligustrum lucidum, Robinia pseudoacacia, Castanopsis echinocarpa, Melia azedarach and Castanea henryi. As the above plants are indigenous to southern climes, we deduce that A. segetum forage on plants in those locales prior to engaging in northward spring migration. Our work validates the use of DNA-assisted approaches in lepidopteran pollination ecology research and provides unique and valuable information on the adult feeding range and geographical origin of A. segetum. Our findings also enable targeted (area-wide) pest management interventions or guide the future isolation of volatile attractants.},
}
@article {pmid29436716,
year = {2018},
author = {Endara, MJ and Coley, PD and Wiggins, NL and Forrister, DL and Younkin, GC and Nicholls, JA and Pennington, RT and Dexter, KG and Kidner, CA and Stone, GN and Kursar, TA},
title = {Chemocoding as an identification tool where morphological- and DNA-based methods fall short: Inga as a case study.},
journal = {The New phytologist},
volume = {218},
number = {2},
pages = {847-858},
doi = {10.1111/nph.15020},
pmid = {29436716},
issn = {1469-8137},
mesh = {DNA, Plant/*genetics ; Fabaceae/*anatomy &amp; histology/*classification ; Geography ; Metabolomics/*methods ; Multivariate Analysis ; Phylogeny ; South America ; Species Specificity ; },
abstract = {The need for species identification and taxonomic discovery has led to the development of innovative technologies for large-scale plant identification. DNA barcoding has been useful, but fails to distinguish among many species in species-rich plant genera, particularly in tropical regions. Here, we show that chemical fingerprinting, or 'chemocoding', has great potential for plant identification in challenging tropical biomes. Using untargeted metabolomics in combination with multivariate analysis, we constructed species-level fingerprints, which we define as chemocoding. We evaluated the utility of chemocoding with species that were defined morphologically and subject to next-generation DNA sequencing in the diverse and recently radiated neotropical genus Inga (Leguminosae), both at single study sites and across broad geographic scales. Our results show that chemocoding is a robust method for distinguishing morphologically similar species at a single site and for identifying widespread species across continental-scale ranges. Given that species are the fundamental unit of analysis for conservation and biodiversity research, the development of accurate identification methods is essential. We suggest that chemocoding will be a valuable additional source of data for a quick identification of plants, especially for groups where other methods fall short.},
}
@article {pmid29435248,
year = {2018},
author = {Liu, G and Shafer, ABA and Hu, X and Li, L and Ning, Y and Gong, M and Cui, L and Li, H and Hu, D and Qi, L and Tian, H and Wang, B},
title = {Meta-barcoding insights into the spatial and temporal dietary patterns of the threatened Asian Great Bustard (Otis tarda dybowskii) with potential implications for diverging migratory strategies.},
journal = {Ecology and evolution},
volume = {8},
number = {3},
pages = {1736-1745},
pmid = {29435248},
issn = {2045-7758},
abstract = {Food resources are often not sufficient to satisfy the nutritional and energetic requirements during winter conditions at high latitudes. Dietary analysis is a prerequisite to fully understanding the feeding ecology of a species and the nature of trophic interactions. Previous dietary studies of Asian Great Bustard (Otis tarda dybowskii) relied on behavioral observations, resulting in categorization of diet limited to broad taxonomic groupings. Here, we applied a high-throughput sequencing meta-barcoding approach to quantify the diet of resident and migratory Asian Great Bustard in three wintering sites during early winter and late winter. We detected 57 unique plant taxa in the bustard diet, among which 15 species were confirmed by a local plant database we generated. Both agricultural and natural foods were detected, indicating a relatively broad dietary niche. Spatiotemporal dietary changes were discovered, revealing diet differences among wintering sites and a general shift toward lower plant diversity later in winter. For the nonmigratory population, we detected a significantly more diverse array of plant species in their diet. We hypothesize that dietary variation between resident and migratory populations could be involved in the recent transition to partial migration in this species, although climate change can not be excluded. Collectively, these results support protecting unharvested grain fields and naturally unplowed lands to help conserve and promote population growth of Asian Great Bustard.},
}
@article {pmid29434487,
year = {2018},
author = {Swanteson-Franz, RJ and Marquez, DA and Goldstein, CI and Andreas Schmidt-Rhaesa, and Bolek, MG and Hanelt, B},
title = {New hairworm (Nematomorpha, Gordiida) species described from the Arizona Madrean Sky Islands.},
journal = {ZooKeys},
volume = {},
number = {733},
pages = {131-145},
pmid = {29434487},
issn = {1313-2989},
support = {P20 RR018754/RR/NCRR NIH HHS/United States ; },
abstract = {Gordiids, or freshwater hairworms, are members of the phylum Nematomorpha that use terrestrial definitive hosts (arthropods) and live as adults in rivers, lakes, or streams. The genus Paragordius consists of 18 species, one of which was described from the Nearctic in 1851. More than 150 years later, we are describing a second Paragordius species from a unique habitat within the Nearctic; the Madrean Sky Island complex. The Madrean Sky Islands are a series of isolated high mountains in northern Mexico and the southwestern United States (Arizona and New Mexico), and are well known for their high diversity and endemicity. The new species is described based on both molecular data (COI barcoding) and morphological characters of the eggs, larvae, cysts, and adults. Adult females have unique small oblong mounds present on the interior of the trifurcating lobes with randomly dispersed long hairs extending from the furrows between the mounds. Marked genetic differences support observed morphological differences. This species represents the second new hairworm to be described from the Madrean Sky Islands, and it may represent the first endemic hairworm from this biodiversity hotspot.},
}
@article {pmid29434377,
year = {2018},
author = {Preissl, S and Fang, R and Huang, H and Zhao, Y and Raviram, R and Gorkin, DU and Zhang, Y and Sos, BC and Afzal, V and Dickel, DE and Kuan, S and Visel, A and Pennacchio, LA and Zhang, K and Ren, B},
title = {Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation.},
journal = {Nature neuroscience},
volume = {21},
number = {3},
pages = {432-439},
pmid = {29434377},
issn = {1546-1726},
support = {T32 GM008806/GM/NIGMS NIH HHS/United States ; R01 GM065490/GM/NIGMS NIH HHS/United States ; P50 GM085764/GM/NIGMS NIH HHS/United States ; U19 MH114831/MH/NIMH NIH HHS/United States ; U54 HG006997/HG/NHGRI NIH HHS/United States ; T32 CA009523/CA/NCI NIH HHS/United States ; U01 MH098977/MH/NIMH NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Cell Line ; Chromatin/*metabolism ; DNA-Binding Proteins ; Female ; Gene Expression Regulation, Developmental/*physiology ; Mice ; Mice, Inbred C57BL ; Nerve Tissue Proteins/metabolism ; Neurons/physiology ; Nuclear Proteins/metabolism ; Pregnancy ; Prosencephalon/cytology/*growth &amp; development/metabolism ; Single-Cell Analysis ; },
abstract = {Analysis of chromatin accessibility can reveal transcriptional regulatory sequences, but heterogeneity of primary tissues poses a significant challenge in mapping the precise chromatin landscape in specific cell types. Here we report single-nucleus ATAC-seq, a combinatorial barcoding-assisted single-cell assay for transposase-accessible chromatin that is optimized for use on flash-frozen primary tissue samples. We apply this technique to the mouse forebrain through eight developmental stages. Through analysis of more than 15,000 nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell types. We further define cell-type-specific transcriptional regulatory sequences, infer potential master transcriptional regulators and delineate developmental changes in forebrain cellular composition. Our results provide insight into the molecular and cellular dynamics that underlie forebrain development in the mouse and establish technical and analytical frameworks that are broadly applicable to other heterogeneous tissues.},
}
@article {pmid29433447,
year = {2018},
author = {Carraturo, F and De Castro, O and Troisi, J and De Luca, A and Masucci, A and Cennamo, P and Trifuoggi, M and Aliberti, F and Guida, M},
title = {Comparative assessment of the quality of commercial black and green tea using microbiology analyses.},
journal = {BMC microbiology},
volume = {18},
number = {1},
pages = {4},
pmid = {29433447},
issn = {1471-2180},
mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Bacterial Load ; Chromatography, High Pressure Liquid ; Colony Count, Microbial ; DNA Barcoding, Taxonomic ; Food Contamination/analysis ; Food Microbiology ; Fungi/*classification/genetics/*isolation &amp; purification ; Italy ; Ochratoxins/analysis ; Plant Leaves/chemistry/*microbiology ; Tea/chemistry/*microbiology ; },
abstract = {BACKGROUND: Drinking tea constitutes a tradition which is deeply rooted in the culture of several countries. Moreover, in recent years, tea consumption is growing all over the world. Improper herbal tea storage (long periods, humid environments) represents a relevant health hazard for consumers because of the growth of bacteria and molds.<br><br>RESULTS: This study analyzed 32 samples of commercially available black and green teas - purchased from southern Italy markets and online-shops - and the monitoring of microbiological quality of the tea bag content was performed. Evaluations were conducted with the aim of characterizing pathogens indicated by the European and American guidelines (total bacterial count, fungi and Escherichia coli) and on the research of Pseudomonas spp. and Clostridium perfringens. The presence of ochratoxin A in tea matrix-leaves and infusions was further assessed, using a validated and accredited HPLC-FLD method. Microbial loads, for over 80% samples, ranged from 1.0&#x2009;&#xd7;&#x2009;10[2] to 2.8&#x2009;&#xd7;&#x2009;10[5]&#xa0;CFU/g tea: most of identified microorganisms were classified as Bacillaceae. The utilization of rapid detection and identification methods (PCR and sequencing), allowed the characterization of strains of Pseudomonas psychrotolerans, Staphylococcus warneri, Pantoea gaviniae and the isolation of one strain of Clostridium perfringens, whose ability to produce toxins can result in harmful outcomes for consumers. Fungi were isolated from 70% samples: the most prevalent molds were Aspergillus niger strains, followed by Aspergillus tubingensis. Ochratoxin A was detected in 22 of 32 tea solid samples investigated: concentrations resulted over the indicated limits for food products for 50% samples.<br><br>CONCLUSIONS: Results obtained demonstrated the need to develop targeted regulations for the safety of herbal teas.},
}
@article {pmid29433207,
year = {2018},
author = {Sultana, S and Ali, ME and Hossain, MAM and Asing, and Naquiah, N and Zaidul, ISM},
title = {Universal mini COI barcode for the identification of fish species in processed products.},
journal = {Food research international (Ottawa, Ont.)},
volume = {105},
number = {},
pages = {19-28},
doi = {10.1016/j.foodres.2017.10.065},
pmid = {29433207},
issn = {1873-7145},
mesh = {Animals ; DNA/genetics/isolation &amp; purification ; *DNA Barcoding, Taxonomic ; DNA Primers/genetics/isolation &amp; purification ; Fish Products ; Fishes/*classification ; *Food Labeling ; Genetic Markers ; Malaysia ; Polymerase Chain Reaction ; },
abstract = {Species substitution, the use of a low value fish in place of a high value fish, is the biggest problem in international trade and the leading cause of fraud in the fisheries arena sector. Current DNA barcoding systems have partly solved this problem but also failed in many instances to amplify PCR targets from highly processed products because of the degradation of a longer barcode marker (~650bp). In the present study, a novel mini barcode marker (295bp) was developed to discriminate fish species in raw and processed states forms. The barcode primers were cross-tested against 33 fish species and 15 other animal species and found to be universal for all the tested fish varieties. When 20 commercial fish products of five different categories were screened, all commercial fish sample yielded positive bands for the novel fish barcode. PCR product was sequenced to retrieve the species IDs that reflected 55% (11/20) of Malaysian fish products were mislabeled.},
}
@article {pmid29432417,
year = {2018},
author = {Palm, MM and Elemans, M and Beltman, JB},
title = {Heritable tumor cell division rate heterogeneity induces clonal dominance.},
journal = {PLoS computational biology},
volume = {14},
number = {2},
pages = {e1005954},
pmid = {29432417},
issn = {1553-7358},
mesh = {Animals ; Cell Differentiation ; *Cell Division ; Clone Cells/*cytology ; Computer Simulation ; Genotype ; HeLa Cells ; Humans ; K562 Cells ; Likelihood Functions ; Models, Biological ; Mutation ; Neoplasms/*pathology ; Neoplastic Stem Cells/*cytology ; Phenotype ; Poisson Distribution ; Sequence Analysis, DNA ; Stochastic Processes ; },
abstract = {Tumors consist of a hierarchical population of cells that differ in their phenotype and genotype. This hierarchical organization of cells means that a few clones (i.e., cells and several generations of offspring) are abundant while most are rare, which is called clonal dominance. Such dominance also occurred in published in vitro iterated growth and passage experiments with tumor cells in which genetic barcodes were used for lineage tracing. A potential source for such heterogeneity is that dominant clones derive from cancer stem cells with an unlimited self-renewal capacity. Furthermore, ongoing evolution and selection within the growing population may also induce clonal dominance. To understand how clonal dominance developed in the iterated growth and passage experiments, we built a computational model that accurately simulates these experiments. The model simulations reproduced the clonal dominance that developed in in vitro iterated growth and passage experiments when the division rates vary between cells, due to a combination of initial variation and of ongoing mutational processes. In contrast, the experimental results can neither be reproduced with a model that considers random growth and passage, nor with a model based on cancer stem cells. Altogether, our model suggests that in vitro clonal dominance develops due to selection of fast-dividing clones.},
}
@article {pmid29430207,
year = {2018},
author = {Jelić, D and Jelić, M and Žutinić, P and Šimunović, I and Zupančič, P and Naseka, AM},
title = {Distribution of endangered Italian gudgeon Romanogobio benacensis (Cypriniformes, Cyprinidae, Gobioninae) with remarks on distinguishing morphological characters.},
journal = {ZooKeys},
volume = {},
number = {729},
pages = {103-127},
pmid = {29430207},
issn = {1313-2989},
abstract = {Distribution data on many freshwater fish species in Croatia are scarce and species identifications are difficult, requiring further detailed studies. This paper presents a report of the Italian gudgeon Romanogobio benacensis from the Mirna River in the Istra Peninsula in Croatia, in the south-east from its previously known distribution range. The identification of R. benacensis in Croatia was supported by a morphological comparison with R. benacensis from Italy and Slovenia, the common gudgeon Gobio gobio, and the Danubian gudgeon Gobio obtusirostris from geographically close locations. A combination of character states (number of scales between anus and anal-fin origin, branched pectoral-fin rays, lateral-line scales, total, abdominal, and caudal vertebrae, and the size and number of lateral blotches) distinguishes R. benacensis from both G. gobio and G. obtusirostris. The phylogenetic analyses using mitochondrial sequences of cytochrome b gene confirmed that specimens from the Mirna River belong to R. benacensis. Also, Reka River system (Adriatic Sea basin) in Slovenia is inhabited by a possibly introduced Danubian gudgeon, G. obtusirostris, and not by R. benacensis.},
}
@article {pmid29429333,
year = {2018},
author = {Song, L and Zeng, AP},
title = {Orthogonal Information Encoding in Living Cells with High Error-Tolerance, Safety, and Fidelity.},
journal = {ACS synthetic biology},
volume = {7},
number = {3},
pages = {866-874},
doi = {10.1021/acssynbio.7b00382},
pmid = {29429333},
issn = {2161-5063},
mesh = {*Algorithms ; Base Sequence ; Computer Simulation ; DNA/*genetics ; Escherichia coli/*cytology/genetics ; Nucleic Acid Conformation ; Sequence Analysis, DNA/*methods ; },
abstract = {Information encoding in DNA is of great interest but its applications in vivo might be questionable since errors could be enriched exponentially by cellular replications and the artificial sequences may interfere with the natural ones. Here, a novel self-error-detecting, three-base block encoding scheme (SED3B) is proposed for reliable and orthogonal information encoding in living cells. SED3B utilizes a novel way to add error detecting bases in small data blocks which can combine with the inherent redundancy of DNA molecules for effective error correction. Errors at a rate of 19% can be corrected as shown by error-prone PCR experiments with E. coli cells. Calculations based on this preliminary result show that SED3B encoded information in E. coli can be reliable for more than 12 000 years of continuous replication. Importantly, SED3B encoded sequences do not share sequence space to all reported natural DNA sequences except for some short tandem repeats, indicating a low biological relevance of encoded sequences for the first time. These features make SED3B attractive for broad orthogonal information encoding purposes in living cells, for example, comments/barcodes encoding in synthetic biology. For proof of concept, 10 different barcodes were encoded in E. coli cells. After continuous replications for 10 days including exposure to ultraviolet for 2-3 min (lethality >60%) per day, all barcodes were fully recovered, proving the stability of the encoded information. An online encoding-decoding system is implemented and available at http://biosystem.bt1.tu-harburg.de/sed3b/ .},
}
@article {pmid29429061,
year = {2018},
author = {Loeza-Quintana, T and Adamowicz, SJ},
title = {Iterative Calibration: A Novel Approach for Calibrating the Molecular Clock Using Complex Geological Events.},
journal = {Journal of molecular evolution},
volume = {86},
number = {2},
pages = {118-137},
pmid = {29429061},
issn = {1432-1432},
support = {315757//Consejo Nacional de Ciencia y Tecnolog&#xed;a/International ; 2010-386591//Natural Sciences and Engineering Research Council of Canada/International ; 2016-06199//Natural Sciences and Engineering Research Council of Canada/International ; },
mesh = {Animals ; Biological Evolution ; Calibration ; Echinodermata/*genetics ; Evolution, Molecular ; Fossils ; *Mutation Rate ; Phylogeny ; Phylogeography/*methods ; },
abstract = {During the past 50 years, the molecular clock has become one of the main tools for providing a time scale for the history of life. In the era of robust molecular evolutionary analysis, clock calibration is still one of the most basic steps needing attention. When fossil records are limited, well-dated geological events are the main resource for calibration. However, biogeographic calibrations have often been used in a simplistic manner, for example assuming simultaneous vicariant divergence of multiple sister lineages. Here, we propose a novel iterative calibration approach to define the most appropriate calibration date by seeking congruence between the dates assigned to multiple allopatric divergences and the geological history. Exploring patterns of molecular divergence in 16 trans-Bering sister clades of echinoderms, we demonstrate that the iterative calibration is predominantly advantageous when using complex geological or climatological events-such as the opening/reclosure of the Bering Strait-providing a powerful tool for clock dating that can be applied to other biogeographic calibration systems and further taxa. Using Bayesian analysis, we observed that evolutionary rate variability in the COI-5P gene is generally distributed in a clock-like fashion for Northern echinoderms. The results reveal a large range of genetic divergences, consistent with multiple pulses of trans-Bering migrations. A resulting rate of 2.8% pairwise Kimura-2-parameter sequence divergence per million years is suggested for the COI-5P gene in Northern echinoderms. Given that molecular rates may vary across latitudes and taxa, this study provides a new context for dating the evolutionary history of Arctic marine life.},
}
@article {pmid29426136,
year = {2018},
author = {Ranjbar Jafarabadi, A and Riyahi Bakhtiari, A and Aliabadian, M and Laetitia, H and Shadmehri Toosi, A and Yap, CK},
title = {First report of bioaccumulation and bioconcentration of aliphatic hydrocarbons (AHs) and persistent organic pollutants (PAHs, PCBs and PCNs) and their effects on alcyonacea and scleractinian corals and their endosymbiotic algae from the Persian Gulf, Iran: Inter and intra-species differences.},
journal = {The Science of the total environment},
volume = {627},
number = {},
pages = {141-157},
doi = {10.1016/j.scitotenv.2018.01.185},
pmid = {29426136},
issn = {1879-1026},
mesh = {Animals ; Anthozoa/*drug effects/physiology ; *Coral Reefs ; Hydrocarbons/*metabolism/*toxicity ; Indian Ocean ; Iran ; Middle East ; Polychlorinated Biphenyls/metabolism/toxicity ; Species Specificity ; Water Pollutants, Chemical/*metabolism/*toxicity ; },
abstract = {The coral reefs of the Persian Gulf are the most diverse systems of life in the marine environment of the Middle East. Unfortunately, they are highly threatened by local and global stressors, particularly oil pollutants. This is the first quantitative and qualitative study aimed at assessing the concentration and sources of n-alkanes and POPs (PAHs, PCBs and PCNs) in coral tissues, symbiotic algae (zooxanthellae), reef sediments and seawaters in coral reefs of Lark and Kharg in the Persian Gulf, Iran. This work was conducted on eight species of six genera and three families of hard corals and one family of soft coral. A significant variation in the concentration of ∑30n-alkanes and POPs (∑40PAHs, ∑22PCBs and 20PCNs) was found in the decreasing order: zooxanthellae > coral tissue > skeleton > reef sediment > seawater. The bioaccumulation of these compounds was 2-times higher in ahermatypic than in hermatypic corals, among which significant variations were observed in both sites. In Kharg, Porites lutea had the highest mean concentration of ∑30n-alkanes and ∑40PAHs in soft tissue, whereas the lowest values were in Platygyra daedalea. A contrasting trend was documented for ∑22PCBs and 20PCNs, with the highest level reported in soft tissue of P. daedalea and the lowest in P. lutea at Kharg. Compositional pattern of AHs and PAHs demonstrated the predominance of LMW-PAHs and n-alkanes. In skeleton and reef sediments, tetra, penta and tri-CBs were the most abundant PCBs congeners followed by di-CB > hexa-CB > hepta-CB > octa-CB,whiletri-CB > di-CB > tetra-CB > penta-CB > hexa-CB > hepta-CB > octa-CB was observed for soft tissue, zooxanthellae and seawater. The results of RAD test indicated significantly negative correlation between total concentration of these compounds with zooxanthellae density, the chlorophyll-a and C2 in corals at both reefs. This is the first report on levels, health assessment and source apportionments of POPs in zooxanthellae and a first step in the implementation of specific coral reef management measures.},
}
@article {pmid29425893,
year = {2018},
author = {Bian, J and Zhang, S and Yi, M and Yue, M and Liu, H},
title = {The mechanisms behind decreased internalization of angiotensin II type 1 receptor.},
journal = {Vascular pharmacology},
volume = {103-105},
number = {},
pages = {1-7},
doi = {10.1016/j.vph.2018.01.008},
pmid = {29425893},
issn = {1879-3649},
mesh = {Animals ; Cardiovascular Diseases/*physiopathology ; Cardiovascular System/metabolism/physiopathology ; Endocytosis/physiology ; Humans ; Hypertension/*physiopathology ; Phosphorylation ; Receptor, Angiotensin, Type 1/agonists/*metabolism ; },
abstract = {The internalization of angiotensin II type 1 receptor (AT1R) plays an important role in maintaining cardiovascular homeostasis. Decreased receptor internalization is closely related to cardiovascular diseases induced by the abnormal activation of AT1R, such as hypertension. However, the mechanism behind reduced AT1R internalization is not fully understood. This review focuses on four parts of the receptor internalization process (the combination of agonists and receptors, receptor phosphorylation, endocytosis, and recycling) and summarizes the possible mechanisms by which AT1R internalization is reduced based on these four parts of the process. (1) The agonist has a large molecular weight or a stronger ability to hydrolyze phosphatidylinositol 4,5-bisphosphate (PtdIns (4,5) P2), which can increase the consumption of PtdIns (4,5) P2. (2) AT1R phosphorylation is weakened because of an abnormal function of phosphorylated kinase or changes in phospho-barcoding and GPCR-β-arrestin complex conformation. (3) The abnormal formation of vesicles or AT1R heterodimers with fewer endocytic receptors results in less AT1R endocytosis. (4) The enhanced activity and upregulated expression of small GTP-binding protein 4 (Rab4) and 11 (Rab11), which regulate receptor recycling, and phosphatidylinositol 3-kinase increase AT1R recycling. In addition, lower expression of AT1R-associated protein (ATRAP) or higher expression of AT1R-associated protein 1 (ARAP1) can reduce receptor internalization.},
}
@article {pmid29425132,
year = {2018},
author = {Sann, C and Wemheuer, F and Beaurepaire, A and Daniel, R and Erler, S and Vidal, S},
title = {Preliminary Investigation of Species Diversity of Rice Hopper Parasitoids in Southeast Asia.},
journal = {Insects},
volume = {9},
number = {1},
pages = {},
pmid = {29425132},
issn = {2075-4450},
abstract = {Ongoing intensification of rice production systems in Southeast Asia is causing devastating yield losses each year due to rice hoppers. Their continuing development of immunity to resistant rice varieties and pesticide applications further complicates this problem. Hence, there is a high demand for biological control agents of rice hoppers. Egg parasitoid wasps are among the most important natural enemies of rice hoppers, such as Nilaparvata lugens and Nephotettix spp. However, our knowledge of their diversity is still very limited, due to their small size and the lack of available morphological information. Classifying these parasitoids is the first step to properly understanding their role in the rice agroecosystem. We used traditional morphological identification, as well as DNA sequencing of the 28S rRNA and the COI genes, to investigate the diversity of four important hopper egg parasitoid genera in the Philippines. Parasitoids of the genera Anagrus, Oligosita, Gonatocerus, and Paracentrobia were collected in eight study landscapes located in Luzon. Our findings illustrate that characterization of species diversity using morphological and molecular analyses were concordant only for the genus Paracentrobia. The genera Anagrus and Gonatocerus exhibited more genetic diversity than estimated with the morphological analysis, while the opposite was observed for Oligosita. This is the first study investigating the molecular diversity of rice hopper parasitoids in the Philippines. More research combining morphological, behavioral, and molecular methods, as well as the establishment of a comprehensive DNA database, are urgently needed to assess the performance and suitability of these organisms as biocontrol agents.},
}
@article {pmid29425128,
year = {2018},
author = {Gu, C and Tembrock, LR and Zheng, S and Wu, Z},
title = {The Complete Chloroplast Genome of Catha edulis: A Comparative Analysis of Genome Features with Related Species.},
journal = {International journal of molecular sciences},
volume = {19},
number = {2},
pages = {},
pmid = {29425128},
issn = {1422-0067},
mesh = {Catha/classification/*genetics ; *Genome, Chloroplast ; Open Reading Frames ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Repetitive Sequences, Nucleic Acid ; },
abstract = {Qat (Catha edulis, Celastraceae) is a woody evergreen species with great economic and cultural importance. It is cultivated for its stimulant alkaloids cathine and cathinone in East Africa and southwest Arabia. However, genome information, especially DNA sequence resources, for C. edulis are limited, hindering studies regarding interspecific and intraspecific relationships. Herein, the complete chloroplast (cp) genome of Catha edulis is reported. This genome is 157,960 bp in length with 37% GC content and is structurally arranged into two 26,577 bp inverted repeats and two single-copy areas. The size of the small single-copy and the large single-copy regions were 18,491 bp and 86,315 bp, respectively. The C. edulis cp genome consists of 129 coding genes including 37 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 84 protein coding genes. For those genes, 112 are single copy genes and 17 genes are duplicated in two inverted regions with seven tRNAs, four rRNAs, and six protein coding genes. The phylogenetic relationships resolved from the cp genome of qat and 32 other species confirms the monophyly of Celastraceae. The cp genomes of C. edulis, Euonymus japonicus and seven Celastraceae species lack the rps16 intron, which indicates an intron loss took place among an ancestor of this family. The cp genome of C. edulis provides a highly valuable genetic resource for further phylogenomic research, barcoding and cp transformation in Celastraceae.},
}
@article {pmid29423711,
year = {2018},
author = {Meiklejohn, KA and Jackson, ML and Stern, LA and Robertson, JM},
title = {A protocol for obtaining DNA barcodes from plant and insect fragments isolated from forensic-type soils.},
journal = {International journal of legal medicine},
volume = {132},
number = {6},
pages = {1515-1526},
pmid = {29423711},
issn = {1437-1596},
mesh = {Animals ; DNA/analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/analysis ; Electron Transport Complex IV/genetics ; Insecta/*genetics ; Plants/*genetics ; Polymerase Chain Reaction ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Analysis, DNA ; *Soil ; },
abstract = {Soil is often collected from a suspect's tire, vehicle, or shoes during a criminal investigation and subsequently submitted to a forensic laboratory for analysis. Plant and insect material recovered in such samples is rarely analyzed, as morphological identification is difficult. In this study, DNA barcoding was used for taxonomic identifications by targeting the gene regions known to permit discrimination in plants [maturase K (matK) and ribulose 1,5-biphosphate carboxylase (rbcL)] and insects [cytochrome oxidase subunit I (COI)]. A DNA barcode protocol suitable for processing forensic-type biological fragments was developed and its utility broadly tested with forensic-type fragments (e.g., seeds, leaves, bark, head, legs; n, 213) isolated from soils collected within Virginia, USA (n, 11). Difficulties with PCR inhibitors in plant extracts and obtaining clean Sanger sequence data from insect amplicons were encountered during protocol development; however, the final protocol produced sequences specific to the expected locus and taxa. The overall quantity and quality of DNA extracted from the 213 forensic-type biological fragments was low (< 15 ng/μL). For plant fragments, only the rbcL sequence data was deemed reliable; thus, taxonomic identifications were limited to the family level. The majority of insect sequences matched COI in both GenBank and Barcode of Life DataSystems; however, they were identified as an undescribed environmental contaminant. Although limited taxonomic information was gleaned from the forensic-type fragments processed in this study, the new protocol shows promise for obtaining reliable and specific identifications through DNA barcoding, which could ultimately enhance the information gleaned from soil examinations.},
}
@article {pmid29423464,
year = {2018},
author = {Moon, HS and Je, K and Min, JW and Park, D and Han, KY and Shin, SH and Park, WY and Yoo, CE and Kim, SH},
title = {Inertial-ordering-assisted droplet microfluidics for high-throughput single-cell RNA-sequencing.},
journal = {Lab on a chip},
volume = {18},
number = {5},
pages = {775-784},
doi = {10.1039/c7lc01284e},
pmid = {29423464},
issn = {1473-0189},
mesh = {Animals ; HEK293 Cells ; *High-Throughput Nucleotide Sequencing ; Humans ; K562 Cells ; Mice ; *Microfluidics ; NIH 3T3 Cells ; Particle Size ; *Sequence Analysis, RNA ; *Single-Cell Analysis ; Surface Properties ; },
abstract = {Single-cell RNA-seq reveals the cellular heterogeneity inherent in the population of cells, which is very important in many clinical and research applications. Recent advances in droplet microfluidics have achieved the automatic isolation, lysis, and labeling of single cells in droplet compartments without complex instrumentation. However, barcoding errors occurring in the cell encapsulation process because of the multiple-beads-in-droplet and insufficient throughput because of the low concentration of beads for avoiding multiple-beads-in-a-droplet remain important challenges for precise and efficient expression profiling of single cells. In this study, we developed a new droplet-based microfluidic platform that significantly improved the throughput while reducing barcoding errors through deterministic encapsulation of inertially ordered beads. Highly concentrated beads containing oligonucleotide barcodes were spontaneously ordered in a spiral channel by an inertial effect, which were in turn encapsulated in droplets one-by-one, while cells were simultaneously encapsulated in the droplets. The deterministic encapsulation of beads resulted in a high fraction of single-bead-in-a-droplet and rare multiple-beads-in-a-droplet although the bead concentration increased to 1000 μl[-1], which diminished barcoding errors and enabled accurate high-throughput barcoding. We successfully validated our device with single-cell RNA-seq. In addition, we found that multiple-beads-in-a-droplet, generated using a normal Drop-Seq device with a high concentration of beads, underestimated transcript numbers and overestimated cell numbers. This accurate high-throughput platform can expand the capability and practicality of Drop-Seq in single-cell analysis.},
}
@article {pmid29421668,
year = {2018},
author = {Parra-Giraldo, CM and Valderrama, SL and Cortes-Fraile, G and Garzón, JR and Ariza, BE and Morio, F and Linares-Linares, MY and Ceballos-Garzón, A and de la Hoz, A and Hernandez, C and Alvarez-Moreno, C and Le Pape, P},
title = {First report of sporadic cases of Candida auris in Colombia.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {69},
number = {},
pages = {63-67},
doi = {10.1016/j.ijid.2018.01.034},
pmid = {29421668},
issn = {1878-3511},
mesh = {Aged ; Antifungal Agents/pharmacology ; Candida/drug effects/*genetics/*isolation &amp; purification ; Candida albicans/isolation &amp; purification ; Candidiasis/drug therapy/*epidemiology ; Colombia/epidemiology ; *Disease Outbreaks ; Drug Resistance, Multiple, Fungal/genetics ; Female ; Humans ; Infection Control ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Phenotype ; Sequence Analysis, DNA ; Triazoles/pharmacology ; },
abstract = {BACKGROUND: Candida auris is a recently reported Candida species that is phenotypically similar to Candida haemulonii and related to hospital outbreaks. This organism can be misidentified as Candida haemulonii, Candida famata, Candida catenulata, or Rhodotorula glutinis by phenotypic approaches. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and DNA sequence analysis using internal transcribed spacer rDNA bar-coding provide an accurate identification.<br><br>CASE REPORTS: Three cases of C. auris infection in patients with risk factors for fungal infection (one admitted to the intensive care unit, one with lymphoma, and one with HIV; all three with previous antibiotic use) are reported; these infections were not epidemiologically related. Yeast isolates were recovered from blood, ocular secretion, and bronchoalveolar lavage and were misidentified as C. catenulata and Candida albicans by the phenotypic MicroScan method. The isolates were confirmed to be C. auris by means of MALDI-TOF MS and DNA sequence analysis. Antifungal susceptibility testing was performed on these C. auris isolates, which exhibited high minimum inhibitory concentrations to triazoles and amphotericin B. One patient survived and the other two died. Only one of these deaths was related to fungemia.<br><br>CONCLUSIONS: C. auris is an emerging and opportunistic multidrug-resistant human pathogen. It is necessary to strengthen measures to achieve an accurate and quick identification and also to avoid its dissemination. This will require improvements in health and infection control measures, as well as the promotion of antifungal stewardship in healthcare facilities.},
}
@article {pmid29421101,
year = {2018},
author = {Smith, SDA and Banister, K and Fraser, N and Edgar, RJ},
title = {Tracing the source of marine debris on the beaches of northern New South Wales, Australia: The Bottles on Beaches program.},
journal = {Marine pollution bulletin},
volume = {126},
number = {},
pages = {304-307},
doi = {10.1016/j.marpolbul.2017.11.022},
pmid = {29421101},
issn = {1879-3363},
mesh = {Australia ; Bathing Beaches/*statistics &amp; numerical data ; China ; Environment ; Environmental Monitoring ; Environmental Pollution ; New South Wales ; *Plastics ; Ships ; Waste Products/*statistics &amp; numerical data ; },
abstract = {Identifying the source of marine plastic pollution accumulating on ocean beaches is often difficult as unidentifiable fragments of plastic usually predominate. In this study, we surveyed plastic bottles as a relatively identifiable subset of plastics on 30km of beach along a 200-km section of the north coast of New South Wales, Australia. Source and product type (contents) were determined using barcodes, inscriptions/embossing, or bottle shape and characteristics. Country of origin and product type could be determined for two-thirds of the 694 bottles found. Just over half (51%) of these were of domestic origin with the remainder dominated by bottles from China (24%) and south-east Asian countries (21%). As most of the foreign bottles lacked marine growth, and are unavailable for purchase in the region, passing ships are hypothesised as the primary source.},
}
@article {pmid29416407,
year = {2018},
author = {Roh, SJ and Lee, BW and Byun, BK},
title = {Two new species of the genus Dahlica Enderlein (Lepidoptera, Psychidae) from Korea.},
journal = {ZooKeys},
volume = {},
number = {733},
pages = {49-64},
pmid = {29416407},
issn = {1313-2989},
abstract = {The genus Dahlica Enderlein, 1912 is reported for the first time from Korea with two new species: Dahlica (Dahlica) somae Roh &amp; Byun, sp. n. and Dahlica (Dahlica) ochrostigma Roh &amp; Byun, sp. n. Adults and genitalia are illustrated, and DNA barcodes for precise identification of the species are also provided.},
}
@article {pmid29416071,
year = {2018},
author = {Morard, R and Garet-Delmas, MJ and Mahé, F and Romac, S and Poulain, J and Kucera, M and de Vargas, C},
title = {Surface ocean metabarcoding confirms limited diversity in planktonic foraminifera but reveals unknown hyper-abundant lineages.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {2539},
pmid = {29416071},
issn = {2045-2322},
mesh = {Atlantic Ocean ; *Biodiversity ; DNA, Ribosomal/*genetics ; Ecosystem ; *Foraminifera/classification/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Indian Ocean ; *Plankton/classification/genetics ; RNA, Ribosomal, 18S/*genetics ; },
abstract = {Since the advent of DNA metabarcoding surveys, the planktonic realm is considered a treasure trove of diversity, inhabited by a small number of abundant taxa, and a hugely diverse and taxonomically uncharacterized consortium of rare species. Here we assess if the apparent underestimation of plankton diversity applies universally. We target planktonic foraminifera, a group of protists whose known morphological diversity is limited, taxonomically resolved and linked to ribosomal DNA barcodes. We generated a pyrosequencing dataset of ~100,000 partial 18S rRNA foraminiferal sequences from 32 size fractioned photic-zone plankton samples collected at 8 stations in the Indian and Atlantic Oceans during the Tara Oceans expedition (2009-2012). We identified 69 genetic types belonging to 41 morphotaxa in our metabarcoding dataset. The diversity saturated at local and regional scale as well as in the three size fractions and the two depths sampled indicating that the diversity of foraminifera is modest and finite. The large majority of the newly discovered lineages occur in the small size fraction, neglected by classical taxonomy. These unknown lineages dominate the bulk [>0.8 µm] size fraction, implying that a considerable part of the planktonic foraminifera community biomass has its origin in unknown lineages.},
}
@article {pmid29413969,
year = {2017},
author = {Dharampuriya, PR and Scapin, G and Wong, C and John Wagner, K and Cillis, JL and Shah, DI},
title = {Tracking the origin, development, and differentiation of hematopoietic stem cells.},
journal = {Current opinion in cell biology},
volume = {49},
number = {},
pages = {108-115},
pmid = {29413969},
issn = {1879-0410},
support = {R01 HL131645/HL/NHLBI NIH HHS/United States ; },
mesh = {Cell Differentiation ; Hematopoiesis/*genetics ; Hematopoietic Stem Cells/*metabolism ; Humans ; },
abstract = {PURPOSE OF REVIEW: The hierarchical nature of the hematopoietic system provides an ideal model system to illustrate the features of lineage tracing. We have outlined the utility of lineage tracing methods in establishing the origin and development of hematopoietic cells.<br><br>RECENT FINDINGS: Methods such as CRISPR/Cas9, Polylox barcoding, and single-cell RNA-sequencing have improved our understanding of hematopoiesis.<br><br>SUMMARY: This review chronicles the fate of the hematopoietic cells emerging from the mesoderm that subsequently develops into the adult blood lineages. Specifically, we explain classic techniques utilized in lineage tracing for the hematopoietic system, as well as novel state-of-the-art methods to elucidate clonal hematopoiesis and cell fate mapping at a single-cell level.},
}
@article {pmid29410330,
year = {2018},
author = {Ju, CH and Blum, LK and Kongpachith, S and Lingampalli, N and Mao, R and Brodin, P and Dekker, CL and Davis, MM and Robinson, WH},
title = {Plasmablast antibody repertoires in elderly influenza vaccine responders exhibit restricted diversity but increased breadth of binding across influenza strains.},
journal = {Clinical immunology (Orlando, Fla.)},
volume = {193},
number = {},
pages = {70-79},
pmid = {29410330},
issn = {1521-7035},
support = {U19 AI057229/AI/NIAID NIH HHS/United States ; UL1 RR025744/RR/NCRR NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; },
mesh = {Adult ; Aged ; Aged, 80 and over ; Aging/*immunology ; Antibodies, Viral/genetics/metabolism ; Antibody Affinity ; Antibody Diversity ; Humans ; Influenza A Virus, H1N1 Subtype/*physiology ; Influenza A Virus, H3N2 Subtype/*physiology ; Influenza Vaccines/*immunology ; Influenza, Human/*immunology ; Plasma Cells/*physiology ; Protein Binding ; Receptors, Antigen, B-Cell/genetics ; Vaccination ; Young Adult ; },
abstract = {Seasonal influenza vaccines elicit antibody responses that can prevent infection, but their efficacy is reduced in the elderly. While a subset of elderly individuals can still mount sufficient vaccine-induced antibody responses, little is known about the properties of the vaccine-induced antibody repertoires in elderly as compared to young responders. To gain insights into the effects of aging on influenza vaccine-induced antibody responses, we used flow cytometry and a cell-barcoding method to sequence antibody heavy and light chain gene pairs expressed by individual blood plasmablasts generated in response to influenza vaccination in elderly (aged 70-89) and young (aged 20-29) responders. We found similar blood plasmablast levels in the elderly and young responders seven days post vaccination. Informatics analysis revealed increased clonality, but similar heavy chain V(D)J gene usage in the elderly as compared to young vaccine responders. Although the elderly responders exhibited decreased antibody sequence diversity and fewer consequential mutations relative to young responders, recombinant antibodies from elderly responders bound a broader range of influenza strain HAs. Thus elderly influenza vaccine responders mount plasmablast responses with restricted diversity but with an increased breadth of binding across influenza strains. Our results suggest that the ability to generate plasmablast responses encoding cross-strain binding antibodies likely represents a mechanism important to vaccine responses in the elderly.},
}
@article {pmid29408406,
year = {2018},
author = {Buenaventura, E and Valverde-Castro, C and Wolff, M and Triana-Chavez, O and Gómez-Palacio, A},
title = {DNA barcoding for identifying synanthropic flesh flies (Diptera, Sarcophagidae) of Colombia.},
journal = {Acta tropica},
volume = {182},
number = {},
pages = {291-297},
doi = {10.1016/j.actatropica.2018.01.020},
pmid = {29408406},
issn = {1873-6254},
mesh = {Animals ; Colombia ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Forensic Sciences/methods ; Genes, Mitochondrial ; Phylogeny ; Sarcophagidae/classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {The first step for a successful use of any insect as indicator in forensic sciences is providing a precise taxonomic identification at species level. Due to morphology-based identification of Sarcophaginae flies (Diptera, Sarcophagidae) is often difficult and requires strong taxonomic expertise, their use as forensic indicators has been limited. Consequently, molecular-based approaches have been accepted as alternative means of identification. Thus, we aimed testing the efficiency of the barcode region of the mitochondrial cytochrome oxidase subunit I (COI) gene for identification of synanthropic flesh flies of several species of the genera Peckia, Oxysarcodexia, Ravinia, and Tricharaea collected in Colombia. The 645-bp fragment of COI was amplified and aligned (215 parsimoniously informative variable sites). We calculated Kimura two-parameter genetic distances and reconstruct a Neighbor-Joining phylogenetic tree. Our Neighbor-Joining tree recovered all species as monophyletic, and confirmed a new species of the genus Ravinia as also indicated by the interspecific genetic divergences and morphological observations. We obtained a 100% of identification success. Thus, the COI barcodes showed efficiency as an alternative mean of identification of species of flesh flies collected on decaying organic matter in Colombia.},
}
@article {pmid29398713,
year = {2017},
author = {Garcia-Robledo, C and Horvitz, CC and Kress, WJ and Carvajal-Acosta, AN and Erwin, TL and Staines, CL},
title = {Experimental assemblage of novel plant-herbivore interactions: ecological host shifts after 40 million years of isolation.},
journal = {Biotropica},
volume = {49},
number = {6},
pages = {803-810},
pmid = {29398713},
issn = {0006-3606},
support = {P01 AG022500/AG/NIA NIH HHS/United States ; },
abstract = {Geographic isolation is the first step in insect herbivore diet specialization. Such specialization is postulated to increase insect fitness, but may simultaneously reduce insect ability to colonize novel hosts. During the Paleocene-Eocene, plants from the order Zingiberales became isolated either in the Paleotropics or in the Neotropics. During the Cretaceous, rolled-leaf beetles diversified in the Neotropics concurrently with Neotropical Zingiberales. Using a community of Costa Rican rolled-leaf beetles and their Zingiberales host plants as study system, we explored if previous geographic isolation precludes insects to expand their diets to exotic hosts. We recorded interactions between rolled-leaf beetles and native Zingiberales by combining DNA barcodes and field records for 7450 beetles feeding on 3202 host plants. To determine phylogenetic patterns of diet expansions, we set 20 field plots including five exotic Zingiberales, recording beetles feeding on these exotic hosts. In the laboratory, using both native and exotic host plants, we reared a subset of insect species that had expanded their diets to the exotic plants. The original plant-herbivore community comprised 24 beetle species feeding on 35 native hosts, representing 103 plant-herbivore interactions. After exotic host plant introduction, 20% of the beetle species expanded their diets to exotic Zingiberales. Insects only established on exotic hosts that belong to the same plant family as their native hosts. Laboratory experiments show that beetles are able to complete development on these novel hosts. In conclusion, rolled-leaf beetles are pre-adapted to expand their diets to novel host plants even after millions of years of geographic isolation.},
}
@article {pmid29391478,
year = {2018},
author = {Choe, MK and Lim, M and Kim, JS and Lee, DS and Chung, CK},
title = {Disrupted Resting State Network of Fibromyalgia in Theta frequency.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {2064},
pmid = {29391478},
issn = {2045-2322},
mesh = {Adult ; Female ; Fibromyalgia/*physiopathology ; Humans ; Magnetoencephalography ; Middle Aged ; Temporal Lobe/physiopathology ; *Theta Rhythm ; Visual Cortex/physiopathology ; },
abstract = {Fibromyalgia (FM), chronic widespread pain, exhibits spontaneous pain without external stimuli and is associated with altered brain activities during resting state. To understand the topological features of brain network in FM, we employed persistent homology which is a multiple scale network modeling framework not requiring thresholding. Spontaneous magnetoencephalography (MEG) activity was recorded in 19 healthy controls (HCs) and 18 FM patients. Barcode, single linkage dendrogram and single linkage matrix were generated based on the proposed modeling framework. In theta band, the slope of decrease in the number of connected components in barcodes showed steeper in HC, suggesting FM patients had decreased global connectivity. FM patients had reduced connectivity within default mode network, between middle/inferior temporal gyrus and visual cortex. The longer pain duration was correlated with reduced connectivity between inferior temporal gyrus and visual cortex. Our findings demonstrated that the aberrant resting state network could be associated with dysfunction of sensory processing in chronic pain. The spontaneous nature of FM pain may accrue to disruption of resting state network.},
}
@article {pmid29390935,
year = {2018},
author = {Gowande, GG and Tembe, S and Ghate, HV},
title = {Revisiting DNA barcoding of true bugs of the infraorder Pentatomomorpha (Hemiptera: Heteroptera) from India.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {8},
pages = {1215-1223},
doi = {10.1080/24701394.2018.1431229},
pmid = {29390935},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic/*standards ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Heteroptera/*classification/genetics ; Insect Proteins/genetics ; *Phylogeny ; Reference Standards ; },
abstract = {Cytochrome c oxidase subunit I gene (COI) sequences of roughly 509 bp length for various species of the Infraorder Pentatomomorpha were generated. K2P divergences within and between species and genera were calculated and compared using newly generated sequences and the ones available on online portals. Mean interspecific (within-genus) genetic divergence (14.23%) was ∼ eight times greater than mean intraspecific (within-species) divergence (1.79%). Distance-based as well as character-based approaches were used towards constructing (COI) trees. In total, 20 sequences were of the species that were previously not part of the Barcode Of Life Database (BOLD), hence representing additions to the barcode library of Indian Heteroptera. Some of the analyzed species are well-known agricultural pests. All the COI sequences and the associated specimen data have been deposited on BOLD.},
}
@article {pmid29388716,
year = {2018},
author = {Hao, J and Xu, X and Fei, H and Li, L and Yan, B},
title = {Functionalization of Metal-Organic Frameworks for Photoactive Materials.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {30},
number = {17},
pages = {e1705634},
doi = {10.1002/adma.201705634},
pmid = {29388716},
issn = {1521-4095},
abstract = {Metal-organic frameworks (MOFs) are intriguing platforms with multiple functionalities. Additional functionalization of MOFs generates novel materials for various applications. Here, three main topics are examined regarding the functionalization of MOFs for use as photoactive materials. The first is chemical approaches for postsynthetic modification of the metal clusters and organic linkers in MOFs; that is, sites on pore surfaces and chemical trapping of photoactive moieties within the pores, which create materials with chemical functionalities for water splitting and CO2 reduction by light. The second topic focuses on the functionalization of MOFs for photochemical response and the versatile applications of such materials. State-of-the-art research on functionalizing MOFs through photochemical reactions on the pore surface and within the pores as guests is also summarized. The third topic introduces the functionalization of MOFs for photofunctional materials, including photoluminescent tuning and integration, photoluminescent LED devices and barcodes, and photophysical applications for chemical sensing. Finally, conclusions and perspectives on the fields are given.},
}
@article {pmid29387080,
year = {2018},
author = {Raime, K and Remm, M},
title = {Method for the Identification of Taxon-Specific k-mers from Chloroplast Genome: A Case Study on Tomato Plant (Solanum lycopersicum).},
journal = {Frontiers in plant science},
volume = {9},
number = {},
pages = {6},
pmid = {29387080},
issn = {1664-462X},
abstract = {Polymerase chain reaction and different barcoding methods commonly used for plant identification from metagenomics samples are based on the amplification of a limited number of pre-selected barcoding regions. These methods are often inapplicable due to DNA degradation, low amplification success or low species discriminative power of selected genomic regions. Here we introduce a method for the rapid identification of plant taxon-specific k-mers, that is applicable for the fast detection of plant taxa directly from raw sequencing reads without aligning, mapping or assembling the reads. We identified more than 800 Solanum lycopersicum specific k-mers (32 nucleotides in length) from 42 different chloroplast genome regions using the developed method. We demonstrated that identified k-mers are also detectable in whole genome sequencing raw reads from S. lycopersicum. Also, we demonstrated the usability of taxon-specific k-mers in artificial mixtures of sequences from closely related species. Developed method offers a novel strategy for fast identification of taxon-specific genome regions and offers new perspectives for detection of plant taxa directly from sequencing raw reads.},
}
@article {pmid29386695,
year = {2017},
author = {Krisai-Greilhuber, I and Chen, Y and Jabeen, S and Madrid, H and Marincowitz, S and Razaq, A and Ševčíková, H and Voglmayr, H and Yazici, K and Aptroot, A and Aslan, A and Boekhout, T and Borovička, J and Crous, PW and Ilyas, S and Jami, F and Jiang, YL and Khalid, AN and Kolecka, A and Konvalinková, T and Norphanphoun, C and Shaheen, S and Wang, Y and Wingfield, MJ and Wu, SP and Wu, YM and Yu, JY},
title = {Fungal Systematics and Evolution: FUSE 3.},
journal = {Sydowia},
volume = {69},
number = {},
pages = {229-264},
pmid = {29386695},
issn = {0082-0598},
support = {P 27645/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {The present study introduces seven new species, one new combination, one new variety and several interesting taxonomical notes and/or geographical records. Most of the new taxa are Ascomycetes, but the study also includes a new variety of a Basidiomycete. Novel species include Gyromitra khanspurensis (Discinaceae, Pezizales, Pezizomycetes) from Pakistan growing near Cedrus deoadara and Paramyrothecium guiyangense and Paramyrothecium verruridum (Stachybotriaceae, Hypocreales, Sordariomycetes) both isolated from soil in China. New species from South Africa are Sclerostagonospora elegiae on culm litter of Elegia equisetacea, Sclerostagonospora fusiformis on culm litter of Thamnochortus spicigerus, Sclerostagonospora pinguis on culm litter of Cannomois virgata and Sclerostagonospora sulcata on culm litter of Ischyrolepis subverticellata (Phaeosphaeriaceae, Pleosporales, Dothideomycetes). Hapalocystis berkeleyi var. kickxii with its basionym Hypoxylon kickxii is shown to be a taxon on species level and thus recombined as Hapalocystis kickxii (Sydowiellaceae, Diaporthales, Sordariomycetes), and it is lecto- and epitypified. The new variety Pluteus romellii var. luteoalbus (Pluteaceae, Agaricales, Agaricomycetes) growing on a mossy fallen stem of a deciduous tree is described from Czech Republic. Cortinarius scaurocaninus (Cortinariaceae, Agaricales, Agaricomycetes) is new for Austria, Humicola grisea (Chaetomiaceae, Sordariales, Sordariomycetes) is an interesting new record for Chile. Two taxa are reported as new for Turkey: the lichenicolous fungus Opegrapha parasitica (Opegraphaceae, Arthoniales, Arthoniomycetes) growing partly immersed in the thallus of Aspicilia and the lichen Rinodina zwackhiana (Physciaceae, Teloschistales, Lecanoromycetes) from calcareous rock. Finally, Xerula strigosa (Physalacriaceae, Agaricales, Agaricomycetes), described from China, is confirmed to be present also in Pakistan.},
}
@article {pmid29386579,
year = {2018},
author = {Krawczyk, K and Nobis, M and Myszczyński, K and Klichowska, E and Sawicki, J},
title = {Plastid super-barcodes as a tool for species discrimination in feather grasses (Poaceae: Stipa).},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {1924},
pmid = {29386579},
issn = {2045-2322},
mesh = {Base Pairing/genetics ; Base Sequence ; Chromosome Mapping ; DNA Barcoding, Taxonomic/*methods ; Genetic Loci ; Genetic Variation ; Genome, Plastid ; Open Reading Frames/genetics ; Phylogeny ; Plastids/*genetics ; Poaceae/*genetics ; Polymorphism, Single Nucleotide/genetics ; Species Specificity ; },
abstract = {Present study was designed to verify which or if any of plastome loci is a hotspot region for mutations and hence might be useful for molecular species identification in feather grasses. 21 newly sequenced complete plastid genomes representing 19 taxa from the genus of Stipa were analyzed in search of the most variable and the most discriminative loci within Stipa. The results showed that the problem with selecting a good barcode locus for feather grasses lies in the very low level of genetic diversity within its plastome. None of the single chloroplast loci is polymorphic enough to play a role of a barcode or a phylogenetic marker for Stipa. The biggest number of taxa was successfully identified by the analysis of 600 bp long DNA fragment comprising a part of rbcL gene, the complete rbcL-rpl23 spacer and a part of rpl23 gene. The effectiveness of multi-locus barcode composed of six best-performing loci for Stipa (ndhH, rpl23, ndhF-rpl32, rpl32-ccsA, psbK-psbI and petA-psbJ) didn't reach 70% of analyzed taxa. The analysis of complete plastome sequences as a super-barcode for Stipa although much more effective, still didn't allow for discrimination of all the analyzed taxa of feather grasses.},
}
@article {pmid29386565,
year = {2018},
author = {Jiao, L and Yu, M and Wiedenhoeft, AC and He, T and Li, J and Liu, B and Jiang, X and Yin, Y},
title = {DNA Barcode Authentication and Library Development for the Wood of Six Commercial Pterocarpus Species: the Critical Role of Xylarium Specimens.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {1945},
pmid = {29386565},
issn = {2045-2322},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; *Gene Library ; Genetic Loci ; Phylogeny ; Pterocarpus/anatomy &amp; histology/*genetics ; Species Specificity ; Trees/genetics ; Wood/*genetics ; },
abstract = {DNA barcoding has been proposed as a useful tool for forensic wood identification and development of a reliable DNA reference library is an essential first step. Xylaria (wood collections) are potentially enormous data repositories if DNA information could be extracted from wood specimens. In this study, 31 xylarium wood specimens and 8 leaf specimens of six important commercial species of Pterocarpus were selected to investigate the reliability of DNA barcodes for authentication at the species level and to determine the feasibility of building wood DNA barcode reference libraries from xylarium specimens. Four DNA barcodes (ITS2, matK, ndhF-rpl32 and rbcL) and their combination were tested to evaluate their discrimination ability for Pterocarpus species with both TaxonDNA and tree-based analytical methods. The results indicated that the combination barcode of matK + ndhF-rpl32 + ITS2 yielded the best discrimination for the Pterocarpus species studied. The mini-barcode ndhF-rpl32 (167-173 bps) performed well distinguishing P. santalinus from its wood anatomically inseparable species P. tinctorius. Results from this study verified not only the feasibility of building DNA barcode libraries using xylarium wood specimens, but the importance of using wood rather than leaves as the source tissue, when wood is the botanical material to be identified.},
}
@article {pmid29386333,
year = {2018},
author = {Davidsson, M and Díaz-Fernández, P and Torroba, M and Schwich, OD and Aldrin-Kirk, P and Quintino, L and Heuer, A and Wang, G and Lundberg, C and Björklund, T},
title = {Molecular barcoding of viral vectors enables mapping and optimization of mRNA trans-splicing.},
journal = {RNA (New York, N.Y.)},
volume = {24},
number = {5},
pages = {673-687},
pmid = {29386333},
issn = {1469-9001},
mesh = {Animals ; Brain/metabolism ; Dependovirus/*genetics ; Female ; Gene Library ; *Genetic Vectors ; HEK293 Cells ; HeLa Cells ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Introns ; Lentivirus/*genetics ; Mice, Inbred C57BL ; Sequence Analysis, RNA/*methods ; Synapsins/genetics ; *Trans-Splicing ; },
abstract = {Genome editing has proven to be highly potent in the generation of functional gene knockouts in dividing cells. In the CNS however, efficient technologies to repair sequences are yet to materialize. Reprogramming on the mRNA level is an attractive alternative as it provides means to perform in situ editing of coding sequences without nuclease dependency. Furthermore, de novo sequences can be inserted without the requirement of homologous recombination. Such reprogramming would enable efficient editing in quiescent cells (e.g., neurons) with an attractive safety profile for translational therapies. In this study, we applied a novel molecular-barcoded screening assay to investigate RNA trans-splicing in mammalian neurons. Through three alternative screening systems in cell culture and in vivo, we demonstrate that factors determining trans-splicing are reproducible regardless of the screening system. With this screening, we have located the most permissive trans-splicing sequences targeting an intron in the Synapsin I gene. Using viral vectors, we were able to splice full-length fluorophores into the mRNA while retaining very low off-target expression. Furthermore, this approach also showed evidence of functionality in the mouse striatum. However, in its current form, the trans-splicing events are stochastic and the overall activity lower than would be required for therapies targeting loss-of-function mutations. Nevertheless, the herein described barcode-based screening assay provides a unique possibility to screen and map large libraries in single animals or cell assays with very high precision.},
}
@article {pmid29385868,
year = {2018},
author = {Carvalho, ML and Costa Silva, GJD and Melo, S and Ashikaga, FY and Shimabukuro-Dias, CK and Scacchetti, PC and Devidé, R and Foresti, F and Oliveira, C},
title = {The non-monotypic status of the neotropical fish genus Hemiodontichthys (Siluriformes, Loricariidae) evidenced by genetic approaches.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {8},
pages = {1224-1230},
doi = {10.1080/24701394.2018.1431230},
pmid = {29385868},
issn = {2470-1408},
mesh = {Animals ; Catfishes/classification/*genetics ; Evolution, Molecular ; Genetic Speciation ; *Genetic Variation ; Karyotype ; *Phylogeny ; },
abstract = {The combination of cytogenetic and molecular data with those traditionally obtained in areas like systematics and taxonomy created interesting perspectives for the analysis of natural populations under different aspects. In this context, this study aimed to evaluate the genetic differentiation among populations of the genus Hemiodontichthys Bleeker, 1862, through combined genetic techniques and included the analysis of populations sampled in the Araguaia River, Guamá River, Madeira River and two populations from the Purus River. Hemiodontichthys samples from the two localities in Purus River were also karyotyped in order to address the degree of chromosomal variation between populations. Through GMYC analysis of the COI tree, the patterns of genetic variation among local populations revealed to be higher than the ones found among distinct species from other genera of the subfamily Loricariinae, suggesting the existence of probable four cryptic species in this genus. The possible existence of a species complex in the genus is corroborated by the different cytogenetic patterns between Hemiodontichthys sp. 1 and sp. 2, revealing the necessity of a deep taxonomic review of the group.},
}
@article {pmid29385195,
year = {2018},
author = {Rech, S and Borrell Pichs, YJ and García-Vazquez, E},
title = {Anthropogenic marine litter composition in coastal areas may be a predictor of potentially invasive rafting fauna.},
journal = {PloS one},
volume = {13},
number = {1},
pages = {e0191859},
pmid = {29385195},
issn = {1932-6203},
mesh = {Animals ; Aquatic Organisms/genetics ; Bathing Beaches ; Biota ; Crassostrea ; DNA Barcoding, Taxonomic ; Ecosystem ; Environmental Monitoring ; Environmental Pollution ; *Introduced Species ; *Plastics ; Spain ; Thoracica ; *Waste Products ; },
abstract = {Anthropogenic plastic pollution is a global problem. In the marine environment, one of its less studied effects is the transport of attached biota, which might lead to introductions of non-native species in new areas or aid in habitat expansions of invasive species. The goal of the present work was to assess if the material composition of beached anthropogenic litter is indicative of the rafting fauna in a coastal area and could thus be used as a simple and cost-efficient tool for risk assessment in the future. Beached anthropogenic litter and attached biota along the 200 km coastline of Asturias, central Bay of Biscay, Spain, were analysed. The macrobiotic community attached to fouled litter items was identified using genetic barcoding combined with visual taxonomic analysis, and compared between hard plastics, foams, other plastics and non-plastic items. On the other hand, the material composition of beached litter was analysed in a standardized area on each beach. From these two datasets, the expected frequency of several rafting taxa was calculated for the coastal area and compared to the actually observed frequencies. The results showed that plastics were the most abundant type of beached litter. Litter accumulation was likely driven by coastal sources (industry, ports) and river/sewage inputs and transported by near-shore currents. Rafting vectors were almost exclusively made up of plastics and could mainly be attributed to fishing activity and leisure/ household. We identified a variety of rafting biota, including species of goose barnacles, acorn barnacles, bivalves, gastropods, polychaetes and bryozoan, and hydrozoan colonies attached to stranded litter. Several of these species were non-native and invasive, such as the giant Pacific oyster (Crassostrea gigas) and the Australian barnacle (Austrominius modestus). The composition of attached fauna varied strongly between litter items of different materials. Plastics, except for foam, had a much more diverse attached community than non-plastic materials. The predicted frequency of several taxa attached to beached litter significantly correlated with the actually observed frequencies. Therefore we suggest that the composition of stranded litter on a beach or an area could allow for predictions about the corresponding attached biotic community, including invasive species.},
}
@article {pmid29382048,
year = {2018},
author = {Syromyatnikov, MY and Borodachev, AV and Kokina, AV and Popov, VN},
title = {A Molecular Method for the Identification of Honey Bee Subspecies Used by Beekeepers in Russia.},
journal = {Insects},
volume = {9},
number = {1},
pages = {},
pmid = {29382048},
issn = {2075-4450},
abstract = {Apis mellifera L. includes several recognized subspecies that differ in their biological properties and agricultural characteristics. Distinguishing between honey bee subspecies is complicated. We analyzed the Folmer region of the COX1 gene in honey bee subspecies cultivated at bee farms in Russia and identified subspecies-specific SNPs. DNA analysis revealed two clearly distinct haplogroups in A. melliferamellifera. The first one was characterized by multiple cytosine-thymine (thymine-cytosine) transitions, one adenine-guanine substitution, and one thymine-adenine substitution. The nucleotide sequence of the second haplogroup coincided with sequences from other subspecies, except the unique C/A SNP at position 421 of the 658-bp Folmer region. A. melliferacarnica and A. melliferacarpatica could be distinguished from A. melliferamellifera and A. melliferacaucasica by the presence of the A/G SNP at position 99 of the 658-bp Folmer region. The G/A SNP at position 448 was typical for A. melliferacarnica. A. melliferacaucasicaCOX1 sequence lacked all the above-mentioned sites. We developed a procedure for rapid identification of honey bee subspecies by PCR with restriction fragment length polymorphism (RFLP) using mutagenic primers. The developed molecular method for honey bee subspecies identification is fast and inexpensive.},
}
@article {pmid29376257,
year = {2017},
author = {Chen, YJ and Liu, WJ and Chen, DN and Chieng, SH and Jiang, L},
title = {[A study on identification of edible bird's nests by DNA barcodes].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {42},
number = {23},
pages = {4593-4597},
doi = {10.19540/j.cnki.cjcmm.20171030.018},
pmid = {29376257},
issn = {1001-5302},
mesh = {Animals ; Birds/*classification ; DNA ; *DNA Barcoding, Taxonomic ; Indonesia ; Malaysia ; Phylogeny ; Thailand ; Vietnam ; },
abstract = {To provide theoretical basis for the traceability and quality evaluation of edible bird's nests (EBNs), the Cytb sequence was applied to identify the origin of EBNs. A total of 39 experiment samples were collected from Malaysia, Indonesia, Vietnam and Thailand. Genomic DNA was extracted for the PCR reaction. The amplified products were sequenced. 36 sequences were downloaded from Gen Bank including edible nest swiftlet, black nest swiftlet, mascarene swiftlet, pacific swiftlet and germain's swiftlet. MEGA 7.0 was used to analyze the distinction of sequences by the method of calculating the distances in intraspecific and interspecific divergences and constructing NJ and UPMGA phylogenetic tree based on Kimera-2-parameter model. The results showed that 39 samples were from three kinds of EBNs. Interspecific divergences were significantly greater than the intraspecific one. Samples could be successfully distinguished by NJ and UPMGA phylogenetic tree. In conclusion, Cytb sequence could be used to distinguish the origin of EBNs and it is efficient for tracing the origin species of EBNs.},
}
@article {pmid29375779,
year = {2018},
author = {Weiss, M and Weigand, H and Weigand, AM and Leese, F},
title = {Genome-wide single-nucleotide polymorphism data reveal cryptic species within cryptic freshwater snail species-The case of the Ancylus fluviatilis species complex.},
journal = {Ecology and evolution},
volume = {8},
number = {2},
pages = {1063-1072},
pmid = {29375779},
issn = {2045-7758},
abstract = {DNA barcoding utilizes short standardized DNA sequences to identify species and is increasingly used in biodiversity assessments. The technique has unveiled an unforeseeably high number of morphologically cryptic species. However, if speciation has occurred relatively recently and rapidly, the use of single gene markers, and especially the exclusive use of mitochondrial markers, will presumably fail in delimitating species. Therefore, the true number of biological species might be even higher. One mechanism that can result in rapid speciation is hybridization of different species in combination with polyploidization, that is, allopolyploid speciation. In this study, we analyzed the population genetic structure of the polyploid freshwater snail Ancylus fluviatilis, for which allopolyploidization was postulated as a speciation mechanism. DNA barcoding has already revealed four cryptic species within A. fluviatilis (i.e., A. fluviatilis s. str., Ancylus sp. A-C), but early allozyme data even hint at the presence of additional cryptic lineages in Central Europe. We combined COI sequencing with high-resolution genome-wide SNP data (ddRAD data) to analyze the genetic structure of A. fluviatilis populations in a Central German low mountain range (Sauerland). The ddRAD data results indicate the presence of three cryptic species within A. fluviatilis s. str. occurring in sympatry and even syntopy, whereas mitochondrial sequence data only support the existence of one species, with shared haplotypes between species. Our study hence points to the limitations of DNA barcoding when dealing with organismal groups where speciation is assumed to have occurred rapidly, for example, through the process of allopolyploidization. We therefore emphasize that single marker DNA barcoding can underestimate the true species diversity and argue in strong favor of using genome-wide data for species delimitation in such groups.},
}
@article {pmid29373939,
year = {2018},
author = {Rosas, U and Menendez, F and Cornejo, R and Canales, R and Velez-Zuazo, X},
title = {Fish DNA barcoding around large marine infrastructure for improved biodiversity assessment and monitoring.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {8},
pages = {1174-1179},
doi = {10.1080/24701394.2018.1431225},
pmid = {29373939},
issn = {2470-1408},
mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/methods/*standards ; Databases, Genetic ; Perciformes/classification/*genetics ; Phylogeny ; Reference Values ; },
abstract = {Accurate species-level identification is pivotal for environmental assessments and monitoring. The PERU LNG terminal is composed of large marine infrastructure located on the central coast of Peru. Since construction, taxonomically challenging species such as drum fishes (Sciaenidae) have been attracted to the new hard-bottom habitat. We conducted a DNA barcoding study to investigate fish diversity and constructed a DNA barcode reference library. We examined 56 vouchered specimens and identified 24 unique species. Intra- and interspecific divergence estimates ranged between 0 and 0.64% and 11 and 35.5%, respectively. We assessed the efficiency of the reference library to identify 29 non-vouchered specimens. We had 82.5% efficiency by using both our reference library (n = 17) and GenBank (n = 24). We highlight the importance of implementing molecular barcoding for complementing biodiversity assessments in marine environments. This study represents a first step towards generating a comprehensive DNA barcode reference library for marine fishes in Peru.},
}
@article {pmid29371794,
year = {2017},
author = {Lee, JS and Shin, HD and Lee, HB and Choi, YJ},
title = {Taxonomy and Phylogeny of Peronospora Species (Oomycota) Parasitic to Stellaria and Pseudostellaria in Korea, with the Introduction of Peronospora casparyi sp. nov.},
journal = {Mycobiology},
volume = {45},
number = {4},
pages = {263-269},
pmid = {29371794},
issn = {1229-8093},
abstract = {The genus Peronospora, an obligate biotrophic group belonging to Oomycota, causes serious damage to a variety of wild and ornamental plants, as well as cultivated crops, such as beet, rose, spinach, and tobacco. To investigate the diversity of Peronospora species parasitic to Stellaria and Pseudostellaria (Caryophyllaceae) plants in Korea, we performed a morphological analysis on dried herbarium specimens and molecular phylogenetic inferences based on internal transcribed spacer rDNA and cox2 mitochondrial DNA sequences. As a result, it was confirmed that there are four species of Peronospora parasitic to specific species of Stellaria and Pseudostellaria, all of which were hitherto unrecorded in Korea: P. alsinearum (ex Stellaria media), P. stellariae-aquaticae (ex Stellaria aquatica), P. stellariae-uliginosae (ex Stellaria alsine), and P. pseudostellariae (ex Pseudostellaria palibiniana). In addition, Peronospora specimens parasitic to Pseudostellaria davidii differed morphologically from P. pseudostellariae owing to the large and ellipsoidal conidia; this morphological discrepancy was also validated by the high genetic divergence between the two species. Peronospora casparyi sp. nov. is described and illustrated here.},
}
@article {pmid29363271,
year = {2018},
author = {Blaser, S and Diem, H and von Felten, A and Gueuning, M and Andreou, M and Boonham, N and Tomlinson, J and Müller, P and Utzinger, J and Frey, JE and Bühlmann, A},
title = {From laboratory to point of entry: development and implementation of a loop-mediated isothermal amplification (LAMP)-based genetic identification system to prevent introduction of quarantine insect species.},
journal = {Pest management science},
volume = {74},
number = {6},
pages = {1504-1512},
pmid = {29363271},
issn = {1526-4998},
mesh = {Animals ; Electron Transport Complex IV/analysis ; Hemiptera/*classification/genetics ; Insect Control/*methods ; Insect Proteins/analysis ; Introduced Species ; Nucleic Acid Amplification Techniques/*methods ; Quarantine/*methods ; Switzerland ; Tephritidae/*classification/genetics ; Thysanoptera/*classification/genetics ; },
abstract = {BACKGROUND: Rapid genetic on-site identification methods at points of entry, such as seaports and airports, have the potential to become important tools to prevent the introduction and spread of economically harmful pest species that are unintentionally transported by the global trade of plant commodities. This paper reports the development and evaluation of a loop-mediated isothermal amplification (LAMP)-based identification system to prevent introduction of the three most frequently encountered regulated quarantine insect species groups at Swiss borders, Bemisia tabaci, Thrips palmi and several regulated fruit flies of the genera Bactrocera and Zeugodacus.<br><br>RESULTS: The LAMP primers were designed to target a fragment of the mitochondrial cytochrome c oxidase subunit I gene and were generated based on publicly available DNA sequences. Laboratory evaluations analysing 282 insect specimens suspected to be quarantine organisms revealed an overall test efficiency of 99%. Additional on-site evaluation at a point of entry using 37 specimens performed by plant health inspectors with minimal laboratory training resulted in an overall test efficiency of 95%. During both evaluation rounds, there were no false-positives and the observed false-negatives were attributable to human-induced manipulation errors. To overcome the possibility of accidental introduction of pests as a result of rare false-negative results, samples yielding negative results in the LAMP method were also subjected to DNA barcoding.<br><br>CONCLUSION: Our LAMP assays reliably differentiated between the tested regulated and non-regulated insect species within <1&#x2009;h. Hence, LAMP assays represent suitable tools for rapid on-site identification of harmful pests, which might facilitate an accelerated import control process for plant commodities. &#xa9; 2018 The Authors. Pest Management Science published by John Wiley &amp; Sons Ltd on behalf of Society of Chemical Industry.},
}
@article {pmid29363130,
year = {2018},
author = {Turan, D and Kalayci, G and Kaya, C and Bektaş, Y and Küçük, F},
title = {A new species of Petroleuciscus (Teleostei: Cyprinidae) from the Büyük Menderes River, southwestern Anatolia, Turkey.},
journal = {Journal of fish biology},
volume = {92},
number = {4},
pages = {875-887},
doi = {10.1111/jfb.13525},
pmid = {29363130},
issn = {1095-8649},
mesh = {Animals ; Cyprinidae/anatomy &amp; histology/*classification ; DNA, Mitochondrial/genetics ; Pigmentation ; Rivers ; Turkey ; },
abstract = {Petroleuciscus ninae sp. nov. is described from the Büyük Menderes River drainage. The new species is distinguished by having a black lateral stripe from head to base of caudal fin, stripe distinct anteriorly and posteriorly, wider than eye diameter; numerous black pigments on anal-fin rays; body depth at dorsal-fin origin 27-30% standard length (LS); head width at posterior margin of eye 16-19% LS ; and eye diameter smaller than snout length. Petroleuciscus ninae is also distinguished from other species in adjacent waters by having six fixed diagnostic nucleotide substitutions in the mitochondrial DNA coI barcode region.},
}
@article {pmid29362872,
year = {2018},
author = {Cornara, L and Fortuna-Perez, AP and Bruni, I and Salis, A and Damonte, G and Borghesi, B and Clericuzio, M},
title = {Zornia latifolia: a smart drug being adulterated by Stylosanthes guianensis.},
journal = {International journal of legal medicine},
volume = {132},
number = {5},
pages = {1321-1331},
pmid = {29362872},
issn = {1437-1596},
mesh = {Apigenin ; Brazil ; Chromatography, High Pressure Liquid ; Dose-Response Relationship, Drug ; *Drug Contamination ; Fabaceae/*chemistry ; Flavonoids/*analysis ; Luteolin ; Plant Extracts/*analysis ; Plants ; Quercetin ; },
abstract = {Dried herbal preparations, based on "Zornia latifolia," are commonly sold on web, mainly for their supposed hallucinogenic properties. In this work, we demonstrate that these commercial products contain a different Fabacea, i.e., Stylosanthes guianensis, a cheaper plant, widely cultivated in tropical regions as a fodder legume. We were provided with plant samples of true Zornia latifolia from Brazil, and carried out a thorough comparison of the two species. The assignment of commercial samples was performed by means of micro-morphological analysis, DNA barcoding, and partial phytochemical investigation. We observed that Z. latifolia contains large amounts of flavonoid di-glycosides derived from luteolin, apigenin, and genistein, while in S. guianensis lesser amounts of flavonoids, mainly derived from quercetin, were found. It is likely that the spasmolytic and anxiolytic properties of Z. latifolia, as reported in traditional medicine, derive from its contents in apigenin and/or genistein.},
}
@article {pmid29362550,
year = {2018},
author = {Binh, HT and Ngoc, NV and Bon, TN and Tagane, S and Suyama, Y and Yahara, T},
title = {A new species and two new records of Quercus (Fagaceae) from northern Vietnam.},
journal = {PhytoKeys},
volume = {},
number = {92},
pages = {1-15},
pmid = {29362550},
issn = {1314-2011},
abstract = {A new species, Quercus xuanlienensis Binh, Ngoc &amp; Bon, is described from Xuan Lien Nature Reserve, Vietnam. The new species is morphologically similar to Q. edithiae Skan, in having 8-11 pairs of secondary veins, bowl-shaped cupules and ellipsoid to cylindrical-ellipsoid and basally convex nuts. It differs in having serrulate leaf margins only at apical 1/5-1/7, almost entire margins of bracts on cupule and much longer nuts. The species is also similar to Q. fleuryi Hickel &amp; A. Camus in having leaves glabrous on both surfaces with only an apically serrulate margin but differs in having shorter petioles, cupules enclosing 1/5 of the nut and much longer nuts. In addition, Q. disciformis Chun &amp; Tsiang. and Q. bella Chun &amp; Tsiang., previously known from China, are newly recorded from Ba Vi National Park, Vietnam.},
}
@article {pmid29359196,
year = {2018},
author = {Liu, H and Price, MN and Waters, RJ and Ray, J and Carlson, HK and Lamson, JS and Chakraborty, R and Arkin, AP and Deutschbauer, AM},
title = {Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria.},
journal = {mSystems},
volume = {3},
number = {1},
pages = {},
pmid = {29359196},
issn = {2379-5077},
abstract = {Transposon mutagenesis coupled to next-generation sequencing (TnSeq) is a powerful approach for discovering the functions of bacterial genes. However, the development of a suitable TnSeq strategy for a given bacterium can be costly and time-consuming. To meet this challenge, we describe a part-based strategy for constructing libraries of hundreds of transposon delivery vectors, which we term "magic pools." Within a magic pool, each transposon vector has a different combination of upstream sequences (promoters and ribosome binding sites) and antibiotic resistance markers as well as a random DNA barcode sequence, which allows the tracking of each vector during mutagenesis experiments. To identify an efficient vector for a given bacterium, we mutagenize it with a magic pool and sequence the resulting insertions; we then use this efficient vector to generate a large mutant library. We used the magic pool strategy to construct transposon mutant libraries in five genera of bacteria, including three genera of the phylum Bacteroidetes. IMPORTANCE Molecular genetics is indispensable for interrogating the physiology of bacteria. However, the development of a functional genetic system for any given bacterium can be time-consuming. Here, we present a streamlined approach for identifying an effective transposon mutagenesis system for a new bacterium. Our strategy first involves the construction of hundreds of different transposon vector variants, which we term a "magic pool." The efficacy of each vector in a magic pool is monitored in parallel using a unique DNA barcode that is introduced into each vector design. Using archived DNA "parts," we next reassemble an effective vector for making a whole-genome transposon mutant library that is suitable for large-scale interrogation of gene function using competitive growth assays. Here, we demonstrate the utility of the magic pool system to make mutant libraries in five genera of bacteria.},
}
@article {pmid29358894,
year = {2017},
author = {Zhang, X and Zhao, Z},
title = {A new species of Longicoelotes (Araneae, Agelenidae) from China, with the first description of the male of L. kulianganus (Chamberlin, 1924).},
journal = {ZooKeys},
volume = {},
number = {686},
pages = {137-147},
pmid = {29358894},
issn = {1313-2989},
abstract = {A new Longicoeletes species is described from Jiangxi Province, China: L. geeisp. n. (♂♀). In addition, the male of L. kulianganus (Chamberlin, 1924) is described for the first time. DNA barcodes of the two species are documented for future use and as proof of molecular differences between these species.},
}
@article {pmid29354373,
year = {2018},
author = {Ismail, NZ and Arsad, H and Samian, MR and Hamdan, MR and Othman, AS},
title = {Assessment of three plastid DNA barcode markers for identification of Clinacanthus nutans (Acanthaceae).},
journal = {3 Biotech},
volume = {8},
number = {1},
pages = {62},
pmid = {29354373},
issn = {2190-572X},
abstract = {This study was conducted to determine the feasibility of using three plastid DNA regions (matK, trnH-psbA, and rbcL) as DNA barcodes to identify the medicinal plant Clinacanthus nutans. In this study, C. nutans was collected at several different locations. Total genomic DNA was extracted, amplified by polymerase chain reaction (PCR), and sequenced using matK, trnH-psbA, and rbcL, primers. DNA sequences generated from PCR were submitted to the National Center for Biotechnology Information's (NCBI) GenBank. Identification of C. nutans was carried out using NCBI's Basic Local Alignment Search Tool (BLAST). The rbcL and trnH-psbA regions successfully identified C. nutans with sequencing rates of 100% through BLAST identification. Molecular Evolutionary Genetics Analysis (MEGA) 6.0 was used to analyze interspecific and intraspecific divergence of plastid DNA sequences. rbcL and matK exhibited the lowest average interspecific distance (0.0487 and 0.0963, respectively), whereas trnH-psbA exhibited the highest average interspecific distance (0.2029). The R package Spider revealed that trnH-psbA correctly identified Barcode of Life Data System (BOLD) 96%, best close match 79%, and near neighbor 100% of the species, compared to matK (BOLD 72%; best close match 64%; near neighbor 78%) and rbcL (BOLD 77%; best close match 62%; near neighbor 88%). These results indicate that trnH-psbA is very effective at identifying C. nutans, as it performed well in discriminating species in Acanthaceae.},
}
@article {pmid29352182,
year = {2018},
author = {Bi, Y and Zhang, MF and Xue, J and Dong, R and Du, YP and Zhang, XH},
title = {Chloroplast genomic resources for phylogeny and DNA barcoding: a case study on Fritillaria.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {1184},
pmid = {29352182},
issn = {2045-2322},
mesh = {Computational Biology/methods ; *DNA Barcoding, Taxonomic ; DNA, Chloroplast ; Fritillaria/*classification/*genetics ; *Genome, Chloroplast ; Microsatellite Repeats ; *Phylogeny ; Repetitive Sequences, Nucleic Acid ; Whole Genome Sequencing ; },
abstract = {The genus Fritillaria comprises approximately 130 perennial herbaceous species. In the Pharmacopoeia of the People's Republic of China, the bulbs of 11 Fritillaria species are used in Chinese herbal medicines. However, the traditional methods of morphological classification cannot accurately identify closely related species of Fritillaria. Previous studies have attempted to identify these species with universal molecular markers, but insufficient phylogenetic signal was available. In this study, the complete chloroplast genomes of eight Fritillaria species were compared. The length of the eight Fritillaria chloroplast genomes ranges from 151,009 bp to 152,224 bp. A total of 136 SSR loci were identified, including 124 polymorphic SSR loci. For large repeat sequences, 108 repeat loci and four types of repeats were observed. Ten highly variable regions were identified as potential molecular markers. These SSRs, large repeat sequences and highly variable regions provide important information for the development of genetic markers and DNA fingerprints. Phylogenetic analyses showed that the topological structures of all data sets (except the IR regions) were in complete agreement and well resolved. Overall, this study provides comprehensive chloroplast genomic resources, which will be valuable for future studies of evolution and species identification in Fritillaria.},
}
@article {pmid29345218,
year = {2018},
author = {Duque-Gamboa, DN and Castillo-Cárdenas, MF and Hernández, LM and Guzmán, YC and Manzano, MR and Toro-Perea, N},
title = {Mitochondrial DNA suggests cryptic speciation in Prodiplosis longifila Gagné (Diptera: Cecidomyiidae) associated with geographic distance and host specialization.},
journal = {Bulletin of entomological research},
volume = {108},
number = {6},
pages = {739-749},
doi = {10.1017/S0007485317001298},
pmid = {29345218},
issn = {1475-2670},
mesh = {Animal Distribution ; Animals ; Colombia ; DNA, Mitochondrial/analysis ; DNA, Ribosomal Spacer/analysis ; Diptera/*genetics ; Ecuador ; Electron Transport Complex IV/analysis ; *Evolution, Molecular ; Florida ; *Genetic Speciation ; *Herbivory ; Phylogeny ; Phylogeography ; },
abstract = {Prodiplosis longifila is reported as a pest of a wide range of species cultivated in America, including citrus, solanaceous species and asparagus. This species has different behavioural traits that are primarily centred on the oviposition habit and the feeding of larvae, which can change depending on the host. However, scarce information is available on population studies and the natural history of this insect, and uncertainty exists about the taxonomic identity and the geographic distribution of this species. The main objective was to perform a phylogenetic and genetic study of P. longifila populations and to define whether the North American and South American populations belong to the same species or whether a differentiation process had occurred due to geographic distance. A second objective was to determine whether this species showed genetic differentiation by host specialization in South America. The phylogenetic and population analyses based on DNA barcodes (cytochrome oxidase I gene) and a region of the ribosomal DNA (ITS2) revealed divergent clades attributable to geographic distance and host specificity. The North American and South American P. longifila insects were confirmed to be genetically distinct, and the genetic distances exceeded the values expected for intraspecific variation. In South America, the population analysis of P. longifila from tomato, sweet pepper (Solanaceae), Tahiti lime and key lime (Rutaceae) hosts evidenced high genetic differentiation between populations associated with different hosts and an absence of gene flow between these groups, suggesting the corresponding formation of cryptic species.},
}
@article {pmid29342169,
year = {2018},
author = {Reeves, LE and Krysko, KL and Avery, ML and Gillett-Kaufman, JL and Kawahara, AY and Connelly, CR and Kaufman, PE},
title = {Interactions between the invasive Burmese python, Python bivittatus Kuhl, and the local mosquito community in Florida, USA.},
journal = {PloS one},
volume = {13},
number = {1},
pages = {e0190633},
pmid = {29342169},
issn = {1932-6203},
mesh = {Animals ; Boidae/*physiology ; *Culex ; Female ; Florida ; *Host-Parasite Interactions ; *Introduced Species ; },
abstract = {The Burmese python, Python bivittatus Kuhl, is a well-established invasive species in the greater Everglades ecosystem of southern Florida, USA. Most research on its ecological impacts focuses on its role as a predator and its trophic interactions with native vertebrate species, particularly mammals. Beyond predation, there is little known about the ecological interactions between P. bivittatus and native faunal communities. It is likely that established populations of P. bivittatus in southern Florida serve as hosts for native mosquito communities. To test this concept, we used mitochondrial cytochrome c oxidase subunit I DNA barcoding to determine the hosts of blood fed mosquitoes collected at a research facility in northern Florida where captive P. bivittatus and Argentine black and white tegu, Salvator merianae (Duméril and Bibron), are maintained in outdoor enclosures, accessible to local mosquitoes. We recovered python DNA from the blood meals of three species of Culex mosquitoes: Culex erraticus (Dyar and Knab), Culex quinquefasciatus Say, and Culex pilosus (Dyar and Knab). Culex erraticus conclusively (P = 0.001; Fisher's Exact Test) took more blood meals from P. bivittatus than from any other available host. While the majority of mosquito blood meals in our sample were derived from P. bivittatus, only one was derived from S. merianae. These results demonstrate that local mosquitoes will feed on invasive P. bivittatus, a recently introduced host. If these interactions also occur in southern Florida, P. bivittatus may be involved in the transmission networks of mosquito-vectored pathogens. Our results also illustrate the potential of detecting the presence of P. bivittatus in the field through screening mosquito blood meals for their DNA.},
}
@article {pmid29340236,
year = {2018},
author = {Erasmus, DJ and Yurkowski, EA and Huber, DPW},
title = {DNA barcode-based survey of Trichoptera in the Crooked River reveals three new species records for British Columbia.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e4221},
pmid = {29340236},
issn = {2167-8359},
abstract = {Anthropogenic pressures on aquatic systems have placed a renewed focus on biodiversity of aquatic macroinvertebrates. By combining classical taxonomy and DNA barcoding we identified 39 species of caddisflies from the Crooked River, a unique and sensitive system in the southernmost arctic watershed in British Columbia. Our records include three species never before recorded in British Columbia: Lepidostoma togatum (Lepidostomatidae), Ceraclea annulicornis (Leptoceridae), and possibly Cheumatopsyche harwoodi (Hydropsychidae). Three other specimens may represent new occurrence records and a number of other records seem to be substantial observed geographic range expansions within British Columbia.},
}
@article {pmid29338807,
year = {2018},
author = {Betts, EL and Gentekaki, E and Thomasz, A and Breakell, V and Carpenter, AI and Tsaousis, AD},
title = {Genetic diversity of Blastocystis in non-primate animals.},
journal = {Parasitology},
volume = {145},
number = {9},
pages = {1228-1234},
pmid = {29338807},
issn = {1469-8161},
support = {BB/M009971/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Animals, Zoo/*parasitology ; Birds/parasitology ; Blastocystis/classification/*genetics/pathogenicity ; Blastocystis Infections/*veterinary ; Carrier State/parasitology ; DNA Barcoding, Taxonomic ; DNA, Protozoan/*genetics ; England ; Feces/parasitology ; *Genetic Variation ; Mammals/parasitology ; Phylogeny ; Prevalence ; RNA, Ribosomal/genetics ; },
abstract = {Blastocystis is an anaerobic protist, commonly inhabiting the intestinal tract of both humans and other animals. Blastocystis is extremely diverse comprising 17 genetically distinct subtypes in mammals and birds. Pathogenicity of this enteric microbe is currently disputed and knowledge regarding its distribution, diversity and zoonotic potential is fragmentary. Most research has focused on Blastocystis from primates, while sampling from other animals remains limited. Herein, we investigated the prevalence and distribution of Blastocystis in animals held within a conservation park in South East England. A total of 118 samples were collected from 27 vertebrate species. The barcoding region of the small-subunit ribosomal RNA was used for molecular identification and subtyping. Forty one per cent of the species were sequence positive for Blastocystis indicating a high prevalence and wide distribution among the animals in the park. Six subtypes were identified, one of which is potentially novel. Moreover, the majority of animals were asymptomatic carriers, suggesting that Blastocystis is not pathogenic in animals. This study provides a thorough investigation of Blastocystis prevalence within a wildlife park in the UK and can be used as a platform for further investigations on the distribution of other eukaryotic gut microbes.},
}
@article {pmid29338798,
year = {2018},
author = {Fernández-González, S and Pérez-Rodríguez, A and Proctor, HC and De la Hera, I and Pérez-Tris, J},
title = {High diversity and low genetic structure of feather mites associated with a phenotypically variable bird host.},
journal = {Parasitology},
volume = {145},
number = {9},
pages = {1243-1250},
doi = {10.1017/S0031182017002360},
pmid = {29338798},
issn = {1469-8161},
mesh = {Animal Migration ; Animals ; Bird Diseases/*parasitology ; Canada ; DNA Barcoding, Taxonomic ; Ecosystem ; *Genetic Variation ; *Genetics, Population ; Host-Parasite Interactions ; Mite Infestations/transmission/*veterinary ; Mites/*genetics ; Passeriformes/*parasitology ; Phylogeny ; },
abstract = {Obligate symbionts may be genetically structured among host individuals and among phenotypically distinct host populations. Such processes may in turn determine within-host genetic diversity of symbionts, which is relevant for understanding symbiont population dynamics. We analysed the population genetic structure of two species of feather mites (Proctophyllodes sylviae and Trouessartia bifurcata) in migratory and resident blackcaps Sylvia atricapilla that winter sympatrically. Resident and migratory hosts may provide mites with habitats of different qualities, what might promote specialization of mite populations. We found high genetic diversity of within-host populations for both mite species, but no sign of genetic structure of mites between migratory and resident hosts. Our results suggest that, although dispersal mechanisms between hosts during the non-breeding season are unclear, mite populations are not limited by transmission bottlenecks that would reduce genetic diversity among individuals that share a host. Additionally, there is no evidence that host phenotypic divergence (associated with the evolution of migration and residency) has promoted the evolution of host-specialist mite populations. Unrestricted dispersal among host types may allow symbiotic organisms to avoid inbreeding and to persist in the face of habitat heterogeneity in phenotypically diverse host populations.},
}
@article {pmid29337374,
year = {2018},
author = {Piccioni, F and Younger, ST and Root, DE},
title = {Pooled Lentiviral-Delivery Genetic Screens.},
journal = {Current protocols in molecular biology},
volume = {121},
number = {},
pages = {32.1.1-32.1.21},
doi = {10.1002/cpmb.52},
pmid = {29337374},
issn = {1934-3647},
mesh = {Animals ; *CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats ; *Ectopic Gene Expression ; Gene Editing/methods ; Gene Knockout Techniques/*methods ; *Gene Library ; Genome ; Genomics/*methods ; Humans ; Lentivirus/*genetics ; Mice ; *RNA Interference ; Transduction, Genetic/methods ; },
abstract = {Pooled cell-based screens of mammalian genetic perturbations enable systematic large-scale, even genome-scale, evaluation of gene function. Pooled screens introduce genetic perturbations into a cell population through viral transduction such that each cell integrates into its DNA a single or small number of library perturbations with barcodes identifying the perturbations. One then selects and physically isolates the subset of cells that exhibit the phenotype of interest. Sequencing the barcodes in the hit cells reveals which genes favored or inhibited the hit phenotype. Various genetic perturbations are possible, including CRISPR gene knockout, ectopic gene expression, and RNA interference. Regardless of the type of library being screened or the type of cell model being tested, such screens involve many common steps and procedures. This unit describes detailed experimental protocols for the key steps, and also highlights some of the key factors to achieving a well-powered, reproducible screen result. © 2018 by John Wiley &amp; Sons, Inc.},
}
@article {pmid29336049,
year = {2018},
author = {Lilja, T and Troell, K and Kirik, H and Lindström, A},
title = {A distinct group of north European Aedes vexans as determined by mitochondrial and nuclear markers.},
journal = {Medical and veterinary entomology},
volume = {32},
number = {3},
pages = {282-289},
doi = {10.1111/mve.12294},
pmid = {29336049},
issn = {1365-2915},
mesh = {Aedes/classification/cytology/*genetics ; Animals ; Base Sequence ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Female ; *Genetic Variation ; Phylogeny ; Sweden ; },
abstract = {The floodwater mosquito Aedes (Aedimorphus) vexans (Meigen, 1830) (Diptera: Culicidae) is common in several areas of Sweden and is predicted to become more abundant in the wake of expected changes in precipitation and temperature caused by climate change. As well as being a nuisance, Ae. vexans can act as a vector of over 30 viruses. In the event of an outbreak of disease caused by a vector-borne virus, knowledge of the distribution, population structure and intermixing of populations from different locations will help direct resources to target locations to prevent spread of the pathogen. The present study analysed individual Ae. vexans from eight locations throughout Sweden. Based on the mitochondrial cytochrome oxidase I (COI) marker, a subset of the analysed mosquitoes cluster apart from the other samples. Similarly, two nuclear loci were sequenced and the same phylogenetic structure observed. These results indicate that this group represents a reproductively isolated population among Ae. vexans. Comparisons with COI sequences held in the Barcode of Life Database (BoLD) for Ae. vexans from around the world show that specimens collected in Belgium and Estonia group together with the Swedish group, suggesting that this genotype is present throughout northern Europe. These results suggest there is a cryptic taxonomic unit related to Ae. vexans in northern Europe.},
}
@article {pmid29335281,
year = {2018},
author = {Shukla, CJ and McCorkindale, AL and Gerhardinger, C and Korthauer, KD and Cabili, MN and Shechner, DM and Irizarry, RA and Maass, PG and Rinn, JL},
title = {High-throughput identification of RNA nuclear enrichment sequences.},
journal = {The EMBO journal},
volume = {37},
number = {6},
pages = {},
pmid = {29335281},
issn = {1460-2075},
support = {P01 GM099117/GM/NIGMS NIH HHS/United States ; R01 MH102416/MH/NIMH NIH HHS/United States ; R01 GM083084/GM/NIGMS NIH HHS/United States ; R01 HG005220/HG/NHGRI NIH HHS/United States ; U01 DA040612/DA/NIDA NIH HHS/United States ; },
mesh = {Cell Nucleus/genetics ; HeLa Cells ; High-Throughput Nucleotide Sequencing ; Humans ; In Situ Hybridization, Fluorescence ; RNA, Long Noncoding/*genetics ; Sequence Analysis, RNA ; },
abstract = {In the post-genomic era, thousands of putative noncoding regulatory regions have been identified, such as enhancers, promoters, long noncoding RNAs (lncRNAs), and a cadre of small peptides. These ever-growing catalogs require high-throughput assays to test their functionality at scale. Massively parallel reporter assays have greatly enhanced the understanding of noncoding DNA elements en masse Here, we present a massively parallel RNA assay (MPRNA) that can assay 10,000 or more RNA segments for RNA-based functionality. We applied MPRNA to identify RNA-based nuclear localization domains harbored in lncRNAs. We examined a pool of 11,969 oligos densely tiling 38 human lncRNAs that were fused to a cytosolic transcript. After cell fractionation and barcode sequencing, we identified 109 unique RNA regions that significantly enriched this cytosolic transcript in the nucleus including a cytosine-rich motif. These nuclear enrichment sequences are highly conserved and over-represented in global nuclear fractionation sequencing. Importantly, many of these regions were independently validated by single-molecule RNA fluorescence in situ hybridization. Overall, we demonstrate the utility of MPRNA for future investigation of RNA-based functionalities.},
}
@article {pmid29334378,
year = {2018},
author = {Hu, F and Zeng, C and Long, R and Miao, Y and Wei, L and Xu, Q and Min, W},
title = {Supermultiplexed optical imaging and barcoding with engineered polyynes.},
journal = {Nature methods},
volume = {15},
number = {3},
pages = {194-200},
pmid = {29334378},
issn = {1548-7105},
support = {DP2 EB016573/EB/NIBIB NIH HHS/United States ; R01 EB020892/EB/NIBIB NIH HHS/United States ; },
mesh = {Cell Survival ; Fluorescent Dyes/*chemistry ; HeLa Cells ; Humans ; Optical Imaging/*instrumentation/*methods ; Optics and Photonics ; Polyynes/*chemistry ; Spectrum Analysis, Raman/*methods ; },
abstract = {Optical multiplexing has a large impact in photonics, the life sciences and biomedicine. However, current technology is limited by a 'multiplexing ceiling' from existing optical materials. Here we engineered a class of polyyne-based materials for optical supermultiplexing. We achieved 20 distinct Raman frequencies, as 'Carbon rainbow', through rational engineering of conjugation length, bond-selective isotope doping and end-capping substitution of polyynes. With further probe functionalization, we demonstrated ten-color organelle imaging in individual living cells with high specificity, sensitivity and photostability. Moreover, we realized optical data storage and identification by combinatorial barcoding, yielding to our knowledge the largest number of distinct spectral barcodes to date. Therefore, these polyynes hold great promise in live-cell imaging and sorting as well as in high-throughput diagnostics and screening.},
}
@article {pmid29334293,
year = {2018},
author = {Liu, J and Zhang, H},
title = {DNA barcoding for species identification in deep-sea clams (Mollusca: Bivalvia: Vesicomyidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {8},
pages = {1165-1173},
doi = {10.1080/24701394.2018.1424843},
pmid = {29334293},
issn = {2470-1408},
mesh = {Animals ; Bivalvia/*classification/genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Phylogeny ; },
abstract = {Deep-sea clams (Bivalvia: Vesicomyidae) have been found in reduced environments over the world oceans, but taxonomy of this group remains confusing at species and supraspecific levels due to their high-morphological similarity and plasticity. In the present study, we collected mitochondrial COI sequences to evaluate the utility of DNA barcoding on identifying vesicomyid species. COI dataset identified 56 well-supported putative species/operational taxonomic units (OTUs), approximately covering half of the extant vesicomyid species. One species (OTU2) was first detected, and may represent a new species. Average distances between species ranged from 1.65 to 29.64%, generally higher than average intraspecific distances (0-1.41%) when excluding Pliocardia sp.10 cf. venusta (average intraspecific distance 1.91%). Local barcoding gap existed in 33 of the 35 species when comparing distances of maximum interspecific and minimum interspecific distances with two exceptions (Abyssogena southwardae and Calyptogena rectimargo-starobogatovi). The barcode index number (BIN) system determined 41 of the 56 species/OTUs, each with a unique BIN, indicating their validity. Three species were found to have two BINs, together with their high level of intraspecific variation, implying cryptic diversity within them. Although fewer 16 S sequences were collected, similar results were obtained. Nineteen putative species were determined and no overlap observed between intra- and inter-specific variation. Implications of DNA barcoding for the Vesicomyidae taxonomy were then discussed. Findings of this study will provide important evidence for taxonomic revision in this problematic clam group, and accelerate the discovery of new vesicomyid species in the future.},
}
@article {pmid29333345,
year = {2018},
author = {Li, JY and Guo, DH and Wu, PC and He, LS},
title = {Ontogeny reversal and phylogenetic analysis of Turritopsis sp.5 (Cnidaria, Hydrozoa, Oceaniidae), a possible new species endemic to Xiamen, China.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e4225},
pmid = {29333345},
issn = {2167-8359},
abstract = {Ontogeny reversal, as seen in some cnidarians, is an unprecedented phenomenon in the animal kingdom involving reversal of the ordinary life cycle. Three species of Turritopsis have been shown to be capable of inverted metamorphosis, a process in which the pelagic medusa transforms back into a juvenile benthic polyp stage when faced with adverse conditions. Turritopsis sp.5 is a species of Turritopsis collected from Xiamen, China which presents a similar ability, being able to reverse its life cycle if injured by mechanical stress. Phylogenetic analysis based on both 16S rDNA and cytochrome c oxidase subunit I (COI) genetic barcodes shows that Turritopsis sp.5 is phylogenetically clustered in a clade separate from other species of Turritopsis. The genetic distance between T. sp.5 and the Japanese species T. sp.2 is the shortest, when measured by the Kimura 2-Parameter metric, and the distance to the New Zealand species T. rubra is the largest. An experimental assay on the induction of reverse development in this species was initiated by cutting medusae into upper and lower parts. We show, for the first time, that the two dissected parts have significantly different potentials to transform into polyps. Also, a series of morphological changes of the reversed life cycle can be recognised, including medusa stage, contraction stage I, contraction stage II, cyst, cyst with stolons, and polyp. The discovery of species capable of reverse ontogeny caused by unfavorable conditions adds to the available systems with which to study the cell types that contribute to the developmental reversal and the molecular mechanisms of the directional determination of ontogeny.},
}
@article {pmid29330936,
year = {2018},
author = {Abrego, N and Norros, V and Halme, P and Somervuo, P and Ali-Kovero, H and Ovaskainen, O},
title = {Give me a sample of air and I will tell which species are found from your region: Molecular identification of fungi from airborne spore samples.},
journal = {Molecular ecology resources},
volume = {18},
number = {3},
pages = {511-524},
doi = {10.1111/1755-0998.12755},
pmid = {29330936},
issn = {1755-0998},
mesh = {*Air Microbiology ; Biodiversity ; DNA Barcoding, Taxonomic ; Finland ; Fungi/classification/*genetics ; Seasons ; Species Specificity ; Spores, Fungal/*genetics/isolation &amp; purification ; },
abstract = {Fungi are a megadiverse group of organisms, they play major roles in ecosystem functioning and are important for human health, food production and nature conservation. Our knowledge on fungal diversity and fungal ecology is however still very limited, in part because surveying and identifying fungi is time demanding and requires expert knowledge. We present a method that allows anyone to generate a list of fungal species likely to occur in a region of interest, with minimal effort and without requiring taxonomical expertise. The method consists of using a cyclone sampler to acquire fungal spores directly from the air to an Eppendorf tube, and applying DNA barcoding with probabilistic species identification to generate a list of species from the sample. We tested the feasibility of the method by acquiring replicate air samples from different geographical regions within Finland. Our results show that air sampling is adequate for regional-level surveys, with samples collected >100 km apart varying but samples collected <10 km apart not varying in their species composition. The data show marked phenology, and thus obtaining a representative species list requires aerial sampling that covers the entire fruiting season. In sum, aerial sampling combined with probabilistic molecular species identification offers a highly effective method for generating a species list of air-dispersing fungi. The method presented here has the potential to revolutionize fungal surveys, as it provides a highly cost-efficient way to include fungi as a part of large-scale biodiversity assessments and monitoring programs.},
}
@article {pmid29329703,
year = {2018},
author = {Tang, S and Gu, Y and Lu, H and Dong, H and Zhang, K and Dai, W and Meng, X and Yang, F and Zhang, X},
title = {Highly-sensitive microRNA detection based on bio-bar-code assay and catalytic hairpin assembly two-stage amplification.},
journal = {Analytica chimica acta},
volume = {1004},
number = {},
pages = {1-9},
doi = {10.1016/j.aca.2017.12.004},
pmid = {29329703},
issn = {1873-4324},
mesh = {*Biosensing Techniques ; Catalysis ; DNA/chemistry ; DNA Probes/chemistry ; Metal Nanoparticles/chemistry ; MicroRNAs/*analysis ; *Nucleic Acid Hybridization ; },
abstract = {Herein, a highly-sensitive microRNA (miRNA) detection strategy was developed by combining bio-bar-code assay (BBA) with catalytic hairpin assembly (CHA). In the proposed system, two nanoprobes of magnetic nanoparticles functionalized with DNA probes (MNPs-DNA) and gold nanoparticles with numerous barcode DNA (AuNPs-DNA) were designed. In the presence of target miRNA, the MNP-DNA and AuNP-DNA hybridized with target miRNA to form a "sandwich" structure. After "sandwich" structures were separated from the solution by the magnetic field and dehybridized by high temperature, the barcode DNA sequences were released by dissolving AuNPs. The released barcode DNA sequences triggered the toehold strand displacement assembly of two hairpin probes, leading to recycle of barcode DNA sequences and producing numerous fluorescent CHA products for miRNA detection. Under the optimal experimental conditions, the proposed two-stage amplification system could sensitively detect target miRNA ranging from 10 pM to 10 aM with a limit of detection (LOD) down to 97.9 zM. It displayed good capability to discriminate single base and three bases mismatch due to the unique sandwich structure. Notably, it presented good feasibility for selective multiplexed detection of various combinations of synthetic miRNA sequences and miRNAs extracted from different cell lysates, which were in agreement with the traditional polymerase chain reaction analysis. The two-stage amplification strategy may be significant implication in the biological detection and clinical diagnosis.},
}
@article {pmid29326593,
year = {2017},
author = {Liu, J and Shi, L and Song, J and Sun, W and Han, J and Liu, X and Hou, D and Yao, H and Li, M and Chen, S},
title = {BOKP: A DNA Barcode Reference Library for Monitoring Herbal Drugs in the Korean Pharmacopeia.},
journal = {Frontiers in pharmacology},
volume = {8},
number = {},
pages = {931},
pmid = {29326593},
issn = {1663-9812},
abstract = {Herbal drug authentication is an important task in traditional medicine; however, it is challenged by the limitations of traditional authentication methods and the lack of trained experts. DNA barcoding is conspicuous in almost all areas of the biological sciences and has already been added to the British pharmacopeia and Chinese pharmacopeia for routine herbal drug authentication. However, DNA barcoding for the Korean pharmacopeia still requires significant improvements. Here, we present a DNA barcode reference library for herbal drugs in the Korean pharmacopeia and developed a species identification engine named KP-IDE to facilitate the adoption of this DNA reference library for the herbal drug authentication. Using taxonomy records, specimen records, sequence records, and reference records, KP-IDE can identify an unknown specimen. Currently, there are 6,777 taxonomy records, 1,054 specimen records, 30,744 sequence records (ITS2 and psbA-trnH) and 285 reference records. Moreover, 27 herbal drug materials were collected from the Seoul Yangnyeongsi herbal medicine market to give an example for real herbal drugs authentications. Our study demonstrates the prospects of the DNA barcode reference library for the Korean pharmacopeia and provides future directions for the use of DNA barcoding for authenticating herbal drugs listed in other modern pharmacopeias.},
}
@article {pmid29325009,
year = {2018},
author = {Li, R and Xie, M and Dong, N and Lin, D and Yang, X and Wong, MHY and Chan, EW and Chen, S},
title = {Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data.},
journal = {GigaScience},
volume = {7},
number = {3},
pages = {1-9},
pmid = {29325009},
issn = {2047-217X},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple/*genetics ; Genome, Bacterial/genetics ; *High-Throughput Nucleotide Sequencing ; Nanopores ; Plasmids/*genetics ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: Multidrug resistance (MDR)-encoding plasmids are considered major molecular vehicles responsible for transmission of antibiotic resistance genes among bacteria of the same or different species. Delineating the complete sequences of such plasmids could provide valuable insight into the evolution and transmission mechanisms underlying bacterial antibiotic resistance development. However, due to the presence of multiple repeats of mobile elements, complete sequencing of MDR plasmids remains technically complicated, expensive, and time-consuming.<br><br>RESULTS: Here, we demonstrate a rapid and efficient approach to obtaining multiple MDR plasmid sequences through the use of the MinION nanopore sequencing platform, which is incorporated in a portable device. By assembling the long sequencing reads generated by a single MinION run according to a rapid barcoding sequencing protocol, we obtained the complete sequences of 20 plasmids harbored by multiple bacterial strains. Importantly, single long reads covering a plasmid end-to-end were recorded, indicating that de novo assembly may be unnecessary if the single reads exhibit high accuracy.<br><br>CONCLUSIONS: This workflow represents a convenient and cost-effective approach for systematic assessment of MDR plasmids responsible for treatment failure of bacterial infections, offering the opportunity to perform detailed molecular epidemiological studies to probe the evolutionary and transmission mechanisms of MDR-encoding elements.},
}
@article {pmid29321791,
year = {2017},
author = {Zhang, HX and Zhang, ML},
title = {Spatial Patterns of Species Diversity and Phylogenetic Structure of Plant Communities in the Tianshan Mountains, Arid Central Asia.},
journal = {Frontiers in plant science},
volume = {8},
number = {},
pages = {2134},
pmid = {29321791},
issn = {1664-462X},
abstract = {The Tianshan Mountains, located in arid Central Asia, have a humid climate and are biodiversity hotspots. Here, we aimed to clarify whether the pattern of species diversity and the phylogenetic structure of plant communities is affected by environmental variables and glacial refugia. In this study, plant community assemblies of 17 research sites with a total of 35 sample plots were investigated at the grassland/woodland boundaries on the Tianshan Mountains. Community phylogeny of these plant communities was constructed based on two plant DNA barcode regions. The indices of phylogenetic diversity and phylogenetic community structure were calculated for these sample plots. We first estimated the correlation coefficients between species richness (SR) and environmental variables as well as the presence of glacial refugia. We then mapped the significant values of indices of community phylogeny (PD, RPD, NRI, and NTI) to investigate the correlation between community phylogeny and environmental structure or macrozones in the study area. The results showed that a significantly higher value of SR was obtained for the refugial groups than for the colonizing groups (P < 0.05); presence of refugia and environmental variables were highly correlated to the pattern of variation in SR. Indices of community phylogeny were not significantly different between refugial and colonizing regions. Comparison with the humid western part showed that plant communities in the arid eastern part of the Tianshan Mountains tended to display more significant phylogenetic overdispersion. The variation tendency of the PhyloSor index showed that the increase in macro-geographical and environmental distance did not influence obvious phylogenetic dissimilarities between different sample plots. In conclusion, glacial refugia and environmental factors profoundly influenced the pattern of SR, but community phylogenetic structure was not affected by glacial refugia among different plant communities on the Tianshan Mountains. This pattern of community phylogenetic structure could have resulted from shared ancestry and species pool among these sample plots.},
}
@article {pmid29320544,
year = {2018},
author = {González, C and León, C and Paz, A and López, M and Molina, G and Toro, D and Ortiz, M and Cordovez, JM and Atencia, MC and Aguilera, G and Tovar, C},
title = {Diversity patterns, Leishmania DNA detection, and bloodmeal identification of Phlebotominae sand flies in villages in northern Colombia.},
journal = {PloS one},
volume = {13},
number = {1},
pages = {e0190686},
pmid = {29320544},
issn = {1932-6203},
mesh = {Animals ; Colombia ; DNA, Protozoan/*genetics ; *Feeding Behavior ; *Genetic Variation ; Insect Vectors/*parasitology ; Leishmania/*genetics ; Psychodidae/*parasitology/physiology ; },
abstract = {Leishmaniases are neglected tropical diseases exhibiting complex transmission cycles due to the number of parasite species circulating, sand fly species acting as vectors and infected mammals, including humans, which are defined in the New World as accidental hosts. However, current transmission scenarios are changing, and the disease is no longer exclusively related to forested areas but urban transmission foci occur, involving some species of domestic animals as suspected reservoirs. The aim of this study was to determine the transmission cycles in urban environments by evaluating sand fly diversity, detection of Leishmania DNA, and bloodmeal sources through intra and peridomestic collections. The study was carried out in Colombia, in 13 municipalities of Cordoba department, implementing a methodology that could be further used for the evaluation of vector-borne diseases in villages or towns. Our sampling design included 24 houses randomly selected in each of 15 villages distributed in 13 municipalities, which were sampled in two seasons in 2015 and 2016. Sand flies were collected using CDC light traps placed in intra and peridomestic habitats. In addition to the morphological identification, molecular identification through DNA barcodes was also performed. A total of 19,743 sand flies were collected and 13,848 of them (10,268 females and 3,580 males) were used in molecular procedures. Circulation of two known parasite species-Leishmania infantum and Leishmania panamensis was confirmed. Blood source analyses showed that sand flies fed on humans, particularly in the case of the known L. infantum vector, P. evansi; further analyses are advised to evaluate the reservoirs involved in parasite transmission. Our sampling design allowed us to evaluate potential transmission cycles on a department scale, by defining suspected vector species, parasite species present in different municipalities and feeding habits.},
}
@article {pmid29317789,
year = {2017},
author = {Tanney, JB and Visagie, CM and Yilmaz, N and Seifert, KA},
title = {Aspergillus subgenus Polypaecilum from the built environment.},
journal = {Studies in mycology},
volume = {88},
number = {},
pages = {237-267},
pmid = {29317789},
issn = {0166-0616},
abstract = {Xerophilic fungi, especially Aspergillus species, are prevalent in the built environment. In this study, we employed a combined culture-independent (454-pyrosequencing) and culture-dependent (dilution-to-extinction) approach to investigate the mycobiota of indoor dust collected from 93 buildings in 12 countries worldwide. High and low water activity (aw) media were used to capture mesophile and xerophile biodiversity, resulting in the isolation of approximately 9 000 strains. Among these, 340 strains representing seven putative species in Aspergillus subgenus Polypaecilum were isolated, mostly from lowered aw media, and tentatively identified based on colony morphology and internal transcribed spacer rDNA region (ITS) barcodes. Further morphological study and phylogenetic analyses using sequences of ITS, β-tubulin (BenA), calmodulin (CaM), RNA polymerase II second largest subunit (RPB2), DNA topoisomerase 1 (TOP1), and a pre-mRNA processing protein homolog (TSR1) confirmed the isolation of seven species of subgenus Polypaecilum, including five novel species: A. baarnensis, A. keratitidis, A. kalimae sp. nov., A. noonimiae sp. nov., A. thailandensis sp. nov., A. waynelawii sp. nov., and A. whitfieldii sp. nov. Pyrosequencing detected six of the seven species isolated from house dust, as well as one additional species absent from the cultures isolated, and three clades representing potentially undescribed species. Species were typically found in house dust from subtropical and tropical climates, often in close proximity to the ocean or sea. The presence of subgenus Polypaecilum, a recently described clade of xerophilic/xerotolerant, halotolerant/halophilic, and potentially zoopathogenic species, within the built environment is noteworthy.},
}
@article {pmid29316123,
year = {2018},
author = {Kohman, RE and Kunjapur, AM and Hysolli, E and Wang, Y and Church, GM},
title = {From Designing the Molecules of Life to Designing Life: Future Applications Derived from Advances in DNA Technologies.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {57},
number = {16},
pages = {4313-4328},
doi = {10.1002/anie.201707976},
pmid = {29316123},
issn = {1521-3773},
mesh = {*Biotechnology ; DNA/*chemistry/*genetics ; Evolution, Molecular ; Genome/genetics ; *Life ; },
abstract = {Since the elucidation of its structure, DNA has been at the forefront of biological research. In the past half century, an explosion of DNA-based technology development has occurred with the most rapid advances being made for DNA sequencing. In parallel, dramatic improvements have also been made in the synthesis and editing of DNA from the oligonucleotide to the genome scale. In this Review, we will summarize four different subfields relating to DNA technologies following this trajectory of smaller to larger scale. We begin by talking about building materials out of DNA which in turn can act as delivery vehicles in vivo. We then discuss how altering microbial genomes can lead to novel methods of production for industrial biologics. Next, we talk about the future of writing whole genomes as a method of studying evolution. Lastly, we highlight the ways in which barcoding biological systems will allow for their three-dimensional analysis in a highly multiplexed fashion.},
}
@article {pmid29316045,
year = {2018},
author = {Gruber, MS and Strüder-Kypke, M and Agatha, S},
title = {Redescription of Tintinnopsis everta Kofoid and Campbell 1929 (Alveolata, Ciliophora, Tintinnina) Based on Taxonomic and Genetic Analyses-Discovery of a New Complex Ciliary Pattern.},
journal = {The Journal of eukaryotic microbiology},
volume = {65},
number = {4},
pages = {484-504},
pmid = {29316045},
issn = {1550-7408},
mesh = {Alveolata/*classification/genetics/growth &amp; development/*isolation &amp; purification ; Biodiversity ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Phylogeny ; Ribosome Subunits, Small/genetics ; Rivers/parasitology ; Seawater/parasitology ; },
abstract = {The about 1,000 species of tintinnid ciliates are identified and classified almost exclusively based on their lorica features, although the shortcomings of this structure are well-known, e.g. causing uncertain species limitations and nonmonophyletic taxa. Hence, the present redescription of Tintinnopsis everta Kofoid and Campbell, 1929 considers not only the lorica characteristics, but focuses on cell and genetic features. The species is redescribed from the North Atlantic and adjacent sea areas, namely the east coast of the USA, using live observation, protargol-stained material, scanning electron microscopy, and genetic analyses. The main stages of cell division are described, and the species' phylogenetic relationships are inferred from morphological data and the small subunit ribosomal RNA gene sequence. The estimates of its biogeographical distribution and autecology are based on a literature survey. The species is characterised by a complex somatic ciliary pattern with a unique position of the posterior kinety and a conspicuously large distance between the somatic ciliary fields and the collar membranelles. The phylogenetic relationships of Tintinnopsis everta vary in the molecular trees depending on the algorithms used and are, therefore, regarded as unresolved. Nevertheless, the new kind of complex somatic ciliary pattern distinctly contributes to a better understanding of the tintinnid biodiversity and evolution and provides features for a future split of the nonmonophyletic genus Tintinnopsis.},
}
@article {pmid29314756,
year = {2018},
author = {Wang, WY and Srivathsan, A and Foo, M and Yamane, SK and Meier, R},
title = {Sorting specimen-rich invertebrate samples with cost-effective NGS barcodes: Validating a reverse workflow for specimen processing.},
journal = {Molecular ecology resources},
volume = {18},
number = {3},
pages = {490-501},
doi = {10.1111/1755-0998.12751},
pmid = {29314756},
issn = {1755-0998},
mesh = {Animals ; Ants/classification/*genetics ; Biodiversity ; Classification/methods ; DNA Barcoding, Taxonomic/methods ; Databases, Genetic ; Invertebrates/classification/*genetics ; Sequence Analysis, DNA ; Workflow ; },
abstract = {Biologists frequently sort specimen-rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative is barcoding every specimen in a bulk sample and then presorting the specimens using DNA barcodes, thus mitigating downstream morphological work on presorted units. Such a "reverse workflow" is too expensive using Sanger sequencing, but we here demonstrate that is feasible with an next-generation sequencing (NGS) barcoding pipeline that allows for cost-effective high-throughput generation of short specimen-specific barcodes (313 bp of COI; laboratory cost <$0.50 per specimen) through next-generation sequencing of tagged amplicons. We applied our approach to a large sample of tropical ants, obtaining barcodes for 3,290 of 4,032 specimens (82%). NGS barcodes and their corresponding specimens were then sorted into molecular operational taxonomic units (mOTUs) based on objective clustering and Automated Barcode Gap Discovery (ABGD). High diversity of 88-90 mOTUs (4% clustering) was found and morphologically validated based on preserved vouchers. The mOTUs were overwhelmingly in agreement with morphospecies (match ratio 0.95 at 4% clustering). Because of lack of coverage in existing barcode databases, only 18 could be accurately identified to named species, but our study yielded new barcodes for 48 species, including 28 that are potentially new to science. With its low cost and technical simplicity, the NGS barcoding pipeline can be implemented by a large range of laboratories. It accelerates invertebrate species discovery, facilitates downstream taxonomic work, helps with building comprehensive barcode databases and yields precise abundance information.},
}
@article {pmid29310715,
year = {2018},
author = {Bisconti, R and Tenchini, R and Belfiore, C and Nascetti, G and Canestrelli, D},
title = {Fast and accurate identification of cryptic and sympatric mayfly species of the Baetis rhodani group.},
journal = {BMC research notes},
volume = {11},
number = {1},
pages = {7},
pmid = {29310715},
issn = {1756-0500},
mesh = {Animals ; Ephemeroptera/*classification/genetics ; Mediterranean Islands ; Polymerase Chain Reaction ; },
abstract = {OBJECTIVE: Species of the Baetis rhodani group are among the most widespread mayflies of the Palearctic region. However, frequent occurrence of morphologically cryptic species complicates the identification of sympatric species. Here, we proposed and tested a method for the fast, accurate, and cost-effective assignment of a large number of individuals to their putative species, based on high resolution melting profiles of a standard mitochondrial gene fragment. We tested this method using a system of three recently identified cryptic species inhabiting the Tyrrhenian Islands (western Mediterranean basin).<br><br>RESULTS: Highly species-specific high resolution melting profiles were obtained, allowing the unequivocal attribution of each individual to the respective species. This assay provides a convenient and easily customizable alternative to traditional barcoding approaches, provided that the mayfly taxa occurring within the geographic area of interest have been previously identified and their high resolution melting profiles assessed.},
}
@article {pmid29310587,
year = {2018},
author = {MacConaill, LE and Burns, RT and Nag, A and Coleman, HA and Slevin, MK and Giorda, K and Light, M and Lai, K and Jarosz, M and McNeill, MS and Ducar, MD and Meyerson, M and Thorner, AR},
title = {Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {30},
pmid = {29310587},
issn = {1471-2164},
mesh = {Computational Biology/*methods ; *High-Throughput Nucleotide Sequencing/methods/standards ; Humans ; Sensitivity and Specificity ; *Sequence Analysis, DNA/methods/standards ; },
abstract = {BACKGROUND: Sample index cross-talk can result in false positive calls when massively parallel sequencing (MPS) is used for sensitive applications such as low-frequency somatic variant discovery, ancient DNA investigations, microbial detection in human samples, or circulating cell-free tumor DNA (ctDNA) variant detection. Therefore, the limit-of-detection of an MPS assay is directly related to the degree of index cross-talk.<br><br>RESULTS: Cross-talk rates up to 0.29% were observed when using standard, combinatorial adapters, resulting in 110,180 (0.1% cross-talk rate) or 1,121,074 (0.29% cross-talk rate) misassigned reads per lane in non-patterned and patterned Illumina flow cells, respectively. Here, we demonstrate that using unique, dual-matched indexed adapters dramatically reduces index cross-talk to &#x2264;1 misassigned reads per flow cell lane. While the current study was performed using dual-matched indices, using unique, dual-unrelated indices would also be an effective alternative.<br><br>CONCLUSIONS: For sensitive downstream analyses, the use of combinatorial indices for multiplexed hybrid capture and sequencing is inappropriate, as it results in an unacceptable number of misassigned reads. Cross-talk can be virtually eliminated using dual-matched indexed adapters. These results suggest that use of such adapters is critical&#xa0;to reduce false positive rates in assays that aim to identify low allele frequency events, and strongly indicate that dual-matched adapters be implemented for all sensitive MPS applications.},
}
@article {pmid29308026,
year = {2017},
author = {Kang, I and Chapman, EG and Janzen, DH and Hallwachs, W and Tanya Dapkey, and Smith, MA and Sharkey, MJ},
title = {Revision of the species of Lytopylus from Area de Conservación Guanacaste, northwestern Costa Rica (Hymenoptera, Braconidae, Agathidinae).},
journal = {ZooKeys},
volume = {},
number = {721},
pages = {93-158},
pmid = {29308026},
issn = {1313-2989},
abstract = {Thirty two new species of Lytopylus (Agathidinae) are described with image plates for each species: Lytopylus alejandromasisisp. n., Lytopylus alfredomainierisp. n., Lytopylus anamariamongeaesp. n., Lytopylus angelagonzalezaesp. n., Lytopylus cesarmoraisp. n., Lytopylus eddysanchezisp. n., Lytopylus eliethcantillanoaesp. n., Lytopylus ericchapmanisp. n., Lytopylus gahyunaesp. n., Lytopylus gisukaesp. n., Lytopylus guillermopereiraisp. n., Lytopylus gustavoinduniisp. n., Lytopylus hartmanguidoisp. n., Lytopylus hernanbravoisp. n., Lytopylus hokwonisp. n., Lytopylus ivanniasandovalaesp. n., Lytopylus johanvalerioisp. n., Lytopylus josecortesisp. n., Lytopylus luisgaritaisp. n., Lytopylus mariamartachavarriaesp. n., Lytopylus miguelviquezisp. n., Lytopylus motohasegawaisp. n., Lytopylus okchunaesp. n., Lytopylus pablocobbisp. n., Lytopylus robertofernandezisp. n., Lytopylus rogerblancoisp. n., Lytopylus salvadorlopezisp. n., Lytopylus sangyeonisp. n., Lytopylus sarahmeierottoaesp. n., Lytopylus sergiobermudezisp. n., Lytopylus sigifredomarinisp. n., and Lytopylus youngcheaesp. n. A dichotomous key and a link to an electronic, interactive key are included. All specimens were reared from Lepidoptera larvae collected in Area de Conservación Guanacaste (ACG) and all are associated with ecological information including host caterpillar, collection date, eclosion date, caterpillar food plant, and locality. Neighbor-joining and maximum likelihood analyses of the barcode region of the mitochondrial cytochrome c oxidase subunit I gene (COI DNA barcode) were conducted to aid in species delimitation.},
}
@article {pmid29304878,
year = {2018},
author = {Mejía, &#xc1; and Matamoros, G and Fontecha, G and Sosa-Ochoa, W},
title = {Bionomic aspects of Lutzomyia evansi and Lutzomyia longipalpis, proven vectors of Leishmania infantum in an endemic area of non-ulcerative cutaneous leishmaniasis in Honduras.},
journal = {Parasites &amp; vectors},
volume = {11},
number = {1},
pages = {15},
pmid = {29304878},
issn = {1756-3305},
mesh = {Animals ; DNA Barcoding, Taxonomic ; *Ecosystem ; Electron Transport Complex IV/genetics ; Endemic Diseases ; *Feeding Behavior ; Honduras/epidemiology ; Insect Vectors/*classification/*physiology ; Leishmaniasis, Cutaneous/epidemiology ; Psychodidae/*classification/*physiology ; },
abstract = {BACKGROUND: Some Lutzomyia species are the vectors of human leishmaniasis in the Americas. Visceral and cutaneous leishmaniasis are both endemic in the Pacific region of Honduras, but the non-ulcerative form is the more frequent clinical manifestation in this region, where Lutzomyia longipalpis is the most abundant and the only incriminated vector. Taxonomic identification and distribution studies of sand flies are important to understand the epidemiology and to control these neglected tropical diseases.<br><br>RESULTS: Here, we identified more than 13,000 Lutzomyia specimens captured in Isla del Tigre, Honduras, through a classical morphological approach. The two most common species were Lutzomyia evansi and Lu. longipalpis, and this is the first report of three Lutzomyia species on this island. The blood meal source was successfully identified for five sand fly species. A barcode analysis using the cox1 mitochondrial marker proved to be effective in discriminating between species and seems to be a valuable tool for future epidemiological studies including a wider geographical area.<br><br>CONCLUSION: This study updates the diversity and blood meal sources of Lutzomyia species in an island endemic for non-ulcerative cutaneous leishmaniasis in the Pacific region of Honduras, and determines the effectiveness of the barcoding approach to discriminate species, as a complementary tool to classical morphology.},
}
@article {pmid29302302,
year = {2017},
author = {Contreras, R and Figueiras, AM and Gallego, FJ and Benavente, E and Manzaneda, AJ and Benito, C},
title = {Neutral molecular markers support common origin of aluminium tolerance in three congeneric grass species growing in acidic soils.},
journal = {AoB PLANTS},
volume = {9},
number = {6},
pages = {plx060},
pmid = {29302302},
issn = {2041-2851},
abstract = {Aluminium (Al) toxicity is the main abiotic stress limiting plant productivity in acidic soils that are widely distributed among arable lands. Plant species differ in the level of Al resistance showing intraspecific and interspecific variation in many crop species. However, the origin of Al-tolerance is not well known. Three annual species, difficult to distinguish phenotypically and that were until recently misinterpreted as a single complex species under Brachypodium distachyon, have been recently separated into three distinct species: the diploids B. distachyon (2n = 10) and B. stacei (2n = 20), and B. hybridum (2n = 30), the allotetraploid derived from the two diploid species. The aims of this work were to know the origin of Al-tolerance in acidic soil conditions within these three Brachypodium species and to develop new DNA markers for species discrimination. Two multiplex SSR-PCRs allowed to genotype a group of 94 accessions for 17 pentanucleotide microsatellite (SSRs) loci. The variability for 139 inter-microsatellite (ISSRs) markers was also examined. The genetic relationships obtained using those neutral molecular markers (SSRs and ISSRs) support that all Al-tolerant allotetraploid accessions of B. hybridum have a common origin that is related with both geographic location and acidic soils. The possibility that the adaptation to acidic soils caused the isolation of the tolerant B. hybridum populations from the others is discussed. We finally describe a new, easy, DNA barcoding method based in the upstream-intron 1 region of the ALMT1 gene, a tool that is 100 % effective to distinguish among these three Brachypodium species.},
}
@article {pmid29302297,
year = {2017},
author = {Lukhtanov, VA and Dantchenko, AV},
title = {A new butterfly species from south Russia revealed through chromosomal and molecular analysis of the Polyommatus (Agrodiaetus) damonides complex (Lepidoptera, Lycaenidae).},
journal = {Comparative cytogenetics},
volume = {11},
number = {4},
pages = {769-795},
pmid = {29302297},
issn = {1993-0771},
abstract = {Finding a new species is a rare event in easy-to-see and well-studied organisms like butterflies, especially if they inhabit well-explored areas such as the Western Palaearctic. However, even in this region, gaps in taxonomic knowledge still exist and here we report such a discovery. Using a combined analysis of chromosomal and molecular markers we demonstrate that Polyommatus blue populations from Daghestan (South Russia), previously identified as P. aserbeidschanus, represent in fact a new species which is described here as P. australorossicussp. n. We also show that the enigmatic Polyommatus damonides described as a form of Polyommatus damone and later considered as an entity similar to P. poseidon or P. ninae is conspecific with a taxon previously known as P. elbursicus. As a result of our study, we propose several taxonomic changes within the P. damonides species complex and suggest the following new combinations: P. damonides elbursicus Forster, 1956, comb. n. and P. damonides gilanensis Eckweiler, 2002, comb. n.},
}
@article {pmid29302296,
year = {2017},
author = {Lukhtanov, VA and Shapoval, NA},
title = {Chromosomal identification of cryptic species sharing their DNA barcodes: Polyommatus (Agrodiaetus) antidolus and P. (A.) morgani in Iran (Lepidoptera, Lycaenidae).},
journal = {Comparative cytogenetics},
volume = {11},
number = {4},
pages = {759-768},
pmid = {29302296},
issn = {1993-0771},
abstract = {DNA barcoding has been suggested as a universal tool for molecular species identification; however, it cannot be applied in cases when morphologically similar species share their DNA barcodes due to the common ancestry or mitochondrial introgression. Here we analyze the karyotype of Polyommatus (Agrodiaetus) morgani (Le Cerf, 1909) from the region of its type locality in the southern Zagros Mountains in Iran, provide first chromosomal evidence for P. (A.) antidolus (Rebel, 1901) in Iran and demonstrate that these two species can be easily identified through analysis of their karyotypes whereas they share their mitochondrial barcodes.},
}
@article {pmid29299394,
year = {2017},
author = {Kuzmina, ML and Braukmann, TWA and Fazekas, AJ and Graham, SW and Dewaard, SL and Rodrigues, A and Bennett, BA and Dickinson, TA and Saarela, JM and Catling, PM and Newmaster, SG and Percy, DM and Fenneman, E and Lauron-Moreau, A and Ford, B and Gillespie, L and Subramanyam, R and Whitton, J and Jennings, L and Metsger, D and Warne, CP and Brown, A and Sears, E and Dewaard, JR and Zakharov, EV and Hebert, PDN},
title = {Using herbarium-derived DNAs to assemble a large-scale DNA barcode library for the vascular plants of Canada.},
journal = {Applications in plant sciences},
volume = {5},
number = {12},
pages = {},
pmid = {29299394},
issn = {2168-0450},
abstract = {PREMISE OF THE STUDY: Constructing complete, accurate plant DNA barcode reference libraries can be logistically challenging for large-scale floras. Here we demonstrate the promise and challenges of using herbarium collections for building a DNA barcode reference library for the vascular plant flora of Canada.<br><br>METHODS: Our study examined 20,816 specimens representing 5076 of 5190 vascular plant species in Canada (98%). For 98% of the specimens, at least one of the DNA barcode regions was recovered from the plastid loci rbcL and matK and from the nuclear ITS2 region. We used beta regression to quantify the effects of age, type of preservation, and taxonomic affiliation (family) on DNA sequence recovery.<br><br>RESULTS: Specimen age and method of preservation had significant effects on sequence recovery for all markers, but influenced some families more (e.g., Boraginaceae) than others (e.g., Asteraceae).<br><br>DISCUSSION: Our DNA barcode library represents an unparalleled resource for metagenomic and ecological genetic research working on temperate and arctic biomes. An observed decline in sequence recovery with specimen age may be associated with poor primer matches, intragenomic variation (for ITS2), or inhibitory secondary compounds in some taxa.},
}
@article {pmid29299292,
year = {2017},
author = {Boissin, E and Hoareau, TB and Paulay, G and Bruggemann, JH},
title = {DNA barcoding of reef brittle stars (Ophiuroidea, Echinodermata) from the southwestern Indian Ocean evolutionary hot spot of biodiversity.},
journal = {Ecology and evolution},
volume = {7},
number = {24},
pages = {11197-11203},
pmid = {29299292},
issn = {2045-7758},
abstract = {In anticipation of the current biodiversity crisis, it has become critical to rapidly and accurately assess biodiversity. DNA barcoding has proved efficient in facilitating the discovery and description of thousands of species and also provides insight into the dynamics of biodiversity. Here, we sequenced a portion of the mitochondrial cytochrome c oxidase subunit I (COI) gene from all morphospecies of reef brittle stars collected during a large-scale biodiversity survey in the southwestern Indian Ocean (SWIO). Three methods of species delineation (Automatic Barcode Gap Discovery, Generalized Mixed Yule Coalescent model, and Bayesian Poisson Tree Processes) showed concordant results and revealed 51 shallow reef species in the region. Mean intraspecific genetic distances (0.005-0.064) and mean interspecific genetic distances within genera (0.056-0.316) were concordant with previous echinoderm studies. This study revealed that brittle-star biodiversity is underestimated by 20% within SWIO and by >40% when including specimens from the Pacific Ocean. Results are discussed in terms of endemism, diversification processes, and conservation implications for the Indo-West Pacific marine biodiversity. We emphasize the need to further our knowledge on biodiversity of invertebrate groups in peripheral areas.},
}
@article {pmid29298936,
year = {2018},
author = {Luo, SX and Zhang, LJ and Yuan, S and Ma, ZH and Zhang, DX and Renner, SS},
title = {The largest early-diverging angiosperm family is mostly pollinated by ovipositing insects and so are most surviving lineages of early angiosperms.},
journal = {Proceedings. Biological sciences},
volume = {285},
number = {1870},
pages = {},
pmid = {29298936},
issn = {1471-2954},
mesh = {Animals ; Base Sequence ; China ; DNA Barcoding, Taxonomic ; Diptera/*anatomy &amp; histology ; Female ; Flowers/anatomy &amp; histology ; Larva/*anatomy &amp; histology ; Oviposition/*physiology ; Phylogeny ; Pollen ; Pollination/*physiology ; Schisandraceae/*physiology ; },
abstract = {Insect pollination in basal angiosperms is assumed to mostly involve 'generalized' insects looking for food, but direct observations of ANITA grade (283 species) pollinators are sparse. We present new data for numerous Schisandraceae, the largest ANITA family, from fieldwork, nocturnal filming, electron microscopy, barcoding and molecular clocks to infer pollinator/plant interactions over multiple years at sites throughout China to test the extent of pollinator specificity. Schisandraceae are pollinated by nocturnal gall midges that lay eggs in the flowers and whose larvae then feed on floral exudates. At least three Schisandraceae have shifted to beetle pollination. Pollination by a single midge species predominates, but one species was pollinated by different species at three locations and one by two at the same location. Based on molecular clocks, gall midges and Schisandraceae may have interacted since at least the Early Miocene. Combining these findings with a review of all published ANITA pollination data shows that ovipositing flies are the most common pollinators of living representatives of the ANITA grade. Compared to food reward-based pollination, oviposition-based systems are less wasteful of plant gametes because (i) none are eaten and (ii) female insects with herbivorous larvae reliably visit conspecific flowers.},
}
@article {pmid29297332,
year = {2017},
author = {Abugalieva, S and Volkova, L and Genievskaya, Y and Ivaschenko, A and Kotukhov, Y and Sakauova, G and Turuspekov, Y},
title = {Taxonomic assessment of Allium species from Kazakhstan based on ITS and matK markers.},
journal = {BMC plant biology},
volume = {17},
number = {Suppl 2},
pages = {258},
pmid = {29297332},
issn = {1471-2229},
mesh = {Allium/*classification/genetics ; Classification ; DNA, Intergenic/*genetics ; DNA, Plant/genetics ; Genetic Markers/genetics ; Genetic Variation/genetics ; Kazakhstan ; Phylogeny ; Plastids/genetics ; Pyrimidines ; },
abstract = {BACKGROUND: As part of nation-wide project to infer the genetic variation of the native flora in Kazakhstan, a study was attempted to assess phylogenetic relationships of endemic and rare Allium species. In total, 20 Allium species were collected in field trips in five different regions of Kazakhstan during 2015-2016. Most species (9) were collected in the southern part of the country along of Karatau mountains, followed by Altai mountains (5) in eastern Kazakhstan. The ITS and matK DNA regions were applied in order to assess the taxonomic relationships among species. The major goal of the study was to assess the taxonomic position of five endemic and rare species from Allium subgenus Reticulatobulbosa collected in Karatau mountains of Southern Kazakhstan.<br><br>RESULTS: The 20 collected Allium species were assessed using morphological traits and a DNA barcoding approach. The morphological analyses of four different species in subgenus Reticulatobulbosa inferred similarities of A. inconspicuum and A. barszchewskii (both from section Companulata) that were separated from A. oreoscordum and A. oreoprasoides (section Nigrimontana) by several traits, including form of bulbs and leaves, presence of bracts, shape of perianth lobes and style. The Neighbor-Joining method was applied to generate ITS and matK phylogenetic trees for two groups of populations: 1) 20 Allium species collected within the project, and 2) 50 Allium worldwide species.<br><br>CONCLUSIONS: The analyses of nucleotide sequences of ITS and matK robustly confirmed the monophyletic origin of the Allium species. The variability in 20 local Allium species in ITS was 6.6 higher than in matK, therefore the topology of the ITS tree was better resolved. The taxonomy of Allium species largely coincided with a recent classification of this genus. Analyses of both ITS and matK suggest that A. oreoscordum is genetically close to A. oreoprasoides in section Nigrimontana of subgenus Reticulatobulbosa. This result was also confirmed using morphological description of individual plants of four species in subgenus Reticulatobulbosa. The study is another contribution to taxonomy clarification in Allium.},
}
@article {pmid29295259,
year = {2017},
author = {Jáuregui, OI and Bruchanski, L and Rizzato Lede, DA and Otero, CM and Luna, DR},
title = {Improving Patient Safety Through the Design and Development of a Computerized Provider Order Entry for Parenteral Nutrition Linked to a Barcode Medication Administration Record.},
journal = {Studies in health technology and informatics},
volume = {245},
number = {},
pages = {1038-1042},
pmid = {29295259},
issn = {1879-8365},
mesh = {*Electronic Data Processing ; Humans ; *Medical Order Entry Systems ; Medication Errors ; *Parenteral Nutrition ; *Patient Safety ; },
abstract = {Among adverse events related to medication errors, the defects in parenteral nutrition administration pose a special threat to patient safety. Two high impact strategies to reduce these errors require implementing a Computerized Provider Order Entry and the use of bedside bar-code verification prior to medication administration. In this study, we share the deep field analysis of the current workflow performed to include inpatient bedside barcoding verification for parenteral nutrition administration in a large academic health center. Then, we propose a process optimization and a new parenteral nutrition ordering tool embedded in the prescription module. Structuring physicians' ordering and the bar-code verification of administration can increase patient safety. The next steps would involve the creation of a Clinical Decision Support System to improve patient nutrient goals.},
}
@article {pmid29295050,
year = {2017},
author = {Daus, M and Maydana, T and Rizzato Lede, D and Luna, D},
title = {Enhancing Children's Safety by Barcoding Implementation at Breast Milk Feeding.},
journal = {Studies in health technology and informatics},
volume = {245},
number = {},
pages = {49-53},
pmid = {29295050},
issn = {1879-8365},
mesh = {*Breast Feeding ; Child ; Enteral Nutrition ; Female ; Humans ; Infant, Newborn ; Intensive Care Units, Neonatal ; *Milk Banks ; *Milk, Human ; },
abstract = {When newborns remain hospitalized in a neonatal intensive care unit, they are often unable to feed themselves and receive human milk through enteral nutrition devices such as orogastric or nasogastric probes. Therefore, the Nursing staff is responsible for the fractionation, storage and administration of human milk. Breast milk has a great biological complexity being the optimal food for the baby to provide all the nutrients needed. At the same time, it is a bodily fluid that carries the risk of disease transmission if not administered properly. Patient safety should be a priority in healthcare, and health information technologies could be used to avoid preventable adverse events. Barcoding technology has the ability to accurately verify patient identity and prescription accuracy before milk administration. This paper describes the steps followed to implement breast milk barcoding technology in an academic tertiary hospital.},
}
@article {pmid29294404,
year = {2018},
author = {Qu, M and Tang, W and Liu, Q and Wang, D and Ding, S},
title = {Genetic diversity within grouper species and a method for interspecific hybrid identification using DNA barcoding and RYR3 marker.},
journal = {Molecular phylogenetics and evolution},
volume = {121},
number = {},
pages = {46-51},
doi = {10.1016/j.ympev.2017.12.031},
pmid = {29294404},
issn = {1095-9513},
mesh = {Animals ; Biomarkers/*metabolism ; Cell Nucleus/genetics ; China ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Fishes/*genetics ; *Genetic Variation ; Geography ; *Hybridization, Genetic ; Mitochondria/genetics ; Oceans and Seas ; Phylogeny ; Ryanodine Receptor Calcium Release Channel/*genetics ; Species Specificity ; },
abstract = {Groupers (family Epinephelidae) are an assemblage of coral reef fishes comprising more than 160 species in 16 genera, many of which are both environmentally and economically valuable. Because of their similar morphology, variable color patterns, and tendency for interspecies hybridization, morphological identification of groupers usually leads to taxonomic confusion. To find an effective method for identifying different grouper species and hybrids, evaluate genetic diversity and uncover any synonymous or cryptic species, we sampled a total of 221 specimens representing 57 species in 9 genera in the China Seas. Both mitochondrial (mt) cytochrome oxidase subunit I (COI) and NADH dehydrogenase subunit 2 (ND2) were found to be effective barcoding genes. We also developed an efficient protocol for identifying hybrid groupers using mt markers and the nuclear RYR3 gene and found the first record of wide interspecies hybridization in genus Epinephelus. This barcoding study revealed high genetic divergence in many widespread species and possible synonyms. In addition to providing a molecular method for identifying grouper species, this study offers important resources for the further study of grouper conservation genetics, speciation, hybridization and other evolutionary traits.},
}
@article {pmid29292539,
year = {2018},
author = {Porter, TM and Hajibabaei, M},
title = {Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis.},
journal = {Molecular ecology},
volume = {27},
number = {2},
pages = {313-338},
doi = {10.1111/mec.14478},
pmid = {29292539},
issn = {1365-294X},
mesh = {*Biodiversity ; Computational Biology/methods ; DNA/*genetics ; DNA Barcoding, Taxonomic/methods ; *Environmental Monitoring ; *Genomics ; High-Throughput Nucleotide Sequencing ; },
abstract = {The purpose of this review is to present the most common and emerging DNA-based methods used to generate data for biodiversity and biomonitoring studies. As environmental assessment and monitoring programmes may require biodiversity information at multiple levels, we pay particular attention to the DNA metabarcoding method and discuss a number of bioinformatic tools and considerations for producing DNA-based indicators using operational taxonomic units (OTUs), taxa at a variety of ranks and community composition. By developing the capacity to harness the advantages provided by the newest technologies, investigators can "scale up" by increasing the number of samples and replicates processed, the frequency of sampling over time and space, and even the depth of sampling such as by sequencing more reads per sample or more markers per sample. The ability to scale up is made possible by the reduced hands-on time and cost per sample provided by the newest kits, platforms and software tools. Results gleaned from broad-scale monitoring will provide opportunities to address key scientific questions linked to biodiversity and its dynamics across time and space as well as being more relevant for policymakers, enabling science-based decision-making, and provide a greater socio-economic impact. As genomic approaches are continually evolving, we provide this guide to methods used in biodiversity genomics.},
}
@article {pmid29291063,
year = {2017},
author = {Morgan-Richards, M and Bulgarella, M and Sivyer, L and Dowle, EJ and Hale, M and McKean, NE and Trewick, SA},
title = {Explaining large mitochondrial sequence differences within a population sample.},
journal = {Royal Society open science},
volume = {4},
number = {11},
pages = {170730},
pmid = {29291063},
issn = {2054-5703},
abstract = {Mitochondrial DNA sequence is frequently used to infer species' boundaries, as divergence is relatively rapid when populations are reproductively isolated. However, the shared history of a non-recombining gene naturally leads to correlation of pairwise differences, resulting in mtDNA clusters that might be mistaken for evidence of multiple species. There are four distinct processes that can explain high levels of mtDNA sequence difference within a single sample. Here, we examine one case in detail as an exemplar to distinguish among competing hypotheses. Within our sample of tree wētā (Hemideina crassidens; Orthoptera), we found multiple mtDNA haplotypes for a protein-coding region (cytb/ND1) that differed by a maximum of 7.9%. From sequencing the whole mitochondrial genome of two representative individuals, we found evidence of constraining selection. Heterozygotes were as common as expected under random mating at five nuclear loci. Morphological traits and nuclear markers did not resolve the mtDNA groupings of individuals. We concluded that the large differences found among our sample of mtDNA sequences were simply owing to a large population size over an extended period of time allowing an equilibrium between mutation and drift to retain a great deal of genetic diversity within a single species.},
}
@article {pmid29287470,
year = {2018},
author = {Xu, M and Heidmarsson, S and Thorsteinsdottir, M and Kreuzer, M and Hawkins, J and Omarsdottir, S and Olafsdottir, ES},
title = {Authentication of Iceland Moss (Cetraria islandica) by UPLC-QToF-MS chemical profiling and DNA barcoding.},
journal = {Food chemistry},
volume = {245},
number = {},
pages = {989-996},
doi = {10.1016/j.foodchem.2017.11.073},
pmid = {29287470},
issn = {1873-7072},
mesh = {Chromatography, High Pressure Liquid ; *DNA Barcoding, Taxonomic ; Fraud/prevention &amp; control ; Mass Spectrometry ; Parmeliaceae/*chemistry/*classification/genetics ; },
abstract = {The lichen Cetraria islandica or Iceland Moss is commonly consumed as tea, food ingredients (e.g. in soup or bread) and herbal medicines. C. islandica, which has two chemotypes, can be difficult to distinguish from the sister species Cetraria ericetorum. They are collectively referred to as the Cetraria islandica species complex. This study aimed to use an UPLC-QToF-MS chemical profiling together with DNA barcoding to distinguish species and chemotypes of the C. islandica species complex. Our results show that the two chemotypes of C. islandica are clearly distinguishable from each other and from C. ericetorum by the chemometric approach. The RPB2 barcode was able to differentiate C. islandica from C. ericetorum with a barcode gap, but the widely used nrITS barcode failed. Neither of them could discriminate chemotypes of C. islandica. In conclusion, this integrative approach involving chemical profiling and DNA barcoding could be applied for authentication of Iceland Moss materials.},
}
@article {pmid29286260,
year = {2018},
author = {Tseren-Ochir, EO and Yuk, SS and Khishgee, B and Kwon, JH and Noh, JY and Hong, WT and Jeong, JH and Gwon, GB and Jeong, S and Kim, YJ and Kim, JB and Lee, JH and Kim, KJ and Damdinjav, B and Song, CS},
title = {Molecular Characterization of Avian Paramyxovirus Types 4 and 8 Isolated from Wild Migratory Waterfowl in Mongolia.},
journal = {Journal of wildlife diseases},
volume = {54},
number = {2},
pages = {342-346},
doi = {10.7589/2017-03-067},
pmid = {29286260},
issn = {1943-3700},
mesh = {Animals ; *Animals, Wild ; Anseriformes/*virology ; Avulavirus/classification/*genetics ; Avulavirus Infections/epidemiology/*veterinary/virology ; Mongolia/epidemiology ; Phylogeny ; },
abstract = {Avian paramyxoviruses (APMVs) constitute some of the most globally prevalent avian viruses and are frequently isolated from wild migratory bird species. Using 1,907 fresh fecal samples collected during the 2012 avian influenza surveillance program, we identified two serotypes of APMV: APMV-4 (n=10) and APMV-8 (n=1). Sequences for these isolates phylogenetically clustered with Asian APMV-4 and APMV-8 recently isolated from wild birds in Korea, Japan, China, and Kazakhstan. Analysis by DNA barcoding indicated that the Mongolian APMV-4 and APMV-8 strains were isolated from Anseriformes species including Mallards (Anas platyrhynchos) and Whooper Swans (Cygnus cygnus). The close genetic relatedness to Asian isolates, and to similar host species, suggested that wild bird species in the Anatidae family might play an important role as a natural reservoir in the spread of APMV-4 and APMV-8. However, we did not find conclusive evidence to support this hypothesis owing to the limited number of strains that could be isolated. Enhanced surveillance of poultry and wild bird populations in Asia is therefore crucial for the understanding of global AMPV transmission, ecology, evolution, and epidemiology.},
}
@article {pmid29280404,
year = {2018},
author = {Ullah, M and Dong, Y and Qiao, P and Zhang, Y and Yang, Z},
title = {Delineating closely related species of Tylostega Meyrick (Lepidoptera: Crambidae: Spilomelinae) from mainland China using DNA barcodes.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {7},
pages = {1121-1127},
doi = {10.1080/24701394.2017.1419213},
pmid = {29280404},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Genitalia, Male/anatomy &amp; histology ; Insect Proteins/genetics ; Lepidoptera/anatomy &amp; histology/classification/*genetics ; Male ; *Phylogeny ; },
abstract = {Integrative taxonomic study of three species of the genus Tylostega revealed that the genetic distances of the COI gene among the tested species was relatively large (3.27-7.60%). The Automatic Barcode Gap Discovery (ABGD) system performed better than the Barcode Index Number (BIN) in discriminating closely related species. This work provides a molecular baseline for future integrative taxonomic study of Crambidae.},
}
@article {pmid29280363,
year = {2017},
author = {Wang, CX and Xu, X and Li, SQ},
title = {Integrative taxonomy of Leptonetela spiders (Araneae, Leptonetidae), with descriptions of 46 new species.},
journal = {Zoological research},
volume = {38},
number = {6},
pages = {321-448},
pmid = {29280363},
issn = {2095-8137},
mesh = {Animal Distribution ; Animals ; Caves ; China ; Ecosystem ; Species Specificity ; Spiders/*anatomy &amp; histology/*classification/genetics ; },
abstract = {Extreme environments, such as subterranean habitats, are suspected to be responsible for morphologically inseparable cryptic or sibling species and can bias biodiversity assessment. A DNA barcode is a short, standardized DNA sequence used for taxonomic purposes and has the potential to lessen the challenges presented by a biotic inventory. Here, we investigate the diversity of the genus Leptonetela Kratochvíl, 1978 that is endemic to karst systems in Eurasia using DNA barcoding. We analyzed 624 specimens using one mitochondrial gene fragment (COI). The results show that DNA barcoding is an efficient and rapid species identification method in this genus. DNA barcoding gap and automatic barcode gap discovery (ABGD) analyses indicated the existence of 90 species, a result consistent with previous taxonomic hypotheses, and supported the existence of extreme male pedipalpal tibial spine and median apophysis polymorphism in Leptonetela species, with direct implications for the taxonomy of the group and its diversity. Based on the molecular and morphological evidence, we delimit and diagnose 90 Leptonetela species, including the type species Leptonetela kanellisi (Deeleman-Reinhold, 1971). Forty-six of them are previously undescribed. The female of Leptonetela zhai Wang &amp; Li, 2011 is reported for the first time. Leptonetela tianxinensis (Tong &amp; Li, 2008) comb. nov. is transferred from the genus Leptoneta Simon, 1872; the genus Guineta Lin &amp; Li, 2010 syn. nov. is a junior synonym of Leptonetela; Leptonetela gigachela (Lin &amp; Li, 2010) comb. nov. is transferred from Guineta. The genus Sinoneta Lin &amp; Li, 2010 syn. nov. is a junior synonym of Leptonetela; Leptonetela notabilis (Lin &amp; Li, 2010) comb. nov. and Leptonetela sexdigiti (Lin &amp; Li, 2010) comb. nov. are transferred from Sinoneta; Leptonetela sanchahe Wang &amp; Li nom. nov. is proposed as a replacement name for Sinoneta palmata (Chen et al., 2010) because Leptonetela palmata is preoccupied.},
}
@article {pmid29273852,
year = {2017},
author = {Akçaalan, R and Albay, M and Koker, L and Baudart, J and Guillebault, D and Fischer, S and Weigel, W and Medlin, LK},
title = {Seasonal dynamics of freshwater pathogens as measured by microarray at Lake Sapanca, a drinking water source in the north-eastern part of Turkey.},
journal = {Environmental monitoring and assessment},
volume = {190},
number = {1},
pages = {42},
pmid = {29273852},
issn = {1573-2959},
support = {FP7-KBBE-2010-4, 265409//EU/ ; },
mesh = {Bacterial Toxins/analysis ; Cyanobacteria/growth &amp; development ; Cyanobacteria Toxins ; Drinking Water/*microbiology ; Environmental Monitoring/*methods ; Humans ; Lakes/chemistry/*microbiology ; Marine Toxins/analysis ; Microcystins/analysis ; *Seasons ; Turkey ; Water Microbiology/*standards ; *Water Quality ; },
abstract = {Monitoring drinking water quality is an important public health issue. Two objectives from the 4 years, six nations, EU Project μAqua were to develop hierarchically specific probes to detect and quantify pathogens in drinking water using a PCR-free microarray platform and to design a standardised water sampling program from different sources in Europe to obtain sufficient material for downstream analysis. Our phylochip contains barcodes (probes) that specifically identify freshwater pathogens that are human health risks in a taxonomic hierarchical fashion such that if species is present, the entire taxonomic hierarchy (genus, family, order, phylum, kingdom) leading to it must also be present, which avoids false positives. Molecular tools are more rapid, accurate and reliable than traditional methods, which means faster mitigation strategies with less harm to humans and the community. We present microarray results for the presence of freshwater pathogens from a Turkish lake used drinking water and inferred cyanobacterial cell equivalents from samples concentrated from 40 into 1 L in 45 min using hollow fibre filters. In two companion studies from the same samples, cyanobacterial toxins were analysed using chemical methods and those dates with highest toxin values also had highest cell equivalents as inferred from this microarray study.},
}
@article {pmid29272986,
year = {2018},
author = {Vargas-Ortiz, M and Bobadilla, D and Huanca-Mamani, W and Vargas, HA},
title = {Genetic divergence of isolated populations of the native micromoth Bucculatrix mirnae (Lepidoptera: Bucculatricidae) in the arid environments of Northern Chile.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {8},
pages = {1139-1147},
doi = {10.1080/24701394.2017.1419215},
pmid = {29272986},
issn = {2470-1408},
mesh = {Animal Migration ; Animals ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Gene Flow ; Genes, Insect/genetics ; *Genetic Speciation ; *Genetic Variation ; Haplotypes ; Lepidoptera/*genetics ; Male ; },
abstract = {Analysis of maternally inherited genes is especially helpful in population studies of host-specialized insects, as female dispersal is key to find an adequate host plant to ensure larval survival. Bucculatrix mirnae (Lepidoptera: Bucculatricidae) is a little-known Neotropical micromoth native to the arid environments of northern Chile whose hypermetamorphic larvae are miners and skeletonizers on leaves of two species of Baccharis (Asteraceae) shrubs. This micromoth has been detected in three isolated locations embracing a narrow geographic range: two from the coastal valleys of the Atacama Desert near sea level and one from the western slopes of the Andes at about 3000 m elevation. As the dispersal of B. mirnae is mostly restricted to the small adult stage, the altitudinal gradient and desert areas among the three localities could be effective barriers, triggering genetic differentiation among populations. Sequences of the DNA barcode fragment of the cytocrome oxidase subunit I mitochondrial gene were analyzed to assess for the first time the patterns of genetic variation of B. mirnae. Fifteen haplotypes, each exclusive to one locality, were found in the 71 specimens analyzed. Genetic divergence (K2P) between haplotypes of different localities was at least 2.0%. A Bayesian analysis with sequences of congeneric species grouped all the B. mirnae haplotypes in a clade, in which three well-supported locality-specific haplogroups were found. In concordance with this pattern, an analysis of molecular variance showed that the highest genetic variation was found among populations. Furthermore, all the population pairwise comparisons (FST) were significant. These results suggest that female migration between isolated populations of B. mirnae is absent. This pattern must be considered in the current scenario of habitat destruction and modification in the arid environments of northern Chile.},
}
@article {pmid29267311,
year = {2017},
author = {Núñez Pons, L and Calcinai, B and Gates, RD},
title = {Who's there? - First morphological and DNA barcoding catalogue of the shallow Hawai'ian sponge fauna.},
journal = {PloS one},
volume = {12},
number = {12},
pages = {e0189357},
pmid = {29267311},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Hawaii ; Microscopy, Electron, Scanning ; Phylogeny ; Polymerase Chain Reaction ; Porifera/*classification/genetics ; Species Specificity ; },
abstract = {The sponge fauna has been largely overlooked in the Archipelago of Hawai'i, notwithstanding the paramount role of this taxon in marine ecosystems. The lack of knowledge about Porifera populations inhabiting the Hawai'ian reefs limits the development of ecological studies aimed at understanding the functioning of these marine systems. Consequently, this project addresses this gap by describing the most representative sponge species in the shallow waters of the enigmatic bay of Kane'ohe Bay, in O'ahu Island. A total of 30 species (28 demosponges and two calcareous sponges) living associated to the reef structures are here reported. Six of these species are new records to the Hawai'ian Porifera catalogue and are suspected to be recent introductions to these islands. Morphological descriptions of the voucher specimens are provided, along with sequencing data of two partitions involving the mitochondrial cytochrome oxidase subunit 1 (COI) marker and a fragment covering partial (18S and 28S) and full (ITS-1, 5.8S and ITS-2) nuclear ribosomal genes. Species delimitations based on genetic distances were calculated to valitate how taxonomic assignments from DNA barcoding aligned with morphological identifications. Of the 60 sequences submitted to GenBank ~88% are the first sequencing records for the corresponding species and genetic marker. This work compiles the first catalogue combining morphological characters with DNA barcoding of Hawai'ian sponges, and contributes to the repository of public databases through the Sponge Barcoding Project initiative.},
}
@article {pmid29264798,
year = {2018},
author = {Fujinaka, CM and Waas, M and Gundry, RL},
title = {Mass Spectrometry-Based Identification of Extracellular Domains of Cell Surface N-Glycoproteins: Defining the Accessible Surfaceome for Immunophenotyping Stem Cells and Their Derivatives.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1722},
number = {},
pages = {57-78},
pmid = {29264798},
issn = {1940-6029},
support = {R01 HL126785/HL/NHLBI NIH HHS/United States ; R01 HL134010/HL/NHLBI NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Antibodies/immunology ; Epitopes/immunology ; Humans ; Immunophenotyping/*methods ; Mass Spectrometry/*methods ; Membrane Glycoproteins/*analysis ; Protein Domains ; Proteome/*analysis ; Proteomics/methods ; Stem Cells/*classification/immunology ; },
abstract = {Human stem cells and their progeny are valuable for a variety of research applications and have the potential to revolutionize approaches to regenerative medicine. However, we currently have limited tools to permit live isolation of homogeneous populations of cells apt for mechanistic studies or cellular therapies. While these challenges can be overcome through the use of immunophenotyping based on accessible cell surface markers, the success of this process depends on the availability of reliable antibodies and well-characterized markers, which are lacking for most stem cell lineages. This chapter outlines an iterative process for the development of new cell surface marker barcodes for identifying and selecting stem cell derived progeny of specific cell types, subtypes, and maturation stages, where antibody-independent identification of cell surface proteins is achieved using a modern chemoproteomic approach to specifically identify N-glycoproteins localized to the cell surface. By taking advantage of a large repository of available cell surfaceome data, proteins that are unlikely to confer cell type specificity can be rapidly eliminated from consideration. Subsequently, targeted quantitation by mass spectrometry can be used to refine candidates of interest, and a bioinformatic visualization tool is key to mapping experimental data to candidate protein sequences for the purpose of epitope selection during the antibody development phase. Overall, the process of developing cell surface barcodes for immunophenotyping is iterative and can include multiple rounds of discovery, refinement, and validation depending on the phenotypic resolution required.},
}
@article {pmid29261732,
year = {2017},
author = {Titulaer, M and Melgoza-Castillo, A and Panjabi, AO and Sanchez-Flores, A and Martínez-Guerrero, JH and Macías-Duarte, A and Fernandez, JA},
title = {Molecular analysis of stomach contents reveals important grass seeds in the winter diet of Baird's and Grasshopper sparrows, two declining grassland bird species.},
journal = {PloS one},
volume = {12},
number = {12},
pages = {e0189695},
pmid = {29261732},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic ; *Diet ; *Gastrointestinal Contents ; *Grassland ; High-Throughput Nucleotide Sequencing ; *Seasons ; *Seeds ; Sparrows/*physiology ; },
abstract = {We analyzed the diet of Baird's Sparrow (Ammodramus bairdii) and Grasshopper Sparrow (A. savannarum) in three different sites and sampling periods across the Chihuahuan Desert in northern Mexico. DNA from seeds in regurgitated stomach contents was sequenced using NGS technology and identified with a barcoding approach using the P6 loop of the trnL intron as genetic marker. During each sampling period, we collected random soil samples to estimate seed availability in the soil seed bank. Due to the variability and size of the genetic marker, the resolution was limited to a family level resolution for taxonomic classification of seeds, but in several cases a genus level was achieved. Diets contained a high diversity of seeds but were dominated by a limited number of genera/families. Seeds from Panicoideae (from the genera Panicum, Setaria, Eriochloa, Botriochloa, and Hackelochloa) contributed for the largest part to the diets (53 ± 19%), followed by Bouteloua (10 ± 12%). Depending on the site and sampling period, other important seeds in the diets were Eragrostideae, Pleuraphis, Asteraceae, Verbena, and Amaranthus. The most abundant seeds were not always preferred. Aristida and Chloris were common in the soil seed bank but these seeds were avoided by both bird species. Baird's and Grasshopper sparrows did not differ in seed preferences. This work highlights the importance of range management practices that favor seed production of Panicoideae and Bouteloua grasses to enhance winter habitat use and survival of Baird's and Grasshopper sparrows in the Chihuahuan Desert.},
}
@article {pmid29258287,
year = {2017},
author = {Tian, E and Liu, Q and Ye, H and Li, F and Chao, Z},
title = {A DNA Barcode-Based RPA Assay (BAR-RPA) for Rapid Identification of the Dry Root of Ficus hirta (Wuzhimaotao).},
journal = {Molecules (Basel, Switzerland)},
volume = {22},
number = {12},
pages = {},
pmid = {29258287},
issn = {1420-3049},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; DNA, Ribosomal Spacer/genetics ; Ficus/*genetics ; Nucleic Acid Amplification Techniques ; Plant Roots/*genetics ; Recombinases/metabolism ; },
abstract = {Background: Wuzhimaotao (the dry root of Ficus hirta) is used as both medicine and food ingredient by the locals in areas around Nanling Mountains of China. Due to its very similar external morphologies with Duanchangcao (the root of Gelsemium elegans, which contains gelsemine that is extremely neurotoxic) and the associated growth of these two plants, incidents of food poisoning and even death frequently occur, resulting from the misuse of Duanchangcao as Wuzhimaotao. The aim of this study is to develop a fast, even, on-spot approach to identification of Wuzhimaotao. Methods: We used DNA barcode-based recombinase polymerase amplification (BAR-RPA) with species-specific primers targeting the internal transcribed spacer (ITS) region of the rDNA of F. hirta. BAR-RPA reaction time and temperature were optimized and the specificity and sensitivity of BAR-RPA species-specific primers were assessed. Results: This technique showed a high specificity and sensitivity to amplify the genomic DNA of F. hirta and allowed for rapid amplification (within 15 min) of the ITS region under a constant and mild temperature range of 37-42 °C without using thermocyclers. Conclusions: The BAR-RPA assay with a fast DNA extraction protocol provides a simple, energy-saving, and rapid method for identification of Wuzhimaotao in both laboratory and field settings.},
}
@article {pmid29257732,
year = {2017},
author = {Chattopadhyay, P and Banerjee, G and Banerjee, N},
title = {Distinguishing Orchid Species by DNA Barcoding: Increasing the Resolution of Population Studies in Plant Biology.},
journal = {Omics : a journal of integrative biology},
volume = {21},
number = {12},
pages = {711-720},
doi = {10.1089/omi.2017.0131},
pmid = {29257732},
issn = {1557-8100},
mesh = {DNA Barcoding, Taxonomic/*methods ; Dendrobium/classification/*genetics ; Phylogeny ; Plants/classification/*genetics ; Sequence Analysis, DNA/methods ; },
abstract = {Increasing the resolution of population studies in plant biology is one of the leading frontiers for omics sciences. One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets such as individual genes [like ribulose bisphosphate carboxylase large chain (rbcL) and maturase K (matK)] and intergenic spacers (IGS) [like nuclear ribosomal internal transcribed spacer 1 (nrITS 1) and 2 (nrITS 2), and chloroplast IGS between transfer RNA for leucine and phenylalanine (cp trnL-trnF IGS)]. To solve this challenge, we have screened the four well-established candidate gene sequences (i.e., rbcL, matK, trnL-trnF IGS, and 18S-ITS1-5.8S-ITS2-28S nrDNA) of 65 Indian orchid species. We also have included 31 different species of Dendrobium to identify the suitable locus for resolving the phylogeny-related problem below the taxonomic rank of genus. The Consortium for the Barcode of Life has recommended the locus rbcL and matK for barcoding of all land plants, including orchids. However, in this study, matK and rbcL (species resolving capacity 52% and 48%, respectively) were found to work above the taxonomic limit of genus, and thus cannot be considered a suitable tool to resolve closely related species of Dendrobium, whereas, we found that the locus 18S-ITS1-5.8S-ITS2-28S nrDNA is the best choice with the highest species resolving ability (95.23%) and the highest mean Kimura 2-parameter distance (254 for intergeneric and 144 for intrageneric) for phylogeny construction, and thus have been taken as the most promising single-locus barcode for orchids.},
}
@article {pmid29255297,
year = {2018},
author = {Kimmerling, N and Zuqert, O and Amitai, G and Gurevich, T and Armoza-Zvuloni, R and Kolesnikov, I and Berenshtein, I and Melamed, S and Gilad, S and Benjamin, S and Rivlin, A and Ohavia, M and Paris, CB and Holzman, R and Kiflawi, M and Sorek, R},
title = {Quantitative species-level ecology of reef fish larvae via metabarcoding.},
journal = {Nature ecology &amp; evolution},
volume = {2},
number = {2},
pages = {306-316},
doi = {10.1038/s41559-017-0413-2},
pmid = {29255297},
issn = {2397-334X},
mesh = {*Animal Distribution ; Animals ; Coral Reefs ; Electron Transport Complex IV/analysis ; Fish Proteins/analysis ; Fishes/growth &amp; development/*physiology ; Israel ; Larva/growth &amp; development/physiology ; *Metagenome ; Mitochondrial Proteins/analysis ; Oceans and Seas ; Population Density ; Spatio-Temporal Analysis ; },
abstract = {The larval pool of coral reef fish has a crucial role in the dynamics of adult fish populations. However, large-scale species-level monitoring of species-rich larval pools has been technically impractical. Here, we use high-throughput metabarcoding to study larval ecology in the Gulf of Aqaba, a region that is inhabited by >500 reef fish species. We analysed 9,933 larvae from 383 samples that were stratified over sites, depth and time. Metagenomic DNA extracted from pooled larvae was matched to a mitochondrial cytochrome c oxidase subunit I barcode database compiled for 77% of known fish species within this region. This yielded species-level reconstruction of the larval community, allowing robust estimation of larval spatio-temporal distributions. We found significant correlations between species abundance in the larval pool and in local adult assemblages, suggesting a major role for larval supply in determining local adult densities. We documented larval flux of species whose adults were never documented in the region, suggesting environmental filtering as the reason for the absence of these species. Larvae of several deep-sea fishes were found in shallow waters, supporting their dispersal over shallow bathymetries, potentially allowing Lessepsian migration into the Mediterranean Sea. Our method is applicable to any larval community and could assist coral reef conservation and fishery management efforts.},
}
@article {pmid29247217,
year = {2017},
author = {Blut, C and Crespi, A and Mersch, D and Keller, L and Zhao, L and Kollmann, M and Schellscheidt, B and Fülber, C and Beye, M},
title = {Automated computer-based detection of encounter behaviours in groups of honeybees.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {17663},
pmid = {29247217},
issn = {2045-2322},
support = {MC_U105188491/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; Automation, Laboratory ; Bees/*physiology ; Behavior, Animal/*physiology ; Data Curation/*methods ; Diagnosis, Computer-Assisted ; *Machine Learning ; Social Behavior ; Software ; },
abstract = {Honeybees form societies in which thousands of members integrate their behaviours to act as a single functional unit. We have little knowledge on how the collaborative features are regulated by workers' activities because we lack methods that enable collection of simultaneous and continuous behavioural information for each worker bee. In this study, we introduce the Bee Behavioral Annotation System (BBAS), which enables the automated detection of bees' behaviours in small observation hives. Continuous information on position and orientation were obtained by marking worker bees with 2D barcodes in a small observation hive. We computed behavioural and social features from the tracking information to train a behaviour classifier for encounter behaviours (interaction of workers via antennation) using a machine learning-based system. The classifier correctly detected 93% of the encounter behaviours in a group of bees, whereas 13% of the falsely classified behaviours were unrelated to encounter behaviours. The possibility of building accurate classifiers for automatically annotating behaviours may allow for the examination of individual behaviours of worker bees in the social environments of small observation hives. We envisage that BBAS will be a powerful tool for detecting the effects of experimental manipulation of social attributes and sub-lethal effects of pesticides on behaviour.},
}
@article {pmid29245721,
year = {2017},
author = {Prieto, C and Lorenc-Brudecka, J},
title = {Description of Rhamma dawkinsi (Lepidoptera: Lycaenidae) a new mountain butterfly from Colombia.},
journal = {Zootaxa},
volume = {4338},
number = {3},
pages = {587-594},
doi = {10.11646/zootaxa.4338.3.12},
pmid = {29245721},
issn = {1175-5334},
mesh = {Animals ; *Butterflies ; Colombia ; Female ; Genitalia ; Lepidoptera ; Male ; },
abstract = {A preliminary assessment of barcode data for the genus Rhamma suggests the presence of several cryptic species in Colombia. Based on morphology and barcodes, we were able to diagnose one of these lineages as a new species that is described herein as Rhamma dawkinsi, sp. nov. Adult specimens and the genitalia of both sexes are illustrated and compared with R. adunca (Draudt, 1919) and R. comstocki (Johnson, 1992), the most closely related species based on phenotypic appearance.},
}
@article {pmid29245662,
year = {2017},
author = {Erlacher, S and Palma, LM and Erlacher, J},
title = {A systematic revision of Charissa, subgenus Pterygnophos Wehrli, 1951, with description of a new species (Lepidoptera: Geometridae).},
journal = {Zootaxa},
volume = {4341},
number = {3},
pages = {400-418},
doi = {10.11646/zootaxa.4341.3.4},
pmid = {29245662},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; DNA ; Female ; Genitalia ; Male ; Mongolia ; *Moths ; },
abstract = {The subgenus Pterygnophos Wehrli, 1951 within the genus Charissa Curtis, 1826 nomen protectum (= Hyposcotis Hübner, [1825] nomen oblitum) is taxonomically revised based on morphology and DNA barcoding. The subgenus comprises four species in total which are presented in detail. Diagnostic characters are depicted and keys to the species based on the morphology of male and female genitalia are provided. Males and females of each species and their genitalia are illustrated. The distribution of all species is described and figured on a map, and a neighbor joining tree based on DNA barcoding of 17 specimens is presented. Charissa (Pterygnophos) beljaevi spec. nov. from Mongolia is described as new. A neotype for Gnophos creperaria Erschoff, 1877, and lectotypes for Gnophos deliciaria shantungensis Wehrli, 1953, Gnophos dorkadiaria Wehrli, 1922, Gnophos ochrofasciata Staudinger, 1895, and Gnophos finitimaria Fuchs, 1899 are designated. The following synonyms are recognized: Gnophos finitimaria Fuchs, 1899 syn. nov. is a synonym of Gnophos ochrofasciata Staudinger, 1895 and Gnophos deliciaria shantungensis Wehrli, 1953 syn. nov. is a synonym of Gnophos agnitaria Staudinger, 1897.},
}
@article {pmid29245660,
year = {2017},
author = {Hrivniak, &#x13d; and Sroka, P and Godunko, RJ and Žurovcová, M},
title = {Mayflies of the genus Epeorus Eaton, 1881 s.l. (Ephemeroptera: Heptageniidae) from the Caucasus Mountains: a new species of Caucasiron Kluge, 1997 from Georgia and Turkey.},
journal = {Zootaxa},
volume = {4341},
number = {3},
pages = {353-374},
doi = {10.11646/zootaxa.4341.3.2},
pmid = {29245660},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures ; Animals ; *Ephemeroptera ; Georgia (Republic) ; Insecta ; Turkey ; },
abstract = {The new species Epeorus (Caucasiron) bicolliculatus sp. nov. is described based on larvae and adults. Diagnostic characters are given with regard to the related species. The most pronounced difference is represented by protuberances on larval abdominal terga II-IX, present exclusively in E. (C.) bicolliculatus sp. nov. Primary data on the biology and distribution of the new species are also provided. Delimitation of the new species is verified by the analysis of COI (barcode) sequences. Barcode data for all Caucasian species of the subgenus Caucasiron are provided for the first time and compared with E. (C.) bicolliculatus sp. nov.},
}
@article {pmid29245659,
year = {2017},
author = {Brito, R and Lopez-Vaamonde, C and Gonçalves, GL and Becker, VO and Mielke, OHH and Moreira, GRP},
title = {Taxonomic revision of Neotropical Phyllocnistis Zeller, 1848 (Lepidoptera: Gracillariidae), with descriptions of seven new species and host plant associations.},
journal = {Zootaxa},
volume = {4341},
number = {3},
pages = {301-352},
doi = {10.11646/zootaxa.4341.3.1},
pmid = {29245659},
issn = {1175-5334},
mesh = {Animals ; Brazil ; French Guiana ; Genitalia ; *Lepidoptera ; Plants ; },
abstract = {Until now, 20 species of leaf-mining micromoths of the genus Phyllocnistis Zeller (Lepidoptera, Gracillariidae) have been known to occur in the Neotropical region. Here we revise the previously known species and describe seven new species: four from French Guiana, P. kawakitai Brito &amp; Lopez-Vaamonde, sp. nov., P. norak Brito &amp; Lopez-Vaamonde, sp. nov., P. ohshimai Brito &amp; Lopez-Vaamonde, sp. nov., P. petronellii Brito &amp; Lopez-Vaamonde, sp. nov.; and, three from Brazil, P. helios Brito &amp; Moreira, sp. nov., P. jupiter Brito &amp; Moreira, sp. nov. and P. xylopiella Brito &amp; Becker, sp. nov. Lectotypes are designated for P. aurilinea Zeller, 1877; P. citrella Stainton, 1856; P. rotans and P. sexangula Meyrick, 1915. Detailed descriptions of the pattern of forewing fasciae are provided for all species. Host plant associations, photographs of adults and illustrations of genitalia, when available, are provided for the described species of Neotropical Phyllocnistis. In addition, DNA barcodes were used for the delimitation of some species.},
}
@article {pmid29245612,
year = {2017},
author = {Silva, GSC and Covain, R and Oliveira, C and Roxo, FF},
title = {Description of two new species of Lithoxus (Hypostominae: Loricariidae) from rio Jari and rio Amapá basins, Brazilian Guiana Shield.},
journal = {Zootaxa},
volume = {4347},
number = {1},
pages = {151-168},
doi = {10.11646/zootaxa.4347.1.9},
pmid = {29245612},
issn = {1175-5334},
mesh = {Animals ; Brazil ; *Catfishes ; Tooth ; },
abstract = {Two new species of Lithoxus, a genus diagnosed by possessing a dorsoventrally depressed body, a large round oral disk, and small tooth cusps with few teeth, are described from two drainages of the Guiana Shield: Lithoxus jariensis from the rio Jari basin and L. raso from the rio Raso, rio Amapá basin. The new species, L. jariensis, is distinguished from congeners by having an adipose fin, by the number of branched anal-fin and caudal-fin rays, by color pattern of the body, number of teeth, adipose-fin length, dorsal adipose-caudal distance, caudal peduncle depth, cleithral width, and dorsal-anal distance. Lithoxus raso can be diagnosed from congeners by coloration pattern, by having an adipose fin, by the number of branched anal-fin rays, number of teeth, adipose-fin length, dorsal adipose-caudal distance, caudal peduncle depth, and cleithral width. Greater genetic divergence in mitochondrial cytochrome oxidase subunit I (COI) confirms L. jariensis and L. raso as two new species.},
}
@article {pmid29245577,
year = {2017},
author = {Robertson, DR and Angulo, A and Baldwin, CC and Pitassy, D and Driskell, A and Weigt, L and Navarro, IJF},
title = {Deep-water bony fishes collected by the B/O Miguel Oliver on the shelf edge of Pacific Central America: an annotated, illustrated and DNA-barcoded checklist.},
journal = {Zootaxa},
volume = {4348},
number = {1},
pages = {1-125},
doi = {10.11646/zootaxa.4348.1.1},
pmid = {29245577},
issn = {1175-5334},
mesh = {Animals ; Central America ; DNA ; *DNA Barcoding, Taxonomic ; Expeditions ; *Fishes ; Geography ; },
abstract = {An annotated and photographically illustrated checklist with DNA barcodes of the species of bony fishes collected during a month-long research cruise of the Spanish Research vessel B/O Miguel Oliver is presented. The vessel made trawls on the continental shelf of the Pacific coast of Central America, in November-December 2010, at depths of 108-1625 m. This list, based on 707 specimens (of a total of 876 specimens collected during the whole expedition), includes 129 species belonging to 15 orders, 61 families, and 97 genera. New information is presented on the geographical distributions of more than a third of those species, with 29 species (22.4%) representing new records from Central American waters and 17 species (13.2%) having expanded latitudinal ranges. Data on capture depths demonstrate increased depth ranges due to new minimum and/or maximum known depths for 31 species, i.e. 24% of those captured. Tissue samples from frozen specimens were used to obtain DNA barcodes of 682 (96.5%) individuals belonging to 118 species (91.4% of those recorded here), which have been made publically available in Genbank. Those data include barcodes for 84 species (65.1% of the total collected, and 77.1% of those for which barcodes were obtained) and 30 genera (30.9% of those collected) for which no species barcodes have been previously published. Barcodes of 54 species represent the first genetic sequences of any type published for those species. The abundance of new data indicate that there is still much to learn about the composition and geographical and depth distributions of the fish fauna of the shelf edge and continental slope of this region.},
}
@article {pmid29245574,
year = {2017},
author = {Parimuchová, A and Kováč, &#x13d; and Žurovcová, M and Kadebskaya, OI},
title = {A new troglobiotic Protaphorura (Collembola, Hexapoda) from the Siberia, Russia.},
journal = {Zootaxa},
volume = {4350},
number = {1},
pages = {185-195},
doi = {10.11646/zootaxa.4350.1.12},
pmid = {29245574},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; *Arthropods ; Insecta ; Russia ; Siberia ; },
abstract = {A new species of Protaphorura Absolon, 1901 (Collembola, Onychiuridae), P. cykini sp.nov., is described from a cold karst cave in the Irkutsk region, Siberia, Russia. It is an obligate cave species with the largest body size (4.3-5.6 mm) of all congeners. The species is further characteristic by the pseudocellar formula as 3(2)2/022/33343, high number of vesicles in postantennal organ (65-71) and subapical organite protected with two papillae. A partial sequence of cytochrome oxidase I (COI DNA barcoding marker) gene is used to verify the taxonomic status of the new species and the barcode sequence is compared with other congeners available in GenBank database. Distribution and diversity of cave Collembola of Siberia is discussed.},
}
@article {pmid29245545,
year = {2017},
author = {Saldaitis, A and Volynkin, AV and Benedek, B},
title = {On the synonymy of some taxa of the genus Xylena Hübner (Lepidoptera, Noctuidae).},
journal = {Zootaxa},
volume = {4350},
number = {3},
pages = {583-586},
doi = {10.11646/zootaxa.4350.3.10},
pmid = {29245545},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures ; Animals ; China ; Asia, Eastern ; Female ; Male ; *Moths ; Russia ; },
abstract = {Xylena czernilai Volynkin, 2011 was described on the base of a single male from the Russian Altai Mts. (Volynkin 2011). Later, two externally similar taxa, Xylena alexander Benedek, Babics &amp; Saldaitis, 2013 and Xylena andreas Benedek, Babics &amp; Saldaitis, 2013 were described from Sichuan province, China each on the base of a single female (Benedek et al. 2013). In the same year, a female of X. czernilai was described by Volynkin &amp; Knyazev (2013). The female genitalia of X. czernilai are surprisingly similar to those of the both Chinese species therefore we decided to use a DNA analysis to clarify the status of these three taxa. For the analysis we sampled a female of X. czernilai from the Russian Altai, a male of X. czernilai from the Russian Far East and the holotypes of X. alexander and X. andreas. The analysis of COI barcodes of the sampled specimens has shown that X. alexander and X. andreas are conspecific (the difference is 0.15 %), and their COI sequences differ from those of X. czernilai in 0.93 % only. Such difference is too small to treat Chinese populations as a distinct species (for example, the difference between X. czernilai and its closest relative X. vetusta (Hübner, [1813]) is 4.61% . The detailed morphological comparison of czernilai and vetusta has been given by Volynkin (2011) (Fig. 1) therefore here we synonymize X. alexander and X. andreas with X. czernilai.},
}
@article {pmid29245522,
year = {2017},
author = {Brunetti, R and Manni, L and Mastrototaro, F and Gissi, C and Gasparini, F},
title = {Fixation, description and DNA barcode of a neotype for Botryllus schlosseri (Pallas, 1766) (Tunicata, Ascidiacea).},
journal = {Zootaxa},
volume = {4353},
number = {1},
pages = {29-50},
doi = {10.11646/zootaxa.4353.1.2},
pmid = {29245522},
issn = {1175-5334},
mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic ; Italy ; *Urochordata ; },
abstract = {Botryllus schlosseri is a widespread colonial ascidian commonly considered cosmopolitan and amply used as model for researches ranging from developmental biology to immunobiology. Recently, molecular data lead to hypothesize that the species named B. schlosseri may consist of more than a single taxon. Indeed, five highly divergent clades, named A-E, have been genetically identified and are referred as cryptic species. In this context, and lacking both a type and a detailed morphological description, we believe that it is necessary, as a taxonomic reference point, to designate a neotype and re-describe the species. Therefore, a sample from the Lagoon of Venice (Adriatic Sea, Italy) was deposited as neotype in the Natural History Museum of Venice (Italy), preserved both in formalin and in 90% ethanol. Here we provide a morphological description of the suggested neotype of B. schlosseri that takes into account several developmental stages (oozooid, zooid of first blastogenic generations, and mature zooid) and is carefully compared with the previous descriptions of samples coming from other European and non-European localities. Finally, we associate our morphological description to a "DNA barcode", consisting in a long fragment of the mitochondrial COI gene. Our description is associated to clade A, although at now we cannot guarantee that this association is univocal.},
}
@article {pmid29245511,
year = {2017},
author = {Schnabel, KE and Burghardt, I and Ahyong, ST},
title = {Southern high latitude squat lobsters II: description of Uroptychus macquariae sp. nov. from Macquarie Ridge.},
journal = {Zootaxa},
volume = {4353},
number = {2},
pages = {327-338},
doi = {10.11646/zootaxa.4353.2.4},
pmid = {29245511},
issn = {1175-5334},
mesh = {Animals ; *Anomura ; Antarctic Regions ; Indian Ocean ; New Zealand ; },
abstract = {Squat lobsters have only recently been recorded from the Macquarie Ridge, which extends south between New Zealand and Antarctica. Among these, Uroptychus insignis (Henderson, 1885) was recorded for the first time outside the western Indian Ocean, exhibiting only subtle morphological differences. Reexamination of the Macquarie Ridge and Indian Ocean specimens attributed to U. insignis using morphological and molecular data revealed the Macquarie Ridge form to represent a separate species. Subtle but consistent morphological differences are evident and partial CO1 sequence data indicates that the specimens collected on Macquarie Ridge differ from those collected in the Indian Ocean by more than 7%. The Macquarie Ridge species is described herein as Uroptychus macquariae n.sp. Subtle morphological differences between the new species and U. insignis are discussed.},
}
@article {pmid29245492,
year = {2017},
author = {Kanturski, M and Kajtoch, &#x141; and Wieczorek, K},
title = {European species of the aphid genus Eulachnus Del Guercio, 1909 (Hemiptera: Aphididae: Lachninae): revision and molecular phylogeny.},
journal = {Zootaxa},
volume = {4356},
number = {1},
pages = {1-81},
doi = {10.11646/zootaxa.4356.1.1},
pmid = {29245492},
issn = {1175-5334},
mesh = {Animals ; *Aphids ; Croatia ; Czech Republic ; Europe ; Female ; Male ; Phylogeny ; },
abstract = {The aphid genus Eulachnus in Europe is revised to include 12 species, using an integrative taxonomy approach, based on morphometric, molecular and biological traits. Fundatrix, apterous and alate viviparous female of a new species-Eulachnus stekolshchikovi Kanturski sp. nov. are described. Neotypes are designated for E. agilis, E. brevipilosus and E. nigricola. Lectotypes are designated for E. alticola, E. cembrae, E. rileyi and E. tuberculostemmatus. New synonyms are proposed: E. abameleki syn. nov. (= Cinara pini), E. cretaceus syn. nov. (= E. agilis), E. tauricus syn. nov. (= E. rileyi), E. pallidus syn. nov. (= E. tuberculostemmatus). Eulachnus mingazzinii (near Cinara piniphila) and E. nigrofasciatus (near C. brauni) are regarded as incertae sedis. Full species status is given for E. garganicus stat. nov. and E. ibericus stat. nov. Apterous viviparous female of E. cembrae; apterous and alate viviparous females of remaining species are redescribed. Sexual morphs of E. agilis, E. alticola, E. cembrae, E. intermedius, E. nigricola, E. rileyi and oviparous female of E. tuberculostemmatus are fully redescribed and figured for the first time. Fundatrices of E. agilis, E. brevipilosus, E. cembrae, E. rileyi and E. tuberculostemmatus, sexuales of E. brevipilosus and the alate male of E. tuberculostemmatus are described and figured. A new host plant-Pinus cembra for E. brevipilosus is reported, and this species is recorded for the first time from Czech Republic. Eulachnus tuberculostemmatus is reported for the first time from Croatia. Phylogenetic studies, based on the COI and ITS2 molecular markers, are provided to visualize and discuss the relationships within the European species. COI barcodes are provided for seven species.},
}
@article {pmid29245415,
year = {2017},
author = {Tyagi, K and Chakraborty, R and Singha, D and Kumar, V},
title = {A new species of Trichromothrips (Thysanoptera) from India with four new records.},
journal = {Zootaxa},
volume = {4363},
number = {1},
pages = {145-150},
doi = {10.11646/zootaxa.4363.1.8},
pmid = {29245415},
issn = {1175-5334},
mesh = {Animals ; Environment ; India ; Microscopy ; *Thysanoptera ; },
abstract = {Globally 6100 species of the Order Thysanoptera are reported, of which 739 are known from India (Tyagi &amp; Kumar 2016). The purpose here is to describe from India one new species and record for the first time from this country four other species, representing three different families, and full nomenclatural details are available at ThripsWiki (2017). From three of the species, including the holotype of the new species, DNA was isolated and amplification of partial fragment of mtCOI gene was performed (Tyagi et al. 2017) with the sequences submitted to the Barcode of Life Database. Photographs and illustrations were taken through a Leica Trinocular Microscope (Leica DM-1000) using Leica software application suite (LAS EZ 2.1.0). Voucher specimens, also the new holotype, are deposited in the National Zoological Collections (NZC), Zoological Survey of India, Kolkata, India.},
}
@article {pmid29245392,
year = {2017},
author = {Guo, S and He, J and Zhao, Z and Liu, L and Gao, L and Wei, S and Guo, X and Zhang, R and Li, Z},
title = {Identification of Neoceratitis asiatica (Becker) (Diptera: Tephritidae) based on morphological characteristics and DNA barcode.},
journal = {Zootaxa},
volume = {4363},
number = {4},
pages = {553-560},
doi = {10.11646/zootaxa.4363.4.7},
pmid = {29245392},
issn = {1175-5334},
mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV ; Phylogeny ; Sequence Analysis, DNA ; *Tephritidae ; },
abstract = {Neoceratitis asiatica (Becker), which especially infests wolfberry (Lycium barbarum L.), could cause serious economic losses every year in China, especially to organic wolfberry production. In some important wolfberry plantings, it is difficult and time-consuming to rear the larvae or pupae to adults for morphological identification. Molecular identification based on DNA barcode is a solution to the problem. In this study, 15 samples were collected from Ningxia, China. Among them, five adults were identified according to their morphological characteristics. The utility of mitochondrial DNA (mtDNA) cytochrome c oxidase I (COI) gene sequence as DNA barcode in distinguishing N. asiatica was evaluated by analysing Kimura 2-parameter distances and phylogenetic trees. There were significant differences between intra-specific and inter-specific genetic distances according to the barcoding gap analysis. The uncertain larval and pupal samples were within the same cluster as N. asiatica adults and formed sister cluster to N. cyanescens. A combination of morphological and molecular methods enabled accurate identification of N. asiatica. This is the first study using DNA barcode to identify N. asiatica and the obtained DNA sequences will be added to the DNA barcode database.},
}
@article {pmid29245375,
year = {2017},
author = {Ferrari, RR},
title = {Taxonomic revision of the species of Colletes Latreille, 1802 (Hymenoptera: Colletidae: Colletinae) found in Chile.},
journal = {Zootaxa},
volume = {4364},
number = {1},
pages = {1-137},
doi = {10.11646/zootaxa.4364.1.1},
pmid = {29245375},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Bees ; Chile ; Classification ; *Hymenoptera ; },
abstract = {A taxonomic revision of Colletes Latreille species with known geographic distribution in Chile is presented. In addition to the traditional morphological approach to taxonomy, DNA barcoding was employed to facilitate sexual association and cryptic species recognition. I provide diagnoses, synonymies, geographic and floral records, and a fully-illustrated key for 31 recognized species, 23 of them previously described: C. alocochila Moure, C. atacamensis Janvier, C. atripes Smith, C. bicolor Smith, C. chusmiza Rojas &amp; Toro, C. cognatus Spinola, C. cyanescens (Haliday), C. cyaniventris Spinola n. stat., C. flaminii Moure, C. fulvipes Spinola, C. gilvus Vachal, C. guanta Rojas &amp; Toro, C. longiceps Friese, C. lucens Vachal, C. mastochila Moure, C. murinus Friese, C. musculus Friese, C. nigritulus Friese, C. patagonicus Schrottky, C. quelu Rojas &amp; Toro, C. rutilans Vachal, C. sulcatus Vachal, and C. vicugnensis Rojas &amp; Toro. In addition, eight new species are described: C. arthuri n. sp., C. coquimbensis n. sp., C. flavipilosus n. sp., C. kuhlmanni n. sp., C. nigropilosus n. sp., C. simulatus n. sp., C. toroi n. sp., and C. ventricarinatus n. sp. Lectotypes for the following species are designated: Andrena cyanescens, Colletes bicolor, C. campoi Herbst, C. chubutensis Cockerell, C. gilvus, C. lucens, C. patagonicus, C. rufosignatus Cockerell, and C. viridans Vachal. Colletes seminitidus Spinola and C. viridans are both proposed as junior synonyms of C. cyanescens, and C. araucariae Friese is considered a junior synonym of C. sulcatus. Colletes cyaniventris n. stat. is resurrected from synonymy.},
}
@article {pmid29244845,
year = {2017},
author = {Merten, V and Christiansen, B and Javidpour, J and Piatkowski, U and Puebla, O and Gasca, R and Hoving, HT},
title = {Diet and stable isotope analyses reveal the feeding ecology of the orangeback squid Sthenoteuthis pteropus (Steenstrup 1855) (Mollusca, Ommastrephidae) in the eastern tropical Atlantic.},
journal = {PloS one},
volume = {12},
number = {12},
pages = {e0189691},
pmid = {29244845},
issn = {1932-6203},
mesh = {Animals ; Carbon Isotopes ; Crustacea ; DNA Barcoding, Taxonomic ; Decapodiformes/*physiology ; *Ecology ; *Feeding Behavior ; Fishes ; Gastrointestinal Contents/chemistry ; Nitrogen Isotopes ; Nutritional Status ; Seafood ; },
abstract = {In the eastern tropical Atlantic, the orangeback flying squid Sthenoteuthis pteropus (Steenstrup 1855) (Cephalopoda, Ommastrephidae) is a dominant species of the epipelagic nekton community. This carnivore squid has a short lifespan and is one of the fastest-growing squids. In this study, we characterise the role of S. pteropus in the pelagic food web of the eastern tropical Atlantic by investigating its diet and the dynamics of its feeding habits throughout its ontogeny and migration. During three expeditions in the eastern tropical Atlantic in 2015, 129 specimens were caught by hand jigging. Stomach content analyses (via visual identification and DNA barcoding) were combined with stable isotope data (∂15N and ∂13C) of muscle tissue to describe diet, feeding habits and trophic ecology of S. pteropus. Additionally, stable isotope analyses of incremental samples along the squid's gladius-the chitinous spiniform structure supporting the muscles and organs-were carried out to explore possible diet shifts through ontogeny and migration. Our results show that S. pteropus preys mainly on myctophid fishes (e.g. Myctophum asperum, Myctophum nitidulum, Vinciguerria spp.), but also on other teleost species, cephalopods (e.g. Enoploteuthidae, Bolitinidae, Ommastrephidae), crustaceans and possibly on gelatinous zooplankton as well. The squid shows a highly opportunistic feeding behaviour that includes cannibalism. Our study indicates that the trophic position of S. pteropus may increase by approximately one trophic level from a mantle length of 15 cm to 47 cm. The reconstructed isotope-based feeding chronologies of the gladii revealed high intra- and inter-individual variability in the squid's trophic position and foraging area. These findings are not revealed by diet or muscle tissue stable isotope analysis. This suggests a variable and complex life history involving individual variation and migration. The role of S. pteropus in transferring energy and nutrients from lower to higher trophic levels may be underestimated and important for understanding how a changing ocean impacts food webs in the eastern Atlantic.},
}
@article {pmid29242443,
year = {2017},
author = {Chen, YF and Huang, CL and Hsu, YF},
title = {DNA barcoding and morphological data reveal a new Hyposoter (Hymenoptera: Ichneumonidae: Porizontinae) reared from a rare zygaenid moth Artona flavipuncta Hampson, 1900 in Taiwan.},
journal = {Zootaxa},
volume = {4337},
number = {2},
pages = {279-287},
doi = {10.11646/zootaxa.4337.2.6},
pmid = {29242443},
issn = {1175-5334},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Hymenoptera ; Japan ; Moths ; Taiwan ; },
abstract = {A new species of Hyposoter Foerster, 1869 is discovered based on morphology of adults and cocoons, biology, and DNA barcoding evidence. It is herein described as Hyposoter distriangulum Chen, Huang &amp; Hsu sp. nov. , which is a common parasitoid of a rare zygaenid moth Artona flavipuncta Hampson, 1900. The differences between similar Hyposoter species in Japan and Taiwan are also presented.},
}
@article {pmid29241531,
year = {2017},
author = {Chakraborty, D and Paszkowski-Rogacz, M and Berger, N and Ding, L and Mircetic, J and Fu, J and Iesmantavicius, V and Choudhary, C and Anastassiadis, K and Stewart, AF and Buchholz, F},
title = {lncRNA Panct1 Maintains Mouse Embryonic Stem Cell Identity by Regulating TOBF1 Recruitment to Oct-Sox Sequences in Early G1.},
journal = {Cell reports},
volume = {21},
number = {11},
pages = {3012-3021},
doi = {10.1016/j.celrep.2017.11.045},
pmid = {29241531},
issn = {2211-1247},
mesh = {Animals ; Binding Sites ; Cell Line ; Chromatin/chemistry/metabolism ; G1 Phase/*genetics ; *Gene Expression Regulation, Developmental ; Mice ; Mouse Embryonic Stem Cells/cytology/*metabolism ; Nucleotide Motifs ; Octamer Transcription Factor-3/*genetics/metabolism ; Pluripotent Stem Cells/cytology/metabolism ; Promoter Regions, Genetic ; Protein Binding ; RNA, Long Noncoding/*genetics/metabolism ; SOXB1 Transcription Factors/*genetics/metabolism ; Signal Transduction ; },
abstract = {Long noncoding RNAs (lncRNAs) have been implicated in diverse biological processes, including embryonic stem cell (ESC) maintenance. However, their functional mechanisms remain largely undefined. Here, we show that the lncRNA Panct1 regulates the transient recruitment of a putative X-chromosome-encoded protein A830080D01Rik, hereafter referred to as transient octamer binding factor 1 (TOBF1), to genomic sites resembling the canonical Oct-Sox motif. TOBF1 physically interacts with Panct1 and exhibits a cell-cycle-specific punctate localization in ESCs. At the chromatin level, this correlates with its recruitment to promoters of pluripotency genes. Strikingly, mutating an octamer-like motif in Panct1 RNA abrogates the strength of TOBF1 localization and recruitment to its targets. Taken together, our data reveal a tightly controlled spatial and temporal pattern of lncRNA-mediated gene regulation in a cell-cycle-dependent manner and suggest that lncRNAs might function as barcodes for identifying genomic addresses for maintaining cellular states.},
}
@article {pmid29238567,
year = {2017},
author = {Hanisch, PE and Lavinia, PD and Suarez, AV and Lijtmaer, DA and Leponce, M and Paris, CI and Tubaro, PL},
title = {Mind the gap! Integrating taxonomic approaches to assess ant diversity at the southern extreme of the Atlantic Forest.},
journal = {Ecology and evolution},
volume = {7},
number = {23},
pages = {10451-10466},
pmid = {29238567},
issn = {2045-7758},
abstract = {Understanding patterns of species diversity relies on accurate taxonomy which can only be achieved by long-term natural history research and the use of complementary information to establish species boundaries among cryptic taxa. We used DNA barcoding to characterize the ant diversity of Iguazú National Park (INP), a protected area of the Upper Paraná Atlantic Forest ecoregion, located at the southernmost extent of this forest. We assessed ant diversity using both cytochrome c oxidase subunit 1 (COI) sequences and traditional morphological approaches, and compared the results of these two methods. We successfully obtained COI sequences for 312 specimens belonging to 124 species, providing a DNA barcode reference library for nearly 50% of the currently known ant fauna of INP. Our results support a clear barcode gap for all but two species, with a mean intraspecific divergence of 0.72%, and an average congeneric distance of 17.25%. Congruently, the library assembled here was useful for the discrimination of the ants of INP and allowed us to link unidentified males and queens to their worker castes. To detect overlooked diversity, we classified the DNA barcodes into Molecular Operational Taxonomic Units (MOTUs) using three different clustering algorithms, and compared their number and composition to that of reference species identified based on morphology. The MOTU count was always higher than that of reference species regardless of the method, suggesting that the diversity of ants at INP could be between 6% and 10% higher than currently recognized. Lastly, our survey contributed with 78 new barcode clusters to the global DNA barcode reference library, and added 36 new records of ant species for the INP, being 23 of them new citations for Argentina.},
}
@article {pmid29238565,
year = {2017},
author = {Liu, Y and Erséus, C},
title = {New specific primers for amplification of the Internal Transcribed Spacer region in Clitellata (Annelida).},
journal = {Ecology and evolution},
volume = {7},
number = {23},
pages = {10421-10439},
pmid = {29238565},
issn = {2045-7758},
abstract = {Nuclear molecular evidence, for example, the rapidly evolving Internal Transcribed Spacer region (ITS), integrated with maternally inherited (mitochondrial) COI barcodes, has provided new insights into the diversity of clitellate annelids. PCR amplification and sequencing of ITS, however, are often hampered by poor specificity of primers used. Therefore, new clitellate-specific primers for amplifying the whole ITS region (ITS: 29F/1084R) and a part of it (ITS2: 606F/1082R) were developed on the basis of a collection of previously published ITS sequences with flanking rDNA coding regions. The specificity of these and other ITS primers used for clitellates were then tested in silico by evaluating their mismatches with all assembled and annotated sequences (STD, version r127) from EMBL, and the new primers were also tested in vitro for a taxonomically broad sample of clitellate species (71 specimens representing 11 families). The in silico analyses showed that the newly designed primers have a better performance than the universal ones when amplifying clitellate ITS sequences. In vitro PCR and sequencing using the new primers were successful, in particular, for the 606F/1082R pair, which worked well for 65 of the 71 specimens. Thus, using this pair for amplifying the ITS2 will facilitate further molecular systematic investigation of various clitellates. The other pair (29F/1084R), will be a useful complement to existing ITS primers, when amplifying ITS as a whole.},
}
@article {pmid29238531,
year = {2017},
author = {Basset, Y and Lamarre, GPA and Ratz, T and Segar, ST and Decaëns, T and Rougerie, R and Miller, SE and Perez, F and Bobadilla, R and Lopez, Y and Ramirez, JA and Aiello, A and Barrios, H},
title = {The Saturniidae of Barro Colorado Island, Panama: A model taxon for studying the long-term effects of climate change?.},
journal = {Ecology and evolution},
volume = {7},
number = {23},
pages = {9991-10004},
pmid = {29238531},
issn = {2045-7758},
support = {669609/ERC_/European Research Council/International ; },
abstract = {We have little knowledge of the response of invertebrate assemblages to climate change in tropical ecosystems, and few studies have compiled long-term data on invertebrates from tropical rainforests. We provide an updated list of the 72 species of Saturniidae moths collected on Barro Colorado Island (BCI), Panama, during the period 1958-2016. This list will serve as baseline data for assessing long-term changes of saturniids on BCI in the future, as 81% of the species can be identified by their unique DNA Barcode Index Number, including four cryptic species not yet formally described. A local species pool of 60 + species breeding on BCI appears plausible, but more cryptic species may be discovered in the future. We use monitoring data obtained by light trapping to analyze recent population trends on BCI for saturniid species that were relatively common during 2009-2016, a period representing >30 saturniid generations. The abundances of 11 species, of 14 tested, could be fitted to significant time-series models. While the direction of change in abundance was uncertain for most species, two species showed a significant increase over time, and forecast models also suggested continuing increases for most species during 2017-2018, as compared to the 2009 base year. Peaks in saturniid abundance were most conspicuous during El Niño and La Niña years. In addition to a species-specific approach, we propose a reproducible functional classification based on five functional traits to analyze the responses of species sharing similar functional attributes in a fluctuating climate. Our results suggest that the abundances of larger body-size species with good dispersal abilities may increase concomitantly with rising air temperature in the future, because short-lived adults may allocate less time to increasing body temperature for flight, leaving more time available for searching for mating partners or suitable oviposition sites.},
}
@article {pmid29236697,
year = {2017},
author = {Šigut, M and Kostovčík, M and Šigutová, H and Hulcr, J and Drozd, P and Hrček, J},
title = {Performance of DNA metabarcoding, standard barcoding, and morphological approach in the identification of host-parasitoid interactions.},
journal = {PloS one},
volume = {12},
number = {12},
pages = {e0187803},
pmid = {29236697},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Herbivory ; *Host-Parasite Interactions ; Hymenoptera/*growth &amp; development ; *Larva ; Lepidoptera/*growth &amp; development ; Plants/*parasitology ; },
abstract = {Understanding interactions between herbivores and parasitoids is essential for successful biodiversity protection and monitoring and for biological pest control. Morphological identifications employ insect rearing and are complicated by insects' high diversity and crypsis. DNA barcoding has been successfully used in studies of host-parasitoid interactions as it can substantially increase the recovered real host-parasitoid diversity distorted by overlooked species complexes, or by species with slight morphological differences. However, this approach does not allow the simultaneous detection and identification of host(s) and parasitoid(s). Recently, high-throughput sequencing has shown high potential for surveying ecological communities and trophic interactions. Using mock samples comprising insect larvae and their parasitoids, we tested the potential of DNA metabarcoding for identifying individuals involved in host-parasitoid interactions to different taxonomic levels, and compared it to standard DNA barcoding and morphological approaches. For DNA metabarcoding, we targeted the standard barcoding marker cytochrome oxidase subunit I using highly degenerate primers, 2*300 bp sequencing on a MiSeq platform, and RTAX classification using paired-end reads. Additionally, using a large host-parasitoid dataset from a Central European floodplain forest, we assess the completeness and usability of a local reference library by confronting the number of Barcoding Index Numbers obtained by standard barcoding with the number of morphotypes. Overall, metabarcoding recovery was high, identifying 92.8% of the taxa present in mock samples, and identification success within individual taxonomic levels did not significantly differ among metabarcoding, standard barcoding, and morphology. Based on the current local reference library, 39.4% parasitoid and 90.7% host taxa were identified to the species level. DNA barcoding estimated higher parasitoid diversity than morphotyping, especially in groups with high level of crypsis. This study suggests the potential of metabarcoding for effectively recovering host-parasitoid diversity, together with more accurate identifications obtained from building reliable and comprehensive reference libraries, especially for parasitoids.},
}
@article {pmid29235972,
year = {2017},
author = {Balog, JA and Fehér, LZ and Puskás, LG},
title = {Decoding DNA labels by melting curve analysis using real-time PCR.},
journal = {BioTechniques},
volume = {63},
number = {6},
pages = {261-266},
doi = {10.2144/000114618},
pmid = {29235972},
issn = {1940-9818},
mesh = {*DNA/analysis/chemistry ; DNA Primers/chemistry ; Real-Time Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA/*methods ; Transition Temperature ; },
abstract = {Synthetic DNA has been used as an authentication code for a diverse number of applications. However, existing decoding approaches are based on either DNA sequencing or the determination of DNA length variations. Here, we present a simple alternative protocol for labeling different objects using a small number of short DNA sequences that differ in their melting points. Code amplification and decoding can be done in two steps using quantitative PCR (qPCR). To obtain a DNA barcode with high complexity, we defined 8 template groups, each having 4 different DNA templates, yielding 158 (>2.5 billion) combinations of different individual melting temperature (Tm) values and corresponding ID codes. The reproducibility and specificity of the decoding was confirmed by using the most complex template mixture, which had 32 different products in 8 groups with different Tm values. The industrial applicability of our protocol was also demonstrated by labeling a drone with an oil-based paint containing a predefined DNA code, which was then successfully decoded. The method presented here consists of a simple code system based on a small number of synthetic DNA sequences and a cost-effective, rapid decoding protocol using a few qPCR reactions, enabling a wide range of authentication applications.},
}
@article {pmid29233960,
year = {2017},
author = {Winters, IP and Chiou, SH and Paulk, NK and McFarland, CD and Lalgudi, PV and Ma, RK and Lisowski, L and Connolly, AJ and Petrov, DA and Kay, MA and Winslow, MM},
title = {Multiplexed in vivo homology-directed repair and tumor barcoding enables parallel quantification of Kras variant oncogenicity.},
journal = {Nature communications},
volume = {8},
number = {1},
pages = {2053},
pmid = {29233960},
issn = {2041-1723},
support = {R01 HL064274/HL/NHLBI NIH HHS/United States ; R25 CA180993/CA/NCI NIH HHS/United States ; F32 HL119059/HL/NHLBI NIH HHS/United States ; R01 CA175336/CA/NCI NIH HHS/United States ; R01 DK078424/DK/NIDDK NIH HHS/United States ; R01 CA207133/CA/NCI NIH HHS/United States ; R35 GM118165/GM/NIGMS NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; F31 CA210627/CA/NCI NIH HHS/United States ; R21 CA194910/CA/NCI NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; CRISPR-Cas Systems/genetics ; Carcinogenesis/*genetics ; Cost-Benefit Analysis ; DNA Mutational Analysis/economics/*methods ; Feasibility Studies ; Female ; Genomics/economics/methods ; High-Throughput Nucleotide Sequencing/methods ; Male ; Mice ; Mutation ; Neoplasms/*genetics/pathology ; Proto-Oncogene Proteins p21(ras)/*genetics ; Recombinational DNA Repair/*genetics ; Reproducibility of Results ; },
abstract = {Large-scale genomic analyses of human cancers have cataloged somatic point mutations thought to initiate tumor development and sustain cancer growth. However, determining the functional significance of specific alterations remains a major bottleneck in our understanding of the genetic determinants of cancer. Here, we present a platform that integrates multiplexed AAV/Cas9-mediated homology-directed repair (HDR) with DNA barcoding and high-throughput sequencing to simultaneously investigate multiple genomic alterations in de novo cancers in mice. Using this approach, we introduce a barcoded library of non-synonymous mutations into hotspot codons 12 and 13 of Kras in adult somatic cells to initiate tumors in the lung, pancreas, and muscle. High-throughput sequencing of barcoded Kras [HDR] alleles from bulk lung and pancreas reveals surprising diversity in Kras variant oncogenicity. Rapid, cost-effective, and quantitative approaches to simultaneously investigate the function of precise genomic alterations in vivo will help uncover novel biological and clinically actionable insights into carcinogenesis.},
}
@article {pmid29230362,
year = {2017},
author = {Vivien, R and Holzmann, M and Werner, I and Pawlowski, J and Lafont, M and Ferrari, BJD},
title = {Cytochrome c oxidase barcodes for aquatic oligochaete identification: development of a Swiss reference database.},
journal = {PeerJ},
volume = {5},
number = {},
pages = {e4122},
pmid = {29230362},
issn = {2167-8359},
abstract = {INTRODUCTION: Aquatic oligochaetes represent valuable indicators of the quality of sediments of watercourses and lakes, but their difficult identification based on morphological criteria compromises their more common use for eco-diagnostic analyses. This issue could be overcome by using DNA barcodes for species identification. A 10% threshold of cytochrome c oxidase (COI) divergence was proposed for differentiating between oligochaete species based on molecular and morphological data. A Swiss database of COI sequences of aquatic oligochaetes was initiated in 2012. The aim of this study is to complement the Swiss oligochaete database of COI sequences and to confirm the relevance of this threshold for species delimitation.<br><br>METHODS: We sequenced the COI sequence of 216 specimens collected in different regions of Switzerland and ITS2 region of some lineages whose delimitation with COI data was doubtful.<br><br>RESULTS: We distinguished 53 lineages, among which 34 were new for Switzerland and 17 sequenced for the first time. All the lineages were separated by more than 10% of COI variation, with the exception of some species within Nais and Uncinais. In these two genera, the threshold was lowered to 8% to be congruent with the morphological analysis. The total number of lineages reported so far for Switzerland is 75, including 59 morphospecies or unidentified species and 16 cryptic species.<br><br>DISCUSSION: Our study shows that the threshold of 10% of COI divergence is generally appropriate to distinguish aquatic oligochaete lineages, but that it must be adjusted for some species. The database reported here will be complemented in the future in parallel to the development of genetic oligochaete indices.},
}
@article {pmid29229008,
year = {2018},
author = {David, GM and Staentzel, C and Schlumberger, O and Perrot-Minnot, MJ and Beisel, JN and Hardion, L},
title = {A minimalist macroparasite diversity in the round goby of the Upper Rhine reduced to an exotic acanthocephalan lineage.},
journal = {Parasitology},
volume = {145},
number = {8},
pages = {1020-1026},
doi = {10.1017/S0031182017002177},
pmid = {29229008},
issn = {1469-8161},
mesh = {Acanthocephala/*genetics ; Animals ; Biodiversity ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Europe, Eastern/epidemiology ; France/epidemiology ; *Genetic Variation ; Haplotypes ; Helminthiasis, Animal/*epidemiology ; High-Throughput Nucleotide Sequencing ; Introduced Species ; Perciformes/*parasitology ; Phylogeny ; Rivers/*parasitology ; },
abstract = {The round goby, Neogobius melanostomus, is a Ponto-Caspian fish considered as an invasive species in a wide range of aquatic ecosystems. To understand the role that parasites may play in its successful invasion across Western Europe, we investigated the parasitic diversity of the round goby along its invasion corridor, from the Danube to the Upper Rhine rivers, using data from literature and a molecular barcoding approach, respectively. Among 1666 parasites extracted from 179 gobies of the Upper Rhine, all of the 248 parasites barcoded on the c oxidase subunit I gene were identified as Pomphorhynchus laevis. This lack of macroparasite diversity was interpreted as a loss of parasites along its invasion corridor without spillback compensation. The genetic diversity of P. laevis was represented by 33 haplotypes corresponding to a haplotype diversity of 0·65 ± 0·032, but a weak nucleotide diversity of 0·0018 ± 0·00015. Eight of these haplotypes were found in 88·4% of the 248 parasites. These haplotypes belong to a single lineage so far restricted to the Danube, Vistula and Volga rivers (Eastern Europe). This result underlines the exotic status of this Ponto-Caspian lineage in the Upper Rhine, putatively disseminated by the round goby along its invasion corridor.},
}
@article {pmid29227468,
year = {2018},
author = {Beaulaurier, J and Zhu, S and Deikus, G and Mogno, I and Zhang, XS and Davis-Richardson, A and Canepa, R and Triplett, EW and Faith, JJ and Sebra, R and Schadt, EE and Fang, G},
title = {Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.},
journal = {Nature biotechnology},
volume = {36},
number = {1},
pages = {61-69},
pmid = {29227468},
issn = {1546-1696},
support = {R01 GM114472/GM/NIGMS NIH HHS/United States ; },
mesh = {Algorithms ; Bacteria/genetics ; Cluster Analysis ; DNA Methylation/*genetics ; Environmental Microbiology ; Genome, Bacterial/genetics ; Humans ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; Plasmids/genetics ; Sequence Analysis, DNA ; },
abstract = {Shotgun metagenomics methods enable characterization of microbial communities in human microbiome and environmental samples. Assembly of metagenome sequences does not output whole genomes, so computational binning methods have been developed to cluster sequences into genome 'bins'. These methods exploit sequence composition, species abundance, or chromosome organization but cannot fully distinguish closely related species and strains. We present a binning method that incorporates bacterial DNA methylation signatures, which are detected using single-molecule real-time sequencing. Our method takes advantage of these endogenous epigenetic barcodes to resolve individual reads and assembled contigs into species- and strain-level bins. We validate our method using synthetic and real microbiome sequences. In addition to genome binning, we show that our method links plasmids and other mobile genetic elements to their host species in a real microbiome sample. Incorporation of DNA methylation information into shotgun metagenomics analyses will complement existing methods to enable more accurate sequence binning.},
}
@article {pmid29224148,
year = {2018},
author = {Jelinek, J and Lee, JT and Cesaroni, M and Madzo, J and Liang, S and Lu, Y and Issa, JJ},
title = {Digital Restriction Enzyme Analysis of Methylation (DREAM).},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1708},
number = {},
pages = {247-265},
doi = {10.1007/978-1-4939-7481-8_13},
pmid = {29224148},
issn = {1940-6029},
mesh = {CpG Islands ; *DNA Methylation ; DNA Restriction Enzymes/metabolism ; Genome, Human ; Genomic Library ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Restriction Mapping/*methods ; Sequence Analysis, DNA/*methods ; },
abstract = {Digital Restriction Enzyme Analysis of Methylation (DREAM) is a method for quantitative mapping of DNA methylation across genomes using next-generation sequencing (NGS) technology. The method is based on sequential cuts of genomic DNA with a pair of restriction enzymes (SmaI and XmaI) at CCCGGG target sites. Unmethylated sites are first digested with SmaI. This enzyme cuts the sites in the middle at CCC^GGG, leaving behind blunt ended fragments. CpG methylation completely blocks SmaI; therefore, only unmethylated sites are cleaved. The remaining methylated sites are digested with XmaI in the next step. This enzyme is not blocked by CpG methylation. It cuts the recognition site sideways at C^CCGGG forming 5'-CCGG overhangs. The sequential cuts thus create distinct methylation-specific signatures at the ends of restriction fragments: 5'-GGG for unmethylated CpG sites and 5'-CCGGG for methylated sites. The DNA fragments resulting from the digestions are ligated to NGS adapters. Sequencing libraries are prepared using hexanucleotide barcodes for sample identification. Individual libraries with distinct barcodes are pooled and sequenced using a paired ends protocol. The sequencing reads are aligned to the genome and mapped to unique CCCGGG target sites. Methylation at individual CpG sites is calculated as the ratio of sequencing reads with the methylated signature to the total number of reads mapping to the site. Sequencing of 25 million reads per sample typically yields 50,000 unique CpG sites covered with hundreds of reads enabling accurate determination of DNA methylation levels. DREAM does not require bisulfite conversion, has a very low background, and has high sensitivity to low levels of methylation. The method is simple, cost-effective, quantitative, highly reproducible, and can be applied to any species.},
}
@article {pmid29224067,
year = {2018},
author = {Karamitros, T and Magiorkinis, G},
title = {Multiplexed Targeted Sequencing for Oxford Nanopore MinION: A Detailed Library Preparation Procedure.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1712},
number = {},
pages = {43-51},
doi = {10.1007/978-1-4939-7514-3_4},
pmid = {29224067},
issn = {1940-6029},
mesh = {DNA Primers/genetics ; Genome/*genetics ; *Genomic Library ; Multiplex Polymerase Chain Reaction/*methods ; *Nanopores ; Nucleic Acid Hybridization ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA/*methods ; Statistics as Topic ; },
abstract = {MinION is a small form factor sequencer recently retailed by Oxford Nanopore technologies. This lighter-sized USB3.0-interfaced device uses innovative nanotechnology to generate extra-long reads from libraries prepared using only standard molecular biology lab equipment. The flexibility and the portability of the platform makes it ideal for point-of-interest and real-time surveillance applications. However, MinION's limited capacity is not enough for the study of specific targets within larger genomes. Apart from just PCR-amplifying regions of interest, the capture of long reads spanning the edges of known-unknown genomic regions is of great importance for structural studies, such as the identification of mobile elements' integrations sites, bridging over low complexity repetitive regions etc.In this study, using MinION-kit-included and commercially available reagents, we have developed an easy and versatile wet-lab procedure for the targeted enrichment of MinION libraries, capturing DNA fragments of interest before the ligation of the sensitive MinION sequencing-adapters. This method allows for simultaneous target-enrichment and barcode-multiplexing of up to 12 libraries, which can be loaded in the same sequencing run.},
}
@article {pmid29216781,
year = {2018},
author = {da Silva, R and Peloso, PLV and Sturaro, MJ and Veneza, I and Sampaio, I and Schneider, H and Gomes, G},
title = {Comparative analyses of species delimitation methods with molecular data in snappers (Perciformes: Lutjaninae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {7},
pages = {1108-1114},
doi = {10.1080/24701394.2017.1413364},
pmid = {29216781},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods/standards ; Electron Transport Complex IV/genetics ; Fish Proteins/genetics ; Haplotypes ; Perciformes/classification/*genetics ; *Phylogeny ; *Polymorphism, Genetic ; },
abstract = {The integration of approaches that allow the incorporation of stochasticity of gene histories with phylogenetic methods resulted in new approaches for the old issue of species delimitation. Nevertheless, coalescent methods seem problematic for taxa with large effective population size and shallow temporal diversification (like marine fishes). Here, we investigate the performance of single-locus (cytochrome oxidase 1, commonly used in DNA barcoding initiatives) methods for molecular species delimitation in snappers of Lutjaninae from the Western Atlantic and Pacific Eastern. Our results show incongruences among methods. ABGD, PTP and mPTP trend towards a lower number of estimated species. Phylogenetic-coalescent methods with single threshold were majority congruent for a same number of lineages. On the other hand, algorithms with multiple thresholds tend to estimate a higher number of potential species. We do not endorse the use of single-locus for species delimitation, but we do reinforce that single-locus data is sufficient to flag many problems.},
}
@article {pmid29215948,
year = {2017},
author = {Osathanunkul, M and Dheeranupattana, S and Rotarayanont, S and Sookkhee, S and Osathanunkul, K and Madesis, P},
title = {Evaluation of suitable DNA regions for molecular identification of high value medicinal plants in genus Kaempferia.},
journal = {Nucleosides, nucleotides &amp; nucleic acids},
volume = {36},
number = {12},
pages = {726-735},
doi = {10.1080/15257770.2017.1391393},
pmid = {29215948},
issn = {1532-2335},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; DNA, Plant/*chemistry/*genetics ; Data Mining ; Nucleic Acid Denaturation ; Plants, Medicinal/classification/genetics ; Zingiberaceae/*classification/*genetics ; },
abstract = {DNA barcoding coupled high resolution melting (Bar-HRM) is an emerging method for species discrimination based on DNA dissociation kinetics. The aim of this work was to evaluate the suitability of different primer sets, derived from selected DNA regions, for Bar-HRM analysis of species in Kaempferia (Zingiberaceae). Four primer pairs were evaluated (rbcL, rpoC, trnL and ITS1). It was observed that the ITS1 barcode was the most useful DNA barcoding region overall for species discrimination out of all of the regions and primers assessed. Thus, the primer pair derived from the ITS1 region was the single most effective region for the identification of the tested species, whereas the rbcL primer pair gave the lowest resolution. Our Bar-HRM developed here would not only be useful for identification of Kaempferia plant specimens lacking essential parts for morphological identification but will be useful for authenticating products in powdered form of a high value medicinal species Kaempferia parviflora, in particular.},
}
@article {pmid29214218,
year = {2017},
author = {Yang, M and Zhang, W and Yang, J and Hu, B and Cao, F and Zheng, W and Chen, Y and Jiang, X},
title = {Skiving stacked sheets of paper into test paper for rapid and multiplexed assay.},
journal = {Science advances},
volume = {3},
number = {12},
pages = {eaao4862},
pmid = {29214218},
issn = {2375-2548},
abstract = {This paper shows that stacked sheets of paper preincubated with different biological reagents and skiving them into uniform test paper sheets allow mass manufacturing of multiplexed immunoassay devices and simultaneous detection of multiplex targets that can be read out by a barcode scanner. The thickness of one sheet of paper can form the width of a module for the barcode; when stacked, these sheets of paper can form a series of barcodes representing the targets, depending on the color contrast provided by a colored precipitate of an immunoassay. The uniform thickness of sheets of paper allows high-quality signal readout. The manufacturing method allows highly efficient fabrication of the materials and substrates for a straightforward assay of targets that range from drugs of abuse to biomarkers of blood-transmitted infections. In addition, as a novel alternative to the conventional point-of-care testing method, the paper-based barcode assay system can provide highly efficient, accurate, and objective diagnoses.},
}
@article {pmid29213995,
year = {2017},
author = {Luo, R and Sedlazeck, FJ and Darby, CA and Kelly, SM and Schatz, MC},
title = {LRSim: A Linked-Reads Simulator Generating Insights for Better Genome Partitioning.},
journal = {Computational and structural biotechnology journal},
volume = {15},
number = {},
pages = {478-484},
pmid = {29213995},
issn = {2001-0370},
abstract = {Linked-read sequencing, using highly-multiplexed genome partitioning and barcoding, can span hundreds of kilobases to improve de novo assembly, haplotype phasing, and other applications. Based on our analysis of 14 datasets, we introduce LRSim that simulates linked-reads by emulating the library preparation and sequencing process with fine control over variants, linked-read characteristics, and the short-read profile. We conclude from the phasing and assembly of multiple datasets, recommendations on coverage, fragment length, and partitioning when sequencing genomes of different sizes and complexities. These optimizations improve results by orders of magnitude, and enable the development of novel methods. LRSim is available at https://github.com/aquaskyline/LRSIM.},
}
@article {pmid29208648,
year = {2018},
author = {Geister, KA and Timms, AE and Beier, DR},
title = {Optimizing Genomic Methods for Mapping and Identification of Candidate Variants in ENU Mutagenesis Screens Using Inbred Mice.},
journal = {G3 (Bethesda, Md.)},
volume = {8},
number = {2},
pages = {401-409},
pmid = {29208648},
issn = {2160-1836},
support = {R01 HD036404/HD/NICHD NIH HHS/United States ; },
mesh = {Alkylating Agents/toxicity ; Animals ; Chromosome Mapping/*methods ; Embryo, Mammalian/drug effects/embryology/metabolism ; Ethylnitrosourea/toxicity ; Female ; Genes, Dominant/*genetics ; Genomics/*methods ; Genotype ; Male ; Mice, Inbred C57BL ; Mutagenesis/drug effects ; *Mutation ; Phenotype ; },
abstract = {Positional cloning of ENU-induced mutations has traditionally relied on analysis of polymorphic variation between two strains. In contrast, the application of whole-genome sequencing (WGS) has enabled gene discovery in mutant lines maintained on an inbred genetic background. This approach utilizes genetic variation derived from ENU-induced variants for mapping and reduces the likelihood of phenotypic variation, making it an ideal method for genetic modifier screening. Here, we describe the results of such a screen, wherein we determined the minimal number of mutant genomic DNA samples to include in our analyses and improved the sensitivity of our screen by individually barcoding each genomic DNA library. We present several unique cases to illustrate this approach's efficacy, including the discovery of two distinct mutations that generate essentially identical mutant phenotypes, the ascertainment of a non-ENU-induced candidate variant through homozygosity mapping, and an approach for the identification of putative dominant genetic modifiers.},
}
@article {pmid29206876,
year = {2017},
author = {Bączkiewicz, A and Szczecińska, M and Sawicki, J and Stebel, A and Buczkowska, K},
title = {DNA barcoding, ecology and geography of the cryptic species of Aneura pinguis and their relationships with Aneura maxima and Aneura mirabilis (Metzgeriales, Marchantiophyta).},
journal = {PloS one},
volume = {12},
number = {12},
pages = {e0188837},
pmid = {29206876},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic ; *Ecology ; *Genes, Plant ; *Geography ; Haplotypes ; Hepatophyta/classification/*genetics ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {Aneura pinguis is a thalloid liverwort species with broad geographical distribution. It is composed of cryptic species, however, the number of cryptic species within A. pinguis is not known. Five cpDNA regions (matK, rbcL, rpoC1, trnH-psbA and trnL-trnF) and the entire nuclear ITS region were studied in 130 samples of A. pinguis from different geographical regions. The relationships between the cryptic species of A. pinguis, A. maxima and A. mirabilis were analyzed. All of the examined samples were clustered into 10 clades corresponding to 10 cryptic species of A. pinguis (marked A to J). Aneura mirabilis and A. maxima were nested among different cryptic species of A. pinguis, which indicates that A. pinguis is a paraphyletic taxon. Subgroups were found in cryptic species A, B, C and E. As single barcodes, all tested DNA regions had 100% discriminant power and fulfilled DNA barcode criteria for species identification; however, the only combination detected in all subgroups was trnL-trnF with trnH-psbA or ITS2. The distances between cryptic species were 11- to 35-fold higher than intraspecific distances. In all analyzed DNA regions, the distances between most pairs of cryptic A. pinguis species were higher than between A. maxima and A. mirabilis. All cryptic species of A. pinguis clearly differed in their habitat preferences, which suggests that habitat adaptation could be the main driving force behind cryptic speciation within this taxon.},
}
@article {pmid29205973,
year = {2016},
author = {Xia, X and Ding, M},
title = {[Application of COⅠ Gene Mini-barcoding in Species Identification of Hair].},
journal = {Fa yi xue za zhi},
volume = {32},
number = {6},
pages = {441-443},
doi = {10.3969/j.issn.1004-5619.2016.06.012},
pmid = {29205973},
issn = {1004-5619},
mesh = {*Animal Fur ; Animals ; *DNA Barcoding, Taxonomic ; DNA Primers ; *Hair ; Polymerase Chain Reaction ; Species Specificity ; },
abstract = {OBJECTIVES: To identify the species of mammalian hair using COⅠ gene mini-barcoding technology.<br><br>METHODS: A pair of universal primers for mammalian CO&#x2160; gene mini-barcoding were designed. The hair DNA samples of experimental animals from 11 species in 5 orders, mammalia was amplified by PCR technology with universal primers, and the PCR products were sequenced by bi-directional DNA and after the sequences splicing the results were deposited into the BOLD database to perform the homology comparison.<br><br>RESULTS: The DNA of hair from all experiment animal species could be totally amplified by the mini-barcoding universal primers designed in this study. The length of amplified fragment was 147 bp. The result of homology comparison in the database showed that the closest matching species were consistent with the experiment animal species. In addition to the matching degree of Panthera leo &#xff08;98.99%&#xff09;, all homology matching degree of the other experiment animals were 100%, and the intraspecific genetic distance of Panthera leo was 1%. The interspecific genetic distance was ten times more than the intraspecific genetic distance which could be used for species identification.<br><br>CONCLUSIONS: The CO&#x2160; gene mini-barcode technology is established and can provide fast and accurate species identification for hair of mammals.},
}
@article {pmid29204787,
year = {2018},
author = {Harrison, RL and Mowery, JD and Rowley, DL and Bauchan, GR and Theilmann, DA and Rohrmann, GF and Erlandson, MA},
title = {The complete genome sequence of a third distinct baculovirus isolated from the true armyworm, Mythimna unipuncta, contains two copies of the lef-7 gene.},
journal = {Virus genes},
volume = {54},
number = {2},
pages = {297-310},
pmid = {29204787},
issn = {1572-994X},
mesh = {Animals ; Base Composition ; Cluster Analysis ; DNA Barcoding, Taxonomic ; *Genes, Viral ; *Genome, Viral ; Inclusion Bodies, Viral/ultrastructure ; Lepidoptera/*virology ; Nucleopolyhedroviruses/*genetics/isolation &amp; purification/ultrastructure ; Open Reading Frames ; Phylogeny ; Polymerase Chain Reaction ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Virion/ultrastructure ; },
abstract = {A baculovirus isolate from a USDA Forest Service collection was characterized by electron microscopy and analysis of its genome sequence. The isolate, formerly referred to as Pseudoletia (Mythimna) sp. nucleopolyhedrovirus #7 (MyspNPV#7), was determined by barcoding PCR to derive from the host species Mythimna unipuncta (true armyworm) and was renamed Mythimna unipuncta nucleopolyhedrovirus #7 (MyunNPV#7). The occlusion bodies (OBs) and virions exhibited a size and morphology typical for OBs produced by the species of genus Alphabaculovirus, with occlusion-derived virions consisting of 2-5 nucleocapsids within a single envelope. The MyunNPV#7 genome was determined to be 148,482 bp with a 48.58% G+C nucleotide distribution. A total of 159 ORFs of 150 bp or larger were annotated in the genome sequence, including the 38 core genes of family Baculoviridae. The genome contained six homologous repeat regions (hrs) consisting of multiple copies of a 34-bp imperfect palindrome. Phylogenetic inference from concatenated baculovirus core gene amino acid sequence alignments placed MyunNPV#7 with group II alphabaculoviruses isolated from other armyworm and cutworm host species of lepidopteran family Noctuidae. MyunNPV#7 could be distinguished from other viruses in this group on the basis of differences in gene content and order. Pairwise nucleotide distances suggested that MyunNPV#7 represents a distinct species in Alphabaculovirus. The MyunNPV#7 genome was found to contain two copies of the late expression factor-7 (lef-7) gene, a feature not reported for any other baculovirus genome to date. Both copies of lef-7 encoded an F-box domain, which is required for the function of LEF-7 in baculovirus DNA replication.},
}
@article {pmid29202187,
year = {2018},
author = {Barr, NB and Ruiz-Arce, R and Farris, RE and Silva, JG and Lima, KM and Dutra, VS and Ronchi-Teles, B and Kerr, PH and Norrbom, AL and Nolazco, N and Thomas, DB},
title = {Identifying Anastrepha (Diptera; Tephritidae) Species Using DNA Barcodes.},
journal = {Journal of economic entomology},
volume = {111},
number = {1},
pages = {405-421},
doi = {10.1093/jee/tox300},
pmid = {29202187},
issn = {1938-291X},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Female ; Insect Proteins/analysis ; Male ; Sequence Analysis, DNA ; Species Specificity ; Tephritidae/*classification/genetics ; },
abstract = {Molecular identification of fruit flies in the genus Anastrepha (Diptera; Tephritidae) is important to support plant pest exclusion, suppression, and outbreak eradication. Morphological methods of identification of this economically important genus are often not sufficient to identify species when detected as immature life stages. DNA barcoding a segment of the mitochondrial cytochrome oxidase I gene has been proposed as a method to identify pests in the genus. The identification process for these fruit flies, however, has not been explained in prior DNA barcode studies. DNA barcode methods assume that available DNA sequence records are biologically meaningful. These records, however, can be limited to the most common species or lack population-level measurements of diversity for pests. In such cases, the available data used as a reference are insufficient for completing an accurate identification. Using 539 DNA sequence records from 74 species of Anastrepha, we demonstrate that our barcoding data can distinguish four plant pests: Anastrepha grandis (Macquart) (Diptera; Tephritidae), Anastrepha ludens (Loew), Anastrepha serpentina (Wiedemann), and Anastrepha striata Schiner. This is based on genetic distances of barcode records for the pests and expert evaluation of species and population representation in the data set. DNA barcoding of the cytochrome oxidase I gene alone cannot reliably diagnose the pests Anastrepha fraterculus (Wiedemann), Anastrepha obliqua (Macquart), and Anastrepha suspensa (Loew).},
}
@article {pmid29201560,
year = {2017},
author = {Staffen, CF and Staffen, MD and Becker, ML and Löfgren, SE and Muniz, YCN and de Freitas, RHA and Marrero, AR},
title = {DNA barcoding reveals the mislabeling of fish in a popular tourist destination in Brazil.},
journal = {PeerJ},
volume = {5},
number = {},
pages = {e4006},
pmid = {29201560},
issn = {2167-8359},
abstract = {The consumption of raw fish has increased considerably in the West, since it is said to be potentially healthier than processed fish (for containing omega 3 and 6, essential amino acids and vitamins). However this potential benefit, as well as the taste, value and even the risk of extinction are not the same for all species of fish, constituting grounds for fraud. Using the principles of the DNA barcode we revealed mislabelling of fish in Japanese restaurants and fishmarkets in Florianópolis, a popular tourist capital in Brazil. We sequenced the COI gene of 65 samples from fisheries and 80 from restaurants and diagnosed 30% of mislabeled samples in fisheries and 26% in restaurants. We discussed that frauds may have occurred for different reasons: to circumvent surveillance on threatened species; to sell fish with sizes smaller than allowed or abundant species as being a much rarer species (law of supply); to induce product consumption using species with better taste. It should be noted that some substitutions are derived from incorrect identification and are not a fraud per se; they are due to confusion of popular names or misunderstanding by the sellers. Therefore, we suggest the implementation of a systematic regulatory program conducted by governmental agencies to reduce mislabelling in order to avoid further damage to the community (in health and financial issues) and fish stocks.},
}
@article {pmid29200917,
year = {2017},
author = {Liu, T and Wang, S},
title = {First report of the leaf-mining genus Antispila Hübner, [1825] from mainland China, with the description of a new species feeding on Cornus (Lepidoptera, Heliozelidae).},
journal = {ZooKeys},
volume = {},
number = {686},
pages = {95-107},
pmid = {29200917},
issn = {1313-2989},
abstract = {The genus Antispila Hübner, [1825] is newly recorded from mainland China. Antispila sinensissp. n., the first formally named Heliozelidae species in mainland China, is described. The host plant of the new species, Cornus walteri Wangerin (Cornaceae), is widespread through east Asia and is used as a shade tree in city parks in Jinan City, where the moth causes damage to foliage. Morphological and molecular analyses distinguish A. sinensissp. n. from its close relatives. The adult, pupa, larva, host plant, leaf-mines, and the shield of the new species are illustrated, as are male and female genitalia, venation, and larval chaetotaxy. DNA barcodes of the new species are also provided.},
}
@article {pmid29200730,
year = {2017},
author = {Yang, H and Zheng, J and Wang, HY and Li, N and Yang, YY and Shen, YP},
title = {Comparative Proteomic Analysis of Three Gelatinous Chinese Medicines and Their Authentications by Tryptic-digested Peptides Profiling using Matrix-assisted Laser Desorption/Ionization-time of Flight/Time of Flight Mass Spectrometry.},
journal = {Pharmacognosy magazine},
volume = {13},
number = {52},
pages = {663-667},
pmid = {29200730},
issn = {0973-1296},
abstract = {BACKGROUND: Gelatinous Chinese medicines (GCMs) including Asini Corii Colla, Testudinis Carapacis ET Plastri Colla, and Cervi Cornus Colla, were made from reptile shell or mammalian skin or deer horn, and consumed as a popular tonic, as well as hemopoietic and hemostatic agents. Misuse of them would not exert their functions, and fake or adulterate products have caused drug market disorder and affected food and drug safety. GCMs are rich in denatured proteins, but insufficient in available DNA fragments, hence commonly used cytochrome c oxidase I barcoding was not successful for their authentication.<br><br>OBJECTIVE: In this study, we performed comparative proteomic analysis of them and their animal origins to identify the composition of intrinsic proteins for the first time.<br><br>MATERIALS AND METHODS: A reliable and convenient approach was proposed for their authentication, by the incorporation of sodium dodecyl sulfate-polyacrylamide gel electrophoresis, two-dimensional electrophoresis, and matrix-assisted laser desorption/ionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF-MS).<br><br>RESULTS: A total of 26 proteins were identified from medicinal parts of original animals, and GCMs proteins presented in a dispersive manner in electrophoresis analyses due to complicated changes in the structure of original proteins caused by long-term decoction and the addition of ingredients during their manufacturing. In addition, by comparison of MALDI-TOF/TOF-MS profiling, 19 signature peptide fragments originated from the protein of GCM products were selected according to criteria.<br><br>CONCLUSION: These could assist in the discrimination and identification of adulterates of GCMs and other ACMs for their form of raw medicinal material, the pulverized, and even the complex.<br><br>SUMMARY: Comparative proteomic analysis of three gelatinous Chinese medicines was conducted, and their authentications were based on tryptic-digested peptides profiling using matrix-assisted laser desorption/ionization-time of flight/time of flight mass spectrometry. Abbreviations used: GCMs: Gelatinous Chinese medicines, COI: Cytochrome c oxidase I, SDS-PAGE: Sodium dodecyl sulfate polyacrylamide gel electrophoresis, 2-DE: Two-dimensional electrophoresis, MALDI-TOF/TOF-MS: Matrix-assisted laser desorption/ionization-time of flight/time of flight mass spectrometry, LC: Liquid chromatography, ChP: Chinese Pharmacopoeia, HPLC: High performance liquid chromatography, LC-ESI[+]-MS: Liquid chromatography-electro spray ionization-mass spectrometry, IEF: isoelectric focusing, HCCA: &#x3b1;-Cyano-4-hydroxycinnamic acid.},
}
@article {pmid29200712,
year = {2017},
author = {Arshed, MJC and Valdez, MB and Alejandro, GJD},
title = {Evaluating the Feasibility of Five Candidate DNA Barcoding Loci for Philippine Lasianthus Jack (Lasiantheae: Rubiaceae).},
journal = {Pharmacognosy magazine},
volume = {13},
number = {52},
pages = {553-558},
pmid = {29200712},
issn = {0973-1296},
abstract = {INTRODUCTION: The pantropical genus Lasianthus Jack is identified for high phenotypic plasticity making traditional taxonomic identification difficult. Having some members with important medicinal properties, a precise complimentary identification through DNA barcoding is needed for species delineation.<br><br>MATERIALS AND METHODS: In this study, 12 samples representing six Philippine Lasianthus species were used to determine the most efficient barcoding loci among the cpDNA markers (matK, rbcL, rps16, and trnT-F) and nrDNA (ITS) based on the criteria of universality, discriminatory power, and resolution of species.<br><br>RESULTS: The results revealed that ITS has the recommended primer universality, greatest interspecific divergences, and average resolution of species. Among the cpDNA markers, matK and rbcL are recommended but with minimal resolution of species. While trnT-F showed moderate interspecific variations and resolution of Lasianthus species, rps16 has the lowest interspecific divergence and resolution of species.<br><br>CONCLUSION: Consequently, ITS is the potential ideal DNA barcode for Lasianthus species.<br><br>SUMMARY: ITS, matK, and rps16 markers have the excellent amplification and sequence qualityITS marker has the highest interspecific divergence with the maximum values, followed by matK, rbcL, trnT-F, and rps16, respectivelyAll markers except rps16 yielded average resolution to Lasianthus speciesITS marker is the most ideal locus in terms of excellent universality, high interspecific discriminatory ability, and average species resolution. Abbreviations used: ITS: Internal Transcribe Spacer, matK: maturase K, rbcL: ribulose-1,5-biphospahte-carboxylase, rps16: ribosomal protein 16 small subunit gene.},
}
@article {pmid29197405,
year = {2017},
author = {Kudlai, O and Oros, M and Kostadinova, A and Georgieva, S},
title = {Exploring the diversity of Diplostomum (Digenea: Diplostomidae) in fishes from the River Danube using mitochondrial DNA barcodes.},
journal = {Parasites &amp; vectors},
volume = {10},
number = {1},
pages = {592},
pmid = {29197405},
issn = {1756-3305},
support = {P505/12/G112//Czech Science Foundation/ ; 15-14198S//Czech Science Foundation/ ; 15-14198S//Czech Science Foundation/ ; (code ITMS: 26220120022) (0.3)//Research &amp; Development Operational Programme funded by the ERDF/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Eye Diseases/parasitology/veterinary ; Fish Diseases/*parasitology ; Fishes/parasitology ; *Genetic Variation ; Hungary/epidemiology ; Lens, Crystalline/parasitology ; Phylogeny ; Rivers ; Slovakia/epidemiology ; Trematoda/*genetics/isolation &amp; purification ; },
abstract = {BACKGROUND: Metacercariae of Diplostomum are important fish pathogens, but reliable data on their diversity in natural fish populations are virtually lacking. This study was conducted to explore the species diversity and host-parasite association patterns of Diplostomum spp. in a large riverine system in Europe, using molecular and morphological data.<br><br>METHODS: Twenty-eight species of fish of nine families were sampled in the River Danube at Nyerges&#xfa;jfalu in Hungary in 2012 and &#x160;t&#xfa;rovo in Slovakia in 2015. Isolates of Diplostomum spp. were characterised morphologically and molecularly. Partial sequences of the 'barcode' region of the cytochrome c oxidase subunit 1 (cox1) and complete sequences of the nicotinamide adenine dinucleotide dehydrogenase subunit 3 (nad3) mitochondrial genes were amplified for 76 and 30 isolates, respectively. The partial cox1 sequences were used for molecular identification of the isolates and an assessment of haplotype diversity and possible host-associated structuring of the most prevalent parasite species. New primers were designed for amplification of the mitochondrial nad3 gene.<br><br>RESULTS: Only lens-infecting Diplostomum spp. were recovered in 16 fish species of five families. Barcoding of representative isolates provided molecular identification for three species/species-level genetic lineages, D. spathaceum, D. pseudospathaceum and 'D. mergi Lineage 2', and three single isolates potentially representing distinct species. Molecular data helped to elucidate partially the life-cycle of 'D. mergi Lineage 2'. Many of the haplotypes of D. spathaceum (16 in total), D. pseudospathaceum (15 in total) and 'D. mergi Lineage 2' (7 in total) were shared by a number of fish hosts and there was no indication of genetic structuring associated with the second intermediate host. The most frequent Diplostomum spp. exhibited a low host-specificity, predominantly infecting a wide range of cyprinid fishes, but also species of distant fish families such as the Acipenseridae, Lotidae, Percidae and Siluridae. The nad3 gene exhibited distinctly higher levels of interspecific divergence in comparison with the cox1 gene.<br><br>CONCLUSIONS: This first exploration of the species diversity and host ranges of Diplostomum spp., in natural fish populations in the River Danube, provided novel molecular, morphological and host-use data which will advance further ecological studies on the distribution and host ranges of these important fish parasites in Europe. Our results also indicate that the nad3 gene is a good candidate marker for multi-gene approaches to systematic estimates within the genus.},
}
@article {pmid29194624,
year = {2018},
author = {Srivastava, T and Wu, M and Kakhnovich, J and Waithaka, B and Lents, NH},
title = {A Three-Locus, PCR-based Method for Forensic Identification of Plant Material.},
journal = {Journal of forensic sciences},
volume = {63},
number = {4},
pages = {1252-1260},
doi = {10.1111/1556-4029.13715},
pmid = {29194624},
issn = {1556-4029},
mesh = {Botany ; *DNA Barcoding, Taxonomic ; DNA Primers ; DNA, Plant/*genetics ; Forensic Sciences ; *Genetic Loci ; Genome, Plastid/genetics ; Humans ; Mitochondria/genetics ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; },
abstract = {Plant residue is currently an underutilized resource in forensic investigations despite the fact that many crime scenes, as well as suspects and victims, harbor plant-derived residue that could be recovered and analyzed. Notwithstanding the considerable skill of forensic botanists, current methods of species determination could benefit from tools for DNA-based species identification. However, DNA barcoding in plants has been hampered by sequence complications in the plant genome. Following a database search for usable barcodes, broad-spectrum primers were designed and utilized to amplify and sequence the rbcL, trnL-F, and rrn18 genetic loci from a variety of household plants. Once obtained, these DNA sequences were used to design species-targeted primers that could successfully discriminate the source of plant residue from among the 21 species tested.},
}
@article {pmid29192249,
year = {2017},
author = {Liu, J and Jiang, J and Song, S and Tornabene, L and Chabarria, R and Naylor, GJP and Li, C},
title = {Multilocus DNA barcoding - Species Identification with Multilocus Data.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {16601},
pmid = {29192249},
issn = {2045-2322},
mesh = {Animals ; Computational Biology/methods ; *DNA Barcoding, Taxonomic/methods ; Fishes/classification/genetics ; Genetics, Population ; *Multilocus Sequence Typing/methods ; Phylogeny ; },
abstract = {Species identification using DNA sequences, known as DNA barcoding has been widely used in many applied fields. Current barcoding methods are usually based on a single mitochondrial locus, such as cytochrome c oxidase subunit I (COI). This type of barcoding method does not always work when applied to species separated by short divergence times or that contain introgressed genes from closely related species. Herein we introduce a more effective multi-locus barcoding framework that is based on gene capture and "next-generation" sequencing. We selected 500 independent nuclear markers for ray-finned fishes and designed a three-step pipeline for multilocus DNA barcoding. We applied our method on two exemplar datasets each containing a pair of sister fish species: Siniperca chuatsi vs. Sini. kneri and Sicydium altum vs. Sicy. adelum, where the COI barcoding approach failed. Both of our empirical and simulated results demonstrated that under limited gene flow and enough separation time, we could correctly identify species using multilocus barcoding method. We anticipate that, as the cost of DNA sequencing continues to fall that our multilocus barcoding approach will eclipse existing single-locus DNA barcoding methods as a means to better understand the diversity of the living world.},
}
@article {pmid29191745,
year = {2018},
author = {Ni Mhurchu, C and Eyles, H and Jiang, Y and Blakely, T},
title = {Do nutrition labels influence healthier food choices? Analysis of label viewing behaviour and subsequent food purchases in a labelling intervention trial.},
journal = {Appetite},
volume = {121},
number = {},
pages = {360-365},
doi = {10.1016/j.appet.2017.11.105},
pmid = {29191745},
issn = {1095-8304},
mesh = {Adult ; *Choice Behavior ; *Consumer Behavior ; *Diet, Healthy ; Female ; *Food Labeling ; *Food Preferences ; *Health Behavior ; Humans ; Male ; Nutritive Value ; Surveys and Questionnaires ; Young Adult ; },
abstract = {BACKGROUND: There are few objective data on how nutrition labels are used in real-world shopping situations, or how they affect dietary choices and patterns.<br><br>DESIGN: The Starlight study was a four-week randomised, controlled trial of the effects of three different types of nutrition labels on consumer food purchases: Traffic Light Labels, Health Star Rating labels, or Nutrition Information Panels (control). Smartphone technology allowed participants to scan barcodes of packaged foods and receive randomly allocated labels on their phone screen, and to record their food purchases. The study app therefore provided objectively recorded data on label viewing behaviour and food purchases over a four-week period. A post-hoc analysis of trial data was undertaken to assess frequency of label use, label use by food group, and association between label use and the healthiness of packaged food products purchased.<br><br>RESULTS: Over the four-week intervention, study participants (n&#xa0;=&#xa0;1255) viewed nutrition labels for and/or purchased 66,915 barcoded packaged products. Labels were viewed for 23% of all purchased products, with decreasing frequency over time. Shoppers were most likely to view labels for convenience foods, cereals, snack foods, bread and bakery products, and oils. They were least likely to view labels for sugar and honey products, eggs, fish, fruit and vegetables, and meat. Products for which participants viewed the label and subsequently purchased the product during the same shopping episode were significantly healthier than products where labels were viewed but the product was not subsequently purchased: mean difference in nutrient profile score&#xa0;-0.90 (95% CI -1.54 to&#xa0;-0.26).<br><br>CONCLUSIONS: In a secondary analysis of a nutrition labelling intervention trial, there was a significant association between label use and the healthiness of products purchased. Nutrition label use may therefore lead to healthier food purchases.},
}
@article {pmid29190363,
year = {2018},
author = {Chen, X and Sun, YC and Church, GM and Lee, JH and Zador, AM},
title = {Efficient in situ barcode sequencing using padlock probe-based BaristaSeq.},
journal = {Nucleic acids research},
volume = {46},
number = {4},
pages = {e22},
pmid = {29190363},
issn = {1362-4962},
support = {P30 CA045508/CA/NCI NIH HHS/United States ; R35 GM119772/GM/NIGMS NIH HHS/United States ; RF1 MH114132/MH/NIMH NIH HHS/United States ; },
mesh = {Animals ; Cell Lineage ; Cells, Cultured ; High-Throughput Nucleotide Sequencing/*methods ; Neurons/cytology ; Sequence Analysis, RNA/methods ; },
abstract = {Cellular DNA/RNA tags (barcodes) allow for multiplexed cell lineage tracing and neuronal projection mapping with cellular resolution. Conventional approaches to reading out cellular barcodes trade off spatial resolution with throughput. Bulk sequencing achieves high throughput but sacrifices spatial resolution, whereas manual cell picking has low throughput. In situ sequencing could potentially achieve both high spatial resolution and high throughput, but current in situ sequencing techniques are inefficient at reading out cellular barcodes. Here we describe BaristaSeq, an optimization of a targeted, padlock probe-based technique for in situ barcode sequencing compatible with Illumina sequencing chemistry. BaristaSeq results in a five-fold increase in amplification efficiency, with a sequencing accuracy of at least 97%. BaristaSeq could be used for barcode-assisted lineage tracing, and to map long-range neuronal projections.},
}
@article {pmid29187793,
year = {2017},
author = {Lehr, E and von May, R and Moravec, J and Cusi, JC},
title = {A new species of Phrynopus (Amphibia, Anura, Craugastoridae) from upper montane forests and high Andean grasslands of the Pui Pui Protected Forest in central Peru.},
journal = {ZooKeys},
volume = {},
number = {713},
pages = {131-157},
pmid = {29187793},
issn = {1313-2989},
abstract = {We describe a new species of Phrynopus from the upper montane forests and high Andean grasslands (puna) of the Pui Pui Protected Forest and its close surroundings (Región Junín, central Peru) and compare it morphologically and genetically with other species of Phrynopus. Phrynopus intisp. n. is known from four localities outside and two localities inside the Pui Pui Protected Forest between 3350 and 3890 m a.s.l. Studied specimens of the new species are characterized by a snout-vent length of 27.2-35.2 mm in males (n = 6), and 40.4 mm in a single female, by having the skin on dorsum and flanks smooth with scattered tubercles, venter smooth, by lacking a tympanum, and males without vocal slits and nuptial pads. In life, the dorsum is pale grayish brown with or without dark brown blotches, or dorsum blackish brown with small yellow flecks, throat, chest and venter are pale grayish brown with salmon mottling, groin is pale grayish brown with salmon colored flecks, and the iris is golden orange with fine dark brown reticulations. The new species is morphologically most similar to Phrynopus kauneorum and P. juninensis. For the latter we describe the coloration in life for a specimen obtained at the type locality. A molecular phylogenetic analysis based on mitochondrial and nuclear DNA sequences inferred that the new species is most closely related to Phrynopus kauneorum, P. miroslawae, P. tautzorum, and an undescribed species distributed at high elevation in Región Pasco, central Peru.},
}
@article {pmid29186803,
year = {2017},
author = {Neal, B and Crino, M and Dunford, E and Gao, A and Greenland, R and Li, N and Ngai, J and Ni Mhurchu, C and Pettigrew, S and Sacks, G and Webster, J and Wu, JH},
title = {Effects of Different Types of Front-of-Pack Labelling Information on the Healthiness of Food Purchases-A Randomised Controlled Trial.},
journal = {Nutrients},
volume = {9},
number = {12},
pages = {},
pmid = {29186803},
issn = {2072-6643},
mesh = {Adult ; Australia ; Choice Behavior ; *Consumer Behavior ; *Diet, Healthy ; Double-Blind Method ; Female ; Follow-Up Studies ; *Food Labeling ; *Food Preferences ; Health Behavior ; Health Knowledge, Attitudes, Practice ; Humans ; Male ; Middle Aged ; Mobile Applications ; Recommended Dietary Allowances ; Smartphone ; Socioeconomic Factors ; Treatment Outcome ; },
abstract = {BACKGROUND: Front-of-pack nutrition labelling may support healthier packaged food purchases. Australia has adopted a novel Health Star Rating (HSR) system, but the legitimacy of this choice is unknown.<br><br>OBJECTIVE: To define the effects of different formats of front-of-pack labelling on the healthiness of food purchases and consumer perceptions.<br><br>DESIGN: Individuals were assigned at random to access one of four different formats of nutrition labelling-HSR, multiple traffic light labels (MTL), daily intake guides (DIG), recommendations/warnings (WARN)-or control (the nutrition information panel, NIP). Participants accessed nutrition information by using a smartphone application to scan the bar-codes of packaged foods, while shopping. The primary outcome was healthiness defined by the mean transformed nutrient profile score of packaged foods that were purchased over four weeks.<br><br>RESULTS: The 1578 participants, mean age 38 years, 84% female recorded purchases of 148,727 evaluable food items. The mean healthiness of the purchases in the HSR group was non-inferior to MTL, DIG, or WARN (all p < 0.001 at 2% non-inferiority margin). When compared to the NIP control, there was no difference in the mean healthiness of purchases for HSR, MTL, or DIG (all p > 0.07), but WARN resulted in healthier packaged food purchases (mean difference 0.87; 95% confidence interval 0.03 to 1.72; p = 0.04). HSR was perceived by participants as more useful than DIG, and easier to understand than MTL or DIG (all p < 0.05). Participants also reported the HSR to be easier to understand, and the HSR and MTL to be more useful, than NIP (all p < 0.03).<br><br>CONCLUSIONS: These real-world data align with experimental findings and provide support for the policy choice of HSR. Recommendation/warning labels warrant further exploration, as they may be a stronger driver of healthy food purchases.},
}
@article {pmid29186554,
year = {2018},
author = {Zimmerman, RS and Tao, X and Marin, D and Werner, MD and Hong, KH and Lonczak, A and Landis, J and Taylor, D and Zhan, Y and Scott, RT and Treff, NR},
title = {Preclinical validation of a targeted next generation sequencing-based comprehensive chromosome screening methodology in human blastocysts.},
journal = {Molecular human reproduction},
volume = {24},
number = {1},
pages = {37-45},
doi = {10.1093/molehr/gax060},
pmid = {29186554},
issn = {1460-2407},
mesh = {Aneuploidy ; Blastocyst/*cytology/*metabolism ; Cell Line ; Computational Biology ; Female ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Pregnancy ; },
abstract = {STUDY QUESTION: Can a novel targeted next generation sequencing (tNGS) platform accurately detect whole chromosome aneuploidy in a trophectoderm biopsy and provide additional information to improve testing?<br><br>SUMMARY ANSWER: Karyotypes obtained by tNGS were concordant with other validated platforms and single nucleotide polymorphism genotyping information obtained can be used for improved detection and quality control.<br><br>WHAT IS KNOWN ALREADY: qPCR-based whole chromosome aneuploidy screening is highly accurate in comparison to other common methods and has been shown to improve IVF success in two randomized clinical trials. With aneuploidy screening becoming standard of care in many IVF centres, there is a need to develop platforms with high throughput, low cost capabilities.<br><br>STUDY DESIGN SIZE, DURATION: Twelve well-characterized cell lines were obtained from a commercial cell line repository and 31 discarded human blastocysts were obtained from 17 IVF patients who underwent comprehensive chromosome screening (CCS).<br><br>All samples were processed using a unique amplification strategy which directly incorporated sequencing library adapters and barcodes. Sequencing was performed on an Ion Torrent Proton. A custom bioinformatics pipeline was used to determine the karyotype for each sample. The consistency of tNGS diagnoses with either conventional karyotyping of cell lines or quantitative real-time PCR based CCS of blastocyst biopsies was evaluated.<br><br>Overall consistency per sample of tNGS based CCS in 5-cell samples from a variety of cell lines was 99.2%. In the blinded analysis of rebiopsies of aneuploid blastocysts, an overall targeted tNGS CCS consistency of 98.7% was observed per sample. These data demonstrate the ability of tNGS based CCS to provide an accurate and high throughput evaluation of aneuploidy in the human blastocyst.<br><br>LARGE SCALE DATA: Not applicable.<br><br>This study is limited to whole chromosome aneuploidy, as mosaicism and segmental aneuploidy have not been investigated.<br><br>These data show an accurate, high throughput method, and with the greater depth of each amplicon sequenced in comparison to commercial kits, there is greater application available for single nucleotide polymorphism based analysis for quality control.<br><br>This study was funded through intramural research funds provided by the Foundation for Embryonic Competence. There are no competing interests.},
}
@article {pmid29186506,
year = {2018},
author = {Xia, LC and Bell, JM and Wood-Bouwens, C and Chen, JJ and Zhang, NR and Ji, HP},
title = {Identification of large rearrangements in cancer genomes with barcode linked reads.},
journal = {Nucleic acids research},
volume = {46},
number = {4},
pages = {e19},
pmid = {29186506},
issn = {1362-4962},
support = {P01 HG000205/HG/NHGRI NIH HHS/United States ; R01 HG006137/HG/NHGRI NIH HHS/United States ; },
mesh = {Algorithms ; Chromosome Aberrations ; Gastrointestinal Neoplasms/genetics ; Genome, Human ; *Genomic Structural Variation ; Humans ; Neoplasms/*genetics ; Whole Genome Sequencing/*methods ; },
abstract = {Large genomic rearrangements involve inversions, deletions and other structural changes that span Megabase segments of the human genome. This category of genetic aberration is the cause of many hereditary genetic disorders and contributes to pathogenesis of diseases like cancer. We developed a new algorithm called ZoomX for analysing barcode-linked sequence reads-these sequences can be traced to individual high molecular weight DNA molecules (>50 kb). To generate barcode linked sequence reads, we employ a library preparation technology (10X Genomics) that uses droplets to partition and barcode DNA molecules. Using linked read data from whole genome sequencing, we identify large genomic rearrangements, typically greater than 200kb, even when they are only present in low allelic fractions. Our algorithm uses a Poisson scan statistic to identify genomic rearrangement junctions, determine counts of junction-spanning molecules and calculate a Fisher's exact test for determining statistical significance for somatic aberrations. Utilizing a well-characterized human genome, we benchmarked this approach to accurately identify large rearrangement. Subsequently, we demonstrated that our algorithm identifies somatic rearrangements when present in lower allelic fractions as occurs in tumors. We characterized a set of complex cancer rearrangements with multiple classes of structural aberrations and with possible roles in oncogenesis.},
}
@article {pmid29183989,
year = {2018},
author = {Belderbos, ME and Bystrykh, L and de Haan, G},
title = {Left or right? Directions to stem cell engraftment.},
journal = {The Journal of experimental medicine},
volume = {215},
number = {1},
pages = {13-15},
pmid = {29183989},
issn = {1540-9538},
mesh = {Animals ; Cell Differentiation ; Graft Survival ; *Hematopoietic Stem Cell Transplantation ; Hematopoietic Stem Cells ; *Macaca ; },
abstract = {In this issue of JEM, Wu et al. (https://doi.org/10.1084/jem.20171341) use genetic barcoding of macaque hematopoietic stem cells to demonstrate that, after transplantation, HSCs are very asymmetrically distributed and uncover a thymus-independent pathway for mature T cell production in the bone marrow.},
}
@article {pmid29181902,
year = {2017},
author = {Zheng, YM and Hou, ZE},
title = {Myanmarorchestia victoria sp. nov. (Crustacea, Amphipoda, Talitridae), a new species of landhopper from the high altitude forests in Myanmar.},
journal = {Zoological research},
volume = {38},
number = {5},
pages = {281-290},
pmid = {29181902},
issn = {2095-8137},
mesh = {*Altitude ; Amphipoda/*anatomy &amp; histology/*classification/physiology ; Animal Distribution ; Animals ; Female ; *Forests ; Male ; Myanmar ; Species Specificity ; },
abstract = {Myanmarorchestia victoriasp. nov. is described from high altitude habitats in Myanmar. The new species differs morphologically from its congeners by palp of maxilliped narrow; sexually dimorphic gnathopod Ⅱ, propodus of male chelate and propodus of female mitten-shaped; and dimorphic uropod Ⅱ, outer ramus of male with small teeth distally, outer ramus of female with three distal spines. Analysis of DNA barcode sequences and niche distinctiveness support recognition of the new species.},
}
@article {pmid29181898,
year = {2017},
author = {Wu, JL and Luo, YF and Li, SQ},
title = {Nine new species of the spider genus Stedocys (Araneae, Scytodidae) from China and Thailand.},
journal = {Zoological research},
volume = {38},
number = {5},
pages = {215-242},
pmid = {29181898},
issn = {2095-8137},
mesh = {Animal Distribution ; Animals ; China ; Female ; Male ; Species Specificity ; Spiders/*anatomy &amp; histology/*classification/physiology ; Thailand ; },
abstract = {Nine new species of the genus Stedocys Ono, 1995 are described: Stedocys gaolingensis Wu &amp; Li sp. n. (♂♀, Guangxi), S. huangniuensis Wu &amp; Li sp. n. (♀, Guangxi), S. ludiyanensis Wu &amp; Li sp. n. (♂♀, Guangxi), S. matuoensis Wu &amp; Li sp. n. (♀, Guangxi), S. pulianensis Wu &amp; Li sp. n. (♂, Guangxi), S. shilinensis Wu &amp; Li sp. n. (♂♀, Hainan), S. xianrenensis Wu &amp; Li sp. n. (♂♀, Guangxi), S. xiangzhouensis Wu &amp; Li sp. n. (♂♀, Guangxi) from China, and S. zhaoi Wu &amp; Li sp. nov. (♂♀, Kanchanaburi) from Thailand. Diagnoses of nine new species are provided. DNA barcodes for six new species are documented for future use and as proof of molecular differences between these species.},
}
@article {pmid29181454,
year = {2017},
author = {Sandhu, P and Bandyopadhyay, K and Ernst, DJ and Hunt, W and Taylor, TH and Birch, R and Krolak, J and Geaghan, S},
title = {Effectiveness of Laboratory Practices to Reducing Patient Misidentification Due to Specimen Labeling Errors at the Time of Specimen Collection in Healthcare Settings: LMBP™ Systematic Review.},
journal = {The journal of applied laboratory medicine},
volume = {2},
number = {2},
pages = {244-258},
pmid = {29181454},
issn = {2576-9456},
support = {CC999999//Intramural CDC HHS/United States ; },
abstract = {BACKGROUND: Specimen labeling errors have long plagued the laboratory industry putting patients at risk of transfusion-related death, medication errors, misdiagnosis, and patient mismanagement. Many interventions have been implemented and deemed to be effective in reducing sample error rates. The objective of this review was to identify and evaluate the effectiveness of laboratory practices/ interventions to develop evidence based recommendations for the best laboratory practices to reduce labeling errors.<br><br>CONTENT: The standardized LMBP&#x2122; A-6 methods were used to conduct this systematic review. Total evidence included 12 studies published during the time periods of 1980 to September 2015. Combined data from seven studies found that the interventions developed as a result of improved communication and collaboration between the laboratory and clinical staff resulted in substantial decrease in specimen labeling errors (Median relative percent change in labeling errors: -75.86; IQI: -84.77, -58.00). Further data from subset of four studies showed a significant decrease in specimen labeling errors after the institution of the standardized specimen labeling protocols (Median relative percent decrease in specimen labeling errors: -72.45; IQI: -83.25, -46.50).<br><br>SUMMARY: Based on the evidence included in this review, the interventions that enhance the communication and collaboration between laboratory and healthcare professionals can decrease the specimen identification errors in healthcare settings. However, more research is needed to make the conclusion on the effectiveness of other evaluated practices in this review including training and education of the specimen collection staff, audit and feedback of labeling errors, and implementation of new technology (other than barcoding).},
}
@article {pmid29181391,
year = {2017},
author = {Wang, X and Chen, X and Yang, P and Wang, L and Han, J},
title = {Barcoding the Dendrobium (Orchidaceae) Species and Analysis of the Intragenomic Variation Based on the Internal Transcribed Spacer 2.},
journal = {BioMed research international},
volume = {2017},
number = {},
pages = {2734960},
pmid = {29181391},
issn = {2314-6141},
mesh = {Dendrobium/*genetics ; Genetic Markers ; *Phylogeny ; Species Specificity ; },
abstract = {Many species belonging to the genus Dendrobium are of great commercial value. However, their difficult growth conditions and high demand have caused many of these species to become endangered. Indeed, counterfeit Dendrobium products are common, especially in medicinal markets. This study aims to assess the suitability of the internal transcribed spacer 2 (ITS2) region as a marker for identifying Dendrobium and to evaluate its intragenomic variation in Dendrobium species. In total, 29,624 ITS2 copies from 18 species were obtained using 454 pyrosequencing to evaluate intragenomic variation. In addition, 513 ITS2 sequences from 26 Dendrobium species were used to assess its identification suitability. The highest intragenomic genetic distance was observed in Dendrobium chrysotoxum (0.081). The average intraspecific genetic distances of each species ranged from 0 to 0.032. Phylogenetic trees based on ITS2 sequences showed that most Dendrobium species are monophyletic. The intragenomic and intraspecies divergence analysis showed that greater intragenomic divergence is mostly correlated with larger intraspecific variation. As a major ITS2 variant becomes more common in genome, there are fewer intraspecific variable sites in ITS2 sequences at the species level. The results demonstrated that the intragenomic multiple copies of ITS2 did not affect species identification.},
}
@article {pmid29181014,
year = {2017},
author = {Guo, M and Ren, L and Pang, X},
title = {Inspecting the True Identity of Herbal Materials from Cynanchum Using ITS2 Barcode.},
journal = {Frontiers in plant science},
volume = {8},
number = {},
pages = {1945},
pmid = {29181014},
issn = {1664-462X},
abstract = {Cynanchum is a large genus with some important medicinal species in China. The medicinal species in Cynanchum are easily confused, leading to potential safety risks. In this study, the internal transcribed spacer 2 (ITS2) barcode was used to discriminate the medicinal plants in Cynanchum. The identifying capability of ITS2 was assessed using the specific genetic divergence, BLAST1, neighbor-joining (NJ) tree, maximum-likelihood (ML) tree, and single-nucleotide polymorphism (SNP) methods. Results indicated that the intra-specific genetic divergences of Cynanchum species were lower than their inter-specific genetic divergences. Of the 87 samples from 17 species, ITS2 showed a high identification efficiency of 90.8 and 87.4% at the species level through BLAST1 and the nearest distance methods. NJ tree and ML tree also demonstrated the suitability of ITS2 to differentiate Cynanchum species. Meanwhile, a stable SNP was found, and it could accurately authenticate Cynanchum paniculatum and Cynanchum atratum. Furthermore, we collected 64 commercial samples from three commonly used herbal medicines and evaluated the capability of ITS2 to survey their authentication. Of these samples, Cynanchi Atrati Radix et Rhizoma (Baiwei) showed a potential safety problem, and all the 11 test samples were adulterants. In conclusion, ITS2 can distinguish medicinal species in Cynanchum effectively, and its application could greatly improve the identification efficiency and accuracy of commercial herbal medicines in this genus.},
}
@article {pmid29180788,
year = {2017},
author = {Del Campo, J and James, ER and Hirakawa, Y and Fiorito, R and Kolisko, M and Irwin, NAT and Mathur, V and Boscaro, V and Hehenberger, E and Karnkowska, A and Scheffrahn, RH and Keeling, PJ},
title = {Pseudotrichonympha leei, Pseudotrichonympha lifesoni, and Pseudotrichonympha pearti, new species of parabasalian flagellates and the description of a rotating subcellular structure.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {16349},
pmid = {29180788},
issn = {2045-2322},
mesh = {Animals ; Genes, Protozoan ; Isoptera/parasitology ; Microscopy ; Parabasalidea/*classification/*cytology/physiology ; Phylogeny ; RNA, Ribosomal/genetics ; },
abstract = {Pseudotrichonympha is a large and structurally complex genus of parabasalian protists that play a key role in the digestion of lignocellulose in the termite hindgut. Like many termite symbionts, it has a conspicuous body plan that makes genus-level identification relatively easy, but species-level diversity of Pseudotrichonympha is understudied. Molecular surveys have suggested the diversity is much greater than the current number of described species, and that many "species" described in multiple hosts are in fact different, but gene sequences from formally described species remain a rarity. Here we describe three new species from Coptotermes and Prorhinotermes hosts, including small subunit ribosomal RNA (SSU rRNA) sequences from single cells. Based on host identification by morphology and DNA barcoding, as well as the morphology and phylogenetic position of each symbiont, all three represent new Pseudotrichonympha species: P. leei, P. lifesoni, and P. pearti. Pseudotrichonympha leei and P. lifesoni, both from Coptotermes, are closely related to other Coptotermes symbionts including the type species, P. hertwigi. Pseudotrichonympha pearti is the outlier of the trio, more distantly related to P. leei and P. lifesoni than they are to one another, and contains unique features, including an unusual rotating intracellular structure of unknown function.},
}
@article {pmid29179676,
year = {2017},
author = {Segawa, H and Kukita, Y and Kato, K},
title = {HLA genotyping by next-generation sequencing of complementary DNA.},
journal = {BMC genomics},
volume = {18},
number = {1},
pages = {914},
pmid = {29179676},
issn = {1471-2164},
mesh = {DNA, Complementary/*chemistry ; Genotyping Techniques/*methods ; Haplotypes ; *High-Throughput Nucleotide Sequencing ; Histocompatibility Testing/*methods ; *Sequence Analysis, DNA ; Templates, Genetic ; },
abstract = {BACKGROUND: Genotyping of the human leucocyte antigen (HLA) is indispensable for various medical treatments. However, unambiguous genotyping is technically challenging due to high polymorphism of the corresponding genomic region. Next-generation sequencing is changing the landscape of genotyping. In addition to high throughput of data, its additional advantage is that DNA templates are derived from single molecules, which is a strong merit for the phasing problem. Although most currently developed technologies use genomic DNA, use of cDNA could enable genotyping with reduced costs in data production and analysis. We thus developed an HLA genotyping system based on next-generation sequencing of cDNA.<br><br>METHODS: Each HLA gene was divided into 3 or 4 target regions subjected to PCR amplification and subsequent sequencing with Ion Torrent PGM. The sequence data were then subjected to an automated analysis. The principle of the analysis was to construct candidate sequences generated from all possible combinations of variable bases and arrange them in decreasing order of the number of reads. Upon collecting candidate sequences from all target regions, 2 haplotypes were usually assigned. Cases not assigned 2 haplotypes were forwarded to 4 additional processes: selection of candidate sequences applying more stringent criteria, removal of artificial haplotypes, selection of candidate sequences with a relaxed threshold for sequence matching, and countermeasure for incomplete sequences in the HLA database.<br><br>RESULTS: The genotyping system was evaluated using 30 samples; the overall accuracy was 97.0% at the field 3 level and 98.3% at the G group level. With one sample, genotyping of DPB1 was not completed due to short read size. We then developed a method for complete sequencing of individual molecules of the DPB1 gene, using the molecular barcode technology.<br><br>CONCLUSION: The performance of the automatic genotyping system was comparable to that of systems developed in previous studies. Thus, next-generation sequencing of cDNA is a viable option for HLA genotyping.},
}
@article {pmid29175746,
year = {2018},
author = {Lo, YT and Shaw, PC},
title = {DNA barcoding in concentrated Chinese medicine granules using adaptor ligation-mediated polymerase chain reaction.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {149},
number = {},
pages = {512-516},
doi = {10.1016/j.jpba.2017.11.048},
pmid = {29175746},
issn = {1873-264X},
mesh = {Angelica sinensis/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; DNA, Intergenic/genetics/isolation &amp; purification ; DNA, Plant/genetics/isolation &amp; purification ; Drugs, Chinese Herbal/*analysis ; *Medicine, Chinese Traditional ; Panax notoginseng/genetics ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA/methods ; },
abstract = {The use of DNA barcodes for species identification is a common laboratory practice. However, PCR amplification of full-length DNA barcode in processed material is difficult because of severe DNA fragmentation. In this study, an adaptor ligation-mediated PCR protocol was derived to amplify sets of target DNA fragments isolated from two CCMG products. The specially designed adaptor with asymmetric strands and terminal modification avoids amplification of non-target DNA sequences. DNA extracted from Angelica sinensis and Panax notoginseng CCMG were ligated with the adaptors and amplified by an adaptor primer and a single universal barcode primer to obtain partial ITS2 sequence. Results showed that various length of DNA fragments within the ITS2 region were amplified and could be used to identify the concerned species. The adaptor ligation-mediated PCR is therefore a promising universal method for species identification in highly processed herbal products.},
}
@article {pmid29172979,
year = {2017},
author = {Sagi, S and Cohen, HP and Woollett, GR},
title = {Pharmacovigilance of Biologics in a Multisource Environment.},
journal = {Journal of managed care &amp; specialty pharmacy},
volume = {23},
number = {12},
pages = {1249-1254},
pmid = {29172979},
issn = {2376-1032},
mesh = {Adverse Drug Reaction Reporting Systems ; Biological Products/administration &amp; dosage/adverse effects ; Biosimilar Pharmaceuticals/administration &amp; dosage/*adverse effects ; Counterfeit Drugs ; Electronic Data Processing/methods ; Epoetin Alfa/administration &amp; dosage/*adverse effects ; European Union ; Filgrastim/administration &amp; dosage/*adverse effects ; Human Growth Hormone/administration &amp; dosage/*adverse effects ; Humans ; Medication Errors/prevention &amp; control ; *Pharmacovigilance ; United States ; },
abstract = {UNLABELLED: It is important that systems are in place to ensure that appropriate and comprehensive records are kept for use of all medications. It is fundamental to an effective pharmacovigilance system that patient medical records contain sufficient information to identify which medication has been prescribed, when it was administered, and at what dose. The availability of biologics from multiple sponsors has raised questions by some health care providers about the ability of current pharmacovigilance systems to trace specific biologics. In this article, periodic safety update reports were used to assess current postapproval safety monitoring for 3 biosimilars (epoetin alfa, somatropin, and filgrastim) that collectively represented nearly 350 million patient days of treatment worldwide. The reference products have each been marketed for over 10 years, forming a strong baseline of postmarketing safety data against which the safety of biosimilars can be compared. Published data from Denmark were also reviewed as additional evidence of how current pharmacovigilance systems are able to attribute adverse events to particular medicines. Collectively, the data show that spontaneous adverse drug reactions are reported by brand name in the majority of cases and are attributable to a specific medicine. Also discussed are the informational elements critical to monitoring biologics, or indeed any medicine, to ensure the availability of complete information so medicines that a patient has received can be quickly identified should a safety event occur. We support the addition of a single data element, the batch/lot number, to enhance the value of current pharmacovigilance systems. Adoption of 2-D barcodes in the European Union (EU) and standardized numerical identifiers in the United States addresses this need, since they include batch/lot numbers. These identifiers are already being implemented in the United States and the EU to improve patient safety, reduce medication errors, facilitate anticounterfeiting, and enable effective product recalls and adverse event reporting. Importantly, electronic identifiers will ameliorate safety reporting concerns with respect to biosimilars, while concurrently achieving these much broader public health objectives through more complete pharmacovigilance data.<br><br>DISCLOSURES: This work was funded by Sandoz, a Novartis division. The authors were fully responsible for the content, editorial decisions, and opinions expressed in this article. No author received an honorarium related to the development of this manuscript. Sagi and Cohen are employees of Sandoz, and Woollett is an employee of Avalere Health. Study concept and design were contributed by Sagi and Woollett, along with Cohen. Data were primarily collected by Sagi, along with Woollett, and data interpretation was provided by all the authors. The manuscript was written by Woollett, along with Sagi and Cohen, and revised by Sagi and Cohen, along with Woollett.},
}
@article {pmid29171244,
year = {2017},
author = {Fan, CZ and Xu, JG and Li, YW and Li, XJ},
title = {[Identification of origin plant of Uygur medicine mulberry based on DNA barcode].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {42},
number = {16},
pages = {3219-3224},
doi = {10.19540/j.cnki.cjcmm.20170714.019},
pmid = {29171244},
issn = {1001-5302},
mesh = {China ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Geography ; Morus/*classification ; Phylogeny ; Plants, Medicinal/classification ; Trees/classification ; },
abstract = {To provide molecular evidence for medical material identification, we analyzed the nucleotide sequence of ITS2, psbA-trnH gene in Morus genus plants and commercial products which were obtained from different places in Xinjiang. The sequence of ITS2 and psbA-trnH in fifty-one samples were amplified and sequenced, MEGA 6.0 was used to analyze the intra- and interspecific K-2P distances, neighbor-joining (NJ) tree was used to constructing clustering tree. ITS2 sequence analyzed results showed that there is no intra-specific variation among Morus alba, M. alba var. tatarica and M. nigra, but 13 variations sites were exist between M. alba and M. nigra and their inter-specific K-2P distances was 0.04, which indicated that there had significant variation in them. We didn't find informative variation sites between Morus genus plants and commercial products, and we also found that M. nigra can be distinguished from other two species by NJ Tree. PsbA-trnH analysis results showed there was only one variation site between M. alba and M. nigra, but insertion or deletion variation were remarkable evidence among M. alba, M. alba var. tatarica and M. Nigra. Inter-specific variation was accordance with intra-specific variation of commercial products. So ITS2 and psbA-trnH gene were important marker for M. alba, M. alba var. tatarica and M. nigra identification. This study provided important evidence for Uygur medicine identification and market supervision.},
}
@article {pmid29171158,
year = {2018},
author = {Deagle, BE and Clarke, LJ and Kitchener, JA and Polanowski, AM and Davidson, AT},
title = {Genetic monitoring of open ocean biodiversity: An evaluation of DNA metabarcoding for processing continuous plankton recorder samples.},
journal = {Molecular ecology resources},
volume = {18},
number = {3},
pages = {391-406},
doi = {10.1111/1755-0998.12740},
pmid = {29171158},
issn = {1755-0998},
mesh = {Animals ; Aquatic Organisms/*genetics ; *Biodiversity ; DNA Barcoding, Taxonomic ; Ecosystem ; Oceans and Seas ; Plankton/*genetics ; },
abstract = {DNA metabarcoding is an efficient method for measuring biodiversity, but the process of initiating long-term DNA-based monitoring programmes, or integrating with conventional programs, is only starting. In marine ecosystems, plankton surveys using the continuous plankton recorder (CPR) have characterized biodiversity along transects covering millions of kilometres with time-series spanning decades. We investigated the potential for use of metabarcoding in CPR surveys. Samples (n = 53) were collected in two Southern Ocean transects and metazoans identified using standard microscopic methods and by high-throughput sequencing of a cytochrome c oxidase subunit I marker. DNA increased the number of metazoan species identified and provided high-resolution taxonomy of groups problematic in conventional surveys (e.g., larval echinoderms and hydrozoans). Metabarcoding also generally produced more detections than microscopy, but this sensitivity may make cross-contamination during sampling a problem. In some samples, the prevalence of DNA from large plankton such as krill masked the presence of smaller species. We investigated adding a fixed amount of exogenous DNA to samples as an internal control to allow determination of relative plankton biomass. Overall, the metabarcoding data represent a substantial shift in perspective, making direct integration into current long-term time-series challenging. We discuss a number of hurdles that exist for progressing DNA metabarcoding from the current snapshot studies to the requirements of a long-term monitoring programme. Given the power and continually increasing efficiency of metabarcoding, it is almost certain this approach will play an important role in future plankton monitoring.},
}
@article {pmid29170403,
year = {2017},
author = {Yu, G and Rao, D and Matsui, M and Yang, J},
title = {Coalescent-based delimitation outperforms distance-based methods for delineating less divergent species: the case of Kurixalus odontotarsus species group.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {16124},
pmid = {29170403},
issn = {2045-2322},
mesh = {Animals ; Anura/classification/*genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/genetics ; Phylogeny ; Species Specificity ; },
abstract = {Few empirical studies have compared coalescent-based methods to distance-based methods for delimitation of less divergent species. In this study, we used two coalescent-based (BFD and BPP) and two distance-based barcoding (ABGD and jMOTU) methods to delimit closely related species in the Kurixalus odontotarsus species group. Phylogenetic analyses revealed that the K. odontotarsus species group comprises 11 distinct maternal clades with strong support values. Based on the genetic and morphological evidences, we consider that species diversity in the K. odontotarsus species group was underestimated and the 11 clades represent 11 species, of which six are unnamed. The coalescent-based delimitations decisively supported the scenario of 11-species corresponding to the 11 clades. However, the distance-based ABGD only obtained 3-6 candidate species, which is not consistent with morphological evidence. These results indicate that BFD and BPP are more conservative than ABGD to false negatives (lumping). Method of fixed threshold (jMOTU) may obtain a resolution similar to that inferred by BFD and BPP, but it severely relies on subjective choice of the threshold and lacks statistical support. We consider that coalescent-based BFD and BPP approaches outperform distance-based methods for delineation of less divergent species.},
}
@article {pmid29168449,
year = {2018},
author = {Hutchinson, R and Stevens, JR},
title = {Barcoding in trypanosomes.},
journal = {Parasitology},
volume = {145},
number = {5},
pages = {563-573},
doi = {10.1017/S0031182017002049},
pmid = {29168449},
issn = {1469-8161},
mesh = {DNA Barcoding, Taxonomic/*methods ; Genetic Markers ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/genetics ; Trypanosoma/classification/*genetics ; },
abstract = {Trypanosomes (genus Trypanosoma) are parasites of humans, and wild and domestic mammals, in which they cause several economically and socially important diseases, including sleeping sickness in Africa and Chagas disease in the Americas. Despite the development of numerous molecular diagnostics and increasing awareness of the importance of these neglected parasites, there is currently no universal genetic barcoding marker available for trypanosomes. In this review we provide an overview of the methods used for trypanosome detection and identification, discuss the potential application of different barcoding techniques and examine the requirements of the 'ideal' trypanosome genetic barcode. In addition, we explore potential alternative genetic markers for barcoding Trypanosoma species, including an analysis of phylogenetically informative nucleotide changes along the length of the 18S rRNA gene.},
}
@article {pmid29167738,
year = {2017},
author = {Boykin, LM and Savill, A and De Barro, P},
title = {Updated mtCOI reference dataset for the Bemisia tabaci species complex.},
journal = {F1000Research},
volume = {6},
number = {},
pages = {1835},
pmid = {29167738},
issn = {2046-1402},
abstract = {Members of the whitefly Bemisia tabaci species complex cause millions of dollars of damage globally and are considered one of the world's most invasive species. They are capable of causing extensive damage to major vegetable, grain legume and fiber crops. All member of the species complex are morphologically identical therefore, data from the partial mitochondrial cytochrome oxidase subunit I (mtCOI) gene sequence has been used to identify the various species. The current reference dataset that is widely used is found on the CSIRO data portal. However, the reference set stored on the CSIRO data does not include newly added sequences (2013-2017), therefore an updated reference dataset is needed. All mtCOI data for the Bemisia tabaci species complex were downloaded on 22 May 2017 from GenBank and after quality checking, a dataset of 1,071 unique sequences and 696 base pairs was generated (https://doi.org/10.6084/m9.figshare.5437420.v1).},
}
@article {pmid29166859,
year = {2017},
author = {Thielsch, A and Knell, A and Mohammadyari, A and Petrusek, A and Schwenk, K},
title = {Divergent clades or cryptic species? Mito-nuclear discordance in a Daphnia species complex.},
journal = {BMC evolutionary biology},
volume = {17},
number = {1},
pages = {227},
pmid = {29166859},
issn = {1471-2148},
support = {P506/10/P167//Czech Science Foundation/International ; },
mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; Daphnia/*genetics ; *Genetic Variation ; Hybridization, Genetic ; Microsatellite Repeats/genetics ; *Phylogeny ; Species Specificity ; },
abstract = {BACKGROUND: Genetically divergent cryptic species are frequently detected by molecular methods. These discoveries are often a byproduct of molecular barcoding studies in which fragments of a selected marker are used for species identification. Highly divergent mitochondrial lineages and putative cryptic species are even detected in intensively studied animal taxa, such as the crustacean genus Daphnia. Recently, eleven such lineages, exhibiting genetic distances comparable to levels observed among well-defined species, were recorded in the D. longispina species complex, a group that contains several key taxa of freshwater ecosystems. We tested if three of those lineages represent indeed distinct species, by analyzing patterns of variation of ten nuclear microsatellite markers in six populations.<br><br>RESULTS: We observed a discordant pattern between mitochondrial and nuclear DNA, as all individuals carrying one of the divergent mitochondrial lineages grouped at the nuclear level with widespread, well-recognized species coexisting at the same localities (Daphnia galeata, D. longispina, and D. cucullata).<br><br>CONCLUSIONS: A likely explanation for this pattern is the introgression of the mitochondrial genome of undescribed taxa into the common species, either in the distant past or after long-distance dispersal. The occurrence of highly divergent but rare mtDNA lineages in the gene pool of widespread species would suggest that hybridization and introgression in the D. longispina species complex is frequent even across large phylogenetic distances, and that discoveries of such distinct clades must be interpreted with caution. However, maintenance of ancient polymorphisms through selection is another plausible alternative that may cause the observed discordance and cannot be entirely excluded.},
}
@article {pmid29166817,
year = {2018},
author = {Reem, E and Douek, J and Rinkevich, B},
title = {Ambiguities in the taxonomic assignment and species delineation of botryllid ascidians from the Israeli Mediterranean and other coastlines.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {7},
pages = {1073-1080},
doi = {10.1080/24701394.2017.1404047},
pmid = {29166817},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic/*standards ; Electron Transport Complex IV/genetics ; Israel ; Mediterranean Region ; *Phylogeny ; Urochordata/*classification/genetics ; },
abstract = {Based on mtCOI sequences comparisons, recent studies reassigned the 'dwarf Botrylloides leachii' from the Levant as Botrylloides nigrum. Here we conducted a survey of the literature and of deposited mtCOI sequences of botryllid ascidians, elucidating ambiguities in their taxonomy. We found that the species, dwarf morph of Botrylloides leachii, Botrylloides nigrum, Botryllus aster and Botryllus arenaceus are grouped together on a single molecular taxon. Then, results of three additional markers (18S, 28S, H3) contradicted literature suggestions, revealing minute distances between Botrylloides leachii and the 'dwarf Botrylloides leachii'. Moreover, only Botrylloides leachii and the 'dwarf Botrylloides leachii' develop giant ampullae as an allorecognition response. Our results raise the possibility that inadequate identification, together with faults in molecular assignment, including queries regarding the efficacy of the mtCOI as the exclusive barcoding tool in botryllid ascidians, is the major culprits responsible for the emerged inconsistencies between the mtCOI sequences and traditional taxonomy. Thus, we assign the Levantine dwarf form as Botrylloides aff. leachii.},
}
@article {pmid29165730,
year = {2018},
author = {Schmiderer, C and Lukas, B and Ruzicka, J and Novak, J},
title = {What Else Is in Salviae officinalis folium? Comprehensive Species Identification of Plant Raw Material by DNA Metabarcoding.},
journal = {Planta medica},
volume = {84},
number = {6-07},
pages = {428-433},
doi = {10.1055/s-0043-121470},
pmid = {29165730},
issn = {1439-0221},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; Drug Contamination ; High-Throughput Nucleotide Sequencing/methods ; Polymerase Chain Reaction/methods ; Quality Control ; Salvia officinalis/*genetics/microbiology ; },
abstract = {Quality control of drugs consists of identifying the raw material to avoid unwanted admixtures or exchange of material as well as looking for abiotic and biotic contaminations. So far, identity and microbial contamination are analyzed by separate processes and separate methods. Species identification by their DNA ("DNA barcoding") has the potential to supplement existing methods of identification. The introduction of next-generation sequencing methods offers completely new approaches like the identification of whole communities in one analysis, termed "DNA metabarcoding". Here we present a next-generation sequencing assessment to identify plants and fungi of two commercial sage samples (Salvia officinalis) using the standard DNA barcoding region "internal transcribed spacer" consisting of internal transcribed spacer 1 and internal transcribed spacer 2, respectively. The main species in both samples was identified as S. officinalis. The spectrum of accompanying plant and fungal species, however, was completely different between the samples. Additionally, the composition between internal transcribed spacer 1 and internal transcribed spacer 2 within the samples was different and demonstrated the influence of primer selection and therefore the need for harmonization. This next-generation sequencing approach does not result in quantitative species composition but gives deeper insight into the composition of additional species. Therefore, it would allow for a better knowledge-based risk assessment than any other method available. However, the method is only economically feasible in routine analysis if a high sample throughput can be guaranteed.},
}
@article {pmid29165646,
year = {2018},
author = {Yang, F and Lei, Y and Zhou, M and Yao, Q and Han, Y and Wu, X and Zhong, W and Zhu, C and Xu, W and Tao, R and Chen, X and Lin, D and Rahman, K and Tyagi, R and Habib, Z and Xiao, S and Wang, D and Yu, Y and Chen, H and Fu, Z and Cao, G},
title = {Development and application of a recombination-based library versus library high- throughput yeast two-hybrid (RLL-Y2H) screening system.},
journal = {Nucleic acids research},
volume = {46},
number = {3},
pages = {e17},
pmid = {29165646},
issn = {1362-4962},
mesh = {Animals ; Autophagy-Related Proteins/classification/*genetics/metabolism ; Bacterial Proteins/classification/*genetics/metabolism ; CRISPR-Cas Systems ; Deoxyribonucleases, Type II Site-Specific/chemistry ; Gene Editing/methods ; *Gene Library ; Genes, Reporter ; High-Throughput Nucleotide Sequencing ; *High-Throughput Screening Assays ; Host-Pathogen Interactions/*genetics ; Integrases/genetics/metabolism ; Luminescent Proteins/genetics/metabolism ; Mice ; Mycobacterium tuberculosis/*genetics/metabolism ; Phagosomes/metabolism/microbiology ; Plasmids/chemistry/metabolism ; Protein Interaction Mapping/methods ; RAW 264.7 Cells ; Recombination, Genetic ; Siphoviridae/chemistry ; Two-Hybrid System Techniques ; Red Fluorescent Protein ; },
abstract = {Protein-protein interaction (PPI) network maintains proper function of all organisms. Simple high-throughput technologies are desperately needed to delineate the landscape of PPI networks. While recent state-of-the-art yeast two-hybrid (Y2H) systems improved screening efficiency, either individual colony isolation, library preparation arrays, gene barcoding or massive sequencing are still required. Here, we developed a recombination-based 'library vs library' Y2H system (RLL-Y2H), by which multi-library screening can be accomplished in a single pool without any individual treatment. This system is based on the phiC31 integrase-mediated integration between bait and prey plasmids. The integrated fragments were digested by MmeI and subjected to deep sequencing to decode the interaction matrix. We applied this system to decipher the trans-kingdom interactome between Mycobacterium tuberculosis and host cells and further identified Rv2427c interfering with the phagosome-lysosome fusion. This concept can also be applied to other systems to screen protein-RNA and protein-DNA interactions and delineate signaling landscape in cells.},
}
@article {pmid29161943,
year = {2018},
author = {Zolotova, AO and Kartavtsev, YP},
title = {Analysis of sequence divergence in redfin (Cypriniformes, Cyprinidae, Tribolodon) based on mtDNA and nDNA markers with inferences in systematics and genetics of speciation.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {7},
pages = {975-992},
doi = {10.1080/24701394.2017.1404040},
pmid = {29161943},
issn = {2470-1408},
mesh = {Animals ; Cyprinidae/classification/*genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; *Genetic Speciation ; *Phylogeny ; Sequence Homology, Nucleic Acid ; },
abstract = {To clarify relationship of species of the genus Tribolodon in the Russian part of their distribution ranges, two mitochondrial markers (Co-1 and Cyt-b), a nuclear marker (Rho), and a gene marker of rDNA internal transcribed spacer (ITS-1,2) were used. Depending on the marker, different numbers of species groups were detected by the ABGD method, but in combination with the analysis of phylograms, these data generally support the known species clusters and regional intraspecies groups. A complex analysis of sequences from three redfin species within the area of the study, based on four marker genes and using the methods of molecular phylogenetics, ordination of genetic distances, recombinant analysis, and population genetic approaches, has revealed clusters of three commonly recognized species, regional intraspecific groups or individuals of local populations, and few hybrid individuals. DNA barcoding technique proved to be efficient with the use of two mtDNA markers: Co-1 and Cyt-b. It has been found that analysis of insertions and substitutions within the ITS-1,2 gene marker is also suitable for identification of Tribolodon species. Results of the studies of local groups do not confirm a sufficient level of differences for defining any new taxa of a species rank in the genus Tribolodon.},
}
@article {pmid29161485,
year = {2017},
author = {Gómez-Palacio, A and Suaza-Vasco, J and Castaño, S and Triana, O and Uribe, S},
title = {Aedes albopictus (Skuse, 1894) infected with the American-Asian genotype of dengue type 2 virus in Medellín suggests its possible role as vector of dengue fever in Colombia.},
journal = {Biomedica : revista del Instituto Nacional de Salud},
volume = {37},
number = {0},
pages = {135-142},
doi = {10.7705/biomedica.v37i0.3474},
pmid = {29161485},
issn = {2590-7379},
mesh = {Aedes/genetics/*virology ; Animals ; Cities ; Colombia/epidemiology ; DNA, Complementary/analysis ; Dengue/*epidemiology/transmission ; Dengue Virus/classification/genetics/*isolation &amp; purification ; Electron Transport Complex IV/genetics ; Genotype ; Humans ; Insect Proteins/genetics ; Mosquito Vectors/*virology ; Polymerase Chain Reaction ; RNA Helicases/genetics ; Serine Endopeptidases/genetics ; Serotyping ; Viral Nonstructural Proteins/genetics ; },
abstract = {INTRODUCTION: Aedes aegypti and Ae. albopictus are recognized vectors of dengue, yellow fever, chikungunya and Zika arboviruses in several countries worldwide. In Colombia, Ae. albopictus geographical distribution has increased to include highly populated cities such as Cali and Medellín. Although this species has been frequently found in urban and semi-urban zones in the country, its role as vector of the dengue fever is poorly known.<br><br>OBJECTIVE: To identify the presence of Ae. albopictus specimens naturally infected with dengue virus collected in Medell&#xed;n.<br><br>MATERIALS AND METHODS: Insects were collected in the Universidad Nacional de Colombia campus in Medell&#xed;n. Individuals were classified as Ae. albopictus and confirmed by DNA barcode region analysis. Mosquitoes were processed for dengue virus identification, and a fragment of the NS3 gen was sequenced and compared with DENV-2 genotypes reported in the literature.<br><br>RESULTS: Sequence analysis of COI indicated Ae. albopictus individuals were similar to those recently reported in Colombia, and genetically close to those from other regions worldwide. Among the pools tested one was positive for DENV-2, and the NS3 analysis indicated it belonged to the Asian-American clade.<br><br>CONCLUSION: We report the presence Ae. albopictus naturally infected with the Asian-American genotype of DENV-2 in Colombia. The presence of Ae. albopictus specimens carrying the most common genotype infecting humans in a highly populated city such as Medell&#xed;n indicates its potential role as dengue vector in Colombia and highlights the relevance of including it in current vector surveillance strategies.},
}
@article {pmid29157062,
year = {2018},
author = {da Costa-Silva, GJ and Yuldi Ashikaga, F and Kioko Shimabukuro Dias, C and Garcia Pereira, LH and Foresti, F and Oliveira, C},
title = {DNA barcoding techniques used to identify the shared ichthyofauna between the Pantanal floodplain and Upper Parana River.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {7},
pages = {1063-1072},
doi = {10.1080/24701394.2017.1404046},
pmid = {29157062},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Fish Proteins/genetics ; Fishes/*genetics ; Introduced Species ; Paraguay ; },
abstract = {The biological invasion process is widely debated topic, as the population depletion of some species and the extinction of others are related to this process. To accelerate the identification of species and to detect non-native forms, new tools are being developed, such as those based on genetic markers. This study aimed to use Barcode DNA methodology to identify fish species that had translocated between the Parana and Paraguay River Basins. Based on a database of two studies that were conducted in these regions, 289 sequences of Cytochrome Oxidase C subunit 1 (COI) were used for General Mixed Youle Coalecent (GMYC) analysis, including 29 morphospecies that were sampled in both river basins. As a result, we observed that while some morphospecies have low variation, demonstrating a recent occupation of the basins, other morphospecies probably represent species complexes. A third of the morphospecies had well-defined lineages but not enough to be treated as different Molecular Operational Taxonomic Units (MOTUs). These results demonstrate that human interventions possibly participated in the distribution of some lineages. However, biogeographical historical processes are also important for the morphospecies distribution. The data suggest that the number of species that are present in these two basins is underestimated and that human actions can irreversibly affect the natural history of the species in these regions.},
}
@article {pmid29154499,
year = {2018},
author = {Shi, ZY and Yang, CQ and Hao, MD and Wang, XY and Ward, RD and Zhang, AB},
title = {FuzzyID2: A software package for large data set species identification via barcoding and metabarcoding using hidden Markov models and fuzzy set methods.},
journal = {Molecular ecology resources},
volume = {18},
number = {3},
pages = {666-675},
doi = {10.1111/1755-0998.12738},
pmid = {29154499},
issn = {1755-0998},
mesh = {Classification/methods ; DNA Barcoding, Taxonomic ; *Fuzzy Logic ; *Markov Chains ; *Software ; },
abstract = {Species identification through DNA barcoding or metabarcoding has become a key approach for biodiversity evaluation and ecological studies. However, the rapid accumulation of barcoding data has created some difficulties: for instance, global enquiries to a large reference library can take a very long time. We here devise a two-step searching strategy to speed identification procedures of such queries. This firstly uses a Hidden Markov Model (HMM) algorithm to narrow the searching scope to genus level and then determines the corresponding species using minimum genetic distance. Moreover, using a fuzzy membership function, our approach also estimates the credibility of assignment results for each query. To perform this task, we developed a new software pipeline, FuzzyID2, using Python and C++. Performance of the new method was assessed using eight empirical data sets ranging from 70 to 234,535 barcodes. Five data sets (four animal, one plant) deployed the conventional barcode approach, one used metabarcodes, and two were eDNA-based. The results showed mean accuracies of generic and species identification of 98.60% (with a minimum of 95.00% and a maximum of 100.00%) and 94.17% (with a range of 84.40%-100.00%), respectively. Tests with simulated NGS sequences based on realistic eDNA and metabarcode data demonstrated that FuzzyID2 achieved a significantly higher identification success rate than the commonly used Blast method, and the TIPP method tends to find many fewer species than either FuzztID2 or Blast. Furthermore, data sets with tens of thousands of barcodes need only a few seconds for each query assignment using FuzzyID2. Our approach provides an efficient and accurate species identification protocol for biodiversity-related projects with large DNA sequence data sets.},
}
@article {pmid29154110,
year = {2018},
author = {Ruhsam, M and Hollingsworth, PM},
title = {Authentication of Eleutherococcus and Rhodiola herbal supplement products in the United Kingdom.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {149},
number = {},
pages = {403-409},
doi = {10.1016/j.jpba.2017.11.025},
pmid = {29154110},
issn = {1873-264X},
mesh = {DNA Barcoding, Taxonomic ; Dietary Supplements/*analysis/standards ; Eleutherococcus/*chemistry/genetics ; Food Contamination/*analysis ; *Food Labeling ; Medicago sativa/chemistry/genetics ; Phylogeny ; Rhodiola/*chemistry/genetics ; Trigonella/chemistry/genetics ; United Kingdom ; },
abstract = {Siberian ginseng (Eleutherococcus senticosus, Araliaceae) and roseroot (Rhodiola rosea, Rosaceae) are popular herbal supplements which have been shown to improve resilience to conditions such as stress and exhaustion. Using DNA barcoding methods we tested 25 Siberian ginseng and 14 roseroot products which are widely available to UK customers to test whether the herbal ingredient stated on the label is also in the product. All Siberian ginseng supplements contained E. senticosus, however, 36% also contained an Eleutherococcus species other than E. senticosus. In three out of the 13 roseroot products which produced amplifiable DNA, we could only retrieve sequences matching alfalfa (declared on the product label) and fenugreek (not declared). In the other 10 supplements Rhodiola was detected but only five matched the target species R. rosea. As DNA can get severely degraded during the manufacturing process we did not take the absence of Rhodiola DNA as proof for a compromised product. Contamination could explain the presence of non-target species such as fenugreek but is unlikely to be account for the detection of congeneric Rhodiola species in roseroot preparations. Our results therefore suggest that the substitution or mixing of the target medicinal ingredient in these two popular supplements with other species is common.},
}
@article {pmid29151634,
year = {2017},
author = {Crous, PW and Wingfield, MJ and Burgess, TI and Hardy, GESJ and Barber, PA and Alvarado, P and Barnes, CW and Buchanan, PK and Heykoop, M and Moreno, G and Thangavel, R and van der Spuy, S and Barili, A and Barrett, S and Cacciola, SO and Cano-Lira, JF and Crane, C and Decock, C and Gibertoni, TB and Guarro, J and Guevara-Suarez, M and Hubka, V and Kolařík, M and Lira, CRS and Ordoñez, ME and Padamsee, M and Ryvarden, L and Soares, AM and Stchigel, AM and Sutton, DA and Vizzini, A and Weir, BS and Acharya, K and Aloi, F and Baseia, IG and Blanchette, RA and Bordallo, JJ and Bratek, Z and Butler, T and Cano-Canals, J and Carlavilla, JR and Chander, J and Cheewangkoon, R and Cruz, RHSF and da Silva, M and Dutta, AK and Ercole, E and Escobio, V and Esteve-Raventós, F and Flores, JA and Gené, J and Góis, JS and Haines, L and Held, BW and Jung, MH and Hosaka, K and Jung, T and Jurjević, &#x17d; and Kautman, V and Kautmanova, I and Kiyashko, AA and Kozanek, M and Kubátová, A and Lafourcade, M and La Spada, F and Latha, KPD and Madrid, H and Malysheva, EF and Manimohan, P and Manjón, JL and Martín, MP and Mata, M and Merényi, Z and Morte, A and Nagy, I and Normand, AC and Paloi, S and Pattison, N and Pawłowska, J and Pereira, OL and Petterson, ME and Picillo, B and Raj, KNA and Roberts, A and Rodríguez, A and Rodríguez-Campo, FJ and Romański, M and Ruszkiewicz-Michalska, M and Scanu, B and Schena, L and Semelbauer, M and Sharma, R and Shouche, YS and Silva, V and Staniaszek-Kik, M and Stielow, JB and Tapia, C and Taylor, PWJ and Toome-Heller, M and Vabeikhokhei, JMC and van Diepeningen, AD and Van Hoa, N and M, VT and Wiederhold, NP and Wrzosek, M and Zothanzama, J and Groenewald, JZ},
title = {Fungal Planet description sheets: 558-624.},
journal = {Persoonia},
volume = {38},
number = {},
pages = {240-384},
pmid = {29151634},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia: Banksiophoma australiensis (incl. Banksiophoma gen. nov.) on Banksia coccinea, Davidiellomycesaustraliensis (incl. Davidiellomyces gen. nov.) on Cyperaceae, Didymocyrtis banksiae on Banksia sessilis var. cygnorum, Disculoides calophyllae on Corymbia calophylla, Harknessia banksiae on Banksia sessilis, Harknessia banksiae-repens on Banksia repens, Harknessia banksiigena on Banksia sessilis var. cygnorum, Harknessia communis on Podocarpus sp., Harknessia platyphyllae on Eucalyptus platyphylla, Myrtacremonium eucalypti (incl. Myrtacremonium gen. nov.) on Eucalyptus globulus, Myrtapenidiella balenae on Eucalyptus sp., Myrtapenidiella eucalyptigena on Eucalyptus sp., Myrtapenidiella pleurocarpae on Eucalyptuspleurocarpa, Paraconiothyrium hakeae on Hakea sp., Paraphaeosphaeria xanthorrhoeae on Xanthorrhoea sp., Parateratosphaeria stirlingiae on Stirlingia sp., Perthomyces podocarpi (incl. Perthomyces gen. nov.) on Podocarpus sp., Readeriella ellipsoidea on Eucalyptus sp., Rosellinia australiensis on Banksia grandis, Tiarosporella corymbiae on Corymbia calophylla, Verrucoconiothyriumeucalyptigenum on Eucalyptus sp., Zasmidium commune on Xanthorrhoea sp., and Zasmidium podocarpi on Podocarpus sp. Brazil: Cyathus aurantogriseocarpus on decaying wood, Perenniporia brasiliensis on decayed wood, Perenniporia paraguyanensis on decayed wood, and Pseudocercospora leandrae-fragilis on Leandrafragilis.Chile: Phialocephala cladophialophoroides on human toe nail. Costa Rica: Psathyrella striatoannulata from soil. Czech Republic: Myotisia cremea (incl. Myotisia gen. nov.) on bat droppings. Ecuador: Humidicutis dictiocephala from soil, Hygrocybe macrosiparia from soil, Hygrocybe sangayensis from soil, and Polycephalomyces onorei on stem of Etlingera sp. France: Westerdykella centenaria from soil. Hungary: Tuber magentipunctatum from soil. India: Ganoderma mizoramense on decaying wood, Hodophilus indicus from soil, Keratinophyton turgidum in soil, and Russula arunii on Pterigota alata.Italy: Rhodocybe matesina from soil. Malaysia: Apoharknessia eucalyptorum, Harknessia malayensis, Harknessia pellitae, and Peyronellaea eucalypti on Eucalyptus pellita, Lectera capsici on Capsicum annuum, and Wallrothiella gmelinae on Gmelina arborea.Morocco: Neocordana musigena on Musa sp. New Zealand: Candida rongomai-pounamu on agaric mushroom surface, Candida vespimorsuum on cup fungus surface, Cylindrocladiella vitis on Vitis vinifera, Foliocryphia eucalyptorum on Eucalyptus sp., Ramularia vacciniicola on Vaccinium sp., and Rhodotorula ngohengohe on bird feather surface. Poland: Tolypocladium fumosum on a caterpillar case of unidentified Lepidoptera.Russia: Pholiotina longistipitata among moss. Spain: Coprinopsis pseudomarcescibilis from soil, Eremiomyces innocentii from soil, Gyroporus pseudocyanescens in humus, Inocybe parvicystis in humus, and Penicillium parvofructum from soil. Unknown origin: Paraphoma rhaphiolepidis on Rhaphiolepsis indica.USA: Acidiella americana from wall of a cooling tower, Neodactylaria obpyriformis (incl. Neodactylaria gen. nov.) from human bronchoalveolar lavage, and Saksenaea loutrophoriformis from human eye. Vietnam: Phytophthora mekongensis from Citrus grandis, and Phytophthora prodigiosa from Citrus grandis. Morphological and culture characteristics along with DNA barcodes are provided.},
}
@article {pmid29151630,
year = {2017},
author = {Voglmayr, H and Castlebury, LA and Jaklitsch, WM},
title = {Juglanconis gen. nov. on Juglandaceae, and the new family Juglanconidaceae (Diaporthales).},
journal = {Persoonia},
volume = {38},
number = {},
pages = {136-155},
pmid = {29151630},
issn = {0031-5850},
support = {P 27645/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Molecular phylogenetic analyses of ITS-LSU rDNA sequence data demonstrate that Melanconis species occurring on Juglandaceae are phylogenetically distinct from Melanconis s.str., and therefore the new genus Juglanconis is described. Morphologically, the genus Juglanconis differs from Melanconis by light to dark brown conidia with irregular verrucae on the inner surface of the conidial wall, while in Melanconis s.str. they are smooth. Juglanconis forms a separate clade not affiliated with a described family of Diaporthales, and the family Juglanconidaceae is introduced to accommodate it. Data of macro- and microscopic morphology and phylogenetic multilocus analyses of partial nuSSU-ITS-LSU rDNA, cal, his, ms204, rpb1, rpb2, tef1 and tub2 sequences revealed four distinct species of Juglanconis. Comparison of the markers revealed that tef1 introns are the best performing markers for species delimitation, followed by cal, ms204 and tub2. The ITS, which is the primary barcoding locus for fungi, is amongst the poorest performing markers analysed, due to the comparatively low number of informative characters. Melanconium juglandinum (= Melanconis carthusiana), M. oblongum (= Melanconis juglandis) and M. pterocaryae are formally combined into Juglanconis, and J. appendiculata is described as a new species. Melanconium juglandinum and Melanconis carthusiana are neotypified and M. oblongum and Diaporthe juglandis are lectotypified. A short description and illustrations of the holotype of Melanconium ershadii from Pterocarya fraxinifolia are given, but based on morphology it is not considered to belong to Juglanconis. A key to all treated species of Juglanconis is provided.},
}
@article {pmid29149830,
year = {2018},
author = {Bedin, C and Crotti, S and Tasciotti, E and Agostini, M},
title = {Diagnostic Devices for Circulating Biomarkers Detection and Quantification.},
journal = {Current medicinal chemistry},
volume = {25},
number = {34},
pages = {4304-4327},
doi = {10.2174/0929867324666171116124255},
pmid = {29149830},
issn = {1875-533X},
mesh = {Biomarkers, Tumor/*blood ; Biosensing Techniques ; Humans ; MicroRNAs/blood ; Nanoparticles/chemistry ; Nanotechnology/instrumentation/*methods ; Neoplasm Proteins/blood ; Neoplasms/blood/*diagnosis/genetics ; Polymorphism, Single Nucleotide ; },
abstract = {Nowadays, fast and sensitive methods for biomarkers detection exist, but the performance of most of them still rely centralized laboratory testing. The development of small, fast and simple to use medical devices that can help in making diagnosis accurate and with low-invasiveness is now a major challenge for nanotechnology. Nanomaterialsbased systems have significant advantages over current conventional approaches in terms of simplicity, sensitivity, specificity, and rapidity. In this review, we describe the most interesting nanotechnological devices/approaches proposed for circulating biomarkers detection in oncology. In particular, new applicable nanobiosensors for nucleic acids and proteins identification are discussed and classified into four most interesting nanotechnologies: bio-barcodes, quantum dots, metal nanoparticles and carbon-based nanosensors. Their versatility has been demonstrated in different applications aiming to detect and quantify cancer biomarkers in real biological samples, in order to show how these methods can lead, in the future, to the development of devices for routine clinical application.},
}
@article {pmid29144208,
year = {2018},
author = {Kocher, A and Valière, S and Bañuls, AL and Murienne, J},
title = {High-throughput sequencing of kDNA amplicons for the analysis of Leishmania minicircles and identification of Neotropical species.},
journal = {Parasitology},
volume = {145},
number = {5},
pages = {585-594},
doi = {10.1017/S0031182017002013},
pmid = {29144208},
issn = {1469-8161},
mesh = {DNA Barcoding, Taxonomic ; DNA, Kinetoplast/*genetics/isolation &amp; purification ; DNA, Protozoan/*genetics/isolation &amp; purification ; Genetic Variation ; *Genome, Protozoan ; *High-Throughput Nucleotide Sequencing ; Leishmania/classification/*genetics/isolation &amp; purification ; Polymerase Chain Reaction ; },
abstract = {Leishmania kinetoplast DNA contains thousands of small circular molecules referred to as kinetoplast DNA (kDNA) minicercles. kDNA minicircles are the preferred targets for sensitive Leishmania detection, because they are present in high copy number and contain conserved sequence blocks in which polymerase chain reaction (PCR) primers can be designed. On the other hand, the heterogenic nature of minicircle networks has hampered the use of this peculiar genomic region for strain typing. The characterization of Leishmania minicirculomes used to require isolation and cloning steps prior to sequencing. Here, we show that high-throughput sequencing of single minicircle PCR products allows bypassing these laborious laboratory tasks. The 120 bp long minicircle conserved region was amplified by PCR from 18 Leishmania strains representative of the major species complexes found in the Neotropics. High-throughput sequencing of PCR products enabled recovering significant numbers of distinct minicircle sequences from each strain, reflecting minicircle class diversity. Minicircle sequence analysis revealed patterns that are congruent with current hypothesis of Leishmania relationships. Then, we show that a barcoding-like approach based on minicircle sequence comparisons may allow reliable identifications of Leishmania spp. This work opens up promising perspectives for the study of kDNA minicercles and a variety of applications in Leishmania research.},
}
@article {pmid29143601,
year = {2017},
author = {Genievskaya, Y and Abugalieva, S and Zhubanysheva, A and Turuspekov, Y},
title = {Morphological description and DNA barcoding study of sand rice (Agriophyllum squarrosum, Chenopodiaceae) collected in Kazakhstan.},
journal = {BMC plant biology},
volume = {17},
number = {Suppl 1},
pages = {177},
pmid = {29143601},
issn = {1471-2229},
mesh = {Chenopodiaceae/anatomy &amp; histology/*classification/genetics ; DNA Barcoding, Taxonomic ; DNA, Chloroplast ; DNA, Plant ; DNA, Ribosomal Spacer ; Genes, Plant ; Genetic Variation ; Kazakhstan ; Species Specificity ; },
abstract = {BACKGROUND: Sand rice (Agriophyllum squarrosum (L.) Moq.) is an annual shrub-like plant adapted to the mobile sand dunes in desert and semi-desert regions of Asia. It has a balanced nutrient composition with relatively high concentration of lipids and proteins, which results in its nutrition being similar to legumes. Sand rice's proteins contain the full range of essential amino acids. However, calories content is more similar to wheat. These features together with desert stress resistance make sand rice a potential food crop resilient to ongoing climate change. It is also an important fodder crop (on young stages of growth) for cattle in arid regions of Kazakhstan. In our work, sand rice samples were collected from two distant regions of Kazakhstan as a part of the nation-wide project to determine genetic variation of the native flora.<br><br>RESULTS: Samples were collected in western and southeastern parts of Kazakhstan separated by distances of up to 1300&#xa0;km. Sequences of the nuclear ribosomal DNA ITS1-5.8S-ITS2 region and the chloroplast matK gene confirmed the identity of species defined by morphological traits. Comparison with GenBank sequences revealed polymorphic sequence positions among Kazakh populations and GenBank references, and suggested a distinction among local populations of sand rice. The phylogenetic analysis of nucleotide sequences showed a clear partition of A. squarrosum (L.) Moq. from Agriophyllum minus Fisch. &amp; C.A. Mey, which grows in the same sand dunes environment.<br><br>CONCLUSIONS: DNA barcoding analyses of ITS and matK sequences showed a segregation of A. squarrosum from A. minus into separate clades in Maximum-Likelhood dendrograms. ITS analysis can be successfully used to characterize A. squarrosum populations growing quite distant from each other. The data obtained in this work provide the basis for further investigations on A. squarrosum population structure and may play a role in the screening of sand rice plants growing in desert and semi-desert environments of Central Asia and China.},
}
@article {pmid29142319,
year = {2017},
author = {Lobo, J and Shokralla, S and Costa, MH and Hajibabaei, M and Costa, FO},
title = {DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {15618},
pmid = {29142319},
issn = {2045-2322},
mesh = {Biodiversity ; DNA/chemistry/genetics ; DNA Barcoding, Taxonomic/*methods ; *Ecosystem ; Estuaries ; High-Throughput Nucleotide Sequencing ; Marine Biology/*methods ; *Phylogeny ; },
abstract = {Morphology-based profiling of benthic communities has been extensively applied to aquatic ecosystems' health assessment. However, it remains a low-throughput, and sometimes ambiguous, procedure. Despite DNA metabarcoding has been applied to marine benthos, a comprehensive approach providing species-level identifications for estuarine macrobenthos is still lacking. Here we report a combination of experimental and field studies to assess the aptitude of COI metabarcoding to provide robust species-level identifications for high-throughput monitoring of estuarine macrobenthos. To investigate the ability of metabarcoding to detect all species present in bulk DNA extracts, we contrived three phylogenetically diverse communities, and applied four different primer pairs to generate PCR products within the COI barcode region. Between 78-83% of the species in the contrived communities were recovered through HTS. Subsequently, we compared morphology and metabarcoding-based approaches to determine the species composition from four distinct estuarine sites. Our results indicate that species richness would be considerably underestimated if only morphological methods were used: globally 27 species identified through morphology versus 61 detected by metabarcoding. Although further refinement is required to improve efficiency and output of this approach, here we show the great aptitude of COI metabarcoding to provide high quality and auditable species identifications in estuarine macrobenthos monitoring.},
}
@article {pmid29141868,
year = {2018},
author = {Wu, C and Espinoza, DA and Koelle, SJ and Potter, EL and Lu, R and Li, B and Yang, D and Fan, X and Donahue, RE and Roederer, M and Dunbar, CE},
title = {Geographic clonal tracking in macaques provides insights into HSPC migration and differentiation.},
journal = {The Journal of experimental medicine},
volume = {215},
number = {1},
pages = {217-232},
pmid = {29141868},
issn = {1540-9538},
mesh = {Animals ; Biomarkers ; Bone Marrow ; Bone Marrow Cells/cytology/metabolism ; *Cell Differentiation ; Cell Lineage ; *Cell Movement ; *Cell Tracking/methods ; Cellular Microenvironment ; *Clonal Evolution ; *Hematopoiesis ; Hematopoietic Stem Cell Transplantation ; Hematopoietic Stem Cells/*cytology/*metabolism ; Immunophenotyping ; Lymph Nodes/cytology/metabolism ; Macaca mulatta ; Time Factors ; },
abstract = {The geographic distribution of hematopoiesis at a clonal level is of interest in understanding how hematopoietic stem and progenitor cells (HSPCs) and their progeny interact with bone marrow (BM) niches during regeneration. We tagged rhesus macaque autologous HSPCs with genetic barcodes, allowing clonal tracking over time and space after transplantation. We found marked geographic segregation of CD34[+] HSPCs for at least 6 mo posttransplantation, followed by very gradual clonal mixing at different BM sites over subsequent months to years. Clonal mapping was used to document local production of granulocytes, monocytes, B cells, and CD56[+] natural killer (NK) cells. In contrast, CD16[+]CD56[-] NK cells were not produced in the BM, and in fact were clonally distinct from multipotent progenitors producing all other lineages. Most surprisingly, we documented local BM production of CD3[+] T cells early after transplantation, using both clonal mapping and intravascular versus tissue-resident T cell staining, suggesting a thymus-independent T cell developmental pathway operating during BM regeneration, perhaps before thymic recovery.},
}
@article {pmid29139259,
year = {2017},
author = {Xu, Y and Lu, Y and Wu, HP and Bu, Y},
title = {[Progress in molecular identification of snake drugs].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {42},
number = {15},
pages = {2930-2933},
doi = {10.19540/j.cnki.cjcmm.20170714.006},
pmid = {29139259},
issn = {1001-5302},
mesh = {Animals ; Biological Products/pharmacology ; *DNA Barcoding, Taxonomic ; *Medicine, Chinese Traditional ; Polymerase Chain Reaction ; Random Amplified Polymorphic DNA Technique ; *Snakes ; },
abstract = {Snake drugs have high values in clinical medication for anti-inflammatory, analgesia activities and dredging collaterals. However, owing to their deficient resource and substantial profit, many counterfeits for snake drugs have appeared on the market. Traditional methods for Chinese medicine authentication include identification of origin, morphology identification, microscopy and physiochemical identification. But these methods are restricted in application because of their high morphological requirement for specimens, complex process for assays and indeterminate results guided by subjective. With the development of molecular biology and molecular genetic techniques, new theories and technologies for molecular detection have been introduced to the authentication of Chinese medicine, such as RAPD, specific PCR amplification, DNA barcoding analysis and so on, improved the authentication system of Chinese medicine. Here, we will give a brief review of molecular detection methods for snake drugs authentication.},
}
@article {pmid29138618,
year = {2017},
author = {Lee, JS and Lee, HB and Shin, HD and Choi, YJ},
title = {Diversity, Phylogeny, and Host-Specialization of Hyaloperonospora Species in Korea.},
journal = {Mycobiology},
volume = {45},
number = {3},
pages = {139-149},
pmid = {29138618},
issn = {1229-8093},
abstract = {The genus Hyaloperonospora (Peronosporaceae; Oomycota) is an obligate biotrophic group that causes downy mildew disease on the Brassicaceae and allied families of Brassicales, including many economically relevant crops, such as broccoli, cabbage, radish, rape, and wasabi. To investigate the diversity of Hyaloperonospora species in northeast Asia, we performed a morphological analysis for the dried herbarium specimens collected in Korea, along with molecular phylogenetic inferences based on internal transcribed spacer rDNA and cox2 mtDNA sequences. It was confirmed that 14 species of Hyaloperonospora exist in Korea. Of these, three species, previously classified under the genus Peronospora, were combined to Hyaloperonospora: H. arabidis-glabrae comb. nov. (ex Arabis glabra), H. nasturtii-montani comb. nov. (ex Rorippa indica), and H. nasturtii-palustris comb. nov. (ex Rorippa palustris). In addition, finding two potentially new species specific to northeast Asian plants is noteworthy in support of the view that the species abundance of Hyaloperonospora has been underestimated hitherto.},
}
@article {pmid29137957,
year = {2018},
author = {Saunders, GW and Jackson, C and Salomaki, ED},
title = {Phylogenetic analyses of transcriptome data resolve familial assignments for genera of the red-algal Acrochaetiales-Palmariales Complex (Nemaliophycidae).},
journal = {Molecular phylogenetics and evolution},
volume = {119},
number = {},
pages = {151-159},
doi = {10.1016/j.ympev.2017.11.002},
pmid = {29137957},
issn = {1095-9513},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic ; DNA, Intergenic/genetics ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Rhodophyta/*classification/*genetics ; Transcriptome/*genetics ; },
abstract = {Phylogenetic analyses of transcriptome data for representatives of the red algal Acrochaetiales-Palmariales Complex provided robust support for the assignment of genera to the constituent families. In the Acrochaetiales, the genera Acrochaetium, Grania, and an unnamed genus-level lineage (Acrochaetiac sp._1Aus) were assigned to the Acrochaetiaceae, while Audouinella is placed in a resurrected Audouinellaceae and Rhodochorton and Rhododrewia constitute the resurrected Rhodochortonaceae. For the Palmariales, transcriptome data solidly support the inclusion of Camontagnea and Rhodothamniella in the Rhodothamniellaceae, Meiodiscus and Rubrointrusa in the Meiodiscaceae, Rhodonematella and Rhodophysema in the Rhodophysemataceae, while Devaleraea and Palmaria remained in the Palmariaceae. These analyses, however, questioned the monophyly of Palmaria, which prompted a second round of analyses using eight common red algal phylogenetic markers and including a broader sampling of red algal genera in our analyses. These results supported transfer of Palmaria callophylloides and P. mollis to the genus Devaleraea necessitating new combinations, and further added the genus Halosaccion to the Palmariaceae and the genera Kallymenicola and Rhodophysemopsis to the Meiodiscaceae. Finally, DNA barcode (mitochondrial COI-5P) and ITS data were explored and supported the continued recognition of Palmaria palmata as a single species in the North Atlantic.},
}
@article {pmid29134141,
year = {2017},
author = {Yoon, TH and Kang, HE and Lee, SR and Lee, JB and Baeck, GW and Park, H and Kim, HW},
title = {Metabarcoding analysis of the stomach contents of the Antarctic Toothfish (Dissostichus mawsoni) collected in the Antarctic Ocean.},
journal = {PeerJ},
volume = {5},
number = {},
pages = {e3977},
pmid = {29134141},
issn = {2167-8359},
abstract = {Stomach contents of the Antarctic toothfish, Dissostichus mawsoni, collected from subareas 58.4 and 88.3, were analyzed using next generation sequencing (NGS) technology. After processing the raw reads generated by the MiSeq platform, a total of 131,233 contigs (130 operational taxonomic units [OTUs]) were obtained from 163 individuals in subarea 58.4, and 75,961 contigs (105 OTUs) from 164 fish in subarea 88.3. At 98% sequence identity, species names were assigned to most OTUs in this study, indicating the quality of the DNA barcode database for the Antarctic Ocean was sufficient for molecular analysis, especially for fish species. A total of 19 species was identified from the stomach of D. mawsoni in this study, which included 14 fish species and five mollusks. More than 90% of contigs belonged to fish species, supporting the postulate that the major prey of D. mawsoni are fish. Two fish species, Macrourus whitsoni and Chionobathyscus dewitti, were the most important prey items (a finding similar to that of previous studies). We also obtained genotypes of prey items by NGS analysis, identifying an additional 17 representative haplotypes in this study. Comparison with three previous morphological studies and the NGS-based molecular identification in this study extended our knowledge regarding the prey of D. mawsoni, which previously was not possible. These results suggested that NGS-based diet studies are possible, if several current technical limitations, including the quality of the barcode database or the development of precise molecular quantification techniques to link them with morphological values, are overcome. To achieve this, additional studies should be conducted on various marine organisms.},
}
@article {pmid29134072,
year = {2017},
author = {Soler-Membrives, A and Linse, K and Miller, KJ and Arango, CP},
title = {Genetic signature of Last Glacial Maximum regional refugia in a circum-Antarctic sea spider.},
journal = {Royal Society open science},
volume = {4},
number = {10},
pages = {170615},
pmid = {29134072},
issn = {2054-5703},
abstract = {The evolutionary history of Antarctic organisms is becoming increasingly important to understand and manage population trajectories under rapid environmental change. The Antarctic sea spider Nymphon australe, with an apparently large population size compared with other sea spider species, is an ideal target to look for molecular signatures of past climatic events. We analysed mitochondrial DNA of specimens collected from the Antarctic continent and two Antarctic islands (AI) to infer past population processes and understand current genetic structure. Demographic history analyses suggest populations survived in refugia during the Last Glacial Maximum. The high genetic diversity found in the Antarctic Peninsula and East Antarctic (EA) seems related to multiple demographic contraction-expansion events associated with deep-sea refugia, while the low genetic diversity in the Weddell Sea points to a more recent expansion from a shelf refugium. We suggest the genetic structure of N. australe from AI reflects recent colonization from the continent. At a local level, EA populations reveal generally low genetic differentiation, geographically and bathymetrically, suggesting limited restrictions to dispersal. Results highlight regional differences in demographic histories and how these relate to the variation in intensity of glaciation-deglaciation events around Antarctica, critical for the study of local evolutionary processes. These are valuable data for understanding the remarkable success of Antarctic pycnogonids, and how environmental changes have shaped the evolution and diversification of Southern Ocean benthic biodiversity.},
}
@article {pmid29134041,
year = {2017},
author = {Schmidt, O and Hausmann, A and Cancian de Araujo, B and Sutrisno, H and Peggie, D and Schmidt, S},
title = {A streamlined collecting and preparation protocol for DNA barcoding of Lepidoptera as part of large-scale rapid biodiversity assessment projects, exemplified by the Indonesian Biodiversity Discovery and Information System (IndoBioSys).},
journal = {Biodiversity data journal},
volume = {},
number = {5},
pages = {e20006},
pmid = {29134041},
issn = {1314-2828},
abstract = {Here we present a general collecting and preparation protocol for DNA barcoding of Lepidoptera as part of large-scale rapid biodiversity assessment projects, and a comparison with alternative preserving and vouchering methods. About 98% of the sequenced specimens processed using the present collecting and preparation protocol yielded sequences with more than 500 base pairs. The study is based on the first outcomes of the Indonesian Biodiversity Discovery and Information System (IndoBioSys). IndoBioSys is a German-Indonesian research project that is conducted by the Museum für Naturkunde in Berlin and the Zoologische Staatssammlung München, in close cooperation with the Research Center for Biology - Indonesian Institute of Sciences (RCB-LIPI, Bogor).},
}
@article {pmid29134040,
year = {2017},
author = {Schmid-Egger, C and van Achterberg, K and Neumeyer, R and Jérôme Morinière, and Schmidt, S},
title = {Revision of the West Palaearctic Polistes Latreille, with the descriptions of two species - an integrative approach using morphology and DNA barcodes (Hymenoptera, Vespidae).},
journal = {ZooKeys},
volume = {},
number = {713},
pages = {53-112},
pmid = {29134040},
issn = {1313-2989},
abstract = {The genus Polistes is revised for the West Palaearctic region based on morphology and DNA barcodes. The revision includes all known West Palaearctic species, raising the number of species in Europe to 14 and to 17 for the West Palaearctic realm. DNA barcodes were recovered from 15 species, 14 of which belong to the subgenus Polistes, and one, P. wattii, to the subgenus Gyrostoma. An integrative taxonomic approach combining morphology and molecular data (DNA barcoding) was employed to resolve longstanding taxonomic problems in this group. Two species, P. austroccidentalis van Achterberg &amp; Neumeyer, sp. n. (= P. semenowi auctt.) from W and SW Europe and P. maroccanus Schmid-Egger, sp. n. from Morocco are described as new. Polistes bucharensis Erichson, 1849, and P. foederatus Kohl, 1898, were restored from synonymy. The following new synonyms are proposed: P. sulcifer Zimmermann, 1930, and Pseudopolistes sulcifer var. similator Zirngiebl, 1955, under P. semenowi Morawitz, 1889, syn. n.; Polistes iranus Guiglia, 1976, Polistes gallica var. ornata Weyrauch, 1938 and Polistes gallicus muchei Gusenleitner, 1976, under P. bucharensis Erichson, 1849, syn. n.; Polistes omissus var. ordubadensis Zirngiebl, 1955, and P. hellenicus Arens, 2011, under Polistes mongolicus du Buysson, 1911, syn. n. An illustrated key includes all species and additionally three species from the subgenera Aphanilopterus Meunier, 1888 and Gyrostoma Kirby, 1828 (including a Nearctic species recently introduced to Spain and two species occurring in Egypt, the Arabian Peninsula, and SW Asia). A phylogenetic analysis using Bayesian inference provides insights into phylogenetic relationships within the genus Polistes.},
}
@article {pmid29134033,
year = {2017},
author = {Matson, T and Wagner, DL},
title = {A New Cryptic Lactura from Texas (Lepidoptera, Zygaenoidea, Lacturidae).},
journal = {ZooKeys},
volume = {},
number = {711},
pages = {141-150},
pmid = {29134033},
issn = {1313-2989},
abstract = {A new species of Lactura is described from Texas: Lactura rubritegulasp. n. Identity of the new species can be reliably determined by both larval and adult characters, CO1 haplotypes, and its late-spring period of flight activity. Male genitalic features overlap with those of L. basistriga (Barnes &amp; McDunnough, 1913), whereas female structures differ markedly between the pair. The new Sideroxylon-feeding species, rare in collections, is found principally in limestone areas in the vicinity San Antonio, Texas, westward through the southern Hill Country. We illustrate the adult and larval stages and male and female genitalia, review available DNA barcode data that support the recognition of the new Lactura, and briefly characterize its life history.},
}
@article {pmid29134001,
year = {2017},
author = {Zhao, H and Yang, J and Wang, C and Li, P and Murphy, RW and Che, J and Yuan, Z},
title = {A new species of the genus Rana from Henan, central China (Anura, Ranidae).},
journal = {ZooKeys},
volume = {},
number = {694},
pages = {95-108},
pmid = {29134001},
issn = {1313-2989},
abstract = {A new species of brown frog Rana luanchuanensis Zhao &amp; Yuan, sp. n. is described from Luanchuan County, western Henan, central China. The mitochondrial genealogy suggests that the new species is the sister taxon to the clade including R. amurensis and R. coreana, and is separated by uncorrected pairwise distances more than 12.5%. Morphologically, this new species differs from its congeners by a suite of characters. Analyses of partial sequences of cytochrome oxidase subunit I (COI) resolve the new species as a single matriline.},
}
@article {pmid29133989,
year = {2017},
author = {Skowron Volponi, MA and Volponi, P},
title = {A new species of wasp-mimicking clearwing moth from Peninsular Malaysia with DNA barcode and behavioural notes (Lepidoptera, Sesiidae).},
journal = {ZooKeys},
volume = {},
number = {692},
pages = {129-139},
pmid = {29133989},
issn = {1313-2989},
abstract = {A new species of clearwing moth, Pyrophleps ellawi Skowron Volponi, sp. n., is described from Peninsular Malaysia. Information on the habitat, time and conditions of occurrence, flight and mud-puddling behaviour, functional morphology, and DNA barcode are also provided. Photographs and a supplementary video from the wild demonstrate the postures and behaviour of this species of Pyrophleps, whose remaining members were described only on the basis of pinned specimens. This is the first record of this genus in Peninsular Malaysia.},
}
@article {pmid29131846,
year = {2017},
author = {Deichmann, JL and Mulcahy, DG and Vanthomme, H and Tobi, E and Wynn, AH and Zimkus, BM and McDiarmid, RW},
title = {How many species and under what names? Using DNA barcoding and GenBank data for west Central African amphibian conservation.},
journal = {PloS one},
volume = {12},
number = {11},
pages = {e0187283},
pmid = {29131846},
issn = {1932-6203},
mesh = {Africa, Central ; Amphibians/classification/*genetics ; Animals ; *Conservation of Natural Resources ; *DNA Barcoding, Taxonomic ; Species Specificity ; Uncertainty ; },
abstract = {Development projects in west Central Africa are proceeding at an unprecedented rate, often with little concern for their effects on biodiversity. In an attempt to better understand potential impacts of a road development project on the anuran amphibian community, we conducted a biodiversity assessment employing multiple methodologies (visual encounter transects, auditory surveys, leaf litter plots and pitfall traps) to inventory species prior to construction of a new road within the buffer zone of Moukalaba-Doudou National Park, Gabon. Because of difficulties in morphological identification and taxonomic uncertainty of amphibian species observed in the area, we integrated a DNA barcoding analysis into the project to improve the overall quality and accuracy of the species inventory. Based on morphology alone, 48 species were recognized in the field and voucher specimens of each were collected. We used tissue samples from specimens collected at our field site, material available from amphibians collected in other parts of Gabon and the Republic of Congo to initiate a DNA barcode library for west Central African amphibians. We then compared our sequences with material in GenBank for the genera recorded at the study site to assist in identifications. The resulting COI and 16S barcode library allowed us to update the number of species documented at the study site to 28, thereby providing a more accurate assessment of diversity and distributions. We caution that because sequence data maintained in GenBank are often poorly curated by the original submitters and cannot be amended by third-parties, these data have limited utility for identification purposes. Nevertheless, the use of DNA barcoding is likely to benefit biodiversity inventories and long-term monitoring, particularly for taxa that can be difficult to identify based on morphology alone; likewise, inventory and monitoring programs can contribute invaluable data to the DNA barcode library and the taxonomy of complex groups. Our methods provide an example of how non-taxonomists and parataxonomists working in understudied parts of the world with limited geographic sampling and comparative morphological material can use DNA barcoding and publicly available sequence data (GenBank) to rapidly identify the number of species and assign tentative names to aid in urgent conservation management actions and contribute to taxonomic resolution.},
}
@article {pmid29130757,
year = {2017},
author = {Adamowicz, SJ and Hollingsworth, PM and Ratnasingham, S and van der Bank, M},
title = {International Barcode of Life: Focus on big biodiversity in South Africa.},
journal = {Genome},
volume = {60},
number = {11},
pages = {875-879},
doi = {10.1139/gen-2017-0210},
pmid = {29130757},
issn = {1480-3321},
mesh = {Animals ; *Biodiversity ; Computational Biology ; Congresses as Topic ; Conservation of Natural Resources ; *DNA Barcoding, Taxonomic ; *Evolution, Molecular ; High-Throughput Nucleotide Sequencing ; Lepidoptera/genetics ; Phylogeography ; Plants, Medicinal/genetics ; South Africa ; },
abstract = {Participants in the 7th International Barcode of Life Conference (Kruger National Park, South Africa, 20-24 November 2017) share the latest findings in DNA barcoding research and its increasingly diversified applications. Here, we review prevailing trends synthesized from among 429 invited and contributed abstracts, which are collated in this open-access special issue of Genome. Hosted for the first time on the African continent, the 7th Conference places special emphasis on the evolutionary origins, biogeography, and conservation of African flora and fauna. Within Africa and elsewhere, DNA barcoding and related techniques are being increasingly used for wildlife forensics and for the validation of commercial products, such as medicinal plants and seafood species. A striking trend of the conference is the dramatic rise of studies on environmental DNA (eDNA) and on diverse uses of high-throughput sequencing techniques. Emerging techniques in these areas are opening new avenues for environmental biomonitoring, managing species-at-risk and invasive species, and revealing species interaction networks in unprecedented detail. Contributors call for the development of validated community standards for high-throughput sequence data generation and analysis, to enable the full potential of these methods to be realized for understanding and managing biodiversity on a global scale.},
}
@article {pmid29118941,
year = {2017},
author = {Salehi, R and Haghighi, A and Stensvold, CR and Kheirandish, F and Azargashb, E and Raeghi, S and Kohansal, C and Bahrami, F},
title = {Prevalence and subtype identification of Blastocystis isolated from humans in Ahvaz, Southwestern Iran.},
journal = {Gastroenterology and hepatology from bed to bench},
volume = {10},
number = {3},
pages = {235-241},
pmid = {29118941},
issn = {2008-2258},
abstract = {AIM: The aim of the present study was to determine the prevalence and subtype distribution of Blastocystis and its relation with demographic data and symptoms in humans referred to medical centers in Ahvaz 2014-2015.<br><br>BACKGROUND: Infections with intestinal parasites are one of the most important threats to human health worldwide, especially in tropical and subtropical areas. Blastocystis sp. is a common parasite of humans with a vast variety of non-human hosts. We aimed to study the prevalence and subtypes of Blastocystis sp. in individuals referred to medical laboratories in Ahvaz city, southwest Iran.<br><br>METHODS: From September 2014 to September 2015, 618 stool samples were collected from 16 medical laboratories in Ahvaz, and examined using direct wet mount, formalin-ether concentration, a modified version of the Ziehl-Neelsen staining technique, and cultivation in xenic HSr + S medium. Subtypes of positive Blastocysts sp. were obtained using the "barcoding" method. The results were analyzed using SPSS software, version 16, with Chi-square and Fisher's exact test.<br><br>RESULTS: Totally, 325 (52.6%) of the referred individuals were men and 293 (47.4%) were women. Blastocystis sp. was observed in 146 (23.6%) samples. Co-infections with other intestinal parasites were found in 32 (5.17%) cases. Out of the 146 positive isolates, 20.83%, 20.83% and 58.34% belonged to ST1, ST2, ST3 respectively.<br><br>CONCLUSION: Blastocystis sp. was quite common in the study population, with a carrier rate corresponding to nearly one in every four individuals. The subtype distribution identified in the present study was largely identical to that reported from other studies in Iran, with ST3 being the most common.},
}
@article {pmid29118779,
year = {2017},
author = {Song, Y and Chen, Y and Lv, J and Xu, J and Zhu, S and Li, M and Chen, N},
title = {Development of Chloroplast Genomic Resources for Oryza Species Discrimination.},
journal = {Frontiers in plant science},
volume = {8},
number = {},
pages = {1854},
pmid = {29118779},
issn = {1664-462X},
abstract = {Rice is the most important crop in the world as the staple food for over half of the population. The wild species of Oryza represent an enormous gene pool for genetic improvement of rice cultivars. Accurate and rapid identification of these species is critical for effective utilization of the wild rice germplasm. In this study, we developed valuable chloroplast molecular markers by comparing the chloroplast genomes for species identification. Four chloroplast genomes of Oryza were newly sequenced on the Illumina HiSeq platform and other 14 Oryza species chloroplast genomes from Genbank were simultaneously taken into consideration for comparative analyses. Among 18 Oryza chloroplast genomes, five variable regions (rps16-trnQ, trnTEYD, psbE-petL, rpoC2 and rbcL-accD) were detected for DNA barcodes, in addition to differences in simple sequence repeats (SSR) and repeat sequences. The highest species resolution (72.22%) was provided by rpoC2 and rbcL-accD with distance-based methods. Three-marker combinations (rps16-trnQ + trnTEYD + rbcL-accD, rps16-trnQ + trnTEYD + rpoC2 and rpoC2 + trnTEYD + psbE-petL) showed the best species resolution (100%). Phylogenetic analysis based on the chloroplast genome provided the best resolution of Oryza. In the comparison of chloroplast genomes in this study, identification of the most variable regions and assessment of the focal regions of divergence were efficient in developing species-specific DNA barcodes. Based on evaluation of the chloroplast genomic resources, we conclude that chloroplast genome sequences are a reliable and valuable molecular marker for exploring the wild rice genetic resource in rice improvement.},
}
@article {pmid29118648,
year = {2017},
author = {Zúñiga, JD and Gostel, MR and Mulcahy, DG and Barker, K and Asia Hill, and Sedaghatpour, M and Vo, SQ and Funk, VA and Coddington, JA},
title = {Data Release: DNA barcodes of plant species collected for the Global Genome Initiative for Gardens Program, National Museum of Natural History, Smithsonian Institution.},
journal = {PhytoKeys},
volume = {},
number = {88},
pages = {119-122},
pmid = {29118648},
issn = {1314-2011},
abstract = {The Global Genome Initiative has sequenced and released 1961 DNA barcodes for genetic samples obtained as part of the Global Genome Initiative for Gardens Program. The dataset includes barcodes for 29 plant families and 309 genera that did not have sequences flagged as barcodes in GenBank and sequences from officially recognized barcoding genetic markers meet the data standard of the Consortium for the Barcode of Life. The genetic samples were deposited in the Smithsonian Institution's National Museum of Natural History Biorepository and their records were made public through the Global Genome Biodiversity Network's portal. The DNA barcodes are now available on GenBank.},
}
@article {pmid29118627,
year = {2017},
author = {Ding, JH and Sun, JL and Zhang, X},
title = {A new species of the water mite genus Sperchon Kramer, 1877 from China, with identifying Sperchon rostratus Lundblad, 1969 through DNA barcoding (Acari, Hydrachnidia, Sperchontidae).},
journal = {ZooKeys},
volume = {},
number = {707},
pages = {47-61},
pmid = {29118627},
issn = {1313-2989},
abstract = {A new species of the water mite genus Sperchon Kramer, 1877 from China, Sperchon fuxiensis Zhang, sp. n., is described and illustrated in this article. DNA barcoding for the new species is documented for future use. Descriptions of both male and female of Sperchon rostratus Lundblad, 1969 are given in the present study, and DNA barcoding for identifying S. rostratus is also discussed.},
}
@article {pmid29118620,
year = {2017},
author = {Syromyatnikov, MY and Golub, VB and Kokina, AV and Victoria A Soboleva, and Popov, VN},
title = {DNA barcoding and morphological analysis for rapid identification of most economically important crop-infesting Sunn pests belonging to Eurygaster Laporte, 1833 (Hemiptera, Scutelleridae).},
journal = {ZooKeys},
volume = {},
number = {706},
pages = {51-71},
pmid = {29118620},
issn = {1313-2989},
abstract = {The genus Eurygaster Laporte, 1833 includes ten species five of which inhabit the European part of Russia. The harmful species of the genus is E. integriceps. Eurygaster species identification based on the morphological traits is very difficult, while that of the species at the egg or larval stages is extremely difficult or impossible. Eurygaster integriceps, E. maura, and E. testudinaria differ only slightly between each other morphologically, E. maura and E. testudinaria being almost indiscernible. DNA barcoding based on COI sequences have shown that E. integriceps differs significantly from these closely related species, which enables its rapid and accurate identification. Based on COI nucleotide sequences, three species of Sunn pests, E. maura, E. testudinarius, E. dilaticollis, could not be differentiated from each other through DNA barcoding. The difference in the DNA sequences between the COI gene of E. integriceps and COI genes of E. maura and E. testudinarius was more than 4%. In the present study DNA barcoding of two Eurygaster species was performed for the first time on E. integriceps, the most dangerous pest in the genus, and E. dilaticollis that only inhabits natural ecosystems. The PCR-RFLP method was developed in this work for the rapid identification of E. integriceps.},
}
@article {pmid29118612,
year = {2017},
author = {Cecchetto, M and Alvaro, MC and Ghiglione, C and Guzzi, A and Mazzoli, C and Piazza, P and Schiaparelli, S},
title = {Distributional records of Antarctic and sub-Antarctic Ophiuroidea from samples curated at the Italian National Antarctic Museum (MNA): check-list update of the group in the Terra Nova Bay area (Ross Sea) and launch of the MNA 3D model 'virtual gallery'.},
journal = {ZooKeys},
volume = {},
number = {705},
pages = {61-79},
pmid = {29118612},
issn = {1313-2989},
abstract = {The distributional records of Ophiuroidea stored at the Italian National Antarctic Museum (MNA, Section of Genoa) are presented, corresponding to 1595 individuals that belong to 35 species and 17 genera. Specimens were collected in 106 different sampling stations at depths ranging from 21 to 1652 m in the framework of 14 Antarctic expeditions to the Ross Sea, one to the Antarctic Peninsula, and one to the Falkland Islands (Islas Malvinas). Three species, Amphiura joubini Koehler, 1912, Amphiura (Amphiura) angularis Lyman, 1879, and Ophiura flexibilis (Koehler, 1911), are reported as new records for the Terra Nova Bay area, whose check-list of species increases from 15 to 18 species. The determination of these three new records was based both on morphological identification and molecular analyses (COI barcoding). Some of the genetically characterised specimens were also documented through photogrammetry and micro-computed tomography and represent the first bulk of 3D models that will be available through the MNA and Sketchfab websites, both for research and educational purposes.},
}
@article {pmid29118610,
year = {2017},
author = {Hou, Z and Zhao, S},
title = {A new terrestrial talitrid genus, Myanmarorchestia, with two new species from Myanmar (Crustacea, Amphipoda, Talitridae).},
journal = {ZooKeys},
volume = {},
number = {705},
pages = {15-39},
pmid = {29118610},
issn = {1313-2989},
abstract = {Myanmarorchestia Hou, gen. n. with two new species is described from terrestrial habitats in Myanmar. This new genus is characterised by 4-dentate lacinia on left mandible, simple gnathopod I in both sexes, weakly chelate gnathopod II in male, simplidactylate pereopods and complex and lobed gills. Myanmarorchestia peterjaegeri Hou, sp. n. closely resembles M. seabri Hou, sp. n. in gnathopod II merus and carpus protuberant on posterior margin; however, the former is distinguished from the latter by palp of maxilla I with two articles, coxal gills convoluted, and telson with nicks on surface. Additionally, DNA barcodes of the new species are obtained to confirm their distinctiveness.},
}
@article {pmid30451437,
year = {2017},
author = {Munawar, M and Powers, TO and Tian, Z and Harris, T and Higgins, R and Zheng, J},
title = {Description and Distribution of Three Criconematid Nematodes from Hangzhou, Zhejiang Province, China.},
journal = {Journal of nematology},
volume = {50},
number = {1},
pages = {1-24},
pmid = {30451437},
issn = {0022-300X},
abstract = {Populations of Criconemoides parvus , Discocriconemella hengsungica , and Discocriconemella limitanea , isolated in Hangzhou, China from the rhizosphere soil of woody perennials were characterized morphologically and molecularly. The morphometric data of the Chinese populations were compared with populations from other regions of the world. DNA barcoding with the mitochondrial COI gene confirmed conspecificity of Chinese and Costa Rican populations of D. limitanea . Phylogenetic assessment using a near full-length 18S ribosomal DNA sequence provided weak support for a grouping of Criconemoides parvus from China and C. annulatus from western North America. The phylogenetic position of D. hengsungica from China and an unknown species of Discocriconemella from Thailand relative to D. limitanea suggests that the genus Discocriconemella is not monophyletic. The study provides the first record of D. hengsungica in China and confirms the presence of C. parvus previously reported from China. Biogeographic implications of these nematode distributions are discussed.},
}
@article {pmid30308626,
year = {2017},
author = {Garg, S and Biju, SD},
title = {Description of four new species of Burrowing Frogs in the Fejervarya rufescens complex (Dicroglossidae) with notes on morphological affinities of Fejervarya species in the Western Ghats.},
journal = {Zootaxa},
volume = {4277},
number = {4},
pages = {451-490},
doi = {10.11646/zootaxa.4277.4.1},
pmid = {30308626},
issn = {1175-5334},
mesh = {Animals ; *Anura ; Breeding ; *Genes, Mitochondrial ; Homeodomain Proteins ; India ; Phylogeny ; },
abstract = {The Rufescent Burrowing Frog, Fejervarya rufescens, is thought to have a wide distribution across the Western Ghats in Peninsular India. This locally abundant but secretive species has a short breeding period, making it a challenging subject for field studies. We sampled 16 populations of frogs morphologically similar to F. rufescens in order to understand the variation among populations found across the Western Ghats. Our study shows significant morphological and genetic differences among the sampled populations, suggesting that F. 'rufescens' is a complex of several undescribed species. Using evidence from morphology and genetics, we confirm the presence of five distinct species in this group and formally describe four as new. The new species were delineated using a phylogeny based on three mitochondrial genes (16S, COI and Cytb) and a haplotype network of a nuclear gene (Rag1). Hereafter, the distribution of F. rufescens is restricted to the state of Karnataka and adjoining regions of northern Kerala. Three new species (Fejervarya kadar sp. nov., Fejervarya manoharani sp. nov. and Fejervarya neilcoxi sp. nov.) are from regions south of Palghat gap in the state of Kerala, and one (Fejervarya cepfi sp. nov.) from the northern Western Ghats state of Maharashtra. These findings indicate that Fejervarya frogs of the Western Ghats are more diverse than currently known. Our results will also have implications on the conservation status of F. rufescens, which was previously categorized as Least Concern based on its presumed wide geographical distribution. Furthermore, in order to facilitate a better taxonomic understanding of this region's fejervaryan frogs, we divide all the known Fejarvarya species of the Western Ghats into four major groups-Fejervarya nilagirica group, Fejervarya rufescens group, Fejervarya sahyadris group and Fejervarya syhadrensis group, based on their morphological affinities.},
}
@article {pmid30308647,
year = {2017},
author = {Vivero, RJ and Bejarano, EE and Estrada, LG and FlÓrez, F and Ortega-gÓmez, E and Aparicio, Y and Torres-gutiÉrrez, C and Uribe-Soto, S and Muskus-lÓpez, C},
title = {DNA barcode for identification of immature stages of sand flies (Diptera: Psychodidae) collected from natural breeding sites.},
journal = {Zootaxa},
volume = {4277},
number = {2},
pages = {228-236},
doi = {10.11646/zootaxa.4277.2.3},
pmid = {30308647},
issn = {1175-5334},
mesh = {Animals ; Breeding ; Colombia ; *DNA Barcoding, Taxonomic ; Larva ; *Psychodidae ; },
abstract = {Although phlebotomine sand flies breeding sites have been identified and recorded by several studies, the microhabitats exploited by these insects remain little-known and hard to find. In this context, the difficulty of finding immature stages, and the limited number of taxonomic studies to identify immature stages of phlebotomine sand flies, are considered the major obstacles when attempting a complete inventory of Lutzomyia species. The objective of this study is to validate Cytochrome Oxidase I (Barcode region) as a marker for the identification of immature stages of Lutzomyia species recovered from natural breeding sites in Colombia. Among 142 collected sand flies, 18 immature individuals that did not complete their life cycle were identified to species level through sequencing of the COI gene. Values of K2P genetic distance between 0.002-0.031 allowed the identification of larvae at species level. The bootstrap support values (96%) in the Neighbor-Joining dendrogram were consistent for the majority of the established MOTUS of Lutzomyia atroclavata, Lutzomyia micropyga, Lutzomyia serrana, Lutzomyia cayennensis, Lutzomyia rangeliana, Lutzomyia shannoni and some species of the genus Brumptomyia. The COI gene is validated as a marker for the identification of immature stages of the genus Lutzomyia.},
}
@article {pmid29741007,
year = {2017},
author = {Wang, ML and Jia, Y and Cui, JL and Wang, JH},
title = {[Ecological distribution and genetic relation of endophytic fungi in Cynomorium songaricum and its host Nitraria tangutorum].},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {28},
number = {3},
pages = {815-820},
doi = {10.13287/j.1001-9332.201703.008},
pmid = {29741007},
issn = {1001-9332},
mesh = {Biodiversity ; *Cynomorium ; Ecology ; Endophytes ; *Fungi ; Magnoliopsida ; *Phylogeny ; },
abstract = {This is the first report of the distribution and genetic relationships of endophytic fungi from the parasitic plant Cynomorium songaricum and its host Nitraria tangutorum. Endophytic fungi from the root of natural N. tangutorum, parasitic plant C. songaricum and its host N. tangutorum were isolated by tissue culture, and they were identified by morphology combined with molecular barcoding based on ITS-rDNA sequence. The isolation rates, colonization rates, isolation frequency, diversity index, evenness index, similarity coefficient and genetic relationships among fungal taxa were estimated by phylogenetic analysis, and differences in fungal endophyte distribution were investigated. The results showed that a total of 49 isolates were obtained belonging to 18 different taxa. 95.9% of these taxa were in Ascomycota, and the remaining was in Basidiomycota (4.1%). The isolation rate and colonization rate of endophytic fungi were 15.3% and 25.0%, respectively. The Shannon biodiversity index was the highest in the root of natural N. tangutorum at 2.13. The simila-rity coefficient was highest between the stem of C. songaricum and the flower of C. songaricum at0.50. Fusarium was the dominant genus in N. tangutorum, while Penicillium was the primary genus in C. songaricum. The differential distribution of fungal taxa between N. tangutorum and C. songaricum suggested that the parasitic relationship influences the endophytic fungal community.},
}
@article {pmid29979865,
year = {2017},
author = {Liu, XZ and Zhou, LS and Liu, JX and Jia, J and Song, JY and Shi, LC},
title = {[Identification of water buffalo horn and its adulterants using COI barcode].},
journal = {Yao xue xue bao = Acta pharmaceutica Sinica},
volume = {52},
number = {3},
pages = {494-499},
pmid = {29979865},
issn = {0513-4870},
mesh = {Animals ; Biological Products/*chemistry ; Buffaloes ; DNA Barcoding, Taxonomic ; Drugs, Chinese Herbal/*chemistry ; Horns/*chemistry ; Medicine, Chinese Traditional ; },
abstract = {Bubali cornu (water buffalo horn) has been used as the substitute for Cornu rhinoceri asiatici (rhino horn) in clinical applications, and is the essential ingredient of Angong Niuhuang Wan. In recent years, there are a number of adulterants on the commercial herbal medicine markets. An efficient tool is required for species identification. In this study, 155 Bubali cornu samples have been taken from original animals and collected from commercial herbal medicine markets. 153 COI sequences have been successfully obtained from 155 samples through DNA extraction, PCR amplification, bidirectional sequencing and assembly. 93 COI sequences have been added to the DNA barcoding database of traditional Chinese animal medicine after validation using DNA barcoding GAP and tree-based methods. The species identification of the 62 commercial Bubali cornu medicines has been accomplished on the DNA barcoding system for identifying herbal medicine using the updated animal medicine database (www.tcmbarcode.cn). Except two samples failed to obtain COI sequences, 54.8% of the commercial Bubali cornu medicines were water buffalo horns and 29% were yak horns. Our results showed that yak horn was the major adulterant of Bubali cornu and the DNA barcoding method may accurately discriminate Bubali cornu and their adulterants. Therefore, we recommend that supervision on the herbal medicine markets should be strengthened with this new method to warren the effectiveness of herbal medicines.},
}
@article {pmid30134092,
year = {2017},
author = {Guo, YY and Luo, L and Zheng, XL},
title = {[Research progress on application of DNA barcoding technique in Culicidae taxonomy].},
journal = {Zhongguo ji sheng chong xue yu ji sheng chong bing za zhi = Chinese journal of parasitology &amp; parasitic diseases},
volume = {35},
number = {1},
pages = {93-98},
pmid = {30134092},
issn = {1000-7423},
mesh = {Animals ; *Culicidae ; *DNA Barcoding, Taxonomic ; },
abstract = {DNA barcoding technique is a fast and accurate method for species identification. The DNA barcoding based on cytochrome c oxidase subunit Ⅰ (COⅠ) has recently been successfully applied for species identification of Culicidae. In this paper, we introduce the technique and principle of DNA barcoding, application and limitation of the technique based on CO I gene for species identification, as well as research development on applications of other molecular makers such as COⅡ,16S RNA, and the first and the second internal transcribed spacers (ITS1 and ITS2) in species identification and to assist the COⅠ gene in identifying Culicidae species.},
}
@article {pmid29908528,
year = {2016},
author = {Jia, J and Shi, LC and Yao, H and Song, JY and Chen, SL},
title = {[Identification of Bombyx Batryticatus based on DNA barcoding technology].},
journal = {Yao xue xue bao = Acta pharmaceutica Sinica},
volume = {51},
number = {11},
pages = {1784-1790},
pmid = {29908528},
issn = {0513-4870},
mesh = {Animals ; Bombyx/*classification ; *DNA Barcoding, Taxonomic ; },
abstract = {To identify the commercial medicinal materials of Bombyx Batryticatus, two-dimensional DNA barcode was used to construct the "Internet Plus" identification system for Chinese medicine, which should benefit the cross-platform communication of DNA barcode information. Bombyx Batryticatus contained Bombyx mori Linnaeus and Beauveria bassiana (Bals.) Vuillant. Both COI and ITS sequences were obtained via PCR amplification for total genomic DNA extracted from raw materials using the animal genomic DNA kit, while only ITS but no COI sequences was obtained when using the plant genomic DNA kit. The ITS sequences obtained using the animal genomic DNA kit were consistent with those using plant genomic DNA kit. The medicinal materials yielded COI sequences and identified as B. mori. According to analysis of ITS sequences, the main species of the medicinal materials were identified as B. bassiana and few were identified as other fungi. NJ trees analysis based on ITS sequences suggests that it can be easily distinguished from other fungi. Our results showed that total genomic DNA of B. mori and B. bassiana was extracted simultaneously using the animal genomic DNA kit, which could effectively solve the problem in species identification of animal and fungi mixture materials. COI and ITS regions as DNA barcodes can stably and accurately identify Bombyx Batryticatus. The "Internet Plus" two-dimensional DNA barcode system will promote the standardization and normalization of Chinese medicinal materials market.},
}
@article {pmid30128120,
year = {2016},
author = {Kumar, A and Mishra, P and Baskaran, K and Shukla, AK and Shasany, AK and Sundaresan, V},
title = {Higher efficiency of ISSR markers over plastid psbA-trnH region in resolving taxonomical status of genus Ocimum L.},
journal = {Ecology and evolution},
volume = {6},
number = {21},
pages = {7671-7682},
pmid = {30128120},
issn = {2045-7758},
abstract = {High level of morphological as well as chemical variability exists within the genus Ocimum, and its taxonomy and phylogenetic relationships are still doubtful. For evaluating interspecific genetic relationships among the Ocimum species, genotyping with intersimple sequence repeat (ISSR) markers and sequence analyses of noncoding psbA-trnH intergenic region belonging to chloroplast DNA were carried out. Although ISSR markers are highly efficient and reproducible, they have not been used extensively in phylogenetic studies. The use of the plastidial barcode candidate was expected to provide more variable and informative insight into evolutionary rates, and was thus employed as a phylogenetic marker to assess interspecific relationships. This study revealed that the ISSR markers were more efficient than psbA-trnH sequences in resolving the current status of Ocimum L. genus. Distance- and character-based methodological approaches applied on the molecular data with biparental and maternal inheritance were used for deducing the phylogenetic relationships among Ocimum species. Average polymorphic information content (0.344) and resolving power (6.285) depicted through ISSR markers proved to be efficient in discriminating the studied species of Ocimum. The primers used in this study revealed 99.585% polymorphism across the species demonstrating the polymorphic nature of ISSR markers.},
}
@article {pmid30207653,
year = {2016},
author = {},
title = {[Identification on Five Kinds of Easily Confused Bupleurum Medicinal Materials].},
journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials},
volume = {39},
number = {9},
pages = {1975-1981},
pmid = {30207653},
issn = {1001-4454},
mesh = {*Bupleurum ; Chromatography, Thin Layer ; Drugs, Chinese Herbal ; Oleanolic Acid/analogs &amp; derivatives ; Plant Roots ; Saponins ; },
abstract = {OBJECTIVE: Macroscopic identification, thin layer chromatography(TLC) identification and molecular identification based on the Chinese Pharmacopoeia were established to identify five kinds of Bupleurum medicinal materials such as Bupleurum chinense,Bupleurum scorzonerifolium, Bupleurum marginatum, Bupleurum marginatum var. stenophyllum and Bupleurum bicaule,which were easily confused.<br><br>METHODS: According to the Chinese Pharmacopoeia,macroscopic characters of these five kinds of Bupleurum medicinal materials were observed and described; TLC identification method with saikosaponin d and control medicinal material of Bupleuri Radix as reference substances was established. Furthermore, DNA barcode was applied in identification of these confused drugs.<br><br>RESULTS: Five Bupleurum medicinal materials could be easily distinguished by their morphological characters. Moreover, TLC of Bupleurum chinense,Bupleurum scorzonerifolium, Bupleurum marginatum and Bupleurum marginatum var. stenophyllum were extremely similar while being different from that of Bupleurum bicaule. The ITS2 sequences could be used to identify the five Bupleurum medicinal materials.<br><br>CONCLUSION: The established macroscopic identification and TLC for distinguishing of the five kinds of Bupleurum medicinal materials are simple and accurate while DNA barcode technology being effective and extensive. Besides, this study provides scientific basis for the further pharmacodynamic studies on Bupleurum marginatum and Bupleurum marginatum var. stenophyllum.},
}
@article {pmid30207649,
year = {2016},
author = {Cai, X and Qiu, W and Tian, EW and Zhang, HW and Ye, HT and Chao, Z},
title = {[Identification of Original Species of Fish Maw by DNA Barcoding].},
journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials},
volume = {39},
number = {9},
pages = {1956-1959},
pmid = {30207649},
issn = {1001-4454},
mesh = {Animals ; Cluster Analysis ; DNA ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV ; Fishes ; *Phylogeny ; },
abstract = {OBJECTIVE: To identify the original species of fish maw sold in Guangzhou market by DNA barcoding technology.<br><br>METHODS: Mitochondrial cytochrome C subunit I (CO I) gene fragment of eleven fish maw samples were amplified and sequenced with the self-designed primers. UPGMA phylogenetic tree were constructed for clustering analysis. The species origin of each sample was identified with the identification engine provided in the Barcode of Life Data Systems (BOLD).<br><br>RESULTS: The self-designed primers were effective in fish maw CO I amplification and sequencing, with success rates both of 100%. BOLD identification and UPGMA clustering analysis indicated the fish maw samples were derived from five fish species of three families.<br><br>CONCLUSION: DNA barcoding combined with BOLD identification system can accurately identify the species origin of commercial fish maw.},
}
@article {pmid29518303,
year = {2016},
author = {Hodgson, G},
title = {High profile backing for GS1 drive.},
journal = {Health estate},
volume = {70},
number = {8},
pages = {24-28},
pmid = {29518303},
mesh = {Congresses as Topic ; Diffusion of Innovation ; Electronic Data Processing ; England ; *Equipment and Supplies, Hospital ; Humans ; Materials Management, Hospital/*standards ; Product Labeling ; State Medicine ; },
abstract = {At the 2016 GS1 UK Healthcare Conference in London, delegates heard from speakers including Pat Mills, the Department of Health's commercial director, on the ongoing work to embed GS1 standards throughout the NHS in England in line with the DH's eProcurement Strategy, published in April 2014. This mandated that any service or product procured by an English NHS acute Trust comply with the standards--one of the most obvious representations of which is on barcodes--'to enable Trusts to manage their non-pay spending by adopting master procurement data, automating the exchange of such data, and benchmarking their procurement against other Trusts and healthcare providers'. One of six 'demonstrator site' Trusts to provide a speaker at the 2016 GS1 UK national conference to report on their progress to date was Leeds Teaching Hospitals NHS Trust. Shortly after, HEJ editor, Jonathan Baillie, spoke to the Trust's associate director, Commercial and Procurement, Chris Slater, and to head of Healthcare at GS1 UK, Glen Hodgson.},
}
@article {pmid29368907,
year = {2016},
author = {Singh, AK and Kumar, R and Mishra, AK and Singh, M and Baisvar, VS and Chauhan, UK and Kushwaha, B and Nagpure, NS},
title = {Authentication of five Barilius species from Indian waters using DNA barcoding.},
journal = {Genetika},
volume = {52},
number = {8},
pages = {943-950},
pmid = {29368907},
issn = {0016-6758},
mesh = {Animals ; *Cyprinidae/classification/genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Fish Proteins/*genetics ; India ; },
abstract = {Authentic identification of fish species is essential for conserving them as a valuable genetic resource in our environment. DNA barcoding of living beings has become an important and ultimate tool for establishing their molecular identity. Among cyprinids, Barilius is an important genus having nearly 23 species in Indian region whose morphological identification is often difficult due to minute differences in their features. Five species collected from Indian waters and primarily identified as Opsarius bakeri (syn. Barilius bakeri), B. gatensis, B. vagra, B. bendelisis and B. ngawa were authenticated by their DNA barcoding based on mitochondrial COI gene sequences. Five individuals of each species were taken for barcode preparation by COI gene sequencing which yielded one barcode for B. ngawa, two barcodes each for O. bakeri, B. gatensis, B. bendelisis and three barcodes for B. vagra. The order of inter and intra-specific variation was estimated to know a preliminary status of variation prevailing in these cold stream fish species significant for evolution and conservation of these valued species of our ichthyofauna. Average variation within genera was found to be 13.6% with intra-specific variation ranging from 0.0% (B. ngawa) to 0.6% (B. gatensis). These distance data are in the same order found by various researchers globally using COI barcode sequences in different fish species. Phylogenetic relatedness among Barilius species and some other cyprinids validate their status of individual species as established by conventional taxonomy.},
}
@article {pmid30203943,
year = {2016},
author = {Chen, SY and Zhao, R and Xu, L and Feng, QJ and Wang, B and Kang, TQ},
title = {[DNA Barcoding of Mongolian Medicinal Plant Scutellaria scordifolia].},
journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials},
volume = {39},
number = {7},
pages = {1483-1487},
pmid = {30203943},
issn = {1001-4454},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant ; DNA, Ribosomal Spacer ; Phylogeny ; *Plants, Medicinal ; *Scutellaria ; },
abstract = {OBJECTIVE: To authenticate Scutellaria scordifolia and its closely related species using ITS2 sequence.<br><br>METHODS: Total genomic DNA was isolated from Scutellaria scordifolia and its related species. Nuclear DNA ITS2 sequences were amplified and sequenced,and ITS2 sequences of the other species of plants were obtained in Gen Bank,The Kimura 2-parameter(K2P) distances were calculated. Identification analyses were performed using Neighbor-joining(NJ) and secondary structure of ITS2 sequence methods.<br><br>RESULTS: The genetic distances of ITS2 between Scutellaria scordifolia and its closely related species were 0. 014 ~ 0. 141,which were obviously higher than those in the intra-species of Scutellaria scordifolia. The NJ tree and secondary structure of ITS2 sequence can distinguish Scutellaria scordifolia and its closely related species.<br><br>CONCLUSION: ITS2 sequence can effectively and accurately identify the Mongolian medicinal plant Scutellaria scordifolia and its closely relatives.},
}
@article {pmid30156397,
year = {2016},
author = {Yang, LY and Su, RK and Cai, YY and Ye, YH and Li, SY},
title = {[DNA Barcode Screening and Identifying for Anredera cordifolia and Its Related Species].},
journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials},
volume = {39},
number = {6},
pages = {1236-1240},
pmid = {30156397},
issn = {1001-4454},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Chloroplast ; DNA, Ribosomal Spacer ; Plants, Medicinal ; Species Specificity ; Trees ; },
abstract = {OBJECTIVE: To identify Anredera cordifolia and its closely related species using the DNA barcode.<br><br>METHODS: 28 individuals of Anredera cordifolia and its close related species were collected from different habitats. ITS and ITS2 of ribosomal DNA,matK,rbcL and psb A-trn H of chloroplast DNA were amplified and sequenced. The amplification and sequencing success rate,barcoding gap,and NJ trees were used to evaluate the efficiency of species identification.<br><br>RESULTS: After amplified and sequenced, base deletion was occurred in psb A-trnH sequences of Basella alba. The sequencing success rates of mat K,rbc L,ITS and ITS2 were 100%,100%,78. 75% and64. 28%,respectively. Among the four DNA barcoding sequences,ITS and mat K had remarkable barcoding gap. The NJ tree showed that Anredera cordifolia could differed obviously from its closely related species by ITS and mat K.<br><br>CONCLUSION: The sequences of ITS and matK provide an effective and fast tool for the identification and authentication of medicinal plant of Anredera cordifolia and its related species.},
}
@article {pmid30132632,
year = {2016},
author = {Fang, HL and Xia, CL and Duan, BZ and Li, XW},
title = {[Identification of Seeds and Seedlings of Chinese Medicinal Materials Using DNA Barcoding Technology:A Case Study in Paris polyphylla var. yunnanensis].},
journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials},
volume = {39},
number = {5},
pages = {986-990},
pmid = {30132632},
issn = {1001-4454},
mesh = {Base Sequence ; *DNA Barcoding, Taxonomic ; Gene Library ; Liliaceae ; Seedlings ; Seeds ; },
abstract = {OBJECTIVE: To establish a novel approach based on DNA barcode sequence, so as to guarantee the quality stability of Chinese medicinal materials.<br><br>METHODS: Eight species of Paris plants were collected, and a standard DNA barcode library was developed by ITS loci. Furthermore, the barcodes also used to identify the seed and seedling products that purchased from the markets.<br><br>RESULTS: ITS loci can stably and accurately distinguish Paris polyphylla var. yunnanensis and its adulterants.<br><br>CONCLUSION: The seeds and seedlings of Chinese medicinal materials need to be properly authenticated before planting,and DNA barcoding has been found to be effective for this purpose.},
}
@article {pmid29878733,
year = {2016},
author = {Ni, LH and Zhao, ZL and Xiong, B and Gaawe, D and Mi, M},
title = {[A strategy for identifying six species of Sect.Cruciata(Gentiana) in Gansu using DNA barcode sequences].},
journal = {Yao xue xue bao = Acta pharmaceutica Sinica},
volume = {51},
number = {5},
pages = {821-827},
pmid = {29878733},
issn = {0513-4870},
mesh = {China ; *DNA Barcoding, Taxonomic ; DNA, Chloroplast/genetics ; DNA, Plant/genetics ; Genetic Variation ; Gentianaceae/*classification ; Phylogeny ; Rubiaceae ; Tibet ; },
abstract = {Located in the transition zone between the Qinghai-Tibet Plateau and the Loess Plateau, Gansu province is one of the distribution centers of Sect. Cruciata, Gentiana (Gentianaceae) in China. Six species in the section, G. crassicaulis, G. straminea, G. siphonantha, G. officinalis, G. dahurica and G . macrophylla, are native to Gansu. In this paper, samples of 6 species and Halenia elliptica (outgroup) were collected. Nuclear DNA ITS, chloroplast DNA matK, rbcL, rpoC1, trnL (UAA) intron, psbA-trnH, atpB-rbcL, trnS (GCU)-trnG (UCC), rpl20-rps12 and trnL (UAA)-trnF (GAA) were sequenced from these samples. Based on the sequence analyses, high intragenomic polymorphisms were detected in ITS regions of G. crassicaulis, G. straminea, G. siphonantha, G. officinalis and G. dahurica, and they showed incomplete concerted evolution. A methodological study to identifying such close-related species as G. macrophylla, G. officinalis and G. dahurica was carried out based on the special genotypes. The results showed that 7 cp DNA sequence fragments could be used to identify G. crassicaulis, G. straminea and G. siphonantha. With nr ITS genotype II,III and IV of G. dahurica, the species can be distinguished from the close-related G. officinalis using 12 cloned sequences in a sample (with statistical significance).The cp DNA sequences of G. macrophylla were classified into two genotypes, and with genotype II, the species can be distinguished from the close-related G. officinalis and G. dahurica using 6 test samples each(with statistical significance). Furthermore, DNA barcode sequences were determined for all 6 species in Gansu. Also, the studies provide some basic data for analyses of genetic diversity and identification of Gentiana species.},
}
@article {pmid29376929,
year = {2016},
author = {Walch, G and Knapp, M and Rainer, G and Peintner, U},
title = {Colony-PCR Is a Rapid Method for DNA Amplification of Hyphomycetes.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {2},
number = {2},
pages = {},
pmid = {29376929},
issn = {2309-608X},
abstract = {Fungal pure cultures identified with both classical morphological methods and through barcoding sequences are a basic requirement for reliable reference sequences in public databases. Improved techniques for an accelerated DNA barcode reference library construction will result in considerably improved sequence databases covering a wider taxonomic range. Fast, cheap, and reliable methods for obtaining DNA sequences from fungal isolates are, therefore, a valuable tool for the scientific community. Direct colony PCR was already successfully established for yeasts, but has not been evaluated for a wide range of anamorphic soil fungi up to now, and a direct amplification protocol for hyphomycetes without tissue pre-treatment has not been published so far. Here, we present a colony PCR technique directly from fungal hyphae without previous DNA extraction or other prior manipulation. Seven hundred eighty-eight fungal strains from 48 genera were tested with a success rate of 86%. PCR success varied considerably: DNA of fungi belonging to the genera Cladosporium, Geomyces, Fusarium, and Mortierella could be amplified with high success. DNA of soil-borne yeasts was always successfully amplified. Absidia, Mucor, Trichoderma, and Penicillium isolates had noticeably lower PCR success.},
}
@article {pmid29469421,
year = {2016},
author = {Ying, J and Yi, Z and Yun-Hai, G},
title = {[Identification of two Bithynia species from Heng County, Guangxi Zhuang Autonomous Region, China by using morphological and DNA barcoding methods].},
journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control},
volume = {28},
number = {3},
pages = {284-288},
doi = {10.16250/j.32.1374.2016006},
pmid = {29469421},
issn = {1005-6661},
mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; Phylogeny ; Polymerase Chain Reaction ; Reproduction ; Snails/*classification/*genetics/physiology ; },
abstract = {OBJECTIVE: To distinguish two Bithynia species, Bithynia fuchsiana and Bithynia robusta collected from Heng County, Guangxi Zhuang Autonomous Region, by using morphological and DNA barcoding methods.<br><br>METHODS: The adult B. fuchsiana and B. robusta were collected from the biotope such as rivers, ditches and ponds in Heng County of Guangxi Zhuang Autonomous Region, China. The two species specimens were identified by measuring shell morphological parameters, comparing the characters of the male reproductive system, and using the COI gene barcoding technique and building phylogenetic tree.<br><br>RESULTS: B. fuchsiana and B. robusta were similar morphologically in the shell appearance; they had the similar snail height, snail width, shape and male reproductive structure. The DNA sequence analysis showed that the COI gene of the two Bithynia species had low sequence divergence with 11 variation sites among 22 sequences. The length of the COI gene segment was 517 bp and no insertion sites and deletion loci after sequence edited. All individuals of the two species gathered to one clade in the phylogenetic tree based on COI gene.<br><br>CONCLUSIONS: According to the evidence of morphology and COI gene coding sequence, B. fuchsiana and B. robusta from Heng County, Guangxi Zhuang Autonomous Region, are likely to be the same species.},
}
@article {pmid29859033,
year = {2016},
author = {Xiang, L and Zhang, W and Chen, SL},
title = {[Literature study and DNA barcoding of traditional Chinese medicine Qinghao(Artemisia annua L.) ].},
journal = {Yao xue xue bao = Acta pharmaceutica Sinica},
volume = {51},
number = {3},
pages = {486-495},
pmid = {29859033},
issn = {0513-4870},
mesh = {Artemisia annua/*genetics ; Artemisinins ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; *Drugs, Chinese Herbal ; Plants, Medicinal/genetics ; },
abstract = {The original plant of traditional Chinese medicine "Qinghao" is Artemisia annua L. in Chinese Pharmacopoeia. As a different plant, Artemisia carvifolia Buch.-Ham was called "Qinghao" in the Chinese medicine. The relationship of "Qinghao" and Artemisia carvifolia Buch.-Ham was confusion for a long time. In this paper, we summarizes the information of "Qinghao" which is listed in Chinese ancient books, and compared to the identification features of both A. annua and A. carvifolia. The results suggest that "Qinghao" in ancient time includes both A. annua and A. carvifolia. At present, the utilization value of A. annua is low because lack of resources and artemisinin, and most of scholars believe that the original plant of "Qinghao" is A. annua. Then, combined with DNA barcode technology, A. annua and A. carvifolia has been distinguished from each other based on morphological characteristics, phenological period and molecular characteristics.},
}
@article {pmid30121071,
year = {2016},
author = {Jiang, Y and Zhang, Y and Guo, YH},
title = {[Research Progress of DNA Barcoding Technique in Mollusca Taxonomy].},
journal = {Zhongguo ji sheng chong xue yu ji sheng chong bing za zhi = Chinese journal of parasitology &amp; parasitic diseases},
volume = {34},
number = {1},
pages = {80-83},
pmid = {30121071},
issn = {1000-7423},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV ; *Mollusca ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {DNA barcoding technique is a fast and accurate method for species identification. Currently, the barcoding using cytochrome oxidase Ⅰ(COI) gene has been successfully applied for identification of mollusca species. This paper introduces the concept, advantages and limitations of DNA barcoding, and gives an overview on its recent applications in mollusca taxonomy, particularly in classification of mollusca of medical importance. Research on COI gene sequence is also updated.},
}
@article {pmid30080350,
year = {2016},
author = {Chen, SY and Wu, YN and Xu, L and Feng, QJ and Wang, B and Kang, TG and Zhao, R},
title = {[DNA Barcoding of Mongolian Oxytropis Medicinal Materials].},
journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials},
volume = {39},
number = {2},
pages = {284-288},
pmid = {30080350},
issn = {1001-4454},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant ; DNA, Ribosomal Spacer ; *Oxytropis ; Phylogeny ; Plants, Medicinal ; Polymerase Chain Reaction ; },
abstract = {OBJECTIVE: To identify Oxytropis medicinal materials using ITS2 sequence.<br><br>METHODS: The second internal transcribed spacer(ITS2) of Oxytropis fetissovii, Oxytropis myriophylla and Oxytropis grandiflora medicinal material samples was amplified by PCR and sequenced. To expand scope of the research topic,ITS2 sequences of related species were downloaded from Gen Bank. Sequences assembly and consensus sequence generation were performed by ITS2 Database. The related data analysis and processing was performed using software MEGA 5. 10 and the NJ tree was constructed. The ITS2 secondary structure was predicted using ITS2 web server, and the differences of the ITS2 secondary structures of the samples were analyzed.<br><br>RESULTS: Oxytropis medicinal materials ITS2 sequence was shorter, with sequence length of 216 ~ 218 bp, which was in favor of DNA extraction, PCR amplification and sequencing. Genetic distances of Oxytropis myriophylla, Oxytropis fetissovii and Oxytropis grandiflora were much larger than the genetic distances of themselves. In the NJ tree, Oxytropis medicinal materials and counterfeits could be distinguished, and Oxytropis medicinal materials could be distinguished from Astragalus membranaceus.<br><br>CONCLUSION: The DNA barcode based on ITS2 sequence is a powerful and efficient tool for identification of Oxytropis medicinal materials.},
}
@article {pmid29809365,
year = {2016},
author = {Shapoval, N and Lukhtanov, V},
title = {On the Generic Position of Polyommatus avinovi (Lepidoptera: Lycaenidae).},
journal = {Folia biologica},
volume = {64},
number = {4},
pages = {267-273},
doi = {10.3409/fb64_4.267},
pmid = {29809365},
issn = {0015-5497},
mesh = {Animals ; Butterflies/anatomy &amp; histology/*classification/*genetics ; Cytochromes c/genetics ; *Phylogeny ; },
abstract = {Polyommatus avinovi (Stshetkin, 1980), an enigmatic taxon from Tajikistan has been considered in the literature either as a member of the genus Polyonimatus, or a taxon belonging to the genus Rimisia. None of the conclusions on taxonomy and nomenclature of P. avinovi were supported by molecular or cytological data, therefore the problem of identity and phylogenetic position of this taxon has remained unsolved. Here we use the barcoding fragment of the COIgene as a molecular marker to demonstrate that none of these hypotheses are true. Phylogenetic analysis revealed P. avinovi to be strongly differentiated from both Polyommatus and Rimisia. Instead, it formed a separated, well supported monophyletic clade within the genus Afarsia Korb &amp; Bolshakov, 2011. Thus, we propose the following new combinations for this butterfly: Afarsia avinovi comb. nov. and Afarsia avinovi dangara comb. nov.},
}
@article {pmid30287983,
year = {2015},
author = {Simmler, C and Chen, SN and Anderson, J and Lankin, DC and Phansalkar, R and Krause, E and Dietz, B and Bolton, JL and Nikolic, D and van Breemen, RB and Pauli, GF},
title = {Botanical Integrity: The Importance of the Integration of Chemical, Biological, and Botanical Analyses, and the Role of DNA Barcoding.},
journal = {HerbalGram},
volume = {106},
number = {},
pages = {58-60},
pmid = {30287983},
issn = {0899-5648},
support = {P50 AT000155/AT/NCCIH NIH HHS/United States ; },
abstract = {Raw materials, ingredients, and products derived from plants are commonly referred to as herbs or botanicals in both the biomedical literature and the natural products health industry. This overarching term includes the breadth of crude herbs, plant parts, and the ingredients made from them, and also covers finished products such as botanical dietary supplements. Botanical dietary supplements are intended to supplement the human diet and are composed primarily of powdered plant parts, their extracts, or other preparations derived from crude herbal material; some formulations include other ingredients such as vitamins, minerals, and amino acids. Botanical dietary supplements are highly complex mixtures reflecting the diverse chemical constituents that comprise the source plant's raw material. Botanical analysis is an intricate analytical challenge requiring specialized skills and instrumentation that is different from those required for quality control of chemically simpler pharmaceuticals, or for the safety assessment of many conventional food or other products that are generally regarded as safe (GRAS).},
}
@article {pmid29758844,
year = {2013},
author = {Berger, MF},
title = {Harnessing massively parallel DNA sequencing for the personalization of cancer management.},
journal = {Personalized medicine},
volume = {10},
number = {2},
pages = {183-190},
doi = {10.2217/pme.13.2},
pmid = {29758844},
issn = {1744-828X},
abstract = {In order to properly diagnose and classify tumors and select the most appropriate therapies for patients, one must accurately and efficiently identify oncogenic mutations in key cancer-associated genes. Massively parallel DNA sequencing technology has the potential to dramatically enhance the field of molecular diagnostics. For increasingly lower costs, one can interrogate all clinically relevant genes for mutations, copy number alterations and structural rearrangements, with high detection sensitivity in heterogeneous tissue. Advances in exon capture, molecular barcoding and profiling of formalin-fixed paraffin-embedded specimens have further established the clinical potential of massively parallel sequencing. This article discusses promising strategies for DNA sequencing as a clinical tool and also the challenges in its implementation in the clinical arena.},
}
@article {pmid29118596,
year = {2017},
author = {Fisher, JR and Fisher, DM and Skvarla, MJ and Nelson, WA and Dowling, APG},
title = {Revision of torrent mites (Parasitengona, Torrenticolidae, Torrenticola) of the United States and Canada: 90 descriptions, molecular phylogenetics, and a key to species.},
journal = {ZooKeys},
volume = {},
number = {701},
pages = {1-496},
pmid = {29118596},
issn = {1313-2989},
abstract = {The descriptive biology of torrent mites (Parasitengona: Torrenticolidae: Torrenticola) of North America (north of Mexico) is investigated using integrative methods. Material examined includes approximately 2,300 specimens from nearly 500 localities across the United States and Canada, and a few collections in Mexico and Central America. Species hypotheses are derived from a phylogenetic analysis of the barcoding region of cytochrome c oxidase subunit 1 (COI) for 476 specimens and supported with morphology and biogeography. Relationships between species are examined with a combined analysis of COI and two expansion regions (D2-3) of the large ribosomal subunit (28S rDNA) for 57 specimens. All previously described species from the US and Canada are examined. Our results indicate the need to synonymize four species: T. mercedensis (Marshall, 1943) is a junior synonym of T. sierrensis (Marshall, 1943); T. rectiforma Habeeb, 1974 is a junior synonym of T. ellipsoidalis (Marshall, 1943); T. neoconnexa Habeeb, 1957 is a junior synonym of T. magnexa Habeeb, 1955; and T. esbelta Cramer, 1992 is a junior synonym of T. boettgeri KO Viets, 1977. We describe 66 new species and re-describe all previously described regional species. Our findings indicate that total diversity of Torrenticola in the United States and Canada comprises 90 species, 57 known from the east and 33 from the west. We organize these species into four species complexes that include 13 identification groups. An additional 13 species do not fit within an identification group. The southern Appalachians are suspected to contain the highest concentration of remaining undescribed diversity. A key is provided to all known species in the US and Canada.},
}
@article {pmid29118398,
year = {2017},
author = {Ye, H and Wu, CZ and Yang, T and Santosh, M and Yao, XZ and Gao, BF and Wang, XL and Li, W},
title = {Updating the Geologic Barcodes for South China: Discovery of Late Archean Banded Iron Formations in the Yangtze Craton.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {15082},
pmid = {29118398},
issn = {2045-2322},
abstract = {Banded iron formations (BIFs) in Archean cratons provide important "geologic barcodes" for the global correlation of Precambrian sedimentary records. Here we report the first finding of late Archean BIFs from the Yangtze Craton, one of largest Precambrian blocks in East Asia with an evolutionary history of over 3.3 Ga. The Yingshan iron deposit at the northeastern margin of the Yangtze Craton, displays typical features of BIF, including: (i) alternating Si-rich and Fe-rich bands at sub-mm to meter scales; (ii) high SiO2 + Fe2O3total contents (average 90.6 wt.%) and Fe/Ti ratios (average 489); (iii) relative enrichment of heavy rare earth elements and positive Eu anomalies (average 1.42); (iv) and sedimentary Fe isotope compositions (δ[56]FeIRMM-014 as low as -0.36‰). The depositional age of the BIF is constrained at ~2464 ± 24 Ma based on U-Pb dating of zircon grains from a migmatite sample of a volcanic protolith that conformably overlied the Yingshan BIF. The BIF was intruded by Neoproterozoic (805.9 ± 4.7 Ma) granitoids that are unique in the Yangtze Craton but absent in the North China Craton to the north. The discovery of the Yingshan BIF provides new constraints for the tectonic evolution of the Yangtze Craton and has important implications in the reconstruction of Pre-Nuna/Columbia supercontinent configurations.},
}
@article {pmid29117773,
year = {2018},
author = {Jeon, HB and Anderson, D and Won, H and Lim, H and Suk, HY},
title = {Taxonomic characterization of Tanakia species (Acheilognathidae) using DNA barcoding analyses.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {6},
pages = {964-973},
doi = {10.1080/24701394.2017.1398746},
pmid = {29117773},
issn = {2470-1408},
mesh = {Animals ; Cyprinidae/classification/*genetics ; Cytochromes b/genetics ; DNA Barcoding, Taxonomic/*methods/standards ; Electron Transport Complex IV/genetics ; Fish Proteins/genetics ; *Phylogeny ; },
abstract = {Tanakia is a bitterling genus with six species found in Far East Asia. Our aim was to construct the standard DNA barcode database available for the identification of six Tanakia species by comparing the range of intra- and inter-specific genetic distances, identifying the phylogenetic placement of each Tanakia species and providing the unique barcode characteristics that are specific to each species, using cytochrome oxidase I (COI) and cytochrome b (cyt b). Both loci failed to create a perfect barcoding gap between the ranges of inter- and intra-specific genetic distances, though interspecific COI distances were sufficiently greater than intraspecific values with only a few exceptions. In our phylogenetic analyses, T. koreensis and T. signifer did not form a monophyletic cluster of haplotypes in both loci. COI provided clear nucleotide characteristics that distinguish each species, whereas relatively fewer informative sites were found within the range of cyt b. Overall, COI could be regarded as appropriate species identification solution in Tanakia. Our analyses yielded some taxonomic issues that need the further investigation, and are expected to be helpful in the examination for the conservation status of Tanakia species that are on the verge of being endangered.},
}
@article {pmid29117377,
year = {2017},
author = {Wang, J and Wang, W and Wang, R and Zheng, H and Gao, S},
title = {Molecular Detection of Chilo infuscatellus.},
journal = {Journal of insect science (Online)},
volume = {17},
number = {5},
pages = {},
pmid = {29117377},
issn = {1536-2442},
mesh = {Animals ; Base Sequence ; *DNA Barcoding, Taxonomic ; DNA Primers ; Electron Transport Complex IV/genetics ; Female ; Male ; Moths/*classification/genetics ; Polymerase Chain Reaction ; },
abstract = {The Chilo infuscatellus (Snellen; Lepidoptera: Pyralidae) is the main pest of sugarcane in China. The shortage of easily distinguishable morphological characters especially in early stage make it challenging to diagnosed and promptly take steps for pest management. In the present study, we described a PCR method for the molecular identification of based on barcode region of COI sequences between C. infuscatellus and four other sugarcane borer species. A 285bp fragment was successfully amplified from all life stages and different geographical populations. Sensitivity tests revealed that diagnostic bands were generated as low as the DNA template concentration of 5 ng/µl. Our work demonstrated a rapid and accurate way for the molecular diagnosis of C. infuscatellus.},
}
@article {pmid29115074,
year = {2017},
author = {Cho, YC and Lee, SH and Cho, YH and Choy, YB},
title = {Adapter-based Safety Injection System for Prevention of Wrong Route and Wrong Patient Medication Errors.},
journal = {Journal of Korean medical science},
volume = {32},
number = {12},
pages = {1938-1946},
pmid = {29115074},
issn = {1598-6357},
mesh = {Catheters ; Equipment Design ; Humans ; Injections/instrumentation/*methods ; Medication Errors/*prevention &amp; control ; Printing, Three-Dimensional ; },
abstract = {Wrong-route or -patient medication errors due to human mistakes have been considered difficult to resolve in clinical settings. In this study, we suggest a safety injection system that can help to prevent an injection when a mismatch exists between the drug and route or patient. For this, we prepared two distinct adapters with key and keyhole patterns specifically assigned to a pair of drug and route or patient. When connected to a syringe tip and its counterpart, a catheter injection-port, respectively, the adapters allowed for a seamless connection only with their matching patterns. In this study, each of the adapters possessed a specific key and keyhole pattern at one end and the other end was shaped to be a universal fit for syringe tips or catheter injection-ports in clinical use. With the scheme proposed herein, we could generate 27,000 patterns, depending on the location and shape of the key tooth in the adapters. With a rapid prototyping technique, multiple distinct pairs of adapters could be prepared in a relatively short period of time and thus, we envision that a specific adapter pair can be produced on-site after patient hospitalization, much like patient identification barcodes.},
}
@article {pmid29114441,
year = {2017},
author = {Foo, CF and Bennett, VJ and Hale, AM and Korstian, JM and Schildt, AJ and Williams, DA},
title = {Increasing evidence that bats actively forage at wind turbines.},
journal = {PeerJ},
volume = {5},
number = {},
pages = {e3985},
pmid = {29114441},
issn = {2167-8359},
abstract = {Although the ultimate causes of high bat fatalities at wind farms are not well understood, several lines of evidence suggest that bats are attracted to wind turbines. One hypothesis is that bats would be attracted to turbines as a foraging resource if the insects that bats prey upon are commonly present on and around the turbine towers. To investigate the role that foraging activity may play in bat fatalities, we conducted a series of surveys at a wind farm in the southern Great Plains of the US from 2011-2016. From acoustic monitoring we recorded foraging activity, including feeding buzzes indicative of prey capture, in the immediate vicinity of turbine towers from all six bat species known to be present at this site. From insect surveys we found Lepidoptera, Coleoptera, and Orthoptera in consistently high proportions over several years suggesting that food resources for bats were consistently available at wind turbines. We used DNA barcoding techniques to assess bat diet composition of (1) stomach contents from 47 eastern red bat (Lasiurus borealis) and 24 hoary bat (Lasiurus cinereus) carcasses collected in fatality searches, and (2) fecal pellets from 23 eastern red bats that were found on turbine towers, transformers, and tower doors. We found that the majority of the eastern red bat and hoary bat stomachs, the two bat species most commonly found in fatality searches at this site, were full or partially full, indicating that the bats were likely killed while foraging. Although Lepidoptera and Orthoptera dominated the diets of these two bat species, both consumed a range of prey items with individual bats having from one to six insect species in their stomachs at the time of death. The prey items identified from eastern red bat fecal pellets showed similar results. A comparison of the turbine insect community to the diet analysis results revealed that the most abundant insects at wind turbines, including terrestrial insects such as crickets and several important crop pests, were also commonly eaten by eastern red and hoary bats. Collectively, these findings suggest that bats are actively foraging around wind turbines and that measures to minimize bat fatalities should be broadly implemented at wind facilities.},
}
@article {pmid29114215,
year = {2017},
author = {Yoon, YG and Dai, P and Wohlwend, J and Chang, JB and Marblestone, AH and Boyden, ES},
title = {Feasibility of 3D Reconstruction of Neural Morphology Using Expansion Microscopy and Barcode-Guided Agglomeration.},
journal = {Frontiers in computational neuroscience},
volume = {11},
number = {},
pages = {97},
pmid = {29114215},
issn = {1662-5188},
support = {DP1 NS087724/NS/NINDS NIH HHS/United States ; R01 MH110932/MH/NIMH NIH HHS/United States ; R41 MH112318/MH/NIMH NIH HHS/United States ; RM1 HG008525/HG/NHGRI NIH HHS/United States ; },
abstract = {We here introduce and study the properties, via computer simulation, of a candidate automated approach to algorithmic reconstruction of dense neural morphology, based on simulated data of the kind that would be obtained via two emerging molecular technologies-expansion microscopy (ExM) and in-situ molecular barcoding. We utilize a convolutional neural network to detect neuronal boundaries from protein-tagged plasma membrane images obtained via ExM, as well as a subsequent supervoxel-merging pipeline guided by optical readout of information-rich, cell-specific nucleic acid barcodes. We attempt to use conservative imaging and labeling parameters, with the goal of establishing a baseline case that points to the potential feasibility of optical circuit reconstruction, leaving open the possibility of higher-performance labeling technologies and algorithms. We find that, even with these conservative assumptions, an all-optical approach to dense neural morphology reconstruction may be possible via the proposed algorithmic framework. Future work should explore both the design-space of chemical labels and barcodes, as well as algorithms, to ultimately enable routine, high-performance optical circuit reconstruction.},
}
@article {pmid29114162,
year = {2017},
author = {Akkari, N and Komerički, A and Weigand, AM and Edgecombe, GD and Stoev, P},
title = {A new cave centipede from Croatia, Eupolybothrus liburnicus sp. n., with notes on the subgenus Schizopolybothrus Verhoeff, 1934 (Chilopoda, Lithobiomorpha, Lithobiidae).},
journal = {ZooKeys},
volume = {},
number = {687},
pages = {11-43},
pmid = {29114162},
issn = {1313-2989},
abstract = {A new species of Eupolybothrus Verhoeff, 1907 discovered in caves of Velebit Mountain in Croatia is described. E. liburnicussp. n. exhibits a few morphological differences from its most similar congeners, all of which are attributed to the subgenus Schizopolybothrus Verhoeff, 1934, and two approaches to species delimitation using the COI barcode region identify it as distinct from the closely allied E. cavernicolus Stoev &amp; Komerički, 2013. E. spiniger (Latzel, 1888) is redescribed and a lectotype is designated for it as well as E. caesar (Verhoeff, 1899) to stabilize their respective taxonomic status. The subspecies E. acherontis wardaranus Verhoeff, 1937, previously suspected to be a synonym of E. caesar (Verhoeff, 1899), is redescribed and its taxonomy revised after the study of type material whereas the identity of E. acherontis (Verhoeff, 1900) described from a female from southwest Trebinje (Bosnia and Herzegovina) remains unknown. Type material of E. stygis (Folkmanova, 1940) is confirmed to be lost and future designation of neotypes from topotypic specimens is necessary to stabilize its taxonomy. The importance of setal arrangement on the intermediate and 14[th] tergites and the sexual modifications on the male 15[th] prefemur for species identification is discussed in the light of present findings, and a review of the species of E. (Schizopolybothrus) that display these traits is also provided.},
}
@article {pmid29113613,
year = {2018},
author = {Šlapeta, J},
title = {DNA barcoding of Cryptosporidium.},
journal = {Parasitology},
volume = {145},
number = {5},
pages = {574-584},
doi = {10.1017/S0031182017001809},
pmid = {29113613},
issn = {1469-8161},
mesh = {Cryptosporidium/classification/*genetics/pathogenicity ; *DNA Barcoding, Taxonomic ; *Genetic Variation ; Metagenome ; Phenotype ; Virulence Factors/genetics ; Whole Genome Sequencing ; },
abstract = {Cryptosporidium spp. (Apicomplexa) causing cryptosporidiosis are of medical and veterinary significance. The genus Cryptosporidium has benefited from the application of what is considered a DNA-barcoding approach, even before the term 'DNA barcoding' was formally coined. Here, the objective to define the DNA barcode diversity of Cryptosporidium infecting mammals is reviewed and considered to be accomplished. Within the Cryptosporidium literature, the distinction between DNA barcoding and DNA taxonomy is indistinct. DNA barcoding and DNA taxonomy are examined using the latest additions to the growing spectrum of named Cryptosporidium species and within-species and between-species identity is revisited. Ease and availability of whole-genome DNA sequencing of the relatively small Cryptosporidium genome offer an initial perspective on the intra-host diversity. The opportunity emerges to apply a metagenomic approach to purified field/clinical Cryptosporidum isolates. The outstanding question remains a reliable definition of Cryptosporidium phenotype. The complementary experimental infections and metagenome approach will need to be applied simultaneously to address Cryptosporidium phenotype with carefully chosen clinical evaluations enabling identification of virulence factors.},
}
@article {pmid29113594,
year = {2018},
author = {Enabulele, EE and Lawton, SP and Walker, AJ and Kirk, RS},
title = {Molecular and morphological characterization of the cercariae of Lecithodendrium linstowi (Dollfus, 1931), a trematode of bats, and incrimination of the first intermediate snail host, Radix balthica.},
journal = {Parasitology},
volume = {145},
number = {3},
pages = {307-312},
doi = {10.1017/S0031182017001640},
pmid = {29113594},
issn = {1469-8161},
mesh = {Animals ; Cercaria/*anatomy &amp; histology/classification/*genetics/physiology ; Chiroptera/*parasitology ; Cyclooxygenase 1/genetics ; DNA Barcoding, Taxonomic ; DNA, Ribosomal ; DNA, Ribosomal Spacer/genetics ; Life Cycle Stages/genetics ; Phylogeny ; Snails/*parasitology ; Trematoda/classification/*genetics ; Trematode Infections/parasitology/transmission/veterinary ; },
abstract = {Lecithodendrium linstowi is one of the most prevalent and abundant trematodes of bats, but the larval stages and intermediate hosts have not been identified. We present the first molecular and morphological characterization of the cercariae of L. linstowi based on a phylogenetic analysis of partial fragments of LSU and ITS2 rDNA. The first intermediate host was incriminated as Radix balthica by DNA barcoding using cox1 and ITS2 sequences, although the snail morphologically resembled Radix peregra, emphasizing the requirement for molecular identification of lymnaeids as important intermediate hosts of medical and veterinary impact. The application of molecular data in this study has enabled linkage of life cycle stages and accurate incrimination of the first intermediate host.},
}
@article {pmid29113023,
year = {2018},
author = {Andújar, C and Arribas, P and Gray, C and Bruce, C and Woodward, G and Yu, DW and Vogler, AP},
title = {Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill.},
journal = {Molecular ecology},
volume = {27},
number = {1},
pages = {146-166},
doi = {10.1111/mec.14410},
pmid = {29113023},
issn = {1365-294X},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; *Environmental Monitoring ; *Fresh Water ; High-Throughput Nucleotide Sequencing ; Invertebrates/*drug effects ; *Metagenomics ; Pesticides/*toxicity ; Species Specificity ; Water Pollutants, Chemical/*toxicity ; },
abstract = {Biomonitoring underpins the environmental assessment of freshwater ecosystems and guides management and conservation. Current methodology for surveys of (macro)invertebrates uses coarse taxonomic identification where species-level resolution is difficult to obtain. Next-generation sequencing of entire assemblages (metabarcoding) provides a new approach for species detection, but requires further validation. We used metabarcoding of invertebrate assemblages with two fragments of the cox1 "barcode" and partial nuclear ribosomal (SSU) genes, to assess the effects of a pesticide spill in the River Kennet (southern England). Operational taxonomic unit (OTU) recovery was tested under 72 parameters (read denoising, filtering, pair merging and clustering). Similar taxonomic profiles were obtained under a broad range of parameters. The SSU marker recovered Platyhelminthes and Nematoda, missed by cox1, while Rotifera were only amplified with cox1. A reference set was created from all available barcode entries for Arthropoda in the BOLD database and clustered into OTUs. The River Kennet metabarcoding produced matches to 207 of these reference OTUs, five times the number of species recognized with morphological monitoring. The increase was due to the following: greater taxonomic resolution (e.g., splitting a single morphotaxon "Chironomidae" into 55 named OTUs); splitting of Linnaean binomials into multiple molecular OTUs; and the use of a filtration-flotation protocol for extraction of minute specimens (meiofauna). Community analyses revealed strong differences between "impacted" vs. "control" samples, detectable with each gene marker, for each major taxonomic group, and for meio- and macrofaunal samples separately. Thus, highly resolved taxonomic data can be extracted at a fraction of the time and cost of traditional nonmolecular methods, opening new avenues for freshwater invertebrate biodiversity monitoring and molecular ecology.},
}
@article {pmid29112732,
year = {2018},
author = {Elyanow, R and Wu, HT and Raphael, BJ},
title = {Identifying structural variants using linked-read sequencing data.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {2},
pages = {353-360},
pmid = {29112732},
issn = {1367-4811},
support = {R01 CA180776/CA/NCI NIH HHS/United States ; R01 HG005690/HG/NHGRI NIH HHS/United States ; R01 HG007069/HG/NHGRI NIH HHS/United States ; },
abstract = {MOTIVATION: Structural variation, including large deletions, duplications, inversions, translocations and other rearrangements, is common in human and cancer genomes. A number of methods have been developed to identify structural variants from Illumina short-read sequencing data. However, reliable identification of structural variants remains challenging because many variants have breakpoints in repetitive regions of the genome and thus are difficult to identify with short reads. The recently developed linked-read sequencing technology from 10X Genomics combines a novel barcoding strategy with Illumina sequencing. This technology labels all reads that originate from a small number (∼5 to 10) DNA molecules ∼50 Kbp in length with the same molecular barcode. These barcoded reads contain long-range sequence information that is advantageous for identification of structural variants.<br><br>RESULTS: We present Novel Adjacency Identification with Barcoded Reads (NAIBR), an algorithm to identify structural variants in linked-read sequencing data. NAIBR predicts novel adjacencies in an individual genome resulting from structural variants using a probabilistic model that combines multiple signals in barcoded reads. We show that NAIBR outperforms several existing methods for structural variant identification-including two recent methods that also analyze linked-reads-on simulated sequencing data and 10X whole-genome sequencing data from the NA12878 human genome and the HCC1954 breast cancer cell line. Several of the novel somatic structural variants identified in HCC1954 overlap known cancer genes.<br><br>Software is available at compbio.cs.brown.edu/software.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid29107618,
year = {2018},
author = {da Cruz, MOR and Weksler, M},
title = {Impact of tree priors in species delimitation and phylogenetics of the genus Oligoryzomys (Rodentia: Cricetidae).},
journal = {Molecular phylogenetics and evolution},
volume = {119},
number = {},
pages = {1-12},
doi = {10.1016/j.ympev.2017.10.021},
pmid = {29107618},
issn = {1095-9513},
mesh = {Animals ; Arvicolinae/*classification ; Bayes Theorem ; Mitochondria/metabolism ; *Phylogeny ; Probability ; Species Specificity ; Time Factors ; },
abstract = {The use of genetic data and tree-based algorithms to delimit evolutionary lineages is becoming an important practice in taxonomic identification, especially in morphologically cryptic groups. The effects of different phylogenetic and/or coalescent models in the analyses of species delimitation, however, are not clear. In this paper, we assess the impact of different evolutionary priors in phylogenetic estimation, species delimitation, and molecular dating of the genus Oligoryzomys (Mammalia: Rodentia), a group with complex taxonomy and morphological cryptic species. Phylogenetic and coalescent analyses included 20 of the 24 recognized species of the genus, comprising of 416 Cytochrome b sequences, 26 Cytochrome c oxidase I sequences, and 27 Beta-Fibrinogen Intron 7 sequences. For species delimitation, we employed the General Mixed Yule Coalescent (GMYC) and Bayesian Poisson tree processes (bPTP) analyses, and contrasted 4 genealogical and phylogenetic models: Pure-birth (Yule), Constant Population Size Coalescent, Multiple Species Coalescent, and a mixed Yule-Coalescent model. GMYC analyses of trees from different genealogical models resulted in similar species delimitation and phylogenetic relationships, with incongruence restricted to areas of poor nodal support. bPTP results, however, significantly differed from GMYC for 5 taxa. Oligoryzomys early diversification was estimated to have occurred in the Early Pleistocene, between 0.7 and 2.6 MYA. The mixed Yule-Coalescent model, however, recovered younger dating estimates for Oligoryzomys diversification, and for the threshold for the speciation-coalescent horizon in GMYC. Eight of the 20 included Oligoryzomys species were identified as having two or more independent evolutionary units, indicating that current taxonomy of Oligoryzomys is still unsettled.},
}
@article {pmid29097709,
year = {2017},
author = {Mishra, P and Kumar, A and Sivaraman, G and Shukla, AK and Kaliamoorthy, R and Slater, A and Velusamy, S},
title = {Character-based DNA barcoding for authentication and conservation of IUCN Red listed threatened species of genus Decalepis (Apocynaceae).},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {14910},
pmid = {29097709},
issn = {2045-2322},
mesh = {Apocynaceae/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/classification/*genetics ; *Endangered Species ; Gene Library ; Genes, Plant ; Phylogeny ; Polymerase Chain Reaction/methods ; },
abstract = {The steno-endemic species of genus Decalepis are highly threatened by destructive wild harvesting. The medicinally important fleshy tuberous roots of Decalepis hamiltonii are traded as substitute, to meet the international market demand of Hemidesmus indicus. In addition, the tuberous roots of all three species of Decalepis possess similar exudates and texture, which challenges the ability of conventional techniques alone to perform accurate species authentication. This study was undertaken to generate DNA barcodes that could be utilized in monitoring and curtailing the illegal trade of these endangered species. The DNA barcode reference library was developed in BOLD database platform for candidate barcodes rbcL, matK, psbA-trnH, ITS and ITS2. The average intra-specific variations (0-0.27%) were less than the distance to nearest neighbour (0.4-11.67%) with matK and ITS. Anchoring the coding region rbcL in multigene tiered approach, the combination rbcL + matK + ITS yielded 100% species resolution, using the least number of loci combinations either with PAUP or BLOG methods to support a character-based approach. Species-specific SNP position (230 bp) in the matK region that is characteristic of D. hamiltonii could be used to design specific assays, enhancing its applicability for direct use in CITES enforcement for distinguishing it from H. indicus.},
}
@article {pmid29096756,
year = {2017},
author = {Khan, AZ and Amad, I and Shaheen, S and Hussain, K and Hafeez, F and Farooq, M and Noor Ul Ayan, H},
title = {Genetic barcoding and phylogenetic analysis of dusky cotton bug (Oxycarenus hyalinipennis) using mitochondrial cytochrome c oxidase I gene.},
journal = {Cellular and molecular biology (Noisy-le-Grand, France)},
volume = {63},
number = {10},
pages = {59-63},
doi = {10.14715/cmb/2017.63.10.9},
pmid = {29096756},
issn = {1165-158X},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/isolation &amp; purification/metabolism ; Electron Transport Complex IV/classification/*genetics ; Heteroptera/classification/*genetics ; Phylogeny ; },
abstract = {Cotton dusky bug (Oxycarenus spp.) mostly attack on cash crops such as Gossypium, Cola and Hibiscus which affect the national economy therefore sustainable pest management is needed. Cytochrome c oxidase I (COI) gene is utilized as marker gene for DNA barcoding, genetic and ecological study of insects. In present study insect (cotton dusky bug) samples were collected from cotton fields in Faisalabad. COI gene was amplified from genomic DNA of bug and cloned into pTZ57R/T vector (Fermentas). The clone was sent to Macrogen (South Korea) for Sanger sequencing. The phylogenetic analysis and pairwise multiple sequence alignment showed that our cotton dusky bug grouped with two species of Oxycarenus genus and highest sequence identity was 91.1% with Oxycarenus hylinipennis. This is the first report of genetic barcode of Oxycarenus hylinipennis from cotton from Pakistan.},
}
@article {pmid29091798,
year = {2017},
author = {Hewett, DR and Vandyke, K and Lawrence, DM and Friend, N and Noll, JE and Geoghegan, JM and Croucher, PI and Zannettino, ACW},
title = {DNA Barcoding Reveals Habitual Clonal Dominance of Myeloma Plasma Cells in the Bone Marrow Microenvironment.},
journal = {Neoplasia (New York, N.Y.)},
volume = {19},
number = {12},
pages = {972-981},
pmid = {29091798},
issn = {1476-5586},
mesh = {Animals ; Bone Marrow/*pathology ; Cell Line, Tumor ; Cell Proliferation ; Clonal Evolution/*genetics ; *DNA Barcoding, Taxonomic ; Gene Library ; High-Throughput Nucleotide Sequencing ; Humans ; Mice ; Multiple Myeloma/*genetics ; Neoplasm Metastasis ; Plasma Cells/*metabolism/*pathology ; *Tumor Microenvironment ; },
abstract = {Multiple myeloma (MM) is a hematological malignancy resulting from the uncontrolled proliferation of antibody-producing plasma cells in the bone marrow. At diagnosis, independent plasma cell tumors are found throughout the skeleton. The recirculation of mutant plasma cells from the initial lesion and their recolonization of distant marrow sites are thought to occur by a process similar to solid tumor metastasis. However, the efficiency of this bone marrow homing process and the proportion of disseminated cells that actively divide and contribute to new tumor growth in MM are both unknown. We used the C57BL/KaLwRij mouse model of myeloma, lentiviral-mediated DNA barcoding of 5TGM1 myeloma cells, and next-generation sequencing to investigate the relative efficiency of plasma cell migration to, and growth within, the bone marrow. This approach revealed three major findings: firstly, establishment of metastasis within the bone marrow was extremely inefficient, with approximately 0.01% of circulating myeloma cells becoming resident long term in the bone marrow of each long bone; secondly, the individual cells of each metastasis exhibited marked differences in their proliferative fates, with the majority of final tumor burden within a bone being attributable to the progeny of between 1 and 8 cells; and, thirdly, the proliferative fate of individual clonal plasma cells differed at each bone marrow site in which the cells "landed." These findings suggest that individual myeloma plasma cells are subjected to vastly different selection pressures within the bone marrow microenvironment, highlighting the importance of niche-driven factors, which determine the disease course and outcome.},
}
@article {pmid29089113,
year = {2017},
author = {Gavrilović, A and Piria, M and Guo, XZ and Jug-Dujaković, J and Ljubučić, A and Krkić, A and Iveša, N and Marshall, BA and Gardner, JPA},
title = {First evidence of establishment of the rayed pearl oyster, Pinctada imbricata radiata (Leach, 1814), in the eastern Adriatic Sea.},
journal = {Marine pollution bulletin},
volume = {125},
number = {1-2},
pages = {556-560},
doi = {10.1016/j.marpolbul.2017.10.045},
pmid = {29089113},
issn = {1879-3363},
mesh = {Animals ; Croatia ; Ecosystem ; Electron Transport Complex IV/genetics ; Environmental Monitoring ; Haplotypes ; *Introduced Species ; Islands ; Mediterranean Sea ; *Pinctada/genetics ; Sequence Analysis, DNA ; },
abstract = {The Mediterranean Sea is increasingly under threat from invasive species that may negatively affect biodiversity and/or modify ecosystem structure and function. The bivalve mollusc Pinctada imbricata radiata is listed among the 100 most invasive species in the Mediterranean. A first finding of an established population of P. imbricata radiata in the coastal waters of the eastern Adriatic Sea, is presented in this paper. Six and then 30 live specimens were collected in 2015 and in 2017, respectively, at depths of 5 to 15m from the island of Mljet, Croatia. DNA sequencing of the mitochondrial cytochrome c oxidase I gene (COI) revealed three different haplotypes. All samples showed greatest similarity (98 to >99%) to P. radiata COI sequence records in GenBank (=P. imbricata radiata as used in this paper). A Neighbour Joining tree placed all Croatian samples within the 100% bootstrap supported clade for P. imbricata radiata.},
}
@article {pmid29087945,
year = {2017},
author = {Younger, D and Berger, S and Baker, D and Klavins, E},
title = {High-throughput characterization of protein-protein interactions by reprogramming yeast mating.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {114},
number = {46},
pages = {12166-12171},
pmid = {29087945},
issn = {1091-6490},
support = {/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Agglutination/genetics ; *Gene Expression Regulation, Fungal ; Gene Library ; Mating Factor/*genetics/metabolism ; Protein Binding ; Protein Interaction Mapping/*methods ; Saccharomyces cerevisiae/*genetics/metabolism ; *Translocation, Genetic ; Two-Hybrid System Techniques ; },
abstract = {High-throughput methods for screening protein-protein interactions enable the rapid characterization of engineered binding proteins and interaction networks. While existing approaches are powerful, none allow quantitative library-on-library characterization of protein interactions in a modifiable extracellular environment. Here, we show that sexual agglutination of Saccharomyces cerevisiae can be reprogrammed to link interaction strength with mating efficiency using synthetic agglutination (SynAg). Validation of SynAg with 89 previously characterized interactions shows a log-linear relationship between mating efficiency and protein binding strength for interactions with Kds ranging from below 500 pM to above 300 μM. Using induced chromosomal translocation to pair barcodes representing binding proteins, thousands of distinct interactions can be screened in a single pot. We demonstrate the ability to characterize protein interaction networks in a modifiable environment by introducing a soluble peptide that selectively disrupts a subset of interactions in a representative network by up to 800-fold. SynAg enables the high-throughput, quantitative characterization of protein-protein interaction networks in a fully defined extracellular environment at a library-on-library scale.},
}
@article {pmid29084279,
year = {2017},
author = {Birch, JL and Walsh, NG and Cantrill, DJ and Holmes, GD and Murphy, DJ},
title = {Testing efficacy of distance and tree-based methods for DNA barcoding of grasses (Poaceae tribe Poeae) in Australia.},
journal = {PloS one},
volume = {12},
number = {10},
pages = {e0186259},
pmid = {29084279},
issn = {1932-6203},
mesh = {Australia ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; Poaceae/classification/*genetics ; },
abstract = {In Australia, Poaceae tribe Poeae are represented by 19 genera and 99 species, including economically and environmentally important native and introduced pasture grasses [e.g. Poa (Tussock-grasses) and Lolium (Ryegrasses)]. We used this tribe, which are well characterised in regards to morphological diversity and evolutionary relationships, to test the efficacy of DNA barcoding methods. A reference library was generated that included 93.9% of species in Australia (408 individuals, [Formula: see text] = 3.7 individuals per species). Molecular data were generated for official plant barcoding markers (rbcL, matK) and the nuclear ribosomal internal transcribed spacer (ITS) region. We investigated accuracy of specimen identifications using distance- (nearest neighbour, best-close match, and threshold identification) and tree-based (maximum likelihood, Bayesian inference) methods and applied species discovery methods (automatic barcode gap discovery, Poisson tree processes) based on molecular data to assess congruence with recognised species. Across all methods, success rate for specimen identification of genera was high (87.5-99.5%) and of species was low (25.6-44.6%). Distance- and tree-based methods were equally ineffective in providing accurate identifications for specimens to species rank (26.1-44.6% and 25.6-31.3%, respectively). The ITS marker achieved the highest success rate for specimen identification at both generic and species ranks across the majority of methods. For distance-based analyses the best-close match method provided the greatest accuracy for identification of individuals with a high percentage of "correct" (97.6%) and a low percentage of "incorrect" (0.3%) generic identifications, based on the ITS marker. For tribe Poeae, and likely for other grass lineages, sequence data in the standard DNA barcode markers are not variable enough for accurate identification of specimens to species rank. For recently diverged grass species similar challenges are encountered in the application of genetic and morphological data to species delimitations, with taxonomic signal limited by extensive infra-specific variation and shared polymorphisms among species in both data types.},
}
@article {pmid29083401,
year = {2017},
author = {Emanuel, G and Moffitt, JR and Zhuang, X},
title = {High-throughput, image-based screening of pooled genetic-variant libraries.},
journal = {Nature methods},
volume = {14},
number = {12},
pages = {1159-1162},
pmid = {29083401},
issn = {1548-7105},
support = {R01 MH113094/MH/NIMH NIH HHS/United States ; },
mesh = {DNA Barcoding, Taxonomic/*methods ; Escherichia coli/*genetics ; *Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; In Situ Hybridization, Fluorescence/*methods ; Mutation ; Reproducibility of Results ; },
abstract = {We report a high-throughput screening method that allows diverse genotypes and corresponding phenotypes to be imaged in individual cells. We achieve genotyping by introducing barcoded genetic variants into cells as pooled libraries and reading the barcodes out using massively multiplexed fluorescence in situ hybridization. To demonstrate the power of image-based pooled screening, we identified brighter and more photostable variants of the fluorescent protein YFAST among 60,000 variants.},
}
@article {pmid29081915,
year = {2017},
author = {Kristensen, MF and Zeng, G and Neu, TR and Meyer, RL and Baelum, V and Schlafer, S},
title = {Osteopontin adsorption to Gram-positive cells reduces adhesion forces and attachment to surfaces under flow.},
journal = {Journal of oral microbiology},
volume = {9},
number = {1},
pages = {1379826},
pmid = {29081915},
issn = {2000-2297},
abstract = {The bovine milk protein osteopontin (OPN) may be an efficient means to prevent bacterial adhesion to dental tissues and control biofilm formation. This study sought to determine to what extent OPN impacts adhesion forces and surface attachment of different bacterial strains involved in dental caries or medical device-related infections. It further investigated if OPN's effect on adhesion is caused by blocking the accessibility of glycoconjugates on bacterial surfaces. Bacterial adhesion was determined in a shear-controlled flow cell system in the presence of different concentrations of OPN, and interaction forces of single bacteria were quantified using single-cell force spectroscopy before and after OPN exposure. Moreover, the study investigated OPN's effect on the accessibility of cell surface glycoconjugates through fluorescence lectin-binding analysis. OPN strongly affected bacterial adhesion in a dose-dependent manner for all investigated species (Actinomyces naeslundii, Actinomyces viscosus, Lactobacillus paracasei subsp. paracasei, Staphylococcus epidermidis, Streptococcus mitis, and Streptococcus oralis). Likewise, adhesion forces decreased after OPN treatment. No effect of OPN on the lectin-accessibility to glycoconjugates was found. OPN reduces the adhesion and adhesion force/energy of a variety of bacteria and has a potential therapeutic use for biofilm control. OPN acts upon bacterial adhesion without blocking cell surface glycoconjugates.},
}
@article {pmid29078770,
year = {2017},
author = {González, C and Molina, AG and León, C and Salcedo, N and Rondón, S and Paz, A and Atencia, MC and Tovar, C and Ortiz, M},
title = {Entomological characterization of malaria in northern Colombia through vector and parasite species identification, and analyses of spatial distribution and infection rates.},
journal = {Malaria journal},
volume = {16},
number = {1},
pages = {431},
pmid = {29078770},
issn = {1475-2875},
mesh = {Animals ; Anopheles/*parasitology ; Colombia ; Malaria/*transmission ; Mosquito Vectors/*parasitology ; Plasmodium/*isolation &amp; purification/physiology ; Rural Population ; },
abstract = {BACKGROUND: Malaria remains a worldwide public health concern and, in Colombia, despite the efforts to stop malaria transmission, the incidence of cases has increased over the last few years. In this context, it is necessary to evaluate vector diversity, infection rates, and spatial distribution, to better understand disease transmission dynamics. This information may contribute to the planning and development of vector control strategies.<br><br>RESULTS: A total of 778 Anopheles mosquitoes were collected in fifteen localities of C&#xf3;rdoba from August 2015 to October 2016. Six species were identified and overall, Anopheles albimanus was the most widespread and abundant species (83%). Other species of the Nyssorhynchus subgenus were collected, including Anopheles triannulatus (13%), Anopheles nuneztovari (1%), Anopheles argyritarsis (<&#xa0;1%) and two species belonging to the Anopheles subgenus: Anopheles pseudopunctipennis (3%) and Anopheles neomaculipalpus (<&#xa0;1%). Four species were found naturally infected with two Plasmodium species: Anopheles nuneztovari was detected naturally infected with Plasmodium falciparum and Anopheles pseudopunctipennis with Plasmodium vivax, whereas An. albimanus and An. triannulatus were found infected with both parasite species and confirmed by nested PCR.<br><br>CONCLUSIONS: In general, the obtained results were contrasting with previous studies in terms of the most abundant and widespread collected species, and regarding infection rates, which were higher than those previously reported. A positive relationship between mosquito local abundance at the locality level and human infection at the municipality level was found. Mosquito local abundance and the number of houses with mosquitoes in each village are factors explaining malaria human cases in these villages. The obtained results suggest that other factors related to the apparent variation in malaria eco-epidemiology in northern Colombia, must be identified, to provide health authorities with better decision tools aiming to design control and prevention strategies.},
}
@article {pmid29078044,
year = {2018},
author = {Bogdziewicz, M and Bonal, R and Espelta, JM and Kalemba, EM and Steele, MA and Zwolak, R},
title = {Invasive oaks escape pre-dispersal insect seed predation and trap enemies in their seeds.},
journal = {Integrative zoology},
volume = {13},
number = {3},
pages = {228-237},
doi = {10.1111/1749-4877.12285},
pmid = {29078044},
issn = {1749-4877},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Feeding Behavior ; Introduced Species ; Larva ; Lipids/analysis ; *Moths ; Plant Proteins/analysis ; Poland ; Quercus/*physiology ; Seed Dispersal ; Seeds/chemistry/*physiology ; Tannins/analysis ; *Weevils ; },
abstract = {Species introduced to habitats outside their native range often escape control by their natural enemies. Besides competing with native species, an alien species might also affect the native herbivores by introducing a new source of different quality food. Here, we describe the case of northern red oak (Quercus rubra) invasion in Europe. We collected data on insect (moth Cydia spp. and weevil Curculio spp.) seed predation of northern red oak in its native (USA, North America) and invasive (Poland, Europe) range, as well as for sessile oaks (Quercus petrea) in Europe. We also evaluated the quality of acorns as hosts for weevil larvae by collecting infested acorns and measuring weevil developmental success, and quantifying acorn traits such as seed mass, tannins, lipids and protein concentration. We used DNA barcoding to identify insects to the species level. The predation by moths was similar and very low in both species and in both ranges. However, red oaks escape pre-dispersal seed predation by weevils in Europe. Weevil infestation rates of northern red oak acorns in their invasive range were 10 times lower than that of sessile oaks, and also 10 times lower than that of red oaks in North America. Furthermore, even when weevils oviposited into northern red oaks, the larvae failed to develop, suggesting that the exotic host created a trap for the insect. This phenomenon might gradually decrease the local abundance of the seed predator, and further aid the invasion.},
}
@article {pmid29077841,
year = {2017},
author = {Liu, S and Yang, C and Zhou, C and Zhou, X},
title = {Filling reference gaps via assembling DNA barcodes using high-throughput sequencing-moving toward barcoding the world.},
journal = {GigaScience},
volume = {6},
number = {12},
pages = {1-8},
pmid = {29077841},
issn = {2047-217X},
mesh = {Animals ; Biodiversity ; Classification/methods ; *DNA Barcoding, Taxonomic ; *High-Throughput Nucleotide Sequencing ; Insecta/genetics ; Phylogeny ; },
abstract = {Over the past decade, biodiversity researchers have dedicated tremendous efforts to constructing DNA reference barcodes for rapid species registration and identification. Although analytical cost for standard DNA barcoding has been significantly reduced since early 2000, further dramatic reduction in barcoding costs is unlikely because Sanger sequencing is approaching its limits in throughput and chemistry cost. Constraints in barcoding cost not only led to unbalanced barcoding efforts around the globe, but also prevented high-throughput sequencing (HTS)-based taxonomic identification from applying binomial species names, which provide crucial linkages to biological knowledge. We developed an Illumina-based pipeline, HIFI-Barcode, to produce full-length Cytochrome c oxidase subunit I (COI) barcodes from pooled polymerase chain reaction amplicons generated by individual specimens. The new pipeline generated accurate barcode sequences that were comparable to Sanger standards, even for different haplotypes of the same species that were only a few nucleotides different from each other. Additionally, the new pipeline was much more sensitive in recovering amplicons at low quantity. The HIFI-Barcode pipeline successfully recovered barcodes from more than 78% of the polymerase chain reactions that didn't show clear bands on the electrophoresis gel. Moreover, sequencing results based on the single molecular sequencing platform Pacbio confirmed the accuracy of the HIFI-Barcode results. Altogether, the new pipeline can provide an improved solution to produce full-length reference barcodes at about one-tenth of the current cost, enabling construction of comprehensive barcode libraries for local fauna, leading to a feasible direction for DNA barcoding global biomes.},
}
@article {pmid29075838,
year = {2018},
author = {Du, YH and Zhao, YJ and Tang, FH},
title = {A New Molecular Approach Based on the Secondary Structure of Ribosomal RNA for Phylogenetic Analysis of Mobilid Ciliates.},
journal = {Current microbiology},
volume = {75},
number = {3},
pages = {296-304},
pmid = {29075838},
issn = {1432-0991},
mesh = {DNA, Protozoan/*chemistry/genetics ; Nucleic Acid Conformation ; Oligohymenophorea/chemistry/classification/genetics/*isolation &amp; purification ; *Phylogeny ; RNA, Ribosomal/*chemistry/genetics ; },
abstract = {We analyzed the secondary structure of the small subunit (SSU) rRNA genes of Mobilida (Ciliophora, Peritrichia) and found that the secondary structures of some regions within the SSU-rRNA gene are distinct between the families Trichodinidae and Urceolariidae. Therefore, some of these important regions including H10, H11, H17, H47, H29, H30, H37, E10-1, H45-H46, and V4 (E23-4, E23-7) could be used as the barcodes for classification of these two families. In contrast, V4 (E23-1, E23-2) belongs to a hypervariable region and is not a good barcode at the genus level because of its great inter-specific variation. Our results indicated that the comprehensive analysis of the secondary structure of SSU-rRNA genes is a reliable auxiliary approach for phylogenic study of mobilid ciliates. It was further found that the coevolution between hosts or habitats and the Mobilida ciliates was existent, because the host types and their habitats were critical ecological factors that influenced the evolution of Mobilida ciliates.},
}
@article {pmid29075287,
year = {2017},
author = {Ramirez, JL and Birindelli, JL and Carvalho, DC and Affonso, PRAM and Venere, PC and Ortega, H and Carrillo-Avila, M and Rodríguez-Pulido, JA and Galetti, PM},
title = {Revealing Hidden Diversity of the Underestimated Neotropical Ichthyofauna: DNA Barcoding in the Recently Described Genus Megaleporinus (Characiformes: Anostomidae).},
journal = {Frontiers in genetics},
volume = {8},
number = {},
pages = {149},
pmid = {29075287},
issn = {1664-8021},
abstract = {Molecular studies have improved our knowledge on the neotropical ichthyofauna. DNA barcoding has successfully been used in fish species identification and in detecting cryptic diversity. Megaleporinus (Anostomidae) is a recently described freshwater fish genus within which taxonomic uncertainties remain. Here we assessed all nominal species of this genus using a DNA barcode approach (Cytochrome Oxidase subunit I) with a broad sampling to generate a reference library, characterize new molecular lineages, and test the hypothesis that some of the nominal species represent species complexes. The analyses identified 16 (ABGD and BIN) to 18 (ABGD, GMYC, and PTP) different molecular operational taxonomic units (MOTUs) within the 10 studied nominal species, indicating cryptic biodiversity and potential candidate species. Only Megaleporinus brinco, Megaleporinus garmani, and Megaleporinus elongatus showed correspondence between nominal species and MOTUs. Within six nominal species, a subdivision in two MOTUs was found, while Megaleporinus obtusidens was divided in three MOTUs, suggesting that DNA barcode is a very useful approach to identify the molecular lineages of Megaleporinus, even in the case of recent divergence (< 0.5 Ma). Our results thus provided molecular findings that can be used along with morphological traits to better define each species, including candidate new species. This is the most complete analysis of DNA barcode in this recently described genus, and considering its economic value, a precise species identification is quite desirable and fundamental for conservation of the whole biodiversity of this fish.},
}
@article {pmid29073356,
year = {2017},
author = {Du, K and Park, M and Griffiths, A and Carrion, R and Patterson, J and Schmidt, H and Mathies, R},
title = {Microfluidic System for Detection of Viral RNA in Blood Using a Barcode Fluorescence Reporter and a Photocleavable Capture Probe.},
journal = {Analytical chemistry},
volume = {89},
number = {22},
pages = {12433-12440},
pmid = {29073356},
issn = {1520-6882},
support = {R21 AI100229/AI/NIAID NIH HHS/United States ; R33 AI100229/AI/NIAID NIH HHS/United States ; },
mesh = {*DNA Barcoding, Taxonomic ; DNA Probes/*analysis/*chemistry ; Ebolavirus/*genetics ; *Fluorescence ; Humans ; *Microfluidic Analytical Techniques/instrumentation ; Photochemical Processes ; RNA, Viral/*blood ; },
abstract = {A microfluidic sample preparation multiplexer (SPM) and assay procedure is developed to improve amplification-free detection of Ebola virus RNA from blood. While a previous prototype successfully detected viral RNA following off-chip RNA extraction from infected cells, the new device and protocol can detect Ebola virus in raw blood with clinically relevant sensitivity. The Ebola RNA is hybridized with sequence specific capture and labeling DNA probes in solution and then the complex is pulled down onto capture beads for purification and concentration. After washing, the captured RNA target is released by irradiating the photocleavable DNA capture probe with ultraviolet (UV) light. The released, labeled, and purified RNA is detected by a sensitive and compact fluorometer. Exploiting these capabilities, a detection limit of 800 attomolar (aM) is achieved without target amplification. The new SPM can run up to 80 assays in parallel using a pneumatic multiplexing architecture. Importantly, our new protocol does not require time-consuming and problematic off-chip probe conjugation and washing. This improved SPM and labeling protocol is an important step toward a useful POC device and assay.},
}
@article {pmid29072582,
year = {2017},
author = {Masiero, E and Banik, D and Abson, J and Greene, P and Slater, A and Sgamma, T},
title = {Genus-Specific Real-Time PCR and HRM Assays to Distinguish Liriope from Ophiopogon Samples.},
journal = {Plants (Basel, Switzerland)},
volume = {6},
number = {4},
pages = {},
pmid = {29072582},
issn = {2223-7747},
abstract = {Liriope and Ophiopogon species have a long history of use as traditional medicines across East Asia. They have also become widely used around the world for ornamental and landscaping purposes. The morphological similarities between Liriope and Ophiopogon taxa have made the taxonomy of the two genera problematic and caused confusion about the identification of individual specimens. Molecular approaches could be a useful tool for the discrimination of these two genera in combination with traditional methods. Seventy-five Liriope and Ophiopogon samples from the UK National Plant Collections of Ophiopogon and Liriope were analyzed. The 5' end of the DNA barcode region of the gene for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcLa) was used for the discrimination of the two genera. A single nucleotide polymorphism (SNP) between the two genera allowed the development of discriminatory tests for genus-level identification based on specific PCR and high-resolution melt curve (HRM) assays. The study highlights the advantage of incorporating DNA barcoding methods into plant identification protocols and provides simple assays that could be used for the quality assurance of commercially traded plants and herbal drugs.},
}
@article {pmid29071864,
year = {2017},
author = {Wang, MH and Kang, TG and Xu, L and Yang, YY and Cai, ZJ},
title = {[Identification of Ranae Oviductus original animal based on COI sequences].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {42},
number = {8},
pages = {1572-1577},
doi = {10.19540/j.cnki.cjcmm.20170223.016},
pmid = {29071864},
issn = {1001-5302},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Male ; Materia Medica/*analysis ; Phylogeny ; Polymerase Chain Reaction ; Ranidae/*classification ; },
abstract = {Ranae Oviductus has a high economic and social value, but its adulterants are more numerous, which causes a great confusion to the market. Using DNA bar code technology based on COI sequence for PCR amplification and sequencing of the identified Rana dybowskii, R. chensinensis, R. huanrensis and R. amurensiss, the COI gene database of four species of Rana was established, and comparing the measured sequence with the sequence of GenBank, four kinds of Rana were identified. The MEGA (molecular evolutionary genetics analysis) 7 .0 software was used to calculate the genetic distance of K2P and construct the NJ (neighbor-joining) system cluster tree. The sequence of the four species of Rana measured were clustered into one group with the sequence of the four kinds of Rana downloaded from GenBank, but separated from the two outer groups downloaded from GenBank. The COI gene of the R. dybowskii was likely to have regional differences, however this technique failed to distinguish male and female Rana. The results showed that DNA bar code technology could accurately identify the base of original animal of R. oviductus. It indicates that DNA bar code COI provides a new method for the identification of R. oviductus.},
}
@article {pmid29069485,
year = {2017},
author = {Barman, AK and Joyce, AL and Torres, R and Higbee, BS},
title = {Assessing Genetic Diversity in Four Stink Bug Species, Chinavia hilaris, Chlorochroa uhleri, Chlorochroa sayi, and Thyanta pallidovirens (Hemiptera: Pentatomidae), Using DNA Barcodes.},
journal = {Journal of economic entomology},
volume = {110},
number = {6},
pages = {2590-2598},
doi = {10.1093/jee/tox227},
pmid = {29069485},
issn = {1938-291X},
mesh = {Animals ; California ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; *Genetic Variation ; Heteroptera/*genetics ; Insect Proteins/genetics ; Male ; Phylogeny ; Pistacia/growth &amp; development ; Sequence Analysis, DNA ; },
abstract = {Stink bugs (Hemiptera: Pentatomidae) are an economically important group of insects that attack numerous crops in the central valley of California. Management of these pests using pheromones or biological control can be species specific, and proper identification of insect species is essential for effective management. The objective was to examine genetic variability in four species of stink bugs, which included Chinavia hilaris (Say) (= Acrosternum hilare) (Hemiptera: Pentatomidae) , Chlorochroa uhleri (Stål) (Hemiptera: Pentatomidae) , Chlorochroa sayi (Stål) (Hemiptera: Pentatomidae), and Thyanta pallidovirens (Stål) (Hemiptera: Pentatomidae) and to determine whether there may be cryptic species present. Stink bugs were collected in pistachios or on adjacent vegetation when abundant in the central valley of California. The mitochondrial DNA cytochrome oxidase I (COI) gene region (i.e., the barcode) was sequenced for each individual. Data were combined with available GenBank accessions for each species and used to construct a phylogenetic tree. Divergence between genera ranged from 11.2 to 15.7%, whereas divergence between the two Chlorochroa spp. was 4.6%. Genetic variation within Chinavia hilaris collections was up to 4.7%, which suggests the presence of a cryptic species. Genetic divergence was highest between individuals of Chinavia hilaris from the west coast and the east coast of the United States. In contrast, genetic variation within individuals of C. uhleri and Ch. sayi was less than 1%. Nine haplotypes were found for Chinavia hilaris, five for C. uhleri, three for Ch. sayi, and five for T. pallidovirens. The relevance of correct species identification and genetic diversity to stink bug management practices was discussed.},
}
@article {pmid29069318,
year = {2018},
author = {Zhao, L and Liu, Z and Levy, SF and Wu, S},
title = {Bartender: a fast and accurate clustering algorithm to count barcode reads.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {5},
pages = {739-747},
pmid = {29069318},
issn = {1367-4811},
support = {R01 HG008354/HG/NHGRI NIH HHS/United States ; R21 CA205172/CA/NCI NIH HHS/United States ; R21 HG009255/HG/NHGRI NIH HHS/United States ; },
mesh = {Algorithms ; Animals ; Artifacts ; Bacteria ; *Cluster Analysis ; Data Accuracy ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Sequence Analysis, RNA ; *Software ; },
abstract = {MOTIVATION: Barcode sequencing (bar-seq) is a high-throughput, and cost effective method to assay large numbers of cell lineages or genotypes in complex cell pools. Because of its advantages, applications for bar-seq are quickly growing-from using neutral random barcodes to study the evolution of microbes or cancer, to using pseudo-barcodes, such as shRNAs or sgRNAs to simultaneously screen large numbers of cell perturbations. However, the computational pipelines for bar-seq clustering are not well developed. Available methods often yield a high frequency of under-clustering artifacts that result in spurious barcodes, or over-clustering artifacts that group distinct barcodes together. Here, we developed Bartender, an accurate clustering algorithm to detect barcodes and their abundances from raw next-generation sequencing data.<br><br>RESULTS: In contrast with existing methods that cluster based on sequence similarity alone, Bartender uses a modified two-sample proportion test that also considers cluster size. This modification results in higher accuracy and lower rates of under- and over-clustering artifacts. Additionally, Bartender includes unique molecular identifier handling and a 'multiple time point' mode that matches barcode clusters between different clustering runs for seamless handling of time course data. Bartender is a set of simple-to-use command line tools that can be performed on a laptop at comparable run times to existing methods.<br><br>Bartender is available at no charge for non-commercial use at https://github.com/LaoZZZZZ/bartender-1.1.<br><br>CONTACT: sasha.levy@stonybrook.edu or song.wu@stonybrook.edu.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid29069293,
year = {2018},
author = {Yeo, S and Coombe, L and Warren, RL and Chu, J and Birol, I},
title = {ARCS: scaffolding genome drafts with linked reads.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {5},
pages = {725-731},
pmid = {29069293},
issn = {1367-4811},
support = {R01 HG007182/HG/NHGRI NIH HHS/United States ; },
mesh = {*Genome, Human ; Genomics/methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Sequence Analysis, DNA/*methods ; *Software ; },
abstract = {MOTIVATION: Sequencing of human genomes is now routine, and assembly of shotgun reads is increasingly feasible. However, assemblies often fail to inform about chromosome-scale structure due to a lack of linkage information over long stretches of DNA-a shortcoming that is being addressed by new sequencing protocols, such as the GemCode and Chromium linked reads from 10 × Genomics.<br><br>RESULTS: Here, we present ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. We show how the contiguity of an ABySS H.sapiens genome assembly can be increased over six-fold, using moderate coverage (25-fold) Chromium data. We expect ARCS to have broad utility in harnessing the barcoding information contained in linked read data for connecting high-quality sequences in genome assembly drafts.<br><br>https://github.com/bcgsc/ARCS/.<br><br>CONTACT: rwarren@bcgsc.ca.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid29066821,
year = {2017},
author = {Lyons, E and Sheridan, P and Tremmel, G and Miyano, S and Sugano, S},
title = {Large-scale DNA Barcode Library Generation for Biomolecule Identification in High-throughput Screens.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {13899},
pmid = {29066821},
issn = {2045-2322},
mesh = {*DNA Barcoding, Taxonomic ; *Gene Library ; *High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; },
abstract = {High-throughput screens allow for the identification of specific biomolecules with characteristics of interest. In barcoded screens, DNA barcodes are linked to target biomolecules in a manner allowing for the target molecules making up a library to be identified by sequencing the DNA barcodes using Next Generation Sequencing. To be useful in experimental settings, the DNA barcodes in a library must satisfy certain constraints related to GC content, homopolymer length, Hamming distance, and blacklisted subsequences. Here we report a novel framework to quickly generate large-scale libraries of DNA barcodes for use in high-throughput screens. We show that our framework dramatically reduces the computation time required to generate large-scale DNA barcode libraries, compared with a naїve approach to DNA barcode library generation. As a proof of concept, we demonstrate that our framework is able to generate a library consisting of one million DNA barcodes for use in a fragment antibody phage display screening experiment. We also report generating a general purpose one billion DNA barcode library, the largest such library yet reported in literature. Our results demonstrate the value of our novel large-scale DNA barcode library generation framework for use in high-throughput screening applications.},
}
@article {pmid29059215,
year = {2017},
author = {Jakubavičiūtė, E and Bergström, U and Eklöf, JS and Haenel, Q and Bourlat, SJ},
title = {DNA metabarcoding reveals diverse diet of the three-spined stickleback in a coastal ecosystem.},
journal = {PloS one},
volume = {12},
number = {10},
pages = {e0186929},
pmid = {29059215},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Ecosystem ; Smegmamorpha/genetics/*physiology ; },
abstract = {The three-spined stickleback (Gasterosteus aculeatus L., hereafter 'stickleback') is a common mesopredatory fish in marine, coastal and freshwater areas. In large parts of the Baltic Sea, stickleback densities have increased >10-fold during the last decades, and it is now one of the dominating fish species both in terms of biomass and effects on lower trophic levels. Still, relatively little is known about its diet-knowledge which is essential to understand the increasing role sticklebacks play in the ecosystem. Fish diet analyses typically rely on visual identification of stomach contents, a labour-intensive method that is made difficult by prey digestion and requires expert taxonomic knowledge. However, advances in DNA-based metabarcoding methods promise a simultaneous identification of most prey items, even from semi-digested tissue. Here, we studied the diet of stickleback from the western Baltic Sea coast using both DNA metabarcoding and visual analysis of stomach contents. Using the cytochrome oxidase (CO1) marker we identified 120 prey taxa in the diet, belonging to 15 phyla, 83 genera and 84 species. Compared to previous studies, this is an unusually high prey diversity. Chironomids, cladocerans and harpacticoids were dominating prey items. Large sticklebacks were found to feed more on benthic prey, such as amphipods, gastropods and isopods. DNA metabarcoding gave much higher taxonomic resolution (median rank genus) than visual analysis (median rank order), and many taxa identified using barcoding could not have been identified visually. However, a few taxa identified by visual inspection were not revealed by barcoding. In summary, our results suggest that the three-spined stickleback feeds on a wide variety of both pelagic and benthic organisms, indicating that the strong increase in stickleback populations may affect many parts of the Baltic Sea coastal ecosystem.},
}
@article {pmid29055694,
year = {2018},
author = {Mello, &#xc9;M and Furtado, LFV and Rabelo, &#xc9;ML and Pinto, HA},
title = {DNA barcoding of metacestodes found in the Guerlinguetus ingrami (Rodentia: Sciuridae) reveals the occurrence of Hydatigera taeniaeformis sensu stricto (Cyclophyllidea: Taeniidae) in the Americas.},
journal = {Parasitology international},
volume = {67},
number = {2},
pages = {115-118},
doi = {10.1016/j.parint.2017.10.005},
pmid = {29055694},
issn = {1873-0329},
mesh = {Americas/epidemiology ; Animals ; Brazil/epidemiology ; Cestoda/*genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/methods ; Liver/parasitology ; Sciuridae/*parasitology ; Taenia/*genetics/isolation &amp; purification ; Taeniasis/epidemiology/parasitology/transmission ; },
abstract = {The existence of cryptic species in the genus Hydatigera, cyclophillid cestodes, mainly of felids, was recently described based on molecular studies of parasites from Asia, Europe and Africa. However, the occurrence of H. taeniaeformis sensu stricto (s.s.), the species more widely distributed and with a presumed specificity for murid rodents as intermediate hosts, has not been formally described in Americas. In the present study, during necropsy of an Ingram's squirrel specimen, Guerlinguetus ingrami, found dead in the municipality of Belo Horizonte, Minas Gerais state, Brazil, strobilocerci were found in the liver. The metacestodes were subjected to morphological and molecular studies. Sequences of the COI barcode region were obtained and used for phylogenetic analyses. The morphology and measures of the rostellar hooks were compatible with the ones described for H. taeniaeformis s.s. This identification was confirmed by a molecular phylogenetic approach (96.2-99.7% similarity with isolates of the parasite from Europe and Asia). This is the first molecular confirmation of the existence of H. taeniaeformis s.s. on the American continent. Moreover, the involvement of sciurid rodents in the transmission of H. taeniaeformis s.s. is discussed here as a probable case of parasite spillover.},
}
@article {pmid29052405,
year = {2017},
author = {Ren, YY and Jiang, NP and Liu, RY and Song, LK and Tan, R and Gu, J},
title = {[ITS2 sequence analysis and identification of medicinal Artemisia plants].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {42},
number = {7},
pages = {1395-1400},
doi = {10.19540/j.cnki.cjcmm.20170222.016},
pmid = {29052405},
issn = {1001-5302},
mesh = {Artemisia/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/*genetics ; *Phylogeny ; Plants, Medicinal/genetics ; Tibet ; },
abstract = {Artemisia hedinii occupies an important position in the Tibetan medicine. Plants in Artemisia vary a lot and are widely distributed in the Qinghai-Tibet Plateau, many plants in Artemisia look similar, making traditional identification methods laborious. In this article, ITS2 sequences were used as DNA barcoding to identify four kinds of confusable Tibetan medicine plants in Artemisia, aiming to establish a rapid and accurate identification methods. Twenty-one samples in Artemisia were collected from the Qinghai-Tibet Plateau, ITS2 sequence PCR amplification and sequencing were conducted after the extraction of DNA. Another 11 sequence downloaded from Genbank were added to the analysis. Genetic distance calculation and analysis, building Neighbor Joining (NJ) phylogenetic tree were conducted by MEGA 6.0, also comparison of secondary structures of ITS2 sequences among samples. A. hedinii, A. annua, A. dubia and A. argyi shared close genetic distance, but the maximum distance between the four species was much greater than the minimum distance within each species, NJ tree showed that the four species went to four separate branches, differences among secondary structures of ITS2 sequences also made it clear to identify these medical plants. It could be an accurate and rapid method for identification and recognition, as well as the evolutionary relationships between the species by using ITS2 sequence as DNA barcode for plants of Tibetan Artemisia. The study provides theoretical basis for quality control, medication safety and rational exploitation.},
}
@article {pmid29051542,
year = {2017},
author = {Ogawa, T and Kryukov, K and Imanishi, T and Shiroguchi, K},
title = {The efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {13576},
pmid = {29051542},
issn = {2045-2322},
mesh = {DNA ; DNA Barcoding, Taxonomic/*methods ; Polymerase Chain Reaction ; Random Allocation ; Sequence Analysis, RNA/*methods ; },
abstract = {Accurate quantification of biomolecules in system-wide measurements is in high demand, especially for systems with limited sample amounts such as single cells. Because of this, digital quantification of nucleic acid molecules using molecular barcodes has been developed, making, e.g., transcriptome analysis highly reproducible and quantitative. This counting scheme was shown to work using sequence-restricted barcodes, and non-sequence-restricted (random-base) barcodes that may provide a much higher dynamic range at significantly lower cost have been widely used. However, the efficacy of random-base barcodes is significantly affected by base changes due to amplification and/or sequencing errors and has not been investigated experimentally or quantitatively. Here, we show experimentally that random-base barcodes enable absolute and digital quantification of DNA molecules with high dynamic range (from one to more than 10[4], potentially up to 10[15] molecules) conditional on our barcode design and variety, a certain range of sequencing depths, and computational analyses. Moreover, we quantitatively show further functional advantages of the molecular barcodes: the molecular barcodes enable one to find contaminants and misidentifications of target sequences. Our scheme here may be generally used to confirm that the digital quantification works in each platform.},
}
@article {pmid29049373,
year = {2017},
author = {Lavinia, PD and Núñez Bustos, EO and Kopuchian, C and Lijtmaer, DA and García, NC and Hebert, PDN and Tubaro, PL},
title = {Barcoding the butterflies of southern South America: Species delimitation efficacy, cryptic diversity and geographic patterns of divergence.},
journal = {PloS one},
volume = {12},
number = {10},
pages = {e0186845},
pmid = {29049373},
issn = {1932-6203},
mesh = {Animals ; Butterflies/classification/*genetics ; *DNA Barcoding, Taxonomic ; Genetic Variation ; Phylogeography ; Species Specificity ; },
abstract = {Because the tropical regions of America harbor the highest concentration of butterfly species, its fauna has attracted considerable attention. Much less is known about the butterflies of southern South America, particularly Argentina, where over 1,200 species occur. To advance understanding of this fauna, we assembled a DNA barcode reference library for 417 butterfly species of Argentina, focusing on the Atlantic Forest, a biodiversity hotspot. We tested the efficacy of this library for specimen identification, used it to assess the frequency of cryptic species, and examined geographic patterns of genetic variation, making this study the first large-scale genetic assessment of the butterflies of southern South America. The average sequence divergence to the nearest neighbor (i.e. minimum interspecific distance) was 6.91%, ten times larger than the mean distance to the furthest conspecific (0.69%), with a clear barcode gap present in all but four of the species represented by two or more specimens. As a consequence, the DNA barcode library was extremely effective in the discrimination of these species, allowing a correct identification in more than 95% of the cases. Singletons (i.e. species represented by a single sequence) were also distinguishable in the gene trees since they all had unique DNA barcodes, divergent from those of the closest non-conspecific. The clustering algorithms implemented recognized from 416 to 444 barcode clusters, suggesting that the actual diversity of butterflies in Argentina is 3%-9% higher than currently recognized. Furthermore, our survey added three new records of butterflies for the country (Eurema agave, Mithras hannelore, Melanis hillapana). In summary, this study not only supported the utility of DNA barcoding for the identification of the butterfly species of Argentina, but also highlighted several cases of both deep intraspecific and shallow interspecific divergence that should be studied in more detail.},
}
@article {pmid29049301,
year = {2017},
author = {Heckenhauer, J and Abu Salim, K and Chase, MW and Dexter, KG and Pennington, RT and Tan, S and Kaye, ME and Samuel, R},
title = {Plant DNA barcodes and assessment of phylogenetic community structure of a tropical mixed dipterocarp forest in Brunei Darussalam (Borneo).},
journal = {PloS one},
volume = {12},
number = {10},
pages = {e0185861},
pmid = {29049301},
issn = {1932-6203},
support = {P 26548/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Borneo ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; Databases, Genetic ; *Forests ; Likelihood Functions ; *Phylogeny ; Plants/classification/*genetics ; },
abstract = {DNA barcoding is a fast and reliable tool to assess and monitor biodiversity and, via community phylogenetics, to investigate ecological and evolutionary processes that may be responsible for the community structure of forests. In this study, DNA barcodes for the two widely used plastid coding regions rbcL and matK are used to contribute to identification of morphologically undetermined individuals, as well as to investigate phylogenetic structure of tree communities in 70 subplots (10 × 10m) of a 25-ha forest-dynamics plot in Brunei (Borneo, Southeast Asia). The combined matrix (rbcL + matK) comprised 555 haplotypes (from ≥154 genera, 68 families and 25 orders sensu APG, Angiosperm Phylogeny Group, 2016), making a substantial contribution to tree barcode sequences from Southeast Asia. Barcode sequences were used to reconstruct phylogenetic relationships using maximum likelihood, both with and without constraining the topology of taxonomic orders to match that proposed by the Angiosperm Phylogeny Group. A third phylogenetic tree was reconstructed using the program Phylomatic to investigate the influence of phylogenetic resolution on results. Detection of non-random patterns of community assembly was determined by net relatedness index (NRI) and nearest taxon index (NTI). In most cases, community assembly was either random or phylogenetically clustered, which likely indicates the importance to community structure of habitat filtering based on phylogenetically correlated traits in determining community structure. Different phylogenetic trees gave similar overall results, but the Phylomatic tree produced greater variation across plots for NRI and NTI values, presumably due to noise introduced by using an unresolved phylogenetic tree. Our results suggest that using a DNA barcode tree has benefits over the traditionally used Phylomatic approach by increasing precision and accuracy and allowing the incorporation of taxonomically unidentified individuals into analyses.},
}
@article {pmid29049085,
year = {2018},
author = {Evanson, HV and Rodgers, L and Reed, J and Daily, A and Gerlach, K and Greene, M and Koeppl, P and Cox, R and Williams, W},
title = {Experience and Compliance With Scanning Vaccines' Two-Dimensional Barcodes to Record Data.},
journal = {Computers, informatics, nursing : CIN},
volume = {36},
number = {1},
pages = {8-17},
pmid = {29049085},
issn = {1538-9774},
support = {CC999999//Intramural CDC HHS/United States ; },
mesh = {Electronic Data Processing/*statistics &amp; numerical data ; Humans ; Medical Records/*statistics &amp; numerical data ; Risk Assessment ; United States ; Vaccines/*administration &amp; dosage ; },
abstract = {Automated population of data into health information system fields offers the potential to increase efficiencies and save time. Increasingly, as two-dimensional barcoded vaccine products and barcode scanning technology become more widely available, manual recording of vaccine data can be reduced. This evaluation explores how often two-dimensional barcodes on vaccine vials and syringes were scanned and the perceived benefits and challenges reported by vaccine providers. Eighty-two facilities that administer vaccines completed the evaluation. Twenty-seven of those facilities provided records from vaccines administered between July 2014 and January 2015. Among the 63 179 two-dimensional barcoded vaccine administrations recorded, 12 408 (19%) were scanned. We received 116 user surveys from 63 facilities; using content analysis, we identified perceived benefits of scanning, workflow challenges, scanning challenges, and other challenges. The findings of this evaluation can guide health information system developers, vaccine manufacturers, and vaccine providers on how to remove potential barriers to using two-dimensional barcode scanning.},
}
@article {pmid29045665,
year = {2017},
author = {Khamis, FM and Rwomushana, I and Ombura, LO and Cook, G and Mohamed, SA and Tanga, CM and Nderitu, PW and Borgemeister, C and Sétamou, M and Grout, TG and Ekesi, S},
title = {DNA Barcode Reference Library for the African Citrus Triozid, Trioza erytreae (Hemiptera: Triozidae): Vector of African Citrus Greening.},
journal = {Journal of economic entomology},
volume = {110},
number = {6},
pages = {2637-2646},
doi = {10.1093/jee/tox283},
pmid = {29045665},
issn = {1938-291X},
mesh = {Animals ; Citrus/microbiology ; DNA Barcoding, Taxonomic ; Hemiptera/classification/*genetics/growth &amp; development ; Insect Vectors/classification/*genetics/growth &amp; development ; Kenya ; Likelihood Functions ; Nymph/genetics/growth &amp; development ; Phylogeny ; Plant Diseases/microbiology ; Sequence Analysis, DNA ; Tanzania ; },
abstract = {Citrus (Citrus spp.) production continues to decline in East Africa, particularly in Kenya and Tanzania, the two major producers in the region. This decline is attributed to pests and diseases including infestation by the African citrus triozid, Trioza erytreae (Del Guercio) (Hemiptera: Triozidae). Besides direct feeding damage by adults and immature stages, T. erytreae is the main vector of 'Candidatus Liberibacter africanus', the causative agent of Greening disease in Africa, closely related to Huanglongbing. This study aimed to generate a novel barcode reference library for T. erytreae in order to use DNA barcoding as a rapid tool for accurate identification of the pest to aid phytosanitary measures. Triozid samples were collected from citrus orchards in Kenya, Tanzania, and South Africa and from alternative host plants. Sequences generated from populations in the study showed very low variability within acceptable ranges of species. All samples analyzed were linked to T. erytreae of GenBank accession number KU517195. Phylogeny of samples in this study and other Trioza reference species was inferred using the Maximum Likelihood method. The phylogenetic tree was paraphyletic with two distinct branches. The first branch had two clusters: 1) cluster of all populations analyzed with GenBank accession of T. erytreae and 2) cluster of all the other GenBank accession of Trioza species analyzed except T. incrustata Percy, 2016 (KT588307.1), T. eugeniae Froggatt (KY294637.1), and T. grallata Percy, 2016 (KT588308.1) that occupied the second branch as outgroups forming sister clade relationships. These results were further substantiated with genetic distance values and principal component analyses.},
}
@article {pmid29045427,
year = {2017},
author = {Gabel, M and Regoes, RR and Graw, F},
title = {More or less-On the influence of labelling strategies to infer cell population dynamics.},
journal = {PloS one},
volume = {12},
number = {10},
pages = {e0185523},
pmid = {29045427},
issn = {1932-6203},
mesh = {Cell Differentiation ; Cell Proliferation ; Cells/*cytology ; Homeostasis ; Models, Biological ; Staining and Labeling/*methods ; Time Factors ; },
abstract = {The adoptive transfer of labelled cell populations has been an essential tool to determine and quantify cellular dynamics. The experimental methods to label and track cells over time range from fluorescent dyes over congenic markers towards single-cell labelling techniques, such as genetic barcodes. While these methods have been widely used to quantify cell differentiation and division dynamics, the extent to which the applied labelling strategy actually affects the quantification of the dynamics has not been determined so far. This is especially important in situations where measurements can only be obtained at a single time point, as e.g. due to organ harvest. To this end, we studied the appropriateness of various labelling strategies as characterised by the number of different labels and the initial number of cells per label to quantify cellular dynamics. We simulated adoptive transfer experiments in systems of various complexity that assumed either homoeostatic cellular turnover or cell expansion dynamics involving various steps of cell differentiation and proliferation. Re-sampling cells at a single time point, we determined the ability of different labelling strategies to recover the underlying kinetics. Our results indicate that cell transition and expansion rates are differently affected by experimental shortcomings, such as loss of cells during transfer or sampling, dependent on the labelling strategy used. Furthermore, uniformly distributed labels in the transferred population generally lead to more robust and less biased results than non-equal label sizes. In addition, our analysis indicates that certain labelling approaches incorporate a systematic bias for the identification of complex cell expansion dynamics.},
}
@article {pmid29043627,
year = {2018},
author = {Haye-Bertolozzi, JE and Aparicio, OM},
title = {Quantitative Bromodeoxyuridine Immunoprecipitation Analyzed by High-Throughput Sequencing (qBrdU-Seq or QBU).},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1672},
number = {},
pages = {209-225},
doi = {10.1007/978-1-4939-7306-4_16},
pmid = {29043627},
issn = {1940-6029},
support = {R01 GM065494/GM/NIGMS NIH HHS/United States ; },
mesh = {*Bromodeoxyuridine ; DNA Barcoding, Taxonomic ; DNA Replication ; DNA, Fungal ; Gene Library ; *High-Throughput Nucleotide Sequencing/methods ; *Immunoprecipitation/methods ; Quality Control ; Yeasts/genetics ; },
abstract = {Incorporation into DNA of nucleoside analogs like 5-bromo-2'-deoxyuridine (BrdU) is a powerful tool for in vivo studies of DNA synthesis during replication and repair. Immunoprecipitation of BrdU-labeled DNA analyzed by DNA sequencing (BrdU-IP-seq) allows for genome-wide, sequence-specific tracking of replication origin and replication fork dynamics under different conditions, such as DNA damage and replication stress, and in mutant strains. We have recently developed a quantitative method for BrdU-IP-seq (qBrdU-seq) involving DNA barcoding to enable quantitative analysis of multiple experimental samples subjected to BrdU-IP-seq. After initial barcoding of multiple, individually BrdU-labeled genomic DNA samples, a pooling strategy is used for all subsequent steps including immunoprecipitation, amplification, and sequencing, which eliminates sample-to-sample variability in these steps. Parallel processing of an aliquot of the pooled input sample provides a direct control for the normalization of the data and yields results that allow quantitative comparisons of the experimental samples. Though developed for the analysis of S. cerevisiae, this method should be directly adaptable to other model systems.},
}
@article {pmid29039868,
year = {2017},
author = {Yang, M and Zhang, W and Zheng, W and Cao, F and Jiang, X},
title = {Inkjet-printed barcodes for a rapid and multiplexed paper-based assay compatible with mobile devices.},
journal = {Lab on a chip},
volume = {17},
number = {22},
pages = {3874-3882},
doi = {10.1039/c7lc00780a},
pmid = {29039868},
issn = {1473-0189},
mesh = {Animals ; Antibodies, Viral/chemistry/metabolism ; Blood Donors ; *Cell Phone ; Drug Residues/analysis ; Equipment Design ; Humans ; Immunoassay/*instrumentation ; *Lab-On-A-Chip Devices ; Milk/chemistry ; Nucleic Acids/analysis ; Paper ; Printing ; Virus Diseases/diagnosis ; },
abstract = {This study reports a simple, rapid, low-cost, robust, and multiplexed barcoded paper-based assay (BPA) compatible with mobile devices. An inkjet printer and an XYZ dispensing platform were used to realize mass-manufacturing of barcoded paper-based analytical devices (BPADs) with high precision and efficiency. We designed a new group of barcodes and developed an application (APP) for the reading of the new code. The new barcodes possess a 16 times higher coding capacity than the standard Codabar code in our experiment on drug residue detection. The BPA system allows applications in the assays of blood-transmitted infections, drug residues in milk and multiplex nucleic acids. The whole detection process and the readout of the results can be completed within 10 minutes. The limit of detection for enrofloxacin (ENR) (8 ng mL[-1]) satisfies the requirements of drug residue monitoring. Its high rapidity, simplicity, efficiency and selectivity make the BPA system extremely suitable to be applied in rapid and on-site detection.},
}
@article {pmid29038999,
year = {2018},
author = {Idziak-Helmcke, D and Betekhtin, A},
title = {Methods for Cytogenetic Chromosome Barcoding and Chromosome Painting in Brachypodium distachyon and Its Relative Species.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1667},
number = {},
pages = {1-19},
doi = {10.1007/978-1-4939-7278-4_1},
pmid = {29038999},
issn = {1940-6029},
mesh = {Brachypodium/*cytology/*genetics ; Chromosome Painting/*methods ; Chromosomes, Plant/*genetics ; Cytogenetics/*methods ; Genome, Plant ; In Situ Hybridization, Fluorescence/methods ; Karyotype ; Meiosis ; Mitosis ; },
abstract = {Brachypodium distachyon provides a particularly appealing object for molecular cytogenetic analysis due to its compact genome and low repetitive DNA content, as well as low (x = 5) basic number of chromosomes easily identifiable on the basis of their morphometric features. Some of these features, such as genome compactness, are shared by the other members of the genus, thus making them amenable for comparative cytogenetic mapping. Cytogenetic infrastructure established for B. distachyon was initially based on fluorescence in situ hybridization with various tandemly repeated sequences as probes. The molecular cytogenetic studies advanced greatly with the development of B. distachyon large DNA insert genomic libraries. These resources coupled with the access to the fully sequenced genome of B. distachyon enabled chromosome painting in monocots for the first time. This pioneering work was subsequently extended to other Brachypodium species, allowing insight into grass karyotype evolution. In this protocol we describe the methods of making somatic and meiotic chromosome preparations, probe labeling, FISH with BAC clones, a strategy for chromosome barcoding and chromosome painting in B. distachyon, and comparative chromosome painting in the other Brachypodium species.},
}
@article {pmid29038170,
year = {2017},
author = {Jiang, S and Liu, Y and Xu, C and Wang, Y and Gong, J and Shen, Y and Wu, Q and Boeke, JD and Dai, J},
title = {Dissecting Nucleosome Function with a Comprehensive Histone H2A and H2B Mutant Library.},
journal = {G3 (Bethesda, Md.)},
volume = {7},
number = {12},
pages = {3857-3866},
pmid = {29038170},
issn = {2160-1836},
support = {U54 GM103520/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acids/genetics ; DNA Damage/*drug effects ; Gene Library ; Gene Silencing ; Genomic Instability/genetics ; High-Throughput Nucleotide Sequencing ; Histones/*genetics ; Mutant Proteins/genetics ; Nucleosomes/*genetics ; Protein Binding ; Saccharomyces cerevisiae/genetics ; },
abstract = {Using a comprehensive library of histone H2A and H2B mutants, we assessed the biological function of each amino acid residue involved in various stress conditions including exposure to different DNA damage-inducing reagents, different growth temperatures, and other chemicals. H2B N- and H2A C-termini were critical for maintaining nucleosome function and mutations in these regions led to pleiotropic phenotypes. Additionally, two screens were performed using this library, monitoring heterochromatin gene silencing and genome stability, to identify residues that could compromise normal function when mutated. Many distinctive regions within the nucleosome were revealed. Furthermore, we used the barcode sequencing (bar-seq) method to profile the mutant composition of many libraries in one high-throughput sequencing experiment, greatly reducing the labor and increasing the capacity. This study not only demonstrates the applications of the versatile histone library, but also reveals many previously unknown functions of histone H2A and H2B.},
}
@article {pmid29037736,
year = {2018},
author = {Liu, Y and Xiang, L and Zhang, Y and Lai, X and Xiong, C and Li, J and Su, Y and Sun, W and Chen, S},
title = {DNA barcoding based identification of Hippophae species and authentication of commercial products by high resolution melting analysis.},
journal = {Food chemistry},
volume = {242},
number = {},
pages = {62-67},
doi = {10.1016/j.foodchem.2017.09.040},
pmid = {29037736},
issn = {1873-7072},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Intergenic/chemistry/genetics ; DNA, Plant/chemistry/genetics ; Dietary Supplements/*classification ; Drug Contamination/*prevention &amp; control ; Food Contamination/*prevention &amp; control ; Hippophae/*classification/genetics ; Sequence Analysis, DNA ; Transition Temperature ; },
abstract = {Sea buckthorn (Hippophae), an ancient crop with modern virtues, is increasingly consumed in source of foods and nutraceuticals. The growing demand leads to the adulteration of commercial sea buckthorn products, which is a common form of food fraud. Herein, a high resolution melting assay, targeting a DNA barcoding region of the internal transcribed spacer 2 (ITS2) (Bar-HRM) was developed to identify the seven native Chinese Hippophae species, and to authenticate commercial sea buckthorn products. Melting data from the HRM assay demonstrated that all Hippophae species could be clearly distinguished. Then, application to commercial sea buckthorn products indicated the existence of adulterants or contamination, further confirmed using Sanger sequencing results for PCR products from HRM. The Bar-HRM technique proposed in this work could provide a method for regulatory agencies, promoting consumers trust, and raise the quality and safety of sea buckthorn products.},
}
@article {pmid29037251,
year = {2017},
author = {Rodrigues, MS and Morelli, KA and Jansen, AM},
title = {Cytochrome c oxidase subunit 1 gene as a DNA barcode for discriminating Trypanosoma cruzi DTUs and closely related species.},
journal = {Parasites &amp; vectors},
volume = {10},
number = {1},
pages = {488},
pmid = {29037251},
issn = {1756-3305},
mesh = {Brazil/epidemiology ; Chagas Disease/*parasitology ; *DNA Barcoding, Taxonomic ; DNA, Protozoan/genetics ; Electron Transport Complex IV/*genetics ; Genotype ; Glucose-6-Phosphate Isomerase/genetics ; Humans ; Mitochondrial Proteins/genetics ; Trypanosoma/*classification/genetics/isolation &amp; purification ; Trypanosoma cruzi/classification/genetics/isolation &amp; purification ; Trypanosoma rangeli/classification/genetics/isolation &amp; purification ; },
abstract = {BACKGROUND: The DNA barcoding system using the cytochrome c oxidase subunit 1 mitochondrial gene (cox1 or COI) is highly efficient for discriminating vertebrate and invertebrate species. In the present study, we examined the suitability of cox1 as a marker for Trypanosoma cruzi identification from other closely related species. Additionally, we combined the sequences of cox1 and the nuclear gene glucose-6-phosphate isomerase (GPI) to evaluate the occurrence of mitochondrial introgression and the presence of hybrid genotypes.<br><br>METHODS: Sixty-two isolates of Trypanosoma spp. obtained from five of the six Brazilian biomes (Amazon Forest, Atlantic Forest, Caatinga, Cerrado and Pantanal) were sequenced for cox1 and GPI gene fragments. Phylogenetic trees were reconstructed using neighbor-joining, maximum likelihood, parsimony and Bayesian inference methods. Molecular species delimitation was evaluated through pairwise intraspecific and interspecific distances, Automatic Barcode Gap Discovery, single-rate Poisson Tree Processes and multi-rate Poisson Tree Processes.<br><br>RESULTS: Both cox1 and GPI genes recognized and differentiated T. cruzi, Trypanosoma cruzi marinkellei, Trypanosoma dionisii and Trypanosoma rangeli. Cox1 discriminated Tcbat, TcI, TcII, TcIII and TcIV. Additionally, TcV and TcVI were identified as a single group. Cox1 also demonstrated diversity in the discrete typing units (DTUs) TcI, TcII and TcIII and in T. c. marinkellei and T. rangeli. Cox1 and GPI demonstrated TcI and TcII as the most genetically distant branches, and the position of the other T. cruzi DTUs differed according to the molecular marker. The tree reconstructed with concatenated cox1 and GPI sequences confirmed the separation of the subgenus Trypanosoma (Schizotrypanum) sp. and the T. cruzi DTUs TcI, TcII, TcIII and TcIV. The evaluation of single nucleotide polymorphisms (SNPs) was informative for DTU differentiation using both genes. In the cox1 analysis, one SNP differentiated heterozygous hybrids from TcIV sequences. In the GPI analysis one SNP discriminated Tcbat from TcI, while another SNP distinguished TcI from TcIII.<br><br>CONCLUSIONS: DNA barcoding using the cox1 gene is a reliable tool to distinguish T. cruzi from T. c. marinkellei, T. dionisii and T. rangeli and identify the main T. cruzi genotypes.},
}
@article {pmid29032499,
year = {2017},
author = {Hu, L and Yang, Y and Zhao, Y and Niu, D and Yang, R and Wang, R and Lu, Z and Li, X},
title = {DNA barcoding for molecular identification of Demodex based on mitochondrial genes.},
journal = {Parasitology research},
volume = {116},
number = {12},
pages = {3285-3290},
pmid = {29032499},
issn = {1432-1955},
support = {81471972//National Natural Science Foundation of China/ ; 81271856//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Base Sequence ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Dog Diseases ; Dogs ; *Genes, Mitochondrial ; Mite Infestations/parasitology/veterinary ; Mites/*classification ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {There has been no widely accepted DNA barcode for species identification of Demodex. In this study, we attempted to solve this issue. First, mitochondrial cox1-5' and 12S gene fragments of Demodex folloculorum, D. brevis, D. canis, and D. caprae were amplified, cloned, and sequenced for the first time; intra/interspecific divergences were computed and phylogenetic trees were reconstructed. Then, divergence frequency distribution plots of those two gene fragments were drawn together with mtDNA cox1-middle region and 16S obtained in previous studies. Finally, their identification efficiency was evaluated by comparing barcoding gap. Results indicated that 12S had the higher identification efficiency. Specifically, for cox1-5' region of the four Demodex species, intraspecific divergences were less than 2.0%, and interspecific divergences were 21.1-31.0%; for 12S, intraspecific divergences were less than 1.4%, and interspecific divergences were 20.8-26.9%. The phylogenetic trees demonstrated that the four Demodex species clustered separately, and divergence frequency distribution plot showed that the largest intraspecific divergence of 12S (1.4%) was less than cox1-5' region (2.0%), cox1-middle region (3.1%), and 16S (2.8%). The barcoding gap of 12S was 19.4%, larger than cox1-5' region (19.1%), cox1-middle region (11.3%), and 16S (13.0%); the interspecific divergence span of 12S was 6.2%, smaller than cox1-5' region (10.0%), cox1-middle region (14.1%), and 16S (11.4%). Moreover, 12S has a moderate length (517 bp) for sequencing at once. Therefore, we proposed mtDNA 12S was more suitable than cox1 and 16S to be a DNA barcode for classification and identification of Demodex at lower category level.},
}
@article {pmid29031828,
year = {2018},
author = {DeFalco, J and Harbell, M and Manning-Bog, A and Baia, G and Scholz, A and Millare, B and Sumi, M and Zhang, D and Chu, F and Dowd, C and Zuno-Mitchell, P and Kim, D and Leung, Y and Jiang, S and Tang, X and Williamson, KS and Chen, X and Carroll, SM and Espiritu Santo, G and Haaser, N and Nguyen, N and Giladi, E and Minor, D and Tan, YC and Sokolove, JB and Steinman, L and Serafini, TA and Cavet, G and Greenberg, NM and Glanville, J and Volkmuth, W and Emerling, DE and Robinson, WH},
title = {Non-progressing cancer patients have persistent B cell responses expressing shared antibody paratopes that target public tumor antigens.},
journal = {Clinical immunology (Orlando, Fla.)},
volume = {187},
number = {},
pages = {37-45},
doi = {10.1016/j.clim.2017.10.002},
pmid = {29031828},
issn = {1521-7035},
mesh = {Adenocarcinoma of Lung/immunology/secondary ; Adult ; Aged ; Aged, 80 and over ; Antibodies ; Antigens, Neoplasm/*immunology ; B-Lymphocytes/*immunology ; Binding Sites, Antibody/immunology ; Carcinoma, Renal Cell/immunology/secondary ; Disease Progression ; Female ; Humans ; Kidney Neoplasms/immunology/pathology ; Lung Neoplasms/immunology/pathology ; Male ; Melanoma/immunology/secondary ; Middle Aged ; Neoplasm Metastasis ; Neoplasms/*immunology ; Plasma Cells/immunology ; Precursor Cells, B-Lymphoid ; Skin Neoplasms/immunology/pathology ; },
abstract = {There is significant debate regarding whether B cells and their antibodies contribute to effective anti-cancer immune responses. Here we show that patients with metastatic but non-progressing melanoma, lung adenocarcinoma, or renal cell carcinoma exhibited increased levels of blood plasmablasts. We used a cell-barcoding technology to sequence their plasmablast antibody repertoires, revealing clonal families of affinity matured B cells that exhibit progressive class switching and persistence over time. Anti-CTLA4 and other treatments were associated with further increases in somatic hypermutation and clonal family size. Recombinant antibodies from clonal families bound non-autologous tumor tissue and cell lines, and families possessing immunoglobulin paratope sequence motifs shared across patients exhibited increased rates of binding. We identified antibodies that caused regression of, and durable immunity toward, heterologous syngeneic tumors in mice. Our findings demonstrate convergent functional anti-tumor antibody responses targeting public tumor antigens, and provide an approach to identify antibodies with diagnostic or therapeutic utility.},
}
@article {pmid29031541,
year = {2017},
author = {Reich, M and Labes, A},
title = {How to boost marine fungal research: A first step towards a multidisciplinary approach by combining molecular fungal ecology and natural products chemistry.},
journal = {Marine genomics},
volume = {36},
number = {},
pages = {57-75},
doi = {10.1016/j.margen.2017.09.007},
pmid = {29031541},
issn = {1876-7478},
mesh = {Biological Products/*chemistry ; *Fungi ; Interdisciplinary Research ; Marine Biology/*methods ; *Water Microbiology ; },
abstract = {Marine fungi have attracted attention in recent years due to increased appreciation of their functional role in ecosystems and as important sources of new natural products. The concomitant development of various "omic" technologies has boosted fungal research in the fields of biodiversity, physiological ecology and natural product biosynthesis. Each of these research areas has its own research agenda, scientific language and quality standards, which have so far hindered an interdisciplinary exchange. Inter- and transdisciplinary interactions are, however, vital for: (i) a detailed understanding of the ecological role of marine fungi, (ii) unlocking their hidden potential for natural product discovery, and (iii) designing access routes for biotechnological production. In this review and opinion paper, we describe the two different "worlds" of marine fungal natural product chemists and marine fungal molecular ecologists. The individual scientific approaches and tools employed are summarised and explained, and enriched with a first common glossary. We propose a strategy to find a multidisciplinary approach towards a comprehensive view on marine fungi and their chemical potential.},
}
@article {pmid29029619,
year = {2017},
author = {Seck, MC and Thwing, J and Fall, FB and Gomis, JF and Deme, A and Ndiaye, YD and Daniels, R and Volkman, SK and Ndiop, M and Ba, M and Ndiaye, D},
title = {Malaria prevalence, prevention and treatment seeking practices among nomadic pastoralists in northern Senegal.},
journal = {Malaria journal},
volume = {16},
number = {1},
pages = {413},
pmid = {29029619},
issn = {1475-2875},
mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Animal Husbandry ; Child ; Child, Preschool ; DNA Barcoding, Taxonomic ; Female ; Humans ; Infant ; *Malaria/drug therapy/epidemiology/prevention &amp; control ; Male ; Middle Aged ; Patient Acceptance of Health Care/psychology/*statistics &amp; numerical data ; Plasmodium/classification ; Prevalence ; Senegal/epidemiology ; *Transients and Migrants/psychology/statistics &amp; numerical data ; Young Adult ; },
abstract = {BACKGROUND: Malaria transmission in Senegal is highly stratified, from low in the dry north to moderately high in the moist south. In northern Senegal, along the Senegal River Valley and in the Ferlo semi-desert region, annual incidence is less than five cases per 1000 inhabitants. Many nomadic pastoralists have permanent dwellings in the Ferlo Desert and Senegal River Valley, but spend dry season in the south with their herds, returning north when the rains start, leading to a concern that this population could contribute to ongoing transmission in the north.<br><br>METHODS: A modified snowball sampling survey was conducted at six sites in northern Senegal to determine the malaria prevention and treatment seeking practices and parasite prevalence among nomadic pastoralists in the Senegal River Valley and the Ferlo Desert. Nomadic pastoralists aged 6&#xa0;months and older were surveyed during September and October 2014, and data regarding demographics, access to care and preventive measures were collected. Parasite infection was detected using rapid diagnostic tests (RDTs), microscopy (thin and thick smears) and polymerase chain reaction (PCR). Molecular barcodes were determined by high resolution melting (HRM).<br><br>RESULTS: Of 1800 participants, 61% were male. Sixty-four percent had at least one bed net in the household, and 53% reported using a net the night before. Only 29% had received a net from a mass distribution campaign. Of the 8% (142) who reported having had fever in the last month, 55% sought care, 20% of whom received a diagnostic test, one-third of which (n&#xa0;=&#xa0;5) were reported to be positive. Parasite prevalence was 0.44% by thick smear and 0.50% by PCR. None of the molecular barcodes identified among the nomadic pastoralists had been previously identified in Senegal.<br><br>CONCLUSIONS: While access to and utilization of malaria control interventions among nomadic pastoralists was lower than the general population, parasite prevalence was lower than expected and sheds doubt on the perception that they are a source of ongoing transmission in the north. The National Malaria Control Program is making efforts to improve access to malaria prevention and case management for nomadic populations.},
}
@article {pmid29029505,
year = {2017},
author = {Kaistha, BP and Krattenmacher, A and Fredebohm, J and Schmidt, H and Behrens, D and Widder, M and Hackert, T and Strobel, O and Hoheisel, JD and Gress, TM and Buchholz, M},
title = {The deubiquitinating enzyme USP5 promotes pancreatic cancer via modulating cell cycle regulators.},
journal = {Oncotarget},
volume = {8},
number = {39},
pages = {66215-66225},
pmid = {29029505},
issn = {1949-2553},
abstract = {Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal solid tumors. With an overall five-year survival rate remaining below 6%, there is an explicit need to search for new molecular targets for therapeutic interventions. We undertook a barcode labelled short-hairpin (shRNA) library screen in pancreatic cancer cells in order to identify novel genes promoting cancer survival and progression. Among the candidate genes identified in this screen was the deubiquitinase USP5, which subsequent gene expression analyses demonstrated to be significantly upregulated in primary human pancreatic cancer tissues. Using different knockdown approaches, we show that expression of USP5 is essential for the proliferation and survival of pancreatic cancer cells, tested under different 2D and 3D cell culture conditions as well as in in vivo experiments. These growth inhibition effects upon knockdown of USP5 are mediated primarily by the attenuation of G1/S phase transition in the cells, which is accompanied by accumulation of DNA damage, upregulation of p27, and increased apoptosis rates. Since USP5 is overexpressed in cancer tissues, it can thus potentially serve as a new target for therapeutic interventions, especially given the fact that deubiquitinases are currently emerging as new class of attractive drug targets in cancer.},
}
@article {pmid29029146,
year = {2017},
author = {Tembrock, LR and Farris, RE and Ledezma, L and Barr, NB and Gilligan, TM},
title = {A Real-Time PCR Assay for the Separation of Autographa gamma (Noctuidae: Plusiinae) From Morphologically Similar Species in North America.},
journal = {Journal of economic entomology},
volume = {110},
number = {6},
pages = {2609-2617},
doi = {10.1093/jee/tox256},
pmid = {29029146},
issn = {1938-291X},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Insect Proteins/genetics ; *Introduced Species ; Larva/genetics/growth &amp; development ; Moths/*genetics/growth &amp; development ; North America ; Real-Time Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; },
abstract = {The silver Y moth, Autographa gamma L. (Noctuidae: Plusiinae), is a pest of major economic importance in its native range of Europe, Asia, and North Africa. Although not present in North America, larvae of A. gamma are commonly intercepted in commodity shipments at U.S. ports, and adult surveys are conducted each year in more than 20 states. Because of the similarity of A. gamma to several native North American species that are attracted to the same pheromone lure, morphological identification of adults is difficult and requires dissection. In 2010, a specimen of Autographa californica (Speyer, 1875) (Lepidoptera: Noctuidae) from Pennsylvania was incorrectly identified as A. gamma, signaling the need for an alternative method of rapid identification. Here we detail a real-time PCR assay capable of identifying A. gamma specimens in approximately 45 min using extracted DNA. The assay uses a hydrolysis probe that targets a species-specific segment of the CO1 DNA barcode region, while a control probe targets a conserved region of 18S rDNA. The assay was tested with two independent runs of 452 specimens of Plusiinae representing 23 different species. The assay provided unambiguous data 99.7% of the time and did not result in any false positives; these data were used to develop a rule set for interpreting the real-time PCR results. In addition, the same diagnostic probe was tested in bulk sample simulations using real-time PCR and droplet digital PCR where A. gamma could be detected in concentrations as low as 1:1,000,000 (gamma:californica). These experiments provide baseline data for developing a bulk sample assay.},
}
@article {pmid29028869,
year = {2019},
author = {Meyer, F and Bagchi, S and Chaterji, S and Gerlach, W and Grama, A and Harrison, T and Paczian, T and Trimble, WL and Wilke, A},
title = {MG-RAST version 4-lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis.},
journal = {Briefings in bioinformatics},
volume = {20},
number = {4},
pages = {1151-1159},
pmid = {29028869},
issn = {1477-4054},
support = {R01 AI123037/AI/NIAID NIH HHS/United States ; U01 HG006537/HG/NHGRI NIH HHS/United States ; },
mesh = {Algorithms ; Budgets ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/economics/*methods/statistics &amp; numerical data ; Internet ; *Metagenome ; Metagenomics/economics/*methods/statistics &amp; numerical data ; Sequence Analysis, DNA/economics/methods/statistics &amp; numerical data ; *Software ; User-Computer Interface ; Workflow ; },
abstract = {As technologies change, MG-RAST is adapting. Newly available software is being included to improve accuracy and performance. As a computational service constantly running large volume scientific workflows, MG-RAST is the right location to perform benchmarking and implement algorithmic or platform improvements, in many cases involving trade-offs between specificity, sensitivity and run-time cost. The work in [Glass EM, Dribinsky Y, Yilmaz P, et al. ISME J 2014;8:1-3] is an example; we use existing well-studied data sets as gold standards representing different environments and different technologies to evaluate any changes to the pipeline. Currently, we use well-understood data sets in MG-RAST as platform for benchmarking. The use of artificial data sets for pipeline performance optimization has not added value, as these data sets are not presenting the same challenges as real-world data sets. In addition, the MG-RAST team welcomes suggestions for improvements of the workflow. We are currently working on versions 4.02 and 4.1, both of which contain significant input from the community and our partners that will enable double barcoding, stronger inferences supported by longer-read technologies, and will increase throughput while maintaining sensitivity by using Diamond and SortMeRNA. On the technical platform side, the MG-RAST team intends to support the Common Workflow Language as a standard to specify bioinformatics workflows, both to facilitate development and efficient high-performance implementation of the community's data analysis tasks.},
}
@article {pmid29027175,
year = {2018},
author = {Chabbert, CD and Adjalley, SH and Steinmetz, LM and Pelechano, V},
title = {Multiplexed ChIP-Seq Using Direct Nucleosome Barcoding: A Tool for High-Throughput Chromatin Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1689},
number = {},
pages = {177-194},
doi = {10.1007/978-1-4939-7380-4_16},
pmid = {29027175},
issn = {1940-6029},
mesh = {Chromatin/genetics/metabolism ; *Chromatin Immunoprecipitation/methods ; Computational Biology/methods ; *DNA Barcoding, Taxonomic ; Data Interpretation, Statistical ; Gene Library ; *High-Throughput Nucleotide Sequencing/methods ; Nucleosomes/*genetics/metabolism ; Real-Time Polymerase Chain Reaction/methods ; Saccharomyces cerevisiae/genetics/metabolism ; Workflow ; },
abstract = {Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) or microarray hybridization (ChIP-on-chip) are standard methods for the study of transcription factor binding sites and histone chemical modifications. However, these approaches only allow profiling of a single factor or protein modification at a time.In this chapter, we present Bar-ChIP, a higher throughput version of ChIP-Seq that relies on the direct ligation of molecular barcodes to chromatin fragments. Bar-ChIP enables the concurrent profiling of multiple DNA-protein interactions and is therefore amenable to experimental scale-up, without the need for any robotic instrumentation.},
}
@article {pmid29024429,
year = {2018},
author = {Borg Dahl, M and Brejnrod, AD and Unterseher, M and Hoppe, T and Feng, Y and Novozhilov, Y and Sørensen, SJ and Schnittler, M},
title = {Genetic barcoding of dark-spored myxomycetes (Amoebozoa)-Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies.},
journal = {Molecular ecology resources},
volume = {18},
number = {2},
pages = {306-318},
doi = {10.1111/1755-0998.12725},
pmid = {29024429},
issn = {1755-0998},
mesh = {Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Myxomycetes/*classification/*genetics ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; },
abstract = {Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark-spored myxomycetes.},
}
@article {pmid29022235,
year = {2017},
author = {Laha, RC and De Mandal, S and Ralte, L and Ralte, L and Kumar, NS and Gurusubramanian, G and Satishkumar, R and Mugasimangalam, R and Kuravadi, NA},
title = {Correction to: Meta-barcoding in combination with palynological inference is a potent diagnostic marker for honey floral composition.},
journal = {AMB Express},
volume = {7},
number = {1},
pages = {189},
pmid = {29022235},
issn = {2191-0855},
abstract = {In the version of this article that was originally published (Laha et al. 2017) the authors did not properly reference one paragraph in the Introduction section.},
}
@article {pmid29022018,
year = {2017},
author = {Shikha, S and Salafi, T and Cheng, J and Zhang, Y},
title = {Versatile design and synthesis of nano-barcodes.},
journal = {Chemical Society reviews},
volume = {46},
number = {22},
pages = {7054-7093},
doi = {10.1039/c7cs00271h},
pmid = {29022018},
issn = {1460-4744},
abstract = {Encoded nano-structures/particles have been used for barcoding and are in great demand for the simultaneous analysis of multiple targets. Due to their nanoscale dimension(s), nano-barcodes have been implemented favourably for bioimaging, in addition to their security and multiplex bioassay application. In designing nano-barcodes for a specific application, encoding techniques, synthesis strategies, and decoding techniques need to be considered. The encoding techniques to generate unique multiple codes for nano-barcodes are based on certain encoding elements including optical (fluorescent and non-fluorescent), graphical, magnetic, and phase change properties of nanoparticles or their different shapes and sizes. These encoding elements can generally be embedded inside, decorated on the surface of nanostructures or self-assembled to prepare the nano-barcodes. The decoding techniques for each encoding technique are different and need to be suitable for the desired applications. This review will provide a thorough discussion on designing nano-barcodes, focusing on the encoding techniques, synthesis methods, and decoding for applications including bio-detection, imaging, and anti-counterfeiting. Additionally, associated challenges in the field and potential solutions will also be discussed. We believe that a comprehensive understanding on this topic could significantly contribute towards the advancement of nano-barcodes for a broad spectrum of applications.},
}
@article {pmid29020925,
year = {2017},
author = {Christley, S and Levin, MK and Toby, IT and Fonner, JM and Monson, NL and Rounds, WH and Rubelt, F and Scarborough, W and Scheuermann, RH and Cowell, LG},
title = {VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data.},
journal = {BMC bioinformatics},
volume = {18},
number = {1},
pages = {448},
pmid = {29020925},
issn = {1471-2105},
support = {HHSN272201200028C/AI/NIAID NIH HHS/United States ; R01 AI097403/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; B-Lymphocytes/*metabolism ; DNA Primers ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Immunoglobulin G/*genetics ; Mice ; *Software ; Time Factors ; },
abstract = {BACKGROUND: Pre-processing of high-throughput sequencing data for immune repertoire profiling is essential to insure high quality input for downstream analysis. VDJPipe is a flexible, high-performance tool that can perform multiple pre-processing tasks with just a single pass over the data files.<br><br>RESULTS: Processing tasks provided by VDJPipe include base composition statistics calculation, read quality statistics calculation, quality filtering, homopolymer filtering, length and nucleotide filtering, paired-read merging, barcode demultiplexing, 5' and 3' PCR primer matching, and duplicate reads collapsing. VDJPipe utilizes a pipeline approach whereby multiple processing steps are performed in a sequential workflow, with the output of each step passed as input to the next step automatically. The workflow is flexible enough to handle the complex barcoding schemes used in many immunosequencing experiments. Because VDJPipe is designed for computational efficiency, we evaluated this by comparing execution times with those of pRESTO, a widely-used pre-processing tool for immune repertoire sequencing data. We found that VDJPipe requires <10% of the run time required by pRESTO.<br><br>CONCLUSIONS: VDJPipe is a high-performance tool that is optimized for pre-processing large immune repertoire sequencing data sets.},
}
@article {pmid29020743,
year = {2017},
author = {Arulandhu, AJ and Staats, M and Hagelaar, R and Voorhuijzen, MM and Prins, TW and Scholtens, I and Costessi, A and Duijsings, D and Rechenmann, F and Gaspar, FB and Barreto Crespo, MT and Holst-Jensen, A and Birck, M and Burns, M and Haynes, E and Hochegger, R and Klingl, A and Lundberg, L and Natale, C and Niekamp, H and Perri, E and Barbante, A and Rosec, JP and Seyfarth, R and Sovová, T and Van Moorleghem, C and van Ruth, S and Peelen, T and Kok, E},
title = {Development and validation of a multi-locus DNA metabarcoding method to identify endangered species in complex samples.},
journal = {GigaScience},
volume = {6},
number = {10},
pages = {1-18},
pmid = {29020743},
issn = {2047-217X},
mesh = {Animals ; Computational Biology ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; *Endangered Species ; Plants/classification/genetics ; Reproducibility of Results ; },
abstract = {DNA metabarcoding provides great potential for species identification in complex samples such as food supplements and traditional medicines. Such a method would aid Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) enforcement officers to combat wildlife crime by preventing illegal trade of endangered plant and animal species. The objective of this research was to develop a multi-locus DNA metabarcoding method for forensic wildlife species identification and to evaluate the applicability and reproducibility of this approach across different laboratories. A DNA metabarcoding method was developed that makes use of 12 DNA barcode markers that have demonstrated universal applicability across a wide range of plant and animal taxa and that facilitate the identification of species in samples containing degraded DNA. The DNA metabarcoding method was developed based on Illumina MiSeq amplicon sequencing of well-defined experimental mixtures, for which a bioinformatics pipeline with user-friendly web-interface was developed. The performance of the DNA metabarcoding method was assessed in an international validation trial by 16 laboratories, in which the method was found to be highly reproducible and sensitive enough to identify species present in a mixture at 1% dry weight content. The advanced multi-locus DNA metabarcoding method assessed in this study provides reliable and detailed data on the composition of complex food products, including information on the presence of CITES-listed species. The method can provide improved resolution for species identification, while verifying species with multiple DNA barcodes contributes to an enhanced quality assurance.},
}
@article {pmid29020095,
year = {2017},
author = {Cardeñosa, D and Fields, A and Abercrombie, D and Feldheim, K and Shea, SKH and Chapman, DD},
title = {A multiplex PCR mini-barcode assay to identify processed shark products in the global trade.},
journal = {PloS one},
volume = {12},
number = {10},
pages = {e0185368},
pmid = {29020095},
issn = {1932-6203},
mesh = {Animal Fins/physiology ; Animals ; China ; *Commerce ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; *Internationality ; Polymerase Chain Reaction/*methods ; Sharks/*genetics ; Species Specificity ; },
abstract = {Protecting sharks from overexploitation has become global priority after widespread population declines have occurred. Tracking catches and trade on a species-specific basis has proven challenging, in part due to difficulties in identifying processed shark products such as fins, meat, and liver oil. This has hindered efforts to implement regulations aimed at promoting sustainable use of commercially important species and protection of imperiled species. Genetic approaches to identify shark products exist but are typically based on sequencing or amplifying large DNA regions and may fail to work on heavily processed products in which DNA is degraded. Here, we describe a novel multiplex PCR mini-barcode assay based on two short fragments of the cytochrome oxidase I (COI) gene. This assay can identify to species all sharks currently listed on the Convention of International Trade of Endangered Species (CITES) and most shark species present in the international trade. It achieves species diagnosis based on a single PCR and one to two downstream DNA sequencing reactions. The assay is capable of identifying highly processed shark products including fins, cooked shark fin soup, and skin-care products containing liver oil. This is a straightforward and reliable identification method for data collection and enforcement of regulations implemented for certain species at all governance levels.},
}
@article {pmid29018597,
year = {2017},
author = {Shum, P and Moore, L and Pampoulie, C and Di Muri, C and Vandamme, S and Mariani, S},
title = {Harnessing mtDNA variation to resolve ambiguity in 'Redfish' sold in Europe.},
journal = {PeerJ},
volume = {5},
number = {},
pages = {e3746},
pmid = {29018597},
issn = {2167-8359},
abstract = {Morphology-based identification of North Atlantic Sebastes has long been controversial and misidentification may produce misleading data, with cascading consequences that negatively affect fisheries management and seafood labelling. North Atlantic Sebastes comprises of four species, commonly known as 'redfish', but little is known about the number, identity and labelling accuracy of redfish species sold across Europe. We used a molecular approach to identify redfish species from 'blind' specimens to evaluate the performance of the Barcode of Life (BOLD) and Genbank databases, as well as carrying out a market product accuracy survey from retailers across Europe. The conventional BOLD approach proved ambiguous, and phylogenetic analysis based on mtDNA control region sequences provided a higher resolution for species identification. By sampling market products from four countries, we found the presence of two species of redfish (S. norvegicus and S. mentella) and one unidentified Pacific rockfish marketed in Europe. Furthermore, public databases revealed the existence of inaccurate reference sequences, likely stemming from species misidentification from previous studies, which currently hinders the efficacy of DNA methods for the identification of Sebastes market samples.},
}
@article {pmid29017216,
year = {2017},
author = {Sgamma, T and Lockie-Williams, C and Kreuzer, M and Williams, S and Scheyhing, U and Koch, E and Slater, A and Howard, C},
title = {Erratum for: DNA Barcoding for Industrial Quality Assurance.},
journal = {Planta medica},
volume = {83},
number = {18},
pages = {1430},
doi = {10.1055/s-0043-120772},
pmid = {29017216},
issn = {1439-0221},
}
@article {pmid28990202,
year = {2017},
author = {Gabriel, D and Draisma, SGA and Schmidt, WE and Schils, T and Sauvage, T and Maridakis, C and Gurgel, CFD and Harris, DJ and Fredericq, S},
title = {Beneath the hairy look: the hidden reproductive diversity of the Gibsmithia hawaiiensis complex (Dumontiaceae, Rhodophyta).},
journal = {Journal of phycology},
volume = {53},
number = {6},
pages = {1171-1192},
doi = {10.1111/jpy.12593},
pmid = {28990202},
issn = {1529-8817},
mesh = {Algal Proteins/*genetics/metabolism ; Biota ; Phylogeny ; Reproduction ; Rhodophyta/anatomy &amp; histology/*classification/genetics/*physiology ; Sequence Analysis, DNA ; },
abstract = {The tropical alga previously recognized as Gibsmithia hawaiiensis (Dumontiaceae, Rhodophyta) was recently suggested to represent a complex of species distributed throughout the Indo-Pacific Ocean and characterized by a peculiar combination of hairy (pilose) gelatinous lobes growing on cartilaginous stalks. Phylogenetic reconstructions based on three genetic markers are presented here with the inclusion of new samples. Further diversity is reported within the complex, with nine lineages spread in four major phylogenetic groups. The threshold between intra- and interspecific relationships was assessed by species delimitation methods, which indicate the existence of 8-10 putative species in the complex. Two species belonging to the G. hawaiiensis complex are described here: Gibsmithia malayensis sp. nov. from the Coral Triangle and Gibsmithia indopacifica sp. nov., widely distributed in the Central and Eastern Indo-Pacific. Morphological differences in the vegetative and reproductive structures of the newly described species are provided and compared to the previously described species of the complex. Additional lineages represent putative species, which await further investigation to clarify their taxonomic status. Gibsmithia hawaiiensis sensu stricto is confirmed to be endemic to the Hawaiian Islands, and Gibsmithia eilatensis is apparently confined to the Red Sea, with an expanded distribution in the region. New records of the G. hawaiiensis complex are reported from Egypt, Saudi Arabia, Indonesia, Philippines, and the Federated States of Micronesia, indicating that the complex is more broadly distributed than previously considered. The isolated position of Gibsmithia within the Dumontiaceae is corroborated by molecular data.},
}
@article {pmid28988502,
year = {2018},
author = {Santu, KS and Nandan, SB and Cleetus, RI and Harikrishnan, M},
title = {Reassessing the species status of Pseudodiaptomus malayalus Wellershaus, 1969 and P. binghami Sewell, 1912 (Calanoida: Pseudodiaptomidae) from India based on morphology and mitochondrial cytochrome oxidase I gene sequences.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {6},
pages = {885-896},
doi = {10.1080/24701394.2017.1376054},
pmid = {28988502},
issn = {2470-1408},
mesh = {Animals ; Copepoda/anatomy &amp; histology/*classification/genetics ; Electron Transport Complex IV/*genetics ; Female ; Male ; Myanmar ; *Phylogeny ; },
abstract = {Pseudodiaptomus binghami Sewell, 1912 was first described from the Rangoon River (now Yangon River) estuary, Myanmar. Pseudodiaptomus malayalus Wellershaus, 1969 previously known as P. binghami malayalus, is a typical brackish-water calanoid copepod from Cochin Estuary, Kerala. Morphological examination of P. malayalus and P. binghami collected from Cochin Estuary and the Nambur canal in Andhra Pradesh revealed crucial differences between the two congeners. Female specimens of P. malayalus exhibited marked differences from those described by Wellershaus. They are (1) the number of terminal spines on P5, (2) ornamentation of GS, (3) ornamentation of Ur1-4, (4) length ratio of the Ur and CR segments and (5) length:width ratio of the CR setae. Furthermore, significant and discrete morphological differences were observed between the two Indian species in their P5 and urosome. But the male specimens of P. malayalus did not show any major differences from the original description. In addition, distance matrix data revealed 22% interspecific divergence values which in turn confirmed the status of P. malayalus and P. binghami as two distinct species.},
}
@article {pmid28984152,
year = {2018},
author = {Collet, A and Durand, JD and Desmarais, E and Cerqueira, F and Cantinelli, T and Valade, P and Ponton, D},
title = {DNA barcoding post-larvae can improve the knowledge about fish biodiversity: an example from La Reunion, SW Indian Ocean.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {6},
pages = {905-918},
doi = {10.1080/24701394.2017.1383406},
pmid = {28984152},
issn = {2470-1408},
mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods/standards ; Fishes/classification/*genetics/growth &amp; development ; Indian Ocean ; Larva/classification/genetics ; },
abstract = {The aim of this study was to demonstrate that fish larvae identified using their COI sequences offer a unique opportunity for improving the knowledge of local fish richness. Fish larvae were sampled at the end of their pelagic phase using light-traps set off the West Coast of La Reunion Island, southwestern Indian Ocean, once per month from October 2014 to March 2015. Among the 5174 larvae caught, 214 morphologically different specimens were selected, 196 successfully barcoded, giving a total of 101 different Barcode Index Numbers (BINs). Among these BINs, 55 had never been recorded in La Reunion exclusive economic zone (EEZ), and 13 were new for the BOLD database. Even if the sampling effort for collecting fish post-larvae during this study was relatively low, it allowed adding at least nine new species to an updated checklist of fishes of La Reunion EEZ.},
}
@article {pmid28981721,
year = {2017},
author = {Allio, R and Donega, S and Galtier, N and Nabholz, B},
title = {Large Variation in the Ratio of Mitochondrial to Nuclear Mutation Rate across Animals: Implications for Genetic Diversity and the Use of Mitochondrial DNA as a Molecular Marker.},
journal = {Molecular biology and evolution},
volume = {34},
number = {11},
pages = {2762-2772},
doi = {10.1093/molbev/msx197},
pmid = {28981721},
issn = {1537-1719},
mesh = {Animals ; Biological Evolution ; Biomarkers ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; Databases, Nucleic Acid ; Evolution, Molecular ; Genetic Speciation ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome/genetics ; Mitochondria/genetics ; Mutation ; *Mutation Rate ; Phylogeny ; Polymorphism, Genetic/genetics ; Population Density ; Selection, Genetic/genetics ; },
abstract = {It is commonly assumed that mitochondrial DNA (mtDNA) evolves at a faster rate than nuclear DNA (nuDNA) in animals. This has contributed to the popularity of mtDNA as a molecular marker in evolutionary studies. Analyzing 121 multilocus data sets and four phylogenomic data sets encompassing 4,676 species of animals, we demonstrate that the ratio of mitochondrial over nuclear mutation rate is highly variable among animal taxa. In nonvertebrates, such as insects and arachnids, the ratio of mtDNA over nuDNA mutation rate varies between 2 and 6, whereas it is above 20, on average, in vertebrates such as scaled reptiles and birds. Interestingly, this variation is sufficient to explain the previous report of a similar level of mitochondrial polymorphism, on average, between vertebrates and nonvertebrates, which was originally interpreted as reflecting the effect of pervasive positive selection. Our analysis rather indicates that the among-phyla homogeneity in within-species mtDNA diversity is due to a negative correlation between mtDNA per-generation mutation rate and effective population size, irrespective of the action of natural selection. Finally, we explore the variation in the absolute per-year mutation rate of both mtDNA and nuDNA using a reduced data set for which fossil calibration is available, and discuss the potential determinants of mutation rate variation across genomes and taxa. This study has important implications regarding DNA-based identification methods in predicting that mtDNA barcoding should be less reliable in nonvertebrates than in vertebrates.},
}
@article {pmid28981122,
year = {2017},
author = {Yi, S and Liu, NN and Hu, L and Wang, H and Sahni, N},
title = {Base-resolution stratification of cancer mutations using functional variomics.},
journal = {Nature protocols},
volume = {12},
number = {11},
pages = {2323-2341},
pmid = {28981122},
issn = {1750-2799},
support = {P30 CA016672/CA/NCI NIH HHS/United States ; },
mesh = {Cloning, Molecular ; Exome/genetics ; Genomics/*methods ; HEK293 Cells ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Mutagenesis, Site-Directed ; Mutation/*genetics ; Neoplasms/classification/*genetics ; Sequence Analysis, DNA/*methods ; Two-Hybrid System Techniques ; },
abstract = {A complete understanding of human cancer variants requires new methods to systematically and efficiently assess the functional effects of genomic mutations at a large scale. Here, we describe a set of tools to rapidly clone and stratify thousands of cancer mutations at base resolution. This protocol provides a massively parallel pipeline to achieve high stringency and throughput. The approach includes high-throughput generation of mutant clones by Gateway, confirmation of variant identity by barcoding and next-generation sequencing, and stratification of cancer variants by multiplexed interaction profiling. Compared with alternative site-directed mutagenesis methods, our protocol requires less sequencing effort and enables robust statistical calling of allele-specific effects. To ensure the precision of variant interaction profiling, we further describe two complementary methods-a high-throughput enhanced yeast two-hybrid (HT-eY2H) assay and a mammalian-cell-based Gaussia princeps luciferase protein-fragment complementation assay (GPCA). These independent assays with standard controls validate mutational interaction profiles with high quality. This protocol provides experimentally derived guidelines for classifying candidate cancer alleles emerging from whole-genome or whole-exome sequencing projects as 'drivers' or 'passengers'. For ∼100 genomic mutations, the protocol-including target primer design, variant library construction, and sequence verification-can be completed within as little as 2-3 weeks, and cancer variant stratification can be completed within 2 weeks.},
}
@article {pmid28978691,
year = {2017},
author = {Shlemov, A and Bankevich, S and Bzikadze, A and Turchaninova, MA and Safonova, Y and Pevzner, PA},
title = {Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads.},
journal = {Journal of immunology (Baltimore, Md. : 1950)},
volume = {199},
number = {9},
pages = {3369-3380},
pmid = {28978691},
issn = {1550-6606},
support = {P41 GM103484/GM/NIGMS NIH HHS/United States ; },
mesh = {*Algorithms ; Animals ; Antibodies/*genetics ; Humans ; Sequence Analysis, Protein/*methods ; },
abstract = {Transforming error-prone immunosequencing datasets into Ab repertoires is a fundamental problem in immunogenomics, and a prerequisite for studies of immune responses. Although various repertoire reconstruction algorithms were released in the last 3 y, it remains unclear how to benchmark them and how to assess the accuracy of the reconstructed repertoires. We describe an accurate IgReC algorithm for constructing Ab repertoires from high-throughput immunosequencing datasets and a new framework for assessing the quality of reconstructed repertoires. Surprisingly, Ab repertoires constructed by IgReC from barcoded immunosequencing datasets in the blind mode (without using information about unique molecular identifiers) improved upon the repertoires constructed by the state-of-the-art tools that use barcoding. This finding suggests that IgReC may alleviate the need to generate repertoires using the barcoding technology (the workhorse of current immunogenomics efforts) because our computational approach to error correction of immunosequencing data is nearly as powerful as the experimental approach based on barcoding.},
}
@article {pmid28977555,
year = {2017},
author = {Bell, JM and Lau, BT and Greer, SU and Wood-Bouwens, C and Xia, LC and Connolly, ID and Gephart, MH and Ji, HP},
title = {Chromosome-scale mega-haplotypes enable digital karyotyping of cancer aneuploidy.},
journal = {Nucleic acids research},
volume = {45},
number = {19},
pages = {e162},
pmid = {28977555},
issn = {1362-4962},
support = {K08 NS091527/NS/NINDS NIH HHS/United States ; P01 HG000205/HG/NHGRI NIH HHS/United States ; R01 HG006137/HG/NHGRI NIH HHS/United States ; R21 CA193046/CA/NCI NIH HHS/United States ; },
mesh = {*Aneuploidy ; Chromosome Aberrations ; Colorectal Neoplasms/diagnosis/genetics ; DNA Mutational Analysis/methods ; Genome, Human/genetics ; Genomic Instability ; *Haplotypes ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Karyotype ; Karyotyping/methods ; Neoplasms/diagnosis/*genetics ; Reproducibility of Results ; Sensitivity and Specificity ; },
abstract = {Genomic instability is a frequently occurring feature of cancer that involves large-scale structural alterations. These somatic changes in chromosome structure include duplication of entire chromosome arms and aneuploidy where chromosomes are duplicated beyond normal diploid content. However, the accurate determination of aneuploidy events in cancer genomes is a challenge. Recent advances in sequencing technology allow the characterization of haplotypes that extend megabases along the human genome using high molecular weight (HMW) DNA. For this study, we employed a library preparation method in which sequence reads have barcodes linked to single HMW DNA molecules. Barcode-linked reads are used to generate extended haplotypes on the order of megabases. We developed a method that leverages haplotypes to identify chromosomal segmental alterations in cancer and uses this information to join haplotypes together, thus extending the range of phased variants. With this approach, we identified mega-haplotypes that encompass entire chromosome arms. We characterized the chromosomal arm changes and aneuploidy events in a manner that offers similar information as a traditional karyotype but with the benefit of DNA sequence resolution. We applied this approach to characterize aneuploidy and chromosomal alterations from a series of primary colorectal cancers.},
}
@article {pmid28977499,
year = {2017},
author = {Chandrasekaran, AR and Levchenko, O and Patel, DS and MacIsaac, M and Halvorsen, K},
title = {Addressable configurations of DNA nanostructures for rewritable memory.},
journal = {Nucleic acids research},
volume = {45},
number = {19},
pages = {11459-11465},
pmid = {28977499},
issn = {1362-4962},
support = {R35 GM124720/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacteriophage M13/genetics ; *Computers, Molecular ; DNA, Viral/*chemistry/genetics ; Electrophoresis, Agar Gel ; Information Storage and Retrieval/*methods ; Nanostructures/*chemistry ; Reproducibility of Results ; },
abstract = {DNA serves as nature's information storage molecule, and has been the primary focus of engineered systems for biological computing and data storage. Here we combine recent efforts in DNA self-assembly and toehold-mediated strand displacement to develop a rewritable multi-bit DNA memory system. The system operates by encoding information in distinct and reversible conformations of a DNA nanoswitch and decoding by gel electrophoresis. We demonstrate a 5-bit system capable of writing, erasing, and rewriting binary representations of alphanumeric symbols, as well as compatibility with 'OR' and 'AND' logic operations. Our strategy is simple to implement, requiring only a single mixing step at room temperature for each operation and standard gel electrophoresis to read the data. We envision such systems could find use in covert product labeling and barcoding, as well as secure messaging and authentication when combined with previously developed encryption strategies. Ultimately, this type of memory has exciting potential in biomedical sciences as data storage can be coupled to sensing of biological molecules.},
}
@article {pmid28977035,
year = {2017},
author = {Yang, J and Zhang, X and Zhang, W and Sun, J and Xie, Y and Zhang, Y and Burton, GA and Yu, H},
title = {Indigenous species barcode database improves the identification of zooplankton.},
journal = {PloS one},
volume = {12},
number = {10},
pages = {e0185697},
pmid = {28977035},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Databases, Genetic ; Polymerase Chain Reaction ; Zooplankton/*genetics ; },
abstract = {Incompleteness and inaccuracy of DNA barcode databases is considered an important hindrance to the use of metabarcoding in biodiversity analysis of zooplankton at the species-level. Species barcoding by Sanger sequencing is inefficient for organisms with small body sizes, such as zooplankton. Here mitochondrial cytochrome c oxidase I (COI) fragment barcodes from 910 freshwater zooplankton specimens (87 morphospecies) were recovered by a high-throughput sequencing platform, Ion Torrent PGM. Intraspecific divergence of most zooplanktons was < 5%, except Branchionus leydign (Rotifer, 14.3%), Trichocerca elongate (Rotifer, 11.5%), Lecane bulla (Rotifer, 15.9%), Synchaeta oblonga (Rotifer, 5.95%) and Schmackeria forbesi (Copepod, 6.5%). Metabarcoding data of 28 environmental samples from Lake Tai were annotated by both an indigenous database and NCBI Genbank database. The indigenous database improved the taxonomic assignment of metabarcoding of zooplankton. Most zooplankton (81%) with barcode sequences in the indigenous database were identified by metabarcoding monitoring. Furthermore, the frequency and distribution of zooplankton were also consistent between metabarcoding and morphology identification. Overall, the indigenous database improved the taxonomic assignment of zooplankton.},
}
@article {pmid28977016,
year = {2017},
author = {Menegon, M and Cantaloni, C and Rodriguez-Prieto, A and Centomo, C and Abdelfattah, A and Rossato, M and Bernardi, M and Xumerle, L and Loader, S and Delledonne, M},
title = {On site DNA barcoding by nanopore sequencing.},
journal = {PloS one},
volume = {12},
number = {10},
pages = {e0184741},
pmid = {28977016},
issn = {1932-6203},
mesh = {Amphibians/classification/genetics ; Animals ; Base Sequence ; Biodiversity ; *DNA Barcoding, Taxonomic ; Forests ; High-Throughput Nucleotide Sequencing/*methods ; *Nanopores ; Reptiles/classification/genetics ; Sequence Homology, Nucleic Acid ; Tropical Climate ; },
abstract = {Biodiversity research is becoming increasingly dependent on genomics, which allows the unprecedented digitization and understanding of the planet's biological heritage. The use of genetic markers i.e. DNA barcoding, has proved to be a powerful tool in species identification. However, full exploitation of this approach is hampered by the high sequencing costs and the absence of equipped facilities in biodiversity-rich countries. In the present work, we developed a portable sequencing laboratory based on the portable DNA sequencer from Oxford Nanopore Technologies, the MinION. Complementary laboratory equipment and reagents were selected to be used in remote and tough environmental conditions. The performance of the MinION sequencer and the portable laboratory was tested for DNA barcoding in a mimicking tropical environment, as well as in a remote rainforest of Tanzania lacking electricity. Despite the relatively high sequencing error-rate of the MinION, the development of a suitable pipeline for data analysis allowed the accurate identification of different species of vertebrates including amphibians, reptiles and mammals. In situ sequencing of a wild frog allowed us to rapidly identify the species captured, thus confirming that effective DNA barcoding in the field is possible. These results open new perspectives for real-time-on-site DNA sequencing thus potentially increasing opportunities for the understanding of biodiversity in areas lacking conventional laboratory facilities.},
}
@article {pmid28972864,
year = {2018},
author = {Gibbs, J},
title = {DNA barcoding a nightmare taxon: assessing barcode index numbers and barcode gaps for sweat bees.},
journal = {Genome},
volume = {61},
number = {1},
pages = {21-31},
doi = {10.1139/gen-2017-0096},
pmid = {28972864},
issn = {1480-3321},
mesh = {Animals ; Bees/*classification/genetics ; *DNA Barcoding, Taxonomic ; },
abstract = {There is an ongoing campaign to DNA barcode the world's >20 000 bee species. Recent revisions of Lasioglossum (Dialictus) (Hymenoptera: Halictidae) for Canada and the eastern United States were completed using integrative taxonomy. DNA barcode data from 110 species of L. (Dialictus) are examined for their value in identification and discovering additional taxonomic diversity. Specimen identification success was estimated using the best close match method. Error rates were 20% relative to current taxonomic understanding. Barcode Index Numbers (BINs) assigned using Refined Single Linkage Analysis (RESL) and barcode gaps using the Automatic Barcode Gap Discovery (ABGD) method were also assessed. RESL was incongruent for 44.5% of species, although some cryptic diversity may exist. Forty-three of 110 species were part of merged BINs with multiple species. The barcode gap is non-existent for the data set as a whole and ABGD showed levels of discordance similar to the RESL. The viridatum species-group is particularly problematic, so that DNA barcodes alone would be misleading for species delimitation and specimen identification. Character-based methods using fixed nucleotide substitutions could improve specimen identification success in some cases. The use of DNA barcoding for species discovery for standard taxonomic practice in the absence of a well-defined barcode gap is discussed.},
}
@article {pmid28970548,
year = {2017},
author = {Kang, Y and Deng, Z and Zang, R and Long, W},
title = {DNA barcoding analysis and phylogenetic relationships of tree species in tropical cloud forests.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {12564},
pmid = {28970548},
issn = {2045-2322},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/classification/*genetics ; DNA, Ribosomal Spacer/genetics ; Forests ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Tropical Climate ; },
abstract = {DNA barcoding is a useful tool for species identification and phylogenetic construction. But present studies have far reached a consistent result on the universality of DNA barcoding. We tested the universality of tree species DNA barcodes including rbcL, matK, trnH-psbA and ITS, and examined their abilities of species identification and phylogenetic construction in three tropical cloud forests. Results showed that the success rates of PCR amplification of rbcL, matK, trnH-psbA and ITS were 75.26% ± 3.65%, 57.24% ± 4.42%, 79.28% ± 7.08%, 50.31% ± 6.64%, and the rates of DNA sequencing were 63.84% ± 4.32%, 50.82% ± 4.36%, 72.87% ± 11.37%, 45.15% ± 8.91% respectively, suggesting that both rbcL and trnH-psbA are universal for tree species in the tropical cloud forests. The success rates of species identification of the four fragments were higher than 41.00% (rbcL: 41.50% ± 2.81%, matK: 42.88% ± 2.59%, trnH-psbA: 46.16% ± 5.11% and ITS: 47.20% ± 5.76%), demonstrating that these fragments have potentiality in species identification. When the phylogenetic relationships were built with random fragment combinations, optimal evolutionary tree with high supporting values were established using the combinations of rbcL + matK + trnH-psbA in tropical cloud forests.},
}
@article {pmid28966890,
year = {2017},
author = {Bistolas, KSI and Rudstam, LG and Hewson, I},
title = {Gene expression of benthic amphipods (genus: Diporeia) in relation to a circular ssDNA virus across two Laurentian Great Lakes.},
journal = {PeerJ},
volume = {5},
number = {},
pages = {e3810},
pmid = {28966890},
issn = {2167-8359},
abstract = {Circular rep-encoding ssDNA (CRESS-DNA) viruses are common constituents of invertebrate viral consortia. Despite their ubiquity and sequence diversity, the effects of CRESS-DNA viruses on invertebrate biology and ecology remain largely unknown. This study assessed the relationship between the transcriptional profile of benthic amphipods of genus Diporeia and the presence of the CRESS-DNA virus, LM29173, in the Laurentian Great Lakes to provide potential insight into the influence of these viruses on invertebrate gene expression. Twelve transcriptomes derived from Diporeia were compared, representing organisms from two amphipod haplotype clades (Great Lakes Michigan and Superior, defined by COI barcode sequencing) with varying viral loads (up to 3 × 10[6] genome copies organism[-1]). Read recruitment to de novo assembled transcripts revealed 2,208 significantly over or underexpressed contigs in transcriptomes with above average LM29173 load. Of these contigs, 31.5% were assigned a putative function. The greatest proportion of annotated, differentially expressed transcripts were associated with functions including: (1) replication, recombination, and repair, (2) cell structure/biogenesis, and (3) post-translational modification, protein turnover, and chaperones. Contigs putatively associated with innate immunity displayed no consistent pattern of expression, though several transcripts were significantly overexpressed in amphipods with high viral load. Quantitation (RT-qPCR) of target transcripts, non-muscular myosin heavy chain, β-actin, and ubiquitin-conjugating enzyme E2, corroborated transcriptome analysis and indicated that Lake Michigan and Lake Superior amphipods with high LM29173 load exhibit lake-specific trends in gene expression. While this investigation provides the first comparative survey of the transcriptional profile of invertebrates of variable CRESS-DNA viral load, additional inquiry is required to define the scope of host-specific responses to potential infection.},
}
@article {pmid28965311,
year = {2018},
author = {Wang, JD and Wang, WZ and Lin, ZL and Ali, A and Fu, HY and Huang, MT and Gao, SJ and Wang, R},
title = {DNA Barcoding for Identification of Sugarcane Borers in China.},
journal = {Neotropical entomology},
volume = {47},
number = {3},
pages = {362-368},
pmid = {28965311},
issn = {1678-8052},
support = {31601363//National Natural Science Foundation of China/ ; CARS-20-2-4//China Agriculture Research System/ ; 2017J01422//Natural Science Foundation of Fujian Province/ ; JAT160160//Education Department of Fujian scientific research project for youth and middle age teachers/ ; },
mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Herbivory ; Lepidoptera/*classification ; *Phylogeny ; *Saccharum ; },
abstract = {Sugarcane borers are economically damaging insects with species that vary in distribution patterns both geographically and temporally, and vary based on ecological niche. Currently, identification of sugarcane borers is mostly based on morphological characters. However, morphological identification requires taxonomic expertise. An alternative method to identify sugarcane borers is the use of molecular data. DNA barcoding based on partial cytochrome c oxidase subunit 1 (COI) sequences has proven to be a useful tool for rapid and accurate species determination in many insect taxa. This study was conducted to test the effectiveness of DNA barcodes to discriminate among sugarcane borer species in China. Partial sequences of the COI gene (709 bp) were obtained from six species collected from different geographic areas. Results showed that the pairwise intraspecies genetic distance was < 0.02, whereas the interspecies genetic distance ranged from 0.117 to 0.182. Results from a neighbor-joining tree showed that the six sugarcane borer species were certainly separated. These results suggested that the partial COI sequences had high barcoding resolution in discriminating among sugarcane borer species. Our study emphasized the use of DNA barcodes for identification of the analyzed sugarcane borer species and represents an important step for building a comprehensive barcode library for sugarcane borers in China.},
}
@article {pmid28962972,
year = {2017},
author = {Grzebyk, D and Audic, S and Lasserre, B and Abadie, E and de Vargas, C and Bec, B},
title = {Insights into the harmful algal flora in northwestern Mediterranean coastal lagoons revealed by pyrosequencing metabarcodes of the 28S rRNA gene.},
journal = {Harmful algae},
volume = {68},
number = {},
pages = {1-16},
doi = {10.1016/j.hal.2017.06.003},
pmid = {28962972},
issn = {1878-1470},
mesh = {Biomass ; DNA Barcoding, Taxonomic/*methods ; Dinoflagellida/classification/genetics ; *Ecosystem ; *Genes, rRNA ; Geography ; *Harmful Algal Bloom ; High-Throughput Nucleotide Sequencing/*methods ; Mediterranean Sea ; Phylogeny ; Phytoplankton/classification/genetics ; RNA, Ribosomal, 28S/*genetics ; },
abstract = {This study investigated the genetic diversity of phytoplankton communities in six shallow lagoons located on the French coast of the northwestern Mediterranean Sea that represented a trophic gradient ranging from oligotrophic to hypereutrophic. The phytoplankton communities were sampled once a month from spring (May) to the beginning of autumn (September/early October) in 2012 and fractionated by size. Metabarcodes were generated from cDNAs by targeting the D1-D2 region of the 28S rRNA gene and pyrosequenced using Roche 454 technology. Examination of the annotated barcodes revealed harmful algal species not previously documented in these lagoons. Three ichthyotoxic species belonging to Pfiesteriaceae were detected: Luciella masanensis was relatively widespread and abundant in many samples, whereas Pfiesteria piscicida and Stoeckeria changwonensis were found as single barcode sequences. Furthermore, a phylogenetic analysis of barcodes annotated as belonging to Pfiesteriaceae suggested the existence of two previously undescribed clades. The other toxic or potentially harmful dinoflagellates detected through rare barcodes were Dinophysis acuminata, Vulcanodinium rugosum, Alexandrium andersonii and A. ostenfeldii. The two most abundant dinoflagellate taxa were Gymnodinium litoralis and Akashiwo sanguinea with respect to sequence numbers. Four diatom species from the genus Pseudo-nitzschia that potentially produce domoic acid were identified (P. galaxiae, P. delicatissima, P. brasiliana and P. calliantha). These observations are discussed in terms of the literature and monitoring records related to the identified taxa in this Mediterranean area.},
}
@article {pmid28961965,
year = {2017},
author = {Nguyen, SH and Duarte, TPS and Coin, LJM and Cao, MD},
title = {Real-time demultiplexing Nanopore barcoded sequencing data with npBarcode.},
journal = {Bioinformatics (Oxford, England)},
volume = {33},
number = {24},
pages = {3988-3990},
doi = {10.1093/bioinformatics/btx537},
pmid = {28961965},
issn = {1367-4811},
mesh = {Algorithms ; *Electronic Data Processing ; *Nanopores ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; *Software ; },
abstract = {MOTIVATION: The recent introduction of a barcoding protocol for Oxford Nanopore sequencing has increased the versatility of the technology. Several bioinformatics tools have been developed to demultiplex barcoded reads, but none of them supports streaming analysis. This limits the use of multiplexed sequencing in real-time applications, which is one of the main advantages of the technology.<br><br>RESULTS: We introduced npBarcode, an open source and cross-platform tool for barcode demultiplexing in streaming fashion that can be used to pipe data to further real-time analyses. The tool also provides a friendly graphical user interface by integrating the module into npReader, making possible to monitor the progress concurrently when the sequencing is still in progress. We show that our algorithm achieves accuracies at least as good as competing tools.<br><br>npBarcode is bundled in Japsa-a Java tools kit for genome analysis, and is freely available at https://github.com/mdcao/japsa.<br><br>CONTACT: s.nguyen@uq.edu.au or l.coin@imb.uq.edu.au.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid28961510,
year = {2017},
author = {Awad, M and Fahmy, RM and Mosa, KA and Helmy, M and El-Feky, FA},
title = {Identification of effective DNA barcodes for Triticum plants through chloroplast genome-wide analysis.},
journal = {Computational biology and chemistry},
volume = {71},
number = {},
pages = {20-31},
doi = {10.1016/j.compbiolchem.2017.09.003},
pmid = {28961510},
issn = {1476-928X},
mesh = {Computational Biology ; *DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; Genome, Chloroplast/*genetics ; Triticum/*genetics ; },
abstract = {The Egyptian flora is rich with a large number of Triticum plants, which are very difficult to discriminate between in the early developmental stages. This study assesses the significance of using two DNA Barcoding loci (matK and rbcL) in distinguishing between 18 different Triticum accessions in Egypt. We isolated and sequenced 15 rbcL and six matK fragments, but our analysis of the resultant sequences demonstrated a limited ability of matK and rbcL in distinguishing between Triticum accessions. Therefore, we pursued a bioinformatics approach to determine the most useful loci which may be used as DNA barcodes for the Triticum spp. We obtained the 10 available chloroplast genomes of the 10 Triticum species and sub-species from NCBI, and performed chloroplast genome-wide analysis to find the potential barcode loci. A total of 134 chloroplast genes, gene combinations, intergenic regions and intergenic region combinations were tested using a Tree-based method. We were unable to discriminate between Triticum species by using chloroplast genes, gene combinations and intergenic regions. However, a combination of the intergenic region (trnfM-trnT) with either (trnD-psbM), (petN-trnC), (matK-rps16) or (rbcL-psaI) demonstrated a very high discrimination capacity, suggesting their utilization as DNA barcodes for the Triticum plants. Furthermore, our novel DNA barcodes demonstrated high discrimination capacity for other Poaceae members.},
}
@article {pmid28961455,
year = {2017},
author = {Venter, PC and Nitsche, F and Domonell, A and Heger, P and Arndt, H},
title = {The Protistan Microbiome of Grassland Soil: Diversity in the Mesoscale.},
journal = {Protist},
volume = {168},
number = {5},
pages = {546-564},
doi = {10.1016/j.protis.2017.03.005},
pmid = {28961455},
issn = {1618-0941},
mesh = {DNA Barcoding, Taxonomic ; Eukaryota/classification/genetics/*physiology ; Germany ; *Grassland ; High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; Soil/*parasitology ; },
abstract = {Genomic data for less than one quarter of ∼1.8 million named species on earth exist in public databases like GenBank. Little information exists on the estimated one million small sized (1-100μm) heterotrophic nanoflagellates and ciliates and their taxa-area relationship. We analyzed environmental DNA from 150 geo-referenced grassland plots representing topographical and land-use ranges typical for Central Europe. High through-put barcoding allowed the identification of operational taxonomic units (OTUs) at species level, with high pairwise identity to reference sequences (≥99.7%), but also the identification of sequences at the genus (≥97%) and class (≥80%) taxonomic level. Species richness analyses revealed, on average, 100 genus level OTUs (332 unique individual read (UIR) and 56 class level OTUs per gram of soil sample in the mesoscale (1-1000km). Database shortfalls were highlighted by increased uncertain taxonomic lineages at lower resolution (≥80% sequence identity). No single barcode occurred ubiquitously across all sites. Taxa-area relationships indicated that OTUs spread over the entire mesoscale were more similar than in the local scale and increased land-use (fertilization, mowing and grazing) promoted taxa-area separation. Only a small fraction of sequences strictly matched reference library sequences, suggesting a large protistan "dark matter" in soil which warrants further research.},
}
@article {pmid28961406,
year = {2018},
author = {Feng, S and Jiao, K and Zhu, Y and Wang, H and Jiang, M and Wang, H},
title = {Molecular identification of species of Physalis (Solanaceae) using a candidate DNA barcode: the chloroplast psbA-trnH intergenic region.},
journal = {Genome},
volume = {61},
number = {1},
pages = {15-20},
doi = {10.1139/gen-2017-0115},
pmid = {28961406},
issn = {1480-3321},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Intergenic/*chemistry ; DNA, Plant/chemistry ; *Genes, Chloroplast ; Genetic Variation ; Photosystem II Protein Complex/genetics ; Physalis/anatomy &amp; histology/*classification/*genetics ; Polymerase Chain Reaction ; },
abstract = {Physalis L., an important genus of the family Solanaceae, includes many commercially important edible and medicinal species. Traditionally, species identification is based on morphological traits; however, the highly similar morphological traits among species of Physalis make this approach difficult. In this study, we evaluated the feasibility of using a popular DNA barcode, the chloroplast psbA-trnH intergenic region, in the identification of species of Physalis. Thirty-six psbA-trnH regions of species of Physalis and of the closely related plant Nicandra physalodes were analyzed. The success rates of PCR amplification and sequencing of the psbA-trnH region were 100%. MEGA V6.0 was utilized to align the psbA-trnH sequences and to compute genetic distances. The results show an apparent barcoding gap between intra- and interspecific variations. Results of both BLAST1 and nearest-distance methods prove that the psbA-trnH regions can be used to identify all species examined in the present study. In addition, phylogenetic analysis using psbA-trnH data revealed a distinct boundary between species. It also confirmed the relationship between species of Physalis and closely related species, as established by previous studies. In conclusion, the psbA-trnH intergenic region can be used as an efficient DNA barcode for the identification of species of Physalis.},
}
@article {pmid28960408,
year = {2018},
author = {Gaksch, L and Kashofer, K and Heitzer, E and Quehenberger, F and Daga, S and Hofer, S and Halbwedl, I and Graf, R and Krisper, N and Hoefler, G and Zebisch, A and Sill, H and Wölfler, A},
title = {Residual disease detection using targeted parallel sequencing predicts relapse in cytogenetically normal acute myeloid leukemia.},
journal = {American journal of hematology},
volume = {93},
number = {1},
pages = {23-30},
doi = {10.1002/ajh.24922},
pmid = {28960408},
issn = {1096-8652},
mesh = {Adult ; Aged ; Biomarkers, Tumor/*genetics ; Cytogenetics/*methods ; Female ; Humans ; Leukemia, Myeloid, Acute/*diagnosis/mortality ; Male ; Middle Aged ; Prognosis ; Young Adult ; },
abstract = {Despite achieving complete remission after intensive therapy, most patients with cytogenetically normal (CN) AML relapse due to the persistence of submicroscopic residual disease. In this pilot study, we hypothesized that detection of leukemia-specific mutations following consolidation treatment using a targeted parallel sequencing approach predicts relapse. We included 34 AML patients of whom diagnostic material and remission bone marrow slides after at least one cycle of consolidation were available. Isolated DNA was screened for mutations in 19 genes using an Ion Torrent sequencing platform. Furthermore, the variant allelic frequency of distinct mutations was validated by digital PCR and sequencing using a barcoding approach. Twenty-seven out of 34 patients could be analyzed for mutation clearance. We identified 68 somatic mutations at diagnosis (median, 3 mutations per patient; range 1-5) and 22 of these were still detected in 16 patients after consolidation therapy with a reliable sensitivity of 0.5% (median, 1 mutation; range 0-3). The most frequent noncleared mutations were found in DNMT3A. However, as persistence of these mutations has recently been shown to be without any impact on relapse risk, we performed survival and relapse risk analysis excluding DNMT3A mutations. Importantly, persistence of non-DNMT3A mutations was associated with a higher risk of AML relapse (7/8 pts versus 6/19 pts; P = .013) and with a shorter relapse-free survival (333 days vs. not reached; log-rank P = .0219). Detection of residual disease by routine targeted parallel sequencing proved feasible and effective as persistence of somatic mutations other than DNMT3A were prognostic for relapse in CN AML.},
}
@article {pmid28957705,
year = {2018},
author = {Xu, Y and Wang, H and Luan, C and Liu, Y and Chen, B and Zhao, Y},
title = {Aptamer-based hydrogel barcodes for the capture and detection of multiple types of pathogenic bacteria.},
journal = {Biosensors &amp; bioelectronics},
volume = {100},
number = {},
pages = {404-410},
doi = {10.1016/j.bios.2017.09.032},
pmid = {28957705},
issn = {1873-4235},
mesh = {Aptamers, Nucleotide/*chemistry ; Bacteria/*isolation &amp; purification ; Bacterial Infections/microbiology ; Biosensing Techniques/*methods ; Escherichia coli/isolation &amp; purification ; Escherichia coli Infections/microbiology ; Humans ; Hydrogel, Polyethylene Glycol Dimethacrylate/*chemistry ; Magnetite Nanoparticles/*chemistry ; Polyethylene Glycols/*chemistry ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/isolation &amp; purification ; },
abstract = {Rapid and sensitive diagnosing hematological infections based on the separation and detection of pathogenic bacteria in the patient's blood is a significant challenge. To address this, we herein present a new barcodes technology that can simultaneously capture and detect multiple types of pathogenic bacteria from a complex sample. The barcodes are poly (ethylene glycol) (PEG) hydrogel inverse opal particles with characteristic reflection peak codes that remain stable during bacteria capture on their surfaces. As the spherical surface of the particles has ordered porous nanostructure, the barcodes can provide not only more surface area for probe immobilization and reaction, but also a nanopatterned platform for highly efficient bioreactions. In addition, the PEG hydrogel scaffold could decrease the non-specificity adsorption by its anti-adhesive effect, and the decorated aptamer probes in the scaffolds could increase the sensitivity, reliability, and specificity of the bacteria capture and detection. Moreover, the tagged magnetic nanoparticles in the PEG scaffold could impart the barcodes with controllable movement under magnetic fields, which can be used to significantly increase the reaction speed and simplify the processing of the bioassays. Based on the describe barcodes, it was demonstrated that the bacteria could be captured and identified even at low bacterial concentrations (100 CFU mL[-1]) within 2.5h, which is effectively shortened in comparison with the "gold standard" in clinic. These features make the barcodes ideal for capturing and detecting multiple bacteria from clinical samples for hematological infection diagnostics.},
}
@article {pmid28955369,
year = {2017},
author = {Zhang, X and Zhou, T and Kanwal, N and Zhao, Y and Bai, G and Zhao, G},
title = {Completion of Eight Gynostemma BL. (Cucurbitaceae) Chloroplast Genomes: Characterization, Comparative Analysis, and Phylogenetic Relationships.},
journal = {Frontiers in plant science},
volume = {8},
number = {},
pages = {1583},
pmid = {28955369},
issn = {1664-462X},
abstract = {Gynostemma BL., belonging to the family Cucurbitaceae, is a genus containing 17 creeping herbaceous species mainly distributed in East Asia. It can be divided into two subgenera based on different fruit morphology. Herein, we report eight complete chloroplast genome sequences of the genus Gynostemma, which were obtained by Illumina paired-end sequencing, assembly, and annotation. The length of the eight complete cp genomes ranged from 157,576 bp (G. pentaphyllum) to 158,273 bp (G. laxiflorum). Each encoded 133 genes, including 87 protein-coding genes, 37 tRNA genes, eight rRNA genes, and one pseudogene. The four types of repeated sequences had been discovered and indicated that the repeated structure for species in the Subgen. Triostellum was greater than that for species in the Subgen. Gynostemma. The percentage of variation of the eight cp genomes in different regions were calculated, which demonstrated that the coding and inverted repeats regions were highly conserved. Phylogenetic analysis based on Bayesian inference and maximum likelihood methods strongly supported the phylogenetic position of the genus Gynostemma as a member of family Cucurbitaceae. The phylogenetic relationships among the eight species were clearly resolved using the complete cp genome sequences in this study. It will also provide potential molecular markers and candidate DNA barcodes for future studies and enrich the valuable complete cp genome resources of Cucurbitaceae.},
}
@article {pmid28952271,
year = {2017},
author = {Huang, YX and Guo, YM and Zhou, YF and Zhang, CE and Jing, J and Liu, SJ and Zhang, NN and Song, JY and Xiao, XH and Wang, JB},
title = {[Dictamni Cortex powder-induced liver injury based on integrated evidence chain].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {42},
number = {3},
pages = {600-606},
doi = {10.19540/j.cnki.cjcmm.2017.0015},
pmid = {28952271},
issn = {1001-5302},
mesh = {*Chemical and Drug Induced Liver Injury ; Dictamnus/*adverse effects ; Drugs, Chinese Herbal/*adverse effects ; Humans ; },
abstract = {A typical clinical case of taking Dictamni Cortex(Baixianpi) powder was analyzed to study liver damage caused by Dictamni Cortex. Liver damage was diagnosed according to the integrated evidence chain method recommended by the Guideline for Diagnosis and Treatment of Herb-Induced Liver Injury. By analyzing clinical history and biochemistry and imaging examinations, underlying diseases, such as viral hepatitis, autoimmune liver disease and alcoholic liver disease, were excluded. Through the investigation of medication history, we made it clear that the patient only took Dictamni Cortex powder during the period, and thus suspected that the liver injury was induced by Dictamni Cortex. Furthermore, the quality of the drug was tested, and the results showed it was consistent with the quality standard of Chinese Pharmacopoeia. DNA barcoding showed that the drug was 100% similar with Dictamnus dasycarpus. Moreover, exogenous harmful substances and chemical drug additions were tested, and the results showed that the content of heavy metal, pesticide residues and microbial toxin were consistent with the required standards, and no chemical drug additions were found in Agilent Fake TCM-Drugs database. In summary, we confirmed that the clinical case of drug-induced liver injury was induced by D. dasycarpus with the dose of 15 g•d[-1], which exceeded the prescribed amount of Chinese Pharmacopoeia. According to the Guideline for Diagnosis and Treatment of Herb-Induced Liver Injury, the case of drug-induced liver injury induced by D. dasycarpus was confirmed, which provided a direct and reliable evidence for the study of risk of liver injury induced by D. dasycarpus and its relevant preparations.},
}
@article {pmid28952249,
year = {2017},
author = {Yang, S and Xue, YY and Li, MH and Zhao, FX and Zhao, H and Zhang, W},
title = {[Application of phylogenetic information of ITS2 secondary structure in DNA barcoding of Solanum medicinal plant].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {42},
number = {3},
pages = {456-464},
doi = {10.19540/j.cnki.cjcmm.20170103.003},
pmid = {28952249},
issn = {1001-5302},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/*genetics ; Nucleic Acid Conformation ; *Phylogeny ; Plants, Medicinal/genetics ; Solanum/*genetics ; },
abstract = {Internal transcript spacer 2 (ITS2) is one of the broadly used standard core barcodes and also the only nuclear barcode in identification of Chinese traditional medicine. Although the DNA barcode method based on ITS2 is popular and has been used in Chinese Pharmacopoeia, its low discriminatory efficiency is still a problem to its extensive application. Therefore, further study is still necessary to explore its phylogenetic information for medicinal plants identification. In cells, ITS2 activity is based on its secondary structure. The secondary structures are particularly useful in phylogenetic analysis because they include information not found in the primary sequence. In this study ITS2 secondary structure of 40 samples from 26 species were predicted and used to explore their utility in addressing the identification problems of Chinese traditional medicine in Solanum. The secondary structures were predicted and aligned, and their consensus models were generated using the three different software of LocARNA, MASTR and PicXAA-R. RNAstat software was used to transform the secondary structures into 28 symbol code data for maximum parsimony (MP) analysis. The results showed that the phylogenetic information increased 88.57% after ITS2 secondary structure information has been added, and then the support values above 50%, 75% and 90% in the tree increased 19.05%, 66.67% and 66.67%, respectively, indicating that the identification of Solanum medical plants has been well resolved. Thus, our analysis suggests that ITS2 secondary structure information should be incorporated into the current DNA barcoding analysis as a beneficial supplement of phylogenetic information.},
}
@article {pmid28948681,
year = {2017},
author = {Pan, M and Zhu, YX and Wu, K and Chen, L and Hou, YJ and Yin, SY and Wang, HP and Fan, YN and Su, CY},
title = {Epitaxial Growth of Hetero-Ln-MOF Hierarchical Single Crystals for Domain- and Orientation-Controlled Multicolor Luminescence 3D Coding Capability.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {56},
number = {46},
pages = {14582-14586},
doi = {10.1002/anie.201708802},
pmid = {28948681},
issn = {1521-3773},
abstract = {Core-shell or striped heteroatomic lanthanide metal-organic framework hierarchical single crystals were obtained by liquid-phase anisotropic epitaxial growth, maintaining identical periodic organization while simultaneously exhibiting spatially segregated structure. Different types of domain and orientation-controlled multicolor photophysical models are presented, which show either visually distinguishable or visible/near infrared (NIR) emissive colors. This provides a new bottom-up strategy toward the design of hierarchical molecular systems, offering high-throughput and multiplexed luminescence color tunability and readability. The unique capability of combining spectroscopic coding with 3D (three-dimensional) microscale spatial coding is established, providing potential applications in anti-counterfeiting, color barcoding, and other types of integrated and miniaturized optoelectronic materials and devices.},
}
@article {pmid28948100,
year = {2017},
author = {Baeza, JA and Behringer, DC},
title = {Integrative taxonomy of the ornamental 'peppermint' shrimp public market and population genetics of Lysmata boggessi, the most heavily traded species worldwide.},
journal = {PeerJ},
volume = {5},
number = {},
pages = {e3786},
pmid = {28948100},
issn = {2167-8359},
abstract = {The ornamental trade is a worldwide industry worth >15 billion USD with a problem of rampant product misidentification. Minimizing misidentification is critical in the face of overexploitation of species in the trade. We surveyed the peppermint shrimp ornamental marketplace in the southeastern USA, the most intense market for peppermint shrimps worldwide, to characterize the composition of species in the trade, reveal the extent of misidentification, and describe the population genetics of the true target species. Shrimps were bought from aquarium shops in FL, GA, SC, and NC. We demonstrated, contrary to popular belief (information from dealers), that the most heavily traded species in the market was Lysmata boggessi, an endemic species to the eastern Gulf of Mexico, and not Lysmata wurdemanni. Importantly, only when color pattern or genetic markers in conjunction with morphological traits were employed, was it was possible to unequivocally identify L. boggessi as the only species in the trade. The intensity of the market for peppermint shrimps in the USA has led to L. boggessi being the most traded species worldwide. Misidentification in the shrimp aquarium trade is accidental and involuntary, and is explained by remarkable similarity among congeneric species. Using sequences of the 16S-mt-DNA marker, we found no indication of population genetic structure in the endemic L. boggessi across 550 km of linear coast. Therefore, this species can be considered genetically homogeneous and a single fished stock. Still, we argue in favor of additional studies using more powerful markers (e.g., SNPs) capable of revealing genetic structure at a finer spatial-scale. Our results will help advance management and conservation policies in this lucrative yet understudied fishery. Future studies of other ornamental fisheries will benefit from using an integrative taxonomic approach, as we demonstrate here.},
}
@article {pmid28946337,
year = {2018},
author = {Zhang, Y and Zhao, C and Tian, G and Lu, C and Li, Y and He, L and Xiao, H and Zheng, J},
title = {Simultaneous characterization of chemical structures and bioactivities of citrus-derived components using SERS barcodes.},
journal = {Food chemistry},
volume = {240},
number = {},
pages = {743-750},
doi = {10.1016/j.foodchem.2017.07.103},
pmid = {28946337},
issn = {1873-7072},
mesh = {Citrus ; Molecular Structure ; *Spectrum Analysis, Raman ; Structure-Activity Relationship ; },
abstract = {Rapid detection of bioactive components in food has attracted great attention. Herein, we report a novel method through surface-enhanced Raman spectroscopy (SERS) spectra based barcodes for simultaneous characterization of chemical structures and bioactivities of nine citrus components for the first time. SERS barcodes were successfully used to characterize and discriminate all the components with high sensitivity down to 40-60ng. Importantly, SERS barcodes exhibited the 'identity' characteristics. Beyond the molecular structure information, bioactivity information can also be read from the barcodes according to the bioactivity assay and structure-activity relationship. Hence, a simple and intuitive SERS barcoding approach used for simultaneous characterization of chemical structures and bioactivities was established. With a large database of barcodes, there is high potential that the SERS barcoding approach could be further developed to be a rapid, simple and effective foodomics-like approach for bioactive compound identification from a complex food matrix.},
}
@article {pmid28944019,
year = {2017},
author = {Hosein, FN and Austin, N and Maharaj, S and Johnson, W and Rostant, L and Ramdass, AC and Rampersad, SN},
title = {Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad.},
journal = {Ecology and evolution},
volume = {7},
number = {18},
pages = {7311-7333},
pmid = {28944019},
issn = {2045-7758},
abstract = {The islands of the Caribbean are considered to be a "biodiversity hotspot." Collectively, a high level of endemism for several plant groups has been reported for this region. Biodiversity conservation should, in part, be informed by taxonomy, population status, and distribution of flora. One taxonomic impediment to species inventory and management is correct identification as conventional morphology-based assessment is subject to several caveats. DNA barcoding can be a useful tool to quickly and accurately identify species and has the potential to prompt the discovery of new species. In this study, the ability of DNA barcoding to confirm the identities of 14 endangered endemic vascular plant species in Trinidad was assessed using three DNA barcodes (matK, rbcL, and rpoC1). Herbarium identifications were previously made for all species under study. matK, rbcL, and rpoC1 markers were successful in amplifying target regions for seven of the 14 species. rpoC1 sequences required extensive editing and were unusable. rbcL primers resulted in cleanest reads, however, matK appeared to be superior to rbcL based on a number of parameters assessed including level of DNA polymorphism in the sequences, genetic distance, reference library coverage based on BLASTN statistics, direct sequence comparisons within "best match" and "best close match" criteria, and finally, degree of clustering with moderate to strong bootstrap support (>60%) in neighbor-joining tree-based comparisons. The performance of both markers seemed to be species-specific based on the parameters examined. Overall, the Trinidad sequences were accurately identified to the genus level for all endemic plant species successfully amplified and sequenced using both matK and rbcL markers. DNA barcoding can contribute to taxonomic and biodiversity research and will complement efforts to select taxa for various molecular ecology and population genetics studies.},
}
@article {pmid28943295,
year = {2017},
author = {Wahlestedt, M and Bryder, D},
title = {The slippery slope of hematopoietic stem cell aging.},
journal = {Experimental hematology},
volume = {56},
number = {},
pages = {1-6},
doi = {10.1016/j.exphem.2017.09.008},
pmid = {28943295},
issn = {1873-2399},
mesh = {Animals ; *Cellular Senescence ; *Epigenesis, Genetic ; *Hematopoiesis ; Hematopoietic Stem Cells/*metabolism ; Humans ; Induced Pluripotent Stem Cells/metabolism ; },
abstract = {The late stages of life, in most species including humans, are associated with a decline in the overall maintenance and health of the organism. This applies also to the hematopoietic system, where aging is not only associated with an increased predisposition for hematological malignancies, but also identified as a strong comorbidity factor for other diseases. Research during the last two decades has proposed that alterations at the level of hematopoietic stem cells (HSCs) might be a root cause for the hematological changes observed with age. However, the recent realization that not all HSCs are alike with regard to fundamental stem cell properties such as self-renewal and lineage potential has several implications for HSC aging, including the synchrony and the stability of the aging HSC state. To approach HSC aging from a clonal perspective, we recently took advantage of technical developments in cellular barcoding and combined this with the derivation of induced pluripotent stem cells (iPSCs). This allowed us to selectively approach HSCs functionally affected by age. The finding that such iPSCs were capable of fully regenerating multilineage hematopoiesis upon morula/blastocyst complementation provides compelling evidence that many aspects of HSC aging can be reversed, which indicates that a central mechanism underlying HSC aging is a failure to uphold the epigenomes associated with younger age. Here we discuss these findings in the context of the underlying causes that might influence HSC aging and the requirements and prospects for restoration of the aging HSC epigenome.},
}
@article {pmid28942722,
year = {2019},
author = {Reichard, JS and Garbarz, DM and Teachey, AL and Allgood, J and Brown, MJ},
title = {Pharmacy workload benchmarking: Establishing a health-system outpatient infusion productivity metric.},
journal = {Journal of oncology pharmacy practice : official publication of the International Society of Oncology Pharmacy Practitioners},
volume = {25},
number = {1},
pages = {172-178},
doi = {10.1177/1078155217730663},
pmid = {28942722},
issn = {1477-092X},
mesh = {Ambulatory Care/methods/*standards ; Ambulatory Care Facilities/standards ; Antineoplastic Agents/*administration &amp; dosage ; Benchmarking/methods/*standards ; Humans ; Infusions, Intravenous ; Pharmacies/standards ; Pharmacists/*standards ; Pharmacy Service, Hospital/methods/*standards ; Workload/*standards ; },
abstract = {BACKGROUND AND OBJECTIVES: Current productivity assessment models lack the ability to measure the quality of pharmacy services through workload validation. The goal of our efforts was to create a model to more accurately assess workload at multiple outpatient infusion centers.<br><br>METHOD: Current procedural terminology codes were identified as representative of the key drivers of pharmacy workload. Fourteen current procedural terminology codes representing medication orders were selected and categorized into eight distinctive groups associated with varying amounts of pharmacy workload. A three-month average of current procedural terminology volumes were calculated and used to create a workload baseline.<br><br>RESULTS: Our study found a usable productivity assessment and coefficient to compare relevant clinical workload across outpatient oncology sites. The current procedural terminology codes were readily retrievable from our system electronic medical record. By assigning activities, e.g. clinical review, verification, barcoding, batch preparation, we were able to compute a workload and then adjust staffing to achieve a median coefficient across sites.<br><br>DISCUSSION: This study evaluated the use of administration current procedural terminology codes for an outpatient oncology productivity model. Based upon our analysis, it can be successfully used to determine workload for pharmacists and technicians across variable locations. We believe it is the first study to demonstrate a productivity model for this setting.},
}
@article {pmid28940935,
year = {2018},
author = {Lekishvili, T and Campbell, JJ},
title = {Rapid comparative immunophenotyping of human mesenchymal stromal cells by a modified fluorescent cell barcoding flow cytometric assay.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {93},
number = {9},
pages = {905-915},
doi = {10.1002/cyto.a.23248},
pmid = {28940935},
issn = {1552-4930},
mesh = {Antibodies/metabolism ; Biological Assay/methods ; Cells, Cultured ; Flow Cytometry/*methods ; Fluorescent Dyes/*administration &amp; dosage ; Humans ; Immunophenotyping/*methods ; Mesenchymal Stem Cells/*cytology/metabolism ; Reproducibility of Results ; },
abstract = {Flow cytometry immunophenotyping is a sensitive technique allowing rapid characterization of single cells within heterogeneous populations, but it includes several subjective steps during sample analysis that impact the development of standardized methodology. Proposed strategies to overcome these limitations include fluorescent cell barcoding (FCB), which facilitates multiplexed sample evaluation with increased data reproducibility whilst reducing labeling variation, materials, and time. To date, the FCB assay has found utility for analyzing the phosphorylation status of intracellular targets but has not been intensively employed for cellular immunophenotypic analyses using cell surface markers. In this study we developed a modified FCB assay for multiplexed analysis of human mesenchymal stromal cells (hMSCs) to evaluate the quality of these cells during bioprocessing. A panel of fluorochrome-conjugated antibodies was used to target 15 ubiquitously expressed or stage-specific markers together with a fixable viability dye eFluor 506 acting as the cell barcoding agent. Critical technical considerations and validation steps were presented in the context of monitoring hMSC status, defined by generic, and specific surface markers for cell identity and quality. It was found that at discrete passages, inter-analyst expression patterns between hMSCs cultures were similar, but in contrast, diverse marker expression was evident between passages. A side-by-side analysis of barcoded and non-barcoded cells demonstrated the potential of this technique for the rapid phenotypic characterization of cells exposed to different bioprocessing conditions. Additionally, the method incorporates fewer subjective factors; including sample preparation and instrument day-to-day variations and is customizable across a diversity of cell types. © 2017 International Society for Advancement of Cytometry.},
}
@article {pmid28934929,
year = {2017},
author = {Lau, BT and Ji, HP},
title = {Single molecule counting and assessment of random molecular tagging errors with transposable giga-scale error-correcting barcodes.},
journal = {BMC genomics},
volume = {18},
number = {1},
pages = {745},
pmid = {28934929},
issn = {1471-2164},
support = {P01 HG000205/HG/NHGRI NIH HHS/United States ; R01 HG006137/HG/NHGRI NIH HHS/United States ; },
mesh = {DNA Transposable Elements/*genetics ; DNA, Complementary/genetics ; Gene Expression Profiling ; Sequence Analysis, RNA/*methods ; },
abstract = {BACKGROUND: RNA-Seq measures gene expression by counting sequence reads belonging to unique cDNA fragments. Molecular barcodes commonly in the form of random nucleotides were recently introduced to improve gene expression measures by detecting amplification duplicates, but are susceptible to errors generated during PCR and sequencing. This results in false positive counts, leading to inaccurate transcriptome quantification especially at low input and single-cell RNA amounts where the total number of molecules present is minuscule. To address this issue, we demonstrated the systematic identification of molecular species using transposable error-correcting barcodes that are exponentially expanded to tens of billions of unique labels.<br><br>RESULTS: We experimentally showed random-mer molecular barcodes suffer from substantial and persistent errors that are difficult to resolve. To assess our method's performance, we applied it to the analysis of known reference RNA standards. By including an inline random-mer molecular barcode, we systematically characterized the presence of sequence errors in random-mer molecular barcodes. We observed that such errors are extensive and become more dominant at low input amounts.<br><br>CONCLUSIONS: We described the first study to use transposable molecular barcodes and its use for studying random-mer molecular barcode errors. Extensive errors found in random-mer molecular barcodes may warrant the use of error correcting barcodes for transcriptome analysis as input amounts decrease.},
}
@article {pmid28928943,
year = {2017},
author = {White, R and Pellefigues, C and Ronchese, F and Lamiable, O and Eccles, D},
title = {Investigation of chimeric reads using the MinION.},
journal = {F1000Research},
volume = {6},
number = {},
pages = {631},
pmid = {28928943},
issn = {2046-1402},
abstract = {Following a nanopore sequencing run of PCR products of three amplicons less than 1kb, an abundance of reads failed quality control due to template/complement mismatch. A BLAST search demonstrated that some of the failed reads mapped to two different genes -- an unexpected observation, given that PCR was carried out separately for each amplicon. A further investigation was carried out specifically to search for chimeric reads, using separate barcodes for each amplicon and trying two different ligation methods prior to sample loading. Despite the separation of ligation products, chimeric reads formed from different amplicons were still observed in the base-called sequence. The long-read nature of nanopore sequencing presents an effective tool for the discovery and filtering of chimeric reads. We have found that at least 1.7% of reads prepared using the Nanopore LSK002 2D Ligation Kit include post-amplification chimeric elements. This finding has potential implications for other amplicon sequencing technologies, as the process is unlikely to be specific to the sample preparation used for nanopore sequencing.},
}
@article {pmid28934362,
year = {2017},
author = {Yao, PC and Gao, HY and Wei, YN and Zhang, JH and Chen, XY and Li, HQ},
title = {Evaluating sampling strategy for DNA barcoding study of coastal and inland halo-tolerant Poaceae and Chenopodiaceae: A case study for increased sample size.},
journal = {PloS one},
volume = {12},
number = {9},
pages = {e0185311},
pmid = {28934362},
issn = {1932-6203},
mesh = {*Adaptation, Physiological ; Chenopodiaceae/*classification/genetics/*physiology ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; Ecosystem ; Genetic Variation ; Poaceae/*classification/genetics/*physiology ; *Salinity ; Sample Size ; },
abstract = {Environmental conditions in coastal salt marsh habitats have led to the development of specialist genetic adaptations. We evaluated six DNA barcode loci of the 53 species of Poaceae and 15 species of Chenopodiaceae from China's coastal salt marsh area and inland area. Our results indicate that the optimum DNA barcode was ITS for coastal salt-tolerant Poaceae and matK for the Chenopodiaceae. Sampling strategies for ten common species of Poaceae and Chenopodiaceae were analyzed according to optimum barcode. We found that by increasing the number of samples collected from the coastal salt marsh area on the basis of inland samples, the number of haplotypes of Arundinella hirta, Digitaria ciliaris, Eleusine indica, Imperata cylindrica, Setaria viridis, and Chenopodium glaucum increased, with a principal coordinate plot clearly showing increased distribution points. The results of a Mann-Whitney test showed that for Digitaria ciliaris, Eleusine indica, Imperata cylindrica, and Setaria viridis, the distribution of intraspecific genetic distances was significantly different when samples from the coastal salt marsh area were included (P < 0.01). These results suggest that increasing the sample size in specialist habitats can improve measurements of intraspecific genetic diversity, and will have a positive effect on the application of the DNA barcodes in widely distributed species. The results of random sampling showed that when sample size reached 11 for Chloris virgata, Chenopodium glaucum, and Dysphania ambrosioides, 13 for Setaria viridis, and 15 for Eleusine indica, Imperata cylindrica and Chenopodium album, average intraspecific distance tended to reach stability. These results indicate that the sample size for DNA barcode of globally distributed species should be increased to 11-15.},
}
@article {pmid28931735,
year = {2017},
author = {de Boer, HJ and Ghorbani, A and Manzanilla, V and Raclariu, AC and Kreziou, A and Ounjai, S and Osathanunkul, M and Gravendeel, B},
title = {DNA metabarcoding of orchid-derived products reveals widespread illegal orchid trade.},
journal = {Proceedings. Biological sciences},
volume = {284},
number = {1863},
pages = {},
pmid = {28931735},
issn = {1471-2954},
mesh = {Beverages/*analysis ; *Commerce ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Germany ; Greece ; Orchidaceae/*classification ; },
abstract = {In eastern Mediterranean countries orchids continue to be collected from the wild for the production of salep, a beverage made of dried orchid tubers. In this study we used nrITS1 and nrITS2 DNA metabarcoding to identify orchid and other plant species present in 55 commercial salep products purchased in Iran, Turkey, Greece and Germany. Thirty samples yielded a total of 161 plant taxa, and 13 products (43%) contained orchid species and these belonged to 10 terrestrial species with tuberous roots. Another 70% contained the substitute ingredient Cyamopsis tetraganoloba (Guar). DNA metabarcoding using the barcoding markers nrITS1 and nrITS2 shows the potential of these markers and approach for identification of species used in salep products. The analysis of interspecific genetic distances between sequences of these markers for the most common salep orchid genera shows that species level identifications can be made with a high level of confidence. Understanding the species diversity and provenance of salep orchid tubers will enable the chain of commercialization of endangered species to be traced back to the harvesters and their natural habitats, and thus allow for targeted efforts to protect or sustainably use wild populations of these orchids.},
}
@article {pmid28931084,
year = {2017},
author = {Conte-Grand, C and Britz, R and Dahanukar, N and Raghavan, R and Pethiyagoda, R and Tan, HH and Hadiaty, RK and Yaakob, NS and Rüber, L},
title = {Barcoding snakeheads (Teleostei, Channidae) revisited: Discovering greater species diversity and resolving perpetuated taxonomic confusions.},
journal = {PloS one},
volume = {12},
number = {9},
pages = {e0184017},
pmid = {28931084},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; DNA/chemistry/*metabolism ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Fishes/classification/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Snakehead fishes of the family Channidae are predatory freshwater teleosts from Africa and Asia comprising 38 valid species. Snakeheads are important food fishes (aquaculture, live food trade) and have been introduced widely with several species becoming highly invasive. A channid barcode library was recently assembled by Serrao and co-workers to better detect and identify potential and established invasive snakehead species outside their native range. Comparing our own recent phylogenetic results of this taxonomically confusing group with those previously reported revealed several inconsistencies that prompted us to expand and improve on previous studies. By generating 343 novel snakehead coxI sequences and combining them with an additional 434 coxI sequences from GenBank we highlight several problems with previous efforts towards the assembly of a snakehead reference barcode library. We found that 16.3% of the channid coxI sequences deposited in GenBank are based on misidentifications. With the inclusion of our own data we were, however, able to solve these cases of perpetuated taxonomic confusion. Different species delimitation approaches we employed (BIN, GMYC, and PTP) were congruent in suggesting a potentially much higher species diversity within snakeheads than currently recognized. In total, 90 BINs were recovered and within a total of 15 currently recognized species multiple BINs were identified. This higher species diversity is mostly due to either the incorporation of undescribed, narrow range, endemics from the Eastern Himalaya biodiversity hotspot or the incorporation of several widespread species characterized by deep genetic splits between geographically well-defined lineages. In the latter case, over-lumping in the past has deflated the actual species numbers. Further integrative approaches are clearly needed for providing a better taxonomic understanding of snakehead diversity, new species descriptions and taxonomic revisions of the group.},
}
@article {pmid28931082,
year = {2017},
author = {Kenchington, EL and Baillie, SM and Kenchington, TJ and Bentzen, P},
title = {Barcoding Atlantic Canada's mesopelagic and upper bathypelagic marine fishes.},
journal = {PloS one},
volume = {12},
number = {9},
pages = {e0185173},
pmid = {28931082},
issn = {1932-6203},
mesh = {Animals ; Atlantic Ocean ; Canada ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Databases, Genetic ; Fishes/*classification/*genetics ; Haplotypes ; },
abstract = {DNA barcode sequences were developed from 557 mesopelagic and upper bathypelagic teleost specimens collected in waters off Atlantic Canada. Confident morphological identifications were available for 366 specimens, of 118 species and 93 genera, which yielded 328 haplotypes. Five of the species were novel to the Barcode of Life Database (BOLD). Most of the 118 species conformed to expectations of monophyly and the presence of a "barcode gap", though some known weaknesses in existing taxonomy were confirmed and a deficiency in published keys was revealed. Of the specimens for which no firm morphological identification was available, 156 were successfully identified to species, and a further 11 to genus, using their barcode sequences and a combination of distance- and character-based methods. The remaining 24 specimens were from species for which no reference barcode is yet available or else ones confused by apparent misidentification of publicly available sequences in BOLD. Addition of the new sequences to those previously in BOLD contributed support to recent taxonomic revisions of Chiasmodon and Poromitra, while it also revealed 18 cases of potential cryptic speciation. Most of the latter appear to result from genetic divergence among populations in different ocean basins, while the general lack of strong horizontal environmental gradients within the deep sea has allowed morphology to be conserved. Other examples of divergence appear to distinguish individuals living under the sub-tropical gyre of the North Atlantic from those under that ocean's sub-polar gyre. In contrast, the available sequences for two myctophid species, Benthosema glaciale and Notoscopelus elongatus, showed genetic structuring on finer geographic scales. The observed structure was not consistent with recent suggestions that "resident" populations of myctophids can maintain allopatry despite the mixing of ocean waters. Rather, it indicates that the very rapid speciation characteristic of the Myctophidae is both on-going and detectable using barcodes.},
}
@article {pmid28924511,
year = {2017},
author = {Morgan, BST and Egerton-Warburton, LM},
title = {Barcoded NS31/AML2 primers for sequencing of arbuscular mycorrhizal communities in environmental samples.},
journal = {Applications in plant sciences},
volume = {5},
number = {8},
pages = {},
pmid = {28924511},
issn = {2168-0450},
abstract = {PREMISE OF THE STUDY: Arbuscular mycorrhizal fungi (AMF) are globally important root symbioses that enhance plant growth and nutrition and influence ecosystem structure and function. To better characterize levels of AMF diversity relevant to ecosystem function, deeper sequencing depth in environmental samples is needed. In this study, Illumina barcoded primers and a bioinformatics pipeline were developed and applied to study AMF diversity and community structure in environmental samples.<br><br>METHODS: Libraries of small subunit ribosomal RNA fragment amplicons were amplified from environmental DNA using a single-step PCR reaction with barcoded NS31/AML2 primers. Amplicons were sequenced on an Illumina MiSeq sequencer using version 2, 2 &#xd7; 250-bp paired-end chemistry, and analyzed using QIIME and RDP Classifier.<br><br>RESULTS: Sequencing captured 196 to 6416 operational taxonomic units (OTUs; depending on clustering parameters) representing nine AMF genera. Regardless of clustering parameters, &#x223c;20 OTUs dominated AMF communities (78-87% reads) with the remaining reads distributed among other OTUs. Analyses also showed significant biogeographic differences in AMF communities and that community composition could be linked to specific edaphic factors.<br><br>DISCUSSION: Barcoded NS31/AML2 primers and Illumina MiSeq sequencing provide a powerful approach to address AMF diversity and variations in fungal assemblages across host plants, ecosystems, and responses to environmental drivers including global change.},
}
@article {pmid28923557,
year = {2017},
author = {Vella, A and Vella, N and Schembri, S},
title = {A molecular approach towards taxonomic identification of elasmobranch species from Maltese fisheries landings.},
journal = {Marine genomics},
volume = {36},
number = {},
pages = {17-23},
doi = {10.1016/j.margen.2017.08.008},
pmid = {28923557},
issn = {1876-7478},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Fish Proteins/*genetics ; *Fisheries ; Malta ; Mediterranean Sea ; Mitochondrial Proteins/genetics ; NADH Dehydrogenase/genetics ; Sharks/*classification ; },
abstract = {The mitochondrial genome, through the application of DNA barcoding, provides a powerful tool for identifying species even when specimens are either incomplete or belong to species that exhibit cryptic diversity. In fisheries management accurate identification of whole or part of the specimens landed is a fundamental requirement for the conservation of species affected directly or indirectly by the fisheries activities. In this study cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 2 (ND2) sequences were used to genetically distinguish 36 elasmobranch species collected from Maltese (Central Mediterranean) commercial fisheries landings. Each species was analysed using these two mtDNA loci where COI (610bp) and ND2 (990bp) efficiently distinguished between the various species studied, leading to the identification of 101 haplotypes, with the intraspecific p-distance ranging between 0 and 0.75% (mean 0.10%, SD ±0.13%). This study enhances the molecular data available on elasmobranchs by providing new ND2 sequences for various species, while providing both COI and ND2 data for poorly studied Mediterranean species including: the large pelagic sharks Alopias vulpinus, A. superciliosus, Carcharhinus altimus, C. plumbeus, Carcharadon carcharias, Isurus oxyrinchus, Prionace glauca and Odontaspis ferox; the smaller demersal sharks Somniosus rostratus, Squatina aculeata, S. oculata and Squalus sp.; and the endemic stingray Dasyatis tortonesei. It also confirmed the landings of species whose identification relies strongly on molecular tools, namely Squalus sp. and D. tortonesei, which are both first confirmed records amongst Maltese fisheries landings. Morphologically, the latter two species, can be easily misidentified with S. blainville and D. pastinaca respectively. Additionally, this study evaluated the genetic differences between different polychromatic forms of Raja clavata, R. radula and Dipturus oxyrinchus. Based on the currently analysed specimens, no significant genetic differences were found between the various forms and thus no further speciation within the species was identified.},
}
@article {pmid28921904,
year = {2018},
author = {Hou, G and Chen, WT and Lu, HS and Cheng, F and Xie, SG},
title = {Developing a DNA barcode library for perciform fishes in the South China Sea: Species identification, accuracy and cryptic diversity.},
journal = {Molecular ecology resources},
volume = {18},
number = {1},
pages = {137-146},
doi = {10.1111/1755-0998.12718},
pmid = {28921904},
issn = {1755-0998},
mesh = {Animals ; China ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; *Genetic Variation ; Oceans and Seas ; Perciformes/*classification/*genetics ; Phylogeny ; },
abstract = {DNA barcodes were studied for 1,353 specimens representing 272 morphological species belonging to 149 genera and 55 families of Perciformes from the South China Sea (SCS). The average Kimura 2-parameter (K2P) distances within species, genera and families were 0.31%, 8.71% and 14.52%, respectively. A neighbour-joining (NJ) tree, Bayesian inference (BI) and maximum-likelihood (ML) trees and Automatic Barcode Gap Discovery (ABGD) revealed 260, 253 and 259 single-species-representing clusters, respectively. Barcoding gap analysis (BGA) demonstrated that barcode gaps were present for 178 of 187 species analysed with multiple specimens (95.2%), with the minimum interspecific distance to the nearest neighbour larger than the maximum intraspecific distance. A group of three Thunnus species (T. albacares, T. obesus and T. tonggol), a pair of Gerres species (G. oyena and G. japonicus), a pair of Istiblennius species (I. edentulous and I. lineatus) and a pair of Uranoscopus species (U. oligolepis and U. kaianus) were observed with low interspecific distances and overlaps between intra- and interspecific genetic distances. Three species (Apogon ellioti, Naucrates ductor and Psenopsis anomala) showed deep intraspecific divergences and generated two lineages each, suggesting the possibility of cryptic species. Our results demonstrated that DNA barcodes are highly reliable for delineating species of Perciformes in the SCS. The DNA barcode library established in this study will shed light on further research on the diversity of Perciformes in the SCS.},
}
@article {pmid28919968,
year = {2017},
author = {Lukhtanov, VA},
title = {A new species of Melitaea from Israel, with notes on taxonomy, cytogenetics, phylogeography and interspecific hybridization in the Melitaea persea complex (Lepidoptera, Nymphalidae).},
journal = {Comparative cytogenetics},
volume = {11},
number = {2},
pages = {325-357},
pmid = {28919968},
issn = {1993-0771},
abstract = {Specimens with intermediate morphology are often considered to be the result of ongoing interspecific hybridization; however, this conclusion is difficult to prove without analysis of chromosomal and/or molecular markers. In the butterfly genus Melitaea, such an intermediacy can be detected in male genitalia, and is more or less regularly observed in localities where two closely related, presumably parental species are found in sympatry. Here I analyze a high altitude Melitaea population from Mt. Hermon in north Israel and show that its male genitalia are clearly differentiated from those found in phenotypically similar M. persea and M. didyma, but in some aspects intermediate between them. This hybrid-like population is unique because, although M. didyma is present on Mt. Hermon, the true, low-altitude M. persea has never been reported from Israel. Cytogenetic analysis revealed no apomorphic chromosomal characters to distinguish the Mt. Hermon population from other known taxa of the M. persea and M. didyma species groups. At the same time, DNA barcode-based phylogeographic study showed that this population is ancient. It was estimated to originate 1-1.6 million years ago in the Levantine refugium from a common ancestor with M. persea. Generally, the data obtained are incompatible with interpretation of the studied population as a taxon conspecific with M. persea or M. didyma, or a swarm of recent hybrids between M. persea and M. didyma, although the possibility of ancient homoploid hybrid speciation cannot be ruled out. I also argue that the name Melitaea montium assigned to butterflies from north Lebanon cannot be applied to the studied taxon from Mt. Hermon. Here I describe this morphologically and ecologically distinct entity as a new species Melitaea acentriasp. n., and compare it with other taxa of the M. persea complex.},
}
@article {pmid28915829,
year = {2017},
author = {Brugman, VA and England, ME and Stoner, J and Tugwell, L and Harrup, LE and Wilson, AJ and Medlock, JM and Logan, JG and Fooks, AR and Mertens, PPC and Johnson, N and Carpenter, S},
title = {How often do mosquitoes bite humans in southern England? A standardised summer trial at four sites reveals spatial, temporal and site-related variation in biting rates.},
journal = {Parasites &amp; vectors},
volume = {10},
number = {1},
pages = {420},
pmid = {28915829},
issn = {1756-3305},
support = {BBS/E/I/00001701/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/I/00007033/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/I/00007036/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/I/00007038/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Anopheles/physiology ; Blood/virology ; Culex/physiology ; *Culicidae/classification/physiology/virology ; Feeding Behavior ; Humans ; Insect Bites and Stings/*epidemiology ; Mosquito Vectors/physiology/virology ; Spatio-Temporal Analysis ; United Kingdom/epidemiology ; Virus Diseases/transmission ; },
abstract = {BACKGROUND: This field-based study examined the abundance and species complement of mosquitoes (Diptera: Culicidae) attracted to humans at four sites in the United Kingdom (UK). The study used a systematic approach to directly measure feeding by mosquitoes on humans at multiple sites and using multiple volunteers. Quantifying how frequently humans are bitten in the field by mosquitoes is a fundamental parameter in assessing arthropod-borne virus transmission.<br><br>METHODS: Human landing catches were conducted using a standardised protocol by multiple volunteers at four rural sites between July and August 2013. Collections commenced two hours prior to sunset and lasted for a total of four hours. To reduce bias occurring due to collection point or to the individual attractiveness of the volunteer to mosquitoes, each collection was divided into eight collection periods, with volunteers rotated by randomised Latin square design between four sampling points per site. While the aim was to collect mosquitoes prior to feeding, the source of blood meals from any engorged specimens was also identified by DNA barcoding.<br><br>RESULTS: Three of the four sites yielded human-biting mosquito populations for a total of 915 mosquitoes of fifteen species/species groups. Mosquito species composition and biting rates differed significantly between sites, with individual volunteers collecting between 0 and 89 mosquitoes (over 200 per hour) of up to six species per collection period. Coquillettidia richiardii (Ficalbi, 1889) was responsible for the highest recorded biting rates at any one site, reaching 161 bites per hour, whilst maximum biting rates of 55 bites per hour were recorded for Culex modestus (Ficalbi, 1889). Human-biting by Culex pipiens (L., 1758) form pipiens was also observed at two sites, but at much lower rates when compared to other species.<br><br>CONCLUSIONS: Several mosquito species are responsible for human nuisance biting pressure in southern England, although human exposure to biting may be largely limited to evening outdoor activities. This study indicates Cx. modestus can be a major human-biting species in the UK whilst Cx. pipiens f. pipiens may show greater opportunistic human-biting than indicated by earlier studies.},
}
@article {pmid28914776,
year = {2017},
author = {Chan, TYK},
title = {Worldwide Occurrence and Investigations of Contamination of Herbal Medicines by Tropane Alkaloids.},
journal = {Toxins},
volume = {9},
number = {9},
pages = {},
pmid = {28914776},
issn = {2072-6651},
mesh = {Alkaloids ; *Drug Contamination ; Humans ; *Plants, Medicinal ; *Tropanes ; },
abstract = {Tropane alkaloids occur mainly in Solanaceae plants. In the present review, the main objective is to describe the worldwide occurrence and investigations of anticholinergic poisoning due to the contamination of herbal teas and herbs by tropane alkaloids. Tropane alkaloid poisoning can occur after consumption of any medicinal plant if Solanaceae plants or plant parts are present as contaminants. Globally, almost all reports in 1978-2014 involve herbal teas and one of the prescribed herbs in composite formulae. Contamination most likely occurs during harvest or processing. As for prescribed herbs, on-site inspection is necessary to exclude cross-contamination and accidental mix-up at the retail level. The diagnosis is confirmed by screening for the presence of Solanaceae species and tropane alkaloids. Herbal teas and herbs contaminated by tropane alkaloids can pose a serious health hazard because these relatively heat-stable alkaloids may exist in large quantities. The WHO repeatedly emphasises the importance of good agricultural and collection practices for medicinal plants. DNA barcoding is increasingly used to exclude the presence of contaminants (particularly toxic species) and product substitution. All suspected cases should be reported to health authorities so that investigations along the supply chain and early intervention measures to protect the public can be initiated.},
}
@article {pmid28911667,
year = {2017},
author = {Lee, SC and Wang, CH and Yen, CE and Chang, C},
title = {DNA barcode and identification of the varieties and provenances of Taiwan's domestic and imported made teas using ribosomal internal transcribed spacer 2 sequences.},
journal = {Journal of food and drug analysis},
volume = {25},
number = {2},
pages = {260-274},
pmid = {28911667},
issn = {2224-6614},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic ; DNA, Chloroplast ; DNA, Intergenic ; DNA, Plant ; DNA, Ribosomal Spacer ; Phylogeny ; *Ribosomes ; Taiwan ; },
abstract = {The major aim of made tea identification is to identify the variety and provenance of the tea plant. The present experiment used 113 tea plants [Camellia sinensis (L.) O. Kuntze] housed at the Tea Research and Extension Substation, from which 113 internal transcribed spacer 2 (ITS2) fragments, 104 trnL intron, and 98 trnL-trnF intergenic sequence region DNA sequences were successfully sequenced. The similarity of the ITS2 nucleotide sequences between tea plants housed at the Tea Research and Extension Substation was 0.379-0.994. In this polymerase chain reaction-amplified noncoding region, no varieties possessed identical sequences. Compared with the trnL intron and trnL-trnF intergenic sequence fragments of chloroplast cpDNA, the proportion of ITS2 nucleotide sequence variation was large and is more suitable for establishing a DNA barcode database to identify tea plant varieties. After establishing the database, 30 imported teas and 35 domestic made teas were used in this model system to explore the feasibility of using ITS2 sequences to identify the varieties and provenances of made teas. A phylogenetic tree was constructed using ITS2 sequences with the unweighted pair group method with arithmetic mean, which indicated that the same variety of tea plant is likely to be successfully categorized into one cluster, but contamination from other tea plants was also detected. This result provides molecular evidence that the similarity between important tea varieties in Taiwan remains high. We suggest a direct, wide collection of made tea and original samples of tea plants to establish an ITS2 sequence molecular barcode identification database to identify the varieties and provenances of tea plants. The DNA barcode comparison method can satisfy the need for a rapid, low-cost, frontline differentiation of the large amount of made teas from Taiwan and abroad, and can provide molecular evidence of their varieties and provenances.},
}
@article {pmid28910286,
year = {2017},
author = {Wu, F and Ma, J and Meng, Y and Zhang, D and Pascal Muvunyi, B and Luo, K and Di, H and Guo, W and Wang, Y and Feng, B and Zhang, J},
title = {Potential DNA barcodes for Melilotus species based on five single loci and their combinations.},
journal = {PloS one},
volume = {12},
number = {9},
pages = {e0182693},
pmid = {28910286},
issn = {1932-6203},
mesh = {Chloroplasts/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Chloroplast/genetics ; DNA, Intergenic ; DNA, Plant/*genetics ; Genetic Loci ; Genetic Variation ; Melilotus/*classification/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {Melilotus, an annual or biennial herb, belongs to the tribe Trifolieae (Leguminosae) and consists of 19 species. As an important green manure crop, diverse Melilotus species have different values as feed and medicine. To identify different Melilotus species, we examined the efficiency of five candidate regions as barcodes, including the internal transcribed spacer (ITS) and two chloroplast loci, rbcL and matK, and two non-coding loci, trnH-psbA and trnL-F. In total, 198 individuals from 98 accessions representing 18 Melilotus species were sequenced for these five potential barcodes. Based on inter-specific divergence, we analysed sequences and confirmed that each candidate barcode was able to identify some of the 18 species. The resolution of a single barcode and its combinations ranged from 33.33% to 88.89%. Analysis of pairwise distances showed that matK+rbcL+trnL-F+trnH-psbA+ITS (MRTPI) had the greatest value and rbcL the least. Barcode gap values and similarity value analyses confirmed these trends. The results indicated that an ITS region, successfully identifying 13 of 18 species, was the most appropriate single barcode and that the combination of all five potential barcodes identified 16 of the 18 species. We conclude that MRTPI is the most effective tool for Melilotus species identification. Taking full advantage of the barcode system, a clear taxonomic relationship can be applied to identify Melilotus species and enhance their practical production.},
}
@article {pmid28906059,
year = {2018},
author = {Raclariu, AC and Heinrich, M and Ichim, MC and de Boer, H},
title = {Benefits and Limitations of DNA Barcoding and Metabarcoding in Herbal Product Authentication.},
journal = {Phytochemical analysis : PCA},
volume = {29},
number = {2},
pages = {123-128},
pmid = {28906059},
issn = {1099-1565},
mesh = {*DNA Barcoding, Taxonomic ; European Union ; Herbal Medicine/legislation &amp; jurisprudence/*standards ; Quality Control ; Reference Standards ; },
abstract = {INTRODUCTION: Herbal medicines play an important role globally in the health care sector and in industrialised countries they are often considered as an alternative to mono-substance medicines. Current quality and authentication assessment methods rely mainly on morphology and analytical phytochemistry-based methods detailed in pharmacopoeias. Herbal products however are often highly processed with numerous ingredients, and even if these analytical methods are accurate for quality control of specific lead or marker compounds, they are of limited suitability for the authentication of biological ingredients.<br><br>OBJECTIVE: To review the benefits and limitations of DNA barcoding and metabarcoding in complementing current herbal product authentication.<br><br>METHOD: Recent literature relating to DNA based authentication of medicinal plants, herbal medicines and products are summarised to provide a basic understanding of how DNA barcoding and metabarcoding can be applied to this field.<br><br>RESULTS: Different methods of quality control and authentication have varying resolution and usefulness along the value chain of these products. DNA barcoding can be used for authenticating products based on single herbal ingredients and DNA metabarcoding for assessment of species diversity in processed products, and both methods should be used in combination with appropriate hyphenated chemical methods for quality control.<br><br>CONCLUSIONS: DNA barcoding and metabarcoding have potential in the context of quality control of both well and poorly regulated supply systems. Standardisation of protocols for DNA barcoding and DNA sequence-based identification are necessary before DNA-based biological methods can be implemented as routine analytical approaches and approved by the competent authorities for use in regulated procedures. &#xa9; 2017 The Authors. Phytochemical Analysis Published by John Wiley &amp; Sons Ltd.},
}
@article {pmid28906012,
year = {2018},
author = {Tedersoo, L and Tooming-Klunderud, A and Anslan, S},
title = {PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives.},
journal = {The New phytologist},
volume = {217},
number = {3},
pages = {1370-1385},
doi = {10.1111/nph.14776},
pmid = {28906012},
issn = {1469-8137},
mesh = {Base Sequence ; Bias ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/metabolism ; Eukaryota/*genetics ; Fungi/*genetics ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal/genetics ; },
abstract = {Second-generation, high-throughput sequencing methods have greatly improved our understanding of the ecology of soil microorganisms, yet the short barcodes (< 500 bp) provide limited taxonomic and phylogenetic information for species discrimination and taxonomic assignment. Here, we utilized the third-generation Pacific Biosciences (PacBio) RSII and Sequel instruments to evaluate the suitability of full-length internal transcribed spacer (ITS) barcodes and longer rRNA gene amplicons for metabarcoding Fungi, Oomycetes and other eukaryotes in soil samples. Metabarcoding revealed multiple errors and biases: Taq polymerase substitution errors and mis-incorporating indels in sequencing homopolymers constitute major errors; sequence length biases occur during PCR, library preparation, loading to the sequencing instrument and quality filtering; primer-template mismatches bias the taxonomic profile when using regular and highly degenerate primers. The RSII and Sequel platforms enable the sequencing of amplicons up to 3000 bp, but the sequence quality remains slightly inferior to Illumina sequencing especially in longer amplicons. The full ITS barcode and flanking rRNA small subunit gene greatly improve taxonomic identification at the species and phylum levels, respectively. We conclude that PacBio sequencing provides a viable alternative for metabarcoding of organisms that are of relatively low diversity, require > 500-bp barcode for reliable identification or when phylogenetic approaches are intended.},
}
@article {pmid28905379,
year = {2017},
author = {Engin, S and Seyhan, D},
title = {A new species of Pomatoschistus (Teleostei, Gobiidae): the Mediterranean's smallest marine fish.},
journal = {Journal of fish biology},
volume = {91},
number = {4},
pages = {1208-1223},
doi = {10.1111/jfb.13455},
pmid = {28905379},
issn = {1095-8649},
mesh = {Animals ; Body Size ; DNA Barcoding, Taxonomic ; Female ; Fishes/anatomy &amp; histology/*classification/genetics ; Male ; Mediterranean Sea ; },
abstract = {The new sand goby species Pomatoschistus nanus (Teleostei: Gobiidae) is described from the northern coast of the Levantine Sea (eastern Mediterranean Sea) based on both morphological and DNA barcoding data. The new species is the smallest fish in the Mediterranean Sea and may be distinguished from congeners by the following features: predorsal area, first dorsal-fin base and breast naked; δ-pore missing; anterior point of the suborbital row b not reaching level of posterior point of suborbital row d; slightly emarginated caudal fin and nape coloration pattern. DNA barcode data clearly discriminate Pomatoschistus spp. in the neighbour-joining tree with an average of 17·7% interspecific K2P distance. The most closely related taxon to P. nanus sp. nov. is Pomatoschistus bathi and the most distantly related is Pomatoschistus tortonesei with 11·9 and 21·9% K2P distances respectively. Morphometric and genetic data are also provided for Pomatoschistus bathi.},
}
@article {pmid28905200,
year = {2018},
author = {Kostric, M and Milger, K and Krauss-Etschmann, S and Engel, M and Vestergaard, G and Schloter, M and Schöler, A},
title = {Development of a Stable Lung Microbiome in Healthy Neonatal Mice.},
journal = {Microbial ecology},
volume = {75},
number = {2},
pages = {529-542},
pmid = {28905200},
issn = {1432-184X},
mesh = {Animals ; Animals, Newborn/microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Lung/*microbiology ; Mice ; Mice, Inbred BALB C ; *Microbiota ; },
abstract = {The lower respiratory tract has been previously considered sterile in a healthy state, but advances in culture-independent techniques for microbial identification and characterization have revealed that the lung harbors a diverse microbiome. Although research on the lung microbiome is increasing and important questions were already addressed, longitudinal studies aiming to describe developmental stages of the microbial communities from the early neonatal period to adulthood are lacking. Thus, little is known about the early-life development of the lung microbiome and the impact of external factors during these stages. In this study, we applied a barcoding approach based on high-throughput sequencing of 16S ribosomal RNA gene amplicon libraries to determine age-dependent differences in the bacterial fraction of the murine lung microbiome and to assess potential influences of differing "environmental microbiomes" (simulated by the application of used litter material to the cages). We could clearly show that the diversity of the bacterial community harbored in the murine lung increases with age. Interestingly, bacteria belonging to the genera Delftia and Rhodococcus formed an age-independent core microbiome. The addition of the used litter material influenced the lung microbiota of young mice but did not significantly alter the community composition of adult animals. Our findings elucidate the dynamic nature of the early-life lung microbiota and its stabilization with age. Further, this study indicates that even slight environmental changes modulate the bacterial community composition of the lung microbiome in early life, whereas the lung microbes of adults demonstrate higher resilience towards environmental variations.},
}
@article {pmid28905136,
year = {2018},
author = {Masunaga, N and Kagara, N and Motooka, D and Nakamura, S and Miyake, T and Tanei, T and Naoi, Y and Shimoda, M and Shimazu, K and Kim, SJ and Noguchi, S},
title = {Highly sensitive detection of ESR1 mutations in cell-free DNA from patients with metastatic breast cancer using molecular barcode sequencing.},
journal = {Breast cancer research and treatment},
volume = {167},
number = {1},
pages = {49-58},
doi = {10.1007/s10549-017-4487-y},
pmid = {28905136},
issn = {1573-7217},
mesh = {Adult ; Aged ; Breast Neoplasms/*blood/genetics/pathology ; Cell-Free Nucleic Acids/*blood ; DNA Barcoding, Taxonomic ; DNA, Neoplasm/*blood ; Estrogen Receptor alpha/*blood ; Female ; Gene Frequency ; High-Throughput Nucleotide Sequencing ; Humans ; Middle Aged ; Mutation/genetics ; Neoplasm Metastasis ; },
abstract = {PURPOSE: We aimed to develop a highly sensitive method to detect ESR1 mutations in cell-free DNA (cfDNA) using next-generation sequencing with molecular barcode (MB-NGS) targeting the hotspot segment (c.1600-1713).<br><br>METHODS: The sensitivity of MB-NGS was tested using serially diluted ESR1 mutant DNA and then cfDNA samples from 34 patients with metastatic breast cancer were analyzed with MB-NGS. The results of MB-NGS were validated in comparison with conventional NGS and droplet digital PCR (ddPCR).<br><br>RESULTS: MB-NGS showed a higher sensitivity (0.1%) than NGS without barcode (1%) by reducing background errors. Of the cfDNA samples from 34 patients with metastatic breast cancer, NGS without barcode revealed seven mutations in six patients (17.6%) and MB-NGS revealed six additional mutations including three mutations not reported in the COSMIC database of breast cancer, resulting in total 13 ESR1 mutations in ten patients (29.4%). Regarding the three hotspot mutations, all the patients with mutations detected by MB-NGS had identical mutations detected by droplet digital PCR (ddPCR), and mutant allele frequency correlated very well between both (r&#xa0;=&#xa0;0.850, p&#xa0;<&#xa0;0.01). Moreover, all the patients without these mutations by MB-NGS were found to have no mutations by ddPCR.<br><br>CONCLUSION: In conclusion, MB-NGS could successfully detect ESR1 mutations in cfDNA with a higher sensitivity of 0.1% than conventional NGS and was considered as clinically useful as ddPCR.},
}
@article {pmid28904776,
year = {2017},
author = {Avin, FA and Subha, B and Tan, YS and Braukmann, TWA and Vikineswary, S and Hebert, PDN},
title = {Escaping introns in COI through cDNA barcoding of mushrooms: Pleurotus as a test case.},
journal = {Ecology and evolution},
volume = {7},
number = {17},
pages = {6972-6980},
pmid = {28904776},
issn = {2045-7758},
abstract = {DNA barcoding involves the use of one or more short, standardized DNA fragments for the rapid identification of species. A 648-bp segment near the 5' terminus of the mitochondrial cytochrome c oxidase subunit I (COI) gene has been adopted as the universal DNA barcode for members of the animal kingdom, but its utility in mushrooms is complicated by the frequent occurrence of large introns. As a consequence, ITS has been adopted as the standard DNA barcode marker for mushrooms despite several shortcomings. This study employed newly designed primers coupled with cDNA analysis to examine COI sequence diversity in six species of Pleurotus and compared these results with those for ITS. The ability of the COI gene to discriminate six species of Pleurotus, the commonly cultivated oyster mushroom, was examined by analysis of cDNA. The amplification success, sequence variation within and among species, and the ability to design effective primers was tested. We compared ITS sequences to their COI cDNA counterparts for all isolates. ITS discriminated between all six species, but some sequence results were uninterpretable, because of length variation among ITS copies. By comparison, a complete COI sequences were recovered from all but three individuals of Pleurotus giganteus where only the 5' region was obtained. The COI sequences permitted the resolution of all species when partial data was excluded for P. giganteus. Our results suggest that COI can be a useful barcode marker for mushrooms when cDNA analysis is adopted, permitting identifications in cases where ITS cannot be recovered or where it offers higher resolution when fresh tissue is. The suitability of this approach remains to be confirmed for other mushrooms.},
}
@article {pmid28904771,
year = {2017},
author = {Elbrecht, V and Peinert, B and Leese, F},
title = {Sorting things out: Assessing effects of unequal specimen biomass on DNA metabarcoding.},
journal = {Ecology and evolution},
volume = {7},
number = {17},
pages = {6918-6926},
pmid = {28904771},
issn = {2045-7758},
abstract = {Environmental bulk samples often contain many different taxa that vary several orders of magnitude in biomass. This can be problematic in DNA metabarcoding and metagenomic high-throughput sequencing approaches, as large specimens contribute disproportionately high amounts of DNA template. Thus, a few specimens of high biomass will dominate the dataset, potentially leading to smaller specimens remaining undetected. Sorting of samples by specimen size (as a proxy for biomass) and balancing the amounts of tissue used per size fraction should improve detection rates, but this approach has not been systematically tested. Here, we explored the effects of size sorting on taxa detection using two freshwater macroinvertebrate bulk samples, collected from a low-mountain stream in Germany. Specimens were morphologically identified and sorted into three size classes (body size < 2.5 × 5, 5 × 10, and up to 10 × 20 mm). Tissue powder from each size category was extracted individually and pooled based on tissue weight to simulate samples that were not sorted by biomass ("Unsorted"). Additionally, size fractions were pooled so that each specimen contributed approximately equal amounts of biomass ("Sorted"). Mock samples were amplified using four different DNA metabarcoding primer sets targeting the Cytochrome c oxidase I (COI) gene. Sorting taxa by size and pooling them proportionately according to their abundance lead to a more equal amplification of taxa compared to the processing of complete samples without sorting. The sorted samples recovered 30% more taxa than the unsorted samples at the same sequencing depth. Our results imply that sequencing depth can be decreased approximately fivefold when sorting the samples into three size classes and pooling by specimen abundance. Even coarse size sorting can substantially improve taxa detection using DNA metabarcoding. While high-throughput sequencing will become more accessible and cheaper within the next years, sorting bulk samples by specimen biomass or size is a simple yet efficient method to reduce current sequencing costs.},
}
@article {pmid28902202,
year = {2017},
author = {Luan, C and Xu, Y and Fu, F and Wang, H and Xu, Q and Chen, B and Zhao, Y},
title = {Responsive photonic barcodes for sensitive multiplex bioassay.},
journal = {Nanoscale},
volume = {9},
number = {37},
pages = {14111-14117},
doi = {10.1039/c7nr04867j},
pmid = {28902202},
issn = {2040-3372},
mesh = {*Biological Assay ; Biomarkers, Tumor/*analysis ; Carcinoembryonic Antigen/*analysis ; Humans ; Limit of Detection ; *Photons ; Reproducibility of Results ; alpha-Fetoproteins/*analysis ; },
abstract = {Barcodes have a demonstrated value for multiplex high-throughput bioassays. The tendency of this technology is to pursue high sensitivity target screening. Herein, we presented a new type of inverse opal-structured poly(N-isopropylacrylamide) (pNIPAM) hydrogel photonic crystal (PhC) barcodes with the function of fluorescent signal self-amplification for the detection. During the bio-reaction process at body temperature, the pNIPAM hydrogel barcodes kept swelling, and their inverse opal structure with interconnected pores provided unblocked channels for the targets to diffuse into the voids of the barcodes and react. During the detection process, the barcodes were kept at a volume phase transition temperature (VPTT) to shrink their volume; this resulted in an obvious increase in the density of fluorescent molecules and signal amplification. It was demonstrated that the responsive barcodes could achieve the limits of detection (LOD) of α-fetoprotein (AFP) and carcinoembryonic antigen (CEA) at 0.623 ng mL[-1] and 0.492 ng mL[-1], respectively. In addition, the proposed barcodes showed good multiplex detection capacity with acceptable cross-reactivity, accuracy, and reproducibility, and the results were consistent with those of common clinical laboratory methods for the detection of clinical samples. These features of the inverse opal-structured responsive hydrogel barcodes indicate that they are ideal technology for high-sensitive multiplex bioassays.},
}
@article {pmid28902130,
year = {2017},
author = {Jiang, D and Zhao, Z and Zhang, T and Zhong, W and Liu, C and Yuan, Q and Huang, L},
title = {The Chloroplast Genome Sequence of Scutellaria baicalensis Provides Insight into Intraspecific and Interspecific Chloroplast Genome Diversity in Scutellaria.},
journal = {Genes},
volume = {8},
number = {9},
pages = {},
pmid = {28902130},
issn = {2073-4425},
abstract = {Scutellaria baicalensis Georgi (Lamiaceae) is the source of the well-known traditional Chinese medicine "HuangQin" (Radix Scutellariae). Natural sources of S. baicalensis are rapidly declining due to high market demand and overexploitation. Moreover, the commercial products of Radix Scutellariae have often been found to contain adulterants in recent years, which may give rise to issues regarding drug efficacy and safety. In this study, we developed valuable chloroplast molecular resources by comparing intraspecific and interspecific chloroplast genome. The S. baicalensis chloroplast genome is a circular molecule consisting of two single-copy regions separated by a pair of inverted repeats. Comparative analyses of three Scutellaria chloroplast genomes revealed six variable regions (trnH-psbA, trnK-rps16, petN-psbM, trnT-trnL, petA-psbJ, and ycf1) that could be used as DNA barcodes. There were 25 single nucleotide polymorphisms(SNPs) and 29 indels between the two S. baicalensis genotypes. All of the indels occurred within non-coding regions. Phylogenetic analysis suggested that Scutellarioideae is a sister taxon to Lamioideae. These resources could be used to explore the variation present in Scutellaria populations and for further evolutionary, phylogenetic, barcoding and genetic engineering studies, in addition to effective exploration and conservation of S. baicalensis.},
}
@article {pmid28901371,
year = {2017},
author = {Han, S and Lee, JS and Lee, JB},
title = {Synthesis of a multi-functional DNA nanosphere barcode system for direct cell detection.},
journal = {Nanoscale},
volume = {9},
number = {37},
pages = {14094-14102},
doi = {10.1039/c7nr03615a},
pmid = {28901371},
issn = {2040-3372},
mesh = {*Biosensing Techniques ; Biotin ; DNA ; *DNA Barcoding, Taxonomic ; HeLa Cells ; Humans ; *Nanospheres ; *Nucleic Acid Amplification Techniques ; Streptavidin ; },
abstract = {Nucleic acid-based technologies have been applied to numerous biomedical applications. As a novel material for target detection, DNA has been used to construct a barcode system with a range of structures. This paper reports multi-functionalized DNA nanospheres (DNANSs) by rolling circle amplification (RCA) with several functionalized nucleotides. DNANSs with a barcode system were designed to exhibit fluorescence for coding enhanced signals and contain biotin for more functionalities, including targeting through the biotin-streptavidin (biotin-STA) interaction. Functionalized deoxynucleotide triphosphates (dNTPs) were mixed in the RCA process and functional moieties can be expressed on the DNANSs. The anti-epidermal growth factor receptor antibodies (anti-EGFR Abs) can be conjugated on DNANSs for targeting cancer cells specifically. As a proof of concept, the potential of the multi-functional DNANS barcode was demonstrated by direct cell detection as a simple detection method. The DNANS barcode provides a new route for the simple and rapid selective recognition of cancer cells.},
}
@article {pmid28895964,
year = {2017},
author = {Lussier, F and Brulé, T and Bourque, MJ and Ducrot, C and Trudeau, L&#xc9; and Masson, JF},
title = {Dynamic SERS nanosensor for neurotransmitter sensing near neurons.},
journal = {Faraday discussions},
volume = {205},
number = {},
pages = {387-407},
doi = {10.1039/c7fd00131b},
pmid = {28895964},
issn = {1364-5498},
support = {//CIHR/Canada ; },
mesh = {Acetylcholine/analysis ; Animals ; Dopamine/analysis ; Glutamic Acid/analysis ; Green Fluorescent Proteins/genetics/metabolism ; Mice ; Mice, Transgenic ; Microscopy, Fluorescence ; Neurons/metabolism/pathology ; Neurotransmitter Agents/*analysis ; Spectrum Analysis, Raman/*methods ; gamma-Aminobutyric Acid/analysis ; },
abstract = {Current electrophysiology and electrochemistry techniques have provided unprecedented understanding of neuronal activity. However, these techniques are suited to a small, albeit important, panel of neurotransmitters such as glutamate, GABA and dopamine, and these constitute only a subset of the broader range of neurotransmitters involved in brain chemistry. Surface-enhanced Raman scattering (SERS) provides a unique opportunity to detect a broader range of neurotransmitters in close proximity to neurons. Dynamic SERS (D-SERS) nanosensors based on patch-clamp-like nanopipettes decorated with gold nanoraspberries can be located accurately under a microscope using techniques analogous to those used in current electrophysiology or electrochemistry experiments. In this manuscript, we demonstrate that D-SERS can measure in a single experiment ATP, glutamate (glu), acetylcholine (ACh), GABA and dopamine (DA), among other neurotransmitters, with the potential for detecting a greater number of neurotransmitters. The SERS spectra of these neurotransmitters were identified with a barcoding data processing method and time series of the neurotransmitter levels were constructed. The D-SERS nanosensor was then located near cultured mouse dopaminergic neurons. The detection of neurotransmitters was performed in response to a series of K[+] depolarisations, and allowed the detection of elevated levels of both ATP and dopamine. Control experiments were also performed near glial cells, showing only very low basal detection neurotransmitter events. This paper demonstrates the potential of D-SERS to detect neurotransmitter secretion events near living neurons, but also constitutes a strong proof-of-concept for the broad application of SERS to the detection of secretion events by neurons or other cell types in order to study normal or pathological cell functions.},
}
@article {pmid28894108,
year = {2017},
author = {Kanzaki, N and Kiontke, K and Tanaka, R and Hirooka, Y and Schwarz, A and Müller-Reichert, T and Chaudhuri, J and Pires-daSilva, A},
title = {Description of two three-gendered nematode species in the new genus Auanema (Rhabditina) that are models for reproductive mode evolution.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {11135},
pmid = {28894108},
issn = {2045-2322},
support = {R01 GM100140/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Biological Evolution ; Female ; Life Cycle Stages ; Male ; Phylogeny ; *Reproduction ; Rhabditida/anatomy &amp; histology/classification/*physiology ; Rhabditida Infections/diagnosis/parasitology ; },
abstract = {The co-existence of males, females and hermaphrodites, a rare mating system known as trioecy, has been considered as an evolutionarily transient state. In nematodes, androdioecy (males/hermaphrodites) as found in Caenorhabditis elegans, is thought to have evolved from dioecy (males/females) through a trioecious intermediate. Thus, trioecious species are good models to understand the steps and requirements for the evolution of new mating systems. Here we describe two new species of nematodes with trioecy, Auanema rhodensis and A. freiburgensis. Along with molecular barcodes, we provide a detailed analysis of the morphology of these species, and document it with drawings and light and SEM micrographs. Based on morphological data, these free-living nematodes were assigned to a new genus, Auanema, together with three other species described previously. Auanema species display convergent evolution in some features with parasitic nematodes with complex life cycles, such as the production of few males after outcrossing and the obligatory development of dauers into self-propagating adults.},
}
@article {pmid28892487,
year = {2017},
author = {Ereskovsky, AV and Richter, DJ and Lavrov, DV and Schippers, KJ and Nichols, SA},
title = {Transcriptome sequencing and delimitation of sympatric Oscarella species (O. carmela and O. pearsei sp. nov) from California, USA.},
journal = {PloS one},
volume = {12},
number = {9},
pages = {e0183002},
pmid = {28892487},
issn = {1932-6203},
mesh = {Animals ; California ; Computational Biology/methods ; DNA Barcoding, Taxonomic ; Gene Expression Profiling ; Genome, Mitochondrial ; *High-Throughput Nucleotide Sequencing ; Phylogeny ; Porifera/classification/*genetics ; Sympatry/*genetics ; *Transcriptome ; },
abstract = {The homoscleromorph sponge Oscarella carmela, first described from central California, USA is shown to represent two superficially similar but both morphologically and phylogenetically distinct species that are co-distributed. We here describe a new species as Oscarella pearsei, sp. nov. and re-describe Oscarella carmela; the original description was based upon material from both species. Further, we correct the identification of published genomic/transcriptomic resources that were originally attributed to O. carmela, and present new Illumina-sequenced transcriptome assemblies for each of these species, and the mitochondrial genome sequence for O. pearsei sp. nov. Using SSU and LSU ribosomal DNA and the mitochondrial genome, we report the phylogenetic relationships of these species relative to other Oscarella species, and find strong support for the placement of O. pearsei sp. nov. in a distinct clade within genus Oscarella defined by the presence of spherulous cells that contain paracrystalline inclusions; O. carmela lacks this cell type. Oscarella pearsei sp. nov and O. carmela can be tentatively distinguished based upon gross morphological differences such as color, surface texture and extent of mucus production, but can be more reliably identified using mitochondrial and nuclear barcode sequencing, ultrastructural characteristics of cells in the mesohyl, and the morphology of the follicle epithelium which surrounds the developing embryo in reproductively active individuals.},
}
@article {pmid28888791,
year = {2018},
author = {Furfaro, G and Salvi, D and Mancini, E and Mariottini, P},
title = {A multilocus view on Mediterranean aeolid nudibranchs (Mollusca): Systematics and cryptic diversity of Flabellinidae and Piseinotecidae.},
journal = {Molecular phylogenetics and evolution},
volume = {118},
number = {},
pages = {13-22},
doi = {10.1016/j.ympev.2017.09.001},
pmid = {28888791},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Biodiversity ; Gastropoda/anatomy &amp; histology/*classification/genetics ; Likelihood Functions ; Mediterranean Sea ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/genetics ; },
abstract = {Recent molecular studies revealed high level of endemism and numerous cryptic species within opisthobranchs, with Mediterranean taxa clearly understudied. Here we used genetic data from both mitochondrial and nuclear gene fragments as well as morphological data from taxonomically relevant characters to investigate the phylogenetic relationships and systematics of Mediterranean taxa of the Flabellinidae and Piseinotecidae families. Phylogenetic analyses based on Bayesian and Maximum-Likelihood methods indicate that Flabellinidae and Pisenotecidae taxa and species within the genera Flabellina, Calmella and Piseinotecus do not form monophyletic clades. These results are supported by our morphological analyses which allowed the re-evaluation of the triseriate radula condition in Pisenotecidae and Calmella taxa and their inclusion in the genus Flabellina as Flabellina gaditanacomb. nov. (synonym of F. confusa), Flabellina gabiniereicomb. nov. and Flabellina cavolinicomb. nov. Species delimitation and barcoding gap analyses allowed uncovering cryptic species within Flabellina gracilis (Alder and Hancock, 1844), F. trophina (Bergh, 1890), F. verrucosa (M. Sars, 1829) and F. ischitana Hirano and Thompson, 1990, the latter with an Atlantic form which is under description. This study corroborates the relevance of combining molecular and morphological data from multiple populations and species in the assessment of nudibranch diversity and classification.},
}
@article {pmid28885183,
year = {2018},
author = {Popescu, L and Cao, ZP},
title = {From Microscopy to Genomic Approach in Soil Biodiversity Assessment.},
journal = {Current issues in molecular biology},
volume = {27},
number = {},
pages = {195-198},
doi = {10.21775/cimb.027.195},
pmid = {28885183},
issn = {1467-3045},
mesh = {Animals ; Bacteria/classification/*genetics ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Bacterial/genetics ; Ecosystem ; Fungi/classification/*genetics ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Microbial Consortia/genetics ; Microscopy ; Nematoda/classification/*genetics ; Plant Roots/microbiology ; Plants/microbiology ; *Soil Microbiology ; },
abstract = {Soil biota represents a major component of the earth's biodiversity and for over 200 years, the microscopy approach was the only way to explore it. In the last decade, the DNA-based technique has been adopted in soil ecology. Due to the rapid development of cutting-edge technology, the field is transitioning from barcoding individuals to metabarcoding communities. With the advent of next-generation sequencing and a rapid decline in sequencing cost, it has become feasible to assess soil biodiversity at species level. This review article summarizes current approaches in soil biodiversity research along with their advantages and disadvantages.},
}
@article {pmid28883648,
year = {2017},
author = {Palomares-Rius, JE and Cantalapiedra-Navarrete, C and Archidona-Yuste, A and Subbotin, SA and Castillo, P},
title = {The utility of mtDNA and rDNA for barcoding and phylogeny of plant-parasitic nematodes from Longidoridae (Nematoda, Enoplea).},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {10905},
pmid = {28883648},
issn = {2045-2322},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Helminth/chemistry/*genetics ; DNA, Mitochondrial/chemistry/*genetics ; DNA, Ribosomal/chemistry/*genetics ; Electron Transport Complex IV/genetics ; Nematoda/*classification/genetics/*isolation &amp; purification ; Phylogeny ; Plant Diseases/*parasitology ; Sequence Analysis, DNA ; },
abstract = {The traditional identification of plant-parasitic nematode species by morphology and morphometric studies is very difficult because of high morphological variability that can lead to considerable overlap of many characteristics and their ambiguous interpretation. For this reason, it is essential to implement approaches to ensure accurate species identification. DNA barcoding aids in identification and advances species discovery. This study sought to unravel the use of the mitochondrial marker cytochrome c oxidase subunit 1 (coxI) as barcode for Longidoridae species identification, and as a phylogenetic marker. The results showed that mitochondrial and ribosomal markers could be used as barcoding markers, except for some species from the Xiphinema americanum group. The ITS1 region showed a promising role in barcoding for species identification because of the clear molecular variability among species. Some species presented important molecular variability in coxI. The analysis of the newly provided sequences and the sequences deposited in GenBank showed plausible misidentifications, and the use of voucher species and topotype specimens is a priority for this group of nematodes. The use of coxI and D2 and D3 expansion segments of the 28S rRNA gene did not clarify the phylogeny at the genus level.},
}
@article {pmid28882174,
year = {2017},
author = {Fang, Y and Shi, WQ and Zhang, Y},
title = {Molecular phylogeny of Anopheles hyrcanus group members based on ITS2 rDNA.},
journal = {Parasites &amp; vectors},
volume = {10},
number = {1},
pages = {417},
pmid = {28882174},
issn = {1756-3305},
mesh = {Animals ; Anopheles/*classification/*genetics ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/*genetics ; Genetic Variation ; Malaria/transmission ; Mosquito Vectors/*classification/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; },
abstract = {BACKGROUND: The Anopheles hyrcanus group includes 25 species, and is widely distributed in the Oriental and Palaearctic regions. Several species within this group are vectors of malaria, lymphatic filariasis and Japanese encephalitis. It is difficult or impossible to identify cryptic species based on their morphological characteristics, with some closely related species of the Hyrcanus Group have similar adult morphological characteristics. Thus, their molecular identification has been an important complementary method to traditional morphological taxonomy.<br><br>METHODS: We used 461 ribosomal DNA (rDNA) internal transcribed spacer 2 (ITS2) sequences relating to 19 species to reconstruct the molecular phylogeny of the&#xa0;Hyrcanus Group across its range. In addition, we compared the performance of rDNA ITS2 to that of mitochondrial DNA (mtDNA) cytochrome c oxidase subunit 1 gene (cox1) to assess the genetic divergence of Hyrcanus Group sibling species.<br><br>RESULTS: Based on Kimura's 2-parameter (K2P) distance model, the average conspecific ITS2 divergence was 0.003, whereas sequence divergence between species averaged 0.480. Average ITS2 sequence divergences were almost 160 times higher among the Hyrcanus Group members than within each species. Two sets of sibling species, An. lesteri Baisas &amp; Hu, 1936 and An. paraliae Sandosham, 1959; and An. sinensis Wiedemann, 1828, An. belenrae Rueda, 2005, and An. kleini Rueda, 2005, were resolved by ITS2. Each of these species was represented as an independent lineage in the phylogenetic tree. Results suggest that An. pseudopictus Grassi, 1899 and An. hyrcanus (Pallas, 1771) are most likely a single species. We uncovered two new ITS2 lineages that require further study before resolving their true taxonomic status, and designed a diagnostic polymerase chain reaction (PCR) assay to distinguish five morphologically similar species.<br><br>CONCLUSIONS: Nuclear and mitochondrial genes generally provided consistent results for subgroup division. Compared to cox1, ITS2 is a more reliable tool for studying phylogenetic relationships among closely related mosquito taxa. Based on species-specific differences in ITS2 sequences, the multiplex PCR assay developed here can be used to improve the efficiency of vector identification. Thus, this research will promote the progress of malaria vector surveillance in both epidemic and non-epidemic areas of South and East Asia.},
}
@article {pmid28881498,
year = {2017},
author = {Múrria, C and Bonada, N and Vellend, M and Zamora-Muñoz, C and Alba-Tercedor, J and Sainz-Cantero, CE and Garrido, J and Acosta, R and El Alami, M and Barquín, J and Derka, T and Álvarez-Cabria, M and Sáinz-Bariain, M and Filipe, AF and Vogler, AP},
title = {Local environment rather than past climate determines community composition of mountain stream macroinvertebrates across Europe.},
journal = {Molecular ecology},
volume = {26},
number = {21},
pages = {6085-6099},
doi = {10.1111/mec.14346},
pmid = {28881498},
issn = {1365-294X},
mesh = {Animals ; *Biodiversity ; *Climate ; Europe ; Geography ; Haplotypes ; Insecta/*classification ; Phylogeny ; *Rivers ; Species Specificity ; },
abstract = {Community assembly is determined by a combination of historical events and contemporary processes that are difficult to disentangle, but eco-evolutionary mechanisms may be uncovered by the joint analysis of species and genetic diversity across multiple sites. Mountain streams across Europe harbour highly diverse macroinvertebrate communities whose composition and turnover (replacement of taxa) among sites and regions remain poorly known. We studied whole-community biodiversity within and among six mountain regions along a latitudinal transect from Morocco to Scandinavia at three levels of taxonomic hierarchy: genus, species and haplotypes. Using DNA barcoding of four insect families (>3100 individuals, 118 species) across 62 streams, we found that measures of local and regional diversity and intraregional turnover generally declined slightly towards northern latitudes. However, at all hierarchical levels we found complete (haplotype) or high (species, genus) turnover among regions (and even among sites within regions), which counters the expectations of Pleistocene postglacial northward expansion from southern refugia. Species distributions were mostly correlated with environmental conditions, suggesting a strong role of lineage- or species-specific traits in determining local and latitudinal community composition, lineage diversification and phylogenetic community structure (e.g., loss of Coleoptera, but not Ephemeroptera, at northern sites). High intraspecific genetic structure within regions, even in northernmost sites, reflects species-specific dispersal and demographic histories and indicates postglacial migration from geographically scattered refugia, rather than from only southern areas. Overall, patterns were not strongly concordant across hierarchical levels, but consistent with the overriding influence of environmental factors determining community composition at the species and genus levels.},
}
@article {pmid28874906,
year = {2017},
author = {Amon, DJ and Ziegler, AF and Drazen, JC and Grischenko, AV and Leitner, AB and Lindsay, DJ and Voight, JR and Wicksten, MK and Young, CM and Smith, CR},
title = {Megafauna of the UKSRL exploration contract area and eastern Clarion-Clipperton Zone in the Pacific Ocean: Annelida, Arthropoda, Bryozoa, Chordata, Ctenophora, Mollusca.},
journal = {Biodiversity data journal},
volume = {},
number = {5},
pages = {e14598},
pmid = {28874906},
issn = {1314-2828},
abstract = {BACKGROUND: There is growing interest in mining polymetallic nodules from the abyssal Clarion-Clipperton Zone (CCZ) in the tropical Pacific Ocean. Despite having been the focus of environmental studies for decades, the benthic megafauna of the CCZ remain poorly known. To predict and manage the environmental impacts of mining in the CCZ, baseline knowledge of the megafauna is essential. The ABYSSLINE Project has conducted benthic biological baseline surveys in the UK Seabed Resources Ltd polymetallic-nodule exploration contract area (UK-1). Prior to ABYSSLINE research cruises in 2013 and 2015, no biological studies had been done in this area of the eastern CCZ.<br><br>NEW INFORMATION: Using a Remotely Operated Vehicle and Autonomous Underwater Vehicle (as well as several other pieces of equipment), the megafauna within the UK Seabed Resources Ltd exploration contract area (UK-1) and at a site ~250 km east of the UK-1 area were surveyed, allowing us to make the first estimates of megafaunal morphospecies richness from the imagery collected. Here, we present an atlas of the abyssal annelid, arthropod, bryozoan, chordate, ctenophore and molluscan megafauna observed and collected during the ABYSSLINE cruises to the UK-1 polymetallic-nodule exploration contract area in the CCZ. There appear to be at least 55 distinct morphospecies (8 Annelida, 12 Arthropoda, 4 Bryozoa, 22 Chordata, 5 Ctenophora, and 4 Mollusca) identified mostly by morphology but also using molecular barcoding for a limited number of animals that were collected. This atlas will aid the synthesis of megafaunal presence/absence data collected by contractors, scientists and other stakeholders undertaking work in the CCZ, ultimately helping to decipher the biogeography of the megafauna in this threatened habitat.},
}
@article {pmid28874686,
year = {2017},
author = {Alcaide, M and Yu, S and Davidson, J and Albuquerque, M and Bushell, K and Fornika, D and Arthur, S and Grande, BM and McNamara, S and Tertre, MCD and Batist, G and Huntsman, DG and Cavallone, L and Aguilar, A and Basik, M and Johnson, NA and Deyell, RJ and Rassekh, SR and Morin, RD},
title = {Targeted error-suppressed quantification of circulating tumor DNA using semi-degenerate barcoded adapters and biotinylated baits.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {10574},
pmid = {28874686},
issn = {2045-2322},
support = {//CIHR/Canada ; },
mesh = {*Biomarkers, Tumor ; *Circulating Tumor DNA/chemistry/genetics ; Consensus Sequence ; DNA Barcoding, Taxonomic ; DNA, Neoplasm/*blood ; *Genetic Testing/methods ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Humans ; Neoplasms/*diagnosis/*genetics ; Precision Medicine/methods ; },
abstract = {Ultrasensitive methods for rare allele detection are critical to leverage the full potential offered by liquid biopsies. Here, we describe a novel molecular barcoding method for the precise detection and quantification of circulating tumor DNA (ctDNA). The major benefits of our design include straightforward and cost-effective production of barcoded adapters to tag individual DNA molecules before PCR and sequencing, and better control over cross-contamination between experiments. We validated our approach in a cohort of 24 patients with a broad spectrum of cancer diagnoses by targeting and quantifying single-nucleotide variants (SNVs), indels and genomic rearrangements in plasma samples. By using personalized panels targeting a priori known mutations, we demonstrate comprehensive error-suppression capabilities for SNVs and detection thresholds for ctDNA below 0.1%. We also show that our semi-degenerate barcoded adapters hold promise for noninvasive genotyping in the absence of tumor biopsies and monitoring of minimal residual disease in longitudinal plasma samples. The benefits demonstrated here include broad applicability, flexibility, affordability and reproducibility in the research and clinical settings.},
}
@article {pmid28873965,
year = {2017},
author = {Mohd Salleh, F and Ramos-Madrigal, J and Peñaloza, F and Liu, S and Mikkel-Holger, SS and Riddhi, PP and Martins, R and Lenz, D and Fickel, J and Roos, C and Shamsir, MS and Azman, MS and Burton, KL and Stephen, JR and Wilting, A and Gilbert, MTP},
title = {An expanded mammal mitogenome dataset from Southeast Asia.},
journal = {GigaScience},
volume = {6},
number = {8},
pages = {1-8},
pmid = {28873965},
issn = {2047-217X},
mesh = {Animals ; Asia, Southeastern ; Biodiversity ; Computational Biology/methods ; DNA Barcoding, Taxonomic ; *Databases, Nucleic Acid ; Genetic Variation ; *Genome, Mitochondrial ; Genomics/methods ; Mammals/*genetics ; Molecular Sequence Annotation ; Phylogeny ; Phylogeography ; Reproducibility of Results ; },
abstract = {Southeast (SE) Asia is 1 of the most biodiverse regions in the world, and it holds approximately 20% of all mammal species. Despite this, the majority of SE Asia's genetic diversity is still poorly characterized. The growing interest in using environmental DNA to assess and monitor SE Asian species, in particular threatened mammals-has created the urgent need to expand the available reference database of mitochondrial barcode and complete mitogenome sequences. We have partially addressed this need by generating 72 new mitogenome sequences reconstructed from DNA isolated from a range of historical and modern tissue samples. Approximately 55 gigabases of raw sequence were generated. From this data, we assembled 72 complete mitogenome sequences, with an average depth of coverage of ×102.9 and ×55.2 for modern samples and historical samples, respectively. This dataset represents 52 species, of which 30 species had no previous mitogenome data available. The mitogenomes were geotagged to their sampling location, where known, to display a detailed geographical distribution of the species. Our new database of 52 taxa will strongly enhance the utility of environmental DNA approaches for monitoring mammals in SE Asia as it greatly increases the likelihoods that identification of metabarcoding sequencing reads can be assigned to reference sequences. This magnifies the confidence in species detections and thus allows more robust surveys and monitoring programmes of SE Asia's threatened mammal biodiversity. The extensive collections of historical samples from SE Asia in western and SE Asian museums should serve as additional valuable material to further enrich this reference database.},
}
@article {pmid28873765,
year = {2017},
author = {Bosmali, I and Ordoudi, SA and Tsimidou, MZ and Madesis, P},
title = {Greek PDO saffron authentication studies using species specific molecular markers.},
journal = {Food research international (Ottawa, Ont.)},
volume = {100},
number = {Pt 1},
pages = {899-907},
doi = {10.1016/j.foodres.2017.08.001},
pmid = {28873765},
issn = {1873-7145},
mesh = {Chromatography, High Pressure Liquid ; Crocus/*chemistry/classification/*genetics ; Curcuma/chemistry ; DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Flowers/chemistry ; Food Contamination/*analysis ; Greece ; Polymerase Chain Reaction ; Sensitivity and Specificity ; Spices/*analysis ; },
abstract = {Saffron, the spice produced from the red stigmas of the flower of Crocus sativus L. is a frequent target of fraud and mislabeling practices that cannot be fully traced using the ISO 3632 trade standard specifications and test methods. A molecular approach is proposed herein as a promising branding strategy for the authentication of highly esteemed saffron brands such as the Greek Protected Designation of Origin (PDO) "Krokos Kozanis". Specific ISSR (inter-simple sequence repeat) markers were used to assess for the first time, the within species variability of several populations of C. sativus L. from the cultivation area of "Krokos Kozanis" as well as the potential differences with the band pattern produced by other Crocus species. Then, species-specific markers were developed taking advantage of an advanced molecular technique such as the HRM analysis coupled with universal DNA barcoding regions (trnL) (Bar-HRM) and applied to saffron admixtures with some of the most common plant adulterants (Calendula officinalis, Carthamus tinctorius, Gardenia jasminoides, Zea mays and Curcuma longa). The sensitivity of the procedure was tested for turmeric as a case study whereas HPLC-fluorescence determination of secondary metabolites was also employed for comparison. The overall results indicated that the Bar-HRM approach is quite effective in terms of specificity and sensitivity. Its effectiveness regarding the detection of turmeric was comparable to that of a conventional HPLC method (0.5% vs 1.0%, w/w). Yet, the proposed DNA-based method is much faster, cost-effective and can be used even by non-geneticists, in any laboratory having access to an HRM-capable real-time PCR instrumentation. It can be, thus, regarded as a strong analytical tool in saffron authentication studies.},
}
@article {pmid28873426,
year = {2017},
author = {Borrell, YJ and Miralles, L and Do Huu, H and Mohammed-Geba, K and Garcia-Vazquez, E},
title = {DNA in a bottle-Rapid metabarcoding survey for early alerts of invasive species in ports.},
journal = {PloS one},
volume = {12},
number = {9},
pages = {e0183347},
pmid = {28873426},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Bays ; Biodiversity ; DNA/*analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; Environmental Monitoring/*methods ; Geography ; *Introduced Species ; Sequence Analysis, DNA ; Spain ; *Surveys and Questionnaires ; Time Factors ; },
abstract = {Biota monitoring in ports is increasingly needed for biosecurity reasons and safeguarding marine biodiversity from biological invasion. Present and future international biosecurity directives can be accomplished only if the biota acquired by maritime traffic in ports is controlled. Methodologies for biota inventory are diverse and now rely principally on extensive and labor-intensive sampling along with taxonomic identification by experts. In this study, we employed an extremely simplified environmental DNA (eDNA) sampling methodology from only three 1-L bottles of water per port, followed by metabarcoding (high-throughput sequencing and DNA-based species identification) using 18S rDNA and Cytochrome oxidase I as genetic barcodes. Eight Bay of Biscay ports with available inventory of fouling invertebrates were employed as a case study. Despite minimal sampling efforts, three invasive invertebrates were detected: the barnacle Austrominius modestus, the tubeworm Ficopomatus enigmaticus and the polychaete Polydora triglanda. The same species have been previously found from visual and DNA barcoding (genetic identification of individuals) surveys in the same ports. The current costs of visual surveys, conventional DNA barcoding and this simplified metabarcoding protocol were compared. The results encourage the use of metabarcoding for early biosecurity alerts.},
}
@article {pmid28872382,
year = {2018},
author = {Chen, YC and Wang, CT and Lees, DC and Wu, LW},
title = {Higher DNA insert fragment sizes improve mitogenomic assemblies from metagenomic pyrosequencing datasets: an example using Limenitidinae butterflies (Lepidoptera, Nymphalidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {6},
pages = {840-845},
doi = {10.1080/24701394.2017.1373106},
pmid = {28872382},
issn = {2470-1408},
mesh = {Animals ; Butterflies/*genetics ; Contig Mapping/*methods ; DNA Barcoding, Taxonomic/*methods ; *Genome, Mitochondrial ; Sequence Analysis, DNA/*methods ; },
abstract = {A large number of diverse mitogenomic sequences can be obtained more easily and affordably via mitochondrial metagenomics, which generates high-throughput sequences directly from sheared DNA extractions and assembles mitogenomic sequences using a few bioinformatic processing steps. However, following de novo assembly analysis, the optimal DNA fragment insert size is unclear. In this study, four extracted Limenitidinae butterfly DNA samples were sonically fragmented, and two fragment size ranges (200-400 and 400-600 bp) of each sample were tagged with different barcodes, producing pyrosequencing datasets. The results show that the datasets generated from longer DNA insert fragments result in better coverage and more complete mitogenomic sequences, and the phylogenetic analysis shows high support at nodes, revealing that Athyma butterflies do not represent a monophyletic group. Therefore, we recommend using longer insert DNA fragment sizes to generate high-throughput datasets for obtaining complete mitogenomic sequences which can improve phylogenetic studies.},
}
@article {pmid28872375,
year = {2018},
author = {Mantelatto, FL and Terossi, M and Negri, M and Buranelli, RC and Robles, R and Magalhães, T and Tamburus, AF and Rossi, N and Miyazaki, MJ},
title = {DNA sequence database as a tool to identify decapod crustaceans on the São Paulo coastline.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {805-815},
doi = {10.1080/24701394.2017.1365848},
pmid = {28872375},
issn = {2470-1408},
mesh = {Animals ; Biodiversity ; Brazil ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/genetics ; Databases, Nucleic Acid ; Decapoda/*genetics ; Electron Transport Complex IV/genetics ; Estuaries ; Genetic Markers ; Genetic Variation ; Genome, Mitochondrial/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
abstract = {DNA barcoding has emerged as an efficient tool for taxonomy and other biodiversity fields. The vast and speciose group of decapod crustaceans is not an exception in the current scenario and comparing short DNA fragments has enabled researchers to overcome some taxonomic impediments to help broadening knowledge on the diversity of this group of crustaceans. Brazil is considered as an important area in terms of global marine biodiversity and some regions stand out in terms of decapod fauna, such as the São Paulo coastline. Thus, the aim of this study is to obtain sequences of the mitochondrial markers (COI and 16S) for decapod crustaceans distributed at the São Paulo coastline and to test the accuracy of these markers for species identification from this region by comparing our sequences to those already present in the GenBank database. We sampled along almost the 300 km of the São Paulo coastline from estuaries to offshore islands during the development of a multidisciplinary research project that took place for 5 years. All the species were processed to obtain the DNA sequences. The diversity of the decapod fauna on the São Paulo coastline comprises at least 404 species. We were able to collect 256 of those species and sequence of at least one of the target genes from 221. By testing the accuracy of these two DNA markers as a tool for identification, we were able to check our own identifications, including new records in GenBank, spot potential mistakes in GenBank, and detect potential new species.},
}
@article {pmid28867876,
year = {2017},
author = {Paracchini, V and Petrillo, M and Lievens, A and Puertas Gallardo, A and Martinsohn, JT and Hofherr, J and Maquet, A and Silva, APB and Kagkli, DM and Querci, M and Patak, A and Angers-Loustau, A},
title = {Novel nuclear barcode regions for the identification of flatfish species.},
journal = {Food control},
volume = {79},
number = {},
pages = {297-308},
pmid = {28867876},
issn = {0956-7135},
abstract = {The development of an efficient seafood traceability framework is crucial for the management of sustainable fisheries and the monitoring of potential substitution fraud across the food chain. Recent studies have shown the potential of DNA barcoding methods in this framework, with most of the efforts focusing on using mitochondrial targets such as the cytochrome oxidase 1 and cytochrome b genes. In this article, we show the identification of novel targets in the nuclear genome, and their associated primers, to be used for the efficient identification of flatfishes of the Pleuronectidae family. In addition, different in silico methods are described to generate a dataset of barcode reference sequences from the ever-growing wealth of publicly available sequence information, replacing, where possible, labour-intensive laboratory work. The short amplicon lengths render the analysis of these new barcode target regions ideally suited to next-generation sequencing techniques, allowing characterisation of multiple fish species in mixed and processed samples. Their location in the nucleus also improves currently used methods by allowing the identification of hybrid individuals.},
}
@article {pmid28865184,
year = {2018},
author = {Xu, SZ and Li, ZY and Jin, XH},
title = {DNA barcoding of invasive plants in China: A resource for identifying invasive plants.},
journal = {Molecular ecology resources},
volume = {18},
number = {1},
pages = {128-136},
doi = {10.1111/1755-0998.12715},
pmid = {28865184},
issn = {1755-0998},
mesh = {China ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; *Introduced Species ; Phylogeny ; Plant Proteins/genetics ; Plants/*classification/*genetics ; },
abstract = {Invasive plants have aroused attention globally for causing ecological damage and having a negative impact on the economy and human health. However, it can be extremely challenging to rapidly and accurately identify invasive plants based on morphology because they are an assemblage of many different families and many plant materials lack sufficient diagnostic characteristics during border inspections. It is therefore urgent to evaluate candidate loci and build a reliable genetic library to prevent invasive plants from entering China. In this study, five common single markers (ITS, ITS2, matK, rbcL and trnH-psbA) were evaluated using 634 species (including 469 invasive plant species in China, 10 new records to China, 16 potentially invasive plant species around the world but not introduced into China yet and 139 plant species native to China) based on three different methods. Our results indicated that ITS2 displayed largest intra- and interspecific divergence (1.72% and 91.46%). Based on NJ tree method, ITS2, ITS, matK, rbcL and trnH-psbA provided 76.84%, 76.5%, 63.21%, 52.86% and 50.68% discrimination rates, respectively. The combination of ITS + matK performed best and provided 91.03% discriminatory power, followed by ITS2 + matK (85.78%). For identifying unknown individuals, ITS + matK had 100% correct identification rate based on our database, followed by ITS/ITS2 (both 93.33%) and ITS2 + matK (91.67%). Thus, we propose ITS/ITS2 + matK as the most suitable barcode for invasive plants in China. This study also demonstrated that DNA barcoding is an efficient tool for identifying invasive species.},
}
@article {pmid28865158,
year = {2018},
author = {Borrelli, C and Hou, Y and Pawlowski, JW and Holzmann, M and Katz, ME and Chandler, GT and Bowser, SS},
title = {Assessing SSU rDNA Barcodes in Foraminifera: A Case Study using Bolivina quadrata.},
journal = {The Journal of eukaryotic microbiology},
volume = {65},
number = {2},
pages = {220-235},
doi = {10.1111/jeu.12471},
pmid = {28865158},
issn = {1550-7408},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Ribosomal/*genetics ; Foraminifera/classification/*genetics ; Phylogeny ; Ribosome Subunits, Small, Eukaryotic/*genetics ; },
abstract = {The Small Subunit Ribosomal RNA gene (SSU rDNA) is a widely used tool to reconstruct phylogenetic relationships among foraminiferal species. Recently, the highly variable regions of this gene have been proposed as DNA barcodes to identify foraminiferal species. However, the resolution of these barcodes has not been well established, yet. In this study, we evaluate four SSU rDNA hypervariable regions (37/f, 41/f, 43/e, and 45/e) as DNA barcodes to distinguish among species of the genus Bolivina, with particular emphasis on Bolivina quadrata for which ten new sequences (KY468817-KY468826) were obtained during this study. Our analyses show that a single SSU rDNA hypervariable sequence is insufficient to resolve all Bolivina species and that some regions (37/f and 41/f) are more useful than others (43/e and 45/e) to distinguish among closely related species. In addition, polymorphism analyses reveal a high degree of variability. In the context of barcoding studies, these results emphasize the need to assess the range of intraspecific variability of DNA barcodes prior to their application to identify foraminiferal species in environmental samples; our results also highlight the possibility that a longer SSU rDNA region might be required to distinguish among species belonging to the same taxonomic group (i.e. genus).},
}
@article {pmid28865135,
year = {2018},
author = {Storm, AJ and Jensen, PA},
title = {Designing Randomized DNA Sequences Free of Restriction Enzyme Recognition Sites.},
journal = {Biotechnology journal},
volume = {13},
number = {1},
pages = {},
pmid = {28865135},
issn = {1860-7314},
support = {R03 DE026817/DE/NIDCR NIH HHS/United States ; },
mesh = {Algorithms ; Base Sequence/*genetics ; Computational Biology/methods ; *DNA Barcoding, Taxonomic ; DNA Restriction Enzymes/chemistry/genetics ; Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Software ; },
abstract = {DNA libraries containing random "barcodes" complicate synthetic biology workflows that utilize restriction enzymes since restriction sites can appear inside some barcodes. By removing bases at particular sites in the barcodes, it is possible to create semi-random pools of barcodes that do not contain any restriction sites. The challenge is to remove as few bases as possible to maximize the number of sequences in the pool while ensuring all sequences are free of restriction sites. The authors present CutFree, a computational approach to create pools of random DNA barcodes that lack a pre-defined set of restriction sites. The resulting pools can be inexpensively produced en masse with standard DNA synthesis techniques. CutFree is experimentally validated by blocking digestion of pools of barcodes designed to frequently contain restriction sites. Using CutFree, a pool of 1.3 billion barcodes that are free from recognition sites for 182 commercially available restriction enzymes is designed. CutFree is available as a software package and an online tool (http://jensenlab.net/tools).},
}
@article {pmid28863163,
year = {2017},
author = {Park, I and Kim, WJ and Yang, S and Yeo, SM and Li, H and Moon, BC},
title = {The complete chloroplast genome sequence of Aconitum coreanum and Aconitum carmichaelii and comparative analysis with other Aconitum species.},
journal = {PloS one},
volume = {12},
number = {9},
pages = {e0184257},
pmid = {28863163},
issn = {1932-6203},
mesh = {Aconitum/classification/*genetics ; Base Composition ; DNA Primers/genetics ; Evolution, Molecular ; Gene Order ; Genes, Plant ; *Genome, Chloroplast ; Genomics ; Microsatellite Repeats ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Aconitum species (belonging to the Ranunculaceae) are well known herbaceous medicinal ingredients and have great economic value in Asian countries. However, there are still limited genomic resources available for Aconitum species. In this study, we sequenced the chloroplast (cp) genomes of two Aconitum species, A. coreanum and A. carmichaelii, using the MiSeq platform. The two Aconitum chloroplast genomes were 155,880 and 157,040 bp in length, respectively, and exhibited LSC and SSC regions separated by a pair of inverted repeat regions. Both cp genomes had 38% GC content and contained 131 unique functional genes including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The gene order, content, and orientation of the two Aconitum cp genomes exhibited the general structure of angiosperms, and were similar to those of other Aconitum species. Comparison of the cp genome structure and gene order with that of other Aconitum species revealed general contraction and expansion of the inverted repeat regions and single copy boundary regions. Divergent regions were also identified. In phylogenetic analysis, Aconitum species positon among the Ranunculaceae was determined with other family cp genomes in the Ranunculales. We obtained a barcoding target sequence in a divergent region, ndhC-trnV, and successfully developed a SCAR (sequence characterized amplified region) marker for discrimination of A. coreanum. Our results provide useful genetic information and a specific barcode for discrimination of Aconitum species.},
}
@article {pmid28861070,
year = {2017},
author = {Defois, C and Ratel, J and Denis, S and Batut, B and Beugnot, R and Peyretaillade, E and Engel, E and Peyret, P},
title = {Environmental Pollutant Benzo[a]Pyrene Impacts the Volatile Metabolome and Transcriptome of the Human Gut Microbiota.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {1562},
pmid = {28861070},
issn = {1664-302X},
abstract = {Benzo[a]pyrene (B[a]P) is a ubiquitous, persistent, and carcinogenic pollutant that belongs to the large family of polycyclic aromatic hydrocarbons. Population exposure primarily occurs via contaminated food products, which introduces the pollutant to the digestive tract. Although the metabolism of B[a]P by host cells is well known, its impacts on the human gut microbiota, which plays a key role in health and disease, remain unexplored. We performed an in vitro assay using 16S barcoding, metatranscriptomics and volatile metabolomics to study the impact of B[a]P on two distinct human fecal microbiota. B[a]P exposure did not induce a significant change in the microbial structure; however, it altered the microbial volatolome in a dose-dependent manner. The transcript levels related to several metabolic pathways, such as vitamin and cofactor metabolism, cell wall compound metabolism, DNA repair and replication systems, and aromatic compound metabolism, were upregulated, whereas the transcript levels related to the glycolysis-gluconeogenesis pathway and bacterial chemotaxis toward simple carbohydrates were downregulated. These primary findings show that food pollutants, such as B[a]P, alter human gut microbiota activity. The observed shift in the volatolome demonstrates that B[a]P induces a specific deviation in the microbial metabolism.},
}
@article {pmid28860009,
year = {2017},
author = {Dyomin, A and Volodkina, V and Koshel, E and Galkina, S and Saifitdinova, A and Gaginskaya, E},
title = {Evolution of ribosomal internal transcribed spacers in Deuterostomia.},
journal = {Molecular phylogenetics and evolution},
volume = {116},
number = {},
pages = {87-96},
doi = {10.1016/j.ympev.2017.08.015},
pmid = {28860009},
issn = {1095-9513},
mesh = {Animals ; Base Composition ; Base Sequence ; DNA, Ribosomal Spacer/classification/*genetics ; Databases, Genetic ; *Evolution, Molecular ; Phylogeny ; },
abstract = {Sequences of ribosomal internal transcribed spacers (ITSs) are of great importance to molecular phylogenetics and DNA barcoding, but remain unstudied in some large taxa of Deuterostomia. We have analyzed complete ITS1 and ITS2 sequences in 62 species from 16 Deuterostomia classes, with ITS sequences in 24 species from 11 classes initially obtained using unannotated contigs and raw read sequences. A general tendency for both ITS length and GC-content increase from interior to superior Deuterostomia taxa, a uniform GC-content in both ITSs within the same species, thymine content decrease in sense DNA sequences of both ITSs are shown. A possible role of GC-based gene conversion in Deuterostomia ITS evolutionary changes is hypothesized. The first example of non-LTR retrotransposon insertion into ITS sequence in Deuterostomia is described in turtle Geochelone nigra. The roles of mobile genetic element insertions in the evolution of ITS sequences in some Sauropsida taxa are discussed as well.},
}
@article {pmid28859676,
year = {2017},
author = {Young, KI and Mundis, S and Widen, SG and Wood, TG and Tesh, RB and Cardosa, J and Vasilakis, N and Perera, D and Hanley, KA},
title = {Abundance and distribution of sylvatic dengue virus vectors in three different land cover types in Sarawak, Malaysian Borneo.},
journal = {Parasites &amp; vectors},
volume = {10},
number = {1},
pages = {406},
pmid = {28859676},
issn = {1756-3305},
support = {R24 AI120942/AI/NIAID NIH HHS/United States ; U01 AI115577/AI/NIAID NIH HHS/United States ; },
mesh = {*Aedes/virology ; Animal Distribution ; Animals ; Borneo/epidemiology ; Dengue/epidemiology/transmission ; Dengue Virus/genetics/*isolation &amp; purification/physiology ; *Forests ; High-Throughput Nucleotide Sequencing ; Humans ; *Insect Vectors/virology ; Larva/virology ; Malaysia/epidemiology ; Primates/virology ; Severe Dengue/epidemiology/transmission/virology ; },
abstract = {BACKGROUND: Mosquito-borne dengue virus (DENV) is maintained in a sylvatic, enzootic cycle of transmission between canopy-dwelling non-human primates and Aedes mosquitoes in Borneo. Sylvatic DENV can spill over into humans living in proximity to forest foci of transmission, in some cases resulting in severe dengue disease. The most likely vectors of such spillover (bridge vectors) in Borneo are Ae. albopictus and Ae. niveus. Borneo is currently experiencing extensive forest clearance. To gauge the effect of this change in forest cover on the likelihood of sylvatic DENV spillover, it is first necessary to characterize the distribution of bridge vectors in different land cover types. In the current study, we hypothesized that Ae. niveus and Ae. albopictus would show significantly different distributions in different land cover types; specifically, we predicted that Ae. niveus would be most abundant in forests whereas Ae. albopictus would have a more even distribution in the landscape.<br><br>RESULTS: Mosquitoes were collected from a total of 15 sites using gravid traps and a backpack aspirator around Kampong Puruh Karu, Sarawak, Malaysian Borneo, where sylvatic DENV spillover has been documented. A total of 2447 mosquitoes comprising 10 genera and 4 species of Aedes, were collected over the three years, 2013, 2014 and 2016, in the three major land cover types in the area, homestead, agriculture and forest. Mosquitoes were identified morphologically, pooled by species and gender, homogenized, and subject to DNA barcoding of each Aedes species and to arbovirus screening. As predicted, Ae. niveus was found almost exclusively in forests whereas Ae. albopictus was collected in all land cover types. Aedes albopictus was significantly (P&#xa0;=&#xa0;0.04) more abundant in agricultural fields than forests. Sylvatic DENV was not detected in any Aedes mosquito pools, however genomes of 14 viruses were detected using next generation sequencing.<br><br>CONCLUSIONS: Land cover type affects the abundance and distribution of the most likely bridge vectors of sylvatic DENV in Malaysia Borneo. Conversion of forests to agriculture will likely decrease the range and abundance of Ae. niveus but enhance the abundance of Ae. albopictus.},
}
@article {pmid28859638,
year = {2017},
author = {Suesatpanit, T and Osathanunkul, K and Madesis, P and Osathanunkul, M},
title = {Should DNA sequence be incorporated with other taxonomical data for routine identifying of plant species?.},
journal = {BMC complementary and alternative medicine},
volume = {17},
number = {1},
pages = {437},
pmid = {28859638},
issn = {1472-6882},
mesh = {Acanthaceae/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; Plants, Medicinal/*classification/genetics ; Thailand ; },
abstract = {BACKGROUND: A variety of plants in Acanthaceae have long been used in traditional Thai ailment and commercialised with significant economic value. Nowadays medicinal plants are sold in processed forms and thus morphological authentication is almost impossible. Full identification requires comparison of the specimen with some authoritative sources, such as a full and accurate description and verification of the species deposited in herbarium. Intake of wrong herbals can cause adverse effects. Identification of both raw materials and end products is therefore needed.<br><br>METHODS: Here, the potential of a DNA-based identification method, called Bar-HRM (DNA barcoding coupled with High Resolution Melting analysis), in raw material species identification is investigated. DNA barcode sequences from five regions (matK, rbcL, trnH-psbA spacer region, trnL and ITS2) of Acanthaceae species were retrieved for in silico analysis. Then the specific primer pairs were used in HRM assay to generate unique melting profiles for each plants species.<br><br>RESULTS: The method allows identification of samples lacking necessary morphological parts. In silico analyses of all five selected regions suggested that ITS2 is the most suitable marker for Bar-HRM in this study. The HRM analysis on dried samples of 16 Acanthaceae medicinal species was then performed using primer pair derived from ITS2 region. 100% discrimination of the tested samples at both genus and species level was observed. However, two samples documented as Clinacanthus nutans and Clinacanthus siamensis were recognised as the same species from the HRM analysis. Further investigation reveals that C. siamensis is now accepted as C. nutans.<br><br>CONCLUSIONS: The results here proved that Bar-HRM is a promising technique in species identification of the studied medicinal plants in Acanthaceae. In addition, molecular biological data is currently used in plant taxonomy and increasingly popular in recent years. Here, DNA barcode sequence data should be incorporated with morphological characters in the species identification.},
}
@article {pmid28855685,
year = {2017},
author = {Zhu, RW and Li, YC and Zhong, DL and Zhang, JQ},
title = {Establishment of the most comprehensive ITS2 barcode database to date of the traditional medicinal plant Rhodiola (Crassulacaee).},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {10051},
pmid = {28855685},
issn = {2045-2322},
mesh = {China ; DNA Barcoding, Taxonomic/*methods ; DNA, Intergenic/classification/*genetics ; DNA, Plant/classification/*genetics ; Haplotypes ; Humans ; Nucleic Acid Conformation ; *Phylogeny ; Plant Extracts/chemistry ; Plant Roots/chemistry/genetics ; Plants, Medicinal ; Rhizome/chemistry/genetics ; Rhodiola/classification/*genetics ; },
abstract = {The roots and rhizomes of Rhodiola crenulata and R. rosea have been used worldwide as adaptogens for hundreds of years. However, rapid growth in demand has resulted in merchants using other species of Rhodiola as adulterants. Here, we surveyed 518 individuals representing 47 of the 55 species in the genus, including 253 R. crenulata individuals from 16 populations and 98 R. rosea individuals from 11 populations, to evaluate the utility of the internal transcribed spacer 2 (ITS2) barcode for identification of Rhodiola species. We detected six haplotypes in R. crenulata and only one haplotype in R. rosea. An obvious overlap between intra- and inter-specific distance was detected, and the authentication efficacy of ITS2, which was assessed by BLAST1, a nearest distance method, and a tree test, was much lower than in other groups. However, R. crenulata and R. rosea could be exactly identified. Analysis showed that the secondary structure of ITS2 differs in R. crenulata and its closest relatives. Our results demonstrated that both a mini barcode from ITS2 and the structure of ITS2 are effective markers for the identification of R. crenulata and R. rosea. This study represents the most comprehensive database of ITS2 barcodes in Rhodiola to date and will be useful in Rhodiola species identification.},
}
@article {pmid28855105,
year = {2018},
author = {Merat, SJ and van de Berg, D and Bru, C and Yasuda, E and Breij, E and Kootstra, N and Prins, M and Molenkamp, R and Bakker, AQ and de Jong, MD and Spits, H and Schinkel, J and Beaumont, T},
title = {Multiplex flow cytometry-based assay to study the breadth of antibody responses against E1E2 glycoproteins of hepatitis C virus.},
journal = {Journal of immunological methods},
volume = {454},
number = {},
pages = {15-26},
doi = {10.1016/j.jim.2017.07.015},
pmid = {28855105},
issn = {1872-7905},
mesh = {Antibodies, Neutralizing/metabolism ; Antibody Formation ; Cell Separation ; Cross Reactions ; Epitopes, B-Lymphocyte/genetics/*immunology ; Flow Cytometry/*methods ; Fluorescence ; HEK293 Cells ; Hepacivirus/*immunology ; Hepatitis C Antibodies/metabolism ; Hepatitis C, Chronic/immunology/*metabolism ; High-Throughput Screening Assays ; Humans ; Neutralization Tests ; Transgenes/genetics ; Viral Envelope Proteins/genetics/*immunology ; },
abstract = {Hepatitis C virus (HCV) infection is a major global public health problem. Early induction of cross-reactive neutralizing antibodies during acute infection correlates with the spontaneous clearance of HCV. Understanding the antibody response in multiple subjects in large-scale studies would greatly benefit vaccine development. To determine the breadth of a polyclonal-serum antibody response, and or, the monoclonal antibodies against the different HCV E1E2 genotypes, we developed a quick and high throughput flow cytometry assay using fluorescent cell barcoding to distinguish cells transfected with different E1E2 sequences in a single measurement. HCV-specific antibodies recognizing conformational epitopes were tested for binding to cells transfected with E1E2 from six genotypes. In this assay, 1500 samples can be analyzed for specific binding to 6 different HCV E1E2 sequences within 8h. Plasma of HCV infected subjects were tested in our assay allowing us to determine the breadth of their antibody response. In summary, we developed a quick and high throughput assay to study the specificity of an antibody response against multiple HCV E1E2 sequences simultaneously. This assay can also be used to facilitate the discovery of novel antibodies, and because other flavi- and picornaviruses have similar intracellular assembly mechanisms, this approach can be used to study the antibody response against such viruses.},
}
@article {pmid28852760,
year = {2017},
author = {Loo, J and Yang, C and Tsang, HL and Lau, PM and Yong, KT and Ho, HP and Kong, SK},
title = {An Aptamer Bio-barCode (ABC) assay using SPR, RNase H, and probes with RNA and gold-nanorods for anti-cancer drug screening.},
journal = {The Analyst},
volume = {142},
number = {19},
pages = {3579-3587},
doi = {10.1039/c7an01026e},
pmid = {28852760},
issn = {1364-5528},
mesh = {Antineoplastic Agents/*pharmacology ; Aptamers, Nucleotide/*chemistry ; *Biosensing Techniques ; Cytochromes c/analysis ; *Drug Screening Assays, Antitumor ; Gold ; Hep G2 Cells ; Humans ; Nanotubes ; RNA ; Ribonuclease H/*chemistry ; *Surface Plasmon Resonance ; },
abstract = {With modifications to an ultra-sensitive bio-barcode (BBC) assay, we have developed a next generation aptamer-based bio-barcode (ABC) assay to detect cytochrome-c (Cyto-c), a cell death marker released from cancer cells, for anti-cancer drug screening. An aptamer is a short single-stranded DNA selected from a synthetic DNA library that is capable of binding to its target with high affinity and specificity based on its unique DNA sequence and 3D structure after folding. Similar to the BBC assay, Cyto-c is captured by a micro-magnetic particle (MMP) coated with capturing antibodies (Ab) and an aptamer specifically against Cyto-c to form sandwich structures ([MMP-Ab]-[Cyto-c]-[Aptamer]). After washing and melting, our aptamers, acting as a DNA bio-barcode, are released from the sandwiches and hybridized with the probes specially designed for RNase H for surface plasmon resonance (SPR) sensing. In an aptamer-probe duplex, RNase H digests the RNA in the probe and releases the intact aptamer for another round of hybridization and digestion. With signal enhancement effects from gold-nanorods (Au-NRs) on probes for SPR sensing, the detection limit was found to be 1 nM for the aptamer and 80 pM for Cyto-c. Without the time-consuming DNA amplification steps by PCR, the detection process of this new ABC assay can be completed within three hours. As a proof-of-concept, phenylarsine oxide was found to be a potent agent to kill liver cancer cells with multi-drug resistance at the nano-molar level. This approach thus provides a fast, sensitive and robust tool for anti-cancer drug screening.},
}
@article {pmid28852323,
year = {2017},
author = {Ortiz, AS and Rubio, RM and Guerrero, JJ and Garre, MJ and Serrano, J and Hebert, PDN and Hausmann, A},
title = {Close congruence between Barcode Index Numbers (bins) and species boundaries in the Erebidae (Lepidoptera: Noctuoidea) of the Iberian Peninsula.},
journal = {Biodiversity data journal},
volume = {},
number = {5},
pages = {e19840},
pmid = {28852323},
issn = {1314-2828},
abstract = {The DNA barcode reference library for Lepidoptera holds much promise as a tool for taxonomic research and for providing the reliable identifications needed for conservation assessment programs. We gathered sequences for the barcode region of the mitochondrial cytochrome c oxidase subunit I gene from 160 of the 176 nominal species of Erebidae moths (Insecta: Lepidoptera) known from the Iberian Peninsula. These results arise from a research project which constructing a DNA barcode library for the insect species of Spain. New records for 271 specimens (122 species) are coupled with preexisting data for 38 species from the Iberian fauna. Mean interspecific distance was 12.1%, while the mean nearest neighbour divergence was 6.4%. All 160 species possessed diagnostic barcode sequences, but one pair of congeneric taxa (Eublemma rosea and Eublemma rietzi) were assigned to the same BIN. As well, intraspecific sequence divergences higher than 1.5% were detected in four species which likely represent species complexes. This study reinforces the effectiveness of DNA barcoding as a tool for monitoring biodiversity in particular geographical areas and the strong correspondence between sequence clusters delineated by BINs and species recognized through detailed taxonomic analysis.},
}
@article {pmid28849536,
year = {2017},
author = {Zhang, R and Zhao, A and Wang, X and Zhang, Z},
title = {Diversity of tick species on domestic animals in Shandong Province, China, using DNA barcoding.},
journal = {Experimental &amp; applied acarology},
volume = {73},
number = {1},
pages = {79-89},
pmid = {28849536},
issn = {1572-9702},
support = {81401693//National Natural Sciences Foundation of China/ ; 81572028//National Natural Sciences Foundation of China/ ; },
mesh = {Animals ; Arthropod Proteins/analysis ; *Biodiversity ; Cattle ; Cattle Diseases/*epidemiology/parasitology ; China/epidemiology ; DNA Barcoding, Taxonomic ; Dog Diseases/*epidemiology/parasitology ; Dogs ; Electron Transport Complex IV/analysis ; Goat Diseases/*epidemiology/parasitology ; Goats ; Ixodidae/classification/*physiology ; Mitochondrial Proteins/analysis ; Rhipicephalus/classification/physiology ; Sheep ; Sheep Diseases/*epidemiology/parasitology ; },
abstract = {Ticks are considered to be second only to mosquitoes as vectors of diseases. In recent years, severe fever with thrombocytopenia syndrome, a new emerging tick-borne disease has been detected in many areas of China, including Shandong Province, Eastern China. Here, we report the tick species diversity based on surveys between 2014 and 2016 covering 16 locations in seven cities of Shandong. Based on DNA barcoding, 1859 ticks belonging to three species were identified: Haemaphysalis longicornis, Rhipicephalus turanicus and Haemaphysalis verticalis. Samples of the same species clustered together in a neighbor-joining phylogenetic tree, with intraspecific distances between 0 and 3.0% and interspecific distances ranged between 15.5 and 24.3%. Goats and dogs were the major hosts of ticks and H. longicornis was regarded as predominant tick species of Shandong. In order to reduce tick populations and prevent tick-borne diseases, effective control measures should be implemented on human and domestic animals, respectively.},
}
@article {pmid28848534,
year = {2017},
author = {Thorgersen, MP and Lancaster, WA and Ge, X and Zane, GM and Wetmore, KM and Vaccaro, BJ and Poole, FL and Younkin, AD and Deutschbauer, AM and Arkin, AP and Wall, JD and Adams, MWW},
title = {Mechanisms of Chromium and Uranium Toxicity in Pseudomonas stutzeri RCH2 Grown under Anaerobic Nitrate-Reducing Conditions.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {1529},
pmid = {28848534},
issn = {1664-302X},
abstract = {Chromium and uranium are highly toxic metals that contaminate many natural environments. We investigated their mechanisms of toxicity under anaerobic conditions using nitrate-reducing Pseudomonas stutzeri RCH2, which was originally isolated from a chromium-contaminated aquifer. A random barcode transposon site sequencing library of RCH2 was grown in the presence of the chromate oxyanion (Cr[VI][Formula: see text]) or uranyl oxycation (U[VI][Formula: see text]). Strains lacking genes required for a functional nitrate reductase had decreased fitness as both metals interacted with heme-containing enzymes required for the later steps in the denitrification pathway after nitrate is reduced to nitrite. Cr[VI]-resistance also required genes in the homologous recombination and nucleotide excision DNA repair pathways, showing that DNA is a target of Cr[VI] even under anaerobic conditions. The reduced thiol pool was also identified as a target of Cr[VI] toxicity and psest_2088, a gene of previously unknown function, was shown to have a role in the reduction of sulfite to sulfide. U[VI] resistance mechanisms involved exopolysaccharide synthesis and the universal stress protein UspA. As the first genome-wide fitness analysis of Cr[VI] and U[VI] toxicity under anaerobic conditions, this study provides new insight into the impact of Cr[VI] and U[VI] on an environmental isolate from a chromium contaminated site, as well as into the role of a ubiquitous protein, Psest_2088.},
}
@article {pmid28847169,
year = {2017},
author = {Aranyossy, T and Thielecke, L and Glauche, I and Fehse, B and Cornils, K},
title = {Genetic Barcodes Facilitate Competitive Clonal Analyses In Vivo.},
journal = {Human gene therapy},
volume = {28},
number = {10},
pages = {926-937},
doi = {10.1089/hum.2017.124},
pmid = {28847169},
issn = {1557-7422},
mesh = {Animals ; Bone Marrow Cells/cytology/metabolism ; Clonal Evolution/*genetics ; *Clone Cells ; Gene Expression ; Gene Order ; Genetic Vectors/genetics ; Hematopoietic Stem Cells/cytology/metabolism ; Humans ; Lentivirus/genetics ; Mice ; Promoter Regions, Genetic ; Transduction, Genetic ; Transgenes ; },
abstract = {Monitoring the fate of individual cell clones is an important task to better understand normal tissue regeneration, for example after hematopoietic stem cell (HSC) transplantation, but also cancerogenesis. Based on their integration into the host cell's genome, retroviral vectors are commonly used to stably mark target cells and their progeny. The development of genetic barcoding techniques has opened new possibilities to determine clonal composition and dynamics in great detail. A modular genetic barcode was recently introduced consisting of 32 variable positions (BC32) with a customized backbone, and its advantages were demonstrated with regard to barcode calling and quantification. The study presented applied the BC32 system in a complex in vivo situation, namely to analyze clonal reconstitution dynamics for HSC grafts consisting of up to three cell populations with distinguishable barcodes using different alpha- and lentiviral vectors. In a competitive transplantation setup, it was possible to follow the differently marked cell populations within individual animals. This enabled the clonal contribution of the different BC32 constructs during reconstitution and long-term hematopoiesis in the peripheral blood and the spatial distribution in bone marrow and spleen to be identified. Thus, it was demonstrated that the system allows the output of individually marked cells to be tracked in vivo and their influence on clonal dynamics to be analyzed. Successful application of the BC32 system in a complex, competitive in vivo situation provided proof-of-principle that its high complexity and the large Hamming distance between individual barcodes, combined with the easy customization, facilitate efficient and precise quantification, even without prior knowledge of individual barcode sequences. Importantly, simultaneous high-sensitivity analyses of different cell populations in single animals may significantly reduce numbers of animals required to investigate specific scientific questions in accordance with RRR principles. It is concluded that this BC32 system will be excellently suited for various research applications in regenerative medicine and cancer biology.},
}
@article {pmid28842669,
year = {2017},
author = {Steinke, D and Bernard, AM and Horn, RL and Hilton, P and Hanner, R and Shivji, MS},
title = {DNA analysis of traded shark fins and mobulid gill plates reveals a high proportion of species of conservation concern.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {9505},
pmid = {28842669},
issn = {2045-2322},
mesh = {*Animal Fins ; Animals ; *Biological Evolution ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Endangered Species ; *Gills ; RNA, Ribosomal, 16S ; Sharks/classification/*genetics ; },
abstract = {Continuously increasing demand for plant and animal products causes unsustainable depletion of biological resources. It is estimated that one-quarter of sharks and rays are threatened worldwide and although the global fin trade is widely recognized as a major driver, demand for meat, liver oil, and gill plates also represents a significant threat. This study used DNA barcoding and 16 S rRNA sequencing as a method to identify shark and ray species from dried fins and gill plates, obtained in Canada, China, and Sri Lanka. 129 fins and gill plates were analysed and searches on BOLD produced matches to 20 species of sharks and five species of rays or - in two cases - to a species pair. Twelve of the species found are listed or have been approved for listing in 2017 in the appendices of the Convention on International Trade in Endangered Species of Fauna and Flora (CITES), including the whale shark (Rhincodon typus), which was surprisingly found among both shark fin and gill plate samples. More than half of identified species fall under the IUCN Red List categories 'Endangered' and 'Vulnerable', raising further concerns about the impacts of this trade on the sustainability of these low productivity species.},
}
@article {pmid28841714,
year = {2017},
author = {Zhai, Q and Xue, GX and Li, M},
title = {DNA barcoding-based sexual association of Sovia lucasii and S. lii (Lepidoptera: Hesperiidae), with description of a new subspecies.},
journal = {PloS one},
volume = {12},
number = {8},
pages = {e0183847},
pmid = {28841714},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Female ; Lepidoptera/anatomy &amp; histology/classification/*genetics ; Phylogeny ; },
abstract = {Both sexes of two sympatric and sexually dimorphic species, Sovia lucasii (Mabille, 1876) and S. lii Xue, 2015, are associated based on DNA barcoding using the COI (mitochondrial cytochrome coxidase I) gene. The females are thus identified for the first time, and their wing patterns and genitalia are described and illustrated for the convenience of morphological identification hereafter. A new subspecies, S. lucasii minor ssp. nov., from the northeastern and eastern parts of the Sichuan Basin of China, is reported. External and genital differences between the new taxon and the nominate subspecies, which is distributed in western Sichuan and newly discovered in northwestern Guangxi, are illustrated and discussed.},
}
@article {pmid28840814,
year = {2017},
author = {Boscaro, V and James, ER and Fiorito, R and Hehenberger, E and Karnkowska, A and Del Campo, J and Kolisko, M and Irwin, NAT and Mathur, V and Scheffrahn, RH and Keeling, PJ},
title = {Molecular characterization and phylogeny of four new species of the genus Trichonympha (Parabasalia, Trichonymphea) from lower termite hindguts.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {67},
number = {9},
pages = {3570-3575},
doi = {10.1099/ijsem.0.002169},
pmid = {28840814},
issn = {1466-5034},
mesh = {Animals ; Australia ; Base Composition ; Digestive System/*microbiology ; Ecuador ; Hypermastigia/*classification/genetics/isolation &amp; purification ; Isoptera/*microbiology ; Peru ; *Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; Symbiosis ; },
abstract = {Members of the genus Trichonympha are among the most well-known, recognizable and widely distributed parabasalian symbionts of lower termites and the wood-eating cockroach species of the genus Cryptocercus. Nevertheless, the species diversity of this genus is largely unknown. Molecular data have shown that the superficial morphological similarities traditionally used to identify species are inadequate, and have challenged the view that the same species of the genus Trichonympha can occur in many different host species. Ambiguities in the literature, uncertainty in identification of both symbiont and host, and incomplete samplings are limiting our understanding of the systematics, ecology and evolution of this taxon. Here we describe four closely related novel species of the genus Trichonympha collected from South American and Australian lower termites: Trichonympha hueyi sp. nov. from Rugitermes laticollis, Trichonympha deweyi sp. nov. from Glyptotermes brevicornis, Trichonympha louiei sp. nov. from Calcaritermes temnocephalus and Trichonympha webbyae sp. nov. from Rugitermes bicolor. We provide molecular barcodes to identify both the symbionts and their hosts, and infer the phylogeny of the genus Trichonympha based on small subunit rRNA gene sequences. The analysis confirms the considerable divergence of symbionts of members of the genus Cryptocercus, and shows that the two clades of the genus Trichonympha harboured by termites reflect only in part the phylogeny of their hosts.},
}
@article {pmid28839956,
year = {2017},
author = {Marino, FZ and Accardo, M and Franco, R},
title = {CRISPR-barcoding in non small cell lung cancer: from intratumor genetic heterogeneity modeling to cancer therapy application.},
journal = {Journal of thoracic disease},
volume = {9},
number = {7},
pages = {1759-1762},
pmid = {28839956},
issn = {2072-1439},
}
@article {pmid28835125,
year = {2017},
author = {Grimm, D and Büning, H},
title = {Small But Increasingly Mighty: Latest Advances in AAV Vector Research, Design, and Evolution.},
journal = {Human gene therapy},
volume = {28},
number = {11},
pages = {1075-1086},
doi = {10.1089/hum.2017.172},
pmid = {28835125},
issn = {1557-7422},
mesh = {Capsid Proteins/genetics ; DNA/genetics ; DNA Barcoding, Taxonomic ; Dependovirus/*genetics ; Gene Transfer Techniques/*trends ; Genetic Therapy/*trends ; Genetic Vectors/genetics/*therapeutic use ; Genome, Viral ; Humans ; Integrases/genetics ; },
abstract = {Recombinant gene delivery vectors derived from naturally occurring or genetically engineered adeno-associated viruses (AAV) have taken center stage in human gene therapy, fueled by rapidly accumulating and highly encouraging clinical data. Nonetheless, it has also become evident that the current generation of AAV vectors will require improvements in transduction potency, antibody evasion, and cell specificity in order to realize their full potential and to widen applicability in larger patient cohorts. Fortunately, in the recent past, the field has seen a flurry of exciting new developments that enhance our understanding of AAV vector biology, including virus-host interactions, and/or that expand our arsenal of technologies for AAV capsid design and evolution. This review highlights a collection of latest advances in these areas, which, in the authors' opinion, hold particular promise to propel the AAV vector field forward in the near future, especially when applied in combination. These include fundamental novel insights into the AAV life cycle, from an unexpected role of autophagy and interactions with other viruses to the (re-)discovery of a universal AAV receptor and the function of AAV-AAP for capsid assembly. Concurrently, recent successes in the rational design of next-generation synthetic AAV capsids are pointed out, exemplified by the structure-guided derivation of AAV mutants displaying robust in vivo immune evasion. Finally, a variety of new and innovative strategies for high-throughput generation and screening of AAV capsid libraries are briefly reviewed, including Cre recombinase-based selection, ancestral AAV capsid reconstruction, and DNA barcoding of AAV genomes. All of these examples showcase the present momentum in the AAV field and, together with work by many other academic or industrial entities, raise substantial optimism that the remaining hurdles for human gene therapy with AAV vectors will (soon) be overcome.},
}
@article {pmid28833851,
year = {2017},
author = {Karamessini, D and Poyer, S and Charles, L and Lutz, JF},
title = {2D Sequence-Coded Oligourethane Barcodes for Plastic Materials Labeling.},
journal = {Macromolecular rapid communications},
volume = {38},
number = {24},
pages = {},
doi = {10.1002/marc.201700426},
pmid = {28833851},
issn = {1521-3927},
mesh = {Mass Spectrometry ; Plastics/chemical synthesis/*chemistry ; Polyethylene Terephthalates/*chemistry ; Polystyrenes/*chemistry ; Polyvinyl Chloride/*chemistry ; Urethane/chemical synthesis/*chemistry ; },
abstract = {Mixtures of uniform sequence-defined oligourethanes are evaluated as 2D molecular barcodes for labeling three different commodity polymers, namely polystyrene, polyvinylchloride and polyethylene terephthalate. Six different oligourethanes are synthesized by solid-phase iterative synthesis and are coded using a binary monomer alphabet. High-resolution mass spectrometry studies indicate that all oligomers are uniform and sequence-defined. However, instead of using them as individual coded chains, oligomers with different chain-length, mass and sequence are mixed into intentionally polydispersed libraries. In particular, a three-component library and a four-component library are created to encode a 2-bytes model binary sequence. These 2D-coded libraries are incorporated in all commodity plastics via a simple solvent casting procedure. Furthermore, in all cases, the oligomer mixtures can be extracted from the host polymer films and deciphered by mass spectrometry, thus opening interesting avenues for anti-counterfeiting and traceability applications.},
}
@article {pmid28829803,
year = {2017},
author = {Mishra, P and Kumar, A and Nagireddy, A and Shukla, AK and Sundaresan, V},
title = {Evaluation of single and multilocus DNA barcodes towards species delineation in complex tree genus Terminalia.},
journal = {PloS one},
volume = {12},
number = {8},
pages = {e0182836},
pmid = {28829803},
issn = {1932-6203},
mesh = {Combretaceae/*genetics ; DNA Barcoding, Taxonomic/*methods ; Genes, Plant ; Species Specificity ; },
abstract = {DNA barcoding is used as a universal tool for delimiting species boundaries in taxonomically challenging groups, with different plastid and nuclear regions (rbcL, matK, ITS and psbA-trnH) being recommended as primary DNA barcodes for plants. We evaluated the feasibility of using these regions in the species-rich genus Terminalia, which exhibits various overlapping morphotypes with pantropical distribution, owing to its complex taxonomy. Terminalia bellerica and T. chebula are ingredients of the famous Ayurvedic Rasayana formulation Triphala, used for detoxification and rejuvenation. High demand for extracted phytochemicals as well as the high trade value of several species renders mandatory the need for the correct identification of traded plant material. Three different analytical methods with single and multilocus barcoding regions were tested to develop a DNA barcode reference library from 222 individuals representing 41 Terminalia species. All the single barcodes tested had a lower discriminatory power than the multilocus regions, and the combination of matK+ITS had the highest resolution rate (94.44%). The average intra-specific variations (0.0188±0.0019) were less than the distance to the nearest neighbour (0.106±0.009) with matK and ITS. Distance-based Neighbour Joining analysis outperformed the character-based Maximum Parsimony method in the identification of traded species such as T. arjuna, T. chebula and T. tomentosa, which are prone to adulteration. rbcL was shown to be a highly conservative region with only 3.45% variability between all of the sequences. The recommended barcode combination, rbcL+matK, failed to perform in the genus Terminalia. Considering the complexity of resolution observed with single regions, the present study proposes the combination of matK+ITS as the most successful barcode in Terminalia.},
}
@article {pmid28828267,
year = {2017},
author = {Pinochet, J and Leclerc, JC and Brante, A and Daguin-Thiébaut, C and Díaz, C and Tellier, F and Viard, F},
title = {Presence of the tunicate Asterocarpa humilis on ship hulls and aquaculture facilities in the coast of the Biobío Region, south central Chile.},
journal = {PeerJ},
volume = {5},
number = {},
pages = {e3672},
pmid = {28828267},
issn = {2167-8359},
abstract = {Non-native ascidians are important members of the fouling community associated with artificial substrata and man-made structures. Being efficient fouling species, they are easily spread by human-mediated transports (e.g., with aquaculture trade and maritime transports). This is exemplified by the ascidian Asterocarpa humilis which displays a wide distribution in the Southern Hemisphere and has been recently reported in the Northern Hemisphere (NW Europe). In continental Chile, its first report dates back from 2000 for the locality of Antofagasta (23°S). Although there was no evidence about the vectors of introduction and spread, nor the source, some authors suggested maritime transport by ship hulls and aquaculture devices as putative introduction pathways and vectors. In the present study, we report for the first time the presence of A. humilis on the hull of an international ship in a commercial port in Concepción bay (36°S), south central Chile. We also found one individual associated to a seashell farm, 70 km far from Concepción bay. Further individuals were subsequently identified within Concepción bay: one juvenile settled upon international harbor pilings and a dozen individuals along aquaculture seashell longlines. For the first specimens sampled, species identification was ascertained using both morphological criteria and molecular barcoding, using the mitochondrial gene cytochrome c oxidase subunit I (COI) and a nuclear gene (ribosomal RNA 18S). The nuclear 18S gene and the mitochondrial gene COI clearly assigned the specimens to A. humilis, confirming our morphological identification. Two haplotypes were obtained with COI corresponding to haplotypes previously obtained with European and Northern Chilean specimens. The present study thus reports for the first time the presence of A. humilis in the Araucanian ecoregion, documenting the apparent expansion of this non-native tunicate in Chile over 2,000 km, spanning over three ecoregions. In addition we reveal the potential implication of the international maritime transport as a vector of spread of this species along the Eastern Pacific coast, and the putative role of aquaculture facilities in promoting local establishments of non-native tunicates.},
}
@article {pmid28825134,
year = {2017},
author = {Yu, M and Jiao, L and Guo, J and Wiedenhoeft, AC and He, T and Jiang, X and Yin, Y},
title = {DNA barcoding of vouchered xylarium wood specimens of nine endangered Dalbergia species.},
journal = {Planta},
volume = {246},
number = {6},
pages = {1165-1176},
pmid = {28825134},
issn = {1432-2048},
mesh = {DNA Barcoding, Taxonomic/*methods ; Dalbergia/*classification/genetics ; Endangered Species ; Feasibility Studies ; Genetic Markers/genetics ; Species Specificity ; Wood/classification/genetics ; },
abstract = {ITS2+ trnH - psbA was the best combination of DNA barcode to resolve the Dalbergia wood species studied. We demonstrate the feasibility of building a DNA barcode reference database using xylarium wood specimens. The increase in illegal logging and timber trade of CITES-listed tropical species necessitates the development of unambiguous identification methods at the species level. For these methods to be fully functional and deployable for law enforcement, they must work using wood or wood products. DNA barcoding of wood has been promoted as a promising tool for species identification; however, the main barrier to extensive application of DNA barcoding to wood is the lack of a comprehensive and reliable DNA reference library of barcodes from wood. In this study, xylarium wood specimens of nine Dalbergia species were selected from the Wood Collection of the Chinese Academy of Forestry and DNA was then extracted from them for further PCR amplification of eight potential DNA barcode sequences (ITS2, matK, trnL, trnH-psbA, trnV-trnM1, trnV-trnM2, trnC-petN, and trnS-trnG). The barcodes were tested singly and in combination for species-level discrimination ability by tree-based [neighbor-joining (NJ)] and distance-based (TaxonDNA) methods. We found that the discrimination ability of DNA barcodes in combination was higher than any single DNA marker among the Dalbergia species studied, with the best two-marker combination of ITS2+trnH-psbA analyzed with NJ trees performing the best (100% accuracy). These barcodes are relatively short regions (<350 bp) and amplification reactions were performed with high success (≥90%) using wood as the source material, a necessary factor to apply DNA barcoding to timber trade. The present results demonstrate the feasibility of using vouchered xylarium specimens to build DNA barcoding reference databases.},
}
@article {pmid28824845,
year = {2017},
author = {Crous, PW and Groenewald, JZ},
title = {The Genera of Fungi - G 4: Camarosporium and Dothiora.},
journal = {IMA fungus},
volume = {8},
number = {1},
pages = {131-152},
pmid = {28824845},
issn = {2210-6340},
abstract = {The current paper represents the fourth contribution in the Genera of Fungi series, linking type species of fungal genera to their morphology and DNA sequence data. The present paper focuses on two genera of microfungi, Camarosporium and Dothiora, which are respectively epi- and neotypified. The genus Camarosporium is typified by C. quaternatum, which has a karstenula-like sexual morph, and phoma-like synasexual morph. Furthermore, Camarosporomyces, Foliophoma and Hazslinszkyomyces are introduced as new camarosporium-like genera, while Querciphoma is introduced as a new phoma-like genus. Libertasomycetaceae is introduced as a new family to accommodate Libertasomyces and Neoplatysporoides. Dothiora, which is typified by D. pyrenophora, is shown to produce dothichiza- and hormonema-like synasexual morphs in culture, and D. cactacearum is introduced as a new species. In addition to their typification, ex-type cultures have been deposited in the Westerdijk Fungal Biodiversity Institute (CBS Culture Collection), and species-specific DNA barcodes in GenBank. Authors interested in contributing accounts of individual genera to larger multi-authored papers in this series should contact the associate editors listed on the List of Protected Generic Names for Fungi.},
}
@article {pmid28824841,
year = {2017},
author = {Bezerra, JDP and Sandoval-Denis, M and Paiva, LM and Silva, GA and Groenewald, JZ and Souza-Motta, CM and Crous, PW},
title = {New endophytic Toxicocladosporium species from cacti in Brazil, and description of Neocladosporium gen. nov.},
journal = {IMA fungus},
volume = {8},
number = {1},
pages = {77-97},
pmid = {28824841},
issn = {2210-6340},
abstract = {Brazil harbours a unique ecosystem, the Caatinga, which belongs to the tropical dry forest biome. This region has an important diversity of organisms, and recently several new fungal species have been described from different hosts and substrates within it. During a survey of fungal endophyte diversity from cacti in this forest, we isolated cladosporium-like fungi that were subjected to morphological and multigene phylogenetic analyses including actA, ITS, LSU, rpb2 and tub2 gene sequences. Based on these analyses we identified two new species belonging to the genus Toxicocladosporium, described here as T. cacti and T. immaculatum spp. nov., isolated from Pilosocereus gounellei subsp. gounellei and Melocactus zehntneri, respectively. To improve the species recognition and assess species diversity in Toxicocladosporium we studied all ex-type strains of the genus, for which actA, rpb2 and tub2 barcodes were also generated. After phylogenetic reconstruction using five loci, we differentiated 13 species in the genus. Toxicocladosporium velox and T. chlamydosporum are synonymized based on their phylogenetic position and limited number of unique nucleotide differences. Six strains previously assigned to T. leucadendri, including the ex-type strain (CBS 131317) of that species, were found to belong to an undescribed genus here named as Neocladosporium gen. nov., with N. leucadendri comb. nov. as type species. Furthermore, this study proposes the actA, ITS, rpb2 and tub2 as main phylogenetic loci to recognise Toxicocladosporium species.},
}
@article {pmid28822148,
year = {2017},
author = {Tang, H and Xiang, L and Li, XW and Sun, W and Wang, MN and Huang, YF and Ye, M},
title = {[DNA barcoding identification of endangered medicinal plants of Orchidaceae].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {42},
number = {11},
pages = {2058-2067},
doi = {10.19540/j.cnki.cjcmm.2017.0090},
pmid = {28822148},
issn = {1001-5302},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Endangered Species ; Genes, Plant ; Orchidaceae/*classification ; Plants, Medicinal/*classification ; },
abstract = {In this study, DNA barcoding was used to validate the traditional morphological classification of medicinal plants of Orchidaceae. The 163 samples of 135 species belong to 49 genera which have been confirmed by morphological identification were collected. Candidate sequences, including matK, psbA-trnH and ITS2 sequences, were amplified, bidirectionally sequenced, and assembled. All the sequences were blasted to GenBank database at NCBI, then analyzed using Neighbor-joining tree method by MEGA 7.0. The results showed that the DNAs of 163 samples were successfully extracted. The amplification efficiency of matK, psbA-trnH and ITS2 sequences were 100%, 100% and 98.77%, respectively. The 487 sequences were obtained, 345 sequences of which have matched corresponding sequences in the GenBank database and 142 sequences were new sequences. The topology of NJ tree which were constructed with the matK sequences was better than the trees of psbA-trnH and ITS2 sequences. In conclusion, the matK, psbA-trnH and ITS2 sequences were complementary and suitable for identification of medicinal plants of Orchidaceae. DNA barcoding can be used as an auxiliary means for identification of medicinal plants of Orchidaceae.},
}
@article {pmid28817640,
year = {2017},
author = {Saddhe, AA and Jamdade, RA and Kumar, K},
title = {Evaluation of multilocus marker efficacy for delineating mangrove species of West Coast India.},
journal = {PloS one},
volume = {12},
number = {8},
pages = {e0183245},
pmid = {28817640},
issn = {1932-6203},
mesh = {Avicennia/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; *Genetic Markers ; India ; Multilocus Sequence Typing/*methods ; Phylogeny ; Poisson Distribution ; },
abstract = {The plant DNA barcoding is a complex and requires more than one marker(s) as compared to animal barcoding. Mangroves are diverse estuarine ecosystem prevalent in the tropical and subtropical zone, but anthropogenic activity turned them into the vulnerable ecosystem. There is a need to build a molecular reference library of mangrove plant species based on molecular barcode marker along with morphological characteristics. In this study, we tested the core plant barcode (rbcL and matK) and four promising complementary barcodes (ITS2, psbK-psbI, rpoC1 and atpF-atpH) in 14 mangroves species belonging to 5 families from West Coast India. Data analysis was performed based on barcode gap analysis, intra- and inter-specific genetic distance, Automated Barcode Gap Discovery (ABGD), TaxonDNA (BM, BCM), Poisson Tree Processes (PTP) and General Mixed Yule-coalescent (GMYC). matK+ITS2 marker based on GMYC method resolved 57.14% of mangroves species and TaxonDNA, ABGD, and PTP discriminated 42.85% of mangrove species. With a single locus analysis, ITS2 exhibited the higher discriminatory power (87.82%) and combinations of matK + ITS2 provided the highest discrimination success (89.74%) rate except for Avicennia genus. Further, we explored 3 additional markers (psbK-psbI, rpoC1, and atpF-atpH) for Avicennia genera (A. alba, A. officinalis and A. marina) and atpF-atpH locus was able to discriminate three species of Avicennia genera. Our analysis underscored the efficacy of matK + ITS2 markers along with atpF-atpH as the best combination for mangrove identification in West Coast India regions.},
}
@article {pmid28814920,
year = {2017},
author = {Toyama, H and Dang, VS and Tagane, S and Nguyen, NV and Naiki, A and Nagamasu, H and Yahara, T},
title = {Garcinia hopii (Clusiaceae), a new species from Bidoup Nui Ba National Park, southern Vietnam.},
journal = {PhytoKeys},
volume = {},
number = {77},
pages = {63-70},
pmid = {28814920},
issn = {1314-2011},
abstract = {A new species, Garcinia hopii H.Toyama &amp; V.S.Dang is described from Bidoup Nui Ba National Park, southern Vietnam. This species is similar to Garcinia hendersoniana Whitmore but differs from that species in having larger leaves, clustered pistillate flowers, a greater number of sterile anthers and a larger stigma of young fruits. A description, preliminary conservation assessment, illustration, photographs and DNA barcodes of the new species are provided, as well as an updated key to Garcinia sect. Hebradendron in Indochina.},
}
@article {pmid28813413,
year = {2017},
author = {Pei, W and Feyerabend, TB and Rössler, J and Wang, X and Postrach, D and Busch, K and Rode, I and Klapproth, K and Dietlein, N and Quedenau, C and Chen, W and Sauer, S and Wolf, S and Höfer, T and Rodewald, HR},
title = {Polylox barcoding reveals haematopoietic stem cell fates realized in vivo.},
journal = {Nature},
volume = {548},
number = {7668},
pages = {456-460},
pmid = {28813413},
issn = {1476-4687},
support = {742883/ERC_/European Research Council/International ; },
mesh = {Animals ; Attachment Sites, Microbiological/*genetics ; Cell Lineage/*genetics ; Cell Tracking/*methods ; Clone Cells/cytology/metabolism ; DNA Barcoding, Taxonomic/*methods ; Embryo, Mammalian/cytology ; Erythroid Cells/cytology/metabolism ; Female ; Hematopoietic Stem Cells/*cytology/metabolism ; Integrases/metabolism ; Lymphocytes/cytology/metabolism ; Male ; Mice ; Mosaicism ; Myeloid Cells/cytology/metabolism ; Recombination, Genetic/*genetics ; Single-Cell Analysis/*methods ; },
abstract = {Developmental deconvolution of complex organs and tissues at the level of individual cells remains challenging. Non-invasive genetic fate mapping has been widely used, but the low number of distinct fluorescent marker proteins limits its resolution. Much higher numbers of cell markers have been generated using viral integration sites, viral barcodes, and strategies based on transposons and CRISPR-Cas9 genome editing; however, temporal and tissue-specific induction of barcodes in situ has not been achieved. Here we report the development of an artificial DNA recombination locus (termed Polylox) that enables broadly applicable endogenous barcoding based on the Cre-loxP recombination system. Polylox recombination in situ reaches a practical diversity of several hundred thousand barcodes, allowing tagging of single cells. We have used this experimental system, combined with fate mapping, to assess haematopoietic stem cell (HSC) fates in vivo. Classical models of haematopoietic lineage specification assume a tree with few major branches. More recently, driven in part by the development of more efficient single-cell assays and improved transplantation efficiencies, different models have been proposed, in which unilineage priming may occur in mice and humans at the level of HSCs. We have introduced barcodes into HSC progenitors in embryonic mice, and found that the adult HSC compartment is a mosaic of embryo-derived HSC clones, some of which are unexpectedly large. Most HSC clones gave rise to multilineage or oligolineage fates, arguing against unilineage priming, and suggesting coherent usage of the potential of cells in a clone. The spreading of barcodes, both after induction in embryos and in adult mice, revealed a basic split between common myeloid-erythroid development and common lymphocyte development, supporting the long-held but contested view of a tree-like haematopoietic structure.},
}
@article {pmid28811535,
year = {2017},
author = {Sun, X and Zhang, F and Ding, Y and Davies, TW and Li, Y and Wu, D},
title = {Delimiting species of Protaphorura (Collembola: Onychiuridae): integrative evidence based on morphology, DNA sequences and geography.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {8261},
pmid = {28811535},
issn = {2045-2322},
mesh = {Animals ; Arthropods/*anatomy &amp; histology/classification/*genetics ; Bayes Theorem ; Geography ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Species delimitation remains a significant challenge when the diagnostic morphological characters are limited. Integrative taxonomy was applied to the genus Protaphorura (Collembola: Onychiuridae), which is one of most difficult soil animals to distinguish taxonomically. Three delimitation approaches (morphology, molecular markers and geography) were applied providing rigorous species validation criteria with an acceptably low error rate. Multiple molecular approaches, including distance- and evolutionary model-based methods, were used to determine species boundaries based on 144 standard barcode sequences. Twenty-two molecular putative species were consistently recovered across molecular and geographical analyses. Geographic criteria were was proved to be an efficient delimitation method for onychiurids. Further morphological examination, based on the combination of the number of pseudocelli, parapseudocelli and ventral mesothoracic chaetae, confirmed 18 taxa of 22 molecular units, with six of them described as new species. These characters were found to be of high taxonomical value. This study highlights the potential benefits of integrative taxonomy, particularly simultaneous use of molecular/geographical tools, as a powerful way of ascertaining the true diversity of the Onychiuridae. Our study also highlights that discovering new morphological characters remains central to achieving a full understanding of collembolan taxonomy.},
}
@article {pmid28810700,
year = {2017},
author = {Modave, E and MacDonald, AJ and Sarre, SD},
title = {A single mini-barcode test to screen for Australian mammalian predators from environmental samples.},
journal = {GigaScience},
volume = {6},
number = {8},
pages = {1-13},
pmid = {28810700},
issn = {2047-217X},
mesh = {Animals ; Australia ; Computational Biology/methods ; DNA Barcoding, Taxonomic/*methods ; DNA Primers ; *Genetic Markers ; Mammals/*genetics ; RNA, Ribosomal ; Real-Time Polymerase Chain Reaction ; Sensitivity and Specificity ; Species Specificity ; },
abstract = {Identification of species from trace samples is now possible through the comparison of diagnostic DNA fragments against reference DNA sequence databases. DNA detection of animals from non-invasive samples, such as predator faeces (scats) that contain traces of DNA from their species of origin, has proved to be a valuable tool for the management of elusive wildlife. However, application of this approach can be limited by the availability of appropriate genetic markers. Scat DNA is often degraded, meaning that longer DNA sequences, including standard DNA barcoding markers, are difficult to recover. Instead, targeted short diagnostic markers are required to serve as diagnostic mini-barcodes. The mitochondrial genome is a useful source of such trace DNA markers because it provides good resolution at the species level and occurs in high copy numbers per cell. We developed a mini-barcode based on a short (178 bp) fragment of the conserved 12S ribosomal ribonucleic acid mitochondrial gene sequence, with the goal of discriminating amongst the scats of large mammalian predators of Australia. We tested the sensitivity and specificity of our primers and can accurately detect and discriminate amongst quolls, cats, dogs, foxes, and devils from trace DNA samples. Our approach provides a cost-effective, time-efficient, and non-invasive tool that enables identification of all 8 medium-large mammal predators in Australia, including native and introduced species, using a single test. With modification, this approach is likely to be of broad applicability elsewhere.},
}
@article {pmid28808549,
year = {2017},
author = {Kusche, H and Côté, G and Hernandez, C and Normandeau, E and Boivin-Delisle, D and Bernatchez, L},
title = {Characterization of natural variation in North American Atlantic Salmon populations (Salmonidae: Salmo salar) at a locus with a major effect on sea age.},
journal = {Ecology and evolution},
volume = {7},
number = {15},
pages = {5797-5807},
pmid = {28808549},
issn = {2045-7758},
abstract = {Age at maturity is a key life-history trait of most organisms. In anadromous salmonid fishes such as Atlantic Salmon (Salmo salar), age at sexual maturity is associated with sea age, the number of years spent at sea before the spawning migration. For the first time, we investigated the presence of two nonsynonymous vgll3 polymorphisms in North American Atlantic Salmon populations that relate to sea age in European salmon and quantified the natural variation at these and two additional candidate SNPs from two other genes. A targeted resequencing assay was developed and 1,505 returning adult individuals of size-inferred sea age and sex from four populations were genotyped. Across three of four populations sampled in Québec, Canada, the late-maturing component (MSW) of the population of a given sex exhibited higher proportions of SNP genotypes 54Thr vgll3 and 323Lys vgll3 compared to early-maturing fish (1SW), for example, 85% versus 53% of females from Trinité River carried 323Lys vgll3 (nMSW = 205 vs. n1SW = 30; p < .001). However, the association between vgll3 polymorphism and sea age was more pronounced in females than in males in the rivers we studied. Logistic regression analysis of vgll3 SNP genotypes revealed increased probabilities of exhibiting higher sea age for 54Thr vgll3 and 323Lys vgll3 genotypes compared to alternative genotypes, depending on population and sex. Moreover, individuals carrying the heterozygous vgll3 SNP genotypes were more likely (>66%) to be female. In summary, two nonsynonymous vgll3 polymorphisms were confirmed in North American populations of Atlantic Salmon and our results suggest that variation at those loci correlates with sea age and sex. Our results also suggest that this correlation varies among populations. Future work would benefit from a more balanced sampling and from adding data on juvenile riverine life stages to contrast our data.},
}
@article {pmid28808384,
year = {2017},
author = {Umdale, SD and Kshirsagar, PR and Lekhak, MM and Gaikwad, NB},
title = {Molecular Authentication of the Traditional Medicinal Plant "Lakshman Booti" (Smithia conferta Sm.) and Its Adulterants through DNA Barcoding.},
journal = {Pharmacognosy magazine},
volume = {13},
number = {Suppl 2},
pages = {S224-S229},
pmid = {28808384},
issn = {0973-1296},
abstract = {BACKGROUND: Smithia conferta Sm. is an annual herb widely used in Indian traditional medical practice and commonly known as "Lakshman booti" in Sanskrit. Morphological resemblance among the species of genus Smithia Aiton. leads to inaccurate identification and adulteration. This causes inconsistent therapeutic effects and also affects the quality of herbal medicine.<br><br>AIM: This study aimed to generate potential barcode for authentication of S. conferta and its adulterants through DNA barcoding technique.<br><br>MATERIALS AND METHODS: Genomic DNA extracted from S. conferta and its adulterants was used as templates for polymerase chain reaction amplification of the barcoding regions. The amplicons were directed for sequencing, and species identification was conducted using BLASTn and unweighted pair-group method with arithmetic mean trees. In addition, the secondary structures of internal transcribed spacer (ITS) 2 region were predicted.<br><br>RESULTS: The nucleotide sequence of ITS provides species-specific single nucleotide polymorphisms and sequence divergence (22%) than psbA-trnH (10.9%) and rbcL (3.1%) sequences. The ITS barcode indicates that S. conferta and Smithia sensitiva are closely related compared to other species.<br><br>CONCLUSION: ITS is the most applicable barcode for molecular authentication of S. conferta, and further chloroplast barcodes should be tested for phylogenetic analysis of genus Smithia.<br><br>SUMMARY: The present investigation is the first effort of utilization of DNA barcode for molecular authentication of S. conferta and its adulterants. Also, this study expanded the application of the ITS2 sequence data in the authentication. The ITS has been proved as a potential and reliable candidate barcode for the authentication of S. conferta. Abbreviations used: BLASTn: Basic Local Alignment Search Tool for Nucleotide; MEGA: Molecular Evolutionary Genetic Analysis; EMBL: European Molecular Biology Laboratory; psbA-trnH: Photosystem II protein D1- stuctural RNA: His tRNA gene; rbcL: Ribulose 1,5 bi-phosphate carboxylase/oxygenase large subunit gene.},
}
@article {pmid28807221,
year = {2017},
author = {Song, M and Dong, GQ and Zhang, YQ and Liu, X and Sun, W},
title = {Identification of processed Chinese medicinal materials using DNA mini-barcoding.},
journal = {Chinese journal of natural medicines},
volume = {15},
number = {7},
pages = {481-486},
doi = {10.1016/S1875-5364(17)30073-0},
pmid = {28807221},
issn = {1875-5364},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; Discriminant Analysis ; Drugs, Chinese Herbal/*chemistry/classification ; Introns ; Plant Proteins/genetics ; Plants, Medicinal/chemistry/classification/*genetics ; },
abstract = {Most of Chinese medicinal herbs are subjected to traditional processing procedures, including stir-frying, charring, steaming, boiling, and calcining before they are released into dispensaries. The marketing and identification of processed medicinal materials is a growing issue in the marketplace. However, conventional methods of identification have limitations, while DNA mini-barcoding, based on the sequencing of a short-standardized region, has received considerable attention as a new potential means to identify processed medicinal materials. In the present study, six DNA barcode loci including ITS2, psbA-trnH, rbcL, matK, trnL (UAA) intron and its P6 loop, were employed for the authentication of 45 processed samples belonging to 15 species. We evaluated the amplification efficiency of each locus. We also examined the identification accuracy of the potential mini-barcode locus, of trnL (UAA) intron P6 loop. Our results showed that the five primary barcode loci were successfully amplified in only 8.89%-20% of the processed samples, while the amplification rates of the trnL (UAA) intron P6 loop were higher, at 75.56% successful amplification. We compared the mini-barcode sequences with Genbank using the Blast program. The analysis showed that 45.23% samples could be identified to genus level, while only one sample could be identified to the species level. We conclude that trnL (UAA) p6 loop is a candidate mini-barcode that has shown its potential and may become a universal mini-barcode as complementary barcode for authenticity testing and will play an important role in medicinal materials control.},
}
@article {pmid28803843,
year = {2017},
author = {Lu, M and Chan, BM and Schow, PW and Chang, WS and King, CT},
title = {High-throughput screening of hybridoma supernatants using multiplexed fluorescent cell barcoding on live cells.},
journal = {Journal of immunological methods},
volume = {451},
number = {},
pages = {20-27},
doi = {10.1016/j.jim.2017.08.002},
pmid = {28803843},
issn = {1872-7905},
mesh = {Animals ; Antibodies, Monoclonal/biosynthesis/immunology/*metabolism ; Antibody Formation ; Antibody Specificity ; Antigens, Surface/genetics/*immunology ; Binding Sites, Antibody ; CHO Cells ; Cell Separation/*methods ; Cricetulus ; Female ; Flow Cytometry/*methods ; Fluorescent Dyes/*chemistry ; HEK293 Cells ; High-Throughput Screening Assays/*methods ; Humans ; Hybridomas/immunology/*metabolism ; Mice, Inbred C57BL ; Predictive Value of Tests ; Protein Binding ; Reproducibility of Results ; Transfection ; },
abstract = {With current available assay formats using either immobilized protein (ELISA, enzyme-linked immunosorbent assay) or immunostaining of fixed cells for primary monoclonal antibody (mAb) screening, researchers often fail to identify and characterize antibodies that recognize the native conformation of cell-surface antigens. Therefore, screening using live cells has become an integral and important step contributing to the successful identification of therapeutic antibody candidates. Thus the need for developing high-throughput screening (HTS) technologies using live cells has become a major priority for therapeutic mAb discovery and development. We have developed a novel technique called Multiplexed Fluorescent Cell Barcoding (MFCB), a flow cytometry-based method based upon the Fluorescent Cell Barcoding (FCB) technique and the Luminex fluorescent bead array system, but is applicable to high-through mAb screens on live cells. Using this technique in our system, we can simultaneously identify or characterize the antibody-antigen binding of up to nine unique fluorescent labeled cell populations in the time that it would normally take to process a single population. This has significantly reduced the amount of time needed for the identification of potential lead candidates. This new technology enables investigators to conduct large-scale primary hybridoma screens using flow cytometry. This in turn has allowed us to screen antibodies more efficiently than before and streamline identification and characterization of lead molecules.},
}
@article {pmid28802879,
year = {2017},
author = {Pérez-Juárez, H and Serrano-Vázquez, A and Kosakyan, A and Mitchell, EAD and Rivera Aguilar, VM and Lahr, DJG and Hernández Moreno, MM and Cuellar, HM and Eguiarte, LE and Lara, E},
title = {Quadrulella texcalense sp. nov. from a Mexican desert: An unexpected new environment for hyalospheniid testate amoebae.},
journal = {European journal of protistology},
volume = {61},
number = {Pt A},
pages = {253-264},
doi = {10.1016/j.ejop.2017.06.008},
pmid = {28802879},
issn = {1618-0429},
mesh = {*Desert Climate ; Electron Transport Complex IV/genetics ; Lobosea/*classification/cytology/genetics ; Mexico ; *Phylogeny ; Soil/*parasitology ; Species Specificity ; },
abstract = {Quadrulella (Amoebozoa, Arcellinida, Hyalospheniidae) is a genus of testate amoebae with unmistakable morphology, which secretes characteristic square plates to reinforce the test. They are mainly known from fens and freshwater habitats and have never been documented in deserts. We describe a new species, Quadrulella texcalense, from biological soil crusts in the intertropical desert of Tehuacán (state of Puebla, Mexico). Quadrulella texcalense occurred only at altitudes between 2140 and 2221m.a.s.l., together with the bryophyte genera Pseudocrossidium, Weissia, Bryum, Didymodon, Neohyophyla and Aloina. The soil was extremely dry (moisture of 1.97-2.6%), which contrasts sharply with previous reports for the Quadrulella genus. Single cell mitochondrial cytochrome oxidase I (COI) barcoding of thirteen isolated cells showed an important morphological variability despite having all the same COI barcode sequence. Quadrulella texcalense was placed in a tree containing other Hyalsopheniidae, including a newly barcoded South African species, Q. elegans. Q. texcalense unambiguously branched within genus Quadrulella in a compact clade but with a long branch, suggesting accelerated evolution due to a transition towards a new environment and/or under-sampling.},
}
@article {pmid28799720,
year = {2017},
author = {Berruti, A and Desirò, A and Visentin, S and Zecca, O and Bonfante, P},
title = {ITS fungal barcoding primers versus 18S AMF-specific primers reveal similar AMF-based diversity patterns in roots and soils of three mountain vineyards.},
journal = {Environmental microbiology reports},
volume = {9},
number = {5},
pages = {658-667},
doi = {10.1111/1758-2229.12574},
pmid = {28799720},
issn = {1758-2229},
mesh = {Biodiversity ; *DNA Barcoding, Taxonomic ; *DNA, Fungal ; *DNA, Intergenic ; Mycorrhizae/*classification/*genetics ; Phylogeny ; Plant Roots/*microbiology ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {ITS primers commonly used to describe soil fungi are flawed for AMF although it is unknown the extent to which they distort the interpretation of community patterns. Here, we focus on how the use of a specific ITS2 fungal barcoding primer pair biased for AMF changes the interpretation of AMF community patterns from three mountain vineyards compared to a novel AMF-specific approach on the 18S. We found that although discrepancies were present in the taxonomic composition of the two resulting datasets, the estimation of diversity patterns among AMF communities was similar and resulted in both primer systems being able to correctly assess the community-structuring effect of location, compartment (root vs. soil) and environment. Both methodologies made it possible to detect the same alpha-diversity trend among the locations under study but not between root and soil transects. We show that the ITS2 primer system for fungal barcoding provides a good estimate of both AMF community structure and relation to environmental variables. However, this primer system does not fit in with cross-compartment surveys (roots vs. soil) as it can underestimate AMF diversity in soil samples. When specifically focusing on AMF, the 18S primer system resulted in wide coverage and marginal non-target amplification.},
}
@article {pmid28798064,
year = {2017},
author = {Reid-Bayliss, KS and Loeb, LA},
title = {Accurate RNA consensus sequencing for high-fidelity detection of transcriptional mutagenesis-induced epimutations.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {114},
number = {35},
pages = {9415-9420},
pmid = {28798064},
issn = {1091-6490},
support = {P01 CA077852/CA/NCI NIH HHS/United States ; R01 CA160674/CA/NCI NIH HHS/United States ; T32 AG000057/AG/NIA NIH HHS/United States ; T32 GM007266/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Base Sequence ; *Epigenesis, Genetic ; *Mutagenesis ; Mutation ; Oxidative Stress ; RNA/*genetics ; Saccharomyces ; Transcription, Genetic ; },
abstract = {Transcriptional mutagenesis (TM) due to misincorporation during RNA transcription can result in mutant RNAs, or epimutations, that generate proteins with altered properties. TM has long been hypothesized to play a role in aging, cancer, and viral and bacterial evolution. However, inadequate methodologies have limited progress in elucidating a causal association. We present a high-throughput, highly accurate RNA sequencing method to measure epimutations with single-molecule sensitivity. Accurate RNA consensus sequencing (ARC-seq) uniquely combines RNA barcoding and generation of multiple cDNA copies per RNA molecule to eliminate errors introduced during cDNA synthesis, PCR, and sequencing. The stringency of ARC-seq can be scaled to accommodate the quality of input RNAs. We apply ARC-seq to directly assess transcriptome-wide epimutations resulting from RNA polymerase mutants and oxidative stress.},
}
@article {pmid28795701,
year = {2017},
author = {Kim, D and Jetson, RR and Krusemark, CJ},
title = {A DNA-assisted immunoassay for enzyme activity via a DNA-linked, activity-based probe.},
journal = {Chemical communications (Cambridge, England)},
volume = {53},
number = {68},
pages = {9474-9477},
doi = {10.1039/c7cc05236g},
pmid = {28795701},
issn = {1364-548X},
mesh = {Base Sequence ; DNA/*chemistry ; DNA Probes/*chemistry ; Hydrolases/*genetics/*metabolism ; *Immunoassay ; Oligonucleotides/chemistry/metabolism ; Phosphates/chemistry/metabolism ; Polymerase Chain Reaction ; Serine/genetics/metabolism ; },
abstract = {Here, we describe an immunoassay approach for the detection of enzyme activity by quantitative PCR (qPCR) or parallel DNA sequencing which relies on activity-based probes linked to barcoding DNAs. We demonstrate this technique in the detection of serine hydrolase activities using a fluorophosphonate-oligonucleotide conjugate.},
}
@article {pmid28794672,
year = {2017},
author = {Lehr, E and von May, R},
title = {A new species of terrestrial-breeding frog (Amphibia, Craugastoridae, Pristimantis) from high elevations of the Pui Pui Protected Forest in central Peru.},
journal = {ZooKeys},
volume = {},
number = {660},
pages = {17-42},
pmid = {28794672},
issn = {1313-2989},
abstract = {We describe a new species of Pristimantis from upper montane forests and high Andean grasslands of the Pui Pui Protected Forest and its close surroundings, Región Junín, central Peru. The description of the new species is based on 34 specimens found at elevations between 3400 and 3936 m a.s.l. Pristimantis attenboroughisp. n. is characterized by a snout-vent length of 14.6-19.2 mm in adult males (n = 21), 19.2-23.0 mm in adult females (n = 10), and is compared morphologically and genetically with other taxonomically and biogeographically relevant species of Pristimantis. The new species is characterized by having narrow digits that lack circumferential grooves, irregularly shaped, discontinuous dorsolateral folds, and absence of both tympanic membrane and tympanic annulus. The high similarity in morphology between P. attenboroughisp. n. and members of the Andean genera Phrynopus and Bryophryne provides an example for convergent evolution, and highlights the importance of using molecular data to justify generic assignment. Pristimantis attenboroughisp. n. is most similar to Phrynopus chaparroi from the Región Junín, suggesting that the generic placement of this species needs to be revised. Phylogenetically the new species belongs to the Pristimantis danae species Group, a clade that includes several Pristimantis species distributed in the montane forests of central Peru, including P. albertus, P. aniptopalmatus, P. ornatus, and P. stictogaster.},
}
@article {pmid28793855,
year = {2017},
author = {Palandačić, A and Naseka, A and Ramler, D and Ahnelt, H},
title = {Contrasting morphology with molecular data: an approach to revision of species complexes based on the example of European Phoxinus (Cyprinidae).},
journal = {BMC evolutionary biology},
volume = {17},
number = {1},
pages = {184},
pmid = {28793855},
issn = {1471-2148},
mesh = {Animals ; Cell Nucleus/genetics ; Cyprinidae/*anatomy &amp; histology/classification/*genetics ; DNA, Mitochondrial/genetics ; Europe ; Geography ; Haplotypes/genetics ; Phylogeny ; Species Specificity ; },
abstract = {BACKGROUND: Molecular taxonomy studies and barcoding projects can provide rapid means of detecting cryptic diversity. Nevertheless, the use of molecular data for species delimitation should be undertaken with caution. Especially the single-gene approaches are linked with certain pitfalls for taxonomical inference. In the present study, recent and historical species descriptions based upon morphology were used as primary species hypotheses, which were then evaluated with molecular data (including in type and historical museum material) to form secondary species hypotheses. As an example of cryptic diversity and taxonomic controversy, the European Phoxinus phoxinus species complex was used.<br><br>RESULTS: The results of the revision showed that of the fourteen primary species hypotheses, three were rejected, namely P. ketmaieri, P. likai, and P. apollonicus. For three species (P. strandjae, P. strymonicus, P. morella), further investigation with increased data sampling was suggested, while two primary hypotheses, P. bigerri and P. colchicus, were supported as secondary species hypotheses. Finally, six of the primary species hypotheses (P. phoxinus, P. lumaireul, P. karsticus, P. septimanae, P. marsilii and P. csikii) were well supported by mitochondrial but only limitedly corroborated by nuclear data analysis.<br><br>CONCLUSION: The approach has proven useful for revision of species complexes, and the study can serve as an overview of the Phoxinus genus in Europe, as well as a solid basis for further work.},
}
@article {pmid28792677,
year = {2017},
author = {Weigand, H and Weiss, M and Cai, H and Li, Y and Yu, L and Zhang, C and Leese, F},
title = {Deciphering the origin of mito-nuclear discordance in two sibling caddisfly species.},
journal = {Molecular ecology},
volume = {26},
number = {20},
pages = {5705-5715},
doi = {10.1111/mec.14292},
pmid = {28792677},
issn = {1365-294X},
mesh = {Animals ; *Biological Evolution ; Cell Nucleus/genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Europe ; Gene Flow ; Genetic Markers ; Genome, Insect ; *Hybridization, Genetic ; Insecta/*classification ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {An increasing number of phylogenetic studies have reported discordances among nuclear and mitochondrial markers. These discrepancies are highly relevant to widely used biodiversity assessment approaches, such as DNA barcoding, that rely almost exclusively on mitochondrial markers. Although the theoretical causes of mito-nuclear discordances are well understood, it is often extremely challenging to determine the principal underlying factor in a given study system. In this study, we uncovered significant mito-nuclear discordances in a pair of sibling caddisfly species. Application of genome sequencing, ddRAD and DNA barcoding revealed ongoing hybridization, as well as historical hybridization in Pleistocene refugia, leading us to identify introgression as the ultimate cause of the observed discordance pattern. Our novel genomic data, the discovery of a European-wide hybrid zone and the availability of established techniques for laboratory breeding make this species pair an ideal model system for studying species boundaries with ongoing gene flow.},
}
@article {pmid28791769,
year = {2017},
author = {Andreiuk, B and Reisch, A and Lindecker, M and Follain, G and Peyriéras, N and Goetz, JG and Klymchenko, AS},
title = {Fluorescent Polymer Nanoparticles for Cell Barcoding In Vitro and In Vivo.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {13},
number = {38},
pages = {},
doi = {10.1002/smll.201701582},
pmid = {28791769},
issn = {1613-6829},
mesh = {Animals ; Carbocyanines/chemistry ; Cell Survival ; Cell Tracking ; Color ; Embryo, Nonmammalian/cytology/metabolism ; Fluorescence ; HeLa Cells ; Humans ; Mice ; Nanoparticles/*chemistry/ultrastructure ; Polymers/*chemistry ; Zebrafish/embryology ; },
abstract = {Fluorescent polymer nanoparticles for long-term labeling and tracking of living cells with any desired color code are developed. They are built from biodegradable poly(lactic-co-glycolic acid) polymer loaded with cyanine dyes (DiO, DiI, and DiD) with the help of bulky fluorinated counterions, which minimize aggregation-caused quenching. At the single particle level, these particles are ≈20-fold brighter than quantum dots of similar color. Due to their identical 40 nm size and surface properties, these nanoparticles are endocytosed equally well by living cells. Mixing nanoparticles of three colors in different proportions generates a homogeneous RGB (red, green, and blue) barcode in cells, which is transmitted through many cell generations. Cell barcoding is validated on 7 cell lines (HeLa, KB, embryonic kidney (293T), Chinese hamster ovary, rat basophilic leucemia, U97, and D2A1), 13 color codes, and it enables simultaneous tracking of co-cultured barcoded cell populations for >2 weeks. It is also applied to studying competition among drug-treated cell populations. This technology enabled six-color imaging in vivo for (1) tracking xenografted cancer cells and (2) monitoring morphogenesis after microinjection in zebrafish embryos. In addition to a robust method of multicolor cell labeling and tracking, this work suggests that multiple functions can be co-localized inside cells by combining structurally close nanoparticles carrying different functions.},
}
@article {pmid28791201,
year = {2017},
author = {Wang, J and Zhang, L and Zhang, QL and Zhou, MQ and Wang, XT and Yang, XZ and Yuan, ML},
title = {Comparative mitogenomic analysis of mirid bugs (Hemiptera: Miridae) and evaluation of potential DNA barcoding markers.},
journal = {PeerJ},
volume = {5},
number = {},
pages = {e3661},
pmid = {28791201},
issn = {2167-8359},
abstract = {The family Miridae is one of the most species-rich families of insects. To better understand the diversity and evolution of mirids, we determined the mitogenome of Lygus pratenszs and re-sequenced the mitogenomes of four mirids (i.e., Apolygus lucorum, Adelphocoris suturalis, Ade. fasciaticollis and Ade. lineolatus). We performed a comparative analysis for 15 mitogenomic sequences representing 11 species of five genera within Miridae and evaluated the potential of these mitochondrial genes as molecular markers. Our results showed that the general mitogenomic features (gene content, gene arrangement, base composition and codon usage) were well conserved among these mirids. Four protein-coding genes (PCGs) (cox1, cox3, nad1 and nad3) had no length variability, where nad5 showed the largest size variation; no intraspecific length variation was found in PCGs. Two PCGs (nad4 and nad5) showed relatively high substitution rates at the nucleotide and amino acid levels, where cox1 had the lowest substitution rate. The Ka/Ks values for all PCGs were far lower than 1 (<0.59), but the Ka/Ks values of cox1-barcode sequences were always larger than 1 (1.34 -15.20), indicating that the 658 bp sequences of cox1 may be not the appropriate marker due to positive selection or selection relaxation. Phylogenetic analyses based on two concatenated mitogenomic datasets consistently supported the relationship of Nesidiocoris + (Trigonotylus + (Adelphocoris + (Apolygus + Lygus))), as revealed by nad4, nad5, rrnL and the combined 22 transfer RNA genes (tRNAs), respectively. Taken sequence length, substitution rate and phylogenetic signal together, the individual genes (nad4, nad5 and rrnL) and the combined 22 tRNAs could been used as potential molecular markers for Miridae at various taxonomic levels. Our results suggest that it is essential to evaluate and select suitable markers for different taxa groups when performing phylogenetic, population genetic and species identification studies.},
}
@article {pmid28785816,
year = {2018},
author = {Schmidt, PA and Schmitt, I and Otte, J and Bandow, C and Römbke, J and Bálint, M and Rolshausen, G},
title = {Season-Long Experimental Drought Alters Fungal Community Composition but Not Diversity in a Grassland Soil.},
journal = {Microbial ecology},
volume = {75},
number = {2},
pages = {468-478},
pmid = {28785816},
issn = {1432-184X},
mesh = {Biodiversity ; Droughts ; Ecosystem ; Fungi/classification/genetics/*isolation &amp; purification ; Grassland ; Mycobiome ; Phylogeny ; Seasons ; Soil/chemistry ; *Soil Microbiology ; Water/analysis ; },
abstract = {Using terrestrial model ecosystems (TMEs), we investigated how reduced moisture conditions impact soil fungal communities from a temperate grassland over the course of an entire season. Starting at about 65% of the soil's maximum water holding capacity (WHCmax), TME soils were adjusted to three moisture levels for 15 weeks: 70% WHCmax, approximating starting conditions, 50% WHCmax, and 30% WHCmax, representing reduced moisture conditions. Diversity and abundances of soil fungi at the start and at the end of the experiment were characterized using Illumina meta-barcoding. Community diversity at the end of the experiment did not differ between experimental moisture levels and was comparable to diversity measures from the field. However, fungal communities did change compositionally in both abundances and presence/absence of species. Analyzing class-level and individual contributions of fungi to these changes revealed that only a minor portion reacted significantly, indicating that most compositional change was likely driven by many consistent small-scale shifts in presence/absences or abundances. Together, our results show that prolonged reduction in soil moisture conditions will trigger compositional changes in soil fungal communities but not necessarily change overall diversity. We highlight the cumulative contribution of minor but consistent changes among community members, as opposed to significant responses of individual species. We also detected a strong general experimental effect on soil fungi that are moved from the field to experimental TMEs, suggesting the importance of acclimatization effects in these communities under laboratory conditions.},
}
@article {pmid28785163,
year = {2017},
author = {Souladeth, P and Tagane, S and Zhang, M and Okabe, N and Yahara, T},
title = {Flora of Nam Kading National Protected Area I: a new species of yellow-flowered Strobilanthes (Acanthaceae), S. namkadingensis.},
journal = {PhytoKeys},
volume = {},
number = {81},
pages = {11-17},
pmid = {28785163},
issn = {1314-2011},
abstract = {A new species of Acanthaceae, Strobilanthes namkadingensis Soulad. &amp; Tagane from Nam Kading National Protected Area, Bolikhamxay Province, central Laos, is described and illustrated. It is characterized by long spicate inflorescences consisting of 6-32 flowers, yellow corolla, the absence of long white hairs on the bracts and 4-6 seeds per capsule. Three DNA barcode regions of the partial genes for the large sub-unit ribulose-1,5-bisphosphate carboxylase oxygenase (rbcL) and maturase K (matK) and internal transcribed spacers (ITS) are also provided.},
}
@article {pmid28781562,
year = {2017},
author = {Tagane, S and Dang, VS and Ngoc, NV and Binh, HT and Komada, N and Wai, JS and Naiki, A and Nagamasu, H and Toyama, H and Yahara, T},
title = {Macrosolen bidoupensis (Loranthaceae), a new species from Bidoup Nui Ba National Park, southern Vietnam.},
journal = {PhytoKeys},
volume = {},
number = {80},
pages = {113-120},
pmid = {28781562},
issn = {1314-2011},
abstract = {Macrosolen bidoupensis Tagane &amp; V.S.Dang, sp. nov. (Loranthaceae) is newly described from Bidoup Nui Ba National Park in Lam Dong Province, southern Vietnam. The new species is characterized by small broadly elliptic to circular leaves, sessile to short petioles, slightly cordate to rounded leaf bases, 4-5 pairs of lateral veins and a basally green corolla tube. An illustration, a summary of DNA barcoding of the plastid genes rbcL and matK, and a key to the species of Macrosolen in Vietnam are provided.},
}
@article {pmid28780857,
year = {2017},
author = {Ahmad, R and Jang, H and Batule, BS and Park, HG},
title = {Barcode DNA-Mediated Signal Amplifying Strategy for Ultrasensitive Biomolecular Detection on Matrix-Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) Mass Spectrometry.},
journal = {Analytical chemistry},
volume = {89},
number = {17},
pages = {8966-8973},
doi = {10.1021/acs.analchem.7b01535},
pmid = {28780857},
issn = {1520-6882},
mesh = {Aptamers, Peptide/chemistry ; Biotin/chemistry ; DNA/*analysis/chemistry ; Gold/chemistry ; Graphite/chemistry ; Limit of Detection ; Metal Nanoparticles/chemistry ; Potassium Cyanide/chemistry ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Thrombin/analysis/chemistry ; },
abstract = {We have devised a barcode DNA-mediated signal amplifying strategy for ultrasensitive biomolecular detection by utilizing matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). As a model target, thrombin was first captured by specific aptamer15 functionalized on magnetic beads (MBs-apt15) and sandwiched through the simultaneous interaction with gold nanoparticles modified with another specific aptamer29 and barcode DNA molecules (apt29-AuNPs-bcDNAs). The sandwiched complex was collected by convenient magnetic separation and then treated with potassium cyanide (KCN) to dissolve the gold nanoparticles (AuNPs) and consequently release the barcode DNA molecules (bcDNAs), which were then again magnetically separated and analyzed by using MALDI-TOF MS. Under optimized conditions, this strategy revealed an excellent sensitivity with a limit of detection of 0.89 aM in a wide linear detection range from 0 aM to 0.1 nM and exhibited an acceptable recovery for thrombin detection in complex biological matrices. This signal amplifying strategy based on MALDI-TOF MS could greatly enable the ultrasensitive detection of various low abundant biomolecules.},
}
@article {pmid28779732,
year = {2016},
author = {Aziz, NMA and Esa, Y and Arshad, A},
title = {DNA barcoding and phylogenetic analysis of Malaysian groupers (Subfamily: Epinephelinae) using mitochondrial Cytochrome c oxidase I (COI) gene.},
journal = {Journal of environmental biology},
volume = {37},
number = {4 Spec No},
pages = {725-733},
pmid = {28779732},
issn = {0254-8704},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Fishes/*genetics ; Haplotypes ; Mitochondria/*enzymology ; *Phylogeny ; Species Specificity ; },
abstract = {The present study was carried out to examine the species identification and phylogenetic relationships of groupers in Malaysia using mitochondrial Cytochrome c Oxidase I (COI) gene, commonly known as barcoding gene. A total of 63 individuals comprising 10 species from three genera were collected from the coastal areas of Johor, Kelantan, Pahang, Perak, Selangor and Terengganu. All the individuals were morphologically identified and molecular works involved polymerase chain reaction (PCR) and sequencing of COI barcoding fragment (655 base pairs). Results from the BLAST search showed that 55 sequences could be assigned to 10 grouper species with high percentage identity index (≥95% to 100%), while eight grouper individuals showed discrepancies in their taxonomic identification based on the morphology and the COI barcoding results. The histogram of distances showed that there was a clear-cut barcode gap present in the sequences indicating a clear separation between intraspecific and interspecific distances. The pairwise genetic distances showed lowest pairwise distance between P. leopardus and P. maculatus (4.4%), while the highest pairwise distance was between E. bleekeri and P. maculatus (23.5%), supporting their morphological and habitat similarities and differences. Phylogenetic analysis (Neighbor-Joining) showed the presence of two major clades (1) genus Epinephelus vs (2) genus Plectropomus and Cephalopholis). In conclusion, the present study has managed to show the accuracy of DNA barcoding method for species identification, and utilization of COI gene for phylogenetic study among groupers. ?},
}
@article {pmid28778818,
year = {2017},
author = {Janssen, T and Karssen, G and Orlando, V and Subbotin, SA and Bert, W},
title = {Molecular characterization and species delimiting of plant-parasitic nematodes of the genus Pratylenchus from the penetrans group (Nematoda: Pratylenchidae).},
journal = {Molecular phylogenetics and evolution},
volume = {117},
number = {},
pages = {30-48},
doi = {10.1016/j.ympev.2017.07.027},
pmid = {28778818},
issn = {1095-9513},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic ; Genes, Mitochondrial/genetics ; Haplotypes/genetics ; *Phylogeny ; Plant Diseases/parasitology ; Plant Roots/parasitology ; Plants/*parasitology ; Ribosomal Proteins/genetics ; Species Specificity ; Tylenchoidea/anatomy &amp; histology/*classification/*genetics/isolation &amp; purification ; },
abstract = {Root-lesion nematodes of the genus Pratylenchus are an important pest parasitizing a wide range of vascular plants including several economically important crops. However, morphological diagnosis of the more than 100 species is problematic due to the low number of diagnostic features, high morphological plasticity and incomplete taxonomic descriptions. In order to employ barcoding based diagnostics, a link between morphology and species specific sequences has to be established. In this study, we reconstructed a multi-gene phylogeny of the Penetrans group using nuclear ribosomal and mitochondrial gene sequences. A combination of this phylogenetic framework with molecular species delineation analysis, population genetics, morphometric information and sequences from type location material allowed us to establish the species boundaries within the Penetrans group and as such clarify long-standing controversies about the taxonomic status of P. penetrans, P. fallax and P. convallariae. Our study also reveals a remarkable amount of cryptic biodiversity within the genus Pratylenchus confirming that identification on morphology alone can be inconclusive in this taxonomically confusing genus.},
}
@article {pmid28774799,
year = {2017},
author = {Gómez, GF and Correa, MM},
title = {Discrimination of Neotropical Anopheles species based on molecular and wing geometric morphometric traits.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {54},
number = {},
pages = {379-386},
doi = {10.1016/j.meegid.2017.07.028},
pmid = {28774799},
issn = {1567-7257},
mesh = {Animals ; Anopheles/anatomy &amp; histology/*classification/*genetics ; DNA Barcoding, Taxonomic ; Organ Size ; Phylogeny ; Quantitative Trait Loci ; Species Specificity ; Wings, Animal/*anatomy &amp; histology ; },
abstract = {Morphological similarities among closely related Anopheles species that differ in biological traits and malaria transmission represent a challenge in medical entomology; therefore, new tools are constantly tested to bring solutions. Particularly, in this work, a geometric morphometric analysis of wing geometry variation, based on morphologically and molecularly identified specimens, was applied for the discrimination of fourteen Anopheles species belonging to the Nyssorhynchus, Anopheles and Kerteszia subgenera. DNA barcodes helped to confirm species assignation and the geometric morphometric approach revealed wing form differences not only at the subgenera but also at the species level. Each subgenus presented a particular wing size trend, possibly related to the evolutionary history of these lineages. Wing shape allowed species discrimination, except for some very closely related taxa. The current findings highlight the importance of using complementary approaches involving morphological and molecular data for Anopheles species discrimination.},
}
@article {pmid28771612,
year = {2017},
author = {Nelson, EJH and Holden, J and Eves, R and Tufts, B},
title = {Comparison of diets for Largemouth and Smallmouth Bass in Eastern Lake Ontario using DNA barcoding and stable isotope analysis.},
journal = {PloS one},
volume = {12},
number = {8},
pages = {e0181914},
pmid = {28771612},
issn = {1932-6203},
mesh = {Animals ; DNA/*analysis ; DNA Barcoding, Taxonomic/*methods ; Diet/*veterinary ; Food Analysis/*methods ; Isotope Labeling/*methods ; Perciformes/*physiology ; },
abstract = {Largemouth (LMB: Micropterus salmoides) and Smallmouth Bass (SMB: Micropterus dolomieu) are important species in the recreational fisheries of the Laurentian Great Lakes. The invasion of the Round Goby (Neogobius melanostomus) into these lakes has changed several facets of black bass biology, but there is still much to learn about the relationship between these species. Previous dietary analyses have shown Round Goby to be important prey for bass, but have been limited by low visual identification rates of dissected stomach items. Within the present study, DNA barcoding and stable isotope analysis improve prey identification and provide a more quantitative dietary analysis of adult black bass in Lake Ontario, comparing the importance of Round Goby as prey between these two species. Eighty-four LMB (406mm fork length ±4mm SEM) and two hundred sixty-four SMB (422mm ±2mm) obtained as tournament mortalities had prey identified using DNA-based methods. Round Goby was the most prevalent prey species for both predators. The diet of LMB was three times more diverse than that of SMB, which almost entirely consists of Round Goby. Our results provide further support that recent increases in the size of Lake Ontario bass are a result of Round Goby consumption, and that the effects of this dietary shift on body condition are greater for SMB. Techniques developed in this study include reverse-oriented dual priming oligonucleotides used as blocking primers for predator DNA, and an automated design approach of restriction fragment length polymorphism tests for identifying prey DNA barcodes.},
}
@article {pmid28771590,
year = {2017},
author = {Isari, S and Pearman, JK and Casas, L and Michell, CT and Curdia, J and Berumen, ML and Irigoien, X},
title = {Exploring the larval fish community of the central Red Sea with an integrated morphological and molecular approach.},
journal = {PloS one},
volume = {12},
number = {8},
pages = {e0182503},
pmid = {28771590},
issn = {1932-6203},
mesh = {Animals ; Electron Transport Complex IV/*genetics ; Fish Proteins/genetics ; Fishes/*anatomy &amp; histology/*classification/genetics ; Indian Ocean ; Larva/anatomy &amp; histology/classification/genetics ; Phylogeny ; Population Dynamics ; Saudi Arabia ; Seasons ; Sequence Analysis, DNA/methods ; },
abstract = {An important aspect of population dynamics for coral reef fishes is the input of new individuals from the pelagic larval pool. However, the high biodiversity and the difficulty of identifying larvae of closely related species represent obstacles to more fully understanding these populations. In this study, we combined morphology and genetic barcoding (Cytochrome Oxidase I gene) to characterize the seasonal patterns of the larval fish community at two sites in close proximity to coral reefs in the central-north Red Sea: one shallower inshore location (50 m depth) and a nearby site located in deeper and more offshore waters (~ 500 m depth). Fish larvae were collected using oblique tows of a 60 cm-bongo net (500 μm mesh size) every month for one year (2013). During the warmer period of the year (June-November), the larval fish stock was comparable between sampling sites. However, during the colder months, abundances were higher in the inshore than in the offshore waters. Taxonomic composition and temporal variation of community structure differed notably between sites, potentially reflecting habitat differences, reproductive patterns of adults, and/or advective processes in the area. Eleven out of a total of 62 recorded families comprised 69-94% of the fish larval community, depending on sampling site and month. Richness of taxa was notably higher in the inshore station compared to the offshore, particularly during the colder period of the year and especially for the gobiids and apogonids. Two mesopelagic taxa (Vinciguerria sp. and Benthosema spp.) comprised an important component of the larval community at the deeper site with only a small and sporadic occurrence in the shallower inshore waters. Our data provide an important baseline reference for the larval fish communities of the central Red Sea, representing the first such study from Saudi Arabian waters.},
}
@article {pmid28770676,
year = {2017},
author = {Tominaga, H and Hirose, M and Igarashi, H and Kiyomoto, M and Komatsu, M},
title = {A New Species of Sexually Dimorphic Brittle Star of the Genus Ophiodaphne (Echinodermata: Ophiuroidea).},
journal = {Zoological science},
volume = {34},
number = {4},
pages = {351-360},
doi = {10.2108/zs160215},
pmid = {28770676},
issn = {0289-0003},
mesh = {Animal Distribution ; Animals ; Echinodermata/*classification/genetics ; Female ; Japan ; Male ; Phylogeny ; Species Specificity ; },
abstract = {We describe a new species of sexually dimorphic brittle star, Ophiodaphne spinosa, from Japan associated with the irregular sea urchin, Clypeaster japonicus based on its external morphology, and phylogenetic analyses of mitochondrial COI (cytochrome c oxidase subunit I). Females of this new species of Ophiodaphne are characterized mainly by the presence of wavy grooves on the surface of the radial shields, needle-like thorns on the oral skeletal jaw structures, and a low length-to-width ratio of the jaw angle in comparison with those of type specimens of its Ophiodaphne congeners: O. scripta, O. materna, and O. formata. A tabular key to the species characteristics of Ophiodaphne is provided. Phylogenetic analyses indicate that the new species of Ophiodaphne, O. scripta, and O. formata are monophyletic. Our results indicate that the Japanese Ophiodaphne include both the new species and O. scripta, and that there are four Ophiodaphne species of sexually dimorphic brittle stars with androphorous habit.},
}
@article {pmid28769736,
year = {2017},
author = {Buchner, P and Corley, M and Junnilainen, J},
title = {Three new species and one new subspecies of Depressariinae (Lepidoptera) from Europe.},
journal = {ZooKeys},
volume = {},
number = {684},
pages = {119-154},
pmid = {28769736},
issn = {1313-2989},
abstract = {The species Depressaria albarracinella Corley, sp. n., Agonopterix carduncelli Corley, sp. n. and Agonopterix pseudoferulae Buchner &amp; Junnilainen, sp. n. and the subspecies Depressaria saharae Gastón &amp; Vives ssp. tabelli Buchner, ssp. n. are described. Depressaria albarracinella was first found in Spain in 1969 and recognised as apparently new but the specimens in NHMUK have remained undescribed. Additional Spanish material has been located in ZMUC and other collections and three specimens have been found from Greece. Agonopterix carduncelli. A single male of an unidentified Agonopterix of the pallorella group was found in Algarve, Portugal in 2010. A search for larvae in March 2011 was successful and one male and one female were reared from Carthamus caeruleus. Additional specimens of the new species have been located in collections from Spain, Greece and Morocco. Agonopterix pseudoferulae. A specimen from Greece with the name Agonopterix ferulae (Zeller, 1847) found in the Klimesch collection in ZSM had forewing markings which suggested that it might be a different species. Further specimens from Italy and Greece have been examined, among them two reared from Elaeoselinum asclepium (Apiaceae). Both genitalia and barcode show that this is an undescribed species. Depressaria saharae Gastón &amp; Vives, 2017 was described very recently (Gastón and Vives 2017) from northern Spain with a brief description, and figures of two males and male genitalia. Here the new species is redescribed, and additional data on distribution and relationships of the new species added. The opportunity is also taken to show that Canary Islands specimens with the same male genitalia should be treated as a new subspecies D. saharae ssp. tabelli Buchner, ssp. n.},
}
@article {pmid28769720,
year = {2017},
author = {Arriaga-Varela, E and Seidel, M and Deler-Hernández, A and Viktor Senderov, and Fikáček, M},
title = {A review of the Cercyon Leach (Coleoptera, Hydrophilidae, Sphaeridiinae) of the Greater Antilles.},
journal = {ZooKeys},
volume = {},
number = {681},
pages = {39-93},
pmid = {28769720},
issn = {1313-2989},
abstract = {The representatives of the genus Cercyon Leach occurring in the Greater Antilles are reviewed. Ten species are recorded, of which five are described here as new: C. gimmelisp. n. (Dominican Republic), C. armatipenissp. n. (Dominican Republic), C. tainosp. n. (Dominican Republic), C. sklodowskaesp. n. (Jamaica) and C. spiniventrissp. n. (Dominican Republic). Diagnoses and detailed distributional data are also provided for C. floridanus Horn, 1890 (distributed in southeastern United States of America and Cayman Islands), C. insularis Chevrolat, 1863 (endemic to the Antilles) C. praetextatus (Say, 1825) (widely distributed in the New World incl. Greater Antilles), C. quisquilius (Linnaeus, 1761) (an adventive species of Paleartic origin) and C. nigriceps (Marshall, 1802) (an adventive species probably of Oriental origin). Cercyon armatipenis, C. gimmeli, C. taino form a group of closely related species only distinguishable by male genitalia and DNA sequences. A key to the Great Antillean Cercyon is provided and important diagnostic characters are illustrated. The larvae of C. insularis and C. taino were associated with adults using COI barcode sequences, illustrated and diagnosed. Full occurrence data, additional images and COI barcode sequences were submitted to open access on-line depositories in an effort to provide access to complete data.},
}
@article {pmid28769719,
year = {2017},
author = {Voigtländer, K and Iorio, E and Decker, P and Spelda, J},
title = {The subgenus Monotarsobius in the Iberian Peninsula with a description of a new pseudo-cryptic species from Northern Spain revealed by an integrative revision of Lithobius crassipes L. Koch, 1862 (Chilopoda, Lithobiomorpha, Lithobiidae).},
journal = {ZooKeys},
volume = {},
number = {681},
pages = {1-38},
pmid = {28769719},
issn = {1313-2989},
abstract = {The widespread European centipede species Lithobius (Monotarsobius) crassipes L. Koch, 1862 was revised using an integrative approach incorporating sequence data and morphology. The partial mitochondrial cytochrome c oxidase subunit I (COI) barcoding gene was amplified and sequenced for 21 individuals from northern Spain, France and Germany as well as for individuals of three other species of the subgenus Monotarsobius Verhoeff, 1905. The dataset was used for molecular phylogenetic analysis and genetic distance determination. In addition, Monotarsobius specimens from more than 100 localities in northern Spain, France, and Germany were morphologically investigated. Both morphological and molecular data indicate that specimens from the Navarre and Gipuzkoa provinces, northern Spain, represent a distinct pseudo-cryptic species, only differing in some minor characters from L. crassipes. The new species L. (Monotarsobius) crassipesoides sp. n. is described and compared to L. crassipes in detail using morphology and morphometric statistics for body, head, and antennae length, number of ocelli and coxal pores, as well as the starting leg for legpair spines Vmt and DaP. The Iberian and European records of L. crassipes are discussed. The subspecies L. crassipes morenoi Garcia Ruiz, 2014 from Southern Spain is elevated to species as L. morenoistat. n. A checklist, distribution map and key to all five species of Monotarsobius of the Iberian Peninsula are presented.},
}
@article {pmid28769712,
year = {2017},
author = {Lehmann, AW and Devriese, H and Tumbrinck, J and Skejo, J and Lehmann, GUC and Hochkirch, A},
title = {The importance of validated alpha taxonomy for phylogenetic and DNA barcoding studies: a comment on species identification of pygmy grasshoppers (Orthoptera, Tetrigidae).},
journal = {ZooKeys},
volume = {},
number = {679},
pages = {139-144},
pmid = {28769712},
issn = {1313-2989},
abstract = {In a recently published paper on colour polymorphism in a Pygmy grasshopper from China (Zhao et al 2016) an unidentified Paratettix sp. was misidentified as Tetrix bolivari. This case highlights the need for correct species identification and provides an opportunity to recommend some aspects of Good Taxonomic Practice (GTP) in Tetrigidae to reduce the number of erroneous identifications.},
}
@article {pmid28769709,
year = {2017},
author = {Ullah, M and Yang, Z and Qiao, P and Zhang, Y},
title = {A new cryptic species of Nagiella Munroe from China revealed by DNA barcodes and morphological evidence (Lepidoptera, Crambidae, Spilomelinae).},
journal = {ZooKeys},
volume = {},
number = {679},
pages = {65-76},
pmid = {28769709},
issn = {1313-2989},
abstract = {Nagiella occultalis Misbah &amp; Yang, sp. n. from China is described and illustrated. This new species is very similar to N. quadrimaculalis (Kollar, 1844) in general morphological characters of forewing and male genitalia. Molecular evidence shows that these two species diverge in COI barcode region by more than 3.2%. Sequence divergence among the two species is congruent with subtle morphological differences. Wing venation and male genitalia of the two species are compared and illustrated.},
}
@article {pmid28769662,
year = {2017},
author = {Liu, YQ and Gao, QS and Chen, HW},
title = {The genus Scaptodrosophila Duda part I: the brunnea species group from the Oriental Region, with morphological and molecular evidence (Diptera, Drosophilidae).},
journal = {ZooKeys},
volume = {},
number = {671},
pages = {87-118},
pmid = {28769662},
issn = {1313-2989},
abstract = {Seven new species of the Scaptodrosophila brunnea species group are described from east Asia: S. maculatasp. n., S. melanogastersp. n., S. nigricostatasp. n., S. nigripectasp. n., S. obscuratasp. n., S. protenipenissp. n. and S. rhinasp. n. Three known species, S. parabrunnea (Tsacas &amp; Chassagnard), S. pressobrunnea (Tsacas &amp; Chassagnard) and S. scutellimargo (Duda) are redescribed. A key to all the examined species in the brunnea group is provided. Species delimitations have been improved by integrating the DNA sequences with morphological information. The intra- and interspecific pairwise p-distances (proportional distance) are summarized. Some nucleotide sites with fixed status in the alignment of the COI sequences (664 nucleotide sites in length) are used as "pure" molecular diagnostic characters to delineate species in the brunnea group.},
}
@article {pmid28769654,
year = {2017},
author = {Cacciali, P and Martínez, N and Köhler, G},
title = {Revision of the phylogeny and chorology of the tribe Iphisini with the revalidation of Colobosaura kraepelini Werner, 1910 (Reptilia, Squamata, Gymnophthalmidae).},
journal = {ZooKeys},
volume = {},
number = {669},
pages = {89-105},
pmid = {28769654},
issn = {1313-2989},
abstract = {The family Gymnophthalmidae contains nearly 235 species with a distribution range from southern Mexico to central Argentina as well as in the Antilles. Among gymnophthalmids, the genus Colobosaura is a member of the tribe Iphisini, and currently is considered monotypic (C. modesta). The diversity of the tribe was studied recently, with the erection of several new genera. In this work genetic and morphological data of specimens of Colobosaura recently collected in Paraguay were analyzed. Genetic (16S barcode) data indicate that these samples are not conspecific with C. modesta and they are allocated to the nominal species C. kraepelini. Because the original primary type of the latter taxon is considered to be lost, a neotype (SMF 101370) is designated for this species and a redescription provided based on our material. Colobosaura kraepelini is distributed in the Humid Chaco, being the only member of the whole tribe in this ecoregion.},
}
@article {pmid28769640,
year = {2017},
author = {Palasio, RGS and Guimarães, MCA and Ohlweiler, FP and Tuan, R},
title = {Molecular and morphological identification of Biomphalaria species from the state of São Paulo, Brazil.},
journal = {ZooKeys},
volume = {},
number = {668},
pages = {11-32},
pmid = {28769640},
issn = {1313-2989},
abstract = {DNA barcoding and morphological characters were used to identify adult snails belonging to the genus Biomphalaria from 17 municipalities in the state of São Paulo, Brazil. The DNA barcode analysis also included twenty-nine sequences retrieved from GenBank. The final data set of 104 sequences of the mitochondrial cytochrome oxidase I (COI) gene was analyzed for K2P intraspecific and interspecific divergences, through tree-reconstruction methods (Neighbor-Joining, Maximum Likelihood and Bayesian inference), and by applying different models (ABGD, bPTP, GMYC) to partition the sequences according to the pattern of genetic variation. Twenty-seven morphological parameters of internal organs were used to identify specimens. The molecular taxonomy of Biomphalaria agreed with the morphological identification of specimens from the same collection locality. DNA barcoding may therefore be a useful supporting tool for identifying Biomphalaria snails in areas at risk for schistosomiasis.},
}
@article {pmid28769639,
year = {2017},
author = {Warren, AD and Grishin, NV},
title = {A new species of Oxynetra from Mexico (Hesperiidae, Pyrginae, Pyrrhopygini).},
journal = {ZooKeys},
volume = {},
number = {667},
pages = {155-164},
pmid = {28769639},
issn = {1313-2989},
abstract = {Oxynetra aureopectasp. n. is described from the Sierra Madre Oriental of east-central Mexico. Visually similar to Mesoamerican O. hopfferi Staudinger, 1888 in having five orange bands on the abdomen above, it is diagnosed by orange forecoxae and palpi beneath, narrower forewing hyaline bands and a prominent 6% difference in the COI DNA barcode sequence. It is the northernmost representative of the hopfferi species group that also includes O. stangelandi Grishin &amp; Burns, 2013, characterized by a single-banded abdomen and currently known only from the Area de Conservación Guanacaste in northwestern Costa Rica. Both O. hopfferi and O. stangelandi possess white forecoxae and ventral palpi. This new discovery brings the total number of Oxynetra C. &amp; R. Felder, 1862 species to five.},
}
@article {pmid28769630,
year = {2017},
author = {Yang, JH and Toda, MJ and Suwito, A and Hashim, R and Gao, JJ},
title = {A new species group in the genus Dichaetophora, with descriptions of six new species from the Oriental region (Diptera, Drosophilidae).},
journal = {ZooKeys},
volume = {},
number = {665},
pages = {121-146},
pmid = {28769630},
issn = {1313-2989},
abstract = {The genus Dichaetophora Duda comprises 61 described species classified into four species groups: agbo, tenuicauda, acutissima and sinensis. This genus is distributed exclusively in the Old World, and is rich in species in the tropical and subtropical areas of the Oriental, Australasian, and Afrotropical regions. In this paper, a new species group, the trilobita group, is established for six new species discovered from the Oriental region. The delimitation of these species is firstly performed in light of morphology and further with the aid of DNA sequences of the mitochondrial COI and COII (cytochrome c oxydase, subunits I and II, respectively) genes, considering also their respective geographical origins. Then, the new species (trilobita Yang &amp; Gao, sp. n., heterochroma Yang &amp; Gao, sp. n., flatosternata Yang &amp; Gao, sp. n., borneoensis Yang &amp; Gao, sp. n., javaensis Yang &amp; Gao, sp. n., and sumatraensis Yang &amp; Gao, sp. n.) are described, and a key, based on not only morphological but also molecular information, is provided.},
}
@article {pmid28769617,
year = {2017},
author = {Zhang, X and Zhao, Z and Zheng, G and Li, S},
title = {A survey of five Pireneitega species (Agelenidae, Coelotinae) from China.},
journal = {ZooKeys},
volume = {},
number = {663},
pages = {45-64},
pmid = {28769617},
issn = {1313-2989},
abstract = {Five species of Pireneitega spiders from China are surveyed, of which three are new to science: P. huashanensis Zhao &amp; Li, sp. n. (♂♀), P. lushuiensis Zhao &amp; Li, sp. n. (♂♀), P. xiyankouensis Zhao &amp; Li, sp. n. (♂♀). Two known species are redescribed: P. liansui (Bao &amp; Yin, 2004) and P. triglochinata (Zhu &amp; Wang, 1991). The males of P. liansui and P. triglochinata (Zhu &amp; Wang, 1991) are described for the first time. DNA barcodes for five species are documented for future use and as proof of molecular differences between species.},
}
@article {pmid28769614,
year = {2017},
author = {Ståhls, G and Barkalov, AV},
title = {Taxonomic review of the Palaearctic species of the Cheilosia caerulescens-group (Diptera, Syrphidae).},
journal = {ZooKeys},
volume = {},
number = {662},
pages = {137-171},
pmid = {28769614},
issn = {1313-2989},
abstract = {The Palaearctic species of the Cheilosia caerulescens group (Diptera: Syrphidae) are revised in this work. The species group belongs to the genus Cheilosia subgenus Taeniocheilosia Oldenberg. One new species is described from north Caucasus, Cheilosia (Taeniocheilosia) circassica sp. n.Cheilosia primulae Hering is established as a junior synonym of Cheilosia laeviventris Loew. Four lectotype designations are made. The species of the Cheilosia caerulescens group are redescribed and illustrated, and a table of diagnostic characters and an identification key to species are provided. MtDNA COI barcodes were generated for several specimens of C. (T.) caerulescens Meigen and other Cheilosia (Taeniocheilosia) and Cheilosia s. str. taxa. Parsimony and maximum likelihood analyses did not place the morphologically similar C. hercyniae Loew in the C. caerulescens group but among other Cheilosia (Taeniocheilosia) taxa. The following eight taxa are included in the Cheilosia (T.) caerulescens group of species: Cheilosia armeniaca Stackelberg, 1960, C. caerulescens caerulescens (Meigen, 1822), C. caerulescens calculosa Skufjin, 1977, C. circassica sp. n., C. herculana Brădescu, 1982, C. kerteszi Szilády, 1938, C. laeviventris Loew, 1857, and C. venosa Loew, 1857.},
}
@article {pmid28765814,
year = {2017},
author = {Li, Q and Xu, J and Han, L and Gao, C and Lu, J and Du, G and Sun, X},
title = {Evaluation of ITS2 for intraspecific identification of Paeonia lactiflora cultivars.},
journal = {Biotechnology reports (Amsterdam, Netherlands)},
volume = {15},
number = {},
pages = {101-106},
pmid = {28765814},
issn = {2215-017X},
abstract = {Herbaceous peony (Paeonia lactiflora Pall.) is an important ornamental and medicinal plant. DNA barcodes can reveal species identity via the nucleotide diversity of short DNA segments. In this study, two main candidate DNA barcodes (ITS2 and psbA-trnH) were tested to identify twenty-one cutting cultivars of P. lactiflora and their wild species. The efficacy of the candidate DNA barcodes was assessed by PCR amplification, sequence quality, sequence diversity, rate of correct identification, and phylogenetic analysis. ITS2 was easy to be amplified and sequenced among the samples. The identification by Blastn and phylogenetic analysis was 95.4% and 63.6%, respectively. For psbA-trnH, the presence of poly A-T led to sequencing failure which limited its use as DNA barcode candidate. Moreover, the authentic efficiency of psbA-trnH was lower than ITS2. The results showed that ITS2 is suitable as a candidate DNA barcode for the intraspecific identification of P. lactiflora cultivars.},
}
@article {pmid28765727,
year = {2017},
author = {Steinke, D and deWaard, JR and Gomon, MF and Johnson, JW and Larson, HK and Lucanus, O and Moore, GI and Reader, S and Ward, RD},
title = {DNA barcoding the fishes of Lizard Island (Great Barrier Reef).},
journal = {Biodiversity data journal},
volume = {},
number = {5},
pages = {e12409},
pmid = {28765727},
issn = {1314-2828},
}
@article {pmid28765722,
year = {2017},
author = {Amon, DJ and Ziegler, AF and Kremenetskaia, A and Mah, CL and Mooi, R and O'Hara, T and Pawson, DL and Roux, M and Smith, CR},
title = {Megafauna of the UKSRL exploration contract area and eastern Clarion-Clipperton Zone in the Pacific Ocean: Echinodermata.},
journal = {Biodiversity data journal},
volume = {},
number = {5},
pages = {e11794},
pmid = {28765722},
issn = {1314-2828},
abstract = {BACKGROUND: There is growing interest in mining polymetallic nodules from the abyssal Clarion-Clipperton Zone (CCZ) in the tropical Pacific Ocean. Despite being the focus of environmental studies for decades, the benthic megafauna of the CCZ remain poorly known. In order to predict and manage the environmental impacts of mining in the CCZ, baseline knowledge of the megafauna is essential. The ABYSSLINE Project has conducted benthic biological baseline surveys in the UK Seabed Resources Ltd polymetallic-nodule exploration contract area (UK-1). Prior to these research cruises in 2013 and 2015, no biological studies had been done in this area of the eastern CCZ.<br><br>NEW INFORMATION: Using a Remotely Operated Vehicle and Autonomous Underwater Vehicle, the megafauna within the UKSRL exploration contract area (UK-1) and at a site ~250 km east of the UK-1 area were surveyed, allowing us to make the first estimates of megafaunal morphospecies richness from the imagery collected. Here, we present an atlas of the abyssal echinoderm megafauna observed and collected during the ABYSSLINE cruises to the UK-1 polymetallic-nodule exploration contract area in the CCZ. There appear to be at least 62 distinct morphospecies (13 Asteroidea, 5 Crinoidea, 9 Echinoidea, 29 Holothuroidea and 6 Ophiuroidea) identified mostly by imagery but also using molecular barcoding for a limited number of animals that were collected. This atlas will aid the synthesis of megafaunal presence/absence data collected by contractors, scientists and other stakeholders undertaking work in the CCZ, ultimately helping to decipher the biogeography of the megafauna in this threatened habitat.},
}
@article {pmid28764816,
year = {2018},
author = {Kosoy, M and McKee, C and Albayrak, L and Fofanov, Y},
title = {Genotyping of Bartonella bacteria and their animal hosts: current status and perspectives.},
journal = {Parasitology},
volume = {145},
number = {5},
pages = {543-562},
doi = {10.1017/S0031182017001263},
pmid = {28764816},
issn = {1469-8161},
mesh = {Animals ; Arthropods ; Bartonella/classification/*genetics ; Genetic Variation ; *Genotyping Techniques ; Mammals ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Whole Genome Sequencing ; },
abstract = {Growing evidence demonstrates that bacterial species diversity is substantial, and many of these species are pathogenic in some contexts or hosts. At the same time, laboratories and museums have collected valuable animal tissue and ectoparasite samples that may contain substantial novel information on bacterial prevalence and diversity. However, the identification of bacterial species is challenging, partly due to the difficulty in culturing many microbes and the reliance on molecular data. Although the genomics revolution will surely add to our knowledge of bacterial systematics, these approaches are not accessible to all researchers and rely predominantly on cultured isolates. Thus, there is a need for comprehensive molecular analyses capable of accurately genotyping bacteria from animal tissues or ectoparasites using common methods that will facilitate large-scale comparisons of species diversity and prevalence. To illustrate the challenges of genotyping bacteria, we focus on the genus Bartonella, vector-borne bacteria common in mammals. We highlight the value and limitations of commonly used techniques for genotyping bartonellae and make recommendations for researchers interested in studying the diversity of these bacteria in various samples. Our recommendations could be applicable to many bacterial taxa (with some modifications) and could lead to a more complete understanding of bacterial species diversity.},
}
@article {pmid28763495,
year = {2017},
author = {Koroiva, R and Pepinelli, M and Rodrigues, ME and Roque, FO and Lorenz-Lemke, AP and Kvist, S},
title = {DNA barcoding of odonates from the Upper Plata basin: Database creation and genetic diversity estimation.},
journal = {PloS one},
volume = {12},
number = {8},
pages = {e0182283},
pmid = {28763495},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; Brazil ; *DNA Barcoding, Taxonomic ; *Databases, Genetic ; Electron Transport Complex IV/*genetics ; *Genetic Variation ; Geography ; Odonata/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {We present a DNA barcoding study of Neotropical odonates from the Upper Plata basin, Brazil. A total of 38 species were collected in a transition region of "Cerrado" and Atlantic Forest, both regarded as biological hotspots, and 130 cytochrome c oxidase subunit I (COI) barcodes were generated for the collected specimens. The distinct gap between intraspecific (0-2%) and interspecific variation (15% and above) in COI, and resulting separation of Barcode Index Numbers (BIN), allowed for successful identification of specimens in 94% of cases. The 6% fail rate was due to a shared BIN between two separate nominal species. DNA barcoding, based on COI, thus seems to be a reliable and efficient tool for identifying Neotropical odonate specimens down to the species level. These results underscore the utility of DNA barcoding to aid specimen identification in diverse biological hotspots, areas that require urgent action regarding taxonomic surveys and biodiversity conservation.},
}
@article {pmid28762205,
year = {2017},
author = {Weinmann, J and Grimm, D},
title = {Next-generation AAV vectors for clinical use: an ever-accelerating race.},
journal = {Virus genes},
volume = {53},
number = {5},
pages = {707-713},
pmid = {28762205},
issn = {1572-994X},
support = {SFB1129 - TP2//Deutsche Forschungsgemeinschaft/ ; TRR179 - TP18//Deutsche Forschungsgemeinschaft/ ; Cluster of Excellence CellNetworks EXC81//Deutsche Forschungsgemeinschaft/ ; 667751 - MYOCURE//Horizon 2020 Framework Programme/ ; Smart-HaemoCare//E-Rare JTC 2015/ ; },
mesh = {Animals ; Capsid/physiology ; Capsid Proteins/genetics ; Dependovirus/*genetics ; Gene Library ; Genetic Therapy/methods ; Genetic Vectors/*genetics ; Humans ; },
abstract = {During the past five decades, it has become evident that Adeno-associated virus (AAV) represents one of the most potent, most versatile, and thus most auspicious platforms available for gene delivery into cells, animals and, ultimately, humans. Particularly attractive is the ease with which the viral capsid-the major determinant of virus-host interaction including cell specificity and antibody recognition-can be modified and optimized at will. This has motivated countless researchers to develop high-throughput technologies in which genetically engineered AAV capsid libraries are subjected to a vastly hastened emulation of natural evolution, with the aim to enrich novel synthetic AAV capsids displaying superior features for clinical application. While the power and potential of these forward genetics approaches is undisputed, they are also inherently challenging as success depends on a combination of library quality, fidelity, and complexity. Here, we will describe and discuss two original, very exciting strategies that have emerged over the last three years and that promise to alleviate at least some of these concerns, namely, (i) a reverse genetics approach termed "ancestral AAV sequence reconstruction," and (ii) AAV genome barcoding as a technology that can advance both, forward and reverse genetics stratagems. Notably, despite the conceptual differences of these two technologies, they pursue the same goal which is tailored acceleration of AAV evolution and thus winning the race for the next-generation AAV vectors for clinical use.},
}
@article {pmid28761780,
year = {2017},
author = {Yusseff-Vanegas, SZ and Agnarsson, I},
title = {DNA-barcoding of forensically important blow flies (Diptera: Calliphoridae) in the Caribbean Region.},
journal = {PeerJ},
volume = {5},
number = {},
pages = {e3516},
pmid = {28761780},
issn = {2167-8359},
abstract = {Correct identification of forensically important insects, such as flies in the family Calliphoridae, is a crucial step for them to be used as evidence in legal investigations. Traditional identification based on morphology has been effective, but has some limitations when it comes to identifying immature stages of certain species. DNA-barcoding, using COI, has demonstrated potential for rapid and accurate identification of Calliphoridae, however, this gene does not reliably distinguish among some recently diverged species, raising questions about its use for delimitation of species of forensic importance. To facilitate DNA based identification of Calliphoridae in the Caribbean we developed a vouchered reference collection from across the region, and a DNA sequence database, and further added the nuclear ITS2 as a second marker to increase accuracy of identification through barcoding. We morphologically identified freshly collected specimens, did phylogenetic analyses and employed several species delimitation methods for a total of 468 individuals representing 19 described species. Our results show that combination of COI + ITS2 genes yields more accurate identification and diagnoses, and better agreement with morphological data, than the mitochondrial barcodes alone. All of our results from independent and concatenated trees and most of the species delimitation methods yield considerably higher diversity estimates than the distance based approach and morphology. Molecular data support at least 24 distinct clades within Calliphoridae in this study, recovering substantial geographic variation for Lucilia eximia, Lucilia retroversa, Lucilia rica and Chloroprocta idioidea, probably indicating several cryptic species. In sum, our study demonstrates the importance of employing a second nuclear marker for barcoding analyses and species delimitation of calliphorids, and the power of molecular data in combination with a complete reference database to enable identification of taxonomically and geographically diverse insects of forensic importance.},
}
@article {pmid28761482,
year = {2017},
author = {Daneshparvar, A and Mowlavi, G and Mirjalali, H and Hajjaran, H and Mobedi, I and Naddaf, SR and Shidfar, M and Sadat Makki, M},
title = {Molecular Characterization and Analysis of 16S Ribosomal DNA in Some Isolates of Demodex folicullorum.},
journal = {Iranian journal of parasitology},
volume = {12},
number = {2},
pages = {224-229},
pmid = {28761482},
issn = {1735-7020},
abstract = {BACKGROUND: Demodicosis is one of the most prevalent skin diseases resulting from infestation by Demodex mites. This parasite usually inhabits in follicular infundibulum or sebaceous duct and transmits through close contact with an infested host.<br><br>METHODS: This study was carried from September 2014 to January 2016 at Tehran University of Medical Sciences, Tehran, Iran. DNA extraction and amplification of 16S ribosomal RNA was performed on four isolates, already obtained from four different patients and identified morphologically though clearing with 10% Potassium hydroxide (KOH) and microscopical examination. Amplified fragments from the isolates were compared with GeneBank database and phylogenetic analysis was carried out using MEGA6 software.<br><br>RESULTS: A 390 bp fragment of 16S rDNA was obtained in all isolates and analysis of generated sequences showed high similarity with those submitted to GenBank, previously. Intra-species similarity and distance also showed 99.983% and 0.017, respectively, for the studied isolates. Multiple alignments of the isolates showed Single Nucleotide Polymorphisms (SNPs) in 16S rRNA fragment. Phylogenetic analysis revealed that all 4 isolates clustered with other D. folliculorum, recovered from GenBank database. Our accession numbers KF875587 and KF875589 showed more similarity together in comparison with two other studied isolates.<br><br>CONCLUSION: Mitochondrial 16S rDNA is one of the most suitable molecular barcodes for identification D. folliculorum and this fragment can use for intra-species characterization of the most human-infected mites.},
}
@article {pmid28758818,
year = {2018},
author = {Manger, A and Behere, GT and Firake, DM and Sharma, B and Deshmukh, NA and Firake, PD and Azad Thakur, NS and Ngachan, SV},
title = {Genetic characterization of Bactrocera fruit flies (Diptera: Tephritidae) from Northeastern India based on DNA barcodes.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {792-799},
doi = {10.1080/24701394.2017.1357713},
pmid = {28758818},
issn = {2470-1408},
mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Speciation ; Genome, Mitochondrial/genetics ; India ; Mitochondria/genetics ; Perciformes/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Tephritidae/*genetics ; },
abstract = {The Northeastern region of India, one of the mega biodiversity hot spots has enormous potential for the production of fruits and vegetables. Fruit flies of the genus Bactrocera Macquart are important pests of fruits and vegetables, and one of the limiting factors in successful production of these commodities. The relationship among some of the species is unclear due to their high molecular and morphological similarities. Moreover, due to the significant morphological resemblance between fruit fly species, reliable identification is very difficult task. We genetically characterized 10 fruit fly species of the genus Bactrocera by using standard DNA barcoding region of COI gene. The characterization and identification of eight species were straight forward. This study was unable to establish the molecular identity of Bactrocera sp. 2. Within the 547 bp region of partial COI gene, there were 157 variable sites of which 110 sites were parsimony informative, 153 were synonymous substitutions and 4 were non-synonymous substitutions. The estimate of genetic divergence among the ten species was in the range of 0-21.9% and the pairwise genetic distance of Bactrocera. (Bactrocera) dorsalis (Hendel) with B. (B.) carambolae was only 0.7%. Phylogenetic analysis formed separate clades for fruit and vegetable infesting fruit flies. B. (B.) aethriobasis Hardy, B. (B.) thailandica and B. (B.) tuberculata (Bezzi) have been reported for the first time from the Northeastern India. The information generated from this study would certainly have implications for pest management, taxonomy, quarantine and trade.},
}
@article {pmid28757445,
year = {2017},
author = {Scheffer, SJ and Davies, KA and Taylor, GS and Thornhill, AH and Lewis, ML and Winkler, IS and Yeates, DK and Purcell, MF and Makinson, J and Giblin-Davis, RM},
title = {Phylogenetics of Australasian gall flies (Diptera: Fergusoninidae): Evolutionary patterns of host-shifting and gall morphology.},
journal = {Molecular phylogenetics and evolution},
volume = {115},
number = {},
pages = {140-160},
doi = {10.1016/j.ympev.2017.07.023},
pmid = {28757445},
issn = {1095-9513},
mesh = {Animals ; Australia ; Biological Evolution ; Diptera/*classification/genetics ; Electron Transport Complex IV/classification/genetics ; Genetic Variation ; Host Specificity ; Host-Parasite Interactions/physiology ; Myrtaceae/anatomy &amp; histology/metabolism ; Phylogeny ; Plant Tumors/*classification ; },
abstract = {This study investigated host-specificity and phylogenetic relationships in Australian galling flies, Fergusonina Malloch (Diptera: Fergusoninidae), in order to assess diversity and explore the evolutionary history of host plant affiliation and gall morphology. A DNA barcoding approach using COI data from 203 Fergusonina specimens from 5gall types on 56 host plant species indicated 85 presumptive fly species. These exhibited a high degree of host specificity; of the 40 species with multiple representatives, each fed only on a single host genus, 29 (72.5%) were strictly monophagous, and 11 (27.5%) were reared from multiple closely related hosts. COI variation within species was not correlated with either sample size or geographic distance. However variation was greater within oligophagous species, consistent with expectations of the initial stages of host-associated divergence during speciation. Phylogenetic analysis using both nuclear and mitochondrial genes revealed host genus-restricted clades but also clear evidence of multiple colonizations of both host plant genus and host species. With the exception of unilocular peagalls, evolution of gall type was somewhat constrained, but to a lesser degree than host plant association. Unilocular peagalls arose more often than any other gall type, were primarily located at the tips of the phylogeny, and did not form clades comprising more than a few species. For ecological reasons, species of this gall type are predicted to harbor substantially less genetic variation than others, possibly reducing evolutionary flexibility resulting in reduced diversification in unilocular gallers.},
}
@article {pmid28754835,
year = {2017},
author = {Bortolotti, F and Ruozi, G and Falcione, A and Doimo, S and Dal Ferro, M and Lesizza, P and Zentilin, L and Banks, L and Zacchigna, S and Giacca, M},
title = {In Vivo Functional Selection Identifies Cardiotrophin-1 as a Cardiac Engraftment Factor for Mesenchymal Stromal Cells.},
journal = {Circulation},
volume = {136},
number = {16},
pages = {1509-1524},
doi = {10.1161/CIRCULATIONAHA.117.029003},
pmid = {28754835},
issn = {1524-4539},
mesh = {Animals ; Apoptosis ; Cell Adhesion ; Cell Proliferation ; Cell Survival ; Cells, Cultured ; Cytokines/genetics/*metabolism ; Dependovirus/genetics ; Disease Models, Animal ; Focal Adhesion Kinase 1/metabolism ; Gene Library ; Genetic Vectors ; Graft Survival ; Male ; *Mesenchymal Stem Cell Transplantation ; Mesenchymal Stem Cells/*metabolism ; Mice, Inbred C57BL ; Myocardial Contraction ; Myocardial Infarction/genetics/metabolism/pathology/*surgery ; Myocardium/*metabolism/pathology ; Recovery of Function ; *Regeneration ; STAT3 Transcription Factor/metabolism ; Signal Transduction ; Time Factors ; Transduction, Genetic ; Transfection/methods ; },
abstract = {BACKGROUND: Transplantation of cells into the infarcted heart has significant potential to improve myocardial recovery; however, low efficacy of cell engraftment still limits therapeutic benefit. Here, we describe a method for the unbiased, in vivo selection of cytokines that improve mesenchymal stromal cell engraftment into the heart both in normal conditions and after myocardial infarction.<br><br>METHODS: An arrayed library of 80 secreted factors, including most of the currently known interleukins and chemokines, were individually cloned into adeno-associated viral vectors. Pools from this library were then used for the batch transduction of bone marrow-derived mesenchymal stromal cells ex vivo, followed by intramyocardial cell administration in normal and infarcted mice. Three weeks after injection, vector genomes were recovered from the few persisting cells and identified by sequencing DNA barcodes uniquely labeling each of the tested cytokines.<br><br>RESULTS: The most effective molecule identified by this competitive engraftment screening was cardiotrophin-1, a member of the interleukin-6 family. Intracardiac injection of mesenchymal stromal cells transiently preconditioned with cardiotrophin-1 preserved cardiac function and reduced infarct size, parallel to the persistence of the transplanted cells in the healing hearts for at least 2 months after injection. Engraftment of cardiotrophin-1-treated mesenchymal stromal cells was consequent to signal transducer and activator of transcription 3-mediated activation of the focal adhesion kinase and its associated focal adhesion complex and the consequent acquisition of adhesive properties by the cells.<br><br>CONCLUSIONS: These results support the feasibility of selecting molecules in vivo for their functional properties with adeno-associated viral vector libraries and identify cardiotrophin-1 as a powerful cytokine promoting cell engraftment and thus improving cell therapy of the infarcted myocardium.},
}
@article {pmid28753409,
year = {2017},
author = {Vierna, J and Doña, J and Vizcaíno, A and Serrano, D and Jovani, R},
title = {PCR cycles above routine numbers do not compromise high-throughput DNA barcoding results.},
journal = {Genome},
volume = {60},
number = {10},
pages = {868-873},
doi = {10.1139/gen-2017-0081},
pmid = {28753409},
issn = {1480-3321},
mesh = {Animals ; Cephalopoda/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; *Mutation ; Polymerase Chain Reaction/*methods ; },
abstract = {High-throughput DNA barcoding has become essential in ecology and evolution, but some technical questions still remain. Increasing the number of PCR cycles above the routine 20-30 cycles is a common practice when working with old-type specimens, which provide little amounts of DNA, or when facing annealing issues with the primers. However, increasing the number of cycles can raise the number of artificial mutations due to polymerase errors. In this work, we sequenced 20 COI libraries in the Illumina MiSeq platform. Libraries were prepared with 40, 45, 50, 55, and 60 PCR cycles from four individuals belonging to four species of four genera of cephalopods. We found no relationship between the number of PCR cycles and the number of mutations despite using a nonproofreading polymerase. Moreover, even when using a high number of PCR cycles, the resulting number of mutations was low enough not to be an issue in the context of high-throughput DNA barcoding (but may still remain an issue in DNA metabarcoding due to chimera formation). We conclude that the common practice of increasing the number of PCR cycles should not negatively impact the outcome of a high-throughput DNA barcoding study in terms of the occurrence of point mutations.},
}
@article {pmid28752775,
year = {2018},
author = {Wang, ZD and Liao, J and Huang, CQ and Long, SS and Zhang, S and Guo, YS and Liu, L and Liu, CW},
title = {Significant genetic differentiation of Gobiopterus lacustris, a newly recorded transparent goby in China.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {785-791},
doi = {10.1080/24701394.2017.1357712},
pmid = {28752775},
issn = {2470-1408},
mesh = {Animals ; China ; Cyclooxygenase 1/*genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/genetics ; Gene Flow ; Genetic Drift ; Genetic Variation/genetics ; Genetics, Population ; Genome, Mitochondrial/genetics ; Haplotypes ; Mitochondria/genetics ; Perciformes/*genetics ; Phenotype ; Philippines ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/methods ; },
abstract = {In our recent survey, the transparent small Lacustrine goby, Gobiopterus lacustris had reported as the endemic species of Luzon, Philippines, was identified as an abundant species in mangroves of Leizhou Peninsula, China. Here, high diversity and significant differentiation of five sites of samples representing the west and east populations were revealed by mitochondrial DNA sequences. Five haplotypes of 56 cytochrome oxidase subunit I (Cox1) with the lengths of 623 base pairs (bp) have the high pairwise identity (>98.8%). Moreover, a total of 31 haplotypes for 129 partial D-loop regions were clustered into two clades corresponding to the east and west sampling sites. The strong population structure was confirmed (ΦST = 0.43017, p < .0001) with high haplotype diversity (h = 0.880 ± 0.017) and low nucleotide diversity (p=.00484). Moreover, both the mismatch distribution analysis and neutral test of D-loop revealed that the west group might experience a recent demographic expansion. Lastly, the isolation-with-migration analysis supported the expansion and indicated that the east-west split happened at approximately 7.1 kyr ago. Given the distribution and diversity, G. lacustris could be a good model for the study of the sea-level fluctuations and coast evolution of the South China Sea.},
}
@article {pmid28752773,
year = {2018},
author = {Koroiva, R and Kvist, S},
title = {Estimating the barcoding gap in a global dataset of cox1 sequences for Odonata: close, but no cigar.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {765-771},
doi = {10.1080/24701394.2017.1357709},
pmid = {28752773},
issn = {2470-1408},
mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Speciation ; Genetic Variation ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Odonata/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {We evaluated the extent of intraspecific and interspecific genetic distances for two highly diverse infraorders of Odonata: Anisoptera and Zygoptera. All cytochrome c oxidase subunit I sequences (cox1), the region chosen for zoological DNA barcoding, present in GenBank for each infraorder were downloaded and curated. For Anisoptera, the final dataset consisted of 2,961 individual cox1 sequences for 536 species and the equivalent numbers for Zygoptera were 2,477 sequences for 497 species. More than 7 million individual genetic comparisons were made and the results indicated that there is a tendency towards a barcoding gap, but that the size of the gap may not be sufficient to robustly infer identities for some taxa. DNA barcoding may be of less use for some odonate taxa, perhaps pertaining to misidentifications in global databases. However, at local scales or with more confined taxonomical sampling, this tool may yet be beneficial in identifying these charismatic organisms.},
}
@article {pmid28748632,
year = {2017},
author = {Martínez-DE LA Puente, J and Navarro, J and Ferraguti, M and Soriguer, R and Figuerola, J},
title = {First molecular identification of the vertebrate hosts of Culicoides imicola in Europe and a review of its blood-feeding patterns worldwide: implications for the transmission of bluetongue disease and African horse sickness.},
journal = {Medical and veterinary entomology},
volume = {31},
number = {4},
pages = {333-339},
doi = {10.1111/mve.12247},
pmid = {28748632},
issn = {1365-2915},
mesh = {African Horse Sickness/*transmission ; Animals ; Bluetongue/*transmission ; Ceratopogonidae/genetics/*physiology ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Feeding Behavior ; Female ; Insect Proteins/genetics ; Sequence Analysis, DNA ; Spain ; },
abstract = {Culicoides (Diptera: Ceratopogonidae) are vectors of pathogens that affect wildlife, livestock and, occasionally, humans. Culicoides imicola (Kieffer, 1913) is considered to be the main vector of the pathogens that cause bluetongue disease (BT) and African horse sickness (AHS) in southern Europe. The study of blood-feeding patterns in Culicoides is an essential step towards understanding the epidemiology of these pathogens. Molecular tools that increase the accuracy and sensitivity of traditional methods have been developed to identify the hosts of potential insect vectors. However, to the present group's knowledge, molecular studies that identify the hosts of C. imicola in Europe are lacking. The present study genetically characterizes the barcoding region of C. imicola trapped on farms in southern Spain and identifies its vertebrate hosts in the area. The report also reviews available information on the blood-feeding patterns of C. imicola worldwide. Culicoides imicola from Spain feed on blood of six mammals that include species known to be hosts of the BT and AHS viruses. This study provides evidence of the importance of livestock as sources of bloodmeals for C. imicola and the relevance of this species in the transmission of BT and AHS viruses in Europe.},
}
@article {pmid28747591,
year = {2017},
author = {Duan, Z and Song, W and Chen, K and Qiao, X and Ye, M},
title = {Assessment of Genetic and Chemical Variability in Curcumae Longae Rhizoma (Curcuma longa) Based on DNA Barcoding Markers and HPLC Fingerprints.},
journal = {Biological &amp; pharmaceutical bulletin},
volume = {40},
number = {10},
pages = {1638-1645},
doi = {10.1248/bpb.b17-00020},
pmid = {28747591},
issn = {1347-5215},
mesh = {Chromatography, High Pressure Liquid/methods ; Cluster Analysis ; Curcuma/*chemistry/*genetics ; *DNA Barcoding, Taxonomic ; Drugs, Chinese Herbal/chemistry ; Plant Extracts/chemistry/genetics ; Rhizome/chemistry/genetics ; },
abstract = {Curcumae Longae Rhizoma (Curcuma longa L.) is an important traditional Chinese medicine with multiple beneficial effects. To elucidate the genetic and chemical differences among Curcumae Longae Rhizoma samples, three DNA barcoding markers (rbcL, matK, and ITS-LSU D1/D3) and HPLC fingerprinting were employed in this study. The discriminatory power of rbcL and matK was low, as they only detected one sequence type that showed 100% similarity with more than 20 congeneric species in the Barcode of Life Data Systems (BOLD) database. In contrast, ITS-LSU D1/D3 showed sufficient discriminatory power to precisely identify all of the market samples as C. longa L. in a BLAST search as well as differentiate each sample based on 2-10 ITS-LSU D1/D3 haplotypes with intragenomic variability (mean p-distance: 0.7%, range: 0-2.6%; mean number of differences: 9.6 sites, range: 0-38 sites). HPLC fingerprinting of 13 commercial samples showed a similarity that ranged from 0.769 to 0.996, indicating that the sample quality varied. A cluster analysis based on 5 common peak areas from the HPLC chromatogram resulted in two groups. Group I included 9 samples with a relatively high chemical content, and group II contained 4 samples with a low chemical content. A Mantel test revealed a low correlation (r=0.1721, p=0.047) between genetic and chemical differences. Our findings suggest that the integrated approach of ITS-LSU D1/D3 DNA barcoding and HPLC fingerprinting provides a comprehensive, precise, and convenient method to clarify the genetic and chemical differences in Curcumae Longae Rhizoma.},
}
@article {pmid28747472,
year = {2017},
author = {Wang, C and Zhang, T and Wang, Y and Katz, LA and Gao, F and Song, W},
title = {Disentangling sources of variation in SSU rDNA sequences from single cell analyses of ciliates: impact of copy number variation and experimental error.},
journal = {Proceedings. Biological sciences},
volume = {284},
number = {1859},
pages = {},
pmid = {28747472},
issn = {1471-2954},
support = {R15 GM113177/GM/NIGMS NIH HHS/United States ; },
mesh = {Ciliophora/*genetics ; *DNA Copy Number Variations ; DNA, Ribosomal/*genetics ; Phylogeny ; Scientific Experimental Error ; Single-Cell Analysis ; },
abstract = {Small subunit ribosomal DNA (SSU rDNA) is widely used for phylogenetic inference, barcoding and other taxonomy-based analyses. Recent studies indicate that SSU rDNA of ciliates may have a high level of sequence variation within a single cell, which impacts the interpretation of rDNA-based surveys. However, sequence variation can come from a variety of sources including experimental errors, especially the mutations generated by DNA polymerase in PCR. In the present study, we explore the impact of four DNA polymerases on sequence variation and find that low-fidelity polymerases exaggerate the estimates of single-cell sequence variation. Therefore, using a polymerase with high fidelity is essential for surveys of sequence variation. Another source of variation results from errors during amplification of SSU rDNA within the polyploidy somatic macronuclei of ciliates. To investigate further the impact of SSU rDNA copy number variation, we use a high-fidelity polymerase to examine the intra-individual SSU rDNA polymorphism in ciliates with varying levels of macronuclear amplification: Halteria grandinella, Blepharisma americanum and Strombidium stylifer We estimate the rDNA copy numbers of these three species by single-cell quantitative PCR. The results indicate that: (i) sequence variation of SSU rDNA within a single cell is authentic in ciliates, but the level of intra-individual SSU rDNA polymorphism varies greatly among species; (ii) rDNA copy numbers vary greatly among species, even those within the same class; (iii) the average rDNA copy number of Halteria grandinella is about 567 893 (s.d. = 165 481), which is the highest record of rDNA copy number in ciliates to date; and (iv) based on our data and the records from previous studies, it is not always true in ciliates that rDNA copy numbers are positively correlated with cell or genome size.},
}
@article {pmid28744301,
year = {2017},
author = {Li, L and Josef, BA and Liu, B and Zheng, S and Huang, L and Chen, S},
title = {Three-Dimensional Evaluation on Ecotypic Diversity of Traditional Chinese Medicine: A Case Study of Artemisia annua L.},
journal = {Frontiers in plant science},
volume = {8},
number = {},
pages = {1225},
pmid = {28744301},
issn = {1664-462X},
abstract = {Artemisinin is the first-line drug for anti-malaria recommended by the World Health Organization (WHO). As the sole natural plant source of artemisinin, ecotypes of Artemisia annua L. vary widely in artemisinin content between nations, and China is the main producing area of A. annua. Here we present a three-dimensional evaluation on ecotypic diversity of A. annua from 12 main producing areas in China using high-performance liquid chromatography coupled with evaporative light scattering detection (HPLC-ELSD) method, DNA barcoding and ecological analyses. The results indicated that A. annua exhibited high ecotypic diversity. A. annua grown in the South of the Qinling Mountains-Huaihe River Line had a high artemisinin content, whereas the northern ones were low. Similar pattern was noted in the genetic diversity. The southern A. annua had high intraspecific variation in contrast to the northern A. annua. In terms of ecological analyses, humidity and sunshine time could be the major limiting ecological factors that affect the accumulation of artemisinin. This is the first reported three-dimensional evaluation integrating chemical, molecular and ecological analyses of the ecotypic diversity of A. annua. The work will facilitate exploring the genetic basis of chemical variations and developing strategies for the breeding and cultivation of high quality A. annua.},
}
@article {pmid28743954,
year = {2017},
author = {Alamaru, A and Hoeksema, BW and van der Meij, SET and Huchon, D},
title = {Molecular diversity of benthic ctenophores (Coeloplanidae).},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {6365},
pmid = {28743954},
issn = {2045-2322},
mesh = {Animals ; Ctenophora/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; *Genetic Markers ; Genetic Variation ; Indian Ocean ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; },
abstract = {Coeloplanidae, the largest family of benthic ctenophores, comprises 33 species, all described based on traditional morphological characteristics, such as coloration, length, and number of aboral papillae, which are highly variable and can be affected by fixation methods and environmental conditions. Thus, there is a need for reliable genetic markers to complement the morphological identifications at the species level. Here, we analyzed 95 specimens from 11 morphologically distinct species of benthic ctenophores from the Red Sea and Sulu Sea, and tested selected regions of four genetic markers (ITS1, 18S rRNA, 28S rRNA and COI) for their ability to differentiate between species. We show that the barcoding region of the mitochondrial gene, cytochrome oxidase subunit I (COI), is highly variable among species of Coeloplanidae, and effectively discriminates between species in this family. The average Kimura-2-parameter (K2P) distance between species-level clades was 10%, while intraspecific variation was ~30 times lower (0.36%). COI-based phylogeny supported the delineation of four recently described new species from the Red Sea. The other nuclear markers tested were found to be too conserved in order to separate between species. We conclude that COI is a potential molecular barcode for the family Coeloplanidae and suggest to test it in pelagic ctenophores.},
}
@article {pmid28743946,
year = {2017},
author = {Leung, LM and Fondrie, WE and Doi, Y and Johnson, JK and Strickland, DK and Ernst, RK and Goodlett, DR},
title = {Identification of the ESKAPE pathogens by mass spectrometric analysis of microbial membrane glycolipids.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {6403},
pmid = {28743946},
issn = {2045-2322},
support = {R01 AI104895/AI/NIAID NIH HHS/United States ; T32 HL007698/HL/NHLBI NIH HHS/United States ; R35 HL135743/HL/NHLBI NIH HHS/United States ; R01 GM111066/GM/NIGMS NIH HHS/United States ; R21 AI123747/AI/NIAID NIH HHS/United States ; R01 HL120388/HL/NHLBI NIH HHS/United States ; },
mesh = {Blood/microbiology ; Drug Resistance, Bacterial ; Glycolipids/*analysis/isolation &amp; purification ; Gram-Negative Bacteria/*chemistry/drug effects/isolation &amp; purification ; Gram-Positive Bacteria/*chemistry/drug effects/isolation &amp; purification ; Humans ; Limit of Detection ; Membrane Lipids/*analysis/isolation &amp; purification ; Reproducibility of Results ; Software ; Species Specificity ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; },
abstract = {Rapid diagnostics that enable identification of infectious agents improve patient outcomes, antimicrobial stewardship, and length of hospital stay. Current methods for pathogen detection in the clinical laboratory include biological culture, nucleic acid amplification, ribosomal protein characterization, and genome sequencing. Pathogen identification from single colonies by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis of high abundance proteins is gaining popularity in clinical laboratories. Here, we present a novel and complementary approach that utilizes essential microbial glycolipids as chemical fingerprints for identification of individual bacterial species. Gram-positive and negative bacterial glycolipids were extracted using a single optimized protocol. Extracts of the clinically significant ESKAPE pathogens: E nterococcus faecium, S taphylococcus aureus, K lebsiella pneumoniae, A cinetobacter baumannii, P seudomonas aeruginosa, and E nterobacter spp. were analyzed by MALDI-TOF-MS in negative ion mode to obtain glycolipid mass spectra. A library of glycolipid mass spectra from 50 microbial entries was developed that allowed bacterial speciation of the ESKAPE pathogens, as well as identification of pathogens directly from blood bottles without culture on solid medium and determination of antimicrobial peptide resistance. These results demonstrate that bacterial glycolipid mass spectra represent chemical barcodes that identify pathogens, potentially providing a useful alternative to existing diagnostics.},
}
@article {pmid28743640,
year = {2017},
author = {Rubinstein, R and Goodman, KM and Maniatis, T and Shapiro, L and Honig, B},
title = {Structural origins of clustered protocadherin-mediated neuronal barcoding.},
journal = {Seminars in cell &amp; developmental biology},
volume = {69},
number = {},
pages = {140-150},
pmid = {28743640},
issn = {1096-3634},
support = {R01 GM062270/GM/NIGMS NIH HHS/United States ; R01 NS043915/NS/NINDS NIH HHS/United States ; R01 GM107571/GM/NIGMS NIH HHS/United States ; R01 NS088476/NS/NINDS NIH HHS/United States ; R01 MH114817/MH/NIMH NIH HHS/United States ; S10 OD012351/OD/NIH HHS/United States ; S10 OD021764/OD/NIH HHS/United States ; },
mesh = {Animals ; Cadherins/*chemistry/*metabolism ; Humans ; Models, Molecular ; Neurons/*metabolism ; Phylogeny ; Protein Multimerization ; Structure-Activity Relationship ; },
abstract = {Clustered protocadherins mediate neuronal self-recognition and non-self discrimination-neuronal "barcoding"-which underpin neuronal self-avoidance in vertebrate neurons. Recent structural, biophysical, computational, and cell-based studies on protocadherin structure and function have led to a compelling molecular model for the barcoding mechanism. Protocadherin isoforms assemble into promiscuous cis-dimeric recognition units and mediate cell-cell recognition through homophilic trans-interactions. Each recognition unit is composed of two arms extending from the membrane proximal EC6 domains. A cis-dimeric recognition unit with each arm coding adhesive trans homophilic specificity can generate a zipper-like assembly that in turn suggests a chain termination mechanism for self-vs-non-self-discrimination among vertebrate neurons.},
}
@article {pmid28742835,
year = {2017},
author = {Lim, VC and Ramli, R and Bhassu, S and Wilson, JJ},
title = {A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library.},
journal = {PloS one},
volume = {12},
number = {7},
pages = {e0179555},
pmid = {28742835},
issn = {1932-6203},
mesh = {Animals ; Chiroptera/classification/*genetics ; DNA/*genetics ; *DNA Barcoding, Taxonomic ; Female ; Gene Library ; Malaysia ; Male ; Phylogeny ; },
abstract = {Several published checklists of bat species have covered Peninsular Malaysia as part of a broader region and/or in combination with other mammal groups. Other researchers have produced comprehensive checklists for specific localities within the peninsula. To our knowledge, a comprehensive checklist of bats specifically for the entire geopolitical region of Peninsular Malaysia has never been published, yet knowing which species are present in Peninsular Malaysia and their distributions across the region are crucial in developing suitable conservation plans. Our literature search revealed that 110 bat species have been documented in Peninsular Malaysia; 105 species have precise locality records while five species lack recent and/or precise locality records. We retrieved 18 species from records dated before the year 2000 and seven species have only ever been recorded once. Our search of Barcode of Life Datasystems (BOLD) found that 86 (of the 110) species have public records of which 48 species have public DNA barcodes available from bats sampled in Peninsular Malaysia. Based on Neighbour-Joining tree analyses and the allocation of DNA barcodes to Barcode Index Number system (BINs) by BOLD, several DNA barcodes recorded under the same species name are likely to represent distinct taxa. We discuss these cases in detail and highlight the importance of further surveys to determine the occurences and resolve the taxonomy of particular bat species in Peninsular Malaysia, with implications for conservation priorities.},
}
@article {pmid28742772,
year = {2017},
author = {Lobaugh, LMY and Martin, LD and Schleelein, LE and Tyler, DC and Litman, RS},
title = {Medication Errors in Pediatric Anesthesia: A Report From the Wake Up Safe Quality Improvement Initiative.},
journal = {Anesthesia and analgesia},
volume = {125},
number = {3},
pages = {936-942},
doi = {10.1213/ANE.0000000000002279},
pmid = {28742772},
issn = {1526-7598},
mesh = {Adverse Drug Reaction Reporting Systems/standards/trends ; Anesthesia/adverse effects/*standards/trends ; Databases, Factual/*standards/trends ; Humans ; Medication Errors/*prevention &amp; control/trends ; Pediatrics/*standards/trends ; Quality Improvement/*standards/trends ; Research Report/*standards/trends ; *Wakefulness ; },
abstract = {BACKGROUND: Wake Up Safe is a quality improvement initiative of the Society for Pediatric Anesthesia that contains a deidentified registry of serious adverse events occurring in pediatric anesthesia. The aim of this study was to describe and characterize reported medication errors to find common patterns amenable to preventative strategies.<br><br>METHODS: In September 2016, we analyzed approximately 6 years' worth of medication error events reported to Wake Up Safe. Medication errors were classified by: (1) medication category; (2) error type by phase of administration: prescribing, preparation, or administration; (3) bolus or infusion error; (4) provider type and level of training; (5) harm as defined by the National Coordinating Council for Medication Error Reporting and Prevention; and (6) perceived preventability.<br><br>RESULTS: From 2010 to the time of our data analysis in September 2016, 32 institutions had joined and submitted data on 2087 adverse events during 2,316,635 anesthetics. These reports contained details of 276 medication errors, which comprised the third highest category of events behind cardiac and respiratory related events. Medication errors most commonly involved opioids and sedative/hypnotics. When categorized by phase of handling, 30 events occurred during preparation, 67 during prescribing, and 179 during administration. The most common error type was accidental administration of the wrong dose (N = 84), followed by syringe swap (accidental administration of the wrong syringe, N = 49). Fifty-seven (21%) reported medication errors involved medications prepared as infusions as opposed to 1 time bolus administrations. Medication errors were committed by all types of anesthesia providers, most commonly by attendings. Over 80% of reported medication errors reached the patient and more than half of these events caused patient harm. Fifteen events (5%) required a life sustaining intervention. Nearly all cases (97%) were judged to be either likely or certainly preventable.<br><br>CONCLUSIONS: Our findings characterize the most common types of medication errors in pediatric anesthesia practice and provide guidance on future preventative strategies. Many of these errors will be almost entirely preventable with the use of prefilled medication syringes to avoid accidental ampule swap, bar-coding at the point of medication administration to prevent syringe swap and to confirm the proper dose, and 2-person checking of medication infusions for accuracy.},
}
@article {pmid28740083,
year = {2017},
author = {Bush, EC and Ray, F and Alvarez, MJ and Realubit, R and Li, H and Karan, C and Califano, A and Sims, PA},
title = {PLATE-Seq for genome-wide regulatory network analysis of high-throughput screens.},
journal = {Nature communications},
volume = {8},
number = {1},
pages = {105},
pmid = {28740083},
issn = {2041-1723},
support = {K01 EB016071/EB/NIBIB NIH HHS/United States ; U54 CA209997/CA/NCI NIH HHS/United States ; S10 OD012351/OD/NIH HHS/United States ; U01 CA217858/CA/NCI NIH HHS/United States ; S10 OD021764/OD/NIH HHS/United States ; R35 CA197745/CA/NCI NIH HHS/United States ; },
mesh = {Antineoplastic Agents/pharmacology ; Cell Line, Tumor ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Neoplastic/drug effects ; *Gene Regulatory Networks ; Genome/genetics ; Genome-Wide Association Study/*methods ; Genomics/methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Reproducibility of Results ; },
abstract = {Pharmacological and functional genomic screens play an essential role in the discovery and characterization of therapeutic targets and associated pharmacological inhibitors. Although these screens affect thousands of gene products, the typical readout is based on low complexity rather than genome-wide assays. To address this limitation, we introduce pooled library amplification for transcriptome expression (PLATE-Seq), a low-cost, genome-wide mRNA profiling methodology specifically designed to complement high-throughput screening assays. Introduction of sample-specific barcodes during reverse transcription supports pooled library construction and low-depth sequencing that is 10- to 20-fold less expensive than conventional RNA-Seq. The use of network-based algorithms to infer protein activity from PLATE-Seq data results in comparable reproducibility to 30 M read sequencing. Indeed, PLATE-Seq reproducibility compares favorably to other large-scale perturbational profiling studies such as the connectivity map and library of integrated network-based cellular signatures.Despite the importance of pharmacological and functional genomic screens the readouts are of low complexity. Here the authors introduce PLATE-Seq, a low-cost genome-wide mRNA profiling method to complement high-throughput screening.},
}
@article {pmid28738203,
year = {2017},
author = {Trebitz, AS and Hoffman, JC and Darling, JA and Pilgrim, EM and Kelly, JR and Brown, EA and Chadderton, WL and Egan, SP and Grey, EK and Hashsham, SA and Klymus, KE and Mahon, AR and Ram, JL and Schultz, MT and Stepien, CA and Schardt, JC},
title = {Early detection monitoring for aquatic non-indigenous species: Optimizing surveillance, incorporating advanced technologies, and identifying research needs.},
journal = {Journal of environmental management},
volume = {202},
number = {Pt 1},
pages = {299-310},
pmid = {28738203},
issn = {1095-8630},
support = {EPA999999//Intramural EPA/United States ; EPA999999//Intramural EPA/ ; },
mesh = {Animals ; DNA ; Environmental Monitoring ; Great Lakes Region ; *Introduced Species ; Lakes ; Risk Assessment ; },
abstract = {Following decades of ecologic and economic impacts from a growing list of nonindigenous and invasive species, government and management entities are committing to systematic early- detection monitoring (EDM). This has reinvigorated investment in the science underpinning such monitoring, as well as the need to convey that science in practical terms to those tasked with EDM implementation. Using the context of nonindigenous species in the North American Great Lakes, this article summarizes the current scientific tools and knowledge - including limitations, research needs, and likely future developments - relevant to various aspects of planning and conducting comprehensive EDM. We begin with the scope of the effort, contrasting target-species with broad-spectrum monitoring, reviewing information to support prioritization based on species and locations, and exploring the challenge of moving beyond individual surveys towards a coordinated monitoring network. Next, we discuss survey design, including effort to expend and its allocation over space and time. A section on sample collection and analysis overviews the merits of collecting actual organisms versus shed DNA, reviews the capabilities and limitations of identification by morphology, DNA target markers, or DNA barcoding, and examines best practices for sample handling and data verification. We end with a section addressing the analysis of monitoring data, including methods to evaluate survey performance and characterize and communicate uncertainty. Although the body of science supporting EDM implementation is already substantial, research and information needs (many already actively being addressed) include: better data to support risk assessments that guide choice of taxa and locations to monitor; improved understanding of spatiotemporal scales for sample collection; further development of DNA target markers, reference barcodes, genomic workflows, and synergies between DNA-based and morphology-based taxonomy; and tools and information management systems for better evaluating and communicating survey outcomes and uncertainty.},
}
@article {pmid28738081,
year = {2017},
author = {Nagoshi, RN and Koffi, D and Agboka, K and Tounou, KA and Banerjee, R and Jurat-Fuentes, JL and Meagher, RL},
title = {Comparative molecular analyses of invasive fall armyworm in Togo reveal strong similarities to populations from the eastern United States and the Greater Antilles.},
journal = {PloS one},
volume = {12},
number = {7},
pages = {e0181982},
pmid = {28738081},
issn = {1932-6203},
mesh = {Africa ; Agriculture ; Animals ; Bacillus thuringiensis/genetics ; DNA Barcoding, Taxonomic/methods ; Genetic Markers/genetics ; Haplotypes ; Larva ; Moths/classification/genetics/microbiology ; Puerto Rico ; Sorghum/microbiology ; Spodoptera/*classification/*genetics/microbiology ; Togo ; United States ; Zea mays ; },
abstract = {The fall armyworm (Spodoptera frugiperda, J.E. Smith) is a noctuid moth that is a major and ubiquitous agricultural pest in the Western Hemisphere. Infestations have recently been identified in several locations in Africa, indicating its establishment in the Eastern Hemisphere where it poses an immediate and significant economic threat. Genetic methods were used to characterize noctuid specimens infesting multiple cornfields in the African nation of Togo that were tentatively identified as fall armyworm by morphological criteria. Species identification was confirmed by DNA barcoding and the specimens were found to be primarily of the subgroup that preferentially infests corn and sorghum in the Western Hemisphere. The mitochondrial haplotype configuration was most similar to that found in the Caribbean region and the eastern coast of the United States, identifying these populations as the likely originating source of the Togo infestations. A genetic marker linked with resistance to the Cry1Fa toxin from Bacillus thuringiensis (Bt) expressed in transgenic corn and common in Puerto Rico fall armyworm populations was not found in the Togo collections. These observations demonstrate the usefulness of genetic surveys to characterize fall armyworm populations from Africa.},
}
@article {pmid28734268,
year = {2017},
author = {Grzywacz, A and Wyborska, D and Piwczyński, M},
title = {DNA barcoding allows identification of European Fanniidae (Diptera) of forensic interest.},
journal = {Forensic science international},
volume = {278},
number = {},
pages = {106-114},
doi = {10.1016/j.forsciint.2017.06.023},
pmid = {28734268},
issn = {1872-6283},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Databases, Genetic ; Diptera/*genetics ; Electron Transport Complex IV/*genetics ; Forensic Sciences ; Polymerase Chain Reaction ; },
abstract = {In forensic entomology practice, species identification is a prerequisite for any further analysis of collected material. Although morphology-based taxonomy may be hindered by a range of factors, these are not obstacles for a molecular identification approach, so-called DNA barcoding. The Fanniidae are a dipteran family that is attracted to and breeds in decomposing animal carrion and dead human bodies. However, morphological identification of fanniids, both at adult and immature stages, is considered to be difficult, particularly for non-experts. We investigated the usefulness of molecular taxonomy methods as an alternative/supplement for morphology-based identification in European Fanniidae of forensic interest. The material used in this study was collected from various regions in Asia, Europe and North America. We sequenced a barcode region of the mitochondrial cytochrome c oxidase subunit I (COI) in 27 species. For 13 species, including some taxa breeding in dead bodies, this study describes COI sequences for the first time. Our analysis revealed that both mini-barcode and full-length COI barcode sequences give very high specimen identification success. Despite the large number of COI barcode sequences referring to Fanniidae in the BOLD and GenBank databases, previous identification of forensically relevant Fanniidae was hindered by uneven taxonomic sampling. The majority of available sequences refer to species that are not of medico-legal interest, and many species of forensic interest are unrepresented or represented only by a single sequence. Because of erroneous data that are present in depository databases, DNA barcoding must be used with caution and cannot be considered to be the sole alternative to other identification methods. Wolbachia infections in the examined material did not disrupt specimen identification. The obtained results will facilitate precise identification of European Fanniidae of forensic interest, badly preserved material with degraded DNA, as well as matching of unidentified females and immature stages to already described specimens.},
}
@article {pmid28727769,
year = {2017},
author = {Dario, MA and Moratelli, R and Schwabl, P and Jansen, AM and Llewellyn, MS},
title = {Small subunit ribosomal metabarcoding reveals extraordinary trypanosomatid diversity in Brazilian bats.},
journal = {PLoS neglected tropical diseases},
volume = {11},
number = {7},
pages = {e0005790},
pmid = {28727769},
issn = {1935-2735},
support = {R15 AI105749/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Brazil ; Chiroptera/*parasitology ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/*genetics ; *Genetic Variation ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA ; Trypanosoma/*classification/*genetics/isolation &amp; purification ; },
abstract = {BACKGROUND: Bats are a highly successful, globally dispersed order of mammals that occupy a wide array of ecological niches. They are also intensely parasitized and implicated in multiple viral, bacterial and parasitic zoonoses. Trypanosomes are thought to be especially abundant and diverse in bats. In this study, we used 18S ribosomal RNA metabarcoding to probe bat trypanosome diversity in unprecedented detail.<br><br>Total DNA was extracted from the blood of 90 bat individuals (17 species) captured along Atlantic Forest fragments of Esp&#xed;rito Santo state, southeast Brazil. 18S ribosomal RNA was amplified by standard and/or nested PCR, then deep sequenced to recover and identify Operational Taxonomic Units (OTUs) for phylogenetic analysis. Blood samples from 34 bat individuals (13 species) tested positive for infection by 18S rRNA amplification. Amplicon sequences clustered to 14 OTUs, of which five were identified as Trypanosoma cruzi I, T. cruzi III/V, Trypanosoma cruzi marinkellei, Trypanosoma rangeli, and Trypanosoma dionisii, and seven were identified as novel genotypes monophyletic to basal T. cruzi clade types of the New World. Another OTU was identified as a trypanosome like those found in reptiles. Surprisingly, the remaining OTU was identified as Bodo saltans-closest non-parasitic relative of the trypanosomatid order. While three blood samples featured just one OTU (T. dionisii), all others resolved as mixed infections of up to eight OTUs.<br><br>CONCLUSIONS/SIGNIFICANCE: This study demonstrates the utility of next-generation barcoding methods to screen parasite diversity in mammalian reservoir hosts. We exposed high rates of local bat parasitism by multiple trypanosome species, some known to cause fatal human disease, others non-pathogenic, novel or yet little understood. Our results highlight bats as a long-standing nexus among host-parasite interactions of multiple niches, sustained in part by opportunistic and incidental infections of consequence to evolutionary theory as much as to public health.},
}
@article {pmid28725363,
year = {2016},
author = {Thaler, DS and Stoeckle, MY},
title = {Bridging two scholarly islands enriches both: COI DNA barcodes for species identification versus human mitochondrial variation for the study of migrations and pathologies.},
journal = {Ecology and evolution},
volume = {6},
number = {19},
pages = {6824-6835},
pmid = {28725363},
issn = {2045-7758},
abstract = {DNA barcodes for species identification and the analysis of human mitochondrial variation have developed as independent fields even though both are based on sequences from animal mitochondria. This study finds questions within each field that can be addressed by reference to the other. DNA barcodes are based on a 648-bp segment of the mitochondrially encoded cytochrome oxidase I. From most species, this segment is the only sequence available. It is impossible to know whether it fairly represents overall mitochondrial variation. For modern humans, the entire mitochondrial genome is available from thousands of healthy individuals. SNPs in the human mitochondrial genome are evenly distributed across all protein-encoding regions arguing that COI DNA barcode is representative. Barcode variation among related species is largely based on synonymous codons. Data on human mitochondrial variation support the interpretation that most - possibly all - synonymous substitutions in mitochondria are selectively neutral. DNA barcodes confirm reports of a low variance in modern humans compared to nonhuman primates. In addition, DNA barcodes allow the comparison of modern human variance to many other extant animal species. Birds are a well-curated group in which DNA barcodes are coupled with census and geographic data. Putting modern human variation in the context of intraspecies variation among birds shows humans to be a single breeding population of average variance.},
}
@article {pmid28724933,
year = {2017},
author = {Gao, Z and Liu, Y and Wang, X and Song, J and Chen, S and Ragupathy, S and Han, J and Newmaster, SG},
title = {Derivative Technology of DNA Barcoding (Nucleotide Signature and SNP Double Peak Methods) Detects Adulterants and Substitution in Chinese Patent Medicines.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {5858},
pmid = {28724933},
issn = {2045-2322},
mesh = {Biological Products/analysis ; DNA Barcoding, Taxonomic/*methods ; *Drug Contamination ; Drugs, Chinese Herbal/*standards ; Nonprescription Drugs/*standards ; Polymorphism, Single Nucleotide/*genetics ; Reproducibility of Results ; },
abstract = {Lonicerae japonicae Flos has been used to produce hundred kinds of Chinese patent medicines (CPMs) in China. Economically motivated adulterants have been documented, leading to market instability and a decline in consumer confidence. ITS2 has been used to identify raw medicinal materials, but it's not suitable for the identification of botanical extracts and complex CPMs. Therefore, a short barcode for the identification of processed CPMs would be profitable. A 34 bp nucleotide signature (5' CTAGCGGTGGTCGTACGATAGCCAATGCATGAGT 3') was developed derived from ITS2 region of Eucommiae Folium based on unique motifs. Mixtures of powdered Lonicerae japonicae Flos and Lonicerae Flos resulted in double peaks at the expected SNP (Single Nucleotide Polymorphisms) positions, of which the height of the peaks were roughly indicative of the species' ratio in the mixed powder. Subsequently we tested 20 extracts and 47 CPMs labelled as containing some species of Lonicera. The results revealed only 17% of the extracts and 22% of the CPMs were authentic, others exist substitution or adulterant; 7% were shown to contain both of two adulterants Eucommiae Folium and Lonicerae Flos. The methods developed in this study will widely broaden the application of DNA barcode in quality assurance of natural health products.},
}
@article {pmid28724197,
year = {2017},
author = {Sutour, S and Esselin, H and Bighelli, A and Casanova, J and Le Gall, L and Tomi, F},
title = {Discrimination and Characterization of Two Mediterranean Species from the Laurencia Complex (Rhodomelacea) Using an NMR-Based Metabolomic Approach.},
journal = {Chemistry &amp; biodiversity},
volume = {14},
number = {11},
pages = {},
doi = {10.1002/cbdv.201700226},
pmid = {28724197},
issn = {1612-1880},
mesh = {Carbon Isotopes/chemistry ; DNA, Mitochondrial/metabolism ; Discriminant Analysis ; Laurencia/*chemistry/metabolism ; Magnetic Resonance Spectroscopy ; *Metabolomics ; Phenotype ; Plant Extracts/*chemistry ; Principal Component Analysis ; },
abstract = {Generic and specific determination among the Laurencia complex is a challenging task. DNA barcoding combined with phenotypic investigations are mandatory for species differentiation. In this study, two morphologically different members of the Laurencia complex were investigated using untargeted [1] H-NMR-based metabolomics. Twenty-one population samples were collected in order to evaluate both temporal and geographical homogeneity. Data obtained from [1] H-NMR analysis followed by statistical analysis allowed a clear separation of all the samples into two groups. DNA mitochondrial tests confirmed this pattern and identified the two species as Laurenciella sp. and Laurencia obtusa. In addition, metabolites responsible of this discrimination were investigated directly in crude extracts by [13] C-NMR using an in-house computer-assisted method. The combination of both untargeted ([1] H) and targeted ([13] C) NMR-based metabolomic approaches proves to be a powerful and complementary approach to discriminate species from the Laurencia complex.},
}
@article {pmid28718629,
year = {2017},
author = {Andrews, NLP and Ferguson, T and Rangaswamy, AMM and Bernicky, AR and Henning, N and Dudelzak, A and Reich, O and Barnes, JA and Loock, HP},
title = {Hadamard-Transform Fluorescence Excitation-Emission-Matrix Spectroscopy.},
journal = {Analytical chemistry},
volume = {89},
number = {16},
pages = {8554-8564},
doi = {10.1021/acs.analchem.7b02400},
pmid = {28718629},
issn = {1520-6882},
abstract = {We present a fluorescence excitation-emission-matrix spectrometer with superior data acquisition rates over previous instruments. Light from a white light emitting diode (LED) source is dispersed onto a digital micromirror array (DMA) and encoded using binary n-size Walsh functions ("barcodes"). The encoded excitation light is used to irradiate the liquid sample and its fluorescence is dispersed and detected using a conventional array spectrometer. After exposure to excitation light encoded in n different ways, the 2-dimensional excitation-emission-matrix (EEM) spectrum is obtained by inverse Hadamard transformation. Using this technique we examined the kinetics of the fluorescence of rhodamine B as a function of temperature and the acid-driven demetalation of chlorophyll-a into pheophytin-a. For these experiments, EEM spectra with 31 excitation channels and 2048 emission channels were recorded every 15 s. In total, data from over 3000 EEM spectra were included in this report. It is shown that the increase in data acquisition rate can be as high as [{n(n + 1)}
/2]-fold over conventional EEM spectrometers. Spectral acquisition rates of more than two spectra per second were demonstrated.},
}
@article {pmid28717207,
year = {2017},
author = {Brennan, IG and Bauer, AM and Van Tri, N and Wang, YY and Wang, WZ and Zhang, YP and Murphy, RW},
title = {Barcoding utility in a mega-diverse, cross-continental genus: keeping pace with Cyrtodactylus geckos.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {5592},
pmid = {28717207},
issn = {2045-2322},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Ecosystem ; *Evolution, Molecular ; Geography ; Lizards/*classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {Over the past decade, DNA barcoding has become a staple of low-cost molecular systematic investigations. The availability of universal primers and subsidized sequencing projects (PolarBOL, SharkBOL, SpongeBOL) have driven this popularity, often without appropriate investigation into the utility of barcoding data for the taxonomic group of interest. Here, our primary aim is to determine the phylogenetic value of DNA barcoding (mitochondrial locus COI) within the gecko genus Cyrtodactylus. With >40 new species described since last systematic investigation, Cyrtodactylus represents one of the most diverse extant squamate genera, and their contemporary distribution spans the Indian subcontinent, eastward through Indochina, and into AustraloPapua. The complex biogeographic history of this group, and morphology-only designation of many species have complicated our phylogenetic understanding of Cyrtodactylus. To highlight the need for continued inclusive molecular assessment, we use Vietnamese Cyrtodactylus as a case study showing the geopolitically paraphyletic nature of their history. We compare COI to the legacy marker ND2, and discuss the value of COI as an interspecific marker, as well as its shortcomings at deeper evolutionary scales. We draw attention back to the Cold Code as a subsidized method for incorporating molecular methods into species descriptions in the effort to maintain accurate phylogenies.},
}
@article {pmid28716927,
year = {2017},
author = {Janzen, DH and Burns, JM and Cong, Q and Hallwachs, W and Dapkey, T and Manjunath, R and Hajibabaei, M and Hebert, PDN and Grishin, NV},
title = {Nuclear genomes distinguish cryptic species suggested by their DNA barcodes and ecology.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {114},
number = {31},
pages = {8313-8318},
pmid = {28716927},
issn = {1091-6490},
support = {R01 GM094575/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; Base Sequence ; Biodiversity ; Butterflies/*classification/*genetics ; Costa Rica ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Moths/*classification/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Tropical Climate ; },
abstract = {DNA sequencing brings another dimension to exploration of biodiversity, and large-scale mitochondrial DNA cytochrome oxidase I barcoding has exposed many potential new cryptic species. Here, we add complete nuclear genome sequencing to DNA barcoding, ecological distribution, natural history, and subtleties of adult color pattern and size to show that a widespread neotropical skipper butterfly known as Udranomia kikkawai (Weeks) comprises three different species in Costa Rica. Full-length barcodes obtained from all three century-old Venezuelan syntypes of U. kikkawai show that it is a rainforest species occurring from Costa Rica to Brazil. The two new species are Udranomia sallydaleyae Burns, a dry forest denizen occurring from Costa Rica to Mexico, and Udranomia tomdaleyi Burns, which occupies the junction between the rainforest and dry forest and currently is known only from Costa Rica. Whereas the three species are cryptic, differing but slightly in appearance, their complete nuclear genomes totaling 15 million aligned positions reveal significant differences consistent with their 0.00065-Mbp (million base pair) mitochondrial barcodes and their ecological diversification. DNA barcoding of tropical insects reared by a massive inventory suggests that the presence of cryptic species is a widespread phenomenon and that further studies will substantially increase current estimates of insect species richness.},
}
@article {pmid28716157,
year = {2018},
author = {Guernier, V and Allan, KJ and Goarant, C},
title = {Advances and challenges in barcoding pathogenic and environmental Leptospira.},
journal = {Parasitology},
volume = {145},
number = {5},
pages = {595-607},
pmid = {28716157},
issn = {1469-8161},
support = {096400//Wellcome Trust/United Kingdom ; },
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Disease Reservoirs/*microbiology ; *Environmental Microbiology ; Genotyping Techniques/methods ; Humans ; Leptospira/classification/*genetics/*pathogenicity ; Leptospirosis/microbiology ; Phylogeny ; Zoonoses/microbiology ; },
abstract = {Leptospirosis is a zoonotic bacterial disease of global importance. A large spectrum of asymptomatic animal hosts can carry the infection and contribute to the burden of human disease. Environmental sources of human contamination also point to the importance of a hydrotelluric reservoir. Leptospirosis can be caused by as many as 15 different pathogenic or intermediate Leptospira species. However, classification of these bacteria remains complicated through the use of both serological and genetic classification systems that show poor correlation. With the advent of molecular techniques, DNA-based barcoding offers a conceptual framework that can be used for leptospirosis surveillance as well as source tracking. In this review, we summarize some of the current techniques, highlight significant successes and weaknesses and point to the future opportunities and challenges to successfully establish a widely applicable barcoding scheme for Leptospira.},
}
@article {pmid28714986,
year = {2017},
author = {Spies, N and Weng, Z and Bishara, A and McDaniel, J and Catoe, D and Zook, JM and Salit, M and West, RB and Batzoglou, S and Sidow, A},
title = {Genome-wide reconstruction of complex structural variants using read clouds.},
journal = {Nature methods},
volume = {14},
number = {9},
pages = {915-920},
pmid = {28714986},
issn = {1548-7105},
support = {R01 CA183904/CA/NCI NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; },
mesh = {*Algorithms ; Chromosome Mapping/*methods ; DNA Mutational Analysis/*methods ; Genetic Variation/*genetics ; Genome/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Sequence Analysis, DNA/*methods ; },
abstract = {In read cloud approaches, microfluidic partitioning of long genomic DNA fragments and barcoding of shorter fragments derived from these fragments retains long-range information in short sequencing reads. This combination of short reads with long-range information represents a powerful alternative to single-molecule long-read sequencing. We develop Genome-wide Reconstruction of Complex Structural Variants (GROC-SVs) for SV detection and assembly from read cloud data and apply this method to Illumina-sequenced 10x Genomics sarcoma and breast cancer data sets. Compared with short-fragment sequencing, GROC-SVs substantially improves the specificity of breakpoint detection at comparable sensitivity. This approach also performs sequence assembly across multiple breakpoints simultaneously, enabling the reconstruction of events exhibiting remarkable complexity. We show that chromothriptic rearrangements occurred before copy number amplifications, and that rates of single-nucleotide variants and SVs are not correlated. Our results support the use of read cloud approaches to advance the characterization of large and complex structural variation.},
}
@article {pmid28712341,
year = {2018},
author = {Choudhary, JS and Naaz, N and Lemtur, M and Das, B and Singh, AK and Bhatt, BP and Prabhakar, CS},
title = {Genetic analysis of Bactrocera zonata (Diptera: Tephritidae) populations from India based on cox1 and nad1 gene sequences.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {727-736},
doi = {10.1080/24701394.2017.1350952},
pmid = {28712341},
issn = {2470-1408},
mesh = {Animals ; Cyclooxygenase 1/*genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/genetics ; Diptera/genetics ; Electron Transport Complex I/*genetics ; Gene Flow ; Genetic Speciation ; Genetic Variation ; Genetics, Population/methods ; Genome, Mitochondrial ; Haplotypes ; India ; Phylogeny ; Tephritidae/*genetics ; },
abstract = {The peach fruit fly, Bactrocera zonata, is among the most serious and polyphagous insect pest of fruit crops in many parts of the world under genus Bactrocera. In the present study, the genetic structure, diversity and demographic history of B. zonata in India were inferred from mitochondrial cytochrome oxidase 1 (cox1) and NADH dehydrogenase 1 (nad1) sequences. The efficiency of DNA barcodes for identification of B. zonata was also tested. Genetic diversity indices [number of haplotypes (H), haplotype diversity (Hd), nucleotide diversity (π) and average number of nucleotide differences (k)] of B. zonata populations across India maintain high level of genetic diversity without isolation by distance among the geographic regions. Non-significant negative correlation between pairwise Fst and geographic distance suggests a high level of gene flow among studied populations of B. zonata. The possibility of sudden expansion of B. zonata revealed through mismatch distribution analysis as well as negative Tajima's D and Fu's Fs values further supported by star-like network of haplotypes. DNA barcoding analysis suggests that B. zonata specimens can be clearly differentiated from other species with 100% accuracy of identification. Therefore, cytochrome oxidase 1 (cox1) barcode sequences generated in the present study could be a valuable source for the rapid identification and global population genetic study of B. zonata.},
}
@article {pmid28712321,
year = {2018},
author = {Wang, ZL and Yang, XQ and Wang, TZ and Yu, X},
title = {Assessing the effectiveness of mitochondrial COI and 16S rRNA genes for DNA barcoding of farmland spiders in China.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {695-702},
doi = {10.1080/24701394.2017.1350949},
pmid = {28712321},
issn = {2470-1408},
mesh = {Animals ; China ; DNA ; DNA Barcoding, Taxonomic/methods ; Electron Transport Complex IV/*genetics ; Farms ; Genetic Speciation ; Genetic Variation ; Genome, Insect/*genetics ; Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Spiders/*genetics ; },
abstract = {DNA barcoding has been widely used to identify and discover new species in a wide range of taxa. In order to assess the effectiveness of COI (cytochrome C oxidase subunit I) and 16S (16S ribosomal RNA) in the discrimination of spiders, we have generated 289 barcodes for a total of 56 farmland spider species from 14 different families for the first time in China. Our results reveal that the standard barcoding marker COI can be used to distinguish the farmland spiders both in species and family level by NJ tree-based method, despite the absence of a barcode gap between the intra- and inter-specific genetic divergences. 16S has a lower species identification success as compared with COI. However, almost 98% of the species can be correctly distinguished for both COI and 16S when a threshold of 3% nucleotide divergence was used for species discrimination. Our study significantly improves the barcode reference sequence library for Chinese farmland spiders, and will be very useful in pest management and eco-environmental monitoring and protection.},
}
@article {pmid28711357,
year = {2017},
author = {Celiński, K and Kijak, H and Wojnicka-Półtorak, A and Buczkowska-Chmielewska, K and Sokołowska, J and Chudzińska, E},
title = {Effectiveness of the DNA barcoding approach for closely related conifers discrimination: A case study of the Pinus mugo complex.},
journal = {Comptes rendus biologies},
volume = {340},
number = {6-7},
pages = {339-348},
doi = {10.1016/j.crvi.2017.06.002},
pmid = {28711357},
issn = {1768-3238},
abstract = {DNA barcoding is a standard and efficient method, frequently used for identification, discrimination and discovery of new species. Although this approach is very useful for classifying the world's biodiversity, little is known about its usefulness in barcoding at lower taxonomic level and its discrimination rate for closely related species, like conifers. In this study, we compared the genetic variation of eight chloroplast DNA barcode regions (matK, rbcL, trnH-psbA, trnL-trnF, rpl20-rps18, trnV, ycf1, ycf2) in 17 conifers - three closely related pines from Pinus mugo complex and 14 more distant conifers representing two genera and four sections of the Pinaceae family. The discrimination rate for a single and for multiple DNA barcode regions analyzed in this study was estimated using the Tree-Building and PWG-Distance methods. The usefulness of the DNA barcoding approach for analyzing and resolving taxonomic inconsistency among closely related and more phylogenetically distant conifers was evaluated and discussed.},
}
@article {pmid28711044,
year = {2017},
author = {Reinhart, WF and Reifenberger, JG and Gupta, D and Muralidhar, A and Sheats, J and Cao, H and Dorfman, KD},
title = {Erratum: "Distribution of distances between DNA barcode labels in nanochannels close to the persistence length" [J. Chem. Phys. 142, 064902 (2015)].},
journal = {The Journal of chemical physics},
volume = {147},
number = {2},
pages = {029901},
pmid = {28711044},
issn = {1089-7690},
support = {R01 HG006851/HG/NHGRI NIH HHS/United States ; },
}
@article {pmid28709463,
year = {2017},
author = {Cornils, K and Thielecke, L and Winkelmann, D and Aranyossy, T and Lesche, M and Dahl, A and Roeder, I and Fehse, B and Glauche, I},
title = {Clonal competition in BcrAbl-driven leukemia: how transplantations can accelerate clonal conversion.},
journal = {Molecular cancer},
volume = {16},
number = {1},
pages = {120},
pmid = {28709463},
issn = {1476-4598},
mesh = {Animals ; Base Sequence ; Carcinogenesis/pathology ; Clone Cells ; Computer Simulation ; Gene Expression Regulation, Leukemic ; Genetic Vectors/metabolism ; Interleukin-3/metabolism ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics/*pathology ; Mice, Inbred BALB C ; Models, Biological ; *Neoplasm Transplantation ; RNA, Messenger/genetics/metabolism ; Transcriptome/genetics ; },
abstract = {BACKGROUND: Clonal competition in cancer describes the process in which the progeny of a cell clone supersedes or succumbs to other competing clones due to differences in their functional characteristics, mostly based on subsequently acquired mutations. Even though the patterns of those mutations are well explored in many tumors, the dynamical process of clonal selection is underexposed.<br><br>METHODS: We studied the dynamics of clonal competition in a BcrAbl-induced leukemia using a &#x3b3;-retroviral vector library encoding the oncogene in conjunction with genetic barcodes. To this end, we studied the growth dynamics of transduced cells on the clonal level both in vitro and in vivo in transplanted mice.<br><br>RESULTS: While we detected moderate changes in clonal abundancies in vitro, we observed monoclonal leukemias in 6/30 mice after transplantation, which intriguingly were caused by only two different BcrAbl clones. To analyze the success of these clones, we applied a mathematical model of hematopoietic tissue maintenance, which indicated that a differential engraftment capacity of these two dominant clones provides a possible explanation of our observations. These findings were further supported by additional transplantation experiments and increased BcrAbl transcript levels in both clones.<br><br>CONCLUSION: Our findings show that clonal competition is not an absolute process based on mutations, but highly dependent on selection mechanisms in a given environmental context.},
}
@article {pmid28707027,
year = {2017},
author = {Jia, S and Nakano, T and Hattori, M and Nara, K},
title = {Root-associated fungal communities in three Pyroleae species and their mycobiont sharing with surrounding trees in subalpine coniferous forests on Mount Fuji, Japan.},
journal = {Mycorrhiza},
volume = {27},
number = {8},
pages = {733-745},
pmid = {28707027},
issn = {1432-1890},
mesh = {Ascomycota/physiology ; Forests ; Japan ; Mycorrhizae/*physiology ; Pyrola/*microbiology ; Pyrolaceae/microbiology ; Sympatry ; Trees/*microbiology ; },
abstract = {Pyroleae species are perennial understory shrubs, many of which are partial mycoheterotrophs. Most fungi colonizing Pyroleae roots are ectomycorrhizal (ECM) and share common mycobionts with their Pyroleae hosts. However, such mycobiont sharing has neither been examined in depth before nor has the interspecific variation in sharing among Pyroleae species. Here, we examined root-associated fungal communities in three co-existing Pyroleae species, including Pyrola alpina, Pyrola incarnata, and Orthilia secunda, with reference to co-existing ECM fungi on the surrounding trees in the same soil blocks in subalpine coniferous forests. We identified 42, 75, and 18 fungal molecular operational taxonomic units in P. alpina, P. incarnata, and O. secunda roots, respectively. Mycobiont sharing with surrounding trees, which was defined as the occurrence of the same mycobiont between Pyroleae and surrounding trees in each soil block, was most frequent among P. incarnata (31 of 44 plants). In P. alpina, sharing was confirmed in 12 of 37 plants, and the fungal community was similar to that of P. incarnata. Mycobiont sharing was least common in O. secunda, found in only 5 of 32 plants. Root-associated fungi of O. secunda were dominated by Wilcoxina species, which were absent from the surrounding ECM roots in the same soil blocks. These results indicate that mycobiont sharing with surrounding trees does not equally occur among Pyroleae plants, some of which may develop independent mycorrhizal associations with ECM fungi, as suggested in O. secunda at our research sites.},
}
@article {pmid28706318,
year = {2017},
author = {Kolombia, YA and Karssen, G and Viaene, N and Kumar, PL and de Sutter, N and Joos, L and Coyne, DL and Bert, W},
title = {Diversity of Root-knot Nematodes Associated with Tubers of Yam (Dioscorea spp.) Established Using Isozyme Analysis and Mitochondrial DNA-based Identification.},
journal = {Journal of nematology},
volume = {49},
number = {2},
pages = {177-188},
pmid = {28706318},
issn = {0022-300X},
abstract = {The root-knot nematodes (RKN), Meloidogyne spp., represent an important threat to yam (Dioscorea spp.) production in West Africa. With the aim to establish the diversity of RKN species affecting yam tubers, for control and resistance screening purposes, surveys were conducted in the main yam producing areas of Nigeria. Galled tubers (N = 48) were collected from farmers' stores and markets in nine states in Nigeria and in one district in Ghana. RKN isolated from yam tubers were identified using enzyme phenotyping (esterase and malate dehydrogenase) and mitochondrial DNA (mtDNA) NADH dehydrogenase subunit 5 (Nad5) barcoding. Examination of 48 populations revealed that yam tubers were infested by Meloidogyne incognita (69%), followed by M. javanica (13%), M. enterolobii (2%), and M. arenaria (2%). Most of the tubers sampled (86%) were infected by a single species, and multiple species of RKN were detected in 14% of the samples. Results of both identification methods revealed the same species, confirming their accuracy for the identification of these tropical RKN species. In addition to M. incognita, M. javanica, and M. enterolobii, we report for the first time M. arenaria infecting yam tubers in Nigeria. This finding extends the list of yam pests and calls for caution when developing practices for yam pest management.},
}
@article {pmid28706316,
year = {2017},
author = {Kim, J and Kim, T and Park, JK},
title = {Description of Pseudacrobeles (Pseudacrobeles) curvatus sp. n. (Cephalobidae: Rhabditida) in South Korea.},
journal = {Journal of nematology},
volume = {49},
number = {2},
pages = {162-167},
pmid = {28706316},
issn = {0022-300X},
abstract = {Pseudacrobeles (Pseudacrobeles) curvatus sp. n. was collected from potato fields in Gyeongsangnam-do, South Korea. The new species shares morphological characters typical of the genus Pseudacrobeles, including three lateral incisures that fade posteriorly near the phasmid openings. The new species differs from other Pseudacrobeles species by its smaller body size and a comparatively shorter corpus relative to the isthmus length. In this study, we provide a comparison of morphometrics and diagnostic features of Pseudacrobeles species and molecular sequence data from the D2-D3 regions of the 28S ribosomal DNA (rDNA) and ITS1-5.8S-ITS2 region of rDNA from the new species, which can be used as molecular barcode sequences.},
}
@article {pmid28705884,
year = {2017},
author = {Celaj, A and Schlecht, U and Smith, JD and Xu, W and Suresh, S and Miranda, M and Aparicio, AM and Proctor, M and Davis, RW and Roth, FP and St Onge, RP},
title = {Quantitative analysis of protein interaction network dynamics in yeast.},
journal = {Molecular systems biology},
volume = {13},
number = {7},
pages = {934},
pmid = {28705884},
issn = {1744-4292},
support = {P01 HG000205/HG/NHGRI NIH HHS/United States ; P50 HG004233/HG/NHGRI NIH HHS/United States ; R21 HG005785/HG/NHGRI NIH HHS/United States ; U01 GM110706/GM/NIGMS NIH HHS/United States ; U41 HG001715/HG/NHGRI NIH HHS/United States ; },
mesh = {Computer Simulation ; DNA Barcoding, Taxonomic ; Gene Expression Profiling ; Models, Biological ; Peptide Hydrolases/chemistry/genetics/metabolism ; Protein Interaction Mapping/methods ; *Protein Interaction Maps ; RNA, Fungal/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Systems Biology ; },
abstract = {Many cellular functions are mediated by protein-protein interaction networks, which are environment dependent. However, systematic measurement of interactions in diverse environments is required to better understand the relative importance of different mechanisms underlying network dynamics. To investigate environment-dependent protein complex dynamics, we used a DNA-barcode-based multiplexed protein interaction assay in Saccharomyces cerevisiae to measure in vivo abundance of 1,379 binary protein complexes under 14 environments. Many binary complexes (55%) were environment dependent, especially those involving transmembrane transporters. We observed many concerted changes around highly connected proteins, and overall network dynamics suggested that "concerted" protein-centered changes are prevalent. Under a diauxic shift in carbon source from glucose to ethanol, a mass-action-based model using relative mRNA levels explained an estimated 47% of the observed variance in binary complex abundance and predicted the direction of concerted binary complex changes with 88% accuracy. Thus, we provide a resource of yeast protein interaction measurements across diverse environments and illustrate the value of this resource in revealing mechanisms of network dynamics.},
}
@article {pmid28704452,
year = {2017},
author = {Engel, M and Endesfelder, D and Schloter-Hai, B and Kublik, S and Granitsiotis, MS and Boschetto, P and Stendardo, M and Barta, I and Dome, B and Deleuze, JF and Boland, A and Müller-Quernheim, J and Prasse, A and Welte, T and Hohlfeld, J and Subramanian, D and Parr, D and Gut, IG and Greulich, T and Koczulla, AR and Nowinski, A and Gorecka, D and Singh, D and Gupta, S and Brightling, CE and Hoffmann, H and Frankenberger, M and Hofer, TP and Burggraf, D and Heiss-Neumann, M and Ziegler-Heitbrock, L and Schloter, M and Zu Castell, W},
title = {Influence of lung CT changes in chronic obstructive pulmonary disease (COPD) on the human lung microbiome.},
journal = {PloS one},
volume = {12},
number = {7},
pages = {e0180859},
pmid = {28704452},
issn = {1932-6203},
mesh = {Aged ; Bacteria/*classification/genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/methods ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Humans ; Lung/diagnostic imaging/*microbiology ; Male ; Microbiota ; Middle Aged ; Prevotella/classification/genetics/isolation &amp; purification ; Pulmonary Disease, Chronic Obstructive/complications/*diagnostic imaging ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; Streptococcus/classification/genetics/isolation &amp; purification ; Tomography, X-Ray Computed/*methods ; },
abstract = {BACKGROUND: Changes in microbial community composition in the lung of patients suffering from moderate to severe COPD have been well documented. However, knowledge about specific microbiome structures in the human lung associated with CT defined abnormalities is limited.<br><br>METHODS: Bacterial community composition derived from brush samples from lungs of 16 patients suffering from different CT defined subtypes of COPD and 9 healthy subjects was analyzed using a cultivation independent barcoding approach applying 454-pyrosequencing of 16S rRNA gene fragment amplicons.<br><br>RESULTS: We could show that bacterial community composition in patients with changes in CT (either airway or emphysema type changes, designated as severe subtypes) was different from community composition in lungs of patients without visible changes in CT as well as from healthy subjects (designated as mild COPD subtype and control group) (PC1, Padj = 0.002). Higher abundance of Prevotella in samples from patients with mild COPD subtype and from controls and of Streptococcus in the severe subtype cases mainly contributed to the separation of bacterial communities of subjects. No significant effects of treatment with inhaled glucocorticoids on bacterial community composition were detected within COPD cases with and without abnormalities in CT in PCoA. Co-occurrence analysis suggests the presence of networks of co-occurring bacteria. Four communities of positively correlated bacteria were revealed. The microbial communities can clearly be distinguished by their associations with the CT defined disease phenotype.<br><br>CONCLUSION: Our findings indicate that CT detectable structural changes in the lung of COPD patients, which we termed severe subtypes, are associated with alterations in bacterial communities, which may induce further changes in the interaction between microbes and host cells. This might result in a changed interplay with the host immune system.},
}
@article {pmid28701875,
year = {2017},
author = {Cai, Y and Li, P and Li, XW and Zhao, J and Chen, H and Yang, Q and Hu, H},
title = {Converting Panax ginseng DNA and chemical fingerprints into two-dimensional barcode.},
journal = {Journal of ginseng research},
volume = {41},
number = {3},
pages = {339-346},
pmid = {28701875},
issn = {1226-8453},
abstract = {BACKGROUND: In this study, we investigated how to convert the Panax ginseng DNA sequence code and chemical fingerprints into a two-dimensional code. In order to improve the compression efficiency, GATC2Bytes and digital merger compression algorithms are proposed.<br><br>METHODS: HPLC chemical fingerprint data of 10 groups of P.&#xa0;ginseng from Northeast China and the internal transcribed spacer 2 (ITS2) sequence code as the DNA sequence code were ready for conversion. In order to convert such data into a two-dimensional code, the following six steps were performed: First, the chemical fingerprint characteristic data sets were obtained through the inflection filtering algorithm. Second, precompression processing of such data sets is undertaken. Third, precompression processing was undertaken with the P.&#xa0;ginseng DNA (ITS2) sequence codes. Fourth, the precompressed chemical fingerprint data and the DNA (ITS2) sequence code were combined in accordance with the set data format. Such combined data can be compressed by Zlib, an open source data compression algorithm. Finally, the compressed data generated a two-dimensional code called a quick response code (QR code).<br><br>RESULTS: Through the abovementioned converting process, it can be found that the number of bytes needed for storing P.&#xa0;ginseng chemical fingerprints and its DNA (ITS2) sequence code can be greatly reduced. After GTCA2Bytes algorithm processing, the ITS2 compression rate reaches 75% and the chemical fingerprint compression rate exceeds 99.65% via filtration and digital merger compression algorithm processing. Therefore, the overall compression ratio even exceeds 99.36%. The capacity of the formed QR code is around 0.5k, which can easily and successfully be read and identified by any smartphone.<br><br>CONCLUSION: P.&#xa0;ginseng chemical fingerprints and its DNA (ITS2) sequence code can form a QR code after data processing, and therefore the QR code can be a perfect carrier of the authenticity and quality of P.&#xa0;ginseng information. This study provides a theoretical basis for the development of a quality traceability system of traditional Chinese medicine based on a two-dimensional code.},
}
@article {pmid28701020,
year = {2018},
author = {Reunov, A and Reunova, G and Atopkin, D and Reunova, Y and Muzarok, T and Zakharov, E and Zhuravlev, Y},
title = {The Identification of Araliaceae Species by ITS2 Genetic Barcoding and Pollen Morphology.},
journal = {Planta medica},
volume = {84},
number = {1},
pages = {42-48},
doi = {10.1055/s-0043-114425},
pmid = {28701020},
issn = {1439-0221},
mesh = {Aralia/genetics/ultrastructure ; Araliaceae/*genetics/ultrastructure ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/genetics ; Eleutherococcus/genetics/ultrastructure ; Oplopanax/genetics/ultrastructure ; Panax/genetics/ultrastructure ; Phylogeny ; Pollen/*ultrastructure ; Species Specificity ; },
abstract = {The genetic barcode ITS2 (ITS: internal transcribed spacer) and pollen morphology were used for the identification of the pharmacologically valuable wild Araliaceae species Panax ginseng, Oplopanax elatus, Aralia elata, Aralia continentalis, Eleutherococcus senticosus, and Eleutherococcus sessiliflorus inhabiting the natural forests of Primorye, Russia. The ITS2 locus successfully identified all six species, which supports the use of ITS2 as a standard barcode for medicinal plants. However, the ITS2 locus was insufficient for intra-specific discrimination in these species, neither within Primorye nor from other world representatives within GenBank. Araliaceae pollen was confirmed to undergo size-reducing metamorphosis. The final morphotypes were species-specific for each of the six species but could not discriminate intra-species geographic localities within Primorye. The morphologies of the final pollen morphotypes from homologous species inhabiting other parts of the world are not yet known. Therefore, whether pollen is applicable for Araliaceae intra-species discrimination between Primorye and other world localities could not be established. Based on these findings, we propose that the ITS2 genetic barcode and the final pollen morphotypes are suitable for the identification of Araliaceae species. However, further studies will be needed to determine the suitability of genetic and pollen traits for Araliaceae geographic authentication.},
}
@article {pmid28698913,
year = {2017},
author = {Atiphasaworn, P and Monggoot, S and Gentekaki, E and Brooks, S and Pripdeevech, P},
title = {Antibacterial and Antioxidant Constituents of Extracts of Endophytic Fungi Isolated from Ocimum basilicum var. thyrsiflora Leaves.},
journal = {Current microbiology},
volume = {74},
number = {10},
pages = {1185-1193},
pmid = {28698913},
issn = {1432-0991},
mesh = {Anti-Bacterial Agents/*isolation &amp; purification/*metabolism ; *Antibiosis ; Antioxidants/*isolation &amp; purification/*pharmacology ; Bacteria/drug effects ; *Endophytes ; Fungi/*metabolism ; Gas Chromatography-Mass Spectrometry ; Microbial Sensitivity Tests ; Ocimum basilicum/*microbiology ; Plant Leaves/*microbiology ; },
abstract = {Fourteen fungal endophytes were isolated from the Ocimum basilicum var. thyrsiflora leaves collected from Northern Thailand. Eight genera were identified including Aspergillus, Ascochyta, Nigrospora, Blastomyces, Colletotrichum, Exidia, Clitopilus, and Nomuraea. The antibacterial activity of crude extracts from all endophytic fungi was tested against nine human bacterial pathogens: Staphylococcus aureus, Staphylococcus epidermidis, Bacillus subtilis, Bacillus cereus, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Vibrio cholerae, and Vibrio parahaemolyticus. All crude extracts showed some degree of antibacterial activity, but the crude extract from Nigrospora MFLUCC16-0605 exhibited broad spectrum activity with MIC values ranging from 7.81 to 250 µg/mL. The antioxidant activity of all crude extracts was also investigated by DPPH radical scavenging assay. Crude extract from MFLUCC16-0605 had high antioxidant activity (IC50 value of 15.36 μg/mL) comparable to the trolox and gallic acid standards showing IC50 values of 2.56 and 12.89 μg/mL, respectively. The chemical composition of the crude extract from MFLUCC16-0605 was determined using GC-MS. Sixty-two compounds were identified representing 92.09% of crude extract with six major components including 5E,9E-farnesyl acetone, columellarin, totarene, laurenan-2-one, and 8S,13-cedranediol. PCR amplification and sequencing of the barcoding region identified MFLUCC16-0605 as belonging to Nigrospora genus. The notable activities of MFLUCC16-0605 indicate that the endophyte is a potent natural resource and its use as an antibacterial/antioxidant agent should be further explored.},
}
@article {pmid28698616,
year = {2017},
author = {Yu, N and Wei, YL and Zhang, X and Zhu, N and Wang, YL and Zhu, Y and Zhang, HP and Li, FM and Yang, L and Sun, JQ and Sun, AD},
title = {Barcode ITS2: a useful tool for identifying Trachelospermum jasminoides and a good monitor for medicine market.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {5037},
pmid = {28698616},
issn = {2045-2322},
mesh = {Apocynaceae/*genetics ; Base Sequence ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/chemistry/*genetics ; Genetic Variation ; Nucleic Acid Conformation ; Phylogeny ; Plants, Medicinal/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Trachelospermum jasminoides is commonly used in traditional Chinese medicine. However, the use of the plant's local alternatives is frequent, causing potential clinical problems. The T. jasminoides sold in the medicine market is commonly dried and sliced, making traditional identification methods difficult. In this study, the ITS2 region was evaluated on 127 sequences representing T. jasminoides and its local alternatives according to PCR and sequencing rates, intra- and inter-specific divergences, secondary structure, and discrimination capacity. Results indicated the 100% success rates of PCR and sequencing and the obvious presence of a barcoding gap. Results of BLAST 1, nearest distance and neighbor-joining tree methods showed that barcode ITS2 could successfully identify all the texted samples. The secondary structures of the ITS2 region provided another dimensionality for species identification. Two-dimensional images were obtained for better and easier identification. Previous studies on DNA barcoding concentrated more on the same family, genus, or species. However, an ideal barcode should be variable enough to identify closely related species. Meanwhile, the barcodes should also be conservative in identifying distantly related species. This study highlights the application of barcode ITS2 in solving practical problems in the distantly related local alternatives of medical plants.},
}
@article {pmid28692789,
year = {2017},
author = {Giudice, V and Feng, X and Kajigaya, S and Young, NS and Biancotto, A},
title = {Optimization and standardization of fluorescent cell barcoding for multiplexed flow cytometric phenotyping.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {91},
number = {7},
pages = {694-703},
pmid = {28692789},
issn = {1552-4930},
support = {Z99 HL999999//Intramural NIH HHS/United States ; },
mesh = {Adult ; Antibodies/*immunology ; Cytokines/metabolism ; Drug Evaluation, Preclinical/methods ; Female ; *Flow Cytometry/methods ; Fluorescent Dyes ; Humans ; *Immunophenotyping/methods ; Lymphocytes/*cytology ; Male ; Signal Transduction/physiology ; Staining and Labeling/methods ; },
abstract = {Fluorescent cell barcoding (FCB) is a cell-based multiplexing technique for high-throughput flow cytometry. Barcoded samples can be stained and acquired collectively, minimizing staining variability and antibody consumption, and decreasing required sample volumes. Combined with functional measurements, FCB can be used for drug screening, signaling profiling, and cytokine detection, but technical issues are present. We optimized the FCB technique for routine utilization using DyLight 350, DyLight 800, Pacific Orange, and CBD500 for barcoding six, nine, or 36 human peripheral blood specimens. Working concentrations of FCB dyes ranging from 0 to 500 μg/ml were tested, and viability dye staining was optimized to increase robustness of data. A five-color staining with surface markers for Vβ usage analysis in CD4[+] and CD8[+] T cells was achieved in combination with nine sample barcoding. We provide improvements of the FCB technique that should be useful for multiplex drug screening and for lymphocyte characterization and perturbations in the diagnosis and during the course of disease. Published 2017 by Wiley Periodicals, Inc., on behalf of International Society for Advancement of Cytometry. This article is a US government work and as such, is in the public domain in the United States of America.},
}
@article {pmid28691083,
year = {2017},
author = {Woehrstein, JB and Strauss, MT and Ong, LL and Wei, B and Zhang, DY and Jungmann, R and Yin, P},
title = {Sub-100-nm metafluorophores with digitally tunable optical properties self-assembled from DNA.},
journal = {Science advances},
volume = {3},
number = {6},
pages = {e1602128},
pmid = {28691083},
issn = {2375-2548},
support = {680241/ERC_/European Research Council/International ; R21 HD072481/HD/NICHD NIH HHS/United States ; R01 EB018659/EB/NIBIB NIH HHS/United States ; K99 EB015331/EB/NIBIB NIH HHS/United States ; DP2 OD007292/OD/NIH HHS/United States ; },
mesh = {Biophysical Phenomena ; DNA/*chemistry ; Fluorescent Dyes/*chemistry ; Microscopy, Fluorescence ; Nanostructures/*chemistry ; Nanotechnology ; Nucleic Acid Conformation ; Nucleic Acids/chemistry ; },
abstract = {Fluorescence microscopy allows specific target detection down to the level of single molecules and has become an enabling tool in biological research. To transduce the biological information to an imageable signal, we have developed a variety of fluorescent probes, such as organic dyes or fluorescent proteins with different colors. Despite their success, a limitation on constructing small fluorescent probes is the lack of a general framework to achieve precise and programmable control of critical optical properties, such as color and brightness. To address this challenge, we introduce metafluorophores, which are constructed as DNA nanostructure-based fluorescent probes with digitally tunable optical properties. Each metafluorophore is composed of multiple organic fluorophores, organized in a spatially controlled fashion in a compact sub-100-nm architecture using a DNA nanostructure scaffold. Using DNA origami with a size of 90 × 60 nm[2], substantially smaller than the optical diffraction limit, we constructed small fluorescent probes with digitally tunable brightness, color, and photostability and demonstrated a palette of 124 virtual colors. Using these probes as fluorescent barcodes, we implemented an assay for multiplexed quantification of nucleic acids. Additionally, we demonstrated the triggered in situ self-assembly of fluorescent DNA nanostructures with prescribed brightness upon initial hybridization to a nucleic acid target.},
}
@article {pmid28690934,
year = {2017},
author = {Byers, DL and Chang, SM},
title = {Studying plant-pollinator interactions facing climate change and changing environments.},
journal = {Applications in plant sciences},
volume = {5},
number = {6},
pages = {},
pmid = {28690934},
issn = {2168-0450},
abstract = {Plant-pollinator interactions are essential for successful plant reproduction in both natural and agricultural systems. These interactions are negatively impacted by recent large-scale alterations of the environments, particularly climate change. The responses of plants and pollinators to changing abiotic conditions that vary seasonally and geographically are often uncoordinated, potentially leading to the breakdown of this interaction. The complexity of the responses of plants and pollinators to our changing climate necessitates creative approaches. The six articles in this special issue directly address this need by providing a variety of key methods and reviews of current methodology. The articles include: DNA barcoding methods for use on pollen collected from visiting bees; methods for assessment of plant attraction traits (nectar and review of floral volatiles methods); a field sampling method for ground nesting bees; a review of using spatial and temporal transplants for addressing changing dynamics of plant-pollinator interactions; and a review of approaches used to assess potential shifts in phenology of plants and pollinators. Collectively, these articles illustrate some of the breadth of approaches needed to address the changing dynamics of plant-pollinator interactions.},
}
@article {pmid28690814,
year = {2017},
author = {Moreno, E and Conde-Porcuna, JM and Gómez, A},
title = {Barcoding rotifer biodiversity in Mediterranean ponds using diapausing egg banks.},
journal = {Ecology and evolution},
volume = {7},
number = {13},
pages = {4855-4867},
pmid = {28690814},
issn = {2045-7758},
abstract = {The biodiversity of Mediterranean freshwater bodies is among the most threatened worldwide; therefore, its accurate estimation is an urgent issue. However, traditional methods are likely to underestimate freshwater zooplankton biodiversity due to its high species seasonality and cryptic diversity. We test the value of applying DNA barcoding to diapausing egg banks, in combination with the creation of a reference collection of DNA barcodes using adult individual samples, to characterize rotifer communities. We use monogonont rotifers from two lakes in Doñana National Park and one from Ruidera Natural Park in Spain as models to create a reference collection of DNA barcodes for taxonomically diagnosed adult individuals sampled from the water column, to compare with the sequences obtained from individual eggs from the diapausing egg banks. We apply two different approaches to carry out DNA taxonomy analyses, the generalized mixed Yule coalescent method (GMYC) and the Automatic Barcode Gap Discovery (ABGD), to the obtained sequences and to publicly available rotifer sequences. We obtained a total of 210 new rotifer COI sequences from all three locations (151 diapausing eggs and 59 adults). Both GMYC and ABGD generated the same 35 operational taxonomic units (OTUs), revealing four potential cryptic species. Most sequences obtained from diapausing eggs (85%) clustered with sequences obtained from morphologically diagnosed adults. Our approach, based on a single sediment sample, retrieved estimates of rotifer biodiversity higher than or similar to those of previous studies based on a number of seasonal samples. This study shows that DNA barcoding of diapausing egg banks is an effective aid to characterize rotifer diversity in Mediterranean freshwater bodies.},
}
@article {pmid28690801,
year = {2017},
author = {Yang, CH and Wu, KC and Dahms, HU and Chuang, LY and Chang, HW},
title = {Single nucleotide polymorphism barcoding of cytochrome c oxidase I sequences for discriminating 17 species of Columbidae by decision tree algorithm.},
journal = {Ecology and evolution},
volume = {7},
number = {13},
pages = {4717-4725},
pmid = {28690801},
issn = {2045-7758},
abstract = {DNA barcodes are widely used in taxonomy, systematics, species identification, food safety, and forensic science. Most of the conventional DNA barcode sequences contain the whole information of a given barcoding gene. Most of the sequence information does not vary and is uninformative for a given group of taxa within a monophylum. We suggest here a method that reduces the amount of noninformative nucleotides in a given barcoding sequence of a major taxon, like the prokaryotes, or eukaryotic animals, plants, or fungi. The actual differences in genetic sequences, called single nucleotide polymorphism (SNP) genotyping, provide a tool for developing a rapid, reliable, and high-throughput assay for the discrimination between known species. Here, we investigated SNPs as robust markers of genetic variation for identifying different pigeon species based on available cytochrome c oxidase I (COI) data. We propose here a decision tree-based SNP barcoding (DTSB) algorithm where SNP patterns are selected from the DNA barcoding sequence of several evolutionarily related species in order to identify a single species with pigeons as an example. This approach can make use of any established barcoding system. We here firstly used as an example the mitochondrial gene COI information of 17 pigeon species (Columbidae, Aves) using DTSB after sequence trimming and alignment. SNPs were chosen which followed the rule of decision tree and species-specific SNP barcodes. The shortest barcode of about 11 bp was then generated for discriminating 17 pigeon species using the DTSB method. This method provides a sequence alignment and tree decision approach to parsimoniously assign a unique and shortest SNP barcode for any known species of a chosen monophyletic taxon where a barcoding sequence is available.},
}
@article {pmid28690303,
year = {2017},
author = {Nomura, C and Masayama, A and Yamaguchi, M and Sakuma, D and Kajimura, K},
title = {[PCR-Based Method for the Detection of Toxic Mushrooms Causing Food-Poisoning Incidents].},
journal = {Shokuhin eiseigaku zasshi. Journal of the Food Hygienic Society of Japan},
volume = {58},
number = {3},
pages = {132-142},
doi = {10.3358/shokueishi.58.132},
pmid = {28690303},
issn = {1882-1006},
mesh = {Agaricales/genetics/*isolation &amp; purification ; Base Sequence ; DNA Barcoding, Taxonomic/methods ; DNA Primers ; DNA, Fungal/genetics/isolation &amp; purification ; Foodborne Diseases/*diagnosis/*etiology ; Gastric Juice ; Japan ; Polymerase Chain Reaction/*methods ; Time Factors ; },
abstract = {In this study, species-specific identification of five toxic mushrooms, Chlorophyllum molybdites, Gymnopilus junonius, Hypholoma fasciculare, Pleurocybella porrigens, and Tricholoma ustale, which have been involved in food-poisoning incidents in Japan, was investigated. Specific primer pairs targeting internal transcribed spacer (ITS) regions were designed for PCR detection. The specific amplicons were obtained from fresh, cooked, and simulated gastric fluid (SGF)-treated samples. No amplicons were detected from other mushrooms with similar morphology. Our method using one-step extraction of mushrooms allows rapid detection within 2.5 hr. It could be utilized for rapid identification or screening of toxic mushrooms.},
}
@article {pmid28688979,
year = {2018},
author = {Garcia, HA and Rodrigues, CMF and Rodrigues, AC and Pereira, DL and Pereira, CL and Camargo, EP and Hamilton, PB and Teixeira, MMG},
title = {Remarkable richness of trypanosomes in tsetse flies (Glossina morsitans morsitans and Glossina pallidipes) from the Gorongosa National Park and Niassa National Reserve of Mozambique revealed by fluorescent fragment length barcoding (FFLB).},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {63},
number = {},
pages = {370-379},
doi = {10.1016/j.meegid.2017.07.005},
pmid = {28688979},
issn = {1567-7257},
mesh = {Animals ; Animals, Wild/parasitology ; Artiodactyla/parasitology ; DNA Barcoding, Taxonomic/*methods ; *Genetic Variation ; Genotype ; Humans ; Intestines/parasitology ; Livestock/parasitology ; Mozambique ; Parks, Recreational ; Perissodactyla/parasitology ; Trypanosoma/classification/*genetics/isolation &amp; purification/pathogenicity ; Trypanosoma brucei brucei/classification/*genetics/isolation &amp; purification/pathogenicity ; Trypanosoma congolense/classification/*genetics/isolation &amp; purification/pathogenicity ; Trypanosoma vivax/classification/*genetics/isolation &amp; purification/pathogenicity ; Tsetse Flies/classification/*parasitology ; },
abstract = {Trypanosomes of African wild ungulates transmitted by tsetse flies can cause human and livestock diseases. However, trypanosome diversity in wild tsetse flies remains greatly underestimated. We employed FFLB (fluorescent fragment length barcoding) for surveys of trypanosomes in tsetse flies (3086) from the Gorongosa National Park (GNP) and Niassa National Reserve (NNR) in Mozambique (MZ), identified as Glossina morsitans morsitans (GNP/NNR=77.6%/90.5%) and Glossina pallidipes (22.4%/9.5%). Trypanosomes were microscopically detected in 8.3% of tsetse guts. FFLB of gut samples revealed (GNP/NNR): Trypanosoma congolense of Savannah (27%/63%), Kilifi (16.7%/29.7%) and Forest (1.0%/0.3%) genetic groups; T. simiae Tsavo (36.5%/6.1%); T. simiae (22.2%/17.7%); T. godfreyi (18.2%/7.0%); subgenus Trypanozoon (20.2%/25.7%); T. vivax/T. vivax-like (1.5%/5.2%); T. suis/T. suis-like (9.4%/11.9%). Tsetse proboscises exhibited similar species composition, but most prevalent species were (GNP/NNR): T. simiae (21.9%/28%), T. b. brucei (19.2%/31.7%), and T. vivax/T. vivax-like (19.2%/28.6%). Flies harboring mixtures of trypanosomes were common (~ 64%), and combinations of more than four trypanosomes were especially abundant in the pristine NNR. The non-pathogenic T. theileri was found in 2.5% while FFLB profiles of unknown species were detected in 19% of flies examined. This is the first report on molecular diversity of tsetse flies and their trypanosomes in MZ; all trypanosomes pathogenic for ungulates were detected, but no human pathogens were detected. Overall, two species of tsetse flies harbor 12 species/genotypes of trypanosomes. This notable species richness was likely uncovered because flies were captured in wildlife reserves and surveyed using the method of FFLB able to identify, with high sensitivity and accuracy, known and novel trypanosomes. Our findings importantly improve the knowledge on trypanosome diversity in tsetse flies, revealed the greatest species richness so far reported in tsetse fly of any African country, and indicate the existence of a hidden trypanosome diversity to be discovered in African wildlife protected areas.},
}
@article {pmid28687754,
year = {2017},
author = {Tyagi, K and Kumar, V and Singha, D and Chandra, K and Laskar, BA and Kundu, S and Chakraborty, R and Chatterjee, S},
title = {DNA Barcoding studies on Thrips in India: Cryptic species and Species complexes.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {4898},
pmid = {28687754},
issn = {2045-2322},
mesh = {Animals ; Bayes Theorem ; DNA/*classification/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Genetic Variation ; *Genome, Insect ; Haplotypes ; India ; *Phylogeny ; Plants/parasitology ; Thysanoptera/classification/*genetics ; },
abstract = {Thrips are one of the major sucking pest and vector of plant viruses causing huge economic loss in agriculture. The accurate identification of thrips is crucial for effective pest management strategies. However, morphology based identification has limitations and warrants integration of molecular data. We attempted the largest DNA barcoding initiative on 370 sequences of 89 thrips morphospecies including 104 novel sequences from 39 morphospecies, including the type specimens of four species. The results of multiple species delimitation methods (BIN, ABGD, GMYC and bPTP) were consistent for 73 species (82%) with their morphological identifications. A total of 107 molecular operational taxonomic units (MOTUs) was recovered for 89 morphospecies by superimposing multiple methods and applying a three level nomenclature system. We detected more than one MOTU in 14 morphospecies indicating to have cryptic diversity including, two major vector species (Frankliniella schultzei and Thrips palmi). However, four morphospecies (Thrips moundi, Thrips carthami, Haplothrips andersi and Haplothrips gowdeyi) showed low genetic distances between them with overlapping in barcode gap that requires further analysis with multiple molecular markers and more specimens from wide geographical areas for better taxonomic judgment. We also presented the advantage of simultaneous use of multiple delimitation methods for detection and identification of cryptic species.},
}
@article {pmid28686280,
year = {2017},
author = {Humar, M and Upadhya, A and Yun, SH},
title = {Spectral reading of optical resonance-encoded cells in microfluidics.},
journal = {Lab on a chip},
volume = {17},
number = {16},
pages = {2777-2784},
pmid = {28686280},
issn = {1473-0189},
support = {DP1 EB024242/EB/NIBIB NIH HHS/United States ; P01 HL120839/HL/NHLBI NIH HHS/United States ; P41 EB015903/EB/NIBIB NIH HHS/United States ; R01 CA192878/CA/NCI NIH HHS/United States ; },
mesh = {Algorithms ; *Electronic Data Processing ; Fluorescent Dyes/chemistry ; Microfluidic Analytical Techniques/*instrumentation ; Microscopy, Fluorescence ; Microspheres ; Polystyrenes ; Single-Cell Analysis/*instrumentation/*methods ; },
abstract = {The ability to label individual cells is useful for single-cell-level studies of complex cellular interactions and heterogeneity. Optically readable cell labeling is attractive as it can be investigated non-invasively and repeatedly at high speeds. Here, we demonstrate the feasibility of large-scale cell barcoding and identification using fluorescent polystyrene microbeads loaded into cells. Intracellular beads with different diameters in a range of 5 to 12 μm generate spectrally distinguished features or barcodes. A microfluidic chip was used to measure fluorescence resonance peaks emitted from individual cells. An algorithm comparing the peak wavelengths to a reference barcode library allowed barcode identification with high accuracy. This work provides a guideline to increase the number of unique identifiers and reduce various false-positive and false-negative errors.},
}
@article {pmid28683838,
year = {2017},
author = {de Muinck, EJ and Trosvik, P and Gilfillan, GD and Hov, JR and Sundaram, AYM},
title = {A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform.},
journal = {Microbiome},
volume = {5},
number = {1},
pages = {68},
pmid = {28683838},
issn = {2049-2618},
mesh = {Bacteria/genetics ; Computational Biology ; DNA Barcoding, Taxonomic ; *Gene Library ; High-Throughput Nucleotide Sequencing/economics/instrumentation/*methods ; Metagenomics ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/instrumentation/methods ; },
abstract = {BACKGROUND: Advances in sequencing technologies and bioinformatics have made the analysis of microbial communities almost routine. Nonetheless, the need remains to improve on the techniques used for gathering such data, including increasing throughput while lowering cost and benchmarking the techniques so that potential sources of bias can be better characterized.<br><br>METHODS: We present a triple-index amplicon sequencing strategy to sequence large numbers of samples at significantly lower c ost and in a shorter timeframe compared to existing methods. The design employs a two-stage PCR protocol, incorpo rating three barcodes to each sample, with the possibility to add a fourth-index. It also includes heterogeneity spacers to overcome low complexity issues faced when sequencing amplicons on Illumina platforms.<br><br>RESULTS: The library preparation method was extensively benchmarked through analysis of a mock community in order to assess biases introduced by sample indexing, number of PCR cycles, and template concentration. We further evaluated the method through re-sequencing of a standardized environmental sample. Finally, we evaluated our protocol on a set of fecal samples from a small cohort of healthy adults, demonstrating good performance in a realistic experimental setting. Between-sample variation was mainly related to batch effects, such as DNA extraction, while sample indexing was also a significant source of bias. PCR cycle number strongly influenced chimera formation and affected relative abundance estimates of species with high GC content. Libraries were sequenced using the Illumina HiSeq and MiSeq platforms to demonstrate that this protocol is highly scalable to sequence thousands of samples at a very low cost.<br><br>CONCLUSIONS: Here, we provide the most comprehensive study of performance and bias inherent to a 16S rRNA gene amplicon sequencing method to date. Triple-indexing greatly reduces the number of long custom DNA oligos required for library preparation, while the inclusion of variable length heterogeneity spacers minimizes the need for PhiX spike-in. This design results in a significant cost reduction of highly multiplexed amplicon sequencing. The biases we characterize highlight the need for highly standardized protocols. Reassuringly, we find that the biological signal is a far stronger structuring factor than the various sources of bias.},
}
@article {pmid28680426,
year = {2017},
author = {Estendorfer, J and Stempfhuber, B and Haury, P and Vestergaard, G and Rillig, MC and Joshi, J and Schröder, P and Schloter, M},
title = {The Influence of Land Use Intensity on the Plant-Associated Microbiome of Dactylis glomerata L.},
journal = {Frontiers in plant science},
volume = {8},
number = {},
pages = {930},
pmid = {28680426},
issn = {1664-462X},
abstract = {In this study, we investigated the impact of different land use intensities (LUI) on the root-associated microbiome of Dactylis glomerata (orchardgrass). For this purpose, eight sampling sites with different land use intensity levels but comparable soil properties were selected in the southwest of Germany. Experimental plots covered land use levels from natural grassland up to intensively managed meadows. We used 16S rRNA gene based barcoding to assess the plant-associated community structure in the endosphere, rhizosphere and bulk soil of D. glomerata. Samples were taken at the reproductive stage of the plant in early summer. Our data indicated that roots harbor a distinct bacterial community, which clearly differed from the microbiome of the rhizosphere and bulk soil. Our results revealed Pseudomonadaceae, Enterobacteriaceae and Comamonadaceae as the most abundant endophytes independently of land use intensity. Rhizosphere and bulk soil were dominated also by Proteobacteria, but the most abundant families differed from those obtained from root samples. In the soil, the effect of land use intensity was more pronounced compared to root endophytes leading to a clearly distinct pattern of bacterial communities under different LUI from rhizosphere and bulk soil vs. endophytes. Overall, a change of community structure on the plant-soil interface was observed, as the number of shared OTUs between all three compartments investigated increased with decreasing land use intensity. Thus, our findings suggest a stronger interaction of the plant with its surrounding soil under low land use intensity. Furthermore, the amount and quality of available nitrogen was identified as a major driver for shifts in the microbiome structure in all compartments.},
}
@article {pmid28680424,
year = {2017},
author = {Liu, Y and Wang, XY and Gao, ZT and Han, JP and Xiang, L},
title = {Detection of Ophiocordyceps sinensis and Its Common Adulterates Using Species-Specific Primers.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {1179},
pmid = {28680424},
issn = {1664-302X},
abstract = {Ophiocordyceps sinensis is a fungus that infects Hepialidae caterpillars, mummifying the larvae and producing characteristic fruiting bodies (stromata) that are processed into one of the most valued traditional Chinese medicines (TCM). The product commands a very high price due to a high demand but a very limited supply. Adulteration with other fungi is a common problem and there is a need to test preparation for the presence of the correct fungus. In the current study, a PCR-based approach for the identification of O. sinensis based on a segment of the internal transcribed spacer (ITS) region was developed. The segments is 146-bp in size and is likely to be amplified even in materials where processing led to DNA fragmentation. Primer development was based on the alignment of sequence data generated from a total of 89 samples of O. sinensis and potential adulterants as well as sequences date from 41 Ophiocordyceps species and 26 Cordyceps species available in GenBank. Tests with primer pair, DCF4/DCR4, demonstrated generation of an amplicon from DNA extracted from O. sinensis stromata, but not from extracts derived from adulterants. Species-specific primer pairs were also developed and tested for detection of the common adulterants, Cordyceps gunnii, Cordyceps cicadae, Cordyceps militaris, Cordyceps liangshanensis and Ophiocordyceps nutans. The collection of primers developed in the present study will be useful for the authentication of preparation claiming to only contain O. sinensis and for the detection of fungi used as adulterants in these preparations.},
}
@article {pmid28675688,
year = {2017},
author = {van der Valk, T and Lona Durazo, F and Dalén, L and Guschanski, K},
title = {Whole mitochondrial genome capture from faecal samples and museum-preserved specimens.},
journal = {Molecular ecology resources},
volume = {17},
number = {6},
pages = {e111-e121},
doi = {10.1111/1755-0998.12699},
pmid = {28675688},
issn = {1755-0998},
mesh = {Animals ; DNA, Mitochondrial/chemistry/*genetics/*isolation &amp; purification ; Feces/*chemistry ; *Fossils ; *Genome, Mitochondrial ; Gorilla gorilla ; Pan troglodytes ; *Sequence Analysis, DNA ; },
abstract = {Population-scale molecular studies of endangered and cryptic species are often limited by access to high-quality samples. The use of noninvasively collected samples or museum-preserved specimens reduces the pressure on modern populations by removing the need to capture and handle live animals. However, endogenous DNA content in such samples is low, making shotgun sequencing a financially prohibitive approach. Here, we apply a target enrichment method to retrieve mitochondrial genomes from 65 museum specimens and 56 noninvasively collected faecal samples of two endangered great ape species, Grauer's gorilla and the eastern chimpanzee. We show that the applied method is suitable for a wide range of sample types that differ in endogenous DNA content, increasing the proportion of target reads to over 300-fold. By systematically evaluating biases introduced during target enrichment of pooled museum samples, we show that capture is less efficient for fragments shorter or longer than the baits, that the proportion of human contaminating reads increases postcapture although capture efficiency is lower for human compared to gorilla fragments with a gorilla-generated bait, and that the rate of jumping PCR is considerable, but can be controlled for with a double-barcoding approach. We succeed in capturing complete mitochondrial genomes from faecal samples, but observe reduced capture efficiency as sequence divergence increases between the bait and target species. As previously shown for museum specimens, we demonstrate here that mitochondrial genome capture from field-collected faecal samples is a robust and reliable approach for population-wide studies of nonmodel organisms.},
}
@article {pmid28671248,
year = {2017},
author = {Ali, MA and Lee, J and Al-Hemaid, F},
title = {Generic relationships among Molluginaceae inferred from a molecular phylogenetic analysis of the matK gene.},
journal = {Genetics and molecular research : GMR},
volume = {16},
number = {2},
pages = {},
doi = {10.4238/gmr16029295},
pmid = {28671248},
issn = {1676-5680},
mesh = {*Genes, Chloroplast ; Molluginaceae/classification/*genetics ; *Phylogeny ; Polymorphism, Genetic ; },
abstract = {The family Molluginaceae (order Caryophyllales) is considered polyphyletic based on the photosynthetic pathway, C4 evolution, and phylogeny of the family. This inference was made based on photosynthetic, anatomical, and molecular datasets. The generic circumscription of this family has greatly been changed owing to the placement of several of its genera into the Caryophyllaceae, Microteaceae, Lophiocarpaceae, and Limeaceae families. However, the generic relationships are largely unknown. By virtue of high substitution rates within the species and the ability to resolve the phylogenetic position of morphologically very closely related species and species complexes, the matK gene has emerged as one of the potential chloroplast DNA molecular markers in plant molecular phylogenetics and DNA barcoding studies. We herein used molecular phylogenetic analyses of matK gene sequences using maximum parsimony and maximum likelihood analyses to infer the generic relationships among currently recognized genera circumscribed under the family Molluginaceae. The resulting phylogenetic tree confirmed the polyphyly of the family Molluginaceae. The genus Hypertelis was found at the base of the Molluginaceae clade. The genus Glinus was close to Glischrothamnus and Mollugo, Suessenguthiella was close to Coelanthum and Pharnaceum, whereas Polpoda grouped with Adenogramma and Psammotropha. The present study constitutes a robust investigation of the molecular phylogenetic relationships among members of the family Molluginaceae. Future study should combine by combined analyses of morphological characters and multiple nuclear and chloroplast DNA sequences with a more comprehensive taxon sampling of the family Molluginaceae.},
}
@article {pmid28664166,
year = {2017},
author = {Maetzig, T and Ruschmann, J and Sanchez Milde, L and Lai, CK and von Krosigk, N and Humphries, RK},
title = {Lentiviral Fluorescent Genetic Barcoding for Multiplex Fate Tracking of Leukemic Cells.},
journal = {Molecular therapy. Methods &amp; clinical development},
volume = {6},
number = {},
pages = {54-65},
pmid = {28664166},
issn = {2329-0501},
abstract = {Tracking the behavior of leukemic samples both in vitro and in vivo plays an increasingly large role in efforts to better understand the leukemogenic processes and the effects of potential new therapies. Such work can be accelerated and made more efficient by methodologies enabling the characterization of leukemia samples in multiplex assays. We recently developed three sets of lentiviral fluorescent genetic barcoding (FGB) vectors that create 26, 14, and 6 unique immunophenotyping-compatible color codes from GFP-, yellow fluorescent protein (YFP)-, and monomeric kusabira orange 2 (mKO2)-derived fluorescent proteins. These vectors allow for labeling and tracking of individual color-coded cell populations in mixed samples by real-time flow cytometry. Using the prototypical Hoxa9/Meis1 murine model of acute myeloid leukemia, we describe the application of the 6xFGB vector system for assessing leukemic cell characteristics in multiplex assays. By transplanting color-coded cell mixes, we investigated the competitive growth behavior of individual color-coded populations, determined leukemia-initiating cell frequencies, and assessed the dose-dependent potential of cells exposed to the histone deacetylase inhibitor Entinostat for bone marrow homing. Thus, FGB provides a useful tool for the multiplex characterization of leukemia samples in a wide variety of applications with a concomitant reduction in workload, processing times, and mouse utilization.},
}
@article {pmid28663753,
year = {2017},
author = {Yang, L and Danzberger, J and Schöler, A and Schröder, P and Schloter, M and Radl, V},
title = {Dominant Groups of Potentially Active Bacteria Shared by Barley Seeds become Less Abundant in Root Associated Microbiome.},
journal = {Frontiers in plant science},
volume = {8},
number = {},
pages = {1005},
pmid = {28663753},
issn = {1664-462X},
abstract = {Endophytes are microorganisms colonizing plant internal tissues. They are ubiquitously associated with plants and play an important role in plant growth and health. In this work, we grew five modern cultivars of barley in axenic systems using sterile sand mixture as well as in greenhouse with natural soil. We characterized the potentially active microbial communities associated with seeds and roots using rRNA based amplicon sequencing. The seeds of the different cultivars share a great part of their microbiome, as we observed a predominance of a few bacterial OTUs assigned to Phyllobacterium, Paenibacillus, and Trabusiella. Seed endophytes, particularly members of the Enterobacteriacea and Paenibacillaceae, were important members of root endophytes in axenic systems, where there were no external microbes. However, when plants were grown in soil, seed endophytes became less abundant in root associated microbiome. We observed a clear enrichment of Actinobacteriacea and Rhizobiaceae, indicating a strong influence of the soil bacterial communities on the composition of the root microbiome. Two OTUs assigned to Phyllobacteriaceae were found in all seeds and root samples growing in soil, indicating a relationship between seed-borne and root associated microbiome in barley. Even though the role of endophytic bacteria remains to be clarified, it is known that many members of the genera detected in our study produce phytohormones, shape seedling exudate profile and may play an important role in germination and establishment of the seedlings.},
}
@article {pmid28663602,
year = {2017},
author = {Marin-Felix, Y and Groenewald, JZ and Cai, L and Chen, Q and Marincowitz, S and Barnes, I and Bensch, K and Braun, U and Camporesi, E and Damm, U and de Beer, ZW and Dissanayake, A and Edwards, J and Giraldo, A and Hernández-Restrepo, M and Hyde, KD and Jayawardena, RS and Lombard, L and Luangsa-Ard, J and McTaggart, AR and Rossman, AY and Sandoval-Denis, M and Shen, M and Shivas, RG and Tan, YP and van der Linde, EJ and Wingfield, MJ and Wood, AR and Zhang, JQ and Zhang, Y and Crous, PW},
title = {Genera of phytopathogenic fungi: GOPHY 1.},
journal = {Studies in mycology},
volume = {86},
number = {},
pages = {99-216},
pmid = {28663602},
issn = {0166-0616},
abstract = {Genera of Phytopathogenic Fungi (GOPHY) is introduced as a new series of publications in order to provide a stable platform for the taxonomy of phytopathogenic fungi. This first paper focuses on 21 genera of phytopathogenic fungi: Bipolaris, Boeremia, Calonectria, Ceratocystis, Cladosporium, Colletotrichum, Coniella, Curvularia, Monilinia, Neofabraea, Neofusicoccum, Pilidium, Pleiochaeta, Plenodomus, Protostegia, Pseudopyricularia, Puccinia, Saccharata, Thyrostroma, Venturia and Wilsonomyces. For each genus, a morphological description and information about its pathology, distribution, hosts and disease symptoms are provided. In addition, this information is linked to primary and secondary DNA barcodes of the presently accepted species, and relevant literature. Moreover, several novelties are introduced, i.e. new genera, species and combinations, and neo-, lecto- and epitypes designated to provide a stable taxonomy. This first paper includes one new genus, 26 new species, ten new combinations, and four typifications of older names.},
}
@article {pmid28662530,
year = {2017},
author = {Sgamma, T and Lockie-Williams, C and Kreuzer, M and Williams, S and Scheyhing, U and Koch, E and Slater, A and Howard, C},
title = {DNA Barcoding for Industrial Quality Assurance.},
journal = {Planta medica},
volume = {83},
number = {14-15},
pages = {1117-1129},
doi = {10.1055/s-0043-113448},
pmid = {28662530},
issn = {1439-0221},
mesh = {Computational Biology ; DNA Barcoding, Taxonomic/*methods ; European Union ; Herbal Medicine/*standards ; High-Throughput Nucleotide Sequencing ; Plants, Medicinal/*classification ; Quality Control ; Sequence Analysis, DNA ; },
abstract = {DNA barcoding methods originally developed for the identification of plant specimens have been applied to the authentication of herbal drug materials for industrial quality assurance. These methods are intended to be complementary to current morphological and chemical methods of identification. The adoption of these methods by industry will be accelerated by the introduction of DNA-based identification techniques into regulatory standards and monographs. The introduction of DNA methods into the British Pharmacopoeia is described, along with a reference standard for use as a positive control for DNA extraction and polymerase chain reaction (PCR). A general troubleshooting chart is provided to guide the user through the problems that may be encountered during this process. Nevertheless, the nature of the plant materials and the demands of industrial quality control procedures mean that conventional DNA barcoding is not the method of choice for industrial quality control. The design of DNA barcode-targeted quantitative PCR and high resolution melt curve tests is one strategy for developing rapid, robust, and reliable protocols for high-throughput screening of raw materials. The development of authentication tests for wild-harvested Rhodiola rosea L. is used as a case study to exemplify these relatively simple tests. By way of contrast, the application of next-generation sequencing to create a complete profile of all the biological entities in a mixed herbal drug is described and its potential for industrial quality assurance discussed.},
}
@article {pmid28654351,
year = {2017},
author = {Araya-Jaime, C and Mateussi, NTB and Utsunomia, R and Costa-Silva, GJ and Oliveira, C and Foresti, F},
title = {ZZ/Z0: The New System of Sex Chromosomes in Eigenmannia aff. trilineata (Teleostei: Gymnotiformes: Sternopygidae) Characterized by Molecular Cytogenetics and DNA Barcoding.},
journal = {Zebrafish},
volume = {14},
number = {5},
pages = {464-470},
doi = {10.1089/zeb.2017.1422},
pmid = {28654351},
issn = {1557-8542},
mesh = {Animals ; Chromosome Mapping ; DNA Barcoding, Taxonomic/*methods ; Gymnotiformes/classification/*genetics ; Karyotyping ; *Repetitive Sequences, Nucleic Acid ; *Sex Chromosomes ; },
abstract = {The cytogenetic characteristics of Eigenmannia aff. trilineata were analyzed by basic and molecular cytogenetics, applying fluorescent in situ hybridization, with 18S and 5S rDNA and U2 snRNA probes. The species revealed a kind of polymorphism associated to ZZ/Z0 type sex chromosomes, with 2n = 32 (8m+2sm+22a, NF = 42) in all males under analysis, whereas females evidenced 2n = 31 (8m+1sm+22a, NF = 40). C-banding showed constitutive heterochromatin restricted to the pericentromeric region of all chromosomes and single-nucleolus organized regions on pair 11. A site for rDNA 5S was synthetic with a cluster of rDNA 18S near the centromere on the long arm of only one homologue of pair 11. Other clusters for 5S rDNA were sited on pairs 7, 10, 12, 13, and 16. Further, 5S rDNA was co-located with U2 cluster in the pericentromeric region of pair 12. Joint analysis of DNA barcoding from cytochrome c oxidase subunit I (COI) sequences, generated from the karyotyped samples of E. aff. trilineata, and sequences of other Gymnotiforms recognized E. aff. trilineata as an Operational Taxonomic Unit. Results foreground the hypothesis that cytotypes are independent evolution units as cryptic species with a low morphological differentiation level, although with high genetic/karyotype differentiation rates.},
}
@article {pmid28653593,
year = {2017},
author = {Caffara, M and Locke, SA and Echi, PC and Halajian, A and Benini, D and Luus-Powell, WJ and Tavakol, S and Fioravanti, ML},
title = {A morphological and molecular study of Clinostomid metacercariae from African fish with a redescription of Clinostomum tilapiae.},
journal = {Parasitology},
volume = {144},
number = {11},
pages = {1519-1529},
doi = {10.1017/S0031182017001068},
pmid = {28653593},
issn = {1469-8161},
mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA, Helminth/*genetics ; DNA, Mitochondrial ; DNA, Ribosomal Spacer ; Fish Diseases/*parasitology ; Fishes/*parasitology ; Fresh Water/parasitology ; Metacercariae/anatomy &amp; histology/genetics ; South Africa ; Trematoda/*anatomy &amp; histology/classification/*genetics/physiology ; Trematode Infections/parasitology/*veterinary ; },
abstract = {The genus Clinostomum Leidy, 1856 (Digenea: Clinostomidae) has been reported in all ecozones of the world and a clear separation between the species of the 'Old World' and 'New World' has been recognized based on molecular studies. Recent works on Afrotropical species include redescriptions of C. cutaneum and C. phalacrocoracis, while C. tilapiae has yet to be studied using modern taxonomic approaches. In the present research, morphological redescription of C. tilapiae metacercariae from a new host, Synodontis batensoda sampled at Anambra River Basin, Nigeria, together with molecular analysis of nuclear internal transcribed spacer rDNA and cytochrome c oxidase 1 mtDNA are reported. We also provide morphological and molecular data from four further putative species of Clinostomum (morphotypes 1-4) from different areas of Africa, as well as the first report of C. phalacrocoracis in South Africa.},
}
@article {pmid28652184,
year = {2017},
author = {Dhar, B and Ghosh, SK},
title = {Mini-DNA barcode in identification of the ornamental fish: A case study from Northeast India.},
journal = {Gene},
volume = {627},
number = {},
pages = {248-254},
doi = {10.1016/j.gene.2017.06.043},
pmid = {28652184},
issn = {1879-0038},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods/standards ; Fishes/classification/*genetics ; },
abstract = {The ornamental fishes were exported under the trade names or generic names, thus creating problems in species identification. In this regard, DNA barcoding could effectively elucidate the actual species status. However, the problem arises if the specimen is having taxonomic disputes, falsified by trade/generic names, etc., On the other hand, barcoding the archival museum specimens would be of greater benefit to address such issues as it would create firm, error-free reference database for rapid identification of any species. This can be achieved only by generating short sequences as DNA from chemically preserved are mostly degraded. Here we aimed to identify a short stretch of informative sites within the full-length barcode segment, capable of delineating diverse group of ornamental fish species, commonly traded from NE India. We analyzed 287 full-length barcode sequences from the major fish orders and compared the interspecific K2P distance with nucleotide substitutions patterns and found a strong correlation of interspecies distance with transversions (0.95, p<0.001). We, therefore, proposed a short stretch of 171bp (transversion rich) segment as mini-barcode. The proposed segment was compared with the full-length barcodes and found to delineate the species effectively. Successful PCR amplification and sequencing of the 171bp segment using designed primers for different orders validated it as mini-barcodes for ornamental fishes. Thus, our findings would be helpful in strengthening the global database with the sequence of archived fish species as well as an effective identification tool of the traded ornamental fish species, as a less time consuming, cost effective field-based application.},
}
@article {pmid28651582,
year = {2017},
author = {He, XL and Li, Q and Peng, WH and Zhou, J and Cao, XL and Wang, D and Huang, ZQ and Tan, W and Li, Y and Gan, BC},
title = {Intra- and inter-isolate variation of ribosomal and protein-coding genes in Pleurotus: implications for molecular identification and phylogeny on fungal groups.},
journal = {BMC microbiology},
volume = {17},
number = {1},
pages = {139},
pmid = {28651582},
issn = {1471-2180},
mesh = {Cloning, Molecular ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/*genetics ; Fungal Proteins/*genetics ; Peptide Elongation Factor 1/*genetics ; Phylogeny ; Pleurotus/*classification/genetics ; Polymorphism, Genetic ; RNA Polymerase II/*genetics ; Reproducibility of Results ; Ribosomal Proteins/genetics ; Sequence Analysis, DNA/methods ; Species Specificity ; },
abstract = {BACKGROUND: The internal transcribed spacer (ITS), RNA polymerase II second largest subunit (RPB2), and elongation factor 1-alpha (EF1α) are often used in fungal taxonomy and phylogenetic analysis. As we know, an ideal molecular marker used in molecular identification and phylogenetic studies is homogeneous within species, and interspecific variation exceeds intraspecific variation. However, during our process of performing ITS, RPB2, and EF1α sequencing on the Pleurotus spp., we found that intra-isolate sequence polymorphism might be present in these genes because direct sequencing of PCR products failed in some isolates. Therefore, we detected intra- and inter-isolate variation of the three genes in Pleurotus by polymerase chain reaction amplification and cloning in this study.<br><br>RESULTS: Results showed that intra-isolate variation of ITS was not uncommon but the polymorphic level in each isolate was relatively low in Pleurotus; intra-isolate variations of EF1&#x3b1; and RPB2 sequences were present in an unexpectedly high amount. The polymorphism level differed significantly between ITS, RPB2, and EF1&#x3b1; in the same individual, and the intra-isolate heterogeneity level of each gene varied between isolates within the same species. Intra-isolate and intraspecific variation of ITS in the tested isolates was less than interspecific variation, and intra-isolate and intraspecific variation of RPB2 was probably equal with interspecific divergence. Meanwhile, intra-isolate and intraspecific variation of EF1&#x3b1; could exceed interspecific divergence. These findings suggested that RPB2 and EF1&#x3b1; are not desirable barcoding candidates for Pleurotus. We also discussed the reason why rDNA and protein-coding genes showed variants within a single isolate in Pleurotus, but must be addressed in further research.<br><br>CONCLUSIONS: Our study demonstrated that intra-isolate variation of ribosomal and protein-coding genes are likely widespread in fungi. This has implications for studies on fungal evolution, taxonomy, phylogenetics, and population genetics. More extensive sampling of these genes and other candidates will be required to ensure reliability as phylogenetic markers and DNA barcodes.},
}
@article {pmid28651381,
year = {2017},
author = {Laha, RC and De Mandal, S and Ralte, L and Ralte, L and Kumar, NS and Gurusubramanian, G and Satishkumar, R and Mugasimangalam, R and Kuravadi, NA},
title = {Meta-barcoding in combination with palynological inference is a potent diagnostic marker for honey floral composition.},
journal = {AMB Express},
volume = {7},
number = {1},
pages = {132},
pmid = {28651381},
issn = {2191-0855},
abstract = {Identification of floral samples present in honey is important in order to determine the medicinal value, enhance the production of honey as well as to conserve the honey bees. Traditional approaches for studying pollen samples are based on microscopic observation which is laborious, time intensive and requires specialized palynological knowledge. Present study compares two composite honey metagenome collected from 20 samples in Mizoram, Northeast India using three gene loci- rbcL, matK and ITS2 that was sequenced using a next-generation sequencing (NGS) platform (Illumina Miseq). Furthermore, a classical palynology study for all 20 samples was carried out to evaluate the NGS approach. NGS based approach and pollen microscopic studies were able to detect the most abundant floral components of honey. We investigated the plants that were frequently used by honey bees by examining the results obtained from both the techniques. Microscopic examination of pollens detected plants with a broad taxonomic range covering 26 families. NGS based multigene approach revealed diverse plant species, which was higher than in any other previously reported techniques using a single locus. Frequently found herbaceous species were from the family Poaceae, Myrtaceae, Fabaceae and Asteraceae. The future NGS based approach using multi-loci target, with the help of an improved and robust plant database, can be a potential replacement technique for tedious microscopic studies to identify the polleniferous plants.},
}
@article {pmid28651291,
year = {2017},
author = {Zhang, N and Ramachandran, P and Wen, J and Duke, JA and Metzman, H and McLaughlin, W and Ottesen, AR and Timme, RE and Handy, SM},
title = {Development of a Reference Standard Library of Chloroplast Genome Sequences, GenomeTrakrCP.},
journal = {Planta medica},
volume = {83},
number = {18},
pages = {1420-1430},
doi = {10.1055/s-0043-113449},
pmid = {28651291},
issn = {1439-0221},
mesh = {DNA Barcoding, Taxonomic ; DNA, Chloroplast/chemistry/genetics ; Databases, Nucleic Acid/*standards ; Genome, Chloroplast/*genetics ; Molecular Sequence Annotation ; Plant Leaves/classification/genetics ; Plants/*classification/genetics ; Reference Standards ; Species Specificity ; United States ; United States Food and Drug Administration ; },
abstract = {Precise, species-level identification of plants in foods and dietary supplements is difficult. While the use of DNA barcoding regions (short regions of DNA with diagnostic utility) has been effective for many inquiries, it is not always a robust approach for closely related species, especially in highly processed products. The use of fully sequenced chloroplast genomes, as an alternative to short diagnostic barcoding regions, has demonstrated utility for closely related species. The U. S. Food and Drug Administration (FDA) has also developed species-specific DNA-based assays targeting plant species of interest by utilizing chloroplast genome sequences. Here, we introduce a repository of complete chloroplast genome sequences called GenomeTrakrCP, which will be publicly available at the National Center for Biotechnology Information (NCBI). Target species for inclusion are plants found in foods and dietary supplements, toxin producers, common contaminants and adulterants, and their close relatives. Publicly available data will include annotated assemblies, raw sequencing data, and voucher information with each NCBI accession associated with an authenticated reference herbarium specimen. To date, 40 complete chloroplast genomes have been deposited in GenomeTrakrCP (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA325670/), and this will be expanded in the future.},
}
@article {pmid28650462,
year = {2017},
author = {Zhang, F and Christiansen, L and Thomas, J and Pokholok, D and Jackson, R and Morrell, N and Zhao, Y and Wiley, M and Welch, E and Jaeger, E and Granat, A and Norberg, SJ and Halpern, A and C Rogert, M and Ronaghi, M and Shendure, J and Gormley, N and Gunderson, KL and Steemers, FJ},
title = {Haplotype phasing of whole human genomes using bead-based barcode partitioning in a single tube.},
journal = {Nature biotechnology},
volume = {35},
number = {9},
pages = {852-857},
pmid = {28650462},
issn = {1546-1696},
mesh = {DNA Barcoding, Taxonomic/*methods ; Genome, Human/*genetics ; Genomics/*methods ; Haplotypes/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; },
abstract = {Haplotype-resolved genome sequencing promises to unlock a wealth of information in population and medical genetics. However, for the vast majority of genomes sequenced to date, haplotypes have not been determined because of cumbersome haplotyping workflows that require fractions of the genome to be sequenced in a large number of compartments. Here we demonstrate barcode partitioning of long DNA molecules in a single compartment using "on-bead" barcoded tagmentation. The key to the method that we call "contiguity preserving transposition" sequencing on beads (CPTv2-seq) is transposon-mediated transfer of homogenous populations of barcodes from beads to individual long DNA molecules that get fragmented at the same time (tagmentation). These are then processed to sequencing libraries wherein all sequencing reads originating from each long DNA molecule share a common barcode. Single-tube, bulk processing of long DNA molecules with ∼150,000 different barcoded bead types provides a barcode-linked read structure that reveals long-range molecular contiguity. This technology provides a simple, rapid, plate-scalable and automatable route to accurate, haplotype-resolved sequencing, and phasing of structural variants of the genome.},
}
@article {pmid28646202,
year = {2017},
author = {Proença, DN and Francisco, R and Kublik, S and Schöler, A and Vestergaard, G and Schloter, M and Morais, PV},
title = {The Microbiome of Endophytic, Wood Colonizing Bacteria from Pine Trees as Affected by Pine Wilt Disease.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {4205},
pmid = {28646202},
issn = {2045-2322},
mesh = {Bacteria/*genetics/isolation &amp; purification ; Biodiversity ; Colony Count, Microbial ; DNA Barcoding, Taxonomic ; DNA Fingerprinting ; Endophytes/*genetics ; Microbiota/*genetics ; Phylogeny ; Pinus/*microbiology ; Plant Diseases/*microbiology ; Principal Component Analysis ; Wood/*microbiology ; },
abstract = {Pine wilt disease (PWD) is a devastating forest disease present worldwide. In this study we analyzed the effects of the invasion of the pinewood nematode Bursaphelenchus xylophilus, the major pathogen causing PWD, on the endophytic microbiome of adult P. pinaster trees. Wood samples from trees with different degrees of PWD disease were collected at two sites (A and M) in Portugal. Endophytic bacteria were characterized based on directly extracted DNA by fingerprinting and barcoding using the 16S rRNA gene as marker. Furthermore, cultivation-based approaches were used to obtain isolates of the major taxa to study their ecophysiology. The endophytic microbiome from P. pinaster trees differed significantly between the two sampling sites. Main bacterial OTUs belonged to the Proteobacteria (39% (site M) - 97% (site A)), and Firmicutes (0.70% (site A) - 44% (site M)). However, consequences of the invasion with the pathogen were comparable. Interestingly diversity of wood endophytic bacteria increased with the severity of the diseases, with highest diversity levels observed in in the most affected trees. Our results suggest that in the first stages of the disease, the defence mechanisms of plants are repressed by the pathogen, resulting in a colonization of the wood interior by soil microorganisms.},
}
@article {pmid28645767,
year = {2017},
author = {Suchan, T and Espíndola, A and Rutschmann, S and Emerson, BC and Gori, K and Dessimoz, C and Arrigo, N and Ronikier, M and Alvarez, N},
title = {Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study.},
journal = {Molecular phylogenetics and evolution},
volume = {114},
number = {},
pages = {189-198},
doi = {10.1016/j.ympev.2017.06.012},
pmid = {28645767},
issn = {1095-9513},
mesh = {Animals ; Base Sequence ; Biological Evolution ; DNA/*chemistry/isolation &amp; purification/metabolism ; DNA Restriction Enzymes/metabolism ; DNA, Mitochondrial/classification/metabolism ; Diptera/*classification/genetics ; Genetic Loci ; Genetic Markers/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Determining phylogenetic relationships among recently diverged species has long been a challenge in evolutionary biology. Cytoplasmic DNA markers, which have been widely used, notably in the context of molecular barcoding, have not always proved successful in resolving such phylogenies. However, with the advent of next-generation-sequencing technologies and associated techniques of reduced genome representation, phylogenies of closely related species have been resolved at a much higher detail in the last couple of years. Here we examine the potential and limitations of one of such techniques-Restriction-site Associated DNA (RAD) sequencing, a method that produces thousands of (mostly) anonymous nuclear markers, in disentangling the phylogeny of the fly genus Chiastocheta (Diptera: Anthomyiidae). In Europe, this genus encompasses seven species of seed predators, which have been widely studied in the context of their ecological and evolutionary interactions with the plant Trollius europaeus (Ranunculaceae). So far, phylogenetic analyses using mitochondrial markers failed to resolve monophyly of most of the species from this recently diversified genus, suggesting that their taxonomy may need a revision. However, relying on a single, non-recombining marker and ignoring potential incongruences between mitochondrial and nuclear loci may provide an incomplete account of the lineage history. In this study, we applied both classical Sanger sequencing of three mtDNA regions and RAD-sequencing, for reconstructing the phylogeny of the genus. Contrasting with results based on mitochondrial markers, RAD-sequencing analyses retrieved the monophyly of all seven species, in agreement with the morphological species assignment. We found robust nuclear-based species assignment of individual samples, and low levels of estimated contemporary gene flow among them. However, despite recovering species' monophyly, interspecific relationships varied depending on the set of RAD loci considered, producing contradictory topologies. Moreover, coalescence-based phylogenetic analyses revealed low supports for most of the interspecific relationships. Our results indicate that despite the higher performance of RAD-sequencing in terms of species trees resolution compared to cytoplasmic markers, reconstructing inter-specific relationships among recently-diverged lineages may lie beyond the possibilities offered by large sets of RAD-sequencing markers in cases of strong gene tree incongruence.},
}
@article {pmid28642581,
year = {2017},
author = {Cock, MJW and Beseh, PK and Buddie, AG and Cafá, G and Crozier, J},
title = {Molecular methods to detect Spodoptera frugiperda in Ghana, and implications for monitoring the spread of invasive species in developing countries.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {4103},
pmid = {28642581},
issn = {2045-2322},
mesh = {Animals ; Developing Countries ; Genes, Mitochondrial ; Ghana ; *Introduced Species ; Phylogeny ; Spodoptera/classification/*genetics ; Zea mays/parasitology ; },
abstract = {Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) is a polyphagous pest indigenous throughout the Americas, which recently appeared in Africa, first reported from São Tomé, Nigeria, Bénin and Togo in 2016, and which we now report from Ghana. This species is recognised to comprise two morphologically identical but genetically distinct strains or species in the Americas, and we found both to be present in Ghana. We discuss possible routes of entry to Africa, of which the likeliest is adults and/or egg masses transported on direct commercial flights between the Americas and West Africa, followed by dispersal by adult flight within Africa. Identification of Lepidoptera is normally based on the markings and morphology of adults, and not on the larvae which actually cause the damage, and therefore larvae have to be reared through to adult for authoritative identification. We confirmed that the use of DNA barcoding allowed unequivocal identification of this new pest from Ghana based on the larvae alone. As authenticated barcodes for vouchered specimens of more pests become available, this approach has the potential to become a valuable in-country tool to support national capability in rapid and reliable pest diagnosis and identification.},
}
@article {pmid28642488,
year = {2017},
author = {Damase, TR and Spencer, A and Samuel, B and Allen, PB},
title = {Biomimetic Molecular Signaling using DNA Walkers on Microparticles.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {4081},
pmid = {28642488},
issn = {2045-2322},
support = {P20 GM103408/GM/NIGMS NIH HHS/United States ; },
mesh = {*Biomimetics/methods ; DNA/*chemistry ; DNA, Catalytic ; Fluorescent Dyes ; Hydrogels/chemistry ; Nanoparticles/*chemistry ; Nanotechnology ; },
abstract = {We report the release of catalytic DNA walkers from hydrogel microparticles and the detection of those walkers by substrate-coated microparticles. This might be considered a synthetic biology analog of molecular signal release and reception. One type of particles was coated with components of a DNA one-step strand displacement (OSD) reaction to release the walker. A second type of particle was coated with substrate (or "track") for the molecular walker. We distinguish these particle types using fluorescence barcoding: we synthesized and distinguished multiple particle types with multicolor fluorescence microscopy and automated image analysis software. This represents a step toward amplified, multiplex, and microscopically localized detection based on DNA nanotechnology.},
}
@article {pmid28640821,
year = {2017},
author = {Torche, PC and Müller, V and Westerlund, F and Ambjörnsson, T},
title = {Noise reduction in single time frame optical DNA maps.},
journal = {PloS one},
volume = {12},
number = {6},
pages = {e0179041},
pmid = {28640821},
issn = {1932-6203},
mesh = {*Optical Phenomena ; Plasmids/genetics ; Sequence Analysis, DNA/*methods ; *Signal-To-Noise Ratio ; Time Factors ; },
abstract = {In optical DNA mapping technologies sequence-specific intensity variations (DNA barcodes) along stretched and stained DNA molecules are produced. These "fingerprints" of the underlying DNA sequence have a resolution of the order one kilobasepairs and the stretching of the DNA molecules are performed by surface adsorption or nano-channel setups. A post-processing challenge for nano-channel based methods, due to local and global random movement of the DNA molecule during imaging, is how to align different time frames in order to produce reproducible time-averaged DNA barcodes. The current solutions to this challenge are computationally rather slow. With high-throughput applications in mind, we here introduce a parameter-free method for filtering a single time frame noisy barcode (snap-shot optical map), measured in a fraction of a second. By using only a single time frame barcode we circumvent the need for post-processing alignment. We demonstrate that our method is successful at providing filtered barcodes which are less noisy and more similar to time averaged barcodes. The method is based on the application of a low-pass filter on a single noisy barcode using the width of the Point Spread Function of the system as a unique, and known, filtering parameter. We find that after applying our method, the Pearson correlation coefficient (a real number in the range from -1 to 1) between the single time-frame barcode and the time average of the aligned kymograph increases significantly, roughly by 0.2 on average. By comparing to a database of more than 3000 theoretical plasmid barcodes we show that the capabilities to identify plasmids is improved by filtering single time-frame barcodes compared to the unfiltered analogues. Since snap-shot experiments and computational time using our method both are less than a second, this study opens up for high throughput optical DNA mapping with improved reproducibility.},
}
@article {pmid28635635,
year = {2017},
author = {Dalén, L and Lagerholm, VK and Nylander, JAA and Barton, N and Bochenski, ZM and Tomek, T and Rudling, D and Ericson, PGP and Irestedt, M and Stewart, JR},
title = {Identifying Bird Remains Using Ancient DNA Barcoding.},
journal = {Genes},
volume = {8},
number = {6},
pages = {},
pmid = {28635635},
issn = {2073-4425},
abstract = {Bird remains that are difficult to identify taxonomically using morphological methods, are common in the palaeontological record. Other types of challenging avian material include artefacts and food items from endangered taxa, as well as remains from aircraft strikes. We here present a DNA-based method that enables taxonomic identification of bird remains, even from material where the DNA is heavily degraded. The method is based on the amplification and sequencing of two short variable parts of the 16S region in the mitochondrial genome. To demonstrate the applicability of this approach, we evaluated the method on a set of Holocene and Late Pleistocene postcranial bird bones from several palaeontological and archaeological sites in Europe with good success.},
}
@article {pmid28634359,
year = {2017},
author = {Weissenböck, H and Bagó, Z and Kolodziejek, J and Hager, B and Palmetzhofer, G and Dürrwald, R and Nowotny, N},
title = {Infections of horses and shrews with Bornaviruses in Upper Austria: a novel endemic area of Borna disease.},
journal = {Emerging microbes &amp; infections},
volume = {6},
number = {6},
pages = {e52},
pmid = {28634359},
issn = {2222-1751},
mesh = {Animals ; Antigens, Viral ; Austria/epidemiology ; Borna Disease/complications/*epidemiology/pathology/*virology ; Borna disease virus/genetics/*isolation &amp; purification ; Disease Reservoirs/*veterinary/virology ; Encephalitis, Viral/epidemiology/etiology/veterinary ; Endemic Diseases/*veterinary ; Horses ; Phylogeny ; Polymerase Chain Reaction ; RNA, Viral/genetics ; Shrews/*virology ; },
abstract = {Borna disease, a lethal infection with Borna disease virus-1 (BoDV-1), was diagnosed in four horses from Upper Austria in 2015 and 2016. All cases occurred in winter (two cases in February 2015 and two cases in December 2016), and the maximal distance of the affected stables was 17 km. To demonstrate whether the causative agent was also harbored by its reservoir host, the bicolored white-toothed shrew (Crocidura leucodon), 28 shrews from this geographic area were collected in 2015 and investigated for the presence of BoDV-1. The shrew species were identified according to taxonomic clues and molecular barcodes. Affected horses and all shrews were investigated using histology, immunohistochemistry (IHC) and reverse transcription PCR. The horses exhibited severe nonpurulent encephalitis. Large amounts of BoDV-1 antigen were identified in their CNS. Among the 28 shrews, nine were identified as C. leucodon and 13 as Sorex araneus (Common shrew; Eurasian shrew). Six C. leucodon (66.7%) and one S. araneus (7.7%) had BoDV-1 infections. In accordance with previous findings, the IHC of C. leucodon exhibited a high amount of viral antigen in many neural and extraneural tissues. By contrast, the single positive S. araneus had an exclusively neural staining pattern. Of all positive samples, whole-genome BoDV-1 sequences were generated. The acquired sequences of the affected shrews were not identical to each other and clustered around the sequences of the diseased horses belonging, surprisingly, to the German 'strain V' cluster.},
}
@article {pmid28633080,
year = {2017},
author = {Schmid-Burgk, JL},
title = {Disruptive non-disruptive applications of CRISPR/Cas9.},
journal = {Current opinion in biotechnology},
volume = {48},
number = {},
pages = {203-209},
doi = {10.1016/j.copbio.2017.06.001},
pmid = {28633080},
issn = {1879-0429},
mesh = {Base Sequence ; CRISPR-Cas Systems/*genetics ; Computational Biology ; Epigenesis, Genetic ; Genome ; RNA Editing/genetics ; },
abstract = {The bacterial type II Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR Associated (Cas) systems, and in particular Streptococcus pyogenes CRISPR-Cas9, have been broadly applied to edit the genome of bacterial and eukaryotic cells. Cas9, which is an RNA-guided programmable nuclease, is a powerful tool for disrupting protein-coding genes. Cas9 cleaves target sites to generate a double-strand break (DSB) that is repaired via an error-prone repair process, leading to insertion/deletion mutations and gene knockouts. However, Cas9 can also be used to modulate genome function without gene disruption, enabling base editing, transcriptional and epigenetic reprogramming, genome imaging, cellular barcoding, genetic recording, and genetic computation.},
}
@article {pmid28630464,
year = {2017},
author = {McCarthy, RL and Mak, DH and Burks, JK and Barton, MC},
title = {Rapid monoisotopic cisplatin based barcoding for multiplexed mass cytometry.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {3779},
pmid = {28630464},
issn = {2045-2322},
support = {P30 CA016672/CA/NCI NIH HHS/United States ; },
mesh = {Cell Line ; Cisplatin/*pharmacokinetics/*pharmacology ; Human Embryonic Stem Cells/cytology/*metabolism ; Humans ; Mass Spectrometry/*methods ; Molecular Typing/*methods ; },
abstract = {Mass cytometry presents an exceptional opportunity to interrogate the biology of highly heterogeneous cell populations, owing to the ability to collect highly parametric proteomic data at a single cell level. However, sample-to-sample variability, due to antibody staining and/or instrument sensitivity, can introduce substantial artifacts into the data, which can in turn lead to erroneous conclusions. This variability can be eliminated by sample barcoding which enables samples to be pooled, stained and run simultaneously. Existing mass cytometry barcoding approaches require time intensive labeling, reduce the number of biologically meaningful parameters and/or rely on expensive reagents. We present an approach utilizing monoisotopic cisplatin to perform cell barcoding that does not require cell permeabilization, can be completed in 10 minutes and can be utilized in combination with existing barcoding techniques to greatly increase the number of samples which can be multiplexed to improve throughput and consistency.},
}
@article {pmid28629531,
year = {2017},
author = {Duan, BZ and Fang, HL and Li, XW and Huang, LF and Ping, W and Chen, SL},
title = {Survey of traditional Dai medicine reveals species confusion and potential safety concerns: a case study on Radix Clerodendri Japonicum.},
journal = {Chinese journal of natural medicines},
volume = {15},
number = {6},
pages = {417-426},
doi = {10.1016/S1875-5364(17)30063-8},
pmid = {28629531},
issn = {1875-5364},
mesh = {Clerodendrum/classification/*genetics ; *DNA Barcoding, Taxonomic ; *Drug Contamination ; *Medicine, Chinese Traditional/adverse effects ; Polymerase Chain Reaction ; },
abstract = {The adulteration of herbal products is a threat to consumer safety. In the present study, we surveyed the species composition of commercial Radix Clerodendri Japonicum products using DNA barcoding as a supervisory method. A reference database for plant-material DNA-barcode was successfully constructed with 48 voucher samples from 12 Clerodendrum species. The database was used to identify 27 Radix Clerodendri Japonicum decoction piece samples purchased from drug stores and hospitals. The DNA sequencing results revealed that only 1 decoction piece (3.70%) was authentic C. japonicum, as recorded in the Dai Pharmacopeia, whereas the other samples were all adulterants, indicating a potential safety issue. The results indicate that decoction pieces that are available in the market have complex origins and that DNA barcoding is a suitable tool for regulation of Dai medicines.},
}
@article {pmid28629429,
year = {2017},
author = {Greer, SU and Nadauld, LD and Lau, BT and Chen, J and Wood-Bouwens, C and Ford, JM and Kuo, CJ and Ji, HP},
title = {Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases.},
journal = {Genome medicine},
volume = {9},
number = {1},
pages = {57},
pmid = {28629429},
issn = {1756-994X},
support = {K08 CA166512/CA/NCI NIH HHS/United States ; P01 HG000205/HG/NHGRI NIH HHS/United States ; R01 HG006137/HG/NHGRI NIH HHS/United States ; P30 DK056339/DK/NIDDK NIH HHS/United States ; },
mesh = {Genome, Human ; Genomics/methods ; Haplotypes ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Mutation ; *Neoplasm Metastasis ; Sequence Analysis, DNA/*methods ; Stomach Neoplasms/*genetics/pathology ; },
abstract = {BACKGROUND: Genome rearrangements are critical oncogenic driver events in many malignancies. However, the identification and resolution of the structure of cancer genomic rearrangements remain challenging even with whole genome sequencing.<br><br>METHODS: To identify oncogenic genomic rearrangements and resolve their structure, we analyzed linked read sequencing. This approach relies on a microfluidic droplet technology to produce libraries derived from single, high molecular weight DNA molecules, 50 kb in size or greater. After sequencing, the barcoded sequence reads provide long range genomic information, identify individual high molecular weight DNA molecules, determine the haplotype context of genetic variants that occur across contiguous megabase-length segments of the genome and delineate the structure of complex rearrangements. We applied linked read sequencing of whole genomes to the analysis of a set of synchronous metastatic diffuse gastric cancers that occurred in the same individual.<br><br>RESULTS: When comparing metastatic sites, our analysis implicated a complex somatic rearrangement that was present in the metastatic tumor. The oncogenic event associated with the identified complex rearrangement resulted in an amplification of the known cancer driver gene FGFR2. With further investigation using these linked read data, the FGFR2 copy number alteration was determined to be a deletion-inversion motif that underwent tandem duplication, with unique breakpoints in each metastasis. Using a three-dimensional organoid tissue model, we functionally validated the metastatic potential of an FGFR2 amplification in gastric cancer.<br><br>CONCLUSIONS: Our study demonstrates that linked read sequencing is useful in characterizing oncogenic rearrangements in cancer metastasis.},
}
@article {pmid28624254,
year = {2017},
author = {Assouly, P},
title = {[Of corkscrews and barcodes].},
journal = {Annales de dermatologie et de venereologie},
volume = {144},
number = {8-9},
pages = {488-489},
doi = {10.1016/j.annder.2017.05.011},
pmid = {28624254},
issn = {0151-9638},
mesh = {*Dermoscopy/methods ; Diagnosis, Differential ; Hair/*pathology ; Hair Diseases/*diagnosis ; Humans ; Scalp Dermatoses/*diagnosis ; Staining and Labeling/methods ; },
}
@article {pmid28622748,
year = {2018},
author = {Iswarya Deepti, V and Kandula, S and Khedkar, GD},
title = {DNA barcoding of five species of groupers (Pisces: Serranidae) off Visakhapatnam, central eastern coast of India.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {659-663},
doi = {10.1080/24701394.2017.1339188},
pmid = {28622748},
issn = {2470-1408},
mesh = {Animals ; Bass/*genetics ; DNA ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Genetic Speciation ; Genome, Mitochondrial/*genetics ; India ; Mitochondria/genetics ; Perciformes/genetics ; Phylogeny ; },
abstract = {Grouper species of Epinephelus - E. epistictus, E. heniochus, E. latifasciatus, E. magniscuttis and E. radiatus exhibit overlapping colour pattern that often leads to misidentification in the field. Even the colour pattern of juveniles of these species in different size groups varies considerably with that of adults. DNA barcoding of these five species was carried out to reinforce our knowledge on existing taxonomic relationships derived based on morphological and biochemical genetic studies that were previously done from Indian waters. Mean interspecific genetic distance is in the range 0.079-0.164.The phylogeny tree revealed distinct clades for species that are in concurrence with previous taxonomic and allozyme electrophoretic studies carried out from central eastern coast of India. Barcode sequences generated for the first time for species E. heniochus from Indian waters for E. magniscuttis so far there are no reference sequences in GenBank.},
}
@article {pmid28620408,
year = {2017},
author = {Jia, J and Xu, Z and Xin, T and Shi, L and Song, J},
title = {Quality Control of the Traditional Patent Medicine Yimu Wan Based on SMRT Sequencing and DNA Barcoding.},
journal = {Frontiers in plant science},
volume = {8},
number = {},
pages = {926},
pmid = {28620408},
issn = {1664-462X},
abstract = {Substandard traditional patent medicines may lead to global safety-related issues. Protecting consumers from the health risks associated with the integrity and authenticity of herbal preparations is of great concern. Of particular concern is quality control for traditional patent medicines. Here, we establish an effective approach for verifying the biological composition of traditional patent medicines based on single-molecule real-time (SMRT) sequencing and DNA barcoding. Yimu Wan (YMW), a classical herbal prescription recorded in the Chinese Pharmacopoeia, was chosen to test the method. Two reference YMW samples were used to establish a standard method for analysis, which was then applied to three different batches of commercial YMW samples. A total of 3703 and 4810 circular-consensus sequencing (CCS) reads from two reference and three commercial YMW samples were mapped to the ITS2 and psbA-trnH regions, respectively. Moreover, comparison of intraspecific genetic distances based on SMRT sequencing data with reference data from Sanger sequencing revealed an ITS2 and psbA-trnH intergenic spacer that exhibited high intraspecific divergence, with the sites of variation showing significant differences within species. Using the CCS strategy for SMRT sequencing analysis was adequate to guarantee the accuracy of identification. This study demonstrates the application of SMRT sequencing to detect the biological ingredients of herbal preparations. SMRT sequencing provides an affordable way to monitor the legality and safety of traditional patent medicines.},
}
@article {pmid28620101,
year = {2017},
author = {Larsson, J},
title = {Barcodes show family trees in ALL.},
journal = {Blood},
volume = {129},
number = {24},
pages = {3139-3140},
doi = {10.1182/blood-2017-05-780023},
pmid = {28620101},
issn = {1528-0020},
mesh = {*DNA Barcoding, Taxonomic ; *Pedigree ; Phylogeny ; },
}
@article {pmid28616174,
year = {2017},
author = {Gaitán-Espitia, JD and Gómez, D and Hobday, AJ and Daley, R and Lamilla, J and Cárdenas, L},
title = {Spatial overlap of shark nursery areas and the salmon farming industry influences the trophic ecology of Squalus acanthias on the southern coast of Chile.},
journal = {Ecology and evolution},
volume = {7},
number = {11},
pages = {3773-3783},
pmid = {28616174},
issn = {2045-7758},
abstract = {Potential interactions between marine predators and humans arise in the southern coast of Chile where predator feeding and reproduction sites overlap with fisheries and aquaculture. Here, we assess the potential effects of intensive salmon aquaculture on food habits, growth, and reproduction of a common predator, the spiny dogfish-identified as Squalus acanthias via genetic barcoding. A total of 102 (89 females and 13 males) individuals were collected during winter and summer of 2013-2014 from the Chiloé Sea where salmon aquaculture activities are concentrated. The low frequency of males in our study suggests spatial segregation of sex, while immature and mature females spatially overlapped in both seasons. Female spiny dogfish showed a functional specialist behavior as indicated by the small number of prey items and the relative high importance of the austral hake and salmon pellets in the diet. Immature sharks fed more on pellets and anchovies than the larger hake-preferring mature females. Our results also indicate that spiny dogfish switch prey (anchovy to hake) to take advantage of seasonal changes in prey availability. Despite differences in the trophic patterns of S. acanthias due to the spatial association with intensive salmon farming, in this region, there appears to be no difference in fecundity or size at maturity compared to other populations. Although no demographic effects were detected, we suggest that a range of additional factors should be considered before concluding that intensive aquaculture does not have any impact on these marine predators.},
}
@article {pmid28615189,
year = {2017},
author = {Fernius, J and Starkenberg, A and Thor, S},
title = {Bar-coding neurodegeneration: identifying subcellular effects of human neurodegenerative disease proteins using Drosophila leg neurons.},
journal = {Disease models &amp; mechanisms},
volume = {10},
number = {8},
pages = {1027-1038},
pmid = {28615189},
issn = {1754-8411},
mesh = {Actin Cytoskeleton/metabolism ; Actins/metabolism ; Animals ; Biomarkers/metabolism ; Cell Nucleus/metabolism ; Cell Survival ; Drosophila melanogaster/*metabolism ; Extremities/*innervation/pathology ; Fluorescence ; Genes, Reporter ; Glutamates/metabolism ; Green Fluorescent Proteins/metabolism ; Humans ; Longevity ; Mitochondria/metabolism ; Motor Neurons/metabolism ; Movement ; Nerve Degeneration/*pathology ; Nerve Tissue Proteins/*metabolism ; Neurodegenerative Diseases/*pathology ; Neurons/*metabolism/pathology ; Sensory Receptor Cells/metabolism ; Subcellular Fractions/metabolism ; },
abstract = {Genetic, biochemical and histological studies have identified a number of different proteins as key drivers of human neurodegenerative diseases. Although different proteins are typically involved in different diseases, there is also considerable overlap. Addressing disease protein dysfunction in an in vivo neuronal context is often time consuming and requires labor-intensive analysis of transgenic models. To facilitate the rapid, cellular analysis of disease protein dysfunction, we have developed a fruit fly (Drosophila melanogaster) adult leg neuron assay. We tested the robustness of 41 transgenic fluorescent reporters and identified a number that were readily detected in the legs and could report on different cellular events. To test these reporters, we expressed a number of human proteins involved in neurodegenerative disease, in both their mutated and wild-type versions, to address the effects on reporter expression and localization. We observed strikingly different effects of the different disease proteins upon the various reporters with, for example, Aβ[1-42] being highly neurotoxic, tau, parkin and HTT[128Q] affecting mitochondrial distribution, integrity or both, and Aβ[1-42], tau, HTT[128Q] and ATX1[82Q] affecting the F-actin network. This study provides proof of concept for using the Drosophila adult leg for inexpensive and rapid analysis of cellular effects of neurodegenerative disease proteins in mature neurons.},
}
@article {pmid28611392,
year = {2017},
author = {Wang, Q and Wang, X and Tang, PS and O'leary, GM and Zhang, M},
title = {Targeted sequencing of both DNA strands barcoded and captured individually by RNA probes to identify genome-wide ultra-rare mutations.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {3356},
pmid = {28611392},
issn = {2045-2322},
mesh = {DNA/*analysis/genetics ; DNA Mutational Analysis/*methods ; Genome, Human ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Mutation ; Neoplasm Proteins/*genetics ; Neoplasms/*genetics ; RNA/*analysis/genetics ; RNA Probes/chemistry/genetics ; },
abstract = {Next Generation Sequencing (NGS) has been widely implemented in biological research and has made a profound impact on patient care. One of the essential NGS applications is to identify disease-causing sequence variants, where high coverage and accuracy are needed. Here, we reported a novel NGS pipeline, termed a Sequencing System of Digitalized Barcode Encrypted Single-stranded Library from Extremely Low (quality and quantity) DNA Input with Probe-based DNA Enrichment by RNA probes targeting DNA duplex (DEEPER-Seq). This method combines an ultra-sensitive single-stranded library construction with barcoding error correction, termed DEEPER-Library; and a DNA capture approach using RNA probes targeting both DNA strands, termed DEEPER-Capture. DEEPER-Seq can create NGS libraries from as little as 20 pg DNA with PCR error correcting capabilities, and capture target sequences at an average ratio of 29.2% by targeting both DNA strands simultaneously with an over 98.6% coverage. Our method tags and sequences each of the two strands of a DNA duplex independently and only scores mutations that are found at the same position in both strands, which allows us to identify mutations with allelic fractions down to 0.03% in a whole exome sequencing (WES) study with a background error rate of one artificial error per 4.8 × 10[9] nucleotides.},
}
@article {pmid28611359,
year = {2017},
author = {Song, Y and Wang, S and Ding, Y and Xu, J and Li, MF and Zhu, S and Chen, N},
title = {Chloroplast Genomic Resource of Paris for Species Discrimination.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {3427},
pmid = {28611359},
issn = {2045-2322},
mesh = {DNA Barcoding, Taxonomic/*methods ; Genes, Plant ; *Genome, Chloroplast ; Melanthiaceae/classification/*genetics ; Microsatellite Repeats ; Phylogeny ; Plants, Medicinal/classification/genetics ; },
abstract = {Paris is famous in China for its medicinal value and has been included in the Chinese Pharmacopoeia. Inaccurate identification of these species could confound their effective exploration, conservation, and domestication. Due to the plasticity of the morphological characteristics, correct identification among Paris species remains problematic. In this regard, we report the complete chloroplast genome of P. thibetica and P. rugosa to develop highly variable molecular markers. Comparing three chloroplast genomes, we sought out the most variable regions to develop the best cpDNA barcodes for Paris. The size of Paris chloroplast genome ranged from 162,708 to 163,200 bp. A total of 134 genes comprising 81 protein coding genes, 45 tRNA genes and 8 rRNA genes were observed in all three chloroplast genomes. Eight rapidly evolving regions were detected, as well as the difference of simple sequence repeats (SSR) and repeat sequence. Two regions of the coding gene ycf1, ycf1a and ycf1b, evolved the quickest and were proposed as core barcodes for Paris. The complete chloroplast genome sequences provide more integrated and adequate information for better understanding the phylogenetic pattern and improving efficient discrimination during species identification.},
}
@article {pmid28610364,
year = {2017},
author = {Yu, D and Ding, Y and Ma, Y},
title = {Revision of Tomocerus similis Chen &amp; Ma, with discussion of the kinoshitai complex and the distal tibiotarsal chaetae in Tomocerinae (Collembola, Tomoceridae).},
journal = {Zootaxa},
volume = {4268},
number = {3},
pages = {395-410},
doi = {10.11646/zootaxa.4268.3.5},
pmid = {28610364},
issn = {1175-5334},
mesh = {Animals ; *Arthropods ; China ; Ecology ; },
abstract = {Molecular analysis and a detailed morphological comparison revealed that Tomocerus similis Chen &amp; Ma was described from individuals belonging to several species from several localities. Based on both old and new material from Anhui and Jiangsu Provinces, China, T. similis is redescribed and two new species are described. The three species are morphologically similar. Tomocerus persimilis sp. nov. differs from the others by the presence of central macrochaeta on head and of several distinct distal inner teeth on unguis. Tomocerus dissimilis sp. nov. is characterised by pointed tenent hairs on anterior legs. Remarks are made on the systematics and ecology of the kinoshitai complex, and on the taxonomic value of tenent hair and its adjacent chaetae.},
}
@article {pmid28610305,
year = {2017},
author = {Lin, YP and Ding, ZY and Gullan, PJ and Cook, LG},
title = {A newly recognised Australian endemic species of Austrolecanium Gullan &amp; Hodgson 1998 (Hemiptera: Coccidae) from Queensland.},
journal = {Zootaxa},
volume = {4272},
number = {1},
pages = {119-130},
doi = {10.11646/zootaxa.4272.1.6},
pmid = {28610305},
issn = {1175-5334},
mesh = {Animals ; Australia ; Female ; *Hemiptera ; Phylogeny ; Plant Leaves ; Queensland ; },
abstract = {Austrolecanium cryptocaryae Lin &amp; Cook sp. n. is described based on adult female morphology and DNA sequences from mitochondrial and nuclear loci. This Australian endemic species was found on the underside of leaves of Cryptocarya microneura (Lauraceae) in Queensland. All phylogenetic analyses of four independent DNA loci and a concatenated dataset show that A. cryptocaryae is monophyletic and closely related to A. sassafras Gullan &amp; Hodgson, the type species of Austrolecanium Gullan &amp; Hodgson. The adult female of A. cryptocaryae is described and illustrated and a table is provided of the characters that differ among adult females of the three species of Austrolecanium currently recognised (A. cappari (Froggatt), A. cryptocaryae sp. n. and A. sassafras).},
}
@article {pmid28610239,
year = {2017},
author = {Zupolini, LL and Magalhães, T and Pileggi, LG and Mantelatto, FL},
title = {Taxonomic revision of the speckled crabs, genus Arenaeus Dana, 1851 (Brachyura: Portunidae) based on morphological and molecular data.},
journal = {Zootaxa},
volume = {4273},
number = {3},
pages = {362-380},
doi = {10.11646/zootaxa.4273.3.3},
pmid = {28610239},
issn = {1175-5334},
mesh = {Americas ; Animals ; *Brachyura ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV ; Male ; Phylogeny ; RNA, Ribosomal, 16S ; },
abstract = {The family Portunidae Rafinesque, 1815 presents a series of taxonomic problems such as paraphyletic groups, synonymizations, and unresolved complexes of cryptic species. Arenaeus Dana, 1851, encompasses only two species with mirrored distributions along the coasts of the Americas. Despite of comprising two widespread species, there is a scarcity of information on their biology and ecology and on the relationships with other genera in the family. Because of the lack of studies comprising both species and the imprecise or erroneous taxonomic descriptions for the species of Arenaeus, we conducted a thorough taxonomic revision of the genus and used data from fragments of the 16S rRNA and the cytochrome oxidase I (COI) genes to investigate the validity of Arenaeus cribrarius (Lamarck, 1818) and Arenaeus mexicanus (Gerstaecker, 1856). A range of easily discernible and objective characteristics distinguish the species, including the number of rostral teeth, the number of carpal spines, and the presence of a spine on the epistome region. This last feature, although never properly addressed in the literature, was diagnostic in discriminating the taxa. Results of molecular analyses also supported the separate identity of the two species. Assemblages generated in COI analyses reflected no geographic pattern or geographic partitioning, suggesting that dispersion and gene flow could be sufficiently high to hinder genetic differentiation through the extensive distribution range of the Atlantic species, A. cribrarius. Furthermore, molecular results and morphological analyses may indicate a closer relationship among particular groups of portunids and Arenaeus. Morphology of the carapace and of the first male gonopods may be the most prominent characteristics supporting such view. We have shed light on the status of the genus Arenaeus and its members, clarified some taxonomical issues, and provide an identification key for the species.},
}
@article {pmid28610228,
year = {2017},
author = {Majnon-Jahromi, B and Gheibi, M and Fallahzadeh, M and Kehlmaier, C and Hesami, S},
title = {Pipunculidae (Diptera) from southern Iran, including two new species of the genus Tomosvaryella Aczél.},
journal = {Zootaxa},
volume = {4273},
number = {4},
pages = {488-500},
doi = {10.11646/zootaxa.4273.4.2},
pmid = {28610228},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; *Diptera ; Female ; Genes, Mitochondrial ; Iran ; Male ; Muscidae ; },
abstract = {We provide data on the distribution of 23 big-headed fly species (Diptera: Brachycera: Pipunculidae) from Fars province, southern Iran. Two new species of the genus Tomosvaryella Aczél, T. angulata sp. nov. and T. pistacia sp. nov., are described and illustrated. The new species show a clear morphological affiliation to the T. congoana species-group that was hitherto only known from the Afrotropical region. Nine species recorded herein represent first records for Iran. The number of pipunculid species recorded from Iran is now raised to 30. By DNA barcoding of the mitochondrial COI gene, males and females could be unequivocally associated with each other for most species.},
}
@article {pmid28610203,
year = {2017},
author = {Tiunova, TM and Semenchenko, AA and Velyaev, OA},
title = {New species of Ameletus Eaton, 1885 from the Russian Far East with notes on Ameletus camtschaticus Ulmer 1927 (Ephemeroptera: Ameletidae).},
journal = {Zootaxa},
volume = {4276},
number = {2},
pages = {151-176},
doi = {10.11646/zootaxa.4276.2.1},
pmid = {28610203},
issn = {1175-5334},
mesh = {Animal Structures ; Animals ; *Ephemeroptera ; Asia, Eastern ; Male ; Ovum ; Phylogeny ; Russia ; },
abstract = {The male imagoes, larvae, and eggs of Ameletus allengaensis sp. nov. and Ameletus sirotskii sp. nov. from the Russian Far East are described. Based on the structure of the male genitalia, the imago and larvae of A. allengaensis sp. nov. and A. sirotskii sp. nov. are similar to those of A. camtschaticus, but the discovery of these new species and separation from A. camtschaticus were confirmed by studies of the morphology of the larvae and male imago, as well as molecular analysis. Identity of various developmental stages of the new species were confirmed by analysis of the mitochondrial gene cytochrome oxidase 1 (COI) DNA barcode, which was also used to reconstruct the phylogenetic relationships within the genus Ameletus. The intraspecific sequence divergence based on the Kimura-2-parameter (K2P) distance ranged from 0.0-2.5%, whereas the interspecific sequence divergence based on the K2P distance ranged from 6.2-7.9% within A. sirotskii sp. nov., A. allengaensis sp. nov. and A. camtschaticus. Male imagoes of A. allengaensis sp. nov., A. sirotskii sp. nov., and A. camtschaticus can be distinguished by the size and location of small denticles on the ventral plate of the penis. The larvae of A. allengaensis sp. nov. differ from those of A. sirotskii sp. nov. by the size of gills I and II. In A. allengaensis sp. nov., gill I is almost twice as small as gill II; in A. sirotskii sp. nov., gill I is only slightly smaller than gill II. Both new species differ from A. camtschaticus by gill II, which does not have an anal rib on the anal margin.},
}
@article {pmid28610139,
year = {2017},
author = {Liu, W and Wesener, T and Golovatch, S and Tian, M},
title = {Contributions to the millipede genus Nepalella Shear, 1979 from China, with four new species and first results on phylogeny based on DNA-barcoding (Diplopoda, Chordeumatida, Megalotylidae).},
journal = {Zootaxa},
volume = {4243},
number = {3},
pages = {455-482},
doi = {10.11646/zootaxa.4243.3.3},
pmid = {28610139},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures ; Animals ; *Arthropods ; China ; DNA ; DNA Barcoding, Taxonomic ; Europe ; Phylogeny ; },
abstract = {Four new species of the chordeumatidan millipede genus Nepalella Shear, 1979, family Megalotylidae, are described from caves in southern China: N. troglodytes sp. nov., N. lobata sp. nov., N. jinfoshan sp. nov., and N. wangi sp. nov. Three of them (except N. lobata sp. nov.) are presumed troglobites. Additional locality records of two cave congeners, N. caeca Shear, 1999 and N. grandoides Golovatch, Geoffroy &amp; Mauriès, 2006, are also provided. DNA-barcoding based on the COI mitochondrial gene is documented in this genus and for species of the order Chordeumatida outside Europe for the first time. Interspecific p-distances between Nepalella species amount to 8.5-15.9%, while intraspecific p-distances are 0-6.8%. The species of Nepalella are found to show a surprisingly low genetic distance from the European genus Atractosoma Fanzago, 1876, family Craspedosomatidae Gray in Jones, 1843, potentially based on the very limited number of barcoding sequences of the order Chordeumatida being available.},
}
@article {pmid28610112,
year = {2017},
author = {Riedel, A},
title = {The weevil genera Nyphaeba Pascoe and Pantiala Pascoe and the problems of an unstable nomenclature in orphaned taxa.},
journal = {Zootaxa},
volume = {4244},
number = {3},
pages = {377-389},
doi = {10.11646/zootaxa.4244.3.6},
pmid = {28610112},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures ; Animals ; *Weevils ; },
abstract = {The genera Nyphaeba Pascoe and Pantiala Pascoe of Cryptorhynchinae are redescribed and revised. Lectotypes are designated for the names Nyphaeba monommoides Pascoe and Pantiala illusa Pascoe. This facilitates the description of Nyphaeba mimica sp. n. represented by two paralectotypes of Pantiala illusa. Both genera are excluded from the subtribe Tylodina Lacordaire based on their possession of wings and a distinct metanepisternum. The following new combination for a species originally described in Pantiala is proposed: Nyphaeba germari (Faust). A femora-abdominal stridulatory mechanism is observed for Nyphaeba. This case illustrates how nomenclatural problems evident from type material can persist in an understudied taxon for more than a century. Such problems severely affect modern research and databasing.},
}
@article {pmid28610073,
year = {2017},
author = {Makarchenko, EA and Makarchenko, MA and Semenchenko, AA},
title = {New or little-known species of Chaetocladius s. str. Kieffer, 1911 (Diptera: Chironomidae: Orthocladiinae) from the Amur River basin (Russian Far East).},
journal = {Zootaxa},
volume = {4247},
number = {3},
pages = {313-330},
doi = {10.11646/zootaxa.4247.3.5},
pmid = {28610073},
issn = {1175-5334},
mesh = {Animals ; *Chironomidae ; Asia, Eastern ; Larva ; Male ; Phylogeny ; Rivers ; Russia ; },
abstract = {Chironomids of the subgenus Chaetocladius s. str. from the Amur River basin are revised using both morphological characters and molecular data. Three new species, C. egorych sp. nov., C. lopatinskiy sp. nov. and C. yavorskayae sp. nov., are described and figured. The pupa of C. fedotkin is described for the first time. Adult males of C. ligni and C. piger, little-known in the Far East, are redescribed and annotated, and key to males of the Chaetocladius s. str. from the Amur River basin is provided. A reference 658 bp barcode sequence from a fragment of the mitochondrial gene cytochrome oxidase I (COI) was used as a tool for species delimitation. Comparisons with corresponding regions of COI between 5 species in the subgenus produced K2P genetic distances of 8.3-12.6%, values well associated with interspecific variation. Molecular data were also used for the reconstruction of the phylogenetic relationships within the subgenus Chaetocladius s. str.},
}
@article {pmid28610069,
year = {2017},
author = {Huang, J and Su, Y and Chen, H},
title = {The genus Leucophenga (Diptera, Drosophilidae), part VII: the subpollinosa species group from China, with morphological and molecular evidence.},
journal = {Zootaxa},
volume = {4247},
number = {3},
pages = {201-245},
doi = {10.11646/zootaxa.4247.3.1},
pmid = {28610069},
issn = {1175-5334},
mesh = {Animals ; Argentina ; Bayes Theorem ; China ; Databases, Nucleic Acid ; Diptera ; *Drosophilidae ; Phylogeny ; Taiwan ; },
abstract = {Seventeen species of Leucophenga subpollinosa species group are described from China (including 11 new species): L. argentina (de Meijere, 1924); L. flavicosta Duda, 1926; L. formosa Okada, 1987; L. nigroscutellata Duda, 1924; L. subpollinosa (de Meijere, 1914); L. umbratula Duda, 1924; L. aculeata sp. nov.; L. acuticauda sp. nov.; L. cultella sp. nov.; L. cyclophylla sp. nov.; L. flaviclypeata sp. nov.; L. fuscipedes sp. nov.; L. gracilenta sp. nov.; L. latipenis sp. nov.; L. magnicauda sp. nov.; L. rhombura sp. nov.; L. rugatifolia sp. nov. A key to all examined species of the subpollinosa group in the present study is provided. The phylogenetic relationships among the 17 species of the subpollinosa group are reconstructed by NJ (Neighbor-joining) and Bayesian analyses using 98 DNA sequences of COI (cytochrome c oxidase subunit I) gene. The pairwise intra- and interspecific p-distances of aforementioned sequences are summarized.},
}
@article {pmid28610033,
year = {2017},
author = {Hernández-Triana, LM and Brugman, VA and Prosser, SWJ and Weland, C and Nikolova, N and Thorne, L and Marco, MF and Fooks, AR and Johnson, N},
title = {Molecular approaches for blood meal analysis and species identification of mosquitoes (Insecta: Diptera: Culicidae) in rural locations in southern England, United Kingdom.},
journal = {Zootaxa},
volume = {4250},
number = {1},
pages = {67-76},
doi = {10.11646/zootaxa.4250.1.5},
pmid = {28610033},
issn = {1175-5334},
mesh = {Animals ; Anopheles ; Cattle ; Culex ; *Culicidae ; Dogs ; England ; Female ; Humans ; Insect Vectors ; Sequence Analysis, DNA ; United Kingdom ; West Nile virus ; },
abstract = {Thirty-four species of Culicidae are present in the UK, of which 15 have been implicated as potential vectors of arthropod-borne viruses such as West Nile virus. Identification of mosquito feeding preferences is paramount to the understanding of vector-host-pathogen interactions which, in turn, would assist in the control of disease outbreaks. Results are presented on the application of DNA barcoding for vertebrate species identification in blood-fed female mosquitoes in rural locations. Blood-fed females (n = 134) were collected in southern England from rural sites and identified based on morphological criteria. Blood meals from 59 specimens (44%) were identified as feeding on eight hosts: European rabbit, cow, human, barn swallow, dog, great tit, magpie and blackbird. Analysis of the cytochrome c oxidase subunit I mtDNA barcoding region and the internal transcribed spacer 2 rDNA region of the specimens morphologically identified as Anopheles maculipennis s.l. revealed the presence of An. atroparvus and An. messeae. A similar analysis of specimens morphologically identified as Culex pipiens/Cx. torrentium showed all specimens to be Cx. pipiens (typical form). This study demonstrates the importance of using molecular techniques to support species-level identification in blood-fed mosquitoes to maximize the information obtained in studies investigating host feeding patterns.},
}
@article {pmid28610027,
year = {2017},
author = {Feng, L and Zhang, Y},
title = {Two new species in the genus Kolla Distant (Hemiptera: Cicadellidae: Cicadellinae) from China, with DNA barcoding data.},
journal = {Zootaxa},
volume = {4250},
number = {2},
pages = {191-197},
doi = {10.11646/zootaxa.4250.2.5},
pmid = {28610027},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures ; Animals ; China ; *DNA Barcoding, Taxonomic ; *Hemiptera ; },
abstract = {Two new species of the genus Kolla from China, K. medsimilis and K. brevis spp. nov., are described and illustrated. Sequence data for the barcoding region of mitochondrial gene COI for these two new species were obtained and deposited in GenBank.},
}
@article {pmid28610009,
year = {2017},
author = {Liu, T and Yan, J},
title = {Review of the Palearctic Atemelia Herrich-Schäffer (Lepidoptera, Yponomeutoidea, Praydidae), with description of a new leafmining species.},
journal = {Zootaxa},
volume = {4250},
number = {4},
pages = {327-336},
doi = {10.11646/zootaxa.4250.4.3},
pmid = {28610009},
issn = {1175-5334},
mesh = {Animals ; China ; Europe ; Genitalia ; *Lepidoptera ; Plant Leaves ; },
abstract = {The Palearctic Atemelia Herrich-Schäffer, 1853 is reviewed. Two species are treated, one of which is described as new: A. fusca Liu, sp. nov. The genus Atemelia is recorded in China for the first time, and it is also newly recorded from the Eastern Palearctic region. Larvae of A. fusca sp. nov. mine leaves of Ulmus pumila (Ulmaceae), sharing the same host plant genus with another leaf miner A. torquatella (Lienig &amp; Zeller, 1846) from Europe, but they are distinctive from the Nearctic and the Neotropical Atemelia species in host plant families and life styles. Photographs of adults and genitalia of the Palearctic Atemelia are provided. Additional photographs of immature stages, leafmines, and host plant are provided for the new species. In addition, three DNA barcodes are provided for A. fusca sp. nov.},
}
@article {pmid28610001,
year = {2017},
author = {Kovačić, M and Ordines, F and Schliewen, UK},
title = {A new species of Buenia (Teleostei: Gobiidae) from the western Mediterranean Sea, with the description of this genus.},
journal = {Zootaxa},
volume = {4250},
number = {5},
pages = {447-460},
doi = {10.11646/zootaxa.4250.5.3},
pmid = {28610001},
issn = {1175-5334},
mesh = {Animals ; Fishes ; Male ; Mediterranean Sea ; *Perciformes ; Phylogeny ; Spain ; },
abstract = {A new miniature gobiid species, Buenia massutii sp. nov. (Teleostei: Gobiidae) is described from the circalittoral bottom off the Balearic Islands, western Mediterranean. Phylogenetic analysis of the mitochondrial COI-barcoding fragment supports its species-level distinctiveness and the monophyly of the genus Buenia. A description and diagnosis of the genus Buenia is for the first time provided. Material of the new species was collected in 57-67 m depth from beam trawl samples carried out on red algae beds. The traits that differentiate the new species from two congeneric species are: anterior oculoscapular canal only semiclosed with pores σ, λ, κ, ω, α, ρ and additional pores and open furrows from interorbital part to pore ρ; posterior oculoscapular canal absent; suborbital row c with 5 papillae; scales in lateral series 26-28; pectoral fin rays 16; the second spine of the first dorsal fin the longest, reaching to or behind posterior end of the second dorsal fin in males when folded down; pelvic fin anterior membrane one sixth or less of length of spinous ray in midline depth; head length 31.2-32.5% of standard length; eye 32.8-35.7% of head length; caudal fin length 21.5-24.0% of standard length.},
}
@article {pmid28609994,
year = {2017},
author = {Razowski, J and Pelz, V and Tarcz, S},
title = {Uncovering the hidden biodiversity of natural history collections: Insights from DNA barcoding and morphological characters of the Neotropical genus Orthocomotis Dognin (Lepidoptera: Tortricidae).},
journal = {Zootaxa},
volume = {4250},
number = {6},
pages = {541-559},
doi = {10.11646/zootaxa.4250.6.3},
pmid = {28609994},
issn = {1175-5334},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Ecuador ; *Lepidoptera ; Peru ; Phylogeny ; },
abstract = {We used a 227-bp fragment of the mitochondrial gene cytochrome oxidase I (DNA "barcode") in conjunction with morphological data to study specimens of the Neotropical genus Orthocomotis Dognin, 1906, acquired from natural history collections. We examined over 20 species of Orthocomotis from 17 localities in Colombia, Ecuador, and Peru. The analysis identified 32 haplotypes among the 62 specimens and found no haplotypes shared among species. The molecular study revealed not only the usefulness of short COI sequences in discriminating among Orthocomotis species but also showed distinctness of four clusters which correspond to those based on morphological (genitalia) characters. Moreover, the molecular results suggest the occurrence of rapid speciation in Orthocomotis. We hypothesize that this may be linked to the great biodiversity of potential host plants in Neotropical ecosystems.},
}
@article {pmid28609983,
year = {2017},
author = {Ibáñez, RD and Griffith, EJ and Lips, KR and Crawford, AJ},
title = {Altitudinal distribution and advertisement call of Colostethus latinasus (Amphibia: Dendrobatidae), endemic species from eastern Panama and type species of Colostethus , with a molecular assessment of similar sympatric species.},
journal = {Zootaxa},
volume = {4254},
number = {1},
pages = {91-101},
doi = {10.11646/zootaxa.4254.1.5},
pmid = {28609983},
issn = {1175-5334},
mesh = {Animals ; *Anura ; DNA ; Panama ; Phylogeny ; *Sympatry ; },
abstract = {We conducted a molecular assessment of Colostethus-like frogs along an elevational gradient in the Serranía de Pirre, above Santa Cruz de Cana, eastern Panama, aiming to establish their species identity and to determine the altitudinal distribution of C. latinasus. Our findings confirm the view of C. latinasus as an endemic species restricted to the highlands of this mountain range, i.e., 1350-1475 m.a.s.l., considered to be type locality of this species. We described the advertisement call of C. latinasus that consists of a series of 4-18 single, short and relatively loud "peep"-like notes given in rapid succession, and its spectral and temporal features were compared with calls of congeneric species. For the first time, DNA sequences from C. latinasus were obtained, since previously reported sequences were based on misidentified specimens. This is particularly important because C. latinasus is the type species of Colostethus, a genus considered paraphyletic according to recent phylogenetic analyses based on molecular data.},
}
@article {pmid28609930,
year = {2017},
author = {Ortega-Morales, AI and Rodríguez, QKS and Garza-Hernández, JA and Adeniran, AA and Hernández-Triana, LM and Rodríguez-Pérez, MA},
title = {First record of the ant cricket Myrmecophilus (Myrmecophilina) americanus (Orthoptera: Myrmecophilidae) in Mexico.},
journal = {Zootaxa},
volume = {4258},
number = {2},
pages = {195-200},
doi = {10.11646/zootaxa.4258.2.9},
pmid = {28609930},
issn = {1175-5334},
mesh = {Animals ; *Gryllidae ; Mexico ; },
abstract = {In September 2004, the New World ant cricket, Myrmecophilus americanus Saussure, 1877, was collected in association with longhorn crazy ants, Paratrechina longicornis (Latreille. 1802), in the state of Coahuila, Mexico. We are reporting the DNA barcode using the mitochrondrial cytochrome oxidase subunit I for this first record of M. americanus in Mexico.},
}
@article {pmid28609869,
year = {2017},
author = {Sagorny, C and Wesener, T},
title = {Two new giant pill-millipede species of the genus Zoosphaerium endemic to the Bemanevika area in northern Madagascar (Diplopoda, Sphaerotheriida, Arthrosphaeridae).},
journal = {Zootaxa},
volume = {4263},
number = {2},
pages = {273-294},
doi = {10.11646/zootaxa.4263.2.4},
pmid = {28609869},
issn = {1175-5334},
mesh = {Animals ; *Arthropods ; Biodiversity ; Female ; Madagascar ; },
abstract = {Madagascar is one of the world's most important hotspots of biodiversity and a center for localized endemism. Among the highly endemic faunal elements are the giant pill-millipedes, order Sphaerotheriida, which are severely understudied in Madagascar. Here we provide descriptions of two new species of endemic giant-pill millipedes of the genus Zoosphaerium Pocock, 1895: Zoosphaerium bemanevika n. sp. and Zoosphaerium minutus n. sp.. Zoosphaerium bemanevika n. sp. belongs to the Z. coquerelianum species-group, while Z. minutus n. sp. is not assignable to a species-group. An updated key to the 19 species of the Z. coquerelianum group is provided. Zoosphaerium minutus n. sp. has a body length of <20 mm and thus is the smallest known member of the genus, being of similar size as the larger species of Microsphaerotherium Wesener &amp; VandenSpiegel, 2007. Both species are described utilizing drawings, scanning electron microscopy and genetic barcoding based on the mitochondrial COI gene. MicroCT imaging is applied to study internal morphology non-destructively and in situ, allowing for a reconstruction of the head skeleton. Our results show that females of Z. bemanevika n. sp. exhibit island gigantism. The two newly described species are not closely related to one another but each to different species from the Marojejy Mountain and the lowland rainforest of the east coast. Both species occur sympatrically as microendemics in small patches of humid evergreen forest near Bemanevika in northern Madagascar, an only recently protected area that represents a Malagasy center of endemism.},
}
@article {pmid28609860,
year = {2017},
author = {Fusu, L and Polaszek, A},
title = {Description, DNA barcoding and phylogenetic placement of a remarkable new species of Eopelma (Hymenoptera: Eupelmidae) from Borneo.},
journal = {Zootaxa},
volume = {4263},
number = {3},
pages = {557-566},
doi = {10.11646/zootaxa.4263.3.7},
pmid = {28609860},
issn = {1175-5334},
mesh = {Animals ; Borneo ; *DNA Barcoding, Taxonomic ; Male ; Phylogeny ; *Wasps ; },
abstract = {Eopelma gibsoni sp. nov. is described based on a male recently collected in Borneo. It is the second species of the genus to be described, and the first species of chalcid wasp in which a pattern of dark stripes on the compound eye is described. The presence of similar dark stripes on the eyes of other chalcid wasps is discussed, highlighting the importance of citizen science. The description is accompanied by a DNA barcode sequence to assist future identification and association of the sexes. The phylogenetic position of E. gibsoni based on 28S DNA sequences is discussed.},
}
@article {pmid28605074,
year = {2017},
author = {Gao, Z and Wei, C and Yan, Y and Zhang, W and Dong, H and Zhao, J and Yi, J and Zhang, C and Li, YJ and Zhao, YS},
title = {Covert Photonic Barcodes Based on Light Controlled Acidichromism in Organic Dye Doped Whispering-Gallery-Mode Microdisks.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {29},
number = {30},
pages = {},
doi = {10.1002/adma.201701558},
pmid = {28605074},
issn = {1521-4095},
abstract = {Photonic barcodes with a small footprint have demonstrated a great value for multiplexed high-throughput bioassays and tracking systems. Attempts to develop coding technology tend to focus on the generation of featured barcodes both with high coding capacity and accurate recognition. In this work, a strategy to design photonic barcodes is proposed based on whispering-gallery-mode (WGM) modulations in dye-doped microdisk resonant cavities, where each modulated photoluminescence spectrum constitutes the fingerprint of a corresponding microdisk. The WGM-based barcodes can achieve infinite encoding capacity through tuning the dimensions of the microdisks. These photonic barcodes can be well disguised and decoded based on the light controlled proton release and acidichromism of the organic materials, which are essential to fulfill the functions of anti-counterfeiting, information security, and so on. The results will pave an avenue to new types of flexible WGM-based components for optical data recording and security labels.},
}
@article {pmid28597155,
year = {2017},
author = {Maloukh, L and Kumarappan, A and Jarrar, M and Salehi, J and El-Wakil, H and Rajya Lakshmi, TV},
title = {Discriminatory power of rbcL barcode locus for authentication of some of United Arab Emirates (UAE) native plants.},
journal = {3 Biotech},
volume = {7},
number = {2},
pages = {144},
pmid = {28597155},
issn = {2190-572X},
abstract = {DNA barcoding of United Arab Emirates (UAE) native plants is of high practical and scientific value as the plants adapt to very harsh environmental conditions that challenge their identification. Fifty-one plant species belonged to 22 families, 2 monocots, and 20 eudicots; a maximum number of species being legumes and grasses were collected. To authenticate the morphological identification of the wild plant taxa, rbcL and matK regions were used in the study. The primer universality and discriminatory power of rbcL is 100%, while it is 35% for matK locus for these plant species. The sequences were submitted to GenBank; accession numbers were obtained for all the rbcL sequences and for 6 of matK sequences. We suggest rbcL as a promising barcode locus for the tested group of 51 plants. In the present study, an inexpensive, simple method of identification of rare desert plant taxa through rbcL barcode is being reported.},
}
@article {pmid28595682,
year = {2017},
author = {Mangini, L and Wick, JY},
title = {Wandering: Unearthing New Tracking Devices.},
journal = {The Consultant pharmacist : the journal of the American Society of Consultant Pharmacists},
volume = {32},
number = {6},
pages = {324-331},
doi = {10.4140/TCP.n.2017.324},
pmid = {28595682},
issn = {0888-5109},
mesh = {Alzheimer Disease/complications/drug therapy ; Caregivers ; Dementia/*complications/*drug therapy ; Humans ; Mental Disorders/*drug therapy/*etiology ; Wandering Behavior/*physiology ; },
abstract = {Wandering away from home or facilities is dangerous for patients with dementia and stressful for families and caregivers when those who go missing cannot be located. Up to 60% of Alzheimer's disease patients wander, and up to 50% of those who are not found within 24 hours face serious injury or death. Currently, no effective drug therapies exist to abate wandering, which has multiple causes, but emerging technologies offer a promise of comfort in being able to easily locate a missing loved one. As of 2012, 41 states had enacted Silver Alert programs that broadcast information about missing, vulnerable adults. Numerous technologies, such as wearable global positioning system trackers and temporary barcodes worn on fingernails, exist to ease the fears of families and caregivers, locate residents, and hasten their return. While these strategies offer promise, issues of expense, effectiveness, privacy, and ethics remain.},
}
@article {pmid28595314,
year = {2017},
author = {Sternes, PR and Lee, D and Kutyna, DR and Borneman, AR},
title = {A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation.},
journal = {GigaScience},
volume = {6},
number = {7},
pages = {1-10},
pmid = {28595314},
issn = {2047-217X},
mesh = {DNA Barcoding, Taxonomic/*methods ; *Fermentation ; *Metagenome ; Saccharomyces cerevisiae/*genetics/metabolism ; Wine/*microbiology ; },
abstract = {Wine is a complex beverage, comprising hundreds of metabolites produced through the action of yeasts and bacteria in fermenting grape must. Commercially, there is now a growing trend away from using wine yeast (Saccharomyces) starter cultures, toward the historic practice of uninoculated or "wild" fermentation, where the yeasts and bacteria associated with the grapes and/or winery perform the fermentation. It is the varied metabolic contributions of these numerous non-Saccharomyces species that are thought to impart complexity and desirable taste and aroma attributes to wild ferments in comparison to their inoculated counterparts. To map the microflora of spontaneous fermentation, metagenomic techniques were employed to characterize and monitor the progression of fungal species in 5 different wild fermentations. Both amplicon-based ribosomal DNA internal transcribed spacer (ITS) phylotyping and shotgun metagenomics were used to assess community structure across different stages of fermentation. While providing a sensitive and highly accurate means of characterizing the wine microbiome, the shotgun metagenomic data also uncovered a significant overabundance bias in the ITS phylotyping abundance estimations for the common non-Saccharomyces wine yeast genus Metschnikowia. By identifying biases such as that observed for Metschnikowia, abundance measurements from future ITS phylotyping datasets can be corrected to provide more accurate species representation. Ultimately, as more shotgun metagenomic and single-strain de novo assemblies for key wine species become available, the accuracy of both ITS-amplicon and shotgun studies will greatly increase, providing a powerful methodology for deciphering the influence of the microbial community on the wine flavor and aroma.},
}
@article {pmid28590228,
year = {2017},
author = {Phunngam, P and Chareonviriyaphap, T and Bangs, MJ and Arunyawat, U},
title = {Phylogenetic Relationships Among Malaria Vectors and Closely Related Species in Thailand Using Multilocus DNA Sequences.},
journal = {Journal of the American Mosquito Control Association},
volume = {33},
number = {2},
pages = {91-102},
doi = {10.2987/17-6637.1},
pmid = {28590228},
issn = {8756-971X},
mesh = {Animals ; Anopheles/*classification/genetics ; Malaria/transmission ; Mosquito Vectors/*classification/genetics ; Multilocus Sequence Typing ; Phylogeny ; Thailand ; },
abstract = {The evolutionary and taxonomic status is important for understanding speciation events and phylogenetic relationships between closely related vector and nonvector species. This information is useful for targeting important disease vector species groups for the development of novel genetic-based vector and pathogen control methods. In this study, different phylogenetic analyses were performed to reconstruct phylogenetic trees for the primary malaria vectors in Thailand based on sequence information of 4 DNA fragments from the nuclear and mitochondrial regions. The primary Anopheles species in the subgenus Cellia involved in malaria transmission in Thailand separate clearly into 3 distinct clades: the Leucosphyrus group, Minimus subgroup, and Maculatus group. The phylogenetic trees based on different reconstructed algorithms and different gene regions provided congruent phylogenetic status of the mosquito species studied. The phylogenetic relationships of malaria vector species examined followed similar patterns based on morphological characters. An estimate of the divergence time among the Anopheles species infers that they were present during the Eocene and Miocene periods (>41 million years ago). Congruent phylogenetic analysis of malaria vectors is presented with different algorithms and gene regions. The nuclear TOLL6 fragment appears useful for molecular phylogenetic, species DNA barcode, and Anopheles population genetic analyses.},
}
@article {pmid28579999,
year = {2017},
author = {Yang, J and Vázquez, L and Chen, X and Li, H and Zhang, H and Liu, Z and Zhao, G},
title = {Development of Chloroplast and Nuclear DNA Markers for Chinese Oaks (Quercus Subgenus Quercus) and Assessment of Their Utility as DNA Barcodes.},
journal = {Frontiers in plant science},
volume = {8},
number = {},
pages = {816},
pmid = {28579999},
issn = {1664-462X},
abstract = {Chloroplast DNA (cpDNA) is frequently used for species demography, evolution, and species discrimination of plants. However, the lack of efficient and universal markers often brings particular challenges for genetic studies across different plant groups. In this study, chloroplast genomes from two closely related species (Quercus rubra and Castanea mollissima) in Fagaceae were compared to explore universal cpDNA markers for the Chinese oak species in Quercus subgenus Quercus, a diverse species group without sufficient molecular differentiation. With the comparison, nine and 14 plastid markers were selected as barcoding and phylogeographic candidates for the Chinese oaks. Five (psbA-trnH, matK-trnK, ycf3-trnS, matK, and ycf1) of the nine plastid candidate barcodes, with the addition of newly designed ITS and a single-copy nuclear gene (SAP), were then tested on 35 Chinese oak species employing four different barcoding approaches (genetic distance-, BLAST-, character-, and tree-based methods). The four methods showed different species identification powers with character-based method performing the best. Of the seven barcodes tested, a barcoding gap was absent in all of them across the Chinese oaks, while ITS and psbA-trnH provided the highest species resolution (30.30%) with the character- and BLAST-based methods, respectively. The six-marker combination (psbA-trnH + matK-trnK + matK + ycf1 + ITS + SAP) showed the best species resolution (84.85%) using the character-based method for barcoding the Chinese oaks. The barcoding results provided additional implications for taxonomy of the Chinese oaks in subg. Quercus, basically identifying three major infrageneric clades of the Chinese oaks (corresponding to Groups Quercus, Cerris, and Ilex) referenced to previous phylogenetic classification of Quercus. While the morphology-based allocations proposed for the Chinese oaks in subg. Quercus were challenged. A low variation rate of the chloroplast genome, and complex speciation patterns involving incomplete lineage sorting, interspecific hybridization and introgression, possibly have negative impacts on the species assignment and phylogeny of oak species.},
}
@article {pmid28579404,
year = {2017},
author = {McGlincy, NJ and Ingolia, NT},
title = {Transcriptome-wide measurement of translation by ribosome profiling.},
journal = {Methods (San Diego, Calif.)},
volume = {126},
number = {},
pages = {112-129},
pmid = {28579404},
issn = {1095-9130},
support = {DP2 CA195768/CA/NCI NIH HHS/United States ; P50 GM102706/GM/NIGMS NIH HHS/United States ; R21 ES022575/ES/NIEHS NIH HHS/United States ; S10 OD018174/OD/NIH HHS/United States ; },
mesh = {Gene Expression Profiling/*methods ; Oligonucleotides/*genetics/metabolism ; Protein Biosynthesis/*physiology ; Ribosomes/*genetics/metabolism ; Transcriptome/*physiology ; },
abstract = {Translation is one of the fundamental processes of life. It comprises the assembly of polypeptides whose amino acid sequence corresponds to the codon sequence of an mRNA's ORF. Translation is performed by the ribosome; therefore, in order to understand translation and its regulation we must be able to determine the numbers and locations of ribosomes on mRNAs in vivo. Furthermore, we must be able to examine their redistribution in different physiological contexts and in response to experimental manipulations. The ribosome profiling method provides us with an opportunity to learn these locations, by sequencing a cDNA library derived from the short fragments of mRNA covered by the ribosome. Since its original description, the ribosome profiling method has undergone continuing development; in this article we describe the method's current state. Important improvements include: the incorporation of sample barcodes to enable library multiplexing, the incorporation of unique molecular identifiers to enable to removal of duplicated sequences, and the replacement of a gel-purification step with the enzymatic degradation of unligated linker.},
}
@article {pmid28578677,
year = {2017},
author = {Sarvašová, A and Kočišová, A and Candolfi, E and Mathieu, B},
title = {Description of Culicoides (Culicoides) bysta n. sp., a new member of the Pulicaris group (Diptera: Ceratopogonidae) from Slovakia.},
journal = {Parasites &amp; vectors},
volume = {10},
number = {1},
pages = {279},
pmid = {28578677},
issn = {1756-3305},
mesh = {Animals ; Arboviruses ; Bluetongue/transmission ; Bluetongue virus ; Ceratopogonidae/anatomy &amp; histology/*classification/genetics/virology ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Genes, Mitochondrial/genetics ; Insect Vectors/anatomy &amp; histology/*classification/genetics/virology ; Male ; Mitochondria/enzymology/genetics ; *Phylogeny ; Slovakia ; Species Specificity ; },
abstract = {BACKGROUND: Species of the genus Culicoides Latreille, 1809 (Diptera: Ceratopogonidae) are mainly known as vectors of arboviruses such as bluetongue (BTV) and Schmallenberg (SBV). Among the known vectors, few species within the subgenus Culicoides Latreille, 1809 have been implicated in the transmission of BTV and SBV. Nevertheless, phylogenetic studies had revealed the presence of cryptic and undescribed species in Europe, raising questions about their vectorial role. A previous integrative study, associating morphology and barcode data, raised the hypothesis of the presence of undescribed species in Slovakia. The present study, combining morphological and molecular approaches, is aimed to support the hypothesis and a description of Culicoides bysta n. sp. is provided.<br><br>METHODS: Series of male and female specimens were dissected and several of them were sequenced for the barcode region of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1). Bayesian inference phylogenetic analyses based on 72 cox1 sequences of the species belonging to the Pulicaris group of the subgenus Culicoides, were carried out and the frequencies of intra/interspecific variations were analyzed. The morphology of abundant material of the new species (31 females and 12 males) was examined and compared with the paratypes of Culicoides boyi Nielsen, Kristensen &amp; Pape, 2015 and with specimens of Culicoides pulicaris Linnaeus, 1758. For females, suture distances on the eyes were newly evaluated as a diagnostic character and for males we assessed a new measurement on the ninth tergite and on the apicolateral processes.<br><br>RESULTS: Both phylogenetic analysis and barcode distances supported the distinct status of the new species, Culicoides bysta n. sp. described as a member of the Pulicaris group based on the morphology of males and females. The new species is closely related to C. boyi and C. pulicaris but can be distinguished on the basis of the wing pattern and the ratio between the two eye sutures. Both newly evaluated characters, i.e. eyes in females and male genitalia appeared to be diagnostic for distinguishing the new species described herein.<br><br>CONCLUSIONS: The vector potential of the recently described species C. boyi and C. bysta n. sp. to transmit arboviruses, such as BTV and SBV, is unknown. When considering these two species as being close to C. pulicaris, the previous data, such as the vector implication for C. pulicaris in BTV transmission, should be revaluated in future.},
}
@article {pmid28578667,
year = {2017},
author = {Weeraratne, TC and Surendran, SN and Reimer, LJ and Wondji, CS and Perera, MDB and Walton, C and Parakrama Karunaratne, SHP},
title = {Molecular characterization of Anopheline (Diptera: Culicidae) mosquitoes from eight geographical locations of Sri Lanka.},
journal = {Malaria journal},
volume = {16},
number = {1},
pages = {234},
pmid = {28578667},
issn = {1475-2875},
mesh = {Animals ; Anopheles/anatomy &amp; histology/*classification/genetics ; DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Insect Proteins/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Sri Lanka ; },
abstract = {BACKGROUND: Genus Anopheles is a major mosquito group of interest in Sri Lanka as it includes vectors of malaria and its members exist as species complexes. Taxonomy of the group is mainly based on morphological features, which are not conclusive and can be easily erased while handling the specimens. A combined effort, using morphology and DNA barcoding (using the markers cytochrome c oxidase subunit I (COI) gene and internal transcribed spacer 2 (ITS2) region, was made during the present study to recognize anophelines collected from eight districts of Sri Lanka for the first time.<br><br>METHODS: Cytochrome c oxidase subunit I and ITS2 regions of morphologically identified anopheline mosquitoes from Sri Lanka were sequenced. These sequences together with GenBank sequences were used in phylogenetic tree construction and molecular characterization of mosquitoes.<br><br>RESULTS: According to morphological identification, the field-collected adult mosquitoes belonged to 15 species, i.e., Anopheles aconitus, Anopheles annularis, Anopheles barbirostris, Anopheles culicifacies, Anopheles jamesii, Anopheles karwari, Anopheles maculatus, Anopheles nigerrimus, Anopheles pallidus, Anopheles peditaeniatus, Anopheles pseudojamesi, Anopheles subpictus, Anopheles tessellatus, Anopheles vagus, and Anopheles varuna. However, analysis of 123 COI sequences (445&#xa0;bp) (16 clades supported by strong bootstrap value in the neighbour joining tree and inter-specific distances of&#xa0;>3%) showed that there are 16 distinct species. Identity of the morphologically identified species, except An. subpictus, was comparable with the DNA barcoding results. COI sequence analysis showed that morphologically identified An. subpictus is composed of two genetic entities: An. subpictus species A and species B (inter-specific K2P distance 0.128). All the four haplotypes of An. culicifacies discovered during the present study belonged to a single species. ITS2 sequences (542&#xa0;bp) were obtained for all the species except for An. barbirostris, An. subpictus species B, An. tessellatus, and An. varuna. Each of these sequences was represented by a single species-specific haplotype.<br><br>CONCLUSIONS: The present study reflects the importance and feasibility of COI and ITS2 genetic markers in identifying anophelines and their sibling species, and the significance of integrated systematic approach in mosquito taxonomy. Wide distribution of malaria vectors in the country perhaps indicates the potential for re-emergence of malaria in the country.},
}
@article {pmid28575090,
year = {2017},
author = {Talaga, S and Leroy, C and Guidez, A and Dusfour, I and Girod, R and Dejean, A and Murienne, J},
title = {DNA reference libraries of French Guianese mosquitoes for barcoding and metabarcoding.},
journal = {PloS one},
volume = {12},
number = {6},
pages = {e0176993},
pmid = {28575090},
issn = {1932-6203},
mesh = {Animals ; Culicidae/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; French Guiana ; Phylogeny ; },
abstract = {The mosquito family (Diptera: Culicidae) constitutes the most medically important group of arthropods because certain species are vectors of human pathogens. In some parts of the world, the diversity is so high that the accurate delimitation and/or identification of species is challenging. A DNA-based identification system for all animals has been proposed, the so-called DNA barcoding approach. In this study, our objectives were (i) to establish DNA barcode libraries for the mosquitoes of French Guiana based on the COI and the 16S markers, (ii) to compare distance-based and tree-based methods of species delimitation to traditional taxonomy, and (iii) to evaluate the accuracy of each marker in identifying specimens. A total of 266 specimens belonging to 75 morphologically identified species or morphospecies were analyzed allowing us to delimit 86 DNA clusters with only 21 of them already present in the BOLD database. We thus provide a substantial contribution to the global mosquito barcoding initiative. Our results confirm that DNA barcodes can be successfully used to delimit and identify mosquito species with only a few cases where the marker could not distinguish closely related species. Our results also validate the presence of new species identified based on morphology, plus potential cases of cryptic species. We found that both COI and 16S markers performed very well, with successful identifications at the species level of up to 98% for COI and 97% for 16S when compared to traditional taxonomy. This shows great potential for the use of metabarcoding for vector monitoring and eco-epidemiological studies.},
}
@article {pmid28575022,
year = {2017},
author = {Smith, MA and Boyd, A and Chan, A and Clout, S and des Brisay, P and Dolson, S and Eagalle, T and Espinola, S and Fairweather, A and Frank, S and Fruetel, C and Garrido Cortes, C and Hall, J and Ho, C and Matczak, E and McCubbin, S and McPhee, M and Pare, KA and Paris, K and Richard, E and Roblin, M and Russell, C and Snyder, R and Trombley, C and Schmitt, T and Vandermeer, C and Warne, C and Welch, N and Xavier-Blower, C},
title = {Investigating the effect of forestry on leaf-litter arthropods (Algonquin Park, Ontario, Canada).},
journal = {PloS one},
volume = {12},
number = {6},
pages = {e0178568},
pmid = {28575022},
issn = {1932-6203},
mesh = {Animals ; Arthropods/classification/genetics/*physiology ; Biodiversity ; DNA Barcoding, Taxonomic ; *Forestry ; Ontario ; *Plant Leaves ; },
abstract = {Arthropods are the most diverse taxonomic group of terrestrial eukaryotes and are sensitive to physical alterations in their environment such as those caused by forestry. With their enormous diversity and physical omnipresence, arthropods could be powerful indicators of the effects of disturbance following forestry. When arthropods have been used to measure the effects of disturbance, the total diversity of some groups is often found to increase following forestry. However, these findings are frequently derived using a coarse taxonomic grain (family or order) to accommodate for various taxonomic impediments (including cryptic diversity and poorly resourced taxonomists). Our intent with this work was to determine the diversity of arthropods in and around Algonquin Park, and how this diversity was influenced by disturbance (in this case, forestry within the past 25 years). We used DNA barcode-derived diversity estimates (Barcode Index Number (BIN) richness) to avoid taxonomic impediments and as a source of genetic information with which we could conduct phylogenetic estimates of diversity (PD). Diversity patterns elucidated with PD are often, but not always congruent with taxonomic estimates-and departures from these expectations can help clarify disturbance effects that are hidden from richness studies alone. We found that BIN richness and PD were greater in disturbed (forested) areas, however when we controlled for the expected relationship between PD and BIN richness, we found that cut sites contained less PD than expected and that this diversity was more phylogenetically clustered than would be predicted by taxonomic richness. While disturbance may cause an evident increase in diversity, this diversity may not reflect the full evolutionary history of the assemblage within that area and thus a subtle effect of disturbance can be found decades following forestry.},
}
@article {pmid28575004,
year = {2017},
author = {Yu, XQ and Drew, BT and Yang, JB and Gao, LM and Li, DZ},
title = {Comparative chloroplast genomes of eleven Schima (Theaceae) species: Insights into DNA barcoding and phylogeny.},
journal = {PloS one},
volume = {12},
number = {6},
pages = {e0178026},
pmid = {28575004},
issn = {1932-6203},
mesh = {Chloroplasts/*genetics ; *DNA Barcoding, Taxonomic ; *Genome, Plant ; Phylogeny ; Species Specificity ; Theaceae/*genetics ; },
abstract = {Schima is an ecologically and economically important woody genus in tea family (Theaceae). Unresolved species delimitations and phylogenetic relationships within Schima limit our understanding of the genus and hinder utilization of the genus for economic purposes. In the present study, we conducted comparative analysis among the complete chloroplast (cp) genomes of 11 Schima species. Our results indicate that Schima cp genomes possess a typical quadripartite structure, with conserved genomic structure and gene order. The size of the Schima cp genome is about 157 kilo base pairs (kb). They consistently encode 114 unique genes, including 80 protein-coding genes, 30 tRNAs, and 4 rRNAs, with 17 duplicated in the inverted repeat (IR). These cp genomes are highly conserved and do not show obvious expansion or contraction of the IR region. The percent variability of the 68 coding and 93 noncoding (>150 bp) fragments is consistently less than 3%. The seven most widely touted DNA barcode regions as well as one promising barcode candidate showed low sequence divergence. Eight mutational hotspots were identified from the 11 cp genomes. These hotspots may potentially be useful as specific DNA barcodes for species identification of Schima. The 58 cpSSR loci reported here are complementary to the microsatellite markers identified from the nuclear genome, and will be leveraged for further population-level studies. Phylogenetic relationships among the 11 Schima species were resolved with strong support based on the cp genome data set, which corresponds well with the species distribution pattern. The data presented here will serve as a foundation to facilitate species identification, DNA barcoding and phylogenetic reconstructions for future exploration of Schima.},
}
@article {pmid28572216,
year = {2017},
author = {Giessler, KM and Kleinheinz, K and Huebschmann, D and Balasubramanian, GP and Dubash, TD and Dieter, SM and Siegl, C and Herbst, F and Weber, S and Hoffmann, CM and Fronza, R and Buchhalter, I and Paramasivam, N and Eils, R and Schmidt, M and von Kalle, C and Schneider, M and Ulrich, A and Scholl, C and Fröhling, S and Weichert, W and Brors, B and Schlesner, M and Ball, CR and Glimm, H},
title = {Genetic subclone architecture of tumor clone-initiating cells in colorectal cancer.},
journal = {The Journal of experimental medicine},
volume = {214},
number = {7},
pages = {2073-2088},
pmid = {28572216},
issn = {1540-9538},
mesh = {Animals ; Clone Cells/metabolism ; Colorectal Neoplasms/*genetics/metabolism/pathology ; *DNA Copy Number Variations ; DNA Mutational Analysis/methods ; Genetic Heterogeneity ; Genomics/methods ; Humans ; Interleukin Receptor Common gamma Subunit/deficiency/genetics ; Mice, Inbred NOD ; Mice, Knockout ; Mice, SCID ; Mutation ; Neoplastic Stem Cells/*metabolism ; Spheroids, Cellular/*metabolism ; Transplantation, Heterologous ; Tumor Cells, Cultured ; },
abstract = {A hierarchically organized cell compartment drives colorectal cancer (CRC) progression. Genetic barcoding allows monitoring of the clonal output of tumorigenic cells without prospective isolation. In this study, we asked whether tumor clone-initiating cells (TcICs) were genetically heterogeneous and whether differences in self-renewal and activation reflected differential kinetics among individual subclones or functional hierarchies within subclones. Monitoring genomic subclone kinetics in three patient tumors and corresponding serial xenografts and spheroids by high-coverage whole-genome sequencing, clustering of genetic aberrations, subclone combinatorics, and mutational signature analysis revealed at least two to four genetic subclones per sample. Long-term growth in serial xenografts and spheroids was driven by multiple genomic subclones with profoundly differing growth dynamics and hence different quantitative contributions over time. Strikingly, genetic barcoding demonstrated stable functional heterogeneity of CRC TcICs during serial xenografting despite near-complete changes in genomic subclone contribution. This demonstrates that functional heterogeneity is, at least frequently, present within genomic subclones and independent of mutational subclone differences.},
}
@article {pmid28572161,
year = {2017},
author = {Waalkes, A and Penewit, K and Wood, BL and Wu, D and Salipante, SJ},
title = {Ultrasensitive detection of acute myeloid leukemia minimal residual disease using single molecule molecular inversion probes.},
journal = {Haematologica},
volume = {102},
number = {9},
pages = {1549-1557},
pmid = {28572161},
issn = {1592-8721},
support = {R33 CA192980/CA/NCI NIH HHS/United States ; },
mesh = {Adult ; Aged ; Female ; Humans ; Leukemia, Myeloid, Acute/*blood/*diagnosis ; Male ; Middle Aged ; Molecular Probes/*chemistry ; Neoplasm, Residual/blood/diagnosis ; },
abstract = {The identification of minimal residual disease is the primary diagnostic finding which predicts relapse in patients treated for acute myeloid leukemia. Ultrasensitive detection of minimal residual disease would enable better patient risk stratification and could open opportunities for early therapeutic intervention. Herein we apply single molecule molecular inversion probe capture, a technology combining multiplexed targeted sequencing with error correction schemes based on molecular barcoding, in order to detect mutations identifying minimal residual disease with ultrasensitive and quantitative precision. We designed a single molecule molecular inversion probe capture panel spanning >50 kb and targeting 32 factors relevant to acute myeloid leukemia pathogenesis. We demonstrate linearity and quantitative precision over 100-fold relative abundance of mutant cells (1 in 100 to 1 in 1,500), with estimated error rates approaching 1 in 1,200 base pairs sequenced and maximum theoretical limits of detection exceeding 1 in 60,000 mutant alleles. In 3 of 4 longitudinally collected specimens from patients with acute myeloid leukemia, we find that single molecule molecular inversion probe capture detects somatic mutations identifying minimal residual disease at substantially earlier time points and with greater sensitivity than clinical diagnostic approaches used as current standard of care (flow cytometry and conventional molecular diagnosis), and identifies persisting neoplastic cells during clinical remission. In 2 patients, single molecule molecular inversion probe capture detected heterogeneous, subclonal acute myeloid leukemia populations carrying distinct mutational signatures. Single molecule molecular inversion probe technology uniquely couples scalable target enrichment with sequence read error correction, providing an integrated, ultrasensitive approach for detecting minimal residual disease identifying mutations.},
}
@article {pmid28570635,
year = {2017},
author = {Zahiri, R and Lafontaine, JD and Schmidt, BC and deWaard, JR and Zakharov, EV and Hebert, PDN},
title = {Probing planetary biodiversity with DNA barcodes: The Noctuoidea of North America.},
journal = {PloS one},
volume = {12},
number = {6},
pages = {e0178548},
pmid = {28570635},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Genes, Insect ; Lepidoptera/*genetics ; North America ; },
abstract = {This study reports the assembly of a DNA barcode reference library for species in the lepidopteran superfamily Noctuoidea from Canada and the USA. Based on the analysis of 69,378 specimens, the library provides coverage for 97.3% of the noctuoid fauna (3565 of 3664 species). In addition to verifying the strong performance of DNA barcodes in the discrimination of these species, the results indicate close congruence between the number of species analyzed (3565) and the number of sequence clusters (3816) recognized by the Barcode Index Number (BIN) system. Distributional patterns across 12 North American ecoregions are examined for the 3251 species that have GPS data while BIN analysis is used to quantify overlap between the noctuoid faunas of North America and other zoogeographic regions. This analysis reveals that 90% of North American noctuoids are endemic and that just 7.5% and 1.8% of BINs are shared with the Neotropics and with the Palearctic, respectively. One third (29) of the latter species are recent introductions and, as expected, they possess low intraspecific divergences.},
}
@article {pmid28569159,
year = {2017},
author = {Echeverry, DF and Deason, NA and Makuru, V and Davidson, J and Xiao, H and Niedbalski, J and Yu, X and Stevenson, JC and Bugoro, H and Aparaimo, A and Reuben, H and Cooper, R and Burkot, TR and Russell, TL and Collins, FH and Lobo, NF},
title = {Fast and robust single PCR for Plasmodium sporozoite detection in mosquitoes using the cytochrome oxidase I gene.},
journal = {Malaria journal},
volume = {16},
number = {1},
pages = {230},
pmid = {28569159},
issn = {1475-2875},
mesh = {Animals ; Anopheles/parasitology ; Electron Transport Complex IV/analysis ; Female ; High-Throughput Nucleotide Sequencing/*methods ; Melanesia ; Plasmodium falciparum/enzymology/*isolation &amp; purification ; Plasmodium knowlesi/enzymology/*isolation &amp; purification ; Plasmodium vivax/enzymology/*isolation &amp; purification ; Polymerase Chain Reaction/*methods ; Protozoan Proteins/*analysis ; RNA, Ribosomal, 18S/analysis ; Sensitivity and Specificity ; Sporozoites/enzymology/isolation &amp; purification ; },
abstract = {BACKGROUND: Molecular tools for detecting malaria-infected mosquitoes with improved practicality, sensitivity and specificity, and high-throughput are required. A common PCR technique used to detect mosquitoes infected with Plasmodium spp. is a nested PCR assay based on the 18s-rRNA gene. However, this technique has several technical limitations, is laborious and time consuming.<br><br>METHODS: In this study, a PCR-based on the Plasmodium cytochrome oxidase I (COX-I) gene was compared with the 18s-rRNA nested PCR using serial dilutions (330-0.0012&#xa0;pg) of DNA from Plasmodium vivax, Plasmodium falciparum and Plasmodium knowlesi and with DNA from 48 positive and negative Kenyan mosquitoes (previously detected by using both ELISA and PCR). This assay for Plasmodium spp. DNA detection using the fast COX-I PCR assay was then performed individually on 2122 field collected mosquitoes (from the Solomon Islands) in which DNA was extracted from head and thorax.<br><br>RESULTS: The fast COX-I PCR assay took 1&#xa0;h to run and consistently detected as low as to 0.043&#xa0;pg of parasite DNA (equivalent to two parasites) in a single PCR, while analyses with the 18s-rRNA nested PCR required 4&#xa0;h to complete with a consistent detection threshold of 1.5&#xa0;pg of DNA. Both assays produced concordant results when applied to the 48 Kenyan control samples with known Plasmodium spp. infection status. The fast COX-I PCR identified 23/2122 Plasmodium-infected mosquitoes from the Solomon Islands.<br><br>CONCLUSIONS: This new COX-I PCR adapted for a single PCR reaction is a faster, simpler, cheaper, more sensitive technique amenable to high-throughput analyses for Plasmodium DNA detection in mosquitoes and is comparable to the 18s-rRNA nested PCR. The improved sensitivity seen with the fast COX-I PCR will improve the accuracy of mosquito infection rate determination.},
}
@article {pmid28569133,
year = {2017},
author = {Charbonneau, ARL and Forman, OP and Cain, AK and Newland, G and Robinson, C and Boursnell, M and Parkhill, J and Leigh, JA and Maskell, DJ and Waller, AS},
title = {Defining the ABC of gene essentiality in streptococci.},
journal = {BMC genomics},
volume = {18},
number = {1},
pages = {426},
pmid = {28569133},
issn = {1471-2164},
support = {G1100100/MRC_/Medical Research Council/United Kingdom ; 1503883/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Genes, Bacterial/*genetics ; Genes, Essential/genetics ; Genomics ; *High-Throughput Nucleotide Sequencing ; Mutation ; Streptococcus/*genetics ; },
abstract = {BACKGROUND: Utilising next generation sequencing to interrogate saturated bacterial mutant libraries provides unprecedented information for the assignment of genome-wide gene essentiality. Exposure of saturated mutant libraries to specific conditions and subsequent sequencing can be exploited to uncover gene essentiality relevant to the condition. Here we present a barcoded transposon directed insertion-site sequencing (TraDIS) system to define an essential gene list for Streptococcus equi subsp. equi, the causative agent of strangles in horses, for the first time. The gene essentiality data for this group C Streptococcus was compared to that of group A and B streptococci.<br><br>RESULTS: Six barcoded variants of pGh9:ISS1 were designed and used to generate mutant libraries containing between 33,000-66,000 unique mutants. TraDIS was performed on DNA extracted from each library and data were analysed separately and as a combined master pool. Gene essentiality determined that 19.5% of the S. equi genome was essential. Gene essentialities were compared to those of group A and group B streptococci, identifying concordances of 90.2% and 89.4%, respectively and an overall concordance of 83.7% between the three species.<br><br>CONCLUSIONS: The use of barcoded pGh9:ISS1 to generate mutant libraries provides a highly useful tool for the assignment of gene function in S. equi and other streptococci. The shared essential gene set of group A, B and C streptococci provides further evidence of the close genetic relationships between these important pathogenic bacteria. Therefore, the ABC of gene essentiality reported here provides a solid foundation towards reporting the functional genome of streptococci.},
}
@article {pmid28566083,
year = {2017},
author = {Başaran, S and Karabıçak, N and Şimşek Yavuz, S and Wiederhold, NP and Şafak, S and Sarıbuğa, A and Sutton, DA and Bingöl, Z and Çağatay, A and Özsüt, H and Kılıçaslan, Z and Eraksoy, H},
title = {[A case of coccidioidomycosis in Turkey imported from the United States of America].},
journal = {Mikrobiyoloji bulteni},
volume = {51},
number = {2},
pages = {183-190},
doi = {10.5578/mb.54033},
pmid = {28566083},
issn = {0374-9096},
mesh = {Adult ; Amoxicillin-Potassium Clavulanate Combination/pharmacology/therapeutic use ; Antifungal Agents/pharmacology/*therapeutic use ; Arizona ; Coccidioides/drug effects/growth &amp; development/*isolation &amp; purification ; Coccidioidomycosis/drug therapy/*microbiology ; Fluconazole/pharmacology/therapeutic use ; Humans ; Itraconazole/pharmacology/therapeutic use ; Male ; Penicillanic Acid/analogs &amp; derivatives/pharmacology/therapeutic use ; Piperacillin/pharmacology/therapeutic use ; Piperacillin, Tazobactam Drug Combination ; Pleura/microbiology ; Recurrence ; Spores, Fungal/drug effects/growth &amp; development/isolation &amp; purification ; Travel ; Turkey ; },
abstract = {Coccidioidomycosis caused by Coccidioides immitis or Coccidioides posadasii is a rare infectious disease except in endemic regions. In this report the third documented imported case of coccidioidomycosis in Turkey was presented. A thirty-year-old male patient was admitted to our hospital with fever and purulent drainage from his chest tube. He had worked in Arizona, USA, until 4 months before this presentation. While in Arizona, he experienced cough and hemoptysis and was diagnosed as pulmonary coccidioidomycosis. He was treated with itraconazole for two months and he had no symptoms for 3 years. He then returned to Turkey and 2 months after his return to Turkey, he was admitted to another hospital in Istanbul with dyspnea and diagnosed as hydro-pneumothorax, and pleural fluid obtained from the inserted chest tube was found to be purulent. One gram of BID amoxicillin-clavulanate was given. Physical examination on admission revealed a purulent drainage on the right side chest tube, a temperature of 38.5°C and decreased breath sounds on the right lung. Piperacillin-tazobactam 3 x 4.5 g intravenous and fluconazole 400 mg intravenous once daily were started. Human immunodeficiency virus test was negative. Gram-negative diplococci and rods, gram-positive cocci and septate hyphae were seen in the Gram stain of his pleural fluid. Pleural fluid culture revealed Moraxella catarrhalis after 24 hours incubation and a mold after 72 hours of incubation. Anti-coccidioidal antibodies were found positive in a titer of 1/2. Hydro-pneumothorax, atelectasis and a 3 mm nodules in the right lung were seen in his thorax CT. The patient's pleural fluid and the culture plates were sent to the Public Health Institute of Turkey, Mycology Reference Laboratory (PHIT-MRL), with a clinical suspicion of coccidioidomycosis. The specimen and plates were submitted to the PHIT-MRL Bio Safety Level-3 laboratory for mycological evaluation. The microscopic examination of 15% KOH preparations of pleural fluid specimens revealed septate hyphae which appear to be in the early stages of forming arthroconidia. The pleural fluid culture grew buff-white coloured colonies with aerial hyphae, which were suspected of being a Coccidioides spp. The strain was identified as C.immitis/posadasii by direct microscopy and culture, and subsequently confirmed by the FDA-approved DNA probe. DNA sequence analysis of the ITS and D1/D2 rDNA regions confirmed the isolate to be C.posadasii species [ITS 100% match to GenBank Accession No. AB232901 (630/630 base pair match), and D1/D2 100% match to GenBank Accession No. AB232884 (617/617 base pair match)]. ITS1 and ITS2 barcode analysis also confirmed the species to be C.posadasii, which is the species endemic in Arizona. Susceptibility testing was performed according to Clinical and Laboratory Standards Institute M38-A2 guidelines in the Fungus Testing Laboratory of the University of Texas Health Science Center at San Antonio and minimal inhibitory concentration values were; 0.125 µg/ml for amphotericin B, posaconazole and voriconazole, 0.5 µg/ml for itraconazole and 8 µg/ml for fluconazole. He had decortication of the pleura and was discharged from hospital after six weeks treatment with intravenous fluconazole which was continued orally for one year. Anti-coccidioidal antibodies were negative after two months of treatment. The patient is currently asymptomatic. The presented case is the third case reported from Turkey and provides additional contribution to the existing literature with regard to the appearance of arthroconidium, which is the unusual hyphal form, instead of the expected spherules in the infected tissue.},
}
@article {pmid28553940,
year = {2017},
author = {Lan, F and Demaree, B and Ahmed, N and Abate, AR},
title = {Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding.},
journal = {Nature biotechnology},
volume = {35},
number = {7},
pages = {640-646},
pmid = {28553940},
issn = {1546-1696},
support = {R01 HG008978/HG/NHGRI NIH HHS/United States ; R21 HG007233/HG/NHGRI NIH HHS/United States ; DP2 AR068129/AR/NIAMS NIH HHS/United States ; R01 EB019453/EB/NIBIB NIH HHS/United States ; U01 AI129206/AI/NIAID NIH HHS/United States ; },
mesh = {Cell Separation/instrumentation ; Chromosome Mapping/*instrumentation ; DNA Barcoding, Taxonomic/*instrumentation ; Equipment Design ; Equipment Failure Analysis ; Genome/*genetics ; High-Throughput Nucleotide Sequencing/*instrumentation ; *Lab-On-A-Chip Devices ; Tissue Array Analysis/*instrumentation ; },
abstract = {The application of single-cell genome sequencing to large cell populations has been hindered by technical challenges in isolating single cells during genome preparation. Here we present single-cell genomic sequencing (SiC-seq), which uses droplet microfluidics to isolate, fragment, and barcode the genomes of single cells, followed by Illumina sequencing of pooled DNA. We demonstrate ultra-high-throughput sequencing of >50,000 cells per run in a synthetic community of Gram-negative and Gram-positive bacteria and fungi. The sequenced genomes can be sorted in silico based on characteristic sequences. We use this approach to analyze the distributions of antibiotic-resistance genes, virulence factors, and phage sequences in microbial communities from an environmental sample. The ability to routinely sequence large populations of single cells will enable the de-convolution of genetic heterogeneity in diverse cell populations.},
}
@article {pmid28551127,
year = {2017},
author = {Tian, A and Liu, Y and Gao, J},
title = {Sensitive SERS detection of lead ions via DNAzyme based quadratic signal amplification.},
journal = {Talanta},
volume = {171},
number = {},
pages = {185-189},
doi = {10.1016/j.talanta.2017.04.049},
pmid = {28551127},
issn = {1873-3573},
mesh = {Biosensing Techniques/*methods ; DNA, Catalytic/*chemistry ; Lead/*analysis/chemistry ; *Limit of Detection ; *Spectrum Analysis, Raman ; },
abstract = {Highly sensitive detection of Pb[2+] is very necessary for water quality control, clinical toxicology, and industrial monitoring. In this work, a simple and novel DNAzyme-based SERS quadratic amplification method is developed for the detection of Pb[2+]. This strategy possesses some remarkable features compared to the conventional DNAzyme-based SERS methods, which are as follows: (i) Coupled DNAzyme-activated hybridization chain reaction (HCR) with bio barcodes; a quadratic amplification method is designed using the unique catalytic selectivity of DNAzyme. The SERS signal is significantly amplified. This method is rapid with a detection time of 2h. (ii) The problem of high background induced by excess bio barcodes is circumvented by using magnetic beads (MBs) as the carrier of signal-output products, and this sensing system is simple in design and can easily be carried out by simple mixing and incubation. Given the unique and attractive characteristics, a simple and universal strategy is designed to accomplish sensitive detection of Pb[2+]. The detection limit of Pb[2+] via SERS detection is 70 fM, with the linear range from 1.0×10[-13]M to 1.0×10[-7]M. The method can be further extended to the quantitative detection of a variety of targets by replacing the lead-responsive DNAzyme with other functional DNA.},
}
@article {pmid28548029,
year = {2017},
author = {Basu, AS},
title = {Digital Assays Part II: Digital Protein and Cell Assays.},
journal = {SLAS technology},
volume = {22},
number = {4},
pages = {387-405},
doi = {10.1177/2472630317705681},
pmid = {28548029},
issn = {2472-6311},
mesh = {Chemistry Techniques, Analytical/*methods ; Cytological Techniques/*methods ; *Data Interpretation, Statistical ; Microfluidic Analytical Techniques/*methods ; Specimen Handling/*methods ; },
abstract = {A digital assay is one in which the sample is partitioned into many containers such that each partition contains a discrete number of biological entities (0, 1, 2, 3, . . .). A powerful technique in the biologist's toolkit, digital assays bring a new level of precision in quantifying nucleic acids, measuring proteins and their enzymatic activity, and probing single-cell genotype and phenotype. Where part I of this review focused on the fundamentals of partitioning and digital PCR, part II turns its attention to digital protein and cell assays. Digital enzyme assays measure the kinetics of single proteins with enzymatic activity. Digital enzyme-linked immunoassays (ELISAs) quantify antigenic proteins with 2 to 3 log lower detection limit than conventional ELISA, making them well suited for low-abundance biomarkers. Digital cell assays probe single-cell genotype and phenotype, including gene expression, intracellular and surface proteins, metabolic activity, cytotoxicity, and transcriptomes (scRNA-seq). These methods exploit partitioning to 1) isolate single cells or proteins, 2) detect their activity via enzymatic amplification, and 3) tag them individually by coencapsulating them with molecular barcodes. When scaled, digital assays reveal stochastic differences between proteins or cells within a population, a key to understanding biological heterogeneity. This review is intended to give a broad perspective to scientists interested in adopting digital assays into their workflows.},
}
@article {pmid28546554,
year = {2017},
author = {Nag, S and Dalgaard, MD and Kofoed, PE and Ursing, J and Crespo, M and Andersen, LO and Aarestrup, FM and Lund, O and Alifrangis, M},
title = {High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {2398},
pmid = {28546554},
issn = {2045-2322},
mesh = {Antimalarials/*pharmacology/therapeutic use ; DNA, Protozoan/genetics ; *Drug Resistance ; *High-Throughput Nucleotide Sequencing ; Humans ; Malaria, Falciparum/drug therapy/epidemiology/*parasitology ; Mutation ; Plasmodium falciparum/*drug effects/*genetics ; Polymorphism, Single Nucleotide ; Prevalence ; Protozoan Proteins/genetics ; Tetrahydrofolate Dehydrogenase/genetics ; },
abstract = {Genetic polymorphisms in P. falciparum can be used to indicate the parasite's susceptibility to antimalarial drugs as well as its geographical origin. Both of these factors are key to monitoring development and spread of antimalarial drug resistance. In this study, we combine multiplex PCR, custom designed dual indexing and Miseq sequencing for high throughput SNP-profiling of 457 malaria infections from Guinea-Bissau, at the cost of 10 USD per sample. By amplifying and sequencing 15 genetic fragments, we cover 20 resistance-conferring SNPs occurring in pfcrt, pfmdr1, pfdhfr, pfdhps, as well as the entire length of pfK13, and the mitochondrial barcode for parasite origin. SNPs of interest were sequenced with an average depth of 2,043 reads, and bases were called for the various SNP-positions with a p-value below 0.05, for 89.8-100% of samples. The SNP data indicates that artemisinin resistance-conferring SNPs in pfK13 are absent from the studied area of Guinea-Bissau, while the pfmdr1 86 N allele is found at a high prevalence. The mitochondrial barcodes are unanimous and accommodate a West African origin of the parasites. With this method, very reliable high throughput surveillance of antimalarial drug resistance becomes more affordable than ever before.},
}
@article {pmid28545995,
year = {2017},
author = {Gao, F and Huang, J and Zhao, Y and Li, L and Liu, W and Miao, M and Zhang, Q and Li, J and Yi, Z and El-Serehy, HA and Warren, A and Song, W},
title = {Systematic studies on ciliates (Alveolata, Ciliophora) in China: Progress and achievements based on molecular information.},
journal = {European journal of protistology},
volume = {61},
number = {Pt B},
pages = {409-423},
doi = {10.1016/j.ejop.2017.04.009},
pmid = {28545995},
issn = {1618-0429},
mesh = {China ; Ciliophora/*classification/*genetics ; *Classification ; *Molecular Biology ; Research/*trends ; },
abstract = {Due to complex morphological and convergent morphogenetic characters, the systematics of ciliates has long been ambiguous. Since 1990, the Laboratory of Protozoology, Ocean University of China, in collaboration with other research groups worldwide, has carried out a series of integrative investigations on ciliate systematics. To date, genomic DNA has been extracted from about 1700 ciliate strains, and phylogenetic analyses have been performed for two-thirds of orders. Main findings are: (1) Classifications of about 50 hypotrichous species have been resolved, although the monophylies of three hypotrichous orders remain unconfirmed; (2) Euplotia and two orders and all seven families within them are monophyletic assemblages; (3) Lynnella represents an order-level taxon, and is separated from two sister monophyletic subclasses Oligotrichia and Choreotrichia; (4) the peritrich families Zoothamniidae and Vorticellidae are separated from each other, and Zoothamnium exhibits a high genetic diversity; (5) the scuticociliate order Philasterida is monophyletic and separated from loxocephalids, and the thigmotrichids is a suborder within Pleuronematida; (6) 14 classes were recovered including one new class Protocruziea, and Mesodiniea is basal to subphyla Intramacronucleata and Postciliodesmatophora; (7) mitochondrial cytochrome c oxidase subunit I heteroplasmy was reported in ciliates for the first time, and candidate barcoding genes for Frontonia species identification were identified.},
}
@article {pmid28545896,
year = {2017},
author = {Montes, MM and Castro-Romero, R and Martorelli, SR},
title = {Morphological identification and DNA barcoding of a new species of Parabrachiella (Siphonostomatoida: Lernaeopodidae) with aspects of their intraspecific variation.},
journal = {Acta tropica},
volume = {173},
number = {},
pages = {34-44},
doi = {10.1016/j.actatropica.2017.05.025},
pmid = {28545896},
issn = {1873-6254},
mesh = {Animals ; Argentina ; Copepoda/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Fish Diseases/epidemiology/*parasitology ; Fishes ; },
abstract = {We present a detailed morphological description and a DNA barcoding of Parabrachiella platensis n. sp. collected from Mugil liza Valenciennes in Samborombon Bay (Buenos Aires, Argentina). This new species was compared with two Parabrachiella species parasitic on mugilids: Parabrachiella exilis (Shiino, 1956) and Parabrachiella mugilis (Kabata, Raibaut et Ben Hassine, 1971). Parabrachiella platensis n. sp. differs from those species in the shape of posterior processes, the anal slit with two pairs of bipartite papillae, the size of cephalothorax, the trunk, the maxilla, the microhabitat on the host, and the lack of caudal rami. On the host, the new species was in the nostrils (a new site for a species of the genus Parabrachiella) and in the fins base. Some minor morphological differences were observed in relation to the locations on the host. The molecular analysis conducted based on mtDNA-COI between specimens of the new species on the fins and nostrils showed a genetic similarity of 99.8%. This percentage supports that the specimens found in nostrils and fins base could represent a single species. New studies on P. platensis n. sp., including infection of the same fish with the two forms, could bring some new information. Anyway according to the genetic information provided and the minimal morphological differences spotted we conclude that the two forms are a single specie. The differences observed are possibly influenced by the place of the host where the two forms of copepods were found, nostrils and fins. The new species was also molecularly compared to other five species of Parabrachiella including P. exilis (parasitizing mugilid from Chile), Parabrachiella anisotremis, Parabrachiella auriculata, Parabrachiella merluccii, and P. hugu (the last two sequences were taken from the GenBank). The genetic distance of 9% among P. platensis n. sp. and P. exilis, which is the close morphological related species, allow to states that these two copepods on mugilids belong to different species and then validating the morphological differences found between them.},
}
@article {pmid28544553,
year = {2017},
author = {Valentini, P and Galimberti, A and Mezzasalma, V and De Mattia, F and Casiraghi, M and Labra, M and Pompa, PP},
title = {DNA Barcoding Meets Nanotechnology: Development of a Universal Colorimetric Test for Food Authentication.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {56},
number = {28},
pages = {8094-8098},
doi = {10.1002/anie.201702120},
pmid = {28544553},
issn = {1521-3773},
mesh = {Colorimetry/*methods ; Commerce ; *DNA Barcoding, Taxonomic ; DNA Primers ; Datasets as Topic ; Food Contamination/*analysis ; Indicators and Reagents/chemistry ; *Nanotechnology ; Polymerase Chain Reaction/methods ; Proof of Concept Study ; },
abstract = {Food trade globalization and the growing demand for selected food varieties have led to the intensification of adulteration cases, especially in the form of species substitution and mixing with cheaper taxa. This phenomenon has huge economic impact and sometimes even public health implications. DNA barcoding represents a well-proven molecular approach to assess the authenticity of food items, although its use is hampered by analytical constraints and timeframes that are often prohibitive for the food market. To address such issues, we have introduced a new technology, named NanoTracer, that allows for rapid and naked-eye molecular traceability of any food and requires limited instrumentation and cost-effective reagents. Moreover, unlike sequencing, this method can be used to identify not only the substitution of a fine ingredient, but also its dilution with cheaper ones.},
}
@article {pmid28542606,
year = {2017},
author = {De Castro, O and Comparone, M and Di Maio, A and Del Guacchio, E and Menale, B and Troisi, J and Aliberti, F and Trifuoggi, M and Guida, M},
title = {What is in your cup of tea? DNA Verity Test to characterize black and green commercial teas.},
journal = {PloS one},
volume = {12},
number = {5},
pages = {e0178262},
pmid = {28542606},
issn = {1932-6203},
mesh = {Camellia sinensis/classification/*genetics ; Chloroplasts/genetics ; *DNA Barcoding, Taxonomic ; *DNA, Plant ; Food Analysis/*methods ; *Genotyping Techniques ; Italy ; Quality Control ; Tea/*genetics ; },
abstract = {In this study, we used several molecular techniques to develop a fast and reliable protocol (DNA Verity Test, DVT) for the characterization and confirmation of the species or taxa present in herbal infusions. As a model plant for this protocol, Camellia sinensis, a traditional tea plant, was selected due to the following reasons: its historical popularity as a (healthy) beverage, its high selling value, the importation of barely recognizable raw product (i.e., crushed), and the scarcity of studies concerning adulterants or contamination. The DNA Verity Test includes both the sequencing of DNA barcoding markers and genotyping of labeled-PCR DNA barcoding fragments for each sample analyzed. This protocol (DVT) was successively applied to verify the authenticity of 32 commercial teas (simple or admixture), and the main results can be summarized as follows: (1) the DVT protocol is suitable to detect adulteration in tea matrices (contaminations or absence of certified ingredients), and the method can be exported for the study of other similar systems; (2) based on the BLAST analysis of the sequences of rbcL+matK±rps7-trnV(GAC) chloroplast markers, C. sinensis can be taxonomically characterized; (3) rps7-trnV(GAC) can be employed to discriminate C. sinensis from C. pubicosta; (4) ITS2 is not an ideal DNA barcode for tea samples, reflecting potential incomplete lineage sorting and hybridization/introgression phenomena in C. sinensis taxa; (5) the genotyping approach is an easy, inexpensive and rapid pre-screening method to detect anomalies in the tea templates using the trnH(GUG)-psbA barcoding marker; (6) two herbal companies provided no authentic products with a contaminant or without some of the listed ingredients; and (7) the leaf matrices present in some teabags could be constituted using an admixture of different C. sinensis haplotypes and/or allied species (C. pubicosta).},
}
@article {pmid28542495,
year = {2017},
author = {Xu, M and Heidmarsson, S and Thorsteinsdottir, M and Eiriksson, FF and Omarsdottir, S and Olafsdottir, ES},
title = {DNA barcoding and LC-MS metabolite profiling of the lichen-forming genus Melanelia: Specimen identification and discrimination focusing on Icelandic taxa.},
journal = {PloS one},
volume = {12},
number = {5},
pages = {e0178012},
pmid = {28542495},
issn = {1932-6203},
mesh = {Ascomycota/classification/*genetics/metabolism ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/*genetics ; DNA, Plant/*genetics ; DNA, Ribosomal Spacer/*genetics ; Iceland ; Lichens/classification/*genetics ; Principal Component Analysis ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Taxa in the genus Melanelia (Parmeliaceae, Ascomycota) belong to a group of saxicolous lichens with brown to black foliose thalli, which have recently undergone extensive changes in circumscription. Taxa belonging to Parmeliaceae are prolific producers of bioactive compounds, which have also been traditionally used for chemotaxonomic purposes. However, the chemical diversity of the genus Melanelia and the use of chemical data for species discrimination in this genus are largely unexplored. In addition, identification based on morphological characters is challenging due to few taxonomically informative characters. Molecular identification methods, such as DNA barcoding, have rarely been applied to this genus. This study aimed to identify the Melanelia species from Iceland using DNA barcoding approach, and to explore their chemical diversity using chemical profiling. Chemometric tools were used to see if lichen metabolite profiles determined by LC-MS could be used for the identification of Icelandic Melanelia species. Barcoding using the fungal nuclear ribosomal internal transcribed spacer region (nrITS) successfully identified three Melalenlia species occurring in Iceland, together with Montanelia disjuncta (Basionym: Melanelia disjuncta). All species formed monophyletic clades in the neighbor-joining nrITS gene tree. However, high intraspecific genetic distance of M. stygia suggests the potential of unrecognized species lineages. Principal component analysis (PCA) of metabolite data gave a holistic overview showing that M. hepatizon and M. disjuncta were distinct from the rest, without the power to separate M. agnata and M. stygia due to their chemical similarity. Orthogonal partial least-squares to latent structures-discriminate analysis (OPLS-DA), however, successfully distinguished M. agnata and M. stygia by identifying statistically significant metabolites, which lead to class differentiation. This work has demonstrated the potential of DNA barcoding, chemical profiling and chemometrics in identification of Melanelia species.},
}
@article {pmid28542160,
year = {2017},
author = {Nadin-Davis, S and Alnabelseya, N and Knowles, MK},
title = {The phylogeography of Myotis bat-associated rabies viruses across Canada.},
journal = {PLoS neglected tropical diseases},
volume = {11},
number = {5},
pages = {e0005541},
pmid = {28542160},
issn = {1935-2735},
mesh = {Animals ; Canada ; Chiroptera/classification/genetics/*virology ; DNA Barcoding, Taxonomic ; Genome, Viral ; *Phylogeography ; Rabies virus/*classification/genetics/*isolation &amp; purification ; Sequence Analysis, DNA ; },
abstract = {As rabies in carnivores is increasingly controlled throughout much of the Americas, bats are emerging as a significant source of rabies virus infection of humans and domestic animals. Knowledge of the bat species that maintain rabies is a crucial first step in reducing this public health problem. In North America, several bat species are known to be rabies virus reservoirs but the role of bats of the Myotis genus has been unclear due to the scarcity of laboratory confirmed cases and the challenges encountered in species identification of poorly preserved diagnostic submissions by morphological traits alone. This study has employed a collection of rabid bat specimens collected across Canada over a 25 year period to clearly define the role of particular Myotis species as rabies virus reservoirs. The virus was characterised by partial genome sequencing and host genetic barcoding, used to confirm species assignment of specimens, proved crucial to the identification of certain bat species as disease reservoirs. Several variants were associated with Myotis species limited in their Canadian range to the westernmost province of British Columbia while others were harboured by Myotis species that circulate across much of eastern and central Canada. All of these Myotis-associated viral variants, except for one, clustered as a monophyletic MYCAN clade, which has emerged from a lineage more broadly distributed across North America; in contrast one distinct variant, associated with the long-legged bat in Canada, represents a relatively recent host jump from a big brown bat reservoir. Together with evidence from South America, these findings demonstrate that rabies virus has emerged in the Myotis genus independently on multiple occasions and highlights the potential for emergence of new viral-host associations within this genus.},
}
@article {pmid28541403,
year = {2017},
author = {Roehr, JT and Dieterich, C and Reinert, K},
title = {Flexbar 3.0 - SIMD and multicore parallelization.},
journal = {Bioinformatics (Oxford, England)},
volume = {33},
number = {18},
pages = {2941-2942},
doi = {10.1093/bioinformatics/btx330},
pmid = {28541403},
issn = {1367-4811},
mesh = {Animals ; Caenorhabditis elegans/genetics ; Genome, Helminth ; High-Throughput Nucleotide Sequencing/*methods ; Sequence Alignment/methods ; Sequence Analysis, DNA/methods ; *Software ; },
abstract = {MOTIVATION: High-throughput sequencing machines can process many samples in a single run. For Illumina systems, sequencing reads are barcoded with an additional DNA tag that is contained in the respective sequencing adapters. The recognition of barcode and adapter sequences is hence commonly needed for the analysis of next-generation sequencing data. Flexbar performs demultiplexing based on barcodes and adapter trimming for such data. The massive amounts of data generated on modern sequencing machines demand that this preprocessing is done as efficiently as possible.<br><br>RESULTS: We present Flexbar 3.0, the successor of the popular program Flexbar. It employs now twofold parallelism: multi-threading and additionally SIMD vectorization. Both types of parallelism are used to speed-up the computation of pair-wise sequence alignments, which are used for the detection of barcodes and adapters. Furthermore, new features were included to cover a wide range of applications. We evaluated the performance of Flexbar based on a simulated sequencing dataset. Our program outcompetes other tools in terms of speed and is among the best tools in the presented quality benchmark.<br><br>https://github.com/seqan/flexbar.<br><br>CONTACT: johannes.roehr@fu-berlin.de or knut.reinert@fu-berlin.de.},
}
@article {pmid28541284,
year = {2017},
author = {Schlecht, U and Liu, Z and Blundell, JR and St Onge, RP and Levy, SF},
title = {A scalable double-barcode sequencing platform for characterization of dynamic protein-protein interactions.},
journal = {Nature communications},
volume = {8},
number = {},
pages = {15586},
pmid = {28541284},
issn = {2041-1723},
support = {R01 HG008354/HG/NHGRI NIH HHS/United States ; U01 HL127522/HL/NHLBI NIH HHS/United States ; },
mesh = {DNA Barcoding, Taxonomic/*methods ; Protein Interaction Mapping/*methods ; *Protein Interaction Maps ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Tetrahydrofolate Dehydrogenase/metabolism ; },
abstract = {Several large-scale efforts have systematically catalogued protein-protein interactions (PPIs) of a cell in a single environment. However, little is known about how the protein interactome changes across environmental perturbations. Current technologies, which assay one PPI at a time, are too low throughput to make it practical to study protein interactome dynamics. Here, we develop a highly parallel protein-protein interaction sequencing (PPiSeq) platform that uses a novel double barcoding system in conjunction with the dihydrofolate reductase protein-fragment complementation assay in Saccharomyces cerevisiae. PPiSeq detects PPIs at a rate that is on par with current assays and, in contrast with current methods, quantitatively scores PPIs with enough accuracy and sensitivity to detect changes across environments. Both PPI scoring and the bulk of strain construction can be performed with cell pools, making the assay scalable and easily reproduced across environments. PPiSeq is therefore a powerful new tool for large-scale investigations of dynamic PPIs.},
}
@article {pmid28536641,
year = {2017},
author = {Mohammed Abubakar, B and Mohd Salleh, F and Shamsir Omar, MS and Wagiran, A},
title = {Review: DNA Barcoding and Chromatography Fingerprints for the Authentication of Botanicals in Herbal Medicinal Products.},
journal = {Evidence-based complementary and alternative medicine : eCAM},
volume = {2017},
number = {},
pages = {1352948},
pmid = {28536641},
issn = {1741-427X},
abstract = {In the last two decades, there has been a tremendous increase in the global use of herbal medicinal products (HMPs) due to their claimed health benefits. This has led to increase in their demand and consequently, also, resulted in massive adulteration. This is due to the fact that most of the traditional methods cannot identify closely related species in a process product form. Therefore the urgent need for simple and rapid identification methods resulted in the discovery of a novel technique. DNA barcoding is a process that uses short DNA sequence from the standard genome for species identification. This technique is reliable and is not affected by external factors such as climates, age, or plant part. The difficulties in isolation of DNA of high quality in addition to other factors are among the challenges encountered using the DNA barcoding in the authentication of HMP. These limitations indicated that using DNA barcoding alone may ineffectively authenticate the HMP. Therefore, the combination of DNA barcoding with chromatographic fingerprint, a popular and generally accepted technique for the assessment and quality control of HMP, will offer an efficient solution to effectively evaluate the authenticity and quality consistency of HMP. Detailed and quality information about the main composition of the HMPs will help to ascertain their efficacy and safety as these are very important for quality control.},
}
@article {pmid28533898,
year = {2017},
author = {Erickson, DL and Reed, E and Ramachandran, P and Bourg, NA and McShea, WJ and Ottesen, A},
title = {Reconstructing a herbivore's diet using a novel rbcL DNA mini-barcode for plants.},
journal = {AoB PLANTS},
volume = {9},
number = {3},
pages = {plx015},
pmid = {28533898},
issn = {2041-2851},
abstract = {Next Generation Sequencing and the application of metagenomic analyses can be used to answer questions about animal diet choice and study the consequences of selective foraging by herbivores. The quantification of herbivore diet choice with respect to native versus exotic plant species is particularly relevant given concerns of invasive species establishment and their effects on ecosystems. While increased abundance of white-tailed deer (Odocoileus virginianus) appears to correlate with increased incidence of invasive plant species, data supporting a causal link is scarce. We used a metabarcoding approach (PCR amplicons of the plant rbcL gene) to survey the diet of white-tailed deer (fecal samples), from a forested site in Warren County, Virginia with a comprehensive plant species inventory and corresponding reference collection of plant barcode and chloroplast sequences. We sampled fecal pellet piles and extracted DNA from 12 individual deer in October 2014. These samples were compared to a reference DNA library of plant species collected within the study area. For 72 % of the amplicons, we were able to assign taxonomy at the species level, which provides for the first time-sufficient taxonomic resolution to quantify the relative frequency at which native and exotic plant species are being consumed by white-tailed deer. For each of the 12 individual deer we collected three subsamples from the same fecal sample, resulting in sequencing 36 total samples. Using Qiime, we quantified the plant DNA found in all 36 samples, and found that variance within samples was less than variance between samples (F = 1.73, P = 0.004), indicating additional subsamples may not be necessary. Species level diversity ranged from 60 to 93 OTUs per individual and nearly 70 % of all plant sequences recovered were from native plant species. The number of species detected did reduce significantly (range 4-12) when we excluded species whose OTU composed <1 % of each sample's total. When compared to the abundance of native and non-natives plants inventoried in the local community, our results support the observation that white-tailed deer have strong foraging preferences, but these preferences were not consistent for species in either class. Deer forage behaviour may favour some exotic species, but not all.},
}
@article {pmid28530655,
year = {2017},
author = {Rogers, ZN and McFarland, CD and Winters, IP and Naranjo, S and Chuang, CH and Petrov, D and Winslow, MM},
title = {A quantitative and multiplexed approach to uncover the fitness landscape of tumor suppression in vivo.},
journal = {Nature methods},
volume = {14},
number = {7},
pages = {737-742},
pmid = {28530655},
issn = {1548-7105},
support = {R25 CA180993/CA/NCI NIH HHS/United States ; R01 CA175336/CA/NCI NIH HHS/United States ; R01 CA207133/CA/NCI NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; R35 GM118165/GM/NIGMS NIH HHS/United States ; R21 CA194910/CA/NCI NIH HHS/United States ; S10 OD018220/OD/NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; },
mesh = {Adenocarcinoma/genetics ; Animals ; DNA/genetics/isolation &amp; purification/metabolism ; DNA Barcoding, Taxonomic ; Female ; Genetic Engineering ; Humans ; Lentivirus/genetics ; Lung/metabolism ; Lung Neoplasms/genetics ; Male ; Mice ; Models, Genetic ; Neoplasms, Experimental/*metabolism ; Plasmids ; Proto-Oncogene Proteins p21(ras)/genetics/metabolism ; Tumor Suppressor Proteins/genetics/*metabolism ; },
abstract = {Cancer growth is a multistage, stochastic evolutionary process. While cancer genome sequencing has been instrumental in identifying the genomic alterations that occur in human tumors, the consequences of these alterations on tumor growth remain largely unexplored. Conventional genetically engineered mouse models enable the study of tumor growth in vivo, but they are neither readily scalable nor sufficiently quantitative to unravel the magnitude and mode of action of many tumor-suppressor genes. Here, we present a method that integrates tumor barcoding with ultradeep barcode sequencing (Tuba-seq) to interrogate tumor-suppressor function in mouse models of human cancer. Tuba-seq uncovers genotype-dependent distributions of tumor sizes. By combining Tuba-seq with multiplexed CRISPR-Cas9-mediated genome editing, we quantified the effects of 11 tumor-suppressor pathways that are frequently altered in human lung adenocarcinoma. Tuba-seq enables the broad quantification of the function of tumor-suppressor genes with unprecedented resolution, parallelization, and precision.},
}
@article {pmid28529702,
year = {2017},
author = {Muchlisin, ZA and Batubara, AS and Fadli, N and Muhammadar, AA and Utami, AI and Farhana, N and Siti-Azizah, MN},
title = {Assessing the species composition of tropical eels (Anguillidae) in Aceh Waters, Indonesia, with DNA barcoding gene cox1.},
journal = {F1000Research},
volume = {6},
number = {},
pages = {258},
pmid = {28529702},
issn = {2046-1402},
abstract = {The objective of the present study was to evaluate the species diversity of eels native to Aceh waters based on genetic data. Sampling was conducted in western coast waters of Aceh Province, Indonesia, from July to August 2016. Genomic DNA was extracted from the samples, a genomic region from the 5' region of the cox1 gene was amplified and sequenced, and this was then used to analyse genetic variation. The genetic sequences were blasted into the NCBI database. Based on this analysis there were three valid species of eels that occurred in Aceh waters, namely Anguilla marmorata, A. bicolor bicolor, and A. bengalensis bengalensis.},
}
@article {pmid28525570,
year = {2017},
author = {Redin, D and Borgström, E and He, M and Aghelpasand, H and Käller, M and Ahmadian, A},
title = {Droplet Barcode Sequencing for targeted linked-read haplotyping of single DNA molecules.},
journal = {Nucleic acids research},
volume = {45},
number = {13},
pages = {e125},
pmid = {28525570},
issn = {1362-4962},
mesh = {Alleles ; DNA Barcoding, Taxonomic/*methods ; Gene Library ; HLA-A Antigens/genetics ; *Haplotypes ; High-Throughput Nucleotide Sequencing ; Humans ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {Data produced with short-read sequencing technologies result in ambiguous haplotyping and a limited capacity to investigate the full repertoire of biologically relevant forms of genetic variation. The notion of haplotype-resolved sequencing data has recently gained traction to reduce this unwanted ambiguity and enable exploration of other forms of genetic variation; beyond studies of just nucleotide polymorphisms, such as compound heterozygosity and structural variations. Here we describe Droplet Barcode Sequencing, a novel approach for creating linked-read sequencing libraries by uniquely barcoding the information within single DNA molecules in emulsion droplets, without the aid of specialty reagents or microfluidic devices. Barcode generation and template amplification is performed simultaneously in a single enzymatic reaction, greatly simplifying the workflow and minimizing assay costs compared to alternative approaches. The method has been applied to phase multiple loci targeting all exons of the highly variable Human Leukocyte Antigen A (HLA-A) gene, with DNA from eight individuals present in the same assay. Barcode-based clustering of sequencing reads confirmed analysis of over 2000 independently assayed template molecules, with an average of 753 reads in support of called polymorphisms. Our results show unequivocal characterization of all alleles present, validated by correspondence against confirmed HLA database entries and haplotyping results from previous studies.},
}
@article {pmid28515454,
year = {2017},
author = {Takase, S and Kurokawa, R and Arai, D and Kanemoto Kanto, K and Okino, T and Nakao, Y and Kushiro, T and Yoshida, M and Matsumoto, K},
title = {A quantitative shRNA screen identifies ATP1A1 as a gene that regulates cytotoxicity by aurilide B.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {2002},
pmid = {28515454},
issn = {2045-2322},
mesh = {Cell Line, Tumor ; Cell Survival/drug effects/genetics ; Etoposide/pharmacology ; Gene Library ; Humans ; Peptides, Cyclic/*pharmacology ; Pharmacogenomic Testing ; Pharmacogenomic Variants/*drug effects ; *RNA Interference ; RNA, Small Interfering/*genetics ; Sodium-Potassium-Exchanging ATPase/*genetics ; },
abstract = {Genome-wide RNA interference (RNAi) with pooled and barcoded short-hairpin RNA (shRNA) libraries provides a powerful tool for identifying cellular components that are relevant to the modes/mechanisms of action (MoA) of bioactive compounds. shRNAs that affect cellular sensitivity to a given compound can be identified by deep sequencing of shRNA-specific barcodes. We used multiplex barcode sequencing technology by adding sample-specific index tags to PCR primers during sequence library preparation, enabling parallel analysis of multiple samples. An shRNA library screen with this system revealed that downregulation of ATP1A1, an α-subunit of Na[+]/K[+] ATPase, conferred significant sensitivity to aurilide B, a natural marine product that induces mitochondria-mediated apoptosis. Combined treatment with ouabain which inhibits Na[+]/K[+] ATPase by targeting α-subunits potentiated sensitivity to aurilide B, suggesting that ATP1A1 regulates mitochondria-mediated apoptosis. Our results indicate that multiplex sequencing facilitates the use of pooled shRNA library screening for the identification of combination drug therapy targets.},
}
@article {pmid28515435,
year = {2017},
author = {Amouroux, P and Crochard, D and Germain, JF and Correa, M and Ampuero, J and Groussier, G and Kreiter, P and Malausa, T and Zaviezo, T},
title = {Genetic diversity of armored scales (Hemiptera: Diaspididae) and soft scales (Hemiptera: Coccidae) in Chile.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {2014},
pmid = {28515435},
issn = {2045-2322},
mesh = {Animals ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial ; *Genetic Variation ; Haplotypes ; Hemiptera/classification/*genetics ; Phylogeny ; },
abstract = {Scale insects (Sternorrhyncha: Coccoidea) are one of the most invasive and agriculturally damaging insect groups. Their management and the development of new control methods are currently jeopardized by the scarcity of identification data, in particular in regions where no large survey coupling morphological and DNA analyses have been performed. In this study, we sampled 116 populations of armored scales (Hemiptera: Diaspididae) and 112 populations of soft scales (Hemiptera: Coccidae) in Chile, over a latitudinal gradient ranging from 18°S to 41°S, on fruit crops, ornamental plants and trees. We sequenced the COI and 28S genes in each population. In total, 19 Diaspididae species and 11 Coccidae species were identified morphologically. From the 63 COI haplotypes and the 54 28S haplotypes uncovered, and using several DNA data analysis methods (Automatic Barcode Gap Discovery, K2P distance, NJ trees), up to 36 genetic clusters were detected. Morphological and DNA data were congruent, except for three species (Aspidiotus nerii, Hemiberlesia rapax and Coccus hesperidum) in which DNA data revealed highly differentiated lineages. More than 50% of the haplotypes obtained had no high-scoring matches with any of the sequences in the GenBank database. This study provides 63 COI and 54 28S barcode sequences for the identification of Coccoidea from Chile.},
}
@article {pmid28514600,
year = {2017},
author = {Parveen, I and Singh, HK and Malik, S and Raghuvanshi, S and Babbar, SB},
title = {Evaluating five different loci (rbcL, rpoB, rpoC1, matK, and ITS) for DNA barcoding of Indian orchids.},
journal = {Genome},
volume = {60},
number = {8},
pages = {665-671},
doi = {10.1139/gen-2016-0215},
pmid = {28514600},
issn = {1480-3321},
mesh = {DNA Barcoding, Taxonomic/*methods ; Gene Amplification ; *Genes, Plant ; Genetic Variation ; Orchidaceae/*classification/*genetics ; Plants, Medicinal ; },
abstract = {Orchidaceae, one of the largest families of angiosperms, is represented in India by 1600 species distributed in diverse habitats. Orchids are in high demand owing to their beautiful flowers and therapeutic properties. Overexploitation and habitat destruction have made many orchid species endangered. In the absence of effective identification methods, illicit trade of orchids continues unabated. Considering DNA barcoding as a potential identification tool, species discrimination capability of five loci, ITS, matK, rbcL, rpoB, and rpoC1, was tested in 393 accessions of 94 Indian orchid species belonging to 47 genera, including one listed in Appendix I of CITES and 26 medicinal species. ITS provided the highest species discrimination rate of 94.9%. While, among the chloroplast loci, matK provided the highest species discrimination rate of 85.7%. None of the tested loci individually discriminated 100% of the species. Therefore, multi-locus combinations of up to five loci were tested for their species resolution capability. Among two-locus combinations, the maximum species resolution (86.7%) was provided by ITS+matK. ITS and matK sequences of the medicinal orchids were species specific, thus providing unique molecular identification tags for their identification and detection. These observations emphasize the need for the inclusion of ITS in the core barcode for plants, whenever required and available.},
}
@article {pmid28512377,
year = {2017},
author = {Olson, M and Harris, T and Higgins, R and Mullin, P and Powers, K and Olson, S and Powers, TO},
title = {Species Delimitation and Description of Mesocriconema nebraskense n. sp. (Nematoda: Criconematidae), a Morphologically Cryptic, Parthenogenetic Species from North American Grasslands.},
journal = {Journal of nematology},
volume = {49},
number = {1},
pages = {42-66},
pmid = {28512377},
issn = {0022-300X},
abstract = {Nematode surveys of North American grasslands conducted from 2010 to 2015 frequently recovered a species of criconematid nematode morphologically resembling Mesocriconema curvatum. These specimens were recovered from remnant native prairies in the central tallgrass ecoregion of North America, and not from surrounding agroecosystems. Historical records indicate that M. curvatum is a cosmopolitan species feeding on a wide range of agronomic and native plants. DNA barcoding indicates North American grasslands contain at least 10 phylogenetically distinct lineages of Mesocriconema that resemble, but are not, M. curvatum. Analysis of the two most common lineages reveals two distinctly different population structures. The variation in population structure suggests unique evolutionary histories associated with their diversification. These two major lineages share a sympatric distribution and their slight morphological differences contrast with a high level of genetic separation. Based on their genetic divergence, fixed diagnostic nucleotides, population structure, species delimitation metrics, and a sympatric distribution, we believe that one of these distinct lineages warrants formal nomenclatural recognition. Herein, we provide formal recognition for Mesocriconema nebraskense n. sp. and discuss its relationship to other Mesocriconema lineages discovered in native North American grasslands.},
}
@article {pmid28507815,
year = {2017},
author = {Sellers, GS and Griffin, LR and Hänfling, B and Gómez, A},
title = {A new molecular diagnostic tool for surveying and monitoring Triops cancriformis populations.},
journal = {PeerJ},
volume = {5},
number = {},
pages = {e3228},
pmid = {28507815},
issn = {2167-8359},
abstract = {The tadpole shrimp, Triops cancriformis, is a freshwater crustacean listed as endangered in the UK and Europe living in ephemeral pools. Populations are threatened by habitat destruction due to land development for agriculture and increased urbanisation. Despite this, there is a lack of efficient methods for discovering and monitoring populations. Established macroinvertebrate monitoring methods, such as net sampling, are unsuitable given the organism's life history, that include long lived diapausing eggs, benthic habits and ephemerally active populations. Conventional hatching methods, such as sediment incubation, are both time consuming and potentially confounded by bet-hedging hatching strategies of diapausing eggs. Here we develop a new molecular diagnostic method to detect viable egg banks of T. cancriformis, and compare its performance to two conventional monitoring methods involving diapausing egg hatching. We apply this method to a collection of pond sediments from the Wildfowl &amp; Wetlands Trust Caerlaverock National Nature Reserve, which holds one of the two remaining British populations of T. cancriformis. DNA barcoding of isolated eggs, using newly designed species-specific primers for a large region of mtDNA, was used to estimate egg viability. These estimates were compared to those obtained by the conventional methods of sediment and isolation hatching. Our method outperformed the conventional methods, revealing six ponds holding viable T. cancriformis diapausing egg banks in Caerlaverock. Additionally, designed species-specific primers for a short region of mtDNA identified degraded, inviable eggs and were used to ascertain the levels of recent mortality within an egg bank. Together with efficient sugar flotation techniques to extract eggs from sediment samples, our molecular method proved to be a faster and more powerful alternative for assessing the viability and condition of T. cancriformis diapausing egg banks.},
}
@article {pmid28503829,
year = {2017},
author = {González-Varo, JP and Carvalho, CS and Arroyo, JM and Jordano, P},
title = {Unravelling seed dispersal through fragmented landscapes: Frugivore species operate unevenly as mobile links.},
journal = {Molecular ecology},
volume = {26},
number = {16},
pages = {4309-4321},
doi = {10.1111/mec.14181},
pmid = {28503829},
issn = {1365-294X},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; *Ecosystem ; Forests ; Fruit ; Herbivory ; Microsatellite Repeats ; *Seed Dispersal ; Seeds ; Trees/*classification ; },
abstract = {Seed dispersal constitutes a pivotal process in an increasingly fragmented world, promoting population connectivity, colonization and range shifts in plants. Unveiling how multiple frugivore species disperse seeds through fragmented landscapes, operating as mobile links, has remained elusive owing to methodological constraints for monitoring seed dispersal events. We combine for the first time DNA barcoding and DNA microsatellites to identify, respectively, the frugivore species and the source trees of animal-dispersed seeds in forest and matrix of a fragmented landscape. We found a high functional complementarity among frugivores in terms of seed deposition at different habitats (forest vs. matrix), perches (isolated trees vs. electricity pylons) and matrix sectors (close vs. far from the forest edge), cross-habitat seed fluxes, dispersal distances and canopy-cover dependency. Seed rain at the landscape-scale, from forest to distant matrix sectors, was characterized by turnovers in the contribution of frugivores and source-tree habitats: open-habitat frugivores replaced forest-dependent frugivores, whereas matrix trees replaced forest trees. As a result of such turnovers, the magnitude of seed rain was evenly distributed between habitats and landscape sectors. We thus uncover key mechanisms behind "biodiversity-ecosystem function" relationships, in this case, the relationship between frugivore diversity and landscape-scale seed dispersal. Our results reveal the importance of open-habitat frugivores, isolated fruiting trees and anthropogenic perching sites (infrastructures) in generating seed dispersal events far from the remnant forest, highlighting their potential to drive regeneration dynamics through the matrix. This study helps to broaden the "mobile-link" concept in seed dispersal studies by providing a comprehensive and integrative view of the way in which multiple frugivore species disseminate seeds through real-world landscapes.},
}
@article {pmid28502206,
year = {2018},
author = {Akram, S and Arshan, KML and H Abdul, J},
title = {DNA barcoding and phylogenetic analysis of five ascidians (Phlebobranchia) distributed in Gulf of Mannar, India.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {4},
pages = {581-586},
doi = {10.1080/24701394.2017.1325479},
pmid = {28502206},
issn = {2470-1408},
mesh = {Animals ; Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; *Genes, Mitochondrial ; *Genome, Mitochondrial ; India ; *Phylogeny ; Urochordata/*classification/*genetics ; },
abstract = {DNA barcoding has played a significant role in biodiversity assessment as well as its conservation. This technique involves sequencing of mitochondrial marker gene including a short COI gene, known as barcode gene. It has proved its efficiency in identifying several species and resolving the limitations incurred during identification through conventional taxonomy. This study involves the use of DNA barcoding of ascidian species belonging to order Phlebobranchia. A total of 14 individuals, covering two families, three genera and five species, were barcoded. COI gene sequences of all the five species were deposited for the first time in NCBI as well as BOLD. The NJ tree revealed identical phylogenetic relationship among the individuals collected from three different stations. Mean Kimura 2-parameter (K2P) distances within-species, genus, family and order were 0.08%, 6.69%, 9.49% and 18.58%, respectively. This result concludes that COI gene sequencing is the efficient tool in identifying ascidians of the order Phlebobranchia. We report for the first time the COI gene sequences of four species of ascidians studied.},
}
@article {pmid28501957,
year = {2017},
author = {Pires, AA and Ramirez, JL and Galetti, PM and Troy, WP and Freitas, PD},
title = {Molecular analysis reveals hidden diversity in Zungaro (Siluriformes: Pimelodidade): a genus of giant South American catfish.},
journal = {Genetica},
volume = {145},
number = {3},
pages = {335-340},
pmid = {28501957},
issn = {1573-6857},
mesh = {Animals ; Catfishes/classification/*genetics ; Electron Transport Complex IV/chemistry/genetics ; Fish Proteins/chemistry/genetics ; *Phylogeny ; *Polymorphism, Genetic ; },
abstract = {The genus Zungaro contains some of the largest catfish in South America. Two valid species are currently recognized: Zungaro jahu, inhabiting the Paraná and Paraguay basins, and Zungaro zungaro, occurring in the Amazonas and Orinoco basins. Analysing Zungaro specimens from the Amazonas, Orinoco, Paraguay and Paraná basins, based on the sequencing of COI and D-loop, we found at least three MOTUs, indicating the existence of hidden diversity within this fish group. Considering the ecological and economic values of this fish, our results are surely welcomed for its conservation, disclosing new findings on its diversity and pointing out the necessity for a detailed taxonomic revision.},
}
@article {pmid28499337,
year = {2017},
author = {Kuo, CT and Peng, HS and Rong, Y and Yu, J and Sun, W and Fujimoto, B and Chiu, DT},
title = {Optically Encoded Semiconducting Polymer Dots with Single-Wavelength Excitation for Barcoding and Tracking of Single Cells.},
journal = {Analytical chemistry},
volume = {89},
number = {11},
pages = {6232-6238},
pmid = {28499337},
issn = {1520-6882},
support = {R01 MH113333/MH/NIMH NIH HHS/United States ; R21 CA186798/CA/NCI NIH HHS/United States ; },
mesh = {Boron Compounds/chemistry ; Color ; Fluorenes/chemistry ; Fluorescent Dyes/chemical synthesis/*chemistry ; Humans ; Hydrogen-Ion Concentration ; MCF-7 Cells ; Molecular Structure ; Optical Phenomena ; Particle Size ; Polymers/chemical synthesis/*chemistry ; Quantum Dots/*chemistry ; Semiconductors ; *Single-Cell Analysis ; Surface Properties ; Temperature ; Tumor Cells, Cultured ; },
abstract = {Multiplexed optical encoding is emerging as a powerful technique for high-throughput cellular analysis and molecular assays. Most of the developed optical barcodes, however, either suffer from large particle size or are incompatible with most commercial optical instruments. Here, a new type of nanoscale fluorescent barcode (Pdot barcodes) was prepared from semiconducting polymers. The Pdot barcodes possess the merits of small size (∼20 nm in diameter), narrow emission bands (full-width-at-half-maximum (fwhm) of 30-40 nm), three-color emissions (blue, green, and red) under single-wavelength excitation, a high brightness, good pH and thermal stability, and efficient cellular uptake. The Pdot barcodes were prepared using a three-color and six-intensity encoding strategy; for ratiometric readout of the barcodes, one of the colors might be used as an internal reference. We used the Pdot barcodes to label 20 sets of cancer cells and then distinguished and identified each set based on the Pdot barcodes using flow cytometry. We also monitored and tracked single cells labeled with different Pdot barcodes, even through rounds of cell division. These results suggest Pdot barcodes are strong candidates for discriminating different labeled cell and for long-term cell tracking.},
}
@article {pmid28499063,
year = {2018},
author = {Wang, P and Zhang, J and Sun, L and Ma, Y and Xu, J and Liang, S and Deng, J and Tan, J and Zhang, Q and Tu, L and Daniell, H and Jin, S and Zhang, X},
title = {High efficient multisites genome editing in allotetraploid cotton (Gossypium hirsutum) using CRISPR/Cas9 system.},
journal = {Plant biotechnology journal},
volume = {16},
number = {1},
pages = {137-150},
pmid = {28499063},
issn = {1467-7652},
mesh = {CRISPR-Cas Systems/*genetics ; Gene Editing/*methods ; Genome, Plant/*genetics ; Gossypium/*genetics ; Plants, Genetically Modified/*genetics ; Xylem/genetics ; },
abstract = {Gossypium hirsutum is an allotetraploid with a complex genome. Most genes have multiple copies that belong to At and Dt subgenomes. Sequence similarity is also very high between gene homologues. To efficiently achieve site/gene-specific mutation is quite needed. Due to its high efficiency and robustness, the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 system has exerted broad site-specific genome editing from prokaryotes to eukaryotes. In this study, we utilized a CRISPR/Cas9 system to generate two sgRNAs in a single vector to conduct multiple sites genome editing in allotetraploid cotton. An exogenously transformed gene Discosoma red fluorescent protein2(DsRed2) and an endogenous gene GhCLA1 were chosen as targets. The DsRed2-edited plants in T0 generation reverted its traits to wild type, with vanished red fluorescence the whole plants. Besides, the mutated phenotype and genotype were inherited to their T1 progenies. For the endogenous gene GhCLA1, 75% of regenerated plants exhibited albino phenotype with obvious nucleotides and DNA fragments deletion. The efficiency of gene editing at each target site is 66.7-100%. The mutation genotype was checked for both genes with Sanger sequencing. Barcode-based high-throughput sequencing, which could be highly efficient for genotyping to a population of mutants, was conducted in GhCLA1-edited T0 plants and it matched well with Sanger sequencing results. No off-target editing was detected at the potential off-target sites. These results prove that the CRISPR/Cas9 system is highly efficient and reliable for allotetraploid cotton genome editing.},
}
@article {pmid28493919,
year = {2017},
author = {Diez Benavente, E and Ward, Z and Chan, W and Mohareb, FR and Sutherland, CJ and Roper, C and Campino, S and Clark, TG},
title = {Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure.},
journal = {PloS one},
volume = {12},
number = {5},
pages = {e0177134},
pmid = {28493919},
issn = {1932-6203},
support = {MC_PC_15103/MRC_/Medical Research Council/United Kingdom ; MR/K000551/1/MRC_/Medical Research Council/United Kingdom ; MR/M01360X/1/MRC_/Medical Research Council/United Kingdom ; MR/N010469/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Antigens, Protozoan/genetics ; DNA, Protozoan/genetics ; Genetics, Population ; Genomics ; Humans ; Linkage Disequilibrium/genetics ; Malaria, Vivax/genetics/parasitology ; Plasmodium falciparum/genetics ; Plasmodium vivax/*genetics ; Polymorphism, Single Nucleotide/genetics ; Protozoan Proteins/genetics ; Selection, Genetic/*genetics ; },
abstract = {BACKGROUND: Although Plasmodium vivax contributes to almost half of all malaria cases outside Africa, it has been relatively neglected compared to the more deadly P. falciparum. It is known that P. vivax populations possess high genetic diversity, differing geographically potentially due to different vector species, host genetics and environmental factors.<br><br>RESULTS: We analysed the high-quality genomic data for 46 P. vivax isolates spanning 10 countries across 4 continents. Using population genetic methods we identified hotspots of selection pressure, including the previously reported MRP1 and DHPS genes, both putative drug resistance loci. Extra copies and deletions in the promoter region of another drug resistance candidate, MDR1 gene, and duplications in the Duffy binding protein gene (PvDBP) potentially involved in erythrocyte invasion, were also identified. For surveillance applications, continental-informative markers were found in putative drug resistance loci, and we show that organellar polymorphisms could classify P. vivax populations across continents and differentiate between Plasmodia spp.<br><br>CONCLUSIONS: This study has shown that genomic diversity that lies within and between P. vivax populations can be used to elucidate potential drug resistance and invasion mechanisms, as well as facilitate the molecular barcoding of the parasite for surveillance applications.},
}
@article {pmid28487542,
year = {2017},
author = {Elder, A and Bomken, S and Wilson, I and Blair, HJ and Cockell, S and Ponthan, F and Dormon, K and Pal, D and Heidenreich, O and Vormoor, J},
title = {Abundant and equipotent founder cells establish and maintain acute lymphoblastic leukaemia.},
journal = {Leukemia},
volume = {31},
number = {12},
pages = {2577-2586},
pmid = {28487542},
issn = {1476-5551},
support = {NC/P002412/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; A12788/CRUK_/Cancer Research UK/United Kingdom ; 23389/CRUK_/Cancer Research UK/United Kingdom ; 12788/CRUK_/Cancer Research UK/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; G0802259/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; *Biomarkers, Tumor ; *Cell Transformation, Neoplastic/genetics/metabolism ; Clonal Evolution/genetics ; Computational Biology/methods ; Disease Models, Animal ; Gene Expression Profiling ; Heterografts ; High-Throughput Nucleotide Sequencing ; Humans ; Mice ; Models, Biological ; Neoplastic Stem Cells/*metabolism/pathology ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/*etiology/pathology ; },
abstract = {High frequencies of blasts in primary acute lymphoblastic leukaemia (ALL) samples have the potential to induce leukaemia and to engraft mice. However, it is unclear how individual ALL cells each contribute to drive leukaemic development in a bulk transplant and the extent to which these blasts vary functionally. We used cellular barcoding as a fate mapping tool to track primograft ALL blasts in vivo. Our results show that high numbers of ALL founder cells contribute at similar frequencies to leukaemic propagation over serial transplants, without any clear evidence of clonal succession. These founder cells also exhibit equal capacity to home and engraft to different organs, although stochastic processes may alter the composition in restrictive niches. Our findings enhance the stochastic stem cell model of ALL by demonstrating equal functional abilities of singular ALL blasts and show that successful treatment strategies must eradicate the entire leukaemic cell population.},
}
@article {pmid28487426,
year = {2017},
author = {Martin, CJ and Cadena, AM and Leung, VW and Lin, PL and Maiello, P and Hicks, N and Chase, MR and Flynn, JL and Fortune, SM},
title = {Digitally Barcoding Mycobacterium tuberculosis Reveals In Vivo Infection Dynamics in the Macaque Model of Tuberculosis.},
journal = {mBio},
volume = {8},
number = {3},
pages = {},
pmid = {28487426},
issn = {2150-7511},
support = {R01 AI114674/AI/NIAID NIH HHS/United States ; T32 AI049928/AI/NIAID NIH HHS/United States ; T32 AI089443/AI/NIAID NIH HHS/United States ; P30 AI060354/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Computational Biology ; Granuloma/*microbiology ; Humans ; Latent Tuberculosis/microbiology ; Lung/microbiology ; Macaca fascicularis ; Models, Animal ; Mycobacterium tuberculosis/*genetics/*physiology ; Positron Emission Tomography Computed Tomography ; Tuberculosis/*microbiology ; },
abstract = {Infection with Mycobacterium tuberculosis causes a spectrum of outcomes; the majority of individuals contain but do not eliminate the infection, while a small subset present with primary active tuberculosis (TB) disease. This variability in infection outcomes is recapitulated at the granuloma level within each host, such that some sites of infection can be fully cleared while others progress. Understanding the spectrum of TB outcomes requires new tools to deconstruct the mechanisms underlying differences in granuloma fate. Here, we use novel genome-encoded barcodes to uniquely tag individual M. tuberculosis bacilli, enabling us to quantitatively track the trajectory of each infecting bacterium in a macaque model of TB. We also introduce a robust bioinformatics pipeline capable of identifying and counting barcode sequences within complex mixtures and at various read depths. By coupling this tagging strategy with serial positron emission tomography coregistered with computed tomography (PET/CT) imaging of lung pathology in macaques, we define a lesional map of M. tuberculosis infection dynamics. We find that there is no significant infection bottleneck, but there are significant constraints on productive bacterial trafficking out of primary granulomas. Our findings validate our barcoding approach and demonstrate its utility in probing lesion-specific biology and dissemination. This novel technology has the potential to greatly enhance our understanding of local dynamics in tuberculosis.IMPORTANCE Classically, M. tuberculosis infection was thought to result in either latent infection or active disease. More recently, the field has recognized that there is a spectrum of M. tuberculosis infection clinical outcomes. Within a single host, this spectrum is recapitulated at the granuloma level, where there can simultaneously be lesional sterilization and poorly contained disease. To better understand the lesional biology of TB infection, we digitally barcoded M. tuberculosis to quantitatively track the fate of each infecting bacterium. By combining this technology with serial PET-CT imaging, we can dynamically track both bacterial populations and granuloma trajectories. We demonstrate that there is little constraint on the bacterial population at the time of infection. However, the granuloma imposes a strong bottleneck on dissemination, and the subset of granulomas at risk of dissemination can be distinguished by physical features.},
}
@article {pmid28484137,
year = {2017},
author = {Ushiyama, A and Akaboshi, C and Ohsawa, N and Shimizu, T and Matsushima, Y and Shimizu, H and Hashiguchi, S},
title = {[Identification of Datura Species Involved in a Food-Poisoning Case Using LC-MS/MS and DNA Barcording].},
journal = {Shokuhin eiseigaku zasshi. Journal of the Food Hygienic Society of Japan},
volume = {58},
number = {2},
pages = {86-95},
doi = {10.3358/shokueishi.58.86},
pmid = {28484137},
issn = {1882-1006},
mesh = {Atropine/analysis/isolation &amp; purification ; Chromatography, Liquid/*methods ; DNA Barcoding, Taxonomic/*methods ; Datura/chemistry/classification/*genetics/*poisoning ; Foodborne Diseases/*etiology ; Humans ; Scopolamine/analysis/isolation &amp; purification ; Solanaceae ; Tandem Mass Spectrometry/*methods ; },
abstract = {A food-poisoning case due to eating the roots of Datura occurred in Kawasaki City, Japan in 2014. The Datura plant was mistakenly collected instead of burdock in a domestic garden. The roots of these plants are quite similar to each other. We presumed that the specimen was the root of Datura, but it was difficult to classify it only from the morphology. Using LC-MS/MS, we detected atropine and scopolamine from the remaining plant specimen. Therefore, we applied the DNA barcoding method. The results showed that the specimen was classified into Solanaceae family, but not Asteraceae family. Thus, the specimen was confirmed to be Datura species based on both chemical and genetic analyses.},
}
@article {pmid28484128,
year = {2017},
author = {Onuma, M and Kakogawa, M and Yanagisawa, M and Haga, A and Okano, T and Neagari, Y and Okano, T and Goka, K and Asakawa, M},
title = {Characterizing the temporal patterns of avian influenza virus introduction into Japan by migratory birds.},
journal = {The Journal of veterinary medical science},
volume = {79},
number = {5},
pages = {943-951},
pmid = {28484128},
issn = {1347-7439},
mesh = {*Animal Migration ; Animals ; Animals, Wild/virology ; Birds/virology ; Ducks/virology ; Feces/virology ; Genes, Viral/genetics ; Influenza A virus/genetics ; Influenza in Birds/*epidemiology ; Japan/epidemiology ; Seasons ; },
abstract = {The objectives of the present study were to observe the temporal pattern of avian influenza virus (AIV) introduction into Japan and to determine which migratory birds play an important role in introducing AIV. In total, 19,407 fecal samples from migratory birds were collected at 52 sites between October 2008 and May 2015. Total nucleic acids extracted from the fecal samples were subjected to reverse transcription loop-mediated isothermal amplification to detect viral RNA. Species identification of host migratory birds was conducted by DNA barcoding for positive fecal samples. The total number of positive samples was 352 (prevalence, 1.8%). The highest prevalence was observed in autumn migration, and a decrease in prevalence was observed. During autumn migration, central to southern Japan showed a prevalence higher than the overall prevalence. Thus, the main AIV entry routes may involve crossing the Sea of Japan and entry through the Korean Peninsula. Species identification was successful in 221 of the 352 positive samples. Two major species sequences were identified: the Mallard/Eastern Spot-billed duck group (115 samples; 52.0%) and the Northern pintail (61 samples; 27.6%). To gain a better understanding of the ecology of AIV in Japan and the introduction pattern of highly pathogenic avian influenza viruses, information regarding AIV prevalence by species, the prevalence of hatch-year migratory birds, migration patterns and viral subtypes in fecal samples using egg inoculation and molecular-based methods in combination is required.},
}
@article {pmid28483762,
year = {2017},
author = {Zink, F and Stacey, SN and Norddahl, GL and Frigge, ML and Magnusson, OT and Jonsdottir, I and Thorgeirsson, TE and Sigurdsson, A and Gudjonsson, SA and Gudmundsson, J and Jonasson, JG and Tryggvadottir, L and Jonsson, T and Helgason, A and Gylfason, A and Sulem, P and Rafnar, T and Thorsteinsdottir, U and Gudbjartsson, DF and Masson, G and Kong, A and Stefansson, K},
title = {Clonal hematopoiesis, with and without candidate driver mutations, is common in the elderly.},
journal = {Blood},
volume = {130},
number = {6},
pages = {742-752},
pmid = {28483762},
issn = {1528-0020},
support = {R01 DA017932/DA/NIDA NIH HHS/United States ; R01 DA034076/DA/NIDA NIH HHS/United States ; },
mesh = {Adult ; Age Factors ; Aged ; Aged, 80 and over ; Clone Cells ; DNA (Cytosine-5-)-Methyltransferases/*genetics ; DNA Methyltransferase 3A ; DNA-Binding Proteins/*genetics ; Dioxygenases ; Female ; Hematologic Neoplasms/epidemiology/genetics ; *Hematopoiesis ; Hematopoietic Stem Cells/*cytology/metabolism ; Humans ; Male ; Middle Aged ; *Mutation ; Protein Phosphatase 2C/*genetics ; Proto-Oncogene Proteins/*genetics ; Repressor Proteins/*genetics ; Risk Factors ; },
abstract = {Clonal hematopoiesis (CH) arises when a substantial proportion of mature blood cells is derived from a single dominant hematopoietic stem cell lineage. Somatic mutations in candidate driver (CD) genes are thought to be responsible for at least some cases of CH. Using whole-genome sequencing of 11 262 Icelanders, we found 1403 cases of CH by using barcodes of mosaic somatic mutations in peripheral blood, whether or not they have a mutation in a CD gene. We find that CH is very common in the elderly, trending toward inevitability. We show that somatic mutations in TET2, DNMT3A, ASXL1, and PPM1D are associated with CH at high significance. However, known CD mutations were evident in only a fraction of CH cases. Nevertheless, the highly prevalent CH we detect associates with increased mortality rates, risk for hematological malignancy, smoking behavior, telomere length, Y-chromosome loss, and other phenotypic characteristics. Modeling suggests some CH cases could arise in the absence of CD mutations as a result of neutral drift acting on a small population of active hematopoietic stem cells. Finally, we find a germline deletion in intron 3 of the telomerase reverse transcriptase (TERT) gene that predisposes to CH (rs34002450; P = 7.4 × 10[-12]; odds ratio, 1.37).},
}
@article {pmid28481646,
year = {2018},
author = {Kartavtsev, YP},
title = {Barcode index number, taxonomic rank and modes of speciation: examples from fish.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {4},
pages = {535-542},
doi = {10.1080/24701394.2017.1315570},
pmid = {28481646},
issn = {2470-1408},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Fishes/classification/*genetics ; *Genetic Speciation ; },
abstract = {Species delimitation by DNA sequence data or DNA barcoding is successful, as confirmed by the vast BOLD data base. However, the theory that would explain this fact has not been developed yet. An approach based on Barcoding Index Number (BIN), suggested in the assignment, allows delimiting of taxa of three ranks (species, genera, and families) and statistical validation with a high precision of delimiting (over 80%), as well as shows for majority of Co-1-based single gene trees good correspondence between their topology and conventional taxa content for analyzed fish species (R[2] ≈ 0.84-0.98). Knowledge of deviations from these data can help to find out new taxa and improve biodiversity description. It is concluded that delimiting is successful for bulk of cases because the geographic mode of speciation prevails in nature. It takes a long time for new taxa to form in isolation, which allows accumulation of random mutations and many different nucleotide substitutions between them that can be detected by molecular markers and give unique DNA barcodes. The use of BIN approach, described here, can aid greatly in making this important question clearer especially under wider examination of other organisms.},
}
@article {pmid28481470,
year = {2017},
author = {Chen, B and Kong, W and Liu, Y and Lu, Y and Li, M and Qiao, X and Fan, X and Wang, F},
title = {Crystalline Hollow Microrods for Site-Selective Enhancement of Nonlinear Photoluminescence.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {56},
number = {35},
pages = {10383-10387},
doi = {10.1002/anie.201703600},
pmid = {28481470},
issn = {1521-3773},
abstract = {A class of one-dimensional hollow microstructure is described, which was formed by a kinetically controlled crystal growth process. A hexagonal-phase NaYbF4 microrod comprising isolated holes along the longitudinal axis was synthesized by a one-pot hydrothermal method with the assistance of citrate ligands. The structural void feature modulates light intensity across the microrods as a result of interference arising from light scattering and reflection by the inner walls. A single crystal comprising a structural void was doped with upconverting lanthanide ions. Upon near-infrared excitation of the doped crystal spatially resolvable optical codes were produced.},
}
@article {pmid28480366,
year = {2016},
author = {Zhang, D and Jiang, B and Duan, L and Zhou, N},
title = {INTERNAL TRANSCRIBED SPACER (ITS), AN IDEAL DNA BARCODE FOR SPECIES DISCRIMINATION IN CRAWFURDIA WALL. (GENTIANACEAE).},
journal = {African journal of traditional, complementary, and alternative medicines : AJTCAM},
volume = {13},
number = {6},
pages = {101-106},
pmid = {28480366},
issn = {2505-0044},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/*genetics ; Gentianaceae/*genetics ; Species Specificity ; },
abstract = {BACKGROUND: DNA barcoding is a technique used to identify species based on species-specific differences in short regions of their DNA. It is widely used in species discrimination of medicinal plants and traditional medicines.<br><br>MATERIALS AND METHODS: In the present study, four potential DNA barcodes, namely rbcL, matK, trnH-psbA and ITS (nuclear ribosomal internal transcribed spacer) were adopted for species discrimination in Crawfurdia Wall (Genetiaceae). Identification ability of these DNA barcodes and combinations were evaluated using three classic methods (Distance, Blast and Tree-Building).<br><br>RESULTS: As a result, ITS, trnH-psbA and rbcL regions showed great universality for a success rate of 100%; whereas matK was disappointing for which only 65% samples gained useful DNA sequences. ITS region, which could clearly and effectively identify the five species in Crawfurdia, performed very well in this study. On the contrary, trnH-psbA and rbcL performed poorly in discrimination among these species.<br><br>CONCLUSION: ITS marker was an ideal DNA barcode in Crawfurdia and it should be incorporated into one of the core barcodes for seed plants.},
}
@article {pmid28480363,
year = {2016},
author = {Zhang, D and Mo, X and Xiang, J and Zhou, N},
title = {MOLECULAR IDENTIFICATION OF ORIGINAL PLANTS OF FRITILLARIAE CIRRHOSAE BULBUS, A TRADTIONAL CHINESE MEDICINE (TCM) USING PLANT DNA BARCODING.},
journal = {African journal of traditional, complementary, and alternative medicines : AJTCAM},
volume = {13},
number = {6},
pages = {74-82},
pmid = {28480363},
issn = {2505-0044},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*analysis ; DNA, Ribosomal Spacer/genetics ; Drugs, Chinese Herbal/*analysis ; Fritillaria/*genetics ; Plastids/genetics ; },
abstract = {BACKGROUND: DNA barcoding is a widely used tool that enables rapid and accurate identification of species based on standardized DNA regions.<br><br>MATERIALS AND METHODS: In this study, potential DNA barcodes, namely three plastid regions (rbcL, trnH-psbA and matK) and one nuclear ribosomal internal transcribed spacer (ITS) were adopted for species identification of original plants of Fritillariae Cirrhosae Bulbus.<br><br>RESULTS: The rbcL and trnH-psbA regions showed better success rate of PCR amplification and DNA sequencing, as well as superior discriminatory ability. On the contrary, ITS region did not possess effective genetic variation and matK was faced with low success rate of sequencing. Combination of multi-loci sequences could improve identification ability of DNA barcoding. The trnH-psbA + rbcL could discriminate 25% - 100% species based on the Blast, Tree-Building and Distance methods.<br><br>CONCLUSION: The potential DNA barcodes could not completely solving species identification of botanic origins of Fritillariae Cirrhosae Bulbus. In future, we should pay more attention to super-barcoding or specific barcode that enhance ability to discriminate the closely related plants.},
}
@article {pmid28478763,
year = {2017},
author = {Fang, Y and Shi, WQ and Zhang, Y},
title = {Molecular phylogeny of Anopheles hyrcanus group (Diptera: Culicidae) based on mtDNA COI.},
journal = {Infectious diseases of poverty},
volume = {6},
number = {1},
pages = {61},
pmid = {28478763},
issn = {2049-9957},
mesh = {Animals ; Anopheles/*classification/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Insect Proteins/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The Anopheles hyrcanus group, which includes at least 25 species, is widely distributed in the Oriental and Palearctic regions. Some group members have been incriminated as vectors of malaria and other mosquito-borne diseases. It is difficult to identify Hyrcanus Group members by morphological features. Thus, molecular phylogeny has been proposed as an important complementary method to traditional morphological taxonomy.<br><br>METHODS: Based on the GenBank database and our original study data, we used 466 mitochondrial DNA COI sequences belonging to 18 species to reconstruct the molecular phylogeny of the Hyrcanus Group across its worldwide geographic range.<br><br>RESULTS: The results are as follows. 1) The average conspecific K2P divergence was 0.008 (range 0.002-0.017), whereas sequence divergence between congroup species averaged 0.064 (range 0.026-0.108). 2) The topology of COI tree of the Hyrcanus Group was generally consistent with classical morphological taxonomy in terms of species classification, but disagreed in subgroup division. In the COI tree, the group was divided into at least three main clusters. The first cluster contained An. nimpe; the second was composed of the Nigerrimus Subgroup and An. argyropus; and the third cluster was comprised of the Lesteri Subgroup and other unassociated species. 3) Phylogenetic analysis of COI indicated that ancient hybridizations probably occurred among the three closely related species, An. sinensis, An. belenrae, and An. kleini. 4) The results supported An. paraliae as a probable synonym of An. lesteri, and it was possible that An. pseudopictus and An. hyrcanus were the same species, as evident from their extremely low interspecific genetic divergence (0.020 and 0.007, respectively) and their phylogenetic positions.<br><br>CONCLUSIONS: In summary, we reconstructed the molecular phylogeny and analysed genetic divergence of the Hyrcanus Group using mitochondrial COI sequences. Our results suggest that in the future of malaria surveillance, we should not only pay much attention to those known vectors of malaria, but also their closely related species.},
}
@article {pmid28475900,
year = {2017},
author = {Lavin, Y and Kobayashi, S and Leader, A and Amir, ED and Elefant, N and Bigenwald, C and Remark, R and Sweeney, R and Becker, CD and Levine, JH and Meinhof, K and Chow, A and Kim-Shulze, S and Wolf, A and Medaglia, C and Li, H and Rytlewski, JA and Emerson, RO and Solovyov, A and Greenbaum, BD and Sanders, C and Vignali, M and Beasley, MB and Flores, R and Gnjatic, S and Pe'er, D and Rahman, A and Amit, I and Merad, M},
title = {Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses.},
journal = {Cell},
volume = {169},
number = {4},
pages = {750-765.e17},
pmid = {28475900},
issn = {1097-4172},
support = {R01 CA164729/CA/NCI NIH HHS/United States ; U19 AI128949/AI/NIAID NIH HHS/United States ; R01 CA154947/CA/NCI NIH HHS/United States ; R01 CA190400/CA/NCI NIH HHS/United States ; DP1 HD084071/HD/NICHD NIH HHS/United States ; U19 AI117873/AI/NIAID NIH HHS/United States ; T32 GM008798/GM/NIGMS NIH HHS/United States ; R01 CA173861/CA/NCI NIH HHS/United States ; U24 AI118644/AI/NIAID NIH HHS/United States ; },
mesh = {Adenocarcinoma/*immunology/*pathology ; Adenocarcinoma of Lung ; Dendritic Cells/pathology ; Humans ; *Immunity, Innate ; Killer Cells, Natural/pathology ; Lung Neoplasms/*immunology/*pathology ; Macrophages/pathology ; Single-Cell Analysis/*methods ; T-Lymphocytes/pathology ; Tumor Microenvironment ; },
abstract = {To guide the design of immunotherapy strategies for patients with early stage lung tumors, we developed a multiscale immune profiling strategy to map the immune landscape of early lung adenocarcinoma lesions to search for tumor-driven immune changes. Utilizing a barcoding method that allows a simultaneous single-cell analysis of the tumor, non-involved lung, and blood cells, we provide a detailed immune cell atlas of early lung tumors. We show that stage I lung adenocarcinoma lesions already harbor significantly altered T cell and NK cell compartments. Moreover, we identified changes in tumor-infiltrating myeloid cell (TIM) subsets that likely compromise anti-tumor T cell immunity. Paired single-cell analyses thus offer valuable knowledge of tumor-driven immune changes, providing a powerful tool for the rational design of immune therapies. VIDEO ABSTRACT.},
}
@article {pmid28472365,
year = {2017},
author = {Maclean, CJ and Metzger, BPH and Yang, JR and Ho, WC and Moyers, B and Zhang, J},
title = {Deciphering the Genic Basis of Yeast Fitness Variation by Simultaneous Forward and Reverse Genetics.},
journal = {Molecular biology and evolution},
volume = {34},
number = {10},
pages = {2486-2502},
doi = {10.1093/molbev/msx151},
pmid = {28472365},
issn = {1537-1719},
support = {R01 GM103232/GM/NIGMS NIH HHS/United States ; },
mesh = {Cell Proliferation/genetics ; Chromosome Mapping/methods ; Genetic Fitness/*genetics ; Genetic Variation/genetics ; Genome, Fungal/genetics ; Genome-Wide Association Study/methods ; Genomics ; Phenotype ; Reverse Genetics/*methods ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/genetics ; },
abstract = {The budding yeast Saccharomyces cerevisiae is the best studied eukaryote in molecular and cell biology, but its utility for understanding the genetic basis of phenotypic variation in natural populations is limited by inefficient association mapping due to strong and complex population structure. To overcome this challenge, we generated genome sequences for 85 strains and performed a comprehensive population genomic survey of a total of 190 diverse strains. We identified considerable variation in population structure among chromosomes and identified 181 genes that are absent from the reference genome. Many of these nonreference genes are expressed and we functionally confirmed that two of these genes confer increased resistance to antifungals. Next, we simultaneously measured the growth rates of over 4,500 laboratory strains, each of which lacks a nonessential gene, and 81 natural strains across multiple environments using unique DNA barcode present in each strain. By combining the genome-wide reverse genetic information gained from the gene deletion strains with a genome-wide association analysis from the natural strains, we identified genomic regions associated with fitness variation in natural populations. To experimentally validate a subset of these associations, we used reciprocal hemizygosity tests, finding that while the combined forward and reverse genetic approaches can identify a single causal gene, the phenotypic consequences of natural genetic variation often follow a complicated pattern. The resources and approach provided outline an efficient and reliable route to association mapping in yeast and significantly enhance its value as a model for understanding the genetic mechanisms underlying phenotypic variation and evolution in natural populations.},
}
@article {pmid28472156,
year = {2017},
author = {Fennessey, CM and Pinkevych, M and Immonen, TT and Reynaldi, A and Venturi, V and Nadella, P and Reid, C and Newman, L and Lipkey, L and Oswald, K and Bosche, WJ and Trivett, MT and Ohlen, C and Ott, DE and Estes, JD and Del Prete, GQ and Lifson, JD and Davenport, MP and Keele, BF},
title = {Genetically-barcoded SIV facilitates enumeration of rebound variants and estimation of reactivation rates in nonhuman primates following interruption of suppressive antiretroviral therapy.},
journal = {PLoS pathogens},
volume = {13},
number = {5},
pages = {e1006359},
pmid = {28472156},
issn = {1553-7374},
mesh = {Animals ; Anti-Retroviral Agents/therapeutic use ; CD4-Positive T-Lymphocytes/virology ; Genetic Markers/genetics ; *Genetic Variation ; Genome, Viral/*genetics ; Macaca mulatta ; Male ; *Models, Theoretical ; Sequence Analysis, DNA ; Simian Acquired Immunodeficiency Syndrome/drug therapy/*virology ; Simian Immunodeficiency Virus/drug effects/genetics/*physiology ; Viral Load ; Viremia ; *Virus Replication ; },
abstract = {HIV and SIV infection dynamics are commonly investigated by measuring plasma viral loads. However, this total viral load value represents the sum of many individual infection events, which are difficult to independently track using conventional sequencing approaches. To overcome this challenge, we generated a genetically tagged virus stock (SIVmac239M) with a 34-base genetic barcode inserted between the vpx and vpr accessory genes of the infectious molecular clone SIVmac239. Next-generation sequencing of the virus stock identified at least 9,336 individual barcodes, or clonotypes, with an average genetic distance of 7 bases between any two barcodes. In vitro infection of rhesus CD4+ T cells and in vivo infection of rhesus macaques revealed levels of viral replication of SIVmac239M comparable to parental SIVmac239. After intravenous inoculation of 2.2x105 infectious units of SIVmac239M, an average of 1,247 barcodes were identified during acute infection in 26 infected rhesus macaques. Of the barcodes identified in the stock, at least 85.6% actively replicated in at least one animal, and on average each barcode was found in 5 monkeys. Four infected animals were treated with combination antiretroviral therapy (cART) for 82 days starting on day 6 post-infection (study 1). Plasma viremia was reduced from >106 to <15 vRNA copies/mL by the time treatment was interrupted. Virus rapidly rebounded following treatment interruption and between 87 and 136 distinct clonotypes were detected in plasma at peak rebound viremia. This study confirmed that SIVmac239M viremia could be successfully curtailed with cART, and that upon cART discontinuation, rebounding viral variants could be identified and quantified. An additional 6 animals infected with SIVmac239M were treated with cART beginning on day 4 post-infection for 305, 374, or 482 days (study 2). Upon treatment interruption, between 4 and 8 distinct viral clonotypes were detected in each animal at peak rebound viremia. The relative proportions of the rebounding viral clonotypes, spanning a range of 5 logs, were largely preserved over time for each animal. The viral growth rate during recrudescence and the relative abundance of each rebounding clonotype were used to estimate the average frequency of reactivation per animal. Using these parameters, reactivation frequencies were calculated and ranged from 0.33-0.70 events per day, likely representing reactivation from long-lived latently infected cells. The use of SIVmac239M therefore provides a powerful tool to investigate SIV latency and the frequency of viral reactivation after treatment interruption.},
}
@article {pmid28470316,
year = {2017},
author = {Xie, P and Cao, X and Lin, Z and Javanmard, M},
title = {Top-down fabrication meets bottom-up synthesis for nanoelectronic barcoding of microparticles.},
journal = {Lab on a chip},
volume = {17},
number = {11},
pages = {1939-1947},
doi = {10.1039/c7lc00035a},
pmid = {28470316},
issn = {1473-0189},
mesh = {Biomarkers ; Electric Impedance ; Electronic Data Processing/*methods ; Microspheres ; Nanotechnology/*methods ; Oxides ; },
abstract = {Traditional optical and plasmonic techniques for barcoding of micro-particles for multiplexed bioassays are generally high in throughput, however bulky instrumentation is often required for performing readout. Electrical impedance based detection allows for ultra-compact instrumentation footprint necessary for wearable devices, however to date, the lack of ability to electronically barcode micro-particles has been a long standing bottleneck towards enabling multiplexed electronic biomarker assays. Nanoelectronic barcoding, which to the best of our knowledge is the first impedance based solution for micro-particle barcoding, works by forming tunable nano-capacitors on the surface of micro-spheres, effectively modulating the frequency dependent dielectric properties of the spheres allowing one bead barcode to be distinguished from another. Nanoelectronic barcoding uses a well-known, but unexplored electromagnetic phenomenon of micro-particles: the Clausius-Mossotti (CM) factor spectrum of a Janus particle (JP) shifts depending on the zeta (wall) potential of the metallic half of the microsphere, and the fact that the complex impedance spectrum of a particle directly corresponds to the CM factor spectrum. A one-to-one correspondence will be established between each biomarker and the corresponding engineered microsphere. This transformative new method for barcoding will enable a new class of handheld and wearable biosensors capable of multiplexed continuous temporal bio-monitoring. The proposed nano-electronically barcoded particles utilize both bottom-up synthesis and top-down fabrication to enable precisely engineered frequency dependent dielectric signatures. Multi-frequency lock-in measurements of the complex impedance, in conjunction with multi-variate analysis of impedance data, allows for particle differentiation using a fully functional ultra-compact electronic detector.},
}
@article {pmid28468764,
year = {2017},
author = {Parker, S and Fraczek, MG and Wu, J and Shamsah, S and Manousaki, A and Dungrattanalert, K and de Almeida, RA and Estrada-Rivadeneyra, D and Omara, W and Delneri, D and O'Keefe, RT},
title = {A resource for functional profiling of noncoding RNA in the yeast Saccharomyces cerevisiae.},
journal = {RNA (New York, N.Y.)},
volume = {23},
number = {8},
pages = {1166-1171},
pmid = {28468764},
issn = {1469-9001},
support = {//Wellcome Trust/United Kingdom ; BB/M017702/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 094225//Wellcome Trust/United Kingdom ; 104981//Wellcome Trust/United Kingdom ; },
mesh = {*Genome, Fungal ; RNA, Fungal/genetics/*metabolism ; RNA, Untranslated/genetics/*metabolism ; Saccharomyces cerevisiae/*genetics/growth &amp; development/metabolism ; Sequence Deletion ; },
abstract = {Eukaryotic genomes are extensively transcribed, generating many different RNAs with no known function. We have constructed 1502 molecular barcoded ncRNA gene deletion strains encompassing 443 ncRNAs in the yeast Saccharomyces cerevisiae as tools for ncRNA functional analysis. This resource includes deletions of small nuclear RNAs (snRNAs), transfer RNAs (tRNAs), small nucleolar RNAs (snoRNAs), and other annotated ncRNAs as well as the more recently identified stable unannotated transcripts (SUTs) and cryptic unstable transcripts (CUTs) whose functions are largely unknown. Specifically, deletions have been constructed for ncRNAs found in the intergenic regions, not overlapping genes or their promoters (i.e., at least 200 bp minimum distance from the closest gene start codon). The deletion strains carry molecular barcodes designed to be complementary with the protein gene deletion collection enabling parallel analysis experiments. These strains will be useful for the numerous genomic and molecular techniques that utilize deletion strains, including genome-wide phenotypic screens under different growth conditions, pooled chemogenomic screens with drugs or chemicals, synthetic genetic array analysis to uncover novel genetic interactions, and synthetic dosage lethality screens to analyze gene dosage. Overall, we created a valuable resource for the RNA community and for future ncRNA research.},
}
@article {pmid28467234,
year = {2018},
author = {Barik, TK and Swain, SN and Sahu, B and Tripathy, B and Acharya, UR},
title = {Morphological and genetic analyses of the first record of longrakered trevally, Ulua mentalis (Perciformes: Carangidae) and of the pinjalo snapper, Pinjalo pinjalo (Perciformes: Lutjanidae) in the Odisha coast, Bay of Bengal.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {4},
pages = {552-560},
doi = {10.1080/24701394.2017.1320993},
pmid = {28467234},
issn = {2470-1408},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Fish Proteins/genetics ; Genome, Mitochondrial ; India ; Perciformes/*classification/*genetics ; *Phylogeny ; },
abstract = {Identification of fish species have so far been carried out mostly by classical morpho-taxonomy. In the present study, however, an attempt has been taken to identify two species of fishes Ulua mentalis and Pinjalo pinjalo of order Perciformes which happens to be the first record in Odisha coast Bay of Bengal, India during the year 2015, using DNA barcoding technique for reconfirmation over conventional morpho-taxonomy. During recent past, study of molecular-taxonomical profile of mitochondrial DNA in general and Cytochrome Oxidase subunit I (COI) gene in particular has gained enormous importance for accurate identification of species. In the present study, the partial COI sequence of Ulua mentalis and Pinjalo pinjalo were generated. Analysis using the COI gene produced phylogenetic trees in concurrence with other multi gene studies and we came across the identical phylogenetic relationship considering Neighbor-Joining and Maximum Likelihood tree. Moreover, these molecular data set further testified in Bayesian framework to reevaluate the exact taxonomic groupings within the family. Surprisingly, Ulua mentalis and Pinjalo pinjalo seems to be closely related to their sister taxa.},
}
@article {pmid28462938,
year = {2017},
author = {Ahn, J and Hwang, B and Young Kim, H and Jang, H and Kim, HP and Han, SW and Kim, TY and Hyun Lee, J and Bang, D},
title = {Asymmetrical barcode adapter-assisted recovery of duplicate reads and error correction strategy to detect rare mutations in circulating tumor DNA.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {46678},
pmid = {28462938},
issn = {2045-2322},
mesh = {Circulating Tumor DNA/chemistry/*genetics ; DNA Mutational Analysis/methods ; DNA, Neoplasm/chemistry/*genetics ; Genotype ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Mutation ; Neoplasms/diagnosis/genetics ; Reproducibility of Results ; Sensitivity and Specificity ; },
abstract = {Deep sequencing is required for the highly sensitive detection of rare variants in circulating tumor DNA (ctDNA). However, there remains a challenge for improved sensitivity and specificity. Maximum-depth sequencing is crucial to detect minority mutations that contribute to cancer progression. The associated costs become prohibitive as the numbers of targets and samples increase. We describe the targeted sequencing of KRAS in plasma samples using an efficient barcoding approach to recover discarded reads marked as duplicates. Combined with an error-removal strategy, we anticipate that our method could improve the accuracy of genotype calling, especially to detect rare mutations in the monitoring of ctDNA.},
}
@article {pmid28462038,
year = {2017},
author = {Stern, DB and Castro Nallar, E and Rathod, J and Crandall, KA},
title = {DNA Barcoding analysis of seafood accuracy in Washington, D.C. restaurants.},
journal = {PeerJ},
volume = {5},
number = {},
pages = {e3234},
pmid = {28462038},
issn = {2167-8359},
abstract = {In Washington D.C., recent legislation authorizes citizens to test if products are properly represented and, if they are not, to bring a lawsuit for the benefit of the general public. Recent studies revealing the widespread phenomenon of seafood substitution across the United States make it a fertile area for consumer protection testing. DNA barcoding provides an accurate and cost-effective way to perform these tests, especially when tissue alone is available making species identification based on morphology impossible. In this study, we sequenced the 5' barcoding region of the Cytochrome Oxidase I gene for 12 samples of vertebrate and invertebrate food items across six restaurants in Washington, D.C. and used multiple analytical methods to make identifications. These samples included several ambiguous menu listings, sequences with little genetic variation among closely related species and one sequence with no available reference sequence. Despite these challenges, we were able to make identifications for all samples and found that 33% were potentially mislabeled. While we found a high degree of mislabeling, the errors involved closely related species and we did not identify egregious substitutions as have been found in other cities. This study highlights the efficacy of DNA barcoding and robust analyses in identifying seafood items for consumer protection.},
}
@article {pmid28454189,
year = {2017},
author = {Pawar, RS and Handy, SM and Cheng, R and Shyong, N and Grundel, E},
title = {Assessment of the Authenticity of Herbal Dietary Supplements: Comparison of Chemical and DNA Barcoding Methods.},
journal = {Planta medica},
volume = {83},
number = {11},
pages = {921-936},
doi = {10.1055/s-0043-107881},
pmid = {28454189},
issn = {1439-0221},
mesh = {Biomarkers/*analysis ; *DNA Barcoding, Taxonomic ; DNA, Plant ; Dietary Supplements/*analysis/standards ; Drug Contamination ; Drug Labeling ; Genes, Chloroplast ; Genes, Plant ; Plants, Medicinal/*chemistry/classification ; Quality Control ; },
abstract = {About 7 % of the U. S. population reports using botanical dietary supplements. Increased use of such supplements has led to discussions related to their authenticity and quality. Reports of adulteration with substandard materials or pharmaceuticals are of concern because such substitutions, whether inadvertent or deliberate, may reduce the efficacy of specific botanicals or lead to adverse events. Methods for verifying the identity of botanicals include macroscopic and microscopic examinations, chemical analysis, and DNA-based methods including DNA barcoding. Macroscopic and microscopic examinations may fail when a supplement consists of botanicals that have been processed beyond the ability to provide morphological characterizations. Chemical analysis of specific marker compounds encounters problems when these compounds are not distinct to a given species or when purified reference standards are not available. Recent investigations describing DNA barcoding analysis of botanical dietary supplements have raised concerns about the authenticity of the supplements themselves as well as the appropriateness of using DNA barcoding techniques with finished botanical products. We collected 112 market samples of frequently consumed botanical dietary supplements of ginkgo, soy, valerian, yohimbe, and St. John's wort and analyzed each for specific chemical markers (i.e., flavonol glycosides, total isoflavones, total valerenic acids, yohimbine, and hypericins, respectively). We used traditional DNA barcoding techniques targeting the nuclear ITS2 gene and the chloroplast gene psbA-trnH on the same samples to determine the presence of DNA of the labelled ingredient. We compared the results obtained by both methods to assess the contribution of each in determining the identity of the samples.},
}
@article {pmid28453569,
year = {2017},
author = {Lo, PC and Liu, SH and Nor, SAM and Chen, WJ},
title = {Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade.},
journal = {PloS one},
volume = {12},
number = {4},
pages = {e0176623},
pmid = {28453569},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; Perciformes/*classification ; Phylogeny ; },
abstract = {The family Sciaenidae, known as croakers or drums, is one of the largest perciform fish families. A recent multi-gene based study investigating the phylogeny and biogeography of global sciaenids revealed that the origin and early diversification of this family occurred in tropical America during the Late Oligocene-Early Miocene before undergoing range expansions to other seas including the Indo-West Pacific, where high species richness is observed. Despite this clarification of the overall evolutionary history of the family, knowledge of the taxonomy and phylogeny of sciaenid genera endemic to the Indo-West Pacific is still limited due to lack of a thorough survey of all taxa. In this study, we used DNA-based approaches to investigate the evolutionary relationships, to explore the species diversity, and to elucidate the taxonomic status of sciaenid species/genera within the Indo-West Pacific clade. Three datasets were herein built for the above objectives: the combined dataset (248 samples from 45 currently recognized species) from one nuclear gene (RAG1) and one mitochondrial gene (COI); the dataset with only RAG1 gene sequences (245 samples from 44 currently recognized species); and the dataset with only COI gene sequences (308 samples from 51 currently recognized species). The latter was primarily used for our biodiversity exploration with two different species delimitation methods (Automatic Barcode Gap Discovery, ABGD and Generalized Mixed Yule Coalescent, GMYC). The results were further evaluated with help of four supplementary criteria for species delimitation (genetic similarity, monophyly inferred from individual gene and combined data trees, geographic distribution, and morphology). Our final results confirmed the validity of 32 currently recognized species and identified several potential new species waiting for formal descriptions. We also reexamined the taxonomic status of the genera, Larimichthys, Nibea, Protonibea and Megalonibea, and suggested a revision of Nibea and proposed a new genus Pseudolarimichthys.},
}
@article {pmid28449947,
year = {2017},
author = {Bahouth, SW and Nooh, MM},
title = {Barcoding of GPCR trafficking and signaling through the various trafficking roadmaps by compartmentalized signaling networks.},
journal = {Cellular signalling},
volume = {36},
number = {},
pages = {42-55},
pmid = {28449947},
issn = {1873-3913},
support = {R01 HL085848/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Endosomes/metabolism ; Feedback, Physiological ; Humans ; Protein Processing, Post-Translational ; *Protein Transport ; Receptors, G-Protein-Coupled/*metabolism ; Signal Transduction ; },
abstract = {Proper signaling by G protein coupled receptors (GPCR) is dependent on the specific repertoire of transducing, enzymatic and regulatory kinases and phosphatases that shape its signaling output. Activation and signaling of the GPCR through its cognate G protein is impacted by G protein-coupled receptor kinase (GRK)-imprinted "barcodes" that recruit β-arrestins to regulate subsequent desensitization, biased signaling and endocytosis of the GPCR. The outcome of agonist-internalized GPCR in endosomes is also regulated by sequence motifs or "barcodes" within the GPCR that mediate its recycling to the plasma membrane or retention and eventual degradation as well as its subsequent signaling in endosomes. Given the vast number of diverse sequences in GPCR, several trafficking mechanisms for endosomal GPCR have been described. The majority of recycling GPCR, are sorted out of endosomes in a "sequence-dependent pathway" anchored around a type-1 PDZ-binding module found in their C-tails. For a subset of these GPCR, a second "barcode" imprinted onto specific GPCR serine/threonine residues by compartmentalized kinase networks was required for their efficient recycling through the "sequence-dependent pathway". Mutating the serine/threonine residues involved, produced dramatic effects on GPCR trafficking, indicating that they played a major role in setting the trafficking itinerary of these GPCR. While endosomal SNX27, retromer/WASH complexes and actin were required for efficient sorting and budding of all these GPCR, additional proteins were required for GPCR sorting via the second "barcode". Here we will review recent developments in GPCR trafficking in general and the human β1-adrenergic receptor in particular across the various trafficking roadmaps. In addition, we will discuss the role of GPCR trafficking in regulating endosomal GPCR signaling, which promote biochemical and physiological effects that are distinct from those generated by the GPCR signal transduction pathway in membranes.},
}
@article {pmid28449274,
year = {2017},
author = {Morinière, J and Hendrich, L and Balke, M and Beermann, AJ and König, T and Hess, M and Koch, S and Müller, R and Leese, F and Hebert, PDN and Hausmann, A and Schubart, CD and Haszprunar, G},
title = {A DNA barcode library for Germany's mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera).},
journal = {Molecular ecology resources},
volume = {17},
number = {6},
pages = {1293-1307},
doi = {10.1111/1755-0998.12683},
pmid = {28449274},
issn = {1755-0998},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; *Databases, Genetic ; Ephemeroptera/*classification/*genetics ; Germany ; Holometabola/*classification/*genetics ; },
abstract = {Mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera) are prominent representatives of aquatic macroinvertebrates, commonly used as indicator organisms for water quality and ecosystem assessments. However, unambiguous morphological identification of EPT species, especially their immature life stages, is a challenging, yet fundamental task. A comprehensive DNA barcode library based upon taxonomically well-curated specimens is needed to overcome the problematic identification. Once available, this library will support the implementation of fast, cost-efficient and reliable DNA-based identifications and assessments of ecological status. This study represents a major step towards a DNA barcode reference library as it covers for two-thirds of Germany's EPT species including 2,613 individuals belonging to 363 identified species. As such, it provides coverage for 38 of 44 families (86%) and practically all major bioindicator species. DNA barcode compliant sequences (≥500 bp) were recovered from 98.74% of the analysed specimens. Whereas most species (325, i.e., 89.53%) were unambiguously assigned to a single Barcode Index Number (BIN) by its COI sequence, 38 species (18 Ephemeroptera, nine Plecoptera and 11 Trichoptera) were assigned to a total of 89 BINs. Most of these additional BINs formed nearest neighbour clusters, reflecting the discrimination of geographical subclades of a currently recognized species. BIN sharing was uncommon, involving only two species pairs of Ephemeroptera. Interestingly, both maximum pairwise and nearest neighbour distances were substantially higher for Ephemeroptera compared to Plecoptera and Trichoptera, possibly indicating older speciation events, stronger positive selection or faster rate of molecular evolution.},
}
@article {pmid28449263,
year = {2017},
author = {Xue, AT and Hickerson, MJ},
title = {multi-dice: r package for comparative population genomic inference under hierarchical co-demographic models of independent single-population size changes.},
journal = {Molecular ecology resources},
volume = {17},
number = {6},
pages = {e212-e224},
pmid = {28449263},
issn = {1755-0998},
support = {R15 GM096267/GM/NIGMS NIH HHS/United States ; },
mesh = {Biostatistics/*methods ; *Metagenomics ; *Population Density ; *Software ; },
abstract = {Population genetic data from multiple taxa can address comparative phylogeographic questions about community-scale response to environmental shifts, and a useful strategy to this end is to employ hierarchical co-demographic models that directly test multi-taxa hypotheses within a single, unified analysis. This approach has been applied to classical phylogeographic data sets such as mitochondrial barcodes as well as reduced-genome polymorphism data sets that can yield 10,000s of SNPs, produced by emergent technologies such as RAD-seq and GBS. A strategy for the latter had been accomplished by adapting the site frequency spectrum to a novel summarization of population genomic data across multiple taxa called the aggregate site frequency spectrum (aSFS), which potentially can be deployed under various inferential frameworks including approximate Bayesian computation, random forest and composite likelihood optimization. Here, we introduce the r package multi-dice, a wrapper program that exploits existing simulation software for flexible execution of hierarchical model-based inference using the aSFS, which is derived from reduced genome data, as well as mitochondrial data. We validate several novel software features such as applying alternative inferential frameworks, enforcing a minimal threshold of time surrounding co-demographic pulses and specifying flexible hyperprior distributions. In sum, multi-dice provides comparative analysis within the familiar R environment while allowing a high degree of user customization, and will thus serve as a tool for comparative phylogeography and population genomics.},
}
@article {pmid28449067,
year = {2017},
author = {Peikon, ID and Kebschull, JM and Vagin, VV and Ravens, DI and Sun, YC and Brouzes, E and Corrêa, IR and Bressan, D and Zador, AM},
title = {Using high-throughput barcode sequencing to efficiently map connectomes.},
journal = {Nucleic acids research},
volume = {45},
number = {12},
pages = {e115},
pmid = {28449067},
issn = {1362-4962},
support = {R01 CA181595/CA/NCI NIH HHS/United States ; RF1 MH114132/MH/NIMH NIH HHS/United States ; },
mesh = {Animals ; Calcium-Binding Proteins ; Cell Adhesion Molecules, Neuronal/*genetics/metabolism ; Connectome/*methods ; Embryo, Mammalian ; Gene Expression Regulation ; Genes, Reporter ; Genetic Vectors/chemistry/metabolism ; Green Fluorescent Proteins/genetics/metabolism ; HEK293 Cells ; High-Throughput Nucleotide Sequencing ; Hippocampus/cytology/*metabolism ; Humans ; Luminescent Proteins/genetics/metabolism ; Mice ; Neural Cell Adhesion Molecules/*genetics/metabolism ; Neurons/cytology/*metabolism ; Plasmids/chemistry/metabolism ; Polymerase Chain Reaction/methods ; Primary Cell Culture ; RNA/*genetics/metabolism ; Sindbis Virus/genetics/metabolism ; Synapses/metabolism ; Synaptic Transmission ; Transfection ; Red Fluorescent Protein ; },
abstract = {The function of a neural circuit is determined by the details of its synaptic connections. At present, the only available method for determining a neural wiring diagram with single synapse precision-a 'connectome'-is based on imaging methods that are slow, labor-intensive and expensive. Here, we present SYNseq, a method for converting the connectome into a form that can exploit the speed and low cost of modern high-throughput DNA sequencing. In SYNseq, each neuron is labeled with a unique random nucleotide sequence-an RNA 'barcode'-which is targeted to the synapse using engineered proteins. Barcodes in pre- and postsynaptic neurons are then associated through protein-protein crosslinking across the synapse, extracted from the tissue, and joined into a form suitable for sequencing. Although our failure to develop an efficient barcode joining scheme precludes the widespread application of this approach, we expect that with further development SYNseq will enable tracing of complex circuits at high speed and low cost.},
}
@article {pmid28448639,
year = {2017},
author = {Lee, Y and Lee, W and Kanturski, M and Foottit, RG and Akimoto, SI and Lee, S},
title = {Cryptic diversity of the subfamily Calaphidinae (Hemiptera: Aphididae) revealed by comprehensive DNA barcoding.},
journal = {PloS one},
volume = {12},
number = {4},
pages = {e0176582},
pmid = {28448639},
issn = {1932-6203},
mesh = {Animals ; Aphids/classification/*genetics ; DNA Barcoding, Taxonomic ; Genetic Variation ; Phylogeny ; },
abstract = {Aphids are a species rich group comprising many important pests. However, species identification can be very difficult for aphids due to their morphological ambiguity. DNA barcoding has been widely adopted for rapid and reliable species identification as well as cryptic species detection. In this study, we investigated cryptic diversity in the subfamily Calaphidinae (Hemiptera: Aphididae) based on 899 sequences of cytochrome c oxidase I (COI) for 115 morphospecies (78 species collected in this study and sequences of 73 species downloaded from Genbank). Among these 115 morphospecies, DNA barcoding results of 90 (78.3%) species were identical to results of morphological identification. However, 25 (21.7%) morphospecies showed discrepancies between DNA barcoding and traditional taxonomy. Among these 25 discordances, a total of 15 cryptic species were identified from 12 morphospecies. We also found three morphologically distinct species pairs that sharing DNA barcoding. Based on molecular operational taxonomic unit (MOTU) estimation, we discussed on species delimitation threshold value for these taxa. Our findings confirm that Calaphidinae has high cryptic diversity even though aphids are relatively well-studied.},
}
@article {pmid28447448,
year = {2017},
author = {Silva, JYR and da Luz, LL and Mauricio, FGM and Vasconcelos Alves, IB and Ferro, JNS and Barreto, E and Weber, IT and de Azevedo, WM and Júnior, SA},
title = {Lanthanide-Organic Gels as a Multifunctional Supramolecular Smart Platform.},
journal = {ACS applied materials &amp; interfaces},
volume = {9},
number = {19},
pages = {16458-16465},
doi = {10.1021/acsami.6b15667},
pmid = {28447448},
issn = {1944-8252},
abstract = {A multifunctional smart supramolecular platform based on a lanthanide-organic hydrogel is presented. This platform, which provides unique biocompatibility and tunable optical properties, is synthesized by a simple, fast, and reproducible eco-friendly microwave-assisted route. Photoluminescent properties enable the production of coated light-emitting diodes (LED), unique luminescent barcodes dependent on the excitation wavelength and thin-films for use in tamper seals. Moreover, piroxicam entrapped in hydrogel acts as a transdermal drug release device efficient in inhibiting edemas as compared to a commercial reference.},
}
@article {pmid28446707,
year = {2017},
author = {Yunusova, AM and Fishman, VS and Vasiliev, GV and Battulin, NR},
title = {Deterministic versus stochastic model of reprogramming: new evidence from cellular barcoding technique.},
journal = {Open biology},
volume = {7},
number = {4},
pages = {},
pmid = {28446707},
issn = {2046-2441},
mesh = {Animals ; Cells, Cultured ; *Cellular Reprogramming ; Doxycycline/pharmacology ; Embryo, Mammalian/cytology ; Fibroblasts/cytology/metabolism ; Genetic Vectors/genetics/metabolism ; Green Fluorescent Proteins/genetics/metabolism ; High-Throughput Nucleotide Sequencing ; Induced Pluripotent Stem Cells/cytology/drug effects/*metabolism ; Lentivirus/genetics ; Mice ; *Models, Biological ; Recombinant Fusion Proteins/biosynthesis/genetics ; Sequence Analysis, DNA ; Time-Lapse Imaging ; Transcription Factors/genetics/metabolism ; },
abstract = {Factor-mediated reprogramming of somatic cells towards pluripotency is a low-efficiency process during which only small subsets of cells are successfully reprogrammed. Previous analyses of the determinants of the reprogramming potential are based on average measurements across a large population of cells or on monitoring a relatively small number of single cells with live imaging. Here, we applied lentiviral genetic barcoding, a powerful tool enabling the identification of familiar relationships in thousands of cells. High-throughput sequencing of barcodes from successfully reprogrammed cells revealed a significant number of barcodes from related cells. We developed a computer model, according to which a probability of synchronous reprogramming of sister cells equals 10-30%. We conclude that the reprogramming success is pre-established in some particular cells and, being a heritable trait, can be maintained through cell division. Thus, reprogramming progresses in a deterministic manner, at least at the level of cell lineages.},
}
@article {pmid28445658,
year = {2017},
author = {Pham, KK and Hipp, AL and Manos, PS and Cronn, RC},
title = {A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny.},
journal = {Genome},
volume = {60},
number = {9},
pages = {720-732},
doi = {10.1139/gen-2016-0191},
pmid = {28445658},
issn = {1480-3321},
mesh = {DNA, Plant ; Evolution, Molecular ; Gene Flow ; Genes, Plant ; Phylogeny ; Phylogeography ; Plastids/genetics ; Quercus/*genetics ; Sequence Analysis, DNA ; },
abstract = {Owing to high rates of introgressive hybridization, the plastid genome is poorly suited to fine-scale DNA barcoding and phylogenetic studies of the oak genus (Quercus, Fagaceae). At the tips of the oak plastome phylogeny, recent gene migration and reticulation generally cause topology to reflect geographic structure, while deeper branches reflect lineage divergence. In this study, we quantify the simple and partial effects of geographic proximity and nucleome-inferred phylogenetic history on oak plastome phylogeny at different evolutionary scales. Our study compares pairwise phylogenetic distances based on complete plastome sequences, pairwise phylogenetic distances from nuclear restriction site-associated DNA sequences (RADseq), and pairwise geographic distances for 34 individuals of the white oak clade representing 24 North American and Eurasian species. Within the North American white oak clade alone, phylogenetic history has essentially no effect on plastome variation, while geography explains 11%-21% of plastome phylogenetic variance. However, across multiple continents and clades, phylogeny predicts 30%-41% of plastome variation, geography 3%-41%. Tipwise attenuation of phylogenetic informativeness in the plastome means that in practical terms, plastome data has little use in solving phylogenetic questions, but can still be a useful barcoding or phylogenetic marker for resolving questions among major clades.},
}
@article {pmid28445483,
year = {2017},
author = {Langer, JAF and Sharma, R and Schmidt, SI and Bahrdt, S and Horn, HG and Algueró-Muñiz, M and Nam, B and Achterberg, EP and Riebesell, U and Boersma, M and Thines, M and Schwenk, K},
title = {Community barcoding reveals little effect of ocean acidification on the composition of coastal plankton communities: Evidence from a long-term mesocosm study in the Gullmar Fjord, Skagerrak.},
journal = {PloS one},
volume = {12},
number = {4},
pages = {e0175808},
pmid = {28445483},
issn = {1932-6203},
mesh = {Alveolata/genetics/growth &amp; development/metabolism ; Carbon Dioxide/analysis ; Chlorophyll/analysis ; Chlorophyll A ; Cryptophyta/genetics/growth &amp; development/metabolism ; DNA/chemistry/isolation &amp; purification/metabolism ; *DNA Barcoding, Taxonomic ; Fungi/genetics/growth &amp; development/metabolism ; High-Throughput Nucleotide Sequencing ; Hydrogen-Ion Concentration ; Oceans and Seas ; Plankton/genetics/*growth &amp; development/metabolism ; RNA, Ribosomal, 18S/chemistry/isolation &amp; purification/metabolism ; Sequence Analysis, DNA ; Sweden ; },
abstract = {The acidification of the oceans could potentially alter marine plankton communities with consequences for ecosystem functioning. While several studies have investigated effects of ocean acidification on communities using traditional methods, few have used genetic analyses. Here, we use community barcoding to assess the impact of ocean acidification on the composition of a coastal plankton community in a large scale, in situ, long-term mesocosm experiment. High-throughput sequencing resulted in the identification of a wide range of planktonic taxa (Alveolata, Cryptophyta, Haptophyceae, Fungi, Metazoa, Hydrozoa, Rhizaria, Straminipila, Chlorophyta). Analyses based on predicted operational taxonomical units as well as taxonomical compositions revealed no differences between communities in high CO2 mesocosms (~ 760 μatm) and those exposed to present-day CO2 conditions. Observed shifts in the planktonic community composition were mainly related to seasonal changes in temperature and nutrients. Furthermore, based on our investigations, the elevated CO2 did not affect the intraspecific diversity of the most common mesozooplankter, the calanoid copepod Pseudocalanus acuspes. Nevertheless, accompanying studies found temporary effects attributed to a raise in CO2. Differences in taxa composition between the CO2 treatments could, however, only be observed in a specific period of the experiment. Based on our genetic investigations, no compositional long-term shifts of the plankton communities exposed to elevated CO2 conditions were observed. Thus, we conclude that the compositions of planktonic communities, especially those in coastal areas, remain rather unaffected by increased CO2.},
}
@article {pmid28444386,
year = {2017},
author = {Luo, SX and Liu, TT and Cui, F and Yang, ZY and Hu, XY and Renner, SS},
title = {Coevolution with pollinating resin midges led to resin-filled nurseries in the androecia, gynoecia and tepals of Kadsura (Schisandraceae).},
journal = {Annals of botany},
volume = {120},
number = {5},
pages = {653-664},
pmid = {28444386},
issn = {1095-8290},
mesh = {Animals ; *Biological Coevolution ; China ; Diptera/*physiology ; Evolution, Molecular ; Flowers/anatomy &amp; histology/chemistry ; Kadsura/*anatomy &amp; histology/*chemistry ; Odorants/*analysis ; Phylogeny ; *Pollination ; Symbiosis ; },
abstract = {BACKGROUND AND AIMS: Resin is a defence against herbivores and a floral reward in a few African and South American species whose bee pollinators collect it for nest construction. Here we describe a new role for floral resin from the Asian genus Kadsura (Schisandraceae). Kadsura tepals tightly cover a globe formed by carpels (in females) or near-fused stamens with fleshy connectives (in male flowers of most, but not all species).<br><br>METHODS: We carried out field observations at four sites in China and used pollinator behavioural assays, chemical analyses and time-calibrated insect and plant phylogenies to investigate the specificity of the interactions and their relationship to floral structure.<br><br>KEY RESULTS: Nocturnal resin midges (Resseliella , Cecidomyiidae) walk around on the flowers' sexual organs to oviposit, thereby transferring pollen and wounding tissues. The larvae then develop in resin-filled chambers. Male and female floral scents are dominated by &#x3b1;-pinene, while the resinous exudate is dominated by caryophyllene. As revealed by barcoding of multiple midge larvae per flower species, the mutualisms are species specific and appear to have evolved over the past 6-9 million years.<br><br>CONCLUSIONS: Resin feeding, not pollen or ovule feeding, by midge larvae explains the abundant Kadsura exudates, highlighting the poorly known world of nocturnal flower-fly interactions.},
}
@article {pmid28439828,
year = {2017},
author = {Michaels, YS and Wu, Q and Fulga, TA},
title = {Interrogation of Functional miRNA-Target Interactions by CRISPR/Cas9 Genome Engineering.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1580},
number = {},
pages = {79-97},
doi = {10.1007/978-1-4939-6866-4_7},
pmid = {28439828},
issn = {1940-6029},
support = {G0902418/MRC_/Medical Research Council/United Kingdom ; BB/N006550/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L010275/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; 105605/Z/14/Z//Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *CRISPR-Cas Systems ; Cell Culture Techniques/methods ; Cell Line ; Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Editing/*methods ; Genome ; Humans ; MicroRNAs/*genetics ; Mutation ; RNA, Guide, CRISPR-Cas Systems/genetics ; Response Elements ; Transfection/methods ; },
abstract = {Post-transcriptional silencing by microRNAs (miRNAs) is a critical constituent of eukaryotic gene regulation. miRNAs are short (~22nt) noncoding RNAs capable of specifically targeting the miRNA-induced-silencing-complex (miRISC) to transcripts bearing a complementary miRNA response element (MRE). Although recent methodological advances have greatly improved our understanding of miRNA biogenesis and the mechanisms by which miRNAs repress their cognate targets, exploring the physiological relevance of direct miRNA-target interactions in vivo has remained an outstanding challenge. Here we describe the experimental protocol underlying a novel approach, which allows direct interrogation of specific miRNA-MRE interactions by CRISPR/Cas9-mediated genome engineering. In this instance, the CRISPR/Cas9 system is first used to catalyze homology-directed replacement of candidate MREs with molecular barcodes at endogenous loci. Subsequently, the effect of MRE mutation on transcript abundance (i.e., MRE activity) can be rapidly evaluated by routine quantitative PCR. This strategy enables functional investigation of a putative miRNA-target pair in a pool of transiently transfected cells, obviating the need for generation of clonal cell lines or transgenic animals. This protocol can be implemented in any cell line in less than 2 weeks, and can readily be scaled up for multiplex studies. To facilitate the conceptual workflow underlying this strategy, we also describe a genome-wide resource for automated design and computational evaluation of CRISPR/Cas9 guide RNAs targeting all predicted MREs in various species (miR-CRISPR).},
}
@article {pmid28438699,
year = {2017},
author = {Vacher, JP and Kok, PJR and Rodrigues, MT and Lima, JD and Lorenzini, A and Martinez, Q and Fallet, M and Courtois, EA and Blanc, M and Gaucher, P and Dewynter, M and Jairam, R and Ouboter, P and Thébaud, C and Fouquet, A},
title = {Cryptic diversity in Amazonian frogs: Integrative taxonomy of the genus Anomaloglossus (Amphibia: Anura: Aromobatidae) reveals a unique case of diversification within the Guiana Shield.},
journal = {Molecular phylogenetics and evolution},
volume = {112},
number = {},
pages = {158-173},
doi = {10.1016/j.ympev.2017.04.017},
pmid = {28438699},
issn = {1095-9513},
mesh = {Acoustics ; Animals ; Anura/*classification/*genetics ; Bayes Theorem ; Brazil ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Ecosystem ; *Genetic Variation ; Larva/growth &amp; development ; Likelihood Functions ; Phylogeny ; Principal Component Analysis ; Reproduction ; Species Specificity ; },
abstract = {Lack of resolution on species boundaries and distribution can hamper inferences in many fields of biology, notably biogeography and conservation biology. This is particularly true in megadiverse and under-surveyed regions such as Amazonia, where species richness remains vastly underestimated. Integrative approaches using a combination of phenotypic and molecular evidence have proved extremely successful in reducing knowledge gaps in species boundaries, especially in animal groups displaying high levels of cryptic diversity like amphibians. Here we combine molecular data (mitochondrial 16S rRNA and nuclear TYR, POMC, and RAG1) from 522 specimens of Anomaloglossus, a frog genus endemic to the Guiana Shield, including 16 of the 26 nominal species, with morphometrics, bioacoustics, tadpole development mode, and habitat use to evaluate species delineation in two lowlands species groups. Molecular data reveal the existence of 18 major mtDNA lineages among which only six correspond to described species. Combined with other lines of evidence, we confirm the existence of at least 12 Anomaloglossus species in the Guiana Shield lowlands. Anomaloglossus appears to be the only amphibian genus to have largely diversified within the eastern part of the Guiana Shield. Our results also reveal strikingly different phenotypic evolution among lineages. Within the A. degranvillei group, one subclade displays acoustic and morphological conservatism, while the second subclade displays less molecular divergence but clear phenotypic divergence. In the A. stepheni species group, a complex evolutionary diversification in tadpole development is observed, notably with two closely related lineages each displaying exotrophic and endotrophic tadpoles.},
}
@article {pmid28437475,
year = {2017},
author = {Steinke, D and Breton, V and Berzitis, E and Hebert, PDN},
title = {The School Malaise Trap Program: Coupling educational outreach with scientific discovery.},
journal = {PLoS biology},
volume = {15},
number = {4},
pages = {e2001829},
pmid = {28437475},
issn = {1545-7885},
mesh = {Adolescent ; Animals ; *Biodiversity ; Canada ; Child ; *Community-Institutional Relations/trends ; DNA Barcoding, Taxonomic/veterinary ; Genomics/*education/trends ; Humans ; Insecta/classification/*genetics/growth &amp; development/physiology ; *Schools/trends ; Teaching/trends ; Workforce ; },
abstract = {The School Malaise Trap Program (SMTP) provides a technologically sophisticated and scientifically relevant educational experience that exposes students to the diversity of life, enhancing their understanding of biodiversity while promoting environmental stewardship. Since 2013, the SMTP has allowed 15,000 students at 350 primary and secondary schools to explore insect diversity in Canadian schoolyards. Students at each school collected hundreds of insects for an analysis of DNA sequence variation that enabled their rapid identification to a species. Through this hands-on approach, they participated in a learning exercise that conveys a real sense of scientific discovery. As well, the students contributed valuable data to the largest biodiversity genomics initiative ever undertaken: the International Barcode of Life project. To date, the SMTP has sequenced over 80,000 insect specimens, which includes representatives of 7,990 different species, nearly a tenth of the Canadian fauna. Both surprisingly and importantly, the collections generated the first DNA barcode records for 1,288 Canadian species.},
}
@article {pmid28432095,
year = {2017},
author = {Castaño, C and Oliva, J and Martínez de Aragón, J and Alday, JG and Parladé, J and Pera, J and Bonet, JA},
title = {Mushroom Emergence Detected by Combining Spore Trapping with Molecular Techniques.},
journal = {Applied and environmental microbiology},
volume = {83},
number = {13},
pages = {},
pmid = {28432095},
issn = {1098-5336},
mesh = {Agaricales/classification/genetics/growth &amp; development/*isolation &amp; purification ; Fruiting Bodies, Fungal/classification/genetics/growth &amp; development/isolation &amp; purification ; Mycological Typing Techniques/instrumentation/*methods ; Real-Time Polymerase Chain Reaction ; Soil Microbiology ; Spores, Fungal/classification/genetics/growth &amp; development/*isolation &amp; purification ; },
abstract = {Obtaining reliable and representative mushroom production data requires time-consuming sampling schemes. In this paper, we assessed a simple methodology to detect mushroom emergence by trapping the fungal spores of the fruiting body community in plots where mushroom production was determined weekly. We compared the performance of filter paper traps with that of funnel traps and combined these spore trapping methods with species-specific quantitative real-time PCR and Illumina MiSeq to determine the spore abundance. Significantly more MiSeq proportional reads were generated for both ectomycorrhizal and saprotrophic fungal species using filter traps than were obtained using funnel traps. The spores of 37 fungal species that produced fruiting bodies in the study plots were identified. Spore community composition changed considerably over time due to the emergence of ephemeral fruiting bodies and rapid spore deposition (lasting from 1 to 2 weeks), which occurred in the absence of rainfall events. For many species, the emergence of epigeous fruiting bodies was followed by a peak in the relative abundance of their airborne spores. There were significant positive relationships between fruiting body yields and spore abundance in time for five of seven fungal species. There was no relationship between fruiting body yields and their spore abundance at plot level, indicating that some of the spores captured in each plot were arriving from the surrounding areas. Differences in fungal detection capacity by spore trapping may indicate different dispersal ability between fungal species. Further research can help to identify the spore rain patterns for most common fungal species.IMPORTANCE Mushroom monitoring represents a serious challenge in economic and logistical terms because sampling approaches demand extensive field work at both the spatial and temporal scales. In addition, the identification of fungal taxa depends on the expertise of experienced fungal taxonomists. Similarly, the study of fungal dispersal has been constrained by technological limitations, especially because the morphological identification of spores is a challenging and time-consuming task. Here, we demonstrate that spores from ectomycorrhizal and saprotrophic fungal species can be identified using simple spore traps together with either MiSeq fungus-specific amplicon sequencing or species-specific quantitative real-time PCR. In addition, the proposed methodology can be used to characterize the airborne fungal community and to detect mushroom emergence in forest ecosystems.},
}
@article {pmid28431229,
year = {2017},
author = {van Arensbergen, J and van Steensel, B},
title = {Functional Enhancer Screening in Single Cells.},
journal = {Molecular cell},
volume = {66},
number = {2},
pages = {167-168},
doi = {10.1016/j.molcel.2017.03.018},
pmid = {28431229},
issn = {1097-4164},
mesh = {*Enhancer Elements, Genetic ; *Gene Expression Regulation ; Promoter Regions, Genetic ; RNA/genetics ; },
abstract = {In this issue of Molecular Cell, Xie et al. (2017) introduce Mosaic-seq, a powerful technology that combines CRISPRi and single-cell RNA-seq. This method enables the high-throughput assessment of contributions of enhancers to gene regulation.},
}
@article {pmid28431212,
year = {2017},
author = {Sheth, BP and Thaker, VS},
title = {DNA barcoding and traditional taxonomy: an integrated approach for biodiversity conservation.},
journal = {Genome},
volume = {60},
number = {7},
pages = {618-628},
doi = {10.1139/gen-2015-0167},
pmid = {28431212},
issn = {1480-3321},
mesh = {Animals ; Biodiversity ; Classification/*methods ; Conservation of Natural Resources/methods ; DNA Barcoding, Taxonomic/*methods ; },
abstract = {Biological diversity is depleting at an alarming rate. Additionally, a vast amount of biodiversity still remains undiscovered. Taxonomy has been serving the purpose of describing, naming, and classifying species for more than 250 years. DNA taxonomy and barcoding have accelerated the rate of this process, thereby providing a tool for conservation practice. DNA barcoding and traditional taxonomy have their own inherent merits and demerits. The synergistic use of both methods, in the form of integrative taxonomy, has the potential to contribute to biodiversity conservation in a pragmatic timeframe and overcome their individual drawbacks. In this review, we discuss the basics of both these methods of biological identification (traditional taxonomy and DNA barcoding), the technical advances in integrative taxonomy, and future trends. We also present a comprehensive compilation of published examples of integrative taxonomy that refer to nine topics within biodiversity conservation. Morphological and molecular species limits were observed to be congruent in ∼41% of the 58 source studies. The majority of the studies highlighted the description of cryptic diversity through the use of molecular data, whereas research areas like endemism, biological invasion, and threatened species were less discussed in the literature.},
}
@article {pmid28428844,
year = {2017},
author = {Dittrich, C and Struck, U and Rödel, MO},
title = {Stable isotope analyses-A method to distinguish intensively farmed from wild frogs.},
journal = {Ecology and evolution},
volume = {7},
number = {8},
pages = {2525-2534},
pmid = {28428844},
issn = {2045-7758},
abstract = {Consumption of frog legs is increasing worldwide, with potentially dramatic effects for ecosystems. More and more functioning frog farms are reported to exist. However, due to the lack of reliable methods to distinguish farmed from wild-caught individuals, the origin of frogs in the international trade is often uncertain. Here, we present a new methodological approach to this problem. We investigated the isotopic composition of legally traded frog legs from suppliers in Vietnam and Indonesia. Muscle and bone tissue samples were examined for δ[15]N, δ[13]C, and δ[18]O stable isotope compositions, to elucidate the conditions under which the frogs grew up. We used DNA barcoding (16S rRNA) to verify species identities. We identified three traded species (Hoplobatrachus rugulosus, Fejervarya cancrivora and Limnonectes macrodon); species identities were partly deviating from package labeling. Isotopic values of δ[15]N and δ[18]O showed significant differences between species and country of origin. Based on low δ[15]N composition and generally little variation in stable isotope values, our results imply that frogs from Vietnam were indeed farmed. In contrast, the frogs from the Indonesian supplier likely grew up under natural conditions, indicated by higher δ[15]N values and stronger variability in the stable isotope composition. Our results indicate that stable isotope analyses seem to be a useful tool to distinguish between naturally growing and intensively farmed frogs. We believe that this method can be used to improve the control in the international trade of frog legs, as well as for other biological products, thus supporting farming activities and decreasing pressure on wild populations. However, we examined different species from different countries and had no access to samples of individuals with confirmed origin and living conditions. Therefore, we suggest improving this method further with individuals of known origin and history, preferably including samples of the respective nutritive bases.},
}
@article {pmid28428147,
year = {2017},
author = {Chi, H and Taik, P and Foley, EJ and Racicot, AC and Gray, HM and Guzzetta, KE and Lin, HY and Song, YL and Tung, CH and Zenke, K and Yoshinaga, T and Cheng, CY and Chang, WJ and Gong, H},
title = {High genetic diversities between isolates of the fish parasite Cryptocaryon irritans (Ciliophora) suggest multiple cryptic species.},
journal = {Molecular phylogenetics and evolution},
volume = {112},
number = {},
pages = {47-52},
doi = {10.1016/j.ympev.2017.04.015},
pmid = {28428147},
issn = {1095-9513},
mesh = {Animals ; Aquaculture ; China ; Fishes/parasitology ; Genetic Speciation ; *Genetic Variation ; Hymenostomatida/*genetics ; Japan ; Phylogeny ; Taiwan ; },
abstract = {The ciliate protozoan Cryptocaryon irritans parasitizes marine fish and causes lethal white spot disease. Sporadic infections as well as large-scale outbreaks have been reported globally and the parasite's broad host range poses particular threat to the aquaculture and ornamental fish markets. In order to better understand C. irritans' population structure, we sequenced and compared mitochondrial cox-1, SSU rRNA, and ITS-1 sequences from 8 new isolates of C. irritans collected in China, Japan, and Taiwan. We detected two SSU rRNA haplotypes, which differ at three positions, separating the isolates into two main groups (I and II). Cox-1 sequences also support the division into two groups, and the cox-1 divergence between these two groups is unexpectedly high (9.28% for 1582 nucleotide positions). The divergence is much greater than that detected in Ichthyophthirius multifiliis, the ciliate protozoan causing freshwater white spot disease in fish, where intraspecies divergence on cox-1 sequence is only 1.95%. ITS-1 sequences derived from these eight isolates and from all other C. irritans isolates (deposited in the GenBank) not only support the two groups, but further suggest the presence of a third group with even greater sequence divergence. Finally, a small Ka/Ks ratio estimated from cox-1 sequences suggests that this gene in C. irritans remains under strong purifying selection. Taken together, the C. irritans species may consists of many subspecies and/or syngens. Further work is needed to determine if there is reproductive isolation between the groups we have defined.},
}
@article {pmid28427715,
year = {2017},
author = {Takei, Y and Shah, S and Harvey, S and Qi, LS and Cai, L},
title = {Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH.},
journal = {Biophysical journal},
volume = {112},
number = {9},
pages = {1773-1776},
pmid = {28427715},
issn = {1542-0086},
support = {R01 DA036858/DA/NIDA NIH HHS/United States ; U01 DA047732/DA/NIDA NIH HHS/United States ; U01 EB021240/EB/NIBIB NIH HHS/United States ; },
mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; CRISPR-Associated Protein 9 ; Chromosomes/*metabolism ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Embryonic Stem Cells/metabolism ; Endonucleases/genetics/metabolism ; *Genetic Loci ; Green Fluorescent Proteins/genetics/metabolism ; *In Situ Hybridization, Fluorescence ; Mice ; Streptococcus pyogenes ; },
abstract = {Visualization of chromosome dynamics allows the investigation of spatiotemporal chromatin organization and its role in gene regulation and other cellular processes. However, current approaches to label multiple genomic loci in live cells have a fundamental limitation in the number of loci that can be labeled and uniquely identified. Here we describe an approach we call "track first and identify later" for multiplexed visualization of chromosome dynamics by combining two techniques: CRISPR imaging and DNA sequential fluorescence in situ hybridization. Our approach first labels and tracks chromosomal loci in live cells with the CRISPR-Cas9 system, then barcodes those loci by DNA sequential fluorescence in situ hybridization in fixed cells and resolves their identities. We demonstrate our approach by tracking telomere dynamics, identifying 12 unique subtelomeric regions with variable detection efficiencies, and tracking back the telomere dynamics of respective chromosomes in mouse embryonic stem cells.},
}
@article {pmid28419283,
year = {2017},
author = {Bharti, M and Singh, B},
title = {DNA-Based Identification of Forensically Important Blow Flies (Diptera: Calliphoridae) From India.},
journal = {Journal of medical entomology},
volume = {54},
number = {5},
pages = {1151-1156},
doi = {10.1093/jme/tjx084},
pmid = {28419283},
issn = {1938-2928},
mesh = {Animals ; Biological Evolution ; DNA Fingerprinting ; Diptera/*genetics ; Electron Transport Complex IV/*genetics ; *Forensic Sciences ; },
abstract = {Correct species identification is the first and the most important criteria in entomological evidence-based postmortem interval (PMI) estimation. Although morphological keys are available for species identification of adult blow flies, keys for immature stages are either lacking or are incomplete. In this study, cytochrome oxidase subunit 1 (COI) reference data were developed from nine species (belonging to three subfamilies, namely, Calliphorinae, Luciliinae, and Chrysomyinae) of blow flies from India. Seven of the nine species included in this study were found suitable for DNA-based identification using COI gene, because they showed nonoverlapping intra- (0.0-0.3%) and inter-(1.96-18.14%) specific diversity, and formed well-supported monophyletic clade in phylogenetic analysis. The remaining two species (i.e., Chrysomya megacephala (Fabricius) and Chrysomya chani Kurahashi) cannot be distinguished reliably using our database because they had a very low interspecific diversity (0.11%), and Ch. megacephala was paraphyletic with respect to Ch. chani in the phylogenetic analysis. We conclude that the COI gene is a useful marker for DNA-based identification of blow flies from India.},
}
@article {pmid28419161,
year = {2017},
author = {Ghorbani, A and Saeedi, Y and de Boer, HJ},
title = {Unidentifiable by morphology: DNA barcoding of plant material in local markets in Iran.},
journal = {PloS one},
volume = {12},
number = {4},
pages = {e0175722},
pmid = {28419161},
issn = {1932-6203},
mesh = {Amaranthus ; Cell Nucleus/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Chloroplast/chemistry/genetics ; DNA, Plant/chemistry/*genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Plants, Medicinal/*anatomy &amp; histology/classification/*genetics ; RNA, Transfer/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; },
abstract = {Local markets provide a rapid insight into the medicinal plants growing in a region as well as local traditional health concerns. Identification of market plant material can be challenging as plants are often sold in dried or processed forms. In this study, three approaches of DNA barcoding-based molecular identification of market samples are evaluated, two objective sequence matching approaches and an integrative approach that coalesces sequence matching with a priori and a posteriori data from other markers, morphology, ethnoclassification and species distribution. Plant samples from markets and herbal shops were identified using morphology, descriptions of local use, and vernacular names with relevant floras and pharmacopoeias. DNA barcoding was used for identification of samples that could not be identified to species level using morphology. Two methods based on BLAST similarity-based identification, were compared with an integrative identification approach. Integrative identification combining the optimized similarity-based approach with a priori and a posteriori information resulted in a 1.67, 1.95 and 2.00 fold increase for ITS, trnL-F spacer, and both combined, respectively. DNA barcoding of traded plant material requires objective strategies to include data from multiple markers, morphology, and traditional knowledge to optimize species level identification success.},
}
@article {pmid28417591,
year = {2018},
author = {Batovska, J and Lynch, SE and Cogan, NOI and Brown, K and Darbro, JM and Kho, EA and Blacket, MJ},
title = {Effective mosquito and arbovirus surveillance using metabarcoding.},
journal = {Molecular ecology resources},
volume = {18},
number = {1},
pages = {32-40},
pmid = {28417591},
issn = {1755-0998},
mesh = {Animals ; Computational Biology ; DNA Barcoding, Taxonomic/*methods ; Entomology/*methods ; *Epidemiological Monitoring ; Metagenomics/*methods ; Mosquito Vectors/*classification/genetics/*virology ; Reverse Transcriptase Polymerase Chain Reaction ; Ross River virus/genetics/*isolation &amp; purification ; Sequence Analysis, DNA ; },
abstract = {Effective vector and arbovirus surveillance requires timely and accurate screening techniques that can be easily upscaled. Next-generation sequencing (NGS) is a high-throughput technology that has the potential to modernize vector surveillance. When combined with DNA barcoding, it is termed 'metabarcoding.' The aim of our study was to establish a metabarcoding protocol to characterize pools of mosquitoes and screen them for virus. Pools contained 100 morphologically identified individuals, including one Ross River virus (RRV) infected mosquito, with three species present at different proportions: 1, 5, 94%. Nucleic acid extracted from both crude homogenate and supernatant was used to amplify a 269-bp section of the mitochondrial cytochrome c oxidase subunit I (COI) locus. Additionally, a 67-bp region of the RRV E2 gene was amplified from synthesized cDNA to screen for RRV. Amplicon sequencing was performed using an Illumina MiSeq, and bioinformatic analysis was performed using a DNA barcode database of Victorian mosquitoes. Metabarcoding successfully detected all mosquito species and RRV in every positive sample tested. The limits of species detection were also examined by screening a pool of 1000 individuals, successfully identifying the species and RRV from a single mosquito. The primers used for amplification, number of PCR cycles and total number of individuals present all have effects on the quantification of species in mixed bulk samples. Based on the results, a number of recommendations for future metabarcoding studies are presented. Overall, metabarcoding shows great promise for providing a new alternative approach to screening large insect surveillance trap catches.},
}
@article {pmid28417460,
year = {2017},
author = {Jiao, S and Cao, H and Dai, Y and Wu, J and Lv, J and Du, R and Han, B},
title = {Effect of high-fat diet and growth stage on the diversity and composition of intestinal microbiota in healthy bovine livestock.},
journal = {Journal of the science of food and agriculture},
volume = {97},
number = {14},
pages = {5004-5013},
doi = {10.1002/jsfa.8380},
pmid = {28417460},
issn = {1097-0010},
mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Cattle/*growth &amp; development/*metabolism/microbiology ; Diet, High-Fat ; Fats/*metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; Male ; },
abstract = {BACKGROUND: This study aimed to investigate the composition of bacteria in the bovine rectum and their functions during growth, in relation to different diets. Fecal samples were collected from 6-, 12-, 18- and 24-month cattle fed high-fat diet, and healthy female parents fed regular diet. Total DNA was amplified (V3-V4 of 16S rRNA) and submitted to barcode-DNA pyrosequencing. Intestinal microbiota profiles and functions were then analyzed.<br><br>RESULTS: A total of 114 512 operational taxonomic units were detected from the 1 802 243 sequences obtained. In 6-month-old and female parent groups, the top three abundant phyla were Bacteroidetes (37.6%, 32.2%), Firmicutes (34.4%, 48.2%) and Proteobacteria (9.1%, 6.3%); in the 12-, 18- and 24-month groups, they were Proteobacteria (45.5%, 47.1%, 38.8%), Firmicutes (27.4%, 22.2%, 20.1%) and Bacteroidetes (14.9%, 19.4%, 17.7%), respectively. Paludibacter and Desulfopila in abundance showed negative (P < 0.001) and positive (P < 0.05) correlation, respectively, to cattle weight gain through metagenomic functional prediction of methane, cysteine and methionine metabolism. Meanwhile, cofactor/vitamin and amino acid metabolic processes were significantly higher in bacteria from the regular diet group than high-fat diet groups, with markedly lower cellular processes and signaling, and reduced glycan biosynthesis and metabolism (P < 0.01).<br><br>CONCLUSIONS: The 6-month cattle and female parents shared similar intestinal bacteria; the community structure of fecal microbiota was significantly affected by high-fat diet in older cattle. &#xa9; 2017 Society of Chemical Industry.},
}
@article {pmid28416672,
year = {2017},
author = {Mattox, AK and Wang, Y and Springer, S and Cohen, JD and Yegnasubramanian, S and Nelson, WG and Kinzler, KW and Vogelstein, B and Papadopoulos, N},
title = {Bisulfite-converted duplexes for the strand-specific detection and quantification of rare mutations.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {114},
number = {18},
pages = {4733-4738},
pmid = {28416672},
issn = {1091-6490},
support = {P30 CA006973/CA/NCI NIH HHS/United States ; P50 CA062924/CA/NCI NIH HHS/United States ; T32 GM007309/GM/NIGMS NIH HHS/United States ; T32 GM007814/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {DNA Mutational Analysis/methods ; DNA, Neoplasm/chemistry/*genetics ; Humans ; Mutation ; Neoplasms/*genetics ; Sulfites/*chemistry ; },
abstract = {The identification of mutations that are present at low frequencies in clinical samples is an essential component of precision medicine. The development of molecular barcoding for next-generation sequencing has greatly enhanced the sensitivity of detecting such mutations by massively parallel sequencing. However, further improvements in specificity would be useful for a variety of applications. We herein describe a technology (BiSeqS) that can increase the specificity of sequencing by at least two orders of magnitude over and above that achieved with molecular barcoding and can be applied to any massively parallel sequencing instrument. BiSeqS employs bisulfite treatment to distinguish the two strands of molecularly barcoded DNA; its specificity arises from the requirement for the same mutation to be identified in both strands. Because no library preparation is required, the technology permits very efficient use of the template DNA as well as sequence reads, which are nearly all confined to the amplicons of interest. Such efficiency is critical for clinical samples, such as plasma, in which only tiny amounts of DNA are often available. We show here that BiSeqS can be applied to evaluate transversions, as well as small insertions or deletions, and can reliably detect one mutation among >10,000 wild-type molecules.},
}
@article {pmid28416409,
year = {2017},
author = {Sanz López, E and Sánchez Luna, M and Rite Gracia, S and Benavente Fernández, I and Leante Castellanos, JL and Pérez Muñuzuri, A and Ruiz Campillo, CW and Sánchez Redondo, MD and , },
title = {[Recommendations for the unequivocal identification of the newborn].},
journal = {Anales de pediatria (Barcelona, Spain : 2003)},
volume = {87},
number = {4},
pages = {235.e1-235.e4},
doi = {10.1016/j.anpedi.2017.03.008},
pmid = {28416409},
issn = {1695-9531},
mesh = {*DNA Fingerprinting ; Humans ; Infant, Newborn ; Patient Identification Systems/*methods/*standards ; },
abstract = {Newborn identification is a legal right recognised by international and national laws. Moreover, improving the accuracy of correct patient identification is an important goal of patient safety solutions programs. In this article, the Standards Committee of the Spanish Society of Neonatology establishes recommendations to ensure correct identification of the newborn whilst in hospital. Currently, the most reliable method of identification of the newborn is the combination of identification cord clamp and bracelets (mother bracelet, newborn bracelet and cord clamp with the same number and identical and exclusive barcode system for each newborn) and the collection of maternal and umbilical cord blood samples (for DNA testing only for identification purposes).},
}
@article {pmid28416141,
year = {2017},
author = {Xie, S and Duan, J and Li, B and Zhou, P and Hon, GC},
title = {Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells.},
journal = {Molecular cell},
volume = {66},
number = {2},
pages = {285-299.e5},
doi = {10.1016/j.molcel.2017.03.007},
pmid = {28416141},
issn = {1097-4164},
mesh = {CRISPR-Cas Systems ; Cell Separation/methods ; Databases, Genetic ; *Enhancer Elements, Genetic ; Flow Cytometry ; Gene Expression Profiling/*methods ; Gene Expression Regulation ; Genotype ; HEK293 Cells ; *High-Throughput Nucleotide Sequencing ; Humans ; K562 Cells ; Penetrance ; Phenotype ; RNA Polymerase II/genetics/metabolism ; RNA, Guide, CRISPR-Cas Systems/genetics/metabolism ; Single-Cell Analysis/*methods ; Transcription Factors/*genetics/metabolism ; *Transcription, Genetic ; *Transcriptional Activation ; *Transcriptome ; Transfection ; Transposases/genetics/metabolism ; p300-CBP Transcription Factors/genetics/metabolism ; },
abstract = {The study of enhancers has been hampered by the scarcity of methods to systematically quantify their endogenous activity. We develop Mosaic-seq to systematically perturb enhancers and measure their endogenous activities at single-cell resolution. Mosaic-seq uses a CRISPR barcoding system to jointly measure a cell's transcriptome and its sgRNA modulators, thus quantifying the effects of dCas9-KRAB-mediated enhancer repression in single cells. Applying Mosaic-seq to 71 constituent enhancers from 15 super-enhancers, our analysis of 51,448 sgRNA-induced transcriptomes finds that only a small number of constituents are major effectors of target gene expression. Binding of p300 and RNAPII are key features of these constituents. We determine two key parameters of enhancer activity in single cells: their penetrance in a population and their contribution to expression in these cells. Through combinatorial interrogation, we find that simultaneous repression of multiple weak constituents can alter super-enhancer activity in a manner greatly exceeding repression of individual constituents.},
}
@article {pmid28414813,
year = {2017},
author = {Liu, ZF and Ci, XQ and Li, L and Li, HW and Conran, JG and Li, J},
title = {DNA barcoding evaluation and implications for phylogenetic relationships in Lauraceae from China.},
journal = {PloS one},
volume = {12},
number = {4},
pages = {e0175788},
pmid = {28414813},
issn = {1932-6203},
mesh = {China ; *DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; Lauraceae/*classification/*genetics ; Phylogeny ; Species Specificity ; },
abstract = {Lauraceae are an important component of tropical and subtropical forests and have major ecological and economic significance. Owing to lack of clear-cut morphological differences between genera and species, this family is an ideal case for testing the efficacy of DNA barcoding in the identification and discrimination of species and genera. In this study, we evaluated five widely recommended plant DNA barcode loci matK, rbcL, trnH-psbA, ITS2 and the entire ITS region for 409 individuals representing 133 species, 12 genera from China. We tested the ability of DNA barcoding to distinguish species and as an alternative tool for correcting species misidentification. We also used the rbcL+matK+trnH-psbA+ITS loci to investigate the phylogenetic relationships of the species examined. Among the gene regions and their combinations, ITS was the most efficient for identifying species (57.5%) and genera (70%). DNA barcoding also had a positive role for correcting species misidentification (10.8%). Furthermore, based on the results of the phylogenetic analyses, Chinese Lauraceae species formed three supported monophyletic clades, with the Cryptocarya group strongly supported (PP = 1.00, BS = 100%) and the clade including the Persea group, Laureae and Cinnamomum also receiving strong support (PP = 1.00, BS = 98%), whereas the Caryodaphnopsis-Neocinnamomum received only moderate support (PP = 1.00 and BS = 85%). This study indicates that molecular barcoding can assist in screening difficult to identify families like Lauraceae, detecting errors of species identification, as well as helping to reconstruct phylogenetic relationships. DNA barcoding can thus help with large-scale biodiversity inventories and rare species conservation by improving accuracy, as well as reducing time and costs associated with species identification.},
}
@article {pmid28410643,
year = {2017},
author = {D'Antonio, M and Woodruff, G and Nathanson, JL and D'Antonio-Chronowska, A and Arias, A and Matsui, H and Williams, R and Herrera, C and Reyna, SM and Yeo, GW and Goldstein, LSB and Panopoulos, AD and Frazer, KA},
title = {High-Throughput and Cost-Effective Characterization of Induced Pluripotent Stem Cells.},
journal = {Stem cell reports},
volume = {8},
number = {4},
pages = {1101-1111},
pmid = {28410643},
issn = {2213-6711},
support = {U01 DK105541/DK/NIDDK NIH HHS/United States ; R01 EY021237/EY/NEI NIH HHS/United States ; DP3 DK112155/DK/NIDDK NIH HHS/United States ; R41 HG008118/HG/NHGRI NIH HHS/United States ; U01 HL107442/HL/NHLBI NIH HHS/United States ; R01 HG004659/HG/NHGRI NIH HHS/United States ; P30 CA023100/CA/NCI NIH HHS/United States ; T32 GM008666/GM/NIGMS NIH HHS/United States ; R44 HG008118/HG/NHGRI NIH HHS/United States ; R01 NS075449/NS/NINDS NIH HHS/United States ; },
mesh = {Biomarkers/metabolism ; Cell Differentiation ; Cell Line ; Cellular Reprogramming/genetics ; Cost-Benefit Analysis ; *Genetic Variation ; Genotype ; High-Throughput Screening Assays/economics/instrumentation/*methods ; Humans ; Induced Pluripotent Stem Cells/cytology/*metabolism ; Karyotyping/economics/*methods ; Myocytes, Cardiac/cytology/*metabolism ; Neurons/cytology/*metabolism ; Phenotype ; },
abstract = {Reprogramming somatic cells to induced pluripotent stem cells (iPSCs) offers the possibility of studying the molecular mechanisms underlying human diseases in cell types difficult to extract from living patients, such as neurons and cardiomyocytes. To date, studies have been published that use small panels of iPSC-derived cell lines to study monogenic diseases. However, to study complex diseases, where the genetic variation underlying the disorder is unknown, a sizable number of patient-specific iPSC lines and controls need to be generated. Currently the methods for deriving and characterizing iPSCs are time consuming, expensive, and, in some cases, descriptive but not quantitative. Here we set out to develop a set of simple methods that reduce cost and increase throughput in the characterization of iPSC lines. Specifically, we outline methods for high-throughput quantification of surface markers, gene expression analysis of in vitro differentiation potential, and evaluation of karyotype with markedly reduced cost.},
}
@article {pmid28407939,
year = {2017},
author = {Fernandes, TJR and Costa, J and Oliveira, MBPP and Mafra, I},
title = {DNA barcoding coupled to HRM analysis as a new and simple tool for the authentication of Gadidae fish species.},
journal = {Food chemistry},
volume = {230},
number = {},
pages = {49-57},
doi = {10.1016/j.foodchem.2017.03.015},
pmid = {28407939},
issn = {1873-7072},
mesh = {Animals ; Base Sequence ; Cytochromes b/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Gadiformes/classification/*genetics/metabolism ; Real-Time Polymerase Chain Reaction ; Sequence Alignment ; },
abstract = {This work aimed to exploit the use of DNA mini-barcodes combined with high resolution melting (HRM) for the authentication of gadoid species: Atlantic cod (Gadus morhua), Pacific cod (Gadus macrocephalus), Alaska pollock (Theragra chalcogramma) and saithe (Pollachius virens). Two DNA barcode regions, namely cytochrome c oxidase subunit I (COI) and cytochrome b (cytb), were analysed in silico to identify genetic variability among the four species and used, subsequently, to develop a real-time PCR method coupled with HRM analysis. The cytb mini-barcode enabled best discrimination of the target species with a high level of confidence (99.3%). The approach was applied successfully to identify gadoid species in 30 fish-containing foods, 30% of which were not as declared on the label. Herein, a novel approach for rapid, simple and cost-effective discrimination/clustering, as a tool to authenticate Gadidae fish species, according to their genetic relationship, is proposed.},
}
@article {pmid28407723,
year = {2018},
author = {Huang, Z and Ruan, R},
title = {DNA barcodes and insights into the phylogenetic relationships of Corvidae (Aves: Passeriformes).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {4},
pages = {529-534},
doi = {10.1080/24701394.2017.1315569},
pmid = {28407723},
issn = {2470-1408},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Genome, Mitochondrial ; Mitochondria/*enzymology ; Passeriformes/*classification/*genetics ; *Phylogeny ; },
abstract = {DNA barcoding has become a promising tool for species identification and phylogeny in a wide range of animal taxa using mitochondrial cytochrome c oxidase subunit I (COI). The Corvidae (Aves: Passeriformes) is a species rich and morphologically diverse family. In the present study, we analyzed the COI barcodes of 39 species from 12 genera of Corvidae. COI gene was also used to examine phylogenetic relationships of Corvidae. Every species possessed a barcode distinct from that of other species. Kimura two-parameter distances were calculated between species barcodes. The average genetic distance between the species was 22 times higher compared to the average genetic distance within species. Maximum likelihood method was used to construct a phylogenetic tree. All the species could be discriminated by their distinct clades in the phylogenetic tree. COI gene data provided good evidence for the monophyly of the Corvidae. Members of Cyanopica and Pyrrhocorax were the first to split from the Corvidae lineage. Analysis of COI genes supported the others genera fell into two clades. DNA barcoding is an effective molecular tool for Corvidae species identification and phylogenetic inference.},
}
@article {pmid28407030,
year = {2017},
author = {Qazi, MA and Vora, P and Venugopal, C and Sidhu, SS and Moffat, J and Swanton, C and Singh, SK},
title = {Intratumoral heterogeneity: pathways to treatment resistance and relapse in human glioblastoma.},
journal = {Annals of oncology : official journal of the European Society for Medical Oncology},
volume = {28},
number = {7},
pages = {1448-1456},
doi = {10.1093/annonc/mdx169},
pmid = {28407030},
issn = {1569-8041},
mesh = {Animals ; Antineoplastic Agents/*therapeutic use ; Biomarkers, Tumor/genetics/metabolism ; Brain Neoplasms/*drug therapy/genetics/metabolism/pathology ; Disease Progression ; *Drug Resistance/drug effects ; Glioblastoma/*drug therapy/genetics/metabolism/secondary ; Humans ; *Neoplasm Recurrence, Local ; Treatment Outcome ; },
abstract = {Intratumoral heterogeneity (ITH) has increasingly being described for multiple cancers as the root cause of therapy resistance. Recent studies have started to explore the scope of ITH in glioblastoma (GBM), a highly aggressive and fatal form of brain tumor, to explain its inevitable therapy resistance and disease relapse. In this review, we detail the emerging data that explores the extensive genetic, cellular and functional ITH present in GBM. We discuss current experimental models of human GBM recurrence and suggest harnessing new technologies (CRISPR-Cas9 screening, CyTOF, cellular barcoding, single cell analysis) to delineate GBM ITH and identify treatment-refractory cell populations, thus opening new therapeutic windows. We will also explore why current therapeutics have failed in clinical trials and how ITH can inform us on developing empiric therapies for the treatment of recurrent GBM.},
}
@article {pmid28406914,
year = {2017},
author = {Rach, J and Bergmann, T and Paknia, O and DeSalle, R and Schierwater, B and Hadrys, H},
title = {The marker choice: Unexpected resolving power of an unexplored CO1 region for layered DNA barcoding approaches.},
journal = {PloS one},
volume = {12},
number = {4},
pages = {e0174842},
pmid = {28406914},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Genetic Markers ; Insect Proteins/*genetics ; Mitochondrial Proteins/*genetics ; NADH Dehydrogenase/*genetics ; Odonata/classification/*genetics ; },
abstract = {The potential of DNA barcoding approaches to identify single species and characterize species compositions strongly depends on the marker choice. The prominent "Folmer region", a 648 basepair fragment at the 5' end of the mitochondrial CO1 gene, has been traditionally applied as a universal DNA barcoding region for metazoans. In order to find a suitable marker for biomonitoring odonates (dragonflies and damselflies), we here explore a new region of the CO1 gene (CO1B) for DNA barcoding in 51 populations of 23 dragonfly and damselfly species. We compare the "Folmer region", the mitochondrial ND1 gene (NADH dehydrogenase 1) and the new CO1 region with regard to (i) speed and reproducibility of sequence generation, (ii) levels of homoplasy and (iii) numbers of diagnostic characters for discriminating closely related sister taxa and populations. The performances of the gene regions regarding these criteria were quite different. Both, the amplification of CO1B and ND1 was highly reproducible and CO1B showed the highest potential for discriminating sister taxa at different taxonomic levels. In contrast, the amplification of the "Folmer region" using the universal primers was difficult and the third codon positions of this fragment have experienced nucleotide substitution saturation. Most important, exploring this new barcode region of the CO1 gene identified a higher discriminating power between closely related sister taxa. Together with the design of layered barcode approaches adapted to the specific taxonomic "environment", this new marker will further enhance the discrimination power at the species level.},
}
@article {pmid28406446,
year = {2017},
author = {Breviario, D},
title = {Is There any Alternative to Canonical DNA Barcoding of Multicellular Eukaryotic Species? A Case for the Tubulin Gene Family.},
journal = {International journal of molecular sciences},
volume = {18},
number = {4},
pages = {},
pmid = {28406446},
issn = {1422-0067},
mesh = {DNA/chemistry/metabolism ; *DNA Barcoding, Taxonomic ; Eukaryota/*genetics ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Tubulin/*genetics ; },
abstract = {Modern taxonomy is largely relying on DNA barcoding, a nucleotide sequence-based approach that provides automated species identification using short orthologous DNA regions, mainly of organellar origin when applied to multicellular Eukaryotic species. Target DNA loci have been selected that contain a minimal amount of nucleotide sequence variation within species while diverging among species. This strategy is quite effective for the identification of vertebrates and other animal lineages but poses a problem in plants where different combinations of two or three loci are constantly used. Even so, species discrimination in such plant categories as ornamentals and herbals remain problematic as well as the confident identification of subspecies, ecotypes, and closely related or recently evolved species. All these limitations may be successfully solved by the application of a different strategy, based on the use of a multi-locus, ubiquitous, nuclear marker, that is tubulin. In fact, the tubulin-based polymorphism method can release specific genomic profiles to any plant species independently from its taxonomic group. This offers the rare possibility of an effective yet generic genomic fingerprint. In a more general context, the issue is raised about the possibility that approaches alternative to systematic DNA sequencing may still provide useful and simple solutions.},
}
@article {pmid28405837,
year = {2017},
author = {Lehmitz, R and Decker, P},
title = {The nuclear 28S gene fragment D3 as species marker in oribatid mites (Acari, Oribatida) from German peatlands.},
journal = {Experimental &amp; applied acarology},
volume = {71},
number = {3},
pages = {259-276},
pmid = {28405837},
issn = {1572-9702},
mesh = {Animals ; Base Sequence ; DNA, Ribosomal/*chemistry/genetics ; Europe ; *Evolution, Molecular ; Genetic Markers ; Germany ; Mites/classification/*genetics ; Molecular Sequence Data ; Parthenogenesis/genetics ; Phylogeny ; RNA, Ribosomal, 28S/*chemistry/genetics ; Sequence Alignment ; Species Specificity ; },
abstract = {To make oribatid mites an applicable tool in monitoring programs it is necessary to find a molecular species marker that allows distinct, rapid and easy species identification. In previous studies, the common barcoding sequence COI showed to be too variable to serve as species marker in oribatid mites. The aim of the present study is to evaluate the potential use of the D3 region of the nuclear 28S rDNA gene for species identification. Therefore, we generated a reference DNA library of 28S D3 to identify specimens of the Oribatida from Germany, with focus on species occurring in peatlands being one of the most endangered habitats in Europe. New DNA sequences were obtained from 325 individuals and 64 species (58 genera, 34 families). By adding 28S D3-sequences from GenBank we altogether analysed 385 sequences from 89 German species, 32 of them restricted to peatlands and further 42 occurring in peatlands occasionally, representing 46 and 33% of the oribatids in German peatlands, respectively. P-distances were measured between species within families as well as for intraspecific divergence. 28S D3 showed low intraspecific genetic p-distances between 0 and 0.5%, interspecific distances within families varied between 0 and 9.7%. Most species pairs within families were further separated by one to four indels in addition to substitutions. Altogether, 93% of all analysed species are clearly delineated by 28S D3. Our study emphasises that 28S D3 rDNA is a useful barcode for the identification of oribatid mite specimens and represents an important step in building-up a comprehensive barcode library to allow metabarcoding analyses of environmental peatland samples for Oribatida in Germany as well as in Central Europe.},
}
@article {pmid28401958,
year = {2017},
author = {Wilkinson, MJ and Szabo, C and Ford, CS and Yarom, Y and Croxford, AE and Camp, A and Gooding, P},
title = {Replacing Sanger with Next Generation Sequencing to improve coverage and quality of reference DNA barcodes for plants.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {46040},
pmid = {28401958},
issn = {2045-2322},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; Databases, Genetic ; High-Throughput Nucleotide Sequencing/*methods ; Phylogeny ; Plants/*genetics ; Reference Standards ; Sonication ; Species Specificity ; },
abstract = {We estimate the global BOLD Systems database holds core DNA barcodes (rbcL + matK) for about 15% of land plant species and that comprehensive species coverage is still many decades away. Interim performance of the resource is compromised by variable sequence overlap and modest information content within each barcode. Our model predicts that the proportion of species-unique barcodes reduces as the database grows and that 'false' species-unique barcodes remain >5% until the database is almost complete. We conclude the current rbcL + matK barcode is unfit for purpose. Genome skimming and supplementary barcodes could improve diagnostic power but would slow new barcode acquisition. We therefore present two novel Next Generation Sequencing protocols (with freeware) capable of accurate, massively parallel de novo assembly of high quality DNA barcodes of >1400 bp. We explore how these capabilities could enhance species diagnosis in the coming decades.},
}
@article {pmid28399228,
year = {2017},
author = {Mashaly, A and Alajmi, R and Mustafa, AE and Rady, A and Alkhedir, H},
title = {Species Abundance and Identification of Forensically Important Flies of Saudi Arabia by DNA Barcoding.},
journal = {Journal of medical entomology},
volume = {54},
number = {4},
pages = {837-843},
doi = {10.1093/jme/tjx049},
pmid = {28399228},
issn = {1938-2928},
mesh = {Animals ; *Biota ; DNA Barcoding, Taxonomic ; Diptera/classification/genetics/*physiology ; Electron Transport Complex IV/genetics ; *Forensic Sciences ; Insect Proteins/genetics ; Phylogeny ; Population Density ; Saudi Arabia ; Sequence Analysis, DNA ; },
abstract = {Because they may demonstrate characteristics of the environment where a body has been laying prior to the discovery, flies are insects of forensic interest. We investigated the fly abundance and the effect of location in Kingdom of Saudi Arabia on fly species diversity that attack decomposing human and animal remains. Using baited traps deployed in each location, we collected 3,697 flies of seven species belonging to three families. Chrysomya albiceps Wiedmann represented 60.86% of the collected flies, whereas Musca domestica L. represented 25.8%; the other species made up < 6% each. To facilitate species identification by DNA barcoding, we sequenced a 710-bp "Folmer region" of cytochrome oxidase subunit 1 (COI) gene for 22 samples from collection sites distributed through entire Saudi Arabia. The COI sequences from Musca albina Wiedmann, Musca lucidula Loew, Musca calleva Walker, Musca sorbens Wiedmann, and Physiphora alceae Preyssler were obtained for the first time. This primary study indicates that even when Folmer primers were widely used in DNA barcoding, the Folmer's region is not adequate when discriminating between Musca species, and sequencing the whole COI or other genes is required for forensic purpose.},
}
@article {pmid28399227,
year = {2017},
author = {Inci, A and Yildirim, A and Duzlu, O and Onder, Z and Ciloglu, A and Seitz, G and Adler, PH},
title = {Genetic Diversity and Identification of Palearctic Black Flies in the Subgenus Wilhelmia (Diptera: Simuliidae).},
journal = {Journal of medical entomology},
volume = {54},
number = {4},
pages = {888-894},
doi = {10.1093/jme/tjw246},
pmid = {28399227},
issn = {1938-2928},
mesh = {Animals ; Electron Transport Complex IV/genetics ; Europe ; Female ; *Genetic Variation ; Insect Proteins/genetics ; Larva/classification/genetics ; Phylogeny ; Sequence Analysis, DNA ; Simuliidae/*classification/genetics/growth &amp; development ; Turkey ; },
abstract = {Accurate species identifications are the essential first step in understanding the medical, economic, and ecological importance of black flies. The utility of DNA barcoding based on cytochrome c oxidase subunit 1 (COI) sequences was evaluated for identifying six common species of Palearctic black flies in the subgenus Wilhelmia, including several that are virulent pests. Chromosomally identified larvae from Turkey and Germany and COI sequences in GenBank were analyzed. Intraspecific genetic divergence was 0.7-3.5% (mean 1.6%), whereas interspecific genetic divergence was 2.7-16.9%. On the basis of COI barcodes, the six nominal species of Simulium (Wilhelmia) were clustered in three distinct clades with high levels of genetic divergence, using maximum likelihood and Bayesian analyses. All specimens of Simulium equinum (L.), Simulium pseudequinum Séguy, and Simulium paraequinum Puri were correctly identified. However, >75% of identifications were ambiguous for Simulium lineatum (Meigen) and Simulium turgaicum Rubtsov (Meigen) because of overlapping intra- and interspecific divergence of the two species and Simulium balcanicum (Enderlein), all three of which are chromosomally similar and nearly isomorphic. Phylogenetic evaluation showed that S. balcanicum, S. equinum, S. pseudequinum, and S. paraequinum were monophyletic, with high bootstrap and posterior probability values, but it also showed that S. lineatum and S. turgaicum were paraphyletic, each clustering in two distinct groups, suggesting the presence of cryptic taxa. Although DNA barcoding provided a partial means of identification and indications of additional biodiversity, other molecular markers are needed to clarify the limits of all pest species of the subgenus Wilhelmia.},
}
@article {pmid28399213,
year = {2017},
author = {Solgi, R and Djadid, ND and Eslamifar, A and Raz, A and Zakeri, S},
title = {Morphological and Molecular Characteristic of Megaselia scalaris (Diptera: Phoridae) Larvae as the Cause of Urinary Myiasis.},
journal = {Journal of medical entomology},
volume = {54},
number = {3},
pages = {781-784},
doi = {10.1093/jme/tjw204},
pmid = {28399213},
issn = {1938-2928},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Diptera/anatomy &amp; histology/genetics/*physiology ; Electron Transport Complex IV/genetics ; Humans ; Insect Proteins/genetics ; Iran ; Larva/anatomy &amp; histology/genetics/physiology ; Male ; Middle Aged ; Myiasis/*diagnosis/parasitology ; Sequence Analysis, DNA ; Thailand ; Urologic Diseases/*diagnosis/parasitology ; },
abstract = {We report a case of urinary myiasis occurring in a 60-yr-old Iranian male patient with urinary tract problems and a history of travel to Thailand who was referred to Shafagh Medical Laboratory in Tehran (Iran). Larvae excreted in the patient's urine were confirmed by morphological identification key and DNA barcoding to belong to the species Megaselia scalaris Loew, which is known as the scuttle fly. Based on the patient's history, he was infected with M. scalaris in Thailand. To the best of our knowledge, this is the first report of urinary myiasis caused by M. scalaris in Thailand.},
}
@article {pmid28399170,
year = {2017},
author = {Wang, A and Gopurenko, D and Wu, H and Lepschi, B},
title = {Evaluation of six candidate DNA barcode loci for identification of five important invasive grasses in eastern Australia.},
journal = {PloS one},
volume = {12},
number = {4},
pages = {e0175338},
pmid = {28399170},
issn = {1932-6203},
mesh = {Australia ; *DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; *Introduced Species ; Phylogeny ; Poaceae/classification/*genetics ; Polymerase Chain Reaction ; },
abstract = {Invasive grass weeds reduce farm productivity, threaten biodiversity, and increase weed control costs. Identification of invasive grasses from native grasses has generally relied on the morphological examination of grass floral material. DNA barcoding may provide an alternative means to identify co-occurring native and invasive grasses, particularly during early growth stages when floral characters are unavailable for analysis. However, there are no universal loci available for grass barcoding. We herein evaluated the utility of six candidate loci (atpF intron, matK, ndhK-ndhC, psbE-petL, ETS and ITS) for barcode identification of several economically important invasive grass species frequently found among native grasses in eastern Australia. We evaluated these loci in 66 specimens representing five invasive grass species (Chloris gayana, Eragrostis curvula, Hyparrhenia hirta, Nassella neesiana, Nassella trichotoma) and seven native grass species. Our results indicated that, while no single locus can be universally used as a DNA barcode for distinguishing the grass species examined in this study, two plastid loci (atpF and matK) showed good distinguishing power to separate most of the taxa examined, and could be used as a dual locus to distinguish several of the invasive from the native species. Low PCR success rates were evidenced among two nuclear loci (ETS and ITS), and few species were amplified at these loci, however ETS was able to genetically distinguish the two important invasive Nassella species. Multiple loci analyses also suggested that ETS played a crucial role in allowing identification of the two Nassella species in the multiple loci combinations.},
}
@article {pmid28398809,
year = {2017},
author = {Mandecki, W and Kopacka, WM and Qian, Z and Ertwine, V and Gedzberg, K and Gruda, M and Reinhardt, D and Rodriguez, E},
title = {Tagging of Test Tubes with Electronic p-Chips for Use in Biorepositories.},
journal = {Biopreservation and biobanking},
volume = {15},
number = {4},
pages = {293-304},
pmid = {28398809},
issn = {1947-5543},
mesh = {*Biological Specimen Banks ; Computer Peripherals/economics/*standards ; Radio Frequency Identification Device/economics/standards ; Robotics ; Software ; Specimen Handling/*instrumentation/standards ; Temperature ; },
abstract = {A system has been developed to electronically tag and track test tubes used in biorepositories. The system is based on a light-activated microtransponder, also known as a "p-Chip." One of the pressing problems with storing and retrieving biological samples at low temperatures is the difficulty of reliably reading the identification (ID) number that links each storage tube with the database containing sample details. Commonly used barcodes are not always reliable at low temperatures because of poor adhesion of the label to the test tube and problems with reading under conditions of frost and ice accumulation. Traditional radio frequency identification (RFID) tags are not cost effective and are too large for this application. The system described herein consists of the p-Chip, p-Chip-tagged test tubes, two ID readers (for single tubes or for racks of tubes), and software. We also describe a robot that is configured for retrofitting legacy test tubes in biorepositories with p-Chips while maintaining the temperature of the sample below -50°C at all times. The main benefits of the p-Chip over other RFID devices are its small size (600 × 600 × 100 μm) that allows even very small tubes or vials to be tagged, low cost due to the chip's unitary construction, durability, and the ability to read the ID through frost and ice.},
}
@article {pmid28397362,
year = {2017},
author = {Roy, M and Vasco-Palacios, A and Geml, J and Buyck, B and Delgat, L and Giachini, A and Grebenc, T and Harrower, E and Kuhar, F and Magnago, A and Rinaldi, AC and Schimann, H and Selosse, MA and Sulzbacher, MA and Wartchow, F and Neves, MA},
title = {The (re)discovery of ectomycorrhizal symbioses in Neotropical ecosystems sketched in Florianópolis.},
journal = {The New phytologist},
volume = {214},
number = {3},
pages = {920-923},
doi = {10.1111/nph.14531},
pmid = {28397362},
issn = {1469-8137},
mesh = {Brazil ; Congresses as Topic ; DNA Barcoding, Taxonomic ; *Ecosystem ; Mycorrhizae/*physiology ; Plant Roots/*microbiology ; *Symbiosis ; },
}
@article {pmid28396495,
year = {2017},
author = {Belderbos, ME and Koster, T and Ausema, B and Jacobs, S and Sowdagar, S and Zwart, E and de Bont, E and de Haan, G and Bystrykh, LV},
title = {Clonal selection and asymmetric distribution of human leukemia in murine xenografts revealed by cellular barcoding.},
journal = {Blood},
volume = {129},
number = {24},
pages = {3210-3220},
doi = {10.1182/blood-2016-12-758250},
pmid = {28396495},
issn = {1528-0020},
mesh = {Adolescent ; Animals ; Child ; Child, Preschool ; Female ; Heterografts ; Humans ; Male ; Mice ; Mice, Inbred NOD ; Mice, Knockout ; Mice, SCID ; *Models, Immunological ; Neoplasm Transplantation ; Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/*immunology/pathology ; },
abstract = {Genetic and phenotypic heterogeneity of human leukemia is thought to drive leukemia progression through a Darwinian process of selection and evolution of increasingly malignant clones. However, the lack of markers that uniquely identify individual leukemia clones precludes high-resolution tracing of their clonal dynamics. Here, we use cellular barcoding to analyze the clonal behavior of patient-derived leukemia-propagating cells (LPCs) in murine xenografts. Using a leukemic cell line and diagnostic bone marrow cells from 6 patients with B-progenitor cell acute lymphoblastic leukemia, we demonstrate that patient-derived xenografts were highly polyclonal, consisting of tens to hundreds of LPC clones. The number of clones was stable within xenografts but strongly reduced upon serial transplantation. In contrast to primary recipients, in which clonal composition was highly diverse, clonal composition in serial xenografts was highly similar between recipients of the same donor and reflected donor clonality, supporting a deterministic, clone-size-based model for clonal selection. Quantitative analysis of clonal abundance in several anatomic sites identified 2 types of anatomic asymmetry. First, clones were asymmetrically distributed between different bones. Second, clonal composition in the skeleton significantly differed from extramedullary sites, showing similar numbers but different clone sizes. Altogether, this study shows that cellular barcoding and xenotransplantation providea useful model to study the behavior of patient-derived LPC clones, which provides insights relevant for experimental studies on cancer stem cells and for clinical protocols for the diagnosis and treatment of leukemia.},
}
@article {pmid28395577,
year = {2017},
author = {Renoux, LP and Dolan, MC and Cook, CA and Smit, NJ and Sikkel, PC},
title = {Developing an Apicomplexan DNA Barcoding System to Detect Blood Parasites of Small Coral Reef Fishes.},
journal = {The Journal of parasitology},
volume = {103},
number = {4},
pages = {366-376},
doi = {10.1645/16-93},
pmid = {28395577},
issn = {1937-2345},
mesh = {Animals ; Apicomplexa/*classification/genetics ; Bayes Theorem ; Coral Reefs ; *DNA Barcoding, Taxonomic/veterinary ; DNA, Protozoan/blood/chemistry ; DNA, Ribosomal/chemistry ; Fish Diseases/blood/epidemiology/*parasitology ; Fishes ; Likelihood Functions ; Parasitemia/epidemiology/parasitology/*veterinary ; Phylogeny ; Polymerase Chain Reaction/veterinary ; Protozoan Infections, Animal/blood/epidemiology/*parasitology ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Alignment ; United States Virgin Islands/epidemiology ; },
abstract = {Apicomplexan parasites are obligate parasites of many species of vertebrates. To date, there is very limited understanding of these parasites in the most-diverse group of vertebrates, actinopterygian fishes. While DNA barcoding targeting the eukaryotic 18S small subunit rRNA gene sequence has been useful in identifying apicomplexans in tetrapods, identification of apicomplexans infecting fishes has relied solely on morphological identification by microscopy. In this study, a DNA barcoding method was developed that targets the 18S rRNA gene primers for identifying apicomplexans parasitizing certain actinopterygian fishes. A lead primer set was selected showing no cross-reactivity to the overwhelming abundant host DNA and successfully confirmed 37 of the 41 (90.2%) microscopically verified parasitized fish blood samples analyzed in this study. Furthermore, this DNA barcoding method identified 4 additional samples that screened negative for parasitemia, suggesting this molecular method may provide improved sensitivity over morphological characterization by microscopy. In addition, this PCR screening method for fish apicomplexans, using Whatman FTA preserved DNA, was tested in efforts leading to a more simplified field collection, transport, and sample storage method as well as a streamlining sample processing important for DNA barcoding of large sample sets.},
}
@article {pmid28395362,
year = {2017},
author = {Tomasello, S and Heubl, G},
title = {Phylogenetic Analysis and Molecular Characterization of Xanthium sibiricum Using DNA Barcoding, PCR-RFLP, and Specific Primers.},
journal = {Planta medica},
volume = {83},
number = {11},
pages = {946-953},
doi = {10.1055/s-0043-106585},
pmid = {28395362},
issn = {1439-0221},
mesh = {DNA Barcoding, Taxonomic ; DNA Primers ; Genetic Markers ; Molecular Typing/*methods ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Xanthium/*classification/genetics ; },
abstract = {The fruits of Xanthium sibiricum have been widely used in traditional Chinese medicine for the treatment of nasal sinusitis and headaches. The genus Xanthium (cocklebur) is a taxonomically complex genus. Different taxonomic concepts have been proposed, some including several species, others lumping the different taxa in a few extremely polymorphic species. Due to the morphological similarities between species, the correct authentication of X. sibiricum is very difficult. Therefore, we established a polymerase chain reaction-restriction fragment length polymorphism method and diagnostic PCR based on nuclear internal transcribed spacer and chloroplast trnQ-rps16 barcodes to differentiate X. sibirium from related species.Results from the phylogenetic analyses based on sequence information from four marker regions (plastidal psbA-trnH and trnQ-rps16 and nuclear ITS and D35) support those taxonomic concepts accepting a reduced number of species, as four to five major clades are revealed in the phylogenetic reconstructions. X. sibiricum, together with some accessions from closely related taxa, is always supported as monophyletic, constituting a well-defined genetic entity. Allele-specific primer pairs for ITS and trnQ-rps16 were designed to amplify diagnostic products from the genomic DNA of X. sibiricum. Specific PCR in combination with digestion using the restriction enzyme MseI allowed for the identification of X. sibiricum by producing specific restriction patterns. The results demonstrate that the applied techniques provide effective and accurate authentication of X. sibiricum.},
}
@article {pmid28394451,
year = {2017},
author = {Der Sarkissian, C and Pichereau, V and Dupont, C and Ilsøe, PC and Perrigault, M and Butler, P and Chauvaud, L and Eiríksson, J and Scourse, J and Paillard, C and Orlando, L},
title = {Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past.},
journal = {Molecular ecology resources},
volume = {17},
number = {5},
pages = {835-853},
doi = {10.1111/1755-0998.12679},
pmid = {28394451},
issn = {1755-0998},
mesh = {*Animal Shells ; Animals ; Aquatic Organisms/genetics ; *Body Remains ; DNA/chemistry/genetics/isolation &amp; purification ; DNA, Ancient/*analysis/chemistry ; DNA, Bacterial/chemistry/genetics/isolation &amp; purification ; Metagenomics/*methods ; Mollusca/*genetics ; *Sequence Analysis, DNA ; Vibrio/genetics ; },
abstract = {Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro-) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA extraction, high-throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome-scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA research, with the potential to reconstruct the evolutionary history of molluscs, microbial communities and pathogens in the face of environmental changes. Other future applications include conservation of endangered mollusc species and aquaculture management.},
}
@article {pmid28392984,
year = {2017},
author = {Bieler, R and Granados-Cifuentes, C and Rawlings, TA and Sierwald, P and Collins, TM},
title = {Non-native molluscan colonizers on deliberately placed shipwrecks in the Florida Keys, with description of a new species of potentially invasive worm-snail (Gastropoda: Vermetidae).},
journal = {PeerJ},
volume = {5},
number = {},
pages = {e3158},
pmid = {28392984},
issn = {2167-8359},
abstract = {Artificial reefs created by deliberately sinking ships off the coast of the Florida Keys island chain are providing new habitat for marine invertebrates. This newly developing fouling community includes the previously reported invasive orange tube coral Tubastraea coccinea and the non-native giant foam oyster Hyotissa hyotis. New SCUBA-based surveys involving five shipwrecks spanning the upper, middle, and lower Florida Keys, show T. coccinea now also established in the lower Keys and H. hyotis likewise extending to new sites. Two additional mollusks found on the artificial reefs, the amathinid gastropod Cyclothyca pacei and gryphaeid oyster Hyotissa mcgintyi, the latter also common in the natural reef areas, are discussed as potentially non-native. A new species of sessile, suspension-feeding, worm-snail, Thylacodes vandyensis Bieler, Rawlings &amp; Collins n. sp. (Vermetidae), is described from the wreck of the USNS Vandenberg off Key West and discussed as potentially invasive. This new species is compared morphologically and by DNA barcode markers to other known members of the genus, and may be a recent arrival from the Pacific Ocean. Thylacodes vandyensis is polychromatic, with individuals varying in both overall head-foot coloration and mantle margin color pattern. Females brood stalked egg capsules attached to their shell within the confines of their mantle cavity, and give rise to crawl-away juveniles. Such direct-developing species have the demonstrated capacity for colonizing habitats isolated far from their native ranges and establishing rapidly growing founder populations. Vermetid gastropods are common components of the marine fouling community in warm temperate and tropical waters and, as such, have been tagged as potentially invasive or with a high potential to be invasive in the Pacific Ocean. As vermetids can influence coral growth/composition in the Pacific and have been reported serving as intermediate hosts for blood flukes of loggerhead turtles, such new arrivals in the Florida Keys National Marine Sanctuary are of concern. Growing evidence indicates that artificial reefs can act as permanent way-stations for arriving non-natives, providing nurseries within which populations may grow in an environment with reduced competition compared to native habitats. Consequently, artificial reefs can act as sentinels for the appearance of new species. Ongoing monitoring of the developing molluscan fauna on the artificial reefs of the Florida Keys is necessary to recognize new invasions and identify potential eradication targets, thereby assuring the health of the nearby natural barrier reef.},
}
@article {pmid28390505,
year = {2017},
author = {Luo, J and Walsh, E and Miller, S and Blystone, D and Dighton, J and Zhang, N},
title = {Root endophytic fungal communities associated with pitch pine, switchgrass, and rosette grass in the pine barrens ecosystem.},
journal = {Fungal biology},
volume = {121},
number = {5},
pages = {478-487},
doi = {10.1016/j.funbio.2017.01.005},
pmid = {28390505},
issn = {1878-6146},
mesh = {*Biota ; DNA Barcoding, Taxonomic ; Endophytes/*classification/cytology/genetics/*isolation &amp; purification ; Phylogeny ; Pinus/*microbiology ; Plant Roots/*microbiology ; Poaceae/*microbiology ; },
abstract = {Almost all plants in nature harbour fungi in their roots but the knowledge on distribution and the underlying principles of assemblage is still poorly developed for the root-associated fungi. In this study we analysed the root endophytic fungal communities associated with switchgrass, rosette grass, and pitch pine in the acidic, oligotrophic pine barrens ecosystem. A total of 434 fungal isolates were obtained from 600 root segments of 60 plant samples. DNA barcoding and morphological analyses identified 92 fungal species, which belong to 39 genera in six classes. Compared to other ecosystems, the pine barrens has a higher proportion of Leotiomycetes. The fungal community associated with pitch pine was significantly different from those associated with the grasses, while less difference was found between those associated with the two grasses. Our results suggest that edaphic factors and host specificity play a role in shaping root endophytic fungal community. This study also corroborates our previous finding that plant roots in the pine barrens are a rich reservoir of novel fungi.},
}
@article {pmid28386949,
year = {2017},
author = {Gomes, P and Vieira, AR and Oliveira, R and Silva, H and Martins, R and Carneiro, M},
title = {First record of Cynoscion regalis (Pisces, Sciaenidae) in Portuguese continental waters.},
journal = {Journal of fish biology},
volume = {90},
number = {6},
pages = {2470-2474},
doi = {10.1111/jfb.13318},
pmid = {28386949},
issn = {1095-8649},
mesh = {Animal Distribution ; Animals ; Atlantic Ocean ; Fishes/anatomy &amp; histology/*classification/physiology ; Genes, Mitochondrial ; Portugal ; },
abstract = {The occurrence of Cynoscion regalis in Portuguese continental waters is reported for the first time, with six specimens collected in 2015 from three areas: Tagus Estuary, Sado Estuary and Praia da Vieira (central-west coast). Analyses of morphometric and meristic characteristics confirmed all six specimens as C. regalis; further validation was obtained by sequencing a 675 bp region of the mitochondrial cytochrome c oxidase I gene. These records constitute a range extension of C. regalis into the southern north-east Atlantic Ocean.},
}
@article {pmid28382937,
year = {2017},
author = {de Brida, AL and Rosa, JM and Oliveira, CM and Castro, BM and Serrão, JE and Zanuncio, JC and Leite, LG and Wilcken, SR},
title = {Entomopathogenic nematodes in agricultural areas in Brazil.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {45254},
pmid = {28382937},
issn = {2045-2322},
mesh = {Agriculture ; Animals ; Brazil ; DNA Barcoding, Taxonomic ; Lepidoptera/*parasitology ; Nematoda/genetics/growth &amp; development/isolation &amp; purification/*pathogenicity ; RNA, Ribosomal, 28S/genetics ; Soil/*parasitology ; },
abstract = {Entomopathogenic nematodes (EPNs) (Steinernematidae and Heterorhabditidae) can control pests due to the mutualistic association with bacteria that kill the host by septicemia and make the environment favorable for EPNs development and reproduction. The diversity of EPNs in Brazilian soils requires further study. The identification of EPNs, adapted to environmental and climatic conditions of cultivated areas is important for sustainable pest suppression in integrated management programs in agricultural areas of Brazil. The objective was to identify EPNs isolated from agricultural soils with annual, fruit and forest crops in Brazil. Soil samples were collected and stored in 250 ml glass vials. The nematodes were isolated from these samples with live bait traps ([Galleria mellonella L. (Lepidoptera: Pyralidae) larvae]. Infective juveniles were collected with White traps and identified by DNA barcoding procedures by sequencing the D2/D3 expansion of the 28S rDNA region by PCR. EPNs identified in agricultural areas in Brazil were Heterorhabditis amazonensis, Metarhabditis rainai, Oscheios tipulae and Steinernema rarum. These species should be considered pest biocontrol agents in Brazilian agricultural areas.},
}
@article {pmid28382652,
year = {2017},
author = {Pérez-Izquierdo, L and Morin, E and Maurice, JP and Martin, F and Rincón, A and Buée, M},
title = {A new promising phylogenetic marker to study the diversity of fungal communities: The Glycoside Hydrolase 63 gene.},
journal = {Molecular ecology resources},
volume = {17},
number = {6},
pages = {e1-e11},
doi = {10.1111/1755-0998.12678},
pmid = {28382652},
issn = {1755-0998},
mesh = {Cluster Analysis ; DNA Primers/genetics ; DNA, Fungal/chemistry/genetics ; Fungi/*classification/*enzymology/genetics ; *Genetic Variation ; Glycoside Hydrolases/*genetics ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {In molecular ecology, the development of efficient molecular markers for fungi remains an important research domain. Nuclear ribosomal internal transcribed spacer (ITS) region was proposed as universal DNA barcode marker for fungi, but this marker was criticized for Indel-induced alignment problems and its potential lack of phylogenetic resolution. Our main aim was to develop a new phylogenetic gene and a putative functional marker, from single-copy gene, to describe fungal diversity. Thus, we developed a series of primers to amplify a polymorphic region of the Glycoside Hydrolase GH63 gene, encoding exo-acting α-glucosidases, in basidiomycetes. These primers were validated on 125 different fungal genomic DNAs, and GH63 amplification yield was compared with that of already published functional markers targeting genes coding for laccases, N-acetylhexosaminidases, cellobiohydrolases and class II peroxidases. Specific amplicons were recovered for 95% of the fungal species tested, and GH63 amplification success was strikingly higher than rates obtained with other functional genes. We downloaded the GH63 sequences from 483 fungal genomes publicly available at the JGI mycocosm database. GH63 was present in 461 fungal genomes belonging to all phyla, except Microsporidia and Neocallimastigomycota divisions. Moreover, the phylogenetic trees built with both GH63 and Rpb1 protein sequences revealed that GH63 is also a promising phylogenetic marker. Finally, a very high proportion of GH63 proteins was predicted to be secreted. This molecular tool could be a new phylogenetic marker of fungal species as well as potential indicator of functional diversity of basidiomycetes fungal communities in term of secretory capacities.},
}
@article {pmid28371153,
year = {2017},
author = {Qiu, X and Guo, J and Jin, Z and Petreto, A and Medintz, IL and Hildebrandt, N},
title = {Multiplexed Nucleic Acid Hybridization Assays Using Single-FRET-Pair Distance-Tuning.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {13},
number = {25},
pages = {},
doi = {10.1002/smll.201700332},
pmid = {28371153},
issn = {1613-6829},
abstract = {Multiplexed photoluminescence (PL) detection plays an important role in chemical and biological sensing. Here, it is shown that time-gated (TG) detection of a single terbium-donor-based Förster resonance energy transfer (FRET) pair can be used to selectively quantify low nanomolar concentrations of multiple DNAs or microRNAs in a single sample. This study demonstrates the applicability of single-TG-FRET-pair multiplexing for molecular (Tb-to-dye) and nanoparticle (Tb-to-quantum-dot) biosensing. Both systems use acceptor-sensitization and donor-quenching for quantifying biomolecular recognition and modification of the donor-acceptor distance for tuning the PL decays. TG intensity detection provides extremely low background noise and a quick and simple one-step assay format. Single-TG-FRET-pair multiplexing can be combined with spectral and spatial resolution, paving the way for biosensing with unprecedented high-order multiplexing capabilities.},
}
@article {pmid28370147,
year = {2017},
author = {Talavera, S and Muñoz-Muñoz, F and Verdún, M and Pagès, N},
title = {Morphology and DNA barcoding reveal three species in one: description of Culicoides cryptipulicaris sp. nov. and Culicoides quasipulicaris sp. nov. in the subgenus Culicoides.},
journal = {Medical and veterinary entomology},
volume = {31},
number = {2},
pages = {178-191},
doi = {10.1111/mve.12228},
pmid = {28370147},
issn = {1365-2915},
mesh = {Animals ; Bluetongue/virology ; Ceratopogonidae/anatomy &amp; histology/*classification/genetics ; DNA Barcoding, Taxonomic/veterinary ; Female ; Insect Vectors/anatomy &amp; histology/*classification/genetics ; Male ; Phylogeny ; Sequence Analysis, DNA/veterinary ; Spain ; },
abstract = {Species of the genus Culicoides (Diptera: Ceratopogonidae) are well known for their importance in the field of medical and veterinary entomology. Culicoides spp. transmit a wide variety of pathogens, primarily viruses that affect animals and humans. In Europe, the most economically important disease transmitted by Culicoides is bluetongue (BT). Culicoides spp. have been recently involved as primary vectors for Schmallenberg disease. The taxonomy within the subgenus Culicoides has been historically difficult and reorganizations have been proposed regularly. The subgenus Culicoides includes species that are considered to be potential vectors for BT. High morphological intraspecific variability has been attributed to these species. This highlights the apparent presence of previously undetected cryptic species diversity in the subgenus. In the present study, a detailed morphological and molecular study of specimens belonging to Culicoides pulicaris s.l. and specimens resembling a cross between C. pulicaris and Culicoides punctatus revealed the presence of two new species: Culicoides cryptipulicaris and Culicoides quasipulicaris. Females of C. quasipulicaris and males of both species were morphologically distinguished from C. pulicaris (Linnaeus, 1758), whereas females of C. cryptipulicaris were identified using molecular techniques exclusively.},
}
@article {pmid28370102,
year = {2017},
author = {Xi, X and Yang, Y and Yang, Y and Segoli, M and Sun, S},
title = {Plant-mediated resource partitioning by coexisting parasitoids.},
journal = {Ecology},
volume = {98},
number = {6},
pages = {1660-1670},
doi = {10.1002/ecy.1834},
pmid = {28370102},
issn = {0012-9658},
mesh = {Animals ; Asteraceae ; *Ecosystem ; *Herbivory ; *Host-Parasite Interactions ; Phenotype ; *Plants ; Wasps ; },
abstract = {Although it has been frequently suggested that resource partitioning of species coexisting at the same trophic level can be mediated by interactions with species at non-adjacent trophic levels, empirical evidence supporting this claim is scarce. Here we demonstrate that plants may mediate resource partitioning for two parasitoids that share the same herbivorous host. The tephritid fly Tephritis femoralis is the primary pre-dispersal seed predator of two Asteraceae species, Saussurea nigrescens and Anaphalis flavescens, both of which dominate the plant community in the alpine meadows of the Tibetan Plateau. Field surveys and molecular barcoding analyses showed that the identity of the fly's main predator depended on the plant in which the fly developed. Tephritid flies that developed in S. nigrescens were preyed upon mainly by the parasitoid wasp Pteromalus albipennis, while the parasitoid Mesopolobus sp. was the main predator of flies that developed in A. flavescens. Microcosm experiments revealed that P. albipennis could not exploit the host flies within the capitula of A. flavescens due to food limitation (capitula are too small), while Mesopolobus sp. could not exploit the host flies within the capitula of S. nigrescens due to its inability to reach the host with its ovipositor (capitula are too large). Such bottom-up control of plant species traits may facilitate the coexistence of parasitoid wasps sharing a common host in this system. We suggest that interactions between non-adjacent trophic levels may potentially promote species coexistence and diversity in biological communities.},
}
@article {pmid28367371,
year = {2017},
author = {Santos, L and Alves, A and Alves, R},
title = {Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe.},
journal = {PeerJ},
volume = {5},
number = {},
pages = {e3120},
pmid = {28367371},
issn = {2167-8359},
abstract = {BACKGROUND: Species identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genus Diaporthe. Accurate Diaporthe species separation requires using multi-loci phylogenies. However, defining the optimal set of loci that can be used for species identification is still an open problem.<br><br>METHODS: Here we addressed that problem by identifying five loci that have been sequenced in 142 Diaporthe isolates representing 96 species: TEF1, TUB, CAL, HIS and ITS. We then used every possible combination of those loci to build, analyse, and compare phylogenetic trees.<br><br>RESULTS: As expected, species separation is better when all five loci are simultaneously used to build the phylogeny of the isolates. However, removing the ITS locus has little effect on reconstructed phylogenies, identifying the TEF1-TUB-CAL-HIS 4-loci tree as almost equivalent to the 5-loci tree. We further identify the best 3-loci, 2-loci, and 1-locus trees that should be used for species separation in the genus.<br><br>DISCUSSION: Our results question the current use of the ITS locus for DNA barcoding in the genus Diaporthe and suggest that TEF1 might be a better choice if one locus barcoding needs to be done.},
}
@article {pmid28367369,
year = {2017},
author = {Montes, M and Rico, JM and García-Vazquez, E and Borrell Pichs, YJ},
title = {Molecular barcoding confirms the presence of exotic Asian seaweeds (Pachymeniopsis gargiuli and Grateloupia turuturu) in the Cantabrian Sea, Bay of Biscay.},
journal = {PeerJ},
volume = {5},
number = {},
pages = {e3116},
pmid = {28367369},
issn = {2167-8359},
abstract = {BACKGROUND: The introduction of exotic species can have serious consequences for marine ecosystems. On the shores of the Cantabrian Sea (North of Spain) there are no routine examinations of seaweeds that combine molecular and morphological methods for early detection of exotic species making it difficult to assess in the early stages their establishment and expansion processes as a result of anthropogenic activities (e.g., shipping and/or aquaculture).<br><br>METHODS: In this work we used both morphological identification and molecular barcoding (COI-5P and rbcL genes) of red algae collected in Asturias, Bay of Biscay (Gij&#xf3;n and Cand&#xe1;s harbours) and from the University of Oviedo's herbarium samples.<br><br>RESULTS: The results confirmed the presence of exotic Asian seaweeds Pachymeniopsis gargiuli and Grateloupia turuturu Yamada on Cantabrian Sea shores. Several individuals of these species were fertile and developing cystocarps when collected, underlining the risk of possible expansion or continued establishment. This study constitutes the first report of the Asian P. gargiuli in this area of the Bay of Biscay.<br><br>CONCLUSIONS: Here the presence of the exotic species of the Halymeniales P.&#xa0;gargiuli is confirmed. We hypothesize that this species may have been established some time ago as a cryptic introduction with G. turuturu in Galician shores. The detection of these species on the shores of the Cantabrian Sea is relevant since introductions of Pachymeniopsis species could have been overlooked on other European coasts, probably mixed with G. turuturu and P. lanceolata. Our results confirm one new alien seaweed species that has been detected using molecular methods (COI-5P region and rbcL genes barcoding) on North Atlantic shores: the Asian native P. gargiuli. This demonstrates that routine screening for early detection of exotic algae in the Cantabrian Sea can be used for risk assessment. Genetic barcoding should be done using both rbcL gene and COI-5P regions since, although COI-databases are still poorer in sequences and this inhibits successful outcomes in Grateloupia-related species identifications, it is nonetheless a useful marker for species-level identifications in seaweeds.},
}
@article {pmid28366623,
year = {2017},
author = {Kikkawa, HS and Tsuge, K and Kubota, S and Aragane, M and Ohta, H and Sugita, R},
title = {Species identification of white false hellebore (Veratrum album subsp. oxysepalum) using real-time PCR.},
journal = {Forensic science international},
volume = {275},
number = {},
pages = {160-166},
doi = {10.1016/j.forsciint.2017.02.002},
pmid = {28366623},
issn = {1872-6283},
mesh = {DNA, Plant/genetics ; Foodborne Diseases ; Humans ; Multiplex Polymerase Chain Reaction/methods ; Plants, Toxic/*genetics ; Real-Time Polymerase Chain Reaction/*methods ; Veratrum/*genetics ; },
abstract = {Food poisoning is frequently caused by the accidental ingestion of toxic plants that possess strong morphological similarities to edible plants. False helleborine (Veratrum album) is one of the most common plants involved in such accidents. In cases of poisoning by toxic plants, rapid and accurate identification, usually based on the morphological or chemical analysis of plant parts, is required for appropriate medical treatment or forensic investigation. However, morphological examinations require experience in systematic botany because the samples are fragmentary, and chemical analysis of natural compounds can be difficult. In this study, we developed a TaqMan real-time PCR method using trnH-psbA and trnL-trnF that could be carried out in 30-60min. The lower detection limit was less than 10pg of DNA and the primer sets were specific to V. album and Veratrum stamineum. Mixed samples, cooked samples, and simulated gastric contents were successfully identified, and a multiplex assay of two regions was also possible. These results indicate that the TaqMan real-time PCR analysis is a very effective method to detect small samples of V. album and V. stamineum accurately and rapidly in poisoning cases.},
}
@article {pmid28365726,
year = {2017},
author = {Li, FW and Rushworth, CA and Beck, JB and Windham, MD},
title = {Boechera microsatellite website: an online portal for species identification and determination of hybrid parentage.},
journal = {Database : the journal of biological databases and curation},
volume = {2017},
number = {1},
pages = {},
pmid = {28365726},
issn = {1758-0463},
mesh = {Alleles ; Arabidopsis/classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; Evolution, Molecular ; *Internet ; *Microsatellite Repeats ; *Sequence Analysis, DNA ; },
abstract = {UNLABELLED: Boechera (Brassicaceae) has many features to recommend it as a model genus for ecological and evolutionary research, including species richness, ecological diversity, experimental tractability and close phylogenetic proximity to Arabidopsis . However, efforts to realize the full potential of this model system have been thwarted by the frequent inability of researchers to identify their samples and place them in a broader evolutionary context. Here we present the Boechera Microsatellite Website (BMW), a portal that archives over 55 000 microsatellite allele calls from 4471 specimens (including 133 nomenclatural types). The portal includes analytical tools that utilize data from 15 microsatellite loci as a highly effective DNA barcoding system. The BMW facilitates the accurate identification of Boechera samples and the investigation of reticulate evolution among the ±83 sexual diploid taxa in the genus, thereby greatly enhancing Boechera 's potential as a model system.<br><br>DATABASE URL: http://sites.biology.duke.edu/windhamlab/.},
}
@article {pmid28362164,
year = {2017},
author = {Maschmann, A and Kounovsky-Shafer, KL},
title = {Determination of restriction enzyme activity when cutting DNA labeled with the TOTO dye family.},
journal = {Nucleosides, nucleotides &amp; nucleic acids},
volume = {36},
number = {6},
pages = {406-417},
doi = {10.1080/15257770.2017.1300665},
pmid = {28362164},
issn = {1532-2335},
mesh = {DNA/*chemistry/*metabolism ; DNA Restriction Enzymes/antagonists &amp; inhibitors/*metabolism ; Fluorescent Dyes/*chemistry ; Models, Molecular ; Nucleic Acid Conformation ; Quinolinium Compounds/*chemistry ; Staining and Labeling ; Thiazoles/*chemistry ; },
abstract = {Optical mapping, a single DNA molecule genome analysis platform that can determine methylation profiles, uses fluorescently labeled DNA molecules that are elongated on the surface and digested with a restriction enzyme to produce a barcode of that molecule. Understanding how the cyanine fluorochromes affect enzyme activity can lead to other fluorochromes used in the optical mapping system. The effects of restriction digestion on fluorochrome labeled DNA (Ethidium Bromide, DAPI, H33258, EthD-1, TOTO-1) have been analyzed previously. However, TOTO-1 is a part of a family of cyanine fluorochromes (YOYO-1, TOTO-1, BOBO-1, POPO-1, YOYO-3, TOTO-3, BOBO-3, and POPO-3) and the rest of the fluorochromes have not been examined in terms of their effects on restriction digestion. In order to determine if the other dyes in the TOTO-1 family inhibit restriction enzymes in the same way as TOTO-1, lambda DNA was stained with a dye from the TOTO family and digested. The restriction enzyme activity in regards to each dye, as well as each restriction enzyme, was compared to determine the extent of digestion. YOYO-1, TOTO-1, and POPO-1 fluorochromes inhibited ScaI-HF, PmlI, and EcoRI restriction enzymes. Additionally, the mobility of labeled DNA fragments in an agarose gel changed depending on which dye was intercalated.},
}
@article {pmid28358863,
year = {2017},
author = {Schäffer, S and Zachos, FE and Koblmüller, S},
title = {Opening the treasure chest: A DNA-barcoding primer set for most higher taxa of Central European birds and mammals from museum collections.},
journal = {PloS one},
volume = {12},
number = {3},
pages = {e0174449},
pmid = {28358863},
issn = {1932-6203},
mesh = {Animals ; Birds/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; Europe ; Mammals/*classification/*genetics ; *Museums ; },
abstract = {DNA-barcoding is a rapidly developing method for efficiently identifying samples to species level by means of short standard DNA sequences. However, reliable species assignment requires the availability of a comprehensive DNA barcode reference library, and hence numerous initiatives aim at generating such barcode databases for particular taxa or geographic regions. Historical museum collections represent a potentially invaluable source for the DNA-barcoding of many taxa. This is particularly true for birds and mammals, for which collecting fresh (voucher) material is often very difficult to (nearly) impossible due to the special animal welfare and conservation regulations that apply to vertebrates in general, and birds and mammals in particular. Moreover, even great efforts might not guarantee sufficiently complete sampling of fresh material in a short period of time. DNA extracted from historical samples is usually degraded, such that only short fragments can be amplified, rendering the recovery of the barcoding region as a single fragment impossible. Here, we present a new set of primers that allows the efficient amplification and sequencing of the entire barcoding region in most higher taxa of Central European birds and mammals in six overlapping fragments, thus greatly increasing the value of historical museum collections for generating DNA barcode reference libraries. Applying our new primer set in recently established NGS protocols promises to further increase the efficiency of barcoding old bird and mammal specimens.},
}
@article {pmid28355106,
year = {2017},
author = {Santos, ARD and Usso, MC and Gouveia, JG and Araya-Jaime, C and Frantine-Silva, W and Giuliano-Caetano, L and Foresti, F and Dias, AL},
title = {Chromosomal Mapping of Repetitive DNA Sequences in the Genus Bryconamericus (Characidae) and DNA Barcoding to Differentiate Populations.},
journal = {Zebrafish},
volume = {14},
number = {3},
pages = {261-271},
doi = {10.1089/zeb.2016.1380},
pmid = {28355106},
issn = {1557-8542},
mesh = {Animals ; Characidae/*classification/*genetics ; Chromosome Mapping/*methods ; DNA Barcoding, Taxonomic/*methods ; Genetic Variation ; *Genetics, Population ; In Situ Hybridization, Fluorescence/methods ; Karyotyping ; *Repetitive Sequences, Nucleic Acid ; },
abstract = {The mapping of repetitive DNA sites by fluorescence in situ hybridization has been widely used for karyotype studies in different species of fish, especially when dealing with related species or even genera presenting high chromosome variability. This study analyzed three populations of Bryconamericus, with diploid number preserved, but with different karyotype formulae. Bryconamericus ecai, from the Forquetinha river/RS, presented three new cytotypes, increasing the number of karyotype forms to seven in this population. Other two populations of Bryconamericus sp. from the Vermelho stream/PR and Cambuta river/PR exhibited interpopulation variation. The chromosome mapping of rDNA sites revealed unique markings among the three populations, showing inter- and intrapopulation variability located in the terminal region. The molecular analysis using DNA barcoding complementing the cytogenetic analysis also showed differentiation among the three populations. The U2 small nuclear DNA repetitive sequence exhibited conserved features, being located in the interstitial region of a single chromosome pair. This is the first report on its occurrence in the genus Bryconamericus. Data obtained revealed a karyotype variability already assigned to the genus, along with polymorphism of ribosomal sites, demonstrating that this group of fish can be undergoing a divergent evolutionary process, constituting a substantive model for studies of chromosomal evolution.},
}
@article {pmid28346340,
year = {2017},
author = {Waterworth, SC and Jiwaji, M and Kalinski, JJ and Parker-Nance, S and Dorrington, RA},
title = {A Place to Call Home: An Analysis of the Bacterial Communities in Two Tethya rubra Samaai and Gibbons 2005 Populations in Algoa Bay, South Africa.},
journal = {Marine drugs},
volume = {15},
number = {4},
pages = {},
pmid = {28346340},
issn = {1660-3397},
mesh = {Animals ; Bacteria/*genetics ; Bays/*microbiology ; Biodiversity ; DNA, Bacterial/genetics ; Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA/methods ; South Africa ; },
abstract = {Sponges are important sources of bioactive secondary metabolites. These compounds are frequently synthesized by bacterial symbionts, which may be recruited from the surrounding seawater or transferred to the sponge progeny by the parent. In this study, we investigated the bacterial communities associated with the sponge Tethya rubra Samaai and Gibbons 2005. Sponge specimens were collected from Evans Peak and RIY Banks reefs in Algoa Bay, South Africa and taxonomically identified by spicule analysis and molecular barcoding. Crude chemical extracts generated from individual sponges were profiled by ultraviolet high performance liquid chromatography (UV-HPLC) and subjected to bioactivity assays in mammalian cells. Next-generation sequencing analysis of 16S rRNA gene sequences was used to characterize sponge-associated bacterial communities. T. rubra sponges collected from the two locations were morphologically and genetically indistinguishable. Chemical extracts from sponges collected at RIY banks showed mild inhibition of the metabolic activity of mammalian cells and their UV-HPLC profiles were distinct from those of sponges collected at Evans Peak. Similarly, the bacterial communities associated with sponges from the two locations were distinct with evidence of vertical transmission of symbionts from the sponge parent to its embryos. We conclude that these distinct bacterial communities may be responsible for the differences observed in the chemical profiles of the two Algoa Bay T. rubra Samaai and Gibbons 2005 populations.},
}
@article {pmid28342375,
year = {2017},
author = {Lin, X and Liu, Y and Tao, Z and Gao, J and Deng, J and Yin, J and Wang, S},
title = {Nanozyme-based bio-barcode assay for high sensitive and logic-controlled specific detection of multiple DNAs.},
journal = {Biosensors &amp; bioelectronics},
volume = {94},
number = {},
pages = {471-477},
doi = {10.1016/j.bios.2017.01.008},
pmid = {28342375},
issn = {1873-4235},
mesh = {*Biosensing Techniques ; DNA, Viral/chemistry/*isolation &amp; purification ; HIV/chemistry/*isolation &amp; purification ; HIV Infections/diagnosis/virology ; Hepacivirus/chemistry/*isolation &amp; purification ; Hepatitis C/diagnosis/virology ; Humans ; Nanoparticles/chemistry ; Spectrometry, Fluorescence ; },
abstract = {Since HCV and HIV share a common transmission path, high sensitive detection of HIV and HCV gene is of significant importance to improve diagnosis accuracy and cure rate at early stage for HIV virus-infected patients. In our investigation, a novel nanozyme-based bio-barcode fluorescence amplified assay is successfully developed for simultaneous detection of HIV and HCV DNAs with excellent sensitivity in an enzyme-free and label-free condition. Here, bimetallic nanoparticles, PtAuNPs, present outstanding peroxidase-like activity and act as barcode to catalyze oxidation of nonfluorescent substrate of amplex red (AR) into fluorescent resorufin generating stable and sensitive "Turn On" fluorescent output signal, which is for the first time to be integrated with bio-barcode strategy for fluorescence detection DNA. Furthermore, the provided strategy presents excellent specificity and can distinguish single-base mismatched mutant from target DNA. What interesting is that cascaded INHIBIT-OR logic gate is integrated with biosensors for the first time to distinguish individual target DNA from each other under logic function control, which presents great application in development of rapid and intelligent detection.},
}
@article {pmid28341701,
year = {2017},
author = {Crepeau, MW and Langley, CH and Stevens, KA},
title = {From Pine Cones to Read Clouds: Rescaffolding the Megagenome of Sugar Pine (Pinus lambertiana).},
journal = {G3 (Bethesda, Md.)},
volume = {7},
number = {5},
pages = {1563-1568},
pmid = {28341701},
issn = {2160-1836},
mesh = {Algorithms ; Balsams ; Contig Mapping/*methods/standards ; *Genome, Plant ; Pinus/*genetics ; Plant Extracts/*genetics ; Reference Standards ; Whole Genome Sequencing/*methods/standards ; },
abstract = {We investigate the utility and scalability of new read cloud technologies to improve the draft genome assemblies of the colossal, and largely repetitive, genomes of conifers. Synthetic long read technologies have existed in various forms as a means of reducing complexity and resolving repeats since the outset of genome assembly. Recently, technologies that combine subhaploid pools of high molecular weight DNA with barcoding on a massive scale have brought new efficiencies to sample preparation and data generation. When combined with inexpensive light shotgun sequencing, the resulting data can be used to scaffold large genomes. The protocol is efficient enough to consider routinely for even the largest genomes. Conifers represent the largest reference genome projects executed to date. The largest of these is that of the conifer Pinus lambertiana (sugar pine), with a genome size of 31 billion bp. In this paper, we report on the molecular and computational protocols for scaffolding the P. lambertiana genome using the library technology from 10× Genomics. At 247,000 bp, the NG50 of the existing reference sequence is the highest scaffold contiguity among the currently published conifer assemblies; this new assembly's NG50 is 1.94 million bp, an eightfold increase.},
}
@article {pmid28340301,
year = {2017},
author = {Bezeng, BS and Davies, TJ and Daru, BH and Kabongo, RM and Maurin, O and Yessoufou, K and van der Bank, H and van der Bank, M},
title = {Ten years of barcoding at the African Centre for DNA Barcoding.},
journal = {Genome},
volume = {60},
number = {7},
pages = {629-638},
doi = {10.1139/gen-2016-0198},
pmid = {28340301},
issn = {1480-3321},
mesh = {Africa ; Animals ; Biodiversity ; Chloroplast Proteins/genetics ; Conservation of Natural Resources ; DNA Barcoding, Taxonomic/methods/*trends ; Electron Transport Complex IV/genetics ; Phylogeny ; Plants/*classification/genetics ; },
abstract = {The African Centre for DNA Barcoding (ACDB) was established in 2005 as part of a global initiative to accurately and rapidly survey biodiversity using short DNA sequences. The mitochondrial cytochrome c oxidase 1 gene (CO1) was rapidly adopted as the de facto barcode for animals. Following the evaluation of several candidate loci for plants, the Plant Working Group of the Consortium for the Barcoding of Life in 2009 recommended that two plastid genes, rbcLa and matK, be adopted as core DNA barcodes for terrestrial plants. To date, numerous studies continue to test the discriminatory power of these markers across various plant lineages. Over the past decade, we at the ACDB have used these core DNA barcodes to generate a barcode library for southern Africa. To date, the ACDB has contributed more than 21 000 plant barcodes and over 3000 CO1 barcodes for animals to the Barcode of Life Database (BOLD). Building upon this effort, we at the ACDB have addressed questions related to community assembly, biogeography, phylogenetic diversification, and invasion biology. Collectively, our work demonstrates the diverse applications of DNA barcoding in ecology, systematics, evolutionary biology, and conservation.},
}
@article {pmid28339501,
year = {2017},
author = {Ashfaq, M and Akhtar, S and Rafi, MA and Mansoor, S and Hebert, PD},
title = {Mapping global biodiversity connections with DNA barcodes: Lepidoptera of Pakistan.},
journal = {PloS one},
volume = {12},
number = {3},
pages = {e0174749},
pmid = {28339501},
issn = {1932-6203},
mesh = {Animal Distribution ; Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Lepidoptera/*genetics ; Pakistan ; },
abstract = {Sequences from the DNA barcode region of the mitochondrial COI gene are an effective tool for specimen identification and for the discovery of new species. The Barcode of Life Data Systems (BOLD) (www.boldsystems.org) currently hosts 4.5 million records from animals which have been assigned to more than 490,000 different Barcode Index Numbers (BINs), which serve as a proxy for species. Because a fourth of these BINs derive from Lepidoptera, BOLD has a strong capability to both identify specimens in this order and to support studies of faunal overlap. DNA barcode sequences were obtained from 4503 moths from 329 sites across Pakistan, specimens that represented 981 BINs from 52 families. Among 379 species with a Linnaean name assignment, all were represented by a single BIN excepting five species that showed a BIN split. Less than half (44%) of the 981 BINs had counterparts in other countries; the remaining BINs were unique to Pakistan. Another 218 BINs of Lepidoptera from Pakistan were coupled with the 981 from this study before being compared with all 116,768 BINs for this order. As expected, faunal overlap was highest with India (21%), Sri Lanka (21%), United Arab Emirates (20%) and with other Asian nations (2.1%), but it was very low with other continents including Africa (0.6%), Europe (1.3%), Australia (0.6%), Oceania (1.0%), North America (0.1%), and South America (0.1%). This study indicates the way in which DNA barcoding facilitates measures of faunal overlap even when taxa have not been assigned to a Linnean species.},
}
@article {pmid28339012,
year = {2017},
author = {Pappalardo, AM and Copat, C and Ferrito, V and Grasso, A and Ferrante, M},
title = {Heavy metal content and molecular species identification in canned tuna: Insights into human food safety.},
journal = {Molecular medicine reports},
volume = {15},
number = {5},
pages = {3430-3437},
doi = {10.3892/mmr.2017.6376},
pmid = {28339012},
issn = {1791-3004},
mesh = {Animals ; Cadmium/analysis ; Food Analysis ; *Food Preservation ; Food Safety ; Humans ; Lead/analysis ; Mass Spectrometry ; Mercury/analysis ; Metals, Heavy/*analysis ; Olive Oil/chemistry ; Risk Assessment ; Seafood/*analysis ; *Tuna ; },
abstract = {Canned tuna in olive oil and in brine of the most popular brands sold in Italian markets were analyzed to verify the authentication of transformed products, with the aim to unveil commercial frauds due to the substitutions of high value species with species of low commercial value, and to assess the health risk of consumers related to cadmium (Cd), lead (Pb) and mercury (Hg) contents. Species authentication was evaluated with amplification of COI DNA barcode and confirmed the declared species. Among tested metals, Hg had the highest concentrations, followed by Cd and Pb. None of the tested samples surpassed the European regulatory limits no. 1881/2006 fixed for Hg and Pb, whereas one batch of canned tuna in olive oil exceeded standard for Cd. Risk for human health was evaluated by the metals daily intake and target hazard quotient (THQ). As a result, Cd and Pb did not exceed the toxicological reference values established by World Health Organization (WHO) and the Environmental Protection Agency (EPA). Conversely, Hg content suggests a consumption no more than once a week and a continuous surveillance of this fishery products for consumer protection.},
}
@article {pmid28337390,
year = {2017},
author = {Bell, KL and Loeffler, VM and Brosi, BJ},
title = {An rbcL reference library to aid in the identification of plant species mixtures by DNA metabarcoding.},
journal = {Applications in plant sciences},
volume = {5},
number = {3},
pages = {},
pmid = {28337390},
issn = {2168-0450},
abstract = {PREMISE OF THE STUDY: DNA metabarcoding has broad-ranging applications in ecology, aerobiology, biosecurity, and forensics. A bioinformatics pipeline has recently been published for identification using a comprehensive database of ITS2, one of the common plant DNA barcoding markers. There is, however, no corresponding database for rbcL, the other primary marker used in plants.<br><br>METHODS: Using publicly available data, we compiled a reference library of rbcL sequences and trained databases for use with UTAX and RDP classifier algorithms. We used this reference library, along with the existing bioinformatics pipeline and ITS2 reference library, to identify species in an artificial mixture of nine species of pollen. We have made this database publicly available in multiple formats, to allow use with multiple bioinformatics pipelines, now and in the future.<br><br>RESULTS: Using the rbcL database, in addition to the ITS2 database, we succeeded in making species-level identifications for eight species and a family-level identification of the ninth species. This is an improvement on ITS2 sequence alone.<br><br>DISCUSSION: The reference library described here will assist with identification of plant species using rbcL. By making another gene region available for standard barcoding, this will increase the resolution and accuracy of identifications.},
}
@article {pmid28337181,
year = {2017},
author = {Iskandar, CF and Borges, F and Taminiau, B and Daube, G and Zagorec, M and Remenant, B and Leisner, JJ and Hansen, MA and Sørensen, SJ and Mangavel, C and Cailliez-Grimal, C and Revol-Junelles, AM},
title = {Comparative Genomic Analysis Reveals Ecological Differentiation in the Genus Carnobacterium.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {357},
pmid = {28337181},
issn = {1664-302X},
abstract = {Lactic acid bacteria (LAB) differ in their ability to colonize food and animal-associated habitats: while some species are specialized and colonize a limited number of habitats, other are generalist and are able to colonize multiple animal-linked habitats. In the current study, Carnobacterium was used as a model genus to elucidate the genetic basis of these colonization differences. Analyses of 16S rRNA gene meta-barcoding data showed that C. maltaromaticum followed by C. divergens are the most prevalent species in foods derived from animals (meat, fish, dairy products), and in the gut. According to phylogenetic analyses, these two animal-adapted species belong to one of two deeply branched lineages. The second lineage contains species isolated from habitats where contact with animal is rare. Genome analyses revealed that members of the animal-adapted lineage harbor a larger secretome than members of the other lineage. The predicted cell-surface proteome is highly diversified in C. maltaromaticum and C. divergens with genes involved in adaptation to the animal milieu such as those encoding biopolymer hydrolytic enzymes, a heme uptake system, and biopolymer-binding adhesins. These species also exhibit genes for gut adaptation and respiration. In contrast, Carnobacterium species belonging to the second lineage encode a poorly diversified cell-surface proteome, lack genes for gut adaptation and are unable to respire. These results shed light on the important genomics traits required for adaptation to animal-linked habitats in generalist Carnobacterium.},
}
@article {pmid28336417,
year = {2018},
author = {Héritier, L and Verneau, O and Smith, KG and Coetzer, C and Du Preez, LH},
title = {Demonstrating the value and importance of combining DNA barcodes and discriminant morphological characters for polystome taxonomy (Platyhelminthes, Monogenea).},
journal = {Parasitology international},
volume = {67},
number = {1},
pages = {38-46},
doi = {10.1016/j.parint.2017.03.002},
pmid = {28336417},
issn = {1873-0329},
mesh = {Animals ; Classification/*methods ; DNA Barcoding, Taxonomic/*veterinary ; Electron Transport Complex IV/genetics ; Florida ; France ; Helminth Proteins/genetics ; North Carolina ; Photography ; Trematoda/anatomy &amp; histology/*classification/genetics ; Turtles/*parasitology ; },
abstract = {Polystomes are monogenean parasites that infest mainly semi aquatic vertebrates, such as amphibians and chelonians. Owing to the lack of discriminative morphological characters and because polystomes are considered to be strictly host- and site-specific, host identity is often used as an additional character for parasite identification. Recent genetic studies, however, showed that polystomes infecting freshwater turtles in outdoor turtle enclosures and natural environments, were not strictly host-specific. Therefore, we proposed a new procedure for turtle polystome taxonomy based on the combination of Cytochrome c Oxydase I sequences and two discriminant morphological characters, namely the number of genital spines and the testis shape. We tested the validity of this procedure with Polystomoides oris, which was collected from the pharyngeal cavity of the American painted turtle Chrysemys picta and two undescribed species, both collected from the pharyngeal cavity of the American slider Trachemys scripta and two other European turtles, namely the European pond turtle Emys orbicularis and the Mediterranean turtle Mauremys leprosa. A Principal Component Analysis based on both morphological characters allowed the separation of all specimens in three morphological groups, which matched well with the molecular data. As a result, we describe two new polystome species, i.e., Polystomoides soredensis n. sp. and Polystomoides scriptanus n. sp.},
}
@article {pmid28334157,
year = {2017},
author = {Debroas, D and Domaizon, I and Humbert, JF and Jardillier, L and Lepère, C and Oudart, A and Taïb, N},
title = {Overview of freshwater microbial eukaryotes diversity: a first analysis of publicly available metabarcoding data.},
journal = {FEMS microbiology ecology},
volume = {93},
number = {4},
pages = {},
doi = {10.1093/femsec/fix023},
pmid = {28334157},
issn = {1574-6941},
mesh = {Cryptophyta/classification ; Ecosystem ; Eukaryota/*classification ; Fungi/classification ; Lakes/microbiology ; Phylogeny ; Plankton/*classification ; Stramenopiles/classification ; },
abstract = {Although they are widespread, diverse and involved in biogeochemical cycles, microbial eukaryotes attract less attention than their prokaryotic counterparts in environmental microbiology. In this study, we used publicly available 18S barcoding data to define biases that may limit such analyses and to gain an overview of the planktonic microbial eukaryotic diversity in freshwater ecosystems. The richness of the microbial eukaryotes was estimated to 100 798 operational taxonomic units (OTUs) delineating 1267 clusters or phylogenetic units (PUs, i.e. monophyletic groups of OTUs that are phylogenetically close). By summing the richness found in aquatic environments, we can predict the microbial eukaryotic richness to be around 200 000-250 000 species. The molecular diversity of protists in freshwater environments is generally higher than that of the morphospecies and cultivated species catalogued in public databases. Amoebozoa, Viridiplantae, Ichthyosporea, and Cryptophyta are the most phylogenetically diverse taxa, and characterisation of these groups is still needed. A network analysis showed that Fungi, Stramenopiles and Viridiplantae play central role in lake ecosystems. Finally, this work provides guidance for compiling metabarcoding data and identifies missing data that should be obtained to increase our knowledge on microbial eukaryote diversity.},
}
@article {pmid28332322,
year = {2017},
author = {Chakraborty, M and Dhar, B and Ghosh, SK},
title = {Design of character-based DNA barcode motif for species identification: A computational approach and its validation in fishes.},
journal = {Molecular ecology resources},
volume = {17},
number = {6},
pages = {1359-1370},
doi = {10.1111/1755-0998.12671},
pmid = {28332322},
issn = {1755-0998},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Electron Transport Complex IV/*genetics ; Fishes/*classification/*genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {The DNA barcodes are generally interpreted using distance-based and character-based methods. The former uses clustering of comparable groups, based on the relative genetic distance, while the latter is based on the presence or absence of discrete nucleotide substitutions. The distance-based approach has a limitation in defining a universal species boundary across the taxa as the rate of mtDNA evolution is not constant throughout the taxa. However, character-based approach more accurately defines this using a unique set of nucleotide characters. The character-based analysis of full-length barcode has some inherent limitations, like sequencing of the full-length barcode, use of a sparse-data matrix and lack of a uniform diagnostic position for each group. A short continuous stretch of a fragment can be used to resolve the limitations. Here, we observe that a 154-bp fragment, from the transversion-rich domain of 1367 COI barcode sequences can successfully delimit species in the three most diverse orders of freshwater fishes. This fragment is used to design species-specific barcode motifs for 109 species by the character-based method, which successfully identifies the correct species using a pattern-matching program. The motifs also correctly identify geographically isolated population of the Cypriniformes species. Further, this region is validated as a species-specific mini-barcode for freshwater fishes by successful PCR amplification and sequencing of the motif (154 bp) using the designed primers. We anticipate that use of such motifs will enhance the diagnostic power of DNA barcode, and the mini-barcode approach will greatly benefit the field-based system of rapid species identification.},
}
@article {pmid28331407,
year = {2017},
author = {Jimi, N and Salazar-Vallejo, SI and Kajihara, H},
title = {Designation of a neotype and redescription of Hesione reticulata von Marenzeller, 1879 from Japan (Annelida, Hesionidae).},
journal = {ZooKeys},
volume = {},
number = {657},
pages = {29-41},
pmid = {28331407},
issn = {1313-2989},
abstract = {The hesionid polychaete Hesione reticulata von Marenzeller, 1879 was described from Enoshima Island, Japan and has been recorded also from the Red Sea. Depending on researchers, it has been regarded as either a distinct species or synonymous with older established ones. The type specimen has been lost. In order to clarify its taxonomic status, Hesione reticulata is herein redescribed, illustrated, and a neotype is proposed based on recent material collected near the type locality. The diagnostic features include the presence of several dorsal, discontinuous longitudinal bands, interrupted by pale segmental spots; prostomium with tiny antennae; a tuberculated dorsal integument; acicular lobes double; and neurochaetal blades with guards approaching the distal tooth. The dorsal color pattern in life enables a clear distinction from similar species such as Hesione intertexta Grube, 1878 amongst others. Mitochondrial COI barcoding sequences are deposited in the DNA Data Bank of Japan. A key to Hesione species from Japan is also included.},
}
@article {pmid28331401,
year = {2017},
author = {Zhu, XC and Chen, J and Chen, R and Jiang, LY and Qiao, GX},
title = {DNA barcoding and species delimitation of Chaitophorinae (Hemiptera, Aphididae).},
journal = {ZooKeys},
volume = {},
number = {656},
pages = {25-50},
pmid = {28331401},
issn = {1313-2989},
abstract = {Chaitophorinae aphids are widespread across Eurasia and North America, and include some important agricultural and horticultural pests. So, accurate rapid species identification is very important. Here, we used three mitochondrial genes and one endosymbiont gene to calculate and analyze the genetic distances within different datasets. For species delimitation, two distance-based methods were employed, threshold with NJ (neighbor-joining) and ABGD (Automatic Barcode Gap Discovery), and two tree-based approaches, GMYC (General Mixed Yule Coalescent) and PTP (Poisson Tree Process). The genetic interspecific divergence was clearly larger than the intraspecific divergence for four molecular markers. COI and COII genes were found to be more suitable for Chaitophorinae DNA barcoding. For species delimitation, at least one distance-based method combined with one tree-based method would be preferable. Based on the data for Chaitophorus saliniger and Laingia psammae, DNA barcoding may also reveal geographical variation.},
}
@article {pmid28330505,
year = {2017},
author = {Lwande, OW and Bucht, G and Ahlm, C and Ahlm, K and Näslund, J and Evander, M},
title = {Mosquito-borne Inkoo virus in northern Sweden - isolation and whole genome sequencing.},
journal = {Virology journal},
volume = {14},
number = {1},
pages = {61},
pmid = {28330505},
issn = {1743-422X},
mesh = {Aedes/classification/genetics/*virology ; Animals ; Electron Transport Complex IV/genetics ; *Genome, Viral ; Mosquito Vectors/classification/genetics/*virology ; Mutation ; Orthobunyavirus/*genetics/*isolation &amp; purification ; RNA, Viral/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; *Sequence Analysis, DNA ; Sweden ; Viral Proteins/genetics ; Virus Cultivation ; },
abstract = {BACKGROUND: Inkoo virus (INKV) is a less known mosquito-borne virus belonging to Bunyaviridae, genus Orthobunyavirus, California serogroup. Studies indicate that INKV infection is mainly asymptomatic, but can cause mild encephalitis in humans. In northern Europe, the sero-prevalence against INKV is high, 41% in Sweden and 51% in Finland. Previously, INKV RNA has been detected in adult Aedes (Ae.) communis, Ae. hexodontus and Ae. punctor mosquitoes and Ae. communis larvae, but there are still gaps of knowledge regarding mosquito vectors and genetic diversity. Therefore, we aimed to determine the occurrence of INKV in its mosquito vector and characterize the isolates.<br><br>METHODS: About 125,000 mosquitoes were collected during a mosquito-borne virus surveillance in northern Sweden during the summer period of 2015. Of these, 10,000 mosquitoes were processed for virus isolation and detection using cell culture and RT-PCR. Virus isolates were further characterized by whole genome sequencing. Genetic typing of mosquito species was conducted by cytochrome oxidase subunit I (COI) gene amplification and sequencing (genetic barcoding).<br><br>RESULTS: Several Ae. communis mosquitoes were found positive for INKV RNA and two isolates were obtained. The first complete sequences of the small (S), medium (M), and large (L) segments of INKV in Sweden were obtained. Phylogenetic analysis showed that the INKV genome was most closely related to other INKV isolates from Sweden and Finland. Of the three INKV genome segments, the INKV M segment had the highest frequency of non-synonymous mutations. The overall G/C-content of INKV genes was low for the N/NSs genes (43.8-45.5%), polyprotein (Gn/Gc/NSm) gene (35.6%) and the RNA polymerase gene (33.8%) This may be due to the fact that INKV in most instances utilized A or T in the third codon position.<br><br>CONCLUSIONS: INKV is frequently circulating in northern Sweden and Ae. communis is the key vector. The high mutation rate of the INKV M segment may have consequences on virulence.},
}
@article {pmid28329763,
year = {2017},
author = {Wylie, AA and Schoepfer, J and Jahnke, W and Cowan-Jacob, SW and Loo, A and Furet, P and Marzinzik, AL and Pelle, X and Donovan, J and Zhu, W and Buonamici, S and Hassan, AQ and Lombardo, F and Iyer, V and Palmer, M and Berellini, G and Dodd, S and Thohan, S and Bitter, H and Branford, S and Ross, DM and Hughes, TP and Petruzzelli, L and Vanasse, KG and Warmuth, M and Hofmann, F and Keen, NJ and Sellers, WR},
title = {The allosteric inhibitor ABL001 enables dual targeting of BCR-ABL1.},
journal = {Nature},
volume = {543},
number = {7647},
pages = {733-737},
doi = {10.1038/nature21702},
pmid = {28329763},
issn = {1476-4687},
mesh = {Allosteric Regulation/drug effects ; Allosteric Site/*drug effects ; Animals ; Catalytic Domain/drug effects ; Cell Proliferation/drug effects ; Dasatinib/therapeutic use ; Drug Resistance, Neoplasm/drug effects/genetics ; Drug Therapy, Combination ; Fusion Proteins, bcr-abl/*antagonists &amp; inhibitors/chemistry/genetics ; Humans ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/*drug therapy/enzymology/genetics/pathology ; Mice ; Mutation ; Niacinamide/*analogs &amp; derivatives/pharmacology/therapeutic use ; Pyrazoles/*pharmacology/therapeutic use ; Pyrimidines/pharmacology/therapeutic use ; Xenograft Model Antitumor Assays ; },
abstract = {Chronic myeloid leukaemia (CML) is driven by the activity of the BCR-ABL1 fusion oncoprotein. ABL1 kinase inhibitors have improved the clinical outcomes for patients with CML, with over 80% of patients treated with imatinib surviving for more than 10 years. Second-generation ABL1 kinase inhibitors induce more potent molecular responses in both previously untreated and imatinib-resistant patients with CML. Studies in patients with chronic-phase CML have shown that around 50% of patients who achieve and maintain undetectable BCR-ABL1 transcript levels for at least 2 years remain disease-free after the withdrawal of treatment. Here we characterize ABL001 (asciminib), a potent and selective allosteric ABL1 inhibitor that is undergoing clinical development testing in patients with CML and Philadelphia chromosome-positive (Ph[+]) acute lymphoblastic leukaemia. In contrast to catalytic-site ABL1 kinase inhibitors, ABL001 binds to the myristoyl pocket of ABL1 and induces the formation of an inactive kinase conformation. ABL001 and second-generation catalytic inhibitors have similar cellular potencies but distinct patterns of resistance mutations, with genetic barcoding studies revealing pre-existing clonal populations with no shared resistance between ABL001 and the catalytic inhibitor nilotinib. Consistent with this profile, acquired resistance was observed with single-agent therapy in mice; however, the combination of ABL001 and nilotinib led to complete disease control and eradicated CML xenograft tumours without recurrence after the cessation of treatment.},
}
@article {pmid28327913,
year = {2017},
author = {Bayliss, SC and Hunt, VL and Yokoyama, M and Thorpe, HA and Feil, EJ},
title = {The use of Oxford Nanopore native barcoding for complete genome assembly.},
journal = {GigaScience},
volume = {6},
number = {3},
pages = {1-6},
pmid = {28327913},
issn = {2047-217X},
support = {MR/R00241X/1/MRC_/Medical Research Council/United Kingdom ; BB/M026388/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Bacterial/genetics ; Genome, Bacterial/*genetics ; Genomic Library ; Genomics/methods ; High-Throughput Nucleotide Sequencing/*methods ; Methicillin-Resistant Staphylococcus aureus/classification/genetics ; *Nanopores ; Reproducibility of Results ; Species Specificity ; },
abstract = {BACKGROUND: The Oxford Nanopore Technologies MinION(TM) is a mobile DNA sequencer that can produce long read sequences with a short turn-around time. Here we report the first demonstration of single contig genome assembly using Oxford Nanopore native barcoding when applied to a multiplexed library of 12 samples and combined with existing Illumina short read data. This paves the way for the closure of multiple bacterial genomes from a single MinION(TM) sequencing run, given the availability of existing short read data. The strain we used, MHO_001, represents the important community-acquired methicillin-resistant Staphylococcus aureus lineage USA300.<br><br>FINDINGS: Using a hybrid assembly of existing short read and barcoded long read sequences from multiplexed data, we completed a genome of the S. aureus USA300 strain MHO_001. The long read data represented only &#x223c;5% to 10% of an average MinION(TM) run (&#x223c;7x genomic coverage), but, using standard tools, this was sufficient to complete the circular chromosome of S. aureus strain MHO_001 (2.86 Mb) and two complete plasmids (27 Kb and 3 Kb). Minor differences were noted when compared to USA300 reference genome, USA300_FPR3757, including the translocation, loss, and gain of mobile genetic elements.<br><br>CONCLUSION: Here we demonstrate that MinION(TM) reads, multiplexed using native barcoding, can be used in combination with short read data to fully complete a bacterial genome. The ability to complete multiple genomes, for which short read data is already available, from a single MinION(TM) run is set to impact our understanding of accessory genome content, plasmid diversity, and genome rearrangements.},
}
@article {pmid28325987,
year = {2017},
author = {Salmela, J and Kolcsár, LP},
title = {New and poorly known Palaearctic fungus gnats (Diptera, Sciaroidea).},
journal = {Biodiversity data journal},
volume = {},
number = {5},
pages = {e11760},
pmid = {28325987},
issn = {1314-2828},
abstract = {BACKGROUND: Fungus gnats (Sciaroidea) are a globally species rich group of lower Diptera. In Europe, Fennoscandian peninsula in particular holds a notable diversity, ca. 1000 species, of which 10 % are still unnamed. Fungus gnats are predominantly terrestrial insects, but some species dwell in wetland habitats.<br><br>NEW INFORMATION: Eight new fungus gnat species, belonging to the families Keroplatidae (Orfelia boreoalpina Salmela sp.n.) and Mycetophilidae (Sciophila holopaineni Salmela sp.n., S. curvata Salmela sp.n., Boletina sasakawai Salmela &amp; Kolcs&#xe1;r sp.n., B. norokorpii Salmela &amp; Kolcs&#xe1;r sp.n., Phronia sompio Salmela sp.n., P. reducta Salmela sp.n., P. prolongata Salmela sp.n.), are described. Four of the species are known from Fennoscandia only whilst two are supposed to have boreo-alpine disjunct ranges, i.e. having populations in Fennoscandia and the Central European Alps. One of the species probably has a boreal range (Finnish Lapland and Central Siberia). Type material of Boletina curta Sasakawa &amp; Kimura from Japan was found to consist of two species, and a further species close to these taxa is described from Finland. Phronia elegantula Hackman is redescribed and reported for the first time from Norway. DNA barcodes are provided for the first time for five species.},
}
@article {pmid28325970,
year = {2017},
author = {Percy, DM},
title = {Making the most of your host: the Metrosideros-feeding psyllids (Hemiptera, Psylloidea) of the Hawaiian Islands.},
journal = {ZooKeys},
volume = {},
number = {649},
pages = {1-163},
pmid = {28325970},
issn = {1313-2989},
abstract = {The Hawaiian psyllids (Psylloidea, Triozidae) feeding on Metrosideros (Myrtaceae) constitute a remarkable radiation of more than 35 species. This monophyletic group has diversified on a single, highly polymorphic host plant species, Metrosideros polymorpha. Eleven Metrosideros-feeding species included in the Insects of Hawaii by Zimmerman are redescribed, and an additional 25 new species are described. Contrary to previous classifications that placed the Metrosideros-feeders in two genera, Trioza Foerster, 1848 and Kuwayama Crawford, 1911, all 36 named species are placed in Pariaconus Enderlein, 1926; and the relationship of this genus to other Pacific taxa within the family Triozidae, and other Austro-Pacific taxa feeding on host plants in Myrtaceae is clarified. The processes of diversification in Pariaconus include shifts in galling habit, geographic isolation within and between islands, and preferences for different morphotypes of the host plant. Four species groups are recognized: the bicoloratus and minutus groups are free-living or form pit galls, and together with the kamua group (composing all of the Kauai species) form a basal assemblage; the more derived closed gall species in the ohialoha group are found on all major islands except Kauai. The diversification of Pariaconus has likely occurred over several million years. Within island diversification is exemplified in the kamua group, and within species variation in the ohialoha group, but species discovery rates suggest this radiation remains undersampled. Mitochondrial DNA barcodes are provided for 28 of the 36 species. Genetic divergence, intraspecific genetic structure, and parallel evolution of different galling biologies and morphological traits are discussed within a phylogenetic framework. Outgroup analysis for the genus Pariaconus and ancestral character state reconstruction suggest pit-galling may be the ancestral state, and the closest outgroups are Palaearctic-Australasian taxa rather than other Pacific Metrosideros-feeders.},
}
@article {pmid28325121,
year = {2018},
author = {Olekšáková, T and Žurovcová, M and Klimešová, V and Barták, M and Šuláková, H},
title = {DNA extraction and barcode identification of development stages of forensically important flies in the Czech Republic.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {3},
pages = {427-430},
doi = {10.1080/24701394.2017.1298102},
pmid = {28325121},
issn = {2470-1408},
mesh = {Animals ; Czech Republic ; DNA/*isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Diptera/*classification/genetics/*growth &amp; development ; Electron Transport Complex IV/genetics ; Forensic Genetics/methods ; Insect Proteins/genetics ; Reagent Kits, Diagnostic ; Sequence Analysis, DNA ; },
abstract = {Several methods of DNA extraction, coupled with 'DNA barcoding' species identification, were compared using specimens from early developmental stages of forensically important flies from the Calliphoridae and Sarcophagidae families. DNA was extracted at three immature stages - eggs, the first instar larvae, and empty pupal cases (puparia) - using four different extraction methods, namely, one simple 'homemade' extraction buffer protocol and three commercial kits. The extraction conditions, including the amount of proteinase K and incubation times, were optimized. The simple extraction buffer method was successful for half of the eggs and for the first instar larval samples. The DNA Lego Kit and DEP-25 DNA Extraction Kit were useful for DNA extractions from the first instar larvae samples, and the DNA Lego Kit was also successful regarding the extraction from eggs. The QIAamp DNA mini kit was the most effective; the extraction was successful with regard to all sample types - eggs, larvae, and pupari.},
}
@article {pmid28320321,
year = {2017},
author = {Schuster, A and Lopez, JV and Becking, LE and Kelly, M and Pomponi, SA and Wörheide, G and Erpenbeck, D and Cárdenas, P},
title = {Evolution of group I introns in Porifera: new evidence for intron mobility and implications for DNA barcoding.},
journal = {BMC evolutionary biology},
volume = {17},
number = {1},
pages = {82},
pmid = {28320321},
issn = {1471-2148},
mesh = {Animals ; Base Sequence ; Biological Evolution ; *DNA Barcoding, Taxonomic ; Endonucleases/genetics ; *Introns ; Mitochondria/genetics ; Open Reading Frames ; Phylogeny ; Porifera/classification/*genetics ; RNA Splicing ; },
abstract = {BACKGROUND: Mitochondrial introns intermit coding regions of genes and feature characteristic secondary structures and splicing mechanisms. In metazoans, mitochondrial introns have only been detected in sponges, cnidarians, placozoans and one annelid species. Within demosponges, group I and group II introns are present in six families. Based on different insertion sites within the cox1 gene and secondary structures, four types of group I and two types of group II introns are known, which can harbor up to three encoding homing endonuclease genes (HEG) of the LAGLIDADG family (group I) and/or reverse transcriptase (group II). However, only little is known about sponge intron mobility, transmission, and origin due to the lack of a comprehensive dataset. We analyzed the largest dataset on sponge mitochondrial group I introns to date: 95 specimens, from 11 different sponge genera which provided novel insights into the evolution of group I introns.<br><br>RESULTS: For the first time group I introns were detected in four genera of the sponge family Scleritodermidae (Scleritoderma, Microscleroderma, Aciculites, Setidium). We demonstrated that group I introns in sponges aggregate in the most conserved regions of cox1. We showed that co-occurrence of two introns in cox1 is unique among metazoans, but not uncommon in sponges. However, this combination always associates an active intron with a degenerating one. Earlier hypotheses of HGT were confirmed and for the first time VGT and secondary losses of introns conclusively demonstrated.<br><br>CONCLUSION: This study validates the subclass Spirophorina (Tetractinellida) as an intron hotspot in sponges. Our analyses confirm that most sponge group I introns probably originated from fungi. DNA barcoding is discussed and the application of alternative primers suggested.},
}
@article {pmid28317543,
year = {2017},
author = {Cruywagen, EM and Slippers, B and Roux, J and Wingfield, MJ},
title = {Phylogenetic species recognition and hybridisation in Lasiodiplodia: A case study on species from baobabs.},
journal = {Fungal biology},
volume = {121},
number = {4},
pages = {420-436},
doi = {10.1016/j.funbio.2016.07.014},
pmid = {28317543},
issn = {1878-6146},
mesh = {Adansonia/*microbiology ; Africa ; Ascomycota/*classification/genetics/*isolation &amp; purification ; DNA, Fungal/*genetics ; *Phylogeny ; Plant Diseases/microbiology ; *Recombination, Genetic ; Sequence Analysis, DNA ; },
abstract = {Lasiodiplodia species (Botryosphaeriaceae, Ascomycota) infect a wide range of typically woody plants on which they are associated with many different disease symptoms. In this study, we determined the identity of Lasiodiplodia isolates obtained from baobab (Adansonia species) trees in Africa and reviewed the molecular markers used to describe Lasiodiplodia species. Publicly available and newly produced sequence data for some of the type strains of Lasiodiplodia species showed incongruence amongst phylogenies of five nuclear loci. We conclude that several of the previously described Lasiodiplodia species are hybrids of other species. Isolates from baobab trees in Africa included nine species of Lasiodiplodia and two hybrid species. Inoculation trials with the most common Lasiodiplodia species collected from these trees produced significant lesions on young baobab trees. There was also variation in aggressiveness amongst isolates from the same species. The apparently widespread tendency of Lasiodiplodia species to hybridise demands that phylogenies from multiple loci (more than two and preferably four or more) are compared for congruence prior to new species being described. This will avoid hybrids being incorrectly described as new taxa, as has clearly occurred in the past.},
}
@article {pmid28314956,
year = {2017},
author = {Bentzen, AK and Hadrup, SR},
title = {Evolution of MHC-based technologies used for detection of antigen-responsive T cells.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {66},
number = {5},
pages = {657-666},
pmid = {28314956},
issn = {1432-0851},
mesh = {Antigens/*immunology ; Humans ; Major Histocompatibility Complex/*immunology ; Receptors, Antigen, T-Cell/*immunology ; T-Lymphocytes/*immunology ; },
abstract = {T cell-mediated recognition of peptide-major histocompatibility complex (pMHC) class I and II molecules is crucial for the control of intracellular pathogens and cancer, as well as for stimulation and maintenance of efficient cytotoxic responses. Such interactions may also play a role in the development of autoimmune diseases. Novel insights into this mechanism are crucial to understanding disease development and establishing new treatment strategies. MHC multimers have been used for detection of antigen-responsive T cells since the first report by Altman et al. showed that tetramerization of pMHC class I molecules provided sufficient stability to T cell receptor (TCR)-pMHC interactions, allowing detection of MHC multimer-binding T cells using flow cytometry. Since this breakthrough the scientific community has aimed for expanding the capacity of MHC multimer-based detection technologies to facilitate large-scale epitope discovery and immune monitoring in limited biological material. Screening of T cell specificity using large libraries of pMHC molecules is suitable for analyses of T cell recognition potentially at genome-wide levels rather than analyses restricted to a selection of model antigens. Such strategies provide novel insights into the immune specificities involved in disease development and response to immunotherapy, and extend fundamental knowledge related to T cell recognition patterns and cross-recognition by TCRs. MHC multimer-based technologies have now evolved from detection of 1-2 different T cell specificities per cell sample, to include more than 1000 evaluable pMHC molecules using novel technologies. Here, we provide an overview of MHC multimer-based detection technologies developed over two decades, focusing primarily on MHC class I interactions.},
}
@article {pmid28304358,
year = {2017},
author = {Flaviani, F and Schroeder, DC and Balestreri, C and Schroeder, JL and Moore, K and Paszkiewicz, K and Pfaff, MC and Rybicki, EP},
title = {A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater.},
journal = {Viruses},
volume = {9},
number = {3},
pages = {},
pmid = {28304358},
issn = {1999-4915},
mesh = {Bacteria/*classification/genetics ; Eukaryota/*classification/genetics ; *Microbiota ; Seawater/*microbiology ; Viruses/*classification/genetics ; },
abstract = {The aquatic microbiome is composed of a multi-phylotype community of microbes, ranging from the numerically dominant viruses to the phylogenetically diverse unicellular phytoplankton. They influence key biogeochemical processes and form the base of marine food webs, becoming food for secondary consumers. Due to recent advances in next-generation sequencing, this previously overlooked component of our hydrosphere is starting to reveal its true diversity and biological complexity. We report here that 250 mL of seawater is sufficient to provide a comprehensive description of the microbial diversity in an oceanic environment. We found that there was a dominance of the order Caudovirales (59%), with the family Myoviridae being the most prevalent. The families Phycodnaviridae and Mimiviridae made up the remainder of pelagic double-stranded DNA (dsDNA) virome. Consistent with this analysis, the Cyanobacteria dominate (52%) the prokaryotic diversity. While the dinoflagellates and their endosymbionts, the superphylum Alveolata dominates (92%) the microbial eukaryotic diversity. A total of 834 prokaryotic, 346 eukaryotic and 254 unique virus phylotypes were recorded in this relatively small sample of water. We also provide evidence, through a metagenomic-barcoding comparative analysis, that viruses are the likely source of microbial environmental DNA (meDNA). This study opens the door to a more integrated approach to oceanographic sampling and data analysis.},
}
@article {pmid28303008,
year = {2017},
author = {Zhang, N and Erickson, DL and Ramachandran, P and Ottesen, AR and Timme, RE and Funk, VA and Luo, Y and Handy, SM},
title = {An analysis of Echinacea chloroplast genomes: Implications for future botanical identification.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {216},
pmid = {28303008},
issn = {2045-2322},
mesh = {Chloroplasts/*genetics ; DNA Barcoding, Taxonomic ; DNA, Chloroplast/analysis ; DNA, Plant/analysis ; Echinacea/*classification/cytology/genetics ; *Genome, Chloroplast ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/*methods ; },
abstract = {Echinacea is a common botanical used in dietary supplements, primarily to treat upper respiratory tract infections and to support immune function. There are currently thought to be nine species in the genus Echinacea. Due to very low molecular divergence among sister species, traditional DNA barcoding has not been successful for differentiation of Echinacea species. Here, we present the use of full chloroplast genomes to distinguish between all 9 reported species. Total DNA was extracted from specimens stored at the National Museum of Natural History, Smithsonian Institution, which had been collected from the wild with species identification documented by experts in the field. We used Next Generation Sequencing (NGS) and CLC Genomics Workbench to assemble complete chloroplast genomes for all nine species. Full chloroplasts unambiguously differentiated all nine species, compared with the very few single nucleotide polymorphisms (SNPs) available with core DNA barcoding markers. SNPs for any two Echinacea chloroplast genomes ranged from 181 to 910, and provided robust data for unambiguous species delimitation. Implications for DNA-based species identification assays derived from chloroplast genome sequences are discussed in light of product safety, adulteration and quality issues.},
}
@article {pmid28296890,
year = {2017},
author = {Shu, JP and Shang, H and Jin, D and Wei, HJ and Zhou, XL and Liu, HM and Gu, YF and Wang, Y and Wang, FG and Shen, H and Zhang, R and Adjie, B and Yan, YH},
title = {Re-establishment of species from synonymies based on DNA barcoding and phylogenetic analysis using Diplopterygium simulans (Gleicheniaceae) as an example.},
journal = {PloS one},
volume = {12},
number = {3},
pages = {e0164604},
pmid = {28296890},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; Ferns/*genetics ; *Phylogeny ; },
abstract = {Because synonymy treatment traditionally relies on morphological judgments, it usually causes many problems in species delimitation and in the biodiversity catalogue. For example, Diplopterygium simulans, which belongs to the Gleicheniaceae family, has been considered to be synonymous with D. glaucum or D. giganteum based mainly on the morphology of its pinna rachis and blade. In the absence of molecular evidence, these revisions remain doubtful. DNA barcoding, which is considered to be a powerful method for species-level identification, was employed to assess the genetic distance among 9 members of the Diplopterygium genus. The results indicate that D. simulans is an independent species rather than a synonymy of D. glaucum or D. giganteum. Moreover, phylogenetic analysis uncovered the sisterhood of D. simulans and D. cantonense, which is supported by their geographical distributions and morphological traits. Incorrect synonymy treatment is prevalent in the characterization of biological diversity, and our study proposes a convenient and effective method for validating synonym treatments and discovering cryptic species.},
}
@article {pmid28296214,
year = {2017},
author = {Matteucci, E and Occhipinti, A and Piervittori, R and Maffei, ME and Favero-Longo, SE},
title = {Morphological, Secondary Metabolite and ITS (rDNA) Variability within Usnic Acid-Containing Lichen Thalli of Xanthoparmelia Explored at the Local Scale of Rock Outcrop in W-Alps.},
journal = {Chemistry &amp; biodiversity},
volume = {14},
number = {6},
pages = {},
doi = {10.1002/cbdv.201600483},
pmid = {28296214},
issn = {1612-1880},
mesh = {Benzofurans ; Chromatography, High Pressure Liquid ; DNA, Ribosomal/*genetics ; Europe ; Haplotypes ; Italy ; Lichens/chemistry/*metabolism ; Parmeliaceae/*chemistry/classification ; Secondary Metabolism ; Tandem Mass Spectrometry ; },
abstract = {Lichen secondary metabolites (LSMs) are regarded with interest for valuable biological properties, but chemical variability among/within lichen taxa has been only fragmentarily characterized by advanced analytical techniques. Knowledge of variability at a local geographic scale has been particularly neglected, while it should address the collection of chemically homogeneous materials to test and exploit LSMs. Here we evaluated the chemical variability of 48 Xanthoparmelia specimens from two rock outcrops in Western Italian Alps, representative of nine morphotypes and sixteen rDNA ITS haplotypes. Qualitative and quantitative analyses were performed by HPLC-DAD-ESI-MS2 and UPLC-HDR-DAD, respectively, and revealed the occurrence of 18 LSMs. Chemical partition allowed distinguishing six chemical groups, only partially overlapping with distinct morphotypes and three divergent haplotype groups, which, overall, accounted for the co-occurrence of different taxa only in part identifiable with species described for Europe. Some morphotypes were variable in presence and concentration of LSMs, and chemical divergences also characterized single ITS haplotypes. Accordingly, the collection of chemically homogeneous materials, even at a local scale, may be not properly addressed by morphological features and ITS barcoding, and should be confirmed by a specimen-level chemical characterization.},
}
@article {pmid28290550,
year = {2017},
author = {Shahi, P and Kim, SC and Haliburton, JR and Gartner, ZJ and Abate, AR},
title = {Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {44447},
pmid = {28290550},
issn = {2045-2322},
support = {R01 HG008978/HG/NHGRI NIH HHS/United States ; T32 GM008284/GM/NIGMS NIH HHS/United States ; R21 HG007233/HG/NHGRI NIH HHS/United States ; T32 EB009383/EB/NIBIB NIH HHS/United States ; DP2 AR068129/AR/NIAMS NIH HHS/United States ; R01 EB019453/EB/NIBIB NIH HHS/United States ; },
mesh = {DNA Barcoding, Taxonomic ; Dietary Proteins/*analysis/chemistry ; High-Throughput Nucleotide Sequencing ; Humans ; Microfluidics/methods ; Proteins/chemistry/*genetics ; *Single-Cell Analysis ; },
abstract = {Proteins are the primary effectors of cellular function, including cellular metabolism, structural dynamics, and information processing. However, quantitative characterization of proteins at the single-cell level is challenging due to the tiny amount of protein available. Here, we present Abseq, a method to detect and quantitate proteins in single cells at ultrahigh throughput. Like flow and mass cytometry, Abseq uses specific antibodies to detect epitopes of interest; however, unlike these methods, antibodies are labeled with sequence tags that can be read out with microfluidic barcoding and DNA sequencing. We demonstrate this novel approach by characterizing surface proteins of different cell types at the single-cell level and distinguishing between the cells by their protein expression profiles. DNA-tagged antibodies provide multiple advantages for profiling proteins in single cells, including the ability to amplify low-abundance tags to make them detectable with sequencing, to use molecular indices for quantitative results, and essentially limitless multiplexing.},
}
@article {pmid28290255,
year = {2017},
author = {Motley, K and Havill, NP and Arsenault-Benoit, AL and Mayfield, AE and Ott, DS and Ross, D and Whitmore, MC and Wallin, KF},
title = {Feeding by Leucopis argenticollis and Leucopis piniperda (Diptera: Chamaemyiidae) from the western USA on Adelges tsugae (Hemiptera: Adelgidae) in the eastern USA.},
journal = {Bulletin of entomological research},
volume = {107},
number = {5},
pages = {699-704},
doi = {10.1017/S0007485317000219},
pmid = {28290255},
issn = {1475-2670},
mesh = {Animals ; Diptera/*growth &amp; development ; Female ; Food Chain ; *Hemiptera ; Male ; *Pest Control, Biological ; *Predatory Behavior ; Tsuga ; United States ; },
abstract = {Leucopis argenticollis (Zetterstedt) and Leucopis piniperda (Malloch) are known to feed on the lineage of Adelges tsugae Annand that is native to western North America, but it is not known if they will survive on the lineage that was introduced from Japan to the eastern USA. In 2014, western Leucopis spp. larvae were brought to the laboratory and placed on A. tsugae collected in either Washington (North American A. tsugae lineage) or Connecticut (Japanese lineage). There were no significant differences in survival or developmental times between flies reared on the two different adelgid lineages. In 2015 and 2016, western Leucopis spp. adults were released at two different densities onto enclosed branches of A. tsugae infested eastern hemlock (Tsuga canadensis (L.) Carr.) in Tennessee and New York. Cages were recovered and their contents examined 4 weeks after release at each location. Leucopis spp. larvae and puparia of the F1 generation were recovered at both release locations and adults of the F1 generation were collected at the Tennessee location. The number of Leucopis spp. offspring collected increased with increasing adelgid density, but did not differ by the number of adult flies released. Flies recovered from cages and flies collected from the source colony were identified as L.argenticollis and L. piniperda using DNA barcoding. These results demonstrate that Leucopis spp. from the Pacific Northwest are capable of feeding and developing to the adult stage on A. tsugae in the eastern USA and they are able to tolerate environmental conditions during late spring and early summer at the southern and northern extent of the area invaded by A. tsugae in the eastern USA.},
}
@article {pmid28290215,
year = {2018},
author = {Chatterjee, N and Dhar, B and Bhattarcharya, D and Deori, S and Doley, J and Bam, J and Das, PJ and Bera, AK and Deb, SM and Devi, NN and Paul, R and Malvika, S and Ghosh, SK},
title = {Genetic assessment of leech species from yak (Bos grunniens) in the tract of Northeast India.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {1},
pages = {73-81},
doi = {10.1080/24701394.2016.1238914},
pmid = {28290215},
issn = {2470-1408},
mesh = {Animals ; Cattle/parasitology ; DNA Barcoding, Taxonomic ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; *Genes, Mitochondrial ; India ; Leeches/classification/*genetics ; Phylogeny ; },
abstract = {Yak is an iconic symbol of Tibet and high altitudes of Northeast India. It is highly cherished for milk, meat, and skin. However, yaks suffer drastic change in milk production, weight loss, etc, when infested by parasites. Among them, infestation by leeches is a serious problem in the Himalayan belt of Northeast India. The parasite feeds on blood externally or from body orifices, like nasopharynx, oral, rectum, etc. But there has been limited data about the leech species infesting the yak in that region because of the difficulties in morphological identification due to plasticity of the body, changes in shape, and surface structure and thus, warrants for the molecular characterization of leech. In anticipation, this study would be influential in proper identification of leech species infesting yak track and also helpful in inventorying of leech species in Northeast India. Here, we investigated, through combined approach of molecular markers and morphological parameters for the identification of leech species infesting yak. The DNA sequences of COI barcode fragment, 18S and 28S rDNA, were analyzed for species identification. The generated sequences were subjected to similarity match in global database and analyzed further through Neighbour-Joining, K2P distance based as well as ML approach. Among the three markers, only COI was successful in delineating species whereas the 18S and 28S failed to delineate the species. Our study confirmed the presence of the species from genus Hirudinaria, Haemadipsa, Whitmania, and one species Myxobdella annandalae, which has not been previously reported from this region.},
}
@article {pmid28288827,
year = {2017},
author = {Guernet, A and Grumolato, L},
title = {CRISPR/Cas9 editing of the genome for cancer modeling.},
journal = {Methods (San Diego, Calif.)},
volume = {121-122},
number = {},
pages = {130-137},
doi = {10.1016/j.ymeth.2017.03.007},
pmid = {28288827},
issn = {1095-9130},
mesh = {Animals ; Bacterial Proteins/*genetics/metabolism ; CRISPR-Associated Protein 9 ; *CRISPR-Cas Systems ; Cell Transformation, Neoplastic/genetics/metabolism/pathology ; *Clustered Regularly Interspaced Short Palindromic Repeats ; DNA End-Joining Repair ; DNA, Neoplasm/*genetics/metabolism ; Disease Models, Animal ; Endonucleases/*genetics/metabolism ; Gene Editing/*methods ; Genome ; Humans ; Intestinal Neoplasms/*genetics/metabolism/pathology ; Models, Genetic ; Mutation ; RNA, Guide, CRISPR-Cas Systems/*genetics/metabolism ; Recombinational DNA Repair ; },
abstract = {The CRISPR/Cas9 revolution has democratized access to genome editing in many biological fields, including cancer research. Cancer results from the multistep accumulation of mutations that confer to the transformed cells certain biological hallmarks typical of the malignant phenotype. One of the major goals in cancer research is to characterize such mutations and assess their implication in the oncogenic process. Through CRISPR/Cas9 technology, genetic aberrations identified in a patient's tumor can now be easily recreated in experimental models, which can then be used for basic research or for more translational applications. Here we review the different CRISPR/Cas9 strategies that have been implemented to recapitulate oncogenic mutations in both in vitro and in vivo systems, including novel strategies to model tumor evolution and genetic heterogeneity.},
}
@article {pmid28287980,
year = {2018},
author = {Wang, B and Zheng, X and Zhou, S and Zhou, C and Wei, X and Zhang, Q and Wei, Z},
title = {Constructing DNA Barcode Sets Based on Particle Swarm Optimization.},
journal = {IEEE/ACM transactions on computational biology and bioinformatics},
volume = {15},
number = {3},
pages = {999-1002},
doi = {10.1109/TCBB.2017.2679004},
pmid = {28287980},
issn = {1557-9964},
mesh = {*Algorithms ; DNA/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; Genome, Human/*genetics ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; Sequence Analysis, DNA ; },
abstract = {Following the completion of the human genome project, a large amount of high-throughput bio-data was generated. To analyze these data, massively parallel sequencing, namely next-generation sequencing, was rapidly developed. DNA barcodes are used to identify the ownership between sequences and samples when they are attached at the beginning or end of sequencing reads. Constructing DNA barcode sets provides the candidate DNA barcodes for this application. To increase the accuracy of DNA barcode sets, a particle swarm optimization (PSO) algorithm has been modified and used to construct the DNA barcode sets in this paper. Compared with the extant results, some lower bounds of DNA barcode sets are improved. The results show that the proposed algorithm is effective in constructing DNA barcode sets.},
}
@article {pmid28287390,
year = {2017},
author = {Moravec, F and Chaabane, A and Neifar, L and Gey, D and Justine, JL},
title = {Species of Philometra (Nematoda, Philometridae) from fishes off the Mediterranean coast of Africa, with a description of Philometra rara n. sp. from Hyporthodus haifensis and a molecular analysis of Philometra saltatrix from Pomatomus saltatrix.},
journal = {Parasite (Paris, France)},
volume = {24},
number = {},
pages = {8},
pmid = {28287390},
issn = {1776-1042},
mesh = {Animals ; Bass/genetics/*parasitology ; DNA Barcoding, Taxonomic/veterinary ; Dracunculoidea/anatomy &amp; histology/*classification/genetics/ultrastructure ; Female ; Fish Diseases/epidemiology/*parasitology ; Fishes ; Libya ; Male ; Mediterranean Sea ; Microscopy, Electron, Scanning ; Prevalence ; Spirurida Infections/epidemiology/parasitology/*veterinary ; Tunisia ; },
abstract = {Two gonad-infecting species of Philometra Costa, 1845 (Nematoda, Philometridae) were recorded for the first time from marine perciform fishes off Tunisia and Libya: Philometra rara n. sp. from the rare, deep-water Haifa grouper Hyporthodus haifensis (Serranidae) off Libya and Philometra saltatrix Ramachandran, 1973 from the bluefish Pomatomus saltatrix (Pomatomidae) off Tunisia. Identification of both fish species was confirmed by molecular barcoding. Light and scanning electron microscope studies of Ph. rara n. sp. showed that it is characterized by the length of spicules (216-219 μm) and the gubernaculum (90-93 μm), the gubernaculum/spicules length ratio (1:2.32-2.43), and mainly by the shape and structure of the distal end of the gubernaculum (shovel-shaped with a wide median smooth field in dorsal view), appearing as having a dorsal protuberance in lateral view, and by the structure of the male caudal mound (dorsally interrupted); large subgravid females (70-137 mm long) are characterized by the presence of four oval submedian cephalic elevations, each of them bearing a pair of cephalic papillae of the outer circle. The finding of Ph. saltatrix off Tunisia confirms that this species is widespread throughout the Mediterranean region. A molecular analysis of our Ph. saltatrix specimens and other available philometrid cytochrome c oxidase 1 (COI) sequences showed that most species have robust clades. Sequences of Ph. saltatrix from Tunisia diverge from Ph. saltatrix from Brazil and the USA, suggesting that speciation is currently occurring between populations from both sides of the Atlantic Ocean.},
}
@article {pmid28287117,
year = {2017},
author = {Myhrvold, C and Baym, M and Hanikel, N and Ong, LL and Gootenberg, JS and Yin, P},
title = {Barcode extension for analysis and reconstruction of structures.},
journal = {Nature communications},
volume = {8},
number = {},
pages = {14698},
pmid = {28287117},
issn = {2041-1723},
mesh = {Base Sequence ; DNA/chemistry/*ultrastructure ; DNA Barcoding, Taxonomic/*methods ; Electrophoresis, Agar Gel ; Microscopy, Atomic Force ; Microscopy, Electron, Transmission ; Nanostructures/chemistry/*ultrastructure ; Nanotechnology/*methods ; Nucleic Acid Conformation ; Sequence Analysis, DNA ; },
abstract = {Collections of DNA sequences can be rationally designed to self-assemble into predictable three-dimensional structures. The geometric and functional diversity of DNA nanostructures created to date has been enhanced by improvements in DNA synthesis and computational design. However, existing methods for structure characterization typically image the final product or laboriously determine the presence of individual, labelled strands using gel electrophoresis. Here we introduce a new method of structure characterization that uses barcode extension and next-generation DNA sequencing to quantitatively measure the incorporation of every strand into a DNA nanostructure. By quantifying the relative abundances of distinct DNA species in product and monomer bands, we can study the influence of geometry and sequence on assembly. We have tested our method using 2D and 3D DNA brick and DNA origami structures. Our method is general and should be extensible to a wide variety of DNA nanostructures.},
}
@article {pmid28284548,
year = {2017},
author = {Beaumelle, L and Hedde, M and Vandenbulcke, F and Lamy, I},
title = {Relationships between metal compartmentalization and biomarkers in earthworms exposed to field-contaminated soils.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {224},
number = {},
pages = {185-194},
doi = {10.1016/j.envpol.2017.01.078},
pmid = {28284548},
issn = {1873-6424},
mesh = {Animals ; Biological Availability ; Biomarkers/metabolism ; *Environmental Exposure ; Environmental Monitoring ; France ; Metallothionein/metabolism ; Metals/analysis/*metabolism ; Oligochaeta/*drug effects/*metabolism ; Soil/*chemistry ; Soil Pollutants/analysis/*metabolism/*pharmacology ; Subcellular Fractions ; Toxicity Tests ; },
abstract = {Partitioning tissue metal concentration into subcellular compartments reflecting toxicologically available pools may provide good descriptors of the toxicological effects of metals on organisms. Here we investigated the relationships between internal compartmentalization of Cd, Pb and Zn and biomarker responses in a model soil organism: the earthworm. The aim of this study was to identify metal fractions reflecting the toxic pressure in an endogeic, naturally occurring earthworm species (Aporrectodea caliginosa) exposed to realistic field-contaminated soils. After a 21 days exposure experiment to 31 field-contaminated soils, Cd, Pb and Zn concentrations in earthworms and in three subcellular fractions (cytosol, debris and granules) were quantified. Different biomarkers were measured: the expression of a metallothionein gene (mt), the activity of catalase (CAT) and of glutathione-s-transferase (GST), and the protein, lipid and glycogen reserves. Biomarkers were further combined into an integrated biomarker index (IBR). The subcellular fractionation provided better predictors of biomarkers than the total internal contents hence supporting its use when assessing toxicological bioavailability of metals to earthworms. The most soluble internal pools of metals were not always the best predictors of biomarker responses. metallothionein expression responded to increasing concentrations of Cd in the insoluble fraction (debris + granules). Protein and glycogen contents were also mainly related to Cd and Pb in the insoluble fraction. On the other hand, GST activity was better explained by Pb in the cytosolic fraction. CAT activity and lipid contents variations were not related to metal subcellular distribution. The IBR was best explained by both soluble and insoluble fractions of Pb and Cd. This study further extends the scope of mt expression as a robust and specific biomarker in an ecologically representative earthworm species exposed to field-contaminated soils. The genetic lineage of the individuals, assessed by DNA barcoding with cytochrome c oxidase subunit I, did not influence mt expression.},
}
@article {pmid28281309,
year = {2017},
author = {Yang, Z and Rannala, B},
title = {Bayesian species identification under the multispecies coalescent provides significant improvements to DNA barcoding analyses.},
journal = {Molecular ecology},
volume = {26},
number = {11},
pages = {3028-3036},
doi = {10.1111/mec.14093},
pmid = {28281309},
issn = {1365-294X},
mesh = {Bayes Theorem ; Computer Simulation ; *DNA Barcoding, Taxonomic ; Gene Library ; Genes, Mitochondrial ; *Models, Genetic ; },
abstract = {DNA barcoding methods use a single locus (usually the mitochondrial COI gene) to assign unidentified specimens to known species in a library based on a genetic distance threshold that distinguishes between-species divergence from within-species diversity. Recently developed species delimitation methods based on the multispecies coalescent (MSC) model offer an alternative approach to individual assignment using either single-locus or multiloci sequence data. Here, we use simulations to demonstrate three features of an MSC method implemented in the program bpp. First, we show that with one locus, MSC can accurately assign individuals to species without the need for arbitrarily determined distance thresholds (as required for barcoding methods). We provide an example in which no single threshold or barcoding gap exists that can be used to assign all specimens without incurring high error rates. Second, we show that bpp can identify cryptic species that may be misidentified as a single species within the library, potentially improving the accuracy of barcoding libraries. Third, we show that taxon rarity does not present any particular problems for species assignments using bpp and that accurate assignments can be achieved even when only one or a few loci are available. Thus, concerns that have been raised that MSC methods may have problems analysing rare taxa (singletons) are unfounded. Currently, barcoding methods enjoy a huge computational advantage over MSC methods and may be the only approach feasible for massively large data sets, but MSC methods may offer a more stringent test for species that are tentatively assigned by barcoding.},
}
@article {pmid28280591,
year = {2017},
author = {Brasier, MJ and Wiklund, H and Neal, L and Jeffreys, R and Linse, K and Ruhl, H and Glover, AG},
title = {Correction to 'DNA barcoding uncovers cryptic diversity in 50% of deep-sea Antarctic polychaetes'.},
journal = {Royal Society open science},
volume = {4},
number = {1},
pages = {160937},
doi = {10.1098/rsos.160937},
pmid = {28280591},
issn = {2054-5703},
abstract = {[This corrects the article DOI: 10.1098/rsos.160432.].},
}
@article {pmid28280149,
year = {2017},
author = {Zhang, W and Zhao, G and Luo, Z and Lin, Y and Wang, L and Guo, Y and Wang, A and Jiang, S and Jiang, Q and Gong, J and Wang, Y and Hou, S and Huang, J and Li, T and Qin, Y and Dong, J and Qin, Q and Zhang, J and Zou, X and He, X and Zhao, L and Xiao, Y and Xu, M and Cheng, E and Huang, N and Zhou, T and Shen, Y and Walker, R and Luo, Y and Kuang, Z and Mitchell, LA and Yang, K and Richardson, SM and Wu, Y and Li, BZ and Yuan, YJ and Yang, H and Lin, J and Chen, GQ and Wu, Q and Bader, JS and Cai, Y and Boeke, JD and Dai, J},
title = {Engineering the ribosomal DNA in a megabase synthetic chromosome.},
journal = {Science (New York, N.Y.)},
volume = {355},
number = {6329},
pages = {},
doi = {10.1126/science.aaf3981},
pmid = {28280149},
issn = {1095-9203},
support = {BB/M005690/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Cell Nucleus/genetics/ultrastructure ; Chromosomes, Artificial, Yeast/*chemistry/genetics/ultrastructure ; DNA, Ribosomal/*genetics ; Genetic Engineering/*methods ; *Genome, Fungal ; Saccharomyces cerevisiae/*genetics/ultrastructure ; Synthetic Biology/*methods ; Transcriptome ; },
abstract = {We designed and synthesized a 976,067-base pair linear chromosome, synXII, based on native chromosome XII in Saccharomyces cerevisiae SynXII was assembled using a two-step method, specified by successive megachunk integration and meiotic recombination-mediated assembly, producing a functional chromosome in S. cerevisiae. Minor growth defect "bugs" detected in synXII, caused by deletion of tRNA genes, were rescued by introducing an ectopic copy of a single tRNA gene. The ribosomal gene cluster (rDNA) on synXII was left intact during the assembly process and subsequently replaced by a modified rDNA unit used to regenerate rDNA at three distinct chromosomal locations. The signature sequences within rDNA, which can be used to determine species identity, were swapped to generate a Saccharomyces synXII strain that would be identified as Saccharomyces bayanus by standard DNA barcoding procedures.},
}
@article {pmid28278695,
year = {2018},
author = {Barman, AS and Singh, M and Pandey, PK},
title = {DNA barcoding and genetic diversity analyses of fishes of Kaladan River of Indo-Myanmar biodiversity hotspot.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {3},
pages = {367-378},
doi = {10.1080/24701394.2017.1285290},
pmid = {28278695},
issn = {2470-1408},
mesh = {Animals ; Bayes Theorem ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Fishes/*classification/genetics ; *Genetic Variation ; Phylogeny ; Rivers ; Sequence Analysis, DNA/*methods ; },
abstract = {Species are considered as a fundamental unit of biodiversity. Therefore, the prerequisite for biodiversity management and conservation is to know the number of species one is dealing with. Consequently, the need of the present study was conceptualized, which dealt with the comprehensive molecular appraisal of Kaladan's Fish fauna. A total of 291 specimens representing 49 species, 28 genera, 11 families, and 4 orders, were collected from 11 sampling stations situated along the main Kaladan River and its four major tributaries, i.e. Tiau, Tuipui, Mat, and Tuichang, flowing in Mizoram state of India (part of Indo-Myanmar biodiversity hotspot) and COI sequences of all the 291 samples were generated. All the analyses conducted in the present study, i.e. K2P genetic divergence, bPTP and Neighbour-Joining suggest that DNA Barcoding is an efficient and reliable tool for species identification and deciding the species boundary. Most of the species of Kaladan showed the clear existence of barcode gap. However, the presence of intra-specific and inter-specific genetic distance overlap in two species revealed the existence of putative sibling species or hidden taxa. This study also revealed the presence of two cryptic species and putative previously unknown species of genus Garra and Schistura. The COI barcode database of Kaladan's fish fauna, established in the present study, may serve as a reference library for accurate identification of fishes and will help ichthyologist, researcher, students, biodiversity managers and policy makers in proper planning with regard to conservation and management of the resources.},
}
@article {pmid28278693,
year = {2018},
author = {Huang, H and Chen, Z and Wei, Z and Bu, R and Wu, Z},
title = {DNA barcoding revises a misidentification on mossy frog: new record and distribution extension of Theloderma corticale Boulenger, 1903 (Amphibia: Anura: Rhacophoridae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {2},
pages = {273-280},
doi = {10.1080/24701394.2016.1275601},
pmid = {28278693},
issn = {2470-1408},
mesh = {Animals ; Anura/*classification/genetics ; China ; Conservation of Natural Resources ; DNA Barcoding, Taxonomic/*methods ; Endangered Species ; Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {As an endangered animal group, mossy frog (genus Theloderma) has attracted the attention of biologists and wildlife conservationists. Clarifying the taxonomic status and distribution of each species in Theloderma is important to determine the conservation status for each species, establish appropriate conservation strategies and probe the speciation process. Recently, we discovered a medium-sized species of mossy frog of the genus Theloderma in April 2015 during municipal surveys of amphibians in Dayao Mountain of Jinxiu. It was collected from the water-filled tree cavities. However, there remains some uncertainty about the species determination of the mossy frog in the Yinshan station of Dayao Mountain in Guangxi Province, China. Previously, the mossy frog in Guangxi Province was recognized as Th. kwangsiense. In order to clarify the species status of the mossy frog obtained from Guangxi, we sequenced 2414 bp of the 12S and 16S genes in the sample collected from the Dayao Mountain. Combining all the sequence in NCBI, genetic analyses from the data suggest that the sample from the Dayao Mountain is Th. corticale rather than Th. kwangsiense. It is most likely that the most previous studies had wrong species identification. And, it is the first time we use DNA barcoding to prove that the species obtained from Guangxi is a new distribution of Th. corticale.},
}
@article {pmid28272801,
year = {2017},
author = {Truong, C and Mujic, AB and Healy, R and Kuhar, F and Furci, G and Torres, D and Niskanen, T and Sandoval-Leiva, PA and Fernández, N and Escobar, JM and Moretto, A and Palfner, G and Pfister, D and Nouhra, E and Swenie, R and Sánchez-García, M and Matheny, PB and Smith, ME},
title = {How to know the fungi: combining field inventories and DNA-barcoding to document fungal diversity.},
journal = {The New phytologist},
volume = {214},
number = {3},
pages = {913-919},
doi = {10.1111/nph.14509},
pmid = {28272801},
issn = {1469-8137},
mesh = {*Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Fungi/*classification ; Plants/microbiology ; South America ; Symbiosis ; },
}
@article {pmid28270824,
year = {2017},
author = {Pei, N and Chen, B and Kress, WJ},
title = {Advances of Community-Level Plant DNA Barcoding in China.},
journal = {Frontiers in plant science},
volume = {8},
number = {},
pages = {225},
pmid = {28270824},
issn = {1664-462X},
abstract = {DNA barcoding is a commonly used bio-technology in multiple disciplines including biology, environmental science, forensics and inspection, etc. Forest dynamic plots provide a unique opportunity to carry out large-scale, comparative, and multidisciplinary research for plant DNA barcoding. The paper concisely reviewed four previous progresses in China; specifically, species discrimination, community phylogenetic reconstruction, phylogenetic community structure exploration, and biodiversity index evaluation. Further, we demonstrated three major challenges; specifically, building the impetus to generate DNA barcodes using multiple plant DNA markers for all woody species at forest community levels, analyzing massive DNA barcoding sequence data, and promoting theoretical innovation. Lastly, we raised five possible directions; specifically, proposing a "purpose-driven barcode" fit for multi-level applications, developing new integrative sequencing strategies, pushing DNA barcoding beyond terrestrial ecosystem, constructing national-level DNA barcode sequence libraries for special plant groups, and establishing intelligent identification systems or online server platforms. These efforts will be potentially valuable to explore large-scale biodiversity patterns, the origin and evolution of life, and will also facilitate preservation and utilization of biodiversity resources.},
}
@article {pmid28267567,
year = {2017},
author = {VanderMolen, KM and Little, JG and Sica, VP and El-Elimat, T and Raja, HA and Oberlies, NH and Baker, TR and Mahony, C},
title = {Safety assessment of mushrooms in dietary supplements by combining analytical data with in silico toxicology evaluation.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {103},
number = {},
pages = {133-147},
doi = {10.1016/j.fct.2017.03.005},
pmid = {28267567},
issn = {1873-6351},
mesh = {Agaricales/*chemistry/genetics ; Computer Simulation ; Dietary Supplements/*adverse effects/toxicity ; Humans ; Toxicology/*methods ; },
abstract = {Despite growing popularity in dietary supplements, many medicinal mushrooms have not been evaluated for their safe human consumption using modern techniques. The multifaceted approach described here relies on five key principles to evaluate the safety of non-culinary fungi for human use: (1) identification by sequencing the nuclear ribosomal internal transcribed spacer (ITS) region (commonly referred to as ITS barcoding), (2) screening an extract of each fungal raw material against a database of known fungal metabolites, (3) comparison of these extracts to those prepared from grocery store-bought culinary mushrooms using UHPLCPDA-ELS-HRMS, (4) review of the toxicological and chemical literature for each fungus, and (5) evaluation of data establishing presence in-market. This weight-of-evidence approach was used to evaluate seven fungal raw materials and determine safe human use for each. Such an approach may provide an effective alternative to conventional toxicological animal studies (or more efficiently identifies when studies are necessary) for the safety assessment of fungal dietary ingredients.},
}
@article {pmid28266019,
year = {2019},
author = {Agapouda, A and Booker, A and Kiss, T and Hohmann, J and Heinrich, M and Csupor, D},
title = {Quality control of Hypericum perforatum L. analytical challenges and recent progress.},
journal = {The Journal of pharmacy and pharmacology},
volume = {71},
number = {1},
pages = {15-37},
doi = {10.1111/jphp.12711},
pmid = {28266019},
issn = {2042-7158},
support = {GINOP-2.3.2-15-2016-00012//J&#xe1;nos Bolyai Research Scholarship of the Hungarian Academy of Sciences/ ; },
mesh = {Animals ; Chromatography, Liquid/methods ; Humans ; Hypericum/*chemistry/metabolism ; Plant Extracts/*analysis/chemistry/standards ; *Quality Control ; Secondary Metabolism ; Spectrum Analysis/methods ; },
abstract = {OBJECTIVES: The most widely applied qualitative and quantitative analytical methods in the quality control of Hypericum perforatum extracts will be reviewed, including routine analytical tools and most modern approaches.<br><br>KEY FINDINGS: Biologically active components of H. perforatum are chemically diverse; therefore, different chromatographic and detection methods are required for the comprehensive analysis of St. John's wort extracts. Naphthodianthrones, phloroglucinols and flavonoids are the most widely analysed metabolites of this plant. For routine quality control, detection of major compounds belonging to these groups seems to be sufficient; however, closer characterization requires the detection of minor compounds as well.<br><br>CONCLUSIONS: TLC and HPTLC are basic methods in the routine analysis, whereas HPLC-DAD is the most widely applied method for quantitative analysis due to its versatility. LC-MS is gaining importance in pharmacokinetic studies due to its sensitivity. Modern approaches, such as DNA barcoding, NIRS and NMR metabolomics, may offer new possibilities for the more detailed characterization of secondary metabolite profile of H. perforatum extracts.},
}
@article {pmid28264564,
year = {2017},
author = {Schmidt, ST and Zimmerman, SM and Wang, J and Kim, SK and Quake, SR},
title = {Quantitative Analysis of Synthetic Cell Lineage Tracing Using Nuclease Barcoding.},
journal = {ACS synthetic biology},
volume = {6},
number = {6},
pages = {936-942},
pmid = {28264564},
issn = {2161-5063},
support = {P40 OD010440/OD/NIH HHS/United States ; U01 HL099995/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; CRISPR-Cas Systems/genetics ; Caenorhabditis elegans/classification/genetics ; Cell Lineage/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Helminth/genetics ; INDEL Mutation/genetics ; Models, Genetic ; Synthetic Biology/*methods ; },
abstract = {Lineage tracing by the determination and mapping of progeny arising from single cells is an important approach enabling the elucidation of mechanisms underlying diverse biological processes ranging from development to disease. We developed a dynamic sequence-based barcode system for synthetic lineage tracing and have demonstrated its performance in C. elegans, a model organism whose lineage tree is well established. The strategy we use creates lineage trees based upon the introduction of synthetically controlled mutations into cells and the propagation of these mutations to daughter cells at each cell division. We analyzed this experimental proof of concept along with a corresponding simulation and analytical model to gain a deeper understanding of the coding capacity of the system. Our results provide specific bounds on the fidelity of lineage tracing using such approaches.},
}
@article {pmid28264417,
year = {2017},
author = {Qi, X and Wang, XH and Andersen, T and Lin, XL},
title = {A new species of Manoa Fittkau (Diptera: Chironomidae), with DNA barcodes from Xianju National Park, Oriental China.},
journal = {Zootaxa},
volume = {4231},
number = {3},
pages = {zootaxa.4231.3.6},
doi = {10.11646/zootaxa.4231.3.6},
pmid = {28264417},
issn = {1175-5334},
mesh = {Animals ; China ; *Chironomidae ; *DNA Barcoding, Taxonomic ; Female ; Male ; Parks, Recreational ; },
abstract = {The genus Manoa and the tribe Pseudochironomini are recorded from the Oriental region for the first time. Manoa xianjuensis Qi &amp; Lin sp. n. from Xianju National Park, Zhejiang, China is described and illustrated as adult male and female, the latter associated with the male by standard DNA barcodes. A neighbor joining tree based on available Pseudochironomini DNA barcodes and keys to the adults in Manoa are given.},
}
@article {pmid28264353,
year = {2017},
author = {Jarzabek-Müller, A and Morinière, J and Varandi, HB and Müller, J},
title = {Synaptus iranicus sp. nov., a second species of the genus Synaptus Eschscholtz, 1829 from Iran (Coleoptera: Elateridae) discovered by an integrative approach.},
journal = {Zootaxa},
volume = {4232},
number = {4},
pages = {zootaxa.4232.4.6},
doi = {10.11646/zootaxa.4232.4.6},
pmid = {28264353},
issn = {1175-5334},
mesh = {Animals ; *Coleoptera ; Female ; Iran ; Male ; },
abstract = {Synaptus filiformis Fabricius, 1781 has been recognized as a rather variable elaterid species. Based on morphological distinctness of 3 specimens (2 males, 1 female) from Mazandaran, Iran, a new species is here hypothesised. COI barcoding supports the new species as a new Barcode Index Number with a distance of mean 13.5% to the three other BINs available on the Barcode of Life Database. The new species Synaptus iranicus sp. nov. (BOLD: ACZ9929) and its distinctive features are described. Moreover the results of the DNA barcoding suggest that Synaptus filiformis as yet described is not a single species, but rather a complex of several morphologically similar species.},
}
@article {pmid28264285,
year = {2017},
author = {Tachi, T},
title = {Description of the female of Ceromya glaucescens Tachi &amp; Shima (Diptera: Tachinidae) and discovery of unusual sexual dimorphism in this species.},
journal = {Zootaxa},
volume = {4237},
number = {3},
pages = {zootaxa.4237.3.10},
doi = {10.11646/zootaxa.4237.3.10},
pmid = {28264285},
issn = {1175-5334},
mesh = {Animals ; *Diptera ; Extremities ; Female ; Insecta ; Male ; Sex Characteristics ; Wings, Animal ; },
abstract = {Sexual dimorphism is a phenomenon in which the male and female of a species differ in features of the external morphology such as size, shape, colour, or the development of appendages. In the Diptera, stalked compound eyes, leg modifications and wing patterns are well-known examples of sexual dimorphism (McAlpine 1979; Zeil 1983; Adler &amp; Adler 1991; Meyerrochow &amp; Reid 1994; Wilkinson &amp; Dodson 1996; Sivinski 1997; Baker &amp; Wilkinson 2001; Eberhard 2002; Puniamoorthy et al. 2008). Males and females of sexually dimorphic species are often described as separate species due to the dissimilarity in external characters, thus leading to problems in identification and proper association of the sexes. In contrast to characters that are usually involved in sexual dimorphism, leg chaetotaxy is considered one of the invariable character systems, irrespective of sex, in the tribe Siphonini of the Tachinidae, and is thus widely used in keys to genera and species (O'Hara 1989; Andersen 1996). Species' identification by DNA barcoding has been used in various groups of organisms (Hebert et al. 2003; Ratnasingham &amp; Hebert 2013). In insects, males, usually more easily identified by morphological characters (e.g., postabdominal features) than females, are often used for barcoding. The identification of females will improve as sequence data accumulate, such as data from pairs collected in copula. In this paper, I describe sexual dimorphism in the Japanese endemic species of tachinid fly Ceromya glaucescens Tachi &amp; Shima, 2000 of the tribe Siphonini, and use molecular and morphological data for the identification of this species. Sequence data of C. silacea (Meigen, 1824) are also included for comparison.},
}
@article {pmid28264279,
year = {2017},
author = {Costa, GJ and Nunes, VL and Marabuto, E and Mendes, R and Laurentino, TG and Quartau, JA and Paulo, OS and Simões, PC},
title = {Morphology, songs and genetics identify two new cicada species from Morocco: Tettigettalna afroamissa sp. nov. and Berberigetta dimelodica gen. nov. &amp; sp. nov. (Hemiptera: Cicadettini).},
journal = {Zootaxa},
volume = {4237},
number = {3},
pages = {zootaxa.4237.3.4},
doi = {10.11646/zootaxa.4237.3.4},
pmid = {28264279},
issn = {1175-5334},
mesh = {Animals ; Bayes Theorem ; Europe ; *Hemiptera ; Morocco ; Phylogeny ; },
abstract = {Morocco has been the subject of very few expeditions on the last century with the objective of studying small cicadas. In the summer of 2014 an expedition was carried out to Morocco to update our knowledge with acoustic recordings and genetic data of these poorly known species. We describe here two new small-sized cicadas that could not be directly assigned to any species of North African cicadas: Tettigettalna afroamissa sp. nov. and Berberigetta dimelodica gen. nov. &amp; sp. nov. In respect to T. afroamissa it is the first species of the genus to be found outside Europe and we frame this taxon within the evolutionary history of the genus. Acoustic analysis of this species allows us to confidently separate T. afroamissa from its congeners. With B. dimelodica, a small species showing a remarkable calling song characterized by an abrupt frequency modulation, a new genus had to be erected. Bayesian inference and maximum likelihood phylogenetic analyses with DNA-barcode sequences of Cytochrome C Oxidase 1 support the monophyly of both species, their distinctness and revealed genetic structure within B. dimelodica. Alongside the descriptions we also provide GPS coordinates of collection points, distributions and habitat preferences.},
}
@article {pmid28264271,
year = {2017},
author = {Yan, C and Song, C and Liu, T and Zhao, G and Hou, Z and Cao, W and Wang, X},
title = {Two new and one newly recorded species of Polypedilum Kieffer 1912 with DNA barcodes from Oriental China (Chironomidae: Diptera).},
journal = {Zootaxa},
volume = {4238},
number = {1},
pages = {zootaxa.4238.1.8},
doi = {10.11646/zootaxa.4238.1.8},
pmid = {28264271},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures ; Animals ; Body Size ; China ; *Chironomidae ; *DNA Barcoding, Taxonomic ; Male ; Organ Size ; },
abstract = {Polypedilum (Tripodura) enshiense Song &amp; Wang sp. n. and P. (Tripodura) jianfengense Song &amp; Wang sp. n. are described and illustrated as male imagines from China. P. (Uresipedilum) paraconvictum Yamamoto, Yamamoto &amp; Hirowatari, 2016 is recorded from China for the first time. Cytochrome coxidase subunit I (COI) sequence of above species are uploaded to Barcode of Life Data Systems (BOLD).},
}
@article {pmid28263836,
year = {2017},
author = {Medina, DX and Householder, KT and Ceton, R and Kovalik, T and Heffernan, JM and Shankar, RV and Bowser, RP and Wechsler-Reya, RJ and Sirianni, RW},
title = {Optical barcoding of PLGA for multispectral analysis of nanoparticle fate in vivo.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {253},
number = {},
pages = {172-182},
doi = {10.1016/j.jconrel.2017.02.033},
pmid = {28263836},
issn = {1873-4995},
mesh = {Animals ; Brain/*metabolism ; Brain Neoplasms/metabolism ; Cell Line, Tumor ; Cell Survival/drug effects ; *Cell-Penetrating Peptides/administration &amp; dosage/chemistry/pharmacokinetics ; Gene Products, tat ; HEK293 Cells ; Humans ; *Lactic Acid/administration &amp; dosage/chemistry/pharmacokinetics ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; *Nanoparticles/administration &amp; dosage/chemistry ; Optical Phenomena ; *Polyglycolic Acid/administration &amp; dosage/chemistry/pharmacokinetics ; Polylactic Acid-Polyglycolic Acid Copolymer ; Tissue Distribution ; },
abstract = {Understanding of the mechanisms by which systemically administered nanoparticles achieve delivery across biological barriers remains incomplete, due in part to the challenge of tracking nanoparticle fate in the body. Here, we develop a new approach for "barcoding" nanoparticles composed of poly(lactic-co-glycolic acid) (PLGA) with bright, spectrally defined quantum dots (QDs) to enable direct, fluorescent detection of nanoparticle fate with subcellular resolution. We show that QD labeling does not affect major biophysical properties of nanoparticles or their interaction with cells and tissues. Live cell imaging enabled simultaneous visualization of the interaction of control and targeted nanoparticles with bEnd.3 cells in a flow chamber, providing direct evidence that surface modification of nanoparticles with the cell-penetrating peptide TAT increases their biophysical association with cell surfaces over very short time periods under convective current. We next developed this technique for quantitative biodistribution analysis in vivo. These studies demonstrate that nanoparticle surface modification with the cell penetrating peptide TAT facilitates brain-specific delivery that is restricted to brain vasculature. Although nanoparticle entry into the healthy brain parenchyma is minimal, with no evidence for movement of nanoparticles across the blood-brain barrier (BBB), we observed that nanoparticles are able to enter to the central nervous system (CNS) through regions of altered BBB permeability - for example, into circumventricular organs in the brain or leaky vasculature of late-stage intracranial tumors. In sum, these data demonstrate a new, multispectral approach for barcoding PLGA, which enables simultaneous, quantitative analysis of the fate of multiple nanoparticle formulations in vivo.},
}
@article {pmid28262116,
year = {2016},
author = {Xiong, C and Hu, ZG and Tu, Y and Liu, HG and Wang, P and Zhao, MM and SHIi, YH and Wu, L and Sun, W and Chen, SL},
title = {ITS2 barcoding DNA region combined with high resolution melting (HRM) analysis of Hyoscyami Semen, the mature seed of Hyoscyamus niger.},
journal = {Chinese journal of natural medicines},
volume = {14},
number = {12},
pages = {898-903},
doi = {10.1016/S1875-5364(17)30014-6},
pmid = {28262116},
issn = {1875-5364},
mesh = {China ; DNA Barcoding, Taxonomic/*methods ; DNA, Intergenic/chemistry/*genetics ; DNA, Plant/chemistry/*genetics ; Discriminant Analysis ; Drug Contamination ; Drugs, Chinese Herbal/*chemistry ; Hyoscyamus/genetics/*growth &amp; development ; Seeds/genetics/*growth &amp; development ; Transition Temperature ; },
abstract = {Hyoscyami Semen, the mature dried seed of Hyoscyamus niger L., has long been used as a traditional Chinese medicine to treat human diseases. Hyoscyami Semen is found in local markets in China. In markets, sellers and buyers commonly inadvertently mix the seeds of H. niger with the seeds of related species such as Hygrophila salicifolia (Vahl) Nees, Astragalus complanatus R. Br., Cuscuta australis R. Br., Cuscuta chinensis Lam., and Impatiens balsamina L. because of their similar morphologies or similar names. Thus, developing a reliable method for discriminating H. niger seeds from its adulterants is necessary to reduce confusion and ensure the safe use of Hyoscyami Semen. The present study was designed to evaluate the efficiency of high-resolution melting analysis combined with DNA barcoding (Bar-HRM) with internal transcribed spacer 2 to discriminate H. niger. Our results show that Bar-HRM successfully identified the adulterants and detected the proportion of H. niger DNA extract within an admixture. In particular, HRM detected H. niger DNA extract in A. complanatus DNA extract at concentrations as low as 1%. In conclusion, the Bar-HRM method developed in the present study for authenticating H. niger is rapid and cost-effective. It can be used in the future to guarantee the purity of Hyoscyami Semen for the clinical use.},
}
@article {pmid28262023,
year = {2017},
author = {Oracz, J and Adolfsson, K and Westphal, V and Radzewicz, C and Borgström, MT and Sahl, SJ and Prinz, CN and Hell, SW},
title = {Ground State Depletion Nanoscopy Resolves Semiconductor Nanowire Barcode Segments at Room Temperature.},
journal = {Nano letters},
volume = {17},
number = {4},
pages = {2652-2659},
pmid = {28262023},
issn = {1530-6992},
abstract = {Nanowires hold great promise as tools for probing and interacting with various molecular and biological systems. Their unique geometrical properties (typically <100 nm in diameter and a few micrometers in length) enable minimally invasive interactions with living cells, so that electrical signals or forces can be monitored. All such experiments require in situ high-resolution imaging to provide context. While there is a clear need to extend visualization capabilities to the nanoscale, no suitable super-resolution far-field photoluminescence microscopy of extended semiconductor emitters has been described. Here, we report that ground state depletion (GSD) nanoscopy resolves heterostructured semiconductor nanowires formed by alternating GaP/GaInP segments ("barcodes") at a 5-fold resolution enhancement over confocal imaging. We quantify the resolution and contrast dependence on the dimensions of GaInP photoluminescence segments and illustrate the effects by imaging different nanowire barcode geometries. The far-red excitation wavelength (∼700 nm) and low excitation power (∼3 mW) make GSD nanoscopy attractive for imaging semiconductor structures in biological applications.},
}
@article {pmid28261587,
year = {2017},
author = {Yang, Y and Ricke, SC and Tellez, G and Kwon, YM},
title = {Quantitative Tracking of Salmonella Enteritidis Transmission Routes Using Barcode-Tagged Isogenic Strains in Chickens: Proof-of-Concept Study.},
journal = {Frontiers in veterinary science},
volume = {4},
number = {},
pages = {15},
pmid = {28261587},
issn = {2297-1769},
abstract = {Salmonella is an important foodborne bacterial pathogen, however, a fundamental understanding on Salmonella transmission routes within a poultry flock remains unclear. In this study, a series of barcode-tagged strains were constructed by inserting six random nucleotides into a functionally neutral region on the chromosome of S. Enteritidis as a tool for quantitative tracking of Salmonella transmission in chickens. Six distinct barcode-tagged strains were used for infection or contamination at either low dose (10[3] CFUs; three strains) or high dose (10[5] CFUs; three strains) in three independent experiments (Experiment 1 oral gavage; Experiment 2 contaminated feed; Experiment 3 contaminated water). For all chick experiments, cecal and foot-wash samples were collected from a subset of the chickens at days 7 or/and 14, from which genomic DNA was extracted and used to amplify the barcode regions. After the resulting PCR amplicons were pooled and analyzed by MiSeq sequencing, a total of approximately 1.5 million reads containing the barcode sequences were analyzed to determine the relative frequency of every barcode-tagged strain in each sample. In Experiment 1, the high dose of oral infection was correlated with greater dominance of the strains in the ceca of the respective seeder chickens and also in the contact chickens yet at lesser degrees. When chicks were exposed to contaminated feed (Experiment 2) or water (Experiment 3), there were no clear patterns of the barcode-tagged strains in relation to the dosage, except that the strains introduced at low dose required a longer time to colonize the ceca with contaminated feed. Most foot-wash samples contained only one to three strains for the majority of the samples, suggesting potential existence of an unknown mechanism(s) for strain exclusion. These results demonstrated the proof of concept of using barcode tagged to investigate transmission dynamics of Salmonella in chickens in a quantitative manner.},
}
@article {pmid28257512,
year = {2017},
author = {Comte, A and Gräfenhan, T and Links, MG and Hemmingsen, SM and Dumonceaux, TJ},
title = {Quantitative molecular diagnostic assays of grain washes for Claviceps purpurea are correlated with visual determinations of ergot contamination.},
journal = {PloS one},
volume = {12},
number = {3},
pages = {e0173495},
pmid = {28257512},
issn = {1932-6203},
mesh = {Chaperonins/*genetics ; Claviceps/classification/*isolation &amp; purification/pathogenicity ; DNA Barcoding, Taxonomic ; Edible Grain/genetics/*microbiology ; Seeds/genetics/microbiology ; },
abstract = {We examined the epiphytic microbiome of cereal grain using the universal barcode chaperonin-60 (cpn60). Microbial community profiling of seed washes containing DNA extracts prepared from field-grown cereal grain detected sequences from a fungus identified only to Class Sordariomycetes. To identify the fungal sequence and to improve the reference database, we determined cpn60 sequences from field-collected and reference strains of the ergot fungus, Claviceps purpurea. These data allowed us to identify this fungal sequence as deriving from C. purpurea, and suggested that C. purpurea DNA is readily detectable on agricultural commodities, including those for which ergot was not identified as a grading factor. To get a sense of the prevalence and level of C. purpurea DNA in cereal grains, we developed a quantitative PCR assay based on the fungal internal transcribed spacer (ITS) and applied it to 137 samples from the 2014 crop year. The amount of Claviceps DNA quantified correlated strongly with the proportion of ergot sclerotia identified in each grain lot, although there was evidence that non-target organisms were responsible for some false positives with the ITS-based assay. We therefore developed a cpn60-targeted loop-mediated isothermal amplification assay and applied it to the same grain wash samples. The time to positive displayed a significant, inverse correlation to ergot levels determined by visual ratings. These results indicate that both laboratory-based and field-adaptable molecular diagnostic assays can be used to detect and quantify pathogen load in bulk commodities using cereal grain washes.},
}
@article {pmid28257471,
year = {2017},
author = {Hoshino, T and Inagaki, F},
title = {Correction: Application of Stochastic Labeling with Random-Sequence Barcodes for Simultaneous Quantification and Sequencing of Environmental 16S rRNA Genes.},
journal = {PloS one},
volume = {12},
number = {3},
pages = {e0173546},
pmid = {28257471},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0169431.].},
}
@article {pmid28256524,
year = {2017},
author = {Thielecke, L and Aranyossy, T and Dahl, A and Tiwari, R and Roeder, I and Geiger, H and Fehse, B and Glauche, I and Cornils, K},
title = {Limitations and challenges of genetic barcode quantification.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {43249},
pmid = {28256524},
issn = {2045-2322},
support = {R01 AG040118/AG/NIA NIH HHS/United States ; },
mesh = {Cell Count/*methods ; DNA Barcoding, Taxonomic/*methods ; HEK293 Cells ; Humans ; Nucleic Acid Amplification Techniques ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Analysis, DNA ; },
abstract = {Genetic barcodes are increasingly used to track individual cells and to quantitatively assess their clonal contributions over time. Although barcode quantification relies entirely on counting sequencing reads, detailed studies about the method's accuracy are still limited. We report on a systematic investigation of the relation between barcode abundance and resulting read counts after amplification and sequencing using cell-mixtures that contain barcodes with known frequencies ("miniBulks"). We evaluated the influence of protocol modifications to identify potential sources of error and elucidate possible limitations of the quantification approach. Based on these findings we designed an advanced barcode construct (BC32) to improved barcode calling and quantification, and to ensure a sensitive detection of even highly diluted barcodes. Our results emphasize the importance of using curated barcode libraries to obtain interpretable quantitative data and underline the need for rigorous analyses of any utilized barcode library in terms of reliability and reproducibility.},
}
@article {pmid28253481,
year = {2017},
author = {Maetzig, T and Ruschmann, J and Lai, CK and Ngom, M and Imren, S and Rosten, P and Norddahl, GL and von Krosigk, N and Sanchez Milde, L and May, C and Selich, A and Rothe, M and Dhillon, I and Schambach, A and Humphries, RK},
title = {A Lentiviral Fluorescent Genetic Barcoding System for Flow Cytometry-Based Multiplex Tracking.},
journal = {Molecular therapy : the journal of the American Society of Gene Therapy},
volume = {25},
number = {3},
pages = {606-620},
pmid = {28253481},
issn = {1525-0024},
support = {//CIHR/Canada ; },
mesh = {Cell Differentiation ; Cell Tracking/*methods ; Codon ; Flow Cytometry ; *Gene Expression ; Gene Order ; Gene Transfer Techniques ; *Genes, Reporter ; Genetic Vectors/*genetics ; Hematopoietic Stem Cells/cytology/metabolism ; Homeodomain Proteins/genetics ; Humans ; Lentivirus/*genetics ; Luminescent Proteins/*genetics/metabolism ; MicroRNAs/genetics ; Reproducibility of Results ; Transduction, Genetic ; },
abstract = {Retroviral integration site analysis and barcoding have been instrumental for multiplex clonal fate mapping, although their use imposes an inherent delay between sample acquisition and data analysis. Monitoring of multiple cell populations in real time would be advantageous, but multiplex assays compatible with flow cytometric tracking of competitive growth behavior are currently limited. We here describe the development and initial validation of three generations of lentiviral fluorescent genetic barcoding (FGB) systems that allow the creation of 26, 14, or 6 unique labels. Color-coded populations could be tracked in multiplex in vitro assays for up to 28 days by flow cytometry using all three vector systems. Those involving lower levels of multiplexing eased color-code generation and the reliability of vector expression and enabled functional in vitro and in vivo studies. In proof-of-principle experiments, FGB vectors facilitated in vitro multiplex screening of microRNA (miRNA)-induced growth advantages, as well as the in vivo recovery of color-coded progeny of murine and human hematopoietic stem cells. This novel series of FGB vectors provides new tools for assessing comparative growth properties in in vitro and in vivo multiplexing experiments, while simultaneously allowing for a reduction in sample numbers by up to 26-fold.},
}
@article {pmid28253235,
year = {2017},
author = {Ståhlberg, A and Krzyzanowski, PM and Egyud, M and Filges, S and Stein, L and Godfrey, TE},
title = {Simple multiplexed PCR-based barcoding of DNA for ultrasensitive mutation detection by next-generation sequencing.},
journal = {Nature protocols},
volume = {12},
number = {4},
pages = {664-682},
doi = {10.1038/nprot.2017.006},
pmid = {28253235},
issn = {1750-2799},
support = {R21 CA172999/CA/NCI NIH HHS/United States ; },
mesh = {DNA Mutational Analysis/*methods ; DNA Primers/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Limit of Detection ; Multiplex Polymerase Chain Reaction/*methods ; },
abstract = {Detection of extremely rare variant alleles within a complex mixture of DNA molecules is becoming increasingly relevant in many areas of clinical and basic research, such as the detection of circulating tumor DNA in the plasma of cancer patients. Barcoding of DNA template molecules early in next-generation sequencing (NGS) library construction provides a way to identify and bioinformatically remove polymerase errors that otherwise make detection of these rare variants very difficult. Several barcoding strategies have been reported, but all require long and complex library preparation protocols. Simple, multiplexed, PCR-based barcoding of DNA for sensitive mutation detection using sequencing (SiMSen-seq) was developed to generate targeted barcoded libraries with minimal DNA input, flexible target selection and a very simple, short (∼4 h) library construction protocol. The protocol comprises a three-cycle barcoding PCR step followed directly by adaptor PCR to generate the library and then bead purification before sequencing. Thus, SiMSen-seq allows detection of variant alleles at <0.1% frequency with easy customization of library content (from 1 to 40+ PCR amplicons) and a protocol that can be implemented in any molecular biology laboratory. Here, we provide a detailed protocol for assay development and describe software to process the barcoded sequence reads.},
}
@article {pmid28250597,
year = {2017},
author = {Enan, MR and Palakkott, AR and Ksiksi, TS},
title = {DNA barcoding of selected UAE medicinal plant species: a comparative assessment of herbarium and fresh samples.},
journal = {Physiology and molecular biology of plants : an international journal of functional plant biology},
volume = {23},
number = {1},
pages = {221-227},
pmid = {28250597},
issn = {0971-5894},
abstract = {It is commonly difficult to extract and amplify DNA from herbarium samples as they are old and preserved using different compounds. In addition, such samples are subjected to the accumulation of intrinsically produced plant substances over long periods (up to hundreds of years). DNA extraction from desert flora may pause added difficulties as many contain high levels of secondary metabolites. Herbarium samples from the Biology Department (UAE University) plant collection and fresh plant samples, collected from around Al-Ain (UAE), were used in this study. The three barcode loci for the coding genes matK, rbcL and rpoC1-were amplified. Our results showed that T. terresteris, H. robustum,T. pentandrus and Z. qatarense were amplified using all three primers for both fresh and herbaium samples. Both fresh and herbarium samples of C. comosum, however, were not amplified at all, using the three primers. Herbarium samples from A. javanica, C. imbricatum, T. aucherana and Z. simplex were not amplified with any of the three primers. For fresh samples 90, 90 and 80% of the samples were amplified using matK, rbcL and rpoC1, respectively. In short, fresh samples were significantly better amplified than those from herbarium sources, using the three primers. Both fresh and herbarium samples from one species (C. comosum), however, were not successfully amplified. It is also concluded that the rbcL regions showed real potentials to distinguish the UAE species under investigation into the appropriate family and genus.},
}
@article {pmid28248920,
year = {2017},
author = {Pettitt, SJ and Krastev, DB and Pemberton, HN and Fontebasso, Y and Frankum, J and Rehman, FL and Brough, R and Song, F and Bajrami, I and Rafiq, R and Wallberg, F and Kozarewa, I and Fenwick, K and Armisen-Garrido, J and Swain, A and Gulati, A and Campbell, J and Ashworth, A and Lord, CJ},
title = {Genome-wide barcoded transposon screen for cancer drug sensitivity in haploid mouse embryonic stem cells.},
journal = {Scientific data},
volume = {4},
number = {},
pages = {170020},
pmid = {28248920},
issn = {2052-4463},
support = {14276/CRUK_/Cancer Research UK/United Kingdom ; },
mesh = {Animals ; Antineoplastic Agents/pharmacology ; *DNA Transposable Elements ; Genome-Wide Association Study ; Haploidy ; Mice ; *Mouse Embryonic Stem Cells ; *Neoplasms/drug therapy/genetics ; },
abstract = {We describe a screen for cellular response to drugs that makes use of haploid embryonic stem cells. We generated ten libraries of mutants with piggyBac gene trap transposon integrations, totalling approximately 100,000 mutant clones. Random barcode sequences were inserted into the transposon vector to allow the number of cells bearing each insertion to be measured by amplifying and sequencing the barcodes. These barcodes were associated with their integration sites by inverse PCR. We exposed these libraries to commonly used cancer drugs and profiled changes in barcode abundance by Ion Torrent sequencing in order to identify mutations that conferred sensitivity. Drugs tested included conventional chemotherapeutics as well as targeted inhibitors of topoisomerases, poly(ADP-ribose) polymerase (PARP), Hsp90 and WEE1.},
}
@article {pmid28246190,
year = {2017},
author = {Yang, Z and Yang, F and Zhang, D and Liu, Z and Lin, A and Liu, C and Xiao, P and Yu, X and Sun, JP},
title = {Phosphorylation of G Protein-Coupled Receptors: From the Barcode Hypothesis to the Flute Model.},
journal = {Molecular pharmacology},
volume = {92},
number = {3},
pages = {201-210},
doi = {10.1124/mol.116.107839},
pmid = {28246190},
issn = {1521-0111},
mesh = {Animals ; Humans ; Phosphorylation ; Protein Conformation ; Receptors, G-Protein-Coupled/chemistry/*metabolism ; Signal Transduction/physiology ; beta-Arrestin 1/physiology ; },
abstract = {Seven transmembrane G protein-coupled receptors (GPCRs) are often phosphorylated at the C terminus and on intracellular loops in response to various extracellular stimuli. Phosphorylation of GPCRs by GPCR kinases and certain other kinases can promote the recruitment of arrestin molecules. The arrestins critically regulate GPCR functions not only by mediating receptor desensitization and internalization, but also by redirecting signaling to G protein-independent pathways via interactions with numerous downstream effector molecules. Accumulating evidence over the past decade has given rise to the phospho-barcode hypothesis, which states that ligand-specific phosphorylation patterns of a receptor direct its distinct functional outcomes. Our recent work using unnatural amino acid incorporation and fluorine-19 nuclear magnetic resonance ([19]F-NMR) spectroscopy led to the flute model, which provides preliminary insight into the receptor phospho-coding mechanism, by which receptor phosphorylation patterns are recognized by an array of phosphate-binding pockets on arrestin and are translated into distinct conformations. These selective conformations are recognized by various effector molecules downstream of arrestin. The phospho-barcoding mechanism enables arrestin to recognize a wide range of phosphorylation patterns of GPCRs, contributing to their diverse functions.},
}
@article {pmid28243532,
year = {2017},
author = {Garg, S and Suyesh, R and Sukesan, S and Biju, SD},
title = {Seven new species of Night Frogs (Anura, Nyctibatrachidae) from the Western Ghats Biodiversity Hotspot of India, with remarkably high diversity of diminutive forms.},
journal = {PeerJ},
volume = {5},
number = {},
pages = {e3007},
pmid = {28243532},
issn = {2167-8359},
abstract = {The Night Frog genus Nyctibatrachus (Family Nyctibatrachidae) represents an endemic anuran lineage of the Western Ghats Biodiversity Hotspot, India. Until now, it included 28 recognised species, of which more than half were described recently over the last five years. Our amphibian explorations have further revealed the presence of undescribed species of Nights Frogs in the southern Western Ghats. Based on integrated molecular, morphological and bioacoustic evidence, seven new species are formally described here as Nyctibatrachus athirappillyensis sp. nov., Nyctibatrachus manalari sp. nov., Nyctibatrachus pulivijayani sp. nov., Nyctibatrachus radcliffei sp. nov., Nyctibatrachus robinmoorei sp. nov., Nyctibatrachus sabarimalai sp. nov. and Nyctibatrachus webilla sp. nov., thereby bringing the total number of valid Nyctibatrachus species to 35 and increasing the former diversity estimates by a quarter. Detailed morphological descriptions, comparisons with other members of the genus, natural history notes, and genetic relationships inferred from phylogenetic analyses of a mitochondrial dataset are presented for all the new species. Additionally, characteristics of male advertisement calls are described for four new and three previously known species. Among the new species, six are currently known to be geographically restricted to low and mid elevation regions south of Palghat gap in the states of Kerala and Tamil Nadu, and one is probably endemic to high-elevation mountain streams slightly northward of the gap in Tamil Nadu. Interestingly, four new species are also among the smallest known Indian frogs. Hence, our discovery of several new species, particularly of easily overlooked miniaturized forms, reiterates that the known amphibian diversity of the Western Ghats of India still remains underestimated.},
}
@article {pmid28235609,
year = {2017},
author = {Serrania, J and Johner, T and Rupp, O and Goesmann, A and Becker, A},
title = {Massive parallel insertion site sequencing of an arrayed Sinorhizobium meliloti signature-tagged mini-Tn 5 transposon mutant library.},
journal = {Journal of biotechnology},
volume = {257},
number = {},
pages = {9-12},
doi = {10.1016/j.jbiotec.2017.02.019},
pmid = {28235609},
issn = {1873-4863},
mesh = {Bacterial Proteins/genetics ; Base Sequence ; DNA Transposable Elements/*genetics ; DNA, Bacterial/genetics ; Gene Library ; Genes, Bacterial ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing/*methods ; Mutagenesis, Insertional ; Mutation/*genetics ; Nitrogen-Fixing Bacteria/genetics ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/*methods ; Sinorhizobium meliloti/*genetics ; Symbiosis/genetics ; },
abstract = {Transposon mutagenesis in conjunction with identification of genomic transposon insertion sites is a powerful tool for gene function studies. We have implemented a protocol for parallel determination of transposon insertion sites by Illumina sequencing involving a hierarchical barcoding method that allowed for tracking back insertion sites to individual clones of an arrayed signature-tagged transposon mutant library. This protocol was applied to further characterize a signature-tagged mini-Tn 5 mutant library comprising about 12,000 mutants of the symbiotic nitrogen-fixing alphaproteobacterium Sinorhizobium meliloti (Pobigaylo et al., 2006; Appl. Environ. Microbiol. 72, 4329-4337). Previously, insertion sites have been determined for 5000 mutants of this library. Combining an adapter-free, inverse PCR method for sequencing library preparation with next generation sequencing, we identified 4473 novel insertion sites, increasing the total number of transposon mutants with known insertion site to 9562. The number of protein-coding genes that were hit at least once by a transposon increased by 1231 to a total number of 3673 disrupted genes, which represents 59% of the predicted protein-coding genes in S. meliloti.},
}
@article {pmid28234729,
year = {2021},
author = {Hutton, K and Ding, Q and Wellman, G},
title = {The Effects of Bar-coding Technology on Medication Errors: A Systematic Literature Review.},
journal = {Journal of patient safety},
volume = {17},
number = {3},
pages = {e192-e206},
pmid = {28234729},
issn = {1549-8425},
mesh = {Electronic Data Processing ; Humans ; *Medication Errors/prevention &amp; control ; *Medication Systems, Hospital ; Prospective Studies ; Technology ; United States ; },
abstract = {BACKGROUND: The bar-coding technology adoptions have risen drastically in U.S. health systems in the past decade. However, few studies have addressed the impact of bar-coding technology with strong prospective methodologies and the research, which has been conducted from both in-pharmacy and bedside implementations.<br><br>OBJECTIVE: This systematic literature review is to examine the effectiveness of bar-coding technology on preventing medication errors and what types of medication errors may be prevented in the hospital setting.<br><br>METHODS: A systematic search of databases was performed from 1998 to December 2016. Studies measuring the effect of bar-coding technology on medication errors were included in a full-text review. Studies with the outcomes other than medication errors such as efficiency or workarounds were excluded. The outcomes were measured and findings were summarized for each retained study.<br><br>RESULTS: A total of 2603 articles were initially identified and 10 studies, which used prospective before-and-after study design, were fully reviewed in this article. Of the 10 included studies, 9 took place in the United States, whereas the remaining was conducted in the United Kingdom. One research article focused on bar-coding implementation in a pharmacy setting, whereas the other 9 focused on bar coding within patient care areas. All 10 studies showed overall positive effects associated with bar-coding implementation.<br><br>CONCLUSIONS: The results of this review show that bar-coding technology may reduce medication errors in hospital settings, particularly on preventing targeted wrong dose, wrong drug, wrong patient, unauthorized drug, and wrong route errors.},
}
@article {pmid28232868,
year = {2017},
author = {Burkepile, DE and Parker, JD},
title = {Recent advances in plant-herbivore interactions.},
journal = {F1000Research},
volume = {6},
number = {},
pages = {119},
pmid = {28232868},
issn = {2046-1402},
abstract = {Plant-herbivore interactions shape community dynamics across marine, freshwater, and terrestrial habitats. From amphipods to elephants and from algae to trees, plant-herbivore relationships are the crucial link generating animal biomass (and human societies) from mere sunlight. These interactions are, thus, pivotal to understanding the ecology and evolution of virtually any ecosystem. Here, we briefly highlight recent advances in four areas of plant-herbivore interactions: (1) plant defense theory, (2) herbivore diversity and ecosystem function, (3) predation risk aversion and herbivory, and (4) how a changing climate impacts plant-herbivore interactions. Recent advances in plant defense theory, for example, highlight how plant life history and defense traits affect and are affected by multiple drivers, including enemy pressure, resource availability, and the local plant neighborhood, resulting in trait-mediated feedback loops linking trophic interactions with ecosystem nutrient dynamics. Similarly, although the positive effect of consumer diversity on ecosystem function has long been recognized, recent advances using DNA barcoding to elucidate diet, and Global Positioning System/remote sensing to determine habitat selection and impact, have shown that herbivore communities are probably even more functionally diverse than currently realized. Moreover, although most diversity-function studies continue to emphasize plant diversity, herbivore diversity may have even stronger impacts on ecosystem multifunctionality. Recent studies also highlight the role of risk in plant-herbivore interactions, and risk-driven trophic cascades have emerged as landscape-scale patterns in a variety of ecosystems. Perhaps not surprisingly, many plant-herbivore interactions are currently being altered by climate change, which affects plant growth rates and resource allocation, expression of chemical defenses, plant phenology, and herbivore metabolism and behavior. Finally, we conclude by noting that although the field is advancing rapidly, the world is changing even more rapidly, challenging our ability to manage these pivotal links in the food chain.},
}
@article {pmid28232766,
year = {2016},
author = {Crous, PW and Wingfield, MJ and Burgess, TI and Hardy, GE and Crane, C and Barrett, S and Cano-Lira, JF and Le Roux, JJ and Thangavel, R and Guarro, J and Stchigel, AM and Martín, MP and Alfredo, DS and Barber, PA and Barreto, RW and Baseia, IG and Cano-Canals, J and Cheewangkoon, R and Ferreira, RJ and Gené, J and Lechat, C and Moreno, G and Roets, F and Shivas, RG and Sousa, JO and Tan, YP and Wiederhold, NP and Abell, SE and Accioly, T and Albizu, JL and Alves, JL and Antoniolli, ZI and Aplin, N and Araújo, J and Arzanlou, M and Bezerra, JD and Bouchara, JP and Carlavilla, JR and Castillo, A and Castroagudín, VL and Ceresini, PC and Claridge, GF and Coelho, G and Coimbra, VR and Costa, LA and da Cunha, KC and da Silva, SS and Daniel, R and de Beer, ZW and Dueñas, M and Edwards, J and Enwistle, P and Fiuza, PO and Fournier, J and García, D and Gibertoni, TB and Giraud, S and Guevara-Suarez, M and Gusmão, LF and Haituk, S and Heykoop, M and Hirooka, Y and Hofmann, TA and Houbraken, J and Hughes, DP and Kautmanová, I and Koppel, O and Koukol, O and Larsson, E and Latha, KP and Lee, DH and Lisboa, DO and Lisboa, WS and López-Villalba, &#xc1; and Maciel, JL and Manimohan, P and Manjón, JL and Marincowitz, S and Marney, TS and Meijer, M and Miller, AN and Olariaga, I and Paiva, LM and Piepenbring, M and Poveda-Molero, JC and Raj, KN and Raja, HA and Rougeron, A and Salcedo, I and Samadi, R and Santos, TA and Scarlett, K and Seifert, KA and Shuttleworth, LA and Silva, GA and Silva, M and Siqueira, JP and Souza-Motta, CM and Stephenson, SL and Sutton, DA and Tamakeaw, N and Telleria, MT and Valenzuela-Lopez, N and Viljoen, A and Visagie, CM and Vizzini, A and Wartchow, F and Wingfield, BD and Yurchenko, E and Zamora, JC and Groenewald, JZ},
title = {Fungal Planet description sheets: 469-557.},
journal = {Persoonia},
volume = {37},
number = {},
pages = {218-403},
pmid = {28232766},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia: Apiognomonia lasiopetali on Lasiopetalum sp., Blastacervulus eucalyptorum on Eucalyptus adesmophloia, Bullanockia australis (incl. Bullanockia gen. nov.) on Kingia australis, Caliciopsis eucalypti on Eucalyptus marginata, Celerioriella petrophiles on Petrophile teretifolia, Coleophoma xanthosiae on Xanthosia rotundifolia, Coniothyrium hakeae on Hakea sp., Diatrypella banksiae on Banksia formosa, Disculoides corymbiae on Corymbia calophylla, Elsinoë eelemani on Melaleuca alternifolia, Elsinoë eucalyptigena on Eucalyptus kingsmillii, Elsinoë preissianae on Eucalyptus preissiana, Eucasphaeria rustici on Eucalyptus creta, Hyweljonesia queenslandica (incl. Hyweljonesia gen. nov.) on the cocoon of an unidentified microlepidoptera, Mycodiella eucalypti (incl. Mycodiella gen. nov.) on Eucalyptus diversicolor, Myrtapenidiella sporadicae on Eucalyptus sporadica, Neocrinula xanthorrhoeae (incl. Neocrinula gen. nov.) on Xanthorrhoea sp., Ophiocordyceps nooreniae on dead ant, Phaeosphaeriopsis agavacearum on Agave sp., Phlogicylindrium mokarei on Eucalyptus sp., Phyllosticta acaciigena on Acacia suaveolens, Pleurophoma acaciae on Acacia glaucoptera, Pyrenochaeta hakeae on Hakea sp., Readeriella lehmannii on Eucalyptus lehmannii, Saccharata banksiae on Banksia grandis, Saccharata daviesiae on Daviesia pachyphylla, Saccharata eucalyptorum on Eucalyptus bigalerita, Saccharata hakeae on Hakea baxteri, Saccharata hakeicola on Hakea victoria, Saccharata lambertiae on Lambertia ericifolia, Saccharata petrophiles on Petrophile sp., Saccharata petrophilicola on Petrophile fastigiata, Sphaerellopsis hakeae on Hakea sp., and Teichospora kingiae on Kingia australis.Brazil: Adautomilanezia caesalpiniae (incl. Adautomilanezia gen. nov.) on Caesalpina echinata, Arthrophiala arthrospora (incl. Arthrophiala gen. nov.) on Sagittaria montevidensis, Diaporthe caatingaensis (endophyte from Tacinga inamoena), Geastrum ishikawae on sandy soil, Geastrum pusillipilosum on soil, Gymnopus pygmaeus on dead leaves and sticks, Inonotus hymenonitens on decayed angiosperm trunk, Pyricularia urashimae on Urochloa brizantha, and Synnemellisia aurantia on Passiflora edulis. Chile: Tubulicrinis australis on Lophosoria quadripinnata.France: Cercophora squamulosa from submerged wood, and Scedosporium cereisporum from fluids of a wastewater treatment plant. Hawaii: Beltraniella acaciae, Dactylaria acaciae, Rhexodenticula acaciae, Rubikia evansii and Torula acaciae (all on Acacia koa).India: Lepidoderma echinosporum on dead semi-woody stems, and Rhodocybe rubrobrunnea from soil. Iran: Talaromyces kabodanensis from hypersaline soil. La Réunion: Neocordana musarum from leaves of Musa sp. Malaysia: Anungitea eucalyptigena on Eucalyptus grandis × pellita, Camptomeriphila leucaenae (incl. Camptomeriphila gen. nov.) on Leucaena leucocephala, Castanediella communis on Eucalyptus pellita, Eucalyptostroma eucalypti (incl. Eucalyptostroma gen. nov.) on Eucalyptus pellita, Melanconiella syzygii on Syzygium sp., Mycophilomyces periconiae (incl. Mycophilomyces gen. nov.) as hyperparasite on Periconia on leaves of Albizia falcataria, Synnemadiella eucalypti (incl. Synnemadiella gen. nov.) on Eucalyptus pellita, and Teichospora nephelii on Nephelium lappaceum.Mexico: Aspergillus bicephalus from soil. New Zealand: Aplosporella sophorae on Sophora microphylla, Libertasomyces platani on Platanus sp., Neothyronectria sophorae (incl. Neothyronectria gen. nov.) on Sophora microphylla, Parastagonospora phoenicicola on Phoenix canariensis, Phaeoacremonium pseudopanacis on Pseudopanax crassifolius, Phlyctema phoenicis on Phoenix canariensis, and Pseudoascochyta novae-zelandiae on Cordyline australis.Panama: Chalara panamensis from needle litter of Pinus cf. caribaea. South Africa: Exophiala eucalypti on leaves of Eucalyptus sp., Fantasmomyces hyalinus (incl. Fantasmomyces gen. nov.) on Acacia exuvialis, Paracladophialophora carceris (incl. Paracladophialophora gen. nov.) on Aloe sp., and Umthunziomyces hagahagensis (incl. Umthunziomyces gen. nov.) on Mimusops caffra.Spain: Clavaria griseobrunnea on bare ground in Pteridium aquilinum field, Cyathus ibericus on small fallen branches of Pinus halepensis, Gyroporus pseudolacteus in humus of Pinus pinaster, and Pseudoascochyta pratensis (incl. Pseudoascochyta gen. nov.) from soil. Thailand: Neoascochyta adenii on Adenium obesum, and Ochroconis capsici on Capsicum annuum. UK: Fusicolla melogrammae from dead stromata of Melogramma campylosporum on bark of Carpinus betulus. Uruguay: Myrmecridium pulvericola from house dust. USA: Neoscolecobasidium agapanthi (incl. Neoscolecobasidium gen. nov.) on Agapanthus sp., Polyscytalum purgamentum on leaf litter, Pseudopithomyces diversisporus from human toenail, Saksenaea trapezispora from knee wound of a soldier, and Sirococcus quercus from Quercus sp. Morphological and culture characteristics along with DNA barcodes are provided.},
}
@article {pmid28232764,
year = {2016},
author = {Orihara, T and Lebel, T and Ge, ZW and Smith, ME and Maekawa, N},
title = {Evolutionary history of the sequestrate genus Rossbeevera (Boletaceae) reveals a new genus Turmalinea and highlights the utility of ITS minisatellite-like insertions for molecular identification.},
journal = {Persoonia},
volume = {37},
number = {},
pages = {173-198},
pmid = {28232764},
issn = {0031-5850},
abstract = {The sequestrate (truffle-like) basidiomycete genera Rossbeevera, Chamonixia, and Octaviania are closely related to the epigeous mushroom genera Leccinum and Leccinellum. In order to elucidate the properties and placement of several undescribed sequestrate taxa in the group and to reveal the evolutionary history of Rossbeevera and its allies, we conducted phylogenetic analyses based on three nuclear (ITS, nLSU, EF-1α) and two mitochondrial DNA loci (ATP6 and mtSSU) as well as precise morphological observations. Phylogenetic analyses of three nuclear loci suggest a complex evolutionary history with sequestrate fruiting bodies present in several clades, including a previously unrecognized sister clade to Rossbeevera. Here we propose a new sequestrate genus, Turmalinea, with four new species and one new subspecies as well as two new species of Rossbeevera. The three-locus nuclear phylogeny resolves species-level divergence within the Rossbeevera-Turmalinea lineage, whereas a separate phylogeny based on two mitochondrial genes corresponds to geographic distance within each species-level lineage and suggests incomplete lineage sorting (ILS) and gene introgression within several intraspecific lineages of Rossbeevera. Furthermore, topological incongruence among the three nuclear single-locus phylogenies suggests that ancient speciation within Rossbeevera probably involved considerable ILS. We also found an unusually long, minisatellite-like insertion within the ITS2 in all Rossbeevera and Turmalinea species. A barcode gap analysis demonstrates that the insertion is more informative for discrimination at various taxonomic levels than the rest of the ITS region and could therefore serve as a unique molecular barcode for these genera.},
}
@article {pmid28232231,
year = {2017},
author = {Breitwieser, M and Viricel, A and Churlaud, C and Guillot, B and Martin, E and Stenger, PL and Huet, V and Fontanaud, A and Thomas-Guyon, H},
title = {First data on three bivalve species exposed to an intra-harbour polymetallic contamination (La Rochelle, France).},
journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP},
volume = {199},
number = {},
pages = {28-37},
doi = {10.1016/j.cbpc.2017.02.006},
pmid = {28232231},
issn = {1532-0456},
mesh = {Animals ; Atlantic Ocean ; Biomarkers/analysis ; Crassostrea/classification/*drug effects/growth &amp; development/metabolism ; DNA Barcoding, Taxonomic ; Digestive System/chemistry/drug effects/growth &amp; development/metabolism ; Environmental Exposure/*adverse effects ; Environmental Monitoring ; France ; Glutathione Transferase/metabolism ; Lipid Peroxidation/drug effects ; Metals, Heavy/analysis/*toxicity ; Mytilus/classification/*drug effects/growth &amp; development/metabolism ; Oxidative Stress/*drug effects ; Oxidoreductases/metabolism ; Pectinidae/classification/*drug effects/growth &amp; development/metabolism ; Species Specificity ; Tissue Distribution ; Toxicokinetics ; Water Pollutants, Chemical/analysis/*toxicity ; },
abstract = {Evaluating diffuse sediment contamination in the environment is a major concern with the aim of reaching a good chemical and ecological state of the littoral zone. In this study the risks of chronic chemical contamination and consequences in the bivalves Crassostrea gigas, Mytilus sp. and Mimachlamys varia were evaluated in coastal environments. The objective here was to understand the anthropological phenomena that affect the functioning of the marina of La Rochelle (semi-closed environment). Harbours seeking ecomanagement accreditations (such as the international reference ISO 14001) constitute zones of interest to implement biomonitoring studies. The biological effects of chemical pollution in the Marina of La Rochelle were studied to develop a multi-biomarker biomonitoring approach on specific marine species of this site. Moreover, a genetic (DNA barcoding) approach was applied to validate the species identity of collected bivalves. Of the three species tested the scallop, M. varia, was the most sensitive to metal exposure.},
}
@article {pmid28228677,
year = {2017},
author = {Nazari, V},
title = {Review of Neopalpa Povolný, 1998 with description of a new species from California and Baja California, Mexico (Lepidoptera, Gelechiidae).},
journal = {ZooKeys},
volume = {},
number = {646},
pages = {79-94},
pmid = {28228677},
issn = {1313-2989},
abstract = {The monotypic genus Neopalpa was described in 1998 by Czech entomologist Dalibor Povolný based on two male specimens from Santa Catalina Island, California, which he named Neopalpa neonata. The female of this species was discovered recently based on a DNA barcode match and is described. In addition, a new species with marked differences in morphology and DNA barcodes from southern California and Baja California Mexico is described as Neopalpa donaldtrumpisp. n. Adults and genitalia of both species are illustrated, new diagnosis for the genus Neopalpa is provided, and its position within Gelechiidae is briefly discussed.},
}
@article {pmid28228669,
year = {2017},
author = {Lehr, E and Moravec, J},
title = {A new species of Pristimantis (Amphibia, Anura, Craugastoridae) from a montane forest of the Pui Pui Protected Forest in central Peru (Región Junín).},
journal = {ZooKeys},
volume = {},
number = {645},
pages = {85-102},
pmid = {28228669},
issn = {1313-2989},
abstract = {A new species of frog of the genus Pristimantis is described from a montane forest between 1700 and 1800 m a.s.l. of the Pui Pui Protected Forest (Región Junín) in central Peru. Pristimantis ashaninkasp. n. is described based on five adult females (snout-vent length 23.1-26.7 mm) and ten juveniles (snout-vent length 10.6-13.4). It differs from its congeners by having the skin on dorsum shagreen with many conical tubercles giving it a spinose appearance, lacking a tympanum, having groin, anterior and posterior surfaces of thighs uniformly grayish brown, and a pale bronze iris with fine black reticulations, a median reddish hint horizontally across iris, and a black narrow vertical streak from pupil across lower and upper half of iris. Among the Peruvian Pristimantis that lack a tympanum, Pristimantis ashaninkasp. n. is morphologically most similar to Pristimantis lirellus, Pristimantis martiae, and Pristimantis rhabdocnemus. However, 16S DNA barcoding revealed clear distinctions between all four species of Pristimantis.},
}
@article {pmid28228107,
year = {2017},
author = {Badotti, F and de Oliveira, FS and Garcia, CF and Vaz, AB and Fonseca, PL and Nahum, LA and Oliveira, G and Góes-Neto, A},
title = {Effectiveness of ITS and sub-regions as DNA barcode markers for the identification of Basidiomycota (Fungi).},
journal = {BMC microbiology},
volume = {17},
number = {1},
pages = {42},
pmid = {28228107},
issn = {1471-2180},
mesh = {Basidiomycota/classification/*genetics/*isolation &amp; purification ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal ; DNA, Ribosomal Spacer/*genetics ; Databases, Nucleic Acid ; Fungi/genetics ; Genes, Fungal/genetics ; Genetic Markers/*genetics ; Molecular Typing/methods ; Mycological Typing Techniques/methods ; *Phylogeny ; RNA, Fungal/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND: Fungi are among the most abundant and diverse organisms on Earth. However, a substantial amount of the species diversity, relationships, habitats, and life strategies of these microorganisms remain to be discovered and characterized. One important factor hindering progress is the difficulty in correctly identifying fungi. Morphological and molecular characteristics have been applied in such tasks. Later, DNA barcoding has emerged as a new method for the rapid and reliable identification of species. The nrITS region is considered the universal barcode of Fungi, and the ITS1 and ITS2 sub-regions have been applied as metabarcoding markers. In this study, we performed a large-scale analysis of all the available Basidiomycota sequences from GenBank. We carried out a rigorous trimming of the initial dataset based in methodological principals of DNA Barcoding. Two different approaches (PCI and barcode gap) were used to determine the performance of the complete ITS region and sub-regions.<br><br>RESULTS: For most of the Basidiomycota genera, the three genomic markers performed similarly, i.e., when one was considered a good marker for the identification of a genus, the others were also; the same results were observed when the performance was insufficient. However, based on barcode gap analyses, we identified genomic markers that had a superior identification performance than the others and genomic markers that were not indicated for the identification of some genera. Notably, neither the complete ITS nor the sub-regions were useful in identifying 11 of the 113 Basidiomycota genera. The complex phylogenetic relationships and the presence of cryptic species in some genera are possible explanations of this limitation and are discussed.<br><br>CONCLUSIONS: Knowledge regarding the efficiency and limitations of the barcode markers that are currently used for the identification of organisms is crucial because it benefits research in many areas. Our study provides information that may guide researchers in choosing the most suitable genomic markers for identifying Basidiomycota species.},
}
@article {pmid28224997,
year = {2017},
author = {Wahlestedt, M and Erlandsson, E and Kristiansen, T and Lu, R and Brakebusch, C and Weissman, IL and Yuan, J and Martin-Gonzalez, J and Bryder, D},
title = {Clonal reversal of ageing-associated stem cell lineage bias via a pluripotent intermediate.},
journal = {Nature communications},
volume = {8},
number = {},
pages = {14533},
pmid = {28224997},
issn = {2041-1723},
mesh = {Aging/*physiology ; Animals ; *Cell Lineage/genetics ; Cellular Reprogramming/genetics ; *Cellular Senescence/genetics ; Clone Cells/*cytology ; Gene Expression Regulation, Developmental ; Hematopoietic Stem Cells/*cytology/metabolism ; Induced Pluripotent Stem Cells/*cytology/metabolism ; Mice, Inbred C57BL ; T-Lymphocytes/cytology/metabolism ; },
abstract = {Ageing associates with significant alterations in somatic/adult stem cells and therapies to counteract these might have profound benefits for health. In the blood, haematopoietic stem cell (HSC) ageing is linked to several functional shortcomings. However, besides the recent realization that individual HSCs might be preset differentially already from young age, HSCs might also age asynchronously. Evaluating the prospects for HSC rejuvenation therefore ultimately requires approaching those HSCs that are functionally affected by age. Here we combine genetic barcoding of aged murine HSCs with the generation of induced pluripotent stem (iPS) cells. This allows us to specifically focus on aged HSCs presenting with a pronounced lineage skewing, a hallmark of HSC ageing. Functional and molecular evaluations reveal haematopoiesis from these iPS clones to be indistinguishable from that associating with young mice. Our data thereby provide direct support to the notion that several key functional attributes of HSC ageing can be reversed.},
}
@article {pmid28222945,
year = {2017},
author = {Blandenier, Q and Lara, E and Mitchell, EA and Alcantara, DM and Siemensma, FJ and Todorov, M and Lahr, DJ},
title = {NAD9/NAD7 (mitochondrial nicotinamide adenine dinucleotide dehydrogenase gene)-A new "Holy Grail" phylogenetic and DNA-barcoding marker for Arcellinida (Amoebozoa)?.},
journal = {European journal of protistology},
volume = {58},
number = {},
pages = {175-186},
doi = {10.1016/j.ejop.2016.12.002},
pmid = {28222945},
issn = {1618-0429},
mesh = {Amoebozoa/*classification/enzymology/*genetics ; DNA Barcoding, Taxonomic/*standards ; Genes, Protozoan/genetics ; Genetic Markers/genetics ; NADH Dehydrogenase/*genetics ; *Phylogeny ; Species Specificity ; },
abstract = {Molecular phylogeny is an indispensable tool for assessing evolutionary relationships among protists. The most commonly used marker is the small subunit ribosomal RNA gene, a conserved gene present in many copies in the nuclear genomes. However, this marker is not variable enough at a fine-level taxonomic scale, and intra-genomic polymorphism has already been reported. Finding a marker that could be useful at both deep and fine taxonomic resolution levels seemed like a utopic dream. We designed Amoebozoa-specific primers to amplify a region including partial sequences of two subunits of the mitochondrial nicotinamide adenine dinucleotide dehydrogenase gene (NAD9/NAD7). We applied them to arcellinids belonging to distantly related genera (Arcella, Difflugia, Netzelia and Hyalosphenia) and to Arcellinid-rich environmental samples to obtain additional Amoebozoa sequences. Tree topology was congruent with previous phylogenies, all nodes being highly supported, suggesting that this marker is well-suited for deep phylogenies in Arcellinida and perhaps Amoebozoa. Furthermore, it enabled discrimination of close-related taxa. This short genetic marker (ca. 250bp) can therefore be used at different taxonomic levels, due to a fast-varying intergenic region presenting either a small intergenic sequence or an overlap, depending on the species.},
}
@article {pmid28218638,
year = {2017},
author = {Noune, C and Hauxwell, C},
title = {MetaGaAP: A Novel Pipeline to Estimate Community Composition and Abundance from Non-Model Sequence Data.},
journal = {Biology},
volume = {6},
number = {1},
pages = {},
pmid = {28218638},
issn = {2079-7737},
abstract = {Next generation sequencing and bioinformatic approaches are increasingly used to quantify microorganisms within populations by analysis of 'meta-barcode' data. This approach relies on comparison of amplicon sequences of 'barcode' regions from a population with public-domain databases of reference sequences. However, for many organisms relevant 'barcode' regions may not have been identified and large databases of reference sequences may not be available. A workflow and software pipeline, 'MetaGaAP,' was developed to identify and quantify genotypes through four steps: shotgun sequencing and identification of polymorphisms in a metapopulation to identify custom 'barcode' regions of less than 30 polymorphisms within the span of a single 'read', amplification and sequencing of the 'barcode', generation of a custom database of polymorphisms, and quantitation of the relative abundance of genotypes. The pipeline and workflow were validated in a 'wild type' Alphabaculovirus isolate, Helicoverpa armigera single nucleopolyhedrovirus (HaSNPV-AC53) and a tissue-culture derived strain (HaSNPV-AC53-T2). The approach was validated by comparison of polymorphisms in amplicons and shotgun data, and by comparison of predicted dominant and co-dominant genotypes with Sanger sequences. The computational power required to generate and search the database effectively limits the number of polymorphisms that can be included in a barcode to 30 or less. The approach can be used in quantitative analysis of the ecology and pathology of non-model organisms.},
}
@article {pmid28218290,
year = {2017},
author = {Greff, S and Aires, T and Serrão, EA and Engelen, AH and Thomas, OP and Pérez, T},
title = {The interaction between the proliferating macroalga Asparagopsis taxiformis and the coral Astroides calycularis induces changes in microbiome and metabolomic fingerprints.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {42625},
pmid = {28218290},
issn = {2045-2322},
mesh = {Animals ; Anthozoa/*microbiology/*physiology ; *Metabolome ; *Metabolomics/methods ; *Microbial Interactions ; *Microbiota ; Seawater/chemistry ; Seaweed/*physiology ; Spectrometry, Mass, Electrospray Ionization ; Temperature ; },
abstract = {Mediterranean Sea ecosystems are considered as hotspots of biological introductions, exposed to possible negative effects of non-indigenous species. In such temperate marine ecosystems, macroalgae may be dominant, with a great percentage of their diversity represented by introduced species. Their interaction with temperate indigenous benthic organisms have been poorly investigated. To provide new insights, we performed an experimental study on the interaction between the introduced proliferative red alga Asparagopsis taxiformis and the indigenous Mediterranean coral Astroides calycularis. The biological response measurements included meta-barcoding of the associated microbial communities and metabolomic fingerprinting of both species. Significant changes were detected among both associated microbial communities, the interspecific differences decreasing with stronger host interaction. No short term effects of the macroalga on the coral health, neither on its polyp activity or its metabolism, were detected. In contrast, the contact interaction with the coral induced a change in the macroalgal metabolomic fingerprint with a significant increase of its bioactivity against the marine bacteria Aliivibrio fischeri. This induction was related to the expression of bioactive metabolites located on the macroalgal surface, a phenomenon which might represent an immediate defensive response of the macroalga or an allelopathic offense against coral.},
}
@article {pmid28216881,
year = {2017},
author = {Han, BX and Yuan, Y and Huang, LQ and Zhao, Q and Tan, LL and Song, XW and He, XM and Xu, T and Liu, F and Wang, J},
title = {Specific PCR Identification between Peucedanum praeruptorum and Angelica decursiva and Identification between Them and Adulterant Using DNA Barcode.},
journal = {Pharmacognosy magazine},
volume = {13},
number = {49},
pages = {38-45},
pmid = {28216881},
issn = {0973-1296},
abstract = {BACKGROUND: The traditional Chinese medicine (TCM) Qianhu and Zihuaqianhu are the dried roots of Peucedanum praeruptorum and Angelica decursiva, respectively. Since the plant sources of Qianhu and Zihuaqianhu are more complex, the chemical compositions of P. praeruptorum and A. decursiva are significantly different, and many adulterants exist because of the differences in traditional understanding and medication habits. Therefore, the rapid and accurate identification methods are required.<br><br>OBJECTIVE: The aim was to study the feasibility of using DNA barcoding to distinguish between Traditional Chinese medicine Qianhu (Peucedanum praeruptorum), Zihuaqianhu (Angelica decursiva), and common adulterants, based on internal transcribed spacer (ITS) sequences, as well as specific PCR identification between P. praeruptorum and A. decursiva.<br><br>MATERIALS AND METHODS: The ITS sequences of P. praeruptorum, A. decursiva, and adulterant were studied, and a phylogenetic tree was constructed. Based on the ITS barcode, the specific PCR primer pairs QH-CP19s/QH-CP19a and ZHQH-CP3s/ZHQH-CP3a were designed for P. praeruptorum and A. decursiva, respectively. The amplification conditions were optimized, and specific PCR products were obtained.<br><br>RESULTS: The results showed that the phylogenetic trees constructed using the BI and MP methods were consistent, and P. praeruptorum and A. decursiva sequence haplotypes formed their own monophyly. The experimental results showed that in PCR products, the target bands appeared in the genuine drug and not in the adulterant, which suggests the high specificity of the two primer pairs.<br><br>CONCLUSION: The ITS sequence was ideal DNA barcode to identify P. praeruptorum, A. decursiva, and adulterant. The specific PCR is a quick and effective method to distinguish between P. praeruptorum and A. decursiva.<br><br>SUMMARY: Peucedanum praeruptorum and Angelica decursiva sequence haplotypes formed their own monophyly.The ITS sequence was ideal DNA barcode to identify P. praeruptorum, A. decursiva, and adulterant.Specific PCR is a quick and effective method to distinguish between P. praeruptorum and A. decursiva. Abbreviations used: TCM: The traditional Chinese medicine, P.: Peucedanum, A.: Angelica, ITS: The internal transcribed spacer, PCR: Polymerase chain reaction, NCBI: National Center for Biotechnology Information, NI: Number of individuals, HN: Haplotype number; GAN: Gen Bank accession numbers, L.: Ligusticum, O.: Ostericum, A.: Angelica, P.: Pimpinella, BI: Bayesian inference, MP: Maximum parsimony, AIC: Akaike Information Criterion, MCMC: Markov Chains Monte Carlo, TBR: Tree bisection-reconnection, LPP: Length of PCR product, PRP: PCR reaction procedure, SNP: Single nucleotide polymorphisms, PP: Posterior probability, BS: Bootstrap.Qun Zhao.},
}
@article {pmid28215349,
year = {2017},
author = {Robicheau, BM and Young, AP and LaButti, K and Grigoriev, IV and Walker, AK},
title = {The complete mitochondrial genome of the conifer needle endophyte, Phialocephala scopiformis DAOMC 229536 confirms evolutionary division within the fungal Phialocephala fortinii s.l. - Acephala appalanata species complex.},
journal = {Fungal biology},
volume = {121},
number = {3},
pages = {212-221},
doi = {10.1016/j.funbio.2016.11.007},
pmid = {28215349},
issn = {1878-6146},
mesh = {Ascomycota/classification/*genetics ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Endophytes/classification/*genetics ; Gene Order ; Genes, Fungal ; *Genome, Fungal ; *Genome, Mitochondrial ; Phylogeny ; Sequence Analysis, DNA ; Synteny ; Tracheophyta/microbiology ; },
abstract = {Despite the recent surge in mitochondrial (mt) genome sequencing, Kingdom Fungi remains underrepresented with respect to mtDNA. We describe the mt genome of the conifer needle endophyte, Phialocephala scopiformis DAOMC 229536 (Helotiales, Ascomycota). This strain is of interest to the Canadian forestry industry as it produces the anti-insectan compound rugulosin. Sequence was obtained from whole genome shotgun sequencing. Comparison to the only other published Phialocephala mt genome, Phialocephala subalpina, indicates that the suite of common mt genes - cox1-3, cob, nad1-6 and 4L, atp6, 8 and 9, as well as rrnL and rrnS - has retained an identical order. Nad4L remains one of the most conserved mitochondrial genes within Phialocephala. Members of the closely related Phialocephala fortinii s.l. - Acephala appalanata species complex (PAC) share too much sequence similarity to properly resolve lineages using ITS barcoding alone. Using P. scopiformis sequence as an outgroup, we determined ancestral gene states that help confirm clades within Phialocephala. Our results show: (1) the complete mt genome of P. scopiformis, representing the 10th complete mt genome for the order Helotiales (containing >3800 species), and (2) how large-scale genomic patterns, such as mitochondrial gene order, can be used to confirm lineages within fungal species complexes.},
}
@article {pmid28215207,
year = {2017},
author = {Boon, NAM and Fannes, W and Rombouts, S and Polman, K and Volckaert, FAM and Huyse, T},
title = {Detecting hybridization in African schistosome species: does egg morphology complement molecular species identification?.},
journal = {Parasitology},
volume = {144},
number = {7},
pages = {954-964},
doi = {10.1017/S0031182017000087},
pmid = {28215207},
issn = {1469-8161},
mesh = {Adolescent ; Animals ; Child ; Child, Preschool ; DNA, Helminth/genetics ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Female ; Helminth Proteins/genetics ; Humans ; *Hybridization, Genetic ; Male ; Mitochondrial Proteins/genetics ; Ovum/*cytology ; Schistosoma/classification/*cytology/genetics ; Schistosoma haematobium/classification/cytology/genetics ; Senegal ; Young Adult ; },
abstract = {Hybrid parasites may have an increased transmission potential and higher virulence compared to their parental species. Consequently, hybrid detection is critical for disease control. Previous crossing experiments showed that hybrid schistosome eggs have distinct morphotypes. We therefore compared the performance of egg morphology with molecular markers with regard to detecting hybridization in schistosomes. We studied the morphology of 303 terminal-spined eggs, originating from 19 individuals inhabiting a hybrid zone with natural crosses between the human parasite Schistosoma haematobium and the livestock parasite Schistosoma bovis in Senegal. The egg sizes showed a high variability and ranged between 92·4 and 176·4 µm in length and between 35·7 and 93·0 µm in width. No distinct morphotypes were found and all eggs resembled, to varying extent, the typical S. haematobium egg type. However, molecular analyses on the same eggs clearly showed the presence of two distinct partial mitochondrial cox1 profiles, namely S. bovis and S. haematobium, and only a single nuclear ITS rDNA profile (S. haematobium). Therefore, in these particular crosses, egg morphology appears not a good indicator of hybrid ancestry. We conclude by discussing strengths and limitations of molecular methods to detect hybrids in the context of high-throughput screening of field samples.},
}
@article {pmid28215143,
year = {2017},
author = {Gao, B and Fang, Y and Zhang, J and Wu, R and Xu, B and Xie, L},
title = {A DNA Barcoding Based Study to Identify Main Mosquito Species in Taiwan and its Difference from Those in Mainland China.},
journal = {Combinatorial chemistry &amp; high throughput screening},
volume = {20},
number = {2},
pages = {147-152},
doi = {10.2174/1386207320666170217153548},
pmid = {28215143},
issn = {1875-5402},
mesh = {Animals ; Base Sequence ; China ; Classification/methods ; Culicidae/*classification/genetics ; *DNA Barcoding, Taxonomic ; Phylogeny ; Taiwan ; },
abstract = {AIM AND OBJECTIVE: Mosquitoes can transmit many types of viruses such as West Nile virus and Zika virus and are responsible for a number of virus-causing diseases including malaria, dengue fever, yellow fever, lymphatic filariasis, and Japanese B encephalitis. On January 19, 2016, the first case of Zika virus infection was identified in Taiwan, which presents the need for studying the mosquito species in the Taiwan Strait and evaluating the risk of the outbreak of this infection.<br><br>MATERIALS AND METHOD: In this study, we have collected 144 mosquito specimens from 42 species belonging to nine genera from both sides of the Taiwan Strait during 2013 and 2014. We then applied the COI DNA Barcoding technique to classify the specimens and performed a phylogenetic analysis to infer the evolutionary history of these mosquitoes. Based on the analyses, we found that though the mosquitoes from different sides of the Taiwan Strait share a lot of commonality, they have a few regional specificities.<br><br>RESULTS: Our results also suggested a very small divergences (1%~9%) between specimens from the same mosquito species and relatively large divergences (8%~25%) between specimens from different mosquito species. Within the same species, the divergence of specimens from the same region is significantly smaller than that between two regions. A few highly divergent species between Fujian and Taiwan (e.g., An.maculatus and Ae.elsiae) might be formed due to the so-called "cryptic evolutionary events", in which the species has differentiation into cryptic species due to geographical differences without changing morphological characteristics.<br><br>CONCLUSION: In conclusion, the phylogenetic analyses showed a very similar taxonomy to the historical one based on morphological characteristics, validating again the application of COI DNA Barcoding technique in classifying mosquito species. However, there are also some inconsistencies between COI DNA Barcoding and historical taxonomy, which points out the differences between mosquito DNA and morphological characteristics and suggests the possibility to improve mosquito taxonomy based on DNA techniques.},
}
@article {pmid28211676,
year = {2017},
author = {Acero Sánchez, JL and Joda, H and Henry, OY and Solnestam, BW and Kvastad, L and Akan, PS and Lundeberg, J and Laddach, N and Ramakrishnan, D and Riley, I and Schwind, C and Latta, D and O'Sullivan, CK},
title = {Electrochemical Genetic Profiling of Single Cancer Cells.},
journal = {Analytical chemistry},
volume = {89},
number = {6},
pages = {3378-3385},
doi = {10.1021/acs.analchem.6b03973},
pmid = {28211676},
issn = {1520-6882},
mesh = {*Biosensing Techniques ; Breast Neoplasms/*genetics/pathology ; *Electrochemical Techniques ; Female ; Genetic Profile ; Humans ; Neoplastic Cells, Circulating/*pathology ; RNA, Messenger/*genetics ; *Single-Cell Analysis ; },
abstract = {Recent understandings in the development and spread of cancer have led to the realization of novel single cell analysis platforms focused on circulating tumor cells (CTCs). A simple, rapid, and inexpensive analytical platform capable of providing genetic information on these rare cells is highly desirable to support clinicians and researchers alike to either support the selection or adjustment of therapy or provide fundamental insights into cell function and cancer progression mechanisms. We report on the genetic profiling of single cancer cells, exploiting a combination of multiplex ligation-dependent probe amplification (MLPA) and electrochemical detection. Cells were isolated using laser capture and lysed, and the mRNA was extracted and transcribed into DNA. Seven markers were amplified by MLPA, which allows for the simultaneous amplification of multiple targets with a single primer pair, using MLPA probes containing unique barcode sequences. Capture probes complementary to each of these barcode sequences were immobilized on a printed circuit board (PCB) manufactured electrode array and exposed to single-stranded MLPA products and subsequently to a single stranded DNA reporter probe bearing a HRP molecule, followed by substrate addition and fast electrochemical pulse amperometric detection. We present a simple, rapid, flexible, and inexpensive approach for the simultaneous quantification of multiple breast cancer related mRNA markers, with single tumor cell sensitivity.},
}
@article {pmid28208623,
year = {2017},
author = {Neu, TR and Kuhlicke, U},
title = {Fluorescence Lectin Bar-Coding of Glycoconjugates in the Extracellular Matrix of Biofilm and Bioaggregate Forming Microorganisms.},
journal = {Microorganisms},
volume = {5},
number = {1},
pages = {},
pmid = {28208623},
issn = {2076-2607},
abstract = {Microbial biofilm systems are defined as interface-associated microorganisms embedded into a self-produced matrix. The extracellular matrix represents a continuous challenge in terms of characterization and analysis. The tools applied in more detailed studies comprise extraction/chemical analysis, molecular characterization, and visualisation using various techniques. Imaging by laser microscopy became a standard tool for biofilm analysis, and, in combination with fluorescently labelled lectins, the glycoconjugates of the matrix can be assessed. By employing this approach a wide range of pure culture biofilms from different habitats were examined using the commercially available lectins. From the results, a binary barcode pattern of lectin binding can be generated. Furthermore, the results can be fine-tuned and transferred into a heat map according to signal intensity. The lectin barcode approach is suggested as a useful tool for investigating the biofilm matrix characteristics and dynamics at various levels, e.g. bacterial cell surfaces, adhesive footprints, individual microcolonies, and the gross biofilm or bio-aggregate. Hence fluorescence lectin bar-coding (FLBC) serves as a basis for a subsequent tailor-made fluorescence lectin-binding analysis (FLBA) of a particular biofilm. So far, the lectin approach represents the only tool for in situ characterization of the glycoconjugate makeup in biofilm systems. Furthermore, lectin staining lends itself to other fluorescence techniques in order to correlate it with cellular biofilm constituents in general and glycoconjugate producers in particular.},
}
@article {pmid28202776,
year = {2017},
author = {Shalek, AK},
title = {Baring cellular souls.},
journal = {Science translational medicine},
volume = {9},
number = {377},
pages = {},
doi = {10.1126/scitranslmed.aam6064},
pmid = {28202776},
issn = {1946-6242},
mesh = {Cell Nucleus ; *DNA Barcoding, Taxonomic ; *High-Throughput Nucleotide Sequencing ; },
abstract = {Coupling chemical approaches for disrupting DNA-protein complexes in intact nuclei with combinatorial barcoding enables high-throughput single-cell DNA sequencing.},
}
@article {pmid28202626,
year = {2017},
author = {Mathis, RA and Sokol, ES and Gupta, PB},
title = {Cancer cells exhibit clonal diversity in phenotypic plasticity.},
journal = {Open biology},
volume = {7},
number = {2},
pages = {},
pmid = {28202626},
issn = {2046-2441},
support = {R01 GM124491/GM/NIGMS NIH HHS/United States ; T32 GM007287/GM/NIGMS NIH HHS/United States ; },
mesh = {Antineoplastic Agents/*pharmacology ; Cell Line, Tumor ; Cell Plasticity ; DNA Barcoding, Taxonomic ; DNA, Neoplasm/*genetics ; Drug Resistance, Bacterial ; *Epithelial-Mesenchymal Transition/drug effects ; HEK293 Cells ; Humans ; Neoplasm Invasiveness ; Neoplasms/drug therapy/*genetics/pathology ; Phenotype ; },
abstract = {Phenotypic heterogeneity in cancers is associated with invasive progression and drug resistance. This heterogeneity arises in part from the ability of cancer cells to switch between phenotypic states, but the dynamics of this cellular plasticity remain poorly understood. Here we apply DNA barcodes to quantify and track phenotypic plasticity across hundreds of clones in a population of cancer cells exhibiting epithelial or mesenchymal differentiation phenotypes. We find that the epithelial-to-mesenchymal cell ratio is highly variable across the different clones in cancer cell populations, but remains stable for many generations within the progeny of any single clone-with a heritability of 0.89. To estimate the effects of combination therapies on phenotypically heterogeneous tumours, we generated quantitative simulations incorporating empirical data from our barcoding experiments. These analyses indicated that combination therapies which alternate between epithelial- and mesenchymal-specific treatments eventually select for clones with increased phenotypic plasticity. However, this selection could be minimized by increasing the frequency of alternation between treatments, identifying designs that may minimize selection for increased phenotypic plasticity. These findings establish new insights into phenotypic plasticity in cancer, and suggest design principles for optimizing the effectiveness of combination therapies for phenotypically heterogeneous tumours.},
}
@article {pmid28199790,
year = {2017},
author = {MacConnell, AB and Price, AK and Paegel, BM},
title = {An Integrated Microfluidic Processor for DNA-Encoded Combinatorial Library Functional Screening.},
journal = {ACS combinatorial science},
volume = {19},
number = {3},
pages = {181-192},
pmid = {28199790},
issn = {2156-8944},
support = {DP2 OD008535/OD/NIH HHS/United States ; },
mesh = {Base Sequence ; Cathepsin D/antagonists &amp; inhibitors ; Combinatorial Chemistry Techniques/*instrumentation ; DNA/*chemistry ; Drug Evaluation, Preclinical/*instrumentation ; Enzyme Inhibitors/chemistry/pharmacology ; Equipment Design ; Gene Library ; Humans ; *Lab-On-A-Chip Devices ; Microspheres ; Pepstatins/chemistry/pharmacology ; },
abstract = {DNA-encoded synthesis is rekindling interest in combinatorial compound libraries for drug discovery and in technology for automated and quantitative library screening. Here, we disclose a microfluidic circuit that enables functional screens of DNA-encoded compound beads. The device carries out library bead distribution into picoliter-scale assay reagent droplets, photochemical cleavage of compound from the bead, assay incubation, laser-induced fluorescence-based assay detection, and fluorescence-activated droplet sorting to isolate hits. DNA-encoded compound beads (10-μm diameter) displaying a photocleavable positive control inhibitor pepstatin A were mixed (1920 beads, 729 encoding sequences) with negative control beads (58 000 beads, 1728 encoding sequences) and screened for cathepsin D inhibition using a biochemical enzyme activity assay. The circuit sorted 1518 hit droplets for collection following 18 min incubation over a 240 min analysis. Visual inspection of a subset of droplets (1188 droplets) yielded a 24% false discovery rate (1166 pepstatin A beads; 366 negative control beads). Using template barcoding strategies, it was possible to count hit collection beads (1863) using next-generation sequencing data. Bead-specific barcodes enabled replicate counting, and the false discovery rate was reduced to 2.6% by only considering hit-encoding sequences that were observed on >2 beads. This work represents a complete distributable small molecule discovery platform, from microfluidic miniaturized automation to ultrahigh-throughput hit deconvolution by sequencing.},
}
@article {pmid28199378,
year = {2017},
author = {O Elansary, H and Ashfaq, M and Ali, HM and Yessoufou, K},
title = {The first initiative of DNA barcoding of ornamental plants from Egypt and potential applications in horticulture industry.},
journal = {PloS one},
volume = {12},
number = {2},
pages = {e0172170},
pmid = {28199378},
issn = {1932-6203},
mesh = {Arecaceae/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Plant/chemistry/isolation &amp; purification/*metabolism ; Egypt ; Plant Proteins/genetics/metabolism ; Plants, Medicinal/genetics ; Ribulose-Bisphosphate Carboxylase/genetics/metabolism ; Sequence Analysis, DNA ; },
abstract = {DNA barcoding relies on short and standardized gene regions to identify species. The agricultural and horticultural applications of barcoding such as for marketplace regulation and copyright protection remain poorly explored. This study examines the effectiveness of the standard plant barcode markers (matK and rbcL) for the identification of plant species in private and public nurseries in northern Egypt. These two markers were sequenced from 225 specimens of 161 species and 62 plant families of horticultural importance. The sequence recovery was similar for rbcL (96.4%) and matK (84%), but the number of specimens assigned correctly to the respective genera and species was lower for rbcL (75% and 29%) than matK (85% and 40%). The combination of rbcL and matK brought the number of correct generic and species assignments to 83.4% and 40%, respectively. Individually, the efficiency of both markers varied among different plant families; for example, all palm specimens (Arecaceae) were correctly assigned to species while only one individual of Asteraceae was correctly assigned to species. Further, barcodes reliably assigned ornamental horticultural and medicinal plants correctly to genus while they showed a lower or no success in assigning these plants to species and cultivars. For future, we recommend the combination of a complementary barcode (e.g. ITS or trnH-psbA) with rbcL + matK to increase the performance of taxa identification. By aiding species identification of horticultural crops and ornamental palms, the analysis of the barcode regions will have large impact on horticultural industry.},
}
@article {pmid28199101,
year = {2017},
author = {Raja, HA and Miller, AN and Pearce, CJ and Oberlies, NH},
title = {Fungal Identification Using Molecular Tools: A Primer for the Natural Products Research Community.},
journal = {Journal of natural products},
volume = {80},
number = {3},
pages = {756-770},
pmid = {28199101},
issn = {1520-6025},
support = {P01 CA125066/CA/NCI NIH HHS/United States ; },
mesh = {Biological Products/*chemistry ; DNA/chemistry/genetics ; Fungi/*chemistry ; Molecular Structure ; *Phylogeny ; Research ; },
abstract = {Fungi are morphologically, ecologically, metabolically, and phylogenetically diverse. They are known to produce numerous bioactive molecules, which makes them very useful for natural products researchers in their pursuit of discovering new chemical diversity with agricultural, industrial, and pharmaceutical applications. Despite their importance in natural products chemistry, identification of fungi remains a daunting task for chemists, especially those who do not work with a trained mycologist. The purpose of this review is to update natural products researchers about the tools available for molecular identification of fungi. In particular, we discuss (1) problems of using morphology alone in the identification of fungi to the species level; (2) the three nuclear ribosomal genes most commonly used in fungal identification and the potential advantages and limitations of the ITS region, which is the official DNA barcoding marker for species-level identification of fungi; (3) how to use NCBI-BLAST search for DNA barcoding, with a cautionary note regarding its limitations; (4) the numerous curated molecular databases containing fungal sequences; (5) the various protein-coding genes used to augment or supplant ITS in species-level identification of certain fungal groups; and (6) methods used in the construction of phylogenetic trees from DNA sequences to facilitate fungal species identification. We recommend that, whenever possible, both morphology and molecular data be used for fungal identification. Our goal is that this review will provide a set of standardized procedures for the molecular identification of fungi that can be utilized by the natural products research community.},
}
@article {pmid28196276,
year = {2017},
author = {Evans, JR and Saunders, GW},
title = {PCR fishing for red endophytes in British Columbia Kallymeniaceae (Gigartinales, Florideophyceae) uncovers the species-rich Kallymenicola gen. nov. (Palmariales, Nemaliophycidae).},
journal = {Journal of phycology},
volume = {53},
number = {3},
pages = {577-588},
doi = {10.1111/jpy.12522},
pmid = {28196276},
issn = {1529-8817},
mesh = {British Columbia ; DNA Barcoding, Taxonomic ; Endophytes/*classification/*genetics ; Polymerase Chain Reaction ; Rhodophyta/*classification/*genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; },
abstract = {Unexpected contaminants uncovered during routine COI-5P DNA barcoding of British Columbia Kallymeniaceae indicated the presence of a novel lineage allied to the family Meiodiscaceae, Palmariales. Available rbcL data for species of this family were used to design specific primers to screen for the presence of the meiodiscacean species in 534 kallymeniacean specimens primarily from British Columbia, Canada. Ultimately, 43 positive PCR products representing six diverse genetic groups from nine host species were uncovered; three are described here in the new genus Kallymenicola gen. nov., viz., K. invisiblis sp. nov., K penetrans sp. nov., and K superficialis sp. nov. Although genetic groups loosely displayed evidence of host specificity and cospeciation, examples of host switching with interesting biogeographical patterns were also documented.},
}
@article {pmid28193505,
year = {2017},
author = {Vilsen, SB and Tvedebrink, T and Mogensen, HS and Morling, N},
title = {Statistical modelling of Ion PGM HID STR 10-plex MPS data.},
journal = {Forensic science international. Genetics},
volume = {28},
number = {},
pages = {82-89},
doi = {10.1016/j.fsigen.2017.01.017},
pmid = {28193505},
issn = {1878-0326},
mesh = {Alleles ; *DNA Fingerprinting ; *Data Interpretation, Statistical ; Heterozygote ; *High-Throughput Nucleotide Sequencing ; Humans ; *Microsatellite Repeats ; *Models, Statistical ; },
abstract = {We investigated the results of short tandem repeat (STR) markers of dilution series experiments and reference profiles generated using the Ion PGM massively parallel sequencing platform utilising the HID STR 10-plex panel. The STR markers were identified by the marker specific flanking regions of the STR region. We investigated the following: (1) the usage of quality measures for identifying substitution errors, (2) the heterozygote balance and compared it to that of capillary electrophoresis (CE), (3) the stability of the coverage and the consequence of IonExpress Barcode adapter (IBA) sampling with decreasing amounts of template DNA, (4) the hypothesis that the parental longest uninterrupted stretch (LUS) is a better linear predictor of stutter ratio than the parent allele length, (5) the use of parental allele length as a predictor of shoulder ratio, and (6) the removal of non-systematic erroneous sequences using dynamic thresholds created by fitting the distribution of the non-systematic erroneous sequences. We found that, due to MID sampling, the average coverage on a marker could not be used as an apt predictor of the amount of template DNA. The parental LUS was shown to be better predictor of stutter ratio than the parental allele repeat length, when markers with compound and complex repeat patterns or markers which contained micro-variants were considered, such as marker TH01 showed R[2] of 0.02 and 0.78 for parent allele repeat length and LUS, respectively. The one-inflated negative binomial method (OINB) and geometric model that can be used to remove non-systematic noise left on average 1.8 and 1.2 systematic errors per STR system, respectively.},
}
@article {pmid28192986,
year = {2017},
author = {Song, W and Qiao, X and Chen, K and Wang, Y and Ji, S and Feng, J and Li, K and Lin, Y and Ye, M},
title = {Biosynthesis-Based Quantitative Analysis of 151 Secondary Metabolites of Licorice To Differentiate Medicinal Glycyrrhiza Species and Their Hybrids.},
journal = {Analytical chemistry},
volume = {89},
number = {5},
pages = {3146-3153},
doi = {10.1021/acs.analchem.6b04919},
pmid = {28192986},
issn = {1520-6882},
mesh = {Chromatography, High Pressure Liquid ; DNA Barcoding, Taxonomic ; Flavonoids/chemistry ; Genotype ; Glycosides/*analysis/metabolism ; Glycyrrhiza/*chemistry/genetics/metabolism ; *Metabolomics ; Phenols/*analysis/metabolism ; Plants, Medicinal/*chemistry/genetics/metabolism ; Principal Component Analysis ; Saponins/*analysis/metabolism ; Spectrophotometry, Ultraviolet ; Tandem Mass Spectrometry ; },
abstract = {Secondary metabolites are usually the bioactive components of medicinal plants. The difference in the secondary metabolisms of closely related plant species and their hybrids has rarely been addressed. In this study, we conducted a holistic secondary metabolomics analysis of three medicinal Glycyrrhiza species (G. uralensis, G. glabra, and G. inflata), which are used as the popular herbal medicine licorice. The Glycyrrhiza species (genotype) for 95 batches of samples were identified by DNA barcodes of the internal transcribed spacer and trnV-ndhC regions, and the chemotypes were revealed by LC/UV- or LC/MS/MS-based quantitative analysis of 151 bioactive secondary metabolites, including 17 flavonoid glycosides, 24 saponins, and 110 free phenolic compounds. These compounds represented key products in the biosynthetic pathways of licorice. For the 76 homozygous samples, the three Glycyrrhiza species showed significant biosynthetic preferences, especially in coumarins, chalcones, isoflavanes, and flavonols. In total, 27 species-specific chemical markers were discovered. The 19 hybrid samples indicated that hybridization could remarkably alter the chemical composition and that the male parent contributed more to the offspring than the female parent did. This is hitherto the largest-scale targeted secondary metabolomics study of medicinal plants and the first report on uniparental inheritance in plant secondary metabolism. The results are valuable for biosynthesis, inheritance, and quality control studies of licorice and other medicinal plants.},
}
@article {pmid28192446,
year = {2017},
author = {Farías-Curtidor, N and Barragán-Barrera, DC and Chávez-Carreño, PA and Jiménez-Pinedo, C and Palacios, DM and Caicedo, D and Trujillo, F and Caballero, S},
title = {Range extension for the common dolphin (Delphinus sp.) to the Colombian Caribbean, with taxonomic implications from genetic barcoding and phylogenetic analyses.},
journal = {PloS one},
volume = {12},
number = {2},
pages = {e0171000},
pmid = {28192446},
issn = {1932-6203},
mesh = {Animals ; Caribbean Region ; Cetacea/classification/genetics ; Colombia ; Common Dolphins/classification/*genetics/physiology ; Cytochromes b/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/chemistry/*genetics ; Geography ; *Phylogeny ; Polymerase Chain Reaction ; Population Dynamics ; Sequence Analysis, DNA/methods ; Species Specificity ; Venezuela ; },
abstract = {The nearest known population of common dolphins (Delphinus sp.) to the Colombian Caribbean occurs in a fairly restricted range in eastern Venezuela. These dolphins have not been previously reported in the Colombian Caribbean, likely because of a lack of study of the local cetacean fauna. We collected cetacean observations in waters of the Guajira Department, northern Colombia (~11°N, 73°W) during two separate efforts: (a) a seismic vessel survey (December 2009-March 2010), and (b) three coastal surveys from small boats (May-July 2012, May 2013, and May 2014). Here we document ten sightings of common dolphins collected during these surveys, which extend the known range of the species by ~1000 km into the southwestern Caribbean. We also collected nine skin biopsies in 2013 and 2014. In order to determine the taxonomic identity of the specimens, we conducted genetic barcoding and phylogenetic analyses using two mitochondrial markers, the Control Region (mtDNA) and Cytochrome b (Cytb). Results indicate that these specimens are genetically closer to the short-beaked common dolphin (Delphinus delphis) even though morphologically they resemble a long-beaked form (Delphinus sp.). However, the specific taxonomic status of common dolphins in the Caribbean and in the Western Atlantic remains unresolved. It is also unclear whether the distribution of the species between northern Colombia and eastern Venezuela is continuous or disjoined, or whether they can be considered part of the same stock.},
}
@article {pmid28191885,
year = {2017},
author = {Chuang, CH and Greenside, PG and Rogers, ZN and Brady, JJ and Yang, D and Ma, RK and Caswell, DR and Chiou, SH and Winters, AF and Grüner, BM and Ramaswami, G and Spencley, AL and Kopecky, KE and Sayles, LC and Sweet-Cordero, EA and Li, JB and Kundaje, A and Winslow, MM},
title = {Molecular definition of a metastatic lung cancer state reveals a targetable CD109-Janus kinase-Stat axis.},
journal = {Nature medicine},
volume = {23},
number = {3},
pages = {291-300},
pmid = {28191885},
issn = {1546-170X},
support = {T32 CA009302/CA/NCI NIH HHS/United States ; F32 CA189659/CA/NCI NIH HHS/United States ; R01 CA175336/CA/NCI NIH HHS/United States ; T15 LM007033/LM/NLM NIH HHS/United States ; R01 GM102484/GM/NIGMS NIH HHS/United States ; R01 CA157510/CA/NCI NIH HHS/United States ; R01 CA204620/CA/NCI NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; },
mesh = {Adenocarcinoma/*genetics/metabolism ; Animals ; Antigens, CD/*genetics ; Blotting, Western ; Cell Line, Tumor ; Disease Models, Animal ; Gene Expression Regulation, Neoplastic/*genetics ; Gene Knockdown Techniques ; Janus Kinase 1/genetics ; Janus Kinase 3/genetics ; Janus Kinases/*genetics ; Lung Neoplasms/*genetics/metabolism ; Mice ; Molecular Targeted Therapy ; Neoplasm Metastasis/genetics ; Neoplasm Proteins/*genetics ; Polymerase Chain Reaction ; Protein Kinase Inhibitors ; Proto-Oncogene Proteins p21(ras)/genetics ; STAT3 Transcription Factor/*genetics ; Signal Transduction ; Tumor Suppressor Protein p53/genetics ; },
abstract = {Lung cancer is the leading cause of cancer deaths worldwide, with the majority of mortality resulting from metastatic spread. However, the molecular mechanism by which cancer cells acquire the ability to disseminate from primary tumors, seed distant organs, and grow into tissue-destructive metastases remains incompletely understood. We combined tumor barcoding in a mouse model of human lung adenocarcinoma with unbiased genomic approaches to identify a transcriptional program that confers metastatic ability and predicts patient survival. Small-scale in vivo screening identified several genes, including Cd109, that encode novel pro-metastatic factors. We uncovered signaling mediated by Janus kinases (Jaks) and the transcription factor Stat3 as a critical, pharmacologically targetable effector of CD109-driven lung cancer metastasis. In summary, by coupling the systematic genomic analysis of purified cancer cells in distinct malignant states from mouse models with extensive human validation, we uncovered several key regulators of metastatic ability, including an actionable pro-metastatic CD109-Jak-Stat3 axis.},
}
@article {pmid28190875,
year = {2017},
author = {Clyde, D},
title = {Technique: Barcoding the nucleus.},
journal = {Nature reviews. Genetics},
volume = {18},
number = {4},
pages = {211},
pmid = {28190875},
issn = {1471-0064},
mesh = {*Cell Nucleus ; *DNA Barcoding, Taxonomic ; Humans ; Phylogeny ; },
}
@article {pmid28189584,
year = {2017},
author = {Yin, HQ and Ji, CF and Yang, XQ and Wang, R and Yang, S and Zhang, HQ and Zhang, JG},
title = {An improved gold nanoparticle probe-based assay for HCV core antigen ultrasensitive detection.},
journal = {Journal of virological methods},
volume = {243},
number = {},
pages = {142-145},
doi = {10.1016/j.jviromet.2017.02.007},
pmid = {28189584},
issn = {1879-0984},
mesh = {Antigens, Viral/*analysis ; *Gold ; Hepacivirus/*isolation &amp; purification ; Hepatitis C/*diagnosis ; Humans ; Immunoassay/*methods ; *Nanoparticles ; Reproducibility of Results ; Sensitivity and Specificity ; Viral Core Proteins/*analysis ; },
abstract = {A gold nanoparticle probe-based assay (GNPA) was developed for ultrasensitive detection of Hepatitis C virus (HCV) core antigen. In the GNPA, after anti-HCV core antigen polyclonal antibodies and single-stranded barcode signal DNA were labeled on gold nanoparticle probe (NP), DNA enzyme was used to degrade the unbound barcode DNAs. The anti-HCV core antigen monoclonal antibodies were coated on magnetic microparticles probe (MMP). Then the NP-HCV core antigen-MMP sandwich immuno-complex was formed when the target antigen protein was added and captured. Magnetically separated, the immuno-complex containing the single-stranded barcode signal DNA was characterized by TaqMan probe based real-time fluorescence PCR. A detection limit of 1 fg/ml was determined for the HCV core antigen which is magnitude greater than that of ELISA (2ng/ml). The coefficients of variation (CV) of intra-assay and inter-assay respectively ranged from 0.22-2.62% and 1.92-3.01%. The improved GNPA decreased the interference of unbound barcode DNAs and may be an new way for HCV core antigen detection.},
}
@article {pmid28187661,
year = {2017},
author = {Shinohara, A and Hara, H and Kramp, K and Blank, SM and Kameda, Y},
title = {Bird droppings on chestnut leaves or sawfly larvae: DNA barcodes verify the occurrence of the archaic Megaxyela togashii (Hymenoptera, Xyelidae) in Hokkaido, Japan.},
journal = {Zootaxa},
volume = {4221},
number = {2},
pages = {zootaxa.4221.2.6},
doi = {10.11646/zootaxa.4221.2.6},
pmid = {28187661},
issn = {1175-5334},
mesh = {Animals ; Birds ; *DNA Barcoding, Taxonomic ; *Hymenoptera ; Japan ; Larva ; Phylogeny ; },
abstract = {We made a molecular phylogenetic analysis using mitochondrial cytochrome oxidase subunit 1 (COI) gene sequences for ten unidentified Megaxyela larvae from Hokkaido, Honshu and Shikoku, Japan, and 15 identified adults of four Megaxyela, one Macroxyela and three Xyela species. It revealed that all larvae belonged to M. togashii Shinohara, 1992, which showed rather large intraspecific genetic variability even among the individuals from the same population. This is the first distribution record of M. togashii from Hokkaido. Megaxyela togashii is a univoltine species with a very short larval feeding period, only nine days in one rearing experiment from egg to larval maturation. The larva is a solitary, external leaf-feeder on Juglans ailanthifolia, resting curled around the central leaf vein at the apex of a leaflet, and may resemble the excrement of birds. The prepupa overwinters in an earthen cell whose wall is made only of soil, neither parchment-like nor containing fiber. The mature larva is described and several life traits are discussed.},
}
@article {pmid28187647,
year = {2017},
author = {Corley, MF and Ferreira, S},
title = {DNA Barcoding reveals sexual dimorphism in Isotrias penedana Trematerra, 2013 (Lepidoptera: Tortricidae, Chlidanotinae).},
journal = {Zootaxa},
volume = {4221},
number = {5},
pages = {zootaxa.4221.5.7},
doi = {10.11646/zootaxa.4221.5.7},
pmid = {28187647},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Female ; *Lepidoptera ; Male ; Portugal ; Sex Characteristics ; Spain ; },
abstract = {Isotrias penedana Trematerra, 2013 was described from north Portugal based on males alone. Unidentified females were associated with the males using DNA barcoding, revealing sexual dimorphism in the species. Males and females differ in forewing shape, markings, and size, with females significantly smaller than males. The female is described and illustrated for the first time. We also document the species' occurrence in northern Spain.},
}
@article {pmid28187642,
year = {2017},
author = {Zhang, F and Greenslade, P and Stevens, MI},
title = {A revision of the genus Lepidobrya Womersley (Collembola: Entomobryidae) based on morphology and sequence data of the genotype.},
journal = {Zootaxa},
volume = {4221},
number = {5},
pages = {zootaxa.4221.5.2},
doi = {10.11646/zootaxa.4221.5.2},
pmid = {28187642},
issn = {1175-5334},
mesh = {Animals ; *Arthropods ; Ecology ; Genotype ; },
abstract = {The genus Lepidobrya Womersley, previously placed in Willowsiini, is re-diagnosed based on a redescription of the type species L. mawsoni (Tillyard) and its DNA barcode. Specimens possess narrow, pointed scales on the dens, two inner teeth on unguis, a truncate unguiculus with an outer tooth, a bidentate mucro with a basal spine and ordinary tergal S-chaetae 2, 2|1, 2, 2, ?, 3, so belongs to the Entomobryinae. Its systematic position and relationships to other scaled Entomobryinae genera are discussed and comments are made on the distribution of the genus as well as on ecology.},
}
@article {pmid28187619,
year = {2017},
author = {Tantawi, TI and Whitworth, TL and Sinclair, BJ},
title = {Revision of the Nearctic Calliphora Robineau-Desvoidy (Diptera: Calliphoridae).},
journal = {Zootaxa},
volume = {4226},
number = {3},
pages = {zootaxa.4226.3.1},
doi = {10.11646/zootaxa.4226.3.1},
pmid = {28187619},
issn = {1175-5334},
mesh = {Animals ; *Diptera ; Female ; Male ; Montana ; North America ; Orthoptera ; },
abstract = {The Nearctic species of Calliphora Robineau-Desvoidy are revised and all species are redescribed and/or diagnosed. Diagnostic characters to permit reliable identification of both sexes of Calliphora aldrichia (Shannon) and C. montana (Shannon) and detailed distributional records for both species are provided for the first time. A lectotype is designated for Calliphora loewi Enderlein, 1903. A revised key to the 13 species of Nearctic Calliphora is also included. The key is based on examination of over 1,000 specimens from across North America and the structure of the terminalia of both sexes of each species. Complete illustrations of the terminalia of both sexes are provided for all species, including those of eight poorly known species: Calliphora alaskensis (Shannon), C. aldrichia (Shannon), C. coloradensis Hough, C. grahami Aldrich, C. latifrons Hough, C. livida Hall, C. montana (Shannon) and C. terraenovae Macquart. The female terminalia of C. alaskensis, C. aldrichia, C. coloradensis, C. livida and C. montana are illustrated for the first time. Barcode data for all 13 species of Nearctic Calliphora are provided, several for the first time. Results support current species concepts but barcodes failed to distinguish C. aldrichia and C. montana.},
}
@article {pmid28187592,
year = {2017},
author = {Li, JH and Gopurenko, D and Cai, DC and Yang, YM and Hu, R and Thepparat, A and Wardhana, AH and Kim, HC and Klein, TA and Kim, MS and Bellis, GA},
title = {Culicoides Latreille biting midges (Diptera: Ceratopogonidae) of the Dongzhaigang mangrove forest, Hainan Province, China.},
journal = {Zootaxa},
volume = {4227},
number = {1},
pages = {zootaxa.4227.1.2},
doi = {10.11646/zootaxa.4227.1.2},
pmid = {28187592},
issn = {1175-5334},
mesh = {Animals ; *Ceratopogonidae ; China ; DNA ; DNA Barcoding, Taxonomic ; Wetlands ; },
abstract = {The biting midge fauna of Dongzhaigang Mangrove Forest, Hainan Province, China was sampled on 14 October 2015 using three methods: a pan light trap operated from dusk until dawn the following morning and sweep net and human landing collections performed between 16:15-17:15 hr. Eight species, including two new records for China, Culicoides palawanensis and C. niphanae, and one new record for Hainan, C. circumbasalis, were collected. A key to assist with identification of specimens of these species is provided. DNA barcodes supported the morphological identification of some of these species and identified the potential presence of cryptic species and/or deep population structure in others. The newly recorded species were morphologically similar to species previously reported from Hainan, highlighting the need for further investigation into the taxonomy of biting midges in this region. Species composition and abundance varied considerably between the three collection techniques suggesting that multiple techniques likely provide a more comprehensive sample of biting midge fauna.},
}
@article {pmid28187569,
year = {2017},
author = {Taeger, A and Shinohara, A and Kramp, K},
title = {Pachyprotasis kojimai sp. nov.-the "Pachyprotasis nigronotata" of Japanese authors (Hymenoptera: Tenthredinidae).},
journal = {Zootaxa},
volume = {4227},
number = {4},
pages = {zootaxa.4227.4.8},
doi = {10.11646/zootaxa.4227.4.8},
pmid = {28187569},
issn = {1175-5334},
mesh = {Animals ; *Hymenoptera ; Japan ; },
abstract = {The species formerly known as Pachyprotasis nigronotata Kriechbaumer, 1874 in Japan is described as P. kojimai Taeger &amp; Shinohara, sp. nov. Both taxa are not very closely related, but were hitherto mixed up because of their similar coloration. The new species is endemic to the mountains of central Honshu and P. nigronotata is to be deleted from the fauna of Japan.},
}
@article {pmid28187567,
year = {2017},
author = {Motamedinia, B and Kehlmaier, C and Mokhtari, A and Rakhshani, E and Gilasian, E},
title = {Discovery of the genus Claraeola Aczél in Iran with the description of two new species (Diptera: Pipunculidae).},
journal = {Zootaxa},
volume = {4227},
number = {4},
pages = {zootaxa.4227.4.6},
doi = {10.11646/zootaxa.4227.4.6},
pmid = {28187567},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; *Diptera ; Genes, Mitochondrial ; Iran ; },
abstract = {The genus Claraeola Aczél is recorded from Iran for the first time. Two new species, Claraeola parnianae Motamedinia &amp; Kehlmaier sp. nov. and Claraeola khorshidae Motamedinia &amp; Kehlmaier sp. nov., are described and illustrated. An updated identification key to the Western Palaearctic species of the genus Claraeola is provided. Both species were characterized morphologically and by DNA barcoding of the mitochondrial COI gene.},
}
@article {pmid28186159,
year = {2017},
author = {Chen, X and Xiang, L and Shi, L and Li, G and Yao, H and Han, J and Lin, Y and Song, J and Chen, S},
title = {Identification of crude drugs in the Japanese pharmacopoeia using a DNA barcoding system.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {42325},
pmid = {28186159},
issn = {2045-2322},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/genetics ; Databases as Topic ; Pharmaceutical Preparations/*analysis ; *Pharmacopoeias as Topic ; Plants, Medicinal/genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; Statistics as Topic ; },
abstract = {Kampo is the general designation for traditional Japanese herbal medicines, which are recognized as official medicines and listed in the Japanese pharmacopoeia (JP). In most cases, it is difficult to identify the crude drug materials to species level using only traditional identification methods. We report the first online DNA barcode identification system, which includes standard barcode sequences from approximately 95% of the species recorded in the JP (16[th] edition). This tool provides users with basic information on each crude drug recorded in the JP, DNA barcoding identification of herbal material, and the standard operating procedure (SOP) from sampling to data analysis. ITS2 sequences (psbA-trnH was an alternative when ITS2 could not be amplified) were generated from a total of 576 samples to establish the database. An additional 100 samples (from different medicinal parts, from both single origin and multiple origins and from both retailers and the planting base) were identified using the system. A total of 78% of the test samples were identified as the species listed on their label. This system establishes a model platform for other pharmacopeias from countries like China, Korea, the US and the European Union, for the safe and effective utilization of traditional herbal medicines.},
}
@article {pmid28182661,
year = {2017},
author = {Filzen, TM and Kutchukian, PS and Hermes, JD and Li, J and Tudor, M},
title = {Representing high throughput expression profiles via perturbation barcodes reveals compound targets.},
journal = {PLoS computational biology},
volume = {13},
number = {2},
pages = {e1005335},
pmid = {28182661},
issn = {1553-7358},
mesh = {Animals ; Cell Physiological Phenomena/*drug effects ; Drug Evaluation, Preclinical/*methods ; Gene Expression/drug effects/*genetics ; Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Molecular Targeted Therapy/*methods ; Pharmaceutical Preparations/*administration &amp; dosage ; },
abstract = {High throughput mRNA expression profiling can be used to characterize the response of cell culture models to perturbations such as pharmacologic modulators and genetic perturbations. As profiling campaigns expand in scope, it is important to homogenize, summarize, and analyze the resulting data in a manner that captures significant biological signals in spite of various noise sources such as batch effects and stochastic variation. We used the L1000 platform for large-scale profiling of 978 representative genes across thousands of compound treatments. Here, a method is described that uses deep learning techniques to convert the expression changes of the landmark genes into a perturbation barcode that reveals important features of the underlying data, performing better than the raw data in revealing important biological insights. The barcode captures compound structure and target information, and predicts a compound's high throughput screening promiscuity, to a higher degree than the original data measurements, indicating that the approach uncovers underlying factors of the expression data that are otherwise entangled or masked by noise. Furthermore, we demonstrate that visualizations derived from the perturbation barcode can be used to more sensitively assign functions to unknown compounds through a guilt-by-association approach, which we use to predict and experimentally validate the activity of compounds on the MAPK pathway. The demonstrated application of deep metric learning to large-scale chemical genetics projects highlights the utility of this and related approaches to the extraction of insights and testable hypotheses from big, sometimes noisy data.},
}
@article {pmid28182623,
year = {2017},
author = {Wang, DY and Wang, Q and Wang, YL and Xiang, XG and Huang, LQ and Jin, XH},
title = {Evaluation of DNA barcodes in Codonopsis (Campanulaceae) and in some large angiosperm plant genera.},
journal = {PloS one},
volume = {12},
number = {2},
pages = {e0170286},
pmid = {28182623},
issn = {1932-6203},
mesh = {Codonopsis/*classification/*genetics ; *DNA Barcoding, Taxonomic ; *Genome, Plastid ; *Phylogeny ; },
abstract = {DNA barcoding is expected to be one of the most promising tools in biological taxonomy. However, there have been no agreements on which core barcode should be used in plants, especially in species-rich genera with wide geographical distributions. To evaluate their discriminatory power in large genera, four of the most widely used DNA barcodes, including three plastid regions (matK, rbcL, trnH-psbA) and nuclear internal transcribed spacer (nrITS), were tested in seven species-rich genera (Ficus, Pedicularis, Rhodiola, Rhododendron,Viburnum, Dendrobium and Lysimachia) and a moderate size genus, Codonopsis. All of the sequences from the aforementioned seven large genera were downloaded from NCBI. The related barcodes for Codonopsis were newly generated in this study. Genetics distances, DNA barcoding gaps and phylogenetic trees of the four single barcodes and their combinations were calculated and compared in the seven genera. As for single barcode, nrITS has the most variable sites, the clearest intra- and inter-specific divergences and the highest discrimination rates in the seven genera. Among the combinations of barcodes, ITS+matK performed better than all the single barcodes in most cases and even the three- and four-loci combinations in the seven genera. Therefore, we recommend ITS+matK as the core barcodes for large plant genera.},
}
@article {pmid28179510,
year = {2017},
author = {Cong, Q and Shen, J and Borek, D and Robbins, RK and Opler, PA and Otwinowski, Z and Grishin, NV},
title = {When COI barcodes deceive: complete genomes reveal introgression in hairstreaks.},
journal = {Proceedings. Biological sciences},
volume = {284},
number = {1848},
pages = {},
pmid = {28179510},
issn = {1471-2954},
support = {R01 GM094575/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Butterflies/*growth &amp; development ; Central America ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; *Genome, Insect ; *Genome, Mitochondrial ; Phylogeny ; United States ; },
abstract = {Two species of hairstreak butterflies from the genus Calycopis are known in the United States: C. cecrops and C. isobeon Analysis of mitochondrial COI barcodes of Calycopis revealed cecrops-like specimens from the eastern US with atypical barcodes that were 2.6% different from either USA species, but similar to Central American Calycopis species. To address the possibility that the specimens with atypical barcodes represent an undescribed cryptic species, we sequenced complete genomes of 27 Calycopis specimens of four species: C. cecrops, C. isobeon, C. quintana and C. bactra Some of these specimens were collected up to 60 years ago and preserved dry in museum collections, but nonetheless produced genomes as complete as fresh samples. Phylogenetic trees reconstructed using the whole mitochondrial and nuclear genomes were incongruent. While USA Calycopis with atypical barcodes grouped with Central American species C. quintana by mitochondria, nuclear genome trees placed them within typical USA C. cecrops in agreement with morphology, suggesting mitochondrial introgression. Nuclear genomes also show introgression, especially between C. cecrops and C. isobeon About 2.3% of each C. cecrops genome has probably (p-value < 0.01, FDR < 0.1) introgressed from C. isobeon and about 3.4% of each C. isobeon genome may have come from C. cecrops. The introgressed regions are enriched in genes encoding transmembrane proteins, mitochondria-targeting proteins and components of the larval cuticle. This study provides the first example of mitochondrial introgression in Lepidoptera supported by complete genome sequencing. Our results caution about relying solely on COI barcodes and mitochondrial DNA for species identification or discovery.},
}
@article {pmid28178222,
year = {2017},
author = {He, L and Qian, J and Li, X and Sun, Z and Xu, X and Chen, S},
title = {Complete Chloroplast Genome of Medicinal Plant Lonicera japonica: Genome Rearrangement, Intron Gain and Loss, and Implications for Phylogenetic Studies.},
journal = {Molecules (Basel, Switzerland)},
volume = {22},
number = {2},
pages = {},
pmid = {28178222},
issn = {1420-3049},
mesh = {Base Composition ; DNA, Chloroplast/*genetics ; Evolution, Molecular ; Gene Rearrangement ; *Genome, Chloroplast ; Introns ; Lonicera/*genetics ; Phylogeny ; Plants, Medicinal/genetics ; Sequence Analysis, DNA ; },
abstract = {The complete chloroplast (cp) genome of Lonicera japonica, a common ornamental and medicinal plant in North America and East Asia, was sequenced and analyzed. The length of the L. japonica cp genome is 155,078 bp, contains a pair of inverted repeat regions (IRa and IRb), of 23,774 bp each, as well as large (LSC, 88,858 bp) and small (SSC, 18,672 bp) single-copy regions. A total of 129 genes were identified in the cp genome, 16 of which were duplicated within the IR regions. Relative to other plant cp genomes, the L. japonica cp genome had a unique rearrangement between trnI-CAU and trnN-GUU. In L. japonica cpDNA, rps19, rpl2, and rpl23 move to the LSC region, from the IR region. The ycf1 pesudogene in the IR region is lost, and only one copy locates in the SSC region. Comparative cp DNA sequence analyses of L. japonica with other cp genomes reveal that the gene order, and the gene and intron contents, are slightly different. The introns in ycf2 and rps18 genes are found for the first time. Four genes (clpP, petB, petD, and rpl16) lost introns. However, its genome structure, GC content, and codon usage were similar to those of typical angiosperm cp genomes. All preferred synonymous codons were found to use codons ending with A/T. The AT-rich sequences were less abundant in the coding regions than in the non-coding ones. A phylogenetic analysis based on 71 protein-coding genes supported the idea that L. japonica is a sister of the Araliaceae species. This study identified unique characteristics of the L. japonica cp genome that contribute to our understanding of the cpDNA evolution. It offers valuable information for the phylogenetic and specific barcoding of this medicinal plant.},
}
@article {pmid28177847,
year = {2017},
author = {Mwale, M and Dalton, DL and Jansen, R and De Bruyn, M and Pietersen, D and Mokgokong, PS and Kotzé, A},
title = {Forensic application of DNA barcoding for identification of illegally traded African pangolin scales.},
journal = {Genome},
volume = {60},
number = {3},
pages = {272-284},
doi = {10.1139/gen-2016-0144},
pmid = {28177847},
issn = {1480-3321},
mesh = {Africa ; Animals ; Asia ; Conservation of Natural Resources ; Crime ; Cytochromes b/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Ecosystem ; Electron Transport Complex IV/metabolism ; Geography ; Mammals/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The escalating growth in illegal wildlife trade and anthropogenic habitat changes threaten the survival of pangolin species worldwide. All eight extant species have experienced drastic population size reductions globally with a high extinction risk in Asia. Consequently, forensic services have become critical for law enforcement, with a need for standardised and validated genetic methods for reliable identifications. The seizure of three tonnes of pangolin scales, believed to have originated from Africa, by Hong Kong Customs Authorities provided an opportunity for the application of DNA barcoding in identifying scales. Three mitochondrial DNA gene regions (COI, Cyt b, and D-loop) were amplified for a subsample of the confiscated material and compared with taxonomically verified references. All four African species were recovered as monophyletic with high interspecific uncorrected p-distance estimates (0.048-0.188) among genes. However, only three of four African species (Phataginus tricuspis, Phataginus tetradactyla, and Smutsia gigantea, originating from West and Central Africa) and one of four Asian species (Manis javanica from Southeast Asia) were identified among scales. Although the assignment of unknown scales to specific species was reliable, additional genetic tools and representative reference material are required to determine geographic origins of confiscated pangolin specimens.},
}
@article {pmid28177842,
year = {2017},
author = {Packer, L and Ruz, L},
title = {DNA barcoding the bees (Hymenoptera: Apoidea) of Chile: species discovery in a reasonably well known bee fauna with the description of a new species of Lonchopria (Colletidae).},
journal = {Genome},
volume = {60},
number = {5},
pages = {414-430},
doi = {10.1139/gen-2016-0071},
pmid = {28177842},
issn = {1480-3321},
mesh = {Animals ; Bees/anatomy &amp; histology/classification/*genetics ; Chile ; DNA Barcoding, Taxonomic/*methods ; Female ; Hymenoptera/anatomy &amp; histology/classification/*genetics ; Male ; Species Specificity ; },
abstract = {We compare the diversity of bees in the Chilean fauna as understood from traditional taxonomy-based catalogues with that currently known from DNA barcodes using the BIN system informed by ongoing morphology-based taxonomic research. While DNA barcode surveys of the Chilean bee fauna remain incomplete, it is clear that new species can readily be distinguished using this method and that morphological differentiation of distinct barcode clusters is sometimes very easy. We assess the situation in two genera in some detail. In Lonchopria Vachal one "species" is readily separable into two BINs that are easily differentiated based upon male mandibular and genitalic morphology (characters generally used in this group) as well as female hair patterns. Consequently, we describe Lonchopria (Lonchopria) heberti Packer and Ruz, new species. For Liphanthus Reed, a large number of new species has been detected using DNA barcoding and considerable additional traditional morphological work will be required to describe them. When we add the number of BINs (whether identified to named species or not) to the number of Chilean bee species that we know have not been barcoded (both described and new species under study in our laboratories) we conclude that the bee fauna of Chile is substantially greater than the 436 species currently known. Spanish language abstract available as supplementary data [1] .},
}
@article {pmid28177841,
year = {2017},
author = {Hernández-Triana, LM and Montes De Oca, F and Prosser, SW and Hebert, PD and Gregory, TR and McMurtrie, S},
title = {DNA barcoding as an aid for species identification in austral black flies (Insecta: Diptera: Simuliidae).},
journal = {Genome},
volume = {60},
number = {4},
pages = {348-357},
doi = {10.1139/gen-2015-0168},
pmid = {28177841},
issn = {1480-3321},
mesh = {Animals ; Argentina ; Australia ; Chile ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Insect Proteins/genetics ; New Zealand ; Phylogeny ; Phylogeography ; Simuliidae/*classification/*genetics ; Species Specificity ; },
abstract = {In this paper, the utility of a partial sequence of the COI gene, the DNA barcoding region, for the identification of species of black flies in the austral region was assessed. Twenty-eight morphospecies were analyzed: eight of the genus Austrosimulium (four species in the subgenus Austrosimulium s. str., three species in the subgenus Novaustrosimulium, and one species unassigned to subgenus), two of the genus Cnesia, eight of Gigantodax, three of Paracnephia, one of Paraustrosimulium, and six of Simulium (subgenera Morops, Nevermannia, and Pternaspatha). The neighbour-joining tree derived from the DNA barcode sequences grouped most specimens according to species or species groups recognized by morphotaxonomic studies. Intraspecific sequence divergences within morphologically distinct species ranged from 0% to 1.8%, while higher divergences (2%-4.2%) in certain species suggested the presence of cryptic diversity. The existence of well-defined groups within S. simile revealed the likely inclusion of cryptic diversity. DNA barcodes also showed that specimens identified as C. dissimilis, C. nr. pussilla, and C. ornata might be conspecific, suggesting possible synonymy. DNA barcoding combined with a sound morphotaxonomic framework would provide an effective approach for the identification of black flies in the region.},
}
@article {pmid28177838,
year = {2017},
author = {Daru, BH and van der Bank, M and Bello, A and Yessoufou, K},
title = {Testing the reliability of standard and complementary DNA barcodes for the monocot subfamily Alooideae from South Africa.},
journal = {Genome},
volume = {60},
number = {4},
pages = {337-347},
doi = {10.1139/gen-2015-0183},
pmid = {28177838},
issn = {1480-3321},
mesh = {Asparagales/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Complementary/*genetics ; DNA, Plant/genetics ; Evolution, Molecular ; Genetic Markers/*genetics ; Genetic Variation ; Phylogeny ; Reproducibility of Results ; South Africa ; Species Specificity ; },
abstract = {Although a standard DNA barcode has been identified for plants, it does not always provide species-level specimen identifications for investigating important ecological questions. In this study, we assessed the species-level discriminatory power of standard (rbcLa + matK) and complementary barcodes (ITS1 and trnH-psbA) within the subfamily Alooideae (Asphodelaceae), a large and recent plant radiation, whose species are important in horticulture yet are threatened. Alooideae has its centre of endemism in southern Africa, with some outlier species occurring elsewhere in Africa and Madagascar. We sampled 360 specimens representing 235 species within all 11 genera of the subfamily. With three distance-based methods, all markers performed poorly for our combined data set, with the highest proportion of correct species-level specimen identifications (30%) found for ITS1. However, when performance was assessed across genera, the discriminatory power varied from 0% for all single markers and combinations in Gasteria to 63% in Haworthiopsis, again for ITS1, suggesting that DNA barcoding success may be related to the evolutionary history of the lineage considered. Although ITS1 could be a good barcode for Haworthiopsis, the generally poor performance of all markers suggests that Alooideae remains a challenge. As species boundaries within Alooideae remain controversial, we call for continued search for suitable markers or the use of genomics approaches to further explore species discrimination in the group.},
}
@article {pmid28177833,
year = {2017},
author = {Freeland, JR},
title = {The importance of molecular markers and primer design when characterizing biodiversity from environmental DNA.},
journal = {Genome},
volume = {60},
number = {4},
pages = {358-374},
doi = {10.1139/gen-2016-0100},
pmid = {28177833},
issn = {1480-3321},
mesh = {Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/*genetics ; Environment ; Genetic Markers/*genetics ; Species Specificity ; },
abstract = {Environmental DNA (eDNA) comprises DNA fragments that have been shed into the environment by organisms, and which can be extracted from environmental samples such as water or soil. Characterization of eDNA can allow researchers to infer the presence or absence of species from a particular site without the need to locate and identify individuals, and therefore may provide an extremely valuable tool for quantifying biodiversity. However, as is often the case with relatively new protocols, methodological challenges remain. A number of earlier reviews have discussed these challenges, but none have provided extensive treatment of the critical decisions surrounding molecular markers and primer development for use in eDNA assays. This review discusses a number of options and approaches that can be used when determining which primers and gene regions are most appropriate for either targeted species detection or metabarcoding macro-organisms from eDNA. The latter represents a new field that is growing rapidly, and which has the potential to revolutionize future assessments of community and ecosystem diversity.},
}
@article {pmid28174497,
year = {2016},
author = {Baldwin, CC and Robertson, DR and Nonaka, A and Tornabene, L},
title = {Two new deep-reef basslets (Teleostei, Grammatidae, Lipogramma), with comments on the eco-evolutionary relationships of the genus.},
journal = {ZooKeys},
volume = {},
number = {638},
pages = {45-82},
pmid = {28174497},
issn = {1313-2989},
abstract = {The banded basslet, Lipogramma evides Robins &amp; Colin, 1979, is shown to comprise two species: Lipogramma evides, which inhabits depths of 133-302 m, and a new species described here as Lipogramma levinsoni, which inhabits depths of 108-154 m and previously was considered to represent the juvenile of Lipogramma evides. A second new species of banded basslet, described here as Lipogramma haberi, inhabits depths of 152-233 m and was previously not reported in the literature. Morphologically, the three species differ in color patterns and modal numbers of gill rakers, whereas various other morphological features distinguish Lipogramma levinsoni from Lipogramma evides and Lipogramma haberi. DNA barcode data and multilocus, coalescent-based, species-delimitation analysis support the recognition of the three species. Phylogenetic analysis of mitochondrial and nuclear genetic data supports a sister-group relationship between the two deepest-living of the three species, Lipogramma evides and Lipogramma haberi, and suggests that the shallower Lipogramma levinsoni is more closely related to Lipogramma anabantoides Böhlke, 1960, which inhabits depths < 120 m. Evolutionary relationships within Lipogramma thus appear to be correlated with species depth ranges, an eco-evolutionary pattern that has been observed in other Caribbean marine teleosts and that warrants further investigation. The new species represent the eleventh and twelfth new fish species described in recent years from exploratory submersible diving in the Caribbean in the globally poorly studied depth zone of 50-300 m. This study suggests that there are at least two additional cryptic species of Lipogramma, which are being analyzed in ongoing investigations of Caribbean deep-reef ecosystems.},
}
@article {pmid28171784,
year = {2017},
author = {Jäger, AC and Alvarez, ML and Davis, CP and Guzmán, E and Han, Y and Way, L and Walichiewicz, P and Silva, D and Pham, N and Caves, G and Bruand, J and Schlesinger, F and Pond, SJK and Varlaro, J and Stephens, KM and Holt, CL},
title = {Developmental validation of the MiSeq FGx Forensic Genomics System for Targeted Next Generation Sequencing in Forensic DNA Casework and Database Laboratories.},
journal = {Forensic science international. Genetics},
volume = {28},
number = {},
pages = {52-70},
doi = {10.1016/j.fsigen.2017.01.011},
pmid = {28171784},
issn = {1878-0326},
mesh = {Amelogenin/genetics ; Animals ; *DNA Fingerprinting ; Female ; Genotype ; High-Throughput Nucleotide Sequencing/*instrumentation ; Humans ; Male ; Microsatellite Repeats ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Reproducibility of Results ; Species Specificity ; },
abstract = {Human DNA profiling using PCR at polymorphic short tandem repeat (STR) loci followed by capillary electrophoresis (CE) size separation and length-based allele typing has been the standard in the forensic community for over 20 years. Over the last decade, Next-Generation Sequencing (NGS) matured rapidly, bringing modern advantages to forensic DNA analysis. The MiSeq FGx™ Forensic Genomics System, comprised of the ForenSeq™ DNA Signature Prep Kit, MiSeq FGx™ Reagent Kit, MiSeq FGx™ instrument and ForenSeq™ Universal Analysis Software, uses PCR to simultaneously amplify up to 231 forensic loci in a single multiplex reaction. Targeted loci include Amelogenin, 27 common, forensic autosomal STRs, 24 Y-STRs, 7 X-STRs and three classes of single nucleotide polymorphisms (SNPs). The ForenSeq™ kit includes two primer sets: Amelogenin, 58 STRs and 94 identity informative SNPs (iiSNPs) are amplified using DNA Primer Set A (DPMA; 153 loci); if a laboratory chooses to generate investigative leads using DNA Primer Set B, amplification is targeted to the 153 loci in DPMA plus 22 phenotypic informative (piSNPs) and 56 biogeographical ancestry SNPs (aiSNPs). High-resolution genotypes, including detection of intra-STR sequence variants, are semi-automatically generated with the ForenSeq™ software. This system was subjected to developmental validation studies according to the 2012 Revised SWGDAM Validation Guidelines. A two-step PCR first amplifies the target forensic STR and SNP loci (PCR1); unique, sample-specific indexed adapters or "barcodes" are attached in PCR2. Approximately 1736 ForenSeq™ reactions were analyzed. Studies include DNA substrate testing (cotton swabs, FTA cards, filter paper), species studies from a range of nonhuman organisms, DNA input sensitivity studies from 1ng down to 7.8pg, two-person human DNA mixture testing with three genotype combinations, stability analysis of partially degraded DNA, and effects of five commonly encountered PCR inhibitors. Calculations from ForenSeq™ STR and SNP repeatability and reproducibility studies (1ng template) indicate 100.0% accuracy of the MiSeq FGx™ System in allele calling relative to CE for STRs (1260 samples), and >99.1% accuracy relative to bead array typing for SNPs (1260 samples for iiSNPs, 310 samples for aiSNPs and piSNPs), with >99.0% and >97.8% precision, respectively. Call rates of >99.0% were observed for all STRs and SNPs amplified with both ForenSeq™ primer mixes. Limitations of the MiSeq FGx™ System are discussed. Results described here demonstrate that the MiSeq FGx™ System meets forensic DNA quality assurance guidelines with robust, reliable, and reproducible performance on samples of various quantities and qualities.},
}
@article {pmid28169275,
year = {2017},
author = {Shin, G and Grimes, SM and Lee, H and Lau, BT and Xia, LC and Ji, HP},
title = {CRISPR-Cas9-targeted fragmentation and selective sequencing enable massively parallel microsatellite analysis.},
journal = {Nature communications},
volume = {8},
number = {},
pages = {14291},
pmid = {28169275},
issn = {2041-1723},
support = {P01 HG000205/HG/NHGRI NIH HHS/United States ; R01 HG006137/HG/NHGRI NIH HHS/United States ; R33 CA174575/CA/NCI NIH HHS/United States ; },
mesh = {Alleles ; *CRISPR-Cas Systems ; *Genomic Library ; Haplotypes/genetics ; High-Throughput Nucleotide Sequencing/*methods ; *Human Genome Project ; Humans ; Microsatellite Repeats/*genetics ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/*methods ; },
abstract = {Microsatellites are multi-allelic and composed of short tandem repeats (STRs) with individual motifs composed of mononucleotides, dinucleotides or higher including hexamers. Next-generation sequencing approaches and other STR assays rely on a limited number of PCR amplicons, typically in the tens. Here, we demonstrate STR-Seq, a next-generation sequencing technology that analyses over 2,000 STRs in parallel, and provides the accurate genotyping of microsatellites. STR-Seq employs in vitro CRISPR-Cas9-targeted fragmentation to produce specific DNA molecules covering the complete microsatellite sequence. Amplification-free library preparation provides single molecule sequences without unique molecular barcodes. STR-selective primers enable massively parallel, targeted sequencing of large STR sets. Overall, STR-Seq has higher throughput, improved accuracy and provides a greater number of informative haplotypes compared with other microsatellite analysis approaches. With these new features, STR-Seq can identify a 0.1% minor genome fraction in a DNA mixture composed of different, unrelated samples.},
}
@article {pmid28167778,
year = {2017},
author = {Dahlman, JE and Kauffman, KJ and Xing, Y and Shaw, TE and Mir, FF and Dlott, CC and Langer, R and Anderson, DG and Wang, ET},
title = {Barcoded nanoparticles for high throughput in vivo discovery of targeted therapeutics.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {114},
number = {8},
pages = {2060-2065},
pmid = {28167778},
issn = {1091-6490},
support = {DP5 OD017865/OD/NIH HHS/United States ; P30 CA014051/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Cell Separation ; DNA Barcoding, Taxonomic/*methods ; Drug Delivery Systems/methods ; Drug Discovery/*methods ; Factor VII/genetics ; Female ; Flow Cytometry ; Liver/cytology/drug effects ; Lung/cytology/drug effects ; Mice ; Mice, Inbred C57BL ; Molecular Targeted Therapy/methods ; Nanoparticles/*chemistry ; Nucleic Acids/*administration &amp; dosage/therapeutic use ; Pharmaceutical Preparations/administration &amp; dosage ; RNA Interference ; RNA, Small Interfering/*administration &amp; dosage/therapeutic use ; Tissue Distribution ; },
abstract = {Nucleic acid therapeutics are limited by inefficient delivery to target tissues and cells and by an incomplete understanding of how nanoparticle structure affects biodistribution to off-target organs. Although thousands of nanoparticle formulations have been designed to deliver nucleic acids, most nanoparticles have been tested in cell culture contexts that do not recapitulate systemic in vivo delivery. To increase the number of nanoparticles that could be tested in vivo, we developed a method to simultaneously measure the biodistribution of many chemically distinct nanoparticles. We formulated nanoparticles to carry specific nucleic acid barcodes, administered the pool of particles, and quantified particle biodistribution by deep sequencing the barcodes. This method distinguished previously characterized lung- and liver- targeting nanoparticles and accurately reported relative quantities of nucleic acid delivered to tissues. Barcode sequences did not affect delivery, and no evidence of particle mixing was observed for tested particles. By measuring the biodistribution of 30 nanoparticles to eight tissues simultaneously, we identified chemical properties promoting delivery to some tissues relative to others. Finally, particles that distributed to the liver also silenced gene expression in hepatocytes when formulated with siRNA. This system can facilitate discovery of nanoparticles targeting specific tissues and cells and accelerate the study of relationships between chemical structure and delivery in vivo.},
}
@article {pmid28166371,
year = {2017},
author = {Bondarenko, NI and Bondarenko, AS and Smirnov, AV},
title = {Lineage-Specific and Highly Derived Gene Sequences Among Amoebozoa, Revealed by the Comparative Analysis of Transcriptomes from Twelve Amoebozoan Species.},
journal = {The Journal of eukaryotic microbiology},
volume = {64},
number = {5},
pages = {622-631},
doi = {10.1111/jeu.12397},
pmid = {28166371},
issn = {1550-7408},
mesh = {Amoebozoa/classification/*genetics ; DNA Barcoding, Taxonomic/methods ; Evolution, Molecular ; Gene Expression Profiling/*methods ; Molecular Sequence Annotation ; Phylogeny ; Protozoan Proteins/*genetics ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
abstract = {Amoebozoa represent a difficult group for traditional morphology-based taxonomy. Molecular approaches, such as gene sequencing and DNA barcoding have greatly enhanced our knowledge of the diversity of these organisms. However, metagenomic studies of Amoebozoa still did not provide as impressive results as they did among some other groups of protists. In environmental DNA surveys done on fragments of SSU rDNA gene and other traditional DNA barcodes, Amoebozoa genes normally constitute a minor part of the total gene diversity and represent only the most abundant lineages. A potential way to resolve this problem is the usage of DNA barcodes based on genes, which are unique or highly derived in this group of organisms. In the present study, we attempted to find such genes and gene families with a low level of paralogy, potentially appropriate as Amoebozoa-specific DNA barcodes. For this we re-assembled transcriptomes of 12 amoebozoan species available from the public databases and performed gene annotation and identification of orthologous genes. In our analysis Amoebozoa-specific and highly derived sequences formed 53,182 clusters of orthologs, containing from 2 to 299 proteins each. Some of these genes may be a potential target for DNA barcoding of Amoebozoa.},
}
@article {pmid28165046,
year = {2017},
author = {Cruaud, P and Rasplus, JY and Rodriguez, LJ and Cruaud, A},
title = {High-throughput sequencing of multiple amplicons for barcoding and integrative taxonomy.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {41948},
pmid = {28165046},
issn = {2045-2322},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Ficus/*physiology ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing/*methods ; Insect Proteins/*genetics ; Sequence Analysis, DNA/*methods ; Wasps/classification/*genetics ; },
abstract = {Until now, the potential of NGS for the construction of barcode libraries or integrative taxonomy has been seldom realised. Here, we amplified (two-step PCR) and simultaneously sequenced (MiSeq) multiple markers from hundreds of fig wasp specimens. We also developed a workflow for quality control of the data. Illumina and Sanger sequences accumulated in the past years were compared. Interestingly, primers and PCR conditions used for the Sanger approach did not require optimisation to construct the MiSeq library. After quality controls, 87% of the species (76% of the specimens) had a valid MiSeq sequence for each marker. Importantly, major clusters did not always correspond to the targeted loci. Nine specimens exhibited two divergent sequences (up to 10%). In 95% of the species, MiSeq and Sanger sequences obtained from the same sampling were similar. For the remaining 5%, species were paraphyletic or the sequences clustered into divergent groups on the Sanger + MiSeq trees (>7%). These problematic cases may represent coding NUMTS or heteroplasms. Our results illustrate that Illumina approaches are not artefact-free and confirm that Sanger databases can contain non-target genes. This highlights the importance of quality controls, working with taxonomists and using multiple markers for DNA-taxonomy or species diversity assessment.},
}
@article {pmid28161911,
year = {2017},
author = {Blair, C and Bryson, RW},
title = {Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae: Phrynosoma).},
journal = {Molecular ecology resources},
volume = {17},
number = {6},
pages = {1168-1182},
doi = {10.1111/1755-0998.12658},
pmid = {28161911},
issn = {1755-0998},
mesh = {Animals ; *Cluster Analysis ; Computational Biology/*methods ; *Genetic Loci ; *Genetic Variation ; Lizards/*classification/*genetics ; Mitochondrial Proteins/genetics ; NADH Dehydrogenase/genetics ; },
abstract = {Biodiversity reduction and loss continues to progress at an alarming rate, and thus, there is widespread interest in utilizing rapid and efficient methods for quantifying and delimiting taxonomic diversity. Single-locus species delimitation methods have become popular, in part due to the adoption of the DNA barcoding paradigm. These techniques can be broadly classified into tree-based and distance-based methods depending on whether species are delimited based on a constructed genealogy. Although the relative performance of these methods has been tested repeatedly with simulations, additional studies are needed to assess congruence with empirical data. We compiled a large data set of mitochondrial ND4 sequences from horned lizards (Phrynosoma) to elucidate congruence using four tree-based (single-threshold GMYC, multiple-threshold GMYC, bPTP, mPTP) and one distance-based (ABGD) species delimitation models. We were particularly interested in cases with highly uneven sampling and/or large differences in intraspecific diversity. Results showed a high degree of discordance among methods, with multiple-threshold GMYC and bPTP suggesting an unrealistically high number of species (29 and 26 species within the P. douglasii complex alone). The single-threshold GMYC model was the most conservative, likely a result of difficulty in locating the inflection point in the genealogies. mPTP and ABGD appeared to be the most stable across sampling regimes and suggested the presence of additional cryptic species that warrant further investigation. These results suggest that the mPTP model may be preferable in empirical data sets with highly uneven sampling or large differences in effective population sizes of species.},
}
@article {pmid28158202,
year = {2017},
author = {Adomako-Ankomah, Y and Chenoweth, MS and Durfee, K and Doumbia, S and Konate, D and Doumbouya, M and Keita, AS and Nikolaeva, D and Tullo, GS and Anderson, JM and Fairhurst, RM and Daniels, R and Volkman, SK and Diakite, M and Miura, K and Long, CA},
title = {High Plasmodium falciparum longitudinal prevalence is associated with high multiclonality and reduced clinical malaria risk in a seasonal transmission area of Mali.},
journal = {PloS one},
volume = {12},
number = {2},
pages = {e0170948},
pmid = {28158202},
issn = {1932-6203},
support = {T32 GM007309/GM/NIGMS NIH HHS/United States ; },
mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; Female ; Humans ; Infant ; Longitudinal Studies ; Malaria, Falciparum/*epidemiology/*parasitology ; Male ; Mali/epidemiology ; Middle Aged ; Plasmodium falciparum/*pathogenicity ; Polymerase Chain Reaction ; Prevalence ; Young Adult ; },
abstract = {The effects of persistent Plasmodium falciparum (Pf) infection and multiclonality on subsequent risk of clinical malaria have been reported, but the relationship between these 2 parameters and their relative impacts on the clinical outcome of infection are not understood. A longitudinal cohort study was conducted in a seasonal and high-transmission area of Mali, in which 500 subjects aged 1-65 years were followed for 1 year. Blood samples were collected every 2 weeks, and incident malaria cases were diagnosed and treated. Pf infection in each individual at each time point was assessed by species-specific nested-PCR, and Pf longitudinal prevalence per person (PfLP, proportion of Pf-positive samples over 1 year) was calculated. Multiclonality of Pf infection was measured using a 24-SNP DNA barcoding assay at 4 time-points (two in wet season, and two in dry season) over one year. PfLP was positively correlated with multiclonality at each time point (all r≥0.36; all P≤0.011). When host factors (e.g., age, gender), PfLP, and multiclonality (at the beginning of the transmission season) were analyzed together, only increasing age and high PfLP were associated with reduced clinical malaria occurrence or reduced number of malaria episodes (for both outcomes, P<0.001 for age, and P = 0.005 for PfLP). When age, PfLP and baseline Pf positivity were analyzed together, the effect of high PfLP remained significant even after adjusting for the other two factors (P = 0.001 for malaria occurrence and P<0.001 for number of episodes). In addition to host age and baseline Pf positivity, both of which have been reported as important modifiers of clinical malaria risk, our results demonstrate that persistent parasite carriage, but not baseline multiclonality, is associated with reduced risk of clinical disease in this population. Our study emphasizes the importance of considering repeated parasite exposure in future studies that evaluate clinical malaria risk.},
}
@article {pmid28157916,
year = {2017},
author = {Li, WS and Shen, Y and Chen, ZJ and Cui, Q and Li, SS and Chen, LJ},
title = {Demonstration of patterned polymer-stabilized cholesteric liquid crystal textures for anti-counterfeiting two-dimensional barcodes.},
journal = {Applied optics},
volume = {56},
number = {3},
pages = {601-606},
doi = {10.1364/AO.56.000601},
pmid = {28157916},
issn = {1539-4522},
abstract = {We evaluated the feasibility of embedding periodically arranged squares with planar and vertical texture into a background with a developable-modulation (DM) type cholesteric liquid crystal (CLC) fingerprint texture by a two-step ultraviolet-induced polymerization method. Checker-patterned optical diffractive elements, which can be seen as a variation of a two-dimensional (2D) barcode, were first realized and the dependence of diffraction behaviors on incident light polarization and applied voltage were investigated. Taking advantage of the natural randomness and uncontrollable variations of a DM-type fingerprint textures, a polymer-stabilized CLC (PSCLC) graphic symbol with a 2D barcode pattern was then implemented with enhanced anti-counterfeiting features that are difficult to falsify or duplicate. The results indicate that the multiplexing of nonuniform DM-type fingerprint gratings, cross-polarized light readout, and unique polarization diffraction characteristics can improve the level of security.},
}
@article {pmid28155635,
year = {2016},
author = {Mun, J and Kim, DU and Hoe, KL and Kim, SY},
title = {Genome-wide functional analysis using the barcode sequence alignment and statistical analysis (Barcas) tool.},
journal = {BMC bioinformatics},
volume = {17},
number = {Suppl 17},
pages = {475},
pmid = {28155635},
issn = {1471-2105},
mesh = {Algorithms ; Animals ; CRISPR-Cas Systems ; Data Interpretation, Statistical ; *Genome ; Humans ; Mice ; RNA, Small Interfering ; Sequence Alignment/*methods ; Sequence Analysis, DNA/*methods ; *Software ; },
abstract = {BACKGROUND: Pooled library screen analysis using shRNAs or CRISPR-Cas9 hold great promise to genome-wide functional studies. While pooled library screens are effective tools, erroneous barcodes can potentially be generated during the production of many barcodes. However, no current tools can distinguish erroneous barcodes from PCR or sequencing errors in a data preprocessing step.<br><br>RESULTS: We developed the Barcas program, a specialized program for the mapping and analysis of multiplexed barcode sequencing (barcode-seq) data. For fast and efficient mapping, Barcas uses a trie data structure based imperfect matching algorithm which generates precise mapping results containing mismatches, shifts, insertions and deletions (indel) in a flexible manner. Barcas provides three functions for quality control (QC) of a barcode library and distinguishes erroneous barcodes from PCR or sequencing errors. It also provides useful functions for data analysis and visualization.<br><br>CONCLUSIONS: Barcas is an all-in-one package providing useful functions including mapping, data QC, library QC, statistical analysis and visualization in genome-wide pooled screens.},
}
@article {pmid28155593,
year = {2018},
author = {Casas, PAS and Sing, KW and Lee, PS and Nuñeza, OM and Villanueva, RJT and Wilson, JJ},
title = {DNA barcodes for dragonflies and damselflies (Odonata) of Mindanao, Philippines.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {2},
pages = {206-211},
doi = {10.1080/24701394.2016.1267157},
pmid = {28155593},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Evolution, Molecular ; Genetic Speciation ; Odonata/*classification/genetics ; Philippines ; Phylogeny ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
abstract = {Reliable species identification provides a sounder basis for use of species in the order Odonata as biological indicators and for their conservation, an urgent concern as many species are threatened with imminent extinction. We generated 134 COI barcodes from 36 morphologically identified species of Odonata collected from Mindanao Island, representing 10 families and 19 genera. Intraspecific sequence divergences ranged from 0 to 6.7% with four species showing more than 2%, while interspecific sequence divergences ranged from 0.5 to 23.3% with seven species showing less than 2%. Consequently, no distinct gap was observed between intraspecific and interspecific DNA barcode divergences. The numerous islands of the Philippine archipelago may have facilitated rapid speciation in the Odonata and resulted in low interspecific sequence divergences among closely related groups of species. This study contributes DNA barcodes for 36 morphologically identified species of Odonata reported from Mindanao including 31 species with no previous DNA barcode records.},
}
@article {pmid28152034,
year = {2017},
author = {Chaabane, A and Neifar, L and Justine, JL},
title = {Diplectanids from Mycteroperca spp. (Epinephelidae) in the Mediterranean Sea: Redescriptions of six species from material collected off Tunisia and Libya, proposal for the 'Pseudorhabdosynochus riouxi group', and a taxonomic key.},
journal = {PloS one},
volume = {12},
number = {2},
pages = {e0171392},
pmid = {28152034},
issn = {1932-6203},
mesh = {Animals ; Bass/*parasitology ; Cestode Infections/diagnosis/*veterinary ; Female ; Fish Diseases/diagnosis/*parasitology ; Male ; Mediterranean Sea ; Platyhelminths/anatomy &amp; histology/*classification ; },
abstract = {Diplectanid monogeneans are gill parasites that can infect fish in huge numbers and thus become harmful, especially in maricultured fish. It is therefore useful to have taxonomic tools, such as keys, to identify species. The following diplectanid species from groupers of the Mediterranean Sea were studied: five species of Pseudorhabdosynochus Yamaguti, 1958, including P. riouxi (Oliver, 1986) Kritsky &amp; Beverley-Burton, 1986 from the dusky grouper Mycteroperca marginata, P. enitsuji Neifar &amp; Euzet, 2007, P. bouaini Neifar &amp; Euzet, 2007, P. dolicocolpos Neifar &amp; Euzet, 2007 and P. sinediscus Neifar &amp; Euzet, 2007 from the goldblotch grouper M. costae, and Echinoplectanum echinophallus (Euzet &amp; Oliver, 1965) Justine &amp; Euzet, 2006 from the dusky grouper. New material was obtained from fish collected from off Tunisia and Libya and compared to the type-material and voucher specimens in museum collections. Identifications of fish were confirmed by barcoding of cytochrome c oxidase subunit I (COI) sequences. The sclerotized vagina was considered the most important structure for systematics. The three species P. riouxi, P. bouaini, and P. enitsuji share a common general structure of the sclerotized vagina with a conspicuous spherical secondary chamber. We thus propose the 'Pseudorhabdosynochus riouxi group' to accommodate them. Pseudorhabdosynochus dolicocolpos has an elongate vaginal structure that is completely different from all its congeneric species reported from the Mediterranean Sea, and Pseudorhabdosynochus sinediscus has a sclerotized vagina in which the secondary chamber is not visible, and a haptor without squamodiscs. A taxonomic key to diplectanid species on Mycteroperca spp. in the Mediterranean Sea is proposed; it includes ten species of Pseudorhabdosynochus and one species of Echinoplectanum.},
}
@article {pmid28151699,
year = {2017},
author = {de Sousa, TP and Marques, DK and Vitorino, CA and Faria, KC and Braga, GD and Ferreira, DC and Venere, PC},
title = {Cytogenetic and Molecular Data Support the Occurrence of Three Gymnotus Species (Gymnotiformes: Gymnotidae) Used as Live Bait in Corumbá, Brazil: Implications for Conservation and Management of Professional Fishing.},
journal = {Zebrafish},
volume = {14},
number = {2},
pages = {177-186},
doi = {10.1089/zeb.2016.1356},
pmid = {28151699},
issn = {1557-8542},
mesh = {Animals ; Brazil ; *Conservation of Natural Resources ; *Fisheries ; Genetic Variation ; Gymnotiformes/*genetics ; Karyotype ; Species Specificity ; },
abstract = {In the Pantanal of Mato Grosso do Sul, electric fish (Gymnotus spp.) are the primary source of live bait, accounting for more than three-quarters of total sales. Based on chromosomal and molecular markers, the present study attempted to identify the Gymnotus species used as bait in the region of Corumbá, Mato Grosso do Sul, Brazil. Three species were detected, based on their distinct karyotypes: G. paraguensis (2n = 54), G. sylvius (2n = 40), and G. pantanal (2n = 39-40, X1X2Y/X1X1X2X2), with no evidence being found of interspecific hybrids. All three species presented a single nucleolar organizer regions (NOR) (heterochromatin CMA3[+]/DAPI[-]) and pericentromeric heterochromatin in almost all chromosomes, with a few distal and/or interstitial blocks. G. sylvius and G. pantanal had one and two pairs of chromosomes with 5S rDNA sites, respectively, while G. paraguensis had 17 chromosome pairs with these markers. The three species formed well-defined clusters in the DNA barcoding analysis. The integrated analysis of the cytogenetic and DNA barcoding data confirmed that the diversity of Gymnotus species exploited as live bait in the study region has been underestimated. These findings indicate that the markers analyzed represent valuable tools for the conservation and fishery management of the Gymnotus stocks exploited.},
}
@article {pmid28150727,
year = {2017},
author = {Yang, Q and Franco, CM and Sorokin, SJ and Zhang, W},
title = {Development of a multilocus-based approach for sponge (phylum Porifera) identification: refinement and limitations.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {41422},
pmid = {28150727},
issn = {2045-2322},
mesh = {Animals ; Base Sequence ; DNA Barcoding, Taxonomic/*methods ; Databases, Genetic ; *Genetic Loci ; Genetic Markers ; *Phylogeny ; Porifera/*classification/*genetics ; Reproducibility of Results ; Species Specificity ; },
abstract = {For sponges (phylum Porifera), there is no reliable molecular protocol available for species identification. To address this gap, we developed a multilocus-based Sponge Identification Protocol (SIP) validated by a sample of 37 sponge species belonging to 10 orders from South Australia. The universal barcode COI mtDNA, 28S rRNA gene (D3-D5), and the nuclear ITS1-5.8S-ITS2 region were evaluated for their suitability and capacity for sponge identification. The highest Bit Score was applied to infer the identity. The reliability of SIP was validated by phylogenetic analysis. The 28S rRNA gene and COI mtDNA performed better than the ITS region in classifying sponges at various taxonomic levels. A major limitation is that the databases are not well populated and possess low diversity, making it difficult to conduct the molecular identification protocol. The identification is also impacted by the accuracy of the morphological classification of the sponges whose sequences have been submitted to the database. Re-examination of the morphological identification further demonstrated and improved the reliability of sponge identification by SIP. Integrated with morphological identification, the multilocus-based SIP offers an improved protocol for more reliable and effective sponge identification, by coupling the accuracy of different DNA markers.},
}
@article {pmid28148503,
year = {2017},
author = {Ni Mhurchu, C and Volkova, E and Jiang, Y and Eyles, H and Michie, J and Neal, B and Blakely, T and Swinburn, B and Rayner, M},
title = {Effects of interpretive nutrition labels on consumer food purchases: the Starlight randomized controlled trial.},
journal = {The American journal of clinical nutrition},
volume = {105},
number = {3},
pages = {695-704},
doi = {10.3945/ajcn.116.144956},
pmid = {28148503},
issn = {1938-3207},
mesh = {Adult ; *Commerce ; Comprehension ; *Consumer Behavior ; Family Characteristics ; Female ; Food Labeling/*methods ; Food Packaging ; *Food Preferences ; *Health Behavior ; Health Promotion/*methods ; Humans ; Male ; Mobile Applications ; New Zealand ; Smartphone ; Young Adult ; },
abstract = {Background: Nutrition labeling is a prominent policy to promote healthy eating.Objective: We aimed to evaluate the effects of 2 interpretive nutrition labels compared with a noninterpretive label on consumer food purchases.Design: In this parallel-group randomized controlled trial, we enrolled household shoppers across New Zealand who owned smartphones and were aged ≥18 y. Eligible participants were randomly assigned (1:1:1) to receive either traffic light labels (TLLs), Health Star Rating labels (HSRs), or a control [nutrition information panel (NIP)]. Smartphone technology allowed participants to scan barcodes of packaged foods and to receive allocated labels on their smartphone screens. The primary outcome was the mean healthiness of all packaged food purchases over the 4-wk intervention period, which was measured by using the Food Standards Australia New Zealand Nutrient Profiling Scoring Criterion (NPSC).Results: Between October 2014 and November 2015, 1357 eligible shoppers were randomly assigned to TLL (n = 459), HSR (n = 443), or NIP (n = 455) labels. Overall difference in the mean transformed NPSC score for the TLL group compared with the NIP group was -0.20 (95% CI: -0.94, 0.54; P = 0.60). The corresponding difference for HSR compared with NIP was -0.60 (95% CI: -1.35, 0.15; P = 0.12). In an exploratory per-protocol analysis of participants who used the labeling intervention more often than average (n = 423, 31%), those who were assigned to TLL and HSR had significantly better NPSC scores [TLL compared with NIP: -1.33 (95% CI: -2.63, -0.04; P = 0.04); HSR compared with NIP: -1.70 (95% CI: -2.97, -0.43; P = 0.01)]. Shoppers who were randomly assigned to HSR and TLL also found the labels significantly more useful and easy to understand than the NIP (all P values <0.001).Conclusions: At the relatively low level of use observed in this trial, interpretive nutrition labels had no significant effect on food purchases. However, shoppers who used interpretive labels found them to be significantly more useful and easy to understand, and compared with frequent NIP users, frequent TLL and HSR users had significantly healthier food purchases. This trial was registered at the Australian New Zealand Clinical Trials Registry (https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=366446&amp;isReview=true) as ACTRN12614000644662.},
}
@article {pmid28145743,
year = {2017},
author = {Hollatz, C and Leite, BR and Lobo, J and Froufe, H and Egas, C and Costa, FO},
title = {Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities.},
journal = {Genome},
volume = {60},
number = {3},
pages = {260-271},
doi = {10.1139/gen-2015-0220},
pmid = {28145743},
issn = {1480-3321},
mesh = {Animals ; Annelida/genetics ; Arthropods/genetics ; *Biodiversity ; Biomass ; Chordata/genetics ; Cnidaria/genetics ; Computer Simulation ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/*genetics ; Echinodermata/genetics ; Ecosystem ; Electron Transport Complex IV/genetics ; Gene Library ; High-Throughput Nucleotide Sequencing ; Mollusca/genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {In marine and estuarine benthic communities, the inventory and estimation of species richness are often hampered by the need for broad taxonomic expertise across several phyla. The use of DNA metabarcoding has emerged as a powerful tool for the fast assessment of species composition in a diversity of ecological communities. Here, we tested the amplification success of five primer sets targeting different COI-5P regions by 454 pyrosequencing to maximize the recovery of two simulated macrobenthic communities containing 21 species (SimCom1 and SimCom 2). Species identification was first performed against a compiled reference library of macrobenthic species. Reads with similarity results to reference sequences between 70% and 97% were then submitted to GenBank and BOLD to attempt the identification of concealed species in the bulk sample. The combination of at least three primer sets was able to recover more species than any primer set alone, achieving 85% of represented species in SimCom1 and 76% in SimCom2. Our approach was successful to detect low-frequency specimens, as well as concealed species, in the bulk sample, indicating the potential for the application of this approach on marine bioassessment and inventory, including the detection of "hidden" biodiversity that would hardly be possible based on morphology only.},
}
@article {pmid28143579,
year = {2017},
author = {Li, X and Jiang, W},
title = {Method for generating multiple risky barcodes of complex diseases using ant colony algorithm.},
journal = {Theoretical biology &amp; medical modelling},
volume = {14},
number = {1},
pages = {4},
pmid = {28143579},
issn = {1742-4682},
mesh = {*Algorithms ; Animals ; Ants ; Breast Neoplasms/diagnosis/*genetics ; DNA Barcoding, Taxonomic/*methods ; Female ; Humans ; *Models, Genetic ; Polymorphism, Single Nucleotide/*genetics ; Risk Factors ; },
abstract = {BACKGROUND: Susceptible barcode recognition plays an important role in the diagnosis and treatment of complex diseases. Numerous approaches have been proposed to identify risky barcodes involved in the progress of complex diseases. However, some methods only consider differences in barcode frequencies between the control and disease groups; as such, these methods may be partial or even wrong. For example, some barcodes with a high risk ratio yield a low frequency on cases or exhibit a high frequency on controls, which may unreasonable from a statistical point.<br><br>RESULTS: In our study, a stricter criteria, maximum discrepancy and maximum constituency, is designed to evaluate each barcode and ant colony algorithm is used to search combination space of epistasis. For complex diseases with multi-subtypes, our method can list several potential barcodes contributing to different subtypes of complex diseases. Another contribution of this work is to introduce a method for determining the length of barcodes and excluding noisy barcodes whose frequencies are abnormal. In addition, common pathogenic genes shared by different risky barcodes are also recognized, which may provide key clue for further study, such as gene function analysis.<br><br>CONCLUSIONS: Experimental results reveal that our method can find multiple risky barcodes whose risk ratio and odds ratio are >1. These barcodes could be related to different subtypes of complex diseases.},
}
@article {pmid28138848,
year = {2017},
author = {McElwain, MA and Zhang, RY and Drmanac, R and Peters, BA},
title = {Long Fragment Read (LFR) Technology: Cost-Effective, High-Quality Genome-Wide Molecular Haplotyping.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1551},
number = {},
pages = {191-205},
doi = {10.1007/978-1-4939-6750-6_11},
pmid = {28138848},
issn = {1940-6029},
mesh = {Genome, Human/genetics ; Genomics ; Haplotypes/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA ; Whole Genome Sequencing ; },
abstract = {In this chapter, we describe Long Fragment Read (LFR) technology, a DNA preprocessing method for genome-wide haplotyping by whole genome sequencing (WGS). The addition of LFR prior to WGS on any high-throughput DNA sequencer (e.g., Complete Genomics Revolocity™, BGISEQ-500, Illumina HiSeq, etc.) enables the assignment of single-nucleotide polymorphisms (SNPs) and other genomic variants onto contigs representing contiguous DNA from a single parent (haplotypes) with N50 lengths of up to ~1 Mb. Importantly, this is achieved independent of any parental sequencing data or knowledge of parental haplotypes. Further, the nature of this method allows for the correction of most amplification, sequencing, and mapping errors, resulting in false-positive error rates as low as 10[-9]. This method can be employed either manually using hand-held micropipettors or in the preferred, automated manner described below, utilizing liquid-handling robots capable of pipetting in the nanoliter range. Automating the method limits the amount of hands-on time and allows significant reduction in reaction volumes. Further, the cost of LFR, as described in this chapter, is moderate, while it adds invaluable whole genome haplotype data to almost any WGS process.},
}
@article {pmid28138840,
year = {2017},
author = {Zhang, W and Messing, J},
title = {PacBio for Haplotyping in Gene Families.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1551},
number = {},
pages = {61-71},
doi = {10.1007/978-1-4939-6750-6_3},
pmid = {28138840},
issn = {1940-6029},
mesh = {Haplotypes/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Sequence Analysis, DNA ; },
abstract = {The throughput and read length provided by Pacific Bioscience (PacBio) Single Molecule Real Time (SMRT) sequencing platform makes it feasible to construct contiguous, non-chimeric sequences. This is especially useful for genes with repetitive sequences in their gene bodies in gene families. We illustrate the use of PacBio to sequence and assemble hundreds of transcripts of gluten gene families from different cultivars of wheat using sequence from a single SMRT cell. To this end, we barcoded amplicons from different cultivars, then pooled these into one library for sequencing. Sequencing reads were later separated by the barcodes and further sorted into different gene groups by blast. The reads from each gene are then assembled by SeqmanNGen software. Given the length of 1 kb for each sequence derived from an initial molecule, the phase of the polymorphisms is not lost and can be used to infer also haplotype differences between different cultivars.},
}
@article {pmid28138277,
year = {2016},
author = {Estupiñán, RA and Ferrari, SF and Gonçalves, EC and Barbosa, MS and Vallinoto, M and Schneider, MP},
title = {Evaluating the diversity of Neotropical anurans using DNA barcodes.},
journal = {ZooKeys},
volume = {},
number = {637},
pages = {89-106},
pmid = {28138277},
issn = {1313-2989},
abstract = {This study tested the effectiveness of COI barcodes for the discrimination of anuran species from the Amazon basin and other Neotropical regions. Barcodes were determined for a total of 59 species, with a further 58 species being included from GenBank. In most cases, distinguishing species using the barcodes was straightforward. Each species had a distinct COI barcode or codes, with intraspecific distances ranging from 0% to 9.9%. However, relatively high intraspecific divergence (11.4-19.4%) was observed in some species, such as Ranitomeya ventrimaculata, Craugastor fitzingeri, Hypsiboas leptolineatus, Scinax fuscomarginatus and Leptodactylus knudseni, which may reflect errors of identification or the presence of a species complex. Intraspecific distances recorded in species for which samples were obtained from GenBank (Engystomops pustulosus, Atelopus varius, Craugastor podiciferus, and Dendropsophus labialis) were greater than those between many pairs of species. Interspecific distances ranged between 11-39%. Overall, the clear differences observed between most intra- and inter-specific distances indicate that the COI barcode is an effective tool for the identification of Neotropical species in most of the cases analyzed in the present study.},
}
@article {pmid28127700,
year = {2017},
author = {Ahmed, I and Huebner, H and Mamoori, YI and Buchholz, R},
title = {Identification of newly established Spodoptera littoralis cell lines by two DNA barcoding markers.},
journal = {In vitro cellular &amp; developmental biology. Animal},
volume = {53},
number = {4},
pages = {288-292},
pmid = {28127700},
issn = {1543-706X},
mesh = {Animals ; Base Sequence ; Cell Line/*cytology ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Electrophoresis, Agar Gel ; Genetic Markers ; Phylogeny ; Sequence Alignment ; Spodoptera/*cytology/*genetics ; },
abstract = {Cell line authentication is crucial in determining the identity of cell lines and detecting any cross-contamination. The identity of three newly established Spodoptera littoralis cell lines (Spli-C, Spli-B, and Spli-S) was confirmed by DNA fingerprinting. In this study, we used two universal primers sets to amplify two DNA fragments in different positions in the mitochondrial cytochrome C oxidase 1 gene (COI). The PCR reaction succeeded in amplifying two target DNA amplicons. The first amplicon had ~650 bp, while the second had ~410 bp. By comparing the obtained informative sequences with those in the GenBank sequence database, the results showed 100% similarity between the S. littoralis cell lines and their host. The same similarity ratio was observed between the Sf21, Tni, and Cp cell lines, which are used widely, and their hosts. The informative sequences were then used for phylogenetic analyses. In addition to the high efficiency of this technique, it showed high reproducibility in two different laboratories. DNA barcoding using the two sets of the universal primers used in this study can be a fast and a reliable method for insect cell line identification.},
}
@article {pmid28126462,
year = {2017},
author = {Vadivalagan, C and Karthika, P and Murugan, K and Panneerselvam, C and Del Serrone, P and Benelli, G},
title = {Exploring genetic variation in haplotypes of the filariasis vector Culex quinquefasciatus (Diptera: Culicidae) through DNA barcoding.},
journal = {Acta tropica},
volume = {169},
number = {},
pages = {43-50},
doi = {10.1016/j.actatropica.2017.01.020},
pmid = {28126462},
issn = {1873-6254},
mesh = {Animals ; Culex/*genetics ; DNA Barcoding, Taxonomic/*methods ; Filariasis/*epidemiology/genetics ; *Genetic Variation ; Haplotypes/*genetics ; Humans ; India ; Insect Vectors/*genetics ; RNA, Ribosomal, 16S/genetics ; Rift Valley Fever/*epidemiology/genetics ; Rift Valley fever virus/genetics/*pathogenicity ; },
abstract = {Culex quinquefasciatus (Diptera: Culicidae) is a vector of many pathogens and parasites of humans, as well as domestic and wild animals. In urban and semi-urban Asian countries, Cx. quinquefasciatus is a main vector of nematodes causing lymphatic filariasis. In the African region, it vectors the Rift Valley fever virus, while in the USA it transmits West Nile, St. Louis encephalitis and Western equine encephalitis virus. In this study, DNA barcoding was used to explore the genetic variation of Cx. quinquefasciatus populations from 88 geographical regions. We presented a comprehensive approach analyzing the effectiveness of two gene markers, i.e. CO1 and 16S rRNA. The high threshold genetic divergence of CO1 (0.47%) gene was reported as an ideal marker for molecular identification of this mosquito vector. Furthermore, null substitutions were lower in CO1 if compared to 16S rRNA, which influenced its differentiating potential among Indian haplotypes. NJ tree was well supported with high branch values for CO1 gene than 16S rRNA, indicating ideal genetic differentiation among haplotypes. TCS haplotype network revealed 14 distinct clusters. The intra- and inter-population polymorphism were calculated among the global and Indian Cx. quinquefasciatus lineages. The genetic diversity index Tajima' D showed negative values for all the 4 intra-population clusters (G2-4, G10). Fu's FS showed negative value for G10 cluster, which was significant and indicated recent population expansion. However, the G2-G4 (i.e. Indian lineages) had positive values, suggesting a bottleneck effect. Overall, our research firstly shed light on the genetic differences among the haplotypes of Cx. quinquefasciatus species complex, adding basic knowledge to the molecular ecology of this important mosquito vector.},
}
@article {pmid28124752,
year = {2017},
author = {Nassar, AF and Wisnewski, AV and Raddassi, K},
title = {Automation of sample preparation for mass cytometry barcoding in support of clinical research: protocol optimization.},
journal = {Analytical and bioanalytical chemistry},
volume = {409},
number = {9},
pages = {2363-2372},
pmid = {28124752},
issn = {1618-2650},
support = {R01 OH010941/OH/NIOSH CDC HHS/United States ; },
mesh = {Antibodies/analysis ; *Automation ; Flow Cytometry/*methods ; Humans ; Single-Cell Analysis/*methods ; *Specimen Handling ; },
abstract = {Analysis of multiplexed assays is highly important for clinical diagnostics and other analytical applications. Mass cytometry enables multi-dimensional, single-cell analysis of cell type and state. In mass cytometry, the rare earth metals used as reporters on antibodies allow determination of marker expression in individual cells. Barcode-based bioassays for CyTOF are able to encode and decode for different experimental conditions or samples within the same experiment, facilitating progress in producing straightforward and consistent results. Herein, an integrated protocol for automated sample preparation for barcoding used in conjunction with mass cytometry for clinical bioanalysis samples is described; we offer results of our work with barcoding protocol optimization. In addition, we present some points to be considered in order to minimize the variability of quantitative mass cytometry measurements. For example, we discuss the importance of having multiple populations during titration of the antibodies and effect of storage and shipping of labelled samples on the stability of staining for purposes of CyTOF analysis. Data quality is not affected when labelled samples are stored either frozen or at 4 °C and used within 10 days; we observed that cell loss is greater if cells are washed with deionized water prior to shipment or are shipped in lower concentration. Once the labelled samples for CyTOF are suspended in deionized water, the analysis should be performed expeditiously, preferably within the first hour. Damage can be minimized if the cells are resuspended in phosphate-buffered saline (PBS) rather than deionized water while waiting for data acquisition.},
}
@article {pmid28123689,
year = {2016},
author = {Pazhenkova, EA and Lukhtanov, VA},
title = {Chromosomal and mitochondrial diversity in Melitaea didyma complex (Lepidoptera, Nymphalidae): eleven deeply diverged DNA barcode groups in one non-monophyletic species?.},
journal = {Comparative cytogenetics},
volume = {10},
number = {4},
pages = {697-717},
pmid = {28123689},
issn = {1993-0771},
abstract = {It is generally accepted that cases of species' polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, and the detected cases reflect misidentifications or/and methodological errors. Here we studied the problem of species' non-monophyly through chromosomal and molecular analysis of butterfly taxa close to Melitaea didyma (Esper, 1779) (Lepidoptera, Nymphalidae). We found absence or low interspecific chromosome number variation and presence of intraspecific variation, therefore we conclude that in this group, chromosome numbers have relatively low value as taxonomic markers. Despite low karyotype variability, the group was found to have unexpectedly high mitochondrial haplotype diversity. These haplotypes were clustered in 23 highly diverged haplogroups. Twelve of these haplogroups are associated with nine traditionally recognized and morphologically distinct species Melitaea chitralensis Moore, 1901, Melitaea deserticola Oberthür, 1909, Melitaea didymoides Eversmann, 1847, Melitaea gina Higgins, 1941, Melitaea interrupta Colenati, 1846, Melitaea latonigena Eversmann, 1847, Melitaea mixta Evans, 1912, Melitaea saxatilis Christoph, 1873 and Melitaea sutschana Staudinger, 1892. The rest of the haplogroups (11 lineages) belong to a well-known west-palaearctic species Melitaea didyma. The last species is particularly unusual in the haplotypes we obtained. First, it is clearly polyphyletic with respect to COI gene. Second, the differentiation in COI gene between these mostly allopatric (but in few cases sympatric) eleven lineages is extremely high (up to 7.4%), i.e. much deeper than the "standard" DNA barcode species threshold (2.7-3%). This level of divergence normally could correspond not even to different species, but to different genera. Despite this divergence, the bearers of these haplogroups were found to be morphologically indistinguishable and, most importantly, to share absolutely the same ecological niches, i.e. demonstrating the pattern which is hardly compatible with hypothesis of multiple cryptic species. Most likely such a profound irregularity in barcodes is caused by reasons other than speciation and represents an extraordinary example of intra-species barcode variability. Given the deep level of genetic differentiation between the lineages, we assume that there was a long period (up to 5.0 My) of allopatric differentiation when the lineages were separated by geographic or/and ecological barriers and evolved in late Pliocene and Pleistocene refugia of north Africa, the Iberian and Balkan Peninsulas, the Middle East and Central Asia. We discuss the refugia-within-refugia concept as a mechanism explaining the presence of additional diverged minor haplogroups within the areas of the major haplogroups. We also provide the first record of Melitaea gina in Azerbaijan and the record of Melitaea didyma turkestanica as a new taxon for Russia and Europe.},
}
@article {pmid28123687,
year = {2016},
author = {Lukhtanov, VA and Pazhenkova, EA and Novikova, AV},
title = {Mitochondrial chromosome as a marker of animal migratory routes: DNA barcoding revealed Asian (non-African) origin of a tropical migrant butterfly Junonia orithya in south Israel.},
journal = {Comparative cytogenetics},
volume = {10},
number = {4},
pages = {671-677},
pmid = {28123687},
issn = {1993-0771},
abstract = {The blue pansy Junonia orithya Linnaeus, 1758 (Lepidoptera, Nymphalidae) is widely distributed along the tropical areas of Africa, Asia and Australia. It is also known as a migrant species in the Levant. Here we record Junonia orithya in south Israel and provide a DNA-barcode-based evidence for its Asian (non-African) origin.},
}
@article {pmid28120184,
year = {2017},
author = {Fattahi, S and Pilehchian Langroudi, M and Samadani, AA and Nikbakhsh, N and Asouri, M and Akhavan-Niaki, H},
title = {Application of unique sequence index (USI) barcode to gene expression profiling in gastric adenocarcinoma.},
journal = {Journal of cell communication and signaling},
volume = {11},
number = {1},
pages = {97-104},
pmid = {28120184},
issn = {1873-9601},
abstract = {Accurate expression profiling is imperative for understanding the biological roles of mRNAs. Real-time PCR have been at the forefront of biological innovation in detection and monitoring of gene expression, however, fluorophore-labeled oligonucleotides and double-stranded DNA binding dyes, the two most frequently used dyes in RNA detection, are not very cost effective and have poor specificity, respectively. We have developed a cost effective and specific approach for mRNA expression profiling via added unique sequence index (USI) to cDNAs before amplification. USI is a barcode which enable the detection of each target RNA. Using this method, caudal type homeobox 1 (CDX1) and FAT atypical cadherin 4 (FAT4) expressions were investigated in tumoral and non-tumoral tissues of gastric cancer patients and compared with commercial ABI kit. Both methods indicated that FAT4 and CDX1 expression were significantly reduced in gastric cancer tissues compared with adjacent noncancerous tissues. Moreover, we have shown that this assay is highly sensitive, linear and reproducible. USI barcode not only provides a powerful tool for mRNA detection due to its sensitivity, specificity and cost-effectiveness, but also allows comfortable design for real-time qPCR assays within the least time and empowers the analysis of many transcripts of virtually any organism. Furthermore, USI barcode is highly affordable for large numbers of different samples or small sample sizes without microarray and expensive commercial platforms.},
}
@article {pmid28118403,
year = {2017},
author = {Kus, A and Kwasniewska, J and Hasterok, R},
title = {Brachypodium distachyon - A Useful Model in the Qualification of Mutagen-Induced Micronuclei Using Multicolor FISH.},
journal = {PloS one},
volume = {12},
number = {1},
pages = {e0170618},
pmid = {28118403},
issn = {1932-6203},
mesh = {Brachypodium/drug effects/*genetics ; Centromere/drug effects/ultrastructure ; Chromosome Painting/*methods ; Chromosomes, Artificial, Bacterial/drug effects ; Chromosomes, Plant/*drug effects/ultrastructure ; DNA Probes ; DNA, Ribosomal/genetics ; Genome, Plant ; Germination ; Interphase ; Maleic Hydrazide/*pharmacology ; Micronuclei, Chromosome-Defective/*chemically induced ; Micronucleus Tests/*methods ; Mitosis ; *Mutagenesis ; Mutagens/*pharmacology ; Plant Roots ; RNA, Plant/biosynthesis/genetics ; Seeds/drug effects ; Telomere/drug effects/ultrastructure ; },
abstract = {Brachypodium distachyon (Brachypodium) is now intensively utilized as a model grass species in various biological studies. Its favorable cytological features create a unique foundation for a convenient system in mutagenesis, thereby potentially enabling the 'hot spots' and 'cold spots' of DNA damage in its genome to be analyzed. The aim of this study was to analyze the involvement of 5S rDNA, 25S rDNA, the Arabidopsis-type (TTTAGGG)n telomeric sequence and the Brachypodium-originated centromeric BAC clone CB33J12 in the micronuclei formation in Brachypodium root tip cells that were subjected to the chemical clastogenic agent maleic hydrazide (MH). To the best of our knowledge, this is the first use of a multicolor fluorescence in situ hybridization (mFISH) with four different DNA probes being used simultaneously to study plant mutagenesis. A quantitative analysis allowed ten types of micronuclei, which were characterized by the presence or absence of specific FISH signal(s), to be distinguished, thus enabling some specific rules governing the composition of the MH-induced micronuclei with the majority of them originating from the terminal regions of chromosomes, to be identified. The application of rDNA sequences as probes showed that 5S rDNA-bearing chromosomes are involved in micronuclei formation more frequently than the 25S rDNA-bearing chromosomes. These findings demonstrate the promising potential of Brachypodium to be a useful model organism to analyze the effects of various genotoxic agents on the plant nuclear genome stability, especially when the complex FISH-based and chromosome-specific approaches such as chromosome barcoding and chromosome painting will be applied in future studies.},
}
@article {pmid28118315,
year = {2017},
author = {Guillonneau, C and David, L and Anegon, I},
title = {Improved Analyses of CD8+ T Cell Specificities Using Multimers of Peptide MHC Complexes Coupled to DNA Barcodes.},
journal = {Transplantation},
volume = {101},
number = {2},
pages = {219-221},
doi = {10.1097/TP.0000000000001601},
pmid = {28118315},
issn = {1534-6080},
mesh = {CD8-Positive T-Lymphocytes/immunology ; *DNA Barcoding, Taxonomic ; HLA-A2 Antigen/*genetics ; Histocompatibility Antigens Class I/chemistry ; Humans ; Peptides/genetics ; },
}
@article {pmid28117350,
year = {2017},
author = {Levitt, B and Obala, A and Langdon, S and Corcoran, D and O'Meara, WP and Taylor, SM},
title = {Overlap Extension Barcoding for the Next Generation Sequencing and Genotyping of Plasmodium falciparum in Individual Patients in Western Kenya.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {41108},
pmid = {28117350},
issn = {2045-2322},
support = {K08 AI100924/AI/NIAID NIH HHS/United States ; UL1 TR001117/TR/NCATS NIH HHS/United States ; },
mesh = {*DNA Barcoding, Taxonomic ; Genotyping Techniques ; High-Throughput Nucleotide Sequencing ; Humans ; Malaria, Falciparum/*genetics ; Plasmodium falciparum/*genetics ; *Polymorphism, Genetic ; },
abstract = {Large-scale molecular epidemiologic studies of Plasmodium falciparum parasites have provided insights into parasite biology and transmission, can identify the spread of drug resistance, and are useful in assessing vaccine targets. The polyclonal nature infections in high transmission settings is problematic for traditional genotyping approaches. Next-generation sequencing (NGS) approaches to parasite genotyping allow sensitive detection of minority variants, disaggregation of complex parasite mixtures, and scalable processing of large samples sets. Therefore, we designed, validated, and applied to field parasites an approach that leverages sequencing of individually barcoded samples in a multiplex manner. We utilize variant barcodes, invariant linker sequences and modular template-specific primers to allow for the simultaneous generation of high-dimensional sequencing data of multiple gene targets. This modularity permits a cost-effective and reproducible way to query many genes at once. In mixtures of reference parasite genomes, we quantitatively detected unique haplotypes comprising as little as 2% of a polyclonal infection. We applied this genotyping approach to field-collected parasites collected in Western Kenya in order to simultaneously obtain parasites genotypes at three unlinked loci. In summary, we present a rapid, scalable, and flexible method for genotyping individual parasites that enables molecular epidemiologic studies of parasite evolution, population structure and transmission.},
}
@article {pmid28116647,
year = {2017},
author = {Marín, MA and Cadavid, IC and Valdés, L and Álvarez, CF and Uribe, SI and Vila, R and Pyrcz, TW},
title = {DNA Barcoding of an Assembly of Montane Andean Butterflies (Satyrinae): Geographical Scale and Identification Performance.},
journal = {Neotropical entomology},
volume = {46},
number = {5},
pages = {514-523},
pmid = {28116647},
issn = {1678-8052},
support = {2014/16481-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 528/2011//Departamento Administrativo de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; BIOCON08_021//Fundaci&#xf3;n BBVA/ ; FCAA-07 2010//Corporaci&#xf3;n Universitaria Lasallista/ ; },
mesh = {Animals ; Butterflies/*classification ; Colombia ; *DNA Barcoding, Taxonomic ; Genetic Variation ; Genetics, Population ; Geography ; *Phylogeny ; },
abstract = {DNA barcoding is a technique used primarily for the documentation and identification of biological diversity based on mitochondrial DNA sequences. Butterflies have received particular attention in DNA barcoding studies, although varied performance may be obtained due to different scales of geographic sampling and speciation processes in various groups. The montane Andean Satyrinae constitutes a challenging study group for taxonomy. The group displays high richness, with more of 550 species, and remarkable morphological similarity among taxa, which renders their identification difficult. In the present study, we evaluated the effectiveness of DNA barcodes in the identification of montane Andean satyrines and the effect of increased geographical scale of sampling on identification performance. Mitochondrial sequences were obtained from 104 specimens of 39 species and 16 genera, collected in a forest remnant in the northwest Andes. DNA barcoding has proved to be a useful tool for the identification of the specimens, with a well-defined gap and producing clusters with unambiguous identifications for all the morphospecies in the study area. The expansion of the geographical scale with published data increased genetic distances within species and reduced those among species, but did not generally reduce the success of specimen identification. Only in Forsterinaria rustica (Butler, 1868), a taxon with high intraspecific variation, the barcode gap was lost and low support for monophyly was obtained. Likewise, expanded sampling resulted in a substantial increase in the intraspecific distance in Morpho sulkowskyi (Kollar, 1850); Panyapedaliodes drymaea (Hewitson, 1858); Lymanopoda obsoleta (Westwood, 1851); and Lymanopoda labda Hewitson, 1861; but for these species, the barcode gap was maintained. These divergent lineages are nonetheless worth a detailed study of external and genitalic morphology variation, as well as ecological features, in order to determine the potential existence of cryptic species. Even including these cases, DNA barcoding performance in specimen identification was 100% successful based on monophyly, an unexpected result in such a taxonomically complicated group.},
}
@article {pmid28114306,
year = {2017},
author = {Gandolfi, A and Crestanello, B and Fagotti, A and Simoncelli, F and Chiesa, S and Girardi, M and Giovagnoli, E and Marangoni, C and Di Rosa, I and Lucentini, L},
title = {New Evidences of Mitochondrial DNA Heteroplasmy by Putative Paternal Leakage between the Rock Partridge (Alectoris graeca) and the Chukar Partridge (Alectoris chukar).},
journal = {PloS one},
volume = {12},
number = {1},
pages = {e0170507},
pmid = {28114306},
issn = {1932-6203},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; Galliformes/*genetics ; Hybridization, Genetic ; Phylogeny ; Species Specificity ; },
abstract = {The rock partridge, Alectoris graeca, is a polytypic species declining in Italy mostly due to anthropogenic causes, including the massive releases of the closely related allochthonous chukar partridge Alectoris chukar which produced the formation of hybrids. Molecular approaches are fundamental for the identification of evolutionary units in the perspective of conservation and management, and to correctly select individuals to be used in restocking campaigns. We analyzed a Cytochrome oxidase I (COI) fragment of contemporary and historical A. graeca and A. chukar samples, using duplicated analyses to confirm results and nuclear DNA microsatellites to exclude possible sample cross-contamination. In two contemporary specimens of A. graeca, collected from an anthropogenic hybrid zone, we found evidence of the presence of mtDNA heteroplasmy possibly associated to paternal leakage and suggesting hybridization with captive-bred exotic A. chukar. These results underline significant limitations in the reliability of mtDNA barcoding-based species identification and could have relevant evolutionary and ecological implications that should be accounted for when interpreting data aimed to support conservation actions.},
}
@article {pmid28112435,
year = {2017},
author = {Tonti-Filippini, J and Nevill, PG and Dixon, K and Small, I},
title = {What can we do with 1000 plastid genomes?.},
journal = {The Plant journal : for cell and molecular biology},
volume = {90},
number = {4},
pages = {808-818},
doi = {10.1111/tpj.13491},
pmid = {28112435},
issn = {1365-313X},
mesh = {Chloroplasts/genetics ; DNA, Plant/genetics ; Genome, Plant/genetics ; Genome, Plastid/*genetics ; Genomics/*methods ; Phylogeny ; },
abstract = {The plastid genome of plants is the smallest and most gene-rich of the three genomes in each cell and the one generally present in the highest copy number. As a result, obtaining plastid DNA sequence is a particularly cost-effective way of discovering genetic information about a plant. Until recently, the sequence information gathered in this way was generally limited to small portions of the genome amplified by polymerase chain reaction, but recent advances in sequencing technology have stimulated a substantial rate of increase in the sequencing of complete plastid genomes. Within the last year, the number of complete plastid genomes accessible in public sequence repositories has exceeded 1000. This sudden flood of data raises numerous challenges in data analysis and interpretation, but also offers the keys to potential insights across large swathes of plant biology. We examine what has been learnt so far, what more could be learnt if we look at the data in the right way, and what we might gain from the tens of thousands more genome sequences that will surely arrive in the next few years. The most exciting new discoveries are likely to be made at the interdisciplinary interfaces between molecular biology and ecology.},
}
@article {pmid28105307,
year = {2016},
author = {Ankenbrand, MJ and Terhoeven, N and Hohlfeld, S and Förster, F and Keller, A},
title = {biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format.},
journal = {F1000Research},
volume = {5},
number = {},
pages = {2348},
pmid = {28105307},
issn = {2046-1402},
abstract = {The Biological Observation Matrix (BIOM) format is widely used to store data from high-throughput studies. It aims at increasing interoperability of bioinformatic tools that process this data. However, due to multiple versions and implementation details, working with this format can be tricky. Currently, libraries in Python, R and Perl are available, whilst such for JavaScript are lacking. Here, we present a BioJS component for parsing BIOM data in all format versions. It supports import, modification, and export via a unified interface. This module aims to facilitate the development of web applications that use BIOM data. Finally, we demonstrate its usefulness by two applications that already use this component. Availability: https://github.com/molbiodiv/biojs-io-biom, https://dx.doi.org/10.5281/zenodo.218277.},
}
@article {pmid28110431,
year = {2017},
author = {Bishoyi, AK and Kavane, A and Sharma, A and Geetha, KA},
title = {A report on identification of sequence polymorphism in barcode region of six commercially important Cymbopogon species.},
journal = {Molecular biology reports},
volume = {44},
number = {1},
pages = {19-24},
pmid = {28110431},
issn = {1573-4978},
mesh = {Base Sequence ; Cymbopogon/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Phylogeny ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/methods ; Species Specificity ; },
abstract = {CYMBOPOGON: is an important member of grass family Poaceae, cultivated for essential oils which have greater medicinal and industrial value. Taxonomic identification of Cymbopogon species is determined mainly by morphological markers, odour of essential oils and concentration of bioactive compounds present in the oil matrices which are highly influenced by environment. Authenticated molecular marker based taxonomical identification is also lacking in the genus; hence effort was made to evaluate potential DNA barcode loci in six commercially important Cymbopogon species for their individual discrimination and authentication at the species level. Four widely used DNA barcoding regions viz., ITS 1 &amp; ITS 2 spacers, matK, psbA-trnH and rbcL were taken for the study. Gene sequences of the same or related genera of the concerned loci were mined from NCBI domain and primers were designed and validated for barcode loci amplification. Out of the four loci studied, sequences from matK and ITS spacer loci revealed 0.46% and 5.64% nucleotide sequence diversity, respectively whereas the other two loci i.e., psbA-trnH and rbcL showed 100% sequence homology. The newly developed primers can be used for barcode loci amplification in the genus Cymbopogon. The identified Single Nucleotide Polymorphisms from the studied sequences may be used as barcodes for the six Cymbopogon species. The information generated can also be utilized for barcode development of the genus by including more number of Cymbopgon species in future.},
}
@article {pmid28109958,
year = {2017},
author = {Mohme, M and Maire, CL and Riecken, K and Zapf, S and Aranyossy, T and Westphal, M and Lamszus, K and Fehse, B},
title = {Optical Barcoding for Single-Clone Tracking to Study Tumor Heterogeneity.},
journal = {Molecular therapy : the journal of the American Society of Gene Therapy},
volume = {25},
number = {3},
pages = {621-633},
pmid = {28109958},
issn = {1525-0024},
mesh = {Cell Line ; Cell Tracking/*methods ; *Clonal Evolution ; Flow Cytometry ; Fluorescent Dyes ; Gene Order ; Genetic Vectors/genetics ; Humans ; Lentivirus/genetics ; Neoplasms/*pathology ; Reproducibility of Results ; Sensitivity and Specificity ; Staining and Labeling ; },
abstract = {Intratumoral heterogeneity has been identified as one of the strongest drivers of treatment resistance and tumor recurrence. Therefore, investigating the complex clonal architecture of tumors over time has become a major challenge in cancer research. We developed a new fluorescent "optical barcoding" technique that allows fast tracking, identification, and quantification of live cell clones in vitro and in vivo using flow cytometry (FC). We optically barcoded two cell lines derived from malignant glioma, an exemplary heterogeneous brain tumor. In agreement with mathematical combinatorics, we demonstrate that up to 41 clones can unambiguously be marked using six fluorescent proteins and a maximum of three colors per clone. We show that optical barcoding facilitates sensitive, precise, rapid, and inexpensive analysis of clonal composition kinetics of heterogeneous cell populations by FC. We further assessed the quantitative contribution of multiple clones to glioblastoma growth in vivo and we highlight the potential to recover individual viable cell clones by fluorescence-activated cell sorting. In summary, we demonstrate that optical barcoding is a powerful technique for clonal cell tracking in vitro and in vivo, rendering this approach a potent tool for studying the heterogeneity of complex tissues, in particular, cancer.},
}
@article {pmid28108445,
year = {2017},
author = {Kapli, P and Lutteropp, S and Zhang, J and Kobert, K and Pavlidis, P and Stamatakis, A and Flouri, T},
title = {Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo.},
journal = {Bioinformatics (Oxford, England)},
volume = {33},
number = {11},
pages = {1630-1638},
pmid = {28108445},
issn = {1367-4811},
mesh = {*Algorithms ; Animals ; Classification/*methods ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial ; *Markov Chains ; *Monte Carlo Method ; Phylogeny ; },
abstract = {MOTIVATION: In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced "Poisson Tree Processes" (PTP) method is a phylogeny-aware approach that does not rely on such thresholds. Yet, two weaknesses of PTP impact its accuracy and practicality when applied to large datasets; it does not account for divergent intraspecific variation and is slow for a large number of sequences.<br><br>RESULTS: We introduce the multi-rate PTP (mPTP), an improved method that alleviates the theoretical and technical shortcomings of PTP. It incorporates different levels of intraspecific genetic diversity deriving from differences in either the evolutionary history or sampling of each species. Results on empirical data suggest that mPTP is superior to PTP and popular distance-based methods as it, consistently yields more accurate delimitations with respect to the taxonomy (i.e., identifies more taxonomic species, infers species numbers closer to the taxonomy). Moreover, mPTP does not require any similarity threshold as input. The novel dynamic programming algorithm attains a speedup of at least five orders of magnitude compared to PTP, allowing it to delimit species in large (meta-) barcoding data. In addition, Markov Chain Monte Carlo sampling provides a comprehensive evaluation of the inferred delimitation in just a few seconds for millions of steps, independently of tree size.<br><br>mPTP is implemented in C and is available for download at http://github.com/Pas-Kapli/mptp under the GNU Affero 3 license. A web-service is available at http://mptp.h-its.org .<br><br>CONTACT: : paschalia.kapli@h-its.org or alexandros.stamatakis@h-its.org or tomas.flouri@h-its.org.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid28107413,
year = {2017},
author = {Cariani, A and Messinetti, S and Ferrari, A and Arculeo, M and Bonello, JJ and Bonnici, L and Cannas, R and Carbonara, P and Cau, A and Charilaou, C and El Ouamari, N and Fiorentino, F and Follesa, MC and Garofalo, G and Golani, D and Guarniero, I and Hanner, R and Hemida, F and Kada, O and Lo Brutto, S and Mancusi, C and Morey, G and Schembri, PJ and Serena, F and Sion, L and Stagioni, M and Tursi, A and Vrgoc, N and Steinke, D and Tinti, F},
title = {Improving the Conservation of Mediterranean Chondrichthyans: The ELASMOMED DNA Barcode Reference Library.},
journal = {PloS one},
volume = {12},
number = {1},
pages = {e0170244},
pmid = {28107413},
issn = {1932-6203},
mesh = {Animals ; *Conservation of Natural Resources ; *DNA Barcoding, Taxonomic ; Fishes/classification/*genetics ; Mediterranean Region ; Species Specificity ; },
abstract = {Cartilaginous fish are particularly vulnerable to anthropogenic stressors and environmental change because of their K-selected reproductive strategy. Accurate data from scientific surveys and landings are essential to assess conservation status and to develop robust protection and management plans. Currently available data are often incomplete or incorrect as a result of inaccurate species identifications, due to a high level of morphological stasis, especially among closely related taxa. Moreover, several diagnostic characters clearly visible in adult specimens are less evident in juveniles. Here we present results generated by the ELASMOMED Consortium, a regional network aiming to sample and DNA-barcode the Mediterranean Chondrichthyans with the ultimate goal to provide a comprehensive DNA barcode reference library. This library will support and improve the molecular taxonomy of this group and the effectiveness of management and conservation measures. We successfully barcoded 882 individuals belonging to 42 species (17 sharks, 24 batoids and one chimaera), including four endemic and several threatened ones. Morphological misidentifications were found across most orders, further confirming the need for a comprehensive DNA barcoding library as a valuable tool for the reliable identification of specimens in support of taxonomist who are reviewing current identification keys. Despite low intraspecific variation among their barcode sequences and reduced samples size, five species showed preliminary evidence of phylogeographic structure. Overall, the ELASMOMED initiative further emphasizes the key role accurate DNA barcoding libraries play in establishing reliable diagnostic species specific features in otherwise taxonomically problematic groups for biodiversity management and conservation actions.},
}
@article {pmid28106469,
year = {2017},
author = {Sikes, DS and Bowser, M and Morton, JM and Bickford, C and Meierotto, S and Hildebrandt, K},
title = {Building a DNA barcode library of Alaska's non-marine arthropods.},
journal = {Genome},
volume = {60},
number = {3},
pages = {248-259},
doi = {10.1139/gen-2015-0203},
pmid = {28106469},
issn = {1480-3321},
mesh = {Alaska ; Animals ; Arthropods/*genetics ; Biodiversity ; Canada ; DNA/analysis ; DNA Barcoding, Taxonomic/*methods ; Ecology ; Gene Library ; Genetic Variation ; Geography ; Insecta/*genetics ; Models, Genetic ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Temperature ; },
abstract = {Climate change may result in ecological futures with novel species assemblages, trophic mismatch, and mass extinction. Alaska has a limited taxonomic workforce to address these changes. We are building a DNA barcode library to facilitate a metabarcoding approach to monitoring non-marine arthropods. Working with the Canadian Centre for DNA Barcoding, we obtained DNA barcodes from recently collected and authoritatively identified specimens in the University of Alaska Museum (UAM) Insect Collection and the Kenai National Wildlife Refuge collection. We submitted tissues from 4776 specimens, of which 81% yielded DNA barcodes representing 1662 species and 1788 Barcode Index Numbers (BINs), of primarily terrestrial, large-bodied arthropods. This represents 84% of the species available for DNA barcoding in the UAM Insect Collection. There are now 4020 Alaskan arthropod species represented by DNA barcodes, after including all records in Barcode of Life Data Systems (BOLD) of species that occur in Alaska - i.e., 48.5% of the 8277 Alaskan, non-marine-arthropod, named species have associated DNA barcodes. An assessment of the identification power of the library in its current state yielded fewer species-level identifications than expected, but the results were not discouraging. We believe we are the first to deliberately begin development of a DNA barcode library of the entire arthropod fauna for a North American state or province. Although far from complete, this library will become increasingly valuable as more species are added and costs to obtain DNA sequences fall.},
}
@article {pmid28105291,
year = {2016},
author = {Vishnevskaya, MS and Saifitdinova, AF and Lukhtanov, VA},
title = {Karyosystematics and molecular taxonomy of the anomalous blue butterflies (Lepidoptera, Lycaenidae) from the Balkan Peninsula.},
journal = {Comparative cytogenetics},
volume = {10},
number = {5},
pages = {1-85},
pmid = {28105291},
issn = {1993-0771},
abstract = {The Balkan Peninsula represents one of the hottest biodiversity spots in Europe. However, the invertebrate fauna of this region is still insufficiently investigated, even in respect of such well-studied organisms as Lepidoptera. Here we use a combination of chromosomal, molecular and morphological markers to rearrange the group of so-called anomalous blue butterflies (also known as 'brown complex' of the subgenus Agrodiaetus Hübner, [1822] and as the Polyommatus (Agrodiaetus) admetus (Esper, 1783) species group) and to reveal its cryptic taxonomic structure. We demonstrate that Polyommatus aroaniensis (Brown, 1976) is not as widespread in the Balkans as was previously thought. In fact, it has a dot-like distribution range restricted to the Peloponnese Peninsula in South Greece. Polyommatus orphicus Kolev, 2005 is not as closely related to the Turkish species Polyommatus dantchenkoi (Lukhtanov &amp; Wiemers, 2003) as was supposed earlier. Instead, it is a Balkan endemic represented by two subspecies: Polyommatus orphicus orphicus (Bulgaria) and Polyommatus orphicus eleniae Coutsis &amp; De Prins, 2005 (Northern Greece). Polyommatus ripartii (Freyer, 1830) is represented in the Balkans by an endemic subspecies Polyommatus ripartii pelopi. The traditionally recognized Polyommatus admetus (Esper, 1783) is shown to be a heterogeneous complex and is divided into Polyommatus admetus sensu stricto (the Balkans and west Turkey) and Polyommatus yeranyani (Dantchenko &amp; Lukhtanov, 2005) (east Turkey, Armenia, Azerbaijan and Iran). Polyommatus nephohiptamenos (Brown &amp; Coutsis, 1978) is confirmed to be a species with a dot-like distribution range in Northern Greece. Finally, from Central Greece (Timfristos and Parnassos mountains) we describe Polyommatus timfristos Lukhtanov, Vishnevskaya &amp; Shapoval, sp. n. which differs by its haploid chromosome number (n=38) from the closely related and morphologically similar Polyommatus aroaniensis (n=47-48) and Polyommatus orphicus (n=41-42). We provide chromosomal evidence for three separate south Balkan Pleistocene refugia (Peloponnesse, Central Greece and Northern Greece/South Bulgaria) and stress the biogeographic importance of Central Greece as a place of diversification. Then we argue that the data obtained have direct implications for butterfly karyology, taxonomy, biogeography and conservation.},
}
@article {pmid28104454,
year = {2017},
author = {Poveda, C and Higuera, A and Urbano, P and Ramírez, JD},
title = {Ecology of Trypanosoma cruzi I genotypes across Rhodnius prolixus captured in Attalea butyracea palms.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {49},
number = {},
pages = {146-150},
doi = {10.1016/j.meegid.2017.01.017},
pmid = {28104454},
issn = {1567-7257},
mesh = {Animals ; Arecaceae/parasitology ; Chagas Disease/*transmission ; Colombia ; DNA, Protozoan/*genetics ; Ecosystem ; Genotype ; Humans ; Insect Control/organization &amp; administration ; Insect Vectors/*parasitology ; Molecular Typing ; Phylogeny ; Plant Leaves/*parasitology ; Rhodnius/*parasitology ; Trypanosoma cruzi/classification/*genetics/isolation &amp; purification ; },
abstract = {Trypanosoma cruzi, the agent of Chagas disease exhibits significant genetic diversity. This parasite is divided into six discrete typing units (DTUs) where T. cruzi I (TcI) is the most widespread in the Americas. TcI genotypes have been associated to domestic and sylvatic cycles of transmission (TcIDom and sylvatic TcI). Due to the importance of the enzootic transmission, we determined the frequency of TcI genotypes present in Rhodnius prolixus captured in different regions of the palm A. butyracea to understand the ecology of the disease and the importance of A. butyracea palms as ecotopes of R. prolixus. Forty A. butyracea palms were sampled (base crown, mid-point and crown) capturing 105 individuals identified as R. prolixus by morphological and molecular barcoding. We conducted molecular detection and typing of T. cruzi across 59 individuals. The results showed that all the insects were infected with TcI; 28.57% were sylvatic TcI, 12.38% TcIDom and 15,24% mixed infections (TcIDom/sylvatic TcI). Statistical analysis showed a similar behavior between TcIDom and mixed infections in the mid-point and at the crown of the palm, being more frequent in the crown, while sylvatic TcI does not seem to have a specific association with any of the sampled areas. These findings are consistent with other studies showing high mobility of the insect vector between different ecotopes, increasing the need to develop improvements in the programs of disease control.},
}
@article {pmid28104086,
year = {2017},
author = {Li, J and Wang, Y and Jin, H and Li, W and Yan, C and Yan, P and Zhang, X and He, S and Song, Z},
title = {Identification of Triplophysa species from the Qinghai-Tibetan Plateau (QTP) and its adjacent regions through DNA barcodes.},
journal = {Gene},
volume = {605},
number = {},
pages = {12-19},
doi = {10.1016/j.gene.2016.11.045},
pmid = {28104086},
issn = {1879-0038},
mesh = {Animals ; Artifacts ; Cypriniformes/classification/*genetics ; Cytochromes c1/*genetics ; DNA/*genetics ; DNA Barcoding, Taxonomic/methods ; Fish Proteins/*genetics ; Gene Expression ; Genetic Variation ; *Phylogeny ; Phylogeography ; Tibet ; },
abstract = {The genus Triplophysa is the largest and most difficult to identity morphologically fish group of superfamily Cobitoidea with 140 currently valid species, and is mainly distributed in the Qinghai-Tibetan Plateau (QTP) and adjacent regions. Most species within this genus possess highly similar morphological characteristics for adaption to the highland environment and are very difficult to be identified only based on morphology. The traditional species identification, mainly based on external morphological diagnostic characters, leads to inconsistent results in many cases. Herein, we provided a molecular method based on mitochondrial cytochrome c subunit I (COI) for the identification of Triplophysa fishes. Thirty-three Triplophysa species, 244 individuals, were used to determine whether barcoding was effective in discriminating species for this genus. The mean intraspecific and interspecific K2P distances ranged from 0 to 14.9% (mean, 2.9%) and 0 to 23.4% (mean, 9.7%), respectively. The tree-based analysis displayed most of species formed discrete clusters with strong bootstrap support values (>90%). The results showed that most of Triplophysa species could be identified by DNA barcode and indicated DNA barcode could be used as a molecular marker for these species.},
}
@article {pmid28103323,
year = {2017},
author = {Harrison, RL and Rowley, DL and Mowery, J and Bauchan, GR and Theilmann, DA and Rohrmann, GF and Erlandson, MA},
title = {The Complete Genome Sequence of a Second Distinct Betabaculovirus from the True Armyworm, Mythimna unipuncta.},
journal = {PloS one},
volume = {12},
number = {1},
pages = {e0170510},
pmid = {28103323},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; DNA Barcoding, Taxonomic ; DNA, Viral/genetics ; *Genome, Viral ; Granulovirus/*genetics/*isolation &amp; purification/ultrastructure ; Lepidoptera/*virology ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Open Reading Frames ; Phylogeny ; Viral Proteins/genetics ; },
abstract = {The betabaculovirus originally called Pseudaletia (Mythimna) sp. granulovirus #8 (MyspGV#8) was examined by electron microscopy, host barcoding PCR, and determination of the nucleotide sequence of its genome. Scanning and transmission electron microscopy revealed that the occlusion bodies of MyspGV#8 possessed the characteristic size range and morphology of betabaculovirus granules. Barcoding PCR using cytochrome oxidase I primers with DNA from the MyspGV#8 collection sample confirmed that it had been isolated from the true armyworm, Mythimna unipuncta (Lepidoptera: Noctuidae) and therefore was renamed MyunGV#8. The MyunGV#8 genome was found to be 144,673 bp in size with a nucleotide distribution of 49.9% G+C, which was significantly smaller and more GC-rich than the genome of Pseudaletia unipuncta granulovirus H (PsunGV-H), another M. unipuncta betabaculovirus. A phylogeny based on concatenated baculovirus core gene amino acid sequence alignments placed MyunGV#8 in clade a of genus Betabaculovirus. Kimura-2-parameter nucleotide distances suggested that MyunGV#8 represents a virus species different and distinct from other species of Betabaculovirus. Among the 153 ORFs annotated in the MyunGV#8 genome, four ORFs appeared to have been obtained from or donated to the alphabaculovirus lineage represented by Leucania separata nucleopolyhedrovirus AH1 (LeseNPV-AH1) during co-infection of Mythimna sp. larvae. A set of 33 ORFs was identified that appears only in other clade a betabaculovirus isolates. This clade a-specific set includes an ORF that encodes a polypeptide sequence containing a CIDE_N domain, which is found in caspase-activated DNAse/DNA fragmentation factor (CAD/DFF) proteins. CAD/DFF proteins are involved in digesting DNA during apoptosis.},
}
@article {pmid28103008,
year = {2017},
author = {Zeitoun, RI and Pines, G and Grau, WC and Gill, RT},
title = {Quantitative Tracking of Combinatorially Engineered Populations with Multiplexed Binary Assemblies.},
journal = {ACS synthetic biology},
volume = {6},
number = {4},
pages = {619-627},
doi = {10.1021/acssynbio.6b00376},
pmid = {28103008},
issn = {2161-5063},
mesh = {*Algorithms ; Escherichia coli/genetics ; Gene Library ; *Genetic Engineering ; Genome, Bacterial ; Genotype ; High-Throughput Nucleotide Sequencing ; Plasmids/genetics/metabolism ; Sequence Analysis, DNA ; },
abstract = {Advances in synthetic biology and genomics have enabled full-scale genome engineering efforts on laboratory time scales. However, the absence of sufficient approaches for mapping engineered genomes at system-wide scales onto performance has limited the adoption of more sophisticated algorithms for engineering complex biological systems. Here we report on the development and application of a robust approach to quantitatively map combinatorially engineered populations at scales up to several dozen target sites. This approach works by assembling genome engineered sites with cell-specific barcodes into a format compatible with high-throughput sequencing technologies. This approach, called barcoded-TRACE (bTRACE) was applied to assess E. coli populations engineered by recursive multiplex recombineering across both 6-target sites and 31-target sites. The 31-target library was then tracked throughout growth selections in the presence and absence of isopentenol (a potential next-generation biofuel). We also use the resolution of bTRACE to compare the influence of technical and biological noise on genome engineering efforts.},
}
@article {pmid28100584,
year = {2017},
author = {Smith, T and Heger, A and Sudbery, I},
title = {UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy.},
journal = {Genome research},
volume = {27},
number = {3},
pages = {491-499},
pmid = {28100584},
issn = {1549-5469},
support = {MC_PC_15065/MRC_/Medical Research Council/United Kingdom ; G1000902/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; Sequence Analysis, DNA/methods/*standards ; *Software ; },
abstract = {Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes that are increasingly used in high-throughput sequencing experiments. Through a UMI, identical copies arising from distinct molecules can be distinguished from those arising through PCR amplification of the same molecule. However, bioinformatic methods to leverage the information from UMIs have yet to be formalized. In particular, sequencing errors in the UMI sequence are often ignored or else resolved in an ad hoc manner. We show that errors in the UMI sequence are common and introduce network-based methods to account for these errors when identifying PCR duplicates. Using these methods, we demonstrate improved quantification accuracy both under simulated conditions and real iCLIP and single-cell RNA-seq data sets. Reproducibility between iCLIP replicates and single-cell RNA-seq clustering are both improved using our proposed network-based method, demonstrating the value of properly accounting for errors in UMIs. These methods are implemented in the open source UMI-tools software package.},
}
@article {pmid28100169,
year = {2017},
author = {Chen, GG and Gross, JA and Lutz, PE and Vaillancourt, K and Maussion, G and Bramoulle, A and Théroux, JF and Gardini, ES and Ehlert, U and Bourret, G and Masurel, A and Lepage, P and Mechawar, N and Turecki, G and Ernst, C},
title = {Medium throughput bisulfite sequencing for accurate detection of 5-methylcytosine and 5-hydroxymethylcytosine.},
journal = {BMC genomics},
volume = {18},
number = {1},
pages = {96},
pmid = {28100169},
issn = {1471-2164},
support = {R01 DA033684/DA/NIDA NIH HHS/United States ; MOP93775//CIHR/Canada ; MOP11260//CIHR (Canadian Institutes of Health Research)/International ; MOP119429//CIHR (Canadian Institutes of Health Research)/International ; MOP119430//CIHR (Canadian Institutes of Health Research)/International ; },
mesh = {5-Methylcytosine/*analogs &amp; derivatives/*metabolism ; Adult ; DNA Methylation/drug effects ; Humans ; Male ; Oxidation-Reduction ; Sequence Analysis, DNA/*methods ; Sulfites/*pharmacology ; },
abstract = {BACKGROUND: Epigenetic modifications of DNA, such as 5-methylcytosine and 5-hydroxymethycytosine, play important roles in development and disease. Here, we present a cost-effective and versatile methodology for the analysis of DNA methylation in targeted genomic regions, which comprises multiplexed, PCR-based preparation of bisulfite DNA libraries followed by customized MiSeq sequencing.<br><br>RESULTS: Using bisulfite and oxidative bisulfite conversion of DNA, we have performed multiplexed targeted sequencing to analyse several kilobases of genomic DNA in up to 478 samples, and achieved high coverage data of 5-methylcytosine and 5-hydroxymethycytosine at single-base resolution. Our results demonstrate the ability of this methodology to detect all levels of cytosine modifications at greater than 100&#xd7; coverage in large sample sets at low cost compared to other targeted methods.<br><br>CONCLUSIONS: This approach can be applied to multiple settings, from candidate gene to clinical studies, and is especially useful for validation of differentially methylated or hydroxymethylated regions following whole-genome analyses.},
}
@article {pmid28099773,
year = {2017},
author = {Suetsugu, K and Yamato, M and Miura, C and Yamaguchi, K and Takahashi, K and Ida, Y and Shigenobu, S and Kaminaka, H},
title = {Comparison of green and albino individuals of the partially mycoheterotrophic orchid Epipactis helleborine on molecular identities of mycorrhizal fungi, nutritional modes and gene expression in mycorrhizal roots.},
journal = {Molecular ecology},
volume = {26},
number = {6},
pages = {1652-1669},
doi = {10.1111/mec.14021},
pmid = {28099773},
issn = {1365-294X},
mesh = {Carbon Isotopes/analysis ; Mycorrhizae/*classification ; Orchidaceae/genetics/*microbiology ; Oxidative Stress ; Plant Roots/*genetics/microbiology ; Symbiosis ; },
abstract = {Some green orchids obtain carbon from their mycorrhizal fungi, as well as from photosynthesis. These partially mycoheterotrophic orchids sometimes produce fully achlorophyllous, leaf-bearing (albino) variants. Comparing green and albino individuals of these orchids will help to uncover the molecular mechanisms associated with mycoheterotrophy. We compared green and albino Epipactis helleborine by molecular barcoding of mycorrhizal fungi, nutrient sources based on [15] N and [13] C abundances and gene expression in their mycorrhizae by RNA-seq and cDNA de novo assembly. Molecular identification of mycorrhizal fungi showed that green and albino E. helleborine harboured similar mycobionts, mainly Wilcoxina. Stable isotope analyses indicated that albino E. helleborine plants were fully mycoheterotrophic, whereas green individuals were partially mycoheterotrophic. Gene expression analyses showed that genes involved in antioxidant metabolism were upregulated in the albino variants, which indicates that these plants experience greater oxidative stress than the green variants, possibly due to a more frequent lysis of intracellular pelotons. It was also found that some genes involved in the transport of some metabolites, including carbon sources from plant to fungus, are higher in albino than in green variants. This result may indicate a bidirectional carbon flow even in the mycoheterotrophic symbiosis. The genes related to mycorrhizal symbiosis in autotrophic orchids and arbuscular mycorrhizal plants were also upregulated in the albino variants, indicating the existence of common molecular mechanisms among the different mycorrhizal types.},
}
@article {pmid28095828,
year = {2017},
author = {Kia, A and Gloeckner, C and Osothprarop, T and Gormley, N and Bomati, E and Stephenson, M and Goryshin, I and He, MM},
title = {Improved genome sequencing using an engineered transposase.},
journal = {BMC biotechnology},
volume = {17},
number = {1},
pages = {6},
pmid = {28095828},
issn = {1472-6750},
mesh = {AT Rich Sequence/genetics ; Chromosome Mapping/*methods ; DNA/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; *Protein Engineering ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Analysis, DNA/*methods ; Transposases/*genetics ; },
abstract = {BACKGROUND: Next-generation sequencing (NGS) has transformed genomic research by reducing turnaround time and cost. However, no major breakthrough has been made in the upstream library preparation methods until the transposase-based Nextera method was invented. Nextera combines DNA fragmentation and barcoding in a single tube reaction and therefore enables a very fast workflow to sequencing-ready DNA libraries within a couple of hours. When compared to the traditional ligation-based methods, transposed-based Nextera has a slight insertion bias.<br><br>RESULTS: Here we present the discovery of a mutant transposase (Tn5-059) with a lowered GC insertion bias through protein engineering. We demonstrate Tn5-059 reduces AT dropout and increases uniformity of genome coverage in both bacterial genomes and human genome. We also observe higher library diversity generated by Tn5-059 when compared to Nextera v2 for human exomes, which leads to less sequencing and lower cost per genome. In addition, when used for human exomes, Tn5-059 delivers consistent library insert size over a range of input DNA, allowing up to a tenfold variance from the 50&#xa0;ng input recommendation.<br><br>CONCLUSIONS: Enhanced DNA input tolerance of Tn5-059 can translate to flexibility and robustness of workflow. DNA input tolerance together with superior uniformity of coverage and lower AT dropouts extend the applications of transposase based library preps. We discuss possible mechanisms of improvements in Tn5-059, and potential advantages of using the new mutant in varieties of applications including microbiome sequencing and chromatin profiling.},
}
@article {pmid28094568,
year = {2017},
author = {Young, RG and Abbott, CL and Therriault, TW and Adamowicz, SJ},
title = {Barcode-based species delimitation in the marine realm: a test using Hexanauplia (Multicrustacea: Thecostraca and Copepoda).},
journal = {Genome},
volume = {60},
number = {2},
pages = {169-182},
doi = {10.1139/gen-2015-0209},
pmid = {28094568},
issn = {1480-3321},
mesh = {Animals ; Biodiversity ; Canada ; Cluster Analysis ; Copepoda/anatomy &amp; histology/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Genetic Variation ; Geography ; Phenotype ; Phylogeny ; },
abstract = {DNA barcoding has been used successfully for identifying specimens belonging to marine planktonic groups. However, the ability to delineate species within taxonomically diverse and widely distributed marine groups, such as the Copepoda and Thecostraca, remains largely untested. We investigate whether a cytochrome c oxidase subunit I (COI-5P) global pairwise sequence divergence threshold exists between intraspecific and interspecific divergences in the copepods plus the thecostracans (barnacles and allies). Using publicly accessible sequence data, we applied a graphical method to determine an optimal threshold value. With these thresholds, and using a newly generated planktonic marine data set, we quantify the degree of concordance using a bidirectional analysis and discuss different analytical methods for sequence-based species delimitation (e.g., BIN, ABGD, jMOTU, UPARSE, Mothur, PTP, and GMYC). Our results support a COI-5P threshold between 2.1% and 2.6% p-distance across methods for these crustacean taxa, yielding molecular groupings largely concordant with traditional, morphologically defined species. The adoption of internal methods for clustering verification enables rapid biodiversity studies and the exploration of unknown faunas using DNA barcoding. The approaches taken here for concordance assessment also provide a more quantitative comparison of clustering results (as contrasted with "success/failure" of barcoding), and we recommend their further consideration for barcoding studies.},
}
@article {pmid28092571,
year = {2018},
author = {Ma, EYT and Ratnasingham, S and Kremer, SC},
title = {Machine Learned Replacement of N-Labels for Basecalled Sequences in DNA Barcoding.},
journal = {IEEE/ACM transactions on computational biology and bioinformatics},
volume = {15},
number = {1},
pages = {191-204},
doi = {10.1109/TCBB.2016.2598752},
pmid = {28092571},
issn = {1557-9964},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Genomics/*methods ; Humans ; *Machine Learning ; Neural Networks, Computer ; },
abstract = {This study presents a machine learning method that increases the number of identified bases in Sanger Sequencing. The system post-processes a KB basecalled chromatogram. It selects a recoverable subset of N-labels in the KB-called chromatogram to replace with basecalls (A,C,G,T). An N-label correction is defined given an additional read of the same sequence, and a human finished sequence. Corrections are added to the dataset when an alignment determines the additional read and human agree on the identity of the N-label. KB must also rate the replacement with quality value of in the additional read. Corrections are only available during system training. Developing the system, nearly 850,000 N-labels are obtained from Barcode of Life Datasystems, the premier database of genetic markers called DNA Barcodes. Increasing the number of correct bases improves reference sequence reliability, increases sequence identification accuracy, and assures analysis correctness. Keeping with barcoding standards, our system maintains an error rate of percent. Our system only applies corrections when it estimates low rate of error. Tested on this data, our automation selects and recovers: 79 percent of N-labels from COI (animal barcode); 80 percent from matK and rbcL (plant barcodes); and 58 percent from non-protein-coding sequences (across eukaryotes).},
}
@article {pmid28092170,
year = {2017},
author = {Techen, N and Parveen, I and Khan, IA},
title = {A single molecular marker to distinguish between species of Dioscorea.},
journal = {Genome},
volume = {60},
number = {3},
pages = {201-207},
doi = {10.1139/gen-2015-0105},
pmid = {28092170},
issn = {1480-3321},
support = {U01 FD004246/FD/FDA HHS/United States ; },
mesh = {DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; Dioscorea/classification/*genetics ; *Genetic Markers ; Genetic Variation ; Genome, Plant ; Genomics ; Introns ; Oligonucleotides/genetics ; Phylogeny ; Plant Tubers/chemistry ; Polymerase Chain Reaction ; Saponins/analysis ; Species Specificity ; },
abstract = {Yams are species of the genus Dioscorea (family Dioscoreaceae), which consists of approximately 630 species. The majority of the world production of yams occurs in Africa with 58.8 million t annually, but they are also produced in the Americas and Asia. The saponins in yams have been reported to possess various properties to improve health. The tuber and aerial parts of various species often share morphological similarities, which can cause problems in the proper identification of sample material. For example, the rootstocks and aerial parts of Dioscorea villosa L. share similarities with Dioscorea polystachia Turcz. Dioscorea bulbifera L. may be mistaken for Dioscorea alata L. owing to similar morphologies. Various molecular analyses have been published to help with the identification of species and varieties within the genus Dioscorea. The multi-loci or single-locus analysis has resulted in varying success, some with only a limited discrimination rate. In the present study, a single nuclear genomic region, biparentally inherited, was analyzed for its usefulness as a molecular marker for species identification and discrimination between D. bulbifera, D. villosa, D. nipponica, D. alata, D. caucasica, and D. deltoidea samples. The results of this study show that the LFY genomic region can be useful as a molecular marker to distinguish between samples.},
}
@article {pmid28091577,
year = {2017},
author = {Wu, Y and Trepanowski, NF and Molongoski, JJ and Reagel, PF and Lingafelter, SW and Nadel, H and Myers, SW and Ray, AM},
title = {Identification of wood-boring beetles (Cerambycidae and Buprestidae) intercepted in trade-associated solid wood packaging material using DNA barcoding and morphology.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {40316},
pmid = {28091577},
issn = {2045-2322},
mesh = {Animals ; Bayes Theorem ; Coleoptera/*anatomy &amp; histology/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; Geography ; Larva/physiology ; Phylogeny ; *Product Packaging ; United States ; Wood/*parasitology ; },
abstract = {Global trade facilitates the inadvertent movement of insect pests and subsequent establishment of populations outside their native ranges. Despite phytosanitary measures, nonnative insects arrive at United States (U.S.) ports of entry as larvae in solid wood packaging material (SWPM). Identification of wood-boring larval insects is important for pest risk analysis and management, but is difficult beyond family level due to highly conserved morphology. Therefore, we integrated DNA barcoding and rearing of larvae to identify wood-boring insects in SWPM. From 2012 to 2015, we obtained larvae of 338 longhorned beetles (Cerambycidae) and 38 metallic wood boring beetles (Buprestidae) intercepted in SWPM associated with imported products at six U.S. ports. We identified 265 specimens to species or genus using DNA barcodes. Ninety-three larvae were reared to adults and identified morphologically. No conflict was found between the two approaches, which together identified 275 cerambycids (23 genera) and 16 buprestids (4 genera). Our integrated approach confirmed novel DNA barcodes for seven species (10 specimens) of woodborers not in public databases. This study demonstrates the utility of DNA barcoding as a tool for regulatory agencies. We provide important documentation of potential beetle pests that may cross country borders through the SWPM pathway.},
}
@article {pmid28090577,
year = {2016},
author = {Guernet, A and Aaronson, SA and Anouar, Y and Grumolato, L},
title = {Modeling intratumor heterogeneity through CRISPR-barcodes.},
journal = {Molecular &amp; cellular oncology},
volume = {3},
number = {6},
pages = {e1227894},
pmid = {28090577},
issn = {2372-3556},
abstract = {We have devised a barcoding strategy to recapitulate cancer evolution through the emergence of subclonal mutations of interest, whose effects can be monitored in a dynamic manner. This approach can be easily adapted for a variety of applications, including combined modeling of multiple mechanisms of drug resistance or repair of oncogenic driver mutations in addicted cancer cells.},
}
@article {pmid28090265,
year = {2017},
author = {Doh, EJ and Kim, JH and Oh, SE and Lee, G},
title = {Identification and monitoring of Korean medicines derived from Cinnamomum spp. by using ITS and DNA marker.},
journal = {Genes &amp; genomics},
volume = {39},
number = {1},
pages = {101-109},
pmid = {28090265},
issn = {1976-9571},
abstract = {In this study, we identified and evaluated the genetic relationships among Cinnamomum plants, which are used in traditional medicine. We also attempted to monitor the distribution of traditional medicines derived from Cinnamomum cassia by using DNA barcoding and a species-specific DNA marker. Plants of the genus Cinnamomum, and in particular C. cassia, are commonly used as medicinal herbs in the form of Cinnamomi Ramulus, Cinnamomi Cortex, and Cassiae Cortex Interior. However, it is difficult to distinguish among different Cinnamomum species based on morphological features, and so to overcome this limitation, nucleotide sequences of the internal transcribed spacer (ITS) region of Cinnamomum DNA were determined and compared. On the basis of the discrepancy in determined ITS sequences, a 408-bp product, amplified by the primer pair CC F1/CC R3, was developed as a C. cassia-specific DNA marker. Using the developed DNA marker in combination with the ITS 2 nucleotide sequence, we monitored imported and commercially supplied medicinal products derived from Cinnamomum plants in markets in Korean, China, and Japan. The results revealed that most of the specimens monitored were derived from C. cassia.},
}
@article {pmid28089841,
year = {2017},
author = {Tarvin, RD and Powell, EA and Santos, JC and Ron, SR and Cannatella, DC},
title = {The birth of aposematism: High phenotypic divergence and low genetic diversity in a young clade of poison frogs.},
journal = {Molecular phylogenetics and evolution},
volume = {109},
number = {},
pages = {283-295},
doi = {10.1016/j.ympev.2016.12.035},
pmid = {28089841},
issn = {1095-9513},
mesh = {Amphibian Venoms ; Animals ; Anura/anatomy &amp; histology/*classification ; Biological Evolution ; *Biological Mimicry/genetics ; DNA, Mitochondrial ; Genetic Speciation ; *Genetic Variation ; Phylogeny ; },
abstract = {Rapid radiation coupled with low genetic divergence often hinders species delimitation and phylogeny estimation even if putative species are phenotypically distinct. Some aposematic species, such as poison frogs (Dendrobatidae), have high levels of intraspecific color polymorphism, which can lead to overestimation of species when phenotypic divergence primarily guides species delimitation. We explored this possibility in the youngest origin of aposematism (3-7 MYA) in poison frogs, Epipedobates, by comparing genetic divergence with color and acoustic divergence. We found low genetic divergence (2.6% in the 16S gene) despite substantial differences in color and acoustic signals. While chemical defense is inferred to have evolved in the ancestor of Epipedobates, aposematic coloration evolved at least twice or was lost once in Epipedobates, suggesting that it is evolutionarily labile. We inferred at least one event of introgression between two cryptically colored species with adjacent ranges (E. boulengeri and E. machalilla). We also find evidence for peripheral isolation resulting in phenotypic divergence and potential speciation of the aposematic E. tricolor from the non-aposematic E. machalilla. However, we were unable to estimate a well-supported species tree or delimit species using multispecies coalescent models. We attribute this failure to factors associated with recent speciation including mitochondrial introgression, incomplete lineage sorting, and too few informative molecular characters. We suggest that species delimitation within young aposematic lineages such as Epipedobates will require genome-level molecular studies. We caution against relying solely on DNA barcoding for species delimitation or identification and highlight the value of phenotypic divergence and natural history in delimiting species.},
}
@article {pmid28088131,
year = {2017},
author = {Sardari, S},
title = {Study Break: Number Crunching towards Molecular Barcoding.},
journal = {Iranian biomedical journal},
volume = {21},
number = {2},
pages = {67-68},
pmid = {28088131},
issn = {2008-823X},
}
@article {pmid28087539,
year = {2017},
author = {Koelle, SJ and Espinoza, DA and Wu, C and Xu, J and Lu, R and Li, B and Donahue, RE and Dunbar, CE},
title = {Quantitative stability of hematopoietic stem and progenitor cell clonal output in rhesus macaques receiving transplants.},
journal = {Blood},
volume = {129},
number = {11},
pages = {1448-1457},
pmid = {28087539},
issn = {1528-0020},
mesh = {Animals ; Cell Differentiation ; Cell Lineage ; Cell Self Renewal ; Clone Cells/cytology ; Hematopoiesis ; *Hematopoietic Stem Cell Transplantation ; Hematopoietic Stem Cells/*cytology ; Macaca mulatta ; },
abstract = {Autologous transplantation of hematopoietic stem and progenitor cells lentivirally labeled with unique oligonucleotide barcodes flanked by sequencing primer targets enables quantitative assessment of the self-renewal and differentiation patterns of these cells in a myeloablative rhesus macaque model. Compared with other approaches to clonal tracking, this approach is highly quantitative and reproducible. We documented stable multipotent long-term hematopoietic clonal output of monocytes, granulocytes, B cells, and T cells from a polyclonal pool of hematopoietic stem and progenitor cells in 4 macaques observed for up to 49 months posttransplantation. A broad range of clonal behaviors characterized by contribution level and biases toward certain cell types were extremely stable over time. Correlations between granulocyte and monocyte clonalities were greatest, followed by correlations between these cell types and B cells. We also detected quantitative expansion of T cell-biased clones consistent with an adaptive immune response. In contrast to recent data from a nonquantitative murine model, there was little evidence for clonal succession after initial hematopoietic reconstitution. These findings have important implications for human hematopoiesis, given the similarities between macaque and human physiologies.},
}
@article {pmid28083107,
year = {2016},
author = {Farrell, ED and Carlsson, JE and Carlsson, J},
title = {Next Gen Pop Gen: implementing a high-throughput approach to population genetics in boarfish (Capros aper).},
journal = {Royal Society open science},
volume = {3},
number = {12},
pages = {160651},
pmid = {28083107},
issn = {2054-5703},
abstract = {The recently developed approach for microsatellite genotyping by sequencing (GBS) using individual combinatorial barcoding was further improved and used to assess the genetic population structure of boarfish (Capros aper) across the species' range. Microsatellite loci were developed de novo and genotyped by next-generation sequencing. Genetic analyses of the samples indicated that boarfish can be subdivided into at least seven biological units (populations) across the species' range. Furthermore, the recent apparent increase in abundance in the northeast Atlantic is better explained by demographic changes within this area than by influx from southern or insular populations. This study clearly shows that the microsatellite GBS approach is a generic, cost-effective, rapid and powerful method suitable for full-scale population genetic studies-a crucial element for assessment, sustainable management and conservation of valuable biological resources.},
}
@article {pmid28082759,
year = {2016},
author = {Lombard, L and Wingfield, MJ and Alfenas, AC and Crous, PW},
title = {The forgotten Calonectria collection: Pouring old wine into new bags.},
journal = {Studies in mycology},
volume = {85},
number = {},
pages = {159-198},
pmid = {28082759},
issn = {0166-0616},
abstract = {The genus Calonectria with its Cylindrocladium asexual morphs has been subject to several taxonomic revisions in the past. These have resulted in the recognition of 116 species, of which all but two species (C. hederae and C. pyrochroa) are supported by ex-type cultures and supplemented with DNA barcodes. The present study is based on a large collection of unidentified Calonectria isolates that have been collected over a period of 20 years from various substrates worldwide, which has remained unstudied in the basement of the CBS-KNAW Fungal Biodiversity Centre. Employing a polyphasic approach, the identities of these isolates were resolved and shown to represent many new phylogenetic species. Of these, 24 are newly described, while C. uniseptata is reinstated at species level. We now recognise 141 species that include some of the most important plant pathogens globally.},
}
@article {pmid28080994,
year = {2016},
author = {Crous, PW and Groenewald, JZ and Slippers, B and Wingfield, MJ},
title = {Global food and fibre security threatened by current inefficiencies in fungal identification.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1709},
pages = {},
pmid = {28080994},
issn = {1471-2970},
mesh = {*Dietary Fiber/analysis ; *Food Supply ; Fungi/*isolation &amp; purification ; Mycoses/*classification/microbiology/prevention &amp; control ; Plant Diseases/*classification/microbiology/prevention &amp; control ; },
abstract = {Fungal pathogens severely impact global food and fibre crop security. Fungal species that cause plant diseases have mostly been recognized based on their morphology. In general, morphological descriptions remain disconnected from crucially important knowledge such as mating types, host specificity, life cycle stages and population structures. The majority of current fungal species descriptions lack even the most basic genetic data that could address at least some of these issues. Such information is essential for accurate fungal identifications, to link critical metadata and to understand the real and potential impact of fungal pathogens on production and natural ecosystems. Because international trade in plant products and introduction of pathogens to new areas is likely to continue, the manner in which fungal pathogens are identified should urgently be reconsidered. The technologies that would provide appropriate information for biosecurity and quarantine already exist, yet the scientific community and the regulatory authorities are slow to embrace them. International agreements are urgently needed to enforce new guidelines for describing plant pathogenic fungi (including key DNA information), to ensure availability of relevant data and to modernize the phytosanitary systems that must deal with the risks relating to trade-associated plant pathogens.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.},
}
@article {pmid28080142,
year = {2017},
author = {Bourque, DA and Naaum, AM and Distel, DL and Hanner, RH},
title = {Whole Genome Amplification Provides Suitable Control DNA for Use in DNA Barcoding Applications.},
journal = {Biopreservation and biobanking},
volume = {15},
number = {3},
pages = {277-279},
doi = {10.1089/bio.2016.0078},
pmid = {28080142},
issn = {1947-5543},
mesh = {Animals ; Biological Specimen Banks ; DNA Barcoding, Taxonomic/*methods ; Fishes/*classification/genetics ; Genome ; Polymerase Chain Reaction/*methods ; },
}
@article {pmid28075039,
year = {2017},
author = {Willette, DA and Simmonds, SE and Cheng, SH and Esteves, S and Kane, TL and Nuetzel, H and Pilaud, N and Rachmawati, R and Barber, PH},
title = {Using DNA barcoding to track seafood mislabeling in Los Angeles restaurants.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {31},
number = {5},
pages = {1076-1085},
doi = {10.1111/cobi.12888},
pmid = {28075039},
issn = {1523-1739},
mesh = {Animals ; Conservation of Natural Resources ; *DNA Barcoding, Taxonomic ; *Food Labeling ; Los Angeles ; *Restaurants ; *Seafood ; },
abstract = {Seafood mislabeling is common in both domestic and international markets. Studies on seafood fraud often report high rates of mislabeling (e.g., >70%), but these studies have been limited to a single sampling year, which means it is difficult to assess the impact of stricter governmental truth-in-labeling regulations. We used DNA barcoding to assess seafood labeling in 26 sushi restaurants in Los Angeles over 4 years. Seafood from 3 high-end grocery stores were also sampled (n = 16) in 2014. We ordered 9 common sushi fish from menus, preserved tissue samples in 95% ethanol, extracted the genomic DNA, amplified and sequenced a portion of the mtDNA COI gene, and identified the resulting sequence to known fish sequences from the National Center for Biotechnology Information nucleotide database. We compared DNA results with the U.S. Food and Drug Administration (FDA) list of acceptable market names and retail names. We considered sushi-sample labels that were inconsistent with FDA names mislabeled. Sushi restaurants had a consistently high percentage of mislabeling (47%; 151 of 323) from 2012 to 2015, yet mislabeling was not homogenous across species. Halibut, red snapper, yellowfin tuna, and yellowtail had consistently high (<77%) occurrences of mislabeling on menus, whereas mislabeling of salmon and mackerel were typically low (>15%). All sampled sushi restaurants had at least one case of mislabeling. Mislabeling of sushi-grade fish from high-end grocery stores was also identified in red snapper, yellowfin tuna, and yellowtail, but at a slightly lower frequency (42%) than sushi restaurants. Despite increased regulatory measures and media attention, we found seafood mislabeling continues to be prevalent.},
}
@article {pmid28074500,
year = {2017},
author = {Novoa, A and Le Roux, JJ and Richardson, DM and Wilson, JRU},
title = {Level of environmental threat posed by horticultural trade in Cactaceae.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {31},
number = {5},
pages = {1066-1075},
doi = {10.1111/cobi.12892},
pmid = {28074500},
issn = {1523-1739},
mesh = {Animals ; *Cactaceae ; *Conservation of Natural Resources ; Endangered Species ; *Introduced Species ; South Africa ; },
abstract = {Ornamental horticulture has been identified as an important threat to plant biodiversity and is a major pathway for plant invasions worldwide. In this context, the family Cactaceae is particularly challenging because it is considered the fifth most threatened large taxonomic group in the world; several species are among the most widespread and damaging invasive species; and Cactaceae is one of the most popular horticultural plant groups. Based on the Convention on International Trade in Endangered Species of Wild Flora and Fauna and the 11 largest online auction sites selling cacti, we documented the international cactus trade. To provide an in-depth look at the dynamics of the industry, we surveyed the businesses involved in the cactus trade in South Africa (a hotspot of cactus trade and invasions). We purchased seeds of every available species and used DNA barcoding to identify species to the genus level. Although <20% of this trade involved threatened species and <3% involved known invasive species, many species were identified by a common name. However, only 0.02% of the globally traded cacti were collected from wild populations. Despite a large commercial network, all South African imports (of which 15% and 1.5% were of species listed as threatened and invasive, respectively) came from the same source. With DNA barcoding, we identified 24% of the species to genus level. Based on our results, we believe that if trade restrictions are placed on the small proportion of cacti that are invasive and there is no major increase in harvesting of native populations, then the commercial trade in cactus poses a negligible environmental threat. However, there are currently no effective methods for easily identifying which cacti are traded, and both the illicit harvesting of cacti from the wild and the informal trade in invasive taxa pose on-going conservation challenges.},
}
@article {pmid28072819,
year = {2017},
author = {Braukmann, TW and Kuzmina, ML and Sills, J and Zakharov, EV and Hebert, PD},
title = {Testing the Efficacy of DNA Barcodes for Identifying the Vascular Plants of Canada.},
journal = {PloS one},
volume = {12},
number = {1},
pages = {e0169515},
pmid = {28072819},
issn = {1932-6203},
mesh = {Canada ; *DNA Barcoding, Taxonomic ; *DNA, Plant ; DNA, Ribosomal Spacer ; Genes, Plant ; Phylogeny ; Plants/*classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {Their relatively slow rates of molecular evolution, as well as frequent exposure to hybridization and introgression, often make it difficult to discriminate species of vascular plants with the standard barcode markers (rbcL, matK, ITS2). Previous studies have examined these constraints in narrow geographic or taxonomic contexts, but the present investigation expands analysis to consider the performance of these gene regions in discriminating the species in local floras at sites across Canada. To test identification success, we employed a DNA barcode reference library with sequence records for 96% of the 5108 vascular plant species known from Canada, but coverage varied from 94% for rbcL to 60% for ITS2 and 39% for matK. Using plant lists from 27 national parks and one scientific reserve, we tested the efficacy of DNA barcodes in identifying the plants in simulated species assemblages from six biogeographic regions of Canada using BLAST and mothur. Mean pairwise distance (MPD) and mean nearest taxon distance (MNTD) were strong predictors of barcode performance for different plant families and genera, and both metrics supported ITS2 as possessing the highest genetic diversity. All three genes performed strongly in assigning the taxa present in local floras to the correct genus with values ranging from 91% for rbcL to 97% for ITS2 and 98% for matK. However, matK delivered the highest species discrimination (~81%) followed by ITS2 (~72%) and rbcL (~44%). Despite the low number of plant taxa in the Canadian Arctic, DNA barcodes had the least success in discriminating species from this biogeographic region with resolution ranging from 36% with rbcL to 69% with matK. Species resolution was higher in the other settings, peaking in the Woodland region at 52% for rbcL and 87% for matK. Our results indicate that DNA barcoding is very effective in identifying Canadian plants to a genus, and that it performs well in discriminating species in regions where floristic diversity is highest.},
}
@article {pmid28070758,
year = {2017},
author = {Janique, S and Sriratanasak, W and Ketsuwan, K and Jairin, J and Jeratthitikul, E},
title = {Phylogeography of the Asian rice gall midge Orseolia oryzae (Wood Mason) (Diptera: Cecidomyiidae) in Thailand.},
journal = {Genetica},
volume = {145},
number = {1},
pages = {37-49},
pmid = {28070758},
issn = {1573-6857},
mesh = {Animals ; Base Sequence ; DNA, Mitochondrial ; Diptera/*classification/*genetics ; Genetic Variation ; Haplotypes ; Oryza/*parasitology ; *Phylogeny ; *Phylogeography ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Thailand ; },
abstract = {The Asian rice gall midge (RGM) Orseolia oryzae (Wood Mason) (Diptera: Cecidomyiidae) is a major pest of rice, leading to yield losses in Thailand and many Asian countries. Despite an increasing number of reported midge outbreaks and the presence of many susceptible rice varieties, only a few studies have focused on the genetic variation of the midges. Therefore, we analyzed the phylogeography among Thai RGM populations covering north, northeast and central Thailand. Two mitochondrial DNA genes, cytochrome C oxidase I (COI) and 12S, and a non-coding repeat region (RR) situated just before COI were amplified. Overall, the haplotype diversity for COI and 12S genes of the Thai population was high, but the nucleotide diversity was quite low. Altogether, the phylogenetic tree and pairwise F st values indicated that Thai RGM populations recently expanded and were homogeneously distributed throughout the country, except for some populations in the north, which most likely became recently isolated from the main population. Two non-coding repeat motifs, that were recently observed in the mitogenome of RGM in India, were absent in Thai populations and replaced by an 89 bp non-coding sequence. Tandem nucleotide repeats of the sequence TA were also observed. The repeat copy number varied from 2 to 11 and was not correlated with geographical repartition of the midge. Finally, COI barcoding divergence between Indian and Thai populations was high (6.3% in average), giving insights into the potential existence of an RGM species complex in Asia.},
}
@article {pmid28067539,
year = {2017},
author = {Nithaniyal, S and Vassou, SL and Poovitha, S and Raju, B and Parani, M},
title = {Identification of species adulteration in traded medicinal plant raw drugs using DNA barcoding.},
journal = {Genome},
volume = {60},
number = {2},
pages = {139-146},
doi = {10.1139/gen-2015-0225},
pmid = {28067539},
issn = {1480-3321},
mesh = {Computational Biology/methods ; *DNA Barcoding, Taxonomic ; DNA, Plant ; Plants, Medicinal/*classification/*genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {Plants are the major source of therapeutic ingredients in complementary and alternative medicine (CAM). However, species adulteration in traded medicinal plant raw drugs threatens the reliability and safety of CAM. Since morphological features of medicinal plants are often not intact in the raw drugs, DNA barcoding was employed for species identification. Adulteration in 112 traded raw drugs was tested after creating a reference DNA barcode library consisting of 1452 rbcL and matK barcodes from 521 medicinal plant species. Species resolution of this library was 74.4%, 90.2%, and 93.0% for rbcL, matK, and rbcL + matK, respectively. DNA barcoding revealed adulteration in about 20% of the raw drugs, and at least 6% of them were derived from plants with completely different medicinal or toxic properties. Raw drugs in the form of dried roots, powders, and whole plants were found to be more prone to adulteration than rhizomes, fruits, and seeds. Morphological resemblance, co-occurrence, mislabeling, confusing vernacular names, and unauthorized or fraudulent substitutions might have contributed to species adulteration in the raw drugs. Therefore, this library can be routinely used to authenticate traded raw drugs for the benefit of all stakeholders: traders, consumers, and regulatory agencies.},
}
@article {pmid28067010,
year = {2017},
author = {Zimmermann, G and Li, Y and Rieder, U and Mattarella, M and Neri, D and Scheuermann, J},
title = {Hit-Validation Methodologies for Ligands Isolated from DNA-Encoded Chemical Libraries.},
journal = {Chembiochem : a European journal of chemical biology},
volume = {18},
number = {9},
pages = {853-857},
pmid = {28067010},
issn = {1439-7633},
support = {163479/SNSF_/Swiss National Science Foundation/Switzerland ; 670603/ERC_/European Research Council/International ; },
mesh = {Acetazolamide/chemistry/metabolism ; Carbonic Anhydrase IX/chemistry/metabolism ; DNA/*chemistry/metabolism ; Drug Discovery ; Fluorescent Dyes/chemistry ; High-Throughput Nucleotide Sequencing ; Ligands ; Nucleic Acid Hybridization ; Oligonucleotides/chemistry/metabolism ; Protein Binding ; Sequence Analysis, DNA ; Small Molecule Libraries/*chemistry ; },
abstract = {DNA-encoded chemical libraries (DECLs) are large collections of compounds linked to DNA fragments, serving as amplifiable barcodes, which can be screened on target proteins of interest. In typical DECL selections, preferential binders are identified by high-throughput DNA sequencing, by comparing their frequency before and after the affinity capture step. Hits identified in this procedure need to be confirmed, by resynthesis and by performing affinity measurements. In this article we present new methods based on hybridization of oligonucleotide conjugates with fluorescently labeled complementary oligonucleotides; these facilitate the determination of affinity constants and kinetic dissociation constants. The experimental procedures were demonstrated with acetazolamide, a binder to carbonic anhydrase IX with a dissociation constant in the nanomolar range. The detection of binding events was compatible not only with fluorescence polarization methodologies, but also with Alphascreen technology and with microscale thermophoresis.},
}
@article {pmid28059130,
year = {2017},
author = {Shi, Y and Zhao, M and Yao, H and Yang, P and Xin, T and Li, B and Sun, W and Chen, S},
title = {Rapidly discriminate commercial medicinal Pulsatilla chinensis (Bge.) Regel from its adulterants using ITS2 barcoding and specific PCR-RFLP assay.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {40000},
pmid = {28059130},
issn = {2045-2322},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/*genetics ; Drug Contamination ; Medicine, Chinese Traditional ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Pulsatilla/*classification/genetics ; },
abstract = {Pulsatillae radix is a conventional traditional Chinese medicine (TCM) with common name Baitouweng, and has notable effects on inflammation and dysentery. Pulsatilla chinensis (Bge.) Regel is the only source plant of Baitouweng recorded in Chinese Pharmacopoeia, but its adulteration often occurs in the market that possibly affects medicinal efficacy and safety. We have established an internal transcribed spacer 2 (ITS2) barcode library based on 105 plant samples from 12 Pulsatilla species and 10 common adulterants. Results indicate that ITS2 barcoding can accurately distinguish Pulsatilla species from their adulterants. Pulsatilla chinensis can be discriminated from 11 congeneric species by two stable single nucleotide polymorphisms (SNPs) in the ITS2 region. Additionally, a quick specific PCR-RFLP identification assay based on the ITS2 barcode was developed. Using specific primers ITS2/PR1 combined with restriction enzyme Bgl I, Pu. chinensis can rapidly be differentiated from other species via simple and low-cost test procedures. Furthermore, 30 commercial Baitouweng products were tested and only two products were derived from authentic Pu. chinensis. Thus, these two molecular approaches provide practical tools for quick identification of commercial Baitouweng products and can help ensure the safe use of this TCM product.},
}
@article {pmid28053872,
year = {2017},
author = {Peninal, S and Subramanian, J and Elavarasi, A and Kalaiselvam, M},
title = {Genetic identification of marine eels through DNA barcoding from Parangipettai coastal waters.},
journal = {Genomics data},
volume = {11},
number = {},
pages = {81-84},
pmid = {28053872},
issn = {2213-5960},
abstract = {Anguilliformes, also known as "true eels", are an ecologically diverse group of predominantly marine origin whose members were easily recognized by their extremely elongated bodies with reduced cross-sectional areas and universal lack of pelvic fins. The Marine Eels were collected from landing centres of Parangipettai coastal waters and identified based on their morphometric and meristic characters. The newly recorded species were used for the barcoding analysis. Information on molecular taxonomy of marine eels was very meagre and hence, the present study was aimed to study the barcoding of marine eels which were present along the southeast coast of India. The cube of lateral muscle was exercised for DNA isolation followed by its amplification. Cluster IX 2.06 was used to align the nucleotide sequences (Thomson, 1997). The evolutionary history was inferred using the Neighbor-Joining method (Saitou and Nei, 1987). The evolutionary distances were computed using the Maximum Composite Likelihood method (Tamura et al., 2004). The barcodes sequences were submitted in NCBI (National centre for Biotechnological Information). The species within genera of Muraenidae, Muraenesocidae and Ophichthidae family were clustered in a same clade with high bootstrap value. The evolutionary relationships of six species were analyzed using neighbor joining method. This results of phylogenetic tree showed maximum genetic relatedness with the sequenced results which were submitted in gene bank.},
}
@article {pmid28052927,
year = {2017},
author = {Buschmann, T},
title = {DNABarcodes: an R package for the systematic construction of DNA sample tags.},
journal = {Bioinformatics (Oxford, England)},
volume = {33},
number = {6},
pages = {920-922},
doi = {10.1093/bioinformatics/btw759},
pmid = {28052927},
issn = {1367-4811},
mesh = {Algorithms ; DNA Barcoding, Taxonomic/*methods ; *Software ; },
abstract = {MOTIVATION: DNA barcodes are commonly used for counting and discriminating purposes in molecular and cell biology. Not every set of DNA sequences is equally suitable for this goal. There is a growing demand for more sophisticated barcode designs, with only few tools available. We prepared an R package that combines known algorithms and innovative methods for the efficient, flexible and near-optimal generation of robust barcode sets.<br><br>RESULTS: Our R-software package 'DNABarcodes' generates sets of DNA barcodes from a few basic input parameters (e.g. length, distance metric, minimum distance, chemical properties). It satisfies the specifics of most particular experimental demands in de novo design of barcodes. Additionally, the package allows analysing existing sets of DNA barcodes as well as the generation of subsets of those existing sets to improve their error correction and detection properties. 'DNABarcodes' was designed for speed, versatility, provable correctness and large set sizes.<br><br>The DNABarcodes R package is available from Bioconductor at http://bioconductor.org/packages/DNABarcodes under the GPL-2 license.<br><br>CONTACT: tilo.buschmann@izi.fraunhofer.de.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid28052139,
year = {2017},
author = {Hoshino, T and Inagaki, F},
title = {Application of Stochastic Labeling with Random-Sequence Barcodes for Simultaneous Quantification and Sequencing of Environmental 16S rRNA Genes.},
journal = {PloS one},
volume = {12},
number = {1},
pages = {e0169431},
pmid = {28052139},
issn = {1932-6203},
mesh = {Base Sequence ; *DNA Barcoding, Taxonomic ; *Environment ; Gene Dosage ; High-Throughput Nucleotide Sequencing/*methods ; RNA, Ribosomal, 16S/*genetics ; Stochastic Processes ; },
abstract = {Next-generation sequencing (NGS) is a powerful tool for analyzing environmental DNA and provides the comprehensive molecular view of microbial communities. For obtaining the copy number of particular sequences in the NGS library, however, additional quantitative analysis as quantitative PCR (qPCR) or digital PCR (dPCR) is required. Furthermore, number of sequences in a sequence library does not always reflect the original copy number of a target gene because of biases caused by PCR amplification, making it difficult to convert the proportion of particular sequences in the NGS library to the copy number using the mass of input DNA. To address this issue, we applied stochastic labeling approach with random-tag sequences and developed a NGS-based quantification protocol, which enables simultaneous sequencing and quantification of the targeted DNA. This quantitative sequencing (qSeq) is initiated from single-primer extension (SPE) using a primer with random tag adjacent to the 5' end of target-specific sequence. During SPE, each DNA molecule is stochastically labeled with the random tag. Subsequently, first-round PCR is conducted, specifically targeting the SPE product, followed by second-round PCR to index for NGS. The number of random tags is only determined during the SPE step and is therefore not affected by the two rounds of PCR that may introduce amplification biases. In the case of 16S rRNA genes, after NGS sequencing and taxonomic classification, the absolute number of target phylotypes 16S rRNA gene can be estimated by Poisson statistics by counting random tags incorporated at the end of sequence. To test the feasibility of this approach, the 16S rRNA gene of Sulfolobus tokodaii was subjected to qSeq, which resulted in accurate quantification of 5.0 × 103 to 5.0 × 104 copies of the 16S rRNA gene. Furthermore, qSeq was applied to mock microbial communities and environmental samples, and the results were comparable to those obtained using digital PCR and relative abundance based on a standard sequence library. We demonstrated that the qSeq protocol proposed here is advantageous for providing less-biased absolute copy numbers of each target DNA with NGS sequencing at one time. By this new experiment scheme in microbial ecology, microbial community compositions can be explored in more quantitative manner, thus expanding our knowledge of microbial ecosystems in natural environments.},
}
@article {pmid28050055,
year = {2016},
author = {Vu, D and Groenewald, M and Szöke, S and Cardinali, G and Eberhardt, U and Stielow, B and de Vries, M and Verkleij, GJ and Crous, PW and Boekhout, T and Robert, V},
title = {DNA barcoding analysis of more than 9 000 yeast isolates contributes to quantitative thresholds for yeast species and genera delimitation.},
journal = {Studies in mycology},
volume = {85},
number = {},
pages = {91-105},
pmid = {28050055},
issn = {0166-0616},
abstract = {DNA barcoding is a global initiative for species identification through sequencing of short DNA sequence markers. Sequences of two loci, ITS and LSU, were generated as barcode data for all (ca. 9k) yeast strains included in the CBS collection, originally assigned to ca. 2 000 species. Taxonomic sequence validation turned out to be the most severe bottleneck due to the large volume of generated trace files and lack of reference sequences. We have analysed and validated CBS strains and barcode sequences automatically. Our analysis shows that there were 6 and 9.5 % of CBS yeast species that could not be distinguished by ITS and LSU, respectively. Among them, ∼3 % were indistinguishable by both loci. Except for those species, both loci were successfully resolving yeast species as the grouping of yeast DNA barcodes with the predicted taxonomic thresholds was more than 90 % similar to the grouping with respect to the expected taxon names. The taxonomic thresholds predicted to discriminate yeast species were 98.41 % for ITS and 99.51 % for LSU. To discriminate current yeast genera, thresholds were 96.31 % for ITS and 97.11 % for LSU. Using ITS and LSU barcodes, we were also able to show that the recent reclassifications of basidiomycetous yeasts in 2015 have made a significant improvement for the generic taxonomy of those organisms. The barcodes of 4 730 (51 %) CBS yeast strains of 1 351 (80 %) accepted yeast species that were manually validated have been released to GenBank and the CBS-KNAW website as reference sequences for yeast identification.},
}
@article {pmid28049922,
year = {2017},
author = {An, C and Okamoto, Y and Xu, S and Eo, KY and Kimura, J and Yamamoto, N},
title = {Comparison of fecal microbiota of three captive carnivore species inhabiting Korea.},
journal = {The Journal of veterinary medical science},
volume = {79},
number = {3},
pages = {542-546},
pmid = {28049922},
issn = {1347-7439},
mesh = {Animals ; Animals, Zoo/microbiology ; Bacteria/classification/*isolation &amp; purification ; DNA Barcoding, Taxonomic ; Feces/microbiology ; Felidae/*microbiology ; Female ; *Gastrointestinal Microbiome ; Male ; Otters/*microbiology ; Raccoon Dogs/*microbiology ; Seoul ; },
abstract = {This study aimed at characterizing fecal microbiota of three captive carnivore species of leopard cats Prionailurus bengalensis, Eurasian otters Lutra lutra and raccoon dogs Nyctereutes procyonoides. We used DNA barcoding sequencing to analyze 16S rRNA genes of uncultured bacteria in the feces collected in the Seoul Zoo. The sequencing analyses revealed that: 1) Firmicutes was the most dominant phylum for all three animals; 2) bacterial genus-rank compositions were distinct across species of the animals; and 3) bacterial community memberships were different across species of the studied animals. We expect such baseline information is useful for better understanding of these endangered species and future management of their health in zoos.},
}
@article {pmid28049435,
year = {2017},
author = {Xu, C and Nezami Ranjbar, MR and Wu, Z and DiCarlo, J and Wang, Y},
title = {Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller.},
journal = {BMC genomics},
volume = {18},
number = {1},
pages = {5},
pmid = {28049435},
issn = {1471-2164},
mesh = {*Alleles ; *Base Sequence ; Computational Biology/methods ; *DNA Barcoding, Taxonomic ; *Gene Frequency ; *Genetic Variation ; Models, Statistical ; Multiplex Polymerase Chain Reaction ; Reproducibility of Results ; Sensitivity and Specificity ; },
abstract = {BACKGROUND: Detection of DNA mutations at very low allele fractions with high accuracy will significantly improve the effectiveness of precision medicine for cancer patients. To achieve this goal through next generation sequencing, researchers need a detection method that 1) captures rare mutation-containing DNA fragments efficiently in the mix of abundant wild-type DNA; 2) sequences the DNA library extensively to deep coverage; and 3) distinguishes low level true variants from amplification and sequencing errors with high accuracy. Targeted enrichment using PCR primers provides researchers with a convenient way to achieve deep sequencing for a small, yet most relevant region using benchtop sequencers. Molecular barcoding (or indexing) provides a unique solution for reducing sequencing artifacts analytically. Although different molecular barcoding schemes have been reported in recent literature, most variant calling has been done on limited targets, using simple custom scripts. The analytical performance of barcode-aware variant calling can be significantly improved by incorporating advanced statistical models.<br><br>RESULTS: We present here a highly efficient, simple and scalable enrichment protocol that integrates molecular barcodes in multiplex PCR amplification. In addition, we developed smCounter, an open source, generic, barcode-aware variant caller based on a Bayesian probabilistic model. smCounter was optimized and benchmarked on two independent read sets with SNVs and indels at 5 and 1% allele fractions. Variants were called with very good sensitivity and specificity within coding regions.<br><br>CONCLUSIONS: We demonstrated that we can accurately detect somatic mutations with allele fractions as low as 1% in coding regions using our enrichment protocol and variant caller.},
}
@article {pmid28044459,
year = {2017},
author = {Qiu, D and Cook, CE and Yue, Q and Hu, J and Wei, X and Chen, J and Liu, D and Wu, K},
title = {Species-level identification of the blowfly Chrysomya megacephala and other Diptera in China by DNA barcoding.},
journal = {Genome},
volume = {60},
number = {2},
pages = {158-168},
doi = {10.1139/gen-2015-0174},
pmid = {28044459},
issn = {1480-3321},
mesh = {Animals ; Biodiversity ; China ; *DNA Barcoding, Taxonomic ; Diptera/*classification/*genetics ; Electron Transport Complex IV/genetics ; Genetic Variation ; Geography ; Phylogeny ; },
abstract = {The blowfly Chrysomya megacephala, or oriental latrine fly, is the most common human-associated fly of the oriental and Australasian regions. Chrysomya megacephala is of particular interest for its use in forensic entomology and because it is a disease vector. The larvae are economically important as feed for livestock and in traditional Chinese medicine. Identification of adults is straightforward, but larvae and fragments of adults are difficult to identify. We collected C. megacephala, its allies Chrysomya pinguis and Protophormia terraenovae, as well as flies from 11 other species from 52 locations around China, then sequenced 658 base pairs of the COI barcode region from 645 flies of all 14 species, including 208 C. megacephala, as the basis of a COI barcode library for flies in China. While C. megacephala and its closest relative C. pinguis are closely related (mean K2P divergence of 0.022), these species are completely non-overlapping in their barcode divergences, thus demonstrating the utility of the COI barcode region for the identification of C. megacephala. We combined the 208 C. megacephala sequences from China with 98 others from public databases and show that worldwide COI barcode diversity is low, with 70% of all individuals belonging to one of three haplotypes that differ by one or two substitutions from each other, reflecting recent anthropogenic dispersal from its native range in Eurasia.},
}
@article {pmid28044453,
year = {2017},
author = {Lobo, J and Ferreira, MS and Antunes, IC and Teixeira, MA and Borges, LM and Sousa, R and Gomes, PA and Costa, MH and Cunha, MR and Costa, FO},
title = {Contrasting morphological and DNA barcode-suggested species boundaries among shallow-water amphipod fauna from the southern European Atlantic coast.},
journal = {Genome},
volume = {60},
number = {2},
pages = {147-157},
doi = {10.1139/gen-2016-0009},
pmid = {28044453},
issn = {1480-3321},
mesh = {Amphipoda/*anatomy &amp; histology/classification/*genetics ; Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; Electron Transport Complex IV/genetics ; Europe ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Geography ; Phylogeny ; },
abstract = {In this study we compared DNA barcode-suggested species boundaries with morphology-based species identifications in the amphipod fauna of the southern European Atlantic coast. DNA sequences of the cytochrome c oxidase subunit I barcode region (COI-5P) were generated for 43 morphospecies (178 specimens) collected along the Portuguese coast which, together with publicly available COI-5P sequences, produced a final dataset comprising 68 morphospecies and 295 sequences. Seventy-five BINs (Barcode Index Numbers) were assigned to these morphospecies, of which 48 were concordant (i.e., 1 BIN = 1 species), 8 were taxonomically discordant, and 19 were singletons. Twelve species had matching sequences (<2% distance) with conspecifics from distant locations (e.g., North Sea). Seven morphospecies were assigned to multiple, and highly divergent, BINs, including specimens of Corophium multisetosum (18% divergence) and Dexamine spiniventris (16% divergence), which originated from sampling locations on the west coast of Portugal (only about 36 and 250 km apart, respectively). We also found deep divergence (4%-22%) among specimens of seven species from Portugal compared to those from the North Sea and Italy. The detection of evolutionarily meaningful divergence among populations of several amphipod species from southern Europe reinforces the need for a comprehensive re-assessment of the diversity of this faunal group.},
}
@article {pmid28031795,
year = {2016},
author = {Hambäck, PA and Weingartner, E and Dalén, L and Wirta, H and Roslin, T},
title = {Spatial subsidies in spider diets vary with shoreline structure: Complementary evidence from molecular diet analysis and stable isotopes.},
journal = {Ecology and evolution},
volume = {6},
number = {23},
pages = {8431-8439},
pmid = {28031795},
issn = {2045-7758},
abstract = {Inflow of matter and organisms may strongly affect the local density and diversity of organisms. This effect is particularly evident on shores where organisms with aquatic larval stages enter the terrestrial food web. The identities of such trophic links are not easily estimated as spiders, a dominant group of shoreline predator, have external digestion. We compared trophic links and the prey diversity of spiders on different shore types along the Baltic Sea: on open shores and on shores with a reed belt bordering the water. A priori, we hypothesized that the physical structure of the shoreline reduces the flow between ecosystem and the subsidies across the sea-land interface. To circumvent the lack of morphologically detectable remains of spider prey, we used a combination of stable isotope and molecular gut content analyses. The two tools used for diet analysis revealed complementary information on spider diets. The stable isotope analysis indicated that spiders on open shores had a marine signal of carbon isotopes, while spiders on reedy shores had a terrestrial signal. The molecular analysis revealed a diverse array of dipteran and lepidopteran prey, where spiders on open and reedy shores shared a similar diet with a comparable proportion of chironomids, the larvae of which live in the marine system. Comparing the methods suggests that differences in isotope composition of the two spider groups occurred because of differences in the chironomid diets: as larvae, chironomids of reedy shores likely fed on terrestrial detritus and acquired a terrestrial isotope signature, while chironomids of open shores utilized an algal diet and acquired a marine isotope signature. Our results illustrate how different methods of diet reconstruction may shed light on complementary aspects of nutrient transfer. Overall, they reveal that reed belts can reduce connectivity between habitats, but also function as a source of food for predators.},
}
@article {pmid28029226,
year = {2017},
author = {Lyra, ML and Haddad, CFB and de Azeredo-Espin, AML},
title = {Meeting the challenge of DNA barcoding Neotropical amphibians: polymerase chain reaction optimization and new COI primers.},
journal = {Molecular ecology resources},
volume = {17},
number = {5},
pages = {966-980},
doi = {10.1111/1755-0998.12648},
pmid = {28029226},
issn = {1755-0998},
mesh = {Amphibians/*classification/*genetics ; Animals ; Brazil ; DNA Barcoding, Taxonomic/*methods ; *DNA Primers ; Electron Transport Complex IV/*genetics ; Polymerase Chain Reaction/*methods ; },
abstract = {Amphibians are one of the most threatened vertebrate classes, yet at the same time new species are being described every year, demonstrating that the number of existing species is grossly underestimated. In groups such as amphibians, with high extinction rates and poorly known species boundaries, DNA barcoding is a tool that can rapidly assess genetic diversity and estimate species richness for prioritizing conservation decisions. However, reliable recovery of the 5' region of the cytochrome c oxidase subunit 1 (COI) gene is critical for the ongoing effort to gather DNA barcodes for all amphibian species. Here, we provide new PCR conditions and tested new primers that increase the efficiency of barcode recovery in amphibians. We found that a low extension temperature for PCR cycles significantly improves the efficiency of amplification for all combinations of primers. Combining low PCR extension temperature and primers AnF1 + AnR1, we were able to recover COI sequences for 100% of the species analysed (N = 161), encompassing ~15% of the species known from Brazil (representing 77 genera and 23 families), which is an important improvement over previous studies. The preliminary assessment of species diversity suggested that number of species might be underestimated by about 25%. We conclude that DNA barcoding is an efficient, simple, and standardized protocol for identifying cryptic diversity in amphibians and advocate for its use in biodiversity inventories and across widespread populations within known species.},
}
@article {pmid28028141,
year = {2017},
author = {Jewiss-Gaines, A and Barelli, L and Hunter, FF},
title = {First Records of Culicoides sonorensis (Diptera: Ceratopogonidae), a Known Vector of Bluetongue Virus, in Southern Ontario.},
journal = {Journal of medical entomology},
volume = {54},
number = {3},
pages = {757-762},
doi = {10.1093/jme/tjw215},
pmid = {28028141},
issn = {1938-2928},
mesh = {*Animal Distribution ; Animals ; Base Sequence ; Bluetongue virus/physiology ; Ceratopogonidae/genetics/*physiology ; Insect Proteins/*genetics ; Insect Vectors/genetics/*physiology ; Introns ; Ontario ; Peptide Elongation Factor 1/*genetics ; },
abstract = {Ceratopogonidae (Diptera) were collected on sheep farms in southern Ontario to establish whether Culicoides spp. pose a threat to the livestock industry. Specimens were collected in modified CO2-baited Centers for Disease Control and Prevention light traps, returned to the laboratory, freeze-killed, and identified to species under a microscope. In addition to Culicoides variipennis (Coquillet), we found that Culicoides sonorensis Wirth &amp; Jones occurred on a number of farms over a 2-yr period. These records represent a significant departure from C. sonorensis' previously known geographical distribution. We present spatial and temporal distribution data for both species, with an emphasis on C. sonorensis. DNA sequence information is presented so that researchers lacking the necessary taxonomic skills can determine whether C. sonorensis is present in their collections. To differentiate C. sonorensis from C. variipennis, taxonomically reliable and informative traits were found in EF1α and, to a lesser extent, in ITS1, whereas the universal barcode region of cytochrome oxidase subunit 1 (CO1) was unsuitable.},
}
@article {pmid28024146,
year = {2017},
author = {van Arensbergen, J and FitzPatrick, VD and de Haas, M and Pagie, L and Sluimer, J and Bussemaker, HJ and van Steensel, B},
title = {Genome-wide mapping of autonomous promoter activity in human cells.},
journal = {Nature biotechnology},
volume = {35},
number = {2},
pages = {145-153},
pmid = {28024146},
issn = {1546-1696},
support = {R01 HG003008/HG/NHGRI NIH HHS/United States ; S10 OD021764/OD/NIH HHS/United States ; T32 GM008281/GM/NIGMS NIH HHS/United States ; 293662/ERC_/European Research Council/International ; T32 GM008798/GM/NIGMS NIH HHS/United States ; },
mesh = {Chromosome Mapping/*methods ; DNA/genetics ; Gene Library ; Genome, Human/*genetics ; Humans ; K562 Cells ; Promoter Regions, Genetic/*genetics ; Sequence Analysis, DNA/*methods ; *Transcription Initiation, Genetic ; Transcriptional Activation/*genetics ; },
abstract = {Previous methods to systematically characterize sequence-intrinsic activity of promoters have been limited by relatively low throughput and the length of the sequences that could be tested. Here we present 'survey of regulatory elements' (SuRE), a method that assays more than 10[8] DNA fragments, each 0.2-2 kb in size, for their ability to drive transcription autonomously. In SuRE, a plasmid library of random genomic fragments upstream of a 20-bp barcode is constructed, and decoded by paired-end sequencing. This library is used to transfect cells, and barcodes in transcribed RNA are quantified by high-throughput sequencing. When applied to the human genome, we achieve 55-fold genome coverage, allowing us to map autonomous promoter activity genome-wide in K562 cells. By computational modeling we delineate subregions within promoters that are relevant for their activity. We show that antisense promoter transcription is generally dependent on the sense core promoter sequences, and that most enhancers and several families of repetitive elements act as autonomous transcription initiation sites.},
}
@article {pmid28018653,
year = {2016},
author = {Lim, NK and Tay, YC and Srivathsan, A and Tan, JW and Kwik, JT and Baloğlu, B and Meier, R and Yeo, DC},
title = {Next-generation freshwater bioassessment: eDNA metabarcoding with a conserved metazoan primer reveals species-rich and reservoir-specific communities.},
journal = {Royal Society open science},
volume = {3},
number = {11},
pages = {160635},
pmid = {28018653},
issn = {2054-5703},
abstract = {Freshwater habitats are of high conservation value and provide a wide range of ecosystem services. Effective management requires regular monitoring. However, conventional methods based on direct observation or specimen collection are so invasive, expensive and labour-intensive that frequent monitoring is uncommon. Here, we test whether the evaluation of environmental DNA (eDNA) from water based on a simple protocol can be used for assessing biodiversity. We use universal metazoan primers for characterizing water eDNA across horizontal and vertical spatial dimensions in two reservoirs with known species diversity for two key taxa. eDNA obtained directly from 42 samples × 15 ml water (total = 630 ml) per reservoir yielded DNA signatures for more than 500 metazoan species, of which 105 could be identified to species/genus based on DNA barcodes. We show that eDNA can be used to assign each water sample to its reservoir of origin, and that eDNA outperforms conventional survey methods in single-sample richness comparisons, while revealing evidence for hundreds of unknown species that are undetected by conventional bioassessment methods. eDNA also confirms the presence of a recently discovered invasive snail species and provides evidence for the continued survival of a rare native species of goby not sighted in that habitat since 2007. eDNA thus promises to be a useful addition to the bioassessment toolbox for freshwater systems.},
}
@article {pmid28018624,
year = {2016},
author = {Brasier, MJ and Wiklund, H and Neal, L and Jeffreys, R and Linse, K and Ruhl, H and Glover, AG},
title = {DNA barcoding uncovers cryptic diversity in 50% of deep-sea Antarctic polychaetes.},
journal = {Royal Society open science},
volume = {3},
number = {11},
pages = {160432},
pmid = {28018624},
issn = {2054-5703},
abstract = {The Antarctic marine environment is a diverse ecosystem currently experiencing some of the fastest rates of climatic change. The documentation and management of these changes requires accurate estimates of species diversity. Recently, there has been an increased recognition of the abundance and importance of cryptic species, i.e. those that are morphologically identical but genetically distinct. This article presents the largest genetic investigation into the prevalence of cryptic polychaete species within the deep Antarctic benthos to date. We uncover cryptic diversity in 50% of the 15 morphospecies targeted through the comparison of mitochondrial DNA sequences, as well as 10 previously overlooked morphospecies, increasing the total species richness in the sample by 233%. Our ability to describe universal rules for the detection of cryptic species within polychaetes, or normalization to expected number of species based on genetic data is prevented by taxon-specific differences in phylogenetic outputs and genetic variation between and within potential cryptic species. These data provide the foundation for biogeographic and functional analysis that will provide insight into the drivers of species diversity and its role in ecosystem function.},
}
@article {pmid28011296,
year = {2017},
author = {Nitsche, F and Thomsen, HA and Richter, DJ},
title = {Bridging the gap between morphological species and molecular barcodes - Exemplified by loricate choanoflagellates.},
journal = {European journal of protistology},
volume = {57},
number = {},
pages = {26-37},
doi = {10.1016/j.ejop.2016.10.006},
pmid = {28011296},
issn = {1618-0429},
mesh = {Biodiversity ; Choanoflagellata/classification/*cytology/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Ribosomal/genetics ; Phylogeny ; Species Specificity ; },
abstract = {Translating the vast amounts of molecular barcodes from global surveys of microbial eukaryotes into ecological insight depends critically on a well-curated reference database with adequate taxonomic coverage. In this respect, the choanoflagellates resemble other eukaryotic lineages: reasonable coverage at higher taxonomic levels, but missing diversity at the species level. The acanthoecid (loricate) choanoflagellates are well-characterized morphologically, with over 115 species described, but less than 10% with any sequence data. Because lorica shape is species-specific, the acanthoecids represent an opportunity to link morphological with molecular data within a lineage of eukaryotes. To match morphospecies to sequences, we sampled the Kattegat and the Isefjord in Denmark in September 2014 and February 2015. We identified 45 morphospecies and sequenced ribosomal DNA of nine previously unsequenced species, roughly doubling the number of acanthoecid species with sequence data, including the first data representing five genera: Bicosta, Calliacantha, Cosmoeca, Crinolina and Pleurasiga. Our phylogenetic analysis is mainly congruent with morphology-based systematics. Five of the newly sequenced species match a previously unidentified barcode from Tara Oceans, providing access to the global distribution of species isolated from Danish waters. One species, Calliacantha natans, is the second most globally abundant choanoflagellate present in Tara Oceans. Our project translating new ribosomal DNA sequences to distributions of described species on a global scale supports the approach linking morphology to molecular barcodes for microbial eukaryote ecology.},
}
@article {pmid28004880,
year = {2017},
author = {Kamil Reza, K and Wang, J and Vaidyanathan, R and Dey, S and Wang, Y and Trau, M},
title = {Electrohydrodynamic-Induced SERS Immunoassay for Extensive Multiplexed Biomarker Sensing.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {13},
number = {9},
pages = {},
doi = {10.1002/smll.201602902},
pmid = {28004880},
issn = {1613-6829},
mesh = {Biomarkers, Tumor/*blood ; Biosensing Techniques/*methods ; *Electricity ; ErbB Receptors/metabolism ; Humans ; *Hydrodynamics ; Immunoassay/*methods ; Spectrum Analysis, Raman ; },
abstract = {Cancer diagnosis and patient monitoring require sensitive and simultaneous measurement of multiple cancer biomarkers considering that single biomarker analysis present inadequate information on the underlying biological transformations. Thus, development of sensitive and selective assays for multiple biomarker detection might improve clinical diagnosis and expedite the treatment process. Herein, a microfluidic platform for the rapid, sensitive, and parallel detection of multiple cancer-specific protein biomarkers from complex biological samples is presented. This approach utilizes alternating current electrohydrodynamic-induced surface shear forces that provide exquisite control over fluid flow thereby enhancing target-sensor interactions and minimizing non-specific binding. Further, the use of surface-enhanced Raman scattering-based spectral encoding with individual barcodes for different targets enables specific and simultaneous detection of captured protein biomarkers. Using this approach, the specific and sensitive detection of clinically relevant biomarkers including human epidermal growth factor receptor 2 (HER2); Mucin 1, cell surface associated (MUC1); epidermal growth factor receptor; and Mucin 16, cell surface associated (MUC16) at concentrations as low as 10 fg mL[-1] in patient serum is demonstrated. Successful target detection from patient samples further demonstrates the potential of this current approach for the clinical diagnosis, which envisages a clinical translation for a rapid and sensitive appraisal of clinical samples in cancer diagnostics.},
}
@article {pmid28004878,
year = {2017},
author = {Sullivan, BK and Robinson, KL and Trevathan-Tackett, SM and Lilje, ES and Gleason, FH and Lilje, O},
title = {The First Isolation and Characterisation of the Protist Labyrinthula sp. in Southeastern Australia.},
journal = {The Journal of eukaryotic microbiology},
volume = {64},
number = {4},
pages = {504-513},
doi = {10.1111/jeu.12387},
pmid = {28004878},
issn = {1550-7408},
mesh = {Australia ; Climate Change ; DNA Barcoding, Taxonomic/*methods ; DNA, Algal/genetics ; DNA, Ribosomal/genetics ; Haplotypes ; Host-Parasite Interactions ; Magnoliopsida/*parasitology ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Stramenopiles/*classification/genetics/*isolation &amp; purification ; },
abstract = {As a result of anthropogenic influences and global climate change, emerging infectious marine diseases are thought to be increasingly more common and more severe than in the past. The aim of our investigation was to confirm the presence of Labyrinthula, the aetiological agent of the seagrass wasting disease, in Southeastern Australia and provide the first isolation and characterisation of this protist, in Australia. Colonies and individual cells were positively identified as Labyrinthula using published descriptions, diagrams, and photographs. Their identity was then confirmed using DNA barcoding of a region of the 18S rRNA gene. Species level identification of isolates was not possible as the taxonomy of the Labyrinthula is still poorly resolved. Still, a diversity of Labyrinthula was isolated from small sections of the southeast coast of Australia. The isolates were grouped into three haplotypes that are biogeographically restricted. These haplotypes are closely related to previously identified saprotrophic clades. The study highlights the need for further investigation into the global distribution of Labyrinthula, including phylogenetic pathogenicity and analysis of host-parasite interactions in response to stressors. Given the results of our analyses, it is prudent to continue research into disease and epidemic agents to better prepare researchers for potential future outbreaks.},
}
@article {pmid28002414,
year = {2016},
author = {Baseia, IG and Silva, BD and Ishikawa, NK and Soares, JV and França, IF and Ushijima, S and Maekawa, N and Martín, MP},
title = {Discovery or Extinction of New Scleroderma Species in Amazonia?.},
journal = {PloS one},
volume = {11},
number = {12},
pages = {e0167879},
pmid = {28002414},
issn = {1932-6203},
mesh = {Animals ; Basidiomycota/classification/genetics/*isolation &amp; purification ; Brazil ; DNA, Fungal/chemistry/isolation &amp; purification/metabolism ; Forests ; Phylogeny ; },
abstract = {The Amazon Forest is a hotspot of biodiversity harboring an unknown number of undescribed taxa. Inventory studies are urgent, mainly in the areas most endangered by human activities such as extensive dam construction, where species could be in risk of extinction before being described and named. In 2015, intensive studies performed in a few locations in the Brazilian Amazon rainforest revealed three new species of the genus Scleroderma: S. anomalosporum, S. camassuense and S. duckei. The two first species were located in one of the many areas flooded by construction of hydroelectric dams throughout the Amazon; and the third in the Reserva Florestal Adolpho Ducke, a protected reverse by the INPA. The species were identified through morphology and molecular analyses of barcoding sequences (Internal Transcribed Spacer nrDNA). Scleroderma anomalosporum is characterized mainly by the smooth spores under LM in mature basidiomata (under SEM with small, unevenly distributed granules, a characteristic not observed in other species of the genus), the large size of the basidiomata, up to 120 mm diameter, and the stelliform dehiscence; S. camassuense mainly by the irregular to stellate dehiscence, the subreticulated spores and the bright sulfur-yellow colour, and Scleroderma duckei mainly by the verrucose exoperidium, stelliform dehiscence, and verrucose spores. Description, illustration and affinities with other species of the genus are provided.},
}
@article {pmid27997843,
year = {2016},
author = {David, V and Archibald, JM},
title = {Evolution: Plumbing the Depths of Diplonemid Diversity.},
journal = {Current biology : CB},
volume = {26},
number = {24},
pages = {R1290-R1292},
doi = {10.1016/j.cub.2016.10.050},
pmid = {27997843},
issn = {1879-0445},
mesh = {*Biological Evolution ; Ecosystem ; Euglenozoa/*genetics/physiology ; Genetic Variation/*genetics ; Genome, Protozoan ; Genomics/methods ; },
abstract = {Environmental molecular sequence surveys have opened a window on the hidden riches of the microbial biosphere. Recent genetic 'barcoding' and single-cell genomics studies have provided a snapshot of the biology of diplonemids - abundant, diverse, marine heterotrophic protists whose ecological roles are becoming clearer.},
}
@article {pmid27994958,
year = {2016},
author = {Mishra, P and Kumar, A and Rodrigues, V and Shukla, AK and Sundaresan, V},
title = {Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae).},
journal = {PeerJ},
volume = {4},
number = {},
pages = {e2638},
pmid = {27994958},
issn = {2167-8359},
abstract = {PREMISE OF THE STUDY: The internal transcribed spacer (ITS) region is situated between 18S and 26S in a polycistronic rRNA precursor transcript. It had been proved to be the most commonly sequenced region across plant species to resolve phylogenetic relationships ranging from shallow to deep taxonomic levels. Despite several taxonomical revisions in Cassiinae, a stable phylogeny remains elusive at the molecular level, particularly concerning the delineation of species in the genera Cassia, Senna and Chamaecrista. This study addresses the comparative potential of ITS datasets (ITS1, ITS2 and concatenated) in resolving the underlying morphological disparity in the highly complex genera, to assess their discriminatory power as potential barcode candidates in Cassiinae.<br><br>METHODOLOGY: A combination of experimental data and an in-silico approach based on threshold genetic distances, sequence similarity based and hierarchical tree-based methods was performed to decipher the discriminating power of ITS datasets on 18 different species of Cassiinae complex. Lab-generated sequences were compared against those available in the GenBank using BLAST and were aligned through MUSCLE 3.8.31 and analysed in PAUP 4.0 and BEAST1.8 using parsimony ratchet, maximum likelihood and Bayesian inference (BI) methods of gene and species tree reconciliation with bootstrapping. DNA barcoding gap was realized based on the Kimura two-parameter distance model (K2P) in TaxonDNA and MEGA.<br><br>PRINCIPAL FINDINGS: Based on the K2P distance, significant divergences between the inter- and intra-specific genetic distances were observed, while the presence of a DNA barcoding gap was obvious. The ITS1 region efficiently identified 81.63% and 90% of species using TaxonDNA and BI methods, respectively. The PWG-distance method based on simple pairwise matching indicated the significance of ITS1 whereby highest number of variable (210) and informative sites (206) were obtained. The BI tree-based methods outperformed the similarity-based methods producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses.<br><br>CONCLUSION: The reticulated phylogenetic hypothesis using the ITS1 region mainly supported the relationship between the species of Cassiinae established by traditional morphological methods. The ITS1 region showed a higher discrimination power and desirable characteristics as compared to ITS2 and ITS1 + 2, thereby concluding to be the locus of choice. Considering the complexity of the group and the underlying biological ambiguities, the results presented here are encouraging for developing DNA barcoding as a useful tool for resolving taxonomical challenges in corroboration with morphological framework.},
}
@article {pmid27994608,
year = {2016},
author = {Li, Y and Tong, Y and Xing, F},
title = {DNA Barcoding Evaluation and Its Taxonomic Implications in the Recently Evolved Genus Oberonia Lindl. (Orchidaceae) in China.},
journal = {Frontiers in plant science},
volume = {7},
number = {},
pages = {1791},
pmid = {27994608},
issn = {1664-462X},
abstract = {The orchid genus Oberonia Lindl., is a taxonomically complex genus characterized by recent species radiations and many closely related species. All Oberonia species are under conservation as listed in the CITES and the IUCN Red List Categories and Criteria. Given its difficulties in taxonomy and conservation status, Oberonia is an excellent model for developing DNA barcodes. Three analytical methods and five DNA barcoding regions (rbcL, matK, trnH-psbA, ITS, and ITS2) were evaluated on 127 individuals representing 40 species and 1 variety of Oberonia from China. All the three plastid candidates tested (rbcL, matK, and trnH-psbA) have a lower discriminatory power than the nuclear regions (ITS and ITS2), and ITS had the highest resolution rate (82.14%). Two to four combinations of these gene sets were not better than the ITS alone, but when considering modes of inheritance, rbcL+ITS and matK+ITS were the best barcodes for identifying Oberonia species. Furthermore, the present barcoding system has many new insights in the current Oberonia taxonomy, such as correcting species identification, resolving taxonomic uncertainties, and the underlying presence of new or cryptic species in a genus with a complex speciation history.},
}
@article {pmid27992652,
year = {2017},
author = {Wade, RM and Sherwood, AR},
title = {Molecular determination of kleptoplast origins from the sea slug Plakobranchus ocellatus (Sacoglossa, Gastropoda) reveals cryptic bryopsidalean (Chlorophyta) diversity in the Hawaiian Islands.},
journal = {Journal of phycology},
volume = {53},
number = {3},
pages = {467-475},
doi = {10.1111/jpy.12503},
pmid = {27992652},
issn = {1529-8817},
mesh = {Algal Proteins/genetics ; Animals ; *Biodiversity ; Chlorophyta/*classification/genetics ; Chloroplast Proteins/*genetics ; Chloroplasts/genetics ; DNA Barcoding, Taxonomic ; Gastropoda/*physiology ; Hawaii ; Microalgae/*classification/genetics ; Ribulose-Bisphosphate Carboxylase/genetics ; *Symbiosis ; },
abstract = {The sacoglossan sea slug species complex Plakobranchus ocellatus is a common algivore throughout the tropical Pacific, including the Hawaiian Islands. Plakobranchus ocellatus is kleptoplastic-it sequesters and retains algal chloroplasts-a characteristic that can be exploited to molecularly characterize diminutive bryopsidalean algae that are typically difficult to locate, collect, and identify. Previous DNA barcode analyses of both P. ocellatus and its kleptoplasts have been conducted primarily in the western Pacific and have only minimally sampled the most eastern populations in the Hawaiian Islands. Using two chloroplast markers, rbcL and tufA, kleptoplast samples from an Oahu population of P. ocellatus were amplified and cloned to identify their algal sources. Plakobranchus ocellatus sequester chloroplasts from up to 11 bryopsidalean algal species, all but one being diminutive in thallus size. Notably, eight of the detected algal species were new records to the Hawaiian Islands. A sequestration preference study demonstrated that the O'ahu population of P. ocellatus preferentially sequesters chloroplasts from diminutive, epilithic taxa. Using coxI barcoding of P. ocellatus, we showed the O'ahu population to be part of a clade that includes sequences from the neighboring island Maui, Australia, and the Philippines. The use of P. ocellatus as a novel sampling tool allows the exploration of the green algal community diversity and composition at a fine scale.},
}
@article {pmid27992537,
year = {2016},
author = {Rossini, BC and Oliveira, CA and Melo, FA and Bertaco, VA and Astarloa, JM and Rosso, JJ and Foresti, F and Oliveira, C},
title = {Highlighting Astyanax Species Diversity through DNA Barcoding.},
journal = {PloS one},
volume = {11},
number = {12},
pages = {e0167203},
pmid = {27992537},
issn = {1932-6203},
mesh = {Animals ; Bayes Theorem ; Characidae/*classification/genetics ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; Genetic Variation ; Phylogeny ; Sequence Analysis, DNA/methods ; Species Specificity ; },
abstract = {DNA barcoding has been used extensively to solve taxonomic questions and identify new species. Neotropical fishes are found in a wide variety of shapes and sizes, with a large number of species yet to be described, many of which are very difficult to identify. Characidae is the most species-rich family of the Characiformes, and many of its genera are affected by taxonomic uncertainties, including the widely-distributed, species-rich genus Astyanax. In this study, we present an extensive analysis of Astyanax covering almost its entire area of occurrence, based on DNA barcoding. The use of different approaches (ABGD, GMYC and BIN) to the clustering of the sequences revealed ample consistency in the results obtained by the initial cutoff value of 2% divergence for putative species in the Neighbor-Joining analysis using the Kimura-2-parameter model. The results indicate the existence of five Astyanax lineages. Some groups, such as that composed by the trans-Andean forms, are mostly composed of well-defined species, and in others a number of nominal species are clustered together, hampering the delimitation of species, which in many cases proved impossible. The results confirm the extreme complexity of the systematics of the genus Astyanax and show that DNA barcoding can be an useful tool to address these complexes questions.},
}
@article {pmid27991489,
year = {2016},
author = {Cao, X and Liu, J and Chen, J and Zheng, G and Kuntner, M and Agnarsson, I},
title = {Rapid dissemination of taxonomic discoveries based on DNA barcoding and morphology.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {37066},
pmid = {27991489},
issn = {2045-2322},
mesh = {Animals ; Biodiversity ; China ; Classification/*methods ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Datasets as Topic ; Electron Transport Complex IV/genetics ; Female ; Gene Library ; Genitalia/anatomy &amp; histology ; *Information Dissemination ; Male ; Sequence Analysis, DNA ; Species Specificity ; Spiders/anatomy &amp; histology/*classification/genetics ; Taiwan ; },
abstract = {The taxonomic impediment is characterized by dwindling classical taxonomic expertise, and slow pace of revisionary work, thus more rapid taxonomic assessments are needed. Here we pair rapid DNA barcoding methods with swift assessment of morphology in an effort to gauge diversity, establish species limits, and rapidly disseminate taxonomic information prior to completion of formal taxonomic revisions. We focus on a poorly studied, but diverse spider genus, Pseudopoda, from East Asia. We augmented the standard barcoding locus (COI) with nuclear DNA sequence data (ITS2) and analyzed congruence among datasets and species delimitation methods for a total of 572 individuals representing 23 described species and many potentially new species. Our results suggest that a combination of CO1 + ITS2 fragments identify and diagnose species better than the mitochondrial barcodes alone, and that certain tree based methods yield considerably higher diversity estimates than the distance-based approaches and morphology. Combined, through an extensive field survey, we detect a twofold increase in species diversity in the surveyed area, at 42-45, with most species representing short range endemics. Our study demonstrates the power of biodiversity assessments and swift dissemination of taxonomic data through rapid inventory, and through a combination of morphological and multi-locus DNA barcoding diagnoses of diverse arthropod lineages.},
}
@article {pmid27990256,
year = {2016},
author = {Falade, MO and Opene, AJ and Benson, O},
title = {DNA barcoding of Clarias gariepinus, Coptodon zillii and Sarotherodon melanotheron from Southwestern Nigeria.},
journal = {F1000Research},
volume = {5},
number = {},
pages = {1268},
pmid = {27990256},
issn = {2046-1402},
abstract = {DNA barcoding has been adopted as a gold standard rapid, precise and unifying identification system for animal species and provides a database of genetic sequences that can be used as a tool for universal species identification. In this study, we employed mitochondrial genes 16S rRNA (16S) and cytochrome oxidase subunit I (COI) for the identification of some Nigerian freshwater catfish and Tilapia species. Approximately 655 bp were amplified from the 5' region of the mitochondrial cytochrome C oxidase subunit I (COI) gene whereas 570 bp were amplified for the 16S rRNA gene. Nucleotide divergences among sequences were estimated based on Kimura 2-parameter distances and the genetic relationships were assessed by constructing phylogenetic trees using the neighbour-joining (NJ) and maximum likelihood (ML) methods. Analyses of consensus barcode sequences for each species, and alignment of individual sequences from within a given species revealed highly consistent barcodes (99% similarity on average), which could be compared with deposited sequences in public databases. The nucleotide distance between species belonging to different genera based on COI ranged from 0.17% between Sarotherodonmelanotheron and Coptodon zillii to 0.49% between Clarias gariepinus and C. zillii, indicating that S. melanotheron and C. zillii are closely related. Based on the data obtained, the utility of COI gene was confirmed in accurate identification of three fish species from Southwest Nigeria.},
}
@article {pmid27990177,
year = {2016},
author = {More, RP and Mane, RC and Purohit, HJ},
title = {matK-QR classifier: a patterns based approach for plant species identification.},
journal = {BioData mining},
volume = {9},
number = {},
pages = {39},
pmid = {27990177},
issn = {1756-0381},
abstract = {BACKGROUND: DNA barcoding is widely used and most efficient approach that facilitates rapid and accurate identification of plant species based on the short standardized segment of the genome. The nucleotide sequences of maturaseK (matK) and ribulose-1, 5-bisphosphate carboxylase (rbcL) marker loci are commonly used in plant species identification. Here, we present a new and highly efficient approach for identifying a unique set of discriminating nucleotide patterns to generate a signature (i.e. regular expression) for plant species identification.<br><br>METHODS: In order to generate molecular signatures, we used matK and rbcL loci datasets, which encompass 125 plant species in 52 genera reported by the CBOL plant working group. Initially, we performed Multiple Sequence Alignment (MSA) of all species followed by Position Specific Scoring Matrix (PSSM) for both loci to achieve a percentage of discrimination among species. Further, we detected Discriminating Patterns (DP) at genus and species level using PSSM for the matK dataset. Combining DP and consecutive pattern distances, we generated molecular signatures for each species. Finally, we performed a comparative assessment of these signatures with the existing methods including BLASTn, Support Vector Machines (SVM), Jrip-RIPPER, J48 (C4.5 algorithm), and the Na&#xef;ve Bayes (NB) methods against NCBI-GenBank matK dataset.<br><br>RESULTS: Due to the higher discrimination success obtained with the matK as compared to the rbcL, we selected matK gene for signature generation. We generated signatures for 60 species based on identified discriminating patterns at genus and species level. Our comparative assessment results suggest that a total of 46 out of 60 species could be correctly identified using generated signatures, followed by BLASTn (34 species), SVM (18 species), C4.5 (7 species), NB (4 species) and RIPPER (3 species) methods As a final outcome of this study, we converted signatures into QR codes and developed a software matK-QR Classifier (http://www.neeri.res.in/matk_classifier/index.htm), which search signatures in the query matK gene sequences and predict corresponding plant species.<br><br>CONCLUSIONS: This novel approach of employing pattern-based signatures opens new avenues for the classification of species. In addition to existing methods, we believe that matK-QR Classifier would be a valuable tool for molecular taxonomists enabling precise identification of plant species.},
}
@article {pmid27988936,
year = {2017},
author = {Sherwood, AR and Dittbern, MN and Johnston, ET and Conklin, KY},
title = {A metabarcoding comparison of windward and leeward airborne algal diversity across the Ko'olau mountain range on the island of O'ahu, Hawai'i[1].},
journal = {Journal of phycology},
volume = {53},
number = {2},
pages = {437-445},
doi = {10.1111/jpy.12502},
pmid = {27988936},
issn = {1529-8817},
mesh = {Chlorophyta/classification/*genetics ; Cyanobacteria/classification/genetics ; DNA, Algal/genetics ; Ecosystem ; Hawaii ; },
abstract = {Airborne algae from sites on the windward (n = 3) and leeward (n = 3) sides of the Ko'olau Mountain range of O'ahu, Hawai'i, were sampled for a 16 d period during January and February 2015 using passive collection devices and were characterized using Illumina MiSeq sequencing of the universal plastid amplicon marker. Amplicons were assigned to 3,023 operational taxonomic units (OTUs), which included 1,189 cyanobacteria, 1,009 heterotrophic bacteria, and 304 Eukaryota (of which 284 were algae and land plants). Analyses demonstrated substantially more OTUs at windward than leeward O'ahu sites during the sampling period. Removal of nonalgal OTUs revealed a greater number of algal reads recovered from windward (839,853) than leeward sites (355,387), with the majority of these being cyanobacteria. The 1,234 total algal OTUs included cyanobacteria, diatoms, cryptophytes, brown algae, chlorophyte green algae, and charophyte green algae. A total of 208 algal OTUs were identified from leeward side samplers (including OTUs in common among samplers) and 1,995 algal OTUs were identified from windward samplers. Barcoding analyses of the most abundant algal OTUs indicated that very few were shared between the windward and leeward sides of the Ko'olau Mountains, highlighting the localized scale at which these airborne algae communities differ. Back trajectories of air masses arriving on O'ahu during the sampling period were calculated using the NOAA HY-SPLIT model and suggested that the sampling period was composed of three large-scale meteorological events, indicating a diversity of potential sources of airborne algae outside of the Hawaiian Islands.},
}
@article {pmid27988774,
year = {2016},
author = {Bañón, R and Arronte, JC and Armesto, &#xc1; and Barros-García, D and Carlos, A},
title = {Halosaur fishes (Notacanthiformes: Halosauridae) from Atlantic Spanish waters according to integrative taxonomy.},
journal = {Zootaxa},
volume = {4184},
number = {3},
pages = {zootaxa.4184.3.3},
doi = {10.11646/zootaxa.4184.3.3},
pmid = {27988774},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Atlantic Ocean ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry/genetics ; Fishes/anatomy &amp; histology/*classification/genetics ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Spain ; },
abstract = {From 2009 to 2011 thirty-five specimens belonging to six halosaurid species of the family Halosauridae were captured in two different locations in the northern waters of Spain. The specimens were identified as belonging to the genera Halosauropsis Collett, 1896, Halosaurus Johnson, 1864 and Aldrovandia Goode &amp; Bean, 1896, including the following species: Halosauropsis macrochir (Günther, 1878), Halosaurus ovenii Johnson, 1864, Halosaurus johnsonianus Vaillant, 1888, Aldrovandia affinis (Günther, 1877), Aldrovandia phalacra (Vaillant, 1888) and Aldrovandia oleosa Sulak, 1977. The morphometric measurements and meristic characters of these specimens are given. As a result, a new northern limit of distribution of A. oleosa from the northeastern Atlantic is reported. Using a taxonomical integrative approach, the mitochondrial DNA COI gene sequences from all individuals where determined and their comparison with morphological characters showed no incongruities. Among these specimens, the highest genetic distance within species was 0.8% while the lowest value between species was 3.3%. This ample barcoding gap has allowed the delimitation and assignment of all species reported in a way that matches the traditional taxonomical methods previously employed.},
}
@article {pmid27988719,
year = {2016},
author = {Furfaro, G and Picton, B and Martynov, A and Mariottini, P},
title = {Diaphorodoris alba Portmann &amp; Sandmeier, 1960 is a valid species: molecular and morphological comparison with D. luteocincta (M. Sars, 1870) (Gastropoda: Nudibranchia).},
journal = {Zootaxa},
volume = {4193},
number = {2},
pages = {zootaxa.4193.2.6},
doi = {10.11646/zootaxa.4193.2.6},
pmid = {27988719},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Atlantic Ocean ; Base Sequence ; Body Size ; DNA, Ribosomal/chemistry/genetics ; Gastropoda/*anatomy &amp; histology/classification/*genetics/growth &amp; development ; Mediterranean Sea ; Molecular Sequence Data ; Organ Size ; Phylogeny ; },
abstract = {The nudibranch Diaphorodoris luteocincta (M. Sars, 1870) shows two colour morphotypes defined as D. luteocincta var. alba and D. luteocincta var. reticulata, which are easy to identify and which share an overlapping distribution in the Mediterranean Sea and the North-Eastern Atlantic Ocean. Their systematics has long been discussed by several authors until recently when a molecular study proposed the two varieties as intraspecific colour variability occurring within D. luteocincta species. In order to solve their ranking status, we have carried out a morphological study on anatomical characters and molecular analyses on the mitochondrial markers (COI and 16S rDNA) and the nuclear H3 gene. Results proved the usefulness of the integrative taxonomy approach in assessing species delimitation; in fact Diaphorodoris alba stat. nov. and D. luteocincta were revealed to be two different species. D. luteocincta var. reticulata is confirmed as synonym of D. luteocincta s.str. A hypothesis on phylogenetic relationship among most of the currently recognised species of the genus Diaphorodoris Iredale &amp; O'Donoghue, 1923 is also here presented.},
}
@article {pmid27988704,
year = {2016},
author = {Cruz, IN and Nuñeza, OM and Lin, CP},
title = {Description of a new Oriental stonefly species, Phanoperla constanspina (Plecoptera: Perlidae) from Mindanao, Philippines and association of life stages using DNA barcoding.},
journal = {Zootaxa},
volume = {4193},
number = {1},
pages = {zootaxa.4193.1.4},
doi = {10.11646/zootaxa.4193.1.4},
pmid = {27988704},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; DNA/genetics ; DNA Barcoding, Taxonomic ; Ecosystem ; Female ; Insecta/*anatomy &amp; histology/*classification/genetics/growth &amp; development ; Male ; Organ Size ; Philippines ; },
abstract = {A new perlid stonefly, Phanoperla constanspina sp. nov. is described from Mt. Malindang, northern Mindanao, Philippines. The male of the new species is distinguished by lacking lobes on penial sac and large black spines at the penial apex. The female is distinguished by the egg. DNA barcoding was used to associate male, female, and nymphal specimens with 0% divergence. Morphological variation was observed in the shape of the hemitergal anterior processes and the 9th tergal setal patches of male adult and body pigmentation of the nymph. A key to the Philippine Phanoperla species and a checklist of Oriental Phanoperla are also provided.},
}
@article {pmid27988652,
year = {2016},
author = {Zawierucha, K and Kolicka, M and Kaczmarek, &#x141;},
title = {Re-description of the Arctic tardigrade Tenuibiotus voronkovi (Tumanov, 2007 (Eutardigrada; Macrobiotidea), with the first molecular data for the genus.},
journal = {Zootaxa},
volume = {4196},
number = {4},
pages = {zootaxa.4196.4.2},
doi = {10.11646/zootaxa.4196.4.2},
pmid = {27988652},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Ovum ; Species Specificity ; Svalbard ; Tardigrada/*anatomy &amp; histology/*classification/genetics ; },
abstract = {Tardigrada is phylum of micrometazoans widely distributed throughout the world, because of old descriptions and insufficient morphometric data, many species currently need revision and re-description. Tenuibiotus voronkovi (Tumanov, 2007) is tardigrade previously only recorded from the Svalbard archipelago. This species' original description was based on two individuals with destroyed claws on the fourth pair of legs and a lack of complete morphometric data for buccal tube and claws. In this paper, we present a re-description of T. voronkovi, supplementing the original description using the original paratype and additional material from Svalbard: Spitsbergen, Nordaustlandet and Edgeøya. This species is characterised by two macroplacoids and a microplacoid, claws of Tenuibiotus type, dentate lunules under claw IV, and faint granulation on legs I-III and strong granulation on the legs IV. We include a new morphological description with microphotographs, morphometric, and molecular data (including: mitochondrial cytochrome c oxidase subunit I (COI), internal transcribed spacers (ITS1-5.8S rDNA-ITS2), and nuclear ribosome subunits 28S rRNA and 18S rRNA). These are the first published molecular data for the genus Tenuibiotus Pilato and Lisi, 2011, analysis of which indicated an affiliation of Tenuibiotus to the family Macrobiotidae. We found no differences in body size between individuals from different islands (Nordaustlandet and Edgeøya), but did observe variability in the eggs. After revision of the literature and the published figures, we concluded that Dastych's (1985) report of T. willardi (Pilato, 1976) from Svalbard, was actually T. voronkovi, which has the greater distribution in Svalbard, and other Arctic locations, than previously believed.},
}
@article {pmid27988644,
year = {2016},
author = {Khalaji-Pirbalouty, V and Raupach, MJ},
title = {DNA barcoding and morphological studies confirm the occurrence of three Atarbolana (Crustacea: Isopoda: Cirolanidae) species along the coastal zone of the Persian Gulf and Gulf of Oman.},
journal = {Zootaxa},
volume = {4200},
number = {1},
pages = {zootaxa.4200.1.7},
doi = {10.11646/zootaxa.4200.1.7},
pmid = {27988644},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Female ; Indian Ocean ; Isopoda/anatomy &amp; histology/*classification/genetics ; Male ; },
abstract = {Two species of Atarbolana (Cirolanidae: Isopoda) from the intertidal zone of the Gulf of Oman and the Persian Gulf were studied and redescribed. The known distribution of this small genus is limited to the northern areas of the Indian Ocean, from the Pakistan coasts to the Persian Gulf. The analyses of DNA barcodes as well as detailed morphological studies clearly support the existence of three distinct Atarbolana species along the coastal zone of the Persian Gulf and northern Arabian Sea. Furthermore, A. dasycolus Yasmeen, 2004 is synonymized with A. setosa Javed and Yasmeen, 1989.},
}
@article {pmid27988638,
year = {2016},
author = {Silva, GS and Melo, BF and Oliveira, C and Benine, RC},
title = {Revision of the South American genus Tetragonopterus Cuvier, 1816 (Teleostei: Characidae) with description of four new species.},
journal = {Zootaxa},
volume = {4200},
number = {1},
pages = {zootaxa.4200.1.1},
doi = {10.11646/zootaxa.4200.1.1},
pmid = {27988638},
issn = {1175-5334},
mesh = {Animals ; Characidae/anatomy &amp; histology/*classification ; Female ; Male ; Phylogeny ; Rivers ; South America ; },
abstract = {The systematics of the characid genus Tetragonopterus is reviewed based on morphological and molecular data of specimens from its entire geographical range encompassing all major South American river drainages from Orinoco basin southward to the La Plata basin. Eight previously described species (T. anostomus, T. araguaiensis, T. argenteus, T. carvalhoi, T. chalceus, T. denticulatus, T. georgiae n. comb., and T. rarus) are recognized as valid, four of which are redescribed (T. argenteus, T. chalceus, T. georgiae, and T. rarus), and four new species from the Brazilian Shield in the Amazon and São Francisco river basins are herein described. We also provide evidence for the reallocation of Moenkhausia georgiae into Tetragonopterus and recognize T. akamai as junior synonym of T. anostomus. DNA barcodes of Tetragonopterus revealed genetic support for each recognized species and provided valuable population-level information within T. argenteus, T. chalceus, T. georgiae, and T. rarus.},
}
@article {pmid27988605,
year = {2016},
author = {Jiang, N and Stüning, D and Xue, D and Han, H},
title = {Revision of the genus Metaterpna Yazaki, 1992 (Lepidoptera, Geometridae, Geometrinae), with description of a new species from China.},
journal = {Zootaxa},
volume = {4200},
number = {4},
pages = {zootaxa.4200.4.3},
doi = {10.11646/zootaxa.4200.4.3},
pmid = {27988605},
issn = {1175-5334},
mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; Female ; Male ; Moths/anatomy &amp; histology/*classification/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The genus Metaterpna is revised. The two species known, M. differens (Warren, 1909) and M. thyatiraria (Oberthür, 1913), are redescribed, with emphasis on the considerable variability of M. thyatiraria, and the status of the related type specimen was discussed. In addition, one new species, M. batangensis sp. nov., is described from Batang and Daocheng, Sichuan province, and Lijiang, Yunnan province, southwestern China. M. thyatiraria and M. batangensis show clear distance by DNA barcode sequences. Illustrations of moths and genitalia are presented.},
}
@article {pmid27988576,
year = {2016},
author = {Grebennikov, VV},
title = {Flightless Catapionus (Coleoptera: Curculionidae: Entiminae) in Southwest China survive the Holocene trapped on mountaintops: new species, unknown phylogeny and clogging taxonomy.},
journal = {Zootaxa},
volume = {4205},
number = {3},
pages = {zootaxa.4205.3.4},
doi = {10.11646/zootaxa.4205.3.4},
pmid = {27988576},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Asia ; Body Size ; China ; DNA, Mitochondrial/genetics ; Ecosystem ; Female ; Male ; Organ Size ; *Phylogeny ; Weevils/anatomy &amp; histology/*classification/genetics/growth &amp; development ; },
abstract = {This paper reports the first discovery of the weevil genus Catapionus in Southwest China. Eighteen specimens of C. mopsus sp.n. were collected in two high altitude localities some 360 km apart: Mt. Haba in Yunnan (the type locality) at 4,158-4,195 m and Mt. Gongga in Sichuan at 3,533-4,143 m. Habitus and genitalia of a male and a female from each locality are extensively illustrated. Six specimens from each locality were DNA barcoded (dx.doi.org/10.5883/DS-CATAPCH). Taxonomic validation of the new species name was made by referring to high quality illustrations of the holotype and to its DNA barcode, and without providing a customary verbal description. This novel approach was chosen partly due to the redundancy of description in the presence of high quality images, and partly due to the lack of adequate and unambiguously identified comparative material. Analysis of mtDNA sequences dated the separation of both geographical populations at about 3.65 Ma. The disjunct distribution of Catapionus in Asia is discussed and mapped for the first time. Monophyly and internal relationships of the genus are discussed and remain untested, together with the generic assignment to the phylogenetically vague Cneorhinini and/or Dermatodini. Discovery of the southernmost members of Catapionus high in the mountains of Southwest China evokes a hypothesis on interglacial refugia. A new term "clogging taxonomy" is introduced for situations as encountered in Catapionus when an abundance of obscure historical species-group names impedes further research.},
}
@article {pmid27988533,
year = {2016},
author = {Stec, D and Morek, W and Gąsiorek, P and Kaczmarek, &#x141; and Michalczyk, &#x141;},
title = {Determinants and taxonomic consequences of extreme egg shell variability in Ramazzottius subanomalus (Biserov, 1985) (Tardigrada).},
journal = {Zootaxa},
volume = {4208},
number = {2},
pages = {zootaxa.4208.2.5},
doi = {10.11646/zootaxa.4208.2.5},
pmid = {27988533},
issn = {1175-5334},
mesh = {Animals ; Classification ; Egg Shell/*anatomy &amp; histology ; Female ; Genotype ; Species Specificity ; Tardigrada/*anatomy &amp; histology/*classification/genetics ; },
abstract = {Nearly a half of known eutardigrade species lay ornamented eggs. The ornamentation is thought to provide attachment of the egg to the substrate and protection for the developing embryo, but from the taxonomic point of view chorion morphology may also provide key characters for species differentiation and identification, especially between closely related taxa. Nonetheless, despite the evolutionary and taxonomic importance of the egg shell, the determinants of its morphology are very poorly, if at all, understood. Here, we combine morphological, molecular and experimental approaches in an attempt to separate the genetic and environmental factors that shape egg chorion morphology in Ramazzottius subanomalus (Biserov, 1985). Our integrative study, based on a population of R. subanomalus isolated from a single moss sample, revealed (1) remarkable variation in egg shell morphology, but (2) relatively little variation in animal morphometric traits, and (3) genetic differentiation, expressed as two ITS-2 haplotypes, but no parallel polymorphism in COI. Although animals did not differ morphometrically between the haplotypes, eggs laid by haplotype 1 and 2 females exhibited highly statistically significant differences in all measured traits. The study demonstrates, for the first time, a correlation between phenotypic and genetic variability within a tardigrade species. The revealed congruence between genetic and morphological traits might be viewed as an example of incipient speciation that illustrates early evolutionary steps leading to species complexes that differ primarily in terms of egg shell morphology. Moreover, our data confirm the value of the ITS-2 fragment in distinguishing very closely related tardigrade lineages.},
}
@article {pmid27988531,
year = {2016},
author = {Heiss, E and Grebennikov, V},
title = {Monophyly, review, six new species and DNA barcode of micropterous Afromontane Afropictinus (Heteroptera: Aradidae).},
journal = {Zootaxa},
volume = {4208},
number = {2},
pages = {zootaxa.4208.2.3},
doi = {10.11646/zootaxa.4208.2.3},
pmid = {27988531},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; *DNA Barcoding, Taxonomic ; Heteroptera/*anatomy &amp; histology/*classification/genetics ; Rwanda ; Species Specificity ; },
abstract = {The micropterous East African flat bug genus Afropictinus Heiss, 1986 (Heteroptera: Aradidae: Mezirinae) is revised. In addition to the type and only known species A. congoensis (Hoberlandt, 1956) from Rwanda, four new species from Tanzania (A. castor sp. nov., A. hylas sp. nov., A. idas sp. nov., A. nauplius sp. nov.), one new species from the Democratic Republic of the Congo (A. kahuzianus sp. nov.), and one new species from Ethiopia (A. nabu sp. nov.) are described and illustrated. An identification key is presented to all seven nominal species of Afropictinus. DNA barcodes of 28 individuals of Afropictinus species were newly generated and together with 12 sequences of other Aradidae were made publicly available at dx.doi.org/10.5883/DS-AFROPICT. These mtDNA sequences were analyzed phylogenetically using Maximum Likelihood approach with 500 bootstraps. Obtained topology reveals a monophyletic Afropictinus with high statistical support (84%), although its sister group remains elusive. Both specimens of non-Tanzanian Afropictinus species included in the study (A. kahuzianus and A. nabu) were nested among Tanzanian congeners. The internal clades within Afropictinus, except for those at species and population level, had lesser statistical support. Despite of intense sampling, no Afropictinus species was found in mountain forests of geologically young (<2 Ma) volcanic highlands of the Ngorongoro-Kilimanjaro Volcanic Belt, which suggest reduced dispersal capacities.},
}
@article {pmid27987268,
year = {2017},
author = {Carew, ME and Metzeling, L and St Clair, R and Hoffmann, AA},
title = {Detecting invertebrate species in archived collections using next-generation sequencing.},
journal = {Molecular ecology resources},
volume = {17},
number = {5},
pages = {915-930},
doi = {10.1111/1755-0998.12644},
pmid = {27987268},
issn = {1755-0998},
mesh = {Animals ; Aquatic Organisms ; *Body Remains ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing ; Invertebrates/*classification/*genetics ; Metagenomics/*methods ; *Preservation, Biological ; },
abstract = {Invertebrate biodiversity measured at mostly family level is widely used in biological monitoring programmes to assess anthropogenic impacts on ecosystems. However, next-generation sequencing (NGS) could allow development of new more sensitive biomonitoring tools by allowing rapid species identification. This could be accelerated if archived invertebrate collections and environmental information from past programmes are used to understand species distributions and their environmental responses. In this study, we take archived macroinvertebrate samples from two sites collected on multiple occasions and test whether NGS can successfully detect species. Samples had been stored in 70% ethanol at room temperature for up to 12 years. Three amplicons ranging from 197 to 274 bps within the DNA barcode region were amplified from samples and compared to DNA barcoding libraries to identify species. We were able to amplify partial DNA barcodes from most samples, and species were often detected with multiple amplicons. However, some singletons and taxa poorly covered by DNA barcoding were missed. This suggests additional DNA barcodes will be required to fill 'gaps' in current DNA barcode libraries for aquatic macroinvertebrates and/or that it may not be possible to detect all taxa in a sample. Furthermore, older samples often detected fewer taxa and were less reliable for amplification, suggesting NGS is best used on samples within 8 years of collection. Nevertheless, many common taxa with existing DNA barcodes were reliably identified with NGS and were often present at sites across multiple years, showing the potential of NGS for detecting common and abundant species in archived material.},
}
@article {pmid27986545,
year = {2017},
author = {Ya'cob, Z and Takaoka, H and Low, VL and Sofian-Azirun, M},
title = {First description of a new cryptic species, Simulium vanluni from Peninsular Malaysia: An integrated morpho-taxonomical and genetic approach for naming cryptic species in the family Simuliidae.},
journal = {Acta tropica},
volume = {167},
number = {},
pages = {31-39},
doi = {10.1016/j.actatropica.2016.12.009},
pmid = {27986545},
issn = {1873-6254},
mesh = {Animals ; Larva/anatomy &amp; histology/genetics ; Malaysia ; Pupa/anatomy &amp; histology/genetics ; Simuliidae/anatomy &amp; histology/*classification/genetics ; Species Specificity ; },
abstract = {In recent decades, the numbers of cryptic taxa have increased significantly with current progress in DNA barcoding, yet, most of these cryptic taxa have not been formally named and recognized as valid species. To address this issue, we provide a guide for applying the procedure of describing new cryptic species in the family Simuliidae. Simulium (Simulium) vanluni from Pahang, Peninsular Malaysia, previously treated as S. nobile De Meijere, is described as a new species by using an integrated morpho-taxonomical and genetic approach. This new species is morphologically identical to S. nobile from Java and S. kiuliense Smart &amp; Clifford from Borneo, but their distinctiveness is supported by an expanded multigene phylogeny analysis.},
}
@article {pmid27984733,
year = {2016},
author = {Adamson, B and Norman, TM and Jost, M and Cho, MY and Nuñez, JK and Chen, Y and Villalta, JE and Gilbert, LA and Horlbeck, MA and Hein, MY and Pak, RA and Gray, AN and Gross, CA and Dixit, A and Parnas, O and Regev, A and Weissman, JS},
title = {A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response.},
journal = {Cell},
volume = {167},
number = {7},
pages = {1867-1882.e21},
pmid = {27984733},
issn = {1097-4172},
support = {U01 CA168370/CA/NCI NIH HHS/United States ; R00 CA204602/CA/NCI NIH HHS/United States ; R35 GM118061/GM/NIGMS NIH HHS/United States ; K99 CA204602/CA/NCI NIH HHS/United States ; T32 EB009383/EB/NIBIB NIH HHS/United States ; R01 GM102790/GM/NIGMS NIH HHS/United States ; T32 GM007618/GM/NIGMS NIH HHS/United States ; F32 GM116331/GM/NIGMS NIH HHS/United States ; P50 GM102706/GM/NIGMS NIH HHS/United States ; R01 DA036858/DA/NIDA NIH HHS/United States ; R01 AG041826/AG/NIA NIH HHS/United States ; P50 HG006193/HG/NHGRI NIH HHS/United States ; RM1 HG006193/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; Clustered Regularly Interspaced Short Palindromic Repeats ; Endoribonucleases ; Feedback ; Humans ; Models, Molecular ; Protein Serine-Threonine Kinases ; RNA, Guide, CRISPR-Cas Systems/metabolism ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis/*methods ; Transcription, Genetic ; Unfolded Protein Response ; },
abstract = {Functional genomics efforts face tradeoffs between number of perturbations examined and complexity of phenotypes measured. We bridge this gap with Perturb-seq, which combines droplet-based single-cell RNA-seq with a strategy for barcoding CRISPR-mediated perturbations, allowing many perturbations to be profiled in pooled format. We applied Perturb-seq to dissect the mammalian unfolded protein response (UPR) using single and combinatorial CRISPR perturbations. Two genome-scale CRISPR interference (CRISPRi) screens identified genes whose repression perturbs ER homeostasis. Subjecting ∼100 hits to Perturb-seq enabled high-precision functional clustering of genes. Single-cell analyses decoupled the three UPR branches, revealed bifurcated UPR branch activation among cells subject to the same perturbation, and uncovered differential activation of the branches across hits, including an isolated feedback loop between the translocon and IRE1α. These studies provide insight into how the three sensors of ER homeostasis monitor distinct types of stress and highlight the ability of Perturb-seq to dissect complex cellular responses.},
}
@article {pmid27980066,
year = {2017},
author = {Wei, X and Xu, Z and Wang, G and Hou, J and Ma, X and Liu, H and Liu, J and Chen, B and Luo, M and Xie, B and Li, R and Ruan, J and Liu, X},
title = {pBACode: a random-barcode-based high-throughput approach for BAC paired-end sequencing and physical clone mapping.},
journal = {Nucleic acids research},
volume = {45},
number = {7},
pages = {e52},
pmid = {27980066},
issn = {1362-4962},
mesh = {Animals ; *Chromosomes, Artificial, Bacterial ; *Cloning, Molecular ; Flounder/genetics ; Gene Library ; Genome ; High-Throughput Nucleotide Sequencing/*methods ; Physical Chromosome Mapping/*methods ; Saccharomyces cerevisiae/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {Applications that use Bacterial Artificial Chromosome (BAC) libraries often require paired-end sequences and knowledge of the physical location of each clone in plates. To facilitate obtaining this information in high-throughput, we generated pBACode vectors: a pool of BAC cloning vectors, each with a pair of random barcodes flanking its cloning site. In a pBACode BAC library, the BAC ends and their linked barcodes can be sequenced in bulk. Barcode pairs are determined by sequencing the empty pBACode vectors, which allows BAC ends to be paired according to their barcodes. For physical clone mapping, the barcodes are used as unique markers for their linked genomic sequence. After multi-dimensional pooling of BAC clones, the barcodes are sequenced and deconvoluted to locate each clone. We generated a pBACode library of 94,464 clones for the flounder Paralichthys olivaceus and obtained paired-end sequence from 95.4% of the clones. Incorporating BAC paired-ends into the genome preassembly improved its continuity by over 10-fold. Furthermore, we were able to use the barcodes to map the physical locations of each clone in just 50 pools, with up to 11 808 clones per pool. Our physical clone mapping located 90.2% of BAC clones, enabling targeted characterization of chromosomal rearrangements.},
}
@article {pmid27979055,
year = {2017},
author = {Uncu, AT and Uncu, AO and Frary, A and Doganlar, S},
title = {Barcode DNA length polymorphisms vs fatty acid profiling for adulteration detection in olive oil.},
journal = {Food chemistry},
volume = {221},
number = {},
pages = {1026-1033},
doi = {10.1016/j.foodchem.2016.11.059},
pmid = {27979055},
issn = {1873-7072},
mesh = {Chromatography, Gas/methods ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*analysis/genetics ; Electrophoresis, Capillary/methods ; Fatty Acids/*analysis/genetics ; Food Contamination/*analysis ; Humans ; Olive Oil/*analysis/standards ; Plant Oils/analysis/standards ; Polymerase Chain Reaction/methods ; *Polymorphism, Genetic/genetics ; },
abstract = {The aim of this study was to compare the performance of a DNA-barcode assay with fatty acid profile analysis to authenticate the botanical origin of olive oil. To achieve this aim, we performed a PCR-capillary electrophoresis (PCR-CE) approach on olive oil: seed oil blends using the plastid trnL (UAA) intron barcode. In parallel to genomic analysis, we subjected the samples to gas chromatography analysis of fatty acid composition. While the PCR-CE assay proved equally efficient as gas chromatography analysis in detecting adulteration with soybean, palm, rapeseed, sunflower, sesame, cottonseed and peanut oils, it was superior to the widely utilized analytical chemistry approach in revealing the adulterant species and detecting small quantities of corn and safflower oils in olive oil. Moreover, the DNA-based test correctly identified all tested olive oil: hazelnut oil blends whereas it was not feasible to detect hazelnut oil adulteration through fatty acid profile analysis. Thus, the present research has shown the feasibility of a PCR-CE barcode assay to detect adulteration in olive oil.},
}
@article {pmid27965081,
year = {2017},
author = {Tritsch, C and Martens, J and Sun, YH and Heim, W and Strutzenberger, P and Päckert, M},
title = {Improved sampling at the subspecies level solves a taxonomic dilemma - A case study of two enigmatic Chinese tit species (Aves, Passeriformes, Paridae, Poecile).},
journal = {Molecular phylogenetics and evolution},
volume = {107},
number = {},
pages = {538-550},
doi = {10.1016/j.ympev.2016.12.014},
pmid = {27965081},
issn = {1095-9513},
mesh = {Animals ; China ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Genetic Loci ; Passeriformes/*classification/genetics ; Phylogeny ; Phylogeography ; Species Specificity ; },
abstract = {A recent full species-level phylogeny of tits, titmice and chickadees (Paridae) has placed the Chinese endemic black-bibbed tit (Poecile hypermelaenus) as the sister to the Palearctic willow tit (P. montanus). Because this sister-group relationship is in striking disagreement with the traditional affiliation of P. hypermelaenus close to the marsh tit (P. palustris) we tested this phylogenetic hypothesis in a multi-locus analysis with an extended taxon sampling including sixteen subspecies of willow tits and marsh tits. As a taxonomic reference we included type specimens in our analysis. The molecular genetic study was complemented with an analysis of biometric data obtained from museum specimens. Our phylogenetic reconstructions, including a comparison of all GenBank data available for our target species, clearly show that the genetic lineage previously identified as P. hypermelaenus actually refers to P. weigoldicus because sequences were identical to that of a syntype of this taxon. The close relationship of P. weigoldicus and P. montanus - despite large genetic distances between the two taxa - is in accordance with current taxonomy and systematics. In disagreement with the previous phylogenetic hypothesis but in accordance with most taxonomic authorities, all our P. hypermelaenus specimens fell in the sister clade of all western and eastern Palearctic P. palustris. Though shared haplotypes among the Chinese populations of the two latter species might indicate mitochondrial introgression in this part of the breeding range, further research is needed here due to the limitations of our own sampling.},
}
@article {pmid27960232,
year = {2017},
author = {Griffin, J and Treanor, D},
title = {Digital pathology in clinical use: where are we now and what is holding us back?.},
journal = {Histopathology},
volume = {70},
number = {1},
pages = {134-145},
doi = {10.1111/his.12993},
pmid = {27960232},
issn = {1365-2559},
mesh = {Humans ; Image Interpretation, Computer-Assisted/*methods ; Pathology, Surgical/*methods/trends ; Telepathology/*methods/trends ; },
abstract = {Whole slide imaging is being used increasingly in research applications and in frozen section, consultation and external quality assurance practice. Digital pathology, when integrated with other digital tools such as barcoding, specimen tracking and digital dictation, can be integrated into the histopathology workflow, from specimen accession to report sign-out. These elements can bring about improvements in the safety, quality and efficiency of a histopathology department. The present paper reviews the evidence for these benefits. We then discuss the challenges of implementing a fully digital pathology workflow, including the regulatory environment, validation of whole slide imaging and the evidence for the design of a digital pathology workstation.},
}
@article {pmid27941803,
year = {2017},
author = {Garst, AD and Bassalo, MC and Pines, G and Lynch, SA and Halweg-Edwards, AL and Liu, R and Liang, L and Wang, Z and Zeitoun, R and Alexander, WG and Gill, RT},
title = {Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering.},
journal = {Nature biotechnology},
volume = {35},
number = {1},
pages = {48-55},
doi = {10.1038/nbt.3718},
pmid = {27941803},
issn = {1546-1696},
mesh = {Algorithms ; Chromosome Mapping/*methods ; DNA Mutational Analysis/*methods ; Gene Editing/*methods ; Genome, Bacterial/genetics ; Genome, Fungal/genetics ; High-Throughput Nucleotide Sequencing ; Metabolic Engineering/*methods ; Metabolome/genetics ; Nucleotides/genetics ; Polymorphism, Single Nucleotide/*genetics ; Protein Engineering/*methods ; Proteome/genetics ; Reproducibility of Results ; Sensitivity and Specificity ; Software ; },
abstract = {Improvements in DNA synthesis and sequencing have underpinned comprehensive assessment of gene function in bacteria and eukaryotes. Genome-wide analyses require high-throughput methods to generate mutations and analyze their phenotypes, but approaches to date have been unable to efficiently link the effects of mutations in coding regions or promoter elements in a highly parallel fashion. We report that CRISPR-Cas9 gene editing in combination with massively parallel oligomer synthesis can enable trackable editing on a genome-wide scale. Our method, CRISPR-enabled trackable genome engineering (CREATE), links each guide RNA to homologous repair cassettes that both edit loci and function as barcodes to track genotype-phenotype relationships. We apply CREATE to site saturation mutagenesis for protein engineering, reconstruction of adaptive laboratory evolution experiments, and identification of stress tolerance and antibiotic resistance genes in bacteria. We provide preliminary evidence that CREATE will work in yeast. We also provide a webtool to design multiplex CREATE libraries.},
}
@article {pmid27940562,
year = {2017},
author = {Arguel, MJ and LeBrigand, K and Paquet, A and Ruiz García, S and Zaragosi, LE and Barbry, P and Waldmann, R},
title = {A cost effective 5΄ selective single cell transcriptome profiling approach with improved UMI design.},
journal = {Nucleic acids research},
volume = {45},
number = {7},
pages = {e48},
pmid = {27940562},
issn = {1362-4962},
mesh = {Cells, Cultured ; DNA, Complementary ; Gene Expression Profiling/economics/*methods ; HEK293 Cells ; Humans ; Sequence Analysis, RNA/economics/*methods ; Single-Cell Analysis ; },
abstract = {Single cell RNA sequencing approaches are instrumental in studies of cell-to-cell variability. 5΄ selective transcriptome profiling approaches allow simultaneous definition of the transcription start size and have advantages over 3΄ selective approaches which just provide internal sequences close to the 3΄ end. The only currently existing 5΄ selective approach requires costly and labor intensive fragmentation and cell barcoding after cDNA amplification. We developed an optimized 5΄ selective workflow where all the cell indexing is done prior to fragmentation. With our protocol, cell indexing can be performed in the Fluidigm C1 microfluidic device, resulting in a significant reduction of cost and labor. We also designed optimized unique molecular identifiers that show less sequence bias and vulnerability towards sequencing errors resulting in an improved accuracy of molecule counting. We provide comprehensive experimental workflows for Illumina and Ion Proton sequencers that allow single cell sequencing in a cost range comparable to qPCR assays.},
}
@article {pmid27938420,
year = {2017},
author = {Héritier, L and Verneau, O and Breuil, G and Meistertzheim, AL},
title = {The high resolution melting analysis (HRM) as a molecular tool for monitoring parasites of the wildlife.},
journal = {Parasitology},
volume = {144},
number = {5},
pages = {563-570},
doi = {10.1017/S0031182016002183},
pmid = {27938420},
issn = {1469-8161},
mesh = {Animals ; Animals, Wild ; *Biodiversity ; DNA Primers/genetics ; DNA, Ribosomal/genetics ; Endangered Species ; Female ; France ; Male ; Ovum ; Platyhelminths/classification/genetics/*isolation &amp; purification ; Sequence Alignment/veterinary ; Transition Temperature ; Turtles/*parasitology ; },
abstract = {In an interconnected world, the international pet trade on wild animals is becoming increasingly important. As a consequence, non-native parasite species are introduced, which affect the health of wildlife and contribute to the loss of biodiversity. Because the investigation of parasite diversity within vulnerable host species implies the molecular identification of large samples of parasite eggs, the sequencing of DNA barcodes is time-consuming and costly. Thereby, the objectives of our study were to apply the high resolution melting (HRM) approach for species determination from pools of parasite eggs. Molecular assays were validated on flatworm parasites (polystomes) infecting the Mediterranean pond turtle Mauremys leprosa and the invasive red-eared slider Trachemys scripta elegans in French natural environments. HRM analysis results indicated that double or multiple parasitic infections could be detected from wild animal populations. They also showed that the cycle of parasite eggs production was not regular over time and may depend on several factors, among which the ecological niche and the target species. Thereby, monitoring parasites from wild endangered animals implies periodic parasitological surveys to avoid false negative diagnostics, based solely on eggs production.},
}
@article {pmid27936933,
year = {2017},
author = {Lim, BK},
title = {Review of genetic diversification of bats in the Caribbean and biogeographic relationships to Neotropical species based on DNA barcodes.},
journal = {Genome},
volume = {60},
number = {1},
pages = {65-73},
doi = {10.1139/gen-2015-0204},
pmid = {27936933},
issn = {1480-3321},
mesh = {Animals ; Biodiversity ; Caribbean Region ; Chiroptera/*classification/*genetics ; *DNA Barcoding, Taxonomic ; *Genetic Variation ; Mutation ; *Phylogeny ; Phylogeography ; },
abstract = {DNA barcoding is helping in discovering high levels of cryptic species and an underestimation of biodiversity in many groups of organisms. Although mammals are arguably the most studied and one of the least speciose taxonomic classes, the rate of species discovery is increasing and biased for small mammals on islands. An earlier study found bats in the Caribbean as a taxonomic and geographic deficiency in the International Barcode of Life initiative to establish a genetic reference database to enable specimen identification to species. Recent surveys in Dominican Republic, Jamaica, and Martinique have documented and barcoded half of the 58 bat species known from the Caribbean. I analyze all available barcode data of Caribbean bats to investigate biogeography and cryptic species in the Neotropical region. Analysis of the mitochondrial DNA gene cytochrome c oxidase subunit 1 results in a phylogenetic tree with all but one species as well-supported and reciprocally monophyletic. With a broader sampling across the Neotropics, there are also divergent lineages that exhibit biogeographic structuring: (i) a phylogenetic split between northern and southern Dominican Republic in three species, (ii) two taxa with cryptic species associated with higher degree of island endemism, (iii) populations of two widely distributed species with deep divergence between the Caribbean and North and Central America, and (iv) one species in the Caribbean with affinities to taxa in South America.},
}
@article {pmid27932930,
year = {2016},
author = {Geiger, MF and Moriniere, J and Hausmann, A and Haszprunar, G and Wägele, W and Hebert, PD and Rulik, B},
title = {Testing the Global Malaise Trap Program - How well does the current barcode reference library identify flying insects in Germany?.},
journal = {Biodiversity data journal},
volume = {},
number = {4},
pages = {e10671},
pmid = {27932930},
issn = {1314-2828},
abstract = {BACKGROUND: Biodiversity patterns are inherently complex and difficult to comprehensively assess. Yet, deciphering shifts in species composition through time and space are crucial for efficient and successful management of ecosystem services, as well as for predicting change. To better understand species diversity patterns, Germany participated in the Global Malaise Trap Program, a world-wide collection program for arthropods using this sampling method followed by their DNA barcode analysis. Traps were deployed at two localities: "Nationalpark Bayerischer Wald" in Bavaria, the largest terrestrial Natura 2000 area in Germany, and the nature conservation area Landskrone, an EU habitats directive site in the Rhine Valley. Arthropods were collected from May to September to track shifts in the taxonomic composition and temporal succession at these locations.<br><br>NEW INFORMATION: In total, 37,274 specimens were sorted and DNA barcoded, resulting in 5,301 different genetic clusters (BINs, Barcode Index Numbers, proxy for species) with just 7.6% of their BINs shared. Accumulation curves for the BIN count versus the number of specimens analyzed suggest that about 63% of the potential diversity at these sites was recovered with this single season of sampling. Diversity at both sites rose from May (496 &amp; 565 BINs) to July (1,236 &amp; 1,522 BINs) before decreasing in September (572 &amp; 504 BINs). Unambiguous species names were assigned to 35% of the BINs (1,868) which represented 12,640 specimens. Another 7% of the BINs (386) with 1,988 specimens were assigned to genus, while 26% (1,390) with 12,092 specimens were only placed to a family. These results illustrate how a comprehensive DNA barcode reference library can identify unknown specimens, but also reveal how this potential is constrained by gaps in the quantity and quality of records in BOLD, especially for Hymenoptera and Diptera. As voucher specimens are available for morphological study, we invite taxonomic experts to assist in the identification of unnamed BINs.},
}
@article {pmid27932928,
year = {2016},
author = {Holovachov, O},
title = {Metabarcoding of marine nematodes - evaluation of similarity scores used in alignment-based taxonomy assignment approach.},
journal = {Biodiversity data journal},
volume = {},
number = {4},
pages = {e10647},
pmid = {27932928},
issn = {1314-2828},
abstract = {BACKGROUND: The diversity of organisms is being commonly accessed using metabarcoding of environmental samples. Reliable identification of barcodes is one of the critical steps in the process and several taxonomy assignment methods were proposed to accomplish this task, including alignment-based approach that uses Basic Local Alignment Search Tool (BLAST) algorithm. This publication evaluates the variability of 5' end of 18S rRNA barcoding region as expressed by similarity scores (alignment score and identity score) produced by BLAST, and its impact on barcode identification to family-level taxonomic categories.<br><br>NEW INFORMATION: In alignment-based taxonomy assignment approach, reliable identification of anonymous OTUs to supraspecific taxa depends on the correct application of similarity thresholds. Since various taxa show different level of genetic variation, practical application of alignment-based approach requires the determination and use of taxon-specific similarity thresholds.},
}
@article {pmid27932926,
year = {2016},
author = {Kano, Y and Musikasinthorn, P and Iwata, A and Tun, S and Yun, L and Win, SS and Matsui, S and Tabata, R and Yamasaki, T and Watanabe, K},
title = {A dataset of fishes in and around Inle Lake, an ancient lake of Myanmar, with DNA barcoding, photo images and CT/3D models.},
journal = {Biodiversity data journal},
volume = {},
number = {4},
pages = {e10539},
pmid = {27932926},
issn = {1314-2828},
abstract = {BACKGROUND: Inle (Inlay) Lake, an ancient lake of Southeast Asia, is located at the eastern part of Myanmar, surrounded by the Shan Mountains. Detailed information on fish fauna in and around the lake has long been unknown, although its outstanding endemism was reported a century ago.<br><br>NEW INFORMATION: Based on the fish specimens collected from markets, rivers, swamps, ponds and ditches around Inle Lake as well as from the lake itself from 2014 to 2016, we recorded a total of 948 occurrence data (2120 individuals), belonging to 10 orders, 19 families, 39 genera and 49 species. Amongst them, 13 species of 12 genera are endemic or nearly endemic to the lake system and 17 species of 16 genera are suggested as non-native. The data are all accessible from the document "A dataset of Inle Lake fish fauna and its distribution (http://ipt.pensoft.net/resource.do?r=inle_fish_2014-16)", as well as DNA barcoding data (mitochondrial COI) for all species being available from the DDBJ/EMBL/GenBank (Accession numbers: LC189568-LC190411). Live photographs of almost all the individuals and CT/3D model data of several specimens are also available at the graphical fish biodiversity database (http://ffish.asia/INLE2016; http://ffish.asia/INLE2016-3D). The information can benefit the clarification, public concern and conservation of the fish biodiversity in the region.},
}
@article {pmid27929523,
year = {2017},
author = {Zilionis, R and Nainys, J and Veres, A and Savova, V and Zemmour, D and Klein, AM and Mazutis, L},
title = {Single-cell barcoding and sequencing using droplet microfluidics.},
journal = {Nature protocols},
volume = {12},
number = {1},
pages = {44-73},
doi = {10.1038/nprot.2016.154},
pmid = {27929523},
issn = {1750-2799},
mesh = {Equipment Design ; High-Throughput Nucleotide Sequencing/*instrumentation ; *Lab-On-A-Chip Devices ; Sequence Analysis, RNA/*instrumentation ; Single-Cell Analysis/*instrumentation ; },
abstract = {Single-cell RNA sequencing has recently emerged as a powerful tool for mapping cellular heterogeneity in diseased and healthy tissues, yet high-throughput methods are needed for capturing the unbiased diversity of cells. Droplet microfluidics is among the most promising candidates for capturing and processing thousands of individual cells for whole-transcriptome or genomic analysis in a massively parallel manner with minimal reagent use. We recently established a method called inDrops, which has the capability to index >15,000 cells in an hour. A suspension of cells is first encapsulated into nanoliter droplets with hydrogel beads (HBs) bearing barcoding DNA primers. Cells are then lysed and mRNA is barcoded (indexed) by a reverse transcription (RT) reaction. Here we provide details for (i) establishing an inDrops platform (1 d); (ii) performing hydrogel bead synthesis (4 d); (iii) encapsulating and barcoding cells (1 d); and (iv) RNA-seq library preparation (2 d). inDrops is a robust and scalable platform, and it is unique in its ability to capture and profile >75% of cells in even very small samples, on a scale of thousands or tens of thousands of cells.},
}
@article {pmid27929459,
year = {2016},
author = {Fourie, NH and Peace, RM and Abey, SK and Sherwin, LB and Wiley, JW and Henderson, WA},
title = {Perturbations of Circulating miRNAs in Irritable Bowel Syndrome Detected Using a Multiplexed High-throughput Gene Expression Platform.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {117},
pages = {},
pmid = {27929459},
issn = {1940-087X},
support = {R01 DK098205/DK/NIDDK NIH HHS/United States ; ZIA NR000018/ImNIH/Intramural NIH HHS/United States ; },
mesh = {DNA Probes ; Gene Expression ; *Gene Expression Profiling ; Genes, Reporter ; Humans ; *Irritable Bowel Syndrome ; *MicroRNAs ; Nucleic Acid Hybridization ; Reproducibility of Results ; },
abstract = {The gene expression platform assay allows for robust and highly reproducible quantification of the expression of up to 800 transcripts (mRNA or miRNAs) in a single reaction. The miRNA assay counts transcripts by directly imaging and digitally counting miRNA molecules that are labeled with color-coded fluorescent barcoded probe sets (a reporter probe and a capture probe). Barcodes are hybridized directly to mature miRNAs that have been elongated by ligating a unique oligonucleotide tag (miRtag) to the 3' end. Reverse transcription and amplification of the transcripts are not required. Reporter probes contain a sequence of six color positions populated using a combination of four fluorescent colors. The four colors over six positions are used to construct a gene-specific color barcode sequence. Post-hybridization processing is automated on a robotic prep station. After hybridization, the excess probes are washed away, and the tripartite structures (capture probe-miRNA-reporter probe) are fixed to a streptavidin-coated slide via the biotin-labeled capture probe. Imaging and barcode counting is done using a digital analyzer. The immobilized barcoded miRNAs are visualized and imaged using a microscope and camera, and the unique barcodes are decoded and counted. Data quality control (QC), normalization, and analysis are facilitated by a custom-designed data processing and analysis software that accompanies the assay software. The assay demonstrates high linearity over a broad range of expression, as well as high sensitivity. Sample and assay preparation does not involve enzymatic reactions, reverse transcription, or amplification; has few steps; and is largely automated, reducing investigator effects and resulting in high consistency and technical reproducibility. Here, we describe the application of this technology to identifying circulating miRNA perturbations in irritable bowel syndrome.},
}
@article {pmid27928939,
year = {2017},
author = {Lal, S and Pearce, M and Achilles-Day, UE and Day, JG and Morton, LH and Crean, SJ and Singhrao, SK},
title = {Developing an ecologically relevant heterogeneous biofilm model for dental-unit waterlines.},
journal = {Biofouling},
volume = {33},
number = {1},
pages = {75-87},
doi = {10.1080/08927014.2016.1260710},
pmid = {27928939},
issn = {1029-2454},
mesh = {Biofilms/*growth &amp; development ; Colony Count, Microbial ; Dental Equipment/*microbiology ; Disinfectants/pharmacology ; Equipment Contamination/*prevention &amp; control ; Fungi/drug effects/isolation &amp; purification ; Klebsiella/drug effects/isolation &amp; purification ; Legionella pneumophila/drug effects/isolation &amp; purification ; *Microbial Consortia ; *Models, Biological ; Pseudomonas/drug effects/isolation &amp; purification ; Water Microbiology/*standards ; },
abstract = {This study monitored the biodiversity of microbes cultured from a heterogeneous biofilm which had formed on the lumen of a section of dental waterline tubing over a period of 910 days. By day 2 bacterial counts on the outlet-water showed that contamination of the system had occurred. After 14 days, a biofilm comparable to that of clinical waterlines, consisting of bacteria, fungi and amoebae had formed. This showed that the proprietary silver coating applied to the luminal surface of the commercial waterline tubing failed to prevent biofilm formation. Molecular barcoding of isolated culturable microorganisms showed some degree of the diversity of taxa in the biofilm, including the opportunistic pathogen Legionella pneumophila. Whilst the system used for isolation and identification of contaminating microorganisms may underestimate the diversity of organisms in the biofilm, their similarity to those found in the clinical environment makes this a promising test-bed for future biocide testing.},
}
@article {pmid27928533,
year = {2016},
author = {Doosti, S and Yaghoobi-Ershadi, MR and Schaffner, F and Moosa-Kazemi, SH and Akbarzadeh, K and Gooya, MM and Vatandoost, H and Shirzadi, MR and Mosta-Favi, E},
title = {Mosquito Surveillance and the First Record of the Invasive Mosquito Species Aedes (Stegomyia) albopictus (Skuse) (Diptera: Culicidae) in Southern Iran.},
journal = {Iranian journal of public health},
volume = {45},
number = {8},
pages = {1064-1073},
pmid = {27928533},
issn = {2251-6085},
abstract = {BACKGROUND: Epidemics of mosquito-borne viral infections such as dengue, chikungunya, West Nile and Rift Valley fevers in neighbouring countries and risk of introduction of exotic vectors into Iran have placed this country at a significant risk for these mosquito-borne diseases.<br><br>METHODS: After the first dengue case reported in Iran in 2008, active entomological surveillance of Aedes albopictus (Skuse) and Ae. aegypti (Linnaeus) were conducted in May/Jun, Sep, and Oct/Nov, 2008-2014. Based on occurrence of dengue cases and the presence of potential entry sides including ports and boarder gates, 121 sites in eight provinces were monitored for mosquito vectors. Larval collections were carried out using droppers or dippers and adult collections with CDC light traps, human landing catches, aspirator and Pyrethrum spray space catches.<br><br>RESULTS: A total of 8,186 larvae and 3,734 adult mosquitoes were collected belonging to 23 Culicinae species, including 13 of the genus Culex, 1 Culiseta, 1 Uranotaenia, and 8 of the genus Aedes. Five Aedes albopictus larvae were identified from the Sistan &amp; Baluchestan province bordering Pakistan in 2009. In 2013, seven Ae. albopictus adult mosquitoes were also collected in a coastal locality near the city of Chabahar in the same province.<br><br>CONCLUSION: The detection of larvae and adults of this species in different parts of this province reveal its probable establishment in southeast Iran, which has implications for public health and requires active entomological surveillance as well as the implementation of vector control to prevent the further spread of this critical vector.},
}
@article {pmid27926379,
year = {2016},
author = {Chuang, LY and Moi, SH and Lin, YD and Yang, CH},
title = {A comparative analysis of chaotic particle swarm optimizations for detecting single nucleotide polymorphism barcodes.},
journal = {Artificial intelligence in medicine},
volume = {73},
number = {},
pages = {23-33},
doi = {10.1016/j.artmed.2016.09.002},
pmid = {27926379},
issn = {1873-2860},
mesh = {*Algorithms ; Breast Neoplasms/*genetics ; Chi-Square Distribution ; Humans ; Models, Genetic ; *Neural Networks, Computer ; Pattern Recognition, Automated ; Polymorphism, Single Nucleotide ; },
abstract = {OBJECTIVE: Evolutionary algorithms could overcome the computational limitations for the statistical evaluation of large datasets for high-order single nucleotide polymorphism (SNP) barcodes. Previous studies have proposed several chaotic particle swarm optimization (CPSO) methods to detect SNP barcodes for disease analysis (e.g., for breast cancer and chronic diseases). This work evaluated additional chaotic maps combined with the particle swarm optimization (PSO) method to detect SNP barcodes using a high-dimensional dataset.<br><br>METHODS AND MATERIAL: Nine chaotic maps were used to improve PSO method results and compared the searching ability amongst all CPSO methods. The XOR and ZZ disease models were used to compare all chaotic maps combined with PSO method. Efficacy evaluations of CPSO methods were based on statistical values from the chi-square test (&#x3c7;[2]).<br><br>RESULTS: The results showed that chaotic maps could improve the searching ability of PSO method when population are trapped in the local optimum. The minor allele frequency (MAF) indicated that, amongst all CPSO methods, the numbers of SNPs, sample size, and the highest &#x3c7;[2] value in all datasets were found in the Sinai chaotic map combined with PSO method. We used the simple linear regression results of the gbest values in all generations to compare the all methods. Sinai chaotic map combined with PSO method provided the highest &#x3b2; values (&#x3b2;&#x2265;0.32 in XOR disease model and &#x3b2;&#x2265;0.04 in ZZ disease model) and the significant p-value (p-value<0.001 in both the XOR and ZZ disease models).<br><br>CONCLUSION: The Sinai chaotic map was found to effectively enhance the fitness values (&#x3c7;[2]) of PSO method, indicating that the Sinai chaotic map combined with PSO method is more effective at detecting potential SNP barcodes in both the XOR and ZZ disease models.},
}
@article {pmid27924536,
year = {2017},
author = {Peterson, SW},
title = {Targeting Conserved Genes in Penicillium Species.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1542},
number = {},
pages = {149-157},
doi = {10.1007/978-1-4939-6707-0_9},
pmid = {27924536},
issn = {1940-6029},
mesh = {Computational Biology/methods ; *Conserved Sequence ; DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/genetics ; Databases, Nucleic Acid ; Evolution, Molecular ; Genes, Essential ; *Genes, Fungal ; Penicillium/*classification/*genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Software ; Web Browser ; },
abstract = {Polymerase chain reaction amplification of conserved genes and sequence analysis provides a very powerful tool for the identification of toxigenic as well as non-toxigenic Penicillium species. Sequences are obtained by amplification of the gene fragment, sequencing via capillary electrophoresis of dideoxynucleotide-labeled fragments or NGS. The sequences are compared to a database of validated isolates. Identification of species indicates the potential of the fungus to make particular mycotoxins.},
}
@article {pmid27923068,
year = {2016},
author = {Cohen, EM and Kobiler, O},
title = {Gene Expression Correlates with the Number of Herpes Viral Genomes Initiating Infection in Single Cells.},
journal = {PLoS pathogens},
volume = {12},
number = {12},
pages = {e1006082},
pmid = {27923068},
issn = {1553-7374},
mesh = {Animals ; Cell Line, Tumor ; Cell Separation ; Chlorocebus aethiops ; DNA Barcoding, Taxonomic ; Genome, Viral ; Herpesviridae Infections/*virology ; Herpesvirus 1, Human/*physiology ; Host-Pathogen Interactions/*physiology ; Humans ; Image Processing, Computer-Assisted ; Polymerase Chain Reaction ; Vero Cells ; Virus Replication/*physiology ; },
abstract = {Viral gene expression varies significantly among genetically identical cells. The sources of these variations are not well understood and have been suggested to involve both deterministic host differences and stochastic viral host interactions. For herpesviruses, only a limited number of incoming viral genomes initiate expression and replication in each infected cell. To elucidate the effect of this limited number of productively infecting genomes on viral gene expression in single cells, we constructed a set of fluorescence-expressing genetically tagged herpes recombinants. The number of different barcodes originating from a single cell is a good representative of the number of incoming viral genomes replicating (NOIVGR) in that cell. We identified a positive correlation between the NOIVGR and viral gene expression, as measured by the fluorescent protein expressed from the viral genome. This correlation was identified in three distinct cell-types, although the average NOIVGR per cell differed among these cell-types. Among clonal single cells, high housekeeping gene expression levels are not supportive of high viral gene expression, suggesting specific host determinants effecting viral infection. We developed a model to predict NOIVGR from cellular parameters, which supports the notion that viral gene expression is tightly linked to the NOIVGR in single-cells. Our results support the hypothesis that the stochastic nature of viral infection and host cell determinants contribute together to the variability observed among infected cells.},
}
@article {pmid27922451,
year = {2016},
author = {Vlaming, H and Molenaar, TM and van Welsem, T and Poramba-Liyanage, DW and Smith, DE and Velds, A and Hoekman, L and Korthout, T and Hendriks, S and Altelaar, AFM and van Leeuwen, F},
title = {Direct screening for chromatin status on DNA barcodes in yeast delineates the regulome of H3K79 methylation by Dot1.},
journal = {eLife},
volume = {5},
number = {},
pages = {},
pmid = {27922451},
issn = {2050-084X},
mesh = {Chromatin/*chemistry ; Chromatin Immunoprecipitation ; DNA, Fungal/chemistry/genetics/*metabolism ; *Gene Expression Regulation, Fungal ; Genetic Testing ; Genetics, Microbial/methods ; Histone-Lysine N-Methyltransferase/*metabolism ; Histones/*metabolism ; Methylation ; Molecular Biology/methods ; Nuclear Proteins/*metabolism ; *Protein Processing, Post-Translational ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/*metabolism ; Sequence Analysis, DNA ; },
abstract = {Given the frequent misregulation of chromatin in cancer, it is important to understand the cellular mechanisms that regulate chromatin structure. However, systematic screening for epigenetic regulators is challenging and often relies on laborious assays or indirect reporter read-outs. Here we describe a strategy, Epi-ID, to directly assess chromatin status in thousands of mutants. In Epi-ID, chromatin status on DNA barcodes is interrogated by chromatin immunoprecipitation followed by deep sequencing, allowing for quantitative comparison of many mutants in parallel. Screening of a barcoded yeast knock-out collection for regulators of histone H3K79 methylation by Dot1 identified all known regulators as well as novel players and processes. These include histone deposition, homologous recombination, and adenosine kinase, which influences the methionine cycle. Gcn5, the acetyltransferase within the SAGA complex, was found to regulate histone methylation and H2B ubiquitination. The concept of Epi-ID is widely applicable and can be readily applied to other chromatin features.},
}
@article {pmid27918555,
year = {2017},
author = {Bresler, SC and Min, L and Rodig, SJ and Walls, AC and Xu, S and Geng, S and Hodi, FS and Murphy, GF and Lian, CG},
title = {Gene expression profiling of anti-CTLA4-treated metastatic melanoma in patients with treatment-induced autoimmunity.},
journal = {Laboratory investigation; a journal of technical methods and pathology},
volume = {97},
number = {2},
pages = {207-216},
pmid = {27918555},
issn = {1530-0307},
mesh = {Adult ; Aged ; Aged, 80 and over ; Antibodies, Monoclonal/*therapeutic use ; Autoimmunity/*drug effects/genetics ; CTLA-4 Antigen/*antagonists &amp; inhibitors/genetics/immunology ; Cell Cycle Proteins/genetics/metabolism ; Cluster Analysis ; Female ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Neoplastic/drug effects ; Genetic Predisposition to Disease/genetics ; Humans ; Immunohistochemistry ; Inhibitor of Apoptosis Proteins/genetics/metabolism ; Ipilimumab ; Male ; Melanoma/*drug therapy/genetics/pathology ; Middle Aged ; Neoplasm Metastasis ; Protein Serine-Threonine Kinases/genetics/metabolism ; Protein-Tyrosine Kinases/genetics/metabolism ; Skin Neoplasms/*drug therapy/genetics/pathology ; Survivin ; },
abstract = {Ipilimumab (IPI) is a monoclonal antibody that targets the inhibitory CTLA4 receptor of T cells, enhancing T-cell-driven antitumor responses. IPI therapy in metastatic melanoma results in significant improvement in disease-free and overall survival, although after initial responses disease progression generally ensues. Identification of specific responses in tissue where melanoma tumor cells are subjected to IPI-driven immune attack may reveal mechanisms of treatment efficacy or resistance, permitting refinement of targeted therapeutic approaches. We used NanoString digital barcoding chemistry to identify changes in the transcriptome of metastatic melanoma cells before and after IPI treatment using two comprehensive panels containing a total of 1330 unique genes. Only patients who developed autoimmune disorders following treatment, signifying a robust immune response, were included. Despite evidence of an enhanced immune response, most patients eventually exhibited disease progression. Overall, data from five pre-IPI tumors and four post-IPI tumor samples (from three patients) permitted identification of several candidate genes that showed increased expression based on normalized counts after therapy. These included TTK (~3.1-fold, P=1.18e-4), which encodes a dual-specificity protein tyrosine kinase, a known cell cycle regulator, and BIRC5 (~3.0-fold, P=9.36e-4), which encodes the antiapoptotic protein survivin. Both TTK (MPS1) and survivin are targetable proteins against which a number of pharmacologic agents have been developed. CDK1, which encodes a protein tyrosine kinase known to phosphorylate survivin, was also upregulated (~3.2-fold, P=2.80-3). Tumor cell expression of TTK and survivin proteins was confirmed using immunohistochemistry in an expanded patient cohort. Differences in gene expression for several commonly encountered immune antigens, such as CD3, CD4, CD8, and CTLA4, were not statistically significant, likely reflecting the long length of time (average 323 days) between the last IPI dose and post-treatment biopsies. Although our sample size is limited, these results for the first time identify targetable genes that are significantly altered by interaction between a highly activated, IPI-treated immune system and melanoma cells.},
}
@article {pmid27918539,
year = {2017},
author = {Kalhor, R and Mali, P and Church, GM},
title = {Rapidly evolving homing CRISPR barcodes.},
journal = {Nature methods},
volume = {14},
number = {2},
pages = {195-200},
pmid = {27918539},
issn = {1548-7105},
support = {P50 HG005550/HG/NHGRI NIH HHS/United States ; R01 MH103910/MH/NIMH NIH HHS/United States ; RM1 HG008525/HG/NHGRI NIH HHS/United States ; },
mesh = {Bacterial Proteins/genetics/metabolism ; CRISPR-Associated Protein 9 ; CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Endonucleases/genetics/metabolism ; Genetic Vectors ; Green Fluorescent Proteins/genetics/metabolism ; HEK293 Cells ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Lentivirus/genetics ; RNA, Guide, CRISPR-Cas Systems ; },
abstract = {We present an approach for engineering evolving DNA barcodes in living cells. A homing guide RNA (hgRNA) scaffold directs the Cas9-hgRNA complex to the DNA locus of the hgRNA itself. We show that this homing CRISPR-Cas9 system acts as an expressed genetic barcode that diversifies its sequence and that the rate of diversification can be controlled in cultured cells. We further evaluate these barcodes in cell populations and show that they can be used to record lineage history and that the barcode RNA can be amplified in situ, a prerequisite for in situ sequencing. This integrated approach will have wide-ranging applications, such as in deep lineage tracing, cellular barcoding, molecular recording, dissecting cancer biology, and connectome mapping.},
}
@article {pmid27918193,
year = {2017},
author = {Ondrejicka, DA and Morey, KC and Hanner, RH},
title = {DNA barcodes identify medically important tick species in Canada.},
journal = {Genome},
volume = {60},
number = {1},
pages = {74-84},
doi = {10.1139/gen-2015-0179},
pmid = {27918193},
issn = {1480-3321},
mesh = {Animals ; Biodiversity ; Borrelia burgdorferi/genetics ; Canada ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial ; Geography ; Humans ; Ixodes/classification/genetics/microbiology ; Phylogeny ; Sequence Analysis, DNA ; Ticks/*classification/*genetics/microbiology ; },
abstract = {Medically important ticks (Acari: Ixodidae) are often difficult to identify morphologically. A standardized, molecular approach using a 658 base pair DNA barcode sequence (from the 5' region of the mitochondrial cytochrome c oxidase subunit I gene) was evaluated for its effectiveness in discriminating ticks in North America, with an emphasis on Canadian ticks. DNA barcodes were generated for 96 of 154 specimens representing 26 ixodid species. A genetic cluster analysis was performed on the barcode sequences, which separated specimens into haplogroups closely corresponding with morphologically identified species. The tree topology was further supported by a BIN analysis. COI sequences generated were found to have a mean maximum intraspecific divergence of 1.59% and a mean nearest neighbour divergence of 12.8%, indicating a significant "barcode gap". This study also revealed possible cryptic diversity among specimens morphologically identified as Ixodes soricis and Ixodes texanus. A PCR-based test for Borrelia burgdorferi determined that 18.1% of Lyme-competent ticks in this study were positive. This study is also the first to record a B. burgdorferi-positive exoskeleton. In conclusion, DNA barcoding is a powerful tool that clinicians can use to determine the identification of tick specimens which can help them to suggest whether an attached tick is a potential health risk.},
}
@article {pmid27917695,
year = {2017},
author = {Tsang, HF and Xue, VW and Koh, SP and Chiu, YM and Ng, LP and Wong, SC},
title = {NanoString, a novel digital color-coded barcode technology: current and future applications in molecular diagnostics.},
journal = {Expert review of molecular diagnostics},
volume = {17},
number = {1},
pages = {95-103},
doi = {10.1080/14737159.2017.1268533},
pmid = {27917695},
issn = {1744-8352},
mesh = {Gene Expression Profiling/*methods ; Humans ; Molecular Diagnostic Techniques/*methods ; Nucleic Acid Amplification Techniques/*methods ; *Paraffin Embedding ; Specimen Handling/*methods ; },
abstract = {Formalin-fixed, paraffin-embedded (FFPE) tissue sample is a gold mine of resources for molecular diagnosis and retrospective clinical studies. Although molecular technologies have expanded the range of mutations identified in FFPE samples, the applications of existing technologies are limited by the low nucleic acids yield and poor extraction quality. As a result, the routine clinical applications of molecular diagnosis using FFPE samples has been associated with many practical challenges. NanoString technologies utilize a novel digital color-coded barcode technology based on direct multiplexed measurement of gene expression and offer high levels of precision and sensitivity. Each color-coded barcode is attached to a single target-specific probe corresponding to a single gene which can be individually counted without amplification. Therefore, NanoString is especially useful for measuring gene expression in degraded clinical specimens. Areas covered: This article describes the applications of NanoString technologies in molecular diagnostics and challenges associated with its applications and the future development. Expert commentary: Although NanoString technology is still in the early stages of clinical use, it is expected that NanoString-based cancer expression panels would play more important roles in the future in classifying cancer patients and in predicting the response to therapy for better personal therapeutic care.},
}
@article {pmid27917068,
year = {2016},
author = {Esmaeili, HR and Sayyadzadeh, G and Seehausen, O},
title = {Iranocichla persa, a new cichlid species from southern Iran (Teleostei, Cichlidae).},
journal = {ZooKeys},
volume = {},
number = {636},
pages = {141-161},
pmid = {27917068},
issn = {1313-2989},
abstract = {Iranocichla persasp. n. is described from the Shur, Hasanlangi and Minab River drainages flowing into the Persian Gulf at the Strait of Hormuz in southern Iran. It is distinguished from Iranocichla hormuzensis, from the Mehran River drainage, by nuptial males having a bright orange breast and lower part of the head (vs. black), a poorly developed or invisible (vs. distinctive) "Tilapia-mark" in the dorsal fin and very clear white spots making almost wavy bars or stripes on the caudal fin (vs. without or with very few white spots). Mitochondrial DNA sequence characters suggest that both Iranocichla species are closely related but form two distinct clades, diagnosable by several fixed mutations in ND2, D-loop and partially by COI sequences. Populations from Kol River drainage, which is situated in-between the Mehran and the Shur River drainages, are more similar to Iranocichla hormuzensis in terms of their male nuptial coloration but to Iranocichla persasp. n. in their mitochondrial sequence characters. Their status requires further investigation.},
}
@article {pmid27917059,
year = {2016},
author = {Zhang, X and Marusik, YM},
title = {A survey of Pireneitega from Tajikistan (Agelenidae, Coelotinae).},
journal = {ZooKeys},
volume = {},
number = {635},
pages = {89-107},
pmid = {27917059},
issn = {1313-2989},
abstract = {Five new species of Pireneitega species from Tajikistan are described: Pireneitega zonsteinisp. n. (♂♀), Pireneitega muratovisp. n. (♀), Pireneitega tyuraisp. n. (♀), Pireneitega ramitensissp. n. (♀) and Pireneitega kovblyukisp. n. (♂). Pireneitega major (Kroneberg, 1875) is redescribed for the first time based on the lectotype designated here. DNA barcodes for the five new species are documented for future use and as proof of molecular differences between these species.},
}
@article {pmid27917041,
year = {2016},
author = {Cao, Q and Li, S and Żabka, M},
title = {The jumping spiders from Xishuangbanna, Yunnan, China (Araneae, Salticidae).},
journal = {ZooKeys},
volume = {},
number = {630},
pages = {43-104},
pmid = {27917041},
issn = {1313-2989},
abstract = {Twenty one jumping spider species from South Yunnan are reported, diagnosed, described and illustrated; 19 of them are described as new: Afraflacilla ballarini Cao &amp; Li, sp. n. (♂), Agorius tortilis Cao &amp; Li, sp. n. (♂♀), Bavia exilis Cao &amp; Li, sp. n. (♂), Carrhotus kevinlii Cao &amp; Li, sp. n. (♂♀), Carrhotus sarahcrewsae Cao &amp; Li, sp. n. (♂), Chinattus wengnanensis Cao &amp; Li, sp. n. (♂♀), Chinophrys mengyangensis Cao &amp; Li, sp. n. (♂♀), Cocalus menglaensis Cao &amp; Li, sp. n. (♂♀), Cosmophasis xiaolonghaensis Cao &amp; Li, sp. n. (♂♀), Cytaea yunnanensis Cao &amp; Li, sp. n. (♂), Gedea pinguis Cao &amp; Li, sp. n. (♂), Gelotia zhengi Cao &amp; Li, sp. n. (♂), Icius bamboo Cao &amp; Li, sp. n. (♂), Nannenus menghaiensis Cao &amp; Li, sp. n. (♂♀), Pancorius latus Cao &amp; Li, sp. n. (♂), Phintella lepidus Cao &amp; Li, sp. n. (♂♀), Phintella sancha Cao &amp; Li, sp. n. (♂), Ptocasius paraweyersi Cao &amp; Li, sp. n. (♂♀), and Stenaelurillus fuscus Cao &amp; Li, sp. n. (♂). Females of Bavia capistrata (C.L. Koch, 1846) and Phintella suavisoides Lei &amp; Peng, 2013 are described for the first time. DNA barcodes of 12 species were obtained for future use.},
}
@article {pmid27917038,
year = {2016},
author = {van Nieukerken, EJ and Doorenweerd, C and Hoare, RJ and Davis, DR},
title = {Revised classification and catalogue of global Nepticulidae and Opostegidae (Lepidoptera, Nepticuloidea).},
journal = {ZooKeys},
volume = {},
number = {628},
pages = {65-246},
pmid = {27917038},
issn = {1313-2989},
abstract = {A catalogue of all named Nepticulidae and Opostegidae is presented, including fossil species. The catalogue is simultaneously published online in the scratchpad http://nepticuloidea.info/ and in Catalogue of Life (http://www.catalogueoflife.org/col/details/database/id/172). We provide a historical overview of taxonomic research on Nepticuloidea and a brief 'state of the art'. A DNA barcode dataset with 3205 barcodes is made public at the same time, providing DNA barcodes of ca. 779 species, of which 2563 are identified as belonging to 444 validly published species. We recognise 862 extant and 18 fossil species of Nepticulidae in 22 extant genera and the fossil form genus Stigmellites. We count 192 valid Opostegidae species in 7 genera, without fossils. We also list seven dubious Nepticulidae names that cannot be placed due to absent type material and poor descriptions, 18 unavailable names in Nepticulidae that cannot be placed and we also list the 33 names (including four fossils) that once were placed as Nepticulidae or Opostegidae but are now excluded. All synonyms and previous combinations are listed. The generic classification follows the Molecular phylogeny that is published almost simultaneously. Subfamilies and tribes are not recognised, Trifurculinae Scoble, 1983 is synonymised with Nepticulidae Stainton, 1854 and Opostegoidinae Kozlov, 1987 is synonymised with Opostegidae Meyrick, 1893. The status of Casanovula Hoare, 2013, Etainia Beirne, 1945, Fomoria Beirne, 1945, Glaucolepis Braun, 1917, Menurella Hoare, 2013, Muhabbetana Koçak &amp; Kemal, 2007 and Zimmermannia Hering, 1940 is changed from subgenus to full genus, whereas two genera are considered synonyms again: Manoneura Davis, 1979, a synonym of Enteucha Meyrick, 1915 and Levarchama Beirne, 1945, a synonym of Trifurcula Zeller, 1848. We propose 87 new combinations in Nepticulidae and 10 in Opostegidae, largely due to the new classification, and re-examination of some species. We propose the following 37 new synonymies for species (35 in Nepticulidae, 2 in Opostegidae): Stigmella acerifoliella Dovnar-Zapolski, 1969 (unavailable, = Stigmella acerna Puplesis, 1988), Stigmella nakamurai Kemperman &amp; Wilkinson, 1985 (= Stigmella palionisi Puplesis, 1984), Nepticula amseli Skala, 1941 (unavailable = Stigmella birgittae Gustafsson, 1985), Stigmella cathepostis Kemperman &amp; Wilkinson, 1985 (= Stigmella microtheriella (Stainton, 1854)), Stigmella populnea Kemperman &amp; Wilkinson, 1985 (= Stigmella nivenburgensis (Preissecker, 1942)), Nepticula obscurella Braun, 1912 (revised synonymy, = Stigmella myricafoliella (Busck, 1900)), Nepticula mandingella Gustafsson, 1972 (= Stigmella wollofella (Gustafsson, 1972)), Stigmella rosaefoliella pectocatena Wilkinson &amp; Scoble, 1979 (= Stigmella centifoliella (Zeller, 1848)), Micropteryx pomivorella Packard, 1870 (= Stigmella oxyacanthella (Stainton, 1854)), Stigmella crataegivora Puplesis, 1985 (= Stigmella micromelis Puplesis, 1985), Stigmella scinanella Wilkinson &amp; Scoble, 1979 (= Stigmella purpuratella (Braun, 1917)), Stigmella palmatae Puplesis, 1984 (= Stigmella filipendulae (Wocke, 1871)), Stigmella sesplicata Kemperman &amp; Wilkinson, 1985 (= Stigmella lediella (Schleich, 1867)), Stigmella rhododendrifolia Dovnar-Zapolski &amp; Tomilova, 1978 (unavailable, = Stigmella lediella (Schleich, 1867)), Stigmella oa Kemperman &amp; Wilkinson, 1985 (= Stigmella spiculifera Kemperman &amp; Wilkinson, 1985), Stigmella gracilipae Hirano, 2014 (= Stigmella monticulella Puplesis, 1984), Nepticula chaoniella Herrich-Schäffer, 1863 (= Stigmella samiatella (Zeller, 1839)), Bohemannia piotra Puplesis, 1984 (= Bohemannia pulverosella (Stainton, 1849)), Bohemannia nipponicella Hirano, 2010 (= Bohemannia manschurella Puplesis, 1984), Sinopticula sinica Yang, 1989 (= Glaucolepis oishiella (Matsumura, 1931)), Trifurcula collinella Nel, 2012 (= Glaucolepis magna (A. Laštuvka &amp; Z. Laštuvka, 1997)), Obrussa tigrinella Puplesis, 1985 (= Etainia trifasciata (Matsumura, 1931)), Microcalyptris vittatus Puplesis, 1984 and Microcalyptris arenosus Falkovitsh, 1986 (both = Acalyptris falkovitshi (Puplesis, 1984)), Ectoedemia castaneae Busck, 1913, Ectoedemia heinrichi Busck, 1914 and Ectoedemia helenella Wilkinson, 1981 (all three = Zimmermannia bosquella (Chambers, 1878)), Ectoedemia chloranthis Meyrick, 1928 and Ectoedemia acanthella Wilkinson &amp; Newton, 1981 (both = Zimmermannia grandisella (Chambers, 1880)), Ectoedemia coruscella Wilkinson, 1981 (= Zimmermannia mesoloba (Davis, 1978)), Ectoedemia piperella Wilkinson &amp; Newton, 1981 and Ectoedemia reneella Wilkinson, 1981 (both = Zimmermannia obrutella (Zeller, 1873)), Ectoedemia similigena Puplesis, 1994 (= Ectoedemia turbidella (Zeller, 1848)), Ectoedemia andrella Wilkinson, 1981 (= Ectoedemia ulmella (Braun, 1912)), Nepticula canadensis Braun, 1917 (= Ectoedemia minimella (Zetterstedt, 1839)), Opostega rezniki Kozlov, 1985 (= Opostega cretatella Chrétien, 1915), Pseudopostega cyrneochalcopepla Nel &amp; Varenne, 2012 (= Pseudopostega chalcopepla (Walsingham, 1908)). Stigmella caryaefoliella (Clemens, 1861) and Zimmermannia bosquella (Chambers, 1878) are taken out of synonymy and re-instated as full species. Lectotypes are designated for Trifurcula obrutella Zeller, 1873 and Nepticula grandisella Chambers, 1880.},
}
@article {pmid27916561,
year = {2017},
author = {Le Lam, TN and Morvan, C and Liu, W and Bohn, C and Jaszczyszyn, Y and Bouloc, P},
title = {Finding sRNA-associated phenotypes by competition assays: An example with Staphylococcus aureus.},
journal = {Methods (San Diego, Calif.)},
volume = {117},
number = {},
pages = {21-27},
doi = {10.1016/j.ymeth.2016.11.018},
pmid = {27916561},
issn = {1095-9130},
mesh = {*Biological Assay ; DNA Barcoding, Taxonomic ; Escherichia coli/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Genetic Fitness ; Microbial Interactions/*genetics ; Mutation ; Phenotype ; Plasmids/chemistry/metabolism ; RNA, Bacterial/*genetics/metabolism ; RNA, Small Untranslated/*genetics/metabolism ; Sequence Analysis, RNA ; Sigma Factor/genetics/metabolism ; Staphylococcus aureus/*genetics/metabolism ; Transcription, Genetic ; Transformation, Bacterial ; },
abstract = {Bacteria optimize their fitness in response to a changing environment by tight regulation of gene expression. Regulation can be controlled at both transcriptional and post-transcriptional levels via key players such as sigma factors, regulatory proteins and regulatory RNAs. The identification of phenotypes associated with gene deletions is the established method for finding gene functions but may require testing many conditions for each studied mutant. As regulatory RNAs often contribute to fine-tuning gene expression, phenotypes associated with their inactivation are often weak and difficult to detect. Nevertheless, minor phenotypes conferring modest advantages, may allow bacteria to emerge after some generations under selective pressure. A strategy employing DNA barcodes can be used to perform competition experiments between mutants and to monitor fitness associated with mutations in different growth conditions. We combined this strategy with deep sequencing to study regulatory RNAs in Staphylococcus aureus, a major opportunistic pathogen.},
}
@article {pmid27915305,
year = {2017},
author = {Fidler, G and Kocsube, S and Leiter, E and Biro, S and Paholcsek, M},
title = {DNA Barcoding Coupled with High Resolution Melting Analysis Enables Rapid and Accurate Distinction of Aspergillus species.},
journal = {Medical mycology},
volume = {55},
number = {6},
pages = {642-659},
doi = {10.1093/mmy/myw127},
pmid = {27915305},
issn = {1460-2709},
mesh = {Aspergillosis/diagnosis/*microbiology ; Aspergillus/*classification/*genetics/isolation &amp; purification ; *DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; Fungi/classification/genetics ; Humans ; Limit of Detection ; Mycological Typing Techniques/*methods/standards ; *Polymerase Chain Reaction ; Reproducibility of Results ; Species Specificity ; Tubulin/genetics ; },
abstract = {We describe a high-resolution melting (HRM) analysis method that is rapid, reproducible, and able to identify reference strains and further 40 clinical isolates of Aspergillus fumigatus (14), A. lentulus (3), A. terreus (7), A. flavus (8), A. niger (2), A. welwitschiae (4), and A. tubingensis (2). Asp1 and Asp2 primer sets were designed to amplify partial sequences of the Aspergillus benA (beta-tubulin) genes in a closed-, single-tube system. Human placenta DNA, further Aspergillus (3), Candida (9), Fusarium (6), and Scedosporium (2) nucleic acids from type strains and clinical isolates were also included in this study to evaluate cross reactivity with other relevant pathogens causing invasive fungal infections. The barcoding capacity of this method proved to be 100% providing distinctive binomial scores; 14, 34, 36, 35, 25, 15, 26 when tested among species, while the within-species distinction capacity of the assay proved to be 0% based on the aligned thermodynamic profiles of the Asp1, Asp2 melting clusters allowing accurate species delimitation of all tested clinical isolates. The identification limit of this HRM assay was also estimated on Aspergillus reference gDNA panels where it proved to be 10-102 genomic equivalents (GE) except the A. fumigatus panel where it was 103 only. Furthermore, misidentification was not detected with human genomic DNA or with Candida, Fusarium, and Scedosporium strains. Our DNA barcoding assay introduced here provides results within a few hours, and it may possess further diagnostic utility when analyzing standard cultures supporting adequate therapeutic decisions.},
}
@article {pmid27905467,
year = {2016},
author = {Müller, V and Rajer, F and Frykholm, K and Nyberg, LK and Quaderi, S and Fritzsche, J and Kristiansson, E and Ambjörnsson, T and Sandegren, L and Westerlund, F},
title = {Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {37938},
pmid = {27905467},
issn = {2045-2322},
mesh = {Bacteria/*genetics ; Bacterial Proteins/*genetics ; CRISPR-Cas Systems ; Chromosome Mapping ; DNA, Bacterial/genetics ; *Drug Resistance, Microbial ; Nanotechnology ; Plasmids/*genetics ; RNA, Guide, CRISPR-Cas Systems/genetics ; Single Molecule Imaging ; },
abstract = {Bacterial plasmids are extensively involved in the rapid global spread of antibiotic resistance. We here present an assay, based on optical DNA mapping of single plasmids in nanofluidic channels, which provides detailed information about the plasmids present in a bacterial isolate. In a single experiment, we obtain the number of different plasmids in the sample, the size of each plasmid, an optical barcode that can be used to identify and trace the plasmid of interest and information about which plasmid that carries a specific resistance gene. Gene identification is done using CRISPR/Cas9 loaded with a guide-RNA (gRNA) complementary to the gene of interest that linearizes the circular plasmids at a specific location that is identified using the optical DNA maps. We demonstrate the principle on clinically relevant extended spectrum beta-lactamase (ESBL) producing isolates. We discuss how the gRNA sequence can be varied to obtain the desired information. The gRNA can either be very specific to identify a homogeneous group of genes or general to detect several groups of genes at the same time. Finally, we demonstrate an example where we use a combination of two gRNA sequences to identify carbapenemase-encoding genes in two previously not characterized clinical bacterial samples.},
}
@article {pmid27903261,
year = {2016},
author = {Wang, C and Agrawal, S and Laudien, J and Häussermann, V and Held, C},
title = {Discrete phenotypes are not underpinned by genome-wide genetic differentiation in the squat lobster Munida gregaria (Crustacea: Decapoda: Munididae): a multi-marker study covering the Patagonian shelf.},
journal = {BMC evolutionary biology},
volume = {16},
number = {1},
pages = {258},
pmid = {27903261},
issn = {1471-2148},
mesh = {Animals ; Anomura/*genetics ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Ecotype ; Female ; *Genetic Variation ; Genotype ; Haplotypes ; Male ; Microsatellite Repeats ; Phenotype ; Phylogeny ; South America ; },
abstract = {BACKGROUND: DNA barcoding has demonstrated that many discrete phenotypes are in fact genetically distinct (pseudo)cryptic species. Genetically identical, isogenic individuals, however, can also express similarly different phenotypes in response to a trigger condition, e.g. in the environment. This alternative explanation to cryptic speciation often remains untested because it requires considerable effort to reject the hypothesis that the observed underlying genetic homogeneity of the different phenotypes may be trivially caused by too slowly evolving molecular markers. The widespread squat lobster Munida gregaria comprises two discrete ecotypes, gregaria s. str. and subrugosa, which were long regarded as different species due to marked differences in morphological, ecological and behavioral traits. We studied the morphometry and genetics of M. gregaria s. l. and tested (1) whether the phenotypic differences remain stable after continental-scale sampling and inclusion of different life stages, (2) and whether each phenotype is underpinned by a specific genotype.<br><br>RESULTS: A total number of 219 gregaria s. str. and subrugosa individuals from 25 stations encompassing almost entire range in South America were included in morphological and genetic analyses using nine unlinked hypervariable microsatellites and new COI sequences. Results from the PCA and using discriminant functions demonstrated that the morphology of the two forms remains discrete. The mitochondrial data showed a shallow, star-like haplotype network and complete overlap of genetic distances within and among ecotypes. Coalescent-based species delimitation methods, PTP and GMYC, coherently suggested that haplotypes of both ecotypes forms a single species. Although all microsatellite markers possess sufficient genetic variation, AMOVA, PCoA and Bayesian clustering approaches revealed no genetic clusters corresponding to ecotypes or geographic units across the entire South-American distribution. No evidence of isolation-by-distance could be detected for this species in South America.<br><br>CONCLUSIONS: Despite their pronounced bimodal morphologies and different lifestyles, the gregaria s. str. and subrugosa ecotypes form a single, dimorphic species M. gregaria s. l.. Based on adequate geographic coverage and multiple independent polymorphic loci, there is no indication that each phenotype may have a unique genetic basis, leaving phenotypic plasticity or localized genomic islands of speciation as possible explanations.},
}
@article {pmid27901268,
year = {2017},
author = {Vamosi, JC and Gong, YB and Adamowicz, SJ and Packer, L},
title = {Forecasting pollination declines through DNA barcoding: the potential contributions of macroecological and macroevolutionary scales of inquiry.},
journal = {The New phytologist},
volume = {214},
number = {1},
pages = {11-18},
doi = {10.1111/nph.14356},
pmid = {27901268},
issn = {1469-8137},
mesh = {*Biological Evolution ; DNA Barcoding, Taxonomic/*methods ; *Ecosystem ; Plants ; Pollination/*physiology ; Time Factors ; },
abstract = {While pollinators are widely acknowledged as important contributors to seed production in plant communities, we do not yet have a good understanding of the importance of pollinator specialists for this ecosystem service. Determination of the prevalence of pollinator specialists is often hindered by the occurrence of cryptic species and the limitations of observational data on pollinator visitation rates, two areas where DNA barcoding of pollinators and pollen can be useful. Further, the demonstrated adequacy of pollen DNA barcoding from historical records offers opportunities to observe the effects of pollinator loss over longer timescales, and phylogenetic approaches can elucidate the historical rates of extinction of specialist lineages. In this Viewpoint article, we review how advances in DNA barcoding and metabarcoding of plants and pollinators have brought important developments to our understanding of specialization in plant-pollinator interactions. We then put forth several lines of inquiry that we feel are especially promising for providing insight on changes in plant-pollinator interactions over space and time. Obtaining estimates of the effects of reductions in specialists will contribute to forecasting the loss of ecosystem services that will accompany the erosion of plant and pollinator diversity.},
}
@article {pmid27900685,
year = {2017},
author = {Wemheuer, B and Wemheuer, F},
title = {Assessing Bacterial and Fungal Diversity in the Plant Endosphere.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1539},
number = {},
pages = {75-84},
doi = {10.1007/978-1-4939-6691-2_6},
pmid = {27900685},
issn = {1940-6029},
mesh = {Bacteria/*classification/*genetics ; Biodiversity ; Computational Biology/methods ; DNA Barcoding, Taxonomic ; *Endophytes ; Fungi/*classification/*genetics ; Metagenome ; Metagenomics/methods ; Phylogeny ; Plants/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Plants are colonized various microorganisms including endophytes. These microbes can play an important role in agricultural production as they promote plant growth and/or enhance the resistance of their host plant against diseases and environmental stress conditions. Although culture-independent molecular approaches such as DNA barcoding have greatly enhanced our understanding of bacterial and fungal endophyte communities, there are some methodical problems when investigating endophyte diversity. One main issue are sequence contaminations such as plastid-derived rRNA gene sequences which are co-amplified due to their high homology to bacterial 16S rRNA genes. The same is true for plant and fungal ITS sequences. The application of highly specific-primers suppressing co-amplification of these sequence contaminations is a good solution for this issue. Here, we describe a detailed protocol for assessing bacterial and fungal endophyte diversity in plants using these primers in combination with next-generation sequencing.},
}
@article {pmid27899929,
year = {2016},
author = {Han, YW and Duan, D and Ma, XF and Jia, Y and Liu, ZL and Zhao, GF and Li, ZH},
title = {Efficient Identification of the Forest Tree Species in Aceraceae Using DNA Barcodes.},
journal = {Frontiers in plant science},
volume = {7},
number = {},
pages = {1707},
pmid = {27899929},
issn = {1664-462X},
abstract = {Aceraceae is a large forest tree family that comprises many economically and ecologically important species. However, because interspecific and/or intraspecific morphological variations result from frequent interspecific hybridization and introgression, it is challenging for non-taxonomists to accurately recognize and identify the tree species in Aceraceae based on a traditional approach. DNA barcoding is a powerful tool that has been proposed to accurately distinguish between species. In this study, we assessed the effectiveness of three core standard markers (matK, rbcL and ITS) plus the chloroplast locus trnS-trnG as Aceraceae barcodes. A total of 231 sequences representing 85 species in this forest family were collected. Of these four barcode markers, the discrimination power was highest for the ITS (I) region (50%) and was progressively reduced in the other three chloroplast barcodes matK (M), trnS-trnG (T) and rbcL (R); the discrimination efficiency of the ITS marker was also greater than any two-locus combination of chloroplast barcodes. However, the combinations of ITS plus single or combined chloroplast barcodes could improve species resolution significantly; T+I (90.5% resolution) and R+M+T+I (90.5% resolution) differentiated the highest portion of species in Aceraceae. Our current results show that the nuclear ITS fragment represents a more promising DNA barcode marker than the maternally inherited chloroplast barcodes. The most efficient and economical method to identify tree species in Aceraceae among single or combined DNA barcodes is the combination of T+I (90.5% resolution).},
}
@article {pmid27897009,
year = {2017},
author = {Fread, KI and Strickland, WD and Nolan, GP and Zunder, ER},
title = {AN UPDATED DEBARCODING TOOL FOR MASS CYTOMETRY WITH CELL TYPE-SPECIFIC AND CELL SAMPLE-SPECIFIC STRINGENCY ADJUSTMENT.},
journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing},
volume = {22},
number = {},
pages = {588-598},
doi = {10.1142/9789813207813_0054},
pmid = {27897009},
issn = {2335-6936},
support = {F32 GM093508/GM/NIGMS NIH HHS/United States ; },
mesh = {*Algorithms ; Biological Assay/*statistics &amp; numerical data ; Computational Biology ; Flow Cytometry/*statistics &amp; numerical data ; Fluorescent Dyes ; Humans ; Software ; },
abstract = {Pooled sample analysis by mass cytometry barcoding carries many advantages: reduced antibody consumption, increased sample throughput, removal of cell doublets, reduction of cross-contamination by sample carryover, and the elimination of tube-to-tube-variability in antibody staining. A single-cell debarcoding algorithm was previously developed to improve the accuracy and yield of sample deconvolution, but this method was limited to using fixed parameters for debarcoding stringency filtering, which could introduce cell-specific or sample-specific bias to cell yield in scenarios where barcode staining intensity and variance are not uniform across the pooled samples. To address this issue, we have updated the algorithm to output debarcoding parameters for every cell in the sample-assigned FCS files, which allows for visualization and analysis of these parameters via flow cytometry analysis software. This strategy can be used to detect cell type-specific and sample-specific effects on the underlying cell data that arise during the debarcoding process. An additional benefit to this strategy is the decoupling of barcode stringency filtering from the debarcoding and sample assignment process. This is accomplished by removing the stringency filters during sample assignment, and then filtering after the fact with 1- and 2-dimensional gating on the debarcoding parameters which are output with the FCS files. These data exploration strategies serve as an important quality check for barcoded mass cytometry datasets, and allow cell type and sample-specific stringency adjustment that can remove bias in cell yield introduced during the debarcoding process.},
}
@article {pmid27895525,
year = {2016},
author = {Lin, Y and Ballarin, F and Li, S},
title = {A survey of the spider family Nesticidae (Arachnida, Araneae) in Asia and Madagascar, with the description of forty-three new species.},
journal = {ZooKeys},
volume = {},
number = {627},
pages = {1-168},
pmid = {27895525},
issn = {1313-2989},
abstract = {Forty-three new species of Nesticidae are described from China, Indonesia, Philippines, Singapore, Thailand, Vietnam and Madagascar, and two new junior synonyms are suggested. A new genus, Speleoticusgen. n., is described with Nesticus navicellatus Liu &amp; Li, 2013 as the type species, and four species are transferfed from Nesticus, i.e., Speleoticus globosus (Liu &amp; Li, 2013), comb. n., Speleoticus libo (Chen &amp; Zhu, 2005), comb. n., Speleoticus navicellatus (Liu &amp; Li, 2015), comb. n. and Speleoticus uenoi (Yaginuma, 1972), comb. n. The new species described in this paper belong to four genera and are: Hamus cornutussp. n. (♂♀), Hamus kangdingensissp. n. (♂), Hamus luzonsp. n. (♀), Hamus mangunensissp. n. (♂), Nescina kohisp. n. (♂♀), Nesticella baiseensissp. n. (♂♀), Nesticella baobabsp. n. (♂), Nesticella caecasp. n. (♂♀), Nesticella chongqingsp. n. (♀), Nesticella dazhuangensissp. n. (♂♀), Nesticella fuliangensissp. n. (♂♀), Nesticella gazuidasp. n. (♀), Nesticella gongshanensissp. n. (♀), Nesticella griswoldisp. n. (♂♀), Nesticella hongheensissp. n. (♂♀), Nesticella huomachongensissp. n. (♂♀), Nesticella jingposp. n. (♀), Nesticella kaohsiungensissp. n. (♂♀), Nesticella lisusp. n. (♂♀), Nesticella liuzhaiensissp. n. (♀), Nesticella nandanensissp. n. (♂♀), Nesticella phamisp. n. (♂♀), Nesticella potalasp. n. (♀), Nesticella qiaoqiensissp. n. (♀), Nesticella qiongensissp. n. (♂♀), Nesticella robustasp. n. (♂♀), Nesticella rongtangensissp. n. (♂), Nesticella sanchaheensissp. n. (♂♀), Nesticella sulawesisp. n. (♀), Nesticella sumatranasp. n. (♂), Nesticella tibetanasp. n. (♂♀), Nesticella vanlangsp. n. (♀), Nesticella wanzaiensissp. n. (♂♀), Nesticella xiongmaosp. n. (♂♀), Nesticella xixiasp. n. (♂♀), Nesticella yanbeiensissp. n. (♂♀), Nesticella yaosp. n. (♀), Nesticella zhiyuanisp. n. (♂♀), Pseudonesticus dafangensissp. n. (♂♀), Pseudonesticus miaosp. n. (♂♀), Pseudonesticus spinosussp. n. (♂♀), Pseudonesticus wumengensissp. n. (♀), Pseudonesticus ziyunensissp. n. (♂♀). Nesticella inthanoni (Lehtinen &amp; Saaristo, 1980), syn. n. is synonymised with Nesticella mollicula (Thorell, 1898); Nesticella taiwan Tso &amp; Yoshida, 2000, syn. n. is synonymised with Nesticella odonta (Chen, 1984). The female of Nesticella connectens Wunderlich, 1995, so far unknown, is described and recorded from Thailand. Nesticidae are reported from Madagascar for the first time. Nesticella nepalensis (Hubert, 1973) is recorded for the first time from China. Types of Nesticella odonta (Chen, 1984), Nesticella songi Chen &amp; Zhu, 2004 and Nesticella yui Wunderlich &amp; Song, 1995 are re-examined and photographed. The entire genus Nesticella is reviewed, and four species groups are recognised. DNA barcodes of the new species are obtained to confirm their correct identifications.},
}
@article {pmid27893773,
year = {2016},
author = {Anibaldi, A and Benassi Franciosi, C and Massari, F and Tinti, F and Piccinetti, C and Riccioni, G},
title = {Morphology and Species Composition of Southern Adriatic Sea Leptocephali Evaluated Using DNA Barcoding.},
journal = {PloS one},
volume = {11},
number = {11},
pages = {e0166137},
pmid = {27893773},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/methods ; Eels/*classification/*genetics ; Larva/classification/genetics/physiology ; Mediterranean Region ; },
abstract = {Leptocephali are the characteristic larvae of the superorder Elopomorpha that are difficult to identify at the species level. In this study, we used DNA barcoding (i.e. short genetic sequences of DNA used as unique species tags) coupled with classical taxonomic methods to identify leptocephali in the southern Adriatic Sea. This information will provide an assessment of the biodiversity of the eel larvae in this region. A total of 2,785 leptocephali were collected, and using external morphology were assigned to seven morphotypes: Ariosoma balearicum, Conger conger, Gnathophis mystax, Facciolella sp., Nettastoma melanurum, Dalophis imberbis and Chlopsis bicolor. Collectively, these seven morphotypes are considered to be a good proxy for the Anguilliformes community (the main order of the Elopomorpha) in the southern Adriatic Sea (to date, seven families and sixteen species have been recorded in this region). Interestingly, the higher number of G. mystax larvae collected suggests an increased abundance of this genus. To validate the morphological identifications, we sequenced 61 leptocephali (at a 655 bp fragment from the cytochrome oxidase subunit 1 mitochondrial region) and developed barcode vouchers for the seven morphotypes. Using genetic information from reference databases, we validated three of these morphotypes. Where reference sequences were unavailable, we generated barcodes for both adult and juvenile forms to provide additional genetic information. Using this integrated approach allowed us to characterize a new species of Facciolella in the Adriatic Sea for the first time. Moreover, we also revealed a lack of differentiation, at the species level, between G. mistax and G. bathytopos, a western Atlantic Ocean species. Our morphological and barcode data have been published in the Barcoding of the Adriatic Leptocephali database. This work represents the first contribution to a wider project that aims to create a barcode database to support the assessment of leptocephali diversity in the Mediterranean Sea.},
}
@article {pmid27889948,
year = {2017},
author = {Arrigoni, R and Vacherie, B and Benzoni, F and Stefani, F and Karsenti, E and Jaillon, O and Not, F and Nunes, F and Payri, C and Wincker, P and Barbe, V},
title = {A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications.},
journal = {Molecular ecology resources},
volume = {17},
number = {5},
pages = {1054-1071},
doi = {10.1111/1755-0998.12640},
pmid = {27889948},
issn = {1755-0998},
mesh = {Animals ; Anthozoa/*classification/*genetics ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; *Genetic Variation ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; },
abstract = {Scleractinian corals (i.e. hard corals) play a fundamental role in building and maintaining coral reefs, one of the most diverse ecosystems on Earth. Nevertheless, their phylogenies remain largely unresolved and little is known about dispersal and survival of their planktonic larval phase. The small subunit ribosomal RNA (SSU rRNA) is a commonly used gene for DNA barcoding in several metazoans, and small variable regions of SSU rRNA are widely adopted as barcode marker to investigate marine plankton community structure worldwide. Here, we provide a large sequence data set of the complete SSU rRNA gene from 298 specimens, representing all known extant reef coral families and a total of 106 genera. The secondary structure was extremely conserved within the order with few exceptions due to insertions or deletions occurring in the variable regions. Remarkable differences in SSU rRNA length and base composition were detected between and within acroporids (Acropora, Montipora, Isopora and Alveopora) compared to other corals. The V4 and V9 regions seem to be promising barcode loci because variation at commonly used barcode primer binding sites was extremely low, while their levels of divergence allowed families and genera to be distinguished. A time-calibrated phylogeny of Scleractinia is provided, and mutation rate heterogeneity is demonstrated across main lineages. The use of this data set as a valuable reference for investigating aspects of ecology, biology, molecular taxonomy and evolution of scleractinian corals is discussed.},
}
@article {pmid27876850,
year = {2016},
author = {Zeng, Y and Wu, Z and Zhang, C and Meng, Z and Jiang, Z and Zhang, J},
title = {DNA barcoding of Mobulid Ray Gill Rakers for Implementing CITES on Elasmobranch in China.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {37567},
pmid = {27876850},
issn = {2045-2322},
mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; *Endangered Species ; Gills/anatomy &amp; histology ; *Internationality ; Skates, Fish/*genetics ; Species Specificity ; },
abstract = {The Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) has been counted on for conserving threatened marine fish since it regulates the commercial international trade of these species. Implementation of the international treaty for Mantas included on CITES Appendix II is challenging due to insufficient information on species identification and markets management. To fill the gap in such aspects, we identified five species of Mobulid rays (Mobula spps. and Manta spp) by using COI and NADH2 mtDNA markers in dried ray gill rakers from Chinese markets, namely, Mobula japonica (representing 54.8% of the sample set), M. tarapacana (14.4%), M. kuhlii (13.3%), M. thurstoni (6.4%), along with Manta birostris (11.2%; CITES Appendix II). The utilization and conservation statuses of these species were discussed. Based on combination of DNA barcodes and key morphological characters, we developed a three-step process for identifying the gill rakers of Mobulid rays which has been adopted by frontline enforcement in China. We hope that our work can serve as a foundation and basis to reinforce objectives of international treaties, regulation of consumer-driven markets, regional cooperation, and national fishery management on endangered elasmobranchs in China as well as related countries.},
}
@article {pmid27874090,
year = {2016},
author = {Davidsson, M and Diaz-Fernandez, P and Schwich, OD and Torroba, M and Wang, G and Björklund, T},
title = {A novel process of viral vector barcoding and library preparation enables high-diversity library generation and recombination-free paired-end sequencing.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {37563},
pmid = {27874090},
issn = {2045-2322},
mesh = {Dependovirus/*genetics ; *Gene Library ; Genetic Vectors/*genetics ; High-Throughput Nucleotide Sequencing ; RNA/*genetics ; Recombination, Genetic ; },
abstract = {Detailed characterization and mapping of oligonucleotide function in vivo is generally a very time consuming effort that only allows for hypothesis driven subsampling of the full sequence to be analysed. Recent advances in deep sequencing together with highly efficient parallel oligonucleotide synthesis and cloning techniques have, however, opened up for entirely new ways to map genetic function in vivo. Here we present a novel, optimized protocol for the generation of universally applicable, barcode labelled, plasmid libraries. The libraries are designed to enable the production of viral vector preparations assessing coding or non-coding RNA function in vivo. When generating high diversity libraries, it is a challenge to achieve efficient cloning, unambiguous barcoding and detailed characterization using low-cost sequencing technologies. With the presented protocol, diversity of above 3 million uniquely barcoded adeno-associated viral (AAV) plasmids can be achieved in a single reaction through a process achievable in any molecular biology laboratory. This approach opens up for a multitude of in vivo assessments from the evaluation of enhancer and promoter regions to the optimization of genome editing. The generated plasmid libraries are also useful for validation of sequencing clustering algorithms and we here validate the newly presented message passing clustering process named Starcode.},
}
@article {pmid27872997,
year = {2017},
author = {Baudart, J and Guillebault, D and Mielke, E and Meyer, T and Tandon, N and Fischer, S and Weigel, W and Medlin, LK},
title = {Microarray (phylochip) analysis of freshwater pathogens at several sites along the Northern German coast transecting both estuarine and freshwaters.},
journal = {Applied microbiology and biotechnology},
volume = {101},
number = {2},
pages = {871-886},
doi = {10.1007/s00253-016-7937-2},
pmid = {27872997},
issn = {1432-0614},
mesh = {Bacterial Toxins/*analysis/genetics ; Cyanobacteria/classification/genetics/*isolation &amp; purification ; Fresh Water/*microbiology ; Germany ; Humans ; Microarray Analysis/*methods ; Seawater/*microbiology ; },
abstract = {Monitoring the quality of drinking water is an important issue for public health. Two of the main objectives of the European Project μAQUA were (i) the development of specific probes to detect and quantify pathogens in drinking water and (ii) the design of standardized sampling programs of water from different sources in Europe in order to obtain sufficient material for downstream analysis. Our phylochip contains barcodes that specifically identify freshwater pathogens for enabling the detection of organisms that can be risks for human health. Monitoring for organisms with molecular tools is rapid, more accurate and more reliable than traditional methods. Rapid detection means that mitigation strategies come into play faster with less harm to the community and to humans. Samples were collected from several waters in France, Germany, Ireland, Italy and Turkey over 2 years. We present microarray results for the presence of freshwater pathogens from brackish and freshwater sites in Northern Germany, and cyanobacterial cell numbers inferred from these sites. In a companion study from the same samples, cyanobacterial toxins were analyzed using two methods and those sites with highest toxin values also had highest cell numbers as inferred from this microarray study.},
}
@article {pmid27871217,
year = {2018},
author = {Hou, F and Wen, L and Peng, C and Guo, J},
title = {Identification of marine traditional Chinese medicine dried seahorses in the traditional Chinese medicine market using DNA barcoding.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {1},
pages = {107-112},
doi = {10.1080/24701394.2016.1248430},
pmid = {27871217},
issn = {2470-1408},
mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Endangered Species ; *Genes, Mitochondrial ; Medicine, Chinese Traditional ; Phylogeny ; Smegmamorpha/*classification/genetics ; },
abstract = {Seahorse documented in Chinese pharmacopeia possess important medicinal efficacy and are used as an ingredient in traditional Chinese medicines. The growing international trade threatens the species. DNA barcoding holds a great application potentiality in wildlife conservation and might prevent the illegal trade of threatened species. The COI gene was used to identify seahorse, and nine Hippocampus species were found in the three large traditional Chinese medicines markets of China. All inter-specific genetic variations were larger than 2%. Mean genetic distances between species were 17-fold larger than those within the species. Phylogenetic tree showed that each species clustered in the appropriate branch. All results demonstrated that COI-based barcoding technique could be used to identify seahorse species and played a major role in monitoring the seahorse trade.},
}
@article {pmid27871204,
year = {2017},
author = {H Abdul, J and Akram, S and Arshan, KML},
title = {DNA barcoding of a colonial ascidian, Lissoclinum fragile (Van Name, 1902).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {6},
pages = {810-813},
doi = {10.1080/24701394.2016.1192615},
pmid = {27871204},
issn = {2470-1408},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Genes, Mitochondrial ; India ; *Phylogeny ; Sequence Analysis, DNA ; Urochordata/classification/enzymology/*genetics ; },
abstract = {Ascidians (tunicates) are marine benthic organisms possessing various pharmacological activities, including anti-oxidant, anti-tumour, antimicrobial, etc. They also play a key role as model organisms to study various neurobehavioral disorders. Ascidian diversity is reportedly less in India due to lack of taxonomists as well as the limitations in morphology based taxonomy. Molecular taxonomy, comprising the sequencing of cytochrome c oxidase 1 gene (barcode region) otherwise known as DNA barcoding reduces these bottlenecks. Since several species of the family Didemnidae closely resemble in morphology, the present study was aimed to develop DNA barcodes of a colonial ascidian, Lissoclinum fragile belonging to the family Didemnidae. CO1 gene of L. fragile from Thoothukudi, Mandapam, and Vizhinjam waters were sequenced and submitted in GenBank, NCBI through Barcode submission tool. BLAST results showed maximum identity (97-100%) for L. fragile collected from different stations. The pairwise genetic distances within species and genera were calculated using Kimura two parameter (K2P) and the phylogenetic tree was constructed using Neighbour-Joining Tree.},
}
@article {pmid27870868,
year = {2016},
author = {Layton, KK and Corstorphine, EA and Hebert, PD},
title = {Exploring Canadian Echinoderm Diversity through DNA Barcodes.},
journal = {PloS one},
volume = {11},
number = {11},
pages = {e0166118},
pmid = {27870868},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; Canada ; DNA Barcoding, Taxonomic/*methods ; Echinodermata/*classification/genetics ; Female ; Male ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/*methods ; },
abstract = {DNA barcoding has proven an effective tool for species identification in varied groups of marine invertebrates including crustaceans, molluscs, polychaetes and echinoderms. In this study, we further validate its utility by analyzing almost half of the 300 species of Echinodermata known from Canadian waters. COI sequences from 999 specimens were assigned to 145 BINs. In most cases, species discrimination was straightforward due to the large difference (25-fold) between mean intra- (0.48%) and inter- (12.0%) specific divergence. Six species were flagged for further taxonomic investigation because specimens assigned to them fell into two or three discrete sequence clusters. The potential influence of larval dispersal capacity and glacial events on patterns of genetic diversity is discussed for 19 trans-oceanic species. Although additional research is needed to clarify biogeographic patterns and resolve taxonomic questions, this study represents an important step in the assembly of a DNA barcode library for all Canadian echinoderms, a valuable resource for future biosurveillance programs.},
}
@article {pmid27870830,
year = {2017},
author = {Henninger, J and Santoso, B and Hans, S and Durand, E and Moore, J and Mosimann, C and Brand, M and Traver, D and Zon, L},
title = {Clonal fate mapping quantifies the number of haematopoietic stem cells that arise during development.},
journal = {Nature cell biology},
volume = {19},
number = {1},
pages = {17-27},
pmid = {27870830},
issn = {1476-4679},
support = {U01 HL134812/HL/NHLBI NIH HHS/United States ; R01 DK074482/DK/NIDDK NIH HHS/United States ; P30 DK049216/DK/NIDDK NIH HHS/United States ; P01 HL032262/HL/NHLBI NIH HHS/United States ; R01 HL048801/HL/NHLBI NIH HHS/United States ; R01 DK053298/DK/NIDDK NIH HHS/United States ; /HHMI_/Howard Hughes Medical Institute/United States ; F31 HL126338/HL/NHLBI NIH HHS/United States ; U01 HL100001/HL/NHLBI NIH HHS/United States ; U54 DK110805/DK/NIDDK NIH HHS/United States ; R24 DK092760/DK/NIDDK NIH HHS/United States ; },
mesh = {Aging ; Animals ; Blood Vessels/embryology ; Bone Marrow Cells/cytology ; Bone Marrow Transplantation ; Cell Count ; *Cell Lineage ; Clone Cells ; Embryo, Nonmammalian/cytology ; *Embryonic Development ; Erythroid Cells/cytology ; Granulocytes/cytology ; Hematopoiesis ; Hematopoietic Stem Cells/*cytology ; Lasers ; Platelet Membrane Glycoprotein IIb/metabolism ; Staining and Labeling ; Transgenes ; Zebrafish/embryology ; },
abstract = {Haematopoietic stem cells (HSCs) arise in the developing aorta during embryogenesis. The number of HSC clones born has been estimated through transplantation, but experimental approaches to assess the absolute number of forming HSCs in a native setting have remained challenging. Here, we applied single-cell and clonal analysis of HSCs in zebrafish to quantify developing HSCs. Targeting creER[T2] in developing cd41:eGFP[+] HSCs enabled long-term assessment of their blood contribution. We also applied the Brainbow-based multicolour Zebrabow system with drl:creER[T2] that is active in early haematopoiesis to induce heritable colour barcoding unique to each HSC and its progeny. Our findings reveal that approximately 21 HSC clones exist prior to HSC emergence and 30 clones are present during peak production from aortic endothelium. Our methods further reveal that stress haematopoiesis, including sublethal irradiation and transplantation, reduces clonal diversity. Our findings provide quantitative insights into the early clonal events that regulate haematopoietic development.},
}
@article {pmid27867826,
year = {2016},
author = {Wang, H and Hao, N and Chen, L and Li, G},
title = {Development of intron polymorphism markers in major latex-like protein gene for locality-level and cultivar identification of Salvia miltiorrhiza.},
journal = {SpringerPlus},
volume = {5},
number = {1},
pages = {1919},
pmid = {27867826},
issn = {2193-1801},
abstract = {BACKGROUND: Salvia miltiorrhiza (Danshen) is one of the most widely used medicinal herbs in traditional Chinese medicine. Locality-level and cultivar identification is of great importance not only for protecting highest therapeutic effectiveness of Daodi Danshen, but also for the genetic conservation and utilization of existing S. miltiorrhiza populations.<br><br>RESULTS: Intron polymorphisms including SNPs (single nucleotide polymorphisms) and indels were exploited in major latex-like protein (MLP) gene. Based on these markers, genetic relationships among S. miltiorrhiza cultivar and populations in different locations were evaluated by constructing a dendrogram. Moreover, S. miltiorrhiza specimens from Laiwu region were geographically distinguishable by the developed SNP marker. A 204&#xa0;bp-indel marker was exploited for the first space breeding cultivar Luyuan Danshen-1 (LD-1), and an effective real-time PCR assay was successfully developed for fast screening of LD-1 among local landraces.<br><br>CONCLUSIONS: MLP intron is a valuable DNA barcode for intra-specific study of S. miltiorrhiza populations, and the developed markers can serve as a useful tool for molecular identification of LD-1 cultivar and geographically distinct populations of S. miltiorrhiza.},
}
@article {pmid27863033,
year = {2017},
author = {Hawlitschek, O and Morinière, J and Lehmann, GUC and Lehmann, AW and Kropf, M and Dunz, A and Glaw, F and Detcharoen, M and Schmidt, S and Hausmann, A and Szucsich, NU and Caetano-Wyler, SA and Haszprunar, G},
title = {DNA barcoding of crickets, katydids and grasshoppers (Orthoptera) from Central Europe with focus on Austria, Germany and Switzerland.},
journal = {Molecular ecology resources},
volume = {17},
number = {5},
pages = {1037-1053},
doi = {10.1111/1755-0998.12638},
pmid = {27863033},
issn = {1755-0998},
mesh = {Animals ; Austria ; *DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; Electron Transport Complex IV/genetics ; Germany ; International Cooperation ; Orthoptera/*classification/*genetics ; Switzerland ; Wolbachia/genetics ; },
abstract = {We present a DNA barcoding study on the insect order Orthoptera that was generated in collaboration between four barcoding projects in three countries, viz. Barcoding Fauna Bavarica (Germany), German Barcode of Life, Austrian Barcode of Life and Swiss Barcode of Life. Our data set includes 748 COI sequences from 127 of the 162 taxa (78.4%) recorded in the three countries involved. Ninety-three of these 122 species (76.2%, including all Ensifera) can be reliably identified using DNA barcodes. The remaining 26 caeliferan species (families Acrididae and Tetrigidae) form ten clusters that share barcodes among up to five species, in three cases even across different genera, and in six cases even sharing individual barcodes. We discuss incomplete lineage sorting and hybridization as most likely causes of this phenomenon, as the species concerned are phylogenetically young and hybridization has been previously observed. We also highlight the problem of nuclear mitochondrial pseudogenes (numts), a known problem in the barcoding of orthopteran species, and the possibility of Wolbachia infections. Finally, we discuss the possible taxonomic implications of our barcoding results and point out future research directions.},
}
@article {pmid27861494,
year = {2016},
author = {Tian, Q and Zhao, W and Lu, S and Zhu, S and Li, S},
title = {DNA Barcoding for Efficient Species- and Pathovar-Level Identification of the Quarantine Plant Pathogen Xanthomonas.},
journal = {PloS one},
volume = {11},
number = {11},
pages = {e0165995},
pmid = {27861494},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic ; Evolution, Molecular ; Genes, Bacterial ; Genetic Markers ; Phylogeny ; Plants/*microbiology ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; Xanthomonas/*classification/*genetics ; },
abstract = {Genus Xanthomonas comprises many economically important plant pathogens that affect a wide range of hosts. Indeed, fourteen Xanthomonas species/pathovars have been regarded as official quarantine bacteria for imports in China. To date, however, a rapid and accurate method capable of identifying all of the quarantine species/pathovars has yet to be developed. In this study, we therefore evaluated the capacity of DNA barcoding as a digital identification method for discriminating quarantine species/pathovars of Xanthomonas. For these analyses, 327 isolates, representing 45 Xanthomonas species/pathovars, as well as five additional species/pathovars from GenBank (50 species/pathovars total), were utilized to test the efficacy of four DNA barcode candidate genes (16S rRNA gene, cpn60, gyrB, and avrBs2). Of these candidate genes, cpn60 displayed the highest rate of PCR amplification and sequencing success. The tree-building (Neighbor-joining), 'best close match', and barcode gap methods were subsequently employed to assess the species- and pathovar-level resolution of each gene. Notably, all isolates of each quarantine species/pathovars formed a monophyletic group in the neighbor-joining tree constructed using the cpn60 sequences. Moreover, cpn60 also demonstrated the most satisfactory results in both barcoding gap analysis and the 'best close match' test. Thus, compared with the other markers tested, cpn60 proved to be a powerful DNA barcode, providing a reliable and effective means for the species- and pathovar-level identification of the quarantine plant pathogen Xanthomonas.},
}
@article {pmid27859248,
year = {2017},
author = {Sakinan, S and Karahan, A and Ok, M},
title = {Integration of DNA barcoding for the initial recordings of Lessepsian fishes: a case study of the Indo-Pacific slender ponyfish Equulites elongatus.},
journal = {Journal of fish biology},
volume = {90},
number = {3},
pages = {1054-1061},
doi = {10.1111/jfb.13207},
pmid = {27859248},
issn = {1095-8649},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Fishes/*genetics ; Mediterranean Sea ; Turkey ; },
abstract = {In this study, the DNA barcode of a regional Lessepsian sighting of the slender ponyfish Equulites elongatus is integrated with morphometric and meristic descriptors as a case study to address further identification problems in the Mediterranean Sea. The study also aims to contribute to the regional mitochondrial cytochrome oxidase I information pool, to support other potential uses. The initial sighting of E. elongatus from the north-eastern Mediterranean coast of Turkey is provided from a trawl survey on 3 June 2015, where 76 specimens were captured during a 15 min tow.},
}
@article {pmid27859230,
year = {2017},
author = {McKenzie, JL and Alvarado Bremer, JR},
title = {Genetic identification of istiophorid larvae from the Gulf of Mexico based on the analysis of mitochondrial DNA control region sequences.},
journal = {Journal of fish biology},
volume = {90},
number = {3},
pages = {1070-1079},
doi = {10.1111/jfb.13212},
pmid = {27859230},
issn = {1095-8649},
mesh = {Animals ; Atlantic Ocean ; DNA Primers ; DNA, Mitochondrial/*genetics ; Fishes/classification/*genetics ; *Genetic Variation ; Gulf of Mexico ; Larva/classification/genetics ; Life Cycle Stages/genetics/physiology ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Assigning relative importance of spawning and nursery habitats for threatened and endangered teleosts, such as those seen in the Gulf of Mexico (GoM), relies on the proper identification of the early life-history stages of the species of concern. Here, sequencing a portion of the mitochondrial DNA (mtDNA) control region (CR) I as barcodes is recommended to identify istiophorid (billfish) larvae in the Atlantic Ocean because of its high resolution and the intrinsic value of the levels of genetic variation that can be extracted from these data. The universality of the primers employed here demonstrates their utility for not only the positive identification of istiophorids in the GoM, but for any larval teleost occurring in areas recognized as larval hotspots worldwide.},
}
@article {pmid27858971,
year = {2016},
author = {Stensvold, CR and Clark, CG},
title = {Molecular Identification and Subtype Analysis of Blastocystis.},
journal = {Current protocols in microbiology},
volume = {43},
number = {},
pages = {20A.2.1-20A.2.10},
doi = {10.1002/cpmc.17},
pmid = {27858971},
issn = {1934-8533},
mesh = {Blastocystis/*genetics/*isolation &amp; purification/metabolism ; Blastocystis Infections/*parasitology ; Cell Culture Techniques/*methods ; Culture Media/chemistry/metabolism ; DNA, Protozoan/genetics/isolation &amp; purification ; Feces/parasitology ; Genotype ; Humans ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA/*methods ; },
abstract = {Several typing methods have been used in studies aiming to unravel the molecular epidemiology of Blastocystis, which is one of the most common intestinal parasites in human and many non-human hosts. Such studies have the potential to add to knowledge on Blastocystis transmission, host specificity, phylogeography, and clinical and public health significance, but rely on robust, standardized methods by which data can be generated and compared directly between studies. One of the most used methods is "barcoding,", which involves single-round PCR amplification and sequencing of partial small subunit ribosomal RNA genes of the parasites. Recently, a publicly available online facility was developed for quick and standardized identification of subtypes (ribosomal lineages) and subtype alleles (variation within subtypes) based on sequence data obtained by barcoding PCR. Moreover, a modified barcoding approach is now available using nested PCR, which enables detection of mixed subtype infections. © 2016 by John Wiley &amp; Sons, Inc.},
}
@article {pmid27855191,
year = {2016},
author = {Yang, T and Zhang, TL and Guo, YH and Liu, X},
title = {Identification of Hybrids in Potamogeton: Incongruence between Plastid and ITS Regions Solved by a Novel Barcoding Marker PHYB.},
journal = {PloS one},
volume = {11},
number = {11},
pages = {e0166177},
pmid = {27855191},
issn = {1932-6203},
mesh = {Chimera/*genetics ; DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/genetics ; Genetic Markers ; Phylogeny ; Plastids/genetics ; Potamogetonaceae/classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {Potamogeton is one of the most difficult groups to clarify in aquatic plants, which has an extensive range of interspecific morphological and ecological diversity. Internal transcribed spacer (ITS) is prevalent for phylogenetic analysis in plants. However, most researches demonstrate that ITS has a high percentage of homoplasy in phylogenetic datasets. In this study, eighteen materials were collected in Potamogeton from China and incongruence was shown between the rbcL and ITS phylogenies. To solve the discrepancy, we employed a novel barcode PHYB to improve resolution and accuracy of the phylogenetic relationships. The PHYB phylogeny successfully resolved the incongruence between the rbcL and ITS phylogenies. In addition, six hybrids were confirmed using PHYB, including P. compressus × P. pusillus, P. octandrus × P. oxyphyllus, P. gramineus × P. lucens, P. distinctus × P. natans, P. distinctus × P. wrightii, and S. pectinata × S. amblyophylla. Whereas, only one hybrid was identified (P. compressus × P. pusillus) by ITS, indicating that ITS homoplasy was present in Potamogeton and ITS was completely homogenized to one parental lineage. Thus, ITS might have limited utility for phylogenetic relationships in Potamogeton. It is recommended that a three-locus combination of chloroplast DNA gene, ITS and PHYB is potential to effectively reveal more robust phylogenetic relationships and species identification.},
}
@article {pmid27852862,
year = {2017},
author = {Earley, LF and Powers, JM and Adachi, K and Baumgart, JT and Meyer, NL and Xie, Q and Chapman, MS and Nakai, H},
title = {Adeno-associated Virus (AAV) Assembly-Activating Protein Is Not an Essential Requirement for Capsid Assembly of AAV Serotypes 4, 5, and 11.},
journal = {Journal of virology},
volume = {91},
number = {3},
pages = {},
pmid = {27852862},
issn = {1098-5514},
support = {R01 GM066875/GM/NIGMS NIH HHS/United States ; T32 AI007472/AI/NIAID NIH HHS/United States ; T32 GM071338/GM/NIGMS NIH HHS/United States ; T32 EY023211/EY/NEI NIH HHS/United States ; P41 RR006009/RR/NCRR NIH HHS/United States ; R01 DK078388/DK/NIDDK NIH HHS/United States ; R01 NS088399/NS/NINDS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Capsid/*metabolism ; Capsid Proteins/chemistry/genetics/*metabolism ; Dependovirus/classification/*physiology/ultrastructure ; Gene Expression ; Genetic Complementation Test ; Genetic Vectors/genetics ; Humans ; Serogroup ; Viral Proteins/chemistry/genetics/*metabolism ; Virion ; *Virus Assembly ; Virus Replication ; },
abstract = {UNLABELLED: Adeno-associated virus (AAV) vectors have made great progress in their use for gene therapy; however, fundamental aspects of AAV's capsid assembly remain poorly characterized. In this regard, the discovery of assembly-activating protein (AAP) sheds new light on this crucial part of AAV biology and vector production. Previous studies have shown that AAP is essential for assembly; however, how its mechanistic roles in assembly might differ among AAV serotypes remains uncharacterized. Here, we show that biological properties of AAPs and capsid assembly processes are surprisingly distinct among AAV serotypes 1 to 12. In the study, we investigated subcellular localizations and assembly-promoting functions of AAP1 to -12 (i.e., AAPs derived from AAV1 to -12, respectively) and examined the AAP dependence of capsid assembly processes of these 12 serotypes using combinatorial approaches that involved immunofluorescence and transmission electron microscopy, barcode-Seq (i. e., a high-throughput quantitative method using DNA barcodes and a next-generation sequencing technology), and quantitative dot blot assays. This study revealed that AAP1 to -12 are all localized in the nucleus with serotype-specific differential patterns of nucleolar association; AAPs and assembled capsids do not necessarily colocalize; AAPs are promiscuous in promoting capsid assembly of other serotypes, with the exception of AAP4, -5, -11, and -12; assembled AAV5, -8, and -9 capsids are excluded from the nucleolus, in contrast to the nucleolar enrichment of assembled AAV2 capsids; and, surprisingly, AAV4, -5, and -11 capsids are not dependent on AAP for assembly. These observations highlight the serotype-dependent heterogeneity of the capsid assembly process and challenge current notions about the role of AAP and the nucleolus in capsid assembly.<br><br>IMPORTANCE: Assembly-activating protein (AAP) is a recently discovered adeno-associated virus (AAV) protein that promotes capsid assembly and provides new opportunities for research in assembly. Previous studies on AAV serotype 2 (AAV2) showed that assembly takes place in the nucleolus and is dependent on AAP and that capsids colocalize with AAP in the nucleolus during the assembly process. However, through the investigation of 12 different AAV serotypes (AAV1 to -12), we find that AAP is not an essential requirement for capsid assembly of AAV4, -5, and -11, and AAP, assembled capsids, and the nucleolus do not colocalize for all the serotypes. In addition, we find that there are both serotype-restricted and serotype-promiscuous AAPs in their assembly roles. These findings challenge widely held beliefs about the importance of the nucleolus and AAP in AAV assembly and show the heterogeneous nature of the assembly process within the AAV family.},
}
@article {pmid27851823,
year = {2016},
author = {Garg, S and Biju, SD},
title = {Molecular and Morphological Study of Leaping Frogs (Anura, Ranixalidae) with Description of Two New Species.},
journal = {PloS one},
volume = {11},
number = {11},
pages = {e0166326},
pmid = {27851823},
issn = {1932-6203},
mesh = {Animals ; Anura/*anatomy &amp; histology/*genetics ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Ecosystem ; Female ; Likelihood Functions ; Male ; *Phylogeny ; Species Specificity ; },
abstract = {The monotypic anuran family Ranixalidae is endemic to India, with a predominant distribution in the Western Ghats, a region that is home to several unique amphibian lineages. It is also one of the three ancient anuran families that diversified on the Indian landmass long before several larger radiations of extant frogs in this region. In recent years, ranixalids have been subjected to DNA barcoding and systematic studies. Nearly half of the presently recognized species in this family have been described over the last three years, along with recognition of a new genus to accommodate three previously known members. Our surveys in the Western Ghats further suggest the presence of undescribed diversity in this group, thereby increasing former diversity estimates. Based on rapid genetic identification using a mitochondrial gene, followed by phylogenetic analyses with an additional nuclear gene and detailed morphological studies including examination of museum specimens, new collections, and available literature, here we describe two new species belonging to the genus Indirana from the Western Ghats states of Karnataka and Kerala. We also provide new genetic and morphological data along with confirmed distribution records for all the species known prior to this study. This updated systematic revision of family Ranixalidae will facilitate future studies and provide vital information for conservation assessment of these relic frogs.},
}
@article {pmid27845571,
year = {2016},
author = {Bringloe, TT and Cottenie, K and Martin, GK and Adamowicz, SJ},
title = {The importance of taxonomic resolution for additive beta diversity as revealed through DNA barcoding.},
journal = {Genome},
volume = {59},
number = {12},
pages = {1130-1140},
doi = {10.1139/gen-2016-0080},
pmid = {27845571},
issn = {1480-3321},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Insecta/*classification/*genetics ; Manitoba ; Pennsylvania ; },
abstract = {Additive diversity partitioning (α, β, and γ) is commonly used to study the distribution of species-level diversity across spatial scales. Here, we first investigate whether published studies of additive diversity partitioning show signs of difficulty attaining species-level resolution due to inherent limitations with morphological identifications. Second, we present a DNA barcoding approach to delineate specimens of stream caddisfly larvae (order Trichoptera) and consider the importance of taxonomic resolution on classical (additive) measures of beta (β) diversity. Caddisfly larvae were sampled using a hierarchical spatial design in two regions (subarctic Churchill, Manitoba, Canada; temperate Pennsylvania, USA) and then additively partitioned according to Barcode Index Numbers (molecular clusters that serve as a proxy for species), genus, and family levels; diversity components were expressed as proportional species turnover. We screened 114 articles of additive diversity partitioning and found that a third reported difficulties with achieving species-level identifications, with a clear taxonomic tendency towards challenges identifying invertebrate taxa. Regarding our own study, caddisfly BINs appeared to show greater subregional turnover (e.g., proportional additive β) compared to genus or family levels. Diversity component studies failing to achieve species resolution due to morphological identifications may therefore be underestimating diversity turnover at larger spatial scales.},
}
@article {pmid27843766,
year = {2016},
author = {Green, R and Wilkins, C and Thomas, S and Sekine, A and Ireton, RC and Ferris, MT and Hendrick, DM and Voss, K and de Villena, FP and Baric, R and Heise, M and Gale, M},
title = {Identifying protective host gene expression signatures within the spleen during West Nile virus infection in the collaborative cross model.},
journal = {Genomics data},
volume = {10},
number = {},
pages = {114-117},
pmid = {27843766},
issn = {2213-5960},
support = {P51 OD010425/OD/NIH HHS/United States ; R01 AI104002/AI/NIAID NIH HHS/United States ; U19 AI083019/AI/NIAID NIH HHS/United States ; U19 AI100625/AI/NIAID NIH HHS/United States ; },
abstract = {Flaviviruses are hematophagous arthropod-viruses that pose global challenges to human health. Like Zika virus, West Nile Virus (WNV) is a flavivirus for which no approved vaccine exists [1]. The role host genetics play in early detection and response to WNV still remains largely unexplained. In order to capture the impact of genetic variation on innate immune responses, we studied gene expression following WNV infection using the collaborative cross (CC). The CC is a mouse genetics resource composed of hundreds of independently bred, octo-parental recombinant inbred mouse lines [2]. To accurately capture the host immune gene expression signatures of West Nile infection, we used the nanostring platform to evaluate expression in spleen tissue isolated from CC mice infected with WNV over a time course of 4, 7, and 12 days' post-infection [3]. Nanostring is a non-amplification based digital method to quantitate gene expression that uses color-coded molecular barcodes to detect hundreds of transcripts in a sample. Using this approach, we identified unique gene signatures in spleen tissue at days 4, 7, and 12 following WNV infection, which delineated distinct differences between asymptomatic and symptomatic CC lines. We also identified novel immune genes. Data was deposited into the Gene Expression Omnibus under accession GSE86000.},
}
@article {pmid27842955,
year = {2017},
author = {Krueger, A and Ziętara, N and Łyszkiewicz, M},
title = {T Cell Development by the Numbers.},
journal = {Trends in immunology},
volume = {38},
number = {2},
pages = {128-139},
doi = {10.1016/j.it.2016.10.007},
pmid = {27842955},
issn = {1471-4981},
mesh = {Animals ; *Cell Differentiation ; Cell Lineage ; Hematopoiesis ; Humans ; Immunoassay ; Lymphocyte Activation ; *Models, Theoretical ; Precursor Cells, T-Lymphoid/*physiology ; Receptors, Antigen, T-Cell/genetics/metabolism ; T-Lymphocytes/*physiology ; Thymus Gland/*immunology ; },
abstract = {T cells are continually generated in the thymus in a highly dynamic process comprising discrete steps of lineage commitment, T cell receptor (TCR) gene rearrangement, and selection. These steps are linked to distinct rates of proliferation, survival, and cell death, but a quantitative picture of T cell development is only beginning to emerge. Here we summarize recent technical advances, including genetic fate mapping, barcoding, and molecular timers, that have allowed the implementation of computational models to quantify developmental dynamics in the thymus. Coupling new techniques with mathematical models has recently resulted in the emergence of new paradigms in early hematopoiesis and might similarly open new perspectives on T cell development.},
}
@article {pmid27841048,
year = {2018},
author = {Naseem, S and Tahir, HM},
title = {Use of mitochondrial COI gene for the identification of family Salticidae and Lycosidae of spiders.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {1},
pages = {96-101},
doi = {10.1080/24701394.2016.1248428},
pmid = {27841048},
issn = {2470-1408},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Genes, Mitochondrial ; Reproducibility of Results ; Spiders/*classification/genetics/metabolism ; },
abstract = {In recent years, DNA barcoding has become quite popular for molecular identification of species because it is simple, quick and an affordable method. Present study was conducted to identify spiders of most abundant families, i.e. Salticidae and Lycosidae from citrus orchards in Sargodha district using DNA barcoding. A total of 160 specimens were subjected to DNA barcoding but, sequences up to 600 bp were recovered for 156 specimens. This molecular approach proved helpful to assign the exact taxon to those specimens which were misidentified through morphological characters in the study. We were succeeded to discriminate six species of Lycosidae and nine species of Salticidae through DNA barcoding. Results revealed the presence of clear barcode gap (discontinuity in intra- and inter-specific divergences) for members of both families. Furthermore, the maximum intra-specific divergence was less than NN (nearest neighbour) distance for all species. This suggested the reliability of DNA barcoding for spider's identification up to species level. We got 98% success in our study. It is concluded from present study that DNA barcoding is more reliable tool especially for immature spiders, when morphological characters are ambiguous.},
}
@article {pmid27840197,
year = {2017},
author = {Ayadi, ZEM and Gey, D and Justine, JL and Tazerouti, F},
title = {A new species of Microcotyle (Monogenea: Microcotylidae) from Scorpaena notata (Teleostei: Scorpaenidae) in the Mediterranean Sea.},
journal = {Parasitology international},
volume = {66},
number = {2},
pages = {37-42},
doi = {10.1016/j.parint.2016.11.004},
pmid = {27840197},
issn = {1873-0329},
mesh = {Algeria ; Animals ; DNA Barcoding, Taxonomic ; Gills/parasitology ; Mediterranean Sea ; Perciformes/*parasitology ; Phylogeny ; Trematoda/*anatomy &amp; histology/classification/*genetics/isolation &amp; purification ; },
abstract = {We collected specimens of Microcotyle spp. from two species of scorpaeniform fishes off Algeria, namely Scorpaena notata and Helicolenus dactylopterus. The identification of both fishes was confirmed by molecular barcoding of the COI gene. Sequences of COI gene were also obtained for both parasite species. The species from S. notata is described as Microcotyle algeriensis n. sp., on the basis of morphological differences from other species (number of clamps, number of spines in genital atrium, number of testes). Its COI sequence differs from M. sebastis Goto, 1894 (from Sebastes schlegeli from a fish farm in South Korea) by 14.6%. The species from H. dactylopterus is distinct from M. algeriensis on the basis of morphology (number of clamps, number of spines in genital atrium) and COI sequence (4.5% divergence) and is also distinct from M. sebastis in its COI sequence (12.3%). We refrained from describing it as new because M. sebastis, a species originally described from scorpaeniform fishes off Japan, has been recorded in various hosts in the North and South Pacific, Atlantic and Mediterranean (for the latter, in the same host, H. dactylopterus). We believe that correct specific assignment of species of Microcotyle from scorpaeniform fishes needs a detailed morphological and molecular study of representatives from various locations and hosts.},
}
@article {pmid27838750,
year = {2017},
author = {Ito, H and Tanaka, M and Zhou, Y and Nashimoto, Y and Takahashi, Y and Ino, K and Matsue, T and Shiku, H},
title = {Continuous collection and simultaneous detection of picoliter volume of nucleic acid samples using a mille-feuille probe.},
journal = {Analytical and bioanalytical chemistry},
volume = {409},
number = {4},
pages = {961-969},
doi = {10.1007/s00216-016-0006-y},
pmid = {27838750},
issn = {1618-2650},
mesh = {Base Sequence ; DNA, Complementary/*analysis ; Humans ; Limit of Detection ; MCF-7 Cells ; *Molecular Probes ; Polymerase Chain Reaction/methods ; RNA, Messenger/*analysis ; },
abstract = {Investigation of the positional heterogeneity of messenger RNA (mRNA) expression in tissues requires a technology that facilitates analysis of mRNA expression in the selected single cells. We developed a mille-feuille probe (MP) that allows the lamination of the aqueous and organic phases in a nanopipette under voltage control. The MP was used for continuous collection of different nucleic acid samples and sequential evaluation of gene expression with mRNA barcoding tags. First, we found that the aqueous phases could be laminated into five individual layers and separated by the plugs of the organic phases in a nanopipette when the salt (THATPBCl) concentration in the organic phase was 100 mM. Second, the aspiration rate of the MP was stabilized and the velocity of the aqueous phase in the MP was lowered at higher THATPBCl concentrations in the organic phase. This was because the force during ingression of the aqueous phase into the organic - phase-filled nanopipette induced an electro-osmotic flow between the inside wall of the nanopipette and THATPBCl in the organic phase. Third, inclusion of mRNA barcoding tags in the MP facilitated complementary DNA construction and sequential analysis of gene expression. This technique has potential to be applicable to RNA sequencing from different cell samples across the life sciences. Graphical abstract We developed a mille-feuille probe (MP) that allows the lamination of the aqueous and organic phases in a nanopipette under voltage control.},
}
@article {pmid27838203,
year = {2017},
author = {Amini, B and Kamali, M and Salouti, M and Yaghmaei, P},
title = {Fluorescence bio-barcode DNA assay based on gold and magnetic nanoparticles for detection of Exotoxin A gene sequence.},
journal = {Biosensors &amp; bioelectronics},
volume = {92},
number = {},
pages = {679-686},
doi = {10.1016/j.bios.2016.10.030},
pmid = {27838203},
issn = {1873-4235},
mesh = {ADP Ribose Transferases/*genetics ; Bacterial Toxins/*genetics ; Biosensing Techniques/methods ; DNA Probes/chemistry/genetics ; DNA, Bacterial/analysis/*genetics ; Exotoxins/*genetics ; Gold/*chemistry ; Humans ; Limit of Detection ; Magnetite Nanoparticles/*chemistry/ultrastructure ; Metal Nanoparticles/*chemistry/ultrastructure ; Pseudomonas Infections/diagnosis/microbiology ; Pseudomonas aeruginosa/*genetics ; Spectrometry, Fluorescence/methods ; Virulence Factors/*genetics ; Pseudomonas aeruginosa Exotoxin A ; },
abstract = {Bio-barcode DNA based on gold nanoparticle (bDNA-GNPs) as a new generation of biosensor based detection tools, holds promise for biological science studies. They are of enormous importance in the emergence of rapid and sensitive procedures for detecting toxins of microorganisms. Exotoxin A (ETA) is the most toxic virulence factor of Pseudomonas aeruginosa. ETA has ADP-ribosylation activity and decisively affects the protein synthesis of the host cells. In the present study, we developed a fluorescence bio-barcode technology to trace P. aeruginosa ETA. The GNPs were coated with the first target-specific DNA probe 1 (1pDNA) and bio-barcode DNA, which acted as a signal reporter. The magnetic nanoparticles (MNPs) were coated with the second target-specific DNA probe 2 (2pDNA) that was able to recognize the other end of the target DNA. After binding the nanoparticles with the target DNA, the following sandwich structure was formed: MNP 2pDNA/tDNA/1pDNA-GNP-bDNA. After isolating the sandwiches by a magnetic field, the DNAs of the probes which have been hybridized to their complementary DNA, GNPs and MNPs, via the hydrogen, electrostatic and covalently bonds, were released from the sandwiches after dissolving in dithiothreitol solution (DTT 0.8M). This bio-barcode DNA with known DNA sequence was then detected by fluorescence spectrophotometry. The findings showed that the new method has the advantages of fast, high sensitivity (the detection limit was 1.2ng/ml), good selectivity, and wide linear range of 5-200ng/ml. The regression analysis also showed that there was a good linear relationship (∆F=0.57 [target DNA]+21.31, R[2]=0.9984) between the fluorescent intensity and the target DNA concentration in the samples.},
}
@article {pmid27833426,
year = {2016},
author = {Salles, FF and Domínguez, E and Mariano, R and Paresque, R},
title = {The imagos of some enigmatic members of the Hermanella complex (Ephemeroptera, Leptophlebiidae).},
journal = {ZooKeys},
volume = {},
number = {625},
pages = {45-66},
pmid = {27833426},
issn = {1313-2989},
abstract = {The imago stages of three species of the Hermanella complex are described mostly based on material from Roraima, northern Brazil: Hydrosmilodon gilliesae, Hydromastodon sallesi and Leentvaaria palpalis. Male imagos of Hydrosmilodon gilliesae and Leentvaaria palpalis both have a pair of large, broad projections at the posterior margin of the styliger plate, nearly covering the penis lobes; in Leentvaaria palpalis, however, these projections are fused. The male imago of Hydromastodon sallesi resembles Hydrosmilodon plagatus in that both species have a styliger plate with a robust projection that is curved towards the penis lobes. DNA barcoding is likely to be a powerful investigative tool for identifying and understanding species limits among these Ephemeroptera taxa, especially if it is used within an integrative taxonomic context. An updated identification key to the genera of the Hermanella complex is proposed.},
}
@article {pmid27830705,
year = {2016},
author = {Yaari, Z and da Silva, D and Zinger, A and Goldman, E and Kajal, A and Tshuva, R and Barak, E and Dahan, N and Hershkovitz, D and Goldfeder, M and Roitman, JS and Schroeder, A},
title = {Theranostic barcoded nanoparticles for personalized cancer medicine.},
journal = {Nature communications},
volume = {7},
number = {},
pages = {13325},
pmid = {27830705},
issn = {2041-1723},
mesh = {Animals ; Antineoplastic Agents/chemistry/therapeutic use ; Base Sequence ; Cell Line, Tumor ; DNA/*chemistry/genetics ; Drug Carriers/chemistry ; Female ; Humans ; Kaplan-Meier Estimate ; Mice, Inbred BALB C ; Nanoparticles/*chemistry/ultrastructure ; Neoplasms/diagnosis/drug therapy/genetics ; Precision Medicine/*methods ; Theranostic Nanomedicine/*methods ; Triple Negative Breast Neoplasms/diagnosis/drug therapy/genetics ; },
abstract = {Personalized medicine promises to revolutionize cancer therapy by matching the most effective treatment to the individual patient. Using a nanoparticle-based system, we predict the therapeutic potency of anticancer medicines in a personalized manner. We carry out the diagnostic stage through a multidrug screen performed inside the tumour, extracting drug activity information with single cell sensitivity. By using 100 nm liposomes, loaded with various cancer drugs and corresponding synthetic DNA barcodes, we find a correlation between the cell viability and the drug it was exposed to, according to the matching barcodes. Based on this screen, we devise a treatment protocol for mice bearing triple-negative breast-cancer tumours, and its results confirm the diagnostic prediction. We show that the use of nanotechnology in cancer care is effective for generating personalized treatment protocols.},
}
@article {pmid27830049,
year = {2016},
author = {Gomes Júnior, RG and Schneider, CH and de Lira, T and Carvalho, ND and Feldberg, E and da Silva, MN and Gross, MC},
title = {Intense genomic reorganization in the genus Oecomys (Rodentia, Sigmodontinae): comparison between DNA barcoding and mapping of repetitive elements in three species of the Brazilian Amazon.},
journal = {Comparative cytogenetics},
volume = {10},
number = {3},
pages = {401-426},
pmid = {27830049},
issn = {1993-0771},
abstract = {Oecomys Thomas, 1906 is one of the most diverse and widely distributed genera within the tribe Oryzomyini. At least sixteen species in this genus have been described to date, but it is believed this genus contains undescribed species. Morphological, molecular and cytogenetic study has revealed an uncertain taxonomic status for several Oecomys species, suggesting the presence of a complex of species. The present work had the goal of contributing to the genetic characterization of the genus Oecomys in the Brazilian Amazon. Thirty specimens were collected from four locations in the Brazilian Amazon and three nominal species recognized: Oecomys auyantepui (Tate, 1939), Oecomys bicolor (Tomes, 1860) and Oecomys rutilus (Anthony, 1921). COI sequence analysis grouped Oecomys auyantepui, Oecomys bicolor and Oecomys rutilus specimens into one, three and two clades, respectively, which is consistent with their geographic distribution. Cytogenetic data for Oecomys auyantepui revealed the sympatric occurrence of two different diploid numbers, 2n=64/NFa=110 and 2n=66/NFa=114, suggesting polymorphism while Oecomys bicolor exhibited 2n=80/NFa=142 and Oecomys rutilus 2n=54/NFa=90. The distribution of constitutive heterochromatin followed a species-specific pattern. Interspecific variation was evident in the chromosomal location and number of 18S rDNA loci. However, not all loci showed signs of activity. All three species displayed a similar pattern for 5S rDNA, with only one pair carrying this locus. Interstitial telomeric sites were found only in Oecomys auyantepui. The data presented in this work reinforce intra- and interspecific variations observed in the diploid number of Oecomys species and indicate that chromosomal rearrangements have led to the appearance of different diploid numbers and karyotypic formulas.},
}
@article {pmid27829794,
year = {2016},
author = {Chaveerach, A and Tanee, T and Sanubol, A and Monkheang, P and Sudmoon, R},
title = {Efficient DNA barcode regions for classifying Piper species (Piperaceae).},
journal = {PhytoKeys},
volume = {},
number = {70},
pages = {1-10},
pmid = {27829794},
issn = {1314-2011},
abstract = {Piper species are used for spices, in traditional and processed forms of medicines, in cosmetic compounds, in cultural activities and insecticides. Here barcode analysis was performed for identification of plant parts, young plants and modified forms of plants. Thirty-six Piper species were collected and the three barcode regions, matK, rbcL and psbA-trnH spacer, were amplified, sequenced and aligned to determine their genetic distances. For intraspecific genetic distances, the most effective values for the species identification ranged from no difference to very low distance values. However, Piper betle had the highest values at 0.386 for the matK region. This finding may be due to Piper betle being an economic and cultivated species, and thus is supported with growth factors, which may have affected its genetic distance. The interspecific genetic distances that were most effective for identification of different species were from the matK region and ranged from a low of 0.002 in 27 paired species to a high of 0.486. Eight species pairs, Piper kraense and Piper dominantinervium, Piper magnibaccum and Piper kraense, Piper phuwuaense and Piper dominantinervium, Piper phuwuaense and Piper kraense, Piper pilobracteatum and Piper dominantinervium, Piper pilobracteatum and Piper kraense, Piper pilobracteatum and Piper phuwuaense and Piper sylvestre and Piper polysyphonum, that presented a genetic distance of 0.000 and were identified by independently using each of the other two regions. Concisely, these three barcode regions are powerful for further efficient identification of the 36 Piper species.},
}
@article {pmid27829786,
year = {2016},
author = {Burridge, AK and Janssen, AW and Peijnenburg, KT},
title = {Revision of the genus Cuvierina Boas, 1886 based on integrative taxonomic data, including the description of a new species from the Pacific Ocean (Gastropoda, Thecosomata).},
journal = {ZooKeys},
volume = {},
number = {619},
pages = {1-12},
pmid = {27829786},
issn = {1313-2989},
abstract = {Shelled pteropods (Gastropoda, Thecosomata, Euthecosomata) are a group of holoplanktonic gastropods that occur predominantly in the surface layers of the world's oceans. Accurate species identifications are essential for tracking changes in species assemblages of planktonic gastropods, because different species are expected to have different sensitivities to ocean changes. The genus Cuvierina has a worldwide warm water distribution pattern between ~36°N and ~39°S. Based on an integrative taxonomic approach combining morphometric, genetic, and biogeographic information, the two subgenera of Cuvierina, Cuvierinas. str. and Urceolarica, are rejected. A new species is introduced: Cuvierina tsudaisp. n., which has to date been considered the same species as Cuvierina pacifica. Cuvierina tsudaisp. n. is endemic to the Pacific Ocean and is characterised by a shell height of 7.2-8.0 mm, a moderately cylindrical shell shape, the absence of micro-ornamentation and a triangular aperture. Cuvierina pacifica is restricted to the centre of the oligotrophic southern Pacific gyre, has a shell height of 6.6-8.5 mm, a more cylindrical shell shape, no micro-ornamentation and a less triangular aperture than Cuvierina tsudaisp. n.},
}
@article {pmid27829307,
year = {2016},
author = {Adamowicz, SJ and Chain, FJ and Clare, EL and Deiner, K and Dincă, V and Elías-Gutiérrez, M and Hausmann, A and Hogg, ID and Kekkonen, M and Lijtmaer, DA and Naaum, A and Steinke, D and Valdez-Moreno, M and Van der Bank, M and Wilson, JJ and Xu, J},
title = {From Barcodes to Biomes: Special Issues from the 6th International Barcode of Life Conference.},
journal = {Genome},
volume = {59},
number = {11},
pages = {v-ix},
doi = {10.1139/gen-2016-0195},
pmid = {27829307},
issn = {1480-3321},
mesh = {Animals ; Biodiversity ; *DNA Barcoding, Taxonomic/methods/standards ; Ecosystem ; Humans ; International Cooperation ; Inventions ; },
}
@article {pmid27829306,
year = {2016},
author = {Xu, J},
title = {Fungal DNA barcoding.},
journal = {Genome},
volume = {59},
number = {11},
pages = {913-932},
doi = {10.1139/gen-2016-0046},
pmid = {27829306},
issn = {1480-3321},
mesh = {Animals ; Biodiversity ; *DNA Barcoding, Taxonomic/methods/standards ; DNA, Fungal ; DNA, Intergenic ; Databases, Nucleic Acid/standards ; Environmental Microbiology ; Food Microbiology ; Fungi/*classification/*genetics/metabolism ; Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; Microbiota ; Mouth/microbiology ; Research ; Sequence Analysis, DNA/methods ; Soil Microbiology ; },
abstract = {Fungi are ubiquitous in both natural and human-made environments. They play important roles in the health of plants, animals, and humans, and in broad ecosystem functions. Thus, having an efficient species-level identification system could significantly enhance our ability to treat fungal diseases and to monitor the spatial and temporal patterns of fungal distributions and migrations. DNA barcoding is a potent approach for rapid identification of fungal specimens, generating novel species hypothesis, and guiding biodiversity and ecological studies. In this mini-review, I briefly summarize (i) the history of DNA sequence-based fungal identification; (ii) the emergence of the ITS region as the consensus primary fungal barcode; (iii) the use of the ITS barcodes to address a variety of issues on fungal diversity from local to global scales, including generating a large number of species hypothesis; and (iv) the problems with the ITS barcode region and the approaches to overcome these problems. Similar to DNA barcoding research on plants and animals, significant progress has been achieved over the last few years in terms of both the questions being addressed and the foundations being laid for future research endeavors. However, significant challenges remain. I suggest three broad areas of research to enhance the usefulness of fungal DNA barcoding to meet the current and future challenges: (i) develop a common set of primers and technologies that allow the amplification and sequencing of all fungi at both the primary and secondary barcode loci; (ii) compile a centralized reference database that includes all recognized fungal species as well as species hypothesis, and allows regular updates from the research community; and (iii) establish a consensus set of new species recognition criteria based on barcode DNA sequences that can be applied across the fungal kingdom.},
}
@article {pmid27829305,
year = {2016},
author = {},
title = {Barcodes to Biomes / Codes barres pour biomes.},
journal = {Genome},
volume = {59},
number = {11},
pages = {iii},
doi = {10.1139/gen-2016-0194},
pmid = {27829305},
issn = {1480-3321},
}
@article {pmid27829037,
year = {2016},
author = {von Beeren, C and Maruyama, M and Kronauer, DJ},
title = {Community Sampling and Integrative Taxonomy Reveal New Species and Host Specificity in the Army Ant-Associated Beetle Genus Tetradonia (Coleoptera, Staphylinidae, Aleocharinae).},
journal = {PloS one},
volume = {11},
number = {11},
pages = {e0165056},
pmid = {27829037},
issn = {1932-6203},
mesh = {Animals ; Ants/classification/*parasitology ; Aspartate Carbamoyltransferase/classification/genetics ; *Biodiversity ; Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing)/classification/genetics ; Coleoptera/classification/genetics/*physiology ; Costa Rica ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/chemistry/genetics ; Dihydroorotase/classification/genetics ; Electron Transport Complex IV/classification/genetics ; Host Specificity ; Insect Proteins/classification/genetics ; Phylogeny ; Species Specificity ; *Symbiosis ; },
abstract = {Army ant colonies host a diverse community of arthropod symbionts. Among the best-studied symbiont communities are those of Neotropical army ants of the genus Eciton. It is clear, however, that even in these comparatively well studied systems, a large proportion of symbiont biodiversity remains unknown. Even more striking is our lack of knowledge regarding the nature and specificity of these host-symbiont interactions. Here we surveyed the diversity and host specificity of rove beetles of the genus Tetradonia Wasmann, 1894 (Staphylinidae: Aleocharinae). Systematic community sampling of 58 colonies of the six local Eciton species at La Selva Biological Station, Costa Rica, combined with an integrative taxonomic approach, allowed us to uncover species diversity, host specificity, and co-occurrence patterns of symbionts in unprecedented detail. We used an integrative taxonomic approach combining morphological and genetic analyses, to delineate species boundaries. Mitochondrial DNA barcodes were analyzed for 362 Tetradonia specimens, and additional nuclear markers for a subset of 88 specimens. All analyses supported the presence of five Tetradonia species, including two species new to science. Host specificity is highly variable across species, ranging from generalists such as T. laticeps, which parasitizes all six local Eciton species, to specialists such as T. lizonae, which primarily parasitizes a single species, E. hamatum. Here we provide a dichotomous key along with diagnostic molecular characters for identification of Tetradonia species at La Selva Biological Station. By reliably assessing biodiversity and providing tools for species identification, we hope to set the baseline for future studies of the ecological and evolutionary dynamics in these species-rich host-symbiont networks.},
}
@article {pmid27828981,
year = {2016},
author = {Cramer, CA and Melo de Sousa, L},
title = {A New Species of Tiger Pleco Panaqolus (Siluriformes: Loricariidae) from the Xingu Basin, Brazil.},
journal = {PloS one},
volume = {11},
number = {11},
pages = {e0165388},
pmid = {27828981},
issn = {1932-6203},
mesh = {Animal Distribution/*physiology ; Animal Fins/anatomy &amp; histology ; Animals ; Body Size ; Brazil ; Catfishes/anatomy &amp; histology/classification/*genetics ; *DNA Barcoding, Taxonomic ; Databases, Nucleic Acid ; Electron Transport Complex IV/*genetics ; Female ; Male ; *Phylogeny ; Pigmentation/physiology ; Power Plants ; Rivers ; },
abstract = {Panaqolus tankei is described from the Xingu River, Brazil. The new species is diagnosed from P. albomaculatus, P. dentex, P. nix, P. nocturnus, and P. koko by its color pattern consisting of dark and light diagonal bars on the body and bands on the fins (vs. body and fins without bars or bands); from P. albivermis, P. maccus, and P. purusiensis by the width of the dark bars being more or less the same of the light bars (vs. dark bars at least two or three times wider than light bars) and from P. changae by the absence of vermiculation on the head (vs. vermiculation present on head). The new species differs from P. gnomus by the orientation of the bars from posterodorsal to anteroventral direction (vs. anterodorsal to posteroventral direction), and from P. claustellifer by the orientation of the bands in the dorsal fin that are not parallel to the margin (vs. parallel to the margin). The barcoding region (COI) was sequenced for the new species, sequences were deposited in GenBank and were compared with congeners from other drainages. With regard to the current construction of a hydroelectric power plant (a so-called mega dam) in the Xingu River, herewith we increase knowledge of the river Xingu's ichthyofauna and, thus improve the assessment of the impacts of that construction on the river.},
}
@article {pmid27827440,
year = {2016},
author = {Zou, S and Fei, C and Wang, C and Gao, Z and Bao, Y and He, M and Wang, C},
title = {How DNA barcoding can be more effective in microalgae identification: a case of cryptic diversity revelation in Scenedesmus (Chlorophyceae).},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {36822},
pmid = {27827440},
issn = {2045-2322},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal/genetics ; Phylogeny ; Plant Proteins/*genetics ; Scenedesmus/*classification/genetics ; Species Specificity ; },
abstract = {Microalgae identification is extremely difficult. The efficiency of DNA barcoding in microalgae identification involves ideal gene markers and approaches employed, which however, is still under the way. Although Scenedesmus has obtained much research in producing lipids its identification is difficult. Here we present a comprehensive coalescent, distance and character-based DNA barcoding for 118 Scenedesmus strains based on rbcL, tufA, ITS and 16S. The four genes, and their combined data rbcL + tufA + ITS + 16S, rbcL + tufA and ITS + 16S were analyzed by all of GMYC, P ID, PTP, ABGD, and character-based barcoding respectively. It was apparent that the three combined gene data showed a higher proportion of resolution success than the single gene. In comparison, the GMYC and PTP analysis produced more taxonomic lineages. The ABGD generated various resolution in discrimination among the single and combined data. The character-based barcoding was proved to be the most effective approach for species discrimination in both single and combined data which produced consistent species identification. All the integrated results recovered 11 species, five out of which were revealed as potential cryptic species. We suggest that the character-based DNA barcoding together with other approaches based on multiple genes and their combined data could be more effective in microalgae diversity revelation.},
}
@article {pmid27824508,
year = {2016},
author = {Barreira, AS and Lijtmaer, DA and Tubaro, PL},
title = {The multiple applications of DNA barcodes in avian evolutionary studies.},
journal = {Genome},
volume = {59},
number = {11},
pages = {899-911},
doi = {10.1139/gen-2016-0086},
pmid = {27824508},
issn = {1480-3321},
mesh = {Animals ; Biodiversity ; Birds/*classification/*genetics ; *DNA Barcoding, Taxonomic ; *Evolution, Molecular ; Genes, Mitochondrial ; Genetic Variation ; Phylogeny ; Phylogeography ; },
abstract = {DNA barcodes of birds are currently available for 41% of known species and for many different geographic areas; therefore, they are a rich data source to answer evolutionary questions. We review studies that have used DNA barcodes to investigate evolutionary processes in birds using diverse approaches. We also review studies that have investigated species in depth where taxonomy and DNA barcodes present inconsistencies. Species that showed low genetic interspecific divergence and lack of reciprocal monophyly either are the result of recent radiation and (or) hybridize, while species with large genetic splits in their COI sequences were determined to be more than one independent evolutionary unit. In addition, we review studies that employed large DNA barcode datasets to study the molecular evolution of mitochondrial genes and the biogeography of islands, continents, and even at a multi-continental scale. These studies showed that DNA barcodes offer high-quality data well beyond their main purpose of serving as a molecular tool for species identification.},
}
@article {pmid27824505,
year = {2016},
author = {Ouvrard, P and Hicks, DM and Mouland, M and Nicholls, JA and Baldock, KC and Goddard, MA and Kunin, WE and Potts, SG and Thieme, T and Veromann, E and Stone, GN},
title = {Molecular taxonomic analysis of the plant associations of adult pollen beetles (Nitidulidae: Meligethinae), and the population structure of Brassicogethes aeneus.},
journal = {Genome},
volume = {59},
number = {12},
pages = {1101-1116},
doi = {10.1139/gen-2016-0020},
pmid = {27824505},
issn = {1480-3321},
mesh = {Animals ; Brassica napus/*parasitology ; Coleoptera/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Genetic Variation ; Genetics, Population ; Haplotypes ; Phylogeny ; Selection, Genetic ; Sequence Analysis, DNA ; },
abstract = {Pollen beetles (Nitidulidae: Meligethinae) are among the most abundant flower-visiting insects in Europe. While some species damage millions of hectares of crops annually, the biology of many species is little known. We assessed the utility of a 797 base pair fragment of the cytochrome oxidase 1 gene to resolve molecular operational taxonomic units (MOTUs) in 750 adult pollen beetles sampled from flowers of 63 plant species sampled across the UK and continental Europe. We used the same locus to analyse region-scale patterns in population structure and demography in an economically important pest, Brassicogethes aeneus. We identified 44 Meligethinae at ∼2% divergence, 35 of which contained published sequences. A few specimens could not be identified because the MOTUs containing them included published sequences for multiple Linnaean species, suggesting either retention of ancestral haplotype polymorphism or identification errors in published sequences. Over 90% of UK specimens were identifiable as B. aeneus. Plant associations of adult B. aeneus were found to be far wider taxonomically than for their larvae. UK B. aeneus populations showed contrasting affiliations between the north (most similar to Scandinavia and the Baltic) and south (most similar to western continental Europe), with strong signatures of population growth in the south.},
}
@article {pmid27822864,
year = {2017},
author = {Vossen, RH and Buermans, HP},
title = {Full-Length Mitochondrial-DNA Sequencing on the PacBio RSII.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1492},
number = {},
pages = {179-184},
doi = {10.1007/978-1-4939-6442-0_12},
pmid = {27822864},
issn = {1940-6029},
mesh = {DNA, Mitochondrial/*genetics ; Humans ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA/*methods ; },
abstract = {Conventional mitochondrial-DNA (MT DNA) sequencing approaches use Sanger sequencing of 20-40 partially overlapping PCR fragments per individual, which is a time- and resource-consuming process. We have developed a high-throughput, accurate, fast, and cost-effective human MT DNA sequencing approach. In this setup we first generate long-range PCR products for two partially overlapping 7.7 and 9.2 kb MT DNA-specific amplicons, add sample-specific barcodes, and sequence these on the PacBio RSII system to obtain full-length MT DNA sequences for genotyping/haplotyping purposes.},
}
@article {pmid27822858,
year = {2017},
author = {Cantsilieris, S and Stessman, HA and Shendure, J and Eichler, EE},
title = {Targeted Capture and High-Throughput Sequencing Using Molecular Inversion Probes (MIPs).},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1492},
number = {},
pages = {95-106},
pmid = {27822858},
issn = {1940-6029},
support = {/HHMI_/Howard Hughes Medical Institute/United States ; T32 HG000035/HG/NHGRI NIH HHS/United States ; },
mesh = {High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Molecular Probes ; Polymerase Chain Reaction ; },
abstract = {Molecular inversion probes (MIPs) in combination with massively parallel DNA sequencing represent a versatile, yet economical tool for targeted sequencing of genomic DNA. Several thousand genomic targets can be selectively captured using long oligonucleotides containing unique targeting arms and universal linkers. The ability to append sequencing adaptors and sample-specific barcodes allows large-scale pooling and subsequent high-throughput sequencing at relatively low cost per sample. Here, we describe a "wet bench" protocol detailing the capture and subsequent sequencing of >2000 genomic targets from 192 samples, representative of a single lane on the Illumina HiSeq 2000 platform.},
}
@article {pmid27822536,
year = {2016},
author = {Moser, LA and Ramirez-Carvajal, L and Puri, V and Pauszek, SJ and Matthews, K and Dilley, KA and Mullan, C and McGraw, J and Khayat, M and Beeri, K and Yee, A and Dugan, V and Heise, MT and Frieman, MB and Rodriguez, LL and Bernard, KA and Wentworth, DE and Stockwell, TB and Shabman, RS},
title = {A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses.},
journal = {mSystems},
volume = {1},
number = {3},
pages = {},
pmid = {27822536},
issn = {2379-5077},
abstract = {Several biosafety level 3 and/or 4 (BSL-3/4) pathogens are high-consequence, single-stranded RNA viruses, and their genomes, when introduced into permissive cells, are infectious. Moreover, many of these viruses are select agents (SAs), and their genomes are also considered SAs. For this reason, cDNAs and/or their derivatives must be tested to ensure the absence of infectious virus and/or viral RNA before transfer out of the BSL-3/4 and/or SA laboratory. This tremendously limits the capacity to conduct viral genomic research, particularly the application of next-generation sequencing (NGS). Here, we present a sequence-independent method to rapidly amplify viral genomic RNA while simultaneously abolishing both viral and genomic RNA infectivity across multiple single-stranded positive-sense RNA (ssRNA+) virus families. The process generates barcoded DNA amplicons that range in length from 300 to 1,000 bp, which cannot be used to rescue a virus and are stable to transport at room temperature. Our barcoding approach allows for up to 288 barcoded samples to be pooled into a single library and run across various NGS platforms without potential reconstitution of the viral genome. Our data demonstrate that this approach provides full-length genomic sequence information not only from high-titer virion preparations but it can also recover specific viral sequence from samples with limited starting material in the background of cellular RNA, and it can be used to identify pathogens from unknown samples. In summary, we describe a rapid, universal standard operating procedure that generates high-quality NGS libraries free of infectious virus and infectious viral RNA. IMPORTANCE This report establishes and validates a standard operating procedure (SOP) for select agents (SAs) and other biosafety level 3 and/or 4 (BSL-3/4) RNA viruses to rapidly generate noninfectious, barcoded cDNA amenable for next-generation sequencing (NGS). This eliminates the burden of testing all processed samples derived from high-consequence pathogens prior to transfer from high-containment laboratories to lower-containment facilities for sequencing. Our established protocol can be scaled up for high-throughput sequencing of hundreds of samples simultaneously, which can dramatically reduce the cost and effort required for NGS library construction. NGS data from this SOP can provide complete genome coverage from viral stocks and can also detect virus-specific reads from limited starting material. Our data suggest that the procedure can be implemented and easily validated by institutional biosafety committees across research laboratories.},
}
@article {pmid27821633,
year = {2017},
author = {Jaffe, M and Sherlock, G and Levy, SF},
title = {iSeq: A New Double-Barcode Method for Detecting Dynamic Genetic Interactions in Yeast.},
journal = {G3 (Bethesda, Md.)},
volume = {7},
number = {1},
pages = {143-153},
pmid = {27821633},
issn = {2160-1836},
support = {R01 GM110275/GM/NIGMS NIH HHS/United States ; R01 HG008354/HG/NHGRI NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; },
mesh = {Aneuploidy ; Epistasis, Genetic ; Gene Expression Regulation, Fungal/genetics ; Gene Regulatory Networks/*genetics ; Gene-Environment Interaction ; Genotype ; Mutation ; Oligonucleotide Array Sequence Analysis/*methods ; Saccharomyces cerevisiae/*genetics ; Systems Biology/*methods ; },
abstract = {Systematic screens for genetic interactions are a cornerstone of both network and systems biology. However, most screens have been limited to characterizing interaction networks in a single environment. Moving beyond this static view of the cell requires a major technological advance to increase the throughput and ease of replication in these assays. Here, we introduce iSeq-a platform to build large double barcode libraries and rapidly assay genetic interactions across environments. We use iSeq in yeast to measure fitness in three conditions of nearly 400 clonal strains, representing 45 possible single or double gene deletions, including multiple replicate strains per genotype. We show that iSeq fitness and interaction scores are highly reproducible for the same clonal strain across replicate cultures. However, consistent with previous work, we find that replicates with the same putative genotype have highly variable genetic interaction scores. By whole-genome sequencing 102 of our strains, we find that segregating variation and de novo mutations, including aneuploidy, occur frequently during strain construction, and can have large effects on genetic interaction scores. Additionally, we uncover several new environment-dependent genetic interactions, suggesting that barcode-based genetic interaction assays have the potential to significantly expand our knowledge of genetic interaction networks.},
}
@article {pmid27816670,
year = {2017},
author = {Nooh, MM and Bahouth, SW},
title = {Two barcodes encoded by the type-1 PDZ and by phospho-Ser[312] regulate retromer/WASH-mediated sorting of the ß1-adrenergic receptor from endosomes to the plasma membrane.},
journal = {Cellular signalling},
volume = {29},
number = {},
pages = {192-208},
doi = {10.1016/j.cellsig.2016.10.014},
pmid = {27816670},
issn = {1873-3913},
mesh = {Cell Membrane/drug effects/*metabolism ; Down-Regulation/drug effects ; Endocytosis/drug effects ; Endosomes/drug effects/*metabolism ; HEK293 Cells ; Humans ; Isoproterenol/pharmacology ; Membrane Proteins/metabolism ; Models, Biological ; Multiprotein Complexes/chemistry/*metabolism ; *PDZ Domains ; Phosphate-Binding Proteins ; Phosphatidylinositol Phosphates/metabolism ; Phosphorylation/drug effects ; Phosphoserine/*metabolism ; Protein Binding/drug effects ; Protein Structure, Secondary ; Protein Transport/drug effects ; Proteins/metabolism ; RNA, Small Interfering/metabolism ; Receptors, Adrenergic, beta-1/*chemistry/*metabolism ; Sorting Nexins/metabolism ; Structure-Activity Relationship ; Tacrolimus Binding Proteins ; Wiskott-Aldrich Syndrome Protein Family ; rab GTP-Binding Proteins/metabolism ; rab7 GTP-Binding Proteins ; },
abstract = {Recycling of the majority of agonist-internalized GPCR is dependent on a type I-PDZ "barcode" in their C-tail. The recycling of wild-type (WT) ß1-AR is also dependent on its default "type-1 PDZ barcode", but trafficking of the ß1-AR is inhibited when PKA or its substrate serine at position 312 (Ser[312]) are inactivated. We tested the hypothesis that phospho-Ser[312] provided a second barcode for ß1-AR sorting from endosomes to the plasma membrane by determining the role of retromer/WASH complexes in ß1-AR trafficking. Recycling of WT ß1-AR or WT ß2-AR was dependent on targeting the retromer to endosomal membranes via SNX3 and rab7a, and on complexing the retromer to the WASH pentamer via the C-tail of FAM21 (FAM21C). These maneuvers however, did not inhibit the recycling of a phospho-Ser[312] ß1-AR mimic ((S312D) ß1-AR). Knockdown of the trans-acting PDZ protein sorting nexin27 (SNX27) inhibited the recycling of WT ß1-AR and WT ß2-AR, but had no effect on (S312D) ß1-AR∆PDZ or on phosphorylation of WT ß1-AR by PKA at Ser[312]. However, depletion of FKBP15, a FAM21C-binding endosomal protein, selectively inhibited WT ß1-AR but not ß2-AR recycling, suggesting divergence might exist in GPCR trafficking roadmaps. These results indicate that two barcodes are involved in sorting WT ß1-AR out of early endosomes. The first and antecedent "barcode" was the "type-1 PDZ", followed by a second reversible "phospho-Ser[312]" verification "barcode". This organization allows tight regulation of ß1-AR density to signaling intensity in conditions associated with aberrant ß1-AR signaling such as in hypertension and heart failure.},
}
@article {pmid27816015,
year = {2016},
author = {Zlatogursky, VV and Klimov, VI},
title = {Barcoding Heliozoa: Perspectives of 18S rDNA for Distinguishing Between Acanthocystis Species.},
journal = {Protist},
volume = {167},
number = {6},
pages = {555-567},
doi = {10.1016/j.protis.2016.09.004},
pmid = {27816015},
issn = {1618-0941},
mesh = {DNA Barcoding, Taxonomic ; DNA, Protozoan/*genetics ; Eukaryota/*classification/genetics/ultrastructure ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; *Phylogeny ; RNA, Ribosomal, 18S/*genetics ; },
abstract = {The first application of DNA-barcoding for the centrohelids is reported. The character-rich genus Acanthocystis was chosen to compare sequence divergence and morphological similarity. Acanthocystis nichollsi, an easily identifiable and well outlined species, was isolated from four remote locations; A. costata; A. takahashii (2 strains) and A. turfacea were studied as well. Detailed light- and electron-microscopic data were obtained and a fragment of 18S rDNA (mostly V5 to V8 regions) was cloned and multiple clones were sequenced. Obtained data allowed a comparison of the level of genetic divergence between several strains of one and the same morphospecies from remote locations and several strains of different morphospecies. This analysis showed no overlap between intraspecific and interspecific divergence. Phylogenetic analysis also recovered the clades for all species correctly. The genetic divergence between individual molecular clones obtained from the same clonal culture allowed accessing the genetic structure of the local populations of heliozoans. The level of divergence inside of the morphological species suggests a possible cryptic speciation. In some subclades of A. nichollsi the sequence polymorphism caused mingling of strains on the tree. 18S rDNA was shown to be an appropriate barcode at the specific level, but the intra-strain polymorphism needs further attention.},
}
@article {pmid27814676,
year = {2016},
author = {Hansen, P and Hecht, J and Ibn-Salem, J and Menkuec, BS and Roskosch, S and Truss, M and Robinson, PN},
title = {Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus.},
journal = {BMC genomics},
volume = {17},
number = {1},
pages = {873},
pmid = {27814676},
issn = {1471-2164},
mesh = {Algorithms ; Binding Sites ; *Chromatin Immunoprecipitation ; Computational Biology/*methods ; DNA-Binding Proteins/metabolism ; *High-Throughput Nucleotide Sequencing ; Nucleotide Motifs ; Protein Binding ; Reproducibility of Results ; *Software ; Transcription Factors/metabolism ; },
abstract = {BACKGROUND: ChIP-nexus, an extension of the ChIP-exo protocol, can be used to map the borders of protein-bound DNA sequences at nucleotide resolution, requires less input DNA and enables selective PCR duplicate removal using random barcodes. However, the use of random barcodes requires additional preprocessing of the mapping data, which complicates the computational analysis. To date, only a very limited number of software packages are available for the analysis of ChIP-exo data, which have not yet been systematically tested and compared on ChIP-nexus data.<br><br>RESULTS: Here, we present a comprehensive software package for ChIP-nexus data that exploits the random barcodes for selective removal of PCR duplicates and for quality control. Furthermore, we developed bespoke methods to estimate the width of the protected region resulting from protein-DNA binding and to infer binding positions from ChIP-nexus data. Finally, we applied our peak calling method as well as the two other methods MACE and MACS2 to the available ChIP-nexus data.<br><br>CONCLUSIONS: The Q-nexus software is efficient and easy to use. Novel statistics about duplication rates in consideration of random barcodes are calculated. Our method for the estimation of the width of the protected region yields unbiased signatures that are highly reproducible for biological replicates and at the same time very specific for the respective factors analyzed. As judged by the irreproducible discovery rate (IDR), our peak calling algorithm shows a substantially better reproducibility. An implementation of Q-nexus is available at http://charite.github.io/Q/ .},
}
@article {pmid27814365,
year = {2016},
author = {Pohjoismäki, JL and Kahanpää, J and Mutanen, M},
title = {DNA Barcodes for the Northern European Tachinid Flies (Diptera: Tachinidae).},
journal = {PloS one},
volume = {11},
number = {11},
pages = {e0164933},
pmid = {27814365},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; Cluster Analysis ; Coleoptera/genetics ; DNA/*genetics ; DNA Barcoding, Taxonomic/methods ; Diptera/*genetics ; Lepidoptera/genetics ; Parasites/genetics ; },
abstract = {This data release provides COI barcodes for 366 species of parasitic flies (Diptera: Tachinidae), enabling the DNA based identification of the majority of northern European species and a large proportion of Palearctic genera, regardless of the developmental stage. The data will provide a tool for taxonomists and ecologists studying this ecologically important but challenging parasitoid family. A comparison of minimum distances between the nearest neighbors revealed the mean divergence of 5.52% that is approximately the same as observed earlier with comparable sampling in Lepidoptera, but clearly less than in Coleoptera. Full barcode-sharing was observed between 13 species pairs or triplets, equaling to 7.36% of all species. Delimitation based on Barcode Index Number (BIN) system was compared with traditional classification of species and interesting cases of possible species oversplits and cryptic diversity are discussed. Overall, DNA barcodes are effective in separating tachinid species and provide novel insight into the taxonomy of several genera.},
}
@article {pmid27811849,
year = {2017},
author = {Zvyagin, IV and Mamedov, IZ and Tatarinova, OV and Komech, EA and Kurnikova, EE and Boyakova, EV and Brilliantova, V and Shelikhova, LN and Balashov, DN and Shugay, M and Sycheva, AL and Kasatskaya, SA and Lebedev, YB and Maschan, AA and Maschan, MA and Chudakov, DM},
title = {Tracking T-cell immune reconstitution after TCRαβ/CD19-depleted hematopoietic cells transplantation in children.},
journal = {Leukemia},
volume = {31},
number = {5},
pages = {1145-1153},
doi = {10.1038/leu.2016.321},
pmid = {27811849},
issn = {1476-5551},
mesh = {Adolescent ; *Antigens, CD19 ; Child ; Child, Preschool ; *Graft Survival ; Hematologic Diseases/*therapy ; Hematopoietic Stem Cell Transplantation/*methods ; Humans ; Infant ; Lymphocyte Depletion/*methods ; *Receptors, Antigen, T-Cell, alpha-beta ; T-Lymphocytes/*immunology ; Time Factors ; Young Adult ; },
abstract = {αβT-cell-depleted allogeneic hematopoietic cell transplantation holds promise for the safe and accessible therapy of both malignant and non-malignant blood disorders. Here we employed molecular barcoding normalized T-cell receptor (TCR) profiling to quantitatively track T-cell immune reconstitution after TCRαβ-/CD19-depleted transplantation in children. We demonstrate that seemingly early reconstitution of αβT-cell counts 2 months after transplantation is based on only several hundred rapidly expanded clones originating from non-depleted graft cells. In further months, frequency of these hyperexpanded clones declines, and after 1 year the observed T-cell counts and TCRβ diversity are mostly provided by the newly produced T cells. We also demonstrate that high TCRβ diversity at day 60 observed for some of the patients is determined by recipient T cells and intrathymic progenitors that survived conditioning regimen. Our results indicate that further efforts on optimization of TCRαβ-/CD19-depleted transplantation protocols should be directed toward providing more efficient T-cell defense in the first months after transplantation.},
}
@article {pmid27811752,
year = {2016},
author = {Barone, ML and Werenkraut, V and Ramírez, MJ},
title = {New species and phylogenetic relationships of the spider genus Coptoprepes using morphological and sequence data (Araneae: Anyphaenidae).},
journal = {Zootaxa},
volume = {4175},
number = {5},
pages = {436-448},
doi = {10.11646/zootaxa.4175.5.2},
pmid = {27811752},
issn = {1175-5334},
mesh = {Animals ; Argentina ; Chile ; DNA Barcoding, Taxonomic ; Female ; Forests ; Male ; Phylogeny ; Species Specificity ; Spiders/*anatomy &amp; histology/*classification/genetics ; },
abstract = {We present evidence from the standard cytochrome c oxidase subunit I (COI) barcoding marker and from new collections, showing that the males and females of C. ecotono Werenkraut &amp; Ramírez were mismatched, and describe the female of that species for the first time. An undescribed male from Chile is assigned to the new species Coptoprepes laudani, together with the female that was previously thought as C. ecotono. The matching of sexes is justified after a dual cladistics analysis of morphological and sequence data in combination. New locality data and barcoding sequences are provided for other species of Coptoprepes, all endemic of the temperate forests of Chile and adjacent Argentina. Although morphology and sequences are not conclusive on the relationships of Coptoprepes species, the sequence data suggests that the species without a retrolateral tibial apophysis may belong to an independent lineage.},
}
@article {pmid27811749,
year = {2016},
author = {López-Rubio, A and Suaza-Vasco, J and Marcet, PL and Ruíz-Molina, N and Cáceres, L and Porter, C and Uribe, S},
title = {Use of DNA barcoding to distinguish the malaria vector Anopheles neivai in Colombia.},
journal = {Zootaxa},
volume = {4175},
number = {4},
pages = {377-389},
pmid = {27811749},
issn = {1175-5334},
support = {CC999999//Intramural CDC HHS/United States ; },
mesh = {Animals ; Anopheles/*genetics/parasitology ; Colombia ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Female ; Genetic Variation/genetics ; Malaria, Falciparum/*transmission ; Male ; Plasmodium falciparum ; },
abstract = {A reference 535 bp barcode sequence from a fragment of the mitochondrial gene cytochrome oxidase I (COI), acquired from specimens of An. neivai Howard, Dyar &amp; Knab, 1913 from its type locality in Panama, was used as a tool for distinguishing this species from others in the subgenus Kerteszia. Comparisons with corresponding regions of COI between An. neivai and other species in the subgenus (An. bellator Dyar &amp; Knab 1906, An. homunculus Komp 1937, An cruzii Dyar &amp; Knab, 1908 and An. laneanus Corrêa &amp; Cerqueira, 1944) produced K2P genetic distances of 8.3-12.6%, values well above those associated with intraspecific variation. In contrast, genetic distances among 55 specimens from five municipalities in the Colombian Pacific coastal state of Chocó were all within the range of 0-2.5%, with an optimized barcode threshold of 1.3%, the limit for unambiguous differentiation of An. neivai. Among specimens from the Chocó region, 18 haplotypes were detected, two of which were widely distributed over the municipalities sampled. The barcode sequence permits discrimination of An. neivai from sympatric species and indicates genetic variability within the species; aspects key to malaria surveillance and control as well as defining geographic distribution and dispersion patterns.},
}
@article {pmid27811739,
year = {2016},
author = {Schuchert, P},
title = {The polyps of Oceania armata identified by DNA barcoding (Cnidaria, Hydrozoa).},
journal = {Zootaxa},
volume = {4175},
number = {6},
pages = {539-555},
doi = {10.11646/zootaxa.4175.6.3},
pmid = {27811739},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Hydrozoa/*classification/genetics/*growth &amp; development ; Phylogeny ; Species Specificity ; },
abstract = {The polyps of the widely distributed medusa Oceania armata have never been found in nature and only the primary polyp is known from breeding experiments. The fully developed colony is so far unknown. This report shows that DNA sequence data of the medusa stage of O. armata permits to identify several hydroid colonies from different geographic origins as the most likely polyp stage of this medusa. These hydroids had previously been misidentified as Turritopsis species, a closely related genus which also produces medusae resembling Oceania armata. It is concluded that most Turritopsis hydroids are not reliably identifiable to species level using morphological traits only. However, DNA barcodes, particularly 16S sequences, are an excellent tool to identify the species, although we still lack information on a few nominal species and the identities of some sequence-delimited clades need to be corroborated by the addition of topotype samples.},
}
@article {pmid27811724,
year = {2016},
author = {Jamhour, A and Mitrović, M and Petrović, A and Starý, P and Tomanović, &#x17d;},
title = {Re-visiting the Aphidius urticae s. str. group: re-description of Aphidius rubi Starý and A. silvaticus Starý (Hymenoptera: Braconidae: Aphidiinae).},
journal = {Zootaxa},
volume = {4178},
number = {2},
pages = {278-288},
doi = {10.11646/zootaxa.4178.2.6},
pmid = {27811724},
issn = {1175-5334},
mesh = {Animals ; Aphids/*classification/genetics ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Male ; Mitochondrial Proteins/genetics ; Phylogeny ; Species Specificity ; Wasps/*parasitology ; },
abstract = {Here we tested Aphidius urticae s. str. host-associated lineages from Microlophium carnosum (Buckton), Amphorophora rubi (Kaltenbach), Macrosiphum funestum (Macchiati) and Aulacorthum vaccinii Hille Ris Lambers with the barcoding region of the mitochondrial cytochrome oxidase subunit I gene used to analyse population differences and elucidate phylogenetic relationships between the separated taxa. This molecular marker has been shown to be the most informative molecular marker in resolving species complexes in aphidiine parasitoids. Analyses of the mitochondrial sequences revealed the existence of three clearly separated mitochondrial lineages of A. urticae s. str. group associated with: i) Macrosiphum funestum and Aulacorthum vaccinii aphid hosts, ii) Microlophium carnosum and iii) Amphorophora rubi. This corresponds to the initial descriptions of A. rubi, A. silvaticus and A. urticae and their aphid host associations prior to synonymization of A. rubi and A. silvaticus with A. urticae. On the other hand, significant evolutionary distances ranging from 2.3 to 9.2% between the three mitochondrial lineages were not accompanied by clear morphological differences. Therefore, re-descriptions of A. rubi and A. silvaticus are presented, together with their morphological differentiation in a key, as well as their phylogenetic relationships and genetical differentiation.},
}
@article {pmid27811722,
year = {2016},
author = {Mock, A and Tajovský, K and Žurovcová, M and Jarošová, A and Kocourek, P and Gruber, J and Angyal, D and Spelda, J},
title = {Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology.},
journal = {Zootaxa},
volume = {4178},
number = {2},
pages = {234-256},
doi = {10.11646/zootaxa.4178.2.4},
pmid = {27811722},
issn = {1175-5334},
mesh = {Animals ; Arthropods/*anatomy &amp; histology/*classification/genetics/microbiology ; Caves ; DNA Barcoding, Taxonomic ; Ecosystem ; Female ; Hungary ; Male ; Parthenogenesis ; Species Specificity ; Wolbachia/genetics ; },
abstract = {Hungarosoma bokori Verhoeff, 1928 is a millipede species which was originally classified solely on the basis of a female specimen. Subsequently, a long history of field searching for and surmising about the systematic position of this small, enigmatic species followed. In April 2013, 85 years after its first description, a series of nine specimens were sampled in the type locality, the Abaliget Cave, in southern Hungary. An adult male was collected for the first time, along with females and juveniles. Descriptions of the gonopods and the female vulvae, both important for considerations of the systematic position of the species, are presented for the first time. Revision and re-designation of the type material was made.The cryptic life of the species is connected with its activity in winter, and its known fragmented distribution corresponds with its presence in undisturbed microhabitats having a specific microclimate, often in the soil at cave entrances.Molecular methods showed a positive detection of the intracellular prokaryotic parasite Wolbachia in H. bokori, reflecting its highly probable parthenogenetic character in the main part of its known area of occurrence. This is the first demonstration of Wolbachia in a millipede.The legitimacy of the family Hungarosomatidae Ceuca, 1974, as a separate taxon was analysed using morphological and molecular approaches. Results of both methods confirmed the existence of a distinct phyletic line. DNA barcoding has shown its closest position to Attemsiidae Verhoeff, 1899, or Neoatractosomatidae Verhoeff, 1901. Based on records from Austria, the Czech Republic, Hungary and Slovakia, the residual circum-pannonic distribution that the whole genus (family) probably represents is proposed.},
}
@article {pmid27811713,
year = {2016},
author = {Gilligan, T and Huemer, P and Wiesmair, B},
title = {Different continents, same species? Resolving the taxonomy of some Holarctic Ancylis Hübner (Lepidoptera: Tortricidae).},
journal = {Zootaxa},
volume = {4178},
number = {3},
pages = {347-370},
doi = {10.11646/zootaxa.4178.3.3},
pmid = {27811713},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Female ; Male ; Moths/*anatomy &amp; histology/*classification/genetics ; Species Specificity ; },
abstract = {Several species of Ancylis related to A. unguicella (Linnaeus) and A. geminana (Donovan) have been presumed by previous authors to be Holarctic. However, difficulty in identifying genitalic characters to define and separate these taxa has brought into question their true distribution and led to inconsistencies in their taxonomic treatment in Europe and North America. Here we use a combination of DNA barcode sequence data and morphology to resolve these taxonomic differences, determine the actual geographic range of these taxa, and describe three new species. In the A. unguicella group, only A. unguicella and A. uncella (Denis &amp; Schiffermüller) are Holarctic in distribution. In the A. geminana group, none of the taxa are Holarctic in their distribution. Three species are described as new: A. christiandiana Huemer and Wiesmair, sp.n. (Austria, Germany); A. oregonensis Gilligan and Huemer, sp.n. (USA: Oregon); and A. saliana Gilligan and Huemer, sp.n. (USA: Florida). In addition, Ancylis carbonana Heinrich, syn.n., is synonymized with A. uncella; A. cuspidana (Treitschke), syn.rev., is synonymized with A. diminutana (Haworth); and A. diminuatana Kearfott, stat.rev., and A. subarcuana (Douglas), stat.rev., are raised from synonymy.},
}
@article {pmid27811699,
year = {2016},
author = {Grebennikov, VV and Morimoto, K},
title = {Flightless litter-dwelling Cotasterosoma (Coleoptera: Curculionidae: Cossoninae) found outside of Japan, with mtDNA phylogeography of a new species from Southwest China.},
journal = {Zootaxa},
volume = {4179},
number = {1},
pages = {133-138},
doi = {10.11646/zootaxa.4179.1.11},
pmid = {27811699},
issn = {1175-5334},
mesh = {Animals ; China ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Female ; Male ; Phylogeny ; Species Specificity ; Weevils/*anatomy &amp; histology/*classification/genetics ; },
abstract = {The herein reported beetles (Figs 1, 2) were repeatedly sampled by the first author since 2008 by sifting leaf litter in two forested localities in Southwest China: Cang Shan Mountain Range in Yunnan and Mount Emei in Sichuan (Fig. 3). The specimens' characteristic appearance and edaphic way of life were consistent with those of various members of the subfamily Cossoninae (Morimoto 1973, 1993, 1995), although a more precise taxonomic assignment remained elusive. In 2015 the second author saw images of these beetles and suggested their affinities to the genus Cotasterosoma Konishi, 1962. This taxon until present was known from a single specimen collected in 1954 in Shikoku, Japan, and illustrated in Morimoto (1993), although additional congeneric specimens are known to the second author. The purpose of this paper is to document our discovery of the genus in Southwest China by describing a new species, illustrating its external and genital morphological characters, releasing DNA barcode data and providing phylogeographic interpretations of our findings.},
}
@article {pmid27809975,
year = {2016},
author = {Fernández de Marco, M and Brugman, VA and Hernández-Triana, LM and Thorne, L and Phipps, LP and Nikolova, NI and Fooks, AR and Johnson, N},
title = {Detection of Theileria orientalis in mosquito blood meals in the United Kingdom.},
journal = {Veterinary parasitology},
volume = {229},
number = {},
pages = {31-36},
doi = {10.1016/j.vetpar.2016.09.012},
pmid = {27809975},
issn = {1873-2550},
mesh = {Animals ; Blood/*parasitology ; Cattle ; Culicidae/*parasitology ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; Species Specificity ; Theileria/genetics/*isolation &amp; purification ; Theileriasis/epidemiology/parasitology ; United Kingdom/epidemiology ; },
abstract = {Theileria spp. are tick-borne protozoan parasites that infect a wide range of wild and domestic animals. In this study, the utility of xenosurveillance of blood-fed specimens of Culiseta annulata for detecting the presence of piroplasms in livestock was investigated. Blood-fed mosquitoes were collected at Elmley National Nature Reserve, Kent, United Kingdom. All specimens were morphologically identified, and DNA barcoding was used to confirm the morphological identification. Both the vertebrate host species and Theileria genome was detected within the bloodmeal by real-time PCR. Sequencing was used to confirm the identity of all amplicons. In total, 105 blood-fed mosquitoes morphologically identified as Cs. annulata were collected. DNA barcoding revealed that 102 specimens were Cs. annulata (99%), while a single specimen was identified as Anopheles messeae. Two specimens could not be identified molecularly due to PCR amplification failure. Blood meal analysis revealed that Cs. annulata fed almost exclusively on cattle at the collection site (n=100). The application of a pan-piroplasm PCR detected 16 positive samples (15.2%) and sequence analysis of the amplicons demonstrated that the piroplasms present in the blood meal belonged to the Theileria orientalis group. This study demonstrates how xenosurveillance can be applied to detecting pathogens in livestock and confirms the presence of Theileria species in livestock from the United Kingdom.},
}
@article {pmid27809602,
year = {2016},
author = {Sirianni, NM and Yuan, H and Rice, JE and Kaufman, RS and Deng, J and Fulton, C and Wangh, LJ},
title = {Closed-Tube Barcoding.},
journal = {Genome},
volume = {59},
number = {11},
pages = {1049-1061},
doi = {10.1139/gen-2016-0026},
pmid = {27809602},
issn = {1480-3321},
mesh = {Animals ; Bacterial Proteins/genetics ; *Biodiversity ; Cluster Analysis ; Computational Biology/methods ; DNA Barcoding, Taxonomic/*methods ; DNA-Directed RNA Polymerases/genetics ; Electron Transport Complex IV/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Polymerase Chain Reaction/methods ; Workflow ; },
abstract = {Here, we present a new approach for increasing the rate and lowering the cost of identifying, cataloging, and monitoring global biodiversity. These advances, which we call Closed-Tube Barcoding, are one application of a suite of proven PCR-based technologies invented in our laboratory. Closed-Tube Barcoding builds on and aims to enhance the profoundly important efforts of the International Barcode of Life initiative. Closed-Tube Barcoding promises to be particularly useful when large numbers of small or rare specimens need to be screened and characterized at an affordable price. This approach is also well suited for automation and for use in portable devices.},
}
@article {pmid27605155,
year = {2016},
author = {Mehta, B and Daniel, R and Phillips, C and Doyle, S and Elvidge, G and McNevin, D},
title = {Massively parallel sequencing of customised forensically informative SNP panels on the MiSeq.},
journal = {Electrophoresis},
volume = {37},
number = {21},
pages = {2832-2840},
doi = {10.1002/elps.201600190},
pmid = {27605155},
issn = {1522-2683},
mesh = {DNA/*analysis/genetics ; Female ; Forensic Genetics/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Humic Substances ; Male ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide/*genetics ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; },
abstract = {Forensic DNA-based intelligence, or forensic DNA phenotyping, utilises SNPs to infer the biogeographical ancestry and externally visible characteristics of the donor of evidential material. SNaPshot[®] is a commonly employed forensic SNP genotyping technique, which is limited to multiplexes of 30-40 SNPs in a single reaction and prone to PCR contamination. Massively parallel sequencing has the ability to genotype hundreds of SNPs in multiple samples simultaneously by employing an oligonucleotide sample barcoding strategy. This study of the Illumina MiSeq massively parallel sequencing platform analysed 136 unique SNPs in 48 samples from SNaPshot PCR amplicons generated by five established forensic DNA phenotyping assays comprising the SNPforID 52-plex, SNPforID 34-plex, Eurasiaplex, Pacifiplex and IrisPlex. Approximately 3 GB of sequence data were generated from two MiSeq flow cells and profiles were obtained from just 0.25 ng of DNA. Compared with SNaPshot, an average 98% genotyping concordance was achieved. Our customised approach was successful in attaining SNP profiles from extremely degraded, inhibited, and compromised casework samples. Heterozygote imbalance and sequence coverage in negative controls highlight the need to establish baseline sequence coverage thresholds and refine allele frequency thresholds. This study demonstrates the potential of the MiSeq for forensic SNP analysis.},
}
@article {pmid27546764,
year = {2016},
author = {Namas, RA and Almahmoud, K and Mi, Q and Ghuma, A and Namas, R and Zaaqoq, A and Zhu, X and Abdul-Malak, O and Sperry, J and Zamora, R and Billiar, TR and Vodovotz, Y},
title = {Individual-specific principal component analysis of circulating inflammatory mediators predicts early organ dysfunction in trauma patients.},
journal = {Journal of critical care},
volume = {36},
number = {},
pages = {146-153},
pmid = {27546764},
issn = {1557-8615},
support = {P50 GM053789/GM/NIGMS NIH HHS/United States ; T32 GM008516/GM/NIGMS NIH HHS/United States ; },
mesh = {Accidental Falls ; Accidents, Traffic ; Adult ; Biomarkers/blood ; Cluster Analysis ; Cytokines/*blood ; Female ; Humans ; Inflammation/blood ; Inflammation Mediators/blood ; Injury Severity Score ; Length of Stay ; Male ; Middle Aged ; Multiple Organ Failure/*blood/epidemiology ; Principal Component Analysis ; Respiration, Artificial ; Survivors ; Wounds, Nonpenetrating/*blood/epidemiology ; },
abstract = {PURPOSE: We hypothesized that early inflammation can drive, or impact, later multiple organ dysfunction syndrome (MODS), that patient-specific principal component analysis (PCA) of circulating inflammatory mediators could reveal conserved dynamic responses which would not be apparent from the unprocessed data, and that this computational approach could segregate trauma patients with regard to subsequent MODS.<br><br>METHODS: From a cohort of 472 blunt trauma survivors, 2 separate subcohorts of moderately/severely injured patients were studied. Multiple inflammatory mediators were assessed in serial blood samples in the first 24 hours postinjury. PCA of these time course data was used to derive patient-specific "inflammation barcodes," followed by hierarchical clustering to define patient subgroups. To define the generalizability of this approach, 2 different but overlapping Luminex kits were used.<br><br>RESULTS: PCA/hierarchical clustering of 24-hour Luminex data segregated the patients into 2 groups that differed significantly in their Marshall multiple organ dysfunction score on subsequent days, independently of the specific set of inflammatory mediators analyzed. Multiple inflammatory mediators and their dynamic networks were significantly different in the 2 groups in both patient cohorts, demonstrating that the groups were defined based on "core" early responses exhibit truly different dynamic inflammatory trajectories.<br><br>CONCLUSION: Identification of patient-specific "core responses" can lead to early segregation of diverse trauma patients with regard to later MODS. Hence, we suggest that a focus on dynamic inflammatory networks rather than individual biomarkers is warranted.},
}
@article {pmid27808270,
year = {2016},
author = {He, Q and Liu, Y and He, Y and Zhu, L and Zhang, Y and Shen, Z},
title = {Digital barcodes of suspension array using laser induced breakdown spectroscopy.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {36511},
pmid = {27808270},
issn = {2045-2322},
abstract = {We show a coding method of suspension array based on the laser induced breakdown spectroscopy (LIBS), which promotes the barcodes from analog to digital. As the foundation of digital optical barcodes, nanocrystals encoded microspheres are prepared with self-assembly encapsulation method. We confirm that digital multiplexing of LIBS-based coding method becomes feasible since the microsphere can be coded with direct read-out data of wavelengths, and the method can avoid fluorescence signal crosstalk between barcodes and analyte tags, which lead to overall advantages in accuracy and stability to current fluorescent multicolor coding method. This demonstration increases the capability of multiplexed detection and accurate filtrating, expanding more extensive applications of suspension array in life science.},
}
@article {pmid27808223,
year = {2016},
author = {Ueda, S and Komatsu, T and Itino, T and Arai, R and Sakamoto, H},
title = {Host-ant specificity of endangered large blue butterflies (Phengaris spp., Lepidoptera: Lycaenidae) in Japan.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {36364},
pmid = {27808223},
issn = {2045-2322},
mesh = {Animals ; Ants/*physiology ; Butterflies/*anatomy &amp; histology/*classification/genetics ; Electron Transport Complex IV/genetics ; Endangered Species ; Host Specificity ; Insect Proteins/genetics ; Phylogeny ; },
abstract = {Large blue butterflies, Phengaris (Maculinea), are an important focus of endangered-species conservation in Eurasia. Later-instar Phengaris caterpillars live in Myrmica ant nests and exploit the ant colony's resources, and they are specialized to specific host-ant species. For example, local extinction of P. arion in the U. K. is thought to have been due to the replacement of its host-ant species with a less-suitable congener, as a result of changes in habitat. In Japan, Myrmica kotokui hosts P. teleius and P. arionides caterpillars. We recently showed, however, that the morphological species M. kotokui actually comprises four genetic clades. Therefore, to determine to which group of ants the hosts of these two Japanese Phengaris species belong, we used mitochondrial COI-barcoding of M. kotokui specimens from colonies in the habitats of P. teleius and P. arionides to identify the ant clade actually parasitized by the caterpillars of each species. We found that these two butterfly species parasitize different ant clades within M. kotokui.},
}
@article {pmid27799340,
year = {2017},
author = {Batovska, J and Cogan, NO and Lynch, SE and Blacket, MJ},
title = {Using Next-Generation Sequencing for DNA Barcoding: Capturing Allelic Variation in ITS2.},
journal = {G3 (Bethesda, Md.)},
volume = {7},
number = {1},
pages = {19-29},
pmid = {27799340},
issn = {2160-1836},
mesh = {Alleles ; Animals ; Culicidae/classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Intergenic/*genetics ; *High-Throughput Nucleotide Sequencing ; INDEL Mutation/genetics ; Polymorphism, Single Nucleotide/genetics ; },
abstract = {Internal Transcribed Spacer 2 (ITS2) is a popular DNA barcoding marker; however, in some animal species it is hypervariable and therefore difficult to sequence with traditional methods. With next-generation sequencing (NGS) it is possible to sequence all gene variants despite the presence of single nucleotide polymorphisms (SNPs), insertions/deletions (indels), homopolymeric regions, and microsatellites. Our aim was to compare the performance of Sanger sequencing and NGS amplicon sequencing in characterizing ITS2 in 26 mosquito species represented by 88 samples. The suitability of ITS2 as a DNA barcoding marker for mosquitoes, and its allelic diversity in individuals and species, was also assessed. Compared to Sanger sequencing, NGS was able to characterize the ITS2 region to a greater extent, with resolution within and between individuals and species that was previously not possible. A total of 382 unique sequences (alleles) were generated from the 88 mosquito specimens, demonstrating the diversity present that has been overlooked by traditional sequencing methods. Multiple indels and microsatellites were present in the ITS2 alleles, which were often specific to species or genera, causing variation in sequence length. As a barcoding marker, ITS2 was able to separate all of the species, apart from members of the Culex pipiens complex, providing the same resolution as the commonly used Cytochrome Oxidase I (COI). The ability to cost-effectively sequence hypervariable markers makes NGS an invaluable tool with many applications in the DNA barcoding field, and provides insights into the limitations of previous studies and techniques.},
}
@article {pmid27806089,
year = {2016},
author = {Ferrão, M and Colatreli, O and de Fraga, R and Kaefer, IL and Moravec, J and Lima, AP},
title = {High Species Richness of Scinax Treefrogs (Hylidae) in a Threatened Amazonian Landscape Revealed by an Integrative Approach.},
journal = {PloS one},
volume = {11},
number = {11},
pages = {e0165679},
pmid = {27806089},
issn = {1932-6203},
mesh = {Acoustics ; Animals ; Anura/*classification/genetics/*physiology ; Brazil ; DNA Barcoding, Taxonomic ; Ecosystem ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Rainforest ; Species Specificity ; },
abstract = {Rising habitat loss is one of the main drivers of the global amphibian decline. Nevertheless, knowledge of amphibian diversity needed for effective habitat protection is still highly inadequate in remote tropical regions, the greater part of the Amazonia. In this study we integrated molecular, morphological and bioacoustic evidence to evaluate the species richness of the treefrogs genus Scinax over a 1000 km transect across rainforest of the Purus-Madeira interfluve, and along the east bank of the upper Madeira river, Brazilian Amazonia. Analysis revealed that 82% of the regional species richness of Scinax is still undescribed; two nominal species, seven confirmed candidate species, two unconfirmed candidate species, and one deep conspecific lineage were detected in the study area. DNA barcoding based analysis of the 16s rRNA gene indicates possible existence of three discrete species groups within the genus Scinax, in addition to the already-known S. rostratus species Group. Quantifying and characterizing the number of undescribed Scinax taxa on a regional scale, we provide a framework for future taxonomic study in Amazonia. These findings indicate that the level to which Amazonian anura species richness has been underestimated is far greater than expected. Consequently, special attention should be paid both to taxonomic studies and protection of the still-neglected Amazonian Scinax treefrogs.},
}
@article {pmid27717215,
year = {2017},
author = {Chang, CH and Shao, KT and Lin, HY and Chiu, YC and Lee, MY and Liu, SH and Lin, PL},
title = {DNA barcodes of the native ray-finned fishes in Taiwan.},
journal = {Molecular ecology resources},
volume = {17},
number = {4},
pages = {796-805},
doi = {10.1111/1755-0998.12601},
pmid = {27717215},
issn = {1755-0998},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Fishes/*classification ; Taiwan ; },
abstract = {Species identification based on the DNA sequence of a fragment of the cytochrome c oxidase subunit I gene in the mitochondrial genome, DNA barcoding, is widely applied to assist in sustainable exploitation of fish resources and the protection of fish biodiversity. The aim of this study was to establish a reliable barcoding reference database of the native ray-finned fishes in Taiwan. A total of 2993 individuals, belonging to 1245 species within 637 genera, 184 families and 29 orders of ray-finned fishes and representing approximately 40% of the recorded ray-finned fishes in Taiwan, were PCR amplified at the barcode region and bidirectionally sequenced. The mean length of the 2993 barcodes is 549 bp. Mean congeneric K2P distance (15.24%) is approximately 10-fold higher than the mean conspecific one (1.51%), but approximately 1.4-fold less than the mean genetic distance between families (20.80%). The Barcode Index Number (BIN) discordance report shows that 2993 specimens represent 1275 BINs and, among them, 86 BINs are singletons, 570 BINs are taxonomically concordant, and the other 619 BINs are taxonomically discordant. Barcode gap analysis also revealed that more than 90% of the collected fishes in this study can be discriminated by DNA barcoding. Overall, the barcoding reference database established by this study reveals the need for taxonomic revisions and voucher specimen rechecks, in addition to assisting in the management of Taiwan's fish resources and diversity.},
}
@article {pmid27616166,
year = {2016},
author = {Stern, N and Rinkevich, B and Goren, M},
title = {Integrative approach revises the frequently misidentified species of Sardinella (Clupeidae) of the Indo-West Pacific Ocean.},
journal = {Journal of fish biology},
volume = {89},
number = {5},
pages = {2282-2305},
doi = {10.1111/jfb.13114},
pmid = {27616166},
issn = {1095-8649},
mesh = {Animals ; Fishes/anatomy &amp; histology/*classification/genetics ; Genetic Variation ; Indian Ocean ; Islands ; Pacific Ocean ; Philippines ; Phylogeny ; },
abstract = {To deal with the difficulties of species differentiation and delimitation among the commercially important sardines from the genus Sardinella, an integrative approach was adopted, incorporating traditional taxonomy with four DNA markers (coI, cytb, 16s and nuclear rag2). Combining these methodologies has enabled a thorough re-description of three of the most common species of Sardinella of the Indo-west Pacific Ocean: white sardinella Sardinella albella, fringescale sardinella Sardinella fimbriata and the goldstripe sardinella Sardinella gibbosa, as well as a description of a new species, Gon's sardinella Sardinella goni, from the island of Boracay, Philippines. In addition, extensive widespread sampling of S. gibbosa reveals a significant genetic separation between the populations from the western Indian Ocean and the west Pacific Ocean, despite no supporting morphological differentiation. An updated morphological key of the species of Sardinella of the Indo-west Pacific Ocean is also provided in order to minimize future misidentifications within these economically important taxa. Finally, the genetic and morphological variabilities within and between the investigated species are used to discuss their biogeographical distribution and possible processes of speciation.},
}
@article {pmid27601081,
year = {2016},
author = {Zhang, X and Li, N and Yao, Y and Liang, X and Qu, X and Liu, X and Zhu, Y and Yang, D and Sun, W},
title = {Identification of Species in Tripterygium (Celastraceae) Based on DNA Barcoding.},
journal = {Biological &amp; pharmaceutical bulletin},
volume = {39},
number = {11},
pages = {1760-1766},
doi = {10.1248/bpb.b15-00956},
pmid = {27601081},
issn = {1347-5215},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Intergenic/genetics ; DNA, Plant/genetics ; Plant Leaves/classification/genetics ; Tripterygium/classification/*genetics ; },
abstract = {Species of genus Tripterygium (Celastraceae) have attracted much attention owing to their excellent effect on treating autoimmune and inflammatory diseases. However, due to high market demand causing overexploitation, natural populations of genus Tripterygium have rapidly declined. Tripterygium medicinal materials are mainly collected from the wild, making the quality of medicinal materials unstable. Additionally, identification of herbal materials from Tripterygium species and their adulterants is difficult based on morphological characters. Therefore, an accurate, convenient, and stability method is urgently needed. In this wok, we developed a DNA barcoding technique to distinguish T. wilfordii HOOK. f., T. hypoglaucum (LÉVL.) HUTCH, and T. regelii SPRAGUE et TAKEDA and their adulterants based on four uniform and standard DNA regions (internal transcribed spacer 2 (ITS2), matK, rbcL, and psbA-trnH). DNA was extracted from 26 locations of fresh leaves. Phylogenetic tree was constructed with Neighbor-Joining (NJ) method, while barcoding gap was analyzed to assess identification efficiency. Compared with the other DNA barcodes applied individually or in combination, ITS2+psbA-trnH was demonstrated as the optimal barcode. T. hypoglaucum and T. wilfordii can be considered as conspecific, while T. regelii was recognized as a separate species. Furthermore, identification of commercial Tripterygium samples was conducted using BLAST against GenBank and Species Identification System for Traditional Chinese Medicine. Our results indicated that DNA barcoding is a convenient, effective, and stability method to identify and distinguish Tripterygium and its adulterants, and could be applied as the quality control for Tripterygium medicinal preparations and monitoring of the medicinal herb trade in markets.},
}
@article {pmid27801965,
year = {2016},
author = {Madden, AA and Barberán, A and Bertone, MA and Menninger, HL and Dunn, RR and Fierer, N},
title = {The diversity of arthropods in homes across the United States as determined by environmental DNA analyses.},
journal = {Molecular ecology},
volume = {25},
number = {24},
pages = {6214-6224},
doi = {10.1111/mec.13900},
pmid = {27801965},
issn = {1365-294X},
mesh = {Allergens ; Animals ; Arthropods/*classification ; DNA/analysis ; Dust/*analysis ; Food Chain ; *Housing ; United States ; },
abstract = {We spend most of our lives inside homes, surrounded by arthropods that impact our property as pests and our health as disease vectors and producers of sensitizing allergens. Despite their relevance to human health and well-being, we know relatively little about the arthropods that exist in our homes and the factors structuring their diversity. As previous work has been limited in scale by the costs and time associated with collecting arthropods and the subsequent morphological identification, we used a DNA-based method for investigating the arthropod diversity in homes via high-throughput marker gene sequencing of home dust. Settled dust samples were collected by citizen scientists from both inside and outside more than 700 homes across the United States, yielding the first continental-scale estimates of arthropod diversity associated with our residences. We were able to document food webs and previously unknown geographic distributions of diverse arthropods - from allergen producers to invasive species and nuisance pests. Home characteristics, including the presence of basements, home occupants and surrounding land use, were more useful than climate parameters in predicting arthropod diversity in homes. These noninvasive, scalable tools and resultant findings not only provide the first continental-scale maps of household arthropod diversity, but our analyses also provide valuable baseline information on arthropod allergen exposures and the distributions of invasive pests inside homes.},
}
@article {pmid27798817,
year = {2017},
author = {Sumatoh, HR and Teng, KW and Cheng, Y and Newell, EW},
title = {Optimization of mass cytometry sample cryopreservation after staining.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {91},
number = {1},
pages = {48-61},
doi = {10.1002/cyto.a.23014},
pmid = {27798817},
issn = {1552-4930},
mesh = {Cell Survival/genetics ; Cryopreservation/*methods ; Flow Cytometry/*methods ; Humans ; Single-Cell Analysis/*methods ; Staining and Labeling ; T-Lymphocytes/ultrastructure ; },
abstract = {The advent of mass cytometry has facilitated highly multi-parametric single-cell analysis allowing for the deep assessment of cellular diversity. While the data and analytical power of this approach are well described, associated technical and experimental hurdles remain. Issues like equipment breakdown and sampling of large-scale batches, which may require multiple days of data acquisition, are minor but critical obstacles that prompt a technical solution, especially when dealing with precious samples. An ability to cryopreserve mass cytometry samples that have already been stained would alleviate numerous technical limitations we face with currently used sample-handling approaches. Here, we evaluated two protocols for freezing of already-stained and fixed cellular samples and compared them with standard sample refrigeration in staining buffer. A comprehensive human T cell staining phenotypic and functional profiling panel was used and the signal intensity and reliability of each marker was assessed over a 4-week period. In general, cellular viability, DNA Ir-Intercalator and barcode staining were minimally affected by freezing compared to refrigeration, and the signal intensities for cell surface markers and receptors were not compromised. Intracellular cytokine staining did show some decreases in signal intensity after freezing, with the decreases more prominent in a methanol-based protocol compared to a protocol involving the use of 10% DMSO in FBS. We conclude that freezing already-stained samples suspended in 10% DMSO in FBS is practical and efficient way to preserve already-stained samples when needed. © 2016 International Society for Advancement of Cytometry.},
}
@article {pmid27798706,
year = {2016},
author = {Yin, Y and Lan, JH and Nguyen, D and Valenzuela, N and Takemura, P and Bolon, YT and Springer, B and Saito, K and Zheng, Y and Hague, T and Pasztor, A and Horvath, G and Rigo, K and Reed, EF and Zhang, Q},
title = {Application of High-Throughput Next-Generation Sequencing for HLA Typing on Buccal Extracted DNA: Results from over 10,000 Donor Recruitment Samples.},
journal = {PloS one},
volume = {11},
number = {10},
pages = {e0165810},
pmid = {27798706},
issn = {1932-6203},
mesh = {Alleles ; Exons ; Gene Frequency ; Genotype ; HLA Antigens/*genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Histocompatibility Testing/methods ; Humans ; Mouth Mucosa/*metabolism ; Multiplex Polymerase Chain Reaction ; Sequence Analysis, DNA ; Tissue Donors ; Workflow ; },
abstract = {BACKGROUND: Unambiguous HLA typing is important in hematopoietic stem cell transplantation (HSCT), HLA disease association studies, and solid organ transplantation. However, current molecular typing methods only interrogate the antigen recognition site (ARS) of HLA genes, resulting in many cis-trans ambiguities that require additional typing methods to resolve. Here we report high-resolution HLA typing of 10,063 National Marrow Donor Program (NMDP) registry donors using long-range PCR by next generation sequencing (NGS) approach on buccal swab DNA.<br><br>METHODS: Multiplex long-range PCR primers amplified the full-length of HLA class I genes (A, B, C) from promotor to 3' UTR. Class II genes (DRB1, DQB1) were amplified from exon 2 through part of exon 4. PCR amplicons were pooled and sheared using Covaris fragmentation. Library preparation was performed using the Illumina TruSeq Nano kit on the Beckman FX automated platform. Each sample was tagged with a unique barcode, followed by 2&#xd7;250 bp paired-end sequencing on the Illumina MiSeq. HLA typing was assigned using Omixon Twin software that combines two independent computational algorithms to ensure high confidence in allele calling. Consensus sequence and typing results were reported in Histoimmunogenetics Markup Language (HML) format. All homozygous alleles were confirmed by Luminex SSO typing and exon novelties were confirmed by Sanger sequencing.<br><br>RESULTS: Using this automated workflow, over 10,063 NMDP registry donors were successfully typed under high-resolution by NGS. Despite known challenges of nucleic acid degradation and low DNA concentration commonly associated with buccal-based specimens, 97.8% of samples were successfully amplified using long-range PCR. Among these, 98.2% were successfully reported by NGS, with an accuracy rate of 99.84% in an independent blind Quality Control audit performed by the NDMP. In this study, NGS-HLA typing identified 23 null alleles (0.023%), 92 rare alleles (0.091%) and 42 exon novelties (0.042%).<br><br>CONCLUSION: Long-range, unambiguous HLA genotyping is achievable on clinical buccal swab-extracted DNA. Importantly, full-length gene sequencing and the ability to curate full sequence data will permit future interrogation of the impact of introns, expanded exons, and other gene regulatory sequences on clinical outcomes in transplantation.},
}
@article {pmid27798407,
year = {2017},
author = {Chesters, D},
title = {Construction of a Species-Level Tree of Life for the Insects and Utility in Taxonomic Profiling.},
journal = {Systematic biology},
volume = {66},
number = {3},
pages = {426-439},
pmid = {27798407},
issn = {1076-836X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Classification/*methods ; Insecta/*classification/genetics ; *Phylogeny ; },
abstract = {Although comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis. I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta). Matrix-building requires separately optimized pipelines for nuclear transcriptomic, mitochondrial genomic, and species-rich markers, whereas tree-building requires hierarchical inference in order to capture species-breadth while retaining deep-level resolution. The phylogeny of insects contains 49,358 species, 13,865 genera, 760 families. Deep-level splits largely reflected previous findings for sections of the tree that are data rich or unambiguous, such as inter-ordinal Endopterygota and Dictyoptera, the recently evolved and relatively homogeneous Lepidoptera, Hymenoptera, Brachycera (Diptera), and Cucujiformia (Coleoptera). However, analysis of bias, matrix construction and gene-tree variation suggests confidence in some relationships (such as in Polyneoptera) is less than has been indicated by the matrix bootstrap method. To assess the utility of the insect tree as a tool in query profiling several tree-based taxonomic assignment methods are compared. Using test data sets with existing taxonomic annotations, a tendency is observed for greater accuracy of species-level assignments where using a fixed comprehensive tree of life in contrast to methods generating smaller de novo reference trees. Described herein is a solution to the discrepancy in the way data are fit into supermatrices. The resulting tree facilitates wider studies of insect diversification and application of advanced descriptions of diversity in community studies, among other presumed applications. [Data integration; data mining; insects; phylogenomics; phyloinformatics; tree of life.].},
}
@article {pmid27797448,
year = {2017},
author = {Richardson, RT and Bengtsson-Palme, J and Johnson, RM},
title = {Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence data.},
journal = {Molecular ecology resources},
volume = {17},
number = {4},
pages = {760-769},
doi = {10.1111/1755-0998.12628},
pmid = {27797448},
issn = {1755-0998},
mesh = {Bayes Theorem ; Computer Simulation ; DNA Barcoding, Taxonomic/*methods ; *Software ; },
abstract = {The taxonomic classification of DNA sequences has become a critical component of numerous ecological research applications; however, few studies have evaluated the strengths and weaknesses of commonly used sequence classification approaches. Further, the methods and software available for sequence classification are diverse, creating an environment in which it may be difficult to determine the best course of action and the trade-offs made using different classification approaches. Here, we provide an in silico evaluation of three DNA sequence classifiers, the rdp Naïve Bayesian Classifier, rtax and utax. Further, we discuss the results, merits and limitations of both the classifiers and our method of classifier evaluation. Our methods of comparison are simple, yet robust, and will provide researchers a methodological and conceptual foundation for making such evaluations in a variety of research situations. Generally, we found a considerable trade-off between accuracy and sensitivity for the classifiers tested, indicating a need for further improvement of sequence classification tools.},
}
@article {pmid27796590,
year = {2017},
author = {Mezzasalma, V and Ganopoulos, I and Galimberti, A and Cornara, L and Ferri, E and Labra, M},
title = {Poisonous or non-poisonous plants? DNA-based tools and applications for accurate identification.},
journal = {International journal of legal medicine},
volume = {131},
number = {1},
pages = {1-19},
pmid = {27796590},
issn = {1437-1596},
mesh = {DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Forensic Toxicology ; High-Throughput Nucleotide Sequencing ; Humans ; Plants, Toxic/*genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {Plant exposures are among the most frequently reported cases to poison control centres worldwide. This is a growing condition due to recent societal trends oriented towards the consumption of wild plants as food, cosmetics, or medicine. At least three general causes of plant poisoning can be identified: plant misidentification, introduction of new plant-based supplements and medicines with no controls about their safety, and the lack of regulation for the trading of herbal and phytochemical products. Moreover, an efficient screening for the occurrence of plants poisonous to humans is also desirable at the different stages of the food supply chain: from the raw material to the final transformed product. A rapid diagnosis of intoxication cases is necessary in order to provide the most reliable treatment. However, a precise taxonomic characterization of the ingested species is often challenging. In this review, we provide an overview of the emerging DNA-based tools and technologies to address the issue of poisonous plant identification. Specifically, classic DNA barcoding and its applications using High Resolution Melting (Bar-HRM) ensure high universality and rapid response respectively, whereas High Throughput Sequencing techniques (HTS) provide a complete characterization of plant residues in complex matrices. The pros and cons of each approach have been evaluated with the final aim of proposing a general user's guide to molecular identification directed to different stakeholder categories interested in the diagnostics of poisonous plants.},
}
@article {pmid27693386,
year = {2017},
author = {Bashford-Rogers, RJ and Palser, AL and Hodkinson, C and Baxter, J and Follows, GA and Vassiliou, GS and Kellam, P},
title = {Dynamic variation of CD5 surface expression levels within individual chronic lymphocytic leukemia clones.},
journal = {Experimental hematology},
volume = {46},
number = {},
pages = {31-37.e10},
pmid = {27693386},
issn = {1873-2399},
support = {/WT_/Wellcome Trust/United Kingdom ; MC_PC_12009/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Antigens, CD/genetics/metabolism ; B-Lymphocytes/metabolism/pathology ; Biomarkers ; CD5 Antigens/genetics/*metabolism ; Cell Membrane/*metabolism ; Gene Expression ; Humans ; Immunophenotyping ; Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis/genetics/*metabolism ; Receptors, Antigen, B-Cell/metabolism ; Sequence Analysis, DNA ; },
abstract = {Chronic lymphocytic leukemia (CLL) is characterized by the accumulation of clonally derived mature CD5[high] B cells; however, the cellular origin of CLL is still unknown. Patients with CLL also harbor variable numbers of CD5[low] B cells, but the clonal relationship of these cells to the bulk disease is unknown and can have important implications for monitoring, treating, and understanding the biology of CLL. Here, we use B-cell receptors (BCRs) as molecular barcodes to first show by single-cell BCR sequencing that the great majority of CD5[low] B cells in the blood of CLL patients are clonally related to CD5[high] CLL B cells. We investigate whether CD5 state switching was likely to occur continuously as a common event or as a rare event in CLL by tracking somatic BCR mutations in bulk CLL B cells and using them to reconstruct the phylogenetic relationships and evolutionary history of the CLL in four patients. Using statistical methods, we show that there is no parsimonious route from a single or low number of CD5[low] switch events to the CD5[high] population, but rather, large-scale and/or dynamic switching between these CD5 states is the most likely explanation. The overlapping BCR repertoires between CD5[high] and CD5[low] cells from CLL patient peripheral blood reveal that CLL exists in a continuum of CD5 expression. The major proportion of CD5[low] B cells in patients are leukemic, thus identifying CD5[low] B cells as an important component of CLL, with implications for CLL pathogenesis, clinical monitoring, and the development of anti-CD5-directed therapies.},
}
@article {pmid27792411,
year = {2016},
author = {Hodgetts, J and Ostojá-Starzewski, JC and Prior, T and Lawson, R and Hall, J and Boonham, N},
title = {DNA barcoding for biosecurity: case studies from the UK plant protection program.},
journal = {Genome},
volume = {59},
number = {11},
pages = {1033-1048},
doi = {10.1139/gen-2016-0010},
pmid = {27792411},
issn = {1480-3321},
mesh = {Animals ; Coleoptera/classification/genetics ; Conservation of Natural Resources ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Invertebrates/*classification/*genetics ; Nematoda/classification/genetics ; Phylogeny ; Pinus/parasitology ; Plants/parasitology ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; United Kingdom ; },
abstract = {Since its conception, DNA barcoding has seen a rapid uptake within the research community. Nevertheless, as with many new scientific tools, progression towards the point of routine deployment within diagnostic laboratories has been slow. In this paper, we discuss the application of DNA barcoding in the Defra plant health diagnostic laboratories, where DNA barcoding is used primarily for the identification of invertebrate pests. We present a series of case studies that demonstrate the successful application of DNA barcoding but also reveal some potential limitations to expanded use. The regulated plant pest, Bursephalenchus xylophilus, and one of its vectors, Monochamus alternatus, were found in dining chairs. Some traded wood products are potentially high risk, allowing the movement of longhorn beetles; Trichoferus campestris, Leptura quadrifasciata, and Trichoferus holosericeus were found in a wooden cutlery tray, a railway sleeper, and a dining chair, respectively. An outbreak of Meloidogyne fallax was identified in Allium ampeloprasum and in three weed species. Reference sequences for UK native psyllids were generated to enable the development of rapid diagnostics to be used for monitoring following the release of Aphalara itadori as a biological control agent for Fallopia japonica.},
}
@article {pmid27609637,
year = {2016},
author = {Torres-Gutierrez, C and Bergo, ES and Emerson, KJ and de Oliveira, TMP and Greni, S and Sallum, MAM},
title = {Mitochondrial COI gene as a tool in the taxonomy of mosquitoes Culex subgenus Melanoconion.},
journal = {Acta tropica},
volume = {164},
number = {},
pages = {137-149},
doi = {10.1016/j.actatropica.2016.09.007},
pmid = {27609637},
issn = {1873-6254},
mesh = {Animals ; Bayes Theorem ; Brazil ; Cluster Analysis ; Culex/classification/*genetics ; Cyclooxygenase 1/*genetics ; DNA Barcoding, Taxonomic ; Insect Proteins/*analysis ; Insect Vectors/classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {The subgenus Melanoconion is the second largest subgenus within the genus Culex, with 160 described species. Several of the species are proven vectors of arboviruses, including West Nile virus, Venezuelan equine encephalitis virus complex and Eastern equine encephalomyelitis virus. Species of Melanoconion are well distributed from southern North America to most countries of South America and display the highest species diversity in tropical regions. Taxonomical identification within this group has been primarily based on morphological characters, with the male genitalia as the source of the most solid diagnostic features. The difficulty in reaching accurate species determinations when studying specimens of Culex (Melanoconion) has been extensively documented as a real limitation to expand knowledge of these insects. We tested the utility of the mitochondrial gene COI as a complementary tool in the taxonomy of Melanoconion. Using a data set of 120 COI sequences from Culex specimen captured in several localities in Brazil, the utility of COI barcodes for species delimitation is discussed through the evaluation of genetic divergences among specimens and the clustering patterns of species in three topologies obtained with Neighbor Joining, Maximum Likelihood and Bayesian phylogenetic inference. For all specimens included in this study a previous morphological examination was performed, and most of the taxonomical determinations were corroborated using the COI barcode. We generated COI sequences that belong to 48 species of Melanoconion, with a mean intraspecific K2P genetic divergence of 3%; and all interspecific divergence values higher than the intraspecific divergence values. This is the first comprehensive study of subgenus Melanoconion, with evidence of COI as a useful and accessible DNA barcode.},
}
@article {pmid27609635,
year = {2016},
author = {Dokianakis, E and Tsirigotakis, N and Christodoulou, V and Poulakakis, N and Antoniou, M},
title = {DNA sequencing confirms PCR-RFLP identification of wild caught Larroussius sand flies from Crete and Cyprus.},
journal = {Acta tropica},
volume = {164},
number = {},
pages = {314-320},
doi = {10.1016/j.actatropica.2016.09.003},
pmid = {27609635},
issn = {1873-6254},
mesh = {Amplified Fragment Length Polymorphism Analysis/*methods ; Animals ; Base Sequence ; Bayes Theorem ; Cyprus ; Dogs ; Female ; Geography ; Greece ; Humans ; Leishmania/growth &amp; development ; Leishmaniasis/transmission ; Male ; Phylogeny ; *Polymorphism, Restriction Fragment Length ; Psychodidae/*genetics/parasitology ; Sequence Analysis, DNA/*methods ; },
abstract = {Many Phlebotomine sand fly species (Diptera, Psychodidae) are vectors of the protozoan parasite Leishmania causing a group of diseases called the leishmaniases. The subgenus Larroussius includes sand fly vectors found in South East Mediterranean Basin responsible for Visceral (VL) and Cutaneous human leishmaniasis (CL). It is important to monitor these medically important insects in order to safely predict possible Leishmania transmission cycles. Leishmania infantum is endemic in the islands of Crete and Cyprus with increasing VL cases in humans and dogs and in Cyprus the newly introduced Leishmania donovani causes both VL and CL in humans. The morphological identification of the females of the subgenus Larroussius often presents difficulties. Morphology and COI PCR - RFLP were used to identify wild caught Larroussius sand flies belonging to Phlebotomus tobbi, P. perfiliewi, and P. neglectus species from Crete and Cyprus. The identification results were further confirmed by sequencing (DNA barcoding) and Bayesian phylogenetic analysis. COI PCR - RFLP, when correctly optimized and with respect to geographical origin, can serve as an initial patterning identification tool when large sand fly numbers need to be identified. It could accurately assign Larroussius females and males to their taxa overcoming the difficulties of morphological identification. Finally, DNA barcoding will contribute to a molecular identification database to be used for in-depth species studies.},
}
@article {pmid27542536,
year = {2016},
author = {Pramual, P and Thaijarern, J and Wongpakam, K},
title = {DNA barcoding of human-biting black flies (Diptera: Simuliidae) in Thailand.},
journal = {Acta tropica},
volume = {164},
number = {},
pages = {33-40},
doi = {10.1016/j.actatropica.2016.08.016},
pmid = {27542536},
issn = {1873-6254},
mesh = {Animals ; Bites and Stings ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Genetic Variation ; Humans ; Phylogeny ; Simuliidae/classification/*genetics ; Thailand ; },
abstract = {Black flies (Diptera: Simuliidae) are important insect vectors and pests of humans and animals. Accurate identification, therefore, is important for control and management. In this study, we used mitochondrial cytochrome oxidase I (COI) barcoding sequences to test the efficiency of species identification for the human-biting black flies in Thailand. We used human-biting specimens because they enabled us to link information with previous studies involving the immature stages. Three black fly taxa, Simulium nodosum, S. nigrogilvum and S. doipuiense complex, were collected. The S. doipuiense complex was confirmed for the first time as having human-biting habits. The COI sequences revealed considerable genetic diversity in all three species. Comparisons to a COI sequence library of black flies in Thailand and in a public database indicated a high efficiency for specimen identification for S. nodosum and S. nigrogilvum, but this method was not successful for the S. doipuiense complex. Phylogenetic analyses revealed two divergent lineages in the S. doipuiense complex. Human-biting specimens formed a separate clade from other members of this complex. The results are consistent with the Barcoding Index Number System (BINs) analysis that found six BINs in the S. doipuiense complex. Further taxonomic work is needed to clarify the species status of these human-biting specimens.},
}
@article {pmid27759756,
year = {2016},
author = {Jalali, M and Yu, Y and Xu, K and Ng, RJ and Dong, Z and Wang, L and Safari Dinachali, S and Hong, M and Yang, JK},
title = {Stacking of colors in exfoliable plasmonic superlattices.},
journal = {Nanoscale},
volume = {8},
number = {42},
pages = {18228-18234},
doi = {10.1039/c6nr03466g},
pmid = {27759756},
issn = {2040-3372},
abstract = {Color printing with plasmonic resonators can overcome limitations in pigment-based printing approaches. While layering in pigment-based prints results in familiar color mixing effects, the color effects of stacking plasmonic resonator structures have not been investigated. Here, we demonstrate an experimental strategy to fabricate a 3-tiered complex superlattice of nanostructures with multiple sets of building blocks. Laser interference lithography was used to fabricate the nanostructures and a thin-layer of aluminum was deposited to introduce plasmonic colors. Interestingly, the structures exhibited drastic color changes when the layers of structures were sequentially exfoliated. Our theoretical analysis shows that the colors of the superlattice nanostructure were predominantly determined by the plasmonic properties of the two topmost layers. These results suggest the feasibility of the sub-wavelength vertical stacking of multiple plasmonic colors for applications in sensitive tamper-evident seals, dense 3D barcoding, and substrates for plasmonic color laser printing.},
}
@article {pmid27742219,
year = {2016},
author = {Daily, A and Kennedy, ED and Fierro, LA and Reed, JH and Greene, M and Williams, WW and Evanson, HV and Cox, R and Koeppl, P and Gerlach, K},
title = {Evaluation of scanning 2D barcoded vaccines to improve data accuracy of vaccines administered.},
journal = {Vaccine},
volume = {34},
number = {47},
pages = {5802-5807},
pmid = {27742219},
issn = {1873-2518},
support = {CC999999//Intramural CDC HHS/United States ; },
mesh = {*Data Accuracy ; Documentation/standards ; Electronic Data Processing/*methods/standards ; Electronic Health Records/standards ; Humans ; Multivariate Analysis ; Product Labeling/standards ; Quality Control ; United States ; United States Food and Drug Administration ; Vaccination/*standards ; Vaccines/administration &amp; dosage/*standards ; },
abstract = {BACKGROUND AND OBJECTIVE: Accurately recording vaccine lot number, expiration date, and product identifiers, in patient records is an important step in improving supply chain management and patient safety in the event of a recall. These data are being encoded on two-dimensional (2D) barcodes on most vaccine vials and syringes. Using electronic vaccine administration records, we evaluated the accuracy of lot number and expiration date entered using 2D barcode scanning compared to traditional manual or drop-down list entry methods.<br><br>METHODS: We analyzed 128,573 electronic records of vaccines administered at 32 facilities. We compared the accuracy of records entered using 2D barcode scanning with those entered using traditional methods using chi-square tests and multilevel logistic regression.<br><br>RESULTS: When 2D barcodes were scanned, lot number data accuracy was 1.8 percentage points higher (94.3-96.1%, P<0.001) and expiration date data accuracy was 11 percentage points higher (84.8-95.8%, P<0.001) compared with traditional methods. In multivariate analysis, lot number was more likely to be accurate (aOR=1.75; 99% CI, 1.57-1.96) as was expiration date (aOR=2.39; 99% CI, 2.12-2.68). When controlling for scanning and other factors, manufacturer, month vaccine was administered, and vaccine type were associated with variation in accuracy for both lot number and expiration date.<br><br>CONCLUSION: Two-dimensional barcode scanning shows promise for improving data accuracy of vaccine lot number and expiration date records. Adapting systems to further integrate with 2D barcoding could help increase adoption of 2D barcode scanning technology.},
}
@article {pmid27780256,
year = {2016},
author = {Cai, Y and Li, X and Wang, R and Yang, Q and Li, P and Hu, H},
title = {Quality Traceability System of Traditional Chinese Medicine Based on Two Dimensional Barcode Using Mobile Intelligent Technology.},
journal = {PloS one},
volume = {11},
number = {10},
pages = {e0165263},
pmid = {27780256},
issn = {1932-6203},
mesh = {Algorithms ; Chromatography, High Pressure Liquid/methods ; DNA Barcoding, Taxonomic/*methods ; Drugs, Chinese Herbal/*chemistry/classification ; Mobile Applications ; },
abstract = {Currently, the chemical fingerprint comparison and analysis is mainly based on professional equipment and software, it's expensive and inconvenient. This study aims to integrate QR (Quick Response) code with quality data and mobile intelligent technology to develop a convenient query terminal for tracing quality in the whole industrial chain of TCM (traditional Chinese medicine). Three herbal medicines were randomly selected and their chemical two-dimensional barcode (2D) barcodes fingerprints were constructed. Smartphone application (APP) based on Android system was developed to read initial data of 2D chemical barcodes, and compared multiple fingerprints from different batches of same species or different species. It was demonstrated that there were no significant differences between original and scanned TCM chemical fingerprints. Meanwhile, different TCM chemical fingerprint QR codes could be rendered in the same coordinate and showed the differences very intuitively. To be able to distinguish the variations of chemical fingerprint more directly, linear interpolation angle cosine similarity algorithm (LIACSA) was proposed to get similarity ratio. This study showed that QR codes can be used as an effective information carrier to transfer quality data. Smartphone application can rapidly read quality information in QR codes and convert data into TCM chemical fingerprints.},
}
@article {pmid27775220,
year = {2017},
author = {Bjørnsgaard Aas, A and Davey, ML and Kauserud, H},
title = {ITS all right mama: investigating the formation of chimeric sequences in the ITS2 region by DNA metabarcoding analyses of fungal mock communities of different complexities.},
journal = {Molecular ecology resources},
volume = {17},
number = {4},
pages = {730-741},
doi = {10.1111/1755-0998.12622},
pmid = {27775220},
issn = {1755-0998},
mesh = {Algorithms ; *DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/*genetics ; Fungi/*classification ; Polymerase Chain Reaction ; },
abstract = {The formation of chimeric sequences can create significant methodological bias in PCR-based DNA metabarcoding analyses. During mixed-template amplification of barcoding regions, chimera formation is frequent and well documented. However, profiling of fungal communities typically uses the more variable rDNA region ITS. Due to a larger research community, tools for chimera detection have been developed mainly for the 16S/18S markers. However, these tools are widely applied to the ITS region without verification of their performance. We examined the rate of chimera formation during amplification and 454 sequencing of the ITS2 region from fungal mock communities of different complexities. We evaluated the chimera detecting ability of two common chimera-checking algorithms: perseus and uchime. Large proportions of the chimeras reported were false positives. No false negatives were found in the data set. Verified chimeras accounted for only 0.2% of the total ITS2 reads, which is considerably less than what is typically reported in 16S and 18S metabarcoding analyses. Verified chimeric 'parent sequences' had significantly higher per cent identity to one another than to random members of the mock communities. Community complexity increased the rate of chimera formation. GC content was higher around the verified chimeric break points, potentially facilitating chimera formation through base pair mismatching in the neighbouring regions of high similarity in the chimeric region. We conclude that the hypervariable nature of the ITS region seems to buffer the rate of chimera formation in comparison with other, less variable barcoding regions, due to shorter regions of high sequence similarity.},
}
@article {pmid27770759,
year = {2016},
author = {Adao, DE and Dela Serna, AO and Belleza, ML and Bolo, NR and Rivera, WL},
title = {Subtype analysis of Blastocystis sp. isolates from asymptomatic individuals in an urban community in the Philippines.},
journal = {Annals of parasitology},
volume = {62},
number = {3},
pages = {193&#x2013;200},
doi = {10.17420/ap6203.53},
pmid = {27770759},
issn = {2299-0631},
mesh = {Blastocystis/*classification/genetics/isolation &amp; purification ; Blastocystis Infections/*epidemiology/*parasitology ; Feces/parasitology ; Humans ; Philippines/epidemiology ; Phylogeny ; Urban Population ; },
abstract = {Blastocystis sp. is a commonly reported enteric protistan parasite in faecal specimens with a worldwide distribution afflicting both humans and a wide range of animals. The aim of this study is to characterize the subtypes (STs) of Blastocystis sp. isolates from asymptomatic individuals in an urban community in Pateros, Metro Manila, Philippines. The 600-bp small subunit ribosomal RNA (SSU rRNA) barcoding region of Blastocystis sp. isolates was amplified and sequenced using the primers RD5 and BhRDr. Subtypes were identified by uploading the sequences onto the Basic Local Alignment and Search Tool (BLAST) websites, the Blastocystis Subtype (18S) and Sequence Typing (MLST) Database and by construction of a phylogenetic tree. Twenty-nine (29) out of 35 individuals were detected positive for Blastocystis sp. ST3 is the most common among the three STs detected (65.5%), followed by ST1 (31.0%) and ST4 (3.44%). This study showed that DNA barcoding can serve as a helpful tool to investigate the diversity of Blastocystis sp. in the Philippines.},
}
@article {pmid27623220,
year = {2016},
author = {Hartikainen, H and Bass, D and Briscoe, AG and Knipe, H and Green, AJ and Okamura, B},
title = {Assessing myxozoan presence and diversity using environmental DNA.},
journal = {International journal for parasitology},
volume = {46},
number = {12},
pages = {781-792},
doi = {10.1016/j.ijpara.2016.07.006},
pmid = {27623220},
issn = {1879-0135},
mesh = {Amphipoda/parasitology ; Animals ; *Biodiversity ; Birds ; DNA/analysis ; DNA Barcoding, Taxonomic ; Environment ; Feces/*parasitology ; Fresh Water ; Invertebrates/parasitology ; Myxozoa/classification/genetics/*isolation &amp; purification ; Otters/*parasitology ; Parasitic Diseases, Animal/*parasitology ; Phylogeny ; Polymerase Chain Reaction ; Seawater ; United Kingdom ; Water/*parasitology ; },
abstract = {Amplicon sequencing on a High Throughput Sequencing platform (custom barcoding) was used to detect and characterise myxosporean communities in environmental DNA samples from marine and freshwater environments and in faeces of animals that may serve as hosts or whose prey may host myxosporean infections. A diversity of myxozoans in filtered water samples and in faeces of piscivores (otters and great cormorants) was detected, demonstrating the suitability of lineage-specific amplicons for characterising otherwise difficult to sample parasite communities. The importance of using this approach was highlighted by the lack of myxosporean detection using commonly employed, broadly targeted eukaryotic primers. These results suggest that, despite being frequently present in eDNA samples, myxozoans have been generally overlooked in "eukaryote-wide" surveys. Lineage-specific primers, in contrast, detected 107 operational taxonomic units that were assigned to both the "freshwater" and "marine" myxosporean lineages. Only 7% of these OTUs clustered with sequences in GenBank, providing evidence for substantial undescribed myxosporean diversity. Many new operational taxonomic units, including those found in otter faeces, clustered with a clade of myxosporeans previously characterised by sequences from invertebrate hosts and water samples only. Because myxozoan species identification is heavily reliant on molecular signatures, lineage-specific amplicon sequencing offers an effective and non-destructive means of improving our knowledge of myxozoan diversity. In addition, the analysis of myxozoan DNA in faeces of piscivores offers a potentially efficient method of sampling for diversity and revealing life cycles as piscivore activities may integrate myxozoan infections in fish over relatively broad spatial scales.},
}
@article {pmid27507088,
year = {2016},
author = {Yang, CH and Lin, YD and Chuang, LY and Chang, HW},
title = {Analysis of high-order SNP barcodes in mitochondrial D-loop for chronic dialysis susceptibility.},
journal = {Journal of biomedical informatics},
volume = {63},
number = {},
pages = {112-119},
doi = {10.1016/j.jbi.2016.08.009},
pmid = {27507088},
issn = {1532-0480},
mesh = {*Algorithms ; *DNA, Mitochondrial ; *Electronic Data Processing ; Genotype ; Humans ; *Polymorphism, Single Nucleotide ; Renal Dialysis/statistics &amp; numerical data ; },
abstract = {OBJECTIVES: Positively identifying disease-associated single nucleotide polymorphism (SNP) markers in genome-wide studies entails the complex association analysis of a huge number of SNPs. Such large numbers of SNP barcode (SNP/genotype combinations) continue to pose serious computational challenges, especially for high-dimensional data.<br><br>METHODS: We propose a novel exploiting SNP barcode method based on differential evolution, termed IDE (improved differential evolution). IDE uses a "top combination strategy" to improve the ability of differential evolution to explore high-order SNP barcodes in high-dimensional data.<br><br>RESULTS: We simulate disease data and use real chronic dialysis data to test four global optimization algorithms. In 48 simulated disease models, we show that IDE outperforms existing global optimization algorithms in terms of exploring ability and power to detect the specific SNP/genotype combinations with a maximum difference between cases and controls. In real data, we show that IDE can be used to evaluate the relative effects of each individual SNP on disease susceptibility.<br><br>CONCLUSION: IDE generated significant SNP barcode with less computational complexity than the other algorithms, making IDE ideally suited for analysis of high-order SNP barcodes.},
}
@article {pmid27769448,
year = {2016},
author = {Orozco, J and Villa, E and Manes, CL and Medlin, LK and Guillebault, D},
title = {Electrochemical RNA genosensors for toxic algal species: enhancing selectivity and sensitivity.},
journal = {Talanta},
volume = {161},
number = {},
pages = {560-566},
doi = {10.1016/j.talanta.2016.08.073},
pmid = {27769448},
issn = {1873-3573},
mesh = {Biosensing Techniques ; Dinoflagellida/*genetics ; Electrochemical Techniques ; Electrodes ; Environmental Monitoring ; Gold/chemistry ; Harmful Algal Bloom ; RNA, Algal/*analysis ; Water Pollutants ; },
abstract = {Harmful algal blooms (HABs) are becoming more frequent as climate changes, with tropical species moving northward. Monitoring programs detecting the presence of toxic algae before they bloom are of paramount importance to protect aquatic ecosystems, aquaculture, human health and local economies. Rapid and reliable species identification methods using molecular barcodes coupled to biosensor detection tools have received increasing attention over the past decade as an alternative to the impractical standard microscopic counting-based techniques. This work reports on a PCR amplification-free electrochemical genosensor for the enhanced selective and sensitive detection of RNA from multiple Mediterranean toxic algal species. For a sandwich hybridization (SHA), we designed longer capture and signal probes for more specific target discrimination against a single base-pair mismatch from closely related species and for reproducible signals. We optimized experimental conditions, viz., minimal probe concentration in the SHA on a screen-printed gold electrode and selected the best electrochemical mediator. Probes from 13 Mediterranean dinoflagellate species were tested under optimized conditions and the format further tested for quantification of RNA from environmental samples. We not only enhanced the selectivity and sensitivity of the state-of-the-art toxic algal genosensors but also increased the repertoire of toxic algal biosensors in the Mediterranean, towards an integral and automatic monitoring system.},
}
@article {pmid27768252,
year = {2017},
author = {Ghorbani, A and Gravendeel, B and Selliah, S and Zarré, S and de Boer, H},
title = {DNA barcoding of tuberous Orchidoideae: a resource for identification of orchids used in Salep.},
journal = {Molecular ecology resources},
volume = {17},
number = {2},
pages = {342-352},
doi = {10.1111/1755-0998.12615},
pmid = {27768252},
issn = {1755-0998},
mesh = {Cities ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Intergenic ; DNA, Plant/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; *Genetic Variation ; Iran ; Orchidaceae/anatomy &amp; histology/*classification/*genetics ; Phylogeny ; Plant Proteins/genetics ; Plant Tubers/anatomy &amp; histology/*classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {Tubers of terrestrial orchids are harvested and traded from the eastern Mediterranean to the Caspian Sea for the traditional product Salep. Overexploitation of wild populations and increased middle-class prosperity have escalated prices for Salep, causing overharvesting, depletion of native populations and providing an incentive to expand harvesting to untapped areas in Iran. Limited morphological distinctiveness among traded Salep tubers renders species identification impossible, making it difficult to establish which species are targeted and affected the most. In this study, a reference database of 490 nrITS, trnL-F spacer and matK sequences of 133 taxa was used to identify 150 individual tubers from 31 batches purchased in 12 cities in Iran to assess species diversity in commerce. The sequence reference database consisted of 211 nrITS, 158 trnL-F and 121 matK sequences, including 238 new sequences from collections made for this study. The markers enabled unambiguous species identification with tree-based methods for nrITS in 67% of the tested tubers, 58% for trnL-F and 59% for matK. Species in the genera Orchis (34%), Anacamptis (27%) and Dactylorhiza (19%) were the most common in Salep. Our study shows that all tuberous orchid species in this area are threatened by this trade, and further stresses the urgency of controlling illegal harvesting and cross-border trade of Salep tubers.},
}
@article {pmid27768250,
year = {2017},
author = {Schmidt, S and Taeger, A and Morinière, J and Liston, A and Blank, SM and Kramp, K and Kraus, M and Schmidt, O and Heibo, E and Prous, M and Nyman, T and Malm, T and Stahlhut, J},
title = {Identification of sawflies and horntails (Hymenoptera, 'Symphyta') through DNA barcodes: successes and caveats.},
journal = {Molecular ecology resources},
volume = {17},
number = {4},
pages = {670-685},
doi = {10.1111/1755-0998.12614},
pmid = {27768250},
issn = {1755-0998},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Europe ; Hymenoptera/*classification ; Larva ; *Phylogeny ; },
abstract = {The 'Symphyta' is a paraphyletic assemblage at the base of the order Hymenoptera, comprising 14 families and about 8750 species. All have phytophagous larvae, except for the Orussidae, which are parasitoids. This study presents and evaluates the results of DNA barcoding of approximately 5360 specimens of 'Symphyta', mainly adults, and 4362 sequences covering 1037 species were deemed of suitable quality for inclusion in the analysis. All extant families are represented, except for the Anaxyelidae. The majority of species and specimens are from Europe, but approximately 38% of the species and 13% of the specimens are of non-European origin. The utility of barcoding for species identification and taxonomy of 'Symphyta' is discussed on the basis of examples from each of the included families. A significant level of cryptic species diversity was apparent in many groups. Other attractive applications include the identification of immature stages without the need to rear them, community analyses based on metabarcoding of bulk samples and association of the sexes of adults.},
}
@article {pmid27768246,
year = {2017},
author = {MacDonald, AJ and Sarre, SD},
title = {A framework for developing and validating taxon-specific primers for specimen identification from environmental DNA.},
journal = {Molecular ecology resources},
volume = {17},
number = {4},
pages = {708-720},
doi = {10.1111/1755-0998.12618},
pmid = {27768246},
issn = {1755-0998},
mesh = {Animals ; Australia ; DNA/*isolation &amp; purification ; *DNA Primers ; Murinae/genetics ; *Phylogeny ; Polymerase Chain Reaction ; Species Specificity ; },
abstract = {Taxon-specific DNA tests are applied to many ecological and management questions, increasingly using environmental DNA (eDNA). eDNA facilitates noninvasive ecological studies but introduces additional risks of bias and error. For effective application, PCR primers must be developed for each taxon and validated in each system. We outline a nine step framework for the development and validation of taxon-specific primers for eDNA analysis in ecological studies, involving reference database construction, phylogenetic evaluation of the target gene, primer design, primer evaluation in silico, and laboratory evaluation of primer specificity, sensitivity and utility. Our framework makes possible a rigorous evaluation of likely sources of error. The first five steps can be conducted relatively rapidly and (where reference DNA sequences are available) require minimal laboratory resources, enabling assessment of primer suitability before investing in further work. Steps six to eight require more costly laboratory analyses but are essential to evaluate risks of false-positive and false-negative results, while step 9 relates to field implementation. As an example, we have developed and evaluated primers to specifically amplify part of the mitochondrial ND2 gene from Australian bandicoots. If adopted during the early stages of primer development, our framework will facilitate large-scale implementation of well-designed DNA tests to detect specific wildlife from eDNA samples. This will provide researchers and managers with an understanding of the strengths and limitations of their data and the conclusions that can be drawn from them.},
}
@article {pmid27767337,
year = {2016},
author = {Littlefair, JE and Clare, EL},
title = {Barcoding the food chain: from Sanger to high-throughput sequencing.},
journal = {Genome},
volume = {59},
number = {11},
pages = {946-958},
doi = {10.1139/gen-2016-0028},
pmid = {27767337},
issn = {1480-3321},
mesh = {Agriculture ; Animals ; *Biodiversity ; Crops, Agricultural/parasitology ; *DNA Barcoding, Taxonomic ; Ecosystem ; *Food Chain ; Food Safety ; Food Supply ; Humans ; },
abstract = {Society faces the complex challenge of supporting biodiversity and ecosystem functioning, while ensuring food security by providing safe traceable food through an ever-more-complex global food chain. The increase in human mobility brings the added threat of pests, parasites, and invaders that further complicate our agro-industrial efforts. DNA barcoding technologies allow researchers to identify both individual species, and, when combined with universal primers and high-throughput sequencing techniques, the diversity within mixed samples (metabarcoding). These tools are already being employed to detect market substitutions, trace pests through the forensic evaluation of trace "environmental DNA", and to track parasitic infections in livestock. The potential of DNA barcoding to contribute to increased security of the food chain is clear, but challenges remain in regulation and the need for validation of experimental analysis. Here, we present an overview of the current uses and challenges of applied DNA barcoding in agriculture, from agro-ecosystems within farmland to the kitchen table.},
}
@article {pmid27767335,
year = {2016},
author = {Mitterboeck, TF and Fu, J and Adamowicz, SJ},
title = {Rates and patterns of molecular evolution in freshwater versus terrestrial insects.},
journal = {Genome},
volume = {59},
number = {11},
pages = {968-980},
doi = {10.1139/gen-2016-0030},
pmid = {27767335},
issn = {1480-3321},
mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic ; Ecosystem ; Electron Transport Complex IV/genetics ; Energy Metabolism ; *Evolution, Molecular ; Fresh Water/parasitology ; Insecta/*classification/*genetics/metabolism ; Phylogeny ; Population Density ; },
abstract = {Insect lineages have crossed between terrestrial and aquatic habitats many times, for both immature and adult life stages. We explore patterns in molecular evolutionary rates between 42 sister pairs of related terrestrial and freshwater insect clades using publicly available protein-coding DNA sequence data from the orders Coleoptera, Diptera, Lepidoptera, Hemiptera, Mecoptera, Trichoptera, and Neuroptera. We furthermore test for habitat-associated convergent molecular evolution in the cytochrome c oxidase subunit I (COI) gene in general and at a particular amino acid site previously reported to exhibit habitat-linked convergence within an aquatic beetle group. While ratios of nonsynonymous-to-synonymous substitutions across available loci were higher in terrestrial than freshwater-associated taxa in 26 of 42 lineage pairs, a stronger trend was observed (20 of 31, pbinomial = 0.15, pWilcoxon = 0.017) when examining only terrestrial-aquatic pairs including fully aquatic taxa. We did not observe any widespread changes at particular amino acid sites in COI associated with habitat shifts, although there may be general differences in selection regime linked to habitat.},
}
@article {pmid27767334,
year = {2016},
author = {Thomas, VG and Hanner, RH and Borisenko, AV},
title = {DNA-based identification of invasive alien species in relation to Canadian federal policy and law, and the basis of rapid-response management.},
journal = {Genome},
volume = {59},
number = {11},
pages = {1023-1031},
doi = {10.1139/gen-2016-0022},
pmid = {27767334},
issn = {1480-3321},
mesh = {Animals ; Canada ; *DNA Barcoding, Taxonomic/methods ; Humans ; *Introduced Species ; Plants/classification/genetics ; Public Policy ; },
abstract = {Managing invasive alien species in Canada requires reliable taxonomic identification as the basis of rapid-response management. This can be challenging, especially when organisms are small and lack morphological diagnostic features. DNA-based techniques, such as DNA barcoding, offer a reliable, rapid, and inexpensive toolkit for taxonomic identification of individual or bulk samples, forensic remains, and even environmental DNA. Well suited for this requirement, they could be more broadly deployed and incorporated into the operating policy and practices of Canadian federal departments and should be authorized under these agencies' articles of law. These include Fisheries and Oceans Canada, Canadian Food Inspection Agency, Transport Canada, Environment Canada, Parks Canada, and Health Canada. These efforts should be harmonized with the appropriate provisions of provincial jurisdictions, for example, the Ontario Invasive Species Act. This approach necessitates that a network of accredited, certified laboratories exists, and that updated DNA reference libraries are readily accessible. Harmonizing this approach is vital among Canadian federal agencies, and between the federal and provincial levels of government. Canadian policy and law must also be harmonized with that of the USA when detecting, and responding to, invasive species in contiguous lands and waters. Creating capacity in legislation for use of DNA-based identifications brings the authority to fund, train, deploy, and certify staff, and to refine further developments in this molecular technology.},
}
@article {pmid27766152,
year = {2016},
author = {Shaik, RS and Zhu, X and Clements, DR and Weston, LA},
title = {Understanding invasion history and predicting invasive niches using genetic sequencing technology in Australia: case studies from Cucurbitaceae and Boraginaceae.},
journal = {Conservation physiology},
volume = {4},
number = {1},
pages = {cow030},
pmid = {27766152},
issn = {2051-1434},
abstract = {Part of the challenge in dealing with invasive plant species is that they seldom represent a uniform, static entity. Often, an accurate understanding of the history of plant introduction and knowledge of the real levels of genetic diversity present in species and populations of importance is lacking. Currently, the role of genetic diversity in promoting the successful establishment of invasive plants is not well defined. Genetic profiling of invasive plants should enhance our understanding of the dynamics of colonization in the invaded range. Recent advances in DNA sequencing technology have greatly facilitated the rapid and complete assessment of plant population genetics. Here, we apply our current understanding of the genetics and ecophysiology of plant invasions to recent work on Australian plant invaders from the Cucurbitaceae and Boraginaceae. The Cucurbitaceae study showed that both prickly paddy melon (Cucumis myriocarpus) and camel melon (Citrullus lanatus) were represented by only a single genotype in Australia, implying that each was probably introduced as a single introduction event. In contrast, a third invasive melon, Citrullus colocynthis, possessed a moderate level of genetic diversity in Australia and was potentially introduced to the continent at least twice. The Boraginaceae study demonstrated the value of comparing two similar congeneric species; one, Echium plantagineum, is highly invasive and genetically diverse, whereas the other, Echium vulgare, exhibits less genetic diversity and occupies a more limited ecological niche. Sequence analysis provided precise identification of invasive plant species, as well as information on genetic diversity and phylogeographic history. Improved sequencing technologies will continue to allow greater resolution of genetic relationships among invasive plant populations, thereby potentially improving our ability to predict the impact of these relationships upon future spread and better manage invaders possessing potentially diverse biotypes and exhibiting diverse breeding systems, life histories and invasion histories.},
}
@article {pmid27765655,
year = {2016},
author = {Rajvanshi, S and Choudhary, K and Agrawal, N},
title = {Threading: A novel insilico indagation method for genetic characterization of some diplostomoid metacercariae (Digenea:Diplostomidae Poirier, 1886).},
journal = {Experimental parasitology},
volume = {171},
number = {},
pages = {71-76},
doi = {10.1016/j.exppara.2016.10.013},
pmid = {27765655},
issn = {1090-2449},
mesh = {Amino Acid Sequence ; Amino Acids/analysis ; Animals ; Cyclooxygenase 1/genetics ; DNA, Mitochondrial/chemistry ; Fish Diseases/parasitology ; Fishes ; Helminth Proteins/*chemistry/genetics ; Imaging, Three-Dimensional ; Metacercariae/chemistry/classification/genetics ; Mitochondria/enzymology ; Models, Biological ; Models, Structural ; Molecular Conformation ; Phylogeny ; Protein Conformation ; Proteomics ; Trematoda/chemistry/classification/*genetics ; Trematode Infections/parasitology/veterinary ; },
abstract = {The protein encoding zone of Mitochondrial DNA region (inherited from single lineage) seems most suitable and effective for taxonomic, systematic, ecological, evolutionary, DNA barcoding, cryptic species and population studies, exploiting nucleotide/amino acid datasets (1D/2D/3D conformational level). Nowadays, expeditious computerized methods are in trend for analyzing genetic material to demonstrate variations at various levels of protein structures. Structural proteomics have implemented here for genetic identification, differentiation and relationship of species from information rich data of mt COI gene of the family Diplostomidae with inclusion of molecular tools. Various aspects have been utilized herein for re-validation and infallible discrimination of Trematode diplostomoid metacercariae (Tetracotyle lucknowensis Pandey, 1971; T. xenentodoni Chakrabarti, 1970; T. fausti Rai and Pande, 1969; T. muscularius Chakrabarti, 1970 and Diplostomulum minutum Pandey, 1968), the infective stage in the life cycle, causing severe damage to fish host, whose adults are found mainly in fish eating birds and mammals.},
}
@article {pmid27764218,
year = {2016},
author = {Baldow, C and Thielecke, L and Glauche, I},
title = {Model Based Analysis of Clonal Developments Allows for Early Detection of Monoclonal Conversion and Leukemia.},
journal = {PloS one},
volume = {11},
number = {10},
pages = {e0165129},
pmid = {27764218},
issn = {1932-6203},
mesh = {Clone Cells/*cytology/pathology ; Genetic Therapy ; Genetic Vectors/genetics ; Hematopoietic Stem Cells/*cytology/pathology ; Humans ; Leukemia/*diagnosis/pathology/therapy ; Models, Theoretical ; Retroviridae ; },
abstract = {The availability of several methods to unambiguously mark individual cells has strongly fostered the understanding of clonal developments in hematopoiesis and other stem cell driven regenerative tissues. While cellular barcoding is the method of choice for experimental studies, patients that underwent gene therapy carry a unique insertional mark within the transplanted cells originating from the integration of the retroviral vector. Close monitoring of such patients allows accessing their clonal dynamics, however, the early detection of events that predict monoclonal conversion and potentially the onset of leukemia are beneficial for treatment. We developed a simple mathematical model of a self-stabilizing hematopoietic stem cell population to generate a wide range of possible clonal developments, reproducing typical, experimentally and clinically observed scenarios. We use the resulting model scenarios to suggest and test a set of statistical measures that should allow for an interpretation and classification of relevant clonal dynamics. Apart from the assessment of several established diversity indices we suggest a measure that quantifies the extension to which the increase in the size of one clone is attributed to the total loss in the size of all other clones. By evaluating the change in relative clone sizes between consecutive measurements, the suggested measure, referred to as maximum relative clonal expansion (mRCE), proves to be highly sensitive in the detection of rapidly expanding cell clones prior to their dominant manifestation. This predictive potential places the mRCE as a suitable means for the early recognition of leukemogenesis especially in gene therapy patients that are closely monitored. Our model based approach illustrates how simulation studies can actively support the design and evaluation of preclinical strategies for the analysis and risk evaluation of clonal developments.},
}
@article {pmid27764148,
year = {2016},
author = {Nazari, V and Schmidt, BC and Prosser, S and Hebert, PD},
title = {Century-Old DNA Barcodes Reveal Phylogenetic Placement of the Extinct Jamaican Sunset Moth, Urania sloanus Cramer (Lepidoptera: Uraniidae).},
journal = {PloS one},
volume = {11},
number = {10},
pages = {e0164405},
pmid = {27764148},
issn = {1932-6203},
mesh = {Animals ; Bayes Theorem ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry/isolation &amp; purification/metabolism ; Evolution, Molecular ; Jamaica ; Male ; Moths/classification/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Analysis of the DNA barcode region of the cytochrome c oxidase 1 gene from a specimen of the extinct Jamaican sunset moth, Urania sloanus, places this species as a sister to the Central American U. fulgens. We found that all Urania F. species were closely related (<2.8% maximum divergence at COI), with the Cuban endemic U. boisduvalii appearing as sister to the rest. The low divergence in DNA barcodes and genitalic structures indicate that the Cuban U. poeyi and eastern Brazilian U. brasiliensis are geographic segregates of U. fulgens and U. leilus respectively, so the former two taxa are accordingly recognized as subspecies.},
}
@article {pmid27762295,
year = {2016},
author = {Sommeria-Klein, G and Zinger, L and Taberlet, P and Coissac, E and Chave, J},
title = {Inferring neutral biodiversity parameters using environmental DNA data sets.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {35644},
pmid = {27762295},
issn = {2045-2322},
mesh = {*Biodiversity ; Biostatistics ; Computer Simulation ; DNA/*analysis/*genetics ; DNA Barcoding, Taxonomic/methods ; *Ecosystem ; Metagenomics/methods ; Polymerase Chain Reaction ; },
abstract = {The DNA present in the environment is a unique and increasingly exploited source of information for conducting fast and standardized biodiversity assessments for any type of organisms. The datasets resulting from these surveys are however rarely compared to the quantitative predictions of biodiversity models. In this study, we simulate neutral taxa-abundance datasets, and artificially noise them by simulating noise terms typical of DNA-based biodiversity surveys. The resulting noised taxa abundances are used to assess whether the two parameters of Hubbell's neutral theory of biodiversity can still be estimated. We find that parameters can be inferred provided that PCR noise on taxa abundances does not exceed a certain threshold. However, inference is seriously biased by the presence of artifactual taxa. The uneven contribution of organisms to environmental DNA owing to size differences and barcode copy number variability does not impede neutral parameter inference, provided that the number of sequence reads used for inference is smaller than the number of effectively sampled individuals. Hence, estimating neutral parameters from DNA-based taxa abundance patterns is possible but requires some caution. In studies that include empirical noise assessments, our comprehensive simulation benchmark provides objective criteria to evaluate the robustness of neutral parameter inference.},
}
@article {pmid27762185,
year = {2017},
author = {Laidemitt, MR and Zawadzki, ET and Brant, SV and Mutuku, MW and Mkoji, GM and Loker, ES},
title = {Loads of trematodes: discovering hidden diversity of paramphistomoids in Kenyan ruminants.},
journal = {Parasitology},
volume = {144},
number = {2},
pages = {131-147},
pmid = {27762185},
issn = {1469-8161},
support = {P30 GM110907/GM/NIGMS NIH HHS/United States ; R01 AI101438/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; DNA, Ribosomal Spacer/genetics ; Kenya/epidemiology ; Livestock/*parasitology ; Paramphistomatidae/anatomy &amp; histology/genetics/*isolation &amp; purification ; Phylogeny ; Ruminants/*parasitology ; Snails/parasitology ; Trematode Infections/epidemiology/parasitology/*veterinary ; },
abstract = {Paramphistomoids are ubiquitous and widespread digeneans that infect a diverse range of definitive hosts, being particularly speciose in ruminants. We collected adult worms from cattle, goats and sheep from slaughterhouses, and cercariae from freshwater snails from ten localities in Central and West Kenya. We sequenced cox1 (690 bp) and internal transcribed region 2 (ITS2) (385 bp) genes from a small piece of 79 different adult worms and stained and mounted the remaining worm bodies for comparisons with available descriptions. We also sequenced cox1 and ITS2 from 41 cercariae/rediae samples collected from four different genera of planorbid snails. Combining morphological observations, host use information, genetic distance values and phylogenetic methods, we delineated 16 distinct clades of paramphistomoids. For four of the 16 clades, sequences from adult worms and cercariae/rediae matched, providing an independent assessment for their life cycles. Much work is yet to be done to resolve fully the relationships among paramphistomoids, but some correspondence between sequence- and anatomically based classifications were noted. Paramphistomoids of domestic ruminants provide one of the most abundant sources of parasitic flatworm biomass, and because of the predilection of several species use Bulinus and Biomphalaria snail hosts, have interesting linkages with the biology of animal and human schistosomes to in Africa.},
}
@article {pmid27762049,
year = {2017},
author = {Biedrzycka, A and Sebastian, A and Migalska, M and Westerdahl, H and Radwan, J},
title = {Testing genotyping strategies for ultra-deep sequencing of a co-amplifying gene family: MHC class I in a passerine bird.},
journal = {Molecular ecology resources},
volume = {17},
number = {4},
pages = {642-655},
doi = {10.1111/1755-0998.12612},
pmid = {27762049},
issn = {1755-0998},
mesh = {Animals ; *Genes, MHC Class I ; Genotyping Techniques ; High-Throughput Nucleotide Sequencing ; Passeriformes/*genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; },
abstract = {Characterization of highly duplicated genes, such as genes of the major histocompatibility complex (MHC), where multiple loci often co-amplify, has until recently been hindered by insufficient read depths per amplicon. Here, we used ultra-deep Illumina sequencing to resolve genotypes at exon 3 of MHC class I genes in the sedge warbler (Acrocephalus schoenobaenus). We sequenced 24 individuals in two replicates and used this data, as well as a simulated data set, to test the effect of amplicon coverage (range: 500-20 000 reads per amplicon) on the repeatability of genotyping using four different genotyping approaches. A third replicate employed unique barcoding to assess the extent of tag jumping, that is swapping of individual tag identifiers, which may confound genotyping. The reliability of MHC genotyping increased with coverage and approached or exceeded 90% within-method repeatability of allele calling at coverages of >5000 reads per amplicon. We found generally high agreement between genotyping methods, especially at high coverages. High reliability of the tested genotyping approaches was further supported by our analysis of the simulated data set, although the genotyping approach relying primarily on replication of variants in independent amplicons proved sensitive to repeatable errors. According to the most repeatable genotyping method, the number of co-amplifying variants per individual ranged from 19 to 42. Tag jumping was detectable, but at such low frequencies that it did not affect the reliability of genotyping. We thus demonstrate that gene families with many co-amplifying genes can be reliably genotyped using HTS, provided that there is sufficient per amplicon coverage.},
}
@article {pmid27761337,
year = {2016},
author = {Fourdrilis, S and Mardulyn, P and Hardy, OJ and Jordaens, K and de Frias Martins, AM and Backeljau, T},
title = {Mitochondrial DNA hyperdiversity and its potential causes in the marine periwinkle Melarhaphe neritoides (Mollusca: Gastropoda).},
journal = {PeerJ},
volume = {4},
number = {},
pages = {e2549},
pmid = {27761337},
issn = {2167-8359},
abstract = {We report the presence of mitochondrial DNA (mtDNA) hyperdiversity in the marine periwinkle Melarhaphe neritoides (Linnaeus, 1758), the first such case among marine gastropods. Our dataset consisted of concatenated 16S-COI-Cytb gene fragments. We used Bayesian analyses to investigate three putative causes underlying genetic variation, and estimated the mtDNA mutation rate, possible signatures of selection and the effective population size of the species in the Azores archipelago. The mtDNA hyperdiversity in M. neritoides is characterized by extremely high haplotype diversity (Hd = 0.999 ± 0.001), high nucleotide diversity (π = 0.013 ± 0.001), and neutral nucleotide diversity above the threshold of 5% (πsyn = 0.0677). Haplotype richness is very high even at spatial scales as small as 100m[2]. Yet, mtDNA hyperdiversity does not affect the ability of DNA barcoding to identify M. neritoides. The mtDNA hyperdiversity in M. neritoides is best explained by the remarkably high mutation rate at the COI locus (μ = 5.82 × 10[-5] per site per year or μ = 1.99 × 10[-4] mutations per nucleotide site per generation), whereas the effective population size of this planktonic-dispersing species is surprisingly small (Ne = 5, 256; CI = 1,312-3,7495) probably due to the putative influence of selection. Comparison with COI nucleotide diversity values in other organisms suggests that mtDNA hyperdiversity may be more frequently linked to high μ values and that mtDNA hyperdiversity may be more common across other phyla than currently appreciated.},
}
@article {pmid27761307,
year = {2016},
author = {Ardura, A and Morote, E and Kochzius, M and Garcia-Vazquez, E},
title = {Diversity of planktonic fish larvae along a latitudinal gradient in the Eastern Atlantic Ocean estimated through DNA barcodes.},
journal = {PeerJ},
volume = {4},
number = {},
pages = {e2438},
pmid = {27761307},
issn = {2167-8359},
abstract = {Mid-trophic pelagic fish are essential components of marine ecosystems because they represent the link between plankton and higher predators. Moreover, they are the basis of the most important fisheries resources; for example, in African waters. In this study, we have sampled pelagic fish larvae in the Eastern Atlantic Ocean along a latitudinal gradient between 37°N and 2°S. We have employed Bongo nets for plankton sampling and sorted visually fish and fish larvae. Using the cytochrome oxidase I gene (COI) as a DNA barcode, we have identified 44 OTUs down to species level that correspond to 14 families, with Myctophidae being the most abundant. A few species were cosmopolitan and others latitude-specific, as was expected. The latitudinal pattern of diversity did not exhibit a temperate-tropical cline; instead, it was likely correlated with environmental conditions with a decline in low-oxygen zones. Importantly, gaps and inconsistencies in reference DNA databases impeded accurate identification to the species level of 49% of the individuals. Fish sampled from tropical latitudes and some orders, such as Perciformes, Myctophiformes and Stomiiformes, were largely unidentified due to incomplete references. Some larvae were identified based on morphology and COI analysis for comparing time and costs employed from each methodology. These results suggest the need of reinforcing DNA barcoding reference datasets of Atlantic bathypelagic tropical fish that, as main prey of top predators, are crucial for ecosystem-based management of fisheries resources.},
}
@article {pmid27759467,
year = {2018},
author = {Levin, BA and Simonov, E and Matveyev, MP and Artaev, ON and Mustafayev, NJ and Pashkov, AN and Roubenyan, HR},
title = {DNA barcoding of the fishes of the genus Alburnoides (Actinopterygii, Cyprinidae) from Caucasus.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {1},
pages = {49-55},
doi = {10.1080/24701394.2016.1238900},
pmid = {27759467},
issn = {2470-1408},
mesh = {Animals ; Cyprinidae/*classification/genetics ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Genes, Mitochondrial ; Genome, Mitochondrial ; *Phylogeny ; },
abstract = {Spirlins of the genus Alburnoides are widespread fishes, which taxonomy has been rapidly developing in recent years. Mitochondrial cytochrome c oxidase subunit I (COI) was used as DNA barcode marker to create a reference dataset of Caucasian Alburnoides and to test its barcoding efficiency. All four previously known Caucasian species of Alburnoides were confirmed as valid species with high genetic distances to sister species as well confirmed as Caucasian endemics. Alburnoides samiii, previously known from Sefidroud basin (Iran), was discovered in Transcaucasia. The accuracy of species identification of Ponto-Caspian Alburnoides by DNA barcodes was 100%. In addition, one potentially new species within A. gmelini was revealed. Despite the limited ability of COI to infer phylogenetic relationships, study provided evidence that Ponto-Caspian lineage of Alburnoides includes significantly larger number of species from Caspian Sea basin and inland basins of Central Asia.},
}
@article {pmid27759464,
year = {2017},
author = {Sukantamala, J and Sing, KW and Jaturas, N and Polseela, R and Wilson, JJ},
title = {Unexpected diversity of sandflies (Diptera: Psychodidae) in tourist caves in Northern Thailand.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {6},
pages = {949-955},
doi = {10.1080/24701394.2016.1214728},
pmid = {27759464},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; *Genes, Mitochondrial ; *Genetic Variation ; *Phylogeny ; Psychodidae/classification/enzymology/*genetics ; Sequence Analysis, DNA ; },
abstract = {Certain species of Phlebotomine sandflies (Diptera: Psychodidae) are vectors of the protozoa which causes leishmaniasis. Sandflies are found breeding in enclosed places like caves. Thailand is a popular tourist destination, including for ecotourism activities like caving, which increases the risk of contact between tourists and sandflies. Surveillance of sandflies is important for monitoring this risk but identification of species based on morphology is challenged by phenotypic plasticity and cryptic diversity. DNA barcodes have been used for the identification of sandflies in Thailand. We collected sandflies using CDC light trap from four tourist caves in Northern Thailand. Female sandflies were provisionally sorted into 13 morphospecies and 19 unidentified specimens. DNA was extracted from the thorax and legs of sandflies and the DNA barcode region of cytochrome c oxidase I mtDNA amplified and sequenced. The specimens were sorted into 22 molecular operational taxonomic units (MOTU) based on the 145 DNA barcodes, which is significantly more than the morphospecies. Several of the taxa thought to be present in multiple caves, based on morphospecies sorting, split into cave-specific MOTU which likely represent cryptic species. Several MOTU reported in an earlier study from Wihan Cave, Thailand, were also found in these caves. This supports the use of DNA barcodes to investigate species diversity of sandflies and their useful role in surveillance of sandflies in Thailand.},
}
@article {pmid27758125,
year = {2018},
author = {Muangkram, Y and Wajjwalku, W and Amano, A and Sukmak, M},
title = {The novel primers for mammal species identification-based mitochondrial cytochrome b sequence: implication for reserved wild animals in Thailand and endangered mammal species in Southeast Asia.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {1},
pages = {62-72},
doi = {10.1080/24701394.2016.1238902},
pmid = {27758125},
issn = {2470-1408},
mesh = {Animals ; Base Sequence ; Cytochromes b/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA Primers ; *Endangered Species ; *Genes, Mitochondrial ; Mammals/classification/genetics ; Perissodactyla/classification/*genetics ; Phylogeny ; Sequence Alignment ; Thailand ; },
abstract = {We presented the powerful techniques for species identification using the short amplicon of mitochondrial cytochrome b gene sequence. Two faecal samples and one single hair sample of the Asian tapir were tested using the new cytochrome b primers. The results showed a high sequence similarity with the mainland Asian tapir group. The comparative sequence analysis of the reserved wild mammals in Thailand and the other endangered mammal species from Southeast Asia comprehensibly verified the potential of our novel primers. The forward and reverse primers were 94.2 and 93.2%, respectively, by the average value of the sequence identity among 77 species sequences, and the overall mean distance was 35.9%. This development technique could provide rapid, simple, and reliable tools for species confirmation. Especially, it could recognize the problematic biological specimens contained less DNA material from illegal products and assist with wildlife crime investigation of threatened species and related forensic casework.},
}
@article {pmid27753524,
year = {2016},
author = {Poovitha, S and Stalin, N and Balaji, R and Parani, M},
title = {Multi-locus DNA barcoding identifies matK as a suitable marker for species identification in Hibiscus L.},
journal = {Genome},
volume = {59},
number = {12},
pages = {1150-1156},
doi = {10.1139/gen-2015-0205},
pmid = {27753524},
issn = {1480-3321},
mesh = {*DNA Barcoding, Taxonomic/methods ; DNA, Intergenic ; *Genes, Plant ; *Genetic Markers ; Hibiscus/*classification/*genetics ; India ; Multilocus Sequence Typing ; Phylogeny ; },
abstract = {The genus Hibiscus L. includes several taxa of medicinal value and species used for the extraction of natural dyes. These applications require the use of authentic plant materials. DNA barcoding is a molecular method for species identification, which helps in reliable authentication by using one or more DNA barcode marker. In this study, we have collected 44 accessions, representing 16 species of Hibiscus, distributed in the southern peninsular India, to evaluate the discriminatory power of the two core barcodes rbcLa and matK together with the suggested additional regions trnH-psbA and ITS2. No intraspecies divergence was observed among the accessions studied. Interspecies divergence was 0%-9.6% with individual markers, which increased to 0%-12.5% and 0.8%-20.3% when using two- and three-marker combinations, respectively. Differentiation of all the species of Hibiscus was possible with the matK DNA barcode marker. Also, in two-marker combinations, only those combinations with matK differentiated all the species. Though all the three-marker combinations showed 100% species differentiation, species resolution was consistently better when the matK marker formed part of the combination. These results clearly showed that matK is more suitable when compared to rbcLa, trnH-psbA, and ITS2 for species identification in Hibiscus.},
}
@article {pmid27753511,
year = {2016},
author = {Ashfaq, M and Hebert, PD},
title = {DNA barcodes for bio-surveillance: regulated and economically important arthropod plant pests.},
journal = {Genome},
volume = {59},
number = {11},
pages = {933-945},
doi = {10.1139/gen-2016-0024},
pmid = {27753511},
issn = {1480-3321},
mesh = {Animals ; Arthropods/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Environmental Monitoring ; Insect Control ; Introduced Species ; Plants/*parasitology ; Quarantine ; },
abstract = {Many of the arthropod species that are important pests of agriculture and forestry are impossible to discriminate morphologically throughout all of their life stages. Some cannot be differentiated at any life stage. Over the past decade, DNA barcoding has gained increasing adoption as a tool to both identify known species and to reveal cryptic taxa. Although there has not been a focused effort to develop a barcode library for them, reference sequences are now available for 77% of the 409 species of arthropods documented on major pest databases. Aside from developing the reference library needed to guide specimen identifications, past barcode studies have revealed that a significant fraction of arthropod pests are a complex of allied taxa. Because of their importance as pests and disease vectors impacting global agriculture and forestry, DNA barcode results on these arthropods have significant implications for quarantine detection, regulation, and management. The current review discusses these implications in light of the presence of cryptic species in plant pests exposed by DNA barcoding.},
}
@article {pmid27753507,
year = {2016},
author = {Leyva-Cruz, E and Vásquez-Yeomans, L and Carrillo, L and Valdez-Moreno, M},
title = {Identifying pelagic fish eggs in the southeast Yucatan Peninsula using DNA barcodes.},
journal = {Genome},
volume = {59},
number = {12},
pages = {1117-1129},
doi = {10.1139/gen-2015-0151},
pmid = {27753507},
issn = {1480-3321},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Fishes/*classification/*genetics ; Geography ; Mexico ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {In the waters surrounding Banco Chinchorro in the Mexican Caribbean are spawning and nursery areas for many types of fish. In this natural environment, as opposed to under controlled laboratory conditions, it is almost impossible to link an individual egg to the adult that laid it. This makes identifying the species of the eggs difficult. However, DNA barcodes have made this easier. In the present study, 300 eggs were processed for molecular analysis, from which 139 sequences were obtained. We identified 42 taxa (33 species with their binomial names), 35 genera, and 24 families. The identified eggs included those from Ariomma melanum, which is the first recording of this species in the Mexican Caribbean. Eggs from economically important fish species were also identified, including frigate tuna (Auxis thazard), crevalle jack (Caranx hippos), common dolphinfish (Coryphaena hippurus), sailfish (Istiophorus platypterus), white marlin (Kajikia albida), skipjack tuna (Katsuwonus pelamis), blackfin tuna (Thunnus atlanticus), and swordfish (Xiphias gladius). We have also described new morphological characteristics and captured photographs for 21 species, as well as obtained new information about spawning locality and time for 16 species. This valuable information will provide the basis to develop more effective conservation measures for sustainable fisheries and protection of the Mesoamerican Barrier Reef System.},
}
@article {pmid27748984,
year = {2017},
author = {Zhao, G and Yin, G and Inamdar, AA and Luo, J and Zhang, N and Yang, I and Buckley, B and Bennett, JW},
title = {Volatile organic compounds emitted by filamentous fungi isolated from flooded homes after Hurricane Sandy show toxicity in a Drosophila bioassay.},
journal = {Indoor air},
volume = {27},
number = {3},
pages = {518-528},
doi = {10.1111/ina.12350},
pmid = {27748984},
issn = {1600-0668},
mesh = {*Air Microbiology ; Air Pollution, Indoor/analysis ; Animals ; Biological Assay ; Cyclonic Storms ; Drosophila/*drug effects ; Fungi/isolation &amp; purification/*metabolism ; Housing ; Humans ; New Jersey ; Solid Phase Microextraction ; Toxicity Tests ; Volatile Organic Compounds/*analysis ; },
abstract = {Superstorm Sandy provided an opportunity to study filamentous fungi (molds) associated with winter storm damage. We collected 36 morphologically distinct fungal isolates from flooded buildings. By combining traditional morphological and cultural characters with an analysis of ITS sequences (the fungal DNA barcode), we identified 24 fungal species that belong to eight genera: Penicillium (11 species), Fusarium (four species), Aspergillus (three species), Trichoderma (two species), and one species each of Metarhizium, Mucor, Pestalotiopsis, and Umbelopsis. Then, we used a Drosophila larval assay to assess possible toxicity of volatile organic compounds (VOCs) emitted by these molds. When cultured in a shared atmosphere with growing cultures of molds isolated after Hurricane Sandy, larval toxicity ranged from 15 to 80%. VOCs from Aspergillus niger 129B were the most toxic yielding 80% mortality to Drosophila after 12 days. The VOCs from Trichoderma longibrachiatum 117, Mucor racemosus 138a, and Metarhizium anisopliae 124 were relatively non-toxigenic. A preliminary analysis of VOCs was conducted using solid-phase microextraction-gas chromatography-mass spectrometry from two of the most toxic, two of the least toxic, and two species of intermediate toxicity. The more toxic molds produced higher concentrations of 1-octen-3-ol, 3-octanone, 3-octanol, 2-octen-1-ol, and 2-nonanone; while the less toxic molds produced more 3-methyl-1-butanol and 2-methyl-1-propanol, or an overall lower amount of volatiles. Our data support the hypothesis that at certain concentrations, some VOCs emitted by indoor molds are toxigenic.},
}
@article {pmid27743236,
year = {2016},
author = {Souidenne, D and Florent, I and Dellinger, M and Romdhane, MS and Grellier, P and Furuya, H},
title = {Redescription of Dicyemennea eledones (Wagener, 1857) (Phylum Dicyemida) from Eledone cirrhosa (Lamarck, 1798) (Mollusca: Cephalopoda: Octopoda).},
journal = {Systematic parasitology},
volume = {93},
number = {9},
pages = {905-915},
pmid = {27743236},
issn = {1573-5192},
mesh = {Animals ; DNA Barcoding, Taxonomic ; France ; Genetic Variation ; Invertebrates/anatomy &amp; histology/*classification/genetics ; Octopodiformes/*parasitology ; RNA, Ribosomal, 18S/genetics ; Species Specificity ; Tunisia ; },
abstract = {Dicyemids are common parasites found in the kidneys of many cephalopods. Species identification previously relied on old species descriptions containing considerable confusions, casting doubt on taxonomy and identification. Detailed morphological description and genotyping of all developmental stages are required for an exact taxonomy. To this end, we undertook the redescription of the dicyemid Dicyemennea eledones (Wagener, 1857), infecting the cephalopod Eledone cirrhosa (Lamarck). Samples were collected off Concarneau in the Bay of Biscay, France, and off La Goulette in the Gulf of Tunis, Tunisia. Dicyemennea eledones is a large species, with adults reaching c.7,000 μm in length. The vermiform stages are characterised by having 23 peripheral cells, a conical calotte and an axial cell that extends to the base of the propolar cells. An anterior abortive axial cell is present in vermiform embryos. Infusoriform embryos consist of 37 cells; a single nucleus is present in each urn cell and the refringent bodies, which were not always seen, are possibly liquid. For the first time, an 18S rDNA sequence is generated for D. eledones, illustrating genetic differences with the other dicyemid 18S rDNA sequences available in databases. This sequence can now be used for D. eledones barcoding, making the identification of the species easier and more reliable.},
}
@article {pmid27742095,
year = {2016},
author = {Leavitt, SD and Esslinger, TL and Divakar, PK and Crespo, A and Lumbsch, HT},
title = {Hidden diversity before our eyes: Delimiting and describing cryptic lichen-forming fungal species in camouflage lichens (Parmeliaceae, Ascomycota).},
journal = {Fungal biology},
volume = {120},
number = {11},
pages = {1374-1391},
doi = {10.1016/j.funbio.2016.06.001},
pmid = {27742095},
issn = {1878-6146},
mesh = {Ascomycota/*classification/*genetics/growth &amp; development/isolation &amp; purification ; Base Sequence ; DNA, Fungal/genetics ; *Genetic Variation ; Lichens/*microbiology ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Molecular data provide unprecedented insight into diversity of lichenized fungi, although morphologically cryptic species-level lineages circumscribed from sequence data often remain undescribed even in well-studies groups. Using diagnostic characters from DNA sequence data and support from the multispecies coalescent model, we formally describe a total of eleven new species and resurrect two others in the hyperdiverse lichen-forming fungal family Parmeliaceae. These include: four in the genus Melanelixia - M. ahtii sp. nov., M. epilosa comb. nov., M. hawksworthii sp. nov., and M. robertsoniorum sp. nov.; six in Melanohalea - M. austroamericana sp. nov., M. beringiana sp. nov., M. clari sp. nov., M. columbiana sp. nov., M. davidii sp. nov., and M. tahltan sp. nov.; and three species in Montanelia - M. occultipanniformis sp. nov., M. saximontana comb. nov., and M. secwepemc sp. nov. Morphological, ecological and geographical features were revised to corroborate species descriptions. These species can consistently be distinguished by differences in nucleotide position characters in the fungal barcoding marker (ITS) and high speciation probabilities. This study helps close the "taxonomic gap" between molecular species delimitation studies and formal taxonomy by incorporating statistical evaluation of lineage independence, diagnostic differences in DNA data, and additional consideration of differences in morphology and species distributions.},
}
@article {pmid27739429,
year = {2016},
author = {Vickovic, S and Ståhl, PL and Salmén, F and Giatrellis, S and Westholm, JO and Mollbrink, A and Navarro, JF and Custodio, J and Bienko, M and Sutton, LA and Rosenquist, R and Frisén, J and Lundeberg, J},
title = {Massive and parallel expression profiling using microarrayed single-cell sequencing.},
journal = {Nature communications},
volume = {7},
number = {},
pages = {13182},
pmid = {27739429},
issn = {2041-1723},
mesh = {Animals ; Biotechnology/*methods ; Cells, Cultured ; Flow Cytometry ; Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Leukemia, Lymphocytic, Chronic, B-Cell/genetics/pathology ; MCF-7 Cells ; Mice ; NIH 3T3 Cells ; Single-Cell Analysis/*methods ; },
abstract = {Single-cell transcriptome analysis overcomes problems inherently associated with averaging gene expression measurements in bulk analysis. However, single-cell analysis is currently challenging in terms of cost, throughput and robustness. Here, we present a method enabling massive microarray-based barcoding of expression patterns in single cells, termed MASC-seq. This technology enables both imaging and high-throughput single-cell analysis, characterizing thousands of single-cell transcriptomes per day at a low cost (0.13 USD/cell), which is two orders of magnitude less than commercially available systems. Our novel approach provides data in a rapid and simple way. Therefore, MASC-seq has the potential to accelerate the study of subtle clonal dynamics and help provide critical insights into disease development and other biological processes.},
}
@article {pmid27739061,
year = {2016},
author = {Oliveira, LM and Knebelsberger, T and Landi, M and Soares, P and Raupach, MJ and Costa, FO},
title = {Assembling and auditing a comprehensive DNA barcode reference library for European marine fishes.},
journal = {Journal of fish biology},
volume = {89},
number = {6},
pages = {2741-2754},
doi = {10.1111/jfb.13169},
pmid = {27739061},
issn = {1095-8649},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Europe ; Fishes/*genetics ; *Gene Library ; Molecular Sequence Annotation ; },
abstract = {A large-scale comprehensive reference library of DNA barcodes for European marine fishes was assembled, allowing the evaluation of taxonomic uncertainties and species genetic diversity that were otherwise hidden in geographically restricted studies. A total of 4118 DNA barcodes were assigned to 358 species generating 366 Barcode Index Numbers (BIN). Initial examination revealed as much as 141 BIN discordances (more than one species in each BIN). After implementing an auditing and five-grade (A-E) annotation protocol, the number of discordant species BINs was reduced to 44 (13% grade E), while concordant species BINs amounted to 271 (78% grades A and B) and 14 other had insufficient data (grade D). Fifteen species displayed comparatively high intraspecific divergences ranging from 2·6 to 18·5% (grade C), which is biologically paramount information to be considered in fish species monitoring and stock assessment. On balance, this compilation contributed to the detection of 59 European fish species probably in need of taxonomic clarification or re-evaluation. The generalized implementation of an auditing and annotation protocol for reference libraries of DNA barcodes is recommended.},
}
@article {pmid27736878,
year = {2016},
author = {Yang, Z and Landry, JF and Hebert, PD},
title = {A DNA Barcode Library for North American Pyraustinae (Lepidoptera: Pyraloidea: Crambidae).},
journal = {PloS one},
volume = {11},
number = {10},
pages = {e0161449},
pmid = {27736878},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Gene Library ; Genetic Variation ; Lepidoptera/classification/*genetics ; North America ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Although members of the crambid subfamily Pyraustinae are frequently important crop pests, their identification is often difficult because many species lack conspicuous diagnostic morphological characters. DNA barcoding employs sequence diversity in a short standardized gene region to facilitate specimen identifications and species discovery. This study provides a DNA barcode reference library for North American pyraustines based upon the analysis of 1589 sequences recovered from 137 nominal species, 87% of the fauna. Data from 125 species were barcode compliant (>500bp, <1% n), and 99 of these taxa formed a distinct cluster that was assigned to a single BIN. The other 26 species were assigned to 56 BINs, reflecting frequent cases of deep intraspecific sequence divergence and a few instances of barcode sharing, creating a total of 155 BINs. Two systems for OTU designation, ABGD and BIN, were examined to check the correspondence between current taxonomy and sequence clusters. The BIN system performed better than ABGD in delimiting closely related species, while OTU counts with ABGD were influenced by the value employed for relative gap width. Different species with low or no interspecific divergence may represent cases of unrecognized synonymy, whereas those with high intraspecific divergence require further taxonomic scrutiny as they may involve cryptic diversity. The barcode library developed in this study will also help to advance understanding of relationships among species of Pyraustinae.},
}
@article {pmid27734964,
year = {2016},
author = {Pentinsaari, M and Salmela, H and Mutanen, M and Roslin, T},
title = {Molecular evolution of a widely-adopted taxonomic marker (COI) across the animal tree of life.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {35275},
pmid = {27734964},
issn = {2045-2322},
mesh = {Animals ; DNA Barcoding, Taxonomic ; *Evolution, Molecular ; *Genetic Markers ; },
abstract = {DNA barcodes are widely used for identification and discovery of species. While such use draws on information at the DNA level, the current amassment of ca. 4.7 million COI barcodes also offers a unique resource for exploring functional constraints on DNA evolution. Here, we explore amino acid variation in a crosscut of the entire animal kingdom. Patterns of DNA variation were linked to functional constraints at the level of the amino acid sequence in functionally important parts of the enzyme. Six amino acid sites show variation with possible effects on enzyme function. Overall, patterns of amino acid variation suggest convergent or parallel evolution at the protein level connected to the transition into a parasitic life style. Denser sampling of two diverse insect taxa revealed that the beetles (Coleoptera) show more amino acid variation than the butterflies and moths (Lepidoptera), indicating fundamental difference in patterns of molecular evolution in COI. Several amino acid sites were found to be under notably strong purifying selection in Lepidoptera as compared to Coleoptera. Overall, these findings demonstrate the utility of the global DNA barcode library to extend far beyond identification and taxonomy, and will hopefully be followed by a multitude of work.},
}
@article {pmid27734501,
year = {2016},
author = {Darienko, T and Gustavs, L and Pröschold, T},
title = {Species concept and nomenclatural changes within the genera Elliptochloris and Pseudochlorella (Trebouxiophyceae) based on an integrative approach.},
journal = {Journal of phycology},
volume = {52},
number = {6},
pages = {1125-1145},
doi = {10.1111/jpy.12481},
pmid = {27734501},
issn = {1529-8817},
mesh = {Amino Acid Sequence ; Base Sequence ; Chlorophyta/*classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Algal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Phylogeny ; Sequence Alignment ; Species Specificity ; },
abstract = {The genera Elliptochloris and Pseudochlorella were erected for Chlorella-like green algae producing two types of autospores and cell packages, respectively. Both genera are widely distributed in different soil habitats, either as free living or as photobionts of lichens. The species of these genera are often difficult to identify because of the high phenotypic plasticity and occasional lack of characteristic features. The taxonomic and nomenclatural status of these species, therefore, remains unclear. In this study, 34 strains were investigated using an integrative approach. Phylogenetic analyses demonstrated that the isolates belong to two independent lineages of the Trebouxiophyceae (Elliptochloris and Prasiola clades) and confirmed that the genera are not closely related. The comparison of morphology, molecular phylogeny, and analyses of secondary structures of SSU and ITS rDNA sequences revealed that all of the strains belong to three genera: Elliptochloris, Pseudochlorella, and Edaphochlorella. As a consequence of the taxonomic revisions, we propose two new combinations (Elliptochloris antarctica and Pseudochlorella signiensis) and validate Elliptochloris reniformis, which is invalidly described according to the International Code for Nomenclature (ICN), by designating a holotype. To reflect the high phenotypic plasticity of P. signiensis, two new varieties were described: P. signiensis var. magna and P. signiensis var. communis. Chlorella mirabilis was not closely related to any of these genera and was, therefore, transferred to the new genus Edaphochlorella. All of the taxonomic changes were highly supported by all phylogenetic analyses and were confirmed by the ITS-2 Barcodes using the ITS-2/CBC approach.},
}
@article {pmid27728993,
year = {2018},
author = {Jaffarali, HA and Akram, S and Arshan, KM},
title = {Identification of four Indian ascidians based on COI gene sequences.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {1},
pages = {14-18},
doi = {10.1080/24701394.2016.1233531},
pmid = {27728993},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; Electron Transport Complex IV/genetics ; *Genes, Mitochondrial ; Genome, Mitochondrial ; *Phylogeny ; Urochordata/*classification/genetics ; },
abstract = {DNA barcoding involving the sequencing of a short mitochondrial DNA segment, cytochrome c oxidase subunit 1 (COI) gene, is a specialized technique for the identification of species even at the early embryonic and larval stages, which is quite difficult in morphology-based taxonomy. Ascidians are sessile invertebrate chordates possessing numerous biochemical as well as pharmacological activities. In this study, a total of 36 ascidian samples belonging to the family Didemnidae were sequenced for a 650 bp region of the mitochondrial COI gene. All the species were represented by multiple specimens. The barcode sequences showed no stop-codons and indels in the alignments. The aligned sequences were submitted in Barcode submission tool, NCBI, and the accession numbers were obtained. The minimum intraspecific distance was found to be 0.00% and the maximum was 2.23%. Mean Kimura 2-parameter (K2P) distances within-species, genus, and family were 0.88, 5.98, and 20.03%, respectively. The mean interspecific distance is more than the mean intraspecific divergence, which indicates efficiency of DNA barcoding for identification of ascidians.},
}
@article {pmid27718207,
year = {2017},
author = {Wiley, SR and Raman, VS},
title = {Molecular Methods and Bioinformatic Tools for Adjuvant Characterization by High-Throughput Sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1494},
number = {},
pages = {353-368},
doi = {10.1007/978-1-4939-6445-1_26},
pmid = {27718207},
issn = {1940-6029},
mesh = {Adjuvants, Immunologic/*pharmacology ; Animals ; B-Lymphocytes/*immunology ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Immunoglobulin Heavy Chains/genetics/immunology ; *Immunoglobulin Light Chains/genetics/immunology ; Mice ; Vaccines/*pharmacology ; },
abstract = {Adjuvants in vaccine formulations are designed to enhance immune responses against a target antigen or pathogen. The ability of these vaccines to induce activation and differentiation of mature naïve B cells to produce pathogen-specific antibodies (immunoglobulins; Ig) helps guarantee long-lived humoral immunity. This process involves clonal expansion of antigen-specific B cells, genomic rearrangement of Ig heavy (IgH) and light (IgL) loci, somatic hypermutation (SHM), and clonal selection for affinity-matured antibody, resulting in a vast but directed repertoire of B cells expressing highly specific antibody proteins. High-throughput sequencing of the IgH and IgL complementary determining regions (CDRs) derived from various B cell populations provides an unprecedented way to observe dynamic responses of the humoral immune repertoire in response to vaccination. However, applying high-throughput sequencing (HTS) methodologies to multi-armed in vivo experiments requires careful coordination of sample preparation with downstream bioinformatics, particularly with regard to issues of quantitation, sequence fidelity, bar-coding, and multiplexing strategies. Here, we overview strategies of high-throughput sequencing and analysis of the adaptive immune complex loci applied to multi-armed, multiplexed experiments.},
}
@article {pmid27718041,
year = {2016},
author = {Adebowale, A and Lamb, J and Nicholas, A and Naidoo, Y},
title = {ITS2 secondary structure for species circumscription: case study in southern African Strychnos L. (Loganiaceae).},
journal = {Genetica},
volume = {144},
number = {6},
pages = {639-650},
pmid = {27718041},
issn = {1573-6857},
mesh = {Base Sequence ; DNA, Intergenic/*genetics ; Evolution, Molecular ; Phylogeny ; Strychnos/*classification/*genetics ; },
abstract = {Recently developed computational tools in ITS2 sequence-structure phylogenetics are improving tree robustness by exploitation of the added information content of the secondary structure. Despite this strength, however, their adoption for species-level clarifications in angiosperms has been slow. We investigate the utility of combining ITS2 sequence and secondary structure to separate species of southern African Strychnos, and assess correlation between compensatory base changes (CBCs) and currently recognised species boundaries. Combined phylogenetic analysis of sequence and secondary structure datasets performed better, in terms of robustness and species resolution, than analysis involving primary sequences only, achieving 100 and 88.2 % taxa discriminations respectively. Further, the Strychnos madagascariensis complex is well-resolved by sequence-structure phylogenetic analysis. The 17 Strychnos species corresponded to 14 ITS2 CBC clades. Four of the five taxa in section Densiflorae belong to a single CBC clade, whose members tend to form natural hybrids. Our finding supports the application of ITS2 as a complementary barcoding marker for species identification. It also highlights the potential of comparative studies of ITS2 CBC features among prospective parental pairs in breeding experiments as a rapid proxy for cross compatibility assessment. This could save valuable time in crop improvement. Patterns of CBC evolution and species boundaries in Strychnos suggests a positive correlation. We conclude that the CBC pattern coupled with observed ITS2 sequence paraphyly in section Densiflorae points to a speciation work-in-progress.},
}
@article {pmid27717395,
year = {2016},
author = {Kasper-Pakosz, R and Pietras, M and Łuczaj, &#x141;},
title = {Wild and native plants and mushrooms sold in the open-air markets of south-eastern Poland.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {12},
number = {1},
pages = {45},
pmid = {27717395},
issn = {1746-4269},
mesh = {*Agaricales ; DNA Barcoding, Taxonomic ; *Ethnobotany ; Plants, Edible ; Plants, Medicinal ; Poland ; },
abstract = {BACKGROUND: The study of plants and fungi sold in open-air markets is an important part of ethnobotanical enquiry. Only few such studies were carried out in Europe.<br><br>METHODS: Four of the largest open-air markets of south-eastern Poland were visited regularly, and the plants sold in them were recorded between 2013 and 2015. The aim of the study was to record native and/or wild species sold in the markets. All the plants sold in the markets were photographed regularly. In each market, 25 sellers were interviewed. Voucher specimens were collected and fungi were identified using DNA barcoding.<br><br>RESULTS: Altogether, 468 species of plants were recorded, 117 of them native to south-eastern Poland - 19 only collected from the wild and 11 both wild and cultivated. Seventeen of the species are under legal protection. Most protected plants were sold from cultivation, although proper authorization procedures had not been performed. Thirty-two species of fungi were sold (including two cultivated species), all of them for culinary purposes. Two species (Lactarius quieticolor, Leccinum schistophilum) are new to the mycobiota of Poland. Ornamental plants constituted a large section of the market, and they dominated the group of native species. Food plants dominated among wild-collected plants and were sold mainly as fruits for jams, juices and alcoholic drinks, or as culinary herbs. Very few medicinal or green vegetable plants were sold. An interesting feature of the markets was the sale of Ledum palustre as an insect repellent.<br><br>CONCLUSIONS: Finding two species of fungi which are new to Poland highlights the importance of DNA barcoding in ethnomycological studies. Most items in the markets are ornamental plants, or edible fruits and mushrooms. Very few medicinal plants and green vegetables are sold, which differentiates the markets from southern European ones. Such a pattern is probably the model for most central European markets.},
}
@article {pmid27717304,
year = {2016},
author = {Girardot, C and Scholtalbers, J and Sauer, S and Su, SY and Furlong, EE},
title = {Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers.},
journal = {BMC bioinformatics},
volume = {17},
number = {1},
pages = {419},
pmid = {27717304},
issn = {1471-2105},
mesh = {Electronic Data Processing/*methods ; *Gene Library ; Genomics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: The yield obtained from next generation sequencers has increased almost exponentially in recent years, making sample multiplexing common practice. While barcodes (known sequences of fixed length) primarily encode the sample identity of sequenced DNA fragments, barcodes made of random sequences (Unique Molecular Identifier or UMIs) are often used to distinguish between PCR duplicates and transcript abundance in, for example, single-cell RNA sequencing (scRNA-seq). In paired-end sequencing, different barcodes can be inserted at each fragment end to either increase the number of multiplexed samples in the library or to use one of the barcodes as UMI. Alternatively, UMIs can be combined with the sample barcodes into composite barcodes, or with standard Illumina® indexing. Subsequent analysis must take read duplicates and sample identity into account, by identifying UMIs.<br><br>RESULTS: Existing tools do not support these complex barcoding configurations and custom code development is frequently required. Here, we present Je, a suite of tools that accommodates complex barcoding strategies, extracts UMIs and filters read duplicates taking UMIs into account. Using Je on publicly available scRNA-seq and iCLIP data containing UMIs, the number of unique reads increased by up to 36&#xa0;%, compared to when UMIs are ignored.<br><br>CONCLUSIONS: Je is implemented in JAVA and uses the Picard API. Code, executables and documentation are freely available at http://gbcs.embl.de/Je . Je can also be easily installed in Galaxy through the Galaxy toolshed.},
}
@article {pmid27716950,
year = {2017},
author = {Cross, H and Sønstebø, JH and Nagy, NE and Timmermann, V and Solheim, H and Børja, I and Kauserud, H and Carlsen, T and Rzepka, B and Wasak, K and Vivian-Smith, A and Hietala, AM},
title = {Fungal diversity and seasonal succession in ash leaves infected by the invasive ascomycete Hymenoscyphus fraxineus.},
journal = {The New phytologist},
volume = {213},
number = {3},
pages = {1405-1417},
pmid = {27716950},
issn = {1469-8137},
mesh = {Ascomycota/classification/*physiology ; *Biodiversity ; DNA, Intergenic ; Fraxinus/*microbiology ; *Introduced Species ; Plant Leaves/*microbiology ; Principal Component Analysis ; *Seasons ; },
abstract = {High biodiversity is regarded as a barrier against biological invasions. We hypothesized that the invasion success of the pathogenic ascomycete Hymenoscyphus fraxineus threatening common ash in Europe relates to differences in dispersal and colonization success between the invader and the diverse native competitors. Ash leaf mycobiome was monitored by high-throughput sequencing of the fungal internal transcribed spacer region (ITS) and quantitative PCR profiling of H. fraxineus DNA. Initiation of ascospore production by H. fraxineus after overwintering was followed by pathogen accumulation in asymptomatic leaves. The induction of necrotic leaf lesions coincided with escalation of H. fraxineus DNA levels and changes in proportion of biotrophs, followed by an increase of ubiquitous endophytes with pathogenic potential. H. fraxineus uses high propagule pressure to establish in leaves as quiescent thalli that switch to pathogenic mode once these thalli reach a certain threshold - the massive feedback from the saprophytic phase enables this fungus to challenge host defenses and the resident competitors in mid-season when their density in host tissues is still low. Despite the general correspondence between the ITS-1 and ITS-2 datasets, marker biases were observed, which suggests that multiple barcodes provide better overall representation of mycobiomes.},
}
@article {pmid27715419,
year = {2016},
author = {Tomioka, S and Kondoh, T and Sato-Okoshi, W and Ito, K and Kakui, K and Kajihara, H},
title = {Cosmopolitan or Cryptic Species? A Case Study of Capitella teleta (Annelida: Capitellidae).},
journal = {Zoological science},
volume = {33},
number = {5},
pages = {545-554},
doi = {10.2108/zs160059},
pmid = {27715419},
issn = {0289-0003},
mesh = {Animals ; Annelida/*genetics/ultrastructure ; California ; DNA Barcoding, Taxonomic ; Databases, Factual ; Electron Transport Complex IV/genetics ; Gene Expression Regulation, Enzymologic ; Introduced Species ; Japan ; Massachusetts ; Phylogeny ; Phylogeography ; Species Specificity ; },
abstract = {Capitella teleta Blake et al., 2009 is an opportunistic capitellid originally described from Massachusetts (USA), but also reported from the Mediterranean, NW Atlantic, and North Pacific, including Japan. This putatively wide distribution had not been tested with DNA sequence data; intraspecific variation in morphological characters diagnostic for the species had not been assessed with specimens from non-type localities, and the species status of the Japanese population(s) was uncertain. We examined the morphology and mitochondrial COI (cytochrome c oxidase subunit I) gene sequences of Capitella specimens from two localities (Ainan and Gamo) in Japan. Specimens from Ainan and Gamo differed from C. teleta from Massachusetts in methyl-green staining pattern, shape of the genital spines, and shape of the capillary chaetae; we concluded that these characters vary intraspecifically. Species delimitation analyses of COI sequences suggested that worms from Ainan and Massachusetts represent C. teleta; these populations share a COI haplotype. The specimens from Gamo may represent a distinct species and comprise a sister group to C. teleta s. str.; we refer to the Gamo population as Capitella aff. teleta. The average Kimura 2-parameter (K2P) distance between C. teleta s. str. and C. aff. teleta was 3.7%. The COI data indicate that C. teleta actually occurs in both the NW Atlantic and NW Pacific. Given the short planktonic larval duration of C. teleta, this broad distribution may have resulted from anthropogenic dispersal.},
}
@article {pmid27713564,
year = {2016},
author = {Wang, X and Liu, Y and Wang, L and Han, J and Chen, S},
title = {A Nucleotide Signature for the Identification of Angelicae Sinensis Radix (Danggui) and Its Products.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {34940},
pmid = {27713564},
issn = {2045-2322},
mesh = {Angelica sinensis/*chemistry/*genetics ; Base Sequence ; Computer Systems ; Counterfeit Drugs ; DNA Barcoding, Taxonomic ; DNA Primers/genetics ; DNA, Plant/*genetics ; Drug Contamination ; Drugs, Chinese Herbal/*chemistry ; Humans ; Nonprescription Drugs/chemistry ; Nucleotide Motifs ; },
abstract = {It is very difficult to identify Angelicae sinensis radix (Danggui) when it is processed into Chinese patent medicines. The proposed internal transcribed spacer 2 (ITS2) is not sufficient to resolve heavily processed materials. Therefore, a short barcode for the identification of processed materials is urgently needed. In this study, 265 samples of Angelicae sinensis radix and adulterants were collected. The ITS2 region was sequenced, and based on one single nucleotide polymorphism(SNP) site unique to Angelica sinensis, a nucleotide signature consisting of 37-bp (5'-aatccgcgtc atcttagtga gctcaaggac ccttagg-3') was developed. It is highly conserved and specific within Angelica sinensis while divergent among other species. Then, we designed primers (DG01F/DG01R) to amplify the nucleotide signature region from processed materials. 15 samples procured online were analysed. By seeking the signature, we found that 7 of them were counterfeits. 28 batches of Chinese patent medicines containing Danggui were amplified. 19 of them were found to contain the signature, and adulterants such as Ligusticum sinense, Notopterygium incisum, Angelica decursiva and Angelica gigas were detected in other batches. Thus, this nucleotide signature, with only 37-bp, will broaden the application of DNA barcoding to identify the components in decoctions, Chinese patent medicines and other products with degraded DNA.},
}
@article {pmid27710790,
year = {2016},
author = {Turrero García, M and Mazzola, E and Harwell, CC},
title = {Lineage Relationships Do Not Drive MGE/PoA-Derived Interneuron Clustering in the Brain.},
journal = {Neuron},
volume = {92},
number = {1},
pages = {52-58},
pmid = {27710790},
issn = {1097-4199},
support = {K01 NS089720/NS/NINDS NIH HHS/United States ; },
mesh = {Cluster Analysis ; *Interneurons ; Preoptic Area/*physiology ; Prosencephalon ; },
abstract = {Neocortical excitatory and inhibitory neurons derive from distinct progenitor domains during embryonic development and migrate to their final positions, where they assemble into functional circuits. This process appears to be influenced by lineage relationships among locally born excitatory neurons, raising the intriguing possibility that this might be true for cortical interneurons. Two recent articles by the Fishell laboratory and our own used retrovirus-encoded DNA barcodes as unambiguous lineage-tracing tools to address this question, finding that clonally related inhibitory interneurons dispersed widely across the forebrain (Harwell et al., 2015; Mayer et al., 2015). This Matters Arising Response addresses the Sultan et al. (2016) Matters Arising paper, published concurrently in Neuron, where the authors reanalyze the datasets from both studies and propose a new interpretation, whereby clonally related interneurons would be considered clustered according to specific spatial constraints. After studying the report from Sultan et al. (2016) and carefully revisiting previously published studies, we find no evidence of lineage-dependent MGE/PoA-derived interneuron clustering in the forebrain.},
}
@article {pmid27706726,
year = {2016},
author = {Miz, RB and Tacuatiá, LO and Cidade, FW and de Souza, AP and Bered, F and Eggers, L and de Souza-Chies, TT},
title = {Isolation and characterization of microsatellite loci in Sisyrinchium (Iridaceae) and cross amplification in other genera.},
journal = {Genetics and molecular research : GMR},
volume = {15},
number = {3},
pages = {},
doi = {10.4238/gmr.15038474},
pmid = {27706726},
issn = {1676-5680},
mesh = {Iridaceae/*genetics ; Microsatellite Repeats/*genetics ; *Phylogeny ; Polymorphism, Genetic ; Species Specificity ; },
abstract = {Recent phylogenetic studies on Sisyrinchium strongly suggest that species classified in section Hydastylus and section Viperella belong to a single group of plants in recent adaptive radiation (Clade IV). These species neither present clear morphological differentiation among them nor show clear identification using DNA barcode markers. Thus, the main goal of this study was to develop a set of polymorphic microsatellite markers compatible for representative species of both sections to ensure variability that could be revealed by SSR markers. Therefore, microsatellite primers were isolated and characterized for Sisyrinchium palmifolium and S. marchioides. In addition, transferability of the developed primers was tested in Iridoideae, primarily in closely related species of Sisyrinchium. Sixteen microsatellite loci were developed from enriched genomic libraries, of which ten were polymorphic. GST values indicated higher differentiation among subpopulations of S. palmifolium than those from S. marchioides. Major transferability was obtained using primers isolated from S. marchioides. All primers exhibited higher rates of cross-amplification for species belonging to Clade IV of Sisyrinchium, as well as to the genera Calydorea and Herbertia. These developed microsatellite markers can be used as an efficient tool for characterization of genetic variability in species belonging to Iridoideae, as well as for studies on population dynamics, genetic structure, and mating system in other Sisyrinchium species.},
}
@article {pmid27706636,
year = {2016},
author = {Nascimento, MH and Almeida, MS and Veira, MN and Limeira Filho, D and Lima, RC and Barros, MC and Fraga, EC},
title = {DNA barcoding reveals high levels of genetic diversity in the fishes of the Itapecuru Basin in Maranhão, Brazil.},
journal = {Genetics and molecular research : GMR},
volume = {15},
number = {3},
pages = {},
doi = {10.4238/gmr.15038476},
pmid = {27706636},
issn = {1676-5680},
mesh = {Animals ; Brazil ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Fish Proteins/*genetics ; Fishes/classification/*genetics ; Genetic Speciation ; Genetic Variation ; *Genome ; *Phylogeny ; Rivers ; },
abstract = {DNA barcoding is a useful complementary tool for use in traditional taxonomic studies due to its ability to detect cryptic species, and may be particularly efficient in the identification of fish species. The fish fauna of the Itapecuru River represents an important fishery resource in the Brazilian State of Maranhão, although it is currently suffering increasing degradation as a result of anthropogenic impacts. Therefore, DNA barcoding was used in the present study to identify fish species and establish a database of the rich freshwater fish fauna of Maranhão. A total of 440 specimens were analyzed, corresponding to 64 species belonging to 59 genera, 31 families, and 10 orders. Overall, 92.19% of these species could be identified by DNA barcoding, and were characterized by low levels (average 0.80%) of intra-specific divergence. However, five species (Anableps anableps, Gymnotus carapo, Sciades couma, Pseudauchenipterus nodosus, and Leporinus piau) presented values of mean genetic divergence above 3%, indicating the existence of cryptic diversity in these fishes. The DNA barcoding approach permitted the analysis of a large number of specimens and facilitated the discrimination and identification of closely related fish species in the Itapecuru Basin.},
}
@article {pmid27706576,
year = {2016},
author = {Huang, ZH and Li, MF and Qin, JW},
title = {DNA barcoding and phylogenetic relationships of Ardeidae (Aves: Ciconiiformes).},
journal = {Genetics and molecular research : GMR},
volume = {15},
number = {3},
pages = {},
doi = {10.4238/gmr.15038270},
pmid = {27706576},
issn = {1676-5680},
mesh = {Animals ; Birds/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Phylogeny ; },
abstract = {The avian family Ardeidae comprises long-legged freshwater and coastal birds. There has been considerable disagreement concerning the intrafamilial relationships of Ardeidae. Mitochondrial cytochrome c oxidase subunit I (COI) was used as a marker for the identification and phylogenetic analysis of avian species. In the present study, we analyzed the COI barcodes of 32 species from 17 genera belonging to the family Ardeidae. Each bird species possessed a barcode distinct from that of other bird species except for Egretta thula and E. garzetta, which shared one barcoding sequence. Kimura two-parameter distances were calculated between barcodes. The average genetic distance between species was 34-fold higher than the average genetic distance within species. Neighbor-joining and maximum likelihood methods were used to construct phylogenetic trees. Most species could be discriminated by their distinct clades in the phylogenetic tree. Both methods of phylogenetic reconstruction suggested that Zebrilus, Tigrisoma, and Cochlearius were an offshoot of the primitive herons. COI gene analysis suggested that the other herons could be divided into two clades: Botaurinae and Ardeinae. Our results support the Great Egret and Intermediate Egret being in separate genera, Casmerodius and Mesophoyx, respectively.},
}
@article {pmid27704526,
year = {2017},
author = {Mallott, EK and Garber, PA and Malhi, RS},
title = {Integrating feeding behavior, ecological data, and DNA barcoding to identify developmental differences in invertebrate foraging strategies in wild white-faced capuchins (Cebus capucinus).},
journal = {American journal of physical anthropology},
volume = {162},
number = {2},
pages = {241-254},
doi = {10.1002/ajpa.23113},
pmid = {27704526},
issn = {1096-8644},
mesh = {Animals ; Anthropology, Physical ; Cebus/*physiology ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/analysis/genetics/isolation &amp; purification ; *Ecology ; Feces/chemistry ; Feeding Behavior/*classification/*physiology ; Female ; Invertebrates/classification/*genetics ; Male ; },
abstract = {OBJECTIVES: Invertebrate foraging strategies in nonhuman primates often require complex extractive foraging or prey detection techniques. As these skills take time to master, juveniles may have reduced foraging efficiency or concentrate their foraging efforts on easier to acquire prey than adults.<br><br>MATERIALS AND METHODS: We use DNA barcoding, behavioral observations, and ecological data to assess age-based differences in invertebrate prey foraging strategies in a group of white-faced capuchins (Cebus capucinus) in northeastern Costa Rica. Invertebrate availability was monitored using canopy traps and sweep netting. Fecal samples were collected from adult female, adult male, and juvenile white-faced capuchins (n&#x2009;=&#x2009;225). COI mtDNA sequences were compared with known sequences in GenBank and the Barcode of Life Database.<br><br>RESULTS: Frequencies of Lepidoptera and Hymenoptera consumption were higher in juveniles than in adults. A significantly smaller proportion of juvenile fecal samples contained Gryllidae and Cercopidae sequences, compared with adults (0% and 4.2% vs. 4.6% and 12.5%), and a significantly larger proportion contained Tenthredinidae, Culicidae, and Crambidae (5.6%, 9.7%, and 5.6% vs. 1.3%, 0.7%, and 1.3%). Juveniles spent significantly more time feeding and foraging than adults, and focused their foraging efforts on prey that require different skills to capture or extract. Arthropod availability was not correlated with foraging efficiency, and the rate of consumption of specific orders of invertebrates was not correlated with the availability of those same taxa.<br><br>DISCUSSION: Our data support the hypothesis that juveniles are concentrating their foraging efforts on different prey than adults, potentially focusing their foraging efforts on more easily acquired types of prey.},
}
@article {pmid27701290,
year = {2016},
author = {Hiruta, SF and Kakui, K},
title = {Three new brackish-water thalassocypridine species (Crustacea: Ostracoda: Paracyprididae) from the Ryukyu Islands, southwestern Japan.},
journal = {Zootaxa},
volume = {4169},
number = {3},
pages = {515-539},
doi = {10.11646/zootaxa.4169.3.6},
pmid = {27701290},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Crustacea/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Ecosystem ; Female ; Islands ; Japan ; Male ; Mitochondria/genetics ; Organ Size ; Phylogeny ; },
abstract = {We describe three new species of brackish-water ostracods representing two genera in the ostracod tribe Thalassocypridini from mangrove forests in the Ryukyu Islands, subtropical southwestern Japan, and provide their barcoding sequences for the mitochondrial cytochrome c oxidase subunit I (COI) gene. Mangalocypria ryukyuensis sp. nov. was found on Okinawa Island. We also found a Mangalocypria population on Ishigaki Island that was morphologically identical to M. ryukyuensis on Okinawa, but an individual differed by 4.7% in COI sequence (K2P distance) from an individual from Okinawa. This is the first record for Japan of a species in Mangalocypria. Paracypria longiseta sp. nov., obtained from Okinawa Island, is similar to Pontoparta hartmanni. Paracypria plumosa sp. nov. from Ishigaki Island is similar to Pa. adnata described from Yakushima Island, Japan. The COI genetic distance between individuals of Pa. longiseta and Pa. plumosa was roughly as large as that between either of these species and individuals in the Mangalocypria populations. Our study underscores that genera in Thalassocypridini may not represent natural groups, and that this tribe needs taxonomic revision.},
}
@article {pmid27701286,
year = {2016},
author = {Erlacher, S and Erlacher, J},
title = {A systematic revision of the genus Gnophopsodos Wehrli, 1945, with description of two new species (Lepidoptera: Geometridae).},
journal = {Zootaxa},
volume = {4169},
number = {3},
pages = {435-456},
doi = {10.11646/zootaxa.4169.3.2},
pmid = {27701286},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Female ; Kyrgyzstan ; Lepidoptera/*anatomy &amp; histology/*classification/growth &amp; development ; Male ; Organ Size ; Russia ; Uzbekistan ; },
abstract = {In a comprehensive morphological study besides results of DNA barcoding the genus Gnophopsodos Wehrli, 1945 is taxonomically revised. The taxon comprises nine species. Diagnostic characters are depicted and a key to the species based on the morphology of male genitalia is provided. Males and females (if available) of each species and their genitalia are illustrated. The distribution of all species is described and figured on maps. Gnophopsodos hilmari spec. nov. from Uzbekistan and Kyrgyzstan, Gnophopsodos sabine spec. nov. and Gnophopsodos ravistriolaria pantherinus subspec. nov., both from the Russian part of the Altai Mountains, are described as new. Gnophopsodos puengeleri (Bohatsch, 1910) stat. rev. is re-established as a separate species. The following synonyms are recognized: Chelegnophos Wehrli, 1951 syn. nov. of Gnophopsodos Wehrli, 1945; Chelegnophos alaianus Viidalepp, 1988 syn. nov. of Gnophopsodos puengeleri (Bohatsch, 1910), Psodos altissimaria Oberthür, 1913 syn. nov. of Gnophopsodos gnophosaria (Oberthür, 1893), and Gnophos orbicularia Püngeler, 1904 syn. nov. of Gnophopsodos stemmataria (Eversmann, 1848) comb. nov. The latter is transferred from the genus Gnophos Treitschke, 1825 to the genus Gnophopsodos.},
}
@article {pmid27701253,
year = {2016},
author = {Grebennikov, VV},
title = {The genus Prothrombosternus (Coleoptera: Curculionidae: Molytinae) rediscovered: a male from Rubeho Mountains, Tanzania.},
journal = {Zootaxa},
volume = {4171},
number = {1},
pages = {170-174},
doi = {10.11646/zootaxa.4171.1.7},
pmid = {27701253},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Insect Proteins/genetics ; Male ; Phylogeny ; Sequence Analysis, DNA ; Tanzania ; Weevils/*anatomy &amp; histology/*classification/genetics/physiology ; },
abstract = {A male specimen of the monotypic weevil genus, Prothrombosternus Voss, 1965, so far known on the basis of only five syntypes from Mt. Meru and Mt. Hanang, Tanzania, is reported from the Rubeho Mountains, Tanzania. The lectotype of Prothrombosternus tarsalis Voss, 1965 is designated using a male from Mt. Meru. The Rubeho specimen shares the same external and genital morphological characters with the lectotype (both extensively illustrated) and, therefore, both are considered conspecific. The DNA barcode of the Rubeho specimen is publicly available at dx.doi.org/10.5883/DS-PROTHRO. All six known specimens of Prothrombosternus are flightless and were found by sifting leaf litter at elevations between 1833-2500 m in wet Afromontane forests. The genus is, therefore, thought to be restricted to this highly fragmented habitat threatened by human encroachment. Presence of the genus on both geologically old (Rubeho Mountains; >10Ma) and young (Mt. Meru and Mt. Hanang volcanoes, <2Ma) forested highlands suggests presently unknown means of dispersal. The phylogenetic position of the genus is unknown and its taxonomic placement in Cycloterini cannot be presently tested.},
}
@article {pmid27701235,
year = {2016},
author = {Pérez-Asso, AR and Núñez-Aguila, R and Genaro, JA},
title = {Morphology and COI barcodes reveal four new species in the lycieus group of Calisto (Lepidoptera, Nymphalidae, Satyrinae).},
journal = {Zootaxa},
volume = {4170},
number = {3},
pages = {401-450},
doi = {10.11646/zootaxa.4170.3.1},
pmid = {27701235},
issn = {1175-5334},
mesh = {Animals ; Butterflies/*anatomy &amp; histology/*classification/genetics ; DNA Barcoding, Taxonomic ; Dominican Republic ; Female ; Male ; Phylogeny ; Species Specificity ; },
abstract = {The predominantly Greater Antillean endemic genus Calisto Hübner, 1823 is highly diversified on several islands being more species rich on Hispaniola. We conducted expeditions during five years in the Dominican Republic resulting in new findings related with lyceius species group. Material belonging to this group was examined following the traditional morphological characters employed in genus taxonomy, and the COI barcode sequences obtained were analyzed through different approaches: Neighbor Joining clustering, ABGD, Maximum Likelihood (ML), and Bayesian Inference (BI). Analysis yielded 12 groups representing putative species: eight corresponding to previously named ones and four new species which are described in the present work: C. mariposa sp. nov., C. azua sp. nov., C. victori sp. nov., and C. samana sp. nov. The results also confirmed a single taxonomic entity within C. pulchella Lathy and the conspecific nature of C. franciscoi Gali and C. hendersoni. A dichotomic key for identification of species within the group is also given. Both phylogenetic reconstruction methods (ML and BI) employing molecular data achieved similar results with the relationships among the majority of taxa being supported by some ecological and morphological features. The exceptions were C. zangis Fabricius, C. raburni Gali, and C. pulchella, grouped together in a weakly supported clade. These species possess a highly differentiated adult and immature morphology which indicates an earlier divergence.},
}
@article {pmid27701182,
year = {2016},
author = {Freyhof, J and Abdullah, YS and Ararat, K and Ibrahim, H and Geiger, MF},
title = {Eidinemacheilus proudlovei, a new subterranean loach from Iraqi Kurdistan (Teleostei; Nemacheilidae).},
journal = {Zootaxa},
volume = {4173},
number = {3},
pages = {225-236},
doi = {10.11646/zootaxa.4173.3.2},
pmid = {27701182},
issn = {1175-5334},
mesh = {Animals ; Caves ; Cypriniformes/*anatomy &amp; histology/*classification/genetics ; DNA Barcoding, Taxonomic ; Iraq ; Species Specificity ; },
abstract = {Eidinemacheilus proudlovei, new species, is described from subterranean waters in the Little Zab River drainage in Iraqi Kurdistan. After the discovery of E. smithi in 1976, E. proudlovei is the second troglomorphic nemacheilid loach found in the Middle East and the second species placed in Eidinemacheilus. Eidinemacheilus proudlovei is distinguished from E. smithi by having 8+8 or 8+7 branched caudal-fin rays, no adipose keel on the caudal peduncle, enlarged jaws and a fully developed head canal system. It furthers differs substantially in its DNA barcode (>8% K2P distance) from all other nemacheilid loaches in the Middle East, Europe and Western India.},
}
@article {pmid27698441,
year = {2016},
author = {Wang, Y and Zhou, QS and Qiao, HJ and Zhang, AB and Yu, F and Wang, XB and Zhu, CD and Zhang, YZ},
title = {Formal nomenclature and description of cryptic species of the Encyrtus sasakii complex (Hymenoptera: Encyrtidae).},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {34372},
pmid = {27698441},
issn = {2045-2322},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Hymenoptera/*classification/*genetics ; RNA, Ribosomal, 28S/*genetics ; },
abstract = {With the recent development of molecular approaches to species delimitation, a growing number of cryptic species have been discovered in what had previously been thought to be single morpho-species. Molecular methods, such as DNA barcoding, have greatly enhanced our knowledge of taxonomy, but taxonomy remains incomplete and needs a formal species nomenclature and description to facilitate its use in other scientific fields. A previous study using DNA barcoding, geometric morphometrics and mating tests revealed at least two cryptic species in the Encyrtus sasakii complex. (Hymenoptera: Encyrtidae). To describe these two new species formally (Encyrtus eulecaniumiae sp. nov. and Encyrtus rhodococcusiae sp. nov.), a detailed morphometric study of Encyrtus spp. was performed in addition to the molecular analysis and evaluation of biological data. Morphometric analyses, a multivariate ratio analysis (MRA) and a geometric morphometric analysis (GMA) revealed a great number of differences between the species, but reliable characteristics were not observed for diagnosing the cryptic species. We thus diagnosed these three Encyrtus species on the basis of the characteristics that resulted from genetic markers (mitochondrial cytochrome c oxidase subunit I and nuclear 28S rRNA) and biological data. A formal nomenclature and description of cryptic species was provided on the basis of an integrated taxonomy.},
}
@article {pmid27696907,
year = {2016},
author = {Lee, PS and Gan, HM and Clements, GR and Wilson, JJ},
title = {Field calibration of blowfly-derived DNA against traditional methods for assessing mammal diversity in tropical forests.},
journal = {Genome},
volume = {59},
number = {11},
pages = {1008-1022},
doi = {10.1139/gen-2015-0193},
pmid = {27696907},
issn = {1480-3321},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Diptera/*classification/*genetics ; *Forests ; Geography ; Malaysia ; Mammals/*classification/*genetics ; *Tropical Climate ; },
abstract = {Mammal diversity assessments based on DNA derived from invertebrates have been suggested as alternatives to assessments based on traditional methods; however, no study has field-tested both approaches simultaneously. In Peninsular Malaysia, we calibrated the performance of mammal DNA derived from blowflies (Diptera: Calliphoridae) against traditional methods used to detect species. We first compared five methods (cage trapping, mist netting, hair trapping, scat collection, and blowfly-derived DNA) in a forest reserve with no recent reports of megafauna. Blowfly-derived DNA and mist netting detected the joint highest number of species (n = 6). Only one species was detected by multiple methods. Compared to the other methods, blowfly-derived DNA detected both volant and non-volant species. In another forest reserve, rich in megafauna, we calibrated blowfly-derived DNA against camera traps. Blowfly-derived DNA detected more species (n = 11) than camera traps (n = 9), with only one species detected by both methods. The rarefaction curve indicated that blowfly-derived DNA would continue to detect more species with greater sampling effort. With further calibration, blowfly-derived DNA may join the list of traditional field methods. Areas for further investigation include blowfly feeding and dispersal biology, primer biases, and the assembly of a comprehensive and taxonomically-consistent DNA barcode reference library.},
}
@article {pmid27692487,
year = {2016},
author = {Sanyal, O and Shinde, VL and Meena, RM and Damare, S and Shenoy, BD},
title = {The ITS-based phylogeny of fungi associated with tarballs.},
journal = {Marine pollution bulletin},
volume = {113},
number = {1-2},
pages = {277-281},
doi = {10.1016/j.marpolbul.2016.09.052},
pmid = {27692487},
issn = {1879-3363},
mesh = {Bathing Beaches/standards ; Biodegradation, Environmental ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer ; Humans ; India ; Petroleum/*microbiology ; Phylogeny ; Saccharomycetales/genetics/*isolation &amp; purification ; Sequence Analysis, DNA ; Tars/*chemistry ; *Water Pollutants, Chemical ; },
abstract = {Tarballs, the remnants of crude oil which change into semi-solid phase due to various weathering processes in the sea, are rich in hydrocarbons, including toxic and almost non-degradable hydrocarbons. Certain microorganisms such as fungi are known to utilize hydrocarbons present in tarballs as sole source of carbon for nutrition. Previous studies have reported 53 fungal taxa associated with tarballs. There is apparently no gene sequence-data available for the published taxa so as to verify the fungal identification using modern taxonomic tools. The objective of the present study is to isolate fungi from tarballs collected from Candolim beach in Goa, India and investigate their phylogenetic diversity based on 5.8S rRNA gene and the flanking internal transcribed spacer regions (ITS) sequence analysis. In the ITS-based NJ tree, eight tarball-associated fungal isolates clustered with 3 clades of Dothideomycetes and 2 clades of Saccharomycetes. To the best of our knowledge, this is the first study that has employed ITS-based phylogeny to characterize the fungal diversity associated with tarballs. Further studies are warranted to investigate the role of the tarball-associated fungi in degradation of recalcitrant hydrocarbons present in tarballs and the role of tarballs as carriers of human pathogenic fungi.},
}
@article {pmid27688026,
year = {2016},
author = {Shanmughanandhan, D and Ragupathy, S and Newmaster, SG and Mohanasundaram, S and Sathishkumar, R},
title = {Estimating Herbal Product Authentication and Adulteration in India Using a Vouchered, DNA-Based Biological Reference Material Library.},
journal = {Drug safety},
volume = {39},
number = {12},
pages = {1211-1227},
pmid = {27688026},
issn = {1179-1942},
mesh = {*DNA Barcoding, Taxonomic ; *Drug Contamination ; Humans ; India ; Phytotherapy/*standards ; Plants, Medicinal/*genetics ; Quality Control ; Reference Values ; },
abstract = {INTRODUCTION: India is considered the 'medicinal garden' of the world, with 8000 medicinal plants of which 960 are commercial species that are traded nationally and globally. Although scientific studies estimate herbal product adulteration as 42-66 % in North America, India does not have any published marketplace studies and subsequent estimates of adulteration in an industry facing considerable supply demands.<br><br>OBJECTIVES: The goal of this project is to provide an initial assessment of herbal product authentication and adulteration in the marketplace in India by (1) developing a biological reference material (BRM) herbal DNA library for Indian herbal species using DNA barcode regions (ITS2 and rbcL) in order to facilitate accurate species resolution when testing the herbal products; and (2) assessing herbal product identification using our BRM library; and (3) comparing the use of our BRM library to identify herbal products with that of GenBank.<br><br>METHODS: A BRM herbal DNA library consisting of 187 herbal species was prepared to authenticate the herbal products within India. Ninty-three herbal products representing ten different companies were procured from local stores located at Coimbatore, India. These samples were subjected to blind testing for authenticity using the DNA barcode regions rbcL and ITS2.<br><br>RESULTS: The results indicate that 40&#xa0;% of the products tested are authentic, and 60&#xa0;% of the products may be adulterated (i.e. contained species of plants not listed on the product labels). The adulterated samples included contamination (50&#xa0;%), substitution (10&#xa0;%) and fillers (6&#xa0;%). Our BRM library provided a 100&#xa0;% Basic Local Alignment Search Tool (BLAST) match for all species, whereas the GenBank match was 64&#xa0;%.<br><br>CONCLUSIONS: Our findings suggest that most Indian herbal medicinal products are essentially mixed with one or a few other herbs that could lessen the therapeutic activity of the main ingredients. We do not recommend the use of GenBank to identify herbal products because the use of this non-curated and/or vouchered database will result in inaccurate species identification. These DNA-based tools provide a scientific foundation for herbal pharmacovigilance to ensure the safety and efficacy of natural drugs. This study provides curated BRMs that will underpin innovations in molecular diagnostic biotechnology, which will soon provide more robust estimates of adulteration and commercial tools that will strengthen due diligence in quality assurance within the herbal industry.},
}
@article {pmid27686791,
year = {2016},
author = {Li, XF and Han, C and Zhong, CR and Xu, JQ and Huang, JR},
title = {Identification of Sphaeroma terebrans via morphology and the mitochondrial cytochrome c oxidase subunit I (COI) gene.},
journal = {Zoological research},
volume = {37},
number = {5},
pages = {307-312},
pmid = {27686791},
issn = {2095-8137},
mesh = {Animals ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Genetic Variation ; Haplotypes ; Isopoda/*anatomy &amp; histology/enzymology/*genetics ; Mitochondria/*enzymology ; Phylogeny ; },
abstract = {Sphaeroma terebrans, a wood-boring isopoda, is distributed worldwide in tropical and subtropical mangroves. The taxonomy of S. terebrans is usually based on morphological characteristics, with its molecular identification still poorly understood. The number of teeth on the uropodal exopod and the length of the propodus of the seventh pereopod are considered as the major morphological characteristics in S. terebrans, which can cause difficulty in regards to accurate identification. In this study, we identified S. terebrans via molecular and morphological data. Furthermore, the validity of the mitochondrial cytochrome c oxidase subunit I (COI) gene as a DNA barcode for the identification of genus Sphaeroma, including species S. terebrans, S. retrolaeve, and S. serratum, was examined. The mitochondrial COI gene sequences of all specimens were sequenced and analysed. The interspecific Kimura 2-parameter distances were higher than intraspecific distances and no intraspecific-interspecific distance overlaps were observed. In addition, genetic distance and nucleotide diversity (π) exhibited no differences within S. terebrans. Our results revealed that the mitochondrial COI gene can serve as a valid DNA barcode for the identification of S. terebrans. Furthermore, the number of teeth on the uropodal exopod and the length of the propodus of the seventh pereopod were found to be unreliable taxonomic characteristics for S. terebrans.},
}
@article {pmid27683367,
year = {2016},
author = {Tiusanen, M and Hebert, PD and Schmidt, NM and Roslin, T},
title = {One fly to rule them all-muscid flies are the key pollinators in the Arctic.},
journal = {Proceedings. Biological sciences},
volume = {283},
number = {1839},
pages = {},
pmid = {27683367},
issn = {1471-2954},
abstract = {Global change is causing drastic changes in the pollinator communities of the Arctic. While arctic flowers are visited by a wide range of insects, flies in family Muscidae have been proposed as a pollinator group of particular importance. To understand the functional outcome of current changes in pollinator community composition, we examined the role of muscids in the pollination of a key plant species, the mountain avens (Dryas). We monitored the seed set of Dryas across 15 sites at Zackenberg, northeast Greenland, and used sticky flower mimics and DNA barcoding to describe the flower-visiting community at each site. To evaluate the consequences of shifts in pollinator phenology under climate change, we compared the flower visitors between the early and the late season. Our approach revealed a diverse community of insects visiting Dryas, including two-thirds of all insect species known from the area. Even against this diverse background, the abundance of muscid flies emerged as a key predictor for seed set in Dryas, whereas overall insect abundance and species richness had little or no effect. With muscid flies as the main drivers of the pollinating function in the High Arctic, a recently observed decline in their abundances offers cause for concern.},
}
@article {pmid27681175,
year = {2016},
author = {Astrin, JJ and Höfer, H and Spelda, J and Holstein, J and Bayer, S and Hendrich, L and Huber, BA and Kielhorn, KH and Krammer, HJ and Lemke, M and Monje, JC and Morinière, J and Rulik, B and Petersen, M and Janssen, H and Muster, C},
title = {Towards a DNA Barcode Reference Database for Spiders and Harvestmen of Germany.},
journal = {PloS one},
volume = {11},
number = {9},
pages = {e0162624},
pmid = {27681175},
issn = {1932-6203},
abstract = {As part of the German Barcode of Life campaign, over 3500 arachnid specimens have been collected and analyzed: ca. 3300 Araneae and 200 Opiliones, belonging to almost 600 species (median: 4 individuals/species). This covers about 60% of the spider fauna and more than 70% of the harvestmen fauna recorded for Germany. The overwhelming majority of species could be readily identified through DNA barcoding: median distances between closest species lay around 9% in spiders and 13% in harvestmen, while in 95% of the cases, intraspecific distances were below 2.5% and 8% respectively, with intraspecific medians at 0.3% and 0.2%. However, almost 20 spider species, most notably in the family Lycosidae, could not be separated through DNA barcoding (although many of them present discrete morphological differences). Conspicuously high interspecific distances were found in even more cases, hinting at cryptic species in some instances. A new program is presented: DiStats calculates the statistics needed to meet DNA barcode release criteria. Furthermore, new generic COI primers useful for a wide range of taxa (also other than arachnids) are introduced.},
}
@article {pmid27678125,
year = {2017},
author = {Sjögren, P and Edwards, ME and Gielly, L and Langdon, CT and Croudace, IW and Merkel, MK and Fonville, T and Alsos, IG},
title = {Lake sedimentary DNA accurately records 20[th] Century introductions of exotic conifers in Scotland.},
journal = {The New phytologist},
volume = {213},
number = {2},
pages = {929-941},
pmid = {27678125},
issn = {1469-8137},
mesh = {DNA, Plant/*genetics ; Geography ; *Geologic Sediments ; *Introduced Species ; *Lakes ; Models, Theoretical ; Pollen/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Scotland ; Time Factors ; Tracheophyta/*genetics ; },
abstract = {Sedimentary DNA (sedDNA) has recently emerged as a new proxy for reconstructing past vegetation, but its taphonomy, source area and representation biases need better assessment. We investigated how sedDNA in recent sediments of two small Scottish lakes reflects a major vegetation change, using well-documented 20[th] Century plantations of exotic conifers as an experimental system. We used next-generation sequencing to barcode sedDNA retrieved from subrecent lake sediments. For comparison, pollen was analysed from the same samples. The sedDNA record contains 73 taxa (mainly genus or species), all but one of which are present in the study area. Pollen and sedDNA shared 35% of taxa, which partly reflects a difference in source area. More aquatic taxa were recorded in sedDNA, whereas taxa assumed to be of regional rather than local origin were recorded only as pollen. The chronology of the sediments and planting records are well aligned, and sedDNA of exotic conifers appears in high quantities with the establishment of plantations around the lakes. SedDNA recorded other changes in local vegetation that accompanied afforestation. There were no signs of DNA leaching in the sediments or DNA originating from pollen.},
}
@article {pmid27673501,
year = {2016},
author = {González-Vaquero, RA and Roig-Alsina, A and Packer, L},
title = {DNA barcoding as a useful tool in the systematic study of wild bees of the tribe Augochlorini (Hymenoptera: Halictidae).},
journal = {Genome},
volume = {59},
number = {10},
pages = {889-898},
doi = {10.1139/gen-2016-0006},
pmid = {27673501},
issn = {1480-3321},
mesh = {Animals ; Argentina ; Bees/*classification/*genetics ; Chile ; *DNA Barcoding, Taxonomic ; Female ; Genes, Insect ; Male ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Special care is needed in the delimitation and identification of halictid bee species, which are renowned for being morphologically monotonous. Corynura Spinola and Halictillus Moure (Halictidae: Augochlorini) contain species that are key elements in southern South American ecosystems. These bees are very difficult to identify due to close morphological similarity among species and high sexual dimorphism. We analyzed 170 barcode-compliant COI sequences from 19 species. DNA barcodes were useful to confirm gender associations and to detect two new cryptic species. Interspecific distances were significantly higher than those reported for other bees. Maximum intraspecific divergence was less than 1% in 14 species. Barcode index numbers (BINs) were useful to identify putative species that need further study. More than one BIN was assigned to five species. The name Corynura patagonica (Cockerell) probably refers to two cryptic species. The results suggest that Corynura and Halictillus species can be identified using DNA barcodes. The sequences of the species included in this study can be used as a reference to assess the identification of unknown specimens. This study provides additional support for the use of DNA barcodes in bee taxonomy and the identification of specimens, which is particularly relevant in insects of ecological importance such as pollinators.},
}
@article {pmid27673405,
year = {2016},
author = {Kunprom, C and Pramual, P},
title = {DNA barcode variability and host plant usage of fruit flies (Diptera: Tephritidae) in Thailand.},
journal = {Genome},
volume = {59},
number = {10},
pages = {792-804},
doi = {10.1139/gen-2015-0110},
pmid = {27673405},
issn = {1480-3321},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Genetic Variation ; Geography ; Host Specificity/*genetics ; Phylogeny ; Plants/parasitology ; Sequence Analysis, DNA ; Tephritidae/*classification/*genetics ; Thailand ; },
abstract = {The objectives of this study were to examine the genetic variation in fruit flies (Diptera: Tephritidae) in Thailand and to test the efficiency of the mitochondrial cytochrome c oxidase subunit I (COI) barcoding region for species-level identification. Twelve fruit fly species were collected from 24 host plant species of 13 families. The number of host plant species for each fruit fly species ranged between 1 and 11, with Bactrocera correcta found in the most diverse host plants. A total of 123 COI sequences were obtained from these fruit fly species. Sequences from the NCBI database were also included, for a total of 17 species analyzed. DNA barcoding identification analysis based on the best close match method revealed a good performance, with 94.4% of specimens correctly identified. However, many specimens (3.6%) had ambiguous identification, mostly due to intra- and interspecific overlap between members of the B. dorsalis complex. A phylogenetic tree based on the mitochondrial barcode sequences indicated that all species, except for the members of the B. dorsalis complex, were monophyletic with strong support. Our work supports recent calls for synonymization of these species. Divergent lineages were observed within B. correcta and B. tuberculata, and this suggested that these species need further taxonomic reexamination.},
}
@article {pmid27672058,
year = {2016},
author = {McGugan, JR and Byrd, GD and Roland, AB and Caty, SN and Kabir, N and Tapia, EE and Trauger, SA and Coloma, LA and O'Connell, LA},
title = {Response to Heethoff, Norton, and Raspotnig: Ant and Mite Diversity Drives Toxin Variation in the Little Devil Poison Frog and Erratum.},
journal = {Journal of chemical ecology},
volume = {42},
number = {8},
pages = {845-848},
pmid = {27672058},
issn = {1573-1561},
abstract = {Our recent publication titled "Ant and Mite Diversity Drives Toxin Variation in the Little Devil Poison Frog" aimed to describe how variation in diet contributes to population differences in toxin profiles of poison frogs. Some poison frogs (Family Dendrobatidae) sequester alkaloid toxins from their arthropod diet, which is composed mainly of ants and mites. Our publication demonstrated that arthropods from the stomach contents of three different frog populations were diverse in both chemistry and species composition. To make progress towards understanding this trophic relationship, our main goal was to identify alkaloids that are found in either ants or mites. With the remaining samples that were not used for chemical analysis, we attempted to identify the arthropods using DNA barcoding of cytochrome oxidase 1 (CO1). The critique of Heethoff, Norton, and Raspotnig refers to the genetic analysis of a small number of mites. Here, we respond to the general argument of the critique as well as other minor issues detailed by Heethoff, Norton, and Raspotnig.},
}
@article {pmid27671940,
year = {2017},
author = {Kim, J and Kim, DU and Hoe, KL},
title = {Gene Deletion by Synthesis in Yeast.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1472},
number = {},
pages = {169-185},
doi = {10.1007/978-1-4939-6343-0_13},
pmid = {27671940},
issn = {1940-6029},
mesh = {Base Sequence ; *Gene Deletion ; Gene Targeting ; Genes, Fungal ; Mutagenesis, Insertional ; Oligonucleotides/genetics ; Schizosaccharomyces/*genetics ; Transformation, Genetic ; },
abstract = {Targeted gene deletion is a useful tool for understanding the function of a gene and its protein product. We have developed an efficient and robust gene deletion approach in yeast that employs oligonucleotide-based gene synthesis. This approach requires a deletion cassette composed of three modules: a central 1397-bp KanMX4 selection marker module and two 366-bp gene-specific flanking modules. The invariable KanMX4 module can be used in combination with different pairs of flanking modules targeting different genes. The two flanking modules consist of both sequences unique to each cassette (chromosomal homologous regions and barcodes) and those common to all deletion constructs (artificial linkers and restriction enzyme sites). Oligonucleotides for each module and junction regions are designed using the BatchBlock2Oligo program and are synthesized on a 96-well basis. The oligonucleotides are ligated into a single deletion cassette by ligase chain reaction, which is then amplified through two rounds of nested PCR to obtain sufficient quantities for yeast transformation. After removal of the artificial linkers, the deletion cassettes are transformed into wild-type diploid fission yeast SP286 cells. Verification of correct clone and gene deletion is achieved by performing check PCR and tetrad analysis. This method with proven effectiveness, as evidenced by a high success rate of gene deletion, can be potentially applicable to create systematic gene deletion libraries in a variety of yeast species.},
}
@article {pmid27668281,
year = {2016},
author = {Rodrigues, AD and Brandão, JH and Bitencourt, JA and Jucá-Chagas, R and Sampaio, I and Schneider, H and Affonso, PR},
title = {Molecular Identification and Traceability of Illegal Trading in Lignobrycon myersi (Teleostei: Characiformes), a Threatened Brazilian Fish Species, Using DNA Barcode.},
journal = {TheScientificWorldJournal},
volume = {2016},
number = {},
pages = {9382613},
pmid = {27668281},
issn = {1537-744X},
abstract = {Lignobrycon myersi is a threatened freshwater fish species and endemic of a few coastal rivers in northeastern Brazil. Even though the Brazilian laws prohibit the fisheries of threatened species, L. myersi is occasionally found in street markets, being highly appreciated by local population. In order to provide a reliable DNA barcode dataset for L. myersi, we compared mitochondrial sequences of cytochrome c oxidase subunit I (COI) from fresh, frozen, and salt-preserved specimens. Phylogenetically related species (Triportheus spp.) and other fish species (Astyanax fasciatus) commonly mixed with L. myersi in street markets were also included to test the efficiency of molecular identification. In spite of the differences in conservation processes and advanced deterioration of some commercial samples, high-quality COI sequences were obtained and effective in discriminating L. myersi specimens. In addition, while populations from Contas and Almada River basins seem to comprise a single evolutionary lineage, the specimens from Cachoeira River were genetically differentiated, indicating population structuring. Therefore, DNA barcoding has proved to be useful to trace the illegal trading of L. myersi and to manage threatened populations, which should focus on conservation of distinct genetic stocks and mitigation on human impacts along their range.},
}
@article {pmid27667958,
year = {2016},
author = {Thiel, R and Knebelsberger, T},
title = {How reliably can northeast Atlantic sand lances of the genera Ammodytes and Hyperoplus be distinguished? A comparative application of morphological and molecular methods.},
journal = {ZooKeys},
volume = {},
number = {617},
pages = {139-164},
pmid = {27667958},
issn = {1313-2989},
abstract = {Accurate stock assessments for each of the dominant species of sand lances in the northeast Atlantic Ocean and adjacent areas are not available due to the lack of a reliable identification procedure; therefore, appropriate measures of fisheries management or conservation of sand lances cannot be implemented. In this study, detailed morphological and molecular features are assessed to discriminate between four species of sand lances belonging to the genera Ammodytes and Hyperoplus. Morphological characters described by earlier authors as useful for identification of the genera are confirmed, and two additional distinguishing characters are added. A combination of the following morphological characters is recommended to distinguish between the genera Hyperoplus and Ammodytes: the protrusibility of the premaxillae, the presence of hooked ends of the prevomer, the number of dermal plicae, and the pectoral-fin length as a percentage of the standard length. The discriminant function analysis revealed that morphometric data are not very useful to distinguish the species of each of the two genera. The following meristic characters improve the separation of Hyperoplus lanceolatus from Hyperoplus immaculatus: the number of lower arch gill rakers, total number of gill rakers, numbers of caudal vertebrae and total vertebrae, and numbers of dorsal-fin and anal-fin rays. It is confirmed that Ammodytes tobianus differs from Ammodytes marinus by its belly scales that are organised in tight chevrons, scales which are present over the musculature at the base of the caudal fin, as well as by the lower numbers of dermal plicae, dorsal-fin rays, and total vertebrae. In contrast to the morphological data, mitochondrial COI sequences (DNA barcodes) failed to separate unambiguously the four investigated species. Ammodytes tobianus and Hyperoplus lanceolatus showed an overlap between intraspecific and interspecific K2P genetic distances and cannot be reliably distinguished using the common DNA barcoding approach. Ammodytes marinus and Hyperoplus immaculatus exhibited gaps between intraspecific and interspecific K2P distances of 2.73 and 3.34% respectively, indicating that their DNA barcodes can be used for species identification. As an alternative, short nuclear Rhodopsin sequences were analysed and one diagnostic character was found for each of the species Ammodytes marinus, Hyperoplus lanceolatus, and Hyperoplus immaculatus. Ammodytes tobianus can be characterised by the lack of species-specific mutations when compared to the other three species. In contrast to COI, the short nuclear sequences represent a useful alternative for rapid species identification whenever an examination of morphological characters is not available.},
}
@article {pmid27667932,
year = {2016},
author = {Chen, L and Zhao, Z and Li, S},
title = {Sinocoelotes gen. n., a new genus of the subfamily Coelotinae (Araneae, Agelenidae) from Southeast Asia.},
journal = {ZooKeys},
volume = {},
number = {614},
pages = {51-86},
pmid = {27667932},
issn = {1313-2989},
abstract = {A new genus of the spider subfamily Coelotinae, Sinocoelotes gen. n., with nine new species, is described from Yunnan and Sichuan Provinces in southern China. The new species are: Sinocoelotes cangshanensis sp. n. (♀), Sinocoelotes hehuaensis sp. n. (♂♀), Sinocoelotes luoshuiensis sp. n. (♀), Sinocoelotes mangbangensis sp. n. (♀) from Yunnan; Sinocoelotes kangdingensis sp. n. (♀), Sinocoelotes ludingensis sp. n. (♂♀), Sinocoelotes mahuanggouensis sp. n. (♀), Sinocoelotes muliensis sp. n. (♀), and Sinocoelotes yanyuanensis sp. n. (♂) from Sichuan. In addition, six Coelotes species are transferred to the new genus: Sinocoelotes acicularis (Wang, Griswold &amp; Ubick, 2009), comb. n. (♂♀), Sinocoelotes forficatus (Liu &amp; Li, 2010), comb. n. (♂♀), Sinocoelotes guangxian (Zhang, Yang, Zhu &amp; Song, 2003), comb. n. (♂♀), Sinocoelotes pseudoterrestris (Schenkel, 1963), comb. n. (♂♀), Sinocoelotes pseudoyunnanensis (Wang, Griswold &amp; Ubick, 2009), comb. n. (♂♀) and Sinocoelotes thailandensis (Dankittipakul &amp; Wang, 2003), comb. n. (♂♀). DNA barcodes of all the species were documented for future use.},
}
@article {pmid27666088,
year = {2016},
author = {Hsiao, ST and Chuang, SC and Chen, KS and Ho, PH and Wu, CL and Chen, CA},
title = {DNA barcoding reveals that the common cupped oyster in Taiwan is the Portuguese oyster Crassostrea angulata (Ostreoida; Ostreidae), not C. gigas.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {34057},
pmid = {27666088},
issn = {2045-2322},
abstract = {The Pacific cupped oyster, Crassostrea gigas, is one of the major aquacultural shellfish species that has been introduced to Europe and America from its native source in the West Pacific. In Taiwan, the cultivated cupped oysters along the west coast have been identified as C. gigas for over centuries; however, several molecular phylogenetic studies have cast doubt upon the existence of this species in Taiwan and adjacent waters. Indeed, our analyses of mitochondrial cytochrome oxidase I (COI) sequences from 313 Crassostrea collected from 12 locations along Taiwanese and southern Chinese coastlines confirm that all samples were the Portuguese oyster, C. angulata, rather than C. gigas. Multiple lines of evidence, including haplotypic and nucleotide diversity of the COI gene, demographic history, and population genetics, suggest that Taiwanese C. angulata is unique, probably experienced a sudden population expansion after the Last Glacial Maxima around 20,000 years ago, and has a significantly limited genetic connectivity across the Taiwan Strait. Our study applies an extended sampling and DNA barcoding to confirm the absence of C. gigas in natural and cultivated populations in Taiwan and southern China, where we only found C. angulata. We highlight the importance of conserving the gene pool of the C. angulata population in Taiwan, particularly considering the current threats by large-scale environmental disturbances such as marine pollution, habitat destruction, and climate change.},
}
@article {pmid27660534,
year = {2016},
author = {Heron, J and Sheffield, C},
title = {First Canadian record of the water mite Thermacarus nevadensis Marshall, 1928 (Arachnida: Acariformes: Hydrachnidiae: Thermacaridae) from hot springs in British Columbia.},
journal = {Biodiversity data journal},
volume = {},
number = {4},
pages = {e9550},
pmid = {27660534},
issn = {1314-2828},
abstract = {BACKGROUND: Thermacarus nevadensis Marshall, 1928 is an uncommonly collected mite associated with hot spring environments in the western United States. Information on its distribution and ecology are incomplete.<br><br>NEW INFORMATION: In this paper, we report Thermacarus nevadensis from northern British Columbia. These records represent the first of Thermacaridae from Canada, the most northern records of this species in North America, and the most northern records for the family globally. We also provide short notes and images of the habitats in which specimens have been collected in Canada.},
}
@article {pmid27660533,
year = {2016},
author = {Dahlgren, TG and Wiklund, H and Rabone, M and Amon, DJ and Ikebe, C and Watling, L and Smith, CR and Glover, AG},
title = {Abyssal fauna of the UK-1 polymetallic nodule exploration area, Clarion-Clipperton Zone, central Pacific Ocean: Cnidaria.},
journal = {Biodiversity data journal},
volume = {},
number = {4},
pages = {e9277},
pmid = {27660533},
issn = {1314-2828},
abstract = {BACKGROUND: We present data from a DNA taxonomy register of the abyssal Cnidaria collected as part of the Abyssal Baseline (ABYSSLINE) environmental survey cruise 'AB01' to the UK Seabed Resources Ltd (UKSRL) polymetallic-nodule exploration area 'UK-1' in the eastern Clarion-Clipperton Zone (CCZ), central Pacific Ocean abyssal plain. This is the second paper in a series to provide regional taxonomic data for a region that is undergoing intense deep-sea mineral exploration for high-grade polymetallic nodules. Data were collected from the UK-1 exploration area following the methods described in Glover et al. (2015b).<br><br>NEW INFORMATION: Morphological and genetic data are presented for 10 species and 18 records identified by a combination of morphological and genetic data, including molecular phylogenetic analyses. These included 2 primnoid octocorals, 2 isidid octocorals, 1 anemone, 4 hydroids (including 2 pelagic siphonophores accidentally caught) and a scyphozoan jellyfish (in the benthic stage of the life cycle). Two taxa matched previously published genetic sequences (pelagic siphonophores), two taxa matched published morphological descriptions (abyssal primnoids described from the same locality in 2015) and the remaining 6 taxa are potentially new species, for which we make the raw data, imagery and vouchers available for future taxonomic study. We have used a precautionary approach in taxon assignments to avoid over-estimating species ranges. The Clarion-Clipperton Zone is a region undergoing intense exploration for potential deep-sea mineral extraction. We present these data to facilitate future taxonomic and environmental impact study by making both data and voucher materials available through curated and accessible biological collections. For some of the specimens we also provide image data collected at the seabed by ROV, wich may facilitate more accurate taxon designation in coming ROV or AUV surveys.},
}
@article {pmid27657915,
year = {2016},
author = {Lim, H and Zainal Abidin, M and Pulungan, CP and de Bruyn, M and Mohd Nor, SA},
title = {DNA Barcoding Reveals High Cryptic Diversity of the Freshwater Halfbeak Genus Hemirhamphodon from Sundaland.},
journal = {PloS one},
volume = {11},
number = {9},
pages = {e0163596},
pmid = {27657915},
issn = {1932-6203},
abstract = {DNA barcoding of the cytochrome oxidase subunit I (COI) gene was utilized to assess the species diversity of the freshwater halfbeak genus Hemirhamphodon. A total of 201 individuals from 46 locations in Peninsular Malaysia, north Borneo (Sarawak) and Sumatra were successfully amplified for 616 base pairs of the COI gene revealing 231 variable and 213 parsimony informative sites. COI gene trees showed that most recognized species form monophyletic clades with high bootstrap support. Pairwise within species comparisons exhibited a wide range of intraspecific diversity from 0.0% to 14.8%, suggesting presence of cryptic diversity. This finding was further supported by barcode gap analysis, ABGD and the constructed COI gene trees. In particular, H. pogonognathus from Kelantan (northeast Peninsular Malaysia) diverged from the other H. pogonognathus groups with distances ranging from 7.8 to 11.8%, exceeding the nearest neighbor taxon. High intraspecific diversity was also observed in H. byssus and H. kuekanthali, but of a lower magnitude. This study also provides insights into endemism and phylogeographic structuring, and limited support for the Paleo-drainage divergence hypothesis as a driver of speciation in the genus Hemirhamphodon.},
}
@article {pmid27656642,
year = {2016},
author = {Cui, C and Shu, W and Li, P},
title = {Fluorescence In situ Hybridization: Cell-Based Genetic Diagnostic and Research Applications.},
journal = {Frontiers in cell and developmental biology},
volume = {4},
number = {},
pages = {89},
pmid = {27656642},
issn = {2296-634X},
abstract = {Fluorescence in situ hybridization (FISH) is a macromolecule recognition technology based on the complementary nature of DNA or DNA/RNA double strands. Selected DNA strands incorporated with fluorophore-coupled nucleotides can be used as probes to hybridize onto the complementary sequences in tested cells and tissues and then visualized through a fluorescence microscope or an imaging system. This technology was initially developed as a physical mapping tool to delineate genes within chromosomes. Its high analytical resolution to a single gene level and high sensitivity and specificity enabled an immediate application for genetic diagnosis of constitutional common aneuploidies, microdeletion/microduplication syndromes, and subtelomeric rearrangements. FISH tests using panels of gene-specific probes for somatic recurrent losses, gains, and translocations have been routinely applied for hematologic and solid tumors and are one of the fastest-growing areas in cancer diagnosis. FISH has also been used to detect infectious microbias and parasites like malaria in human blood cells. Recent advances in FISH technology involve various methods for improving probe labeling efficiency and the use of super resolution imaging systems for direct visualization of intra-nuclear chromosomal organization and profiling of RNA transcription in single cells. Cas9-mediated FISH (CASFISH) allowed in situ labeling of repetitive sequences and single-copy sequences without the disruption of nuclear genomic organization in fixed or living cells. Using oligopaint-FISH and super-resolution imaging enabled in situ visualization of chromosome haplotypes from differentially specified single-nucleotide polymorphism loci. Single molecule RNA FISH (smRNA-FISH) using combinatorial labeling or sequential barcoding by multiple round of hybridization were applied to measure mRNA expression of multiple genes within single cells. Research applications of these single molecule single cells DNA and RNA FISH techniques have visualized intra-nuclear genomic structure and sub-cellular transcriptional dynamics of many genes and revealed their functions in various biological processes.},
}
@article {pmid27654850,
year = {2016},
author = {Walker, FM and Williamson, CH and Sanchez, DE and Sobek, CJ and Chambers, CL},
title = {Species From Feces: Order-Wide Identification of Chiroptera From Guano and Other Non-Invasive Genetic Samples.},
journal = {PloS one},
volume = {11},
number = {9},
pages = {e0162342},
pmid = {27654850},
issn = {1932-6203},
abstract = {Bat guano is a relatively untapped reservoir of information, having great utility as a DNA source because it is often available at roosts even when bats are not and is an easy type of sample to collect from a difficult-to-study mammalian order. Recent advances from microbial community studies in primer design, sequencing, and analysis enable fast, accurate, and cost-effective species identification. Here, we borrow from this discipline to develop an order-wide DNA mini-barcode assay (Species from Feces) based on a segment of the mitochondrial gene cytochrome c oxidase I (COI). The assay works effectively with fecal DNA and is conveniently transferable to low-cost, high-throughput Illumina MiSeq technology that also allows simultaneous pairing with other markers. Our PCR primers target a region of COI that is highly discriminatory among Chiroptera (92% species-level identification of barcoded species), and are sufficiently degenerate to allow hybridization across diverse bat taxa. We successfully validated our system with 54 bat species across both suborders. Despite abundant arthropod prey DNA in guano, our primers were highly specific to bats; no arthropod DNA was detected in thousands of feces run on Sanger and Illumina platforms. The assay is extendable to fecal pellets of unknown age as well as individual and pooled guano, to allow for individual (using singular fecal pellets) and community (using combined pellets collected from across long-term roost sites) analyses. We developed a searchable database (http://nau.edu/CEFNS/Forestry/Research/Bats/Search-Tool/) that allows users to determine the discriminatory capability of our markers for bat species of interest. Our assay has applications worldwide for examining disease impacts on vulnerable species, determining species assemblages within roosts, and assessing the presence of bat species that are vulnerable or facing extinction. The development and analytical pathways are rapid, reliable, and inexpensive, and can be applied to ecology and conservation studies of other taxa.},
}
@article {pmid27653702,
year = {2016},
author = {Pedales, RD and Damatac, AM and Limbo, CA and Marquez, CM and Navarro, AI and Molina, J},
title = {DNA Barcoding of Philippine Herbal Medicinal Products.},
journal = {Journal of AOAC International},
volume = {99},
number = {6},
pages = {1479-1489},
doi = {10.5740/jaoacint.16-0185},
pmid = {27653702},
issn = {1944-7922},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/*analysis/*genetics ; Databases, Genetic ; Drug Contamination ; *Herbal Medicine/standards ; Philippines ; Phylogeny ; Plants, Medicinal/*classification/*genetics ; },
abstract = {The Philippine government established the Traditional and Alternative Medicine Act in 1997 to promote traditionally used herbal products and to provide an effective yet affordable alternative to conventional medicines. However, government regulation of herbal medicinal products (HMPs) is not stringent, relying only on submitted quality data from the manufacturer. In this study we validated the taxonomic identity of 26 plant samples contained within 22 HMPs, each produced by different local manufacturers, through DNA barcoding of the nuclear internal transcribed spacer-2 (ITS2) region. We recovered 19 ITS2 barcodes from 26 samples. These were compared to sequences in GenBank using MEGABLAST, but ambiguous results (similar max scores for different species) were phylogenetically analyzed. Twelve of the 19 samples matched the indicated species on the product label, three were equivocal in specific identity but were placed in the expected genus, and four other samples from three manufacturers contained contamination and/or substitution. GenBank's reference database was at times problematic because some sequences were lacking or were misidentified, but the database was still useful. Overall, ITS2 barcoding was successful in authenticating the HMPs, and it is recommended during the premarket evaluation process so as to obtain a certificate of registration from the government. The government should also develop a comprehensive database of barcodes for Philippine plants, and should prioritize the development of the traditional pharmacopeia because many locally produced HMPs are not indigenous.},
}
@article {pmid27653340,
year = {2016},
author = {Steinke, D and Connell, AD and Hebert, PD},
title = {Linking adults and immatures of South African marine fishes.},
journal = {Genome},
volume = {59},
number = {11},
pages = {959-967},
doi = {10.1139/gen-2015-0212},
pmid = {27653340},
issn = {1480-3321},
mesh = {Animals ; Biodiversity ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Fishes/*classification/*genetics ; Phylogeny ; Sequence Analysis, DNA ; South Africa ; },
abstract = {The early life-history stages of fishes are poorly known, impeding acquisition of the identifications needed to monitor larval recruitment and year-class strength. A comprehensive database of COI sequences, linked to authoritatively identified voucher specimens, promises to change this situation, representing a significant advance for fisheries science. Barcode records were obtained from 2526 early larvae and pelagic eggs of fishes collected on the inshore shelf within 5 km of the KwaZulu-Natal coast, about 50 km south of Durban, South Africa. Barcodes were also obtained from 3215 adults, representing 946 South African fish species. Using the COI reference library on BOLD based on adults, 89% of the immature fishes could be identified to a species level; they represented 450 species. Most of the uncertain sequences could be assigned to a genus, family, or order; only 92 specimens (4%) were unassigned. Accumulation curves based on inference of phylogenetic diversity indicate near-completeness of the collecting effort. The entire set of adult and larval fishes included 1006 species, representing 43% of all fish species known from South African waters. However, this total included 189 species not previously recorded from this region. The fact that almost 90% of the immatures gained a species identification demonstrates the power and completeness of the DNA barcode reference library for fishes generated during the 10 years of FishBOL.},
}
@article {pmid27652127,
year = {2016},
author = {Saddhe, AA and Jamdade, RA and Kumar, K},
title = {Assessment of mangroves from Goa, west coast India using DNA barcode.},
journal = {SpringerPlus},
volume = {5},
number = {1},
pages = {1554},
pmid = {27652127},
issn = {2193-1801},
abstract = {Mangroves are salt-tolerant forest ecosystems of tropical and subtropical intertidal regions. They are among most productive, diverse, biologically important ecosystem and inclined toward threatened system. Identification of mangrove species is of critical importance in conserving and utilizing biodiversity, which apparently hindered by a lack of taxonomic expertise. In recent years, DNA barcoding using plastid markers rbcL and matK has been suggested as an effective method to enrich traditional taxonomic expertise for rapid species identification and biodiversity inventories. In the present study, we performed assessment of available 14 mangrove species of Goa, west coast India based on core DNA barcode markers, rbcL and matK. PCR amplification success rate, intra- and inter-specific genetic distance variation and the correct identification percentage were taken into account to assess candidate barcode regions. PCR and sequence success rate were high in rbcL (97.7 %) and matK (95.5 %) region. The two candidate chloroplast barcoding regions (rbcL, matK) yielded barcode gaps. Our results clearly demonstrated that matK locus assigned highest correct identification rates (72.09 %) based on TaxonDNA Best Match criteria. The concatenated rbcL + matK loci were able to adequately discriminate all mangrove genera and species to some extent except those in Rhizophora, Sonneratia and Avicennia. Our study provides the first endorsement of the species resolution among mangroves using plastid genes with few exceptions. Our future work will be focused on evaluation of other barcode markers to delineate complete resolution of mangrove species and identification of putative hybrids.},
}
@article {pmid27648231,
year = {2016},
author = {Paterson, ID and Mangan, R and Downie, DA and Coetzee, JA and Hill, MP and Burke, AM and Downey, PO and Henry, TJ and Compton, SG},
title = {Two in one: cryptic species discovered in biological control agent populations using molecular data and crossbreeding experiments.},
journal = {Ecology and evolution},
volume = {6},
number = {17},
pages = {6139-6150},
pmid = {27648231},
issn = {2045-7758},
abstract = {There are many examples of cryptic species that have been identified through DNA-barcoding or other genetic techniques. There are, however, very few confirmations of cryptic species being reproductively isolated. This study presents one of the few cases of cryptic species that has been confirmed to be reproductively isolated and therefore true species according to the biological species concept. The cryptic species are of special interest because they were discovered within biological control agent populations. Two geographically isolated populations of Eccritotarsus catarinensis (Carvalho) [Hemiptera: Miridae], a biological control agent for the invasive aquatic macrophyte, water hyacinth, Eichhornia crassipes (Mart.) Solms [Pontederiaceae], in South Africa, were sampled from the native range of the species in South America. Morphological characteristics indicated that both populations were the same species according to the current taxonomy, but subsequent DNA analysis and breeding experiments revealed that the two populations are reproductively isolated. Crossbreeding experiments resulted in very few hybrid offspring when individuals were forced to interbreed with individuals of the other population, and no hybrid offspring were recorded when a choice of mate from either population was offered. The data indicate that the two populations are cryptic species that are reproductively incompatible. Subtle but reliable diagnostic characteristics were then identified to distinguish between the two species which would have been considered intraspecific variation without the data from the genetics and interbreeding experiments. These findings suggest that all consignments of biological control agents from allopatric populations should be screened for cryptic species using genetic techniques and that the importation of multiple consignments of the same species for biological control should be conducted with caution.},
}
@article {pmid27646634,
year = {2016},
author = {Jeffet, J and Kobo, A and Su, T and Grunwald, A and Green, O and Nilsson, AN and Eisenberg, E and Ambjörnsson, T and Westerlund, F and Weinhold, E and Shabat, D and Purohit, PK and Ebenstein, Y},
title = {Super-Resolution Genome Mapping in Silicon Nanochannels.},
journal = {ACS nano},
volume = {10},
number = {11},
pages = {9823-9830},
doi = {10.1021/acsnano.6b05398},
pmid = {27646634},
issn = {1936-086X},
support = {337830/ERC_/European Research Council/International ; },
abstract = {Optical genome mapping in nanochannels is a powerful genetic analysis method, complementary to deoxyribonucleic acid (DNA) sequencing. The method is based on detecting a pattern of fluorescent labels attached along individual DNA molecules. When such molecules are extended in nanochannels, the labels create a fluorescent genetic barcode that is used for mapping the DNA molecule to its genomic locus and identifying large-scale variation from the genome reference. Mapping resolution is currently limited by two main factors: the optical diffraction limit and the thermal fluctuations of DNA molecules suspended in the nanochannels. Here, we utilize single-molecule tracking and super-resolution localization in order to improve the mapping accuracy and resolving power of this genome mapping technique and achieve a 15-fold increase in resolving power compared to currently practiced methods. We took advantage of a naturally occurring genetic repeat array and labeled each repeat with custom-designed Trolox conjugated fluorophores for enhanced photostability. This model system allowed us to acquire extremely long image sequences of the equally spaced fluorescent markers along DNA molecules, enabling detailed characterization of nanoconfined DNA dynamics and quantitative comparison to the Odijk theory for confined polymer chains. We present a simple method to overcome the thermal fluctuations in the nanochannels and exploit single-step photobleaching to resolve subdiffraction spaced fluorescent markers along fluctuating DNA molecules with ∼100 bp resolution. In addition, we show how time-averaging over just ∼50 frames of 40 ms enhances mapping accuracy, improves mapping P-value scores by 3 orders of magnitude compared to nonaveraged alignment, and provides a significant advantage for analyzing structural variations between DNA molecules with similar sequence composition.},
}
@article {pmid27643687,
year = {2016},
author = {Gavazzi, F and Braglia, L and Mastromauro, F and Gianì, S and Morello, L and Breviario, D},
title = {The Tubulin-Based-Polymorphism Method Provides a Simple and Effective Alternative to the Genomic Profiling of Grape.},
journal = {PloS one},
volume = {11},
number = {9},
pages = {e0163335},
pmid = {27643687},
issn = {1932-6203},
mesh = {*Genes, Plant ; *Polymorphism, Genetic ; Tubulin/*metabolism ; Vitis/*genetics ; },
abstract = {The TBP (Tubulin-Based-Polymorphism) method, based on a nuclear ILP (Intron-Length-Polymorphism) molecular marker, has been used for genotyping 37 accessions of the genus Vitis inclusive of different species, rootstocks, wild and cultivated subspecies. A distinct DNA barcode made up by a different number of amplicons, was attributed to each of the different accessions. TBP data were compared with those obtained, with the use of an internationally validated set of six SSR markers. Genetic relationships among the different accessions, dendrogram distributions, correlation values and polymorphic index values (PICs) were definitively comparable when not in favor of TBP. Such an experimental consistency is based upon a genomic organization of the multiple members of the β-tubulin gene family, the targets of TBP-mediated amplification, that is conserved in Vitis as in any other plant species. The TBP amplicons can actually be used as a useful source of sequence polymorphisms for generating primer pairs capable of identifying specific cultivars in a simple assay. An example for the identification of the 'Sangiovese' cv. is reported. More generally, these data are discussed in terms of the actual advantages that the introduction of the TBP method in the field of grape characterization and genotyping can provide.},
}
@article {pmid27640980,
year = {2016},
author = {Yates, D},
title = {Techniques: Neuronal barcoding.},
journal = {Nature reviews. Neuroscience},
volume = {17},
number = {10},
pages = {605},
pmid = {27640980},
issn = {1471-0048},
}
@article {pmid27640675,
year = {2016},
author = {Sun, S and Li, Q and Kong, L and Yu, H and Zheng, X and Yu, R and Dai, L and Sun, Y and Chen, J and Liu, J and Ni, L and Feng, Y and Yu, Z and Zou, S and Lin, J},
title = {DNA barcoding reveal patterns of species diversity among northwestern Pacific molluscs.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {33367},
pmid = {27640675},
issn = {2045-2322},
mesh = {Animals ; Base Sequence ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Genetic Variation ; Geography ; Mollusca/*classification/genetics ; Pacific Ocean ; Phylogeny ; Species Specificity ; },
abstract = {This study represents the first comprehensive molecular assessment of northwestern Pacific molluscs. In total, 2801 DNA barcodes belonging to 569 species from China, Japan and Korea were analyzed. An overlap between intra- and interspecific genetic distances was present in 71 species. We tested the efficacy of this library by simulating a sequence-based specimen identification scenario using Best Match (BM), Best Close Match (BCM) and All Species Barcode (ASB) criteria with three threshold values. BM approach returned 89.15% true identifications (95.27% when excluding singletons). The highest success rate of congruent identifications was obtained with BCM at 0.053 threshold. The analysis of our barcode library together with public data resulted in 582 Barcode Index Numbers (BINs), 72.2% of which was found to be concordantly with morphology-based identifications. The discrepancies were divided in two groups: sequences from different species clustered in a single BIN and conspecific sequences divided in one more BINs. In Neighbour-Joining phenogram, 2,320 (83.0%) queries fromed 355 (62.4%) species-specific barcode clusters allowing their successful identification. 33 species showed paraphyletic and haplotype sharing. 62 cases are represented by deeply diverged lineages. This study suggest an increased species diversity in this region, highlighting taxonomic revision and conservation strategy for the cryptic complexes.},
}
@article {pmid27639480,
year = {2017},
author = {Martinsson, S and Erséus, C},
title = {Cryptic speciation and limited hybridization within Lumbricus earthworms (Clitellata: Lumbricidae).},
journal = {Molecular phylogenetics and evolution},
volume = {106},
number = {},
pages = {18-27},
doi = {10.1016/j.ympev.2016.09.011},
pmid = {27639480},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Cytochromes b/classification/genetics ; DNA/chemistry/isolation &amp; purification/metabolism ; Europe ; Haplotypes ; Histones/classification/genetics ; *Hybridization, Genetic ; Oligochaeta/*classification/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Cryptic mitochondrial (mt) lineages are known to exist in the earthworm morphospecies Lumbricus rubellus and L. terrestris. The latter was recently split into two species, L. terrestris and L. herculeus, based on large genetic distances and a statistical difference in body size. There is support for the separation of some lineages in L. rubellus into species, whereas other lineages, separated by similar mt genetic distances, have been found to be part of the same species. However, no study has evaluated the status of the cryptic mt lineages in L. terrestris-L. herculeus and L. rubellus using nuclear genes. We use a combination of methods to reveal extensive cryptic speciation and limited hybridization in Lumbricus, based on one nuclear (H3) and one mitochondrial (COI) marker. Using a Bayesian multi-locus species delimitation method, as well as single gene haplotype networks and gene trees, we delimit seven well supported cryptic species within the morphospecies L. rubellus, and confirm the split within the species-pair L. terrestris-L. herculeus. Limited hybridization was found between the most common species of L. rubellus (A) in northern Europe and two other species (B and H) in this complex, as well as between L. terrestris and L. herculeus. Deep mt divergence was found within L. terrestris s.str. but no support for further splitting of this taxon was found. Both L. rubellus and L. terrestris are well studied model organisms, and considering that cryptic species and hybridization were found within them, it is important that they are properly identified in future studies.},
}
@article {pmid27638734,
year = {2016},
author = {Fajfer, M and Melnikov, D and Dabert, M},
title = {Three new species of the genus Pterygosoma Peters, 1849 (Acariformes: Pterygosomatidae) from agamid lizards (Sauria: Agaminae) with DNA barcode data.},
journal = {Systematic parasitology},
volume = {93},
number = {8},
pages = {791-814},
pmid = {27638734},
issn = {1573-5192},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Lizards/*parasitology ; Mites/anatomy &amp; histology/*classification/*genetics ; RNA, Ribosomal, 28S/genetics ; Species Specificity ; },
abstract = {Three new species of the genus Pterygosoma Peters, 1849 parasitising lizards of the subfamily Agaminae (Squamata: Agamidae) are described: P. pallidum n. sp. from Trapelus pallidus (Merrem) and P. parasiniatum n. sp. from Pseudotrapelus cf. sinaitus (Heyden) (both from Jordan); and P. theobaldi n. sp. from Phrynocephalus theobaldi Blyth from North India. We extend the standard morphological description of the new species by using DNA barcode markers, partial sequences of the mitochondrial cytochrome c oxidase subunit I (cox1) gene and the hypervariable region D2 of the nuclear 28S rRNA gene. A key to the species group inermis is constructed based on female morphology. The agamid genus Phrynocephalus Kaup, 1825 is recorded as a host of Pterygosoma for the first time.},
}
@article {pmid27633310,
year = {2016},
author = {Coskun, A and Malatyali, E and Ertabaklar, H and Yasar, MB and Karaoglu, AO and Ertug, S},
title = {Blastocystis in ulcerative colitis patients: Genetic diversity and analysis of laboratory findings.},
journal = {Asian Pacific journal of tropical medicine},
volume = {9},
number = {9},
pages = {916-919},
doi = {10.1016/j.apjtm.2016.07.018},
pmid = {27633310},
issn = {2352-4146},
abstract = {OBJECTIVE: To determine Blastocystis frequency and subtypes (ST) in ulcerative colitis (UC) patients and analyse some laboratory findings between Blastocystis positive and negative cases.<br><br>METHODS: Faecal samples from 150 UC patients in Adnan Menderes University, Training and Research Hospital were examined by direct microscopy and cultivated in Jones medium. Blastocystis positive cultures were subjected to DNA isolation and subtypes were identified by sequencing of barcode region. A retrospective analysis was conducted on C reactive protein (CRP), leucocyte counts (WBC), neutrophil counts, and sedimentation rates.<br><br>RESULTS: The overall positive rate of Blastocystis was 8% (12 patients) and the most abundant subtype was ST3 (eight isolates, 66.7%), followed by ST1, ST2 and ST7. Laboratory findings between Blastocystis infected and non-infected UC patients were not significantly different. Blastocystis frequency was 3.8% among the patients in active stage, while it was 11.8% among the patients in remission stage.<br><br>CONCLUSIONS: The present study confirms previous findings that have indicated the predominance of Blastocystis ST3 in humans and contributes additional evidence that suggests the low colonisation of Blastocystis infection in ulcerative colitis patients during active stage.},
}
@article {pmid27632899,
year = {2016},
author = {Laopichienpong, N and Muangmai, N and Supikamolseni, A and Twilprawat, P and Chanhome, L and Suntrarachun, S and Peyachoknagul, S and Srikulnath, K},
title = {Assessment of snake DNA barcodes based on mitochondrial COI and Cytb genes revealed multiple putative cryptic species in Thailand.},
journal = {Gene},
volume = {594},
number = {2},
pages = {238-247},
doi = {10.1016/j.gene.2016.09.017},
pmid = {27632899},
issn = {1879-0038},
mesh = {Animals ; *Biodiversity ; Cytochromes b/*genetics ; *DNA Barcoding, Taxonomic ; *Databases, Genetic ; Electron Transport Complex IV/*genetics ; Mitochondrial Proteins/*genetics ; Snakes/*genetics ; Species Specificity ; Thailand ; },
abstract = {DNA barcodes of mitochondrial cytochrome c oxidase I (COI), cytochrome b (Cytb) genes, and their combined data sets were constructed from 35 snake species in Thailand. No barcoding gap was detected in either of the two genes from the observed intra- and interspecific sequence divergences. Intra- and interspecific sequence divergences of the COI gene differed 14 times, with barcode cut-off scores ranging over 2%-4% for threshold values differentiated among most of the different species; the Cytb gene differed 6 times with cut-off scores ranging over 2%-6%. Thirty-five specific nucleotide mutations were also found at interspecific level in the COI gene, identifying 18 snake species, but no specific nucleotide mutation was observed for Cytb in any single species. This suggests that COI barcoding was a better marker than Cytb. Phylogenetic clustering analysis indicated that most species were represented by monophyletic clusters, suggesting that these snake species could be clearly differentiated using COI barcodes. However, the two-marker combination of both COI and Cytb was more effective, differentiating snake species by over 2%-4%, and reducing species numbers in the overlap value between intra- and interspecific divergences. Three species delimitation algorithms (general mixed Yule-coalescent, automatic barcoding gap detection, and statistical parsimony network analysis) were extensively applied to a wide range of snakes based on both barcodes. This revealed cryptic diversity for eleven snake species in Thailand. In addition, eleven accessions from the database previously grouped under the same species were represented at different species level, suggesting either high genetic diversity, or the misidentification of these sequences in the database as a consequence of cryptic species.},
}
@article {pmid27631279,
year = {2016},
author = {Kaczanowski, A and Brunk, CF and Kazubski, SL},
title = {Cohesion of Clonal Life History, Senescence and Rejuvenation Induced by Autogamy of the Histophagous Ciliate Tetrahymena rostrata.},
journal = {Protist},
volume = {167},
number = {5},
pages = {490-510},
doi = {10.1016/j.protis.2016.08.003},
pmid = {27631279},
issn = {1618-0941},
mesh = {Animals ; *Life History Traits ; Poland ; RNA, Protozoan/genetics ; RNA, Ribosomal/genetics ; Reproduction ; Sequence Analysis, RNA ; Snails/parasitology ; Tetrahymena/genetics/*physiology ; },
abstract = {The histophagous ciliate Tetrahymena rostrata was found as a parasite in the renal organs of the land snails Zonitoides nitidus and Cochlicopa lubrica. A starvation medium induced encystment, meiosis, autogamy, and development of new macronuclei. The cell division rate declined linearly with number of divisions from the last autogamy until senescence. The senescing strains were rejuvenated by further encystment-induced autogamy. It is expected, that these processes contribute to genetic variability among the local, small, and isolated T. rostrata populations. Consistent with this expectation, small divergences in the cox-1 sequences appeared even among these strains, which had been isolated from different specimens of the same host species at the same site. The divergences in this gene between our T. rostrata strains from Z. nitidus and other strains from C. lubrica, Helix aspersa, and Deroceras reticulatum in Spain (Segade et al. 2009, Parasitology 136:771-782), were beyond the limits of intra-species variability within the genus Tetrahymena. However there is the lack of inter-strain differences in the life history and cytology among our, the Spanish, and those T.rostrata strains, that are not available for "barcoding" anymore. Therefore, variability in the life history and morphology within T .rostrata is constrained by natural selection.},
}
@article {pmid27629021,
year = {2016},
author = {Reeves, LE and Holderman, CJ and Gillett-Kaufman, JL and Kawahara, AY and Kaufman, PE},
title = {Maintenance of host DNA integrity in field-preserved mosquito (Diptera: Culicidae) blood meals for identification by DNA barcoding.},
journal = {Parasites &amp; vectors},
volume = {9},
number = {1},
pages = {503},
pmid = {27629021},
issn = {1756-3305},
mesh = {Aedes/*physiology ; Animals ; *Blood ; Cold Temperature ; DNA/*blood/chemistry/isolation &amp; purification/*metabolism ; *DNA Barcoding, Taxonomic ; Desiccation ; Ethanol/chemistry ; Feeding Behavior ; Filtration ; Mosquito Vectors/*physiology ; Paper ; Polymerase Chain Reaction ; Preservation, Biological/*methods/*standards ; Specimen Handling/methods ; },
abstract = {BACKGROUND: Determination of the interactions between hematophagous arthropods and their hosts is a necessary component to understanding the transmission dynamics of arthropod-vectored pathogens. Current molecular methods to identify hosts of blood-fed arthropods require the preservation of host DNA to serve as an amplification template. During transportation to the laboratory and storage prior to molecular analysis, genetic samples need to be protected from nucleases, and the degradation effects of hydrolysis, oxidation and radiation. Preservation of host DNA contained in field-collected blood-fed specimens has an additional caveat: suspension of the degradative effects of arthropod digestion on host DNA. Unless effective preservation methods are implemented promptly after blood-fed specimens are collected, host DNA will continue to degrade. Preservation methods vary in their efficacy, and need to be selected based on the logistical constraints of the research program.<br><br>METHODS: We compared four preservation methods (cold storage at -20 &#xb0;C, desiccation, ethanol storage of intact mosquito specimens and crushed specimens on filter paper) for field storage of host DNA from blood-fed mosquitoes across a range of storage and post-feeding time periods. The efficacy of these techniques in maintaining host DNA integrity was evaluated using a polymerase chain reaction (PCR) to detect the presence of a sufficient concentration of intact host DNA templates for blood meal analysis. We applied a logistic regression model to assess the effects of preservation method, storage time and post-feeding time on the binomial response variable, amplification success.<br><br>RESULTS: Preservation method, storage time and post-feeding time all significantly impacted PCR amplification success. Filter papers and, to a lesser extent, 95 % ethanol, were the most effective methods for the maintenance of host DNA templates. Amplification success of host DNA preserved in cold storage at -20 &#xb0;C and desiccation was poor.<br><br>CONCLUSIONS: Our data suggest that, of the methods tested, host DNA template integrity was most stable when blood meals were preserved using filter papers. Filter paper preservation is effective over short- and long-term storage, while ethanol preservation is only suitable for short-term storage. Cold storage at -20 &#xb0;C, and desiccation of blood meal specimens, even for short time periods, should be avoided.},
}
@article {pmid27627901,
year = {2016},
author = {Urumarudappa, SK and Gogna, N and Newmaster, SG and Venkatarangaiah, K and Subramanyam, R and Saroja, SG and Gudasalamani, R and Dorai, K and Ramanan, US},
title = {DNA barcoding and NMR spectroscopy-based assessment of species adulteration in the raw herbal trade of Saraca asoca (Roxb.) Willd, an important medicinal plant.},
journal = {International journal of legal medicine},
volume = {130},
number = {6},
pages = {1457-1470},
pmid = {27627901},
issn = {1437-1596},
mesh = {Commerce ; Conservation of Natural Resources ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Drug Contamination ; Humans ; India ; *Magnetic Resonance Spectroscopy ; Phytotherapy ; Plant Extracts/genetics ; Plants, Medicinal/*genetics ; Polymerase Chain Reaction ; },
abstract = {Saraca asoca (Roxb.) Willd, commonly known as "Asoka" or "Ashoka," is one of the most important medicinal plants used in raw herbal trade in India. The bark extracts of the tree are used in the treatment of leucorrhea and other uterine disorders besides also having anti-inflammatory, anti-bacterial, anti-pyretic, anti-helminthic, and analgesic activity. The indiscriminate and rampant extraction of the wood to meet the ever-increasing market demand has led to a sharp decline in naturally occurring populations of the species in the country. Consequently, the species has recently been classified as "vulnerable" by the International Union for Conservation of Nature (IUCN). Increasing deforestation and increasing demand for this medicinal plant have resulted in a limited supply and suspected widespread adulteration of the species in the raw herbal trade market. Adulteration is a serious concern due to: (i) reduction in the efficacy of this traditional medicine, (ii) considerable health risk to consumers, and (iii) fraudulent product substitution that impacts the economy for the Natural Health Product (NHP) Industry and consumers. In this paper, we provide the first attempt to assess the extent of adulteration in the raw herbal trade of S. asoca using DNA barcoding validated by NMR spectroscopic techniques. Analyzing market samples drawn from 25 shops, mostly from peninsular India, we show that more than 80 % of the samples were spurious, representing plant material from at least 7 different families. This is the first comprehensive and large-scale study to demonstrate the widespread adulteration of market samples of S. asoca in India. These results pose grave implications for the use of raw herbal drugs, such as that of S. asoca, on consumer health and safety. Based on these findings, we argue for a strong and robust regulatory framework to be put in place, which would ensure the quality of raw herbal trade products and reassure consumer confidence in indigenous medicinal systems. Graphical Abstract DNA barcoding and NMR spectroscopy-based assessment of adulteration in Saraca asoca.},
}
@article {pmid27626403,
year = {2016},
author = {Yu, N and Gu, H and Wei, Y and Zhu, N and Wang, Y and Zhang, H and Zhu, Y and Zhang, X and Ma, C and Sun, A},
title = {Suitable DNA Barcoding for Identification and Supervision of Piper kadsura in Chinese Medicine Markets.},
journal = {Molecules (Basel, Switzerland)},
volume = {21},
number = {9},
pages = {},
pmid = {27626403},
issn = {1420-3049},
mesh = {China ; *DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; *Drugs, Chinese Herbal ; *Genetic Loci ; Piper/*chemistry ; },
abstract = {Piper kadsura is a vine-like medicinal plant which is widely used in clinical treatment. However, P. kadsura is often substituted by other materials in the markets, thereby causing health risks. In this study, 38 P. kadsura samples and eight sequences from GenBank, including a closely-related species and common adulterants were collected. This study aimed to identify an effective DNA barcode from four popular DNA loci for P. kadsura authentication. The success rates of PCR amplification, sequencing, and sequence acquisition of matK were 10.5%, 75%, and 7.9%, respectively; for rbcL they were 89.5%, 8.8%, and 7.9%, respectively; ITS2 rates were 86.8%, 3.0%, and 2.6%, respectively, while for psbA-trnH they were all 100%, which is much higher than for the other three loci. The sequences were aligned using Muscle, genetic distances were computed using MEGA 5.2.2, and barcoding gap was performed using TAXON DNA. Phylogenetic analysis showed that psbA-trnH could clearly distinguish P. kadsura from its closely related species and the common adulterant. psbA-trnH was then used to evaluate the fake proportions of P. kadsura. Results showed that 18.4% of P. kadsura samples were fake, indicating that adulterant species exist in the Chinese markets. Two-dimensional DNA barcoding imaging of P. kadsura was conducted, which was beneficial to the management of P. kadsura. We conclude that the psbA-trnH region is a powerful tool for P. kadsura identification and supervision in the current medicine markets.},
}
@article {pmid27625426,
year = {2016},
author = {Moffitt, JR and Hao, J and Wang, G and Chen, KH and Babcock, HP and Zhuang, X},
title = {High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {113},
number = {39},
pages = {11046-11051},
pmid = {27625426},
issn = {1091-6490},
support = {R01 MH113094/MH/NIMH NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Algorithms ; Cell Division ; Cell Line, Tumor ; DNA Replication ; Fluorescent Dyes/metabolism ; Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Image Processing, Computer-Assisted ; In Situ Hybridization, Fluorescence/*methods ; RNA/metabolism ; Reproducibility of Results ; Single-Cell Analysis/*methods ; },
abstract = {Image-based approaches to single-cell transcriptomics, in which RNA species are identified and counted in situ via imaging, have emerged as a powerful complement to single-cell methods based on RNA sequencing of dissociated cells. These image-based approaches naturally preserve the native spatial context of RNAs within a cell and the organization of cells within tissue, which are important for addressing many biological questions. However, the throughput of these image-based approaches is relatively low. Here we report advances that lead to a drastic increase in the measurement throughput of multiplexed error-robust fluorescence in situ hybridization (MERFISH), an image-based approach to single-cell transcriptomics. In MERFISH, RNAs are identified via a combinatorial labeling approach that encodes RNA species with error-robust barcodes followed by sequential rounds of single-molecule fluorescence in situ hybridization (smFISH) to read out these barcodes. Here we increase the throughput of MERFISH by two orders of magnitude through a combination of improvements, including using chemical cleavage instead of photobleaching to remove fluorescent signals between consecutive rounds of smFISH imaging, increasing the imaging field of view, and using multicolor imaging. With these improvements, we performed RNA profiling in more than 100,000 human cells, with as many as 40,000 cells measured in a single 18-h measurement. This throughput should substantially extend the range of biological questions that can be addressed by MERFISH.},
}
@article {pmid27622637,
year = {2016},
author = {Paula, DP and Linard, B and Crampton-Platt, A and Srivathsan, A and Timmermans, MJ and Sujii, ER and Pires, CS and Souza, LM and Andow, DA and Vogler, AP},
title = {Uncovering Trophic Interactions in Arthropod Predators through DNA Shotgun-Sequencing of Gut Contents.},
journal = {PloS one},
volume = {11},
number = {9},
pages = {e0161841},
pmid = {27622637},
issn = {1932-6203},
mesh = {Animals ; Coleoptera/*physiology ; *Food Chain ; Gastrointestinal Contents/*chemistry ; Insecta/*physiology ; Sequence Analysis, DNA/*methods ; },
abstract = {Characterizing trophic networks is fundamental to many questions in ecology, but this typically requires painstaking efforts, especially to identify the diet of small generalist predators. Several attempts have been devoted to develop suitable molecular tools to determine predatory trophic interactions through gut content analysis, and the challenge has been to achieve simultaneously high taxonomic breadth and resolution. General and practical methods are still needed, preferably independent of PCR amplification of barcodes, to recover a broader range of interactions. Here we applied shotgun-sequencing of the DNA from arthropod predator gut contents, extracted from four common coccinellid and dermapteran predators co-occurring in an agroecosystem in Brazil. By matching unassembled reads against six DNA reference databases obtained from public databases and newly assembled mitogenomes, and filtering for high overlap length and identity, we identified prey and other foreign DNA in the predator guts. Good taxonomic breadth and resolution was achieved (93% of prey identified to species or genus), but with low recovery of matching reads. Two to nine trophic interactions were found for these predators, some of which were only inferred by the presence of parasitoids and components of the microbiome known to be associated with aphid prey. Intraguild predation was also found, including among closely related ladybird species. Uncertainty arises from the lack of comprehensive reference databases and reliance on low numbers of matching reads accentuating the risk of false positives. We discuss caveats and some future prospects that could improve the use of direct DNA shotgun-sequencing to characterize arthropod trophic networks.},
}
@article {pmid27621286,
year = {2016},
author = {Desjardin, DE and Perry, BA and Stevani, CV},
title = {New luminescent mycenoid fungi (Basidiomycota, Agaricales) from São Paulo State, Brazil.},
journal = {Mycologia},
volume = {108},
number = {6},
pages = {1165-1174},
doi = {10.3852/16-077},
pmid = {27621286},
issn = {0027-5514},
mesh = {Agaricales/chemistry/*classification/growth &amp; development/*isolation &amp; purification ; Brazil ; Cluster Analysis ; DNA Barcoding, Taxonomic ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Luminescence ; Microscopy ; Phylogeny ; },
abstract = {Four species of mycenoid fungi are reported as luminescent (or putatively luminescent) on the basis of specimens collected from São Paulo State, Brazil. Two of them represent new species (Mycena oculisnymphae, Resinomycena petarensis), and two represent new reports of luminescence in previously described species (M. deformis, M. globulispora). Comprehensive descriptions, illustrations, photographs, and comparisons with phenetically similar species are provided. Sequences of nuc rDNA internal transcribed spacer regions were generated for barcoding purposes and for comparisons with similar species.},
}
@article {pmid27619348,
year = {2016},
author = {Lewińska, AM and Peuhkuri, RH and Rode, C and Andersen, B and Hoof, JB},
title = {Rapid detection and identification of Stachybotrys and Chaetomium species using tissue PCR analysis.},
journal = {Journal of microbiological methods},
volume = {130},
number = {},
pages = {115-122},
doi = {10.1016/j.mimet.2016.09.005},
pmid = {27619348},
issn = {1872-8359},
mesh = {Air Microbiology ; Air Pollution, Indoor/*analysis ; Base Sequence ; Chaetomium/classification/*genetics/growth &amp; development/*isolation &amp; purification ; DNA Barcoding, Taxonomic/methods ; DNA, Fungal/analysis/isolation &amp; purification ; Environmental Monitoring/methods ; Genes, Fungal ; Histones/genetics ; Mitogen-Activated Protein Kinases/genetics ; Phylogeny ; Polymerase Chain Reaction/*methods ; Risk Assessment/methods ; Sequence Analysis, DNA/methods ; Stachybotrys/classification/*genetics/growth &amp; development/*isolation &amp; purification ; Time Factors ; },
abstract = {Indoor fungi are a worldwide problem causing negative health effects for infected building's occupants and even deterioration of building structures. Different fungal species affect buildings and their inhabitants differently. Therefore, rapid and accurate identification of fungi to the species level is essential for health risk assessment and building remediation. This study focuses on molecular identification of two common indoor fungal genera: Stachybotrys and Chaetomium. This study proposes two new DNA barcode candidates for Stachybotrys and Chaetomium: the gene encoding mitogen activated protein kinase (hogA) and the intergenic region between histone 3 and histone 4 (h3-h4) as well as it introduces a rapid - 3.5h - protocol for direct Stachybotrys and Chaetomium species identification, which bypasses culture cultivation, DNA extraction and DNA sequencing.},
}
@article {pmid27618948,
year = {2017},
author = {Haverkort, JJM and Bouman, JH and Wind, JDD and Leenen, LPH},
title = {Continuous Development of a Major Incident In-Hospital Victim Tracking and Tracing System, Withstanding the Challenges of Time.},
journal = {Disaster medicine and public health preparedness},
volume = {11},
number = {2},
pages = {244-250},
doi = {10.1017/dmp.2016.122},
pmid = {27618948},
issn = {1938-744X},
mesh = {Disaster Planning/methods ; Hospitals/statistics &amp; numerical data/*trends ; Humans ; Mass Casualty Incidents/*statistics &amp; numerical data ; Netherlands ; Patient Identification Systems/*methods ; Surge Capacity/standards ; Teaching/trends ; },
abstract = {OBJECTIVE: To describe the development of the Patient Barcode Registration System (PBRS) over time and confirm the usability and feasibility of the system's latest version during a large trauma drill.<br><br>METHODS: The development of a PBRS started around 1993 aiming to provide an effective tool for patient registration, tracking, and tracing during major incidents. The PBRS uses wristbands with barcodes to follow and register patients in the care process. During a large trauma drill, 120 patients and 40 relatives were registered and traced in the system. Errors in registration, tracking, and tracing of persons were registered.<br><br>RESULTS: Of the 120 patients, no patient data were lost and patients could be traced in real time throughout the treatment process by the command team. Strategic decisions could be made based on the information provided by the system. Patient relatives were easily matched and government agencies received regular updates on the number and characteristics of the patients.<br><br>CONCLUSION: The PBRS is a usable, feasible, and sustainable patient tracking and tracing tool to be used during the hospital response to major incidents. Lessons learned during the last 20 years include the need for continuous updates to withstand the challenge of time. (Disaster Med Public Health Preparedness. 2017;11:244-250).},
}
@article {pmid27617390,
year = {2016},
author = {Grüner, BM and Schulze, CJ and Yang, D and Ogasawara, D and Dix, MM and Rogers, ZN and Chuang, CH and McFarland, CD and Chiou, SH and Brown, JM and Cravatt, BF and Bogyo, M and Winslow, MM},
title = {An in vivo multiplexed small-molecule screening platform.},
journal = {Nature methods},
volume = {13},
number = {10},
pages = {883-889},
pmid = {27617390},
issn = {1548-7105},
support = {R25 CA180993/CA/NCI NIH HHS/United States ; R01 DA033760/DA/NIDA NIH HHS/United States ; R01 CA132630/CA/NCI NIH HHS/United States ; R21 CA188863/CA/NCI NIH HHS/United States ; R01 HL122283/HL/NHLBI NIH HHS/United States ; F32 CA200078/CA/NCI NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Cell Adhesion/drug effects ; Cell Line, Tumor ; Cell Movement/drug effects ; Cell Proliferation/drug effects ; Dose-Response Relationship, Drug ; Drug Evaluation, Preclinical/*methods ; Gene Knockdown Techniques ; High-Throughput Screening Assays/*methods ; Humans ; Liver Neoplasms/metabolism/secondary ; Mice ; Mice, SCID ; Molecular Imaging/*methods ; Monoacylglycerol Lipases/antagonists &amp; inhibitors/genetics ; Neoplasm Transplantation ; Pancreatic Neoplasms/metabolism/pathology ; Small Molecule Libraries/*pharmacology ; },
abstract = {Phenotype-based small-molecule screening is a powerful method to identify molecules that regulate cellular functions. However, such screens are generally performed in vitro under conditions that do not necessarily model complex physiological conditions or disease states. Here, we use molecular cell barcoding to enable direct in vivo phenotypic screening of small-molecule libraries. The multiplexed nature of this approach allows rapid in vivo analysis of hundreds to thousands of compounds. Using this platform, we screened >700 covalent inhibitors directed toward hydrolases for their effect on pancreatic cancer metastatic seeding. We identified multiple hits and confirmed the relevant target of one compound as the lipase ABHD6. Pharmacological and genetic studies confirmed the role of this enzyme as a regulator of metastatic fitness. Our results highlight the applicability of this multiplexed screening platform for investigating complex processes in vivo.},
}
@article {pmid27616795,
year = {2016},
author = {Crous, PW and Wingfield, MJ and Richardson, DM and Le Roux, JJ and Strasberg, D and Edwards, J and Roets, F and Hubka, V and Taylor, PW and Heykoop, M and Martín, MP and Moreno, G and Sutton, DA and Wiederhold, NP and Barnes, CW and Carlavilla, JR and Gené, J and Giraldo, A and Guarnaccia, V and Guarro, J and Hernández-Restrepo, M and Kolařík, M and Manjón, JL and Pascoe, IG and Popov, ES and Sandoval-Denis, M and Woudenberg, JH and Acharya, K and Alexandrova, AV and Alvarado, P and Barbosa, RN and Baseia, IG and Blanchette, RA and Boekhout, T and Burgess, TI and Cano-Lira, JF and Čmoková, A and Dimitrov, RA and Dyakov, MY and Dueñas, M and Dutta, AK and Esteve-Raventós, F and Fedosova, AG and Fournier, J and Gamboa, P and Gouliamova, DE and Grebenc, T and Groenewald, M and Hanse, B and Hardy, GE and Held, BW and Jurjević, &#x17d; and Kaewgrajang, T and Latha, KP and Lombard, L and Luangsa-Ard, JJ and Lysková, P and Mallátová, N and Manimohan, P and Miller, AN and Mirabolfathy, M and Morozova, OV and Obodai, M and Oliveira, NT and Ordóñez, ME and Otto, EC and Paloi, S and Peterson, SW and Phosri, C and Roux, J and Salazar, WA and Sánchez, A and Sarria, GA and Shin, HD and Silva, BD and Silva, GA and Smith, MT and Souza-Motta, CM and Stchigel, AM and Stoilova-Disheva, MM and Sulzbacher, MA and Telleria, MT and Toapanta, C and Traba, JM and Valenzuela-Lopez, N and Watling, R and Groenewald, JZ},
title = {Fungal Planet description sheets: 400-468.},
journal = {Persoonia},
volume = {36},
number = {},
pages = {316-458},
pmid = {27616795},
issn = {0031-5850},
abstract = {Novel species of fungi described in the present study include the following from Australia: Vermiculariopsiella eucalypti, Mulderomyces natalis (incl. Mulderomyces gen. nov.), Fusicladium paraamoenum, Neotrimmatostroma paraexcentricum, and Pseudophloeospora eucalyptorum on leaves of Eucalyptus spp., Anungitea grevilleae (on leaves of Grevillea sp.), Pyrenochaeta acaciae (on leaves of Acacia sp.), and Brunneocarpos banksiae (incl. Brunneocarpos gen. nov.) on cones of Banksia attenuata. Novel foliicolous taxa from South Africa include Neosulcatispora strelitziae (on Strelitzia nicolai), Colletotrichum ledebouriae (on Ledebouria floridunda), Cylindrosympodioides brabejum (incl. Cylindrosympodioides gen. nov.) on Brabejum stellatifolium, Sclerostagonospora ericae (on Erica sp.), Setophoma cyperi (on Cyperus sphaerocephala), and Phaeosphaeria breonadiae (on Breonadia microcephala). Novelties described from Robben Island (South Africa) include Wojnowiciella cissampeli and Diaporthe cissampeli (both on Cissampelos capensis), Phaeotheca salicorniae (on Salicornia meyeriana), Paracylindrocarpon aloicola (incl. Paracylindrocarpon gen. nov.) on Aloe sp., and Libertasomyces myopori (incl. Libertasomyces gen. nov.) on Myoporum serratum. Several novelties are recorded from La Réunion (France), namely Phaeosphaeriopsis agapanthi (on Agapanthus sp.), Roussoella solani (on Solanum mauritianum), Vermiculariopsiella acaciae (on Acacia heterophylla), Dothiorella acacicola (on Acacia mearnsii), Chalara clidemiae (on Clidemia hirta), Cytospora tibouchinae (on Tibouchina semidecandra), Diaporthe ocoteae (on Ocotea obtusata), Castanediella eucalypticola, Phaeophleospora eucalypticola and Fusicladium eucalypticola (on Eucalyptus robusta), Lareunionomyces syzygii (incl. Lareunionomyces gen. nov.) and Parawiesneriomyces syzygii (incl. Parawiesneriomyces gen. nov.) on leaves of Syzygium jambos. Novel taxa from the USA include Meristemomyces arctostaphylos (on Arctostaphylos patula), Ochroconis dracaenae (on Dracaena reflexa), Rasamsonia columbiensis (air of a hotel conference room), Paecilomyces tabacinus (on Nicotiana tabacum), Toxicocladosporium hominis (from human broncoalveolar lavage fluid), Nothophoma macrospora (from respiratory secretion of a patient with pneumonia), and Penidiellopsis radicularis (incl. Penidiellopsis gen. nov.) from a human nail. Novel taxa described from Malaysia include Prosopidicola albizziae (on Albizzia falcataria), Proxipyricularia asari (on Asarum sp.), Diaporthe passifloricola (on Passiflora foetida), Paramycoleptodiscus albizziae (incl. Paramycoleptodiscus gen. nov.) on Albizzia falcataria, and Malaysiasca phaii (incl. Malaysiasca gen. nov.) on Phaius reflexipetalus. Two species are newly described from human patients in the Czech Republic, namely Microascus longicollis (from toenails of patient with suspected onychomycosis), and Chrysosporium echinulatum (from sole skin of patient). Furthermore, Alternaria quercicola is described on leaves of Quercus brantii (Iran), Stemphylium beticola on leaves of Beta vulgaris (The Netherlands), Scleroderma capeverdeanum on soil (Cape Verde Islands), Scleroderma dunensis on soil, and Blastobotrys meliponae from bee honey (Brazil), Ganoderma mbrekobenum on angiosperms (Ghana), Geoglossum raitviirii and Entoloma kruticianum on soil (Russia), Priceomyces vitoshaensis on Pterostichus melas (Carabidae) (Bulgaria) is the only one for which the family is listed, Ganoderma ecuadoriense on decaying wood (Ecuador), Thyrostroma cornicola on Cornus officinalis (Korea), Cercophora vinosa on decorticated branch of Salix sp. (France), Coprinus pinetorum, Coprinus littoralis and Xerocomellus poederi on soil (Spain). Two new genera from Colombia include Helminthosporiella and Uwemyces on leaves of Elaeis oleifera. Two species are described from India, namely Russula intervenosa (ectomycorrhizal with Shorea robusta), and Crinipellis odorata (on bark of Mytragyna parviflora). Novelties from Thailand include Cyphellophora gamsii (on leaf litter), Pisolithus aureosericeus and Corynascus citrinus (on soil). Two species are newly described from Citrus in Italy, namely Dendryphiella paravinosa on Citrus sinensis, and Ramularia citricola on Citrus floridana. Morphological and culture characteristics along with ITS nrDNA barcodes are provided for all taxa.},
}
@article {pmid27616793,
year = {2016},
author = {Sandoval-Denis, M and Gené, J and Sutton, DA and Wiederhold, NP and Cano-Lira, JF and Guarro, J},
title = {New species of Cladosporium associated with human and animal infections.},
journal = {Persoonia},
volume = {36},
number = {},
pages = {281-298},
pmid = {27616793},
issn = {0031-5850},
abstract = {Cladosporium is mainly known as a ubiquitous environmental saprobic fungus or plant endophyte, and to date, just a few species have been documented as etiologic agents in vertebrate hosts, including humans. In the present study, 10 new species of the genus were isolated from human and animal clinical specimens from the USA. They are proposed and characterized on the basis of their morphology and a molecular phylogenetic analysis using DNA sequences from three loci (the ITS region of the rDNA, and partial fragments of the translation elongation factor 1-alpha and actin genes). Six of those species belong to the C. cladosporioides species complex, i.e., C. alboflavescens, C. angulosum, C. anthropophilum, C. crousii, C. flavovirens and C. xantochromaticum, three new species belong to the C. herbarum species complex, i.e., C. floccosum, C. subcinereum and C. tuberosum; and one to the C. sphaerospermum species complex, namely, C. succulentum. Differential morphological features of the new taxa are provided together with molecular barcodes to distinguish them from the currently accepted species of the genus.},
}
@article {pmid27616789,
year = {2016},
author = {Wang, XW and Lombard, L and Groenewald, JZ and Li, J and Videira, SI and Samson, RA and Liu, XZ and Crous, PW},
title = {Phylogenetic reassessment of the Chaetomium globosum species complex.},
journal = {Persoonia},
volume = {36},
number = {},
pages = {83-133},
pmid = {27616789},
issn = {0031-5850},
abstract = {Chaetomium globosum, the type species of the genus, is ubiquitous, occurring on a wide variety of substrates, in air and in marine environments. This species is recognised as a cellulolytic and/or endophytic fungus. It is also known as a source of secondary metabolites with various biological activities, having great potential in the agricultural, medicinal and industrial fields. On the negative side, C. globosum has been reported as an air contaminant causing adverse health effects and as causal agent of human fungal infections. However, the taxonomic status of C. globosum is still poorly understood. The contemporary species concept for this fungus includes a broadly defined morphological diversity as well as a large number of synonymies with limited phylogenetic evidence. The aim of this study is, therefore, to resolve the phylogenetic limits of C. globosum s.str. and related species. Screening of isolates in the collections of the CBS-KNAW Fungal Biodiversity Centre (The Netherlands) and the China General Microbiological Culture Collection Centre (China) resulted in recognising 80 representative isolates of the C. globosum species complex. Thirty-six species are identified based on phylogenetic inference of six loci, supported by typical morphological characters, mainly ascospore shape. Of these, 12 species are newly described here. Additionally, C. cruentum, C. mollipilium, C. rectum, C. subterraneum and two varieties of C. globosum are synonymised under C. globosum s.str., and six species are resurrected, i.e. C. angustispirale, C. coarctatum, C. cochliodes, C. olivaceum, C. spiculipilium and C. subglobosum. Chaetomium ascotrichoides is segregated from C. madrasense and the genus name Chaetomidium is rejected. Five species, including C. globosum s.str., are typified here to stabilise their taxonomic status. A further evaluation of the six loci used in this study as potential barcodes indicated that the 28S large subunit (LSU) nrDNA and the internal transcribed spacer regions and intervening 5.8S nrRNA (ITS) gene regions were unreliable to resolve species, whereas β-tubulin (tub2) and RNA polymerase II second largest subunit (rpb2) showed the greatest promise as DNA barcodes for differentiating Chaetomium species. This study provides a starting point to establish a more robust classification system for Chaetomium and for the Chaetomiaceae.},
}
@article {pmid27615897,
year = {2016},
author = {Bogorodsky, SV and Alpermann, TJ and Mal, AO},
title = {Redescription of Cheilinus quinquecinctus Rüppell, 1835 (Pisces: Perciformes, Labridae), a valid endemic Red Sea wrasse.},
journal = {Zootaxa},
volume = {4158},
number = {4},
pages = {451-472},
doi = {10.11646/zootaxa.4158.4.1},
pmid = {27615897},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Ecosystem ; Female ; Indian Ocean ; Male ; Organ Size ; Perciformes/*anatomy &amp; histology/*classification/genetics/growth &amp; development ; Phylogeny ; },
abstract = {The labrid fish Cheilinus quinquecinctus Rüppell, originally described from the Red Sea, has long been regarded as a junior synonym of C. fasciatus (Bloch). Herein, both nominal species are redescribed, based on examination of the types and additional material from the Red Sea (for C. quinquecinctus) and the Indo-West Pacific (for C. fasciatus). Rüppell's description of Cheilinus quinquecinctus was originally based on three syntypes, and the most representative adult specimen is designated as the lectotype. We show that Cheilinus quinquecinctus is restricted to the Red Sea and the Gulf of Aden, and it differs from the similar C. fasciatus in having modally fewer gill rakers on the first gill arch, a total of 13-16 (mean 13.9, usually 13 or 14) (vs. 13-16, mean 14.7, usually 14 or 15), in developing a ragged posterior margin of the caudal fin with age (versus only upper and lower caudal-fin lobes developing with age), and in its color pattern. The phylogenetic analysis of the COI barcoding region accords with the species status of C. quinquecinctus with the placement of the two sister species in two divergent and reciprocally monophyletic evolutionary lineages. A full description of C. quinquecinctus and diagnosis of C. fasciatus is provided here for comparison. In addition, the data include a table of the results of the meristic and morphological examination of type and additional specimens of both species from throughout their distribution ranges as well as a table of gill-raker counts of all examined specimens. Underwater color photographs are provided for comparison of juveniles, females and males of both species.},
}
@article {pmid27615321,
year = {2016},
author = {Moravec, F and Gey, D and Justine, JL},
title = {Nematode parasites of four species of Carangoides (Osteichthyes: Carangidae) in New Caledonian waters, with a description of Philometra dispar n. sp. (Philometridae).},
journal = {Parasite (Paris, France)},
volume = {23},
number = {},
pages = {40},
pmid = {27615321},
issn = {1776-1042},
mesh = {Animals ; Ascaridoidea/classification/isolation &amp; purification/ultrastructure ; Dracunculoidea/classification/isolation &amp; purification/ultrastructure ; Female ; Fish Diseases/epidemiology/*parasitology ; Fishes ; Male ; Microscopy, Electron, Scanning/veterinary ; Nematoda/classification/genetics/*isolation &amp; purification/ultrastructure ; Nematode Infections/epidemiology/parasitology/*veterinary ; New Caledonia/epidemiology ; Spiruroidea/classification/isolation &amp; purification/ultrastructure ; },
abstract = {Parasitological examination of marine perciform fishes belonging to four species of Carangoides, i.e. C. chrysophrys, C. dinema, C. fulvoguttatus and C. hedlandensis (Carangidae), from off New Caledonia revealed the presence of nematodes. The identification of carangids was confirmed by barcoding of the COI gene. The eight nematode species found were: Capillariidae gen. sp. (females), Cucullanus bulbosus (Lane, 1916) (male and females), Hysterothylacium sp. third-stage larvae, Raphidascaris (Ichthyascaris) sp. (female and larvae), Terranova sp. third-stage larvae, Philometra dispar n. sp. (male), Camallanus carangis Olsen, 1954 (females) and Johnstonmawsonia sp. (female). The new species P. dispar from the abdominal cavity of C. dinema is mainly characterised by the body length (5.14 mm), the lengths of markedly unequal spicules (163 and 96 μm) and gubernaculum (102 μm long) provided with a dorsal protuberance and a small, reflexed dorsal barb on its posterior portion. The finding of C. bulbosus represents the first record of this parasite a century after its discovery; the first study of this species by scanning electron microscopy (SEM) enabled detailed redescription. The finding of Johnstonmawsonia sp. in C. fulvoguttatus is the first record of a rhabdochonid nematode from a host belonging to the Carangidae family. Johnstonmawsonia africana Moravec &amp; Puylaert, 1970 and J. campanae Puylaert, 1973 are transferred to Prosungulonema Roytman, 1963 as P. africanum (Moravec &amp; Puylaert, 1970) comb. n. and P. campanae (Puylaert, 1973) n. comb.},
}
@article {pmid27611699,
year = {2016},
author = {Adamowicz, SJ and Chain, FJ and Clare, EL and Deiner, K and Dincă, V and Elías-Gutiérrez, M and Hausmann, A and Hogg, ID and Kekkonen, M and Lijtmaer, DA and Naaum, A and Steinke, D and Valdez-Moreno, M and Van der Bank, M and Wilson, JJ and Xu, J},
title = {From Barcodes to Biomes: Special Issues from the 6th International Barcode of Life Conference.},
journal = {Genome},
volume = {59},
number = {9},
pages = {v-ix},
doi = {10.1139/gen-2016-0159},
pmid = {27611699},
issn = {1480-3321},
mesh = {Biodiversity ; *DNA Barcoding, Taxonomic ; *Genomics/methods ; },
}
@article {pmid27611698,
year = {2016},
author = {},
title = {Barcodes to Biomes / Codes barres pour biomes.},
journal = {Genome},
volume = {59},
number = {9},
pages = {iii},
doi = {10.1139/gen-2016-0156},
pmid = {27611698},
issn = {1480-3321},
}
@article {pmid27608754,
year = {2016},
author = {Yonehara, K and Roska, B},
title = {"MAPseq"-uencing Long-Range Neuronal Projections.},
journal = {Neuron},
volume = {91},
number = {5},
pages = {945-947},
doi = {10.1016/j.neuron.2016.08.029},
pmid = {27608754},
issn = {1097-4199},
mesh = {Brain ; Brain Mapping ; *Neurites ; *Neurons ; RNA, Messenger ; },
abstract = {Kebschull et al. (2016a) describe "MAPseq," which tags individual neurons from a specific brain region with individual mRNA barcodes and sequences these barcodes in other brain regions. This allows the simultaneous mapping of long-range neuronal projections at single-cell resolution.},
}
@article {pmid27608265,
year = {2016},
author = {Barreto, SB and Nunes, LA and da Silva, AT and Jucá-Chagas, R and Diniz, D and Sampaio, I and Schneider, H and Affonso, PR},
title = {Is Nematocharax (Actinopterygii, Characiformes) a monotypic fish genus?.},
journal = {Genome},
volume = {59},
number = {10},
pages = {851-865},
doi = {10.1139/gen-2015-0166},
pmid = {27608265},
issn = {1480-3321},
mesh = {Animals ; Brazil ; Characiformes/anatomy &amp; histology/*classification/*genetics ; Chromium Alloys ; Cobalt ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Genomics/methods ; Geography ; Haplotypes ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The combination of DNA barcodes and geometric morphometrics is useful to discriminate taxonomically controversial species, providing more precise estimates of biodiversity. Therefore, our goal was to assess the genetic and morphometric diversity in Nematocharax, a controversial monotypic and sexually dimorphic genus of Neotropical fish, based on sequencing of cytochrome c oxidase subunit I (COI) and morphometric analyses in seven populations of N. venustus from coastal rivers in Brazil. The average pairwise intrapopulation divergence in COI ranged from 0 to 2.2%, while the average pairwise interpopulation divergence varied from 0 to 7.5%. The neighbour-joining (NJ) tree resulted in five genetic groups (bootstrap ≥ 97%), which correspond to the five clusters delimited by the BIN System, GMYC, and bPTP, indicating that there might be at least five species (or OTUs) within Nematocharax. Morphometric differences among these genetic lineages were also identified. Apparently, sexual selection, restricted dispersal, and geographic isolation might have acted synergistically to cause the evolutionary split of populations. These data challenge the current view that Nematocharax is a monotypic genus inasmuch as evolutionarily significant units or even distinguished species were identified. Therefore, we recommend that the highly impacted coastal basins in northeastern Brazil should be prioritized in conservation plans.},
}
@article {pmid27607516,
year = {2017},
author = {Liu, G and Ning, H and Ayidaerhan, N and Aisa, HA},
title = {Evaluation of DNA barcode candidates for the discrimination of Artemisia L.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {6},
pages = {956-964},
doi = {10.1080/24701394.2016.1219729},
pmid = {27607516},
issn = {2470-1408},
mesh = {Artemisia/classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Plant ; *Genetic Variation ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Because of the very similar morphologies and wide diversity of Artemisia L. varieties, they are difficult to identify, and there have been many arguments about the systematic classification Artemisia L., especially concerning the division of species. DNA barcode technology is used to rapidly identify species based on standard short DNA sequences. To evaluate seven candidate DNA barcodes (ITS, ITS2, psbA-trnH, rbcL, matK, rpoB, and rpoC1) regarding their ability to identify closely related species of the Artemisia genus in Xinjiang. The corresponding PCR amplification efficiency, detectable genetic divergence, identification efficiency and phylogenetic tree were assessed. We found that the internal transcribed spacer (ITS) region exhibited the highest interspecific divergence, which was significantly higher than the observed intraspecific variation and showed the highest identification efficiency, followed by ITS2, psbA-trnH and, finally, rpoB. matK, rbcL, and rpoC1 performed poorly in this evaluation. ITS, ITS2, and psbA-trnH were able to perfectly identify the tested species Artemisia annua, A. absinthium, A. rupestris, A. tonurnefortiana, A. austriaca, A. dracunculus, A. vulgaris, and A. macrocephala. Therefore, we propose the ITS, ITS2, and psbA-trnH regions as promising DNA barcodes for the closely related species of Artemisia L. in Xinjiang.},
}
@article {pmid27603700,
year = {2016},
author = {Wang, FH and Lu, JM and Wen, J and Ebihara, A and Li, DZ},
title = {Applying DNA Barcodes to Identify Closely Related Species of Ferns: A Case Study of the Chinese Adiantum (Pteridaceae).},
journal = {PloS one},
volume = {11},
number = {9},
pages = {e0160611},
pmid = {27603700},
issn = {1932-6203},
mesh = {Adiantum/classification/*genetics ; China ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Ferns/classification/*genetics ; Species Specificity ; },
abstract = {DNA barcoding is a fast-developing technique to identify species by using short and standard DNA sequences. Universal selection of DNA barcodes in ferns remains unresolved. In this study, five plastid regions (rbcL, matK, trnH-psbA, trnL-F and rps4-trnS) and eight nuclear regions (ITS, pgiC, gapC, LEAFY, ITS2, IBR3_2, DET1, and SQD1_1) were screened and evaluated in the fern genus Adiantum from China and neighboring areas. Due to low primer universality (matK) and/or the existence of multiple copies (ITS), the commonly used barcodes matK and ITS were not appropriate for Adiantum. The PCR amplification rate was extremely low in all nuclear genes except for IBR3_2. rbcL had the highest PCR amplification rate (94.33%) and sequencing success rate (90.78%), while trnH-psbA had the highest species identification rate (75%). With the consideration of discriminatory power, cost-efficiency and effort, the two-barcode combination of rbcL+ trnH-psbA seems to be the best choice for barcoding Adiantum, and perhaps basal polypod ferns in general. The nuclear IBR3_2 showed 100% PCR amplification success rate in Adiantum, however, it seemed that only diploid species could acquire clean sequences without cloning. With cloning, IBR3_2 can successfully distinguish cryptic species and hybrid species from their related species. Because hybridization and allopolyploidy are common in ferns, we argue for including a selected group of nuclear loci as barcodes, especially via the next-generation sequencing, as it is much more efficient to obtain single-copy nuclear loci without the cloning procedure.},
}
@article {pmid27603265,
year = {2016},
author = {Ankenbrand, MJ and Keller, A},
title = {bcgTree: automatized phylogenetic tree building from bacterial core genomes.},
journal = {Genome},
volume = {59},
number = {10},
pages = {783-791},
doi = {10.1139/gen-2015-0175},
pmid = {27603265},
issn = {1480-3321},
mesh = {Bacteria/*classification/*genetics ; Computational Biology/*methods ; *Genome, Bacterial ; Lactobacillus/classification/genetics ; Markov Chains ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; *Software ; Web Browser ; Workflow ; },
abstract = {The need for multi-gene analyses in scientific fields such as phylogenetics and DNA barcoding has increased in recent years. In particular, these approaches are increasingly important for differentiating bacterial species, where reliance on the standard 16S rDNA marker can result in poor resolution. Additionally, the assembly of bacterial genomes has become a standard task due to advances in next-generation sequencing technologies. We created a bioinformatic pipeline, bcgTree, which uses assembled bacterial genomes either from databases or own sequencing results from the user to reconstruct their phylogenetic history. The pipeline automatically extracts 107 essential single-copy core genes, found in a majority of bacteria, using hidden Markov models and performs a partitioned maximum-likelihood analysis. Here, we describe the workflow of bcgTree and, as a proof-of-concept, its usefulness in resolving the phylogeny of 293 publically available bacterial strains of the genus Lactobacillus. We also evaluate its performance in both low- and high-level taxonomy test sets. The tool is freely available at github (https://github.com/iimog/bcgTree) and our institutional homepage (http://www.dna-analytics.biozentrum.uni-wuerzburg.de).},
}
@article {pmid27602259,
year = {2016},
author = {Chaabane, A and Justine, JL and Gey, D and Bakenhaster, MD and Neifar, L},
title = {Pseudorhabdosynochus sulamericanus (Monogenea, Diplectanidae), a parasite of deep-sea groupers (Serranidae) occurs transatlantically on three congeneric hosts (Hyporthodus spp.), one from the Mediterranean Sea and two from the western Atlantic.},
journal = {PeerJ},
volume = {4},
number = {},
pages = {e2233},
pmid = {27602259},
issn = {2167-8359},
abstract = {Little is known of the diversity of the monogenean parasites infesting deep-sea groupers, and there is even less information available about their geographic distributions within the ranges of their hosts. To improve our understanding of these host-parasite relationships we conducted parasitological evaluations of the deep-water Haifa grouper Hyporthodus haifensis from the southern Mediterranean off Tunisia and Libya. We collected more than one species of diplectanid monogeneans from this host, but among these only one dominant species was abundant. This proved to be morphologically very similar to Pseudorhabdosynochus sulamericanus Santos, Buchmann &amp; Gibson, 2000, a species originally described from the congeneric host H. niveatus off Brazil and also recorded from H. niveatus and H. nigritus off Florida. Here, we conducted a morphological comparison between newly collected specimens and those previously deposited in museum collections by other authors. Further, we used COI barcoding to ascertain the specific identity of the three host species to better elucidate the circumstances that might explain the unexpectedly broad distribution of P. sulamericanus. We assigned our specimens from H. haifensis to P. sulamericanus primarily on the basis of morphological characteristics of the sclerotized vagina. We also noted morphological characteristics of eastern and western Atlantic specimens that are not clearly described or not given in previous descriptions and so prepared a redescription of the species. We confirmed, by COI barcoding, that no sister-species relationships were evident among the three hosts of P. sulamericanus. Our observation that P. sulamericanus infects unrelated host species with putatively allopatric distributions was unexpected given the very limited dispersive capabilities and the high degree of host specificity common to members of Pseudorhabdosynochus. This transatlantic distribution raises questions with regard to phylogeography and assumptions about the allopatry of Atlantic grouper species from the Americas and Afro-Eurasia. Here, we propose some hypothetical explanations for our findings.},
}
@article {pmid27601530,
year = {2016},
author = {Gosselin, P and Rando, G and Fleury-Olela, F and Schibler, U},
title = {Unbiased identification of signal-activated transcription factors by barcoded synthetic tandem repeat promoter screening (BC-STAR-PROM).},
journal = {Genes &amp; development},
volume = {30},
number = {16},
pages = {1895-1907},
pmid = {27601530},
issn = {1549-5477},
mesh = {Animals ; Antineoplastic Agents/pharmacology ; Cell Line ; Cytoskeleton/drug effects ; Depsipeptides/pharmacology ; Gene Knockdown Techniques ; Genes, Synthetic ; Genetic Association Studies/*methods ; Genetic Techniques/standards ; Humans ; Mice ; Promoter Regions, Genetic/*genetics ; Serum Response Factor/genetics ; Signal Transduction ; Tandem Repeat Sequences/*genetics ; Transcription Factors/*genetics ; Vinblastine/pharmacology ; },
abstract = {The discovery of transcription factors (TFs) controlling pathways in health and disease is of paramount interest. We designed a widely applicable method, dubbed barcorded synthetic tandem repeat promoter screening (BC-STAR-PROM), to identify signal-activated TFs without any a priori knowledge about their properties. The BC-STAR-PROM library consists of ∼3000 luciferase expression vectors, each harboring a promoter (composed of six tandem repeats of synthetic random DNA) and an associated barcode of 20 base pairs (bp) within the 3' untranslated mRNA region. Together, the promoter sequences encompass >400,000 bp of random DNA, a sequence complexity sufficient to capture most TFs. Cells transfected with the library are exposed to a signal, and the mRNAs that it encodes are counted by next-generation sequencing of the barcodes. This allows the simultaneous activity tracking of each of the ∼3000 synthetic promoters in a single experiment. Here we establish proof of concept for BC-STAR-PROM by applying it to the identification of TFs induced by drugs affecting actin and tubulin cytoskeleton dynamics. BC-STAR-PROM revealed that serum response factor (SRF) is the only immediate early TF induced by both actin polymerization and microtubule depolymerization. Such changes in cytoskeleton dynamics are known to occur during the cell division cycle, and real-time bioluminescence microscopy indeed revealed cell-autonomous SRF-myocardin-related TF (MRTF) activity bouts in proliferating cells.},
}
@article {pmid27597158,
year = {2016},
author = {Zlatogursky, VV and Kudryavtsev, A and Udalov, IA and Bondarenko, N and Pawlowski, J and Smirnov, A},
title = {Genetic structure of a morphological species within the amoeba genus Korotnevella (Amoebozoa: Discosea), revealed by the analysis of two genes.},
journal = {European journal of protistology},
volume = {56},
number = {},
pages = {102-111},
doi = {10.1016/j.ejop.2016.08.001},
pmid = {27597158},
issn = {1618-0429},
mesh = {Amoebozoa/cytology/*genetics ; Ecosystem ; Electron Transport Complex IV/genetics ; Fresh Water/parasitology ; Genes, Protozoan/*genetics ; Polymorphism, Genetic ; RNA, Ribosomal, 18S/genetics ; Russia ; },
abstract = {Amoebae of the genus Korotnevella are covered with scales, the structure of which is believed to be species-specific and allows distinguishing species reliably at the morphological level. We studied members of this genus in order to assess the genetic structure of the local populations of amoebae. For the present study we isolated nine freshwater strains of Korotnevella, belonging to three species, from two locations in North-Western Russia. In order to obtain data on the population structure of these amoebae, we identified all isolates based on the light-microscopic morphology and scale structure and investigated both inter-strain and intra-strain polymorphism of Cox I and 18S rRNA genes. Results show that both genes provide congruent patterns of population structure. The Cox I gene appears to be more reliable DNA barcode while the 18S rRNA gene shows an interesting pattern of polymorphism, which may represent phylotypes of amoebae. Local population of amoebae in every studied species consists of a number of genetic lineages (phylotypes), some shared between the populations while others are unique to a local habitat.},
}
@article {pmid27595914,
year = {2016},
author = {Williamson, J and Maurin, O and Shiba, SN and van der Bank, H and Pfab, M and Pilusa, M and Kabongo, RM and van der Bank, M},
title = {Exposing the illegal trade in cycad species (Cycadophyta: Encephalartos) at two traditional medicine markets in South Africa using DNA barcoding.},
journal = {Genome},
volume = {59},
number = {9},
pages = {771-781},
doi = {10.1139/gen-2016-0032},
pmid = {27595914},
issn = {1480-3321},
mesh = {Biodiversity ; Cycadopsida/*classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Intergenic ; DNA, Plant ; *Medicine, Traditional ; Phylogeny ; South Africa ; },
abstract = {Species in the cycad genus Encephalartos are listed in CITES Appendix I and as Threatened or Protected Species in terms of South Africa's National Environmental Management: Biodiversity Act (NEM:BA) of 2004. Despite regulations, illegal plant harvesting for medicinal trade has continued in South Africa and resulted in declines in cycad populations and even complete loss of sub-populations. Encephalartos is traded at traditional medicine markets in South Africa in the form of bark strips and stem sections; thus, determining the species traded presents a major challenge due to a lack of characteristic plant parts. Here, a case study is presented on the use of DNA barcoding to identify cycads sold at the Faraday and Warwick traditional medicine markets in Johannesburg and Durban, respectively. Market samples were sequenced for the core DNA barcodes (rbcLa and matK) as well as two additional regions: nrITS and trnH-psbA. The barcoding database for cycads at the University of Johannesburg was utilized to assign query samples to known species. Three approaches were followed: tree-based, similarity-based, and character-based (BRONX) methods. Market samples identified were Encephalartos ferox (Near Threatened), Encephalartos lebomboensis (Endangered), Encephalartos natalensis (Near Threatened), Encephalartos senticosus (Vulnerable), and Encephalartos villosus (Least Concern). Results from this study are crucial for making appropriate assessments and decisions on how to manage these markets.},
}
@article {pmid27594428,
year = {2016},
author = {Venkataram, S and Dunn, B and Li, Y and Agarwala, A and Chang, J and Ebel, ER and Geiler-Samerotte, K and Hérissant, L and Blundell, JR and Levy, SF and Fisher, DS and Sherlock, G and Petrov, DA},
title = {Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast.},
journal = {Cell},
volume = {166},
number = {6},
pages = {1585-1596.e22},
pmid = {27594428},
issn = {1097-4172},
support = {R01 GM115919/GM/NIGMS NIH HHS/United States ; R01 GM110275/GM/NIGMS NIH HHS/United States ; R01 HD036601/HD/NICHD NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; R35 GM118165/GM/NIGMS NIH HHS/United States ; S10 RR027431/RR/NCRR NIH HHS/United States ; R01 GM097415/GM/NIGMS NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; R01 HG003328/HG/NHGRI NIH HHS/United States ; },
mesh = {Adaptation, Physiological/*genetics ; Diploidy ; *Evolution, Molecular ; Genetic Fitness/*genetics ; *Genetic Techniques ; Genome, Fungal/genetics ; Genotype ; Haploidy ; Mutagenesis ; Mutation ; Saccharomyces cerevisiae/*genetics/*metabolism ; },
abstract = {Adaptive evolution plays a large role in generating the phenotypic diversity observed in nature, yet current methods are impractical for characterizing the molecular basis and fitness effects of large numbers of individual adaptive mutations. Here, we used a DNA barcoding approach to generate the genotype-to-fitness map for adaptation-driving mutations from a Saccharomyces cerevisiae population experimentally evolved by serial transfer under limiting glucose. We isolated and measured the fitness of thousands of independent adaptive clones and sequenced the genomes of hundreds of clones. We found only two major classes of adaptive mutations: self-diploidization and mutations in the nutrient-responsive Ras/PKA and TOR/Sch9 pathways. Our large sample size and precision of measurement allowed us to determine that there are significant differences in fitness between mutations in different genes, between different paralogs, and even between different classes of mutations within the same gene.},
}
@article {pmid27593700,
year = {2016},
author = {Qin, Y and Man, B and Kosakyan, A and Lara, E and Gu, Y and Wang, H and Mitchell, EA},
title = {Nebela jiuhuensis nov. sp. (Amoebozoa; Arcellinida; Hyalospheniidae): A New Member of the Nebela saccifera - equicalceus - ansata Group Described from Sphagnum Peatlands in South-Central China.},
journal = {The Journal of eukaryotic microbiology},
volume = {63},
number = {5},
pages = {558-566},
doi = {10.1111/jeu.12300},
pmid = {27593700},
issn = {1550-7408},
mesh = {Amoeba/classification ; Amoebozoa/*classification/cytology/genetics/*isolation &amp; purification ; Animals ; Biodiversity ; China ; Classification ; DNA, Protozoan ; Ecology ; Ecosystem ; Electron Transport Complex IV/genetics ; Environmental Pollution ; Lobosea/*classification/cytology/genetics/*isolation &amp; purification ; Microscopy, Electron, Scanning ; Mitochondria/enzymology ; *Phylogeny ; Phylogeography ; Soil/parasitology ; Species Specificity ; Sphagnopsida/*parasitology ; },
abstract = {Hyalospheniids are among the most common and conspicuous testate amoebae in high-latitude peatlands and forest humus. These testate amoebae were widely studied as bioindicators and are increasingly used as models in microbial biogeography. However, data on their diversity and ecology are still very unevenly distributed geographically: notably, data are lacking for low-latitude peatlands. We describe here a new species, Nebela jiuhuensis, from peatlands near the Middle Yangtze River reach of south-central China with characteristic morphology. The test (shell) has hollow horn-like lateral extensions also found in N. saccifera, N. equicalceus (=N. hippocrepis), and N. ansata, three large species restricted mostly to Sphagnum peatlands of Eastern North America. Mitochondrial cytochrome oxidase (COI) data confirm that N. jiuhuensis is closely related to the morphologically very similar North American species N. saccifera and more distantly to N. ansata within the N. penardiana group. These species are all found in wet mosses growing in poor fens. Earlier reports of morphologically similar specimens found in South Korea peatlands suggest that N. jiuhuensis may be distributed in comparable peatlands in Eastern Asia (China and Korea). The discovery of such a conspicuous new species in Chinese peatlands suggests that many new testate amoebae species are yet to be discovered, including potential regional endemics. Furthermore, human activities (e.g., drainage, agriculture, and pollution) have reduced the known habitat of N. jiuhuensis, which can thus be considered as locally endangered. We, therefore, suggest that this very conspicuous micro-organism with a probably limited geographical distribution and specific habitat requirement should be considered as a flagship species for microbial biogeography as well as local environmental conservation and management.},
}
@article {pmid27593164,
year = {2016},
author = {Arrigoni, R and Berumen, ML and Chen, CA and Terraneo, TI and Baird, AH and Payri, C and Benzoni, F},
title = {Species delimitation in the reef coral genera Echinophyllia and Oxypora (Scleractinia, Lobophylliidae) with a description of two new species.},
journal = {Molecular phylogenetics and evolution},
volume = {105},
number = {},
pages = {146-159},
doi = {10.1016/j.ympev.2016.08.023},
pmid = {27593164},
issn = {1095-9513},
mesh = {Animals ; Anthozoa/*classification/genetics ; Comoros ; Coral Reefs ; Indian Ocean Islands ; Phylogeny ; },
abstract = {Scleractinian corals are affected by environment-induced phenotypic plasticity and intraspecific morphological variation caused by genotype. In an effort to identify new strategies for resolving this taxonomic issue, we applied a molecular approach for species evaluation to two closely related genera, Echinophyllia and Oxypora, for which few molecular data are available. A robust multi-locus phylogeny using DNA sequence data across four loci of both mitochondrial (COI, ATP6-NAD4) and nuclear (histone H3, ITS region) origin from 109 coral colonies was coupled with three independent putative species delimitation methods based on barcoding threshold (ABGD) and coalescence theory (PTP, GMYC). Observed overall congruence across multiple genetic analyses distinguished two traditional species (E. echinoporoides and O. convoluta), a species complex composed of E. aspera, E. orpheensis, E. tarae, and O. glabra, whereas O. lacera and E. echinata were indistinguishable with the sequenced loci. The combination of molecular species delimitation approaches and skeletal character observations allowed the description of two new reef coral species, E. bulbosa sp. n. from the Red Sea and E. gallii sp. n. from the Maldives and Mayotte. This work demonstrated the efficiency of multi-locus phylogenetic analyses and recently developed molecular species delimitation approaches as valuable tools to disentangle taxonomic issues caused by morphological ambiguities and to re-assess the diversity of scleractinian corals.},
}
@article {pmid27587784,
year = {2016},
author = {Nislow, C and Wong, LH and Lee, AH and Giaever, G},
title = {Functional Genomics Using the Saccharomyces cerevisiae Yeast Deletion Collections.},
journal = {Cold Spring Harbor protocols},
volume = {2016},
number = {9},
pages = {},
doi = {10.1101/pdb.top080945},
pmid = {27587784},
issn = {1559-6095},
support = {//CIHR/Canada ; },
mesh = {*Gene Expression Regulation, Fungal ; Gene Library ; *Genes, Fungal ; Genomics ; Saccharomyces cerevisiae/*genetics/*physiology ; Saccharomyces cerevisiae Proteins/*genetics/*metabolism ; *Sequence Deletion ; },
abstract = {Constructed by a consortium of 16 laboratories, the Saccharomyces genome-wide deletion collections have, for the past decade, provided a powerful, rapid, and inexpensive approach for functional profiling of the yeast genome. Loss-of-function deletion mutants were systematically created using a polymerase chain reaction (PCR)-based gene deletion strategy to generate a start-to-stop codon replacement of each open reading frame by homologous recombination. Each strain carries two molecular barcodes that serve as unique strain identifiers, enabling their growth to be analyzed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays or through the use of next-generation sequencing technologies. Functional profiling of the deletion collections, using either strain-by-strain or parallel assays, provides an unbiased approach to systematically survey the yeast genome. The Saccharomyces yeast deletion collections have proved immensely powerful in contributing to the understanding of gene function, including functional relationships between genes and genetic pathways in response to diverse genetic and environmental perturbations.},
}
@article {pmid27587778,
year = {2016},
author = {Suresh, S and Schlecht, U and Xu, W and Miranda, M and Davis, RW and Nislow, C and Giaever, G and St Onge, RP},
title = {Identification of Chemical-Genetic Interactions via Parallel Analysis of Barcoded Yeast Strains.},
journal = {Cold Spring Harbor protocols},
volume = {2016},
number = {9},
pages = {},
doi = {10.1101/pdb.prot088054},
pmid = {27587778},
issn = {1559-6095},
support = {P01 HG000205/HG/NHGRI NIH HHS/United States ; R01 HG003317/HG/NHGRI NIH HHS/United States ; //CIHR/Canada ; },
mesh = {Antifungal Agents/*pharmacology ; Drug Evaluation, Preclinical/*methods ; *Gene Deletion ; Gene Library ; *Genes, Fungal ; Genetic Testing ; Growth Inhibitors/*pharmacology ; Saccharomyces cerevisiae/*drug effects/genetics/*growth &amp; development ; },
abstract = {The Yeast Knockout Collection is a complete set of gene deletion strains for the budding yeast, Saccharomyces cerevisiae In each strain, one of approximately 6000 open-reading frames is replaced with a dominant selectable marker flanked by two DNA barcodes. These barcodes, which are unique to each gene, allow the growth of thousands of strains to be individually measured from a single pooled culture. The collection, and other resources that followed, has ushered in a new era in chemical biology, enabling unbiased and systematic identification of chemical-genetic interactions (CGIs) with remarkable ease. CGIs link bioactive compounds to biological processes, and hence can reveal the mechanism of action of growth-inhibitory compounds in vivo, including those of antifungal, antibiotic, and anticancer drugs. The chemogenomic profiling method described here measures the sensitivity induced in yeast heterozygous and homozygous deletion strains in the presence of a chemical inhibitor of growth (termed haploinsufficiency profiling and homozygous profiling, respectively, or HIPHOP). The protocol is both scalable and amenable to automation. After competitive growth of yeast knockout collection cultures, with and without chemical inhibitors, CGIs can be identified and quantified using either array- or sequencing-based approaches as described here.},
}
@article {pmid27587776,
year = {2016},
author = {Nislow, C and Wong, LH and Lee, AH and Giaever, G},
title = {Functional Profiling Using the Saccharomyces Genome Deletion Project Collections.},
journal = {Cold Spring Harbor protocols},
volume = {2016},
number = {9},
pages = {},
doi = {10.1101/pdb.prot088039},
pmid = {27587776},
issn = {1559-6095},
mesh = {*Gene Library ; Genes, Fungal ; Genetics, Microbial/methods ; *Genome, Fungal ; Microbiological Techniques/methods ; Molecular Biology/methods ; Saccharomyces cerevisiae/*genetics/*physiology ; Saccharomyces cerevisiae Proteins/*genetics/*metabolism ; *Sequence Deletion ; },
abstract = {The ability to measure and quantify the fitness of an entire organism requires considerably more complex approaches than simply using traditional "omic" methods that examine, for example, the abundance of RNA transcripts, proteins, or metabolites. The yeast deletion collections represent the only systematic, comprehensive set of null alleles for any organism in which such fitness measurements can be assayed. Generated by the Saccharomyces Genome Deletion Project, these collections allow the systematic and parallel analysis of gene functions using any measurable phenotype. The unique 20-bp molecular barcodes engineered into the genome of each deletion strain facilitate the massively parallel analysis of individual fitness. Here, we present functional genomic protocols for use with the yeast deletion collections. We describe how to maintain, propagate, and store the deletion collections and how to perform growth fitness assays on single and parallel screening platforms. Phenotypic fitness analyses of the yeast mutants, described in brief here, provide important insights into biological functions, mechanisms of drug action, and response to environmental stresses. It is important to bear in mind that the specific assays described in this protocol represent some of the many ways in which these collections can be assayed, and in this description particular attention is paid to maximizing throughput using growth as the phenotypic measure.},
}
@article {pmid27584940,
year = {2016},
author = {Al-Rshaidat, MM and Snider, A and Rosebraugh, S and Devine, AM and Devine, TD and Plaisance, L and Knowlton, N and Leray, M},
title = {Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea.},
journal = {Genome},
volume = {59},
number = {9},
pages = {724-737},
doi = {10.1139/gen-2015-0208},
pmid = {27584940},
issn = {1480-3321},
mesh = {Animals ; Anthozoa/*classification/*genetics ; *Biodiversity ; *Coral Reefs ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Geography ; *High-Throughput Nucleotide Sequencing ; Indian Ocean ; Jordan ; Phylogeny ; },
abstract = {High-throughput sequencing (HTS) of DNA barcodes (metabarcoding), particularly when combined with standardized sampling protocols, is one of the most promising approaches for censusing overlooked cryptic invertebrate communities. We present biodiversity estimates based on sequencing of the cytochrome c oxidase subunit 1 (COI) gene for coral reefs of the Gulf of Aqaba, a semi-enclosed system in the northern Red Sea. Samples were obtained from standardized sampling devices (Autonomous Reef Monitoring Structures (ARMS)) deployed for 18 months. DNA barcoding of non-sessile specimens >2 mm revealed 83 OTUs in six phyla, of which only 25% matched a reference sequence in public databases. Metabarcoding of the 2 mm - 500 μm and sessile bulk fractions revealed 1197 OTUs in 15 animal phyla, of which only 4.9% matched reference barcodes. These results highlight the scarcity of COI data for cryptobenthic organisms of the Red Sea. Compared with data obtained using similar methods, our results suggest that Gulf of Aqaba reefs are less diverse than two Pacific coral reefs but much more diverse than an Atlantic oyster reef at a similar latitude. The standardized approaches used here show promise for establishing baseline data on biodiversity, monitoring the impacts of environmental change, and quantifying patterns of diversity at regional and global scales.},
}
@article {pmid27584861,
year = {2016},
author = {Janzen, DH and Hallwachs, W},
title = {DNA barcoding the Lepidoptera inventory of a large complex tropical conserved wildland, Area de Conservacion Guanacaste, northwestern Costa Rica.},
journal = {Genome},
volume = {59},
number = {9},
pages = {641-660},
doi = {10.1139/gen-2016-0005},
pmid = {27584861},
issn = {1480-3321},
mesh = {Animals ; Biodiversity ; Cluster Analysis ; Conservation of Natural Resources ; Costa Rica ; *DNA Barcoding, Taxonomic ; Lepidoptera/*classification/*genetics ; Tropical Climate ; },
abstract = {The 37-year ongoing inventory of the estimated 15 000 species of Lepidoptera living in the 125 000 terrestrial hectares of Area de Conservacion Guanacaste, northwestern Costa Rica, has DNA barcode documented 11 000+ species, and the simultaneous inventory of at least 6000+ species of wild-caught caterpillars, plus 2700+ species of parasitoids. The inventory began with Victorian methodologies and species-level perceptions, but it was transformed in 2004 by the full application of DNA barcoding for specimen identification and species discovery. This tropical inventory of an extraordinarily species-rich and complex multidimensional trophic web has relied upon the sequencing services provided by the Canadian Centre for DNA Barcoding, and the informatics support from BOLD, the Barcode of Life Data Systems, major tools developed by the Centre for Biodiversity Genomics at the Biodiversity Institute of Ontario, and available to all through couriers and the internet. As biodiversity information flows from these many thousands of undescribed and often look-alike species through their transformations to usable product, we see that DNA barcoding, firmly married to our centuries-old morphology-, ecology-, microgeography-, and behavior-based ways of taxonomizing the wild world, has made possible what was impossible before 2004. We can now work with all the species that we find, as recognizable species-level units of biology. In this essay, we touch on some of the details of the mechanics of actually using DNA barcoding in an inventory.},
}
@article {pmid27582332,
year = {2016},
author = {Mei, Q and Chen, X and Xiang, L and Liu, Y and Su, Y and Gao, Y and Dai, W and Dong, P and Chen, S},
title = {DNA Barcode for Identifying Folium Artemisiae Argyi from Counterfeits.},
journal = {Biological &amp; pharmaceutical bulletin},
volume = {39},
number = {9},
pages = {1531-1537},
doi = {10.1248/bpb.b16-00336},
pmid = {27582332},
issn = {1347-5215},
mesh = {Artemisia/classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Phylogeny ; Plant Leaves/classification/*genetics ; Species Specificity ; },
abstract = {Folium Artemisiae Argyi is an important herb in traditional Chinese medicine. It is commonly used in moxibustion, medicine, etc. However, identifying Artemisia argyi is difficult because this herb exhibits similar morphological characteristics to closely related species and counterfeits. To verify the applicability of DNA barcoding, ITS2 and psbA-trnH were used to identify A. argyi from 15 closely related species and counterfeits. Results indicated that total DNA was easily extracted from all the samples and that both ITS2 and psbA-trnH fragments can be easily amplified. ITS2 was a more ideal barcode than psbA-trnH and ITS2+psbA-trnH to identify A. argyi from closely related species and counterfeits on the basis of sequence character, genetic distance, and tree methods. The sequence length was 225 bp for the 56 ITS2 sequences of A. argyi, and no variable site was detected. For the ITS2 sequences, A. capillaris, A. anomala, A. annua, A. igniaria, A. maximowicziana, A. princeps, Dendranthema vestitum, and D. indicum had single nucleotide polymorphisms (SNPs). The intraspecific Kimura 2-Parameter distance was zero, which is lower than the minimum interspecific distance (0.005). A. argyi, the closely related species, and counterfeits, except for Artemisia maximowicziana and Artemisia sieversiana, were separated into pairs of divergent clusters by using the neighbor joining, maximum parsimony, and maximum likelihood tree methods. Thus, the ITS2 sequence was an ideal barcode to identify A. argyi from closely related species and counterfeits to ensure the safe use of this plant.},
}
@article {pmid27581143,
year = {2016},
author = {Jelinek, J and Madzo, J},
title = {DREAM: A Simple Method for DNA Methylation Profiling by High-throughput Sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1465},
number = {},
pages = {111-127},
doi = {10.1007/978-1-4939-4011-0_10},
pmid = {27581143},
issn = {1940-6029},
support = {P01 CA049639/CA/NCI NIH HHS/United States ; },
mesh = {CpG Islands ; *DNA Methylation ; DNA Primers ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Restriction Mapping/*methods ; Sequence Analysis, DNA/*methods ; },
abstract = {The digital restriction enzyme analysis of methylation (DREAM) is a simple method for DNA methylation analysis at tens of thousands of CpG sites across the genome. The method creates specific signatures at unmethylated and methylated CpG sites by sequential digests of genomic DNA with restriction endonucleases SmaI and XmaI, respectively. Both enzymes have the same CCCGGG recognition site; however, they differ in their sensitivity to CpG methylation and their cutting pattern. SmaI cuts only unmethylated sites leaving blunt 5'-GGG ends. XmaI cuts remaining methylated CC(me)CGG sites leaving 5'-CCGGG ends. Restriction fragments with distinct signatures at their ends are ligated to Illumina sequencing adaptors with sample-specific barcodes. High-throughput sequencing of pooled libraries follows. Sequencing reads are mapped to the restriction sites in the reference genome, and signatures corresponding to methylation status of individual DNA molecules are resolved. Methylation levels at target CpG sites are calculated as the proportion of sequencing reads with the methylated signature to the total number of reads mapping to the particular restriction site. Aligning the reads to the reference genome of any species is straightforward, since the method does not rely on bisulfite conversion of DNA. Sequencing of 25 million reads per human DNA library yields over 50,000 unique CpG sites with high coverage enabling accurate determination of DNA methylation levels. DREAM has a background less than 1 % making it suitable for accurate detection of low methylation levels. In summary, the method is simple, robust, highly reproducible, and cost-effective.},
}
@article {pmid27572819,
year = {2017},
author = {Chroni, A and Djan, M and Vidaković, DO and Petanidou, T and Vujić, A},
title = {Molecular species delimitation in the genus Eumerus (Diptera: Syrphidae).},
journal = {Bulletin of entomological research},
volume = {107},
number = {1},
pages = {126-138},
doi = {10.1017/S0007485316000729},
pmid = {27572819},
issn = {1475-2670},
mesh = {Africa ; Animals ; DNA Barcoding, Taxonomic ; Diptera/*classification/*genetics ; Electron Transport Complex IV/*genetics ; Europe ; *Genetic Variation ; Insect Proteins/*genetics ; Mitochondrial Proteins/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Eumerus is one of the most diverse genera of hoverfly worldwide. Species delimitation within genus is considered to be difficult due to: (a) lack of an efficient key; (b) non-defined taxonomical status of a large number of species; and (c) blurred nomenclature. Here, we present the first molecular study to delimit species of the genus by using a fragment of the mitochondrial cytochrome-c oxidase subunit I gene (COI) gene. We assessed 75 specimens assigned to 28 taxa originating from two biogeographic zones: 22 from the western Palaearctic and six from the Afrotropical region. Two datasets were generated based on different sequence lengths to explore the significance of availability of more polymorphic sites for species delimitation; dataset A with a total length of 647 bp and dataset B with 746 bp. Various tree inference approaches and Poisson tree processes models were applied to evaluate the putative 'taxonomical' vs. 'molecular' taxa clusters. All analyses resulted in high taxonomic resolution and clear species delimitation for both the dataset lengths. Furthermore, we revealed a high number of mitochondrial haplotypes and high intraspecific variability. We report two major monophyletic clades, and seven 'molecular' groups of taxa formed, which are congruent with morphology-based taxonomy. Our results support the use of the mitochondrial COI gene in species diagnosis of Eumerus.},
}
@article {pmid27571850,
year = {2016},
author = {Pérez-Ponce DE León, G and García-Varela, M and Pinacho-Pinacho, CD and Sereno-Uribe, AL and Poulin, R},
title = {Species delimitation in trematodes using DNA sequences: Middle-American Clinostomum as a case study.},
journal = {Parasitology},
volume = {143},
number = {13},
pages = {1773-1789},
doi = {10.1017/S0031182016001517},
pmid = {27571850},
issn = {1469-8161},
mesh = {Animals ; Central America ; Cluster Analysis ; DNA, Helminth/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; *Phylogeny ; Sequence Analysis, DNA ; Trematoda/*classification/*genetics ; },
abstract = {The recent development of genetic methods allows the delineation of species boundaries, especially in organisms where morphological characters are not reliable to differentiate species. However, few empirical studies have used these tools to delineate species among parasitic metazoans. Here we investigate the species boundaries of Clinostomum, a cosmopolitan trematode genus with complex life cycle. We sequenced a mitochondrial [cytochrome c oxidase subunit I (COI)] gene for multiple individuals (adults and metacercariae) from Middle-America. Bayesian phylogenetic analysis of the COI uncovered five reciprocally monophyletic clades. COI sequences were then explored using the Automatic Barcode Gap Discovery to identify putative species; this species delimitation method recognized six species. A subsample was sequenced for a nuclear gene (ITS1, 5·8S, ITS2), and a concatenated phylogenetic analysis was performed through Bayesian inference. The species delimitation of Middle-American Clinostomum was finally validated using a multispecies coalescent analysis (species tree). In total, five putative species are recognized among our samples. Mapping the second intermediate hosts (fish) onto the species tree suggests that metacercariae of these five species exhibit some level of host specificity towards their fish intermediate host (at the family level), irrespective of geographical distribution.},
}
@article {pmid27571370,
year = {2016},
author = {Bentzen, AK and Marquard, AM and Lyngaa, R and Saini, SK and Ramskov, S and Donia, M and Such, L and Furness, AJ and McGranahan, N and Rosenthal, R and Straten, PT and Szallasi, Z and Svane, IM and Swanton, C and Quezada, SA and Jakobsen, SN and Eklund, AC and Hadrup, SR},
title = {Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes.},
journal = {Nature biotechnology},
volume = {34},
number = {10},
pages = {1037-1045},
pmid = {27571370},
issn = {1546-1696},
support = {20265/CRUK_/Cancer Research UK/United Kingdom ; 20466/CRUK_/Cancer Research UK/United Kingdom ; },
mesh = {Antigens/*genetics/*immunology ; CD8-Positive T-Lymphocytes/*immunology ; Cells, Cultured ; DNA Barcoding, Taxonomic ; Genes, MHC Class I/*genetics/immunology ; High-Throughput Screening Assays/*methods ; Humans ; Immunoassay/*methods ; Peptides/genetics/immunology ; Protein Multimerization/genetics/immunology ; Staining and Labeling/methods ; },
abstract = {Identification of the peptides recognized by individual T cells is important for understanding and treating immune-related diseases. Current cytometry-based approaches are limited to the simultaneous screening of 10-100 distinct T-cell specificities in one sample. Here we use peptide-major histocompatibility complex (MHC) multimers labeled with individual DNA barcodes to screen >1,000 peptide specificities in a single sample, and detect low-frequency CD8 T cells specific for virus- or cancer-restricted antigens. When analyzing T-cell recognition of shared melanoma antigens before and after adoptive cell therapy in melanoma patients, we observe a greater number of melanoma-specific T-cell populations compared with cytometry-based approaches. Furthermore, we detect neoepitope-specific T cells in tumor-infiltrating lymphocytes and peripheral blood from patients with non-small cell lung cancer. Barcode-labeled pMHC multimers enable the combination of functional T-cell analysis with large-scale epitope recognition profiling for the characterization of T-cell recognition in various diseases, including in small clinical samples.},
}
@article {pmid27570325,
year = {2016},
author = {Videira, SI and Groenewald, JZ and Braun, U and Shin, HD and Crous, PW},
title = {All that glitters is not Ramularia.},
journal = {Studies in mycology},
volume = {83},
number = {},
pages = {49-163},
pmid = {27570325},
issn = {0166-0616},
abstract = {Ramularia is a species-rich genus that harbours plant pathogens responsible for yield losses to many important crops, including barley, sugar beet and strawberry. Species of Ramularia are hyphomycetes with hyaline conidiophores and conidia with distinct, thickened, darkened, refractive conidiogenous loci and conidial hila, and Mycosphaerella sexual morphs. Because of its simple morphology and general lack of DNA data in public databases, several allied genera are frequently confused with Ramularia. In order to improve the delimitation of Ramularia from allied genera and the circumscription of species within the genus Ramularia, a polyphasic approach based on multilocus DNA sequences, morphological and cultural data were used in this study. A total of 420 isolates belonging to Ramularia and allied genera were targeted for the amplification and sequencing of six partial genes. Although Ramularia and Ramulariopsis proved to be monophyletic, Cercosporella and Pseudocercosporella were polyphyletic. Phacellium isolates clustered within the Ramularia clade and the genus is thus tentatively reduced to synonymy under Ramularia. Cercosporella and Pseudocercosporella isolates that were not congeneric with the ex-type strains of the type species of those genera were assigned to existing genera or to the newly introduced genera Teratoramularia and Xenoramularia, respectively. Teratoramularia is a genus with ramularia-like morphology belonging to the Teratosphaeriaceae, and Xenoramularia was introduced to accommodate hyphomycetous species closely related to Zymoseptoria. The genera Apseudocercosporella, Epicoleosporium, Filiella, Fusidiella, Neopseudocercosporella, and Mycosphaerelloides were also newly introduced to accommodate species non-congeneric with their purported types. A total of nine new combinations and 24 new species were introduced in this study.},
}
@article {pmid27567602,
year = {2017},
author = {Swiderska, B and Kedracka-Krok, S and Panz, T and Morgan, AJ and Falniowski, A and Grzmil, P and Plytycz, B},
title = {Lysenin family proteins in earthworm coelomocytes - Comparative approach.},
journal = {Developmental and comparative immunology},
volume = {67},
number = {},
pages = {404-412},
doi = {10.1016/j.dci.2016.08.011},
pmid = {27567602},
issn = {1879-0089},
mesh = {Animals ; Cells, Cultured ; *Hemolysis ; Mass Spectrometry ; Oligochaeta/*immunology ; Phagocytes/*immunology ; Pore Forming Cytotoxic Proteins/metabolism ; Protein Binding ; Proteins/genetics/*metabolism ; Species Specificity ; Sphingomyelins/metabolism ; Toxins, Biological/genetics/*metabolism ; },
abstract = {Sphingomyelin-binding proteins of the lysenin family were originally identified in earthworms belonging to the genus Eisenia comprised of at least two distinct species, E. andrei and E. fetida, until recently considered subspecies or morphotypes of E. foetida (sic). In the present study the presence of lysenin and lysenin-related protein 2 (LRP-2, known also as fetidin) was detected in coelomocytes retrieved from all investigated adult specimens of E. andrei, and E. fetida. They were accompanied by LRP-3 and LRP-1 in some specimens of E. andrei and E. fetida, respectively. Lysenins were not observed in a third composting lumbricid species, Dendrobaena veneta, which served as a convenient negative reference for techniques and procedures used in the study. The pore-forming potential of soluble and cellular fractions of coelomic fluid was studied towards sheep red blood cells and sphingomyelin-rich liposomes. After experimental depletion the potential was restored in parallel with restoration of chloragocyte-derived eleocytes in both E. andrei and E. fetida.},
}
@article {pmid27567252,
year = {2017},
author = {Xu, Y and Zhang, X and Luan, C and Wang, H and Chen, B and Zhao, Y},
title = {Hybrid hydrogel photonic barcodes for multiplex detection of tumor markers.},
journal = {Biosensors &amp; bioelectronics},
volume = {87},
number = {},
pages = {264-270},
doi = {10.1016/j.bios.2016.08.063},
pmid = {27567252},
issn = {1873-4235},
mesh = {Antibodies, Immobilized/chemistry ; Biomarkers, Tumor/blood ; Biosensing Techniques/*methods ; Carcinoembryonic Antigen/*blood ; Humans ; Hydrogel, Polyethylene Glycol Dimethacrylate/*chemistry ; Immunoassay/methods ; Limit of Detection ; Neoplasms/blood ; Polyethylene Glycols/*chemistry ; Reproducibility of Results ; Sepharose/*chemistry ; alpha-Fetoproteins/*analysis ; },
abstract = {Barcodes-based suspension array have for demonstrated values in multiplex assay of tumor markers. Photonic barcodes which are encoded by their characteristic reflection peaks are the important supports for suspension array due to their stable code, low fluorescent background and high surface-volume ratio. Attempts to develop this technology tend to improve the function of the photonic barcodes. Here, we present a new type of hybrid hydrogel photonic barcodes for efficient multiplex assays. This photonic barcodes are hybrid inverse opal hydrogel composed of poly(ethylene glycol) diacrylate (PEG-DA) and agarose. The polymerized PEG-DA hydrogel could guarantee the stabilities of the inverse opal structure and its resultant code, while the agarose could offer active chemical groups for the probe immobilization and homogeneous water surrounding for the bioassay. In addition, the interconnected pores inverse opal structure could provide channels for biomolecules diffusing and reaction into the voids of barcodes. These features imparted the hybrid hydrogel photonic barcodes with limits of detection (LOD) of 0.78ng/mL for carcinoembryonic antigen (CEA) and 0.21ng/mL for α-fetoprotein (AFP), respectively. It was also demonstrated that the proposed barcodes showed acceptable accuracy and detection reproducibility, and the results were in acceptable agreement with those from common clinic method for the detections of practical clinical samples. Thus, our technique provides a new platform for simultaneous multiplex immunoassay.},
}
@article {pmid27563229,
year = {2016},
author = {Cabelin, VL and Alejandro, GJ},
title = {Efficiency of matK, rbcL, trnH-psbA, and trnL-F (cpDNA) to Molecularly Authenticate Philippine Ethnomedicinal Apocynaceae Through DNA Barcoding.},
journal = {Pharmacognosy magazine},
volume = {12},
number = {Suppl 3},
pages = {S384-8},
pmid = {27563229},
issn = {0973-1296},
abstract = {BACKGROUND: The Philippines is home to some ethnomedicinal Apocynaceae that has been used to cure common ailments. They are perceived to be safe, but misidentification can lead to substitution and adulteration. Morphological characters are primarily utilized to identify these species but a new method utilizing molecular characters called DNA barcoding has emerged. In this study, the efficiency of matK, rbcL, trnH-psbA, and trnL-F to molecularly authenticate selected Apocynaceae species were tested.<br><br>MATERIALS AND METHODS: Genomic DNA from silica-dried leaf samples were isolated and used as a template for generating DNA barcodes. Pair-wise sequence divergence using Kimura-2-Parameter was used to analyze inter-specific and intraspecific variations among the barcodes, whereas basic local alignment search tool (BLAST) and neighbor-joining (NJ) analyses were employed to examine discrimination success.<br><br>RESULTS: The results show that matK is the best barcode for Apocynaceae as it has the highest amplification and sequencing success together with rbcL while having high inter-specific and low intra-specific divergence relative to the other candidate barcodes. Furthermore, matK provided the highest discrimination both in BLAST and NJ analyses.<br><br>CONCLUSION: This study proposes the use of matK as the principal barcode for Apocynaceae.<br><br>SUMMARY: Both matK and rbcL have higher universality compared to trnH-psbA and trnL-F matK has relatively high inter-specific divergence and very minimal intra-specific divergencematK is the best barcode to molecularly authenticate Apocynaceae with either trnH-psbA or trnL-F as supplements. Abbreviations used: K2P: Kimura-2-parameter, BLAST: Basic local alignment search tool, NJ: Neighbor-joining.},
}
@article {pmid27563228,
year = {2016},
author = {Sharma, S and Shrivastava, N},
title = {DNA-based Simultaneous Identification of Three Terminalia Species Targeting Adulteration.},
journal = {Pharmacognosy magazine},
volume = {12},
number = {Suppl 3},
pages = {S379-83},
pmid = {27563228},
issn = {0973-1296},
abstract = {BACKGROUND: Various parts of three Terminalia species, namely, Terminalia arjuna (stem bark), Terminalia bellirica (fruit), and Terminalia chebula (fruit) are widely known for their therapeutic principles and other commercial values. However, stem bark of T. bellirica and T. chebula along with Terminalia tomentosa are reported as adulterants of T. arjuna. Correct botanical identification is very critical for safe and effective herbal drugs. DNA-based identification approaches are advancing the conventional methods and sometime proved more beneficial.<br><br>OBJECTIVE: The purpose of the study was to develop polymerase chain reaction (PCR) method using internal transcribed spacer (ITS) region to ascertain the identity of T. arjuna herbal material as well as detection of mixing of other three Terminalia species.<br><br>MATERIALS AND METHODS: DNA from stem barks samples were isolated and subjected to ITS region amplification and sequencing. Sequences were compared for polymorphic nucleotides determination to develop species-specific primers. Final primers were selected on the basis of in silico analysis and experimentally validated. PCR assays for botanical identification of Terminalia species were developed. Sensitivity testing and assay validation were also performed.<br><br>RESULTS: The PCR assays developed for Terminalia species were resulted in definite amplicons of the corresponding species. No cross-reactivity of the primers was detected. Sensitivity was found enough to amplify as low as 2 ng of DNA. Mixing of DNA in various concentrations for validation also proved the sensitivity of assay to detect original botanicals in the mixture. The developed methods proved very specific and sensitive to authenticate Arjuna bark to develop evidence-based herbal medicines.<br><br>SUMMARY: Internal transcribed spacer-based species-specific polymerase chain reaction.(PCR) assays were developed to authenticate Terminalia arjuna stem bark and to identify substitution/adulteration of Terminalia bellirica and Terminalia chebula in the genuine starting materialDefinite amplicons were obtained specific to particular species and the assay was found of profound sensitivity to amplify as low as 2 ng of DNAResults of method validation proved that the assay can identify adulterant Terminalia species even when present in lower amountsThe DNA barcodes and PCR methods can also be used to identify Terminalia bellirica and T. chebula related herbal medicinal material. Abbreviations used: ITS: Internal transcribed spacer, BSA: Bovine serum albumin, DMSO: Dimethyl sulfoxide.},
}
@article {pmid27558664,
year = {2016},
author = {Guo, L and Ganguly, A and Sun, L and Suo, F and Du, LL and Russell, P},
title = {Global Fitness Profiling Identifies Arsenic and Cadmium Tolerance Mechanisms in Fission Yeast.},
journal = {G3 (Bethesda, Md.)},
volume = {6},
number = {10},
pages = {3317-3333},
pmid = {27558664},
issn = {2160-1836},
support = {P42 ES010337/ES/NIEHS NIH HHS/United States ; R01 CA077325/CA/NCI NIH HHS/United States ; R01 CA117638/CA/NCI NIH HHS/United States ; R01 GM059447/GM/NIGMS NIH HHS/United States ; },
mesh = {*Adaptation, Biological ; Arsenic/metabolism/*pharmacology ; Biological Transport ; Cadmium/metabolism/*pharmacology ; Cluster Analysis ; Computational Biology/methods ; Cysteine/biosynthesis ; DNA Damage ; Gene Expression Profiling ; Gene Expression Regulation, Fungal ; Gene Ontology ; *Genetic Fitness ; Heavy Metal Poisoning ; Membrane Transport Proteins/metabolism ; Metabolic Networks and Pathways ; Microbial Sensitivity Tests ; Mitochondria/metabolism ; Mutation ; Oxidation-Reduction ; Oxidative Stress ; Peroxisomes/metabolism ; Phenotype ; Phytochelatins/biosynthesis ; Poisoning ; Schizosaccharomyces/*drug effects/*genetics/metabolism ; Schizosaccharomyces pombe Proteins/metabolism ; Transcription Factors/metabolism ; Vitamin B 6/metabolism ; },
abstract = {Heavy metals and metalloids such as cadmium [Cd(II)] and arsenic [As(III)] are widespread environmental toxicants responsible for multiple adverse health effects in humans. However, the molecular mechanisms underlying metal-induced cytotoxicity and carcinogenesis, as well as the detoxification and tolerance pathways, are incompletely understood. Here, we use global fitness profiling by barcode sequencing to quantitatively survey the Schizosaccharomyces pombe haploid deletome for genes that confer tolerance of cadmium or arsenic. We identified 106 genes required for cadmium resistance and 110 genes required for arsenic resistance, with a highly significant overlap of 36 genes. A subset of these 36 genes account for almost all proteins required for incorporating sulfur into the cysteine-rich glutathione and phytochelatin peptides that chelate cadmium and arsenic. A requirement for Mms19 is explained by its role in directing iron-sulfur cluster assembly into sulfite reductase as opposed to promoting DNA repair, as DNA damage response genes were not enriched among those required for cadmium or arsenic tolerance. Ubiquinone, siroheme, and pyridoxal 5'-phosphate biosynthesis were also identified as critical for Cd/As tolerance. Arsenic-specific pathways included prefoldin-mediated assembly of unfolded proteins and protein targeting to the peroxisome, whereas cadmium-specific pathways included plasma membrane and vacuolar transporters, as well as Spt-Ada-Gcn5-acetyltransferase (SAGA) transcriptional coactivator that controls expression of key genes required for cadmium tolerance. Notable differences are apparent with corresponding screens in the budding yeast Saccharomyces cerevisiae, underscoring the utility of analyzing toxic metal defense mechanisms in both organisms.},
}
@article {pmid27558458,
year = {2016},
author = {Jiang, GF and Hinsinger, DD and Strijk, JS},
title = {Comparison of intraspecific, interspecific and intergeneric chloroplast diversity in Cycads.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {31473},
pmid = {27558458},
issn = {2045-2322},
mesh = {Chloroplasts/*genetics ; Cycadopsida/classification/*genetics ; DNA, Chloroplast/genetics ; Evolution, Molecular ; Genes, Chloroplast/genetics ; *Genetic Variation ; Genome, Chloroplast/*genetics ; Microsatellite Repeats/genetics ; Phylogeny ; Species Specificity ; },
abstract = {Cycads are among the most threatened plant species. Increasing the availability of genomic information by adding whole chloroplast data is a fundamental step in supporting phylogenetic studies and conservation efforts. Here, we assemble a dataset encompassing three taxonomic levels in cycads, including ten genera, three species in the genus Cycas and two individuals of C. debaoensis. Repeated sequences, SSRs and variations of the chloroplast were analyzed at the intraspecific, interspecific and intergeneric scale, and using our sequence data, we reconstruct a phylogenomic tree for cycads. The chloroplast was 162,094 bp in length, with 133 genes annotated, including 87 protein-coding, 37 tRNA and 8 rRNA genes. We found 7 repeated sequences and 39 SSRs. Seven loci showed promising levels of variations for application in DNA-barcoding. The chloroplast phylogeny confirmed the division of Cycadales in two suborders, each of them being monophyletic, revealing a contradiction with the current family circumscription and its evolution. Finally, 10 intraspecific SNPs were found. Our results showed that despite the extremely restricted distribution range of C. debaoensis, using complete chloroplast data is useful not only in intraspecific studies, but also to improve our understanding of cycad evolution and in defining conservation strategies for this emblematic group.},
}
@article {pmid27556403,
year = {2016},
author = {Bekker, EI and Karabanov, DP and Galimov, YR and Kotov, AA},
title = {DNA Barcoding Reveals High Cryptic Diversity in the North Eurasian Moina Species (Crustacea: Cladocera).},
journal = {PloS one},
volume = {11},
number = {8},
pages = {e0161737},
pmid = {27556403},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; Cladocera/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Genes, Mitochondrial ; Genetic Variation ; Genetics, Population ; Genotype ; Haplotypes ; *Phylogeny ; Polymorphism, Genetic ; Siberia ; },
abstract = {Species of the genus Moina Baird (Cladocera: Moinidae) often dominate freshwater crustacean communities in temporary water bodies. Several species of Moina are used as food for fish larvae in aquaculture, as bioindicators in toxicological studies, and as common subjects for physiological studies. The aim of this paper is to estimate biodiversity of Moina in northern Eurasia using the standard DNA barcoding approach based on the cytochrome c oxidase subunit I (COI) gene. We analysed 160 newly obtained and 157 existing COI sequences, and found evidence for 21 phylogroups of Moina, some of which were detected here for the first time. Our study confirmed the opinion that the actual species diversity of cladocerans is several times higher than is presently accepted. Our results also indicated that Moina has the second richest species diversity among the cladoceran genera (with only Daphnia O. F. Mueller having a greater diversity of species). Our study strongly supports division of Moina into two faunistic groups: European-Western Siberian and Eastern Siberian-Far Eastern, with a transitional zone at the Yenisey River basin (Eastern Siberia). Here, we refrain from taxonomic descriptions of new species, as this requires a thorough morphological and taxonomic study for each putative taxon.},
}
@article {pmid27551226,
year = {2016},
author = {Baldwin, CC and Pitassy, DE and Robertson, DR},
title = {A new deep-reef scorpionfish (Teleostei, Scorpaenidae, Scorpaenodes) from the southern Caribbean with comments on depth distributions and relationships of western Atlantic members of the genus.},
journal = {ZooKeys},
volume = {},
number = {606},
pages = {141-158},
pmid = {27551226},
issn = {1313-2989},
abstract = {A new species of scorpionfish, Scorpaenodes barrybrowni Pitassy &amp; Baldwin, sp. n. which is described, was collected during submersible diving in the southern Caribbean as part of the Smithsonian's Deep Reef Observation Project (DROP). It differs from the other two western Atlantic species of the genus, Scorpaenodes caribbaeus and Scorpaenodes tredecimspinosus, in various features, including its color pattern, having an incomplete lateral line comprising 8-10 pored scales, tending to be more elongate, usually having the 11(th)-12(th) pectoral-fin rays elongate, and by 20-23% divergence in the cytochrome c oxidase I (COI) DNA barcode sequences. It further differs from one or the other of those species in head spination and in numbers of soft dorsal-fin rays, pectoral-fin rays, and precaudal + caudal vertebrae. Inhabiting depths of 95-160 m, the new species is the deepest western Atlantic member of the genus (Scorpaenodes caribbaeus occurs at depths < 35 m and Scorpaenodes tredecimspinosus from 7 to 82 m). DNA barcode data do not rigorously resolve relationships among the ten species of the genus for which those data are available.},
}
@article {pmid27551210,
year = {2016},
author = {Stoffels, BE and van der Meij, SE and Hoeksema, BW and van Alphen, J and van Alen, T and Meyers-Muñoz, MA and de Voogd, NJ and Tuti, Y and van der Velde, G},
title = {Phylogenetic relationships within the Phyllidiidae (Opisthobranchia, Nudibranchia).},
journal = {ZooKeys},
volume = {},
number = {605},
pages = {1-35},
pmid = {27551210},
issn = {1313-2989},
abstract = {The Phyllidiidae (Gastropoda, Heterobranchia, Nudibranchia) is a family of colourful nudibranchs found on Indo-Pacific coral reefs. Despite the abundant and widespread occurrence of many species, their phylogenetic relationships are not well known. The present study is the first contribution to fill the gap in our knowledge on their phylogeny by combining morphological and molecular data. For that purpose 99 specimens belonging to 16 species were collected at two localities in Indonesia. They were photographed and used to make a phylogeny reconstruction based on newly obtained cytochrome oxidase subunit (COI) sequences as well as sequence data from GenBank. All mitochondrial 16S sequence data available from GenBank were used in a separate phylogeny reconstruction to obtain information for species we did not collect. COI data allowed the distinction of the genera and species, whereas the 16S data gave a mixed result with respect to the genera Phyllidia and Phyllidiella. Specimens which could be ascribed to species level based on their external morphology and colour patterns showed low variation in COI sequences, but there were two exceptions: three specimens identified as Phyllidia cf. babai represent two to three different species, while Phyllidiella pustulosa showed highly supported subclades. The barcoding marker COI also confirms that the species boundaries in morphologically highly variable species such as Phyllidia elegans, Phyllidia varicosa, and Phyllidiopsis krempfi, are correct as presently understood. In the COI as well as the 16S cladogram Phyllidiopsis cardinalis was located separately from all other Phyllidiidae, whereas Phyllidiopsis fissuratus was positioned alone from the Phyllidiella species by COI data only. Future studies on phyllidiid systematics should continue to combine morphological information with DNA sequences to obtain a clearer insight in their phylogeny.},
}
@article {pmid27551204,
year = {2016},
author = {Wall-Palmer, D and Burridge, AK and Peijnenburg, KT},
title = {Atlanta ariejansseni, a new species of shelled heteropod from the Southern Subtropical Convergence Zone (Gastropoda, Pterotracheoidea).},
journal = {ZooKeys},
volume = {},
number = {604},
pages = {13-30},
pmid = {27551204},
issn = {1313-2989},
abstract = {The Atlantidae (shelled heteropods) is a family of microscopic aragonite shelled holoplanktonic gastropods with a wide biogeographical distribution in tropical, sub-tropical and temperate waters. The aragonite shell and surface ocean habitat of the atlantids makes them particularly susceptible to ocean acidification and ocean warming, and atlantids are likely to be useful indicators of these changes. However, we still lack fundamental information on their taxonomy and biogeography, which is essential for monitoring the effects of a changing ocean. Integrated morphological and molecular approaches to taxonomy have been employed to improve the assessment of species boundaries, which give a more accurate picture of species distributions. Here a new species of atlantid heteropod is described based on shell morphology, DNA barcoding of the Cytochrome Oxidase I gene, and biogeography. All specimens of Atlanta ariejansseni sp. n. were collected from the Southern Subtropical Convergence Zone of the Atlantic and Indo-Pacific oceans suggesting that this species has a very narrow latitudinal distribution (37-48°S). Atlanta ariejansseni sp. n. was found to be relatively abundant (up to 2.3 specimens per 1000 m(3) water) within this narrow latitudinal range, implying that this species has adapted to the specific conditions of the Southern Subtropical Convergence Zone and has a high tolerance to the varying ocean parameters in this region.},
}
@article {pmid27551203,
year = {2016},
author = {Bu, Y and Ma, Y and Luan, YX},
title = {Paracerella Imadaté in China: the description of a new species and the analysis of genetic differences between populations (Protura, Acerentomata, Nipponentomidae).},
journal = {ZooKeys},
volume = {},
number = {604},
pages = {1-11},
pmid = {27551203},
issn = {1313-2989},
abstract = {The genus Paracerella Imadaté, 1980 is recorded from China for the first time, with the description of a new species, Paracerella sinensis sp. n. Paracerella sinensis is characterized by four pairs of A-setae on tergite I, the presence of setae Pc and P3a on tergite VII, eight A-setae on tergite VIII, the presence of seta Pc on both sternites VI and VII, and 4/2 setae on sternite VIII, which are different from all other members of the genus. The key to the four species of the genus is updated. In addition, DNA barcodes of four populations are sequenced and their genetic differences are analyzed.},
}
@article {pmid27551188,
year = {2016},
author = {Zhang, X and Zhao, Z and Zheng, G and Li, S},
title = {A further study of the spider genus Notiocoelotes (Araneae, Agelenidae) from Hainan Island, China.},
journal = {ZooKeys},
volume = {},
number = {601},
pages = {75-87},
pmid = {27551188},
issn = {1313-2989},
abstract = {Two new Notiocoelotes species, Notiocoelotes maoganensis sp. n. (♂♀) and Notiocoelotes qiongzhongensis sp. n. (♂♀) are described from Hainan Island, China. In addition, the female of Notiocoelotes membranaceus Liu &amp; Li, 2010 is described for the first time. DNA barcodes of three species treated in this paper were obtained for future use.},
}
@article {pmid27551187,
year = {2016},
author = {Zhang, X and Zhao, Z and Zheng, G and Li, S},
title = {Nine new species of the spider genus Pireneitega Kishida, 1955 (Agelenidae, Coelotinae) from Xinjiang, China.},
journal = {ZooKeys},
volume = {},
number = {601},
pages = {49-74},
pmid = {27551187},
issn = {1313-2989},
abstract = {Nine new Pireneitega species collected from Xinjiang, China are described as new to science: Pireneitega burqinensis sp. n. (♂♀), Pireneitega fuyunensis sp. n. (♂♀), Pireneitega gongliuensis sp. n. (♂♀), Pireneitega huochengensis sp. n. (♂♀), Pireneitega lini sp. n. (♀), Pireneitega liui sp. n. (♂♀), Pireneitega wensuensis sp. n. (♂), Pireneitega wui sp. n. (♂) and Pireneitega yaoi sp. n. (♀). DNA barcodes were obtained for all these species for future use.},
}
@article {pmid27549737,
year = {2016},
author = {Mark, K and Cornejo, C and Keller, C and Flück, D and Scheidegger, C},
title = {Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation.},
journal = {Genome},
volume = {59},
number = {9},
pages = {685-704},
doi = {10.1139/gen-2015-0189},
pmid = {27549737},
issn = {1480-3321},
mesh = {Biodiversity ; Biological Evolution ; Computational Biology ; Consensus Sequence ; *DNA Barcoding, Taxonomic ; *Genetic Variation ; *High-Throughput Nucleotide Sequencing/instrumentation/methods ; Lichens/*classification/*genetics ; Molecular Typing/instrumentation/methods ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Although lichens (lichen-forming fungi) play an important role in the ecological integrity of many vulnerable landscapes, only a minority of lichen-forming fungi have been barcoded out of the currently accepted ∼18 000 species. Regular Sanger sequencing can be problematic when analyzing lichens since saprophytic, endophytic, and parasitic fungi live intimately admixed, resulting in low-quality sequencing reads. Here, high-throughput, long-read 454 pyrosequencing in a GS FLX+ System was tested to barcode the fungal partner of 100 epiphytic lichen species from Switzerland using fungal-specific primers when amplifying the full internal transcribed spacer region (ITS). The present study shows the potential of DNA barcoding using pyrosequencing, in that the expected lichen fungus was successfully sequenced for all samples except one. Alignment solutions such as BLAST were found to be largely adequate for the generated long reads. In addition, the NCBI nucleotide database-currently the most complete database for lichen-forming fungi-can be used as a reference database when identifying common species, since the majority of analyzed lichens were identified correctly to the species or at least to the genus level. However, several issues were encountered, including a high sequencing error rate, multiple ITS versions in a genome (incomplete concerted evolution), and in some samples the presence of mixed lichen-forming fungi (possible lichen chimeras).},
}
@article {pmid27549620,
year = {2016},
author = {Niskanen, T and Liimatainen, K and Kytövuori, I and Lindström, H and Dentinger, BT and Ammirati, JF},
title = {Cortinarius subgenus Callistei in North America and Europe-type studies, diversity, and distribution of species.},
journal = {Mycologia},
volume = {108},
number = {5},
pages = {1018-1027},
doi = {10.3852/16-033},
pmid = {27549620},
issn = {0027-5514},
mesh = {Americas ; *Biodiversity ; Cortinarius/*cytology/genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic ; Europe ; North America ; },
abstract = {Five species of Cortinarius subgenus Callistei, are recognized in Europe and North America. Cortinarius callisteus, C. infucatus, and C. neocallisteus sp. nov. have a broad distribution, extending from western North America to Europe. Cortinarius tofaceus is known from eastern North America and Europe, while C. callistei sp. is known only from one locality in Sweden. All five species are primarily associated with coniferous trees. Previously the species were included either in subgenus Leprocybe or subgenus Cortinarius, but recently they have been separated into subgenus Callistei based on molecular data. Type specimens of the names associated with this subgenus were studied and a neotype proposed for C. tofaceus and an epitype for C. infucatus Barcodes for the species are deposited in RefSeq and UNITE.},
}
@article {pmid27549575,
year = {2017},
author = {Radhika, R and Bijoy Nandan, S and Harikrishnan, M},
title = {Morphological and molecular identification of marine copepod Dioithona rigida Giesbrecht, 1896 (Crustacea:Cyclopoida) based on mitochondrial COI gene sequences, from Lakshadweep sea, India.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {6},
pages = {872-879},
doi = {10.1080/24701394.2016.1202941},
pmid = {27549575},
issn = {2470-1408},
mesh = {Animals ; Copepoda/*anatomy &amp; histology/classification/enzymology/*genetics ; Electron Transport Complex IV/genetics ; Female ; *Genes, Mitochondrial ; Genetic Variation ; India ; Molecular Typing ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Morphological identification of the marine cyclopoid copepod Dioithona rigida in combination with sequencing a 645 bp fragment of mitochondrial cytochrome oxidase c subunit I (mtCOI) gene, collected from offshore waters of Kavarathi Island, Lakshadweep Sea, is presented in this study. Kiefer in 1935 classified Dioithona as a separate genus from Oithona. The main distinguishing characters observed in the collected samples, such as the presence of well-developed P5 with 2 setae, 5 segmented urosome, 12 segmented antennule, compact dagger-like setae on the inner margin of proximal segment of exopod ramus in P1-P4 and engorged portion of P1-bearing a spine, confirmed their morphology to D. rigida. A comparison of setal formulae of the exopod and endopod of D. rigida with those recorded previously by various authors are also presented here. Maximum likelihood Tree analysis exhibited the clustering of D. rigida sequences into a single clade (accession numbers KP972540.1-KR528588.1), which in contrast was 37-42% divergent from other Oithona species. Further intra-specific divergence values of 0-2% also confirmed the genetic identity of D. rigida species. Paracyclopina nana was selected as an out group displayed a diverged array. The present results distinctly differentiated D. rigida from other Oithona species.},
}
@article {pmid27549513,
year = {2016},
author = {Hausmann, A and Miller, SE and Holloway, JD and deWaard, JR and Pollock, D and Prosser, SW and Hebert, PD},
title = {Calibrating the taxonomy of a megadiverse insect family: 3000 DNA barcodes from geometrid type specimens (Lepidoptera, Geometridae).},
journal = {Genome},
volume = {59},
number = {9},
pages = {671-684},
doi = {10.1139/gen-2015-0197},
pmid = {27549513},
issn = {1480-3321},
mesh = {Animals ; *Biodiversity ; DNA ; *DNA Barcoding, Taxonomic ; Insecta/*classification/*genetics ; Lepidoptera ; Nucleic Acid Amplification Techniques ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {It is essential that any DNA barcode reference library be based upon correctly identified specimens. The Barcode of Life Data Systems (BOLD) requires information such as images, geo-referencing, and details on the museum holding the voucher specimen for each barcode record to aid recognition of potential misidentifications. Nevertheless, there are misidentifications and incomplete identifications (e.g., to a genus or family) on BOLD, mainly for species from tropical regions. Unfortunately, experts are often unavailable to correct taxonomic assignments due to time constraints and the lack of specialists for many groups and regions. However, considerable progress could be made if barcode records were available for all type specimens. As a result of recent improvements in analytical protocols, it is now possible to recover barcode sequences from museum specimens that date to the start of taxonomic work in the 18th century. The present study discusses success in the recovery of DNA barcode sequences from 2805 type specimens of geometrid moths which represent 1965 species, corresponding to about 9% of the 23 000 described species in this family worldwide and including 1875 taxa represented by name-bearing types. Sequencing success was high (73% of specimens), even for specimens that were more than a century old. Several case studies are discussed to show the efficiency, reliability, and sustainability of this approach.},
}
@article {pmid27549137,
year = {2016},
author = {Harrup, LE and Laban, S and Purse, BV and Reddy, YK and Reddy, YN and Byregowda, SM and Kumar, N and Purushotham, KM and Kowalli, S and Prasad, M and Prasad, G and Bettis, AA and De Keyser, R and Logan, J and Garros, C and Gopurenko, D and Bellis, G and Labuschagne, K and Mathieu, B and Carpenter, S},
title = {DNA barcoding and surveillance sampling strategies for Culicoides biting midges (Diptera: Ceratopogonidae) in southern India.},
journal = {Parasites &amp; vectors},
volume = {9},
number = {1},
pages = {461},
pmid = {27549137},
issn = {1756-3305},
support = {BB/H009167/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/H009493/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/H009205/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/K021214/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animal Distribution ; Animals ; Ceratopogonidae/*genetics ; DNA/*genetics ; *DNA Barcoding, Taxonomic ; India ; Phylogeny ; Population Surveillance ; Species Specificity ; },
abstract = {BACKGROUND: Culicoides spp. biting midges transmit bluetongue virus (BTV), the aetiological agent of bluetongue (BT), an economically important disease of ruminants. In southern India, hyperendemic outbreaks of BT exert high cost to subsistence farmers in the region, impacting on sheep production. Effective Culicoides spp. monitoring methods coupled with accurate species identification can accelerate responses for minimising BT outbreaks. Here, we assessed the utility of sampling methods and DNA barcoding for detection and identification of Culicoides spp. in southern India, in order to provide an informed basis for future monitoring of their populations in the region.<br><br>METHODS: Culicoides spp. collected from Tamil Nadu and Karnataka were used to construct a framework for future morphological identification in surveillance, based on sequence comparison of the DNA barcode region of the mitochondrial cytochrome c oxidase I (COI) gene and achieving quality standards defined by the Barcode of Life initiative. Pairwise catches of Culicoides spp. were compared in diversity and abundance between green (570&#xa0;nm) and ultraviolet (UV) (390&#xa0;nm) light emitting diode (LED) suction traps at a single site in Chennai, Tamil Nadu over 20 nights of sampling in November 2013.<br><br>RESULTS: DNA barcode sequences of Culicoides spp. were mostly congruent both with existing DNA barcode data from other countries and with morphological identification of major vector species. However, sequence differences symptomatic of cryptic species diversity were present in some groups which require further investigation. While the diversity of species collected by the UV LED Center for Disease Control (CDC) trap did not significantly vary from that collected by the green LED CDC trap, the UV CDC significantly outperformed the green LED CDC trap with regard to the number of Culicoides individuals collected.<br><br>CONCLUSIONS: Morphological identification of the majority of potential vector species of Culicoides spp. samples within southern India appears relatively robust; however, potential cryptic species diversity was present in some groups requiring further investigation. The UV LED CDC trap is recommended for surveillance of Culicoides in southern India.},
}
@article {pmid27547527,
year = {2016},
author = {Coddington, JA and Agnarsson, I and Cheng, RC and Čandek, K and Driskell, A and Frick, H and Gregorič, M and Kostanjšek, R and Kropf, C and Kweskin, M and Lokovšek, T and Pipan, M and Vidergar, N and Kuntner, M},
title = {DNA barcode data accurately assign higher spider taxa.},
journal = {PeerJ},
volume = {4},
number = {},
pages = {e2201},
pmid = {27547527},
issn = {2167-8359},
abstract = {The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios "barcodes" (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families-taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level assignment. We used BLAST queries of each sequence against the entire library and got the top ten hits. The percent sequence identity was reported from these hits (PIdent, range 75-100%). Accurate assignment of higher taxa (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values >95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for accurate generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all higher taxon assignments were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of the underlying database impacts accuracy of results; many outliers in our dataset could be attributed to taxonomic and/or sequencing errors in BOLD and GenBank. It seems that an accurate and complete reference library of families and genera of life could provide accurate higher level taxonomic identifications cheaply and accessibly, within years rather than decades.},
}
@article {pmid27547517,
year = {2016},
author = {Jaskuła, R and Rewicz, T and Płóciennik, M and Grabowski, M},
title = {Pleistocene phylogeography and cryptic diversity of a tiger beetle, Calomera littoralis, in North-Eastern Mediterranean and Pontic regions inferred from mitochondrial COI gene sequences.},
journal = {PeerJ},
volume = {4},
number = {},
pages = {e2128},
pmid = {27547517},
issn = {2167-8359},
abstract = {Background. Calomera littoralis is a Palearctic species, widely distributed in Europe; inhabiting predominantly its Atlantic, Mediterranean and Black Sea coastlines. Methods. Its phylogeography on the Balkan Peninsula and on the north-western Black Sea coast was inferred using a 697 bp long portion of the mitochondrial COI gene, amplified from 169 individuals collected on 43 localities. Results. The results revealed two genetically divergent groups/lineages, the southern one inhabiting both the Balkan Peninsula and the Pontic Region and the northern one found exclusively in the Pontic Region. Species delimitation based on DNA barcoding gap suggested an interspecific level of divergence between these groups. Multivariate analysis of eight male and female morphometric traits detected no difference between the groups, implying they may represent cryptic species. The Bayesian time-calibrated reconstruction of phylogeny suggested that the lineages diverged ca. 2.3 Ma, in early Pleistocene. Discussion. The presence of the two genetically divergent groups results most likely from contemporary isolation of the Pontic basin from the Mediterranean that broke the continuous strip of coastal habitats inhabited by C. littoralis. Demographic analyses indicated that both lineages have been in demographic and spatial expansion since ca. 0.15 Ma. It coincides with the terminal stage of MIS-6, i.e., Wartanian/Saalian glaciation, and beginning of MIS-5e, i.e., Eemian interglacial, during which, due to eustatic sea level rise, a wide connection between Mediterranean and the Pontic basin was re-established. This, along with re-appearance of coastal habitats could initiate north-east expansion of the southern lineage and its secondary contact with the northern one. The isolation of the Pontic basin from the Mediterranean during the Weichselian glaciation most likely did not have any effect on their phylogeography.},
}
@article {pmid27547514,
year = {2016},
author = {Sánchez, JA and Fuentes-Pardo, AP and Ní Almhain, &#xcd; and Ardila-Espitia, NE and Cantera-Kintz, J and Forero-Shelton, M},
title = {The masquerade game: marine mimicry adaptation between egg-cowries and octocorals.},
journal = {PeerJ},
volume = {4},
number = {},
pages = {e2051},
pmid = {27547514},
issn = {2167-8359},
abstract = {Background. Background matching, as a camouflage strategy, is one of the most outstanding examples of adaptation, where little error or mismatch means high vulnerability to predation. It is assumed that the interplay of natural selection and adaptation are the main evolutionary forces shaping the great diversity of phenotypes observed in mimicry; however, there may be other significant processes that intervene in the development of mimicry such as phenotypic plasticity. Based on observations of background mismatching during reproduction events of egg-cowries, sea snails of the family Ovulidae that mimic the octocoral where they inhabit, we wondered if they match the host species diversity. Using observations in the field and molecular systematics, we set out to establish whether the different egg-cowrie color/shape polymorphisms correspond to distinct lineages restricted to specific octocoral species. Methods. Collection and observations of egg-cowries and their octocoral hosts were done using SCUBA diving between 2009 and 2012 at two localities in the Tropical Eastern Pacific (TEP), Malpelo Island and Cabo Corrientes (Colombia). Detailed host preference observations were done bi-annually at Malpelo Island. We analyzed the DNA sequence of the mitochondrial genes COIand 16S rDNA, extensively used in phylogenetic and DNA barcoding studies, to assess the evolutionary relationship among different egg-cowrie colorations and morphologies. Results. No genetic divergence among egg-cowries associated to different species of the same octocoral genus was observed based on the two mitochondrial genes analyzed. For instance, all egg-cowrie individuals from the two sampled localities observed on 8 different Pacifigorgia-Eugorgia species showed negligible mitochondrial divergence yet large morphologic divergence, which suggests that morphologies belonging to at least two sea snail species, Simnia avena(=S. aequalis) and Simnialena rufa, can cross-fertilize. Discussion. Our study system comprised background-matching mimicry, of the masquerade type, between egg-cowries (Simnia/Simnialena) and octocorals (Pacifigorgia/Eugorgia/Leptogorgia). We observed mimicry mismatches related to fitness trade-offs, such as reproductive aggregations vs. vulnerability against predators. Despite the general assumption that coevolution of mimicry involves speciation, egg-cowries with different hosts and colorations comprise the same lineages. Consequently, we infer that there would be significant tradeoffs between mimicry and the pursuit of reproductive aggregations in egg-cowries. The findings of this study not only contribute to the understanding of the evolution of mimicry in egg-cowries, a poorly studied group of marine gastropods, but also to the development of a new biologically meaningful board game that could be implemented as a learning tool.},
}
@article {pmid27547358,
year = {2016},
author = {Hill, GE},
title = {Mitonuclear coevolution as the genesis of speciation and the mitochondrial DNA barcode gap.},
journal = {Ecology and evolution},
volume = {6},
number = {16},
pages = {5831-5842},
pmid = {27547358},
issn = {2045-7758},
abstract = {Mitochondrial genes are widely used in taxonomy and systematics because high mutation rates lead to rapid sequence divergence and because such changes have long been assumed to be neutral with respect to function. In particular, the nucleotide sequence of the mitochondrial gene cytochrome c oxidase subunit 1 has been established as a highly effective DNA barcode for diagnosing the species boundaries of animals. Rarely considered in discussions of mitochondrial evolution in the context of systematics, speciation, or DNA barcodes, however, is the genomic architecture of the eukaryotes: Mitochondrial and nuclear genes must function in tight coordination to produce the complexes of the electron transport chain and enable cellular respiration. Coadaptation of these interacting gene products is essential for organism function. I extend the hypothesis that mitonuclear interactions are integral to the process of speciation. To maintain mitonuclear coadaptation, nuclear genes, which code for proteins in mitochondria that cofunction with the products of mitochondrial genes, must coevolve with rapidly changing mitochondrial genes. Mitonuclear coevolution in isolated populations leads to speciation because population-specific mitonuclear coadaptations create between-population mitonuclear incompatibilities and hence barriers to gene flow between populations. In addition, selection for adaptive divergence of products of mitochondrial genes, particularly in response to climate or altitude, can lead to rapid fixation of novel mitochondrial genotypes between populations and consequently to disruption in gene flow between populations as the initiating step in animal speciation. By this model, the defining characteristic of a metazoan species is a coadapted mitonuclear genotype that is incompatible with the coadapted mitochondrial and nuclear genotype of any other population.},
}
@article {pmid27547308,
year = {2016},
author = {Lu, Z and Zhang, D and Liu, S and Yang, X and Liu, X and Liu, J},
title = {Species delimitation of Chinese hop-hornbeams based on molecular and morphological evidence.},
journal = {Ecology and evolution},
volume = {6},
number = {14},
pages = {4731-4740},
pmid = {27547308},
issn = {2045-7758},
abstract = {Species delimitation through which infers species boundaries is emerging as a major work in modern systematics. Hop-hornbeam species in Ostrya (Betulaceae) are well known for their hard and heavy woods. Five species were described in China and their interspecific delimitations remain unclear. In this study, we firstly explored their distributions in all recorded field sites distributed in China. We then selected 110 samples from 22 natural populations of five species from this genus and one type specimen of O. yunnanensis, for molecular barcoding analyses. We sequenced four chloroplast (cp) DNA fragments (trnH-psbA, trnL-trnF, rps16, and trnG) and the nuclear internal transcribed spacer (ITS) region for all samples. Sequence variations of Ostrya from four cpDNA fragments identified three groups that showed no correspondence to any morphological delimitation because of the incomplete lineage sorting and/or possible interspecific introgression in the history. However, phylogenetic analyses of ITS sequence variations discerned four species, O. japonica, O. rehderiana, O. trichocarpa, and O. multinervis while O. yunnanensis nested within O. multinervis. Morphological clustering also discerned four species and showed the complete consistency with molecular evidence. Moreover, our phylogenetic analyses-based ITS sequence variations suggested that O. trichocarpa comprised an isolated lineage different from the other Eurasian ones. Based on these results, hop-hornbeams in China should be treated as four separate species. Our results further highlight the importance of ITS sequence variations in delimitating and discerning the closely related species in plants.},
}
@article {pmid27545715,
year = {2016},
author = {Kebschull, JM and Garcia da Silva, P and Reid, AP and Peikon, ID and Albeanu, DF and Zador, AM},
title = {High-Throughput Mapping of Single-Neuron Projections by Sequencing of Barcoded RNA.},
journal = {Neuron},
volume = {91},
number = {5},
pages = {975-987},
pmid = {27545715},
issn = {1097-4199},
support = {P30 CA045508/CA/NCI NIH HHS/United States ; R01 DA036913/DA/NIDA NIH HHS/United States ; R01 NS073129/NS/NINDS NIH HHS/United States ; },
mesh = {Animals ; Brain Mapping/*methods ; Cerebral Cortex/cytology/metabolism ; High-Throughput Nucleotide Sequencing/*methods ; Locus Coeruleus/cytology/metabolism ; Mice ; Neural Pathways/metabolism ; Neuroanatomical Tract-Tracing Techniques/*methods ; Neurons/*cytology/*metabolism ; RNA/*analysis/*genetics ; Sequence Analysis, RNA/*methods ; },
abstract = {Neurons transmit information to distant brain regions via long-range axonal projections. In the mouse, area-to-area connections have only been systematically mapped using bulk labeling techniques, which obscure the diverse projections of intermingled single neurons. Here we describe MAPseq (Multiplexed Analysis of Projections by Sequencing), a technique that can map the projections of thousands or even millions of single neurons by labeling large sets of neurons with random RNA sequences ("barcodes"). Axons are filled with barcode mRNA, each putative projection area is dissected, and the barcode mRNA is extracted and sequenced. Applying MAPseq to the locus coeruleus (LC), we find that individual LC neurons have preferred cortical targets. By recasting neuroanatomy, which is traditionally viewed as a problem of microscopy, as a problem of sequencing, MAPseq harnesses advances in sequencing technology to permit high-throughput interrogation of brain circuits.},
}
@article {pmid27541167,
year = {2016},
author = {Giri, D and Li, Z and Ashraf, KM and Collinson, MM and Higgins, DA},
title = {Molecular Combing of λ-DNA using Self-Propelled Water Droplets on Wettability Gradient Surfaces.},
journal = {ACS applied materials &amp; interfaces},
volume = {8},
number = {36},
pages = {24265-24272},
doi = {10.1021/acsami.6b08607},
pmid = {27541167},
issn = {1944-8252},
mesh = {DNA ; Hydrophobic and Hydrophilic Interactions ; Surface Tension ; Water ; *Wettability ; },
abstract = {Surface wettability gradients were used to elongate and align double stranded λ-DNA. Gradients were prepared by vapor phase deposition of octyltrichlorosilane (C8-silane) and fluorinated octyltrichlorosilane (F-silane) precursors. Gradient formation was confirmed by water contact angle and ellipsometric film thickness measurements. Placement of a droplet of aqueous DNA solution on the hydrophobic end of each gradient led to spontaneous motion of the droplet toward the hydrophilic end and deposition of the DNA. Fluorescence imaging of surface-adsorbed YOYO-1 labeled DNA molecules revealed that they are elongated and aligned perpendicular to the droplet-surface contact line at all positions along the gradient, consistent with a dominant role played by surface tension forces in elongating the DNA. The density of adsorbed DNA was found to be greatest on the C8-silane gradient at its hydrophobic end. DNA density decreased toward the hydrophilic end, while the length of the elongated DNA was less dependent on position. The elongation of DNA molecules by spontaneous droplet motion on chemical gradient surfaces has possible applications in DNA barcoding and studies of DNA-protein interactions.},
}
@article {pmid27533015,
year = {2016},
author = {Kristiansen, TA and Jaensson Gyllenbäck, E and Zriwil, A and Björklund, T and Daniel, JA and Sitnicka, E and Soneji, S and Bryder, D and Yuan, J},
title = {Cellular Barcoding Links B-1a B Cell Potential to a Fetal Hematopoietic Stem Cell State at the Single-Cell Level.},
journal = {Immunity},
volume = {45},
number = {2},
pages = {346-357},
doi = {10.1016/j.immuni.2016.07.014},
pmid = {27533015},
issn = {1097-4180},
mesh = {Animals ; Animals, Newborn ; B-Lymphocytes/*physiology ; Cell Differentiation/genetics ; Cell Plasticity ; Cell Self Renewal ; Clone Cells ; DNA-Binding Proteins/genetics/*metabolism ; Female ; Hematopoiesis/genetics ; Hematopoietic Stem Cells/*physiology ; Immunophenotyping ; Liver/*physiology ; Lymphocyte Subsets/*physiology ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; RNA-Binding Proteins ; Single-Cell Analysis ; },
abstract = {Hematopoietic stem cells (HSCs) undergo a functional switch in neonatal mice hallmarked by a decrease in self-renewing divisions and entry into quiescence. Here, we investigated whether the developmental attenuation of B-1a cell output is a consequence of a shift in stem cell state during ontogeny. Using cellular barcoding for in vivo single-cell fate analyses, we found that fetal liver definitive HSCs gave rise to both B-1a and B-2 cells. Whereas B-1a potential diminished in all HSCs with time, B-2 output was maintained. B-1a and B-2 plasticity could be reinitiated in a subset of adult HSCs by ectopic expression of the RNA binding protein LIN28B, a key regulator of fetal hematopoiesis, and this coincided with the clonal reversal to fetal-like elevated self-renewal and repopulation potential. These results anchor the attenuation of B-1a cell output to fetal HSC behavior and demonstrate that the developmental decline in regenerative potential represents a reversible HSC state.},
}
@article {pmid27532108,
year = {2016},
author = {Chaabane, A and Neifar, L and Gey, D and Justine, JL},
title = {Species of Pseudorhabdosynochus (Monogenea, Diplectanidae) from Groupers (Mycteroperca spp., Epinephelidae) in the Mediterranean and Eastern Atlantic Ocean, with Special Reference to the 'Beverleyburtonae Group' and Description of Two New Species.},
journal = {PloS one},
volume = {11},
number = {8},
pages = {e0159886},
pmid = {27532108},
issn = {1932-6203},
mesh = {Animals ; Atlantic Ocean ; Base Sequence ; Electron Transport Complex IV/genetics ; Female ; Fish Diseases/*parasitology ; Gills/*parasitology ; Libya ; Male ; Mediterranean Region ; Perciformes/*parasitology ; Platyhelminths/*anatomy &amp; histology/*classification/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Tunisia ; },
abstract = {Pseudorhabdosynochus Yamaguti, 1958 is a species-rich diplectanid genus, mainly restricted to the gills of groupers (Epinephelidae) and especially abundant in warm seas. Species from the Mediterranean are not fully documented. Two new and two previously known species from the gills of Mycteroperca spp. (M. costae, M. rubra, and M. marginata) in the Mediterranean and Eastern Atlantic Ocean are described here from new material and slides kept in collections. Identifications of newly collected fish were ascertained by barcoding of cytochrome c oxidase subunit I (COI) sequences. Pseudorhabdosynochus beverleyburtonae (Oliver, 1984) Kritsky &amp; Beverley-Burton, 1986 and P. sosia Neifar &amp; Euzet 2007 are redescribed from type-specimens and new specimens collected off Tunisia and Libya from M. marginata and M. costae, respectively. Pseudorhabdosynochus oliveri n. sp., from M. marginata (type-host) off the Mediterranean coast of France (type-locality), is described from specimens found among voucher specimens of P. beverleyburtonae deposited by Guy Oliver in the collection of the Muséum National d'Histoire Naturelle, Paris. Pseudorhabdosynochus oliveri is distinguished by the shape of its sclerotised vagina; it was not found in the other localities investigated. Pseudorhabdosynochus hayet n. sp. is described from M. rubra (type host) off Senegal (type-locality) and Tunisia. Pseudorhabdosynochus hayet is morphologically similar to P. sosia (type-host: M. costae) but was distinguished by differences in measurements of the vagina and male copulatory organ, different host, and divergent COI sequences. The four species (P. beverleyburtonae, P. sosia, P. oliveri, and P. hayet) share common characteristics such as squamodiscs with 2 innermost circular rows of rodlets and a similar general structure of the sclerotised vagina; we propose to group them into a 'beverleyburtonae group' within Pseudorhabdosynochus.},
}
@article {pmid27528664,
year = {2016},
author = {Hoang, ML and Kinde, I and Tomasetti, C and McMahon, KW and Rosenquist, TA and Grollman, AP and Kinzler, KW and Vogelstein, B and Papadopoulos, N},
title = {Genome-wide quantification of rare somatic mutations in normal human tissues using massively parallel sequencing.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {113},
number = {35},
pages = {9846-9851},
pmid = {27528664},
issn = {1091-6490},
support = {P50 CA062924/CA/NCI NIH HHS/United States ; R01 CA057345/CA/NCI NIH HHS/United States ; R37 CA043460/CA/NCI NIH HHS/United States ; R37 CA057345/CA/NCI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Cell Nucleus/genetics ; Child ; Child, Preschool ; DNA, Mitochondrial/chemistry/genetics ; Female ; Genome, Human/*genetics ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Male ; Middle Aged ; *Mutation ; Young Adult ; },
abstract = {We present the bottleneck sequencing system (BotSeqS), a next-generation sequencing method that simultaneously quantifies rare somatic point mutations across the mitochondrial and nuclear genomes. BotSeqS combines molecular barcoding with a simple dilution step immediately before library amplification. We use BotSeqS to show age- and tissue-dependent accumulations of rare mutations and demonstrate that somatic mutational burden in normal human tissues can vary by several orders of magnitude, depending on biologic and environmental factors. We further show major differences between the mutational patterns of the mitochondrial and nuclear genomes in normal tissues. Lastly, the mutation spectra of normal tissues were different from each other, but similar to those of the cancers that arose in them. This technology can provide insights into the number and nature of genetic alterations in normal tissues and can be used to address a variety of fundamental questions about the genomes of diseased tissues.},
}
@article {pmid27527375,
year = {2016},
author = {Miralles, L and Ardura, A and Arias, A and Borrell, YJ and Clusa, L and Dopico, E and de Rojas, AH and Lopez, B and Muñoz-Colmenero, M and Roca, A and Valiente, AG and Zaiko, A and Garcia-Vazquez, E},
title = {Barcodes of marine invertebrates from north Iberian ports: Native diversity and resistance to biological invasions.},
journal = {Marine pollution bulletin},
volume = {112},
number = {1-2},
pages = {183-188},
doi = {10.1016/j.marpolbul.2016.08.022},
pmid = {27527375},
issn = {1879-3363},
mesh = {Animals ; Aquatic Organisms ; *Biodiversity ; Biota ; Bivalvia ; Crassostrea ; *DNA Barcoding, Taxonomic ; *Introduced Species ; *Invertebrates/genetics ; Ships ; Spain ; },
abstract = {Ports are gateways for many marine organisms transported by ships worldwide, especially non-indigenous species (NIS). In this study carried out in North Iberian ports (Cantabrian Sea, Bay of Biscay) we have observed 38% of exotic macroinvertebrates. Four species, namely the barnacle Austrominius modestus, the tubeworm Ficopomatus enigmaticus, the Pacific oyster Crassostrea gigas and the pygmy mussel Xenostrobus securis, exhibited clear signs of invasiveness. A total of 671 barcode (cytochrome oxidase subunit I or 18S rRNA) genes were obtained and confirmed the species status of some cryptic NIS. Negative and significant correlation between diversity estimators of native biota and proportion of NIS suggests biotic resistance in ports. This could be applied to management of port biota for contributing to prevent the settlement of biopollutants in these areas which are very sensitive to biological invasions.},
}
@article {pmid27527172,
year = {2016},
author = {Moufawad El Achkar, C and Lenoble-Hoskovec, C and Paraschiv-Ionescu, A and Major, K and Büla, C and Aminian, K},
title = {Physical Behavior in Older Persons during Daily Life: Insights from Instrumented Shoes.},
journal = {Sensors (Basel, Switzerland)},
volume = {16},
number = {8},
pages = {},
pmid = {27527172},
issn = {1424-8220},
mesh = {Activities of Daily Living ; Aged ; Gait/*physiology ; Humans ; Monitoring, Physiologic/*methods ; *Shoes ; Walking/*physiology ; },
abstract = {Activity level and gait parameters during daily life are important indicators for clinicians because they can provide critical insights into modifications of mobility and function over time. Wearable activity monitoring has been gaining momentum in daily life health assessment. Consequently, this study seeks to validate an algorithm for the classification of daily life activities and to provide a detailed gait analysis in older adults. A system consisting of an inertial sensor combined with a pressure sensing insole has been developed. Using an algorithm that we previously validated during a semi structured protocol, activities in 10 healthy elderly participants were recorded and compared to a wearable reference system over a 4 h recording period at home. Detailed gait parameters were calculated from inertial sensors. Dynamics of physical behavior were characterized using barcodes that express the measure of behavioral complexity. Activity classification based on the algorithm led to a 93% accuracy in classifying basic activities of daily life, i.e., sitting, standing, and walking. Gait analysis emphasizes the importance of metrics such as foot clearance in daily life assessment. Results also underline that measures of physical behavior and gait performance are complementary, especially since gait parameters were not correlated to complexity. Participants gave positive feedback regarding the use of the instrumented shoes. These results extend previous observations in showing the concurrent validity of the instrumented shoes compared to a body-worn reference system for daily-life physical behavior monitoring in older adults.},
}
@article {pmid27525917,
year = {2016},
author = {Kim, WJ and Ji, Y and Choi, G and Kang, YM and Yang, S and Moon, BC},
title = {Molecular identification and phylogenetic analysis of important medicinal plant species in genus Paeonia based on rDNA-ITS, matK, and rbcL DNA barcode sequences.},
journal = {Genetics and molecular research : GMR},
volume = {15},
number = {3},
pages = {},
doi = {10.4238/gmr.15038472},
pmid = {27525917},
issn = {1676-5680},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant ; *DNA, Ribosomal ; Paeonia/*classification/*genetics ; *Phylogeny ; Plants, Medicinal/*classification/*genetics ; },
abstract = {This study was performed to identify and analyze the phylogenetic relationship among four herbaceous species of the genus Paeonia, P. lactiflora, P. japonica, P. veitchii, and P. suffruticosa, using DNA barcodes. These four species, which are commonly used in traditional medicine as Paeoniae Radix and Moutan Radicis Cortex, are pharmaceutically defined in different ways in the national pharmacopoeias in Korea, Japan, and China. To authenticate the different species used in these medicines, we evaluated rDNA-internal transcribed spacers (ITS), matK and rbcL regions, which provide information capable of effectively distinguishing each species from one another. Seventeen samples were collected from different geographic regions in Korea and China, and DNA barcode regions were amplified using universal primers. Comparative analyses of these DNA barcode sequences revealed species-specific nucleotide sequences capable of discriminating the four Paeonia species. Among the entire sequences of three barcodes, marker nucleotides were identified at three positions in P. lactiflora, eleven in P. japonica, five in P. veitchii, and 25 in P. suffruticosa. Phylogenetic analyses also revealed four distinct clusters showing homogeneous clades with high resolution at the species level. The results demonstrate that the analysis of these three DNA barcode sequences is a reliable method for identifying the four Paeonia species and can be used to authenticate Paeoniae Radix and Moutan Radicis Cortex at the species level. Furthermore, based on the assessment of amplicon sizes, inter/intra-specific distances, marker nucleotides, and phylogenetic analysis, rDNA-ITS was the most suitable DNA barcode for identification of these species.},
}
@article {pmid27525916,
year = {2016},
author = {Enan, MR and Ahmed, A},
title = {Cultivar-level phylogeny using chloroplast DNA barcode psbK-psbI spacers for identification of Emirati date palm (Phoenix dactylifera L.) varieties.},
journal = {Genetics and molecular research : GMR},
volume = {15},
number = {3},
pages = {},
doi = {10.4238/gmr.15038470},
pmid = {27525916},
issn = {1676-5680},
mesh = {*DNA Barcoding, Taxonomic ; *DNA, Chloroplast ; Genetic Variation ; Haplotypes ; Phoeniceae/*classification/*genetics ; },
abstract = {The efficacy of genetic material for use as DNA barcodes is under constant evaluation and improvement as new barcodes offering better resolution and efficiency of amplification for specific species groups are identified. In this study, the chloroplast intergenic spacer psbK-psbI was evaluated for the first time as a DNA barcode for distinguishing date palm cultivars. Nucleotide sequences were aligned using MEGA 6.0 to calculate pairwise divergence among the cultivars. The analyzed data illustrated a considerable level of variability in the genetic pool of the selected cultivars (0.009). In fact, five haplotypes were detected among 30 cultivars examined, yielding a haplotype diversity of 0.685. An unweighted pair group method with arithmetic mean phylogenetic tree was constructed and shows a well-defined relationship among date palm cultivar varieties. On the other hand, selective neutrality investigations using Tajima test and Fu and Li tests were negative, providing evidence that date palm has been undergoing rapid expansion and recent population growth. Thus, we suggest that the psbK-psbI spacer can be successfully used to construct reliable phylogenetic trees for P. dactylifera.},
}
@article {pmid27525660,
year = {2016},
author = {Ng, TH and Tan, SK and Wong, WH and Meier, R and Chan, SY and Tan, HH and Yeo, DC},
title = {Molluscs for Sale: Assessment of Freshwater Gastropods and Bivalves in the Ornamental Pet Trade.},
journal = {PloS one},
volume = {11},
number = {8},
pages = {e0161130},
pmid = {27525660},
issn = {1932-6203},
mesh = {Animals ; *Bivalvia/classification ; Commerce/*statistics &amp; numerical data ; DNA Barcoding, Taxonomic ; *Fresh Water ; *Gastropoda/classification ; Pets/*economics ; },
abstract = {The ornamental pet trade is often considered a key culprit for conservation problems such as the introduction of invasive species (including infectious diseases) and overharvesting of rare species. Here, we present the first assessment of the biodiversity of freshwater molluscs in the ornamental pet trade in Singapore, one of the most important global hubs of the ornamental aquarium trade, and discuss associated conservation concerns. We recorded freshwater molluscs from ornamental pet shops and major exporters including non-ornamental species (e.g., hitchhikers, molluscs sold as fish feed). We recorded an unexpectedly high diversity-59 species-of freshwater bivalves and gastropods, with the majority (38 species or 64%) being from the Oriental region. In addition to morphological examination, we sequenced the DNA barcode region of mitochondrial CO1 and 16S genes to provide molecular data for the confirmation of the identification and for future re-identification. DNA barcodes were obtained for 50 species, and all but four were separated by > 3% uncorrected pairwise distances. The trade has been considered a main introduction pathway for non-native species to Singapore, and we found that out of 15 species in the trade as well as in the wild in Singapore, 12 are either introduced or of unknown origin, representing almost half of the known non-native freshwater molluscs in Singapore. Particularly prevalent are non-ornamental species: six hitchhikers on aquarium plants and six species sold as fish feed. We found that a quarter of the trade species have a history of introduction, which includes 11 known or potentially invasive species. We conclude that potential overharvesting is difficult to assess because only half of the trade species have been treated by IUCN. Of these, 21 species are of Least Concern and three are Data Deficient. Our checklist, with accompanying DNA barcodes, images, and museum vouchers, provides an important reference library for future monitoring, and constitutes a step toward creating a more sustainable ornamental pet trade.},
}
@article {pmid27524652,
year = {2016},
author = {Stokholm, MS and Wulff, EG and Zida, EP and Thio, IG and Néya, JB and Soalla, RW and Głazowska, SE and Andresen, M and Topbjerg, HB and Boelt, B and Lund, OS},
title = {DNA barcoding and isolation of vertically transmitted ascomycetes in sorghum from Burkina Faso: Epicoccum sorghinum is dominant in seedlings and appears as a common root pathogen.},
journal = {Microbiological research},
volume = {191},
number = {},
pages = {38-50},
doi = {10.1016/j.micres.2016.05.004},
pmid = {27524652},
issn = {1618-0623},
mesh = {Ascomycota/*classification/*genetics/isolation &amp; purification ; Burkina Faso ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; *Genetic Variation ; Phylogeny ; Plant Diseases/microbiology ; Plant Roots/microbiology ; RNA, Ribosomal, 18S/genetics ; Seedlings/microbiology ; Sequence Analysis, DNA ; Sorghum/*microbiology ; },
abstract = {Molecular identification of fungal taxa commonly transmitted through seeds of sorghum in Western Africa is lacking. In the present study, farm-saved seeds, collected from four villages in Northern Burkina Faso, were surface sterilized and the distribution of fungal DNA in seeds and seven-day-old seedlings was analyzed by 18S ribosomal DNA (rDNA) amplicon sequencing. More than 99% of the fungal rDNA was found to originate from ascomycetes. The distribution of ascomycetes at species level was subsequently analyzed by barcoding of ITS2 rDNA. Eighteen Operational Taxonomic Units (OTUs) were identified from seedlings, compared to 29 OTUs from seeds. The top-eight most abundant ascomycete OTUs from seedlings were annotated as: Epicoccum sorghinum, Fusarium thapsinum, four different Curvularia spp., Exserohilum rostratum and Alternaria longissima. These OTUs were also present in amplicons from seed samples collected in Central Burkina Faso confirming a common occurrence. E. sorghinum was highly predominant in seedlings both measured by DNA analysis and by isolation. The dominance of E. sorghinum was particularly strong in roots from poorly growing seedlings. Pathogenicity of E. sorghinum isolates was compared to F. thapsinum by inoculation to seeds in vitro. Both fungal species caused significant inhibition of seedling growth (P<0.001) and Koch's postulates were fulfilled. Extensive, dark necrosis in roots was a typical symptom of E. sorghinum, whereas wilting of leaves was caused primarily by F. thapsinum. This study provides the first molecular approach to characterize the seedling mycoflora of sorghum in Western Africa and suggests E. sorghinum as a common root pathogen.},
}
@article {pmid27522369,
year = {2016},
author = {Broda, L and Dabert, M and Glowska, E},
title = {Aulonastus similis n. sp., a new quill mite species (Syringophilidae) parasitising passeriform birds (Tyrannidae and Cardinalidae) in Mexico.},
journal = {Systematic parasitology},
volume = {93},
number = {7},
pages = {715-719},
pmid = {27522369},
issn = {1573-5192},
mesh = {Animals ; Electron Transport Complex IV/genetics ; Feathers/parasitology ; Female ; Mexico ; Mites/anatomy &amp; histology/*classification/genetics ; Passeriformes/*parasitology ; RNA, Ribosomal, 28S/*genetics ; Species Specificity ; },
abstract = {A new quill mite species, Aulonastus similis n. sp. (Acariformes: Syringophilidae), parasitising Myiozetetes similis (Spix) (Tyrannidae) and Habia fuscicauda (Cabanis) (Cardinalidae) in Mexico is described and DNA barcode sequences of the mitochondrial cytochrome c oxidase subunit I (cox1) and D1-D3 region of the nuclear 28S rRNA gene are provided. Morphologically, females of A. similis are close to A. euphagus Skoracki, Hendricks &amp; Spicer, 2010 but differ from this species in the length ratios of the idiosomal setae: ve:si (2-2.3:1 vs 1:1) and f2:f1 (4.7-6.3:1 vs 3.3:1).},
}
@article {pmid27515647,
year = {2016},
author = {Pyataeva, SV and Hopcroft, RR and Lindsay, DJ and Collins, AG},
title = {DNA barcodes unite two problematic taxa: the meiobenthic Boreohydra simplex is a life-cycle stage of Plotocnide borealis (Hydrozoa: Aplanulata).},
journal = {Zootaxa},
volume = {4150},
number = {1},
pages = {85-92},
doi = {10.11646/zootaxa.4150.1.5},
pmid = {27515647},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Hydrozoa/*anatomy &amp; histology/*classification/genetics ; Life Cycle Stages/*genetics ; Phylogeny ; },
abstract = {Genetic barcodes of arctic medusae and meiobenthic cnidarians have uncovered a fortuitous connection between the medusa Plotocnide borealis Wagner, 1885 and the minute, mud-dwelling polyp Boreohydra simplex Westblad, 1937. Little to no sequence differences exist among independently collected samples identified as Boreohydra simplex and Plotocnide borealis, showing that the two different forms represent a single species that is henceforth known by the older name Plotocnide borealis Wagner, 1885. The polyp form has been observed to produce bulges previously hypothesized to be gonophores, and the results here are consistent with that view. Interestingly, the polyp has also been reported to produce egg cells in the epiderm, a surprising phenomenon that we document here for only the second time. Thus, P. borealis produces eggs in two different life stages, polyp and medusa. This is the first documented case of a metagenetic medusozoan species being able to produce gametes in both the medusa and polyp stage. It remains unclear what environmental/ecological conditions modulate the production of eggs and/or medusa buds in the polyp stage. Similarly, sperm production, fertilization and development are unknown, warranting further studies.},
}
@article {pmid27515644,
year = {2016},
author = {Iaciofano, D and Brutto, SL},
title = {Re-description of Orchestia stephenseni Cecchini, 1928: designation of neotype and senior synonym to Orchestia constricta A. Costa, 1853 (Crustacea: Amphipoda: Talitridae) by Reversal of Precedence.},
journal = {Zootaxa},
volume = {4150},
number = {1},
pages = {40-60},
doi = {10.11646/zootaxa.4150.1.2},
pmid = {27515644},
issn = {1175-5334},
mesh = {Amphipoda/*anatomy &amp; histology/*classification/genetics ; Animal Structures/anatomy &amp; histology ; Animals ; Body Size ; DNA Barcoding, Taxonomic ; Male ; Mediterranean Sea ; Phylogeny ; Sicily ; },
abstract = {The beach flea Orchestia stephenseni was originally described by Cecchini (1928), and successively by Karaman (1973). The description of this species will be herein revised by focusing on the variation of the gnathopod 2 in males, as detected during its growth period. An analysis of DNA Barcoding was performed to support the assignment of the taxonomic species to five morphotypes. As the type specimen has not yet been designated, a neotype is assigned. The name of the species is here presented as a valid name as it satisfies the requirements of a Reversal of the Principle of Priority: Orchestia stephenseni takes precedence over the objective synonym Orchestia constricta A. Costa, 1853, in accordance with Article 23.9.2. of the International Code of Zoological Nomenclature. Orchestia stephenseni Cecchini, 1928 becomes nomen protectum, and Orchestia constricta nomen oblitum. The results presented in this paper also support the status of Orchestia stephenseni as a Mediterranean endemic species, thereby rejecting previous Atlantic records. The synonymies for O. stephenseni are revised accordingly.},
}
@article {pmid27515641,
year = {2016},
author = {Krug, PJ and Vendetti, JE and Valdés, &#xc1;},
title = {Molecular and morphological systematics of Elysia Risso, 1818 (Heterobranchia: Sacoglossa) from the Caribbean region.},
journal = {Zootaxa},
volume = {4148},
number = {1},
pages = {1-137},
doi = {10.11646/zootaxa.4148.1.1},
pmid = {27515641},
issn = {1175-5334},
mesh = {Animals ; Caribbean Region ; Female ; Gastropoda/*anatomy &amp; histology/*physiology ; Larva ; Male ; },
abstract = {The Caribbean is a biodiversity hotspot for photosynthetic sea slugs, with about 27 described species in the genus Elysia Risso, 1818. However, many species are poorly known or have complex taxonomic histories, complicating assessments of regional biodiversity and impeding studies of plastid symbiosis, speciation, and larval biology. Using an integrative approach, we address the taxonomy and systematics of Caribbean elysiids by performing robust tests of existing species hypotheses, and describe six new species. Species delimitation included DNA barcoding of up to 189 nominal conspecific specimens; nuclear gene sequences were then used to confirm that divergent lineages were genetically distinct candidate species. New synonymies and species descriptions are based on external anatomy, penial and radular morphology, developmental characters, and host ecology of all species described from the region, plus a critical review of the literature. We synonymized three species (Elysia annedupontae Ortea, Espinosa &amp; Caballer in Ortea, Caballer, Moro &amp; Espinosa, 2005, Elysia clarki Pierce et al. 2006, and Elysia leeanneae Caballer, Ortea &amp; Espinosa in Ortea, Espinosa, Buske &amp; Caballer, 2013), transfered one species from Bosellia (Elysia marcusi), and described six new species (Elysia pawliki n. sp., Elysia zemi n. sp., Elysia christinae n. sp., Elysia hamanni n. sp., Elysia taino n. sp., and Elysia buonoi n. sp.). We resurrected the name Elysia velutinus Pruvot-Fol, 1947, a senior synonym of Elysia tuca Ev. Marcus &amp; Er. Marcus, 1967. Based on a four-gene phylogeny of 76 Elysia spp., we identified shifts in host use and penial armature that may explain patterns of endemic diversification in Elysia, invoking both ecological and non-ecological mechanisms. Non-monophyly of stylet-bearing species rejects previous attempts to classify species based on presence of a stylet (i.e., the genus Checholysia Ortea, Caballer, Moro &amp; Espinosa, 2005). Our findings show how integrative approaches can resolve the taxonomic status of problematic species (e.g., Elysia papillosa Verrill, 1901) for soft-bodied marine taxa.},
}
@article {pmid27515166,
year = {2016},
author = {Ahumada, ML and Orjuela, LI and Pareja, PX and Conde, M and Cabarcas, DM and Cubillos, EF and Lopez, JA and Beier, JC and Herrera, S and Quiñones, ML},
title = {Spatial distributions of Anopheles species in relation to malaria incidence at 70 localities in the highly endemic Northwest and South Pacific coast regions of Colombia.},
journal = {Malaria journal},
volume = {15},
number = {1},
pages = {407},
pmid = {27515166},
issn = {1475-2875},
support = {U19 AI089702/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Anopheles/*classification/*growth &amp; development ; Cluster Analysis ; Colombia/epidemiology ; Cross-Sectional Studies ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Electron Transport Complex IV/genetics ; Female ; Humans ; Incidence ; Malaria/*epidemiology ; Male ; Mosquito Vectors/*classification/*growth &amp; development ; Phylogeny ; *Phylogeography ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Spatial Analysis ; *Topography, Medical ; },
abstract = {BACKGROUND: A proper identification of malaria vectors is essential for any attempt to control this disease. Between 40 and 47 Anopheles species have been recorded in Colombia, and eight species complexes have been identified in the last decade. An update of Anopheles species distribution and its relationship with malaria is required, particularly for newly identified members of species complexes.<br><br>METHODS: A cross-sectional entomological study was conducted at 70 localities in the highest malaria transmission areas in Colombia. In each locality, immature and adult mosquitoes were collected. All specimens were determined using morphological characters and confirmed used restriction profiles of Internal Transcribed Spacer 2 (PCR-RFLP-ITS2), and Cytochrome c Oxidase I (COI) sequence gene. To detect natural Plasmodium infections, enzyme-linked immunosorbent assay and nested PCR analysis were used. Distribution of Anopheles species was spatially associated with malaria incidence.<br><br>RESULTS: A total of 1736 larvae and 12,052 adult mosquitoes were determined in the 70 localities. Thirteen Anopheles species were identified. COI sequence analysis suggested 4 new lineages for Colombia: for Anopheles albimanus (An. albimanus B), Anopheles pseudopunctipennis s.l., Anopheles neivai (An. neivai nr. neivai 4), and Anopheles apicimacula. Two members of species complexes were identified, as: Anopheles nuneztovari C, and Anopheles albitarsis I. Another seven species were confirmed. Four mosquitoes were infected with Plasmodium species, An. albimanus B and An. nuneztovari C. In Northwest of Colombia, An. nuneztovari C, An. albimanus, and Anopheles darlingi were present in the municipalities with highest annual parasitic index (API) (>35 cases/1000 inhabitants). In the north of South Pacific coast, with a similar API, An. nuneztovari C were widely distributed inland, and the main species in coastal regions were An. albimanus B and An. neivai s.l. In the South Pacific coast bordering with Ecuador, 3 Anopheles species were found in municipalities with high API (15-88 cases/1000 inhabitants): An. albimanus B, Anopheles calderoni and An. neivai s.l.<br><br>CONCLUSIONS: In the highest malaria areas of Colombia, 13 Anopheles species and four new lineages were found, which highlights the need for updating the species distribution. A DNA barcode analysis allowed the taxonomic identification to be refined, particularly for species complexes, and to improve the further understanding of their relation with malaria transmission.},
}
@article {pmid27513649,
year = {2016},
author = {Del-Prado, R and Divakar, PK and Lumbsch, HT and Crespo, AM},
title = {Hidden Genetic Diversity in an Asexually Reproducing Lichen Forming Fungal Group.},
journal = {PloS one},
volume = {11},
number = {8},
pages = {e0161031},
pmid = {27513649},
issn = {1932-6203},
mesh = {Bayes Theorem ; Biological Evolution ; DNA Barcoding, Taxonomic ; DNA, Fungal/*genetics ; *Genetic Variation ; Lichens/*genetics ; Phylogeny ; Reproduction, Asexual/*genetics ; },
abstract = {Asexual species with vegetative propagation of both symbiont partners (soredia) in lichens may harbor lower species diversity because they may indeed represent evolutionary dead ends or clones. In this study we aim to critically examine species boundaries in the sorediate lichen forming fungi Parmotrema reticulatum-Parmotrema pseudoreticulatum complex applying coalescent-based approaches and other recently developed DNA-based methods. To this end, we gathered 180 samples from Africa, Asia, Australasia, Europe, North and South America and generated sequences of internal transcribed spacer of nuclear ribosomal DNA (ITS) and DNA replication licensing factor MCM7 (MCM7). The dataset was analysed using different approaches such as traditional phylogeny-maximum likelihood and Bayesian-genetic distances, automatic barcode gap discovery and coalescent-based methods-PTP, GMYC, spedeSTEM and *Beast-in order to test congruence among results. Additionally, the divergence times were also estimated to elucidate diversification events. Delimitations inferred from the different analyses are comparable with only minor differences, and following a conservative approach we propose that the sampled specimens of the P. reticulatum-P. pseudoreticulatum complex belong to at least eight distinct species-level lineages. Seven are currently classified under P. reticulatum and one as P. pseudoreticulatum. In this work we discuss one of only few examples of cryptic species that have so far been found in sorediate reproducing lichen forming fungi. Additionally our estimates suggest a recent origin of the species complex-during the Miocene. Consequently, the wide distribution of several of the cryptic species has to be explained by intercontinental long-distance dispersal events.},
}
@article {pmid27509323,
year = {2017},
author = {Zhang, Q and Agatha, S and Zhang, W and Dong, J and Yu, Y and Jiao, N and Gong, J},
title = {Three rDNA Loci-Based Phylogenies of Tintinnid Ciliates (Ciliophora, Spirotrichea, Choreotrichida).},
journal = {The Journal of eukaryotic microbiology},
volume = {64},
number = {2},
pages = {226-241},
pmid = {27509323},
issn = {1550-7408},
support = {P 28790/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Biodiversity ; China ; Ciliophora/*classification/cytology/*genetics/isolation &amp; purification ; DNA, Protozoan/genetics ; DNA, Ribosomal/*genetics ; France ; Genetic Variation ; Microscopy ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; RNA, Ribosomal, 5.8S/genetics ; Seawater/parasitology ; Species Specificity ; },
abstract = {To improve understanding of diversity, phylogeny and evolution in tintinnid ciliates, it is essential to link multiple molecular markers with properly identified and documented morphospecies. Accordingly, 54 tintinnid morphospecies/isolates mainly from the Yellow and East China Seas were collected and analysed. Using single-cell approaches, sequences were obtained for three rDNA loci (18S, ITS1-5.8S-ITS2, D1-D5 region of 28S). Twenty-six tintinnid morphospecies (29 isolates) are documented by micrographs, measurements, morphologically described, and compared with the original species description. Three rDNA loci-based phylogenetic analyses were then performed for these identified isolates. Sequences from 25 unidentified species/isolates were also included in the comparison of the three rDNA loci. Ribosomal DNA genes of the genus Leprotintinnus were analysed for the first time, showing that Leprotintinnus was closely related to Tintinnopsis radix and branched distinctly apart from the family Tintinnidiidae. Four novel clades (VI to IX) of the Tintinnopsis complex emerged in the 18S genealogies. Analyses of the relative variability in the ITS and 28S regions vs. the 18S rDNA showed that the ITS1-5.8S-ITS2 and ITS2 regions well co-varied with the 18S rDNA when the variations of the latter were less than 3%, whereas at difference of less than 1%, no correlation was found between the compared loci. These findings highlight the difficulties in using variable locus-based cut-off divergences in circumscribing tintinnid morphospecies.},
}
@article {pmid27509042,
year = {2016},
author = {Mitchell, A and Gopurenko, D},
title = {DNA Barcoding the Heliothinae (Lepidoptera: Noctuidae) of Australia and Utility of DNA Barcodes for Pest Identification in Helicoverpa and Relatives.},
journal = {PloS one},
volume = {11},
number = {8},
pages = {e0160895},
pmid = {27509042},
issn = {1932-6203},
mesh = {Animals ; Australia ; DNA Barcoding, Taxonomic ; Moths/*classification/*genetics ; Pest Control ; Phylogeny ; },
abstract = {Helicoverpa and Heliothis species include some of the world's most significant crop pests, causing billions of dollars of losses globally. As such, a number are regulated quarantine species. For quarantine agencies, the most crucial issue is distinguishing native species from exotics, yet even this task is often not feasible because of poorly known local faunas and the difficulties of identifying closely related species, especially the immature stages. DNA barcoding is a scalable molecular diagnostic method that could provide the solution to this problem, however there has been no large-scale test of the efficacy of DNA barcodes for identifying the Heliothinae of any region of the world to date. This study fills that gap by DNA barcoding the entire heliothine moth fauna of Australia, bar one rare species, and comparing results with existing public domain resources. We find that DNA barcodes provide robust discrimination of all of the major pest species sampled, but poor discrimination of Australian Heliocheilus species, and we discuss ways to improve the use of DNA barcodes for identification of pests.},
}
@article {pmid27507959,
year = {2016},
author = {Ahmed, A},
title = {Analysis of Metagenomics Next Generation Sequence Data for Fungal ITS Barcoding: Do You Need Advance Bioinformatics Experience?.},
journal = {Frontiers in microbiology},
volume = {7},
number = {},
pages = {1061},
pmid = {27507959},
issn = {1664-302X},
abstract = {During the last few decades, most of microbiology laboratories have become familiar in analyzing Sanger sequence data for ITS barcoding. However, with the availability of next-generation sequencing platforms in many centers, it has become important for medical mycologists to know how to make sense of the massive sequence data generated by these new sequencing technologies. In many reference laboratories, the analysis of such data is not a big deal, since suitable IT infrastructure and well-trained bioinformatics scientists are always available. However, in small research laboratories and clinical microbiology laboratories the availability of such resources are always lacking. In this report, simple and user-friendly bioinformatics work-flow is suggested for fast and reproducible ITS barcoding of fungi.},
}
@article {pmid27507489,
year = {2017},
author = {Raja, HA and Baker, TR and Little, JG and Oberlies, NH},
title = {DNA barcoding for identification of consumer-relevant mushrooms: A partial solution for product certification?.},
journal = {Food chemistry},
volume = {214},
number = {},
pages = {383-392},
doi = {10.1016/j.foodchem.2016.07.052},
pmid = {27507489},
issn = {1873-7072},
mesh = {Agaricales/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {One challenge in the dietary supplement industry is confirmation of species identity for processed raw materials, i.e. those modified by milling, drying, or extraction, which move through a multilevel supply chain before reaching the finished product. This is particularly difficult for samples containing fungal mycelia, where processing removes morphological characteristics, such that they do not present sufficient variation to differentiate species by traditional techniques. To address this issue, we have demonstrated the utility of DNA barcoding to verify the taxonomic identity of fungi found commonly in the food and dietary supplement industry; such data are critical for protecting consumer health, by assuring both safety and quality. By using DNA barcoding of nuclear ribosomal internal transcribed spacer (ITS) of the rRNA gene with fungal specific ITS primers, ITS barcodes were generated for 33 representative fungal samples, all of which could be used by consumers for food and/or dietary supplement purposes. In the majority of cases, we were able to sequence the ITS region from powdered mycelium samples, grocery store mushrooms, and capsules from commercial dietary supplements. After generating ITS barcodes utilizing standard procedures accepted by the Consortium for the Barcode of Life, we tested their utility by performing a BLAST search against authenticate published ITS sequences in GenBank. In some cases, we also downloaded published, homologous sequences of the ITS region of fungi inspected in this study and examined the phylogenetic relationships of barcoded fungal species in light of modern taxonomic and phylogenetic studies. We anticipate that these data will motivate discussions on DNA barcoding based species identification as applied to the verification/certification of mushroom-containing dietary supplements.},
}
@article {pmid27501051,
year = {2016},
author = {Chand Dakal, T and Giudici, P and Solieri, L},
title = {Contrasting Patterns of rDNA Homogenization within the Zygosaccharomyces rouxii Species Complex.},
journal = {PloS one},
volume = {11},
number = {8},
pages = {e0160744},
pmid = {27501051},
issn = {1932-6203},
mesh = {DNA, Fungal/*genetics ; DNA, Ribosomal/*genetics ; DNA, Ribosomal Spacer/*genetics ; Evolution, Molecular ; Phylogeny ; Polymorphism, Genetic/*genetics ; Repetitive Sequences, Nucleic Acid/*genetics ; Zygosaccharomyces/*genetics ; },
abstract = {Arrays of repetitive ribosomal DNA (rDNA) sequences are generally expected to evolve as a coherent family, where repeats within such a family are more similar to each other than to orthologs in related species. The continuous homogenization of repeats within individual genomes is a recombination process termed concerted evolution. Here, we investigated the extent and the direction of concerted evolution in 43 yeast strains of the Zygosaccharomyces rouxii species complex (Z. rouxii, Z. sapae, Z. mellis), by analyzing two portions of the 35S rDNA cistron, namely the D1/D2 domains at the 5' end of the 26S rRNA gene and the segment including the internal transcribed spacers (ITS) 1 and 2 (ITS regions). We demonstrate that intra-genomic rDNA sequence variation is unusually frequent in this clade and that rDNA arrays in single genomes consist of an intermixing of Z. rouxii, Z. sapae and Z. mellis-like sequences, putatively evolved by reticulate evolutionary events that involved repeated hybridization between lineages. The levels and distribution of sequence polymorphisms vary across rDNA repeats in different individuals, reflecting four patterns of rDNA evolution: I) rDNA repeats that are homogeneous within a genome but are chimeras derived from two parental lineages via recombination: Z. rouxii in the ITS region and Z. sapae in the D1/D2 region; II) intra-genomic rDNA repeats that retain polymorphisms only in ITS regions; III) rDNA repeats that vary only in their D1/D2 domains; IV) heterogeneous rDNA arrays that have both polymorphic ITS and D1/D2 regions. We argue that an ongoing process of homogenization following allodiplodization or incomplete lineage sorting gave rise to divergent evolutionary trajectories in different strains, depending upon temporal, structural and functional constraints. We discuss the consequences of these findings for Zygosaccharomyces species delineation and, more in general, for yeast barcoding.},
}
@article {pmid27494556,
year = {2016},
author = {Drost, J and Clevers, H},
title = {Who Is in the Driver's Seat: Tracing Cancer Genes Using CRISPR-Barcoding.},
journal = {Molecular cell},
volume = {63},
number = {3},
pages = {352-354},
doi = {10.1016/j.molcel.2016.07.013},
pmid = {27494556},
issn = {1097-4164},
mesh = {*Clustered Regularly Interspaced Short Palindromic Repeats ; Humans ; Mutation ; *Oncogenes ; },
abstract = {Intratumor heterogeneity is thought to be the driving force of tumor evolution and therapy resistance. Yet tools to study these processes are limited. In this issue, Guernet et al. (2016) devised clustered regularly interspaced short palindromic repeats (CRISPR)-barcoding to functionally annotate specific mutations and study clonal evolution in heterogeneous cell populations.},
}
@article {pmid27493679,
year = {2016},
author = {Yang, GQ and Chen, YM and Wang, JP and Guo, C and Zhao, L and Wang, XY and Guo, Y and Li, L and Li, DZ and Guo, ZH},
title = {Development of a universal and simplified ddRAD library preparation approach for SNP discovery and genotyping in angiosperm plants.},
journal = {Plant methods},
volume = {12},
number = {},
pages = {39},
pmid = {27493679},
issn = {1746-4811},
abstract = {BACKGROUND: The double digest restriction-site associated DNA sequencing technology (ddRAD-seq) is a reduced representation sequencing technology by sampling genome-wide enzyme loci developed on the basis of next-generation sequencing. ddRAD-seq has been widely applied to SNP marker development and genotyping on animals, especially on marine animals as the original ddRAD protocol is mainly built and trained based on animal data. However, wide application of ddRAD-seq technology in plant species has not been achieved so far. Here, we aim to develop an optimized ddRAD library preparation protocol be accessible to most angiosperm plant species without much startup pre-experiment and costs.<br><br>RESULTS: We first tested several combinations of enzymes by in silico analysis of 23 plant species covering 17 families of angiosperm and 1 family of bryophyta and found AvaII&#xa0;+&#xa0;MspI enzyme pair produced consistently higher number of fragments in a broad range of plant species. Then we removed two purifying and one quantifying steps of the original protocol, replaced expensive consumables and apparatuses by conventional experimental apparatuses. Besides, we shortened P1 adapter from 37 to 25&#xa0;bp and designed a new barcode-adapter system containing 20 pairs of barcodes of varying length. This is an optimized ddRAD strategy for angiosperm plants that is economical, time-saving and requires little technical expertise or investment in laboratory equipment. We refer to this simplified protocol as MiddRAD and we demonstrated the utility and flexibility of our approach by resolving phylogenetic relationships of two genera of woody bamboos (Dendrocalamus and Phyllostachys). Overall our results provide empirical evidence for using this method on different model and non-model plants to produce consistent data.<br><br>CONCLUSIONS: As MiddRAD adopts an enzyme pair that works for a broad range of angiosperm plants, simplifies library constructing procedure and requires less DNA input, it will greatly facilitate designing a ddRAD project. Our optimization of this method may make ddRAD be widely used in fields of plant population genetics, phylogenetics, phylogeography and molecular breeding.},
}
@article {pmid27490633,
year = {2016},
author = {Turchaninova, MA and Davydov, A and Britanova, OV and Shugay, M and Bikos, V and Egorov, ES and Kirgizova, VI and Merzlyak, EM and Staroverov, DB and Bolotin, DA and Mamedov, IZ and Izraelson, M and Logacheva, MD and Kladova, O and Plevova, K and Pospisilova, S and Chudakov, DM},
title = {High-quality full-length immunoglobulin profiling with unique molecular barcoding.},
journal = {Nature protocols},
volume = {11},
number = {9},
pages = {1599-1616},
pmid = {27490633},
issn = {1750-2799},
mesh = {Animals ; Base Sequence ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Immunoglobulin Heavy Chains/*genetics ; Immunoglobulin Light Chains/*genetics ; Mice ; Mutation ; Quality Control ; Sequence Analysis, DNA/*methods ; },
abstract = {High-throughput sequencing analysis of hypermutating immunoglobulin (IG) repertoires remains a challenging task. Here we present a robust protocol for the full-length profiling of human and mouse IG repertoires. This protocol uses unique molecular identifiers (UMIs) introduced in the course of cDNA synthesis to control bottlenecks and to eliminate PCR and sequencing errors. Using asymmetric 400+100-nt paired-end Illumina sequencing and UMI-based assembly with the new version of the MIGEC software, the protocol allows up to 750-nt lengths to be sequenced in an almost error-free manner. This sequencing approach should also be applicable to various tasks beyond immune repertoire studies. In IG profiling, the achieved length of high-quality sequence covers the variable region of even the longest chains, along with the fragment of a constant region carrying information on the antibody isotype. The whole protocol, including preparation of cells and libraries, sequencing and data analysis, takes 5 to 6 d.},
}
@article {pmid27489493,
year = {2016},
author = {Ngoc, NV and Tagane, S and Binh, HT and Toyama, H and Okabe, N and Duy, CN and Yahara, T},
title = {Popowia bachmaensis (Annonaceae), a new species from Bach Ma National Park, Central Vietnam.},
journal = {PhytoKeys},
volume = {},
number = {65},
pages = {125-131},
pmid = {27489493},
issn = {1314-2011},
abstract = {A new species, Popowia bachmaensis Ngoc, Tagane &amp; Yahara, sp. nov. is described from Bach Ma National Park in Thua Thien Hue Province, Central Vietnam. This species is morphologically similar to Popowia pisocarpa (Blume) Endl. ex Walp., but can be readily distinguished from it by its lower stems, smaller leaves, shorter flowering pedicels, shorter carpels, longer sepals and inner petals. A detailed description, comprising illustrations, and supplemented with DNA barcodes of the two regions of rbcL and matK, are provided.},
}
@article {pmid27489488,
year = {2016},
author = {Toyama, H and Tagane, S and Dang, VS and Tran, H and Nagamasu, H and Naiki, A and Yahara, T},
title = {A new species of Eustigma (Hamamelidaceae) from Hon Ba Nature Reserve, Vietnam.},
journal = {PhytoKeys},
volume = {},
number = {65},
pages = {47-55},
pmid = {27489488},
issn = {1314-2011},
abstract = {A new species of Hamamelidaceae, Eustigma honbaense H.Toyama, Tagane &amp; V.S.Dang, sp. nov., is described from Hon Ba Nature Reserve, Vietnam. This species is similar to Eustigma oblongifolium Gardner &amp; Champ., but differs from it in having entire leaves, longer infructescences, capsules with a longer apical part and seeds with a larger hilum. A description, preliminary conservation assessment, illustration and photographs of the new species are provided, as well as an updated key to the genus Eustigma.},
}
@article {pmid27489487,
year = {2016},
author = {Yahara, T and Tagane, S and Mase, K and Chhang, P and Toyama, H},
title = {Flora of Bokor National Park V: Two new species of Machilus (Lauraceae), M. bokorensis and M. brevipaniculata.},
journal = {PhytoKeys},
volume = {},
number = {65},
pages = {35-46},
pmid = {27489487},
issn = {1314-2011},
abstract = {Two new species, Machilus bokorensis Yahara &amp; Tagane and Machilus brevipaniculata Yahara &amp; Tagane (Lauraceae) are described from Bokor National Park, Cambodia with their illustrations and DNA barcodes of the two plastid regions of rbcL and matK and the nuclear region of ITS.},
}
@article {pmid27486467,
year = {2016},
author = {Feng, S and Jiang, M and Shi, Y and Jiao, K and Shen, C and Lu, J and Ying, Q and Wang, H},
title = {Application of the Ribosomal DNA ITS2 Region of Physalis (Solanaceae): DNA Barcoding and Phylogenetic Study.},
journal = {Frontiers in plant science},
volume = {7},
number = {},
pages = {1047},
pmid = {27486467},
issn = {1664-462X},
abstract = {Recently, commercial interest in Physalis species has grown worldwide due to their high nutritional value, edible fruit, and potential medicinal properties. However, many Physalis species have similar shapes and are easily confused, and consequently the phylogenetic relationships between Physalis species are poorly understood. This hinders their safe utilization and genetic resource conservation. In this study, the nuclear ribosomal ITS2 region was used to identify species and phylogenetically examine Physalis. Eighty-six ITS2 regions from 45 Physalis species were analyzed. The ITS2 sequences were aligned using Clustal W and genetic distances were calculated using MEGA V6.0. The results showed that ITS2 regions have significant intra- and inter-specific divergences, obvious barcoding gaps, and higher species discrimination rates (82.2% for both the BLASTA1 and nearest distance methods). In addition, the secondary structure of ITS2 provided another way to differentiate species. Cluster analysis based on ITS2 regions largely concurred with the relationships among Physalis species established by many previous molecular analyses, and showed that most sections of Physalis appear to be polyphyletic. Our results demonstrated that ITS2 can be used as an efficient and powerful marker in the identification and phylogenetic study of Physalis species. The technique provides a scientific basis for the conservation of Physalis plants and for utilization of resources.},
}
@article {pmid27485345,
year = {2016},
author = {Li, C and Chng, KR and Boey, EJ and Ng, AH and Wilm, A and Nagarajan, N},
title = {INC-Seq: accurate single molecule reads using nanopore sequencing.},
journal = {GigaScience},
volume = {5},
number = {1},
pages = {34},
pmid = {27485345},
issn = {2047-217X},
mesh = {Algorithms ; Bacteria/*classification/genetics ; DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Genomics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Nanopores ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: Nanopore sequencing provides a rapid, cheap and portable real-time sequencing platform with the potential to revolutionize genomics. However, several applications are limited by relatively high single-read error rates (>10 %), including RNA-seq, haplotype sequencing and 16S sequencing.<br><br>RESULTS: We developed the Intramolecular-ligated Nanopore Consensus Sequencing (INC-Seq) as a strategy for obtaining long and accurate nanopore reads, starting with low input DNA. Applying INC-Seq for 16S rRNA-based bacterial profiling generated full-length amplicon sequences with a median accuracy >97&#xa0;%.<br><br>CONCLUSIONS: INC-Seq reads enabled accurate species-level classification, identification of species at 0.1&#xa0;% abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling on the MinION system.},
}
@article {pmid27484303,
year = {2016},
author = {Laure, C and Karamessini, D and Milenkovic, O and Charles, L and Lutz, JF},
title = {Coding in 2D: Using Intentional Dispersity to Enhance the Information Capacity of Sequence-Coded Polymer Barcodes.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {55},
number = {36},
pages = {10722-10725},
doi = {10.1002/anie.201605279},
pmid = {27484303},
issn = {1521-3773},
abstract = {A 2D approach was studied for the design of polymer-based molecular barcodes. Uniform oligo(alkoxyamine amide)s, containing a monomer-coded binary message, were synthesized by orthogonal solid-phase chemistry. Sets of oligomers with different chain-lengths were prepared. The physical mixture of these uniform oligomers leads to an intentional dispersity (1st dimension fingerprint), which is measured by electrospray mass spectrometry. Furthermore, the monomer sequence of each component of the mass distribution can be analyzed by tandem mass spectrometry (2nd dimension sequencing). By summing the sequence information of all components, a binary message can be read. A 4-bytes extended ASCII-coded message was written on a set of six uniform oligomers. Alternatively, a 3-bytes sequence was written on a set of five oligomers. In both cases, the coded binary information was recovered.},
}
@article {pmid27484156,
year = {2016},
author = {Roslin, T and Majaneva, S},
title = {The use of DNA barcodes in food web construction-terrestrial and aquatic ecologists unite!.},
journal = {Genome},
volume = {59},
number = {9},
pages = {603-628},
doi = {10.1139/gen-2015-0229},
pmid = {27484156},
issn = {1480-3321},
mesh = {Animals ; Biodiversity ; *DNA Barcoding, Taxonomic/methods ; Ecosystem ; *Food Chain ; Genomics/methods ; Humans ; },
abstract = {By depicting who eats whom, food webs offer descriptions of how groupings in nature (typically species or populations) are linked to each other. For asking questions on how food webs are built and work, we need descriptions of food webs at different levels of resolution. DNA techniques provide opportunities for highly resolved webs. In this paper, we offer an exposé of how DNA-based techniques, and DNA barcodes in particular, have recently been used to construct food web structure in both terrestrial and aquatic systems. We highlight how such techniques can be applied to simultaneously improve the taxonomic resolution of the nodes of the web (i.e., the species), and the links between them (i.e., who eats whom). We end by proposing how DNA barcodes and DNA information may allow new approaches to the construction of larger interaction webs, and overcome some hurdles to achieving adequate sample size. Most importantly, we propose that the joint adoption and development of these techniques may serve to unite approaches to food web studies in aquatic and terrestrial systems-revealing the extent to which food webs in these environments are structured similarly to or differently from each other, and how they are linked by dispersal.},
}
@article {pmid27482137,
year = {2016},
author = {Hachesu, PR and Zyaei, L and Hassankhani, H},
title = {Recommendations for Using Barcode in Hospital Process.},
journal = {Acta informatica medica : AIM : journal of the Society for Medical Informatics of Bosnia &amp; Herzegovina : casopis Drustva za medicinsku informatiku BiH},
volume = {24},
number = {3},
pages = {206-210},
pmid = {27482137},
issn = {0353-8109},
abstract = {BACKGROUND: Lack of attention to the proper barcode using leads to lack of use or misuse in the hospitals. The present research aimed to investigate the requirements and barrier for using barcode technology and presenting suggestions to use it.<br><br>METHODS: The research is observational-descriptive. The data was collected using the designed checklist which its validity was assessed. This check list consists of two parts: "Requirements" and "barrier" of using the barcodes. Research community included 10 teaching hospitals and a class of 65 participants included people in the hospitals. The collected data was analyzed using descriptive statistics.<br><br>RESULTS: Required changes of workflow processes in the hospital and compliance them with the hospital policy are such requirements that had been infringed in the 90 % of hospitals. Prioritization of some hospital processes for barcoding, system integration with Hospital Information system (HIS), training of staff and budgeting are requirements for the successful implementation which had been infringed in the 80% of hospitals. Dissatisfaction with the quality of barcode labels and lacks of adequate scanners both whit the rate of 100 %, and the lack of understanding of the necessary requirements for implementation of barcodes as 80% were the most important barrier.<br><br>CONCLUSION: Integrate bar code system with clinical workflow should be considered. Lack of knowledge and understanding toward the infrastructure, inadequate staff training and technologic problems are considered as the greatest barriers.},
}
@article {pmid27481793,
year = {2016},
author = {Zhou, X and Frandsen, PB and Holzenthal, RW and Beet, CR and Bennett, KR and Blahnik, RJ and Bonada, N and Cartwright, D and Chuluunbat, S and Cocks, GV and Collins, GE and deWaard, J and Dean, J and Flint, OS and Hausmann, A and Hendrich, L and Hess, M and Hogg, ID and Kondratieff, BC and Malicky, H and Milton, MA and Morinière, J and Morse, JC and Mwangi, FN and Pauls, SU and Gonzalez, MR and Rinne, A and Robinson, JL and Salokannel, J and Shackleton, M and Smith, B and Stamatakis, A and StClair, R and Thomas, JA and Zamora-Muñoz, C and Ziesmann, T and Kjer, KM},
title = {The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1702},
pages = {},
pmid = {27481793},
issn = {1471-2970},
support = {P 23687/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Animals ; Biodiversity ; *DNA Barcoding, Taxonomic ; Haplotypes ; Insecta/*classification/genetics ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between 'Barcode Index Numbers' (BINs) and 'species' that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description.This article is part of the themed issue 'From DNA barcodes to biomes'.},
}
@article {pmid27481792,
year = {2016},
author = {Henter, HJ and Imondi, R and James, K and Spencer, D and Steinke, D},
title = {DNA barcoding in diverse educational settings: five case studies.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1702},
pages = {},
pmid = {27481792},
issn = {1471-2970},
mesh = {*Biodiversity ; Biology/*education ; Canada ; Community Participation ; *Conservation of Natural Resources ; *DNA Barcoding, Taxonomic ; School Teachers ; Students ; United States ; },
abstract = {Despite 250 years of modern taxonomy, there remains a large biodiversity knowledge gap. Most species remain unknown to science. DNA barcoding can help address this gap and has been used in a variety of educational contexts to incorporate original research into school curricula and informal education programmes. A growing body of evidence suggests that actively conducting research increases student engagement and retention in science. We describe case studies in five different educational settings in Canada and the USA: a programme for primary and secondary school students (ages 5-18), a year-long professional development programme for secondary school teachers, projects embedding this research into courses in a post-secondary 2-year institution and a degree-granting university, and a citizen science project. We argue that these projects are successful because the scientific content is authentic and compelling, DNA barcoding is conceptually and technically straightforward, the workflow is adaptable to a variety of situations, and online tools exist that allow participants to contribute high-quality data to the international research effort. Evidence of success includes the broad adoption of these programmes and assessment results demonstrating that participants are gaining both knowledge and confidence. There are exciting opportunities for coordination among educational projects in the future.This article is part of the themed issue 'From DNA barcodes to biomes'.},
}
@article {pmid27481791,
year = {2016},
author = {Miller, SE and Hausmann, A and Hallwachs, W and Janzen, DH},
title = {Advancing taxonomy and bioinventories with DNA barcodes.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1702},
pages = {},
pmid = {27481791},
issn = {1471-2970},
mesh = {Animals ; *Biodiversity ; Classification/*methods ; Conservation of Natural Resources/*methods ; Costa Rica ; *DNA Barcoding, Taxonomic ; Moths ; Papua New Guinea ; },
abstract = {We use three examples-field and ecology-based inventories in Costa Rica and Papua New Guinea and a museum and taxonomic-based inventory of the moth family Geometridae-to demonstrate the use of DNA barcoding (a short sequence of the mitochondrial COI gene) in biodiversity inventories, from facilitating workflows of identification of freshly collected specimens from the field, to describing the overall diversity of megadiverse taxa from museum collections, and most importantly linking the fresh specimens, the general museum collections and historic type specimens. The process also flushes out unexpected sibling species hiding under long-applied scientific names, thereby clarifying and parsing previously mixed collateral data. The Barcode of Life Database has matured to an essential interactive platform for the multi-authored and multi-process collaboration. The BIN system of creating and tracking DNA sequence-based clusters as proxies for species has become a powerful way around some parts of the 'taxonomic impediment', especially in entomology, by providing fast but testable and tractable species hypotheses, tools for visualizing the distribution of those in time and space and an interim naming system for communication.This article is part of the themed issue 'From DNA barcodes to biomes'.},
}
@article {pmid27481790,
year = {2016},
author = {Hollingsworth, PM and Li, DZ and van der Bank, M and Twyford, AD},
title = {Telling plant species apart with DNA: from barcodes to genomes.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1702},
pages = {},
pmid = {27481790},
issn = {1471-2970},
mesh = {Biodiversity ; *DNA Barcoding, Taxonomic ; *Genome, Plant ; Plants/*classification/genetics ; },
abstract = {Land plants underpin a multitude of ecosystem functions, support human livelihoods and represent a critically important component of terrestrial biodiversity-yet many tens of thousands of species await discovery, and plant identification remains a substantial challenge, especially where material is juvenile, fragmented or processed. In this opinion article, we tackle two main topics. Firstly, we provide a short summary of the strengths and limitations of plant DNA barcoding for addressing these issues. Secondly, we discuss options for enhancing current plant barcodes, focusing on increasing discriminatory power via either gene capture of nuclear markers or genome skimming. The former has the advantage of establishing a defined set of target loci maximizing efficiency of sequencing effort, data storage and analysis. The challenge is developing a probe set for large numbers of nuclear markers that works over sufficient phylogenetic breadth. Genome skimming has the advantage of using existing protocols and being backward compatible with existing barcodes; and the depth of sequence coverage can be increased as sequencing costs fall. Its non-targeted nature does, however, present a major informatics challenge for upscaling to large sample sets.This article is part of the themed issue 'From DNA barcodes to biomes'.},
}
@article {pmid27481789,
year = {2016},
author = {La Salle, J and Williams, KJ and Moritz, C},
title = {Biodiversity analysis in the digital era.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1702},
pages = {},
pmid = {27481789},
issn = {1471-2970},
mesh = {Australia ; *Biodiversity ; Classification/*methods ; *Computational Biology ; *DNA Barcoding, Taxonomic ; Phylogeny ; },
abstract = {This paper explores what the virtual biodiversity e-infrastructure will look like as it takes advantage of advances in 'Big Data' biodiversity informatics and e-research infrastructure, which allow integration of various taxon-level data types (genome, morphology, distribution and species interactions) within a phylogenetic and environmental framework. By overcoming the data scaling problem in ecology, this integrative framework will provide richer information and fast learning to enable a deeper understanding of biodiversity evolution and dynamics in a rapidly changing world. The Atlas of Living Australia is used as one example of the advantages of progressing towards this future. Living in this future will require the adoption of new ways of integrating scientific knowledge into societal decision making.This article is part of the themed issue 'From DNA barcodes to biomes'.},
}
@article {pmid27481788,
year = {2016},
author = {Yahr, R and Schoch, CL and Dentinger, BT},
title = {Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1702},
pages = {},
pmid = {27481788},
issn = {1471-2970},
mesh = {*Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Fungal/*genetics ; DNA, Ribosomal Spacer/genetics ; Fungi/*classification ; },
abstract = {The fungal kingdom is a hyperdiverse group of multicellular eukaryotes with profound impacts on human society and ecosystem function. The challenge of documenting and describing fungal diversity is exacerbated by their typically cryptic nature, their ability to produce seemingly unrelated morphologies from a single individual and their similarity in appearance to distantly related taxa. This multiplicity of hurdles resulted in the early adoption of DNA-based comparisons to study fungal diversity, including linking curated DNA sequence data to expertly identified voucher specimens. DNA-barcoding approaches in fungi were first applied in specimen-based studies for identification and discovery of taxonomic diversity, but are now widely deployed for community characterization based on sequencing of environmental samples. Collectively, fungal barcoding approaches have yielded important advances across biological scales and research applications, from taxonomic, ecological, industrial and health perspectives. A major outstanding issue is the growing problem of 'sequences without names' that are somewhat uncoupled from the traditional framework of fungal classification based on morphology and preserved specimens. This review summarizes some of the most significant impacts of fungal barcoding, its limitations, and progress towards the challenge of effective utilization of the exponentially growing volume of data gathered from high-throughput sequencing technologies.This article is part of the themed issue 'From DNA barcodes to biomes'.},
}
@article {pmid27481787,
year = {2016},
author = {Mallo, D and Posada, D},
title = {Multilocus inference of species trees and DNA barcoding.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1702},
pages = {},
pmid = {27481787},
issn = {1471-2970},
support = {203161/ERC_/European Research Council/International ; },
mesh = {*Biological Evolution ; *DNA Barcoding, Taxonomic ; *Genetic Speciation ; *Phylogeny ; },
abstract = {The unprecedented amount of data resulting from next-generation sequencing has opened a new era in phylogenetic estimation. Although large datasets should, in theory, increase phylogenetic resolution, massive, multilocus datasets have uncovered a great deal of phylogenetic incongruence among different genomic regions, due both to stochastic error and to the action of different evolutionary process such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence violates one of the fundamental assumptions of the DNA barcoding approach, which assumes that gene history and species history are identical. In this review, we explain some of the most important challenges we will have to face to reconstruct the history of species, and the advantages and disadvantages of different strategies for the phylogenetic analysis of multilocus data. In particular, we describe the evolutionary events that can generate species tree-gene tree discordance, compare the most popular methods for species tree reconstruction, highlight the challenges we need to face when using them and discuss their potential utility in barcoding. Current barcoding methods sacrifice a great amount of statistical power by only considering one locus, and a transition to multilocus barcodes would not only improve current barcoding methods, but also facilitate an eventual transition to species-tree-based barcoding strategies, which could better accommodate scenarios where the barcode gap is too small or inexistent.This article is part of the themed issue 'From DNA barcodes to biomes'.},
}
@article {pmid27481786,
year = {2016},
author = {Page, RD},
title = {DNA barcoding and taxonomy: dark taxa and dark texts.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1702},
pages = {},
pmid = {27481786},
issn = {1471-2970},
mesh = {Biodiversity ; Classification/*methods ; *DNA Barcoding, Taxonomic ; *Periodicals as Topic ; Specimen Handling ; },
abstract = {Both classical taxonomy and DNA barcoding are engaged in the task of digitizing the living world. Much of the taxonomic literature remains undigitized. The rise of open access publishing this century and the freeing of older literature from the shackles of copyright have greatly increased the online availability of taxonomic descriptions, but much of the literature of the mid- to late-twentieth century remains offline ('dark texts'). DNA barcoding is generating a wealth of computable data that in many ways are much easier to work with than classical taxonomic descriptions, but many of the sequences are not identified to species level. These 'dark taxa' hamper the classical method of integrating biodiversity data, using shared taxonomic names. Voucher specimens are a potential common currency of both the taxonomic literature and sequence databases, and could be used to help link names, literature and sequences. An obstacle to this approach is the lack of stable, resolvable specimen identifiers. The paper concludes with an appeal for a global 'digital dashboard' to assess the extent to which biodiversity data are available online.This article is part of the themed issue 'From DNA barcodes to biomes'.},
}
@article {pmid27481785,
year = {2016},
author = {Hebert, PD and Ratnasingham, S and Zakharov, EV and Telfer, AC and Levesque-Beaudin, V and Milton, MA and Pedersen, S and Jannetta, P and deWaard, JR},
title = {Counting animal species with DNA barcodes: Canadian insects.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1702},
pages = {},
pmid = {27481785},
issn = {1471-2970},
mesh = {Animals ; *Biodiversity ; Canada ; *DNA Barcoding, Taxonomic ; Insecta/*classification/genetics ; },
abstract = {Recent estimates suggest that the global insect fauna includes fewer than six million species, but this projection is very uncertain because taxonomic work has been limited on some highly diverse groups. Validation of current estimates minimally requires the investigation of all lineages that are diverse enough to have a substantial impact on the final species count. This study represents a first step in this direction; it employs DNA barcoding to evaluate patterns of species richness in 27 orders of Canadian insects. The analysis of over one million specimens revealed species counts congruent with earlier results for most orders. However, Diptera and Hymenoptera were unexpectedly diverse, representing two-thirds of the 46 937 barcode index numbers (=species) detected. Correspondence checks between known species and barcoded taxa showed that sampling was incomplete, a result confirmed by extrapolations from the barcode results which suggest the occurrence of at least 94 000 species of insects in Canada, a near doubling from the prior estimate of 54 000 species. One dipteran family, the Cecidomyiidae, was extraordinarily diverse with an estimated 16 000 species, a 10-fold increase from its predicted diversity. If Canada possesses about 1% of the global fauna, as it does for known taxa, the results of this study suggest the presence of 10 million insect species with about 1.8 million of these taxa in the Cecidomyiidae. If so, the global species count for this fly family may exceed the combined total for all 142 beetle families. If extended to more geographical regions and to all hyperdiverse groups, DNA barcoding can rapidly resolve the current uncertainty surrounding a species count for the animal kingdom. A newly detailed understanding of species diversity may illuminate processes important in speciation, as suggested by the discovery that the most diverse insect lineages in Canada employ an unusual mode of reproduction, haplodiploidy.This article is part of the themed issue 'From DNA barcodes to biomes'.},
}
@article {pmid27481784,
year = {2016},
author = {Speller, C and van den Hurk, Y and Charpentier, A and Rodrigues, A and Gardeisen, A and Wilkens, B and McGrath, K and Rowsell, K and Spindler, L and Collins, M and Hofreiter, M},
title = {Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1702},
pages = {},
pmid = {27481784},
issn = {1471-2970},
mesh = {Animals ; Archaeology/methods ; Biodiversity ; Cetacea/*classification ; Classification/*methods ; Collagen/analysis ; *DNA Barcoding, Taxonomic ; High-Throughput Nucleotide Sequencing/methods ; North Sea ; },
abstract = {Over the last few centuries, many cetacean species have witnessed dramatic global declines due to industrial overharvesting and other anthropogenic influences, and thus are key targets for conservation. Whale bones recovered from archaeological and palaeontological contexts can provide essential baseline information on the past geographical distribution and abundance of species required for developing informed conservation policies. Here we review the challenges with identifying whale bones through traditional anatomical methods, as well as the opportunities provided by new molecular analyses. Through a case study focused on the North Sea, we demonstrate how the utility of this (pre)historic data is currently limited by a lack of accurate taxonomic information for the majority of ancient cetacean remains. We then discuss current opportunities presented by molecular identification methods such as DNA barcoding and collagen peptide mass fingerprinting (zooarchaeology by mass spectrometry), and highlight the importance of molecular identifications in assessing ancient species' distributions through a case study focused on the Mediterranean. We conclude by considering high-throughput molecular approaches such as hybridization capture followed by next-generation sequencing as cost-effective approaches for enhancing the ecological informativeness of these ancient sample sets.This article is part of the themed issue 'From DNA barcodes to biomes'.},
}
@article {pmid27481783,
year = {2016},
author = {Leray, M and Knowlton, N},
title = {Censusing marine eukaryotic diversity in the twenty-first century.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1702},
pages = {},
pmid = {27481783},
issn = {1471-2970},
mesh = {Aquatic Organisms/*classification ; *Biodiversity ; Conservation of Natural Resources/methods ; DNA Barcoding, Taxonomic ; Eukaryota/*classification ; Marine Biology/methods ; Oceans and Seas ; },
abstract = {The ocean constitutes one of the vastest and richest biomes on our planet. Most recent estimations, all based on indirect approaches, suggest that there are millions of marine eukaryotic species. Moreover, a large majority of these are small (less than 1 mm), cryptic and still unknown to science. However, this knowledge gap, caused by the lack of diagnostic morphological features in small organisms and the limited sampling of the global ocean, is currently being filled, thanks to new DNA-based approaches. The molecular technique of PCR amplification of homologous gene regions combined with high-throughput sequencing, routinely used to census unculturable prokaryotes, is now also being used to characterize whole communities of marine eukaryotes. Here, we review how this methodological advancement has helped to better quantify the magnitude and patterns of marine eukaryotic diversity, with an emphasis on taxonomic groups previously largely overlooked. We then discuss obstacles remaining to achieve a global understanding of marine eukaryotic diversity. In particular, we argue that 18S variable regions do not provide sufficient taxonomic resolution to census marine life, and suggest combining broad eukaryotic surveys targeting the 18S rRNA region with more taxon-focused analyses of hypervariable regions to improve our understanding of the diversity of species, the functional units of marine ecosystems.This article is part of the themed issue 'From DNA barcodes to biomes'.},
}
@article {pmid27481782,
year = {2016},
author = {Hajibabaei, M and Baird, DJ and Fahner, NA and Beiko, R and Golding, GB},
title = {A new way to contemplate Darwin's tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1702},
pages = {},
pmid = {27481782},
issn = {1471-2970},
mesh = {Biodiversity ; Computational Biology/*methods ; Conservation of Natural Resources/*methods ; DNA Barcoding, Taxonomic/*methods ; Environmental Monitoring/*methods ; },
abstract = {Encompassing the breadth of biodiversity in biomonitoring programmes has been frustrated by an inability to simultaneously identify large numbers of species accurately and in a timely fashion. Biomonitoring infers the state of an ecosystem from samples collected and identified using the best available taxonomic knowledge. The advent of DNA barcoding has now given way to the extraction of bulk DNA from mixed samples of organisms in environmental samples through the development of high-throughput sequencing (HTS). This DNA metabarcoding approach allows an unprecedented view of the true breadth and depth of biodiversity, but its adoption poses two important challenges. First, bioinformatics techniques must simultaneously perform complex analyses of large datasets and translate the results of these analyses to a range of users. Second, the insights gained from HTS need to be amalgamated with concepts such as Linnaean taxonomy and indicator species, which are less comprehensive but more intuitive. It is clear that we are moving beyond proof-of-concept studies to address the challenge of implementation of this new approach for environmental monitoring and regulation. Interpreting Darwin's 'tangled bank' through a DNA lens is now a reality, but the question remains: how can this information be generated and used reliably, and how does it relate to accepted norms in ecosystem study?This article is part of the themed issue 'From DNA barcodes to biomes'.},
}
@article {pmid27481781,
year = {2016},
author = {Blaxter, M},
title = {Imagining Sisyphus happy: DNA barcoding and the unnamed majority.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1702},
pages = {},
pmid = {27481781},
issn = {1471-2970},
support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Eukaryota/*classification/genetics ; },
abstract = {The vast majority of life on the Earth is physically small, and is classifiable as micro- or meiobiota. These organisms are numerically dominant and it is likely that they are also abundantly speciose. By contrast, the vast majority of taxonomic effort has been expended on 'charismatic megabionts': larger organisms where a wealth of morphology has facilitated Linnaean species definition. The hugely successful Linnaean project is unlikely to be extensible to the totality of approximately 10 million species in a reasonable time frame and thus alternative toolkits and methodologies need to be developed. One such toolkit is DNA barcoding, particularly in its metabarcoding or metagenetics mode, where organisms are identified purely by the presence of a diagnostic DNA sequence in samples that are not processed for morphological identification. Building on secure Linnaean foundations, classification of unknown (and unseen) organisms to molecular operational taxonomic units (MOTUs) and deployment of these MOTUs in biodiversity science promises a rewarding resolution to the Sisyphean task of naming all the world's species.This article is part of the themed issue 'From DNA barcodes to biomes'.},
}
@article {pmid27481780,
year = {2016},
author = {Baker, CC and Bittleston, LS and Sanders, JG and Pierce, NE},
title = {Dissecting host-associated communities with DNA barcodes.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1702},
pages = {},
pmid = {27481780},
issn = {1471-2970},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; *Symbiosis ; },
abstract = {DNA barcoding and metabarcoding methods have been invaluable in the study of interactions between host organisms and their symbiotic communities. Barcodes can help identify individual symbionts that are difficult to distinguish using morphological characters, and provide a way to classify undescribed species. Entire symbiont communities can be characterized rapidly using barcoding and especially metabarcoding methods, which is often crucial for isolating ecological signal from the substantial variation among individual hosts. Furthermore, barcodes allow the evolutionary histories of symbionts and their hosts to be assessed simultaneously and in reference to one another. Here, we describe three projects illustrating the utility of barcodes for studying symbiotic interactions: first, we consider communities of arthropods found in the ant-occupied domatia of the East African ant-plant Vachellia (Acacia) drepanolobium; second, we examine communities of arthropod and protozoan inquilines in three species of Nepenthes pitcher plant in South East Asia; third, we investigate communities of gut bacteria of South American ants in the genus Cephalotes Advances in sequencing and computation, and greater database connectivity, will continue to expand the utility of barcoding methods for the study of species interactions, especially if barcoding can be approached flexibly by making use of alternative genetic loci, metagenomes and whole-genome data.This article is part of the themed issue 'From DNA barcodes to biomes'.},
}
@article {pmid27481779,
year = {2016},
author = {McLean, AH and Parker, BJ and Hrček, J and Henry, LM and Godfray, HC},
title = {Insect symbionts in food webs.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1702},
pages = {},
pmid = {27481779},
issn = {1471-2970},
mesh = {Animals ; Aphids/*microbiology/*physiology ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; *Food Chain ; *Symbiosis ; },
abstract = {Recent research has shown that the bacterial endosymbionts of insects are abundant and diverse, and that they have numerous different effects on their hosts' biology. Here we explore how insect endosymbionts might affect the structure and dynamics of insect communities. Using the obligate and facultative symbionts of aphids as an example, we find that there are multiple ways that symbiont presence might affect food web structure. Many symbionts are now known to help their hosts escape or resist natural enemy attack, and others can allow their hosts to withstand abiotic stress or affect host plant use. In addition to the direct effect of symbionts on aphid phenotypes there may be indirect effects mediated through trophic and non-trophic community interactions. We believe that by using data from barcoding studies to identify bacterial symbionts, this extra, microbial dimension to insect food webs can be better elucidated.This article is part of the themed issue 'From DNA barcodes to biomes'.},
}
@article {pmid27481778,
year = {2016},
author = {Hebert, PD and Hollingsworth, PM and Hajibabaei, M},
title = {From writing to reading the encyclopedia of life.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1702},
pages = {},
pmid = {27481778},
issn = {1471-2970},
mesh = {Archaea/genetics ; Bacteria/genetics ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Eukaryota/genetics ; },
abstract = {Prologue 'As the study of natural science advances, the language of scientific description may be greatly simplified and abridged. This has already been done by Linneaus and may be carried still further by other invention. The descriptions of natural orders and genera may be reduced to short definitions, and employment of signs, somewhat in the manner of algebra, instead of long descriptions. It is more easy to conceive this, than it is to conceive with what facility, and in how short a time, a knowledge of all the objects of natural history may ultimately be acquired; and that which is now considered learning and science, and confined to a few specially devoted to it, may at length be universally possessed in every civilized country and in every rank of life'. J. C. Louden 1829. Magazine of natural history, vol. 1: This article is part of the themed issue 'From DNA barcodes to biomes'.},
}
@article {pmid27481285,
year = {2016},
author = {Veach, AM and Stegen, JC and Brown, SP and Dodds, WK and Jumpponen, A},
title = {Spatial and successional dynamics of microbial biofilm communities in a grassland stream ecosystem.},
journal = {Molecular ecology},
volume = {25},
number = {18},
pages = {4674-4688},
doi = {10.1111/mec.13784},
pmid = {27481285},
issn = {1365-294X},
mesh = {Bacteria/*classification ; *Biofilms ; Chlorophyll ; Chlorophyll A ; *Grassland ; Kansas ; Phylogeny ; RNA, Ribosomal, 16S ; Rivers/*microbiology ; *Water Microbiology ; },
abstract = {Biofilms represent a metabolically active and structurally complex component of freshwater ecosystems. Ephemeral prairie streams are hydrologically harsh and prone to frequent perturbation. Elucidating both functional and structural community changes over time within prairie streams provides a general understanding of microbial responses to environmental disturbance. We examined microbial succession of biofilm communities at three sites in a third-order stream at Konza Prairie over a 2- to 64-day period. Microbial abundance (bacterial abundance, chlorophyll a concentrations) increased and never plateaued during the experiment. Net primary productivity (net balance of oxygen consumption and production) of the developing biofilms did not differ statistically from zero until 64 days suggesting a balance of the use of autochthonous and allochthonous energy sources until late succession. Bacterial communities (MiSeq analyses of the V4 region of 16S rRNA) established quickly. Bacterial richness, diversity and evenness were high after 2 days and increased over time. Several dominant bacterial phyla (Beta-, Alphaproteobacteria, Bacteroidetes, Gemmatimonadetes, Acidobacteria, Chloroflexi) and genera (Luteolibacter, Flavobacterium, Gemmatimonas, Hydrogenophaga) differed in relative abundance over space and time. Bacterial community composition differed across both space and successional time. Pairwise comparisons of phylogenetic turnover in bacterial community composition indicated that early-stage succession (≤16 days) was driven by stochastic processes, whereas later stages were driven by deterministic selection regardless of site. Our data suggest that microbial biofilms predictably develop both functionally and structurally indicating distinct successional trajectories of bacterial communities in this ecosystem.},
}
@article {pmid27479214,
year = {2016},
author = {Paoletti, MG and Blakemore, RJ and Csuzdi, C and Dorigo, L and Dreon, AL and Gavinelli, F and Lazzarini, F and Manno, N and Moretto, E and Porco, D and Ruzzier, E and Toniello, V and Squartini, A and Concheri, G and Zanardo, M and Alba-Tercedor, J},
title = {Correction: Barcoding Eophila crodabepis sp. nov. (Annelida, Oligochaeta, Lumbricidae), a Large Stripy Earthworm from Alpine Foothills of Northeastern Italy Similar to Eophila tellinii (Rosa, 1888).},
journal = {PloS one},
volume = {11},
number = {8},
pages = {e0160218},
pmid = {27479214},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0151799.].},
}
@article {pmid27478996,
year = {2016},
author = {Hanson, WM and Chen, Z and Jackson, LK and Attaf, M and Sewell, AK and Heemstra, JM and Phillips, JD},
title = {Reversible Oligonucleotide Chain Blocking Enables Bead Capture and Amplification of T-Cell Receptor α and β Chain mRNAs.},
journal = {Journal of the American Chemical Society},
volume = {138},
number = {35},
pages = {11073-11076},
pmid = {27478996},
issn = {1520-5126},
support = {R37 DK020503/DK/NIDDK NIH HHS/United States ; R01 DK090257/DK/NIDDK NIH HHS/United States ; U54 DK110858/DK/NIDDK NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R56 DK020503/DK/NIDDK NIH HHS/United States ; R01 DK020503/DK/NIDDK NIH HHS/United States ; },
mesh = {High-Throughput Nucleotide Sequencing ; *Microspheres ; Models, Molecular ; Nucleic Acid Amplification Techniques/*methods ; Nucleic Acid Conformation ; Oligonucleotides/*chemistry ; RNA, Messenger/chemistry/genetics ; Receptors, Antigen, T-Cell, alpha-beta/*genetics ; Sequence Analysis, RNA ; },
abstract = {Next-generation sequencing (NGS) has proven to be an exceptionally powerful tool for studying genetic variation and differences in gene expression profiles between cell populations. However, these population-wide studies are limited by their inability to detect variation between individual cells within a population, inspiring the development of single-cell techniques such as Drop-seq, which add a unique barcode to the mRNA from each cell prior to sequencing. Current Drop-seq technology enables capture, amplification, and barcoding of the entire mRNA transcriptome of individual cells. NGS can then be used to sequence the 3'-end of each message to build a cell-specific transcriptional landscape. However, current technology does not allow high-throughput capture of information distant from the mRNA poly-A tail. Thus, gene profiling would have much greater utility if beads could be generated having multiple transcript-specific capture sequences. Here we report the use of a reversible chain blocking group to enable synthesis of DNA barcoded beads having capture sequences for the constant domains of the T-cell receptor α and β chain mRNAs. We demonstrate that these beads can be used to capture and pair TCRα and TCRβ sequences from total T-cell RNA, enabling reverse transcription and PCR amplification of these sequences. This is the first example of capture beads having more than one capture sequence, and we envision that this technology will be of high utility for applications such as pairing the antigen receptor chains that give rise to autoimmune diseases or measuring the ratios of mRNA splice variants in cancer stem cells.},
}
@article {pmid27477486,
year = {2016},
author = {Zimmermann, G and Neri, D},
title = {DNA-encoded chemical libraries: foundations and applications in lead discovery.},
journal = {Drug discovery today},
volume = {21},
number = {11},
pages = {1828-1834},
pmid = {27477486},
issn = {1878-5832},
support = {163479/SNSF_/Swiss National Science Foundation/Switzerland ; 670603/ERC_/European Research Council/International ; },
mesh = {*DNA ; *Drug Discovery ; *Small Molecule Libraries ; },
abstract = {DNA-encoded chemical libraries have emerged as a powerful tool for hit identification in the pharmaceutical industry and in academia. Similar to biological display techniques (such as phage display technology), DNA-encoded chemical libraries contain a link between the displayed chemical building block and an amplifiable genetic barcode on DNA. Using routine procedures, libraries containing millions to billions of compounds can be easily produced within a few weeks. The resulting compound libraries are screened in a single test tube against proteins of pharmaceutical interest and hits can be identified by PCR amplification of DNA barcodes and subsequent high-throughput sequencing.},
}
@article {pmid27473771,
year = {2016},
author = {Zieritz, A and Lopes-Lima, M and Bogan, AE and Sousa, R and Walton, S and Rahim, KA and Wilson, JJ and Ng, PY and Froufe, E and McGowan, S},
title = {Factors driving changes in freshwater mussel (Bivalvia, Unionida) diversity and distribution in Peninsular Malaysia.},
journal = {The Science of the total environment},
volume = {571},
number = {},
pages = {1069-1078},
doi = {10.1016/j.scitotenv.2016.07.098},
pmid = {27473771},
issn = {1879-1026},
mesh = {*Animal Distribution ; Animals ; *Biodiversity ; Bivalvia/*physiology ; *Conservation of Natural Resources ; Malaysia ; Water Pollution, Chemical/*analysis ; },
abstract = {Freshwater mussels (Bivalvia, Unionida) fulfil important ecosystem functions and are one of the most threatened freshwater taxa globally. Knowledge of freshwater mussel diversity, distribution and ecology in Peninsular Malaysia is extremely poor, and the conservation status of half of the species presumed to occur in the region has yet to be assessed. We conducted the first comprehensive assessment of Peninsular Malaysia's freshwater mussels based on species presence/absence and environmental data collected from 155 sites spanning all major river catchments and diverse habitat types. Through an integrative morphological-molecular approach we recognised nine native and one widespread non-native species, i.e. Sinanodonta woodiana. Two species, i.e. Pilsbryoconcha compressa and Pseudodon cambodjensis, had not been previously recorded from Malaysia, which is likely a result of morphological misidentifications of historical records. Due to their restriction to single river catchments and declining distributions, Hyriopsis bialata, possibly endemic to Peninsular Malaysia, Ensidens ingallsianus, possibly already extinct in the peninsula, and Rectidens sumatrensis, particularly require conservation attention. Equally, the Pahang, the Perak and the north-western river catchments are of particular conservation value due to the presence of a globally unique freshwater mussel fauna. Statistical relationships of 15 water quality parameters and mussel presence/absence identified acidification and nutrient pollution (eutrophication) as the most important anthropogenic factors threatening freshwater mussel diversity in Peninsular Malaysia. These factors can be linked to atmospheric pollution, deforestation, oil-palm plantations and a lack of functioning waste water treatment, and could be mitigated by establishing riparian buffers and improving waste water treatment for rivers running through agricultural and residential land.},
}
@article {pmid27471065,
year = {2016},
author = {Pallen, MJ},
title = {Microbial bioinformatics 2020.},
journal = {Microbial biotechnology},
volume = {9},
number = {5},
pages = {681-686},
pmid = {27471065},
issn = {1751-7915},
mesh = {Computational Biology/*methods/trends ; Databases, Nucleic Acid ; Genomics/*methods/trends ; Internet ; },
abstract = {Microbial bioinformatics in 2020 will remain a vibrant, creative discipline, adding value to the ever-growing flood of new sequence data, while embracing novel technologies and fresh approaches. Databases and search strategies will struggle to cope and manual curation will not be sustainable during the scale-up to the million-microbial-genome era. Microbial taxonomy will have to adapt to a situation in which most microorganisms are discovered and characterised through the analysis of sequences. Genome sequencing will become a routine approach in clinical and research laboratories, with fresh demands for interpretable user-friendly outputs. The "internet of things" will penetrate healthcare systems, so that even a piece of hospital plumbing might have its own IP address that can be integrated with pathogen genome sequences. Microbiome mania will continue, but the tide will turn from molecular barcoding towards metagenomics. Crowd-sourced analyses will collide with cloud computing, but eternal vigilance will be the price of preventing the misinterpretation and overselling of microbial sequence data. Output from hand-held sequencers will be analysed on mobile devices. Open-source training materials will address the need for the development of a skilled labour force. As we boldly go into the third decade of the twenty-first century, microbial sequence space will remain the final frontier!},
}
@article {pmid28895322,
year = {2016},
author = {Liao, LX and Zeng, KW and Tu, PF},
title = {[Hydrophidae identification through analysis on cytochrome c oxydase I（COI） and ribosome 16s rDNA gene barcode].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {41},
number = {10},
pages = {1792-1796},
doi = {10.4268/cjcmm20161005},
pmid = {28895322},
issn = {1001-5302},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Hydrophiidae/*classification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Hydrophidae, one of the precious traditional Chinese medicines, is generally drily preserved to prevent corruption, but it is hard to identify the species of Hydrophidae through the appearance because of the change due to the drying process. The identification through analysis on gene barcode, a new technique in species identification, can avoid this problem. The gene barcodes of the 5 species of Hydrophidae, Lapemis hardwickii, Hydrophis fasciatus, Aipysurus eydouxii, Hydrophis belcher and Hydrophis lamberti, were acquired through DNA extraction and gene sequencing. These barcodes were then in sequence alignment and test the identification efficiency by BLAST. Our results showed that the 16S rDNA sequences identified Hydrophidae briefly and the COI sequenceshad obvious difference between intra-and inter-species, indicating that DNA bar-coding was an efficiency method of Hydrophidae identification.},
}
@article {pmid28871675,
year = {2016},
author = {Liu, Y and Liu, C and Tan, E and Fan, G and Xiang, L and Li, XD and Zhang, Y},
title = {[Genetic and chemical discrimination of traditional Tibetan medicine seabuckthorn based on DNA barcode and [1]H-NMR metabolic method].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {41},
number = {4},
pages = {578-585},
doi = {10.4268/cjcmm20160405},
pmid = {28871675},
issn = {1001-5302},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; Discriminant Analysis ; Drugs, Chinese Herbal/*analysis/*chemistry ; Genetic Variation ; Hippophae/*chemistry/classification/*genetics/metabolism ; Medicine, Tibetan Traditional ; Metabolomics/*methods ; Phylogeny ; Proton Magnetic Resonance Spectroscopy/*methods ; },
abstract = {To differentiate three medicinal Hippopahe species of seabuckthorn, a combined genetic and chemical identification method was established in this study. ITS2 and psbA-trnH were tested for identification of 3 species of seabuckthorn. Detection of the kimura 2-parameter (K2P) distance, the neighbor-joining (NJ) tree and the barcoding gap were used to assess the identification efficiency. [1]H-NMR based metabolic method was applied to acquire the profile of metabolites. PCA was used to analysis the metabolite data. The results indicated that DNA barcode combined [1]H-NMR based metabolic method is a powerful tool for the identification of 3 medicinal Hippopahe species of seabuckthorn. The finding demonstrated that different genetic variation and chemical constituents existed among 3 medicinal Hippopahe species of seabuckthorn. The combined identification method will improve the reliability of species discrimination and could be applicable to much other ethnic medicine which has various origins in China.},
}
@article {pmid28871674,
year = {2016},
author = {Zhang, YX and Li, CY and Liu, C and Xu, J and Xiang, L and Fan, G and Zhang, Y},
title = {[Study on genetic-chemical relation of Pterocephali Herba based on DNA barcode and UFLC].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {41},
number = {4},
pages = {572-577},
doi = {10.4268/cjcmm20160404},
pmid = {28871674},
issn = {1001-5302},
mesh = {Caprifoliaceae/*chemistry/classification/*genetics ; Chromatography, High Pressure Liquid/*methods ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; Drugs, Chinese Herbal/*analysis ; Medicine, Tibetan Traditional ; Phylogeny ; },
abstract = {DNA barcoding technique in combination with UFLC analysis technology was used to evaluate the quality of Tibetan medicine Pterocephalus hookeri from species identification and chemical qualitative and other aspects. Hybrid identification was established by DNA barcoding; UFLC-PDA was adopted to analyse fingerprint of different parts of Pterocephali Herba, and SPSS and Grey relation software were used for data analysis. The result showed that DNA barcoding is an accurate and reliable method in origin identification of Pterocephalus hookeri. The compounds in overground is more than underground by analysis of the different part fingerprint by UFLC. The genetic gene may be involved in the secondary metabolites of iridoid glycosides. Pertinence between gene and chemical component, as a new model established, could be suited for quality evaluation and resources protection.},
}
@article {pmid28871673,
year = {2016},
author = {Liu, C and Zhang, YX and Liu, Y and Chen, YL and Fan, G and Xiang, L and Xu, J and Zhang, Y},
title = {[Identification of Tibetan medicine "Dida" of Gentianaceae using DNA barcoding].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {41},
number = {4},
pages = {567-571},
doi = {10.4268/cjcmm20160403},
pmid = {28871673},
issn = {1001-5302},
mesh = {DNA Barcoding, Taxonomic/*methods ; Drugs, Chinese Herbal/chemistry ; Medicine, Tibetan Traditional ; Phylogeny ; Plants, Medicinal/chemistry/classification/*genetics ; },
abstract = {The ITS2 barcode was used toidentify Tibetan medicine "Dida", and tosecure its quality and safety in medication. A total of 13 species, 151 experimental samples for the study from the Tibetan Plateau, including Gentianaceae Swertia, Halenia, Gentianopsis, Comastoma, Lomatogonium ITS2 sequences were amplified, and purified PCR products were sequenced. Sequence assembly and consensus sequence generation were performed using the CodonCode Aligner V3.7.1. The Kimura 2-Parameter (K2P) distances were calculated using MEGA 6.0. The neighbor-joining (NJ) phylogenetic trees were constructed. There are 31 haplotypes among 231 bp after alignment of all ITS2 sequence haplotypes, and the average G±C content of 61.40%. The NJ tree strongly supported that every species clustered into their own clade and high identification success rate, except that Swertia bifolia and Swertia wolfangiana could not be distinguished from each other based on the sequence divergences. DNA barcoding could be used as a fast and accurate identification method to distinguish Tibetan medicine "Dida" to ensure its safe use.},
}
@article {pmid28871672,
year = {2016},
author = {Li, XH and Zhao, CY and Liu, Y and Wan, L and Jia, MR and Xie, CX and Zhang, Y},
title = {[Research progress on resources and quality evaluation of Tibetan medicine in Qinghai-Tibet Plateau].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {41},
number = {4},
pages = {562-566},
doi = {10.4268/cjcmm20160402},
pmid = {28871672},
issn = {1001-5302},
mesh = {Conservation of Natural Resources ; Drugs, Chinese Herbal/chemistry/*standards ; Medicine, Tibetan Traditional/*standards ; Plants, Medicinal/*chemistry/genetics ; Quality Control ; Tibet ; },
abstract = {With the development of Tibetan medicine industry, the demands for Tibetan medicine were rising sharply. In addition, with the eco-environment vulnerability of Qinghai-Tibet Plateau region and the phenomenon of synonymies and homonymies in Tibetan medicine, there were a lack of resources and varieties in the clinical application of Tibetan medicine. At present, the shortage of Tibetan medicine and the inadequacy of its quality standard have become the two major problems that seriously restricted the sustainable development of Tibetan medicine industry. Therefore, it is important to develop the resources investigation and quality evaluation for Tibetan medicine, which were contribute to its resources protection and sustainable utilization. In this paper, current status of resources investigation, quality standardization, artificial breeding and germplasm resources of Tibetan medicine were presented by the integrated application of the new technologies, such as DNA barcoding and 1H-NMR, which provided a reference information for resources protection, sustainable utilization, variety identification and quality standardization of Tibetan medicine resources in Qinghai-Tibet Plateau.},
}
@article {pmid28871671,
year = {2016},
author = {Fan, G and Jia, MR and Liu, Y and Zhang, Y},
title = {[Advances of species identification and quality control for Tibetan medicines].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {41},
number = {4},
pages = {559-561},
doi = {10.4268/cjcmm20160401},
pmid = {28871671},
issn = {1001-5302},
mesh = {Humans ; Medicine, Tibetan Traditional/*standards ; Metabolomics ; Plants, Medicinal/*chemistry/classification/genetics ; Proton Magnetic Resonance Spectroscopy ; Quality Control ; },
abstract = {Species identification and quality control of Tibetan medicines are an important part of its modernization studies, and they have important significance for ensuring the safety and effectiveness of Tibetan medicines in clinical application. In order to provide a reference for the modernization research of Tibetan medicines, this paper summarized the research progress of species identification, quality standards and quality evaluation of Tibetan medicines in the past 10 years. It also introduces the application examples of some new technologies and methods, such as DNA barcoding, infrared spectroscopy and 1H NMR-based metabolomics.},
}
@article {pmid28868852,
year = {2016},
author = {Zhang, GX and Jin, Y and Jia, J and Song, JY and Shi, LC and Chen, SL},
title = {[Identification of Notopterygium seeds using DNA barcoding method].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {41},
number = {3},
pages = {390-395},
doi = {10.4268/cjcmm20160305},
pmid = {28868852},
issn = {1001-5302},
mesh = {Apiaceae/classification/*genetics ; China ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; Phylogeny ; Seeds/classification/genetics ; },
abstract = {In order to guarantee the species correction of Notopterygium seeds, a molecular identification method with ITS2 as DNA barcode has been verified. In this study, 27 samples of Notopterygium seeds were collected from the main producing area of Notopterygium. The morphological characteristics of the Notopterygium seeds were firstly surveyed. Then the DNA extraction, PCR amplification, DNA sequencing and DNA assembly were carried out. The species identification for a Notopterygium seed was implemented through distance method, NJ-tree method and the DNA barcoding system for traditional Chinese medicine (www.tcmbarcode.cn). The results showed that the seeds of N. incisum and N. franchetii had similar morphological characteristics and were difficult to distinguish clearly based on morphological descriptions. With the results of molecular identification, 24 samples were genuine including 13 N. incisum seeds samples and 11 N. franchetii genuine seeds samples. In conclusion, DNA barcode technology can accurately and efficiently identify the species of Notopterygium seeds. Furthermore, this study will provide a new method for germplasm resources identification of medicinal materials and supplies some guidelines for establishing Chinese herbal seeds and seedlings quality standards.},
}
@article {pmid29081469,
year = {2016},
author = {Minamoto, T},
title = {[Expectation for infectious disease studies using environmental DNA].},
journal = {Uirusu},
volume = {66},
number = {2},
pages = {171-178},
doi = {10.2222/jsv.66.171},
pmid = {29081469},
issn = {0042-6857},
abstract = {Environmental DNA analysis for micro- and macro-organisms is rapidly developing. Environmental DNA means total DNA present in environmental media such as water or soil, and includes DNA contained in the organisms themselves and extra-organism DNA of macro-organisms. Analysis of environmental DNA can be divided into two methods, species-specific detection and meta-barcoding, which can be used according to each purpose. Applicable subjects are all organisms (including viruses in this case) with DNA as genes, and application to rivers, ponds, lakes and marines has been reported. In this paper, the present situation of environmental DNA analysis of macro organisms is described, and the possibility of application to infectious disease studies and the problems to be solved are discussed.},
}
@article {pmid29023041,
year = {2016},
author = {Ahmed, MI and Sabrah, MM and Heneish, RA and El-Alwany, M},
title = {DNA Barcoding Uncover Cryptic Diversity in Goat Fishes (Family: Mullidae) Across the Egyptian Coastal Waters.},
journal = {Pakistan journal of biological sciences : PJBS},
volume = {19},
number = {2},
pages = {65-70},
doi = {10.3923/pjbs.2016.65.70},
pmid = {29023041},
issn = {1028-8880},
abstract = {Despite ongoing efforts to protect species and ecosystems in the egyptian costs of the Red Sea and Mediterranean Sea, habitat degradation, overfishing and pollution have posed serious challenges to marine natural resources. In spite of the accumulated knowledge on the systematics of commercial fishes in Egypt recent results suggested that we are far from having a complete picture of egyptian fish diversity. The accurate identification of species is a very important component in many fields of biological research and conservation efforts. The high level of expertise and time consuming process needed means a loss in biodiversity. Successful species identification is now frequently based on a combination of approaches including morphometrics and the sequencing of the mitochondrial COI gene known as the DNA barcoding. This study employed COI sequencing alongside traditional taxonomic identification methods and uncovered cryptic diversity within the goat fish species of Family Mullidae, four species collected from both the Red Sea and the Mediterranean Sea. Upeneus pori, Upeneus vittatus, Mullus surmuletus and Mullus barbatus samples from the Red Sea and the Mediterranean were clustered separately in a NJ tree indicating the possibility of the presence of cryptic species complex. All species could be differentiated by their COI sequence.},
}
@article {pmid28330205,
year = {2016},
author = {Ragupathy, S and Dhivya, S and Patel, K and Sritharan, A and Sambandan, K and Gartaula, H and Sathishkumar, R and Khadka, K and Nirmala, BC and Kumari, AN and Newmaster, SG},
title = {DNA record of some traditional small millet landraces in India and Nepal.},
journal = {3 Biotech},
volume = {6},
number = {2},
pages = {133},
pmid = {28330205},
issn = {2190-572X},
abstract = {Despite the extensive use of small millet landraces as an important source of nutrition for people living in semi-arid regions, they are presently marginalized and their diversity and distribution are threatened at a global scale. Local farmers have developed ancient breeding programs entrenched in traditional knowledge (TK) that has sustained rural cultures for thousands of years. The convention on biological diversity seeks fair and equitable sharing of genetic resources arising from local knowledge and requires signatory nations to provide appropriate policy and legal framework to farmers' rights over plant genetic resources and associated TK. DNA barcoding employed in this study is proposed as a model for conservation of genetic diversity and an essential step towards documenting and protecting farmers' rights and TK. Our study focuses on 32 landraces of small millets that are still used by indigenous farmers located in the rain fed areas of rural India and Nepal. Traditional knowledge of traits and utility was gathered using participatory methods and semi-structured interviews with key informants. DNA was extracted and sequenced (rbcL, trnH-psbA and ITS2) from 160 samples. Both multivariate analysis of traits and phylogenetic analyses were used to assess diversity among small millet landraces. Our research revealed considerable variation in traits and DNA sequences among the 32 small millet landraces. We utilized a tiered approach using ITS2 DNA barcode to make 100 % accurate landrace (32 landraces) and species (six species) assignments for all 160 blind samples in our study. We have also recorded precious TK of nutritional value, ecological and agricultural traits used by local farmers for each of these traditional landraces. This research demonstrates the potential of DNA barcoding as a reliable identification tool and for use in evaluating and conserving genetic diversity of small millets. We suggest ways in which DNA barcodes could be used in the Protection of Plant Varieties and Farmers' Rights in India and Nepal.},
}
@article {pmid28347096,
year = {2015},
author = {Wang, M and Duong, B and Su, M},
title = {Organic Phase Change Nanoparticles for in-Product Labeling of Agrochemicals.},
journal = {Nanomaterials (Basel, Switzerland)},
volume = {5},
number = {4},
pages = {1810-1819},
pmid = {28347096},
issn = {2079-4991},
abstract = {There is an urgent need to develop in-product covert barcodes for anti-counterfeiting of agrochemicals. This paper reports a new organic nanoparticle-based in-product barcode system, in which a panel of organic phase change nanoparticles is added as a barcode into in a variety of chemicals (herein agrochemicals). The barcode is readout by detecting melting peaks of organic nanoparticles using differential scanning calorimetry. This method has high labeling capacity due to small sizes of nanoparticles, sharp melting peaks, and large scan range of thermal analysis. The in-product barcode can be effectively used to protect agrochemical products from being counterfeited due to its large coding capacity, technical readiness, covertness, and robustness.},
}
@article {pmid27800410,
year = {2015},
author = {Tantillo, G and Marchetti, P and Mottola, A and Terio, V and Bottaro, M and Bonerba, E and Bozzo, G and Di Pinto, A},
title = {Occurrence of Mislabelling in Prepared Fishery Products in Southern Italy.},
journal = {Italian journal of food safety},
volume = {4},
number = {3},
pages = {5358},
pmid = {27800410},
issn = {2239-7132},
abstract = {Fish authentication is a major concern not only for the prevention of commercial fraud, but also for the assessment of safety risks deriving from the undeclared introduction of potentially dangerous toxic or allergenic substances or environmentally damaging fish where endangered species are involved. Moreover, food authentication might affect the diet of certain groups of consumers, such as followers of religious practices. Considering the authentication of fish products is one of the key issues in food safety, quality and sustainability, the aim of this work was to investigate the prevalence of mislabelling in sole (Solea solea), plaice (Pleuronectes platessa), Atlantic salmon (Salmo salar), and hake (Merluccius merluccius) fillets from markets and supermarkets located in Apulia (Southern Italy) using DNA barcoding. The results of the molecular investigations reveal that 42/98 (42.8%) fillet samples were not correctly labelled. In particular, 12/27 (44.4%) fillets of sole (Solea solea) were identified as belonging to Solea senegalensis. In addition, 13/28 (46.4%) plaice (Pleuronectes platessa) samples were identified as Pangasius hypophtalmus. All Atlantic salmon (Salmo salar) samples were correctly labelled. Post-sequencing data analysis revealed that 17/30 (56.6%) hake fillets (Merluccius merluccius) were not correctly labelled, of which 8/30 samples identified as Merluccius hubbsi, 5/30 samples as Merluccius products and 4/30 as Merluccius capensis. The study reveals a high occurrence of species mislabelling in the prepared fish fillet products, further evidence of the need for increased traceability and assessment of the authenticity of food products.},
}
@article {pmid28959279,
year = {2015},
author = {Huang, WJ and Li, FF and Liu, YJ and Long, CL},
title = {Identification of Crocus sativus and its Adulterants from Chinese Markets by using DNA Barcoding Technique.},
journal = {Iranian journal of biotechnology},
volume = {13},
number = {1},
pages = {36-42},
pmid = {28959279},
issn = {1728-3043},
abstract = {BACKGROUND: Saffron (Crocus sativus L.) is a common but very expensive herbal medicine. As an important traditional medicine, it has an outstanding effect in treating irregular and painful menstruation. Recently, the over-demand tendency of saffron results in an unusual phenomenon in the medicinal markets. Adulterants and saffron-like substitutes are intentionally mixed into medicinal markets and pharmacies or online stores, affecting drug safety and food quality.<br><br>OBJECTIVES: Our study aimed to identify saffron from its adulterants via DNA barcoding.<br><br>MATERIALS AND METHODS: Samples (13 saffron + 4 others containing Carthamus tinctorius or Chrysanthemum x morifolium) obtained from 12 different provinces of China. Through DNA barcoding, samples were compared using three candidate markers, trnH-psbA, rbcL-a and ITS2.<br><br>RESULTS: trnH-psbA and rbcL-a were capable of distinguishing different accessions. ITS2 could identify samples even at intra-specific level. According to these three barcodes, four samples were identified saffron-like substitutes.<br><br>CONCLUSIONS: The adulterant rate in Chinese markets reaches as high as 33.33% that may cause health risks and further may reduce saffron efficacy once is being used as herbal remedy. In order to make a distinction between C. sativus with other genera as adulterants, DNA barcoding is suggested.},
}
@article {pmid28462014,
year = {2015},
author = {Bénard-Capelle, J and Guillonneau, V and Nouvian, C and Fournier, N and Le Loët, K and Dettai, A},
title = {Fish mislabelling in France: substitution rates and retail types.},
journal = {PeerJ},
volume = {2},
number = {},
pages = {e714},
pmid = {28462014},
issn = {2167-8359},
abstract = {Market policies have profound implications for consumers as well as for the management of resources. One of the major concerns in fish trading is species mislabelling: the commercial name used does not correspond to the product, most often because the product is in fact a cheaper or a more easily available species. Substitution rates depend heavily on species, some often being sold mislabelled while others rarely or never mislabelled. Rates also vary largely depending on countries. In this study, we analyse the first market-wide dataset collected for France, the largest sea food market in Europe, for fish species substitution. We sequenced and analysed 371 samples bearing 55 commercial species names, collected in fishmonger shops, supermarkets and restaurants; the largest dataset assembled to date in an European country. Sampling included fish fillets, both fresh and frozen, and prepared meals. We found a total of 14 cases of mislabelling in five species: bluefin tuna, cod, yellowfin tuna, sole and seabream, setting the overall substitution rate at 3.7% CI [2.2-6.4], one of the lowest observed for comparable surveys with large sampling. We detected no case of species mislabelling among the frozen fillets or in industrially prepared meals, and all the substitutions were observed in products sold in fishmongers shops or restaurants. The rate of mislabelling does not differ between species, except for bluefin tuna. Despite a very small sample size (n = 6), the rate observed for this species (83.3% CI [36-99]) stands in sharp contrast with the low substitution rate observed for the other substituted species. In agreement with studies from other countries, this work shows that fish mislabelling can vary greatly within a country depending on the species. It further suggests that more efforts should be directed to the control of high value species like bluefin tuna.},
}
@article {pmid27843991,
year = {2015},
author = {Esmaeili, HR and Pirvar, Z and Ebrahimi, M and F Geiger, M},
title = {Karyological and molecular analysis of three endemic loaches (Actinopterygii: Cobitoidea) from Kor River basin, Iran.},
journal = {Molecular biology research communications},
volume = {4},
number = {1},
pages = {1-13},
pmid = {27843991},
issn = {2322-181X},
abstract = {This study provides new data on chromosomal characteristics and DNA barcoding of three endemic loaches of Iran: spiny southern loach Cobitis linea (Heckel, 1847), Persian stream loach Oxynoemacheilus persa (Heckel, 1848) and Tongiorgi stream loach Oxynoemacheilus tongiorgii (Nalbant &amp; Bianco, 1998). The chromosomes of these fishes were investigated by examining metaphase chromosome spreads obtained from epithelial gill and kidney cells. The diploid chromosome numbers of all three species were 2n=50. The karyotypes of C. linea consisted of 4M + 40SM + 6ST, NF=94; of O. persa by 20M + 22SM + 8ST, NF=90 and of O. tongiorgii by 18M + 24SM + 8ST, NF= 92. Sex chromosomes were cytologically indistinguishable in these loaches. Maximum likelihood-based estimation of the phylogenetic relationships based on the COI barcode region clearly separates the three Iranian loach species of the Kor River basin. All species distinguished by morphological characters were recovered as monophyletic clades by the COI barcodes. The obtained results could be used for population studies, management and conservation programs.},
}
@article {pmid27800370,
year = {2014},
author = {Debenedetti, F and Dalmasso, A and Bottero, MT and Gilli, M and Gili, S and Tepedino, V and Civera, T},
title = {Application of DNA Barcoding for Controlling of the Species from Octopus Genus.},
journal = {Italian journal of food safety},
volume = {3},
number = {4},
pages = {4521},
pmid = {27800370},
issn = {2239-7132},
abstract = {The DNA barcoding proposes the use of a particular sequence from a single genomic region as the base for an identifying system capable to determine all animal species. This methodology comprises the analysis of a 655 base-pair region from the mithocondrial cytochrome C oxidase gene (COI). Its application in the species identification of fishery products has been very promising. However, in the last years some doubts about its usage have emerged. In this work, we make use of the DNA barcoding for the identification of some of the octopus species with higher commercial interest (Octopus membranaceus, Octopus vulgaris, Octopus aegina, Octopus cyanea) focusing the attention on the reliability and completeness of the available information on the databases. The study looked over 51 individuals apparently belonging to the Octopus genus. For the identification of O.aegina, O.cyanea, O.vulgaris species no particular problems were found. On the other hand, most of the samples of O.membranaceus, though they clearly presented the morphological characteristics of the species, were not identified with the biomolecular analyses.},
}
@article {pmid27630534,
year = {2014},
author = {Ott, JA and Gruber-Vodicka, HR and Leisch, N and Zimmermann, J},
title = {Phylogenetic confirmation of the genus Robbea (Nematoda: Desmodoridae, Stilbonematinae) with the description of three new species.},
journal = {Systematics and biodiversity},
volume = {12},
number = {4},
pages = {434-455},
pmid = {27630534},
issn = {1477-2000},
support = {P 22470/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {The Stilbonematinae are a monophyletic group of marine nematodes that are characterized by a coat of thiotrophic bacterial symbionts. Among the ten known genera of the Stilbonematinae, the genus Robbea Gerlach 1956 had a problematic taxonomic history of synonymizations and indications of polyphyletic origin. Here we describe three new species of the genus, R. hypermnestra sp. nov., R. ruetzleri sp. nov. and R. agricola sp. nov., using conventional light microscopy, interference contrast microscopy and SEM. We provide 18S rRNA gene sequences of all three species, together with new sequences for the genera Catanema and Leptonemella. Both our morphological analyses as well as our phylogenetic reconstructions corroborate the genus Robbea. In our phylogenetic analysis the three species of the genus Robbea form a distinct clade in the Stilbonematinae radiation and are clearly separated from the clade of the genus Catanema, which has previously been synonymized with Robbea. Surprisingly, in R. hypermnestra sp. nov. all females are intersexes exhibiting male sexual characters. Our extended dataset of Stilbonematinae 18S rRNA genes for the first time allows the identification of the different genera, e.g. in a barcoding approach. http://zoobank.org/urn:lsid:zoobank.org:pub:D37C3F5A-CF2B-40E6-8B09-3C72EEED60B0.},
}
@article {pmid28788127,
year = {2014},
author = {Ferré-Borrull, J and Pallarès, J and Macías, G and Marsal, LF},
title = {Nanostructural Engineering of Nanoporous Anodic Alumina for Biosensing Applications.},
journal = {Materials (Basel, Switzerland)},
volume = {7},
number = {7},
pages = {5225-5253},
pmid = {28788127},
issn = {1996-1944},
abstract = {Modifying the diameter of the pores in nanoporous anodic alumina opens new possibilities in the application of this material. In this work, we review the different nanoengineering methods by classifying them into two kinds: in situ and ex situ. Ex situ methods imply the interruption of the anodization process and the addition of intermediate steps, while in situ methods aim at realizing the in-depth pore modulation by continuous changes in the anodization conditions. Ex situ methods permit a greater versatility in the pore geometry, while in situ methods are simpler and adequate for repeated cycles. As an example of ex situ methods, we analyze the effect of changing drastically one of the anodization parameters (anodization voltage, electrolyte composition or concentration). We also introduce in situ methods to obtain distributed Bragg reflectors or rugate filters in nanoporous anodic alumina with cyclic anodization voltage or current. This nanopore engineering permits us to propose new applications in the field of biosensing: using the unique reflectance or photoluminescence properties of the material to obtain photonic barcodes, applying a gold-coated double-layer nanoporous alumina to design a self-referencing protein sensor or giving a proof-of-concept of the refractive index sensing capabilities of nanoporous rugate filters.},
}
@article {pmid27485984,
year = {2014},
author = {Szalay, KZ and Nussinov, R and Csermely, P},
title = {Attractor Structures of Signaling Networks: Consequences of Different Conformational Barcode Dynamics and Their Relations to Network-Based Drug Design.},
journal = {Molecular informatics},
volume = {33},
number = {6-7},
pages = {463-468},
doi = {10.1002/minf.201400029},
pmid = {27485984},
issn = {1868-1743},
abstract = {Conformational barcodes tag functional sites of proteins and are decoded by interacting molecules transmitting the incoming signal. Conformational barcodes are modified by all co-occurring allosteric events induced by post-translational modifications, pathogen, drug binding, etc. We argue that fuzziness (plasticity) of conformational barcodes may be increased by disordered protein structures, by integrative plasticity of multi-phosphorylation events, by increased intracellular water content (decreased molecular crowding) and by increased action of molecular chaperones. This leads to increased plasticity of signaling and cellular networks. Increased plasticity is both substantiated by and inducing an increased noise level. Using the versatile network dynamics tool, Turbine (www.turbine.linkgroup.hu), here we show that the 10 % noise level expected in cellular systems shifts a cancer-related signaling network of human cells from its proliferative attractors to its largest, apoptotic attractor representing their health-preserving response in the carcinogen containing and tumor suppressor deficient environment modeled in our study. Thus, fuzzy conformational barcodes may not only make the cellular system more plastic, and therefore more adaptable, but may also stabilize the complex system allowing better access to its largest attractor.},
}
@article {pmid28324311,
year = {2014},
author = {Gantait, S and Debnath, S and Nasim Ali, M},
title = {Genomic profile of the plants with pharmaceutical value.},
journal = {3 Biotech},
volume = {4},
number = {6},
pages = {563-578},
pmid = {28324311},
issn = {2190-572X},
abstract = {There is an ample genetic diversity of plants with medicinal importance around the globe and this pool of genetic variation serves as the base for selection as well as for plant improvement. Thus, identification, characterization and documentation of the gene pool of medicinal plants are essential for this purpose. Genomic information of many a medicinal plant species has increased rapidly since the past decade and genetic resources available for domestication and improvement programs include genome sequencing, expressed sequence tags sequencing, transcript profiling, gene transmit, molecular markers in favor of mapping and breeding. In recent years, multiple endeavors have been undertaken for genomic characterization of medicinal plant species with the aid of molecular markers for sustainable utilization of gene pool, its conservation and future studies. Recent advancement in genomics is so fast that only some researches have been published till date and to a large extent documentation is restricted to electronic resources. Whole genome profiling of the identified medicinal plant species, carried out by several researchers, based on the DNA fingerprinting, is well documented in the present review. This review will facilitate preparing a database of the widely used, economically important medicinal plant species, based on their genomic organization.},
}
@article {pmid28040099,
year = {2014},
author = {Wang, L and Zhuang, Y and Zhang, H and Lin, X and Lin, S},
title = {DNA barcoding species in Alexandrium tamarense complex using ITS and proposing designation of five species.},
journal = {Harmful algae},
volume = {31},
number = {},
pages = {100-113},
doi = {10.1016/j.hal.2013.10.013},
pmid = {28040099},
issn = {1878-1470},
abstract = {Alexandrium species can be very difficult to identify, with A. catenella, A. tamarense, and A. fundyense that compose "Alexandrium tamarense species complex" (Atama complex) as a distinct example. DNA barcoding is promising to offer a solution but remains to be established. In this study, we examined the utility of ITS in resolving the Atama species complex, by analyzing previously studied strains plus unstudied Chinese strains within the LSU- and SSU-rDNA based group/clade frameworks recently established. We further investigated the presence of intragenomic polymorphism and its implications in species delimitation. Similar to the previous SSU and LSU results, our ITS-based phylogenies divided the complex to five clusters, but with longer and evener branch lengths between the clusters. Based on the ITS region, the inter-cluster genetic distances (p=0.134-0.216) were consistently and substantially greater than intra-cluster genetic distances (p=0.000-0.066), with an average inter-cluster (species) distance (p=0.167) 7.6-fold of the average intraspecific difference (p=0.022), qualifying the approximately 510-520bp ITS as a DNA barcode for Atama complex. We detected varying levels of intragenomic polymorphism in ITS but found that this did not impact the taxon-resolving power of this gene. With this DNA barcode, the new East and South China Sea strains and one Antarctic strain were placed in Clade IIC/Group IV, even though there were 7-10 polymorphic sites in their ITS, in contrast to none in SSU. Furthermore, our results suggest that the five clusters are recognizable as distinct species according to the phylogenetic species concept. Based on the phylogenetic placements of the type-locality strains of the existing three morphospecies and the dominant localities of other strains, we propose that Group I/Clade I be designated as A. fundyense, Group III/Clade IIB as A. tamarense, Group IV/Clade IIC as A. catenella, Group II/Clade IIA as A. mediterranis, and Group V/Clade IID as A. australis.},
}
@article {pmid28510869,
year = {2013},
author = {Yang, MY and Geraldino, PJL and Kim, MS},
title = {DNA barcode assessment of Gracilaria salicornia (Gracilariaceae, Rhodophyta) from Southeast Asia.},
journal = {Botanical studies},
volume = {54},
number = {1},
pages = {27},
pmid = {28510869},
issn = {1817-406X},
abstract = {BACKGROUND: DNA barcoding is becoming a widely applied tool for the quick and accurate identification of species. The evolution of the mitochondrial cytochrome c oxidase subunit I (COI) gene is sufficiently rapid to allow discrimination between closely related species and biogeographic subgroups within species. Gracilaria salicornia was originally described as being from Manila, the Philippines, and is distributed throughout Asia and the Indian Ocean. To more accurately define this species and its genetic diversity owing to the confusion of identification historically, DNA barcoding using the 5' end of the COI gene of the mitochondrial genome was applied to specimens collected from the Philippines, Malaysia, Thailand, China, and Japan, and they were compared to other gracilarian species.<br><br>RESULTS: Within species, the COI marker yielded two clusters with nucleotide divergences of 0.0-1.3%. This divergence is slightly higher than the typical intraspecific variation for red algae. A total of eight COI haplotypes were found for G. salicornia, comprising the following groups: H1-H3 from the Philippines; H4 from Okinawa in Japan; H5-H7 from Malaysia, Thailand, and China; and H8 from Thailand.<br><br>CONCLUSION: Although this work concentrated on a limited geographical region of a widespread taxon, the data shows intraspecific molecular divergences in G. salicornia and provides further evidence that DNA barcodes are useful tools for identifying species boundaries and examining biogeographical haplotypes for the genus Gracilaria.},
}
@article {pmid27605186,
year = {2013},
author = {Lung, O and Nadin-Davis, S and Fisher, M and Erickson, A and Knowles, MK and Furukawa-Stoffer, T and Ambagala, A},
title = {Microarray for Identification of the Chiropteran Host Species of Rabies Virus in Canada.},
journal = {Microarrays (Basel, Switzerland)},
volume = {2},
number = {2},
pages = {153-169},
pmid = {27605186},
issn = {2076-3905},
abstract = {Species identification through genetic barcoding can augment traditional taxonomic methods, which rely on morphological features of the specimen. Such approaches are especially valuable when specimens are in poor condition or comprise very limited material, a situation that often applies to chiropteran (bat) specimens submitted to the Canadian Food Inspection Agency for rabies diagnosis. Coupled with phenotypic plasticity of many species and inconclusive taxonomic keys, species identification using only morphological traits can be challenging. In this study, a microarray assay with associated PCR of the mitochondrial cytochrome c oxidase subunit I (COI) gene was developed for differentiation of 14 bat species submitted to the Canadian Food Inspection Agency from 1985-2012 for rabies diagnosis. The assay was validated with a reference collection of DNA from 153 field samples, all of which had been barcoded previously. The COI gene from 152 samples which included multiple specimens of each target species were successfully amplified by PCR and accurately identified by the microarray. One sample that was severely decomposed failed to amplify with PCR primers developed in this study, but amplified weakly after switching to alternate primers and was accurately typed by the microarray. Thus, the chiropteran microarray was able to accurately differentiate between the 14 species of Canadian bats targeted. This PCR and microarray assay would allow unequivocal identification to species of most, if not all, bat specimens submitted for rabies diagnosis in Canada.},
}
@article {pmid27605333,
year = {2011},
author = {Peršoh, D and Weig, AR and Rambold, G},
title = {A Transcriptome-Targeting EcoChip for Assessing Functional Mycodiversity.},
journal = {Microarrays (Basel, Switzerland)},
volume = {1},
number = {1},
pages = {25-41},
pmid = {27605333},
issn = {2076-3905},
abstract = {A functional biodiversity microarray (EcoChip) prototype has been developed to facilitate the analysis of fungal communities in environmental samples with broad functional and phylogenetic coverage and to enable the incorporation of nucleic acid sequence data as they become available from large-scale (next generation) sequencing projects. A dual probe set (DPS) was designed to detect a) functional enzyme transcripts at conserved protein sites and b) phylogenetic barcoding transcripts at ITS regions present in precursor rRNA. Deviating from the concept of GeoChip-type microarrays, the presented EcoChip microarray phylogenetic information was obtained using a dedicated set of barcoding microarray probes, whereas functional gene expression was analyzed by conserved domain-specific probes. By unlinking these two target groups, the shortage of broad sequence information of functional enzyme-coding genes in environmental communities became less important. The novel EcoChip microarray could be successfully applied to identify specific degradation activities in environmental samples at considerably high phylogenetic resolution. Reproducible and unbiased microarray signals could be obtained with chemically labeled total RNA preparations, thus avoiding the use of enzymatic labeling steps. ITS precursor rRNA was detected for the first time in a microarray experiment, which confirms the applicability of the EcoChip concept to selectively quantify the transcriptionally active part of fungal communities at high phylogenetic resolution. In addition, the chosen microarray platform facilitates the conducting of experiments with high sample throughput in almost any molecular biology laboratory.},
}
@article {pmid27715281,
year = {2006},
author = {},
title = {[Not Available].},
journal = {Emergency nurse : the journal of the RCN Accident and Emergency Nursing Association},
volume = {14},
number = {8},
pages = {2},
doi = {10.7748/en.14.8.2.s3},
pmid = {27715281},
issn = {1354-5752},
abstract = {Blood test:emergency nurses and other clinical staff who are involved in blood transfusions should have their competencies assessed formally every three years, according to the National Patient Safety Agency. The advice last month to all NHS organisations also urges the risk assessment of local transfusion procedures and using barcodes or other electronic identification systems to track blood. The safer practice notice and associated blood safety resources are available at www.npsa.nhs.uk/health/alerts/.},
}
@article {pmid27391275,
year = {2016},
author = {Pérez-Flores, J and Rueda-Calderon, H and Kvist, S and Siddall, ME and Oceguera-Figueroa, A},
title = {From the Worm in a Bottle of Mezcal: iDNA Confirmation of a Leech Parasitizing the Antillean Manatee.},
journal = {The Journal of parasitology},
volume = {102},
number = {5},
pages = {553-555},
doi = {10.1645/16-46},
pmid = {27391275},
issn = {1937-2345},
mesh = {Agave/*parasitology ; Animals ; DNA Barcoding, Taxonomic/*veterinary ; Female ; Fixatives ; Fruit and Vegetable Juices/*parasitology ; Leeches/*classification/genetics ; Mexico ; Phylogeny ; Trichechus/blood/*parasitology ; West Indies ; },
abstract = {Invertebrate-derived ingested DNA (iDNA) is quickly proving to be a valuable, non-invasive tool for monitoring vertebrate species of conservation concern. Using the DNA barcoding locus, we successfully identified both the blood-feeding leech Haementeria acuecueyetzin and its blood meal-the latter is shown to be derived from the Caribbean manatee, Trichechus manatus . DNA amplification was successful despite the fact that the specimen was fixed in Mezcal (a beverage distilled from agave). We report the first confirmed case of a leech feeding on a manatee, the first record of H. acuecueyetzin for the State of Chiapas and, to our knowledge, the first case of successful DNA amplification of a biological sample fixed in Mezcal other than the caterpillar "worms" more commonly found in that beverage.},
}
@article {pmid27470820,
year = {2016},
author = {Palero, F and Genis-Armero, R and Hall, MR and Clark, PF},
title = {DNA barcoding the phyllosoma of Scyllarides squammosus (H. Milne Edwards, 1837) (Decapoda: Achelata: Scyllaridae).},
journal = {Zootaxa},
volume = {4139},
number = {4},
pages = {481-498},
doi = {10.11646/zootaxa.4139.4.2},
pmid = {27470820},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; DNA/genetics ; DNA Barcoding, Taxonomic ; Decapoda/anatomy &amp; histology/*classification/*genetics/growth &amp; development ; Ecosystem ; Larva/anatomy &amp; histology/classification/genetics/growth &amp; development ; Organ Size ; Phylogeny ; },
abstract = {Scyllarides has the largest number of species with commercial importance within the Scyllaridae family. As for other achelate lobsters, however, little is known of the unique long-lived planktonic phyllosoma stages of any of these tropical and temperate species. Recently, a large and diverse collection of Scyllaridae phyllosoma, compiled from cruises along the Coral Sea and spanning several years, has been analysed. Molecular evidence from DNA-barcoding and phylogenetic analyses is provided here on the identity of S. squammosus phyllosoma larvae, including stages that were previously undescribed or poorly known. As a consequence, the growth and morphological changes that occur during the mid- to late-stages of S. squammosus larval development is now well-documented. Furthermore, an additional collection of S. squammosus larvae, described by Alain Michel and thought to be no longer extant, were discovered in the crustacean collection of the Muséum national d'Histoire naturelle, Paris. This new molecular and morphological information is complemented by a review of the literature. As a result, descriptions of key larval characters by a number of authors were evaluated and appear to suggest the existence of distinct groups of larvae within Scyllarides. From a combination of adult and larval morphology, and molecular data, the results presented here revealed inconsistencies with regard to the affinities of species assigned to Scyllarides. This new evidence will contribute to future studies addressing the phylogenetic relationships within the genus.},
}
@article {pmid27470742,
year = {2016},
author = {Seidel, M},
title = {Morphology and DNA barcoding reveal a new species of Eudicella from East Africa (Coleoptera: Scarabaeidae: Cetoniinae).},
journal = {Zootaxa},
volume = {4137},
number = {4},
pages = {535-544},
doi = {10.11646/zootaxa.4137.4.5},
pmid = {27470742},
issn = {1175-5334},
mesh = {Animals ; Coleoptera/*anatomy &amp; histology/*classification/genetics ; DNA/genetics ; DNA Barcoding, Taxonomic ; Kenya ; Species Specificity ; Uganda ; },
abstract = {A new species of Eudicella White, 1839 (Coleoptera: Scarabaeidae: Cetoniinae), is described from Uganda and Kenya: E. nana new species. Morphological and genetic analyses of the new taxon and phenotypically allied species are given. Eudicella nana is compared with its hypothesized sister species, E. darwiniana Kraatz, 1880, and diagnostic characters that distinguish it from other species occurring in the same region are provided.},
}
@article {pmid27465030,
year = {2016},
author = {Hwang, Y and Yoon, D and Ahn, EK and Hwang, H and Park, RW},
title = {Provider risk factors for medication administration error alerts: analyses of a large-scale closed-loop medication administration system using RFID and barcode.},
journal = {Pharmacoepidemiology and drug safety},
volume = {25},
number = {12},
pages = {1387-1396},
doi = {10.1002/pds.4068},
pmid = {27465030},
issn = {1099-1557},
mesh = {*Electronic Data Processing ; Humans ; Logistic Models ; Medical Order Entry Systems ; Medication Errors/prevention &amp; control/*statistics &amp; numerical data ; Medication Systems, Hospital ; Nurses/organization &amp; administration ; Pharmaceutical Preparations/*administration &amp; dosage ; Point-of-Care Systems ; *Radio Frequency Identification Device ; Risk Factors ; Time Factors ; Work Schedule Tolerance ; },
abstract = {PURPOSE: To determine the risk factors and rate of medication administration error (MAE) alerts by analyzing large-scale medication administration data and related error logs automatically recorded in a closed-loop medication administration system using radio-frequency identification and barcodes.<br><br>METHODS: The subject hospital adopted a closed-loop medication administration system. All medication administrations in the general wards were automatically recorded in real-time using radio-frequency identification, barcodes, and hand-held point-of-care devices. MAE alert logs recorded during a full 1&#x2009;year of 2012. We evaluated risk factors for MAE alerts including administration time, order type, medication route, the number of medication doses administered, and factors associated with nurse practices by logistic regression analysis.<br><br>RESULTS: A total of 2&#x2009;874&#x2009;539 medication dose records from 30&#x2009;232 patients (882.6 patient-years) were included in 2012. We identified 35&#x2009;082 MAE alerts (1.22% of total medication doses). The MAE alerts were significantly related to administration at non-standard time [odds ratio (OR) 1.559, 95% confidence interval (CI) 1.515-1.604], emergency order (OR 1.527, 95%CI 1.464-1.594), and the number of medication doses administered (OR 0.993, 95%CI 0.992-0.993). Medication route, nurse's employment duration, and working schedule were also significantly related.<br><br>CONCLUSION: The MAE alert rate was 1.22% over the 1-year observation period in the hospital examined in this study. The MAE alerts were significantly related to administration time, order type, medication route, the number of medication doses administered, nurse's employment duration, and working schedule. The real-time closed-loop medication administration system contributed to improving patient safety by preventing potential MAEs. Copyright &#xa9; 2016 John Wiley &amp; Sons, Ltd.},
}
@article {pmid27463361,
year = {2016},
author = {Geary, J and Camicioli, E and Bubela, T},
title = {DNA barcoding in the media: does coverage of cool science reflect its social context?.},
journal = {Genome},
volume = {59},
number = {9},
pages = {738-750},
doi = {10.1139/gen-2015-0210},
pmid = {27463361},
issn = {1480-3321},
mesh = {*DNA Barcoding, Taxonomic ; Humans ; Newspapers as Topic ; Science ; *Social Media ; },
abstract = {Paul Hebert and colleagues first described DNA barcoding in 2003, which led to international efforts to promote and coordinate its use. Since its inception, DNA barcoding has generated considerable media coverage. We analysed whether this coverage reflected both the scientific and social mandates of international barcoding organizations. We searched newspaper databases to identify 900 English-language articles from 2003 to 2013. Coverage of the science of DNA barcoding was highly positive but lacked context for key topics. Coverage omissions pose challenges for public understanding of the science and applications of DNA barcoding; these included coverage of governance structures and issues related to the sharing of genetic resources across national borders. Our analysis provided insight into how barcoding communication efforts have translated into media coverage; more targeted communication efforts may focus media attention on previously omitted, but important topics. Our analysis is timely as the DNA barcoding community works to establish the International Society for the Barcode of Life.},
}
@article {pmid27463035,
year = {2016},
author = {Beet, CR and Hogg, ID and Collins, GE and Cowan, DA and Wall, DH and Adams, BJ},
title = {Genetic diversity among populations of Antarctic springtails (Collembola) within the Mackay Glacier ecotone.},
journal = {Genome},
volume = {59},
number = {9},
pages = {762-770},
doi = {10.1139/gen-2015-0194},
pmid = {27463035},
issn = {1480-3321},
mesh = {Animals ; Antarctic Regions ; Arthropods/*classification/*genetics ; DNA, Mitochondrial ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; *Genetic Variation ; *Genetics, Population ; Haplotypes ; Phylogeny ; },
abstract = {Climate changes are likely to have major influences on the distribution and abundance of Antarctic terrestrial biota. To assess arthropod distribution and diversity within the Ross Sea region, we examined mitochondrial DNA (COI) sequences for three currently recognized species of springtail (Collembola) collected from sites in the vicinity, and to the north of, the Mackay Glacier (77°S). This area acts as a transition between two biogeographic regions (northern and southern Victoria Land). We found populations of highly divergent individuals (5%-11.3% intraspecific sequence divergence) for each of the three putative springtail species, suggesting the possibility of cryptic diversity. Based on molecular clock estimates, these divergent lineages are likely to have been isolated for 3-5 million years. It was during this time that the Western Antarctic Ice Sheet (WAIS) was likely to have completely collapsed, potentially facilitating springtail dispersal via rafting on running waters and open seaways. The reformation of the WAIS would have isolated newly established populations, with subsequent dispersal restricted by glaciers and ice-covered areas. Given the currently limited distributions for these genetically divergent populations, any future changes in species' distributions can be easily tracked through the DNA barcoding of springtails from within the Mackay Glacier ecotone.},
}
@article {pmid27460437,
year = {2016},
author = {Nyberg, LK and Quaderi, S and Emilsson, G and Karami, N and Lagerstedt, E and Müller, V and Noble, C and Hammarberg, S and Nilsson, AN and Sjöberg, F and Fritzsche, J and Kristiansson, E and Sandegren, L and Ambjörnsson, T and Westerlund, F},
title = {Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {30410},
pmid = {27460437},
issn = {2045-2322},
mesh = {Bacteria/genetics ; DNA/*chemistry ; DNA Barcoding, Taxonomic/*methods ; Drug Resistance, Bacterial/*genetics ; Fluorescent Dyes ; Microfluidics/*methods ; Optical Imaging/*methods ; Plasmids/*genetics ; },
abstract = {The rapid spread of antibiotic resistance - currently one of the greatest threats to human health according to WHO - is to a large extent enabled by plasmid-mediated horizontal transfer of resistance genes. Rapid identification and characterization of plasmids is thus important both for individual clinical outcomes and for epidemiological monitoring of antibiotic resistance. Toward this aim, we have developed an optical DNA mapping procedure where individual intact plasmids are elongated within nanofluidic channels and visualized through fluorescence microscopy, yielding barcodes that reflect the underlying sequence. The assay rapidly identifies plasmids through statistical comparisons with barcodes based on publicly available sequence repositories and also enables detection of structural variations. Since the assay yields holistic sequence information for individual intact plasmids, it is an ideal complement to next generation sequencing efforts which involve reassembly of sequence reads from fragmented DNA molecules. The assay should be applicable in microbiology labs around the world in applications ranging from fundamental plasmid biology to clinical epidemiology and diagnostics.},
}
@article {pmid27460382,
year = {2016},
author = {Aylagas, E and Rodríguez-Ezpeleta, N},
title = {Analysis of Illumina MiSeq Metabarcoding Data: Application to Benthic Indices for Environmental Monitoring.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1452},
number = {},
pages = {237-249},
doi = {10.1007/978-1-4939-3774-5_16},
pmid = {27460382},
issn = {1940-6029},
mesh = {Animals ; Biodiversity ; Electron Transport Complex IV/genetics ; Environmental Monitoring/*methods ; High-Throughput Nucleotide Sequencing/methods ; Invertebrates/classification/genetics ; Mitochondrial Proteins/genetics ; },
abstract = {This protocol details the analysis of Illumina MiSeq amplicon libraries derived from marine benthic macroinvertebrate samples and based on two barcodes of the mitochondrial cytochrome oxidase 1 (CO1) gene: a "short region," covered by overlapping forward and reverse reads and a "long region" for which forward and reverse reads do not overlap. Aside from providing guidelines for analyzing both types of amplicons, we show how amplicon reads can be used for the calculation of benthic indices for environmental monitoring.},
}
@article {pmid27460378,
year = {2016},
author = {Fonseca, VG and Lallias, D},
title = {Metabarcoding Marine Sediments: Preparation of Amplicon Libraries.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1452},
number = {},
pages = {183-196},
doi = {10.1007/978-1-4939-3774-5_12},
pmid = {27460378},
issn = {1940-6029},
mesh = {Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Geologic Sediments/*analysis ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; },
abstract = {The accurate assessment of community composition and ultimately species identification is of utmost importance in any ecological and evolutionary study. Advances in sequencing technologies have allowed the unraveling of levels of biodiversity never imagined before when applied to large-scale environmental DNA studies (also termed metabarcoding/metagenetics/metasystematics/environmental barcoding). Here, we describe a detailed protocol to assess eukaryotic biodiversity in marine sediments, identifying key steps that should not be neglected when preparing Next-Generation Sequencing (NGS) amplicon libraries: DNA extraction, multiple PCR amplification of DNA barcode markers with index/ tag-primers, and final Illumina MiSeq sequencing library preparation.},
}
@article {pmid27460377,
year = {2016},
author = {Nikinmaa, M and Götting, M},
title = {DNA Barcoding Marine Biodiversity: Steps from Mere Cataloguing to Giving Reasons for Biological Differences.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1452},
number = {},
pages = {169-182},
doi = {10.1007/978-1-4939-3774-5_11},
pmid = {27460377},
issn = {1940-6029},
mesh = {Biodiversity ; DNA/*genetics ; DNA Barcoding, Taxonomic/*methods ; Marine Biology/*methods ; },
abstract = {DNA barcoding has become a useful tool in many contexts and has opened up a completely new avenue for taxonomy. DNA barcoding has its widest application in biodiversity and ecological research to detect and describe diversity whenever morphological discrimination is difficult or impossible (e.g., in the case of species lacking diagnostic characters, early life stages, or cryptic species). In this chapter, we outline the utility of including physiological parameters as part of species description in publicly available databases that catalog taxonomic information resulting from barcoding projects. Cryptic species or different life stages of a species often differ in their physiological traits. Thus, if physiological aspects were included in species definitions, the presently cryptic species could be distinguished. We furthermore give suggestions for physiological information that should be included in a species description and describe potential applications of DNA barcoding for research with physiological components.},
}
@article {pmid27460376,
year = {2016},
author = {Steinke, D and Prosser, SW and Hebert, PD},
title = {DNA Barcoding of Marine Metazoans.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1452},
number = {},
pages = {155-168},
doi = {10.1007/978-1-4939-3774-5_10},
pmid = {27460376},
issn = {1940-6029},
mesh = {Animals ; Aquatic Organisms/*classification/genetics ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; },
abstract = {The accumulation of DNA barcode sequences will provide an increasingly useful and comprehensive library for species identification and discovery of marine metazoans. Here we present a summary of protocols designed to obtain DNA barcodes of marine metazoans from diverse phyla.},
}
@article {pmid27460369,
year = {2016},
author = {Briscoe, AG and Hopkins, KP and Waeschenbach, A},
title = {High-Throughput Sequencing of Complete Mitochondrial Genomes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1452},
number = {},
pages = {45-64},
doi = {10.1007/978-1-4939-3774-5_3},
pmid = {27460369},
issn = {1940-6029},
mesh = {Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; },
abstract = {Next-generation sequencing has revolutionized mitogenomics, turning a cottage industry into a high throughput process. This chapter outlines methodologies used to sequence, assemble, and annotate mitogenomes of non-model organisms using Illumina sequencing technology, utilizing either long-range PCR amplicons or gDNA as starting template. Instructions are given on how to extract DNA, conduct long-range PCR amplifications, generate short Sanger barcode tag sequences, prepare equimolar sample pools, construct and assess quality library preparations, assemble Illumina reads using either seeded reference mapping or de novo assembly, and annotate mitogenomes in the absence of an automated pipeline. Notes and recommendations, derived from our own experience, are given throughout this chapter.},
}
@article {pmid27454470,
year = {2016},
author = {Vassou, SL and Nithaniyal, S and Raju, B and Parani, M},
title = {Creation of reference DNA barcode library and authentication of medicinal plant raw drugs used in Ayurvedic medicine.},
journal = {BMC complementary and alternative medicine},
volume = {16 Suppl 1},
number = {Suppl 1},
pages = {186},
pmid = {27454470},
issn = {1472-6882},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/classification/*genetics ; *Medicine, Ayurvedic ; Phylogeny ; Plant Extracts/*classification/genetics ; Plants, Medicinal/*classification/*genetics ; },
abstract = {BACKGROUND: Ayurveda is a system of traditional medicine that originated in ancient India, and it is still in practice. Medicinal plants are the backbone of Ayurveda, which heavily relies on the plant-derived therapeutics. While Ayurveda is becoming more popular in several countries throughout the World, lack of authenticated medicinal plant raw drugs is a growing concern. Our aim was to DNA barcode the medicinal plants that are listed in the Ayurvedic Pharmacopoeia of India (API) to create a reference DNA barcode library, and to use the same to authenticate the raw drugs that are sold in markets.<br><br>METHODS: We have DNA barcoded 347 medicinal plants using rbcL marker, and curated rbcL DNA barcodes for 27 medicinal plants from public databases. These sequences were used to create Ayurvedic Pharmacopoeia of India - Reference DNA Barcode Library (API-RDBL). This library was used to authenticate 100 medicinal plant raw drugs, which were in the form of powders (82) and seeds (18).<br><br>RESULTS: Ayurvedic Pharmacopoeia of India - Reference DNA Barcode Library (API-RDBL) was created with high quality and authentic rbcL barcodes for 374 out of the 395 medicinal plants that are included in the API. The rbcL DNA barcode differentiated 319 species (85&#xa0;%) with the pairwise divergence ranging between 0.2 and 29.9&#xa0;%. PCR amplification and DNA sequencing success rate of rbcL marker was 100&#xa0;% even for the poorly preserved medicinal plant raw drugs that were collected from local markets. DNA barcoding revealed that only 79&#xa0;% raw drugs were authentic, and the remaining 21&#xa0;% samples were adulterated. Further, adulteration was found to be much higher with powders (ca. 25&#xa0;%) when compared to seeds (ca. 5&#xa0;%).<br><br>CONCLUSIONS: The present study demonstrated the utility of DNA barcoding in authenticating medicinal plant raw drugs, and found that approximately one fifth of the market samples were adulterated. Powdered raw drugs, which are very difficult to be identified by taxonomists as well as common people, seem to be the easy target for adulteration. Developing a quality control protocol for medicinal plant raw drugs by incorporating DNA barcoding as a component is essential to ensure safety to the consumers.},
}
@article {pmid27454456,
year = {2017},
author = {Montecinos, AE and Couceiro, L and Peters, AF and Desrut, A and Valero, M and Guillemin, ML},
title = {Species delimitation and phylogeographic analyses in the Ectocarpus subgroup siliculosi (Ectocarpales, Phaeophyceae).},
journal = {Journal of phycology},
volume = {53},
number = {1},
pages = {17-31},
doi = {10.1111/jpy.12452},
pmid = {27454456},
issn = {1529-8817},
mesh = {Chile ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Europe ; *Genetic Variation ; Phaeophyceae/*classification/*genetics ; *Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The genus Ectocarpus (Ectocarpales, Phaeophyceae) contains filamentous algae widely distributed in marine and estuarine habitats of temperate regions in both hemispheres. While E. siliculosus has become a model organism for genomics and genetics of the brown macroalgae, accurate species delineation, distribution patterns and diversity for the genus Ectocarpus remain problematic. In this study, we used three independent species delimitation approaches to generate a robust species hypothesis for 729 Ectocarpus specimens collected mainly along the European and Chilean coasts. These approaches comprised phylogenetic reconstructions and two bioinformatics tools developed to objectively define species boundaries (General Mixed Yule Coalescence Method and Automatic Barcode Gap Discovery). Our analyses were based on DNA sequences of two loci: the mitochondrial cytochrome oxidase subunit 1 and the nuclear internal transcribed spacer 1 of the ribosomal DNA. Our analyses showed the presence of at least 15 cryptic species and suggest the existence of incomplete lineage sorting or introgression between five of them. These results suggested the possible existence of different levels of reproductive barriers within this species complex. We also detected differences among species in their phylogeographic patterns, range and depth distributions, which may suggest different biogeographic histories (e.g., endemic species or recent introductions).},
}
@article {pmid27454455,
year = {2016},
author = {Lanzén, A and Lekang, K and Jonassen, I and Thompson, EM and Troedsson, C},
title = {High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities.},
journal = {Molecular ecology},
volume = {25},
number = {17},
pages = {4392-4406},
doi = {10.1111/mec.13761},
pmid = {27454455},
issn = {1365-294X},
mesh = {Animals ; *Biodiversity ; Ciliophora ; *DNA Barcoding, Taxonomic ; Ecosystem ; *Environmental Monitoring ; Food Chain ; Geologic Sediments ; *Oil and Gas Fields ; },
abstract = {As global exploitation of available resources increases, operations extend towards sensitive and previously protected ecosystems. It is important to monitor such areas in order to detect, understand and remediate environmental responses to stressors. The natural heterogeneity and complexity of communities means that accurate monitoring requires high resolution, both temporally and spatially, as well as more complete assessments of taxa. Increased resolution and taxonomic coverage is economically challenging using current microscopy-based monitoring practices. Alternatively, DNA sequencing-based methods have been suggested for cost-efficient monitoring, offering additional insights into ecosystem function and disturbance. Here, we applied DNA metabarcoding of eukaryotic communities in marine sediments, in areas of offshore drilling on the Norwegian continental shelf. Forty-five samples, collected from seven drilling sites in the Troll/Oseberg region, were assessed, using the small subunit ribosomal RNA gene as a taxonomic marker. In agreement with results based on classical morphology-based monitoring, we were able to identify changes in sediment communities surrounding oil platforms. In addition to overall changes in community structure, we identified several potential indicator taxa, responding to pollutants associated with drilling fluids. These included the metazoan orders Macrodasyida, Macrostomida and Ceriantharia, as well as several ciliates and other protist taxa, typically not targeted by environmental monitoring programmes. Analysis of a co-occurrence network to study the distribution of taxa across samples provided a framework for better understanding the impact of anthropogenic activities on the benthic food web, generating novel, testable hypotheses of trophic interactions structuring benthic communities.},
}
@article {pmid27453044,
year = {2016},
author = {Guernet, A and Mungamuri, SK and Cartier, D and Sachidanandam, R and Jayaprakash, A and Adriouch, S and Vezain, M and Charbonnier, F and Rohkin, G and Coutant, S and Yao, S and Ainani, H and Alexandre, D and Tournier, I and Boyer, O and Aaronson, SA and Anouar, Y and Grumolato, L},
title = {CRISPR-Barcoding for Intratumor Genetic Heterogeneity Modeling and Functional Analysis of Oncogenic Driver Mutations.},
journal = {Molecular cell},
volume = {63},
number = {3},
pages = {526-538},
pmid = {27453044},
issn = {1097-4164},
support = {P01 CA080058/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Antineoplastic Combined Chemotherapy Protocols/pharmacology ; Biomarkers, Tumor/*genetics ; *CRISPR-Cas Systems ; Carcinoma, Non-Small-Cell Lung/drug therapy/*genetics/metabolism/pathology ; Cell Lineage ; Clone Cells/drug effects/metabolism/pathology ; DNA Mutational Analysis ; DNA, Neoplasm/*genetics ; Dose-Response Relationship, Drug ; Drug Resistance, Neoplasm/genetics ; ErbB Receptors/antagonists &amp; inhibitors/genetics/metabolism ; Gene Editing/*methods ; *Genetic Heterogeneity ; Genetic Predisposition to Disease ; HCT116 Cells ; HEK293 Cells ; High-Throughput Nucleotide Sequencing ; Humans ; Lung Neoplasms/drug therapy/*genetics/metabolism/pathology ; MCF-7 Cells ; Male ; Mice, SCID ; Multiplex Polymerase Chain Reaction ; *Oncogenes ; Phenotype ; *Point Mutation ; Protein Kinase Inhibitors/pharmacology ; Time Factors ; Tumor Microenvironment ; Xenograft Model Antitumor Assays ; },
abstract = {Intratumor genetic heterogeneity underlies the ability of tumors to evolve and adapt to different environmental conditions. Using CRISPR/Cas9 technology and specific DNA barcodes, we devised a strategy to recapitulate and trace the emergence of subpopulations of cancer cells containing a mutation of interest. We used this approach to model different mechanisms of lung cancer cell resistance to EGFR inhibitors and to assess effects of combined drug therapies. By overcoming intrinsic limitations of current approaches, CRISPR-barcoding also enables investigation of most types of genetic modifications, including repair of oncogenic driver mutations. Finally, we used highly complex barcodes inserted at a specific genome location as a means of simultaneously tracing the fates of many thousands of genetically labeled cancer cells. CRISPR-barcoding is a straightforward and highly flexible method that should greatly facilitate the functional investigation of specific mutations, in a context that closely mimics the complexity of cancer.},
}
@article {pmid27452291,
year = {2016},
author = {Alajmi, RA and AlGhufaili, H and Farrukh, A and Aljohani, H and Mashaly, AM},
title = {First Report of Necrophagous Insects on Human Corpses in Riyadh, Saudi Arabia.},
journal = {Journal of medical entomology},
volume = {53},
number = {6},
pages = {1276-1282},
doi = {10.1093/jme/tjw113},
pmid = {27452291},
issn = {1938-2928},
mesh = {Animals ; Base Sequence ; Cadaver ; Coleoptera/classification/genetics/growth &amp; development/*physiology ; Diptera/classification/genetics/growth &amp; development/*physiology ; Electron Transport Complex IV/genetics ; Entomology ; Forensic Sciences ; Humans ; Insect Proteins/genetics ; Larva/classification/genetics/growth &amp; development/physiology ; Mitochondrial Proteins/genetics ; Saudi Arabia ; Sequence Alignment ; },
abstract = {Necrophagous species of insects provide useful complementary data to estimate the postmortem interval in forensic cases. Here, for the first time, we report on insect specimens collected from human corpses in Riyadh, Kingdom of Saudi Arabia. During the study, 14 beetle larvae were collected from the outdoor corpse (case report one) and five flies and seven beetles were collected from the indoor corpse (case report two). Sequencing was performed to study the mitochondrial DNA (mtDNA) as the prospective basis of an identification technique. The sequencing focused on a section of the cytochrome oxidase I encoding region of mtDNA. Two beetle species, Dermestes frischii (Kugelann) and Dermestes maculatus (De Geer) (Coleoptera: Dermestidae), and one fly species, Chrysomya albiceps (Wiedemann) (Diptera: Calliphoridae), were identified. These results will be instrumental in the implementation of a Saudi database of forensically relevant insects.},
}
@article {pmid27447221,
year = {2016},
author = {Glowska, E and Broda, L and Gebhard, CA and Dabert, M},
title = {A new quill mite Syringophiloidus plocei sp. nov. (Prostigmata: Syringophilidae) parasitizing ploceid birds (Passeriformes) in Gabon - a combined description using morphology and DNA barcoding.},
journal = {Acta parasitologica},
volume = {61},
number = {3},
pages = {562-566},
doi = {10.1515/ap-2016-0075},
pmid = {27447221},
issn = {1896-1851},
mesh = {Animals ; Bird Diseases/*parasitology ; DNA/genetics ; DNA Barcoding, Taxonomic ; Female ; Gabon ; Mite Infestations/parasitology/*veterinary ; Mites/classification/*genetics/*growth &amp; development ; Passeriformes/parasitology ; },
abstract = {A new species of quill mites (Syringophilidae) Syringophiloidus plocei sp. nov. parasitizing Ploceus cucullatus (St. Muller) (type host), P. aurantius (Vieillot) and P. nigerrimus (Vieillot) (Ploceidae: Passeriformes) in Gabon is described using external morphology and DNA barcode data (the mitochondrial cytochrome c oxidase subunit I sequences (COI) and D1-D3 region of the nuclear 28S rRNA gene). Females of S. plocei sp. nov. differ from S. pseudonigritae Glowska, Dragun-Damian and Dabert, 2012 by the length of setae ag3 190-230 (vs 145-160). The genetic distances (K2P) between COI haplotypes of S. plocei sp. nov. individuals (from P. cucullatus, P. nigerrimus and P. aurantius) and S. pseudonigritae ranges from 13.1-13.7%.},
}
@article {pmid27442864,
year = {2016},
author = {Avraham, R and Haseley, N and Fan, A and Bloom-Ackermann, Z and Livny, J and Hung, DT},
title = {A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes.},
journal = {Nature protocols},
volume = {11},
number = {8},
pages = {1477-1491},
pmid = {27442864},
issn = {1750-2799},
mesh = {Animals ; Bone Marrow Cells/cytology ; Gene Expression Profiling/*methods ; *Host-Pathogen Interactions ; Limit of Detection ; Macrophages/*metabolism/microbiology ; Mice ; RNA, Bacterial/*genetics ; Salmonella/cytology/*genetics/*physiology ; Sequence Analysis, RNA/*methods ; Time Factors ; },
abstract = {The ability to simultaneously characterize the bacterial and host expression programs during infection would facilitate a comprehensive understanding of pathogen-host interactions. Although RNA sequencing (RNA-seq) has greatly advanced our ability to study the transcriptomes of prokaryotes and eukaryotes separately, limitations in existing protocols for the generation and analysis of RNA-seq data have hindered simultaneous profiling of host and bacterial pathogen transcripts from the same sample. Here we provide a detailed protocol for simultaneous analysis of host and bacterial transcripts by RNA-seq. Importantly, this protocol details the steps required for efficient host and bacteria lysis, barcoding of samples, technical advances in sample preparation for low-yield sample inputs and a computational pipeline for analysis of both mammalian and microbial reads from mixed host-pathogen RNA-seq data. Sample preparation takes 3 d from cultured cells to pooled libraries. Data analysis takes an additional day. Compared with previous methods, the protocol detailed here provides a sensitive, facile and generalizable approach that is suitable for large-scale studies and will enable the field to obtain in-depth analysis of host-pathogen interactions in infection models.},
}
@article {pmid27442116,
year = {2016},
author = {Díaz, J and Villanova, GV and Brancolini, F and Del Pazo, F and Posner, VM and Grimberg, A and Arranz, SE},
title = {First DNA Barcode Reference Library for the Identification of South American Freshwater Fish from the Lower Paraná River.},
journal = {PloS one},
volume = {11},
number = {7},
pages = {e0157419},
pmid = {27442116},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Fishes/*genetics ; *Fresh Water ; *Gene Library ; Genetic Variation ; Geography ; Imaging, Three-Dimensional ; Likelihood Functions ; *Rivers ; South America ; Species Specificity ; },
abstract = {Valid fish species identification is essential for biodiversity conservation and fisheries management. Here, we provide a sequence reference library based on mitochondrial cytochrome c oxidase subunit I for a valid identification of 79 freshwater fish species from the Lower Paraná River. Neighbour-joining analysis based on K2P genetic distances formed non-overlapping clusters for almost all species with a ≥99% bootstrap support each. Identification was successful for 97.8% of species as the minimum genetic distance to the nearest neighbour exceeded the maximum intraspecific distance in all these cases. A barcoding gap of 2.5% was apparent for the whole data set with the exception of four cases. Within-species distances ranged from 0.00% to 7.59%, while interspecific distances varied between 4.06% and 19.98%, without considering Odontesthes species with a minimum genetic distance of 0%. Sequence library validation was performed by applying BOLDs BIN analysis tool, Poisson Tree Processes model and Automatic Barcode Gap Discovery, along with a reliable taxonomic assignment by experts. Exhaustive revision of vouchers was performed when a conflicting assignment was detected after sequence analysis and BIN discordance evaluation. Thus, the sequence library presented here can be confidently used as a benchmark for identification of half of the fish species recorded for the Lower Paraná River.},
}
@article {pmid27439517,
year = {2016},
author = {Akkaya, B and Miozzo, P and Holstein, AH and Shevach, EM and Pierce, SK and Akkaya, M},
title = {A Simple, Versatile Antibody-Based Barcoding Method for Flow Cytometry.},
journal = {Journal of immunology (Baltimore, Md. : 1950)},
volume = {197},
number = {5},
pages = {2027-2038},
pmid = {27439517},
issn = {1550-6606},
support = {ZIA AI000899-15//Intramural NIH HHS/United States ; },
mesh = {Animals ; Antibodies/chemistry/classification/*isolation &amp; purification ; Electronic Data Processing/*methods ; Flow Cytometry/*methods ; Fluorescent Dyes/chemistry ; Humans ; Mice ; Staining and Labeling ; },
abstract = {Barcoding of biological samples is a commonly used strategy to mark or identify individuals within a complex mixture. However, cell barcoding has not yet found wide use in flow cytometry that would benefit greatly from the ability to analyze pooled experimental samples simultaneously. This is due, in part, to technical and practical limitations of current fluorescent dye-based methods. In this study, we describe a simple, versatile barcoding strategy that relies on combinations of a single Ab conjugated to different fluorochromes and thus in principle can be integrated into any flow cytometry application. To demonstrate the efficacy of the approach, we describe the results of a variety of experiments using live cells as well as fixed and permeabilized cells. The results of these studies show that Ab-based barcoding provides a simple, practical method for identifying cells from individual samples pooled for analysis by flow cytometry that has broad applications in immunological research.},
}
@article {pmid27437861,
year = {2017},
author = {Zhang, HG and Lv, MH and Yi, WB and Zhu, WB and Bu, WJ},
title = {Species diversity can be overestimated by a fixed empirical threshold: insights from DNA barcoding of the genus Cletus (Hemiptera: Coreidae) and the meta-analysis of COI data from previous phylogeographical studies.},
journal = {Molecular ecology resources},
volume = {17},
number = {2},
pages = {314-323},
doi = {10.1111/1755-0998.12571},
pmid = {27437861},
issn = {1755-0998},
mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Heteroptera/*classification/enzymology/*genetics ; Metagenomics/*methods ; },
abstract = {The use of genetic distances to identify species within the framework of DNA barcoding has to some extent improved the development of biodiversity studies. However, using a fixed empirical threshold to delimit species may lead to overestimating species diversity. In this study, we use a new data set of COI sequences for 366 specimens within the genus of Cletus as well as conduct an analysis on the same genetic data for collected morphologically defined species from previous phylogeographical studies, to test whether high intraspecific genetic divergences are common with the premises of comprehensive sampling. The results indicate C. graminis Hsiao &amp; Cheng , is the same species with C. punctiger (Dallas, 1852) and should be synonymized and that the distributional record of C. pugnator (Fabricius, 1787) in China is correct. High intraspecific genetic differentiations (0%-4.35%) were found in C. punctiger. Furthermore, as to the mined data, the maximum intraspecific K2P distances of 186 species (48.44% of 384) exceed 3%, and 101 species (26.30%) can be divided into two or more clusters with a threshold of 3% in cluster analysis. If genetic distance is used to delimit species boundaries, the minimum interspecific K2P distance of the congeneric species should be considered rather than only using the fixed empirical value; otherwise, the species richness may be overestimated in some cases.},
}
@article {pmid27435430,
year = {2016},
author = {Lima, LHGM and Mesquita, MR and Skrip, L and de Souza Freitas, MT and Silva, VC and Kirstein, OD and Abassi, I and Warburg, A and Balbino, VQ and Costa, CHN},
title = {DNA barcode for the identification of the sand fly Lutzomyia longipalpis plant feeding preferences in a tropical urban environment.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {29742},
pmid = {27435430},
issn = {2045-2322},
support = {T32 AI007404/AI/NIAID NIH HHS/United States ; },
mesh = {Anacardiaceae/genetics/parasitology ; Animals ; Brazil/epidemiology ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/analysis/genetics ; Endemic Diseases ; Fabaceae/genetics/parasitology ; Feeding Behavior/*physiology ; Insect Vectors/genetics/parasitology/*physiology ; Leishmania infantum/physiology ; Leishmaniasis, Visceral/epidemiology/parasitology ; Meliaceae/genetics/parasitology ; Plants/genetics/*parasitology ; Psychodidae/classification/genetics/*physiology ; Ribulose-Bisphosphate Carboxylase/genetics ; },
abstract = {Little is known about the feeding behavior of hematophagous insects that require plant sugar to complete their life cycles. We studied plant feeding of Lutzomyia longipalpis sand flies, known vectors of Leishmania infantum/chagasi parasites, in a Brazilian city endemic with visceral leishmaniasis. The DNA barcode technique was applied to identify plant food source of wild-caught L. longipalpis using specific primers for a locus from the chloroplast genome, ribulose diphosphate carboxylase. DNA from all trees or shrubs within a 100-meter radius from the trap were collected to build a barcode reference library. While plants from the Anacardiaceae and Meliaceae families were the most abundant at the sampling site (25.4% and 12.7% of the local plant population, respectively), DNA from these plant families was found in few flies; in contrast, despite its low abundance (2.9%), DNA from the Fabaceae family was detected in 94.7% of the sand flies. The proportion of sand flies testing positive for DNA from a given plant family was not significantly associated with abundance, distance from the trap, or average crown expansion of plants from that family. The data suggest that there may indeed be a feeding preference of L. longipalpis for plants in the Fabaceae family.},
}
@article {pmid27433442,
year = {2016},
author = {Visagie, CM and Seifert, KA and Houbraken, J and Samson, RA and Jacobs, K},
title = {A phylogenetic revision of Penicillium sect. Exilicaulis, including nine new species from fynbos in South Africa.},
journal = {IMA fungus},
volume = {7},
number = {1},
pages = {75-117},
pmid = {27433442},
issn = {2210-6340},
abstract = {A survey of the fynbos biome in South Africa resulted in the isolation of 61 Penicillium species from Protea repens infructescences, air, and soil samples. Fourteen of these belong to Penicillium sect. Exilicaulis and therefore we considered it an opportunity to re-evaluate the taxonomy of the section. Phylogenetic comparisons of the ITS, β-tubulin, calmodulin and RPB2 gene regions of the 76 section Exilicaulis species, revealed 52 distinct species, including nine new species from fynbos. Morphological comparisons confirmed the novelty for most of these, however, new species closely related to P. rubefaciens did not show significant or consistent morphological differences and we thus placed a bias on phylogenetic data applying the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) concept. In this paper we describe the nine new species and update the accepted species list and resolve synonyms in the section. Importantly, we reveal that P. citreosulfuratum is the correct name for the clade previously considered to represent P. toxicarium fide Serra et al. (2008). The nine new species are: Penicillium atrolazulinum, P. consobrinum, P. cravenianum, P. hemitrachum, P. pagulum, P. repensicola, P. momoii, P. subturcoseum, and P. xanthomelinii spp. nov.},
}
@article {pmid27432350,
year = {2016},
author = {Cheng, YC and Lin, CP},
title = {Dietary Niche Partitioning of Euphaea formosa and Matrona cyanoptera (Odonata: Zygoptera) on the Basis of DNA Barcoding of Larval Feces.},
journal = {Journal of insect science (Online)},
volume = {16},
number = {1},
pages = {},
pmid = {27432350},
issn = {1536-2442},
mesh = {Animals ; DNA Barcoding, Taxonomic ; *Diet ; Feces/chemistry ; Insect Proteins/genetics ; Larva/genetics/growth &amp; development/physiology ; Nymph/genetics/growth &amp; development/physiology ; Odonata/genetics/growth &amp; development/*physiology ; *Predatory Behavior ; Sequence Analysis, DNA ; Taiwan ; },
abstract = {Odonate larvae are commonly considered opportunistic general predators in freshwater ecosystems. However, the dietary breadth of most odonate larvae in forest streams is still poorly documented. We characterized the prey species and estimated the level of dietary niche overlap of two damselflies, Euphaea formosa Hagen 1869 and Matrona cyanoptera Hämäläinen and Yeh, 2000 in a forest stream of central Taiwan on the basis of DNA barcoding of larval feces. A collection of 23 successfully identified cytochrome c oxidase 1 (CO1) barcoding sequences suggested that the mayflies (Ephemeroptera), caddisflies (Trichoptera), and midges (Diptera) comprise the majority (43%, 6/14) of prey species consumed by E. formosa larvae, whereas the identified prey for M. cyanoptera were mainly zooplankton (56%, 5/9). Statistical analysis of dietary overlap indicated that these two species occupy different dietary niches (Pianka's index = 0.219). DNA barcoding analysis of damselfly larval feces was effective in detecting less sclerotized prey such as vertebrates (fish and frog) and small zooplankton. However, a moderately successful rate (<70%) of PCR amplification by universal CO1 primers and a low percentage (<60%) of identifiable sequences in public databases indicate the limitations of naive DNA barcoding in fecal analysis.},
}
@article {pmid27430899,
year = {2016},
author = {Jaksch, K and Eschner, A and Rintelen, TV and Haring, E},
title = {DNA analysis of molluscs from a museum wet collection: a comparison of different extraction methods.},
journal = {BMC research notes},
volume = {9},
number = {},
pages = {348},
pmid = {27430899},
issn = {1756-0500},
mesh = {Animals ; Austria ; DNA/genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic/*standards ; DNA Primers/chemistry ; Electron Transport Complex IV/genetics ; Formaldehyde/chemistry ; Liquid Phase Microextraction/methods ; Mollusca/classification/*genetics ; Museums ; Polymerase Chain Reaction/*standards ; RNA, Ribosomal, 16S/genetics ; Reagent Kits, Diagnostic/*standards ; Solid Phase Microextraction/methods ; Tissue Banks ; },
abstract = {BACKGROUND: DNA isolation and PCR amplification from molluscan taxa is considered as problematic because polysaccharides in tissue and mucus presumably co-precipitate with the DNA and inhibit the activity of DNA polymerase. In the present study we tested two common extraction methods on specimens from the mollusc collection of the Natural History Museum Vienna (NHMW). We analysed a broad variety of taxa covering a large temporal span (acquisition years 1877 to 1999), which distinguishes our study from previous ones where mostly fresh material was used. We also took other factors into account: effects of sample age, effects of formaldehyde treatment and taxon-specific problems. We used several primer combinations to amplify amplicons of different lengths of two mitochondrial genes: cytochrome c oxidase subunit 1 (COI) and 16S rRNA gene (16S).<br><br>RESULTS: Overall PCR success was 43&#xa0;% in the 576 extractions (including all primer combinations). The smallest amplicon (~240&#xa0;bp) showed the best results (49&#xa0;% positive reactions), followed by the 400&#xa0;bp amplicon (40.5&#xa0;%). Both short sections yielded significantly better results than the 700&#xa0;bp long amplicon (27&#xa0;%). Comparatively, the Gen-ial-First, All-tissue DNA-Kit-extraction method performed significantly better than Promega-Tissue and Hair Extraction Kit. Generally, PCR success is age-dependent. Nonetheless, we were able to obtain the longest amplicon even from 137-year-old material. Importantly, formaldehyde traces did not totally inhibit amplification success, although very high concentrations did.<br><br>CONCLUSIONS: Museum material has gained importance for DNA analysis in recent years, especially for DNA barcoding projects. In some cases, however, the amplification of the standard barcoding region (partial sequence of the COI) is problematic with old material. Our study clearly shows that the COI barcoding region could be amplified in up to 49&#xa0;% of PCRs (varying with amplicon length), which is, for museum samples, quite a high percentage. The difference between extraction methods was minimal and we recommend using an established kit for a first attempt because experience and routine in handling might be more important than slight performance differences of the various kits. Finally, we identify fixation, storage, sample conservation and documentation of the specimens' history rather than the DNA extraction method to be the most crucial factors for PCR success.},
}
@article {pmid27427438,
year = {2016},
author = {Patil, TS and Tamboli, AS and Patil, SM and Bhosale, AR and Govindwar, SP and Muley, DV},
title = {Relative profile analysis of molecular markers for identification and genetic discrimination of loaches (Pisces, Nemacheilidae).},
journal = {Comptes rendus biologies},
volume = {339},
number = {9-10},
pages = {364-370},
doi = {10.1016/j.crvi.2016.06.001},
pmid = {27427438},
issn = {1768-3238},
mesh = {Alleles ; Animals ; Classification ; Cypriniformes/*genetics ; DNA/genetics ; DNA Barcoding, Taxonomic ; Gene Frequency ; Genetic Markers/*genetics ; Genetic Variation ; Heterozygote ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic/genetics ; Polymorphism, Restriction Fragment Length ; Species Specificity ; },
abstract = {Genus Nemacheilus, Nemachilichthys and Schistura belong to the family Nemacheilidae of the order Cypriniformes. The present investigation was undertaken to observe genetic diversity, phylogenetic relationship and to develop a molecular-based tool for taxonomic identification. For this purpose, four different types of molecular markers were utilized in which 29 random amplified polymorphic DNA (RAPD), 25 inter-simple sequence repeat (ISSR) markers, and 10 amplified fragment length polymorphism (AFLP) marker sets were screened and mitochondrial COI gene was sequenced. This study added COI barcodes for the identification of Nemacheilus anguilla, Nemachilichthys rueppelli and Schistura denisoni. RAPD showed higher polymorphism (100%) than the ISSR (93.75-100%) and AFLP (93.86-98.96%). The polymorphic information content (PIC), heterozygosity, multiplex ratio, and gene diversity was observed highest for AFLP primers, whereas the major allele frequency was observed higher for RAPD (0.5556) and lowest for AFLP (0.1667). The COI region of all individuals was successfully amplified and sequenced, which gave a 100% species resolution.},
}
@article {pmid27423443,
year = {2020},
author = {Sigamani, S and Perumal, M and Thivakaran, GA and Thangavel, B and Kandasamy, K},
title = {DNA barcoding of macrofauna act as a tool for assessing marine ecosystem.},
journal = {Marine pollution bulletin},
volume = {152},
number = {},
pages = {107891},
doi = {10.1016/j.marpolbul.2016.07.017},
pmid = {27423443},
issn = {1879-3363},
mesh = {*DNA Barcoding, Taxonomic ; *Ecosystem ; Environmental Monitoring ; },
abstract = {Nowadays, marine ecosystem monitoring and assessment are increasingly depending on variety of molecular tools. With these background, DNA barcoding play a key role in species identification with increasing speed and accuracy, and although the suitability for developing genetic tools like genomic AMBI (gAMBI). Presently we have submitted 13 benthic polychaete species using mtCOI to GenBank. Of these, nine species were newly submitted, and hence they act as a benchmark and reference organism for identifying respective polychaete species worldwide in the near future. Based on that, our study results tend to be helpful for motivating among the researcher in order to implementing the genomic AMBI (gAMBI).},
}
@article {pmid27422709,
year = {2016},
author = {Volik, S and Alcaide, M and Morin, RD and Collins, C},
title = {Cell-free DNA (cfDNA): Clinical Significance and Utility in Cancer Shaped By Emerging Technologies.},
journal = {Molecular cancer research : MCR},
volume = {14},
number = {10},
pages = {898-908},
doi = {10.1158/1541-7786.MCR-16-0044},
pmid = {27422709},
issn = {1557-3125},
support = {//CIHR/Canada ; },
mesh = {Cell-Free System ; DNA, Neoplasm/*blood ; Disease Progression ; Humans ; Neoplasms/*genetics ; Precision Medicine ; },
abstract = {Precision oncology is predicated upon the ability to detect specific actionable genomic alterations and to monitor their adaptive evolution during treatment to counter resistance. Because of spatial and temporal heterogeneity and comorbidities associated with obtaining tumor tissues, especially in the case of metastatic disease, traditional methods for tumor sampling are impractical for this application. Known to be present in the blood of cancer patients for decades, cell-free DNA (cfDNA) is beginning to inform on tumor genetics, tumor burden, and mechanisms of progression and drug resistance. This substrate is amenable for inexpensive noninvasive testing and thus presents a viable approach to serial sampling for screening and monitoring tumor progression. The fragmentation, low yield, and variable admixture of normal DNA present formidable technical challenges for realization of this potential. This review summarizes the history of cfDNA discovery, its biological properties, and explores emerging technologies for clinically relevant sequence-based analysis of cfDNA in cancer patients. Molecular barcoding (or Unique Molecular Identifier, UMI)-based methods currently appear to offer an optimal balance between sensitivity, flexibility, and cost and constitute a promising approach for clinically relevant assays for near real-time monitoring of treatment-induced mutational adaptations to guide evidence-based precision oncology. Mol Cancer Res; 14(10); 898-908. ©2016 AACR.},
}
@article {pmid27420996,
year = {2016},
author = {Zhao, YY and Su, LN and Zhang, ZM and Wang, XY},
title = {Phylogenetic relationships of Pseudohynobius (Urodela, Hynobiidae) inferred from DNA barcoding analysis.},
journal = {Genetics and molecular research : GMR},
volume = {15},
number = {2},
pages = {},
doi = {10.4238/gmr.15028155},
pmid = {27420996},
issn = {1676-5680},
mesh = {Animals ; Bayes Theorem ; Cytochromes b/genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Caudata/*genetics ; },
abstract = {As a proven tool, DNA barcoding can identify species rapidly and unambiguously. In this study, we used mtDNA cyt b, COI, and 16s rRNA sequences of six species of Pseudohynobius, Protohynobius puxiongensis, Liua shihi, Ranodon sibiricus, and Pachyhynobius shangchengensis, to reconstruct the phylogenetic relationships using Bayesian inference and maximum likelihood methods. Approximate lineage divergence times were also estimated, the divergence between them was calculated to have taken place mainly in Miocene. Our results showed that: 1) Ps. guizhouensis is an independent and valid species that is a sister species to Ps. kuankuoshuiensis; 2) five Pseudohynobius species formed a monophyletic group; 3) Ps. tsinpaensis is different from L. shihi, and should be classified as belonging to the Liua genus; and 4) Pr. puxiongensis is the sister lineage to all Pseudohynobius species, and should therefore be named Pseudohynobius puxiongensis.},
}
@article {pmid27420974,
year = {2016},
author = {Hou, DY and Wang, GP and Zhi, LH and Xu, HW and Liang, HL and Yang, MM and Shi, GA},
title = {Molecular identification of Achyranthis Bidentatae Radix by using DNA barcoding.},
journal = {Genetics and molecular research : GMR},
volume = {15},
number = {2},
pages = {},
doi = {10.4238/gmr.15028783},
pmid = {27420974},
issn = {1676-5680},
mesh = {Achyranthes/classification/*genetics ; DNA Barcoding, Taxonomic ; DNA, Intergenic ; Genome, Plant ; Photosystem II Protein Complex/genetics ; *Phylogeny ; *Polymorphism, Genetic ; },
abstract = {Achyranthis Bidentatae Radix has a long history in China as a commonly used herb that can be used to treat various diseases, including those related to the liver, muscles, bones, and kidneys. Recently, an increase in the number of adulterants has been reported, which affects the clinical safety of Achyranthis Bidentatae Radix. To identify adulterants of Achyranthis Bidentatae Radix, we collected samples from major regions and conducted an in-depth genetic comparison of the herb and its commonly used adulterants. We amplified and sequenced three genomic regions, internal transcribed spacer (ITS), psbA-trnH, and internal transcribed spacer 2 (ITS2), to confirm whether ITS2 is a suitable identifier for Achyranthis Bidentatae Radix. Results showed that the ITS2 sequence length of Achyranthis Bidentatae Radix was 199 bp, with no variation between samples. The inter-specific genetic distance of ITS2 between Achyranthis Bidentatae Radix and its adulterants was 0.390. Neighbor-joining trees showed that Achyranthis Bidentatae Radix and its adulterants are easily differentiated by monophyly. In conclusion, ITS2 regions accurately and effectively distinguished between Achyranthis Bidentatae Radix and its adulterants.},
}
@article {pmid27413214,
year = {2016},
author = {Khatua, S and Acharya, K},
title = {Influence of extraction parameters on physico-chemical characters and antioxidant activity of water soluble polysaccharides from Macrocybe gigantea (Massee) Pegler &amp; Lodge.},
journal = {Journal of food science and technology},
volume = {53},
number = {4},
pages = {1878-1888},
pmid = {27413214},
issn = {0022-1155},
abstract = {Polysaccharides from mushrooms are potentially active pharmaceutical ingredients and their action is dependent upon conformation, composition, size etc. In this context, three water soluble crude polysaccharide rich fractions viz. hot water extracted polysaccharide (HWP), cold alkaline extracted polysaccharide (CAP) and hot alkaline extracted polysaccharide (HAP) have been isolated using varying extraction parameters from Macrocybe gigantea, a well-known edible mushroom collected from Gangetic plain of West Bengal and authenticated by DNA barcoding of nrDNA ITS region. Physico-chemical investigation revealed that the fractions were mainly composed of β-configuration in pyranose form of sugars conjugated with small amount of protein. Further analysis presented that polysaccharides were composed of same monosaccharide even in similar order of ratio (D-glucose > D-galactose > D-mannose > D-xylose). However, D-glucose as well as β-glucan were found to be in the highest amount in CAP. The helical structure was determined by Congo red assay which indicated that polysaccharides were in aggregate forms except HWP which consisted of tertiary structure. These diverse structural features may have imparted effect on free radical scavenging activity of polysaccharides where HWP was the most active in all assays. HWP was proved to be a good scavenger of free radicals, strong chelator of ferrous ion and had high reducing power. Thus it can be inferred that HWP may foster further studies for searching active compound which might be used as ingredients of functional foods, nutraceuticals and pharmaceuticals. Moreover, to the best of our knowledge this is the first report on chemical composition and antioxidant activity of different crude polysaccharides from M. gigantea.},
}
@article {pmid27411567,
year = {2016},
author = {Vivien, R and Ferrari, BJ and Pawlowski, J},
title = {DNA barcoding of formalin-fixed aquatic oligochaetes for biomonitoring.},
journal = {BMC research notes},
volume = {9},
number = {},
pages = {342},
pmid = {27411567},
issn = {1756-0500},
mesh = {Animals ; DNA/*genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Ethanol/chemistry ; Fixatives/*chemistry ; Formaldehyde/*chemistry ; Gene Library ; Guanidine/chemistry ; High-Throughput Nucleotide Sequencing ; Liquid-Liquid Extraction/methods ; Oligochaeta/classification/*genetics ; *Phylogeny ; Polymerase Chain Reaction ; Tissue Fixation/methods ; },
abstract = {BACKGROUND: Oligochaetes are valuable bioindicators of the quality of watercourse and lake sediments. The morphological identification of aquatic oligochaetes is difficult, prompting the development of new molecular oligochaete indices based on DNA barcoding and Next-generation sequencing of sorted specimens. In general, the samples for DNA barcoding are fixed in absolute ethanol. However, in the case of aquatic oligochaetes, this medium is not appropriate as it can induce a modification of specimen abundances and of the composition of communities. Therefore, we investigated the possibility to amplify and sequence aquatic oligochaetes fixed in formalin for a short time. We performed guanidine extraction and polymerase chain reaction (PCR) amplification/sequencing of the cytochrome c oxydase I (COI) gene on tissue fragments fixed in formalin for different periods of time (from 1 h to 1 week) and in ethanol.<br><br>RESULTS: The large majority of aquatic oligochaete specimens fixed in formalin for up to 1&#xa0;week could be successfully amplified and all obtained sequences were of high quality. The amplification and sequencing success rate of formalin-fixed samples and ethanol-fixed samples was similar. These results suggest that formalin fixation of aquatic oligochaete tissues for a short time does not cause serious damages to DNA and inhibit PCR amplification.<br><br>CONCLUSION: The possibility to fix aquatic oligochaetes with formalin before genetic analyses is very promising for diversity monitoring, for construction of a comprehensive DNA barcode library and for development of an index based on Next-generation sequencing analysis of samples composed of sorted specimens.},
}
@article {pmid27408618,
year = {2016},
author = {Clark, LV and Sacks, EJ},
title = {TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data.},
journal = {Source code for biology and medicine},
volume = {11},
number = {},
pages = {11},
pmid = {27408618},
issn = {1751-0473},
abstract = {BACKGROUND: In genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), read depth is important for assessing the quality of genotype calls and estimating allele dosage in polyploids. However, existing pipelines for GBS and RAD-seq do not provide read counts in formats that are both accurate and easy to access. Additionally, although existing pipelines allow previously-mined SNPs to be genotyped on new samples, they do not allow the user to manually specify a subset of loci to examine. Pipelines that do not use a reference genome assign arbitrary names to SNPs, making meta-analysis across projects difficult.<br><br>RESULTS: We created the software TagDigger, which includes three programs for analyzing GBS and RAD-seq data. The first script, tagdigger_interactive.py, rapidly extracts read counts and genotypes from FASTQ files using user-supplied sets of barcodes and tags. Input and output is in CSV format so that it can be opened by spreadsheet software. Tag sequences can also be imported from the Stacks, TASSEL-GBSv2, TASSEL-UNEAK, or pyRAD pipelines, and a separate file can be imported listing the names of markers to retain. A second script, tag_manager.py, consolidates marker names and sequences across multiple projects. A third script, barcode_splitter.py, assists with preparing FASTQ data for deposit in a public archive by splitting FASTQ files by barcode and generating MD5 checksums for the resulting files.<br><br>CONCLUSIONS: TagDigger is open-source and freely available software written in Python 3. It uses a scalable, rapid search algorithm that can process over 100 million FASTQ reads per hour. TagDigger will run on a laptop with any operating system, does not consume hard drive space with intermediate files, and does not require programming skill to use.},
}
@article {pmid27408604,
year = {2016},
author = {Verovnik, R and Wiemers, M},
title = {Species delimitation in the Grayling genus Pseudochazara (Lepidoptera, Nymphalidae, Satyrinae) supported by DNA barcodes.},
journal = {ZooKeys},
volume = {},
number = {600},
pages = {131-154},
pmid = {27408604},
issn = {1313-2989},
abstract = {The Palaearctic Grayling genus Pseudochazara encompasses a number of petrophilous butterfly species, most of which are local endemics especially in their centre of radiation in SW Asia and the Balkans. Due to a lack of consistent morphological characters, coupled with habitat induced variability, their taxonomy is poorly understood and species delimitation is hampered. We employed a DNA barcoding approach to address the question of separate species status for several European taxa and provide first insight into the phylogeny of the genus. Unexpectedly we found conflicting patterns with deep divergences between presumably conspecific taxa and lack of divergence among well-defined species. We propose separate species status for Pseudochazara tisiphone, Pseudochazara amalthea, Pseudochazara amymone, and Pseudochazara kermana all of which have separate well supported clades, with the majority of them becoming local endemics. Lack of resolution in the 'Mamurra' species group with well-defined species (in terms of wing pattern and coloration) such as Pseudochazara geyeri, Pseudochazara daghestana and Pseudochazara alpina should be further explored using nuclear molecular markers with higher genetic resolution.},
}
@article {pmid27408584,
year = {2016},
author = {Magoga, G and Sassi, D and Daccordi, M and Leonardi, C and Mirzaei, M and Regalin, R and Lozzia, G and Montagna, M},
title = {Barcoding Chrysomelidae: a resource for taxonomy and biodiversity conservation in the Mediterranean Region.},
journal = {ZooKeys},
volume = {},
number = {597},
pages = {27-38},
pmid = {27408584},
issn = {1313-2989},
abstract = {The Mediterranean Region is one of the world's biodiversity hot-spots, which is also characterized by high level of endemism. Approximately 2100 species of leaf beetle (Coleoptera; Chrysomelidae) are known from this area, a number that increases year after year and represents 5/6% of the known species. These features, associated with the urgent need to develop a DNA-based species identification approach for a broad spectrum of leaf beetle species, prompted us to develop a database of nucleotide sequences, with a solid taxonomic background, for all the Chrysomelidae Latreille, 1802 sensu latu inhabiting the Mediterranean region. The Mediterranean Chrysomelidae Barcoding project, which has started in 2009, involves more than fifty entomologists and molecular biologists from different European countries. Numerous collecting campaigns have been organized during the first seven years of the project, which led to the collection of more than 5000 leaf beetle specimens. In addition, during these collecting campaigns two new allochthonous species for Europe, namely Ophraella communa LeSage, 1986 and Colasposoma dauricum Mannerheim, 1849, were intercepted and some species new to science were discovered (e.g., Pachybrachis sassii Montagna, 2011 and Pachybrachis holerorum Montagna et al., 2013). DNA was extracted from 1006 specimens (~13% of the species inhabiting the Mediterranean region) and a total of 910 cox1 gene sequences were obtained (PCR amplification efficiency of 93.8%). Here we report the list of the barcoded subfamilies, genera and the number of species for which cox1 gene sequences were obtained; the metadata associated with each specimen and a list of problematic species for which marker amplification failed. In addition, the nucleotide divergence within and between species and genera was estimated and values of intraspecific nucleotide divergence greater than the average have been discussed. Cryptocephalus quadripunctatus G. A. Olivier, 1808, Cryptocephalus rugicollis G. A. Olivier, 1791 and Exosoma lusitanicum Linnaeus, 1767) are representatives of these cases.},
}
@article {pmid27408581,
year = {2016},
author = {Tornabene, L and Robertson, DR and Baldwin, CC},
title = {Varicus lacerta, a new species of goby (Teleostei, Gobiidae, Gobiosomatini, Nes subgroup) from a mesophotic reef in the southern Caribbean.},
journal = {ZooKeys},
volume = {},
number = {596},
pages = {143-156},
pmid = {27408581},
issn = {1313-2989},
abstract = {We describe a new species of goby, Varicus lacerta sp. n., which was collected from a mesophotic reef at Curacao, southern Caribbean. The new species is the tenth species of Varicus, all of which occur below traditional SCUBA depths in the wider Caribbean area. Its placement in the genus Varicus is supported by a molecular phylogenetic analysis of three nuclear genes and the mitochondrial gene cytochrome b. In addition, the new species has one anal-fin pterygiophore inserted anterior to the first haemal spine, which distinguishes Varicus species from most species in the closely related and morphologically similar genus Psilotris. Varicus lacerta sp. n. is distinguished from all other named species of Varicus by the absence of scales, having highly branched, feather-like pelvic-fin rays, and in its live coloration. We provide the cytochrome c oxidase I DNA barcode of the holotype and compare color patterns of all species of Varicus and Psilotris for which color photographs or illustrations are available. This study is one of several recent studies demonstrating the utility of manned submersibles in exploring the diversity of poorly studied but species-rich deep-reef habitats.},
}
@article {pmid27408576,
year = {2016},
author = {Guo, HF and Guan, B and Shi, FM and Zhou, ZJ},
title = {DNA Barcoding of genus Hexacentrus in China reveals cryptic diversity within Hexacentrus japonicus (Orthoptera, Tettigoniidae).},
journal = {ZooKeys},
volume = {},
number = {596},
pages = {53-63},
pmid = {27408576},
issn = {1313-2989},
abstract = {DNA barcoding has been proved successful to provide resolution beyond the boundaries of morphological information. Hence, a study was undertaken to establish DNA barcodes for all morphologically determined Hexacentrus species in China collections. In total, 83 specimens of five Hexacentrus species were barcoded using standard mitochondrial cytochrome c oxidase subunit I (COI) gene. Except for Hexacentrus japonicus, barcode gaps were present in the remaining Hexacentrus species. Taxon ID tree generated seven BOLD's barcode index numbers (BINs), four of which were in agreement with the morphological species. For Hexacentrus japonicus, the maximum intraspecific divergence (4.43%) produced a minimal overlap (0.64%), and 19 specimens were divided into three different BINs. There may be cryptic species within the current Hexacentrus japonicus. This study adds to a growing body of DNA barcodes that have become available for katydids, and shows that a DNA barcoding approach enables the identification of known Hexacentrus species with a very high resolution.},
}
@article {pmid27408547,
year = {2016},
author = {Raupach, MJ and Hannig, K and Morinière, J and Hendrich, L},
title = {A DNA barcode library for ground beetles (Insecta, Coleoptera, Carabidae) of Germany: The genus Bembidion Latreille, 1802 and allied taxa.},
journal = {ZooKeys},
volume = {},
number = {592},
pages = {121-141},
pmid = {27408547},
issn = {1313-2989},
abstract = {As molecular identification method, DNA barcoding based on partial cytochrome c oxidase subunit 1 (COI) sequences has been proven to be a useful tool for species determination in many insect taxa including ground beetles. In this study we tested the effectiveness of DNA barcodes to discriminate species of the ground beetle genus Bembidion and some closely related taxa of Germany. DNA barcodes were obtained from 819 individuals and 78 species, including sequences from previous studies as well as more than 300 new generated DNA barcodes. We found a 1:1 correspondence between BIN and traditionally recognized species for 69 species (89%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for three species pairs, including two species pairs with haplotype sharing (Bembidion atrocaeruleum/Bembidion varicolor and Bembidion guttula/Bembidion mannerheimii). In contrast to this, deep intraspecific sequence divergences with distinct lineages were revealed for two species (Bembidion geniculatum/Ocys harpaloides). Our study emphasizes the use of DNA barcodes for the identification of the analyzed ground beetles species and represents an important step in building-up a comprehensive barcode library for the Carabidae in Germany and Central Europe as well.},
}
@article {pmid27408541,
year = {2016},
author = {Monckton, SK},
title = {A revision of Chilicola (Heteroediscelis), a subgenus of xeromelissine bees (Hymenoptera, Colletidae) endemic to Chile: taxonomy, phylogeny, and biogeography, with descriptions of eight new species.},
journal = {ZooKeys},
volume = {},
number = {591},
pages = {1-144},
pmid = {27408541},
issn = {1313-2989},
abstract = {The bee subgenus Chilicola (Heteroediscelis) Toro &amp; Moldenke, 1979 (Hymenoptera, Colletidae, Xeromelissinae) is revised. The subgenus is considered endemic to Chile and occurs across a broad range of habitats. Eight new species are described: Chilicola (Heteroediscelis) charizard Monckton, sp. n., Chilicola (Heteroediscelis) curvapeligrosa Monckton, sp. n., Chilicola (Heteroediscelis) guanicoe Monckton, sp. n., Chilicola (Heteroediscelis) katherinae Monckton, sp. n., Chilicola (Heteroediscelis) lickana Monckton, sp. n., Chilicola (Heteroediscelis) mayu Monckton, sp. n., Chilicola (Heteroediscelis) packeri Monckton, sp. n., and Chilicola (Heteroediscelis) randolphi Monckton, sp. n. One of the existing species, Chilicola (Heteroediscelis) valparaiso Toro &amp; Moldenke, 1979, syn. n., is treated as a junior synonym of Chilicola (Heteroediscelis) mantagua Toro &amp; Moldenke, 1979, and the nine remaining valid species are redescribed. Thoroughly illustrated keys to species for males and females are provided, along with habitus images, images of male terminalia, distribution maps for each species, and a map of relevant Chilean biogeographic regions. Results of phylogenetic analyses are presented, based upon 74 morphological characters and on CO1 barcode sequences, analyzed both separately and as a combined dataset. Monophyly of the subgenus is supported, and groupings within the subgenus are discussed in light of a biogeographic analysis of their species distributions (spatial analysis of vicariance), whereby divergence between taxa is found to occur primarily via north-south disjunctions.},
}
@article {pmid27406498,
year = {2016},
author = {Moore, A},
title = {The benefits of keeping track.},
journal = {Nursing standard (Royal College of Nursing (Great Britain) : 1987)},
volume = {30},
number = {46},
pages = {25-26},
doi = {10.7748/ns.30.46.25.s25},
pmid = {27406498},
issn = {2047-9018},
mesh = {*Electronic Data Processing ; *Nursing ; State Medicine ; *Time Management ; United Kingdom ; },
abstract = {Barcodes are familiar to everyone from their supermarket shop, but the potential they offer for improving health care in the NHS is only just being explored.},
}
@article {pmid27404885,
year = {2016},
author = {Duarte, JH},
title = {Tracing cell lineages with mutable barcodes.},
journal = {Nature biotechnology},
volume = {34},
number = {7},
pages = {725},
pmid = {27404885},
issn = {1546-1696},
mesh = {*Cell Lineage ; *DNA Barcoding, Taxonomic ; Humans ; Phylogeny ; },
}
@article {pmid27404207,
year = {2016},
author = {Perié, L and Duffy, KR},
title = {Retracing the in vivo haematopoietic tree using single-cell methods.},
journal = {FEBS letters},
volume = {590},
number = {22},
pages = {4068-4083},
doi = {10.1002/1873-3468.12299},
pmid = {27404207},
issn = {1873-3468},
mesh = {Cell Differentiation/*genetics ; Cell Lineage/*genetics ; Cell Proliferation/genetics ; Erythroid Precursor Cells/cytology/metabolism ; Hematopoietic Stem Cells/*cytology/metabolism ; Humans ; Lymphocytes/cytology/metabolism ; Myeloid Cells/cytology/metabolism ; *Single-Cell Analysis ; },
abstract = {The dynamic process by which self-renewing stem cells and their offspring proliferate and differentiate to create the erythroid, myeloid and lymphoid lineages of the blood system has long since been an important topic of study. A range of recent single cell and family tracing methodologies such as massively parallel single-cell RNA-sequencing, mass cytometry, integration site barcoding, cellular barcoding and transposon barcoding are enabling unprecedented analysis, dissection and re-evaluation of the haematopoietic tree. In addition to the substantial experimental advances, these new techniques have required significant theoretical development in order to make biological deductions from their data. Here, we review these approaches from both an experimental and inferential point of view, considering their discoveries to date, their capabilities, limitations and opportunities for further development.},
}
@article {pmid27402888,
year = {2016},
author = {Ajamma, YU and Villinger, J and Omondi, D and Salifu, D and Onchuru, TO and Njoroge, L and Muigai, AW and Masiga, DK},
title = {Composition and Genetic Diversity of Mosquitoes (Diptera: Culicidae) on Islands and Mainland Shores of Kenya's Lakes Victoria and Baringo.},
journal = {Journal of medical entomology},
volume = {53},
number = {6},
pages = {1348-1363},
pmid = {27402888},
issn = {1938-2928},
support = {//Wellcome Trust/United Kingdom ; 087540//Wellcome Trust/United Kingdom ; },
mesh = {*Animal Distribution ; Animals ; Biota ; Culicidae/anatomy &amp; histology/genetics/growth &amp; development/*physiology ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Female ; *Genetic Variation ; Insect Proteins/genetics ; Islands ; Kenya ; Lakes ; Larva/anatomy &amp; histology/genetics/growth &amp; development/physiology ; Male ; Mosquito Vectors/anatomy &amp; histology/genetics/growth &amp; development/*physiology ; Ovum/growth &amp; development/physiology ; Phylogeny ; Population Density ; Pupa/anatomy &amp; histology/genetics/growth &amp; development/physiology ; Sequence Analysis, DNA ; },
abstract = {The Lake Baringo and Lake Victoria regions of Kenya are associated with high seroprevalence of mosquito-transmitted arboviruses. However, molecular identification of potential mosquito vector species, including morphologically identified ones, remains scarce. To estimate the diversity, abundance, and distribution of mosquito vectors on the mainland shores and adjacent inhabited islands in these regions, we collected and morphologically identified adult and immature mosquitoes and obtained the corresponding sequence variation at cytochrome c oxidase 1 (COI) and internal transcribed spacer region 2 (ITS2) gene regions. A total of 63 species (including five subspecies) were collected from both study areas, 47 of which have previously been implicated as disease vectors. Fourteen species were found only on island sites, which are rarely included in mosquito diversity surveys. We collected more mosquitoes, yet with lower species composition, at Lake Baringo (40,229 mosquitoes, 32 species) than at Lake Victoria (22,393 mosquitoes, 54 species). Phylogenetic analysis of COI gene sequences revealed Culex perexiguus and Cx tenagius that could not be distinguished morphologically. Most Culex species clustered into a heterogeneous clade with closely related sequences, while Culex pipiens clustered into two distinct COI and ITS2 clades. These data suggest limitations in current morphological identification keys. This is the first DNA barcode report of Kenyan mosquitoes. To improve mosquito species identification, morphological identifications should be supported by their molecular data, while diversity surveys should target both adults and immatures. The diversity of native mosquito disease vectors identified in this study impacts disease transmission risks to humans and livestock.},
}
@article {pmid27402509,
year = {2016},
author = {Dulla, EL and Kathera, C and Gurijala, HK and Mallakuntla, TR and Srinivasan, P and Prasad, V and Mopati, RD and Jasti, PK},
title = {Highlights of DNA Barcoding in identification of salient microorganisms like fungi.},
journal = {Journal de mycologie medicale},
volume = {26},
number = {4},
pages = {291-297},
doi = {10.1016/j.mycmed.2016.05.006},
pmid = {27402509},
issn = {1773-0449},
mesh = {Biodiversity ; *DNA Barcoding, Taxonomic ; Fungi/*classification/*genetics/isolation &amp; purification ; Genome, Fungal ; Humans ; Mycological Typing Techniques/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Fungi, the second largest kingdom of eukaryotic life, are diverse and widespread. Fungi play a distinctive role in the production of different products on industrial scale, like fungal enzymes, antibiotics, fermented foods, etc., to give storage stability and improved health to meet major global challenges. To utilize algae perfectly for human needs, and to pave the way for getting a healthy relationship with fungi, it is important to identify them in a quick and robust manner with molecular-based identification system. So, there is a technique that aims to provide a well-organized method for species level identifications and to contribute powerfully to taxonomic and biodiversity research is DNA Barcoding. DNA Barcoding is generally achieved by the retrieval of a short DNA sequence - the 'barcode' - from a standard part of the genome and that barcode is then compared with a library of reference barcode sequences derived from individuals of known identity for identification.},
}
@article {pmid27402361,
year = {2016},
author = {Sack, LM and Davoli, T and Xu, Q and Li, MZ and Elledge, SJ},
title = {Sources of Error in Mammalian Genetic Screens.},
journal = {G3 (Bethesda, Md.)},
volume = {6},
number = {9},
pages = {2781-2790},
pmid = {27402361},
issn = {2160-1836},
mesh = {Animals ; Cell Culture Techniques/standards ; DNA Barcoding, Taxonomic/*standards ; Genetic Testing/*standards ; Genetic Vectors ; Genome ; Mammals/*genetics ; Plasmids/genetics ; Polymerase Chain Reaction/standards ; RNA, Small Interfering/genetics ; },
abstract = {Genetic screens are invaluable tools for dissection of biological phenomena. Optimization of such screens to enhance discovery of candidate genes and minimize false positives is thus a critical aim. Here, we report several sources of error common to pooled genetic screening techniques used in mammalian cell culture systems, and demonstrate methods to eliminate these errors. We find that reverse transcriptase-mediated recombination during retroviral replication can lead to uncoupling of molecular tags, such as DNA barcodes (BCs), from their associated library elements, leading to chimeric proviral genomes in which BCs are paired to incorrect ORFs, shRNAs, etc This effect depends on the length of homologous sequence between unique elements, and can be minimized with careful vector design. Furthermore, we report that residual plasmid DNA from viral packaging procedures can contaminate transduced cells. These plasmids serve as additional copies of the PCR template during library amplification, resulting in substantial inaccuracies in measurement of initial reference populations for screen normalization. The overabundance of template in some samples causes an imbalance between PCR cycles of contaminated and uncontaminated samples, which results in a systematic artifactual depletion of GC-rich library elements. Elimination of contaminating plasmid DNA using the bacterial endonuclease Benzonase can restore faithful measurements of template abundance and minimize GC bias.},
}
@article {pmid27401671,
year = {2016},
author = {Rozenberg, A and Leese, F and Weiss, LC and Tollrian, R},
title = {Digital gene expression analysis with sample multiplexing and PCR duplicate detection: A straightforward protocol.},
journal = {BioTechniques},
volume = {61},
number = {1},
pages = {26-32},
doi = {10.2144/000114434},
pmid = {27401671},
issn = {1940-9818},
mesh = {Animals ; Daphnia/genetics ; Female ; Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Polymerase Chain Reaction/*methods ; Polymorphism, Single Nucleotide/genetics ; RNA/analysis/genetics ; Reproducibility of Results ; *Software ; },
abstract = {Tag-Seq is a high-throughput approach used for discovering SNPs and characterizing gene expression. In comparison to RNA-Seq, Tag-Seq eases data processing and allows detection of rare mRNA species using only one tag per transcript molecule. However, reduced library complexity raises the issue of PCR duplicates, which distort gene expression levels. Here we present a novel Tag-Seq protocol that uses the least biased methods for RNA library preparation combined with a novel approach for joint PCR template and sample labeling. In our protocol, input RNA is fragmented by hydrolysis, and poly(A)-bearing RNAs are selected and directly ligated to mixed DNA-RNA P5 adapters. The P5 adapters contain i5 barcodes composed of sample-specific (moderately) degenerate base regions (mDBRs), which later allow detection of PCR duplicates. The P7 adapter is attached via reverse transcription with individual i7 barcodes added during the amplification step. The resulting libraries can be sequenced on an Illumina sequencer. After sample demultiplexing and PCR duplicate removal with a free software tool we designed, the data are ready for downstream analysis. Our protocol was tested on RNA samples from predator-induced and control Daphnia microcrustaceans.},
}
@article {pmid27400629,
year = {2016},
author = {Trunz, V and Packer, L and Vieu, J and Arrigo, N and Praz, CJ},
title = {Comprehensive phylogeny, biogeography and new classification of the diverse bee tribe Megachilini: Can we use DNA barcodes in phylogenies of large genera?.},
journal = {Molecular phylogenetics and evolution},
volume = {103},
number = {},
pages = {245-259},
doi = {10.1016/j.ympev.2016.07.004},
pmid = {27400629},
issn = {1095-9513},
mesh = {Animals ; Bees/*classification/genetics ; Biological Evolution ; Cytochromes c/classification/genetics/metabolism ; DNA/chemistry/isolation &amp; purification/metabolism ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/classification/genetics/metabolism ; Likelihood Functions ; Phylogeny ; Phylogeography ; Protein Serine-Threonine Kinases/classification/genetics/metabolism ; RNA, Ribosomal, 28S/classification/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Classification and evolutionary studies of particularly speciose clades pose important challenges, as phylogenetic analyses typically sample a small proportion of the existing diversity. We examine here one of the largest bee genera, the genus Megachile - the dauber and leafcutting bees. Besides presenting a phylogeny based on five nuclear genes (5480 aligned nucleotide positions), we attempt to use the phylogenetic signal of mitochondrial DNA barcodes, which are rapidly accumulating and already include a substantial proportion of the known species diversity in the genus. We used barcodes in two ways: first, to identify particularly divergent lineages and thus to guide taxon sampling in our nuclear phylogeny; second, to augment taxon sampling by combining nuclear markers (as backbone for ancient divergences) with DNA barcodes. Our results indicate that DNA barcodes bear phylogenetic signal limited to very recent divergences (3-4 my before present). Sampling within clades of very closely related species may be augmented using this technique, but our results also suggest statistically supported, but incongruent placements of some taxa. However, the addition of one single nuclear gene (LW-rhodopsin) to the DNA barcode data was enough to recover meaningful placement with high clade support values for nodes up to 15 million years old. We discuss different proposals for the generic classification of the tribe Megachilini. Finding a classification that is both in agreement with our phylogenetic hypotheses and practical in terms of diagnosability is particularly challenging as our analyses recover several well-supported clades that include morphologically heterogeneous lineages. We favour a classification that recognizes seven morphologically well-delimited genera in Megachilini: Coelioxys, Gronoceras, Heriadopsis, Matangapis, Megachile, Noteriades and Radoszkowskiana. Our results also lead to the following classification changes: the groups known as Dinavis, Neglectella, Eurymella and Phaenosarus are reestablished as valid subgenera of the genus Megachile, while the subgenus Alocanthedon is placed in synonymy with M. (Callomegachile), the subgenera Parachalicodoma and Largella with M. (Pseudomegachile), Anodonteutricharaea with M. (Paracella), Platysta with M. (Eurymella), and Grosapis and Eumegachile with M. (Megachile) (new synonymies). In addition, we use maximum likelihood reconstructions of ancestral geographic ranges to infer the origin of the tribe and reconstruct the main dispersal routes explaining the current, cosmopolitan distribution of this genus.},
}
@article {pmid27396012,
year = {2016},
author = {Avelino-Capistrano, F and Barbosa, LS and Takiya, DM},
title = {Description of a new Kempnyia Klapálek from Brazil (Plecoptera: Perlidae) with life stages associated using DNA barcodes.},
journal = {Zootaxa},
volume = {4079},
number = {3},
pages = {372-380},
doi = {10.11646/zootaxa.4079.3.5},
pmid = {27396012},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Brazil ; DNA Barcoding, Taxonomic ; Female ; Insecta/anatomy &amp; histology/*classification/genetics/*growth &amp; development ; Life Cycle Stages ; Male ; Nymph/anatomy &amp; histology/classification/genetics/growth &amp; development ; Organ Size ; Phylogeny ; },
abstract = {Kempnyia couriae sp. nov. is described from specimens (male, female, and nymphs) collected in Rio de Janeiro State, southeastern Brazil. This species is distinguished from its congeners by the male penial armature, having an elongate gonopore, surpassing the hooks, hooks with penial apex forming a globular membranous structure, and by ventrally curved hooks. Females and a nymph were associated with males using DNA barcoding.},
}
@article {pmid27395923,
year = {2016},
author = {Nadolny, AA and Omelko, MM and Marusik, YM and Blagoev, G},
title = {A new species of spider belonging to the Pardosa lugubris-group (Araneae: Lycosidae) from Far East Asia.},
journal = {Zootaxa},
volume = {4072},
number = {2},
pages = {263-281},
doi = {10.11646/zootaxa.4072.2.8},
pmid = {27395923},
issn = {1175-5334},
mesh = {Animals ; Asia, Eastern ; Female ; Male ; Spiders/*anatomy &amp; histology/*classification ; },
abstract = {A new species, Pardosa koponeni sp. n., is described. The new species is widely distributed in Far East Asia. It was previously confused with P. lugubris (Walckenaer, 1802). The two species have very similar copulatory organs but differ in the colouration of legs II-IV in males and the carapace/femur I ratio in both sexes. The distribution of the new species is mapped using material examined and literature data. To provide a more complete understanding of the boundaries between such closely related species, morphological and DNA barcoding approaches for species discrimination were integrated. Two species of the Pardosa lugubris-group (P. lugubris and P. alacris) were found to share haplotypes, suggesting evidence of hybridization or incomplete lineage sorting, or they are perhaps separate morphotypes of the same species. This is another example of complexity and the value of comparing morphology and DNA barcode data among spiders.},
}
@article {pmid27395920,
year = {2016},
author = {Pérez-Bañón, C and Radenković, S and Vujić, A and Petanidou, T},
title = {Brachyopa minima (Diptera: Syrphidae), a new species from Greece with notes on the biodiversity and conservation of the genus Brachyopa Meigen in the Northern Aegean Islands.},
journal = {Zootaxa},
volume = {4072},
number = {2},
pages = {217-234},
doi = {10.11646/zootaxa.4072.2.5},
pmid = {27395920},
issn = {1175-5334},
mesh = {Animals ; Diptera/*anatomy &amp; histology/*classification ; Female ; Greece ; Islands ; Larva/anatomy &amp; histology ; Male ; },
abstract = {An on-going study of the hoverfly fauna of the Northern Aegean Islands (Greece) has revealed the presence of four species of the genus Brachyopa Meigen. During the survey the following species were found: B. bicolor (Fallén), B. quadrimaculosa Thompson in Kaplan &amp; Thompson, B. minima Vujić &amp; Pérez-Bañón sp. nov. and an unidentified species very close to B. pilosa (Collin). Morphological characters and mitochondrial COI barcodes were used to link different life stages of B. minima, and to identify a larval specimen of B. bicolor. In this study adult and larval morphology and habitat preferences for B. minima are described. The description of larval morphology of B. bicolor and Brachyopa sp. aff. pilosa is amended too. An identification key to the adults of the B. quadrimaculosa group sensu Kassebeer (2002) in the Eastern Mediterranean (Greece, Israel and Turkey) is provided. The importance of specific microhabitats for the continued existence of these taxa is discussed.},
}
@article {pmid27395917,
year = {2016},
author = {Attaran-Farimani, G and Estekani, S and Springer, VG and Crimmen, O and Johnson, GD and Baldwin, CC},
title = {Validation of the synonymy of the teleost blenniid fish species Salarias phantasticus Boulenger 1897 and Salarias anomalus Regan 1905 with Ecsenius pulcher (Murray 1887) based on DNA barcoding and morphology.},
journal = {Zootaxa},
volume = {4072},
number = {2},
pages = {171-184},
doi = {10.11646/zootaxa.4072.2.2},
pmid = {27395917},
issn = {1175-5334},
mesh = {Animals ; Female ; Fishes/*anatomy &amp; histology/*classification ; Iran ; Male ; },
abstract = {As currently recognized, Ecsenius pulcher includes Salarias pulcher (type material has a banded color pattern), S. anomalus (non-banded), and S. phantasticus (banded). The color patterns are not sex linked, and no other morphological features apparently distinguish the three nominal species. The recent collection of banded and non-banded specimens of Ecsenius pulcher from Iran has provided the first tissue samples for genetic analyses. Here we review the taxonomic history of E. pulcher and its included synonyms and genetically analyze tissue samples of both color patterns. Salarias anomalus is retained as a synonym of E. pulcher because DNA barcode data suggest that they represent banded and non-banded color morphs of a single species. Furthermore, the large size of the largest type specimen of S. anomalus (herein designated as the lectotype) suggests that it belongs to E. pulcher. A single non-banded specimen from Iran is genetically distinct from E. pulcher and appears to represent an undescribed species. Salarias phantasticus is retained as a synonym of E. pulcher because the primary morphological difference between the two nominal species-presence of spots on the dorsal fin in E. pulcher and absence of those spots in S. phantasticus-is not a valid taxonomic character; rather, the spots represent galls that contain the larval stages of a parasitic crustacean. As males and females of Ecsenius species have been confused in the literature, we describe and illustrate the genital regions of both and comment on possible new blenniid synapomorphies that our investigation revealed.},
}
@article {pmid27395909,
year = {2016},
author = {Pramual, P and Simwisat, K and Martin, J},
title = {Identification and reassessment of the specific status of some tropical freshwater midges (Diptera: Chironomidae) using DNA barcode data.},
journal = {Zootaxa},
volume = {4072},
number = {1},
pages = {39-60},
doi = {10.11646/zootaxa.4072.1.2},
pmid = {27395909},
issn = {1175-5334},
mesh = {Animals ; Chironomidae/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Larva ; Male ; Thailand ; },
abstract = {Chironomidae are a highly diverse group of insects. Members of this family are often included in programs monitoring the health of freshwater ecosystems. However, a difficulty in morphological identification, particularly of larval stages is the major obstacle to this application. In this study, we tested the efficiency of mitochondrial cytochrome c oxidase I (COI) sequences as the DNA barcoding region for species identification of Chironomidae in Thailand. The results revealed 14 species with a high success rate (>90%) for the correct species identification, which suggests the potential usefulness of the technique. However, some morphological species possess high (>3%) intraspecific genetic divergence that suggests these species could be species complexes and need further morphological or cytological examination. Sequence-based species delimitation analyses indicated that most specimens identified as Chironomus kiiensis, Tokunaga 1936, in Japan are conspecific with C. striatipennis, Kieffer 1912, although a small number form a separate cluster. A review of the descriptions of Kiefferulus tainanus (Kieffer 1912) and its junior synonym, K. biroi (Kieffer 1918), following our results, suggests that this synonymy is probably not correct and that K. tainanus occurs in Japan, China and Singapore, while K. biroi occurs in India and Thailand. Our results therefore revealed the usefulness of DNA barcoding for correct species identification of Chironomidae, particularly the immature stages. In addition, DNA barcodes could also uncover hidden diversity that can guide further taxonomic study, and offer a more efficient way to identify species than morphological analysis where large numbers of specimens are involved, provided the identifications of DNA barcodes in the databases are correct. Our studies indicate that this is not the case, and we identify cases of misidentifications for C. flaviplumus, Tokunaga 1940 and K. tainanus.},
}
@article {pmid27395843,
year = {2016},
author = {Bartilotti, C and Salabert, J and Santos, AD},
title = {Complete larval development of Thor amboinensis (De Man, 1888) Decapoda: Thoridae) described from laboratory-reared material &lt;br /&gt;and identified by DNA barcoding.},
journal = {Zootaxa},
volume = {4066},
number = {4},
pages = {399-420},
doi = {10.11646/zootaxa.4066.4.3},
pmid = {27395843},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Decapoda/anatomy &amp; histology/classification/*genetics/growth &amp; development ; Ecosystem ; Female ; Laboratories ; Larva/anatomy &amp; histology/classification/genetics/*growth &amp; development ; Male ; Organ Size ; Phylogeny ; },
abstract = {Of the 12 species of Thor described until present date, only three (25%) have their complete larval development known. Present work describes the complete larval development of Thor amboinensis, based on laboratory-reared material. The spent females were identified through the analysis of the partial sequences of the mitochondrial DNA barcode, also used for the reconstruction of the phylogenetic relationships within the recently resurrected and recognized family Thoridae Kingsley, 1879. Eight zoeal stages and one decapodid complete this species larval development. In the genus Thor, the number of zoeal stages varies greatly from two (T. dobkini) to eight (T. amboinensis and T. floridanus). The larvae of T. ambionensis and T. floridanus are readily distinguished from each other by the ornamentation of the ventral margin of the carapace and the pereiopods development. The first zoeal stage of T. amboinensis described by Yang &amp; Okuno (2004) and the one described in present study are very similar. A brief discussion on the morphological characters and on the number of zoeal stages of the genus, as well as of the previous larval descriptions is made. The phylogenetic analysis suggest cryptic speciation for geographical separated populations of T. amboinensis, paraphyly of the genus Eualus, and the reassignment of E. cranchii to a different genus.},
}
@article {pmid27395728,
year = {2016},
author = {Ekins, M and Erpenbeck, D and Wörheide, G and Hooper, JN},
title = {A new species of lithistid sponge hiding within the Isabella mirabilis species complex (Porifera: Demospongiae: Tetractinellida) from seamounts of the Norfolk Ridge.},
journal = {Zootaxa},
volume = {4136},
number = {3},
pages = {433-460},
doi = {10.11646/zootaxa.4136.3.2},
pmid = {27395728},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Ecosystem ; Organ Size ; Pacific Ocean ; Phylogeny ; Porifera/anatomy &amp; histology/*classification/genetics/growth &amp; development ; },
abstract = {A population level study of the lithistid ('rock') sponge, Isabella mirabilis, revealed a new species, Isabella tanoa sp. nov., living on five seamounts on the Norfolk Ridge, SW Pacific, and representing the third species to be discovered since the genus was first described in 2005. Comparisons between the three species showed significant differences in morphological characters that corresponded to differences in their respective CO1 barcoding sequences. Conversely, three of the four genotypes of Isabella mirabilis remain unresolved using morphological markers.},
}
@article {pmid27395720,
year = {2016},
author = {Li, Z and Tian, L and Cuccodoro, G and Chen, L and Lu, C},
title = {Taxonomic note of Oberea fuscipennis (Chevrolat, 1852) based on morphological and DNA barcode data (Coleoptera, Cerambycidae, Lamiinae).},
journal = {Zootaxa},
volume = {4136},
number = {2},
pages = {360-372},
doi = {10.11646/zootaxa.4136.2.6},
pmid = {27395720},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Coleoptera/*anatomy &amp; histology/*classification/genetics/growth &amp; development ; DNA Barcoding, Taxonomic ; Female ; Male ; Organ Size ; Phylogeny ; },
abstract = {Oberea fuscipennis (Chevrolat, 1852) species group is revised based on morphology and DNA barcode data. Oberea diversipes Pic, 1919 and O. infratestacea Pic, 1936 are restored from synonymy. The following two new synonymies are proposed: Oberea fuscipennis ssp. fairmairei Breuning, 1962 = Oberea diversipes Pic, 1919; and Oberea hanoiensis Pic, 1923 = O. fuscipennis (Chevrolat, 1852).},
}
@article {pmid27395596,
year = {2016},
author = {Mapalo, MA and Stec, D and Mirano-Bascos, D and Michalczyk, &#x141;},
title = {Mesobiotus philippinicus sp. nov., the first limnoterrestrial tardigrade from the Philippines.},
journal = {Zootaxa},
volume = {4126},
number = {3},
pages = {411-426},
doi = {10.11646/zootaxa.4126.3.6},
pmid = {27395596},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Base Sequence ; Body Size ; Bryophyta/parasitology ; Ecosystem ; Female ; Molecular Sequence Data ; Organ Size ; Philippines ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Tardigrada/anatomy &amp; histology/*classification/genetics/growth &amp; development ; },
abstract = {The limnoterrestrial tardigrade fauna of the Philippines is completely unknown. In this paper, we describe the first ever limnoterrestrial water bear species from this southeast Asian country, Mesobiotus philippinicus sp. nov., found in a moss sample collected in Quezon City. Apart from morphometrics and imaging in light microscopy, we also analysed the new species under scanning electron microscope and sequenced four DNA markers differing in mutation rates, three nuclear (18S rRNA, 28S rRNA, and ITS-2) and one mitochondrial (COI). This allowed not only a detailed description but also provided barcodes to aid future species identification. The new species belongs to the harmsworthi group and is most similar to M. diffusus (Binda &amp; Pilato, 1987), M. pseudocoronatus (Pilato et al., 2006), M. montanus (Murray, 1910) and M. mottai (Binda &amp; Pilato, 1994), but differs from these species by whorled egg processes and dimensions of some morphometric traits. The 28S rRNA, ITS-2 and COI sequences presented in this paper are the first published DNA sequences for the genus Mesobiotus.},
}
@article {pmid27395556,
year = {2016},
author = {Wijayathilaka, N and Garg, S and Senevirathne, G and Karunarathna, N and Biju, SD and Meegaskumbura, M},
title = {A new species of Microhyla (Anura: Microhylidae) from Sri Lanka: an integrative taxonomic approach.},
journal = {Zootaxa},
volume = {4066},
number = {3},
pages = {331-342},
doi = {10.11646/zootaxa.4066.3.9},
pmid = {27395556},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Anura/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Body Size ; Female ; India ; Male ; Organ Size ; RNA, Ribosomal, 16S/genetics ; Sri Lanka ; Vocalization, Animal ; },
abstract = {Species boundaries of Microhyla rubra of India and Sri Lanka were assessed using the following criteria: genetic barcoding, morphology, and vocalization. We use a ca. 500 bp fragment of the 16S rRNA mitochondrial gene and show that there is an uncorrected pairwise distance of 2.7-3.2% between the Indian and Sri Lankan populations of M. rubra. We show that they are different in several call characteristics such as, dominant frequency, call duration, call rise time and pulse rate. Morphologically, the Sri Lankan population can be distinguished from the typical M. rubra described from southern India, by a combination of characters: body size, skin texture, and feet dimensions. We recognize the population from Sri Lanka as a new species, Microhyla mihintalei sp. nov., a widely distributed lowland species with an elevational distribution of up to 500 m a.s.l.},
}
@article {pmid27395200,
year = {2016},
author = {Fu, Z and Toda, MJ and Li, NN and Zhang, YP and Gao, JJ},
title = {A new genus of anthophilous drosophilids, Impatiophila (Diptera, Drosophilidae): morphology, DNA barcoding and molecular phylogeny, with descriptions of thirty-nine new species.},
journal = {Zootaxa},
volume = {4120},
number = {1},
pages = {1-100},
doi = {10.11646/zootaxa.4120.1.1},
pmid = {27395200},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; China ; DNA Barcoding, Taxonomic ; Drosophilidae/*anatomy &amp; histology/*classification/genetics/growth &amp; development ; Ecosystem ; Female ; Larva/anatomy &amp; histology/classification/genetics/growth &amp; development ; Male ; Mitochondria/genetics ; Organ Size ; *Phylogeny ; },
abstract = {Breeding habits of essential dependence on flowers for larval food resources have evolved repeatedly in separate lineages of the Drosophilidae. However, flowers of Impatiens L. have never been recognized as hosts for drosophilid flies until recently: two Hirtodrosophila species, H. actinia (Okada) and H. yapingi Gao, were found feeding and breeding on Impatiens flowers. During our recent field surveys in central and southern China, a great number of drosophilid flies morphologically resembling the two species were collected, almost exclusively from flowers of Impatiens (family Balsaminaceae) and the family Gesneriaceae. In the present study, these specimens were identified on the basis of morphological characters and/or partial DNA sequences of the mitochondrial COI (cytochrome c oxidase subunit I gene, used as a barcoding marker). As a result, 39 new species were recognized. We then reconstructed the phylogenetic relationships among most of them, based on concatenated DNA sequences (3047 nucleotide sites) of two mitochondrial (COI and COII, i.e., cytochrome c oxidase subunits I and II, respectively) and three nuclear genes (ATPsyn-alpha, alphaTub84B and Hsc70cb, i.e., ATP synthase alpha, alpha-Tubulin at 84B and Hsc70Cb isoform H, respectively). In the resulting Bayesian and ML (maximum likelihood) trees, three well-supported clades were recognized, with a few species having remained uncertain for their phylogenetic positions. We also conducted a cladistic analysis with data of adult morphological characters to investigate the phylogenetic positions of a few species of which DNA sequence data were not available, and to investigate the classification of species groups with definition of their diagnoses. In consequence, we established a new genus, Impatiophila, for the species visiting flowers of Impatiens and Gesneriaceae, described all the new species, and revised the taxonomy of some known species.},
}
@article {pmid27395114,
year = {2016},
author = {Lis, JA and Lis, B and Ziaja, DJ},
title = {In BOLD we trust? A commentary on the reliability of specimen identification for DNA barcoding: a case study on burrower bugs (Hemiptera: Heteroptera: Cydnidae).},
journal = {Zootaxa},
volume = {4114},
number = {1},
pages = {83-86},
doi = {10.11646/zootaxa.4114.1.6},
pmid = {27395114},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; DNA/genetics ; DNA Barcoding, Taxonomic ; Heteroptera/*classification/*genetics ; },
abstract = {An assessment was performed regarding the accuracy of various types of data deposited in the Barcode of Life Data system (BOLD) related to the true bug family Cydnidae (Hemiptera: Heteroptera). Taxonomic nomenclature and classification, identification reliability, and the correctness of the data provided in the "Taxon description" were analyzed and commented on with respect to both available versions of the BOLD system, i.e. version 3 and beta version 4. Numerous mistakes in taxonomy, the relevance of the taxa names, and species misidentifications in BOLD version 3 were found and, more importantly, similar errors were detected in BOLD version 4 as well. We suggest that if the BOLD system is presumed to be taxonomically trustworthy, it can't exist without an adequate a priori identification of barcoded specimens. Otherwise, the erroneous data deposited onto the BOLD platform will have a negative impact on studies in which molecular data imported from BOLD are utilized.},
}
@article {pmid27395101,
year = {2016},
author = {Cumming, HJ and Wheeler, TA},
title = {Revision of the Nearctic species of Callomyia Meigen (Diptera: Platypezidae) and phylogeny of the genus.},
journal = {Zootaxa},
volume = {4111},
number = {5},
pages = {501-554},
doi = {10.11646/zootaxa.4111.5.1},
pmid = {27395101},
issn = {1175-5334},
mesh = {Animals ; Arctic Regions ; DNA Barcoding, Taxonomic ; Diptera/anatomy &amp; histology/*classification/genetics ; Female ; Male ; Maximal Voluntary Ventilation ; Phylogeny ; },
abstract = {The Nearctic fauna of the genus Callomyia Meigen is revised and a phylogeny of the world species, based on morphological characters, is presented. Although morphological data are used primarily to delimit species, molecular sequence data (DNA barcodes) are used where possible, to help determine species boundaries and associate sexes. Species descriptions, diagnoses, and distribution maps are presented, along with illustrations of habitus, male terminalia, and additional important diagnostic characters. A key to the Nearctic species is provided. Ten species are recorded from the Nearctic Region including three new species: C. argentea Cumming sp. nov., C. arnaudi Cumming sp. nov., C. bertae Kessel, C. browni Cumming sp. nov., C. calla Kessel, C. corvina Kessel, C. gilloglyorum Kessel, C. proxima Johnson, C. velutina Johnson, and C. venusta Snow. The female of C. velutina is described, and three new synonyms are proposed: C. cleta Kessel is a junior synonym of C. calla syn. nov.; C. clara Kessel is a junior synonym of C. corvina syn. nov.; and C. liardia Kessel &amp; Buegler is a junior synonym of C. proxima syn. nov. Phylogenetic relationships within the genus are reconstructed. The genus is monophyletic based primarily on the setulose R1 wing vein, female antennal size and three larval characters. The Nearctic species do not form a monophyletic group with respect to the Old World species.},
}
@article {pmid27395098,
year = {2016},
author = {Spasojevic, T and Kropf, C and Nentwig, W and Lasut, L},
title = {Combining morphology, DNA sequences, and morphometrics: revising closely related species in the orb-weaving spider genus Araniella (Araneae, Araneidae).},
journal = {Zootaxa},
volume = {4111},
number = {4},
pages = {448-470},
doi = {10.11646/zootaxa.4111.4.6},
pmid = {27395098},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/*anatomy &amp; histology/growth &amp; development ; Animals ; Asia ; Body Size ; DNA/genetics ; Europe ; Female ; Male ; North America ; Organ Size ; Phylogeny ; Spiders/anatomy &amp; histology/*classification/*genetics/growth &amp; development ; },
abstract = {The integration of independent data sets could solve problems in both traditional and DNA-based taxonomy. The aim of this study is to investigate the power of CO1 sequences and of morphometrics to distinguish closely related species in the spider genus Araniella. We put special emphasis on the species pair A. cucurbitina (Clerck, 1757) and A. opisthographa (Kulczyński, 1905) since the females are morphologically difficult to distinguish and often misidentified. A total of 216 sequences of eight Araniella species from seven European countries, North America and Asia were included in the molecular analysis. The results from both maximum likelihood and Bayesian phylogenetic inference indicate successful separation of six out of eight Araniella species, including A. cucurbitina and A. opisthographa. For the same six species, we detect no overlap of intra- and interspecific genetic divergence, leading to successful species identification with a threshold approach. In addition, morphometric analysis of the epigyna of A. cucurbitina and A. opisthographa supports species separation by two best explanatory ratios: receptaculum length and distance between receptaculum and copulatory duct. Although a small overlap in the ratios exists, the species identification rate increases when combining morphometric and molecular data, which demonstrates the efficiency of integrative approaches for distinguishing closely related species. However, none of the molecular approaches was able to separate closely related A. alpica (L. Koch, 1869) and A. inconspicua (Simon, 1874) due to shared CO1 haplotypes. Considering the clear morphological separation of the males and different habitat preferences, incomplete lineage sorting or introgressive hybridization could have led to identical CO1 sequences. Therefore, DNA-barcoding must be thoroughly tested even within small homogenous genera of spiders.},
}
@article {pmid27395088,
year = {2016},
author = {Williams, JT and Viviani, J},
title = {Pseudogramma polyacantha complex (Serranidae, tribe Grammistini): DNA barcoding results lead to the discovery of three cryptic species, including two new species from French Polynesia.},
journal = {Zootaxa},
volume = {4111},
number = {3},
pages = {246-260},
doi = {10.11646/zootaxa.4111.3.3},
pmid = {27395088},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Bass/anatomy &amp; histology/*classification/*genetics/growth &amp; development ; Body Size ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Ecosystem ; Female ; Hawaii ; Male ; Organ Size ; Phylogeny ; Polynesia ; South Africa ; },
abstract = {The Pseudogramma polyacantha species complex was found to harbor cryptic taxonomic diversity with three similar, but genetically divergent, species previously hidden in the complex. The true Pseudogramma polyacantha occurs from French Polynesia to South Africa and has modally 19 (many with 20) segmented dorsal-fin rays, modally 16 segmented anal-fin rays, a relatively short lateral line, no dermal flap or small tentacle dorsally on eye, and extensive scalation on the interorbital, suborbital and dentary. Pseudogramma brederi (previously synonymized with P. polyacantha) is recognized as a valid species occurring from Hawaii to Mauritius and having modally 21 segmented dorsal-fin rays, modally 17 segmented anal-fin rays, a relatively long lateral line, no dermal flap or small tentacle dorsally on eye, and relatively well-developed scalation on the interorbital, suborbital and dentary. Pseudogramma galzini n. sp. is described as a new species known only from French Polynesia and having modally 22 segmented dorsal-fin rays, modally 17 segmented anal-fin rays, a relatively long lateral line, no dermal flap or small tentacle dorsally on eye, and limited scalation on the interorbital, suborbital and dentary. Pseudogramma paucilepis n. sp. is described as a new species known only from French Polynesia and having 20 segmented dorsal-fin rays, modally 16 segmented anal-fin rays, a relatively long lateral line, no dermal flap or small tentacle dorsally on eye, and relatively reduced scalation on the interorbital, suborbital and dentary. A mtDNA COI analysis including all available Pseudogramma sequences shows well-supported genetic divergence between the two new species and among congeners.},
}
@article {pmid27394907,
year = {2016},
author = {Baldizzone, G and Landry, JF},
title = {Coleophora ericarnella Baldizzone, a new species of the C. pyrrhulipennella group (Lepidoptera: Coleophoridae) from the South-Eastern Alps.},
journal = {Zootaxa},
volume = {4111},
number = {2},
pages = {177-186},
doi = {10.11646/zootaxa.4111.2.6},
pmid = {27394907},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Ecosystem ; Female ; Italy ; Larva/anatomy &amp; histology/classification/growth &amp; development ; Male ; Moths/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Organ Size ; Phylogeny ; Slovenia ; },
abstract = {Coleophora ericarnella Baldizzone, n. sp. is described from the East-Central Alps region (Italy and Slovenia). It belongs to the C. pyrrhulipennella group. Its larval host plant is Erica carnea (Ericaceae). The adult habitus and genitalia as well as its larval case are illustrated and compared with those of Coleophora pulchripennella Baldizzone, 2011 and C. pyrrhulipennella Zeller, 1849. DNA barcodes also distinguish all three species from each other in congruence with genitalia morphology.},
}
@article {pmid27394871,
year = {2016},
author = {Metzler, EH and Landry, JF},
title = {The Lepidoptera of White Sands National Monument, Otero County, New Mexico, USA 10. A remarkable new white species of Chionodes Hübner (Gelechiidae).},
journal = {Zootaxa},
volume = {4109},
number = {3},
pages = {372-380},
doi = {10.11646/zootaxa.4109.3.7},
pmid = {27394871},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Ecosystem ; Genitalia, Male/anatomy &amp; histology/growth &amp; development ; Male ; Moths/anatomy &amp; histology/*classification/genetics/growth &amp; development ; New Mexico ; Organ Size ; Parks, Recreational ; Phylogeny ; United States ; },
abstract = {The U.S. National Park Service initiated a 10-year study, in late 2006, of the Lepidoptera at White Sands National Monument, Otero County, New Mexico. Chionodes bustosorum sp. n., described here, was discovered in 2010, during the third year of the study. The male imago and male genitalia are illustrated, and its DNA barcode is compared to that of seven other species of Chionodes from western North America.},
}
@article {pmid27394867,
year = {2016},
author = {Cranston, PS},
title = {Conochironomus (Diptera: Chironomidae) in Asia: new and redescribed species and vouchering issues.},
journal = {Zootaxa},
volume = {4109},
number = {3},
pages = {315-331},
doi = {10.11646/zootaxa.4109.3.3},
pmid = {27394867},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Asia ; Body Size ; Chironomidae/*anatomy &amp; histology/*classification/growth &amp; development ; Ecosystem ; Female ; Larva/anatomy &amp; histology/classification/growth &amp; development ; Male ; Organ Size ; Pupa/anatomy &amp; histology/classification/growth &amp; development ; },
abstract = {The presence of the Afro-Australian genus Conochironomus Freeman, 1961 (Diptera: Chironomidae) in Asia has been recognised only informally. An unpublished thesis included Conochironomus from Singapore, and the genus has been keyed from Malaysia without named species. Here, the Sumatran Conochironomus tobaterdecimus (Kikuchi &amp; Sasa, 1980) comb. n. is recorded from Singapore and Thailand. The species is transferred from Sumatendipes Kikuchi &amp; Sasa, 1980, rendering the latter a junior synonym (syn. n.) of Conochironomus Freeman. Conochironomus nuengthai sp. n. and Conochironomus sawngthai sp. n. are described as new to science, based on adult males from Chiang Mai, Thailand. All species conform to existing generic diagnoses for all life stages, with features from male and female genitalia, pupal cephalic tubercles and posterolateral 'spurs' of tergite VIII providing evidence for species distinction. Some larvae are linked to C. tobaterdecimus through molecular barcoding. Variation in other larvae, which clearly belong to Conochironomus and are common throughout Thailand, means that they cannot be segregated to species. Larval habitats include pools in river beds, urban storage reservoirs, drains with moderately high nutrient loadings, and peat swamps. Endochironomus effusus Dutta, 1994 from north-eastern India may be a congener but may differ in adult morphology, thereby precluding formal new combination until discrepancies can be reconciled. Many problems with vouchering taxonomic and molecular material are identified that need to be rectified in the future.},
}
@article {pmid27394805,
year = {2016},
author = {Freyhof, J and Geiger, MF and Golzarianpour, K and Patimar, R},
title = {Sasanidus, a new generic name for Noemacheilus kermanshahensis Bănărescu &amp; Nalbant, with discussion of Ilamnemacheilus and Schistura (Teleostei; Nemacheilidae).},
journal = {Zootaxa},
volume = {4107},
number = {1},
pages = {65-80},
doi = {10.11646/zootaxa.4107.1.3},
pmid = {27394805},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Cypriniformes/anatomy &amp; histology/*classification/genetics/physiology ; Ecosystem ; Female ; India ; Male ; Organ Size ; Phylogeny ; Sex Characteristics ; Terminology as Topic ; },
abstract = {Sasanidus, new genus, is described for Noemacheilus kermanshahensis Bănărescu &amp; Nalbant, endemic to the Karkheh and Karun drainages in Iran. Sasanidus kermanshahensis was initially identified as a species in Oxynoemacheilus, from which it is distinguished by the absence of an external sexual dimorphism (i.e. longer pectoral fin, and nuptial tubercles on fins, head and back in males). Sasanidus is distinguished from all other genera of Nemacheilidae in the Middle East by a combination of the following character states: pelvic-fin origin behind of a vertical of the dorsal-fin origin, anus about one eye diameter in front of the anal-fin origin, dorsal adipose keel absent, a high crest on the bony capsule of the swim bladder present and colour pattern marbled or mottled or with an irregularly shaped midlateral stripe. Ilamnemacheilus longipinnis was examined and no difference could be found between Ilamnemacheilus and Oxynoemacheilus. Therefore, Ilamnemacheilus is treated as a synonym of Oxynoemacheilus. COI barcode sequences from all nemacheilid loach genera occurring in the Middle East and western India are analysed jointly for the first time. The view that Schistura is a paraphyletic assemblage is supported by the clustering of DNA sequences from 45 specimens placed in at least 20 species in the genus Schistura analysed here.},
}
@article {pmid27394798,
year = {2016},
author = {Grebennikov, VV and Kolov, SV},
title = {Flightless Notaris (Coleoptera: Curculionidae: Brachycerinae: Erirhinini) in Southwest China: monophyly, mtDNA phylogeography and evolution of habitat associations.},
journal = {Zootaxa},
volume = {4105},
number = {6},
pages = {557-574},
doi = {10.11646/zootaxa.4105.6.3},
pmid = {27394798},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; China ; DNA, Mitochondrial/genetics ; Ecosystem ; Evolution, Molecular ; Female ; Male ; Organ Size ; Phylogeography ; Weevils/anatomy &amp; histology/*classification/*genetics/growth &amp; development ; },
abstract = {This paper reports the recent discovery of flightless populations of weevils of the genus Notaris in Yunnan and Sichuan provinces of China. Specimens were found in the middle or high altitude mountains (2440-4195 m), by either sifting leaf litter in the deciduous forest and among alpine Rhododendron shrubs, or by turning rocks in the alpine zone. These finds extend southwards the Asian range of this Holarctic genus and report its highest altitudinal records. DNA barcodes of 127 specimens were phylogenetically analysed, of them 42 are those of newly discovered Notaris from Southwest China. The genera Notaris and Tournotaris consistently formed a clade, with Tournotaris nested inside Notaris in Maximum Parsimony (MP) and Maximum Likelihood (ML) analysis. The newly discovered flightless Notaris from Southwest China were either monophyletic (MP) or paraphyletic with respect to volant Holarctic N. aethiops (ML); the latter placement being likely an artefact. A strict linear molecular clock approach suggests a pre-Pliocene separation of Notaris populations in Southwest China. Habitat associations of these high-altitude flightless Notaris contrast sharply with that of the predominantly volant lowland riparian Notaris and other Erirhinini. We hypothesis that evolution of habitat selection in Notaris went from lowland riparian, to high altitude (via uplift of the Tibetan Plateau and adjacent regions of Central Asia), and then to forest leaf litter (via subsequent erosions of isolated mountains such as Emei Shan in Sichuan losing the alpine zone and forcing Notaris into the forest floor). Taxonomic uncertainty of Asian Notaris is addressed and remains unresolved due to uninformative morphology and conflicting DNA signal. Identities of two obscure and likely closely related species, Notaroides brevirostris and Notaris kozlovi from nearby SE Qinghai and NW Sichuan, respectively, are discussed and illustrated. Pending further research, all reported flightless Notaris from Yunnan and Sichuan are hypothesised to form a clade, for which the available name N. kozlovi is used. Habitus and genitalia of Notaris specimens from the newly detected populations are illustrated.},
}
@article {pmid27394741,
year = {2016},
author = {Liu, SP and Pan, Z and Ren, GD},
title = {Identification of three morphologically indistinguishable Epicauta species (Coleoptera, Meloidae, Epicautini) through DNA barcodes and morphological comparisons.},
journal = {Zootaxa},
volume = {4103},
number = {4},
pages = {361-373},
doi = {10.11646/zootaxa.4103.4.4},
pmid = {27394741},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Coleoptera/*anatomy &amp; histology/*classification/genetics/growth &amp; development ; DNA Barcoding, Taxonomic ; Male ; Organ Size ; Phylogeny ; },
abstract = {Three species that belong to the genus Epicauta (Coleopera: Meloidae), E. chinensis, E. dubia, and E. sibirica, appear morphologically indistinguishable. The present study aims to resolve the taxonomic status and the relationships among these three species. Identifying adult morphological characters among the three species were compared and illustrated and partial fragments of the mitochondrial gene (COI) for 77 samples, representing seven meloid species, were obtained and analyzed. Analyses of nucleotide composition, genetic distances and phylogenetics were performed. The results of the morphological studies and molecular analyses showed concordance, indicating that the three species are closely related and indistinguishable from one another. Consequently, two new synonyms are proposed: E. chinensis (Laporte, 1840) syn. n. = E. sibirica (Pallas, 1773) and E. dubia (Fabricius, 1781) syn. n. = E. sibirica (Pallas, 1773).},
}
@article {pmid27394588,
year = {2016},
author = {Marceniuk, AP and Caires, R and Siccha-Ramirez, R and Oliveira, C},
title = {Review of the harvestfishes, genus Peprilus (Perciformes: Stromateidae), &lt;br /&gt;of the Atlantic coast of South America.},
journal = {Zootaxa},
volume = {4098},
number = {2},
pages = {311-332},
doi = {10.11646/zootaxa.4098.2.6},
pmid = {27394588},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Atlantic Ocean ; Body Size ; Ecosystem ; Female ; Male ; Organ Size ; Perciformes/anatomy &amp; histology/*classification/growth &amp; development ; South America ; },
abstract = {Currently, seven valid species are recognized in the genus Peprilus. Found from United States to Argentina, Peprilus paru has a complex nomenclatural history, with seven junior synonyms, three from North America and four from South America. As there has been no recent research, it remains unclear whether species representatives in the north-south axis represent different populations of a single species or distinct species. By comparison of type specimens as well as a comprehensive collection of non-type specimens, this paper aims to clarify the taxonomic status of the nominal species listed as junior synonyms of Peprilus paru in the Atlantic side of South America. Based on morphological data and DNA barcoding, Peprilus crenulatus Cuvier, 1829 and P. xanthurus (Quoy &amp; Gaimard, 1825) are resurrected, while Rhombus argentipinnis Cuvier, 1833 and Rhombus orbicularis Guichenot, 1866, are considered to be junior synonyms of P. crenulatus.},
}
@article {pmid27394568,
year = {2016},
author = {Baldizzone, G and Tabell, J},
title = {Coleophora sabina Baldizzone &amp; Tabell, sp. nov. (Lepidoptera: Coleophoridae) from Central Italy.},
journal = {Zootaxa},
volume = {4097},
number = {4},
pages = {575-583},
doi = {10.11646/zootaxa.4097.4.9},
pmid = {27394568},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Ecosystem ; Female ; Italy ; Male ; Moths/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Organ Size ; Phylogeny ; },
abstract = {Coleophora sabina sp. nov. is described from Italian mainland. Habitus of the adult and the genitalia of both sexes are illustrated. The species is compared especially to C. fringillella Zeller, 1839. DNA barcodes are shown to be distinct and congruent with morphological differences.},
}
@article {pmid27394557,
year = {2016},
author = {Miglietta, MP},
title = {Turritopsis fascicularis Fraser, 1943 (Cnidaria: Hydrozoa): redescription and discussion of its phylogenetic position within the genus.},
journal = {Zootaxa},
volume = {4097},
number = {3},
pages = {426-433},
doi = {10.11646/zootaxa.4097.3.10},
pmid = {27394557},
issn = {1175-5334},
mesh = {Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Florida ; Hydrozoa/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Organ Size ; *Phylogeny ; },
abstract = {Turritopsis fascicularis Fraser, 1943 was first described off Alligator Reef, Florida, USA, at a depth of 216 m. Presumably a deep-sea species, its validity has often been questioned due to the scarcity of available records. In this paper, T. fascicularis is re-described from some mature colonies from the upper slope of the Gulf of Mexico. Furthermore, new pictures of the colony, polyps, and medusa buds, are provided. A ~600bp sequence of the large ribosomal subunit of the mitochondrial RNA (lsu-rRNA, 16S), also known as the Hydrozoan barcoding molecule, is used for the first time to confirm the validity of T. fascicularis as a species, and analyze its phylogenetic position within the genus Turritopsis.},
}
@article {pmid27394494,
year = {2016},
author = {Cumming, JM and Brooks, SE and Sinclair, BJ},
title = {Review of the little-known western Nearctic fly genus Philetus Melander (Diptera: Empididae), with a discussion of its phylogenetic assignment.},
journal = {Zootaxa},
volume = {4093},
number = {2},
pages = {261-274},
doi = {10.11646/zootaxa.4093.2.7},
pmid = {27394494},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; British Columbia ; DNA, Mitochondrial/genetics ; Diptera/anatomy &amp; histology/*classification/*genetics/physiology ; Electron Transport Complex IV/genetics ; Female ; Gene Expression Regulation, Enzymologic ; Male ; *Phylogeny ; Species Specificity ; },
abstract = {The western North American empidid genus Philetus Melander is reviewed, including redescription of the two included species, P. memorandus Melander and P. schizophorus Melander. A lectotype is designated for P. schizophorus. The distributions of both species are mapped and the male terminalia are illustrated. The female of P. schizophorus is discovered for the first time through comparison of COI mitochondrial DNA barcode sequences. The phylogenetic assignment of Philetus within the Empididae is discussed based on a reinterpretation of male terminalia homologies.},
}
@article {pmid27394306,
year = {2016},
author = {Wang, X and Qiu, Y and Wei, C},
title = {A new species of the genus Hyalessa (Hemiptera, Cicadidae) from China, with DNA barcoding data and a key to related species.},
journal = {Zootaxa},
volume = {4085},
number = {2},
pages = {296-300},
doi = {10.11646/zootaxa.4085.2.10},
pmid = {27394306},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; China ; DNA Barcoding, Taxonomic ; Ecosystem ; Hemiptera/anatomy &amp; histology/*classification/*genetics/growth &amp; development ; Male ; Organ Size ; },
abstract = {One new species of the genus Hyalessa China, H. wangi sp. nov., from Yunnan, China is described. Partial mitochondrial COI gene (DNA barcoding) of this new species is sequenced and uploaded to GenBank. A key to all species of Hyalessa is provided.},
}
@article {pmid27394254,
year = {2016},
author = {Yu, D and Yao, J and Hu, F},
title = {Two new species of Tomocerus ocreatus complex (Collembola, Tomoceridae) from Nanjing, China.},
journal = {Zootaxa},
volume = {4084},
number = {1},
pages = {125-134},
doi = {10.11646/zootaxa.4084.1.6},
pmid = {27394254},
issn = {1175-5334},
mesh = {Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Arthropods/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Body Size ; China ; DNA Barcoding, Taxonomic ; Female ; Organ Size ; Phylogeny ; },
abstract = {Two new species of Tomocerus Nicolet, 1842 are described from Nanjing, China. Tomocerus qinae sp. nov. is similar to the Vietnamese species Tomocerus ocreatus, but is different from the latter mainly in the colour pattern, the length of antennae, and the pattern of ungual teeth. Tomocerus qixiaensis sp. nov. is similar to Tomocerus ocreatus and Tomocerus qinae sp. nov., but can be distinguished from them by the short antennae and the blunt prominent macrochaetae on manubrium and dens. DNA barcode sequences of the new species are provided.},
}
@article {pmid27394243,
year = {2016},
author = {Simões, PI},
title = {A new species of nurse-frog (Aromobatidae, Allobates) from the Madeira River basin with a small geographic range.},
journal = {Zootaxa},
volume = {4083},
number = {4},
pages = {501-525},
doi = {10.11646/zootaxa.4083.4.3},
pmid = {27394243},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Anura/anatomy &amp; histology/*classification/growth &amp; development/physiology ; Body Size ; Brazil ; DNA, Ribosomal/genetics ; Ecosystem ; Female ; Genes, Mitochondrial ; Male ; Organ Size ; Phylogeny ; Rivers ; Vocalization, Animal ; },
abstract = {I describe the seventh species of nurse-frog (Allobates) from the Madeira River basin in Brazilian Amazonia. The new species is distinguished from similar congeneric species by its small body size (snout-to-vent length ranging between 14.0-14.7 mm in adult males and between 14.7-14.9 mm in adult females), by the absence of dark brown regular shapes (e.g. hourglass, "X" or polygon-like marks) on the dorsum, by the absence of transverse dark bars on the dorsal surface of the thigh, and by the light gray to white ventral surfaces, light to dark gray only on throat in live male and female specimens. Males have a distinctive advertisement call characterized by the emission of long (7-11 s) trills of short notes (0.04 s in average) with dominant frequency at 5.9-6.3 kHz and emission rate ranging between 6.7-8.7 notes/s. DNA barcode analyses based on a fragment of the 16S rDNA mitochondrial gene provides additional support to the recognition of the new taxon, which is probably distributed on the east riverbank of the Madeira River, in the interfluve between the Aripuanã and Ji-Paraná rivers.},
}
@article {pmid27394221,
year = {2016},
author = {Steinhoff, PO and Butler, SG and Dow, RA},
title = {Description of the final instar larva of Orthetrum borneense Kimmins, 1936 (Odonata, Libellulidae), using rearing and molecular methods.},
journal = {Zootaxa},
volume = {4083},
number = {1},
pages = {99-108},
doi = {10.11646/zootaxa.4083.1.5},
pmid = {27394221},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Borneo ; Ecosystem ; Female ; Larva/*anatomy &amp; histology/classification/genetics/growth &amp; development ; Malaysia ; Male ; Odonata/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Organ Size ; Phylogeny ; },
abstract = {The final instar larva of Orthetrum borneense Kimmins, 1936, is described and figured for the first time based on exuviae from three male and six female larvae collected in Sarawak, Borneo (East Malaysia). It is compared with an early instar larva, which was matched to the adult O. borneense by DNA barcoding, and the known larvae of other species of this genus that occur in the region.},
}
@article {pmid27394216,
year = {2016},
author = {Young, AD and Marshall, SA and Skevington, JH},
title = {Revision of Platycheirus Lepeletier and Serville (Diptera: Syrphidae) in the Nearctic north of Mexico.},
journal = {Zootaxa},
volume = {4082},
number = {1},
pages = {1-317},
doi = {10.11646/zootaxa.4082.1.1},
pmid = {27394216},
issn = {1175-5334},
mesh = {Animals ; Diptera/*anatomy &amp; histology/*classification ; Female ; Male ; Mexico ; },
abstract = {The 75 Nearctic species of Platycheirus Lepeletier and Serville found north of Mexico are revised, including five species new to North America: Platycheirus alpigenus Barkalov and Nielsen, Platycheirus brunnifrons Nielsen, Platycheirus clausseni Nielsen, Platycheirus speighti Doczkal, Stuke &amp; Goeldlin, and Platycheirus splendidus Rotheray. Platycheirus rufimaculatus Vockeroth, Melanostoma willistoni Goot, and Melanostoma concinnus Snow are recognized as junior synonyms of Platycheirus pictipes (Bigot). Melanostoma carinata Curran is recognized as a junior synonym of Platycheirus chilosia (Curran). Melanostoma atra Curran is recognized as a junior synonym of Platycheirus luteipennis (Curran). Platycheirus holarcticus Vockeroth is recognized as a junior synonym of Syrphus naso Walker. Platycheirus trichopus (Thomson) is resurrected and represents what was previously considered the western population of Platycheirus obscurus (Say). One new species, Platycheirus neoperpallidus Young sp. nov., is described. Females of 26 species are described for the first time, and an illustrated key to Nearctic Platycheirus is presented. DNA barcode data are presented for 60 Nearctic species and a COI gene tree of all available world Platycheirus species, as well as morphological and combined morphological/COI phylogenetic analyses of the Platycheirus albimanus species group are presented and discussed.},
}
@article {pmid27394207,
year = {2016},
author = {Song, C and Wang, Q and Zhang, R and Sun, B and Wang, X},
title = {Exploring the utility of DNA barcoding in species delimitation of Polypedilum (Tripodura) non-biting midges (Diptera: Chironomidae).},
journal = {Zootaxa},
volume = {4079},
number = {5},
pages = {534-550},
doi = {10.11646/zootaxa.4079.5.2},
pmid = {27394207},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Chironomidae/anatomy &amp; histology/*classification/*genetics/growth &amp; development ; DNA Barcoding, Taxonomic ; Ecosystem ; Female ; Male ; Organ Size ; Phylogeny ; },
abstract = {In this study, we tested the utility of the mitochondrial gene cytochrome c oxidase subunit 1 (CO1) as the barcode region to deal with taxonomical problems of Polypedilum (Tripodura) non-biting midges (Diptera: Chironomidae). The 114 DNA barcodes representing 27 morphospecies are divided into 33 well separated clusters based on both Neighbor Joining and Maximum Likelihood methods. DNA barcodes revealed an 82% success rate in matching with morphospecies. The selected DNA barcode data support 37-64 operational taxonomic units (OTUs) based on the methods of Automatic Barcode Gap Discovery (ABGD) and Poisson Tree Process (PTP). Furthermore, a priori species based on consistent phenotypic variations were attested by molecular analysis, and a taxonomical misidentification of barcode sequences from GenBank was found. We could not observe a distinct barcode gap but an overlap ranged from 9-12%. Our results supported DNA barcoding as an ideal method to detect cryptic species, delimit sibling species, and associate different life stages in non-biting midges.},
}
@article {pmid27393648,
year = {2016},
author = {Meher, PK and Sahu, TK and Rao, AR},
title = {Identification of species based on DNA barcode using k-mer feature vector and Random forest classifier.},
journal = {Gene},
volume = {592},
number = {2},
pages = {316-324},
doi = {10.1016/j.gene.2016.07.010},
pmid = {27393648},
issn = {1879-0038},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Invertebrates/classification/genetics ; Plants/classification/genetics ; *Software ; },
abstract = {DNA barcoding is a molecular diagnostic method that allows automated and accurate identification of species based on a short and standardized fragment of DNA. To this end, an attempt has been made in this study to develop a computational approach for identifying the species by comparing its barcode with the barcode sequence of known species present in the reference library. Each barcode sequence was first mapped onto a numeric feature vector based on k-mer frequencies and then Random forest methodology was employed on the transformed dataset for species identification. The proposed approach outperformed similarity-based, tree-based, diagnostic-based approaches and found comparable with existing supervised learning based approaches in terms of species identification success rate, while compared using real and simulated datasets. Based on the proposed approach, an online web interface SPIDBAR has also been developed and made freely available at http://cabgrid.res.in:8080/spidbar/ for species identification by the taxonomists.},
}
@article {pmid27392246,
year = {2016},
author = {Parveen, I and Gafner, S and Techen, N and Murch, SJ and Khan, IA},
title = {DNA Barcoding for the Identification of Botanicals in Herbal Medicine and Dietary Supplements: Strengths and Limitations.},
journal = {Planta medica},
volume = {82},
number = {14},
pages = {1225-1235},
doi = {10.1055/s-0042-111208},
pmid = {27392246},
issn = {1439-0221},
support = {U01 FD004246/FD/FDA HHS/United States ; },
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant ; *Dietary Supplements/standards ; *Herbal Medicine/standards ; Plants, Medicinal/*classification/genetics ; Reproducibility of Results ; },
abstract = {In the past decades, the use of traditional medicine has increased globally, leading to a booming herbal medicine and dietary supplement industry. The increased popularity of herbal products has led to a rise in demand for botanical raw materials. Accurate identification of medicinal herbs is a legal requirement in most countries and prerequisite for delivering a quality product that meets consumer expectations. Traditional identification methods include botanical taxonomy, macroscopic and microscopic examination, and chemical methods. Advances in the identification of biological species using DNA-based techniques have led to the development of a DNA marker-based platform for authentication of plant materials. DNA barcoding, in particular, has been proposed as a means to identify herbal ingredients and to detect adulteration. However, general barcoding techniques using universal primers have been shown to provide mixed results with regard to data accuracy. Further technological advances such as mini-barcodes, digital polymerase chain reaction, and next generation sequencing provide additional tools for the authentication of herbs, and may be successful in identifying processed ingredients used in finished herbal products. This review gives an overview on the strengths and limitations of DNA barcoding techniques for botanical ingredient identification. Based on the available information, we do not recommend the use of universal primers for DNA barcoding of processed plant material as a sole means of species identification, but suggest an approach combining DNA-based methods using genus- or species-specific primers, chemical analysis, and microscopic and macroscopic methods for the successful authentication of botanical ingredients used in the herbal dietary supplement industry.},
}
@article {pmid27392036,
year = {2016},
author = {Monaghan, KA},
title = {Four Reasons to Question the Accuracy of a Biotic Index; the Risk of Metric Bias and the Scope to Improve Accuracy.},
journal = {PloS one},
volume = {11},
number = {7},
pages = {e0158383},
pmid = {27392036},
issn = {1932-6203},
mesh = {Animals ; *Biota ; *Body Size ; *Data Accuracy ; *Models, Theoretical ; },
abstract = {Natural ecological variability and analytical design can bias the derived value of a biotic index through the variable influence of indicator body-size, abundance, richness, and ascribed tolerance scores. Descriptive statistics highlight this risk for 26 aquatic indicator systems; detailed analysis is provided for contrasting weighted-average indices applying the example of the BMWP, which has the best supporting data. Differences in body size between taxa from respective tolerance classes is a common feature of indicator systems; in some it represents a trend ranging from comparatively small pollution tolerant to larger intolerant organisms. Under this scenario, the propensity to collect a greater proportion of smaller organisms is associated with negative bias however, positive bias may occur when equipment (e.g. mesh-size) selectively samples larger organisms. Biotic indices are often derived from systems where indicator taxa are unevenly distributed along the gradient of tolerance classes. Such skews in indicator richness can distort index values in the direction of taxonomically rich indicator classes with the subsequent degree of bias related to the treatment of abundance data. The misclassification of indicator taxa causes bias that varies with the magnitude of the misclassification, the relative abundance of misclassified taxa and the treatment of abundance data. These artifacts of assessment design can compromise the ability to monitor biological quality. The statistical treatment of abundance data and the manipulation of indicator assignment and class richness can be used to improve index accuracy. While advances in methods of data collection (i.e. DNA barcoding) may facilitate improvement, the scope to reduce systematic bias is ultimately limited to a strategy of optimal compromise. The shortfall in accuracy must be addressed by statistical pragmatism. At any particular site, the net bias is a probabilistic function of the sample data, resulting in an error variance around an average deviation. Following standardized protocols and assigning precise reference conditions, the error variance of their comparative ratio (test-site:reference) can be measured and used to estimate the accuracy of the resultant assessment.},
}
@article {pmid27388757,
year = {2016},
author = {Montagna, M and Mereghetti, V and Lencioni, V and Rossaro, B},
title = {Correction: Integrated Taxonomy and DNA Barcoding of Alpine Midges (Diptera: Chironomidae).},
journal = {PloS one},
volume = {11},
number = {7},
pages = {e0159124},
pmid = {27388757},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0149673.].},
}
@article {pmid27383475,
year = {2016},
author = {Baek, SY and Jang, KH and Choi, EH and Ryu, SH and Kim, SK and Lee, JH and Lim, YJ and Lee, J and Jun, J and Kwak, M and Lee, YS and Hwang, JS and Venmathi Maran, BA and Chang, CY and Kim, IH and Hwang, UW},
title = {DNA Barcoding of Metazoan Zooplankton Copepods from South Korea.},
journal = {PloS one},
volume = {11},
number = {7},
pages = {e0157307},
pmid = {27383475},
issn = {1932-6203},
mesh = {Animals ; Copepoda/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Genes, Mitochondrial ; Genetic Variation ; Geography ; Phylogeny ; Republic of Korea ; Sequence Analysis, DNA ; Species Specificity ; Zooplankton/*genetics ; },
abstract = {Copepods, small aquatic crustaceans, are the most abundant metazoan zooplankton and outnumber every other group of multicellular animals on earth. In spite of ecological and biological importance in aquatic environment, their morphological plasticity, originated from their various lifestyles and their incomparable capacity to adapt to a variety of environments, has made the identification of species challenging, even for expert taxonomists. Molecular approaches to species identification have allowed rapid detection, discrimination, and identification of cryptic or sibling species based on DNA sequence data. We examined sequence variation of a partial mitochondrial cytochrome C oxidase I gene (COI) from 133 copepod individuals collected from the Korean Peninsula, in order to identify and discriminate 94 copepod species covering six copepod orders of Calanoida, Cyclopoida, Harpacticoida, Monstrilloida, Poecilostomatoida and Siphonostomatoida. The results showed that there exists a clear gap with ca. 20 fold difference between the averages of within-specific sequence divergence (2.42%) and that of between-specific sequence divergence (42.79%) in COI, suggesting the plausible utility of this gene in delimitating copepod species. The results showed, with the COI barcoding data among 94 copepod species, that a copepod species could be distinguished from the others very clearly, only with four exceptions as followings: Mesocyclops dissimilis-Mesocyclops pehpeiensis (0.26% K2P distance in percent) and Oithona davisae-Oithona similis (1.1%) in Cyclopoida, Ostrincola japonica-Pseudomyicola spinosus (1.5%) in Poecilostomatoida, and Hatschekia japonica-Caligus quadratus (5.2%) in Siphonostomatoida. Thus, it strongly indicated that COI may be a useful tool in identifying various copepod species and make an initial progress toward the construction of a comprehensive DNA barcode database for copepods inhabiting the Korean Peninsula.},
}
@article {pmid27375591,
year = {2016},
author = {Herbold, CW and Pelikan, C and Kuzyk, O and Hausmann, B and Angel, R and Berry, D and Loy, A},
title = {Corrigendum: A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes.},
journal = {Frontiers in microbiology},
volume = {7},
number = {},
pages = {870},
doi = {10.3389/fmicb.2016.00870},
pmid = {27375591},
issn = {1664-302X},
support = {P 25111/FWF_/Austrian Science Fund FWF/Austria ; P 25700/FWF_/Austrian Science Fund FWF/Austria ; P 26127/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {[This corrects the article on p. 731 in vol. 6, PMID: 26236305.].},
}
@article {pmid27374145,
year = {2017},
author = {Guimaraes, S and Pruvost, M and Daligault, J and Stoetzel, E and Bennett, EA and Côté, NM and Nicolas, V and Lalis, A and Denys, C and Geigl, EM and Grange, T},
title = {A cost-effective high-throughput metabarcoding approach powerful enough to genotype ~44 000 year-old rodent remains from Northern Africa.},
journal = {Molecular ecology resources},
volume = {17},
number = {3},
pages = {405-417},
doi = {10.1111/1755-0998.12565},
pmid = {27374145},
issn = {1755-0998},
mesh = {Animals ; Archaeology ; *DNA Barcoding, Taxonomic ; Genotype ; High-Throughput Nucleotide Sequencing ; Morocco ; Phylogeny ; Rodentia/*classification ; },
abstract = {We present a cost-effective metabarcoding approach, aMPlex Torrent, which relies on an improved multiplex PCR adapted to highly degraded DNA, combining barcoding and next-generation sequencing to simultaneously analyse many heterogeneous samples. We demonstrate the strength of these improvements by generating a phylochronology through the genotyping of ancient rodent remains from a Moroccan cave whose stratigraphy covers the last 120 000 years. Rodents are important for epidemiology, agronomy and ecological investigations and can act as bioindicators for human- and/or climate-induced environmental changes. Efficient and reliable genotyping of ancient rodent remains has the potential to deliver valuable phylogenetic and paleoecological information. The analysis of multiple ancient skeletal remains of very small size with poor DNA preservation, however, requires a sensitive high-throughput method to generate sufficient data. We show this approach to be particularly adapted at accessing this otherwise difficult taxonomic and genetic resource. As a highly scalable, lower cost and less labour-intensive alternative to targeted sequence capture approaches, we propose the aMPlex Torrent strategy to be a useful tool for the genetic analysis of multiple degraded samples in studies involving ecology, archaeology, conservation and evolutionary biology.},
}
@article {pmid27373803,
year = {2016},
author = {Sousa, LL and Xavier, R and Costa, V and Humphries, NE and Trueman, C and Rosa, R and Sims, DW and Queiroz, N},
title = {DNA barcoding identifies a cosmopolitan diet in the ocean sunfish.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {28762},
pmid = {27373803},
issn = {2045-2322},
mesh = {Animals ; Atlantic Ocean ; Cnidaria/genetics/physiology ; Crustacea/genetics/physiology ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; *Diet ; Feeding Behavior/*physiology ; Fishes/genetics/physiology ; Food Chain ; Oceans and Seas ; Plankton/genetics/physiology ; Predatory Behavior/*physiology ; Tetraodontiformes/*physiology ; },
abstract = {The ocean sunfish (Mola mola) is the world's heaviest bony fish reaching a body mass of up to 2.3 tonnes. However, the prey M. mola consumes to fuel this prodigious growth remains poorly known. Sunfish were thought to be obligate gelatinous plankton feeders, but recent studies suggest a more generalist diet. In this study, through molecular barcoding and for the first time, the diet of sunfish in the north-east Atlantic Ocean was characterised. Overall, DNA from the diet content of 57 individuals was successfully amplified, identifying 41 different prey items. Sunfish fed mainly on crustaceans and teleosts, with cnidarians comprising only 16% of the consumed prey. Although no adult fishes were sampled, we found evidence for an ontogenetic shift in the diet, with smaller individuals feeding mainly on small crustaceans and teleost fish, whereas the diet of larger fish included more cnidarian species. Our results confirm that smaller sunfish feed predominantly on benthic and on coastal pelagic species, whereas larger fish depend on pelagic prey. Therefore, sunfish is a generalist predator with a greater diversity of links in coastal food webs than previously realised. Its removal as fisheries' bycatch may have wider reaching ecological consequences, potentially disrupting coastal trophic interactions.},
}
@article {pmid27369043,
year = {2016},
author = {Davies, R and Vogelsang, P and Jonsson, R and Appel, S},
title = {An optimized multiplex flow cytometry protocol for the analysis of intracellular signaling in peripheral blood mononuclear cells.},
journal = {Journal of immunological methods},
volume = {436},
number = {},
pages = {58-63},
doi = {10.1016/j.jim.2016.06.007},
pmid = {27369043},
issn = {1872-7905},
mesh = {B-Lymphocytes/*cytology ; Cell Culture Techniques ; Flow Cytometry/*methods ; Humans ; Monocytes/*cytology ; Phosphoproteins/metabolism ; Phosphorylation ; *Signal Transduction ; T-Lymphocytes/*cytology ; },
abstract = {Phosphoflow cytometry is increasingly being used as a tool for the discovery of biomarkers used in the treatment and monitoring of disease and therapy. The ability to measure numerous phospho-protein targets simultaneously at a single cell level accurately and rapidly provides significant advantages over other methods. We here discuss important considerations required to successfully implement these methods. Three different blood collection tubes (lithium-heparin tubes, CPT with sodium citrate and CPT with sodium heparin) were evaluated, with PBMC isolated through lithium-heparin tubes/lymphoprep displaying reduced basal and increased stimulation induced phosphorylation compared to the other two methods. Further, we provide a protocol outlining an 8 color assay developed for the study of intracellular signaling in peripheral blood mononuclear cells. The assay allows for the quantitative measurement of the phospho-proteins ERK1/2, NF-κB p65, Stat1 (Y701), Stat1 (S727), Stat3 (Y705), Stat3 (S727), Stat4 (Y693), p38 and Stat5 (Y694), as well as the identification of T cells, B cells, natural killer cells and monocytes. The assay additionally incorporates fluorescent cell barcoding, reducing assay costs and increasing throughput while increasing data robustness. Inter-assay precision was assessed over a month long period for all experimental variables (phospho-protein measured, cell type and stimulant). Coefficient of variations (CVs) calculated from process triplicates of normalized median fluorescence intensity (MFI) of the phospho-proteins displayed median CVs under 10% when grouped according to cell type, stimulation agent and phospho-protein measured, while the CV for each triplicate did not exceed 20%.},
}
@article {pmid27365449,
year = {2016},
author = {Ståhl, PL and Salmén, F and Vickovic, S and Lundmark, A and Navarro, JF and Magnusson, J and Giacomello, S and Asp, M and Westholm, JO and Huss, M and Mollbrink, A and Linnarsson, S and Codeluppi, S and Borg, &#xc5; and Pontén, F and Costea, PI and Sahlén, P and Mulder, J and Bergmann, O and Lundeberg, J and Frisén, J},
title = {Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.},
journal = {Science (New York, N.Y.)},
volume = {353},
number = {6294},
pages = {78-82},
doi = {10.1126/science.aaf2403},
pmid = {27365449},
issn = {1095-9203},
mesh = {Animals ; Brain/metabolism ; Breast Neoplasms/metabolism ; DNA, Complementary/biosynthesis ; Female ; Gene Expression Profiling/*methods ; Humans ; Mice ; Organ Specificity ; RNA, Messenger/metabolism ; Sequence Analysis, RNA/*methods ; *Transcriptome ; },
abstract = {Analysis of the pattern of proteins or messengerRNAs (mRNAs) in histological tissue sections is a cornerstone in biomedical research and diagnostics. This typically involves the visualization of a few proteins or expressed genes at a time. We have devised a strategy, which we call "spatial transcriptomics," that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections. By positioning histological sections on arrayed reverse transcription primers with unique positional barcodes, we demonstrate high-quality RNA-sequencing data with maintained two-dimensional positional information from the mouse brain and human breast cancer. Spatial transcriptomics provides quantitative gene expression data and visualization of the distribution of mRNAs within tissue sections and enables novel types of bioinformatics analyses, valuable in research and diagnostics.},
}
@article {pmid27363727,
year = {2016},
author = {Weber, TS and Dukes, M and Miles, DC and Glaser, SP and Naik, SH and Duffy, KR},
title = {Site-specific recombinatorics: in situ cellular barcoding with the Cre Lox system.},
journal = {BMC systems biology},
volume = {10},
number = {1},
pages = {43},
pmid = {27363727},
issn = {1752-0509},
mesh = {Animals ; CD8-Positive T-Lymphocytes/metabolism ; Genetic Engineering/*methods ; Genetic Variation ; Integrases/*metabolism ; Inverted Repeat Sequences/genetics ; Mice ; *Recombination, Genetic ; },
abstract = {BACKGROUND: Cellular barcoding is a recently developed biotechnology tool that enables the familial identification of progeny of individual cells in vivo. In immunology, it has been used to track the burst-sizes of multiple distinct responding T cells over several adaptive immune responses. In the study of hematopoiesis, it revealed fate heterogeneity amongst phenotypically identical multipotent cells. Most existing approaches rely on ex vivo viral transduction of cells with barcodes followed by adoptive transfer into an animal, which works well for some systems, but precludes barcoding cells in their native environment such as those inside solid tissues.<br><br>RESULTS: With a view to overcoming this limitation, we propose a new design for a genetic barcoding construct based on the Cre Lox system that induces randomly created stable barcodes in cells in situ by exploiting inherent sequence distance constraints during site-specific recombination. We identify the cassette whose provably maximal code diversity is several orders of magnitude higher than what is attainable with previously considered Cre Lox barcoding approaches, exceeding the number of lymphocytes or hematopoietic progenitor cells in mice.<br><br>CONCLUSIONS: Its high diversity and in situ applicability, make the proposed Cre Lox based tagging system suitable for whole tissue or even whole animal barcoding. Moreover, it can be built using established technology.},
}
@article {pmid27362639,
year = {2016},
author = {Malausa, T and Delaunay, M and Fleisch, A and Groussier-Bout, G and Warot, S and Crochard, D and Guerrieri, E and Delvare, G and Pellizzari, G and Kaydan, MB and Al-Khateeb, N and Germain, JF and Brancaccio, L and Le Goff, I and Bessac, M and Ris, N and Kreiter, P},
title = {Investigating Biological Control Agents for Controlling Invasive Populations of the Mealybug Pseudococcus comstocki in France.},
journal = {PloS one},
volume = {11},
number = {6},
pages = {e0157965},
pmid = {27362639},
issn = {1932-6203},
mesh = {Animals ; Biological Control Agents ; DNA Barcoding, Taxonomic ; France ; Hemiptera/*parasitology ; Host-Parasite Interactions ; Insect Control/*methods ; Parasites/*classification/isolation &amp; purification/physiology ; Pest Control, Biological/*methods ; Phylogeny ; Population Control ; },
abstract = {Pseudococcus comstocki (Hemiptera: Pseudococcidae) is a mealybug species native to Eastern Asia and present as an invasive pest in northern Italy and southern France since the start of the century. It infests apple and pear trees, grapevines and some ornamental trees. Biocontrol programmes against this pest proved successful in central Asia and North America in the second half of the 20th century. In this study, we investigated possible biocontrol agents against P. comstocki, with the aim of developing a biocontrol programme in France. We carried out systematic DNA-barcoding at each step in the search for a specialist parasitoid. First we characterised the French target populations of P. comstocki. We then identified the parasitoids attacking P. comstocki in France. Finally, we searched for foreign mealybug populations identified a priori as P. comstocki and surveyed their hymenopteran parasitoids. Three mealybug species (P. comstocki, P. viburni and P. cryptus) were identified during the survey, together with at least 16 different parasitoid taxa. We selected candidate biological control agent populations for use against P. comstocki in France, from the species Allotropa burrelli (Hymenoptera: Platygastridae) and Acerophagus malinus (Hymenoptera: Encyrtidae). The coupling of molecular and morphological characterisation for both pests and natural enemies facilitated the programme development and the rejection of unsuitable or generalist parasitoids.},
}
@article {pmid27362258,
year = {2016},
author = {Hassold, S and Lowry, PP and Bauert, MR and Razafintsalama, A and Ramamonjisoa, L and Widmer, A},
title = {DNA Barcoding of Malagasy Rosewoods: Towards a Molecular Identification of CITES-Listed Dalbergia Species.},
journal = {PloS one},
volume = {11},
number = {6},
pages = {e0157881},
pmid = {27362258},
issn = {1932-6203},
mesh = {Conservation of Natural Resources ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; Dalbergia/*classification/genetics ; Endangered Species ; Madagascar ; Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA/*methods ; Species Specificity ; Tropical Climate ; },
abstract = {Illegal selective logging of tropical timber is of increasing concern worldwide. Madagascar is a biodiversity hotspot and home to some of the world's most sought after tropical timber species. Malagasy rosewoods belong to the genus Dalbergia (Fabaceae), which is highly diverse and has a pantropical distribution, but these timber species are among the most threatened as a consequence of intensive illegal selective logging and deforestation. Reliable identification of Dalbergia species from Madagascar is important for law enforcement but is almost impossible without fertile plant material, which is often unavailable during forest inventories or when attempting to identify logged trees of cut wood. DNA barcoding has been promoted as a promising tool for species identification in such cases. In this study we tested whether DNA barcoding with partial sequences of three plastid markers (matK, rbcL and trnL (UAA)) can distinguish between Dalbergia from Madagascar and from other areas of its distributional range, and whether Malagasy species can be distinguished from one another. Phylogenetic analyses revealed that the Malagasy Dalbergia species studied form two monophyletic groups, each containing two subgroups, only one of which corresponds to a single species. We characterized diagnostic polymorphisms in the three DNA barcoding markers that allow rapid discrimination between Dalbergia from Madagascar and from other areas of its distribution range. Species identification success based on individual barcoding markers or combinations was poor, whereas subgroup identification success was much higher (up to 98%), revealing both the value and limitations of a DNA barcoding approach for the identification of closely related Malagasy rosewoods.},
}
@article {pmid27356376,
year = {2015},
author = {Da, GZ and Zhang, XQ and Yao, H and Wang, ZP and Zhao, B and Zhang, C and Hu, ZG},
title = {[Identification of Ardisiae Japonicae Herba by ITS2 Sequence].},
journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials},
volume = {38},
number = {11},
pages = {2277-2280},
pmid = {27356376},
issn = {1001-4454},
mesh = {Ardisia/classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/*genetics ; *Phylogeny ; Plants, Medicinal/classification/genetics ; },
abstract = {OBJECTIVE: The ITS2 sequence was used to identify Ardisiae Japonicae Herba collected from the market, in order to ensure the medicine quality of the market and to provide a reliable technical method.<br><br>METHODS: The certified samples, including Ardisia japonica and its adulterants, were 56 samples of 17 species. All the sequences of the samples including six related sequences downloaded from NCBI were analyzed by computing the Kimura 2-parameter (K2P) genetic distance and the neighbor-joining (NJ) phylogenetic tree, then the method of DNA barcoding identification technology of Ardisiae Japonicae Herba based on ITS2 sequence was established. Combined with online comparison of sequences, the method was used to detect 15 samples of Ardisiae Japonicae Herba from the market to distinguish authenticity.<br><br>RESULTS: The maximum and the average intra-specific K2P genetic distance of Ardisia japonica were all less than the minimum and the average inter-specific K2P genetic distance, and Ardisia japonica and its adulterants could be separated by computing the NJ phylogenetic tree. The identification results of online comparison and DNA barcoding identification were the same. In all of the 15 samples, 13 of them were genuine, and the other two samples were fake.<br><br>CONCLUSION: The DNA barcoding identification technique method of Ardisiae Japonicae Herba is established based on ITS2 sequence, and it provides a reference method to distinguish the authenticity of Ardisiae Japonicae Herba quickly by gene recognition.},
}
@article {pmid27355872,
year = {2016},
author = {Yavorski, JM and Blanck, G},
title = {TCGA: Increased oncoprotein coding region mutations correlate with a greater expression of apoptosis-effector genes and a positive outcome for stomach adenocarcinoma.},
journal = {Cell cycle (Georgetown, Tex.)},
volume = {15},
number = {16},
pages = {2157-2163},
pmid = {27355872},
issn = {1551-4005},
mesh = {Adenocarcinoma/*genetics ; Amino Acids/genetics ; Apoptosis/*genetics ; *Databases, Genetic ; *Gene Expression Regulation, Neoplastic ; Genes, Tumor Suppressor ; Humans ; Mutation/*genetics ; Neoplasm Proteins/genetics/metabolism ; Open Reading Frames/*genetics ; Stomach Neoplasms/*genetics ; Treatment Outcome ; },
abstract = {Oncogene mutations are primarily thought to facilitate uncontrolled cell growth. However, overexpression of oncoproteins likely leads to apoptosis in a feed forward mechanism, whereby a certain level of oncoprotein leads to the activation of pro-proliferation effector genes and higher levels lead to activation of pro-apoptotic effector genes. TCGA STAD barcodes having no oncoprotein coding region mutations represented reduced expression of the apoptosis-effector genes compared with barcodes with multiple oncoprotein coding region mutations. Furthermore, STAD barcodes in a "no-subsequent tumor" group, representing 224 samples, and in a "positive outcome" group, had more oncoprotein coding regions mutated, on average, than barcodes of the new tumor and negative outcome groups, respectively. BRAF, CTNNB1, KRAS and MTOR coding region mutations (as a group) had the strongest association with the no-subsequent tumor group. Tumor suppressor coding region mutations were also correlated with no-subsequent tumor. These results are consistent with an oncoprotein-mediated, feed-forward mechanism of apoptosis in patients. Importantly, the no-subsequent tumor group also had more overall mutations. This result leads to considerations of unhealthy cells or cells with more neo-antigens for immune rejection. However, a probabilistic aspect of mutagenesis is also consistent with more oncoprotein and tumor suppressor protein mutations, in cases of more overall mutations, and thus a higher likelihood of activation of feed forward apoptosis pathways.},
}
@article {pmid27353563,
year = {2016},
author = {Lan, F and Haliburton, JR and Yuan, A and Abate, AR},
title = {Droplet barcoding for massively parallel single-molecule deep sequencing.},
journal = {Nature communications},
volume = {7},
number = {},
pages = {11784},
pmid = {27353563},
issn = {2041-1723},
support = {T32 GM008284/GM/NIGMS NIH HHS/United States ; R21 HG007233/HG/NHGRI NIH HHS/United States ; T32 EB009383/EB/NIBIB NIH HHS/United States ; DP2 AR068129/AR/NIAMS NIH HHS/United States ; R01 EB019453/EB/NIBIB NIH HHS/United States ; },
mesh = {DNA/*genetics ; DNA Barcoding, Taxonomic/*methods ; Haplotypes ; High-Throughput Nucleotide Sequencing/*methods ; *Microfluidics ; Mutation ; Sequence Analysis, DNA/*methods ; },
abstract = {The ability to accurately sequence long DNA molecules is important across biology, but existing sequencers are limited in read length and accuracy. Here, we demonstrate a method to leverage short-read sequencing to obtain long and accurate reads. Using droplet microfluidics, we isolate, amplify, fragment and barcode single DNA molecules in aqueous picolitre droplets, allowing the full-length molecules to be sequenced with multi-fold coverage using short-read sequencing. We show that this approach can provide accurate sequences of up to 10 kb, allowing us to identify rare mutations below the detection limit of conventional sequencing and directly link them into haplotypes. This barcoding methodology can be a powerful tool in sequencing heterogeneous populations such as viruses.},
}
@article {pmid27352804,
year = {2016},
author = {Zhang, T and Wang, YJ and Guo, W and Luo, D and Wu, Y and Kučerová, Z and Stejskal, V and Opit, G and Cao, Y and Li, FJ and Li, ZH},
title = {DNA barcoding, species-specific PCR and real-time PCR techniques for the identification of six Tribolium pests of stored products.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {28494},
pmid = {27352804},
issn = {2045-2322},
mesh = {Animals ; Base Sequence ; DNA/*chemistry/isolation &amp; purification/metabolism ; *DNA Barcoding, Taxonomic ; DNA Primers/metabolism ; Electron Transport Complex IV/chemistry/genetics ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Sequence Alignment ; Species Specificity ; Tribolium/*classification/*genetics ; },
abstract = {Flour beetles of the genus Tribolium Macleay (Coleoptera: Tenebrionidae) are important stored product pests in China and worldwide. They are often found or are intercepted in grain depots, flour mills, and entry-exit ports, etc. Traditionally, Tribolium species are identified according to the morphological characteristics of the adult. However, it is almost impossible to rapidly identify adult fragments and non-adult stages based on external morphological characteristics. Molecular techniques for the rapid and accurate identification of Tribolium species are required, particularly for pest monitoring and the quarantine of stored products pests. Here, we establish DNA barcoding, species-specific PCR, and real-time PCR techniques for the identification of six stored-product pest Tribolium species including T. castaneum, T. confusum, T. destructor, T. madens, T. freemani and T. brevicornis. We detected the mitochondrial DNA cytochrome oxidase subunit I (COI) barcodes for Tribolium from 18 geographic populations and 101 individuals, built a Tribolium DNA barcode library, and designed species-specific primers and TaqMan probes for the above six Tribolium species. The three techniques were applied to identify Tribolium collected from stored samples and samples captured from quarantine ports. The results demonstrated that three techniques were all able to identify the six species of Tribolium both rapidly and accurately.},
}
@article {pmid27347459,
year = {2016},
author = {Guo, LC and Zhao, MM and Sun, W and Teng, HL and Huang, BS and Zhao, XP},
title = {Differentiation of the Chinese minority medicinal plant genus Berchemia spp. by evaluating three candidate barcodes.},
journal = {SpringerPlus},
volume = {5},
number = {1},
pages = {658},
pmid = {27347459},
issn = {2193-1801},
abstract = {The genus Berchemia comprises important Chinese plants with considerable medicinal value; however, these plants are often misidentified in the herbal medicinal market. To differentiate the various morphotypes of Berchemia species, a proficient method employing the screening of universal DNA barcodes was used in this work. Three candidate barcoding loci, namely, psbA-trnH, rbcL, and the second internal transcribed spacer (ITS2), were used to identify an effective DNA barcode that can differentiate the various Berchemia species. Additionally, PCR amplification, efficient sequencing, intra- and inter-specific divergences, and DNA barcoding gaps were employed to assess the ability of each barcode to identify these diverse Berchemia plants authentically; the species were differentiated using the Kimura two-parameter and maximum composite likelihood methods. Sequence data analysis showed that the ITS2 region was the most suitable candidate barcode and exhibited the highest interspecific divergence among the three DNA-barcoding sequences. A clear differentiation was observed at the species level, in which a maximum distance of 0.264 was exhibited between dissimilar species. Clustal analysis also demonstrated that ITS2 clearly differentiated the test species in a more effective manner than that with the two other barcodes at both the hybrid and variety levels. Results indicate that DNA barcoding is ideal for species-level identification of Berchemia and provides a foundation for further identification at the molecular level of other Rhamnaceae medicinal plants.},
}
@article {pmid27347449,
year = {2016},
author = {Heckenhauer, J and Barfuss, MH and Samuel, R},
title = {Universal multiplexable matK primers for DNA barcoding of angiosperms.},
journal = {Applications in plant sciences},
volume = {4},
number = {6},
pages = {},
pmid = {27347449},
issn = {2168-0450},
support = {P 26548/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {PREMISE OF THE STUDY: PCR amplification of the matK barcoding region is often difficult when dealing with multiple angiosperm families. We developed a primer cocktail to amplify this region efficiently across angiosperm diversity.<br><br>METHODS AND RESULTS: We developed 14 matK primers (seven forward, seven reverse) for multiplex PCR, using sequences available in GenBank for 178 taxa belonging to 123 genera in 41 families and 18 orders. Universality of these new multiplexed primers was tested with 53 specimens from 44 representative angiosperm families in 23 different orders. Our primers showed high PCR amplification and sequencing success.<br><br>CONCLUSIONS: These results show that our newly developed primers are highly effective for multiplex PCR and can be employed in future barcode projects involving taxonomically diverse samples across angiosperms. Using multiplex primers for barcoding will reduce the cost and time needed for PCR amplification.},
}
@article {pmid27341687,
year = {2016},
author = {Wilson, JJ and Sing, KW and Lee, PS and Wee, AK},
title = {Application of DNA barcodes in wildlife conservation in Tropical East Asia.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {30},
number = {5},
pages = {982-989},
doi = {10.1111/cobi.12787},
pmid = {27341687},
issn = {1523-1739},
mesh = {Animals ; Animals, Wild ; Asia ; *Biodiversity ; *Conservation of Natural Resources ; DNA ; *DNA Barcoding, Taxonomic ; },
abstract = {Over the past 50 years, Tropical East Asia has lost more biodiversity than any tropical region. Tropical East Asia is a megadiverse region with an acute taxonomic impediment. DNA barcodes are short standardized DNA sequences used for taxonomic purposes and have the potential to lessen the challenges of biodiversity inventory and assessments in regions where they are most needed. We reviewed DNA barcoding efforts in Tropical East Asia relative to other tropical regions. We suggest DNA barcodes (or metabarcodes from next-generation sequencers) may be especially useful for characterizing and connecting species-level biodiversity units in inventories encompassing taxa lacking formal description (particularly arthropods) and in large-scale, minimal-impact approaches to vertebrate monitoring and population assessments through secondary sources of DNA (invertebrate derived DNA and environmental DNA). We suggest interest and capacity for DNA barcoding are slowly growing in Tropical East Asia, particularly among the younger generation of researchers who can connect with the barcoding analogy and understand the need for new approaches to the conservation challenges being faced.},
}
@article {pmid27339043,
year = {2016},
author = {Bell, C and Guerinet, J and Atkinson, KM and Wilson, K},
title = {Feasibility and Limitations of Vaccine Two-Dimensional Barcoding Using Mobile Devices.},
journal = {Journal of medical Internet research},
volume = {18},
number = {6},
pages = {e143},
pmid = {27339043},
issn = {1438-8871},
mesh = {*Cell Phone ; Cost-Benefit Analysis ; Data Accuracy ; *Documentation ; *Drug Labeling ; Electronic Data Processing ; Feasibility Studies ; Humans ; Point-of-Care Systems ; Vaccination ; *Vaccines ; },
abstract = {BACKGROUND: Two-dimensional (2D) barcoding has the potential to enhance documentation of vaccine encounters at the point of care. However, this is currently limited to environments equipped with dedicated barcode scanners and compatible record systems. Mobile devices may present a cost-effective alternative to leverage 2D vaccine vial barcodes and improve vaccine product-specific information residing in digital health records.<br><br>OBJECTIVE: Mobile devices have the potential to capture product-specific information from 2D vaccine vial barcodes. We sought to examine the feasibility, performance, and potential limitations of scanning 2D barcodes on vaccine vials using 4 different mobile phones.<br><br>METHODS: A unique barcode scanning app was developed for Android and iOS operating systems. The impact of 4 variables on the scan success rate, data accuracy, and time to scan were examined: barcode size, curvature, fading, and ambient lighting conditions. Two experimenters performed 4 trials 10 times each, amounting to a total of 2160 barcode scan attempts.<br><br>RESULTS: Of the 1832 successful scans performed in this evaluation, zero produced incorrect data. Five-millimeter barcodes were the slowest to scan, although only by 0.5 seconds on average. Barcodes with up to 50% fading had a 100% success rate, but success rate deteriorated beyond 60% fading. Curved barcodes took longer to scan compared with flat, but success rate deterioration was only observed at a vial diameter of 10 mm. Light conditions did not affect success rate or scan time between 500 lux and 20 lux. Conditions below 20 lux impeded the device's ability to scan successfully. Variability in scan time was observed across devices in all trials performed.<br><br>CONCLUSIONS: 2D vaccine barcoding is possible using mobile devices and is successful under the majority of conditions examined. Manufacturers utilizing 2D barcodes should take into consideration the impact of factors that limit scan success rates. Future studies should evaluate the effect of mobile barcoding on workflow and vaccine administrator acceptance.},
}
@article {pmid27336462,
year = {2016},
author = {Clare, EL and Chain, FJ and Littlefair, JE and Cristescu, ME},
title = {The effects of parameter choice on defining molecular operational taxonomic units and resulting ecological analyses of metabarcoding data.},
journal = {Genome},
volume = {59},
number = {11},
pages = {981-990},
doi = {10.1139/gen-2015-0184},
pmid = {27336462},
issn = {1480-3321},
mesh = {*Biodiversity ; Computational Biology/methods ; *DNA Barcoding, Taxonomic/methods ; Ecology ; *Ecosystem ; Electron Transport Complex IV/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {The combination of DNA barcoding and high-throughput (next-generation) sequencing (metabarcoding) provides many promises but also serious challenges. Generating a reliable comparable estimate of biodiversity remains a central challenge to the application of the technology. Many approaches have been used to turn millions of sequences into distinct taxonomic units. However, the extent to which these methods impact the outcome of simple ecological analyses is not well understood. Here we performed a simple analysis of dietary overlap by skinks and shrews on Ile Aux Aigrettes, Mauritius. We used a combination of filtering thresholds and clustering algorithms on a COI metabarcoding dataset and demonstrate that all bioinformatics parameters will have interacting effects on molecular operational taxonomic unit (MOTU) recovery rates. These effects generated estimates covering two orders of magnitude. However, the effect on a simple ecological analysis was not large and, despite the wide variation in estimates of niche overlap, the same ecological conclusion was drawn in most cases. We advise that a conservative clustering programme coupled with larger sequence divergences to define a cluster, the removal of singletons, rigorous length filtering, and stringent match criteria for Molecular Identifier tags are preferable to avoid MOTU inflation and that the same parameters be used in all comparative analyses.},
}
@article {pmid27333330,
year = {2016},
author = {Jisming-See, SW and Sing, KW and Wilson, JJ},
title = {DNA barcodes and citizen science provoke a diversity reappraisal for the "ring" butterflies of Peninsular Malaysia (Ypthima: Satyrinae: Nymphalidae: Lepidoptera).},
journal = {Genome},
volume = {59},
number = {10},
pages = {879-888},
doi = {10.1139/gen-2015-0156},
pmid = {27333330},
issn = {1480-3321},
mesh = {Animals ; *Biodiversity ; Butterflies/anatomy &amp; histology/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Malaysia ; Phenotype ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The "rings" belonging to the genus Ypthima are amongst the most common butterflies in Peninsular Malaysia. However, the species can be difficult to tell apart, with keys relying on minor and often non-discrete ring characters found on the hindwing. Seven species have been reported from Peninsular Malaysia, but this is thought to be an underestimate of diversity. DNA barcodes of 165 individuals, and wing and genital morphology, were examined to reappraise species diversity of this genus in Peninsular Malaysia. DNA barcodes collected during citizen science projects-School Butterfly Project and Peninsular Malaysia Butterfly Count-recently conducted in Peninsular Malaysia were included. The new DNA barcodes formed six groups with different Barcode Index Numbers (BINs) representing four species reported in Peninsular Malaysia. When combined with public DNA barcodes from the Barcode Of Life Datasystems, several taxonomic issues arose. We consider the taxon Y. newboldi, formerly treated as a subspecies of Y. baldus, as a distinct species. DNA barcodes also supported an earlier suggestion that Y. nebulosa is a synonym under Y. horsfieldii humei. Two BINs of the genus Ypthima comprising DNA barcodes collected during citizen science projects did not correspond to any species previously reported in Peninsular Malaysia.},
}
@article {pmid27327818,
year = {2016},
author = {Sing, KW and Wang, WZ and Wan, T and Lee, PS and Li, ZX and Chen, X and Wang, YY and Wilson, JJ},
title = {Diversity and human perceptions of bees (Hymenoptera: Apoidea) in Southeast Asian megacities.},
journal = {Genome},
volume = {59},
number = {10},
pages = {827-839},
doi = {10.1139/gen-2015-0159},
pmid = {27327818},
issn = {1480-3321},
mesh = {Animals ; Asia, Southeastern ; *Bees/classification/genetics ; *Biodiversity ; *Cities ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Geography ; Humans ; *Perception ; Population Dynamics ; Public Opinion ; Surveys and Questionnaires ; },
abstract = {Urbanization requires the conversion of natural land cover to cover with human-constructed elements and is considered a major threat to biodiversity. Bee populations, globally, are under threat; however, the effect of rapid urban expansion in Southeast Asia on bee diversity has not been investigated. Given the pressing issues of bee conservation and urbanization in Southeast Asia, coupled with complex factors surrounding human-bee coexistence, we investigated bee diversity and human perceptions of bees in four megacities. We sampled bees and conducted questionnaires at three different site types in each megacity: a botanical garden, central business district, and peripheral suburban areas. Overall, the mean species richness and abundance of bees were significantly higher in peripheral suburban areas than central business districts; however, there were no significant differences in the mean species richness and abundance between botanical gardens and peripheral suburban areas or botanical gardens and central business districts. Urban residents were unlikely to have seen bees but agreed that bees have a right to exist in their natural environment. Residents who did notice and interact with bees, even though being stung, were more likely to have positive opinions towards the presence of bees in cities.},
}
@article {pmid27323800,
year = {2016},
author = {Nassar, AF and Wisnewski, AV and Raddassi, K},
title = {Progress in automation of mass cytometry barcoding for drug development.},
journal = {Bioanalysis},
volume = {8},
number = {14},
pages = {1429-1435},
doi = {10.4155/bio-2016-0135},
pmid = {27323800},
issn = {1757-6199},
support = {R01 OH010941/OH/NIOSH CDC HHS/United States ; },
mesh = {Animals ; Cytophotometry/instrumentation/*methods ; Drug Discovery/instrumentation/*methods ; High-Throughput Screening Assays/instrumentation/*methods ; Humans ; Mass Spectrometry/instrumentation/*methods ; Palladium/chemistry ; },
}
@article {pmid27323714,
year = {2016},
author = {Uesugi, T and Nakano, M and Selosse, MA and Obase, K and Matsuda, Y},
title = {Pyrola japonica, a partially mycoheterotrophic Ericaceae, has mycorrhizal preference for russulacean fungi in central Japan.},
journal = {Mycorrhiza},
volume = {26},
number = {8},
pages = {819-829},
pmid = {27323714},
issn = {1432-1890},
mesh = {Basidiomycota/*classification/physiology ; Cloning, Molecular ; Japan ; Mycorrhizae/*classification/physiology ; Phylogeny ; Pyrola/*microbiology ; },
abstract = {Mycorrhizal symbiosis often displays low specificity, except for mycoheterotrophic plants that obtain carbon from their mycorrhizal fungi and often have higher specificity to certain fungal taxa. Partially mycoheterotrophic (or mixotrophic, MX) plant species tend to have a larger diversity of fungal partners, e.g., in the genus Pyrola (Monotropoideae, Ericaceae). Preliminary evidence however showed that the Japanese Pyrola japonica has preference for russulacean fungi based on direct sequencing of the fungal internal transcribed spacer (ITS) region from a single site. The present study challenges this conclusion using (1) sampling of P. japonica in different Japanese regions and forest types and (2) fungal identification by ITS cloning. Plants were sampled from eight sites in three regions, in one of which the fungal community on tree ectomycorrhizal (ECM) tips surrounding P. japonica was also analyzed. In all, 1512 clone sequences were obtained successfully from 35 P. japonica plants and 137 sequences from ECM communities. These sequences were collectively divided into 74 molecular operational taxonomic units (MOTUs) (51 and 33 MOTUs, respectively). MOTUs from P. japonica involved 36 ECM taxa (96 % of all clones), and 17 of these were Russula spp. (76.2 % of all clones), which colonized 33 of the 35 sampled plants. The MOTU composition significantly differed between P. japonica and ECM tips, although shared species represented 26.3 % of the ECM tips community in abundance. This suggests that P. japonica has a preference for russulacean fungi.},
}
@article {pmid27322652,
year = {2016},
author = {Bell, KL and de Vere, N and Keller, A and Richardson, RT and Gous, A and Burgess, KS and Brosi, BJ},
title = {Pollen DNA barcoding: current applications and future prospects.},
journal = {Genome},
volume = {59},
number = {9},
pages = {629-640},
doi = {10.1139/gen-2015-0200},
pmid = {27322652},
issn = {1480-3321},
mesh = {Allergens/genetics/immunology ; Biodiversity ; Computational Biology/methods ; *DNA Barcoding, Taxonomic ; *DNA, Plant ; Databases, Genetic ; Food Quality ; Genetic Markers ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Plants/*classification/*genetics ; Pollen/*genetics ; },
abstract = {Identification of the species origin of pollen has many applications, including assessment of plant-pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and has few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. In this paper, we review the nascent field of pollen DNA barcoding and discuss potential new applications of this technology, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications.},
}
@article {pmid27320797,
year = {2016},
author = {Kim, SM and Wang, Y and Nabavi, N and Liu, Y and Correia, MA},
title = {Hepatic cytochromes P450: structural degrons and barcodes, posttranslational modifications and cellular adapters in the ERAD-endgame.},
journal = {Drug metabolism reviews},
volume = {48},
number = {3},
pages = {405-433},
pmid = {27320797},
issn = {1097-9883},
support = {P41 GM103481/GM/NIGMS NIH HHS/United States ; R01 GM044037/GM/NIGMS NIH HHS/United States ; R01 DK026506/DK/NIDDK NIH HHS/United States ; P30 DK026743/DK/NIDDK NIH HHS/United States ; R56 DK026506/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Cytochrome P-450 Enzyme System/*metabolism ; *Endoplasmic Reticulum-Associated Degradation ; Humans ; Liver/cytology/*enzymology/*metabolism ; Lysosomes/metabolism ; Models, Biological ; *Proteolysis ; Receptors, Autocrine Motility Factor/metabolism ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitination ; },
abstract = {The endoplasmic reticulum (ER)-anchored hepatic cytochromes P450 (P450s) are enzymes that metabolize endo- and xenobiotics i.e. drugs, carcinogens, toxins, natural and chemical products. These agents modulate liver P450 content through increased synthesis or reduction via inactivation and/or proteolytic degradation, resulting in clinically significant drug-drug interactions. P450 proteolytic degradation occurs via ER-associated degradation (ERAD) involving either of two distinct routes: Ubiquitin (Ub)-dependent 26S proteasomal degradation (ERAD/UPD) or autophagic lysosomal degradation (ERAD/ALD). CYP3A4, the major human liver/intestinal P450, and the fast-turnover CYP2E1 species are degraded via ERAD/UPD entailing multisite protein phosphorylation and subsequent ubiquitination by gp78 and CHIP E3 Ub-ligases. We are gaining insight into the nature of the structural determinants involved in CYP3A4 and CYP2E1 molecular recognition in ERAD/UPD [i.e. K48-linked polyUb chains and linear and/or "conformational" phosphodegrons consisting either of consecutive sequences on surface loops and/or disordered regions, or structurally-assembled surface clusters of negatively charged acidic (Asp/Glu) and phosphorylated (Ser/Thr) residues, within or vicinal to which, Lys-residues are targeted for ubiquitination]. Structural inspection of select human liver P450s reveals that such linear or conformational phosphodegrons may indeed be a common P450-ERAD/UPD feature. By contrast, although many P450s such as the slow-turnover CYP2E1 species and rat liver CYP2B1 and CYP2C11 are degraded via ERAD/ALD, little is known about the mechanism of their ALD-targeting. On the basis of our current knowledge of ALD-substrate targeting, we propose a tripartite conjunction of K63-linked Ub-chains, P450 structural "LIR" motifs and selective cellular "cargo receptors" as plausible P450-ALD determinants.},
}
@article {pmid27317884,
year = {2016},
author = {Łukomska-Kowalczyk, M and Karnkowska, A and Krupska, M and Milanowski, R and Zakryś, B},
title = {DNA barcoding in autotrophic euglenids: evaluation of COI and 18s rDNA.},
journal = {Journal of phycology},
volume = {52},
number = {6},
pages = {951-960},
doi = {10.1111/jpy.12439},
pmid = {27317884},
issn = {1529-8817},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Protozoan/genetics ; Electron Transport Complex IV/genetics ; Euglenida/*classification/genetics ; Protozoan Proteins/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; },
abstract = {Autotrophic euglenids (Euglenophyceae) are a common and abundant group of microbial eukaryotes in freshwater habitats. They have a limited number of features, which can be observed using light microscopy, thus species identification is often problematic. Establishing a barcode for this group is therefore an important step toward the molecular identification of autotrophic euglenids. Based on the literature, we selected verified species and used a plethora of available methods to validate two molecular markers: COI and 18S rDNA (the whole sequence and three fragments separately) as potential DNA barcodes. Analyses of the COI gene were performed based on the data set of 43 sequences (42 obtained in this study) representing 24 species and the COI gene was discarded as a DNA barcode mainly due to a lack of universal primer sites. For 18S rDNA analyses we used a data set containing 263 sequences belonging to 86 taxonomically verified species. We demonstrated that the whole 18S rDNA is too long to be a useful marker, but from the three shorter analyzed variable regions we recommend variable regions V2V3 and V4 of 18S rDNA as autotrophic euglenid barcodes due to their high efficiency (above 95% and 90%, respectively).},
}
@article {pmid27317177,
year = {2016},
author = {Wang, W and Bartholomae, CC and Gabriel, R and Deichmann, A and Schmidt, M},
title = {The LAM-PCR Method to Sequence LV Integration Sites.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1448},
number = {},
pages = {107-120},
doi = {10.1007/978-1-4939-3753-0_9},
pmid = {27317177},
issn = {1940-6029},
mesh = {*Gene Transfer Techniques ; Genetic Therapy/methods ; Genetic Vectors ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Lentivirus/*genetics ; Polymerase Chain Reaction/methods ; Virus Integration/*genetics ; },
abstract = {Integrating viral gene transfer vectors are commonly used gene delivery tools in clinical gene therapy trials providing stable integration and continuous gene expression of the transgene in the treated host cell. However, integration of the reverse-transcribed vector DNA into the host genome is a potentially mutagenic event that may directly contribute to unwanted side effects. A comprehensive and accurate analysis of the integration site (IS) repertoire is indispensable to study clonality in transduced cells obtained from patients undergoing gene therapy and to identify potential in vivo selection of affected cell clones. To date, next-generation sequencing (NGS) of vector-genome junctions allows sophisticated studies on the integration repertoire in vitro and in vivo. We have explored the use of the Illumina MiSeq Personal Sequencer platform to sequence vector ISs amplified by non-restrictive linear amplification-mediated PCR (nrLAM-PCR) and LAM-PCR. MiSeq-based high-quality IS sequence retrieval is accomplished by the introduction of a double-barcode strategy that substantially minimizes the frequency of IS sequence collisions compared to the conventionally used single-barcode protocol. Here, we present an updated protocol of (nr)LAM-PCR for the analysis of lentiviral IS using a double-barcode system and followed by deep sequencing using the MiSeq device.},
}
@article {pmid27314400,
year = {2016},
author = {Sing, KW and Dong, H and Wang, WZ and Wilson, JJ},
title = {Can butterflies cope with city life? Butterfly diversity in a young megacity in southern China.},
journal = {Genome},
volume = {59},
number = {9},
pages = {751-761},
doi = {10.1139/gen-2015-0192},
pmid = {27314400},
issn = {1480-3321},
mesh = {Animals ; *Biodiversity ; *Butterflies/classification/genetics ; China ; *Cities ; Ecosystem ; *Life Style ; Urbanization ; },
abstract = {During 30 years of unprecedented urbanization, plant diversity in Shenzhen, a young megacity in southern China, has increased dramatically. Although strongly associated with plant diversity, butterfly diversity generally declines with urbanization, but this has not been investigated in Shenzhen. Considering the speed of urbanization in Shenzhen and the large number of city parks, we investigated butterfly diversity in Shenzhen parks. We measured butterfly species richness in four microhabitats (groves, hedges, flowerbeds, and unmanaged areas) across 10 parks and examined the relationship with three park variables: park age, park size, and distance from the central business district. Butterflies were identified based on wing morphology and DNA barcoding. We collected 1933 butterflies belonging to 74 species from six families; 20% of the species were considered rare. Butterfly species richness showed weak negative correlations with park age and distance from the central business district, but the positive correlation with park size was statistically significant (p = 0.001). Among microhabitat types, highest species richness was recorded in unmanaged areas. Our findings are consistent with others in suggesting that to promote urban butterfly diversity it is necessary to make parks as large as possible and to set aside areas for limited management. In comparison to neighbouring cities, Shenzhen parks have high butterfly diversity.},
}
@article {pmid27314158,
year = {2016},
author = {Geiger, MF and Astrin, JJ and Borsch, T and Burkhardt, U and Grobe, P and Hand, R and Hausmann, A and Hohberg, K and Krogmann, L and Lutz, M and Monje, C and Misof, B and Morinière, J and Müller, K and Pietsch, S and Quandt, D and Rulik, B and Scholler, M and Traunspurger, W and Haszprunar, G and Wägele, W},
title = {How to tackle the molecular species inventory for an industrialized nation-lessons from the first phase of the German Barcode of Life initiative GBOL (2012-2015).},
journal = {Genome},
volume = {59},
number = {9},
pages = {661-670},
doi = {10.1139/gen-2015-0185},
pmid = {27314158},
issn = {1480-3321},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; *Databases, Genetic ; Developed Countries ; Germany ; Guideline Adherence ; Humans ; International Cooperation ; Libraries ; Reproducibility of Results ; },
abstract = {Biodiversity loss is mainly driven by human activity. While concern grows over the fate of hot spots of biodiversity, contemporary species losses still prevail in industrialized nations. Therefore, strategies were formulated to halt or reverse the loss, driven by evidence for its value for ecosystem services. Maintenance of the latter through conservation depends on correctly identified species. To this aim, the German Federal Ministry of Education and Research is funding the GBOL project, a consortium of natural history collections, botanic gardens, and universities working on a barcode reference database for the country's fauna and flora. Several noticeable findings could be useful for future campaigns: (i) validating taxon lists to serve as a taxonomic backbone is time-consuming, but without alternative; (ii) offering financial incentives to taxonomic experts, often citizen scientists, is indispensable; (iii) completion of the libraries for widespread species enables analyses of environmental samples, but the process may not hold pace with technological advancements; (iv) discoveries of new species are among the best stories for the media; (v) a commitment to common data standards and repositories is needed, as well as transboundary cooperation between nations; (vi) after validation, all data should be published online via the BOLD to make them searchable for external users and to allow cross-checking with data from other countries.},
}
@article {pmid27310720,
year = {2016},
author = {Fahner, NA and Shokralla, S and Baird, DJ and Hajibabaei, M},
title = {Large-Scale Monitoring of Plants through Environmental DNA Metabarcoding of Soil: Recovery, Resolution, and Annotation of Four DNA Markers.},
journal = {PloS one},
volume = {11},
number = {6},
pages = {e0157505},
pmid = {27310720},
issn = {1932-6203},
mesh = {Alberta ; DNA Barcoding, Taxonomic ; DNA, Intergenic/*genetics ; DNA, Plant/*genetics ; Databases, Genetic ; Ecosystem ; Genetic Markers ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Molecular Sequence Annotation ; *Phylogeny ; Plants/classification/*genetics ; Pollen/genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; Seeds/genetics ; Soil/chemistry ; },
abstract = {In a rapidly changing world we need methods to efficiently assess biodiversity in order to monitor ecosystem trends. Ecological monitoring often uses plant community composition to infer quality of sites but conventional aboveground surveys only capture a snapshot of the actively growing plant diversity. Environmental DNA (eDNA) extracted from soil samples, however, can include taxa represented by both active and dormant tissues, seeds, pollen, and detritus. Analysis of this eDNA through DNA metabarcoding provides a more comprehensive view of plant diversity at a site from a single assessment but it is not clear which DNA markers are best used to capture this diversity. Sequence recovery, annotation, and sequence resolution among taxa were evaluated for four established DNA markers (matK, rbcL, ITS2, and the trnL P6 loop) in silico using database sequences and in situ using high throughput sequencing of 35 soil samples from a remote boreal wetland. Overall, ITS2 and rbcL are recommended for DNA metabarcoding of vascular plants from eDNA when not using customized or geographically restricted reference databases. We describe a new framework for evaluating DNA metabarcodes and, contrary to existing assumptions, we found that full length DNA barcode regions could outperform shorter markers for surveying plant diversity from soil samples. By using current DNA barcoding markers rbcL and ITS2 for plant metabarcoding, we can take advantage of existing resources such as the growing DNA barcode database. Our work establishes the value of standard DNA barcodes for soil plant eDNA analysis in ecological investigations and biomonitoring programs and supports the collaborative development of DNA barcoding and metabarcoding.},
}
@article {pmid27308864,
year = {2016},
author = {Brankovics, B and Zhang, H and van Diepeningen, AD and van der Lee, TA and Waalwijk, C and de Hoog, GS},
title = {GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research.},
journal = {PLoS computational biology},
volume = {12},
number = {6},
pages = {e1004753},
pmid = {27308864},
issn = {1553-7358},
mesh = {Algorithms ; Computational Biology ; Computer Simulation ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; Fusarium/genetics ; Genome, Fungal ; Genome, Mitochondrial ; Genomics/*methods/statistics &amp; numerical data ; High-Throughput Nucleotide Sequencing/statistics &amp; numerical data ; *Software ; },
abstract = {GRAbB (Genomic Region Assembly by Baiting) is a new program that is dedicated to assemble specific genomic regions from NGS data. This approach is especially useful when dealing with multi copy regions, such as mitochondrial genome and the rDNA repeat region, parts of the genome that are often neglected or poorly assembled, although they contain interesting information from phylogenetic or epidemiologic perspectives, but also single copy regions can be assembled. The program is capable of targeting multiple regions within a single run. Furthermore, GRAbB can be used to extract specific loci from NGS data, based on homology, like sequences that are used for barcoding. To make the assembly specific, a known part of the region, such as the sequence of a PCR amplicon or a homologous sequence from a related species must be specified. By assembling only the region of interest, the assembly process is computationally much less demanding and may lead to assemblies of better quality. In this study the different applications and functionalities of the program are demonstrated such as: exhaustive assembly (rDNA region and mitochondrial genome), extracting homologous regions or genes (IGS, RPB1, RPB2 and TEF1a), as well as extracting multiple regions within a single run. The program is also compared with MITObim, which is meant for the exhaustive assembly of a single target based on a similar query sequence. GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs. The program is available with explanatory documentation at https://github.com/b-brankovics/grabb. GRAbB has been tested on Ubuntu (12.04 and 14.04), Fedora (23), CentOS (7.1.1503) and Mac OS X (10.7). Furthermore, GRAbB is available as a docker repository: brankovics/grabb (https://hub.docker.com/r/brankovics/grabb/).},
}
@article {pmid27306741,
year = {2016},
author = {Ramirez, LM and He, M and Mailloux, S and George, J and Wang, J},
title = {Microparticles: Facile and High-Throughput Synthesis of Functional Microparticles with Quick Response Codes (Small 24/2016).},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {12},
number = {24},
pages = {3258},
doi = {10.1002/smll.201670118},
pmid = {27306741},
issn = {1613-6829},
mesh = {*Cell Phone ; Cell-Derived Microparticles ; Electronic Data Processing ; },
abstract = {Microparticles carrying quick response (QR) barcodes are fabricated by J. Wang and co-workers on page 3259, using a massive coding of dissociated elements (MiCODE) technology. Each microparticle can bear a special custom-designed QR code that enables encryption or tagging with unlimited multiplexity, and the QR code can be easily read by cellphone applications. The utility of MiCODE particles in multiplexed DNA detection and microtagging for anti-counterfeiting is explored.},
}
@article {pmid27306051,
year = {2016},
author = {Gill, BA and Kondratieff, BC and Casner, KL and Encalada, AC and Flecker, AS and Gannon, DG and Ghalambor, CK and Guayasamin, JM and Poff, NL and Simmons, MP and Thomas, SA and Zamudio, KR and Funk, WC},
title = {Cryptic species diversity reveals biogeographic support for the 'mountain passes are higher in the tropics' hypothesis.},
journal = {Proceedings. Biological sciences},
volume = {283},
number = {1832},
pages = {},
pmid = {27306051},
issn = {1471-2954},
mesh = {Animals ; *Biodiversity ; Climate ; Colorado ; DNA Barcoding, Taxonomic ; Ecuador ; Insecta/*classification ; Species Specificity ; },
abstract = {The 'mountain passes are higher in the tropics' (MPHT) hypothesis posits that reduced climate variability at low latitudes should select for narrower thermal tolerances, lower dispersal and smaller elevational ranges compared with higher latitudes. These latitudinal differences could increase species richness at low latitudes, but that increase may be largely cryptic, because physiological and dispersal traits isolating populations might not correspond to morphological differences. Yet previous tests of the MPHT hypothesis have not addressed cryptic diversity. We use integrative taxonomy, combining morphology (6136 specimens) and DNA barcoding (1832 specimens) to compare the species richness, cryptic diversity and elevational ranges of mayflies (Ephemeroptera) in the Rocky Mountains (Colorado; approx. 40°N) and the Andes (Ecuador; approx. 0°). We find higher species richness and smaller elevational ranges in Ecuador than Colorado, but only after quantifying and accounting for cryptic diversity. The opposite pattern is found when comparing diversity based on morphology alone, underscoring the importance of uncovering cryptic species to understand global biodiversity patterns.},
}
@article {pmid27305769,
year = {2016},
author = {An, JH and Lee, KJ and Choi, JW},
title = {Gold Nanoparticles-Based Barcode Analysis for Detection of Norepinephrine.},
journal = {Journal of biomedical nanotechnology},
volume = {12},
number = {2},
pages = {357-365},
doi = {10.1166/jbn.2016.2185},
pmid = {27305769},
issn = {1550-7033},
mesh = {Annexin A5/metabolism ; Apoptosis ; Cell Line, Tumor ; Fluorescein-5-isothiocyanate/metabolism ; Gold/*chemistry ; Humans ; Metal Nanoparticles/*chemistry/ultrastructure ; Molecular Probes/chemical synthesis/chemistry ; Norepinephrine/*analysis ; Nucleic Acid Amplification Techniques/*methods ; Propidium/metabolism ; Reproducibility of Results ; Spectrum Analysis, Raman ; },
abstract = {Nanotechnology-based bio-barcode amplification analysis offers an innovative approach for detecting neurotransmitters. We evaluated the efficacy of this method for detecting norepinephrine in normal and oxidative-stress damaged dopaminergic cells. Our approach use a combination of DNA barcodes and bead-based immunoassays for detecting neurotransmitters with surface-enhanced Raman spectroscopy (SERS), and provides polymerase chain reaction (PCR)-like sensitivity. This method relies on magnetic Dynabeads containing antibodies and nanoparticles that are loaded both with DNA barcords and with antibodies that can sandwich the target protein captured by the Dynabead-bound antibodies. The aggregate sandwich structures are magnetically separated from the solution and treated to remove the conjugated barcode DNA. The DNA barcodes are then identified by SERS and PCR analysis. The concentration of norepinephrine in dopaminergic cells can be readily detected using the bio-barcode assay, which is a rapid, high-throughput screening tool for detecting neurotransmitters.},
}
@article {pmid27304905,
year = {2016},
author = {Costion, CM and Kress, WJ and Crayn, DM},
title = {DNA Barcodes Confirm the Taxonomic and Conservation Status of a Species of Tree on the Brink of Extinction in the Pacific.},
journal = {PloS one},
volume = {11},
number = {6},
pages = {e0155118},
pmid = {27304905},
issn = {1932-6203},
mesh = {Conservation of Natural Resources/*methods ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/chemistry/genetics ; Endangered Species ; Extinction, Biological ; Genome, Plastid/genetics ; Geography ; Pacific Ocean ; Palau ; Phylogeny ; Population Density ; Ribulose-Bisphosphate Carboxylase/genetics ; Rubiaceae/anatomy &amp; histology/classification/*genetics ; Sequence Analysis, DNA ; Species Specificity ; Trees/anatomy &amp; histology/classification/*genetics ; },
abstract = {The taxonomic status of a single island, narrow range endemic plant species from Palau, Micronesia (Timonius salsedoi) was assessed using DNA barcode markers, additional plastid loci, and morphology in order to verify its conservation status. DNA barcode loci distinguished T. salsedoi from all other Timonius species sampled from Palau, and were supported by sequence data from the atpB-rbcL intergenic spacer region. Timonius salsedoi was only known from two mature individual trees in 2012. Due to its extremely narrow range and population size, it had previously been recommended to be listed as Critically Endangered Status under three separate IUCN Criteria. In 2014 a second survey of the population following a typhoon revealed that the only two known trees had died suggesting that this species may now be extinct. Comprehensive follow up surveys of suitable habitat for this species are urgently required.},
}
@article {pmid27304877,
year = {2016},
author = {Bilgin, R and Ebeoğlu, N and İnak, S and Kırpık, MA and Horns, JJ and Şekercioğlu, &#xc7;H},
title = {DNA Barcoding of Birds at a Migratory Hotspot in Eastern Turkey Highlights Continental Phylogeographic Relationships.},
journal = {PloS one},
volume = {11},
number = {6},
pages = {e0154454},
pmid = {27304877},
issn = {1932-6203},
mesh = {Animal Migration ; Animals ; Birds/classification/*genetics/physiology ; Climate Change ; DNA Barcoding, Taxonomic/*methods ; *Ecosystem ; Electron Transport Complex IV/genetics ; Gene Frequency ; *Genetic Variation ; Phylogeny ; Phylogeography ; Protein Subunits/genetics ; Rivers ; Seasons ; Species Specificity ; Turkey ; Wetlands ; },
abstract = {The combination of habitat loss, climate change, direct persecution, introduced species and other components of the global environmental crisis has resulted in a rapid loss of biodiversity, including species, population and genetic diversity. Birds, which inhabit a wide spectrum of different habitat types, are particularly sensitive to and indicative of environmental changes. The Caucasus endemic bird area, part of which covers northeastern Turkey, is one of the world's key regions harboring a unique bird community threatened with habitat loss. More than 75% of all bird species native to Turkey have been recorded in this region, in particular along the Kars-Iğdır migratory corridor, stopover, wintering and breeding sites along the Aras River, whose wetlands harbor at least 264 bird species. In this study, DNA barcoding technique was used for evaluating the genetic diversity of land bird species of Aras River Bird Paradise at the confluence of Aras River and Iğdır Plains key biodiversity areas. Seventy three COI sequences from 33 common species and 26 different genera were newly generated and used along with 301 sequences that were retrieved from the Barcoding of Life Database (BOLD). Using the sequences obtained in this study, we made global phylogeographic comparisons to define four categories of species, based on barcoding suitability, intraspecific divergence and taxonomy. Our findings indicate that the landbird community of northeastern Turkey has a genetical signature mostly typical of northern Palearctic bird communities while harboring some unique variations. The study also provides a good example of how DNA barcoding can build upon its primary mission of species identification and use available data to integrate genetic variation investigated at the local scale into a global framework. However, the rich bird community of the Aras River wetlands is highly threatened with the imminent construction of the Tuzluca Dam by the government.},
}
@article {pmid27298183,
year = {2016},
author = {Zhang, Z and Zhang, Y and Zhang, Z and Yao, H and Liu, H and Zhang, B and Liao, Y},
title = {Comparative Analysis of DNA Barcoding and HPLC Fingerprint to Trace Species of Phellodendri Cortex, an Important Traditional Chinese Medicine from Multiple Sources.},
journal = {Biological &amp; pharmaceutical bulletin},
volume = {39},
number = {8},
pages = {1325-1330},
doi = {10.1248/bpb.b16-00210},
pmid = {27298183},
issn = {1347-5215},
mesh = {Chromatography, High Pressure Liquid ; DNA Barcoding, Taxonomic ; DNA, Intergenic/genetics ; DNA, Plant/genetics ; Medicine, Chinese Traditional ; *Phellodendron/chemistry/classification/genetics ; Plant Bark/chemistry/classification/genetics ; },
abstract = {Phellodendri Cortex is derived from the dried barks of Phellodendron genus species, has been extensively used in traditional Chinese medicine. The cortex is divided into two odorless crude drugs Guanhuangbo and Huangbo. Historically, it has been difficult to distinguish their identities due to a lack of identification methods. This study was executed to confirm the identity and to ensure the species traceability of Phellodendri Cortex. In the current study, analysis is based on the internal transcribed spacer (ITS) and psbA-trnH intergenic spacer (psbA-trnH) barcodes and HPLC fingerprint was carried out to guarantee the species traceability of Guanhuangbo and Huangbo. DNA barcoding data successfully identified the three plants of the Phellodendron genus species by ITS+psbA-trnH, with the ability to distinguish the species origin of Huangbo. Moreover, the psbA-trnH data distinguished Guanhuangbo and Huangbo except to trace species. The HPLC fingerprint data showed that Guanhuangbo was clearly different from Huangbo, but there was no difference between the two origins of Huangbo. Additionally, the result of hierarchical clustering analysis, based on chlorogenic acid, phellodendrine, magnoflorine, jatrorrhizine, palmatine and berberine, was consistent with the HPLC fingerprint analysis. These results show that DNA barcoding and HPLC fingerprint can discriminate Guanhuangbo and Huangbo. However, DNA barcoding is more powerful than HPLC fingerprint for species traceability in the identification of related species that are genetically similar. DNA barcoding is a useful scientific tool to accurately confirm the identities of medicinal materials from multiple sources.},
}
@article {pmid27296980,
year = {2016},
author = {Somervuo, P and Koskela, S and Pennanen, J and Henrik Nilsson, R and Ovaskainen, O},
title = {Unbiased probabilistic taxonomic classification for DNA barcoding.},
journal = {Bioinformatics (Oxford, England)},
volume = {32},
number = {19},
pages = {2920-2927},
doi = {10.1093/bioinformatics/btw346},
pmid = {27296980},
issn = {1367-4811},
mesh = {*DNA Barcoding, Taxonomic ; *Phylogeny ; *Software ; },
abstract = {MOTIVATION: When targeted to a barcoding region, high-throughput sequencing can be used to identify species or operational taxonomical units from environmental samples, and thus to study the diversity and structure of species communities. Although there are many methods which provide confidence scores for assigning taxonomic affiliations, it is not straightforward to translate these values to unbiased probabilities. We present a probabilistic method for taxonomical classification (PROTAX) of DNA sequences. Given a pre-defined taxonomical tree structure that is partially populated by reference sequences, PROTAX decomposes the probability of one to the set of all possible outcomes. PROTAX accounts for species that are present in the taxonomy but that do not have reference sequences, the possibility of unknown taxonomical units, as well as mislabeled reference sequences. PROTAX is based on a statistical multinomial regression model, and it can utilize any kind of sequence similarity measures or the outputs of other classifiers as predictors.<br><br>RESULTS: We demonstrate the performance of PROTAX by using as predictors the output from BLAST, the phylogenetic classification software TIPP, and the RDP classifier. We show that PROTAX improves the predictions of the baseline implementations of TIPP and RDP classifiers, and that it is able to combine complementary information provided by BLAST and TIPP, resulting in accurate and unbiased classifications even with very challenging cases such as 50% mislabeling of reference sequences.<br><br>Perl/R implementation of PROTAX is available at http://www.helsinki.fi/science/metapop/Software.htm<br><br>CONTACT: panu.somervuo@helsinki.fi<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid27293094,
year = {2016},
author = {Bigildeev, AE and Cornils, K and Aranyossy, T and Sats, NV and Petinati, NA and Shipounova, IN and Surin, VL and Pshenichnikova, OS and Riecken, K and Fehse, B and Drize, NI},
title = {Investigation of the Mesenchymal Stem Cell Compartment by Means of a Lentiviral Barcode Library.},
journal = {Biochemistry. Biokhimiia},
volume = {81},
number = {4},
pages = {373-381},
doi = {10.1134/S0006297916040076},
pmid = {27293094},
issn = {1608-3040},
mesh = {Animals ; Bone Marrow Cells/cytology ; Cells, Cultured ; Female ; Gene Library ; Lentivirus/*genetics ; Mesenchymal Stem Cells/cytology/*metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Inbred CBA ; Plasmids/genetics/metabolism ; Polymerase Chain Reaction ; },
abstract = {The hematopoietic bone marrow microenvironment is formed by proliferation and differentiation of mesenchymal stem cells (MSCs). The MSC compartment has been less studied than the hematopoietic stem cell compartment. To characterize the structure of the MSC compartment, it is necessary to trace the fate of distinct mesenchymal cells. To do so, mesenchymal progenitors need to be marked at the single-cell level. A method for individual marking of normal and cancer stem cells based on genetic "barcodes" has been developed for the last 10 years. Such approach has not yet been applied to MSCs. The aim of this study was to evaluate the possibility of using such barcoding strategy to mark MSCs and their descendants, colony-forming units of fibroblasts (CFU-Fs). Adherent cell layers (ACLs) of murine long-term bone marrow cultures (LTBMCs) were transduced with a lentiviral library with barcodes consisting of 32 + 3 degenerate nucleotides. Infected ACLs were suspended, and CFU-F derived clones were obtained. DNA was isolated from each individual colony, and barcodes were analyzed in marked CFU-F-derived colonies by means of conventional polymerase chain reaction and Sanger sequencing. Barcodes were identified in 154 marked colonies. All barcodes appeared to be unique: there were no two distinct colonies bearing the same barcode. It was shown that ACLs included CFU-Fs with different proliferative potential. MSCs are located higher in the hierarchy of mesenchymal progenitors than CFU-Fs, so the presented data indicate that MSCs proliferate rarely in LTBMCs. A method of stable individual marking and comparing the markers in mesenchymal progenitor cells has been developed in this work. We show for the first time that a barcoded library of lentiviruses is an effective tool for studying stromal progenitor cells.},
}
@article {pmid27292571,
year = {2017},
author = {Pentinsaari, M and Vos, R and Mutanen, M},
title = {Algorithmic single-locus species delimitation: effects of sampling effort, variation and nonmonophyly in four methods and 1870 species of beetles.},
journal = {Molecular ecology resources},
volume = {17},
number = {3},
pages = {393-404},
doi = {10.1111/1755-0998.12557},
pmid = {27292571},
issn = {1755-0998},
mesh = {Animals ; Biodiversity ; Cluster Analysis ; Coleoptera/*classification ; *DNA Barcoding, Taxonomic ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The vast number of undescribed species and the fast rate of biodiversity loss call for new approaches to speed up alpha taxonomy. A plethora of methods for delimiting species or operational taxonomic units (OTUs) based on sequence data have been published in recent years. We test the ability of four delimitation methods (BIN, ABGD, GMYC, PTP) to reproduce established species boundaries on a carefully curated DNA barcode data set of 1870 North European beetle species. We also explore how sampling effort, intraspecific variation, nearest neighbour divergence and nonmonophyly affect the OTU delimitations. All methods produced approximately 90% identity between species and OTUs. The effects of variation and sampling differed between methods. ABGD was sensitive to singleton sequences, while GMYC showed tendencies for oversplitting. The best fit between species and OTUs was achieved using simple rules to find consensus between discordant OTU delimitations. Using several approaches simultaneously allows the methods to compensate for each other's weaknesses. Barcode-based OTU-picking is an efficient way to delimit putative species from large data sets where the use of more sophisticated methods based on multilocus or genomic data is not feasible.},
}
@article {pmid27292284,
year = {2017},
author = {Kocher, A and Gantier, JC and Gaborit, P and Zinger, L and Holota, H and Valiere, S and Dusfour, I and Girod, R and Bañuls, AL and Murienne, J},
title = {Vector soup: high-throughput identification of Neotropical phlebotomine sand flies using metabarcoding.},
journal = {Molecular ecology resources},
volume = {17},
number = {2},
pages = {172-182},
doi = {10.1111/1755-0998.12556},
pmid = {27292284},
issn = {1755-0998},
mesh = {Animals ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; French Guiana ; *Insect Vectors ; Metagenomics/*methods ; Phylogeny ; Psychodidae/*classification/*genetics/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Phlebotomine sand flies are haematophagous dipterans of primary medical importance. They represent the only proven vectors of leishmaniasis worldwide and are involved in the transmission of various other pathogens. Studying the ecology of sand flies is crucial to understand the epidemiology of leishmaniasis and further control this disease. A major limitation in this regard is that traditional morphological-based methods for sand fly species identifications are time-consuming and require taxonomic expertise. DNA metabarcoding holds great promise in overcoming this issue by allowing the identification of multiple species from a single bulk sample. Here, we assessed the reliability of a short insect metabarcode located in the mitochondrial 16S rRNA for the identification of Neotropical sand flies, and constructed a reference database for 40 species found in French Guiana. Then, we conducted a metabarcoding experiment on sand flies mixtures of known content and showed that the method allows an accurate identification of specimens in pools. Finally, we applied metabarcoding to field samples caught in a 1-ha forest plot in French Guiana. Besides providing reliable molecular data for species-level assignations of phlebotomine sand flies, our study proves the efficiency of metabarcoding based on the mitochondrial 16S rRNA for studying sand fly diversity from bulk samples. The application of this high-throughput identification procedure to field samples can provide great opportunities for vector monitoring and eco-epidemiological studies.},
}
@article {pmid27288478,
year = {2016},
author = {Mutanen, M and Kivelä, SM and Vos, RA and Doorenweerd, C and Ratnasingham, S and Hausmann, A and Huemer, P and Dincă, V and van Nieukerken, EJ and Lopez-Vaamonde, C and Vila, R and Aarvik, L and Decaëns, T and Efetov, KA and Hebert, PD and Johnsen, A and Karsholt, O and Pentinsaari, M and Rougerie, R and Segerer, A and Tarmann, G and Zahiri, R and Godfray, HC},
title = {Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera.},
journal = {Systematic biology},
volume = {65},
number = {6},
pages = {1024-1040},
pmid = {27288478},
issn = {1076-836X},
mesh = {Animals ; Bias ; Classification/*methods ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; Genes, Mitochondrial ; Lepidoptera/*classification/*genetics ; *Phylogeny ; },
abstract = {The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service "Monophylizer" to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6%) of the detected cases of non-monophyly. Furthermore, we observed that in about 20% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric-conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors.},
}
@article {pmid27279702,
year = {2016},
author = {Yu, X and Xie, Z and Wu, J and Tao, J and Xu, X},
title = {DNA Barcoding Identification of Kadsurae Caulis and Spatholobi Caulis Based on Internal Transcribed Spacer 2 Region and Secondary Structure Prediction.},
journal = {Pharmacognosy magazine},
volume = {12},
number = {Suppl 2},
pages = {S165-9},
pmid = {27279702},
issn = {0973-1296},
abstract = {BACKGROUND: Kadsurae Caulis and Spatholobi Caulis have very similar Chinese names. Their commodities were hard to distinguish because their stems were very alike after dried and processed. These two herbal drugs were often mixed in clinical use.<br><br>OBJECTIVE: Authenticity assurance is crucial for quality control of herbal drugs. Therefore, it is essential to establish a method for identifying the two herbs.<br><br>MATERIALS AND METHODS: In this paper, we used the DNA barcoding technology, based on the internal transcribed spacer 2 (ITS2) regions, to differentiate Kadsurae Caulis and Spatholobi Caulis.<br><br>RESULTS: The ITS2 of these two herbs were very different. They were successfully differentiated using the DNA barcoding technique.<br><br>CONCLUSIONS: DNA barcoding was a promising and reliable tool for the identification of medicinal plants. It can be a powerful complementary method for traditional authentication.<br><br>SUMMARY: The internal transcribed spacer 2 (ITS2) regions between Kadsurae Caulis and Spatholobi Caulis varied considerably, totally 139 variable sitesSample 1 was not Kadsurae Caulis as it labeled, but it should be Spatholobi Caulis in fact based on ITS2 regionThe secondary structure can also separate Kadsurae Caulis and Spatholobi Caulis effectivelyDNA barcoding provided an accurate and strong prove to identify these two herbs. Abbreviations used: CTAB: hexadecyltrimethylammonium bromide, DNA: deoxyribonucleic acid, ITS2:internal transcribed spacer 2, PCR: polymerase chain reaction.},
}
@article {pmid27273876,
year = {2016},
author = {Kinslow, JD and Blum, LK and Deane, KD and Demoruelle, MK and Okamoto, Y and Parish, MC and Kongpachith, S and Lahey, LJ and Norris, JM and Robinson, WH and Holers, VM},
title = {Elevated IgA Plasmablast Levels in Subjects at Risk of Developing Rheumatoid Arthritis.},
journal = {Arthritis &amp; rheumatology (Hoboken, N.J.)},
volume = {68},
number = {10},
pages = {2372-2383},
pmid = {27273876},
issn = {2326-5205},
support = {R01 AR063676/AR/NIAMS NIH HHS/United States ; T32 AR007534/AR/NIAMS NIH HHS/United States ; T32 AR050942/AR/NIAMS NIH HHS/United States ; U01 AI101981/AI/NIAID NIH HHS/United States ; },
mesh = {Adult ; Arthritis, Rheumatoid/*immunology ; Autoantibodies/genetics/immunology ; Female ; Genes, Immunoglobulin Heavy Chain/genetics ; Genes, Immunoglobulin Light Chain/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Immunoglobulin A/genetics/*immunology ; Immunoglobulin G/genetics/immunology ; Male ; Middle Aged ; Peptides, Cyclic/*immunology ; Plasma Cells/*immunology ; Rheumatoid Factor/*immunology ; Risk ; Sequence Analysis, DNA ; },
abstract = {OBJECTIVE: The disease process in rheumatoid arthritis (RA) starts years before the clinical diagnosis is made, and elevated levels of disease-specific autoantibodies can be detected during this period. Early responses to known or novel autoantigens likely drive the eventual production of pathogenic autoimmunity. Importantly, the presence of disease-specific autoantibodies can identify individuals who are at high risk of developing RA but who do not currently have arthritis. The goal of the current study was to characterize plasmablasts from individuals at risk of developing RA.<br><br>METHODS: We investigated antibody-secreting plasmablasts derived from a well-characterized cohort of individuals who were at risk of developing RA, based on RA-related serum autoantibody positivity, as compared to patients with early (<1 year) seropositive RA as well as healthy control subjects. The plasmablast antibody repertoires of at-risk subjects were analyzed using DNA barcode-based methods with paired heavy- and light-chain gene sequencing. Cells were single-cell sorted, the cell- and plate-specific DNA barcodes were sequentially added, and next-generation sequencing was performed.<br><br>RESULTS: Total plasmablast levels were similar in the antibody-positive (1%) and control (0.4-1.6%) groups. However, increased frequencies of IgA+ versus IgG+ plasmablasts were observed in the antibody-positive group (39% IgA+ and 37% IgG+) as compared to other groups (1-9% IgA+ and 71-87% IgG+). Paired antibody sequences from antibody-positive subjects revealed cross-isotype clonal families and similar sequence characteristics in the IgA and IgG plasmablast repertoires. Antibody-positive individuals also demonstrated elevated serum levels of IgA isotype anti-cyclic citrullinated peptide 3 antibodies.<br><br>CONCLUSION: The IgA plasmablast dominance in these antibody-positive individuals suggests that a subset of RA-related autoantibodies may arise from mucosal immune responses and may be involved in early disease pathogenesis in individuals who are at risk of developing RA.},
}
@article {pmid27271592,
year = {2016},
author = {Liu, Y and Fu, X and Mao, L and Xing, Z and Wu, K},
title = {Host Plants Identification for Adult Agrotis ipsilon, a Long-Distance Migratory Insect.},
journal = {International journal of molecular sciences},
volume = {17},
number = {6},
pages = {},
pmid = {27271592},
issn = {1422-0067},
mesh = {*Animal Migration ; Animals ; Host-Parasite Interactions ; Moths/*physiology ; Plants/*parasitology ; Pollen/ultrastructure ; },
abstract = {In this study, we determined the host relationship of Agrotis ipsilon moths by identifying pollen species adhering them during their long-distance migration. Pollen carried by A. ipsilon moths was collected from 2012 to 2014 on a small island in the center of the Bohai Strait, which is a seasonal migration pathway of this pest species. Genomic DNA of single pollen grains was amplified by using whole genome amplification technology, and a portion of the chloroplast rbcL sequence was then amplified from this material. Pollen species were identified by a combination of DNA barcoding and pollen morphology. We found 28 species of pollen from 18 families on the tested moths, mainly from Angiosperm, Dicotyledoneae. From this, we were able to determine that these moths visit woody plants more than herbaceous plants that they carry more pollen in the early and late stages of the migration season, and that the amounts of pollen transportation were related to moth sex, moth body part, and plant species. In general, 31% of female and 26% of male moths were found to be carrying pollen. Amounts of pollen on the proboscis was higher for female than male moths, while the reverse was true for pollen loads on the antennae. This work provides a new approach to study the interactions between noctuid moth and their host plants. Identification of plant hosts for adult moths furthers understanding of the coevolution processes between moths and their host plants.},
}
@article {pmid27271198,
year = {2016},
author = {Coskun, AF and Cai, L},
title = {Dense transcript profiling in single cells by image correlation decoding.},
journal = {Nature methods},
volume = {13},
number = {8},
pages = {657-660},
pmid = {27271198},
issn = {1548-7105},
support = {R01 HD075605/HD/NICHD NIH HHS/United States ; R01 HD076915/HD/NICHD NIH HHS/United States ; },
mesh = {Animals ; Dietary Proteins/*metabolism ; *Gene Expression Profiling ; In Situ Hybridization, Fluorescence/*methods ; Mice ; NIH 3T3 Cells ; Nucleic Acid Hybridization ; RNA, Messenger/*genetics ; Ribosomal Proteins/genetics ; Single-Cell Analysis/*methods ; Transcription, Genetic ; },
abstract = {Sequential barcoded fluorescent in situ hybridization (seqFISH) allows large numbers of molecular species to be accurately detected in single cells, but multiplexing is limited by the density of barcoded objects. We present correlation FISH (corrFISH), a method to resolve dense temporal barcodes in sequential hybridization experiments. Using corrFISH, we quantified highly expressed ribosomal protein genes in single cultured cells and mouse thymus sections, revealing cell-type-specific gene expression.},
}
@article {pmid27268483,
year = {2016},
author = {Velmurugan, J and Mollison, E and Barth, S and Marshall, D and Milne, L and Creevey, CJ and Lynch, B and Meally, H and McCabe, M and Milbourne, D},
title = {An ultra-high density genetic linkage map of perennial ryegrass (Lolium perenne) using genotyping by sequencing (GBS) based on a reference shotgun genome assembly.},
journal = {Annals of botany},
volume = {118},
number = {1},
pages = {71-87},
pmid = {27268483},
issn = {1095-8290},
mesh = {*Chromosome Mapping ; Genetic Linkage ; Genome, Plant ; Genotyping Techniques/methods ; High-Throughput Nucleotide Sequencing ; Homozygote ; Lolium/*genetics ; *Polymorphism, Single Nucleotide ; },
abstract = {BACKGROUND AND AIMS: High density genetic linkage maps that are extensively anchored to assembled genome sequences of the organism in question are extremely useful in gene discovery. To facilitate this process in perennial ryegrass (Lolium perenne L.), a high density single nucleotide polymorphism (SNP)- and presence/absence variant (PAV)-based genetic linkage map has been developed in an F2 mapping population that has been used as a reference population in numerous studies. To provide a reference sequence to which to align genotyping by sequencing (GBS) reads, a shotgun assembly of one of the grandparents of the population, a tenth-generation inbred line, was created using Illumina-based sequencing.<br><br>METHODS: The assembly was based on paired-end Illumina reads, scaffolded by mate pair and long jumping distance reads in the range of 3-40&#x2009;kb, with >200-fold initial genome coverage. A total of 169 individuals from an F2 mapping population were used to construct PstI-based GBS libraries tagged with unique 4-9 nucleotide barcodes, resulting in 284 million reads, with approx. 1&#xb7;6 million reads per individual. A bioinformatics pipeline was employed to identify both SNPs and PAVs. A core genetic map was generated using high confidence SNPs, to which lower confidence SNPs and PAVs were subsequently fitted in a straightforward binning approach.<br><br>KEY RESULTS: The assembly comprises 424&#x2009;750 scaffolds, covering 1&#xb7;11 Gbp of the 2&#xb7;5 Gbp perennial ryegrass genome, with a scaffold N50 of 25 212&#x2009;bp and a contig N50 of 3790&#x2009;bp. It is available for download, and access to a genome browser has been provided. Comparison of the assembly with available transcript and gene model data sets for perennial ryegrass indicates that approx. 570 Mbp of the gene-rich portion of the genome has been captured. An ultra-high density genetic linkage map with 3092 SNPs and 7260 PAVs was developed, anchoring just over 200&#x2009;Mb of the reference assembly.<br><br>CONCLUSIONS: The combined genetic map and assembly, combined with another recently released genome assembly, represent a significant resource for the perennial ryegrass genetics community.},
}
@article {pmid27264730,
year = {2016},
author = {Bláha, M and Patoka, J and Kozák, P and Kouba, A},
title = {Unrecognized diversity in New Guinean crayfish species (Decapoda, Parastacidae): The evidence from molecular data.},
journal = {Integrative zoology},
volume = {11},
number = {6},
pages = {457-468},
doi = {10.1111/1749-4877.12211},
pmid = {27264730},
issn = {1749-4877},
mesh = {Animals ; Astacoidea/*classification/*genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; New Guinea ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; },
abstract = {The phylogenetic relationships among imported ornamental crayfish belonging to the genus Cherax were inferred from a combined dataset of 3 mitochondrial genes (COI, 16S and 12S) and by comparison with available GenBank sequences of 14 Cherax species. Furthermore, the concordance of previously described species obtained from a wholesaler (Cherax boesemani, C. holthuisi and C. peknyi) with available GenBank sequences was verified based on COI with special respect to comparison with sequences assigned as Cherax species. Recently described species C. gherardiae, C. pulcher and C. subterigneus belong to the northern group of Cherax species. Comparison and analysis with other GenBank COI sequences show previously unreported diversity of New Guinean species, suggesting 5 putative new species. Surprisingly, species assigned to the subgenus Astaconephrops do not form a monophyletic clade; this subgenus should be reappraised relative to the purported typical morphological characteristic of the uncalcified patch on male chelae. Increasing importation of crayfish underscores the importance of accurate species identification. Use of basic molecular methods is a necessary requisite for documenting occurrence, abundance and population trends of target species. Consequently, it helps to support eventual conservation decision-making by stakeholders.},
}
@article {pmid27260665,
year = {2016},
author = {Madeira, T and Souza, CM and Cordeiro, J and Thyssen, PJ},
title = {The use of DNA barcode for identifying species of Oxysarcodexia Townsend (Diptera: Sarcophagidae): A preliminary survey.},
journal = {Acta tropica},
volume = {161},
number = {},
pages = {73-78},
doi = {10.1016/j.actatropica.2016.05.017},
pmid = {27260665},
issn = {1873-6254},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Genome, Insect ; Humans ; Phylogeny ; Sarcophagidae/*classification/*genetics ; Sequence Analysis, DNA ; Surveys and Questionnaires ; },
abstract = {Oxysarcodexia is one of the Neotropical richest genera within the Sarcophagidae family. Medical, veterinary and forensic importance of these flies are due to their association with corpses, cases of myiasis in humans and domestic animals, and being pathogen carriers. Regarding morphological identification, molecular techniques, especially the DNA-based ones, arise as useful alternatives or complementary methodologies for species identification. Thus, in this study we aimed to investigate the potential of the COI marker (barcode region) to delimit Oxysarcodexia species in comparison with the morphological identification criteria. A COI fragment was amplified and the length of the sequences after alignment were of 648bp (149 parsimoniously informative variable sites). According to the Neighbor-Joining phylogenetic tree, specimens of the same morphological species were clustered in monophyletic clades (82-100% bootstrap branch support). Species-level resolution thus achieved was successful, despite low interspecific divergence (1.8-2.3%) and since interspecific variation was higher than intraspecific divergence (0.1-1.2%). Therefore, the use of COI barcode sequences supports differentiation and identification of the Oxysarcodexia species studied.},
}
@article {pmid27259539,
year = {2017},
author = {Ezpeleta, J and Krsticevic, FJ and Bulacio, P and Tapia, E},
title = {Designing robust watermark barcodes for multiplex long-read sequencing.},
journal = {Bioinformatics (Oxford, England)},
volume = {33},
number = {6},
pages = {807-813},
doi = {10.1093/bioinformatics/btw322},
pmid = {27259539},
issn = {1367-4811},
mesh = {Computer Simulation ; High-Throughput Nucleotide Sequencing/*methods ; Sequence Analysis, DNA/*methods ; *Software ; },
abstract = {MOTIVATION: To attain acceptable sample misassignment rates, current approaches to multiplex single-molecule real-time sequencing require upstream quality improvement, which is obtained from multiple passes over the sequenced insert and significantly reduces the effective read length. In order to fully exploit the raw read length on multiplex applications, robust barcodes capable of dealing with the full single-pass error rates are needed.<br><br>RESULTS: We present a method for designing sequencing barcodes that can withstand a large number of insertion, deletion and substitution errors and are suitable for use in multiplex single-molecule real-time sequencing. The manuscript focuses on the design of barcodes for full-length single-pass reads, impaired by challenging error rates in the order of 11%. The proposed barcodes can multiplex hundreds or thousands of samples while achieving sample misassignment probabilities as low as 10-7 under the above conditions, and are designed to be compatible with chemical constraints imposed by the sequencing process.<br><br>Software tools for constructing watermark barcode sets and demultiplexing barcoded reads, together with example sets of barcodes and synthetic barcoded reads, are freely available at www.cifasis-conicet.gov.ar/ezpeleta/NS-watermark .<br><br>CONTACT: ezpeleta@cifasis-conicet.gov.ar.},
}
@article {pmid27251364,
year = {2016},
author = {Kang, J and Kang, Y and Ji, X and Guo, Q and Jacques, G and Pietras, M and Łuczaj, N and Li, D and Łuczaj, &#x141;},
title = {Wild food plants and fungi used in the mycophilous Tibetan community of Zhagana (Tewo County, Gansu, China).},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {12},
number = {1},
pages = {21},
pmid = {27251364},
issn = {1746-4269},
mesh = {*Agaricales ; *Ethnobotany ; Humans ; *Plants, Edible ; Tibet ; },
abstract = {BACKGROUND: The aim of the study was to investigate knowledge and use of wild food plants and fungi in a highland valley in the Gannan Tibetan Autonomous Region on the north-eastern edges of the Tibetan Plateau.<br><br>METHODS: Field research was carried out in four neighbouring villages in a mountain valley of the Diebu (Tewo) county, surrounded by spruce forests. The study consisted of 30 interviews with single informants, or group interviews (altogether 63 informants). Apart from collecting voucher specimens, we also identified fungi using DNA barcoding.<br><br>RESULTS: We recorded the use of 54 species of vascular plants. We also recorded the use of 22 mushroom taxa, which made up the largest category of wild foods. Fruits formed the largest category of food plants, with 21 species, larger than the wild greens category, which consisted of 20 species eaten after boiling or frying and 7 as raw snacks. We also recorded the alimentary use of 10 species of edible flowers and 3 species with underground edible organs. On average, 20.8 edible taxa were listed per interview (median - 21). The most listed category of wild foods was green vegetables (mean - 7.5 species, median - 8 species), but fruits and mushrooms were listed nearly as frequently (mean - 6.3, median - 6 and mean - 5.8, - median 6 respectively). Other category lists were very short, e.g., flowers (mean - 1.3, median - 1) and underground edible parts (mean - 0.7, median - 1). Wild vegetables are usually boiled and/or fried and served as side-dishes, or their green parts are eaten as snacks during mountain treks (e.g., peeled rhubarb shoots). Wild fruits are mainly collected by children and eaten raw, they are not stored for further use. The most widely used wild staple foods are Potetilla anserina roots, an important ceremonial food served on such occasions as New Year or at funerals. They are boiled and served with sugar and butter. The most important famine plants remembered by people are the aerial bulbils of Persicaria vivipara. Flowers are used as children's snacks - their nectar is sucked.<br><br>CONCLUSIONS: The number of wild taxa eaten in the studied valley is similar to that of other Tibetan areas. The structure of wild food plant taxa is also very typical for Tibetan speaking areas (e.g., the use of rhubarb shoots, Potentilla anserina, Persicaria vivipara). The studied community show a high level of mycophilia.},
}
@article {pmid27250946,
year = {2016},
author = {Boye, E and Anda, S and Rothe, C and Stokke, T and Grallert, B},
title = {Analyzing Schizosaccharomyces pombe DNA Content by Flow Cytometry.},
journal = {Cold Spring Harbor protocols},
volume = {2016},
number = {6},
pages = {},
doi = {10.1101/pdb.prot091280},
pmid = {27250946},
issn = {1559-6095},
mesh = {DNA, Fungal/*analysis ; Flow Cytometry/*methods ; Schizosaccharomyces/*genetics ; },
abstract = {Flow cytometry can be used to measure the DNA content of individual cells. The data are usually presented as DNA histograms that can be used to examine the cells' progression through the cell cycle. Under standard growth conditions, fission yeast cells do not complete cytokinesis until after G1 phase; therefore, DNA histograms show one major peak representing cells in G1 (2×1C DNA) and G2 phase (1×2C DNA). By analysis of the duration of the fluorescence signal as well as the intensity of the DNA-related signal, it is possible to discriminate between cells in M/G1, S, and G2 This protocol describes how to prepare cells for flow cytometry and analyze them. We also describe the application of barcoding for more accurate comparison of samples.},
}
@article {pmid27249833,
year = {2016},
author = {Chen, C and Huang, W and Zhou, B and Liu, C and Mow, WH},
title = {PiCode: A New Picture-Embedding 2D Barcode.},
journal = {IEEE transactions on image processing : a publication of the IEEE Signal Processing Society},
volume = {25},
number = {8},
pages = {3444-3458},
doi = {10.1109/TIP.2016.2573592},
pmid = {27249833},
issn = {1941-0042},
mesh = {*Algorithms ; *Electronic Data Processing ; Humans ; },
abstract = {Nowadays, 2D barcodes have been widely used as an interface to connect potential customers and advertisement contents. However, the appearance of a conventional 2D barcode pattern is often too obtrusive for integrating into an aesthetically designed advertisement. Besides, no human readable information is provided before the barcode is successfully decoded. This paper proposes a new picture-embedding 2D barcode, called PiCode, which mitigates these two limitations by equipping a scannable 2D barcode with a picturesque appearance. PiCode is designed with careful considerations on both the perceptual quality of the embedded image and the decoding robustness of the encoded message. Comparisons with the existing beautified 2D barcodes show that PiCode achieves one of the best perceptual qualities for the embedded image, and maintains a better tradeoff between image quality and decoding robustness in various application conditions. PiCode has been implemented in the MATLAB on a PC and some key building blocks have also been ported to Android and iOS platforms. Its practicality for real-world applications has been successfully demonstrated.},
}
@article {pmid27246435,
year = {2017},
author = {de Carvalho Lima, TP and do Egito, AA and Feijó, GLD and de Arruda Mauro, R and Ferraz, ALJ},
title = {Molecular identification and phylogenetic analysis of Siluriformes from the Paraguay River basin, Brazil.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {4},
pages = {536-543},
doi = {10.3109/24701394.2016.1149825},
pmid = {27246435},
issn = {2470-1408},
mesh = {Animals ; Brazil ; Catfishes/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*genetics ; Fish Proteins/genetics ; Phylogeny ; Rivers ; },
abstract = {The objective of this study was to identify, through the DNA barcode, fishable Siluriformes which were collected from the Paraguay River basin in Pantanal. It was analyzed for genetic distance calculation using the Kimura-two-model parameters and the dendrogram was builtusing the Neighbour-Joining algorithm. The average genetic distance within species, genus and families were 0.2%, 1.6% and 4.2%, respectively. These values were lower than those reported in studies from other continents, probably due to the recent radiation process undergone by Neotropical fish. The dendrogram revealed two possible cases of hybridization, one individual Pseudoplatystoma corruscans, it was not possible to identify whether it was a natural event or commercial production exhaust and other of Pimelodus cf. argenteus leading to the assumption that the aspects of reproductive isolation cannot be clearly defined. Besides, the populations of the species Hemisorubim platyrhynchos and e Platydora armatulus may be undergoing a substructuring process, with genetic differences 3% and 4%, respectively.},
}
@article {pmid27244120,
year = {2016},
author = {Zhong, X and Qiao, L and Gasilova, N and Liu, B and Girault, HH},
title = {Mass Barcode Signal Amplification for Multiplex Allergy Diagnosis by MALDI-MS.},
journal = {Analytical chemistry},
volume = {88},
number = {12},
pages = {6184-6189},
doi = {10.1021/acs.analchem.6b01142},
pmid = {27244120},
issn = {1520-6882},
mesh = {Animals ; Cattle ; Gold/chemistry ; Humans ; Hypersensitivity/*diagnosis ; Immunoglobulin E/*blood/immunology/isolation &amp; purification ; Immunomagnetic Separation ; Lactoferrin/immunology ; Metal Nanoparticles/chemistry ; Milk/immunology/metabolism ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {A highly sensitive method based on mass-barcoded gold nanoparticles (AuNPs) and immunomagnetic separation has been developed for multiplex allergy diagnosis by MALDI mass spectrometry in a component-resolved manner. Different analytical probes were prepared by coating AuNPs with individual allergenic proteins and mass barcode, represented by polyethylene glycol molecules of various chain lengths. Magnetic beads (MBs) functionalized with antihuman IgE antibodies (Abs) were used as immunomagnetic capture probes. IgE Abs were extracted from a patient's blood serum by the formation of a sandwich structure between the AuNPs and MBs. Multiple specific IgE Abs were simultaneously identified by mass spectrometry detection of the mass barcodes, providing an efficient component-resolved allergy diagnosis. Because of the signal amplification provided by the mass barcodes, the developed diagnosis method is very sensitive, with a limit of detection down to picograms per milliliter level for specific IgE Abs. The method can be potentially useful when the sample amount is highly limited and a multiplex diagnostic procedure is required.},
}
@article {pmid27235386,
year = {2016},
author = {Jiang, F and Fu, W and Clarke, AR and Schutze, MK and Susanto, A and Zhu, S and Li, Z},
title = {A high-throughput detection method for invasive fruit fly (Diptera: Tephritidae) species based on microfluidic dynamic array.},
journal = {Molecular ecology resources},
volume = {16},
number = {6},
pages = {1378-1388},
doi = {10.1111/1755-0998.12542},
pmid = {27235386},
issn = {1755-0998},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Entomology/*methods ; Microfluidics/*methods ; Plants/parasitology ; Quarantine ; Real-Time Polymerase Chain Reaction ; Tephritidae/*genetics/*growth &amp; development ; Time Factors ; },
abstract = {Invasive species can be detrimental to a nation's ecology, economy and human health. Rapid and accurate diagnostics are critical to limit the establishment and spread of exotic organisms. The increasing rate of biological invasions relative to the taxonomic expertise available generates a demand for high-throughput, DNA-based diagnostics methods for identification. We designed species-specific qPCR primer and probe combinations for 27 economically important tephritidae species in six genera (Anastrepha, Bactrocera, Carpomya, Ceratitis, Dacus and Rhagoletis) based on 935 COI DNA barcode haplotypes from 181 fruit fly species publically available in BOLD, and then tested the specificity for each primer pair and probe through qPCR of 35 of those species. We then developed a standardization reaction system for detecting the 27 target species based on a microfluidic dynamic array and also applied the method to identify unknown immature samples from port interceptions and field monitoring. This method led to a specific and simultaneous detection for all 27 species in 7.5 h, using only 0.2 μL of reaction system in each reaction chamber. The approach successfully discriminated among species within complexes that had genetic similarities of up to 98.48%, while it also identified all immature samples consistent with the subsequent results of morphological examination of adults which were reared from larvae of cohorts from the same samples. We present an accurate, rapid and high-throughput innovative approach for detecting fruit flies of quarantine concern. This is a new method which has broad potential to be one of international standards for plant quarantine and invasive species detection.},
}
@article {pmid27229144,
year = {2016},
author = {McKenna, A and Findlay, GM and Gagnon, JA and Horwitz, MS and Schier, AF and Shendure, J},
title = {Whole-organism lineage tracing by combinatorial and cumulative genome editing.},
journal = {Science (New York, N.Y.)},
volume = {353},
number = {6298},
pages = {aaf7907},
pmid = {27229144},
issn = {1095-9203},
support = {MH105960/MH/NIMH NIH HHS/United States ; T32HL007312/HL/NHLBI NIH HHS/United States ; GM056211/GM/NIGMS NIH HHS/United States ; T32 HL007312/HL/NHLBI NIH HHS/United States ; R37 GM056211/GM/NIGMS NIH HHS/United States ; DP1HG007811/DP/NCCDPHP CDC HHS/United States ; U01 MH105960/MH/NIMH NIH HHS/United States ; R01 HD085905/HD/NICHD NIH HHS/United States ; R01 GM056211/GM/NIGMS NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; HD085905/HD/NICHD NIH HHS/United States ; T32 GM007266/GM/NIGMS NIH HHS/United States ; DP1 HG007811/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; *Bacterial Proteins ; CRISPR-Associated Protein 9 ; *CRISPR-Cas Systems ; Cell Division/genetics ; *Cell Lineage ; Cell Tracking/*methods ; DNA Barcoding, Taxonomic ; *Endonucleases ; Genetic Engineering/*methods ; Mutation ; Single-Cell Analysis ; Stem Cells/cytology/metabolism ; Zebrafish ; Zygote ; },
abstract = {Multicellular systems develop from single cells through distinct lineages. However, current lineage-tracing approaches scale poorly to whole, complex organisms. Here, we use genome editing to progressively introduce and accumulate diverse mutations in a DNA barcode over multiple rounds of cell division. The barcode, an array of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 target sites, marks cells and enables the elucidation of lineage relationships via the patterns of mutations shared between cells. In cell culture and zebrafish, we show that rates and patterns of editing are tunable and that thousands of lineage-informative barcode alleles can be generated. By sampling hundreds of thousands of cells from individual zebrafish, we find that most cells in adult organs derive from relatively few embryonic progenitors. In future analyses, genome editing of synthetic target arrays for lineage tracing (GESTALT) can be used to generate large-scale maps of cell lineage in multicellular systems for normal development and disease.},
}
@article {pmid27220998,
year = {2016},
author = {Dimitrov, D and Iezhova, TA and Zehtindjiev, P and Bobeva, A and Ilieva, M and Kirilova, M and Bedev, K and Sjöholm, C and Valkiūnas, G},
title = {Molecular characterisation of three avian haemoproteids (Haemosporida, Haemoproteidae), with the description of Haemoproteus (Parahaemoproteus) palloris n. sp.},
journal = {Systematic parasitology},
volume = {93},
number = {5},
pages = {431-449},
pmid = {27220998},
issn = {1573-5192},
mesh = {Animals ; Apicoplasts/genetics ; Biodiversity ; Cytochromes b/genetics ; DNA, Protozoan/genetics ; Haemosporida/*classification/*genetics/ultrastructure ; Passeriformes/parasitology ; Phylogeny ; Species Specificity ; },
abstract = {DNA barcoding (molecular characterisation) is a useful tool for describing the taxonomy and systematics of organisms. Over 250 species of avian haemosporidian parasites have been described using morphological characters, yet molecular techniques based on polymerase chain reaction (PCR) suggest this diversity is underestimated. Moreover, molecular techniques are particularly useful for the detection of chronic infections and tissue stages of these parasites. Species delimitation is problematic among haemosporidians, and many questions about the mechanisms and patterns of speciation, host specificity and pathogenicity are still unresolved. Accumulation of additional genetic and morphological information is needed to approach these questions. Here, we combine microscopic examination with PCR-based methods to develop molecular characterisation of Haemoproteus (Parahaemoproteus) manwelli Bennett, 1978 and Haemoproteus (Parahaemoproteus) gavrilovi Valkiūnas &amp; Iezhova, 1990, both of which parasitise the bee-eater Merops apiaster L. We also describe a new species, Haemoproteus (Parahaemoproteus) palloris n. sp., from the blood of the willow warbler Phylloscopus trochilus (L.). We performed phylogenetic analyses with a set of mitochondrial cytochrome b (cyt b) gene lineages, which have been linked to parasite morphospecies and are available in the MalAvi database. Our findings show that morphological characters, which have been traditionally used in the description of haemosporidians, exhibit phylogenetic congruence. This study contributes to a better understanding of avian haemosporidian diversity and provides new molecular markers (cyt b and apicoplast gene sequences) for the diagnostics of inadequately investigated haemosporidian infections.},
}
@article {pmid27220827,
year = {2016},
author = {Pértille, F and Guerrero-Bosagna, C and Silva, VH and Boschiero, C and Nunes, Jde R and Ledur, MC and Jensen, P and Coutinho, LL},
title = {High-throughput and Cost-effective Chicken Genotyping Using Next-Generation Sequencing.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {26929},
pmid = {27220827},
issn = {2045-2322},
mesh = {Animals ; Chickens/*genetics ; Chromosome Mapping ; Cost-Benefit Analysis ; Female ; Genome ; Genome-Wide Association Study ; Genotyping Techniques/*economics ; Heterozygote ; High-Throughput Nucleotide Sequencing/*economics ; Male ; Molecular Sequence Annotation ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/economics ; },
abstract = {Chicken genotyping is becoming common practice in conventional animal breeding improvement. Despite the power of high-throughput methods for genotyping, their high cost limits large scale use in animal breeding and selection. In the present paper we optimized the CornellGBS, an efficient and cost-effective genotyping by sequence approach developed in plants, for its application in chickens. Here we describe the successful genotyping of a large number of chickens (462) using CornellGBS approach. Genomic DNA was cleaved with the PstI enzyme, ligated to adapters with barcodes identifying individual animals, and then sequenced on Illumina platform. After filtering parameters were applied, 134,528 SNPs were identified in our experimental population of chickens. Of these SNPs, 67,096 had a minimum taxon call rate of 90% and were considered 'unique tags'. Interestingly, 20.7% of these unique tags have not been previously reported in the dbSNP. Moreover, 92.6% of these SNPs were concordant with a previous Whole Chicken-genome re-sequencing dataset used for validation purposes. The application of CornellGBS in chickens showed high performance to infer SNPs, particularly in exonic regions and microchromosomes. This approach represents a cost-effective (~US$50/sample) and powerful alternative to current genotyping methods, which has the potential to improve whole-genome selection (WGS), and genome-wide association studies (GWAS) in chicken production.},
}
@article {pmid27217948,
year = {2016},
author = {Batovska, J and Blacket, MJ and Brown, K and Lynch, SE},
title = {Molecular identification of mosquitoes (Diptera: Culicidae) in southeastern Australia.},
journal = {Ecology and evolution},
volume = {6},
number = {9},
pages = {3001-3011},
pmid = {27217948},
issn = {2045-7758},
abstract = {DNA barcoding is a modern species identification technique that can be used to distinguish morphologically similar species, and is particularly useful when using small amounts of starting material from partial specimens or from immature stages. In order to use DNA barcoding in a surveillance program, a database containing mosquito barcode sequences is required. This study obtained Cytochrome Oxidase I (COI) sequences for 113 morphologically identified specimens, representing 29 species, six tribes and 12 genera; 17 of these species have not been previously barcoded. Three of the 29 species ─ Culex palpalis, Macleaya macmillani, and an unknown species originally identified as Tripteroides atripes ─ were initially misidentified as they are difficult to separate morphologically, highlighting the utility of DNA barcoding. While most species grouped separately (reciprocally monophyletic), the Cx. pipiens subgroup could not be genetically separated using COI. The average conspecific and congeneric p-distance was 0.8% and 7.6%, respectively. In our study, we also demonstrate the utility of DNA barcoding in distinguishing exotics from endemic mosquitoes by identifying a single intercepted Stegomyia aegypti egg at an international airport. The use of DNA barcoding dramatically reduced the identification time required compared with rearing specimens through to adults, thereby demonstrating the value of this technique in biosecurity surveillance. The DNA barcodes produced by this study have been uploaded to the 'Mosquitoes of Australia-Victoria' project on the Barcode of Life Database (BOLD), which will serve as a resource for the Victorian Arbovirus Disease Control Program and other national and international mosquito surveillance programs.},
}
@article {pmid27214156,
year = {2016},
author = {Fu, F and Shang, L and Zheng, F and Chen, Z and Wang, H and Wang, J and Gu, Z and Zhao, Y},
title = {Cells Cultured on Core-Shell Photonic Crystal Barcodes for Drug Screening.},
journal = {ACS applied materials &amp; interfaces},
volume = {8},
number = {22},
pages = {13840-13848},
doi = {10.1021/acsami.6b04966},
pmid = {27214156},
issn = {1944-8252},
mesh = {Animals ; Cell Culture Techniques ; Cell Survival/drug effects ; Drug Evaluation, Preclinical/*methods ; HCT116 Cells ; Hep G2 Cells ; Humans ; Hydrogels/chemistry ; Mice ; NIH 3T3 Cells ; Spheroids, Cellular ; Tegafur/toxicity ; },
abstract = {The development of effective drug screening platforms is an important task for biomedical engineering. Here, a novel methacrylated gelatin (GelMA) hydrogel-encapsulated core-shell photonic crystal (PhC) barcode particle was developed for three-dimensional cell aggregation culture and drug screening. The GelMA shells of the barcode particles enable creation of a three-dimensional extracellular matrix (ECM) microenvironment for cell adhesion and growth, while the PhC cores of the barcode particles provide stable diffraction peaks that can encode different cell spheroids during culture and distinguish their biological response during drug testing. The applicability of this cell spheroids-on-barcodes platform was investigated by testing the cytotoxic effect of tegafur (TF), a prodrug of 5-fluorouracil (5-FU), on barcode particle-loaded liver HepG2 and HCT-116 colonic tumor cell spheroids. The cytotoxicity of TF against the HCT-116 tumor cell spheroids was enhanced in systems using cocultures of HepG2 and NIH-3T3 cells, indicating the effectiveness of this multiple cell spheroids-on-barcodes platform for drug screening.},
}
@article {pmid27213560,
year = {2016},
author = {Ng, KKS and Lee, SL and Tnah, LH and Nurul-Farhanah, Z and Ng, CH and Lee, CT and Tani, N and Diway, B and Lai, PS and Khoo, E},
title = {Forensic timber identification: a case study of a CITES listed species, Gonystylus bancanus (Thymelaeaceae).},
journal = {Forensic science international. Genetics},
volume = {23},
number = {},
pages = {197-209},
doi = {10.1016/j.fsigen.2016.05.002},
pmid = {27213560},
issn = {1878-0326},
mesh = {Cluster Analysis ; Conservation of Natural Resources/*legislation &amp; jurisprudence ; Crime ; DNA Barcoding, Taxonomic ; *DNA Fingerprinting ; Databases, Genetic ; Forensic Genetics ; *Genetic Markers ; Humans ; Malaysia ; *Microsatellite Repeats ; Thymelaeaceae/*genetics ; },
abstract = {Illegal logging and smuggling of Gonystylus bancanus (Thymelaeaceae) poses a serious threat to this fragile valuable peat swamp timber species. Using G. bancanus as a case study, DNA markers were used to develop identification databases at the species, population and individual level. The species level database for Gonystylus comprised of an rDNA (ITS2) and two cpDNA (trnH-psbA and trnL) markers based on a 20 Gonystylus species database. When concatenated, taxonomic species recognition was achieved with a resolution of 90% (18 out of the 20 species). In addition, based on 17 natural populations of G. bancanus throughout West (Peninsular Malaysia) and East (Sabah and Sarawak) Malaysia, population and individual identification databases were developed using cpDNA and STR markers respectively. A haplotype distribution map for Malaysia was generated using six cpDNA markers, resulting in 12 unique multilocus haplotypes, from 24 informative intraspecific variable sites. These unique haplotypes suggest a clear genetic structuring of West and East regions. A simulation procedure based on the composition of the samples was used to test whether a suspected sample conformed to a given regional origin. Overall, the observed type I and II errors of the databases showed good concordance with the predicted 5% threshold which indicates that the databases were useful in revealing provenance and establishing conformity of samples from West and East Malaysia. Sixteen STRs were used to develop the DNA profiling databases for individual identification. Bayesian clustering analyses divided the 17 populations into two main genetic clusters, corresponding to the regions of West and East Malaysia. Population substructuring (K=2) was observed within each region. After removal of bias resulting from sampling effects and population subdivision, conservativeness tests showed that the West and East Malaysia databases were conservative. This suggests that both databases can be used independently for random match probability estimation within respective regions. The reliability of the databases was further determined by independent self-assignment tests based on the likelihood of each individual's multilocus genotype occurring in each identified population, genetic cluster and region with an average percentage of correctly assigned individuals of 54.80%, 99.60% and 100% respectively. Thus, after appropriate validation, the genetic identification databases developed for G. bancanus in this study could support forensic applications and help safeguard this valuable species into the future.},
}
@article {pmid27212415,
year = {2016},
author = {Zaiko, A and Schimanski, K and Pochon, X and Hopkins, GA and Goldstien, S and Floerl, O and Wood, SA},
title = {Metabarcoding improves detection of eukaryotes from early biofouling communities: implications for pest monitoring and pathway management.},
journal = {Biofouling},
volume = {32},
number = {6},
pages = {671-684},
doi = {10.1080/08927014.2016.1186165},
pmid = {27212415},
issn = {1029-2454},
mesh = {Biodiversity ; *Biofouling ; Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; Environmental Monitoring/*methods ; *Eukaryota/classification/genetics ; *Geologic Sediments/analysis ; New Zealand ; RNA, Ribosomal, 18S/genetics ; },
abstract = {In this experimental study the patterns in early marine biofouling communities and possible implications for surveillance and environmental management were explored using metabarcoding, viz. 18S ribosomal RNA gene barcoding in combination with high-throughput sequencing. The community structure of eukaryotic assemblages and the patterns of initial succession were assessed from settlement plates deployed in a busy port for one, five and 15 days. The metabarcoding results were verified with traditional morphological identification of taxa from selected experimental plates. Metabarcoding analysis identified > 400 taxa at a comparatively low taxonomic level and morphological analysis resulted in the detection of 25 taxa at varying levels of resolution. Despite the differences in resolution, data from both methods were consistent at high taxonomic levels and similar patterns in community shifts were observed. A high percentage of sequences belonging to genera known to contain non-indigenous species (NIS) were detected after exposure for only one day.},
}
@article {pmid27208009,
year = {2016},
author = {Low, VL and Takaoka, H and Pramual, P and Adler, PH and Ya'cob, Z and Chen, CD and Yotopranoto, S and Zaid, A and Hadi, UK and Lardizabal, ML and Nasruddin-Roshidi, A and Sofian-Azirun, M},
title = {Three Taxa in One: Cryptic Diversity in the Black Fly Simulium nobile (Diptera: Simuliidae) in Southeast Asia.},
journal = {Journal of medical entomology},
volume = {53},
number = {4},
pages = {972-976},
doi = {10.1093/jme/tjw058},
pmid = {27208009},
issn = {1938-2928},
mesh = {Animals ; Electron Transport Complex IV/genetics ; Female ; Genetic Speciation ; *Genetic Variation ; Indonesia ; Insect Proteins/genetics ; Larva/classification/growth &amp; development ; Malaysia ; Male ; Phylogeny ; Pupa/classification/genetics/growth &amp; development ; Sequence Analysis, DNA ; Simuliidae/classification/*genetics/growth &amp; development ; Sympatry ; Thailand ; },
abstract = {We access the molecular diversity of the black fly Simulium nobile De Mejiere, using the universal cytochrome c oxidase subunit I (COI) barcoding gene, across its distributional range in Southeast Asia. Our phylogenetic analyses recovered three well-supported mitochondrial lineages of S. nobile, suggesting the presence of cryptic species. Lineage A is composed of a population from Sabah, East Malaysia (Borneo); lineage B represents the type population from Java, Indonesia; and lineage C includes populations from the mainland of Southeast Asia (Peninsular Malaysia and Thailand). The genetic variation of lineage C on the mainland is greater than that of lineages A and B on the islands of Borneo and Java. Our study highlights the value of a molecular approach in assessing species status of simuliids in geographically distinct regions.},
}
@article {pmid27208008,
year = {2016},
author = {Mokhtar, AS and Sridhar, GS and Mahmud, R and Jeffery, J and Lau, YL and Wilson, JJ and Abdul-Aziz, NM},
title = {First Case Report of Canthariasis in an Infant Caused by the Larvae of Lasioderma serricorne (Coleoptera: Anobiidae).},
journal = {Journal of medical entomology},
volume = {53},
number = {5},
pages = {1234-1237},
pmid = {27208008},
issn = {1938-2928},
abstract = {We report an unusual cause of gastrointestinal infection occurring in a 1-year-old infant patient who was brought to a public hospital in Kuala Lumpur, Malaysia. Larvae passed out in the patient's feces were confirmed by DNA barcoding as belonging to the species, Lasioderma serricorne (F.), known as the cigarette beetle. We postulate that the larvae were acquired from contaminated food and were responsible for gastrointestinal symptoms in the patient. To our knowledge, this the first report of human canthariasis caused by larvae of L. serricorne.},
}
@article {pmid27207383,
year = {2016},
author = {Lang, K and Wagner, I and Schöne, B and Schöfl, G and Birkner, K and Hofmann, JA and Sauter, J and Pingel, J and Böhme, I and Schmidt, AH and Lange, V},
title = {ABO allele-level frequency estimation based on population-scale genotyping by next generation sequencing.},
journal = {BMC genomics},
volume = {17},
number = {},
pages = {374},
pmid = {27207383},
issn = {1471-2164},
mesh = {*ABO Blood-Group System ; *Alleles ; *Gene Frequency ; *Genotype ; High-Throughput Nucleotide Sequencing ; Humans ; Molecular Typing/methods ; Reproducibility of Results ; Workflow ; },
abstract = {BACKGROUND: The characterization of the ABO blood group status is vital for blood transfusion and solid organ transplantation. Several methods for the molecular characterization of the ABO gene, which encodes the alleles that give rise to the different ABO blood groups, have been described. However, the application of those methods has so far been restricted to selected samples and not been applied to population-scale analysis.<br><br>RESULTS: We describe a cost-effective method for high-throughput genotyping of the ABO system by next generation sequencing. Sample specific barcodes and sequencing adaptors are introduced during PCR, rendering the products suitable for direct sequencing on Illumina MiSeq or HiSeq instruments. Complete sequence coverage of exons 6 and 7 enables molecular discrimination of the ABO subgroups and many alleles. The workflow was applied to ABO genotype more than a million samples. We report the allele group frequencies calculated on a subset of more than 110,000 sampled individuals of German origin. Further we discuss the potential of the workflow for high resolution genotyping taking the observed allele group frequencies into account. Finally, sequence analysis revealed 287 distinct so far not described alleles of which the most abundant one was identified in 174 samples.<br><br>CONCLUSIONS: The described workflow delivers high resolution ABO genotyping at low cost enabling population-scale molecular ABO characterization.},
}
@article {pmid27207304,
year = {2016},
author = {Mitake, H and Fujii, Y and Nagai, M and Ito, N and Okadera, K and Okada, K and Nakagawa, K and Kishimoto, M and Mizutani, T and Okazaki, K and Sakoda, Y and Takada, A and Sugiyama, M},
title = {Isolation of a sp. nov. Ljungan virus from wild birds in Japan.},
journal = {The Journal of general virology},
volume = {97},
number = {8},
pages = {1818-1822},
doi = {10.1099/jgv.0.000508},
pmid = {27207304},
issn = {1465-2099},
mesh = {Animals ; Charadriiformes/*virology ; Feces/virology ; Gene Order ; Genome, Viral ; Japan ; Parechovirus/*classification/genetics/*isolation &amp; purification ; Phylogeny ; Picornaviridae Infections/*veterinary/virology ; RNA, Viral/genetics ; Sequence Analysis, DNA ; Sequence Homology ; },
abstract = {Ljungan virus (LV) has been isolated/detected from rodents in a limited area including European countries and the USA. In this study, we isolated an LV strain from faecal samples of wild birds that had been collected in Japan, and determined the nearly complete sequence of the genome. Sequence analyses showed that the isolate possesses an LV-like genomic organization: 5UTR-VP0-VP3-VP1-2A1-2A2-2B-2C-3A-3B-3C-3D-3UTR. Phylogenetic and similarity analyses based on the VP1 region indicated that the strain constitutes a novel genotype within LV. In addition, we identified species origin of the faeces as gull species by using the DNA barcoding technique. These data suggested that the novel LV strain infected a gull species, in which the virus had not been identified. Taken together, this study has provided the first evidence of the presence of a novel LV in Japan, highlighting the possibility of LV infection in birds.},
}
@article {pmid27199612,
year = {2016},
author = {Huemer, P and Lopez-Vaamonde, C and Triberti, P},
title = {A new genus and species of leaf-mining moth from the French Alps, Mercantouria neli gen. n., sp. n. (Lepidoptera, Gracillariidae).},
journal = {ZooKeys},
volume = {},
number = {586},
pages = {145-162},
pmid = {27199612},
issn = {1313-2989},
abstract = {The Alps are a hotspot of biodiversity in Europe with many Lepidoptera species still to be discovered. Here we describe a new gracillariid genus and species, Mercantouria neli gen. n. and sp. n. The morphology of the male genitalia is highly differentiated with unique features. DNA barcodes show that its nearest neighbor is the North American species 'Caloptilia' scutellariella (Braun, 1923). Mercantouria neli is known from four adults (two males and two females) collected at two localities in the French Alps. Its host plant and life cycle remain unknown.},
}
@article {pmid27199603,
year = {2016},
author = {Zhao, Z and Li, S},
title = {Papiliocoelotes gen. n., a new genus of Coelotinae (Araneae, Agelenidae) spiders from the Wuling Mountains, China.},
journal = {ZooKeys},
volume = {},
number = {585},
pages = {33-50},
pmid = {27199603},
issn = {1313-2989},
abstract = {One new genus of the spider subfamily Coelotinae, Papiliocoelotes gen. n., with five new species is described for both sexes: Papiliocoelotes guanyinensis sp. n., Papiliocoelotes guitangensis sp. n., Papiliocoelotes jiepingensis sp. n., Papiliocoelotes meiyuensis sp. n., Papiliocoelotes yezhouensis sp. n. All new species were collected from caves in the Wuling Mountains of Hubei and Hunan Provinces, China. DNA barcodes were obtained for future use.},
}
@article {pmid27199601,
year = {2016},
author = {Chow, S and Konishi, K and Mekuchi, M and Tamaki, Y and Nohara, K and Takagi, M and Niwa, K and Teramoto, W and Manabe, H and Kurogi, H and Suzuki, S and Ando, D and Tadao Jinbo, and Kiyomoto, M and Hirose, M and Shimomura, M and Kurashima, A and Ishikawa, T and Kiyomoto, S},
title = {DNA barcoding and morphological analyses revealed validity of Diadema clarki Ikeda, 1939 (Echinodermata, Echinoidea, Diadematidae).},
journal = {ZooKeys},
volume = {},
number = {585},
pages = {1-16},
pmid = {27199601},
issn = {1313-2989},
abstract = {A long-spined sea urchin Diadema-sp reported from Japanese waters was genetically distinct from all known Diadema species, but it remained undescribed. Extensive field surveys in Japan with molecular identification performed in the present study determined five phenotypes (I to V) in Diadema-sp according to the presence and/or shape of a white streak and blue iridophore lines in the naked space of the interambulacral area. All phenotypes were distinct from Diadema setosum (Leske, 1778) and Diadema savignyi (Audouin, 1829), of which a major type (I) corresponded to Diadema clarki Ikeda, 1939 that was questioned and synonymized with Diadema setosum by Mortensen (1940). The holotype of Diadema clarki has not been found, but three unlabeled dried tests of Diadema were found among Ikeda's original collection held in the Kitakyushu Museum of Natural History and Human History, Fukuoka, Japan. A short mtDNA COI fragment (ca. 350bp) was amplified from one of the tests, and the nucleotide sequence determined (275bp) was nearly identical with that of Diadema-sp. Arrangements of the primary tubercles on the coronal plates in Diadema-sp and the museum specimen also conformed with Diadema clarki, indicating that Diadema-sp is identical to Diadema clarki and a valid species. Narrow latitudinal distribution (31°N to 35°N) of Diadema clarki in Japan was observed, where it co-existed with abundant Diadema setosum and rare Diadema savignyi. No Diadema clarki was found in the southern islands in Japan, such as Satsunan Islands to Ryukyu Islands and Ogasawara Island, where Diadema setosum and Diadema savignyi were commonly observed.},
}
@article {pmid27199600,
year = {2016},
author = {Schmidt, BC and Layberry, RA},
title = {What Azure blues occur in Canada? A re-assessment of Celastrina Tutt species (Lepidoptera, Lycaenidae).},
journal = {ZooKeys},
volume = {},
number = {584},
pages = {135-164},
pmid = {27199600},
issn = {1313-2989},
abstract = {The identity of Celastrina species in eastern Canada is reviewed based on larval host plants, phenology, adult phenotypes, mtDNA barcodes and re-assessment of published data. The status of the Cherry Gall Azure (Celastrina serotina Pavulaan &amp; Wright) as a distinct species in Canada is not supported by any dataset, and is removed from the Canadian fauna. Previous records of this taxon are re-identified as Celastrina lucia (Kirby) and Celastrina neglecta (Edwards). Evidence is presented that both Celastrina lucia and Celastrina neglecta have a second, summer-flying generation in parts of Canada. The summer generation of Celastrina lucia has previously been misidentified as Celastrina neglecta, which differs in phenology, adult phenotype and larval hosts from summer Celastrina lucia. DNA barcodes are highly conserved among at least three North American Celastrina species, and provide no taxonomic information. Celastrina neglecta has a Canadian distribution restricted to southern Ontario, Manitoba, Saskatchewan and easternmost Alberta. The discovery of museum specimens of Celastrina ladon (Cramer) from southernmost Ontario represents a new species for the Canadian butterfly fauna, which is in need of conservation status assessment.},
}
@article {pmid27199599,
year = {2016},
author = {Weng, YM and Yeh, WB and Yang, MM},
title = {A new species of alpine Apenetretus Kurnakov from Taiwan: evidences from DNA barcodes and morphological characteristics (Coleoptera, Carabidae, Patrobini).},
journal = {ZooKeys},
volume = {},
number = {584},
pages = {121-134},
pmid = {27199599},
issn = {1313-2989},
abstract = {There are three isolated mountain ranges in Taiwan including Hsueshan Range, Central Mountain Range, and Yushan Range. The rise of these mountains has resulted in the isolation of some species and caused allopatric distribution resulting in divergence and speciation events of high mountain carabids, especially the flightless carabids such as Epaphiopsis, Apenetretus, and partial Nebria. Genus Apenetretus Kurnakov (1960) is typically distributed in high mountain areas of Taiwan. Three of the currently known Apenetretus species have been described from different mountain ranges. These species include Apenetretus yushanensis Habu, Apenetretus nanhutanus Habu, and Apenetretus smetanai Zamotajlov and Sciaky. In this study, a new species is described from Hsueshan, a mountain separated from the ranges of the previous known species, Apenetretus hsueshanensis sp. n. A key to the Taiwanese Apenetretus is included. A reconstructed phylogeny of the Taiwanese Apenetretus is introduced with the use of mitochondrial cytochrome c oxidase subunit I (COI) gene. Molecular data and geographical distribution of Apenetretus support the morphological characteristics observed among those mountain-isolated species and confirms the new species as being distinctly different. Moreover, lineage calibration suggests that the southern Apenetretus yushanensis is the most distant one compared to the other three northern Apenetretus at ca. 1.81 million years ago (mya), while the divergence time of Apenetretus hsueshanensis to its sister group was dated to 0.94 mya.},
}
@article {pmid27199589,
year = {2016},
author = {Van Dam, MH and Laufa, R and Riedel, A},
title = {Four new species of Trigonopterus Fauvel from the island of New Britain (Coleoptera, Curculionidae).},
journal = {ZooKeys},
volume = {},
number = {582},
pages = {129-141},
pmid = {27199589},
issn = {1313-2989},
abstract = {The hyperdiverse genus Trigonopterus has its center of diversity in Melanesia, but only a single species is recorded from the Bismarck Archipelago to date. Here we describe four new species from the island of New Britain: Trigonopterus chewbacca sp. n., Trigonopterus obsidianus sp. n., Trigonopterus puncticollis sp. n. and Trigonopterus silaliensis sp. n. We provide cytochrome oxidase subunit I (cox1) sequences of the new species and a key to all five species known from the Bismarck Archipelago.},
}
@article {pmid27199587,
year = {2016},
author = {Zhao, L and Lin, LL and Zheng, ZM},
title = {DNA barcoding reveals polymorphism in the pygmy grasshopper Tetrix bolivari (Orthoptera, Tetrigidae).},
journal = {ZooKeys},
volume = {},
number = {582},
pages = {111-120},
pmid = {27199587},
issn = {1313-2989},
abstract = {Many pygmy grasshopper species exhibit colour-marking polymorphism. However, this polymorphism in some species, such as Tetrix bolivari, is almost unknown. The aim of this work is to identify using DNA barcoding the colour-marking polymorphic morphs of this pygmy grasshopper species collected from both grass and sand microhabitats. Analysis by NJ clustering and pairwise distances indicated that all specimens collected showing colour-marking polymorphism are species of Tetrix bolivari. Haplotype network construction showed ten different haplotypes from a total of 57 Tetrix bolivari individuals with H1(82.5%) being the most common type and it also displayed low divergence within Tetrix bolivari population. The haplotype analyses were consistent with the NJ clustering. Our field census showed the frequency of Tetrix bolivari morphs differed significantly, with the rank order of morphs (from high to low) typeA1, type B1, type A2, type A3, type A4, type A5, type A6, type A7, type B2, type B3, and type B4. The most common type A morphs were without contrasting markings, while the rarer type B morphs have contrasting white markings. We suggest that type B morphs have greater camouflage effects against natural backgrounds such as grass or sand than type A morphs. Both our field census and haplotype analysis revealed that type A has higher frequency and more haplotypes than type B.},
}
@article {pmid27199586,
year = {2016},
author = {O'Neill, JC and Fisher, JR and Nelson, WA and Skvarla, MJ and Fisher, DM and Dowling, AP},
title = {Systematics of testudacarine torrent mites (Acari, Hydrachnidia, Torrenticolidae) with descriptions of 13 new species from North America.},
journal = {ZooKeys},
volume = {},
number = {582},
pages = {13-110},
pmid = {27199586},
issn = {1313-2989},
abstract = {Thirteen new species of North American Testudacarus (Torrenticolidae: Testudacarinae) are described: Testudacarus deceptivus O'Neill &amp; Dowling, sp. n., Testudacarus hitchensi O'Neill &amp; Dowling, sp. n., Testudacarus harrisi O'Neill &amp; Dowling, sp. n., Testudacarus dennetti O'Neill &amp; Dowling, sp. n., Testudacarus dawkinsi O'Neill &amp; Dowling, sp. n., Testudacarus radwellae O'Neill &amp; Dowling, sp. n., Testudacarus kirkwoodae O'Neill &amp; Dowling, sp. n., Testudacarus hyporhynchus O'Neill &amp; Dowling, sp. n., Testudacarus smithi O'Neill &amp; Dowling, sp. n., Testudacarus rollerae O'Neill &amp; Dowling, sp. n., Testudacarus elongatus O'Neill &amp; Dowling, sp. n., Testudacarus rectangulatus O'Neill &amp; Dowling, sp. n., and Testudacarus oblongatus O'Neill &amp; Dowling, sp. n. Testudacarus vulgaris Habeeb, 1954 is resurrected from synonymy with Testudacarus minimus and redescribed. Debsacarus (Habeeb, 1961), Testudacarus americanus Marshall, 1943, and Testudacarus minimus Marshall, 1943 are redescribed. All redescriptions are from original types. Species delimination was accomplished through examination of morphology, biogeography, and molecular phylogenetics of the barcoding region of COI. Other species are addressed and a key to world species is presented. For Testudacarinae, this represents the first published: 1) descriptions from multiple specimens (i.e. intraspecific variation); 2) colored photographs; 3) explicit illustrations and discussion of sexual dimorphism within the subfamily; 4) genetic data. A comprehensive testudacarine reference list is also included.},
}
@article {pmid27198103,
year = {2016},
author = {Seidling, HM and Bates, DW},
title = {Evaluating the Impact of Health IT on Medication Safety.},
journal = {Studies in health technology and informatics},
volume = {222},
number = {},
pages = {195-205},
pmid = {27198103},
issn = {1879-8365},
mesh = {Decision Support Systems, Clinical ; Electronic Prescribing/standards ; Evaluation Studies as Topic ; Humans ; Medical Informatics ; Medical Order Entry Systems/*organization &amp; administration ; Medication Errors/*prevention &amp; control ; },
abstract = {Health IT is becoming an increasingly powerful tool for improving medication safety. While errors may happen at all stages of the medication process, different tools have been developed to support the prescribing process (e.g. computerized prescribing with decision support), the dispensing process (e.g. barcoding or automated dispensing and unit-dose systems), or the administration process (e.g. electronic medication administration records and smart pumps). Health IT can reduce medication error and preventable adverse drug event rates by increasing documentation quality and transparency, enhancing accuracy and correctness of the medication process, and supporting information exchange and interlinking different stages of the medication process. Typical evaluated endpoints comprise process-related outcomes such as number of medication errors, harm-related outcomes such as adverse drug events, or cost-related outcomes. Typical study design to measure effectiveness of health IT in medication safety comprises before-after studies and randomized controlled trials. However, implementation is challenging; it often has a major impact on the overall workflow and such technologies must be carefully introduced and their effects must be closely monitored in order to achieve the desired reductions, as in addition to preventing errors they nearly always introduce new ones. As complex interventions, their impact depends crucially on the real world setting and the implementation details and thus, transferability of study results is variable.},
}
@article {pmid27192622,
year = {2016},
author = {Vázquez-Nion, D and Rodríguez-Castro, J and López-Rodríguez, MC and Fernández-Silva, I and Prieto, B},
title = {Subaerial biofilms on granitic historic buildings: microbial diversity and development of phototrophic multi-species cultures.},
journal = {Biofouling},
volume = {32},
number = {6},
pages = {657-669},
doi = {10.1080/08927014.2016.1183121},
pmid = {27192622},
issn = {1029-2454},
mesh = {Architecture/history ; Biodiversity ; Biofilms/*growth &amp; development ; Chlorophyta/classification/*growth &amp; development ; Construction Materials/*microbiology ; Cyanobacteria/classification/*growth &amp; development ; Environmental Microbiology ; Fungi/classification/*growth &amp; development ; History, Medieval ; Phototrophic Processes ; Reproducibility of Results ; Silicon Dioxide/*chemistry ; Spain ; Surface Properties ; },
abstract = {Microbial communities of natural subaerial biofilms developed on granitic historic buildings of a World Heritage Site (Santiago de Compostela, NW Spain) were characterized and cultured in liquid BG11 medium. Environmental barcoding through next-generation sequencing (Pacific Biosciences) revealed that the biofilms were mainly composed of species of Chlorophyta (green algae) and Ascomycota (fungi) commonly associated with rock substrata. Richness and diversity were higher for the fungal than for the algal assemblages and fungi showed higher heterogeneity among samples. Cultures derived from natural biofilms showed the establishment of stable microbial communities mainly composed of Chlorophyta and Cyanobacteria. Although most taxa found in these cultures were not common in the original biofilms, they are likely common pioneer colonizers of building stone surfaces, including granite. Stable phototrophic multi-species cultures of known microbial diversity were thus obtained and their reliability to emulate natural colonization on granite should be confirmed in further experiments.},
}
@article {pmid27191722,
year = {2016},
author = {Morinière, J and Cancian de Araujo, B and Lam, AW and Hausmann, A and Balke, M and Schmidt, S and Hendrich, L and Doczkal, D and Fartmann, B and Arvidsson, S and Haszprunar, G},
title = {Species Identification in Malaise Trap Samples by DNA Barcoding Based on NGS Technologies and a Scoring Matrix.},
journal = {PloS one},
volume = {11},
number = {5},
pages = {e0155497},
pmid = {27191722},
issn = {1932-6203},
mesh = {Animals ; Arthropods/classification/genetics ; Biodiversity ; Cluster Analysis ; Cytochromes c/genetics ; *DNA Barcoding, Taxonomic/methods ; Databases, Nucleic Acid ; Germany ; *High-Throughput Nucleotide Sequencing ; Insecta/*classification/*genetics ; Workflow ; },
abstract = {The German Barcoding initiatives BFB and GBOL have generated a reference library of more than 16,000 metazoan species, which is now ready for applications concerning next generation molecular biodiversity assessments. To streamline the barcoding process, we have developed a meta-barcoding pipeline: We pre-sorted a single malaise trap sample (obtained during one week in August 2014, southern Germany) into 12 arthropod orders and extracted DNA from pooled individuals of each order separately, in order to facilitate DNA extraction and avoid time consuming single specimen selection. Aliquots of each ordinal-level DNA extract were combined to roughly simulate a DNA extract from a non-sorted malaise sample. Each DNA extract was amplified using four primer sets targeting the CO1-5' fragment. The resulting PCR products (150-400bp) were sequenced separately on an Illumina Mi-SEQ platform, resulting in 1.5 million sequences and 5,500 clusters (coverage ≥10; CD-HIT-EST, 98%). Using a total of 120,000 DNA barcodes of identified, Central European Hymenoptera, Coleoptera, Diptera, and Lepidoptera downloaded from BOLD we established a reference sequence database for a local CUSTOM BLAST. This allowed us to identify 529 Barcode Index Numbers (BINs) from our sequence clusters derived from pooled Malaise trap samples. We introduce a scoring matrix based on the sequence match percentages of each amplicon in order to gain plausibility for each detected BIN, leading to 390 high score BINs in the sorted samples; whereas 268 of these high score BINs (69%) could be identified in the combined sample. The results indicate that a time consuming presorting process will yield approximately 30% more high score BINs compared to the non-sorted sample in our case. These promising results indicate that a fast, efficient and reliable analysis of next generation data from malaise trap samples can be achieved using this pipeline.},
}
@article {pmid27185891,
year = {2016},
author = {Lee, DF and Lu, J and Chang, S and Loparo, JJ and Xie, XS},
title = {Mapping DNA polymerase errors by single-molecule sequencing.},
journal = {Nucleic acids research},
volume = {44},
number = {13},
pages = {e118},
pmid = {27185891},
issn = {1362-4962},
support = {R01 GM114065/GM/NIGMS NIH HHS/United States ; R01 EB010244/EB/NIBIB NIH HHS/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; },
mesh = {Chromosome Mapping/methods ; DNA Replication/*genetics ; DNA-Directed DNA Polymerase/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Sequence Analysis, DNA ; },
abstract = {Genomic integrity is compromised by DNA polymerase replication errors, which occur in a sequence-dependent manner across the genome. Accurate and complete quantification of a DNA polymerase's error spectrum is challenging because errors are rare and difficult to detect. We report a high-throughput sequencing assay to map in vitro DNA replication errors at the single-molecule level. Unlike previous methods, our assay is able to rapidly detect a large number of polymerase errors at base resolution over any template substrate without quantification bias. To overcome the high error rate of high-throughput sequencing, our assay uses a barcoding strategy in which each replication product is tagged with a unique nucleotide sequence before amplification. This allows multiple sequencing reads of the same product to be compared so that sequencing errors can be found and removed. We demonstrate the ability of our assay to characterize the average error rate, error hotspots and lesion bypass fidelity of several DNA polymerases.},
}
@article {pmid27181289,
year = {2016},
author = {Otten, L and Vlachou, D and Richards, SJ and Gibson, MI},
title = {Glycan heterogeneity on gold nanoparticles increases lectin discrimination capacity in label-free multiplexed bioassays.},
journal = {The Analyst},
volume = {141},
number = {14},
pages = {4305-4312},
pmid = {27181289},
issn = {1364-5528},
support = {638661/ERC_/European Research Council/International ; },
mesh = {*Biosensing Techniques ; *Gold ; Lectins/*chemistry ; *Metal Nanoparticles ; Polysaccharides/*chemistry ; },
abstract = {The development of new analytical tools as point-of-care biosensors is crucial to combat the spread of infectious diseases, especially in the context of drug-resistant organisms, or to detect biological warfare agents. Glycan/lectin interactions drive a wide range of recognition and signal transduction processes within nature and are often the first site of adhesion/recognition during infection making them appealing targets for biosensors. Glycosylated gold nanoparticles have been developed that change colour from red to blue upon interaction with carbohydrate-binding proteins and may find use as biosensors, but are limited by the inherent promiscuity of some of these interactions. Here we mimic the natural heterogeneity of cell-surface glycans by displaying mixed monolayers of glycans on the surface of gold nanoparticles. These are then used in a multiplexed, label-free bioassay to create 'barcodes' which describe the lectin based on its binding profile. The increased information content encoded by using complex mixtures of a few sugars, rather than increased numbers of different sugars makes this approach both scalable and accessible. These nanoparticles show increased lectin identification power at a range of lectin concentrations, relative to single-channel sensors. It was also found that some information about the concentration of the lectins can be extracted, all from just a simple colour change, taking this technology closer to being a realistic biosensor.},
}
@article {pmid27180824,
year = {2017},
author = {Kaur, H and Sharma, K},
title = {COI-based DNA barcoding of some species of Pentatomidae from North India (Hemiptera: Heteroptera).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {5},
pages = {756-761},
doi = {10.1080/24701394.2016.1180513},
pmid = {27180824},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Heteroptera/*classification/genetics ; India ; Insect Proteins/genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {The family Pentatomidae is one of the largest families of the sub-order Heteroptera, comprising 4722 species belonging to 896 genera. In the present paper, we analysed a partial ∼600 bp COI sequence of 14 species of family Pentatomidae, collected from northern part of India. For seven species viz., Tolumnia antennata Distant, 1902, Cahara jugatoria (Lethierry, 1891), Bagrada hilaris (Burmeister, 1835), Plautia viridicollis (Westwood, 1837), Priassus exemptus (Walker, 1868), Dalpada neoclavata (Rider, 1998) and Dalpada affinis (Dallas, 1851), this is the first ever molecular study which has generated distinct barcodes for each. The COI sequences of these seven species have been added to the existing database at GenBank NCBI which can be used for their identification. The database analysis shows mean K2P divergence of 2.5% at intraspecific level, 11.9% at interspecific level and 16.37% at intergeneric level, thereby indicating a hierarchical increase in K2P mean divergence across different taxonomic levels.},
}
@article {pmid27180732,
year = {2017},
author = {Aksöyek, E and İbiş, O and Özcan, S and Moradi, M and Tez, C},
title = {DNA barcoding of three species (Canis aureus, Canis lupus and Vulpes vulpes) of Canidae.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {5},
pages = {747-755},
doi = {10.1080/24701394.2016.1180512},
pmid = {27180732},
issn = {2470-1408},
mesh = {Animals ; Canidae/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Iran ; Phylogeny ; Sequence Analysis, DNA/*methods ; Species Specificity ; Turkey ; },
abstract = {Sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene have been used for DNA barcoding and determining the genetic diversity of mammal species. In the current study, our intention was to test the validity of COI barcodes for detecting genetic divergence and to reveal whether or not there is a genetic variation at this marker within canids. Three species (Canis aureus, Canis lupus and Vulpes vulpes) from the family Canidae were selected for DNA barcoding using samples collected from Iran and Turkey. All three species had unique barcoding sequences and none of the sequences were shared among these species. The mean sequence divergences within and among the species were 0.61% and 12.32%, respectively, which fell into the mean divergence ranges found in some mammal groups. The genetic diversity of these three canid species was relatively higher than that found in previously reported studies.},
}
@article {pmid27180216,
year = {2016},
author = {Gajapathy, K and Tharmasegaram, T and Eswaramohan, T and Peries, LB and Jayanetti, R and Surendran, SN},
title = {DNA barcoding of Sri Lankan phlebotomine sand flies using cytochrome c oxidase subunit I reveals the presence of cryptic species.},
journal = {Acta tropica},
volume = {161},
number = {},
pages = {1-7},
doi = {10.1016/j.actatropica.2016.05.001},
pmid = {27180216},
issn = {1873-6254},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Disease Vectors/*classification ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Leishmaniasis, Visceral/*parasitology ; Phlebotomus/*classification ; Sequence Analysis, DNA ; Sri Lanka ; },
abstract = {Sri Lanka is known for high diversity of phlebotomine sand flies and prevalence of cutaneous and visceral leishmaniasis; a disease vectored by sand flies. The taxonomy of phlebotomine sand flies is complicated and often the diversity is over/underrated. The current study aims to use the cytochrome c oxidase gene subunit 1 (COI) sequence and formulate a barcode for the sand fly species in Sri Lanka. A total of 70 samples comprising seven species morphologically identified and collected from dry zone districts of Hambantota, Anuradhapura, Vavuniya, Trincomalee and Jaffna were processed. Neighbour-joining (NJ) tree created using the sequences revealed the species identity is compatible with the current morphology based identification. Further the analysis delineated morphologically identified Se. bailyi, Se babu babu and Se babu insularis into genetically distinct groups.},
}
@article {pmid27179810,
year = {2016},
author = {Ahn, S and Hong, M and Van Vrancken, M and Lyou, YJ and Kim, ST and Park, SH and Kang, WK and Park, YS and Jung, SH and Woo, M and Lee, J and Kim, KM},
title = {A nCounter CNV Assay to Detect HER2 Amplification: A Correlation Study with Immunohistochemistry and In Situ Hybridization in Advanced Gastric Cancer.},
journal = {Molecular diagnosis &amp; therapy},
volume = {20},
number = {4},
pages = {375-383},
pmid = {27179810},
issn = {1179-2000},
mesh = {Biomarkers, Tumor ; *DNA Copy Number Variations ; *Gene Amplification ; Humans ; Immunohistochemistry ; In Situ Hybridization, Fluorescence ; Neoplasm Staging ; Receptor, ErbB-2/*genetics ; Reproducibility of Results ; Sensitivity and Specificity ; Stomach Neoplasms/*genetics/metabolism/pathology/surgery ; },
abstract = {AIM: Screening amplified genes for targeted therapy with high-throughput technology is very important. The NanoString nCounter system allows multiplexed digital quantification of target molecules through the use of color-coded barcodes with the great advantage that formalin-fixed, paraffin-embedded (FFPE) tissue can be utilized.<br><br>METHODS: We tested nCounter custom copy number variation (CNV) panels in 220 gastric cancer samples and evaluated the utility of this method as a screening tool for the detection of CNV using HER2. For the validation of results, we compared the nCounter results with immunohistochemistry (IHC), and we further performed in situ hybridization (ISH) in discrepant cases.<br><br>RESULTS: The average HER2 gene copy numbers (CNs) by nCounter were 17.25, 2.0 and 2.61 for the HER2 IHC positive (3+), equivocal (2+), and negative cases, respectively. Out of the 16 IHC 3+ cases, 13 (81.3&#xa0;%) were reported as HER2 CN gain (&#x2265;4). Gastric cancers with homogeneous HER2 overexpression or high tumor purity showed HER2 CN &#x2265;10. Among the 192 cases with HER2 IHC negative and without HER2 gene amplification, 29 showed a HER2 CN &#x2265;4 with the nCounter assay. The nCounter assay had a concordance rate of 83.4&#xa0;% (kappa value, 0.35), a sensitivity of 66.7&#xa0;%, a specificity of 85.2&#xa0;%, a negative predictive value of 96&#xa0;%, and a positive predictive value of 32.6&#xa0;% compared with HER2 IHC/ISH results. Fresh frozen (FF) samples revealed a higher concordance rate (91.5&#xa0;%, kappa value, 0.59) than FFPE samples (78.5&#xa0;%, kappa value 0.27) and showed a high specificity (97.2&#xa0;%).<br><br>CONCLUSION: The nCounter CNV assay is a reliable and practical method to detect high CN variations. Given the intra-tumoral HER2 heterogeneity and normal cell contamination, additional IHC and/or FISH is necessary and needs caution in interpretation, especially in FFPE tissue samples.},
}
@article {pmid27178552,
year = {2016},
author = {Staats, M and Arulandhu, AJ and Gravendeel, B and Holst-Jensen, A and Scholtens, I and Peelen, T and Prins, TW and Kok, E},
title = {Advances in DNA metabarcoding for food and wildlife forensic species identification.},
journal = {Analytical and bioanalytical chemistry},
volume = {408},
number = {17},
pages = {4615-4630},
pmid = {27178552},
issn = {1618-2650},
mesh = {Animals ; Animals, Wild/*genetics ; Computational Biology ; DNA/*genetics ; DNA Barcoding, Taxonomic ; *Food ; *Forensic Genetics ; High-Throughput Nucleotide Sequencing/methods ; Plants/*genetics ; },
abstract = {Species identification using DNA barcodes has been widely adopted by forensic scientists as an effective molecular tool for tracking adulterations in food and for analysing samples from alleged wildlife crime incidents. DNA barcoding is an approach that involves sequencing of short DNA sequences from standardized regions and comparison to a reference database as a molecular diagnostic tool in species identification. In recent years, remarkable progress has been made towards developing DNA metabarcoding strategies, which involves next-generation sequencing of DNA barcodes for the simultaneous detection of multiple species in complex samples. Metabarcoding strategies can be used in processed materials containing highly degraded DNA e.g. for the identification of endangered and hazardous species in traditional medicine. This review aims to provide insight into advances of plant and animal DNA barcoding and highlights current practices and recent developments for DNA metabarcoding of food and wildlife forensic samples from a practical point of view. Special emphasis is placed on new developments for identifying species listed in the Convention on International Trade of Endangered Species (CITES) appendices for which reliable methods for species identification may signal and/or prevent illegal trade. Current technological developments and challenges of DNA metabarcoding for forensic scientists will be assessed in the light of stakeholders' needs.},
}
@article {pmid27178437,
year = {2016},
author = {Caetano Wyler, S and Naciri, Y},
title = {Evolutionary histories determine DNA barcoding success in vascular plants: seven case studies using intraspecific broad sampling of closely related species.},
journal = {BMC evolutionary biology},
volume = {16},
number = {},
pages = {103},
pmid = {27178437},
issn = {1471-2148},
mesh = {*DNA Barcoding, Taxonomic/methods ; *DNA, Plant/genetics ; *Evolution, Molecular ; Magnoliopsida/*genetics ; Phylogeny ; Plastids/genetics ; Trees/genetics ; },
abstract = {BACKGROUND: Four plastid regions, rpoB, rpoC1, matK, and trnH-psbA, have been recommended as DNA barcodes for plants. Their success in delimiting species boundaries depends on the existence of a clear-cut difference between inter- and intraspecific variability. We tested the ability of these regions to discriminate among closely related species in seven genera of flowering plants with different generation times (trees, perennials, and annuals). To ensure a maximum coverage of intraspecific diversity, and therefore to better evaluate the resolution power of each barcode, we applied a population genetics approach by sampling three to 45 individuals per species over a wide geographical range.<br><br>RESULTS: All possible combinations between loci were analysed, which showed that using more than one locus does not always improve the resolution power. The trnH-psbA locus was most effective at discriminating among closely related species (Acer, Lonicera, Geranium, and Veronica), singly or in combination. For Salix, Adenostyles, and Gentiana, the best results were obtained with the combination of matK, rpoB, and trnH-psbA. No barcoding gap was found within six genera analysed, excepting Lonicera. This is due to shared polymorphisms among species, combined with very divergent sequences within species. These genetic patterns reflect incomplete lineage sorting and hybridization events followed by chloroplast capture.<br><br>CONCLUSIONS: Our results strongly suggest that adding trnH-psbA to the two obligate DNA barcodes proposed by the CBOL plant-working group (matK and rbcL) should be mandatory for closely related species. In our sampling, generation time had no influence on DNA barcoding success, as the best and worst identification successes were found for the two tree genera (Acer, 64&#xa0;% success and Salix, 86&#xa0;% failure). Evolutionary histories are the main factor influencing DNA barcoding success in the studied genera.},
}
@article {pmid27175337,
year = {2016},
author = {Sharma, S and Shrivastava, N},
title = {Internal transcribed spacer guided multiplex PCR for species identification of Convolvulus prostratus and Evolvulus alsinoides.},
journal = {Acta pharmaceutica Sinica. B},
volume = {6},
number = {3},
pages = {253-258},
pmid = {27175337},
issn = {2211-3835},
abstract = {Shankhpushpi is a reputed drug from an Indian system of medicine for treating mental disorders and enhancing memory. Two herbs, namely Convolvulus prostratus Forssk. and Evolvulus alsinoides (L.) L., are commonly known as Shankhpushpi. Ambiguous vernacular identity can affect the scientific validity of the Shankpushpi-based herbal drug therapy. In the present investigation, a novel and sensitive multiplex PCR method based on polymorphism in the internal transcribed spacer (ITS) region was developed to establish the molecular identity of C. prostratus and E. alsinoides. DNA was isolated and the ITS region was amplified, sequenced and assembled. Sequences were aligned to identify variable nucleotides in order to develop plant-specific primers. Primers were validated in singleplex reactions and eventually a multiplex assay was developed. This assay was tested for sensitivity and validated by amplifying DNA isolated from the simulated blended powdered plant material. Primers developed for C. prostratus resulted into a 200 bp amplicon and 596 bp for E. alsinoides. The assay was found to be sensitive enough for amplification of low quantities of DNA. The method can detect 10% of the mixing of plants with each other in blended material. This PCR assay can be used for rapid botanical identification of Shankhpushpi plant materials and will improve evidence-based herbal drug therapy.},
}
@article {pmid27173245,
year = {2016},
author = {Su, X and Liu, YP and Chen, Z and Chen, KL},
title = {Evaluation of candidate barcoding markers in Orinus (Poaceae).},
journal = {Genetics and molecular research : GMR},
volume = {15},
number = {2},
pages = {},
doi = {10.4238/gmr.15027714},
pmid = {27173245},
issn = {1676-5680},
mesh = {DNA Barcoding, Taxonomic/methods/*standards ; Genes, Chloroplast ; Genetic Markers ; Inverted Repeat Sequences ; Microsatellite Repeats ; Poaceae/classification/*genetics ; },
abstract = {Orinus is an alpine endemic genus of Poaceae. Because of the imperfect specimens, high level of intraspecific morphological variability, and homoplasies of morphological characters, it is relatively difficult to delimitate species of Orinus by using morphology alone. To this end, the DNA barcoding has shown great potential in identifying species. The present study is the first attempt to test the feasibility of four proposed DNA barcoding markers (matK, rbcL, trnH-psbA, and ITS) in identifying four currently revised species of Orinus from the Qinghai-Tibetan Plateau (QTP). Among all the single-barcode candidates, the differentiation power was the highest for the nuclear internal transcribed spacer (ITS), while the chloroplast barcodes matK (M), rbcL (R), and trnH-psbA (H) could not identify the species. Meanwhile, the differentiation efficiency of the nuclear ITS (I) was also higher than any two- or three-locus combination of chloroplast barcodes, or even a combination of ITS and any chloroplast barcode except H + I and R + I. All the combinations of chloroplast barcodes plus the nuclear ITS, H + I, and R + I differentiated the highest portion of species. The highest differentiation rate for the barcodes or barcode combinations examined here was 100% (H + I and R + I). In summary, this case study showed that the nuclear ITS region represents a more promising barcode than any maternally inherited chloroplast region or combination of chloroplast regions in differentiating Orinus species from the QTP. Moreover, combining the ITS region with chloroplast regions may improve the barcoding success rate.},
}
@article {pmid27172183,
year = {2016},
author = {Larson, A and Fair, BJ and Pleiss, JA},
title = {Interconnections Between RNA-Processing Pathways Revealed by a Sequencing-Based Genetic Screen for Pre-mRNA Splicing Mutants in Fission Yeast.},
journal = {G3 (Bethesda, Md.)},
volume = {6},
number = {6},
pages = {1513-1523},
pmid = {27172183},
issn = {2160-1836},
support = {R01 GM098634/GM/NIGMS NIH HHS/United States ; },
mesh = {Genetic Testing ; Genome-Wide Association Study ; Heterochromatin/genetics/metabolism ; Models, Biological ; *Mutation ; RNA Precursors/*genetics ; RNA Processing, Post-Transcriptional ; *RNA Splicing ; RNA Splicing Factors/genetics/metabolism ; RNA, Messenger/genetics ; Schizosaccharomyces/*genetics/metabolism ; Sequence Analysis, DNA ; },
abstract = {Pre-mRNA splicing is an essential component of eukaryotic gene expression and is highly conserved from unicellular yeasts to humans. Here, we present the development and implementation of a sequencing-based reverse genetic screen designed to identify nonessential genes that impact pre-mRNA splicing in the fission yeast Schizosaccharomyces pombe, an organism that shares many of the complex features of splicing in higher eukaryotes. Using a custom-designed barcoding scheme, we simultaneously queried ∼3000 mutant strains for their impact on the splicing efficiency of two endogenous pre-mRNAs. A total of 61 nonessential genes were identified whose deletions resulted in defects in pre-mRNA splicing; enriched among these were factors encoding known or predicted components of the spliceosome. Included among the candidates identified here are genes with well-characterized roles in other RNA-processing pathways, including heterochromatic silencing and 3' end processing. Splicing-sensitive microarrays confirm broad splicing defects for many of these factors, revealing novel functional connections between these pathways.},
}
@article {pmid27171471,
year = {2016},
author = {Sundberg, P and Kvist, S and Strand, M},
title = {Evaluating the Utility of Single-Locus DNA Barcoding for the Identification of Ribbon Worms (Phylum Nemertea).},
journal = {PloS one},
volume = {11},
number = {5},
pages = {e0155541},
pmid = {27171471},
issn = {1932-6203},
mesh = {Acanthocephala/*genetics ; Animals ; DNA/*genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; *Genetic Loci ; Likelihood Functions ; Species Specificity ; },
abstract = {Whereas many nemerteans (ribbon worms; phylum Nemertea) can be identified from external characters if observed alive, many are still problematic. When it comes to preserved specimens (as in e.g. marine inventories), there is a particular need for specimen identifier alternatives. Here, we evaluate the utility of COI (cytochrome c oxidase subunit I) as a single-locus barcoding gene. We sequenced, data mined, and compared gene fragments of COI for 915 individuals representing 161 unique taxonomic labels for 71 genera, and subjected different constellations of these to both distance-based and character-based DNA barcoding approaches, as well as species delimitation analyses. We searched for the presence or absence of a barcoding gap at different taxonomic levels (phylum, subclass, family and genus) in an attempt to understand at what level a putative barcoding gap presents itself. This was performed both using the taxonomic labels as species predictors and using objectively inferred species boundaries recovered from our species delimitation analyses. Our data suggest that COI works as a species identifier for most groups within the phylum, but also that COI data are obscured by misidentifications in sequence databases. Further, our results suggest that the number of predicted species within the dataset is (in some cases substantially) higher than the number of unique taxonomic labels-this highlights the presence of several cryptic lineages within well-established taxa and underscores the urgency of an updated taxonomic backbone for the phylum.},
}
@article {pmid27170425,
year = {2016},
author = {Pugedo, ML and de Andrade Neto, FR and Pessali, TC and Birindelli, JL and Carvalho, DC},
title = {Integrative taxonomy supports new candidate fish species in a poorly studied neotropical region: the Jequitinhonha River Basin.},
journal = {Genetica},
volume = {144},
number = {3},
pages = {341-349},
pmid = {27170425},
issn = {1573-6857},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Fishes/anatomy &amp; histology/*classification/*genetics ; Genetic Variation ; Phylogeny ; Rivers ; Sequence Analysis, DNA ; },
abstract = {Molecular identification through DNA barcoding has been proposed as a way to standardize a global biodiversity identification system using a partial sequence of the mitochondrial COI gene. We applied an integrative approach using DNA barcoding and traditional morphology-based bioassessment to identify fish from a neotropical region possessing low taxonomic knowledge: the Jequitinhonha River Basin (Southeastern Brazil). The Jequitinhonha River Basin (JRB) has a high rate of endemism and is considered an area of high priority for fish conservation, with estimates indicating the presence of around 110 native and non-indigenous species. DNA barcodes were obtained from 260 individuals belonging to 52 species distributed among 35 genera, 21 families and 6 orders, including threatened and rare species such as Rhamdia jequitinhonha and Steindachneridion amblyurum. The mean Kimura two-parameter genetic distances within species, genera and families were: 0.44, 12.16 and 20.58 %, respectively. Mean intraspecific genetic variation ranged from 0 to 11.43 %, and high values (>2 %) were recovered for five species. Species with a deep intraspecific distance, possibly flagging overlooked taxa, were detected within the genus Pimelodella. Fifteen species, only identified to the genus level, had unique BINs, with a nearest neighbor distance over 2 % and therefore, potential new candidate species supported by DNA barcoding. The integrative taxonomy approach using DNA barcoding and traditional taxonomy may be a remedy to taxonomy impediment, accelerating species identification by flagging potential new candidate species and to adequately conserve the megadiverse neotropical ichthyofauna.},
}
@article {pmid27169389,
year = {2016},
author = {Zinger, L and Philippe, H},
title = {Coalescing molecular evolution and DNA barcoding.},
journal = {Molecular ecology},
volume = {25},
number = {9},
pages = {1908-1910},
doi = {10.1111/mec.13639},
pmid = {27169389},
issn = {1365-294X},
mesh = {DNA/*genetics ; *DNA Barcoding, Taxonomic ; Ecology ; Evolution, Molecular ; },
abstract = {The DNA barcoding concept (Woese et al. ; Hebert et al.) has considerably boosted taxonomy research by facilitating the identification of specimens and discovery of new species. Used alone or in combination with DNA metabarcoding on environmental samples (Taberlet et al.), the approach is becoming a standard for basic and applied research in ecology, evolution and conservation across taxa, communities and ecosystems (Scheffers et al. ; Kress et al.). However, DNA barcoding suffers from several shortcomings that still remain overlooked, especially when it comes to species delineation (Collins &amp; Cruickshank). In this issue of Molecular Ecology, Barley &amp; Thomson () demonstrate that the choice of models of sequence evolution has substantial impacts on inferred genetic distances, with a propensity of the widely used Kimura 2-parameter model to lead to underestimated species richness. While DNA barcoding has been and will continue to be a powerful tool for specimen identification and preliminary taxonomic sorting, this work calls for a systematic assessment of substitution models fit on barcoding data used for species delineation and reopens the debate on the limitation of this approach.},
}
@article {pmid27169292,
year = {2015},
author = {Xiang, L and Tang, H and Cheng, JL and Chen, YL and Deng, W and Zheng, XS and Lai, ZT and Chen, SL},
title = {[The species traceability of the ultrafine powder and the cell wall-broken powder of herbal medicine based on DNA barcoding].},
journal = {Yao xue xue bao = Acta pharmaceutica Sinica},
volume = {50},
number = {12},
pages = {1660-1667},
pmid = {27169292},
issn = {0513-4870},
mesh = {Cell Wall ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Drugs, Chinese Herbal/*analysis ; Phylogeny ; Plants, Medicinal/*classification/genetics ; Powders ; Quality Control ; },
abstract = {Ultrafine powder and cell wall-broken powder of herbal medicine lack of the morphological characters and microscopic identification features. This makes it hard to identify herb's authenticity with traditional methods. We tested ITS2 sequence as DNA barcode in identification of herbal medicine in ultrafine powder and cell wall-broken powder in this study. We extracted genomic DNAs of 93 samples of 31 representative herbal medicines (28 species), which include whole plant, roots and bulbs, stems, leaves, flowers, fruits and seeds. The ITS2 sequences were amplified and sequenced bidirectionally. The ITS2 sequences were identified using Basic Local Alignment Search Tool (BLAST) method in the GenBank database and DNA barcoding system to identify the herbal medicine. The genetic distance was analyzed using the Kimura 2-parameter (K2P) model and the Neighbor-joining (NJ) phylogenetic tree was constructed using MEGA 6.0. The results showed that DNA can be extracted successfully from 93 samples and high quality ITS2 sequences can be amplified. All 31 herbal medicines can get correct identification via BLAST method. The ITS2 sequences of raw material medicines, ultrafine powder and cell wall-broken powder have same sequence in 26 herbal medicines, while the ITS2 sequences in other 5 herbal medicines exhibited variation. The maximum intraspecific genetic-distances of each species were all less than the minimum interspecific genetic distances. ITS2 sequences of each species are all converged to their standard DNA barcodes using NJ method. Therefore, using ITS2 barcode can accurately and effectively distinguish ultrafine powder and cell wall-broken powder of herbal medicine. It provides a new molecular method to identify ultrafine powder and cell wall-broken powder of herbal medicine in the quality control and market supervision.},
}
@article {pmid27169001,
year = {2016},
author = {Santos, AP and Takiya, DM and Nessimian, JL},
title = {Integrative taxonomy of Metrichia Ross (Trichoptera: Hydroptilidae: Ochrotrichiinae) microcaddisflies from Brazil: descriptions of twenty new species.},
journal = {PeerJ},
volume = {4},
number = {},
pages = {e2009},
pmid = {27169001},
issn = {2167-8359},
abstract = {Metrichia is assigned to the Ochrotrichiinae, a group of almost exclusively Neotropical microcaddisflies. Metrichia comprises over 100 described species and, despite its diversity, only one species has been described from Brazil so far. In this paper, we provide descriptions for 20 new species from 8 Brazilian states: M. acuminata sp. nov., M. azul sp. nov., M. bonita sp. nov., M. bracui sp. nov., M. caraca sp. nov., M. circuliforme sp. nov., M. curta sp. nov., M. farofa sp. nov., M. forceps sp. nov., M. formosinha sp. nov., M. goiana sp. nov., M. itabaiana sp. nov., M. longissima sp. nov., M. peluda sp. nov., M. rafaeli sp. nov., M. simples sp. nov., M. talhada sp. nov., M. tere sp. nov., M. ubajara sp. nov., and M. vulgaris sp. nov. DNA barcode sequences (577 bp of the mitochondrial gene COI) were generated for 13 of the new species and two previously known species of Metrichia resulting in 64 sequences. In addition, COI sequences were obtained for other genera of Ochrotrichiinae (Angrisanoia, Nothotrichia, Ochrotrichia, Ragatrichia, and Rhyacopsyche). DNA sequences and morphological data were integrated to evaluate species delimitations. K2P pairwise distances were calculated to generate a neighbor-joining tree. COI sequences also were submitted to ABGD and GMYC methods to assess 'potential species' delimitation. Analyses showed a conspicuous barcoding gap among Metrichia sequences (highest intraspecific divergence: 4.8%; lowest interspecific divergence: 12.6%). Molecular analyses also allowed the association of larvae and adults of Metrichia bonita sp. nov. from Mato Grosso do Sul, representing the first record of microcaddisfly larvae occurring in calcareous tufa (or travertine). ABGD results agreed with the morphological delimitation of Metrichia species, while GMYC estimated a slightly higher number of species, suggesting the division of two morphological species, each one into two potential species. Because this could be due to unbalanced sampling and the lack of morphological diagnostic characters, we have maintained these two species as undivided.},
}
@article {pmid27168243,
year = {2016},
author = {Höfer, T and Busch, K and Klapproth, K and Rodewald, HR},
title = {Fate Mapping and Quantitation of Hematopoiesis In Vivo.},
journal = {Annual review of immunology},
volume = {34},
number = {},
pages = {449-478},
doi = {10.1146/annurev-immunol-032414-112019},
pmid = {27168243},
issn = {1545-3278},
mesh = {Aging/*immunology ; Animals ; *Cell Differentiation ; Cell Lineage ; Cell Self Renewal ; *Hematopoiesis ; Hematopoietic Stem Cells/*physiology ; Humans ; Lymphoid Progenitor Cells/*physiology ; Mice ; Models, Theoretical ; Transcriptome ; },
abstract = {Hematopoietic stem cells (HSCs) and downstream progenitors have long been studied based on phenotype, cell purification, proliferation, and transplantation into myeloablated recipients. These experiments, complemented by data on expression profiles, mouse mutants, and humans with hematopoietic defects, are the foundation for the current hematopoietic differentiation tree. However, there are fundamental gaps in our knowledge of the quantitative and qualitative operation of the HSC/progenitor system under physiological and pathological conditions in vivo. The hallmarks of HSCs, self-renewal and multipotency, are observed in in vitro assays and cell transplantation experiments; however, the extent to which these features occur naturally in HSCs and progenitors remains uncertain. We focus here on work that strives to address these unresolved questions, with emphasis on fate mapping and modeling of the hematopoietic flow from stem cells toward myeloid and lymphoid lineages during development and adult life.},
}
@article {pmid27166994,
year = {2016},
author = {Houghton, J and Hadd, AG and Zeigler, R and Haynes, BC and Latham, GJ},
title = {Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {110},
pages = {e53836},
pmid = {27166994},
issn = {1940-087X},
mesh = {Biopsy, Fine-Needle ; Formaldehyde ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Multiplex Polymerase Chain Reaction ; Mutation ; Neoplasms/*pathology ; },
abstract = {All next-generation sequencing (NGS) procedures include assays performed at the laboratory bench ("wet bench") and data analyses conducted using bioinformatics pipelines ("dry bench"). Both elements are essential to produce accurate and reliable results, which are particularly critical for clinical laboratories. Targeted NGS technologies have increasingly found favor in oncology applications to help advance precision medicine objectives, yet the methods often involve disconnected and variable wet and dry bench workflows and uncoordinated reagent sets. In this report, we describe a method for sequencing challenging cancer specimens with a 21-gene panel as an example of a comprehensive targeted NGS system. The system integrates functional DNA quantification and qualification, single-tube multiplexed PCR enrichment, and library purification and normalization using analytically-verified, single-source reagents with a standalone bioinformatics suite. As a result, accurate variant calls from low-quality and low-quantity formalin-fixed, paraffin-embedded (FFPE) and fine-needle aspiration (FNA) tumor biopsies can be achieved. The method can routinely assess cancer-associated variants from an input of 400 amplifiable DNA copies, and is modular in design to accommodate new gene content. Two different types of analytically-defined controls provide quality assurance and help safeguard call accuracy with clinically-relevant samples. A flexible "tag" PCR step embeds platform-specific adaptors and index codes to allow sample barcoding and compatibility with common benchtop NGS instruments. Importantly, the protocol is streamlined and can produce 24 sequence-ready libraries in a single day. Finally, the approach links wet and dry bench processes by incorporating pre-analytical sample quality control results directly into the variant calling algorithms to improve mutation detection accuracy and differentiate false-negative and indeterminate calls. This targeted NGS method uses advances in both wetware and software to achieve high-depth, multiplexed sequencing and sensitive analysis of heterogeneous cancer samples for diagnostic applications.},
}
@article {pmid27159730,
year = {2017},
author = {Sharina, SN and Chernyshev, AV and Zaslavskaya, NI},
title = {Genetic diversity and phylogeny of limpets of the genus Nipponacmea (Patellogastropoda: Lottiidae) based on mitochondrial DNA sequences.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {5},
pages = {703-710},
doi = {10.3109/24701394.2016.1174224},
pmid = {27159730},
issn = {2470-1408},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Gastropoda/*classification/genetics ; *Genetic Variation ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {Species of the genus Nipponacmea inhabit only the Pacific coast of Asia, including the Russian Far East. Their external morphological characters are highly variable and often lead to misidentifications of species. So far, little research has been conducted using molecular markers. We used sequences from three mitochondrial genes (fragments of cytochrome c oxidase subunit I gene (COI), 12S and 16S rDNA). For comparison, additional genetic and taxonomic data on other species belonging to this genus were derived from GenBank. The molecular phylogenetic trees suggest that the species N. fuscoviridis and N. nigrans are species complexes. N. fuscoviridis is divided into three subgroups with high support and relatively large distances between them (N. fuscoviridis A, B and C); N. nigrans fall into two subgroups and one of them (N. nigrans A) is more closely related to N. moskalevi than to the other subgroup of N. nigrans (B).},
}
@article {pmid27159727,
year = {2017},
author = {Gaikwad, S and Warudkar, A and Shouche, Y},
title = {Efficacy of DNA barcoding for the species identification of spiders from Western Ghats of India.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {5},
pages = {638-644},
doi = {10.3109/24701394.2016.1166219},
pmid = {27159727},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Genetic Variation ; India ; Phylogeny ; Sequence Analysis, DNA/*methods ; Species Specificity ; Spiders/*classification/enzymology/genetics ; },
abstract = {DNA barcoding has emerged as an additional tool for taxonomy and as an aid to taxonomic impediments. Due to their extensive morphological variation, spiders are taxonomically challenging. Therefore, all over the world, attempts are being made to DNA barcode species of spiders. Till now no attempts were made to DNA barcode Indian spiders despite their rich diversity. We have generated DNA barcodes for 60 species (n = 112) of spiders for the first time from India. Although only 17 species were correctly identified at the species level, DNA barcoding correctly discriminated 99% of the species studied here. We have also found high intraspecies nucleotide divergence in Plexippus paykulli suggesting cryptic diversity that needs to be studied in detail. Our study also showed non-specific amplification of the Cytochrome Oxidase I (COI) gene of endosymbiont bacteria Wolbachia. However, these cases are very rare and could be resolved by the use of modified or group specific primers.},
}
@article {pmid27159722,
year = {2017},
author = {Hemalatha, A and Mohammed Esa, SAR and Suresh, M and Thajuddin, N and Anantharaman, P},
title = {Identification of Odontella aurita by rbcL gene sequence - a high antibacterial potential centric marine diatom.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {5},
pages = {655-661},
doi = {10.3109/24701394.2016.1166222},
pmid = {27159722},
issn = {2470-1408},
mesh = {Anti-Bacterial Agents/metabolism/*pharmacology ; Diatoms/genetics/*growth &amp; development/isolation &amp; purification ; Ethanol/metabolism/*pharmacology ; Microbial Sensitivity Tests ; Phylogeny ; Phytoplankton/genetics/growth &amp; development/isolation &amp; purification ; Proteus vulgaris/drug effects ; Ribulose-Bisphosphate Carboxylase/*genetics ; Sequence Analysis, DNA ; Staphylococcus haemolyticus/drug effects ; Vibrio alginolyticus/drug effects ; Water/*parasitology ; },
abstract = {The antibacterial potential of centric marine diatoms has been compared against the clinical pathogens and identified the potential diatom by rbcL gene sequencing. Totally, five diatoms namely Odontella aurita, Thalassiosira subtilis, Chaetoceros curvisetus, Skeletonema costatum and Coscinodiscus centralis were isolated from Cuddalore coastal waters. The diatoms were morphologically identified and isolated using micro capillary-pipette and serial dilution method. The isolated diatoms were cultured in Guillard's f/2 medium to get biomass for the antibacterial study. The dried biomass of the cultured diatoms was individually extracted with methanol, ethanol and hexane. All the obtained extracts were tested against Staphylococcus haemolyticus, Proteus vulgarius and Vibrio alginolyticus. The crude ethanol extract of O. aurita was exhibited highest zone of inhibition against all the test pathogens. The MIC of O. aurita was recorded as 50 μg/ml against both Staphylococcus haemolyticus and Proteus vulgarius whilst 75 μg/ml against Vibrio alginolyticus. This study indicates that O. aurita possesses antibacterial activities but the release of antibiotics depends on physical or chemical rupture of algal cells and extractive solvents. Based on the maximum antibacterial activity, O. aurita was further identified by rbcL gene sequencing. The rbcL gene could be an identical region for the species level identification of diatoms.},
}
@article {pmid27159716,
year = {2017},
author = {Özdemir, E and Altındağ, A and Kandemir, &#x130;},
title = {Molecular diversity of some species belonging to the genus Daphnia O. F. Müller, 1785 (Crustacea: Cladocera) in Turkey.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {3},
pages = {424-433},
doi = {10.3109/19401736.2015.1136303},
pmid = {27159716},
issn = {2470-1408},
mesh = {Animals ; DNA, Mitochondrial ; Daphnia/*genetics ; Electron Transport Complex IV/genetics ; Female ; *Genetic Variation ; *Haplotypes ; *Phylogeny ; Sequence Analysis, DNA ; Turkey ; },
abstract = {Daphnia is a freshwater zooplankton species with controversial taxonomy due to its high morphological variation linked to environmental factors and inter-specific hybridization and polyploidy in some groups. The aim of the present study is to examine molecular diversity of some Daphnia species in Turkey and to establish DNA barcodes of Turkish Daphnia species. Sequence analysis was performed using 540 bp region of cytochrome oxidase subunit I gene of mitochondrial DNA. A total of 34 haplotypes have been identified for Turkey. Daphnia pulex complex was divided into two clades with 16.1% sequence divergence according to molecular taxonomy based on Kimura 2-parameter. The clade which was molecularly diverged from Daphnia pulex with 16.1% sequence divergence was found to show 99% similarity with Daphnia cf. pulicaria (sensu Alonso 1996) instead of Daphnia pulicaria Forbes, 1893. Furthermore, this study has contributed to Turkish zoogeography by demonstrating the distribution of Daphnia species in Turkey.},
}
@article {pmid27159715,
year = {2017},
author = {Janjua, S and Fakhar-I-Abbas, and William, K and Malik, IU and Mehr, J},
title = {DNA Mini-barcoding for wildlife trade control: a case study on identification of highly processed animal materials.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {4},
pages = {544-546},
doi = {10.3109/24701394.2016.1155051},
pmid = {27159715},
issn = {2470-1408},
mesh = {Animals ; Animals, Wild/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Pakistan ; Pest Control ; Species Specificity ; },
abstract = {Although DNA barcoding is an efficient tool for species identification, however, its efficiency is uncertain for samples having degraded DNA and incomplete isolation/amplification of COI gene fragment (>500 bp). DNA mini-barcoding is a solution to this problem because small DNA fragment of COI genes is used for species identification. Twelve highly processed, chemically treated and finished animal skin (coats, tanned skins) and fur (mufflers) samples, received from the Sindh Wildlife Department, Pakistan, were subjected to DNA mini-barcoding. Eight mufflers belonged to Vulpes vulpes, one coat to Ursus thibetanus, one tanned skin to Lutra sumatrana, and one muffler to Vulpes sp. Origin of only one coat sample remained unidentified, success rate of 92% indicative of the fact that the mini barcoding technique can be used as a substitute of conventional barcoding where full length barcode (∼650 bp Folmer region) cannot be generated.},
}
@article {pmid27159710,
year = {2017},
author = {Huang, Z and Tu, F},
title = {DNA barcoding and phylogeny of Calidris and Tringa (Aves: Scolopacidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {4},
pages = {616-619},
doi = {10.3109/24701394.2016.1155121},
pmid = {27159710},
issn = {2470-1408},
mesh = {Animals ; Avian Proteins/genetics ; Birds/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Mitochondrial Proteins/genetics ; Phylogeny ; },
abstract = {The avian genera Calidris and Tringa are the largest of the widespread family of Scolopacidae. The phylogeny of members of the two genera is still a matter of controversial. Mitochondrial cytochrome c oxidase subunit I (COI) can serve as a fast and accurate marker for the identification and phylogeny of animal species. In this study, we analyzed the COI barcodes of thirty-one species of the two genera. All the species had distinct COI sequences. Two hundred and twenty-one variable sites were identified. Kimura two-parameter distances were calculated between barcodes. Neighbor-joining and maximum likelihood methods were used to construct phylogenetic trees. All the species could be discriminated by their distinct clades in the phylogenetic trees. The phylogenetic trees grouped all the species of Calidris and Tringa into different monophyletic clade, respectively. COI data showed a well-supported phylogeny for Calidris and Tringa species.},
}
@article {pmid27159707,
year = {2017},
author = {Shimabukuro-Dias, CK and Costa Silva, GJD and Ashikaga, FY and Foresti, F and Oliveira, C},
title = {Molecular identification of the fish fauna from the pantanal flood plain area in Brazil.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {4},
pages = {588-592},
doi = {10.3109/24701394.2016.1149826},
pmid = {27159707},
issn = {2470-1408},
mesh = {Animals ; Biodiversity ; Brazil ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Fish Proteins/genetics ; Fishes/*classification/genetics ; Phylogeny ; Rivers ; Species Specificity ; },
abstract = {The Pantanal is under the influence of the Paraguay River flood regime is considered to be one of the largest wetlands of the world, and has rich biodiversity, including fishes. Until now, the identification of fish species in this biome has only considered the morphological characteristics of individuals, and the present work aimed to identify the fish species of the Pantanal region through the DNA barcode methodology for investigating the biodiversity in this region. The genetic analysis of 638 samples via the GMYC approach identified 137 operational taxonomic units (OTUs) belonging to 127 species that have previously been described according to their morphological characteristics. Data suggest that 10 cases of morphospecies (Eigenmannia trileneata, E. virescens, Pimelodella gracilis, Brachyhypopomus pinnicaudatus, Brachyhypopomus sp., Ancistrus sp., Hyphessobrycon eques, Jupiaba acanthogaster, and Serrapinnus calliurus) represent complexes of cryptic species, and the number of species described in the Pantanal region has thus potentially been underestimated.},
}
@article {pmid27159705,
year = {2017},
author = {Ordoñez, JFF and Ventolero, MFH and Santos, MD},
title = {Maternal mismatches in farmed tilapia strains (Oreochromis spp.) in the Philippines as revealed by mitochondrial COI gene.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {4},
pages = {526-535},
doi = {10.3109/24701394.2016.1149824},
pmid = {27159705},
issn = {2470-1408},
mesh = {Animals ; Animals, Genetically Modified ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Fisheries ; Genes, Mitochondrial ; Philippines ; Phylogeny ; Tilapia/*genetics ; },
abstract = {The introduction of genetically enhanced tilapia has significantly boosted the performance of Philippine aquaculture industry. While enhanced strains contribute to the increase in tilapia production, genetic characterization of present tilapia stocks is critical to maintain their quality and to ensure the genetic gains are sustained. To understand and determine the genetic relationship of the genetically enhanced strains produced in the Philippines, mitochondrial cytochrome oxidase subunit I (COI) gene using DNA barcoding approach was analyzed. Specimens representing 10 genetically enhanced strains (GIFT, FaST, GET-EXCEL, GST, SST, COLD, YY-male, GMT, Molobicus, and BEST), three red tilapia (Taiwan red, Florida red, and FAC-red), and two pure lines (initially identified as O. aureus and O. spilurus) were collected, sequenced, and identified using DNA barcoding. Results revealed that farmed tilapias consisted of four different Oreochromis species. As expected, COI could not distinguish individuals at the strain level but surprisingly, mismatch between the species of maternal origin and present-day offspring was observed. This particular result may pose a question on the genetic purity and integrity of the strains being distributed to farmers and suggests a re-evaluation of the effectiveness of major tilapia breeding centers in maintaining their stocks.},
}
@article {pmid27159700,
year = {2017},
author = {Kartavtsev, YP and Batischeva, NM and Bogutskaya, NG and Katugina, AO and Hanzawa, N},
title = {Molecular systematics and DNA barcoding of Altai osmans, oreoleuciscus (pisces, cyprinidae, and leuciscinae), and their nearest relatives, inferred from sequences of cytochrome b (Cyt-b), cytochrome oxidase c (Co-1), and complete mitochondrial genome.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {4},
pages = {502-517},
doi = {10.3109/24701394.2016.1149822},
pmid = {27159700},
issn = {2470-1408},
mesh = {Animals ; Cyprinidae/*classification/genetics ; Cytochromes b/*genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Fish Proteins/genetics ; Genome, Mitochondrial ; Phylogeny ; Species Specificity ; },
abstract = {Mitochondrial DNA (mtDNA) at the protein-coding Cyt-b gene along with data retrieved from GenBank for Co-1 gene fragments and complete mitochondrial genome (mitogenome) of Altai osmans and the nearest relatives of Leuciscinae fish species were compared for the estimation of variability and phylogenetic tree building. Phylogenetic trees were built by four techniques: Bayesian (BA), maximum likelihood (ML), maximum parsimony (MP), and neighbor-joining (NJ). Resolution of Cyt-b trees for species of two genera (Oreoleuciscus and Phoxinus) was quite distinct at all the approaches. For Tribolodon, the single gene trees were not well resolved; however, the mitogenome tree was resolved. Species identification on per individual basis (DNA barcoding) was high for both Cyt-b and Co-1 genes. The trees built using the data for 13 protein mitochondrial genes revealed a complicated phylogenetic pattern within the subfamily Leuciscinae. Scores of the average p-distances at three taxonomic levels were considerably different: (1) 1.16 ± 0.96, (2) 8.21 ± 1.01, and (3) 16.41 ± 0.85 for Cyt-b and (1) 1.04 ± 0.78, (2) 8.30 ± 0.92, and (3) 10.74 ± 0.79 for 13 protein genes of mitogenome, where (1) is intraspecies, (2) is intragenus, and (3) is intrasubfamily levels. Data on mitogenome distances were summarized for the taxonomic hierarchy for the first time. A concordant increase in distance score with growth of the rank of taxa (having the minimum score at the intraspecies level), both for a single gene and the whole mitogenome, substantiates the concept that speciation in the subfamily Leuciscinae in most cases follows the geographic mode. The distinct clustering of Altai osmans, Oreoleuciscus potanini and O. humilis, in the Cyt-b and Co-1 gene trees with small overall genetic distances, obtained for both genes, allows us to consider these taxa as separate but genetically sister species.},
}
@article {pmid27159695,
year = {2017},
author = {Bineesh, KK and Gopalakrishnan, A and Akhilesh, KV and Sajeela, KA and Abdussamad, EM and Pillai, NGK and Basheer, VS and Jena, JK and Ward, RD},
title = {DNA barcoding reveals species composition of sharks and rays in the Indian commercial fishery.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {4},
pages = {458-472},
doi = {10.3109/19401736.2015.1137900},
pmid = {27159695},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Fish Proteins/genetics ; Fisheries ; India ; Phylogeny ; Sharks/*classification/genetics ; Skates, Fish/*classification/genetics ; Species Specificity ; },
abstract = {DNA barcoding was successfully used for the accurate identification of chondrichthyans in the Indian commercial marine fishery. About 528 specimens of 111 chondrichthyan species and 34 families, collected from the Indian EEZ, were barcoded for a 655 bp region of the mitochondrial gene cytochrome c oxidase subunit 1 (COI). Generally, five specimens per species were barcoded, but numbers ranged from 2 to 13. The average Kimura 2 parameter (K2P) distance separating individuals within species was 0.32%, and the average distance separating species within genera was 6.73%. Ten species were suggested as putative new species requiring formal descriptions. Based on the morphology and molecular support, 11 elasmobranch species were confirmed first records for Indian waters. The present study confirms the ability of DNA barcoding for the accurate identification of sharks, rays, and their products from Indian waters.},
}
@article {pmid27159693,
year = {2017},
author = {Laskar, BA and Kumar, V and Kundu, S and Tyagi, K and Singha, D and Chakraborty, R and Chatterjee, S and Saha, S},
title = {DNA barcoding of Gobiid fishes (Perciformes: Gobiidae) from eastern and northeastern India with new record of a Gobionellinae species for the region.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {4},
pages = {584-587},
doi = {10.3109/24701394.2016.1143470},
pmid = {27159693},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Fish Proteins/genetics ; India ; Perciformes/*classification/genetics ; Phylogeny ; Species Specificity ; },
abstract = {The study attempted identification of Gobiid fishes from freshwaters in the east and northeast India on a collection of 20 specimens. The DNA barcode data delineated the collected samples into three species clades in the neighbor-joining tree. The results confirmed the identification of five sample sequences belonging to the subfamily Gobionellinae due to cohesive cladding with Awaous congeners. This is a new subfamily record for the northeastern region. Another 15 sample sequences showed conspecific cladding with Glossogobius giuris in the database. Among the 15 sample sequences, 14 sequences cladded with G. giuris sequences of Indian specimens while one sample sequence cladded with G. giuris sequences of South African specimens. This indicated the presence of either a hidden species or a previously synonymized species in the G. giuris complex.},
}
@article {pmid27159689,
year = {2017},
author = {Jose, D and Harikrishnan, M},
title = {Non-homologous COI barcode regions: a serious concern in decapod molecular taxonomy.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {4},
pages = {482-492},
doi = {10.3109/19401736.2015.1137902},
pmid = {27159689},
issn = {2470-1408},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Decapoda/*classification/genetics ; Electron Transport Complex IV/*genetics ; Phylogeny ; },
abstract = {Biodiversity is well defined with the assistance of taxonomy, the science which classifies organisms with "species" as the basic unit. Presently, in taxonomy, morphological type specimen is complimented with its molecular data from "type" gene sequences and species status is granted. For this, DNA barcoding using standardized DNA gene(s) is performed in which Cytochrome c oxidase I gene of mitochondrial DNA is referred as the primary barcode region for animal kingdom. Being a popular mitochondrial marker, this gene is reported to possess two barcode regions with limited overlap, "Folmer" and "Palumbi" regions particularly in decapod crustaceans. Here we demonstrate the issues originated as a result of incorporation of both these barcode regions together in addressing various aspects of DNA barcoding like specimen identification, population analysis, and phylogeny in decapod crustaceans using COI sequences ("Folmer" and "Palumbi") of Macrobrachium rosenbergii as reference sequences.},
}
@article {pmid27159687,
year = {2017},
author = {Basheer, VS and Vineesh, N and Bineesh, KK and Kumar, RG and Mohitha, C and Venu, S and Kathirvelpandian, A and Gopalakrishnan, A and Jena, JK},
title = {Mitochondrial signatures for identification of grouper species from Indian waters.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {4},
pages = {451-457},
doi = {10.3109/19401736.2015.1137899},
pmid = {27159687},
issn = {2470-1408},
mesh = {Animals ; Bass/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Fish Proteins/genetics ; India ; Mitochondria/genetics ; Phylogeny ; Species Specificity ; },
abstract = {Groupers are important commercial fish in many parts of the world. Accurate identification is critical for effective conservation assessment and fisheries management. Genetic barcodes provide a simple and reproducible method for the identification of species even in the absence of taxonomic expertise. The generation of reference barcodes from properly identified specimens is an important first step in this direction. Here, 36 species belonging to the subfamily Epinephelinae (Family: Serranidae) were collected from landings on the west coast of India and Port Blair, Andaman, and partial nucleotide sequence data of the mitochondrial cytochrome C oxidase subunit I (COI) gene was generated. Barcodes for 13 species were developed from Indian waters for the first time. Analysis using the COI gene produced phylogenetic trees in concurrence with other multi-gene studies. Epinephelus fasciatus and E. areolatus were found to be a species complex, as hypothesized in other studies. The DNA barcodes developed in the study can be used for identifying species within Epinehelinae, where taxonomic ambiguity still exists.},
}
@article {pmid27159585,
year = {2017},
author = {Mateussi, NTB and Pavanelli, CS and Oliveira, C},
title = {Molecular identification of cryptic diversity in species of cis-Andean Mylossoma (Characiformes: Serrasalmidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {5},
pages = {778-780},
doi = {10.1080/24701394.2016.1180515},
pmid = {27159585},
issn = {2470-1408},
mesh = {Animals ; Characiformes/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Fish Proteins/genetics ; Genetic Variation ; Genome, Mitochondrial ; Phylogeny ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
abstract = {Mylossoma is a Serrasalmidae genus with only two current valid species in the cis-Andean region but with several available names, today considered as junior synonymous. Morphological information combined with single-locus DNA sequences of cytochrome c oxidase I gene analysed by Barcode Index Number and General Mixed Yule Coalescent model were used in the present study to help the recognition of Operational Taxonomic Units (OTUs) in cis-Andean Mylossoma and discuss species boundaries within the genus. Five OTUs were recognized based on both morphological and molecular approaches. The analysis using the Barcode Index Number resulted in five OTUs, with M. duriventre being split in one unity in the Amazon, one in the Orinoco, one in Paraná-Paraguay and one in Tocantins-Araguaia which is coherent with our morphological results.},
}
@article {pmid27159502,
year = {2017},
author = {Amin Laskar, B and Kumar, V and Darshan, A and Kundu, S and Narayan Das, D},
title = {DNA barcoding of Amblyceps congeners (Siluriformes: Amblycipitidae) from Brahmaputra drainage in northeast India.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {5},
pages = {698-702},
doi = {10.3109/24701394.2016.1174223},
pmid = {27159502},
issn = {2470-1408},
mesh = {Animals ; Bayes Theorem ; Catfishes/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; Genome, Mitochondrial ; India ; Phylogeny ; Rivers ; Sequence Analysis, DNA/*methods ; },
abstract = {The genus Amblyceps is recognized with 18 valid species inhabiting in fast flowing rivers mostly in South and Southeast Asia. We generated 10 mtCOI sequences for four species of Amblyceps from Brahmaputra River drainage that along with conspecific database sequences were analysed in MEGA and Mr. Bayes while Automatic Barcode Gap Discover (ABGD) was performed at web interface. Lowest between species K2P ranged from 8.7% to 16.4% compared to highest within species K2P of only 2.2%. Molecular data clearly delineated studied Amblyceps congeners into four distinct species by all the three methods of analysis employed that was congruent with the morphology based identification at species level, except a minor morphological variation observed for A. mangois specimens. Our results agree with the recent resurrection of A. arunchalensis from synonym of A. mangois. We provide three new sequences for A. laticeps and identified a mislabelled sequence of A. apangi in database.},
}
@article {pmid27159120,
year = {2016},
author = {Tingström, O and Wesula Lwande, O and Näslund, J and Spyckerelle, I and Engdahl, C and Von Schoenberg, P and Ahlm, C and Evander, M and Bucht, G},
title = {Detection of Sindbis and Inkoo Virus RNA in Genetically Typed Mosquito Larvae Sampled in Northern Sweden.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {16},
number = {7},
pages = {461-467},
pmid = {27159120},
issn = {1557-7759},
mesh = {Animals ; Culicidae/genetics/*virology ; Insect Vectors/*virology ; Larva/genetics ; Polymerase Chain Reaction/methods ; RNA, Viral/*isolation &amp; purification ; Sindbis Virus/*isolation &amp; purification ; Sweden ; },
abstract = {INTRODUCTION: Mosquito-borne viruses have a widespread distribution across the globe and are known to pose serious threats to human and animal health. The maintenance and dissemination of these viruses in nature are driven through horizontal and vertical transmission. In the temperate climate of northern Sweden, there is a dearth of knowledge on whether mosquito-borne viruses that occur are transmitted transovarially. To gain a better understanding of mosquito-borne virus circulation and maintenance, mosquito larvae were sampled in northern Sweden during the first and second year after a large outbreak of Ockelbo disease in 2013 caused by Sindbis virus (SINV).<br><br>MATERIALS AND METHODS: A total of 3123 larvae were sampled during the summers of 2014 and 2015 at multiple sites in northern Sweden. The larvae were homogenized and screened for viruses using RT-PCR and sequencing. Species identification of selected larvae was performed by genetic barcoding targeting the cytochrome C oxidase subunit I gene.<br><br>RESULTS AND DISCUSSION: SINV RNA was detected in mosquito larvae of three different species, Ochlerotatus (Oc.) communis, Oc. punctor, and Oc. diantaeus. Inkoo virus (INKV) RNA was detected in Oc. communis larvae. This finding suggested that these mosquitoes could support transovarial transmission of SINV and INKV. Detection of virus in mosquito larva may serve as an early warning for emerging arboviral diseases and add information to epidemiological investigations before, during, and after outbreaks. Furthermore, our results demonstrated the relevance of genetic barcoding as an attractive and effective method for mosquito larva typing. However, further mosquito transmission studies are needed to ascertain the possible role of different mosquito species and developmental stages in the transmission cycle of arboviruses.},
}
@article {pmid27158792,
year = {2016},
author = {K Lim, B and Arcila Hernandez, LM},
title = {DNA barcoding of Jamaican bats: implications to Neotropical biodiversity.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {4},
pages = {3013-3019},
doi = {10.3109/19401736.2015.1063047},
pmid = {27158792},
issn = {2470-1408},
mesh = {Animals ; Biodiversity ; Chiroptera/*classification/*genetics ; *DNA Barcoding, Taxonomic/methods ; Electron Transport Complex IV/genetics ; Geography ; Jamaica ; Phylogeny ; Phylogeography ; },
abstract = {We report on the first comprehensive DNA barcoding survey of bats from Jamaica and compare the genetic variation to similar species on South America and Central America. Bats comprise the majority of mammalian diversity in typical lowland forest in the Neotropics, but the Caribbean is one noticeable geographic gap in the International Barcode of Life reference database. Of the 20 known species reported from Jamaica, half were DNA barcoded and were genetically distinct with interspecific variation ranging from 17 to 33%. By contrast, intraspecific variation ranged from 0 to 0.5% indicating that the barcode gap was sufficient in differentiating bat species diversity in Jamaica. The low levels of intraspecific divergence indicate that the populations within each species are relatively homogeneous across the island. There were, however, several cases of high sequence divergence for widely distributed species that occur on both the Caribbean islands and the continental mainland, which warrant further taxonomic study.},
}
@article {pmid27156886,
year = {2016},
author = {Parekh, S and Ziegenhain, C and Vieth, B and Enard, W and Hellmann, I},
title = {The impact of amplification on differential expression analyses by RNA-seq.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {25533},
pmid = {27156886},
issn = {2045-2322},
mesh = {Databases, Genetic ; Gene Expression Profiling/*methods ; Gene Expression Regulation ; Gene Library ; HCT116 Cells ; Humans ; Sequence Analysis, RNA/*methods ; },
abstract = {Currently, quantitative RNA-seq methods are pushed to work with increasingly small starting amounts of RNA that require amplification. However, it is unclear how much noise or bias amplification introduces and how this affects precision and accuracy of RNA quantification. To assess the effects of amplification, reads that originated from the same RNA molecule (PCR-duplicates) need to be identified. Computationally, read duplicates are defined by their mapping position, which does not distinguish PCR- from natural duplicates and hence it is unclear how to treat duplicated reads. Here, we generate and analyse RNA-seq data sets prepared using three different protocols (Smart-Seq, TruSeq and UMI-seq). We find that a large fraction of computationally identified read duplicates are not PCR duplicates and can be explained by sampling and fragmentation bias. Consequently, the computational removal of duplicates does improve neither accuracy nor precision and can actually worsen the power and the False Discovery Rate (FDR) for differential gene expression. Even when duplicates are experimentally identified by unique molecular identifiers (UMIs), power and FDR are only mildly improved. However, the pooling of samples as made possible by the early barcoding of the UMI-protocol leads to an appreciable increase in the power to detect differentially expressed genes.},
}
@article {pmid27151404,
year = {2016},
author = {Otomo, PV and Otomo, LV and Bezuidenhout, CC and Maboeta, MS},
title = {Preliminary evidence of differences in cadmium tolerance in metal-free stocks of the standard earthworm test species Eisenia andrei (Oligochaeta).},
journal = {Ecotoxicology (London, England)},
volume = {25},
number = {6},
pages = {1119-1125},
pmid = {27151404},
issn = {1573-3017},
mesh = {Adaptation, Physiological ; Animals ; Ecotoxicology ; Metals/*toxicity ; Oligochaeta/*physiology ; Soil Pollutants/*toxicity ; *Toxicity Tests ; },
abstract = {To test whether metal-tolerant and metal-sensitive earthworm specimens could be an inherent part of metal-free earthworm populations, (i) we used DNA barcoding to identify and categorize earthworms from 8 populations of the standard test species Eisenia andrei, and (ii) the earthworms carrying three of the identified COI haplotypes (named Hap1, hap3 and Hap3) were paired up and exposed to Cd in order to assess the difference in Cd sensitivity between the breeding pairs. A total of six breeding pairs were exposed to 0, 25, 50 and 100 mg Cd/kg for 4 weeks at 20 °C. The survival of the breeding pairs, their change in biomass and cocoon production were assessed. For all of the endpoints assessed, the results indicated that couple 6 (Hap3 × Hap3) was the most sensitive breeding pair whereas couple 4 (Hap1 × Hap3) was the least sensitive one. The analysis of Cd tissue contents revealed that with increasing Cd concentration, Cp6 (Hap3 × Hap3) could accumulate significantly more Cd than any other breeding pair (p ≤ 0.01). Our findings indicate that E. andrei may harbour intrinsically Cd-tolerant and Cd-sensitive individuals and that this may be due to individual differences in Cd accumulation kinetics. In the context of ecotoxicological testing, our results underline the importance of using genetically diverse populations in laboratory testing to prevent generating flawed data from genetically homogeneous laboratory stocks. Although we do not regard the present mitochondrial haplotypes as proxy for possibly nuclear encoded traits, we discuss the necessity of a standardised earthworm barcoding protocol that could help not only to confirm the taxonomy of laboratory earthworm stocks but also to select genetically diverse stocks suitable for laboratory testing.},
}
@article {pmid27150996,
year = {2016},
author = {Ma, L and Jiang, YW and Wang, ST and Liu, Q and Cong, X and Shen, J and Cao, YY and Cao, YT},
title = {[Application of High-throughput Sequencing in Acute Myeloid Leukemia Patients with Positive FLT3-ITD].},
journal = {Zhongguo shi yan xue ye xue za zhi},
volume = {24},
number = {2},
pages = {381-387},
doi = {10.7534/j.issn.1009-2137.2016.02.014},
pmid = {27150996},
issn = {1009-2137},
mesh = {Alleles ; DNA Mutational Analysis ; Genotype ; High-Throughput Nucleotide Sequencing ; Humans ; Leukemia, Myeloid, Acute/*genetics ; Mutation ; Polymerase Chain Reaction ; *Tandem Repeat Sequences ; fms-Like Tyrosine Kinase 3/*genetics ; },
abstract = {UNLABELLED: OBJECTICE: To evaluate the application of high-throughput sequencing to sequence the FMS-like Tyrosine Kinase 3 internal tandem duplication (FLT3-ITD) in de novo acute myeloid leukemia (AML) patients with lower allelic ratio FLT3-ITD mutation or more than one ITD, and to analyze the feature of ITD.<br><br>METHODS: The genomic DNA of 23 AML patients with positive FLT3-ITD was amplified by PCR, capillary electrophoresis was used to detect the ITD mutation. Then, the FLT3 gene was amplified using primer with different barcode, and the product was analyzed by illumina Miseq, and the results were compared with UCSC database.<br><br>RESULTS: Out of 23 AML patients, 17 had a single ITD, and 3 had 2 ITDs, and the remaining 3 had 3 ITD detected by capillary electrophoresis. The high-throughput sequencing showed that 17 ITD were the complate duplications of wild-type FLT3, and the remaining 16 ITD were partial duplications in the all 33 ITDs. The same length ITD mutation contained 2 different ITD sequences in one patient with more than one ITD, and the other patient with 2 ITD had the same ITD insertion position. The ITD occurred in the regions from p. Y572 to p. L602 of the FLT3 protein, and all the patient ITD covered one or more amino acid between p. V592 and p. E598.<br><br>CONCLUSION: Illumina Miseq can analyze the sequence of ITDs precisely and accurately. ITD mutation varies widely, but the hotspots are concentrated.},
}
@article {pmid27150350,
year = {2016},
author = {Ortiz, D and Francke, OF},
title = {Two DNA barcodes and morphology for multi-method species delimitation in Bonnetina tarantulas (Araneae: Theraphosidae).},
journal = {Molecular phylogenetics and evolution},
volume = {101},
number = {},
pages = {176-193},
doi = {10.1016/j.ympev.2016.05.003},
pmid = {27150350},
issn = {1095-9513},
mesh = {Animals ; DNA/chemistry/isolation &amp; purification/metabolism ; DNA Barcoding, Taxonomic ; Female ; Male ; Mexico ; Mitochondria/genetics ; Phylogeny ; Spiders/*classification/genetics ; },
abstract = {Determining species boundaries is a central debate in biology. Several recently developed molecular delimitation methods have highlighted extensive inconsistency in classical morphological taxonomy. However, choosing between them is contentious. Molecular studies on theraphosid spiders have found considerable cryptic diversity and many species redundantly described. Most of these studies have relied only on COI, a mitochondrial marker that has proven its efficacy in animal studies, but which also might lead to an over-estimation of diversity. Here we present an integrative approach to species delimitation in Bonnetina, a poorly known group of tarantulas endemic to Mexico. We employed morphological evidence, as well as different setups with distance-based (Hard-Gap barcoding and ABGD) and tree-based (GMYC, PTP and BPP) molecular barcoding approaches, using one mitochondrial (COI) and one nuclear (ITS1) rapidly evolving loci. BPP is also used as a multi-locus method. We also explored the influence of ambiguous alignment choice and of coding gaps as characters in phylogenetic inference and in species delimitation with that marker. Different delimitation methods with COI gave moderately variable results and this gene exhibited a universal barcode gap. The ITS1 gene tree was well supported and robust to alignment choice; with this locus, coding gaps improved branch support and species delimitation with PTP. No universal barcode gap was found with ITS1, and single locus delimitations returned disparate results. However, this locus helped to highlight cases of under- and overestimations by COI. BPP gave solutions with many lineages, in single locus and combined analyses, especially with the recently implemented unguided methodology. We recognize 12 robustly supported species in our data set, of which seven remain undescribed, and three are morphologically cryptic. For COI Bonnetina species identification, we propose intra- and inter-specific thresholds of 2% and 6% sequence divergence, respectively. We conclude that morphological signal for species delimitation in Bonnetina is higher than for other studied tarantulas, but it fails to recognize several lineages in the genus. COI is a functional barcoding marker, and the most reliable source of evidence that we used, but it may also lead to inaccurate delimitations. ITS1 is a highly informative locus for species delimitation and species-level phylogeny, but it performs poorly as a barcoding marker. Due to variability between delimitation methods, we suggest combining evidence from multiple approaches to get better-supported results.},
}
@article {pmid27150245,
year = {2016},
author = {Malakauskas, DM and Snipes, RB and Thompson, AM and Schloesser, DW},
title = {Molecular evidence of undescribed Ceratonova sp. (Cnidaria: Myxosporea) in the freshwater polychaete, Manayunkia speciosa, from western Lake Erie.},
journal = {Journal of invertebrate pathology},
volume = {137},
number = {},
pages = {49-53},
doi = {10.1016/j.jip.2016.05.001},
pmid = {27150245},
issn = {1096-0805},
mesh = {Animals ; Genes, Protozoan/genetics ; Lakes/parasitology ; Michigan ; Myxozoa/*genetics ; Parasitic Diseases, Animal/parasitology ; Phylogeny ; Polychaeta/*parasitology ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {We used PCR to screen pooled individuals of Manayunkia speciosa from western Lake Erie, Michigan, USA for myxosporean parasites. Amplicons from positive PCRs were sequenced and showed a Ceratonova species in an estimated 1.1% (95% CI=0.46%, 1.8%) of M. speciosa individuals. We sequenced 18S, ITS1, 5.8S, ITS2 and most of the 28S rDNA regions of this Ceratonova sp., and part of the protein-coding EF2 gene. Phylogenetic analyses of ribosomal and EF2 sequences showed the Lake Erie Ceratonova sp. is most similar to, but genetically distinct from, Ceratonova shasta. Marked interspecific polymorphism in all genes examined, including the ITS barcoding genes, along with geographic location suggests this is an undescribed Ceratonova species. COI sequences showed M. speciosa individuals in Michigan and California are the same species. These findings represent a third parasite in the genus Ceratonova potentially hosted by M. speciosa.},
}
@article {pmid27149077,
year = {2016},
author = {Meyin A Ebong, S and Petit, E and Le Gall, P and Chen, PP and Nieser, N and Guilbert, E and Njiokou, F and Marsollier, L and Guégan, JF and Pluot-Sigwalt, D and Eyangoh, S and Harry, M},
title = {Molecular Species Delimitation and Morphology of Aquatic and Sub-Aquatic Bugs (Heteroptera) in Cameroon.},
journal = {PloS one},
volume = {11},
number = {5},
pages = {e0154905},
pmid = {27149077},
issn = {1932-6203},
mesh = {Animals ; Aquatic Organisms/genetics ; Biodiversity ; Cameroon ; DNA/genetics ; DNA Barcoding, Taxonomic ; Female ; Heteroptera/anatomy &amp; histology/*genetics ; Male ; Phylogeny ; Sequence Alignment ; },
abstract = {Aquatic and semi-aquatic bugs (Heteroptera) represent a remarkable diversity and a resurging interest has been given to documenting at the species level these insects inhabiting Cameroon in Central Africa due to their potential implication in the transmission of the bacterium Mycobacterium ulcerans, the causal agent of Buruli ulcer, an emerging human disease. A survey was carried out over two years in Cameroon. Morphological analyses were done in two steps. A first step consisted in separating the specimens based on broadly shared characters into morphotypes. The specimens were then separated into two independent batches containing each the same representation of each morphotype. One batch (309 specimens) was used by taxonomy experts on aquatic bugs for species level identification and/or to reconcile nymph with their corresponding adult species. The second batch (188 specimens) was used to define species based on the COI DNA sequences (standard sequence used for "DNA barcoding") and using the Automatic Barcode Gap Discovery (ABGD) method. The first morphological analysis step separated the specimens into 63 different morphotypes (49 adults and 14 nymphs), which were then found to belong to 54 morphological species in the infra-orders Gerromorpha and Nepomorpha based on the species-level morphological identification, and 41-45 putative molecular species according to the gap value retained in the ABGD. Integrating morphology and "DNA barcoding" reconciled all the specimens into 62 aquatic bug species in Cameroon. Generally, we obtained a good congruence between species a priori identified based on morphology from adult morphotypes and molecular putative species. Moreover, molecular identification has allowed the association of 86% of nymphs with adults. This work illustrates the importance of integrative taxonomy.},
}
@article {pmid27148239,
year = {2016},
author = {Aires, T and Serrão, EA and Engelen, AH},
title = {Host and Environmental Specificity in Bacterial Communities Associated to Two Highly Invasive Marine Species (Genus Asparagopsis).},
journal = {Frontiers in microbiology},
volume = {7},
number = {},
pages = {559},
pmid = {27148239},
issn = {1664-302X},
abstract = {As habitats change due to global and local pressures, population resilience, and adaptive processes depend not only on their gene pools but also on their associated bacteria communities. The hologenome can play a determinant role in adaptive evolution of higher organisms that rely on their bacterial associates for vital processes. In this study, we focus on the associated bacteria of the two most invasive seaweeds in southwest Iberia (coastal mainland) and nearby offshore Atlantic islands, Asparagopsis taxiformis and Asparagopsis armata. Bacterial communities were characterized using 16S rRNA barcoding through 454 next generation sequencing and exploratory shotgun metagenomics to provide functional insights and a backbone for future functional studies. The bacterial community composition was clearly different between the two species A. taxiformis and A. armata and between continental and island habitats. The latter was mainly due to higher abundances of Acidimicrobiales, Sphingomonadales, Xanthomonadales, Myxococcales, and Alteromonadales on the continent. Metabolic assignments for these groups contained a higher number of reads in functions related to oxidative stress and resistance to toxic compounds, more precisely heavy metals. These results are in agreement with their usual association with hydrocarbon degradation and heavy-metals detoxification. In contrast, A. taxiformis from islands contained more bacteria related to oligotrophic environments which might putatively play a role in mineralization of dissolved organic matter. The higher number of functional assignments found in the metagenomes of A. taxiformis collected from Cape Verde Islands suggest a higher contribution of bacteria to compensate nutrient limitation in oligotrophic environments. Our results show that Asparagopsis-associated bacterial communities have host-specificity and are modulated by environmental conditions. Whether this environmental effect reflects the host's selective requirements or the locally available bacteria remains to be addressed. However, the known functional capacities of these bacterial communities indicate their potential for eco-physiological functions that could be valuable for the host fitness.},
}
@article {pmid27146045,
year = {2016},
author = {Renner, SS},
title = {A Return to Linnaeus's Focus on Diagnosis, Not Description: The Use of DNA Characters in the Formal Naming of Species.},
journal = {Systematic biology},
volume = {65},
number = {6},
pages = {1085-1095},
doi = {10.1093/sysbio/syw032},
pmid = {27146045},
issn = {1076-836X},
mesh = {Animals ; Classification/*methods ; *DNA ; Phylogeny ; Species Specificity ; *Terminology as Topic ; },
abstract = {Descriptions and diagnoses are alternative choices in all Codes of Nomenclature because Linnaeus relied on diagnoses, not descriptions, to name ca. 13,400 animals, plants, and fungi. A diagnosis names characters in which a new taxon differs from the most similar known taxon; a description mixes taxonomically informative and uninformative features, usually without indicating which is which. The first formal diagnoses of new taxa that included DNA-based characters came out in 2001, and by November 2015, at least 98 names of species of acoels, lichens, angiosperms, annelids, alveolates, arachnids, centipedes, turtles, fishes, butterflies, mollusks, nematodes, and pathogenic fungi have been published based on diagnostic mitochondrial, plastid, or nuclear DNA substitutions, indels, or rarely genetic distances, with or without additional morphological features. Authors have found diverse ways to specify the diagnostic traits (all published studies are here tabulated). While descriptions try to "cover" within-species variation, a goal rarely accomplished because of (i) the stochastic nature of specimen availability (thousands of species are known from single collections) and (ii) the subjective circumscription of species, the purpose of diagnoses was and is speedy identification. Linnaeus tried to achieve this by citing images, geographic occurrence, and previous literature. The renewed attention to sharp diagnosis now coincides with worldwide barcoding efforts, may speed up formal naming, and matches the increasing reliance on DNA for both classification and identification. I argue for DNA-based diagnoses of new species becoming a recommendation in all Codes, not just the bacterial code. [Codes of Nomenclature; description; diagnosis; DNA-based diagnosis; naming new species; nomenclature.},
}
@article {pmid27144464,
year = {2016},
author = {Wang, Y and Ahmad, B and Duan, B and Zeng, R and Huang, L},
title = {Chemical and Genetic Comparative Analysis of Gentiana crassicaulis and Gentiana macrophylla.},
journal = {Chemistry &amp; biodiversity},
volume = {13},
number = {6},
pages = {776-781},
doi = {10.1002/cbdv.201500247},
pmid = {27144464},
issn = {1612-1880},
mesh = {Chromatography, High Pressure Liquid ; *DNA Barcoding, Taxonomic ; Gentiana/*chemistry/*genetics ; Iridoid Glucosides/chemistry ; Iridoids/chemistry ; Pyrones/chemistry ; },
abstract = {Gentiana crassicaulis Duthie ex Burk. and Gentiana macrophylla Pall. are two main sources of Radix Gentianae Macrophyllae (Qinjiao) available in markets, which has a wide range of anti-inflammatory effects and has been extensively used for fighting rheumatoid arthritis. However, they vary in terms of chemical compositions, pharmacological activities, and biomass. In this study, a combined chemical and genetic (HPLC and DNA barcoding) approach was used to compare these two plants. Four predominant bioactive compounds, namely, gentiopicroside, loganic acid, swertiamarin, and sweroside, were used to assess the chemical variations. Based on chemical variations, 15 samples were clustered into two groups through PCA analyses. DNA barcoding utilizing the variable nuclear ITS2 regions were sequenced, aligned, and compared. Together with 61 sequences collected from GenBank, 76 batches of Qinjiao were clustered in two groups according to species origin. The genetic relationships indicated by the ITS2-based NJ tree were consistent with the chemical variations. Thus, the chemical profiles determined by HPLC and DNA profiles obtained from ITS2 region could be applied for the quality control of Qinjiao.},
}
@article {pmid27139454,
year = {2016},
author = {Poulsen, CS and Efunshile, AM and Nelson, JA and Stensvold, CR},
title = {Epidemiological Aspects of Blastocystis Colonization in Children in Ilero, Nigeria.},
journal = {The American journal of tropical medicine and hygiene},
volume = {95},
number = {1},
pages = {175-179},
pmid = {27139454},
issn = {1476-1645},
mesh = {Adolescent ; Africa South of the Sahara ; Age Factors ; Alleles ; Blastocystis/genetics/*isolation &amp; purification ; Blastocystis Infections/diagnosis/*epidemiology ; Child ; Child, Preschool ; Cohort Studies ; DNA, Protozoan/*isolation &amp; purification ; Feces/parasitology ; Female ; Genomics/methods ; Humans ; Male ; Nigeria/epidemiology ; Prevalence ; Sequence Analysis, DNA ; Socioeconomic Factors ; },
abstract = {This study aimed to elucidate aspects of the epidemiology of Blastocystis in Nigerian school children, including the distribution of subtypes (STs) and ST alleles. A total of 199 genomic DNAs extracted from fecal samples from 199 Nigerian children aged 2-14 years were tested by real-time polymerase chain reaction for Blastocystis Positive DNAs were submitted to barcoding by PCR and sequencing to obtain information on STs and ST alleles. A total of 167 (84%) samples were positive for Blastocystis, with prevalence increasing by age. No association between Blastocystis colonization and gender (P = 0.51) or type/presence of toilet facilities (P = 0.21) was observed. Blastocystis carriers were more prone to using water collected from wells than from sachets (P = 0.0044). Moreover, Blastocystis positivity was associated with positivity for fecal-orally transmitted protozoa (P = 0.018) and helminths (P < 0.0001). A clear inverse association of Blastocystis colonization and malaria infection was observed (P < 0.0001); however, malaria-positive children being younger than malaria-negative children, this finding was attributed to the age effect of Blastocystis colonization. ST data were available for 127/167 (76%) samples. Fifty-one children were positive for ST1, while 42 and 33 children were colonized with ST2 and ST3, respectively; a single case of ST7 was observed. By and large, the ST alleles identified for ST1 and ST2 did not differ from those observed in humans in other regions of the world; meanwhile, the distribution of ST3 alleles was remarkably distinct and potentially specific to humans in sub-Saharan Africa.},
}
@article {pmid27128309,
year = {2016},
author = {Lee, SY and Ng, WL and Mahat, MN and Nazre, M and Mohamed, R},
title = {DNA Barcoding of the Endangered Aquilaria (Thymelaeaceae) and Its Application in Species Authentication of Agarwood Products Traded in the Market.},
journal = {PloS one},
volume = {11},
number = {4},
pages = {e0154631},
pmid = {27128309},
issn = {1932-6203},
mesh = {Base Sequence ; *DNA Barcoding, Taxonomic ; DNA Primers/genetics ; DNA, Plant/*genetics ; Endangered Species ; Genes, Plant ; Genetic Variation ; Malaysia ; Phylogeny ; Polymerase Chain Reaction ; Species Specificity ; Thymelaeaceae/*classification/*genetics ; Trees/classification/genetics ; Wood/classification/economics/genetics ; },
abstract = {The identification of Aquilaria species from their resinous non-wood product, the agarwood, is challenging as conventional techniques alone are unable to ascertain the species origin. Aquilaria is a highly protected species due to the excessive exploitation of its precious agarwood. Here, we applied the DNA barcoding technique to generate barcode sequences for Aquilaria species and later applied the barcodes to identify the source species of agarwood found in the market. We developed a reference DNA barcode library using eight candidate barcode loci (matK, rbcL, rpoB, rpoC1, psbA-trnH, trnL-trnF, ITS, and ITS2) amplified from 24 leaf accessions of seven Aquilaria species obtained from living trees. Our results indicated that all single barcodes can be easily amplified and sequenced with the selected primers. The combination of trnL-trnF+ITS and trnL-trnF+ITS2 yielded the greatest species resolution using the least number of loci combination, while matK+trnL-trnF+ITS showed potential in detecting the geographical origins of Aquilaria species. We propose trnL-trnF+ITS2 as the best candidate barcode for Aquilaria as ITS2 has a shorter sequence length compared to ITS, which eases PCR amplification especially when using degraded DNA samples such as those extracted from processed agarwood products. A blind test conducted on eight agarwood samples in different forms using the proposed barcode combination proved successful in their identification up to the species level. Such potential of DNA barcoding in identifying the source species of agarwood will contribute to the international timber trade control, by providing an effective method for species identification and product authentication.},
}
@article {pmid27121950,
year = {2016},
author = {Hashimshony, T and Senderovich, N and Avital, G and Klochendler, A and de Leeuw, Y and Anavy, L and Gennert, D and Li, S and Livak, KJ and Rozenblatt-Rosen, O and Dor, Y and Regev, A and Yanai, I},
title = {CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq.},
journal = {Genome biology},
volume = {17},
number = {},
pages = {77},
pmid = {27121950},
issn = {1474-760X},
mesh = {*Algorithms ; Animals ; Cell Cycle ; Cells, Cultured ; Fibroblasts/cytology/metabolism ; Gene Expression Profiling/*methods ; Mice ; Sensitivity and Specificity ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis/*methods ; },
abstract = {Single-cell transcriptomics requires a method that is sensitive, accurate, and reproducible. Here, we present CEL-Seq2, a modified version of our CEL-Seq method, with threefold higher sensitivity, lower costs, and less hands-on time. We implemented CEL-Seq2 on Fluidigm's C1 system, providing its first single-cell, on-chip barcoding method, and we detected gene expression changes accompanying the progression through the cell cycle in mouse fibroblast cells. We also compare with Smart-Seq to demonstrate CEL-Seq2's increased sensitivity relative to other available methods. Collectively, the improvements make CEL-Seq2 uniquely suited to single-cell RNA-Seq analysis in terms of economics, resolution, and ease of use.},
}
@article {pmid27119149,
year = {2016},
author = {Howard, MG and McDonald, WJ and Forster, PI and Kress, WJ and Erickson, D and Faith, DP and Shapcott, A},
title = {Patterns of Phylogenetic Diversity of Subtropical Rainforest of the Great Sandy Region, Australia Indicate Long Term Climatic Refugia.},
journal = {PloS one},
volume = {11},
number = {4},
pages = {e0153565},
pmid = {27119149},
issn = {1932-6203},
mesh = {Australia ; *Biodiversity ; Geologic Sediments/chemistry ; Peru ; Phylogeny ; Plants/*classification/*genetics ; Rainforest ; Refugium ; Tropical Climate ; },
abstract = {Australia's Great Sandy Region is of international significance containing two World Heritage areas and patches of rainforest growing on white sand. Previous broad-scale analysis found the Great Sandy biogeographic subregion contained a significantly more phylogenetically even subset of species than expected by chance contrasting with rainforest on white sand in Peru. This study aimed to test the patterns of rainforest diversity and relatedness at a finer scale and to investigate why we may find different patterns of phylogenetic evenness compared with rainforests on white sands in other parts of the world. This study focussed on rainforest sites within the Great Sandy and surrounding areas in South East Queensland (SEQ), Australia. We undertook field collections, expanded our three-marker DNA barcode library of SEQ rainforest plants and updated the phylogeny to 95% of the SEQ rainforest flora. We sampled species composition of rainforest in fixed area plots from 100 sites. We calculated phylogenetic diversity (PD) measures as well as species richness (SR) for each rainforest community. These combined with site variables such as geology, were used to evaluate patterns and relatedness. We found that many rainforest communities in the Great Sandy area were significantly phylogenetically even at the individual site level consistent with a broader subregion analysis. Sites from adjacent areas were either not significant or were significantly phylogenetically clustered. Some results in the neighbouring areas were consistent with historic range expansions. In contrast with expectations, sites located on the oldest substrates had significantly lower phylogenetic diversity (PD). Fraser Island was once connected to mainland Australia, our results are consistent with a region geologically old enough to have continuously supported rainforest in refugia. The interface of tropical and temperate floras in part also explains the significant phylogenetic evenness and higher than expected phylogenetic diversity.},
}
@article {pmid27116180,
year = {2016},
author = {Chambers, EA and Hebert, PD},
title = {Assessing DNA Barcodes for Species Identification in North American Reptiles and Amphibians in Natural History Collections.},
journal = {PloS one},
volume = {11},
number = {4},
pages = {e0154363},
pmid = {27116180},
issn = {1932-6203},
mesh = {Amphibians/*classification ; Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*genetics ; Gene Library ; Natural History ; North America ; Reptiles/*classification ; Species Specificity ; },
abstract = {BACKGROUND: High rates of species discovery and loss have led to the urgent need for more rapid assessment of species diversity in the herpetofauna. DNA barcoding allows for the preliminary identification of species based on sequence divergence. Prior DNA barcoding work on reptiles and amphibians has revealed higher biodiversity counts than previously estimated due to cases of cryptic and undiscovered species. Past studies have provided DNA barcodes for just 14% of the North American herpetofauna, revealing the need for expanded coverage.<br><br>This study extends the DNA barcode reference library for North American herpetofauna, assesses the utility of this approach in aiding species delimitation, and examines the correspondence between current species boundaries and sequence clusters designated by the BIN system. Sequences were obtained from 730 specimens, representing 274 species (43%) from the North American herpetofauna. Mean intraspecific divergences were 1% and 3%, while average congeneric sequence divergences were 16% and 14% in amphibians and reptiles, respectively. BIN assignments corresponded with current species boundaries in 79% of amphibians, 100% of turtles, and 60% of squamates. Deep divergences (>2%) were noted in 35% of squamate and 16% of amphibian species, and low divergences (<2%) occurred in 12% of reptiles and 23% of amphibians, patterns reflected in BIN assignments. Sequence recovery declined with specimen age, and variation in recovery success was noted among collections. Within collections, barcodes effectively flagged seven mislabeled tissues, and barcode fragments were recovered from five formalin-fixed specimens.<br><br>CONCLUSIONS/SIGNIFICANCE: This study demonstrates that DNA barcodes can effectively flag errors in museum collections, while BIN splits and merges reveal taxa belonging to deeply diverged or hybridizing lineages. This study is the first effort to compile a reference library of DNA barcodes for herpetofauna on a continental scale.},
}
@article {pmid27116002,
year = {2016},
author = {Ramalho, MO and Martins, C and Silva, LM and Martins, VG and Bueno, OC},
title = {Molecular Profile of the Brazilian Weaver Ant Camponotus textor Forel (Hymenoptera, Formicidae).},
journal = {Neotropical entomology},
volume = {45},
number = {5},
pages = {463-470},
pmid = {27116002},
issn = {1678-8052},
mesh = {Animals ; Ants/*genetics ; Brazil ; *DNA Barcoding, Taxonomic ; *DNA, Ribosomal ; Nesting Behavior ; Phylogeny ; },
abstract = {Camponotus textor Forel is, to date, the only weaver ant recorded from Brazil, and all existing studies on the species are restricted to describing its weaving and nesting behaviors. The aim of this work is to establish the molecular profile of the species. We sampled eight different colonies by sequencing mitochondrial genes (COI, transfer DNA (tRNA), and an intergenic spacer) and the nuclear gene 28S ribosomal DNA (rDNA). We then assessed haplotype diversity and also analyzed distribution patterns of this species based on the correlation between genetic and geographic distances. Our results provide an additional tool for species identification by identifying new regions that can be used as molecular markers for barcoding (such as the intergenic spacer (IGS) and tRNA-Leu). In addition, the phylogenetic analysis revealed that C. textor has features that could be associated with deep population divergences. We identified a wide range of mitotypes and three distinct groups, suggesting a possible reduction of gene flow between colonies.},
}
@article {pmid27114891,
year = {2016},
author = {Elbrecht, V and Taberlet, P and Dejean, T and Valentini, A and Usseglio-Polatera, P and Beisel, JN and Coissac, E and Boyer, F and Leese, F},
title = {Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects.},
journal = {PeerJ},
volume = {4},
number = {},
pages = {e1966},
pmid = {27114891},
issn = {2167-8359},
abstract = {Cytochrome c oxidase I (COI) is a powerful marker for DNA barcoding of animals, with good taxonomic resolution and a large reference database. However, when used for DNA metabarcoding, estimation of taxa abundances and species detection are limited due to primer bias caused by highly variable primer binding sites across the COI gene. Therefore, we explored the ability of the 16S ribosomal DNA gene as an alternative metabarcoding marker for species level assessments. Ten bulk samples, each containing equal amounts of tissue from 52 freshwater invertebrate taxa, were sequenced with the Illumina NextSeq 500 system. The 16S primers amplified three more insect species than the Folmer COI primers and amplified more equally, probably due to decreased primer bias. Estimation of biomass might be less biased with 16S than with COI, although variation in read abundances of two orders of magnitudes is still observed. According to these results, the marker choice depends on the scientific question. If the goal is to obtain a taxonomic identification at the species level, then COI is more appropriate due to established reference databases and known taxonomic resolution of this marker, knowing that a greater proportion of insects will be missed using COI Folmer primers. If the goal is to obtain a more comprehensive survey the 16S marker, which requires building a local reference database, or optimised degenerated COI primers could be more appropriate.},
}
@article {pmid27114859,
year = {2016},
author = {Pineda, J and Cho, W and Starczak, V and Govindarajan, AF and Guzman, HM and Girdhar, Y and Holleman, RC and Churchill, J and Singh, H and Ralston, DK},
title = {A crab swarm at an ecological hotspot: patchiness and population density from AUV observations at a coastal, tropical seamount.},
journal = {PeerJ},
volume = {4},
number = {},
pages = {e1770},
pmid = {27114859},
issn = {2167-8359},
abstract = {A research cruise to Hannibal Bank, a seamount and an ecological hotspot in the coastal eastern tropical Pacific Ocean off Panama, explored the zonation, biodiversity, and the ecological processes that contribute to the seamount's elevated biomass. Here we describe the spatial structure of a benthic anomuran red crab population, using submarine video and autonomous underwater vehicle (AUV) photographs. High density aggregations and a swarm of red crabs were associated with a dense turbid layer 4-10 m above the bottom. The high density aggregations were constrained to 355-385 m water depth over the Northwest flank of the seamount, although the crabs also occurred at lower densities in shallower waters (∼280 m) and in another location of the seamount. The crab aggregations occurred in hypoxic water, with oxygen levels of 0.04 ml/l. Barcoding of Hannibal red crabs, and pelagic red crabs sampled in a mass stranding event in 2015 at a beach in San Diego, California, USA, revealed that the Panamanian and the Californian crabs are likely the same species, Pleuroncodes planipes, and these findings represent an extension of the southern endrange of this species. Measurements along a 1.6 km transect revealed three high density aggregations, with the highest density up to 78 crabs/m(2), and that the crabs were patchily distributed. Crab density peaked in the middle of the patch, a density structure similar to that of swarming insects.},
}
@article {pmid27114581,
year = {2016},
author = {Lavabre, JE and Gilarranz, LJ and Fortuna, MA and Bascompte, J},
title = {How does the functional diversity of frugivorous birds shape the spatial pattern of seed dispersal? A case study in a relict plant species.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1694},
pages = {},
pmid = {27114581},
issn = {1471-2970},
mesh = {Animals ; *Biodiversity ; *Feeding Behavior ; Food Chain ; Genetic Markers ; Models, Biological ; *Seed Dispersal ; Sequence Analysis, DNA ; Songbirds/*physiology ; Spain ; Taxus/genetics/*physiology ; },
abstract = {Genetic markers used in combination with network analysis can characterize the fine spatial pattern of seed dispersal and assess the differential contribution of dispersers. As a case study, we focus on the seed dispersal service provided by a small guild of frugivorous birds to the common yew, Taxus baccata L., in southern Spain. We build the spatial networks of seed dispersal events between trees and seed-plots within the studied population-local network-and the spatial network that includes all dispersal events-regional network. Such networks are structured in well-defined modules, i.e. groups of tightly connected mother trees and seed-plots. Neither geographical distance, nor microhabitat type explained this modular structure, but when long-distance dispersal events are incorporated in the network it shows a relative increase in overall modularity. Independent field observations suggested the co-occurrence of two complementary groups, short- and long-distance dispersers, mostly contributing to the local and regional seed rain, respectively. The main long-distance disperser at our site, Turdus viscivorus, preferentially visits the most productive trees, thus shaping the seed rain at the landscape scale and affecting the local modular organization. We end by discussing how DNA barcoding could serve to better quantify the role of functional diversity.},
}
@article {pmid27113104,
year = {2016},
author = {Simmons, TW and Hutchinson, ML},
title = {A Critical Review of All Known Published Records for Water Mite (Acari: Hydrachnidiae) and Mosquito (Diptera: Culicidae) Parasitic Associations From 1975 to Present.},
journal = {Journal of medical entomology},
volume = {53},
number = {4},
pages = {737-752},
doi = {10.1093/jme/tjw052},
pmid = {27113104},
issn = {1938-2928},
mesh = {Animals ; Culicidae/classification/*parasitology ; Host-Parasite Interactions ; Mites/classification/*physiology ; Species Specificity ; },
abstract = {All published records of water mite-mosquito parasitic associations since Gary R. Mullen's comprehensive review in the 1970s of the literature were critiqued to provide an up-to-date account on the identity of water mites parasitizing mosquitoes and their geographic distribution. In total, 321 records in 62 sources were identified, with each record representing an association specific to a state, province, or region within a country. The greatest number of records were from the United States (120), followed by India (106) and Canada (40). In all, 105 species of mosquitoes were parasitized, with the majority belonging to the genera Aedes sensu lato (30), Anopheles (30), and Culex (21). Records were biased toward mosquito genera with the greatest number of freshwater species and medical importance. Most water mites belonged to the genus Arrenurus, or were Parathyas barbigera (Viets 1908). Arrenurus water mites were often not identified to species, but 15 different Arrenurus species were determined in 119 records. All but one of the species (i.e., Arrenurus madaraszi Daday 1898) were only reported from Canada, Germany, or the United States. Although a greater proportion of sources reviewed by us compared with Mullen's review identified water mites down to the level of genus, to better understand the biological significance of mite and mosquito interactions, more of an effort is needed to identify the species of water mites. The availability of molecular techniques such as DNA barcoding will make this goal more attainable.},
}
@article {pmid27113101,
year = {2016},
author = {Mokhtar, AS and Braima, KA and Peng Chin, H and Jeffery, J and Mohd Zain, SN and Rohela, M and Lau, YL and Jamaiah, I and Wilson, JJ and Abdul-Aziz, NM},
title = {Intestinal Myiasis in a Malaysian Patient Caused by Larvae of Clogmia albipunctatus (Diptera: Psychodidae).},
journal = {Journal of medical entomology},
volume = {53},
number = {4},
pages = {957-960},
doi = {10.1093/jme/tjw014},
pmid = {27113101},
issn = {1938-2928},
mesh = {Adult ; Albendazole/therapeutic use ; Animals ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Feces/parasitology ; Female ; Humans ; Intestines/*parasitology ; Larva/genetics/growth &amp; development/physiology ; Malaysia ; Myiasis/*diagnosis/parasitology ; Phylogeny ; Psychodidae/genetics/growth &amp; development/*physiology ; },
abstract = {We report a case of human intestinal myiasis in a 41-yr-old female patient presented at a clinic in Seri Kembangan, Selangor, Malaysia. Larvae passed out in the patient's feces were sent to the Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia. DNA barcoding confirmed the second case of intestinal myiasis in Malaysia involving the larvae of Clogmia albipunctatus (Duckhouse) (Diptera: Psychodidae). We review reported cases of myiasis and discuss the present case of intestinal myiasis in an urban patient.},
}
@article {pmid27110204,
year = {2016},
author = {Roudbar, AJ and Eagderi, S and Esmaeili, HR and Coad, BW and Bogutskaya, N},
title = {A molecular approach to the genus Alburnoides using COI sequences data set and the description of a new species, A. damghani, from the Damghan River system (the Dasht-e Kavir Basin, Iran) (Actinopterygii, Cyprinidae).},
journal = {ZooKeys},
volume = {},
number = {579},
pages = {157-181},
pmid = {27110204},
issn = {1313-2989},
abstract = {The molecular status of nine species of the genus Alburnoides from different river drainages in Iran and additionally by seven species from Europe was assessed. mtDNA COI gene sequences from freshly collected specimens and available NCBI data revealed four major phylogenetic lineages. Based on the results, a distinct taxon from the Cheshmeh Ali (Ali Spring), a Damghan River tributary in the endorheic Dasht-e Kavir basin, northern Iran, which is the closest sister to Alburnoides namaki (Namak Lake basin) + Alburnoides coadi (Nam River in the endorheic Dasht-e Kavir basin) is considered as a new species, Alburnoides damghani sp. n. It is distinguished from other Alburnoides species in Iran by a combination of character states including: a weakly-developed, variably-scaled, ventral keel from completely scaleless to completely scaled, a short snout with the tip of the mouth cleft on a level with the lower margin of the pupil or slightly lower, a small eye (eye horizontal diameter slightly to markedly less than interorbital width), commonly 8½ branched dorsal-fin rays, commonly 11-12½ branched anal-fin rays, 40-46(47) total lateral-line scales, 2.5-4.2 or 2.5-4.1 pharyngeal teeth, gill rakers short and widely spaced, 6-8 in total, 39-41 (commonly 40), total vertebrae, (19)20(21) abdominal vertebrae, 19-21 (most commonly 20) caudal vertebrae, abdominal vertebral region most commonly equal to or longer than caudal region, and most common vertebral formulae 20+20 and 21+19.},
}
@article {pmid27110203,
year = {2016},
author = {Kirichenko, N and Triberti, P and Mutanen, M and Magnoux, E and Landry, JF and Lopez-Vaamonde, C},
title = {Systematics and biology of some species of Micrurapteryx Spuler (Lepidoptera, Gracillariidae) from the Holarctic Region, with re-description of M. caraganella (Hering) from Siberia.},
journal = {ZooKeys},
volume = {},
number = {579},
pages = {99-156},
pmid = {27110203},
issn = {1313-2989},
abstract = {During a DNA barcoding campaign of leaf-mining insects from Siberia, a genetically divergent lineage of a gracillariid belonging to the genus Micrurapteryx was discovered, whose larvae developed on Caragana Fabr. and Medicago L. (Fabaceae). Specimens from Siberia showed similar external morphology to the Palearctic Micrurapteryx gradatella and the Nearctic Parectopa occulta but differed in male genitalia, DNA barcodes, and nuclear genes histone H3 and 28S. Members of this lineage are re-described here as Micrurapteryx caraganella (Hering, 1957), comb. n., an available name published with only a brief description of its larva and leaf mine. Micrurapteryx caraganella is widely distributed throughout Siberia, from Tyumen oblast in the West to Transbaikalia in the East. Occasionally it may severely affect its main host, Caragana arborescens Lam. This species has been confused in the past with Micrurapteryx gradatella in Siberia, but field observations confirm that Micrurapteryx gradatella exists in Siberia and is sympatric with Micrurapteryx caraganella, at least in the Krasnoyarsk region, where it feeds on different host plants (Vicia amoena Fisch. and Vicia sp.). In addition, based on both morphological and molecular evidence as well as examination of type specimens, the North American Parectopa occulta Braun, 1922 and Parectopa albicostella Braun, 1925 are transferred to Micrurapteryx as Micrurapteryx occulta (Braun, 1922), comb. n. with albicostella as its junior synonym (syn. n.). Characters used to distinguish Micrurapteryx from Parectopa are presented and illustrated. These findings provide another example of the potential of DNA barcoding to reveal overlooked species and illuminate nomenclatural problems.},
}
@article {pmid27110148,
year = {2016},
author = {Wu, Y and Wang, C and Zheng, G and Li, S},
title = {Three new species of the genus Leptonetela from Greece (Araneae, Leptonetidae).},
journal = {ZooKeys},
volume = {},
number = {569},
pages = {23-35},
pmid = {27110148},
issn = {1313-2989},
abstract = {Three new species of the spider genus Leptonetela collected from caves in Greece are described: Leptonetela arvanitidisi sp. n. (male &amp; female), Leptonetela paragamiani sp. n. (male &amp; female) and Leptonetela penevi sp. n. (male &amp; female). Detailed illustrations of the new species are provided. DNA barcodes were obtained for future use.},
}
@article {pmid27109511,
year = {2016},
author = {Pal, D and Blair, HJ and Elder, A and Dormon, K and Rennie, KJ and Coleman, DJ and Weiland, J and Rankin, KS and Filby, A and Heidenreich, O and Vormoor, J},
title = {Long-term in vitro maintenance of clonal abundance and leukaemia-initiating potential in acute lymphoblastic leukaemia.},
journal = {Leukemia},
volume = {30},
number = {8},
pages = {1691-1700},
pmid = {27109511},
issn = {1476-5551},
support = {12788/CRUK_/Cancer Research UK/United Kingdom ; 087961/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Cell Adhesion ; Clone Cells/pathology ; Coculture Techniques/*methods ; Drug Therapy, Combination/methods ; Feeder Cells/cytology ; Heterografts ; Humans ; Mesenchymal Stem Cells/cytology ; Mice ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/*pathology ; },
abstract = {Lack of suitable in vitro culture conditions for primary acute lymphoblastic leukaemia (ALL) cells severely impairs their experimental accessibility and the testing of new drugs on cell material reflecting clonal heterogeneity in patients. We show that Nestin-positive human mesenchymal stem cells (MSCs) support expansion of a range of biologically and clinically distinct patient-derived ALL samples. Adherent ALL cells showed an increased accumulation in the S phase of the cell cycle and diminished apoptosis when compared with cells in the suspension fraction. Moreover, surface expression of adhesion molecules CD34, CDH2 and CD10 increased several fold. Approximately 20% of the ALL cells were in G0 phase of the cell cycle, suggesting that MSCs may support quiescent ALL cells. Cellular barcoding demonstrated long-term preservation of clonal abundance. Expansion of ALL cells for >3 months compromised neither feeder dependence nor cancer initiating ability as judged by their engraftment potential in immunocompromised mice. Finally, we demonstrate the suitability of this co-culture approach for the investigation of drug combinations with luciferase-expressing primograft ALL cells. Taken together, we have developed a preclinical platform with patient-derived material that will facilitate the development of clinically effective combination therapies for ALL.},
}
@article {pmid27107012,
year = {2016},
author = {Yachie, N and Petsalaki, E and Mellor, JC and Weile, J and Jacob, Y and Verby, M and Ozturk, SB and Li, S and Cote, AG and Mosca, R and Knapp, JJ and Ko, M and Yu, A and Gebbia, M and Sahni, N and Yi, S and Tyagi, T and Sheykhkarimli, D and Roth, JF and Wong, C and Musa, L and Snider, J and Liu, YC and Yu, H and Braun, P and Stagljar, I and Hao, T and Calderwood, MA and Pelletier, L and Aloy, P and Hill, DE and Vidal, M and Roth, FP},
title = {Pooled-matrix protein interaction screens using Barcode Fusion Genetics.},
journal = {Molecular systems biology},
volume = {12},
number = {4},
pages = {863},
pmid = {27107012},
issn = {1744-4292},
support = {R21 HG004756/HG/NHGRI NIH HHS/United States ; MOP-123468//Canadian Institutes of Health Research/Canada ; R01 HG001715/HG/NHGRI NIH HHS/United States ; U01 HG001715/HG/NHGRI NIH HHS/United States ; P50 HG004233/HG/NHGRI NIH HHS/United States ; U41 HG001715/HG/NHGRI NIH HHS/United States ; HG004233/HG/NHGRI NIH HHS/United States ; MOP-130507//Canadian Institutes of Health Research/Canada ; R01 GM097358/GM/NIGMS NIH HHS/United States ; HG001715/HG/NHGRI NIH HHS/United States ; },
mesh = {Centrosome/*metabolism ; Chromosomes, Human/metabolism ; Gene Library ; High-Throughput Nucleotide Sequencing ; Humans ; Protein Binding ; Protein Interaction Mapping/*methods ; Proteome/*metabolism ; Saccharomyces cerevisiae/*genetics ; Two-Hybrid System Techniques ; },
abstract = {High-throughput binary protein interaction mapping is continuing to extend our understanding of cellular function and disease mechanisms. However, we remain one or two orders of magnitude away from a complete interaction map for humans and other major model organisms. Completion will require screening at substantially larger scales with many complementary assays, requiring further efficiency gains in proteome-scale interaction mapping. Here, we report Barcode Fusion Genetics-Yeast Two-Hybrid (BFG-Y2H), by which a full matrix of protein pairs can be screened in a single multiplexed strain pool. BFG-Y2H uses Cre recombination to fuse DNA barcodes from distinct plasmids, generating chimeric protein-pair barcodes that can be quantified via next-generation sequencing. We applied BFG-Y2H to four different matrices ranging in scale from ~25 K to 2.5 M protein pairs. The results show that BFG-Y2H increases the efficiency of protein matrix screening, with quality that is on par with state-of-the-art Y2H methods.},
}
@article {pmid27105923,
year = {2016},
author = {Sims, DJ and Harrington, RD and Polley, EC and Forbes, TD and Mehaffey, MG and McGregor, PM and Camalier, CE and Harper, KN and Bouk, CH and Das, B and Conley, BA and Doroshow, JH and Williams, PM and Lih, CJ},
title = {Plasmid-Based Materials as Multiplex Quality Controls and Calibrators for Clinical Next-Generation Sequencing Assays.},
journal = {The Journal of molecular diagnostics : JMD},
volume = {18},
number = {3},
pages = {336-349},
pmid = {27105923},
issn = {1943-7811},
support = {HHSN261200800001C/CA/NCI NIH HHS/United States ; HHSN261200800001E/CA/NCI NIH HHS/United States ; },
mesh = {Computational Biology/methods ; DNA Barcoding, Taxonomic/methods/standards ; Genetic Testing/*methods/*standards ; Genomics/methods/standards ; High-Throughput Nucleotide Sequencing/*methods/*standards ; Humans ; Plasmids/*genetics ; *Quality Control ; *Reference Standards ; Reproducibility of Results ; Workflow ; },
abstract = {Although next-generation sequencing technologies have been widely adapted for clinical diagnostic applications, an urgent need exists for multianalyte calibrator materials and controls to evaluate the performance of these assays. Control materials will also play a major role in the assessment, development, and selection of appropriate alignment and variant calling pipelines. We report an approach to provide effective multianalyte controls for next-generation sequencing assays, referred to as the control plasmid spiked-in genome (CPSG). Control plasmids that contain approximately 1000 bases of human genomic sequence with a specific mutation of interest positioned near the middle of the insert and a nearby 6-bp molecular barcode were synthesized, linearized, quantitated, and spiked into genomic DNA derived from formalin-fixed, paraffin-embedded-prepared hapmap cell lines at defined copy number ratios. Serial titration experiments demonstrated the CPSGs performed with similar efficiency of variant detection as formalin-fixed, paraffin-embedded cell line genomic DNA. Repetitive analyses of one lot of CPSGs 90 times during 18 months revealed that the reagents were stable with consistent detection of each of the plasmids at similar variant allele frequencies. CPSGs are designed to work across most next-generation sequencing methods, platforms, and data analysis pipelines. CPSGs are robust controls and can be used to evaluate the performance of different next-generation sequencing diagnostic assays, assess data analysis pipelines, and ensure robust assay performance metrics.},
}
@article {pmid27104769,
year = {2016},
author = {More, RP and Purohit, HJ},
title = {The Identification of Discriminating Patterns from 16S rRNA Gene to Generate Signature for Bacillus Genus.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {23},
number = {8},
pages = {651-661},
doi = {10.1089/cmb.2016.0002},
pmid = {27104769},
issn = {1557-8666},
mesh = {Bacillus/*classification/*genetics ; Genome, Bacterial ; Phylogeny ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Software ; },
abstract = {The 16S ribosomal RNA (16S rRNA) gene has been widely used for the taxonomic classification of bacteria. A molecular signature is a set of nucleotide patterns, which constitute a regular expression that is specific to each particular taxon. Our main goal was to identify discriminating nucleotide patterns in 16S rRNA gene and then to generate signatures for taxonomic classification. To demonstrate our approach, we used the phylum Firmicutes as a model using representative taxa Bacilli (class), Bacillales (order), Bacillaceae (family), and Bacillus (genus), according to their dominance at each hierarchical taxonomic level. We applied combined composite vector and multiple sequence alignment approaches to generate gene-specific signatures. Further, we mapped all the patterns into the different hypervariable regions of 16S rRNA gene and confirmed the most appropriate distinguishing region as V3-V4 for targeted taxa. We also examined the evolution in discriminating patterns of signatures across taxonomic levels. We assessed the comparative classification accuracy of signatures with other methods (i.e., RDP Classifier, KNN, and SINA). Results revealed that the signatures for taxa Bacilli, Bacillales, Bacillaceae, and Bacillus could correctly classify isolate sequences with sensitivity of 0.99, 0.97, 0.94, and 0.89, respectively, and specificity close to 0.99. We developed signature-based software DNA Barcode Identification (DNA BarID) for taxonomic classification that is available at website http://www.neeri.res.in/DNA_BarID.htm . This pattern-based study provides a deeper understanding of taxon-specific discriminating patterns in 16S rRNA gene with respect to taxonomic classification.},
}
@article {pmid27103937,
year = {2016},
author = {Srivathsan, A and Ang, A and Vogler, AP and Meier, R},
title = {Fecal metagenomics for the simultaneous assessment of diet, parasites, and population genetics of an understudied primate.},
journal = {Frontiers in zoology},
volume = {13},
number = {},
pages = {17},
pmid = {27103937},
issn = {1742-9994},
abstract = {BACKGROUND: Rapid habitat loss and degradation are responsible for population decline in a growing number of species. Understanding the natural history of these species is important for designing conservation strategies, such as habitat enhancements or ex-situ conservation. The acquisition of observational data may be difficult for rare and declining species, but metagenomics and metabarcoding can provide novel kinds of information. Here we use these methods for analysing fecal samples from an endangered population of a colobine primate, the banded leaf monkey (Presbytis femoralis).<br><br>RESULTS: We conducted metagenomics via shotgun sequencing on six fecal samples obtained from a remnant population of P. femoralis in a species-rich rainforest patch in Singapore. Shotgun sequencing and identification against a plant barcode reference database reveals a broad dietary profile consisting of at least 53 plant species from 33 families. The diet includes exotic plant species and is broadly consistent with > 2&#xa0;years of observational data. Metagenomics identified 15 of the 24 plant genera for which there is observational data, but also revealed at least 36 additional species. DNA traces for the diet species were recovered and identifiable in the feces despite long digestion times and a large number of potential food plants within the rainforest habitat (>700 species). We also demonstrate that metagenomics provides greater taxonomic resolution of food plant species by utilizing multiple genetic markers as compared to single-marker metabarcoding. In addition, full mitochondrial genomes of P. femoralis individuals were reconstructed from fecal metagenomic shotgun reads, showing very low levels of genetic diversity in the focal population, and the presence of gut parasites could also be confirmed. Metagenomics thus allows for the simultaneous assessment of diet, population genetics and gut parasites based on fecal samples.<br><br>CONCLUSIONS: Our study demonstrates that metagenomic shotgun sequencing of fecal samples can be successfully used to rapidly obtain natural history data for understudied species with a complex diet. We predict that metagenomics will become a routinely used tool in conservation biology once the cost per sample reduces to ~100 USD within the next few years.},
}
@article {pmid27103875,
year = {2016},
author = {Kawakita, A and Kato, M},
title = {Revision of the Japanese species of Epicephala Meyrick with descriptions of seven new species (Lepidoptera, Gracillariidae).},
journal = {ZooKeys},
volume = {},
number = {568},
pages = {87-118},
pmid = {27103875},
issn = {1313-2989},
abstract = {Epicephala moths are involved in obligate mutualisms with their Phyllanthaceae hosts, in which the female moths assure pollination and, in return, their progeny develop by consuming the seeds. Ecological, molecular and geographical data suggest that the genus includes several hundred species, but the majority remains to be formally described. Here we revise the Japanese species of Epicephala Meyrick, 1880. In addition to two previously named species, seven species are newly described: Epicephala anthophilia sp. n., Epicephala lanceolatella sp. n., Epicephala perplexa sp. n., Epicephala obovatella sp. n., Epicephala corruptrix sp. n., Epicephala parasitica sp. n. and Epicephala nudilingua sp. n. The first four are species involved in obligate pollination mutualism, while the fifth is a pollinating seed parasite and the last two are derived non-pollinating seed parasites of herbaceous Phyllanthus. Each of the nine Japanese Epicephela species is specialized to a single plant species in the genera Glochidion, Breynia or Phyllanthus, except for Epicephala obovatella and Epicephala corruptrix that each utilizes two closely related Glochidion species. Considerable variations are found in pollination and oviposition behaviors among species, which are reflected in their proboscis and ovipositor morphologies, respectively. Molecular phylogeny indicated that there have been repeated transitions in oviposition mode during the diversification of Epicephala, which were accompanied by changes in ovipositor morphology, as suggested by a correlation analysis. Keys to species are provided.},
}
@article {pmid27099956,
year = {2016},
author = {Magalhães, T and Robles, R and Felder, DL and Mantelatto, FL},
title = {Integrative Taxonomic Study of the Purse Crab Genus Persephona Leach, 1817 (Brachyura: Leucosiidae): Combining Morphology and Molecular Data.},
journal = {PloS one},
volume = {11},
number = {4},
pages = {e0152627},
pmid = {27099956},
issn = {1932-6203},
mesh = {Animals ; Brachyura/*classification/*genetics ; Brazil ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Female ; Genes, Mitochondrial/genetics ; Male ; Mexico ; Pacific Ocean ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Shellfish/classification ; },
abstract = {Marine crabs of the genus Persephona Leach, 1817 are restricted to American waters of the western Atlantic and eastern Pacific Oceans. Subfamilial assignment of this taxon has varied between authors and its species composition remain in question. We conducted a comparative study based on morphology and molecular phylogenetics for all ten recognized species of Persephona, along with Iliacantha hancocki. We tested whether Persephona finneganae, P. lichtensteinii, and P. crinita represent a single species as suggested by some authors; whether specimens identified as P. punctata, P. mediterranea, and P. aquilonaris warrant treatment as separate species; and whether I. hancocki should be regarded as a junior synonym of P. subovata. Diagnostic morphological characters (of the carapace, chelipeds, and third maxillipeds) were used along with gonopod (male first pleopod 1) features and live coloration. The 16S rRNA and the Cytochrome Oxidase I (COI) (DNA barcoding) mitochondrial genes were used as molecular markers. Both morphological and molecular analyses revealed that putative specimens of P. crinita from Brazil and those assigned to P. finneganae were no different from specimens presently assignable to P. lichtensteinii. P. finneganae is regarded as a junior synonym of P. lichtensteinii, and we apply P. crinita only to specimens we examined from the Gulf of Mexico. Specimens from Brazil previously reported as P. crinita are herewith concluded to represent P. lichtensteinii. Additionally, P. townsendi is a junior synonym of P. orbicularis, Iliacantha hancocki is concluded to be a junior synonym of P. subovata, while P. aquilonaris and P. mediterranea are found to represent separate species. On the basis of our revisions, eight species of Persephona are considered valid, and the reported distribution for P. crinita is restricted.},
}
@article {pmid27099556,
year = {2016},
author = {Stigenberg, J and Van Achterberg, K},
title = {Review of the Palaearctic (and Oriental) Allurus (Braconidae, Euphorinae) based on material from Sweden.},
journal = {Biodiversity data journal},
volume = {},
number = {4},
pages = {e7853},
pmid = {27099556},
issn = {1314-2828},
abstract = {BACKGROUND: The tribe Centistini includes three genera, Allurus, Centistes and Centistoides (Stigenberg et al. 2015). They are solitary endoparasitoids of adults and final instar larvae of beetles from the family Curculionidae (Jackson 1920, Aeschlimann 1980, Tobias 1986).<br><br>NEW INFORMATION: In this paper we present a key, molecular data (standard DNA barcode, CO1) and images of the two species of Allurus occurring in the Western Palaearctic. A third Oriental species described from China (Taiwan) is also included in the key. Allurus is a Holarctic genus with three known species (A. choui, A. lituratus, A. muricatus). Our sequence data confirms that A. muricatus and A. lituratus are two distinct and separate species and this paper points out good and easy characters to separate them.},
}
@article {pmid27099547,
year = {2016},
author = {Heller, K and Rulik, B},
title = {Ctenosciara alexanderkoenigi sp. n. (Diptera: Sciaridae), an exotic invader in Germany?.},
journal = {Biodiversity data journal},
volume = {},
number = {4},
pages = {e6460},
pmid = {27099547},
issn = {1314-2828},
abstract = {A new species of the genus Ctenosciara Tuomikoski, 1960 is here described based upon a single specimen, obtained from collectings in the garden at Museum Alexander Koenig in Bonn. Ctenosciara alexanderkoenigi sp. n. differs from all other congeneric European species by its striking coloration and distinct male genitalia. However, DNA barcoding reveals associations with two specimens from New Zealand. Therefore a recent migration of Ctenosciara species from the Australasian Region, the likely center of origin of the genus, is discussed. A key to the European species of Ctenosciara is provided. Barcoding results reveale that Ctenosciara exigua is not clearly distinguished from Ctenosciara hyalipennis by its COI sequence (both share the same BIN BOLD:AAH3983) and that its species status may be questionable.},
}
@article {pmid27092945,
year = {2016},
author = {Zou, S and Fei, C and Song, J and Bao, Y and He, M and Wang, C},
title = {Combining and Comparing Coalescent, Distance and Character-Based Approaches for Barcoding Microalgaes: A Test with Chlorella-Like Species (Chlorophyta).},
journal = {PloS one},
volume = {11},
number = {4},
pages = {e0153833},
pmid = {27092945},
issn = {1932-6203},
mesh = {Chlorella/*classification/*genetics ; DNA Barcoding, Taxonomic/methods ; Microalgae/*classification/*genetics ; Phylogeny ; },
abstract = {Several different barcoding methods of distinguishing species have been advanced, but which method is the best is still controversial. Chlorella is becoming particularly promising in the development of second-generation biofuels. However, the taxonomy of Chlorella-like organisms is easily confused. Here we report a comprehensive barcoding analysis of Chlorella-like species from Chlorella, Chloroidium, Dictyosphaerium and Actinastrum based on rbcL, ITS, tufA and 16S sequences to test the efficiency of traditional barcoding, GMYC, ABGD, PTP, P ID and character-based barcoding methods. First of all, the barcoding results gave new insights into the taxonomic assessment of Chlorella-like organisms studied, including the clear species discrimination and resolution of potentially cryptic species complexes in C. sorokiniana, D. ehrenbergianum and C. Vulgaris. The tufA proved to be the most efficient barcoding locus, which thus could be as potential "specific barcode" for Chlorella-like species. The 16S failed in discriminating most closely related species. The resolution of GMYC, PTP, P ID, ABGD and character-based barcoding methods were variable among rbcL, ITS and tufA genes. The best resolution for species differentiation appeared in tufA analysis where GMYC, PTP, ABGD and character-based approaches produced consistent groups while the PTP method over-split the taxa. The character analysis of rbcL, ITS and tufA sequences could clearly distinguish all taxonomic groups respectively, including the potentially cryptic lineages, with many character attributes. Thus, the character-based barcoding provides an attractive complement to coalescent and distance-based barcoding. Our study represents the test that proves the efficiency of multiple DNA barcoding in species discrimination of microalgaes.},
}
@article {pmid27091390,
year = {2016},
author = {Adamčík, S and Slovák, M and Eberhardt, U and Ronikier, A and Jairus, T and Hampe, F and Verbeken, A},
title = {Molecular inference, multivariate morphometrics and ecological assessment are applied in concert to delimit species in the Russula clavipes complex.},
journal = {Mycologia},
volume = {108},
number = {4},
pages = {716-730},
doi = {10.3852/15-194},
pmid = {27091390},
issn = {0027-5514},
mesh = {Basidiomycota/*classification/cytology/genetics/isolation &amp; purification ; Betula/microbiology ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Microscopy ; Phylogeny ; Populus/microbiology ; Salix/microbiology ; Sequence Analysis, DNA ; Tracheophyta/microbiology ; },
abstract = {Species of Russula subsect. Xerampelinae are notoriously difficult to identify and name and have not been subject to molecular study. A group of species, referred to here as the R. clavipes complex, growing in association with Salix, Betula and Populus as well as coniferous tree species from temperate to arctic and alpine habitats, were examined. Analyses of the nuc rDNA internal transcribed spacer (ITS) region and a numerical analysis of morphological characters were used. The R. clavipes complex is a monophyletic group within Russula subsect. Xerampelinae, according to molecular results. The complex includes three species: R. nuoljae is a phylogenetically and morphologically well-supported species while the other two, R. clavipes and R. pascua, are similar based on ITS data and morphology but separate based on their ecology. Russula pseudoolivascens is conspecific with R. clavipes Several combinations of characters traditionally used in the taxonomy of R. subsect. Xerampelinae are inappropriate for species delimitation in this group and the adequacy of the ITS for species identification in this group is discussed. Detailed microscopic observations on the type collection of R. nuoljae are presented and illustrated, along with a key to the European members of R. subsect. Xerampelinae.},
}
@article {pmid27089479,
year = {2016},
author = {Charles, M and Das, S and Daniels, R and Kirkman, L and Delva, GG and Destine, R and Escalante, A and Villegas, L and Daniels, NM and Shigyo, K and Volkman, SK and Pape, JW and Golightly, LM},
title = {Plasmodium falciparum K76T pfcrt Gene Mutations and Parasite Population Structure, Haiti, 2006-2009.},
journal = {Emerging infectious diseases},
volume = {22},
number = {5},
pages = {786-793},
pmid = {27089479},
issn = {1080-6059},
support = {K23 AI073190/AI/NIAID NIH HHS/United States ; K24 AI110732/AI/NIAID NIH HHS/United States ; },
mesh = {DNA Barcoding, Taxonomic ; Geography ; Haiti/epidemiology ; History, 21st Century ; Humans ; Malaria, Falciparum/*epidemiology/history/*parasitology ; Membrane Transport Proteins/*genetics ; *Mutation ; Phylogeography ; Plasmodium falciparum/classification/*genetics ; Protozoan Proteins/*genetics ; Sequence Analysis, DNA ; },
abstract = {Hispaniola is the only Caribbean island to which Plasmodium falciparum malaria remains endemic. Resistance to the antimalarial drug chloroquine has rarely been reported in Haiti, which is located on Hispaniola, but the K76T pfcrt (P. falciparum chloroquine resistance transporter) gene mutation that confers chloroquine resistance has been detected intermittently. We analyzed 901 patient samples collected during 2006-2009 and found 2 samples showed possible mixed parasite infections of genetically chloroquine-resistant and -sensitive parasites. Direct sequencing of the pfcrt resistance locus and single-nucleotide polymorphism barcoding did not definitively identify a resistant population, suggesting that sustained propagation of chloroquine-resistant parasites was not occurring in Haiti during the study period. Comparison of parasites from Haiti with those from Colombia, Panama, and Venezuela reveals a geographically distinct population with highly related parasites. Our findings indicate low genetic diversity in the parasite population and low levels of chloroquine resistance in Haiti, raising the possibility that reported cases may be of exogenous origin.},
}
@article {pmid27085955,
year = {2016},
author = {Sánchez, JL and Henry, OY and Joda, H and Solnestam, BW and Kvastad, L and Johansson, E and Akan, P and Lundeberg, J and Lladach, N and Ramakrishnan, D and Riley, I and O'Sullivan, CK},
title = {Multiplex PCB-based electrochemical detection of cancer biomarkers using MLPA-barcode approach.},
journal = {Biosensors &amp; bioelectronics},
volume = {82},
number = {},
pages = {224-232},
doi = {10.1016/j.bios.2016.04.018},
pmid = {27085955},
issn = {1873-4235},
mesh = {Biomarkers, Tumor/analysis/genetics ; Biosensing Techniques/instrumentation ; Breast/pathology ; Breast Neoplasms/diagnosis/*genetics ; Electrochemical Techniques/*instrumentation ; Female ; Humans ; Multiplex Polymerase Chain Reaction/*instrumentation ; *Nucleic Acid Hybridization ; RNA, Messenger/analysis/*genetics ; Transcriptome ; },
abstract = {Asymmetric multiplex ligation-dependent probe amplification (MLPA) was developed for the amplification of seven breast cancer related mRNA markers and the MLPA products were electrochemically detected via hybridization. Seven breast cancer genetic markers were amplified by means of the MLPA reaction, which allows for multiplex amplification of multiple targets with a single primer pair. Novel synthetic MLPA probes were designed to include a unique barcode sequence in each amplified gene. Capture probes complementary to each of the barcode sequences were immobilized on each electrode of a low-cost electrode microarray manufactured on standard printed circuit board (PCB) substrates. The functionalised electrodes were exposed to the single-stranded MLPA products and following hybridization, a horseradish peroxidase (HRP)-labelled DNA secondary probe complementary to the amplified strand completed the genocomplex, which was electrochemically detected following substrate addition. The electrode arrays fabricated using PCB technology exhibited an excellent electrochemical performance, equivalent to planar photolithographically-fabricated gold electrodes, but at a vastly reduced cost (>50 times lower per array). The optimised system was demonstrated to be highly specific with negligible cross-reactivity allowing the simultaneous detection of the seven mRNA markers, with limits of detections as low as 25pM. This approach provides a novel strategy for the genetic profiling of tumour cells via integrated "amplification-to-detection".},
}
@article {pmid27081333,
year = {2016},
author = {Fossen, EI and Ekrem, T and Nilsson, AN and Bergsten, J},
title = {Species delimitation in northern European water scavenger beetles of the genus Hydrobius (Coleoptera, Hydrophilidae).},
journal = {ZooKeys},
volume = {},
number = {564},
pages = {71-120},
pmid = {27081333},
issn = {1313-2989},
abstract = {The chiefly Holarctic Hydrobius species complex (Coleoptera, Hydrophilidae) currently consists of Hydrobius arcticus Kuwert, 1890, and three morphological variants of Hydrobius fuscipes (Linnaeus, 1758): var. fuscipes, var. rottenbergii and var. subrotundus in northern Europe. Here molecular and morphological data are used to test the species boundaries in this species complex. Three gene segments (COI, H3 and ITS2) were sequenced and analyzed with Bayesian methods to infer phylogenetic relationships. The Generalized Mixed Yule Coalescent (GMYC) model and two versions of the Bayesian species delimitation method BPP, with or without an a priori defined guide tree (v2.2 &amp; v3.0), were used to evaluate species limits. External and male genital characters of primarily Fennoscandian specimens were measured and statistically analyzed to test for significant differences in quantitative morphological characters. The four morphotypes formed separate genetic clusters on gene trees and were delimited as separate species by GMYC and by both versions of BPP, despite specimens of Hydrobius fuscipes var. fuscipes and Hydrobius fuscipes var. subrotundus being sympatric. Hydrobius arcticus and Hydrobius fuscipes var. rottenbergii could only be separated genetically with ITS2, and were delimited statistically with GMYC on ITS2 and with BPP on the combined data. In addition, six or seven potentially cryptic species of the Hydrobius fuscipes complex from regions outside northern Europe were delimited genetically. Although some overlap was found, the mean values of six male genital characters were significantly different between the morphotypes (p < 0.001). Morphological characters previously presumed to be diagnostic were less reliable to separate Hydrobius fuscipes var. fuscipes from Hydrobius fuscipes var. subrotundus, but characters in the literature for Hydrobius arcticus and Hydrobius fuscipes var. rottenbergii were diagnostic. Overall, morphological and molecular evidence strongly suggest that Hydrobius arcticus and the three morphological variants of Hydrobius fuscipes are separate species and Hydrobius rottenbergii Gerhardt, 1872, stat. n. and Hydrobius subrotundus Stephens, 1829, stat. n. are elevated to valid species. An identification key to northern European species of Hydrobius is provided.},
}
@article {pmid27081331,
year = {2016},
author = {Wesener, T and Voigtländer, K and Decker, P and Oeyen, JP and Spelda, J},
title = {Barcoding of Central European Cryptops centipedes reveals large interspecific distances with ghost lineages and new species records from Germany and Austria (Chilopoda, Scolopendromorpha).},
journal = {ZooKeys},
volume = {},
number = {564},
pages = {21-46},
pmid = {27081331},
issn = {1313-2989},
abstract = {In order to evaluate the diversity of Central European Myriapoda species in the course of the German Barcode of Life project, 61 cytochrome c oxidase I sequences of the genus Cryptops Leach, 1815, a centipede genus of the order Scolopendromorpha, were successfully sequenced and analyzed. One sequence of Scolopendra cingulata Latreille, 1829 and one of Theatops erythrocephalus Koch, 1847 were utilized as outgroups. Instead of the expected three species (Cryptops parisi Brolemann, 1920; Cryptops anomalans Newport, 1844; Cryptops hortensis (Donovan, 1810)), analyzed samples included eight to ten species. Of the eight clearly distinguishable morphospecies of Cryptops, five (Cryptops parisi; Cryptops croaticus Verhoeff, 1931; Cryptops anomalans; Cryptops umbricus Verhoeff, 1931; Cryptops hortensis) could be tentatively determined to species level, while a further three remain undetermined (one each from Germany, Austria and Croatia, and Slovenia). Cryptops croaticus is recorded for the first time from Austria. A single specimen (previously suspected as being Cryptops anomalans), was redetermined as Cryptops umbricus Verhoeff, 1931, a first record for Germany. All analyzed Cryptops species are monophyletic and show large genetic distances from one another (p-distances of 13.7-22.2%). Clear barcoding gaps are present in lineages represented by >10 specimens, highlighting the usefulness of the barcoding method for evaluating species diversity in centipedes. German specimens formally assigned to Cryptops parisi are divided into three clades differing by 8.4-11.3% from one another; their intra-lineage genetic distance is much lower at 0-1.1%. The three clades are geographically separate, indicating that they might represent distinct species. Aside from Cryptops parisi, intraspecific distances of Cryptops spp. in Central Europe are low (<3.3%).},
}
@article {pmid27080809,
year = {2016},
author = {Hoinka, J and Przytycka, T},
title = {AptaPLEX - A dedicated, multithreaded demultiplexer for HT-SELEX data.},
journal = {Methods (San Diego, Calif.)},
volume = {106},
number = {},
pages = {82-85},
doi = {10.1016/j.ymeth.2016.04.011},
pmid = {27080809},
issn = {1095-9130},
mesh = {Aptamers, Nucleotide/*genetics ; Computer Simulation ; DNA, Single-Stranded/*chemistry/genetics ; High-Throughput Nucleotide Sequencing ; Ligands ; RNA/chemistry/*genetics ; SELEX Aptamer Technique/*methods ; },
abstract = {Aptamers, short and synthetic RNA/DNA molecules binding distinct targets with high affinity and specificity, are identified via Systematic Evolution of Ligands by Exponential Enrichment (SELEX), an in vitro procedure that, starting from a pool of random ssDNA/RNA sequences, selects sequences by amplifying target-affine species through a series of selection cycles. This versatile protocol has recently been combined with high throughput sequencing, allowing arbitrary stages of the selection to be sequenced and analyzed in silico. As a prerequisite, these data require extensive preprocessing by means of quality controls, error correction and demultiplexing, all while taking into account the specific design of aptamers. Existing solutions addressing this task are currently present only as integrated components in larger pipelines, limiting their applicability in independent software solutions. Here we present AptaPLEX, a standalone and platform independent demultiplexer specifically designed for HT-SELEX data. Given the multiplexed data from one or multiple HT-SELEX experiments, AptaPLEX extracts and restores aptamers into the original selection cycles by identifying the barcode and primer regions in each read. AptaPLEX is capable of fuzzy matching for both the barcode and primers, and automatically corrects mismatches between forward and reverse reads for paired-end data. Our software provides a rich set of additional features and can easily be integrated into existing analysis automation pipelines on multiple platforms ranging from desktop machines to cloud based solutions.},
}
@article {pmid27078660,
year = {2016},
author = {Tambireddy, N and Gayatri, T and Gireesh-Babu, P and Pavan-Kumar, A},
title = {Molecular characterization and phylogeny of some mazocraeidean monogeneans from carangid fish.},
journal = {Acta parasitologica},
volume = {61},
number = {2},
pages = {360-368},
doi = {10.1515/ap-2016-0047},
pmid = {27078660},
issn = {1896-1851},
mesh = {Animals ; Cestode Infections/parasitology/*veterinary ; Cluster Analysis ; DNA, Helminth/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fish Diseases/*parasitology ; Fishes ; Phylogeny ; Platyhelminths/*classification/genetics/*isolation &amp; purification ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; },
abstract = {Polyopisthocotylean monogenean parasites of fishes are highly host specific and have been used as an appropriate model to study the host-parasite co-evolution. In the present study, eight monogeneans of the order Mazocraeidea were characterized by nuclear 28S rDNA sequences and their phylogenetic relationship with other polyopisthocotylean species was investigated. Neighbour-joining, maximum parsimony, maximum likelihood and Bayesian Inference methods were used for phylogenetic reconstruction. The topology sustained by high bootstrap was: (((Hexabothriidae (Mazocraeidae (Discocotylidae (Diplozoidae (Diclidophoridae (Plectanocotylidae (Heteromicrocotylidae (Microcotylidae (Heteraxinidae), (Thoracocotylidae, Gotocotylidae (Gastrocoylidae (Allodiscocotylidae: Protomicrocotylidae))). In addition, we have also developed DNA barcodes (COI sequences) for six species and the barcodes clearly discriminated all the species. The polytomy within Protomicrocotylidae family is resolved in this study for the first time and it appears that within this family, Bilaterocotyloides species are basal compared to Neomicrocotyle and Lethacotyle species while the latter is the more derived.},
}
@article {pmid27076998,
year = {2016},
author = {Gutiérrez-López, N and Ovando-Medina, I and Salvador-Figueroa, M and Molina-Freaner, F and Avendaño-Arrazate, CH and Vázquez-Ovando, A},
title = {Unique haplotypes of cacao trees as revealed by trnH-psbA chloroplast DNA.},
journal = {PeerJ},
volume = {4},
number = {},
pages = {e1855},
pmid = {27076998},
issn = {2167-8359},
abstract = {Cacao trees have been cultivated in Mesoamerica for at least 4,000 years. In this study, we analyzed sequence variation in the chloroplast DNA trnH-psbA intergenic spacer from 28 cacao trees from different farms in the Soconusco region in southern Mexico. Genetic relationships were established by two analysis approaches based on geographic origin (five populations) and genetic origin (based on a previous study). We identified six polymorphic sites, including five insertion/deletion (indels) types and one transversion. The overall nucleotide diversity was low for both approaches (geographic = 0.0032 and genetic = 0.0038). Conversely, we obtained moderate to high haplotype diversity (0.66 and 0.80) with 10 and 12 haplotypes, respectively. The common haplotype (H1) for both networks included cacao trees from all geographic locations (geographic approach) and four genetic groups (genetic approach). This common haplotype (ancient) derived a set of intermediate haplotypes and singletons interconnected by one or two mutational steps, which suggested directional selection and event purification from the expansion of narrow populations. Cacao trees from Soconusco region were grouped into one cluster without any evidence of subclustering based on AMOVA (F ST = 0) and SAMOVA (F ST = 0.04393) results. One population (Mazatán) showed a high haplotype frequency; thus, this population could be considered an important reservoir of genetic material. The indels located in the trnH-psbA intergenic spacer of cacao trees could be useful as markers for the development of DNA barcoding.},
}
@article {pmid27073924,
year = {2016},
author = {Shrubovych, J and Bartel, D and Szucsich, NU and Resch, MC and Pass, G},
title = {Morphological and Genetic Analysis of the Acerentomon doderoi Group (Protura: Acerentomidae) with Description of A. christiani sp. nov.},
journal = {PloS one},
volume = {11},
number = {4},
pages = {e0148033},
pmid = {27073924},
issn = {1932-6203},
support = {P 23251/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Animals ; Arthropod Proteins/*genetics ; *Arthropods/classification/genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; RNA, Ribosomal, 28S/*genetics ; },
abstract = {Acerentomon christiani sp. nov. is described from Vienna, Austria. The new species is a member of the "doderoi" group, characterized by the presence of seta x on tergite VII. It is most similar to A. gallicum, A. brevisetosum and A. tenuisetosum, but differs from these species in the length of foretarsal sensillum c and certain other chaetotaxic measurements and indices. In addition to the morphological description, the DNA barcoding region of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) and the 28S ribosomal RNA of the new species are provided. The morphological characters and the barcode of the new species are discussed in comparison to those of other Acerentomon species. An identification key to all known Acerentomon spp. of the "doderoi" group is given.},
}
@article {pmid27069819,
year = {2016},
author = {Vandamme, SG and Griffiths, AM and Taylor, SA and Di Muri, C and Hankard, EA and Towne, JA and Watson, M and Mariani, S},
title = {Sushi barcoding in the UK: another kettle of fish.},
journal = {PeerJ},
volume = {4},
number = {},
pages = {e1891},
pmid = {27069819},
issn = {2167-8359},
abstract = {Although the spread of sushi restaurants in the European Union and United States is a relatively new phenomenon, they have rapidly become among the most popular food services globally. Recent studies indicate that they can be associated with very high levels (>70%) of fish species substitution. Based on indications that the European seafood retail sector may currently be under better control than its North American counterpart, here we investigated levels of seafood labelling accuracy in sushi bars and restaurants across England. We used the COI barcoding gene to screen samples of tuna, eel, and a variety of other products characterised by less visually distinctive 'white flesh'. Moderate levels of substitution were found (10%), significantly lower than observed in North America, which lends support to the argument that public awareness, policy and governance of seafood labels is more effective in the European Union. Nevertheless, the results highlight that current labelling practice in UK restaurants lags behind the level of detail implemented in the retail sector, which hinders consumer choice, with potentially damaging economic, health and environmental consequences. Specifically, critically endangered species of tuna and eel continue to be sold without adequate information to consumers.},
}
@article {pmid27069650,
year = {2016},
author = {MacIvor, JS},
title = {DNA barcoding to identify leaf preference of leafcutting bees.},
journal = {Royal Society open science},
volume = {3},
number = {3},
pages = {150623},
pmid = {27069650},
issn = {2054-5703},
abstract = {Leafcutting bees (Megachile: Megachilidae) cut leaves from various trees, shrubs, wildflowers and grasses to partition and encase brood cells in hollow plant stems, decaying logs or in the ground. The identification of preferred plant species via morphological characters of the leaf fragments is challenging and direct observation of bees cutting leaves from certain plant species are difficult. As such, data are poor on leaf preference of leafcutting bees. In this study, I use DNA barcoding of the rcbL and ITS2 regions to identify and compare leaf preference of three Megachile bee species widespread in Toronto, Canada. Nests were opened and one leaf piece from one cell per nest of the native M. pugnata Say (N=45 leaf pieces), and the introduced M. rotundata Fabricius (N=64) and M. centuncularis (L.) (N=65) were analysed. From 174 individual DNA sequences, 54 plant species were identified. Preference by M. rotundata was most diverse (36 leaf species, H'=3.08, phylogenetic diversity (pd)=2.97), followed by M. centuncularis (23 species, H'=2.38, pd=1.51) then M. pugnata (18 species, H'=1.87, pd=1.22). Cluster analysis revealed significant overlap in leaf choice of M. rotundata and M. centuncularis. There was no significant preference for native leaves, and only M. centuncularis showed preference for leaves of woody plants over perennials. Interestingly, antimicrobial properties were present in all but six plants collected; all these were exotic plants and none were collected by the native bee, M. pugnata. These missing details in interpreting what bees need offers valuable information for conservation by accounting for necessary (and potentially limiting) nesting materials.},
}
@article {pmid27066827,
year = {2016},
author = {Török, E and Tomazatos, A and Cadar, D and Horváth, C and Keresztes, L and Jansen, S and Becker, N and Kaiser, A and Popescu, O and Schmidt-Chanasit, J and Jöst, H and Lühken, R},
title = {Pilot longitudinal mosquito surveillance study in the Danube Delta Biosphere Reserve and the first reports of Anopheles algeriensis Theobald, 1903 and Aedes hungaricus Mihályi, 1955 for Romania.},
journal = {Parasites &amp; vectors},
volume = {9},
number = {},
pages = {196},
pmid = {27066827},
issn = {1756-3305},
mesh = {Animals ; *Biodiversity ; Culicidae/*classification/genetics/*growth &amp; development ; DNA Barcoding, Taxonomic ; Female ; *Insect Vectors ; Longitudinal Studies ; Romania ; Spatio-Temporal Analysis ; },
abstract = {BACKGROUND: Mosquito-borne viruses (moboviruses) are of growing importance in many countries of Europe. In Romania and especially in the Danube Delta Biosphere Reserve (DDBR), mosquito and mobovirus surveillance are not performed on a regular basis. However, this type of study is crucially needed to evaluate the risk of pathogen transmission, to understand the ecology of emerging moboviruses, or to plan vector control programmes.<br><br>METHODS: We initiated a longitudinal mosquito surveillance study with carbon dioxide-baited Heavy Duty Encephalitis Vector Survey traps at four sampling sites to analyse the spatio-temporal pattern of the (i) mosquito species composition and diversity, (ii) functional groups of mosquitoes (oviposition sites, overwintering stage, and number of generations), and (iii) the occurrence of potential West Nile virus (WNV) vectors.<br><br>RESULTS: During 2014, a total of 240,546 female mosquitoes were collected. All species were identified using morphological characteristics and further confirmed by mitochondrial cytochrome c oxidase subunit I (COI) gene analysis of selected specimens. The two most common taxa were Coquilettidia richiardii (40.9 %) and Anopheles hyrcanus (34.1 %), followed by Culex pipiens (sensu lato) (s.l.)/Cx. torrentium (7.7 %), Aedes caspius (5.7 %), Cx. modestus (4.0 %), An. maculipennis (s.l.) (3.9 %), and Ae. vexans (3.0 %). A further seven species were less common in the area studied, including two new records for Romania: An. algeriensis and Ae. hungaricus. Phylogenetic analysis of COI gene demonstrated the evolutionary relatedness of most species with specimens of the same species collected in other European regions, except Ae. detritus and An. algeriensis, which exhibited high genetic diversity. Due to the dominance of Cq. richiardii and An. hyrcanus (75 % of all collected specimens), the overall phenology and temporal pattern of functional groups basically followed the phenology of both species. A huge proportion of the mosquito population in the course of the entire sampling period can be classified as potential WNV vectors. With 40 % of all collected specimens, the most frequent species Cq. richiardii is probably the most important vector of WNV in the DDBR.<br><br>CONCLUSION: This is the first DNA-barcoding supported analysis of the mosquito fauna in the DDBR. The detection of two new species highlights the lack of knowledge about the mosquito fauna in Romania and in the DDBR in particular. The results provide detailed insights into the spatial-temporal mosquito species composition, which might lead to a better understanding of mobovirus activity in Romania and thus, can be used for the development of vector control programs.},
}
@article {pmid27066250,
year = {2016},
author = {Shen, Y and Guan, L and Wang, D and Gan, X},
title = {DNA barcoding and evaluation of genetic diversity in Cyprinidae fish in the midstream of the Yangtze River.},
journal = {Ecology and evolution},
volume = {6},
number = {9},
pages = {2702-2713},
pmid = {27066250},
issn = {2045-7758},
abstract = {The Yangtze River is the longest river in China and is divided into upstream and mid-downstream regions by the Three Gorges (the natural barriers of the Yangtze River), resulting in a complex distribution of fish. Dramatic changes to habitat environments may ultimately threaten fish survival; thus, it is necessary to evaluate the genetic diversity and propose protective measures. Species identification is the most significant task in many fields of biological research and in conservation efforts. DNA barcoding, which constitutes the analysis of a short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) sequence, has been widely used for species identification. In this study, we collected 561 COI barcode sequences from 35 fish from the midstream of the Yangtze River. The intraspecific distances of all species were below 2% (with the exception of Acheilognathus macropterus and Hemibarbus maculatus). Nevertheless, all species could be unambiguously identified from the trees, barcoding gaps and taxonomic resolution ratio values. Furthermore, the COI barcode diversity was found to be low (≤0.5%), with the exception of H. maculatus (0.87%), A. macropterus (2.02%) and Saurogobio dabryi (0.82%). No or few shared haplotypes were detected between the upstream and downstream populations for ten species with overall nucleotide diversities greater than 0.00%, which indicated the likelihood of significant population genetic structuring. Our analyses indicated that DNA barcoding is an effective tool for the identification of cyprinidae fish in the midstream of the Yangtze River. It is vital that some protective measures be taken immediately because of the low COI barcode diversity.},
}
@article {pmid27066026,
year = {2016},
author = {Sun, W and Li, JJ and Xiong, C and Zhao, B and Chen, SL},
title = {The Potential Power of Bar-HRM Technology in Herbal Medicine Identification.},
journal = {Frontiers in plant science},
volume = {7},
number = {},
pages = {367},
pmid = {27066026},
issn = {1664-462X},
abstract = {The substitution of low-cost or adulterated herbal products for high-priced herbs makes it important to be able to identify and trace herbal plant species and their processed products in the drug supply chain. PCR-based methods play an increasing role in monitoring the safety of herbal medicines by detecting adulteration. Recent studies have shown the potential of DNA barcoding combined with high resolution melting (Bar-HRM) analysis in herbal medicine identification. This method involves precisely monitoring the change in fluorescence caused by the release of an intercalating DNA dye from a DNA duplex as it is denatured by a gradual increase in temperature. Since the melting profile depends on the GC content, length, and strand complementarity of the amplification product, Bar-HRM analysis opens up the possibility of detecting single-base variants or species-specific differences in a short region of DNA. This review summarizes key factors affecting Bar-HRM analysis and describes how Bar-HRM is performed. We then discuss advances in Bar-HRM analysis of medicinal plant ingredients (herbal materia medica) as a contribution toward safe and effective herbal medicines.},
}
@article {pmid27063254,
year = {2016},
author = {Previšić, A and Gelemanović, A and Urbanič, G and Ternjej, I},
title = {Cryptic diversity in the Western Balkan endemic copepod: Four species in one?.},
journal = {Molecular phylogenetics and evolution},
volume = {100},
number = {},
pages = {124-134},
doi = {10.1016/j.ympev.2016.04.010},
pmid = {27063254},
issn = {1095-9513},
mesh = {Animals ; Balkan Peninsula ; Bayes Theorem ; Biodiversity ; Biological Evolution ; Copepoda/*classification/genetics ; DNA/chemistry/isolation &amp; purification/metabolism ; DNA, Mitochondrial/chemistry/metabolism ; Gene Flow ; Genetic Variation ; Histones/genetics ; Male ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {We use mitochondrial (mtCOI) and nuclear (nH3) sequence data to investigate differentiation of Eudiaptomus hadzici, a freshwater copepod endemic to the Western Balkans. E. hadzici has a disjunct distribution and morphological differences were observed at regional scale. In the current study 6 out of 7 known populations are included. We applied several species delimiting approaches, distance based methods (K2P p-distance and Automatic Barcode Gap Discovery, ABGD) using the mtCOI, Bayesian phylogeny and the Bayesian method implemented in bPTP and BPP programs using the concatenated sequences of both genes. Phylogenetic and species delimitation analyses all suggest that the nominal species E. hadzici consists of four isolated, cryptic evolutionary lineages in the Western Balkans. Each of the four lineages inhabits a single lake or a group of lakes in close proximity. They exhibit major differences in secondary sexual characters, e.g. right antennule in males. Denticulation of spine on 13th segment is substantially distinct among the four lineages, having different number and shape of tooth-like protrusions. Gene flow and dispersal are restricted to very small spatial scale, but with local differences, implying that diverse historical and contemporary processes are operating at small spatial scales in E. hadzici. In order to further examine spatial and temporal diversification patterns, we constructed a dated species tree analysis using (*)BEAST. Due to lack of reliable calibration points and taxa specific evolutionary rates, two evolutionary rates were applied and the faster one (2.6% myr) seems more plausible considering the geological history of the region. The divergence of E. hadzici lineages is dated from Early Miocene onwards with geographically close lineages diverging more recently, Late Miocene to Pleistocene and Pleistocene, respectively. Overall, our findings shed light on cryptic genetic complexity of endemics in one of European biodiversity hotspots. Moreover, this study represents one further example of integrative taxonomy, linking DNA methodology and classical taxonomy based on morphology. Therefore, it lays groundwork for future taxonomy and biogeography of freshwater microcrustaceans in the region.},
}
@article {pmid27062810,
year = {2015},
author = {Wang, X and Hou, FX and Wang, YX and Wang, YX and Li, JD and Yuan, Y and Peng, C and Guo, JL},
title = {[Identification of original species of Mantidis Oötheca (Sangpiaoxiao) based on DNA barcoding].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {40},
number = {20},
pages = {3963-3966},
pmid = {27062810},
issn = {1001-5302},
mesh = {Animals ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Insect Proteins/genetics ; Mantodea/*classification/*genetics ; Medicine, Chinese Traditional ; Phylogeny ; },
abstract = {Both market research and literature reports both found that the ootheca of mantodea was all used as medicine. However, Chinese Pharmacopoeia only records the ootheca of three mantis species. The clinical use of ootheca unrecorded in Chinese Pharmacopoeia, will pose potential risks to drug safety. It's urgent to identify the origin of Mantidis Oötheca. The current researches about original animal in Mantidis Oötheca are based on morphology and unanimous. DNA barcoding fill gaps of the traditional morphological identification, which is widely used in animal classification studies. This study first use DNA barcoding to analyze genetic distance among different Mantidis Oötheca types, align COI sequences between mantis and Mantidis Oötheca and construct the phylogeny tree. The result confirmed that Tenodera sinensis and Hierodula patellifera were the origin insects of Tuanpiaoxiao and Heipiaoxiao, respectively, and Statilia maculate and Mantis religiosa were the origin insects of Changpiaoxiao.},
}
@article {pmid27060606,
year = {2017},
author = {Kumar, NP and Rajavel, AR and Jambulingam, P},
title = {Development of a PCR methodology to distinguish species members of Culex vishnui subgroup (Diptera: Culicidae), based on DNA Barcodes.},
journal = {Insect science},
volume = {24},
number = {2},
pages = {336-340},
doi = {10.1111/1744-7917.12344},
pmid = {27060606},
issn = {1744-7917},
mesh = {Animals ; Base Sequence ; Culex/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Insect Proteins/*genetics ; Polymerase Chain Reaction/*methods ; Sequence Alignment ; },
}
@article {pmid27060140,
year = {2016},
author = {Ståhlberg, A and Krzyzanowski, PM and Jackson, JB and Egyud, M and Stein, L and Godfrey, TE},
title = {Simple, multiplexed, PCR-based barcoding of DNA enables sensitive mutation detection in liquid biopsies using sequencing.},
journal = {Nucleic acids research},
volume = {44},
number = {11},
pages = {e105},
pmid = {27060140},
issn = {1362-4962},
support = {R21 CA172999/CA/NCI NIH HHS/United States ; },
mesh = {Biopsy ; Cell Line ; *DNA Barcoding, Taxonomic ; *DNA Mutational Analysis ; DNA Primers/chemistry/genetics ; Gene Library ; High-Throughput Nucleotide Sequencing ; Humans ; *Multiplex Polymerase Chain Reaction ; *Mutation ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Analysis, DNA ; },
abstract = {Detection of cell-free DNA in liquid biopsies offers great potential for use in non-invasive prenatal testing and as a cancer biomarker. Fetal and tumor DNA fractions however can be extremely low in these samples and ultra-sensitive methods are required for their detection. Here, we report an extremely simple and fast method for introduction of barcodes into DNA libraries made from 5 ng of DNA. Barcoded adapter primers are designed with an oligonucleotide hairpin structure to protect the molecular barcodes during the first rounds of polymerase chain reaction (PCR) and prevent them from participating in mis-priming events. Our approach enables high-level multiplexing and next-generation sequencing library construction with flexible library content. We show that uniform libraries of 1-, 5-, 13- and 31-plex can be generated. Utilizing the barcodes to generate consensus reads for each original DNA molecule reduces background sequencing noise and allows detection of variant alleles below 0.1% frequency in clonal cell line DNA and in cell-free plasma DNA. Thus, our approach bridges the gap between the highly sensitive but specific capabilities of digital PCR, which only allows a limited number of variants to be analyzed, with the broad target capability of next-generation sequencing which traditionally lacks the sensitivity to detect rare variants.},
}
@article {pmid27059148,
year = {2016},
author = {Oyafuso, ZS and Toonen, RJ and Franklin, EC},
title = {Temporal and spatial trends in prey composition of wahoo Acanthocybium solandri: a diet analysis from the central North Pacific Ocean using visual and DNA bar-coding techniques.},
journal = {Journal of fish biology},
volume = {88},
number = {4},
pages = {1501-1523},
doi = {10.1111/jfb.12928},
pmid = {27059148},
issn = {1095-8649},
mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Diet/*veterinary ; Ecosystem ; Fisheries ; Gastrointestinal Contents ; Hawaii ; Pacific Ocean ; *Perciformes ; Seasons ; Spatio-Temporal Analysis ; },
abstract = {A diet analysis was conducted on 444 wahoo Acanthocybium solandri caught in the central North Pacific Ocean longline fishery and a nearshore troll fishery surrounding the Hawaiian Islands from June to December 2014. In addition to traditional observational methods of stomach contents, a DNA bar-coding approach was integrated into the analysis by sequencing the cytochrome c oxidase subunit 1 (COI) region of the mtDNA genome to taxonomically identify individual prey items that could not be classified visually to species. For nearshore-caught A. solandri, juvenile pre-settlement reef fish species from various families dominated the prey composition during the summer months, followed primarily by Carangidae in autumn months. Gempylidae, Echeneidae and Scombridae were dominant prey taxa from the offshore fishery. Molidae was a common prey family found in stomachs collected north-east of the Hawaiian Archipelago while tetraodontiform reef fishes, known to have extended pelagic stages, were prominent prey items south-west of the Hawaiian Islands. The diet composition of A. solandri was indicative of an adaptive feeder and thus revealed dominant geographic and seasonal abundances of certain taxa from various ecosystems in the marine environment. The addition of molecular bar-coding to the traditional visual method of prey identifications allowed for a more comprehensive range of the prey field of A. solandri to be identified and should be used as a standard component in future diet studies.},
}
@article {pmid27058734,
year = {2016},
author = {Smart, JJ and Chin, A and Baje, L and Green, ME and Appleyard, SA and Tobin, AJ and Simpfendorfer, CA and White, WT},
title = {Effects of Including Misidentified Sharks in Life History Analyses: A Case Study on the Grey Reef Shark Carcharhinus amblyrhynchos from Papua New Guinea.},
journal = {PloS one},
volume = {11},
number = {4},
pages = {e0153116},
pmid = {27058734},
issn = {1932-6203},
mesh = {Animals ; Conservation of Natural Resources ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Female ; Fisheries ; Male ; Models, Biological ; Papua New Guinea ; Population Dynamics ; Sharks/*classification/genetics/*growth &amp; development ; Species Specificity ; },
abstract = {Fisheries observer programs are used around the world to collect crucial information and samples that inform fisheries management. However, observer error may misidentify similar-looking shark species. This raises questions about the level of error that species misidentifications could introduce to estimates of species' life history parameters. This study addressed these questions using the Grey Reef Shark Carcharhinus amblyrhynchos as a case study. Observer misidentification rates were quantified by validating species identifications using diagnostic photographs taken on board supplemented with DNA barcoding. Length-at-age and maturity ogive analyses were then estimated and compared with and without the misidentified individuals. Vertebrae were retained from a total of 155 sharks identified by observers as C. amblyrhynchos. However, 22 (14%) of these were sharks were misidentified by the observers and were subsequently re-identified based on photographs and/or DNA barcoding. Of the 22 individuals misidentified as C. amblyrhynchos, 16 (73%) were detected using photographs and a further 6 via genetic validation. If misidentified individuals had been included, substantial error would have been introduced to both the length-at-age and the maturity estimates. Thus validating the species identification, increased the accuracy of estimated life history parameters for C. amblyrhynchos. From the corrected sample a multi-model inference approach was used to estimate growth for C. amblyrhynchos using three candidate models. The model averaged length-at-age parameters for C. amblyrhynchos with the sexes combined were L∞ = 159 cm TL and L0 = 72 cm TL. Females mature at a greater length (l50 = 136 cm TL) and older age (A50 = 9.1 years) than males (l50 = 123 cm TL; A50 = 5.9 years). The inclusion of techniques to reduce misidentification in observer programs will improve the results of life history studies and ultimately improve management through the use of more accurate data for assessments.},
}
@article {pmid27056932,
year = {2016},
author = {Lam, VK and Merckx, VS and Graham, SW},
title = {A few-gene plastid phylogenetic framework for mycoheterotrophic monocots.},
journal = {American journal of botany},
volume = {103},
number = {4},
pages = {692-708},
doi = {10.3732/ajb.1500412},
pmid = {27056932},
issn = {1537-2197},
mesh = {*Genes, Plant ; Orchidaceae/*genetics ; Photosynthesis/genetics ; *Phylogeny ; Plastids/*genetics ; },
abstract = {PREMISE OF THE STUDY: Few-gene studies with broad taxon sampling have provided major insights into phylogeny and underpin plant classification. However, they have typically excluded heterotrophic plants because of loss, pseudogenization, or rapid evolution of plastid genes. Here we performed a phylogenetic survey of three commonly retained plastid genes to assess their utility in placing mycoheterotrophs.<br><br>METHODS: We surveyed accD, clpP, and matK for 34 taxa from seven monocot families that include full mycoheterotrophs and a broad sampling of photosynthetic taxa. After screening for weak contaminants, we conducted phylogenetic analyses and characterized among-lineage rate variation.<br><br>KEY RESULTS: Likelihood analyses strongly supported local placements of fully mycoheterotrophic taxa for Corsiaceae, Iridaceae, Orchidaceae, and Petrosaviaceae, in positions consistent with other studies. Depression of likelihood bootstrap support values near mycoheterotrophic clades was alleviated when each mycoheterotrophic family was considered separately. Triuridaceae (Sciaphila) monophyly was recovered in a partitioned likelihood analysis, and the family then placed as sister to Cyclanthaceae-Pandanaceae. Burmanniaceae placed in Dioscoreales with weak to strong support depending on analysis details, and we inferred a plastid-based phylogeny for the family. Thismiaceae species may retain a plastid genome, based on accD retention. The inferred position of Thismiaceae is unstable, but was close to Taccaceae (Dioscoreales) in some analyses.<br><br>CONCLUSIONS: Long branches/elevated substitution rates, missing genes, and occasional contaminants are challenges for plastid-based phylogenetic inference with full mycoheterotrophs. However, most mycoheterotrophs can be readily integrated into the broad picture of plant phylogeny using several plastid genes and broad taxonomic sampling.},
}
@article {pmid27055751,
year = {2016},
author = {Rees, P and Brown, MR and Wills, JW and Summers, H},
title = {An Analysis of the Practicalities of Multi-Color Nanoparticle Cellular Bar-Coding.},
journal = {Combinatorial chemistry &amp; high throughput screening},
volume = {19},
number = {5},
pages = {362-369},
doi = {10.2174/1386207319666160408150649},
pmid = {27055751},
issn = {1875-5402},
mesh = {Animals ; Cell Line ; Cells/*cytology ; Color ; Electronic Data Processing/*methods/standards ; Humans ; Methods ; Nanoparticles/administration &amp; dosage/*analysis ; },
abstract = {Many applications in biomedical research require the long-term identification and tracking of cells over time. In previous work we have demonstrated that by sequentially dosing a cell population with different emission wavelength nanoparticles it is possible to use the random number of nanoparticle loaded vesicles generated by the cells as a barcode for individual cells within the population. In this paper we develop a simple model to describe the number of codes that can be generated using this sequential loading protocol. The methodology is validated by comparison with experiment and subsequently used to predict the effect of varying the number of colors used to encode the cells and also to assess the effect of misreading the cellular code due to errors in imaging the vesicles.},
}
@article {pmid27051224,
year = {2016},
author = {Basavanna, JM and Jain, A and Misra, SK},
title = {Denture barcoding in forensic dentistry: A future option.},
journal = {Journal of forensic dental sciences},
volume = {8},
number = {1},
pages = {52-55},
pmid = {27051224},
issn = {0975-1475},
abstract = {Neurodegenerative disorders are commonly seen in elderly individuals. Parkinson's disease (PD) is the most common example with memory loss, lack of logic, reasoning and analytical thinking. In this case report simple method of 2D Bar code technique of denture marking has been explained which will not only useful in patients with memory loss but it is very helpful in identifying the individuals in case of natural calamities like floods, earthquake, tornedo, state of unconsciousness and accidents. Such patients can be traced easily by denture barcoding. This technique is a major breakthrough in the field of forensic dentistry.},
}
@article {pmid27050315,
year = {2016},
author = {Liu, J and Yan, HF and Ge, XJ},
title = {The Use of DNA Barcoding on Recently Diverged Species in the Genus Gentiana (Gentianaceae) in China.},
journal = {PloS one},
volume = {11},
number = {4},
pages = {e0153008},
pmid = {27050315},
issn = {1932-6203},
mesh = {China ; *DNA Barcoding, Taxonomic ; DNA, Plant ; Gentianaceae/classification/*genetics ; },
abstract = {DNA barcoding of plants poses particular challenges, especially in differentiating, recently diverged taxa. The genus Gentiana (Gentianaceae) is a species-rich plant group which rapidly radiated in the Himalaya-Hengduan Mountains in China. In this study, we tested the core plant barcode (rbcL + matK) and three promising complementary barcodes (trnH-psbA, ITS and ITS2) in 30 Gentiana species across 6 sections using three methods (the genetic distance-based method, Best Close Match and tree-based method). rbcL had the highest PCR efficiency and sequencing success (100%), while the lowest sequence recoverability was from ITS (68.35%). The presence of indels and inversions in trnH-psbA in Gentiana led to difficulties in sequence alignment. When using a single region for analysis, ITS exhibited the highest discriminatory power (60%-74.42%). Of the combinations, matK + ITS provided the highest discrimination success (71.43%-88.24%) and is recommended as the DNA barcode for the genus Gentiana. DNA barcoding proved effective in assigning most species to sections, though it performed poorly in some closely related species in sect. Cruciata because of hybridization events. Our analysis suggests that the status of G. pseudosquarrosa needs to be studied further. The utility of DNA barcoding was also verified in authenticating 'Qin-Jiao' Gentiana medicinal plants (G. macrophylla, G. crassicaulis, G. straminea, and G. dahurica), which can help ensure safe and correct usage of these well-known Chinese traditional medicinal herbs.},
}
@article {pmid27048884,
year = {2016},
author = {Robin, JD and Ludlow, AT and LaRanger, R and Wright, WE and Shay, JW},
title = {Comparison of DNA Quantification Methods for Next Generation Sequencing.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {24067},
pmid = {27048884},
issn = {2045-2322},
support = {R01AG001228/AG/NIA NIH HHS/United States ; UL1 TR001105/TR/NCATS NIH HHS/United States ; C06RR30414/RR/NCRR NIH HHS/United States ; R01 AG001228/AG/NIA NIH HHS/United States ; P50CA70907/CA/NCI NIH HHS/United States ; P50 CA070907/CA/NCI NIH HHS/United States ; TL1 TR001104/TR/NCATS NIH HHS/United States ; C06 RR030414/RR/NCRR NIH HHS/United States ; T32 CA124334/CA/NCI NIH HHS/United States ; },
mesh = {Crystallography, X-Ray ; DNA/*analysis ; G-Quadruplexes ; Genome, Human ; Genomics/methods ; Genotype ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy/methods ; Markov Chains ; Models, Statistical ; Molecular Dynamics Simulation ; Nucleic Acid Conformation ; Probability ; Protein Denaturation ; Thrombin/chemistry ; },
abstract = {Next Generation Sequencing (NGS) is a powerful tool that depends on loading a precise amount of DNA onto a flowcell. NGS strategies have expanded our ability to investigate genomic phenomena by referencing mutations in cancer and diseases through large-scale genotyping, developing methods to map rare chromatin interactions (4C; 5C and Hi-C) and identifying chromatin features associated with regulatory elements (ChIP-seq, Bis-Seq, ChiA-PET). While many methods are available for DNA library quantification, there is no unambiguous gold standard. Most techniques use PCR to amplify DNA libraries to obtain sufficient quantities for optical density measurement. However, increased PCR cycles can distort the library's heterogeneity and prevent the detection of rare variants. In this analysis, we compared new digital PCR technologies (droplet digital PCR; ddPCR, ddPCR-Tail) with standard methods for the titration of NGS libraries. DdPCR-Tail is comparable to qPCR and fluorometry (QuBit) and allows sensitive quantification by analysis of barcode repartition after sequencing of multiplexed samples. This study provides a direct comparison between quantification methods throughout a complete sequencing experiment and provides the impetus to use ddPCR-based quantification for improvement of NGS quality.},
}
@article {pmid27047504,
year = {2016},
author = {Liu, Y and Wang, X and Wang, L and Chen, X and Pang, X and Han, J},
title = {A Nucleotide Signature for the Identification of American Ginseng and Its Products.},
journal = {Frontiers in plant science},
volume = {7},
number = {},
pages = {319},
pmid = {27047504},
issn = {1664-462X},
abstract = {American ginseng (derived from Panax quinquefolius) is one of the most widely used medicinal herbs in the world. Because of its high price and increasing demand, there are many adulterants on the market. The proposed internal transcribed spacer 2 (ITS2) has been used to identify raw medicinal materials, but it is not suitable for the identification of Chinese patent medicine ingredients. Therefore, a short barcode for the identification of processed American ginseng and its corresponding Chinese patent medicines would be profitable. In this study, 94 samples of American ginseng and Asian ginseng were collected from all over the world. The ITS2 region was sequenced, and a nucleotide signature was developed based on one single nucleotide polymorphism (SNP) site unique to American ginseng. The nucleotide signature (atcactcctt tgcgggagtc gaggcgg) consists of 27 bases over the length of the ITS2 sequence (420 bp). Furthermore, we also designed primer pairs to amplify the nucleotide signature; the specific primer pair 4F/4R has been found to be unique to the ginseng species and capable of amplifying the nucleotide signatures from Chinese patent medicines and decoctions. We used the nucleotide signature method to inspect ginseng products in Chinese patent medicines; 24 batches of Chinese patent medicine from stores in Beijing were amplified and sequenced successfully. Using the double peaks at the SNP sites of the nucleotide signature, 5 batches were found to be counterfeits, and 2 batches were found to contain adulterants. Thus, this nucleotide signature, with only 27 bp, has broadened the application of DNA barcoding in identification of decoctions, Chinese patent medicines and other ginseng products with degraded DNA. This method can rapidly identify ginseng products and could also be developed as an on-site detection method.},
}
@article {pmid27044044,
year = {2016},
author = {Bystrykh, LV and Belderbos, ME},
title = {Clonal Analysis of Cells with Cellular Barcoding: When Numbers and Sizes Matter.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1516},
number = {},
pages = {57-89},
doi = {10.1007/7651_2016_343},
pmid = {27044044},
issn = {1940-6029},
mesh = {Cell Differentiation ; Cell Size ; Cell Tracking/*methods ; Cells, Cultured/*cytology ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Stem Cells/*cytology ; },
abstract = {Cellular barcoding is a recently rediscovered tool to trace the clonal output of individual cells with genetically distinct and heritable DNA sequences. Each year a few dozens of papers are published using the cellular barcoding technique. Those publications largely focus on mutually related issues, namely: counting cells capable of clonal proliferation and expansion, monitoring clonal dynamics in time, tracing the origin of differentiated cells, characterizing the differentiation potential of stem cells and similar topics. Apart from their biological content, claims and conclusions, these studies show remarkable diversity in technical aspects of the barcoding method and sometimes in major conclusions. Although a diversity of approaches is quite usual in data analysis, deviant handling of barcode data might directly affect experimental results and their biological interpretation. Here, we will describe typical challenges and caveats in cellular barcoding publications available so far.},
}
@article {pmid27043197,
year = {2016},
author = {Bell, NA and Keyser, UF},
title = {Digitally encoded DNA nanostructures for multiplexed, single-molecule protein sensing with nanopores.},
journal = {Nature nanotechnology},
volume = {11},
number = {7},
pages = {645-651},
pmid = {27043197},
issn = {1748-3395},
mesh = {Binding Sites ; DNA/chemistry/*ultrastructure ; Nanopores/*ultrastructure ; Nanostructures/chemistry/*ultrastructure ; Nanotechnology/*methods ; Proteins/*analysis/chemistry/metabolism ; },
abstract = {The simultaneous detection of a large number of different analytes is important in bionanotechnology research and in diagnostic applications. Nanopore sensing is an attractive method in this regard as the approach can be integrated into small, portable device architectures, and there is significant potential for detecting multiple sub-populations in a sample. Here, we show that highly multiplexed sensing of single molecules can be achieved with solid-state nanopores by using digitally encoded DNA nanostructures. Based on the principles of DNA origami, we designed a library of DNA nanostructures in which each member contains a unique barcode; each bit in the barcode is signalled by the presence or absence of multiple DNA dumbbell hairpins. We show that a 3-bit barcode can be assigned with 94% accuracy by electrophoretically driving the DNA structures through a solid-state nanopore. Select members of the library were then functionalized to detect a single, specific antibody through antigen presentation at designed positions on the DNA. This allows us to simultaneously detect four different antibodies of the same isotype at nanomolar concentration levels.},
}
@article {pmid27041863,
year = {2016},
author = {Osathanunkul, M and Suwannapoom, C and Khamyong, N and Pintakum, D and Lamphun, SN and Triwitayakorn, K and Osathanunkul, K and Madesis, P},
title = {Hybrid analysis (barcode-high resolution melting) for authentication of Thai herbal products, Andrographis paniculata (Burm.f.) Wall.ex Nees.},
journal = {Pharmacognosy magazine},
volume = {12},
number = {Suppl 1},
pages = {S71-5},
pmid = {27041863},
issn = {0973-1296},
abstract = {BACKGROUND: Andrographis paniculata Nees is a medicinal plant with multiple pharmacological properties. It has been used over many centuries as a household remedy. A. paniculata products sold on the markets are in processed forms so it is difficult to authenticate. Therefore buying the herbal products poses a high-risk of acquiring counterfeited, substituted and/or adulterated products. Due to these issues, a reliable method to authenticate products is needed.<br><br>MATERIALS AND METHODS: High resolution melting analysis coupled with DNA barcoding (Bar-HRM) was applied to detect adulteration in commercial herbal products. The rbcL barcode was selected to use in primers design for HRM analysis to produce standard melting profile of A. paniculata species. DNA of the tested commercial products was isolated and their melting profiles were then generated and compared with the standard A. paniculata.<br><br>RESULTS: The melting profiles of the rbcL amplicons of the three closely related herbal species (A. paniculata, Acanthus ebracteatus and Rhinacanthus nasutus) are clearly separated so that they can be distinguished by the developed method. The method was then used to authenticate commercial herbal products. HRM curves of all 10 samples tested are similar to A. paniculata which indicated that all tested products were contained the correct species as labeled.<br><br>CONCLUSION: The method described in this study has been proved to be useful in aiding identification and/or authenticating A. paniculata. This Bar-HRM analysis has allowed us easily to determine the A. paniculata species in herbal products on the markets even they are in processed forms.<br><br>SUMMARY: We propose the use of DNA barcoding combined with High Resolution Melting analysis for authenticating of Andrographis paniculata products.The developed method can be used regardless of the type of the DNA template (fresh or dried tissue, leaf, and stem).rbcL region was chosen for the analysis and work well with our samplesWe can easily determine the A. paniculata species in herbal products tested. Abbreviations used: bp: Base pair, Tm: Melting temperature.},
}
@article {pmid27038897,
year = {2016},
author = {Beltman, JB and Urbanus, J and Velds, A and van Rooij, N and Rohr, JC and Naik, SH and Schumacher, TN},
title = {Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells.},
journal = {BMC bioinformatics},
volume = {17},
number = {},
pages = {151},
pmid = {27038897},
issn = {1471-2105},
mesh = {Animals ; Base Sequence ; DNA/*analysis/chemistry ; *DNA Barcoding, Taxonomic ; *High-Throughput Nucleotide Sequencing ; Mice ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Stem Cells/cytology/metabolism ; },
abstract = {BACKGROUND: Next generation sequencing (NGS) of amplified DNA is a powerful tool to describe genetic heterogeneity within cell populations that can both be used to investigate the clonal structure of cell populations and to perform genetic lineage tracing. For applications in which both abundant and rare sequences are biologically relevant, the relatively high error rate of NGS techniques complicates data analysis, as it is difficult to distinguish rare true sequences from spurious sequences that are generated by PCR or sequencing errors. This issue, for instance, applies to cellular barcoding strategies that aim to follow the amount and type of offspring of single cells, by supplying these with unique heritable DNA tags.<br><br>RESULTS: Here, we use genetic barcoding data from the Illumina HiSeq platform to show that straightforward read threshold-based filtering of data is typically insufficient to filter out spurious barcodes. Importantly, we demonstrate that specific sequencing errors occur at an approximately constant rate across different samples that are sequenced in parallel. We exploit this observation by developing a novel approach to filter out spurious sequences.<br><br>CONCLUSIONS: Application of our new method demonstrates its value in the identification of true sequences amongst spurious sequences in biological data sets.},
}
@article {pmid27037902,
year = {2016},
author = {Filloramo, GV and Saunders, GW},
title = {Application of multigene phylogenetics and site-stripping to resolve intraordinal relationships in the Rhodymeniales (Rhodophyta).},
journal = {Journal of phycology},
volume = {52},
number = {3},
pages = {339-355},
doi = {10.1111/jpy.12418},
pmid = {27037902},
issn = {1529-8817},
mesh = {Algal Proteins/*genetics/metabolism ; Cell Nucleus/genetics ; Chloroplast Proteins/genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; *Phylogeny ; Rhodophyta/*classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {Previous molecular assessments of the red algal order Rhodymeniales have confirmed its monophyly and distinguished the six currently recognized families (viz. Champiaceae, Faucheaceae, Fryeellaceae, Hymenocladiaceae, Lomentariaceae, and Rhodymeniaceae); however, relationships among most of these families have remained unresolved possibly as a result of substitution saturation at deeper phylogenetic nodes. The objective of the current study was to improve rhodymenialean systematics by increasing taxonomic representation and using a more robust multigene dataset of mitochondrial (COB, COI/COI-5P), nuclear (LSU, EF2) and plastid markers (psbA, rbcL). Additionally, we aimed to prevent phylogenetic inference problems associated with substitution saturation (particularly at the interfamilial nodes) by removing fast-evolving sites and analyzing a series of progressively more conservative alignments. The Rhodymeniales was resolved as two major lineages: (i) the Fryeellaceae as sister to the Faucheaceae and Lomentariaceae; and (ii) the Rhodymeniaceae allied to the Champiaceae and Hymenocladiaceae. Support at the interfamilial nodes was highest when 20% of variable sites were removed. Inclusion of Binghamiopsis, Chamaebotrys, and Minium, which were absent in previous phylogenetic investigations, established their phylogenetic affinities while assessment of two genera consistently polyphyletic in phylogenetic analyses, Erythrymenia and Lomentaria, resulted in the proposition of the novel genera Perbella and Fushitsunagia. The taxonomic position of Drouetia was reinvestigated with re-examination of holotype material of D. coalescens to clarify tetrasporangial development in this genus. In addition, we added three novel Australian species to Drouetia as a result of ongoing DNA barcoding assessments-D. aggregata sp. nov., D. scutellata sp. nov., and D. viridescens sp. nov.},
}
@article {pmid27037790,
year = {2016},
author = {Küpper, FC and Peters, AF and Shewring, DM and Sayer, MD and Mystikou, A and Brown, H and Azzopardi, E and Dargent, O and Strittmatter, M and Brennan, D and Asensi, AO and van West, P and Wilce, RT},
title = {Arctic marine phytobenthos of northern Baffin Island.},
journal = {Journal of phycology},
volume = {52},
number = {4},
pages = {532-549},
pmid = {27037790},
issn = {1529-8817},
mesh = {Algal Proteins/genetics ; Arctic Regions ; *Biodiversity ; Chlorophyta/classification/genetics ; Islands ; Nunavut ; Phaeophyceae/classification/genetics ; Phylogeny ; Rhodophyta/classification/genetics ; Seaweed/*classification/genetics ; Sequence Analysis, DNA ; },
abstract = {Global climate change is expected to alter the polar bioregions faster than any other marine environment. This study assesses the biodiversity of seaweeds and associated eukaryotic pathogens of an established study site in northern Baffin Island (72° N), providing a baseline inventory for future work assessing impacts of the currently ongoing changes in the Arctic marine environment. A total of 33 Phaeophyceae, 24 Rhodophyceae, 2 Chlorophyceae, 12 Ulvophyceae, 1 Trebouxiophyceae, and 1 Dinophyceae are reported, based on collections of an expedition to the area in 2009, complemented by unpublished records of Robert T. Wilce and the first-ever photographic documentation of the phytobenthos of the American Arctic. Molecular barcoding of isolates raised from incubated substratum samples revealed the presence of 20 species of brown seaweeds, including gametophytes of kelp and of a previously unsequenced Desmarestia closely related to D. viridis, two species of Pylaiella, the kelp endophyte Laminariocolax aecidioides and 11 previously unsequenced species of the Ectocarpales, highlighting the necessity to include molecular techniques for fully unraveling cryptic algal diversity. This study also includes the first records of Eurychasma dicksonii, a eukaryotic pathogen affecting seaweeds, from the American Arctic. Overall, this study provides both the most accurate inventory of seaweed diversity of the northern Baffin Island region to date and can be used as an important basis to understand diversity changes with climate change.},
}
@article {pmid27035744,
year = {2016},
author = {Kim, J and Biondi, MJ and Feld, JJ and Chan, WC},
title = {Clinical Validation of Quantum Dot Barcode Diagnostic Technology.},
journal = {ACS nano},
volume = {10},
number = {4},
pages = {4742-4753},
doi = {10.1021/acsnano.6b01254},
pmid = {27035744},
issn = {1936-086X},
support = {MOP130143//CIHR/Canada ; COP126588//CIHR/Canada ; },
mesh = {Biological Assay/methods ; DNA, Viral/*blood ; Fluorescent Dyes/chemistry ; Hepatitis B/*diagnosis ; Hepatitis B virus/genetics ; Humans ; Limit of Detection ; Magnetite Nanoparticles/chemistry ; Microscopy, Fluorescence ; Microspheres ; Multiplex Polymerase Chain Reaction ; Quantum Dots/*chemistry ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Surface Properties ; },
abstract = {There has been a major focus on the clinical translation of emerging technologies for diagnosing patients with infectious diseases, cancer, heart disease, and diabetes. However, most developments still remain at the academic stage where researchers use spiked target molecules to demonstrate the utility of a technology and assess the analytical performance. This approach does not account for the biological complexities and variabilities of human patient samples. As a technology matures and potentially becomes clinically viable, one important intermediate step in the translation process is to conduct a full clinical validation of the technology using a large number of patient samples. Here, we present a full detailed clinical validation of Quantum Dot (QD) barcode technology for diagnosing patients infected with Hepatitis B Virus (HBV). We further demonstrate that the detection of multiple regions of the viral genome using multiplexed QD barcodes improved clinical sensitivity from 54.9-66.7% to 80.4-90.5%, and describe how to use QD barcodes for optimal clinical diagnosis of patients. The use of QDs in biology and medicine was first introduced in 1998 but has not reached clinical care. This study describes our long-term systematic development strategy to advance QD technology to a clinically feasible product for diagnosing patients. Our "blueprint" for translating the QD barcode research concept could be adapted for other nanotechnologies, to efficiently advance diagnostic techniques discovered in the academic laboratory to patient care.},
}
@article {pmid27034413,
year = {2016},
author = {Selich, A and Daudert, J and Hass, R and Philipp, F and von Kaisenberg, C and Paul, G and Cornils, K and Fehse, B and Rittinghausen, S and Schambach, A and Rothe, M},
title = {Massive Clonal Selection and Transiently Contributing Clones During Expansion of Mesenchymal Stem Cell Cultures Revealed by Lentiviral RGB-Barcode Technology.},
journal = {Stem cells translational medicine},
volume = {5},
number = {5},
pages = {591-601},
pmid = {27034413},
issn = {2157-6564},
mesh = {Cell Differentiation ; *Cell Proliferation ; Cells, Cultured ; *Cellular Senescence ; *Clonal Evolution ; Clone Cells ; DNA Barcoding, Taxonomic/*methods ; Female ; Flow Cytometry ; Gene Expression Regulation, Developmental ; *Genetic Vectors ; Genotype ; High-Throughput Nucleotide Sequencing ; Humans ; Lentivirus/*genetics ; Mesenchymal Stem Cells/metabolism/*physiology ; Microscopy, Fluorescence ; Phenotype ; Pregnancy ; Time Factors ; Transduction, Genetic ; Umbilical Cord/*cytology ; },
abstract = {UNLABELLED: Mesenchymal stem (or stromal) cells (MSCs) have been used in more than 400 clinical trials for the treatment of various diseases. The clinical benefit and reproducibility of results, however, remain extremely variable. During the in vitro expansion phase, which is necessary to achieve clinically relevant cell numbers, MSCs show signs of aging accompanied by different contributions of single clones to the mass culture. Here we used multicolor lentiviral barcode labeling to follow the clonal dynamics during in vitro MSC expansion from whole umbilical cord pieces (UCPs). The clonal composition was analyzed by a combination of flow cytometry, fluorescence microscopy, and deep sequencing. Starting with highly complex cell populations, we observed a massive reduction in diversity, transiently dominating populations, and a selection of single clones over time. Importantly, the first wave of clonal constriction already occurred in the early passages during MSC expansion. Consecutive MSC cultures from the same UCP implied the existence of more primitive, MSC culture-initiating cells. Our results show that microscopically homogenous MSC mass cultures consist of many subpopulations, which undergo clonal selection and have different capabilities. Among other factors, the clonal composition of the graft might have an impact on the functional properties of MSCs in experimental and clinical settings.<br><br>SIGNIFICANCE: Mesenchymal stem cells (MSCs) can easily be obtained from various adult or embryonal tissues and are frequently used in clinical trials. For their clinical application, MSCs have to be expanded in vitro. This unavoidable step influences the features of MSCs, so that clinical benefit and experimental results are often highly variable. Despite a homogenous appearance under the microscope, MSC cultures undergo massive clonal selection over time. Multicolor fluorescence labeling and deep sequencing were used to demonstrate the dynamic clonal composition of MSC cultures, which might ultimately explain the variable clinical performance of the cells.},
}
@article {pmid27032679,
year = {2016},
author = {Sugita, N and Kawakami, K and Nishiumi, I},
title = {Origin of Japanese White-Eyes and Brown-Eared Bulbuls on the Volcano Islands.},
journal = {Zoological science},
volume = {33},
number = {2},
pages = {146-153},
doi = {10.2108/zs150146},
pmid = {27032679},
issn = {0289-0003},
mesh = {Animals ; Electron Transport Complex IV/genetics/metabolism ; Genetic Variation ; Haplotypes ; Islands ; Japan ; Passeriformes/*genetics/physiology ; Phylogeny ; },
abstract = {The Ogasawara Archipelago comprises two groups of oceanic islands: the Bonin Islands, formed in the Paleogene, and the Volcano Islands, formed in the Quaternary. These groups are located within a moderate distance (ca. 160-270 km) of one another; thus, most land bird species are not distinguished as different subspecies. Two land birds, however, show unusual distribution. The Japanese white-eyes Zosterops japonicus originally inhabited only the Volcano Islands, but has been introduced to the Bonin Islands. The brown-eared bulbuls Hypsipetes amaurotis are distributed as a different subspecies. We investigated their genetic differences and divergences in the Ogasawara Archipelago using mitochondria DNA. The Volcano population of white-eyes had four endemic haplotypes that were divergent from one another, except for the Bonin population, which shared three haplotypes with the Volcano, Izu, and Ryukyu Islands and did not have any endemic haplotype. This is the first genetic suggestion that the Bonin population is a hybrid of introduced populations. With respect to bulbuls, the Volcano and Bonin Islands each had a single endemic haplotype. The Volcano haplotype is closest to a haplotype shared with Izu, the Japanese mainland, Daito and Ryukyu, whereas the Bonin haplotype is closest to one endemic to the south Ryukyu Islands. This indicates that the sources of the two bulbul populations can be geologically and temporally distinguished. The populations of the two species in the Ogasawara Archipelago are irreplaceable, owing to their genetic differences and should be regarded as evolutionarily significant units. In order to prevent introgression between the two populations, we must restrict interisland transfers.},
}
@article {pmid27032370,
year = {2016},
author = {Tamboli, AS and Patil, SM and Gholave, AR and Kadam, SK and Kotibhaskar, SV and Yadav, SR and Govindwar, SP},
title = {Phylogenetic analysis, genetic diversity and relationships between the recently segregated species of Corynandra and Cleoserrata from the genus Cleome using DNA barcoding and molecular markers.},
journal = {Comptes rendus biologies},
volume = {339},
number = {3-4},
pages = {123-132},
doi = {10.1016/j.crvi.2016.02.005},
pmid = {27032370},
issn = {1768-3238},
mesh = {Cleome/classification/*genetics ; *DNA Barcoding, Taxonomic ; *DNA, Plant ; Genetic Markers ; *Genetic Variation ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Random Amplified Polymorphic DNA Technique ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Cleome is the largest genus in the family Cleomaceae and it is known for its various medicinal properties. Recently, some species from the Cleome genus (Cleome viscosa, Cleome chelidonii, Cleome felina and Cleome speciosa) are split into genera Corynandra (Corynandra viscosa, Corynandra chelidonii, Corynandra felina), and Cleoserrata (Cleoserrata speciosa). The objective of this study was to obtain DNA barcodes for these species for their accurate identification and determining phylogenetic relationships. Out of 10 screened barcoding regions, rbcL, matK and ITS1 regions showed higher PCR efficiency and sequencing success. This study added matK, rbcL and ITS1 barcodes for the identification of Corynandra chelidonii, Corynandra felina, Cleome simplicifolia and Cleome aspera species in existing barcode data. Corynandra chelidonii and Corynandra felina species belong to the Corynandra genus, but they are not grouped with the Corynandra viscosa species, however clustered with the Cleome species. Molecular marker analysis showed 100% polymorphism among the studied plant samples. Diversity indices for molecular markers were ranged from He=0.1115-0.1714 and I=0.2268-0.2700, which indicates a significant amount of genetic diversity among studied species. Discrimination of the Cleome and Corynandra species from Cleoserrata speciosa was obtained by two RAPD primers (OPA-4 and RAPD-17) and two ISSR primers (ISSR-1 and ISSR-2). RAPD and ISSR markers are useful for the genetic characterization of these studied species. The present investigation will be helpful to understand the relationships of Cleome lineages with Corynandra and Cleoserrata species.},
}
@article {pmid27027870,
year = {2016},
author = {Senevirathne, G and Garg, S and Kerney, R and Meegaskumbura, M and Biju, SD},
title = {Unearthing the Fossorial Tadpoles of the Indian Dancing Frog Family Micrixalidae.},
journal = {PloS one},
volume = {11},
number = {3},
pages = {e0151781},
pmid = {27027870},
issn = {1932-6203},
mesh = {Animals ; Anura/anatomy &amp; histology/*physiology ; DNA Barcoding, Taxonomic ; Feeding Behavior/*psychology ; Larva/anatomy &amp; histology/physiology ; Metamorphosis, Biological/*physiology ; Ribs/anatomy &amp; histology/*physiology ; Spine/anatomy &amp; histology/*physiology ; },
abstract = {Tadpoles of the monotypic Indian dancing frog family Micrixalidae have remained obscure for over 125 years. Here we report the discovery of the elusive tadpoles of Micrixalus herrei from the sand beds of a forested stream in southern Western Ghats, and confirm their identity through DNA barcoding. These actively burrowing tadpoles lead an entirely fossorial life from eggs to late metamorphic stages. We describe their internal and external morphological characters while highlighting the following features: eel-like appearance, extensively muscularized body and tail, reduced tail fins, skin-covered eyes, delayed development of eye pigmentation in early pre-metamorphic stages (Gosner stages 25-29), prominent tubular sinistral spiracle, large transverse processes on vertebrae II and III, ankylosed ribs on transverse processes of vertebra II, notochord terminating before the atlantal cotyle-occipital condyle junction, absence of keratodonts, serrated well-formed jaw sheaths, and extensive calcified endolymphatic sacs reaching sacrum posteriorly. The tadpole gut contains mostly fine sediments and sand. We discuss the eel-like morphology and feeding habits of M. herrei in the context of convergence with other well-known fossorial tadpoles. This discovery builds the knowledge base for further comparative analyses and conservation of Micrixalus, an ancient and endemic lineage of Indian frogs.},
}
@article {pmid27025372,
year = {2016},
author = {Li, YP and Wang, SJ and Zang, YM and Hu, ZS and Liu, CS},
title = {Sources of varieties and quality of circular Fructus Ligustri Lucidi.},
journal = {Chinese journal of natural medicines},
volume = {14},
number = {3},
pages = {236-240},
doi = {10.1016/S1875-5364(16)30022-X},
pmid = {27025372},
issn = {1875-5364},
mesh = {Chromatography, High Pressure Liquid ; DNA Barcoding, Taxonomic ; DNA, Plant ; Fruit/chemistry ; Glucosides/isolation &amp; purification ; Ligustrum/chemistry/*classification/genetics ; Medicine, Chinese Traditional ; Polymerase Chain Reaction ; Pyrans/isolation &amp; purification ; Quality Control ; },
abstract = {This study aimed to trace sources and quantitatively analyze the specnuezhenide content of circular Fructus Ligustri Lucidi for clinical use. Different specifications of Fructus Ligustri Lucidi were identified using DNA barcoding technology and the specnuezhenide content was analyzed by High Performance Liquid Chromatography (HPLC). The ITS sequence of circular Fructus Ligustri Lucidi was identical to that of standard privet, which was determined through botanical identification. ITS sequence similarity between circular Fructus Ligustri Lucidi and Fructus Ligustri Lucidi which was registered in NCBI ranged from 99.5% to 100%. The sequences of circular and other Fructus Ligustri Lucidi were clustered in a Neighbor-Joining tree with bootstrap value of 95, and these sequences could be distinguished from adulterants. Conforming to pharmacopoeia standard, the average specnuezhenide content of circular Fructus Ligustri Lucidi was higher than that of chicken waist Fructus Ligustri Lucidi. Circular Fructus Ligustri Lucidi derived from Ligustrum lucidum Ait. and the specnuezhenide content was higher in circular Fructus Ligustri Lucidi than that in chicken waist Fructus Ligustri Lucidi.},
}
@article {pmid27023741,
year = {2016},
author = {Leveque, RE and Clark, KJ and Ekker, SC},
title = {Mayo Clinic Zebrafish Facility Overview.},
journal = {Zebrafish},
volume = {13 Suppl 1},
number = {Suppl 1},
pages = {S44-6},
pmid = {27023741},
issn = {1557-8542},
support = {P30 DK084567/DK/NIDDK NIH HHS/United States ; },
mesh = {Animal Husbandry/*methods/organization &amp; administration ; Animals ; *Animals, Laboratory ; Aquaculture/*methods/organization &amp; administration ; *Facility Design and Construction ; Minnesota ; Models, Animal ; *Zebrafish ; },
abstract = {The zebrafish (Danio rerio) is a premier nonmammalian vertebrate model organism. This small aquatic fish is utilized in multiple disciplines in the Mayo Clinic community and by many laboratories around the world because of its biological similarity to humans, its advanced molecular genetics, the elucidation of its genome sequence, and the ever-expanding and outstanding new biological tools now available to the zebrafish researcher. The Mayo Clinic Zebrafish Facility (MCZF) houses ∼2,000 tanks annotated using an in-house, Internet cloud-based bar-coding system tied to our established zfishbook.org web infrastructure. Paramecia are the primary food source for larval fish rearing, using a simplified culture protocol described herein. The MCZF supports the specific ongoing research in a variety of laboratories, while also serving as a local hub for new scientists as they learn to tap into the potential of this model system for understanding normal development, disease, and as models of health.},
}
@article {pmid27020159,
year = {2016},
author = {Jagielski, T and Sandoval-Denis, M and Yu, J and Yao, L and Bakuła, Z and Kalita, J and Skóra, M and Krzyściak, P and de Hoog, GS and Guarro, J and Gené, J},
title = {Molecular taxonomy of scopulariopsis-like fungi with description of new clinical and environmental species.},
journal = {Fungal biology},
volume = {120},
number = {4},
pages = {586-602},
doi = {10.1016/j.funbio.2016.01.014},
pmid = {27020159},
issn = {1878-6146},
mesh = {Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Intergenic/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Humans ; Microscopy ; Multilocus Sequence Typing ; Mycoses/*microbiology ; Peptide Elongation Factor 1/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; Scopulariopsis/*classification/cytology/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Tubulin/genetics ; },
abstract = {The taxonomy of scopulariopsis-like fungi, comprising numerous human opportunistic species, has recently been reassessed with delineation of the genera Microascus, Pithoascus, Pseudoscopulariopsis, and Scopulariopsis, using morphological data and multilocus sequence analysis based on four loci (ITS, LSU, EF-1α, and TUB). In this study, the same genetic markers were used to investigate a set of clinical and environmental isolates, morphologically identified as Microascus and Scopulariopsis spp. The ingroups of the concatenated phylogenetic tree resolved 41 species clades, with isolates distributed in four main lineages corresponding to the genera Microascus, Pithoascus, Scopulariopsis, and newly established genus Fuscoannellis, typified by Scopulariopsis carbonaria. The new species Microascus chinensis, Microascus onychoides, Microascus pseudolongirostris, Pithoascus lunatus, and Scopulariopsis macurae were described. Microascus trigonosporus var. terreus and Scopulariopsis alboflavescens were found different from M. trigonosporus and Scopulariopsis brevicaulis, respectively. All the species identified in the study, except Fuscoannellis carbonaria and S. macurae, originated from clinical samples, suggesting their potential role in human disease. The use of a four marker combination was demonstrated an efficient and reliable approach to infer phylogenetic relationships among the scopulariopsis-like fungi. Yet, the only genetic marker able to discriminate all species was EF-1α, therefore proposed as a secondary barcode for the identification of these fungi.},
}
@article {pmid27019455,
year = {2016},
author = {Peterson, SW and Knox, NC and Golding, GR and Tyler, SD and Tyler, AD and Mabon, P and Embree, JE and Fleming, F and Fanella, S and Van Domselaar, G and Mulvey, MR and Graham, MR},
title = {A Study of the Infant Nasal Microbiome Development over the First Year of Life and in Relation to Their Primary Adult Caregivers Using cpn60 Universal Target (UT) as a Phylogenetic Marker.},
journal = {PloS one},
volume = {11},
number = {3},
pages = {e0152493},
pmid = {27019455},
issn = {1932-6203},
mesh = {Adult ; Biodiversity ; *Caregivers ; Chaperonin 60/*genetics ; Genetic Markers ; Humans ; Infant ; Infant, Newborn ; Microbiota/*genetics ; Nose/*microbiology ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Whereas the infant gut microbiome is the subject of intense study, relatively little is known regarding the nares microbiome in newborns and during early life. This study aimed to survey the typical composition and diversity of human anterior nare microflora for developing infants over time, and to explore how these correlate to their primary caregivers. Single nare swabs were collected at five time points over a one-year period for each subject from infant-caregiver pairs. Our study comprised of 50 infants (recruited at 2 weeks, post delivery) and their 50 primary caregivers. Applying the chaperonin-60 (cpn60) universal target (UT) amplicon as our molecular barcoding marker to census survey the microbial communities, we longitudinally surveyed infant nares microbiota at 5 time points over the course of the first year of life. The inter- and intra-subject diversity was catalogued and compared, both longitudinally and relative to their adult primary caregivers. Although within-subject variability over time and inter-subject variability were both observed, the assessment detected only one or two predominant genera for individual infant samples, belonging mainly to phyla Actinobacteria, Firmicutes, and Proteobacteria. Consistent with previously observed microbial population dynamics in other body sites, the diversity of nares microflora increased over the first year of life and infants showed differential operational taxonomic units (OTUs) relative to their matched primary caregiver. The collected evidence also support that both temporal and seasonal changes occur with respect to carriage of potentially pathogenic bacteria (PPBs), which may influence host predisposition to infection. This pilot study surveying paired infant/caregiver nare microbiomes provides novel longitudinal diversity information that is pertinent to better understanding nare microbiome development in infants.},
}
@article {pmid27019284,
year = {2016},
author = {Paoletti, MG and Blakemore, RJ and Csuzdi, C and Dorigo, L and Dreon, AL and Gavinelli, F and Lazzarini, F and Manno, N and Moretto, E and Porco, D and Ruzzier, E and Toniello, V and Squartini, A and Concheri, G and Zanardo, M and Alba-Tercedor, J},
title = {Barcoding Eophila crodabepis sp. nov. (Annelida, Oligochaeta, Lumbricidae), a Large Stripy Earthworm from Alpine Foothills of Northeastern Italy Similar to Eophila tellinii (Rosa, 1888).},
journal = {PloS one},
volume = {11},
number = {3},
pages = {e0151799},
pmid = {27019284},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/chemistry/*genetics ; Geography ; Italy ; Oligochaeta/anatomy &amp; histology/classification/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
abstract = {A new Italian earthworm morphologically close to the similarly large and anecic Eophila tellinii (Rosa, 1888) is described. Distribution of Eophila crodabepis sp. nov. extends over 750 km2 from East to West on the Asiago Plateau and Vittorio Veneto Hills, from North to South on mounts Belluno Prealps (Praderadego and Cesen), Asiago, Grappa and onto the Montello foothills. This range abuts that of Eophila tellinii in northern Friuli Venezia Giulia region. Known localities of both E. tellinii and E. crodabepis sp. nov. are mapped. mtDNA barcoding definitively separates the new western species from classical Eophila tellinii (Rosa, 1888).},
}
@article {pmid27018799,
year = {2016},
author = {Newman, AM and Lovejoy, AF and Klass, DM and Kurtz, DM and Chabon, JJ and Scherer, F and Stehr, H and Liu, CL and Bratman, SV and Say, C and Zhou, L and Carter, JN and West, RB and Sledge, GW and Shrager, JB and Loo, BW and Neal, JW and Wakelee, HA and Diehn, M and Alizadeh, AA},
title = {Integrated digital error suppression for improved detection of circulating tumor DNA.},
journal = {Nature biotechnology},
volume = {34},
number = {5},
pages = {547-555},
pmid = {27018799},
issn = {1546-1696},
support = {DP2 CA186569/CA/NCI NIH HHS/United States ; CI-71-14/DRCRF/Damon Runyon Cancer Research Foundation/United States ; T32 CA009302/CA/NCI NIH HHS/United States ; T32 CA121940/CA/NCI NIH HHS/United States ; U01 CA194389/CA/NCI NIH HHS/United States ; U01 CA152662/CA/NCI NIH HHS/United States ; K99 CA187192/CA/NCI NIH HHS/United States ; U01 CA196405/CA/NCI NIH HHS/United States ; R01 CA188298/CA/NCI NIH HHS/United States ; },
mesh = {Algorithms ; *Artifacts ; Biomarkers, Tumor/*blood/*genetics ; DNA, Neoplasm/*blood/*genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Neoplastic Cells, Circulating/metabolism ; Reproducibility of Results ; Sensitivity and Specificity ; Signal Processing, Computer-Assisted ; Systems Integration ; },
abstract = {High-throughput sequencing of circulating tumor DNA (ctDNA) promises to facilitate personalized cancer therapy. However, low quantities of cell-free DNA (cfDNA) in the blood and sequencing artifacts currently limit analytical sensitivity. To overcome these limitations, we introduce an approach for integrated digital error suppression (iDES). Our method combines in silico elimination of highly stereotypical background artifacts with a molecular barcoding strategy for the efficient recovery of cfDNA molecules. Individually, these two methods each improve the sensitivity of cancer personalized profiling by deep sequencing (CAPP-Seq) by about threefold, and synergize when combined to yield ∼15-fold improvements. As a result, iDES-enhanced CAPP-Seq facilitates noninvasive variant detection across hundreds of kilobases. Applied to non-small cell lung cancer (NSCLC) patients, our method enabled biopsy-free profiling of EGFR kinase domain mutations with 92% sensitivity and >99.99% specificity at the variant level, and with 90% sensitivity and 96% specificity at the patient level. In addition, our approach allowed monitoring of NSCLC ctDNA down to 4 in 10(5) cfDNA molecules. We anticipate that iDES will aid the noninvasive genotyping and detection of ctDNA in research and clinical settings.},
}
@article {pmid27018769,
year = {2016},
author = {Catena, R and Özcan, A and Zivanovic, N and Bodenmiller, B},
title = {Enhanced multiplexing in mass cytometry using osmium and ruthenium tetroxide species.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {89},
number = {5},
pages = {491-497},
doi = {10.1002/cyto.a.22848},
pmid = {27018769},
issn = {1552-4930},
mesh = {Amino Acids/chemistry ; Antibodies, Monoclonal/chemistry ; Antigens, CD/analysis ; Cell Line, Tumor ; Chelating Agents/chemistry ; Cytophotometry/instrumentation/*methods ; Fatty Acids/chemistry ; Heterocyclic Compounds, 1-Ring/chemistry ; Humans ; Jurkat Cells ; Leukocytes, Mononuclear/classification/cytology ; Mass Spectrometry/instrumentation/*methods ; Osmium Tetroxide/*chemistry ; Palladium/chemistry ; Ruthenium Compounds/*chemistry ; Single-Cell Analysis/instrumentation/*methods ; Staining and Labeling/*methods ; },
abstract = {Mass cytometry facilitates high-dimensional, quantitative, single-cell analysis. The method for sample multiplexing in mass cytometry, called mass-tag cellular barcoding (MCB), relies on the covalent reaction of bifunctional metal chelators with intracellular proteins. Here, we describe the use of osmium and ruthenium tetroxides (OsO4 and RuO4) that bind covalently with fatty acids in the cellular membranes and aromatic amino acids in proteins. Both OsO4 and RuO4 rapidly reacted and allowed for MCB with live cells, crosslinked cells, and permeabilized cells. Given the covalent nature of the labeling reaction, isotope leaching was not observed. OsO4 and RuO4 were used in a 20-sample barcoding protocol together with palladium isotopes. As mass channels occupied by osmium and ruthenium are not used for antibody detection the number of masses effectively utilized in a single experiment is expanded. OsO4 and RuO4 can therefore be used as MCB reagents for a wide range of mass cytometry workflows. © 2016 International Society for Advancement of Cytometry.},
}
@article {pmid27014516,
year = {2016},
author = {Freeman, CJ and Easson, CG},
title = {Sponge distribution and the presence of photosymbionts in Moorea, French Polynesia.},
journal = {PeerJ},
volume = {4},
number = {},
pages = {e1816},
pmid = {27014516},
issn = {2167-8359},
abstract = {Photosymbionts play an important role in the ecology and evolution of diverse host species within the marine environment. Although sponge-photosymbiont interactions have been well described from geographically disparate sites worldwide, our understanding of these interactions from shallow water systems within French Polynesia is limited. We surveyed diverse habitats around the north coast of Moorea, French Polynesia and screened sponges for the presence of photosymbionts. Overall sponge abundance and diversity were low, with <1% cover and only eight putative species identified by 28S barcoding from surveys at 21 sites. Of these eight species, seven were found predominately in shaded or semi-cryptic habitats under overhangs or within caverns. Lendenfeldia chondrodes was the only species that supported a high abundance of photosymbionts and was also the only species found in exposed, illuminated habitats. Interestingly, L. chondrodes was found at three distinct sites, with a massive, fan-shaped growth form at two of the lagoon sites and a thin, encrusting growth form within a bay site. These two growth forms differed in their photosymbiont abundance, with massive individuals of L. chondrodes having higher photosymbiont abundance than encrusting individuals from the bay. We present evidence that some sponges from French Polynesia support abundant photosymbiont communities and provide initial support for the role of these communities in host ecology.},
}
@article {pmid27013796,
year = {2015},
author = {Sheth, BP and Thaker, VS},
title = {Identification of a Herbal Powder by Deoxyribonucleic Acid Barcoding and Structural Analyses.},
journal = {Pharmacognosy magazine},
volume = {11},
number = {Suppl 4},
pages = {S570-4},
pmid = {27013796},
issn = {0973-1296},
abstract = {BACKGROUND: Authentic identification of plants is essential for exploiting their medicinal properties as well as to stop the adulteration and malpractices with the trade of the same.<br><br>OBJECTIVE: To identify a herbal powder obtained from a herbalist in the local vicinity of Rajkot, Gujarat, using deoxyribonucleic acid (DNA) barcoding and molecular tools.<br><br>MATERIALS AND METHODS: The DNA was extracted from a herbal powder and selected Cassia species, followed by the polymerase chain reaction (PCR) and sequencing of the rbcL barcode locus. Thereafter the sequences were subjected to National Center for Biotechnology Information (NCBI) basic local alignment search tool (BLAST) analysis, followed by the protein three-dimension structure determination of the rbcL protein from the herbal powder and Cassia species namely Cassia fistula, Cassia tora and Cassia javanica (sequences obtained in the present study), Cassia Roxburghii, and Cassia abbreviata (sequences retrieved from Genbank). Further, the multiple and pairwise structural alignment were carried out in order to identify the herbal powder.<br><br>RESULTS: The nucleotide sequences obtained from the selected species of Cassia were submitted to Genbank (Accession No. JX141397, JX141405, JX141420). The NCBI BLAST analysis of the rbcL protein from the herbal powder showed an equal sequence similarity (with reference to different parameters like E value, maximum identity, total score, query coverage) to C. javanica and C. roxburghii. In order to solve the ambiguities of the BLAST result, a protein structural approach was implemented. The protein homology models obtained in the present study were submitted to the protein model database (PM0079748-PM0079753). The pairwise structural alignment of the herbal powder (as template) and C. javanica and C. roxburghii (as targets individually) revealed a close similarity of the herbal powder with C. javanica.<br><br>CONCLUSION: A strategy as used here, incorporating the integrated use of DNA barcoding and protein structural analyses could be adopted, as a novel rapid and economic procedure, especially in cases when protein coding loci are considered.<br><br>SUMMARY: Authentic identification of plants is essential for exploiting their medicinal properties as well as to stop the adulteration and malpractices with the trade of the same. A herbal powder was obtained from a herbalist in the local vicinity of Rajkot, Gujarat. An integrated approach using DNA barcoding and structural analyses was carried out to identify the herbal powder. The herbal powder was identified as Cassia javanica L.},
}
@article {pmid27010920,
year = {2016},
author = {Tanabe, AS and Toju, H},
title = {Correction: Two New Computational Methods for Universal DNA Barcoding: A Benchmark Using Barcode Sequences of Bacteria, Archaea, Animals, Fungi, and Land Plants.},
journal = {PloS one},
volume = {11},
number = {3},
pages = {e0152242},
pmid = {27010920},
issn = {1932-6203},
}
@article {pmid27010758,
year = {2016},
author = {Mayer, A and Churchman, LS},
title = {Genome-wide profiling of RNA polymerase transcription at nucleotide resolution in human cells with native elongating transcript sequencing.},
journal = {Nature protocols},
volume = {11},
number = {4},
pages = {813-833},
pmid = {27010758},
issn = {1750-2799},
support = {R01 HG007173/HG/NHGRI NIH HHS/United States ; R01HG007173/HG/NHGRI NIH HHS/United States ; },
mesh = {Cell Fractionation ; Gene Expression Profiling/*methods ; Gene Library ; HeLa Cells ; High-Throughput Nucleotide Sequencing ; Humans ; RNA/genetics/isolation &amp; purification ; RNA Polymerase II/*metabolism ; Sequence Analysis, DNA ; *Transcription, Genetic ; },
abstract = {Many features of how gene transcription occurs in human cells remain unclear, mainly because of a lack of quantitative approaches to follow genome transcription with nucleotide precision in vivo. Here we present a robust genome-wide approach for studying RNA polymerase II (Pol II)-mediated transcription in human cells at single-nucleotide resolution by native elongating transcript sequencing (NET-seq). Elongating RNA polymerase and the associated nascent RNA are prepared by cell fractionation, avoiding immunoprecipitation or RNA labeling. The 3' ends of nascent RNAs are captured through barcode linker ligation and converted into a DNA sequencing library. The identity and abundance of the 3' ends are determined by high-throughput sequencing, which reveals the exact genomic locations of Pol II. Human NET-seq can be applied to the study of the full spectrum of Pol II transcriptional activities, including the production of unstable RNAs and transcriptional pausing. By using the protocol described here, a NET-seq library can be obtained from human cells in 5 d.},
}
@article {pmid27006611,
year = {2016},
author = {Hamilton, CA and Hendrixson, BE and Bond, JE},
title = {Taxonomic revision of the tarantula genus Aphonopelma Pocock, 1901 (Araneae, Mygalomorphae, Theraphosidae) within the United States.},
journal = {ZooKeys},
volume = {},
number = {560},
pages = {1-340},
pmid = {27006611},
issn = {1313-2989},
abstract = {This systematic study documents the taxonomy, diversity, and distribution of the tarantula spider genus Aphonopelma Pocock, 1901 within the United States. By employing phylogenomic, morphological, and geospatial data, we evaluated all 55 nominal species in the United States to examine the evolutionary history of Aphonopelma and the group's taxonomy by implementing an integrative approach to species delimitation. Based on our analyses, we now recognize only 29 distinct species in the United States. We propose 33 new synonymies (Aphonopelma apacheum, Aphonopelma minchi, Aphonopelma rothi, Aphonopelma schmidti, Aphonopelma stahnkei = Aphonopelma chalcodes; Aphonopelma arnoldi = Aphonopelma armada; Aphonopelma behlei, Aphonopelma vogelae = Aphonopelma marxi; Aphonopelma breenei = Aphonopelma anax; Aphonopelma chambersi, Aphonopelma clarum, Aphonopelma cryptethum, Aphonopelma sandersoni, Aphonopelma sullivani = Aphonopelma eutylenum; Aphonopelma clarki, Aphonopelma coloradanum, Aphonopelma echinum, Aphonopelma gurleyi, Aphonopelma harlingenum, Aphonopelma odelli, Aphonopelma waconum, Aphonopelma wichitanum = Aphonopelma hentzi; Aphonopelma heterops = Aphonopelma moderatum; Aphonopelma jungi, Aphonopelma punzoi = Aphonopelma vorhiesi; Aphonopelma brunnius, Aphonopelma chamberlini, Aphonopelma iviei, Aphonopelma lithodomum, Aphonopelma smithi, Aphonopelma zionis = Aphonopelma iodius; Aphonopelma phanum, Aphonopelma reversum = Aphonopelma steindachneri), 14 new species (Aphonopelma atomicum sp. n., Aphonopelma catalina sp. n., Aphonopelma chiricahua sp. n., Aphonopelma icenoglei sp. n., Aphonopelma johnnycashi sp. n., Aphonopelma madera sp. n., Aphonopelma mareki sp. n., Aphonopelma moellendorfi sp. n., Aphonopelma parvum sp. n., Aphonopelma peloncillo sp. n., Aphonopelma prenticei sp. n., Aphonopelma saguaro sp. n., Aphonopelma superstitionense sp. n., and Aphonopelma xwalxwal sp. n.), and seven nomina dubia (Aphonopelma baergi, Aphonopelma cratium, Aphonopelma hollyi, Aphonopelma mordax, Aphonopelma radinum, Aphonopelma rusticum, Aphonopelma texense). Our proposed species tree based on Anchored Enrichment data delimits five major lineages: a monotypic group confined to California, a western group, an eastern group, a group primarily distributed in high-elevation areas, and a group that comprises several miniaturized species. Multiple species are distributed throughout two biodiversity hotspots in the United States (i.e., California Floristic Province and Madrean Pine-Oak Woodlands). Keys are provided for identification of both males and females. By conducting the most comprehensive sampling of a single theraphosid genus to date, this research significantly broadens the scope of prior molecular and morphological investigations, finally bringing a modern understanding of species delimitation in this dynamic and charismatic group of spiders.},
}
@article {pmid27006603,
year = {2016},
author = {Tanaka, H and Dung, le D and Higashi, R and Tsukagoshi, A},
title = {A new interstitial ostracod species of the genus Paracobanocythere from Vietnam, with mitochondrial CO1 sequence data of three Asian species.},
journal = {ZooKeys},
volume = {},
number = {559},
pages = {17-33},
pmid = {27006603},
issn = {1313-2989},
abstract = {This study is a first report of an interstitial ostracod from Southeast Asia. The ostracod species, Paracobanocythere vietnamensis sp. n., was found in the marine interstitial environment of Phu Quoc Island, Vietnam. Thus far, three species of this genus have been described. The morphology of the carapace as well as the appendages of this new species are quite similar to Paracobanocythere hawaiiensis and Paracobanocythere watanabei. However, we found that they could be easily distinguished according to the morphology of the male copulatory organ. Additionally, we estimated the evolutionary distances among these three species based on nucleotide and amino acid sequences of the mitochondrial CO1 gene. Similar morphologies of carapaces and appendages, and relatively small evolutionary distances according to CO1 between Paracobanocythere vietnamensis sp. n. and Paracobanocythere watanabei suggest that these two species are very closely related.},
}
@article {pmid27005905,
year = {2017},
author = {Marcellino, WL and Salih, DA and Njahira, MN and Ndiwa, N and Araba, A and El Hussein, AM and Seitzer, U and Ahmed, JS and Bishop, RP and Skilton, RA},
title = {The Emergence of Theileria parva in Jonglei State, South Sudan: Confirmation Using Molecular and Serological Diagnostic Tools.},
journal = {Transboundary and emerging diseases},
volume = {64},
number = {4},
pages = {1229-1235},
doi = {10.1111/tbed.12495},
pmid = {27005905},
issn = {1865-1682},
mesh = {Animals ; Cattle ; Cross-Sectional Studies ; Enzyme-Linked Immunosorbent Assay/veterinary ; Ixodidae/classification/*parasitology ; Polymerase Chain Reaction/veterinary ; Prevalence ; Rhipicephalus/classification/parasitology ; Seroepidemiologic Studies ; South Sudan/epidemiology ; Theileria parva/*isolation &amp; purification ; Theileriasis/*epidemiology/parasitology ; },
abstract = {A cross-sectional survey was carried out in four counties of Jonglei State, South Sudan, between May and June 2012 to determine the distribution and northern limit of Theileria parva, the causative agent of East Coast fever in cattle, and its tick vector Rhipicephalus appendiculatus, as a prerequisite to the deployment of relevant control strategies. A total of 1636 ticks, 386 serum samples and 399 blood samples were collected from indigenous, apparently healthy, cattle of different age groups. Tick species were identified morphologically, and the identity of R. appendiculatus was confirmed by DNA barcoding. Overall, the T. parva infection rate in R. appendiculatus was 25% as shown by nested PCR. ELISA was used to assess antibodies to T. parva, and the overall seroprevalence was 22.8%. PCR of the blood samples showed 55 (13.8%) were positive for T. parva. This is the first molecular confirmation of T. parva DNA in areas north of Juba, where it was previously known and established. The northern limit of T. parva was determined as N[0]06.17.792, about 242 Km north from Juba. Implication of this limit on the epidemiology and control of ECF is discussed.},
}
@article {pmid27003938,
year = {2016},
author = {Chen, CH and Puliafito, A and Cox, BD and Primo, L and Fang, Y and Di Talia, S and Poss, KD},
title = {Multicolor Cell Barcoding Technology for Long-Term Surveillance of Epithelial Regeneration in Zebrafish.},
journal = {Developmental cell},
volume = {36},
number = {6},
pages = {668-680},
pmid = {27003938},
issn = {1878-1551},
support = {R01 GM074057/GM/NIGMS NIH HHS/United States ; T32 HD040372/HD/NICHD NIH HHS/United States ; },
mesh = {Animal Fins/injuries/physiology ; Animals ; Animals, Genetically Modified ; DNA Barcoding, Taxonomic/*methods ; Epithelial Cells/physiology ; Epithelium/injuries/physiology ; Homeostasis ; Models, Animal ; Reactive Oxygen Species/metabolism ; Regeneration/genetics/physiology ; Skin/injuries ; Skin Pigmentation/genetics/physiology ; Zebrafish/*genetics/*physiology ; },
abstract = {Current fate mapping and imaging platforms are limited in their ability to capture dynamic behaviors of epithelial cells. To deconstruct regenerating adult epithelial tissue at single-cell resolution, we created a multicolor system, skinbow, that barcodes the superficial epithelial cell (SEC) population of zebrafish skin with dozens of distinguishable tags. With image analysis to directly segment and simultaneously track hundreds of SECs in vivo over entire surface lifetimes, we readily quantified the orchestration of cell emergence, growth, repositioning, and loss under homeostatic conditions and after exfoliation or appendage amputation. We employed skinbow-based imaging in conjunction with a live reporter of epithelial stem cell cycle activity and as an instrument to evaluate the effects of reactive oxygen species on SEC behavior during epithelial regeneration. Our findings introduce a platform for large-scale, quantitative in vivo imaging of regenerating skin and reveal unanticipated collective dynamism in epithelial cell size, mobility, and interactions.},
}
@article {pmid27001489,
year = {2016},
author = {Khanam, S and Howitt, R and Mushtaq, M and Russell, JC},
title = {Diet analysis of small mammal pests: A comparison of molecular and microhistological methods.},
journal = {Integrative zoology},
volume = {11},
number = {2},
pages = {98-110},
doi = {10.1111/1749-4877.12172},
pmid = {27001489},
issn = {1749-4877},
mesh = {Animals ; Birds/genetics ; DNA Barcoding, Taxonomic ; Diet/*veterinary ; *Food Chain ; Gastrointestinal Contents/chemistry ; Invertebrates/genetics ; Mice/*physiology ; Pakistan ; Plants/genetics ; Rats/*physiology ; Shrews/*physiology ; },
abstract = {Knowledge of what pest species are eating is important to determine their impact on stored food products and to plan management strategies accordingly. In this study, we investigated the food habits of 2 rodents, Rattus rattus (ship rat) and Mus musculus castaneus (house mouse) as well as an insectivore, Suncus murinus (shrew), present in human dwellings. Both a microhistological approach and a DNA barcoding approach were used in the present study. Following DNA extraction, amplification was performed using group-specific primers targeting birds, plants and invertebrates. Resulting polymerase chain reaction products were sequenced and analyzed to identify the different prey species present in the gut contents. The findings from the application of both techniques were in agreement, but the detection of prey type with each technique was different. The DNA barcoding approach gave greater species-level identification when compared to the microhistological method, especially for the invertebrate and avian prey. Overall, with both techniques, 23 prey taxa were identified in the gut contents of the 3 species, including 15 plants, 7 insects and a single bird species. We conclude that with a selection of suitable "barcode genes" and optimization of polymerase chain reaction protocols, DNA barcoding can provide more accurate and faster results. Prey detection from either technique alone can bias the dietary information. Hence, combining prey information of both microhistological analysis and DNA barcoding is recommended to study pest diet, especially if the pest is an omnivore or insectivore species.},
}
@article {pmid27000429,
year = {2017},
author = {Dahruddin, H and Hutama, A and Busson, F and Sauri, S and Hanner, R and Keith, P and Hadiaty, R and Hubert, N},
title = {Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species.},
journal = {Molecular ecology resources},
volume = {17},
number = {2},
pages = {288-299},
doi = {10.1111/1755-0998.12528},
pmid = {27000429},
issn = {1755-0998},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Ecosystem ; Fishes/*classification/*genetics ; Fresh Water ; Indonesia ; },
abstract = {Among the 899 species of freshwater fishes reported from Sundaland biodiversity hotspot, nearly 50% are endemics. The functional integrity of aquatic ecosystems is currently jeopardized by human activities, and landscape conversion led to the decline of fish populations in several part of Sundaland, particularly in Java. The inventory of the Javanese ichthyofauna has been discontinuous, and the taxonomic knowledge is scattered in the literature. This study provides a DNA barcode reference library for the inland fishes of Java and Bali with the aim to streamline the inventory of fishes in this part of Sundaland. Owing to the lack of available checklist for estimating the taxonomic coverage of this study, a checklist was compiled based on online catalogues. A total of 95 sites were visited, and a library including 1046 DNA barcodes for 159 species was assembled. Nearest neighbour distance was 28-fold higher than maximum intraspecific distance on average, and a DNA barcoding gap was observed. The list of species with DNA barcodes displayed large discrepancies with the checklist compiled here as only 36% (i.e. 77 species) and 60% (i.e. 24 species) of the known species were sampled in Java and Bali, respectively. This result was contrasted by a high number of new occurrences and the ceiling of the accumulation curves for both species and genera. These results highlight the poor taxonomic knowledge of this ichthyofauna, and the apparent discrepancy between present and historical occurrence data is to be attributed to species extirpations, synonymy and misidentifications in previous studies.},
}
@article {pmid26992298,
year = {2016},
author = {Romero-Ricardo, L and Lastre-Meza, N and Pérez-Doria, A and Bejarano, EE},
title = {DNA barcoding to identify species of phlebotomine sand fly (Diptera: Psychodidae) in the mixed leishmaniasis focus of the Colombian Caribbean.},
journal = {Acta tropica},
volume = {159},
number = {},
pages = {125-131},
doi = {10.1016/j.actatropica.2016.03.017},
pmid = {26992298},
issn = {1873-6254},
mesh = {Animals ; Caribbean Region ; Colombia ; *DNA Barcoding, Taxonomic ; Disease Vectors ; Genetic Variation ; Humans ; Leishmaniasis/*parasitology/transmission ; Molecular Sequence Data ; Phlebotomus/*classification/*genetics ; Phylogeny ; },
abstract = {Identification of the species of phlebotomine sand flies present in each focus of leishmaniasis is necessary to incriminate vectors and implement vector control strategies. Although the cytochrome oxidase I (COI) gene has been proposed as a barcode for the identification of animal species, less than 20% of New World phlebotomines have been characterized to date. In this study DNA barcoding was used to identify phlebotomine species of the mixed leishmaniasis focus in the Colombian Caribbean by means of three evolutionary models: Kimura's two parameter (K2P) nucleotide substitution model, that of (Tamura and Nei, 1993) (TN93) and proportional sequence divergence (p-distances). A 681bp sequence of the COI gene was obtained from 66 individuals belonging to 19 species of the genus Lutzomyia (Lu. abonnenci, Lu. atroclavata, Lu. bicolor, Lu. carpenteri, Lu. cayennensis cayennensis, Lu. dubitans, Lu. evansi, Lu. gomezi, Lu. gorbitzi, Lu. longipalpis, Lu. micropyga, Lu. migonei, Lu. panamensis, Lu. (Psathyromyia) sp., Lu. rangeliana, Lu. serrana, Lu. shannoni, Lu. trinidadensis and Lu. venezuelensis) and one of Brumptomyia (B. mesai). The genetic divergence values for TN93 among individuals of the same species fluctuated up to 3.2% (vs. 2.9% for K2P and 2.8% for p-distances), while the values between species ranged from 8.8-43.7% (vs. 6.8-19.6% for K2P and 6.6-17.4% for p-distances). A dendrogram constructed by means of the Neighbor-Joining method grouped phlebotomines into 20 clusters according to species, with bootstrap values of up to 100% in those with more than one individual. However, loss of the phylogenetic signal of the gene COI was observed at the supraspecific level as a consequence of substitutional saturation. In conclusion, irrespective of the evolutionary model selected, all phlebotomines were correctly assigned to species, showing 100% concordance with morphological identification.},
}
@article {pmid26990149,
year = {2016},
author = {Breman, FC and Loix, S and Jordaens, K and Snoeks, J and Van Steenberge, M},
title = {Testing the potential of DNA barcoding in vertebrate radiations: the case of the littoral cichlids (Pisces, Perciformes, Cichlidae) from Lake Tanganyika.},
journal = {Molecular ecology resources},
volume = {16},
number = {6},
pages = {1455-1464},
doi = {10.1111/1755-0998.12523},
pmid = {26990149},
issn = {1755-0998},
mesh = {Adaptation, Biological ; Animals ; Cichlids/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Fishes ; Genetics, Population/*methods ; Lakes ; Phylogeography/*methods ; Sequence Analysis, DNA ; Tanzania ; },
abstract = {We obtained 398 cytochrome c oxidase subunit I barcodes of 96 morphospecies of Lake Tanganyika (LT) cichlids from the littoral zone. The potential of DNA barcoding in these fishes was tested using both species identification and species delineation methods. The best match (BM) and best close match (BCM) methods were used to evaluate the overall identification success. For this, three libraries were analysed in which the specimens were categorized into Operational Taxonomic Units (OTU) in three alternative ways: (A) morphologically distinct, including undescribed, species, (B) valid species and (C) complexes of morphologically similar or closely related species. For libraries A, B and C, 73, 73 and 96% (BM) and 72, 70 and 94% (BCM) of the specimens were correctly identified. Additionally, the potential of two species delineation methods was tested. The General Mixed Yule Coalescent (GMYC) analysis suggested 70 hypothetical species, while the Automatic Barcode Gap Discovery (ABGD) method revealed 115 putative species. Although the ABGD method had a tendency to oversplit, it outperformed the GMYC analysis in retrieving the species. In most cases where ABGD suggested oversplitting, this was due to intraspecific geographical variation. The failure of the GMYC method to retrieve many species could be attributed to discrepancies between mitochondrial gene trees and the evolutionary histories of LT cichlid species. Littoral LT cichlids have complex evolutionary histories that include instances of hybridization, introgression and rapid speciation. Nevertheless, although the utility of DNA barcoding in identification is restricted to the level of complexes, it has potential for species discovery in cichlid radiations.},
}
@article {pmid26989149,
year = {2016},
author = {Rimet, F and Chaumeil, P and Keck, F and Kermarrec, L and Vasselon, V and Kahlert, M and Franc, A and Bouchez, A},
title = {R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring.},
journal = {Database : the journal of biological databases and curation},
volume = {2016},
number = {},
pages = {},
pmid = {26989149},
issn = {1758-0463},
mesh = {*Access to Information ; Base Sequence ; *DNA Barcoding, Taxonomic ; *Data Curation ; *Databases, Genetic ; Diatoms/*classification/genetics ; *Environmental Monitoring ; *Fresh Water ; Phenotype ; Phylogeny ; Statistics as Topic ; },
abstract = {Diatoms are micro-algal indicators of freshwater pollution. Current standardized methodologies are based on microscopic determinations, which is time consuming and prone to identification uncertainties. The use of DNA-barcoding has been proposed as a way to avoid these flaws. Combining barcoding with next-generation sequencing enables collection of a large quantity of barcodes from natural samples. These barcodes are identified as certain diatom taxa by comparing the sequences to a reference barcoding library using algorithms. Proof of concept was recently demonstrated for synthetic and natural communities and underlined the importance of the quality of this reference library. We present an open-access and curated reference barcoding database for diatoms, called R-Syst::diatom, developed in the framework of R-Syst, the network of systematic supported by INRA (French National Institute for Agricultural Research), see http://www.rsyst.inra.fr/en. R-Syst::diatom links DNA-barcodes to their taxonomical identifications, and is dedicated to identify barcodes from natural samples. The data come from two sources, a culture collection of freshwater algae maintained in INRA in which new strains are regularly deposited and barcoded and from the NCBI (National Center for Biotechnology Information) nucleotide database. Two kinds of barcodes were chosen to support the database: 18S (18S ribosomal RNA) and rbcL (Ribulose-1,5-bisphosphate carboxylase/oxygenase), because of their efficiency. Data are curated using innovative (Declic) and classical bioinformatic tools (Blast, classical phylogenies) and up-to-date taxonomy (Catalogues and peer reviewed papers). Every 6 months R-Syst::diatom is updated. The database is available through the R-Syst microalgae website (http://www.rsyst.inra.fr/) and a platform dedicated to next-generation sequencing data analysis, virtual_BiodiversityL@b (https://galaxy-pgtp.pierroton.inra.fr/). We present here the content of the library regarding the number of barcodes and diatom taxa. In addition to these information, morphological features (e.g. biovolumes, chloroplasts…), life-forms (mobility, colony-type) or ecological features (taxa preferenda to pollution) are indicated in R-Syst::diatom. Database URL: http://www.rsyst.inra.fr/.},
}
@article {pmid26987285,
year = {2016},
author = {Sumruayphol, S and Apiwathnasorn, C and Ruangsittichai, J and Sriwichai, P and Attrapadung, S and Samung, Y and Dujardin, JP},
title = {DNA barcoding and wing morphometrics to distinguish three Aedes vectors in Thailand.},
journal = {Acta tropica},
volume = {159},
number = {},
pages = {1-10},
doi = {10.1016/j.actatropica.2016.03.010},
pmid = {26987285},
issn = {1873-6254},
mesh = {Adult ; Aedes/anatomy &amp; histology/*classification/*genetics/virology ; Animals ; Chikungunya Fever/*transmission ; Culex/classification/genetics/virology ; *DNA Barcoding, Taxonomic ; Dengue/*transmission ; Disease Vectors/*classification ; Humans ; Phylogeny ; Reproducibility of Results ; Thailand ; Wings, Animal/*anatomy &amp; histology ; },
abstract = {Aedes aegypti (Diptera: Culicidae) (L.), Ae. albopictus (Skuse), and Ae. scutellaris (Walker) are important mosquito vectors of dengue and chikungunya viruses. They are morphologically similar and sympatric in some parts of their distribution; therefore, there is a risk of incorrect morphological identification. Any confusion could have a negative impact on epidemiological studies or control strategies. Therefore, we explored two modern tools to supplement current morphological identification: DNA barcoding and geometric morphometric analyses. Field larvae were reared to adults and carefully classified based on morphological traits. The genetic analysis was based on the 658bp each of 30COI sequences. Some Culex spp., Mansonia bonneae, were included as outgroups, and inclusion of a few other Aedes spp. facilitated phylogenetic inference of the relationship between Ae. albopictus and Ae. scutellaris. The two species were separated by an average interspecific divergence of 0.123 (0.119-0.127). Morphometric examination included landmark- (392 specimens) and outline-based (317 specimens) techniques. The shape of the wing showed different discriminating power based on sex and digitizing technique. This is the first time that Ae. scutellaris and Ae. albopictus have been compared using these two techniques. We confirm that these morphologically close species are valid, and that geometric morphometrics can considerably increase the reliability of morphological identification.},
}
@article {pmid26986664,
year = {2015},
author = {Geoffroy, A and Mauger, S and De Jode, A and Le Gall, L and Destombe, C},
title = {Molecular evidence for the coexistence of two sibling species in Pylaiella littoralis (Ectocarpales, Phaeophyceae) along the Brittany coast.},
journal = {Journal of phycology},
volume = {51},
number = {3},
pages = {480-489},
doi = {10.1111/jpy.12291},
pmid = {26986664},
issn = {1529-8817},
abstract = {The great phenotypic variability and the lack of diagnostic characters in the genus Pylaiella render the systematic study of this genus problematic. In this study, we investigated the diversity of Pylaiella littoralis along the Brittany (France) coast using a DNA barcoding multilocus approach with mitochondrial (cox1, nad1, and atp9) and chloroplastic (rbcL and atpB) markers associated with a population genetics approach using 10 microsatellite markers. In addition, spatio-temporal sampling was conducted along the Brittany coast. We sampled 140 individuals from four sites located between Saint-Malo and Concarneau (380 km) from April to October. Mitochondrial sequence data revealed the occurrence of two sibling species, with a minimum of 2.4% divergence between them. Microsatellite genotypic data congruently revealed two well-supported clusters matching the two mitochondrial clades of Pylaiella. Although gene flow is limited between species, occurrence of genetic admixtures in some populations suggested that reproductive isolation is not complete. Our study highlighted the complementarity of barcoding and population genetics approaches to shed light on the evolutionary processes that lead to speciation.},
}
@article {pmid26986533,
year = {2015},
author = {Darienko, T and Pröschold, T},
title = {Genetic variability and taxonomic revision of the genus Auxenochlorella (Shihira et Krauss) Kalina et Puncocharova (Trebouxiophyceae, Chlorophyta).},
journal = {Journal of phycology},
volume = {51},
number = {2},
pages = {394-400},
doi = {10.1111/jpy.12279},
pmid = {26986533},
issn = {1529-8817},
abstract = {The monotypic genus Auxenochlorella with its type species A. protothecoides is so far only known from specific habitats such as the sap of several tree species. Several varieties were described according to physiological performances in culture on different organic substrates. However, two strains designated as Auxenochlorella were isolated from other habitats (an endosymbiont of Hydra viridis and an aquatic strain from an acidic volcano stream). We studied those isolates and compared them with six strains of Auxenochlorella belonging to different varieties. The integrative approach used in this study revealed that all strains showed similar morphology but differed in their SSU and ITS rDNA sequences. The Hydra endosymbiont formed a sister taxon to A. protothecoides, which included the varieties protothecoides, galactophila, and communis. The variety acidicola is not closely related to Auxenochlorella and represented its own lineage within the Trebouxiophyceae. In view of these results, we propose a new species of Auxenochlorella, A. symbiontica, for the Hydra symbiont, and a new genus Pumiliosphaera, with its type species, P. acidophila, for acidophilic strain. These results are supported by several compensatory base changes in the conserved region of ITS-2 and ITS-2 DNA barcodes.},
}
@article {pmid26986531,
year = {2015},
author = {Schneider, SC and Rodrigues, A and Moe, TF and Ballot, A},
title = {DNA barcoding the genus Chara: molecular evidence recovers fewer taxa than the classical morphological approach.},
journal = {Journal of phycology},
volume = {51},
number = {2},
pages = {367-380},
doi = {10.1111/jpy.12282},
pmid = {26986531},
issn = {1529-8817},
abstract = {Charophytes (Charales) are benthic algae with a complex morphology. They are vulnerable to ecosystem changes, such as eutrophication, and are red-listed in many countries. Accurate identification of Chara species is critical for understanding their diversity and for documenting changes in species distribution. Species delineation is, however, complicated, because of high phenotypic plasticity. We used barcodes of the ITS2, matK and rbcL regions to test if the distribution of barcode haplotypes among individuals is consistent with species boundaries as they are currently understood. The study included freshly collected and herbarium material of 91 specimens from 10 European countries, Canada and Argentina. Results showed that herbarium specimens are useful as a source of material for genetic analyses for aquatic plants like Chara. rbcL and matK had highest sequence recoverability, but rbcL had a somewhat lower discriminatory power than ITS2 and matK. The tree resulting from the concatenated data matrix grouped the samples into six main groups contrary to a traditional morphological approach that consisted of 14 different taxa. A large unresolved group consisted of C. intermedia, C. hispida, C. horrida, C. baltica, C. polyacantha, C. rudis, C. aculeolata, and C. corfuensis. A second unresolved group consisted of C. virgata and C. strigosa. The taxa within each of the unresolved groups shared identical barcode sequences on the 977 positions of the concatenated data matrix. The morphological differences of taxa within both unresolved groups include the number and length of spine cells, stipulodes, and bract cells. We suggest that these morphological traits have less taxonomic relevance than hitherto assumed.},
}
@article {pmid26986530,
year = {2015},
author = {Lyra, Gde M and Costa, Eda S and de Jesus, PB and de Matos, JC and Caires, TA and Oliveira, MC and Oliveira, EC and Xi, Z and Nunes, JM and Davis, CC},
title = {Phylogeny of Gracilariaceae (Rhodophyta): evidence from plastid and mitochondrial nucleotide sequences.},
journal = {Journal of phycology},
volume = {51},
number = {2},
pages = {356-366},
doi = {10.1111/jpy.12281},
pmid = {26986530},
issn = {1529-8817},
abstract = {Gracilariaceae are mostly pantropical red algae and include ~230 species in seven genera. Infrafamilial classification of the group has long been based on reproductive characters, but previous phylogenies have shown that traditionally circumscribed groups are not monophyletic. We performed phylogenetic analyses using two plastid (universal plastid amplicon and rbcL) and one mitochondrial (cox1) loci from a greatly expanded number of taxa to better assess generic relationships and understand patterns of character distributions. Our analyses produce the most well-supported phylogeny of the family to date, and indicate that key characteristics of spermatangia and cystocarp type do not delineate genera as commonly suggested. Our results further indicate that Hydropuntia is not monophyletic. Given their morphological overlap with closely related members of Gracilaria, we propose that Hydropuntia be synonymized with the former. Our results additionally expand the known ranges of several Gracilariaceae species to include Brazil. Lastly, we demonstrate that the recently described Gracilaria yoneshigueana should be synonymized as G. domingensis based on morphological and molecular characters. These results demonstrate the utility of DNA barcoding for understanding poorly known and fragmentary materials of cryptic red algae.},
}
@article {pmid26985868,
year = {2016},
author = {Kumar, A and Singh, N and Goswami, M and Srivastava, JK and Mishra, AK and Lakra, WS},
title = {Establishment and Characterization of a New Muscle Cell Line of Zebrafish (Danio rerio) as an In Vitro Model for Gene Expression Studies.},
journal = {Animal biotechnology},
volume = {27},
number = {3},
pages = {166-173},
doi = {10.1080/10495398.2016.1147455},
pmid = {26985868},
issn = {1532-2378},
mesh = {Animals ; Cell Culture Techniques ; Cell Cycle ; Cell Line/*cytology ; Cell Proliferation ; Cryopreservation ; Gene Expression Profiling ; Immunohistochemistry ; Male ; *Models, Biological ; Muscles/*cytology ; Transfection ; *Zebrafish ; },
abstract = {A new continuous fibroblast cell line was established from the muscle tissue of healthy juvenile Danio rerio (Zebrafish) through explant method. Fish cell lines serve as useful tool for investigating basic fish biology, as a model for bioassay of environmental toxicant, toxicity ranking, and for developing molecular biomarkers. The cell line was continuously subcultured for a period of 12 months (61 passages) and maintained at 28 °C in L-15 medium supplemented with 10% FBS and 10 ng/mL of basic fibroblastic growth factor (bFGF) without use of antibiotics. Its growth rate was proportional to the FBS concentration, with optimum growth at 15% FBS. DNA barcoding (16SrRNA and COX1) was used to authenticate the cell line. Cells were incubated with propidium iodide and sorted via flow cytometry to calculate the DNA content to confirm the genetic stability. Significant green fluorescent protein (GFP) signals confirmed the utility of cell line in transgenic and genetic manipulation studies. In vitro assay was performed with MTT to examine the growth potential of the cell line. The muscle cell line would provide a novel invaluable in vitro model to identify important genes to understand regulatory mechanisms that govern the molecular regulation of myogenesis and should be useful in biomedical research.},
}
@article {pmid26985574,
year = {2016},
author = {Decurtins, W and Wichert, M and Franzini, RM and Buller, F and Stravs, MA and Zhang, Y and Neri, D and Scheuermann, J},
title = {Automated screening for small organic ligands using DNA-encoded chemical libraries.},
journal = {Nature protocols},
volume = {11},
number = {4},
pages = {764-780},
pmid = {26985574},
issn = {1750-2799},
support = {163479/SNSF_/Swiss National Science Foundation/Switzerland ; 670603/ERC_/European Research Council/International ; },
mesh = {DNA Adducts/*analysis ; High-Throughput Nucleotide Sequencing ; *Ligands ; Mass Screening/*methods ; Oligonucleotides/*chemistry/genetics ; Protein Binding ; *Small Molecule Libraries ; },
abstract = {DNA-encoded chemical libraries (DECLs) are collections of organic compounds that are individually linked to different oligonucleotides, serving as amplifiable identification barcodes. As all compounds in the library can be identified by their DNA tags, they can be mixed and used in affinity-capture experiments on target proteins of interest. In this protocol, we describe the screening process that allows the identification of the few binding molecules within the multiplicity of library members. First, the automated affinity selection process physically isolates binding library members. Second, the DNA codes of the isolated binders are PCR-amplified and subjected to high-throughput DNA sequencing. Third, the obtained sequencing data are evaluated using a C++ program and the results are displayed using MATLAB software. The resulting selection fingerprints facilitate the discrimination of binding from nonbinding library members. The described procedures allow the identification of small organic ligands to biological targets from a DECL within 10 d.},
}
@article {pmid26983732,
year = {2016},
author = {Dunn, G},
title = {Quality Assurance in the Polio Laboratory. Cell Sensitivity and Cell Authentication Assays.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1387},
number = {},
pages = {109-127},
doi = {10.1007/978-1-4939-3292-4_6},
pmid = {26983732},
issn = {1940-6029},
mesh = {Animals ; Cell Culture Techniques/*methods ; Cell Line ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Humans ; Mice ; Phylogeny ; Poliomyelitis/diagnosis/*virology ; Poliovirus/*isolation &amp; purification ; Polymerase Chain Reaction/methods ; Species Specificity ; },
abstract = {The accuracy of poliovirus surveillance is largely dependent on the quality of the cell lines used for virus isolation, which is the foundation of poliovirus diagnostic work. Many cell lines are available for the isolation of enteroviruses, whilst genetically modified L20B cells can be used as a diagnostic tool for the identification of polioviruses. To be confident that cells can consistently isolate the virus of interest, it is necessary to have a quality assurance system in place, which will ensure that the cells in use are not contaminated with other cell lines or microorganisms and that they remain sensitive to the viruses being studied.The sensitivity of cell lines can be assessed by the regular testing of a virus standard of known titer in the cell lines used for virus isolation. The titers obtained are compared to previously obtained titers in the same assay, so that any loss of sensitivity can be detected.However, the detection of cell line cross contamination is more difficult. DNA bar coding is a technique that uses a short DNA sequence from a standardized position in the genome as a molecular diagnostic assay for species-level identification. For almost all groups of higher animals, the cytochrome c oxidase subunit 1 of mitochondrial DNA (CO1) is emerging as the standard barcode region. This region is 648 nucleotide base pairs long in most phylogenetic groups and is flanked by regions of conserved sequences, making it relatively easy to isolate and analyze. DNA barcodes vary among individuals of the same species to a very minor degree (generally less than 1-2 %), and a growing number of studies have shown that the COI sequences of even closely related species differ by several per cent, making it possible to identify different species with high confidence.},
}
@article {pmid26983010,
year = {2016},
author = {Cardoso, AL and Carvalho, HL and Benathar, TC and Serrão, SM and Nagamachi, CY and Pieczarka, JC and Sousa, LM and Ready, JS and Noronha, RC},
title = {Integrated Cytogenetic and Mitochondrial DNA Analyses Indicate That Two Different Phenotypes of Hypancistrus (L066 and L333) Belong to the Same Species.},
journal = {Zebrafish},
volume = {13},
number = {3},
pages = {209-216},
doi = {10.1089/zeb.2015.1213},
pmid = {26983010},
issn = {1557-8542},
mesh = {Animals ; Catfishes/*genetics ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Pigmentation ; Polymorphism, Genetic ; Species Specificity ; },
abstract = {The diversity of Hypancistrus species in the Xingu River is remarkable and the variation in color morphs represents a real challenge to taxonomists to delimit species boundaries. One of the most recognizable Hypancistrus complexes is the worm-lined species, known in the aquarium trade as King Tiger Plec in English, Hypancistrus "pão" in Portuguese or under the L-numbers L066 and L333 that represent two melanic pigment pattern phenotypes. To assess the identity of these two phenotypes, we described their karyotypes and sequenced part of the mitochondrial cytochrome oxidase I gene (DNA barcode). These fishes have 52 chromosomes (40 meta-submetacentric and 12 subtelo-acrocentric) and a strong heteromorphism in chromosome pair 21 was observed, which does not correlate with the two phenotypes or sex. DNA barcodes separated the samples analyzed from Hypancistrus zebra and other publicly available sequences of Loricariidae showing no divergence between the two phenotypes. The data set indicates that worm-lined Hypancistrus from the Xingu form a single species with clear chromosomal and melanic pigment pattern polymorphisms.},
}
@article {pmid26982211,
year = {2016},
author = {Olivar, JE and Alaba, JP and Atienza, JF and Tan, JJ and Umali, MT and Alejandro, GJ},
title = {Establishment of a standard reference material (SRM) herbal DNA barcode library of Vitex negundo L. (lagundi) for quality control measures.},
journal = {Food additives &amp; contaminants. Part A, Chemistry, analysis, control, exposure &amp; risk assessment},
volume = {33},
number = {5},
pages = {741-748},
doi = {10.1080/19440049.2016.1166525},
pmid = {26982211},
issn = {1944-0057},
mesh = {Anti-Asthmatic Agents/analysis/economics/standards ; Antipyretics/analysis/economics/standards ; Antitussive Agents/analysis/economics/standards ; DNA Barcoding, Taxonomic ; DNA, Intergenic/metabolism ; Dietary Supplements/*analysis/economics/standards ; Food Contamination/*prevention &amp; control ; Food Inspection/*methods ; *Gene Library ; *Genes, Plant ; Genetic Loci ; Philippines ; Photosystem II Protein Complex/genetics/metabolism ; Plant Preparations/*analysis/economics/standards ; Protein Subunits/genetics/metabolism ; Proto-Oncogene Proteins pp60(c-src)/genetics/metabolism ; Quality Control ; Reference Standards ; Teas, Herbal/analysis/standards ; Vitex/*genetics/growth &amp; development/metabolism ; },
abstract = {The majority of the population in the Philippines relies on herbal products as their primary source for their healthcare needs. After the recognition of Vitex negundo L. (lagundi) as an important and effective alternative medicine for cough, sore throat, asthma and fever by the Philippine Department of Health (DOH), there was an increase in the production of lagundi-based herbal products in the form of teas, capsules and syrups. The efficiency of these products is greatly reliant on the use of authentic plant material, and to this day no standard protocol has been established to authenticate plant materials. DNA barcoding offers a quick and reliable species authentication tool, but its application to plant material has been less successful due to (1) lack of a standard DNA barcoding loci in plants and (2) poor DNA yield from powderised plant products. This study reports the successful application of DNA barcoding in the authentication of five V. negundo herbal products sold in the Philippines. Also, the first standard reference material (SRM) herbal library for the recognition of authentic V. negundo samples was established using 42 gene accessions of ITS, psbA-trnH and matK barcoding loci. Authentication of the herbal products utilised the SRM following the BLASTn and maximum-likelihood (ML) tree construction criterion. Barcode sequences were retrieved for ITS and psbA-trnH of all products tested and the results of the study revealed that only one out of five herbal products satisfied both BLASTn and ML criterion and was considered to contain authentic V. negundo. The results prompt the urgent need to utilise DNA barcoding in authenticating herbal products available in the Philippine market. Authentication of these products will secure consumer health by preventing the negative effects of adulteration, substitution and contamination.},
}
@article {pmid26980996,
year = {2016},
author = {Trivedi, S and Aloufi, AA and Ansari, AA and Ghosh, SK},
title = {Role of DNA barcoding in marine biodiversity assessment and conservation: An update.},
journal = {Saudi journal of biological sciences},
volume = {23},
number = {2},
pages = {161-171},
pmid = {26980996},
issn = {1319-562X},
abstract = {More than two third area of our planet is covered by oceans and assessment of marine biodiversity is a challenging task. With the increasing global population, there is a tendency to exploit marine resources for food, energy and other requirements. This puts pressure on the fragile marine environment and necessitates sustainable conservation efforts. Marine species identification using traditional taxonomical methods is often burdened with taxonomic controversies. Here we discuss the comparatively new concept of DNA barcoding and its significance in marine perspective. This molecular technique can be useful in the assessment of cryptic species which is widespread in marine environment and linking the different life cycle stages to the adult which is difficult to accomplish in the marine ecosystem. Other advantages of DNA barcoding include authentication and safety assessment of seafood, wildlife forensics, conservation genetics and detection of invasive alien species (IAS). Global DNA barcoding efforts in the marine habitat include MarBOL, CeDAMar, CMarZ, SHARK-BOL, etc. An overview on DNA barcoding of different marine groups ranging from the microbes to mammals is revealed. In conjugation with newer and faster techniques like high-throughput sequencing, DNA barcoding can serve as an effective modern tool in marine biodiversity assessment and conservation.},
}
@article {pmid26977057,
year = {2016},
author = {Chase, MW and Salamin, N and Wilkinson, M and Dunwell, JM and Kesanakurthi, RP and Haider, N and Savolainen, V},
title = {Correction to 'Land plants and DNA barcodes: short-term and long-term goals'.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1691},
pages = {20150063},
doi = {10.1098/rstb.2015.0063},
pmid = {26977057},
issn = {1471-2970},
}
@article {pmid26971231,
year = {2016},
author = {Devloo-Delva, F and Miralles, L and Ardura, A and Borrell, YJ and Pejovic, I and Tsartsianidou, V and Garcia-Vazquez, E},
title = {Detection and characterisation of the biopollutant Xenostrobus securis (Lamarck 1819) Asturian population from DNA Barcoding and eBarcoding.},
journal = {Marine pollution bulletin},
volume = {105},
number = {1},
pages = {23-29},
doi = {10.1016/j.marpolbul.2016.03.008},
pmid = {26971231},
issn = {1879-3363},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA Primers/genetics ; Electron Transport Complex IV/genetics ; *Environmental Monitoring ; Estuaries ; Genetic Variation ; Genetics, Population ; Mytilidae/classification/*genetics ; Polymerase Chain Reaction ; Spain ; Species Specificity ; },
abstract = {DNA efficiently contributes to detect and understand marine invasions. In 2014 the potential biological pollutant pygmy mussel (Xenostrobus securis) was observed for the first time in the Avilés estuary (Asturias, Bay of Biscay). The goal of this study was to assess the stage of invasion, based on demographic and genetic (DNA Barcoding) characteristics, and to develop a molecular tool for surveying the species in environmental DNA. A total of 130 individuals were analysed for the DNA Barcode cytochrome oxidase I gene in order to determine genetic diversity, population structure, expansion trends, and to inferring introduction hits. Reproduction was evidenced by bimodal size distributions of 1597 mussels. High population genetic variation and genetically distinct clades might suggest multiple introductions from several source populations. Finally, species-specific primers were developed within the DNA barcode for PCR amplification from water samples in order to enabling rapid detection of the species in initial expansion stages.},
}
@article {pmid26966652,
year = {2016},
author = {Forster, D and Dunthorn, M and Stoeck, T and Mahé, F},
title = {Comparison of three clustering approaches for detecting novel environmental microbial diversity.},
journal = {PeerJ},
volume = {4},
number = {},
pages = {e1692},
pmid = {26966652},
issn = {2167-8359},
abstract = {Discovery of novel diversity in high-throughput sequencing studies is an important aspect in environmental microbial ecology. To evaluate the effects that amplicon clustering methods have on the discovery of novel diversity, we clustered an environmental marine high-throughput sequencing dataset of protist amplicons together with reference sequences from the taxonomically curated Protist Ribosomal Reference (PR(2)) database using three de novo approaches: sequence similarity networks, USEARCH, and Swarm. The potentially novel diversity uncovered by each clustering approach differed drastically in the number of operational taxonomic units (OTUs) and in the number of environmental amplicons in these novel diversity OTUs. Global pairwise alignment comparisons revealed that numerous amplicons classified as potentially novel by USEARCH and Swarm were more than 97% similar to references of PR(2). Using shortest path analyses on sequence similarity network OTUs and Swarm OTUs we found additional novel diversity within OTUs that would have gone unnoticed without further exploiting their underlying network topologies. These results demonstrate that graph theory provides powerful tools for microbial ecology and the analysis of environmental high-throughput sequencing datasets. Furthermore, sequence similarity networks were most accurate in delineating novel diversity from previously discovered diversity.},
}
@article {pmid26965427,
year = {2016},
author = {Zajac, BK and Sontigun, N and Wannasan, A and Verhoff, MA and Sukontason, K and Amendt, J and Zehner, R},
title = {Application of DNA barcoding for identifying forensically relevant Diptera from northern Thailand.},
journal = {Parasitology research},
volume = {115},
number = {6},
pages = {2307-2320},
pmid = {26965427},
issn = {1432-1955},
mesh = {Animals ; Autopsy/methods ; DNA Barcoding, Taxonomic/*methods ; Diptera/*classification/*genetics ; Electron Transport Complex IV/*genetics ; Entomology/methods ; Forensic Sciences/methods ; Polymerase Chain Reaction ; RNA, Ribosomal, 28S/*genetics ; Sequence Analysis, DNA ; Thailand ; },
abstract = {In recent decades, forensic entomology has become a useful tool in criminal investigations all over the world. Species-specific identification of flies plays an important role in this field and is obligatory for accurate calculation of the post-mortem interval. However, not all important colonizers of a corpse can be identified by common morphological keys. Due to similar morphology and the lack of keys for some taxa, especially for immature stages, DNA barcoding has become more popular during the last recent years. This development is particularly important for countries like Thailand, in which forensic entomology is a newly developing research area and which faces several challenges such as a high biodiversity of fly species. The most commonly used barcoding region in forensic entomology, the mitochondrial cytochrome oxidase subunit 1 (coI) gene, as well as a 1000-bp-long region of the 28S nuclear rRNA gene, was used to analyze and establish the molecular barcodes of 13 different species of flies of forensic relevance in northern Thailand.},
}
@article {pmid26965171,
year = {2016},
author = {Chaskopoulou, A and Giantsis, IA and Demir, S and Bon, MC},
title = {Species composition, activity patterns and blood meal analysis of sand fly populations (Diptera: Psychodidae) in the metropolitan region of Thessaloniki, an endemic focus of canine leishmaniasis.},
journal = {Acta tropica},
volume = {158},
number = {},
pages = {170-176},
doi = {10.1016/j.actatropica.2016.03.006},
pmid = {26965171},
issn = {1873-6254},
mesh = {Animals ; Chickens/parasitology ; DNA Barcoding, Taxonomic ; Disease Vectors ; Dog Diseases/*epidemiology ; Dogs ; Feeding Behavior ; Greece/epidemiology ; Humans ; Leishmania/genetics ; Leishmaniasis/epidemiology/*veterinary ; Phylogeny ; Population Dynamics ; *Psychodidae/classification ; },
abstract = {Species composition, activity patterns and blood meal analysis of sand fly populations were investigated in the metropolitan region of Thessaloniki, North Greece from May to October 2011. Sampling was conducted weekly in 3 different environments (animal facilities, open fields, residential areas) along the outskirts of the city in areas of increased canine leishmania transmission. Six sand fly species (Phlebotomus perfiliewi, Phlebotomus tobbi, Phlebotomus simici, Plebotomus papatasi, Sergentomya minuta and Sergentomya dentata) were identified using both classical and molecular techniques. DNA barcodes were characterized for the first time for two (P. simici and S. dentata) of the six recorded species. Phylogenetic analysis based on the COI gene sequences confirmed the grouping of P. tobbi, P. perniciosus and P. perfiliewi (subgenus Larrousius) and the monophyly of P. simici (subgenus Adlerius). By far the most prevalent species was P. perfiliewi, followed by P. simici and P. tobbi. The largest populations of sand flies were collected from animal facilities, followed by residential areas and open agricultural fields. Peak activity of sand flies overall occurred mid-August to mid-September and then declined sharply in October. Blood meal analysis showed that P. perfiliewi and P. simici feed preferentially on humans (88% &amp; 95%, respectively) but also feed on chickens and goats. When designing a control strategy to alleviate sand fly nuisance in the region of Thessaloniki the following conclusions can be reached from this study: a) August and September are high risk months due to increased sand fly activity levels, b) animal facilities within or adjacent to urban settlements are high risk areas and may act as a maintenance and amplification foci for the vector as well as the parasite, and c) the abundance, ubiquity and feeding behavior of P. perfiliewi and P. simici establishes them as potentially important vectors of Leishmania in the region.},
}
@article {pmid26965054,
year = {2016},
author = {Sauvage, T and Schmidt, WE and Suda, S and Fredericq, S},
title = {A metabarcoding framework for facilitated survey of endolithic phototrophs with tufA.},
journal = {BMC ecology},
volume = {16},
number = {},
pages = {8},
pmid = {26965054},
issn = {1472-6785},
mesh = {Chlorophyta/classification/*genetics ; Cyanobacteria/genetics ; *DNA Barcoding, Taxonomic/methods ; DNA Primers ; DNA, Plant ; Databases, Nucleic Acid ; Peptide Elongation Factor Tu/*genetics ; *Phototrophic Processes ; Rhodophyta/classification/*genetics ; },
abstract = {BACKGROUND: In spite of their ecological importance as primary producers and microbioeroders of marine calcium carbonate (CaCO3) substrata, endolithic phototrophs spanning both prokaryotic (the cyanobacteria) and eukaryotic algae lack established molecular resources for their facilitated survey with high throughput sequencing. Here, the development of a metabarcoding framework for the elongation factor EF-Ttu (tufA) was tested on four Illumina-sequenced marine CaCO3 microfloras for the characterization of their endolithic phototrophs, especially the abundant bioeroding Ostreobium spp. (Ulvophyceae). The framework consists of novel tufA degenerate primers and a comprehensive database enabling Operational Taxonomic Unit (OTU) identification at multiple taxonomic ranks with percent identity thresholds determined herein.<br><br>RESULTS: The newly established tufA database comprises 4057 non-redundant sequences (from 1339 eukaryotic and prokaryotic phototrophs, and 2718 prokaryotic heterotrophs) including 27 classes in 10 phyla of phototrophic diversity summarized from data mining on GenBank(&#xae;), our barcoding of >150 clones produced from coral reef microfloras, and >300 eukaryotic phototrophs (>230 Ulvophyceae including >100 'Ostreobium' spp., and >70 Florideophyceae, Phaeophyceae and miscellaneous taxa). Illumina metabarcoding with the newly designed primers resulted in 802 robust OTUs including 618 phototrophs and 184 heterotrophs (77 and 23% of OTUs, respectively). Phototrophic OTUs belonged to 14 classes of phototrophs found in seven phyla, and represented ~98% of all reads. The phylogenetic profiles of coral reef microfloras showed few OTUs in large abundance (proportion of reads) for the Chlorophyta (Ulvophyceae, i.e. Ostreobium and Phaeophila), the Rhodophyta (Florideophyceae) and Haptophyta (Coccolithophyceae), and a large diversity (richness) of OTUs in lower abundance for the Cyanophyta (Cyanophyceae) and the Ochrophyta (the diatoms, 'Bacillariophyta'). The bioerosive 'Ostreobium' spp. represented four families in a large clade of subordinal divergence, i.e. the Ostreobidineae, and a fifth, phylogenetically remote family in the suborder Halimedineae (provisionally assigned as the 'Pseudostreobiaceae'). Together they harbor 85-95 delimited cryptic species of endolithic microsiphons.<br><br>CONCLUSIONS: The novel degenerate primers allowed for amplification of endolithic phototrophs across a wide phylogenetic breadth as well as their recovery in very large proportions of reads (overall 98%) and diversity (overall 77% of OTUs). The established companion tufA database and determined identity thresholds allow for OTU identification at multiple taxonomic ranks to facilitate the monitoring of phototrophic assemblages via metabarcoding, especially endolithic communities rich in bioeroding Ulvophyceae, such as those harboring 'Ostreobium' spp., Phaeophila spp. and associated algal diversity.},
}
@article {pmid26961079,
year = {2016},
author = {Fitzhugh, K},
title = {Sequence Data, Phylogenetic Inference, and Implications of Downward Causation.},
journal = {Acta biotheoretica},
volume = {64},
number = {2},
pages = {133-160},
doi = {10.1007/s10441-016-9277-0},
pmid = {26961079},
issn = {1572-8358},
mesh = {Animals ; Classification/*methods ; *Evolution, Molecular ; Humans ; Nucleotides/*genetics ; *Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {Framing systematics as a field consistent with scientific inquiry entails that inferences of phylogenetic hypotheses have the goal of producing accounts of past causal events that explain differentially shared characters among organisms. Linking observations of characters to inferences occurs by way of why-questions implied by data matrices. Because of their form, why-questions require the use of common-cause theories. Such theories in phylogenetic inferences include natural selection and genetic drift. Selection or drift can explain 'morphological' characters but selection cannot be causally applied to sequences since fitness differences cannot be directly associated with individual nucleotides or amino acids. The relation of selection to sequence data is by way of downward or top-down causation from those phenotypes upon which selection occurs. The application of phylogenetic inference to explain sequence data is thus restricted to instances where drift is the relevant theory; those nucleotides or amino acids that can be explained via downward causation are precluded from inclusion in the data matrix. The restrictions on the inclusion of sequence data in phylogenetic inferences equally apply to species hypotheses, precluding the more restrictive approach known as DNA barcoding. Not being able to discern drift and selection as relevant causal mechanisms can severely constrain the inclusion and explanations of sequence data. Implications of such exclusion are discussed in relation to the requirement of total evidence.},
}
@article {pmid26959368,
year = {2016},
author = {Brehm, G and Hebert, PD and Colwell, RK and Adams, MO and Bodner, F and Friedemann, K and Möckel, L and Fiedler, K},
title = {Turning Up the Heat on a Hotspot: DNA Barcodes Reveal 80% More Species of Geometrid Moths along an Andean Elevational Gradient.},
journal = {PloS one},
volume = {11},
number = {3},
pages = {e0150327},
pmid = {26959368},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Geography ; Moths/classification/*genetics ; },
abstract = {We sampled 14,603 geometrid moths along a forested elevational gradient from 1020-3021 m in the southern Ecuadorian Andes, and then employed DNA barcoding to refine decisions on species boundaries initially made by morphology. We compared the results with those from an earlier study on the same but slightly shorter gradient that relied solely on morphological criteria to discriminate species. The present analysis revealed 1857 putative species, an 80% increase in species richness from the earlier study that detected only 1010 species. Measures of species richness and diversity that are less dependent on sample size were more than twice as high as in the earlier study, even when analysis was restricted to an identical elevational range. The estimated total number of geometrid species (new dataset) in the sampled area is 2350. Species richness at single sites was 32-43% higher, and the beta diversity component rose by 43-51%. These impacts of DNA barcoding on measures of richness reflect its capacity to reveal cryptic species that were overlooked in the first study. The overall results confirmed unique diversity patterns reported in the first investigation. Species diversity was uniformly high along the gradient, declining only slightly above 2800 m. Species turnover also showed little variation along the gradient, reinforcing the lack of evidence for discrete faunal zones. By confirming these major biodiversity patterns, the present study establishes that incomplete species delineation does not necessarily conceal trends of biodiversity along ecological gradients, but it impedes determination of the true magnitude of diversity and species turnover.},
}
@article {pmid26956219,
year = {2016},
author = {Moravec, F and Chaabane, A and Justine, JL and Neifar, L},
title = {Two gonad-infecting species of Philometra (Nematoda: Philometridae) from groupers (Serranidae) off Tunisia, with a key to Philometra species infecting serranid gonads.},
journal = {Parasite (Paris, France)},
volume = {23},
number = {},
pages = {8},
pmid = {26956219},
issn = {1776-1042},
mesh = {Animals ; Bass/*parasitology ; Dracunculoidea/anatomy &amp; histology/classification/*isolation &amp; purification ; Female ; Fish Diseases/*parasitology ; Food Parasitology ; Male ; Mediterranean Sea ; Ovary/*parasitology ; Species Specificity ; Spirurida Infections/parasitology/*veterinary ; },
abstract = {Based on light and scanning electron microscopical studies of nematode specimens (males and mature females) collected from the ovary of groupers (Serranidae, Perciformes) in the Mediterranean Sea off Tunisia (near Tunis and Sfax), two gonad-infecting species of Philometra Costa, 1845 (Nematoda, Philometridae) are reported: Philometra inexpectata n. sp. from the mottled grouper Mycteroperca rubra and P. jordanoi (López-Neyra, 1951) from the dusky grouper Epinephelus marginatus. Identification of both fish species was confirmed by molecular barcoding. The new species is mainly characterized by the length of equally long spicules (147-165 μm), the gubernaculum (63-93 μm long) bearing at the tip two dorsolateral lamellar parts separated from each other by a smooth median field, a V-shaped mound on the male caudal extremity, the presence of a pair of large caudal papillae located posterior to the cloaca and by the body length of the males (1.97-2.43 mm). Philometra inexpectata n. sp. is the fifth known gonad-infecting philometrid species parasitizing serranid fishes in the Mediterranean region. The males of P. jordanoi were examined by scanning electron microscopy for the first time; this detailed study revealed some new taxonomically important morphological features, such as the number and arrangement of cephalic and caudal papillae, presence of amphids and phasmids and mainly the lamellate structures at the posterior end of the gubernaculum. A key to gonad-infecting species of Philometra parasitic in serranid fishes is provided.},
}
@article {pmid26956060,
year = {2016},
author = {Lavikainen, A and Iwaki, T and Haukisalmi, V and Konyaev, SV and Casiraghi, M and Dokuchaev, NE and Galimberti, A and Halajian, A and Henttonen, H and Ichikawa-Seki, M and Itagaki, T and Krivopalov, AV and Meri, S and Morand, S and Näreaho, A and Olsson, GE and Ribas, A and Terefe, Y and Nakao, M},
title = {Reappraisal of Hydatigera taeniaeformis (Batsch, 1786) (Cestoda: Taeniidae) sensu lato with description of Hydatigera kamiyai n. sp.},
journal = {International journal for parasitology},
volume = {46},
number = {5-6},
pages = {361-374},
doi = {10.1016/j.ijpara.2016.01.009},
pmid = {26956060},
issn = {1879-0135},
mesh = {Africa ; Animals ; Arvicolinae ; Asia ; Australia ; Bayes Theorem ; Cat Diseases/*parasitology ; Cats ; Cestoda/anatomy &amp; histology/*classification/genetics ; Cestode Infections/parasitology/*veterinary ; DNA Barcoding, Taxonomic/veterinary ; DNA, Helminth/chemistry ; Electron Transport Complex IV/genetics ; Europe ; Felidae/*parasitology ; Mice ; Mitochondria/enzymology/genetics ; Murinae ; Phylogeny ; Phylogeography ; Rats ; Rodent Diseases/*parasitology ; },
abstract = {The common cat tapeworm Hydatigera taeniaeformis is a complex of three morphologically cryptic entities, which can be differentiated genetically. To clarify the biogeography and the host spectrum of the cryptic lineages, 150 specimens of H. taeniaeformis in various definitive and intermediate hosts from Eurasia, Africa and Australia were identified with DNA barcoding using partial mitochondrial cytochrome c oxidase subunit 1 gene sequences and compared with previously published data. Additional phylogenetic analyses of selected isolates were performed using nuclear DNA and mitochondrial genome sequences. Based on molecular data and morphological analysis, Hydatigera kamiyai n. sp. Iwaki is proposed for a cryptic lineage, which is predominantly northern Eurasian and uses mainly arvicoline rodents (voles) and mice of the genus Apodemus as intermediate hosts. Hydatigera taeniaeformis sensu stricto (s.s.) is restricted to murine rodents (rats and mice) as intermediate hosts. It probably originates from Asia but has spread worldwide. Despite remarkable genetic divergence between H. taeniaeformis s.s. and H. kamiyai, interspecific morphological differences are evident only in dimensions of rostellar hooks. The third cryptic lineage is closely related to H. kamiyai, but its taxonomic status remains unresolved due to limited morphological, molecular, biogeographical and ecological data. This Hydatigera sp. is confined to the Mediterranean and its intermediate hosts are unknown. Further studies are needed to classify Hydatigera sp. either as a distinct species or a variant of H. kamiyai. According to previously published limited data, all three entities occur in the Americas, probably due to human-mediated introductions.},
}
@article {pmid26953507,
year = {2016},
author = {Otto, A and Laub, A and Wendt, L and Porzel, A and Schmidt, J and Palfner, G and Becerra, J and Krüger, D and Stadler, M and Wessjohann, L and Westermann, B and Arnold, N},
title = {Chilenopeptins A and B, Peptaibols from the Chilean Sepedonium aff. chalcipori KSH 883.},
journal = {Journal of natural products},
volume = {79},
number = {4},
pages = {929-938},
doi = {10.1021/acs.jnatprod.5b01018},
pmid = {26953507},
issn = {1520-6025},
mesh = {Amino Acid Sequence ; Anti-Bacterial Agents/chemistry/*isolation &amp; purification/pharmacology ; Basidiomycota/metabolism ; Chile ; Hypocreales/chemistry ; Molecular Structure ; Peptaibols/chemistry/*isolation &amp; purification/pharmacology ; Peptides/chemistry/isolation &amp; purification/pharmacology ; Trichoderma/chemistry ; },
abstract = {The Chilean Sepedonium aff. chalcipori strain KSH 883, isolated from the endemic Boletus loyo Philippi, was studied in a polythetic approach based on chemical, molecular, and biological data. A taxonomic study of the strain using molecular data of the ITS, EF1-α, and RPB2 barcoding genes confirmed the position of the isolated strain within the S. chalcipori clade, but also suggested the separation of this clade into three different species. Two new linear 15-residue peptaibols, named chilenopeptins A (1) and B (2), together with the known peptaibols tylopeptins A (3) and B (4) were isolated from the semisolid culture of strain KSH 883. The structures of 1 and 2 were elucidated on the basis of HRESIMS(n) experiments in conjunction with comprehensive 1D and 2D NMR analysis. Thus, the sequence of chilenopeptin A (1) was identified as Ac-Aib(1)-Ser(2)-Trp(3)-Aib(4)-Pro(5)-Leu(6)-Aib(7)-Aib(8)-Gln(9)-Aib(10)-Aib(11)-Gln(12)-Aib(13)-Leu(14)-Pheol(15), while chilenopeptin B (2) differs from 1 by the replacement of Trp(3) by Phe(3). Additionally, the total synthesis of 1 and 2 was accomplished by a solid-phase approach, confirming the absolute configuration of all chiral amino acids as l. Both the chilenopeptins (1 and 2) and tylopeptins (3 and 4) were evaluated for their potential to inhibit the growth of phytopathogenic organisms.},
}
@article {pmid26950701,
year = {2016},
author = {Gu, C and Tembrock, LR and Johnson, NG and Simmons, MP and Wu, Z},
title = {The Complete Plastid Genome of Lagerstroemia fauriei and Loss of rpl2 Intron from Lagerstroemia (Lythraceae).},
journal = {PloS one},
volume = {11},
number = {3},
pages = {e0150752},
pmid = {26950701},
issn = {1932-6203},
mesh = {Base Sequence ; Evolution, Molecular ; Genome, Plastid/*genetics ; Genomics ; Introns/*genetics ; Lagerstroemia/*cytology/*genetics ; Microsatellite Repeats/genetics ; Molecular Sequence Annotation ; Phylogeny ; Species Specificity ; },
abstract = {Lagerstroemia (crape myrtle) is an important plant genus used in ornamental horticulture in temperate regions worldwide. As such, numerous hybrids have been developed. However, DNA sequence resources and genome information for Lagerstroemia are limited, hindering evolutionary inferences regarding interspecific relationships. We report the complete plastid genome of Lagerstroemia fauriei. To our knowledge, this is the first reported whole plastid genome within Lythraceae. This genome is 152,440 bp in length with 38% GC content and consists of two single-copy regions separated by a pair of 25,793 bp inverted repeats. The large single copy and the small single copy regions span 83,921 bp and 16,933 bp, respectively. The genome contains 129 genes, including 17 located in each inverted repeat. Phylogenetic analysis of genera sampled from Geraniaceae, Myrtaceae, and Onagraceae corroborated the sister relationship between Lythraceae and Onagraceae. The plastid genomes of L. fauriei and several other Lythraceae species lack the rpl2 intron, which indicating an early loss of this intron within the Lythraceae lineage. The plastid genome of L. fauriei provides a much needed genetic resource for further phylogenetic research in Lagerstroemia and Lythraceae. Highly variable markers were identified for application in phylogenetic, barcoding and conservation genetic applications.},
}
@article {pmid26948627,
year = {2016},
author = {Tagliavia, M and Nicosia, A and Salamone, M and Biondo, G and Bennici, CD and Mazzola, S and Cuttitta, A},
title = {Development of a fast DNA extraction method for sea food and marine species identification.},
journal = {Food chemistry},
volume = {203},
number = {},
pages = {375-378},
doi = {10.1016/j.foodchem.2016.02.095},
pmid = {26948627},
issn = {1873-7072},
mesh = {Animals ; DNA/*analysis/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Fishes/*classification/*genetics ; Seafood/analysis/*classification ; },
abstract = {The authentication of food components is one of the key issues in food safety. Similarly taxonomy, population and conservation genetics as well as food web structure analysis, also rely on genetic analyses including the DNA barcoding technology. In this scenario we developed a fast DNA extraction method without any purification step from fresh and processed seafood, suitable for any PCR analysis. The protocol allows the fast DNA amplification from any sample, including fresh, stored and processed seafood and from any waste of industrial fish processing, independently of the sample storage method. Therefore, this procedure is particularly suitable for the fast processing of samples and to carry out investigations for the authentication of seafood by means of DNA analysis.},
}
@article {pmid26946968,
year = {2016},
author = {Chetoui, I and Denis, F and Boussaid, M and Telahigue, K and El Cafsi, M},
title = {Genetic diversity and phylogenetic analysis of two Tunisian bivalves (Mactridae) Mactra corallina (Linnaeus, 1758) and Eastonia rugosa (Helbling, 1799) based on COI gene sequences.},
journal = {Comptes rendus biologies},
volume = {339},
number = {3-4},
pages = {115-122},
doi = {10.1016/j.crvi.2016.02.001},
pmid = {26946968},
issn = {1768-3238},
mesh = {Animals ; Bivalvia/*genetics ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; *Genetic Variation ; Haplotypes ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Tunisia ; },
abstract = {A partial sequence of mitochondrial cytochrome c oxidase subunit I (COI) was used as a genetic marker for a genetic diversity and phylogenetic analysis (DNA barcoding) of two Mactridae species, Mactra corallina and Eastonia rugosa, collected from the Tunisian coast. These Mactridae species could be distinguished by DNA barcoding techniques and they will be considered as monophyletic clades with the Neighbor-Joining (NJ) tree. The genetic structure detected that E. rugosa presents three haplotypes with a high frequency of HER1 (0.89). However, M. corralina shared 14 haplotypes. The haplotypic diversity (H) was equal to 0.205 and 0.954, respectively, for E. rugosa and M. corallina. While the nucleotide diversity (π) was higher for M. corallina (π=0.0818), the mismatch distribution showed a unimodal curve for E. rugosa (a recent sudden demographic expansion) and a multimodal distribution for M. corallina (size stability).},
}
@article {pmid26946838,
year = {2015},
author = {Lin, LZ and Liu, MC and Ma, HY and Chen, YF and Zhang, DY and Liu, F and Li, SY},
title = {[Identification of Moghania philippinensis and Moghania macrophylla].},
journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials},
volume = {38},
number = {7},
pages = {1417-1421},
pmid = {26946838},
issn = {1001-4454},
mesh = {Chromatography, High Pressure Liquid ; DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Fabaceae/*classification ; Genistein/*analysis ; Plant Roots/*chemistry ; Plants, Medicinal/classification ; },
abstract = {OBJECTIVE: To study the identification methods of Moghania philippinensis and Moghania macrophylla, and to establish a comprehensive precise discrimination method.<br><br>METHODS: TLC and HPLC were applied to analyze genistein in the root of Moghania philippinensis and Moghania macrophylla. DNA barcoding establishment was based on ITS2 sequcence.<br><br>RESULTS: A comprehensive differentiation method for Moghania philippinensis and Moghania macrophylla based on TLC was proposed, which was combined with HPLC for determination of genistein. The plants of Moghania philippinensis and Moghania macrophylla and their related species could be distinguished by DNA barcoding effectively.<br><br>CONCLUSION: TLC and HPLC profiles of Flemingia Radix provide alternative methods of identification using chemical approach. This integrated chemical and molecular approach allows accurate comprehensive fast identification of Moghania philippinensis and Moghania macrophylla, which avoids the methods limitations on the accuracy of identification. The differentiation methods based on TLC, HPLC and DNA barcoding are simple,which provide a new scientific evidence for the identification of authenticity of Flemingia Radix.},
}
@article {pmid26943355,
year = {2016},
author = {Gager, Y and Tarland, E and Lieckfeldt, D and Ménage, M and Botero-Castro, F and Rossiter, SJ and Kraus, RH and Ludwig, A and Dechmann, DK},
title = {The Value of Molecular vs. Morphometric and Acoustic Information for Species Identification Using Sympatric Molossid Bats.},
journal = {PloS one},
volume = {11},
number = {3},
pages = {e0150780},
pmid = {26943355},
issn = {1932-6203},
mesh = {*Acoustics ; Animals ; Body Weight ; Chiroptera/*anatomy &amp; histology/*genetics ; Echolocation ; Extremities/anatomy &amp; histology ; Female ; Genetic Loci ; Male ; Microsatellite Repeats/genetics ; Multigene Family ; Phylogeny ; Principal Component Analysis ; Sample Size ; Skin Pigmentation ; Sound Spectrography ; Species Specificity ; *Sympatry ; Wings, Animal/anatomy &amp; histology ; },
abstract = {A fundamental condition for any work with free-ranging animals is correct species identification. However, in case of bats, information on local species assemblies is frequently limited especially in regions with high biodiversity such as the Neotropics. The bat genus Molossus is a typical example of this, with morphologically similar species often occurring in sympatry. We used a multi-method approach based on molecular, morphometric and acoustic information collected from 962 individuals of Molossus bondae, M. coibensis, and M. molossus captured in Panama. We distinguished M. bondae based on size and pelage coloration. We identified two robust species clusters composed of M. molossus and M. coibensis based on 18 microsatellite markers but also on a more stringently determined set of four markers. Phylogenetic reconstructions using the mitochondrial gene co1 (DNA barcode) were used to diagnose these microsatellite clusters as M. molossus and M. coibensis. To differentiate species, morphological information was only reliable when forearm length and body mass were combined in a linear discriminant function (95.9% correctly identified individuals). When looking in more detail at M. molossus and M. coibensis, only four out of 13 wing parameters were informative for species differentiation, with M. coibensis showing lower values for hand wing area and hand wing length and higher values for wing loading. Acoustic recordings after release required categorization of calls into types, yielding only two informative subsets: approach calls and two-toned search calls. Our data emphasizes the importance of combining morphological traits and independent genetic data to inform the best choice and combination of discriminatory information used in the field. Because parameters can vary geographically, the multi-method approach may need to be adjusted to local species assemblies and populations to be entirely informative.},
}
@article {pmid26938660,
year = {2016},
author = {Montagna, M and Mereghetti, V and Lencioni, V and Rossaro, B},
title = {Integrated Taxonomy and DNA Barcoding of Alpine Midges (Diptera: Chironomidae).},
journal = {PloS one},
volume = {11},
number = {3},
pages = {e0149673},
pmid = {26938660},
issn = {1932-6203},
mesh = {Animals ; Bayes Theorem ; Chironomidae/classification/*genetics ; *DNA Barcoding, Taxonomic ; *Genetic Variation ; Larva/genetics ; *Phylogeny ; Pupa/genetics ; Sequence Analysis, DNA ; },
abstract = {Rapid and efficient DNA-based tools are recommended for the evaluation of the insect biodiversity of high-altitude streams. In the present study, focused principally on larvae of the genus Diamesa Meigen 1835 (Diptera: Chironomidae), the congruence between morphological/molecular delimitation of species as well as performances in taxonomic assignments were evaluated. A fragment of the mitochondrial cox1 gene was obtained from 112 larvae, pupae and adults (Diamesinae, Orthocladiinae and Tanypodinae) that were collected in different mountain regions of the Alps and Apennines. On the basis of morphological characters 102 specimens were attributed to 16 species, and the remaining ten specimens were identified to the genus level. Molecular species delimitation was performed using: i) distance-based Automatic Barcode Gap Discovery (ABGD), with no a priori assumptions on species identification; and ii) coalescent tree-based approaches as the Generalized Mixed Yule Coalescent model, its Bayesian implementation and Bayesian Poisson Tree Processes. The ABGD analysis, estimating an optimal intra/interspecific nucleotide distance threshold of 0.7%-1.4%, identified 23 putative species; the tree-based approaches, identified between 25-26 entities, provided nearly identical results. All species belonging to zernyi, steinboecki, latitarsis, bertrami, dampfi and incallida groups, as well as outgroup species, are recovered as separate entities, perfectly matching the identified morphospecies. In contrast, within the cinerella group, cases of discrepancy arose: i) the two morphologically separate species D. cinerella and D. tonsa are neither monophyletic nor diagnosable exhibiting low values of between-taxa nucleotide mean divergence (0.94%); ii) few cases of larvae morphological misidentification were observed. Head capsule color is confirmed to be a valid character able to discriminate larvae of D. zernyi, D. tonsa and D. cinerella, but it is here better defined as a color gradient between the setae submenti and genal setae. DNA barcodes performances were high: average accuracy was ~89% and precision of ~99%. On the basis of the present data, we can thus conclude that molecular identification represents a promising tool that could be effectively adopted in evaluating biodiversity of high-altitude streams.},
}
@article {pmid26934529,
year = {2016},
author = {Osterhage, D and Pogonoski, JJ and Appleyard, SA and White, WT},
title = {Integrated Taxonomy Reveals Hidden Diversity in Northern Australian Fishes: A New Species of Seamoth (Genus Pegasus).},
journal = {PloS one},
volume = {11},
number = {3},
pages = {e0149415},
pmid = {26934529},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/genetics ; Fishes/*genetics ; Genetic Variation/*genetics ; Phylogeny ; Queensland ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Fishes are one of the most intensively studied marine taxonomic groups yet cryptic species are still being discovered. An integrated taxonomic approach is used herein to delineate and describe a new cryptic seamoth (genus Pegasus) from what was previously a wide-ranging species. Preliminary mitochondrial DNA barcoding indicated possible speciation in Pegasus volitans specimens collected in surveys of the Torres Strait and Great Barrier Reef off Queensland in Australia. Morphological and meristic investigations found key differences in a number of characters between P. volitans and the new species, P. tetrabelos. Further mt DNA barcoding of both the COI and the slower mutating 16S genes of additional specimens provided strong support for two separate species. Pegasus tetrabelos and P. volitans are sympatric in northern Australia and were frequently caught together in trawls at the same depths.},
}
@article {pmid26933250,
year = {2016},
author = {Wang, T and Lander, ES and Sabatini, DM},
title = {Viral Packaging and Cell Culture for CRISPR-Based Screens.},
journal = {Cold Spring Harbor protocols},
volume = {2016},
number = {3},
pages = {pdb.prot090811},
pmid = {26933250},
issn = {1559-6095},
support = {F31 CA189437/CA/NCI NIH HHS/United States ; R01 CA103866/CA/NCI NIH HHS/United States ; },
mesh = {CRISPR-Cas Systems ; Cell Culture Techniques/*methods ; Cell Line ; Gene Knockout Techniques/methods ; Gene Targeting/methods ; Genetic Testing/methods ; Humans ; Lentivirus/genetics/*physiology ; *Virus Assembly ; },
abstract = {This protocol describes how to perform the tissue culture and high-throughput sequencing library preparation for a CRISPR-based screen. First, pantropic lentivirus is prepared from a single guide RNA (sgRNA) plasmid pool and applied to the target cells. Following antibiotic selection and a harvest of the initial population, cells are then cultured under the desired screening condition(s) for 14 population doublings. The sgRNA barcode sequences integrated in the genomic DNA of each cell population are amplified and subject to high-throughput sequencing. Guidelines for downstream analysis of the sequencing data are also provided.},
}
@article {pmid26932125,
year = {2016},
author = {Overdyk, LM and Braid, HE and Naaum, AM and Crawford, SS and Hanner, RH},
title = {Real-time PCR identification of lake whitefish Coregonus clupeaformis in the Laurentian Great Lakes.},
journal = {Journal of fish biology},
volume = {88},
number = {4},
pages = {1460-1474},
doi = {10.1111/jfb.12922},
pmid = {26932125},
issn = {1095-8649},
mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA Primers/genetics ; DNA, Mitochondrial/genetics ; Great Lakes Region ; Lakes ; *Real-Time Polymerase Chain Reaction ; Salmonidae/*classification ; Species Specificity ; },
abstract = {The purpose of this study was to develop a real-time PCR assay to specifically identify lake whitefish Coregonus clupeaformis in larval fish assemblages based on a 122 bp amplicon from the mitochondrial genome. The efficiency of the reaction, as calculated from the standard curve, was 90.77% with the standard curve having an r(2) value of 0.998. Specificity of the assay provided single melt peak in a melt-curve analysis and amplification of only the target species. The assay successfully identified target DNA in as low as 0.1% proportion of a DNA mixture. This assay was designed on the portable Smart Cycler II platform and can be used in both field and laboratory settings to successfully identify C. clupeaformis.},
}
@article {pmid26930979,
year = {2015},
author = {Wu, YN and Xu, L and Chen, L and Wang, B and Zhao, R},
title = {[DNA Molecular Identification of Datura Medicinal Plants Using ITS2 Barcode Sequence].},
journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials},
volume = {38},
number = {9},
pages = {1852-1857},
pmid = {26930979},
issn = {1001-4454},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Datura/*classification/genetics ; Plants, Medicinal/*classification/genetics ; Polymerase Chain Reaction ; Nicotiana/classification/genetics ; },
abstract = {OBJECTIVE: To identify Datura medicinal plants in Solanaceae using DNA barcode technique and ITS2 sequence.<br><br>METHODS: The second internal transcribed spacer (ITS2) of Datura and Nicotiana medicinal plant samples was amplified by PCR and sequenced. To expand scope of the research topic, ITS2 sequences of related species were downloaded from GenBank. Sequence assembly and consensus sequence generation were performed by CodonCode Aligner. All the ITS2 sequences in the study were compared and analyzed using software DNAMAN. The related data analysis and processing were performed using software MEGA 5. 10 and the NJ tree was constructed. The ITS2 secondary structure was predicted using ITS2 web server, and distinguishing differences of the ITS2 secondary structures of the samples.<br><br>RESULTS: In the cluster dendrogram, all of samples were clustered into three branches. The plants of Nicotiana were clustered into a single branch, and the same as Datura (Brugmansia) arborea, which is similar to the results of previous studies. These proved that Brugmansia and Datura belonged to two different genera. Other species of Datura were clustered into a branch where all the intra-species samples were clustered to one branch respectively and obviously distinguished, which showed monophyletic. Bootstrap support rates between each two branches were more than 95%.<br><br>CONCLUSION: ITS2 sequences have great potential in terms of systematics study and variety identification.},
}
@article {pmid26930572,
year = {2016},
author = {Vasconcelos, R and Montero-Mendieta, S and Simó-Riudalbas, M and Sindaco, R and Santos, X and Fasola, M and Llorente, G and Razzetti, E and Carranza, S},
title = {Unexpectedly High Levels of Cryptic Diversity Uncovered by a Complete DNA Barcoding of Reptiles of the Socotra Archipelago.},
journal = {PloS one},
volume = {11},
number = {3},
pages = {e0149985},
pmid = {26930572},
issn = {1932-6203},
mesh = {Animals ; Bayes Theorem ; Biodiversity ; Conservation of Natural Resources/methods ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; *Genetic Variation ; Geography ; Indian Ocean ; Islands ; Phylogeny ; Reptiles/classification/*genetics/growth &amp; development ; },
abstract = {Few DNA barcoding studies of squamate reptiles have been conducted. Due to the significance of the Socotra Archipelago (a UNESCO Natural World Heritage site and a biodiversity hotspot) and the conservation interest of its reptile fauna (94% endemics), we performed the most comprehensive DNA barcoding study on an island group to date to test its applicability to specimen identification and species discovery. Reptiles constitute Socotra's most important vertebrate fauna, yet their taxonomy remains under-studied. We successfully DNA-barcoded 380 individuals of all 31 presently recognized species. The specimen identification success rate is moderate to high, and almost all species presented local barcoding gaps. The unexpected high levels of intra-specific variability found within some species suggest cryptic diversity. Species richness may be under-estimated by 13.8-54.4%. This has implications in the species' ranges and conservation status that should be considered for conservation planning. Other phylogenetic studies using mitochondrial and nuclear markers are congruent with our results. We conclude that, despite its reduced length (663 base pairs), cytochrome c oxidase 1, COI, is very useful for specimen identification and for detecting intra-specific diversity, and has a good phylogenetic signal. We recommend DNA barcoding to be applied to other biodiversity hotspots for quickly and cost-efficiently flagging species discovery, preferentially incorporated into an integrative taxonomic framework.},
}
@article {pmid26930484,
year = {2016},
author = {Crisol-Martínez, E and Moreno-Moyano, LT and Wormington, KR and Brown, PH and Stanley, D},
title = {Using Next-Generation Sequencing to Contrast the Diet and Explore Pest-Reduction Services of Sympatric Bird Species in Macadamia Orchards in Australia.},
journal = {PloS one},
volume = {11},
number = {3},
pages = {e0150159},
pmid = {26930484},
issn = {1932-6203},
mesh = {*Agriculture ; Animals ; Australia ; Birds ; *Conservation of Natural Resources ; Crops, Agricultural ; *Diet ; Ecosystem ; *Feeding Behavior ; High-Throughput Nucleotide Sequencing ; *Macadamia ; *Sympatry ; },
abstract = {Worldwide, avian communities inhabiting agro-ecosystems are threatened as a consequence of agricultural intensification. Unravelling their ecological role is essential to focus conservation efforts. Dietary analysis can elucidate bird-insect interactions and expose avian pest-reduction services, thus supporting avian conservation. In this study, we used next-generation sequencing to analyse the dietary arthropod contents of 11 sympatric bird species foraging in macadamia orchards in eastern Australia. Across all species and based on arthropod DNA sequence similarities ≥98% with records in the Barcode of Life Database, 257 operational taxonomy units were assigned to 8 orders, 40 families, 90 genera and 89 species. These taxa included 15 insect pests, 5 of which were macadamia pests. Among the latter group, Nezara viridula (Pentatomidae; green vegetable bug), considered a major pest, was present in 23% of all faecal samples collected. Results also showed that resource partitioning in this system is low, as most bird species shared large proportion of their diets by feeding primarily on lepidopteran, dipteran and arachnids. Dietary composition differed between some species, most likely because of differences in foraging behaviour. Overall, this study reached a level of taxonomic resolution never achieved before in the studied species, thus contributing to a significant improvement in the avian ecological knowledge. Our results showed that bird communities prey upon economically important pests in macadamia orchards. This study set a precedent by exploring avian pest-reduction services using next-generation sequencing, which could contribute to the conservation of avian communities and their natural habitats in agricultural systems.},
}
@article {pmid26929717,
year = {2016},
author = {Altesor, P and González, A and Schmidt, S},
title = {First report of Tequus schrottkyi (Konow) (Hymenoptera: Pergidae) in Uruguay, and information about its host plant and biology.},
journal = {Biodiversity data journal},
volume = {},
number = {4},
pages = {e7538},
pmid = {26929717},
issn = {1314-2828},
abstract = {BACKGROUND: The sawfly family Pergidae is best represented in South America, and it is the third largest family in the suborder Symphyta. Tequus is a Neotropical genus that has been reported in association with host plants of the genus Solanum (Solanaceae), with little information about the life history of its members. Tequus schrottkyi (Konow, 1906) was described from Paraguay, without any information about its biology and host plant.<br><br>NEW INFORMATION: We report the first record of T. schrottkyi from Uruguay, with information on its host plant and details of its biology. The identification was based on morphology, DNA barcode is provided to allow identification using molecular characters. This sawfly species is associated with Solanum commersonii, a native plant common in Uruguay. Tequus schrottkyi presents several generations between March and July. The larvae feed on leaves and spin a silk cocoon in the soil in which they pupate. The adults exhibit sexual dimorphism, the female being larger than the male and with a different color pattern. The eggs are laid individually in the leaf margins into the leaf tissue. The larvae are unpalatable to a generalist predator, possibly due to defensive compounds sequestered from their host plant, known to contain toxic compounds.},
}
@article {pmid26929438,
year = {2016},
author = {Garnica, S and Schön, ME and Abarenkov, K and Riess, K and Liimatainen, K and Niskanen, T and Dima, B and Soop, K and Frøslev, TG and Jeppesen, TS and Peintner, U and Kuhnert-Finkernagel, R and Brandrud, TE and Saar, G and Oertel, B and Ammirati, JF},
title = {Determining threshold values for barcoding fungi: lessons from Cortinarius (Basidiomycota), a highly diverse and widespread ectomycorrhizal genus.},
journal = {FEMS microbiology ecology},
volume = {92},
number = {4},
pages = {fiw045},
doi = {10.1093/femsec/fiw045},
pmid = {26929438},
issn = {1574-6941},
mesh = {Cortinarius/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Intergenic/*genetics ; Genetic Markers/genetics ; Mycorrhizae/*genetics ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Different distance-based threshold selection approaches were used to assess and compare use of the internal transcribed spacer (ITS) region to distinguish among 901 Cortinarius species represented by >3000 collections. Sources of error associated with genetic markers and selection approaches were explored and evaluated using MOTUs from genus and lineage based-alignments. Our study indicates that 1%-2% more species can be distinguished by using the full-length ITS barcode as compared to either the ITS1 or ITS2 regions alone. Optimal threshold values for different picking approaches and genetic marker lengths inferred from a subset of species containing major lineages ranged from 97.0% to 99.5% sequence similarity using clustering optimization and UNITE SH, and from 1% to 2% sequence dissimilarity with CROP. Errors for the optimal cutoff ranged from 0% to 70%, and these can be reduced to a maximum of 22% when excluding species lacking a barcode gap. A threshold value of 99% is suitable for distinguishing species in the majority of lineages in the genus using the entire ITS region but only 90% of the species could be identified using just the ITS1 or ITS2 region. Prior identification of species, lacking barcode gaps and their subsequent separate analyses, maximized the accuracy of threshold approaches.},
}
@article {pmid26929276,
year = {2016},
author = {Dupont, L and Porco, D and Symondson, WO and Roy, V},
title = {Hybridization relics complicate barcode-based identification of species in earthworms.},
journal = {Molecular ecology resources},
volume = {16},
number = {4},
pages = {883-894},
doi = {10.1111/1755-0998.12517},
pmid = {26929276},
issn = {1755-0998},
mesh = {Animals ; *Chimera ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Helminth/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Genetics, Population/methods ; Genotyping Techniques/*methods ; Microsatellite Repeats ; Oligochaeta/*classification/*genetics ; Phylogeny ; Proteins/genetics ; Sequence Analysis, DNA ; },
abstract = {Introgressive hybridization results in mito-nuclear discordance which could obscure the delimitation of closely related taxa. Although such events are increasingly reported, they have been poorly studied in earthworms. Here, we propose a method for investigating the degree of introgressive hybridization between three taxa of the Allolobophora chlorotica aggregate within two field populations (N = 67 and N = 105) using a reference data set including published DNA barcoding and microsatellite data of all known A. chlorotica lineages (N = 85). For this, we used both molecular phylogenetic and population genetic approaches. The test of correspondence between mitochondrial cytochrome c oxidase I (COI) lineages and clusters of nuclear microsatellite genotypes allowed individuals to be sorted in three categories (matching, admixed and nonmatching) and additional markers (mitochondrial NADH dehydrogenase subunit 1, nuclear Histone 3 and Internal transcribed Spacer Region 2) were used for phylogenetic reconstructions in order to check assignments. Although 15 admixed individuals were observed, no early-generation hybrids were detected within the two populations. Interestingly, 14 nonmatching individuals (i.e. with a mtDNA haplotype that did not correspond to their nuclear cluster) were detected, a pattern that would result after multiple generations of unidirectional hybridization of female from one taxon to male of the other taxon. Because earthworms are simultaneous hermaphrodites, these events of unidirectional hybridization suggest sterility of the male function in several crosses and highlight that some individuals can be misidentified if reliance is placed on COI barcodes alone. These findings could improve the use of these barcodes in earthworms for species delineation.},
}
@article {pmid26929271,
year = {2016},
author = {Mendoza, &#xc1;M and Torres, MF and Paz, A and Trujillo-Arias, N and López-Alvarez, D and Sierra, S and Forero, F and Gonzalez, MA},
title = {Cryptic diversity revealed by DNA barcoding in Colombian illegally traded bird species.},
journal = {Molecular ecology resources},
volume = {16},
number = {4},
pages = {862-873},
doi = {10.1111/1755-0998.12515},
pmid = {26929271},
issn = {1755-0998},
mesh = {Animals ; Birds/*classification/*genetics ; Cluster Analysis ; Colombia ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Genotype ; Sequence Analysis, DNA ; },
abstract = {Colombia is the country with the largest number of bird species worldwide, yet its avifauna is seriously threatened by habitat degradation and poaching. We built a DNA barcode library of nearly half of the bird species listed in the CITES appendices for Colombia, thereby constructing a species identification reference that will help in global efforts for controlling illegal species trade. We obtained the COI barcode sequence of 151 species based on 281 samples, representing 46% of CITES bird species registered for Colombia. The species analysed belong to nine families, where Trochilidae and Psittacidae are the most abundant ones. We sequenced for the first time the DNA barcode of 47 species, mainly hummingbirds endemic of the Northern Andes region. We found a correct match between morphological and genetic identification for 86-92% of the species analysed, depending on the cluster analysis performed (BIN, ABGD and TaxonDNA). Additionally, we identified eleven cases of high intraspecific divergence based on K2P genetic distances (up to 14.61%) that could reflect cryptic diversity. In these cases, the specimens were collected in geographically distant sites such as different mountain systems, opposite flanks of the mountain or different elevations. Likewise, we found two cases of possible hybridization and incomplete lineage sorting. This survey constitutes the first attempt to build the DNA barcode library of endangered bird species in Colombia establishing as a reference for management programs of illegal species trade, and providing major insights of phylogeographic structure that can guide future taxonomic research.},
}
@article {pmid26929112,
year = {2016},
author = {Cornejo, C and Scheidegger, C},
title = {Cyanobacterial gardens: the liverwort Frullania asagrayana acts as a reservoir of lichen photobionts.},
journal = {Environmental microbiology reports},
volume = {8},
number = {3},
pages = {352-357},
doi = {10.1111/1758-2229.12386},
pmid = {26929112},
issn = {1758-2229},
mesh = {Bacterial Proteins/genetics ; *Biodiversity ; Cluster Analysis ; Cyanobacteria/*classification/genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic ; Frullania/*microbiology ; Lichens/*microbiology ; Newfoundland and Labrador ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Cyanobacteria are important mediators of unrelated lichen species, which form epiphytic communities that share the same cyanobiont. No study to date, however, has considered the role of cyanobacteria as mediator between lichens and bryophytes. In the present study, DNA barcoding (16S rDNA, rbcLX) was used to identify filamentous cyanobacteria living in close association with members of an epiphytic liverwort-lichen community on balsam fir in Newfoundland. This study is the first to confirm the presence of Rhizonema strains in boreal forests where they are associated with the liverwort Frullania asagrayana and several lichen species. The majority of cyanobacterial haplotypes can associate with the liverwort, however, some lichen species appear to be more selective for single or closely related haplotypes. Some Rhizonema strains were found exclusively in association with boreal lichens, while others seem to be globally distributed and involved in different lichen symbioses of unrelated fungal lineages and of varying ecological traits. Complex biological interactions in a cyanobacteria-mediated guild are proposed here, which explains composition and dynamics in bryophyte and lichen-dominated epiphytic communities.},
}
@article {pmid26928769,
year = {2016},
author = {Yu, C and Mannan, AM and Yvone, GM and Ross, KN and Zhang, YL and Marton, MA and Taylor, BR and Crenshaw, A and Gould, JZ and Tamayo, P and Weir, BA and Tsherniak, A and Wong, B and Garraway, LA and Shamji, AF and Palmer, MA and Foley, MA and Winckler, W and Schreiber, SL and Kung, AL and Golub, TR},
title = {High-throughput identification of genotype-specific cancer vulnerabilities in mixtures of barcoded tumor cell lines.},
journal = {Nature biotechnology},
volume = {34},
number = {4},
pages = {419-423},
pmid = {26928769},
issn = {1546-1696},
support = {UL1DE019585/DE/NIDCR NIH HHS/United States ; UL1 DE019585/DE/NIDCR NIH HHS/United States ; U54CA112962/CA/NCI NIH HHS/United States ; RL1-GM084437/GM/NIGMS NIH HHS/United States ; RL1-CA133834/CA/NCI NIH HHS/United States ; U54 CA112962/CA/NCI NIH HHS/United States ; RL1 HG004671/HG/NHGRI NIH HHS/United States ; RL1 CA133834/CA/NCI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; RL1 GM084437/GM/NIGMS NIH HHS/United States ; RL1-HG004671/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; Cell Line, Tumor ; DNA Barcoding, Taxonomic/*methods ; Drug Resistance, Neoplasm/*genetics ; Genotyping Techniques/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Mice ; Neoplasms/*classification/*genetics ; },
abstract = {Hundreds of genetically characterized cell lines are available for the discovery of genotype-specific cancer vulnerabilities. However, screening large numbers of compounds against large numbers of cell lines is currently impractical, and such experiments are often difficult to control. Here we report a method called PRISM that allows pooled screening of mixtures of cancer cell lines by labeling each cell line with 24-nucleotide barcodes. PRISM revealed the expected patterns of cell killing seen in conventional (unpooled) assays. In a screen of 102 cell lines across 8,400 compounds, PRISM led to the identification of BRD-7880 as a potent and highly specific inhibitor of aurora kinases B and C. Cell line pools also efficiently formed tumors as xenografts, and PRISM recapitulated the expected pattern of erlotinib sensitivity in vivo.},
}
@article {pmid26926177,
year = {2016},
author = {Osathanunkul, M and Suwannapoom, C and Osathanunkul, K and Madesis, P and de Boer, H},
title = {Evaluation of DNA barcoding coupled high resolution melting for discrimination of closely related species in phytopharmaceuticals.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {23},
number = {2},
pages = {156-165},
doi = {10.1016/j.phymed.2015.11.018},
pmid = {26926177},
issn = {1618-095X},
mesh = {*DNA Barcoding, Taxonomic ; DNA Primers/genetics ; DNA, Chloroplast/genetics ; DNA, Plant/genetics ; Genetic Markers ; Plants, Medicinal/chemistry/*classification ; Quality Control ; Thailand ; },
abstract = {BACKGROUND: Phytopharmaceuticals are increasingly popular as alternative medicines, but poorly regulated in many countries. The manufacturers of these products should be subject to strict controls regarding each product's quality and constituents. Routine testing and identification of raw materials should be performed to ensure that the raw materials used in pharmaceutical products are suitable for their intended use.<br><br>HYPOTHESIS/PURPOSE: We have applied DNA Barcoding - High Resolution Melting (Bar-HRM), an emerging method for identifying of medicinal plant species based on DNA dissociation kinetics and DNA barcoding, for the authentication of medicinal plant species.<br><br>STUDY DESIGN: Commonly commercialized Thai medicinal plants that are widely used for medicinal purposes were used in this study. Publicly available sequences of four plastid markers were used for universal primer design. Species discrimination efficiency of the designed primers was evaluated as single and multi-locus analyses by using the primers sets.<br><br>METHODS: HRM analysis was performed in triplicate on each of the 26 taxa to establish the Tm for each primer set (matK, rbcLA, rbcLB, rbcLC, rpoC1, and trnL). The shapes of the melting curves were analyzed to distinguish the different plant species. Bar-HRM species identification success rates were assessed for each single-locus as well as for multi-locus combinations to establish the optimal combination of primer sets.<br><br>RESULTS: In single locus analysis the rpoC1 primer set gave the highest discrimination (58%), and in multi locus analysis this could be increased from 87% to 99% depending on the total number of regions included. Different combinations proved to be more or less effective at discrimination, depending on the genus or family examined.<br><br>CONCLUSIONS: Bar-HRM has proven to be a cost-effective and reliable method for the identification of species in this study of Thai medicinal plants, and results show an identification success rate of 99% among species in the test set.},
}
@article {pmid26923317,
year = {2016},
author = {Benizri, F and Dalifard, B and Zemmour, C and Henriquet, M and Fougereau, E and Le Franc, B},
title = {DrugCam®-An intelligent video camera system to make safe cytotoxic drug preparations.},
journal = {International journal of pharmaceutics},
volume = {502},
number = {1-2},
pages = {198-207},
doi = {10.1016/j.ijpharm.2016.02.028},
pmid = {26923317},
issn = {1873-3476},
mesh = {*Antineoplastic Agents ; Drug Compounding/*instrumentation/methods ; Drug Packaging ; Syringes ; Video Recording/*instrumentation ; },
abstract = {DrugCam(®) is a new approach to control the chemotherapy preparations with an intelligent video system that enables automatic verification during the critical stages of preparations combined with an a posteriori control with partial or total visualization of the video recording of preparations. The assessment was about the recognizing of anticancer drug vials (qualitative analysis) and syringe volumes (quantitative analysis). The qualitative analysis was conducted for a total of 120 vials with sensitivity of 100% for 84.2% of the vials and at least 97% for all the vials tested. Accuracy was at least 98.5% for all vials. The quantitative analysis was assessed by detecting 10 measures of each graduation for syringes. The identification error rate was 2.1% (244/11,640) i.e. almost 94% to the next graduation. Only 3% (35/1164) of the graduations tested, i.e. 23/35 for volume <0.13 ml of 1 ml syringes, presented a volume error outside the admissible limit of ± 5% of a confidence band constructed for the estimated linear regression line for each syringe. In addition to the vial detection model, barcodes can also read when they are present on vials. DrugCam(®) offers an innovative approach for controlling chemotherapy preparations and constitutes an optimized application of telepharmacy.},
}
@article {pmid26920298,
year = {2016},
author = {Galal-Khallaf, A and Ardura, A and Borrell, YJ and Garcia-Vazquez, E},
title = {PCR-based assessment of shellfish traceability and sustainability in international Mediterranean seafood markets.},
journal = {Food chemistry},
volume = {202},
number = {},
pages = {302-308},
doi = {10.1016/j.foodchem.2016.01.131},
pmid = {26920298},
issn = {1873-7072},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal/genetics ; Egypt ; Electron Transport Complex IV/genetics ; Penaeidae/genetics ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; Seafood ; Shellfish/*classification ; Spain ; },
abstract = {Two mitochondrial markers (cytochrome oxidase COI and 16S rDNA) were employed for species identification of commercial shellfish from two Mediterranean countries. New COI Barcodes were generated for six species: Pleoticus robustus, Metapenaeopsis barbata, Parapenaeus fissuroides, Hymenopenaeus debilis, Metapenaeus affinis and Sepia aculeata. Biodiversity of the seafood species analyzed was greater in Egypt, with nine crustacean and two cephalopod species found compared with only three crustaceans and three cephalopods in Spain. In total, 17.2% and 15.2% products were mislabeled in Egypt and Spain, respectively. Population decline is a problem for some of the substitute species. Others were exotic and/or invasive in exporters' regions. This study offers the first comparable study of shellfish traceability in these Mediterranean markets. The PCR-based method used in this study proved to be reliable, effective and, therefore, could be employed for routine seafood analysis.},
}
@article {pmid26920274,
year = {2016},
author = {Yan, S and Lai, G and Li, L and Xiao, H and Zhao, M and Wang, M},
title = {DNA barcoding reveals mislabeling of imported fish products in Nansha new port of Guangzhou, Guangdong province, China.},
journal = {Food chemistry},
volume = {202},
number = {},
pages = {116-119},
doi = {10.1016/j.foodchem.2016.01.133},
pmid = {26920274},
issn = {1873-7072},
mesh = {Animals ; China ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; *Fish Products ; *Food Labeling ; Perciformes/*classification/genetics ; Phylogeny ; },
abstract = {In the present study, we employed a DNA barcoding approach to authenticate the species of fish imported via one port in China. The fish were identified as smallmouth scad based on morphological characteristics, Alepes apercna (Perciformes, Carangidae), but were labeled as Rastrelliger brachysoma (Perciformes, Scombridae). Fragments of the partial mitochondrial cytochrome c oxidase 1 (COI) gene were sequenced from 12 specimens, and their phylogenetic relationship was subsequently examined. The phylogenetic analysis demonstrated that all of the individuals formed a monophyletic cluster with high bootstrap values and were placed in a sister group with the ancestor of Alepes vari and Alepes melanoptera. The K2P genetic distances at an intraspecific level were significantly smaller than those at an interspecific level. Our results indicated that the fish were A. apercna, rather than R. brachysoma, which confirms the morphological analysis. This study presents a practical demonstration of the use of DNA barcoding to prevent fraud in international trade.},
}
@article {pmid26917782,
year = {2016},
author = {Matsuoka, S and Mori, AS and Kawaguchi, E and Hobara, S and Osono, T},
title = {Disentangling the relative importance of host tree community, abiotic environment and spatial factors on ectomycorrhizal fungal assemblages along an elevation gradient.},
journal = {FEMS microbiology ecology},
volume = {92},
number = {5},
pages = {fiw044},
doi = {10.1093/femsec/fiw044},
pmid = {26917782},
issn = {1574-6941},
mesh = {Altitude ; Biodiversity ; Japan ; Mycorrhizae/*classification/isolation &amp; purification/physiology ; *Soil Microbiology ; Trees/classification/*microbiology/physiology ; },
abstract = {Recent studies have shown that changes in community compositions of ectomycorrhizal (ECM) fungi along elevation gradients are mainly affected by changes in host tree communities and/or in abiotic environments. However, few studies have taken the effects of processes related to fungal dispersal (i.e. spatial processes) into account and distinguished the effects of host community, abiotic environment and spatial processes on community composition along elevation gradients. This has left unclear the relative importance of these factors in structuring the ECM community assemblages. To address this, we investigated the community composition of ECM fungi along an elevation gradient in northern Japan with 454 meta-barcoding. We found that the community composition of ECM fungi changed along the elevation and that all three factors jointly affected the compositional changes. We separated the magnitude of importance of the three factors in structuring ECM fungal communities and found that most of the spatial variation in ECM fungal community was explained by host communities and abiotic environments. Our results suggest that while biotic and/or abiotic environments can be important factors in determining the ECM fungal community composition along an elevation gradient, spatial processes may also be a primary determinant.},
}
@article {pmid26915049,
year = {2016},
author = {Barley, AJ and Thomson, RC},
title = {Assessing the performance of DNA barcoding using posterior predictive simulations.},
journal = {Molecular ecology},
volume = {25},
number = {9},
pages = {1944-1957},
doi = {10.1111/mec.13590},
pmid = {26915049},
issn = {1365-294X},
mesh = {Algorithms ; Bayes Theorem ; Biodiversity ; Cluster Analysis ; *Computer Simulation ; DNA Barcoding, Taxonomic/*methods ; Models, Genetic ; Models, Statistical ; },
abstract = {Accurate estimates of biodiversity are required for research in a broad array of biological subdisciplines including ecology, evolution, systematics, conservation and biodiversity science. The use of statistical models and genetic data, particularly DNA barcoding, has been suggested as an important tool for remedying the large gaps in our current understanding of biodiversity. However, the reliability of biodiversity estimates obtained using these approaches depends on how well the statistical models that are used describe the evolutionary process underlying the genetic data. In this study, we utilize data from the Barcode of Life Database and posterior predictive simulations to assess the performance of DNA barcoding under commonly used substitution models. We demonstrate that the success of DNA barcoding varies widely across DNA substitution models and that model choice has a substantial impact on the number of operational taxonomic units identified (changing results by ~4-31%). Additionally, we demonstrate that the widely followed practice of a priori assuming the Kimura 2-parameter model for DNA barcoding is statistically unjustified and should be avoided. Using both data-based and inference-based test statistics, we detect variation in model performance across taxonomic groups, clustering algorithms, genetic divergence thresholds and substitution models. Taken together, these results illustrate the importance of considering both model selection and model adequacy in studies quantifying biodiversity.},
}
@article {pmid26912871,
year = {2016},
author = {Underwood, E},
title = {Neuroscience. Barcoding the brain.},
journal = {Science (New York, N.Y.)},
volume = {351},
number = {6275},
pages = {799-800},
doi = {10.1126/science.351.6275.799},
pmid = {26912871},
issn = {1095-9203},
mesh = {Animals ; Brain/*physiology ; Brain Mapping/economics/*methods ; DNA/*analysis ; Financing, Organized ; Fluorescence ; Mice ; Nerve Net/physiology ; Neurons/*chemistry ; Neurosciences/economics/trends ; RNA/*analysis ; Synapses/*physiology ; },
}
@article {pmid26909979,
year = {2016},
author = {Moon, BC and Kim, WJ and Ji, Y and Lee, YM and Kang, YM and Choi, G},
title = {Molecular identification of the traditional herbal medicines, Arisaematis Rhizoma and Pinelliae Tuber, and common adulterants via universal DNA barcode sequences.},
journal = {Genetics and molecular research : GMR},
volume = {15},
number = {1},
pages = {},
doi = {10.4238/gmr.15017064},
pmid = {26909979},
issn = {1676-5680},
mesh = {Arisaema/classification/*genetics ; Base Sequence ; *DNA Barcoding, Taxonomic ; *Genes, Plant ; Molecular Sequence Data ; Phylogeny ; Pinellia/classification/*genetics ; Plants, Medicinal/classification/*genetics ; },
abstract = {Methods to identify Pinelliae Tuber and Arisaematis Rhizoma are required because of frequent reciprocal substitution between these two herbal medicines and the existence of several closely related plant materials. As a result of the morphological similarity of dried tubers, correct discrimination of authentic herbal medicines is difficult by conventional methods. Therefore, we analyzed DNA barcode sequences to identify each herbal medicine and the common adulterants at a species level. To verify the identity of these herbal medicines, we collected five authentic species (Pinellia ternata for Pinelliae Tuber, and Arisaema amurense, A. amurense var. serratum, A. erubescens, and A. heterophyllum for Arisaematis Rhizoma) and six common adulterant plant species. Maturase K (matK) and ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) genes were then amplified using universal primers. In comparative analyses of two DNA barcode sequences, we obtained 45 species-specific nucleotides sufficient to identify each species (except A. erubescens with matK) and 28 marker nucleotides for each species (except P. pedatisecta with rbcL). Sequence differences at corresponding positions of the two combined DNA barcodes provided genetic marker nucleotides that could be used to identify specimens of the correct species among the analyzed medicinal plants. Furthermore, we generated a phylogenetic tree showing nine distinct groups depending on the species. These results can be used to authenticate Pinelliae Tuber and Arisaematis Rhizoma from their adulterants and to identify each species. Thus, comparative analyses of plant DNA barcode sequences identified useful genetic markers for the authentication of Pinelliae Tuber and Arisaematis Rhizoma from several adulterant herbal materials.},
}
@article {pmid26909963,
year = {2016},
author = {Souza, HV and Marchesin, SR and Itoyama, MM},
title = {Analysis of the mitochondrial COI gene and its informative potential for evolutionary inferences in the families Coreidae and Pentatomidae (Heteroptera).},
journal = {Genetics and molecular research : GMR},
volume = {15},
number = {1},
pages = {},
doi = {10.4238/gmr.15017428},
pmid = {26909963},
issn = {1676-5680},
mesh = {Animals ; Electron Transport Complex IV/*genetics ; *Evolution, Molecular ; *Genes, Mitochondrial ; Heteroptera/genetics/*metabolism ; Insect Proteins/genetics ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The mitochondrial cytochrome oxidase subunit 1 (COI) gene is one of the most popular markers used for molecular systematics. Fragments of this gene are often used to infer phylogenies, particularly the region near the 5'-end, which is used by the DNA Barcoding Consortium. With a growing number of sequences being deposited in the DNA barcoding database, there is an urgent need to understand the evolution of this gene and its evolutionary relationship among species; it is also important to analyze the informative potential of the gene for phylogenetic inferences for each group used. In this study, the COI gene was divided into three distinct regions: a 5'-region, a central region, and a 3'-region. The nucleotide composition of these regions was analyzed, and their potential for making informative phylogenetic inferences using species in the families Coreidae and Pentatomidae (Heteroptera) was assessed. It was found that the same region in the COI gene may present different behaviors for each family analyzed, and that using additional regions from the same gene may even prejudice the analysis.},
}
@article {pmid26909907,
year = {2016},
author = {Osathanunkul, M and Madesis, P and Ounjai, S and Pumiputavon, K and Somboonchai, R and Lithanatudom, P and Chaowasku, T and Wipasa, J and Suwannapoom, C},
title = {Identification of Uvaria sp by barcoding coupled with high-resolution melting analysis (Bar-HRM).},
journal = {Genetics and molecular research : GMR},
volume = {15},
number = {1},
pages = {},
doi = {10.4238/gmr.15017405},
pmid = {26909907},
issn = {1676-5680},
mesh = {*DNA Barcoding, Taxonomic ; *DNA, Chloroplast ; Nucleic Acid Denaturation ; Uvaria/classification/*genetics ; },
abstract = {DNA barcoding, which was developed about a decade ago, relies on short, standardized regions of the genome to identify plant and animal species. This method can be used to not only identify known species but also to discover novel ones. Numerous sequences are stored in online databases worldwide. One of the ways to save cost and time (by omitting the sequencing step) in species identification is to use available barcode data to design optimized primers for further analysis, such as high-resolution melting analysis (HRM). This study aimed to determine the effectiveness of the hybrid method Bar-HRM (DNA barcoding combined with HRM) to identify species that share similar external morphological features, rather than conduct traditional taxonomic identification that require major parts (leaf, flower, fruit) of the specimens. The specimens used for testing were those, which could not be identified at the species level and could either be Uvaria longipes or Uvaria wrayias, indicated by morphological identification. Primer pairs derived from chloroplast regions (matK, psbA-trnH, rbcL, and trnL) were used in the Bar-HRM. The results obtained from psbA-trnH primers were good enough to help in identifying the specimen while the rest were not. Bar-HRM analysis was proven to be a fast and cost-effective method for plant species identification.},
}
@article {pmid26909185,
year = {2016},
author = {Vartia, S and Villanueva-Cañas, JL and Finarelli, J and Farrell, ED and Collins, PC and Hughes, GM and Carlsson, JE and Gauthier, DT and McGinnity, P and Cross, TF and FitzGerald, RD and Mirimin, L and Crispie, F and Cotter, PD and Carlsson, J},
title = {A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding.},
journal = {Royal Society open science},
volume = {3},
number = {1},
pages = {150565},
pmid = {26909185},
issn = {2054-5703},
abstract = {This study examines the potential of next-generation sequencing based 'genotyping-by-sequencing' (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal primers. Three experimental conditions were employed to explore the possibility of using this approach with existing and novel multiplex marker panels and weighted amplicon mixture. The GBS approach was validated against microsatellite data generated by capillary electrophoresis. GBS allows access to the underlying nucleotide sequences that can reveal homoplasy, even in large datasets and facilitates cross laboratory transfer. GBS of microsatellites, using individual combinatorial barcoding, is potentially faster and cheaper than current microsatellite approaches and offers better and more data.},
}
@article {pmid26903803,
year = {2016},
author = {McNally, AG and Poplawski, SG and Mayweather, BA and White, KM and Abel, T},
title = {Characterization of a Novel Chromatin Sorting Tool Reveals Importance of Histone Variant H3.3 in Contextual Fear Memory and Motor Learning.},
journal = {Frontiers in molecular neuroscience},
volume = {9},
number = {},
pages = {11},
pmid = {26903803},
issn = {1662-5099},
support = {R21 MH102679/MH/NIMH NIH HHS/United States ; T32 GM008076/GM/NIGMS NIH HHS/United States ; },
abstract = {The consolidation of short-term labile memories for long-term storage requires transcription and there is growing interest in defining the epigenetic mechanisms regulating these transcriptional events. In particular, it has been hypothesized that combinations of histone post-translational modifications (PTMs) have the potential to store memory by dynamically defining the transcriptional status of any given gene loci. Studying epigenetic phenomena during long-term memory consolidation, however, is complicated by the complex cellular heterogeneity of the brain, in which epigenetic signal from memory-relevant cells can be obscured or diluted by the surrounding milieu. To address this issue, we have developed a transgenic mouse line expressing a tetO-regulated, hemagglutinin (HA)-tagged histone H3.3 exclusively in excitatory neurons of the forebrain. Unlike canonical histones, histone H3.3 is incorporated at promoter regions of transcriptionally active genes in a DNA replication-independent manner, stably "barcoding" active regions of the genome in post-mitotic cells. Immunoprecipitating H3.3-HA containing nucleosomes from the hippocampus will therefore enrich for memory-relevant chromatin by isolating actively transcribed regions of the excitatory neuron genome. To evaluate the validity of using H3.3 "barcoding" to sort chromatin, we performed a molecular and behavioral characterization of the H3.3-HA transgenic mouse line. Expectedly, we find that H3.3-HA is incorporated preferentially at promoter regions of actively-transcribed neuronal genes and that expression can be effectively regulated by doxycycline. Additionally, H3.3-HA overexpression does not adversely affect exploratory or anxiety-related behaviors, nor does it affect spatial memory. Transgenic animals do, however, exhibit deficits in contextual memory and motor learning, revealing the importance of this histone isoform in the brain. Future studies in the H3.3-HA transgenic mouse line will define the combinatorial histone PTM landscape during spatial memory consolidation and will investigate the important contributions of histone H3.3 to the normal functioning of the brain.},
}
@article {pmid26902862,
year = {2016},
author = {Han, EH and Cho, K and Goo, Y and Kim, M and Shin, YW and Kim, YH and Lee, SW},
title = {Development of molecular markers, based on chloroplast and ribosomal DNA regions, to discriminate three popular medicinal plant species, Cynanchum wilfordii, Cynanchum auriculatum, and Polygonum multiflorum.},
journal = {Molecular biology reports},
volume = {43},
number = {4},
pages = {323-332},
pmid = {26902862},
issn = {1573-4978},
mesh = {Base Sequence ; Cynanchum/classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Chloroplast/genetics ; DNA, Plant/*genetics ; DNA, Ribosomal Spacer/*genetics ; Fallopia multiflora/classification/*genetics ; Molecular Sequence Data ; Plants, Medicinal/classification/genetics ; *Polymorphism, Single Nucleotide ; Real-Time Polymerase Chain Reaction ; Sequence Alignment ; },
abstract = {Identification of plant species is important for standardizing herbal medicine. Cynanchum wilfordii (Baekshuoh in Korean) and Polygonum multiflorum (Hashuoh in Korean) are important oriental medicinal herbs in Korea, Japan, and China. Cynanchum auriculatum is a faster growing and more productive plant than C. wilfordii; and, it is not recognized as a medicinal plant in the Korean Pharmacopoeia. C. wilfordii, P. multiflorum, and C. auriculatum are often misidentified in the Korean herbal medicine marketplace due to their morphological similarities and similar names. In this study, we investigated molecular authentication of these three medicinal plants using DNA sequences in the TrnL-F chloroplast intergenic region. Specific species identification was achieved by detecting allelic variations of single nucleotide polymorphisms (SNPs) using amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) and high resolution melting curve analysis. Our results demonstrate that the intraspecific genetic distance between C. wilfordii and C. auriculatum is relatively low. We also developed a quantitative PCR assay using species-specific TrnL-F primers, which allowed us to estimate the ratio of C. wilfordii and C. auriculatum using varying ratios of mixed genomic DNA template from the two species. Additionally, to identify species in hybrid plants produced by cross-fertilization, we analyzed nuclear ribosomal DNA internal transcribed spacer regions in C. wilfordii and C. auriculatum by ARMS-PCR. Our results indicate that SNP-based molecular markers, usable to barcode tools could provide efficient and rapid authentication of these closely related medicinal plant species, and will be useful for preventing the distribution of products contaminated with adulterants.},
}
@article {pmid26900844,
year = {2016},
author = {Hadi, SI and Santana, H and Brunale, PP and Gomes, TG and Oliveira, MD and Matthiensen, A and Oliveira, ME and Silva, FC and Brasil, BS},
title = {DNA Barcoding Green Microalgae Isolated from Neotropical Inland Waters.},
journal = {PloS one},
volume = {11},
number = {2},
pages = {e0149284},
pmid = {26900844},
issn = {1932-6203},
mesh = {Brazil ; Chlorophyta/*classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Plant ; DNA, Ribosomal Spacer ; Genetic Markers ; Microalgae/*classification/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {This study evaluated the feasibility of using the Ribulose Bisphosphate Carboxylase Large subunit gene (rbcL) and the Internal Transcribed Spacers 1 and 2 of the nuclear rDNA (nuITS1 and nuITS2) markers for identifying a very diverse, albeit poorly known group, of green microalgae from neotropical inland waters. Fifty-one freshwater green microalgae strains isolated from Brazil, the largest biodiversity reservoir in the neotropics, were submitted to DNA barcoding. Currently available universal primers for ITS1-5.8S-ITS2 region amplification were sufficient to successfully amplify and sequence 47 (92%) of the samples. On the other hand, new sets of primers had to be designed for rbcL, which allowed 96% of the samples to be sequenced. Thirty-five percent of the strains could be unambiguously identified to the species level based either on nuITS1 or nuITS2 sequences' using barcode gap calculations. nuITS2 Compensatory Base Change (CBC) and ITS1-5.8S-ITS2 region phylogenetic analysis, together with morphological inspection, confirmed the identification accuracy. In contrast, only 6% of the strains could be assigned to the correct species based solely on rbcL sequences. In conclusion, the data presented here indicates that either nuITS1 or nuITS2 are useful markers for DNA barcoding of freshwater green microalgae, with advantage for nuITS2 due to the larger availability of analytical tools and reference barcodes deposited at databases for this marker.},
}
@article {pmid26899167,
year = {2016},
author = {Zou, S and Li, Q},
title = {Pay Attention to the Overlooked Cryptic Diversity in Existing Barcoding Data: the Case of Mollusca with Character-Based DNA Barcoding.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {18},
number = {3},
pages = {327-335},
pmid = {26899167},
issn = {1436-2236},
mesh = {Animals ; *Biodiversity ; Conservation of Natural Resources ; DNA/genetics ; DNA Barcoding, Taxonomic/*statistics &amp; numerical data ; Electron Transport Complex IV ; *Genetic Speciation ; Genetic Variation ; Mollusca/*classification/genetics ; *Phylogeny ; Species Specificity ; },
abstract = {With the global biodiversity crisis, DNA barcoding aims for fast species identification and cryptic species diversity revelation. For more than 10 years, large amounts of DNA barcode data have been accumulating in publicly available databases, most of which were conducted by distance or tree-building methods that have often been argued, especially for cryptic species revelation. In this context, overlooked cryptic diversity may exist in the available barcoding data. The character-based DNA barcoding, however, has a good chance for detecting the overlooked cryptic diversity. In this study, marine mollusk was as the ideal case for detecting the overlooked potential cryptic species from existing cytochrome c oxidase I (COI) sequences with character-based DNA barcode. A total of 1081 COI sequences of mollusks, belonging to 176 species of 25 families of Gastropoda, Cephalopoda, and Lamellibranchia, were conducted by character analysis. As a whole, the character-based barcoding results were consistent with previous distance and tree-building analysis for species discrimination. More importantly, quite a number of species analyzed were divided into distinct clades with unique diagnostical characters. Based on the concept of cryptic species revelation of character-based barcoding, these species divided into separate taxonomic groups might be potential cryptic species. The detection of the overlooked potential cryptic diversity proves that the character-based barcoding mode possesses more advantages of revealing cryptic biodiversity. With the development of DNA barcoding, making the best use of barcoding data is worthy of our attention for species conservation.},
}
@article {pmid26896098,
year = {2016},
author = {Leal, MC and Ferrier-Pagès, C},
title = {Molecular trophic markers in marine food webs and their potential use for coral ecology.},
journal = {Marine genomics},
volume = {29},
number = {},
pages = {1-7},
doi = {10.1016/j.margen.2016.02.003},
pmid = {26896098},
issn = {1876-7478},
mesh = {Animals ; Anthozoa/*physiology ; Biomarkers/*analysis ; Ecology/*methods ; *Food Chain ; Marine Biology/*methods ; },
abstract = {Notable advances in ecological genomics have been driven by high-throughput sequencing technology and taxonomically broad sequence repositories that allow us to accurately assess species interactions with great taxonomic resolution. The use of DNA as a marker for ingested food is particularly relevant to address predator-prey interactions and disentangle complex marine food webs. DNA-based methods benefit from reductionist molecular approaches to address ecosystem scale processes, such as community structure and energy flow across trophic levels, among others. Here we review how molecular trophic markers have been used to better understand trophic interactions in the marine environment and their advantages and limitations. We focus on animal groups where research has been focused, such as marine mammals, seabirds, fishes, pelagic invertebrates and benthic invertebrates, and use case studies to illustrate how DNA-based methods unraveled food-web interactions. The potential of molecular trophic markers for disentangling the complex trophic ecology of corals is also discussed.},
}
@article {pmid26884709,
year = {2016},
author = {Tagane, S and Nguyen, VH and Ngoc, NV and Son, HT and Toyama, H and Yang, CJ and Yahara, T},
title = {Homalium glandulosum (Salicaceae), a new species from Vu Quang National Park, North Central Vietnam.},
journal = {PhytoKeys},
volume = {},
number = {58},
pages = {97-104},
pmid = {26884709},
issn = {1314-2011},
abstract = {Homalium glandulosum Tagane &amp; V. H. Nguyen, from Vu Quang National Park in northern Vietnam, is newly described. This species is characterized by distinct glands, often stalked, at the base of the lamina and along the margin of the stipules and bracteoles. Illustrations, DNA barcodes of the two regions of rbcL and matK, and a key to the species of Homalium in Vietnam are also provided.},
}
@article {pmid26881847,
year = {2016},
author = {De Luca, D and Catanese, G and Procaccini, G and Fiorito, G},
title = {Octopus vulgaris (Cuvier, 1797) in the Mediterranean Sea: Genetic Diversity and Population Structure.},
journal = {PloS one},
volume = {11},
number = {2},
pages = {e0149496},
pmid = {26881847},
issn = {1932-6203},
mesh = {Alleles ; Animals ; DNA Barcoding, Taxonomic ; Discriminant Analysis ; Genetic Loci ; *Genetic Variation ; *Genetics, Population ; Geography ; Mediterranean Sea ; Microsatellite Repeats/genetics ; Octopodiformes/*genetics ; Principal Component Analysis ; },
abstract = {The common octopus, Octopus vulgaris Cuvier 1797, is a largely exploited cephalopod species in the Mediterranean Sea and the Atlantic Ocean, as well as along the coasts of Africa, Brazil and Japan, where its taxonomic identity is still debated. The assessment of its genetic structure is a pressing need to correctly manage the resource and to avoid overfishing and collapsing of local stocks. Here we analysed genetic variation and population structure of O. vulgaris using thirteen microsatellite loci in seven sampling localities from the Mediterranean Sea and one from the Atlantic Ocean. We also used a DNA barcoding approach by COI gene fragment to understand the phylogenetic relationships among the specimens here investigated and the ones whose sequences are available in literature. Our results reveal high levels of allelic richness and moderate heterozygosity in all samples investigated, and a pronounced differentiation of the Atlantic and Sicilian specimens. This latter aspect seems to support the isolation of the biota within the Strait of Messina. A certain degree of differentiation was detected among the other geographic samples within the Mediterranean Sea, which is more compatible with an island model than isolation by distance. The occurrence of null alleles affected more genetic diversity indices than population structure estimations. This study provides new insights about the genetic diversity and structure of O. vulgaris in the area of interest, which can be used as guidelines for a fisheries management perspective.},
}
@article {pmid26880378,
year = {2016},
author = {Zhao, ZH and Cui, BY and Li, ZH and Jiang, F and Yang, QQ and Kučerová, Z and Stejskal, V and Opit, G and Cao, Y and Li, FJ},
title = {The establishment of species-specific primers for the molecular identification of ten stored-product psocids based on ITS2 rDNA.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {21022},
pmid = {26880378},
issn = {2045-2322},
mesh = {Animals ; *DNA, Intergenic ; *DNA, Ribosomal ; Evolution, Molecular ; Insecta/*classification/*genetics ; Species Specificity ; },
abstract = {Psocids are important stored product pests found worldwide that can be spread through grain trade. Most stored-product psocids, including eggs, nymphs, and adults, are very small (~1 mm) and difficult to identify morphologically. Here, we collected 10 economically important stored-product Liposcelis spp. psocids (L. bostrychophila, L. entomophila, L. decolor, L. paeta, L. brunnea, L. corrodens, L. mendax, L. rufa, L. pearmani, and L. tricolor) from 35 geographical locations in 5 countries (China, Czech Republic, Denmark, Germany, and the United States). The ITS2 rDNA gene was extracted and sequenced. The interspecific genetic distance of the stored-product psocids was significantly higher than the intraspecific genetic distance according to the barcoding gap analysis. Ten pairs of species-specific primers based on the ITS2 rDNA were developed for psocid identification. The sensitivity estimation indicated that the species-specific primers could correctly amplify the target ITS2 gene and successfully identify psocids at 1.0 ng/mL. Additionally, these species-specific primers could quantify specificity and identify 10 stored-product psocids; this approach could also be used to accurately identify other stored-product psocids. This work provides a practical approach for the precise examination of 10 stored-product psocid species and also contributes to the development of an identification method using ITS2 rDNA.},
}
@article {pmid26880148,
year = {2016},
author = {Papakostas, S and Michaloudi, E and Proios, K and Brehm, M and Verhage, L and Rota, J and Peña, C and Stamou, G and Pritchard, VL and Fontaneto, D and Declerck, SA},
title = {Integrative Taxonomy Recognizes Evolutionary Units Despite Widespread Mitonuclear Discordance: Evidence from a Rotifer Cryptic Species Complex.},
journal = {Systematic biology},
volume = {65},
number = {3},
pages = {508-524},
doi = {10.1093/sysbio/syw016},
pmid = {26880148},
issn = {1076-836X},
mesh = {Animals ; Bayes Theorem ; DNA, Ribosomal Spacer/genetics ; Genes, Mitochondrial/*genetics ; Genetic Markers/genetics ; Hybridization, Genetic ; *Phylogeny ; RNA, Ribosomal, 28S/genetics ; Rotifera/*classification/genetics ; Species Specificity ; },
abstract = {Mitonuclear discordance across taxa is increasingly recognized as posing a major challenge to species delimitation based on DNA sequence data. Integrative taxonomy has been proposed as a promising framework to help address this problem. However, we still lack compelling empirical evidence scrutinizing the efficacy of integrative taxonomy in relation to, for instance, complex introgression scenarios involving many species. Here, we report remarkably widespread mitonuclear discordance between about 15 mitochondrial and 4 nuclear Brachionus calyciflorus groups identified using different species delimitation approaches. Using coalescent-, Bayesian admixture-, and allele sharing-based methods with DNA sequence or microsatellite data, we provide strong evidence in support of hybridization as a driver of the observed discordance. We then describe our combined molecular, morphological, and ecological approaches to resolving phylogenetic conflict and inferring species boundaries. Species delimitations based on the ITS1 and 28S nuclear DNA markers proved a more reliable predictor of morphological variation than delimitations using the mitochondrial COI gene. A short-term competition experiment further revealed systematic differences in the competitive ability between two of the nuclear-delimited species under six different growth conditions, independent of COI delimitations; hybrids were also observed. In light of these findings, we discuss the failure of the COI marker to estimate morphological stasis and morphological plasticity in the B. calyciflorus complex. By using B. calyciflorus as a representative case, we demonstrate the potential of integrative taxonomy to guide species delimitation in the presence of mitonuclear phylogenetic conflicts.},
}
@article {pmid26877696,
year = {2016},
author = {Riedel, A and Tänzler, R},
title = {Revision of the Australian species of the weevil genus Trigonopterus Fauvel.},
journal = {ZooKeys},
volume = {},
number = {556},
pages = {97-162},
pmid = {26877696},
issn = {1313-2989},
abstract = {The Australian species of the genus Trigonopterus Fauvel are revised. Eight previously recognized species are redescribed and 24 additional new species are described: Trigonopterus allaetus Riedel, sp. n., Trigonopterus athertonensis Riedel, sp. n., Trigonopterus australinasutus Riedel, sp. n., Trigonopterus australis Riedel, sp. n., Trigonopterus bisignatus Riedel, sp. n., Trigonopterus bisinuatus Riedel, sp. n., Trigonopterus boolbunensis Riedel, sp. n., Trigonopterus cooktownensis Riedel, sp. n., Trigonopterus daintreensis Riedel, sp. n., Trigonopterus deplanatus Riedel, sp. n., Trigonopterus finniganensis Riedel, sp. n., Trigonopterus fraterculus Riedel, sp. n., Trigonopterus garradungensis Riedel, sp. n., Trigonopterus hasenpuschi Riedel, sp. n., Trigonopterus hartleyensis Riedel, sp. n., Trigonopterus kurandensis Riedel, sp. n., Trigonopterus lewisensis Riedel, sp. n., Trigonopterus montanus Riedel, sp. n., Trigonopterus monteithi Riedel, sp. n., Trigonopterus mossmanensis Riedel, sp. n., Trigonopterus oberprieleri Riedel, sp. n., Trigonopterus robertsi Riedel, sp. n., Trigonopterus terraereginae Riedel, sp. n., Trigonopterus yorkensis Riedel, sp. n.. All new species are authored by the taxonomist-in-charge, Alexander Riedel. Lectotypes are designated for the following names: Idotasia aequalis Pascoe, Idotasia albidosparsa Lea, Idotasia evanida Pascoe, Idotasia laeta Lea, Idotasia rostralis Lea, Idotasia sculptirostris Lea, Idotasia squamosa Lea. A new combination of the name Idotasia striatipennis Lea is proposed: Trigonopterus striatipennis (Lea), comb. n.. A key to the species is provided. Australian Trigonopterus occur in coastal Queensland, narrowly crossing into New South Wales. The southern parts of the range are inhabited by species found on foliage. A rich fauna of 19 edaphic species inhabiting the leaf litter of tropical forests is reported for the first time from the Australian Wet Tropics.},
}
@article {pmid26877685,
year = {2016},
author = {Starrett, J and Derkarabetian, S and Richart, CH and Cabrero, A and Hedin, M},
title = {A new monster from southwest Oregon forests: Cryptomaster behemoth sp. n. (Opiliones, Laniatores, Travunioidea).},
journal = {ZooKeys},
volume = {},
number = {555},
pages = {11-35},
pmid = {26877685},
issn = {1313-2989},
abstract = {The monotypic genus Cryptomaster Briggs, 1969 was described based on individuals from a single locality in southwestern Oregon. The described species Cryptomaster leviathan Briggs, 1969 was named for its large body size compared to most travunioid Laniatores. However, as the generic name suggests, Cryptomaster are notoriously difficult to find, and few subsequent collections have been recorded for this genus. Here, we increase sampling of Cryptomaster to 15 localities, extending their known range from the Coast Range northeast to the western Cascade Mountains of southern Oregon. Phylogenetic analyses of mitochondrial and nuclear DNA sequence data reveal deep phylogenetic breaks consistent with independently evolving lineages. We use discovery and validation species delimitation approaches to generate and test species hypotheses, including a coalescent species delimitation method to test multi-species hypotheses. For delimited species, we use light microscopy and SEM to discover diagnostic morphological characters. Although Cryptomaster has a small geographic distribution, this taxon is consistent with other short-range endemics in having deep phylogenetic breaks indicative of species level divergences. Herein we describe Cryptomaster behemoth sp. n., and provide morphological diagnostic characters for identifying Cryptomaster leviathan and Cryptomaster behemoth.},
}
@article {pmid26877679,
year = {2016},
author = {Schneider, C and Porco, D and Deharveng, L},
title = {Two new Megalothorax species of the minimus group (Collembola, Neelidae).},
journal = {ZooKeys},
volume = {},
number = {554},
pages = {37-68},
pmid = {26877679},
issn = {1313-2989},
abstract = {Two new Megalothorax species, Megalothorax potapovi sp. n. from the Russian Far East and Megalothorax sanguineus sp. n. from the French Pyrénées are described. The two new species have a set of morphological characters (including a smooth mucro) that places them among the minimus group sensu Schneider and D'Haese (2013). Megalothorax potapovi characteristics include dorsal protuberance on forehead, peculiar chaetotaxy of antenna III and strong lanceolate chaetae on body. Megalothorax sanguineus characteristics include strong red pigmentation, large network of integumentary channels on head and elongated apex of the two postero-distal spines of dens. The DNA barcodes (cytochrome oxidase subunit I-COI) of the two species are also provided and analyzed among a broader sampling of the genus in order to support further their specific status. A special focus is given to the labral morphological characteristics. Pseudopores-like elements are reported for the first time in the genus. Positions of the τ-chaetae near the dorsal sensory field of thorax II are compared for several species of the genus.},
}
@article {pmid26877675,
year = {2016},
author = {Jiang, N and Liu, S and Xue, D and Han, H},
title = {A review of Cyclidiinae from China (Lepidoptera, Drepanidae).},
journal = {ZooKeys},
volume = {},
number = {553},
pages = {119-148},
pmid = {26877675},
issn = {1313-2989},
abstract = {The subfamily Cyclidiinae from China is reviewed: two genera and seven species are reported from China. One new subspecies, Cyclidia fractifasciata indistincta subsp. n., is described. Two new synonyms are established: Cyclidia substigmaria (Hübner, 1831) (= Cyclidia substigmaria brunna Chu &amp; Wang, 1987, syn. n. = Cyclidia tetraspota Chu &amp; Wang, 1987, syn. n.). One misidentification in Chu &amp; Wang (1987) is corrected. Identification keys and diagnoses for all discussed Chinese species are provided. External features and genitalia are depicted. In addition, results of DNA barcoding for five taxa of Cyclidia are briefly discussed.},
}
@article {pmid26876495,
year = {2016},
author = {Borges, LM and Hollatz, C and Lobo, J and Cunha, AM and Vilela, AP and Calado, G and Coelho, R and Costa, AC and Ferreira, MS and Costa, MH and Costa, FO},
title = {With a little help from DNA barcoding: investigating the diversity of Gastropoda from the Portuguese coast.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {20226},
pmid = {26876495},
issn = {2045-2322},
mesh = {Animal Distribution ; Animals ; Atlantic Ocean ; Bayes Theorem ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Gastropoda/classification/*genetics ; *Phylogeny ; Portugal ; },
abstract = {The Gastropoda is one of the best studied classes of marine invertebrates. Yet, most species have been delimited based on morphology only. The application of DNA barcodes has shown to be greatly useful to help delimiting species. Therefore, sequences of the cytochrome c oxidase I gene from 108 specimens of 34 morpho-species were used to investigate the molecular diversity within the gastropods from the Portuguese coast. To the above dataset, we added available COI-5P sequences of taxonomically close species, in a total of 58 morpho-species examined. There was a good match between ours and sequences from independent studies, in public repositories. We found 32 concordant (91.4%) out of the 35 Barcode Index Numbers (BINs) generated from our sequences. The application of a ranking system to the barcodes yield over 70% with top taxonomic congruence, while 14.2% of the species barcodes had insufficient data. In the majority of the cases, there was a good concordance between morphological identification and DNA barcodes. Nonetheless, the discordance between morphological and molecular data is a reminder that even the comparatively well-known European marine gastropods can benefit from being probed using the DNA barcode approach. Discordant cases should be reviewed with more integrative studies.},
}
@article {pmid26876232,
year = {2016},
author = {Hoffmann, C and Schubert, G and Calvignac-Spencer, S},
title = {Aquatic biodiversity assessment for the lazy.},
journal = {Molecular ecology},
volume = {25},
number = {4},
pages = {846-848},
doi = {10.1111/mec.13535},
pmid = {26876232},
issn = {1365-294X},
mesh = {Amphibians/*classification ; Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Fishes/*classification ; },
abstract = {The world is covered in DNA. In any ecosystem, extracellular DNA fragments can be found that once formed the genomes of a variety of micro- and macroorganisms. A few years ago, it was proposed to use this environmental DNA (eDNA) as a source of information on local vertebrate biodiversity (Ficetola et al. 2008; Taberlet et al. 2012). This idea offered an elegant solution to take up the gauntlet of rapidly increasing monitoring needs. Coupled with barcoding efforts, it promised to be cost-efficient in many respects, for example man-hours and taxonomic expertise. Ecologists and conservation biologists with an interest in aquatic ecosystems have enthusiastically adopted and pioneered this new method, producing dozens of eDNA studies. Most of these studies have, however, focused on a single or a few aquatic species. In this issue of Molecular Ecology, Valentini et al. (2016) move the field a step further by demonstrating that metabarcoding approaches - which simultaneously target large groups of organisms such as amphibians or fish - can match and sometimes even outperform other inventory methods.},
}
@article {pmid26868331,
year = {2016},
author = {Nadimi, M and Daubois, L and Hijri, M},
title = {Mitochondrial comparative genomics and phylogenetic signal assessment of mtDNA among arbuscular mycorrhizal fungi.},
journal = {Molecular phylogenetics and evolution},
volume = {98},
number = {},
pages = {74-83},
doi = {10.1016/j.ympev.2016.01.009},
pmid = {26868331},
issn = {1095-9513},
mesh = {DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; *Genomics ; Glomeromycota/classification/*genetics ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Mycorrhizae/classification/*genetics ; *Phylogeny ; },
abstract = {Mitochondrial (mt) genes, such as cytochrome C oxidase genes (cox), have been widely used for barcoding in many groups of organisms, although this approach has been less powerful in the fungal kingdom due to the rapid evolution of their mt genomes. The use of mt genes in phylogenetic studies of Dikarya has been met with success, while early diverging fungal lineages remain less studied, particularly the arbuscular mycorrhizal fungi (AMF). Advances in next-generation sequencing have substantially increased the number of publically available mtDNA sequences for the Glomeromycota. As a result, comparison of mtDNA across key AMF taxa can now be applied to assess the phylogenetic signal of individual mt coding genes, as well as concatenated subsets of coding genes. Here we show comparative analyses of publically available mt genomes of Glomeromycota, augmented with two mtDNA genomes that were newly sequenced for this study (Rhizophagus irregularis DAOM240159 and Glomus aggregatum DAOM240163), resulting in 16 complete mtDNA datasets. R. irregularis isolate DAOM240159 and G. aggregatum isolate DAOM240163 showed mt genomes measuring 72,293bp and 69,505bp with G+C contents of 37.1% and 37.3%, respectively. We assessed the phylogenies inferred from single mt genes and complete sets of coding genes, which are referred to as "supergenes" (16 concatenated coding genes), using Shimodaira-Hasegawa tests, in order to identify genes that best described AMF phylogeny. We found that rnl, nad5, cox1, and nad2 genes, as well as concatenated subset of these genes, provided phylogenies that were similar to the supergene set. This mitochondrial genomic analysis was also combined with principal coordinate and partitioning analyses, which helped to unravel certain evolutionary relationships in the Rhizophagus genus and for G. aggregatum within the Glomeromycota. We showed evidence to support the position of G. aggregatum within the R. irregularis 'species complex'.},
}
@article {pmid26865235,
year = {2016},
author = {Lane, HS and Webb, SC and Duncan, J},
title = {Bonamia ostreae in the New Zealand oyster Ostrea chilensis: a new host and geographic record for this haplosporidian parasite.},
journal = {Diseases of aquatic organisms},
volume = {118},
number = {1},
pages = {55-63},
doi = {10.3354/dao02960},
pmid = {26865235},
issn = {0177-5103},
mesh = {Animals ; Haplosporida/*physiology ; Host-Parasite Interactions ; New Zealand ; Ostrea/*parasitology ; },
abstract = {Previous reports of the haplosporidian parasite Bonamia ostreae have been restricted to the Northern Hemisphere, including Europe, and both eastern and western North America. This species is reported for the first time in New Zealand infecting the flat oyster Ostrea chilensis. Histological examination of 149 adult oysters identified 119 (79.9%) infected with Bonamia microcells. Bonamia generic PCR of several oysters followed by DNA sequencing of a 300 bp portion of the 18S rDNA gene produced a 100% match with that of B. ostreae. All DNA-sequenced products also produced a B. ostreae PCR-restriction fragment length polymorphism (PCR-RFLP) profile. Bonamia species-specific PCRs further detected single infections of B. exitiosa (2.7%), B. ostreae (40.3%), and concurrent infections (53.7%) with these 2 Bonamia species identifying overall a Bonamia prevalence of 96.6%. Detailed histological inspection revealed 2 microcell types. An infection identified by PCR as B. ostreae histologically presented small microcells (mean ± SE diameter = 1.28 ± 0.16 µm, range = 0.9-2 µm, n = 60) commonly with eccentric nuclei. A B. exitiosa infection exhibited larger microcells (mean ± SE diameter = 2.12 ± 0.27 µm, range = 1.5-4 µm, n = 60) with more concentric nuclei. Concurrent infections of both Bonamia species, as identified by PCR, exhibited both types of microcells. DNA barcoding of the B. ostreae-infected oyster host confirmed the identification as O. chilensis. A suite of other parasites that accompany O. chilensis are reported here for the first time in mixed infection with B. ostreae including apicomplexan X (76.5%), Microsporidium rapuae (0.7%) and Bucephalus longicornutus (30.2%).},
}
@article {pmid26864475,
year = {2016},
author = {Galimberti, A and Spinelli, S and Bruno, A and Mezzasalma, V and De Mattia, F and Cortis, P and Labra, M},
title = {Evaluating the efficacy of restoration plantings through DNA barcoding of frugivorous bird diets.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {30},
number = {4},
pages = {763-773},
doi = {10.1111/cobi.12687},
pmid = {26864475},
issn = {1523-1739},
mesh = {Animals ; Biodiversity ; *Birds ; *Conservation of Natural Resources ; *DNA Barcoding, Taxonomic ; DNA, Plant ; *Diet ; Italy ; Plants ; },
abstract = {Frugivores are critical components of restoration programs because they are seed dispersers. Thus, knowledge about bird-plant trophic relationships is essential in the evaluation of the efficacy of restoration processes. Traditionally, the diet of frugivores is characterized by microscopically identifying plant residues in droppings, which is time-consuming, requires botanical knowledge, and cannot be used for fragments lacking detectable morphological characteristics (e.g., fragmented seeds and skins). We examined whether DNA barcoding can be used as a universal tool to rapidly characterize the diet of a frugivorous bird, Eurasian blackcap (Sylvia atricapilla). We used the DNA barcoding results to assess restoration efforts and monitor the diversity of potentially dispersed plants in a protected area in northern Italy. We collected 642 Eurasian Blackcap droppings at the restored site during the autumn migration over 3 years. Intact seeds and fragmented plant material were analyzed at 2 plastidial barcode loci (rbcL and trnH-psbA), and the resulting plant identifications were validated by comparison with a reference molecular data set of local flora. At least 17 plant species, including 7 of the 11 newly transplanted taxa, were found. Our results demonstrate the potential for DNA barcoding to be used to monitor the effectiveness of restoration plantings and to obtain information about fruit consumption and dispersal of invasive or unexpected plant species. Such an approach provides valuable information that could be used to study local plant biodiversity and to survey its evolution over time.},
}
@article {pmid26863912,
year = {2016},
author = {Santoferrara, LF and Bachy, C and Alder, VA and Gong, J and Kim, YO and Saccà, A and da Silva Neto, ID and Strüder-Kypke, MC and Warren, A and Xu, D and Yi, Z and Agatha, S},
title = {Updating Biodiversity Studies in Loricate Protists: The Case of the Tintinnids (Alveolata, Ciliophora, Spirotrichea).},
journal = {The Journal of eukaryotic microbiology},
volume = {63},
number = {5},
pages = {651-656},
doi = {10.1111/jeu.12303},
pmid = {26863912},
issn = {1550-7408},
mesh = {Alveolata/classification/*cytology/*genetics/isolation &amp; purification ; Animals ; *Biodiversity ; Ciliophora/classification/*cytology/*genetics/isolation &amp; purification ; Classification ; DNA Barcoding, Taxonomic ; DNA, Protozoan ; *Ecology ; Phylogeny ; Species Specificity ; },
abstract = {Species determination is crucial in biodiversity research. In tintinnids, identification is based almost exclusively on the lorica, despite its frequent intraspecific variability and interspecific similarity. We suggest updated procedures for identification and, depending on the aim of the study, further steps to obtain morphological, molecular, and ecological data. Our goal is to help improving the collection of information (e.g. species re-/descriptions and DNA barcodes) that is essential for generating a natural tintinnid classification and a reliable reference for environmental surveys. These suggestions are broadly useful for protistologists because they exemplify data integration, quality/effort compromise, and the need for scientific collaborations.},
}
@article {pmid26863547,
year = {2016},
author = {Xu, W and Solis, NV and Filler, SG and Mitchell, AP},
title = {Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {107},
pages = {e53460},
pmid = {26863547},
issn = {1940-087X},
support = {R01 AI054928/AI/NIAID NIH HHS/United States ; R01 DE017088/DE/NIDCR NIH HHS/United States ; R21 DE023311/DE/NIDCR NIH HHS/United States ; R56 AI111836/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Antifungal Agents/pharmacology ; Candidiasis/drug therapy/*genetics ; Disease Models, Animal ; Gene Expression/*drug effects ; Gene Expression Profiling/*methods ; Mice ; Microarray Analysis ; RNA/metabolism ; },
abstract = {For most mammalian pathogens, gene expression profiling studies have been limited by technical difficulties to accurately quantify pathogen gene transcripts from infected tissues. Pathogen RNA constitutes a tiny portion of the total RNA isolated from infected tissue samples. Both microarray and RNAseq technologies have difficulties in generating reliable reads for weakly expressed pathogen genes. Mutant pathogen strains with reduced in vivo proliferation pose an even bigger challenge. Here we describe an in vivo gene expression profiling protocol that is very fast, extremely sensitive and highly reproducible. We developed this protocol during our investigation of the fungal pathogen Candida albicans in a murine model of hematogenously disseminated candidiasis. Using this protocol, we have documented time courses of dynamically regulated C. albicans gene expression during kidney infection, and discovered unexpected features of gene expression responses to antifungal drug treatment in vivo.},
}
@article {pmid26859488,
year = {2016},
author = {Zenker, MM and Rougerie, R and Teston, JA and Laguerre, M and Pie, MR and Freitas, AV},
title = {Fast Census of Moth Diversity in the Neotropics: A Comparison of Field-Assigned Morphospecies and DNA Barcoding in Tiger Moths.},
journal = {PloS one},
volume = {11},
number = {2},
pages = {e0148423},
pmid = {26859488},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; Brazil ; DNA Barcoding, Taxonomic/methods ; Female ; Genetic Variation ; Male ; Molecular Biology ; Moths/anatomy &amp; histology/*classification/*genetics ; Species Specificity ; Tropical Climate ; },
abstract = {The morphological species delimitations (i.e. morphospecies) have long been the best way to avoid the taxonomic impediment and compare insect taxa biodiversity in highly diverse tropical and subtropical regions. The development of DNA barcoding, however, has shown great potential to replace (or at least complement) the morphospecies approach, with the advantage of relying on automated methods implemented in computer programs or even online rather than in often subjective morphological features. We sampled moths extensively for two years using light traps in a patch of the highly endangered Atlantic Forest of Brazil to produce a nearly complete census of arctiines (Noctuoidea: Erebidae), whose species richness was compared using different morphological and molecular approaches (DNA barcoding). A total of 1,075 barcode sequences of 286 morphospecies were analyzed. Based on the clustering method Barcode Index Number (BIN) we found a taxonomic bias of approximately 30% in our initial morphological assessment. However, a morphological reassessment revealed that the correspondence between morphospecies and molecular operational taxonomic units (MOTUs) can be up to 94% if differences in genitalia morphology are evaluated in individuals of different MOTUs originated from the same morphospecies (putative cases of cryptic species), and by recording if individuals of different genders in different morphospecies merge together in the same MOTU (putative cases of sexual dimorphism). The results of two other clustering methods (i.e. Automatic Barcode Gap Discovery and 2% threshold) were very similar to those of the BIN approach. Using empirical data we have shown that DNA barcoding performed substantially better than the morphospecies approach, based on superficial morphology, to delimit species of a highly diverse moth taxon, and thus should be used in species inventories.},
}
@article {pmid26852345,
year = {2016},
author = {Shen, X and Yan, B},
title = {Barcoded materials based on photoluminescent hybrid system of lanthanide ions-doped metal organic framework and silica via ion exchange.},
journal = {Journal of colloid and interface science},
volume = {468},
number = {},
pages = {220-226},
doi = {10.1016/j.jcis.2016.01.055},
pmid = {26852345},
issn = {1095-7103},
abstract = {A multicolored photoluminescent hybrid system based on lanthanide ions-doped metal organic frameworks/silica composite host has potential in display and barcode applications. By controlling the stoichiometry of the lanthanides via cation exchange, proportional various lanthanide ions are successfully introduced into metal organic frameworks, whose emission intensity is correspondingly proportional to its amount. The resulting luminescent barcodes depend on the lanthanide ions ratios and compositions. Subsequently, the lanthanide ions located in the channels of metal organic frameworks are protected from any interaction with the environment after the modification of silica on the surface. The optical and thermal stability of the hybrid materials are improved for technological application.},
}
@article {pmid26849826,
year = {2016},
author = {Thormann, B and Ahrens, D and Marín Armijos, D and Peters, MK and Wagner, T and Wägele, JW},
title = {Exploring the Leaf Beetle Fauna (Coleoptera: Chrysomelidae) of an Ecuadorian Mountain Forest Using DNA Barcoding.},
journal = {PloS one},
volume = {11},
number = {2},
pages = {e0148268},
pmid = {26849826},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; Coleoptera/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Ecuador ; *Forests ; },
abstract = {BACKGROUND: Tropical mountain forests are hotspots of biodiversity hosting a huge but little known diversity of insects that is endangered by habitat destruction and climate change. Therefore, rapid assessment approaches of insect diversity are urgently needed to complement slower traditional taxonomic approaches. We empirically compare different DNA-based species delimitation approaches for a rapid biodiversity assessment of hyperdiverse leaf beetle assemblages along an elevational gradient in southern Ecuador and explore their effect on species richness estimates.<br><br>Based on a COI barcode data set of 674 leaf beetle specimens (Coleoptera: Chrysomelidae) of 266 morphospecies from three sample sites in the Podocarpus National Park, we employed statistical parsimony analysis, distance-based clustering, GMYC- and PTP-modelling to delimit species-like units and compared them to morphology-based (parataxonomic) species identifications. The four different approaches for DNA-based species delimitation revealed highly similar numbers of molecular operational taxonomic units (MOTUs) (n = 284-289). Estimated total species richness was considerably higher than the sampled amount, 414 for morphospecies (Chao2) and 469-481 for the different MOTU types. Assemblages at different elevational levels (1000 vs. 2000 m) had similar species numbers but a very distinct species composition for all delimitation methods. Most species were found only at one elevation while this turnover pattern was even more pronounced for DNA-based delimitation.<br><br>CONCLUSIONS/SIGNIFICANCE: Given the high congruence of DNA-based delimitation results, probably due to the sampling structure, our study suggests that when applied to species communities on a regionally limited level with high amount of rare species (i.e. ~50% singletons), the choice of species delimitation method can be of minor relevance for assessing species numbers and turnover in tropical insect communities. Therefore, DNA-based species delimitation is confirmed as a valuable tool for evaluating biodiversity of hyperdiverse insect communities, especially when exact taxonomic identifications are missing.},
}
@article {pmid26848744,
year = {2016},
author = {Han, T and Lee, W and Lee, S and Park, IG and Park, H},
title = {Reassessment of Species Diversity of the Subfamily Denticollinae (Coleoptera: Elateridae) through DNA Barcoding.},
journal = {PloS one},
volume = {11},
number = {2},
pages = {e0148602},
pmid = {26848744},
issn = {1932-6203},
mesh = {Animals ; Coleoptera/anatomy &amp; histology/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/chemistry/genetics ; Gene Library ; *Genetic Variation ; Likelihood Functions ; Species Specificity ; },
abstract = {The subfamily Denticollinae is a taxonomically diverse group in the family Elateridae. Denticollinae includes many morphologically similar species and crop pests, as well as many undescribed species at each local fauna. To construct a rapid and reliable identification system for this subfamily, the effectiveness of molecular species identification was assessed based on 421 cytochrome c oxidase subunit I (COI) sequences of 84 morphologically identified species. Among the 84 morphospecies, molecular species identification of 60 species (71.4%) was consistent with their morphological identifications. Six cryptic and/or pseudocryptic species with large genetic divergence (>5%) were confirmed by their sympatric or allopatric distributions. However, 18 species, including a subspecies, had ambiguous genetic distances and shared overlapping intra- and interspecific genetic distances (range: 2.12%-3.67%) suggesting incomplete lineage sorting, introgression of mitochondrial genome, or affection by endosymbionts, such as Wolbachia infection, between species and simple genetic variation within species. In this study, we propose a conservative threshold of 3.6% for convenient molecular operational taxonomic unit (MOTU) identification in the subfamily Denticollinae based on the results of pairwise genetic distances analyses using neighbor-joining, mothur, Automatic Barcode Gap Discovery analysis, and tree-based species delimitation by Poisson Tree Processes analysis. Using the 3.6% threshold, we identified 87 MOTUs and found 8 MOTUs in the interval between 2.5% to 3.5%. Evaluation of MOTUs identified in this range requires integrative species delimitation, including review of morphological and ecological differences as well as sensitive genetic markers. From this study, we confirmed that COI sequence is useful for reassessing species diversity for polymorphic and polytypic species occurring in sympatric and allopatric distributions, and for a single species having an extensively large habitat.},
}
@article {pmid26843891,
year = {2016},
author = {Tang, YL and Wu, YS and Huang, RS and Chao, NX and Liu, Y and Xu, P and Li, KZ and Cai, DZ and Luo, Y},
title = {Molecular identification of Uncaria (Gouteng) through DNA barcoding.},
journal = {Chinese medicine},
volume = {11},
number = {},
pages = {3},
pmid = {26843891},
issn = {1749-8546},
abstract = {BACKGROUND: While DNA barcoding is an important technology for the authentication of the botanical origins of Chinese medicines, the suitable markers for DNA barcoding of the genus Uncaria have not been reported yet. This study aims to determine suitable markers for DNA barcoding of the genus Uncaria (Gouteng).<br><br>METHODS: Genomic DNA was extracted from the freshly dried leaves of Uncaria plants by a Bioteke's Plant Genomic DNA Extraction Kit. Five candidate DNA barcode sites (ITS2, rbcL, psbA-trnH, ITS, and matK) were amplified by PCR with established primers. The purified PCR products were bidirectionally sequenced with appropriate amplification primers in an ABI-PRISM3730 instrument. The candidate DNA barcodes of 257 accessions of Uncaria in GenBank were aligned by ClustalW. Sequence assembly and consensus sequence generation were performed with CodonCode Aligner 3.7.1. The identification efficiency of the candidate DNA barcodes was evaluated with BLAST and nearest distance methods. The interspecific divergence and intraspecific variation were assessed by the Kimura 2-Parameter model. Genetic distances were computed with Molecular Evolutionary Genetics Analysis 6.0.<br><br>RESULTS: The accessions of the five candidate DNA barcodes from 11 of 12 species of Uncaria in China and four species from other countries were included in the analysis, while 54 of total accessions were submitted to GenBank. In a comparison of the interspecific genetic distances of the five candidate barcodes, psbA-trnH exhibited the highest interspecific divergence based on interspecific distance, theta prime, and minimum interspecific distance, followed by ITS2. The distribution of the interspecific distance of ITS2 and psbA-trnH was higher than the corresponding intraspecific distance. Additionally, psbA-trnH showed 95.9&#xa0;% identification efficiency by both the BLAST and nearest distance methods regardless of species or genus level. ITS2 exhibited 92.2&#xa0;% identification efficiency by the nearest distance method, but 87&#xa0;% by the BLAST method.<br><br>CONCLUSION: While psbA-trnH and ITS2 (used alone) were applicable barcodes for species authentication of Uncaria, psbA-trnH was a more suitable barcode for authentication of Uncaria macrophylla.},
}
@article {pmid26843833,
year = {2016},
author = {Ševčík, J and Kaspřák, D and Rulik, B},
title = {A new species of Docosia Winnertz from Central Europe, with DNA barcoding based on four gene markers (Diptera, Mycetophilidae).},
journal = {ZooKeys},
volume = {},
number = {549},
pages = {127-143},
pmid = {26843833},
issn = {1313-2989},
abstract = {A new species of Docosia Winnertz, Docosia dentata sp. n., is described and illustrated, based on a single male specimen collected in Muránska planina National Park in Central Slovakia. DNA sequences (COI, COII, CytB, and ITS2) are included and compared for 13 species of Docosia. There was found only little congruence between the molecular results and previous scarce data about interspecific relationships based on morphology. The COI and CytB gene markers showed the highest interspecific gene distances while ITS2 showed the lowest ones. An updated key to the 23 Central European species of Docosia is also presented.},
}
@article {pmid26842354,
year = {2016},
author = {Mäki, A and Rissanen, AJ and Tiirola, M},
title = {A practical method for barcoding and size-trimming PCR templates for amplicon sequencing.},
journal = {BioTechniques},
volume = {60},
number = {2},
pages = {88-90},
doi = {10.2144/000114380},
pmid = {26842354},
issn = {1940-9818},
mesh = {Algorithms ; DNA/genetics/metabolism ; DNA Barcoding, Taxonomic/*methods ; Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Polymerase Chain Reaction/*methods ; },
abstract = {Sample barcoding facilitates the analysis of tens or even hundreds of samples in a single next-generation sequencing (NGS) run, but more efficient methods are needed for high-throughput barcoding and size-trimming of long PCR products. Here we present a two-step PCR approach for barcoding followed by pool shearing, adapter ligation, and 5' end selection for trimming sets of DNA templates of any size. Our new trimming method offers clear benefits for phylogenetic studies, since targeting exactly the same region maximizes the alignment and enables the use of operational taxonomic unit (OTU)-based algorithms.},
}
@article {pmid26841188,
year = {2016},
author = {Vesterinen, EJ and Ruokolainen, L and Wahlberg, N and Peña, C and Roslin, T and Laine, VN and Vasko, V and Sääksjärvi, IE and Norrdahl, K and Lilley, TM},
title = {What you need is what you eat? Prey selection by the bat Myotis daubentonii.},
journal = {Molecular ecology},
volume = {25},
number = {7},
pages = {1581-1594},
doi = {10.1111/mec.13564},
pmid = {26841188},
issn = {1365-294X},
mesh = {Animals ; Chironomidae ; Chiroptera/*genetics/physiology ; *DNA Barcoding, Taxonomic ; Diet/veterinary ; Feces ; *Feeding Behavior ; Female ; Genotype ; Insecta/*classification/genetics ; Male ; Microsatellite Repeats ; *Predatory Behavior ; Seasons ; Sequence Analysis, DNA ; Simuliidae ; },
abstract = {Optimal foraging theory predicts that predators are selective when faced with abundant prey, but become less picky when prey gets sparse. Insectivorous bats in temperate regions are faced with the challenge of building up fat reserves vital for hibernation during a period of decreasing arthropod abundances. According to optimal foraging theory, prehibernating bats should adopt a less selective feeding behavior--yet empirical studies have revealed many apparently generalized species to be composed of specialist individuals. Targeting the diet of the bat Myotis daubentonii, we used a combination of molecular techniques to test for seasonal changes in prey selectivity and individual-level variation in prey preferences. DNA metabarcoding was used to characterize both the prey contents of bat droppings and the insect community available as prey. To test for dietary differences among M. daubentonii individuals, we used ten microsatellite loci to assign droppings to individual bats. The comparison between consumed and available prey revealed a preference for certain prey items regardless of availability. Nonbiting midges (Chironomidae) remained the most highly consumed prey at all times, despite a significant increase in the availability of black flies (Simuliidae) towards the end of the season. The bats sampled showed no evidence of individual specialization in dietary preferences. Overall, our approach offers little support for optimal foraging theory. Thus, it shows how novel combinations of genetic markers can be used to test general theory, targeting patterns at both the level of prey communities and individual predators.},
}
@article {pmid26840598,
year = {2016},
author = {Gossner, MM and Struwe, JF and Sturm, S and Max, S and McCutcheon, M and Weisser, WW and Zytynska, SE},
title = {Searching for the Optimal Sampling Solution: Variation in Invertebrate Communities, Sample Condition and DNA Quality.},
journal = {PloS one},
volume = {11},
number = {2},
pages = {e0148247},
pmid = {26840598},
issn = {1932-6203},
mesh = {Animals ; Arthropods/*classification/*genetics ; *Biodiversity ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; Sampling Studies ; },
abstract = {There is a great demand for standardising biodiversity assessments in order to allow optimal comparison across research groups. For invertebrates, pitfall or flight-interception traps are commonly used, but sampling solution differs widely between studies, which could influence the communities collected and affect sample processing (morphological or genetic). We assessed arthropod communities with flight-interception traps using three commonly used sampling solutions across two forest types and two vertical strata. We first considered the effect of sampling solution and its interaction with forest type, vertical stratum, and position of sampling jar at the trap on sample condition and community composition. We found that samples collected in copper sulphate were more mouldy and fragmented relative to other solutions which might impair morphological identification, but condition depended on forest type, trap type and the position of the jar. Community composition, based on order-level identification, did not differ across sampling solutions and only varied with forest type and vertical stratum. Species richness and species-level community composition, however, differed greatly among sampling solutions. Renner solution was highly attractant for beetles and repellent for true bugs. Secondly, we tested whether sampling solution affects subsequent molecular analyses and found that DNA barcoding success was species-specific. Samples from copper sulphate produced the fewest successful DNA sequences for genetic identification, and since DNA yield or quality was not particularly reduced in these samples additional interactions between the solution and DNA must also be occurring. Our results show that the choice of sampling solution should be an important consideration in biodiversity studies. Due to the potential bias towards or against certain species by Ethanol-containing sampling solution we suggest ethylene glycol as a suitable sampling solution when genetic analysis tools are to be used and copper sulphate when focusing on morphological species identification and facing financial restrictions in biodiversity studies.},
}
@article {pmid26840220,
year = {2016},
author = {Stiassny, ML and Sakharova, H},
title = {Review of the smiliogastrin cyprinids of the Kwilu River (Kasai Basin, central Africa), revised diagnosis for Clypeobarbus (Cyprinidae: Cyprininae: Smiliogastrini) and description of a new species.},
journal = {Journal of fish biology},
volume = {88},
number = {4},
pages = {1394-1412},
doi = {10.1111/jfb.12901},
pmid = {26840220},
issn = {1095-8649},
mesh = {Africa, Central ; Animals ; Cyprinidae/*anatomy &amp; histology/*classification ; Rivers ; },
abstract = {A revised diagnosis for the smiliogastrin genus Clypeobarbus is provided and a new species, Clypeobarbus breviclipeus, from the Kwilu River (Kasai Basin) of central Africa, is described. Another species co-occurring in the Kwilu system, 'Barbus' matthesi, shares all diagnostic morphological synapomorphies of Clypeobarbus and its generic reassignment is proposed with a taxonomic redescription provided. Nine species are now placed within Clypeobarbus: Clypeobarbus pleuropholis, Clypeobarbus congicus, Clypeobarbus pseudognathodon, Clypeobarbus bomokandi, Clypeobarbus hypsolepis, Clypeobarbus schoutedeni, Clypeobarbus matthesi, Clypeobarbus bellcrossi and Clypeobarbus breviclipeus n. sp.},
}
@article {pmid26838797,
year = {2016},
author = {Chen, R and Jiang, LY and Chen, J and Qiao, GX},
title = {DNA barcoding reveals a mysterious high species diversity of conifer-feeding aphids in the mountains of southwest China.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {20123},
pmid = {26838797},
issn = {2045-2322},
mesh = {Animals ; Aphids/*classification/*genetics ; Biodiversity ; Biological Evolution ; China ; Climate ; DNA Barcoding, Taxonomic/*methods ; Phylogeny ; Sequence Analysis, DNA ; Tracheophyta/*parasitology ; },
abstract = {The mountains of southwest China are one of the hot spots of biodiversity in the world. However, the high-altitude fauna that inhabit these mountains remain a mystery. In this study, the species diversity of the aphids of the genus Cinara from the high-altitude coniferous forests was first assessed, and then the processes and the mechanisms of speciation were discussed. Three hundreds and four aphid samples that contained 3040 individuals were collected during fourteen field surveys. The molecular clusters derived from the DNA barcodes were used to explore the species diversity. Notably, the aphid alpha-diversity was high, with as many as 94 candidate species, and furthermore, 86.2% of the species collected had not been previously recorded. The centers of aphid species richness corresponded to the distributional pattern of the diversity of the host conifer plant species. The divergence time revealed that following the uplift of the Qinghai-Tibetan Plateau during the Pleistocene, the changes in the climate, ecology and host habitats were likely the most important factors that drove the rapid process of evolutionary radiation in the aphids. Our findings revealed the high species diversity of the aphids with DNA barcoding.},
}
@article {pmid26837186,
year = {2015},
author = {Jia, J and Shi, LC and Xu, ZC and Xin, TY and Song, JY and Chen Shi, L},
title = {[Identification of antler powder components based on DNA barcoding technology].},
journal = {Yao xue xue bao = Acta pharmaceutica Sinica},
volume = {50},
number = {10},
pages = {1356-1361},
pmid = {26837186},
issn = {0513-4870},
mesh = {Animals ; *Antlers ; *DNA Barcoding, Taxonomic ; Deer ; *Medicine, Chinese Traditional ; Polymerase Chain Reaction ; Powders ; Quality Control ; },
abstract = {In order to authenticate the components of antler powder in the market, DNA barcoding technology coupled with cloning method were used. Cytochrome c oxidase subunit I (COI) sequences were obtained according to the DNA barcoding standard operation procedure (SOP). For antler powder with possible mixed components, the cloning method was used to get each COI sequence. 65 COI sequences were successfully obtained from commercial antler powders via sequencing PCR products. The results indicates that only 38% of these samples were derived from Cervus nippon Temminck or Cervus elaphus Linnaeus which is recorded in the 2010 edition of "Chinese Pharmacopoeia", while 62% of them were derived from other species. Rangifer tarandus Linnaeus was the most frequent species among the adulterants. Further analysis showed that some samples collected from different regions, companies and prices, contained adulterants. Analysis of 36 COI sequences obtained by the cloning method showed that C. elaphus and C. nippon were main components. In addition, some samples were marked clearly as antler powder on the label, however, C. elaphus or R. tarandus were their main components. In summary, DNA barcoding can accurately and efficiently distinguish the exact content in the commercial antler powder, which provides a new technique to ensure clinical safety and improve quality control of Chinese traditional medicine},
}
@article {pmid26832687,
year = {2016},
author = {Mayhew, D and Mitra, RD},
title = {Calling Card Analysis in Budding Yeast.},
journal = {Cold Spring Harbor protocols},
volume = {2016},
number = {2},
pages = {pdb.prot086918},
doi = {10.1101/pdb.prot086918},
pmid = {26832687},
issn = {1559-6095},
mesh = {Binding Sites ; Chromosome Mapping/methods ; *DNA Transposable Elements ; DNA, Fungal/metabolism ; *Gene Regulatory Networks ; Genetics, Microbial/*methods ; Molecular Biology/*methods ; Protein Binding ; Saccharomyces cerevisiae/*genetics ; Transcription Factors/*metabolism ; },
abstract = {Calling card analysis is a high-throughput method for identifying the genomic binding sites of multiple transcription factors in a single experiment in budding yeast. By tagging a DNA-binding protein with a targeting domain that directs the insertion of the Ty5 retrotransposon, the genomic binding sites for that transcription factor are marked. The transposition locations are then identified en masse by Illumina sequencing. The calling card protocol allows for simultaneous analysis of multiple transcription factors. By cloning barcodes into the Ty5 transposon, it is possible to pair a unique barcode with every transcription factor in the experiment. The method presented here uses expression of transcription factors from their native loci; however, it can also be altered to measure binding sites of transcription factors overexpressed from a plasmid.},
}
@article {pmid26828929,
year = {2016},
author = {Uribe-Convers, S and Settles, ML and Tank, DC},
title = {A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae).},
journal = {PloS one},
volume = {11},
number = {2},
pages = {e0148203},
pmid = {26828929},
issn = {1932-6203},
support = {P20 RR016448/RR/NCRR NIH HHS/United States ; P20 RR016454/RR/NCRR NIH HHS/United States ; P20RR016454/RR/NCRR NIH HHS/United States ; P20RR16448/RR/NCRR NIH HHS/United States ; },
mesh = {Cell Nucleus/genetics ; DNA Primers/metabolism ; DNA, Chloroplast/genetics ; Flowers/genetics ; *Genetic Variation ; *Genome, Plant ; Geography ; High-Throughput Nucleotide Sequencing/*methods ; Microfluidics ; Orobanchaceae/*genetics ; *Phylogeny ; Polymerase Chain Reaction/*methods ; Reproducibility of Results ; Species Specificity ; },
abstract = {Advances in high-throughput sequencing (HTS) have allowed researchers to obtain large amounts of biological sequence information at speeds and costs unimaginable only a decade ago. Phylogenetics, and the study of evolution in general, is quickly migrating towards using HTS to generate larger and more complex molecular datasets. In this paper, we present a method that utilizes microfluidic PCR and HTS to generate large amounts of sequence data suitable for phylogenetic analyses. The approach uses the Fluidigm Access Array System (Fluidigm, San Francisco, CA, USA) and two sets of PCR primers to simultaneously amplify 48 target regions across 48 samples, incorporating sample-specific barcodes and HTS adapters (2,304 unique amplicons per Access Array). The final product is a pooled set of amplicons ready to be sequenced, and thus, there is no need to construct separate, costly genomic libraries for each sample. Further, we present a bioinformatics pipeline to process the raw HTS reads to either generate consensus sequences (with or without ambiguities) for every locus in every sample or--more importantly--recover the separate alleles from heterozygous target regions in each sample. This is important because it adds allelic information that is well suited for coalescent-based phylogenetic analyses that are becoming very common in conservation and evolutionary biology. To test our approach and bioinformatics pipeline, we sequenced 576 samples across 96 target regions belonging to the South American clade of the genus Bartsia L. in the plant family Orobanchaceae. After sequencing cleanup and alignment, the experiment resulted in ~25,300 bp across 486 samples for a set of 48 primer pairs targeting the plastome, and ~13,500 bp for 363 samples for a set of primers targeting regions in the nuclear genome. Finally, we constructed a combined concatenated matrix from all 96 primer combinations, resulting in a combined aligned length of ~40,500 bp for 349 samples.},
}
@article {pmid26828034,
year = {2016},
author = {Che, J and Wang, K},
title = {AmphibiaChina: an online database of Chinese Amphibians.},
journal = {Dong wu xue yan jiu = Zoological research},
volume = {37},
number = {1},
pages = {57-59},
pmid = {26828034},
issn = {2095-8137},
mesh = {*Amphibians/classification ; Animals ; China ; Classification ; *Databases, Factual ; Information Storage and Retrieval ; *Internet ; },
abstract = {AmphibiaChina, an open-access, web-based database, is designed to provide comprehensive and up-to-date information on Chinese amphibians. It offers an integrated module with six major sections. Compared to other known databases including AmphibiaWeb and Amphibian Species of the World, AmphibiaChina has the following new functions: (1) online species identification based on DNA barcode sequences; (2) comparisons and discussions of different major taxonomic systems; and (3) phylogenetic progress on Chinese amphibians. This database offers a window for the world to access available information of Chinese amphibians. AmphibiaChina with its Chinese version can be accessed at http://www.amphibiachina.org.},
}
@article {pmid26828032,
year = {2016},
author = {Jiang, K and Wang, K and Yan, F and Xie, J and Zou, DH and Liu, WL and Jiang, JP and Li, C and Che, J},
title = {A new species of the genus Amolops (Amphibia: Ranidae) from southeastern Tibet, China.},
journal = {Dong wu xue yan jiu = Zoological research},
volume = {37},
number = {1},
pages = {31-40},
pmid = {26828032},
issn = {2095-8137},
mesh = {Animals ; Ecological and Environmental Phenomena ; Female ; Male ; Pigmentation ; Ranidae/anatomy &amp; histology/*classification/genetics ; Tibet ; },
abstract = {A new species of the genus Amolops Cope, 1865 is described from Nyingchi, southeastern Tibet, China, based on morphological and molecular data. The new species, Amolops nyingchiensis sp. nov. is assigned to the Amolops monticola group based on its skin smooth, dorsolateral fold distinct, lateral side of head black, upper lip stripe white extending to the shoulder. Amolops nyingchiensis sp. nov. is distinguished from all other species of Amolops by the following combination of characters: (1) medium body size, SVL 48.5-58.3 mm in males, and 57.6-70.7 mm in females; (2) tympanum distinct, slightly larger than one third of the eye diameter; (3) a small tooth-like projection on anteromedial edge of mandible; (4) the absence of white spine on dorsal surface of body; (5) the presence of circummarginal groove on all fingers; (6) the presence of vomerine teeth; (7) background coloration of dorsal surface brown, lateral body gray with yellow; (8) the presence of transverse bands on the dorsal limbs; (9) the presence of nuptial pad on the first finger in males; (10) the absence of vocal sac in males. Taxonomic status of the populations that were previously identified to A. monticola from Tibet is also discussed.},
}
@article {pmid26828031,
year = {2016},
author = {Jiang, K and Wang, K and Zou, DH and Yan, F and Li, PP and Che, J},
title = {A new species of the genus Scutiger (Anura: Megophryidae) from Medog of southeastern Tibet, China.},
journal = {Dong wu xue yan jiu = Zoological research},
volume = {37},
number = {1},
pages = {21-30},
pmid = {26828031},
issn = {2095-8137},
mesh = {Animals ; Anura/anatomy &amp; histology/*classification ; Female ; Male ; Phylogeny ; Pigmentation ; Tibet ; },
abstract = {A new species of Scutiger Theobald, 1868 is described from Medog, southeastern Tibet, China, based on morphological and molecular data. The new species was previously identified as Scutiger nyingchiensis, but it can be differentiated from the latter and all other congeners by the following combination of characters: (1) medium adult body size, SVL 50.5-55.6 mm in males and 53.8-57.2 mm in females; (2) maxillary teeth absent; (3) web rudimentary between toes; (4) prominent, conical-shaped tubercles on dorsal and lateral surfaces of body and limbs; (5) tubercles covered by black spines in both sexes in breeding condition; (6) a pair of pectoral glands and a pair of axillary glands present and covered by black spines in males in breeding condition, width of axillary gland less than 50% of pectoral gland; (7) nuptial spines present on dorsal surface of first and second fingers, and inner side of third finger in males in breeding condition; (8) spines absent on the abdominal region; (9) vocal sac absent. In addition, the distribution and conservation status of the new species are also discussed.},
}
@article {pmid26827247,
year = {2016},
author = {Simko, I},
title = {High-Resolution DNA Melting Analysis in Plant Research.},
journal = {Trends in plant science},
volume = {21},
number = {6},
pages = {528-537},
doi = {10.1016/j.tplants.2016.01.004},
pmid = {26827247},
issn = {1878-4372},
mesh = {Chromosome Mapping ; DNA Fingerprinting/methods ; Genes, Plant ; Genetic Markers ; Genomics/methods/trends ; Nucleic Acid Denaturation ; Plants/*genetics ; Polymerase Chain Reaction/*methods/trends ; Sequence Analysis, DNA/methods ; },
abstract = {Genetic and genomic studies provide valuable insight into the inheritance, structure, organization, and function of genes. The knowledge gained from the analysis of plant genes is beneficial to all aspects of plant research, including crop improvement. New methods and tools are continually being developed to facilitate rapid and accurate mapping, sequencing, and analyzing of genes. Here, I review the recent progress in the application of high-resolution melting (HRM) analysis of DNA, a method that allows detecting polymorphism in double-stranded DNA by comparing profiles of melting curves. Use of HRM has expanded considerably in the past few years as the method was successfully applied for high-throughput genotyping, mapping genes, testing food products and seeds, and other areas of plant research.},
}
@article {pmid26823636,
year = {2015},
author = {Crous, PW and Wingfield, MJ and Le Roux, JJ and Richardson, DM and Strasberg, D and Shivas, RG and Alvarado, P and Edwards, J and Moreno, G and Sharma, R and Sonawane, MS and Tan, YP and Altés, A and Barasubiye, T and Barnes, CW and Blanchette, RA and Boertmann, D and Bogo, A and Carlavilla, JR and Cheewangkoon, R and Daniel, R and de Beer, ZW and de Jesús Yáñez-Morales, M and Duong, TA and Fernández-Vicente, J and Geering, AD and Guest, DI and Held, BW and Heykoop, M and Hubka, V and Ismail, AM and Kajale, SC and Khemmuk, W and Kolařík, M and Kurli, R and Lebeuf, R and Lévesque, CA and Lombard, L and Magista, D and Manjón, JL and Marincowitz, S and Mohedano, JM and Nováková, A and Oberlies, NH and Otto, EC and Paguigan, ND and Pascoe, IG and Pérez-Butrón, JL and Perrone, G and Rahi, P and Raja, HA and Rintoul, T and Sanhueza, RM and Scarlett, K and Shouche, YS and Shuttleworth, LA and Taylor, PW and Thorn, RG and Vawdrey, LL and Solano-Vidal, R and Voitk, A and Wong, PT and Wood, AR and Zamora, JC and Groenewald, JZ},
title = {Fungal Planet description sheets: 371-399.},
journal = {Persoonia},
volume = {35},
number = {},
pages = {264-327},
pmid = {26823636},
issn = {0031-5850},
abstract = {Novel species of fungi described in the present study include the following from Australia: Neoseptorioides eucalypti gen. &amp; sp. nov. from Eucalyptus radiata leaves, Phytophthora gondwanensis from soil, Diaporthe tulliensis from rotted stem ends of Theobroma cacao fruit, Diaporthe vawdreyi from fruit rot of Psidium guajava, Magnaporthiopsis agrostidis from rotted roots of Agrostis stolonifera and Semifissispora natalis from Eucalyptus leaf litter. Furthermore, Neopestalotiopsis egyptiaca is described from Mangifera indica leaves (Egypt), Roussoella mexicana from Coffea arabica leaves (Mexico), Calonectria monticola from soil (Thailand), Hygrocybe jackmanii from littoral sand dunes (Canada), Lindgomyces madisonensis from submerged decorticated wood (USA), Neofabraea brasiliensis from Malus domestica (Brazil), Geastrum diosiae from litter (Argentina), Ganoderma wiiroense on angiosperms (Ghana), Arthrinium gutiae from the gut of a grasshopper (India), Pyrenochaeta telephoni from the screen of a mobile phone (India) and Xenoleptographium phialoconidium gen. &amp; sp. nov. on exposed xylem tissues of Gmelina arborea (Indonesia). Several novelties are introduced from Spain, namely Psathyrella complutensis on loamy soil, Chlorophyllum lusitanicum on nitrified grasslands (incl. Chlorophyllum arizonicum comb. nov.), Aspergillus citocrescens from cave sediment and Lotinia verna gen. &amp; sp. nov. from muddy soil. Novel foliicolous taxa from South Africa include Phyllosticta carissicola from Carissa macrocarpa, Pseudopyricularia hagahagae from Cyperaceae and Zeloasperisporium searsiae from Searsia chirindensis. Furthermore, Neophaeococcomyces is introduced as a novel genus, with two new combinations, N. aloes and N. catenatus. Several foliicolous novelties are recorded from La Réunion, France, namely Ochroconis pandanicola from Pandanus utilis, Neosulcatispora agaves gen. &amp; sp. nov. from Agave vera-cruz, Pilidium eucalyptorum from Eucalyptus robusta, Strelitziana syzygii from Syzygium jambos (incl. Strelitzianaceae fam. nov.) and Pseudobeltrania ocoteae from Ocotea obtusata (Beltraniaceae emend.). Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.},
}
@article {pmid26823635,
year = {2015},
author = {Stielow, JB and Lévesque, CA and Seifert, KA and Meyer, W and Iriny, L and Smits, D and Renfurm, R and Verkley, GJ and Groenewald, M and Chaduli, D and Lomascolo, A and Welti, S and Lesage-Meessen, L and Favel, A and Al-Hatmi, AM and Damm, U and Yilmaz, N and Houbraken, J and Lombard, L and Quaedvlieg, W and Binder, M and Vaas, LA and Vu, D and Yurkov, A and Begerow, D and Roehl, O and Guerreiro, M and Fonseca, A and Samerpitak, K and van Diepeningen, AD and Dolatabadi, S and Moreno, LF and Casaregola, S and Mallet, S and Jacques, N and Roscini, L and Egidi, E and Bizet, C and Garcia-Hermoso, D and Martín, MP and Deng, S and Groenewald, JZ and Boekhout, T and de Beer, ZW and Barnes, I and Duong, TA and Wingfield, MJ and de Hoog, GS and Crous, PW and Lewis, CT and Hambleton, S and Moussa, TA and Al-Zahrani, HS and Almaghrabi, OA and Louis-Seize, G and Assabgui, R and McCormick, W and Omer, G and Dukik, K and Cardinali, G and Eberhardt, U and de Vries, M and Robert, V},
title = {One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes.},
journal = {Persoonia},
volume = {35},
number = {},
pages = {242-263},
pmid = {26823635},
issn = {0031-5850},
abstract = {The aim of this study was to assess potential candidate gene regions and corresponding universal primer pairs as secondary DNA barcodes for the fungal kingdom, additional to ITS rDNA as primary barcode. Amplification efficiencies of 14 (partially) universal primer pairs targeting eight genetic markers were tested across > 1 500 species (1 931 strains or specimens) and the outcomes of almost twenty thousand (19 577) polymerase chain reactions were evaluated. We tested several well-known primer pairs that amplify: i) sections of the nuclear ribosomal RNA gene large subunit (D1-D2 domains of 26/28S); ii) the complete internal transcribed spacer region (ITS1/2); iii) partial β -tubulin II (TUB2); iv) γ-actin (ACT); v) translation elongation factor 1-α (TEF1α); and vi) the second largest subunit of RNA-polymerase II (partial RPB2, section 5-6). Their PCR efficiencies were compared with novel candidate primers corresponding to: i) the fungal-specific translation elongation factor 3 (TEF3); ii) a small ribosomal protein necessary for t-RNA docking; iii) the 60S L10 (L1) RP; iv) DNA topoisomerase I (TOPI); v) phosphoglycerate kinase (PGK); vi) hypothetical protein LNS2; and vii) alternative sections of TEF1α. Results showed that several gene sections are accessible to universal primers (or primers universal for phyla) yielding a single PCR-product. Barcode gap and multi-dimensional scaling analyses revealed that some of the tested candidate markers have universal properties providing adequate infra- and inter-specific variation that make them attractive barcodes for species identification. Among these gene sections, a novel high fidelity primer pair for TEF1α, already widely used as a phylogenetic marker in mycology, has potential as a supplementary DNA barcode with superior resolution to ITS. Both TOPI and PGK show promise for the Ascomycota, while TOPI and LNS2 are attractive for the Pucciniomycotina, for which universal primers for ribosomal subunits often fail.},
}
@article {pmid26823632,
year = {2015},
author = {Hansen, K and Olariaga, I},
title = {Species limits and relationships within Otidea inferred from multiple gene phylogenies.},
journal = {Persoonia},
volume = {35},
number = {},
pages = {148-165},
pmid = {26823632},
issn = {0031-5850},
abstract = {The genus Otidea is one of the more conspicuous members of the Pyronemataceae, with high species diversity in hemiboreal and boreal forests. The genus is morphologically coherent and in previous higher-level multi-gene analyses it formed a highly supported monophyletic group. Species delimitation within Otidea is controversial and much confusion has prevailed in the naming of taxa. To provide a phylogenetic hypothesis of Otidea, elucidate species diversity and limits we compiled a four-gene dataset including the nuclear LSU rDNA and three nuclear protein-coding genes (RPB1, RPB2 and EF-1α) for 89 specimens (total 4 877 nucleotides). These were selected from a larger sample of material studied using morphology and 146 ITS (ITS1-5.8S-ITS2) and 168 LSU rDNA sequences to represent the full genetic diversity. Using genealogical concordance phylogenetic species recognition (GCPSR), Bayesian and maximum likelihood analyses of the individual datasets resolved 25 species of Otidea. An additional eight singletons are considered to be distinct species, because they were genetically divergent from their sisters. Sequences of multiple genes were included from 13 holotypes, one neotype and three epitypes. Otidea angusta, O. myosotis and O. papillata f. pallidefurfuracea are nested within O. nannfeldtii, O. leporina and O. tuomikoskii, respectively and are considered synonyms. Otidea cantharella var. minor is shown to be a distinct species. Five new species were discovered: O. oregonensis and O. pseudoleporina for North America; and O. borealis, O. brunneoparva and O. subformicarum for Europe. The analyses of the individual four gene datasets yielded phylogenies that were highly concordant topologically, except for the RPB1 that showed supported conflict for some nodes in Bayesian analysis. Excluding the RPB1 from the combined analyses produced an identical topology to the four-gene phylogeny, but with higher support for several basal nodes and lower support for several shallow nodes. We argue to use the three-gene dataset to retrieve the maximum support for the higher-level relationships in Otidea, but still utilise the signal from the RPB1 for the delimitation and relationships of closely related species. From the four gene regions utilised, EF-1α and RPB1 have the strongest species recognition power, and with higher amplification success EF-1α may serve as the best secondary barcoding locus for Otidea (with ITS being a primary). The phylogeny from the three- and four-gene datasets is fully resolved and strongly supported in all branches but one. Two major clades, as part of six inclusive clades A-F, are identified - and ten subclades within these: A) O. platyspora and O. alutacea subclades, and B) O. papillata, O. leporina, O. tuomikoskii, O. cantharella, O. formicarum, O. unicisa, O. bufonia-onotica and O. concinna subclades. Morphological features in Otidea appear to be fast evolving and prone to shifts, and are poor indicators of higher-level relationships. Nevertheless, a conspicuous spore ornament is a synapomorphy for the O. unicisa subclade (/Otideopsis); all other species in Otidea have smooth or verruculose (in SEM) spores. Exclusively pale to bright yellow apothecia and straight to curved, broadly clavate to distinctly capitate paraphyses are synapomorphies for a restricted O. concinna subclade (/Flavoscypha). The curved to hooked apices of the paraphyses is suggested to be a symplesiomorphic trait for the genus. The reaction of resinous exudates on the outermost excipular cells that coalesce into amber drops in Melzer's reagent is likely an ancestral state for clade B. We estimate that Otidea consists of 47 species worldwide, based on all available information (including morphology, ITS or LSU sequences, and literature descriptions). Three fifths of the species occur in Europe, with 20 species recognised as endemic. At least 14 species occur in North America and 17 in Asia, with eight and ten species considered endemic to each continent, respectively. Our knowledge about Otidea in Asia is still fragmentary and the diversity likely much higher.},
}
@article {pmid26822532,
year = {2016},
author = {Tracol, P},
title = {Materials vigilance and traceability.},
journal = {Orthopaedics &amp; traumatology, surgery &amp; research : OTSR},
volume = {102},
number = {1 Suppl},
pages = {S95-103},
doi = {10.1016/j.otsr.2015.05.013},
pmid = {26822532},
issn = {1877-0568},
mesh = {*Equipment Failure ; Equipment and Supplies/classification/standards ; *European Union ; Humans ; *Patient Safety ; Product Labeling/*standards ; Prostheses and Implants/*standards ; Reference Standards ; },
abstract = {Patient safety requires speedy detection of any medical device malfunction; this is known as "materials vigilance". It entails the need to be able to trace back the life-long pathway of a device; this is "traceability". European regulations enact free circulation of medical devices throughout the European Union, with each member state being responsible for safety within its own territory. Medical devices are divided into 3 categories of increasing risk. CE marking mandatory for medical devices distributed within the EU, and count as market authorizations. They are delivered with 5-year validity by what is known as a "notified body". Health authorities are responsible for monitoring the market and any incidents. New regulations are presently being drawn up to improve efficiency and transparency. Materials vigilance is founded on mandatory declaration of medical device incidents. At local level, it comprises local reporters responsible for informing the National Health Products Safety Agency (Agence nationale de sécurité du médicament et des produits de santé [ANSM]) of any incidents and taking all necessary precautions. At national level, the ANSM assesses the safety, efficacy and quality of healthcare products; it centralizes and assesses materials vigilance reports and takes the requisite decisions. Materials vigilance is further organized at the European and international levels, to harmonize legislation regarding medical devices. Traceability is intended to rapidly identify medical device bearers in case of product recall. Each center is to organize the traceability of its devices; manufacturers' obligation of traceability ceases with the healthcare establishment or user. CE marking involves strict labeling rules to ensure safety of use. A change in the organization of traceability is presently underway, in the form of international Unique Device Identifiers, with harmonized label data, barcodes and standardized terminology. A European and later international database will be set up. The objective is to make Unique Device Identifiers mandatory within the EU by 2017.},
}
@article {pmid26821259,
year = {2016},
author = {Coissac, E and Hollingsworth, PM and Lavergne, S and Taberlet, P},
title = {From barcodes to genomes: extending the concept of DNA barcoding.},
journal = {Molecular ecology},
volume = {25},
number = {7},
pages = {1423-1428},
doi = {10.1111/mec.13549},
pmid = {26821259},
issn = {1365-294X},
mesh = {Biodiversity ; *DNA Barcoding, Taxonomic ; *Genomics ; High-Throughput Nucleotide Sequencing ; Plants/classification ; },
abstract = {DNA barcoding has had a major impact on biodiversity science. The elegant simplicity of establishing massive scale databases for a few barcode loci is continuing to change our understanding of species diversity patterns, and continues to enhance human abilities to distinguish among species. Capitalizing on the developments of next generation sequencing technologies and decreasing costs of genome sequencing, there is now the opportunity for the DNA barcoding concept to be extended to new kinds of genomic data. We illustrate the benefits and capacity to do this, and also note the constraints and barriers to overcome before it is truly scalable. We advocate a twin track approach: (i) continuation and acceleration of global efforts to build the DNA barcode reference library of life on earth using standard DNA barcodes and (ii) active development and application of extended DNA barcodes using genome skimming to augment the standard barcoding approach.},
}
@article {pmid26818207,
year = {2016},
author = {Selosse, MA and Vincenot, L and Öpik, M},
title = {Data processing can mask biology: towards better reporting of fungal barcoding data?.},
journal = {The New phytologist},
volume = {210},
number = {4},
pages = {1159-1164},
doi = {10.1111/nph.13851},
pmid = {26818207},
issn = {1469-8137},
mesh = {*DNA Barcoding, Taxonomic ; Heterozygote ; Mycorrhizae/*genetics ; },
}
@article {pmid26811787,
year = {2016},
author = {Jo, H and Ventura, M and Vidal, N and Gim, JS and Buchaca, T and Barmuta, LA and Jeppesen, E and Joo, GJ},
title = {Discovering hidden biodiversity: the use of complementary monitoring of fish diet based on DNA barcoding in freshwater ecosystems.},
journal = {Ecology and evolution},
volume = {6},
number = {1},
pages = {219-232},
pmid = {26811787},
issn = {2045-7758},
abstract = {Ecological monitoring contributes to the understanding of complex ecosystem functions. The diets of fish reflect the surrounding environment and habitats and may, therefore, act as useful integrating indicators of environmental status. It is, however, often difficult to visually identify items in gut contents to species level due to digestion of soft-bodied prey beyond visual recognition, but new tools rendering this possible are now becoming available. We used a molecular approach to determine the species identities of consumed diet items of an introduced generalist feeder, brown trout (Salmo trutta), in 10 Tasmanian lakes and compared the results with those obtained from visual quantification of stomach contents. We obtained 44 unique taxa (OTUs) belonging to five phyla, including seven classes, using the barcode of life approach from cytochrome oxidase I (COI). Compared with visual quantification, DNA analysis showed greater accuracy, yielding a 1.4-fold higher number of OTUs. Rarefaction curve analysis showed saturation of visually inspected taxa, while the curves from the DNA barcode did not saturate. The OTUs with the highest proportions of haplotypes were the families of terrestrial insects Formicidae, Chrysomelidae, and Torbidae and the freshwater Chironomidae. Haplotype occurrence per lake was negatively correlated with lake depth and transparency. Nearly all haplotypes were only found in one fish gut from a single lake. Our results indicate that DNA barcoding of fish diets is a useful and complementary method for discovering hidden biodiversity.},
}
@article {pmid26811761,
year = {2015},
author = {Luo, A and Lan, H and Ling, C and Zhang, A and Shi, L and Ho, SY and Zhu, C},
title = {A simulation study of sample size for DNA barcoding.},
journal = {Ecology and evolution},
volume = {5},
number = {24},
pages = {5869-5879},
pmid = {26811761},
issn = {2045-7758},
abstract = {For some groups of organisms, DNA barcoding can provide a useful tool in taxonomy, evolutionary biology, and biodiversity assessment. However, the efficacy of DNA barcoding depends on the degree of sampling per species, because a large enough sample size is needed to provide a reliable estimate of genetic polymorphism and for delimiting species. We used a simulation approach to examine the effects of sample size on four estimators of genetic polymorphism related to DNA barcoding: mismatch distribution, nucleotide diversity, the number of haplotypes, and maximum pairwise distance. Our results showed that mismatch distributions derived from subsamples of ≥20 individuals usually bore a close resemblance to that of the full dataset. Estimates of nucleotide diversity from subsamples of ≥20 individuals tended to be bell-shaped around that of the full dataset, whereas estimates from smaller subsamples were not. As expected, greater sampling generally led to an increase in the number of haplotypes. We also found that subsamples of ≥20 individuals allowed a good estimate of the maximum pairwise distance of the full dataset, while smaller ones were associated with a high probability of underestimation. Overall, our study confirms the expectation that larger samples are beneficial for the efficacy of DNA barcoding and suggests that a minimum sample size of 20 individuals is needed in practice for each population.},
}
@article {pmid26807711,
year = {2016},
author = {Angers-Loustau, A and Petrillo, M and Paracchini, V and Kagkli, DM and Rischitor, PE and Puertas Gallardo, A and Patak, A and Querci, M and Kreysa, J},
title = {Towards Plant Species Identification in Complex Samples: A Bioinformatics Pipeline for the Identification of Novel Nuclear Barcode Candidates.},
journal = {PloS one},
volume = {11},
number = {1},
pages = {e0147692},
pmid = {26807711},
issn = {1932-6203},
mesh = {Computational Biology ; *DNA Barcoding, Taxonomic ; DNA Primers/*genetics ; DNA, Plant/*genetics ; Plants/genetics ; },
abstract = {Monitoring of the food chain to fight fraud and protect consumer health relies on the availability of methods to correctly identify the species present in samples, for which DNA barcoding is a promising candidate. The nuclear genome is a rich potential source of barcode targets, but has been relatively unexploited until now. Here, we show the development and use of a bioinformatics pipeline that processes available genome sequences to automatically screen large numbers of input candidates, identifies novel nuclear barcode targets and designs associated primer pairs, according to a specific set of requirements. We applied this pipeline to identify novel barcodes for plant species, a kingdom for which the currently available solutions are known to be insufficient. We tested one of the identified primer pairs and show its capability to correctly identify the plant species in simple and complex samples, validating the output of our approach.},
}
@article {pmid26807035,
year = {2015},
author = {Pazhenkova, EA and Zakharov, EV and Lukhtanov, VA},
title = {DNA barcoding reveals twelve lineages with properties of phylogenetic and biological species within Melitaea didyma sensu lato (Lepidoptera, Nymphalidae).},
journal = {ZooKeys},
volume = {},
number = {538},
pages = {35-46},
pmid = {26807035},
issn = {1313-2989},
abstract = {The complex of butterfly taxa close to Melitaea didyma includes the traditionally recognized species Melitaea didyma, Melitaea didymoides and Melitaea sutschana, the taxa that were recognized as species only relatively recently (Melitaea latonigena, Melitaea interrupta, Melitaea chitralensis and Melitaea mixta) as well as numerous described subspecies and forms with unclear taxonomic status. Here analysis of mitochondrial DNA barcodes is used to demonstrate that this complex is monophyletic group consisting of at least 12 major haplogroups strongly differentiated with respect to the gene COI. Six of these haplogroups are shown to correspond to six of the above-mentioned species (Melitaea didymoides, Melitaea sutschana, Melitaea latonigena, Melitaea interrupta, Melitaea chitralensis and Melitaea mixta). It is hypothesized that each of the remaining six haplogroups also represents a distinct species (Melitaea mauretanica, Melitaea occidentalis, Melitaea didyma, Melitaea neera, Melitaea liliputana and Melitaea turkestanica), since merging these haplogroups would result in a polyphyletic assemblage and the genetic distances between them are comparable with those found between the other six previously recognized species.},
}
@article {pmid26807034,
year = {2015},
author = {Lukhtanov, VA and Novikova, AV},
title = {Interpretation of mitochondrial diversity in terms of taxonomy: a case study of Hyponephele lycaon species complex in Israel (Lepidoptera, Nymphalidae, Satyrinae).},
journal = {ZooKeys},
volume = {},
number = {538},
pages = {21-34},
pmid = {26807034},
issn = {1313-2989},
abstract = {It is difficult to interpret mitochondrial diversity in terms of taxonomy even in cases in which a concordance exists between mitochondrial, ecological and morphological markers. Here we demonstrate this difficulty through a study of Israeli Hyponephele butterflies. We show that samples commonly identified as Hyponephele lycaon are represented on Mount Hermon in Israel by two sympatric groups of individuals distinct both in mitochondrial DNA-barcodes (uncorrected p-distance = 3.5%) and hindwing underside pattern. These two groups were collected in different biotopes. They also tended to be different in length of brachia in male genitalia, although the latter character is variable. We reject the hypothesis that the discovered COI haplogroups are selectively neutral intraspecific characters. We hypothesize that they represent: either (1) two different biological species, or (2) a consequence of a strong positive selection acting at intraspecific level and resulting in two intraspecific clusters adapted to low and to high elevations. If we accept the first hypothesis, then provisionally these two haplogroups can be attributed to transpalearctic Hyponephele lycaon sensu stricto and to Hyponephele lycaonoides, previously known from Iran and East Turkey.},
}
@article {pmid26806015,
year = {2016},
author = {Tsang, YH and Dogruluk, T and Tedeschi, PM and Wardwell-Ozgo, J and Lu, H and Espitia, M and Nair, N and Minelli, R and Chong, Z and Chen, F and Chang, QE and Dennison, JB and Dogruluk, A and Li, M and Ying, H and Bertino, JR and Gingras, MC and Ittmann, M and Kerrigan, J and Chen, K and Creighton, CJ and Eterovic, K and Mills, GB and Scott, KL},
title = {Functional annotation of rare gene aberration drivers of pancreatic cancer.},
journal = {Nature communications},
volume = {7},
number = {},
pages = {10500},
pmid = {26806015},
issn = {2041-1723},
support = {P30 CA016672/CA/NCI NIH HHS/United States ; U01 CA168394/CA/NCI NIH HHS/United States ; P30CA125123/CA/NCI NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; R01CA138701/CA/NCI NIH HHS/United States ; U01CA168394/CA/NCI NIH HHS/United States ; R01 CA138701/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Carcinogenesis ; Cell Line, Tumor ; Female ; Humans ; Mice ; Mice, Nude ; Mutation ; Pancreatic Neoplasms/enzymology/*genetics/metabolism/pathology ; Phosphotransferases (Alcohol Group Acceptor)/*genetics ; Reactive Oxygen Species/metabolism ; },
abstract = {As we enter the era of precision medicine, characterization of cancer genomes will directly influence therapeutic decisions in the clinic. Here we describe a platform enabling functionalization of rare gene mutations through their high-throughput construction, molecular barcoding and delivery to cancer models for in vivo tumour driver screens. We apply these technologies to identify oncogenic drivers of pancreatic ductal adenocarcinoma (PDAC). This approach reveals oncogenic activity for rare gene aberrations in genes including NAD Kinase (NADK), which regulates NADP(H) homeostasis and cellular redox state. We further validate mutant NADK, whose expression provides gain-of-function enzymatic activity leading to a reduction in cellular reactive oxygen species and tumorigenesis, and show that depletion of wild-type NADK in PDAC cell lines attenuates cancer cell growth in vitro and in vivo. These data indicate that annotating rare aberrations can reveal important cancer signalling pathways representing additional therapeutic targets.},
}
@article {pmid26805755,
year = {2016},
author = {Geiger, MF and Schreiner, C and Delmastro, GB and Herder, F},
title = {Combining geometric morphometrics with molecular genetics to investigate a putative hybrid complex: a case study with barbels Barbus spp. (Teleostei: Cyprinidae).},
journal = {Journal of fish biology},
volume = {88},
number = {3},
pages = {1038-1055},
doi = {10.1111/jfb.12871},
pmid = {26805755},
issn = {1095-8649},
mesh = {Animals ; Cyprinidae/*anatomy &amp; histology/classification/*genetics ; Electron Transport Complex IV/genetics ; Genotype ; Haplotypes ; *Hybridization, Genetic ; Italy ; Phylogeny ; Species Specificity ; },
abstract = {This integrative study examined the morphological and genetic affinities of three endemic barbel species from Italy (brook barbel Barbus caninus, Italian barbel Barbus plebejus and horse barbel Barbus tyberinus) and of putative hybrid specimens to their species of origin. Two of the species frequently occur together with the non-native barbel Barbus barbus. DNA barcoding indicates that mitochondrial (mt) haplotypes often do not match the species expected from morphology. Linear distance measurements and meristics are not informative for discrimination of the species and putative hybrids, but a discriminant analysis of principal components (DAPC) of geometric landmark data produces reassignments largely in congruence with mt and nuclear genetic data. Cyto-nuclear conflicts confirm the presence of hybridization in B. plebejus and B. tyberinus and identify additional introgressed specimens. A comparison between mixed genotypes and their morphology-based assignment reveals no predictable pattern. The finding that most individuals of the morphologically similar B. plebejus and B. tyberinus have very high assignment probabilities to their respective species suggests that the presented approach may serve as a valuable tool to distinguish morphologically very similar taxa.},
}
@article {pmid26801629,
year = {2016},
author = {Pommier de Santi, V and Girod, R and Mura, M and Dia, A and Briolant, S and Djossou, F and Dusfour, I and Mendibil, A and Simon, F and Deparis, X and Pagès, F},
title = {Epidemiological and entomological studies of a malaria outbreak among French armed forces deployed at illegal gold mining sites reveal new aspects of the disease's transmission in French Guiana.},
journal = {Malaria journal},
volume = {15},
number = {},
pages = {35},
pmid = {26801629},
issn = {1475-2875},
mesh = {Animals ; Anopheles/*parasitology ; Female ; French Guiana/epidemiology ; Gold ; Humans ; Insect Vectors/parasitology ; Malaria/*epidemiology/*transmission ; Male ; *Mining ; Retrospective Studies ; },
abstract = {BACKGROUND: In December 2010, a Plasmodium vivax malaria outbreak occurred among French forces involved in a mission to control illegal gold mining in French Guiana. The findings of epidemiological and entomological investigations conducted after this outbreak are presented here.<br><br>METHODS: Data related to malaria cases reported to the French armed forces epidemiological surveillance system were collected during the epidemic period from December 2010 to April 2011. A retrospective cohort study was conducted to identify presumed contamination sites. Anopheles mosquitoes were sampled at the identified sites using Mosquito Magnet and CDC light traps. Specimens were identified morphologically and confirmed using molecular methods (sequencing of ITS2 gene and/or barcoding). Anopheles infections with Plasmodium falciparum and P. vivax were tested by both enzyme-linked immunosorbent assay and real-time PCR.<br><br>RESULTS: Seventy-two P. vivax malaria cases were reported (three were mixed P. falciparum/P. vivax infections), leading to a global attack rate of 26.5% (72/272). Lack of compliance with vector control measures and doxycycline chemoprophylaxis was reported by patients. Two illegal gold mining sites located in remote areas in the primary forest were identified as places of contamination. In all, 595 Anopheles females were caught and 528 specimens were formally identified: 305 Anopheles darlingi, 145 Anopheles nuneztovari s.l., 63 Anopheles marajoara and 15 Anopheles triannulatus s.l. Three An. darlingi were infected by P. falciparum (infection rate: 1.1%) and four An. marajoara by P. vivax (infection rate: 6.4%).<br><br>DISCUSSION: The main drivers of the outbreak were the lack of adherence by military personnel to malaria prevention measures and the high level of malaria transmission at illegal gold mining sites. Anopheles marajoara was clearly implicated in malaria transmission for the first time in French Guiana. The high infection rates observed confirm that illegal gold mining sites must be considered as high level malaria transmission areas in the territory.<br><br>CONCLUSIONS: Illegal gold mining activities are challenging the control of malaria in French Guiana. Collaboration with neighbouring countries is necessary to take into account mobile populations such as gold miners. Malaria control strategies in the French armed forces must be adapted to P. vivax malaria and sylvatic Anopheles species.},
}
@article {pmid26800992,
year = {2016},
author = {Kikkawa, HS and Tsuge, K and Sugita, R},
title = {Real-Time PCR Quantification of Chloroplast DNA Supports DNA Barcoding of Plant Species.},
journal = {Molecular biotechnology},
volume = {58},
number = {3},
pages = {212-219},
pmid = {26800992},
issn = {1559-0305},
mesh = {Benzothiazoles ; DNA Barcoding, Taxonomic/methods ; DNA Primers/genetics ; DNA, Chloroplast/*analysis/chemistry/classification ; Diamines ; Organic Chemicals/chemistry ; Plants/classification/genetics ; Quinolines ; Real-Time Polymerase Chain Reaction/*methods ; },
abstract = {Species identification from extracted DNA is sometimes needed for botanical samples. DNA quantification is required for an accurate and effective examination. If a quantitative assay provides unreliable estimates, a higher quantity of DNA than the estimated amount may be used in additional analyses to avoid failure to analyze samples from which extracting DNA is difficult. Compared with conventional methods, real-time quantitative PCR (qPCR) requires a low amount of DNA and enables quantification of dilute DNA solutions accurately. The aim of this study was to develop a qPCR assay for quantification of chloroplast DNA from taxonomically diverse plant species. An absolute quantification method was developed using primers targeting the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene using SYBR Green I-based qPCR. The calibration curve was generated using the PCR amplicon as the template. DNA extracts from representatives of 13 plant families common in Japan. This demonstrates that qPCR analysis is an effective method for quantification of DNA from plant samples. The results of qPCR assist in the decision-making will determine the success or failure of DNA analysis, indicating the possibility of optimization of the procedure for downstream reactions.},
}
@article {pmid26800039,
year = {2016},
author = {Kersten, B and Faivre Rampant, P and Mader, M and Le Paslier, MC and Bounon, R and Berard, A and Vettori, C and Schroeder, H and Leplé, JC and Fladung, M},
title = {Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding.},
journal = {PloS one},
volume = {11},
number = {1},
pages = {e0147209},
pmid = {26800039},
issn = {1932-6203},
mesh = {Chloroplasts/*genetics ; *Genome, Plant ; Mitochondria/*genetics ; Phylogeny ; *Plant Breeding ; Populus/classification/*genetics ; },
abstract = {Complete Populus genome sequences are available for the nucleus (P. trichocarpa; section Tacamahaca) and for chloroplasts (seven species), but not for mitochondria. Here, we provide the complete genome sequences of the chloroplast and the mitochondrion for the clones P. tremula W52 and P. tremula x P. alba 717-1B4 (section Populus). The organization of the chloroplast genomes of both Populus clones is described. A phylogenetic tree constructed from all available complete chloroplast DNA sequences of Populus was not congruent with the assignment of the related species to different Populus sections. In total, 3,024 variable nucleotide positions were identified among all compared Populus chloroplast DNA sequences. The 5-prime part of the LSC from trnH to atpA showed the highest frequency of variations. The variable positions included 163 positions with SNPs allowing for differentiating the two clones with P. tremula chloroplast genomes (W52, 717-1B4) from the other seven Populus individuals. These potential P. tremula-specific SNPs were displayed as a whole-plastome barcode on the P. tremula W52 chloroplast DNA sequence. Three of these SNPs and one InDel in the trnH-psbA linker were successfully validated by Sanger sequencing in an extended set of Populus individuals. The complete mitochondrial genome sequence of P. tremula is the first in the family of Salicaceae. The mitochondrial genomes of the two clones are 783,442 bp (W52) and 783,513 bp (717-1B4) in size, structurally very similar and organized as single circles. DNA sequence regions with high similarity to the W52 chloroplast sequence account for about 2% of the W52 mitochondrial genome. The mean SNP frequency was found to be nearly six fold higher in the chloroplast than in the mitochondrial genome when comparing 717-1B4 with W52. The availability of the genomic information of all three DNA-containing cell organelles will allow a holistic approach in poplar molecular breeding in the future.},
}
@article {pmid26799827,
year = {2016},
author = {Chuang, PS and Hung, TC and Chang, HA and Huang, CK and Shiao, JC},
title = {The Species and Origin of Shark Fins in Taiwan's Fishing Ports, Markets, and Customs Detention: A DNA Barcoding Analysis.},
journal = {PloS one},
volume = {11},
number = {1},
pages = {e0147290},
pmid = {26799827},
issn = {1932-6203},
mesh = {Animal Fins ; Animals ; Base Sequence ; Cyclooxygenase 1/genetics ; DNA Barcoding, Taxonomic/*methods ; Diet ; *Endangered Species ; *Feeding Behavior ; Geography ; Humans ; Population Density ; Seafood ; Sequence Analysis, DNA ; Sharks/*classification/*genetics ; Taiwan ; },
abstract = {The increasing consumption of shark products, along with the shark's fishing vulnerabilities, has led to the decrease in certain shark populations. In this study we used a DNA barcoding method to identify the species of shark landings at fishing ports, shark fin products in retail stores, and shark fins detained by Taiwan customs. In total we identified 23, 24, and 14 species from 231 fishing landings, 316 fin products, and 113 detained shark fins, respectively. All the three sample sources were dominated by Prionace glauca, which accounted for more than 30% of the collected samples. Over 60% of the species identified in the fin products also appeared in the port landings, suggesting the domestic-dominance of shark fin products in Taiwan. However, international trade also contributes a certain proportion of the fin product markets, as four species identified from the shark fin products are not found in Taiwan's waters, and some domestic-available species were also found in the customs-detained sample. In addition to the species identification, we also found geographical differentiation in the cox1 gene of the common thresher sharks (Alopias vulpinus), the pelagic thresher shark (A. pelagicus), the smooth hammerhead shark (Sphyrna zygaena), and the scalloped hammerhead shark (S. lewini). This result might allow fishing authorities to more effectively trace the origins as well as enforce the management and conservation of these sharks.},
}
@article {pmid26798309,
year = {2015},
author = {Lehr, E and Dehling, JM and Greenbaum, E and Sinsch, U},
title = {Embryogenesis and tadpole description of Hyperolius castaneus Ahl, 1931 and H. jackie Dehling, 2012 (Anura, Hyperoliidae) from montane bog pools.},
journal = {ZooKeys},
volume = {},
number = {546},
pages = {125-152},
pmid = {26798309},
issn = {1313-2989},
support = {G12 MD007592/MD/NIMHD NIH HHS/United States ; G12 RR008124/RR/NCRR NIH HHS/United States ; },
abstract = {Tadpoles of Hyperolius castaneus and Hyperolius jackie were found in the Nyungwe National Park in Rwanda and adjacent areas. Tadpoles of both species were identified by DNA-barcoding. At the shore of a bog pool three clutches of Hyperolius castaneus of apparently different age, all laid on moss pads (Polytrichum commune, Isotachis aubertii) or grass tussocks (Andropogon shirensis) 2-5 cm above the water level, were found. One clutch of Hyperolius castaneus was infested by larval dipterid flies. The most recently laid clutch contained about 20 eggs within a broad egg-jelly envelope. The eggs were attached to single blades of a tussock and distributed over a vertical distance of 8 cm. A pair of Hyperolius castaneus found in axillary amplexus was transported in a plastic container to the lab for observation. The pair deposited a total of 57 eggs (15 eggs attached to the upper wall of the transport container, 42 eggs floated in the water). Embryogenesis of the clutch was monitored in the plastic container at 20 ± 2 °C (air temperature) and documented by photos until Gosner Stage 25. The description of the tadpole of Hyperolius castaneus is based on a Gosner Stage 29 individual from a series of 57 tadpoles (Gosner stages 25-41). The description of the tadpole of Hyperolius jackie is based on a Gosner Stage 32 individual from a series of 43 tadpoles (Gosner stages 25-41). Egg laying behavior and embryogenesis are unknown for Hyperolius jackie. The labial tooth row formula for both species is 1/3(1) with a narrow median gap of the tooth row. Variation in external morphology was observed in size and labial tooth row formula within the species. With the tadpole descriptions of Hyperolius castaneus and Hyperolius jackie, 36 tadpoles of the 135 known Hyperolius species have been described, including five of the eleven Hyperolius species known from Rwanda.},
}
@article {pmid26798283,
year = {2015},
author = {Neild, AF and Nakahara, S and Zacca, T and Fratello, S and Lamas, G and Le Crom, JF and Dolibaina, DR and Dias, FM and Casagrande, MM and Mielke, OH and Espeland, M},
title = {Two new species of Euptychia Hübner, 1818 from the upper Amazon basin (Lepidoptera, Nymphalidae, Satyrinae).},
journal = {ZooKeys},
volume = {},
number = {541},
pages = {87-108},
pmid = {26798283},
issn = {1313-2989},
abstract = {Two new species of Euptychia Hübner, 1818 are described from the upper Amazon basin: Euptychia attenboroughi Neild, Nakahara, Fratello &amp; Le Crom, sp. n. (type locality: Amazonas, Venezuela), and Euptychia sophiae Zacca, Nakahara, Dolibaina &amp; Dias, sp. n. (type locality: Acre, Brazil). Their unusual facies prompted molecular and phylogenetic analyses of one of the species resulting in support for their classification in monophyletic Euptychia. Diagnostic characters for the two species are presented based on wing morphology, wing pattern, presence of androconial patches on the hindwing, and genitalia. Our results indicate that the projection of the tegumen above the uncus, previously considered a synapomorphy for Euptychia, is not shared by all species in the genus. The adults and their genitalia are documented, and distribution data and a map are provided.},
}
@article {pmid26798245,
year = {2015},
author = {Raupach, MJ and Radulovici, AE},
title = {Looking back on a decade of barcoding crustaceans.},
journal = {ZooKeys},
volume = {},
number = {539},
pages = {53-81},
pmid = {26798245},
issn = {1313-2989},
abstract = {Species identification represents a pivotal component for large-scale biodiversity studies and conservation planning but represents a challenge for many taxa when using morphological traits only. Consequently, alternative identification methods based on molecular markers have been proposed. In this context, DNA barcoding has become a popular and accepted method for the identification of unknown animals across all life stages by comparison to a reference library. In this review we examine the progress of barcoding studies for the Crustacea using the Web of Science data base from 2003 to 2014. All references were classified in terms of taxonomy covered, subject area (identification/library, genetic variability, species descriptions, phylogenetics, methods, pseudogenes/numts), habitat, geographical area, authors, journals, citations, and the use of the Barcode of Life Data Systems (BOLD). Our analysis revealed a total number of 164 barcoding studies for crustaceans with a preference for malacostracan crustaceans, in particular Decapoda, and for building reference libraries in order to identify organisms. So far, BOLD did not establish itself as a popular informatics platform among carcinologists although it offers many advantages for standardized data storage, analyses and publication.},
}
@article {pmid26797695,
year = {2016},
author = {Ahrens, D and Fujisawa, T and Krammer, HJ and Eberle, J and Fabrizi, S and Vogler, AP},
title = {Rarity and Incomplete Sampling in DNA-Based Species Delimitation.},
journal = {Systematic biology},
volume = {65},
number = {3},
pages = {478-494},
doi = {10.1093/sysbio/syw002},
pmid = {26797695},
issn = {1076-836X},
mesh = {Animals ; Classification/*methods ; Coleoptera/classification/genetics ; Computer Simulation ; DNA/genetics ; Electron Transport Complex IV/genetics ; Madagascar ; *Phylogeny ; Population Density ; Sample Size ; },
abstract = {DNA-based species delimitation may be compromised by limited sampling effort and species rarity, including "singleton" representatives of species, which hampers estimates of intra- versus interspecies evolutionary processes. In a case study of southern African chafers (beetles in the family Scarabaeidae), many species and subclades were poorly represented and 48.5% of species were singletons. Using cox1 sequences from >500 specimens and ∼100 species, the Generalized Mixed Yule Coalescent (GMYC) analysis as well as various other approaches for DNA-based species delimitation (Automatic Barcode Gap Discovery (ABGD), Poisson tree processes (PTP), Species Identifier, Statistical Parsimony), frequently produced poor results if analyzing a narrow target group only, but the performance improved when several subclades were combined. Hence, low sampling may be compensated for by "clade addition" of lineages outside of the focal group. Similar findings were obtained in reanalysis of published data sets of taxonomically poorly known species assemblages of insects from Madagascar. The low performance of undersampled trees is not due to high proportions of singletons per se, as shown in simulations (with 13%, 40% and 52% singletons). However, the GMYC method was highly sensitive to variable effective population size ([Formula: see text]), which was exacerbated by variable species abundances in the simulations. Hence, low sampling success and rarity of species affect the power of the GMYC method only if they reflect great differences in [Formula: see text] among species. Potential negative effects of skewed species abundances and prevalence of singletons are ultimately an issue about the variation in [Formula: see text] and the degree to which this is correlated with the census population size and sampling success. Clade addition beyond a limited study group can overcome poor sampling for the GMYC method in particular under variable [Formula: see text] This effect was less pronounced for methods of species delimitation not based on coalescent models.},
}
@article {pmid26793739,
year = {2015},
author = {Marsic, D and Méndez-Gómez, HR and Zolotukhin, S},
title = {High-accuracy biodistribution analysis of adeno-associated virus variants by double barcode sequencing.},
journal = {Molecular therapy. Methods &amp; clinical development},
volume = {2},
number = {},
pages = {15041},
pmid = {26793739},
issn = {2329-0501},
support = {R01 GM082946/GM/NIGMS NIH HHS/United States ; R01 HL097088/HL/NHLBI NIH HHS/United States ; },
abstract = {Biodistribution analysis is a key step in the evaluation of adeno-associated virus (AAV) capsid variants, whether natural isolates or produced by rational design or directed evolution. Indeed, when screening candidate vectors, accurate knowledge about which tissues are infected and how efficiently is essential. We describe the design, validation, and application of a new vector, pTR-UF50-BC, encoding a bioluminescent protein, a fluorescent protein and a DNA barcode, which can be used to visualize localization of transduction at the organism, organ, tissue, or cellular levels. In addition, by linking capsid variants to different barcoded versions of the vector and amplifying the barcode region from various tissue samples using barcoded primers, biodistribution of viral genomes can be analyzed with high accuracy and efficiency.},
}
@article {pmid26793225,
year = {2015},
author = {Gurr, GM and You, M},
title = {Conservation Biological Control of Pests in the Molecular Era: New Opportunities to Address Old Constraints.},
journal = {Frontiers in plant science},
volume = {6},
number = {},
pages = {1255},
pmid = {26793225},
issn = {1664-462X},
abstract = {Biological control has long been considered a potential alternative to pesticidal strategies for pest management but its impact and level of use globally remain modest and inconsistent. A rapidly expanding range of molecular - particularly DNA-related - techniques is currently revolutionizing many life sciences. This review identifies a series of constraints on the development and uptake of conservation biological control and considers the contemporary and likely future influence of molecular methods on these constraints. Molecular approaches are now often used to complement morphological taxonomic methods for the identification and study of biological control agents including microbes. A succession of molecular techniques has been applied to 'who eats whom' questions in food-web ecology. Polymerase chain reaction (PCR) approaches have largely superseded immunological approaches such as enzyme-linked immunosorbent assay (ELISA) and now - in turn - are being overtaken by next generation sequencing (NGS)-based approaches that offer unparalleled power at a rapidly diminishing cost. There is scope also to use molecular techniques to manipulate biological control agents, which will be accelerated with the advent of gene editing tools, the CRISPR/Cas9 system in particular. Gene editing tools also offer unparalleled power to both elucidate and manipulate plant defense mechanisms including those that involve natural enemy attraction to attacked plants. Rapid advances in technology will allow the development of still more novel pest management options for which uptake is likely to be limited chiefly by regulatory hurdles.},
}
@article {pmid26791779,
year = {2016},
author = {Hasvold, G and Lund-Andersen, C and Lando, M and Patzke, S and Hauge, S and Suo, Z and Lyng, H and Syljuåsen, RG},
title = {Hypoxia-induced alterations of G2 checkpoint regulators.},
journal = {Molecular oncology},
volume = {10},
number = {5},
pages = {764-773},
pmid = {26791779},
issn = {1878-0261},
mesh = {Cell Line, Tumor ; DNA Damage ; G2 Phase ; *G2 Phase Cell Cycle Checkpoints ; Gene Expression Regulation, Neoplastic ; Genomic Instability ; Humans ; Hypoxia/*complications/*genetics ; Neoplasms/*complications/*genetics ; },
abstract = {Hypoxia promotes an aggressive tumor phenotype with increased genomic instability, partially due to downregulation of DNA repair pathways. However, genome stability is also surveilled by cell cycle checkpoints. An important issue is therefore whether hypoxia also can influence the DNA damage-induced cell cycle checkpoints. Here, we show that hypoxia (24 h 0.2% O2) alters the expression of several G2 checkpoint regulators, as examined by microarray gene expression analysis and immunoblotting of U2OS cells. While some of the changes reflected hypoxia-induced inhibition of cell cycle progression, the levels of several G2 checkpoint regulators, in particular Cyclin B, were reduced in G2 phase cells after hypoxic exposure, as shown by flow cytometric barcoding analysis of individual cells. These effects were accompanied by decreased phosphorylation of a Cyclin dependent kinase (CDK) target in G2 phase cells after hypoxia, suggesting decreased CDK activity. Furthermore, cells pre-exposed to hypoxia showed increased G2 checkpoint arrest upon treatment with ionizing radiation. Similar results were found following other hypoxic conditions (∼0.03% O2 20 h and 0.2% O2 72 h). These results demonstrate that the DNA damage-induced G2 checkpoint can be altered as a consequence of hypoxia, and we propose that such alterations may influence the genome stability of hypoxic tumors.},
}
@article {pmid26791499,
year = {2016},
author = {Senés-Guerrero, C and Schüßler, A},
title = {DNA-Based Characterization and Identification of Arbuscular Mycorrhizal Fungi Species.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1399},
number = {},
pages = {101-123},
doi = {10.1007/978-1-4939-3369-3_6},
pmid = {26791499},
issn = {1940-6029},
mesh = {DNA, Fungal/genetics ; *High-Throughput Nucleotide Sequencing ; Mycorrhizae/classification/*genetics/isolation &amp; purification ; Plant Roots/*microbiology ; Plants/genetics ; Sequence Analysis, DNA/*methods ; Spores, Fungal/genetics ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) are obligate symbionts of most land plants. They have great ecological and economic importance as they can improve plant nutrition, plant water supply, soil structure, and plant resistance to pathogens. We describe two approaches for the DNA-based characterization and identification of AMF, which both can be used for single fungal spores, soil, or roots samples and resolve closely related AMF species: (a) Sanger sequencing of a 1.5 kb extended rDNA-barcode from clone libraries, e.g., to characterize AMF isolates, and (b) high throughput 454 GS-FLX+ pyrosequencing of a 0.8 kb rDNA fragment, e.g., for in-field monitoring.},
}
@article {pmid26791497,
year = {2016},
author = {Clemmensen, KE and Ihrmark, K and Durling, MB and Lindahl, BD},
title = {Sample Preparation for Fungal Community Analysis by High-Throughput Sequencing of Barcode Amplicons.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1399},
number = {},
pages = {61-88},
doi = {10.1007/978-1-4939-3369-3_4},
pmid = {26791497},
issn = {1940-6029},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Fungi/classification/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Soil Microbiology ; },
abstract = {Fungal species participate in vast numbers of processes in the landscape around us. However, their often cryptic growth, inside various substrates and in highly diverse species assemblages, has been a major obstacle to thorough analysis of fungal communities, hampering exhaustive description of the fungal kingdom. Recent technological developments allowing rapid, high-throughput sequencing of mixed communities from many samples at once are currently having a tremendous impact in fungal community ecology. Universal DNA extraction followed by amplification and sequencing of fungal species-level barcodes such as the nuclear internal transcribed spacer (ITS) region now enable identification and relative quantification of fungal community members across well-replicated experimental settings. Here, we present the sample preparation procedure presently used in our laboratory for fungal community analysis by high-throughput sequencing of amplified ITS2 markers. We focus on the procedure optimized for studies of total fungal communities in humus-rich soils, wood, and litter. However, this procedure can be applied to other sample types and markers. We focus on the laboratory-based part of sample preparation, that is, the procedure from the point where samples enter the laboratory until amplicons are submitted for sequencing. Our procedure comprises four main parts: (1) universal DNA extraction, (2) optimization of PCR conditions, (3) production of tagged ITS amplicons, and (4) preparation of the multiplexed amplicon mix to be sequenced. The presented procedure is independent of the specific high-throughput sequencing technology used, which makes it highly versatile.},
}
@article {pmid26790677,
year = {2016},
author = {Moravec, F and Chaabane, A and Neifar, L and Gey, D and Justine, JL},
title = {Descriptions of Philometra aenei n. sp. and P. tunisiensis n. sp. (Nematoda: Philometridae) from Epinephelus spp. off Tunisia confirm a high degree of host specificity of gonad-infecting species of Philometra Costa, 1845 in groupers (Serranidae).},
journal = {Systematic parasitology},
volume = {93},
number = {2},
pages = {115-128},
pmid = {26790677},
issn = {1573-5192},
mesh = {Animals ; Dracunculoidea/anatomy &amp; histology/*classification/ultrastructure ; Female ; Gonads/parasitology ; *Host Specificity ; Male ; Mediterranean Sea ; Microscopy, Electron, Scanning ; Perciformes/*parasitology ; Species Specificity ; Tunisia ; },
abstract = {Based on light and electron microscopical studies of males and mature females, two new gonad-infecting species of Philometra Costa, 1845 (Nematoda: Philometridae) are described from the ovary of groupers, Epinephelus spp. (Perciformes; Serranidae), in the Mediterranean Sea off Tunisia (near Sfax): Philometra aenei n. sp. from the white grouper E. aeneus (Geoffroy Saint-Hilaire) and P. tunisiensis n. sp. from the goldblotch grouper E. costae (Steindachner). Identification of both fish hosts was confirmed by barcoding of the infected fish specimens. Philometra aenei is mainly characterised by the length of conspicuously distended spicules (108-123 µm), the presence of a distinct dorsal barb at the middle region of the gubernaculum and a distinct protuberance consisting of two dorsolateral lamellar parts separated from each other by a smooth median field at its distal tip, a V-shaped mound on the male caudal extremity and by the body length of the males (2.34-3.05 mm). The male of this species was found to possess minute deirids in the cervical region, which is quite exceptional within the Philometridae. Philometra tunisiensis is distinguished from other gonad-infecting congeneric species parasitising serranids by the length of the needle-like spicules and gubernaculum (201-219 and 78-87 µm, respectively), spicule length representing 9-11% of body length, the gubernaculum/spicules length ratio of 1:2.52-2.77, the length of oesophagus in the male comprising 15-16% of the body length, the absence of a dorsal protuberance on the distal lamellar part of the gubernaculum and a pair of large papillae posterior to the cloaca, a dorsally interrupted mound on the male caudal extremity and the body length of the male (2.01-2.42 mm). The presence of three morphologically very different species of Philometra in congeneric hosts in the Mediterranean Sea confirms a high degree of host specificity of these gonad-infecting nematodes parasitising groupers.},
}
@article {pmid26790288,
year = {2015},
author = {Liao, LX and Zeng, KW and Tu, PF},
title = {[Hydrophidae identification through analysis on Cyt b gene barcode].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {40},
number = {16},
pages = {3179-3182},
pmid = {26790288},
issn = {1001-5302},
mesh = {Animals ; Base Sequence ; China ; Cytochromes b/*genetics ; DNA Barcoding, Taxonomic ; Elapidae/classification/*genetics ; Molecular Sequence Data ; Phylogeny ; Reptilian Proteins/*genetics ; Sequence Analysis, DNA ; },
abstract = {Hydrophidae, one of the precious traditional Chinese medicines, is generally drily preserved to prevent corruption, but it is hard to identify the species of Hydrophidae through the appearance because of the change due to the drying process. The identification through analysis on gene barcode, a new technique in species identification, can avoid the problem. The gene barcodes of the 6 species of Hydrophidae like Lapemis hardwickii were aquired through DNA extraction and gene sequencing. These barcodes were then in sequence alignment and test the identification efficency by BLAST. Our results revealed that the barcode sequences performed high identification efficiency, and had obvious difference between intra- and inter-species. These all indicated that Cyt b DNA barcoding can confirm the Hydrophidae identification.},
}
@article {pmid26788439,
year = {2016},
author = {Shafee, TM and Robinson, AJ and van der Weerden, N and Anderson, MA},
title = {Structural homology guided alignment of cysteine rich proteins.},
journal = {SpringerPlus},
volume = {5},
number = {},
pages = {27},
pmid = {26788439},
issn = {2193-1801},
abstract = {BACKGROUND: Cysteine rich protein families are notoriously difficult to align due to low sequence identity and frequent insertions and deletions.<br><br>RESULTS: Here we present an alignment method that ensures homologous cysteines align by assigning a unique 10 amino acid barcode to those identified as structurally homologous by the DALI webserver. The free inter-cysteine regions of the barcoded sequences can then be aligned using any standard algorithm. Finally the barcodes are replaced with the original columns to yield an alignment which requires the minimum of manual refinement.<br><br>CONCLUSIONS: Using structural homology information to constrain sequence alignments allows the alignment of highly divergent, repetitive sequences that are poorly dealt with by existing algorithms. Tools are provided to perform this method online using the CysBar web-tool (http://CysBar.science.latrobe.edu.au) and offline (python script available from http://github.com/ts404/CysBar).},
}
@article {pmid26783518,
year = {2015},
author = {Ferri, E and Galimberti, A and Casiraghi, M and Airoldi, C and Ciaramelli, C and Palmioli, A and Mezzasalma, V and Bruni, I and Labra, M},
title = {Towards a Universal Approach Based on Omics Technologies for the Quality Control of Food.},
journal = {BioMed research international},
volume = {2015},
number = {},
pages = {365794},
pmid = {26783518},
issn = {2314-6141},
mesh = {*DNA Barcoding, Taxonomic ; *Food Analysis ; Humans ; Magnetic Resonance Spectroscopy ; Mass Spectrometry ; *Metabolomics ; *Quality Control ; },
abstract = {In the last decades, food science has greatly developed, turning from the consideration of food as mere source of energy to a growing awareness on its importance for health and particularly in reducing the risk of diseases. Such vision led to an increasing attention towards the origin and quality of raw materials as well as their derived food products. The continuous advance in molecular biology allowed setting up efficient and universal omics tools to unequivocally identify the origin of food items and their traceability. In this review, we considered the application of a genomics approach known as DNA barcoding in characterizing the composition of foodstuffs and its traceability along the food supply chain. Moreover, metabolomics analytical strategies based on Nuclear Magnetic Resonance (NMR) and Mass Spectroscopy (MS) were discussed as they also work well in evaluating food quality. The combination of both approaches allows us to define a sort of molecular labelling of food that is easily understandable by the operators involved in the food sector: producers, distributors, and consumers. Current technologies based on digital information systems such as web platforms and smartphone apps can facilitate the adoption of such molecular labelling.},
}
@article {pmid26782506,
year = {2015},
author = {Ma, CY and Ma, HY and Ni, Y and Wang, W and Ma, LB},
title = {Molecular identification of the genus Thryssa based on DNA barcoding.},
journal = {Genetics and molecular research : GMR},
volume = {14},
number = {4},
pages = {18580-18586},
doi = {10.4238/2015.December.28.5},
pmid = {26782506},
issn = {1676-5680},
mesh = {Animals ; Base Sequence ; *DNA Barcoding, Taxonomic ; Evolution, Molecular ; Fishes/*classification/*genetics ; Genes, Mitochondrial ; Haplotypes ; Phylogeny ; },
abstract = {DNA barcoding is an effective method for identifying species by analyzing one or a few short standardized DNA sequences. In this study, we examined the utility of mitochondrial cytochrome oxidase subunit I (COI) sequences as a DNA barcode for the identification of six species belonging to the genus Thryssa: T. dussumieri, T. hamiltonii, T. kammalensis, T. mystax, T. setirostris, and T. vitrirostris. We obtained an intraspecific distance of 0.000 for T. vitrirostris and T. hamiltonii, 0.006 for T. mystax, 0.002 for T. dussumieri, and 0.005 for T. kammalensis. The average intraspecific distance was 0.002, while the average interspecific distance was 0.137. Thus, the interspecific genetic distance was approximately 67-fold larger than the intraspecific genetic distance; the average genetic distance among species was greater than the minimum of 0.020 between species suggested elsewhere. The genetic distance between T. vitrirostris and T. mystax was 0.003. A maximum-likelihood phylogenetic tree constructed using best-fitting tree topology showed distinct clusters corresponding to the species (except for T. vitrirostris and T. mystax). The closest relationship was found between T. vitrirostris and T. mystax. These two species clustered together in the phylogenetic tree. This conclusion contradicts the evolutionary relationship based on morphological classification.},
}
@article {pmid26782484,
year = {2015},
author = {Huang, ZH and Tu, FY and Liao, XJ},
title = {DNA barcoding and phylogenetic relationships of genera Picoides and Dendrocopos (Aves: Picidae).},
journal = {Genetics and molecular research : GMR},
volume = {14},
number = {4},
pages = {18370-18375},
doi = {10.4238/2015.December.23.24},
pmid = {26782484},
issn = {1676-5680},
mesh = {Animals ; Birds/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Phylogeny ; },
abstract = {Picoides and Dendrocopos are two closely related genera of woodpeckers (family Picidae), and members of these genera have long been the subjects of phylogenetic debate. Mitochondrial cytochrome c oxidase subunit I (COI) is a powerful marker for the identification and phylogenetic study of animal species. In the present study, we analyzed the COI barcodes of 21 species from the two genera, and 222 variable sites were identified. Kimura two-parameter distances were calculated between barcodes. The average interspecific genetic distance was more than 20 times higher than the average intraspecific genetic distance. The neighbor-joining method was used to construct a phylogenetic tree, and all of the species could be discriminated by their distinct clades. Picoides arcticus was the first to split from the lineage, and the other species were grouped into two divergent clades. The results of this study indicated that the COI genetic data did not support the monophyly of Picoides and Dendrocopos.},
}
@article {pmid26781381,
year = {2016},
author = {Al-Hatmi, AM and Mirabolfathy, M and Hagen, F and Normand, AC and Stielow, JB and Karami-Osbo, R and van Diepeningen, AD and Meis, JF and de Hoog, GS},
title = {DNA barcoding, MALDI-TOF, and AFLP data support Fusarium ficicrescens as a distinct species within the Fusarium fujikuroi species complex.},
journal = {Fungal biology},
volume = {120},
number = {2},
pages = {265-278},
doi = {10.1016/j.funbio.2015.08.001},
pmid = {26781381},
issn = {1878-6146},
mesh = {*Amplified Fragment Length Polymorphism Analysis ; DNA Barcoding, Taxonomic ; Ficus/*microbiology ; Fruit/microbiology ; Fusariosis/*microbiology ; Fusarium/classification/*genetics/*isolation &amp; purification ; Humans ; Molecular Sequence Data ; Phylogeny ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; },
abstract = {The Fusarium fujikuroi species complex (FFSC) is one of the most common groups of fusaria associated with plant diseases, mycotoxin production and traumatic and disseminated human infections. Here we present the description and taxonomy of a new taxon, Fusarium ficicrescens sp. nov., collected from contaminated fig fruits in Iran. Initially this species was identified as Fusarium andiyazi by morphology. In the present study the species was studied by multilocus sequence analysis, amplified fragment length polymorphism (AFLP), matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and phenotypic characters. Multilocus analyses were based on translation elongation factor 1α (TEF1), RNA polymerase subunit (RPB2) and beta-tubulin (BT2) and proved F. ficicrescens as a member of the FFSC. Phylogenetic analysis showed that the fungus is closely related to Fusarium lactis, Fusarium ramigenum, and Fusarium napiforme; known plant pathogens, mycotoxin producers, and occasionally occurring multidrug resistant opportunists. The new species differed by being able to grow at 37 °C and by the absence of mycotoxin production. TEF1 was confirmed as an essential barcode for identifying Fusarium species. In addition to TEF1, we evaluated BT2 and RPB2 in order to provide sufficient genetic and species boundaries information for recognition of the novel species.},
}
@article {pmid26781380,
year = {2016},
author = {Rodrigues, AM and Cruz Choappa, R and Fernandes, GF and de Hoog, GS and de Camargo, ZP},
title = {Sporothrix chilensis sp. nov. (Ascomycota: Ophiostomatales), a soil-borne agent of human sporotrichosis with mild-pathogenic potential to mammals.},
journal = {Fungal biology},
volume = {120},
number = {2},
pages = {246-264},
doi = {10.1016/j.funbio.2015.05.006},
pmid = {26781380},
issn = {1878-6146},
mesh = {Animals ; Humans ; Mammals/*microbiology ; Mice ; Molecular Sequence Data ; Phylogeny ; *Soil Microbiology ; Sporothrix/classification/genetics/*isolation &amp; purification/physiology ; Sporotrichosis/*microbiology/*veterinary ; },
abstract = {A combination of phylogeny, evolution, morphologies and ecologies has enabled major advances in understanding the taxonomy of Sporothrix species, including members exhibiting distinct lifestyles such as saprobes, human/animal pathogens, and insect symbionts. Phylogenetic analyses of ITS1/2 + 5.8s sequences split Sporothrix genus in two well-defined groups with dissimilar ecologies. Species embedded in the Sporothrix schenckii complex are frequently agents of human and animal sporotrichosis, and some of these are responsible for large sapronoses and zoonoses around the warmer temperate regions of the world. At the other extreme, basal saprophytic species evolved in association with decaying wood and soil, and are rarely found to cause human disease. We propose to create a new taxa, Sporothrix chilensis sp. nov., to accommodate strains collected from a clinical case of onychomycosis as well as from environmental origins in Chile. Multigene analyses based on ITS1/2 + 5.8s region, beta-tubulin, calmodulin and translation elongation factor 1α revealed that S. chilensis is a member of the Sporothrix pallida complex, and the nearest taxon is Sporothrix mexicana, a rare soil-borne species, non-pathogenic to humans. The ITS region serves as a primary barcode marker, while each one of the protein-coding loci easily recognized species boundaries providing sufficient information for species identification. A disseminated model of murine sporotrichosis revealed a mild-pathogenic potential, with lung invasion. Although S. chilensis is not a primary pathogen, accidental infection may have an impact in the immunosuppressed population. With the introduction of distinct species with similar routes of transmission but different virulence, identification of Sporothrix agents at the species level is mandatory.},
}
@article {pmid26781379,
year = {2016},
author = {Al-Hatmi, AM and Van Den Ende, AH and Stielow, JB and Van Diepeningen, AD and Seifert, KA and McCormick, W and Assabgui, R and Gräfenhan, T and De Hoog, GS and Levesque, CA},
title = {Evaluation of two novel barcodes for species recognition of opportunistic pathogens in Fusarium.},
journal = {Fungal biology},
volume = {120},
number = {2},
pages = {231-245},
doi = {10.1016/j.funbio.2015.08.006},
pmid = {26781379},
issn = {1878-6146},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/genetics ; Fungal Proteins/genetics ; Fusariosis/*microbiology ; Fusarium/classification/genetics/*isolation &amp; purification ; Humans ; Phylogeny ; },
abstract = {The genus Fusarium includes more than 200 species of which 73 have been isolated from human infections. Fusarium species are opportunistic human pathogens with variable aetiology. Species determination is best made with the combined phylogeny of protein-coding genes such as elongation factor (TEF1), RNA polymerase (RPB2) and the partial β-tubulin (BT2) gene. The internal transcribed spacers 1, 2 and 5.8S rRNA gene (ITS) have also been used, however, ITS cannot discriminate several closely related species and has nonorthologous copies in Fusarium. Currently, morphological approaches and tree-building methods are in use to define species and to discover hitherto undescribed species. Aftter a species is defined, DNA barcoding approaches can be used to identify species by the presence or absence of discrete nucleotide characters. We demonstrate the potential of two recently discovered DNA barcode loci, topoisomerase I (TOP1) and phosphoglycerate kinase (PGK), in combination with other routinely used markers such as TEF1, in an analysis of 144 Fusarium strains belonging to 52 species. Our barcoding study using TOP1 and PKG provided concordance of molecular data with TEF1. The currently accepted Fusarium species sampled were well supported in phylogenetic trees of both new markers.},
}
@article {pmid26781378,
year = {2016},
author = {Samerpitak, K and Gerrits van den Ende, BH and Stielow, JB and Menken, SB and de Hoog, GS},
title = {Barcoding and species recognition of opportunistic pathogens in Ochroconis and Verruconis.},
journal = {Fungal biology},
volume = {120},
number = {2},
pages = {219-230},
doi = {10.1016/j.funbio.2015.08.010},
pmid = {26781378},
issn = {1878-6146},
mesh = {Ascomycota/*classification/genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic ; Fungal Proteins/genetics ; Humans ; Molecular Sequence Data ; Mycoses/*microbiology ; Phylogeny ; },
abstract = {The genera Ochroconis and Verruconis (Sympoventuriaceae, Venturiales) have remarkably high molecular diversity despite relatively high degrees of phenotypic similarity. Tree topologies, inter-specific and intra-specific heterogeneities, barcoding gaps and reciprocal monophyly of all currently known species were analyzed. It was concluded that all currently used genes viz. SSU, ITS, LSU, ACT1, BT2, and TEF1 were unable to reach all 'gold standard' criteria of barcoding markers. They could nevertheless be used for reasonably reliable identification of species, because the markers, although variable, were associated with large inter-specific heterogeneity. Of the coding protein-genes, ACT1 revealed highest potentiality as barcoding marker in mostly all parts of the investigated sequence. SSU, LSU, ITS, and ACT1 yielded consistent monophyly in all investigated species, but only SSU and LSU generated clear barcoding gaps. For phylogeny, LSU was an informative marker, suitable to reconstruct gene-trees showing correct phylogenetic relationships. Cryptic species were revealed especially in complexes with very high intra-specific variability. When all these complexes will be taxonomically resolved, ACT1 will probably appear to be the most reliable barcoding gene for Ochroconis and Verruconis.},
}
@article {pmid26781376,
year = {2016},
author = {Danesi, P and da Rold, G and Rizzoli, A and Hauffe, HC and Marangon, S and Samerpitak, K and Demanche, C and Guillot, J and Capelli, G and de Hoog, SG},
title = {Barcoding markers for Pneumocystis species in wildlife.},
journal = {Fungal biology},
volume = {120},
number = {2},
pages = {191-206},
doi = {10.1016/j.funbio.2015.08.019},
pmid = {26781376},
issn = {1878-6146},
mesh = {Animals ; Animals, Wild/*microbiology ; DNA Barcoding, Taxonomic ; Lung/microbiology ; Molecular Sequence Data ; Phylogeny ; Pneumocystis/classification/genetics/*isolation &amp; purification ; Pneumonia, Pneumocystis/microbiology/*veterinary ; },
abstract = {Lung specimens (n = 216) from six wildlife species were examined for occurrence of Pneumocystis species in pulmonary tissues. Among small mammals the shrew Sorex antinorii (80 %) were most frequently colonized. In contrast, foxes and badgers did not yield positive amplification. Host-specificity was noted, at least at the level of the host genus. Phylogenetic trees based on partial mtLSU and mtSSU showed high diversity of species corresponding to animal host diversity. Nuclear rDNA ITS data confirmed unambiguous separation of species. In conclusion, ITS is an excellent marker to distinguish species of the genus Pneumocystis.},
}
@article {pmid26781375,
year = {2016},
author = {Gouliamova, DE and Dimitrov, RA and Smith, MT and Groenewald, M and Stoilova-Disheva, MM and Guéorguiev, BV and Boekhout, T},
title = {DNA barcoding revealed Nematodospora valgi gen. nov., sp. nov. and Candida cetoniae sp. nov. in the Lodderomyces clade.},
journal = {Fungal biology},
volume = {120},
number = {2},
pages = {179-190},
doi = {10.1016/j.funbio.2015.05.008},
pmid = {26781375},
issn = {1878-6146},
mesh = {Animals ; Candida/classification/genetics/*isolation &amp; purification ; Coleoptera/*microbiology ; DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; Molecular Sequence Data ; Mycological Typing Techniques ; Phylogeny ; Saccharomycetales/classification/genetics/*isolation &amp; purification ; },
abstract = {During a yeast biodiversity survey conducted in 2009-2011 in Bulgaria (South Eastern Europe) five strains of a novel ascomycetous yeast species were isolated from the beetle Valgus hemipterus (Cetoniinae) collected from two localities, namely Osogovska Planina Mountain and Nature Park Zlatni Pyasatsi. Phylogenetic analysis using combined sequences of the D1/D2 domains of the large subunit ribosomal DNA (LSU rDNA) and the internal transcribed spacers 1 + 2 regions (ITS1+2) placed the novel species on a separate branch near the basal part of the Lodderomyces clade. The novel species has a unique ascospore morphology distinct from those of the closely related teleomorphic genus Lodderomyces. Based on phylogenetic analysis and morphology of the ascospores we propose Nematodospora valgi gen. nov., sp. nov. to accommodate these isolates (MB811804 D37S(T), MB802458). Two strains of a novel anamorphic yeast species were isolated from the beetles Cetonia aurata and Oxythyrea funesta (Cetoniinae) collected in East Rhodopies and Sofia city, respectively. DNA barcoding analysis placed the new yeast species within the Candida parapsilosis subclade. Here, we present the description of a new yeast species, Candida cetoniae sp. nov. (IMB1R2(T), MB803501) to accommodate these two strains. The ecology and biogeography of the insect-associated yeasts of the Lodderomyces clade is discussed.},
}
@article {pmid26781374,
year = {2016},
author = {Zhao, L and de Hoog, GS and Cornelissen, A and Lyu, Q and Mou, L and Liu, T and Cao, Y and Vatanshenassan, M and Kang, Y},
title = {Prospective evaluation of the chromogenic medium CandiSelect 4 for differentiation and presumptive identification of non-Candida albicans Candida species.},
journal = {Fungal biology},
volume = {120},
number = {2},
pages = {173-178},
doi = {10.1016/j.funbio.2015.09.006},
pmid = {26781374},
issn = {1878-6146},
mesh = {Candida/classification/growth &amp; development/*isolation &amp; purification/metabolism ; Candida albicans/classification/growth &amp; development/*isolation &amp; purification/metabolism ; Candidiasis/*microbiology ; Culture Media/*chemistry/metabolism ; Humans ; Mycological Typing Techniques/instrumentation/*methods ; },
abstract = {Rapid identification of pathogenic yeasts is a crucial step in timely and appropriate antifungal therapy. For diagnostics in the clinical laboratory, simplified alternatives to barcoding are needed. CandiSelect 4 (CS4) medium, a chromogenic medium for isolation of clinical yeasts, allows routine recognition of Candida albicans and presumptive identification of Candida tropicalis, Candida glabrata, and Candida krusei. We evaluated an extension of this method with 46 non-Candida albicans Candida (NCAC) and 7 Malassezia species. The medium supported growth of all species tested and a wide diversity of cultural types were observed. Colony colours were in violet, turquoise (including green and blue), or white tinges. Eight NCAC species produced violet pigmentation similar to that of C. albicans. Most NCAC species, including C. glabrata and C. tropicalis were distributed in the turquoise group. Malassezia species were invariably blue.},
}
@article {pmid26781372,
year = {2016},
author = {Bernhard, M and Zautner, AE and Steinmann, J and Weig, M and Groß, U and Bader, O},
title = {Towards proteomic species barcoding of fungi - An example using Scedosporium/Pseudallescheria complex isolates.},
journal = {Fungal biology},
volume = {120},
number = {2},
pages = {162-165},
doi = {10.1016/j.funbio.2015.07.001},
pmid = {26781372},
issn = {1878-6146},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/genetics ; Humans ; Mass Spectrometry/*methods ; Mycoses/*microbiology ; Phylogeny ; Proteomics/*methods ; Pseudallescheria/chemistry/genetics/*isolation &amp; purification/metabolism ; Scedosporium/chemistry/genetics/*isolation &amp; purification/metabolism ; },
abstract = {MALDI-ToF mass spectrometry offers fast and reliable species identification for bacteria and yeasts under clinical routine conditions. Here, we produced mass spectra for identification of clinically important species of the Pseudallescheria/Scedosporium complex using the recently suggested new nomenclature and use this example to discuss to what extent the principle of DNA barcoding might be transferred to mass spectrometry.},
}
@article {pmid26781369,
year = {2016},
author = {Chen, M and Zeng, J and De Hoog, GS and Stielow, B and Gerrits Van Den Ende, AH and Liao, W and Lackner, M},
title = {The 'species complex' issue in clinically relevant fungi: A case study in Scedosporium apiospermum.},
journal = {Fungal biology},
volume = {120},
number = {2},
pages = {137-146},
doi = {10.1016/j.funbio.2015.09.003},
pmid = {26781369},
issn = {1878-6146},
mesh = {Actins/genetics ; Fungal Proteins/genetics ; Humans ; Molecular Sequence Data ; Mycological Typing Techniques ; Mycoses/*microbiology ; Phylogeny ; Scedosporium/classification/genetics/*isolation &amp; purification ; Tubulin/genetics ; },
abstract = {The genus Scedosporium currently comprises six species, Scedosporium apiospermum, Scedosporium boydii, Pseudallescheria angusta, Scedosporium minutisporum, Scedosporium dehoogii, and Scedosporium aurantiacum, most of which can be distinguished with the primary fungal DNA barcode, the ITS1/2 region of the rDNA gene cluster. In the present study, four additional genetic loci were explored from a phylogenetic point of view enabling a barcoding approach based on K2P pairwise distances to resolve the taxa Scedosporium. We included partial γ-actin (ACT), β-tubulin (BT2), elongation factor 1α (TEF1), and the small ribosomal protein 60S L10 (L1) (RP60S). Phylogenetic inference of each marker individually showed that four out of six species within Scedosporium can be distinguished unambiguously, while strains of S. apiospermum, S. boydii, and P. angusta showed occasional recombination, and accordingly, no genealogical concordance between markers was obtainable. We defined S. apiospermum, S. boydii, and P. angusta as the 'S. apiospermum species complex' since observed differences were not consistent between lineages, and no clinical differences are known between entities within the complex. While BT2 revealed the best performance among the genetic loci tested at the lineage level, barcoding of the ITS region is sufficient for distinction of all entities in Scedosporium at the species or 'complex' level.},
}
@article {pmid26781368,
year = {2016},
author = {Irinyi, L and Lackner, M and de Hoog, GS and Meyer, W},
title = {DNA barcoding of fungi causing infections in humans and animals.},
journal = {Fungal biology},
volume = {120},
number = {2},
pages = {125-136},
doi = {10.1016/j.funbio.2015.04.007},
pmid = {26781368},
issn = {1878-6146},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Fungi/classification/*genetics/*isolation &amp; purification ; Humans ; Mycological Typing Techniques/*methods ; Mycoses/*microbiology/*veterinary ; Phylogeny ; },
abstract = {Correct species identification is becoming increasingly important in clinical diagnostics. Till now, many mycological laboratories rely on conventional phenotypic identification. But this is slow and strongly operator-dependent. Therefore, to improve the quality of pathogen identification, rapid, reliable, and objective identification methods are essential. One of the most encouraging approaches is molecular barcoding using the internal transcribed spacer (ITS) of the rDNA, which is rapid, easily achievable, accurate, and applicable directly from clinical specimens. It relies on the comparison of a single ITS sequence with a curated reference database. The International Society for Human and Animal Mycology (ISHAM) working group for DNA barcoding has recently established such a database, focusing on the majority of human and animal pathogenic fungi (ISHAM-ITS, freely accessible at http://www.isham.org/ or directly from http://its.mycologylab.org). For some fungi the use of secondary barcodes may be necessary.},
}
@article {pmid26780370,
year = {2016},
author = {Ramirez, LS and Wang, J},
title = {Flow-pattern Guided Fabrication of High-density Barcode Antibody Microarray.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {107},
pages = {},
pmid = {26780370},
issn = {1940-087X},
mesh = {Antibodies/*chemistry ; DNA/*chemistry ; DNA Barcoding, Taxonomic ; DNA, Single-Stranded/chemistry ; Dimethylpolysiloxanes/chemistry ; Immunoconjugates/chemistry ; Microarray Analysis/*methods ; Oligonucleotides/chemistry ; },
abstract = {Antibody microarray as a well-developed technology is currently challenged by a few other established or emerging high-throughput technologies. In this report, we renovate the antibody microarray technology by using a novel approach for manufacturing and by introducing new features. The fabrication of our high-density antibody microarray is accomplished through perpendicularly oriented flow-patterning of single stranded DNAs and subsequent conversion mediated by DNA-antibody conjugates. This protocol outlines the critical steps in flow-patterning DNA, producing and purifying DNA-antibody conjugates, and assessing the quality of the fabricated microarray. The uniformity and sensitivity are comparable with conventional microarrays, while our microarray fabrication does not require the assistance of an array printer and can be performed in most research laboratories. The other major advantage is that the size of our microarray units is 10 times smaller than that of printed arrays, offering the unique capability of analyzing functional proteins from single cells when interfacing with generic microchip designs. This barcode technology can be widely employed in biomarker detection, cell signaling studies, tissue engineering, and a variety of clinical applications.},
}
@article {pmid26776057,
year = {2016},
author = {Erpenbeck, D and Voigt, O and Al-Aidaroos, AM and Berumen, ML and Büttner, G and Catania, D and Guirguis, AN and Paulay, G and Schätzle, S and Wörheide, G},
title = {Molecular biodiversity of Red Sea demosponges.},
journal = {Marine pollution bulletin},
volume = {105},
number = {2},
pages = {507-514},
doi = {10.1016/j.marpolbul.2015.12.004},
pmid = {26776057},
issn = {1879-3363},
mesh = {Animals ; *Biodiversity ; Djibouti ; Indian Ocean ; Phylogeny ; Porifera/*classification/*genetics ; RNA, Ribosomal, 28S/genetics/metabolism ; Saudi Arabia ; Sequence Analysis, DNA ; },
abstract = {Sponges are important constituents of coral reef ecosystems, including those around the Arabian Peninsula. Despite their importance, our knowledge on demosponge diversity in this area is insufficient to recognize, for example, faunal changes caused by anthropogenic disturbances. We here report the first assessment of demosponge molecular biodiversity from Arabia, with focus on the Saudi Arabian Red Sea, based on mitochondrial and nuclear ribosomal molecular markers gathered in the framework of the Sponge Barcoding Project. We use a rapid molecular screening approach on Arabian demosponge collections and analyze results in comparison against published material in terms of biodiversity. We use a variable region of 28S rDNA, applied for the first time in the assessment of demosponge molecular diversity. Our data constitutes a solid foundation for a future more comprehensive understanding of sponge biodiversity of the Red Sea and adjacent waters.},
}
@article {pmid26773328,
year = {2016},
author = {Staal, FJ and Wiekmeijer, AS and Brugman, MH and Pike-Overzet, K},
title = {The functional relationship between hematopoietic stem cells and developing T lymphocytes.},
journal = {Annals of the New York Academy of Sciences},
volume = {1370},
number = {1},
pages = {36-44},
doi = {10.1111/nyas.12995},
pmid = {26773328},
issn = {1749-6632},
mesh = {Animals ; Cell Differentiation/*immunology ; Cell Lineage/*immunology ; Hematopoietic Stem Cells/*cytology/immunology ; Humans ; Mice ; T-Lymphocytes/*cytology/immunology ; Thymus Gland/cytology/immunology ; },
abstract = {In contrast to all other blood and immune cells, T lymphocytes do not develop in the bone marrow (BM), but in the specialized microenvironment provided by the thymus. Similar to the other lineages, however, all T cells arise from multipotent hematopoietic stem cells (HSCs) that reside in the BM. Not all HSCs give rise to T cells; but how many and what kind of developmental checkpoints are located along this intricate differentiation path is the subject of intense research. Traditionally, this process has been studied almost exclusively using mouse cells, but recent advances in immunodeficient mouse models, high-speed cell sorting, lentiviral transduction protocols, and deep sequencing techniques have allowed these questions to be addressed using human cells. Here we review the process of thymic seeding by BM-derived cells and T cell commitment in humans, discussing recent insights into the clonal composition of the thymus and the definition of developmental checkpoints, on the basis of insights from human severe combined immunodeficiency patients.},
}
@article {pmid26768941,
year = {2016},
author = {Yogeswari, S and Srinivasan, R},
title = {A Note on Variations in Morphological Features of the Phlebotomine Sand Fly Sergentomyia bailyi (Diptera: Psychodidae) in a Population From Pondicherry UT, India.},
journal = {Journal of medical entomology},
volume = {53},
number = {3},
pages = {712-716},
doi = {10.1093/jme/tjv249},
pmid = {26768941},
issn = {1938-2928},
mesh = {Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; India ; Male ; Organ Size ; Phlebotomus/*anatomy &amp; histology/genetics/growth &amp; development ; },
abstract = {Morphological variations were observed in specimens of the sand fly species Sergentomyia bailyi Sinton 1931 collected from Pondicherry Union Territory, India. Examination of morphological characteristics showed differences in the length of sensilla chaeticum on antennal flagellomere 3 (A3) in males and females, in the size and shape of the spermathecae in females, and in the position of accessory spines on the gonostyle of males. In our previous study, DNA barcoding characterization of this sand fly species collected from Pondicherry UT revealed molecular variations within the S. bailyi population. This study confirms the existence of a species complex within S. bailyi population at Pondicherry UT.},
}
@article {pmid26760908,
year = {2016},
author = {Zajac, BK and Martin-Vega, D and Feddern, N and Fremdt, H and e Castro, CP and Szpila, K and Reckel, F and Schütt, S and Verhoff, MA and Amendt, J and Zehner, R},
title = {Molecular identification and phylogenetic analysis of the forensically important family Piophilidae (Diptera) from different European locations.},
journal = {Forensic science international},
volume = {259},
number = {},
pages = {77-84},
doi = {10.1016/j.forsciint.2015.12.024},
pmid = {26760908},
issn = {1872-6283},
mesh = {Animals ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Diptera/*genetics ; Entomology/methods ; Europe ; *Forensic Sciences ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA/methods ; Species Specificity ; },
abstract = {Species identification plays an important role in forensic entomology and is mandatory for an accurate calculation of the minimum post-mortem interval. Many important Diptera and Coleoptera taxa of the cadaver community can already be identified by common barcoding approaches, i.e., by sequencing a 658bp region in the mitochondrial cytochrome c oxidase subunit I (coI) gene. Nevertheless, there is still a lack of reference barcodes for species, in particular, that can be found on cadavers at later decomposition stages. Flies of the family Piophilidae illustrate this gap of knowledge perfectly. Due to the fact that a reliable morphological identification key for the immature stages of this flies is still missing and the immature stages of many piophilids cannot be assigned to a certain species, there is need for additional tools to identify forensically relevant taxa. We collected adult piophilid specimens at 10 locations in five European countries: Spain (n=3 locations), Germany (n=3), Portugal (n=2), Poland (n=1) and Switzerland (n=1). Apart from the coI barcoding region, we additionally analyzed a 398bp long region of the nuclear elongation factor 1 alpha (ef1a) and subsequently established the molecular identifier for nine piophilid species. In addition, we present the molecular phylogeny of the examined taxa.},
}
@article {pmid26759636,
year = {2015},
author = {Sheats, J and Reifenberger, JG and Cao, H and Dorfman, KD},
title = {Measurements of DNA barcode label separations in nanochannels from time-series data.},
journal = {Biomicrofluidics},
volume = {9},
number = {6},
pages = {064119},
pmid = {26759636},
issn = {1932-1058},
support = {R01 HG006851/HG/NHGRI NIH HHS/United States ; },
abstract = {We analyzed time-series data for fluctuations of intramolecular segments of barcoded E. coli genomic DNA molecules confined in nanochannels with sizes near the persistence length of DNA. These dynamic data allowed us to measure the probability distribution governing the distance between labels on the DNA backbone, which is a key input into the alignment methods used for genome mapping in nanochannels. Importantly, this dynamic method does not require alignment of the barcode to the reference genome, thereby removing a source of potential systematic error in a previous study of this type. The results thus obtained support previous evidence for a left-skewed probability density for the distance between labels, albeit at a lower magnitude of skewness. We further show that the majority of large fluctuations between labels are short-lived events, which sheds further light upon the success of the linearized DNA genome mapping technique. This time-resolved data analysis will improve existing genome map alignment algorithms, and the overall idea of using dynamic data could potentially improve the accuracy of genome mapping, especially for complex heterogeneous samples such as cancer cells.},
}
@article {pmid26758743,
year = {2016},
author = {Wang, Y and He, K and Fan, L and Wang, Y and Wu, S and Murphy, RW and Wang, W and Zhang, Y},
title = {DNA barcoding reveals commercial fraud related to yak jerky sold in China.},
journal = {Science China. Life sciences},
volume = {59},
number = {1},
pages = {106-108},
doi = {10.1007/s11427-015-4979-0},
pmid = {26758743},
issn = {1869-1889},
mesh = {Animals ; Cattle/*genetics ; China ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Food Contamination ; Food Safety ; Food, Preserved ; *Fraud ; Hazard Analysis and Critical Control Points ; *Meat ; RNA, Ribosomal, 16S/genetics ; },
}
@article {pmid26755361,
year = {2016},
author = {Llanes-Acevedo, IP and Arcones, C and Gálvez, R and Martin, O and Checa, R and Montoya, A and Chicharro, C and Cruz, S and Miró, G and Cruz, I},
title = {DNA sequence analysis suggests that cytb-nd1 PCR-RFLP may not be applicable to sandfly species identification throughout the Mediterranean region.},
journal = {Parasitology research},
volume = {115},
number = {3},
pages = {1287-1295},
pmid = {26755361},
issn = {1432-1955},
mesh = {Animals ; Base Sequence ; Climate ; Cytochromes b/*genetics ; DNA/chemistry/isolation &amp; purification ; Databases, Nucleic Acid ; Electron Transport Complex I/*genetics ; Female ; Male ; Mediterranean Region ; Middle East ; Phlebotomus/classification/genetics ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Psychodidae/*classification/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Spain ; },
abstract = {Molecular methods are increasingly used for both species identification of sandflies and assessment of their population structure. In general, they are based on DNA sequence analysis of targets previously amplified by PCR. However, this approach requires access to DNA sequence facilities, and in some circumstances, it is time-consuming. Though DNA sequencing provides the most reliable information, other downstream PCR applications are explored to assist in species identification. Thus, it has been recently proposed that the amplification of a DNA region encompassing partially both the cytochrome-B (cytb) and the NADH dehydrogenase 1 (nd1) genes followed by RFLP analysis with the restriction enzyme Ase I allows the rapid identification of the most prevalent species of phlebotomine sandflies in the Mediterranean region. In order to confirm the suitability of this method, we collected, processed, and molecularly analyzed a total of 155 sandflies belonging to four species including Phlebotomus ariasi, P. papatasi, P. perniciosus, and Sergentomyia minuta from different regions in Spain. This data set was completed with DNA sequences available at the GenBank for species prevalent in the Mediterranean basin and the Middle East. Additionally, DNA sequences from 13 different phlebotomine species (P. ariasi, P. balcanicus, P. caucasicus, P. chabaudi, P. chadlii, P. longicuspis, P. neglectus, P. papatasi, P. perfiliewi, P. perniciosus, P. riouxi, P. sergenti, and S. minuta), from 19 countries, were added to the data set. Overall, our molecular data revealed that this PCR-RFLP method does not provide a unique and specific profile for each phlebotomine species tested. Intraspecific variability and similar RFLP patterns were frequently observed among the species tested. Our data suggest that this method may not be applicable throughout the Mediterranean region as previously proposed. Other molecular approaches like DNA barcoding or phylogenetic analyses would allow a more precise molecular species identification.},
}
@article {pmid26753115,
year = {2015},
author = {Hajdari, A and Mustafa, B and Ahmeti, G and Pulaj, B and Lukas, B and Ibraliu, A and Stefkov, G and Quave, CL and Novak, J},
title = {Essential oil composition variability among natural populations of Pinus mugo Turra in Kosovo.},
journal = {SpringerPlus},
volume = {4},
number = {},
pages = {828},
pmid = {26753115},
issn = {2193-1801},
abstract = {Pinus mugo Turra, is a native pine species in central and southern Europe, growing in high mountains area (altitudes 1.800-2.300 m.a.s.l.). In Kosovo, it is one of the native pines too, distributed in high altitudes in the Sharri Mountains and Albanian Alps Mountains. Its populations represent an important wealth of essential oil resources available, which make this species very important in terms of economic values. The chemical composition and yields of the essential oils of dwarf pine (Pinus mugo Turra) needles, twigs and cones from six wild populations in Kosovo were investigated with the aim to assess their natural variability. The identity of P. mugo was confirmed by morphology and DNA barcoding. Sixty-two compounds were identified representing 69-95 % of the total identified compounds. The yield ranged from 0.3-0.8 % v/w in needles, 1.0-2.4 % v/w in twigs and 0.1-0.5 % v/w in cones, depending on the origin of plant material and plant organs. α-Pinene (needles: 16.9-24.5 %; twigs: 4.5-8.8 %; cones: 3.1-5.6 %), β-pinene (needles: 1.5-5.4 %; twigs: 2.2-15.4 %; cones: 1.3-14.2 %), δ-3-carene (needles: 15.4-27.8 %; twigs: 24.0-51.6 %; cones: 10.5-31.5 %), limonene + β-phellandrene (needles: 1.9-5.9 %; twigs: 12.6-24.2 %; cones: 2.1-9.3 %), (E)-caryophyllene (needles: 4.4-8.9 %; twigs: 4.0-10.8 %; cones: 10.3-26.9 %) and germacrene D (needles: 4.0-8.3 %; twigs: 0.2-6.19 %; cones: 0.1-12.4 %) were the major components of the essential oil. Principal component analysis (PCA) and hierarchical cluster analyses (HCA) suggests that the population of P. mugo clustering is not related to their geographic location, but rather seemed to be linked to local selective forces acting on chemotype diversity. Low variability related to their geographic location has an economic importance since samples originating from different locations in Kosovo can treated with same standards.},
}
@article {pmid26752741,
year = {2016},
author = {Guo, YY and Huang, LQ and Liu, ZJ and Wang, XQ},
title = {Promise and Challenge of DNA Barcoding in Venus Slipper (Paphiopedilum).},
journal = {PloS one},
volume = {11},
number = {1},
pages = {e0146880},
pmid = {26752741},
issn = {1932-6203},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Chloroplast/*genetics ; DNA, Intergenic/genetics ; DNA, Plant/*genetics ; *Genes, Plant ; Genetic Variation ; Haplotypes ; Orchidaceae/*genetics ; Phylogeny ; Reproducibility of Results ; Species Specificity ; },
abstract = {Orchidaceae are one of the largest families of flowering plants, with over 27,000 species described and all orchids are listed in CITES. Moreover, the seedlings of orchid species from the same genus are similar. The objective of DNA barcoding is rapid, accurate, and automated species identification, which may be used to identify illegally traded endangered species from vegetative specimens of Paphiopedilum (Venus slipper), a flagship group for plant conservation with high ornamental and commercial values. Here, we selected eight chloroplast barcodes and nrITS to evaluate their suitability in Venus slippers. The results indicate that all tested barcodes had no barcoding gap and the core plant barcodes showed low resolution for the identification of Venus slippers (18.86%). Of the single-locus barcodes, nrITS is the most efficient for the species identification of the genus (52.27%), whereas matK + atpF-atpH is the most efficient multi-locus combination (28.97%). Therefore, we recommend the combination of matK + atpF-atpH + ITS as a barcode for Venus slippers. Furthermore, there is an upper limit of resolution of the candidate barcodes, and only half of the taxa with multiple samples were identified successfully. The low efficiency of these candidate barcodes in Venus slippers may be caused by relatively recent speciation, the upper limit of the barcodes, and/or the sampling density. Although the discriminatory power is relatively low, DNA barcoding may be a promising tool to identify species involved in illegal trade, which has broad applications and is valuable for orchid conservation.},
}
@article {pmid26751251,
year = {2016},
author = {Bell, KL and Burgess, KS and Okamoto, KC and Aranda, R and Brosi, BJ},
title = {Review and future prospects for DNA barcoding methods in forensic palynology.},
journal = {Forensic science international. Genetics},
volume = {21},
number = {},
pages = {110-116},
doi = {10.1016/j.fsigen.2015.12.010},
pmid = {26751251},
issn = {1878-0326},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*analysis/*genetics ; Forensic Sciences/methods ; High-Throughput Nucleotide Sequencing/methods ; Paleontology ; Pollen/*genetics ; },
abstract = {Pollen can be a critical forensic marker in cases where determining geographic origin is important, including investigative leads, missing persons cases, and intelligence applications. However, its use has previously been limited by the need for a high level of specialization by expert palynologists, slow speeds of identification, and relatively poor taxonomic resolution (typically to the plant family or genus level). By contrast, identification of pollen through DNA barcoding has the potential to overcome all three of these limitations, and it may seem surprising that the method has not been widely implemented. Despite what might seem a straightforward application of DNA barcoding to pollen, there are technical issues that have delayed progress. However, recent developments of standard methods for DNA barcoding of pollen, along with improvements in high-throughput sequencing technology, have overcome most of these technical issues. Based on these recent methodological developments in pollen DNA barcoding, we believe that now is the time to start applying these techniques in forensic palynology. In this article, we discuss the potential for these methods, and outline directions for future research to further improve on the technology and increase its applicability to a broader range of situations.},
}
@article {pmid26751033,
year = {2015},
author = {Wilson, JJ and Jisming-See, SW and Brandon-Mong, GJ and Lim, AH and Lim, VC and Lee, PS and Sing, KW},
title = {Citizen Science: The First Peninsular Malaysia Butterfly Count.},
journal = {Biodiversity data journal},
volume = {},
number = {3},
pages = {e7159},
pmid = {26751033},
issn = {1314-2828},
abstract = {BACKGROUND: Over the past 50 years, Southeast Asia has suffered the greatest losses of biodiversity of any tropical region in the world. Malaysia is a biodiversity hotspot in the heart of Southeast Asia with roughly the same number of mammal species, three times the number of butterfly species, but only 4% of the land area of Australia. Consequently, in Malaysia, there is an urgent need for biodiversity monitoring and also public engagement with wildlife to raise awareness of biodiversity loss. Citizen science is "on the rise" globally and can make valuable contributions to long-term biodiversity monitoring, but perhaps more importantly, involving the general public in science projects can raise public awareness and promote engagement. Butterflies are often the focus of citizen science projects due to their charisma and familiarity and are particularly valuable "ambassadors" of biodiversity conservation for public outreach.<br><br>NEW INFORMATION: Here we present the data from our citizen science project, the first "Peninsular Malaysia Butterfly Count". Participants were asked to go outdoors on June 6, 2015, and (non-lethally) sample butterfly legs for species identification through DNA barcoding. Fifty-seven citizens responded to our adverts and registered to take part in the butterfly count with many registering on behalf of groups. Collectively the participants sampled 220 butterfly legs from 26 mostly urban and suburban sampling localities. These included our university campus, a highschool, several public parks and private residences. On the basis of 192 usable DNA barcodes, 43 species were sampled by the participants. The most sampled species was Appias olferna, followed by Junonia orithya and Zizina otis. Twenty-two species were only sampled once, five were only sampled twice, and four were only sampled three times. Three DNA barcodes could not be assigned species names. The sampled butterflies revealed that widely distributed, cosmopolitan species, often those recently arrived to the peninsula or with documented "invasive" potential, dominated the habitat types sampled by the participants. Data from this first Butterfly Count helps establish a baseline from which we can monitor the patterns and changes in butterfly communities in Peninsular Malaysia.},
}
@article {pmid26741407,
year = {2016},
author = {Leung, ML and Wang, Y and Kim, C and Gao, R and Jiang, J and Sei, E and Navin, NE},
title = {Highly multiplexed targeted DNA sequencing from single nuclei.},
journal = {Nature protocols},
volume = {11},
number = {2},
pages = {214-235},
pmid = {26741407},
issn = {1750-2799},
support = {P30 CA016672/CA/NCI NIH HHS/United States ; R01 CA169244/CA/NCI NIH HHS/United States ; CA016672/CA/NCI NIH HHS/United States ; TL1TR000369/TR/NCATS NIH HHS/United States ; UL1TR000371/TR/NCATS NIH HHS/United States ; R21 CA174397/CA/NCI NIH HHS/United States ; TL1 TR000369/TR/NCATS NIH HHS/United States ; UL1 TR000371/TR/NCATS NIH HHS/United States ; 1R01CA169244-01/CA/NCI NIH HHS/United States ; R21CA174397-01/CA/NCI NIH HHS/United States ; },
mesh = {*Cell Nucleus ; High-Throughput Nucleotide Sequencing/*methods ; Sequence Analysis, DNA/*methods ; Single-Cell Analysis/*methods ; Time Factors ; },
abstract = {Single-cell DNA sequencing methods are challenged by poor physical coverage, high technical error rates and low throughput. To address these issues, we developed a single-cell DNA sequencing protocol that combines flow-sorting of single nuclei, time-limited multiple-displacement amplification (MDA), low-input library preparation, DNA barcoding, targeted capture and next-generation sequencing (NGS). This approach represents a major improvement over our previous single nucleus sequencing (SNS) Nature Protocols paper in terms of generating higher-coverage data (>90%), thereby enabling the detection of genome-wide variants in single mammalian cells at base-pair resolution. Furthermore, by pooling 48-96 single-cell libraries together for targeted capture, this approach can be used to sequence many single-cell libraries in parallel in a single reaction. This protocol greatly reduces the cost of single-cell DNA sequencing, and it can be completed in 5-6 d by advanced users. This single-cell DNA sequencing protocol has broad applications for studying rare cells and complex populations in diverse fields of biological research and medicine.},
}
@article {pmid26741249,
year = {2015},
author = {Gopurenko, D and Bellis, GA and Yanase, T and Wardhana, AH and Thepparat, A and Wang, J and Cai, D and Mitchell, A},
title = {Integrative taxonomy to investigate species boundaries within Culicoides (Diptera: Ceratopogonidae): a case study using subgenus Avaritia from Australasia and Eastern Asia.},
journal = {Veterinaria italiana},
volume = {51},
number = {4},
pages = {345-378},
doi = {10.12834/VetIt.515.2463.2},
pmid = {26741249},
issn = {1828-1427},
mesh = {Animals ; Asia ; Australasia ; Ceratopogonidae/*classification ; },
abstract = {In this study, species boundaries were examined for 15 described and 2 undescribed species within the economically important Culicoides subg. Avaritia Fox from Australasia and Eastern Asia. We used an integrative taxonomic approach incorporating DNA barcoding, nuclear gene sequencing, and retrospective morphological analyses. Some arbovirus vector species such as Culicoides fulvus Sen and Das Gupta and Culicoides wadai Kitaoka were genetically and morphologically uniform across sampled distributions, but others including Culicoides actoni Smith and Culicoides brevipalpis Delfinado contained 2 or more genetically independent populations of 'cryptic species' that in some cases were sympatric. Some of these 'cryptic species' exhibited consistent morphological differences, while differences are yet to be found for others species. Additionally, an undescribed species, C. Avaritia sp. No. 3, was found to be synonymous with C. fulvus. These results refine our understanding of the distribution of individual species of C. subg. Avaritia and demonstrate that species descriptions and distribution records need revision for part of the Culicoides fauna. Furthermore, because vector competence studies for most of these species are based entirely on Australian populations, the competence of the putative cryptic species identified elsewhere will require independent assessment. Finally, integrative taxonomic assessment requires genetic and morphological assessment of material from the type localities in order to clarify the status and distribution of species, especially for clades containing cryptic species. International collaboration is needed to facilitate this research.},
}
@article {pmid26741134,
year = {2016},
author = {Iftikhar, R and Ashfaq, M and Rasool, A and Hebert, PD},
title = {DNA Barcode Analysis of Thrips (Thysanoptera) Diversity in Pakistan Reveals Cryptic Species Complexes.},
journal = {PloS one},
volume = {11},
number = {1},
pages = {e0146014},
pmid = {26741134},
issn = {1932-6203},
mesh = {Animals ; Bayes Theorem ; Crops, Agricultural/parasitology ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Haplotypes ; Insect Proteins/*genetics ; Mitochondrial Proteins/*genetics ; Multigene Family ; Pakistan ; *Phylogeny ; Thysanoptera/classification/*genetics ; },
abstract = {Although thrips are globally important crop pests and vectors of viral disease, species identifications are difficult because of their small size and inconspicuous morphological differences. Sequence variation in the mitochondrial COI-5' (DNA barcode) region has proven effective for the identification of species in many groups of insect pests. We analyzed barcode sequence variation among 471 thrips from various plant hosts in north-central Pakistan. The Barcode Index Number (BIN) system assigned these sequences to 55 BINs, while the Automatic Barcode Gap Discovery detected 56 partitions, a count that coincided with the number of monophyletic lineages recognized by Neighbor-Joining analysis and Bayesian inference. Congeneric species showed an average of 19% sequence divergence (range = 5.6% - 27%) at COI, while intraspecific distances averaged 0.6% (range = 0.0% - 7.6%). BIN analysis suggested that all intraspecific divergence >3.0% actually involved a species complex. In fact, sequences for three major pest species (Haplothrips reuteri, Thrips palmi, Thrips tabaci), and one predatory thrips (Aeolothrips intermedius) showed deep intraspecific divergences, providing evidence that each is a cryptic species complex. The study compiles the first barcode reference library for the thrips of Pakistan, and examines global haplotype diversity in four important pest thrips.},
}
@article {pmid26740545,
year = {2016},
author = {Tanney, JB and Douglas, B and Seifert, KA},
title = {Sexual and asexual states of some endophytic Phialocephala species of Picea.},
journal = {Mycologia},
volume = {108},
number = {2},
pages = {255-280},
doi = {10.3852/15-136},
pmid = {26740545},
issn = {0027-5514},
mesh = {Animals ; Ascomycota/classification/genetics/*physiology/ultrastructure ; Endophytes/*physiology ; Phylogeny ; Picea/*microbiology ; Reproduction ; Species Specificity ; },
abstract = {Unidentified DNA sequences in isolation-based or culture-free studies of conifer endophytes are a persistent problem that requires a field approach to resolve. An investigation of foliar endophytes of Picea glauca, P. mariana, P. rubens and Pinus strobus in eastern Canada, using a combined field, morphological, cultural and DNA sequencing approach, resulted in the frequent isolation of Phialocephala spp. and the first verified discovery of their mollisia-like sexual states in the field. Phialocephala scopiformis and Ph. piceae were the most frequent species isolated as endophytes from healthy conifer needles. Corresponding Mollisia or mollisioid sexual states for Ph. scopiformis, Ph. piceae and several undescribed species in a clade containing Ph. dimorphospora were collected in the sampling area and characterized by analysis of the nuc internal transcribed spacer rDNA (ITS) and gene for the largest subunit of RNA polymerase II (RPB1) loci. Four novel species and one new combination in a clade containing Ph. dimorphospora, the type of Phialocephala, are presented, accompanied by descriptions of apothecia and previously undocumented synanamorphs. An epitype culture and corresponding reference sequences for Phialocephala dimorphospora are proposed. The resulting ITS barcodes linked with robust taxonomic species concepts are an important resource for future research on forest ecosystems and endophytes.},
}
@article {pmid26740540,
year = {2016},
author = {Kropp, BR},
title = {Russulaceae in American Samoa: new species and further support for an Australasian origin for Samoan ectomycorrhizal fungi.},
journal = {Mycologia},
volume = {108},
number = {2},
pages = {405-413},
doi = {10.3852/15-171},
pmid = {26740540},
issn = {0027-5514},
mesh = {Basidiomycota/*classification/*genetics/isolation &amp; purification/physiology ; Demography ; Mycorrhizae/*classification/*genetics/isolation &amp; purification/physiology ; Phylogeny ; Samoa ; },
abstract = {Two new species from the Russulaceae, Lactifluus aurantiotinctus and Russula pallidirosea, are described from American Samoa. Based on analyses of nuc rDNA internal transcribed spacer region barcodes (ITS), L. aurantiotinctus has an affinity to subgenus Lactariopsis and strong phylogeographic ties to Papua New Guinea. The ITS data indicate that Russula pallidirosea has an affinity to subgenus Heterophyllidia and suggest that it also has phylogeographic ties to Australasia. Both species were associated with the ectomycorrhizal tree Intsia bijuga.},
}
@article {pmid26740340,
year = {2016},
author = {Han, J and Pang, X and Liao, B and Yao, H and Song, J and Chen, S},
title = {An authenticity survey of herbal medicines from markets in China using DNA barcoding.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {18723},
pmid = {26740340},
issn = {2045-2322},
mesh = {China ; *DNA Barcoding, Taxonomic ; Herbal Medicine/*standards ; Medicine, Chinese Traditional/standards ; Plants, Medicinal/*classification ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {Adulterant herbal materials are a threat to consumer safety. In this study, we used DNA barcoding to investigate the proportions and varieties of adulterant species in traditional Chinese medicine (TCM) markets. We used a DNA barcode database of TCM (TCMD) that was established by our group to investigate 1436 samples representing 295 medicinal species from 7 primary TCM markets in China. The results indicate that ITS2 barcodes could be generated for most of the samples (87.7%) using a standard protocol. Of the 1260 samples, approximately 4.2% were identified as adulterants. The adulterant focused on medicinal species such as Ginseng Radix et Rhizoma (Renshen), Radix Rubi Parvifolii (Maomeigen), Dalbergiae odoriferae Lignum (Jiangxiang), Acori Tatarinowii Rhizoma (Shichangpu), Inulae Flos (Xuanfuhua), Lonicerae Japonicae Flos (Jinyinhua), Acanthopanacis Cortex (Wujiapi) and Bupleuri Radix (Chaihu). The survey revealed that adulterant species are present in the Chinese market, and these adulterants pose a risk to consumer health. Thus, regulatory measures should be adopted immediately. We suggest that a traceable platform based on DNA barcode sequences be established for TCM market supervision.},
}
@article {pmid26739287,
year = {2016},
author = {Kakui, K},
title = {Descriptions of two new species of Rhizorhina Hansen, 1892 (Copepoda: Siphonostomatoida: Nicothoidae) parasitic on tanaidacean crustaceans, with a note on their phylogenetic position.},
journal = {Systematic parasitology},
volume = {93},
number = {1},
pages = {57-68},
pmid = {26739287},
issn = {1573-5192},
mesh = {Animals ; China ; Copepoda/anatomy &amp; histology/*classification/genetics ; Crustacea/*parasitology ; Electron Transport Complex IV/genetics ; Pacific Ocean ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; Species Specificity ; },
abstract = {Two new species of nicothoid copepod are described. Rhizorhina ohtsukai n. sp. found on a leptocheliid (Leptochelia sp.) collected at depths of 151-136 m in the North Pacific Ocean is most similar to Rhizorhina aesthetes Boxshall &amp; Harrison, 1988 but can be distinguished by the possession of a narrower body with a rounded anterior end, and in the position of the gonopores. Rhizorhina soyoae n. sp. found on an apseudid (Fageapseudes sp.) collected at depths of 1,595-1,557 m in East China Sea most closely resembles Rhizorhina tanaidaceae Gotto, 1984 but differs in having a narrower body with a rounded anterior end. Partial nucleotide sequences of the cytochrome c oxidase subunit I (COI) gene were obtained from the two copepods in order to enable future barcoding. A phylogenetic reconstruction based on the 18S rRNA gene placed the copepods within the Siphonostomatoida Burmeister, 1835, with the nicothoid Choniosphaera maenadis (Bloch &amp; Gallien, 1933), and separate from the Rhizorhina spp. clade, suggesting that the family Nicothoidae Dana, 1849 is not monophyletic. This is the third report of copepods parasitic on tanaidacean crustaceans.},
}
@article {pmid26732074,
year = {2017},
author = {Brown, MJ and Sainsbury, AW and Vaughan-Higgins, RJ and Measures, GH and Jones, CM and Gammans, N},
title = {Bringing Back a Healthy Buzz? Invertebrate Parasites and Reintroductions: A Case Study in Bumblebees.},
journal = {EcoHealth},
volume = {14},
number = {Suppl 1},
pages = {74-83},
pmid = {26732074},
issn = {1612-9210},
mesh = {Animals ; Bees/*parasitology ; Conservation of Natural Resources ; *Endangered Species ; Parasites/pathogenicity ; },
abstract = {Reintroductions can play a key role in the conservation of endangered species. Parasites may impact reintroductions, both positively and negatively, but few case studies of how to manage parasites during reintroductions exist. Bumblebees are in decline at regional and global scales, and reintroductions can be used to re-establish extinct local populations. Here we report on how the risks associated with parasites are being managed in an ongoing reintroduction of the short-haired bumblebee, Bombus subterraneus, to the UK. Disease risk analysis was conducted and disease risk management plans constructed to design a capture-quarantine-release system that minimised the impacts on both the bumblebees and on their natural parasites. Given that bumblebee parasites are (i) generalists, (ii) geographically ubiquitous, and (iii) show evidence of local adaptation, the disease risk management plan was designed to limit the co-introduction of parasites from the source population in Sweden to the destination site in the UK. Results suggest that this process at best eliminated, or at least severely curtailed the co-introduction of parasites, and ongoing updates of the plan enabled minimization of impacts on natural host-parasite dynamics in the Swedish source population. This study suggests that methods designed for reintroductions of vertebrate species can be successfully applied to invertebrates. Future reintroductions of invertebrates where the parasite fauna is less well known should take advantage of next-generation barcoding and multiple survey years prior to the start of reintroductions, to develop comprehensive disease risk management plans.},
}
@article {pmid26730595,
year = {2016},
author = {Nigro, LM and Angel, MV and Blachowiak-Samolyk, K and Hopcroft, RR and Bucklin, A},
title = {Identification, Discrimination, and Discovery of Species of Marine Planktonic Ostracods Using DNA Barcodes.},
journal = {PloS one},
volume = {11},
number = {1},
pages = {e0146327},
pmid = {26730595},
issn = {1932-6203},
support = {NA050AR4601079/AR/NIAMS NIH HHS/United States ; },
mesh = {Alaska ; Animals ; Atlantic Ocean ; Crustacea/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/chemistry/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Geography ; Greenland ; Haplotypes ; Indian Ocean ; Molecular Sequence Data ; Oceans and Seas ; Phylogeny ; Plankton/classification/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The Ostracoda (Crustacea; Class Ostracoda) is a diverse, frequently abundant, and ecologically important component of the marine zooplankton assemblage. There are more than 200 described species of marine planktonic ostracods, many of which (especially conspecific species) can be identified only by microscopic examination and dissection of fragile morphological characters. Given the complexity of species identification and increasing lack of expert taxonomists, DNA barcodes (short DNA sequences for species discrimination and identification) are particularly useful and necessary. Results are reported from analysis of 210 specimens of 78 species of marine planktonic ostracods, including two novel species, and 51 species for which barcodes have not been previously published. Specimens were collected during 2006 to 2008 from the Atlantic, Indian, and Southern Oceans, Greenland Sea and Gulf of Alaska. Samples were collected from surface to 5,000 m using various collection devices. DNA sequence variation was analyzed for a 598 base-pair region of the mitochondrial cytochrome oxidase subunit I (COI) gene. Kimura-2-Parameter (K2P) genetic distances within described species (mean = 0.010 ± 0.017 SD) were significantly smaller than between species (0.260 + 0.080), excluding eight taxa hypothesized to comprise cryptic species due to morphological variation (especially different size forms) and/or collection from different geographic regions. These taxa showed similar K2P distance values within (0.014 + 0.026) and between (0.221 ± 0.068) species. All K2P distances > 0.1 resulted from comparisons between identified or cryptic species, with no overlap between intra- and interspecific genetic distances. A Neighbor Joining tree resolved nearly all described species analyzed, with multiple sequences forming monophyletic clusters with high bootstrap values (typically 99%). Based on taxonomically and geographically extensive sampling and analysis (albeit with small sample sizes), the COI barcode region was shown to be a valuable character for discrimination, recognition, identification, and discovery of species of marine planktonic ostracods.},
}
@article {pmid26729867,
year = {2016},
author = {García-Robledo, C and Kuprewicz, EK and Staines, CL and Erwin, TL and Kress, WJ},
title = {Limited tolerance by insects to high temperatures across tropical elevational gradients and the implications of global warming for extinction.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {113},
number = {3},
pages = {680-685},
pmid = {26729867},
issn = {1091-6490},
mesh = {Acclimatization ; *Adaptation, Physiological ; *Altitude ; Animals ; Costa Rica ; Electron Transport Complex IV/genetics ; *Extinction, Biological ; Geography ; *Global Warming ; Haplotypes ; Herbivory ; *Hot Temperature ; Humidity ; Insecta/*physiology ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; *Tropical Climate ; },
abstract = {The critical thermal maximum (CTmax), the temperature at which motor control is lost in animals, has the potential to determine if species will tolerate global warming. For insects, tolerance to high temperatures decreases with latitude, suggesting that similar patterns may exist along elevational gradients as well. This study explored how CTmax varies among species and populations of a group of diverse tropical insect herbivores, the rolled-leaf beetles, across both broad and narrow elevational gradients. Data from 6,948 field observations and 8,700 museum specimens were used to map the elevational distributions of rolled-leaf beetles on two mountains in Costa Rica. CTmax was determined for 1,252 individual beetles representing all populations across the gradients. Initial morphological identifications suggested a total of 26 species with populations at different elevations displaying contrasting upper thermal limits. However, compared with morphological identifications, DNA barcodes (cytochrome oxidase I) revealed significant cryptic species diversity. DNA barcodes identified 42 species and haplotypes across 11 species complexes. These 42 species displayed much narrower elevational distributions and values of CTmax than the 26 morphologically defined species. In general, species found at middle elevations and on mountaintops are less tolerant to high temperatures than species restricted to lowland habitats. Species with broad elevational distributions display high CTmax throughout their ranges. We found no significant phylogenetic signal in CTmax, geography, or elevational range. The narrow variance in CTmax values for most rolled-leaf beetles, especially high-elevation species, suggests that the risk of extinction of insects may be substantial under some projected rates of global warming.},
}
@article {pmid26718716,
year = {2016},
author = {Giantsis, IA and Chaskopoulou, A and Bon, MC},
title = {Mild-Vectolysis: A Nondestructive DNA Extraction Method for Vouchering Sand Flies and Mosquitoes.},
journal = {Journal of medical entomology},
volume = {53},
number = {3},
pages = {692-695},
doi = {10.1093/jme/tjv236},
pmid = {26718716},
issn = {1938-2928},
mesh = {Analytic Sample Preparation Methods/*methods ; Animals ; Culicidae/chemistry/*genetics ; DNA/genetics/*isolation &amp; purification ; Phlebotomus/classification/*genetics ; },
abstract = {Nondestructive techniques allow the isolation of genomic DNA, without damaging the morphological features of the specimens. Though such techniques are available for numerous insect groups, they have not been applied to any member of the medically important families of mosquitoes (Diptera: Culicidae) and phlebotomine sand flies (Diptera: Psychodidae). This study presents Mild-Vectolysis, the first nondestructive DNA extraction methodology for vouchering taxa of mosquitoes and sand flies, which provided sufficient amounts of DNA, tested in a verified barcode (cytochrome oxidase I gene), while preserving their morphological integrity. Application of the method to sand flies allowed successful insect identification post DNA extraction, as all basic taxonomical structures necessary for identification (pharynx, cybarium, and genitalia) remained intact. The development of the methodology was more challenging in mosquitoes, due to the fragility of key morphological characters (scales and color). A small modification of the lysis buffer concentration, in combination with the adjustment of the incubation time, a postlysis freezing stage, and the avoidance of ethanol, achieved the extraction of sufficient DNA quantity, while preserving the integument of the mosquitoes, although a small proportion of the scales and the color still appeared to have been lost. In addition to the practicality and efficiency of our methodology, preserving of the original insect specimen post DNA extraction is highly advantageous, as it allows for 1) utilization of the specimen for further analysis and 2) storage for vouchering.},
}
@article {pmid26714125,
year = {2017},
author = {Song, X and Li, Y and Xu, G and Liu, C and Liu, Y and Zhang, X and Liu, Y and Liu, S and Gu, X},
title = {Identification of Notoginseng powder based on similarity to "DNA Barcoding Core-genotype".},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {3},
pages = {355-357},
doi = {10.3109/19401736.2015.1122777},
pmid = {26714125},
issn = {2470-1408},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant ; Drugs, Chinese Herbal ; Panax/classification/*genetics ; },
abstract = {Notoginseng powder is a medicine form of Notoginseng radix et rhizoma in Chinese Pharmacopeia. Common adulterants of Notoginseng powder appeared in the market include powder of Panax ginseng and Panax quinquefolius. Here, "DNA Barcoding Core-Genotype (DBCG)" based on ITS sequences was developed for authenticating Notoginseng powder. DBCG was the genotype with the highest frequency of DNA barcoding in species. The DBCG was found as the reference sequence and minimal-similarity to identify species was calculated by large sample analysis. Then we could calculate similarity index between DBCG and sequences of the unidentified Notoginseng powder and compare it through minimal-similarity to identify the species. This method was simple, efficient, and might be a preferable tool for accurate authentication.},
}
@article {pmid26713226,
year = {2015},
author = {Mahé, F and Rognes, T and Quince, C and de Vargas, C and Dunthorn, M},
title = {Swarm v2: highly-scalable and high-resolution amplicon clustering.},
journal = {PeerJ},
volume = {3},
number = {},
pages = {e1420},
pmid = {26713226},
issn = {2167-8359},
abstract = {Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.},
}
@article {pmid26709635,
year = {2017},
author = {Martinsson, S and Rhodén, C and Erséus, C},
title = {Barcoding gap, but no support for cryptic speciation in the earthworm Aporrectodea longa (Clitellata: Lumbricidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {2},
pages = {147-155},
doi = {10.3109/19401736.2015.1115487},
pmid = {26709635},
issn = {2470-1408},
mesh = {Animals ; Cell Nucleus ; *DNA Barcoding, Taxonomic ; *DNA, Mitochondrial ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial ; Genetic Variation ; Histones/genetics ; Oligochaeta/*classification/genetics/metabolism ; *Phylogeny ; },
abstract = {DNA-barcoding, using the mitochondrial marker COI, has been found successful for the identification of specimens in many animal groups, but may not be suited for species discovery and delimitation if used alone. In this study, we investigate whether two observed COI haplogroups in the earthworm Aporrectodea longa correspond to two cryptic species or if the variation is intraspecific. This is done by complementing COI with two nuclear markers, ITS2 and Histone 3. The variation is studied using distance methods, parsimony networks and Bayesian coalescent trees, and the statistical distinctness of the groups is tested on gene trees using the genealogical sorting index, Rosenberg's PAB and Rodrigo et al.'s P(RD). We also applied multilocus species delimitation based on the multispecies coalescence model. The two haplogroups were found in COI, and all tests except P(RD) found them to be significantly distinct. However, in ITS2, the same groups were not recovered in any analyses or tests. H3 was invariable in A. longa, and was, therefore, included only in the multilocus analysis, which preferred a model treating A. longa as one species over a model splitting it into two. We also compared two measurements of size, body length, and no. of segments between the groups. No difference in body length was found, and although a significant difference in no. of segments was noted the haplogroup with the lower mean showed both the highest and the lowest value. When combined, these results led us to the conclusion that there is no support for the separation of A. longa into two cryptic species. This study again highlights the importance of complementing mitochondrial barcodes with more data when establishing species boundaries.},
}
@article {pmid26705969,
year = {2016},
author = {González-Castro, M and Rosso, JJ and Mabragaña, E and Díaz de Astarloa, JM},
title = {Surfing among species, populations and morphotypes: Inferring boundaries between two species of new world silversides (Atherinopsidae).},
journal = {Comptes rendus biologies},
volume = {339},
number = {1},
pages = {10-23},
doi = {10.1016/j.crvi.2015.11.004},
pmid = {26705969},
issn = {1768-3238},
mesh = {Animals ; Argentina ; Smegmamorpha/anatomy &amp; histology/*classification/genetics ; },
abstract = {Atherinopsidae are widespread freshwater and shallow marine fish with singular economic importance. Morphological, genetical and life cycles differences between marine and estuarine populations were already reported in this family, suggesting ongoing speciation. Also, coexistence and interbreeding between closely related species were documented. The aim of this study was to infer boundaries among: (A) Odontesthes bonariensis and O. argentinensis at species level, and intermediate morphs; (B) the population of O. argentinensis of Mar Chiquita Lagoon and its marine conspecifics. To achieve this, we integrated, meristic, Geometrics Morphometrics and DNA Barcode approaches. Four groups were discriminated and subsequently characterized according to their morphological traits, shape and meristic characters. No shared haplotypes between O. bonariensis and O. argentinensis were found. Significative-meristic and body shape differences between the Mar Chiquita and marine individuals of O. argentinensis were found, suggesting they behave as well differentiated populations, or even incipient ecological species. The fact that the Odontesthes morphotypes shared haplotypes with both, O. argentinensis and O. bonariensis, but also possess meristic and morphometric distinctive traits open new questions related to the origin of this morphogroup.},
}
@article {pmid26703324,
year = {2016},
author = {Lakra, WS and Singh, M and Goswami, M and Gopalakrishnan, A and Lal, KK and Mohindra, V and Sarkar, UK and Punia, PP and Singh, KV and Bhatt, JP and Ayyappan, S},
title = {DNA barcoding Indian freshwater fishes.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4510-4517},
doi = {10.3109/19401736.2015.1101540},
pmid = {26703324},
issn = {2470-1408},
mesh = {Animals ; Catfishes/classification/genetics ; Cypriniformes/classification/genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry/isolation &amp; purification/metabolism ; Databases, Genetic ; Electron Transport Complex IV/classification/genetics/metabolism ; Fishes/classification/*genetics ; Fresh Water ; Genetic Variation ; Perciformes/classification/genetics ; Phylogeny ; },
abstract = {DNA barcoding is a promising technique for species identification using a short mitochondrial DNA sequence of cytochrome c oxidase I (COI) gene. In the present study, DNA barcodes were generated from 72 species of freshwater fish covering the Orders Cypriniformes, Siluriformes, Perciformes, Synbranchiformes, and Osteoglossiformes representing 50 genera and 19 families. All the samples were collected from diverse sites except the species endemic to a particular location. Species were represented by multiple specimens in the great majority of the barcoded species. A total of 284 COI sequences were generated. After amplification and sequencing of 700 base pair fragment of COI, primers were trimmed which invariably generated a 655 base pair barcode sequence. The average Kimura two-parameter (K2P) distances within-species, genera, families, and orders were 0.40%, 9.60%, 13.10%, and 17.16%, respectively. DNA barcode discriminated congeneric species without any confusion. The study strongly validated the efficiency of COI as an ideal marker for DNA barcoding of Indian freshwater fishes.},
}
@article {pmid26702899,
year = {2016},
author = {Garcia, DA and Lasso, CA and Morales, M and Caballero, SJ},
title = {Molecular systematics of the freshwater stingrays (myliobatiformes: potamotrygonidae) of the Amazon, Orinoco, Magdalena, Esequibo, Caribbean, and Maracaibo basins (Colombia - Venezuela): evidence from three mitochondrial genes.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4479-4491},
doi = {10.3109/19401736.2015.1101536},
pmid = {26702899},
issn = {2470-1408},
mesh = {Animals ; Bayes Theorem ; Caribbean Region ; Colombia ; Cytochromes b/classification/genetics/metabolism ; DNA/chemistry/isolation &amp; purification/metabolism ; Electron Transport Complex IV/classification/genetics/metabolism ; Fresh Water ; *Genome, Mitochondrial ; Mitochondrial Proton-Translocating ATPases/classification/genetics/metabolism ; Phylogeny ; Sequence Analysis, DNA ; Sharks/classification/*genetics ; Venezuela ; },
abstract = {Lack of adequate information about the taxonomic and evolutionary relationships, ecology, biology, and distribution of several species belonging to the family Potamotrygonidae makes these species vulnerable to anthropic activities, including commercial overexploitation for the ornamental fish market. The aim of this study was to investigate the systematic relationships among genera and species belonging to this family by analyses of three mitochondrial gene regions. Samples were collected from the main river basins in Colombia and Venezuela for four genera and seven species of the family, as well as for what appear to be unidentified species. Three mitochondrial molecular markers COI, Cytb, and ATP6 were amplified and sequenced. Maximum likelihood and Bayesian inference analysis were performed to obtain topologies for each marker and for a concatenated dataset including the three genes. Small dataset may compromise some methods estimations of sequence divergence in the ATP6 marker. Monophyly of the four genera in Potamotrygonidae was confirmed and phylogenetic relationships among members of the Potamotrygon genus were not clearly resolved. However, results obtained with the molecular marker Cytb appear to offer a good starting point to differentiate among genera and species as a tool that could be used for barcoding. The application of this gene as a barcode could be applied for management and regulation of extraction practices for these genera. Sequencing complete mitochondrial genomes would be the next step for testing evolutionary hypothesis among these genera. Population structure analyses should be undertaken for Paratrygon, Potamotrygon magdalenae and motoro.},
}
@article {pmid26701544,
year = {2015},
author = {Valero, P and Ortiz, AS},
title = {Description and DNA barcoding of a new Iberian species of Pijnackeria (Scali, 2009) from Sierra Nevada, Spain (Phasmida: Diapheromeridae).},
journal = {Zootaxa},
volume = {4058},
number = {4},
pages = {535-550},
doi = {10.11646/zootaxa.4058.4.5},
pmid = {26701544},
issn = {1175-5334},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Female ; Insecta/*anatomy &amp; histology/*classification/genetics ; Male ; Ovum ; Spain ; Species Specificity ; },
abstract = {Male, female and egg of Pijnackeria recondita sp. n. are described from specimens collected at about 2,000 m in Sierra Nevada (Spain) feeding on Cytisus scoparius. The number of antennae segments in males, the smooth thorax in females and the different sculpturing of the egg capsule are the main differences from the other species of the genus. In addition, DNA barcode sequences (COI and COII) clearly differ from the other Iberian species of the genus. For COI, K2P minim-um distance between the new species and the most morphological related species, Pijnackeria hispanica (Bolívar, 1878), showed a mean of 8%. In the case of COII, comparison with the other species of Pijnackeria, showed a K2P minimum distance range from 8 to 10.5% (mean 9.2%); and comparison with the species of the related genus Leptynia, showed a K2P minimum distance range from 7.1 to 10.5%.},
}
@article {pmid26701523,
year = {2015},
author = {Sun, J and Jiang, JB and Zhao, Q and Qiu, JP},
title = {New earthworms of the Amynthas morrisi-group (Oligochaeta, Megascolecidae) from Hainan Island, China.},
journal = {Zootaxa},
volume = {4058},
number = {2},
pages = {257-266},
doi = {10.11646/zootaxa.4058.2.7},
pmid = {26701523},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; China ; Ecosystem ; Female ; Islands ; Male ; Molecular Sequence Data ; Oligochaeta/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Organ Size ; Phylogeny ; },
abstract = {This paper describes two new species of earthworms belonging to the Amynthas morrisi-group from Hainan Island, China: Amynthas zonarius sp. nov. and Amynthas wuzhimontis sp. nov. Both have two pairs of spermathecal pores in 5/6-6/7, and simple intestinal caeca. Amynthas zonarius sp. nov. has a pad-like male porophore, with flat-topped tubercle surrounded by 5 skin folds distal half of the spermathecal diverticulum dilated into band-shaped seminal chamber. Amynthas wuzhimontis sp. nov. has a seminal chamber constricted into moniliform subchambers and a glandular pad-like elliptical male pore porophore surrounded by the tumid area. Partial COI sequences of the holotypes of the two new species have been submitted to GenBank as DNA barcodes to enable molecular species identification.},
}
@article {pmid26701497,
year = {2015},
author = {Ježek, J and Wahab, RA and Ševčík, J and Wahab, RA and Ševčík, J},
title = {Two new species of Sycorax (Diptera: Psychodidae: Sycoracinae) from the Oriental Region.},
journal = {Zootaxa},
volume = {4057},
number = {4},
pages = {539-550},
doi = {10.11646/zootaxa.4057.4.4},
pmid = {26701497},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Female ; Male ; Organ Size ; Psychodidae/anatomy &amp; histology/*classification/genetics/growth &amp; development ; },
abstract = {Two new species of Sycorax Haliday in Curtis, 1839 are described from Ulu Temburong National Park in Brunei Darussalam: Sycorax konopiki sp. nov. and S. tomkineana sp. nov. Both species were found resting on two frog species: Ansonia leptopus (Günther, 1872) and A. longidigita Inger, 1960. Differential diagnoses for males are included and morphological characters illustrated. Possible host associations of the new species are briefly discussed. DNA barcode sequence (COI) for Sycorax konopiki sp. nov. is also provided.},
}
@article {pmid26701482,
year = {2015},
author = {Kočárek, P and Kuřavová, K and Musiolek, D and Abdul Wahab, R and Abdul Kahar, SR},
title = {Synonymy of Discotettix adenanii Mahmood, Idris &amp; Salmah, 2007 with D. belzebuth (Serville, 1838) (Orthoptera: Tetrigidae).},
journal = {Zootaxa},
volume = {4057},
number = {2},
pages = {288-294},
doi = {10.11646/zootaxa.4057.2.10},
pmid = {26701482},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; DNA Barcoding, Taxonomic ; Ecosystem ; Female ; Male ; Organ Size ; Orthoptera/anatomy &amp; histology/*classification/genetics/growth &amp; development ; },
abstract = {According to a study of type specimens of Discotettix adenanii Mahmood, Idris &amp; Salmah, 2007 and copious specimens of D. belzebuth (Serville, 1838) collected in different parts of Borneo, we found that all species-specific morphological characters of D. adenanii, according to its original description, fall into the morphological variability of D. belzebuth. Thus, we synonymize D. adenanii with D. belzebuth. The sequence of a segment of the mitochondrial 16S ribosomal RNA of D. belzebuth was also evaluated and added to GenBank as a DNA barcode.},
}
@article {pmid26701474,
year = {2015},
author = {Liang, F and Dai, Y and Yue, L and Li, F and Liu, X},
title = {DNA barcoding and taxonomic review of the barklouse genus Stenopsocus (Psocoptera: Stenopsocidae) from Taiwan.},
journal = {Zootaxa},
volume = {4057},
number = {2},
pages = {191-209},
doi = {10.11646/zootaxa.4057.2.2},
pmid = {26701474},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; DNA Barcoding, Taxonomic ; Ecosystem ; Female ; Insecta/anatomy &amp; histology/*classification/*genetics/growth &amp; development ; Male ; Molecular Sequence Data ; Organ Size ; Phylogeny ; Taiwan ; },
abstract = {The barklouse genus Stenopsocus Hagen is the most diverse group of the family Stenopsocidae, with 139 described species recorded from China in a previous study. However, due to the considerably similar morphology, species identification in this genus is problematic. In the present study, we used DNA barcoding to delimit the six Stenopsocus species currently recorded in Taiwan. Our results show that S. aphidiformis, S. niger, S. tibialis, S. makii, and S. formosanus can be clearly distinguished based on COI sequences. Although genetic divergence between S. formosanus and S. externus was not detected, we tentatively consider that these two species are valid based on their remarkably different morphological features. Re-descriptions of these six valid species are provided. Stenopsocus niger is newly recorded from Taiwan, and S. formosanus newly recorded from Vietnam.},
}
@article {pmid26700168,
year = {2015},
author = {Cornman, RS and Otto, CR and Iwanowicz, D and Pettis, JS},
title = {Taxonomic Characterization of Honey Bee (Apis mellifera) Pollen Foraging Based on Non-Overlapping Paired-End Sequencing of Nuclear Ribosomal Loci.},
journal = {PloS one},
volume = {10},
number = {12},
pages = {e0145365},
pmid = {26700168},
issn = {1932-6203},
mesh = {Animals ; Bees/*physiology ; DNA, Plant/chemistry ; Geography ; *Phylogeny ; Plants/*classification ; Pollen/*classification/genetics ; Pollination ; Sequence Analysis, DNA ; },
abstract = {Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5' of ITS1 and the 3' of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower "read2" quality, further protocol optimization and/or a modest reduction in multiplex scale should offset this difficulty. As small quantities of pollen are sufficient for amplification, our approach might be extendable to other questions or species for which large pollen samples are not available.},
}
@article {pmid26699756,
year = {2016},
author = {Dolch, K and Wuske, J and Gescher, J},
title = {Genomic Barcode-Based Analysis of Exoelectrogens in Wastewater Biofilms Grown on Anode Surfaces.},
journal = {Journal of microbiology and biotechnology},
volume = {26},
number = {3},
pages = {511-520},
doi = {10.4014/jmb.1510.10102},
pmid = {26699756},
issn = {1738-8872},
mesh = {Bioelectric Energy Sources/*microbiology ; Biofilms ; DNA Barcoding, Taxonomic ; Electricity ; Genomics ; Geobacter/chemistry/genetics/growth &amp; development/*physiology ; Sewage/chemistry/microbiology ; Shewanella/chemistry/genetics/growth &amp; development/*physiology ; Wastewater/*chemistry/microbiology ; },
abstract = {The most energy-demanding step of wastewater treatment is the aeration-dependent elimination of organic carbon. Microbial fuel cells (MFCs) offer an alternative strategy in which carbon elimination is conducted by anaerobic microorganisms that transport respiratory electrons originating from carbon oxidation to an anode. Hence, chemical energy is directly transformed into electrical energy. In this study, the use and stability of barcodecontaining exoelectrogenic model biofilms under non-axenic wastewater treatment conditions are described. Genomic barcodes were integrated in Shewanella oneidensis, Geobacter sulfurreducens, and G. metallireducens. These barcodes are unique for each strain and allow distinction between those cells and naturally occurring wild types as well as quantification of the amount of cells in a biofilm via multiplex qPCR. MFCs were pre-incubated with these three strains, and after 6 days the anodes were transferred into MFCs containing synthetic wastewater with 1% wastewater sludge. Over time, the system stabilized and the coulomb efficiency was constant. Overall, the initial synthetic biofilm community represented half of the anodic population at the end of the experimental timeline. The part of the community that contained a barcode was dominated by G. sulfurreducens cells (61.5%), while S. oneidensis and G. metallireducens cells comprised 10.5% and 17.9%, respectively. To the best of our knowledge, this is the first study to describe the stability of a synthetic exoelectrogenic consortium under non-axenic conditions. The observed stability offers new possibilities for the application of synthetic biofilms and synthetically engineered organisms fed with non-sterile waste streams.},
}
@article {pmid26696760,
year = {2015},
author = {Nielsen, SA and Kristensen, M and Pape, T},
title = {Three new Scandinavian species of Culicoides (Culicoides): Culicoides boyi sp. nov., Culicoides selandicus sp. nov. and Culicoides kalix sp. nov. (Diptera: Ceratopogonidae).},
journal = {Biodiversity data journal},
volume = {},
number = {3},
pages = {e5823},
pmid = {26696760},
issn = {1314-2828},
abstract = {BACKGROUND: In the context of a major monitoring program of Culicoides in Denmark and Sweden due to the appearance of bluetongue disease in 2007-2008, a large number of specimens were collected by light traps and sorted morphologically, with COI barcodes generated for selected specimens.<br><br>NEW INFORMATION: Three species are described as new to science based on both morphological and molecular data: Culicoides (Culicoides) boyi sp. nov. (Denmark: Jutland), C. (C.) selandicus sp. nov. (Denmark: Zealand) and C. (C.) kalix sp. nov. (Sweden: Norrbotten). All are diagnosed morphologically as well as by molecular barcoding. A key to slide-mounted females of all Scandinavian species of Culicoides (Culicoides) is presented.},
}
@article {pmid26692788,
year = {2015},
author = {Mustelin, T and Crabo, LG},
title = {Revision of the genus Aseptis McDunnough (Lepidoptera, Noctuidae, Noctuinae, Xylenini) with a description of two new genera, Paraseptis and Viridiseptis.},
journal = {ZooKeys},
volume = {},
number = {527},
pages = {57-102},
pmid = {26692788},
issn = {1313-2989},
abstract = {The genus Aseptis McDunnough (Lepidoptera, Noctuidae, Noctuinae, Xylenini, Xylenina) is revised to include 15 species based on morphological and molecular data. Several new synonymies are introduced. In addition, two genera are described because of significant morphological differences from Aseptis: Paraseptis gen. n., and Viridiseptis gen. n., resulting in the new combinations Paraseptis adnixa (Grote), comb. n., and Viridiseptis marina (Grote), comb. n. Although this work is primarily based on morphological data, DNA sequence data for the 658-base pair "barcode" segment of the mitochondrial gene for subunit 1 of cytochrome c oxidase was used as a secondary support for taxonomic changes within Aseptis and for the two new genera. Our work should provide clarity and stability in a previously difficult genus.},
}
@article {pmid26692787,
year = {2015},
author = {Crabo, LG},
title = {A new species of Ogdoconta Butler (Lepidoptera, Noctuidae, Condicinae, Condicini) from southeastern Arizona, USA.},
journal = {ZooKeys},
volume = {},
number = {527},
pages = {51-56},
pmid = {26692787},
issn = {1313-2989},
abstract = {A new species of Ogdoconta Butler (Lepidoptera, Noctuidae, Condicinae, Condicini) is described from the Patagonia Mountains, Santa Cruz County, Arizona, USA. Ogdoconta margareta sp. n., is related closely to Ogdoconta tacna (Barnes) from Texas. Modifications are proposed to a recently published key to the Ogdoconta species north of Mexico to allow identification of the new species.},
}
@article {pmid26691851,
year = {2015},
author = {Eeva, T and Andersson, T and Berglund, &#xc5;M and Brommer, JE and Hyvönen, R and Klemola, T and Laaksonen, T and Loukola, O and Morosinotto, C and Rainio, K and Sirkiä, PM and Vesterinen, EJ},
title = {Species and abundance of ectoparasitic flies (Diptera) in pied flycatcher nests in Fennoscandia.},
journal = {Parasites &amp; vectors},
volume = {8},
number = {},
pages = {648},
pmid = {26691851},
issn = {1756-3305},
mesh = {Animals ; Diptera/*classification/*growth &amp; development ; Ectoparasitic Infestations/parasitology/*veterinary ; Europe ; Phylogeography ; Prevalence ; Songbirds/*parasitology ; },
abstract = {BACKGROUND: Birds host several ectoparasitic fly species with negative effects on nestling health and reproductive output, and with the capability of transmitting avian blood parasites. Information on the abundance and distribution of the ectoparasitic fly genera Ornithomya (Hippoboscidae) and Protocalliphora (Calliphoridae) in northern Europe is still generally poor, and we thus explored their geographic range and occurrence of these flies in the nests of a common avian model species, the pied flycatcher Ficedula hypoleuca.<br><br>METHODS: Nests of F. hypoleuca were collected from 21 locations across Fennoscandia in summer 2013, across a latitudinal gradient (between 56 &#xb0;N - 70 &#xb0;N) and examined for the presence of fly puparia. Adult specimens of Ornithomya spp. were also collected for species identification. Fly species were identified morphologically and identifications confirmed with DNA barcoding.<br><br>RESULTS: We found three species: two louse-flies - Ornithomya chloropus and O. avicularia - and one blow-fly, Protocalliphora azurea. The prevalence of O. avicularia was higher in southern latitudes and this species was not encountered beyond 62 &#xb0;N whereas O. chloropus and P. azurea occurred across the whole range of latitudes. The prevalence of O. chloropus further increased with increasing distance from the coast - a pattern not documented before. The three fly species showed no interspecific associations in their prevalence.<br><br>CONCLUSIONS: Our study revealed relatively high prevalence for all the species (O. chloropus 59 %, O. avicularia 20 %, P. azurea 32 %), and an interesting spatial pattern in the prevalence of the two louse fly species. Our sample did not indicate any major range shifts towards the north for the southern species as compared to the information from the past. Morphological identification of O. chloropus did not match with the corresponding sequences published in the GenBank and taxonomy of this group calls for further studies.},
}
@article {pmid26687680,
year = {2016},
author = {van Galen, P and Viny, AD and Ram, O and Ryan, RJ and Cotton, MJ and Donohue, L and Sievers, C and Drier, Y and Liau, BB and Gillespie, SM and Carroll, KM and Cross, MB and Levine, RL and Bernstein, BE},
title = {A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes.},
journal = {Molecular cell},
volume = {61},
number = {1},
pages = {170-180},
pmid = {26687680},
issn = {1097-4164},
support = {U54 HG006991/HG/NHGRI NIH HHS/United States ; U01 HL100395/HL/NHLBI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; HG006991/HG/NHGRI NIH HHS/United States ; U54 HG004570/HG/NHGRI NIH HHS/United States ; HG006193/HG/NHGRI NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; U01HL100395/HL/NHLBI NIH HHS/United States ; },
mesh = {Chromatin/genetics/*metabolism ; *Chromatin Assembly and Disassembly/drug effects ; Chromatin Immunoprecipitation/*methods ; DNA Barcoding, Taxonomic ; Epigenesis, Genetic/drug effects ; Gene Expression Profiling ; Gene Expression Regulation, Leukemic ; Hematopoietic Stem Cells/*metabolism ; High-Throughput Nucleotide Sequencing/*methods ; Histones/genetics/*metabolism ; Humans ; K562 Cells ; Leukemia/genetics/*metabolism ; Multiplex Polymerase Chain Reaction/*methods ; Mutation ; },
abstract = {Genome-wide profiling of histone modifications can provide systematic insight into the regulatory elements and programs engaged in a given cell type. However, conventional chromatin immunoprecipitation and sequencing (ChIP-seq) does not capture quantitative information on histone modification levels, requires large amounts of starting material, and involves tedious processing of each individual sample. Here, we address these limitations with a technology that leverages DNA barcoding to profile chromatin quantitatively and in multiplexed format. We concurrently map relative levels of multiple histone modifications across multiple samples, each comprising as few as a thousand cells. We demonstrate the technology by monitoring dynamic changes following inhibition of p300, EZH2, or KDM5, by linking altered epigenetic landscapes to chromatin regulator mutations, and by mapping active and repressive marks in purified human hematopoietic stem cells. Hence, this technology enables quantitative studies of chromatin state dynamics across rare cell types, genotypes, environmental conditions, and drug treatments.},
}
@article {pmid26683999,
year = {2016},
author = {Tjhung, KF and Kitov, PI and Ng, S and Kitova, EN and Deng, L and Klassen, JS and Derda, R},
title = {Silent Encoding of Chemical Post-Translational Modifications in Phage-Displayed Libraries.},
journal = {Journal of the American Chemical Society},
volume = {138},
number = {1},
pages = {32-35},
doi = {10.1021/jacs.5b10390},
pmid = {26683999},
issn = {1520-5126},
mesh = {Bacteriophage M13/*genetics ; *Protein Processing, Post-Translational ; },
abstract = {In vitro selection of chemically modified peptide libraries presented on phage, while a powerful technology, is limited to one chemical post-translational modification (cPTM) per library. We use unique combinations of redundant codons to encode cPTMs with "silent barcodes" to trace multiple modifications within a mixed modified library. As a proof of concept, we produced phage-displayed peptide libraries Ser-[X]4-Gly-Gly-Gly, with Gly and Ser encoded using unique combinations of codons (TCA-[X]4-GGAGGAGGA, AGT-[X]4-GGTGGTGGT, etc., where [X]4 denotes a random NNK library). After separate chemical modification and pooling, mixed-modified libraries can be panned and deep-sequenced to identify the enriched peptide sequence and the accompanying cPTM simultaneously. We panned libraries bearing combinations of modifications (sulfonamide, biotin, mannose) against matched targets (carbonic anhydrase, streptavidin, concanavalin A) to identify desired ligands. Synthesis and validation of sequences identified by deep sequencing revealed that specific cPTMs are significantly enriched in panning against the specific targets. Panning on carbonic anhydrase yielded a potent ligand, sulfonamide-WIVP, with Kd = 6.7 ± 2.1 nM, a 20-fold improvement compared with the control ligand sulfonamide-GGGG. Silent encoding of multiple cPTMs can be readily incorporated into other in vitro display technologies such as bacteriophage T7 or mRNA display.},
}
@article {pmid26681644,
year = {2016},
author = {K K, B and A, G and J K, J and V S, B and C, M and N, V and M, J and Pillai, NG},
title = {Molecular identification of Bigeyes (Perciformes, Priacanthidae) from Indian waters.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4638-4642},
doi = {10.3109/19401736.2015.1101593},
pmid = {26681644},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; DNA, Mitochondrial/isolation &amp; purification/metabolism ; Electron Transport Complex IV/chemistry/classification/genetics/metabolism ; *Genome, Mitochondrial ; India ; Perciformes/classification/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/genetics ; Sequence Analysis, DNA ; },
abstract = {Thirty-five individuals of six priacanthid fish species were sampled from different localities along the coast of India covering the Arabian Sea and Bay of Bengal. The partial sequence of 16S rRNA and cytochrome oxidase subunit I (COI) genes were analyzed for species identification and phylogenetic relationship among the Indian priacanthids (Priacanthus hamrur, P. prolixus, P. blochii, P. sagittarius, Cookeolus japonicus, and Pristigenys refulgens). The intraspecies genetic distance ranged from 0.000 to 0.002, while distances varied from 0.008 to 0.157 interspecies based on 16S sequences. Using COI data analysis, the intraspecies genetic distance ranged from 0.000 to 0.005, while interspecies distances varied from 0.009 to 0.108. Several sequences labeled Priacanthus hamrur in GenBank are shown to be P. prolixus. We also observed cryptic speciation in Heteropriacanthus cruentatus. Partial sequences of 16S rRNA and COI genes provided phylogenetic information to distinguish thirteen species of priacanthids, indicating the usefulness of molecular markers in species identification.},
}
@article {pmid26681137,
year = {2017},
author = {Katugin, ON and Chichvarkhina, OV and Zolotova, AO and Chichvarkhin, AY},
title = {DNA barcoding for squids of the family Gonatidae (Cephalopoda: Teuthida) from the boreal North Pacific.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {1},
pages = {41-49},
doi = {10.3109/19401736.2015.1110792},
pmid = {26681137},
issn = {2470-1408},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry/isolation &amp; purification/metabolism ; Decapodiformes/cytology/*genetics ; Electron Transport Complex IV/genetics ; Genetic Variation ; Pacific Ocean ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {A fragment of cytochrome c oxidase I was used to assess whether species of the squid family Gonatidae from the North Pacific could be identified using DNA barcoding approach. Pairwise intra- and interspecific p-distances were assessed, and systematic relationships among species were estimated by NJ analysis. Examined species formed well-differentiated species-specific clades on the neighbor-joining and Bayesian trees. Multiple taxa formed clades supported by both tree topologies and species hypothesis-free ABGD method. Species morphologically identified as Gonatus tinro and Gonatopsis okutanii demonstrated intraspecific level of molecular genetic divergence (0.2-0.3%) indicating that they are conspecific. Genetic differences between the G. berryi clade and a squid morphologically close to that species may indicate a new cryptic species. High levels (>6.2%) of genetic differentiation within B. borealis suggested the existence of two cryptic species. This study confirms the usefulness of DNA barcoding for identifying species as well as discovering cryptic diversity in the gonatid squids, and indicates the need for further deeper insights into the phylogeny of the Gonatidae.},
}
@article {pmid26677693,
year = {2015},
author = {Zhang, S and Liu, YJ and Wu, YS and Cao, Y and Yuan, Y},
title = {[Screening potential DNA barcode regions of genus Papaver].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {40},
number = {15},
pages = {2964-2969},
pmid = {26677693},
issn = {1001-5302},
mesh = {DNA Barcoding, Taxonomic/*methods ; Papaver/*classification/genetics ; },
abstract = {DNA barcoding is an effective technique in species identification. To determine the candidate sequences which can be used as DNA barcode to identify in Papaver genus, five potential sequences (ITS, matK, psbA-trnH, rbcL, trnL-trnF) were screened. 69 sequences were downloaded from Genbank, including 21 ITS sequences, 10 matK sequences, 8 psbA-trnH sequences, 14 rbcL sequences and 16 trnL-trnF sequences. Mega 6.0 was used to analysis the comparison of sequences. By the methods of calculating the distances in intraspecific and interspecific divergences, evaluating DNA barcoding gap and constructing NJ and UPMGA phylogenetic trees. The sequence trnL-trnF performed best. In conclusion, trnL-trnF can be considered as a novel DNA barcode in Papaver genus, other four sequences can be as combination barcode for identification.},
}
@article {pmid26675917,
year = {2015},
author = {Camargo, LF and Brito, RA and Penteado-Dias, AM},
title = {Redescription of Campoletis sonorensis (Cameron, 1886) (Hymenoptera, Ichneumonidae, Campopleginae), parasitoid of Spodoptera frugiperda (J. E. Smith, 1797) (Lepidoptera, Noctuidae) in Brazil.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {75},
number = {4},
pages = {989-998},
doi = {10.1590/1519-6984.04914},
pmid = {26675917},
issn = {1678-4375},
mesh = {Animals ; Brazil ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Insect Proteins/genetics ; Male ; Microscopy, Electron, Scanning ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Spodoptera/*parasitology ; Wasps/*anatomy &amp; histology/*genetics/physiology/ultrastructure ; },
abstract = {The fall armyworm Spodoptera frugiperda (Lepidoptera; Noctuidae) is a voracious pest of numerous crops of economic importance throughout the New World. In Brazil, its larvae are attacked by several species of parasitoid wasps, making them potential candidate as biological control agents against this pest. A survey of the parasitoid fauna on S. frugiperda in maize crops throughout Brazil reveals two species of Campoletis, which are morphologicaly very similar species. In this paper we combine these data with pictures from the type material of C. sonorensis and C. flavicincta, as well as their descriptions to provide a redescription to Campoletis sonorensis (Cameron, 1886) using for this both morphological characters and DNA Barcoding (Hebert et al., 2003) information, in an attempt to help with the correct identification of the taxa to improve biological control studies.},
}
@article {pmid26663040,
year = {2016},
author = {Werblow, A and Flechl, E and Klimpel, S and Zittra, C and Lebl, K and Kieser, K and Laciny, A and Silbermayr, K and Melaun, C and Fuehrer, HP},
title = {Direct PCR of indigenous and invasive mosquito species: a time- and cost-effective technique of mosquito barcoding.},
journal = {Medical and veterinary entomology},
volume = {30},
number = {1},
pages = {8-13},
pmid = {26663040},
issn = {1365-2915},
mesh = {Animals ; Culicidae/*genetics/growth &amp; development ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Female ; Insect Proteins/genetics ; *Introduced Species ; Larva/genetics/growth &amp; development ; Male ; Molecular Sequence Data ; *Polymerase Chain Reaction ; Sequence Analysis, DNA ; Specimen Handling ; },
abstract = {Millions of people die each year as a result of pathogens transmitted by mosquitoes. However, the morphological identification of mosquito species can be difficult even for experts. The identification of morphologically indistinguishable species, such as members of the Anopheles maculipennis complex (Diptera: Culicidae), and possible hybrids, such as Culex pipiens pipiens/Culex pipiens molestus (Diptera: Culicidae), presents a major problem. In addition, the detection and discrimination of newly introduced species can be challenging, particularly to researchers without previous experience. Because of their medical importance, the clear identification of all relevant mosquito species is essential. Using the direct polymerase chain reaction (PCR) method described here, DNA amplification without prior DNA extraction is possible and thus species identification after sequencing can be achieved. Different amounts of tissue (leg, head; larvae or adult) as well as different storage conditions (dry, ethanol, -20 and -80 °C) and storage times were successfully applied and showed positive results after amplification and gel electrophoresis. Overall, 28 different indigenous and non-indigenous mosquito species were analysed using a gene fragment of the COX1 gene for species differentiation and identification by sequencing this 658-bp fragment. Compared with standard PCR, this method is time- and cost-effective and could thus improve existing surveillance and control programmes.},
}
@article {pmid26662385,
year = {2015},
author = {Aziz, NA and Ahmad, MI and Naim, DM},
title = {Molecular DNA identification of medicinal plants used by traditional healers in Malaysia.},
journal = {Genetics and molecular research : GMR},
volume = {14},
number = {4},
pages = {15937-15947},
doi = {10.4238/2015.December.7.5},
pmid = {26662385},
issn = {1676-5680},
mesh = {Computational Biology/methods ; *DNA Barcoding, Taxonomic ; DNA, Intergenic ; *DNA, Plant ; Genes, Plant ; Genetic Loci ; *Genetic Markers ; Malaysia ; Phylogeny ; Plants, Medicinal/*classification/*genetics ; Polymorphism, Genetic ; Sequence Analysis, DNA ; },
abstract = {Plants have been used throughout human history for food and medicine. However, many plants are toxic, and cannot easily be morphologically distinguished from non-toxic plants. DNA identification solves this problem and is widely used. Nonetheless, plant DNA barcode identification faces a number of challenges, and many studies have been conducted to find suitable barcodes. The present study was conducted to test the efficiency of commonly used primers, namely ITS2, rpoC1, and trnH-psbA, in order to find the best DNA barcode markers for the identification of medicinal plants in Malaysia. Fresh leaves from 12 medicinal plants that are commonly used by Malay traditional healers were collected from the Tropical Spice Garden, Pulau Pinang, and subjected to polymerase chain reaction amplification using ITS2, rpoC1, and trnH-psbA DNA markers. We found that trnH-psbA is the best DNA marker for the species-level identification of medicinal plants in Malaysia.},
}
@article {pmid26661903,
year = {2016},
author = {Vincent, JB and Weiblen, GD and May, G},
title = {Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees.},
journal = {Molecular ecology},
volume = {25},
number = {3},
pages = {825-841},
doi = {10.1111/mec.13510},
pmid = {26661903},
issn = {1365-294X},
support = {5U01TW006671/TW/FIC NIH HHS/United States ; },
mesh = {*Biodiversity ; DNA, Fungal ; DNA, Ribosomal Spacer/genetics ; Endophytes/*classification/genetics ; Fungi/*classification/genetics ; Molecular Sequence Data ; New Guinea ; Phylogeny ; Plant Leaves/microbiology ; *Rainforest ; Spatial Analysis ; Trees/*microbiology ; },
abstract = {Processes shaping the distribution of foliar fungal endophyte species remain poorly understood. Despite increasing evidence that these cryptic fungal symbionts of plants mediate interactions with pathogens and herbivores, there remain basic questions regarding the extent to which dispersal limitation and host specificity might shape fungal endophyte community composition in rainforests. To assess the relative importance of spatial pattern and host specificity, we isolated fungi from a sample of mapped trees in lowland Papua New Guinea. Sequences of the internal transcribed spacer (ITS) region were obtained for 2079 fungal endophytes from three sites and clustered into molecular operational taxonomic units (MOTUs) at 95% similarity. Multivariate analyses suggest that host affinity plays a significant role in structuring endophyte community composition whereas there was no evidence of endophyte spatial pattern at the scale of tens to hundreds of metres. Differences in endophyte communities between sampled trees were weakly correlated with variation in foliar traits but not with tree species relatedness. The dominance of relatively few generalist endophytes and the presence of a large number of rare MOTUs was a consistent observation at three sites separated by hundreds of kilometres and regional turnover was low. Host specificity appears to play a relatively weak but more important role than dispersal limitation in shaping the distribution of fungal endophyte communities in New Guinea forests. Our results suggest that in the absence of strong ecological gradients and host turnover, beta diversity of endophyte communities could be low in large areas of contiguous forest.},
}
@article {pmid26657936,
year = {2016},
author = {Shen, J and Wen, Z and Qin, X and Shi, Y},
title = {Noninvasive fetal trisomy detection by multiplexed semiconductor sequencing: a barcoding analysis strategy.},
journal = {Journal of human genetics},
volume = {61},
number = {3},
pages = {247-252},
pmid = {26657936},
issn = {1435-232X},
mesh = {*DNA Barcoding, Taxonomic ; Female ; Humans ; Pregnancy ; Prenatal Diagnosis/*methods ; *Semiconductors ; Trisomy/*diagnosis ; },
abstract = {Noninvasive prenatal detection of fetal chromosomal aneuploidies by high-throughput next-generation sequencing proves to be accurate and sensitive. Currently, most of the data analysis methods involve a Z-score test based on the reference distribution of at least dozens of normal samples. This is not only costly but also time consuming. Moreover, as the experimental condition varies between every single run, noises cannot be eliminated and will skew the results. In order to overcome these drawbacks, we have proposed a new analytical strategy based on the multiplex barcoding sequencing of both normal and unknown samples in a single run on Ion Torrent PGM. In this method, only one normal sample is required. By applying this method to 13 single runs with a total number of 44 samples, we achieved the sensitivity and specificity of 100 and 95.181% for T13 detection, 100 and 100% for T18 detection, 90 and 100% for T21 detection, respectively.},
}
@article {pmid26657561,
year = {2015},
author = {Miglietta, MP and Odegard, D and Faure, B and Faucci, A},
title = {Barcoding Techniques Help Tracking the Evolutionary History of the Introduced Species Pennaria disticha (Hydrozoa, Cnidaria).},
journal = {PloS one},
volume = {10},
number = {12},
pages = {e0144762},
pmid = {26657561},
issn = {1932-6203},
mesh = {Animal Distribution ; Animals ; Atlantic Ocean ; *Biological Evolution ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*genetics ; Genetic Variation ; Haplotypes ; Hawaii ; Hydrozoa/classification/*genetics ; Introduced Species ; Pacific Ocean ; Panama ; *Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; },
abstract = {The Christmas tree hydroid Pennaria disticha is listed as one of the most common introduced species in Hawaii. Firstly reported in Kaneohe Bay (Oahu) in 1928, it is now established throughout the entire archipelago, including the Northwestern Hawaiian Islands, a U.S. National Monument and World Heritage site. The Hawaiian population of P. disticha has also been reported as being the source of further introductions to Palmyra Atoll in the U.S. Line Islands. Using a phylogenetic hypothesis based on a 611 base pair fragment of the mitochondrial 16S barcoding gene, we demonstrate that P. disticha is a complex of cryptic species, rather than one species with cosmopolitan distribution. We also show that in Hawaii there are three species of Pennaria, rather than one introduced species. Two of these species share haplotypes with specimens from distant locations such as Florida and Panama and may have been introduced, possibly from the Atlantic Ocean. A third species could either represent a lineage with nearly cosmopolitan distribution, or another introduced species. Our dataset refutes the widely accepted idea that only one lineage of P. disticha is present in Hawaii. On the contrary, P. disticha in Hawaii may be the outcome of multiple independent introductions of several morphologically undistinguishable cryptic lineages. Our results uncover an unsuspected complexity within the very common hydroid P. disticha, and highlight the need for routine use of molecular tools, such as DNA barcoding, to improve the identification and recognition of non-indigenous species.},
}
@article {pmid26654042,
year = {2015},
author = {Fernández-Álvarez, F&#xc1; and García-Jiménez, R and Machordom, A},
title = {Carinina ochracea (Palaeonemertea: Tubulanidae) Reaches Its Southernmost Distribution: New Morphological and Molecular Data.},
journal = {Zoological science},
volume = {32},
number = {6},
pages = {590-595},
doi = {10.2108/zs140228},
pmid = {26654042},
issn = {0289-0003},
mesh = {*Animal Distribution ; Animals ; DNA/genetics ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Estuaries ; Gene Expression Regulation, Enzymologic ; Invertebrates/*genetics ; },
abstract = {New data for Carinina ochracea Sundberg et al., 2009 are provided for the Iberian Peninsula, establishing the southernmost limit of its known distribution. This species was previously known from only two localities: the type locality in Tjärnö (Sweden) and Pouldohan (Brittany, France). The material examined here was obtained during a faunal survey in the Villaviciosa Estuary (Asturias, northern Iberian Peninsula). The identity of the new specimen was confirmed both by DNA barcoding and anatomical examination. The molecular divergence of all available sequences of this species for four molecular markers, cytochrome c oxidase subunit I (COI), 16S, 18S and 28S rDNA, is discussed. For COI, four polymorphic sites were found, indicating: 1) a nuclear pseudogene; 2) heteroplasmy; or 3) gene duplication of a region of the mitochondrial genome. Two previously overlooked morphological characters were found: the presence of a colour ring and a postfixation staining band (pigmented band), which is histologically characterized. This species is the 12th palaeonemertean and the 75th nemertean reported from Iberian waters.},
}
@article {pmid26649264,
year = {2015},
author = {Richardson, RT and Lin, CH and Quijia, JO and Riusech, NS and Goodell, K and Johnson, RM},
title = {Rank-based characterization of pollen assemblages collected by honey bees using a multi-locus metabarcoding approach.},
journal = {Applications in plant sciences},
volume = {3},
number = {11},
pages = {},
pmid = {26649264},
issn = {2168-0450},
abstract = {PREMISE OF THE STUDY: Difficulties inherent in microscopic pollen identification have resulted in limited implementation for large-scale studies. Metabarcoding, a relatively novel approach, could make pollen analysis less onerous; however, improved understanding of the quantitative capacity of various plant metabarcode regions and primer sets is needed to ensure that such applications are accurate and precise.<br><br>METHODS AND RESULTS: We applied metabarcoding, targeting the ITS2, matK, and rbcL loci, to characterize six samples of pollen collected by honey bees, Apis mellifera. Additionally, samples were analyzed by light microscopy. We found significant rank-based associations between the relative abundance of pollen types within our samples as inferred by the two methods.<br><br>CONCLUSIONS: Our findings suggest metabarcoding data from plastid loci, as opposed to the ribosomal locus, are more reliable for quantitative characterization of pollen assemblages. Furthermore, multilocus metabarcoding of pollen may be more reliable than single-locus analyses, underscoring the need for discovering novel barcodes and barcode combinations optimized for molecular palynology.},
}
@article {pmid26647648,
year = {2016},
author = {Otten, L and Fullam, E and Gibson, MI},
title = {Discrimination between bacterial species by ratiometric analysis of their carbohydrate binding profile.},
journal = {Molecular bioSystems},
volume = {12},
number = {2},
pages = {341-344},
pmid = {26647648},
issn = {1742-2051},
support = {104193//Wellcome Trust/United Kingdom ; 638661/ERC_/European Research Council/International ; 104193/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Acetylglucosamine/chemistry ; Arabinose/chemistry ; Bacterial Adhesion ; *Biosensing Techniques ; Cellobiose/chemistry ; Dextrans/chemistry ; Discriminant Analysis ; Escherichia coli/*physiology ; Galactose/chemistry ; Glucose/chemistry ; Glyceraldehyde/chemistry ; Lactose/chemistry ; Mannose/chemistry ; Mycobacterium marinum/*physiology ; Mycobacterium smegmatis/*physiology ; Pseudomonas putida/*physiology ; },
abstract = {Antibiotic resistance is a global health concern meaning there is an urgent need for new treatments and diagnostics. Here glycosylated surfaces are used to profile the binding patterns of a range of Gram-negative, Gram-positive and mycobacteria. This enables the creation of 'barcodes' to enable identification and discrimination between the strains, which could not be achieved by single-point glycan binding and offers a new concept in bacteria detection.},
}
@article {pmid26645448,
year = {2015},
author = {Yen, YT and Chang, SF and Tsai, KL and Chen, CJ and Liu, LC and Fang, YC},
title = {[A Program to Improve the Implementation Rate for the Barcode Medication Administration System].},
journal = {Hu li za zhi The journal of nursing},
volume = {62},
number = {6},
pages = {90-97},
doi = {10.6224/JN62.6.90},
pmid = {26645448},
issn = {0047-262X},
mesh = {*Electronic Data Processing ; Humans ; Medication Errors/*prevention &amp; control ; *Medication Systems, Hospital ; },
abstract = {BACKGROUND &amp; PROBLEM: Fully implementing the barcode medication administration system has been shown to help improve medication safety. We have promoted the barcode medication administration system in our hospital since May of 2014. However, the rate of implementation reached only 32% initially. We identified the major obstacles to fully implementing the barcode system as: (1) the barcodes on patients' wristbands were smudged or broken; (2) the barcodes on transparent drug bags and infusion bags were difficult to scan; (3) nurses were not familiar with the scanner and lacked the skills necessary to conduct barcode scans; (4) poor wireless Internet access inhibited effective barcode scanning; and (5) the beep sound generated during barcode scanning disturbed patients' sleep. The present project was conducted to improve the implementation by nursing staff of the barcode medication administration system.<br><br>PURPOSE: The purpose was to increase the rate of implementation from 32% to 80%.<br><br>RESOLUSIONS: The key members of the project were nurses, computer technicians, and pharmacists. The following procedures were conducted: (1) check the integrity of the wrist band and renew this band periodically; (2) print the barcode against a white background on transparent drug transfusion bags; (3) demonstration the skills of barcode scanning to nurses and inspect the function of scanners periodically; (4) increase the number of access points for the wireless network; (5) demonstrate the procedure for adjusting the sound volume on the scanner; and (6) provide rewards / incentives for using the barcode medication administration system.<br><br>RESULTS: The rate of implementation of the barcode medication administration system increased from 32% to 85.2%.<br><br>CONCLUSIONS: This project significantly increased the use of the barcode medication administration system by our nursing staff. The procedures used in this project may be referenced by administrators at other hospitals with low rates of barcode medication administration system usage.},
}
@article {pmid26643194,
year = {2016},
author = {Zhong, B and Chen, TT and Gong, RY and Zhao, ZX and Wang, B and Fang, C and Mao, HL},
title = {Classification of Pelteobagrus fish in Poyang Lake based on mitochondrial COI gene sequence.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4635-4637},
doi = {10.3109/19401736.2015.1101592},
pmid = {26643194},
issn = {2470-1408},
mesh = {Animals ; Catfishes/classification/*genetics ; Cluster Analysis ; DNA, Mitochondrial/isolation &amp; purification/metabolism ; Electron Transport Complex IV/chemistry/classification/*genetics/metabolism ; Genes, Mitochondrial ; Lakes ; Phylogeny ; },
abstract = {We use DNA molecular marker technology to correct the deficiency of traditional morphological taxonomy. Totality 770 Pelteobagrus fish from Poyang Lake were collected. After preliminary morphological classification, random selected eight samples in each species for DNA extraction. Mitochondrial COI gene sequence was cloned with universal primers and sequenced. The results showed that there are four species of Pelteobagrus living in Poyang Lake. The average of intraspecific genetic distance value was 0.003, while the average interspecific genetic distance was 0.128. The interspecific genetic distance is far more than intraspecific genetic distance. Besides, phylogenetic tree analysis revealed that molecular systematics was in accord with morphological classification. It indicated that COI gene is an effective DNA molecular marker in Pelteobagrus classification. Surprisingly, the intraspecific difference of some individuals (P. e6, P. n6, P. e5, and P. v4) from their original named exceeded species threshold (2%), which should be renewedly classified into Pelteobagrus fulvidraco. However, another individual P. v3 was very different, because its genetic distance was over 8.4% difference from original named Pelteobagrus vachelli. Its taxonomic status remained to be further studied.},
}
@article {pmid26642251,
year = {2015},
author = {Adamowicz, SJ and Steinke, D},
title = {Increasing global participation in genetics research through DNA barcoding.},
journal = {Genome},
volume = {58},
number = {12},
pages = {519-526},
doi = {10.1139/gen-2015-0130},
pmid = {26642251},
issn = {1480-3321},
mesh = {*DNA Barcoding, Taxonomic/methods ; Databases, Genetic ; *Genetic Research ; *Global Health ; Humans ; Meta-Analysis as Topic ; *Social Participation ; },
abstract = {DNA barcoding--the sequencing of short, standardized DNA regions for specimen identification and species discovery--has promised to facilitate rapid access to biodiversity knowledge by diverse users. Here, we advance our opinion that increased global participation in genetics research is beneficial, both to scientists and for science, and explore the premise that DNA barcoding can help to democratize participation in genetics research. We examine publication patterns (2003-2014) in the DNA barcoding literature and compare trends with those in the broader, related domain of genomics. While genomics is the older and much larger field, the number of nations contributing to the published literature is similar between disciplines. Meanwhile, DNA barcoding exhibits a higher pace of growth in the number of publications as well as greater evenness among nations in their proportional contribution to total authorships. This exploration revealed DNA barcoding to be a highly international discipline, with growing participation by researchers in especially biodiverse nations. We briefly consider several of the challenges that may hinder further participation in genetics research, including access to training and molecular facilities as well as policy relating to the movement of genetic resources.},
}
@article {pmid26641858,
year = {2015},
author = {Bennett, KL and Linton, YM and Shija, F and Kaddumukasa, M and Djouaka, R and Misinzo, G and Lutwama, J and Huang, YM and Mitchell, LB and Richards, M and Tossou, E and Walton, C},
title = {Molecular Differentiation of the African Yellow Fever Vector Aedes bromeliae (Diptera: Culicidae) from Its Sympatric Non-vector Sister Species, Aedes lilii.},
journal = {PLoS neglected tropical diseases},
volume = {9},
number = {12},
pages = {e0004250},
pmid = {26641858},
issn = {1935-2735},
mesh = {Aedes/*classification/*genetics ; Animals ; Benin ; Cluster Analysis ; DNA, Ribosomal Spacer/chemistry/genetics ; Ecosystem ; Entomology/*methods ; Humans ; Insect Proteins/genetics ; *Insect Vectors ; Molecular Sequence Data ; Phylogeography ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA ; Tanzania ; Uganda ; Yellow Fever/transmission ; },
abstract = {INTRODUCTION: Yellow fever continues to be a problem in sub-Saharan Africa with repeated epidemics occurring. The mosquito Aedes bromeliae is a major vector of yellow fever, but it cannot be readily differentiated from its non-vector zoophilic sister species Ae. lilii using morphological characters. Genetic differences have been reported between anthropophilic Ae. bromeliae and zoophilic Ae. lilii and between forest and domestic populations. However, due to the application of different molecular markers and non-overlapping populations employed in previous studies, interpretation of species delimitation is unclear.<br><br>DNA sequences were generated from specimens of Ae. simpsoni s.l. from the Republic of Benin, Tanzania and Uganda for two nuclear genes apolipophorin 2 (apoLp2) and cytochrome p450 (CYPJ92), the ribosomal internal transcribed spacer region (ITS) and the mitochondrial cytochrome c oxidase (COI) barcoding region. Nuclear genes apoLp2 and CYPJ92 were unable to differentiate between species Ae. bromeliae and Ae. lilii due to ancestral lineage sorting, while ITS sequence data provided clear topological separation on a phylogeny. The standard COI barcoding region was shown to be subject to species introgression and unable to clearly distinguish the two taxa. Here we present a reliable direct PCR-based method for differentiation of the vector species Ae. bromeliae from its isomorphic, sympatric and non-biomedically important sister taxon, Ae. lilii, based on the ITS region. Using molecular species verification, we describe novel immature habitats for Ae. lilii and report both sympatric and allopatric populations. Whereas only Ae. lilii is found in the Republic of Benin and only Ae. bromeliae in Tanzania, both species are sympatric in Uganda.<br><br>CONCLUSIONS/SIGNIFICANCE: Our accurate identification method will allow informed distribution and detailed ecological studies that will facilitate assessment of arboviral disease risk and development of future targeted vector control.},
}
@article {pmid26640684,
year = {2015},
author = {Bruce, MR and Saunders, GW},
title = {Population genetic analyses are consistent with the introduction of Ceramium secundatum (Ceramiaceae, Rhodophyta) to Narragansett Bay, Rhode Island, USA.},
journal = {Ecology and evolution},
volume = {5},
number = {21},
pages = {5088-5095},
pmid = {26640684},
issn = {2045-7758},
abstract = {During ongoing DNA barcode (COI-5P) surveys of the macroalgal flora along the northwest Atlantic coast, we discovered a population of Ceramium secundatum in Narragansett Bay, Rhode Island, USA. This species is regarded as common and widespread in the northeast Atlantic, ranging from Norway to Morocco, but until now has not been reported from the western Atlantic. Several lines of evidence suggest that C. secundatum may be introduced to Narragansett Bay: (1) despite extensive collecting, specimens have only been obtained from a limited geographic range in the northwest Atlantic; (2) three other nonindigenous seaweed species are reportedly introduced in this region, which is thought to be a consequence of shipping; and (3) this species is introduced to South Africa and New Zealand. To investigate this suspected introduction, we applied population genetic analyses (using the cox2-3 spacer) to compare the Narragansett Bay C. secundatum population to native populations in the Republic of Ireland and the United Kingdom. Collectively, analyses of biogeographical and molecular data indicate that C. secundatum is likely introduced to Narragansett Bay. The implications of this discovery are discussed.},
}
@article {pmid26634467,
year = {2015},
author = {Sun, XQ and Qu, YQ and Yao, H and Zhang, YM and Yan, QQ and Hang, YY},
title = {Applying DNA barcodes for identification of economically important species in Brassicaceae.},
journal = {Genetics and molecular research : GMR},
volume = {14},
number = {4},
pages = {15050-15061},
doi = {10.4238/2015.November.24.13},
pmid = {26634467},
issn = {1676-5680},
mesh = {Brassicaceae/classification/*genetics ; China ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Genetic Loci/genetics ; Genetic Markers/genetics ; *Genetic Variation ; Phylogeny ; Plant Proteins/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Brassicaceae is a large plant family of special interest; it includes many economically important crops, herbs, and ornamentals, as well as model organisms. The taxonomy of the Brassicaceae has long been controversial because of the poorly delimited generic boundaries and artificially circumscribed tribes. Despite great effort to delimitate species and reconstruct the phylogeny of Brassicaceae, little research has been carried out to investigate the applicability and effectiveness of different DNA regions as barcodes - a recent aid for taxonomic identification - to identify economically important species in Brassicaceae. In this study, we evaluated the feasibility of five intensively recommended regions [rbcL, matK, trnH-psbA, internal transcribed spacer (ITS), ITS2] as candidate DNA barcodes to discriminate economic species of Brassicaceae in China and try to establish a new digital identification method for economic plants of Brassicaceae. All sequences of 58 samples from 27 economic species (Brassicaceae) in China were assessed in the success rates of PCR amplifications, intra- and inter-specific divergence, DNA barcoding gaps, and efficiency of identification. Compared with other markers, ITS showed superiority in species discrimination with an accurate identification of 67.2% at the species level. Consequently, as one of the most popular phylogenetic markers, our study indicated that ITS was a powerful but not perfect barcode for Brassicaceae identification. We further discuss the discrimination power of different loci due to inheritance pattern, polyploidization and hybridization in species-specific evolution. Further screening of other nuclear genes related to species isolation as plant barcode candidates is also proposed.},
}
@article {pmid26633636,
year = {2015},
author = {Nguyen, LV and Pellacani, D and Lefort, S and Kannan, N and Osako, T and Makarem, M and Cox, CL and Kennedy, W and Beer, P and Carles, A and Moksa, M and Bilenky, M and Balani, S and Babovic, S and Sun, I and Rosin, M and Aparicio, S and Hirst, M and Eaves, CJ},
title = {Barcoding reveals complex clonal dynamics of de novo transformed human mammary cells.},
journal = {Nature},
volume = {528},
number = {7581},
pages = {267-271},
doi = {10.1038/nature15742},
pmid = {26633636},
issn = {1476-4687},
support = {//Canadian Institutes of Health Research/Canada ; },
mesh = {Animals ; Breast Neoplasms/genetics/*physiopathology ; Carcinoma, Ductal, Breast/genetics/*physiopathology ; Cell Lineage/genetics ; *Cell Transformation, Neoplastic ; Cells, Cultured ; DNA Barcoding, Taxonomic ; Female ; Gene Expression Profiling ; Heterografts ; Humans ; Lentivirus/genetics ; Mammary Glands, Human/cytology/*physiopathology ; Mice ; Mice, Inbred Strains ; Mice, SCID ; Proto-Oncogene Proteins/genetics ; Proto-Oncogene Proteins p21(ras) ; Time Factors ; Transduction, Genetic ; ras Proteins/genetics ; },
abstract = {Most human breast cancers have diversified genomically and biologically by the time they become clinically evident. Early events involved in their genesis and the cellular context in which these events occur have thus been difficult to characterize. Here we present the first formal evidence of the shared and independent ability of basal cells and luminal progenitors, isolated from normal human mammary tissue and transduced with a single oncogene (KRAS(G12D)), to produce serially transplantable, polyclonal, invasive ductal carcinomas within 8 weeks of being introduced either subrenally or subcutaneously into immunodeficient mice. DNA barcoding of the initial cells revealed a dramatic change in the numbers and sizes of clones generated from them within 2 weeks, and the first appearance of many 'new' clones in tumours passaged into secondary recipients. Both primary and secondary tumours were phenotypically heterogeneous and primary tumours were categorized transcriptionally as 'normal-like'. This system challenges previous concepts that carcinogenesis in normal human epithelia is necessarily a slow process requiring the acquisition of multiple driver mutations. It also presents the first description of initial events that accompany the genesis and evolution of malignant human mammary cell populations, thereby contributing new understanding of the rapidity with which heterogeneity in their properties can develop.},
}
@article {pmid26633399,
year = {2015},
author = {Lei, Y and Yang, F and Tang, L and Chen, K and Zhang, GJ},
title = {Identification of Chinese Herbs Using a Sequencing-Free Nanostructured Electrochemical DNA Biosensor.},
journal = {Sensors (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {29882-29892},
pmid = {26633399},
issn = {1424-8220},
mesh = {Biosensing Techniques/*methods ; DNA, Plant/*analysis/classification ; *Drugs, Chinese Herbal ; Electrochemical Techniques/*methods ; Fritillaria/chemistry ; Gold/chemistry ; Metal Nanoparticles/chemistry ; Plant Leaves/chemistry ; },
abstract = {Due to the nearly identical phenotypes and chemical constituents, it is often very challenging to accurately differentiate diverse species of a Chinese herbal genus. Although technologies including DNA barcoding have been introduced to help address this problem, they are generally time-consuming and require expensive sequencing. Herein, we present a simple sequencing-free electrochemical biosensor, which enables easy differentiation between two closely related Fritillaria species. To improve its differentiation capability using trace amounts of DNA sample available from herbal extracts, a stepwise electrochemical deposition of reduced graphene oxide (RGO) and gold nanoparticles (AuNPs) was adopted to engineer a synergistic nanostructured sensing interface. By using such a nanofeatured electrochemical DNA (E-DNA) biosensor, two Chinese herbal species of Fritillaria (F. thunbergii and F. cirrhosa) were successfully discriminated at the DNA level, because a fragment of 16-mer sequence at the spacer region of the 5S-rRNA only exists in F. thunbergii. This E-DNA sensor was capable of identifying the target sequence in the range from 100 fM to 10 nM, and a detection limit as low as 11.7 fM (S/N = 3) was obtained. Importantly, this sensor was applied to detect the unique fragment of the PCR products amplified from F. thunbergii and F. cirrhosa, respectively. We anticipate that such a direct, sequencing-free sensing mode will ultimately pave the way towards a new generation of herb-identification strategies.},
}
@article {pmid26630282,
year = {2015},
author = {Bolson, M and Smidt, Ede C and Brotto, ML and Silva-Pereira, V},
title = {ITS and trnH-psbA as Efficient DNA Barcodes to Identify Threatened Commercial Woody Angiosperms from Southern Brazilian Atlantic Rainforests.},
journal = {PloS one},
volume = {10},
number = {12},
pages = {e0143049},
pmid = {26630282},
issn = {1932-6203},
mesh = {Atlantic Ocean ; Brazil ; *DNA Barcoding, Taxonomic ; DNA, Intergenic/*genetics ; DNA, Plant/*genetics ; *Endangered Species ; Magnoliopsida/*classification/genetics ; Molecular Sequence Data ; *Rainforest ; Sequence Analysis, DNA ; Species Specificity ; *Wood ; },
abstract = {The Araucaria Forests in southern Brazil are part of the Atlantic Rainforest, a key hotspot for global biodiversity. This habitat has experienced extensive losses of vegetation cover due to commercial logging and the intense use of wood resources for construction and furniture manufacturing. The absence of precise taxonomic tools for identifying Araucaria Forest tree species motivated us to test the ability of DNA barcoding to distinguish species exploited for wood resources and its suitability for use as an alternative testing technique for the inspection of illegal timber shipments. We tested three cpDNA regions (matK, trnH-psbA, and rbcL) and nrITS according to criteria determined by The Consortium for the Barcode of Life (CBOL). The efficiency of each marker and selected marker combinations were evaluated for 30 commercially valuable woody species in multiple populations, with a special focus on Lauraceae species. Inter- and intraspecific distances, species discrimination rates, and ability to recover species-specific clusters were evaluated. Among the regions and different combinations, ITS was the most efficient for identifying species based on the 'best close match' test; similarly, the trnH-psbA + ITS combination also demonstrated satisfactory results. When combining trnH-psbA + ITS, Maximum Likelihood analysis demonstrated a more resolved topology for internal branches, with 91% of species-specific clusters. DNA barcoding was found to be a practical and rapid method for identifying major threatened woody angiosperms from Araucaria Forests such as Lauraceae species, presenting a high confidence for recognizing members of Ocotea. These molecular tools can assist in screening those botanical families that are most targeted by the timber industry in southern Brazil and detecting certain species protected by Brazilian legislation and could be a useful tool for monitoring wood exploitation.},
}
@article {pmid26628908,
year = {2015},
author = {Zhu, X and Zhang, Y and Liu, X and Hou, D and Gao, T},
title = {Authentication of commercial processed Glehniae Radix (Beishashen) by DNA barcodes.},
journal = {Chinese medicine},
volume = {10},
number = {},
pages = {35},
pmid = {26628908},
issn = {1749-8546},
abstract = {BACKGROUND: The radix of Glehnia littoralis Fr. Schmidt ex Miq. (Beishashen), is often misidentified and adultered in Chinese medicine. Its seven common adulterants include Chuanminshen violaceum Sheh et Shan (Chuanmingshen), Changium smyrnioides Wolff (Mingdangshen), Sphallerocarpus gracilis (Bess.) K.-Pol. (Miguoqin), Adenophora polyantha Nakai (Shishashen), Silene tatarinowii Regel (Shishengyingzicao), Adenophora tetraphylla (Thunb.) Fisch (Lunyeshashen) and Adenophora stricta Miq. (Shashen). This study aims to evaluate the feasibility of the second internal transcribed spacer (ITS2) DNA barcoding to discriminate between Glehniae Radix and its common adulterants.<br><br>METHODS: In this study, we collected 46 samples of G. littoralis and 59 samples of its seven common adulterants. Genomic DNA sequences were extracted from samples, including original plants and commercially processed crude drugs. The ITS2 of the ribosomal DNA sequences were amplified and sequenced bi-directionally. The sequences were assembled by CodonCode Aligner 3.5.7. The descriptive data analysis was conducted and neighbor-joining (NJ) phylogenetic tree was constructed by MEGA 5.0 in accordance with the kimura 2 -parameter (K2P) model. The identification efficiency was evaluated based on the BLAST1 methods. The ITS2 secondary structures were predicted and compared between Glehniae Radix and its adulterants by the ITS2 database.<br><br>RESULTS: As the 46 ITS2 sequences of G. littoralis were identical to each other, the identification efficiency of the ITS2 region was 100&#xa0;%. A NJ tree based on the ITS2 sequences, and the predicted secondary structures of ITS2, distinguished Glehniae Radix from its adulterants.<br><br>CONCLUSION: DNA barcoding based on ITS2 distinguished commercial processed Glehniae Radix from common herbal adulterants.},
}
@article {pmid26627691,
year = {2016},
author = {Vadivalagan, C and Karthika, P and Murugan, K and Panneerselvam, C and Paulpandi, M and Madhiyazhagan, P and Wei, H and Aziz, AT and Alsalhi, MS and Devanesan, S and Nicoletti, M and Paramasivan, R and Dinesh, D and Benelli, G},
title = {Genetic deviation in geographically close populations of the dengue vector Aedes aegypti (Diptera: Culicidae): influence of environmental barriers in South India.},
journal = {Parasitology research},
volume = {115},
number = {3},
pages = {1149-1160},
pmid = {26627691},
issn = {1432-1955},
mesh = {Aedes/*genetics/virology ; Africa, Western ; Animals ; DNA, Mitochondrial/genetics ; Dengue/transmission ; Dengue Virus/physiology ; *Environment ; Gene Flow ; *Genetic Variation ; Geography ; Haplotypes ; Humans ; India ; Insect Vectors/*genetics ; },
abstract = {Mosquitoes are vectors of devastating pathogens and parasites, causing millions of deaths every year. Dengue is a mosquito-borne viral infection found in tropical and subtropical regions around the world. Recently, dengue transmission has strongly increased in urban and semiurban areas, becoming a major international public health concern. Aedes aegypti (Diptera: Culicidae) is a primary vector of dengue. Shedding light on genetic deviation in A. aegypti populations is of crucial importance to fully understand their molecular ecology and evolution. In this research, haplotype and genetic analyses were conducted using individuals of A. aegypti from 31 localities in the north, southeast, northeast and central regions of Tamil Nadu (South India). The mitochondrial DNA region of cytochrome c oxidase 1 (CO1) gene was used as marker for the analyses. Thirty-one haplotypes sequences were submitted to GenBank and authenticated. The complete haplotype set included 64 haplotypes from various geographical regions clustered into three groups (lineages) separated by three fixed mutational steps, suggesting that the South Indian Ae. aegypti populations were pooled and are linked with West Africa, Columbian and Southeast Asian lineages. The genetic and haplotype diversity was low, indicating reduced gene flow among close populations of the vector, due to geographical barriers such as water bodies. Lastly, the negative values for neutrality tests indicated a bottle-neck effect and supported for low frequency of polymorphism among the haplotypes. Overall, our results add basic knowledge to molecular ecology of the dengue vector A. aegypti, providing the first evidence for multiple introductions of Ae. aegypti populations from Columbia and West Africa in South India.},
}
@article {pmid26626561,
year = {2015},
author = {Glaus, KBJ and Adrian-Kalchhauser, I and Burkhardt-Holm, P and White, WT and Brunnschweiler, JM},
title = {Characteristics of the shark fisheries of Fiji.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {17556},
pmid = {26626561},
issn = {2045-2322},
mesh = {Animals ; Fiji ; Fisheries/*methods ; Sharks/*physiology ; },
abstract = {Limited information is available on artisanal and subsistence shark fisheries across the Pacific. The aim of this study was to investigate Fiji's inshore fisheries which catch sharks. In January and February 2013, 253 semi-directive interviews were conducted in 117 villages and at local harbours on Viti Levu, Vanua Levu, Taveuni, Ovalau and a number of islands of the Mamanuca and Yasawa archipelagos. Of the 253 interviewees, 81.4% reported to presently catch sharks, and 17.4% declared that they did not presently catch any sharks. Of the 206 fishers that reported to catch sharks, 18.4% targeted sharks and 81.6% caught sharks as bycatch. When targeted, primary use of sharks was for consumption or for sale. Sharks caught as bycatch were frequently released (69.6%), consumed (64.9%) or shared amongst the community (26.8%). Fishers' identification based on an identification poster and DNA barcoding revealed that at least 12 species of elasmobranchs, 11 shark and one ray species (Rhynchobatus australiae) were caught. This study, which is the first focused exploration of the shark catch in Fiji's inshore fisheries, suggests that the country's artisanal shark fisheries are small but have the potential to develop into larger and possibly more targeted fisheries.},
}
@article {pmid26624726,
year = {2015},
author = {Jordaens, K and Goergen, G and Kirk-Spriggs, AH and Vokaer, A and Backeljau, T and De Meyer, M},
title = {A second New World hoverfly, Toxomerus floralis (Fabricius) (Diptera: Syrphidae), recorded from the Old World, with description of larval pollen-feeding ecology.},
journal = {Zootaxa},
volume = {4044},
number = {4},
pages = {567-576},
doi = {10.11646/zootaxa.4044.4.6},
pmid = {26624726},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Diptera/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Ecosystem ; Female ; Larva/anatomy &amp; histology/classification/growth &amp; development ; Male ; Organ Size ; Phylogeny ; },
abstract = {Recently (2013-2014), several hoverfly specimens from two localities in Benin and Cameroon (West and Central Africa) were caught from a species that we could not identify using existing identification keys for Afrotropical Syrphidae. Specific identification as Toxomerus floralis (Fabricius) was accomplished using morphology and various Neotropical identification keys. Corroboration of this identification was made by sequencing of the standard COI barcode region and a subsequent BLAST-IDS in BOLD that revealed a 100% sequence similarity with Toxomerus floralis from Suriname (South America). Species identification was further supported by sequencing parts of the nuclear 18S and 28S rRNA genes. The species is widespread in Togo, Benin, Nigeria and Cameroon, and eggs, larvae and adults are abundant at several localities. Yet, the full extent of its geographic distribution within tropical Africa remains to be determined. This is only the second known established introduction of a non-African hoverfly species in the Afrotropics. Interestingly, the larvae of the species have been reported as predators of Aphididae and Delphacidae but we found them to be pollenivorous, which is a rare feeding mode within the subfamily Syrphinae. Moreover, it is the only known Syrphinae species of which the larvae feed on pollen from two plant species from different families (Cyperaceae and Orobranchaceae). This example illustrates how DNA barcoding may allow a fast and accurate identification of introduced species.},
}
@article {pmid26624723,
year = {2015},
author = {Murao, R and Lee, HS and Tadauchi, O},
title = {Bees of the Lasioglossum series (Hymenoptera: Halictidae) in South Korea, with an illustrated keys to species.},
journal = {Zootaxa},
volume = {4044},
number = {4},
pages = {511-534},
doi = {10.11646/zootaxa.4044.4.3},
pmid = {26624723},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Bees/anatomy &amp; histology/*classification/growth &amp; development ; Body Size ; Ecosystem ; Female ; Male ; Organ Size ; Republic of Korea ; },
abstract = {The South Korean fauna of the bee genus Lasioglossum Curtis (Halictidae: Halictini) belonging to the Lasioglossum series (i.e., those with the second submarginal crossvein strong) are reviewed. A total of 12 species are recognized for the country. Lasioglossum circularum Fan &amp; Ebmer is recorded for the first time from the Korean Peninsula and the following species are newly recorded from South Korea: L. denticolle (Morawitz), L. formosae (Strand), L. kansuense (Blüthgen), L. occidens (Smith), L. sutshanicum Pesenko, and L. upinense (Morawitz). Bionomical data as well as illustrated keys to females and males of South Korean species are provided. DNA sequences including a part of barcode region are given for L. kansuense and L. occidens.},
}
@article {pmid26624673,
year = {2015},
author = {Orr, AG and Dow, RA},
title = {Description of the final stadium larvae of Onychargia atrocyana Selys, 1865 from Sarawak, identified using DNA barcoding (Odonata: Zygoptera: Platycnemididae), with an overview of larval characters in the Platycnemididae.},
journal = {Zootaxa},
volume = {4040},
number = {3},
pages = {384-392},
doi = {10.11646/zootaxa.4040.3.9},
pmid = {26624673},
issn = {1175-5334},
mesh = {Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; DNA Barcoding, Taxonomic ; Ecosystem ; Female ; Larva/anatomy &amp; histology/classification/genetics/*growth &amp; development ; Male ; Odonata/anatomy &amp; histology/*classification/*genetics/growth &amp; development ; Organ Size ; Phylogeny ; },
abstract = {The final stadium larva of Onychargia atrocyana Selys, 1865, is described and illustrated based on two female specimens collected at Gunung Mulu National Park, Sarawak, East Malaysia. The larvae were identified by matching the mitochondrial marker COI with that of known adult specimens from Gunung Mulu, Bintulu and Kuching in Sarawak and from Pahang state in West Malaysia. The specimens presented close matches with all adults in this gene. As O. atrocyana is a taxonomically isolated species with no close congeners in Borneo the determination is beyond doubt. O. atrocyana is the only member of the Onychargiinae for which the larva is known. It is compared with the known larvae of other platycnemidid subfamilies, and the possible significance of larval morphology in higher classification of the group is discussed.},
}
@article {pmid26624486,
year = {2015},
author = {Wesener, T},
title = {Integrative redescription of a forgotten Italian pill millipede endemic to the Apuan Alps-Glomeris apuana Verhoeff, 1911 (Diplopoda, Glomerida, Glomeridae).},
journal = {Zootaxa},
volume = {4039},
number = {2},
pages = {391-400},
doi = {10.11646/zootaxa.4039.2.11},
pmid = {26624486},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Arthropods/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Body Size ; Female ; Italy ; Male ; Molecular Sequence Data ; Organ Size ; Phylogeny ; },
abstract = {The Italian pill millipede species Glomeris apuana Verhoeff, 1911, is redescribed from fresh material and its COI barcoding fragment is sequenced. The new specimens were compared to the original type series, of which a lectotype was selected. G. apuana was apparently still viewed as a subspecies of G. ligurica, as its name cannot be found in 'Fauna Europaea', or any faunal lists or catalogues in the last 85 years. We show that the species is both genetically and morphologically unique. G. apuana is easy to identify based on its entirely black coloration in combination with the absence of any main striae on the thoracic shield. Genetically, G. apuana shows large p-distances of >10% to four different populations of G. ligurica Latzel, 1884. G. apuana also differs from other sequenced Glomeris species, G. marginata Latreille, 1803, G. connexa Koch, 1847, and G. klugii Brandt, 1833 by p-distances of >10%. Specimens of G. klugii from a population occurring in sympatry with G. apuana were newly sequenced. All records of G. apuana, a large, easy to identify and conspicuous species, are from a narrow coastal zone of the Apuan Alps, an area in which the species might be microendemic.},
}
@article {pmid26624467,
year = {2015},
author = {Batista, A and Vesely, M and Mebert, K and Lotzkat, S and Köhler, G},
title = {A new species of Dactyloa from eastern Panama, with comments on other Dactyloa species present in the region.},
journal = {Zootaxa},
volume = {4039},
number = {1},
pages = {57-84},
doi = {10.11646/zootaxa.4039.1.2},
pmid = {26624467},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Ecosystem ; Female ; Lizards/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Male ; Molecular Sequence Data ; Organ Size ; Panama ; Phylogeny ; },
abstract = {Giant anoles of the genus Dactyloa have been considered to be represented in eastern Panama by six species. In this contribution, we describe a seventh species that is restricted to the Majé, San Blas, Darién, and Piedras-Pacora mountain ranges. The new species resembles D. ibanezi, D. limon, and D. purpurescens in external morphology but differs from these species in dewlap coloration, dorsal color pattern, morphometrics, and scalation. The recognition of the new species is further supported by DNA barcoding (genetic distances >2.7% in 16S and >7.8% in COI between the new species and all other species of Dactyloa). We discuss the taxonomic identity of D. purpurescens, and, based on morphological evidence, we place D. chocorum in the synonymy of the former species. An identification key for all 11 Dactyloa species occurring in Panama is provided.},
}
@article {pmid26624441,
year = {2015},
author = {Pauly, A and Devalez, J and Sonet, G and Nagy, ZT and Boevé, JL},
title = {DNA barcoding and male genital morphology reveal five new cryptic species in the West Palearctic bee Seladonia smaragdula (Vachal, 1895) (Hymenoptera: Apoidea: Halictidae).},
journal = {Zootaxa},
volume = {4034},
number = {2},
pages = {257-290},
doi = {10.11646/zootaxa.4034.2.2},
pmid = {26624441},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Bees/anatomy &amp; histology/*classification/*genetics/growth &amp; development ; Body Size ; DNA Barcoding, Taxonomic ; Ecosystem ; Female ; Genitalia, Male/anatomy &amp; histology/growth &amp; development ; Male ; Organ Size ; Phylogeny ; },
abstract = {Several forms or variants have long been recognized in the West Palearctic sweat bee Seladonia smaragdula (Vachal, 1895). Using DNA barcoding and morphological characters, primarily of the male genitalia, these variants are here recognized and described as five new species: S. gemmella Pauly sp. nov., S. submediterranea Pauly sp. nov., S. orientana Pauly &amp; Devalez sp. nov., S. phryganica Pauly &amp; Devalez sp. nov., and S. cretella Pauly &amp; Devalez sp. nov. Also, we designate a lectotype for Halictus smaragdulus Vachal, consider Seladonia butea (Warncke, 1975) and S. morinella (Warncke, 1975) as nomina dubia, and discuss the identity of the Seladonia specimens from Australia currently determined as S. smaragdula.},
}
@article {pmid26624433,
year = {2015},
author = {Jendek, E and Grebennikov, VV and Bocak, L},
title = {Undetected for a century: Palaearctic Agrilus ribesi Schaefer (Coleoptera: Buprestidae) on currant in North America, with adult morphology, larval biology and DNA barcode.},
journal = {Zootaxa},
volume = {4034},
number = {1},
pages = {112-126},
doi = {10.11646/zootaxa.4034.1.5},
pmid = {26624433},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Coleoptera/anatomy &amp; histology/*classification/*genetics/growth &amp; development ; DNA Barcoding, Taxonomic ; Female ; Larva/anatomy &amp; histology/classification/genetics/*growth &amp; development ; Male ; Molecular Sequence Data ; North America ; Organ Size ; Phylogeny ; },
abstract = {We report the Eurasian species Agrilus ribesi Schaefer, 1946, for the first time from North America and propose that the damage to currants (Ribes spp.) in Ontario prior to 1940 and ascribed to A. cuprescens were caused by this species. We provide morphological diagnostic characters for A. ribesi and closely related A. cuprescens and we complement this information with DNA barcodes from four alien Agrilus species established in North America (i.e., A. ribesi Schaefer, A. cuprescens (Ménétriés), A. planipennis Fairmaire and A. sulcicollis Lacordaire) to enable DNA-based identification of these invasive species. Additionally, published information on A. ribesi is summarized and new data are provided on the host plants and biology of larva in North America. The distribution of A. ribesi is mapped, both in its native Palaearctic region and in Canada and the USA, together with the range of its potential host plants in North America. A. ribesi was recovered as a sister-species of A. cuprescens on the neighbor joining DNA barcoding tree and low genetic variability of North American populations may indicate a single introduction to North America for each of these species.},
}
@article {pmid26624378,
year = {2015},
author = {Skowron, MA and Munisamy, B and Hamid, SB and Węgrzyn, G},
title = {A new species of clearwing moth (Lepidoptera: Sesiidae: Osminiini) from Peninsular Malaysia, exhibiting bee-like morphology and behaviour.},
journal = {Zootaxa},
volume = {4032},
number = {4},
pages = {426-434},
doi = {10.11646/zootaxa.4032.4.7},
pmid = {26624378},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Behavior, Animal ; Body Size ; Ecosystem ; Female ; Malaysia ; Male ; Moths/anatomy &amp; histology/*classification/growth &amp; development/physiology ; Organ Size ; },
abstract = {A new species of Sesiidae, tribe Osminiini from Peninsular Malaysia, Heterosphecia pahangensis Skowron, displaying numerous bee-mimicking features, is described. DNA barcodes showed significant differences with related taxa. However, the paucity of Sesiidae barcodes from Southeast Asia prevents meaningful taxonomic comparisons. The closest match out of published data on Sesiidae barcodes is Heterosphecia bantanakai, Arita &amp; Gorbunov (2000a) from the tribe Osminiini, which has 9.98% sequence divergence from Heterosphecia pahangensis. Photographs of the moth in its natural habitat are shown. Behavioural aspects, such as mud-puddling and mode of flight, are described and presented in a video.},
}
@article {pmid26624149,
year = {2015},
author = {Schmidt, O},
title = {The genus Visiana Swinhoe (Lepidoptera: Geometridae: Larentiinae) in Australia: resurrection of two species from synonymy.},
journal = {Zootaxa},
volume = {4021},
number = {4},
pages = {501-514},
doi = {10.11646/zootaxa.4021.4.1},
pmid = {26624149},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Australia ; Body Size ; Female ; Male ; Moths/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Organ Size ; Terminology as Topic ; },
abstract = {Based on the study of morphological characters and DNA barcode (CO1) data, the present review revealed the existence of at least three species of Visiana Swinhoe (Lepidoptera: Geometridae: Larentiinae) in Australia. Visiana brujata (Guenée) is redescribed, and two species V. incertata (Walker), stat. rev. and V. repentinata (Walker), stat. rev. are resurrected from synonymy with V. brujata. Visiana breviaria (Walker), syn. rev., previously cited as a synonym of V. brujata, is now considered a synonym of V. incertata. Visiana brujata and V. incertata show close affinities with the sordidata group of species, whereas V. repentinata belongs to the vinosa species group. Images of adults and genitalia of all types are illustrated and the presence of the gnathos in the genus Visiana is discussed.},
}
@article {pmid26624075,
year = {2015},
author = {Meißner, K and Götting, M},
title = {Spionidae (Annelida: 'Polychaeta': Canalipalpata) from Lizard Island, Great Barrier Reef, Australia: the genera Malacoceros, Scolelepis, Spio, Microspio, and Spiophanes.},
journal = {Zootaxa},
volume = {4019},
number = {},
pages = {378-413},
doi = {10.11646/zootaxa.4019.1.15},
pmid = {26624075},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Australia ; Body Size ; Ecosystem ; Female ; Islands ; Male ; Organ Size ; Polychaeta/anatomy &amp; histology/*classification/growth &amp; development ; },
abstract = {Seven species belonging to the spionid genera Malacoceros, Scolelepis, Spio, Microspio, and Spiophanes were found during the polychaete workshop on Lizard Island in August 2013. One species is new to science and named Scolelepis inversa n. sp., another Scolelepis species is probably also a new species but was represented in our samples by only a single specimen and not formally described. All other species have been reported previously from Australia. Species diagnoses of all species found during the workshop and of Scolelepis balihaiensis Hartmann-Schröder, 1979, Microspio microcera (Dorsey, 1977) and M. minuta (Hartmann-Schröder, 1962) have been critically reviewed and amended based on the study of type material. The potential synonymy of Microspio minuta (Hartmann-Schröder, 1962) and M. microcera (Dorsey, 1977) is discussed. The new combination Spio jirkovi (Sikorski, 1992) proposed by Sikorski (2013) is returned to Malacoceros. We added DNA barcodes for five species collected in the Lizard Island area to public databases which will be useful in future phylogenetic and phylogeographic studies. For Microspio we provide the first sequence data for this genus.},
}
@article {pmid26624024,
year = {2015},
author = {Schulze, A and Jansen, M and Köhler, G},
title = {Tadpole diversity of Bolivia's lowland anuran communities: molecular identification, morphological characterisation, and ecological assignment.},
journal = {Zootaxa},
volume = {4016},
number = {},
pages = {1-111},
doi = {10.11646/zootaxa.4016.1.1},
pmid = {26624024},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Anura/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Biodiversity ; Body Size ; Bolivia ; Ecosystem ; Female ; Larva/*anatomy &amp; histology/classification/genetics/growth &amp; development ; Male ; Organ Size ; Phylogeny ; },
abstract = {The last decades have witnessed a rapid increase in our knowledge about amphibian diversity, and a growing number of studies have focused on anuran larval stages. Tadpoles can provide key information for conservation issues and the understanding of amphibian evolution. Moreover, research in tadpoles has the potential to advance species delimitation in the diverse and still understudied Neotropical amphibian fauna. In this study we present morphological tadpole characterisations of 41 lowland species illustrated by detailed imagery (mainly of live specimens). The larvae were identified via captive breeding and genetically using recently published DNA barcodes of adult Bolivian frogs. Tadpoles of three species (Rhinella mirandaribeiroi, Dendropsophus melanargyreus, and D. salli) are described for the first time. The descriptions of 38 tadpoles are at least new for Bolivia (due to the divergent status of many of the Bolivian lineages, further studies are needed to clarify their taxonomy). In addition, we provide information on tadpole habitats, which--combined with morphological data--reveal ecomorphological guilds that further illustrate Bolivia's lowlands tadpole diversity.},
}
@article {pmid26623920,
year = {2015},
author = {Orr, AG and Dow, RA},
title = {ALBERT G. ORR &amp; RORY A. DOW (2015) Description of two final stadium platystictid larvae from Borneo, including that of Drepanosticta ?attala Lieftinck, identified using DNA barcoding (Odonata: Zygoptera: Platystictidae). Zootaxa, 3985 (4): 565-574.},
journal = {Zootaxa},
volume = {4013},
number = {4},
pages = {600},
doi = {10.11646/zootaxa.4013.4.10},
pmid = {26623920},
issn = {1175-5334},
}
@article {pmid26623799,
year = {2015},
author = {Gagnon, JM and Kenchington, E and Port, A and Anstey, LJ and Murillo, FJ},
title = {Morphological and genetic variation in North Atlantic giant file clams, Acesta spp. (Bivalvia: Limidae), with description of a new cryptic species in the northwest Atlantic.},
journal = {Zootaxa},
volume = {4007},
number = {2},
pages = {151-180},
doi = {10.11646/zootaxa.4007.2.1},
pmid = {26623799},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Bivalvia/anatomy &amp; histology/*classification/*genetics/growth &amp; development ; Body Size ; China ; DNA, Mitochondrial/genetics ; Ecosystem ; Genetic Variation ; Molecular Sequence Data ; Organ Size ; Pacific Ocean ; Phylogeny ; },
abstract = {We analyze the morphological and genetic variability within and between seven species of Acesta and specimens recently collected in the northwest Atlantic using traditional morphological measurements, landmark-based geometric morphometrics, and the cytochrome oxidase subunit I (COI) gene sequences, with particular emphasis on North Atlantic species. Shell morphology and external shell appearance do not allow reliable distinction between the widely recognized northeastern Atlantic A. excavata and other northwest Atlantic species or populations of Acesta, with the exception of A. oophaga. Similarly, shape analysis reveals a wide variability within northeastern Atlantic A. excavata, and significant morphological overlap with A. bullisi from the Gulf of Mexico and A. rathbuni from the southwestern Pacific and South China Sea. Specimens from the northwestern and Mid-Atlantic display shell shapes marginally similar to that of A. excavata. These differences are at least partly related to anterior or posterior shifting of the shell body and to the opposite shifting of the hinge line/dorsal region and upper lunule. These morphological variations, along with the midline-width-ratio, explain much of the variability extracted by principal component analysis. Results from a mitochondrial DNA barcode approach (COI), however, suggest that the northwest Atlantic specimens belong to a new species for which we propose the name Acesta cryptadelphe sp. nov. Differences in larval shell sizes between northeastern and northwestern Atlantic specimens are consistent with this result.},
}
@article {pmid26623778,
year = {2015},
author = {Lopes-Andrade, C and Grebennikov, VV},
title = {First record and five new species of Xylographellini (Coleoptera: Ciidae) from China, with online DNA barcode library of the family.},
journal = {Zootaxa},
volume = {4006},
number = {3},
pages = {463-480},
doi = {10.11646/zootaxa.4006.3.3},
pmid = {26623778},
issn = {1175-5334},
mesh = {Animals ; China ; Coleoptera/anatomy &amp; histology/*classification/genetics ; DNA Barcoding, Taxonomic ; Female ; Gene Library ; Male ; Phylogeny ; },
abstract = {We report the first record of the beetle tribe Xylographellini (Ciidae) from the continental Palaearctic Region, represented by five new species discovered in Yunnan and Sichuan provinces, China: Scolytocis danae sp. nov., Syncosmetus euryale sp. nov., Sync. medusa sp. nov., Sync. perseus sp. nov. and Sync. stheno sp. nov. Illustrations and identification keys are provided for these new species, and in order to facilitate further research of Ciidae we present an open-access DNA barcode library (dx.doi.org/10.5883/DS-SYNCOSM) containing 114 records (of 44 species in 14 genera), 15 of which belong to the newly described species. A phylogenetic analysis based on the barcode fragment of the cytochrome oxidase I gene did not recover much tree structure within Ciidae, however both Xylographus Mellié and Syncosmetus Sharp were recovered as clades, with a single Scolytocis Blair being the sister to the latter.},
}
@article {pmid26623757,
year = {2015},
author = {Zhou, L and Chen, HW},
title = {The genus Leucophenga (Diptera, Drosophilidae), part V: the mutabilis species group from East Asia, with morphological and molecular evidence.},
journal = {Zootaxa},
volume = {4006},
number = {1},
pages = {40-58},
doi = {10.11646/zootaxa.4006.1.2},
pmid = {26623757},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Drosophilidae/*anatomy &amp; histology/*classification/genetics ; Electron Transport Complex IV/genetics ; Asia, Eastern ; Female ; Insect Proteins/genetics ; Male ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {A total of seven known species of the Leucophenga mutabilis species group are resurveyed from the East Asia: L. angusta Okada, 1956; L. bellula Bergroth, 1894; L. magnipalpis Duda, 1924; L. nigripalpis Duda, 1924; L. orientalis Lin &amp; Wheeler, 1972; L. striatipennis Okada, 1989 and L. taiwanensis Lin &amp; Wheeler, 1972. The diagnosis of the mutabilis group is revised, and a key to the seven species of this group is provided. DNA sequences of the mitochondrial COI (cytochrome c oxidase subunit I) gene with BOLD process ID and GenBank accession numbers are provided for these species. The pairwise intra- and interspecific Kimura two-parameter COI distances among the aforementioned seven known species are summarized; and the utility of DNA barcoding in the genus Leucophenga is discussed.},
}
@article {pmid26623616,
year = {2015},
author = {Makarchenko, EA and Makarchenko, MA and Semenchenko, AA},
title = {Morphological description and DNA barcoding of Hydrobaenus majus sp. nov. (Diptera: Chironomidae: Orthocladiinae) from the Russian Far East.},
journal = {Zootaxa},
volume = {4000},
number = {2},
pages = {287-293},
doi = {10.11646/zootaxa.4000.2.7},
pmid = {26623616},
issn = {1175-5334},
mesh = {Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Chironomidae/anatomy &amp; histology/*classification/*genetics/growth &amp; development ; DNA Barcoding, Taxonomic ; Female ; Larva/anatomy &amp; histology/classification/genetics/growth &amp; development ; Male ; Molecular Sequence Data ; Organ Size ; Phylogeny ; Pupa/anatomy &amp; histology/classification/genetics/growth &amp; development ; Russia ; },
abstract = {Illustrated descriptions of adult male, pupa and fourth instar larva, as well as DNA barcoding, of Hydrobaenus majus sp. nov. in comparison with the close related species H. sikhotealinensis Makarchenko et Makarchenko from the Russian Far East are provided. The species-specificity of H. majus sp. nov. COI sequences is analyzed and the sequences are presented as diagnostic characters--molecular markers of H. majus and H. sikhotealinensis.},
}
@article {pmid26623596,
year = {2015},
author = {Wesener, T},
title = {No millipede endemics north of the Alps? DNA-Barcoding reveals Glomeris malmivaga Verhoeff, 1912 as a synonym of G. ornata Koch, 1847 (Diplopoda, Glomerida, Glomeridae).},
journal = {Zootaxa},
volume = {3999},
number = {4},
pages = {571-580},
doi = {10.11646/zootaxa.3999.4.7},
pmid = {26623596},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Arthropods/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Body Size ; DNA Barcoding, Taxonomic ; Ecosystem ; Female ; Male ; Organ Size ; Phylogeny ; },
abstract = {In order to evaluate the status of the only species of pill millipede (Glomerida) endemic to Germany, Glomeris malmivaga Verhoeff, 1912, a DNA barcoding study based on the COI mitochondrial gene was conducted. Sequences of G. malmivaga were compared to those of G. ornata Koch, 1847 from Slovenia, of which the former was previously described as a variety of the latter before being elevated to subspecies- and, recently, species-rank. Included in the analysis were specimens of G. helvetica Verhoeff, 1894, also originally described as a variety of G. ornata, which was supposed to be closely related to G. malmivaga based on its morphology, as well as geographical proximity of occurrence. Additionally, G. valesiaca Rothenbühler, 1899, which occurs in sympatry and looks quite similar to G. helvetica was also sequenced for the first time and included in the study. Sequences of four widespread Glomeris species, all occurring in close proximity to G. malmivaga, G. marginata Villers, 1789, G. connexa Koch, 1847, G. klugii Brandt, 1833 and G. intermedia Latzel, 1884 were downloaded from Genbank and incorporated in the analysis. While G. helvetica and G. valesiaca were found to be clearly separate from G. ornata (11.8-14.6% p-distance), G. malmivaga is almost identical to the latter (0.5% p-distance), despite the large geographical distance between both species. Because of their great morphological and genetical similarity, G. malmivaga n. syn. is synonymised under G. ornata.},
}
@article {pmid26623196,
year = {2015},
author = {Falk, BG and Reed, RN},
title = {Challenges to a molecular approach to prey identification in the Burmese python, Python molurus bivittatus.},
journal = {PeerJ},
volume = {3},
number = {},
pages = {e1445},
pmid = {26623196},
issn = {2167-8359},
abstract = {Molecular approaches to prey identification are increasingly useful in elucidating predator-prey relationships, and we aimed to investigate the feasibility of these methods to document the species identities of prey consumed by invasive Burmese pythons in Florida. We were particularly interested in the diet of young snakes, because visual identification of prey from this size class has proven difficult. We successfully extracted DNA from the gastrointestinal contents of 43 young pythons, as well as from several control samples, and attempted amplification of DNA mini-barcodes, a 130-bp region of COX1. Using a PNA clamp to exclude python DNA, we found that prey DNA was not present in sufficient quality for amplification of this locus in 86% of our samples. All samples from the GI tracts of young pythons contained only hair, and the six samples we were able to identify to species were hispid cotton rats. This suggests that young Burmese pythons prey predominantly on small mammals and that prey diversity among snakes of this size class is low. We discuss prolonged gastrointestinal transit times and extreme gastric breakdown as possible causes of DNA degradation that limit the success of a molecular approach to prey identification in Burmese pythons.},
}
@article {pmid26621309,
year = {2015},
author = {Shang, L and Fu, F and Cheng, Y and Wang, H and Liu, Y and Zhao, Y and Gu, Z},
title = {Photonic Crystal Microbubbles as Suspension Barcodes.},
journal = {Journal of the American Chemical Society},
volume = {137},
number = {49},
pages = {15533-15539},
doi = {10.1021/jacs.5b10612},
pmid = {26621309},
issn = {1520-5126},
abstract = {A novel suspension array was developed that uses photonic crystal (PhC) microbubbles as barcode particles. The PhC microbubbles have an outer transparent polymeric shell, a middle PhC shell, and an inner bubble core, and they were achieved by extraction-derived self-assembly of colloidal nanoparticles in semipermeable solid microcapsules. The encoded elements of the microbubbles originated from their PhC structure with a coated shell, which not only improved the stability of the codes but also provided a flexible surface for bioassays. By using multicompartmental microcapsule templates, PhC microbubbles with substantial coding levels and controllable movement could also be achieved. In addition, as the size of the encapsulated bubbles could be tailored, the overall density of the PhC microbubbles could be adjusted to match the density of a detection solution and to remain in suspension. These remarkable properties make the PhC microbubbles excellent barcode particles.},
}
@article {pmid26618779,
year = {2016},
author = {von Beeren, C and Maruyama, M and Kronauer, DJ},
title = {Cryptic diversity, high host specificity and reproductive synchronization in army ant-associated Vatesus beetles.},
journal = {Molecular ecology},
volume = {25},
number = {4},
pages = {990-1005},
doi = {10.1111/mec.13500},
pmid = {26618779},
issn = {1365-294X},
mesh = {Animals ; *Ants ; Biodiversity ; Cell Nucleus/genetics ; Coleoptera/classification/genetics/*physiology ; Costa Rica ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Female ; Larva ; Male ; Reproduction ; Reproductive Physiological Phenomena ; *Symbiosis ; },
abstract = {Army ants and their arthropod symbionts represent one of the most species-rich animal associations on Earth, and constitute a fascinating example of diverse host-symbiont interaction networks. However, despite decades of research, our knowledge of army ant symbionts remains fragmentary due to taxonomic ambiguity and the inability to study army ants in the laboratory. Here, we present an integrative approach that allows us to reliably determine species boundaries, assess biodiversity, match different developmental stages and sexes, and to study the life cycles of army ant symbionts. This approach is based on a combination of community sampling, DNA barcoding, morphology and physiology. As a test case, we applied this approach to the staphylinid beetle genus Vatesus and its different Eciton army ant host species at La Selva Biological Station, Costa Rica. DNA barcoding led to the discovery of cryptic biodiversity and, in combination with extensive community sampling, revealed strict host partitioning with no overlap in host range. Using DNA barcoding, we were also able to match the larval stages of all focal Vatesus species. In combination with studies of female reproductive physiology, this allowed us to reconstruct almost the complete life cycles of the different beetle species. We show that Vatesus beetles are highly adapted to the symbiosis with army ants, in that their reproduction and larval development are synchronized with the stereotypical reproductive and behavioural cycles of their host colonies. Our approach can now be used to study army ant-symbiont communities more broadly, and to obtain novel insights into co-evolutionary and ecological dynamics in species-rich host-symbiont systems.},
}
@article {pmid26616046,
year = {2015},
author = {Chen, W and Ma, X and Shen, Y and Mao, Y and He, S},
title = {The fish diversity in the upper reaches of the Salween River, Nujiang River, revealed by DNA barcoding.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {17437},
pmid = {26616046},
issn = {2045-2322},
mesh = {Animals ; Bayes Theorem ; *Biodiversity ; China ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Fishes/*classification/*genetics ; Genetic Variation ; Geography ; Haplotypes ; Phylogeny ; *Rivers ; },
abstract = {Nujiang River (NR), an essential component of the biodiversity hotspot of the Mountains of Southwest China, possesses a characteristic fish fauna and contains endemic species. Although previous studies on fish diversity in the NR have primarily consisted of listings of the fish species observed during field collections, in our study, we DNA-barcoded 1139 specimens belonging to 46 morphologically distinct fish species distributed throughout the NR basin by employing multiple analytical approaches. According to our analyses, DNA barcoding is an efficient method for the identification of fish by the presence of barcode gaps. However, three invasive species are characterized by deep conspecific divergences, generating multiple lineages and Operational Taxonomic Units (OTUs), implying the possibility of cryptic species. At the other end of the spectrum, ten species (from three genera) that are characterized by an overlap between their intra- and interspecific genetic distances form a single genetic cluster and share haplotypes. The neighbor-joining phenogram, Barcode Index Numbers (BINs) and Automatic Barcode Gap Discovery (ABGD) identified 43 putative species, while the General Mixed Yule-coalescence (GMYC) identified five more OTUs. Thus, our study established a reliable DNA barcode reference library for the fish in the NR and sheds new light on the local fish diversity.},
}
@article {pmid26615752,
year = {2015},
author = {Lee, S and Yamamoto, N},
title = {Accuracy of the high-throughput amplicon sequencing to identify species within the genus Aspergillus.},
journal = {Fungal biology},
volume = {119},
number = {12},
pages = {1311-1321},
doi = {10.1016/j.funbio.2015.10.006},
pmid = {26615752},
issn = {1878-6146},
mesh = {Air Filters/microbiology ; *Air Microbiology ; Aspergillus/classification/genetics/*isolation &amp; purification ; DNA Primers/genetics ; DNA, Fungal/genetics ; Fungal Proteins/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Mycological Typing Techniques/*methods ; },
abstract = {This study characterized the accuracy of high-throughput amplicon sequencing to identify species within the genus Aspergillus. To this end, we sequenced the internal transcribed spacer 1 (ITS1), β-tubulin (BenA), and calmodulin (CaM) gene encoding sequences as DNA markers from eight reference Aspergillus strains with known identities using 300-bp sequencing on the Illumina MiSeq platform, and compared them with the BLASTn outputs. The identifications with the sequences longer than 250 bp were accurate at the section rank, with some ambiguities observed at the species rank due to mostly cross detection of sibling species. Additionally, in silico analysis was performed to predict the identification accuracy for all species in the genus Aspergillus, where 107, 210, and 187 species were predicted to be identifiable down to the species rank based on ITS1, BenA, and CaM, respectively. Finally, air filter samples were analysed to quantify the relative abundances of Aspergillus species in outdoor air. The results were reproducible across biological duplicates both at the species and section ranks, but not strongly correlated between ITS1 and BenA, suggesting the Aspergillus detection can be taxonomically biased depending on the selection of the DNA markers and/or primers.},
}
@article {pmid26608965,
year = {2016},
author = {Karanovic, T and Djurakic, M and Eberhard, SM},
title = {Cryptic Species or Inadequate Taxonomy? Implementation of 2D Geometric Morphometrics Based on Integumental Organs as Landmarks for Delimitation and Description of Copepod Taxa.},
journal = {Systematic biology},
volume = {65},
number = {2},
pages = {304-327},
doi = {10.1093/sysbio/syv088},
pmid = {26608965},
issn = {1076-836X},
mesh = {Animals ; Classification/*methods ; Copepoda/*anatomy &amp; histology/genetics ; Electron Transport Complex IV/genetics ; *Phylogeny ; Species Specificity ; Western Australia ; },
abstract = {Discovery of cryptic species using molecular tools has become common in many animal groups but it is rarely accompanied by morphological revision, creating ongoing problems in taxonomy and conservation. In copepods, cryptic species have been discovered in most groups where fast-evolving molecular markers were employed. In this study at Yeelirrie in Western Australia we investigate a subterranean species complex belonging to the harpacticoid genus Schizopera Sars, 1905, using both the barcoding mitochondrial COI gene and landmark-based two-dimensional geometric morphometrics. Integumental organs (sensilla and pores) are used as landmarks for the first time in any crustacean group. Complete congruence between DNA-based species delimitation and relative position of integumental organs in two independent morphological structures suggests the existence of three distinct evolutionary units. We describe two of them as new species, employing a condensed taxonomic format appropriate for cryptic species. We argue that many supposedly cryptic species might not be cryptic if researchers focus on analyzing morphological structures with multivariate tools that explicitly take into account geometry of the phenotype. A perceived supremacy of molecular methods in detecting cryptic species is in our view a consequence of disparity of investment and unexploited recent advancements in morphometrics among taxonomists. Our study shows that morphometric data alone could be used to find diagnostic morphological traits and gives hope to anyone studying small animals with a hard integument or shell, especially opening the door to assessing fossil diversity and rich museum collections. We expect that simultaneous use of molecular tools with geometry-oriented morphometrics may yield faster formal description of species. Decrypted species in this study are a good example for urgency of formal descriptions, as they display short-range endemism in small groundwater calcrete aquifers in a paleochannel, where their conservation may be threatened by proposed mining.},
}
@article {pmid26602877,
year = {2016},
author = {Thomas, AC and Deagle, BE and Eveson, JP and Harsch, CH and Trites, AW},
title = {Quantitative DNA metabarcoding: improved estimates of species proportional biomass using correction factors derived from control material.},
journal = {Molecular ecology resources},
volume = {16},
number = {3},
pages = {714-726},
doi = {10.1111/1755-0998.12490},
pmid = {26602877},
issn = {1755-0998},
mesh = {Animals ; Biostatistics/*methods ; *Biota ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; },
abstract = {DNA metabarcoding is a powerful new tool allowing characterization of species assemblages using high-throughput amplicon sequencing. The utility of DNA metabarcoding for quantifying relative species abundances is currently limited by both biological and technical biases which influence sequence read counts. We tested the idea of sequencing 50/50 mixtures of target species and a control species in order to generate relative correction factors (RCFs) that account for multiple sources of bias and are applicable to field studies. RCFs will be most effective if they are not affected by input mass ratio or co-occurring species. In a model experiment involving three target fish species and a fixed control, we found RCFs did vary with input ratio but in a consistent fashion, and that 50/50 RCFs applied to DNA sequence counts from various mixtures of the target species still greatly improved relative abundance estimates (e.g. average per species error of 19 ± 8% for uncorrected vs. 3 ± 1% for corrected estimates). To demonstrate the use of correction factors in a field setting, we calculated 50/50 RCFs for 18 harbour seal (Phoca vitulina) prey species (RCFs ranging from 0.68 to 3.68). Applying these corrections to field-collected seal scats affected species percentages from individual samples (Δ 6.7 ± 6.6%) more than population-level species estimates (Δ 1.7 ± 1.2%). Our results indicate that the 50/50 RCF approach is an effective tool for evaluating and correcting biases in DNA metabarcoding studies. The decision to apply correction factors will be influenced by the feasibility of creating tissue mixtures for the target species, and the level of accuracy needed to meet research objectives.},
}
@article {pmid26602739,
year = {2016},
author = {Wirta, H and Várkonyi, G and Rasmussen, C and Kaartinen, R and Schmidt, NM and Hebert, PD and Barták, M and Blagoev, G and Disney, H and Ertl, S and Gjelstrup, P and Gwiazdowicz, DJ and Huldén, L and Ilmonen, J and Jakovlev, J and Jaschhof, M and Kahanpää, J and Kankaanpää, T and Krogh, PH and Labbee, R and Lettner, C and Michelsen, V and Nielsen, SA and Nielsen, TR and Paasivirta, L and Pedersen, S and Pohjoismäki, J and Salmela, J and Vilkamaa, P and Väre, H and von Tschirnhaus, M and Roslin, T},
title = {Establishing a community-wide DNA barcode library as a new tool for arctic research.},
journal = {Molecular ecology resources},
volume = {16},
number = {3},
pages = {809-822},
doi = {10.1111/1755-0998.12489},
pmid = {26602739},
issn = {1755-0998},
mesh = {Animals ; Arctic Regions ; *Biota ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/chemistry/genetics ; *Ecosystem ; Electron Transport Complex IV/genetics ; Greenland ; Phylogeny ; Plants ; Ribulose-Bisphosphate Carboxylase/genetics ; },
abstract = {DNA sequences offer powerful tools for describing the members and interactions of natural communities. In this study, we establish the to-date most comprehensive library of DNA barcodes for a terrestrial site, including all known macroscopic animals and vascular plants of an intensively studied area of the High Arctic, the Zackenberg Valley in Northeast Greenland. To demonstrate its utility, we apply the library to identify nearly 20 000 arthropod individuals from two Malaise traps, each operated for two summers. Drawing on this material, we estimate the coverage of previous morphology-based species inventories, derive a snapshot of faunal turnover in space and time and describe the abundance and phenology of species in the rapidly changing arctic environment. Overall, 403 terrestrial animal and 160 vascular plant species were recorded by morphology-based techniques. DNA barcodes (CO1) offered high resolution in discriminating among the local animal taxa, with 92% of morphologically distinguishable taxa assigned to unique Barcode Index Numbers (BINs) and 93% to monophyletic clusters. For vascular plants, resolution was lower, with 54% of species forming monophyletic clusters based on barcode regions rbcLa and ITS2. Malaise catches revealed 122 BINs not detected by previous sampling and DNA barcoding. The insect community was dominated by a few highly abundant taxa. Even closely related taxa differed in phenology, emphasizing the need for species-level resolution when describing ongoing shifts in arctic communities and ecosystems. The DNA barcode library now established for Zackenberg offers new scope for such explorations, and for the detailed dissection of interspecific interactions throughout the community.},
}
@article {pmid26601279,
year = {2015},
author = {Toju, H and Guimarães, PR and Olesen, JM and Thompson, JN},
title = {Below-ground plant-fungus network topology is not congruent with above-ground plant-animal network topology.},
journal = {Science advances},
volume = {1},
number = {9},
pages = {e1500291},
pmid = {26601279},
issn = {2375-2548},
abstract = {In nature, plants and their pollinating and/or seed-dispersing animals form complex interaction networks. The commonly observed pattern of links between specialists and generalists in these networks has been predicted to promote species coexistence. Plants also build highly species-rich mutualistic networks below ground with root-associated fungi, and the structure of these plant-fungus networks may also affect terrestrial community processes. By compiling high-throughput DNA sequencing data sets of the symbiosis of plants and their root-associated fungi from three localities along a latitudinal gradient, we uncovered the entire network architecture of these interactions under contrasting environmental conditions. Each network included more than 30 plant species and hundreds of mycorrhizal and endophytic fungi belonging to diverse phylogenetic groups. The results were consistent with the notion that processes shaping host-plant specialization of fungal species generate a unique linkage pattern that strongly contrasts with the pattern of above-ground plant-partner networks. Specifically, plant-fungus networks lacked a "nested" architecture, which has been considered to promote species coexistence in plant-partner networks. Rather, the below-ground networks had a conspicuous "antinested" topology. Our findings lead to the working hypothesis that terrestrial plant community dynamics are likely determined by the balance between above-ground and below-ground webs of interspecific interactions.},
}
@article {pmid26595191,
year = {2015},
author = {Axthelm, J and Görls, H and Schubert, US and Schiller, A},
title = {Fluorinated Boronic Acid-Appended Bipyridinium Salts for Diol Recognition and Discrimination via (19)F NMR Barcodes.},
journal = {Journal of the American Chemical Society},
volume = {137},
number = {49},
pages = {15402-15405},
doi = {10.1021/jacs.5b10934},
pmid = {26595191},
issn = {1520-5126},
mesh = {Boronic Acids/*chemistry ; Chemistry Techniques, Analytical/*methods ; *Electronic Data Processing ; Fluorine/*chemistry ; Halogenation ; Hydroxides ; *Magnetic Resonance Spectroscopy ; Models, Molecular ; Phenazopyridine/*chemistry ; Receptors, Cell Surface/chemistry ; },
abstract = {Fluorinated boronic acid-appended benzyl bipyridinium salts, derived from 4,4'-, 3,4'-, and 3,3'-bipyridines, were synthesized and used to detect and differentiate diol-containing analytes at physiological conditions via (19)F NMR spectroscopy. An array of three water-soluble boronic acid receptors in combination with (19)F NMR spectroscopy discriminates nine diol-containing bioanalytes--catechol, dopamine, fructose, glucose, glucose-1-phosphate, glucose-6-phosphate, galactose, lactose, and sucrose--at low mM concentrations. Characteristic (19)F NMR fingerprints are interpreted as two-dimensional barcodes without the need of multivariate analysis techniques.},
}
@article {pmid26588057,
year = {2015},
author = {Shugay, M and Lukyanov, S and Chudakov, DM},
title = {Sequencing rare T-cell populations.},
journal = {Oncotarget},
volume = {6},
number = {37},
pages = {39393-39394},
pmid = {26588057},
issn = {1949-2553},
mesh = {*Gene Expression Profiling ; *High-Throughput Nucleotide Sequencing ; Humans ; *Lymphocyte Count ; Lymphocytes/*metabolism ; Male ; },
}
@article {pmid26584933,
year = {2016},
author = {Landskron, J and Taskén, K},
title = {Phosphoprotein Detection by High-Throughput Flow Cytometry.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1355},
number = {},
pages = {275-290},
doi = {10.1007/978-1-4939-3049-4_19},
pmid = {26584933},
issn = {1940-6029},
mesh = {Animals ; Antibodies/immunology ; Antibody Specificity ; Epitopes ; *Flow Cytometry ; Fluorescent Dyes/chemistry ; *High-Throughput Screening Assays ; Humans ; Luminescent Measurements ; Phosphoproteins/*analysis/chemistry/immunology/metabolism ; Phosphorylation ; Protein Processing, Post-Translational ; Proteomics/*methods ; Workflow ; },
abstract = {Phospho flow cytometry is a powerful technique for the detection of protein phosphorylation events that, like Western blotting, relies on phospho-epitope-specific antibodies. In contrast to the latter, however, multidimensional and directly quantifiable data is obtained at the single-cell level allowing separate analysis of small cell populations in complex cellular mixtures. Furthermore, up to 30 phospho-specific antibodies or antibodies identifying other posttranslational modifications in combination with cell surface markers can be analyzed in a single experiment. Utilizing a technique called fluorescent cell barcoding that enables combination of up to 64 samples into one tube for multiplex analysis and later data deconvolution, phospho flow cytometry is turned into a medium- to high-throughput technology.},
}
@article {pmid26584827,
year = {2016},
author = {Lv, J and Zhang, Y and Feng, C and Yuan, X and Sun, D and Deng, J and Wang, C and Wu, S and Lin, X},
title = {Species discrimination in the subfamily Ostertagiinae of Northern China: assessment of DNA barcode in a taxonomically challenging group.},
journal = {Parasitology research},
volume = {115},
number = {3},
pages = {987-996},
pmid = {26584827},
issn = {1432-1955},
mesh = {Animals ; Cattle ; Cattle Diseases/*parasitology ; China ; DNA Barcoding, Taxonomic/methods ; DNA, Helminth/genetics ; DNA, Mitochondrial/genetics ; Sheep ; Sheep Diseases/*parasitology ; Trichostrongyloidea/*classification/genetics/*isolation &amp; purification ; Trichostrongyloidiasis/parasitology/*veterinary ; },
abstract = {Gastrointestinal nematodes within the subfamily Ostertagiinae (Teladorsagia, Ostertagia, and Marshallagia et al.) are among the most common infections of domesticated livestock. These parasites are of particular interest, as many of the species within this group are of economic importance worldwide. Traditionally, nematode species designations have been based on morphological criteria. However, this group possesses poorly defined species. There is an urgent need to develop a reliable technique that can distinguish species of Ostertagiinae. DNA barcoding has been proved to be a powerful tool to identify species of birds, mammals, and arthropods, but this technique has not yet been examined for identifying species of Ostertagiinae. In this study, a total of 138 mitochondrial DNA (mtDNA) cytochrome c oxidase subunit I (COI) sequences from individuals representing 11 species of Ostertagiinae were acquired by PCR for the first time. The specimens were collected from pastoral area of northern China. Genetic divergence analyses showed that mean interspecific Kimura two-parameter distances of COI (13.61 %) were about four times higher than the mean value of the intraspecific divergence (3.69 %). Then, the performance of the COI to identify species of Ostertagiinae was evaluated by identification success rates using nearest neighbor (NN) and BLASTn. The results indicated that the rates of correct sequence identification for COI were high (>80 %) when using the NN and BLASTn methods. Besides, the deep lineage divergences are detected in Teladorsagia circumcincta. Meanwhile, the analyses also detected no genetic differentiation between some species such as Ostertagia hahurica and Ostertagia buriatica. These results indicate that the traditional status of species within Ostertagiinae should be closely examined based on the molecular data.},
}
@article {pmid26579423,
year = {2015},
author = {Wang, L and Kong, W and Yang, M and Han, J and Chen, S},
title = {Safety issues and new rapid detection methods in traditional Chinese medicinal materials.},
journal = {Acta pharmaceutica Sinica. B},
volume = {5},
number = {1},
pages = {38-46},
pmid = {26579423},
issn = {2211-3835},
abstract = {The safety of traditional Chinese medicine (TCM) is a major strategic issue that involves human health. With the continuous improvement in disease prevention and treatment, the export of TCM and its related products has increased dramatically in China. However, the frequent safety issues of Chinese medicine have become the 'bottleneck' impeding the modernization of TCM. It was proved that mycotoxins seriously affect TCM safety; the pesticide residues of TCM are a key problem in TCM international trade; adulterants have also been detected, which is related to market circulation. These three factors have greatly affected TCM safety. In this study, fast, highly effective, economically-feasible and accurate detection methods concerning TCM safety issues were reviewed, especially on the authenticity, mycotoxins and pesticide residues of medicinal materials.},
}
@article {pmid26577715,
year = {2015},
author = {Ugochukwu, AI and Hobbs, JE and Phillips, PW and Gray, R},
title = {An economic analysis of private incentives to adopt DNA barcoding technology for fish species authentication in Canada.},
journal = {Genome},
volume = {58},
number = {12},
pages = {559-567},
doi = {10.1139/gen-2015-0033},
pmid = {26577715},
issn = {1480-3321},
mesh = {Animals ; Canada ; Cost-Benefit Analysis ; DNA Barcoding, Taxonomic/*economics/*methods ; Fishes/*classification/*genetics ; Food Supply ; Humans ; *Motivation ; Species Specificity ; },
abstract = {The increasing spate of species substitution and mislabelling in fish markets has become a concern to the public and a challenge to both the food industry and regulators. Species substitution and mislabelling within fish supply chains occurs because of price incentives to misrepresent products for economic gain. Emerging authenticity technologies, such as the DNA barcoding technology that has been used to identify plants and animal (particularly fish) species through DNA sequencing, offer a potential technological solution to this information problem. However, the adoption of these authenticity technologies depends also on economic factors. The present study uses economic welfare analysis to examine the effects of species substitution and mislabelling in fish markets, and examines the feasibility of the technology for a typical retail store in Canada. It is assumed that increased accuracy of the technology in detecting fraud and enforcement of legal penalties and other associated costs would be likely to discourage cheating. Empirical results suggest that DNA barcoding technology would be feasible presently for a typical retail store only if authentication is done in a third party laboratory, as it may not be feasible on an individual retail store level once fixed and other associated costs of the technology are considered.},
}
@article {pmid26569490,
year = {2015},
author = {Bhagwat, RM and Dholakia, BB and Kadoo, NY and Balasundaran, M and Gupta, VS},
title = {Two New Potential Barcodes to Discriminate Dalbergia Species.},
journal = {PloS one},
volume = {10},
number = {11},
pages = {e0142965},
pmid = {26569490},
issn = {1932-6203},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; Dalbergia/*classification/genetics ; Genetic Loci ; Genetic Variation ; Geography ; India ; Molecular Sequence Data ; Nucleotides/genetics ; Species Specificity ; },
abstract = {DNA barcoding enables precise identification of species from analysis of unique DNA sequence of a target gene. The present study was undertaken to develop barcodes for different species of the genus Dalbergia, an economically important timber plant and is widely distributed in the tropics. Ten Dalbergia species selected from the Western Ghats of India were evaluated using three regions in the plastid genome (matK, rbcL, trnH-psbA), a nuclear transcribed spacer (nrITS) and their combinations, in order to discriminate them at species level. Five criteria: (i) inter and intraspecific distances, (ii) Neighbor Joining (NJ) trees, (iii) Best Match (BM) and Best Close Match (BCM), (iv) character based rank test and (v) Wilcoxon signed rank test were used for species discrimination. Among the evaluated loci, rbcL had the highest success rate for amplification and sequencing (97.6%), followed by matK (97.0%), trnH-psbA (94.7%) and nrITS (80.5%). The inter and intraspecific distances, along with Wilcoxon signed rank test, indicated a higher divergence for nrITS. The BM and BCM approaches revealed the highest rate of correct species identification (100%) with matK, matK+rbcL and matK+trnH-psb loci. These three loci, along with nrITS, were further supported by character based identification method. Considering the overall performance of these loci and their ranking with different approaches, we suggest matK and matK+rbcL as the most suitable barcodes to unambiguously differentiate Dalbergia species. These findings will potentially be helpful in delineating the various species of Dalbergia genus, as well as other related genera.},
}
@article {pmid26559636,
year = {2015},
author = {Correa, MC and Lombaert, E and Malausa, T and Crochard, D and Alvear, A and Zaviezo, T and Palero, F},
title = {Mealybug species from Chilean agricultural landscapes and main factors influencing the genetic structure of Pseudococcus viburni.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {16483},
pmid = {26559636},
issn = {2045-2322},
mesh = {*Agriculture ; Animals ; Chile ; Cluster Analysis ; *Gene-Environment Interaction ; Genetic Variation ; *Genetics, Population ; *Genome, Insect ; Geography ; Hemiptera/classification/*genetics ; Microsatellite Repeats ; RNA, Ribosomal, 28S/genetics ; },
abstract = {The present study aimed to characterize the distribution of mealybug species along Chilean agro-ecosystems and to determine the relative impact of host plant, management strategy, geography and micro-environment on shaping the distribution and genetic structure of the obscure mealybug Pseudococcus viburni. An extensive survey was completed using DNA barcoding methods to identify Chilean mealybugs to the species level. Moreover, a fine-scale study of Ps. viburni genetic diversity and population structure was carried out, genotyping 529 Ps. viburni individuals with 21 microsatellite markers. Samples from 16 localities were analyzed using Bayesian and spatially-explicit methods and the genetic dataset was confronted to host-plant, management and environmental data. Chilean crops were found to be infested by Ps. viburni, Pseudococcus meridionalis, Pseudococcus longispinus and Planococcus citri, with Ps. viburni and Ps. meridionalis showing contrasting distribution and host-plant preference patterns. Ps. viburni samples presented low genetic diversity levels but high genetic differentiation. While no significant genetic variance could be assigned to host-plant or management strategy, climate and geography were found to correlate significantly with genetic differentiation levels. The genetic characterization of Ps. viburni within Chile will contribute to future studies tracing back the origin and improving the management of this worldwide invader.},
}
@article {pmid26558529,
year = {2015},
author = {Kvastad, L and Werne Solnestam, B and Johansson, E and Nygren, AO and Laddach, N and Sahlén, P and Vickovic, S and Bendigtsen, SC and Aaserud, M and Floer, L and Borgen, E and Schwind, C and Himmelreich, R and Latta, D and Lundeberg, J},
title = {Single cell analysis of cancer cells using an improved RT-MLPA method has potential for cancer diagnosis and monitoring.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {16519},
pmid = {26558529},
issn = {2045-2322},
mesh = {Case-Control Studies ; Cell Line, Tumor ; Gene Expression Profiling ; Humans ; Multiplex Polymerase Chain Reaction/*methods/standards ; Neoplasms/*diagnosis/*genetics ; Neoplastic Cells, Circulating ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Analysis, RNA ; Single-Cell Analysis/*methods ; },
abstract = {Single cell analysis techniques have great potential in the cancer genomics field. The detection and characterization of circulating tumour cells are important for identifying metastatic disease at an early stage and monitoring it. This protocol is based on transcript profiling using Reverse Transcriptase Multiplex Ligation-dependent Probe Amplification (RT-MLPA), which is a specific method for simultaneous detection of multiple mRNA transcripts. Because of the small amount of (circulating) tumour cells, a pre-amplification reaction is performed after reverse transcription to generate a sufficient number of target molecules for the MLPA reaction. We designed a highly sensitive method for detecting and quantifying a panel of seven genes whose expression patterns are associated with breast cancer, and optimized the method for single cell analysis. For detection we used a fluorescence-dependent semi-quantitative method involving hybridization of unique barcodes to an array. We evaluated the method using three human breast cancer cell lines and identified specific gene expression profiles for each line. Furthermore, we applied the method to single cells and confirmed the heterogeneity of a cell population. Successful gene detection from cancer cells in human blood from metastatic breast cancer patients supports the use of RT-MLPA as a diagnostic tool for cancer genomics.},
}
@article {pmid26558366,
year = {2015},
author = {Gilligan, TM and Tembrock, LR and Farris, RE and Barr, NB and van der Straten, MJ and van de Vossenberg, BT and Metz-Verschure, E},
title = {A Multiplex Real-Time PCR Assay to Diagnose and Separate Helicoverpa armigera and H. zea (Lepidoptera: Noctuidae) in the New World.},
journal = {PloS one},
volume = {10},
number = {11},
pages = {e0142912},
pmid = {26558366},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Crops, Agricultural/parasitology ; DNA/*chemistry ; DNA Primers/metabolism ; Larva/genetics ; Molecular Sequence Data ; Moths/*genetics/growth &amp; development ; RNA, Ribosomal, 18S/chemistry/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; Glycine max/parasitology ; },
abstract = {The Old World bollworm, Helicoverpa armigera (Hübner), and the corn earworm, H. zea (Boddie), are two of the most important agricultural pests in the world. Diagnosing these two species is difficult-adults can only be separated with a complex dissection, and larvae cannot be identified to species using morphology, necessitating the use of geographic origin for identification in most instances. With the discovery of H. armigera in the New World, identification of immature Helicoverpa based on origin is no longer possible because H. zea also occurs in all of the geographic regions where H. armigera has been discovered. DNA barcoding and restriction fragment length polymorphism (RFLP) analyses have been reported in publications to distinguish these species, but these methods both require post-PCR processing (i.e., DNA sequencing or restriction digestion) to complete. We report the first real-time PCR assay to distinguish these pests based on two hydrolysis probes that bind to a segment of the internal transcribed spacer region 2 (ITS2) amplified using a single primer pair. One probe targets H. armigera, the second probe targets H. zea, and a third probe that targets a conserved segment of 18S rDNA is used as a control of DNA quality. The assay can be completed in 50 minutes when using isolated DNA and is successfully tested on larvae intercepted at ports of entry and adults captured during domestic surveys. We demonstrate that the assay can be run in triplex with no negative effects on sensitivity, can be run using alternative real-time PCR reagents and instruments, and does not cross react with other New World Heliothinae.},
}
@article {pmid26553779,
year = {2016},
author = {Esteve-Raventós, F and Moreno, G and Alvarado, P and Olariaga, I},
title = {Unraveling the Inocybe praetervisa group through type studies and ITS data: Inocybe praetervisoides sp. nov. from the Mediterranean region.},
journal = {Mycologia},
volume = {108},
number = {1},
pages = {123-134},
doi = {10.3852/15-053},
pmid = {26553779},
issn = {0027-5514},
mesh = {Agaricales/*classification/cytology/genetics ; Base Sequence ; DNA Barcoding, Taxonomic ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Mediterranean Region ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Spores, Fungal ; },
abstract = {Species in the Inocybe praetervisa group are characterized by producing nodulose to angular basidiospores and a bulbous, marginate, white stipe devoid of any pinkish to reddish tinge. Species delimitation problems and common misinterpretations in the I. praetervisa group have not yet been resolved through type studies and analysis of molecular data. This study seeks to clarify the taxonomy and nomenclature of species around I. praetervisa. Analyses of the nuc rDNA internal transcribed regions (ITS) recovered two major groups within the I. praetervisa group that can be separated on the basis of cystidial morphology. The study of three authentic and topotypic specimens in the Bresadola herbarium revealed that the name I. praetervisa has been misapplied often. The ITS region of one of the specimens was obtained, and this specimen is designated as epitype in support of a lectotype. Inocybe rivularis is demonstrated to be a later synonym of I. praetervisa, while Inocybe phaeocystidiosa is the correct name for the species most often misdetermined as I. praetervisa. Inocybe salicis-herbaceae and I. praetervisa var. flavofulvida are shown to be synonyms of I. phaeocystidiosa based on ITS sequence data from type collections. A new species sister to I. phaeocystidiosa with a Mediterranean distribution is described as I. praetervisoides. Cystidial morphology, distribution of caulocystidia, basidiospore morphology and ecology are shown to be the main diagnostic characters for separating the species. Inocybe praetervisa and I. phaeocystidiosa have a transoceanic distribution in Europe and North America, whereas I. praetervisoides so far is known only from the Mediterranean region.},
}
@article {pmid26547515,
year = {2015},
author = {Weber, AA and Mérigot, B and Valière, S and Chenuil, A},
title = {Influence of the larval phase on connectivity: strong differences in the genetic structure of brooders and broadcasters in the Ophioderma longicauda species complex.},
journal = {Molecular ecology},
volume = {24},
number = {24},
pages = {6080-6094},
doi = {10.1111/mec.13456},
pmid = {26547515},
issn = {1365-294X},
mesh = {*Animal Distribution ; Animals ; *Biological Evolution ; DNA, Mitochondrial/genetics ; Echinodermata/*genetics ; Genetic Markers ; Genetic Variation ; *Genetics, Population ; Genotype ; Greece ; Introns ; Larva ; Mediterranean Sea ; Phylogeography ; Reproduction/genetics ; Sequence Analysis, DNA ; Transcriptome ; },
abstract = {Closely related species with divergent life history traits are excellent models to infer the role of such traits in genetic diversity and connectivity. Ophioderma longicauda is a brittle star species complex composed of different genetic clusters, including brooders and broadcasters. These species diverged very recently and some of them are sympatric and ecologically syntopic, making them particularly suitable to study the consequences of their trait differences. At the scale of the geographic distribution of the broadcasters (Mediterranean Sea and northeastern Atlantic), we sequenced the mitochondrial marker COI and genotyped an intron (i51) for 788 individuals. In addition, we sequenced 10 nuclear loci newly developed from transcriptome sequences, for six sympatric populations of brooders and broadcasters from Greece. At the large scale, we found a high genetic structure within the brooders (COI: 0.07 < F(ST) < 0.65) and no polymorphism at the nuclear locus i51. In contrast, the broadcasters displayed lower genetic structure (0 < F(ST) < 0.14) and were polymorphic at locus i51. At the regional scale, the multilocus analysis confirmed the contrasting genetic structure between species, with no structure in the broadcasters (global F(ST) < 0.001) and strong structure in the brooders (global F(ST) = 0.49), and revealed a higher genetic diversity in broadcasters. Our study showed that the lecithotrophic larval stage allows on average a 50-fold increase in migration rates, a 280-fold increase in effective size and a threefold to fourfold increase in genetic diversity. Our work, investigating complementary genetic markers on sympatric and syntopic taxa, highlights the strong impact of the larval phase on connectivity and genetic diversity.},
}
@article {pmid26544710,
year = {2015},
author = {Huang, Y and Xing, N and Wang, Z and Zhang, X and Zhao, X and Du, Q and Chang, L and Tong, D},
title = {Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay.},
journal = {PloS one},
volume = {10},
number = {11},
pages = {e0141545},
pmid = {26544710},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Circovirus/*genetics/*isolation &amp; purification ; DNA Probes/*chemistry/genetics ; Limit of Detection ; Nanoparticles/*chemistry ; Polymerase Chain Reaction/*methods ; Reproducibility of Results ; Swine/virology ; Swine Diseases/diagnosis/virology ; Transmissible gastroenteritis virus/*genetics/*isolation &amp; purification ; },
abstract = {Mixed infection of multiple viruses is common in modern intensive pig rearing. However, there are no methods available to detect DNA and RNA viruses in the same reaction system in preclinical level. In this study, we aimed to develop a duplex ultrasensitive nanoparticle DNA probe-based PCR assay (duplex UNDP-PCR) that was able to simultaneously detect DNA and RNA viruses in the same reaction system. PCV2 and TGEV are selected as representatives of the two different types of viruses. PCV2 DNA and TGEV RNA were simultaneously released from the serum sample by boiling with lysis buffer, then magnetic beads and gold nanoparticles coated with single and/or duplex specific probes for TGEV and PCV2 were added to form a sandwich-like complex with nucleic acids released from viruses. After magnetic separation, DNA barcodes specific for PCV2 and TGEV were eluted using DTT and characterized by specific PCR assay for specific DNA barcodes subsequently. The duplex UNDP-PCR showed similar sensitivity as that of single UNDP-PCR and was able to detect 20 copies each of PCV2 and TGEV in the serum, showing approximately 250-fold more sensitivity than conventional duplex PCR/RT-PCR assays. No cross-reaction was observed with other viruses. The positive detection rate of single MMPs- and duplex MMPs-based duplex UNDP-PCR was identical, with 29.6% for PCV2, 9.3% for TGEV and 3.7% for PCV2 and TGEV mixed infection. This duplex UNDP-PCR assay could detect TGEV (RNA virus) and PCV2 (DNA virus) from large-scale serum samples simultaneously without the need for DNA/RNA extraction, purification and reverse transcription of RNA, and showed a significantly increased positive detection rate for PCV2 (29%) and TGEV (11.7%) preclinical infection than conventional duplex PCR/RT-PCR. Therefore, the established duplex UNDP-PCR is a rapid and economical detection method, exhibiting high sensitivity, specificity and reproducibility.},
}
@article {pmid26544633,
year = {2015},
author = {GilArriortua, M and Saloña-Bordas, MI and Cainé, LM and Pinheiro, F and M de Pancorbo, M},
title = {Technical Note: "Mitochondrial and nuclear DNA approaches for reliable identification of Lucilia (Diptera, Calliphoridae) species of forensic interest from Southern Europe".},
journal = {Forensic science international},
volume = {257},
number = {},
pages = {393-397},
doi = {10.1016/j.forsciint.2015.10.010},
pmid = {26544633},
issn = {1872-6283},
mesh = {Animals ; Cytochromes b/genetics ; DNA/*genetics ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal Spacer/genetics ; Diptera/*genetics ; Electron Transport Complex IV/genetics ; Entomology ; Europe ; Feeding Behavior ; Forensic Sciences ; Haplotypes ; Humans ; Polymerase Chain Reaction ; Postmortem Changes ; Sequence Analysis, DNA ; },
abstract = {In forensic entomology, rapid and unambiguous identification of blowfly species is a critical prerequisite for accurately estimating the post-mortem interval (PMI). The conventional diagnosis of cadaveric entomofauna based on external characters is hampered by the morphological similarities between species, especially in immature stages. Genetic analysis has been shown to allow precise and reliable diagnosis and delimitation of insect species. Nevertheless, the taxonomy of some species remains unresolved. This study was focused on improving the effectiveness and accuracy of analysis based on the widely used cytochrome c oxidase subunit I barcode region (COI barcode, 658 bp), complemented by other mitochondrial and nuclear regions, such as cytochrome b (Cyt-b, 307 bp) and the second internal transcribed spacer (ITS2, 310-331 bp), for the identification of Southern European blowflies. We analyzed a total of 209 specimens, collected from 38 human corpses, belonging to three Calliphoridae genera and seven species: Chrysomya (Ch. albiceps), Calliphora (C. vicina and C. vomitoria), and Lucilia (L. sericata, L. ampullacea, L. caesar and L. illustris). These species are the most common PMI indicators in Portugal. The results revealed that unambiguous separation of species of the Lucilia genus requires different loci from the barcode region. Furthermore, we conclude that the ITS2 (310-331 bp) molecular marker is a promising diagnostic tool because its inter-specific discriminatory power enables unequivocal and consistent distinctions to be made, even between closely related species (L. caesar-L. illustris). This work also contributes new genetic data that may be of interest in performing species diagnosis for Southern European blowflies. Notably, to the best of our knowledge, we provide the first records of the Cyt-b (307 bp) locus for L. illustris and the ITS2 (310-331 bp) region for Iberian Peninsula Lucilia species.},
}
@article {pmid26542714,
year = {2015},
author = {Ullal, AV and Weissleder, R},
title = {Photocleavable DNA Barcoding Antibodies for Multiplexed Protein Analysis in Single Cells.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1346},
number = {},
pages = {47-54},
doi = {10.1007/978-1-4939-2987-0_4},
pmid = {26542714},
issn = {1940-6029},
mesh = {Antibodies/*chemistry ; DNA/*chemistry ; DNA Barcoding, Taxonomic/instrumentation/*methods ; Equipment Design ; Humans ; Immunoconjugates/*chemistry ; Models, Molecular ; Nucleic Acid Hybridization/methods ; Photolysis ; Proteins/*analysis ; Proteomics/methods ; Single-Cell Analysis/instrumentation/*methods ; },
abstract = {We describe a DNA-barcoded antibody sensing technique for single cell protein analysis in which the barcodes are photocleaved and digitally detected without amplification steps (Ullal et al., Sci Transl Med 6:219, 2014). After photocleaving the unique ~70 mer DNA barcodes we use a fluorescent hybridization technology for detection, similar to what is commonly done for nucleic acid readouts. This protocol offers a simple method for multiplexed protein detection using 100+ antibodies and can be performed on clinical samples as well as single cells.},
}
@article {pmid26541238,
year = {2016},
author = {Zhao, Y and Yi, Z and Gentekaki, E and Zhan, A and Al-Farraj, SA and Song, W},
title = {Utility of combining morphological characters, nuclear and mitochondrial genes: An attempt to resolve the conflicts of species identification for ciliated protists.},
journal = {Molecular phylogenetics and evolution},
volume = {94},
number = {Pt B},
pages = {718-729},
doi = {10.1016/j.ympev.2015.10.017},
pmid = {26541238},
issn = {1095-9513},
mesh = {Cell Nucleus ; DNA, Ribosomal ; Genes, Mitochondrial ; *Genetic Markers ; Genetic Variation ; Molecular Typing ; Oligohymenophorea/*classification/genetics ; Phylogeny ; Species Specificity ; },
abstract = {Ciliates comprise a highly diverse protozoan lineage inhabiting all biotopes and playing crucial roles in regulating microbial food webs. Nevertheless, subtle morphological differences and tiny sizes hinder proper species identification for many ciliates. Here, we use the species-rich taxon Frontonia and employ both nuclear and mitochondrial loci. We attempt to assess the level of genetic diversity and evaluate the potential of each marker in delineating species of Frontonia. Morphological features and ecological characteristics are also integrated into genetic results, in an attempt to resolve conflicts of species identification based on morphological and molecular methods. Our studies reveal: (1) the mitochondrial cox1 gene, nuclear ITS1 and ITS2 as well as the hypervariable D2 region of LSU rDNA are promising candidates for species delineation; (2) the cox1 gene provides the best resolution for analyses below the species level; (3) the V2 and V4 hypervariable regions of SSU rDNA, and D1 of LSU rDNA as well as the 5.8S rDNA gene do not show distinct barcoding gap due to overlap between intra- and inter-specific genetic divergences; (4) morphological character-based analysis shows promise for delimitation of Frontonia species; and (5) all gene markers and character-based analyses demonstrate that the genus Frontonia consists of three groups and monophyly of the genus Frontonia is questionable.},
}
@article {pmid26540272,
year = {2016},
author = {Sizhu, Z and Jialin, L and Yihan, W and Yuan, G and Guohui, Z and Xiaojun, Y and Yunfang, C},
title = {DNA barcoding identification of Dermestidae species.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4498-4502},
doi = {10.3109/19401736.2015.1101538},
pmid = {26540272},
issn = {2470-1408},
mesh = {Animals ; Coleoptera/classification/*genetics ; DNA/chemistry/isolation &amp; purification/metabolism ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Electron Transport Complex IV/classification/genetics/metabolism ; Genetic Variation ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Dermestidae species are important stored product insects. The traditional morphological identification has its limitation. The purpose of the study is to explore the effectiveness of identification by DNA barcoding technology in Dermestidae. The COI gene sequences of 39 samples from 17 species of Dermestidae were analyzed, and we evaluated the identification ability of the sequences by the tree building method and the distance evaluation method in this study. The COI sequences whose length was 356 bp had a large difference between intra-specific and inter-specific and a significant barcoding gap. The success rate of identification was 92.5%. The results showed a certain feasibility to identify the most species of Dermestidae by this segment of COI.},
}
@article {pmid26539040,
year = {2015},
author = {Kim, CS and Jo, JW and Kwag, YN and Sung, GH and Lee, SG and Kim, SY and Shin, CH and Han, SK},
title = {Mushroom Flora of Ulleung-gun and a Newly Recorded Bovista Species in the Republic of Korea.},
journal = {Mycobiology},
volume = {43},
number = {3},
pages = {239-257},
pmid = {26539040},
issn = {1229-8093},
abstract = {We conducted five times surveys, in June, September and October in 2012; June and September 2013, to catalog the mushroom flora in Ulleung-gun, Republic of Korea. More than 400 specimens were collected, and 317 of the specimens were successfully sequenced using the ribosomal DNA internal transcribed spacer barcode marker. We also surveyed the morphological characteristics of the sequenced specimens. The specimens were classified into 2 phyla, 7 classes, 21 orders, 59 families, 122 genera, and 221 species, and were deposited in the herbarium of Korea National Arboretum. Among the collected species, 72% were saprophytic, 25% were symbiotic, and 3% were parasitic. The most common order was Agaricales (189 specimens, 132 species), followed by Polyporales (47 specimens, 27 species), Russulales (31 specimens, 22 species), Boletales (10 specimens, 7 species), and so on. Herein, we also reported the first Bovista species in Korea, which was collected from Dokdo, the far-eastern island of Korea.},
}
@article {pmid26538876,
year = {2015},
author = {Dineshshankar, J and Venkateshwaran, R and Vidhya, J and Anuradha, R and Mary, GP and Pradeep, R and Senthileagappan, AR},
title = {Denture bar-coding: An innovative technique in forensic dentistry.},
journal = {Journal of pharmacy &amp; bioallied sciences},
volume = {7},
number = {Suppl 2},
pages = {S350-3},
pmid = {26538876},
issn = {0976-4879},
abstract = {Denture markers play an important role in forensic odontology and also in identifying a person. A number of methods are there for identifying dentures from a less expensive technique to a more expensive technique. Out of different denture markers, the bar-coding system is a way of collecting data from the mobile. Even a huge amount of data can be stored in that. It can be easily incorporated during acrylization of the denture and thus could be helpful in identification. This article reviews the strengths of bar-coding and how easily it can be used in the routine procedure.},
}
@article {pmid26535713,
year = {2015},
author = {Supikamolseni, A and Ngaoburanawit, N and Sumontha, M and Chanhome, L and Suntrarachun, S and Peyachoknagul, S and Srikulnath, K},
title = {Molecular barcoding of venomous snakes and species-specific multiplex PCR assay to identify snake groups for which antivenom is available in Thailand.},
journal = {Genetics and molecular research : GMR},
volume = {14},
number = {4},
pages = {13981-13997},
doi = {10.4238/2015.October.29.18},
pmid = {26535713},
issn = {1676-5680},
mesh = {Animals ; Antivenins ; Cytochromes b/genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial ; Multiplex Polymerase Chain Reaction ; Phylogeny ; Snake Venoms ; Snakes/*classification/*genetics ; Species Specificity ; Thailand ; },
abstract = {DNA barcodes of mitochondrial COI and Cytb genes were constructed from 54 specimens of 16 species for species identification. Intra- and interspecific sequence divergence of the COI gene (10 times) was greater than that of the Cytb gene (4 times), which suggests that the former gene may be a better marker than the latter for species delimitation in snakes. The COI barcode cut-off scores differed by more than 3% between most species, and the minimum interspecific divergence was greater than the maximum intraspecific divergence. Clustering analysis indicated that most species fell into monophyletic clades. These results suggest that these species could be reliably differentiated using COI DNA barcodes. Moreover, a novel species-specific multiplex PCR assay was developed to distinguish between Naja spp, Ophiophagus hannah, Trimeresurus spp, Hydrophiinae, Daboia siamensis, Bungarus fasciatus, and Calloselasma rhodostoma. Antivenom for these species is produced and kept by the Thai Red Cross for clinical use. Our novel PCR assay could easily be applied to venom and saliva samples and could be used effectively for the rapid and accurate identification of species during forensic work, conservation study, and medical research.},
}
@article {pmid26528252,
year = {2015},
author = {Hamilton, PB and Lefebvre, KE and Bull, RD},
title = {Single cell PCR amplification of diatoms using fresh and preserved samples.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {1084},
pmid = {26528252},
issn = {1664-302X},
abstract = {Single cell Chelex® DNA extraction and nested PCR amplification were used to examine partial gene sequences from natural diatom populations for taxonomic and phylogenetic studies at and above the level of species. DNA was extracted from cells that were either fresh collected or stored in RNAlater. Extractions from Lugol's fixation were also attempted with limited success. Three partial gene sequences (rbcL, 18S, and psbA) were recovered using existing and new primers with a nested or double nested PCR approach with amplification and success rates between 70 and 96%. An rbcL consensus tree grouped morphologically similar specimens and was consistent across the two primary sample treatments: fresh and RNAlater. This tool will greatly enhance the number of microscopic diatom taxa (and potentially other microbes) available for barcoding and phylogenetic studies. The near-term increase in sequence data for diatoms generated via routine single cell extractions and PCR will act as a multiproxy validation of longer-term next generation genomics.},
}
@article {pmid26527841,
year = {2015},
author = {Boufahja, F and Semprucci, F and Beyrem, H and Bhadury, P},
title = {Marine Nematode Taxonomy in Africa: Promising Prospects Against Scarcity of Information.},
journal = {Journal of nematology},
volume = {47},
number = {3},
pages = {198-206},
pmid = {26527841},
issn = {0022-300X},
abstract = {From the late 19th century, Africa has faced heavy exploitation of its natural resources with increasing land/water pollution, and several described species have already become extinct or close to extinction. This could also be the case for marine nematodes, which are the most abundant and diverse benthic group in marine sediments, and play major roles in ecosystem functioning. Compared to Europe and North America, only a handful of investigations on marine nematodes have been conducted to date in Africa. This is due to the scarcity of experienced taxonomists, absence of identification guides, as well as local appropriate infrastructures. A pivotal project has started recently between nematologists from Africa (Tunisia), India, and Europe (Italy) to promote taxonomic study and biodiversity estimation of marine nematodes in the African continent. To do this, as a first step, collection of permanent slides of marine nematodes (235 nominal species and 14 new to science but not yet described) was recently established at the Faculty of Sciences of Bizerte (Tunisia). Capacity building of next generation of African taxonomists have been carried out at level of both traditional and molecular taxonomy (DNA barcoding and next-generation sequencing [NGS]), but they need to be implemented. Indeed, the integration of these two approaches appears crucial to overcome lack of information on the taxonomy, ecology, and biodiversity of marine nematodes from African coastal waters.},
}
@article {pmid26525828,
year = {2016},
author = {Lopes-Lima, M and Hinzmann, M and Teixeira, A and Varandas, S and Machado, J and Sousa, R and Froufe, E},
title = {The strange case of the tetragenous Anodonta anatina.},
journal = {Journal of experimental zoology. Part A, Ecological genetics and physiology},
volume = {325},
number = {1},
pages = {52-56},
doi = {10.1002/jez.1995},
pmid = {26525828},
issn = {1932-5231},
mesh = {Animals ; Anodonta/genetics/*growth &amp; development/pathogenicity ; Ecosystem ; Fishes/parasitology ; Fresh Water ; Gills/parasitology ; Lakes ; Larva/classification/*growth &amp; development ; *Life Cycle Stages ; *Phylogeny ; },
abstract = {Unionoid freshwater mussels have a unique life cycle with a form of parental care where the larvae are developed and kept inside the gills until release, followed by an obligate parasitic stage on fish. The size and location of the marsupium have been used as important phylogenetic characters in unionoids and in Anodontini its location was described exclusively on the outer demibranchs. Two recent surveys in a lake in the North of Portugal revealed large anodontine mussels morphological identical to Anodonta anatina but with glochidia in both demibranchs and with an unusual large size. In order to establish the identity of these mussels, a barcoding approach was used and an anatomical description of the gills and glochidia was performed. These mussels were identified as A. anatina and presented an inner demibranch pair with tripartite tubes. The glochidial sizes were much higher than previously reported for the species reaching maximum (length × height) values of 566 × 552 μm. This species reveals a high ecological plasticity being able to change its size and anatomy to increase its fertility as well as infestation performance. J. Exp. Zool. 325A:52-56, 2016. © 2015 Wiley Periodicals, Inc.},
}
@article {pmid26523839,
year = {2016},
author = {Rallis, C and Bähler, J},
title = {Cell-based screens and phenomics with fission yeast.},
journal = {Critical reviews in biochemistry and molecular biology},
volume = {51},
number = {2},
pages = {86-95},
doi = {10.3109/10409238.2015.1103205},
pmid = {26523839},
issn = {1549-7798},
support = {095598//Wellcome Trust/United Kingdom ; 095598/Z/11/Z//Wellcome Trust/United Kingdom ; BB/I012451/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Amino Acids/metabolism ; DNA Transposable Elements ; *Genome, Viral ; Metabolomics ; Models, Biological ; Mutagenesis ; *Phenotype ; Schizosaccharomyces/classification/*genetics ; },
abstract = {Next-generation sequencing approaches have considerably advanced our understanding of genome function and regulation. However, the knowledge of gene function and complex cellular processes remains a challenge and bottleneck in biological research. Phenomics is a rapidly emerging area, which seeks to rigorously characterize all phenotypes associated with genes or gene variants. Such high-throughput phenotyping under different conditions can be a potent approach toward gene function. The fission yeast Schizosaccharomyces pombe (S. pombe) is a proven eukaryotic model organism that is increasingly used for genomewide screens and phenomic assays. In this review, we highlight current large-scale, cell-based approaches used with S. pombe, including computational colony-growth measurements, genetic interaction screens, parallel profiling using barcodes, microscopy-based cell profiling, metabolomic methods and transposon mutagenesis. These diverse methods are starting to offer rich insights into the relationship between genotypes and phenotypes.},
}
@article {pmid26523754,
year = {2015},
author = {Ryberg, M},
title = {Molecular operational taxonomic units as approximations of species in the light of evolutionary models and empirical data from Fungi.},
journal = {Molecular ecology},
volume = {24},
number = {23},
pages = {5770-5777},
doi = {10.1111/mec.13444},
pmid = {26523754},
issn = {1365-294X},
mesh = {Cluster Analysis ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; *Evolution, Molecular ; Fungi/*classification ; *Models, Genetic ; Sequence Analysis, DNA ; },
abstract = {During the last couple of decades, an increasing number of studies use sequence clusters as units for taxonomic diversity. It is well known that such molecular operational taxonomic units (MOTUs) do not necessarily correspond to species, but they are treated as such when measuring diversity and testing theories. Here, I show that data from studies of molecular evolution and species diversification of fungi indicate that commonly used cut-offs are likely to lump species in many cases. At the same time, empirical studies show that the mean within-species variation is close to these cut-offs. That the within-species variation estimates are plausible is supported by coalescence modelling under a range of parameter settings. In addition, studies using crossing tests to delimit species show that there often is an overlap in within- and between-species distances. The available data therefore indicate that sequence clusters are likely to misrepresent species. However, to keep a biological relevance, MOTUs should be kept in close agreement with species. Studies using them should therefore asses how sensitive the results are to differences between MOTUs and species--something that is rarely done. An even better solution is to directly include the uncertainty in species delimitation in the analyses, but in many cases, we need to increase our knowledge of taxonomy and evolution to do this accurately. Even if the empirical data referred to here pertain to the "barcoding" region of rDNA in fungi, there is nothing indicating that the situation is substantially better for other taxa or genes.},
}
@article {pmid26516098,
year = {2015},
author = {Shokralla, S and Hellberg, RS and Handy, SM and King, I and Hajibabaei, M},
title = {A DNA Mini-Barcoding System for Authentication of Processed Fish Products.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {15894},
pmid = {26516098},
issn = {2045-2322},
mesh = {Animals ; DNA/isolation &amp; purification/metabolism ; *DNA Barcoding, Taxonomic ; DNA Primers/metabolism ; Databases, Genetic ; Electron Transport Complex IV/genetics ; Fish Products/*analysis ; Polymerase Chain Reaction ; },
abstract = {Species substitution is a form of seafood fraud for the purpose of economic gain. DNA barcoding utilizes species-specific DNA sequence information for specimen identification. Previous work has established the usability of short DNA sequences-mini-barcodes-for identification of specimens harboring degraded DNA. This study aims at establishing a DNA mini-barcoding system for all fish species commonly used in processed fish products in North America. Six mini-barcode primer pairs targeting short (127-314 bp) fragments of the cytochrome c oxidase I (CO1) DNA barcode region were developed by examining over 8,000 DNA barcodes from species in the U.S. Food and Drug Administration (FDA) Seafood List. The mini-barcode primer pairs were then tested against 44 processed fish products representing a range of species and product types. Of the 44 products, 41 (93.2%) could be identified at the species or genus level. The greatest mini-barcoding success rate found with an individual primer pair was 88.6% compared to 20.5% success rate achieved by the full-length DNA barcode primers. Overall, this study presents a mini-barcoding system that can be used to identify a wide range of fish species in commercial products and may be utilized in high throughput DNA sequencing for authentication of heavily processed fish products.},
}
@article {pmid26507570,
year = {2015},
author = {Bello, A and Daru, BH and Stirton, CH and Chimphango, SB and van der Bank, M and Maurin, O and Muasya, AM},
title = {DNA barcodes reveal microevolutionary signals in fire response trait in two legume genera.},
journal = {AoB PLANTS},
volume = {7},
number = {},
pages = {},
pmid = {26507570},
issn = {2041-2851},
abstract = {Large-scale DNA barcoding provides a new technique for species identification and evaluation of relationships across various levels (populations and species) and may reveal fundamental processes in recently diverged species. Here, we analysed DNA sequence variation in the recently diverged legumes from the Psoraleeae (Fabaceae) occurring in the Cape Floristic Region (CFR) of southern Africa to test the utility of DNA barcodes in species identification and discrimination. We further explored the phylogenetic signal on fire response trait (reseeding and resprouting) at species and generic levels. We showed that Psoraleoid legumes of the CFR exhibit a barcoding gap yielding the combination of matK and rbcLa (matK + rbcLa) data set as a better barcode than single regions. We found a high score (100 %) of correct identification of individuals to their respective genera but a very low score (<50 %) in identifying them to species. We found a considerable match (54 %) between genetic species and morphologically delimited species. We also found that different lineages showed a weak but significant phylogenetic conservatism in their response to fire as reseeders or resprouters, with more clustering of resprouters than would be expected by chance. These novel microevolutionary patterns might be acting continuously over time to produce multi-scale regularities of biodiversity. This study provides the first insight into the DNA barcoding campaign of land plants in species identification and detection of the phylogenetic signal in recently diverged lineages of the CFR.},
}
@article {pmid26507077,
year = {2015},
author = {Truong, AS and Lochbaum, CA and Boyce, MW and Lockett, MR},
title = {Tracking the Invasion of Small Numbers of Cells in Paper-Based Assays with Quantitative PCR.},
journal = {Analytical chemistry},
volume = {87},
number = {22},
pages = {11263-11270},
doi = {10.1021/acs.analchem.5b02362},
pmid = {26507077},
issn = {1520-6882},
mesh = {Breast Neoplasms/genetics/*pathology ; DNA, Neoplasm/analysis/genetics ; Humans ; *Paper ; *Polymerase Chain Reaction ; Tumor Cells, Cultured ; },
abstract = {Paper-based scaffolds are an attractive material for culturing mammalian cells in a three-dimensional environment. There are a number of previously published studies, which utilize these scaffolds to generate models of aortic valves, cardiac ischemia and reperfusion, and solid tumors. These models have largely relied on fluorescence imaging and microscopy to quantify cells in the scaffolds. We present here a polymerase chain reaction (PCR)-based method, capable of quantifying multiple cell types in a single culture with the aid of DNA barcodes: unique sequences of DNA introduced to the genome of individual cells or cell types through lentiviral transduction. PCR-based methods are highly specific and are amenable to high-throughput and multiplexed analyses. To validate this method, we engineered two different breast cancer lines to constitutively express either a green or red fluorescent protein. These cells lines allowed us to directly compare the ability of fluorescence imaging (of the fluorescent proteins) and qPCR (of the unique DNA sequences of the fluorescent proteins) to quantify known numbers of cells in the paper based-scaffolds. We also used both methods to quantify the distribution of these breast cell lines in homotypic and heterotypic invasion assays. In the paper-based invasion assays, a single sheet of paper containing cells suspended in a hydrogel was sandwiched between sheets of paper containing only hydrogel. The stack was incubated, and the cells invaded the adjacent layers. The individual sheets of the invasion assay were then destacked and the number of cells in each layer quantified. Our results show both methods can accurately detect cell populations of greater than 500 cells. The qPCR method can repeatedly and accurately detect as few as 50 cells, allowing small populations of highly invasive cells to be detected and differentiated from other cell types.},
}
@article {pmid26506007,
year = {2015},
author = {Pinto, Ide S and Chagas, BD and Rodrigues, AA and Ferreira, AL and Rezende, HR and Bruno, RV and Falqueto, A and Andrade-Filho, JD and Galati, EA and Shimabukuro, PH and Brazil, RP and Peixoto, AA},
title = {DNA Barcoding of Neotropical Sand Flies (Diptera, Psychodidae, Phlebotominae): Species Identification and Discovery within Brazil.},
journal = {PloS one},
volume = {10},
number = {10},
pages = {e0140636},
pmid = {26506007},
issn = {1932-6203},
mesh = {Animals ; Brazil ; DNA/*genetics ; *DNA Barcoding, Taxonomic ; Female ; Psychodidae/classification/*genetics ; Species Specificity ; },
abstract = {DNA barcoding has been an effective tool for species identification in several animal groups. Here, we used DNA barcoding to discriminate between 47 morphologically distinct species of Brazilian sand flies. DNA barcodes correctly identified approximately 90% of the sampled taxa (42 morphologically distinct species) using clustering based on neighbor-joining distance, of which four species showed comparatively higher maximum values of divergence (range 4.23-19.04%), indicating cryptic diversity. The DNA barcodes also corroborated the resurrection of two species within the shannoni complex and provided an efficient tool to differentiate between morphologically indistinguishable females of closely related species. Taken together, our results validate the effectiveness of DNA barcoding for species identification and the discovery of cryptic diversity in sand flies from Brazil.},
}
@article {pmid26505614,
year = {2016},
author = {Tynan, JA and Kim, SK and Mazloom, AR and Zhao, C and McLennan, G and Tim, R and Liu, L and Hannum, G and Hull, A and Bombard, AT and Oeth, P and Burcham, T and van den Boom, D and Ehrich, M},
title = {Application of risk score analysis to low-coverage whole genome sequencing data for the noninvasive detection of trisomy 21, trisomy 18, and trisomy 13.},
journal = {Prenatal diagnosis},
volume = {36},
number = {1},
pages = {56-62},
doi = {10.1002/pd.4712},
pmid = {26505614},
issn = {1097-0223},
mesh = {Adult ; Chromosome Disorders/*diagnosis/genetics ; Chromosomes, Human, Pair 13/genetics ; Chromosomes, Human, Pair 18/genetics ; *Decision Support Techniques ; Down Syndrome/*diagnosis/genetics ; Female ; *Genome, Human ; *High-Throughput Nucleotide Sequencing ; Humans ; Male ; Maternal Age ; Maternal Serum Screening Tests ; Middle Aged ; Pregnancy ; Retrospective Studies ; Risk Assessment ; Risk Factors ; Sensitivity and Specificity ; Sequence Analysis, DNA/*methods ; Trisomy/*diagnosis/genetics ; Trisomy 13 Syndrome ; Trisomy 18 Syndrome ; Ultrasonography, Prenatal ; },
abstract = {OBJECTIVES: Clinical performance of a low coverage, low cost, massively parallel sequencing (MPS)-based assay to stratify risk of trisomy 21, 18, and 13 pregnancies was determined.<br><br>METHODS: The study included 1100 samples with birth outcome or karyotype results, comprising low-risk patients (84.2%) negative for risk indications from maternal age, serum screening, ultrasound, or family history, and high-risk patients (15.8%) with at least one of the aforementioned indications. Cell free DNA (cfDNA) was extracted from maternal plasma. Library preparation incorporated 96 index barcodes to enable sequencing on a HiSeq 2000 or 2500. Risk scores were calculated using chromosomal representation, fetal fraction, and maternal age at the estimated date of delivery. A risk score greater than or equal to 1 in 100 was used to stratify samples as high risk for trisomy 21, trisomy 18, or trisomy 13.<br><br>RESULTS: Sensitivity and specificity were calculated based on risk group stratification. Trisomy 21, trisomy 18, and trisomy 13 were detected with greater than 99% sensitivity and 99.9% specificity. Fetal sex classification accuracy was 99.3%.<br><br>CONCLUSIONS: We conclude that simplified MPS can be used to stratify the risk of pregnancies for trisomy 21, trisomy 18, and trisomy 13 and accurately determine fetal sex. &#xa9; 2015 John Wiley &amp; Sons, Ltd.},
}
@article {pmid26500674,
year = {2015},
author = {Zhao, S and Chen, X and Song, J and Pang, X and Chen, S},
title = {Internal transcribed spacer 2 barcode: a good tool for identifying Acanthopanacis cortex.},
journal = {Frontiers in plant science},
volume = {6},
number = {},
pages = {840},
pmid = {26500674},
issn = {1664-462X},
abstract = {Acanthopanacis cortex has been used in clinical applications for a long time. Considering some historical and geographical factors, Acanthopanacis cortex is easily confused with other herbs in medicine markets, thereby causing potential safety issues. In this study, we used the internal transcribed spacer 2 (ITS2) barcode to identify 69 samples belonging to six species, including Acanthopanacis cortex and its adulterants. The nearest distance, single-nucleotide polymorphisms (SNPs), and neighbor-joining (NJ) tree methods were used to evaluate the identification ability of the ITS2 barcode. According to the kimura-2-parameter model, the intraspecific distance of Eleutherococcus nodiflorus ITS2 sequences ranged from 0 to 0.0132. The minimum interspecific distance between E. nodiflorus and E. giraldii was 0.0221, which was larger than the maximum intraspecific distance of E. nodiflorus. Three stable SNPs in ITS2 can be used to distinguish Acanthopanacis cortex and its closely related species. The NJ tree indicated that the Acanthopanacis cortex samples clustered into one clade, which can be distinguished clearly from the adulterants of this herb. A secondary structure of ITS2 provided another dimensionality to identify species. In conclusion, the ITS2 barcode effectively identifies Acanthopanacis cortex, and DNA barcoding is a convenient tool for medicine market supervision.},
}
@article {pmid26497143,
year = {2015},
author = {Guo, X and Lehner, K and O'Connell, K and Zhang, J and Dave, SS and Jinks-Robertson, S},
title = {SMRT Sequencing for Parallel Analysis of Multiple Targets and Accurate SNP Phasing.},
journal = {G3 (Bethesda, Md.)},
volume = {5},
number = {12},
pages = {2801-2808},
pmid = {26497143},
issn = {2160-1836},
support = {R01 GM038464/GM/NIGMS NIH HHS/United States ; T32 GM007754/GM/NIGMS NIH HHS/United States ; R01 GM101690/GM/NIGMS NIH HHS/United States ; R01 CA136895/CA/NCI NIH HHS/United States ; GM101690/GM/NIGMS NIH HHS/United States ; GM093197/GM/NIGMS NIH HHS/United States ; R01 GM093197/GM/NIGMS NIH HHS/United States ; GM038464/GM/NIGMS NIH HHS/United States ; CA136895/CA/NCI NIH HHS/United States ; },
mesh = {Alleles ; Cell Line, Tumor ; DNA Barcoding, Taxonomic/methods ; DNA Mutational Analysis/methods ; Genes, Fungal ; Genetic Linkage ; Genomics/methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Lymphoma/genetics ; Mutation ; *Polymorphism, Single Nucleotide ; Recombination, Genetic ; Reproducibility of Results ; Yeasts/classification/genetics ; },
abstract = {Single-molecule real-time (SMRT) sequencing generates much longer reads than other widely used next-generation (next-gen) sequencing methods, but its application to whole genome/exome analysis has been limited. Here, we describe the use of SMRT sequencing coupled with barcoding to simultaneously analyze one or a small number of genomic targets derived from multiple sources. In the budding yeast system, SMRT sequencing was used to analyze strand-exchange intermediates generated during mitotic recombination and to analyze genetic changes in a forward mutation assay. The general barcoding-SMRT approach was then extended to diffuse large B-cell lymphoma primary tumors and cell lines, where detected changes agreed with prior Illumina exome sequencing. A distinct advantage afforded by SMRT sequencing over other next-gen methods is that it immediately provides the linkage relationships between SNPs in the target segment sequenced. The strength of our approach for mutation/recombination studies (as well as linkage identification) derives from its inherent computational simplicity coupled with a lack of reliance on sophisticated statistical analyses.},
}
@article {pmid26492348,
year = {2015},
author = {Tapia, E and Spetale, F and Krsticevic, F and Angelone, L and Bulacio, P},
title = {DNA Barcoding through Quaternary LDPC Codes.},
journal = {PloS one},
volume = {10},
number = {10},
pages = {e0140459},
pmid = {26492348},
issn = {1932-6203},
mesh = {DNA Barcoding, Taxonomic/*methods ; Probability ; },
abstract = {For many parallel applications of Next-Generation Sequencing (NGS) technologies short barcodes able to accurately multiplex a large number of samples are demanded. To address these competitive requirements, the use of error-correcting codes is advised. Current barcoding systems are mostly built from short random error-correcting codes, a feature that strongly limits their multiplexing accuracy and experimental scalability. To overcome these problems on sequencing systems impaired by mismatch errors, the alternative use of binary BCH and pseudo-quaternary Hamming codes has been proposed. However, these codes either fail to provide a fine-scale with regard to size of barcodes (BCH) or have intrinsic poor error correcting abilities (Hamming). Here, the design of barcodes from shortened binary BCH codes and quaternary Low Density Parity Check (LDPC) codes is introduced. Simulation results show that although accurate barcoding systems of high multiplexing capacity can be obtained with any of these codes, using quaternary LDPC codes may be particularly advantageous due to the lower rates of read losses and undetected sample misidentification errors. Even at mismatch error rates of 10(-2) per base, 24-nt LDPC barcodes can be used to multiplex roughly 2000 samples with a sample misidentification error rate in the order of 10(-9) at the expense of a rate of read losses just in the order of 10(-6).},
}
@article {pmid26490301,
year = {2016},
author = {Kinyanjui, G and Khamis, FM and Mohamed, S and Ombura, LO and Warigia, M and Ekesi, S},
title = {Identification of aphid (Hemiptera: Aphididae) species of economic importance in Kenya using DNA barcodes and PCR-RFLP-based approach.},
journal = {Bulletin of entomological research},
volume = {106},
number = {1},
pages = {63-72},
doi = {10.1017/S0007485315000796},
pmid = {26490301},
issn = {1475-2670},
mesh = {Animals ; Aphids/*classification/genetics/growth &amp; development ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics/metabolism ; *Insect Control ; Insect Proteins/genetics/metabolism ; Kenya ; Molecular Sequence Data ; Nymph/classification/genetics/growth &amp; development ; Phylogeny ; *Polymerase Chain Reaction ; *Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; },
abstract = {Aphids are among pests of economic importance throughout the world. Together with transmitting plant viruses, aphids are capable of inflicting severe crop production losses. They also excrete honeydew that favours the growth of sooty mold which reduces the quality of vegetables and fruits and hence their market values. Rapid and accurate identification of aphids to the species level is a critical component in effective pest management and plant quarantine systems. Even though morphological taxonomy has made a tremendous impact on species-level identifications, polymorphism, morphological plasticity and immature stages are among the many challenges to accurate identification. In addition, their small size, presence of cryptic species and damaged specimens dictate the need for a strategy that will ensure timely and accurate identification. In this study, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP)-based on mitochondrial cytochrome c oxidase subunit I gene and DNA barcoding were applied to identify different aphid species collected from different agro-ecological zones of Kenya. Three restriction enzymes RsaI, AluI and Hinf1 produced patterns that allowed unambiguous identification of the species except Aphis craccivora and Aphis fabae. Analyses of the barcode region indicated intraspecific and interspecific sequence divergences of 0.08 and 6.63%, respectively. DNA barcoding identified all species, including the morphologically indistinguishable A. craccivora and A. fabae and separated two subspecies of A. fabae. Based on these results, both PCR-RFLPs and DNA barcoding could provide quick and accurate tools for identification of aphid species within Aphididae subsequently aiding in effective pest management programmes and enhance plant quarantine systems.},
}
@article {pmid26483497,
year = {2015},
author = {Brugman, MH and Wiekmeijer, AS and van Eggermond, M and Wolvers-Tettero, I and Langerak, AW and de Haas, EF and Bystrykh, LV and van Rood, JJ and de Haan, G and Fibbe, WE and Staal, FJ},
title = {Development of a diverse human T-cell repertoire despite stringent restriction of hematopoietic clonality in the thymus.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {112},
number = {44},
pages = {E6020-7},
pmid = {26483497},
issn = {1091-6490},
mesh = {Animals ; Bone Marrow Cells/*cytology ; Humans ; Mice ; Mice, Inbred NOD ; Mice, SCID ; T-Lymphocytes/*cytology ; Thymus Gland/*cytology ; },
abstract = {The fate and numbers of hematopoietic stem cells (HSC) and their progeny that seed the thymus constitute a fundamental question with important clinical implications. HSC transplantation is often complicated by limited T-cell reconstitution, especially when HSC from umbilical cord blood are used. Attempts to improve immune reconstitution have until now been unsuccessful, underscoring the need for better insight into thymic reconstitution. Here we made use of the NOD-SCID-IL-2Rγ(-/-) xenograft model and lentiviral cellular barcoding of human HSCs to study T-cell development in the thymus at a clonal level. Barcoded HSCs showed robust (>80% human chimerism) and reproducible myeloid and lymphoid engraftment, with T cells arising 12 wk after transplantation. A very limited number of HSC clones (<10) repopulated the xenografted thymus, with further restriction of the number of clones during subsequent development. Nevertheless, T-cell receptor rearrangements were polyclonal and showed a diverse repertoire, demonstrating that a multitude of T-lymphocyte clones can develop from a single HSC clone. Our data imply that intrathymic clonal fitness is important during T-cell development. As a consequence, immune incompetence after HSC transplantation is not related to the transplantation of limited numbers of HSC but to intrathymic events.},
}
@article {pmid26483030,
year = {2016},
author = {Malabat, C and Saveanu, C},
title = {Identification of Links Between Cellular Pathways by Genetic Interaction Mapping (GIM).},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1361},
number = {},
pages = {325-343},
doi = {10.1007/978-1-4939-3079-1_18},
pmid = {26483030},
issn = {1940-6029},
mesh = {Chromosome Mapping/methods ; DNA Barcoding, Taxonomic/*methods ; Epistasis, Genetic/*genetics ; *Gene Regulatory Networks ; Oligonucleotide Array Sequence Analysis/methods ; Protein Interaction Mapping/*methods ; Saccharomyces cerevisiae/genetics ; Sequence Deletion/genetics ; Signal Transduction/genetics ; },
abstract = {The yeast systematic deletion collection offered the basis for a number of different strategies that establish functional links between genes by analyzing the phenotype of cells that combine two different deletions or mutations. A distinguishing feature of the collection is the presence of molecular barcodes at each deleted locus, which can be used to quantify the presence and abundance of cells bearing a given allele in a complex mix. As a result, a large number of mutants can be tested in batch cultures, replacing tedious manipulation of thousands of individual strains with a barcode microarray readout. Barcode-based genetic screens like Genetic Interaction Mapping (GIM) thus require little investment in terms of specific equipment, are fast to perform, and allow precise measurements of double mutant growth rates for both aggravating (synthetic sick) and alleviating (epistatic) effects. We describe here protocols for preparing the pools of haploid double mutant S. cerevisiae cells, testing their composition with barcode microarrays, and analyzing the results to extract useful functional information.},
}
@article {pmid26482435,
year = {2015},
author = {Sady, H and Al-Mekhlafi, HM and Webster, BL and Ngui, R and Atroosh, WM and Al-Delaimy, AK and Nasr, NA and Chua, KH and Lim, YA and Surin, J},
title = {New insights into the genetic diversity of Schistosoma mansoni and S. haematobiumin Yemen.},
journal = {Parasites &amp; vectors},
volume = {8},
number = {},
pages = {544},
pmid = {26482435},
issn = {1756-3305},
mesh = {Adolescent ; Africa/epidemiology ; Animals ; Child ; Cohort Studies ; Cross-Sectional Studies ; DNA Barcoding, Taxonomic ; Feces/parasitology ; *Genetic Variation ; Genetics, Population ; Haplotypes ; Humans ; Indian Ocean Islands/epidemiology ; Neglected Diseases ; Phylogeography ; Prevalence ; Schistosoma haematobium/*genetics ; Schistosoma mansoni/*genetics ; Schistosomiasis haematobia/*epidemiology/parasitology ; Schistosomiasis mansoni/*epidemiology/parasitology ; Yemen/epidemiology ; },
abstract = {BACKGROUND: Human schistosomiasis is a neglected tropical disease of great importance that remains highly prevalent in Yemen, especially amongst rural communities. In order to investigate the genetic diversity of human Schistosoma species, a DNA barcoding study was conducted on S. mansoni and S. haematobium in Yemen.<br><br>METHODS: A cross-sectional study was conducted to collect urine and faecal samples from 400 children from five provinces in Yemen. The samples were examined for the presence of Schistosoma eggs. A partial fragment of the schistosome cox1 mitochondrial gene was analysed from each individual sample to evaluate the genetic diversity of the S. mansoni and S. haematobium infections. The data was also analysed together with previous published cox1 data for S. mansoni and S. haematobium from Africa and the Indian Ocean Islands.<br><br>RESULTS: Overall, 31.8&#xa0;% of participants were found to be excreting schistosome eggs in either the urine or faeces (8.0&#xa0;%&#x2009;S. mansoni and 22.5&#xa0;%&#x2009;S. haematobium). Nineteen unique haplotypes of S. mansoni were detected and split into four lineages. Furthermore, nine unique haplotypes of S. haematobium were identified that could be split into two distinct groups.<br><br>CONCLUSION: This study provides novel and interesting insights into the population diversity and structure of S. mansoni and S. haematobium in Yemen. The data adds to our understanding of the evolutionary history and phylogeography of these devastating parasites whilst the genetic information could support the control and monitoring of urogenital and intestinal schistosomiasis in these endemic areas.},
}
@article {pmid26481349,
year = {2016},
author = {McCaffrey, J and Sibert, J and Zhang, B and Zhang, Y and Hu, W and Riethman, H and Xiao, M},
title = {CRISPR-CAS9 D10A nickase target-specific fluorescent labeling of double strand DNA for whole genome mapping and structural variation analysis.},
journal = {Nucleic acids research},
volume = {44},
number = {2},
pages = {e11},
pmid = {26481349},
issn = {1362-4962},
support = {P30 CA010815/CA/NCI NIH HHS/United States ; HG005946/HG/NHGRI NIH HHS/United States ; R21 CA177395/CA/NCI NIH HHS/United States ; R21 HG007205/HG/NHGRI NIH HHS/United States ; CA177395/CA/NCI NIH HHS/United States ; P30 CA006927/CA/NCI NIH HHS/United States ; R01 HG005946/HG/NHGRI NIH HHS/United States ; },
mesh = {Amino Acid Substitution ; Bacterial Proteins/*chemistry/genetics ; CRISPR-Associated Protein 9 ; *CRISPR-Cas Systems ; Chromosome Mapping/*methods ; Chromosomes, Artificial, Bacterial/chemistry/metabolism ; *Clustered Regularly Interspaced Short Palindromic Repeats ; DNA/*chemistry/genetics ; Deoxyribonuclease I/chemistry/genetics ; Endonucleases/*chemistry/genetics ; Fluorescent Dyes/chemistry ; Genome, Human ; HIV-1/chemistry/genetics ; Humans ; In Situ Nick-End Labeling/*methods ; Mutation ; Plasmids/chemistry/metabolism ; Protein Structure, Tertiary ; RNA, Guide, CRISPR-Cas Systems/chemistry/genetics ; },
abstract = {We have developed a new, sequence-specific DNA labeling strategy that will dramatically improve DNA mapping in complex and structurally variant genomic regions, as well as facilitate high-throughput automated whole-genome mapping. The method uses the Cas9 D10A protein, which contains a nuclease disabling mutation in one of the two nuclease domains of Cas9, to create a guide RNA-directed DNA nick in the context of an in vitro-assembled CRISPR-CAS9-DNA complex. Fluorescent nucleotides are then incorporated adjacent to the nicking site with a DNA polymerase to label the guide RNA-determined target sequences. This labeling strategy is very powerful in targeting repetitive sequences as well as in barcoding genomic regions and structural variants not amenable to current labeling methods that rely on uneven distributions of restriction site motifs in the DNA. Importantly, it renders the labeled double-stranded DNA available in long intact stretches for high-throughput analysis in nanochannel arrays as well as for lower throughput targeted analysis of labeled DNA regions using alternative methods for stretching and imaging the labeled long DNA molecules. Thus, this method will dramatically improve both automated high-throughput genome-wide mapping as well as targeted analyses of complex regions containing repetitive and structurally variant DNA.},
}
@article {pmid26478705,
year = {2015},
author = {Jiang, LY and Chen, J and Qiao, GX},
title = {A new species of Mollitrichosiphum Suenaga from Taiwan Island (Hemiptera, Aphididae), based on morphological characteristics and DNA sequences.},
journal = {ZooKeys},
volume = {},
number = {524},
pages = {45-63},
pmid = {26478705},
issn = {1313-2989},
abstract = {A new species of Mollitrichosiphum Suenaga, Mollitrichosiphum tumorisiphum Qiao &amp; Jiang, sp. n., from Fagus longipetiolata in Taiwan island is described. Siphunculi of Mollitrichosiphum tumorisiphum in alatae are distinctly swollen on the distal part, unlike those of the other known species in the genus. Updated keys to apterous and alate viviparous females of all known Chinese species of Mollitrichosiphum are provided. The specimens studied are deposited in the National Zoological Museum of China, Institute of Zoology, Chinese Academy of Sciences, Beijing, China and the Natural History Museum, London, United Kingdom.},
}
@article {pmid26478262,
year = {2015},
author = {Freed, EF and Winkler, JD and Weiss, SJ and Garst, AD and Mutalik, VK and Arkin, AP and Knight, R and Gill, RT},
title = {Genome-Wide Tuning of Protein Expression Levels to Rapidly Engineer Microbial Traits.},
journal = {ACS synthetic biology},
volume = {4},
number = {11},
pages = {1244-1253},
doi = {10.1021/acssynbio.5b00133},
pmid = {26478262},
issn = {2161-5063},
mesh = {Escherichia coli/*genetics ; *Genetic Engineering ; *Genome, Bacterial ; Synthetic Biology ; },
abstract = {The reliable engineering of biological systems requires quantitative mapping of predictable and context-independent expression over a broad range of protein expression levels. However, current techniques for modifying expression levels are cumbersome and are not amenable to high-throughput approaches. Here we present major improvements to current techniques through the design and construction of E. coli genome-wide libraries using synthetic DNA cassettes that can tune expression over a ∼10(4) range. The cassettes also contain molecular barcodes that are optimized for next-generation sequencing, enabling rapid and quantitative tracking of alleles that have the highest fitness advantage. We show these libraries can be used to determine which genes and expression levels confer greater fitness to E. coli under different growth conditions.},
}
@article {pmid26475046,
year = {2016},
author = {de Kock, L and Wang, YC and Revil, T and Badescu, D and Rivera, B and Sabbaghian, N and Wu, M and Weber, E and Sandoval, C and Hopman, SM and Merks, JH and van Hagen, JM and Bouts, AH and Plager, DA and Ramasubramanian, A and Forsmark, L and Doyle, KL and Toler, T and Callahan, J and Engelenberg, C and Bouron-Dal Soglio, D and Priest, JR and Ragoussis, J and Foulkes, WD},
title = {High-sensitivity sequencing reveals multi-organ somatic mosaicism causing DICER1 syndrome.},
journal = {Journal of medical genetics},
volume = {53},
number = {1},
pages = {43-52},
doi = {10.1136/jmedgenet-2015-103428},
pmid = {26475046},
issn = {1468-6244},
mesh = {Child ; Child, Preschool ; Computational Biology/methods ; DEAD-box RNA Helicases/*genetics ; DNA Mutational Analysis ; Female ; *Genetic Association Studies ; High-Throughput Nucleotide Sequencing/*methods/standards ; Humans ; Loss of Heterozygosity ; Male ; *Mosaicism ; *Mutation ; Neoplasms, Multiple Primary/diagnosis/*genetics ; Phenotype ; Ribonuclease III/*genetics ; Sensitivity and Specificity ; Syndrome ; },
abstract = {BACKGROUND: Somatic mosaicism is being increasingly recognised as an important cause of non-Mendelian presentations of hereditary syndromes. A previous whole-exome sequencing study using DNA derived from peripheral blood identified mosaic mutations in DICER1 in two children with overgrowth and developmental delay as well as more typical phenotypes of germline DICER1 mutation. However, very-low-frequency mosaicism is difficult to detect, and thus, causal mutations can go unnoticed. Highly sensitive, cost-effective approaches are needed to molecularly diagnose these persons. We studied four children with multiple primary tumours known to be associated with the DICER1 syndrome, but in whom germline DICER1 mutations were not detected by conventional mutation detection techniques.<br><br>METHODS AND RESULTS: We observed the same missense mutation within the DICER1 RNase IIIb domain in multiple tumours from different sites in each patient, raising suspicion of somatic mosaicism. We implemented three different targeted-capture technologies, including the novel HaloPlex(HS) (Agilent Technologies), followed by deep sequencing, and confirmed that the identified mutations are mosaic in origin in three patients, detectable in 0.24-31% of sequencing reads in constitutional DNA. The mosaic origin of patient 4's mutation remains to be unequivocally established. We also discovered likely pathogenic second somatic mutations or loss of heterozygosity (LOH) in tumours from all four patients.<br><br>CONCLUSIONS: Mosaic DICER1 mutations are an important cause of the DICER1 syndrome in patients with severe phenotypes and often appear to be accompanied by second somatic truncating mutations or LOH in the associated tumours. Furthermore, the molecular barcode-containing HaloPlex(HS) provides the sensitivity required for detection of such low-level mosaic mutations and could have general applicability.},
}
@article {pmid26473612,
year = {2015},
author = {Jordaens, K and Goergen, G and Virgilio, M and Backeljau, T and Vokaer, A and De Meyer, M},
title = {DNA Barcoding to Improve the Taxonomy of the Afrotropical Hoverflies (Insecta: Diptera: Syrphidae).},
journal = {PloS one},
volume = {10},
number = {10},
pages = {e0140264},
pmid = {26473612},
issn = {1932-6203},
mesh = {Africa ; Animals ; Base Sequence ; *DNA Barcoding, Taxonomic ; Diptera/*classification/*genetics ; Molecular Sequence Data ; },
abstract = {The identification of Afrotropical hoverflies is very difficult because of limited recent taxonomic revisions and the lack of comprehensive identification keys. In order to assist in their identification, and to improve the taxonomy of this group, we constructed a reference dataset of 513 COI barcodes of 90 of the more common nominal species from Ghana, Togo, Benin and Nigeria (W Africa) and added ten publically available COI barcodes from nine nominal Afrotropical species to this (total: 523 COI barcodes; 98 nominal species; 26 genera). The identification accuracy of this dataset was evaluated with three methods (K2P distance-based, Neighbor-Joining (NJ) / Maximum Likelihood (ML) analysis, and using SpeciesIdentifier). Results of the three methods were highly congruent and showed a high identification success. Nine species pairs showed a low (< 0.03) mean interspecific K2P distance that resulted in several incorrect identifications. A high (> 0.03) maximum intraspecific K2P distance was observed in eight species and barcodes of these species not always formed single clusters in the NJ / ML analayses which may indicate the occurrence of cryptic species. Optimal K2P thresholds to differentiate intra- from interspecific K2P divergence were highly different among the three subfamilies (Eristalinae: 0.037, Syrphinae: 0.06, Microdontinae: 0.007-0.02), and among the different general suggesting that optimal thresholds are better defined at the genus level. In addition to providing an alternative identification tool, our study indicates that DNA barcoding improves the taxonomy of Afrotropical hoverflies by selecting (groups of) taxa that deserve further taxonomic study, and by attributing the unknown sex to species for which only one of the sexes is known.},
}
@article {pmid26472206,
year = {2016},
author = {Wang, D and Wang, YC and Wu, LJ and Liu, JX and Zhang, P and Jiao, J and Yan, H and Liu, T and Tian, CF and Chen, WX},
title = {Construction and pilot screening of a signature-tagged mutant library of Sinorhizobium fredii.},
journal = {Archives of microbiology},
volume = {198},
number = {2},
pages = {91-99},
doi = {10.1007/s00203-015-1161-9},
pmid = {26472206},
issn = {1432-072X},
mesh = {Cajanus/microbiology ; *Gene Library ; Genes, Bacterial/genetics ; Mutation ; Sinorhizobium fredii/*genetics ; Glycine max/microbiology ; Symbiosis/*genetics ; },
abstract = {Sinorhizobium fredii is well known for its ability to establish symbiosis with diverse legumes such as Glycine max (soybean, determinate nodules) and Cajanus cajan (pigeon pea, indeterminate nodules). In order to make screening of S. fredii genes related to symbiosis cost-effective, we constructed a large Tn5 insertion mutant library of S. fredii CCBAU45436 using the signature-tagged mutagenesis (STM) technique. This STM library contains a total of 25,500 independent mutants distributed in 17 sublibraries tagged by corresponding distinct DNA bar-code sequences. After the pilot screening of 255 mutants in 15 batches, Tag85-4, Tag4-17, Tag4-11 and Tag10-13 were found to have attenuated competitiveness (0-30 % in nodule occupation) compared to the wild-type strain when inoculated on soybean. Further characterization of these mutants suggests that Tag4-11 (a pyrC mutant) and Tag10-13 (a nrdJ mutant) are defective in establishing symbiosis with soybean. The pyrC mutant induced uninfected pseudonodules while the nrdJ mutant formed significantly more nodules containing bacteroids with poor persistence ability. When these two mutants were tested on pigeon pea, host-specific symbiotic defects were found. These results demonstrated the STM library as a valuable resource for identifying S. fredii genes relevant to symbiosis.},
}
@article {pmid26471555,
year = {2016},
author = {Di Pinto, A and Mottola, A and Marchetti, P and Bottaro, M and Terio, V and Bozzo, G and Bonerba, E and Ceci, E and Tantillo, G},
title = {Packaged frozen fishery products: species identification, mislabeling occurrence and legislative implications.},
journal = {Food chemistry},
volume = {194},
number = {},
pages = {279-283},
doi = {10.1016/j.foodchem.2015.07.135},
pmid = {26471555},
issn = {1873-7072},
mesh = {Animals ; DNA/genetics ; DNA Barcoding, Taxonomic ; Fisheries ; Food Labeling/legislation &amp; jurisprudence/standards ; *Food Packaging/legislation &amp; jurisprudence/standards ; Frozen Foods/*standards ; *Gadiformes/genetics ; Italy ; Seafood/*analysis ; },
abstract = {Given the increase in the international trade of packaged frozen fishery products, this study used DNA barcoding to investigate the breaded hake and plaice species, sold in Italian markets. The results of this study generally matched the ingredient list on the food label. Only 6 of the 120 samples were non-compliant. Specifically, breaded merluccius samples match the species shown in the list of ingredients on the label. Of the "breaded plaice" samples, 4/14 contained Lepidopsetta polyxystra and 2/14 Merluccius gayi, thus failing to match the ingredient list on the label. Considering the European legislation indicates that the label must not mislead consumers, but international trade and the use of similar terms for different products makes it complicated when a product from one country is introduced into another in which the niche already exists, clear labeling is strongly recommended in order to ensure that consumers can make conscious choices.},
}
@article {pmid26470942,
year = {2016},
author = {Muhammad Tahir, H and Akhtar, S},
title = {Services of DNA barcoding in different fields.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4463-4474},
doi = {10.3109/19401736.2015.1089572},
pmid = {26470942},
issn = {2470-1408},
mesh = {Animals ; Culicidae/parasitology ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/chemistry/classification/genetics ; Endangered Species ; Food Microbiology ; Forensic Sciences ; Insect Vectors/parasitology ; Mitochondria/genetics ; Water Microbiology ; },
abstract = {DNA barcoding is a new master key for species identification and has greatly accelerated the pace of species discovery. In this novel and cost-effective technique, a short DNA sequence from a standard region of mitochondrial "CO1" gene called "barcode" is used. At present, researchers all over the world are utilizing this powerful tool for investigating biodiversity, differentiating cryptic species, testing food authenticity, identifying parasites, vectors, insect pests, and predators, monitoring of illegal trade of animals and their products, and identifying forensically important insects. In addition, this technique can potentially be used to monitor quality of drinking water, quickly identify the indicator species of lakes, rivers, and streams, identify species with harmful attributes or medicinal properties, monitor smuggling of endangered plants and animals and their products, and disease investigations. Despite non-favorable criticism from a few researchers, DNA barcoding has achieved immense popularity in the scientific community, especially among biologists. The present review provides an overview of DNA barcoding and its practical applications. The limitation, future prospective and main informative platforms for DNA barcoding have also been discussed.},
}
@article {pmid26470715,
year = {2016},
author = {Rebello, E and Kee, S and Kowalski, A and Harun, N and Guindani, M and Goravanchi, F},
title = {Reduction of incorrect record accessing and charting patient electronic medical records in the perioperative environment.},
journal = {Health informatics journal},
volume = {22},
number = {4},
pages = {1055-1062},
doi = {10.1177/1460458215608901},
pmid = {26470715},
issn = {1741-2811},
support = {P30 CA016672/CA/NCI NIH HHS/United States ; },
mesh = {Chi-Square Distribution ; Documentation/*methods/*standards ; Electronic Health Records/*standards ; Forms and Records Control/*methods/standards ; Humans ; Operating Rooms/organization &amp; administration ; Retrospective Studies ; },
abstract = {Opening and charting in the incorrect patient electronic record presents a patient safety issue. The authors investigated the prevalence of reported errors and whether efforts utilizing the anesthesia time-out and barcoding have decreased the incidence of errors in opening and charting in the patient electronic medical record in the perioperative environment. The authors queried the database for all surgeries and procedures requiring anesthesia from January 2009 to September 2012. Of the 115,760 records of anesthesia procedures identified, there were 57 instances of incorrect record opening and charting during the study period. A decreasing trend was observed for all sites combined (p < 0.0001) and at the off-site locations (p = 0.0032). All locations and the off-site locations demonstrated a statistically significant decreasing pattern of errors over time. Barcoding and the anesthesia time-out may play an important role in decreasing errors in incorrect patient record opening in the perioperative environment.},
}
@article {pmid26470300,
year = {2015},
author = {Kang, TH and Lee, KS and Lee, HS},
title = {DNA Barcoding of the Korean Lymantria Hübner, 1819 (Lepidoptera: Erebidae: Lymantriinae) for Quarantine Inspection.},
journal = {Journal of economic entomology},
volume = {108},
number = {4},
pages = {1596-1611},
doi = {10.1093/jee/tov111},
pmid = {26470300},
issn = {0022-0493},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Insect Proteins/genetics ; Male ; Molecular Sequence Data ; Moths/anatomy &amp; histology/*classification/*genetics ; Phylogeny ; Quarantine ; Republic of Korea ; Sequence Analysis, DNA ; Wings, Animal/anatomy &amp; histology ; },
abstract = {DNA barcoding and morphological analyses of Korean Lymantria (Erebidae, Lepidoptera) were conducted for quarantine inspection. In DNA barcoding, Lymantria dispar identified through quarantine inspection was distinguished as three species, L. dispar asiatica, L. albescens, and L. xylina. Lymantria monacha, which is known as a single species in Korea, is revealed as containing three species, L. monacha, L. minomonis, and L. sugii. At the subspecies level, L. dispar dispar formed a single cluster, whereas L. d. asiatica and L. d. japonica formed a cluster containing both subspecies. In morphological re-examination on DNA barcoding results, L. dispar was distinguished from L. albescens by wing pattern, and from L. xylina by papillae anale. L. monacha and the related species were hard to be distinct from each other by using wing pattern, but it was easily distinct through comparison of genitalia. Therefore, DNA barcoding led to accurate identification in species level, but in subspecies level, only a taxon showing geographically far distance was discriminated from the others. These results may provide a taxonomic outline of the Korean Lymantria fauna and may be used as an identification reference for Lymantria species during quarantine inspection.},
}
@article {pmid26468319,
year = {2015},
author = {Liu, Y and Sun, W and Liu, C and Zhang, Y and Chen, Y and Song, M and Fan, G and Liu, X and Xiang, L and Zhang, Y},
title = {Identification of Hippophae species (Shaji) through DNA barcodes.},
journal = {Chinese medicine},
volume = {10},
number = {},
pages = {28},
pmid = {26468319},
issn = {1749-8546},
abstract = {BACKGROUND: The morphological identification of different Hippophae species (Shaji) was difficult. This study aims to discriminate between medicinal and non-medicinal Hippophae species by DNA barcodes, the ITS2, psbA-trnH, and a combination of ITS2 and psbA-trnH (ITS2 + psbA-trnH).<br><br>METHODS: DNA was extracted from the dried fruit samples. Primer pairs ITS2F/3R for ITS2 and psbAF/trnHR for psbA-trnH were used for PCR amplification. The purified PCR products were bidirectionally sequenced. Genetic distances were calculated according to the Kimura 2 parameter model and phylogenetic tree was constructed based on neighbor-joining (NJ) method, barcoding gap was also analyzed to assess identification efficiency.<br><br>RESULTS: Amplification and sequencing efficiencies for both ITS2 and psbA-trnH were 100&#xa0;%. Sequence data revealed that ITS2&#xa0;+&#xa0;psbA-trnH was the most suitable candidate barcode at the species and subspecies level. The closely related Hippophae species were effectively differentiated in the NJ tree.<br><br>CONCLUSION: The combination of the two loci, ITS2&#xa0;+&#xa0;psbA-trnH is applicable to the identification of medicinal and non-medicinal Hippophae species.},
}
@article {pmid26466881,
year = {2015},
author = {Mayers, CG and McNew, DL and Harrington, TC and Roeper, RA and Fraedrich, SW and Biedermann, PHW and Castrillo, LA and Reed, SE},
title = {Three genera in the Ceratocystidaceae are the respective symbionts of three independent lineages of ambrosia beetles with large, complex mycangia.},
journal = {Fungal biology},
volume = {119},
number = {11},
pages = {1075-1092},
doi = {10.1016/j.funbio.2015.08.002},
pmid = {26466881},
issn = {1878-6146},
mesh = {Ambrosia/parasitology ; Animals ; Ascomycota/classification/genetics/*isolation &amp; purification/*physiology ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; *Genetic Variation ; Molecular Sequence Data ; Peptide Elongation Factor 1/genetics ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; Weevils/*microbiology ; },
abstract = {The genus Ambrosiella accommodates species of Ceratocystidaceae (Microascales) that are obligate, mutualistic symbionts of ambrosia beetles, but the genus appears to be polyphyletic and more diverse than previously recognized. In addition to Ambrosiella xylebori, Ambrosiella hartigii, Ambrosiella beaveri, and Ambrosiella roeperi, three new species of Ambrosiella are described from the ambrosia beetle tribe Xyleborini: Ambrosiella nakashimae sp. nov. from Xylosandrus amputatus, Ambrosiella batrae sp. nov. from Anisandrus sayi, and Ambrosiella grosmanniae sp. nov. from Xylosandrus germanus. The genus Meredithiella gen. nov. is created for symbionts of the tribe Corthylini, based on Meredithiella norrisii sp. nov. from Corthylus punctatissimus. The genus Phialophoropsis is resurrected to accommodate associates of the Xyloterini, including Phialophoropsis trypodendri from Trypodendron scabricollis and Phialophoropsis ferruginea comb. nov. from Trypodendron lineatum. Each of the ten named species was distinguished by ITS rDNA barcoding and morphology, and the ITS rDNA sequences of four other putative species were obtained with Ceratocystidaceae-specific primers and template DNA extracted from beetles or galleries. These results support the hypothesis that each ambrosia beetle species with large, complex mycangia carries its own fungal symbiont. Conidiophore morphology and phylogenetic analyses using 18S (SSU) rDNA and TEF1α DNA sequences suggest that these three fungal genera within the Ceratocystidaceae independently adapted to symbiosis with the three respective beetle tribes. In turn, the beetle genera with large, complex mycangia appear to have evolved from other genera in their respective tribes that have smaller, less selective mycangia and are associated with Raffaelea spp. (Ophiostomatales).},
}
@article {pmid26466875,
year = {2015},
author = {Armitage, AD and Barbara, DJ and Harrison, RJ and Lane, CR and Sreenivasaprasad, S and Woodhall, JW and Clarkson, JP},
title = {Discrete lineages within Alternaria alternata species group: Identification using new highly variable loci and support from morphological characters.},
journal = {Fungal biology},
volume = {119},
number = {11},
pages = {994-1006},
doi = {10.1016/j.funbio.2015.06.012},
pmid = {26466875},
issn = {1878-6146},
mesh = {Alternaria/*classification/cytology/genetics ; Cluster Analysis ; Genetic Loci ; *Genetic Variation ; Humans ; Microscopy ; Molecular Sequence Data ; Multilocus Sequence Typing ; *Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; },
abstract = {The Alternaria alternata species group is ubiquitous in the environment acting as saprotrophs, human allergens, and plant pathogens. Many morphological species have been described within the group and it is unclear whether these represent re-descriptions of the same species or discrete evolutionary taxa. Sequencing of five loci identified three major lineages within the A. alternata species group. These loci included three new phylogenetic loci (TMA22, PGS1, and REV3) identified as highly variable based on publically available genome sequence data for Dothideomycete species. Lineages were identified as A. alternata ssp. arborescens, A. alternata ssp. tenuissima, and A. alternata ssp. gaisen in accordance with the placement of reference isolates. The phylogenetic results were supported by morphological analysis, which differentiated strains in A. alternata ssp. arborescens and A. alternata ssp. tenuissima and also aligned with previous morphological species descriptions for A. arborescens and A. tenuissima. However, phylogenetic analysis placed the morphologically described species A. alternata and A. mali within the A. alternata ssp. tenuissima and did not support them as discrete taxa. As A. alternata are of phytosanitary importance, the molecular loci used in this study offer new opportunities for molecular identification of isolates by national plant protection organizations.},
}
@article {pmid26466143,
year = {2015},
author = {Vollmers, C and De Vlaminck, I and Valantine, HA and Penland, L and Luikart, H and Strehl, C and Cohen, G and Khush, KK and Quake, SR},
title = {Monitoring pharmacologically induced immunosuppression by immune repertoire sequencing to detect acute allograft rejection in heart transplant patients: a proof-of-concept diagnostic accuracy study.},
journal = {PLoS medicine},
volume = {12},
number = {10},
pages = {e1001890},
pmid = {26466143},
issn = {1549-1676},
support = {RC4 AI092673/AI/NIAID NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; RC4AI092673/AI/NIAID NIH HHS/United States ; },
mesh = {Allografts ; B-Lymphocytes/*immunology ; Female ; Graft Rejection/*diagnosis/*immunology ; *Heart Transplantation ; Humans ; Immunosuppression Therapy/*methods ; Immunosuppressive Agents/*pharmacology ; Male ; Monitoring, Immunologic/*methods ; Prospective Studies ; Sensitivity and Specificity ; },
abstract = {BACKGROUND: It remains difficult to predict and to measure the efficacy of pharmacological immunosuppression. We hypothesized that measuring the B-cell repertoire would enable assessment of the overall level of immunosuppression after heart transplantation.<br><br>METHODS AND FINDINGS: In this proof-of-concept study, we implemented a molecular-barcode-based immune repertoire sequencing assay that sensitively and accurately measures the isotype and clonal composition of the circulating B cell repertoire. We used this assay to measure the temporal response of the B cell repertoire to immunosuppression after heart transplantation. We selected a subset of 12 participants from a larger prospective cohort study (ClinicalTrials.gov NCT01985412) that is ongoing at Stanford Medical Center and for which enrollment started in March 2010. This subset of 12 participants was selected to represent post-heart-transplant events, with and without acute rejection (six participants with moderate-to-severe rejection and six without). We analyzed 130 samples from these patients, with an average follow-up period of 15 mo. Immune repertoire sequencing enables the measurement of a patient's net state of immunosuppression (correlation with tacrolimus level, r = -0.867, 95% CI -0.968 to -0.523, p = 0.0014), as well as the diagnosis of acute allograft rejection, which is preceded by increased immune activity with a sensitivity of 71.4% (95% CI 30.3% to 94.9%) and a specificity of 82.0% (95% CI 72.1% to 89.1%) (cell-free donor-derived DNA as noninvasive gold standard). To illustrate the potential of immune repertoire sequencing to monitor atypical post-transplant trajectories, we analyzed two more patients, one with chronic infections and one with amyloidosis. A larger, prospective study will be needed to validate the power of immune repertoire sequencing to predict rejection events, as this proof-of-concept study is limited to a small number of patients who were selected based on several criteria including the availability of a large number of samples and the absence or presence of rejection events.<br><br>CONCLUSIONS: If confirmed in larger, prospective studies, the method described here has potential applications in the tailored management of post-transplant immunosuppression and, more broadly, as a method for assessing the overall activity of the immune system.},
}
@article {pmid26465744,
year = {2015},
author = {López, MC and León, CM and Fonseca, J and Reyes, P and Moncada, L and Olivera, MJ and Ramírez, JD},
title = {Molecular Epidemiology of Entamoeba: First Description of Entamoeba moshkovskii in a Rural Area from Central Colombia.},
journal = {PloS one},
volume = {10},
number = {10},
pages = {e0140302},
pmid = {26465744},
issn = {1932-6203},
mesh = {Adolescent ; Child ; Child, Preschool ; Coinfection ; Colombia/epidemiology ; Entamoeba/classification/*genetics ; Entamoebiasis/diagnosis/*epidemiology/*parasitology ; Feces/parasitology ; Humans ; Infant ; Infant, Newborn ; Phylogeny ; Prevalence ; RNA, Ribosomal, 18S/genetics ; *Rural Population ; },
abstract = {BACKGROUND: Entamoeba histolytica, E. dispar and E. moshkovskii are the most frequent species described in human infection where E. histolytica is the only true pathogen. The epidemiology of this infection is complex due to the absence of a routine exam that allows a correct discrimination of the Entamoeba species complex. Therefore, molecular methods appear as the unique epidemiological tool to accomplish the species discrimination. Herein, we conducted a cross-sectional study to determine the frequency of Entamoeba species infections in a group of asymptomatic individuals from a rural area in central Colombia.<br><br>A total of 181 fecal samples from asymptomatic children under 16 years old from the hamlet La V&#xed;rgen, Cundinamarca (Colombia) that voluntarily accepted to participate in the study were collected. The fecal samples were examined by light microscopy and DNA-extracted, subsequently submitted to molecular discrimination of E. dispar/E. histolytica/E. moshkovskii infection based on a multiplex PCR assay targeting the 18S rRNA fragment. To confirm the species description, twenty samples were randomly submitted to DNA sequencing of the aforementioned fragment. By direct microscopic examination, frequency of the complex E. histolytica/E. dispar/E. moshkovskii was 18.8% (34/181). PCR showed a frequency of 49.1% (89/181), discriminated as 23.2% (42/181) that were positive for E. dispar, 25.4% (46/181) for E. moshkovskii and 0.55% (1/ 181) for E. histolytica. Also, mixed infections were detected between E. dispar and E. moshkovskii at 4.42% (8/181) of the samples. Molecular barcoding confirmed the diagnosis depicted by the multiplex PCR assay.<br><br>CONCLUSIONS/SIGNIFICANCE: This is the first description of E. moshkovskii in Colombia and the second report in South-America to our knowledge. Our results suggest the need to unravel the true epidemiology of Entamoeba infections around the world, including the real pathogenic role that E. moshkovskii may have.},
}
@article {pmid26465068,
year = {2016},
author = {Doña, J and Ruiz-Ruano, FJ and Jovani, R},
title = {DNA barcoding of Iberian Peninsula and North Africa Tawny Owls Strix aluco suggests the Strait of Gibraltar as an important barrier for phylogeography.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4475-4478},
doi = {10.3109/19401736.2015.1089573},
pmid = {26465068},
issn = {2470-1408},
mesh = {Africa, Northern ; Animals ; Bayes Theorem ; DNA/chemistry/isolation &amp; purification/metabolism ; *DNA Barcoding, Taxonomic ; Genetic Variation ; Gibraltar ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Strigiformes/classification/*genetics ; },
abstract = {Eight subspecies have been proposed within the Tawny Owl (Strix aluco) species. However, recent molecular data have challenged this view, encouraging further work in this species complex. Here we reevaluated the taxonomic status between the North-Western African Tawny Owl, S. a. mauritanica, and its closest Iberian Tawny Owl population (from the S. a. sylvatica to S. a. aluco clade) separated by the Strait of Gibraltar. The Tawny Owl is a non-migratory and territorial species, and juvenile dispersal is restricted to a few kilometers around the natal site. This limited dispersal and the barrier imposed by the Strait of Gibraltar predicted a strong differentiation between the two populations. We tested this using DNA barcoding, Bayesian phylogenetic and species delimitation analysis. We found that an 81.1% of variation is due to the intergroups variation. In addition, the inter-intraspecific distances distribution revealed a barcoding gap among the two subspecies. Also, posterior probabilities and the PAB value allowed to reject the hypothesis that observed degree of distinctiveness is due to random coalescence processes. These findings clearly support the Strait of Gibraltar as an isolating barrier for this species. The subspecific status is confirmed and species status is even suggested for S. a. mauritanica.},
}
@article {pmid26459131,
year = {2015},
author = {Best, K and Oakes, T and Heather, JM and Shawe-Taylor, J and Chain, B},
title = {Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {14629},
pmid = {26459131},
issn = {2045-2322},
support = {MR/K006584/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Cell Line ; Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods/standards ; DNA Primers ; DNA, Complementary ; Humans ; *Polymerase Chain Reaction/methods/standards ; Software ; },
abstract = {The polymerase chain reaction (PCR) is one of the most widely used techniques in molecular biology. In combination with High Throughput Sequencing (HTS), PCR is widely used to quantify transcript abundance for RNA-seq, and in the context of analysis of T and B cell receptor repertoires. In this study, we combine DNA barcoding with HTS to quantify PCR output from individual target molecules. We develop computational tools that simulate both the PCR branching process itself, and the subsequent subsampling which typically occurs during HTS sequencing. We explore the influence of different types of heterogeneity on sequencing output, and compare them to experimental results where the efficiency of amplification is measured by barcodes uniquely identifying each molecule of starting template. Our results demonstrate that the PCR process introduces substantial amplification heterogeneity, independent of primer sequence and bulk experimental conditions. This heterogeneity can be attributed both to inherited differences between different template DNA molecules, and the inherent stochasticity of the PCR process. The results demonstrate that PCR heterogeneity arises even when reaction and substrate conditions are kept as constant as possible, and therefore single molecule barcoding is essential in order to derive reproducible quantitative results from any protocol combining PCR with HTS.},
}
@article {pmid26458175,
year = {2015},
author = {Rotem, A and Ram, O and Shoresh, N and Sperling, RA and Goren, A and Weitz, DA and Bernstein, BE},
title = {Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state.},
journal = {Nature biotechnology},
volume = {33},
number = {11},
pages = {1165-1172},
pmid = {26458175},
issn = {1546-1696},
support = {U54 HG006991/HG/NHGRI NIH HHS/United States ; U01 HL100395/HL/NHLBI NIH HHS/United States ; U54HG006991/HG/NHGRI NIH HHS/United States ; P50 HG006193/HG/NHGRI NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; P50HG006193/HG/NHGRI NIH HHS/United States ; U01HL100395/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Chromatin/genetics ; Chromatin Immunoprecipitation/*methods ; Computational Biology ; DNA Barcoding, Taxonomic ; Embryonic Stem Cells/*classification/*cytology ; Humans ; Mice ; Microfluidic Analytical Techniques ; Sequence Analysis, DNA ; Single-Cell Analysis/*methods ; },
abstract = {Chromatin profiling provides a versatile means to investigate functional genomic elements and their regulation. However, current methods yield ensemble profiles that are insensitive to cell-to-cell variation. Here we combine microfluidics, DNA barcoding and sequencing to collect chromatin data at single-cell resolution. We demonstrate the utility of the technology by assaying thousands of individual cells and using the data to deconvolute a mixture of ES cells, fibroblasts and hematopoietic progenitors into high-quality chromatin state maps for each cell type. The data from each single cell are sparse, comprising on the order of 1,000 unique reads. However, by assaying thousands of ES cells, we identify a spectrum of subpopulations defined by differences in chromatin signatures of pluripotency and differentiation priming. We corroborate these findings by comparison to orthogonal single-cell gene expression data. Our method for single-cell analysis reveals aspects of epigenetic heterogeneity not captured by transcriptional analysis alone.},
}
@article {pmid26457820,
year = {2016},
author = {Maranan, JB and Basiao, ZU and Quilang, JP},
title = {DNA barcoding of feral tilapias in Philippine lakes.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4302-4313},
doi = {10.3109/19401736.2015.1089478},
pmid = {26457820},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Conserved Sequence/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genetic Variation ; Genome, Mitochondrial/*genetics ; Lakes ; Philippines ; Phylogeny ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; Tilapia/*genetics ; },
abstract = {Tilapia (Oreochromis mossambicus) was first introduced to the Philippines in 1950 for aquaculture. Since then, other species of tilapia have been introduced to the country and some of them (mainly Oreochromis niloticus) have become established in lakes and other water bodies. In this study, DNA barcoding using the mitochondrial cytochrome c oxidase subunit I (COI) gene was done to assess the reliability of morphological identification and the degree of introgression among feral tilapias (Oreochromis spp.) in seven major Philippine lakes, namely Laguna de Bay, Lake Lanao, Taal Lake, Lake Mainit, Lake Naujan, Lake Bato, and Lake Buhi. Specimens were also collected from a private hatchery in Sual, Pangasinan to serve as reference. Morphological traits, Nucleotide BLAST (BLASTn), and Translated BLAST (BLASTx) analyses were used to classify the specimens. A Neighbor-Joining tree was constructed using the Kimura 2-Parameter method, incorporating 66 COI sequences generated from the study and 20 additional reference sequences obtained from GenBank. Three Oreochromis clusters were obtained and were classified as the O. niloticus group, O. mossambicus group, and O. aureus group, with bootstrap support values of 99%, 74%, and 99%, respectively. The mean K2P genetic distances within each group were 0.008%, 0.959%, and 0.086%, respectively. The clustering of COI sequences generated from this study corresponded with the results of the BLASTn analysis. Oreochromis hybrids were also found in all the lakes. The study highlights the usefulness of DNA barcoding for molecular identification and detection of introgressed individuals, with potential applications in management of feral stocks.},
}
@article {pmid26456472,
year = {2015},
author = {Pei, N and Erickson, DL and Chen, B and Ge, X and Mi, X and Swenson, NG and Zhang, JL and Jones, FA and Huang, CL and Ye, W and Hao, Z and Hsieh, CF and Lum, S and Bourg, NA and Parker, JD and Zimmerman, JK and McShea, WJ and Lopez, IC and Sun, IF and Davies, SJ and Ma, K and Kress, WJ},
title = {Closely-related taxa influence woody species discrimination via DNA barcoding: evidence from global forest dynamics plots.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {15127},
pmid = {26456472},
issn = {2045-2322},
mesh = {Chloroplasts/genetics ; Climate ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; Endoribonucleases/genetics ; Forests ; Gene Expression ; Genetic Loci ; Histidine-tRNA Ligase/genetics ; Nucleotidyltransferases/genetics ; Photosystem II Protein Complex/genetics ; *Phylogeny ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Analysis, DNA ; Species Specificity ; Trees/classification/*genetics ; },
abstract = {To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD). We quantified RSD by two DNA barcode combinations (rbcL + matK and rbcL + matK + trnH-psbA) using a monophyly-based method (GARLI). We defined two indexes of closely-related taxa (Gm/Gt and S/G ratios) and correlated these ratios with RSD. The combination of rbcL + matK averagely discriminated 88.65%, 83.84% and 72.51% at the local, regional and global scales, respectively. An additional locus trnH-psbA increased RSD by 2.87%, 1.49% and 3.58% correspondingly. RSD varied along a latitudinal gradient and were negatively correlated with ratios of closely-related taxa. Successes of species discrimination generally depend on scales in global FDPs. We suggested that the combination of rbcL + matK + trnH-psbA is currently applicable for DNA barcoding-based phylogenetic studies on forest communities.},
}
@article {pmid26450644,
year = {2016},
author = {Blanckenhorn, WU and Rohner, PT and Bernasconi, MV and Haugstetter, J and Buser, A},
title = {Is qualitative and quantitative metabarcoding of dung fauna biodiversity feasible?.},
journal = {Environmental toxicology and chemistry},
volume = {35},
number = {8},
pages = {1970-1977},
doi = {10.1002/etc.3275},
pmid = {26450644},
issn = {1552-8618},
mesh = {Animals ; *Biodiversity ; Coleoptera/classification/genetics ; Computational Biology ; *DNA Barcoding, Taxonomic ; Diptera/classification/genetics ; Environmental Monitoring/*methods ; Feasibility Studies ; *Feces ; },
abstract = {In biodiversity assessments, especially of small-bodied organisms for which taxonomic expertise is lacking, identification by genetic barcoding may be a cost-effective and efficient alternative to traditional identification of species by morphology, ecology, and behavior. The authors tested the feasibility and accuracy of such an approach using dung insects of practical relevance in ecotoxicological assessments of veterinary pharmaceutical residues in the environment. They produced 8 known mixtures that varied in absolute and relative composition of small-bodied and large-bodied species to see whether mitochondrial cytochrome c oxidase subunit 1 barcoding picks up all species qualitatively and quantitatively. As demonstrated before in other contexts, such metabarcoding of large numbers of dung insect specimens is principally possible using next-generation sequencing. The authors recovered most species in a sample (low type I error), at minimum permitting analysis of species richness. They obtained even quantitative responses reflecting the body size of the species, although the number of specimens was not well detected. The latter is problematic when calculating diversity indices. Nevertheless, the method yielded too many closely related false positives (type II error), thus generally overestimating species diversity and richness. These errors can be reduced by refining methods and data filtering, although this requires bioinformatics expertise often unavailable where such research is carried out. Identification by barcoding foremost hinges on a good reference database, which does not yet exist for dung organisms but would be worth developing for practical applications. Environ Toxicol Chem 2016;35:1970-1977. © 2015 SETAC.},
}
@article {pmid26448713,
year = {2015},
author = {Hogendoorn, K and Stevens, M and Leijs, R},
title = {DNA barcoding of euryglossine bees and the description of new species of Euhesma Michener (Hymenoptera, Colletidae, Euryglossinae).},
journal = {ZooKeys},
volume = {},
number = {520},
pages = {41-59},
pmid = {26448713},
issn = {1313-2989},
abstract = {This paper launches an open access DNA barcoding project "AUSBS" under the Barcoding of Life Datasystems (BOLD). The aims of the project are to help scientists who lack the necessary morphological knowledge to identify known species using molecular markers, to aid native bee specialists with the recognition of species groups that morphologically are difficult to define, and, eventually, to assist with the recognition of new species among known species. Using integrative taxonomy, i.e. morphological comparison to type specimens in Australian museum collections combined with phylogenetic analysis of a fragment of the mitochondrial DNA cytochrome c oxidase subunit I (mtCOI) gene sequences led to the recognition of four new species of Euhesma Michener (Hymenoptera: Colletidae: Euryglossini) collected during intensive surveys in remote Australian conservation areas, which are described. The new species are Euhesma micans, Euhesma lyngouriae, and Euhesma aulaca in a species group associated with Eremophila flowers, and Euhesma albamala in the walkeriana species group.},
}
@article {pmid26448709,
year = {2015},
author = {Straka, J and Alqarni, AS and Jůzová, K and Hannan, MA and Hinojosa-Díaz, IA and Engel, MS},
title = {Rediscovered parasitism of Andrena savignyi Spinola (Hymenoptera, Andrenidae) by Stylops (Strepsiptera, Stylopidae) and revised taxonomic status of the parasite.},
journal = {ZooKeys},
volume = {},
number = {519},
pages = {117-139},
pmid = {26448709},
issn = {1313-2989},
abstract = {Parasitism of Andrena (Suandrena) savignyi Spinola (Hymenoptera: Andrenidae) by Stylops Kirby (Strepsiptera: Stylopidae) has been recorded only once, and from an individual collected in Egypt almost a century ago, with the parasite described as Stylops savignyi Hofeneder. The recent rediscovery of this Stylops from an individual of Andrena savignyi permits a reinterpretation of the species and its affinities among other Stylops. The bee was collected at flowers of Zilla spinosa (Turra) Prantl. (Brassicaceae) in Amariah, Riyadh, Kingdom of Saudi Arabia. Based on DNA barcode sequences from material sampled across Africa, Asia, and Europe, it is apparent that Stylops savignyi is conspecific with Stylops nassonowi Pierce, and we accordingly synonymize this name (syn. n.), with the latter representing the senior and valid name for the species. A differential diagnosis is provided for Stylops nassonowi and the morphology of the female is described, as well as the first instars.},
}
@article {pmid26444714,
year = {2015},
author = {Adamowicz, SJ},
title = {International Barcode of Life: Evolution of a global research community.},
journal = {Genome},
volume = {58},
number = {5},
pages = {151-162},
doi = {10.1139/gen-2015-0094},
pmid = {26444714},
issn = {1480-3321},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Ecological Parameter Monitoring ; Humans ; },
abstract = {The 6th International Barcode of Life Conference (Guelph, Canada, 18-21 August 2015), themed Barcodes to Biomes, showcases the latest developments in DNA barcoding research and its diverse applications. The meeting also provides a venue for a global research community to share ideas and to initiate collaborations. All plenary and contributed abstracts are being published as an open-access special issue of Genome. Here, I use a comparison with the 3rd Conference (Mexico City, 2009) to highlight 10 recent and emerging trends that are apparent among the contributed abstracts. One of the outstanding trends is the rising proportion of abstracts that focus upon multiple socio-economically important applications of DNA barcoding, including studies of agricultural pests, quarantine and invasive species, wildlife forensics, disease vectors, biomonitoring of ecosystem health, and marketplace surveys evaluating the authenticity of seafood products and medicinal plants. Other key movements include the use of barcoding and metabarcoding approaches for dietary analyses-and for studies of food webs spanning three or more trophic levels-as well as the spread of next-generation sequencing methods in multiple contexts. In combination with the rising taxonomic and geographic scope of many barcoding iniatives, these developments suggest that several important questions in biology are becoming tractable. "What is this specimen on an agricultural shipment?", "Who eats whom in this whole food web?", and even "How many species are there?" are questions that may be answered in time periods ranging from a few years to one or a few decades. The next phases of DNA barcoding may expand yet further into prediction of community shifts with climate change and improved management of biological resources.},
}
@article {pmid26442762,
year = {2015},
author = {Gutzwiller, F and Dedeine, F and Kaiser, W and Giron, D and Lopez-Vaamonde, C},
title = {Correlation between the green-island phenotype and Wolbachia infections during the evolutionary diversification of Gracillariidae leaf-mining moths.},
journal = {Ecology and evolution},
volume = {5},
number = {18},
pages = {4049-4062},
pmid = {26442762},
issn = {2045-7758},
abstract = {Internally feeding herbivorous insects such as leaf miners have developed the ability to manipulate the physiology of their host plants in a way to best meet their metabolic needs and compensate for variation in food nutritional composition. For instance, some leaf miners can induce green-islands on yellow leaves in autumn, which are characterized by photosynthetically active green patches in otherwise senescing leaves. It has been shown that endosymbionts, and most likely bacteria of the genus Wolbachia, play an important role in green-island induction in the apple leaf-mining moth Phyllonorycter blancardella. However, it is currently not known how widespread is this moth-Wolbachia-plant interaction. Here, we studied the co-occurrence between Wolbachia and the green-island phenotype in 133 moth specimens belonging to 74 species of Lepidoptera including 60 Gracillariidae leaf miners. Using a combination of molecular phylogenies and ecological data (occurrence of green-islands), we show that the acquisitions of the green-island phenotype and Wolbachia infections have been associated through the evolutionary diversification of Gracillariidae. We also found intraspecific variability in both green-island formation and Wolbachia infection, with some species being able to form green-islands without being infected by Wolbachia. In addition, Wolbachia variants belonging to both A and B supergroups were found to be associated with green-island phenotype suggesting several independent origins of green-island induction. This study opens new prospects and raises new questions about the ecology and evolution of the tripartite association between Wolbachia, leaf miners, and their host plants.},
}
@article {pmid26437865,
year = {2015},
author = {van Blitterswijk, M and Gendron, TF and Baker, MC and DeJesus-Hernandez, M and Finch, NA and Brown, PH and Daughrity, LM and Murray, ME and Heckman, MG and Jiang, J and Lagier-Tourenne, C and Edbauer, D and Cleveland, DW and Josephs, KA and Parisi, JE and Knopman, DS and Petersen, RC and Petrucelli, L and Boeve, BF and Graff-Radford, NR and Boylan, KB and Dickson, DW and Rademakers, R},
title = {Novel clinical associations with specific C9ORF72 transcripts in patients with repeat expansions in C9ORF72.},
journal = {Acta neuropathologica},
volume = {130},
number = {6},
pages = {863-876},
pmid = {26437865},
issn = {1432-0533},
support = {R21 NS089979/NS/NINDS NIH HHS/United States ; P50 AG005131/AG/NIA NIH HHS/United States ; P50 AG016574/AG/NIA NIH HHS/United States ; U54 NS092091/NS/NINDS NIH HHS/United States ; P01 NS084974/NS/NINDS NIH HHS/United States ; R01 NS080882/NS/NINDS NIH HHS/United States ; },
mesh = {Aged ; Aged, 80 and over ; Amyotrophic Lateral Sclerosis/genetics/metabolism ; C9orf72 Protein ; Cerebellum/*metabolism ; *DNA Repeat Expansion ; Female ; Frontal Lobe/*metabolism ; Frontotemporal Dementia/genetics/metabolism ; Genetic Association Studies ; Genetic Variation ; Heterozygote ; Humans ; Introns ; Male ; Middle Aged ; Motor Neuron Disease/genetics/metabolism ; Promoter Regions, Genetic ; Proteins/*genetics/*metabolism ; Survival Analysis ; Tissue Banks ; },
abstract = {The loss of chromosome 9 open reading frame 72 (C9ORF72) expression, associated with C9ORF72 repeat expansions, has not been examined systematically. Three C9ORF72 transcript variants have been described thus far; the GGGGCC repeat is located between two non-coding exons (exon 1a and exon 1b) in the promoter region of transcript variant 2 (NM_018325.4) or in the first intron of variant 1 (NM_145005.6) and variant 3 (NM_001256054.2). We studied C9ORF72 expression in expansion carriers (n = 56) for whom cerebellum and/or frontal cortex was available. Using quantitative real-time PCR and digital molecular barcoding techniques, we assessed total C9ORF72 transcripts, variant 1, variant 2, variant 3, and intron containing transcripts [upstream of the expansion (intron 1a) and downstream of the expansion (intron 1b)]; the latter were correlated with levels of poly(GP) and poly(GA) proteins aberrantly translated from the expansion as measured by immunoassay (n = 50). We detected a decrease in expansion carriers as compared to controls for total C9ORF72 transcripts, variant 1, and variant 2: the strongest association was observed for variant 2 (quantitative real-time PCR cerebellum: median 43 %, p = 1.26e-06, and frontal cortex: median 58 %, p = 1.11e-05; digital molecular barcoding cerebellum: median 31 %, p = 5.23e-10, and frontal cortex: median 53 %, p = 5.07e-10). Importantly, we revealed that variant 1 levels greater than the 25th percentile conferred a survival advantage [digital molecular barcoding cerebellum: hazard ratio (HR) 0.31, p = 0.003, and frontal cortex: HR 0.23, p = 0.0001]. When focusing on intron containing transcripts, analysis of the frontal cortex revealed an increase of potentially truncated transcripts in expansion carriers as compared to controls [digital molecular barcoding frontal cortex (intron 1a): median 272 %, p = 0.003], with the highest levels in patients pathologically diagnosed with frontotemporal lobar degeneration. In the cerebellum, our analysis suggested that transcripts were less likely to be truncated and, excitingly, we discovered that intron containing transcripts were associated with poly(GP) levels [digital molecular barcoding cerebellum (intron 1a): r = 0.33, p = 0.02, and (intron 1b): r = 0.49, p = 0.0004] and poly(GA) levels [digital molecular barcoding cerebellum (intron 1a): r = 0.34, p = 0.02, and (intron 1b): r = 0.38, p = 0.007]. In summary, we report decreased expression of specific C9ORF72 transcripts and provide support for the presence of truncated transcripts as well as pre-mRNAs that may serve as templates for RAN translation. We further show that higher C9ORF72 levels may have beneficial effects, which warrants caution in the development of new therapeutic approaches.},
}
@article {pmid26426290,
year = {2016},
author = {Prosser, SW and deWaard, JR and Miller, SE and Hebert, PD},
title = {DNA barcodes from century-old type specimens using next-generation sequencing.},
journal = {Molecular ecology resources},
volume = {16},
number = {2},
pages = {487-497},
doi = {10.1111/1755-0998.12474},
pmid = {26426290},
issn = {1755-0998},
support = {5UO1TW006671/TW/FIC NIH HHS/United States ; },
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Lepidoptera/*genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; },
abstract = {Type specimens have high scientific importance because they provide the only certain connection between the application of a Linnean name and a physical specimen. Many other individuals may have been identified as a particular species, but their linkage to the taxon concept is inferential. Because type specimens are often more than a century old and have experienced conditions unfavourable for DNA preservation, success in sequence recovery has been uncertain. This study addresses this challenge by employing next-generation sequencing (NGS) to recover sequences for the barcode region of the cytochrome c oxidase 1 gene from small amounts of template DNA. DNA quality was first screened in more than 1800 century-old type specimens of Lepidoptera by attempting to recover 164-bp and 94-bp reads via Sanger sequencing. This analysis permitted the assignment of each specimen to one of three DNA quality categories--high (164-bp sequence), medium (94-bp sequence) or low (no sequence). Ten specimens from each category were subsequently analysed via a PCR-based NGS protocol requiring very little template DNA. It recovered sequence information from all specimens with average read lengths ranging from 458 bp to 610 bp for the three DNA categories. By sequencing ten specimens in each NGS run, costs were similar to Sanger analysis. Future increases in the number of specimens processed in each run promise substantial reductions in cost, making it possible to anticipate a future where barcode sequences are available from most type specimens.},
}
@article {pmid26423978,
year = {2015},
author = {Poullet, N and Braendle, C},
title = {Sampling and Isolation of C. elegans from the Natural Habitat.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1327},
number = {},
pages = {221-229},
doi = {10.1007/978-1-4939-2842-2_16},
pmid = {26423978},
issn = {1940-6029},
mesh = {Animals ; Caenorhabditis elegans/classification/genetics/*isolation &amp; purification ; Cryopreservation/methods ; *Ecosystem ; Genetic Variation ; },
abstract = {Wild populations of the model organism C. elegans allow characterization of natural genetic variation underlying diverse phenotypic traits. Here we provide a simple protocol on how to sample and rapidly identify C. elegans wild isolates. We outline how to find suitable habitats and organic substrates, followed by describing isolation and identification of C. elegans live cultures based on easily recognizable morphological characteristics, molecular barcodes and/or mating tests. This protocol uses standard laboratory equipment and requires no prior knowledge of C. elegans biology.},
}
@article {pmid26421127,
year = {2015},
author = {Zakeri, H and Shokohi, T and Badali, H and Mayahi, S and Didehdar, M},
title = {Use of Padlock Probes and Rolling Circle Amplification (RCA) for Rapid Identification of Trichophyton Species, Related to Human and Animal Disorder.},
journal = {Jundishapur journal of microbiology},
volume = {8},
number = {7},
pages = {e19107},
pmid = {26421127},
issn = {2008-3645},
abstract = {BACKGROUND: The high degree of phenotypic similarity among Trichophyton species makes their identification difficult.<br><br>OBJECTIVES: The current study aims to establish the use of rolling circle amplification (RCA) based on internal transcribed spacer ribosomal DNA (ITS rDNA) as a powerful, simple, and rapid procedure for distinguishing closely related organisms, and specifically to identify Trichophyton species, which cause human and animal disorders.<br><br>MATERIALS AND METHODS: A total of sixty-one isolates belonging to three species of Trichophyton were identified to the species level based on microscopic and macroscopic examinations and their ITS rDNA regions were sequenced. Three specific circular oligonucleotide probes targeting the ITS1 and ITS2 regions were designed to differentiate Trichophyton rubrum, T. mentagrophytes, and T. tonsurans.<br><br>RESULTS: Of the 61 putative Trichophyton clinical isolates, 52 were identified to the species level. The most common species was T. mentagrophytes var. interdigitale (31 isolates), followed by T. rubrum (11 isolates), T. tonsurans (9 isolates), and T. violaceum (1 isolates); moreover, 9 isolates were identified as non-Trichophyton species. The RCA method correctly identified four Trichophyton species and was 100% specific for each species. Neither cross-reaction between the examined species of Trichophyton nor false positive or false negative results were observed.<br><br>CONCLUSIONS: Species identification of Trichophyton is crucially important for epidemiological and phylogenetic purposes and for genotype delineation. RCA based on ITS polymorphisms can be used to generate identification barcodes and as an alternative to DNA sequencing; it is a very fast, specific, and economical tool for species identification.},
}
@article {pmid26419971,
year = {2015},
author = {Grampp, G and Felix, T},
title = {Pharmacovigilance Considerations for Biosimilars in the USA.},
journal = {BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy},
volume = {29},
number = {5},
pages = {309-321},
pmid = {26419971},
issn = {1179-190X},
mesh = {*Adverse Drug Reaction Reporting Systems ; *Biosimilar Pharmaceuticals ; Humans ; *Pharmacovigilance ; United States ; },
abstract = {In 2015, five or more biosimilars may be approved in the USA. Because no two biologic medicines are identical, postapproval safety monitoring will be critical to detect potential differences in safety signals between a biosimilar, its reference product, and other biosimilars. Postapproval safety monitoring in the USA uses two signal detection systems: spontaneous reporting systems (SRSs) and active surveillance (AS) systems. Both depend on accurate identification of the specific product(s) dispensed or administered to patients, which may be compromised when products from multiple manufacturers share common drug nomenclature or coding. Product identification can present challenges across different healthcare settings, including inpatient and ambulatory care. Common oral-dosage drugs are predominantly dispensed directly to patients by pharmacists, whereas most injectable drugs, including biologics, are administered to patients by healthcare professionals in outpatient clinics or hospitals. Thus, the effectiveness of SRS and AS mechanisms in both pharmacy and medical channels must be given greater consideration as biotechnology matures. In this article, we describe these systems and their limitations. We identify challenges and opportunities for product-specific safety surveillance of biologics in both the pharmacy and medical settings and provide recommendations to improve biologic safety surveillance under the current and future systems envisioned in the Drug Quality and Security Act. As biosimilars are integrated into existing pharmacovigilance systems, distinguishable nonproprietary names and codes for all biologics, as well as other opportunities to improve traceability (e.g., increased use of barcodes), must be considered to ensure patient safety and confidence in this new class of drugs.},
}
@article {pmid26419702,
year = {2015},
author = {Viggiano, D and Srivastava, DP and Speranza, L and Perrone-Capano, C and Bellenchi, GC and di Porzio, U and Buckley, NJ},
title = {Quantifying barcodes of dendritic spines using entropy-based metrics.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {14622},
pmid = {26419702},
issn = {2045-2322},
support = {MR/L021064/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Algorithms ; Animals ; Dendrites ; *Dendritic Spines ; Mice ; Mice, Knockout ; *Models, Biological ; *Neuronal Plasticity ; Neurons/*cytology/*physiology ; },
abstract = {Spine motility analysis has become the mainstay for investigating synaptic plasticity but is limited in its versatility requiring complex, non automatized instrumentations. We describe an entropy-based method for determining the spatial distribution of dendritic spines that allows successful estimation of spine motility from still images. This method has the potential to extend the applicability of spine motility analysis to ex vivo preparations.},
}
@article {pmid26417993,
year = {2015},
author = {Raupach, MJ and Barco, A and Steinke, D and Beermann, J and Laakmann, S and Mohrbeck, I and Neumann, H and Kihara, TC and Pointner, K and Radulovici, A and Segelken-Voigt, A and Wesse, C and Knebelsberger, T},
title = {The Application of DNA Barcodes for the Identification of Marine Crustaceans from the North Sea and Adjacent Regions.},
journal = {PloS one},
volume = {10},
number = {9},
pages = {e0139421},
pmid = {26417993},
issn = {1932-6203},
mesh = {Animals ; Crustacea/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Reproducibility of Results ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {During the last years DNA barcoding has become a popular method of choice for molecular specimen identification. Here we present a comprehensive DNA barcode library of various crustacean taxa found in the North Sea, one of the most extensively studied marine regions of the world. Our data set includes 1,332 barcodes covering 205 species, including taxa of the Amphipoda, Copepoda, Decapoda, Isopoda, Thecostraca, and others. This dataset represents the most extensive DNA barcode library of the Crustacea in terms of species number to date. By using the Barcode of Life Data Systems (BOLD), unique BINs were identified for 198 (96.6%) of the analyzed species. Six species were characterized by two BINs (2.9%), and three BINs were found for the amphipod species Gammarus salinus Spooner, 1947 (0.4%). Intraspecific distances with values higher than 2.2% were revealed for 13 species (6.3%). Exceptionally high distances of up to 14.87% between two distinct but monophyletic clusters were found for the parasitic copepod Caligus elongatus Nordmann, 1832, supporting the results of previous studies that indicated the existence of an overlooked sea louse species. In contrast to these high distances, haplotype-sharing was observed for two decapod spider crab species, Macropodia parva Van Noort &amp; Adema, 1985 and Macropodia rostrata (Linnaeus, 1761), underlining the need for a taxonomic revision of both species. Summarizing the results, our study confirms the application of DNA barcodes as highly effective identification system for the analyzed marine crustaceans of the North Sea and represents an important milestone for modern biodiversity assessment studies using barcode sequences.},
}
@article {pmid26413972,
year = {2015},
author = {Li, N and Shen, Q and Wang, J and Han, C and Ji, R and Li, F and Jiang, T},
title = {Tetrodotoxin detection and species identification of pufferfish in retail roasted fish fillet by DNA barcoding in China.},
journal = {Food additives &amp; contaminants. Part A, Chemistry, analysis, control, exposure &amp; risk assessment},
volume = {32},
number = {12},
pages = {2148-2153},
doi = {10.1080/19440049.2015.1087056},
pmid = {26413972},
issn = {1944-0057},
mesh = {Animals ; China ; Cooking ; DNA/*genetics ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Enzyme-Linked Immunosorbent Assay ; Fish Products/analysis ; Food Contamination/*analysis ; Humans ; Phylogeny ; Poisons/*isolation &amp; purification ; Tetraodontiformes/classification/*physiology ; Tetrodotoxin/*isolation &amp; purification ; },
abstract = {This study identifies the pufferfish species and detects tetrodotoxin (TTX) in roasted fish fillet samples collected in Beijing, Qingdao and Xiamen, China. The cytochrome c oxidase I (COI) gene was used as the target gene for identification of the pufferfish species in the samples. Enzyme-linked immunosorbent assay (ELISA) screened the TTX levels in samples that had been detected as containing pufferfish by DNA barcode. A total of 125 samples were identified by DNA barcodes; 32 (26%) samples contained pufferfish composition and, among them, 26 (81%) were the highly toxic species Lagocephalus lunaris. All 32 samples containing the pufferfish composition were positive for TTX with levels ranging from 100 to 63,800 ng g(-1). Most of the 32 samples contained the highly toxic L. lunaris. Based on the results, we suggest that the monitoring of roasted fish fillet should be strengthened and the processing procedures should be standardised to minimise TTX poisoning caused by pufferfish.},
}
@article {pmid26412424,
year = {2015},
author = {Chen, JJ and Zhao, QS and Liu, YL and Zha, SH and Zhao, B},
title = {Identification of maca (Lepidium meyenii Walp.) and its adulterants by a DNA-barcoding approach based on the ITS sequence.},
journal = {Chinese journal of natural medicines},
volume = {13},
number = {9},
pages = {653-659},
doi = {10.1016/S1875-5364(15)30062-5},
pmid = {26412424},
issn = {1875-5364},
mesh = {DNA Barcoding, Taxonomic/methods ; DNA, Intergenic/*analysis ; DNA, Plant/*analysis ; Drug Contamination/*prevention &amp; control ; Humans ; Lepidium/*genetics ; Phytotherapy ; },
abstract = {Maca (Lepidium meyenii) is an herbaceous plant that grows in high plateaus and has been used as both food and folk medicine for centuries because of its benefits to human health. In the present study, ITS (internal transcribed spacer) sequences of forty-three maca samples, collected from different regions or vendors, were amplified and analyzed. The ITS sequences of nineteen potential adulterants of maca were also collected and analyzed. The results indicated that the ITS sequence of maca was consistent in all samples and unique when compared with its adulterants. Therefore, this DNA-barcoding approach based on the ITS sequence can be used for the molecular identification of maca and its adulterants.},
}
@article {pmid26406615,
year = {2015},
author = {Osathanunkul, M and Suwannapoom, C and Ounjai, S and Rora, JA and Madesis, P and de Boer, H},
title = {Refining DNA Barcoding Coupled High Resolution Melting for Discrimination of 12 Closely Related Croton Species.},
journal = {PloS one},
volume = {10},
number = {9},
pages = {e0138888},
pmid = {26406615},
issn = {1932-6203},
mesh = {Base Composition ; Base Sequence ; Croton/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/*analysis ; DNA, Plant/analysis ; Genetic Markers/genetics ; Phylogeny ; Species Specificity ; },
abstract = {DNA barcoding coupled high resolution melting (Bar-HRM) is an emerging method for species discrimination based on DNA dissociation kinetics. The aim of this work was to evaluate the suitability of different primer sets, derived from selected DNA regions, for Bar-HRM analysis of species in Croton (Euphorbiaceae), one of the largest genera of plants with over 1,200 species. Seven primer pairs were evaluated (matK, rbcL1, rbcL2, rbcL3, rpoC, trnL and ITS1) from four plastid regions, matK, rbcL, rpoC, and trnL, and the nuclear ribosomal marker ITS1. The primer pair derived from the ITS1 region was the single most effective region for the identification of the tested species, whereas the rbcL1 primer pair gave the lowest resolution. It was observed that the ITS1 barcode was the most useful DNA barcoding region overall for species discrimination out of all of the regions and primers assessed. Our Bar-HRM results here also provide further support for the hypothesis that both sequence and base composition affect DNA duplex stability.},
}
@article {pmid26406595,
year = {2015},
author = {Lin, X and Stur, E and Ekrem, T},
title = {Exploring Genetic Divergence in a Species-Rich Insect Genus Using 2790 DNA Barcodes.},
journal = {PloS one},
volume = {10},
number = {9},
pages = {e0138993},
pmid = {26406595},
issn = {1932-6203},
mesh = {Animals ; Chironomidae/*classification/enzymology/genetics ; DNA Barcoding, Taxonomic/*standards ; Databases, Genetic ; Electron Transport Complex IV/*analysis ; Genetic Variation ; Insect Proteins/analysis ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {DNA barcoding using a fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) has proven to be successful for species-level identification in many animal groups. However, most studies have been focused on relatively small datasets or on large datasets of taxonomically high-ranked groups. We explore the quality of DNA barcodes to delimit species in the diverse chironomid genus Tanytarsus (Diptera: Chironomidae) by using different analytical tools. The genus Tanytarsus is the most species-rich taxon of tribe Tanytarsini (Diptera: Chironomidae) with more than 400 species worldwide, some of which can be notoriously difficult to identify to species-level using morphology. Our dataset, based on sequences generated from own material and publicly available data in BOLD, consist of 2790 DNA barcodes with a fragment length of at least 500 base pairs. A neighbor joining tree of this dataset comprises 131 well separated clusters representing 121 morphological species of Tanytarsus: 77 named, 16 unnamed and 28 unidentified theoretical species. For our geographically widespread dataset, DNA barcodes unambiguously discriminate 94.6% of the Tanytarsus species recognized through prior morphological study. Deep intraspecific divergences exist in some species complexes, and need further taxonomic studies using appropriate nuclear markers as well as morphological and ecological data to be resolved. The DNA barcodes cluster into 120-242 molecular operational taxonomic units (OTUs) depending on whether Objective Clustering, Automatic Barcode Gap Discovery (ABGD), Generalized Mixed Yule Coalescent model (GMYC), Poisson Tree Process (PTP), subjective evaluation of the neighbor joining tree or Barcode Index Numbers (BINs) are used. We suggest that a 4-5% threshold is appropriate to delineate species of Tanytarsus non-biting midges.},
}
@article {pmid26399188,
year = {2015},
author = {Balasundaram, SV and Engh, IB and Skrede, I and Kauserud, H},
title = {How many DNA markers are needed to reveal cryptic fungal species?.},
journal = {Fungal biology},
volume = {119},
number = {10},
pages = {940-945},
doi = {10.1016/j.funbio.2015.07.006},
pmid = {26399188},
issn = {1878-6146},
mesh = {Basidiomycota/*classification/*genetics ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Genetic Loci ; *Genetic Markers ; *Genetic Variation ; Molecular Sequence Data ; Mycology/*methods ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {In the fungal kingdom there is a high prevalence of morphologically defined species that includes closely related 'cryptic' biological species with similar phenotypes. Due to evolutionary processes like incomplete lineage sorting and introgression through hybridization, several independent DNA markers are essential to resolve closely related fungal species. In this study we wanted to analyze how many independent loci are necessary to reveal the cryptic species, using the genus Serpula as a model system. DNA sequences from ten different DNA loci, eight nuclear and two mitochondrial DNA markers, were obtained from various cryptic species within Serpula. The inclusion of five loci gave a highly confident separation of the cryptic species. Several other loci performed better than the standard DNA barcoding marker ITS in separating the cryptic species. The DNA loci tub, hsp, rpb2 and tef gave, on average, best support for the different cryptic species in single gene trees. We conclude that the analyses of a few but informative independent DNA loci, such as tub, hsp, rpb2 and tef in addition to the standard DNA barcode ITS, may give a good indication about the existence of cryptic species in fungi.},
}
@article {pmid26392843,
year = {2015},
author = {Sahar, L and Faler, G and Hristov, E and Hughes, S and Lee, L and Westnedge, C and Erickson, B and Nichols, B},
title = {Development of the Inventory Management and Tracking System (IMATS) to Track the Availability of Public Health Department Medical Countermeasures During Public Health Emergencies.},
journal = {Online journal of public health informatics},
volume = {7},
number = {2},
pages = {e212},
pmid = {26392843},
issn = {1947-2579},
abstract = {OBJECTIVE: To bridge gaps identified during the 2009 H1N1 influenza pandemic by developing a system that provides public health departments improved capability to manage and track medical countermeasures at the state and local levels and to report their inventory levels to the Centers for Disease Control and Prevention (CDC).<br><br>MATERIALS AND METHODS: The CDC Countermeasure Tracking Systems (CTS) program designed and implemented the Inventory Management and Tracking System (IMATS) to manage, track, and report medical countermeasure inventories at the state and local levels. IMATS was designed by CDC in collaboration with state and local public health departments to ensure a "user-centered design approach." A survey was completed to assess functionality and user satisfaction.<br><br>RESULTS: IMATS was deployed in September 2011 and is provided at no cost to public health departments. Many state and local public health departments nationwide have adopted IMATS and use it to track countermeasure inventories during public health emergencies and daily operations.<br><br>DISCUSSION: A successful response to public health emergencies requires efficient, accurate reporting of countermeasure inventory levels. IMATS is designed to support both emergency operations and everyday activities. Future improvements to the system include integrating barcoding technology and streamlining user access. To maintain system readiness, we continue to collect user feedback, improve technology, and enhance its functionality.<br><br>CONCLUSION: IMATS satisfies the need for a system for monitoring and reporting health departments' countermeasure quantities so that decision makers are better informed. The "user-centered design approach" was successful, as evident by the many public health departments that adopted IMATS.},
}
@article {pmid26392826,
year = {2015},
author = {Freitag, C and Noble, C and Fritzsche, J and Persson, F and Reiter-Schad, M and Nilsson, AN and Granéli, A and Ambjörnsson, T and Mir, KU and Tegenfeldt, JO},
title = {Visualizing the entire DNA from a chromosome in a single frame.},
journal = {Biomicrofluidics},
volume = {9},
number = {4},
pages = {044114},
pmid = {26392826},
issn = {1932-1058},
abstract = {The contiguity and phase of sequence information are intrinsic to obtain complete understanding of the genome and its relationship to phenotype. We report the fabrication and application of a novel nanochannel design that folds megabase lengths of genomic DNA into a systematic back-and-forth meandering path. Such meandering nanochannels enabled us to visualize the complete 5.7 Mbp (1 mm) stained DNA length of a Schizosaccharomyces pombe chromosome in a single frame of a CCD. We were able to hold the DNA in situ while implementing partial denaturation to obtain a barcode pattern that we could match to a reference map using the Poland-Scheraga model for DNA melting. The facility to compose such long linear lengths of genomic DNA in one field of view enabled us to directly visualize a repeat motif, count the repeat unit number, and chart its location in the genome by reference to unique barcode motifs found at measurable distances from the repeat. Meandering nanochannel dimensions can easily be tailored to human chromosome scales, which would enable the whole genome to be visualized in seconds.},
}
@article {pmid26390647,
year = {2015},
author = {Song, XN and Gu, X and Liu, CS and Li, YP and Zhang, X and Zhang, Y and Liu, Y and Ma, CH},
title = {[DNA barcoding identification of Ginseng Radix et Rhizoma and Panacis Quinquefolii Radix based on trnL-trnF sequences].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {40},
number = {10},
pages = {1914-1918},
pmid = {26390647},
issn = {1001-5302},
mesh = {Chloroplasts/*genetics ; DNA Barcoding, Taxonomic/*methods ; Panax/*classification/genetics ; Phylogeny ; Plant Proteins/*genetics ; Rhizome/classification/genetics ; },
abstract = {To optimize indices of molecular identification for authentication of Ginseng Radix et Rhizoma and Panacis Quinquefolii Radix, four indices, including sequence similarity, specific positions, genetic distance and phylogenetic tree, were compared based on trnL-trnF sequences. Total DNA was extracted from Ginseng Radix et Rhizoma and Panacis Quinquefolii Radix, and trL-trnF sequences were amplified and sequenced. Sequence similarity was calculated by BLAST analysis. Specific positions were compared by DNAman software. Genetic distance and phylogenetic tree were analyzed by Mega software. The results showed that the inter-specific and intra-specific similarity of P. ginseng and P. quinquefolius respectively was 100% and 99. 6%. There were four specific positions at G153A, T463A, C732G and T818C. The inter-specific genetic distance (0) of trL-trnF sequences was lower than intra-specific genetic distance (0. 004). P. ginseng can be distinguished from P. quinquefolius based on the phylogenetic tree. It is concluded that Ginseng Radix et Rhizoma and Panacis Quinquefolii Radix can be authenticated by identification indices of sequence similarity, specific positions, genetic distance and phylogenetic tree. Index of specific positions based on trnL-trnF sequences is the most efficient index to authenticate Ginseng Radix et Rhizoma and Panacis Quinquefolii Radix.},
}
@article {pmid26389887,
year = {2015},
author = {Szczecińska, M and Sawicki, J},
title = {Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae.},
journal = {International journal of molecular sciences},
volume = {16},
number = {9},
pages = {22258-22279},
pmid = {26389887},
issn = {1422-0067},
mesh = {Base Sequence ; Endangered Species ; *Evolution, Molecular ; *Genome, Plant ; *Genome, Plastid ; Molecular Sequence Data ; Mutation Rate ; Polymorphism, Genetic ; Pulsatilla/classification/*genetics ; RNA, Ribosomal/genetics ; Repetitive Sequences, Nucleic Acid ; },
abstract = {BACKGROUND: The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the continent. Most plants of the genus Pulsatilla are rare and endangered, which is why most research efforts focused on their biology, ecology and hybridization. The objective of this study was to develop genomic resources, including complete plastid genomes and nuclear rRNA clusters, for three sympatric Pulsatilla species that are most commonly found in Central Europe. The results will supply valuable information about genetic variation, which can be used in the process of designing primers for population studies and conservation genetics research. The complete plastid genomes together with the nuclear rRNA cluster can serve as a useful tool in hybridization studies.<br><br>Six complete plastid genomes and nuclear rRNA clusters were sequenced from three species of Pulsatilla using the Illumina sequencing technology. Four junctions between single copy regions and inverted repeats and junctions between the identified locally-collinear blocks (LCB) were confirmed by Sanger sequencing. Pulsatilla genomes of 120 unique genes had a total length of approximately 161-162 kb, and 21 were duplicated in the inverted repeats (IR) region. Comparative plastid genomes of newly-sequenced Pulsatilla and the previously-identified plastomes of Aconitum and Ranunculus species belonging to the family Ranunculaceae revealed several variations in the structure of the genome, but the gene content remained constant. The nuclear rRNA cluster (18S-ITS1-5.8S-ITS2-26S) of studied Pulsatilla species is 5795 bp long. Among five analyzed regions of the rRNA cluster, only Internal Transcribed Spacer 2 (ITS2) enabled the molecular delimitation of closely-related Pulsatilla patens and Pulsatilla vernalis.<br><br>CONCLUSIONS/SIGNIFICANCE: The determination of complete plastid genome and nuclear rRNA cluster sequences in three species of the genus Pulsatilla is an important contribution to our knowledge of the evolution and phylogeography of those endangered taxa. The resulting data can be used to identify regions that are particularly useful for barcoding, phylogenetic and phylogeographic studies. The investigated taxa can be identified at each stage of development based on their species-specific SNPs. The nuclear and plastid genomic resources enable advanced studies on hybridization, including identification of parent species, including their roles in that process. The identified nonsynonymous mutations could play an important role in adaptations to changing environments. The results of the study will also provide valuable information about the evolution of the plastome structure in the family Ranunculaceae.},
}
@article {pmid26387459,
year = {2015},
author = {Cho, N and Hwang, B and Yoon, JK and Park, S and Lee, J and Seo, HN and Lee, J and Huh, S and Chung, J and Bang, D},
title = {De novo assembly and next-generation sequencing to analyse full-length gene variants from codon-barcoded libraries.},
journal = {Nature communications},
volume = {6},
number = {},
pages = {8351},
pmid = {26387459},
issn = {2041-1723},
mesh = {Bacterial Proteins/*genetics ; Codon ; *Gene Library ; High-Throughput Nucleotide Sequencing/instrumentation/*methods ; Nostoc/*genetics ; },
abstract = {Interpreting epistatic interactions is crucial for understanding evolutionary dynamics of complex genetic systems and unveiling structure and function of genetic pathways. Although high resolution mapping of en masse variant libraries renders molecular biologists to address genotype-phenotype relationships, long-read sequencing technology remains indispensable to assess functional relationship between mutations that lie far apart. Here, we introduce JigsawSeq for multiplexed sequence identification of pooled gene variant libraries by combining a codon-based molecular barcoding strategy and de novo assembly of short-read data. We first validate JigsawSeq on small sub-pools and observed high precision and recall at various experimental settings. With extensive simulations, we then apply JigsawSeq to large-scale gene variant libraries to show that our method can be reliably scaled using next-generation sequencing. JigsawSeq may serve as a rapid screening tool for functional genomics and offer the opportunity to explore evolutionary trajectories of protein variants.},
}
@article {pmid26385466,
year = {2016},
author = {Phelan, K and Blakeslee, AM and Krause, M and Williams, JD},
title = {First documentation and molecular confirmation of three trematode species (Platyhelminthes: Trematoda) infecting the polychaete Marenzelleria viridis (Annelida: Spionidae).},
journal = {Parasitology research},
volume = {115},
number = {1},
pages = {183-194},
pmid = {26385466},
issn = {1432-1955},
mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA, Helminth/chemistry/isolation &amp; purification ; Documentation ; Ecology ; Estuaries ; Host-Parasite Interactions ; Life Cycle Stages ; Metacercariae/classification/genetics/physiology ; New York ; Phylogeny ; Polychaeta/immunology/*parasitology ; Snails/parasitology ; Trematoda/classification/genetics/*physiology ; },
abstract = {Polychaete worms are hosts to a wide range of marine parasites; yet, studies on trematodes using these ecologically important species as intermediate hosts are lacking. During examination of the spionid polychaete Marenzelleria viridis collected on the north shore of Long Island, New York, putative trematode cysts were discovered in the body cavity of these polychaetes. In order to verify these cysts as metacercariae of trematodes, specimens of the eastern mudsnail Ilyanassa obsoleta (a very common first intermediate host of trematodes in the region) were collected for molecular comparison. DNA barcoding using cytochrome C oxidase I regions confirmed the presence of three species of trematodes (Himasthla quissetensis, Lepocreadium setiferoides, and Zoogonus lasius) in both M. viridis and I. obsoleta hosts. Brown bodies were also recovered from polychaetes, and molecular testing confirmed the presence of L. setiferoides and Z. lasius, indicating an immune response of the polychaete leading to encapsulation of the cysts. From the 125 specimens of M. viridis collected in 2014, 95 (76.8 %) were infected with trematodes; of these 95 infected polychaetes, 86 (90.5 %) contained brown bodies. This is the first confirmation that trematodes use M. viridis as a second intermediate host and that this intermediate host demonstrates a clear immune response to metacercarial infection. Future research should explore the role of these polychaetes in trematode life cycles, the effectiveness of the immune response, and transmission pathways to vertebrate definitive hosts.},
}
@article {pmid26384417,
year = {2016},
author = {Gregory, MT and Bertout, JA and Ericson, NG and Taylor, SD and Mukherjee, R and Robins, HS and Drescher, CW and Bielas, JH},
title = {Targeted single molecule mutation detection with massively parallel sequencing.},
journal = {Nucleic acids research},
volume = {44},
number = {3},
pages = {e22},
pmid = {26384417},
issn = {1362-4962},
support = {P30 CA015704/CA/NCI NIH HHS/United States ; R01ES019319/ES/NIEHS NIH HHS/United States ; F32ES021703/ES/NIEHS NIH HHS/United States ; P50 CA083636/CA/NCI NIH HHS/United States ; R01 ES019319/ES/NIEHS NIH HHS/United States ; },
mesh = {Cell Line ; DNA/*genetics ; Genes, p53 ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Mutation ; Polymerase Chain Reaction/methods ; Saccharomyces cerevisiae/genetics ; },
abstract = {Next-generation sequencing (NGS) technologies have transformed genomic research and have the potential to revolutionize clinical medicine. However, the background error rates of sequencing instruments and limitations in targeted read coverage have precluded the detection of rare DNA sequence variants by NGS. Here we describe a method, termed CypherSeq, which combines double-stranded barcoding error correction and rolling circle amplification (RCA)-based target enrichment to vastly improve NGS-based rare variant detection. The CypherSeq methodology involves the ligation of sample DNA into circular vectors, which contain double-stranded barcodes for computational error correction and adapters for library preparation and sequencing. CypherSeq is capable of detecting rare mutations genome-wide as well as those within specific target genes via RCA-based enrichment. We demonstrate that CypherSeq is capable of correcting errors incurred during library preparation and sequencing to reproducibly detect mutations down to a frequency of 2.4 × 10(-7) per base pair, and report the frequency and spectra of spontaneous and ethyl methanesulfonate-induced mutations across the Saccharomyces cerevisiae genome.},
}
@article {pmid26382887,
year = {2016},
author = {Steer, S and Bhalla, MC and Zalewski, J and Frey, J and Nguyen, V and Mencl, F},
title = {Use of Radio Frequency Identification to Establish Emergency Medical Service Offload Times.},
journal = {Prehospital emergency care},
volume = {20},
number = {2},
pages = {254-259},
doi = {10.3109/10903127.2015.1076093},
pmid = {26382887},
issn = {1545-0066},
mesh = {Ambulances ; Baltimore ; Emergency Medical Services/*statistics &amp; numerical data ; Emergency Service, Hospital/*statistics &amp; numerical data ; Hospitals, Urban ; Humans ; Maryland ; Radio Frequency Identification Device/*methods ; Time Factors ; Transportation of Patients/*statistics &amp; numerical data ; },
abstract = {Emergency medical services (EMS) crews often wait for emergency department (ED) beds to become available to offload their patients. Presently there is no national benchmark for EMS turnaround or offload times, or method for objectively and reliably measuring this. This study introduces a novel method for monitoring offload times and identifying variance. We performed a descriptive, observational study in a large urban community teaching hospital. We affixed radio frequency identification (RFID) tags (Confidex Survivor™, Confidex, Inc., Glen Ellyn, IL) to 65 cots from 19 different EMS agencies and placed a reader (CaptureTech Weatherproof RFID Interpreter, Barcoding Inc., Baltimore, Maryland) in the ED ambulance entrance, allowing for passive recording of traffic. We recorded data for 16 weeks starting December 2009. Offload times were calculated for each visit and analyzed using STATA to show variations in individual and cumulative offload times based on the time of day and day of the week. Results are presented as median times, confidence intervals (CIs), and interquartile ranges (IQRs). We collected data on 2,512 visits. Five hundred and ninety-two were excluded because of incomplete data, leaving 1,920 (76%) complete visits. Average offload time was 13.2 minutes. Median time was 10.7 minutes (IQR 8.1 minutes to 15.4 minutes). A total of 43% of the patients (833/1,920, 95% CI 0.41-0.46) were offloaded in less than 10 minutes, while 27% (513/1,920, 95% CI 0.25-0.29) took greater than 15 minutes. Median times were longest on Mondays (11.5 minutes) and shortest on Wednesdays (10.3 minutes). Longest daily median offload time occurred between 1600 and 1700 (13.5 minutes), whereas the shortest median time was between 0800 and 0900 (9.3 minutes). Cumulative time spent waiting beyond 15 minutes totaled 72.5 hours over the study period. RFID monitoring is a simple and effective means of monitoring EMS traffic and wait times. At our institution, most squads are able to offload their patients within 15 minutes, with many in less than 10 minutes. Variations in wait times are seen and are a topic for future study.},
}
@article {pmid26380710,
year = {2015},
author = {Wirta, HK and Vesterinen, EJ and Hambäck, PA and Weingartner, E and Rasmussen, C and Reneerkens, J and Schmidt, NM and Gilg, O and Roslin, T},
title = {Exposing the structure of an Arctic food web.},
journal = {Ecology and evolution},
volume = {5},
number = {17},
pages = {3842-3856},
pmid = {26380710},
issn = {2045-7758},
abstract = {How food webs are structured has major implications for their stability and dynamics. While poorly studied to date, arctic food webs are commonly assumed to be simple in structure, with few links per species. If this is the case, then different parts of the web may be weakly connected to each other, with populations and species united by only a low number of links. We provide the first highly resolved description of trophic link structure for a large part of a high-arctic food web. For this purpose, we apply a combination of recent techniques to describing the links between three predator guilds (insectivorous birds, spiders, and lepidopteran parasitoids) and their two dominant prey orders (Diptera and Lepidoptera). The resultant web shows a dense link structure and no compartmentalization or modularity across the three predator guilds. Thus, both individual predators and predator guilds tap heavily into the prey community of each other, offering versatile scope for indirect interactions across different parts of the web. The current description of a first but single arctic web may serve as a benchmark toward which to gauge future webs resolved by similar techniques. Targeting an unusual breadth of predator guilds, and relying on techniques with a high resolution, it suggests that species in this web are closely connected. Thus, our findings call for similar explorations of link structure across multiple guilds in both arctic and other webs. From an applied perspective, our description of an arctic web suggests new avenues for understanding how arctic food webs are built and function and of how they respond to current climate change. It suggests that to comprehend the community-level consequences of rapid arctic warming, we should turn from analyses of populations, population pairs, and isolated predator-prey interactions to considering the full set of interacting species.},
}
@article {pmid26379480,
year = {2015},
author = {Lin, G and Fomin, VM and Makarov, D and Schmidt, OG},
title = {Supervised discriminant analysis for droplet micro-magnetofluidics.},
journal = {Microfluidics and nanofluidics},
volume = {19},
number = {2},
pages = {457-464},
pmid = {26379480},
issn = {1613-4982},
abstract = {We apply the technique of supervised discriminant analysis (SDA) for in-flow detection in droplet-based magnetofluidics. Based on the SDA, we successfully discriminate bivariant droplets of different volumes containing different encapsulated magnetic content produced by a GMR-based lab-on-chip platform. We demonstrate that the accuracy of discrimination is superior when the correlation of variables for data training is included to the case when the spatial distribution of variables is considered. Droplets produced with differences in ferrofluid concentration of 2.5 mg/ml and volume of 200 pl have been identified with high accuracy (98 %), indicating the significance of SDA for e.g. the discrimination in magnetic immuno-agglutination assays. Furthermore, the results open the way for the development of a unique magnetofluidic platform for future applications in multiplexed droplet-based barcoding assays and screening.},
}
@article {pmid26379469,
year = {2015},
author = {Telfer, AC and Young, MR and Quinn, J and Perez, K and Sobel, CN and Sones, JE and Levesque-Beaudin, V and Derbyshire, R and Fernandez-Triana, J and Rougerie, R and Thevanayagam, A and Boskovic, A and Borisenko, AV and Cadel, A and Brown, A and Pages, A and Castillo, AH and Nicolai, A and Glenn Mockford, BM and Bukowski, B and Wilson, B and Trojahn, B and Lacroix, CA and Brimblecombe, C and Hay, C and Ho, C and Steinke, C and Warne, CP and Garrido Cortes, C and Engelking, D and Wright, D and Lijtmaer, DA and Gascoigne, D and Hernandez Martich, D and Morningstar, D and Neumann, D and Steinke, D and Marco DeBruin, DD and Dobias, D and Sears, E and Richard, E and Damstra, E and Zakharov, EV and Laberge, F and Collins, GE and Blagoev, GA and Grainge, G and Ansell, G and Meredith, G and Hogg, I and McKeown, J and Topan, J and Bracey, J and Guenther, J and Sills-Gilligan, J and Addesi, J and Persi, J and Layton, KK and D'Souza, K and Dorji, K and Grundy, K and Nghidinwa, K and Ronnenberg, K and Lee, KM and Xie, L and Lu, L and Penev, L and Gonzalez, M and Rosati, ME and Kekkonen, M and Kuzmina, M and Iskandar, M and Mutanen, M and Fatahi, M and Pentinsaari, M and Bauman, M and Nikolova, N and Ivanova, NV and Jones, N and Weerasuriya, N and Monkhouse, N and Lavinia, PD and Jannetta, P and Hanisch, PE and McMullin, RT and Ojeda Flores, R and Mouttet, R and Vender, R and Labbee, RN and Forsyth, R and Lauder, R and Dickson, R and Kroft, R and Miller, SE and MacDonald, S and Panthi, S and Pedersen, S and Sobek-Swant, S and Naik, S and Lipinskaya, T and Eagalle, T and Decaëns, T and Kosuth, T and Braukmann, T and Woodcock, T and Roslin, T and Zammit, T and Campbell, V and Dinca, V and Peneva, V and Hebert, PD and deWaard, JR},
title = {Biodiversity inventories in high gear: DNA barcoding facilitates a rapid biotic survey of a temperate nature reserve.},
journal = {Biodiversity data journal},
volume = {},
number = {3},
pages = {e6313},
pmid = {26379469},
issn = {1314-2828},
abstract = {BACKGROUND: Comprehensive biotic surveys, or 'all taxon biodiversity inventories' (ATBI), have traditionally been limited in scale or scope due to the complications surrounding specimen sorting and species identification. To circumvent these issues, several ATBI projects have successfully integrated DNA barcoding into their identification procedures and witnessed acceleration in their surveys and subsequent increase in project scope and scale. The Biodiversity Institute of Ontario partnered with the rare Charitable Research Reserve and delegates of the 6th International Barcode of Life Conference to complete its own rapid, barcode-assisted ATBI of an established land trust in Cambridge, Ontario, Canada.<br><br>NEW INFORMATION: The existing species inventory for the rare Charitable Research Reserve was rapidly expanded by integrating a DNA barcoding workflow with two surveying strategies - a comprehensive sampling scheme over four months, followed by a one-day bioblitz involving international taxonomic experts. The two surveys resulted in 25,287 and 3,502 specimens barcoded, respectively, as well as 127 human observations. This barcoded material, all vouchered at the Biodiversity Institute of Ontario collection, covers 14 phyla, 29 classes, 117 orders, and 531 families of animals, plants, fungi, and lichens. Overall, the ATBI documented 1,102 new species records for the nature reserve, expanding the existing long-term inventory by 49%. In addition, 2,793 distinct Barcode Index Numbers (BINs) were assigned to genus or higher level taxonomy, and represent additional species that will be added once their taxonomy is resolved. For the 3,502 specimens, the collection, sequence analysis, taxonomic assignment, data release and manuscript submission by 100+ co-authors all occurred in less than one week. This demonstrates the speed at which barcode-assisted inventories can be completed and the utility that barcoding provides in minimizing and guiding valuable taxonomic specialist time. The final product is more than a comprehensive biotic inventory - it is also a rich dataset of fine-scale occurrence and sequence data, all archived and cross-linked in the major biodiversity data repositories. This model of rapid generation and dissemination of essential biodiversity data could be followed to conduct regional assessments of biodiversity status and change, and potentially be employed for evaluating progress towards the Aichi Targets of the Strategic Plan for Biodiversity 2011-2020.},
}
@article {pmid26378526,
year = {2015},
author = {Feng, S and Jiang, Y and Wang, S and Jiang, M and Chen, Z and Ying, Q and Wang, H},
title = {Molecular Identification of Dendrobium Species (Orchidaceae) Based on the DNA Barcode ITS2 Region and Its Application for Phylogenetic Study.},
journal = {International journal of molecular sciences},
volume = {16},
number = {9},
pages = {21975-21988},
pmid = {26378526},
issn = {1422-0067},
mesh = {*DNA Barcoding, Taxonomic ; *DNA, Intergenic ; *DNA, Plant ; Dendrobium/*classification/*genetics ; Genetic Variation ; *Phylogeny ; },
abstract = {The over-collection and habitat destruction of natural Dendrobium populations for their commercial medicinal value has led to these plants being under severe threat of extinction. In addition, many Dendrobium plants are similarly shaped and easily confused during the absence of flowering stages. In the present study, we examined the application of the ITS2 region in barcoding and phylogenetic analyses of Dendrobium species (Orchidaceae). For barcoding, ITS2 regions of 43 samples in Dendrobium were amplified. In combination with sequences from GenBank, the sequences were aligned using Clustal W and genetic distances were computed using MEGA V5.1. The success rate of PCR amplification and sequencing was 100%. There was a significant divergence between the inter- and intra-specific genetic distances of ITS2 regions, while the presence of a barcoding gap was obvious. Based on the BLAST1, nearest distance and TaxonGAP methods, our results showed that the ITS2 regions could successfully identify the species of most Dendrobium samples examined; Second, we used ITS2 as a DNA marker to infer phylogenetic relationships of 64 Dendrobium species. The results showed that cluster analysis using the ITS2 region mainly supported the relationship between the species of Dendrobium established by traditional morphological methods and many previous molecular analyses. To sum up, the ITS2 region can not only be used as an efficient barcode to identify Dendrobium species, but also has the potential to contribute to the phylogenetic analysis of the genus Dendrobium.},
}
@article {pmid26375850,
year = {2015},
author = {Hartvig, I and Czako, M and Kjær, ED and Nielsen, LR and Theilade, I},
title = {The Use of DNA Barcoding in Identification and Conservation of Rosewood (Dalbergia spp.).},
journal = {PloS one},
volume = {10},
number = {9},
pages = {e0138231},
pmid = {26375850},
issn = {1932-6203},
mesh = {*Biodiversity ; *Conservation of Natural Resources ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; Dalbergia/*genetics/growth &amp; development ; Phylogeny ; Sequence Analysis, DNA/methods ; Species Specificity ; },
abstract = {The genus Dalbergia contains many valuable timber species threatened by illegal logging and deforestation, but knowledge on distributions and threats is often limited and accurate species identification difficult. The aim of this study was to apply DNA barcoding methods to support conservation efforts of Dalbergia species in Indochina. We used the recommended rbcL, matK and ITS barcoding markers on 95 samples covering 31 species of Dalbergia, and tested their discrimination ability with both traditional distance-based as well as different model-based machine learning methods. We specifically tested whether the markers could be used to solve taxonomic confusion concerning the timber species Dalbergia oliveri, and to identify the CITES-listed Dalbergia cochinchinensis. We also applied the barcoding markers to 14 samples of unknown identity. In general, we found that the barcoding markers discriminated among Dalbergia species with high accuracy. We found that ITS yielded the single highest discrimination rate (100%), but due to difficulties in obtaining high-quality sequences from degraded material, the better overall choice for Dalbergia seems to be the standard rbcL+matK barcode, as this yielded discrimination rates close to 90% and amplified well. The distance-based method TaxonDNA showed the highest identification rates overall, although a more complete specimen sampling is needed to conclude on the best analytic method. We found strong support for a monophyletic Dalbergia oliveri and encourage that this name is used consistently in Indochina. The CITES-listed Dalbergia cochinchinensis was successfully identified, and a species-specific assay can be developed from the data generated in this study for the identification of illegally traded timber. We suggest that the use of DNA barcoding is integrated into the work flow during floristic studies and at national herbaria in the region, as this could significantly increase the number of identified specimens and improve knowledge about species distributions.},
}
@article {pmid26371156,
year = {2016},
author = {Chen, F and Luo, Y and Keena, MA and Wu, Y and Wu, P and Shi, J},
title = {DNA Barcoding of Gypsy Moths From China (Lepidoptera: Erebidae) Reveals New Haplotypes and Divergence Patterns Within Gypsy Moth Subspecies.},
journal = {Journal of economic entomology},
volume = {109},
number = {1},
pages = {366-374},
doi = {10.1093/jee/tov258},
pmid = {26371156},
issn = {0022-0493},
mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics/metabolism ; Female ; *Genetic Variation ; *Haplotypes ; Insect Proteins/genetics/metabolism ; Male ; Molecular Sequence Data ; Moths/classification/enzymology/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The gypsy moth from Asia (two subspecies) is considered a greater threat to North America than European gypsy moth, because of a broader host range and females being capable of flight. Variation within and among gypsy moths from China (nine locations), one of the native countries of Asian gypsy moth, were compared using DNA barcode sequences (658 bp of mtDNA cytochrome c oxidase subunit 1 [COI] sequence), together with two restriction site mtDNA markers (NlaIII and BamHI in COI), which is the standard system used to distinguish European gypsy moths from Asian gypsy moths. Relatedness of these populations to gypsy moths from seven other world areas was also examined. The restriction site markers showed that two Chinese populations had both Asian and European haplotypes. DNA barcode sequence divergence between the Asian populations and the European populations was three times greater than the variation within each group. Using Bayesian and parsimonious network analyses, nine previously unknown barcode haplotypes were documented from China and a single haplotype was found to be shared by 55% of the Chinese and some Far Eastern Russian and Japanese individuals. Some gypsy moths from two Chinese populations showed genetic affinity with mtDNA haplotypes from Siberia, Russia, suggesting there could be a cryptic new subspecies in Lymantria dispar (L.) or human-aided movement of moths between these two locations at an earlier point in time. The previously unknown haplotype patterns may complicate efforts to identify Asian gypsy moth introductions and require changes in monitoring and exclusion programs.},
}
@article {pmid26370580,
year = {2016},
author = {Polseela, R and Jaturas, N and Thanwisai, A and Sing, KW and Wilson, JJ},
title = {Towards monitoring the sandflies (Diptera: Psychodidae) of Thailand: DNA barcoding the sandflies of Wihan Cave, Uttaradit.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3795-3801},
doi = {10.3109/19401736.2015.1082085},
pmid = {26370580},
issn = {2470-1408},
mesh = {Animal Distribution ; Animals ; Base Sequence ; Caves ; DNA Barcoding, Taxonomic ; Genes, Insect ; Genetic Variation ; Insect Proteins/genetics ; Phylogeny ; Polymerase Chain Reaction ; Psychodidae/*genetics ; Sequence Analysis, DNA ; Thailand ; },
abstract = {Sandflies vary in their distributions and role in pathogen transmission. Attempts to record distributions of sandflies in Thailand have faced difficulties due to their high abundance and diversity. We aim to provide an insight into the diversity of sandflies in Thailand by (i) conducting a literature review, and (ii) DNA barcoding sandflies collected from Wihan Cave where eight morphologically characterized species were recorded. DNA barcodes generated for 193 sandflies fell into 13 distinct species clusters under four genera (Chinius, Idiophlebotomus, Phlebotomus and Sergentomyia). Five of these species could be assigned Linnaean species names unambiguously and two others corresponded to characterized morphospecies. Two species represented a complex under the name Sergentomyia barraudi while the remaining four had not been recognized before in any form. The resulting species checklist and DNA barcode library contribute to a growing set of records for sandflies which is useful for monitoring and vector control.},
}
@article {pmid26369496,
year = {2015},
author = {Vitale, DG and Viscuso, R and D'Urso, V and Gibilras, S and Sardella, A and Marletta, A and Pappalardo, AM},
title = {Morphostructural analysis of the male reproductive system and DNA barcoding in Balclutha brevis Lindberg 1954 (Homoptera, Cicadellidae).},
journal = {Micron (Oxford, England : 1993)},
volume = {79},
number = {},
pages = {36-45},
doi = {10.1016/j.micron.2015.08.002},
pmid = {26369496},
issn = {1878-4291},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Ejaculatory Ducts/anatomy &amp; histology/ultrastructure ; Electron Transport Complex IV/genetics ; Hemiptera/*anatomy &amp; histology/*classification/genetics ; Male ; Microscopy, Electron, Transmission/methods ; Seminal Vesicles/anatomy &amp; histology/ultrastructure ; Spermatozoa/ultrastructure ; Urogenital System/anatomy &amp; histology/ultrastructure ; },
abstract = {Balclutha brevis Lindberg 1954 is an allochthonous leafhopper infesting an invasive grass, Pennisetum setaceum, in Sicily and in mainland Europe; therefore, this species could compete with populations of native species, thus contributing to the loss of biodiversity. Considering the ecological implications of B. brevis, investigations on all its biological aspects represent, therefore, a premise for further studies in applied sciences. Based on the lacking ultrastructural data about the reproductive systems of the Auchenorrhyncha, we carried out morphostructural investigations on the male reproductive system of B. brevis. Further, a first report of DNA barcoding analysis (amplification and sequencing of Cytochrome Oxidase I gene) has also been performed to characterize B. brevis compared to other congeneric species. From a morphological point of view, the male reproductive system of B. brevis has an organization comparable to the general anatomical features of most of the Auchenorrhyncha species; however, comparing our data with those concerning the different groups of Cicadomorpha, some considerations are discussed. As for the histological and ultrastructural investigations, our results show a secretory activity of the various examined structures, mainly in the lateral ejaculatory ducts and in the accessory glands. The latter, in particular, show morphostructural differences comparing the distal tract to the proximal one; moreover, the histochemical techniques showed the possible presence of a lipid component in the peculiar cytoplasmic granules found in the gland cells. The significance of these findings in the accessory glands is discussed. Finally, the ultrastructural features found in the seminal vesicles are different from those of the lateral ejaculatory ducts and are indicative of the different roles played by these structures in the organization of the spermatozoa bundles.},
}
@article {pmid26361047,
year = {2015},
author = {Kono, Y and Kohn, JR},
title = {Range and Frequency of Africanized Honey Bees in California (USA).},
journal = {PloS one},
volume = {10},
number = {9},
pages = {e0137407},
pmid = {26361047},
issn = {1932-6203},
mesh = {Animals ; *Bees/anatomy &amp; histology/genetics ; California ; Genes, Insect ; Genes, Mitochondrial ; Genetics, Population ; Polymorphism, Single Nucleotide ; Population Dynamics ; Sequence Analysis, DNA ; },
abstract = {Africanized honey bees entered California in 1994 but few accounts of their northward expansion or their frequency relative to European honey bees have been published. We used mitochondrial markers and morphometric analyses to determine the prevalence of Africanized honeybees in San Diego County and their current northward progress in California west of the Sierra Nevada crest. The northernmost African mitotypes detected were approximately 40 km south of Sacramento in California's central valley. In San Diego County, 65% of foraging honey bee workers carry African mitochondria and the estimated percentage of Africanized workers using morphological measurements is similar (61%). There was no correlation between mitotype and morphology in San Diego County suggesting Africanized bees result from bidirectional hybridization. Seventy percent of feral hives, but only 13% of managed hives, sampled in San Diego County carried the African mitotype indicating that a large fraction of foraging workers in both urban and rural San Diego County are feral. We also found a single nucleotide polymorphism at the DNA barcode locus COI that distinguishes European and African mitotypes. The utility of this marker was confirmed using 401 georeferenced honey bee sequences from the worldwide Barcode of Life Database. Future censuses can determine whether the current range of the Africanized form is stable, patterns of introgression at nuclear loci, and the environmental factors that may limit the northern range of the Africanized honey bee.},
}
@article {pmid26358100,
year = {2016},
author = {Murugan, K and Vadivalagan, C and Karthika, P and Panneerselvam, C and Paulpandi, M and Subramaniam, J and Wei, H and Aziz, AT and Alsalhi, MS and Devanesan, S and Nicoletti, M and Paramasivan, R and Parajulee, MN and Benelli, G},
title = {DNA barcoding and molecular evolution of mosquito vectors of medical and veterinary importance.},
journal = {Parasitology research},
volume = {115},
number = {1},
pages = {107-121},
pmid = {26358100},
issn = {1432-1955},
mesh = {Aedes/genetics ; Animals ; Anopheles/genetics ; Base Sequence ; Cluster Analysis ; Culex/genetics ; Culicidae/*genetics ; Cyclooxygenase 1/genetics ; *DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/chemistry/isolation &amp; purification ; *Evolution, Molecular ; *Genes, Mitochondrial/genetics ; Genetic Markers ; Humans ; India ; Insect Vectors/*genetics ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {Mosquitoes (Diptera: Culicidae) are a key threat for millions of people worldwide, since they act as vectors for devastating pathogens and parasites. The standard method of utilisation of morphological characters becomes challenging due to various factors such as phenotypical variations. We explored the complementary approach of CO1 gene-based identification, analysing ten species of mosquito vectors belonging to three genera, Aedes, Culex and Anopheles from India. Analysed nucleotide sequences were found without pseudo genes and indels; they match with high similarity in nucleotide Basic Local Alignment Search Tool (BLASTn) search. The partial CO1 sequence of Anopheles niligricus was the first time record submitted to National Center for Biotechnology Information (NCBI). Mean intra- and interspecies divergence was found to be 1.30 and 3.83 %, respectively. The congeneric divergence was three times higher than the conspecifics. Deep intraspecific divergence was noted in three of the species, and the reason could be explained more accurately in the future by improving the sample size across different locations. The transitional and transversional substitutions were tested individually. Ts and Tv substitutions in all the 1st, 2nd and 3rd codons were estimated to be (0.44, 99.51), (40.35, 59.66) and (59.16, 40.84), respectively. Saturation of the sequences was resolved, since both the Ts and Tv exhibited a linear relationship suggesting that the sequences were not saturated. NJ and ML tree analysis showed that the individuals of the same species clustered together based on the CO1 sequence similarity, regardless of their collection site and geographic location. Overall, this study adds basic knowledge to molecular evolution of mosquito vectors of medical and veterinary importance and may be useful to improve biotechnological tools employed in Culicidae control programmes.},
}
@article {pmid26357758,
year = {2015},
author = {Crist, D},
title = {Next-gen barcoding advances quality of care. Barcodes can protect the lives of patients from everyday errors.},
journal = {Health management technology},
volume = {36},
number = {6},
pages = {12-13},
pmid = {26357758},
issn = {1074-4770},
mesh = {*Electronic Data Processing ; Hospitalization ; Medical Errors/*prevention &amp; control ; Patient Safety ; *Quality of Health Care ; United States ; },
}
@article {pmid26355391,
year = {2016},
author = {Mei, HE and Leipold, MD and Maecker, HT},
title = {Platinum-conjugated antibodies for application in mass cytometry.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {89},
number = {3},
pages = {292-300},
doi = {10.1002/cyto.a.22778},
pmid = {26355391},
issn = {1552-4930},
support = {S10RR027582/RR/NCRR NIH HHS/United States ; UL1TR001085/TR/NCATS NIH HHS/United States ; },
mesh = {Antibodies/*chemistry ; Cisplatin/*chemistry ; Flow Cytometry/*methods ; Gene Expression ; Humans ; Immunoconjugates/chemistry ; Immunophenotyping/*methods ; Lanthanoid Series Elements/analysis ; Leukocyte Common Antigens/genetics/immunology ; Lymphocyte Activation ; Mass Spectrometry/instrumentation/*methods ; Monocytes/cytology/immunology ; Single-Cell Analysis/methods ; Staining and Labeling/methods ; T-Lymphocytes/classification/*cytology/immunology ; },
abstract = {Mass cytometry has overcome limitations of fluorescent single cell cytometry by allowing for the measurement of up to currently ∼40 different parameters on a single cell level. However, the cellular proteome comprises many more potential analytes, and current mass cytometry instrumentation allows for theoretically up to 121 different mass detection channels. The labeling of specific probes with appropriate metal ions is a significant hurdle for exploiting more of mass cytometry's analytical capacity. To this end, we here describe the labeling of antibody with natural abundance or isotopically purified platinum as formulated in cisplatin and circumventing the use of chelator-loaded polymers. We confirm the utility of cisplatin-antibody-conjugates for surface, intracellular, and phosphoepitope-specific immunophenotyping, as well as for application in cell surface CD45-based barcoding. Cisplatin-labeling of antibody increases the analytical capacity of the CyTOF(®) platform by two channels based on available reagents, and has the potential to add a total of six channels for detection of specific probes, thus helping to better extend the analytical mass range of mass cytometers.},
}
@article {pmid26355099,
year = {2015},
author = {Lejzerowicz, F and Esling, P and Pillet, L and Wilding, TA and Black, KD and Pawlowski, J},
title = {High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {13932},
pmid = {26355099},
issn = {2045-2322},
mesh = {Animals ; *Aquatic Organisms ; *Biodiversity ; Computational Biology/methods ; DNA Barcoding, Taxonomic ; *Ecosystem ; Environmental Monitoring ; High-Throughput Nucleotide Sequencing ; },
abstract = {Environmental diversity surveys are crucial for the bioassessment of anthropogenic impacts on marine ecosystems. Traditional benthic monitoring relying on morphotaxonomic inventories of macrofaunal communities is expensive, time-consuming and expertise-demanding. High-throughput sequencing of environmental DNA barcodes (metabarcoding) offers an alternative to describe biological communities. However, whether the metabarcoding approach meets the quality standards of benthic monitoring remains to be tested. Here, we compared morphological and eDNA/RNA-based inventories of metazoans from samples collected at 10 stations around a fish farm in Scotland, including near-cage and distant zones. For each of 5 replicate samples per station, we sequenced the V4 region of the 18S rRNA gene using the Illumina technology. After filtering, we obtained 841,766 metazoan sequences clustered in 163 Operational Taxonomic Units (OTUs). We assigned the OTUs by combining local BLAST searches with phylogenetic analyses. We calculated two commonly used indices: the Infaunal Trophic Index and the AZTI Marine Biotic Index. We found that the molecular data faithfully reflect the morphology-based indices and provides an equivalent assessment of the impact associated with fish farms activities. We advocate that future benthic monitoring should integrate metabarcoding as a rapid and accurate tool for the evaluation of the quality of marine benthic ecosystems.},
}
@article {pmid26353811,
year = {2015},
author = {Argüello Caro, EB and Dumón, AD and Mattio, MF and Alemandri, V and Truol, G},
title = {A molecular framework for the identification of planthopper vectors (Hemiptera: Delphacidae) of central Argentina.},
journal = {Bulletin of entomological research},
volume = {105},
number = {6},
pages = {754-762},
doi = {10.1017/S0007485315000735},
pmid = {26353811},
issn = {1475-2670},
mesh = {Animals ; Argentina ; Classification/methods ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/chemistry/*genetics ; Hemiptera/*genetics/virology ; Insect Vectors/*genetics/virology ; Phylogeny ; Plant Diseases/virology ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Planthoppers are important worldwide crop pests as well as vectors of numerous diseases. Different species transmit Mal de Río Cuarto virus, which causes the most economically important corn disease in central Argentina. Epidemiological studies rely on the accurate identification of the species present in the field. Presently, morphological identification of planthoppers requires taxonomic expertise and there are no taxonomic keys for females and nymphs. Nevertheless, no molecular protocols are available for accurate species identification of most frequent delphacid species from central Argentina. In this context, the aim of this study was to evaluate the utility of the cytochrome oxidase I gene (COI) as a DNA barcode and its digestion with restriction enzymes (Restriction Fragment Length Polymorphism, RFLP) for the identification of the most common species of planthoppers in central Argentina. We amplified and sequenced a 843 bp fragment of the COI gene of taxonomically identified specimens and evaluated its use as a DNA barcode. Restriction enzymes were also selected for digesting the COI fragment via RFLP. The high interspecific variability (20.79%; ± 2.32%) and low intraspecific divergence (0.12%; ± 0.17%) observed in the studied species, demonstrate the effectiveness of the COI gene for species identification of major vector delphacids affecting corn crops in Argentina. Moreover, the digestion of this COI gene fragment with Bfa I and Apo I enzymes allows a fast and cost-effective species identification method when numerous specimens need to be processed. Both molecular techniques developed here, allow the accurate identification of planthopper species at regional scale. These new tools would assist traditional identification of these insects, especially for aiding non-experts in morphological taxonomy.},
}
@article {pmid26347956,
year = {2015},
author = {Yang, F and Yu, X and Liu, C and Qu, CX and Gong, Z and Liu, HD and Li, FH and Wang, HM and He, DF and Yi, F and Song, C and Tian, CL and Xiao, KH and Wang, JY and Sun, JP},
title = {Phospho-selective mechanisms of arrestin conformations and functions revealed by unnatural amino acid incorporation and (19)F-NMR.},
journal = {Nature communications},
volume = {6},
number = {},
pages = {8202},
pmid = {26347956},
issn = {2041-1723},
mesh = {Animals ; Arrestins/genetics/*metabolism ; Binding Sites ; Blotting, Western ; Cattle ; Clathrin/metabolism ; Escherichia coli ; Fluorine ; Fluorine-19 Magnetic Resonance Imaging ; G-Protein-Coupled Receptor Kinase 2/metabolism ; G-Protein-Coupled Receptor Kinases/metabolism ; HEK293 Cells ; Humans ; Microscopy, Confocal ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Phosphate-Binding Proteins/metabolism ; Phosphoproteins/*metabolism ; Protein Conformation ; Receptors, G-Protein-Coupled/*metabolism ; Signal Transduction ; Tandem Mass Spectrometry ; Tyrosine/analogs &amp; derivatives/metabolism ; beta-Arrestin 1 ; beta-Arrestins ; },
abstract = {Specific arrestin conformations are coupled to distinct downstream effectors, which underlie the functions of many G-protein-coupled receptors (GPCRs). Here, using unnatural amino acid incorporation and fluorine-19 nuclear magnetic resonance ((19)F-NMR) spectroscopy, we demonstrate that distinct receptor phospho-barcodes are translated to specific β-arrestin-1 conformations and direct selective signalling. With its phosphate-binding concave surface, β-arrestin-1 'reads' the message in the receptor phospho-C-tails and distinct phospho-interaction patterns are revealed by (19)F-NMR. Whereas all functional phosphopeptides interact with a common phosphate binding site and induce the movements of finger and middle loops, different phospho-interaction patterns induce distinct structural states of β-arrestin-1 that are coupled to distinct arrestin functions. Only clathrin recognizes and stabilizes GRK2-specific β-arrestin-1 conformations. The identified receptor-phospho-selective mechanism for arrestin conformation and the spacing of the multiple phosphate-binding sites in the arrestin enable arrestin to recognize plethora phosphorylation states of numerous GPCRs, contributing to the functional diversity of receptors.},
}
@article {pmid26345910,
year = {2015},
author = {Su, LN and Zhao, YY and Wu, XM and Zhang, HF and Li, XC},
title = {Identification of conservation units of the hynobiid salamander Pachyhynobius shangchengensis.},
journal = {Genetics and molecular research : GMR},
volume = {14},
number = {3},
pages = {9772-9778},
doi = {10.4238/2015.August.19.10},
pmid = {26345910},
issn = {1676-5680},
mesh = {Animals ; Biological Evolution ; China ; *DNA, Mitochondrial ; *Evolution, Molecular ; Genes, Mitochondrial ; Haplotypes ; Phylogeny ; Phylogeography ; Caudata/classification/*genetics ; },
abstract = {The evolutionary significant units (ESUs) of the salamander Pachyhynobius shangchengensis (Hynobiidae) in the Dabieshan mountains, southeastern China, were identified based on mitochondrial DNA data. We used methods for detecting cryptic species, such as the minimum spanning tree, the automatic barcode gap discovery, and the generalized mixed Yule-coalescent model; geographical partitioning was also used to identify the ESUs. A total of four ESUs were identified.},
}
@article {pmid26345851,
year = {2015},
author = {Trang, NT and Duc, NM and Sinh, NV and Triest, L},
title = {Application of DNA barcoding markers to the identification of Hopea species.},
journal = {Genetics and molecular research : GMR},
volume = {14},
number = {3},
pages = {9181-9190},
doi = {10.4238/2015.August.7.28},
pmid = {26345851},
issn = {1676-5680},
mesh = {Base Sequence ; *DNA Barcoding, Taxonomic ; DNA, Chloroplast ; DNA, Plant ; Dipterocarpaceae/*classification/*genetics ; Genetic Markers ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Vietnam ; },
abstract = {Hopea chinensis (synonym: H. hongayensis) (Dipterocarpaceae) is a threatened species found so far in only two locations: Quang Ninh (Vietnam) and Guangxi (China). The species shares many morphological characteristics with H. mollissima and the two species are often confused. To overcome this problem of identification and to investigate the genetic relationships of Hopea species with other Dipterocarp species, we sequenced three candidate DNA barcodes for the chloroplast markers rbcL, trnH-psbA, and matK. These markers were used separately and in different combinations to determine whether they could establish an accurate and effective identification system for H. chinensis in Quang Ninh (Vietnam). Our analyses indicated that two of the candidate DNA barcodes, matK and rbcL, performed best. We also generated a neighbor-joining phylogenetic tree and confirmed the presence of four Hopea species (H. odorata, H. hainanensis, H. mollissima, and H. chinensis) in nature reserves and natural parks of Vietnam. These species showed a close relationship with an average genetic distance of 0.0045; both matK and rbcL separated all species, but their use in combination gave higher bootstrap values. The matK region was found to provide the most reliable barcode for the identification of the most closely related Dipterocarp species. Our study provides a means to identify rare Hopea species non-ambiguously and to support the protection of this decreasing natural genetic resource.},
}
@article {pmid26344799,
year = {2015},
author = {Brandon-Mong, GJ and Gan, HM and Sing, KW and Lee, PS and Lim, PE and Wilson, JJ},
title = {DNA metabarcoding of insects and allies: an evaluation of primers and pipelines.},
journal = {Bulletin of entomological research},
volume = {105},
number = {6},
pages = {717-727},
doi = {10.1017/S0007485315000681},
pmid = {26344799},
issn = {1475-2670},
mesh = {Animals ; Arthropods/*genetics ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; *DNA Primers ; DNA, Mitochondrial/chemistry ; Electron Transport Complex IV/chemistry/genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Nucleic Acid Amplification Techniques ; Polymerase Chain Reaction ; },
abstract = {Metabarcoding, the coupling of DNA-based species identification and high-throughput sequencing, offers enormous promise for arthropod biodiversity studies but factors such as cost, speed and ease-of-use of bioinformatic pipelines, crucial for making the leapt from demonstration studies to a real-world application, have not yet been adequately addressed. Here, four published and one newly designed primer sets were tested across a diverse set of 80 arthropod species, representing 11 orders, to establish optimal protocols for Illumina-based metabarcoding of tropical Malaise trap samples. Two primer sets which showed the highest amplification success with individual specimen polymerase chain reaction (PCR, 98%) were used for bulk PCR and Illumina MiSeq sequencing. The sequencing outputs were subjected to both manual and simple metagenomics quality control and filtering pipelines. We obtained acceptable detection rates after bulk PCR and high-throughput sequencing (80-90% of input species) but analyses were complicated by putative heteroplasmic sequences and contamination. The manual pipeline produced similar or better outputs to the simple metagenomics pipeline (1.4 compared with 0.5 expected:unexpected Operational Taxonomic Units). Our study suggests that metabarcoding is slowly becoming as cheap, fast and easy as conventional DNA barcoding, and that Malaise trap metabarcoding may soon fulfill its potential, providing a thermometer for biodiversity.},
}
@article {pmid26340615,
year = {2015},
author = {Nyman, T and Leppänen, SA and Várkonyi, G and Shaw, MR and Koivisto, R and Barstad, TE and Vikberg, V and Roininen, H},
title = {Determinants of parasitoid communities of willow-galling sawflies: habitat overrides physiology, host plant and space.},
journal = {Molecular ecology},
volume = {24},
number = {19},
pages = {5059-5074},
doi = {10.1111/mec.13369},
pmid = {26340615},
issn = {1365-294X},
mesh = {Animals ; DNA Barcoding, Taxonomic ; *Ecosystem ; Food Chain ; Hymenoptera/*parasitology ; Larva/parasitology ; Models, Genetic ; Molecular Sequence Data ; Parasites/classification ; Phylogeny ; Plant Tumors ; Salix ; Wasps/*classification ; },
abstract = {Studies on the determinants of plant-herbivore and herbivore-parasitoid associations provide important insights into the origin and maintenance of global and local species richness. If parasitoids are specialists on herbivore niches rather than on herbivore taxa, then alternating escape of herbivores into novel niches and delayed resource tracking by parasitoids could fuel diversification at both trophic levels. We used DNA barcoding to identify parasitoids that attack larvae of seven Pontania sawfly species that induce leaf galls on eight willow species growing in subarctic and arctic-alpine habitats in three geographic locations in northern Fennoscandia, and then applied distance- and model-based multivariate analyses and phylogenetic regression methods to evaluate the hierarchical importance of location, phylogeny and different galler niche dimensions on parasitoid host use. We found statistically significant variation in parasitoid communities across geographic locations and willow host species, but the differences were mainly quantitative due to extensive sharing of enemies among gallers within habitat types. By contrast, the divide between habitats defined two qualitatively different network compartments, because many common parasitoids exhibited strong habitat preference. Galler and parasitoid phylogenies did not explain associations, because distantly related arctic-alpine gallers were attacked by a species-poor enemy community dominated by two parasitoid species that most likely have independently tracked the gallers' evolutionary shifts into the novel habitat. Our results indicate that barcode- and phylogeny-based analyses of food webs that span forested vs. tundra or grassland environments could improve our understanding of vertical diversification effects in complex plant-herbivore-parasitoid networks.},
}
@article {pmid26339548,
year = {2015},
author = {Knapp, IS and Forsman, ZH and Williams, GJ and Toonen, RJ and Bell, JJ},
title = {Cryptic species obscure introduction pathway of the blue Caribbean sponge (Haliclona (Soestella) caerulea), (order: Haplosclerida) to Palmyra Atoll, Central Pacific.},
journal = {PeerJ},
volume = {3},
number = {},
pages = {e1170},
pmid = {26339548},
issn = {2167-8359},
abstract = {Cryptic species are widespread across the phylum Porifera making the identification of non-indigenous species difficult, an issue not easily resolved by the use of morphological characteristics. The widespread order Haplosclerida is a prime example due to limited and plastic morphological features. Here, we study the reported introduction of Haliclona (Soestella) caerulea from the Caribbean to Palmyra Atoll via Hawai'i using morphological characteristics and genetic analyses based on one nuclear (18s rDNA) and three mitochondrial (COI, the barcoding COI extension (COI ext.) and rnl rDNA) markers. Despite no clear division in lengths of the oxea spicules between the samples, both mtDNA and nDNA phylogenetic trees supported similar topologies resolving two distinct clades. Across the two clades, the concatenated mtDNA tree resolved twelve subclades, with the COI ext. yielding most of the variability between the samples. Low sequence divergence values (0.68%) between two of the subclades indicate that the same species is likely to occur at Palmyra, Hawai'i and the Caribbean, supporting the hypothesis that H. caerulea was introduced to Palmyra from the Caribbean, although whether species came directly from the Caribbean to Palmyra or from Hawai'i remains unresolved. Conversely, the pattern of highly divergent cryptic species supports the notion that traditionally used spicule measurements are taxonomically unreliable in this group. This study illustrates how understanding the scale of within- as opposed to between-species level genetic variation is critical for interpreting biogeographic patterns and inferring the origins of introduced organisms.},
}
@article {pmid26336270,
year = {2015},
author = {Zhang, C and Fu, X and Xie, K and Yan, W and Guo, Y},
title = {MtDNA Analysis for Genetic Identification of Forensically Important Sarcophagid Flies (Diptera: Sarcophagidae) in China.},
journal = {Journal of medical entomology},
volume = {52},
number = {6},
pages = {1225-1233},
doi = {10.1093/jme/tjv131},
pmid = {26336270},
issn = {0022-2585},
mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*chemistry ; Electron Transport Complex IV/genetics ; *Forensic Sciences ; Genetic Variation ; Phylogeny ; Sarcophagidae/*classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {DNA-based technologies have been increasingly used in species determination of forensically important sarcophagids, as they are often not morphologically distinct, especially for the immature specimens. The mitochondrial genome has been broadly used for species-level identifications. Although Chinese sarcophagid sequences of short fragments (200-600 bp) had been deposited in GenBank, the barcode region and the complete cytochrome oxidase subunit I (COI) and COII sequences are still unavailable. In this study, 78 sarcophagid fly specimens, representing 17 Chinese sarcophagid species, were collected from 29 locations in 18 Chinese provinces. Sequence data of the mitochondrial COI and COII of the most important Chinese flesh fly taxa associated with cadavers were presented for first time, which serve as reference standards for Chinese species determination. Phylogenetic analysis showed that the COI and COII sequences were useful for identifying most sarcophagid species. The results of this research will be conductive for implementation of the Chinese Sarcophagidae in forensic entomology. However, the application of mitochondrial DNA as species identifier requires great circumspection and additional markers and methods should be studied to ensure accuracy of identification in the future.},
}
@article {pmid26336248,
year = {2015},
author = {Severini, F and Nocita, E and Tosini, F},
title = {Myiasis of the Tracheostomy Wound Caused by Sarcophaga (Liopygia) argyrostoma (Diptera: Sarcophagidae): Molecular Identification Based on the Mitochondrial Cytochrome c Oxidase I Gene.},
journal = {Journal of medical entomology},
volume = {52},
number = {6},
pages = {1357-1360},
doi = {10.1093/jme/tjv108},
pmid = {26336248},
issn = {0022-2585},
mesh = {Animals ; Child ; Humans ; Male ; Myiasis/*parasitology ; *Sarcophagidae ; Surgical Wound Infection/*parasitology ; *Tracheostomy ; },
abstract = {Wound myiasis is the infestation of open wounds of mammalian hosts caused by larvae of various species of flies. This kind of myiasis can be a serious problem for immobilized patients with open wounds. Here, we identify a dipteran larva found in the tracheostomy wound of a child affected by a severe spinal muscular atrophy. The collected larva was dissected and microscopically analyzed. DNA was extracted from part of the larva and used for the molecular identification. A 487 bp fragment, including part of 5.8 S, the internal transcribed spacer 2 (ITS2), and part of 28S, was amplified using a novel PCR assay to be cloned and sequenced. The barcode region of cytochrome oxidase I (COI) was also cloned and sequenced after PCR amplification. The larva, designated as SASI1, was identified as a third instar of Sarcophaga sp. The COI sequencing confirmed a low similarity with Sarcophaga ruficornis (F.) (95%), yet COI showed a 100% similarity with Sarcophaga argyrostoma (Robineau-Desvoidy, 1830) species. Therefore, SASI1 was identified as a S. argyrostoma larva on the basis of its COI barcode. This is one of the rare cases of myiasis of tracheostomy wound and the first caused by S. argyrostoma.},
}
@article {pmid26334805,
year = {2015},
author = {Salem, AM and Adham, FK and Picard, CJ},
title = {Survey of the Genetic Diversity of Forensically Important Chrysomya (Diptera: Calliphoridae) from Egypt.},
journal = {Journal of medical entomology},
volume = {52},
number = {3},
pages = {320-328},
doi = {10.1093/jme/tjv013},
pmid = {26334805},
issn = {0022-2585},
mesh = {Animals ; Cadaver ; Diptera/*classification/*genetics/growth &amp; development ; Egypt ; Electron Transport Complex IV/genetics/metabolism ; *Forensic Pathology ; *Genetic Variation ; Haplotypes ; Humans ; Insect Proteins/genetics/metabolism ; Larva/classification/genetics/growth &amp; development ; Mitochondrial Proteins/genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Postmortem Changes ; Sequence Analysis, DNA ; },
abstract = {Minimum postmortem interval estimations of a corpse using blow fly larvae in medicolegal investigations require correct identification and the application of appropriate developmental data of the identified fly species. Species identification of forensically relevant blow flies could be very difficult and time consuming when specimens are damaged or in the event of morphologically indistinguishable immature stages, which are most common at crime scenes. In response to this, an alternative, accurate determination of species may depend on sequencing and molecular techniques for identification. Chrysomyinae specimens (n = 158) belonging to three forensically important species [Chrysomya albiceps (Wiedemann), Chrysomya megacephala (F.), and Chrysomya marginalis (Wiedemann)] (Diptera: Calliphoridae) were collected from four locations in Egypt (Giza, Dayrout, Minya, and North Sinai) and sequenced across the mitochondrial cytochrome oxidase subunit I (COI) gene. Phylogenetic analyses using neighbor-joining, maximum likelihood and maximum parsimony methods resulted in the same topological structure and confirmed DNA based identification of all specimens. Interspecific divergence between pairs of species was 5.3% (C. marginalis-C. megacephala), 7% (C. albiceps-C. megacephala), and 8% (C. albiceps-C. marginalis). These divergences are sufficient to confirm the utility of cytochrome oxidase subunit I gene in the molecular identification of these flies in Egypt. Importantly, the maximum intraspecific divergence among individuals within a species was <1% and the least nucleotide divergence between species used for phylogenetic analysis was 3.6%. This study highlights the need for thorough and diverse sampling to capture all of the possible genetic diversity if DNA barcoding is to be used for molecular identification.},
}
@article {pmid26325177,
year = {2015},
author = {Tripathi, M and Das, A},
title = {Genotyping malaria parasites with DNA barcodes.},
journal = {Tropical medicine &amp; international health : TM &amp; IH},
volume = {20},
number = {12},
pages = {1636-1638},
doi = {10.1111/tmi.12594},
pmid = {26325177},
issn = {1365-3156},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Protozoan/*analysis ; Genome, Protozoan ; *Genotype ; Humans ; Malaria, Falciparum/*parasitology ; Malaria, Vivax/*parasitology ; Parasites/genetics ; Plasmodium falciparum/*genetics ; Plasmodium vivax/*genetics ; Polymorphism, Single Nucleotide ; },
}
@article {pmid26320965,
year = {2015},
author = {Chen, J and Ji, X and He, Z},
title = {High-throughput droplet analysis and multiplex DNA detection in the microfluidic platform equipped with a robust sample-introduction technique.},
journal = {Analytica chimica acta},
volume = {888},
number = {},
pages = {110-117},
doi = {10.1016/j.aca.2015.07.054},
pmid = {26320965},
issn = {1873-4324},
mesh = {DNA/*analysis ; DNA Barcoding, Taxonomic/economics/instrumentation ; Dimethylpolysiloxanes/chemistry ; Equipment Design ; Fluorescence ; High-Throughput Screening Assays/economics/*instrumentation ; Microfluidic Analytical Techniques/economics/*instrumentation ; Quantum Dots/*chemistry ; },
abstract = {In this work, a simple, flexible and low-cost sample-introduction technique was developed and integrated with droplet platform. The sample-introduction strategy was realized based on connecting the components of positive pressure input device, sample container and microfluidic chip through the tygon tubing with homemade polydimethylsiloxane (PDMS) adaptor, so the sample was delivered into the microchip from the sample container under the driving of positive pressure. This sample-introduction technique is so robust and compatible that could be integrated with T-junction, flow-focus or valve-assisted droplet microchips. By choosing the PDMS adaptor with proper dimension, the microchip could be flexibly equipped with various types of familiar sample containers, makes the sampling more straightforward without trivial sample transfer or loading. And the convenient sample changing was easily achieved by positioning the adaptor from one sample container to another. Benefiting from the proposed technique, the time-dependent concentration gradient was generated and applied for quantum dot (QD)-based fluorescence barcoding within droplet chip. High-throughput droplet screening was preliminarily demonstrated through the investigation of the quenching efficiency of ruthenium complex to the fluorescence of QD. More importantly, multiplex DNA assay was successfully carried out in the integrated system, which shows the practicability and potentials in high-throughput biosensing.},
}
@article {pmid26319519,
year = {2015},
author = {Ogedengbe, JD and Ogedengbe, ME and Hafeez, MA and Barta, JR},
title = {Molecular phylogenetics of eimeriid coccidia (Eimeriidae, Eimeriorina, Apicomplexa, Alveolata): A preliminary multi-gene and multi-genome approach.},
journal = {Parasitology research},
volume = {114},
number = {11},
pages = {4149-4160},
pmid = {26319519},
issn = {1432-1955},
mesh = {Apicoplasts ; Base Sequence ; Coccidia/*genetics/isolation &amp; purification ; Coccidiosis/*parasitology ; DNA Barcoding, Taxonomic ; DNA, Ribosomal/genetics ; Eimeria/classification ; Genome, Mitochondrial/*genetics ; Genome, Protozoan/*genetics ; Host-Pathogen Interactions ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Coccidia possess three distinct genomes: nuclear, mitochondrial, and plastid. Sequences from five genes located on these three genomes were used to reconstruct the phylogenetic relationships of members of the phylum Apicomplexa: 18S rDNA sequences from the nuclear (nu) genome, partial cytochrome c oxidase subunit I sequences from the mitochondrial (mt) genome, and partial 16S and 23S rDNA sequences and RNA polymerase B sequences from plastid (pl) genomes. Maximum parsimony, maximum likelihood, and Bayesian inference were used in conjunction with nuclear substitution models generated from data subsets in the analyses. Major groups within the Apicomplexa were well supported with the mitochondrial, nuclear, and a combination of mitochondrial, nuclear and concatenated plastid gene sequences. However, the genus Eimeria was paraphyletic in phylogenetic trees based on the nuclear gene. Analyses using the individual genes (18S rDNA and cytochrome c oxidase subunit I) resolved the various apicomplexan groups with high Bayesian posterior probabilities. The multi-gene, multi-genome analyses based on concatenated nu 18S rDNA, pl 16S, pl 23S, pl rPoB, pl rPoB1, and mt COI sequences appeared useful in resolving phylogenetic relationships within the phylum Apicomplexa. Genus-level relationships, or higher, appear best supported by 18S rDNA analyses, and species-level analyses are best investigated using mt COI sequences; for parasites for which both loci are available, nuclear 18S rDNA sequences combined with mitochondrial COI sequences provide a compact and informative molecular dataset for inferring the evolutionary relationships taxa in the Apicomplexa.},
}
@article {pmid26315429,
year = {2015},
author = {Tedersoo, L and Bahram, M and Põlme, S and Anslan, S and Riit, T and Kõljalg, U and Nilsson, RH and Hildebrand, F and Abarenkov, K},
title = {FUNGAL BIOGEOGRAPHY. Response to Comment on "Global diversity and geography of soil fungi".},
journal = {Science (New York, N.Y.)},
volume = {349},
number = {6251},
pages = {936},
doi = {10.1126/science.aaa5594},
pmid = {26315429},
issn = {1095-9203},
mesh = {Fungi/*classification/*physiology ; *Soil ; *Soil Microbiology ; },
abstract = {Schadt and Rosling (Technical Comment, 26 June 2015, p. 1438) argue that primer-template mismatches neglected the fungal class Archaeorhizomycetes in a global soil survey. Amplicon-based metabarcoding of nine barcode-primer pair combinations and polymerase chain reaction (PCR)-free shotgun metagenomics revealed that barcode and primer choice and PCR bias drive the diversity and composition of microorganisms in general, but the Archaeorhizomycetes were little affected in the global study. We urge that careful choice of DNA markers and primers is essential for ecological studies using high-throughput sequencing for identification.},
}
@article {pmid26313186,
year = {2015},
author = {Kajtoch, &#x141; and Mazur, MA},
title = {The Impact of Environmental Conditions on Efficiency of Host Plant DNA Barcoding for Polyphagous Beetles.},
journal = {Environmental entomology},
volume = {44},
number = {2},
pages = {325-329},
doi = {10.1093/ee/nvv019},
pmid = {26313186},
issn = {1938-2936},
mesh = {Animals ; Cold Temperature ; Czech Republic ; Droughts ; *Herbivory ; Poland ; Rain ; Seasons ; *Weather ; Weevils/*physiology ; },
abstract = {Recently, several papers were published dealing with host plant identification for selected species of insects, including beetles. These studies took advantage of the DNA barcoding approach and generally showed that it is possible to identify diet composition from plant DNA present in insect guts. However, none of these studies considered how the impact of environmental conditions affected the likelihood of insect feeding and, therefore, the presence of host plant DNA that could be amplified and sequenced. In the present study, individuals of the polyphagous weevil Centricnemus leucogrammus (Germar, 1824) (Curculionidae: Entiminae) were used to test the hypothesis that harsh environmental conditions limited its feeding activity. The diet of 50 specimens collected during favourable conditions in the middle of the species reproductive period was compared against the diet of 50 specimens collected during harsh environmental conditions. Results clearly showed that almost no weevils fed during rainy and cold conditions and only a minority of individuals (20%) fed during the drought condition (on drought-resistant plants). It is important to consider such factors in any studies dealing with host plant identification and feeding behaviour. Results of ecological studies could lead to erroneous conclusions, e.g., underestimation of number and composition of host plants in the diet of studies species.},
}
@article {pmid26309286,
year = {2014},
author = {Scheffer, SJ and Lewis, ML and Gaimari, SD and Reitz, SR},
title = {Molecular Survey for the Invasive Leafminer Pest Liriomyza huidobrensis (Diptera: Agromyzidae) in California Uncovers Only the Native Pest Liriomyza langei.},
journal = {Journal of economic entomology},
volume = {107},
number = {5},
pages = {1959-1964},
doi = {10.1603/EC13279},
pmid = {26309286},
issn = {0022-0493},
mesh = {Animals ; California ; DNA Barcoding, Taxonomic ; Diptera/classification/*genetics ; Electron Transport Complex IV/genetics ; Female ; Insect Proteins/genetics ; Introduced Species ; Male ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; },
abstract = {Liriomyza huidobrensis (Blanchard) is a highly destructive invasive leafminer pest currently causing extensive damage to vegetable and horticultural crops around the world. Liriomyza langei Frick is a leafminer pest native to California that cannot currently be morphologically distinguished from L. huidobrensis. We used a DNA-barcoding approach, a published PCR-RFLP method, and a new multiplex PCR method to analyze 664 flies matching the morphological description of huidobrensis-langei. We found no evidence for the presence of L. huidobrensis in our extensive samples from California. In addition to the new molecular method, this work is important because it provides definitive data that the California "pea leafminer" is currently, and has probably always been, L. langei. These data will also be important in the event that the highly invasive L. huidobrensis ever becomes established.},
}
@article {pmid26309035,
year = {2015},
author = {Koh, J and Wu, CY and Kittur, H and Di Carlo, D},
title = {Research highlights: microfluidically-fabricated materials.},
journal = {Lab on a chip},
volume = {15},
number = {19},
pages = {3818-3821},
doi = {10.1039/c5lc90092a},
pmid = {26309035},
issn = {1473-0189},
abstract = {Polymer particles with precise shapes or chemistries are finding unique uses in a variety of applications, including tissue engineering, drug delivery, barcoding, and diagnostic imaging. Microfluidic systems have been and are continuing to play a large role in enabling the precision synthesis of designer particles in a uniform manner. To expand the impact of these microfluidic-fabricated materials additional fundamental capabilities should still be developed. The capability to fabricate microparticles with complex three-dimensional shapes and increase the production rate of particles to an industrial scale will allow evaluation of shaped particles in a range of new applications to enhance biological, magnetic, optical, surface wetting, as well as other interfacial or mechanical properties of materials. Here we highlight work applying large collections of simple spherical microgels, with unique surface chemistry that allows in situ particle-particle annealing, to form microporous injectable scaffolds for accelerated tissue regeneration. We also report on two other techniques that are addressing the ability to create 3D-shaped microparticles by first sculpting a fluid precursor stream, and increasing the rate of production of particles using contact lithography to millions of particles per hour. The combination of these capabilities and the applications they will enable suggest a bright future for microfluidics in making the next materials.},
}
@article {pmid26308928,
year = {2015},
author = {Harada, AE and Lindgren, EA and Hermsmeier, MC and Rogowski, PA and Terrill, E and Burton, RS},
title = {Monitoring Spawning Activity in a Southern California Marine Protected Area Using Molecular Identification of Fish Eggs.},
journal = {PloS one},
volume = {10},
number = {8},
pages = {e0134647},
pmid = {26308928},
issn = {1932-6203},
mesh = {Animals ; California ; *Conservation of Natural Resources ; DNA Barcoding, Taxonomic ; Fishes/classification/*physiology ; *Ovum ; RNA, Ribosomal, 16S/genetics ; *Reproduction ; Seasons ; Surface Properties ; Temperature ; },
abstract = {In order to protect the diverse ecosystems of coastal California, a series of marine protected areas (MPAs) have been established. The ability of these MPAs to preserve and potentially enhance marine resources can only be assessed if these habitats are monitored through time. This study establishes a baseline for monitoring the spawning activity of fish in the MPAs adjacent to Scripps Institution of Oceanography (La Jolla, CA, USA) by sampling fish eggs from the plankton. Using vertical plankton net tows, 266 collections were made from the Scripps Pier between 23 August 2012 and 28 August 2014; a total of 21,269 eggs were obtained. Eggs were identified using DNA barcoding: the COI or 16S rRNA gene was amplified from individual eggs and sequenced. All eggs that were successfully sequenced could be identified from a database of molecular barcodes of California fish species, resulting in species-level identification of 13,249 eggs. Additionally, a surface transport model of coastal circulation driven by current maps from high frequency radar was used to construct probability maps that estimate spawning locations that gave rise to the collected eggs. These maps indicated that currents usually come from the north but water parcels tend to be retained within the MPA; eggs sampled at the Scripps Pier have a high probability of having been spawned within the MPA. The surface transport model also suggests that although larvae have a high probability of being retained within the MPA, there is also significant spillover into nearby areas outside the MPA. This study provides an important baseline for addressing the extent to which spawning patterns of coastal California species may be affected by future changes in the ocean environment.},
}
@article {pmid26308620,
year = {2015},
author = {Andreakis, N and Høj, L and Kearns, P and Hall, MR and Ericson, G and Cobb, RE and Gordon, BR and Evans-Illidge, E},
title = {Diversity of Marine-Derived Fungal Cultures Exposed by DNA Barcodes: The Algorithm Matters.},
journal = {PloS one},
volume = {10},
number = {8},
pages = {e0136130},
pmid = {26308620},
issn = {1932-6203},
mesh = {*Algorithms ; Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/genetics ; Fungi/classification/genetics/*isolation &amp; purification ; Genetic Variation/*genetics ; Phylogeny ; Porifera/*microbiology ; Seawater/*microbiology ; Sequence Analysis, DNA/methods ; Species Specificity ; },
abstract = {Marine fungi are an understudied group of eukaryotic microorganisms characterized by unresolved genealogies and unstable classification. Whereas DNA barcoding via the nuclear ribosomal internal transcribed spacer (ITS) provides a robust and rapid tool for fungal species delineation, accurate classification of fungi is often arduous given the large number of partial or unknown barcodes and misidentified isolates deposited in public databases. This situation is perpetuated by a paucity of cultivable fungal strains available for phylogenetic research linked to these data sets. We analyze ITS barcodes produced from a subsample (290) of 1781 cultured isolates of marine-derived fungi in the Bioresources Library located at the Australian Institute of Marine Science (AIMS). Our analysis revealed high levels of under-explored fungal diversity. The majority of isolates were ascomycetes including representatives of the subclasses Eurotiomycetidae, Hypocreomycetidae, Sordariomycetidae, Pleosporomycetidae, Dothideomycetidae, Xylariomycetidae and Saccharomycetidae. The phylum Basidiomycota was represented by isolates affiliated with the genera Tritirachium and Tilletiopsis. BLAST searches revealed 26 unknown OTUs and 50 isolates corresponding to previously uncultured, unidentified fungal clones. This study makes a significant addition to the availability of barcoded, culturable marine-derived fungi for detailed future genomic and physiological studies. We also demonstrate the influence of commonly used alignment algorithms and genetic distance measures on the accuracy and comparability of estimating Operational Taxonomic Units (OTUs) by the automatic barcode gap finder (ABGD) method. Large scale biodiversity screening programs that combine datasets using algorithmic OTU delineation pipelines need to ensure compatible algorithms have been used because the algorithm matters.},
}
@article {pmid26308362,
year = {2015},
author = {Hawkins, J and de Vere, N and Griffith, A and Ford, CR and Allainguillaume, J and Hegarty, MJ and Baillie, L and Adams-Groom, B},
title = {Using DNA Metabarcoding to Identify the Floral Composition of Honey: A New Tool for Investigating Honey Bee Foraging Preferences.},
journal = {PloS one},
volume = {10},
number = {8},
pages = {e0134735},
pmid = {26308362},
issn = {1932-6203},
mesh = {Animals ; *Bees ; *Behavior, Animal ; *DNA Barcoding, Taxonomic ; Flowers/*chemistry/*genetics ; High-Throughput Nucleotide Sequencing ; Honey/*analysis ; Pollen ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Analysis, DNA ; },
abstract = {Identifying the floral composition of honey provides a method for investigating the plants that honey bees visit. We compared melissopalynology, where pollen grains retrieved from honey are identified morphologically, with a DNA metabarcoding approach using the rbcL DNA barcode marker and 454-pyrosequencing. We compared nine honeys supplied by beekeepers in the UK. DNA metabarcoding and melissopalynology were able to detect the most abundant floral components of honey. There was 92% correspondence for the plant taxa that had an abundance of over 20%. However, the level of similarity when all taxa were compared was lower, ranging from 22-45%, and there was little correspondence between the relative abundance of taxa found using the two techniques. DNA metabarcoding provided much greater repeatability, with a 64% taxa match compared to 28% with melissopalynology. DNA metabarcoding has the advantage over melissopalynology in that it does not require a high level of taxonomic expertise, a greater sample size can be screened and it provides greater resolution for some plant families. However, it does not provide a quantitative approach and pollen present in low levels are less likely to be detected. We investigated the plants that were frequently used by honey bees by examining the results obtained from both techniques. Plants with a broad taxonomic range were detected, covering 46 families and 25 orders, but a relatively small number of plants were consistently seen across multiple honey samples. Frequently found herbaceous species were Rubus fruticosus, Filipendula ulmaria, Taraxacum officinale, Trifolium spp., Brassica spp. and the non-native, invasive, Impatiens glandulifera. Tree pollen was frequently seen belonging to Castanea sativa, Crataegus monogyna and species of Malus, Salix and Quercus. We conclude that although honey bees are considered to be supergeneralists in their foraging choices, there are certain key species or plant groups that are particularly important in the honey bees environment. The reasons for this require further investigation in order to better understand honey bee nutritional requirements. DNA metabarcoding can be easily and widely used to investigate floral visitation in honey bees and can be adapted for use with other insects. It provides a starting point for investigating how we can better provide for the insects that we rely upon for pollination.},
}
@article {pmid26306177,
year = {2015},
author = {Holguin, CM and Baeza, JA and Mueller, JD and Agudelo, P},
title = {High genetic diversity and geographic subdivision of three lance nematode species (Hoplolaimus spp.) in the United States.},
journal = {Ecology and evolution},
volume = {5},
number = {14},
pages = {2929-2944},
pmid = {26306177},
issn = {2045-7758},
abstract = {Lance nematodes (Hoplolaimus spp.) feed on the roots of a wide range of plants, some of which are agronomic crops. Morphometric values of amphimictic lance nematode species overlap considerably, and useful morphological characters for their discrimination require high magnification and significant diagnostic time. Given their morphological similarity, these Hoplolaimus species provide an interesting model to investigate hidden diversity in crop agroecosystems. In this scenario, H. galeatus may have been over-reported and the related species that are morphologically similar could be more widespread in the United States that has been recognized thus far. The main objectives of this study were to delimit Hoplolaimus galeatus and morphologically similar species using morphology, phylogeny, and a barcoding approach, and to estimate the genetic diversity and population structure of the species found. Molecular analyses were performed using sequences of the cytochrome c oxidase subunit 1 (Cox1) and the internal transcribed spacer (ITS1) on 23 populations. Four morphospecies were identified: H. galeatus, H. magnistylus, H. concaudajuvencus, and H. stephanus, along with a currently undescribed species. Pronounced genetic structure correlated with geographic origin was found for all species, except for H. galeatus. Hoplolaimus galeatus also exhibited low genetic diversity and the shortest genetic distances among populations. In contrast, H. stephanus, the species with the fewest reports from agricultural soils, was the most common and diverse species found. Results of this project may lead to better delimitation of lance nematode species in the United States by contributing to the understanding the diversity within this group.},
}
@article {pmid26305111,
year = {2015},
author = {Basset, Y and Barrios, H and Segar, S and Srygley, RB and Aiello, A and Warren, AD and Delgado, F and Coronado, J and Lezcano, J and Arizala, S and Rivera, M and Perez, F and Bobadilla, R and Lopez, Y and Ramirez, JA},
title = {The Butterflies of Barro Colorado Island, Panama: Local Extinction since the 1930s.},
journal = {PloS one},
volume = {10},
number = {8},
pages = {e0136623},
pmid = {26305111},
issn = {1932-6203},
mesh = {Animals ; Butterflies/*genetics/physiology ; *DNA Barcoding, Taxonomic ; Ecosystem ; *Extinction, Biological ; Islands ; Panama ; *Phylogeny ; Tropical Climate ; },
abstract = {Few data are available about the regional or local extinction of tropical butterfly species. When confirmed, local extinction was often due to the loss of host-plant species. We used published lists and recent monitoring programs to evaluate changes in butterfly composition on Barro Colorado Island (BCI, Panama) between an old (1923-1943) and a recent (1993-2013) period. Although 601 butterfly species have been recorded from BCI during the 1923-2013 period, we estimate that 390 species are currently breeding on the island, including 34 cryptic species, currently only known by their DNA Barcode Index Number. Twenty-three butterfly species that were considered abundant during the old period could not be collected during the recent period, despite a much higher sampling effort in recent times. We consider these species locally extinct from BCI and they conservatively represent 6% of the estimated local pool of resident species. Extinct species represent distant phylogenetic branches and several families. The butterfly traits most likely to influence the probability of extinction were host growth form, wing size and host specificity, independently of the phylogenetic relationships among butterfly species. On BCI, most likely candidates for extinction were small hesperiids feeding on herbs (35% of extinct species). However, contrary to our working hypothesis, extinction of these species on BCI cannot be attributed to loss of host plants. In most cases these host plants remain extant, but they probably subsist at lower or more fragmented densities. Coupled with low dispersal power, this reduced availability of host plants has probably caused the local extinction of some butterfly species. Many more bird than butterfly species have been lost from BCI recently, confirming that small preserves may be far more effective at conserving invertebrates than vertebrates and, therefore, should not necessarily be neglected from a conservation viewpoint.},
}
@article {pmid26300957,
year = {2015},
author = {Liao, B and Chen, X and Han, J and Dan, Y and Wang, L and Jiao, W and Song, J and Chen, S},
title = {Identification of commercial Ganoderma (Lingzhi) species by ITS2 sequences.},
journal = {Chinese medicine},
volume = {10},
number = {},
pages = {22},
pmid = {26300957},
issn = {1749-8546},
abstract = {BACKGROUND: DNA barcoding can be used to authenticate Ganoderma species for safe use. This study aims to identify commercial products containing Ganoderma using DNA barcoding.<br><br>METHODS: We used 63 internal transcribed spacer (ITS) 2 sequences of Ganoderma species from 33 newly-sequenced wild samples, crude drugs, mycelia, spores, and authentic extracts and spore oils collected from various locations and markets, as well as 30 sequences from GenBank. Sequences were assembled and aligned using CodonCode Aligner V3.71. Intra- and inter-specific distances were estimated by MEGA 6.0, and phylogeny reconstruction was based on the K2P model. SNP(s) and RNA secondary structure of ITS2 were analyzed and compared among closely related Ganoderma species.<br><br>RESULTS: G. lucidum cultivated in China was different from those cultivated in Europe. "Chizhi" (G. lucidum) and "Zizhi" (G. sinense) were clustered into two clades that were separated from the other Ganoderma species. The fruiting bodies and commercial products of G. lucidum and G. sinense were successfully distinguished from those of other Ganoderma species by comparing the ITS2 sequences and RNA secondary structures.<br><br>CONCLUSION: The DNA barcoding method is applicable to the authentication of commercial products containing Ganoderma species.},
}
@article {pmid26299473,
year = {2015},
author = {Mayer, C and Jaglin, XH and Cobbs, LV and Bandler, RC and Streicher, C and Cepko, CL and Hippenmeyer, S and Fishell, G},
title = {Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.},
journal = {Neuron},
volume = {87},
number = {5},
pages = {989-998},
pmid = {26299473},
issn = {1097-4199},
support = {P01 NS074972/NS/NINDS NIH HHS/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; MH095147/MH/NIMH NIH HHS/United States ; P01NS074972/NS/NINDS NIH HHS/United States ; R01 MH095147/MH/NIMH NIH HHS/United States ; R37 MH071679/MH/NIMH NIH HHS/United States ; R01 NS081297/NS/NINDS NIH HHS/United States ; R01 MH071679/MH/NIMH NIH HHS/United States ; NS 081297/NS/NINDS NIH HHS/United States ; },
mesh = {1-Alkyl-2-acetylglycerophosphocholine Esterase/genetics/metabolism ; Animals ; Carrier Proteins/genetics/metabolism ; Cell Differentiation/physiology ; Cell Movement/*physiology ; DNA Barcoding, Taxonomic ; Embryo, Mammalian ; Gene Expression Regulation, Developmental/*physiology ; Gene Library ; Geniculate Bodies/*cytology/embryology ; Interneurons/*physiology ; Luminescent Proteins/genetics/metabolism ; Mice ; Mice, Transgenic ; Microdissection ; Microtubule-Associated Proteins/genetics/metabolism ; Nestin/genetics/metabolism ; Nuclear Proteins/genetics ; Prosencephalon/*cytology/embryology ; Stem Cells/*physiology ; Thyroid Nuclear Factor 1 ; Time Factors ; Transcription Factors/genetics ; },
abstract = {The medial ganglionic eminence (MGE) gives rise to the majority of mouse forebrain interneurons. Here, we examine the lineage relationship among MGE-derived interneurons using a replication-defective retroviral library containing a highly diverse set of DNA barcodes. Recovering the barcodes from the mature progeny of infected progenitor cells enabled us to unambiguously determine their respective lineal relationship. We found that clonal dispersion occurs across large areas of the brain and is not restricted by anatomical divisions. As such, sibling interneurons can populate the cortex, hippocampus striatum, and globus pallidus. The majority of interneurons appeared to be generated from asymmetric divisions of MGE progenitor cells, followed by symmetric divisions within the subventricular zone. Altogether, our findings uncover that lineage relationships do not appear to determine interneuron allocation to particular regions. As such, it is likely that clonally related interneurons have considerable flexibility as to the particular forebrain circuits to which they can contribute.},
}
@article {pmid26286230,
year = {2015},
author = {Seifert, CL and Bodner, F and Brehm, G and Fiedler, K},
title = {Host Plant Associations and Parasitism of South Ecuadorian Eois Species (Lepidoptera: Geometridae) Feeding on Peperomia (Piperaceae).},
journal = {Journal of insect science (Online)},
volume = {15},
number = {1},
pages = {},
pmid = {26286230},
issn = {1536-2442},
mesh = {Animals ; Ecuador ; *Herbivory ; Larva/classification/growth &amp; development/parasitology/physiology ; Moths/classification/growth &amp; development/*parasitology/*physiology ; Peperomia/growth &amp; development ; Species Specificity ; Wasps/*physiology ; },
abstract = {The very species-rich tropical moth genus Eois Hübner (Lepidoptera: Geometridae) is a promising model group for studying host plant specialization and adaptive radiation. While most Eois species are assumed to be specialized herbivores on Piper L. species, records on other plant taxa such as Peperomia Ruiz &amp; Pavón (Piperaceae) are still relatively scarce. Moreover, little is known about life history traits of most species, and only a few caterpillars have been described so far. We collected caterpillars associated with Peperomia (Piperaceae) host plants from June 2012 to January 2013 in three elevational bands of montane and elfin rainforests on the eastern slopes of the Andes in southern Ecuador. Caterpillars were systematically searched and reared to the adult stage. We were able to delimitate ten species of Eois on Peperomia by comparison of larval and adult morphology and by using 658 bp fragments of the mitochondrial COI gene (barcode sequences). Three of these species, Eois albosignata (Dognin), Eois bolana (Dognin), and Eois chasca (Dognin), are validly described whereas the other seven taxa represent interim morphospecies, recognized unequivocally by their DNA barcodes, and their larval and adult morphology. We provide information about their host plants, degree of parasitism, and describe the larval stages in their last instar. Additionally, caterpillars and moths are illustrated in color plates. This is the first comparative study dealing with Eois moths whose caterpillars feed on Peperomia hosts.},
}
@article {pmid26284104,
year = {2015},
author = {Larranaga, N and Hormaza, JI},
title = {DNA barcoding of perennial fruit tree species of agronomic interest in the genus Annona (Annonaceae).},
journal = {Frontiers in plant science},
volume = {6},
number = {},
pages = {589},
pmid = {26284104},
issn = {1664-462X},
abstract = {The DNA barcode initiative aims to establish a universal protocol using short genetic sequences to discriminate among animal and plant species. Although many markers have been proposed to become the barcode of plants, the Consortium for the Barcode of Life (CBOL) Plant Working Group recommended using as a core the combination of two portions of plastid coding region, rbcL and matK. In this paper, specific markers based on matK sequences were developed for 7 closely related Annona species of agronomic interest (Annona cherimola, A. reticulata, A. squamosa, A. muricata, A. macroprophyllata, A. glabra, and A. purpurea) and the discrimination power of both rbcL and matK was tested using also sequences of the genus Annona available in the Barcode of Life Database (BOLD) data systems. The specific sequences developed allowed the discrimination among all those species tested. Moreover, the primers generated were validated in six additional species of the genus (A. liebmanniana, A. longiflora, A. montana, A. senegalensis, A. emarginata and A. neosalicifolia) and in an interspecific hybrid (A. cherimola x A. squamosa). The development of a fast, reliable and economic approach for species identification in these underutilized subtropical fruit crops in a very initial state of domestication is of great importance in order to optimize genetic resource management.},
}
@article {pmid26281578,
year = {2015},
author = {Dou, RK and Bi, ZF and Bai, RX and Ren, YY and Tan, R and Song, LK and Li, DQ and Mao, CQ},
title = {[Identification and analysis of Corydalis boweri, Meconopsis horridula and their close related species of the same genus by using ITS2 DNA barcode].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {40},
number = {8},
pages = {1453-1458},
pmid = {26281578},
issn = {1001-5302},
mesh = {Base Sequence ; China ; Corydalis/chemistry/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/chemistry/*genetics ; DNA, Ribosomal Spacer/chemistry/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Papaveraceae/chemistry/*classification/genetics ; Phylogeny ; Plants, Medicinal/chemistry/classification/genetics ; },
abstract = {The study is aimed to ensure the quality and safety of medicinal plants by using ITS2 DNA barcode technology to identify Corydalis boweri, Meconopsis horridula and their close related species. The DNA of 13 herb samples including C. boweri and M. horridula from Lhasa of Tibet was extracted, ITS PCR were amplified and sequenced. Both assembled and web downloaded 71 ITS2 sequences were removed of 5. 8S and 28S. Multiple sequence alignment was completed and the intraspecific and interspecific genetic distances were calculated by MEGA 5.0, while the neighbor-joining phylogenetic trees were constructed. We also predicted the ITS2 secondary structure of C. boweri, M. horridula and their close related species. The results showed that ITS2 as DNA barcode was able to identify C. boweri, M. horridula as well as well as their close related species effectively. The established based on ITS2 barcode method provides the regular and safe detection technology for identification of C. boweri, M. horridula and their close related species, adulterants and counterfeits, in order to ensure their quality control, safe medication, reasonable development and utilization.},
}
@article {pmid26276524,
year = {2015},
author = {Locke, SA and Al-Nasiri, FS and Caffara, M and Drago, F and Kalbe, M and Lapierre, AR and McLaughlin, JD and Nie, P and Overstreet, RM and Souza, GT and Takemoto, RM and Marcogliese, DJ},
title = {Diversity, specificity and speciation in larval Diplostomidae (Platyhelminthes: Digenea) in the eyes of freshwater fish, as revealed by DNA barcodes.},
journal = {International journal for parasitology},
volume = {45},
number = {13},
pages = {841-855},
doi = {10.1016/j.ijpara.2015.07.001},
pmid = {26276524},
issn = {1879-0135},
mesh = {Animals ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Eye Diseases/parasitology/*veterinary ; Fish Diseases/*parasitology ; Fresh Water/parasitology ; Genetic Variation ; Larva ; Life Cycle Stages/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Trematoda/classification/*genetics/isolation &amp; purification ; },
abstract = {Larvae (metacercariae) in some species of Diplostomidae (Platyhelminthes: Digenea) inhabit fish eyes and are difficult to identify to species based on morphology. DNA barcoding has clarified the diversity and life cycles of diplostomids in North America, Europe and Africa, but has seldom been used in parasites sampled in large numbers or at large spatial scales. Here, distance-based analysis of cytochrome c oxidase 1 barcodes and, in some specimens, internal transcribed spacer (ITS-1, 5.8S, ITS-2) sequences was performed for over 2000 diplostomids from Africa, the Middle East, Europe, Asia and the Americas. Fifty-two species of Diplostomum, Tylodelphys and Austrodiplostomum (Digenea: Diplostomidae) were distinguished. The 52 species comprise 12 identified species, six species in two species complexes and 34 putative species, and 33/52 had been delineated in previous studies. Most (23/40) of the unidentified, putative species distinguished by cytochrome c oxidase 1 distances were supported by at least one additional line of evidence. As the intensity of sampling of the 52 species increased, variation in cytochrome c oxidase 1 decreased between and increased within species, while the spatial scale at which species were sampled had no effect. Nonetheless, variation between species always exceeded variation within species. New life-cycle linkages, geographic and host records, and genetic data were recorded in several species, including Tylodelphys jenynsiae, Tylodelphys immer and Diplostomum ardeae. Species of Diplostomum inhabiting the lens are less host-specific and less numerous than those infecting other tissues, suggesting that reduced immune activity in the lens has influenced rates of speciation.},
}
@article {pmid26270958,
year = {2015},
author = {Wu, L and Sun, W and Wang, B and Zhao, H and Li, Y and Cai, S and Xiang, L and Zhu, Y and Yao, H and Song, J and Cheng, YC and Chen, S},
title = {An integrated system for identifying the hidden assassins in traditional medicines containing aristolochic acids.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {11318},
pmid = {26270958},
issn = {2045-2322},
mesh = {Aristolochiaceae/classification/*genetics/metabolism ; Aristolochic Acids/*analysis/genetics ; DNA Barcoding, Taxonomic/*methods ; Drug Contamination/*prevention &amp; control ; Drugs, Chinese Herbal/*analysis/chemistry ; Medicine, Traditional/methods ; Real-Time Polymerase Chain Reaction/*methods ; Systems Integration ; Technology, Pharmaceutical/methods ; },
abstract = {Traditional herbal medicines adulterated and contaminated with plant materials from the Aristolochiaceae family, which contain aristolochic acids (AAs), cause aristolochic acid nephropathy. Approximately 256 traditional Chinese patent medicines, containing Aristolochiaceous materials, are still being sold in Chinese markets today. In order to protect consumers from health risks due to AAs, the hidden assassins, efficient methods to differentiate Aristolochiaceous herbs from their putative substitutes need to be established. In this study, 158 Aristolochiaceous samples representing 46 species and four genera as well as 131 non-Aristolochiaceous samples representing 33 species, 20 genera and 12 families were analyzed using DNA barcodes based on the ITS2 and psbA-trnH sequences. Aristolochiaceous materials and their non-Aristolochiaceous substitutes were successfully identified using BLAST1, the nearest distance method and the neighbor-joining (NJ) tree. In addition, based on sequence information of ITS2, we developed a Real-Time PCR assay which successfully identified herbal material from the Aristolochiaceae family. Using Ultra High Performance Liquid Chromatography-Mass Spectrometer (UHPLC-HR-MS), we demonstrated that most representatives from the Aristolochiaceae family contain toxic AAs. Therefore, integrated DNA barcodes, Real-Time PCR assays using TaqMan probes and UHPLC-HR-MS system provides an efficient and reliable authentication system to protect consumers from health risks due to the hidden assassins (AAs).},
}
@article {pmid26265257,
year = {2015},
author = {Schwarzfeld, MD and Sperling, FA},
title = {Comparison of five methods for delimitating species in Ophion Fabricius, a diverse genus of parasitoid wasps (Hymenoptera, Ichneumonidae).},
journal = {Molecular phylogenetics and evolution},
volume = {93},
number = {},
pages = {234-248},
doi = {10.1016/j.ympev.2015.08.003},
pmid = {26265257},
issn = {1095-9513},
mesh = {Animals ; DNA Barcoding, Taxonomic/methods ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Genes, Insect ; Genetic Markers ; Insect Proteins/genetics ; Phylogeny ; Sequence Analysis, DNA ; Wasps/*classification/genetics ; },
abstract = {DNA taxonomy has been proposed as a method to quickly assess diversity and species limits in highly diverse, understudied taxa. Here we use five methods for species delimitation and two genetic markers (COI and ITS2) to assess species diversity within the parasitoid genus, Ophion. We searched for compensatory base changes (CBC's) in ITS2, and determined that they are too rare to be of practical use in delimiting species in this genus. The other four methods used both COI and ITS2, and included distance-based (threshold analysis and ABGD) and tree-based (GMYC and PTP) models. We compared the results of these analyses to each other under various parameters and tested their performance with respect to 11 Nearctic species/morphospecies and 15 described Palearctic species. We also computed barcode accumulation curves of COI sequences to assess the completeness of sampling. The species count was highly variable depending on the method and parameters used, ranging from 47 to 168 species, with more conservative estimates of 89-121 species. Despite this range, many of the Nearctic test species were fairly robust with respect to method. We concluded that while there was often good congruence between methods, GMYC and PTP were less reliant on arbitrary parameters than the other two methods and more easily applied to genetic markers other than COI. However, PTP was less successful at delimiting test species than was GMYC. All methods, as well as the barcode accumulation curves, indicate that several Palearctic species remain undescribed and that we have scarcely begun to appreciate the Nearctic diversity within this genus.},
}
@article {pmid26263904,
year = {2015},
author = {Grabner, DS and Weigand, AM and Leese, F and Winking, C and Hering, D and Tollrian, R and Sures, B},
title = {Invaders, natives and their enemies: distribution patterns of amphipods and their microsporidian parasites in the Ruhr Metropolis, Germany.},
journal = {Parasites &amp; vectors},
volume = {8},
number = {},
pages = {419},
pmid = {26263904},
issn = {1756-3305},
mesh = {Amphipoda/genetics/*parasitology ; Animals ; DNA/genetics ; DNA Barcoding, Taxonomic ; Ecosystem ; Germany ; Host-Parasite Interactions ; Introduced Species ; Microsporidia/isolation &amp; purification/*physiology ; Phylogeny ; Rivers ; Species Specificity ; },
abstract = {BACKGROUND: The amphipod and microsporidian diversity in freshwaters of a heterogeneous urban region in Germany was assessed. Indigenous and non-indigenous host species provide an ideal framework to test general hypotheses on potentially new host-parasite interactions, parasite spillback and spillover in recently invaded urban freshwater communities.<br><br>METHODS: Amphipods were sampled in 17 smaller and larger streams belonging to catchments of the four major rivers in the Ruhr Metropolis (Emscher, Lippe, Ruhr, Rhine), including sites invaded and not invaded by non-indigenous amphipods. Species were identified morphologically (hosts only) and via DNA barcoding (hosts and parasites). Prevalence was obtained by newly designed parasite-specific PCR assays.<br><br>RESULTS: Three indigenous and five non-indigenous amphipod species were detected. Gammarus pulex was further distinguished into three clades (C, D and E) and G. fossarum more precisely identified as type B. Ten microsporidian lineages were detected, including two new isolates (designated as Microsporidium sp. nov. RR1 and RR2). All microsporidians occurred in at least two different host clades or species. Seven genetically distinct microsporidians were present in non-invaded populations, six of those were also found in invaded assemblages. Only Cucumispora dikerogammari and Dictyocoela berillonum can be unambiguously considered as non-indigenous co-introduced parasites. Both were rare and were not observed in indigenous hosts. Overall, microsporidian prevalence ranged from 50% (in G. roeselii and G. pulex C) to 73% (G. fossarum) in indigenous and from 10% (Dikerogammarus villosus) to 100 % (Echinogammarus trichiatus) in non-indigenous amphipods. The most common microsporidians belonged to the Dictyocoela duebenum- /D. muelleri- complex, found in both indigenous and non-indigenous hosts. Some haplotype clades were inclusive for a certain host lineage.<br><br>CONCLUSIONS: The Ruhr Metropolis harbours a high diversity of indigenous and non-indigenous amphipod and microsporidian species, and we found indications for an exchange of parasites between indigenous and non-indigenous hosts. No introduced microsporidians were found in indigenous hosts and prevalence of indigenous parasites in non-indigenous hosts was generally low. Therefore, no indication for parasite spillover or spillback was found. We conclude that non-indigenous microsporidians constitute only a minimal threat to the native amphipod fauna. However, this might change e.g. if C. dikerogammari adapts to indigenous amphipod species or if other hosts and parasites invade.},
}
@article {pmid26262221,
year = {2015},
author = {Liu, HC and Li, H and Chang, HF and Lu, MR and Chen, FC},
title = {Application of Barcoding to Reduce Error of Patient Identification and to Increase Patient's Information Confidentiality of Test Tube Labelling in a Psychiatric Teaching Hospital.},
journal = {Studies in health technology and informatics},
volume = {216},
number = {},
pages = {919},
pmid = {26262221},
issn = {1879-8365},
mesh = {Blood Specimen Collection/methods ; *Confidentiality ; *Electronic Data Processing ; Hospitals, Psychiatric ; Hospitals, Teaching ; Humans ; Medical Errors/*prevention &amp; control ; Patient Identification Systems/*methods ; Taiwan ; },
abstract = {Learning from the experience of another medical center in Taiwan, Kaohsiung Municipal Kai-Suan Psychiatric Hospital has changed the nursing informatics system step by step in the past year and a half . We considered ethics in the original idea of implementing barcodes on the test tube labels to process the identification of the psychiatric patients. The main aims of this project are to maintain the confidential information and to transport the sample effectively. The primary nurses had been using different work sheets for this project to ensure the acceptance of the new barcode system. In the past two years the errors in the blood testing process were as high as 11,000 in 14,000 events per year, resulting in wastage of resources. The actions taken by the nurses and the new barcode system implementation can improve the clinical nursing care quality, safety of the patients, and efficiency, while decreasing the cost due to the human error.},
}
@article {pmid26261436,
year = {2015},
author = {Amora, G and Hamada, N and Fusari, LM and Andrade-Souza, V},
title = {An Asiatic Chironomid in Brazil: morphology, DNA barcode and bionomics.},
journal = {ZooKeys},
volume = {},
number = {514},
pages = {129-144},
pmid = {26261436},
issn = {1313-2989},
abstract = {In most freshwater ecosystems, aquatic insects are dominant in terms of diversity; however, there is a disproportionately low number of records of alien species when compared to other freshwater organisms. The Chironomidae is one aquatic insect family that includes some examples of alien species around the world. During a study on aquatic insects in Amazonas state (Brazil), we collected specimens of Chironomidae that are similar, at the morphological level, to Chironomuskiiensis Tokunaga and Chironomusstriatipennis Kieffer, both with distributions restricted to Asia. The objectives of this study were to provide morphological information on this Chironomus population, to investigate its identity using DNA barcoding and, to provide bionomic information about this species. Chironomus DNA barcode data were obtained from GenBank and Barcode of Life Data Systems (BOLD) and, together with our data, were analyzed using the neighbor-joining method with 1000 bootstrap replicates and the genetic distances were estimated using the Kimura-2-parameter. At the morphological level, the Brazilian population cannot be distinguished either from Chironomusstriatipennis or Chironomuskiiensis, configuring a species complex but, at the molecular level our studied population is placed in a clade together with Chironomusstriatipennis, from South Korea. Bionomic characteristics of the Brazilian Chironomus population differ from the ones of Chironomuskiiensis from Japan, the only species in this species complex with bionomic information available. The Brazilian Chironomus population has a smaller size, the double of the number of eggs and inhabits oligotrophic water, in artificial container. In the molecular analysis, populations of Chironomusstriatipennis and Chironomuskiiensis are placed in a clade, formed by two groups: Group A (which includes populations from both named species, from different Asiatic regions and our Brazilian population) and Group B (with populations of Chironomuskiiensis from Japan and South Korea). Genetic distance between the Brazilian population and specimens in Group A suggests that it was recently introduced in Brazil, and that its country of origin is probably South Korea.},
}
@article {pmid26260182,
year = {2016},
author = {Zhao, J and Li, W and Wen, P and Zhang, D and Zhu, X},
title = {Genetic diversity and relationship of Mauremys mutica and M. annamensis assessed by DNA barcoding sequences.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3507-3510},
doi = {10.3109/19401736.2015.1066370},
pmid = {26260182},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Phylogeny ; Turtles/*classification/genetics ; },
abstract = {The mitochondrial DNA cytochrome c oxidase subunit I gene (COI) has been used as an efficient barcoding tool for species identification of animals. In this study, the barcoding sequences were used to assess the genetic diversity and relationship of Mauremy mutica and M. annamensis. Four currently recognized groups of M. mutica were classified into two groups in this study, with 6% intergroup distances, the S group and the N group, consistent to the calling of "southern turtle" and "northern turtle" in folk of China. The north population and Taiwan population formed the N group, and further, the Taiwan population was differentiated as a monophyly originated from the north population, consistent to the calling of "big green head" for the Taiwan population and "small green head" for the north population. The Vietnam, Hainan population, and M. annamensis formed the S group, and the barcoding sequences could not distinguish them from each other. Based on the molecular data and phenotypes of existing hybrids, hybrid origin of M. annamensis may be another possibility.},
}
@article {pmid26258502,
year = {2016},
author = {Tahir, HM and Kanwal, N and Mehwish, },
title = {The sequence divergence in cytochrome C oxidase I gene of Culex quinquefasciatus mosquito and its comparison with four other Culex species.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {4},
pages = {3054-3057},
doi = {10.3109/19401736.2015.1063138},
pmid = {26258502},
issn = {2470-1408},
mesh = {Animals ; Culex/*classification/*genetics ; Databases, Nucleic Acid ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; *Genetic Variation ; Genome, Mitochondrial ; Phylogeny ; Sequence Analysis, DNA ; Whole Genome Sequencing ; },
abstract = {The genetic diversity of Culex quinquefasciatus mosquito based on the standard barcode region of cytochrome C oxidase I (COI) gene fragment was studied in the present study. The COI gene sequences of Cx. quinquefasciatus were also compared with four other species of Genus Culex (i.e. Cx. tritaeniorhynchus, Cx. fuscocephala, Cx. pipiens, and Cx. theileri). Our data set included sequences of Culex mosquitoes from 16 different countries of world. The average intraspecific and interspecific divergences recorded were 0.67% and 8.27%, respectively. The clades for five species were clearly separated except Cx. quinquefasciatus and Cx. pipiens. It is concluded that the DNA barcoding is effective and reliable tool for the identification of selected Culex species but create little problem in case of sister species.},
}
@article {pmid26257572,
year = {2015},
author = {Baldwin, CC and Robertson, DR},
title = {A new, mesophotic Coryphopterus goby (Teleostei, Gobiidae) from the southern Caribbean, with comments on relationships and depth distributions within the genus.},
journal = {ZooKeys},
volume = {},
number = {513},
pages = {123-142},
pmid = {26257572},
issn = {1313-2989},
abstract = {A new species of western Atlantic Coryphopterus is described from mesophotic depths off Curaçao, southern Caribbean. Coryphopteruscurasub sp. n., is similar to Coryphopterusdicrus in, among other features, having two prominent pigment spots of roughly equal intensity on the pectoral-fin base, the pelvic fins fused to form a disk, and no pelvic frenum. The two species can be differentiated by body depth (shallower in Coryphopteruscurasub at origin of dorsal fin and caudal peduncle); differences in the pigmentation on the head, trunk, and basicaudal region; and usually by total number of rays (spinous plus soft) in the second dorsal fin (10-11, usually 11, in Coryphopteruscurasub, 10 in Coryphopterusdicrus). Coryphopteruscurasub differs from other Coryphopterus species that have a prominent pigment spot on the lower portion of the pectoral-fin base (Coryphopteruspunctipectophorus and Coryphopterusvenezuelae) in, among other features, lacking a pelvic frenum. Coryphopteruscurasub was collected between 70 and 80 m, the deepest depth range known for the genus. Collections of Coryphopterusvenezuelae at depths of 65-69 m extend the depth range of that species by approximately 50 m. Mitochondrial cytochrome c oxidase subunit I (COI) data corroborate the recognition of Coryphopteruscurasub as a distinct species but do not rigorously resolve its relationships within the genus. A revised key to the western Atlantic species of Coryphopterus is presented.},
}
@article {pmid26257568,
year = {2015},
author = {Rozo-Lopez, P and Mengual, X},
title = {Mosquito species (Diptera, Culicidae) in three ecosystems from the Colombian Andes: identification through DNA barcoding and adult morphology.},
journal = {ZooKeys},
volume = {},
number = {513},
pages = {39-64},
pmid = {26257568},
issn = {1313-2989},
abstract = {Colombia, one of the world's megadiverse countries, has a highly diverse mosquito fauna and a high prevalence of mosquito-borne diseases. In order to provide relevant information about the diversity and taxonomy of mosquito species in Colombia and to test the usefulness of DNA barcodes, mosquito species collected at different elevations in the departments of Antioquia and Caldas were identified combining adult morphology and barcode sequences. A total of 22 mosquito species from eight genera were identified using these combined techniques. We generated 77 barcode sequences with 16 species submitted as new country records for public databases. We examined the usefulness of DNA barcodes to discriminate mosquito species from the Neotropics by compiling 1,292 sequences from a total of 133 species and using the tree-based methods of neighbor-joining and maximum likelihood. Both methodologies provided similar results by resolving 105 species of mosquitoes separated into distinct clusters. This study shows the importance of combining classic morphological methodologies with molecular tools to accurately identify mosquitoes from Colombia.},
}
@article {pmid26257533,
year = {2015},
author = {Del Latte, L and Bortolin, F and Rota-Stabelli, O and Fusco, G and Bonato, L},
title = {Molecular-based estimate of species number, phylogenetic relationships and divergence times for the genus Stenotaenia (Chilopoda, Geophilomorpha) in the Italian region.},
journal = {ZooKeys},
volume = {},
number = {510},
pages = {31-47},
pmid = {26257533},
issn = {1313-2989},
abstract = {Stenotaenia is one of the largest and most widespread genera of geophilid centipedes in the Western Palearctic, with a very uniform morphology and about fifteen species provisionally recognized. For a better understanding of Stenotaenia species-level taxonomy, we have explored the possibility of using molecular data. As a preliminary assay, we sampled twelve populations, mainly from the Italian region, and analyzed partial sequences of the two genes COI and 28S. We employed a DNA-barcoding approach, complemented by a phylogenetic analysis coupled with divergence time estimation. Assuming a barcoding gap of 10-16% K2P pairwise distances, we found evidence for the presence of at least six Stenotaenia species in the Italian region, which started diverging about 50 million years ago, only partially matching with previously recognized species. We found that small-sized oligopodous species belong to a single clade that originated about 33 million years ago, and obtained some preliminary evidence of the related genus Tuoba being nested within Stenotaenia.},
}
@article {pmid26257532,
year = {2015},
author = {Wesener, T and Voigtländer, K and Decker, P and Oeyen, JP and Spelda, J and Lindner, N},
title = {First results of the German Barcode of Life (GBOL) - Myriapoda project: Cryptic lineages in German Stenotaenialinearis (Koch, 1835) (Chilopoda, Geophilomorpha).},
journal = {ZooKeys},
volume = {},
number = {510},
pages = {15-29},
pmid = {26257532},
issn = {1313-2989},
abstract = {As part of the German Barcode of Life (GBOL) Myriapoda program, which aims to sequence the COI barcoding fragment for 2000 specimens of Germany's 200 myriapod species in the near future, 44 sequences of the centipede order Geophilomorpha are analyzed. The analyses are limited to the genera Geophilus Leach, 1814 and Stenotaenia Koch, 1847 and include a total of six species. A special focus is Stenotaenia, of which 19 specimens from southern, western and eastern Germany could be successfully sequenced. The Stenotaenia data shows the presence of three to four vastly different (13.7-16.7% p-distance) lineages of the genus in Germany. At least two of the three lineages show a wide distribution across Germany, only the lineage including topotypes of Stenotaenialinearis shows a more restricted distribution in southern Germany. In a maximum likelihood phylogenetic analysis the Italian species Stenotaenia 'sorrentina' (Attems, 1903) groups with the different German Stenotaenialinearis clades. The strongly different Stenotaenialinearis lineages within Germany, independent of geography, are a strong hint for the presence of additional, cryptic Stenotaenia species in Germany.},
}
@article {pmid26257385,
year = {2016},
author = {Sebastian, A and Herdegen, M and Migalska, M and Radwan, J},
title = {AMPLISAS: a web server for multilocus genotyping using next-generation amplicon sequencing data.},
journal = {Molecular ecology resources},
volume = {16},
number = {2},
pages = {498-510},
doi = {10.1111/1755-0998.12453},
pmid = {26257385},
issn = {1755-0998},
mesh = {Computational Biology/*methods ; *Genotyping Techniques ; High-Throughput Nucleotide Sequencing ; *Internet ; Multilocus Sequence Typing/*methods ; },
abstract = {Next-generation sequencing (NGS) technologies are revolutionizing the fields of biology and medicine as powerful tools for amplicon sequencing (AS). Using combinations of primers and barcodes, it is possible to sequence targeted genomic regions with deep coverage for hundreds, even thousands, of individuals in a single experiment. This is extremely valuable for the genotyping of gene families in which locus-specific primers are often difficult to design, such as the major histocompatibility complex (MHC). The utility of AS is, however, limited by the high intrinsic sequencing error rates of NGS technologies and other sources of error such as polymerase amplification or chimera formation. Correcting these errors requires extensive bioinformatic post-processing of NGS data. Amplicon Sequence Assignment (AMPLISAS) is a tool that performs analysis of AS results in a simple and efficient way, while offering customization options for advanced users. AMPLISAS is designed as a three-step pipeline consisting of (i) read demultiplexing, (ii) unique sequence clustering and (iii) erroneous sequence filtering. Allele sequences and frequencies are retrieved in excel spreadsheet format, making them easy to interpret. AMPLISAS performance has been successfully benchmarked against previously published genotyped MHC data sets obtained with various NGS technologies.},
}
@article {pmid26250279,
year = {2015},
author = {Eilbracht, J and Fransen, CH},
title = {Periclimenes macrorhynchia sp. nov., a new hydrozoan-associated pontoniine shrimp (Crustacea, Decapoda, Palaemonidae) from North East Kalimantan, Indonesia.},
journal = {Zootaxa},
volume = {3994},
number = {3},
pages = {377-395},
doi = {10.11646/zootaxa.3994.3.3},
pmid = {26250279},
issn = {1175-5334},
mesh = {Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Female ; Hydrozoa/physiology ; Indonesia ; Male ; Organ Size ; Palaemonidae/anatomy &amp; histology/*classification/growth &amp; development ; },
abstract = {A new species of pontoniine shrimp belonging to the 'Periclimenes obscurus species group' is described from the Berau Islands, North East Kalimantan, Indonesia. Specimens were obtained from aglaopheniid hydrozoans of the genus Macrorhynchia. The new species is here described and figured. Its affinities with related species are discussed and a DNA-barcode is provided.},
}
@article {pmid26250173,
year = {2015},
author = {Buchner, P},
title = {Two new species of Agonopterix (Depressariidae, Lepidoptera) from Europe.},
journal = {Zootaxa},
volume = {3986},
number = {1},
pages = {101-114},
doi = {10.11646/zootaxa.3986.1.5},
pmid = {26250173},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Europe ; Female ; Lepidoptera/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Male ; Organ Size ; Phylogeny ; },
abstract = {The species Agonopterix tripunctaria sp. nov. and Agonopterix medelichensis sp. nov. are described. A. tripunctaria, previously misidentified as Agonopterix nodiflorella (Millière, 1866), was recognized as specifically different by the distinctive male genitalia. 19 specimens have been examined, DNA-barcoding yielded full 658 bp fragment of COI from two specimens and a 639 bp sequence from a third, confirming the impression of a rather isolated species. Specimens from Italy, Slovenia, Croatia and Greece had been checked, among them one reared from Ferulago campestris. A. medelichensis was misidentified as Agonopterix rotundella (Douglas, 1846) in NHMV; its male genitalia are erroneously depicted as A. rotundella in Hannemann (1953) and (1995). 20 specimens have been examined, from one a 555 bp fragment of COI was obtained, confirming that it is not closely related to A. rotundella. Specimens from Austria, Italy, Hungary, Slovakia, Croatia and Greece have been checked, among them one reared from Trinia glauca, which had been misidentified as A. hippomarathri. A report of A. rotundella from Russia also belongs to this species.},
}
@article {pmid26250164,
year = {2015},
author = {Orr, AG and Dow, RA},
title = {Description of two final stadium platystictid larvae from Borneo, including that of Drepanosticta ?attala Lieftinck, identified using DNA barcoding (Odonata: Zygoptera: Platystictidae).},
journal = {Zootaxa},
volume = {3985},
number = {4},
pages = {565-574},
doi = {10.11646/zootaxa.3985.4.5},
pmid = {26250164},
issn = {1175-5326},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Borneo ; Coleoptera/anatomy &amp; histology/*classification/growth &amp; development ; DNA Barcoding, Taxonomic ; Ecosystem ; Larva/*anatomy &amp; histology/classification/genetics/growth &amp; development ; Male ; Odonata/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Organ Size ; Phylogeny ; },
abstract = {The final stadium larva of Drepanosticta ?attala Lieftinck, is described and illustrated based on a single male specimen collected at Kuala Belalong Field Studies Centre, Brunei. The larva was identified by matching the mitochondrial marker COI with that of known adult specimens. The larva presented a good match with both D. attala and D. barbatula Lieftinck in this gene, but as adults of only the former species had been collected at the locality, it is presumed more likely to be that species. Another, unidentified platystictid larva, Platystictidae A, collected at the same general locality is also described. The two larvae show significant differences from each other and from D. sundana Krüger, the only other Oriental region member of the family for which larval morphology is known. The three species are also compared with the larvae of the Neotropical genus Palaemnema, which they closely resemble, despite being currently placed in different subfamilies. Based on this known material, Oriental and Neotropical forms differ significantly in details of mandibular morphology, especially the armature of the molar field.},
}
@article {pmid26250161,
year = {2015},
author = {Johnson, JW and Wilmer, JW},
title = {Plectorhinchus caeruleonothus, a new species of sweetlips (Perciformes: &lt;br /&gt;Haemulidae) from northern Australia and the resurrection of P. unicolor (Macleay, 1883), species previously confused with P. schotaf (Forsskål, 1775).},
journal = {Zootaxa},
volume = {3985},
number = {4},
pages = {491-522},
doi = {10.11646/zootaxa.3985.4.2},
pmid = {26250161},
issn = {1175-5326},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Australia ; Body Size ; Ecosystem ; Female ; Male ; Organ Size ; Perciformes/anatomy &amp; histology/*classification/growth &amp; development ; },
abstract = {Two distinct haemulid fishes from Australia and the Indo-Australian Archipelago respectively have long been confused with Plectorhinchus schotaf (Forsskål, 1775). Plectorhinchus caeruleonothus sp. nov. is described from 17 specimens collected off western and far northern Australia, between the Monte Bello Islands, Western Australia and Torres Strait, Queensland. It has also been confirmed outside this range by photographs taken at Ningaloo Reef and Exmouth Gulf, Western Australia, and at Claremont Isles and Lizard Island, Queensland. The new species is unique among the genus in having a combination of dorsal-fin rays XII, 18-20, lateral-line scales 56-61, gill rakers 7-9 on the upper limb and 18-20 on the lower limb of the first arch, nostrils minute, and fresh colouration in adults including body uniformly grey, cheek, opercles and posterior margin of the opercular membrane uniformly blue-grey, and rim of orbit and upper edge of maxilla dusky yellow. In contrast to its closest congeners, the juveniles have a distinctive pattern of narrow creamish-white to pale grey stripes on a dark grey to chocolate brown background on the head and body, and oblique dark stripes progressing with growth to spots on the caudal fin. Plectorhinchus unicolor (Macleay, 1883) from Japan to northern Australia is resurrected from the synonomy of P. schotaf and redescribed on the basis of the holotype and 24 non-type specimens. Plectorhinchus unicolor is most similar to P. schotaf, but can be distinguished by fresh colouration, modal dorsal and pectoral-fin ray counts and DNA barcoding. Plectorhinchus schotaf appears to be restricted to the region from southeast Africa to the Arabian Sea, including the Red Sea and Persian Gulf. Plectorhinchus griseus (Cuvier in Cuvier &amp; Valenciennes, 1830) from Indian and Sri Lankan Seas has previously been treated as a junior synonym of P. schotaf, but in accordance with Smith (1962), is here confirmed as a valid species, readily distinguished from the latter by a concavity in the lateral profile of the snout in adults, deep body and high soft dorsal-fin ray count. Comparison of the CO1 genetic marker utilised in DNA barcoding also resulted in significant genetic divergences between the new species, P. unicolor and their closest sampled congeners. Some behavioural observations are also presented for the species treated, including aggressive interactions between individuals of the new species, the likes of which have not previously been recorded among species of Plectorhinchus.},
}
@article {pmid26250025,
year = {2015},
author = {Pinacho-Pinacho, CD and Sereno-Uribe, AL and De León, GP and García-Varela, M},
title = {Checklist of the species of Neoechinorhynchus (Acanthocephala: Neoechinorhynchidae) in fishes and turtles in Middle-America, and their delimitation based on sequences of the 28S rDNA.},
journal = {Zootaxa},
volume = {3985},
number = {1},
pages = {98-116},
doi = {10.11646/zootaxa.3985.1.5},
pmid = {26250025},
issn = {1175-5326},
mesh = {Acanthocephala/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Central America ; Checklist ; DNA, Helminth/genetics ; DNA, Ribosomal/genetics ; Female ; Fish Diseases/*parasitology ; Fishes ; Helminthiasis, Animal/*parasitology ; Intestines/parasitology ; Male ; Mexico ; Organ Size ; Phylogeny ; RNA, Ribosomal, 28S/*genetics ; Turtles/*parasitology ; },
abstract = {Among the acanthocephalans, Neoechinorhynchus is one of the most speciose genera, with 116 described species distributed worldwide. The adults of Neoechinorhynchus are found in the intestine of freshwater and brackish water fish, as well as in freshwater turtles. In this study, a checklist of the congeneric species of Neoechinorhynchus occurring in Middle-American fish and turtles is presented. The checklist contains the records established in all published accounts, as well as novel data from survey work conducted in the region comprising Neotropical areas of Mexico, as well as some localities in Central America. The species delimitation criteria used to discriminate among species is based on molecular data. In the last years, a large database derived from sequences of the D2 + D3 domains of the large subunit of rDNA (28S) was generated for 262 specimens corresponding to nine species of Neoechinorhynchus. This molecular marker has shown to be useful in establishing species limits within Neoechinorhynchus and in resolving phylogenetic relationships at species level. Based on our results, the domains D2 + D3 of the 28S rDNA could be considered as potential DNA barcodes to complement mitochondrial DNA to discriminate among acanthocephalan species.},
}
@article {pmid26250011,
year = {2015},
author = {Freitas, AV and Barbosa, EP and Siewert, RR and Mielke, OH and Zacca, T and Azeredo-Espin, AM},
title = {Four new species of Moneuptychia (Lepidoptera: Satyrinae: Euptychiina) from Brazil.},
journal = {Zootaxa},
volume = {3981},
number = {4},
pages = {521-541},
doi = {10.11646/zootaxa.3981.4.4},
pmid = {26250011},
issn = {1175-5326},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Brazil ; Butterflies/anatomy &amp; histology/*classification/growth &amp; development ; Ecosystem ; Female ; Male ; Organ Size ; },
abstract = {This paper describes four new species of Moneuptychia as follows: M. montana Freitas, M. vitellina Freitas &amp; Barbosa, M. pervagata Freitas, Siewert &amp; Mielke and M. wahlbergi Freitas, Barbosa, Siewert &amp; Mielke from south and southeastern Brazil. Details are presented on the morphology of adults of all species, and immature stages for two species, and we discuss the taxonomy and identification of the genus Moneuptychia. The mitochondrial CoxI "barcode" region was used for exploring the utility of this DNA marker to identify these species, giving strong support for all new species.},
}
@article {pmid26249957,
year = {2015},
author = {Kaila, L},
title = {The Elachista dispunctella (Duponchel) complex (Lepidoptera, Elachistidae) revisited, with exceptional level of synonymy.},
journal = {Zootaxa},
volume = {3980},
number = {3},
pages = {301-358},
doi = {10.11646/zootaxa.3980.3.1},
pmid = {26249957},
issn = {1175-5326},
mesh = {Animal Distribution ; Animals ; DNA/genetics ; DNA Barcoding, Taxonomic ; Female ; Male ; Moths/*anatomy &amp; histology/*classification/genetics/physiology ; Phylogeny ; Species Specificity ; },
abstract = {The E. dispunctella and E. triseriatella complexes sensu Traugott-Olsen are merged. The newly delineated E. dispunctella complex is re-defined and diagnosed. Until now, a total of 64 species has been assigned to this species complex. The taxonomy of the constituent species has been obscure owing to their identities based on unvalidated traits, in particular subtle differences on branching points of forewing veins. The taxonomy of the E. dispunctella complex is revised on the basis of new material, new and reevaluated information obtained from morphology and biology, as well as from the standard barcode region of COI, with at least partial barcode data derived from 194 recently collected specimens and 33 holotypes. As a result, the number of species considered valid is markedly reduced, with only 19 species now recognized. The following 43 new synonymies are established: Elachista dispunctella (Duponchel, 1843) = E. cahorsensis Traugott-Olsen, 1992, syn. nov., E. imbi Traugott-Olsen, 1992, syn. nov., E. karsholti Traugott-Olsen, 1992, syn. nov., E. mannella Traugott-Olsen, 1992, syn. nov., E. multipunctella Traugott-Olsen, 1992, syn. nov., E. pocopunctella Traugott-Olsen, 1992, syn. nov., E. povolnyi Traugott-Olsen, 1992, syn. nov., E. punctella Traugott-Olsen, 1992, syn. nov., E. hallini Traugott-Olsen, 1992, syn. nov., E. intrigella Traugott-Olsen, 1992, syn. nov., E. skulei Traugott-Olsen, 1992 and E. nielspederi Traugott-Olsen, 1992, syn. nov.; E. tribertiella Traugott-Olsen, 1985 = E. toveella Traugott-Olsen, 1985, syn. nov., E. baldizzonella Traugott-Olsen, 1985, syn. nov., E. veletaella Traugott-Olsen, 1992, syn. nov., E. bazaella Traugott-Olsen, 1992, syn. nov. and E. louiseae Traugott-Olsen, 1992, syn. nov.; E. parvula Parenti, 1978 = E. minusculella Traugott-Olsen, 1992, syn. nov. and E. blancella Traugott-Olsen, 1992, syn. nov.; E. maboulella Chrétien, 1915 = E. catalunella Traugott-Olsen, 1992, syn. nov., E. gerdmaritella Traugott-Olsen, 1992, syn. nov. and E. gielisi Traugott-Olsen, 1992, syn. nov.; E. glaseri Traugott-Olsen, 1992 = E. rikkeae Traugott-Olsen, 1992, syn. nov., E. totanaensis Traugott-Olsen, 1992, syn. nov., E. olemartini Traugott-Olsen, 1992, syn. nov., E. bengtssoni Traugott-Olsen, 1992, syn. nov., E. senecai Traugott-Olsen, 1992, syn. nov., E. wadielhiraensis Traugott-Olsen, 1992, syn. nov., E. rissaniensis Traugott-Olsen, 1992, syn. nov. and E. michelseni Traugott-Olsen, 1992, syn. nov.; E. hispanica Traugott-Olsen, 1992 = E. vivesi Traugott-Olsen, 1992, syn. nov., E. cuencaensis Traugott-Olsen, 1992, syn. nov., E. vanderwolfi Traugott-Olsen, 1992, syn. nov., E. amparoae Traugott-Olsen, 1992, syn. nov., E. varensis Traugott-Olsen, 1992, syn. nov., E. luqueti Traugott-Olsen, 1992, syn. nov., E. occidentella Traugott-Olsen, 1992, syn. nov. and E. clintoni Traugott-Olsen, 1992, syn. nov.; E. berndtiella Traugott-Olsen, 1985 = E. casascoensis Traugott-Olsen, 1992, syn. nov.; E. triseriatella Stainton, 1854 = E. contisella Chrétien, 1922, syn. nov., E. gregori Traugott-Olsen, 1988, syn. nov., and E. lerauti Traugott-Olsen, 1992, syn. nov.; E. elsaella Traugott-Olsen, 1988 = E. svenssoni Traugott-Olsen, 1988, syn. nov.; E. galactitella (Eversmann, 1844) = E. madridensis Traugott-Olsen, 1992, syn. nov. E. deresyensis Traugott-Olsen, 1988 is resurrected as a valid species, stat. rev. Evidence from DNA barcodes suggests that there may exist further species, but in the absence of distinct morphological differences, they are not formally described as new.},
}
@article {pmid26249870,
year = {2015},
author = {Shen, HP and Chang, CH and Chih, WJ},
title = {Earthworms from Matsu, Taiwan with descriptions of new species of the genera Amynthas (Oligochaeta: Megascolecidae) and Drawida (Oligochaeta: Moniligastridae).},
journal = {Zootaxa},
volume = {3973},
number = {3},
pages = {425-450},
doi = {10.11646/zootaxa.3973.3.2},
pmid = {26249870},
issn = {1175-5326},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Ecosystem ; Female ; Male ; Oligochaeta/*anatomy &amp; histology/*classification/genetics/growth &amp; development ; Organ Size ; Phylogeny ; Taiwan ; },
abstract = {In 2012, we conducted earthworm surveys in Matsu Islands, and described five new species of the genera Amynthas and Metaphire and reported two new records, Desmogaster sinensis Gates, 1930 and Ocnerodrilus occidentalis Eisen, 1878. This paper describes three new species, one of them with two new subspecies, Amynthas nanganensis nanganensis sp. nov. et ssp. nov. and Amynthas nanganensis beiganensis ssp. nov., Drawida beiganica sp. nov. and Drawida dongyinica sp. nov., provides a new record of Drawida koreana Kobayashi, 1938 from the remaining specimens collected in the surveys, reports DNA barcodes (the 5' end sequences of the mitochondrial cytochrome c oxidase subunit 1 gene) from type specimens and further reference specimens of the new species, and lists a total of 27 earthworm species and subspecies found from Matsu Islands. Pheretimoid earthworms made up 66.7% of the total number of the species, with Metaphire matsuensis Shen, 2014 and Metaphire californica (Kinberg, 1867) the most dominant. Our findings indicate that the earthworm fauna of Matsu Islands is more closely related to that of warm temperate China than to Taiwan or tropical southern China.},
}
@article {pmid26249440,
year = {2015},
author = {Mecklenburg, CW and Anderson, ME},
title = {Reassessment of multiple species of Gymnelus (Teleostei: Zoarcidae) in Pacific Arctic and boreal regions.},
journal = {Zootaxa},
volume = {3964},
number = {2},
pages = {300},
doi = {10.11646/zootaxa.3964.2.11},
pmid = {26249440},
issn = {1175-5326},
mesh = {Animals ; Arctic Regions ; Perciformes/*classification ; },
abstract = {Recently described new nominal species and resurrected species in the eelpout genus Gymnelus Reinhardt 1834 were reassessed for validity using fresh material collected in Pacific Arctic regions and a large body of data from a previous systematic review of the genus. The analysis reported here included both DNA barcodes and morphology. Only two species were validated: G. viridis (Fabricius 1780) and G. hemifasciatus Andriashev 1937. The latter species occurred as two morphotypes for which there is some evidence of difference in ecological preference, but the available environ-mental data are not robust enough to firmly identify or verify ecophenotypes.},
}
@article {pmid26249388,
year = {2015},
author = {Luo, W and Sullivan, JP and Zhao, HT and Peng, ZG},
title = {Metzia parva, a new cyprinid species (Teleostei: Cypriniformes) from south China.},
journal = {Zootaxa},
volume = {3962},
number = {},
pages = {226-234},
doi = {10.11646/zootaxa.3962.1.14},
pmid = {26249388},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; China ; Cyprinidae/anatomy &amp; histology/*classification/growth &amp; development ; Ecosystem ; Female ; Male ; Organ Size ; },
abstract = {A new species of a small cyprinid fish, Metzia parva sp. nov., is described here based on specimens collected from a tributary of Hongshui-He River in the Pearl River basin at Anyang Town, Du'an County, Guangxi Province, south China. It differs from congeners in having a smaller body with a standard length of 48.3-57.7 mm (vs. 58.3-151.4 mm in other species); a complete lateral line (although some specimens show interruptions on the ventral margin above the anal-fin); 12-14 branched anal-fin rays (vs. 10-11 or 15-20); 10 branched pectoral-fin rays (vs. 11-16); 6 branched pelvic-fin rays (vs. 7-9); a longer caudal peduncle (17.8-21.7% vs. 14.8-17.4% SL); a shorter preanal length (60.9-66.0% vs. 69.0-73.0% SL) and an obviously larger interorbital width (28.4-33.0% vs. 20.2-24.7% of head length). While Metzia parva shares a lateral black stripe from the gill opening to the caudal-fin base with M. formosae, the new species can be distinguished from M. formosae by a deeper head (16.4-19.2% vs. 13.3-15.7% SL) and a longer anal fin (15.4-18.9% vs. 10.0-13.6% SL) in addition to the diagnostic characters above. Kimura's 2-parameter genetic distance between the two species is 6.6% for the barcoding region of the mitochondrial COI gene and 7.3% across the complete mitochondrial genome.},
}
@article {pmid26249088,
year = {2015},
author = {Velonà, A and Brock, PD and Hasenpusch, J and Mantovani, B},
title = {Cryptic diversity in Australian stick insects (Insecta; Phasmida) uncovered by the DNA barcoding approach.},
journal = {Zootaxa},
volume = {3957},
number = {4},
pages = {455-466},
doi = {10.11646/zootaxa.3957.4.6},
pmid = {26249088},
issn = {1175-5334},
mesh = {Animals ; Australia ; DNA Barcoding, Taxonomic ; Female ; Insecta/*classification/*genetics ; Male ; Molecular Sequence Data ; Phylogeny ; },
abstract = {The barcoding approach was applied to analyze 16 Australian morphospecies of the order Phasmida, with the aim to test if it could be suitable as a tool for phasmid species identification and if its discrimination power would allow uncovering of cryptic diversity. Both goals were reached. Eighty-two specimens representing twelve morphospecies (Sipyloidea sp. A, Candovia annulata, Candovia sp. A, Candovia sp. B, Candovia sp. C, Denhama austrocarinata, Xeroderus kirbii, Parapodacanthus hasenpuschorum, Tropidoderus childrenii, Cigarrophasma tessellatum, Acrophylla wuelfingi, Eurycantha calcarata) were correctly recovered as clades through the molecular approach, their sequences forming monophyletic and well-supported clusters. In four instances, Neighbor-Joining tree and barcoding gap analyses supported either a specific (Austrocarausius mercurius, Anchiale briareus) or a subspecific (Anchiale austrotessulata, Extatosoma tiaratum) level of divergence within the analyzed morphospecies. The lack of an appropriate database of homologous coxI sequences prevented more detailed identification of undescribed taxa.},
}
@article {pmid26249084,
year = {2015},
author = {De Prins, J and Gumovsky, A and De Coninck, E},
title = {Discovery of a new species of Caloptilia (Lepidoptera: Gracillariidae) from east and central Africa with its suggested associated host (Gentianales: Rubiaceae) and natural enemies (Hymenoptera: Eulophidae).},
journal = {Zootaxa},
volume = {3957},
number = {4},
pages = {383-407},
doi = {10.11646/zootaxa.3957.4.2},
pmid = {26249084},
issn = {1175-5334},
mesh = {Africa, Central ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Female ; Host-Parasite Interactions ; Male ; Moths/*classification/growth &amp; development/parasitology/physiology ; Organ Size ; Rubiaceae/*parasitology ; Wasps/*physiology ; },
abstract = {A new species of the leaf-mining moth genus Caloptilia (Gracillariidae), C. mwamba sp. nov., suggested to be associated with Cremaspora triflora (Thonn.) K.Schum. (Rubiaceae) is described from east and central Africa. The taxonomic relationships of the new species with its congeners from the Oriental and the Palaearctic regions are discussed. Newly obtained taxonomic and biological data are linked with the DNA barcode workbench in BOLD, providing the molecular, machine-readable identification tag of the new species. New distribution and morphological data for two parasitoid species, Afrotroppopsis risbeci Gumovsky, 2007 and Zaommomentedon newbyi (Kerrich, 1969) (Eulophidae), which were found to be associated with C. mwamba sp. nov., are presented.},
}
@article {pmid26248909,
year = {2015},
author = {Matzke, D and Kocarek, P},
title = {Description and biology of Euborellia arcanum sp. nov., an alien earwig occupying greenhouses in Germany and Austria (Dermaptera: Anisolabididae).},
journal = {Zootaxa},
volume = {3956},
number = {1},
pages = {131-139},
doi = {10.11646/zootaxa.3956.1.8},
pmid = {26248909},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Austria ; Body Size ; Ecosystem ; Female ; Germany ; Insecta/anatomy &amp; histology/*classification/growth &amp; development ; Male ; Organ Size ; },
abstract = {Greenhouses in botanical or zoological gardens are home to dozens of species of invertebrates that were introduced alongside plants or potting soil. Our study presents the description of an alien species of earwig, Euborellia arcanum sp. nov., found in tropical greenhouses in Leipzig and Potsdam (Germany) and in Vienna (Austria), including information about its biology in breeding culture. The species was most likely introduced into Europe by way of plants or plant matter from Florida, but the region of its natural habitat is unknown. The sequence of the mitochondrial gene cytochrome c oxidase subunit I (COI) was also evaluated and added to GenBank as a DNA barcode for further identification.},
}
@article {pmid26248903,
year = {2015},
author = {Antoni, MY and Delpiani, SM and Stewart, AL and González-Castro, M and De Astarloa, JM},
title = {Merluccius tasmanicus Matallanas &amp; Lloris 2006 is a junior synonym of M. australis (Hutton 1872) (Gadiformes: Merluciidae) based on morphological and molecular data.},
journal = {Zootaxa},
volume = {3956},
number = {1},
pages = {29-55},
doi = {10.11646/zootaxa.3956.1.2},
pmid = {26248903},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Argentina ; Body Size ; Female ; Gadiformes/anatomy &amp; histology/*classification/*genetics/growth &amp; development ; Male ; Organ Size ; Phylogeny ; Terminology as Topic ; },
abstract = {The high intraspecific variation among and the conservative external morphology of Merluccius spp. have resulted in serious identification difficulties. Four hundred and twenty fresh and preserved specimens of Merluccius were analyzed, including the type series of Merluccius australis, M. tasmanicus and M. hubbsi; specimens of M. hubbsi from Argentina, Brazil and Uruguay, and individuals of M. australis from Argentina and New Zealand were examined. The nomenclatural status of the type specimens of M. australis is discussed and the designation of a lectotype and a paralectotype is proposed. The comparative study of morphology, meristic, traditional and landmark-based morphometry, both external and internal, and through DNA-based Barcoding molecular tools demonstrates that Merluccius tasmanicus is a junior synonym of Merluccius australis. Meristic and morphometric characters of types of M. tasmanicus completely overlap those of M. australis, whereas M. hubbsi show fewer scales along the lateral line, total vertebrae, second dorsal and anal-fin rays. A trend of a longer snout and wider head in M. australis and M. tasmanicus, and larger eyes and longer pelvic fins, in M. hubbsi was observed. While discriminant characters were found in the internal elements (hyomandibula, urohyal and sagitta otolith) between M. hubbsi and M. australis, none were observed between M. australis and those reported for M. tasmanicus. DNA barcoding analyses found no evidence of the existence of other species of Merluccius besides M. hubbsi and M. australis.},
}
@article {pmid26248563,
year = {2015},
author = {Ankenbrand, MJ and Keller, A and Wolf, M and Schultz, J and Förster, F},
title = {ITS2 Database V: Twice as Much.},
journal = {Molecular biology and evolution},
volume = {32},
number = {11},
pages = {3030-3032},
doi = {10.1093/molbev/msv174},
pmid = {26248563},
issn = {1537-1719},
mesh = {DNA, Ribosomal Spacer/*genetics ; *Databases, Nucleic Acid ; Eukaryota/genetics ; Internet ; Nucleic Acid Conformation ; Phylogeny ; Sequence Alignment/methods ; },
abstract = {The internal transcribed spacer 2 (ITS2) is a well-established marker for phylogenetic analyses in eukaryotes. A reliable resource for reference sequences and their secondary structures is the ITS2 database (http://its2.bioapps.biozentrum.uni-wuerzburg.de/). However, the database was last updated in 2011. Here, we present a major update of the underlying data almost doubling the number of entities. This increases the number of taxa represented within all major eukaryotic clades. Moreover, additional data has been added to underrepresented groups and some new groups have been added. The broader coverage across the tree of life improves phylogenetic analyses and the capability of ITS2 as a DNA barcode.},
}
@article {pmid26248467,
year = {2015},
author = {Peng, Q and Vijaya Satya, R and Lewis, M and Randad, P and Wang, Y},
title = {Reducing amplification artifacts in high multiplex amplicon sequencing by using molecular barcodes.},
journal = {BMC genomics},
volume = {16},
number = {1},
pages = {589},
pmid = {26248467},
issn = {1471-2164},
mesh = {Artifacts ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Multiplex Polymerase Chain Reaction/*methods ; RNA/genetics ; Reproducibility of Results ; Sequence Analysis/methods ; },
abstract = {BACKGROUND: PCR amplicon sequencing has been widely used as a targeted approach for both DNA and RNA sequence analysis. High multiplex PCR has further enabled the enrichment of hundreds of amplicons in one simple reaction. At the same time, the performance of PCR amplicon sequencing can be negatively affected by issues such as high duplicate reads, polymerase artifacts and PCR amplification bias. Recently researchers have made some good progress in addressing these shortcomings by incorporating molecular barcodes into PCR primer design. So far, most work has been demonstrated using one to a few pairs of primers, which limits the size of the region one can analyze.<br><br>RESULTS: We developed a simple protocol, which enables the use of molecular barcodes in high multiplex PCR with hundreds of amplicons. Using this protocol and reference materials, we demonstrated the applications in accurate variant calling at very low fraction over a large region and in targeted RNA quantification. We also evaluated the protocol's utility in profiling FFPE samples.<br><br>CONCLUSIONS: We demonstrated the successful implementation of molecular barcodes in high multiplex PCR, with multiplex scale many times higher than earlier work. We showed that the new protocol combines the benefits of both high multiplex PCR and molecular barcodes, i.e. the analysis of a very large region, low DNA input requirement, very good reproducibility and the ability to detect as low as 1% mutations with minimal false positives (FP).},
}
@article {pmid26247810,
year = {2015},
author = {Balas, B and Huynh, C and Saville, A and Schmidt, J},
title = {Orientation biases for facial emotion recognition during childhood and adulthood.},
journal = {Journal of experimental child psychology},
volume = {140},
number = {},
pages = {171-183},
doi = {10.1016/j.jecp.2015.07.006},
pmid = {26247810},
issn = {1096-0457},
mesh = {Child ; Child Development ; Child, Preschool ; *Emotions ; *Facial Recognition ; Female ; Humans ; Male ; North Dakota ; *Orientation ; Photic Stimulation ; Young Adult ; },
abstract = {Facial emotion recognition develops slowly, with continuing changes in performance observable up to 10 years of age and beyond. In the current study, we chose to examine how the use of specific low-level visual features for emotion recognition may change during childhood. Adults exhibit information biases for face recognition; specific spatial frequency and orientation sub-bands make a larger contribution to recognition than others. This means that depending on the specific task (e.g., identification, emotion recognition), participants will perform worse when some features are removed from the original image and better when those features are included. One example of such an information bias for face recognition is the differential contribution of horizontal orientation energy relative to vertical orientation energy; adult participants are better able to recognize faces and categorize their emotional expressions when horizontal information is included than when only vertical information is included. Although several recent studies have demonstrated various ways in which horizontal orientation energy (and so-called "bar-codes" for face appearance) contribute to adult face processing, there have been as yet no studies describing how such a bias emerges developmentally that may offer insight into the mechanisms underlying the slow development of facial emotion recognition. In the current study, we compared children's (5- and 6-year-olds and 7- and 8-year-olds) and adults' performance in a simple emotion categorization task using orientation-filtered faces to determine the extent to which horizontal and vertical orientation energy contributed to recognition as a function of age. We found that although all three participant groups exhibited a clear bias favoring the use of horizontal orientation energy, the nature of this bias differed as a function of age. Specifically, 5- and 6-year-olds exhibited a disproportionate performance cost when vertical orientation energy was all that was available relative to when stimuli were limited to horizontal orientation energy. One feature of the development of facial emotion recognition, thus, appears to be the capability to use suboptimal or weakly diagnostic information to support recognition.},
}
@article {pmid26246188,
year = {2015},
author = {Guo, JF and Li, HS and Wang, B and Xue, XF and Hong, XY},
title = {DNA barcoding reveals the protogyne and deutogyne of Tegolophus celtis sp. nov. (Acari: Eriophyidae).},
journal = {Experimental &amp; applied acarology},
volume = {67},
number = {3},
pages = {393-410},
pmid = {26246188},
issn = {1572-9702},
mesh = {Animals ; Arthropod Proteins/*genetics/metabolism ; Cell Nucleus/genetics/metabolism ; China ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics/metabolism ; Female ; Food Chain ; Mites/anatomy &amp; histology/*classification/genetics ; Mitochondrial Proteins/genetics/metabolism ; Phylogeny ; Population Dynamics ; RNA, Ribosomal, 18S/genetics/metabolism ; RNA, Ribosomal, 28S/genetics/metabolism ; Ulmaceae/physiology ; },
abstract = {A few eriophyoid mites have two forms of adult female, called protogyne and deutogyne. The latter form is thought to increase survival under unfavorable conditions. The two forms have distinct morphological characters, which often cause them to be recognized as different species. Molecular species delimitation provides a useful tool to solve these misunderstandings. Here we describe a new species of eriophyoid mite, Tegolophus celtis sp. nov., that has protogyne and deutogyne forms infesting Chinese hackberry, Celtis sinensis Pers. (Cannabaceae), an ornamental tree in China. The two forms can be easily differentiated by body shape (fusiform and triangular, respectively) and body color (light yellow and red, respectively). The putative protogyne and deutogyne forms of T. celtis were identified by using fragments of three genes, a mitochondrial gene (COI) and two nuclear genes (18S rRNA and 28S rRNA). Kimura-2-parameter distances of these three fragmental sequences were between 0.0% and 0.9%. Phylogenetic topologies strongly support the occurrence of the protogyne and deutogyne forms with high bootstrap and Bayesian values. The population structure of T. celtis changed with the seasons, with deutogynes being most abundant in summer and protogynes being most abundant in spring. The new species described herein are vagrants on their host plants.},
}
@article {pmid26245790,
year = {2015},
author = {Gonçalves, PF and Oliveira-Marques, AR and Matsumoto, TE and Miyaki, CY},
title = {DNA Barcoding Identifies Illegal Parrot Trade.},
journal = {The Journal of heredity},
volume = {106 Suppl 1},
number = {},
pages = {560-564},
doi = {10.1093/jhered/esv035},
pmid = {26245790},
issn = {1465-7333},
mesh = {Animals ; Animals, Wild/classification/genetics ; Brazil ; Conservation of Natural Resources ; *Crime ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Humans ; Male ; Ovum ; Parrots/*classification/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Illegal trade threatens the survival of many wild species, and molecular forensics can shed light on various questions raised during the investigation of cases of illegal trade. Among these questions is the identity of the species involved. Here we report a case of a man who was caught in a Brazilian airport trying to travel with 58 avian eggs. He claimed they were quail eggs, but authorities suspected they were from parrots. The embryos never hatched and it was not possible to identify them based on morphology. As 29% of parrot species are endangered, the identity of the species involved was important to establish a stronger criminal case. Thus, we identified the embryos' species based on the analyses of mitochondrial DNA sequences (cytochrome c oxidase subunit I gene [COI] and 16S ribosomal DNA). Embryonic COI sequences were compared with those deposited in BOLD (The Barcode of Life Data System) while their 16S sequences were compared with GenBank sequences. Clustering analysis based on neighbor-joining was also performed using parrot COI and 16S sequences deposited in BOLD and GenBank. The results, based on both genes, indicated that 57 embryos were parrots (Alipiopsitta xanthops, Ara ararauna, and the [Amazona aestiva/A. ochrocephala] complex), and 1 was an owl. This kind of data can help criminal investigations and to design species-specific anti-poaching strategies, and demonstrate how DNA sequence analysis in the identification of bird species is a powerful conservation tool.},
}
@article {pmid26244644,
year = {2015},
author = {Klippel, AH and Oliveira, PV and Britto, KB and Freire, BF and Moreno, MR and Dos Santos, AR and Banhos, A and Paneto, GG},
title = {Using DNA Barcodes to Identify Road-Killed Animals in Two Atlantic Forest Nature Reserves, Brazil.},
journal = {PloS one},
volume = {10},
number = {8},
pages = {e0134877},
pmid = {26244644},
issn = {1932-6203},
mesh = {Animals ; Animals, Wild/classification/*genetics ; Brazil ; Conservation of Natural Resources/methods ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; *Forests ; Geography ; Molecular Sequence Data ; Reproducibility of Results ; },
abstract = {Road mortality is the leading source of biodiversity loss in the world, especially due to fragmentation of natural habitats and loss of wildlife. The survey of the main species victims of roadkill is of fundamental importance for the better understanding of the problem, being necessary, for this, the correct species identification. The aim of this study was to verify if DNA barcodes can be applied to identify road-killed samples that often cannot be determined morphologically. For this purpose, 222 vertebrate samples were collected in a stretch of the BR-101 highway that crosses two Discovery Coast Atlantic Forest Natural Reserves, the Sooretama Biological Reserve and the Vale Natural Reserve, in Espírito Santo, Brazil. The mitochondrial COI gene was amplified, sequenced and confronted with the BOLD database. It was possible to identify 62.16% of samples, totaling 62 different species, including Pyrrhura cruentata, Chaetomys subspinosus, Puma yagouaroundi and Leopardus wiedii considered Vulnerable in the National Official List of Species of Endangered Wildlife. The most commonly identified animals were a bat (Molossus molossus), an opossum (Didelphis aurita) and a frog (Trachycephalus mesophaeus) species. Only one reptile was identified using the technique, probably due to lack of reference sequences in BOLD. These data may contribute to a better understanding of the impact of roads on species biodiversity loss and to introduce the DNA barcode technique to road ecology scenarios.},
}
@article {pmid26242876,
year = {2015},
author = {Alkner, S and Tang, MH and Brueffer, C and Dahlgren, M and Chen, Y and Olsson, E and Winter, C and Baker, S and Ehinger, A and Rydén, L and Saal, LH and Fernö, M and Gruvberger-Saal, SK},
title = {Contralateral breast cancer can represent a metastatic spread of the first primary tumor: determination of clonal relationship between contralateral breast cancers using next-generation whole genome sequencing.},
journal = {Breast cancer research : BCR},
volume = {17},
number = {1},
pages = {102},
pmid = {26242876},
issn = {1465-542X},
mesh = {Adult ; Aged, 80 and over ; Breast Neoplasms/*genetics/*pathology ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Middle Aged ; Neoplasm Metastasis/*genetics/*pathology ; Neoplasms, Second Primary/*genetics/*pathology ; },
abstract = {INTRODUCTION: By convention, a contralateral breast cancer (CBC) is treated as a new primary tumor, independent of the first cancer (BC1). Although there have been indications that the second tumor (BC2) sometimes may represent a metastatic spread of BC1, this has never been conclusively shown. We sought to apply next-generation sequencing to determine a "genetic barcode" for each tumor and reveal the clonal relationship of CBCs.<br><br>METHODS: Ten CBC patients with detailed clinical information and available fresh frozen tumor tissue were studied. Using low-coverage whole genome DNA-sequencing data for each tumor, chromosomal rearrangements were enumerated and copy number profiles were generated. Comparisons between tumors provided an estimate of clonal relatedness for tumor pairs within individual patients.<br><br>RESULTS: Between 15-256 rearrangements were detected in each tumor (median 87). For one patient, 76 % (68 out of 90) of the rearrangements were shared between BC1 and BC2, highly consistent with what has been seen for true primary-metastasis pairs (>50 %) and thus confirming a common clonal origin of the two tumors. For most of the remaining cases, BC1 and BC2 had similarly low overlap as unmatched randomized pairs of tumors from different individuals, suggesting the CBC to represent a new independent primary tumor.<br><br>CONCLUSION: Using rearrangement fingerprinting, we show for the first time with certainty that a contralateral BC2 can represent a metastatic spread of BC1. Given the poor prognosis of a generalized disease compared to a new primary tumor, these women need to be identified at diagnosis of CBC for appropriate determination of treatment. Our approach generates a promising new method to assess clonal relationship between tumors. Additional studies are required to confirm the frequency of CBCs representing metastatic events.},
}
@article {pmid26241944,
year = {2015},
author = {Andriollo, T and Naciri, Y and Ruedi, M},
title = {Two Mitochondrial Barcodes for one Biological Species: The Case of European Kuhl's Pipistrelles (Chiroptera).},
journal = {PloS one},
volume = {10},
number = {8},
pages = {e0134881},
pmid = {26241944},
issn = {1932-6203},
mesh = {Africa, Northern ; Alleles ; Animal Distribution ; Animals ; Chiroptera/classification/*genetics ; Cytochromes b/genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Europe ; Genetic Markers ; Genetic Speciation ; *Genetic Variation ; Haplotypes/genetics ; Microsatellite Repeats ; Phylogeny ; Sequence Alignment ; Species Specificity ; Sympatry ; },
abstract = {The Kuhl's pipistrelle (Pipistrellus kuhlii) is a Western Palaearctic species of bat that exhibits several deeply divergent mitochondrial lineages across its range. These lineages could represent cryptic species or merely ancient polymorphism, but no nuclear markers have been studied so far to properly assess the taxonomic status of these lineages. We examined here two lineages occurring in Western Europe, and used both mitochondrial and nuclear markers to measure degrees of genetic isolation between bats carrying them. The sampling focused on an area of strict lineage sympatry in Switzerland but also included bats from further south, in North Africa. All individuals were barcoded for the COI gene to identify their mitochondrial lineages and five highly polymorphic microsatellite loci were used to cluster them according to their nuclear genotypes. Despite this low number of nuclear markers, all North African nuclear genotypes were grouped in a highly distinct subpopulation when compared with European samples sharing the same mitochondrial barcodes. The reverse situation prevailed in Switzerland where bats carrying distinct barcodes had similar nuclear genotypes. There was a weak east/west nuclear structure of populations, but this was independent of mitochondrial lineages as bats carrying either variant were completely admixed. Thus, the divergent mitochondrial barcodes present in Western Europe do not represent cryptic species, but are part of a single biological species. We argue that these distinct barcodes evolved in allopatry and came recently into secondary contact in an area of admixture north of the Alps. Historical records from this area and molecular dating support such a recent bipolar spatial expansion. These results also highlight the need for using appropriate markers before claiming the existence of cryptic species based on highly divergent barcodes.},
}
@article {pmid26240744,
year = {2015},
author = {Cruz, JL and Brown, JN},
title = {Safety risks with investigational drugs: Pharmacy practices and perceptions in the veterans affairs health system.},
journal = {Therapeutic advances in drug safety},
volume = {6},
number = {3},
pages = {103-109},
pmid = {26240744},
issn = {2042-0986},
abstract = {OBJECTIVES: Rigorous practices for safe dispensing of investigational drugs are not standardized. This investigation sought to identify error-prevention processes utilized in the provision of investigational drug services (IDS) and to characterize pharmacists' perceptions about safety risks posed by investigational drugs.<br><br>METHODS: An electronic questionnaire was distributed to an audience of IDS pharmacists within the Veteran Affairs Health System. Multiple facets were examined including demographics, perceptions of medication safety, and standard processes used to support investigational drug protocols.<br><br>RESULTS: Twenty-one respondents (32.8% response rate) from the Northeast, Midwest, South, West, and Non-contiguous United States participated. The mean number of pharmacist full-time equivalents (FTEs) dedicated to the IDS was 0.77 per site with 0.2 technician FTEs. The mean number of active protocols was 22. Seventeen respondents (81%) indicated some level of concern for safety risks. Concerns related to the packaging of medications were expressed, most notably lack of product differentiation, expiration dating, barcodes, and choice of font size or color. Regarding medication safety practices, the majority of sites had specific procedures in place for storing and securing drug supply, temperature monitoring, and prescription labeling. Repackaging bulk items and proactive error-identification strategies were less common. Sixty-seven percent of respondents reported that an independent double check was not routinely performed.<br><br>CONCLUSIONS: Medication safety concerns exist among pharmacists in an investigational drug service; however, a variety of measures have been employed to improve medication safety practices. Best practices for the safe dispensing of investigational medications should be developed in order to standardize these error-prevention strategies.},
}
@article {pmid26240451,
year = {2015},
author = {Crous, PW and Wingfield, MJ and Guarro, J and Hernández-Restrepo, M and Sutton, DA and Acharya, K and Barber, PA and Boekhout, T and Dimitrov, RA and Dueñas, M and Dutta, AK and Gené, J and Gouliamova, DE and Groenewald, M and Lombard, L and Morozova, OV and Sarkar, J and Smith, MT and Stchigel, AM and Wiederhold, NP and Alexandrova, AV and Antelmi, I and Armengol, J and Barnes, I and Cano-Lira, JF and Castañeda Ruiz, RF and Contu, M and Courtecuisse, PR and da Silveira, AL and Decock, CA and de Goes, A and Edathodu, J and Ercole, E and Firmino, AC and Fourie, A and Fournier, J and Furtado, EL and Geering, AD and Gershenzon, J and Giraldo, A and Gramaje, D and Hammerbacher, A and He, XL and Haryadi, D and Khemmuk, W and Kovalenko, AE and Krawczynski, R and Laich, F and Lechat, C and Lopes, UP and Madrid, H and Malysheva, EF and Marín-Felix, Y and Martín, MP and Mostert, L and Nigro, F and Pereira, OL and Picillo, B and Pinho, DB and Popov, ES and Rodas Peláez, CA and Rooney-Latham, S and Sandoval-Denis, M and Shivas, RG and Silva, V and Stoilova-Disheva, MM and Telleria, MT and Ullah, C and Unsicker, SB and van der Merwe, NA and Vizzini, A and Wagner, HG and Wong, PT and Wood, AR and Groenewald, JZ},
title = {Fungal Planet description sheets: 320-370.},
journal = {Persoonia},
volume = {34},
number = {},
pages = {167-266},
pmid = {26240451},
issn = {0031-5850},
abstract = {Novel species of fungi described in the present study include the following from Malaysia: Castanediella eucalypti from Eucalyptus pellita, Codinaea acacia from Acacia mangium, Emarcea eucalyptigena from Eucalyptus brassiana, Myrtapenidiella eucalyptorum from Eucalyptus pellita, Pilidiella eucalyptigena from Eucalyptus brassiana and Strelitziana malaysiana from Acacia mangium. Furthermore, Stachybotrys sansevieriicola is described from Sansevieria ehrenbergii (Tanzania), Phacidium grevilleae from Grevillea robusta (Uganda), Graphium jumulu from Adansonia gregorii and Ophiostoma eucalyptigena from Eucalyptus marginata (Australia), Pleurophoma ossicola from bone and Plectosphaerella populi from Populus nigra (Germany), Colletotrichum neosansevieriae from Sansevieria trifasciata, Elsinoë othonnae from Othonna quinquedentata and Zeloasperisporium cliviae (Zeloasperisporiaceae fam. nov.) from Clivia sp. (South Africa), Neodevriesia pakbiae, Phaeophleospora hymenocallidis and Phaeophleospora hymenocallidicola on leaves of a fern (Thailand), Melanconium elaeidicola from Elaeis guineensis (Indonesia), Hormonema viticola from Vitis vinifera (Canary Islands), Chlorophyllum pseudoglobossum from a grassland (India), Triadelphia disseminata from an immunocompromised patient (Saudi Arabia), Colletotrichum abscissum from Citrus (Brazil), Polyschema sclerotigenum and Phialemonium limoniforme from human patients (USA), Cadophora vitícola from Vitis vinifera (Spain), Entoloma flavovelutinum and Bolbitius aurantiorugosus from soil (Vietnam), Rhizopogon granuloflavus from soil (Cape Verde Islands), Tulasnella eremophila from Euphorbia officinarum subsp. echinus (Morocco), Verrucostoma martinicensis from Danaea elliptica (French West Indies), Metschnikowia colchici from Colchicum autumnale (Bulgaria), Thelebolus microcarpus from soil (Argentina) and Ceratocystis adelpha from Theobroma cacao (Ecuador). Myrmecridium iridis (Myrmecridiales ord. nov., Myrmecridiaceae fam. nov.) is also described from Iris sp. (The Netherlands). Novel genera include (Ascomycetes): Budhanggurabania from Cynodon dactylon (Australia), Soloacrosporiella, Xenocamarosporium, Neostrelitziana and Castanediella from Acacia mangium and Sabahriopsis from Eucalyptus brassiana (Malaysia), Readerielliopsis from basidiomata of Fuscoporia wahlbergii (French Guyana), Neoplatysporoides from Aloe ferox (Tanzania), Wojnowiciella, Chrysofolia and Neoeriomycopsis from Eucalyptus (Colombia), Neophaeomoniella from Eucalyptus globulus (USA), Pseudophaeomoniella from Olea europaea (Italy), Paraphaeomoniella from Encephalartos altensteinii, Aequabiliella, Celerioriella and Minutiella from Prunus (South Africa). Tephrocybella (Basidiomycetes) represents a novel genus from wood (Italy). Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.},
}
@article {pmid26239394,
year = {2015},
author = {Deli Antoni, MY and González-Castro, M and Díaz de Astarloa, JM},
title = {New tools (DNA barcoding), old hypothesis: the case of the taxonomic identity of the Argentine hakes (Actinopterygii: Merluccius).},
journal = {Journal of fish biology},
volume = {87},
number = {3},
pages = {783-793},
doi = {10.1111/jfb.12745},
pmid = {26239394},
issn = {1095-8649},
mesh = {Animals ; Argentina ; Base Sequence ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Gadiformes/*classification/genetics ; Phylogeny ; },
abstract = {The present study evaluated the possible occurrence of cryptic species among Merluccidae from Argentina by examining sequences of cytochrome c oxidase subunit I (coI) mtDNA. This approach can discriminate Merluccius hubbsi and Merluccius australis; specimens with morphological diagnostic characters of Merluccius patagonicus formed a cohesive cluster with M. hubbsi specimens. BIN analysis confirmed the effectiveness of barcoding within a global context.},
}
@article {pmid26238459,
year = {2015},
author = {Ramirez, JL and Galetti, PM},
title = {DNA barcode and evolutionary relationship within Laemolyta Cope 1872 (Characiformes: Anostomidae) through molecular analyses.},
journal = {Molecular phylogenetics and evolution},
volume = {93},
number = {},
pages = {77-82},
doi = {10.1016/j.ympev.2015.07.021},
pmid = {26238459},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Brazil ; Characiformes/*genetics ; Cytochromes c/genetics ; DNA Barcoding, Taxonomic/*methods ; Phylogeny ; },
abstract = {The Laemolyta genus is a monophyletic group with five valid species. Phylogenetic relationships among the species of this genus are unknown. We analyzed four nominal Laemolyta species. The COI gene for all individuals was amplified and the genetic distances were estimated. We performed genetic distance analyses to determine the different MOTUs. Two mitochondrial (COI and CytB) and three nuclear (Myh6, RAG1 and RAG2) markers were amplified for one individual of each identified MOTU. Maximum Parsimony and Maximum Likelihood were conducted using concatenate alignment. In addition, multilocus Bayesian species tree was carried out. By using DNA barcode, we identified six different MOTUs. The COI inter-MOTU distances ranged from 0.92% to 5.76%. The normalized mean intra-MOTU distance was 0.13%. The DNA barcode was useful to diagnose all species. Two clades showing distinct color patterns were recovered in all molecular phylogenetic trees. Clade A joined fishes with no vertical bars (L. garmani, L. taeniata 1 and L. taeniata 2) and clade B, fishes with vertical dark bars (L. fernandezi Araguaia, L. fernandezi Xingu, and L. proxima). The results were able to identify the cryptic biodiversity within the group and obtained the most complete Laemolyta phylogeny.},
}
@article {pmid26237350,
year = {2015},
author = {Kang, H and Jeong, S and Koh, Y and Cha, MG and Yang, JK and Kyeong, S and Kim, J and Kwak, SY and Chang, HJ and Lee, H and Jeong, C and Kim, JH and Jun, BH and Kim, YK and Jeong, DH and Lee, YS},
title = {Corrigendum: Direct Identification of On-Bead Peptides Using Surface-Enhanced Raman Spectroscopic Barcoding System for High-Throughput Bioanalysis.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {12663},
doi = {10.1038/srep12663},
pmid = {26237350},
issn = {2045-2322},
}
@article {pmid26236856,
year = {2015},
author = {Hayward, J and Horton, TR and Pauchard, A and Nuñnez, MA},
title = {A single ectomycorrhizal fungal species can enable a Pinus invasion.},
journal = {Ecology},
volume = {96},
number = {5},
pages = {1438-1444},
doi = {10.1890/14-1100.1},
pmid = {26236856},
issn = {0012-9658},
mesh = {Chile ; DNA, Fungal/genetics ; DNA, Intergenic ; *Ecosystem ; *Introduced Species ; Meristem/microbiology ; Mycorrhizae/*classification/genetics/*physiology ; Pinus/*microbiology ; Species Specificity ; },
abstract = {Like all obligately ectomycorrhizal plants, pines require ectomycorrhizal fungal symbionts to complete their life cycle. Pines introduced into regions far from their native range are typically incompatible with local ectomycorrhizal fungi, and, when they invade, coinvade with fungi from their native range. While the identities and distributions of coinvasive fungal symbionts of pine invasions are poorly known, communities that have been studied are notably depauperate. However, it is not yet clear whether any number of fungal coinvaders is able to support a Pinaceae invasion, or whether very depauperate communities are unable to invade. Here, we ask whether there is evidence for a minimum species richness of fungal symbionts necessary to support a pine/ectomycorrhizal fungus coinvasion. We sampled a Pinus contorta invasion front near Coyhaique, Chile, using molecular barcoding to identify ectomycorrhizal fungi. We report that the site has a total richness of four species, and that many invasive trees appear to be supported by only a single ectomycorrhizal fungus, Suillus luteus. We conclude that a single ectomycorrhizal (ECM) fungus can suffice to enable a pine invasion.},
}
@article {pmid26236400,
year = {2015},
author = {Bernstein, DL and Kameswaran, V and Le Lay, JE and Sheaffer, KL and Kaestner, KH},
title = {The BisPCR(2) method for targeted bisulfite sequencing.},
journal = {Epigenetics &amp; chromatin},
volume = {8},
number = {},
pages = {27},
pmid = {26236400},
issn = {1756-8935},
support = {R01 DK088383/DK/NIDDK NIH HHS/United States ; T32 GM008076/GM/NIGMS NIH HHS/United States ; UC4 DK104119/DK/NIDDK NIH HHS/United States ; UC4 DK116271/DK/NIDDK NIH HHS/United States ; },
abstract = {BACKGROUND: DNA methylation has emerged as an important regulator of development and disease, necessitating the design of more efficient and cost-effective methods for detecting and quantifying this epigenetic modification. Next-generation sequencing (NGS) techniques offer single base resolution of CpG methylation levels with high statistical significance, but are also high cost if performed genome-wide. Here, we describe a simplified targeted bisulfite sequencing approach in which DNA sequencing libraries are prepared following sodium bisulfite conversion and two rounds of PCR for target enrichment and sample barcoding, termed BisPCR(2).<br><br>RESULTS: We have applied the BisPCR(2) technique to validate differential methylation at several type 2 diabetes risk loci identified in genome-wide studies of human islets. We confirmed some previous findings while not others, in addition to identifying novel differentially methylated CpGs at these genes of interest, due to the much higher depth of sequencing coverage in BisPCR(2) compared to prior array-based approaches.<br><br>CONCLUSION: This study presents a robust, efficient, and cost-effective technique for targeted bisulfite NGS, and illustrates its utility by reanalysis of prior findings from genome-wide studies.},
}
@article {pmid26236305,
year = {2015},
author = {Herbold, CW and Pelikan, C and Kuzyk, O and Hausmann, B and Angel, R and Berry, D and Loy, A},
title = {A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {731},
pmid = {26236305},
issn = {1664-302X},
support = {P 25111/FWF_/Austrian Science Fund FWF/Austria ; P 25700/FWF_/Austrian Science Fund FWF/Austria ; P 26127/FWF_/Austrian Science Fund FWF/Austria ; T32 HG002536/HG/NHGRI NIH HHS/United States ; },
abstract = {High throughput sequencing of phylogenetic and functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we introduce a highly adaptable and economical PCR approach to barcoding and pooling libraries of numerous target genes. In this approach, we replace gene- and sequencing platform-specific fusion primers with general, interchangeable barcoding primers, enabling nearly limitless customized barcode-primer combinations. Compared to barcoding with long fusion primers, our multiple-target gene approach is more economical because it overall requires lower number of primers and is based on short primers with generally lower synthesis and purification costs. To highlight our approach, we pooled over 900 different small-subunit rRNA and functional gene amplicon libraries obtained from various environmental or host-associated microbial community samples into a single, paired-end Illumina MiSeq run. Although the amplicon regions ranged in size from approximately 290 to 720 bp, we found no significant systematic sequencing bias related to amplicon length or gene target. Our results indicate that this flexible multiplexing approach produces large, diverse, and high quality sets of amplicon sequence data for modern studies in microbial ecology.},
}
@article {pmid26226748,
year = {2015},
author = {Wu, B and Li, YB and Rao, JB and Zeng, JX and Zhu, JX and Fang, XX and Liu, FQ and Li, HZ and Han, FY and Zhong, GY},
title = {[Study on genetic polymorphism of Platycodon grandiflorum based on barcoding of ITS2].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {40},
number = {6},
pages = {1075-1078},
pmid = {26226748},
issn = {1001-5302},
mesh = {China ; DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; DNA, Ribosomal Spacer/*genetics ; Molecular Sequence Data ; Phylogeny ; Platycodon/*classification/*genetics ; *Polymorphism, Genetic ; },
abstract = {OBJECTIVE: ITS2 of DNA barcoding was used to study genetic polymorphism of Platycodon grandiflorum.<br><br>METHOD: Total genomic DNA was isolated from P. grandiflorum. PCR was used to amplified the region of internal transcribed spacer 2 (ITS2), and PCR products were sequenced. The sequences of ITS2 were analyzed and compared by Clustal. The intraspecies genetic distance was calculated based on Kimura 2-parameter model by using MEGA 5.05. The ITS2 sequence of Codonopsis pilosula was used as the outreach value for plants of the genus, and the phylogenic tree used constructed by Neighbor-Joining (NJ) method.<br><br>RESULT: The K2-P's genetic distance of all samples were ranged from 0 to 0.930. The K2-P's genetic distance of samples at the same area were ranged from 0 to 0.178. The K2-P's genetic distance of samples at different areas were ranged from 0.735 to 0.930. The analytical result showed that the degree of genetic variation were heavy in intraspecies of P. grandiflorum and significantly correlated with geographical location.<br><br>CONCLUSION: The DNA barcoding of ITS2 can applied to study the intraspecific genetic diversity, it provides a reference for further development of DNA barcoding technology applications.},
}
@article {pmid26223793,
year = {2015},
author = {Overy, DP and Marron-Lopez, F and Muckle, A and Bourque, A and Lund, L and MacHattie, D and Lopez, A},
title = {Dermatophytosis in farmed mink (Mustela vison) caused by Trichophyton equinum.},
journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc},
volume = {27},
number = {5},
pages = {621-626},
doi = {10.1177/1040638715596036},
pmid = {26223793},
issn = {1943-4936},
mesh = {Animals ; Base Sequence ; DNA, Fungal/analysis ; Disease Outbreaks/*veterinary ; *Mink ; Molecular Sequence Data ; Nova Scotia/epidemiology ; Phylogeny ; Tinea/epidemiology/*veterinary ; Trichophyton/genetics/*isolation &amp; purification ; },
abstract = {This report details 2 outbreaks of dermatophytosis in 2 different mink ranches. On the first farm, only kits were affected, while on the second farm, small numbers of adults were infected. Affected mink were otherwise clinically healthy and in good body condition. Three animals were euthanized and submitted for autopsy. Grossly, mink exhibited locally extensive to coalescing areas of crusting alopecia but no other significant gross lesions in internal organs. Microscopically, skin lesions were characterized by chronic hyperplastic dermatitis with folliculitis, furunculosis, occasional intracorneal pustules, and large numbers of intrafollicular fungal arthrospores and hyphae. The dermatophyte was cultured and identified as Trichophyton equinum based on molecular barcoding of the internal transcribed spacer region of the ribosomal DNA gene.},
}
@article {pmid26220837,
year = {2015},
author = {Esposito, LA and Bloom, T and Caicedo-Quiroga, L and Alicea-Serrano, AM and Sánchez-Ruíz, JA and May-Collado, LJ and Binford, GJ and Agnarsson, I},
title = {Islands within islands: Diversification of tailless whip spiders (Amblypygi, Phrynus) in Caribbean caves.},
journal = {Molecular phylogenetics and evolution},
volume = {93},
number = {},
pages = {107-117},
doi = {10.1016/j.ympev.2015.07.005},
pmid = {26220837},
issn = {1095-9513},
mesh = {Animal Distribution ; Animals ; Biodiversity ; Caves ; DNA, Mitochondrial/genetics ; Genetic Speciation ; Genetic Variation ; Multilocus Sequence Typing ; Phylogeny ; Phylogeography ; Puerto Rico ; Spiders/classification/*genetics ; },
abstract = {Islands have played a key role in understanding species formation ever since Darwin's work on the Galapagos and Wallace's work in the Malay Archipelago. Like oceanic islands, habitat 'islands', such as mountaintops and caves similarly may drive diversification. Here we examine patterns of diversification in the tailless whip spider genus Phrynus Larmarck, 1809 (Amblypygida: Phrynidae) a system that shows evidence of diversification under the influence of 'islands within islands'. We estimate phylogeographic history and measure genetic diversity among representatives of three nominal Phrynus species from epigean and cave systems of Puerto Rico and nearby islands. Data from five loci (mitochondrial 12S, 16S, Cox1; nuclear H3, 28S) were used to generate phylogenetic hypotheses and to assess species monophyly and phylogeographic relationships. Genetic divergences and population limits were estimated and assessed using the Geneious barcoding plugin and the genealogical sorting index. We find that mtDNA sequence divergences within each of the three Phrynus species range between 15% and 20%. Genetic divergence is structured at three spatial scales: among islands in a manner consistent with the GAARlandia hypothesis, among bedrock formations within Puerto Rico, and among caves within these formations. Every isolated cave system contains a unique mtDNA genetic lineage of Phrynus, with divergence among cave systems far exceeding that within. In some localities epigean specimens nest among cave taxa, in others caves are monophyletic. Remarkably, clades that show up to 20% mtDNA sequence divergence show little or no variation in the nuclear markers. We interpret this pattern as resulting from extreme conservation of our nuclear markers rather than male sex-biased dispersal, based on high conservation of 28S and H3 between our individuals and other amblypygid genera that are restricted to Africa. While this study includes but a tiny fraction of Caribbean caves, our findings suggest Phrynus may be much more diverse than hitherto thought, at least in terms of mtDNA diversity, and that the arthropod fauna of caves may represent a dimension of biodiversity that is yet to be discovered in the Caribbean biodiversity hotspot.},
}
@article {pmid26211788,
year = {2016},
author = {Fučíková, K and Lahr, DJ},
title = {Uncovering Cryptic Diversity in Two Amoebozoan Species Using Complete Mitochondrial Genome Sequences.},
journal = {The Journal of eukaryotic microbiology},
volume = {63},
number = {1},
pages = {112-122},
doi = {10.1111/jeu.12253},
pmid = {26211788},
issn = {1550-7408},
mesh = {Acanthamoeba castellanii/cytology/*genetics ; Amoebozoa/cytology/*genetics ; Animals ; Base Sequence ; DNA, Mitochondrial ; Evolution, Molecular ; *Genetic Variation ; *Genome, Mitochondrial ; Genome, Protozoan ; Nucleic Acid Conformation ; *Phylogeny ; Ribosome Subunits, Small ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {The Amoebozoa are a major eukaryotic lineage that encompasses a wide range of amoeboid organisms. The group is understudied from a systematic perspective: molecular tools have only been applied in the last 15 yr. Hence, there is an undersampling of both genes and taxa in the group especially compared to plants, animals, and fungi. Here, we present the complete mitochondrial genomes of two ubiquitous and abundant morpho-species (Acanthamoeba castellanii and Vermamoeba vermiformis). Both have mitochondrial genomes of close relatives previously available, enabling insights into recent divergences at a genomic scale, while simultaneously offering comparisons with divergence estimates obtained from traditionally used single genes, SSU rDNA and cox1. The newly sequenced mt genomes are significantly divergent from their previously sequenced conspecifics (A. castellannii 16.4% divergence at nucleotide level and 10.4% amino acid; V. vermiformis 21.6% and 13.1%, respectively), while divergence at the small subunit ribosomal DNA is below 1% within both species. Morphological analyses determined that these lineages are indistinguishable from their previously sequenced counterparts. Phylogenetic reconstructions using 26 mt genes also indicate a level of divergence that is comparable to divergence among species, while reconstructions using the small subunit ribosomal DNA (SSU rDNA) do not. In addition, we demonstrate that between closely related taxa, there are high levels of synteny, which can be explored for primer design to obtain larger fragments than the traditional barcoding genes. We conclude that, although most systematic work has relied on SSU, this gene alone can severely underestimate diversity. Thus, we suggest that the mt genome emerges as an alternative for unraveling the lower level phylogenetic relationships of Amoebozoa.},
}
@article {pmid26207903,
year = {2015},
author = {Montano, S and Maggioni, D and Arrigoni, R and Seveso, D and Puce, S and Galli, P},
title = {The Hidden Diversity of Zanclea Associated with Scleractinians Revealed by Molecular Data.},
journal = {PloS one},
volume = {10},
number = {7},
pages = {e0133084},
pmid = {26207903},
issn = {1932-6203},
mesh = {Animals ; Anthozoa/classification/*physiology ; Base Sequence ; Biota ; Coral Reefs ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; Haplotypes/genetics ; Host Specificity ; Hydrozoa/classification/*genetics ; Indian Ocean Islands ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 28S/genetics ; Ribotyping ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Species Specificity ; *Symbiosis ; },
abstract = {Scleractinian reef corals have recently been acknowledged as the most numerous host group found in association with hydroids belonging to the Zanclea genus. However, knowledge of the molecular phylogenetic relationships among Zanclea species associated with scleractinians is just beginning. This study, using the nuclear 28S rDNA region and the fast-evolving mitochondrial 16S rRNA and COI genes, provides the most comprehensive phylogenetic reconstruction of the genus Zanclea with a particular focus on the genetic diversity among Zanclea specimens associated with 13 scleractinian genera. The monophyly of Zanclea associated with scleractinians was strongly supported in all nuclear and mitochondrial phylogenetic reconstructions. Furthermore, a combined mitochondrial 16S and COI phylogenetic tree revealed a multitude of hidden molecular lineages within this group (Clades I, II, III, V, VI, VII, and VIII), suggesting the existence of both host-generalist and genus-specific lineages of Zanclea associated with scleractinians. In addition to Z. gallii living in association with the genus Acropora, we discovered four well-supported lineages (Clades I, II, III, and VII), each one forming a strict association with a single scleractinian genus, including sequences of Zanclea associated with Montipora from two geographically separated areas (Maldives and Taiwan). Two host-generalist Zanclea lineages were also observed, and one of them was formed by Zanclea specimens symbiotic with seven scleractinian genera (Clade VIII). We also found that the COI gene allows the recognition of separated hidden lineages in agreement with the commonly recommended mitochondrial 16S as a DNA barcoding gene for Hydrozoa and shows reasonable potential for phylogenetic and evolutionary analyses in the genus Zanclea. Finally, as no DNA sequences are available for the majority of the nominal Zanclea species known, we note that they will be necessary to elucidate the diversity of the Zanclea-scleractinian association.},
}
@article {pmid26205828,
year = {2015},
author = {Dincă, V and Montagud, S and Talavera, G and Hernández-Roldán, J and Munguira, ML and García-Barros, E and Hebert, PD and Vila, R},
title = {DNA barcode reference library for Iberian butterflies enables a continental-scale preview of potential cryptic diversity.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {12395},
pmid = {26205828},
issn = {2045-2322},
mesh = {Animals ; *Biodiversity ; Butterflies/*genetics ; *DNA Barcoding, Taxonomic ; Spain ; },
abstract = {How common are cryptic species--those overlooked because of their morphological similarity? Despite its wide-ranging implications for biology and conservation, the answer remains open to debate. Butterflies constitute the best-studied invertebrates, playing a similar role as birds do in providing models for vertebrate biology. An accurate assessment of cryptic diversity in this emblematic group requires meticulous case-by-case assessments, but a preview to highlight cases of particular interest will help to direct future studies. We present a survey of mitochondrial genetic diversity for the butterfly fauna of the Iberian Peninsula with unprecedented resolution (3502 DNA barcodes for all 228 species), creating a reliable system for DNA-based identification and for the detection of overlooked diversity. After compiling available data for European butterflies (5782 sequences, 299 species), we applied the Generalized Mixed Yule-Coalescent model to explore potential cryptic diversity at a continental scale. The results indicate that 27.7% of these species include from two to four evolutionary significant units (ESUs), suggesting that cryptic biodiversity may be higher than expected for one of the best-studied invertebrate groups and regions. The ESUs represent important units for conservation, models for studies of evolutionary and speciation processes, and sentinels for future research to unveil hidden diversity.},
}
@article {pmid26205170,
year = {2015},
author = {Dodsworth, S},
title = {Genome skimming for next-generation biodiversity analysis.},
journal = {Trends in plant science},
volume = {20},
number = {9},
pages = {525-527},
doi = {10.1016/j.tplants.2015.06.012},
pmid = {26205170},
issn = {1878-4372},
mesh = {*Biodiversity ; DNA Barcoding, Taxonomic ; *Genome, Plant ; Genomics/*trends ; Phylogeny ; Plants/*classification ; Sequence Analysis, DNA ; },
}
@article {pmid26205052,
year = {2015},
author = {Raveendar, S and Na, YW and Lee, JR and Shim, D and Ma, KH and Lee, SY and Chung, JW},
title = {The complete chloroplast genome of Capsicum annuum var. glabriusculum using Illumina sequencing.},
journal = {Molecules (Basel, Switzerland)},
volume = {20},
number = {7},
pages = {13080-13088},
pmid = {26205052},
issn = {1420-3049},
mesh = {Base Sequence ; Capsicum/*genetics ; Chloroplasts/*genetics ; *Genome, Chloroplast ; Molecular Sequence Data ; },
abstract = {Chloroplast (cp) genome sequences provide a valuable source for DNA barcoding. Molecular phylogenetic studies have concentrated on DNA sequencing of conserved gene loci. However, this approach is time consuming and more difficult to implement when gene organization differs among species. Here we report the complete re-sequencing of the cp genome of Capsicum pepper (Capsicum annuum var. glabriusculum) using the Illumina platform. The total length of the cp genome is 156,817 bp with a 37.7% overall GC content. A pair of inverted repeats (IRs) of 50,284 bp were separated by a small single copy (SSC; 18,948 bp) and a large single copy (LSC; 87,446 bp). The number of cp genes in C. annuum var. glabriusculum is the same as that in other Capsicum species. Variations in the lengths of LSC; SSC and IR regions were the main contributors to the size variation in the cp genome of this species. A total of 125 simple sequence repeat (SSR) and 48 insertions or deletions variants were found by sequence alignment of Capsicum cp genome. These findings provide a foundation for further investigation of cp genome evolution in Capsicum and other higher plants.},
}
@article {pmid26203422,
year = {2015},
author = {Crous, PW and Carris, LM and Giraldo, A and Groenewald, JZ and Hawksworth, DL and Hernández-Restrepo, M and Jaklitsch, WM and Lebrun, MH and Schumacher, RK and Stielow, JB and van der Linde, EJ and Vilcāne, J and Voglmayr, H and Wood, AR},
title = {The Genera of Fungi - fixing the application of the type species of generic names - G 2: Allantophomopsis, Latorua, Macrodiplodiopsis, Macrohilum, Milospium, Protostegia, Pyricularia, Robillarda, Rotula, Septoriella, Torula, and Wojnowicia.},
journal = {IMA fungus},
volume = {6},
number = {1},
pages = {163-198},
pmid = {26203422},
issn = {2210-6340},
support = {P 25870/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {The present paper represents the second contribution in the Genera of Fungi series, linking type species of fungal genera to their morphology and DNA sequence data, and where possible, ecology. This paper focuses on 12 genera of microfungi, 11 of which the type species are neo- or epitypified here: Allantophomopsis (A. cytisporea, Phacidiaceae, Phacidiales, Leotiomycetes), Latorua gen. nov. (Latorua caligans, Latoruaceae, Pleosporales, Dothideomycetes), Macrodiplodiopsis (M. desmazieri, Macrodiplodiopsidaceae, Pleosporales, Dothideomycetes), Macrohilum (M. eucalypti, Macrohilaceae, Diaporthales, Sordariomycetes), Milospium (M. graphideorum, incertae sedis, Pezizomycotina), Protostegia (P. eucleae, Mycosphaerellaceae, Capnodiales, Dothideomycetes), Pyricularia (P. grisea, Pyriculariaceae, Magnaporthales, Sordariomycetes), Robillarda (R. sessilis, Robillardaceae, Xylariales, Sordariomycetes), Rutola (R. graminis, incertae sedis, Pleosporales, Dothideomycetes), Septoriella (S. phragmitis, Phaeosphaeriaceae, Pleosporales, Dothideomycetes), Torula (T. herbarum, Torulaceae, Pleosporales, Dothideomycetes) and Wojnowicia (syn. of Septoriella, S. hirta, Phaeosphaeriaceae, Pleosporales, Dothideomycetes). Novel species include Latorua grootfonteinensis, Robillarda africana, R. roystoneae, R. terrae, Torula ficus, T. hollandica, and T. masonii spp. nov., and three new families: Macrodiplodiopsisceae, Macrohilaceae, and Robillardaceae. Authors interested in contributing accounts of individual genera to larger multi-authored papers to be published in IMA Fungus, should contact the associate editors listed for the major groups of fungi on the List of Protected Generic Names for Fungi (www.generaoffungi.org).},
}
@article {pmid26199185,
year = {2015},
author = {Trebitz, AS and Hoffman, JC and Grant, GW and Billehus, TM and Pilgrim, EM},
title = {Potential for DNA-based identification of Great Lakes fauna: match and mismatch between taxa inventories and DNA barcode libraries.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {12162},
pmid = {26199185},
issn = {2045-2322},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Lakes ; Species Specificity ; },
abstract = {DNA-based identification of mixed-organism samples offers the potential to greatly reduce the need for resource-intensive morphological identification, which would be of value both to bioassessment and non-native species monitoring. The ability to assign species identities to DNA sequences found depends on the availability of comprehensive DNA reference libraries. Here, we compile inventories for aquatic metazoans extant in or threatening to invade the Laurentian Great Lakes and examine the availability of reference mitochondrial COI DNA sequences (barcodes) in the Barcode of Life Data System for them. We found barcode libraries largely complete for extant and threatening-to-invade vertebrates (100% of reptile, 99% of fish, and 92% of amphibian species had barcodes). In contrast, barcode libraries remain poorly developed for precisely those organisms where morphological identification is most challenging; 46% of extant invertebrates lacked reference barcodes with rates especially high among rotifers, oligochaetes, and mites. Lack of species-level identification for many aquatic invertebrates also is a barrier to matching DNA sequences with physical specimens. Attaining the potential for DNA-based identification of mixed-organism samples covering the breadth of aquatic fauna requires a concerted effort to build supporting barcode libraries and voucher collections.},
}
@article {pmid26198870,
year = {2015},
author = {Tyagi, K and Kumar, V and Singha, D and Chakraborty, R},
title = {Morphological and DNA Barcoding Evidence for Invasive Pest Thrips, Thrips parvispinus (Thripidae: Thysanoptera), Newly Recorded From India.},
journal = {Journal of insect science (Online)},
volume = {15},
number = {1},
pages = {},
pmid = {26198870},
issn = {1536-2442},
mesh = {*Animal Distribution ; Animals ; DNA Barcoding, Taxonomic ; Female ; India ; *Introduced Species ; Male ; Thysanoptera/*anatomy &amp; histology/classification/genetics/*physiology ; },
abstract = {South East Asia pest thrips species, Thrips parvispinus (Karny), is a serious pest on a number of agricultural and horticultural crops in a number of plant families. Based on an integrated approach of morphology and DNA barcoding, invasion of this serious pest is reported first time from India on papaya plantations. Molecular data have corroborated with the morphological identification. Haplotyping data suggested that the Indonesia may be a probable source of invasion of this pest to India.},
}
@article {pmid26198227,
year = {2015},
author = {Abe, CA and Faria, CB and de Castro, FF and de Souza, SR and dos Santos, FC and da Silva, CN and Tessmann, DJ and Barbosa-Tessmann, IP},
title = {Fungi Isolated from Maize (Zea mays L.) Grains and Production of Associated Enzyme Activities.},
journal = {International journal of molecular sciences},
volume = {16},
number = {7},
pages = {15328-15346},
pmid = {26198227},
issn = {1422-0067},
mesh = {Amylose/metabolism ; Base Sequence ; Cellulose/metabolism ; DNA, Ribosomal/genetics ; Evolution, Molecular ; Fungi/*enzymology/genetics/*isolation &amp; purification ; Hydrolysis ; Lipolysis ; Proteolysis ; Seeds/*microbiology ; Time Factors ; Zea mays/*microbiology ; },
abstract = {Filamentous fungi produce a great variety of enzymes, and research on their biotechnological potential has recently intensified. The objective of this work was to identify, at the species level, using DNA barcoding, 46 fungal isolates obtained from maize grains with rot symptoms. We also analyzed the production of extracellular amylases, cellulases, proteases and lipases of 33 of those fungal isolates. The enzymatic activities were evaluated by the formation of a clear halo or a white precipitate around the colonies in defined substrate media. The found fungi belong to the genera Talaromyces, Stenocarpella, Penicillium, Phlebiopsis, Cladosporium, Hyphopichia, Epicoccum, Trichoderma, Aspergillus, Irpex, Fusarium, Microdochium, Mucor and Sarocladium. In the genus Fusarium, the species Fusarium verticillioides was predominant and this genus presented the highest diversity, followed by the genera Aspergillus. The best genera for lipase production were Cladosporium and Penicillium; while Cladosporium, Aspergillus and Penicillium were best for cellulase activity; Hyphopichia, Aspergillus and Irpex for amylase activity; and Cladosporium and Sarocladium for proteases activity. In conclusion, a collection of fungi from maize seeds presenting rotten symptoms were obtained, among which exist important producers of hydrolases.},
}
@article {pmid26197545,
year = {2015},
author = {Capecchi, G and Goti, E and Nicolai, E and Bergonzi, MC and Monnanni, R and Bilia, AR},
title = {Goji Berry: Quality Assessment and Crop Adaptation of Plants Cultivated in Tuscany (Italy) by Combination of Carotenoid and DNA Analyses.},
journal = {Natural product communications},
volume = {10},
number = {6},
pages = {1035-1036},
pmid = {26197545},
issn = {1934-578X},
mesh = {Acclimatization ; Antioxidants/analysis ; Carotenoids/*analysis ; DNA, Plant/*genetics ; Fruit/chemistry/genetics/growth &amp; development ; Italy ; Lycium/chemistry/*genetics/growth &amp; development ; Quality Control ; },
abstract = {In this study HPLC analysis for the evaluation of carotenoids and DNA barcoding are reported for three different samples of Lycium cultivated in Tuscany (Italy). These two analytical methods can represent integrative methods for quality control of goji, giving also crucial information on the plant adaptation to different environments. Hence, carotenoids represent the quality markers proposed by the monograph of the European Pharmacopoeia, while DNA barcoding can differentiate between species and populations and is useful for the detection of the homogeneity of the samples.},
}
@article {pmid26196835,
year = {2015},
author = {Kosakyan, A and Mulot, M and Mitchell, EA and Lara, E},
title = {Environmental DNA COI barcoding for quantitative analysis of protists communities: A test using the Nebela collaris complex (Amoebozoa; Arcellinida; Hyalospheniidae).},
journal = {European journal of protistology},
volume = {51},
number = {4},
pages = {311-320},
doi = {10.1016/j.ejop.2015.06.005},
pmid = {26196835},
issn = {1618-0429},
mesh = {Amoebozoa/*classification/*genetics ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Mitochondria/genetics ; Phylogeny ; Soil/parasitology ; },
abstract = {Environmental DNA surveys are used for screening eukaryotic diversity. However, it is unclear how quantitative this approach is and to what extent results from environmental DNA studies can be used for ecological studies requiring quantitative data. Mitochondrial cytochrome oxidase (COI) is used for species-level taxonomic studies of testate amoebae and should allow assessing the community composition from environmental samples, thus bypassing biases due to morphological identification. We tested this using a COI clone library approach and focusing on the Nebela collaris complex. Comparisons with direct microscopy counts showed that the COI clone library diversity data matched the morphologically identified taxa, and that community composition estimates using the two approaches were similar. However, this correlation was improved when microscopy counts were corrected for biovolume. Higher correlation with biovolume-corrected community data suggests that COI clone library data matches the ratio of mitochondria and that within closely-related taxa the density of mitochondria per unit biovolume is approximately constant. Further developments of this metabarcoding approach including quantifying the mitochondrial density among closely-related taxa, experiments on other taxonomic groups and using high throughput sequencing should make if possible to quantitatively estimate community composition of different groups, which would be invaluable for microbial food webs studies.},
}
@article {pmid26196736,
year = {2015},
author = {Lawton, SP and Lim, RM and Dukes, JP and Kett, SM and Cook, RT and Walker, AJ and Kirk, RS},
title = {Unravelling the riddle of Radix: DNA barcoding for species identification of freshwater snail intermediate hosts of zoonotic digeneans and estimating their inter-population evolutionary relationships.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {35},
number = {},
pages = {63-74},
doi = {10.1016/j.meegid.2015.07.021},
pmid = {26196736},
issn = {1567-7257},
mesh = {Animals ; Cyclooxygenase 1/analysis ; DNA/analysis ; DNA Barcoding, Taxonomic/*methods ; Evolution, Molecular ; Fresh Water/*parasitology ; Genetic Variation ; Haplotypes ; Humans ; Introduced Species ; Phylogeny ; Phylogeography ; Snails/*classification/*genetics/parasitology ; Trematode Infections/parasitology/veterinary ; United States ; Zoonoses/parasitology ; },
abstract = {Radix spp. are intermediate host snails for digenean parasites of medical and veterinary importance. Within this genus, species differentiation using shell and internal organ morphology can result in erroneous species identification, causing problems when trying to understand the population biology of Radix. In the present study, DNA barcoding, using cox1 and ITS2 sequences, identified populations of Radix auricularia and Radix balthica from specimens originally morphologically identified as Radix peregra from the UK. Assessment of cox1 and ITS2 as species identification markers showed that, although both markers differentiated species, cox1 possessed greater molecular diversity and higher phylogenetic resolution. Cox1 also proved useful for gaining insights into the evolutionary relationships of Radix species populations. Phylogenetic analysis and haplotype networks of cox1 indicated that R. auricularia appeared to have invaded the UK several times; some haplotypes forming a distinct UK specific clade, whilst others are more akin to those found on mainland Europe. This was in contrast to relationships between R. balthica populations, which had low molecular diversity and no distinct UK specific haplotypes, suggesting recent and multiple invasions from mainland Europe. Molecular techniques therefore appear to be crucial for distinguishing Radix spp., particularly using cox1. This barcoding marker also enables the population biology of Radix spp. to be explored, and is invaluable for monitoring the epidemiology of fluke diseases especially in the light of emerging diseases and food security.},
}
@article {pmid26194794,
year = {2015},
author = {Sickel, W and Ankenbrand, MJ and Grimmer, G and Holzschuh, A and Härtel, S and Lanzen, J and Steffan-Dewenter, I and Keller, A},
title = {Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach.},
journal = {BMC ecology},
volume = {15},
number = {},
pages = {20},
pmid = {26194794},
issn = {1472-6785},
mesh = {Animals ; Bees ; *DNA Barcoding, Taxonomic ; DNA Primers/*genetics ; Databases, Factual ; *High-Throughput Nucleotide Sequencing ; Pollen/*classification ; },
abstract = {BACKGROUND: Meta-barcoding of mixed pollen samples constitutes a suitable alternative to conventional pollen identification via light microscopy. Current approaches however have limitations in practicability due to low sample throughput and/or inefficient processing methods, e.g. separate steps for amplification and sample indexing.<br><br>RESULTS: We thus developed a new primer-adapter design for high throughput sequencing with the Illumina technology that remedies these issues. It uses a dual-indexing strategy, where sample-specific combinations of forward and reverse identifiers attached to the barcode marker allow high sample throughput with a single sequencing run. It does not require further adapter ligation steps after amplification. We applied this protocol to 384 pollen samples collected by solitary bees and sequenced all samples together on a single Illumina MiSeq v2 flow cell. According to rarefaction curves, 2,000-3,000 high quality reads per sample were sufficient to assess the complete diversity of 95% of the samples. We were able to detect 650 different plant taxa in total, of which 95% were classified at the species level. Together with the laboratory protocol, we also present an update of the reference database used by the classifier software, which increases the total number of covered global plant species included in the database from 37,403 to 72,325 (93% increase).<br><br>CONCLUSIONS: This study thus offers improvements for the laboratory and bioinformatical workflow to existing approaches regarding data quantity and quality as well as processing effort and cost-effectiveness. Although only tested for pollen samples, it is furthermore applicable to other research questions requiring plant identification in mixed and challenging samples.},
}
@article {pmid26191499,
year = {2015},
author = {Barar, J and Omidi, Y},
title = {Personalized cell-mediated immunotherapy and vaccination: combating detrimental uprisings of malignancies.},
journal = {BioImpacts : BI},
volume = {5},
number = {2},
pages = {65-69},
pmid = {26191499},
issn = {2228-5652},
abstract = {A large number of researchers worldwide have conducted various investigations to advance the cell-based immunotherapies and to examine their clinical benefits as an ultimate prevention and/or treatment modalities against life-threatening malignancies. This dominion needs integration of science and technology to change the face of treatment of diseases towards much more personalized medicines. It is now plausible to reprogram the human cells for the prevention and treatment of diseases through various mechanisms such as modulation of immune system, nonetheless we should understand the complexity of biological functions of the cells in a holistic way to be able to manipulate the central dogma of the life to prevent any inadvertent mistake. We should, if not must, comprehend the interrelations of the cellular components (e.g., transport machineries) in the developmental processes of diseases. Still, we do not have a complete image of life, perhaps as expressive barcodes, and many pieces are missing. While completing this puzzle to picture the whole image and examine new treatment modalities, we should take extra caution upon unknown/little-known biological phenomena because trifling modulation/ alteration in the complex systems of the life may result in tremendous impacts. In short, it seems we need to consider malignancies as complex systems and treat them in a holistic manner by targeting its hallmarks. Taken all, the immune system reinforcement would be one of the main foundations in combating detrimental malignancy uprising.},
}
@article {pmid26190935,
year = {2015},
author = {López-Legentil, S and Legentil, ML and Erwin, PM and Turon, X},
title = {Harbor networks as introduction gateways: contrasting distribution patterns of native and introduced ascidians.},
journal = {Biological invasions},
volume = {17},
number = {6},
pages = {1623-1638},
pmid = {26190935},
issn = {1387-3547},
abstract = {Harbors and marinas are well known gateways for species introductions in marine environments but little work has been done to ascertain relationships between species diversity, harbor type, and geographic distance to uncover patterns of secondary spread. Here, we sampled ascidians from 32 harbors along ca. 300 km of the NW Mediterranean coast and investigated patterns of distribution and spread related to harbor type (marina, fishing, commercial) and geographic location using multivariate techniques. In total, 28 ascidians were identified at the species level and another 9 at the genus level based on morphology and genetic barcoding. Eight species were assigned to introduced forms, 15 were given native status and 5 were classified as cryptogenic. Aplidium accarense was reported for the first time in the Mediterranean Sea and was especially abundant in 23 of the harbors. Introduced and cryptogenic species were abundant in most of the surveyed harbors, while native forms were rare and restricted to a few harbors. Significant differences in the distribution of ascidians according to harbor type and latitudinal position were observed. These differences were due to the distribution of introduced species. We obtained a significant correlation between geographic distance and ascidian composition, indicating that closely located harbors shared more ascidian species among them. This study showed that harbors act as dispersal strongholds for introduced species, with native species only appearing sporadically, and that harbor type and geographic location should also be considered when developing management plans to constrain the spread of non-indigenous species in highly urbanized coastlines.},
}
@article {pmid26190063,
year = {2015},
author = {Gaudillière, B and Ganio, EA and Tingle, M and Lancero, HL and Fragiadakis, GK and Baca, QJ and Aghaeepour, N and Wong, RJ and Quaintance, C and El-Sayed, YY and Shaw, GM and Lewis, DB and Stevenson, DK and Nolan, GP and Angst, MS},
title = {Implementing Mass Cytometry at the Bedside to Study the Immunological Basis of Human Diseases: Distinctive Immune Features in Patients with a History of Term or Preterm Birth.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {87},
number = {9},
pages = {817-829},
pmid = {26190063},
issn = {1552-4930},
support = {1R01GM10983601/GM/NIGMS NIH HHS/United States ; U19 AI057229/AI/NIAID NIH HHS/United States ; R01CA184968/CA/NCI NIH HHS/United States ; N01-HV-00242/HV/NHLBI NIH HHS/United States ; 41000411217//PHS HHS/United States ; U54CA149145/CA/NCI NIH HHS/United States ; K23 GM111657/GM/NIGMS NIH HHS/United States ; U54 CA149145/CA/NCI NIH HHS/United States ; R01 CA184968/CA/NCI NIH HHS/United States ; 1 R33 CA183654/CA/NCI NIH HHS/United States ; 201303028//PHS HHS/United States ; HHSF223201210194C//PHS HHS/United States ; R33 CA183654/CA/NCI NIH HHS/United States ; 1K23GM111657-01/GM/NIGMS NIH HHS/United States ; U19 AI100627/AI/NIAID NIH HHS/United States ; 1R01NS08953301/NS/NINDS NIH HHS/United States ; 7500108142//PHS HHS/United States ; 5R01AI07372405/AI/NIAID NIH HHS/United States ; R33 CA183692/CA/NCI NIH HHS/United States ; 1U19AI100627/AI/NIAID NIH HHS/United States ; R01 AI100121/AI/NIAID NIH HHS/United States ; },
mesh = {Adult ; Cross-Sectional Studies ; Female ; Flow Cytometry/*methods ; Humans ; Infant, Newborn ; Leukocytes, Mononuclear/*immunology ; *Point-of-Care Testing ; Pregnancy ; Premature Birth/*diagnosis/*immunology ; Term Birth/*immunology ; },
abstract = {Single-cell technologies have immense potential to shed light on molecular and biological processes that drive human diseases. Mass cytometry (or Cytometry by Time Of Flight mass spectrometry, CyTOF) has already been employed in clinical studies to comprehensively survey patients' circulating immune system. As interest in the "bedside" application of mass cytometry is growing, the delineation of relevant methodological issues is called for. This report uses a newly generated dataset to discuss important methodological considerations when mass cytometry is implemented in a clinical study. Specifically, the use of whole blood samples versus peripheral blood mononuclear cells (PBMCs), design of mass-tagged antibody panels, technical and analytical implications of sample barcoding, and application of traditional and unsupervised approaches to analyze high-dimensional mass cytometry datasets are discussed. A mass cytometry assay was implemented in a cross-sectional study of 19 women with a history of term or preterm birth to determine whether immune traits in peripheral blood differentiate the two groups in the absence of pregnancy. Twenty-seven phenotypic and 11 intracellular markers were simultaneously analyzed in whole blood samples stimulated with lipopolysaccharide (LPS at 0, 0.1, 1, 10, and 100 ng mL(-1)) to examine dose-dependent signaling responses within the toll-like receptor 4 (TLR4) pathway. Complementary analyses, grounded in traditional or unsupervised gating strategies of immune cell subsets, indicated that the prpS6 and pMAPKAPK2 responses in classical monocytes are accentuated in women with a history of preterm birth (FDR<1%). The results suggest that women predisposed to preterm birth may be prone to mount an exacerbated TLR4 response during the course of pregnancy. This important hypothesis-generating finding points to the power of single-cell mass cytometry to detect biologically important differences in a relatively small patient cohort.},
}
@article {pmid26188160,
year = {2015},
author = {Buddhachat, K and Osathanunkul, M and Madesis, P and Chomdej, S and Ongchai, S},
title = {Authenticity analyses of Phyllanthus amarus using barcoding coupled with HRM analysis to control its quality for medicinal plant product.},
journal = {Gene},
volume = {573},
number = {1},
pages = {84-90},
doi = {10.1016/j.gene.2015.07.046},
pmid = {26188160},
issn = {1879-0038},
mesh = {Base Sequence ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Molecular Sequence Data ; Phyllanthus/*classification/genetics ; Plants, Medicinal/*classification ; *Quality Control ; Sequence Homology, Nucleic Acid ; },
abstract = {The Phyllanthus genus, a plant used in traditional Thai medicine, has according to several pharmacopeias hepatoprotective properties. Not only is the anatomical morphology of these species relatively similar but they also share the Thai common names Look-Tai-Bai (ลูกใต้ใบ) and Yah-Tai-Bai (หญ้าใต้ใบ), which might cause confusion for laypersons. This study attempted to develop a method for accurate identification of Phyllanthus species, especially Phyllanthus amarus, and to detect contaminants in P. amarus products by using DNA barcoding coupled with high resolution melting (HRM) analysis (bar-HRM). Two plastid loci (rbcL and trnL) were chosen for DNA barcoding to generate a suitable primer for distinguishing Phyllanthus species by HRM analysis. The five species of Phyllanthus were subjected to amplification for testing the specificity and discrimination power of the designed primers derived from rbcL and trnL regions. Sensitivity of the method (DNA barcoding conjugated with HRM) to detect adulterant in P. amarus samples was evaluated. The commercial P. amarus products obtained from a local market were authenticated. The primer pair derived from trnL DNA barcoding (PhylltrnL) had more specificity and power of discrimination for Phyllanthus species than that derived from rbcL DNA barcoding (PhyllrbcL). The result showed that Tm of P. amarus, Phyllanthus urinaria, Phyllanthus debilis, Phyllanthus airy-shawii, and Phyllanthus virgatus was 74.3±0.08, 73.04±0.07, 73.36±0.05, 72.21±0.06, 72.77±0.15°C, respectively. This method proved to be a very sensitive tool that can be used for rapid detection of contamination as low as 1% of other Phyllanthus species in P. amarus admixtures. All commercial products of P. amarus obtained from a local market in Thailand were found to contain pure raw materials of P. amarus without any substitution or contamination. Our results indicated that the use of DNA barcoding coupled with HRM was an efficient molecular tool for correct species identification. This molecular tool provides a noteworthy benefit for quality control of medicinal plants and industry plants for pharmacological prospects.},
}
@article {pmid26186305,
year = {2016},
author = {Suganthi, M and Chandrashekara, KN and Arvinth, S and Raj Kumar, R},
title = {Molecular characterization of tea mosquito bug from tea growing regions of India.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3504-3506},
doi = {10.3109/19401736.2015.1066369},
pmid = {26186305},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Heteroptera/*classification/genetics ; India ; Insect Proteins/genetics ; Phylogeny ; Sequence Analysis, DNA ; Tea/*parasitology ; },
abstract = {The tea mosquito bug, Helopeltis (Hemiptera: Miridae), is an insidious pest that poses a significant economical threat to tea plantations. As a basic first step to control this pest is authentic identification, but the inability to determine morphological characters of Helopeltis species makes this process very difficult. DNA barcoding is a reliable alternative to traditional morphological identification of this pest. Since tea is cultivated in different parts of the country, an attempt was made to molecular characterization of Helopeltis. This is the first report on molecular identification and diversity characterization of Helopeltis collected from tea growing regions of southern and north India, using cytochrome c oxidase subunit I (COI) gene of mitochondrial (mt) DNA. Beginning with the molecular identification of this pest is essential to start an effective pest management strategy, and will provide basic information for diffusion pattern, population dynamics and chemical application.},
}
@article {pmid26186122,
year = {2016},
author = {Kranzfelder, P and Ekrem, T and Stur, E},
title = {Trace DNA from insect skins: a comparison of five extraction protocols and direct PCR on chironomid pupal exuviae.},
journal = {Molecular ecology resources},
volume = {16},
number = {1},
pages = {353-363},
doi = {10.1111/1755-0998.12446},
pmid = {26186122},
issn = {1755-0998},
mesh = {Analytic Sample Preparation Methods/*methods ; Animals ; Chironomidae/classification/*genetics/growth &amp; development ; DNA/genetics/*isolation &amp; purification ; Polymerase Chain Reaction/*methods ; Pupa/classification/*genetics/growth &amp; development ; },
abstract = {Insect skins (exuviae) are of extracellular origin and shed during moulting. The skins do not contain cells or DNA themselves, but epithelial cells and other cell-based structures might accidentally attach as they are shed. This source of trace DNA can be sufficient for PCR amplification and sequencing of target genes and aid in species identification through DNA barcoding or association of unknown life stages. Species identification is essential for biomonitoring programs, as species vary in sensitivities to environmental factors. However, it requires a DNA isolation protocol that optimizes the output of target DNA. Here, we compare the relative effectiveness of five different DNA extraction protocols and direct PCR in isolation of DNA from chironomid pupal exuviae. Chironomidae (Diptera) is a species-rich group of aquatic macroinvertebrates widely distributed in freshwater environments and considered a valuable bioindicator of water quality. Genomic DNA was extracted from 61.2% of 570 sampled pupal exuviae. There were significant differences in the methods with regard to cost, handling time, DNA quantity, PCR success, sequence success and the ability to sequence target taxa. The NucleoSpin(®) Tissue XS Kit, DNeasy(®) Blood and Tissue kit, and QuickExtract(™) DNA Extraction Solution provided the best results in isolating DNA from single pupal exuviae. Direct PCR and DTAB/CTAB methods gave poor results. While the observed differences in DNA isolation methods on trace DNA will be relevant to research that focuses on aquatic macroinvertebrate ecology, taxonomy and systematics, they should also be of interest for studies using environmental barcoding and metabarcoding of aquatic environments.},
}
@article {pmid26186077,
year = {2016},
author = {Decru, E and Moelants, T and De Gelas, K and Vreven, E and Verheyen, E and Snoeks, J},
title = {Taxonomic challenges in freshwater fishes: a mismatch between morphology and DNA barcoding in fish of the north-eastern part of the Congo basin.},
journal = {Molecular ecology resources},
volume = {16},
number = {1},
pages = {342-352},
doi = {10.1111/1755-0998.12445},
pmid = {26186077},
issn = {1755-0998},
mesh = {Animals ; Biodiversity ; Catfishes/classification/genetics ; Congo ; Cyprinidae/anatomy &amp; histology/classification/genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Fish Proteins/genetics ; Fishes/anatomy &amp; histology/*classification/genetics ; Phylogeny ; },
abstract = {This study evaluates the utility of DNA barcoding to traditional morphology-based species identifications for the fish fauna of the north-eastern Congo basin. We compared DNA sequences (COI) of 821 samples from 206 morphologically identified species. Best match, best close match and all species barcoding analyses resulted in a rather low identification success of 87.5%, 84.5% and 64.1%, respectively. The ratio 'nearest-neighbour distance/maximum intraspecific divergence' was lower than 1 for 26.1% of the samples, indicating possible taxonomic problems. In ten genera, belonging to six families, the number of species inferred from mtDNA data exceeded the number of species identified using morphological features; and in four cases indications of possible synonymy were detected. Finally, the DNA barcodes confirmed previously known identification problems within certain genera of the Clariidae, Cyprinidae and Mormyridae. Our results underscore the large number of taxonomic problems lingering in the taxonomy of the fish fauna of the Congo basin and illustrate why DNA barcodes will contribute to future efforts to compile a reliable taxonomic inventory of the Congo basin fish fauna. Therefore, the obtained barcodes were deposited in the reference barcode library of the Barcode of Life Initiative.},
}
@article {pmid26183584,
year = {2016},
author = {Maggi, N and Ruggiero, C and Arrigo, P},
title = {Prediction of potential barcoding sites on ITS1 by wavelet transform.},
journal = {Journal of biomolecular structure &amp; dynamics},
volume = {34},
number = {4},
pages = {814-823},
doi = {10.1080/07391102.2015.1056550},
pmid = {26183584},
issn = {1538-0254},
mesh = {Animals ; Binding Sites ; Computational Biology/methods ; *DNA Barcoding, Taxonomic/methods ; DNA Restriction Enzymes/metabolism ; *DNA, Ribosomal Spacer ; Humans ; Protein Binding ; *Wavelet Analysis ; },
abstract = {For sustainable development, biodiversity conservation and life-quality improvement must be simultaneously considered. Molecular techniques have greatly impacted biotechnology. These methods have, in particular, improved the capability to investigate the fine differences among organisms and, as a consequence, to better investigate the effects on environmental factors on them. We propose an approach to support the optimal selection of molecular probes for barcoding application in many biotechnological fields. The aim of our work is specificity maximization. To this purpose, we have integrated a filter system based on wavelet transforms with biological knowledge about the sequence proneness to mutation and post-translational modification. Specifically, we have tested the proposed method on ITS1 sequences that are a region of the rRNA locus. Our analysis has shown the presence of other local relative stable conformations in addition to known cleavage site. Their characteristics differ within the group of mammals selected for our analysis. These variations could be used to design new species-specific barcoding probes or other quick molecular screening tools.},
}
@article {pmid26176982,
year = {2016},
author = {Kang, HE and Kim, JN and Yoon, TH and Park, KD and Park, WG and Park, H and Kim, HW},
title = {Total mitochondrial genome of mantis shrimp, Squilloides leptosquilla (Brooks, 1886) (Crustacea: Stomatopoda: Squillidae) in Korean waters.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {4},
pages = {2842-2843},
doi = {10.3109/19401736.2015.1053120},
pmid = {26176982},
issn = {2470-1408},
mesh = {Animals ; Crustacea/classification/*genetics ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; },
abstract = {We characterized the complete mitochondrial genome of Squilloides leptosquilla (Brooks, 1886) collected from the southern waters of Korea, which is newly recorded into the Korean carcinological fauna. The total mitochondrial genome length of S. leptosquilla was 16,376 bp. This circular DNA encodes 13 proteins, two ribosomal RNAs, and 22 transfer RNAs, as well as a putative control region. Compared with other decapod crustacean mitochondrial genomes, the overall A + T content was relatively high (71.1%) as those among other stomatopod species. Nine and four protein-coding genes are encoded on the H-strand and on the L-strand, respectively. The short non-coding region (210 bp) between tRNA(Glu) and tRNA(Phe) may be the good candidate as the molecular marker to discriminate S. leptosequilla from other stomatopods.},
}
@article {pmid26175612,
year = {2015},
author = {Wilbrandt, J and Lee, P and Read, H and Wesener, T},
title = {A first integrative study of the identity and origins of the British Dwarf Pill Millipede populations, Trachysphaera cf. lobata (Diplopoda, Glomerida, Glomeridae).},
journal = {Biodiversity data journal},
volume = {},
number = {3},
pages = {e5176},
pmid = {26175612},
issn = {1314-2828},
abstract = {Three populations of the pill millipede genus Trachysphaera Heller 1858 are present in Great Britain, one on the Isle of Wight, one in South Wales and one in mid-Wales. To identify and characterize the British Trachysphaera populations, the intraspecific and interspecific variation of the populations in South Wales and on the Isle of Wight were studied and evaluated in a first integrative study of members of Trachysphaera, utilizing barcoding and SEM. DNA was extracted from 28 British Trachysphaera and 10 French T. lobata (Ribaut 1954) specimens, one each of French T. cf. drescoi (Conde and Demange 1961) and T. pyrenaica (Ribaut 1908), and one of Spanish T. cf. rousseti (Demange 1959); the barcoding fragment of the COI gene was amplified and their genetic intra- and interpopulation distances compared with one another using two Italian T. spp. and one Croatian T. schmidti Heller 1858 specimens as near outgroups. To compare the genetic distances with the morphological characters, 15 characters of a total of 13 British Trachysphaera, together with two specimens of T.pyrenaica, two T. cf. drescoi and one of T. cf. rousseti were imaged, using the same individuals utilized for DNA extraction. Albeit both British populations are genetically distant, they are closely related (1.9-2.5% p-distance) to French T.lobata, corroborating results of earlier studies. Between different Trachysphaera species, genetic distance was high (16.7-18.8%). The morphological study showed the non-reliability of key taxonomic characters in Trachysphaera, with genetically identical individuals exhibiting morphological variation, especially on the telopods. The only observed morphological characters constant within and different between species were the number of rows of sclerotized bacilli on the tergites, as well as the shape of the male and female anal shield. Both, barcoding and the morphological study identify the British Trachysphaera populations as T. lobata.},
}
@article {pmid26175603,
year = {2015},
author = {Angyal, D and Balázs, G and Zakšek, V and Krízsik, V and Fišer, C},
title = {Redescription of two subterranean amphipods Niphargusmolnari Méhely, 1927 and Niphargusgebhardti Schellenberg, 1934 (Amphipoda, Niphargidae) and their phylogenetic position.},
journal = {ZooKeys},
volume = {},
number = {509},
pages = {53-85},
pmid = {26175603},
issn = {1313-2989},
abstract = {A detailed redescription of two endemic, cave-dwelling niphargid species of the Hungarian Mecsek Mts., Niphargusmolnari Méhely, 1927 and Niphargusgebhardti Schellenberg, 1934 is given based on newly collected material. Morphology was studied under light microscopy and with scanning electon microscopy. Morphological descriptions are complemented with mitochondrial cytochrome c oxidase subunit I (COI) sequences as barcodes for both species and with notes on their ecology. Using three independent molecular markers we showed that Niphargusgebhardti belongs to the clade distributed between Central and Eastern Europe, whereas phylogenetic relationship of Niphargusmolnari to the rest of Niphargus species is not clear. The two species from the Mecsek Mts. are phylogenetically not closely related. Both species need to be treated as vulnerable according to IUCN Red List of Threatened Species.},
}
@article {pmid26175299,
year = {2016},
author = {Blagoev, GA and deWaard, JR and Ratnasingham, S and deWaard, SL and Lu, L and Robertson, J and Telfer, AC and Hebert, PD},
title = {Untangling taxonomy: a DNA barcode reference library for Canadian spiders.},
journal = {Molecular ecology resources},
volume = {16},
number = {1},
pages = {325-341},
doi = {10.1111/1755-0998.12444},
pmid = {26175299},
issn = {1755-0998},
mesh = {Animals ; Canada ; DNA Barcoding, Taxonomic/*methods ; Gene Library ; Spiders/*classification/*genetics ; },
abstract = {Approximately 1460 species of spiders have been reported from Canada, 3% of the global fauna. This study provides a DNA barcode reference library for 1018 of these species based upon the analysis of more than 30,000 specimens. The sequence results show a clear barcode gap in most cases with a mean intraspecific divergence of 0.78% vs. a minimum nearest-neighbour (NN) distance averaging 7.85%. The sequences were assigned to 1359 Barcode index numbers (BINs) with 1344 of these BINs composed of specimens belonging to a single currently recognized species. There was a perfect correspondence between BIN membership and a known species in 795 cases, while another 197 species were assigned to two or more BINs (556 in total). A few other species (26) were involved in BIN merges or in a combination of merges and splits. There was only a weak relationship between the number of specimens analysed for a species and its BIN count. However, three species were clear outliers with their specimens being placed in 11-22 BINs. Although all BIN splits need further study to clarify the taxonomic status of the entities involved, DNA barcodes discriminated 98% of the 1018 species. The present survey conservatively revealed 16 species new to science, 52 species new to Canada and major range extensions for 426 species. However, if most BIN splits detected in this study reflect cryptic taxa, the true species count for Canadian spiders could be 30-50% higher than currently recognized.},
}
@article {pmid26174961,
year = {2015},
author = {Rivera-Cabello, D and Huanca-Mamani, W and Vargas, HA},
title = {Macaria mirthae Vargas et al (Lepidoptera: Geometridae): Confirmation of the Use of an Invasive Host Plant in the Northern Atacama Desert of Chile Based on DNA Barcodes.},
journal = {Neotropical entomology},
volume = {44},
number = {4},
pages = {357-364},
pmid = {26174961},
issn = {1678-8052},
mesh = {Animals ; Chile ; DNA Barcoding, Taxonomic ; Desert Climate ; Fabaceae/*parasitology ; Moths/*classification/*genetics ; },
abstract = {Macaria mirthae Vargas et al (Lepidoptera: Geometridae) is a geometrid moth native to the northern Atacama Desert of Chile. Its oligophagous larvae are associated with native hosts of the plant family Fabaceae, the most important of which is Acacia macracantha. The invasive tree Leucaena leucocephala (Fabaceae) was recently recorded as a host plant for M. mirthae based on morphology. The taxonomic status of larvae collected on A. macracantha and L. leucocephala was assessed using sequences of the DNA barcode fragment of the cytochrome c oxidase subunit I (COI) gene. Genetic divergence between samples from the host plants was found to be 0%-0.8% (Kimura 2-parameter model). Neighbor-joining and maximum likelihood analyses were also performed, including additional barcode sequences of Neotropical geometrid moths from GenBank and BOLD databases. Sequences of the larvae from both host plants clustered in a single clade with high statistical support in both analyses. Based on these results, it is concluded that M. mirthae has effectively expanded its host range and its larvae are currently feeding on the exotic tree L. leucocephala. Additionally, the importance of this new host association in a highly disturbed habitat is briefly discussed in terms of the field biology of this native geometrid moth.},
}
@article {pmid26174661,
year = {2015},
author = {Kikkawa, HS and Tahara, M and Sugita, R},
title = {Forensic DNA Analysis of Wheat Flour as Commonly Used in White Powder Cases.},
journal = {Journal of forensic sciences},
volume = {60},
number = {5},
pages = {1316-1321},
doi = {10.1111/1556-4029.12789},
pmid = {26174661},
issn = {1556-4029},
mesh = {DNA Fingerprinting ; DNA, Plant/*genetics ; *Flour ; Forensic Sciences ; Humans ; Microsatellite Repeats ; Molecular Sequence Data ; Polymerase Chain Reaction ; Ribulose-Bisphosphate Carboxylase/*genetics ; Sequence Analysis, DNA ; Terrorism ; Triticum/*genetics ; },
abstract = {In the wake of terrorist attacks using anthrax and ricin, white powder is often encountered in cases of malicious mischief and terrorist threats. Wheat flour is a common white powder encountered in such criminal investigations. We used DNA analysis to investigate wheat flour samples for identification and discrimination as trace evidence. Species identification of commercially available wheat flour was carried out by sequencing a partial region of the ribulose bisphosphate carboxylase large subunit gene (rbcL). Samples were discriminated using short tandem repeat (STR) analysis. The rbcL sequences of all wheat flour samples were identical and showed a high level of similarity to known wheat (Triticum aestivum L.) sequences. Furthermore, flours had characteristic patterns in STR analyses, with specific cultivars showing distinctive patterns. These results suggested that the identification of wheat flour species is possible using rbcL sequencing, and that STR analysis is useful for discriminating between samples.},
}
@article {pmid26173469,
year = {2015},
author = {Patten, MM and Carioscia, SA and Linnen, CR},
title = {Biased introgression of mitochondrial and nuclear genes: a comparison of diploid and haplodiploid systems.},
journal = {Molecular ecology},
volume = {24},
number = {20},
pages = {5200-5210},
doi = {10.1111/mec.13318},
pmid = {26173469},
issn = {1365-294X},
mesh = {Alleles ; Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Diploidy ; Female ; *Genes, Mitochondrial ; Genetic Fitness ; *Genetics, Population ; *Haploidy ; Hybridization, Genetic ; Male ; *Models, Genetic ; },
abstract = {Hybridization between recently diverged species, even if infrequent, can lead to the introgression of genes from one species into another. The rates of mitochondrial and nuclear introgression often differ, with some taxa showing biases for mitochondrial introgression and others for nuclear introgression. Several hypotheses exist to explain such biases, including adaptive introgression, sex differences in dispersal rates, sex-specific prezygotic isolation and sex-specific fitness of hybrids (e.g. Haldane's rule). We derive a simple population genetic model that permits an analysis of sex-specific demographic and fitness parameters and measures the relative rates of mitochondrial and nuclear introgression between hybridizing pairs. We do this separately for diploid and haplodiploid species. For diploid taxa, we recover results consistent with previous hypotheses: an excess of one sex among the hybridizing migrants or sex-specific prezygotic isolation causes a bias for one type of marker or the other; when Haldane's rule is obeyed, we find a mitochondrial bias in XY systems and a nuclear bias in ZW systems. For haplodiploid taxa, the model reveals that owing to their unique transmission genetics, they are seemingly assured of strong mitochondrial biases in introgression rates, unlike diploid taxa, where the relative fitness of male and female hybrids can tip the bias in either direction. This heretofore overlooked aspect of hybridization in haplodiploids provides what is perhaps the most likely explanation for differential introgression of mitochondrial and nuclear markers and raises concerns about the use of mitochondrial DNA barcodes for species delimitation in these taxa.},
}
@article {pmid26173012,
year = {2015},
author = {Vargas, S and Kelly, M and Schnabel, K and Mills, S and Bowden, D and Wörheide, G},
title = {Correction: Diversity in a Cold Hot-Spot: DNA-Barcoding Reveals Patterns of Evolution among Antarctic Demosponges (Class Demospongiae, Phylum Porifera).},
journal = {PloS one},
volume = {10},
number = {7},
pages = {e0133096},
pmid = {26173012},
issn = {1932-6203},
}
@article {pmid26170017,
year = {2015},
author = {Fiannaca, A and La Rosa, M and Rizzo, R and Urso, A},
title = {A k-mer-based barcode DNA classification methodology based on spectral representation and a neural gas network.},
journal = {Artificial intelligence in medicine},
volume = {64},
number = {3},
pages = {173-184},
doi = {10.1016/j.artmed.2015.06.002},
pmid = {26170017},
issn = {1873-2860},
mesh = {Algorithms ; Animals ; Base Sequence ; Cluster Analysis ; Computational Biology ; DNA/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; Databases, Genetic ; Decision Trees ; *Neural Networks, Computer ; Reproducibility of Results ; Species Specificity ; *Supervised Machine Learning ; Support Vector Machine ; },
abstract = {OBJECTIVES: In this paper, an alignment-free method for DNA barcode classification that is based on both a spectral representation and a neural gas network for unsupervised clustering is proposed.<br><br>METHODS: In the proposed methodology, distinctive words are identified from a spectral representation of DNA sequences. A taxonomic classification of the DNA sequence is then performed using the sequence signature, i.e., the smallest set of k-mers that can assign a DNA sequence to its proper taxonomic category. Experiments were then performed to compare our method with other supervised machine learning classification algorithms, such as support vector machine, random forest, ripper, na&#xef;ve Bayes, ridor, and classification tree, which also consider short DNA sequence fragments of 200 and 300 base pairs (bp). The experimental tests were conducted over 10 real barcode datasets belonging to different animal species, which were provided by the on-line resource "Barcode of Life Database".<br><br>RESULTS: The experimental results showed that our k-mer-based approach is directly comparable, in terms of accuracy, recall and precision metrics, with the other classifiers when considering full-length sequences. In addition, we demonstrate the robustness of our method when a classification is performed task with a set of short DNA sequences that were randomly extracted from the original data. For example, the proposed method can reach the accuracy of 64.8% at the species level with 200-bp fragments. Under the same conditions, the best other classifier (random forest) reaches the accuracy of 20.9%.<br><br>CONCLUSIONS: Our results indicate that we obtained a clear improvement over the other classifiers for the study of short DNA barcode sequence fragments.},
}
@article {pmid26167125,
year = {2015},
author = {Stur, E and Ekrem, T},
title = {A review of Norwegian Gymnometriocnemus (Diptera, Chironomidae) including the description of two new species and a new name for Gymnometriocnemusvolitans (Goetghebuer) sensu Brundin.},
journal = {ZooKeys},
volume = {},
number = {508},
pages = {127-142},
pmid = {26167125},
issn = {1313-2989},
abstract = {Examination of the syntypes of Metriocnemusvolitans Goetghebuer, 1940 revealed that these specimens belong to the genus Chaetocladius and are not con-specific with Gymnometriocnemusvolitans (Goetghebuer, 1940) sensu Brundin (1956) and Sæther (1983). A literature search showed that Gymnometriocnemuskamimegavirgus Sasa &amp; Hirabayashi, 1993 fits well with the species figured and diagnosed by Brundin (1956) as well as with specimens of this species from Norway. We present arguments for Chaetocladiusvolitans (Goetghebuer) comb. n. and for the use of Gymnometriocnemuskamimegavirgus for Gymnometriocnemusvolitans sensu Brundin. In addition, we provide DNA barcode data that indicate the presence of at least seven Gymnometriocnemus species in Norway of which six are collected as male adults. Two of these, Gymnometriocnemus (Gymnometriocnemus) pallidussp. n. and Gymnometriocnemus (Raphidocladius) autumnalissp. n. are regarded as new to science and diagnosed based on adult male morphology and DNA barcodes. The species Gymnometriocnemus (Gymnometriocnemus) marionensis Sæther, 1969 is re-established and a key to all Holarctic species is provided.},
}
@article {pmid26167119,
year = {2015},
author = {Jürgenstein, S and Kurina, O and Põldmaa, K},
title = {The Mycetophilaruficollis Meigen (Diptera, Mycetophilidae) group in Europe: elucidating species delimitation with COI and ITS2 sequence data.},
journal = {ZooKeys},
volume = {},
number = {508},
pages = {15-51},
pmid = {26167119},
issn = {1313-2989},
abstract = {European species of the Mycetophilaruficollis group are compared on the basis of morphology and sequences of mitochondrial cytochrome oxidase subunit one (COI) and the ITS2 region of nuclear ribosomal DNA. The study represents the first evaluation of morphology-based species delimitation of closely related fungus gnat species by applying molecular information. Detailed descriptions and illustrations of the male terminalia are presented along with a key for the identification of all nine European species of the group. Phylogenetic analyses of molecular data generally supported the morphological species discrimination. The barcoding region of COI superseded ITS2 rDNA in resolving species. In the COI barcoding region interspecific differences ranged from 2.9 to 10.6% and the intraspecific distance from 0.08 to 0.8%. Only COI data distinguished between the similar and closely related Mycetophilaichneumonea and Mycetophilauninotata of which the latter was observed to include cryptic species. The host range of some species is suggested to be narrower than previously considered and to depend on the forest type. Presented evidence indicates the importance of analysing sequence data of morphologically very similar mycetophages reared from identified host fungi for elucidating species delimitation as well as their geographic and host ranges. New country records, viz. Estonia for Mycetophilaevanida, Georgia for Mycetophilaichneumonea, Mycetophilaidonea and Mycetophilaruficollis, and Norway for Mycetophilastrobli, widen the known distribution ranges of these species.},
}
@article {pmid26165523,
year = {2015},
author = {Saslis-Lagoudakis, CH and Bruun-Lund, S and Iwanycki, NE and Seberg, O and Petersen, G and Jäger, AK and Rønsted, N},
title = {Identification of common horsetail (Equisetum arvense L.; Equisetaceae) using Thin Layer Chromatography versus DNA barcoding.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {11942},
pmid = {26165523},
issn = {2045-2322},
mesh = {*Chromatography, Thin Layer ; DNA/*analysis ; *DNA Barcoding, Taxonomic ; Equisetum/classification/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The global herbal products market has grown in recent years, making regulation of these products paramount for public healthcare. For instance, the common horsetail (Equisetum arvense L.) is used in numerous herbal products, but it can be adulterated with closely related species, especially E. palustre L. that can produce toxic alkaloids. As morphology-based identification is often difficult or impossible, the identification of processed material can be aided by molecular techniques. In this study, we explore two molecular identification techniques as methods of testing the purity of these products: a Thin Layer Chromatography approach (TLC-test) included in the European Pharmacopoeia and a DNA barcoding approach, used in recent years to identify material in herbal products. We test the potential of these methods for distinguishing and identifying these species using material from herbarium collections and commercial herbal products. We find that both methods can discriminate between the two species and positively identify E. arvense. The TLC-test is more cost- and time-efficient, but DNA barcoding is more powerful in determining the identity of adulterant species. Our study shows that, although DNA barcoding presents certain advantages, other established laboratory methods can perform as well or even better in confirming species' identity in herbal products.},
}
@article {pmid26156398,
year = {2015},
author = {de Souza, Rde C and Campolina-Silva, GH and Bezerra, CM and Diotaiuti, L and Gorla, DE},
title = {Does Triatoma brasiliensis occupy the same environmental niche space as Triatoma melanica?.},
journal = {Parasites &amp; vectors},
volume = {8},
number = {},
pages = {361},
pmid = {26156398},
issn = {1756-3305},
mesh = {Animals ; Chagas Disease/parasitology/*transmission ; Ecosystem ; Insect Vectors/classification/genetics/parasitology/*physiology ; Triatoma/classification/genetics/parasitology/*physiology ; Trypanosoma cruzi/physiology ; },
abstract = {BACKGROUND: Triatomines (Hemiptera, Reduviidae) are vectors of Trypanosoma cruzi, the causative agent of Chagas disease, one of the most important vector-borne diseases in Latin America. This study compares the environmental niche spaces of Triatoma brasiliensis and Triatoma melanica using ecological niche modelling and reports findings on DNA barcoding and wing geometric morphometrics as tools for the identification of these species.<br><br>METHODS: We compared the geographic distribution of the species using generalized linear models fitted to elevation and current data on land surface temperature, vegetation cover and rainfall recorded by earth observation satellites for northeastern Brazil. Additionally, we evaluated nucleotide sequence data from the barcode region of the mitochondrial cytochrome c oxidase subunit I (CO1) and wing geometric morphometrics as taxonomic identification tools for T. brasiliensis and T. melanica.<br><br>RESULTS: The ecological niche models show that the environmental spaces currently occupied by T. brasiliensis and T. melanica are similar although not equivalent, and associated with the caatinga ecosystem. The CO1 sequence analyses based on pair wise genetic distance matrix calculated using Kimura 2-Parameter (K2P) evolutionary model, clearly separate the two species, supporting the barcoding gap. Wing size and shape analyses based on seven landmarks of 72 field specimens confirmed consistent differences between T. brasiliensis and T. melanica.<br><br>CONCLUSION: Our results suggest that the separation of the two species should be attributed to a factor that does not include the current environmental conditions. However, as the caatinga is a biome that has existed in the area for at least the last 18,000&#xa0;years, past conditions might have had an influence in the speciation process. The DNA Barcoding approach may be extended to these members of the subfamily Triatominae.},
}
@article {pmid26155738,
year = {2015},
author = {Chen, R and Rishi, HS and Potapov, V and Yamada, MR and Yeh, VJ and Chow, T and Cheung, CL and Jones, AT and Johnson, TD and Keating, AE and DeLoache, WC and Dueber, JE},
title = {A Barcoding Strategy Enabling Higher-Throughput Library Screening by Microscopy.},
journal = {ACS synthetic biology},
volume = {4},
number = {11},
pages = {1205-1216},
pmid = {26155738},
issn = {2161-5063},
support = {R01 GM067681/GM/NIGMS NIH HHS/United States ; GM067681/GM/NIGMS NIH HHS/United States ; },
mesh = {*Electronic Data Processing ; High-Throughput Screening Assays/*methods ; Microscopy/*methods ; Proteins/metabolism ; Synthetic Biology ; },
abstract = {Dramatic progress has been made in the design and build phases of the design-build-test cycle for engineering cells. However, the test phase usually limits throughput, as many outputs of interest are not amenable to rapid analytical measurements. For example, phenotypes such as motility, morphology, and subcellular localization can be readily measured by microscopy, but analysis of these phenotypes is notoriously slow. To increase throughput, we developed microscopy-readable barcodes (MiCodes) composed of fluorescent proteins targeted to discernible organelles. In this system, a unique barcode can be genetically linked to each library member, making possible the parallel analysis of phenotypes of interest via microscopy. As a first demonstration, we MiCoded a set of synthetic coiled-coil leucine zipper proteins to allow an 8 × 8 matrix to be tested for specific interactions in micrographs consisting of mixed populations of cells. A novel microscopy-readable two-hybrid fluorescence localization assay for probing candidate interactions in the cytosol was also developed using a bait protein targeted to the peroxisome and a prey protein tagged with a fluorescent protein. This work introduces a generalizable, scalable platform for making microscopy amenable to higher-throughput library screening experiments, thereby coupling the power of imaging with the utility of combinatorial search paradigms.},
}
@article {pmid26155071,
year = {2015},
author = {van Nieukerken, EJ and Geertsema, H},
title = {A new leafminer on grapevine and Rhoicissus (Vitaceae) in South Africa within an expanded generic concept of Holocacista (Insecta, Lepidoptera, Heliozelidae).},
journal = {ZooKeys},
volume = {},
number = {507},
pages = {41-97},
pmid = {26155071},
issn = {1313-2989},
abstract = {A grapevine leafminer found recently in table grape orchards and vineyards in the Paarl region (Western Cape, South Africa) is described as Holocacistacapensis sp. n. It has also been found on native Rhoicissusdigitata and bred on that species in the laboratory. It is closely related to Holocacistasalutans (Meyrick, 1921), comb. n. (from Antispila), described from Durban in KwaZulu-Natal, but widespread in southern Africa and a native leafminer of various Vitaceae: Rhoicissustomentosa, Rhoicissusdigitata, Rhoicissustridentata and Cissuscornifolia. Holocacistacapensis has been found on Vitisvinifera both in Gauteng and Western Cape, the earliest record being from 1950 in Pretoria. The initial host shift from native Vitaceae to Vitis must have occurred much earlier. The species is sometimes present in high densities, but hitherto no sizeable damage to the crops has been noted. The genus Holocacista Walsingham &amp; Durrant, 1909, previously known from the single European grapevine leafminer Holocacistarivillei (Stainton, 1855), is expanded and redescribed and for the first time reported from Africa, East and South-East Asia and Australia. It comprises seven named species and at least 15 unnamed species. The following species are also recombined with Holocacista: transferred from Antispilina: South-African Holocacistavarii (Mey, 2011), comb. n., feeding on Pelargonium, transferred from Antispila: the Indian species Holocacistamicrarcha (Meyrick, 1926), comb. n. and Holocacistapariodelta (Meyrick, 1929), comb. n., both feeding on Lanneacoromandelica, and Holocacistaselastis (Meyrick, 1926), comb. n. on Psychotriadalzelii. We also remove the following from Antispila: Heliozelaanna (Fletcher, 1920), comb. n. and Heliozelaargyrozona (Meyrick, 1918), comb. n., whereas the following Indian Vitaceae feeding species are confirmed to belong in Antispila s. str.: Antispilaargostoma Meyrick, 1916 and Antispilaaristarcha Meyrick, 1916. Holocacistasalutans and Holocacistavarii are redescribed and diagnosed against Holocacistacapensis and other South African Heliozelidae. DNA barcodes are provided for 13 species of Holocacista.},
}
@article {pmid26154168,
year = {2015},
author = {Elbrecht, V and Leese, F},
title = {Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass--Sequence Relationships with an Innovative Metabarcoding Protocol.},
journal = {PloS one},
volume = {10},
number = {7},
pages = {e0130324},
pmid = {26154168},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; *Biomass ; DNA/analysis ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Diptera/*classification/genetics ; *Ecosystem ; Electron Transport Complex IV/genetics ; Fresh Water ; Haplotypes ; High-Throughput Nucleotide Sequencing ; Odonata/*classification/genetics ; Polymerase Chain Reaction ; Reproducibility of Results ; Species Specificity ; },
abstract = {Metabarcoding is an emerging genetic tool to rapidly assess biodiversity in ecosystems. It involves high-throughput sequencing of a standard gene from an environmental sample and comparison to a reference database. However, no consensus has emerged regarding laboratory pipelines to screen species diversity and infer species abundances from environmental samples. In particular, the effect of primer bias and the detection limit for specimens with a low biomass has not been systematically examined, when processing samples in bulk. We developed and tested a DNA metabarcoding protocol that utilises the standard cytochrome c oxidase subunit I (COI) barcoding fragment to detect freshwater macroinvertebrate taxa. DNA was extracted in bulk, amplified in a single PCR step, and purified, and the libraries were directly sequenced in two independent MiSeq runs (300-bp paired-end reads). Specifically, we assessed the influence of specimen biomass on sequence read abundance by sequencing 31 specimens of a stonefly species with known haplotypes spanning three orders of magnitude in biomass (experiment I). Then, we tested the recovery of 52 different freshwater invertebrate taxa of similar biomass using the same standard barcoding primers (experiment II). Each experiment was replicated ten times to maximise statistical power. The results of both experiments were consistent across replicates. We found a distinct positive correlation between species biomass and resulting numbers of MiSeq reads. Furthermore, we reliably recovered 83% of the 52 taxa used to test primer bias. However, sequence abundance varied by four orders of magnitudes between taxa despite the use of similar amounts of biomass. Our metabarcoding approach yielded reliable results for high-throughput assessments. However, the results indicated that primer efficiency is highly species-specific, which would prevent straightforward assessments of species abundance and biomass in a sample. Thus, PCR-based metabarcoding assessments of biodiversity should rely on presence-absence metrics.},
}
@article {pmid26142058,
year = {2015},
author = {Gomes, LC and Pessali, TC and Sales, NG and Pompeu, PS and Carvalho, DC},
title = {Integrative taxonomy detects cryptic and overlooked fish species in a neotropical river basin.},
journal = {Genetica},
volume = {143},
number = {5},
pages = {581-588},
pmid = {26142058},
issn = {1573-6857},
mesh = {Animals ; Biodiversity ; Brazil ; Characidae/genetics ; Classification ; DNA Barcoding, Taxonomic/*methods ; Fishes/*genetics ; Freshwater Biology ; Phylogeny ; Rivers ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The great freshwater fish diversity found in the neotropical region makes management and conservation actions challenging. Due to shortage of taxonomists and insufficient infrastructure to deal with such great biodiversity (i.e. taxonomic impediment), proposed remedies to accelerate species identification and descriptions include techniques that combine DNA-based identification and concise morphological description. The building of a DNA barcode reference database correlating meristic and genetic data was developed for 75 % of the Mucuri River basin's freshwater fish. We obtained a total of 141 DNA barcode sequences from 37 species belonging to 30 genera, 19 families, and 5 orders. Genetic distances within species, genera, and families were 0.74, 9.5, and 18.86 %, respectively. All species could be clearly identified by the DNA barcodes. Divergences between meristic morphological characteristics and DNA barcodes revealed two cryptic species among the Cyphocharax gilbert and Astyanax gr. bimaculatus specimens, and helped to identify two overlooked species within the Gymnotus and Astyanax taxa. Therefore, using a simplified model of neotropical biodiversity, we tested the efficiency of an integrative taxonomy approach for species discovery, identification of cryptic diversity, and accelerating biodiversity descriptions.},
}
@article {pmid26141432,
year = {2015},
author = {Juan, C and ChengCheng, L and YaE, Z and Li, H and YuanJun, Y and Fan, Y and ZhiYun, S},
title = {Population identification and divergence threshold in Psoroptidae based on ribosomal ITS2 and mitochondrial COI genes.},
journal = {Parasitology research},
volume = {114},
number = {9},
pages = {3497-3507},
pmid = {26141432},
issn = {1432-1955},
mesh = {Animals ; Base Sequence ; Cat Diseases/*parasitology ; Cats ; DNA Barcoding, Taxonomic/veterinary ; DNA, Ribosomal Spacer/chemistry/genetics ; Dog Diseases/*parasitology ; Dogs ; Electron Transport Complex IV/genetics ; Geography ; Mite Infestations/parasitology/*veterinary ; Molecular Sequence Data ; Phylogeny ; Psoroptidae/*classification/genetics ; Sequence Alignment/veterinary ; Sequence Analysis, DNA/veterinary ; },
abstract = {Psoroptidae mites are a type of small mites with a wide range of hosts. The proliferation of Psoroptidae mites could cause symptoms such as severe itching, atopic dermatitis, and hair loss in infected animals. If severely infected, death can also occur. The morphological classification and identification of Psoroptidae mites is problematic due to the overlapping geographical distribution. In addition, there is no divergence threshold for molecular classification and identification. To solve this problem, gDNA was extracted from individual Psoroptes and Otodectes mites (China) for amplification of rDNA ITS2 and mtDNA COI. After that, the sequences obtained were aligned and analyzed with those retrieved from GenBank. Based on rDNA ITS2 sequences, Psoroptidae was divided into three genera, namely, Psoroptes, Chorioptes, and Otodectes, which was in accordance with morphological classification. The intraspecies, interspecies, and intergenera could be differentiated effectively, with thresholds ≤ 5.20, 6.18-14.86, and ≥15.72 %, respectively. However, based on mtDNA COI sequences, Psoroptidae was divided into four genera with Caparinia added, as Caparinia sp did not cluster with the other three genera. The intra- and interspecies could be differentiated effectively, but interspecies and intergenera could not. The intra- and interspecies identification thresholds were ≤ 2.12 and ≥10.93 %. Further analysis showed that host but not geographical isolation was found in Psoroptes and Chorioptes, whereas Otodectes mites parasitizing dogs and cats were the same species; neither host nor geographical isolation was observed. In conclusion, rDNA ITS2 is better than mtDNA COI for DNA barcoding in Psoroptidae.},
}
@article {pmid26140198,
year = {2015},
author = {Chen, J and Jiang, Z and Li, C and Ping, X and Cui, S and Tang, S and Chu, H and Liu, B},
title = {Identification of ungulates used in a traditional Chinese medicine with DNA barcoding technology.},
journal = {Ecology and evolution},
volume = {5},
number = {9},
pages = {1818-1825},
pmid = {26140198},
issn = {2045-7758},
abstract = {Horns of Saiga antelope (Saiga tatarica) have always been an ingredient of "Lingyangjiao", a traditional Chinese medicine (TCM). Persistent hunting for Saiga antelope has already threatened the survival of critical endangered populations in wild. To control the growing pressure, CITES and Chinese government have legislated for monitoring the trade of Saiga horns. However, similar ungulate horns are difficult to identify by their morphological characteristics, which has impeded the law enforcement. Besides Saiga antelope, other seven ungulate species which have similar horns are also sold and marked as "Lingyangjiao" in TCM markets to offset shortage of Saiga antelope horns. Such species are Gazella subgutturosa, Pantholops hodgsonii, Procapra picticaudata, Procapra gutturosa, Procapra przewalskii, Capra hircus, and Ovis aries. Our study aimed at implementing DNA barcoding technology to diagnose Saiga horns and the substitutes. We successfully extracted genomic DNA from horn samples. We recovered COI sequences of 644 bp with specific primers and 349 bp with nested PCR primers designed for degraded horn samples. The mean interspecific genetic distance of data set of the 644-bp full barcodes and the 349-bp mini-barcodes was 14.96% and 15.38%, respectively, and the mean intraspecific distance was 0.24% and 0.20%, respectively. Each species formed independent clades in neighbor-joining (NJ) phylogenetic tree of the two data sets with >99% supporting values, except P. gutturosa and P. przewalskii. The deep genetic distances gap and clear species clades in NJ tree of either full barcodes or mini-barcodes suggest that barcoding technology is an effective tool to diagnose Saiga horns and their substitutes. Barcoding diagnosis protocol developed here will simplify diagnosis of "Lingyangjiao" species and will facilitate conservation of endangered ungulates involved in TCM "Lingyangjiao" markets, especially the Saiga antelope.},
}
@article {pmid26137428,
year = {2015},
author = {Leray, M and Meyer, CP and Mills, SC},
title = {Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet.},
journal = {PeerJ},
volume = {3},
number = {},
pages = {e1047},
pmid = {26137428},
issn = {2167-8359},
abstract = {Understanding the role of predators in food webs can be challenging in highly diverse predator/prey systems composed of small cryptic species. DNA based dietary analysis can supplement predator removal experiments and provide high resolution for prey identification. Here we use a metabarcoding approach to provide initial insights into the diet and functional role of coral-dwelling predatory fish feeding on small invertebrates. Fish were collected in Moorea (French Polynesia) where the BIOCODE project has generated DNA barcodes for numerous coral associated invertebrate species. Pyrosequencing data revealed a total of 292 Operational Taxonomic Units (OTU) in the gut contents of the arc-eye hawkfish (Paracirrhites arcatus), the flame hawkfish (Neocirrhites armatus) and the coral croucher (Caracanthus maculatus). One hundred forty-nine (51%) of them had species-level matches in reference libraries (>98% similarity) while 76 additional OTUs (26%) could be identified to higher taxonomic levels. Decapods that have a mutualistic relationship with Pocillopora and are typically dominant among coral branches, represent a minor contribution of the predators' diets. Instead, predators mainly consumed transient species including pelagic taxa such as copepods, chaetognaths and siphonophores suggesting non random feeding behavior. We also identified prey species known to have direct negative interactions with stony corals, such as Hapalocarcinus sp, a gall crab considered a coral parasite, as well as species of vermetid snails known for their deleterious effects on coral growth. Pocillopora DNA accounted for 20.8% and 20.1% of total number of sequences in the guts of the flame hawkfish and coral croucher but it was not detected in the guts of the arc-eye hawkfish. Comparison of diets among the three fishes demonstrates remarkable partitioning with nearly 80% of prey items consumed by only one predator. Overall, the taxonomic resolution provided by the metabarcoding approach highlights a highly complex interaction web and demonstrates that levels of trophic partitioning among coral reef fishes have likely been underestimated. Therefore, we strongly encourage further empirical approaches to dietary studies prior to making assumptions of trophic equivalency in food web reconstruction.},
}
@article {pmid26136514,
year = {2015},
author = {Kurtzman, CP and Mateo, RQ and Kolecka, A and Theelen, B and Robert, V and Boekhout, T},
title = {Advances in yeast systematics and phylogeny and their use as predictors of biotechnologically important metabolic pathways.},
journal = {FEMS yeast research},
volume = {15},
number = {6},
pages = {},
doi = {10.1093/femsyr/fov050},
pmid = {26136514},
issn = {1567-1364},
mesh = {Biotechnology/methods ; DNA Barcoding, Taxonomic ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Industrial Microbiology/methods ; Metabolic Networks and Pathways/*genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; Yeasts/*classification/*genetics ; },
abstract = {Detection, identification and classification of yeasts have undergone a major transformation in the last decade and a half following application of gene sequence analyses and genome comparisons. Development of a database (barcode) of easily determined DNA sequences from domains 1 and 2 (D1/D2) of the nuclear large subunit rRNA gene and from ITS now permits many laboratories to identify species quickly and accurately, thus replacing the laborious and often inaccurate phenotypic tests previously used. Phylogenetic analysis of gene sequences is leading to a major revision of yeast systematics that will result in redefinition of nearly all genera. This new understanding of species relationships has prompted a change of rules for naming and classifying yeasts and other fungi, and these new rules are presented in the recently implemented International Code of Nomenclature for algae, fungi, and plants (Melbourne Code). The use of molecular methods for species identification and the impact of Code changes on classification will be discussed, as will use of phylogeny for prediction of biotechnological applications.},
}
@article {pmid26130132,
year = {2015},
author = {Fosso, B and Santamaria, M and Marzano, M and Alonso-Alemany, D and Valiente, G and Donvito, G and Monaco, A and Notarangelo, P and Pesole, G},
title = {BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS.},
journal = {BMC bioinformatics},
volume = {16},
number = {},
pages = {203},
pmid = {26130132},
issn = {1471-2105},
mesh = {Bacteria/*genetics ; Biodiversity ; Computational Biology/*methods ; Fungi/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; *Metagenomics ; *Software ; },
abstract = {BACKGROUND: Substantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial communities in any environmental niche. If the investigation is aimed only at the microbiome taxonomic structure, a target-based metagenomic approach, here also referred as Meta-barcoding, is generally applied. This approach commonly involves the selective amplification of a species-specific genetic marker (DNA meta-barcode) in the whole taxonomic range of interest and the exploration of its taxon-related variants through High-Throughput Sequencing (HTS) technologies. The accessibility to proper computational systems for the large-scale bioinformatic analysis of HTS data represents, currently, one of the major challenges in advanced Meta-barcoding projects.<br><br>RESULTS: BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a new bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data upload and cleaning to final taxonomic identification, that are absolutely required in an appropriately designed Meta-barcoding HTS-based experiment. In its current version, BioMaS allows the analysis of both bacterial and fungal environments starting directly from the raw sequencing data from either Roche 454 or Illumina HTS platforms, following two alternative paths, respectively. BioMaS is implemented into a public web service available at https://recasgateway.ba.infn.it/ and is also available in Galaxy at http://galaxy.cloud.ba.infn.it:8080 (only for Illumina data).<br><br>CONCLUSION: BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills. A comparative benchmark, carried out by using a simulated dataset suitably designed to broadly represent the currently known bacterial and fungal world, showed that BioMaS outperforms QIIME and MOTHUR in terms of extent and accuracy of deep taxonomic sequence assignments.},
}
@article {pmid26132382,
year = {2015},
author = {Zhang, W and Yuan, Y and Yang, S and Huang, J and Huang, L},
title = {ITS2 Secondary Structure Improves Discrimination between Medicinal "Mu Tong" Species when Using DNA Barcoding.},
journal = {PloS one},
volume = {10},
number = {7},
pages = {e0131185},
pmid = {26132382},
issn = {1932-6203},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic/*methods ; DNA, Intergenic/*genetics ; DNA, Plant/genetics ; Drugs, Chinese Herbal/*chemistry ; Molecular Sequence Data ; Phylogeny ; Plants/genetics ; Sequence Alignment ; },
abstract = {DNA barcoding is a promising species identification method, but it has proved difficult to find a standardized DNA marker in plant. Although the ITS/ITS2 RNA transcript has been proposed as the core barcode for seed plants, it has been criticized for being too conserved in some species to provide enough information or too variable in some species to align it within the different taxa ranks. We selected 30 individuals, representing 16 species and four families, to explore whether ITS2 can successfully resolve species in terms of secondary structure. Secondary structure was predicted using Mfold software and sequence-structure was aligned by MARNA. RNAstat software transformed the secondary structures into 28 symbol code data for maximum parsimony (MP) analysis. The results showed that the ITS2 structures in our samples had a common four-helix folding type with some shared motifs. This conserved structure facilitated the alignment of ambiguous sequences from divergent families. The structure alignment yielded a MP tree, in which most topological relationships were congruent with the tree constructed using nucleotide sequence data. When the data was combined, we obtained a well-resolved and highly supported phylogeny, in which individuals of a same species were clustered together into a monophyletic group. As a result, the different species that are often referred to as the herb "Mu tong" were successfully identified using short fragments of 250 bp ITS2 sequences, together with their secondary structure. Thus our analysis strengthens the potential of ITS2 as a promising DNA barcode because it incorporates valuable secondary structure information that will help improve discrimination between species.},
}
@article {pmid26131377,
year = {2015},
author = {Justine, JL and Winsor, L and Barrière, P and Fanai, C and Gey, D and Han, AW and La Quay-Velázquez, G and Lee, BP and Lefevre, JM and Meyer, JY and Philippart, D and Robinson, DG and Thévenot, J and Tsatsia, F},
title = {The invasive land planarian Platydemus manokwari (Platyhelminthes, Geoplanidae): records from six new localities, including the first in the USA.},
journal = {PeerJ},
volume = {3},
number = {},
pages = {e1037},
pmid = {26131377},
issn = {2167-8359},
abstract = {The land planarian Platydemus manokwari de Beauchamp, 1963 or "New Guinea flatworm" is a highly invasive species, mainly in the Pacific area, and recently in Europe (France). We report specimens from six additional countries and territories: New Caledonia (including mainland and two of the Loyalty Islands, Lifou and Maré), Wallis and Futuna Islands, Singapore, Solomon Islands, Puerto Rico, and Florida, USA. We analysed the COI gene (barcoding) in these specimens with two sets of primers and obtained 909 bp long sequences. In addition, specimens collected in Townsville (Australia) were also sequenced. Two haplotypes of the COI sequence, differing by 3.7%, were detected: the "World haplotype" found in France, New Caledonia, French Polynesia, Singapore, Florida and Puerto Rico; and the "Australian haplotype" found in Australia. The only locality with both haplotypes was in the Solomon Islands. The country of origin of Platydemus manokwari is New Guinea, and Australia and the Solomon Islands are the countries closest to New Guinea from which we had specimens. These results suggest that two haplotypes exist in the area of origin of the species, but that only one of the two haplotypes (the "World haplotype") has, through human agency, been widely dispersed. However, since P. manokwari is now recorded from 22 countries in the world and we have genetic information from only 8 of these, with none from New Guinea, this analysis provides only partial knowledge of the genetic structure of the invasive species. Morphological analysis of specimens from both haplotypes has shown some differences in ratio of the genital structures but did not allow us to interpret the haplotypes as different species. The new reports from Florida and Puerto Rico are firsts for the USA, for the American continent, and the Caribbean. P. manokwari is a known threat for endemic terrestrial molluscs and its presence is a matter of concern. While most of the infected territories reported until now were islands, the newly reported presence of the species in mainland US in Florida should be considered a potential major threat to the whole US and even the Americas.},
}
@article {pmid26129849,
year = {2016},
author = {Lobo, J and Teixeira, MA and Borges, LM and Ferreira, MS and Hollatz, C and Gomes, PT and Sousa, R and Ravara, A and Costa, MH and Costa, FO},
title = {Starting a DNA barcode reference library for shallow water polychaetes from the southern European Atlantic coast.},
journal = {Molecular ecology resources},
volume = {16},
number = {1},
pages = {298-313},
doi = {10.1111/1755-0998.12441},
pmid = {26129849},
issn = {1755-0998},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Gene Library ; Polychaeta/*classification/*genetics ; Portugal ; Sequence Analysis, DNA ; },
abstract = {Annelid polychaetes have been seldom the focus of dedicated DNA barcoding studies, despite their ecological relevance and often dominance, particularly in soft-bottom estuarine and coastal marine ecosystems. Here, we report the first assessment of the performance of DNA barcodes in the discrimination of shallow water polychaete species from the southern European Atlantic coast, focusing on specimens collected in estuaries and coastal ecosystems of Portugal. We analysed cytochrome oxidase I DNA barcodes (COI-5P) from 164 specimens, which were assigned to 51 morphospecies. To our data set from Portugal, we added available published sequences selected from the same species, genus or family, to inspect for taxonomic congruence among studies and collection location. The final data set comprised 290 specimens and 79 morphospecies, which generated 99 Barcode Index Numbers (BINs) within Barcode of Life Data Systems (BOLD). Among these, 22 BINs were singletons, 47 other BINs were concordant, confirming the initial identification based on morphological characters, and 30 were discordant, most of which consisted on multiple BINs found for the same morphospecies. Some of the most prominent cases in the latter category include Hediste diversicolor (O.F. Müller, 1776) (7), Eulalia viridis (Linnaeus, 1767) (2) and Owenia fusiformis (delle Chiaje, 1844) (5), all of them reported from Portugal and frequently used in ecological studies as environmental quality indicators. Our results for these species showed discordance between molecular lineages and morphospecies, or added additional relatively divergent lineages. The potential inaccuracies in environmental assessments, where underpinning polychaete species diversity is poorly resolved or clarified, demand additional and extensive investigation of the DNA barcode diversity in this group, in parallel with alpha taxonomy efforts.},
}
@article {pmid26126785,
year = {2015},
author = {Banerjee, D and Kumar, V and Maity, A and Ghosh, B and Tyagi, K and Singha, D and Kundu, S and Laskar, BA and Naskar, A and Rath, S},
title = {Identification through DNA barcoding of Tabanidae (Diptera) vectors of surra disease in India.},
journal = {Acta tropica},
volume = {150},
number = {},
pages = {52-58},
doi = {10.1016/j.actatropica.2015.06.023},
pmid = {26126785},
issn = {1873-6254},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Diptera/classification/*genetics ; Genetic Variation ; Insect Vectors/*genetics ; Trypanosomiasis/*transmission ; },
abstract = {Horse flies and deer flies are common names applied to members of the family Tabanidae (Diptera). Tabanid flies are pestiferous and of veterinary and medical importance, with about 244 species in India. They are major vectors of Trypanosoma evansi that causes trypanosomiasis (surra disease). Lack of stable morphological characters, and scarcity of taxonomic expertise, is major impediments for accurate species identification of these important pest and disease vectors. Molecular data, especially DNA barcode data, has been widely used in the identification of Diptera of economic importance. We evaluated the utility of DNA barcode data to discriminate the vectors of surra disease (trypanosomiasis) from India. We used barcode gap and reciprocal monophyly (neighbor-joining and Bayesian tree) criteria to analyze barcode data. A total of 46 specimens belonging to 7 species under four genera in two subfamilies were used for this study. DNA barcode data was not available previously for these species. Analysis revealed that all morphologically identifiable species can be discriminated using DNA barcoding data. Further, our study clearly demonstrated the presence of cryptic species in Chrysops dispar. Moreover, we revealed that closely related species without stable taxonomic distinguishing characters in the "Tabanus striatus species complex" can be discriminated using DNA barcode data.},
}
@article {pmid26126624,
year = {2015},
author = {Kukita, Y and Matoba, R and Uchida, J and Hamakawa, T and Doki, Y and Imamura, F and Kato, K},
title = {High-fidelity target sequencing of individual molecules identified using barcode sequences: de novo detection and absolute quantitation of mutations in plasma cell-free DNA from cancer patients.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {22},
number = {4},
pages = {269-277},
pmid = {26126624},
issn = {1756-1663},
mesh = {DNA Barcoding, Taxonomic ; *DNA, Neoplasm ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Lung Neoplasms/genetics ; Male ; *Mutation ; Neoplasms/*genetics ; Plasma Cells/*metabolism ; Reproducibility of Results ; Stomach Neoplasms/genetics ; },
abstract = {Circulating tumour DNA (ctDNA) is an emerging field of cancer research. However, current ctDNA analysis is usually restricted to one or a few mutation sites due to technical limitations. In the case of massively parallel DNA sequencers, the number of false positives caused by a high read error rate is a major problem. In addition, the final sequence reads do not represent the original DNA population due to the global amplification step during the template preparation. We established a high-fidelity target sequencing system of individual molecules identified in plasma cell-free DNA using barcode sequences; this system consists of the following two steps. (i) A novel target sequencing method that adds barcode sequences by adaptor ligation. This method uses linear amplification to eliminate the errors introduced during the early cycles of polymerase chain reaction. (ii) The monitoring and removal of erroneous barcode tags. This process involves the identification of individual molecules that have been sequenced and for which the number of mutations have been absolute quantitated. Using plasma cell-free DNA from patients with gastric or lung cancer, we demonstrated that the system achieved near complete elimination of false positives and enabled de novo detection and absolute quantitation of mutations in plasma cell-free DNA.},
}
@article {pmid26125940,
year = {2015},
author = {Bhattacharyya, P and Kumaria, S and Tandon, P},
title = {Applicability of ISSR and DAMD markers for phyto-molecular characterization and association with some important biochemical traits of Dendrobium nobile, an endangered medicinal orchid.},
journal = {Phytochemistry},
volume = {117},
number = {},
pages = {306-316},
doi = {10.1016/j.phytochem.2015.06.022},
pmid = {26125940},
issn = {1873-3700},
mesh = {Alkaloids/analysis ; Antioxidants/metabolism/pharmacology ; Bayes Theorem ; DNA Barcoding, Taxonomic ; Dendrobium/classification/*genetics/*metabolism ; Endangered Species ; Flavonoids/analysis ; Genetic Markers ; Genetic Variation ; Genetics, Population ; India ; *Microsatellite Repeats ; *Minisatellite Repeats ; Models, Theoretical ; Plants, Medicinal/genetics ; Secondary Metabolism ; },
abstract = {Dendrobium nobile is an important medicinal orchid having profound importance in traditional herbal drug preparations and pharmacopeias worldwide. Due to various anthropogenic pressures the natural populations of this important orchid species are presently facing threats of extinction. In the present study, genetic and chemical diversity existing amongst 6 natural populations of D. nobile were assessed using molecular markers, and the influence of genetic factors on its phytochemical activity especially antioxidant potential was determined. Molecular fingerprinting of the orchid taxa was performed using ISSR and DAMD markers along with the estimation of total phenolics, flavonoids and alkaloid contents. Antioxidant activity was also measured using DPPH and FRAP assays which cumulatively revealed a significant level of variability across the sampled populations. The representatives from Sikkim in Northeast India revealed higher phytochemical activity whereas those from Mizoram showed lesser activity. Analysis of molecular variance (AMOVA) revealed that variation amongst the populations was significantly higher than within the populations. The data generated by UPGMA and Bayesian analytical models were compared in order to estimate the genetic relationships amongst the D. nobile germplasm sampled from different geographical areas of Northeast India. Interestingly, identical grouping patterns were exhibited by both the approaches. The results of the present study detected a high degree of existing genetic and phytochemical variation amongst the populations in relation to bioclimatic and geographic locations of populations. Our results strongly establish that the cumulative marker approach could be the best suited for assessing the genetic relationships with high accuracy amongst distinct D. nobile accessions.},
}
@article {pmid26125793,
year = {2015},
author = {Huang, ZH and Ke, DH},
title = {DNA barcoding and phylogenetic relationships in Timaliidae.},
journal = {Genetics and molecular research : GMR},
volume = {14},
number = {2},
pages = {5943-5949},
doi = {10.4238/2015.June.1.11},
pmid = {26125793},
issn = {1676-5680},
mesh = {Animals ; DNA/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Passeriformes/*genetics ; *Phylogeny ; },
abstract = {The Timaliidae, a diverse family of oscine passerine birds, has long been a subject of debate regarding its phylogeny. The mitochondrial cytochrome c oxidase subunit I (COI) gene has been used as a powerful marker for identification and phylogenetic studies of animal species. In the present study, we analyzed the COI barcodes of 71 species from 21 genera belonging to the family Timaliidae. Every bird species possessed a barcode distinct from that of other bird species. Kimura two-parameter (K2P) distances were calculated between barcodes. The average genetic distance between species was 18 times higher than the average genetic distance within species. The neighbor-joining method was used to construct a phylogenetic tree and all the species could be discriminated by their distinct clades within the phylogenetic tree. The results indicate that some currently recognized babbler genera might not be monophyletic, with the COI gene data supporting the hypothesis of polyphyly for Garrulax, Alcippe, and Minla. Thus, DNA barcoding is an effective molecular tool for Timaliidae species identification and phylogenetic inference.},
}
@article {pmid26125766,
year = {2015},
author = {Chee, SY},
title = {Limitations of cytochrome oxidase I for the barcoding of Neritidae (Mollusca: Gastropoda) as revealed by Bayesian analysis.},
journal = {Genetics and molecular research : GMR},
volume = {14},
number = {2},
pages = {5677-5684},
doi = {10.4238/2015.May.25.20},
pmid = {26125766},
issn = {1676-5680},
mesh = {Animals ; Bayes Theorem ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Gastropoda/classification/*genetics ; Phylogeny ; },
abstract = {The mitochondrial DNA (mtDNA) cytochrome oxidase I (COI) gene has been universally and successfully utilized as a barcoding gene, mainly because it can be amplified easily, applied across a wide range of taxa, and results can be obtained cheaply and quickly. However, in rare cases, the gene can fail to distinguish between species, particularly when exposed to highly sensitive methods of data analysis, such as the Bayesian method, or when taxa have undergone introgressive hybridization, over-splitting, or incomplete lineage sorting. Such cases require the use of alternative markers, and nuclear DNA markers are commonly used. In this study, a dendrogram produced by Bayesian analysis of an mtDNA COI dataset was compared with that of a nuclear DNA ATPS-α dataset, in order to evaluate the efficiency of COI in barcoding Malaysian nerites (Neritidae). In the COI dendrogram, most of the species were in individual clusters, except for two species: Nerita chamaeleon and N. histrio. These two species were placed in the same subcluster, whereas in the ATPS-α dendrogram they were in their own subclusters. Analysis of the ATPS-α gene also placed the two genera of nerites (Nerita and Neritina) in separate clusters, whereas COI gene analysis placed both genera in the same cluster. Therefore, in the case of the Neritidae, the ATPS-α gene is a better barcoding gene than the COI gene.},
}
@article {pmid26122993,
year = {2015},
author = {Chibwana, FD and Nkwengulila, G and Locke, SA and McLaughlin, JD and Marcogliese, DJ},
title = {Completion of the life cycle of Tylodelphys mashonense (Sudarikov, 1971) (Digenea: Diplostomidae) with DNA barcodes and rDNA sequences.},
journal = {Parasitology research},
volume = {114},
number = {10},
pages = {3675-3682},
pmid = {26122993},
issn = {1432-1955},
mesh = {Animals ; Birds ; Catfishes ; Cercaria ; *DNA Barcoding, Taxonomic ; DNA, Ribosomal/*genetics ; Fish Diseases/parasitology ; Tanzania/epidemiology ; Trematoda/*genetics/*physiology ; Trematode Infections/epidemiology/parasitology/veterinary ; },
abstract = {The life cycle of Tylodelphys mashonense (Digenea: Diplostomidae), whose metacercariae occur in the cranial cavity of the widely cultivated catfish Clarias gariepinus, was resolved by the application of molecular markers. Both COI barcodes and ITS sequences obtained from diplostomid-like cercariae infecting Bulinus spp. from Mindu Dam, Morogoro, matched those acquired from metacercariae from the catfish C. gariepinus, and those from adult T. mashonense from the grey heron Ardea cinerea and the white egret Egretta alba. The success in linking the life cycle stages of T. mashonense using molecular tools highlights the usefulness of this approach in resolving the complex life cycles of digeneans in the absence of experimental establishment.},
}
@article {pmid26122341,
year = {2016},
author = {Jaffar Ali, HA and Ahmed, NS},
title = {DNA barcoding of two solitary ascidians, Herdmania momus Savigny, 1816 and Microcosmus squamiger Michaelsen, 1927 from Thoothukudi coast, India.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {4},
pages = {3005-3007},
doi = {10.3109/19401736.2015.1060479},
pmid = {26122341},
issn = {2470-1408},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; Electron Transport Complex IV/genetics ; India ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Urochordata/*classification/*genetics ; },
abstract = {Morphology-based taxonomical studies of ascidians in India are meagre due to lack of ascidian taxonomist and limitations inherent in conventional system-based identification. The use of short fragment of mitochondrial DNA sequence is proving highly useful in identifying species in a situation where, the traditional morphology-based identification is difficult. In the present study, two adult solitary ascidians collected from the Thoothukudi coast were morphologically identified as Herdmania momus Savigny, 1816 and Microcosmus squamiger Michaelsen, 1927. The genomic DNA of these ascidians was isolated, COI gene was amplified, sequenced and submitted to the GenBank under the accession numbers KM058116, KM411616 and KJ944390. Homology search result using BLAST showed that H. momus showed 100% matched with other H. momus, while M. squamiger showed similarity with Pyura herdmani, a member of the same family Pyuridae. The phylogenetic and genetic distance was maximum in interspecies than in intraspecies. These COI sequences will allow the identification of the species through DNA barcoding technique. Here, we report for the first time the COI gene of H. momus, Savigny 1816 from the Indian coast.},
}
@article {pmid26121045,
year = {2015},
author = {Huang, XC and Ci, XQ and Conran, JG and Li, J},
title = {Application of DNA Barcodes in Asian Tropical Trees--A Case Study from Xishuangbanna Nature Reserve, Southwest China.},
journal = {PloS one},
volume = {10},
number = {6},
pages = {e0129295},
pmid = {26121045},
issn = {1932-6203},
mesh = {China ; *Conservation of Natural Resources ; DNA Barcoding, Taxonomic/*methods ; Likelihood Functions ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; Trees/*genetics ; *Tropical Climate ; },
abstract = {BACKGROUND: Within a regional floristic context, DNA barcoding is more useful to manage plant diversity inventories on a large scale and develop valuable conservation strategies. However, there are no DNA barcode studies from tropical areas of China, which represents one of the biodiversity hotspots around the world.<br><br>A DNA barcoding database of an Asian tropical trees with high diversity was established at Xishuangbanna Nature Reserve, Yunnan, southwest China using rbcL and matK as standard barcodes, as well as trnH-psbA and ITS as supplementary barcodes. The performance of tree species identification success was assessed using 2,052 accessions from four plots belonging to two vegetation types in the region by three methods: Neighbor-Joining, Maximum-Likelihood and BLAST. We corrected morphological field identification errors (9.6%) for the three plots using rbcL and matK based on Neighbor-Joining tree. The best barcode region for PCR and sequencing was rbcL (97.6%, 90.8%), followed by trnH-psbA (93.6%, 85.6%), while matK and ITS obtained relative low PCR and sequencing success rates. However, ITS performed best for both species (44.6-58.1%) and genus (72.8-76.2%) identification. With trnH-psbA slightly less effective for species identification. The two standard barcode rbcL and matK gave poor results for species identification (24.7-28.5% and 31.6-35.3%). Compared with other studies from comparable tropical forests (e.g. Cameroon, the Amazon and India), the overall performance of the four barcodes for species identification was lower for the Xishuangbanna Nature Reserve, possibly because of species/genus ratios and species composition between these tropical areas.<br><br>CONCLUSIONS/SIGNIFICANCE: Although the core barcodes rbcL and matK were not suitable for species identification of tropical trees from Xishuangbanna Nature Reserve, they could still help with identification at the family and genus level. Considering the relative sequence recovery and the species identification performance, we recommend the use of trnH-psbA and ITS in combination as the preferred barcodes for tropical tree species identification in China.},
}
@article {pmid26120347,
year = {2015},
author = {Fan, C and Li, X and Zhu, J and Song, J and Yao, H},
title = {Endangered Uyghur Medicinal Plant Ferula Identification through the Second Internal Transcribed Spacer.},
journal = {Evidence-based complementary and alternative medicine : eCAM},
volume = {2015},
number = {},
pages = {479879},
pmid = {26120347},
issn = {1741-427X},
abstract = {The medicinal plant Ferula has been widely used in Asian medicine, especially in Uyghur medicine in Xinjiang, China. Given that various substitutes and closely related species have similar morphological characteristics, Ferula is difficult to distinguish based on morphology alone, thereby causing confusion and threatening the safe use of Ferula. In this study, internal transcribed spacer 2 (ITS2) sequences were analyzed and assessed for the accurate identification of two salable Ferula species (Ferula sinkiangensis and Ferula fukangensis) and eight substitutes or closely related species. Results showed that the sequence length of ITS2 ranged from 451 bp to 45 bp, whereas guanine and cytosine contents (GC) were from 53.6% to 56.2%. A total of 77 variation sites were detected, including 63 base mutations and 14 insertion/deletion mutations. The ITS2 sequence correctly identified 100% of the samples at the species level using the basic local alignment search tool 1 and nearest-distance method. Furthermore, neighbor-joining tree successfully identified the genuine plants F. sinkiangensis and F. fukangensis from their succedaneum and closely related species. These results indicated that ITS2 sequence could be used as a valuable barcode to distinguish Uyghur medicine Ferula from counterfeits and closely related species. This study may broaden DNA barcoding application in the Uyghur medicinal plant field.},
}
@article {pmid26115486,
year = {2015},
author = {Rocher, S and Jean, M and Castonguay, Y and Belzile, F},
title = {Validation of Genotyping-By-Sequencing Analysis in Populations of Tetraploid Alfalfa by 454 Sequencing.},
journal = {PloS one},
volume = {10},
number = {6},
pages = {e0131918},
pmid = {26115486},
issn = {1932-6203},
mesh = {Alleles ; Base Sequence ; Chromosome Mapping/methods ; DNA Mutational Analysis/methods ; Genome, Plant ; Genotyping Techniques/*methods ; *High-Throughput Nucleotide Sequencing/methods ; Medicago sativa/classification/*genetics ; Medicago truncatula/genetics ; Molecular Sequence Data ; Polymorphism, Single Nucleotide ; Sequence Homology, Nucleic Acid ; *Tetraploidy ; },
abstract = {Genotyping-by-sequencing (GBS) is a relatively low-cost high throughput genotyping technology based on next generation sequencing and is applicable to orphan species with no reference genome. A combination of genome complexity reduction and multiplexing with DNA barcoding provides a simple and affordable way to resolve allelic variation between plant samples or populations. GBS was performed on ApeKI libraries using DNA from 48 genotypes each of two heterogeneous populations of tetraploid alfalfa (Medicago sativa spp. sativa): the synthetic cultivar Apica (ATF0) and a derived population (ATF5) obtained after five cycles of recurrent selection for superior tolerance to freezing (TF). Nearly 400 million reads were obtained from two lanes of an Illumina HiSeq 2000 sequencer and analyzed with the Universal Network-Enabled Analysis Kit (UNEAK) pipeline designed for species with no reference genome. Following the application of whole dataset-level filters, 11,694 single nucleotide polymorphism (SNP) loci were obtained. About 60% had a significant match on the Medicago truncatula syntenic genome. The accuracy of allelic ratios and genotype calls based on GBS data was directly assessed using 454 sequencing on a subset of SNP loci scored in eight plant samples. Sequencing depth in this study was not sufficient for accurate tetraploid allelic dosage, but reliable genotype calls based on diploid allelic dosage were obtained when using additional quality filtering. Principal Component Analysis of SNP loci in plant samples revealed that a small proportion (<5%) of the genetic variability assessed by GBS is able to differentiate ATF0 and ATF5. Our results confirm that analysis of GBS data using UNEAK is a reliable approach for genome-wide discovery of SNP loci in outcrossed polyploids.},
}
@article {pmid26110886,
year = {2015},
author = {Boyle, EE and Adamowicz, SJ},
title = {Community Phylogenetics: Assessing Tree Reconstruction Methods and the Utility of DNA Barcodes.},
journal = {PloS one},
volume = {10},
number = {6},
pages = {e0126662},
pmid = {26110886},
issn = {1932-6203},
mesh = {Animals ; DNA/analysis ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Insecta/enzymology/*genetics/growth &amp; development ; Larva/genetics ; Manitoba ; Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {Studies examining phylogenetic community structure have become increasingly prevalent, yet little attention has been given to the influence of the input phylogeny on metrics that describe phylogenetic patterns of co-occurrence. Here, we examine the influence of branch length, tree reconstruction method, and amount of sequence data on measures of phylogenetic community structure, as well as the phylogenetic signal (Pagel's λ) in morphological traits, using Trichoptera larval communities from Churchill, Manitoba, Canada. We find that model-based tree reconstruction methods and the use of a backbone family-level phylogeny improve estimations of phylogenetic community structure. In addition, trees built using the barcode region of cytochrome c oxidase subunit I (COI) alone accurately predict metrics of phylogenetic community structure obtained from a multi-gene phylogeny. Input tree did not alter overall conclusions drawn for phylogenetic signal, as significant phylogenetic structure was detected in two body size traits across input trees. As the discipline of community phylogenetics continues to expand, it is important to investigate the best approaches to accurately estimate patterns. Our results suggest that emerging large datasets of DNA barcode sequences provide a vast resource for studying the structure of biological communities.},
}
@article {pmid26105653,
year = {2015},
author = {Lv, T and Teng, R and Shao, Q and Wang, H and Zhang, W and Li, M and Zhang, L},
title = {DNA barcodes for the identification of Anoectochilus roxburghii and its adulterants.},
journal = {Planta},
volume = {242},
number = {5},
pages = {1167-1174},
pmid = {26105653},
issn = {1432-2048},
mesh = {DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; DNA, Ribosomal Spacer/*genetics ; Orchidaceae/*genetics ; Sequence Analysis, DNA ; },
abstract = {Chinese medicinal herbs have a similar appearance and are easily confused, complicating identification via traditional methods. This study provided a scientific approach, based on DNA barcoding, to accurately and rapidly identify Anoectochilus roxburghii and its adulterants. This technology complements traditional methods of identification of medicinal herbs. A comparison of the DNA barcodes matK, psbA-trnH and ITS2 was performed to verify that the ITS2 sequence is an effective marker for rapidly and accurately identifying A. roxburghii and its closely related species. Genomic DNA extracted from A. roxburghii and its adulterants were used as templates and the ITS2 sequence was amplified using PCR amplification and sequencing. Species identification was conducted using BLAST1 and neighbor-joining trees. The 12 samples were successfully classified into four species based on the ITS2 sequence. The ITS2 sequence length of A. roxburghii was 253 bp. The average intra-specific genetic distance of A. roxburghii was 0.0021, markedly lower than the inter-specific genetic distance between A. roxburghii and its adulterants (0.0380). Our findings illustrate that ITS2 sequence can accurately and efficiently distinguish A. roxburghii and its adulterants. In addition, the results provided reference for molecular identification of other Chinese herbal medicine.},
}
@article {pmid26103688,
year = {2015},
author = {Wacławik, B and Skalski, T and Lachowska-Cierlik, D},
title = {Species Relationships in the Genus Bryodaemon (Coleoptera: Curculionidae).},
journal = {Folia biologica},
volume = {63},
number = {1},
pages = {69-75},
doi = {10.3409/fb63_1.69},
pmid = {26103688},
issn = {0015-5497},
mesh = {Animals ; Coleoptera/*classification/*genetics ; DNA/genetics ; Phylogeny ; Species Specificity ; },
abstract = {Establishing reliable taxonomy and phylogeny of similar, evolutionarily young species is among the greatest challenges in biology. Clearly the best approach is to use a combination of informative traits, including molecular markers and morphometric measurements. The objective of this study was to verify the taxonomy and phylogeny of four morphologically similar Carpathian species of Bryodaemon Podlussany, 1998 (Coleoptera: Curculionidae). Species relationships were studied using three molecular markers: two nuclear (ITS-2 and EF1-α) and one mitochondrial (COI, barcoding marker). We also took morphometric measurements of 35 taxonomically derived characteristics of body parts and genital apparatus. The potential presence of apomorphic features also was determined. We then compared our results with data concerning the ecology and geography of previously studied species. Our analyses confirmed the monophyly ofthis group and established a phylogeny for the genus. We propose that B. hanakii is the earliest derived species, based on morphometric measurements, apomorphies and the EF-lα phylogeny. The pattern ofnucleotide variation in this marker also indicates that B. rozneri and B. boroveci are the youngest species. This hypothesis is consistent with geographical ranges and ecological preferences of Carpathian Bryodaemon species. We also considered an alternative hypothesis based on the COI gene tree which indicated that B. rozneri was the oldest species. However, this arrangement is inconsistent with our morphological data.},
}
@article {pmid26096026,
year = {2015},
author = {Novo, S and Mora-Espí, I and Gómez-Martínez, R and Barrios, L and Ibáñez, E and Such, X and Duch, M and Mora, X and Plaza, JA and Nogués, C},
title = {Traceability of human sperm samples by direct tagging with polysilicon microbarcodes.},
journal = {Reproductive biomedicine online},
volume = {31},
number = {2},
pages = {162-170},
doi = {10.1016/j.rbmo.2015.04.012},
pmid = {26096026},
issn = {1472-6491},
mesh = {Acrosome Reaction ; Animals ; Cryopreservation ; Female ; Humans ; Insemination, Artificial ; Male ; Pregnancy ; Pregnancy Rate ; Rabbits ; *Silicon ; *Spermatozoa ; },
abstract = {The increasing number of patients undergoing assisted reproductive technology (ART) treatments and of cycles performed in fertility centres has led to some traceability errors. Although the incidence of mismatching errors is extremely low, any error is unacceptable, therefore different strategies have been developed to further minimize these errors, such as manual double-witnessing or electronic witnessing systems. More recently, our group developed a direct tagging method consisting of attaching microbarcodes directly to the zona pellucida of human oocytes/embryos. Here, this method is taken a step further by using these microbarcodes to tag human semen samples, demonstrating that the barcodes are not toxic and do not interfere in the selection of motile spermatozoa nor in the cryopreservation of the sperm samples. In addition, when this tagging system was applied to an animal model (rabbit), pregnancy rate and kitten viability were not affected.},
}
@article {pmid26095583,
year = {2015},
author = {Massana, R},
title = {Getting specific: making taxonomic and ecological sense of large sequencing data sets.},
journal = {Molecular ecology},
volume = {24},
number = {12},
pages = {2904-2906},
doi = {10.1111/mec.13210},
pmid = {26095583},
issn = {1365-294X},
mesh = {*Biodiversity ; Haptophyta/*classification ; *Seasons ; },
abstract = {Eukaryotic microbes comprise a diverse collection of phototrophic and heterotrophic creatures known to play fundamental roles in ecological processes. Some can be identified by light microscopy, generally the largest and with conspicuous shapes, while the smallest can be counted by epifluorescence microscopy or flow cytometry but remain largely unidentified. Microbial diversity studies greatly advanced with the analysis of phylogenetic markers sequenced from natural assemblages. Molecular surveys began in 1990 targeting marine bacterioplankton (Giovannoni et al.) and first approached microbial eukaryotes in three studies published in 2001 (Díez et al. ; López-García et al. ; Moon-van der Staay et al.). These seminal studies, based on cloning and Sanger sequencing the complete 18S rDNA, were critical for obtaining broad pictures of microbial diversity in contrasted habitats and for describing novel lineages by robust phylogenies, but were limited by the number of sequences obtained. So, inventories of species richness in a given sample and community comparisons through environmental gradients were very incomplete. These limitations have been overcome with the advent of high-throughput sequencing (HTS) methods, initially 454-pyrosequencing, today Illumina and soon others to come. In this issue of Molecular Ecology, Egge et al. () show a nice example of the use of HTS to study the biodiversity and seasonal succession of a particularly important group of marine microbial eukaryotes, the haptophytes. Temporal changes were analysed first at the community level, then at the clade level, and finally at the lowest rank comparable to species. Interesting and useful ecological insights were obtained at each taxonomic scale. Haptophyte diversity differed along seasons in a systematic manner, with some species showing seasonal preferences and others being always present. Many of these species had no correspondence with known species, pointing out the high level of novelty in microbial assemblages, only accessible by molecular tools. Moreover, the number of species detected was limited, agreeing with a putative scenario of constrained evolutionary diversification in free-living small eukaryotes. This study illustrates the potential of HTS to address ecological relevant questions in an accessible way by processing large data sets that, nonetheless, need to be treated with a fair understanding of their limitations.},
}
@article {pmid26095230,
year = {2016},
author = {Barco, A and Raupach, MJ and Laakmann, S and Neumann, H and Knebelsberger, T},
title = {Identification of North Sea molluscs with DNA barcoding.},
journal = {Molecular ecology resources},
volume = {16},
number = {1},
pages = {288-297},
doi = {10.1111/1755-0998.12440},
pmid = {26095230},
issn = {1755-0998},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Databases, Nucleic Acid ; Mollusca/classification/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Sequence-based specimen identification, known as DNA barcoding, is a common method complementing traditional morphology-based taxonomic assignments. The fundamental resource in DNA barcoding is the availability of a taxonomically reliable sequence database to use as a reference for sequence comparisons. Here, we provide a reference library including 579 sequences of the mitochondrial cytochrome c oxidase subunit I for 113 North Sea mollusc species. We tested the efficacy of this library by simulating a sequence-based specimen identification scenario using Best Match, Best Close Match (BCM) and All Species Barcode (ASB) criteria with three different threshold values. Each identification result was compared with our prior morphology-based taxonomic assignments. Our simulation resulted in 87.7% congruent identifications (93.8% when excluding singletons). The highest number of congruent identifications was obtained with BCM and ASB and a 0.05 threshold. We also compared identifications with genetic clustering (Barcode Index Numbers, BINs) computed by the Barcode of Life Datasystem (BOLD). About 68% of our morphological identifications were congruent with BINs created by BOLD. Forty-nine sequences were clustered in 16 discordant BINs, and these were divided in two classes: sequences from different species clustered in a single BIN and conspecific sequences divided in more BINs. Whereas former incongruences were probably caused by BOLD entries in need of a taxonomic update, the latter incongruences regarded taxa requiring further investigations. These include species with amphi-Atlantic distribution, whose genetic structure should be evaluated over their entire range to produce a reliable sequence-based identification system.},
}
@article {pmid26092963,
year = {2015},
author = {Pedersen, CA and Schneider, PJ and Scheckelhoff, DJ},
title = {ASHP national survey of pharmacy practice in hospital settings: Dispensing and administration--2014.},
journal = {American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists},
volume = {72},
number = {13},
pages = {1119-1137},
doi = {10.2146/ajhp150032},
pmid = {26092963},
issn = {1535-2900},
mesh = {Drug Compounding/standards ; Drug Packaging ; Drug Prescriptions/statistics &amp; numerical data ; Electronic Data Processing ; Electronic Health Records ; Environment, Controlled ; Hazardous Substances ; Health Facility Size ; Humans ; Medication Systems, Hospital/economics/standards/*statistics &amp; numerical data ; Nutritional Support ; Pharmacists ; Pharmacy Service, Hospital/economics/standards/*statistics &amp; numerical data ; Point-of-Care Systems/statistics &amp; numerical data ; Surveys and Questionnaires ; United States ; },
abstract = {PURPOSE: The results of the 2014 ASHP national survey of pharmacy practice in hospital settings that pertain to dispensing and administration are described.<br><br>METHODS: A stratified random sample of pharmacy directors at 1435 general and children's medical-surgical hospitals in the United States were surveyed by mail.<br><br>RESULTS: In this national probability sample survey, the response rate was 29.7%. Ninety-seven percent of hospitals used automated dispensing cabinets in their medication distribution systems, 65.7% of which used individually secured lidded pockets as the predominant configuration. Overall, 44.8% of hospitals used some form of machine-readable coding to verify doses before dispensing in the pharmacy. Overall, 65% of hospital pharmacy departments reported having a cleanroom compliant with United States Pharmacopeia chapter 797. Pharmacists reviewed and approved all medication orders before the first dose was administered, either onsite or by remote order view, except in procedure areas and emergency situations, in 81.2% of hospitals. Adoption rates of electronic health information have rapidly increased, with the widespread use of electronic health records, computer prescriber order entry, barcodes, and smart pumps. Overall, 31.4% of hospitals had pharmacists practicing in ambulatory or primary care clinics. Transitions-of-care services offered by the pharmacy department have generally increased since 2012. Discharge prescription services increased from 11.8% of hospitals in 2012 to 21.5% in 2014. Approximately 15% of hospitals outsourced pharmacy management operations to a contract pharmacy services provider, an increase from 8% in 2011.<br><br>CONCLUSION: Health-system pharmacists continue to have a positive impact on improving healthcare through programs that improve the efficiency, safety, and clinical outcomes of medication use in health systems.},
}
@article {pmid26091103,
year = {2015},
author = {Vargas, S and Kelly, M and Schnabel, K and Mills, S and Bowden, D and Wörheide, G},
title = {Diversity in a Cold Hot-Spot: DNA-Barcoding Reveals Patterns of Evolution among Antarctic Demosponges (Class Demospongiae, Phylum Porifera).},
journal = {PloS one},
volume = {10},
number = {6},
pages = {e0127573},
pmid = {26091103},
issn = {1932-6203},
mesh = {Animals ; Antarctic Regions ; *Biodiversity ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; Evolution, Molecular ; Phylogeny ; Porifera/*classification/*genetics ; },
abstract = {BACKGROUND: The approximately 350 demosponge species that have been described from Antarctica represent a faunistic component distinct from that of neighboring regions. Sponges provide structure to the Antarctic benthos and refuge to other invertebrates, and can be dominant in some communities. Despite the importance of sponges in the Antarctic subtidal environment, sponge DNA barcodes are scarce but can provide insight into the evolutionary relationships of this unique biogeographic province.<br><br>We sequenced the standard barcoding COI region for a comprehensive selection of sponges collected during expeditions to the Ross Sea region in 2004 and 2008, and produced DNA-barcodes for 53 demosponge species covering about 60% of the species collected. The Antarctic sponge communities are phylogenetically diverse, matching the diversity of well-sampled sponge communities in the Lusitanic and Mediterranean marine provinces in the Temperate Northern Atlantic for which molecular data are readily available. Additionally, DNA-barcoding revealed levels of in situ molecular evolution comparable to those present among Caribbean sponges. DNA-barcoding using the Segregating Sites Algorithm correctly assigned approximately 54% of the barcoded species to the morphologically determined species.<br><br>CONCLUSION/SIGNIFICANCE: A barcode library for Antarctic sponges was assembled and used to advance the systematic and evolutionary research of Antarctic sponges. We provide insights on the evolutionary forces shaping Antarctica's diverse sponge communities, and a barcode library against which future sequence data from other regions or depth strata of Antarctica can be compared. The opportunity for rapid taxonomic identification of sponge collections for ecological research is now at the horizon.},
}
@article {pmid26089942,
year = {2015},
author = {Hu, Z and Tu, Y and Xia, Y and Cheng, P and Sun, W and Shi, Y and Guo, L and He, H and Xiong, C and Chen, S and Zhang, X},
title = {Rapid Identification and Verification of Indirubin-Containing Medicinal Plants.},
journal = {Evidence-based complementary and alternative medicine : eCAM},
volume = {2015},
number = {},
pages = {484670},
pmid = {26089942},
issn = {1741-427X},
abstract = {Indirubin, one of the key components of medicinal plants including Isatis tinctoria, Polygonum tinctorium, and Strobilanthes cusia, possesses great medicinal efficacy in the treatment of chronic myelocytic leukemia (CML). Due to misidentification and similar name, materials containing indirubin and their close relatives frequently fall prey to adulteration. In this study, we selected an internal transcribed spacer 2 (ITS2) for distinguishing these indirubin-containing species from five of their usual adulterants, after assessing identification efficiency of matK, rbcL, psbA-trnH, and ITS2 among these species. The results of genetic distances and neighbor-joining (NJ) phylogenetic tree indicated that ITS2 region is a powerful DNA barcode to accurately identify these indirubin-containing species and discriminate them from their adulterants. Additionally, high performance liquid chromatography (HPLC) was used to verify indirubin in different organs of the above species. The results showed that indirubin had been detected in the leaves of Is. tinctoria, P. tinctorium, S. cusia, and Indigo Naturalis (made from their mixture), but not in their roots, or in the leaves of their adulterants. Therefore, this study provides a novel and rapid method to identify and verify indirubin-containing medicinal plants for effective natural treatment of CML.},
}
@article {pmid26087547,
year = {2015},
author = {Huang, Y and Zhang, YY and Zhao, CJ and Xu, YL and Gu, YL and Huang, WQ and Lin, K and Li, L},
title = {[DNA barcoding and its utility in commonly-used medicinal snakes].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {40},
number = {5},
pages = {868-874},
pmid = {26087547},
issn = {1001-5302},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Medicine, Chinese Traditional ; Molecular Sequence Data ; Phylogeny ; Reptilian Proteins/genetics ; Snakes/*classification/*genetics ; },
abstract = {Identification accuracy of traditional Chinese medicine is crucial for the traditional Chinese medicine research, production and application. DNA barcoding based on the mitochondrial gene coding for cytochrome c oxidase subunit I (COI), are more and more used for identification of traditional Chinese medicine. Using universal barcoding primers to sequence, we discussed the feasibility of DNA barcoding method for identification commonly-used medicinal snakes (a total of 109 samples belonging to 19 species 15 genera 6 families). The phylogenetic trees using Neighbor-joining were constructed. The results indicated that the mean content of G + C(46.5%) was lower than that of A + T (53.5%). As calculated by Kimera-2-parameter model, the mean intraspecies genetic distance of Trimeresurus albolabris, Ptyas dhumnades and Lycodon rufozonatus was greater than 2%. Further phylogenetic relationship results suggested that identification of one sample of T. albolabris was erroneous. The identification of some samples of P. dhumnades was also not correct, namely originally P. korros was identified as P. dhumnades. Factors influence on intraspecific genetic distance difference of L. rufozonatus need to be studied further. Therefore, DNA barcoding for identification of medicinal snakes is feasible, and greatly complements the morphological classification method. It is necessary to further study in identification of traditional Chinese medicine.},
}
@article {pmid26084797,
year = {2015},
author = {Brabec, J and Kostadinova, A and Scholz, T and Littlewood, DT},
title = {Complete mitochondrial genomes and nuclear ribosomal RNA operons of two species of Diplostomum (Platyhelminthes: Trematoda): a molecular resource for taxonomy and molecular epidemiology of important fish pathogens.},
journal = {Parasites &amp; vectors},
volume = {8},
number = {},
pages = {336},
pmid = {26084797},
issn = {1756-3305},
mesh = {Animals ; Cestode Infections/epidemiology/parasitology/*veterinary ; Female ; Fish Diseases/epidemiology/*parasitology ; Fishes ; *Genome, Helminth ; *Genome, Mitochondrial ; Male ; Operon ; Phylogeny ; Platyhelminths/classification/*genetics/isolation &amp; purification ; RNA, Helminth/*genetics ; RNA, Ribosomal/*genetics ; },
abstract = {BACKGROUND: The genus Diplostomum (Platyhelminthes: Trematoda: Diplostomidae) is a diverse group of freshwater parasites with complex life-cycles and global distribution. The larval stages are important pathogens causing eye fluke disease implicated in substantial impacts on natural fish populations and losses in aquaculture. However, the problematic species delimitation and difficulties in the identification of larval stages hamper the assessment of the distributional and host ranges of Diplostomum spp. and their transmission ecology.<br><br>METHODS: Total genomic DNA was isolated from adult worms and shotgun sequenced using Illumina MiSeq technology. Mitochondrial (mt) genomes and nuclear ribosomal RNA (rRNA) operons were assembled using established bioinformatic tools and fully annotated. Mt protein-coding genes and nuclear rRNA genes were subjected to phylogenetic analysis by maximum likelihood and the resulting topologies compared.<br><br>RESULTS: We characterised novel complete mt genomes and nuclear rRNA operons of two closely related species, Diplostomum spathaceum and D. pseudospathaceum. Comparative mt genome assessment revealed that the cox1 gene and its 'barcode' region used for molecular identification are the most conserved regions; instead, nad4 and nad5 genes were identified as most promising molecular diagnostic markers. Using the novel data, we provide the first genome wide estimation of the phylogenetic relationships of the order Diplostomida, one of the two fundamental lineages of the Digenea. Analyses of the mitogenomic data invariably recovered the Diplostomidae as a sister lineage of the order Plagiorchiida rather than as a basal lineage of the Diplostomida as inferred in rDNA phylogenies; this was concordant with the mt gene order of Diplostomum spp. exhibiting closer match to the conserved gene order of the Plagiorchiida.<br><br>CONCLUSIONS: Complete sequences of the mt genome and rRNA operon of two species of Diplostomum provide a valuable resource for novel genetic markers for species delineation and large-scale molecular epidemiology and disease ecology studies based on the most accessible life-cycle stages of eye flukes.},
}
@article {pmid26084789,
year = {2016},
author = {Cheng, T and Xu, C and Lei, L and Li, C and Zhang, Y and Zhou, S},
title = {Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity.},
journal = {Molecular ecology resources},
volume = {16},
number = {1},
pages = {138-149},
doi = {10.1111/1755-0998.12438},
pmid = {26084789},
issn = {1755-0998},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA Primers/*genetics ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/*genetics ; Phylogeny ; Plants/classification/*genetics ; Polymerase Chain Reaction ; Species Specificity ; },
abstract = {The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. Despite this popularity, the universality and specificity of PCR primers for the ITS region are not satisfactory, resulting in amplification and sequencing difficulties. By thoroughly surveying and analysing the 18S, 5.8S and 26S sequences of Plantae and Fungi from GenBank, we designed new universal and plant-specific PCR primers for amplifying the whole ITS region and a part of it (ITS1 or ITS2) of plants. In silico analyses of the new and the existing ITS primers based on these highly representative data sets indicated that (i) the newly designed universal primers are suitable for over 95% of plants in most groups; and (ii) the plant-specific primers are suitable for over 85% of plants in most groups without amplification of fungi. A total of 335 samples from 219 angiosperm families, 11 gymnosperm families, 24 fern and lycophyte families, 16 moss families and 17 fungus families were used to test the performances of these primers. In vitro PCR produced similar results to those from the in silico analyses. Our new primer pairs gave PCR improvements up to 30% compared with common-used ones. The new universal ITS primers will find wide application in both plant and fungal biology, and the new plant-specific ITS primers will, by eliminating PCR amplification of nonplant templates, significantly improve the quality of ITS sequence information collections in plant molecular systematics and DNA barcoding.},
}
@article {pmid26084200,
year = {2015},
author = {Kajtoch, &#x141; and Kubisz, D and Heise, W and Mazur, MA and Babik, W},
title = {Plant-herbivorous beetle networks: molecular characterization of trophic ecology within a threatened steppic environment.},
journal = {Molecular ecology},
volume = {24},
number = {15},
pages = {4023-4038},
doi = {10.1111/mec.13278},
pmid = {26084200},
issn = {1365-294X},
mesh = {Animals ; Coleoptera/*classification ; DNA Barcoding, Taxonomic ; *Ecosystem ; Europe ; *Herbivory ; Molecular Sequence Data ; Phylogeny ; Plants/*classification ; Weevils/*classification ; },
abstract = {DNA barcoding facilitates many evolutionary and ecological studies, including the examination of the dietary diversity of herbivores. In this study, we present a survey of ecological associations between herbivorous beetles and host plants from seriously threatened European steppic grasslands. We determined host plants for the majority (65%) of steppic leaf beetles (55 species) and weevils (59) known from central Europe using two barcodes (trnL and rbcL) and two sequencing strategies (Sanger for mono/oligophagous species and Illumina for polyphagous taxa). To better understand the ecological associations between steppic beetles and their host plants, we tested the hypothesis that leaf beetles and weevils differ in food selection as a result of their phylogenetic relations (within genera and between families) and interactions with host plants. We found 224 links between the beetles and the plants. Beetles belonging to seven genera feed on the same or related plants. Their preferences were probably inherited from common ancestors and/or resulted from the host plant's chemistry. Beetles from four genera feed on different plants, possibly reducing intrageneric competition and possibly due to an adaptation to different plant chemical defences. We found significant correlations between the numbers of leaf beetle and weevil species feeding on particular plants for polyphagous taxa, but not for nonpolyphagous beetles. Finally, we found that the previous identifications of host plants based on direct observations are generally concordant with host plant barcoding from insect gut. Our results expand basic knowledge about the trophic relations of steppic beetles and plants and are immediately useful for conservation purposes.},
}
@article {pmid26082876,
year = {2015},
author = {Prince, LM},
title = {Plastid primers for angiosperm phylogenetics and phylogeography.},
journal = {Applications in plant sciences},
volume = {3},
number = {6},
pages = {},
pmid = {26082876},
issn = {2168-0450},
abstract = {PREMISE OF THE STUDY: PCR primers are available for virtually every region of the plastid genome. Selection of which primer pairs to use is second only to selection of the genic region. This is particularly true for research at the species/population interface.<br><br>METHODS: Primer pairs for 130 regions of the chloroplast genome were evaluated in 12 species distributed across the angiosperms. Likelihood of amplification success was inferred based upon number and location of mismatches to target sequence. Intraspecific sequence variability was evaluated under three different criteria in four species.<br><br>RESULTS: Many published primer pairs should work across all taxa sampled, with the exception of failure due to genomic reorganization events. Universal barcoding primers were the least likely to work (65% success). The list of most variable regions for use within species has little in common with the lists identified in prior studies.<br><br>DISCUSSION: Published primer sequences should amplify a diversity of flowering plant DNAs, even those designed for specific taxonomic groups. "Universal" primers may have extremely limited utility. There was little consistency in likelihood of amplification success for any given publication across lineages or within lineage across publications.},
}
@article {pmid26080899,
year = {2015},
author = {Paz, A and Ibáñez, R and Lips, KR and Crawford, AJ},
title = {Testing the role of ecology and life history in structuring genetic variation across a landscape: a trait-based phylogeographic approach.},
journal = {Molecular ecology},
volume = {24},
number = {14},
pages = {3723-3737},
doi = {10.1111/mec.13275},
pmid = {26080899},
issn = {1365-294X},
mesh = {Animals ; Anura/*genetics ; Bayes Theorem ; DNA, Mitochondrial/genetics ; *Ecosystem ; *Genetic Variation ; Linear Models ; *Models, Genetic ; Molecular Sequence Data ; Panama ; Phylogeography ; Sequence Analysis, DNA ; },
abstract = {Hypotheses to explain phylogeographic structure traditionally invoke geographic features, but often fail to provide a general explanation for spatial patterns of genetic variation. Organisms' intrinsic characteristics might play more important roles than landscape features in determining phylogeographic structure. We developed a novel comparative approach to explore the role of ecological and life-history variables in determining spatial genetic variation and tested it on frog communities in Panama. We quantified spatial genetic variation within 31 anuran species based on mitochondrial DNA sequences, for which hierarchical approximate Bayesian computation analyses rejected simultaneous divergence over a common landscape. Regressing ecological variables, on genetic divergence allowed us to test the importance of individual variables revealing that body size, current landscape resistance, geographic range, biogeographic origin and reproductive mode were significant predictors of spatial genetic variation. Our results support the idea that phylogeographic structure represents the outcome of an interaction between organisms and their environment, and suggest a conceptual integration we refer to as trait-based phylogeography.},
}
@article {pmid26080086,
year = {2015},
author = {Darienko, T and Gustavs, L and Eggert, A and Wolf, W and Pröschold, T},
title = {Evaluating the Species Boundaries of Green Microalgae (Coccomyxa, Trebouxiophyceae, Chlorophyta) Using Integrative Taxonomy and DNA Barcoding with Further Implications for the Species Identification in Environmental Samples.},
journal = {PloS one},
volume = {10},
number = {6},
pages = {e0127838},
pmid = {26080086},
issn = {1932-6203},
mesh = {Biodiversity ; Chlorophyta/classification/*genetics/growth &amp; development ; Classification/methods ; *DNA Barcoding, Taxonomic ; Genetic Markers ; Genetic Variation ; Microalgae/classification/*genetics/growth &amp; development ; Phylogeny ; Species Specificity ; },
abstract = {Integrative taxonomy is an approach for defining species and genera by taking phylogenetic, morphological, physiological, and ecological data into account. This approach is appropriate for microalgae, where morphological convergence and high levels of morphological plasticity complicate the application of the traditional classification. Although DNA barcode markers are well-established for animals, fungi, and higher plants, there is an ongoing discussion about suitable markers for microalgae and protists because these organisms are genetically more diverse compared to the former groups. To solve these problems, we assess the usage of a polyphasic approach combining phenotypic and genetic parameters for species and generic characterization. The application of barcode markers for database queries further allows conclusions about the 'coverage' of culture-based approaches in biodiversity studies and integrates additional aspects into modern taxonomic concepts. Although the culture-dependent approach revealed three new lineages, which are described as new species in this paper, the culture-independent analyses discovered additional putative new species. We evaluated three barcode markers (V4, V9 and ITS-2 regions, nuclear ribosomal operon) and studied the morphological and physiological plasticity of Coccomyxa, which became a model organism because its whole genome sequence has been published. In addition, several biotechnological patents have been registered for Coccomyxa. Coccomyxa representatives are distributed worldwide, are free-living or in symbioses, and colonize terrestrial and aquatic habitats. We investigated more than 40 strains and reviewed the biodiversity and biogeographical distribution of Coccomyxa species using DNA barcoding. The genus Coccomyxa formed a monophyletic group within the Trebouxiophyceae separated into seven independent phylogenetic lineages representing species. Summarizing, the combination of different characteristics in an integrative approach helps to evaluate environmental data and clearly identifies microalgae at generic and species levels.},
}
@article {pmid26079154,
year = {2016},
author = {Mishra, P and Kumar, A and Nagireddy, A and Mani, DN and Shukla, AK and Tiwari, R and Sundaresan, V},
title = {DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market.},
journal = {Plant biotechnology journal},
volume = {14},
number = {1},
pages = {8-21},
pmid = {26079154},
issn = {1467-7652},
mesh = {Commerce ; DNA Barcoding, Taxonomic/*methods ; Genomics ; Industry ; Internationality ; Plants, Medicinal/*genetics ; },
abstract = {The past couple of decades have witnessed global resurgence of herbal-based health care. As a result, the trade of raw drugs has surged globally. Accurate and fast scientific identification of the plant(s) is the key to success for the herbal drug industry. The conventional approach is to engage an expert taxonomist, who uses a mix of traditional and modern techniques for precise plant identification. However, for bulk identification at industrial scale, the process is protracted and time-consuming. DNA barcoding, on the other hand, offers an alternative and feasible taxonomic tool box for rapid and robust species identification. For the success of DNA barcode, the barcode loci must have sufficient information to differentiate unambiguously between closely related plant species and discover new cryptic species. For herbal plant identification, matK, rbcL, trnH-psbA, ITS, trnL-F, 5S-rRNA and 18S-rRNA have been used as successful DNA barcodes. Emerging advances in DNA barcoding coupled with next-generation sequencing and high-resolution melting curve analysis have paved the way for successful species-level resolution recovered from finished herbal products. Further, development of multilocus strategy and its application has provided new vistas to the DNA barcode-based plant identification for herbal drug industry. For successful and acceptable identification of herbal ingredients and a holistic quality control of the drug, DNA barcoding needs to work harmoniously with other components of the systems biology approach. We suggest that for effectively resolving authentication challenges associated with the herbal market, DNA barcoding must be used in conjunction with metabolomics along with need-based transcriptomics and proteomics.},
}
@article {pmid26078770,
year = {2015},
author = {Li, X and Zeng, W and Liao, J and Liang, Z and Huang, S and Chao, Z},
title = {DNA Barcode-Based PCR-RFLP and Diagnostic PCR for Authentication of Jinqian Baihua She (Bungarus Parvus).},
journal = {Evidence-based complementary and alternative medicine : eCAM},
volume = {2015},
number = {},
pages = {402820},
pmid = {26078770},
issn = {1741-427X},
abstract = {We established polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and diagnostic PCR based on cytochrome C oxidase subunit I (COI) barcodes of Bungarus multicinctus, genuine Jinqian Baihua She (JBS), and adulterant snake species. The PCR-RFLP system utilizes the specific restriction sites of SpeI and BstEII in the COI sequence of B. multicinctus to allow its cleavage into 3 fragments (120 bp, 230 bp, and 340 bp); the COI sequences of the adulterants do not contain these restriction sites and therefore remained intact after digestion with SpeI and BstEII (except for that of Zaocys dhumnades, which could be cleaved into a 120 bp and a 570 bp fragment). For diagnostic PCR, a pair of species-specific primers (COI37 and COI337) was designed to amplify a specific 300 bp amplicon from the genomic DNA of B. multicinctus; no such amplicons were found in other allied species. We tested the two methods using 11 commercial JBS samples, and the results demonstrated that barcode-based PCR-RFLP and diagnostic PCR both allowed effective and accurate authentication of JBS.},
}
@article {pmid26078414,
year = {2016},
author = {Wilson, K and Atkinson, KM and Deeks, SL and Crowcroft, NS},
title = {Improving vaccine registries through mobile technologies: a vision for mobile enhanced Immunization information systems.},
journal = {Journal of the American Medical Informatics Association : JAMIA},
volume = {23},
number = {1},
pages = {207-211},
pmid = {26078414},
issn = {1527-974X},
mesh = {Humans ; *Immunization ; *Information Systems ; *Mobile Applications ; Population Surveillance ; *Registries ; Vaccines ; },
abstract = {Immunization registries or information systems are critical to improving the quality and evaluating the ongoing success of immunization programs. However, the completeness of these systems is challenged by a myriad of factors including the fragmentation of vaccine administration, increasing mobility of individuals, new vaccine development, use of multiple products, and increasingly frequent changes in recommendations. Mobile technologies could offer a solution, which mitigates some of these challenges. Engaging individuals to have more control of their own immunization information using their mobile devices could improve the timeliness and accuracy of data in central immunization information systems. Other opportunities presented by mobile technologies that could be exploited to improve immunization information systems include mobile reporting of adverse events following immunization, the capacity to scan 2D barcodes, and enabling bidirectional communication between individuals and public health officials. Challenges to utilizing mobile solutions include ensuring privacy of data, access, and equity concerns, obtaining consent and ensuring adoption of technology at sufficiently high rates. By empowering individuals with their own health information, mobile technologies can also serve as a mechanism to transfer immunization information as individuals cross local, regional, and national borders. Ultimately, mobile enhanced immunization information systems can help realize the goal of the individual, the healthcare provider, and public health officials always having access to the same immunization information.},
}
@article {pmid26076652,
year = {2015},
author = {de Boer, HJ and Ichim, MC and Newmaster, SG},
title = {DNA Barcoding and Pharmacovigilance of Herbal Medicines.},
journal = {Drug safety},
volume = {38},
number = {7},
pages = {611-620},
pmid = {26076652},
issn = {1179-1942},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/*classification/*genetics ; Drug-Related Side Effects and Adverse Reactions/*etiology ; Genetic Markers ; High-Throughput Nucleotide Sequencing ; Humans ; *Pharmacovigilance ; Plant Preparations/*adverse effects/*classification/standards ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Pharmacovigilance of herbal medicines relies on the product label information regarding the ingredients and the adherence to good manufacturing practices along the commercialisation chain. Several studies have shown that substitution of plant species occurs in herbal medicines, and this in turn poses a challenge to herbal pharmacovigilance as adverse reactions might be due to adulterated or added ingredients. Authentication of constituents in herbal medicines using analytical chemistry methods can help detect contaminants and toxins, but are often limited or incapable of detecting the source of the contamination. Recent developments in molecular plant identification using DNA sequence data enable accurate identification of plant species from herbal medicines using defined DNA markers. Identification of multiple constituent species from compound herbal medicines using amplicon metabarcoding enables verification of labelled ingredients and detection of substituted, adulterated and added species. DNA barcoding is proving to be a powerful method to assess species composition in herbal medicines and has the potential to be used as a standard method in herbal pharmacovigilance research of adverse reactions to specific products.},
}
@article {pmid26073745,
year = {2015},
author = {Wang, M and Duong, B and Fenniri, H and Su, M},
title = {Nanomaterial-based barcodes.},
journal = {Nanoscale},
volume = {7},
number = {26},
pages = {11240-11247},
doi = {10.1039/c5nr01948f},
pmid = {26073745},
issn = {2040-3372},
abstract = {Two-dimensional (2D) barcodes ubiquitously used to label, track and authenticate objects face increasing challenges of being damaged, altered and falsified. The past effort in nanomaterials has paved the way for controlled synthesis of nanomaterials with desired size, shape and function. Due to their extremely small sizes, these nanomaterials are promising as next generation barcodes that can be added into or mixed with objects of interest without being noticed. These barcodes can be effectively read owing to their physical properties by manufacturers, law enforcement and security agencies. Meanwhile, nanomaterial-based barcodes are hard to reverse-engineer or imitate without advanced knowledge and technical expertise. This review describes how nanomaterials can be used as barcodes, discusses advantages and limitations of each type of nanomaterial-based barcode, and points out ways that could help design and prepare better nanomaterial-based barcodes.},
}
@article {pmid26072670,
year = {2016},
author = {Failla, AJ and Vasquez, AA and Hudson, P and Fujimoto, M and Ram, JL},
title = {Morphological identification and COI barcodes of adult flies help determine species identities of chironomid larvae (Diptera, Chironomidae).},
journal = {Bulletin of entomological research},
volume = {106},
number = {1},
pages = {34-46},
doi = {10.1017/S0007485315000486},
pmid = {26072670},
issn = {1475-2670},
mesh = {Animals ; Chironomidae/anatomy &amp; histology/*classification/genetics/growth &amp; development ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics/metabolism ; Female ; Insect Proteins/genetics/metabolism ; Lakes ; Larva/anatomy &amp; histology/classification/genetics/growth &amp; development ; Male ; Michigan ; Molecular Sequence Data ; Ohio ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Establishing reliable methods for the identification of benthic chironomid communities is important due to their significant contribution to biomass, ecology and the aquatic food web. Immature larval specimens are more difficult to identify to species level by traditional morphological methods than their fully developed adult counterparts, and few keys are available to identify the larval species. In order to develop molecular criteria to identify species of chironomid larvae, larval and adult chironomids from Western Lake Erie were subjected to both molecular and morphological taxonomic analysis. Mitochondrial cytochrome c oxidase I (COI) barcode sequences of 33 adults that were identified to species level by morphological methods were grouped with COI sequences of 189 larvae in a neighbor-joining taxon-ID tree. Most of these larvae could be identified only to genus level by morphological taxonomy (only 22 of the 189 sequenced larvae could be identified to species level). The taxon-ID tree of larval sequences had 45 operational taxonomic units (OTUs, defined as clusters with >97% identity or individual sequences differing from nearest neighbors by >3%; supported by analysis of all larval pairwise differences), of which seven could be identified to species or 'species group' level by larval morphology. Reference sequences from the GenBank and BOLD databases assigned six larval OTUs with presumptive species level identifications and confirmed one previously assigned species level identification. Sequences from morphologically identified adults in the present study grouped with and further classified the identity of 13 larval OTUs. The use of morphological identification and subsequent DNA barcoding of adult chironomids proved to be beneficial in revealing possible species level identifications of larval specimens. Sequence data from this study also contribute to currently inadequate public databases relevant to the Great Lakes region, while the neighbor-joining analysis reported here describes the application and confirmation of a useful tool that can accelerate identification and bioassessment of chironomid communities.},
}
@article {pmid26071932,
year = {2015},
author = {Karremans, AP and Pupulin, F and Grimaldi, D and Beentjes, KK and Butôt, R and Fazzi, GE and Kaspers, K and Kruizinga, J and Roessingh, P and Smets, EF and Gravendeel, B},
title = {Pollination of Specklinia by nectar-feeding Drosophila: the first reported case of a deceptive syndrome employing aggregation pheromones in Orchidaceae.},
journal = {Annals of botany},
volume = {116},
number = {3},
pages = {437-455},
pmid = {26071932},
issn = {1095-8290},
mesh = {Animals ; Appetitive Behavior ; Drosophila/*physiology ; Female ; Male ; Orchidaceae/*physiology ; Pheromones/*metabolism ; Plant Nectar ; *Pollination ; Species Specificity ; },
abstract = {BACKGROUND AND AIMS: The first documented observation of pollination in Pleurothallidinae was that of Endrés, who noticed that the 'viscid sepals' of Specklinia endotrachys were visited by a 'small fly'. Chase would later identify the visiting flies as being members of the genus Drosophila. This study documents and describes how species of the S. endotrachys complex are pollinated by different Drosophila species.<br><br>METHODS: Specimens of Specklinia and Drosophila were collected in the field in Costa Rica and preserved in the JBL and L herbaria. Flies were photographed, filmed and observed for several days during a 2-year period and were identified by a combination of non-invasive DNA barcoding and anatomical surveys. Tissue samples of the sepals, petals and labellum of Specklinia species were observed and documented by SEM, LM and TEM. Electroantennogram experiments were carried out on Drosophila hydei using the known aggregation pheromones ethyl tiglate, methyl tiglate and isopropyl tiglate. Floral compounds were analysed by gas chromatography-mass spectometry using those same pheromones as standards.<br><br>KEY RESULTS: Flowers of S. endotrachys, S. pfavii, S. remotiflora and S. spectabilis are visited and pollinated by several different but closely related Drosophila species. The flies are arrested by aggregation pheromones, including ethyl tiglate, methyl tiglate and isopropyl tiglate, released by the flowers, and to which at least D. hydei is very sensitive. Visible nectar drops on the adaxial surface of sepals are secreted by nectar-secreting stomata, encouraging male and female Drosophila to linger on the flowers for several hours at a time. The flies frequently show courtship behaviour, occasionally copulating. Several different Drosophila species can be found on a single Specklinia species.<br><br>CONCLUSIONS: Species of the S. endotrachys group share a similar pollination syndrome. There seem to be no species-specific relationships between the orchids and the flies. It is not expected that Specklinia species will hybridize naturally as their populations do not overlap geographically. The combination of pheromone attraction and nectar feeding is likely to be a generalized pollination syndrome in Pleurothallidinae.},
}
@article {pmid26064656,
year = {2015},
author = {Oremus, M and Leqata, J and Baker, CS},
title = {Resumption of traditional drive hunting of dolphins in the Solomon Islands in 2013.},
journal = {Royal Society open science},
volume = {2},
number = {5},
pages = {140524},
pmid = {26064656},
issn = {2054-5703},
abstract = {The 'drive hunting' of dolphins has a long history in the Solomon Islands, specifically at the island of Malaita. In 2010, the most active village, Fanalei, suspended hunting in exchange for financial compensation from an international non-governmental organization but resumed hunting again in early 2013. Here, we report on a visit to Fanalei in March 2013 to document the species and number of dolphins killed in the renewed hunting. Detailed records for the 2013 hunting, up to the time of our visit, included at least 1500 pantropical spotted dolphins (Stenella attenuata), 159 spinner dolphins (Stenella longirostris) and 15 'bottlenose' dolphins, probably Tursiops truncatus. Molecular identification confirmed two of the species, pantropical spotted and spinner dolphins. A summary of all available records from 1976 to 2013 documented a minimum total of 15 454 dolphins killed by the Fanalei villagers alone. We also found the local price of a dolphin tooth had increased from about US$0.14 (SBD$1) in 2004 to about US$0.70 (SBD$5) in 2013. The large number of dolphins killed and the apparent incentive for future hunting offered by the increasing commercial value of teeth, highlight an urgent need to monitor hunts and assess the abundance and trends in local populations.},
}
@article {pmid26062316,
year = {2015},
author = {Prabhakar, A and Malapero, RJ and Gabriel, RA and Kaye, AD and Elhassan, AO and Nelson, ER and Bates, DW and Urman, RD},
title = {Medication errors in anesthesia.},
journal = {The Journal of medical practice management : MPM},
volume = {30},
number = {6 Spec No},
pages = {41-43},
pmid = {26062316},
issn = {8755-0229},
mesh = {Anesthesia/*standards ; Humans ; Medication Errors/*prevention &amp; control ; Patient Safety ; Safety Management/*methods ; },
abstract = {Medication errors represent one of the most common causes of morbidity and mortality in hospitalized patients. Anesthesia has specific medication-related risks; providers must administer many potent intravenous medications quickly, often with minimal to no supervision. Well-described reasons for medication administration errors in anesthesia include medication ampoules with similar appearance and packaging, clinician inattention, ineffective communication, fatigue, and haste. Technologies that are used widely in other parts of the hospital, such as barcoding, are a challenge to implement in anesthesia, and systemic approaches, including color-coding of syringe labels and barcoding technology of syringes, have been evaluated with mixed results. Emphasis should be placed on implementing forcing functions when possible, utilizing technology, standardization, and education about the need for awareness in specific situations. More studies need to be done to define the epidemiology of medication errors in anesthesia, and more importantly, to assess interventions for preventing them.},
}
@article {pmid26061692,
year = {2015},
author = {Kim, K and Lee, SC and Lee, J and Lee, HO and Joh, HJ and Kim, NH and Park, HS and Yang, TJ},
title = {Comprehensive Survey of Genetic Diversity in Chloroplast Genomes and 45S nrDNAs within Panax ginseng Species.},
journal = {PloS one},
volume = {10},
number = {6},
pages = {e0117159},
pmid = {26061692},
issn = {1932-6203},
mesh = {Chloroplasts/*genetics ; DNA, Plant/*genetics ; *Genetic Variation ; Genome, Plant ; INDEL Mutation ; Panax/*genetics ; Polymorphism, Single Nucleotide ; },
abstract = {We report complete sequences of chloroplast (cp) genome and 45S nuclear ribosomal DNA (45S nrDNA) for 11 Panax ginseng cultivars. We have obtained complete sequences of cp and 45S nrDNA, the representative barcoding target sequences for cytoplasm and nuclear genome, respectively, based on low coverage NGS sequence of each cultivar. The cp genomes sizes ranged from 156,241 to 156,425 bp and the major size variation was derived from differences in copy number of tandem repeats in the ycf1 gene and in the intergenic regions of rps16-trnUUG and rpl32-trnUAG. The complete 45S nrDNA unit sequences were 11,091 bp, representing a consensus single transcriptional unit with an intergenic spacer region. Comparative analysis of these sequences as well as those previously reported for three Chinese accessions identified very rare but unique polymorphism in the cp genome within P. ginseng cultivars. There were 12 intra-species polymorphisms (six SNPs and six InDels) among 14 cultivars. We also identified five SNPs from 45S nrDNA of 11 Korean ginseng cultivars. From the 17 unique informative polymorphic sites, we developed six reliable markers for analysis of ginseng diversity and cultivar authentication.},
}
@article {pmid26057013,
year = {2016},
author = {Kundu, S and Laskar, BA and Venkataraman, K and Banerjee, D and Kumar, V},
title = {DNA barcoding of Nilssonia congeners corroborates existence of wild N. nigricans in northeast India.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {4},
pages = {2753-2756},
doi = {10.3109/19401736.2015.1046176},
pmid = {26057013},
issn = {2470-1408},
mesh = {Animals ; Bayes Theorem ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Genome, Mitochondrial/genetics ; India ; Phylogeny ; Sequence Analysis, DNA ; Turtles/classification/*genetics ; },
abstract = {DNA barcode data of soft-shell turtles is limited in global DNA database while it is completely lacking for the highly debated species Nilssonia nigricans. We employed DNA barcoding technique to discriminate the species cluster for Nilssonia congeners, especially for the highly debated N. nigricans from different localities of northeast India. Sampling across the region included a few live specimens from wild, market sold carcass specimens, and a few dry carapaces meant for home decoration purpose. The generated sequences (621 bp of mtCOI) of dry carapaces showed 99-100% homology with the generated sequences of morphologically identified N. nigricans. The COI barcode sequences of N. nigricans (n = 12) showed 3.8% mean genetic divergence with N. hurum (n = 3), 10% with N. gangetica (n = 4), and 9.2% with N. formosa (GenBank sequences). Similarly, the mtCytb sequences of the dry carapace and live specimens of N. nigricans were 99-100% homologous with the conspecific database sequences and formed specific clusters. The inferred Neighbor-Joining (NJ), Maximum Likelihood (ML), and Bayesian (BA) phylogeny based on partial mtCOI gene efficiently discriminated all the congeners of Nilssonia into specific clusters and, therefore, it was helpful to detect the existence of N. nigricans.},
}
@article {pmid26057011,
year = {2016},
author = {Bhattacharya, M and Sharma, AR and Patra, BC and Sharma, G and Seo, EM and Nam, JS and Chakraborty, C and Lee, SS},
title = {DNA barcoding to fishes: current status and future directions.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {4},
pages = {2744-2752},
doi = {10.3109/19401736.2015.1046175},
pmid = {26057011},
issn = {2470-1408},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Fishes/classification/*genetics ; Genome, Mitochondrial/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {DNA barcoding appears to be a promising approach for taxonomic identification, characterization, and discovery of newer species, facilitating biodiversity studies. It helps researchers to appreciate genetic and evolutionary associations by collection of molecular, morphological, and distributional data. Fish DNA barcoding, based on the sequencing of a uniform area of Cytochrome C Oxidase type I (COI) gene, has received significant interest as an accurate tool for species identification, authentication, and phylogenetic analysis. The aim of this review article was to investigate recent global status, approaches, and future direction of DNA barcoding in fisheries sectors. We have tried to highlight its possible impacts, complications, and validation issues at species levels for biodiversity analysis. Moreover, an effort has been put forward to understand issues related to various marker genes associated with barcode process as primer sequences and have concluded barcode promotion as an indispensable tool of molecular biology for the development of taxonomic support systems.},
}
@article {pmid26055759,
year = {2015},
author = {Borgström, E and Redin, D and Lundin, S and Berglund, E and Andersson, AF and Ahmadian, A},
title = {Phasing of single DNA molecules by massively parallel barcoding.},
journal = {Nature communications},
volume = {6},
number = {},
pages = {7173},
pmid = {26055759},
issn = {2041-1723},
mesh = {DNA/*chemistry ; *DNA Barcoding, Taxonomic ; },
abstract = {High-throughput sequencing platforms mainly produce short-read data, resulting in a loss of phasing information for many of the genetic variants analysed. For certain applications, it is vital to know which variant alleles are connected to each individual DNA molecule. Here we demonstrate a method for massively parallel barcoding and phasing of single DNA molecules. First, a primer library with millions of uniquely barcoded beads is generated. When compartmentalized with single DNA molecules, the beads can be used to amplify and tag any target sequences of interest, enabling coupling of the biological information from multiple loci. We apply the assay to bacterial 16S sequencing and up to 94% of the hypothesized phasing events are shown to originate from single molecules. The method enables use of widely available short-read-sequencing platforms to study long single molecules within a complex sample, without losing phase information.},
}
@article {pmid26054647,
year = {2015},
author = {Uncu, AT and Uncu, AO and Frary, A and Doganlar, S},
title = {Authentication of Botanical Origin in Herbal Teas by Plastid Noncoding DNA Length Polymorphisms.},
journal = {Journal of agricultural and food chemistry},
volume = {63},
number = {25},
pages = {5920-5929},
doi = {10.1021/acs.jafc.5b01255},
pmid = {26054647},
issn = {1520-5118},
mesh = {DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; Electrophoresis, Capillary/*methods ; Plants/classification/*genetics ; Plastids/*genetics ; Polymerase Chain Reaction/*methods ; Polymorphism, Genetic ; Teas, Herbal/*analysis/classification ; },
abstract = {The aim of this study was to develop a DNA barcode assay to authenticate the botanical origin of herbal teas. To reach this aim, we tested the efficiency of a PCR-capillary electrophoresis (PCR-CE) approach on commercial herbal tea samples using two noncoding plastid barcodes, the trnL intron and the intergenic spacer between trnL and trnF. Barcode DNA length polymorphisms proved successful in authenticating the species origin of herbal teas. We verified the validity of our approach by sequencing species-specific barcode amplicons from herbal tea samples. Moreover, we displayed the utility of PCR-CE assays coupled with sequencing to identify the origin of undeclared plant material in herbal tea samples. The PCR-CE assays proposed in this work can be applied as routine tests for the verification of botanical origin in herbal teas and can be extended to authenticate all types of herbal foodstuffs.},
}
@article {pmid26051959,
year = {2015},
author = {Kurtzman, CP},
title = {Identification of food and beverage spoilage yeasts from DNA sequence analyses.},
journal = {International journal of food microbiology},
volume = {213},
number = {},
pages = {71-78},
doi = {10.1016/j.ijfoodmicro.2015.05.023},
pmid = {26051959},
issn = {1879-3460},
mesh = {Beverages/*microbiology ; DNA Fingerprinting ; *Food Microbiology ; Phylogeny ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA/methods ; Yeasts/*classification/genetics/isolation &amp; purification ; },
abstract = {Detection, identification and classification of yeasts have undergone major changes in the last decade and a half following application of gene sequence analyses and genome comparisons. Development of a database (barcode) of easily determined DNA sequences from domains 1 and 2 (D1/D2) of the nuclear large subunit rRNA gene and from ITS now permits many laboratories to identify species quickly and accurately, thus replacing the laborious and often inaccurate phenotypic tests previously used. Phylogenetic analysis of gene sequences has resulted in a major revision of yeast systematics resulting in redefinition of nearly all genera. This new understanding of species relationships has prompted a change of rules for naming and classifying yeasts and other fungi, and these new rules are presented in the recently implemented International Code of Nomenclature for algae, fungi, and plants (Melbourne Code). The use of molecular methods for species identification and the impact of Code changes on classification will be discussed, especially in the context of food and beverage spoilage yeasts.},
}
@article {pmid26048340,
year = {2015},
author = {Brassac, J and Blattner, FR},
title = {Species-Level Phylogeny and Polyploid Relationships in Hordeum (Poaceae) Inferred by Next-Generation Sequencing and In Silico Cloning of Multiple Nuclear Loci.},
journal = {Systematic biology},
volume = {64},
number = {5},
pages = {792-808},
pmid = {26048340},
issn = {1076-836X},
mesh = {Classification/*methods ; DNA, Chloroplast/genetics ; Genes, Plant/genetics ; High-Throughput Nucleotide Sequencing ; Hordeum/*classification/*genetics ; *Phylogeny ; *Polyploidy ; },
abstract = {Polyploidization is an important speciation mechanism in the barley genus Hordeum. To analyze evolutionary changes after allopolyploidization, knowledge of parental relationships is essential. One chloroplast and 12 nuclear single-copy loci were amplified by polymerase chain reaction (PCR) in all Hordeum plus six out-group species. Amplicons from each of 96 individuals were pooled, sheared, labeled with individual-specific barcodes and sequenced in a single run on a 454 platform. Reference sequences were obtained by cloning and Sanger sequencing of all loci for nine supplementary individuals. The 454 reads were assembled into contigs representing the 13 loci and, for polyploids, also homoeologues. Phylogenetic analyses were conducted for all loci separately and for a concatenated data matrix of all loci. For diploid taxa, a Bayesian concordance analysis and a coalescent-based dated species tree was inferred from all gene trees. Chloroplast matK was used to determine the maternal parent in allopolyploid taxa. The relative performance of different multilocus analyses in the presence of incomplete lineage sorting and hybridization was also assessed. The resulting multilocus phylogeny reveals for the first time species phylogeny and progenitor-derivative relationships of all di- and polyploid Hordeum taxa within a single analysis. Our study proves that it is possible to obtain a multilocus species-level phylogeny for di- and polyploid taxa by combining PCR with next-generation sequencing, without cloning and without creating a heavy load of sequence data.},
}
@article {pmid26047568,
year = {2015},
author = {Crous, PW and Hawksworth, DL and Wingfield, MJ},
title = {Identifying and naming plant-pathogenic fungi: past, present, and future.},
journal = {Annual review of phytopathology},
volume = {53},
number = {},
pages = {247-267},
doi = {10.1146/annurev-phyto-080614-120245},
pmid = {26047568},
issn = {1545-2107},
mesh = {Biodiversity ; Crops, Agricultural/*microbiology ; Fungi/*classification/physiology ; Genomics ; Plant Diseases/classification/*microbiology ; *Plant Pathology ; },
abstract = {Scientific names are crucial in communicating knowledge about fungi. In plant pathology, they link information regarding the biology, host range, distribution, and potential risk. Our understanding of fungal biodiversity and fungal systematics has undergone an exponential leap, incorporating genomics, web-based systems, and DNA data for rapid identification to link species to metadata. The impact of our ability to recognize hitherto unknown organisms on plant pathology and trade is enormous and continues to grow. Major challenges for phytomycology are intertwined with the Genera of Fungi project, which adds DNA barcodes to known biodiversity and corrects the application of old, established names via epi- or neotypification. Implementing the one fungus-one name system and linking names to validated type specimens, cultures, and reference sequences will provide the foundation on which the future of plant pathology and the communication of names of plant pathogens will rest.},
}
@article {pmid26047179,
year = {2015},
author = {Gutiérrez-López, R and Martínez-de la Puente, J and Gangoso, L and Soriguer, RC and Figuerola, J},
title = {Comparison of manual and semi-automatic DNA extraction protocols for the barcoding characterization of hematophagous louse flies (Diptera: Hippoboscidae).},
journal = {Journal of vector ecology : journal of the Society for Vector Ecology},
volume = {40},
number = {1},
pages = {11-15},
doi = {10.1111/jvec.12127},
pmid = {26047179},
issn = {1948-7134},
mesh = {Animals ; Automation ; Biochemistry/methods ; Chloroform/chemistry ; DNA/*isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Diptera/*genetics ; Electron Transport Complex IV/genetics ; Extremities/physiology ; Pentanols/chemistry ; },
abstract = {The barcoding of life initiative provides a universal molecular tool to distinguish animal species based on the amplification and sequencing of a fragment of the subunit 1 of the cytochrome oxidase (COI) gene. Obtaining good quality DNA for barcoding purposes is a limiting factor, especially in studies conducted on small-sized samples or those requiring the maintenance of the organism as a voucher. In this study, we compared the number of positive amplifications and the quality of the sequences obtained using DNA extraction methods that also differ in their economic costs and time requirements and we applied them for the genetic characterization of louse flies. Four DNA extraction methods were studied: chloroform/isoamyl alcohol, HotShot procedure, Qiagen DNeasy(®) Tissue and Blood Kit and DNA Kit Maxwell(®) 16LEV. All the louse flies were morphologically identified as Ornithophila gestroi and a single COI-based haplotype was identified. The number of positive amplifications did not differ significantly among DNA extraction procedures. However, the quality of the sequences was significantly lower for the case of the chloroform/isoamyl alcohol procedure with respect to the rest of methods tested here. These results may be useful for the genetic characterization of louse flies, leaving most of the remaining insect as a voucher.},
}
@article {pmid26041191,
year = {2015},
author = {Bhau, BS and Gogoi, G and Baruah, D and Ahmed, R and Hazarika, G and Ghosh, S and Borah, B and Gogoi, B and Sarmah, DK and Nath, SC and Wann, SB},
title = {Development of an effective and efficient DNA isolation method for Cinnamomum species.},
journal = {Food chemistry},
volume = {188},
number = {},
pages = {264-270},
doi = {10.1016/j.foodchem.2015.05.004},
pmid = {26041191},
issn = {1873-7072},
mesh = {Cinnamomum/*chemistry ; DNA Primers ; DNA, Plant/*isolation &amp; purification ; Plant Leaves/chemistry ; Polyphenols/analysis ; Polysaccharides/analysis ; Random Amplified Polymorphic DNA Technique/*methods ; },
abstract = {Different species of Cinnamomum are rich in polysaccharide's and secondary metabolites, which hinder the process of DNA extraction. High quality DNA is the pre-requisite for any molecular biology study. In this paper we report a modified method for high quality and quantity of DNA extraction from both lyophilized and non-lyophilized leaf samples. Protocol reported differs from the CTAB procedure by addition of higher concentration of salt and activated charcoal to remove the polysaccharides and polyphenols. Wide utility of the modified protocol was proved by DNA extraction from different woody species and 4 Cinnamomum species. Therefore, this protocol has also been validated in different species of plants containing high levels of polyphenols and polysaccharides. The extracted DNA showed perfect amplification when subjected to RAPD, restriction digestion and amplification with DNA barcoding primers. The DNA extraction protocol is reproducible and can be applied for any plant molecular biology study.},
}
@article {pmid26040695,
year = {2015},
author = {Qin, J and Zhang, Y and Zhou, X and Kong, X and Wei, S and Ward, RD and Zhang, AB},
title = {Mitochondrial phylogenomics and genetic relationships of closely related pine moth (Lasiocampidae: Dendrolimus) species in China, using whole mitochondrial genomes.},
journal = {BMC genomics},
volume = {16},
number = {1},
pages = {428},
pmid = {26040695},
issn = {1471-2164},
mesh = {Animals ; Base Pair Mismatch ; China ; Codon, Initiator/genetics ; DNA, Mitochondrial/analysis/isolation &amp; purification ; Evolution, Molecular ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Mitochondrial Proteins/genetics/metabolism ; Moths/classification/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; RNA, Transfer/genetics/metabolism ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Pine moths (Lepidoptera; Bombycoidea; Lasiocampidae: Dendrolimus spp.) are among the most serious insect pests of forests, especially in southern China. Although COI barcodes (a standardized portion of the mitochondrial cytochrome c oxidase subunit I gene) can distinguish some members of this genus, the evolutionary relationships of the three morphospecies Dendrolimus punctatus, D. tabulaeformis and D. spectabilis have remained largely unresolved. We sequenced whole mitochondrial genomes of eight specimens, including D. punctatus wenshanensis. This is an unambiguous subspecies of D. punctatus, and was used as a reference for inferring the relationships of the other two morphospecies of the D. punctatus complex. We constructed phylogenetic trees from this data, including twelve published mitochondrial genomes of other Bombycoidea species, and examined the relationships of the Dendrolimus taxa using these trees and the genomic features of the mitochondrial genome.<br><br>RESULTS: The eight fully sequenced mitochondrial genomes from the three morphospecies displayed similar genome structures as other Bombycoidea species in terms of gene content, base composition, level of overall AT-bias and codon usage. However, the Dendrolimus genomes possess a unique feature in the large ribosomal 16S RNA subunits (rrnL), which are more than 60 bp longer than other members of the superfamily and have a higher AC proportion. The eight mitochondrial genomes of Dendrolimus were highly conservative in many aspects, for example with identical stop codons and overlapping regions. But there were many differences in start codons, intergenic spacers, and numbers of mismatched base pairs of tRNA (transfer RNA genes). Our results, based on phylogenetic trees, genetic distances, species delimitation and genomic features (such as intergenic spacers) of the mitochondrial genome, indicated that D. tabulaeformis is as close to D. punctatus as is D. punctatus wenshanensis, whereas D. spectabilis evolved independently from D. tabulaeformis and D. punctatus. Whole mitochondrial DNA phylogenies showed that D. spectabilis formed a well-supported monophyletic clade, with a clear species boundary separating it from the other congeners examined here. However, D. tabulaeformis often clustered with D. punctatus and with the subspecies D. punctatus wenshanensis. Genetic distance analyses showed that the distance between D. tabulaeformis and D. punctatus is generally less than the intraspecific distance of D. punctatus and its subspecies D. punctatus wenshanensis. In the species delimitation analysis of Poisson Tree Processes (PTP), D. tabulaeformis, D. punctatus and D. punctatus wenshanensis clustered into a putative species separated from D. spectabilis. In comparison with D. spectabilis, D. tabulaeformis and D. punctatus also exhibit a similar structure in intergenic spacer characterization. These different types of evidence suggest that D. tabulaeformis is very close to D. punctatus and its subspecies D. punctatus wenshanensis, and is likely to be another subspecies of D. punctatus.<br><br>CONCLUSIONS: Whole mitochondrial genomes possess relatively rich genetic information compared with the traditional use of single or multiple genes for phylogenetic purposes. They can be used to better infer phylogenetic relationships and degrees of relatedness of taxonomic groups, at least from the aspect of maternal lineage: caution should be taken due to the maternal-only inheritance of this genome. Our results indicate that D. spectabilis is an independent lineage, while D. tabulaeformis shows an extremely close relationship to D. punctatus.},
}
@article {pmid26025701,
year = {2015},
author = {Nakano, A and Honda, J},
title = {Use of DNA sequences to identify forensically important fly species and their distribution in the coastal region of Central California.},
journal = {Forensic science international},
volume = {253},
number = {},
pages = {1-13},
doi = {10.1016/j.forsciint.2015.05.001},
pmid = {26025701},
issn = {1872-6283},
mesh = {Animals ; California ; Diptera/*genetics ; Ecosystem ; Electron Transport Complex IV/genetics ; Entomology ; Forensic Sciences ; Microclimate ; Polymerase Chain Reaction ; *Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Forensic entomology has gained prominence in recent years, as improvements in DNA technology and molecular methods have allowed insect and other arthropod evidence to become increasingly useful in criminal and civil investigations. However, comprehensive faunal inventories are still needed, including cataloging local DNA sequences for forensically significant Diptera. This multi-year fly-trapping study was built upon and expanded a previous survey of these flies in Santa Clara County, including the addition of genetic barcoding data from collected species of flies. Flies from the families Calliphoridae, Sarcophagidae, and Muscidae were trapped in meat-baited traps set in a variety of locations throughout the county. Flies were identified using morphological features and confirmed by molecular analysis. A total of 16 calliphorid species, 11 sarcophagid species, and four muscid species were collected and differentiated. This study found more species of flies than previous area surveys and established new county records for two calliphorid species: Cynomya cadaverina and Chrysomya rufifacies. Differences were found in fly fauna in different areas of the county, indicating the importance of microclimates in the distribution of these flies. Molecular analysis supported the use of DNA barcoding as an effective method of identifying cryptic fly species.},
}
@article {pmid26025426,
year = {2015},
author = {Leavitt, DH and Starrett, J and Westphal, MF and Hedin, M},
title = {Multilocus sequence data reveal dozens of putative cryptic species in a radiation of endemic Californian mygalomorph spiders (Araneae, Mygalomorphae, Nemesiidae).},
journal = {Molecular phylogenetics and evolution},
volume = {91},
number = {},
pages = {56-67},
doi = {10.1016/j.ympev.2015.05.016},
pmid = {26025426},
issn = {1095-9513},
mesh = {Animals ; California ; Female ; Genes, Mitochondrial ; Male ; Multilocus Sequence Typing ; Phylogeny ; Spiders/anatomy &amp; histology/*classification/genetics ; Sympatry ; },
abstract = {We use mitochondrial and multi-locus nuclear DNA sequence data to infer both species boundaries and species relationships within California nemesiid spiders. Higher-level phylogenetic data show that the California radiation is monophyletic and distantly related to European members of the genus Brachythele. As such, we consider all California nemesiid taxa to belong to the genus Calisoga Chamberlin, 1937. Rather than find support for one or two taxa as previously hypothesized, genetic data reveal Calisoga to be a species-rich radiation of spiders, including perhaps dozens of species. This conclusion is supported by multiple mitochondrial barcoding analyses, and also independent analyses of nuclear data that reveal general genealogical congruence. We discovered three instances of sympatry, and genetic data indicate reproductive isolation when in sympatry. An examination of female reproductive morphology does not reveal species-specific characters, and observed male morphological differences for a subset of putative species are subtle. Our coalescent species tree analysis of putative species lays the groundwork for future research on the taxonomy and biogeographic history of this remarkable endemic radiation.},
}
@article {pmid26024888,
year = {2015},
author = {Singtonat, S and Osathanunkul, M},
title = {Fast and reliable detection of toxic Crotalaria spectabilis Roth. in Thunbergia laurifolia Lindl. herbal products using DNA barcoding coupled with HRM analysis.},
journal = {BMC complementary and alternative medicine},
volume = {15},
number = {},
pages = {162},
pmid = {26024888},
issn = {1472-6882},
mesh = {Acanthaceae/*genetics ; Crotalaria/*genetics ; DNA Barcoding, Taxonomic/*methods ; *DNA, Plant ; *Drug Contamination ; Humans ; Plant Preparations/*analysis ; Plants, Medicinal/*genetics ; },
abstract = {BACKGROUND: Nowadays, medicinal plants are used as a popular alternative to synthetic drugs. Many medicinal plant products have now been commercialized throughout various markets. These products are commonly sold in processed or modified forms such as powders, dried material and capsules, making it almost impossible to accurately identify the constituent species. The herbal plant known as 'Rang Chuet' in Thai has been widely used as remedies for various ailments. However, two medicinal plants species, Thunbergia laurifolia and Crotalaria spectabilis share this name. Duo to the similarity in nomenclature, the commercial products labeled as 'Rang Chuet' could be any of them. Recently, the evidence of hepatotoxic effects linked to use of C. spectabilis were reported and is now seriously concern. There is a need to find an approach that could help with species identification of these herbal products to ensure the safety and efficacy of the herbal drug.<br><br>METHODS: Here DNA barcoding was used in combination with High Resolution Melting analysis (Bar-HRM) to authenticate T. laurifolia species. Four DNA barcodes including matK, rbcL, rpoC and trnL were selected for use in primers design for HRM analysis to produce standard melting profiles of the selected species. Commercial products labeled as 'Rang Chuet' were purchased from Thai markets and authentication by HRM analyses.<br><br>RESULTS: Melting data from the HRM assay using the designed primers showed that the two 'Rang Chuet' species could easily be distinguished from each other. The melting profiles of the all four region amplicons of each species are clearly separated in all three replicates. The method was then applied to authenticate products in powdered form. HRM curves of all ten test samples indicated that three of the tested products did not only contain the T. laurifolia species.<br><br>CONCLUSION: The herbal drugs derived from different plants must be distinguished from each other even they share the same vernacular name. The Bar-HRM method developed here proved useful in the identification and authentication of herbal species in processed samples. In the future, species authentication through Bar-HRM could be used to promote consumer trust, as well as raising the quality of herbal products.},
}
@article {pmid26023287,
year = {2015},
author = {Gutiérrez-Arellano, D and Gutiérrez-Arellano, CR and Zaldívar-Riverón, A},
title = {DNA Barcoding of the parasitoid wasp subfamily Doryctinae (Hymenoptera: Braconidae) from Chamela, Mexico.},
journal = {Biodiversity data journal},
volume = {},
number = {3},
pages = {e5109},
pmid = {26023287},
issn = {1314-2828},
abstract = {Background and aims. The Doryctinae is a considerably diverse, poorly studied group of parasitoid wasps and one of the most diverse subfamilies within Braconidae. Taxonomic knowledge of this group remains highly incomplete, specially in the tropics. In Mexico, it has been reported as the subfamily with the highest number of recorded genera. A preliminary Barcoding study carried out in the Chamela region, located near the Mexican pacific coast in Jalisco, identified 185 barcoding species of Dorytinae assigned to 19 identified doryctine genera. This work updates the later study, representing a three years effort to assess the species richness of this subfamily for the Chamela region. Materials and methods. Ten collecting field trips of 5 to 10 days each were carried out from June 2009 to May 2011. A 2% divergence criterion using the BIN system implemented in BOLD was followed in order to establish species boundaries among the specimens that were collected. Results and conclusions. A total of 961 specimens were collected, from which 883 COI sequences were obtained. The sequences generated corresponded to 289 barcoding species and 30 identified genera. The most speciose genera were Heterospilus Haliday (170 spp.), Ecphylus Förster (19 spp.), Allorhogas Gahan (15 spp.) and Callihormius Ashmead (14 spp.). Addition of previously collected material increased the diversity of the subfamily in the region to 34 genera and 290 species. Paraphyly of Heterospilus with respect to Neoheterospilus and Heterospathius was again recovered. Twenty new species and two new genera (Sabinita Belokobylskij, Zaldívar-Riverón et Martínez, Ficobolus Martínez, Belokobylskij et Zaldívar-Riverón) have been described so far from the material collected in this work.},
}
@article {pmid26021602,
year = {2015},
author = {Leng, Y and Sun, K and Chen, X and Li, W},
title = {Suspension arrays based on nanoparticle-encoded microspheres for high-throughput multiplexed detection.},
journal = {Chemical Society reviews},
volume = {44},
number = {15},
pages = {5552-5595},
pmid = {26021602},
issn = {1460-4744},
support = {Z99 EB999999//Intramural NIH HHS/United States ; ZIA EB000073-06//Intramural NIH HHS/United States ; },
mesh = {Biotechnology ; *High-Throughput Screening Assays ; *Microspheres ; *Nanoparticles ; Nanotechnology ; Spectrum Analysis ; },
abstract = {Spectrometrically or optically encoded microsphere based suspension array technology (SAT) is applicable to the high-throughput, simultaneous detection of multiple analytes within a small, single sample volume. Thanks to the rapid development of nanotechnology, tremendous progress has been made in the multiplexed detecting capability, sensitivity, and photostability of suspension arrays. In this review, we first focus on the current stock of nanoparticle-based barcodes as well as the manufacturing technologies required for their production. We then move on to discuss all existing barcode-based bioanalysis patterns, including the various labels used in suspension arrays, label-free platforms, signal amplification methods, and fluorescence resonance energy transfer (FRET)-based platforms. We then introduce automatic platforms for suspension arrays that use superparamagnetic nanoparticle-based microspheres. Finally, we summarize the current challenges and their proposed solutions, which are centered on improving encoding capacities, alternative probe possibilities, nonspecificity suppression, directional immobilization, and "point of care" platforms. Throughout this review, we aim to provide a comprehensive guide for the design of suspension arrays, with the goal of improving their performance in areas such as multiplexing capacity, throughput, sensitivity, and cost effectiveness. We hope that our summary on the state-of-the-art development of these arrays, our commentary on future challenges, and some proposed avenues for further advances will help drive the development of suspension array technology and its related fields.},
}
@article {pmid26019672,
year = {2015},
author = {Huemer, P and Mutanen, M},
title = {Alpha taxonomy of the genus Kessleria Nowicki, 1864, revisited in light of DNA-barcoding (Lepidoptera, Yponomeutidae).},
journal = {ZooKeys},
volume = {},
number = {503},
pages = {89-133},
pmid = {26019672},
issn = {1313-2989},
abstract = {The taxonomy of Kessleria, a highly specialized montane genus of Yponomeutidae with larval host restriction to Saxifragaceae and Celastraceae (Saxifraga spp. - subgenus Kessleria; Saxifraga spp. and Parnassia spp. - subgenus Hofmannia), is revised based on external morphology, genitalia and DNA barcodes. An integrative taxonomic approach supports the existence of 29 species in Europe (the two known species from Asia and North America are not treated herein). A full 658 bp fragment of COI was obtained from 135 specimens representing 24 species, a further seven sequences are >560 bp. Five new species are described: Kessleriacottiensis sp. n. (Prov. Torino, Italy; Dep. Hautes Alpes, France), Kessleriadimorpha sp. n. (Dep. Alpes-de-Haute-Provence, France), Kessleriaalpmaritimae sp. n. (Dep. Alpes-Maritimes, France), Kessleriaapenninica sp. n. (Prov. Rieti, Prov. L´Aquila, Italy), and Kessleriaorobiae sp. n. (Prov. Bergamo, Italy).},
}
@article {pmid26019671,
year = {2015},
author = {Janion-Scheepers, C and Deharveng, L and Bedos, A and Chown, SL},
title = {Updated list of Collembola species currently recorded from South Africa.},
journal = {ZooKeys},
volume = {},
number = {503},
pages = {55-88},
pmid = {26019671},
issn = {1313-2989},
abstract = {Understanding the abundance and richness of species is one of the most fundamental steps in effecting their conservation. Despite global recognition of the significance of the below-ground component of diversity for ecosystem functioning, the soil remains a poorly studied terrestrial ecosystem. In South Africa, knowledge is increasing for a variety of soil faunal groups, but many still remain poorly understood. We have started to address this gap in the knowledge of South African soil biodiversity by focusing on the Collembola in an integrated project that encompasses systematics, barcoding and ecological assessments. Here we provide an updated list of the Collembola species from South Africa. A total of 124 species from 61 genera and 17 families has been recorded, of which 75 are considered endemic, 24 widespread, and 25 introduced. This total number of species excludes the 36 species we consider to be dubious. From the published data, Collembola species richness is high compared to other African countries, but low compared to European countries. This is largely a consequence of poor sampling in the African region, as our discovery of many new species in South Africa demonstrates. Our analyses also show that much ongoing work will be required before a reasonably comprehensive and spatially explicit picture of South Africa's springtail fauna can be provided, which may well exceed 1000 species. Such work will be necessary to help South Africa meet its commitments to biodiversity conservation, especially in the context of the 2020 Aichi targets of the Convention on Biological Diversity.},
}
@article {pmid26017924,
year = {2015},
author = {Kang, H and Jeong, S and Koh, Y and Geun Cha, M and Yang, JK and Kyeong, S and Kim, J and Kwak, SY and Chang, HJ and Lee, H and Jeong, C and Kim, JH and Jun, BH and Kim, YK and Hong Jeong, D and Lee, YS},
title = {Direct identification of on-bead peptides using surface-enhanced Raman spectroscopic barcoding system for high-throughput bioanalysis.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {10144},
pmid = {26017924},
issn = {2045-2322},
mesh = {Algorithms ; Ligands ; Nanoparticles/chemistry ; Peptide Library ; Peptides/*analysis/chemistry/metabolism ; Protein Binding ; Silicon Dioxide/chemistry ; *Spectrum Analysis, Raman ; },
abstract = {Recently, preparation and screening of compound libraries remain one of the most challenging tasks in drug discovery, biomarker detection, and biomolecular profiling processes. So far, several distinct encoding/decoding methods such as chemical encoding, graphical encoding, and optical encoding have been reported to identify those libraries. In this paper, a simple and efficient surface-enhanced Raman spectroscopic (SERS) barcoding method using highly sensitive SERS nanoparticles (SERS ID) is presented. The 44 kinds of SERS IDs were able to generate simple codes and could possibly generate more than one million kinds of codes by incorporating combinations of different SERS IDs. The barcoding method exhibited high stability and reliability under bioassay conditions. The SERS ID encoding based screening platform can identify the peptide ligand on the bead and also quantify its binding affinity for specific protein. We believe that our SERS barcoding technology is a promising method in the screening of one-bead-one-compound (OBOC) libraries for drug discovery.},
}
@article {pmid26017046,
year = {2016},
author = {Yang, M and Zhai, Q and Yang, Z and Zhang, Y},
title = {DNA barcoding Satyrine butterflies (Lepidoptera: Nymphalidae) in China.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {4},
pages = {2523-2528},
doi = {10.3109/19401736.2015.1038788},
pmid = {26017046},
issn = {2470-1408},
mesh = {Animals ; Aspartate Aminotransferase, Mitochondrial/*genetics ; Biodiversity ; Butterflies/classification/*genetics ; China ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*genetics ; Genetic Variation/genetics ; Sequence Analysis, DNA ; },
abstract = {We investigated the effectiveness of the standard 648 bp mitochondrial COI barcode region in discriminating among Satyrine species from China. A total of 214 COI sequences were obtained from 90 species, including 34 species that have never been barcoded. Analyses of genetic divergence show that the mean interspecific genetic divergence is about 16-fold higher than within species, and little overlap occurs between them. Neighbour-joining (NJ) analyses showed that 48 of the 50 species with two or more individuals, including two cases with deep intraspecific divergence (>3%), are monophyletic. Furthermore, when our sequences are combined with the conspecific sequences sampled from distantly geographic regions, the "barcoding gap" still exists, and all related species are recovered to be monophyletic in NJ analysis. Our study demonstrates that COI barcoding is effective in discriminating among the satyrine species of China, and provides a reference library for their future molecular identification.},
}
@article {pmid26016873,
year = {2016},
author = {Jennings, WB and Wogel, H and Bilate, M and Salles, Rde O and Buckup, PA},
title = {DNA barcoding reveals species level divergence between populations of the microhylid frog genus Arcovomer (Anura: Microhylidae) in the Atlantic Rainforest of southeastern Brazil.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3415-3422},
doi = {10.3109/19401736.2015.1022731},
pmid = {26016873},
issn = {2470-1408},
mesh = {Animals ; Anura/classification/*genetics ; DNA Barcoding, Taxonomic/standards ; Electron Transport Complex IV/genetics ; *Genetic Speciation ; Genome, Mitochondrial ; Phylogeny ; Phylogeography ; *Polymorphism, Genetic ; Reproductive Isolation ; },
abstract = {The microhylid frogs belonging to the genus Arcovomer have been reported from lowland Atlantic Rainforest in the Brazilian states of Espírito Santo, Rio de Janeiro, and São Paulo. Here, we use DNA barcoding to assess levels of genetic divergence between apparently isolated populations in Espírito Santo and Rio de Janeiro. Our mtDNA data consisting of cytochrome oxidase subunit I (COI) nucleotide sequences reveals 13.2% uncorrected and 30.4% TIM2 + I + Γ corrected genetic divergences between these two populations. This level of divergence exceeds the suggested 10% uncorrected divergence threshold for elevating amphibian populations to candidate species using this marker, which implies that the Espírito Santo population is a species distinct from Arcovomer passarellii. Calibration of our model-corrected sequence divergence estimates suggests that the time of population divergence falls between 12 and 29 million years ago.},
}
@article {pmid26014206,
year = {2015},
author = {Schwentner, M and Bosch, TC},
title = {Revisiting the age, evolutionary history and species level diversity of the genus Hydra (Cnidaria: Hydrozoa).},
journal = {Molecular phylogenetics and evolution},
volume = {91},
number = {},
pages = {41-55},
doi = {10.1016/j.ympev.2015.05.013},
pmid = {26014206},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Biodiversity ; Biological Evolution ; DNA, Mitochondrial/chemistry ; Hydra/*classification/genetics ; Phylogeny ; },
abstract = {The genus Hydra has long served as a model system in comparative immunology, developmental and evolutionary biology. Despite its relevance for fundamental research, Hydra's evolutionary origins and species level diversity are not well understood. Detailed previous studies using molecular techniques identified several clades within Hydra, but how these are related to described species remained largely an open question. In the present study, we compiled all published sequence data for three mitochondrial and nuclear genes (COI, 16S and ITS), complemented these with some new sequence data and delimited main genetic lineages (=hypothetical species) objectively by employing two DNA barcoding approaches. Conclusions on the species status of these main lineages were based on inferences of reproductive isolation. Relevant divergence times within Hydra were estimated based on relaxed molecular clock analyses with four genes (COI, 16S, EF1α and 28S) and four cnidarians fossil calibration points All in all, 28 main lineages could be delimited, many more than anticipated from earlier studies. Because allopatric distributions were common, inferences of reproductive isolation often remained ambiguous but reproductive isolation was rarely refuted. Our results support three major conclusions which are central for Hydra research: (1) species level diversity was underestimated by molecular studies; (2) species affiliations of several crucial 'workhorses' of Hydra evolutionary research were wrong and (3) crown group Hydra originated ∼200mya. Our results demonstrate that the taxonomy of Hydra requires a thorough revision and that evolutionary studies need to take this into account when interspecific comparisons are made. Hydra originated on Pangea. Three of four extant groups evolved ∼70mya ago, possibly on the northern landmass of Laurasia. Consequently, Hydra's cosmopolitan distribution is the result of transcontinental and transoceanic dispersal.},
}
@article {pmid26011532,
year = {2015},
author = {Sunshine, AB and Payen, C and Ong, GT and Liachko, I and Tan, KM and Dunham, MJ},
title = {The fitness consequences of aneuploidy are driven by condition-dependent gene effects.},
journal = {PLoS biology},
volume = {13},
number = {5},
pages = {e1002155},
pmid = {26011532},
issn = {1545-7885},
support = {F30 CA165440/CA/NCI NIH HHS/United States ; R01 GM094306/GM/NIGMS NIH HHS/United States ; T32 AG000057/AG/NIA NIH HHS/United States ; T32 GM007266/GM/NIGMS NIH HHS/United States ; },
mesh = {*Aneuploidy ; *Biological Evolution ; Gene Amplification ; *Genetic Fitness ; Genetic Pleiotropy ; Saccharomyces cerevisiae ; *Telomere ; },
abstract = {Aneuploidy is a hallmark of tumor cells, and yet the precise relationship between aneuploidy and a cell's proliferative ability, or cellular fitness, has remained elusive. In this study, we have combined a detailed analysis of aneuploid clones isolated from laboratory-evolved populations of Saccharomyces cerevisiae with a systematic, genome-wide screen for the fitness effects of telomeric amplifications to address the relationship between aneuploidy and cellular fitness. We found that aneuploid clones rise to high population frequencies in nutrient-limited evolution experiments and show increased fitness relative to wild type. Direct competition experiments confirmed that three out of four aneuploid events isolated from evolved populations were themselves sufficient to improve fitness. To expand the scope beyond this small number of exemplars, we created a genome-wide collection of >1,800 diploid yeast strains, each containing a different telomeric amplicon (Tamp), ranging in size from 0.4 to 1,000 kb. Using pooled competition experiments in nutrient-limited chemostats followed by high-throughput sequencing of strain-identifying barcodes, we determined the fitness effects of these >1,800 Tamps under three different conditions. Our data revealed that the fitness landscape explored by telomeric amplifications is much broader than that explored by single-gene amplifications. As also observed in the evolved clones, we found the fitness effects of most Tamps to be condition specific, with a minority showing common effects in all three conditions. By integrating our data with previous work that examined the fitness effects of single-gene amplifications genome-wide, we found that a small number of genes within each Tamp are centrally responsible for each Tamp's fitness effects. Our genome-wide Tamp screen confirmed that telomeric amplifications identified in laboratory-evolved populations generally increased fitness. Our results show that Tamps are mutations that produce large, typically condition-dependent changes in fitness that are important drivers of increased fitness in asexually evolving populations.},
}
@article {pmid26011474,
year = {2015},
author = {Osathanunkul, M and Madesis, P and de Boer, H},
title = {Bar-HRM for Authentication of Plant-Based Medicines: Evaluation of Three Medicinal Products Derived from Acanthaceae Species.},
journal = {PloS one},
volume = {10},
number = {5},
pages = {e0128476},
pmid = {26011474},
issn = {1932-6203},
mesh = {Acanthaceae/*classification/genetics ; Consumer Product Safety ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; Plants, Medicinal/*classification/genetics ; Thailand ; },
abstract = {Medicinal plants are used as a popular alternative to synthetic drugs, both in developed and developing countries. The economic importance of the herbal and natural supplement industry is increasing every year. As the herbal industry grows, consumer safety is one issue that cannot be overlooked. Herbal products in Thai local markets are commonly sold without packaging or labels. Plant powders are stored in large bags or boxes, and therefore buying local herbal products poses a high risk of acquiring counterfeited, substituted and/or adulterated products. Due to these issues, a reliable method to authenticate products is needed. Here DNA barcoding was used in combination with High Resolution Melting analysis (Bar-HRM) to authenticate three medicinal Acanthaceae species (Acanthus ebracteatus, Andrographis paniculata and Rhinacanthus nasutus) commonly used in Thailand. The rbcL barcode was selected for use in primers design for HRM analysis to produce standard melting profiles of the selected species. Melting data from the HRM assay using the designed rbcL primers showed that the three chosen species could be distinguished from each other. HRM curves of all fifteen test samples indicated that three of tested products did not contain the indicated species. Two closely related species (A. paniculata and R. nasutus), which have a high level of morphological similarity, were interchanged with one another in three tested products. Incorrect information on packaging and labels of the tested herbal products was the cause of the results shown here. Morphological similarity among the species of interest also hindered the collection process. The Bar-HRM method developed here proved useful in aiding in the identification and authentication of herbal species in processed samples. In the future, species authentication through Bar-HRM could be used to promote consumer trust, as well as raising the quality of herbal products.},
}
@article {pmid26010570,
year = {2015},
author = {Xiong, F and Obholzer, ND and Noche, RR and Megason, SG},
title = {Multibow: digital spectral barcodes for cell tracing.},
journal = {PloS one},
volume = {10},
number = {5},
pages = {e0127822},
pmid = {26010570},
issn = {1932-6203},
support = {R01 DC010791/DC/NIDCD NIH HHS/United States ; },
mesh = {Animals ; Animals, Genetically Modified ; Cells/*cytology ; Cloning, Molecular ; Developmental Biology/*methods ; Fluorescent Antibody Technique/*methods ; Image Processing, Computer-Assisted ; Microscopy, Confocal ; Molecular Typing/*methods ; Specimen Handling/*methods ; Staining and Labeling/methods ; Zebrafish ; },
abstract = {We introduce a multicolor labeling strategy (Multibow) for cell tracing experiments in developmental and regenerative processes. Building on Brainbow-based approaches that produce colors by differential expression levels of different fluorescent proteins, Multibow adds a layer of label diversity by introducing a binary code in which reporters are initially OFF and then probabilistically ON or OFF following Cre recombination. We have developed a library of constructs that contains seven different colors and three different subcellular localizations. Combining constructs from this library in the presence of Cre generates cells labeled with multiple independently expressed colors based on if each construct is ON or OFF following recombination. These labels form a unique "barcode" that allows the tracking of the cell and its clonal progenies in addition to expression level differences of each color. We tested Multibow in zebrafish which validates its design concept and suggests its utility for cell tracing applications in development and regeneration.},
}
@article {pmid26004249,
year = {2016},
author = {Dang, NX and Sun, FH and Lv, YY and Zhao, BH and Wang, JC and Murphy, RW and Wang, WZ and Li, JT},
title = {DNA barcoding and the identification of tree frogs (Amphibia: Anura: Rhacophoridae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {4},
pages = {2574-2584},
doi = {10.3109/19401736.2015.1041113},
pmid = {26004249},
issn = {2470-1408},
mesh = {Animals ; Anura/classification/*genetics ; Bayes Theorem ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Genome, Mitochondrial/genetics ; Sequence Analysis, DNA ; },
abstract = {The DNA barcoding gene COI (cytochrome c oxidase subunit I) effectively identifies many species. Herein, we barcoded 172 individuals from 37 species belonging to nine genera in Rhacophoridae to test if the gene serves equally well to identify species of tree frogs. Phenetic neighbor joining and phylogenetic Bayesian inference were used to construct phylogenetic trees, which resolved all nine genera as monophyletic taxa except for Rhacophorus, two new matrilines for Liuixalus, and Polypedates leucomystax species complex. Intraspecific genetic distances ranged from 0.000 to 0.119 and interspecific genetic distances ranged from 0.015 to 0.334. Within Rhacophorus and Kurixalus, the intra- and interspecific genetic distances did not reveal an obvious barcode gap. Notwithstanding, we found that COI sequences unambiguously identified rhacophorid species and helped to discover likely new cryptic species via the synthesis of genealogical relationships and divergence patterns. Our results supported that COI is an effective DNA barcoding marker for Rhacophoridae.},
}
@article {pmid26000840,
year = {2015},
author = {Junker, JP and van Oudenaarden, A},
title = {Single-cell transcriptomics enters the age of mass production.},
journal = {Molecular cell},
volume = {58},
number = {4},
pages = {563-564},
doi = {10.1016/j.molcel.2015.05.019},
pmid = {26000840},
issn = {1097-4164},
mesh = {Animals ; Embryonic Stem Cells/*cytology ; Gene Expression Profiling/*methods ; *Genome-Wide Association Study ; *Microfluidic Analytical Techniques ; Retina/*cytology ; Single-Cell Analysis/*methods ; },
abstract = {Two publications in the current issue of Cell introduce novel methods for high-throughput single-cell transcriptomics by using droplet microfluidics and sophisticated barcoding schemes for transcriptional profiling of thousands of individual cells.},
}
@article {pmid26000737,
year = {2015},
author = {Baym, M and Kryazhimskiy, S and Lieberman, TD and Chung, H and Desai, MM and Kishony, R},
title = {Inexpensive multiplexed library preparation for megabase-sized genomes.},
journal = {PloS one},
volume = {10},
number = {5},
pages = {e0128036},
pmid = {26000737},
issn = {1932-6203},
support = {R01 GM081617/GM/NIGMS NIH HHS/United States ; R01 GM104239/GM/NIGMS NIH HHS/United States ; R01-GM081617/GM/NIGMS NIH HHS/United States ; R01-GM104239/GM/NIGMS NIH HHS/United States ; },
mesh = {*Gene Library ; Genomics/economics/*methods ; High-Throughput Nucleotide Sequencing/economics/*methods ; Sequence Analysis, DNA/economics/methods ; },
abstract = {Whole-genome sequencing has become an indispensible tool of modern biology. However, the cost of sample preparation relative to the cost of sequencing remains high, especially for small genomes where the former is dominant. Here we present a protocol for rapid and inexpensive preparation of hundreds of multiplexed genomic libraries for Illumina sequencing. By carrying out the Nextera tagmentation reaction in small volumes, replacing costly reagents with cheaper equivalents, and omitting unnecessary steps, we achieve a cost of library preparation of $8 per sample, approximately 6 times cheaper than the standard Nextera XT protocol. Furthermore, our procedure takes less than 5 hours for 96 samples. Several hundred samples can then be pooled on the same HiSeq lane via custom barcodes. Our method will be useful for re-sequencing of microbial or viral genomes, including those from evolution experiments, genetic screens, and environmental samples, as well as for other sequencing applications including large amplicon, open chromosome, artificial chromosomes, and RNA sequencing.},
}
@article {pmid26000628,
year = {2015},
author = {Rotem, A and Ram, O and Shoresh, N and Sperling, RA and Schnall-Levin, M and Zhang, H and Basu, A and Bernstein, BE and Weitz, DA},
title = {High-Throughput Single-Cell Labeling (Hi-SCL) for RNA-Seq Using Drop-Based Microfluidics.},
journal = {PloS one},
volume = {10},
number = {5},
pages = {e0116328},
pmid = {26000628},
issn = {1932-6203},
support = {P50 HG006193/HG/NHGRI NIH HHS/United States ; U01 HL100395/HL/NHLBI NIH HHS/United States ; P50HG006193/HG/NHGRI NIH HHS/United States ; },
mesh = {DNA, Complementary/genetics ; High-Throughput Nucleotide Sequencing ; Microfluidics/*methods ; Oligonucleotide Array Sequence Analysis ; Sequence Analysis, RNA/methods ; },
abstract = {The importance of single-cell level data is increasingly appreciated, and significant advances in this direction have been made in recent years. Common to these technologies is the need to physically segregate individual cells into containers, such as wells or chambers of a micro-fluidics chip. High-throughput Single-Cell Labeling (Hi-SCL) in drops is a novel method that uses drop-based libraries of oligonucleotide barcodes to index individual cells in a population. The use of drops as containers, and a microfluidics platform to manipulate them en-masse, yields a highly scalable methodological framework. Once tagged, labeled molecules from different cells may be mixed without losing the cell-of-origin information. Here we demonstrate an application of the method for generating RNA-sequencing data for multiple individual cells within a population. Barcoded oligonucleotides are used to prime cDNA synthesis within drops. Barcoded cDNAs are then combined and subjected to second generation sequencing. The data are deconvoluted based on the barcodes, yielding single-cell mRNA expression data. In a proof-of-concept set of experiments we show that this method yields data comparable to other existing methods, but with unique potential for assaying very large numbers of cells.},
}
@article {pmid26000487,
year = {2015},
author = {Klein, AM and Mazutis, L and Akartuna, I and Tallapragada, N and Veres, A and Li, V and Peshkin, L and Weitz, DA and Kirschner, MW},
title = {Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.},
journal = {Cell},
volume = {161},
number = {5},
pages = {1187-1201},
pmid = {26000487},
issn = {1097-4172},
support = {R01 GM026875/GM/NIGMS NIH HHS/United States ; R21 AI101291/AI/NIAID NIH HHS/United States ; P01 GM096971/GM/NIGMS NIH HHS/United States ; P01 HL120839/HL/NHLBI NIH HHS/United States ; R01 HD073104/HD/NICHD NIH HHS/United States ; R01 GM103785/GM/NIGMS NIH HHS/United States ; R01 EB014703/EB/NIBIB NIH HHS/United States ; 5R01HD073104-03/HD/NICHD NIH HHS/United States ; R21DK098818/DK/NIDDK NIH HHS/United States ; R21 DK098818/DK/NIDDK NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Embryonic Stem Cells/*cytology/metabolism ; Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing ; Mice ; *Microfluidic Analytical Techniques ; Sequence Analysis, RNA/methods ; Single-Cell Analysis/*methods ; },
abstract = {It has long been the dream of biologists to map gene expression at the single-cell level. With such data one might track heterogeneous cell sub-populations, and infer regulatory relationships between genes and pathways. Recently, RNA sequencing has achieved single-cell resolution. What is limiting is an effective way to routinely isolate and process large numbers of individual cells for quantitative in-depth sequencing. We have developed a high-throughput droplet-microfluidic approach for barcoding the RNA from thousands of individual cells for subsequent analysis by next-generation sequencing. The method shows a surprisingly low noise profile and is readily adaptable to other sequencing-based assays. We analyzed mouse embryonic stem cells, revealing in detail the population structure and the heterogeneous onset of differentiation after leukemia inhibitory factor (LIF) withdrawal. The reproducibility of these high-throughput single-cell data allowed us to deconstruct cell populations and infer gene expression relationships. VIDEO ABSTRACT.},
}
@article {pmid26000447,
year = {2015},
author = {Guarnizo, CE and Paz, A and Muñoz-Ortiz, A and Flechas, SV and Méndez-Narváez, J and Crawford, AJ},
title = {DNA Barcoding Survey of Anurans across the Eastern Cordillera of Colombia and the Impact of the Andes on Cryptic Diversity.},
journal = {PloS one},
volume = {10},
number = {5},
pages = {e0127312},
pmid = {26000447},
issn = {1932-6203},
mesh = {Animals ; Anura/*genetics ; Colombia ; DNA Barcoding, Taxonomic ; *Genetic Variation ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Colombia hosts the second highest amphibian species diversity on Earth, yet its fauna remains poorly studied, especially using molecular genetic techniques. We present the results of the first wide-scale DNA barcoding survey of anurans of Colombia, focusing on a transect across the Eastern Cordillera. We surveyed 10 sites between the Magdalena Valley to the west and the eastern foothills of the Eastern Cordillera, sequencing portions of the mitochondrial 16S ribosomal RNA and cytochrome oxidase subunit 1 (CO1) genes for 235 individuals from 52 nominal species. We applied two barcode algorithms, Automatic Barcode Gap Discovery and Refined Single Linkage Analysis, to estimate the number of clusters or "unconfirmed candidate species" supported by DNA barcode data. Our survey included ~7% of the anuran species known from Colombia. While barcoding algorithms differed slightly in the number of clusters identified, between three and ten nominal species may be obscuring candidate species (in some cases, more than one cryptic species per nominal species). Our data suggest that the high elevations of the Eastern Cordillera and the low elevations of the Chicamocha canyon acted as geographic barriers in at least seven nominal species, promoting strong genetic divergences between populations associated with the Eastern Cordillera.},
}
@article {pmid25997885,
year = {2015},
author = {Anbalagan, S and Arunprasanna, V and Kannan, M and Dinakaran, S and Krishnan, M},
title = {Simulium (Gomphostilbia) (Diptera: Simuliidae) from Southern Western Ghats, India: two new species and DNA barcoding.},
journal = {Acta tropica},
volume = {149},
number = {},
pages = {94-105},
doi = {10.1016/j.actatropica.2015.05.015},
pmid = {25997885},
issn = {1873-6254},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Female ; India ; Larva/anatomy &amp; histology ; Male ; Phylogeny ; Pupa/anatomy &amp; histology ; Simuliidae/anatomy &amp; histology/*classification/genetics ; },
abstract = {Two new species of Simulium (Gomphostilbia) (Diptera: Simuliidae) are described on the basis of reared adult, pupal and larval specimens collected from Southern Western Ghats India. The morphological data of two new species S. (Gomphostilbia) panagudiense sp. n. and S. (Gomphostilbia) kottoorense sp. n. are assigned to the batoense species group in the subgenus Gomphostilbia. S. (Gomphostilbia) panagudiense sp.n. is characterized in the female by having the scutum without longitudinal vitta and arms of the genital fork wide basally and in the pupa by the stalk of ventral pair medium-long. S. (Gomphostilbia) kottoorense sp.n. is characterized by the arm of genital fork tapered near apex in the female and style in medial view 0.63 times as long as coxite in the male. Phylogeny of members in the genus Simulium was reconstructed based on DNA barcoding gene (cytochrome oxidase c subunit I). Tree analysis using new technology and maximum likelihood analyses are congruent with evidence of two new species in the subgenus Gomphostilbia and separated from other species.},
}
@article {pmid25995738,
year = {2015},
author = {Muslimin, M and Wilson, JJ and Ghazali, AR and Braima, KA and Jeffery, J and Wan-Nor, F and Alaa-Eldin, ME and Mohd-Zin, SW and Wan-Yusoff, WS and Norma-Rashid, Y and Lau, YL and Rohela, M and Abdul-Aziz, NM},
title = {First report of brown widow spider sightings in Peninsular Malaysia and notes on its global distribution.},
journal = {The journal of venomous animals and toxins including tropical diseases},
volume = {21},
number = {},
pages = {11},
pmid = {25995738},
issn = {1678-9199},
abstract = {BACKGROUND: The brown widow spider (Latrodectus geometricus Koch, 1841) has colonised many parts of the world from its continent of origin, Africa. By at least 1841, the species had successfully established populations in South America and has more recently expanded its range to the southern states of North America. This highly adaptable spider has been far more successful in finding its niche around the world than its famous cousins, the black widow, Latrodectus mactans, found in the south-eastern states of North America, and the red-back, Latrodectus hasselti, found mostly in Australia, New Zealand and Japan.<br><br>METHODS: We performed an extensive web search of brown widow sightings and mapped the location of each sighting using ArcGIS. Specimens reputedly of the species L. geometricus were collected at three localities in Peninsular Malaysia. The spiders were identified and documented based on an examination of morphological characteristics and DNA barcoding.<br><br>RESULTS: The spiders found in Peninsular Malaysia were confirmed to be Latrodectus geometricus based on their morphological characteristics and DNA barcodes. We recorded 354 sightings of the brown widow in 58 countries, including Peninsular Malaysia.<br><br>CONCLUSION: Reports from the Americas and the Far East suggest a global-wide invasion of the brown widow spider. Herein we report the arrival of the brown widow spider in Peninsular Malaysia and provide notes on the identification of the species and its recently expanded range.},
}
@article {pmid25991508,
year = {2015},
author = {Reifenberger, JG and Dorfman, KD and Cao, H},
title = {Topological events in single molecules of E. coli DNA confined in nanochannels.},
journal = {The Analyst},
volume = {140},
number = {14},
pages = {4887-4894},
pmid = {25991508},
issn = {1364-5528},
support = {R01 HG006851/HG/NHGRI NIH HHS/United States ; R01-HG006851/HG/NHGRI NIH HHS/United States ; },
mesh = {DNA, Bacterial/*chemistry ; Escherichia coli/*genetics ; *Nanostructures ; },
abstract = {We present experimental data concerning potential topological events such as folds, internal backfolds, and/or knots within long molecules of double-stranded DNA when they are stretched by confinement in a nanochannel. Genomic DNA from E. coli was labeled near the 'GCTCTTC' sequence with a fluorescently labeled dUTP analog and stained with the DNA intercalator YOYO. Individual long molecules of DNA were then linearized and imaged using methods based on the NanoChannel Array technology (Irys® System) available from BioNano Genomics. Data were collected on 189 153 molecules of length greater than 50 kilobases. A custom code was developed to search for abnormal intensity spikes in the YOYO backbone profile along the length of individual molecules. By correlating the YOYO intensity spikes with the aligned barcode pattern to the reference, we were able to correlate the bright intensity regions of YOYO with abnormal stretching in the molecule, which suggests these events were either a knot or a region of internal backfolding within the DNA. We interpret the results of our experiments involving molecules exceeding 50 kilobases in the context of existing simulation data for relatively short DNA, typically several kilobases. The frequency of these events is lower than the predictions from simulations, while the size of the events is larger than simulation predictions and often exceeds the molecular weight of the simulated molecules. We also identified DNA molecules that exhibit large, single folds as they enter the nanochannels. Overall, topological events occur at a low frequency (∼7% of all molecules) and pose an easily surmountable obstacle for the practice of genome mapping in nanochannels.},
}
@article {pmid25991411,
year = {2015},
author = {Blacket, MJ and Rice, AD and Semeraro, L and Malipatil, MB},
title = {DNA-based identifications reveal multiple introductions of the vegetable leafminer Liriomyza sativae (Diptera: Agromyzidae) into the Torres Strait Islands and Papua New Guinea.},
journal = {Bulletin of entomological research},
volume = {105},
number = {5},
pages = {533-544},
doi = {10.1017/S0007485315000383},
pmid = {25991411},
issn = {1475-2670},
mesh = {Animals ; DNA/*genetics ; Diptera/*genetics/physiology ; *Introduced Species ; Larva/genetics/physiology ; Male ; Papua New Guinea ; Queensland ; },
abstract = {Leafmining flies (Diptera: Agromyzidae) can be serious economic pests of horticultural crops. Some genera such as Liriomyza are particularly problematic with numerous species, some of which are highly polyphagous (wide host range), which can only be confidently identified morphologically from adult males. In our study, DNA barcoding was employed to establish new locality records of the vegetable leafminer fly, Liriomyza sativae, from the islands of Torres Strait (Queensland, Australia) and the central highlands of Papua New Guinea (PNG). These records represent significant range extensions of this highly invasive plant pest. Specimens of immature leafminers (from leaf mines) were collected over a 5-year period during routine plant health surveys in ethanol or on FTA® filter paper cards, both methods proved effective at preserving and transporting insect DNA under tropical conditions, with FTA cards possessing some additional logistical benefits. Specimens were identified through sequencing two sections of the cytochrome oxidase I gene and the utility of each was assessed for the identification of species and intra-specific genetic lineages. Our study indicates that multiple haplotypes of L. sativae occur in PNG, while a different haplotype is present in the Torres Strait, with genetic regionalization between these areas apart from a single possible instance - one haplotype 'S.7' appears to be common between these two regions - interestingly this has also been the most common haplotype detected in previous studies of invasive L. sativae populations. The DNA barcoding methods employed here not only identified multiple introductions of L. sativae, but also appear generally applicable to the identification of other agromyzid leafminers (Phytomyzinae and Agromyzinae) and should decrease the likelihood of potentially co-amplifying internal hymenopteran parasitoids. Currently, L. sativae is still not recorded from the Australian mainland; however, further sampling of leafminer flies from Northern Australia and surrounding areas is required, as surveillance for possible Liriomyza incursions, as well as to characterize endemic species with which Liriomyza species might be confused.},
}
@article {pmid25989705,
year = {2015},
author = {Wang, XB and Deng, J and Zhang, JT and Zhou, QS and Zhang, YZ and Wu, SA},
title = {DNA barcoding of common soft scales (Hemiptera: Coccoidea: Coccidae) in China.},
journal = {Bulletin of entomological research},
volume = {105},
number = {5},
pages = {545-554},
doi = {10.1017/S0007485315000413},
pmid = {25989705},
issn = {1475-2670},
mesh = {Animal Distribution ; Animals ; China ; *DNA Barcoding, Taxonomic ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Hemiptera/*genetics ; Phylogeny ; RNA, Ribosomal, 28S/genetics ; Species Specificity ; },
abstract = {The soft scales (Hemiptera: Coccoidea: Coccidae) are a group of sap-sucking plant parasites, many of which are notorious agricultural pests. The quarantine and economic importance of soft scales necessitates rapid and reliable identification of these taxa. Nucleotide sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene (barcoding region) and 28S rDNA were generated from 340 individuals of 36 common soft scales in China. Distance-based [(best match, Automated Barcode Gap Discovery (ABGD)], tree-based (neighbor-joining, Bayesian inference), Klee diagrams, and general mixed Yule coalescent (GMYC) models were used to evaluate barcoding success rates in the data set. Best match showed that COI and 28S sequences could provide 100 and 95.52% correct identification, respectively. The average interspecific divergences were 19.81% for COI data and 20.38% for 28S data, and mean intraspecific divergences were 0.56 and 0.07%, respectively. For COI data, multiple methods (ABGD, Klee, and tree-based methods) resulted in general congruence with morphological identifications. However, GMYC analysis tended to provide more molecular operational taxonomic units (MOTUs). Twelve MOTUs derived from five morphospecies (Rhodococcus sariuoni, Pulvinaria vitis, Pulvinaria aurantii, Parasaissetia nigra, and Ceroplastes rubens) were observed using the GMYC approach. In addition, tree-based methods showed that 28S sequences could be used for species-level identification (except for Ceroplastes ceriferus - Ceroplastes pseudoceriferus), even with low genetic variation (<1%). This report demonstrates the robustness of DNA barcoding for species discrimination of soft scales with two molecular markers (COI and 28S) and provides a reliable barcode library and rapid diagnostic tool for common soft scales in China.},
}
@article {pmid25988313,
year = {2015},
author = {Becker, RA and Sales, NG and Santos, GM and Santos, GB and Carvalho, DC},
title = {DNA barcoding and morphological identification of neotropical ichthyoplankton from the Upper Paraná and São Francisco.},
journal = {Journal of fish biology},
volume = {87},
number = {1},
pages = {159-168},
doi = {10.1111/jfb.12707},
pmid = {25988313},
issn = {1095-8649},
mesh = {Animals ; Brazil ; *DNA Barcoding, Taxonomic ; Fishes/anatomy &amp; histology/*classification ; Larva ; *Ovum ; },
abstract = {The identification of fish larvae from two neotropical hydrographic basins using traditional morphological taxonomy and DNA barcoding revealed no conflicting results between the morphological and barcode identification of larvae. A lower rate (25%) of correct morphological identification of eggs as belonging to migratory or non-migratory species was achieved. Accurate identification of ichthyoplankton by DNA barcoding is an important tool for fish reproductive behaviour studies, correct estimation of biodiversity by detecting eggs from rare species, as well as defining environmental and management strategies for fish conservation in the neotropics.},
}
@article {pmid25981251,
year = {2015},
author = {Contaldo, N and Paltrinieri, S and Makarova, O and Bertaccini, A and Nicolaisen, M},
title = {Q-bank phytoplasma: a DNA barcoding tool for phytoplasma identification.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1302},
number = {},
pages = {123-135},
doi = {10.1007/978-1-4939-2620-6_10},
pmid = {25981251},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Bacterial/*genetics ; Electrophoresis, Agar Gel ; Genes, Bacterial/*genetics ; Phytoplasma/*classification/*genetics ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA/*methods ; },
abstract = {DNA barcoding is an identification method based on comparison of a short DNA sequence with known sequences from a database. A DNA barcoding tool has been developed for phytoplasma identification. This phytoplasma DNA barcoding protocol based on the tuf gene has been shown to identify phytoplasmas belonging to the following groups: 16SrI, 16SrII, 16SrIII, 16SrIV, 16SrV, 16SrVI, 16SrVII, 16SrIX, 16SrX, 16SrXI, 16SrXII, 16SrXIV, 16SrXX, and 16SrXXI.},
}
@article {pmid25980883,
year = {2015},
author = {Ehrler, F and Diener, R and Lovis, C},
title = {Opportunities and limitations in using google glass to assist drug dispensing.},
journal = {Studies in health technology and informatics},
volume = {211},
number = {},
pages = {283-285},
pmid = {25980883},
issn = {1879-8365},
mesh = {Administration, Intravenous/*standards ; *Eyeglasses ; Humans ; Medical Errors/*prevention &amp; control ; Medical Informatics/*instrumentation ; Quality of Health Care ; Software ; },
abstract = {The administration of intravenous drugs is a significant source of medical errors. Protocol based care are have been demonstrated to be an efficient way to favor best practices and to avoid simple errors such as those related to expiration date, hygiene regulation among other. The recent availability of the Google Glass, a hands free wearable device offers new opportunities to access care protocols at patients' bedside. In this article, we present a prototype application for displaying care protocols developed through a user centered design. The software enables the navigation through the different steps of care protocols and their validation using barcodes. Three interactions paradigms, tactile, vocal and by eye blink are proposed in order to provide hands free manipulation when necessary. The realization of a concrete project revealed some limitations that should be taken in account in order to ensure the proper behavior of the tool. If no formal evaluation has been performed, the first feedbacks are very positive and encourage us to go forward and test the tool in real care situations.},
}
@article {pmid25980661,
year = {2016},
author = {Karim, A and Iqbal, A and Akhtar, R and Rizwan, M and Amar, A and Qamar, U and Jahan, S},
title = {Barcoding of fresh water fishes from Pakistan.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {4},
pages = {2685-2688},
doi = {10.3109/19401736.2015.1043544},
pmid = {25980661},
issn = {2470-1408},
mesh = {Animals ; Computational Biology ; Cyprinidae/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Fresh Water ; Genome, Mitochondrial/*genetics ; Sequence Analysis, DNA ; },
abstract = {DNA bar-coding is a taxonomic method that uses small genetic markers in organisms' mitochondrial DNA (mt DNA) for identification of particular species. It uses sequence diversity in a 658-base pair fragment near the 5' end of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene as a tool for species identification. DNA barcoding is more accurate and reliable method as compared with the morphological identification. It is equally useful in juveniles as well as adult stages of fishes. The present study was conducted to identify three farm fish species of Pakistan (Cyprinus carpio, Cirrhinus mrigala, and Ctenopharyngodon idella) genetically. All of them belonged to family cyprinidae. CO1 gene was amplified. PCR products were sequenced and analyzed by bioinformatic software. Conspecific, congenric, and confamilial k2P nucleotide divergence was estimated. From these findings, it was concluded that the gene sequence, CO1, may serve as milestone for the identification of related species at molecular level.},
}
@article {pmid25979965,
year = {2015},
author = {Romeiras, MM and Monteiro, F and Duarte, MC and Schaefer, H and Carine, M},
title = {Patterns of genetic diversity in three plant lineages endemic to the Cape Verde Islands.},
journal = {AoB PLANTS},
volume = {7},
number = {},
pages = {},
pmid = {25979965},
issn = {2041-2851},
abstract = {Conservation of plant diversity on islands relies on a good knowledge of the taxonomy, distribution and genetic diversity of species. In recent decades, a combination of morphology- and DNA-based approaches has become the standard for investigating island plant lineages and this has led, in some cases, to the discovery of previously overlooked diversity, including 'cryptic species'. The flora of the Cape Verde archipelago in the North Atlantic is currently thought to comprise ∼740 vascular plant species, 92 of them endemics. Despite the fact that it is considered relatively well known, there has been a 12 % increase in the number of endemics in the last two decades. Relatively few of the Cape Verde plant lineages have been included in genetic studies so far and little is known about the patterns of diversification in the archipelago. Here we present an updated list for the endemic Cape Verde flora and analyse diversity patterns for three endemic plant lineages (Cynanchum, Globularia and Umbilicus) based on one nuclear (ITS) and four plastid DNA regions. In all three lineages, we find genetic variation. In Cynanchum, we find two distinct haplotypes with no clear geographical pattern, possibly reflecting different ploidy levels. In Globularia and Umbilicus, differentiation is evident between populations from northern and southern islands. Isolation and drift resulting from the small and fragmented distributions, coupled with the significant distances separating the northern and southern islands, could explain this pattern. Overall, our study suggests that the diversity in the endemic vascular flora of Cape Verde is higher than previously thought and further work is necessary to characterize the flora.},
}
@article {pmid25978064,
year = {2015},
author = {Palhares, RM and Gonçalves Drummond, M and Dos Santos Alves Figueiredo Brasil, B and Pereira Cosenza, G and das Graças Lins Brandão, M and Oliveira, G},
title = {Medicinal plants recommended by the world health organization: DNA barcode identification associated with chemical analyses guarantees their quality.},
journal = {PloS one},
volume = {10},
number = {5},
pages = {e0127866},
pmid = {25978064},
issn = {1932-6203},
mesh = {Brazil ; DNA Barcoding, Taxonomic/methods ; DNA, Plant/*genetics ; Flowers/genetics ; Humans ; Plant Leaves/genetics ; Plant Roots/genetics ; Plants, Medicinal/*genetics ; Sequence Analysis, DNA/methods ; World Health Organization ; },
abstract = {Medicinal plants are used throughout the world, and the regulations defining their proper use, such as identification of the correct species and verification of the presence, purity and concentration of the required chemical compounds, are widely recognized. Herbal medicines are made from vegetal drugs, the processed products of medicinal species. These processed materials present a number of challenges in terms of botanical identification, and according to the World Health Organization (WHO), the use of incorrect species is a threat to consumer safety. The samples used in this study consisted of the dried leaves, flowers and roots of 257 samples from 8 distinct species approved by the WHO for the production of medicinal herbs and sold in Brazilian markets. Identification of the samples in this study using DNA barcoding (matK, rbcL and ITS2 regions) revealed that the level of substitutions may be as high as 71%. Using qualitative and quantitative chemical analyses, this study identified situations in which the correct species was being sold, but the chemical compounds were not present. Even more troubling, some samples identified as substitutions using DNA barcoding contained the chemical compounds from the correct species at the minimum required concentration. This last situation may lead to the use of unknown species or species whose safety for human consumption remains unknown. This study concludes that DNA barcoding should be used in a complementary manner for species identification with chemical analyses to detect and quantify the required chemical compounds, thus improving the quality of this class of medicines.},
}
@article {pmid25977611,
year = {2015},
author = {Collins, RA and Duarte Ribeiro, E and Nogueira Machado, V and Hrbek, T and Farias, IP},
title = {A preliminary inventory of the catfishes of the lower Rio Nhamundá, Brazil (Ostariophysi, Siluriformes).},
journal = {Biodiversity data journal},
volume = {},
number = {3},
pages = {e4162},
pmid = {25977611},
issn = {1314-2828},
abstract = {The Rio Nhamundá is a poorly-known clearwater river draining the southern Guiana Shield of Brazil. In this study we report the findings of a preliminary ichthyological survey, focusing on catfishes (Siluriformes). We identify a total of 36 species (31 genera, seven families) from the Nhamundá, including 11 species already recorded from the river. Overall, our survey results show that even rapid surveys can provide important information on Amazon fish biodiversity, suggesting potential new species, providing range extensions for nominal species, and additionally highlighting taxa in need of taxonomic revision and genetic study. As well as the traditional forms of data collected on biodiversity surveys (i.e. preserved specimen vouchers), our study also provides "new" types of data in the form of DNA barcodes and images of fishes exhibiting colouration in life, information that will be invaluable in future work addressing difficult groups. O Rio Nhamundá é um rio de água clara, pouco conhecido, que drena parte do Escudo das Guianas em território brasileiro. Nesse estudo, nós reportamos os resultados de um levantamento ictiofaunístico preliminar dessa área, tendo como foco os bagres (Siluriformes). Nós identificamos um total de 36 espécies (31 gêneros, sete famílias) provenientes de nossa coleta, e adicionamos 11 espécies já conhecidas para o rio. De maneira geral, os resultados de nossa pesquisa mostram que mesmo levantamentos rápidos podem gerar informações importantes sobre a biodiversidade de peixes amazônicos, sugerindo potenciais espécies novas, ampliando a área de distribuição de espécies, além de apontar a necessidade de revisões taxonômicas e estudos genéticos para alguns taxa. Para além das formas tradicionais de dados coletados em pesquisas de biodiversidade (i.e. espécimes preservados), nosso estudo fornece "novas" formas de dados, como DNA barcodes e imagens com o padrão de coloração dos espécimes vivos, informações essas que serão de valor inestimável para futuros estudos que abordem grupos taxonômicos difíceis.},
}
@article {pmid25976414,
year = {2015},
author = {Casero, RD and Mongi, F and Sánchez, A and Ramírez, JD},
title = {Blastocystis and urticaria: Examination of subtypes and morphotypes in an unusual clinical manifestation.},
journal = {Acta tropica},
volume = {148},
number = {},
pages = {156-161},
doi = {10.1016/j.actatropica.2015.05.004},
pmid = {25976414},
issn = {1873-6254},
mesh = {Abdominal Pain/epidemiology/*parasitology ; Adolescent ; Adult ; Alleles ; Argentina/epidemiology ; Asymptomatic Infections ; Blastocystis/classification/*genetics ; Blastocystis Infections/epidemiology/*parasitology ; Child ; Child, Preschool ; Constipation/epidemiology/*parasitology ; Diarrhea/epidemiology/*parasitology ; Feces/parasitology ; Female ; Genetic Variation ; Humans ; Infant ; Male ; Middle Aged ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA ; Urticaria/epidemiology/*parasitology ; Young Adult ; },
abstract = {Blastocystis is a human common enteric protist that may colonize a large variety of non-human hosts linked to symptoms and diseases such as abdominal pain, constipation, diarrhea, urticaria, flatulence and irritable bowel syndrome (IBS). Blastocystis exhibits remarkable genetic diversity and multiple subtypes (STs) within the genus with no absolute associations with clinical symptomatology. Here we analyzed fecal samples from Argentinean patients (n=270) belonging to symptomatic (urticaria and non-specific gastrointestinal symptoms, n=39) and asymptomatic control (n=28). Those patients infected with Blastocystis (n=67) were submitted for morphological analysis, DNA extraction, 18S PCR, sequencing and STs identification according to DNA barcoding. Blastocystis vacuolar forms were the predominant morphotype (75%), ameboid-like forms were evidenced in 1.5% of samples. Blastocystis ST3 was detected in 71.6% (n=48), of which 71.4%, (n=35) and 28.6% (n=14) belonged to symptomatic and asymptomatic respectively. Other subtypes identified were ST1 (14.9%), ST6 (7.5%) and ST2 (5.9%). Blastocystis 18S barcoding evidenced in non-urticaria symptomatic patients and asymptomatic control group the presence of allele 134 (ST3) (p<0.0001), while allele 34 (ST3) was detected in 85.7% (18/21) of symptomatic uricaria as compared with control group (1/21) (p<0.0001). The presence of a particular allele (a34) significantly associated with urticaria patients was detected and the clinical implications of these findings are herein discussed.},
}
@article {pmid25974935,
year = {2015},
author = {van Gennip, Y and Athavale, P and Gilles, J and Choksi, R},
title = {A Regularization Approach to Blind Deblurring and Denoising of QR Barcodes.},
journal = {IEEE transactions on image processing : a publication of the IEEE Signal Processing Society},
volume = {24},
number = {9},
pages = {2864-2873},
doi = {10.1109/TIP.2015.2432675},
pmid = {25974935},
issn = {1941-0042},
abstract = {QR bar codes are prototypical images for which part of the image is a priori known (required patterns). Open source bar code readers, such as ZBar, are readily available. We exploit both these facts to provide and assess purely regularization-based methods for blind deblurring of QR bar codes in the presence of noise.},
}
@article {pmid25972226,
year = {2015},
author = {Galligioni, E and Piras, EM and Galvagni, M and Eccher, C and Caramatti, S and Zanolli, D and Santi, J and Berloffa, F and Dianti, M and Maines, F and Sannicolò, M and Sandri, M and Bragantini, L and Ferro, A and Forti, S},
title = {Integrating mHealth in Oncology: Experience in the Province of Trento.},
journal = {Journal of medical Internet research},
volume = {17},
number = {5},
pages = {e114},
pmid = {25972226},
issn = {1438-8871},
mesh = {Antineoplastic Agents/*therapeutic use ; Asthma/*therapy ; Attitude of Health Personnel ; Cell Phone ; Diabetes Mellitus/*therapy ; Humans ; Hypertension/*therapy ; Information Systems ; Italy ; Mobile Applications ; Neoplasms/*drug therapy ; Oncology Nursing ; Patient Safety ; Patient Satisfaction ; Pilot Projects ; Point-of-Care Systems ; Telemedicine/*methods ; },
abstract = {BACKGROUND: The potential benefits of the introduction of electronic and mobile health (mHealth) information technologies, to support the safe delivery of intravenous chemotherapy or oral anticancer therapies, could be exponential in the context of a highly integrated computerized system.<br><br>OBJECTIVE: Here we describe a safe therapy mobile (STM) system for the safe delivery of intravenous chemotherapy, and a home monitoring system for monitoring and managing toxicity and improving adherence in patients receiving oral anticancer therapies at home.<br><br>METHODS: The STM system is fully integrated with the electronic oncological patient record. After the prescription of chemotherapy, specific barcodes are automatically associated with the patient and each drug, and a bedside barcode reader checks the patient, nurse, infusion bag, and drug sequence in order to trace the entire administration process, which is then entered in the patient's record. The usability and acceptability of the system was investigated by means of a modified questionnaire administered to nurses. The home monitoring system consists of a mobile phone or tablet diary app, which allows patients to record their state of health, the medications taken, their side effects, and a Web dashboard that allows health professionals to check the patient data and monitor toxicity and treatment adherence. A built-in rule-based alarm module notifies health care professionals of critical conditions. Initially developed for chronic patients, the system has been subsequently customized in order to monitor home treatments with capecitabine or sunitinib in cancer patients (Onco-TreC).<br><br>RESULTS: The STM system never failed to match the patient/nurse/drug sequence association correctly, and proved to be accurate and reliable in tracing and recording the entire administration process. The questionnaires revealed that the users were generally satisfied and had a positive perception of the system's usefulness and ease of use, and the quality of their working lives. The pilot studies with the home monitoring system with 43 chronic patients have shown that the approach is reliable and useful for clinicians and patients, but it is also necessary to pay attention to the expectations that mHealth solutions may raise in users. The Onco-TreC version has been successfully laboratory tested, and is now ready for validation.<br><br>CONCLUSIONS: The STM and Onco-TreC systems are fully integrated with our complex and composite information system, which guarantees privacy, security, interoperability, and real-time communications between patients and health professionals. They need to be validated in order to confirm their positive contribution to the safer administration of anticancer drugs.},
}
@article {pmid25968665,
year = {2015},
author = {Ariza-Flores, AD and Mukherjee, A and Antunez, E and Agarwal, V},
title = {Spectral barcodes by superposition of quasiperiodic refractive index profiles.},
journal = {Optics express},
volume = {23},
number = {7},
pages = {8272-8280},
doi = {10.1364/OE.23.008272},
pmid = {25968665},
issn = {1094-4087},
abstract = {Averaging and shifting the refractive index profiles of quasiperiodic structure reveals the formation of several localized modes in the reflectivity spectrum and were used to generate different spectral barcodes. By associating the depth and wavelength of the observed resonant modes to the thickness and position of blackbars, respectively, the possibility to generate multiple codes has been shown. An experimental verification was carried out with multilayered dielectric porous silicon structures with reflectivity spectra revealing unique photonic fingerprints.},
}
@article {pmid25968323,
year = {2015},
author = {Benavente, ED and Coll, F and Furnham, N and McNerney, R and Glynn, JR and Campino, S and Pain, A and Mohareb, FR and Clark, TG},
title = {PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis.},
journal = {BMC bioinformatics},
volume = {16},
number = {1},
pages = {155},
pmid = {25968323},
issn = {1471-2105},
support = {/WT_/Wellcome Trust/United Kingdom ; MR/K020420/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Computer Graphics ; *Genome, Bacterial ; Geography ; Mycobacterium tuberculosis/*genetics ; *Phylogeny ; Polymorphism, Genetic/*genetics ; *Software ; Tuberculosis/*genetics/microbiology ; },
abstract = {BACKGROUND: Phylogenetic-based classification of M. tuberculosis and other bacterial genomes is a core analysis for studying evolutionary hypotheses, disease outbreaks and transmission events. Whole genome sequencing is providing new insights into the genomic variation underlying intra- and inter-strain diversity, thereby assisting with the classification and molecular barcoding of the bacteria. One roadblock to strain investigation is the lack of user-interactive solutions to interrogate and visualise variation within a phylogenetic tree setting.<br><br>RESULTS: We have developed a web-based tool called PhyTB (http://pathogenseq.lshtm.ac.uk/phytblive/index.php) to assist phylogenetic tree visualisation and identification of M. tuberculosis clade-informative polymorphism. Variant Call Format files can be uploaded to determine a sample position within the tree. A map view summarises the geographical distribution of alleles and strain-types. The utility of the PhyTB is demonstrated on sequence data from 1,601 M. tuberculosis isolates.<br><br>CONCLUSION: PhyTB contextualises M. tuberculosis genomic variation within epidemiological, geographical and phylogenic settings. Further tool utility is possible by incorporating large variants and phenotypic data (e.g. drug-resistance profiles), and an assessment of genotype-phenotype associations. Source code is available to develop similar websites for other organisms (http://sourceforge.net/projects/phylotrack).},
}
@article {pmid25966585,
year = {2015},
author = {Ilyasov, RA and Poskryakov, AV and Nikolenko, AG},
title = {[New SNP markers of the honeybee vitellogenin gene (Vg) used for identification of subspecies Apis mellifera mellifera L].},
journal = {Genetika},
volume = {51},
number = {2},
pages = {194-199},
pmid = {25966585},
issn = {0016-6758},
mesh = {Animals ; Bees/*genetics ; DNA Barcoding, Taxonomic ; *Genetic Markers ; Genotype ; Polymorphism, Single Nucleotide/*genetics ; Vitellogenins/*genetics ; },
abstract = {Preservation of the gene pool of honeybee subspecies Apis mellifera mellifera is of vital importance for successful beekeeping development in the northern regions of Eurasia. An effective method of genotyping honeybee colonies used in modern science is the mapping of sites of single nucleotide polymorphism (SNP). The honeybee vitellogenin gene (Vg) encodes a protein that affects reproductive function, behavior, immunity, longevity, and social organization in the honeybee Apis mellifera and is therefore a topical research subject. The results of comparative analysis of honeybee Vg sequences show that there are 26 SNP sites that differentiate M and C evolutionary branches and can be used as markers in selective breeding, DNA-barcoding, and the creation of genetic passports for A. m. mellifera colonies.},
}
@article {pmid25966167,
year = {2015},
author = {Osathanunkul, M and Madesis, P and Ounjai, S and Suwannapoom, C and Jampeetong, A},
title = {Rapid discrimination between four seagrass species using hybrid analysis.},
journal = {Genetics and molecular research : GMR},
volume = {14},
number = {2},
pages = {3957-3963},
doi = {10.4238/2015.April.27.10},
pmid = {25966167},
issn = {1676-5680},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; DNA, Plant/genetics ; Magnoliopsida/*classification/genetics ; Plant Proteins/genetics ; Thailand ; },
abstract = {Biological species are traditionally identified based on their morphological features and the correct identification of species is critical in biological studies. However, some plant types, such as seagrass, are taxonomically problematic and difficult to identify. Furthermore, closely related seagrass species, such as Halophila spp, form a taxonomically unresolved complex. Although some seagrass taxa are easy to recognize, most species are difficult to identify without skilled taxonomic or molecular techniques. Barcoding coupled with High Resolution Melting analysis (BAR-HRM) offers a potentially reliable, rapid, and cost-effective method to confirm species. Here, DNA information of two chloroplast loci was used in combination with HRM analysis to discriminate four species of seagrass collected off the southern coast of Thailand. A distinct melting curve presenting one inflection point was generated for each species using rbcL primers. While the melting profiles of Cymodocea rotundata and Cymodocea serrulata were not statistically different, analysis of the normalized HRM curves produced with the rpoC primers allowed for their discrimination. The Bar-HRM technique showed promise in discriminating seagrass species and with further adaptations and improvements, could make for an effective and power tool for confirming seagrass species.},
}
@article {pmid25962484,
year = {2016},
author = {Cai, Y and Zhang, L and Wang, Y and Liu, Q and Shui, Q and Yue, B and Zhang, Z and Li, J},
title = {Identification of deer species (Cervidae, Cetartiodactyla) in China using mitochondrial cytochrome c oxidase subunit I (mtDNA COI).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4240-4243},
doi = {10.3109/19401736.2014.1003919},
pmid = {25962484},
issn = {2470-1408},
mesh = {Animals ; China ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Deer/*genetics ; Electron Transport Complex IV/*genetics ; Genome, Mitochondrial/genetics ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {In China, many deer species are threatened and their wild populations are decreasing. In this study, a segment of mitochondrial cytochrome oxidase subunit I (COI) was used as a DNA barcode to identify Cervidae species. COI sequences of 30 individuals from nine species were determined. Together with 148 sequences from BOLD and Genbank, a total of 178 sequences from 21 species of the family Cervidae were analyzed. The results showed that all species had unique COI sequences, and there was no barcode sharing among them. The mean K2P distances within species, genus, and family were 1.3%, 3.4%, and 8.9%, respectively. The neighbor-joining (NJ) tree was in most cases concordant with modern deer classification. Three species showed maximum intraspecific divergences higher than their minimum interspecific divergences. However, all species could be discriminated by their diagnostic characters in BLOG analysis. The present study confirmed that COI barcodes can effectively distinguish Cervidae species in China.},
}
@article {pmid25955619,
year = {2015},
author = {Würth, C and Resch-Genger, U},
title = {Determination of photoluminescence quantum yields of scattering media with an integrating sphere: direct and indirect illumination.},
journal = {Applied spectroscopy},
volume = {69},
number = {6},
pages = {749-759},
doi = {10.1366/14-07679},
pmid = {25955619},
issn = {1943-3530},
mesh = {Equipment Design ; Fluorescent Dyes/chemistry ; Light ; Nanoparticles/chemistry ; Particle Size ; Rhodamines/chemistry ; Scattering, Radiation ; Silicon Dioxide/chemistry ; Spectrometry, Fluorescence/*instrumentation/*methods ; },
abstract = {The ever-increasing use of fluorescent nanomaterials and micrometer-sized beads in the life and material sciences requires reliable procedures for the measurement of the key performance parameter fluorescence quantum yield (Φf) of scattering particle dispersions and reference systems to evaluate the performance of such measurements. This encouraged us to systematically study, both theoretically and experimentally, the optical determination of photoluminescent quantum yield as a function of the scattering and absorption properties of the sample and the illumination geometry with an integrating sphere method. The latter included measurements with a direct and an indirect illumination. As a representative and easy-to-prepare reference system, we used ethanolic dispersions of 250 nm sized silica particles and the dye rhodamine 101 and systematically varied the concentration of the dye and particles within the typical ranges of spectroscopic and (bio)analytical applications of fluorescent nanomaterials. Based on our measurements, we recommend indirect sample illumination geometry for the accurate measurement of Φf of samples with low or unknown absorption and high scattering coefficients such as dispersions of luminescent particles or fluorescent reporters in biological matrices. This finding is of utmost relevance for all (bio)analytical applications of fluorescent nanomaterials ranging from particle labels and probes over assay platforms to safety barcodes.},
}
@article {pmid25952855,
year = {2015},
author = {Cawthorn, DM and Duncan, J and Kastern, C and Francis, J and Hoffman, LC},
title = {Fish species substitution and misnaming in South Africa: An economic, safety and sustainability conundrum revisited.},
journal = {Food chemistry},
volume = {185},
number = {},
pages = {165-181},
doi = {10.1016/j.foodchem.2015.03.113},
pmid = {25952855},
issn = {1873-7072},
mesh = {Animals ; *Fishes/genetics ; Food Labeling/legislation &amp; jurisprudence ; *Food Safety ; *Seafood/economics ; South Africa ; },
abstract = {While fish species mislabelling has emerged as a global problem, the tracking of improvements or deteriorations in seafood trading practices is challenging without a consistent basis for monitoring. The aim of this study was to develop a robust, repeatable species authentication protocol that could be used to benchmark the current and future incidences of fish mislabelling in South Africa. Using this approach, 149 fish samples collected from restaurants and retailers in three provinces (KwaZulu-Natal, Western Cape and Gauteng) were identified using DNA barcoding, supplemented in certain cases with mitochondrial control region sequencing. Overall, 18% of samples were incorrectly described in terms of species, with similar misrepresentation rates in restaurants (18%) and retail outlets (19%). While there appears to be some improvement in the transparency of local seafood marketing compared to previous studies, the results remain of concern and signal the need for enhanced seafood labelling regulations, monitoring and law enforcement.},
}
@article {pmid25947776,
year = {2015},
author = {Mecklenburg, CW and Anderson, ME},
title = {Reassessment of multiple species of Gymnelus (Teleostei: Zoarcidae) in Pacific Arctic and boreal regions.},
journal = {Zootaxa},
volume = {3948},
number = {2},
pages = {263-278},
doi = {10.11646/zootaxa.3948.2.7},
pmid = {25947776},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Arctic Regions ; Body Size ; Ecosystem ; Female ; Male ; Organ Size ; Perciformes/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Phylogeny ; },
abstract = {Recently described new nominal species and resurrected species in the eelpout genus Gymnelus Reinhardt 1834 were reassessed for validity using fresh material collected in Pacific Arctic regions and a large body of data from a previous systematic review of the genus. The analysis reported here included both DNA barcodes and morphology. Only two species were validated: G. viridis (Fabricius 1780) and G. hemifasciatus Andriashev 1937. The latter species occurred as two morphotypes for which there is some evidence of difference in ecological preference, but the available environ-mental data are not robust enough to firmly identify or verify ecophenotypes.},
}
@article {pmid25947706,
year = {2015},
author = {Bartlett, CR and Kunz, G},
title = {A new genus and species of delphacid planthopper (Hemiptera: Fulgoroidea: Delphacidae) from Central America with a preliminary regional species list.},
journal = {Zootaxa},
volume = {3946},
number = {4},
pages = {510-518},
doi = {10.11646/zootaxa.3946.4.2},
pmid = {25947706},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Central America ; Female ; Hemiptera/*classification ; Male ; },
abstract = {The new genus Ampliphax, assigned to the Delphacini, is described and illustrated with a single new species A. grandis from Costa Rica and Panama. Ampliphax grandis is a large species with a projected head. DNA barcode data suggest, among currently barcoded taxa, an affinity to the genus Bostaera. A checklist of the delphacid species from Costa Rica, Panama, and Nicaragua based on literature and specimen records is provided.},
}
@article {pmid25947698,
year = {2015},
author = {Kim, MJ and Choi, SW and Kim, I},
title = {Saturnia jonasii Butler, 1877 on Jejudo Island, a new saturnid moth of South Korea with DNA data and morphology (Lepidoptera: Saturniidae).},
journal = {Zootaxa},
volume = {3946},
number = {3},
pages = {374-386},
doi = {10.11646/zootaxa.3946.3.5},
pmid = {25947698},
issn = {1175-5334},
mesh = {Animals ; DNA/*genetics ; Female ; Haplotypes ; Islands ; Male ; Moths/anatomy &amp; histology/*classification/*genetics/physiology ; Phylogeny ; Republic of Korea ; Species Specificity ; },
abstract = {Saturnia (Rinaca) jonasii Butler, 1877 is distributed in Japan, including Tsushima Island and Taiwan, whereas S. boisduvalii Eversmann, 1846 is distributed in northern areas, such as China, Russia, and South Korea. In the present study we found that the specimens from Mt. Hallasan on Jejudo, a southern remote offshore island, were S. jonasii, rather than S. boisduvalii based on morphology, DNA barcode, and nuclear elongation factor 1 alpha (EF-1α) sequences. The major morphological differences between the two species included the shape of wing pattern elements of fore- and hindwings and male and female genitalia. A DNA barcode analysis of the sequences of the Jejudo specimens and S. boisduvalii, along with those of Saturnia species obtained from a public database showed a minimum sequence divergence of 4.26% (28 bp). A phylogenetic analysis also showed clustering of the Jejudo specimens with S. jonasii, separating S. boisduvalii (Bayesian posterior probability = 0.99). The EF-1α-based sequence and phylogenetic analyses of the two species from Jejudo Island and the Korean mainland showed the uniqueness of the Jejudo specimens from S. boisduvalii collected on the Korean mainland, indicating distribution of S. jonasii on Jejudo Island in South Korea, instead of S. boisduvalii.},
}
@article {pmid25947503,
year = {2015},
author = {Filho, LC and Packer, L},
title = {Revision of the Neotropical subgenera Coelioxys (Platycoelioxys) Mitchell and C. (Rhinocoelioxys) Mitchell (Hymenoptera; Megachilidae) with the description of one new species.},
journal = {Zootaxa},
volume = {3941},
number = {2},
pages = {151-203},
doi = {10.11646/zootaxa.3941.2.1},
pmid = {25947503},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Bees/anatomy &amp; histology/*classification/growth &amp; development ; Body Size ; Brazil ; Ecosystem ; Female ; Male ; Organ Size ; },
abstract = {Two Neotropical subgenera of Coelioxys Latreille are revised. The monotypic C. (Platycoelioxys) Mitchell and C. (Rhinocoelioxys) Mitchell has seven valid species; six of them (C. agilis Smith, C. barbata Schwarz &amp; Michener, C. clypearis Friese, C. nasidens Friese, C. paraguayensis Schrottky and C. zapoteca Cresson) previously described, and one, C. platygnatha Rocha-Filho &amp; Packer n. sp. is new from Amazonas State, Brazil. Coelioxys nasidens, previously considered a junior synonym of C. clypeata Smith, is resurrected. Coelioxys crassiceps Friese and C. excisa Friese are synonymized under C. agilis, and C. rostrata Friese is synonymized under C. paraguayensis. Nine names (C. clypeata, C. leucochrysea Cockerell, C. angustivalva Holmberg, C. doelloi Holmberg, C. blabera Holmberg, C. mesopotamica Holmberg, C. bilobata Friese, C. bilobata schenki Friese and C. bullaticeps Friese) are synonymized with C. zapoteca. In the latter species the shape of the apical margin of the clypeus of the female varies widely and, though intermediates occur among all forms, the DNA barcode sequences for the different forms are very similar. One species formerly considered as incertae sedis, C. clypearis, and one belonging to the subgenus C. (Cyrtocoelioxys) Mitchell, C. barbata, are both assigned to the subgenus C. (Rhinocoelioxys). Keys for both sexes of C. (Rhinocoelioxys), distribution maps, host and floral records, redescriptions of species and the description of a new species are provided. In the subgenus C. (Platycoelioxys), only one species, C. alatiformis Friese, is recognized with two junior synonyms: C. crassiceps Friese syn. nov. and C. spatuliventer Cockerell.},
}
@article {pmid25947462,
year = {2015},
author = {Yoshida, T and Hirowatari, T},
title = {Larval and pupal morphology of three species of the genus Psammoecus Latreille (Coleoptera: Silvanidae: Brontinae) in Japan with reference to the number of larval instars.},
journal = {Zootaxa},
volume = {3937},
number = {1},
pages = {90-102},
doi = {10.11646/zootaxa.3937.1.4},
pmid = {25947462},
issn = {1175-5334},
mesh = {Animals ; Coleoptera/anatomy &amp; histology/*growth &amp; development ; Larva/anatomy &amp; histology/growth &amp; development ; Pupa/anatomy &amp; histology ; },
abstract = {The last instar larva and the pupa of Psammoecus scitus Yoshida &amp; Hirowatari, all instar larvae of P. simoni Grouvelle, and the last instar larva of P. hiranoi Yoshida &amp; Hirowatari are described, and their morphologies are compared among species and instars. Larval association for P. simoni was confirmed by DNA barcoding. Apart from a brief description of the pupa of Cryptamorpha brevicornis (White) illustrated by Hudson (1924), the pupal morphology of Brontinae is described in detail for the first time. Potentially informative characters for phylogeny of larval and pupal morphology of Silvanidae are discussed.},
}
@article {pmid25947449,
year = {2015},
author = {Shamshev, I and Grootaert, P and Kustov, S},
title = {New data on the genus Hybos Meigen (Diptera: Hybotidae) from the Palaearctic Region.},
journal = {Zootaxa},
volume = {3936},
number = {4},
pages = {451-484},
doi = {10.11646/zootaxa.3936.4.1},
pmid = {25947449},
issn = {1175-5334},
mesh = {Animals ; Diptera/anatomy &amp; histology/*classification ; Europe ; Female ; Male ; },
abstract = {The taxonomy and distribution of the genus Hybos Meigen in the Palaearctic Region is reviewed with a special reference to the European fauna. Twenty-three species have been recorded from the Palaearctic, of which only four species are known from Europe. We describe two new species, H. andradei sp. nov. (Portugal) and H. mediasiaticus sp. nov. (Middle Asia). The status of two previously considered doubtful species of Hybos are validated: H. striatellus Villeneuve, 1913 (Algeria) and H. vagans Loew, 1874 (the Caucasus). Both species are re-described, and the lectotype of H. striatellus is designated. A key to species of Hybos from the western Palaearctic is compiled. Numerous new data on distributions of H. culiciformis (Fabricius, 1775), H. femoratus (Müller, 1776), H. grossipes (Linné, 1767) and H. vagans are given. Hybos culiciformis is recorded for the first time from Algeria, Byelorussia, Croatia, Cyprus, Lebanon, and Portugal; H. femoratus-from Estonia, Georgia (including Abkhazia), Kazakhstan, Mongolia and Ukraine; H. grossipes-from Byelorussia, Estonia, Kazakhstan, Latvia, Mongolia, Ukraine; H. vagans-from Armenia, Azerbaijan, Georgia (including Abkhazia), Russia, Turkey. The variation of some characters in H. culiciformis is discussed and is confirmed for Portugese specimens by COI barcoding. Female postabdominal structures are examined and described for H. andradei sp. nov., H. culiciformis, H. femoratus, H. grossipes, H. mediasiaticus sp. nov., and H. striatellus. Possible relationships of the West-Palaearctic species are discussed. A check-list of Hybos from the Palaearctic Realm is provided.},
}
@article {pmid25947434,
year = {2015},
author = {Parveen, S and Choudhary, JS and Thomas, A and Ramamurthy, VV},
title = {Biology, morphology and DNA barcodes of Tessaratoma javanica (Thunberg) (Hemiptera: Tessaratomidae).},
journal = {Zootaxa},
volume = {3936},
number = {2},
pages = {261-271},
doi = {10.11646/zootaxa.3936.2.6},
pmid = {25947434},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Ecosystem ; Female ; *Heteroptera/anatomy &amp; histology/classification/genetics/physiology ; India ; Life Cycle Stages/physiology ; Male ; },
abstract = {Tessaratoma javanica (Thunberg) (Hemiptera: Tessaratomidae) an important sucking pest of litchi is studied for supplementing information on its biology, morphometrics of life stages and mtCOI (DNA barcodes). More details generated on the study add to the description of stages namely egg, 1st to 5th nymphal instars and adults. The evaluation of morphometrics of the life stages reveal that the progression of growth is more during 2nd to 3rd nymphal stages, and these are critical as far as the growth and development is concerned. The life cycle takes about 141.7±4.25 days; eggs last for 12.81±1.4 days with 97.14±2.86% hatchability; and duration of 1st , 2nd, 3rd, 4th and 5th nymphal instars were 11.69±0.58, 7.23±0.2, 8.63±0.55, 13.04±0.55 and 26.31±0.97 days, respectively. In addition mtCOI analyses have been done employing standard 658 bp barcode fragments facilitating molecular diagnostics of the adults and other life stages and the phylogenetic tree with available sequence in the GenBank.},
}
@article {pmid25947423,
year = {2015},
author = {Hernández-Triana, LM and Chaverri, LG and Rodríguez- Pérez, MA and Prosser, SW and Hebert, PD and Gregory, TR and Johnson, N},
title = {DNA barcoding of Neotropical black flies (Diptera: Simuliidae): Species identification and discovery of cryptic diversity in Mesoamerica.},
journal = {Zootaxa},
volume = {3936},
number = {1},
pages = {93-114},
doi = {10.11646/zootaxa.3936.1.5},
pmid = {25947423},
issn = {1175-5334},
mesh = {Animals ; Base Sequence ; DNA Barcoding, Taxonomic/*methods ; Female ; Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Simuliidae/anatomy &amp; histology/*classification/genetics ; },
abstract = {Although correct taxonomy is paramount for disease control programs and epidemiological studies, morphology-based taxonomy of black flies is extremely difficult. In the present study, the utility of a partial sequence of the COI gene, the DNA barcoding region, for the identification of species of black flies from Mesoamerica was assessed. A total of 32 morphospecies were analyzed, one belonging to the genus Gigantodax and 31 species to the genus Simulium and six of its subgenera (Aspathia, Eusimulium, Notolepria, Psaroniocompsa, Psilopelmia, Trichodagmia). The Neighbour Joining tree (NJ) derived from the DNA barcodes grouped most specimens according to species or species groups recognized by morphotaxonomic studies. Intraspecific sequence divergences within morphologically distinct species ranged from 0.07% to 1.65%, while higher divergences (2.05%-6.13%) in species complexes suggested the presence of cryptic diversity. The existence of well-defined groups within S. callidum (Dyar &amp; Shannon), S. quadrivittatum Loew, and S. samboni Jennings revealed the likely inclusion of cryptic species within these taxa. In addition, the suspected presence of sibling species within S. paynei Vargas and S. tarsatum Macquart was supported. DNA barcodes also showed that specimens of species that are difficult to delimit morphologically such as S. callidum, S. pseudocallidum Díaz Nájera, S. travisi Vargas, Vargas &amp; Ramírez-Pérez, relatives of the species complexes such as S. metallicum Bellardi s.l. (e.g., S. horacioi Okazawa &amp; Onishi, S. jobbinsi Vargas, Martínez Palacios, Díaz Nájera, and S. puigi Vargas, Martínez Palacios &amp; Díaz Nájera), and S. virgatum Coquillett complex (e.g., S. paynei and S. tarsatum) grouped together in the NJ analysis, suggesting they represent valid species. DNA barcoding combined with a sound morphotaxonomic framework provided an effective approach for the identification of medically important black flies species in Mesoamerica and for the discovery of hidden diversity within this group.},
}
@article {pmid25947419,
year = {2015},
author = {Trivinho-Strixino, S and Pepinelli, M},
title = {A systematic study on Endotribelos Grodhaus (Diptera: Chironomidae) from Brazil including DNA barcoding to link males and females.},
journal = {Zootaxa},
volume = {3936},
number = {1},
pages = {1-41},
doi = {10.11646/zootaxa.3936.1.1},
pmid = {25947419},
issn = {1175-5334},
mesh = {Animals ; Brazil ; Chironomidae/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; Female ; Larva ; Male ; Pupa ; },
abstract = {Six new species of Endotribelos from Brazil are described and illustrated as male, female, pupa and larva: E. bicolor sp. n., E. fulvidus sp. n., E. jaragua sp. n., E. jiboia sp. n., E. semibruneus sp. n. and E. sublettei sp. n. The female of E. calophylli Roque &amp; Trivinho-Strixino and the larvae of four unknown morphotypes are also described. Keys including males and larvae of all known species of Endotribelos are provided. Adults' males and females from five species were linked using DNA Barcoding mtCOI sequences.},
}
@article {pmid25941365,
year = {2015},
author = {Daniels, RF and Schaffner, SF and Wenger, EA and Proctor, JL and Chang, HH and Wong, W and Baro, N and Ndiaye, D and Fall, FB and Ndiop, M and Ba, M and Milner, DA and Taylor, TE and Neafsey, DE and Volkman, SK and Eckhoff, PA and Hartl, DL and Wirth, DF},
title = {Modeling malaria genomics reveals transmission decline and rebound in Senegal.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {112},
number = {22},
pages = {7067-7072},
pmid = {25941365},
issn = {1091-6490},
support = {AI099105/AI/NIAID NIH HHS/United States ; R01 AI106734/AI/NIAID NIH HHS/United States ; T32 AI049928/AI/NIAID NIH HHS/United States ; U19AI089696/AI/NIAID NIH HHS/United States ; K23 AI072033/AI/NIAID NIH HHS/United States ; R01 AI099105/AI/NIAID NIH HHS/United States ; 5D43TW001503/TW/FIC NIH HHS/United States ; K23AI072033/AI/NIAID NIH HHS/United States ; U54 GM088558/GM/NIGMS NIH HHS/United States ; U19 AI089696/AI/NIAID NIH HHS/United States ; U54GM088558/GM/NIGMS NIH HHS/United States ; AI034969/AI/NIAID NIH HHS/United States ; R01 AI034969/AI/NIAID NIH HHS/United States ; D43 TW001503/TW/FIC NIH HHS/United States ; AI106734/AI/NIAID NIH HHS/United States ; },
mesh = {*Epidemiological Monitoring ; *Genetic Variation ; Genetics, Population/*methods ; Genotype ; Humans ; Malaria/*epidemiology/*parasitology/transmission ; Models, Genetic ; Plasmodium falciparum/*genetics ; Senegal/epidemiology ; },
abstract = {To study the effects of malaria-control interventions on parasite population genomics, we examined a set of 1,007 samples of the malaria parasite Plasmodium falciparum collected in Thiès, Senegal between 2006 and 2013. The parasite samples were genotyped using a molecular barcode of 24 SNPs. About 35% of the samples grouped into subsets with identical barcodes, varying in size by year and sometimes persisting across years. The barcodes also formed networks of related groups. Analysis of 164 completely sequenced parasites revealed extensive sharing of genomic regions. In at least two cases we found first-generation recombinant offspring of parents whose genomes are similar or identical to genomes also present in the sample. An epidemiological model that tracks parasite genotypes can reproduce the observed pattern of barcode subsets. Quantification of likelihoods in the model strongly suggests a reduction of transmission from 2006-2010 with a significant rebound in 2012-2013. The reduced transmission and rebound were confirmed directly by incidence data from Thiès. These findings imply that intensive intervention to control malaria results in rapid and dramatic changes in parasite population genomics. The results also suggest that genomics combined with epidemiological modeling may afford prompt, continuous, and cost-effective tracking of progress toward malaria elimination.},
}
@article {pmid25940779,
year = {2015},
author = {Thirumalai, R and Mukhopadhyay, RD and Praveen, VK and Ajayaghosh, A},
title = {A slippery molecular assembly allows water as a self-erasable security marker.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {9842},
pmid = {25940779},
issn = {2045-2322},
abstract = {Protection of currency and valuable documents from counterfeit continues to be a challenge. While there are many embedded security features available for document safety, they are not immune to forgery. Fluorescence is a sensitive property, which responds to external stimuli such as solvent polarity, temperature or mechanical stress, however practical use in security applications is hampered due to several reasons. Therefore, a simple and specific stimuli responsive security feature that is difficult to duplicate is of great demand. Herein we report the design of a fluorescent molecular assembly on which water behaves as a self-erasable security marker for checking the authenticity of documents at point of care. The underlying principle involves the disciplined self-assembly of a tailor-made fluorescent molecule, which initially form a weak blue fluorescence (λem = 425 nm, Φf = 0.13) and changes to cyan emission (λem = 488 nm,Φf = 0.18) in contact with water due to a reversible molecular slipping motion. This simple chemical tool, based on the principles of molecular self-assembly and fluorescence modulation, allows creation of security labels and optically masked barcodes for multiple documents authentication.},
}
@article {pmid25939459,
year = {2015},
author = {Javanbakht, H and Kvičerová, J and Dvořáková, N and Mikulíček, P and Sharifi, M and Kautman, M and Maršíková, A and Široký, P},
title = {Phylogeny, Diversity, Distribution, and Host Specificity of Haemoproteus spp. (Apicomplexa: Haemosporida: Haemoproteidae) of Palaearctic Tortoises.},
journal = {The Journal of eukaryotic microbiology},
volume = {62},
number = {5},
pages = {670-678},
doi = {10.1111/jeu.12227},
pmid = {25939459},
issn = {1550-7408},
mesh = {Animals ; Cytochromes b/genetics ; DNA, Protozoan ; Haemosporida/*classification/cytology/*genetics ; Haplotypes ; *Host Specificity ; Molecular Sequence Data ; Phylogeny ; Protozoan Infections, Animal/*parasitology ; Turtles/*parasitology ; },
abstract = {A complex wide-range study on the haemoproteid parasites of chelonians was carried out for the first time. Altogether, 811 samples from four tortoise species from an extensive area between western Morocco and eastern Afghanistan and between Romania and southern Syria were studied by a combination of microscopic and molecular-genetic methods. Altogether 160 Haemoproteus-positive samples were gathered in the area between central Anatolia and eastern Afghanistan. According to variability in the cytochrome b gene, two monophyletic evolutionary lineages were distinguished; by means of microscopic analysis it was revealed that they corresponded to two previously described species-Haemoproteus anatolicum and Haemoproteus caucasica. Their distribution areas overlap only in a narrow strip along the Zagros Mts. range in Iran. This fact suggests the involvement of two different vector species with separated distribution. Nevertheless, no vectors were confirmed. According to phylogenetic analyses, H. caucasica represented a sister group to H. anatolicum, and both of them were most closely related to H. pacayae and H. peltocephali, described from South American river turtles. Four unique haplotypes were revealed in the population of H. caucasica, compared with seven haplotypes in H. anatolicum. Furthermore, H. caucasica was detected in two tortoise species, Testudo graeca and Testudo horsfieldii, providing evidence that Haemoproteus is not strictly host-specific to the tortoise host species.},
}
@article {pmid25938804,
year = {2015},
author = {Smurthwaite, CA and Williams, W and Fetsko, A and Abbadessa, D and Stolp, ZD and Reed, CW and Dharmawan, A and Wolkowicz, R},
title = {Genetic barcoding with fluorescent proteins for multiplexed applications.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {98},
pages = {},
pmid = {25938804},
issn = {1940-087X},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Fluorescent Dyes/chemistry ; Genetic Markers/genetics ; Green Fluorescent Proteins/chemistry/genetics ; Humans ; Luminescent Proteins/chemistry/*genetics ; Promoter Regions, Genetic ; Protein Engineering/*methods ; Retroviridae/genetics ; },
abstract = {Fluorescent proteins, fluorescent dyes and fluorophores in general have revolutionized the field of molecular cell biology. In particular, the discovery of fluorescent proteins and their genes have enabled the engineering of protein fusions for localization, the analysis of transcriptional activation and translation of proteins of interest, or the general tracking of individual cells and cell populations. The use of fluorescent protein genes in combination with retroviral technology has further allowed the expression of these proteins in mammalian cells in a stable and reliable manner. Shown here is how one can utilize these genes to give cells within a population of cells their own biosignature. As the biosignature is achieved with retroviral technology, cells are barcoded 'indefinitely'. As such, they can be individually tracked within a mixture of barcoded cells and utilized in more complex biological applications. The tracking of distinct populations in a mixture of cells is ideal for multiplexed applications such as discovery of drugs against a multitude of targets or the activation profile of different promoters. The protocol describes how to elegantly develop and amplify barcoded mammalian cells with distinct genetic fluorescent markers, and how to use several markers at once or one marker at different intensities. Finally, the protocol describes how the cells can be further utilized in combination with cell-based assays to increase the power of analysis through multiplexing.},
}
@article {pmid25938480,
year = {2015},
author = {Zhang, J and Chen, M and Dong, X and Lin, R and Fan, J and Chen, Z},
title = {Evaluation of four commonly used DNA barcoding Loci for chinese medicinal plants of the family schisandraceae.},
journal = {PloS one},
volume = {10},
number = {5},
pages = {e0125574},
pmid = {25938480},
issn = {1932-6203},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; *Genetic Loci ; Phylogeny ; Plants, Medicinal/*genetics ; Schisandraceae/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Many species of Schisandraceae are used in traditional Chinese medicine and are faced with contamination and substitution risks due to inaccurate identification. Here, we investigated the discriminatory power of four commonly used DNA barcoding loci (ITS, trnH-psbA, matK, and rbcL) and corresponding multi-locus combinations for 135 individuals from 33 species of Schisandraceae, using distance-, tree-, similarity-, and character-based methods, at both the family level and the genus level. Our results showed that the two spacer regions (ITS and trnH-psbA) possess higher species-resolving power than the two coding regions (matK and rbcL). The degree of species resolution increased with most of the multi-locus combinations. Furthermore, our results implied that the best DNA barcode for the species discrimination at the family level might not always be the most suitable one at the genus level. Here we propose the combination of ITS+trnH-psbA+matK+rbcL as the most ideal DNA barcode for discriminating the medicinal plants of Schisandra and Kadsura, and the combination of ITS+trnH-psbA as the most suitable barcode for Illicium species. In addition, the closely related species Schisandra rubriflora Rehder &amp; E. H. Wilson and Schisandra grandiflora Hook.f. &amp; Thomson, were paraphyletic with each other on phylogenetic trees, suggesting that they should not be distinct species. Furthermore, the samples of these two species from the southern Hengduan Mountains region formed a distinct cluster that was separated from the samples of other regions, implying the presence of cryptic diversity. The feasibility of DNA barcodes for identification of geographical authenticity was also verified here. The database and paradigm that we provide in this study could be used as reference for the authentication of traditional Chinese medicinal plants utilizing DNA barcoding.},
}
@article {pmid25938282,
year = {2016},
author = {Marmiroli, M and Pagano, L and Pasquali, F and Zappettini, A and Tosato, V and Bruschi, CV and Marmiroli, N},
title = {A genome-wide nanotoxicology screen of Saccharomyces cerevisiae mutants reveals the basis for cadmium sulphide quantum dot tolerance and sensitivity.},
journal = {Nanotoxicology},
volume = {10},
number = {1},
pages = {84-93},
doi = {10.3109/17435390.2015.1019586},
pmid = {25938282},
issn = {1743-5404},
mesh = {Cadmium Compounds/*toxicity ; DNA Repair ; Genome, Fungal ; Mutation ; Nystatin/pharmacology ; Oxidative Stress ; *Quantum Dots ; Saccharomyces cerevisiae/*drug effects/genetics ; Sulfides/*toxicity ; },
abstract = {The use of cadmium sulphide quantum dots (CdS QDs) is increasing, particularly in the electronics industry. Their size (1-10 nm in diameter) is, however, such that they can be taken up by living cells. Here, a bakers' yeast (Saccharomyces cerevisiae) deletion mutant collection has been exploited to provide a high-throughput means of revealing the genetic basis for tolerance/susceptibility to CdS QD exposure. The deletion of 112 genes, some associated with the abiotic stress response, some with various metabolic processes, some with mitochondrial organization, some with transport and some with DNA repair, reduced the level of tolerance to CdS QDs. A gene ontology analysis highlighted the role of oxidative stress in determining the cellular response. The transformation of sensitive mutants with centromeric plasmids harbouring DNA from a wild type strain restored the wild type growth phenotype when the complemented genes encoded either HSC82, DSK2 or ALD3. The use of these simple eukaryote knock-out mutants for functional toxicogenomic analysis will inform studies focusing on higher organisms.},
}
@article {pmid25936275,
year = {2015},
author = {Grosjean, S and Ohler, A and Chuaynkern, Y and Cruaud, C and Hassanin, A},
title = {Improving biodiversity assessment of anuran amphibians using DNA barcoding of tadpoles. Case studies from Southeast Asia.},
journal = {Comptes rendus biologies},
volume = {338},
number = {5},
pages = {351-361},
doi = {10.1016/j.crvi.2015.03.015},
pmid = {25936275},
issn = {1768-3238},
mesh = {Animals ; Anura/classification/*physiology ; Asia, Southeastern ; *Biodiversity ; Classification ; Conservation of Natural Resources ; DNA/*genetics ; DNA Barcoding, Taxonomic ; Environmental Monitoring/*methods ; Genetic Markers ; Larva/*physiology ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Reproducibility of Results ; Species Specificity ; },
abstract = {Amphibian populations are dramatically declining, while their inventory is far from being achieved. Tadpoles are usually overlooked from biodiversity survey, whereas their consideration will optimize species counts and knowledge of their ecological and developmental requirements is essential in conservation planning. Two mitochondrial markers, 16S (397 new sequences obtained) and COI (343 new sequences obtained), are used to test DNA barcoding on a set of larval and adult Asian amphibians represented by 83 recognized species from 65 sites. The advantages and drawbacks of each marker are assessed, COI barcoding being advocated for global DNA barcoding, whereas 16S suits for taxonomically or geographically restricted DNA barcoding. About half of the collected tadpoles were badly identified or incompletely named in the field. All tadpole sequences (except one case of probable introgressive hybridization) were correctly assigned to their respective species. Finally six clusters of tadpole sequences without conspecific adults were revealed, stressing the importance of collecting and taking into account tadpoles in biodiversity survey and conservation planning.},
}
@article {pmid25929789,
year = {2015},
author = {Zielske, S and Haase, M},
title = {Molecular phylogeny and a modified approach of character-based barcoding refining the taxonomy of New Caledonian freshwater gastropods (Caenogastropoda, Truncatelloidea, Tateidae).},
journal = {Molecular phylogenetics and evolution},
volume = {89},
number = {},
pages = {171-181},
doi = {10.1016/j.ympev.2015.04.020},
pmid = {25929789},
issn = {1095-9513},
mesh = {Animals ; Australia ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Fresh Water ; Gastropoda/anatomy &amp; histology/*classification/*genetics ; Genetic Markers/genetics ; New Caledonia ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; },
abstract = {The islands of New Caledonia represent one of the world's biodiversity hotspots with many endemic species including freshwater gastropods of the family Tateidae. A phylogenetic analysis based on the mitochondrial COI and 16S rRNA and the nuclear ITS2 genes revealed two cryptic genera, Crosseana gen. n. and Novacaledonia gen. n. In order to provide character-based diagnoses we modified a DNA barcoding approach identifying strings of pairwise diagnostic characters, i.e. alignment positions, at which two genera are alternatively fixed for different nucleotides. The combination or string of all pairwise diagnostic characters was unique for each genus. Inconsistent mitochondrial and nuclear topologies suggest that Hemistomia cockerelli Haase and Bouchet, 1998 and H. fabrorum Haase and Bouchet, 1998, two morphologically well-defined species, hybridize. The age of the most recent common ancestor of the New Caledonian radiation of Tateidae was estimated at 24.6±9.5 MY. These findings are in line with the notion that New Caledonia is rather a Darwinian island that was colonized after an extended phase of submergence - in case of the tateids probably from Australia - despite being a fragment of Gondwanaland.},
}
@article {pmid25926325,
year = {2015},
author = {Zarrei, M and Talent, N and Kuzmina, M and Lee, J and Lund, J and Shipley, PR and Stefanović, S and Dickinson, TA},
title = {DNA barcodes from four loci provide poor resolution of taxonomic groups in the genus Crataegus.},
journal = {AoB PLANTS},
volume = {7},
number = {},
pages = {},
pmid = {25926325},
issn = {2041-2851},
abstract = {DNA barcodes can facilitate identification of organisms especially when morphological characters are limited or unobservable. To what extent this potential is realized in specific groups of plants remains to be determined. Libraries of barcode sequences from well-studied authoritatively identified plants represented by herbarium voucher specimens are needed in order for DNA barcodes to serve their intended purpose, where this is possible, and to understand the reasons behind their failure to do so, when this occurs. We evaluated four loci, widely regarded as universal DNA barcodes for plants, for their utility in hawthorn species identification. Three plastid regions, matK, rbcLa and psbA-trnH, and the internal transcribed spacer 2 (ITS2) of nuclear ribosomal DNA discriminate only some of the species of Crataegus that can be recognized on the basis of their morphology etc. This is, in part, because in Rosaceae tribe Maleae most individual plastid loci yield relatively little taxonomic resolution and, in part, because the effects of allopolyploidization have not been eliminated by concerted evolution of the ITS regions. Although individual plastid markers provided generally poor resolution of taxonomic groups in Crataegus, a few species were notable exceptions. In contrast, analyses of concatenated sequences of the 3 plastid barcode loci plus 11 additional plastid loci gave a well-resolved maternal phylogeny. In the ITS2 tree, different individuals of some species formed groups with taxonomically unrelated species. This is a sign of lineage sorting due to incomplete concerted evolution in ITS2. Incongruence between the ITS2 and plastid trees is best explained by hybridization between different lineages within the genus. In aggregate, limited between-species variation in plastid loci, hybridization and a lack of concerted evolution in ITS2 all combine to limit the utility of standard barcoding markers in Crataegus. These results have implications for authentication of hawthorn materials in natural health products.},
}
@article {pmid25923665,
year = {2015},
author = {Van Steenberge, M and Pariselle, A and Huyse, T and Volckaert, FA and Snoeks, J and Vanhove, MP},
title = {Morphology, molecules, and monogenean parasites: an example of an integrative approach to cichlid biodiversity.},
journal = {PloS one},
volume = {10},
number = {4},
pages = {e0124474},
pmid = {25923665},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; *Biological Evolution ; *Cichlids/classification/parasitology ; Female ; Gills/anatomy &amp; histology/parasitology ; Host Specificity ; Lakes/parasitology ; Male ; *Phylogeny ; Platyhelminths/*classification/physiology/ultrastructure ; Principal Component Analysis ; Species Specificity ; Tanzania ; },
abstract = {The unparalleled biodiversity of Lake Tanganyika (Africa) has fascinated biologists for over a century; its unique cichlid communities are a preferred model for evolutionary research. Although species delineation is, in most cases, relatively straightforward, higher-order classifications were shown not to agree with monophyletic groups. Here, traditional morphological methods meet their limitations. A typical example are the tropheine cichlids currently belonging to Simochromis and Pseudosimochromis. The affiliations of these widespread and abundant cichlids are poorly understood. Molecular work suggested that genus and species boundaries should be revised. Moreover, previous morphological results indicated that intraspecific variation should be considered to delineate species in Lake Tanganyika cichlids. We review the genera Simochromis and Pseudosimochromis using an integrative approach. Besides a morphometric study and a barcoding approach, monogenean Cichlidogyrus (Platyhelminthes: Ancyrocephalidae) gill parasites, often highly species-specific, are used as complementary markers. Six new species are described. Cichlidogyrus raeymaekersi sp. nov., C. muterezii sp. nov. and C. banyankimbonai sp. nov. infect S. diagramma. Cichlidogyrus georgesmertensi sp. nov. was found on S. babaulti and S. pleurospilus, C. franswittei sp. nov. on both S. marginatus and P. curvifrons and C. frankwillemsi sp. nov. only on P. curvifrons. As relatedness between Cichlidogyrus species usually reflects relatedness between hosts, we considered Simochromis monotypic because the three Cichlidogyrus species found on S. diagramma belonged to a different morphotype than those found on the other Simochromis. The transfer of S. babaulti, S. marginatus, S. pleurospilus and S. margaretae to Pseudosimochromis was justified by the similarity of their Cichlidogyrus fauna and the intermediate morphology of S. margaretae. Finally parasite data also supported the synonymy between S. pleurospilus and S. babaulti, a species that contains a large amount of geographical morphological variation.},
}
@article {pmid25923328,
year = {2015},
author = {Gwiazdowski, RA and Foottit, RG and Maw, HE and Hebert, PD},
title = {The hemiptera (insecta) of Canada: constructing a reference library of DNA barcodes.},
journal = {PloS one},
volume = {10},
number = {4},
pages = {e0125635},
pmid = {25923328},
issn = {1932-6203},
mesh = {Animals ; Canada ; *DNA Barcoding, Taxonomic ; *Gene Library ; Hemiptera/classification/*genetics ; Species Specificity ; },
abstract = {DNA barcode reference libraries linked to voucher specimens create new opportunities for high-throughput identification and taxonomic re-evaluations. This study provides a DNA barcode library for about 45% of the recognized species of Canadian Hemiptera, and the publically available R workflow used for its generation. The current library is based on the analysis of 20,851 specimens including 1849 species belonging to 628 genera and 64 families. These individuals were assigned to 1867 Barcode Index Numbers (BINs), sequence clusters that often coincide with species recognized through prior taxonomy. Museum collections were a key source for identified specimens, but we also employed high-throughput collection methods that generated large numbers of unidentified specimens. Many of these specimens represented novel BINs that were subsequently identified by taxonomists, adding barcode coverage for additional species. Our analyses based on both approaches includes 94 species not listed in the most recent Canadian checklist, representing a potential 3% increase in the fauna. We discuss the development of our workflow in the context of prior DNA barcode library construction projects, emphasizing the importance of delineating a set of reference specimens to aid investigations in cases of nomenclatural and DNA barcode discordance. The identification for each specimen in the reference set can be annotated on the Barcode of Life Data System (BOLD), allowing experts to highlight questionable identifications; annotations can be added by any registered user of BOLD, and instructions for this are provided.},
}
@article {pmid25920205,
year = {2014},
author = {Zheng, SH and Li, YK and Ren, WG and Huang, LF},
title = {[Molecular identification in genus of Lilium based on DNA barcoding].},
journal = {Yao xue xue bao = Acta pharmaceutica Sinica},
volume = {49},
number = {12},
pages = {1730-1738},
pmid = {25920205},
issn = {0513-4870},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Lilium/*classification ; },
abstract = {To establish a new method for identifying genus of Lilium by DNA barcoding technology, ITS, ITS2, psbA-trnH, matK and rbcL sequences were analyzed in term of variation of inter- and intra-species, barcoding gap, neighbor-joining tree to distinguish genus of Lilium based on 978 sequences from experimental and GenBank database, and identification efficiency was evaluated by Nearest distance and BLAST1 methods. The results showed that DNA barcoding could identify different species in genus of Lilium. ITS sequence performed higher identification efficiency, and had significant difference between intra- and inter-species. And NJ tree could also divide species into different clades. Results indicate that DNA barcoding can identify genus of Lilium accurately. ITS sequence can be the optimal barcode to identify species of Lilium.},
}
@article {pmid25916734,
year = {2015},
author = {La Rosa, M and Fiannaca, A and Rizzo, R and Urso, A},
title = {Probabilistic topic modeling for the analysis and classification of genomic sequences.},
journal = {BMC bioinformatics},
volume = {16 Suppl 6},
number = {Suppl 6},
pages = {S2},
pmid = {25916734},
issn = {1471-2105},
mesh = {*Algorithms ; Bacteria/*classification/*genetics ; *Genome, Bacterial ; Genomics/*methods ; Models, Statistical ; Sequence Alignment ; Support Vector Machine ; },
abstract = {BACKGROUND: Studies on genomic sequences for classification and taxonomic identification have a leading role in the biomedical field and in the analysis of biodiversity. These studies are focusing on the so-called barcode genes, representing a well defined region of the whole genome. Recently, alignment-free techniques are gaining more importance because they are able to overcome the drawbacks of sequence alignment techniques. In this paper a new alignment-free method for DNA sequences clustering and classification is proposed. The method is based on k-mers representation and text mining techniques.<br><br>METHODS: The presented method is based on Probabilistic Topic Modeling, a statistical technique originally proposed for text documents. Probabilistic topic models are able to find in a document corpus the topics (recurrent themes) characterizing classes of documents. This technique, applied on DNA sequences representing the documents, exploits the frequency of fixed-length k-mers and builds a generative model for a training group of sequences. This generative model, obtained through the Latent Dirichlet Allocation (LDA) algorithm, is then used to classify a large set of genomic sequences.<br><br>RESULTS AND CONCLUSIONS: We performed classification of over 7000 16S DNA barcode sequences taken from Ribosomal Database Project (RDP) repository, training probabilistic topic models. The proposed method is compared to the RDP tool and Support Vector Machine (SVM) classification algorithm in a extensive set of trials using both complete sequences and short sequence snippets (from 400 bp to 25 bp). Our method reaches very similar results to RDP classifier and SVM for complete sequences. The most interesting results are obtained when short sequence snippets are considered. In these conditions the proposed method outperforms RDP and SVM with ultra short sequences and it exhibits a smooth decrease of performance, at every taxonomic level, when the sequence length is decreased.},
}
@article {pmid25913190,
year = {2015},
author = {Wong, MM and Lim, CL and Wilson, JJ},
title = {DNA barcoding implicates 23 species and four orders as potential pollinators of Chinese knotweed (Persicaria chinensis) in Peninsular Malaysia.},
journal = {Bulletin of entomological research},
volume = {105},
number = {4},
pages = {515-520},
doi = {10.1017/S0007485315000358},
pmid = {25913190},
issn = {1475-2670},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Insecta/classification/*genetics/physiology ; Malaysia ; Pollination/*physiology ; Polygonaceae/*physiology ; },
abstract = {Chinese knotweed (Persicaria chinensis) is of ecological and economic importance as a high-risk invasive species and a traditional medicinal herb. However, the insects associated with P. chinensis pollination have received scant attention. As a widespread invasive plant we would expect P. chinensis to be associated with a diverse group of insect pollinators, but lack of taxonomic identification capacity is an impediment to confirm this expectation. In the present study we aimed to elucidate the insect pollinators of P. chinensis in peninsular Malaysia using DNA barcoding. Forty flower visitors, representing the range of morphological diversity observed, were captured at flowers at Ulu Kali, Pahang, Malaysia. Using Automated Barcode Gap Discovery, 17 morphospecies were assigned to 23 species representing at least ten families and four orders. Using the DNA barcode library (BOLD) 30% of the species could be assigned a species name, and 70% could be assigned a genus name. The insects visiting P. chinensis were broadly similar to those previously reported as visiting Persicaria japonica, including honey bees (Apis), droneflies (Eristalis), blowflies (Lucilia) and potter wasps (Eumedes), but also included thrips and ants.},
}
@article {pmid25901115,
year = {2015},
author = {Sohn, JC and Davis, DR and Lopez-Vaamonde, C},
title = {Revision of the genus Philonome Chambers and its proposed reassignment to the family Tineidae (Lepidoptera, Tineoidea).},
journal = {ZooKeys},
volume = {},
number = {494},
pages = {69-106},
pmid = {25901115},
issn = {1313-2989},
abstract = {The New World genus Philonome Chambers, 1874 is revised. This genus comprises twelve species, seven of which are described as new: two species, Philonomenigrescens sp. n. and Philonomewielgusi sp. n., from the United States; four species, Philonomealbivittata sp. n., Philonomecurvilineata sp. n., Philonomekawakitai sp. n., and Philonomelambdagrapha sp. n., from French Guiana; and one species, Philonomepenerivifera sp. n., from Brazil. Lectotypes are designated for Philonomeclemensella Chambers, 1874 and Philonomerivifera Meyrick, 1915. Partially on evidence of their head morphology and particularly from molecular evidence, the genus Philonome, previously associated with Bucculatricidae or Lyonetiidae, is reassigned to Tineidae. A possible systematic position of Philonome within Tineidae is discussed. Eurynome Chambers, 1875, is synonymized with Argyresthia Hübner, 1825 (Argyresthiidae). Photographs of adults and illustrations of genitalia, when available, are provided for all described species of Philonome and two species previously misplaced in Philonome, Argyresthialuteella (Chambers, 1875) and Elachistaalbella (Chambers, 1877). In addition, DNA barcodes were used for the delimitation of most species.},
}
@article {pmid25898573,
year = {2014},
author = {Gu, X and Zhang, XQ and Song, XN and Zang, YM and Li Yan-peng, and Ma, CH and Zhao, BX and Liu, CS},
title = {[A new herbs traceability method based on DNA barcoding-origin-morphology analysis--an example from an adulterant of 'Heiguogouqi'].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {39},
number = {24},
pages = {4759-4762},
pmid = {25898573},
issn = {1001-5302},
mesh = {Berberis/*classification/cytology/genetics ; China ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Drug Contamination ; Drugs, Chinese Herbal/*isolation &amp; purification/standards ; Lycium/*classification/cytology/genetics ; Medicine, Chinese Traditional ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The fruit of Lycium ruthenicum is a common folk medicine in China. Now it is popular for its antioxidative effect and other medical functions. The adulterants of the herb confuse consumers. In order to identify a new adulterant of L. ruthenicum, a research was performed based on NCBI Nucleotide Database ITS Sequence, combined analysis of the origin and morphology of the adulterant to traceable varieties. Total genomic DNA was isolated from the materials, and nuclear DNA ITS sequences were amplified and sequenced; DNA fragments were collated and matched by using ContingExpress. Similarity identification of BLAST analysis was performed. Besides, the distribution of plant origin and morphology were considered to further identification and verification. Families and genera were identified by molecular identification method. The adulterant was identified as plant belonging to Berberis. Origin analysis narrowed the range of sample identification. Seven different kinds of plants in Berberis were potential sources of the sample. Adulterants variety was traced by morphological analysis. The united molecular identification-origin-morphology research proves to be a preceding way to medical herbs traceability with time-saving and economic advantages and the results showed the new adulterant of L. ruthenicum was B. kaschgarica. The main differences between B. kaschgarica and L. ruthenicum are as follows: in terms of the traits, the surface of B. kaschgarica is smooth and crispy, and that of L. ruthenicum is shrinkage, solid and hard. In microscopic characteristics, epicarp cells of B. aschgarica thickening like a string of beads, stone cells as the rectangle, and the stone cell walls of L. ruthenicum is wavy, obvious grain layer. In molecular sequences, the length of ITS sequence of B. kaschgarica is 606 bp, L. ruthenicum is 654 bp, the similarity of the two sequences is 53.32%.},
}
@article {pmid25898278,
year = {2015},
author = {Lee, PS and Sing, KW and Wilson, JJ},
title = {Reading Mammal Diversity from Flies: The Persistence Period of Amplifiable Mammal mtDNA in Blowfly Guts (Chrysomya megacephala) and a New DNA Mini-Barcode Target.},
journal = {PloS one},
volume = {10},
number = {4},
pages = {e0123871},
pmid = {25898278},
issn = {1932-6203},
mesh = {Animals ; Cattle ; DNA, Mitochondrial/*genetics ; Diptera/*chemistry ; Electron Transport Complex IV/genetics ; Gastrointestinal Tract/*chemistry ; Humans ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Most tropical mammal species are threatened or data-deficient. Data collection is impeded by the traditional monitoring approaches which can be laborious, expensive and struggle to detect cryptic diversity. Monitoring approaches using mammal DNA derived from invertebrates are emerging as cost- and time-effective alternatives. As a step towards development of blowfly-derived DNA as an effective method for mammal monitoring in the biodiversity hotspot of Peninsular Malaysia, our objectives were (i) to determine the persistence period of amplifiable mammal mtDNA in blowfly guts through a laboratory feeding experiment (ii) to design and test primers that can selectively amplify mammal COI DNA mini-barcodes in the presence of high concentrations of blowfly DNA. The persistence period of amplifiable mammal mtDNA in blowfly guts was 24 h to 96 h post-feeding indicating the need for collecting flies within 24 h of capture to detect mammal mtDNA of sufficient quantity and quality. We designed a new primer combination for a COI DNA mini-barcode that did not amplify blowfly DNA and showed 89% amplification success for a dataset of mammals from Peninsular Malaysia. The short (205 bp) DNA mini-barcode could distinguish most mammal species (including separating dark taxa) and is of suitable length for high-throughput sequencing. Our new DNA mini-barcode target and a standardized trapping protocol with retrieval of blowflies every 24 h could point the way forward in the development of blowfly-derived DNA as an effective method for mammal monitoring.},
}
@article {pmid25893977,
year = {2015},
author = {Periasamy, M and Schafleitner, R and Muthukalingan, K and Ramasamy, S},
title = {Phylogeographical Structure in Mitochondrial DNA of Legume Pod Borer (Maruca vitrata) Population in Tropical Asia and Sub-Saharan Africa.},
journal = {PloS one},
volume = {10},
number = {4},
pages = {e0124057},
pmid = {25893977},
issn = {1932-6203},
mesh = {Africa South of the Sahara ; Algorithms ; Animals ; Asia ; Australia ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Genetic Variation ; *Genetics, Population ; Geography ; Haplotypes ; Indonesia ; Moths/*genetics ; Papua New Guinea ; Phylogeny ; Phylogeography ; Polymerase Chain Reaction ; Polymorphism, Genetic ; },
abstract = {This study was undertaken to assess the genetic diversity and host plant races of M. vitrata population in South and Southeast Asia and sub-Saharan Africa. The cytochrome c oxidase subunit 1 (cox1) gene was used to understand the phylogenetic relationship of geographically different M. vitrata population, but previous studies did not include population from Southeast Asia, the probable center of origin for Maruca, and from east Africa. Extensive sampling was done from different host plant species in target countries. Reference populations from Oceania and Latin America were used. An amplicon of 658 bp was produced by polymerase chain reaction, and 64 haplotypes were identified in 686 M. vitrata individuals. Phylogenetic analysis showed no difference among the M. vitrata population from different host plants. However, the results suggested that M. vitrata has formed two putative subspecies (which cannot be differentiated based on morphological characters) in Asia and sub-Saharan Africa, as indicated by the high pairwise FST values (0.44-0.85). The extremely high FST values (≥ 0.93) of Maruca population in Latin America and Oceania compared to Asian and African population seem to indicate a different species. On the continental or larger geographical region basis, the genetic differentiation is significantly correlated with the geographical distance. In addition, two putative species of Maruca, including M. vitrata occur in Australia, Indonesia and Papua New Guinea. The negative Tajima's D and Fu's FS values showed the recent demographic expansion of Maruca population. The haplotype network and Automatic Barcode Gap Discovery analyses confirmed the results of phylogenetic analysis. Thus, this study confirmed the presence of three putative Maruca species, including one in Latin America, one in Oceania (including Indonesia) and M. vitrata in Asia, Africa and Oceania. Hence, the genetic differences in Maruca population should be carefully considered while designing the pest management strategies in different regions.},
}
@article {pmid25893251,
year = {2015},
author = {Dickey, AM and Kumar, V and Hoddle, MS and Funderburk, JE and Morgan, JK and Jara-Cavieres, A and Shatters, RG and Osborne, LS and McKenzie, CL},
title = {The Scirtothrips dorsalis Species Complex: Endemism and Invasion in a Global Pest.},
journal = {PloS one},
volume = {10},
number = {4},
pages = {e0123747},
pmid = {25893251},
issn = {1932-6203},
mesh = {Animals ; Bayes Theorem ; Electron Transport Complex IV/genetics ; Genetic Loci ; Genetic Variation ; Genetics, Population ; *Internationality ; *Introduced Species ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Species Specificity ; Thysanoptera/*genetics ; },
abstract = {Invasive arthropods pose unique management challenges in various environments, the first of which is correct identification. This apparently mundane task is particularly difficult if multiple species are morphologically indistinguishable but accurate identification can be determined with DNA barcoding provided an adequate reference set is available. Scirtothrips dorsalis is a highly polyphagous plant pest with a rapidly expanding global distribution and this species, as currently recognized, may be comprised of cryptic species. Here we report the development of a comprehensive DNA barcode library for S. dorsalis and seven nuclear markers via next-generation sequencing for identification use within the complex. We also report the delimitation of nine cryptic species and two morphologically distinguishable species comprising the S. dorsalis species complex using histogram analysis of DNA barcodes, Bayesian phylogenetics, and the multi-species coalescent. One member of the complex, here designated the South Asia 1 cryptic species, is highly invasive, polyphagous, and likely the species implicated in tospovirus transmission. Two other species, South Asia 2, and East Asia 1 are also highly polyphagous and appear to be at an earlier stage of global invasion. The remaining members of the complex are regionally endemic, varying in their pest status and degree of polyphagy. In addition to patterns of invasion and endemism, our results provide a framework both for identifying members of the complex based on their DNA barcode, and for future species delimiting efforts.},
}
@article {pmid25892157,
year = {2016},
author = {Hawlitschek, O and Morinière, J and Dunz, A and Franzen, M and Rödder, D and Glaw, F and Haszprunar, G},
title = {Comprehensive DNA barcoding of the herpetofauna of Germany.},
journal = {Molecular ecology resources},
volume = {16},
number = {1},
pages = {242-253},
doi = {10.1111/1755-0998.12416},
pmid = {25892157},
issn = {1755-0998},
mesh = {Amphibians/*classification/genetics ; Animals ; Biodiversity ; DNA/*genetics ; DNA Barcoding, Taxonomic ; Germany ; Phylogeny ; Reptiles/*classification/genetics ; },
abstract = {We present the first comprehensive DNA barcoding study of German reptiles and amphibians representing likewise the first on the European herpetofauna. A total of 248 barcodes for all native species and subspecies in the country and a few additional taxa were obtained in the framework of the projects 'Barcoding Fauna Bavarica' (BFB) and 'German Barcode of Life' (GBOL). In contrast to many invertebrate groups, the success rate of the identification of mitochondrial lineages representing species via DNA barcode was almost 100% because no cases of Barcode Index Number (BIN) sharing were detected within German native reptiles and amphibians. However, as expected, a reliable identification of the hybridogenetic species complex in the frog genus Pelophylax was not possible. Deep conspecific lineages resulting in the identification of more than one BIN were found in Lissotriton vulgaris, Natrix natrix and the hybridogenetic Pelophylax complex. A high variety of lineages with different BINs was also found in the barcodes of wall lizards (Podarcis muralis), confirming the existence of many introduced lineages and the frequent occurrence of multiple introductions. Besides the reliable species identification of all life stages and even of tissue remains, our study highlights other potential applications of DNA barcoding concerning German amphibians and reptiles, such as the detection of allochthonous lineages, monitoring of gene flow and also noninvasive sampling via environmental DNA. DNA barcoding based on COI has now proven to be a reliable and efficient tool for studying most amphibians and reptiles as it is already for many other organism groups in zoology.},
}
@article {pmid25892063,
year = {2015},
author = {Aivelo, T and Medlar, A and Löytynoja, A and Laakkonen, J and Jernvall, J},
title = {Tracking year-to-year changes in intestinal nematode communities of rufous mouse lemurs (Microcebus rufus).},
journal = {Parasitology},
volume = {142},
number = {8},
pages = {1095-1107},
doi = {10.1017/S0031182015000438},
pmid = {25892063},
issn = {1469-8161},
mesh = {Animals ; Cheirogaleidae/*parasitology ; Feces/parasitology ; Female ; Madagascar/epidemiology ; Male ; Nematoda/*physiology ; Nematode Infections/epidemiology/parasitology/*veterinary ; Parasite Egg Count/veterinary ; Seasons ; },
abstract = {While it is known that intestinal parasite communities vary in their composition over time, there is a lack of studies addressing how variation in component communities (between-hosts) manifests in infracommunities (within-host) during the host lifespan. In this study, we investigate the changes in the intestinal parasite infracommunities in wild-living rufous mouse lemurs (Microcebus rufus) from Ranomafana National Park in southeastern Madagascar from 2010 to 2012. We used high-throughput barcoding of the 18S rRNA gene to interrogate parasite community structure. Our results show that in these nematode communities, there were two frequently occurring putative species and four rarer putative species. All putative species were randomly distributed over host individuals and they did not occur in clear temporal patterns. For the individuals caught in at least two different years, there was high turnover of putative species and high variation in fecal egg counts. Our study shows that while there was remarkable variation in infracommunities over time, the component community was relatively stable. Nevertheless, the patterns of prevalence varied substantially between years in each component community.},
}
@article {pmid25889579,
year = {2015},
author = {Nielsen, SA and Kristensen, M},
title = {Delineation of Culicoides species by morphology and barcode exemplified by three new species of the subgenus Culicoides (Diptera: Ceratopogonidae) from Scandinavia.},
journal = {Parasites &amp; vectors},
volume = {8},
number = {},
pages = {151},
pmid = {25889579},
issn = {1756-3305},
mesh = {*Animal Distribution ; Animals ; Ceratopogonidae/classification/*genetics ; *DNA Barcoding, Taxonomic ; Scandinavian and Nordic Countries ; Species Specificity ; },
abstract = {BACKGROUND: Culicoides biting midges (Diptera: Ceratopogonidae) cause biting nuisance to livestock and humans and are vectors of a range of pathogens of medical and veterinary importance. Despite their economic significance, the delineation and identification of species where only morphology is considered, as well as the evolutionary relationships between species within this genus remains problematic. In recent years molecular barcoding has assisted substantially in the identification of biting midges in the multiple entomological survey projects which were initiated in many European countries following the bluetongue outbreak in 2006-2009. These studies revealed potentially new species and "species-complexes" with large genetic and morphological variability. Here we use molecular barcoding, together with morphological analysis, to study subgenus Culicoides Latreille from Scandinavia with focus on three potentially new species.<br><br>METHODS: Biting midges were collected at various sites in Denmark and Sweden. Culicoides specimens were described by variation of a fragment of their cytochrome c oxidase subunit 1 (COI) gene sequence and wing, palp and antennal characters.<br><br>RESULTS: It is shown that three new species initially separated by DNA barcoding with mitochondrial COI can be distinguished by morphological characters. In this context a key to Scandinavian subgenus Culicoides using wing and maxillary palp characters is presented. The key is including the three new species Culicoides boyi, Culicoides selandicus and Culicoides kalix.<br><br>CONCLUSION: Three new species of Culicoides biting midges were identified and could be identified by both molecular and morphological differences. Evaluation of differences between and within taxa of biting midges using COI barcode yielded a rough estimate of species delineation; interspecies differences across Culicoides subgenera approaches 20%, whereas intraspecies differences are below 4% and in most cases below 1%.},
}
@article {pmid25889204,
year = {2015},
author = {Hammer, JF and Emery, D and Bogema, DR and Jenkins, C},
title = {Detection of Theileria orientalis genotypes in Haemaphysalis longicornis ticks from southern Australia.},
journal = {Parasites &amp; vectors},
volume = {8},
number = {},
pages = {229},
pmid = {25889204},
issn = {1756-3305},
mesh = {Animals ; Arachnid Vectors/*parasitology ; Base Sequence ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Genotype ; Ixodidae/genetics/*parasitology ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; Specimen Handling/methods ; Theileria/*genetics ; Victoria ; },
abstract = {BACKGROUND: Theileria are blood-borne intracellular protozoal parasites belonging to the phylum Apicomplexa. Previously considered a benign parasite in Australia, outbreaks of clinical disease resulting from Theileria orientalis genotypes have been reported in Australia since 2006. Since this time, outbreaks have become widespread in south-eastern Australia, resulting in significant adverse impacts on local dairy and beef industries. This paper provides the first investigation into the possible biological and mechanical vectors involved in the rapid spread of the parasite.<br><br>METHODS: To identify possible vectors for disease, ticks, biting flies and mosquitoes were collected within active outbreak regions of Gippsland, Victoria. Ticks were collected from cattle and wildlife, and mosquitoes and biting flies were collected in traps in close proximity to outbreak herds. Ticks were identified via DNA barcoding of the mitochondrial cytochrome oxidase I gene. Barcoded ticks were pooled according to species or phylogenetic group and tested for the presence of T. orientalis and the genotypes Ikeda, Chitose and Buffeli using real-time PCR.<br><br>RESULTS: DNA barcoding and phylogenetic analysis identified ticks from the following species: Haemaphysalis longicornis, Ixodes holocyclus, Ixodes cornuatus, Ixodes hirsti, and Bothriocroton concolor. Additional Haemaphysalis, Ixodes and Bothriocroton spp. were also identified. Of the ticks investigated, only H. longicornis ticks from cattle carried theilerial DNA, with the genotypes Ikeda, Chitose and Buffeli represented. Mosquitoes collected in close proximity to outbreak herds included; Aedes camptorhynchus, Aedes notoscriptus, Coquillettidia linealis, Culex australicus, and Culex molestus. Low levels of T. orientalis Buffeli genotype were detected in some mosquitoes. The haematophagous flies tested negative.<br><br>CONCLUSIONS: This is the first demonstration of a potential vector for T. orientalis in the current Australasian disease outbreak.},
}
@article {pmid25888466,
year = {2015},
author = {Santiago, M and Matano, LM and Moussa, SH and Gilmore, MS and Walker, S and Meredith, TC},
title = {A new platform for ultra-high density Staphylococcus aureus transposon libraries.},
journal = {BMC genomics},
volume = {16},
number = {1},
pages = {252},
pmid = {25888466},
issn = {1471-2164},
support = {T32 AI007061/AI/NIAID NIH HHS/United States ; F32 AI118160/AI/NIAID NIH HHS/United States ; F32AI118160/AI/NIAID NIH HHS/United States ; F31 AI114131/AI/NIAID NIH HHS/United States ; U19AI109764/AI/NIAID NIH HHS/United States ; P01 AI083214/AI/NIAID NIH HHS/United States ; R01 AI099144/AI/NIAID NIH HHS/United States ; P30 EY014104/EY/NEI NIH HHS/United States ; U19 AI109764/AI/NIAID NIH HHS/United States ; P01AI083214/AI/NIAID NIH HHS/United States ; },
mesh = {Bacteriophages/*genetics ; *DNA Transposable Elements ; Gene Expression ; *Gene Library ; Genes, Essential ; Genetic Vectors/*metabolism ; High-Throughput Nucleotide Sequencing ; Mutation ; Sequence Analysis, DNA ; Staphylococcus aureus/*genetics/growth &amp; development/metabolism ; Temperature ; },
abstract = {BACKGROUND: Staphylococcus aureus readily develops resistance to antibiotics and achieving effective therapies to overcome resistance requires in-depth understanding of S. aureus biology. High throughput, parallel-sequencing methods for analyzing transposon mutant libraries have the potential to revolutionize studies of S. aureus, but the genetic tools to take advantage of the power of next generation sequencing have not been fully developed.<br><br>RESULTS: Here we report a phage-based transposition system to make ultra-high density transposon libraries for genome-wide analysis of mutant fitness in any &#x3a6;11-transducible S. aureus strain. The high efficiency of the delivery system has made it possible to multiplex transposon cassettes containing different regulatory elements in order to make libraries in which genes are over- or under-expressed as well as deleted. By incorporating transposon-specific barcodes into the cassettes, we can evaluate how null mutations and changes in gene expression levels affect fitness in a single sequencing data set. Demonstrating the power of the system, we have prepared a library containing more than 690,000 unique insertions. Because one unique feature of the phage-based approach is that temperature-sensitive mutants are retained, we have carried out a genome-wide study of S. aureus genes involved in withstanding temperature stress. We find that many genes previously identified as essential are temperature sensitive and also identify a number of genes that, when disrupted, confer a growth advantage at elevated temperatures.<br><br>CONCLUSIONS: The platform described here reliably provides mutant collections of unparalleled genotypic diversity and will enable a wide range of functional genomic studies in S. aureus.},
}
@article {pmid25887893,
year = {2015},
author = {Herten, K and Hestand, MS and Vermeesch, JR and Van Houdt, JK},
title = {GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments.},
journal = {BMC bioinformatics},
volume = {16},
number = {1},
pages = {73},
pmid = {25887893},
issn = {1471-2105},
mesh = {DNA Restriction Enzymes ; Genotyping Techniques/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Sequence Analysis, DNA/*methods ; *Software ; },
abstract = {BACKGROUND: Massive parallel sequencing is a powerful tool for variant discovery and genotyping. To reduce costs, sequencing of restriction enzyme based reduced representation libraries can be utilized. This technology is generally referred to as Genotyping By Sequencing (GBS). To deal with GBS experimental design and initial processing specific bioinformatic tools are needed.<br><br>RESULTS: GBSX is a package that assists in selecting the appropriate enzyme and the design of compatible in-line barcodes. Post sequencing, it performs optimized demultiplexing using these barcodes to create fastq files per barcode which can easily be plugged into existing variant analysis pipelines. Here we demonstrate the usability of the GBSX toolkit and demonstrate improved in-line barcode demultiplexing and trimming performance compared to existing tools.<br><br>CONCLUSIONS: GBSX provides an easy to use suite of tools for designing and demultiplexing of GBS experiments.},
}
@article {pmid25887410,
year = {2015},
author = {Kracht, D and Schober, S},
title = {Insertion and deletion correcting DNA barcodes based on watermarks.},
journal = {BMC bioinformatics},
volume = {16},
number = {},
pages = {50},
pmid = {25887410},
issn = {1471-2105},
mesh = {*Algorithms ; Computational Biology/*methods ; DNA/analysis/*chemistry/genetics ; *DNA Barcoding, Taxonomic ; *Gene Library ; *Genome, Human ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: Barcode multiplexing is a key strategy for sharing the rising capacity of next-generation sequencing devices: Synthetic DNA tags, called barcodes, are attached to natural DNA fragments within the library preparation procedure. Different libraries, can individually be labeled with barcodes for a joint sequencing procedure. A post-processing step is needed to sort the sequencing data according to their origin, utilizing these DNA labels. The final separation step is called demultiplexing and is mainly determined by the characteristics of the DNA code words used as labels. Currently, we are facing two different strategies for barcoding: One is based on the Hamming distance, the other uses the edit metric to measure distances of code words. The theory of channel coding provides well-known code constructions for Hamming metric. They provide a large number of code words with variable lengths and maximal correction capability regarding substitution errors. However, some sequencing platforms are known to have exceptional high numbers of insertion or deletion errors. Barcodes based on the edit distance can take insertion and deletion errors into account in the decoding process. Unfortunately, there is no explicit code-construction known that gives optimal codes for edit metric.<br><br>RESULTS: In the present work we focus on an entirely different perspective to obtain DNA barcodes. We consider a concatenated code construction, producing so-called watermark codes, which were first proposed by Davey and Mackay, to communicate via binary channels with synchronization errors. We adapt and extend the concepts of watermark codes to use them for DNA sequencing. Moreover, we provide an exemplary set of barcodes that are experimentally compatible with common next-generation sequencing platforms. Finally, a realistic simulation scenario is use to evaluate the proposed codes to show that the watermark concept is suitable for DNA sequencing applications.<br><br>CONCLUSION: Our adaption of watermark codes enables the construction of barcodes that are capable of correcting substitutions, insertion and deletion errors. The presented approach has the advantage of not needing any markers or technical sequences to recover the position of the barcode in the sequencing reads, which poses a significant restriction with other approaches.},
}
@article {pmid25886285,
year = {2015},
author = {Pan, L and Shah, AN and Phelps, IG and Doherty, D and Johnson, EA and Moens, CB},
title = {Rapid identification and recovery of ENU-induced mutations with next-generation sequencing and Paired-End Low-Error analysis.},
journal = {BMC genomics},
volume = {16},
number = {1},
pages = {83},
pmid = {25886285},
issn = {1471-2164},
support = {U54 HD083091/HD/NICHD NIH HHS/United States ; P30 HD002274/HD/NICHD NIH HHS/United States ; NIH P30:HD002274/HD/NICHD NIH HHS/United States ; NIH R01:HD076585/HD/NICHD NIH HHS/United States ; R01 HD076585/HD/NICHD NIH HHS/United States ; },
mesh = {Animals ; Codon, Nonsense/drug effects ; DNA/analysis/isolation &amp; purification ; Ethylnitrosourea/*toxicity ; Gene Library ; Genome/*drug effects ; Genomics/*methods/standards ; *High-Throughput Nucleotide Sequencing/standards ; Male ; Mutation/drug effects ; RNA Splice Sites/genetics ; Sequence Analysis, DNA ; Spermatozoa/metabolism ; Zebrafish/genetics/metabolism ; },
abstract = {BACKGROUND: Targeting Induced Local Lesions IN Genomes (TILLING) is a reverse genetics approach to directly identify point mutations in specific genes of interest in genomic DNA from a large chemically mutagenized population. Classical TILLING processes, based on enzymatic detection of mutations in heteroduplex PCR amplicons, are slow and labor intensive.<br><br>RESULTS: Here we describe a new TILLING strategy in zebrafish using direct next generation sequencing (NGS) of 250 bp amplicons followed by Paired-End Low-Error (PELE) sequence analysis. By pooling a genomic DNA library made from over 9,000 N-ethyl-N-nitrosourea (ENU) mutagenized F1 fish into 32 equal pools of 288 fish, each with a unique Illumina barcode, we reduce the complexity of the template to a level at which we can detect mutations that occur in a single heterozygous fish in the entire library. MiSeq sequencing generates 250 base-pair overlapping paired-end reads, and PELE analysis aligns the overlapping sequences to each other and filters out any imperfect matches, thereby eliminating variants introduced during the sequencing process. We find that this filtering step reduces the number of false positive calls 50-fold without loss of true variant calls. After PELE we were able to validate 61.5% of the mutant calls that occurred at a frequency between 1 mutant call:100 wildtype calls and 1 mutant call:1000 wildtype calls in a pool of 288 fish. We then use high-resolution melt analysis to identify the single heterozygous mutation carrier in the 288-fish pool in which the mutation was identified.<br><br>CONCLUSIONS: Using this NGS-TILLING protocol we validated 28 nonsense or splice site mutations in 20 genes, at a two-fold higher efficiency than using traditional Cel1 screening. We conclude that this approach significantly increases screening efficiency and accuracy at reduced cost and can be applied in a wide range of organisms.},
}
@article {pmid25884109,
year = {2015},
author = {Shokralla, S and Porter, TM and Gibson, JF and Dobosz, R and Janzen, DH and Hallwachs, W and Golding, GB and Hajibabaei, M},
title = {Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {9687},
pmid = {25884109},
issn = {2045-2322},
mesh = {Animals ; Arthropods/genetics/metabolism ; Base Sequence ; DNA/*analysis ; Electron Transport Complex IV/genetics ; *High-Throughput Nucleotide Sequencing ; Molecular Sequence Data ; *Sequence Analysis, DNA ; },
abstract = {Genetic information is a valuable component of biosystematics, especially specimen identification through the use of species-specific DNA barcodes. Although many genomics applications have shifted to High-Throughput Sequencing (HTS) or Next-Generation Sequencing (NGS) technologies, sample identification (e.g., via DNA barcoding) is still most often done with Sanger sequencing. Here, we present a scalable double dual-indexing approach using an Illumina Miseq platform to sequence DNA barcode markers. We achieved 97.3% success by using half of an Illumina Miseq flowcell to obtain 658 base pairs of the cytochrome c oxidase I DNA barcode in 1,010 specimens from eleven orders of arthropods. Our approach recovers a greater proportion of DNA barcode sequences from individuals than does conventional Sanger sequencing, while at the same time reducing both per specimen costs and labor time by nearly 80%. In addition, the use of HTS allows the recovery of multiple sequences per specimen, for deeper analysis of genetic variation in target gene regions.},
}
@article {pmid25880848,
year = {2015},
author = {Rife, TW and Wu, S and Bowden, RL and Poland, JA},
title = {Spiked GBS: a unified, open platform for single marker genotyping and whole-genome profiling.},
journal = {BMC genomics},
volume = {16},
number = {1},
pages = {248},
pmid = {25880848},
issn = {1471-2164},
mesh = {Algorithms ; Alleles ; Breeding ; Cluster Analysis ; DNA Primers/metabolism ; Genetic Markers/*genetics ; Genome, Plant ; Genotype ; Genotyping Techniques/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Sequence Analysis, DNA ; Triticum/genetics ; },
abstract = {BACKGROUND: In plant breeding, there are two primary applications for DNA markers in selection: 1) selection of known genes using a single marker assay (marker-assisted selection; MAS); and 2) whole-genome profiling and prediction (genomic selection; GS). Typically, marker platforms have addressed only one of these objectives.<br><br>RESULTS: We have developed spiked genotyping-by-sequencing (sGBS), which combines targeted amplicon sequencing with reduced representation genotyping-by-sequencing. To minimize the cost of targeted assays, we utilize a small percent of sequencing capacity available in runs of GBS libraries to "spike" amplified targets of a priori alleles tagged with a different set of unique barcodes. This open platform allows multiple, single-target loci to be assayed while simultaneously generating a whole-genome profile. This dual-genotyping approach allows different sets of samples to be evaluated for single markers or whole genome-profiling. Here, we report the application of sGBS on a winter wheat panel that was screened for converted KASP markers and newly-designed markers targeting known polymorphisms in the leaf rust resistance gene Lr34.<br><br>CONCLUSIONS: The flexibility and low-cost of sGBS will enable a range of applications across genetics research. Specifically in breeding applications, the sGBS approach will allow breeders to obtain a whole-genome profile of important individuals while simultaneously targeting specific genes for a range of selection strategies across the breeding program.},
}
@article {pmid25877341,
year = {2015},
author = {Vargas-Gastélum, L and Romero-Olivares, AL and Escalante, AE and Rocha-Olivares, A and Brizuela, C and Riquelme, M},
title = {Impact of seasonal changes on fungal diversity of a semi-arid ecosystem revealed by 454 pyrosequencing.},
journal = {FEMS microbiology ecology},
volume = {91},
number = {5},
pages = {},
doi = {10.1093/femsec/fiv044},
pmid = {25877341},
issn = {1574-6941},
mesh = {Ascomycota/*classification/genetics ; Base Sequence ; Basidiomycota/*classification/genetics ; Coccidioides/genetics/isolation &amp; purification ; Coccidioidomycosis/*epidemiology/microbiology ; DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/genetics ; Ecology ; Ecosystem ; Mexico ; Seasons ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {Fungi play fundamental ecological roles in terrestrial ecosystems. However, their distribution and diversity remain poorly described in natural communities, particularly in arid and semi-arid ecosystems. In order to identify environmental factors determining fungal community structure in these systems, we assessed their diversity in conjunction with soil physicochemical characteristics in a semi-arid ecosystem in Baja California, Mexico, endemic for Coccidioidomycosis (Valley Fever). Two different microhabitats, burrows (influenced by rodent activity) and topsoil, were compared in winter and summer. Using a metagenomic approach, the ITS1 region of nuclear ribosomal DNA was used as barcode. A total of 1940 Operational Taxonomic Units (OTUs) were identified from 362 332 ITS1 sequences obtained by 454 pyrosequencing. Differences in fungal composition between seasons were clearly identified. Moreover, differences in composition between microhabitats were mainly correlated to significant differences in environmental factors, such as moisture and clay content in topsoil samples, and temperature and electrical conductivity in burrow samples. Overall, the fungal community structure (dominated by Ascomycota and Basidiomycota) was less variable between seasons in burrow than in topsoil samples. Coccidioides spp. went undetected by pyrosequencing. However, a nested PCR approach revealed its higher prevalence in burrows.},
}
@article {pmid25875620,
year = {2015},
author = {Yan, HF and Liu, YJ and Xie, XF and Zhang, CY and Hu, CM and Hao, G and Ge, XJ},
title = {DNA barcoding evaluation and its taxonomic implications in the species-rich genus Primula L. in China.},
journal = {PloS one},
volume = {10},
number = {4},
pages = {e0122903},
pmid = {25875620},
issn = {1932-6203},
mesh = {China ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/*genetics ; Phylogeny ; Plastids/genetics ; Primula/classification/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The genus Primula is extremely diverse in the east Himalaya-Hengduan Mountains (HHM) in China as a result of rapid radiation. In order to overcome the difficulty of morphological classification of this genus, we surveyed three plastid regions (rbcL, matK, and trnH-psbA) and two nuclear markers (ITS and ITS2) from 227 accessions representing 66 Primula species across 18 sections, to assess their discriminatory power as barcodes. We found that ITS alone or combined with plastid regions showed the best discrimination across different infrageneric ranks and at species level. We suggest rbcL + matK + ITS as the first choice at present to barcode Primula plants. Although the present barcoding combination performed poorly in many closely related species of Primula, it still provided many new insights into current Primula taxonomy, such as the underlying presence of cryptic species, and several potential improper taxonomic treatments. DNA barcoding is one useful technique in the integrative taxonomy of the genus Primula, but it still requires further efforts to improve its effectiveness in some taxonomically challenging groups.},
}
@article {pmid25867336,
year = {2015},
author = {Zhao, Y and Li, Y and Liu, Y and Yang, YF},
title = {DNA barcoding for efficient identification of Ixiolirion species (Ixioliriaceae).},
journal = {Genetics and molecular research : GMR},
volume = {14},
number = {1},
pages = {1903-1910},
doi = {10.4238/2015.March.13.19},
pmid = {25867336},
issn = {1676-5680},
mesh = {Chloroplasts/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Chloroplast/genetics ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Genetic Markers ; Genetic Variation ; Introns ; Magnoliopsida/*classification/*genetics ; Polymerase Chain Reaction ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Ixiolirion is a genus of unresolved taxonomy. DNA barcoding is a technique that allows species identification using standardized DNA sequences. In this study, a total of 23 individuals, representing 2 Chinese Ixiolirion species, were sampled to test the effectiveness of 3 DNA barcodes [internal transcribed spacer (ITS), chloroplast tRNA intron, and megakaryocyte-associated tyrosine kinase] for species identification. Of the 3 DNA barcodes, ITS displayed the maximum level of polymerase chain reaction and sequencing success as well as the highest sequence variation. Intra-specific sequence distances of ITS, chloroplast tRNA intron, and megakaryocyte-associated tyrosine kinase were 0, 0, and 0-0.1%, respectively, with 8.3, 0.6, and 0.5% as mean inter-specific distances, respectively. All individuals of each species formed a monophyletic group (clade) in the neighbor-joining trees constructed using the 3 single-DNA barcodes. Our results demonstrated that ITS, chloroplast tRNA intron, and megakaryocyte-associated tyrosine kinase DNA markers could be used to identify Ixiolirion species. Our results indicate that DNA barcoding provides a reliable and effective means for discriminating Ixiolirion species, and is a robust tool for resolving taxonomic controversies of Ixiolirion in combination with morphology-based taxonomy.},
}
@article {pmid25867090,
year = {2015},
author = {Dilworth, D and Nelson, CJ},
title = {Rapid identification of chemical genetic interactions in Saccharomyces cerevisiae.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {98},
pages = {e52345},
pmid = {25867090},
issn = {1940-087X},
mesh = {Antimetabolites, Antineoplastic/*pharmacology ; DNA Repair Enzymes/metabolism ; DNA, Fungal/genetics/metabolism ; Fluorouracil/*pharmacology ; Gene-Environment Interaction ; RNA, Fungal/genetics/metabolism ; Saccharomyces cerevisiae/chemistry/*drug effects/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; },
abstract = {Determining the mode of action of bioactive chemicals is of interest to a broad range of academic, pharmaceutical, and industrial scientists. Saccharomyces cerevisiae, or budding yeast, is a model eukaryote for which a complete collection of ~6,000 gene deletion mutants and hypomorphic essential gene mutants are commercially available. These collections of mutants can be used to systematically detect chemical-gene interactions, i.e. genes necessary to tolerate a chemical. This information, in turn, reports on the likely mode of action of the compound. Here we describe a protocol for the rapid identification of chemical-genetic interactions in budding yeast. We demonstrate the method using the chemotherapeutic agent 5-fluorouracil (5-FU), which has a well-defined mechanism of action. Our results show that the nuclear TRAMP RNA exosome and DNA repair enzymes are needed for proliferation in the presence of 5-FU, which is consistent with previous microarray based bar-coding chemical genetic approaches and the knowledge that 5-FU adversely affects both RNA and DNA metabolism. The required validation protocols of these high-throughput screens are also described.},
}
@article {pmid25865498,
year = {2015},
author = {Xu, C and Dong, W and Shi, S and Cheng, T and Li, C and Liu, Y and Wu, P and Wu, H and Gao, P and Zhou, S},
title = {Accelerating plant DNA barcode reference library construction using herbarium specimens: improved experimental techniques.},
journal = {Molecular ecology resources},
volume = {15},
number = {6},
pages = {1366-1374},
doi = {10.1111/1755-0998.12413},
pmid = {25865498},
issn = {1755-0998},
mesh = {China ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/chemistry/*genetics ; Molecular Sequence Data ; Reference Standards ; Ribulose-Bisphosphate Carboxylase/genetics ; Rosaceae/*classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {A well-covered reference library is crucial for successful identification of species by DNA barcoding. The biggest difficulty in building such a reference library is the lack of materials of organisms. Herbarium collections are potentially an enormous resource of materials. In this study, we demonstrate that it is likely to build such reference libraries using the reconstructed (self-primed PCR amplified) DNA from the herbarium specimens. We used 179 rosaceous specimens to test the effects of DNA reconstruction, 420 randomly sampled specimens to estimate the usable percentage and another 223 specimens of true cherries (Cerasus, Rosaceae) to test the coverage of usable specimens to the species. The barcode rbcLb (the central four-sevenths of rbcL gene) and matK was each amplified in two halves and sequenced on Roche GS 454 FLX+. DNA from the herbarium specimens was typically shorter than 300 bp. DNA reconstruction enabled amplification fragments of 400-500 bp without bringing or inducing any sequence errors. About one-third of specimens in the national herbarium of China (PE) were proven usable after DNA reconstruction. The specimens in PE cover all Chinese true cherry species and 91.5% of vascular species listed in Flora of China. It is very possible to build well-covered reference libraries for DNA barcoding of vascular species in China. As exemplified in this study, DNA reconstruction and DNA-labelled next-generation sequencing can accelerate the construction of local reference libraries. By putting the local reference libraries together, a global library for DNA barcoding becomes closer to reality.},
}
@article {pmid25865150,
year = {2015},
author = {Andújar, C and Arribas, P and Ruzicka, F and Crampton-Platt, A and Timmermans, MJ and Vogler, AP},
title = {Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics.},
journal = {Molecular ecology},
volume = {24},
number = {14},
pages = {3603-3617},
doi = {10.1111/mec.13195},
pmid = {25865150},
issn = {1365-294X},
mesh = {Animals ; Bayes Theorem ; *Biodiversity ; *Biota ; Coleoptera/classification ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; *Phylogeny ; Sequence Analysis, DNA ; Spain ; },
abstract = {High-throughput DNA methods hold great promise for the study of taxonomically intractable mesofauna of the soil. Here, we assess species diversity and community structure in a phylogenetic framework, by sequencing total DNA from bulk specimen samples and assembly of mitochondrial genomes. The combination of mitochondrial metagenomics and DNA barcode sequencing of 1494 specimens in 69 soil samples from three geographic regions in southern Iberia revealed >300 species of soil Coleoptera (beetles) from a broad spectrum of phylogenetic lineages. A set of 214 mitochondrial sequences longer than 3000 bp was generated and used to estimate a well-supported phylogenetic tree of the order Coleoptera. Shorter sequences, including cox1 barcodes, were placed on this mitogenomic tree. Raw Illumina reads were mapped against all available sequences to test for species present in local samples. This approach simultaneously established the species richness, phylogenetic composition and community turnover at species and phylogenetic levels. We find a strong signature of vertical structuring in soil fauna that shows high local community differentiation between deep soil and superficial horizons at phylogenetic levels. Within the two vertical layers, turnover among regions was primarily at the tip (species) level and was stronger in the deep soil than leaf litter communities, pointing to layer-mediated drivers determining species diversification, spatial structure and evolutionary assembly of soil communities. This integrated phylogenetic framework opens the application of phylogenetic community ecology to the mesofauna of the soil, among the most diverse and least well-understood ecosystems, and will propel both theoretical and applied soil science.},
}
@article {pmid25860859,
year = {2015},
author = {Kreipe, V and Corral-Hernández, E and Scheu, S and Schaefer, I and Maraun, M},
title = {Phylogeny and species delineation in European species of the genus Steganacarus (Acari, Oribatida) using mitochondrial and nuclear markers.},
journal = {Experimental &amp; applied acarology},
volume = {66},
number = {2},
pages = {173-186},
pmid = {25860859},
issn = {1572-9702},
mesh = {Acari/*classification/*genetics ; Animals ; Arthropod Proteins/*genetics ; Cell Nucleus/genetics ; Electron Transport Complex IV/genetics ; Europe ; Genetic Markers/*genetics ; Mitochondrial Proteins/*genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Species of the genus Steganacarus are soil-living oribatid mites (Acari, Phthiracaridae) with a ptychoid body. The phylogeny and species status of the species of Steganacarus are not resolved, some authors group all ten German species of Steganacarus within the genus Steganacarus whereas others split them into three subgenera, Steganacarus, Tropacarus and Atropacarus. Additionally, two species, S. magnus and T. carinatus, comprise morphotypes of questionable species status. We investigated the phylogeny and species status of ten European Steganacarus species, i.e. S. applicatus, S. herculeanus, S. magnus forma magna, S. magnus forma anomala, S. spinosus, Tropacarus brevipilus, T. carinatus forma carinata, T. carinatus forma pulcherrima, Atropacarus striculus and Rhacaplacarus ortizi. We used two molecular markers, a 251 bp fragment of the nuclear gene 28S rDNA (D3) and a 477 bp fragment of the mitochondrial COI region. The phylogeny based on a combined analysis of D3 and COI separated four subgenera (Steganacarus, Tropacarus and Atropacarus, Rhacaplacarus) indicating that they form monophyletic groups. The COI region separated all ten species of the genus Steganacarus and showed variation within some species often correlating with the geographic origin of the species. Resolution of the more conserved D3 region was limited, indicating that radiation events are rather recent. Overall, our results indicate that both genes alone cannot be used for phylogeny and barcoding since variation is too low in D3 and too high in COI. However, when used in combination these genes provide reliable insight into the phylogeny, radiation and species status of taxa of the genus Steganacarus.},
}
@article {pmid25860802,
year = {2015},
author = {Mitra, A and Skrzypczak, M and Ginalski, K and Rowicka, M},
title = {Strategies for achieving high sequencing accuracy for low diversity samples and avoiding sample bleeding using illumina platform.},
journal = {PloS one},
volume = {10},
number = {4},
pages = {e0120520},
pmid = {25860802},
issn = {1932-6203},
support = {R01 GM112131/GM/NIGMS NIH HHS/United States ; UL1 TR000071/TR/NCATS NIH HHS/United States ; },
mesh = {*High-Throughput Nucleotide Sequencing ; Humans ; MicroRNAs/*analysis ; Pattern Recognition, Automated ; Research Design ; *Sequence Analysis, RNA ; Software ; },
abstract = {Sequencing microRNA, reduced representation sequencing, Hi-C technology and any method requiring the use of in-house barcodes result in sequencing libraries with low initial sequence diversity. Sequencing such data on the Illumina platform typically produces low quality data due to the limitations of the Illumina cluster calling algorithm. Moreover, even in the case of diverse samples, these limitations are causing substantial inaccuracies in multiplexed sample assignment (sample bleeding). Such inaccuracies are unacceptable in clinical applications, and in some other fields (e.g. detection of rare variants). Here, we discuss how both problems with quality of low-diversity samples and sample bleeding are caused by incorrect detection of clusters on the flowcell during initial sequencing cycles. We propose simple software modifications (Long Template Protocol) that overcome this problem. We present experimental results showing that our Long Template Protocol remarkably increases data quality for low diversity samples, as compared with the standard analysis protocol; it also substantially reduces sample bleeding for all samples. For comprehensiveness, we also discuss and compare experimental results from alternative approaches to sequencing low diversity samples. First, we discuss how the low diversity problem, if caused by barcodes, can be avoided altogether at the barcode design stage. Second and third, we present modified guidelines, which are more stringent than the manufacturer's, for mixing low diversity samples with diverse samples and lowering cluster density, which in our experience consistently produces high quality data from low diversity samples. Fourth and fifth, we present rescue strategies that can be applied when sequencing results in low quality data and when there is no more biological material available. In such cases, we propose that the flowcell be re-hybridized and sequenced again using our Long Template Protocol. Alternatively, we discuss how analysis can be repeated from saved sequencing images using the Long Template Protocol to increase accuracy.},
}
@article {pmid25856442,
year = {2015},
author = {Coutinho Moraes, DF and Still, DW and Lum, MR and Hirsch, AM},
title = {DNA-Based Authentication of Botanicals and Plant-Derived Dietary Supplements: Where Have We Been and Where Are We Going?.},
journal = {Planta medica},
volume = {81},
number = {9},
pages = {687-695},
doi = {10.1055/s-0035-1545843},
pmid = {25856442},
issn = {1439-0221},
mesh = {Botany/*methods ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/chemistry/genetics ; Dietary Supplements/analysis/*standards ; Drug Contamination/prevention &amp; control ; Genetic Markers/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Plant Preparations ; Plants, Medicinal/*classification ; Quality Control ; Sequence Analysis, DNA/methods ; },
abstract = {Herbal medicines and botanicals have long been used as sole or additional medical aids worldwide. Currently, billions of dollars are spent on botanicals and related products, but minimal regulation exists regarding their purity, integrity, and efficacy. Cases of adulteration and contamination have led to severe illness and even death in some cases. Identifying the plant material in botanicals and phytomedicines using organoleptic means or through microscopic observation of plant parts is not trivial, and plants are often misidentified. Recently, DNA-based methods have been applied to these products because DNA is not changed by growth conditions unlike the chemical constituents of many active pharmaceutical agents. In recent years, DNA barcoding methods, which are used to identify species diversity in the Tree of Life, have been also applied to botanicals and plant-derived dietary supplements. In this review, we recount the history of DNA-based methods for identification of botanicals and discuss some of the difficulties in defining a specific bar code or codes to use. In addition, we describe how next generation sequencing technologies have enabled new techniques that can be applied to identifying these products with greater authority and resolution. Lastly, we present case histories where dietary supplements, decoctions, and other products have been shown to contain materials other than the main ingredient stipulated on the label. We conclude that there is a fundamental need for greater quality control in this industry, which if not self-imposed, that may result from legislation.},
}
@article {pmid25856381,
year = {2015},
author = {, },
title = {Correction: DNA barcoding of Japanese click beetles (Coleoptera, Elateridae).},
journal = {PloS one},
volume = {10},
number = {4},
pages = {e0124857},
pmid = {25856381},
issn = {1932-6203},
}
@article {pmid25856230,
year = {2015},
author = {Vivien, R and Wyler, S and Lafont, M and Pawlowski, J},
title = {Molecular barcoding of aquatic oligochaetes: implications for biomonitoring.},
journal = {PloS one},
volume = {10},
number = {4},
pages = {e0125485},
pmid = {25856230},
issn = {1932-6203},
mesh = {Animals ; Aquatic Organisms/classification/*genetics ; Base Sequence ; DNA Barcoding, Taxonomic/*methods ; DNA, Intergenic/*genetics ; Environmental Monitoring/*methods ; Genetic Variation/genetics ; Geologic Sediments ; Oligochaeta/classification/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Aquatic oligochaetes are well recognized bioindicators of quality of sediments and water in watercourses and lakes. However, the difficult taxonomic determination based on morphological features compromises their more common use in eco-diagnostic analyses. To overcome this limitation, we investigated molecular barcodes as identification tool for broad range of taxa of aquatic oligochaetes. We report 185 COI and 52 ITS2 rDNA sequences for specimens collected in Switzerland and belonging to the families Naididae, Lumbriculidae, Enchytraeidae and Lumbricidae. Phylogenetic analyses allowed distinguishing 41 lineages separated by more than 10 % divergence in COI sequences. The lineage distinction was confirmed by Automatic Barcode Gap Discovery (ABGD) method and by ITS2 data. Our results showed that morphological identification underestimates the oligochaete diversity. Only 26 of the lineages could be assigned to morphospecies, of which seven were sequenced for the first time. Several cryptic species were detected within common morphospecies. Many juvenile specimens that could not be assigned morphologically have found their home after genetic analysis. Our study showed that COI barcodes performed very well as species identifiers in aquatic oligochaetes. Their easy amplification and good taxonomic resolution might help promoting aquatic oligochaetes as bioindicators for next generation environmental DNA biomonitoring of aquatic ecosystems.},
}
@article {pmid25855737,
year = {2015},
author = {Fiege, JK and Langlois, RA},
title = {Investigating influenza A virus infection: tools to track infection and limit tropism.},
journal = {Journal of virology},
volume = {89},
number = {12},
pages = {6167-6170},
pmid = {25855737},
issn = {1098-5514},
support = {T32 HL007741/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Genes, Reporter ; *Host-Pathogen Interactions ; Humans ; Influenza A virus/*genetics/*physiology ; Molecular Biology/*methods ; *Viral Tropism ; Virology/*methods ; },
abstract = {Influenza A viruses display a broad cellular tropism within the respiratory tracts of mammalian hosts. Uncovering the relationship between tropism and virus immunity, pathogenesis, and transmission will be critical for the development of therapeutic interventions. Here we discuss recent developments of several recombinant strains of influenza A virus. These viruses have inserted reporters to track tropism, microRNA target sites to restrict tropism, or barcodes to assess transmission dynamics, expanding our understanding of pathogen-host interactions.},
}
@article {pmid25855347,
year = {2015},
author = {Clark, NJ and Adlard, RD and Clegg, SM},
title = {Molecular and morphological characterization of Haemoproteus (Parahaemoproteus) ptilotis, a parasite infecting Australian honeyeaters (Meliphagidae), with remarks on prevalence and potential cryptic speciation.},
journal = {Parasitology research},
volume = {114},
number = {5},
pages = {1921-1928},
pmid = {25855347},
issn = {1432-1955},
mesh = {Animals ; Australia/epidemiology ; Base Sequence ; Bird Diseases/epidemiology/*parasitology ; Cytochromes b/genetics ; DNA Barcoding, Taxonomic/veterinary ; DNA, Protozoan/chemistry/genetics ; Genetic Speciation ; *Genetic Variation ; Haemosporida/cytology/*genetics/isolation &amp; purification ; Host Specificity ; Host-Parasite Interactions ; Molecular Sequence Data ; Passeriformes/*parasitology ; Phylogeny ; Prevalence ; Protozoan Infections, Animal/epidemiology/*parasitology ; Sequence Analysis, DNA/veterinary ; },
abstract = {Avian Haemoproteus (Haemosporida) parasites occur in birds on all continents apart from Antarctica. Molecular screening techniques have uncovered previously unforeseen levels of Haemoproteus lineage diversity; however, fewer than 20% of genetic parasite lineages have been linked to morphological descriptions. The process of linking morphological descriptions to DNA barcodes for Haemoproteus spp. is important for the study of host-parasite interactions and the potential for cryptic speciation. Here, we describe cytochrome-b barcodes and morphological diagnostics for the identification of Haemoproteus (Parahaemoproteus) ptilotis, a systematically confusing parasite found in Australian honeyeaters (family Meliphagidae). We characterised infections from the original type host (Lichenostomus chrysops; Family Meliphagidae) as well as from four co-occurring meliphagid species in southeast Queensland, Australia, to investigate intraspecific variation in morphology and lineage identity. We recorded eight lineages that grouped into a well-supported monophyletic group, supporting the linkage of the described lineages to H. ptilotis. However, comparisons of diagnostics between the type host and co-occurring meliphagid hosts revealed high genetic diversity and variable morphology that could be indicative of cryptic speciation. This study highlights that morphological descriptions alongside molecular characterisation remain crucial if we are to gain an understanding of the true diversity and host specificity of protozoan parasites in Australia and elsewhere.},
}
@article {pmid25853978,
year = {2015},
author = {Parvathy, VA and Swetha, VP and Sheeja, TE and Sasikumar, B},
title = {Detection of plant-based adulterants in turmeric powder using DNA barcoding.},
journal = {Pharmaceutical biology},
volume = {53},
number = {12},
pages = {1774-1779},
doi = {10.3109/13880209.2015.1005756},
pmid = {25853978},
issn = {1744-5116},
mesh = {Curcuma/*genetics ; DNA Barcoding, Taxonomic/*methods ; Food Contamination/*analysis ; Plant Extracts/*analysis/*genetics ; Powders ; Rhizome ; },
abstract = {CONTEXT: In its powdered form, turmeric [Curcuma longa L. (Zingiberaceae)], a spice of medical importance, is often adulterated lowering its quality.<br><br>OBJECTIVE: The study sought to detect plant-based adulterants in traded turmeric powder using DNA barcoding.<br><br>MATERIALS AND METHODS: Accessions of Curcuma longa L., Curcuma zedoaria Rosc. (Zingiberaceae), and cassava starch served as reference samples. Three barcoding loci, namely ITS, rbcL, and matK, were used for PCR amplification of the reference samples and commercial samples representing 10 different companies. PCR success rate, sequencing efficiency, occurrence of SNPs, and BLAST analysis were used to assess the potential of the barcoding loci in authenticating the traded samples of turmeric.<br><br>RESULTS: The PCR and sequencing success of the loci rbcL and ITS were found to be 100%, whereas matK showed no amplification. ITS proved to be the ideal locus because it showed greater variability than rbcL in discriminating the Curcuma species. The presence of C. zedoaria could be detected in one of the samples whereas cassava starch, wheat, barley, and rye in other two samples although the label claimed nothing other than turmeric powder in the samples.<br><br>DISCUSSION AND CONCLUSION: Unlabeled materials in turmeric powder are considered as adulterants or fillers, added to increase the bulk weight and starch content of the commodity for economic gains. These adulterants pose potential health hazards to consumers who are allergic to these plants, lowering the product's medicinal value and belying the claim that the product is gluten free. The study proved DNA barcoding as an efficient tool for testing the integrity and the authenticity of commercial products of turmeric.},
}
@article {pmid25849347,
year = {2015},
author = {Vyas, KN and Love, DM and Ionescu, A and Llandro, J and Kollu, P and Mitrelias, T and Holmes, S and Barnes, CH},
title = {The Scanning TMR Microscope for Biosensor Applications.},
journal = {Biosensors},
volume = {5},
number = {2},
pages = {172-186},
pmid = {25849347},
issn = {2079-6374},
mesh = {Biosensing Techniques/*instrumentation ; Magnetic Fields ; Microscopy, Scanning Tunneling/*instrumentation ; },
abstract = {We present a novel tunnel magnetoresistance (TMR) scanning microscope set-up capable of quantitatively imaging the magnetic stray field patterns of micron-sized elements in 3D. By incorporating an Anderson loop measurement circuit for impedance matching, we are able to detect magnetoresistance changes of as little as 0.006%/Oe. By 3D rastering a mounted TMR sensor over our magnetic barcodes, we are able to characterize the complex domain structures by displaying the real component, the amplitude and the phase of the sensor's impedance. The modular design, incorporating a TMR sensor with an optical microscope, renders this set-up a versatile platform for studying and imaging immobilised magnetic carriers and barcodes currently employed in biosensor platforms, magnetotactic bacteria and other complex magnetic domain structures of micron-sized entities. The quantitative nature of the instrument and its ability to produce vector maps of magnetic stray fields has the potential to provide significant advantages over other commonly used scanning magnetometry techniques.},
}
@article {pmid25849130,
year = {2015},
author = {Bhang, HE and Ruddy, DA and Krishnamurthy Radhakrishna, V and Caushi, JX and Zhao, R and Hims, MM and Singh, AP and Kao, I and Rakiec, D and Shaw, P and Balak, M and Raza, A and Ackley, E and Keen, N and Schlabach, MR and Palmer, M and Leary, RJ and Chiang, DY and Sellers, WR and Michor, F and Cooke, VG and Korn, JM and Stegmeier, F},
title = {Studying clonal dynamics in response to cancer therapy using high-complexity barcoding.},
journal = {Nature medicine},
volume = {21},
number = {5},
pages = {440-448},
pmid = {25849130},
issn = {1546-170X},
support = {U54CA143798/CA/NCI NIH HHS/United States ; },
mesh = {Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Carcinoma, Non-Small-Cell Lung/drug therapy/genetics ; Cell Differentiation ; Cell Line, Tumor ; Crizotinib ; DNA/chemistry ; DNA Barcoding, Taxonomic/*methods ; DNA, Complementary/metabolism ; Epithelial-Mesenchymal Transition ; Erlotinib Hydrochloride ; Fusion Proteins, bcr-abl/genetics ; Gene Dosage ; Gene Library ; Humans ; Lung Neoplasms/drug therapy/genetics ; Models, Theoretical ; Neoplasms/*drug therapy/*genetics ; Oligonucleotides/genetics ; Polymerase Chain Reaction ; Proto-Oncogene Proteins c-abl/antagonists &amp; inhibitors ; Proto-Oncogene Proteins c-met/metabolism ; Pyrazoles/administration &amp; dosage ; Pyridines/administration &amp; dosage ; Quinazolines/administration &amp; dosage ; Sequence Analysis, RNA ; },
abstract = {Resistance to cancer therapies presents a significant clinical challenge. Recent studies have revealed intratumoral heterogeneity as a source of therapeutic resistance. However, it is unclear whether resistance is driven predominantly by pre-existing or de novo alterations, in part because of the resolution limits of next-generation sequencing. To address this, we developed a high-complexity barcode library, ClonTracer, which enables the high-resolution tracking of more than 1 million cancer cells under drug treatment. In two clinically relevant models, ClonTracer studies showed that the majority of resistant clones were part of small, pre-existing subpopulations that selectively escaped under therapeutic challenge. Moreover, the ClonTracer approach enabled quantitative assessment of the ability of combination treatments to suppress resistant clones. These findings suggest that resistant clones are present before treatment, which would make up-front therapeutic combinations that target non-overlapping resistance a preferred approach. Thus, ClonTracer barcoding may be a valuable tool for optimizing therapeutic regimens with the goal of curative combination therapies for cancer.},
}
@article {pmid25849083,
year = {2015},
author = {Kekkonen, M and Mutanen, M and Kaila, L and Nieminen, M and Hebert, PD},
title = {Delineating species with DNA barcodes: a case of taxon dependent method performance in moths.},
journal = {PloS one},
volume = {10},
number = {4},
pages = {e0122481},
pmid = {25849083},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Genetic Loci/genetics ; Moths/anatomy &amp; histology/*classification/genetics ; Reproducibility of Results ; },
abstract = {The accelerating loss of biodiversity has created a need for more effective ways to discover species. Novel algorithmic approaches for analyzing sequence data combined with rapidly expanding DNA barcode libraries provide a potential solution. While several analytical methods are available for the delineation of operational taxonomic units (OTUs), few studies have compared their performance. This study compares the performance of one morphology-based and four DNA-based (BIN, parsimony networks, ABGD, GMYC) methods on two groups of gelechioid moths. It examines 92 species of Finnish Gelechiinae and 103 species of Australian Elachistinae which were delineated by traditional taxonomy. The results reveal a striking difference in performance between the two taxa with all four DNA-based methods. OTU counts in the Elachistinae showed a wider range and a relatively low (ca. 65%) OTU match with reference species while OTU counts were more congruent and performance was higher (ca. 90%) in the Gelechiinae. Performance rose when only monophyletic species were compared, but the taxon-dependence remained. None of the DNA-based methods produced a correct match with non-monophyletic species, but singletons were handled well. A simulated test of morphospecies-grouping performed very poorly in revealing taxon diversity in these small, dull-colored moths. Despite the strong performance of analyses based on DNA barcodes, species delineated using single-locus mtDNA data are best viewed as OTUs that require validation by subsequent integrative taxonomic work.},
}
@article {pmid25840908,
year = {2015},
author = {Liu, F and Mbenoun, M and Barnes, I and Roux, J and Wingfield, MJ and Li, G and Li, J and Chen, S},
title = {New Ceratocystis species from Eucalyptus and Cunninghamia in South China.},
journal = {Antonie van Leeuwenhoek},
volume = {107},
number = {6},
pages = {1451-1473},
doi = {10.1007/s10482-015-0441-3},
pmid = {25840908},
issn = {1572-9699},
mesh = {Ascomycota/*classification/genetics/*isolation &amp; purification/physiology ; China ; Cluster Analysis ; Cunninghamia/*microbiology ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Eucalyptus/*microbiology ; Haplotypes ; Molecular Sequence Data ; Peptide Elongation Factor 1/genetics ; Phylogeny ; Sequence Analysis, DNA ; Tubulin/genetics ; },
abstract = {During routine surveys for possible fungal pathogens in the rapidly expanding plantations of Eucalyptus and Cunninghamia lanceolata in China, numerous isolates of unknown species in the genus Ceratocystis (Microascales) were obtained from tree wounds. In this study we identified the Ceratocystis isolates from Eucalyptus and Cunninghamia in the GuangDong, GuangXi, FuJian and HaiNan Provinces of South China based on morphology and through comparisons of DNA sequence data for the ITS, partial β-tubulin and TEF-1α gene regions. Morphological and DNA sequence comparisons revealed two previously unknown species residing in the Indo-Pacific Clade. These are described here as Ceratocystis cercfabiensis sp. nov. and Ceratocystis collisensis sp. nov. Isolates of Ceratocystis cercfabiensis showed intragenomic variation in their ITS sequences and four strains were selected for cloning of the ITS gene region. Twelve ITS haplotypes were obtained from 17 clones selected for sequencing, differing in up to seven base positions and representing two separate phylogenetic groups. This is the first evidence of multiple ITS types in isolates of Ceratocystis residing in the Indo-Pacific Clade. Caution should thus be exercised when using the ITS gene region as a barcoding marker for Ceratocystis species in this clade. This study also represents the first record of a species of Ceratocystis from Cunninghamia.},
}
@article {pmid25837833,
year = {2015},
author = {, },
title = {Correction: implications of hybridization, NUMTs, and overlooked diversity for DNA barcoding of eurasian ground squirrels.},
journal = {PloS one},
volume = {10},
number = {3},
pages = {e0120631},
pmid = {25837833},
issn = {1932-6203},
}
@article {pmid25837628,
year = {2015},
author = {Giudicelli, GC and Mäder, G and de Freitas, LB},
title = {Efficiency of ITS sequences for DNA barcoding in Passiflora (Passifloraceae).},
journal = {International journal of molecular sciences},
volume = {16},
number = {4},
pages = {7289-7303},
pmid = {25837628},
issn = {1422-0067},
mesh = {DNA Barcoding, Taxonomic/methods ; DNA, Plant/*genetics ; DNA, Ribosomal Spacer/*genetics ; Genetic Variation/genetics ; Passiflora/*genetics ; Phylogeny ; Plastids/genetics ; Sequence Analysis, DNA/methods ; Software ; Species Specificity ; },
abstract = {DNA barcoding is a technique for discriminating and identifying species using short, variable, and standardized DNA regions. Here, we tested for the first time the performance of plastid and nuclear regions as DNA barcodes in Passiflora. This genus is a largely variable, with more than 900 species of high ecological, commercial, and ornamental importance. We analyzed 1034 accessions of 222 species representing the four subgenera of Passiflora and evaluated the effectiveness of five plastid regions and three nuclear datasets currently employed as DNA barcodes in plants using barcoding gap, applied similarity-, and tree-based methods. The plastid regions were able to identify less than 45% of species, whereas the nuclear datasets were efficient for more than 50% using "best match" and "best close match" methods of TaxonDNA software. All subgenera presented higher interspecific pairwise distances and did not fully overlap with the intraspecific distance, and similarity-based methods showed better results than tree-based methods. The nuclear ribosomal internal transcribed spacer 1 (ITS1) region presented a higher discrimination power than the other datasets and also showed other desirable characteristics as a DNA barcode for this genus. Therefore, we suggest that this region should be used as a starting point to identify Passiflora species.},
}
@article {pmid25836364,
year = {2015},
author = {, },
title = {Correction: DNA barcoding in pencilfishes (Lebiasinidae: Nannostomus) reveals cryptic diversity across the Brazilian Amazon.},
journal = {PloS one},
volume = {10},
number = {4},
pages = {e0123363},
pmid = {25836364},
issn = {1932-6203},
}
@article {pmid25835040,
year = {2016},
author = {Kang, AR and Kim, MJ and Park, IA and Kim, KY and Kim, I},
title = {Extent and divergence of heteroplasmy of the DNA barcoding region in Anapodisma miramae (Orthoptera: Acrididae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3405-3414},
doi = {10.3109/19401736.2015.1022730},
pmid = {25835040},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic/methods/*standards ; Electron Transport Complex IV/genetics ; Genetic Variation ; *Genome, Mitochondrial ; Grasshoppers/*genetics ; Haplotypes ; Insect Proteins/genetics ; Pseudogenes ; },
abstract = {A partial sequence of the mitochondrial cytochrome oxidase subunit I (COI) gene is widely used as a molecular marker for species identification in animals, also termed a DNA barcode. However, the presence of more than one sequence type in a single individual, also known as heteroplasmy, is one of the shortcomings of barcode identification. In this study, we examined the extent and divergence of COI heteroplasmy, including nuclear-encoded mitochondrial pseudogenes (NUMTs), at the genomic-DNA level from 13 insect species including orthopteran Anapodisma miramae, and a long fragment of mitochondrial DNA and cDNA from A. miramae as templates. When multiple numbers of clones originated from genomic DNA were sequenced, heteroplasmy was prevalent in all species and NUMTs were observed in five species. Long fragment DNA (∼13.5 kb) also is a source of heteroplasmic amplification, but the divergent haplotypes and NUMTs obtained from genomic DNA were not detected in A. miramae. On the other hand, cDNA was relatively heteroplasmy-free. Consistently, one dominant haplotype was always obtained from the genomic DNA-origin clones in all species and also from the long fragment- and cDNA-origin clones in the two tested individuals of A. miramae. Furthermore, the dominant haplotype was identical in sequence, regardless of the DNA source in A. miramae. Thus, one possible solution to avoid the barcoding problem in relationship to heteroplasmy could be the acquisition of multiple numbers of barcoding sequences to determine a dominant haplotype that can be assigned as barcoding sequence for a given species.},
}
@article {pmid25829855,
year = {2015},
author = {Rougerie, R and Lopez-Vaamonde, C and Barnouin, T and Delnatte, J and Moulin, N and Noblecourt, T and Nusillard, B and Parmain, G and Soldati, F and Bouget, C},
title = {PASSIFOR: A reference library of DNA barcodes for French saproxylic beetles (Insecta, Coleoptera).},
journal = {Biodiversity data journal},
volume = {},
number = {3},
pages = {e4078},
pmid = {25829855},
issn = {1314-2828},
abstract = {Saproxylic beetles - associated with dead wood or with other insects, fungi and microorganisms that decompose it - play a major role in forest nutrient cycling. They are important ecosystem service providers and are used as key bio-indicators of old-growth forests. In France alone, where the present study took place, there are about 2500 species distributed within 71 families. This high diversity represents a major challenge for specimen sorting and identification. The PASSIFOR project aims at developing a DNA metabarcoding approach to facilitate and enhance the monitoring of saproxylic beetles as indicators in ecological studies. As a first step toward that goal we assembled a library of DNA barcodes using the standard genetic marker for animals, i.e. a portion of the COI mitochondrial gene. In the present contribution, we release a library including 656 records representing 410 species in 40 different families. Species were identified by expert taxonomists, and each record is linked to a voucher specimen to enable future morphological examination. We also highlight and briefly discuss cases of low interspecific divergences, as well as cases of high intraspecific divergences that might represent cases of overlooked or cryptic diversity.},
}
@article {pmid25829847,
year = {2015},
author = {Hansson, C and Smith, MA and Janzen, DH and Hallwachs, W},
title = {Integrative taxonomy of New World Euplectrus Westwood (Hymenoptera, Eulophidae), with focus on 55 new species from Area de Conservación Guanacaste, northwestern Costa Rica.},
journal = {ZooKeys},
volume = {},
number = {485},
pages = {1-236},
pmid = {25829847},
issn = {1313-2989},
abstract = {90 species of Euplectrus are treated: 55 newly described, all from Area de Conservación Guanacaste (ACG), and 35 previously described species, of which 20 occur in ACG. Three of the previously described species (Euplectrusbrasiliensis Ashmead, Euplectrushircinus (Say), Euplectrusronnai (Brèthes)) have unknown status, owing to missing or severely damaged type material. The new species, all authored by C. Hansson, are: Euplectrusalejandrovalerioi, Euplectrusalexsmithi, Euplectrusalvarowillei, Euplectrusandybennetti, Euplectrusandydeansi, Euplectrusannettewalkerae, Euplectrusbillbrowni, Euplectrusbobwhartoni, Euplectruscarlosarmientoi, Euplectruscarlrettenmeyeri, Euplectruscharlesmicheneri, Euplectruscharlesporteri, Euplectruschrisdarlingi, Euplectruschrisgrinteri, Euplectruscorriemoreauae, Euplectrusdaveroubiki, Euplectrusdavesmithi, Euplectrusdavidwahli, Euplectrusdianariasae, Euplectrusdonquickei, Euplectruseowilsoni, Euplectrusgarygibsoni, Euplectrusgavinbroadi, Euplectrusgerarddelvarei, Euplectrushenrytownesi, Euplectrushowelldalyi, Euplectrushugokonsi, Euplectrusiangauldi, Euplectrusjacklonginoi, Euplectrusjesusugaldei, Euplectrusjimwhitfieldi, Euplectrusjjrodriguezae, Euplectrusjohnheratyi, Euplectrusjohnlasallei, Euplectrusjohnnoyesi, Euplectrusjosefernandezi, Euplectruslubomirmasneri, Euplectrusmarkshawi, Euplectrusmikegatesi, Euplectrusmikeschauffi, Euplectrusmikesharkeyi, Euplectrusninazitaniae, Euplectruspammitchellae, Euplectruspaulhansoni, Euplectruspaulheberti, Euplectruspaulhurdi, Euplectrusphilwardi, Euplectrusrobbinthorpi, Euplectrusronaldzunigai, Euplectrusroysnellingi, Euplectrusscottshawi, Euplectrussondrawardae, Euplectrussydneycameronae, Euplectrusvictoriapookae, Euplectruswonyoungchoi. The species are described or redescribed, and thoroughly and uniformly illustrated, and included in two identification keys, one for females and one for males. Lectotypes are designated for eight species: Euplectruscatocalae Howard (♂), Euplectrusjunctus Gahan (♀), Euplectrusleucotrophis Howard (♂), Euplectrusmarginatus Ashmead (♀), Euplectruspachyscaphus Girault (♀), Euplectrusplatyhypenae Howard (♂), Euplectrussemimarginatus Girault (♀), Heteroscapusronnai Brèthes (♂). One synonym is established: Euplectruswalteri Schauff is a junior synonym of Euplectrustestaceipes (Cameron). Brief image notes and host records are provided on the natural history of the wasps as well as the details of their morphology. Hosts are known for 74 Euplectrus species.},
}
@article {pmid25827719,
year = {2016},
author = {Wetten, A and Campbell, C and Allainguillaume, J},
title = {High-resolution melt and morphological analyses of mealybugs (Hemiptera: Pseudococcidae) from cacao: tools for the control of Cacao swollen shoot virus spread.},
journal = {Pest management science},
volume = {72},
number = {3},
pages = {527-533},
doi = {10.1002/ps.4017},
pmid = {25827719},
issn = {1526-4998},
mesh = {Animals ; Badnavirus/physiology ; Cacao/*physiology/virology ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Entomology/*methods ; Female ; Food Chain ; Hemiptera/classification/*genetics ; Insect Proteins/genetics ; Molecular Sequence Data ; Plant Diseases/prevention &amp; control ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Mealybugs (Hemiptera: Coccoidea: Pseudococcidae) are key vectors of badnaviruses, including Cacao swollen shoot virus (CSSV), the most damaging virus affecting cacao (Theobroma cacao L.). The effectiveness of mealybugs as virus vectors is species dependent, and it is therefore vital that CSSV resistance breeding programmes in cacao incorporate accurate mealybug identification. In this work, the efficacy of a CO1-based DNA barcoding approach to species identification was evaluated by screening a range of mealybugs collected from cacao in seven countries.<br><br>RESULTS: Morphologically similar adult females were characterised by scanning electron microscopy, and then, following DNA extraction, were screened with CO1 barcoding markers. A high degree of CO1 sequence homology was observed for all 11 individual haplotypes, including those accessions from distinct geographical regions. This has allowed the design of a high-resolution melt (HRM) assay capable of rapid identification of the commonly encountered mealybug pests of cacao.<br><br>CONCLUSIONS: HRM analysis readily differentiated between mealybug pests of cacao that cannot necessarily be identified by conventional morphological analysis. This new approach, therefore, has potential to facilitate breeding for resistance to CSSV and other mealybug-transmitted diseases.},
}
@article {pmid25822483,
year = {2015},
author = {Geisen, S and Tveit, AT and Clark, IM and Richter, A and Svenning, MM and Bonkowski, M and Urich, T},
title = {Metatranscriptomic census of active protists in soils.},
journal = {The ISME journal},
volume = {9},
number = {10},
pages = {2178-2190},
pmid = {25822483},
issn = {1751-7370},
mesh = {Biodiversity ; Eukaryota/classification/genetics/*isolation &amp; purification ; Gene Expression Profiling/methods ; Phylogeny ; RNA, Ribosomal/analysis ; Soil/chemistry/*parasitology ; },
abstract = {The high numbers and diversity of protists in soil systems have long been presumed, but their true diversity and community composition have remained largely concealed. Traditional cultivation-based methods miss a majority of taxa, whereas molecular barcoding approaches employing PCR introduce significant biases in reported community composition of soil protists. Here, we applied a metatranscriptomic approach to assess the protist community in 12 mineral and organic soil samples from different vegetation types and climatic zones using small subunit ribosomal RNA transcripts as marker. We detected a broad diversity of soil protists spanning across all known eukaryotic supergroups and revealed a strikingly different community composition than shown before. Protist communities differed strongly between sites, with Rhizaria and Amoebozoa dominating in forest and grassland soils, while Alveolata were most abundant in peat soils. The Amoebozoa were comprised of Tubulinea, followed with decreasing abundance by Discosea, Variosea and Mycetozoa. Transcripts of Oomycetes, Apicomplexa and Ichthyosporea suggest soil as reservoir of parasitic protist taxa. Further, Foraminifera and Choanoflagellida were ubiquitously detected, showing that these typically marine and freshwater protists are autochthonous members of the soil microbiota. To the best of our knowledge, this metatranscriptomic study provides the most comprehensive picture of active protist communities in soils to date, which is essential to target the ecological roles of protists in the complex soil system.},
}
@article {pmid25821577,
year = {2014},
author = {Tang, CQ and Humphreys, AM and Fontaneto, D and Barraclough, TG and Paradis, E},
title = {Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data.},
journal = {Methods in ecology and evolution},
volume = {5},
number = {10},
pages = {1086-1094},
pmid = {25821577},
issn = {2041-210X},
support = {B/G004250/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/G004250/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The generalised mixed Yule coalescent (GMYC) and the Poisson tree process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes. Here, we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2000 separate species delimitation analyses across 16 empirical data sets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses.},
}
@article {pmid25815866,
year = {2015},
author = {Rajavel, AR and Kumar, NP and Natarajan, R and Vanamail, P and Rathinakumar, A and Jambulingam, P},
title = {Morphological and molecular characterization of the ecological, biological and behavioural variants of the JE vector Culex tritaeniorhynchus: an assessment of its taxonomic status.},
journal = {Journal of vector borne diseases},
volume = {52},
number = {1},
pages = {40-51},
pmid = {25815866},
issn = {0972-9062},
mesh = {Animals ; Base Sequence ; Culex/anatomy &amp; histology/*classification/genetics/physiology ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Ecology ; Electron Transport Complex IV/genetics ; Encephalitis, Japanese/*transmission ; Female ; Humans ; Insect Vectors/anatomy &amp; histology/*classification/genetics/physiology ; Larva ; Male ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND &amp; OBJECTIVES: Culex tritaeniorhynchus (Diptera: Culicidae), an important vector of Japanese encephalitis belongs to the Culex vishnui subgroup which includes two other vector species namely, Cx. Vishnui and Cx. pseudovishnui. Many varieties and types of Cx. tritaeniorhynchus have been reported, besides populations that exhibit behavioural and biological differences. This study was undertaken to find out whether Cx. tritaeniorhynchus populations exhibiting behavioural and biological variations, and those from different geographical areas, are comprised of more than one taxon or belong to a single taxon.<br><br>METHODS: Morphological characterization was done by examining 153 morphological and morphometric characters in the larval (75), pupal (60) and adult stages (18) of five geographical populations of Cx. tritaeniorhynchus. Molecular characterization was done by PCR amplification of mitochondrial cytochrome c oxidase (COI) gene sequences (DNA barcodes) and another hypervariable genetic marker, the ribosomal DNA (16S). One-way ANOVA, principal component analysis (PCA) and discriminant factor analysis (DFA) were done for statistical analyses using the statistical package SPSS IBM version 19.0.<br><br>RESULTS: Morphological characterization showed that no intraspecific differentiation can be made among the five geographical populations of Cx. tritaeniorhynchus. Molecular characterization done by DNA barcoding also showed that the COI sequences of all the five populations of Cx. tritaeniorhynchus grouped into a single taxonomic clade plus the genetic differentiation among these was non-significant and the overall gene flow among the populations was very high. Analysis of the ribosomal DNA also confirmed that the Cx. tritaeniorhynchus populations belonged to a single taxon.<br><br>Culex tritaeniorhynchus is a taxon that does not involve cryptic species.},
}
@article {pmid25815560,
year = {2016},
author = {Ahmed, NS and Jaffar Ali, HA},
title = {Numts: an impediment to DNA barcoding of Polyclinids, Tunicata.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3395-3398},
doi = {10.3109/19401736.2015.1018238},
pmid = {25815560},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic/*standards ; Electron Transport Complex IV/genetics ; Phylogeny ; *Pseudogenes ; Urochordata/classification/*genetics ; },
abstract = {The mitochondrial cytochrome c oxidase subunit I (COI) gene, a widely accepted molecular marker for species identification and classification, has been questioned because of the presence of Numts. In this study we found the presence of Numts in the COI chromatogram of two tunicates, Polyclinum indicum and Polyclinum madrasensis belonging to the genus Polyclinum. Numts were also present in our sequence (Accession Number: KJ944391) and in other sequences belonging to genus Polyclinum in the GenBank record. The GeneBank database of genus Polyclinum contains COI-like sequences and COI pseudogenes, but no record of COI gene from Polyclinids. The prevalence of Numts in Polyclinids belonging to Tunicata, is an impediment to DNA barcoding studies of Polyclinum species.},
}
@article {pmid25812056,
year = {2016},
author = {Lin, J and Kong, L and Li, Q},
title = {DNA barcoding of true limpets (Order Patellogastropoda) along coast of China: a case study.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {4},
pages = {2310-2314},
doi = {10.3109/19401736.2015.1022758},
pmid = {25812056},
issn = {2470-1408},
mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Gastropoda/*classification/*genetics ; Genes, Mitochondrial ; Haplotypes ; Phylogeny ; },
abstract = {In this study, we applied a partial sequence of mitochondrial COI gene as DNA barcode to assess the viability of DNA barcoding for distinguishing Patellogastropoda. One-hundred thirty-five COI gene sequences were obtained from 13 species belonging to Nacellidae (Cellana) and Lottiidae (Lottia, Patelloida and Nipponacmea) along the coast of China. The alignment result of these sequences indicated the existence of insertions in mitochondrial COI gene of Patellogastropoda. The Kimura 2-parameter (K2P) distances within species and genera were 0.00-1.01% (average 0.07%) and 18.09-37.80% (average 24.07%), respectively, an obvious barcoding gap existed. All species in our study were clearly discriminated in all trees (neighbor-joining (NJ), Bayesian, and maximum likelihood (ML) tree) with a highly supported clade node. The character-based barcode method successfully identified 100% of the Patellogastropod species included, and performed well in discriminating Patellogastropod genera. The results of this study affirm that DNA barcoding based on the COI gene can identify species belonging to Patellogastropoda rapidly and accurately.},
}
@article {pmid25811597,
year = {2015},
author = {Karanovic, I},
title = {Barcoding of ancient lake ostracods (crustacea) reveals cryptic speciation with extremely low distances.},
journal = {PloS one},
volume = {10},
number = {3},
pages = {e0121133},
pmid = {25811597},
issn = {1932-6203},
mesh = {Animals ; Crustacea/anatomy &amp; histology/*genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; *Genetic Speciation ; Japan ; *Lakes ; Likelihood Functions ; },
abstract = {Ostracods are drastically reduced crustaceans, with never more than eight appendages enclosed between two valves, leaving only a limited number of morphological characters for species delineation. Conservative morphology of characters used to define genera, along with high variability of characters used to define species are creating problems in applying a morphospecies concept. A high intraspecific variability in a Lake Biwa (Japan) endemic, Physocypria biwaensis (Okubo, 1990), has been observed previously but was never studied in detail. Two sympatric forms, differing in pigmentation and size, suggest a presence of reproductive isolation. The aim of this study is to employ molecular and morphometric tools to aid in species delineation within P. biwaensis complex and reconstruct their phylogenetic relationships. A fragment of the mtCOI gene was amplified from 30 specimens, and an additional 37 specimens were studied for morphological characters. Resulting phylogenies showed that each morphologically distinct form is associated with a distinct phylogenetic group based on mtDNA. The average pairwise distance is very low (5%), indicating a recent divergence time. I speculate that there is a possibility that one of them originated in the lake, while the other probably colonized it afterwards. This seems to be supported with an apparent niche partitioning at different depths. In spite of the fact that traditionally used sexual characters are highly variable in these two species, the morphometric analysis of shell and soft part related characters clearly delineates them and suggests that such characters may be useful for future detection of seemingly cryptic ostracod species.},
}
@article {pmid25803607,
year = {2015},
author = {Shapcott, A and Forster, PI and Guymer, GP and McDonald, WJ and Faith, DP and Erickson, D and Kress, WJ},
title = {Mapping biodiversity and setting conservation priorities for SE Queensland's rainforests using DNA barcoding.},
journal = {PloS one},
volume = {10},
number = {3},
pages = {e0122164},
pmid = {25803607},
issn = {1932-6203},
mesh = {Base Sequence ; *Biodiversity ; Cluster Analysis ; Conservation of Natural Resources/*methods ; DNA Barcoding, Taxonomic/*methods ; Geography ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Phylogeography/methods ; Polymerase Chain Reaction ; Queensland ; *Rainforest ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Australian rainforests have been fragmented due to past climatic changes and more recently landscape change as a result of clearing for agriculture and urban spread. The subtropical rainforests of South Eastern Queensland are significantly more fragmented than the tropical World Heritage listed northern rainforests and are subject to much greater human population pressures. The Australian rainforest flora is relatively taxonomically rich at the family level, but less so at the species level. Current methods to assess biodiversity based on species numbers fail to adequately capture this richness at higher taxonomic levels. We developed a DNA barcode library for the SE Queensland rainforest flora to support a methodology for biodiversity assessment that incorporates both taxonomic diversity and phylogenetic relationships. We placed our SE Queensland phylogeny based on a three marker DNA barcode within a larger international rainforest barcode library and used this to calculate phylogenetic diversity (PD). We compared phylo- diversity measures, species composition and richness and ecosystem diversity of the SE Queensland rainforest estate to identify which bio subregions contain the greatest rainforest biodiversity, subregion relationships and their level of protection. We identified areas of highest conservation priority. Diversity was not correlated with rainforest area in SE Queensland subregions but PD was correlated with both the percent of the subregion occupied by rainforest and the diversity of regional ecosystems (RE) present. The patterns of species diversity and phylogenetic diversity suggest a strong influence of historical biogeography. Some subregions contain significantly more PD than expected by chance, consistent with the concept of refugia, while others were significantly phylogenetically clustered, consistent with recent range expansions.},
}
@article {pmid25802715,
year = {2014},
author = {Alemzadeh, E and Haddad, R and Ahmadi, AR},
title = {Phytoplanktons and DNA barcoding: Characterization and molecular analysis of phytoplanktons on the Persian Gulf.},
journal = {Iranian journal of microbiology},
volume = {6},
number = {4},
pages = {296-302},
pmid = {25802715},
issn = {2008-3289},
abstract = {BACKGROUND AND OBJECTIVES: Phytoplanktons are organisms with a very high diversities and global distribution in different habitats. The high distribution of phytoplankton is due to ecological flexibility and their ability to tolerate different climatic conditions and environmental stress. Phytoplankton is the most sensitive biological indicators of water resources. The purpose of this study was to identify the phytoplankton species with emphasis on DNA bar-coding method. The study of phytoplankton variation and the identification of their species composition can provide useful information about the water quality.<br><br>MATERIALS AND METHODS: In this research project, a clone library of the ribosomal small subunit RNA gene (18S rDNA) in the nuclear genome was constructed by PCR using A and SSU-inR1 primers, and then, after examining the clones, selected clones were sequenced.<br><br>RESULTS: Eleven analyzed sequences were identified correctly and characterized by a similarity search of the GenBank database using BLAST (NCBI). In this study, we revealed a wide range of taxonomic groups in the Alveolata (Ciliphora and Dinophyceae), Stramenopiles (Bacillariophyta and Bicosoecida), Rhodophyta and Haptophyceae. Moreover, we found species of fungi and Metazoa (Arthropoda). Most of the sequences were previously unknown but could still be assigned to important marine phyla.<br><br>CONCLUSION: Clone library of 18S rDNA is an accurate method to identify marine specimens and it is recommended as an efficient method for phylogenic studies in marine environments. There seems to be a high diversity and abundance of small eukaryotes in the marine regions of Persian Gulf.},
}
@article {pmid25802363,
year = {2015},
author = {Irinyi, L and Serena, C and Garcia-Hermoso, D and Arabatzis, M and Desnos-Ollivier, M and Vu, D and Cardinali, G and Arthur, I and Normand, AC and Giraldo, A and da Cunha, KC and Sandoval-Denis, M and Hendrickx, M and Nishikaku, AS and de Azevedo Melo, AS and Merseguel, KB and Khan, A and Parente Rocha, JA and Sampaio, P and da Silva Briones, MR and e Ferreira, RC and de Medeiros Muniz, M and Castañón-Olivares, LR and Estrada-Barcenas, D and Cassagne, C and Mary, C and Duan, SY and Kong, F and Sun, AY and Zeng, X and Zhao, Z and Gantois, N and Botterel, F and Robbertse, B and Schoch, C and Gams, W and Ellis, D and Halliday, C and Chen, S and Sorrell, TC and Piarroux, R and Colombo, AL and Pais, C and de Hoog, S and Zancopé-Oliveira, RM and Taylor, ML and Toriello, C and de Almeida Soares, CM and Delhaes, L and Stubbe, D and Dromer, F and Ranque, S and Guarro, J and Cano-Lira, JF and Robert, V and Velegraki, A and Meyer, W},
title = {International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database--the quality controlled standard tool for routine identification of human and animal pathogenic fungi.},
journal = {Medical mycology},
volume = {53},
number = {4},
pages = {313-337},
doi = {10.1093/mmy/myv008},
pmid = {25802363},
issn = {1460-2709},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/*chemistry/*genetics ; *Databases, Nucleic Acid ; Fungi/*classification/genetics ; Humans ; Molecular Diagnostic Techniques/*methods ; Mycoses/*diagnosis/microbiology/veterinary ; Reference Standards ; },
abstract = {Human and animal fungal pathogens are a growing threat worldwide leading to emerging infections and creating new risks for established ones. There is a growing need for a rapid and accurate identification of pathogens to enable early diagnosis and targeted antifungal therapy. Morphological and biochemical identification methods are time-consuming and require trained experts. Alternatively, molecular methods, such as DNA barcoding, a powerful and easy tool for rapid monophasic identification, offer a practical approach for species identification and less demanding in terms of taxonomical expertise. However, its wide-spread use is still limited by a lack of quality-controlled reference databases and the evolving recognition and definition of new fungal species/complexes. An international consortium of medical mycology laboratories was formed aiming to establish a quality controlled ITS database under the umbrella of the ISHAM working group on "DNA barcoding of human and animal pathogenic fungi." A new database, containing 2800 ITS sequences representing 421 fungal species, providing the medical community with a freely accessible tool at http://www.isham.org/ and http://its.mycologylab.org/ to rapidly and reliably identify most agents of mycoses, was established. The generated sequences included in the new database were used to evaluate the variation and overall utility of the ITS region for the identification of pathogenic fungi at intra-and interspecies level. The average intraspecies variation ranged from 0 to 2.25%. This highlighted selected pathogenic fungal species, such as the dermatophytes and emerging yeast, for which additional molecular methods/genetic markers are required for their reliable identification from clinical and veterinary specimens.},
}
@article {pmid25788971,
year = {2015},
author = {Galindo-González, L and Pinzón-Latorre, D and Bergen, EA and Jensen, DC and Deyholos, MK},
title = {Ion Torrent sequencing as a tool for mutation discovery in the flax (Linum usitatissimum L.) genome.},
journal = {Plant methods},
volume = {11},
number = {},
pages = {19},
pmid = {25788971},
issn = {1746-4811},
abstract = {BACKGROUND: Detection of induced mutations is valuable for inferring gene function and for developing novel germplasm for crop improvement. Many reverse genetics approaches have been developed to identify mutations in genes of interest within a mutagenized population, including some approaches that rely on next-generation sequencing (e.g. exome capture, whole genome resequencing). As an alternative to these genome or exome-scale methods, we sought to develop a scalable and efficient method for detection of induced mutations that could be applied to a small number of target genes, using Ion Torrent technology. We developed this method in flax (Linum usitatissimum), to demonstrate its utility in a crop species.<br><br>RESULTS: We used an amplicon-based approach in which DNA samples from an ethyl methanesulfonate (EMS)-mutagenized population were pooled and used as template in PCR reactions to amplify a region of each gene of interest. Barcodes were incorporated during PCR, and the pooled amplicons were sequenced using an Ion Torrent PGM. A pilot experiment with known SNPs showed that they could be detected at a frequency&#x2009;>&#x2009;0.3% within the pools. We then selected eight genes for which we wanted to discover novel mutations, and applied our approach to screen 768 individuals from the EMS population, using either the Ion 314 or Ion 316 chips. Out of 29 potential mutations identified after processing the NGS reads, 16 mutations were confirmed using Sanger sequencing.<br><br>CONCLUSIONS: The methodology presented here demonstrates the utility of Ion Torrent technology in detecting mutation variants in specific genome regions for large populations of a species such as flax. The methodology could be scaled-up to test >100 genes using the higher capacity chips now available from Ion Torrent.},
}
@article {pmid25782000,
year = {2015},
author = {Jiang, Y and Yang, Z and Wang, X and Hou, Y},
title = {Molecular identification of sibling species of Sclerodermus (Hymenoptera: Bethylidae) that parasitize buprestid and cerambycid beetles by using partial sequences of mitochondrial DNA cytochrome oxidase subunit 1 and 28S ribosomal RNA gene.},
journal = {PloS one},
volume = {10},
number = {3},
pages = {e0119573},
pmid = {25782000},
issn = {1932-6203},
mesh = {Animals ; Electron Transport Complex IV/*genetics ; Hymenoptera/classification/*genetics ; Insect Proteins/*genetics ; Phylogeny ; RNA, Ribosomal, 28S/*genetics ; Sequence Homology ; },
abstract = {The species belonging to Sclerodermus (Hymenoptera: Bethylidae) are currently the most important insect natural enemies of wood borer pests, mainly buprestid and cerambycid beetles, in China. However, some sibling species of this genus are very difficult to distinguish because of their similar morphological features. To address this issue, we conducted phylogenetic and genetic analyses of cytochrome oxidase subunit I (COI) and 28S RNA gene sequences from eight species of Sclerodermus reared from different wood borer pests. The eight sibling species were as follows: S. guani Xiao et Wu, S. sichuanensis Xiao, S. pupariae Yang et Yao, and Sclerodermus spp. (Nos. 1-5). A 594-bp fragment of COI and 750-bp fragment of 28S were subsequently sequenced. For COI, the G-C content was found to be low in all the species, averaging to about 30.0%. Sequence divergences (Kimura-2-parameter distances) between congeneric species averaged to 4.5%, and intraspecific divergences averaged to about 0.09%. Further, the maximum sequence divergences between congeneric species and Sclerodermus sp. (No. 5) averaged to about 16.5%. All 136 samples analyzed were included in six reciprocally monophyletic clades in the COI neighbor-joining (NJ) tree. The NJ tree inferred from the 28S rRNA sequence yielded almost identical results, but the samples from S. guani, S. sichuanensis, S. pupariae, and Sclerodermus spp. (Nos. 1-4) clustered together and only Sclerodermus sp. (No. 5) clustered separately. Our findings indicate that the standard barcode region of COI can be efficiently used to distinguish morphologically similar Sclerodermus species. Further, we speculate that Sclerodermus sp. (No. 5) might be a new species of Sclerodermus.},
}
@article {pmid25781890,
year = {2015},
author = {Baniecki, ML and Faust, AL and Schaffner, SF and Park, DJ and Galinsky, K and Daniels, RF and Hamilton, E and Ferreira, MU and Karunaweera, ND and Serre, D and Zimmerman, PA and Sá, JM and Wellems, TE and Musset, L and Legrand, E and Melnikov, A and Neafsey, DE and Volkman, SK and Wirth, DF and Sabeti, PC},
title = {Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections.},
journal = {PLoS neglected tropical diseases},
volume = {9},
number = {3},
pages = {e0003539},
pmid = {25781890},
issn = {1935-2735},
support = {DP2 OD006514/OD/NIH HHS/United States ; R01 AI097366/AI/NIAID NIH HHS/United States ; T32 CA009337/CA/NCI NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; },
mesh = {Africa/epidemiology ; Asia/epidemiology ; Base Sequence ; Chromosome Mapping ; DNA Barcoding, Taxonomic/*methods ; DNA, Protozoan/*genetics ; Genetic Markers/genetics ; Humans ; Malaria, Vivax/epidemiology/*parasitology ; Plasmodium falciparum/classification/genetics/isolation &amp; purification ; Plasmodium vivax/classification/genetics/*isolation &amp; purification ; Polymorphism, Single Nucleotide ; South America/epidemiology ; },
abstract = {Plasmodium vivax, one of the five species of Plasmodium parasites that cause human malaria, is responsible for 25-40% of malaria cases worldwide. Malaria global elimination efforts will benefit from accurate and effective genotyping tools that will provide insight into the population genetics and diversity of this parasite. The recent sequencing of P. vivax isolates from South America, Africa, and Asia presents a new opportunity by uncovering thousands of novel single nucleotide polymorphisms (SNPs). Genotyping a selection of these SNPs provides a robust, low-cost method of identifying parasite infections through their unique genetic signature or barcode. Based on our experience in generating a SNP barcode for P. falciparum using High Resolution Melting (HRM), we have developed a similar tool for P. vivax. We selected globally polymorphic SNPs from available P. vivax genome sequence data that were located in putatively selectively neutral sites (i.e., intergenic, intronic, or 4-fold degenerate coding). From these candidate SNPs we defined a barcode consisting of 42 SNPs. We analyzed the performance of the 42-SNP barcode on 87 P. vivax clinical samples from parasite populations in South America (Brazil, French Guiana), Africa (Ethiopia) and Asia (Sri Lanka). We found that the P. vivax barcode is robust, as it requires only a small quantity of DNA (limit of detection 0.3 ng/μl) to yield reproducible genotype calls, and detects polymorphic genotypes with high sensitivity. The markers are informative across all clinical samples evaluated (average minor allele frequency > 0.1). Population genetic and statistical analyses show the barcode captures high degrees of population diversity and differentiates geographically distinct populations. Our 42-SNP barcode provides a robust, informative, and standardized genetic marker set that accurately identifies a genomic signature for P. vivax infections.},
}
@article {pmid25781848,
year = {2015},
author = {Van Der Meij, SE and Berumen, ML and Paulay, G},
title = {A new species of Fizesereneia Takeda &amp; Tamura, 1980 (Crustacea: Brachyura: Cryptochiridae) from the Red Sea and Oman.},
journal = {Zootaxa},
volume = {3931},
number = {4},
pages = {585-595},
doi = {10.11646/zootaxa.3931.4.8},
pmid = {25781848},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Brachyura/anatomy &amp; histology/*classification/growth &amp; development ; Female ; Indian Ocean ; Male ; Organ Size ; },
abstract = {A new species of cryptochirid crab, Fizesereneia panda van der Meij, is described and illustrated based on specimens collected from the scleractinian corals Lobophyllia cf. hemprichii and L. cf. corymbosa from the Farasan Banks, Farasan Islands, and the reefs off Thuwal in the Saudi Arabian Red Sea, and from Symphyllia recta from reefs in the Gulf of Oman. This is the second cryptochirid species with the Red Sea as type locality. It can be separated from its congeners by the subrectangular carapace, raised midline and the complete division of the carapace depressions, and reddish black colour pattern of these concavities in live specimens. This new species is the seventh assigned to Fizesereneia. A DNA barcode for the new species has been deposited in GenBank.},
}
@article {pmid25781844,
year = {2015},
author = {Soisook, P and Prajakjitr, A and Karapan, S and Francis, CM and Bates, PJ},
title = {A new genus and species of false vampire (Chiroptera: Megadermatidae) from peninsular Thailand.},
journal = {Zootaxa},
volume = {3931},
number = {4},
pages = {528-550},
doi = {10.11646/zootaxa.3931.4.4},
pmid = {25781844},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Chiroptera/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Ecosystem ; Female ; Legendary Creatures ; Male ; Organ Size ; Phylogeny ; Thailand ; },
abstract = {A new genus and associated species of false vampire, family Megadermatidae, are described based on three specimens from Bala Forest, Narathiwat Province, peninsular Thailand. The new taxon is characterised by a unique combination of distinctive dental, cranial, and external characters, some of which are shared with exclusively African genera and some with Asian genera. These characters are comparable to, or exceed in number, those differentiating currently recognised genera in the family Megadermatidae. They include the absence of a first upper premolar; greatly enlarged upper canine without an anterolingual cingular cusp but with a robust posterolingual cusp; unmodified upper first molar with the preparacrista subequal in length to the postmetacrista, the metastyle not reduced and situated labially; robust lower canine without an anterolingual cusp; the first lower premolar enlarged, equal to or larger than the second lower premolar. In the skull, there is a pronounced rostral depression but no well developed frontal shield with preorbital and/or postorbital processes; the coronoid process is greatly enlarged in each half mandible. Externally, the body size is relatively large and the posterior noseleaf is rounded. The baculum has a robust shaft and two short prongs-the bacula of all five other species of megadermatid are illustrated for the first time; extraordinarily, those of Macroderma gigas and Megaderma lyra comprise two separate bones. DNA barcoding indicate a genetic divergence of about 20 percent (sequence divergence in the mitochondrial gene CO1) between the new genus and species of Megaderma and Cardioderma. Currently, despite numerous bat surveys in peninsular Thailand, the new genus is only known from Bala Forest. The small area of this forest and the very low capture rate suggest that the new species may be extremely rare. Its natural history is little known, although its robust dental and cranial features when coupled with chance observations of its feeding behaviour, suggest it may specialise in eating large beetles. Its conservation status is considered to be at risk owing to the rapid loss of forest habitat in much of the Thai-Malay peninsula.},
}
@article {pmid25781324,
year = {2015},
author = {Pallaoro, A and Hoonejani, MR and Braun, GB and Meinhart, CD and Moskovits, M},
title = {Rapid identification by surface-enhanced Raman spectroscopy of cancer cells at low concentrations flowing in a microfluidic channel.},
journal = {ACS nano},
volume = {9},
number = {4},
pages = {4328-4336},
doi = {10.1021/acsnano.5b00750},
pmid = {25781324},
issn = {1936-086X},
mesh = {Cell Line, Tumor ; Cell Separation/*instrumentation/*methods ; Cell Survival ; Humans ; Hydrodynamics ; *Lab-On-A-Chip Devices ; Least-Squares Analysis ; Principal Component Analysis ; *Spectrum Analysis, Raman ; Surface Properties ; Time Factors ; },
abstract = {Reliable identification and collection of cells from bodily fluids is of growing interest for monitoring patient response to therapy and for early detection of disease or its recurrence. We describe a detection platform that combines microfluidics with surface-enhanced Raman spectroscopy (SERS) for the identification of individual mammalian cells continuously flowing in a microfluidics channel. A mixture of cancerous and noncancerous prostate cells was incubated with SERS biotags (SBTs) developed and synthesized by us, then injected into a flow-focused microfluidic channel, which forces the cells into a single file. The spectrally rich SBTs are based on a silver nanoparticle dimer core labeled with a Raman-active small reporter molecule paired with an affinity biomolecule, providing a unique barcode whose presence in a composite SERS spectrum can be deconvoluted. Individual cancer cells passing through the focused laser beam were correctly identified among a proportionally larger number of other cells by their Raman signatures. We examine two deconvolution strategies: principal component analysis and classical least-squares. The deconvolution strategies are used to unmix the overall spectrum to determine the relative contributions between two SBT barcodes, where one SBT barcode indicates neuropilin-1 overexpression, while a second SBT barcode is more universal and indicates unspecific binding to a cell's membrane. Highly reliable results were obtained for all of the cell mixture ratios tested, the lowest being 1 in 100 cells.},
}
@article {pmid25781250,
year = {2015},
author = {Deharveng, L and Zoughailech, A and Hamra-Kroua, S and Porco, D},
title = {A new species of Deutonura (Collembola: Neanuridae: Neanurinae) from north-eastern Algeria, and characterisation of two intraspecific lineages by their barcodes.},
journal = {Zootaxa},
volume = {3920},
number = {2},
pages = {281-290},
doi = {10.11646/zootaxa.3920.2.4},
pmid = {25781250},
issn = {1175-5334},
mesh = {Algeria ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Arthropods/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Body Size ; Female ; Male ; Organ Size ; *Phylogeny ; },
abstract = {A new species of Deutonura, D. zana sp. nov., is described from north-eastern Algeria. It is morphologically similar in most characters to D. deficiens meridionalis and to D. luberonensis, both members of the D. phlegraea group, differing from the former by the absence of chaeta O on head, and from the later by the separation of tubercles Di and De on Th. I. The muscular insertion pattern of the new species is figured, and suggested as a potential new character for the taxonomy of Neanurinae. Deutonura zana sp. nov. is well characterised by its barcode sequence. Within the new species as morphologically defined, two groups of COI haplotypes, in individuals indistinguishable morphologically, are reported from two distinct mountain ranges. The need of a morphological assessment of demes diverging at significant infra-specific level in their barcodes is stressed.},
}
@article {pmid25781143,
year = {2015},
author = {Grebennikov, VV and Smetana, A},
title = {DNA barcoding and regional diversity of understudied Micropeplinae (Coleoptera: Staphylinidae) in Southwest China: phylogenetic implications and a new Micropeplus from Mount Emei.},
journal = {Zootaxa},
volume = {3919},
number = {3},
pages = {583-599},
doi = {10.11646/zootaxa.3919.3.8},
pmid = {25781143},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Biodiversity ; Body Size ; China ; Coleoptera/anatomy &amp; histology/*classification/genetics/growth &amp; development ; DNA Barcoding, Taxonomic ; Ecosystem ; Female ; Male ; Organ Size ; *Phylogeny ; },
abstract = {Extensive litter sampling at eight forested localities in Yunnan and Sichuan detected 381 specimens of Micropeplinae rove beetles. DNA barcoding data from 85 representative specimens were analysed to delimit species and infer their relationships. Statistical methods were implemented to assess regional species diversity of understudied Micropeplinae. The total number of sampled Micropeplinae species varied between 14 and 17, depending on a splitting versus lumping approach for allopatric populations. A single Micropeplinae species was sampled in six of eight studied localities, three species were found on Mount Gongga, while ten species were discovered on hyperdiverse Mount Emei in Sichuan. All Micropeplinae specimens from our samples belong either to the genus Cerapeplus, or to three other inclusive groups temporarily retained inside Micropeplus sensu lato. Each of the three groups potentially represents a separate genus: tesserula group, sculptus group and Micropeplus sensu stricto. A new species Micropeplus jason sp. n. from Mount Emei in Sichuan is described. Numerous illustrations introduce regional fauna and clarify the discussed morphological characters.},
}
@article {pmid25781095,
year = {2015},
author = {Pan, ZX and Zhang, F and Li, YB},
title = {Two closely related Homidia species (Entomobryidae, Collembola) revealed by morphological and molecular evidence.},
journal = {Zootaxa},
volume = {3918},
number = {2},
pages = {285-294},
doi = {10.11646/zootaxa.3918.2.9},
pmid = {25781095},
issn = {1175-5334},
mesh = {Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Arthropods/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Body Size ; Female ; Male ; Organ Size ; Phylogeny ; },
abstract = {Two closely related Homidia species, H. fascia Wang &amp; Chen, 2001 and H. pseudofascia sp. nov., are recognized by both morphological and molecular approaches. Both species have minor morphological differences except distinct colour patterns on thorax. Genetic distances (18%) of COI barcodes between them greatly exceed commonly employed threshold (3%), also indicating two independent species. The use of colour pattern in taxonomy of Homidia is also discussed.},
}
@article {pmid25781093,
year = {2015},
author = {Packer, L and Martins, DJ},
title = {A new species of Samba s. str. (Hymenoptera: Melittidae) from the Turkana Basin, Kenya with observations on the function of the metatibial spur in females.},
journal = {Zootaxa},
volume = {3918},
number = {2},
pages = {261-272},
doi = {10.11646/zootaxa.3918.2.7},
pmid = {25781093},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Bees/anatomy &amp; histology/*classification/growth &amp; development ; Body Size ; Ecosystem ; Female ; Hymenoptera ; Kenya ; Male ; Organ Size ; Phylogeny ; },
abstract = {The third known species of the Afrotropical subgenus Samba s. str. is described based upon eight females. This is the northernmost and also the most arid habitat record for the genus. Images are provided of the habitus and diagnostic features for the species as well as the subgenus and some notes on floral hosts and habitat are provided. The species is added to a morphology-based phylogeny for the genus and results of barcoding of some species of the genus are presented. Some unusual morphological features of the subgenus are discussed, in particular, the function of the remarkable metatibial spurs of the female is recorded as assisting with removal of pollen from a floral host.},
}
@article {pmid25780764,
year = {2015},
author = {Khatua, S and Dutta, AK and Acharya, K},
title = {Prospecting Russula senecis: a delicacy among the tribes of West Bengal.},
journal = {PeerJ},
volume = {3},
number = {},
pages = {e810},
pmid = {25780764},
issn = {2167-8359},
abstract = {Russula senecis, a worldwide distributed mushroom, is exclusively popular among the tribal communities of West Bengal for food purposes. The present study focuses on its reliable taxonomic identification through macro- and micro-morphological features, DNA barcoding, confirmation of its systematic placement by phylogenetic analyses, myco-chemicals and functional activities. For the first time, the complete Internal Transcribed Spacer region of R. senecis has been sequenced and its taxonomic position within subsection Foetentinae under series Ingratae of the subgen. Ingratula is confirmed through phylogenetic analysis. For exploration of its medicinal properties, dried basidiocarps were subjected for preparation of a heat stable phenol rich extract (RusePre) using water and ethanol as solvent system. The antioxidant activity was evaluated through hydroxyl radical scavenging (EC50 5 µg/ml), chelating ability of ferrous ion (EC50 0.158 mg/ml), DPPH radical scavenging (EC50 1.34 mg/ml), reducing power (EC50 2.495 mg/ml) and total antioxidant activity methods (13.44 µg ascorbic acid equivalent/mg of extract). RusePre exhibited antimicrobial potentiality against Listeria monocytogenes, Bacillus subtilis, Pseudomonas aeruginosa and Staphylococcus aureus. Furthermore, different parameters were tested to investigate its chemical composition, which revealed the presence of appreciable quantity of phenolic compounds, along with carotenoids and ascorbic acid. HPLC-UV fingerprint indicated the probable existence of at least 13 phenolics, of which 10 were identified (pyrogallol > kaempferol > quercetin > chlorogenic acid > ferulic acid, cinnamic acid > vanillic acid > salicylic acid > p-coumaric acid > gallic acid). Result from the present work suggests that the fraction, RusePre, may open novel prospect as a functional ingredient in antioxidant supplements and in drugs to treat infectious disease.},
}
@article {pmid25775791,
year = {2014},
author = {Hou, DY and Song, JY and Yang, P and Zhou, H and Xin, TY and Yao, H},
title = {[Identification of peucedani radix, peucedani decursivi radix and its adulterants using ITS2 sequence].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {39},
number = {21},
pages = {4186-4190},
pmid = {25775791},
issn = {1001-5302},
mesh = {Apiaceae/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer ; *Drug Contamination ; },
abstract = {In order to identify Peucedani Radix, Peucedani Decursivi Radix and their adulterants, the internal transcribed spacer 2 (ITS2) regions of Peucedani Radix, Peucedani Decursivi Radix and their adulterants were amplified and bidirectionally sequenced based on the Principles for Molecular Identification of Traditional Chinese Materia Medica Using DNA Barcoding, which has been promulgated by Chinese Pharmacopoeia Commission. Sequences were analyzed and assembled by Codon Code Aligner V3. 7.1. The relevant data were analyzed by MEGA 5. 0. Species identification analyses were performed by using the nearest distance methods and neighbor-joining (NJ) methods. The result showed that the ITS2 sequence lengths of Peucedani Radix were 229-230 bp and the average intra-specific genetic distances were 0.005. The ITS2 sequence lengths of Peucedani Decursivi Radix were 227 bp and the sequences contained no variation site. The average inter-specific K2P genetic distance of Peucedani Radix, Peucedani Decursivi Radix and their adulterants species were 0.044 and 0.065 respectively. The minimum inter-specific divergence is larger than the maximum intra-specific divergence of Peucedani Decursivi Radix. The nearest distance methods and NJ trees results indicated that Peucedani Radix, Peucedani Decursivi Radix and their adulterants species could be identification clearly. The ITS2 regions can stably and accurately distinguish Peucedani Radix, Peucedani Decursivi Radix and their adulterants.},
}
@article {pmid25774915,
year = {2015},
author = {Zhang, JQ and Meng, SY and Wen, J and Rao, GY},
title = {DNA barcoding of Rhodiola (crassulaceae): a case study on a group of recently diversified medicinal plants from the Qinghai-Tibetan Plateau.},
journal = {PloS one},
volume = {10},
number = {3},
pages = {e0119921},
pmid = {25774915},
issn = {1932-6203},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic ; Molecular Sequence Data ; *Phylogeny ; Plants, Medicinal/classification/*genetics ; Rhodiola/classification/*genetics ; Tibet ; },
abstract = {DNA barcoding, the identification of species using one or a few short standardized DNA sequences, is an important complement to traditional taxonomy. However, there are particular challenges for barcoding plants, especially for species with complex evolutionary histories. We herein evaluated the utility of five candidate sequences - rbcL, matK, trnH-psbA, trnL-F and the internal transcribed spacer (ITS) - for barcoding Rhodiola species, a group of high-altitude plants frequently used as adaptogens, hemostatics and tonics in traditional Tibetan medicine. Rhodiola was suggested to have diversified rapidly recently. The genus is thus a good model for testing DNA barcoding strategies for recently diversified medicinal plants. This study analyzed 189 accessions, representing 47 of the 55 recognized Rhodiola species in the Flora of China treatment. Based on intraspecific and interspecific divergence and degree of monophyly statistics, ITS was the best single-locus barcode, resolving 66% of the Rhodiola species. The core combination rbcL+matK resolved only 40.4% of them. Unsurprisingly, the combined use of all five loci provided the highest discrimination power, resolving 80.9% of the species. However, this is weaker than the discrimination power generally reported in barcoding studies of other plant taxa. The observed complications may be due to the recent diversification, incomplete lineage sorting and reticulate evolution of the genus. These processes are common features of numerous plant groups in the high-altitude regions of the Qinghai-Tibetan Plateau.},
}
@article {pmid25774672,
year = {2015},
author = {Curci, PL and De Paola, D and Danzi, D and Vendramin, GG and Sonnante, G},
title = {Complete chloroplast genome of the multifunctional crop globe artichoke and comparison with other Asteraceae.},
journal = {PloS one},
volume = {10},
number = {3},
pages = {e0120589},
pmid = {25774672},
issn = {1932-6203},
mesh = {Asteraceae/classification/*genetics ; Computational Biology ; Cynara scolymus/classification/*genetics ; DNA Barcoding, Taxonomic ; Evolution, Molecular ; Exons ; Gene Order ; Genes, Plant ; Genetic Structures ; *Genome, Chloroplast ; *Genomics ; High-Throughput Nucleotide Sequencing ; Introns ; Molecular Sequence Annotation ; Molecular Sequence Data ; Phylogeny ; },
abstract = {With over 20,000 species, Asteraceae is the second largest plant family. High-throughput sequencing of nuclear and chloroplast genomes has allowed for a better understanding of the evolutionary relationships within large plant families. Here, the globe artichoke chloroplast (cp) genome was obtained by a combination of whole-genome and BAC clone high-throughput sequencing. The artichoke cp genome is 152,529 bp in length, consisting of two single-copy regions separated by a pair of inverted repeats (IRs) of 25,155 bp, representing the longest IRs found in the Asteraceae family so far. The large (LSC) and the small (SSC) single-copy regions span 83,578 bp and 18,641 bp, respectively. The artichoke cp sequence was compared to the other eight Asteraceae complete cp genomes available, revealing an IR expansion at the SSC/IR boundary. This expansion consists of 17 bp of the ndhF gene generating an overlap between the ndhF and ycf1 genes. A total of 127 cp simple sequence repeats (cpSSRs) were identified in the artichoke cp genome, potentially suitable for future population studies in the Cynara genus. Parsimony-informative regions were evaluated and allowed to place a Cynara species within the Asteraceae family tree. The eight most informative coding regions were also considered and tested for "specific barcode" purpose in the Asteraceae family. Our results highlight the usefulness of cp genome sequencing in exploring plant genome diversity and retrieving reliable molecular resources for phylogenetic and evolutionary studies, as well as for specific barcodes in plants.},
}
@article {pmid25770155,
year = {2015},
author = {},
title = {Barcoding method speeds single-cell expression profiling.},
journal = {Cancer discovery},
volume = {5},
number = {5},
pages = {457-458},
doi = {10.1158/2159-8290.CD-NB2015-030},
pmid = {25770155},
issn = {2159-8290},
mesh = {Gene Expression Profiling/*methods ; Humans ; Single-Cell Analysis/*methods ; },
}
@article {pmid25765919,
year = {2015},
author = {Wolf, M},
title = {ITS so much more.},
journal = {Trends in genetics : TIG},
volume = {31},
number = {4},
pages = {175-176},
doi = {10.1016/j.tig.2015.02.005},
pmid = {25765919},
issn = {0168-9525},
mesh = {Animals ; Humans ; RNA Precursors/*metabolism ; *RNA Processing, Post-Transcriptional ; RNA, Ribosomal/*metabolism ; },
}
@article {pmid25757768,
year = {2015},
author = {Zhang, W and Jiang, J},
title = {Genome-wide mapping of DNase I hypersensitive sites in plants.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1284},
number = {},
pages = {71-89},
doi = {10.1007/978-1-4939-2444-8_4},
pmid = {25757768},
issn = {1940-6029},
mesh = {Arabidopsis/genetics ; Binding Sites/genetics ; *Chromatin Assembly and Disassembly ; *Chromosome Mapping ; DNA, Plant/chemistry/genetics/metabolism ; Deoxyribonuclease I/*metabolism ; Electrophoresis, Gel, Pulsed-Field/methods ; *Genome, Plant ; Genomic Library ; *High-Throughput Nucleotide Sequencing/methods ; Oryza/genetics ; Plants/*genetics ; *Regulatory Sequences, Nucleic Acid ; Reproducibility of Results ; },
abstract = {Genomic regions associated with regulatory proteins are known to be highly sensitive to DNase I digestion and are termed DNase I hypersensitive sites (DHSs). DHSs can be identified by DNase I digestion followed by high-throughput DNA sequencing (DNase-seq). DNase-seq has become a powerful technique for genome-wide mapping of chromatin accessibility in eukaryotes with a sequenced genome. We have developed a DNase-seq procedure in plants. This procedure was adapted from the protocol originally developed for mammalian cell lines. It includes plant nuclei isolation, digestion of purified nuclei with DNase I, recovery of DNase-trimmed DNA fragments, DNase-seq library development, Illumina sequencing and data analysis. We also introduce a barcoding system for library preparation. We have conducted DNase-seq in both Arabidopsis thaliana and rice, and developed genome-wide open chromatin maps in both species. These DHS datasets have been used to detect footprints from regulatory protein binding and to reveal genome-wide nucleosome positioning patterns.},
}
@article {pmid25753913,
year = {2015},
author = {Kohout, P and Doubková, P and Bahram, M and Suda, J and Tedersoo, L and Voříšková, J and Sudová, R},
title = {Niche partitioning in arbuscular mycorrhizal communities in temperate grasslands: a lesson from adjacent serpentine and nonserpentine habitats.},
journal = {Molecular ecology},
volume = {24},
number = {8},
pages = {1831-1843},
doi = {10.1111/mec.13147},
pmid = {25753913},
issn = {1365-294X},
mesh = {DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Dipsacaceae/microbiology ; *Ecosystem ; *Grassland ; Mycorrhizae/classification/*genetics ; Phylogeny ; Plant Roots/microbiology ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) represent an important soil microbial group playing a fundamental role in many terrestrial ecosystems. We explored the effects of deterministic (soil characteristics, host plant life stage, neighbouring plant communities) and stochastic processes on AMF colonization, richness and community composition in roots of Knautia arvensis (Dipsacaceae) plants from three serpentine grasslands and adjacent nonserpentine sites. Methodically, the study was based on 454-sequencing of the ITS region of rDNA. In total, we detected 81 molecular taxonomical operational units (MOTUs) belonging to the Glomeromycota. Serpentine character of the site negatively influenced AMF root colonization, similarly as higher Fe concentration. AMF MOTUs richness linearly increased along a pH gradient from 3.5 to 5.8. Contrary, K and Cr soil concentration had a negative influence on AMF MOTUs richness. We also detected a strong relation between neighbouring plant community composition and AMF MOTUs richness. Although spatial distance between the sampled sites (c. 0.3-3 km) contributed to structuring AMF communities in K. arvensis roots, environmental parameters were key factors in this respect. In particular, the composition of AMF communities was shaped by the complex of serpentine conditions, pH and available soil Ni concentration. The composition of AMF communities was also dependent on host plant life stage (vegetative vs. generative). Our study supports the dominance of deterministic factors in structuring AMF communities in heterogeneous environment composed of an edaphic mosaic of serpentine and nonserpentine soils.},
}
@article {pmid25751057,
year = {2015},
author = {He, Q and Johnston, J and Zeitlinger, J},
title = {ChIP-nexus enables improved detection of in vivo transcription factor binding footprints.},
journal = {Nature biotechnology},
volume = {33},
number = {4},
pages = {395-401},
pmid = {25751057},
issn = {1546-1696},
support = {DP2 OD004561/OD/NIH HHS/United States ; 1DP2 OD004561/OD/NIH HHS/United States ; },
mesh = {Base Sequence ; Binding Sites ; Chromatin Immunoprecipitation/*methods ; DNA/*chemistry/*genetics ; Molecular Sequence Data ; Protein Binding ; Protein Interaction Mapping/*methods ; Reproducibility of Results ; Sensitivity and Specificity ; Transcription Factors/*chemistry/*genetics ; },
abstract = {Understanding how eukaryotic enhancers are bound and regulated by specific combinations of transcription factors is still a major challenge. To better map transcription factor binding genome-wide at nucleotide resolution in vivo, we have developed a robust ChIP-exo protocol called ChIP-nexus (chromatin immunoprecipitation experiments with nucleotide resolution through exonuclease, unique barcode and single ligation), which utilizes an efficient DNA self-circularization step during library preparation. Application of ChIP-nexus to four proteins--human TBP and Drosophila NFkB, Twist and Max--shows that it outperforms existing ChIP protocols in resolution and specificity, pinpoints relevant binding sites within enhancers containing multiple binding motifs, and allows for the analysis of in vivo binding specificities. Notably, we show that Max frequently interacts with DNA sequences next to its motif, and that this binding pattern correlates with local DNA-sequence features such as DNA shape. ChIP-nexus will be broadly applicable to the study of in vivo transcription factor binding specificity and its relationship to cis-regulatory changes in humans and model organisms.},
}
@article {pmid25743182,
year = {2015},
author = {MacColl, E and Therkelsen, MD and Sherpa, T and Ellerbrock, H and Johnston, LA and Jariwala, RH and Chang, W and Gurtowski, J and Schatz, MC and Mozammal Hossain, M and Cassidy-Hanley, DM and Clark, TG and Chang, WJ},
title = {Molecular genetic diversity and characterization of conjugation genes in the fish parasite Ichthyophthirius multifiliis.},
journal = {Molecular phylogenetics and evolution},
volume = {86},
number = {},
pages = {1-7},
doi = {10.1016/j.ympev.2015.02.017},
pmid = {25743182},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Fishes/*parasitology ; Hymenostomatida/*classification/genetics ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; Polymorphism, Single Nucleotide ; Reproduction/genetics ; Sequence Analysis, DNA ; United States ; },
abstract = {Ichthyophthirius multifiliis is the etiologic agent of "white spot", a commercially important disease of freshwater fish. As a parasitic ciliate, I. multifiliis infects numerous host species across a broad geographic range. Although Ichthyophthirius outbreaks are difficult to control, recent sequencing of the I. multifiliis genome has revealed a number of potential metabolic pathways for therapeutic intervention, along with likely vaccine targets for disease prevention. Nonetheless, major gaps exist in our understanding of both the life cycle and population structure of I. multifiliis in the wild. For example, conjugation has never been described in this species, and it is unclear whether I. multifiliis undergoes sexual reproduction, despite the presence of a germline micronucleus. In addition, no good methods exist to distinguish strains, leaving phylogenetic relationships between geographic isolates completely unresolved. Here, we compared nucleotide sequences of SSUrDNA, mitochondrial NADH dehydrogenase subunit I and cox-1 genes, and 14 somatic SNP sites from nine I. multifiliis isolates obtained from four different states in the US since 1995. The mitochondrial sequences effectively distinguished the isolates from one another and divided them into at least two genetically distinct groups. Furthermore, none of the nine isolates shared the same composition of the 14 somatic SNP sites, suggesting that I. multifiliis undergoes sexual reproduction at some point in its life cycle. Finally, compared to the well-studied free-living ciliates Tetrahymena thermophila and Paramecium tetraurelia, I. multifiliis has lost 38% and 29%, respectively, of 16 experimentally confirmed conjugation-related genes, indicating that mechanistic differences in sexual reproduction are likely to exist between I. multifiliis and other ciliate species.},
}
@article {pmid25745100,
year = {2015},
author = {Vandepas, LE and Oliveira, LM and Lee, SS and Hirose, E and Rocha, RM and Swalla, BJ},
title = {Biogeography of Phallusia nigra: is it really black and white?.},
journal = {The Biological bulletin},
volume = {228},
number = {1},
pages = {52-64},
doi = {10.1086/BBLv228n1p52},
pmid = {25745100},
issn = {1939-8697},
mesh = {Animal Distribution ; Animals ; Electron Transport Complex IV/genetics ; Molecular Sequence Data ; *Phylogeny ; Phylogeography ; RNA, Ribosomal, 18S/genetics ; Urochordata/anatomy &amp; histology/*classification/genetics/*physiology ; },
abstract = {Ascidians (Chordata, Tunicata) are an important group for the study of invasive species biology due to rapid generation times, potential for biofouling, and role as filter feeders in an ecosystem. Phallusia nigra is a putative cosmopolitan ascidian that has been described as introduced or invasive in a number of regions in the Indo-Pacific Ocean (India, Japan, and Hawaii) and in the Mediterranean. The taxonomic description of P. nigra includes a striking smooth, black tunic and large size. However, there are at least two similar Phallusia species-P. philippinensis and P. fumigata-which also have dark black tunics and can be difficult to discern from P. nigra. The distribution of P. nigra broadly overlaps with P. philippinensis in the Indo-Pacific and P. fumigata in the Mediterranean. A morphological comparison of P. nigra from Japan, the Caribbean coast of Panama, and Brazil found that Atlantic and Pacific samples were different species and led us to investigate the range of P. nigra using morphological and molecular analyses. We sequenced 18S rDNA and cytochrome oxidase B of individual ascidians from the Red Sea, Greece, Singapore, Japan, Caribbean Panama, Florida, and Brazil. Our results show that identification of the disparate darkly pigmented species has been difficult, and that several reports of P. nigra are likely either P. fumigata or P. philippinensis. Here we include detailed taxonomic descriptions of the distinguishing features of these three species and sequences for molecular barcoding in an effort to have ranges and potential invasions corrected in the ascidian literature.},
}
@article {pmid25741706,
year = {2015},
author = {Brodin, J and Hedskog, C and Heddini, A and Benard, E and Neher, RA and Mild, M and Albert, J},
title = {Challenges with using primer IDs to improve accuracy of next generation sequencing.},
journal = {PloS one},
volume = {10},
number = {3},
pages = {e0119123},
pmid = {25741706},
issn = {1932-6203},
mesh = {Base Sequence ; DNA Primers ; HIV-1/genetics ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Analysis/*methods/standards ; Sequence Homology, Nucleic Acid ; },
abstract = {Next generation sequencing technologies, like ultra-deep pyrosequencing (UDPS), allows detailed investigation of complex populations, like RNA viruses, but its utility is limited by errors introduced during sample preparation and sequencing. By tagging each individual cDNA molecule with barcodes, referred to as Primer IDs, before PCR and sequencing these errors could theoretically be removed. Here we evaluated the Primer ID methodology on 257,846 UDPS reads generated from a HIV-1 SG3Δenv plasmid clone and plasma samples from three HIV-infected patients. The Primer ID consisted of 11 randomized nucleotides, 4,194,304 combinations, in the primer for cDNA synthesis that introduced a unique sequence tag into each cDNA molecule. Consensus template sequences were constructed for reads with Primer IDs that were observed three or more times. Despite high numbers of input template molecules, the number of consensus template sequences was low. With 10,000 input molecules for the clone as few as 97 consensus template sequences were obtained due to highly skewed frequency of resampling. Furthermore, the number of sequenced templates was overestimated due to PCR errors in the Primer IDs. Finally, some consensus template sequences were erroneous due to hotspots for UDPS errors. The Primer ID methodology has the potential to provide highly accurate deep sequencing. However, it is important to be aware that there are remaining challenges with the methodology. In particular it is important to find ways to obtain a more even frequency of resampling of template molecules as well as to identify and remove artefactual consensus template sequences that have been generated by PCR errors in the Primer IDs.},
}
@article {pmid25737601,
year = {2014},
author = {Crous, PW and Wingfield, MJ and Schumacher, RK and Summerell, BA and Giraldo, A and Gené, J and Guarro, J and Wanasinghe, DN and Hyde, KD and Camporesi, E and Gareth Jones, EB and Thambugala, KM and Malysheva, EF and Malysheva, VF and Acharya, K and Álvarez, J and Alvarado, P and Assefa, A and Barnes, CW and Bartlett, JS and Blanchette, RA and Burgess, TI and Carlavilla, JR and Coetzee, MP and Damm, U and Decock, CA and den Breeÿen, A and de Vries, B and Dutta, AK and Holdom, DG and Rooney-Latham, S and Manjón, JL and Marincowitz, S and Mirabolfathy, M and Moreno, G and Nakashima, C and Papizadeh, M and Shahzadeh Fazeli, SA and Amoozegar, MA and Romberg, MK and Shivas, RG and Stalpers, JA and Stielow, B and Stukely, MJ and Swart, WJ and Tan, YP and van der Bank, M and Wood, AR and Zhang, Y and Groenewald, JZ},
title = {Fungal Planet description sheets: 281-319.},
journal = {Persoonia},
volume = {33},
number = {},
pages = {212-289},
pmid = {25737601},
issn = {0031-5850},
abstract = {Novel species of fungi described in the present study include the following from South Africa: Alanphillipsia aloeicola from Aloe sp., Arxiella dolichandrae from Dolichandra unguiscati, Ganoderma austroafricanum from Jacaranda mimosifolia, Phacidiella podocarpi and Phaeosphaeria podocarpi from Podocarpus latifolius, Phyllosticta mimusopisicola from Mimusops zeyheri and Sphaerulina pelargonii from Pelargonium sp. Furthermore, Barssia maroccana is described from Cedrus atlantica (Morocco), Codinaea pini from Pinus patula (Uganda), Crucellisporiopsis marquesiae from Marquesia acuminata (Zambia), Dinemasporium ipomoeae from Ipomoea pes-caprae (Vietnam), Diaporthe phragmitis from Phragmites australis (China), Marasmius vladimirii from leaf litter (India), Melanconium hedericola from Hedera helix (Spain), Pluteus albotomentosus and Pluteus extremiorientalis from a mixed forest (Russia), Rachicladosporium eucalypti from Eucalyptus globulus (Ethiopia), Sistotrema epiphyllum from dead leaves of Fagus sylvatica in a forest (The Netherlands), Stagonospora chrysopyla from Scirpus microcarpus (USA) and Trichomerium dioscoreae from Dioscorea sp. (Japan). Novel species from Australia include: Corynespora endiandrae from Endiandra introrsa, Gonatophragmium triuniae from Triunia youngiana, Penicillium coccotrypicola from Archontophoenix cunninghamiana and Phytophthora moyootj from soil. Novelties from Iran include Neocamarosporium chichastianum from soil and Seimatosporium pistaciae from Pistacia vera. Xenosonderhenia eucalypti and Zasmidium eucalyptigenum are newly described from Eucalyptus urophylla in Indonesia. Diaporthe acaciarum and Roussoella acacia are newly described from Acacia tortilis in Tanzania. New species from Italy include Comoclathris spartii from Spartium junceum and Phoma tamaricicola from Tamarix gallica. Novel genera include (Ascomycetes): Acremoniopsis from forest soil and Collarina from water sediments (Spain), Phellinocrescentia from a Phellinus sp. (French Guiana), Neobambusicola from Strelitzia nicolai (South Africa), Neocladophialophora from Quercus robur (Germany), Neophysalospora from Corymbia henryi (Mozambique) and Xenophaeosphaeria from Grewia sp. (Tanzania). Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.},
}
@article {pmid25737596,
year = {2014},
author = {Liimatainen, K and Niskanen, T and Dima, B and Kytövuori, I and Ammirati, JF and Frøslev, TG},
title = {The largest type study of Agaricales species to date: bringing identification and nomenclature of Phlegmacium (Cortinarius) into the DNA era.},
journal = {Persoonia},
volume = {33},
number = {},
pages = {98-140},
pmid = {25737596},
issn = {0031-5850},
abstract = {Cortinarius is a species-rich and morphologically challenging genus with a cosmopolitan distribution. Many names have not been used consistently and in some instances the same species has been described two or more times under separate names. This study focuses on subg. Phlegmacium as traditionally defined and includes species from boreal and temperate areas of the northern hemisphere. Our goals for this project were to: i) study type material to determine which species already have been described; ii) stabilize the use of Friesian and other older names by choosing a neo- or epitype; iii) describe new species that were discovered during the process of studying specimens; and iv) establish an accurate ITS barcoding database for Phlegmacium species. A total of 236 types representing 154 species were studied. Of these 114 species are described only once whereas 40 species had one ore more synonyms. Of the names studied only 61 were currently represented in GenBank. Neotypes are proposed for 21 species, and epitypes are designated for three species. In addition, 20 new species are described and six new combinations made. As a consequence ITS barcodes for 175 Cortinarius species are released.},
}
@article {pmid25737591,
year = {2014},
author = {Quaedvlieg, W and Binder, M and Groenewald, JZ and Summerell, BA and Carnegie, AJ and Burgess, TI and Crous, PW},
title = {Introducing the Consolidated Species Concept to resolve species in the Teratosphaeriaceae.},
journal = {Persoonia},
volume = {33},
number = {},
pages = {1-40},
pmid = {25737591},
issn = {0031-5850},
abstract = {The Teratosphaeriaceae represents a recently established family that includes numerous saprobic, extremophilic, human opportunistic, and plant pathogenic fungi. Partial DNA sequence data of the 28S rRNA and RPB2 genes strongly support a separation of the Mycosphaerellaceae from the Teratosphaeriaceae, and also provide support for the Extremaceae and Neodevriesiaceae, two novel families including many extremophilic fungi that occur on a diversity of substrates. In addition, a multi-locus DNA sequence dataset was generated (ITS, LSU, Btub, Act, RPB2, EF-1α and Cal) to distinguish taxa in Mycosphaerella and Teratosphaeria associated with leaf disease of Eucalyptus, leading to the introduction of 23 novel genera, five species and 48 new combinations. Species are distinguished based on a polyphasic approach, combining morphological, ecological and phylogenetic species concepts, named here as the Consolidated Species Concept (CSC). From the DNA sequence data generated, we show that each one of the five coding genes tested, reliably identify most of the species present in this dataset (except species of Pseudocercospora). The ITS gene serves as a primary barcode locus as it is easily generated and has the most extensive dataset available, while either Btub, EF-1α or RPB2 provide a useful secondary barcode locus.},
}
@article {pmid25736916,
year = {2015},
author = {Faure, D and Joly, D},
title = {Next-generation sequencing as a powerful motor for advances in the biological and environmental sciences.},
journal = {Genetica},
volume = {143},
number = {2},
pages = {129-132},
pmid = {25736916},
issn = {1573-6857},
mesh = {Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Ecology/methods ; Gene Expression Profiling ; Genomics ; High-Throughput Nucleotide Sequencing/*methods ; },
abstract = {Next-generation sequencing (NGS) provides unprecedented insight into (meta)genomes, (meta)transcriptomes (cDNA) and (meta)barcodes of individuals, populations and communities of Archaea, Bacteria and Eukarya, as well as viruses. This special issue combines reviews and original papers reporting technical and scientific advances in genomics and transcriptomics of non-model species, as well as quantification and functional analyses of biodiversity using NGS technologies of the second and third generations. In addition, certain papers also exemplify the transition from Sanger to NGS barcodes in molecular taxonomy.},
}
@article {pmid25734033,
year = {2014},
author = {Steciow, MM and Lara, E and Paul, C and Pillonel, A and Belbahri, L},
title = {Multiple barcode assessment within the Saprolegnia-Achlya clade (Saprolegniales, Oomycota, Straminipila) brings order in a neglected group of pathogens.},
journal = {IMA fungus},
volume = {5},
number = {2},
pages = {439-448},
pmid = {25734033},
issn = {2210-6340},
abstract = {The Saprolegnia-Achlya clade comprises species of major environmental and economic importance due to their negative impact on aquaculture and aquatic ecosystems by threatening fishes, amphibians, and crustaceans. However, their taxonomy and phylogenetic relationships remain unresolved and suffer from many inconsistencies, which is a major obstacle to the widespread application of molecular barcoding to identify pathogenic strains with quarantine implications. We assessed phylogenetic relationships of major genera using three commonly used markers (ITS, SSU rRNA, and LSU rRNA). A consensus tree of the three genes provided support for nine clades encompassing eleven documented genera and a new clade (SAP1) that has not been described morphologically. In the course of this study, we isolated a new species, Newbya dichotoma sp. nov., which provided the only culture available for this genus. In parallel, we attempted to summarize the evolution of traits in the different genera, but their successive reversals rendered the inference of ancestral states impossible. This highlights even more the importance of a bar-coding strategy for saprolegniacean parasite detection and monitoring.},
}
@article {pmid25731975,
year = {2015},
author = {Mira, JJ and Guilabert, M and Carrillo, I and Fernández, C and Vicente, MA and Orozco-Beltrán, D and Gil-Guillen, VF},
title = {Use of QR and EAN-13 codes by older patients taking multiple medications for a safer use of medication.},
journal = {International journal of medical informatics},
volume = {84},
number = {6},
pages = {406-412},
doi = {10.1016/j.ijmedinf.2015.02.001},
pmid = {25731975},
issn = {1872-8243},
mesh = {Aged ; Female ; Humans ; Information Storage and Retrieval ; Male ; Medication Errors/*prevention &amp; control ; *Mobile Applications ; *Patient Safety ; Software Design ; Surveys and Questionnaires ; *User-Computer Interface ; },
abstract = {BACKGROUND: Older persons following a prolonged complex drug regimen often make mistakes when taking their medication. Currently, the widespread use of tablets and smartphones has encouraged the development of applications to support self-management of medication.<br><br>OBJECTIVE: The aim of this study was to design, develop and assess an app that transforms medication-associated ean-13 (barcodes) and Quick Response codes (QR) into verbal instructions, to enable safer use of medication by the elderly patients taking multiple medications.<br><br>METHODS: Meetings were held in which participated a total of 61 patients.<br><br>RESULTS: The results showed that patients appreciated the application and found it useful for safer use of medicines.<br><br>CONCLUSIONS: The study results support the use of such technology to increase patient safety taking multiple medications safety.},
}
@article {pmid25728598,
year = {2015},
author = {Choi, YJ and Beakes, G and Glockling, S and Kruse, J and Nam, B and Nigrelli, L and Ploch, S and Shin, HD and Shivas, RG and Telle, S and Voglmayr, H and Thines, M},
title = {Towards a universal barcode of oomycetes--a comparison of the cox1 and cox2 loci.},
journal = {Molecular ecology resources},
volume = {15},
number = {6},
pages = {1275-1288},
pmid = {25728598},
issn = {1755-0998},
support = {P 22739/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Oomycetes/*classification/*genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {Oomycetes are a diverse group of eukaryotes in terrestrial, limnic and marine habitats worldwide and include several devastating plant pathogens, for example Phytophthora infestans (potato late blight). The cytochrome c oxidase subunit 2 gene (cox2) has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. The cox1 locus has been used in some studies of Pythium and Phytophthora, but has rarely been used for other oomycetes, as amplification success of cox1 varies with different lineages and sample ages. To determine which out of cox1 or cox2 is best suited as a universal oomycete barcode, we compared these two genes in terms of (i) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (ii) sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding-type material. Sequence data for several historic type specimens exist for cox2, but there are none for cox1. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. The cox2-1 spacer could be a useful marker below species level. Improved protocols and universal primers are presented for all genes to facilitate future barcoding efforts.},
}
@article {pmid25726808,
year = {2016},
author = {Stepanović, S and Kosovac, A and Krstić, O and Jović, J and Toševski, I},
title = {Morphology versus DNA barcoding: two sides of the same coin. A case study of Ceutorhynchus erysimi and C. contractus identification.},
journal = {Insect science},
volume = {23},
number = {4},
pages = {638-648},
doi = {10.1111/1744-7917.12212},
pmid = {25726808},
issn = {1744-7917},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Genotype ; Montenegro ; Peptide Elongation Factor 1/genetics ; Phenotype ; Sequence Analysis, DNA ; Serbia ; Species Specificity ; Weevils/anatomy &amp; histology/*classification/*genetics ; },
abstract = {Genotyping of 2 well-known weevil species from the genus Ceutorhynchus (Coleoptera: Curculionidae) distributed in west Palearctic, C. erysimi and C. contractus, revealed phenotype versus genotype inconsistencies in a set of 56 specimens (25 C. erysimi and 31 C. contractus) collected from 25 locations in Serbia and Montenegro. An analysis of the mitochondrial cytochrome oxidase subunit I gene (COI), widely used as a barcoding region, and a nuclear gene, elongation factor-1α (EF-1α), revealed stable genetic divergence among these species. The average uncorrected pairwise distances for the COI and EF-1α genes were 3.8%, and 1.3%, respectively, indicating 2 genetically well-segregated species. However, the genetic data were not congruent with the phenotypic characteristics of the studied specimens. In the first place, C. erysimi genotypes were attached to specimens with phenotypic characteristics of C. contractus. Species-specific PCR-RFLP assays for the barcoding gene COI were applied for the molecular identification of 101 additional specimens of both morphospecies (33 C. erysimi and 68 C. contractus) and were found to confirm this incongruity. The discrepancy between the genetic and morphological data raises the question of the accuracy of using a barcoding approach, as it may result in misleading conclusions about the taxonomic position of the studied organism. Additionally, the typological species concept shows considerable weakness when genetic data are not supported with phenotypic characteristics as in case of asymmetric introgression, which may cause certain problems, especially in applied studies such as biological control programs in which the biological properties of the studied organisms are the main focus.},
}
@article {pmid25726643,
year = {2014},
author = {Wang, ZT and Hao, H and Lin, LZ and Yu, Y and Li, SY},
title = {[Identification of Smilax glabra and its related species based on psbA-trnH sequence].},
journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials},
volume = {37},
number = {8},
pages = {1368-1371},
pmid = {25726643},
issn = {1001-4454},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic ; DNA, Fungal/*genetics ; DNA, Ribosomal Spacer ; Phylogeny ; Polymerase Chain Reaction ; Smilax/*genetics ; },
abstract = {OBJECTIVE: To identify Smilax glabra and its related species using DNA barcoding technique and psbA-trnH sequence.<br><br>METHODS: Total genomic DNA was isolated as template and the chloroplast gene psbA-trnH region was amplified by PCR technology and sequenced bidirectionally. The sequences and the related data were analyzed using the software CodonCode Aligner and MEGA 6.0; The intra- and inter-specific Kimura-2-Parameter(K2P) distances were calculated and the phylogenetic tree was constructed using the Neighbor-joining method.<br><br>RESULTS: The maximum K2P genetic distance of the plants of Smilax glabra was lower than the minimum K2P genetic distance of its related species. In the cluster dendrogram, the plants of Smilax glabra from various sources showed the monophyletic and simultaneously distinguished from the closely relative species.<br><br>CONCLUSION: psbA-trnH barcoding could be used to distinguish Smilax glabra and its related species effectively, and provide important molecular evidence for identification of original plant of Smilacis Glabrae Rhizoma and clinic safety in medicinal use.},
}
@article {pmid25722943,
year = {2015},
author = {Bach, E and Holmes, DT},
title = {Reqscan: An open source solution for laboratory requisition scanning, archiving and retrieval.},
journal = {Journal of pathology informatics},
volume = {6},
number = {},
pages = {3},
pmid = {25722943},
issn = {2229-5089},
abstract = {Requisition storage and retrieval are an integral part of the outpatient laboratory testing process. It is frequently necessary to review an original requisition to confirm the ordering physician, patient demographics, diagnostic information, and requested tests. Manual retrieval of a paper requisition is time-consuming and tedious. Although commercial solutions exist for the scanning and archiving of barcoded paper requisitions, the tools to accomplish this are freely available from the open source software community. We present a simple dedicated piece of software, Reqscan, for scanning patient laboratory requisitions, finding all barcode information, and saving the requisition as a portable document format named according the barcode(s) found. This Python application offers a simple solution to patient requisition digitization. Reqscan has been successfully tested and implemented into routine practice for storage and retrieval of outpatient requisitions at St. Paul's Hospital, Department of Pathology and Laboratory Medicine in Vancouver, British Columbia, Canada.},
}
@article {pmid25722736,
year = {2015},
author = {Sint, D and Thurner, I and Kaufmann, R and Traugott, M},
title = {Sparing spiders: faeces as a non-invasive source of DNA.},
journal = {Frontiers in zoology},
volume = {12},
number = {},
pages = {3},
pmid = {25722736},
issn = {1742-9994},
support = {P 20859/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {INTRODUCTION: Spiders are important arthropod predators in many terrestrial ecosystems, and molecular tools have boosted our ability to investigate this taxon, which can be difficult to study with conventional methods. Nonetheless, it has typically been necessary to kill spiders to obtain their DNA for molecular applications, especially when studying their diet.<br><br>RESULTS: We successfully tested the novel approach of employing spider faeces as a non-invasive source of DNA for species identification and diet analysis. Although the overall concentration of DNA in the samples was very low, consumer DNA, suitable for species identification, was amplified from 84% of the faecal pellets collected from lycosid spiders. Moreover, the most important prey types detected in the gut content of the lycosids were also amplified from the faecal samples.<br><br>CONCLUSION: The ability to amplify DNA from spider faeces with specific and general primers suggests that this sample type can be used for diagnostic PCR and sequence-based species and prey identification such as DNA barcoding and next generation sequencing, respectively. These findings demonstrate that faeces provide a non-invasive alternative to full-body DNA extracts for molecular studies on spiders when killing or injuring the animal is not an option.},
}
@article {pmid25712507,
year = {2015},
author = {Paknia, O and Bergmann, T and Hadrys, H},
title = {Some 'ant'swers: Application of a layered barcode approach to problems in ant taxonomy.},
journal = {Molecular ecology resources},
volume = {15},
number = {6},
pages = {1262-1274},
doi = {10.1111/1755-0998.12395},
pmid = {25712507},
issn = {1755-0998},
mesh = {Animals ; Ants/*classification/*genetics ; Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; *Genetic Variation ; RNA, Ribosomal, 28S/genetics ; Rhodopsin/genetics ; },
abstract = {DNA barcoding has emerged as a routine tool in modern taxonomy. Although straightforward, this approach faces new challenges, when applied to difficult situation such as defining cryptic biodiversity. Ants are prime examples for high degrees of cryptic biodiversity due to complex population differentiation, hybridization and speciation processes. Here, we test the DNA barcoding region, cytochrome c oxidase 1 and two supplementary markers, 28S ribosomal DNA and long-wavelength rhodopsin, commonly used in ant taxonomy, for their potential in a layered, character-based barcoding approach across different taxonomic levels. Furthermore, we assess performance of the character-based barcoding approach to determine cryptic species diversity in ants. We found (i) that the barcode potential of a specific genetic marker varied widely among taxonomic levels in ants; (ii) that application of a layered, character-based barcode for identification of specimens can be a solution to taxonomical challenging groups; (iii) that the character-based barcoding approach allows us to differentiate specimens even within locations based on pure characters. In summary, (layered) character-based barcoding offers a reliable alternative for problematic species identification in ants and can be used as a fast and cost-efficient approach to estimate presence, absence or frequency of cryptic species.},
}
@article {pmid25710377,
year = {2015},
author = {Derocles, SA and Evans, DM and Nichols, PC and Evans, SA and Lunt, DH},
title = {Determining plant-leaf miner-parasitoid interactions: a DNA barcoding approach.},
journal = {PloS one},
volume = {10},
number = {2},
pages = {e0117872},
pmid = {25710377},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; *DNA Barcoding, Taxonomic ; DNA Primers/genetics/metabolism ; Electron Transport Complex IV/classification/genetics ; Food Chain ; Insecta/growth &amp; development ; Larva/physiology ; Molecular Sequence Data ; Phylogeny ; Plant Leaves/genetics/parasitology ; Plants/*genetics/parasitology ; },
abstract = {A major challenge in network ecology is to describe the full-range of species interactions in a community to create highly-resolved food-webs. We developed a molecular approach based on DNA full barcoding and mini-barcoding to describe difficult to observe plant-leaf miner-parasitoid interactions, consisting of animals commonly regarded as agricultural pests and their natural enemies. We tested the ability of universal primers to amplify the remaining DNA inside leaf miner mines after the emergence of the insect. We compared the results of a) morphological identification of adult specimens; b) identification based on the shape of the mines; c) the COI Mini-barcode (130 bp) and d) the COI full barcode (658 bp) fragments to accurately identify the leaf-miner species. We used the molecular approach to build and analyse a tri-partite ecological network of plant-leaf miner-parasitoid interactions. We were able to detect the DNA of leaf-mining insects within their feeding mines on a range of host plants using mini-barcoding primers: 6% for the leaves collected empty and 33% success after we observed the emergence of the leaf miner. We suggest that the low amplification success of leaf mines collected empty was mainly due to the time since the adult emerged and discuss methodological improvements. Nevertheless our approach provided new species-interaction data for the ecological network. We found that the 130 bp fragment is variable enough to identify all the species included in this study. Both COI fragments reveal that some leaf miner species could be composed of cryptic species. The network built using the molecular approach was more accurate in describing tri-partite interactions compared with traditional approaches based on morphological criteria.},
}
@article {pmid25703851,
year = {2016},
author = {Bamaniya, DC and Pavan-Kumar, A and Gireesh-Babu, P and Sharma, N and Reang, D and Krishna, G and Lakra, WS},
title = {DNA barcoding of marine ornamental fishes from India.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3093-3097},
doi = {10.3109/19401736.2014.1003923},
pmid = {25703851},
issn = {2470-1408},
mesh = {Animals ; Biodiversity ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Fishes/*classification/*genetics ; Genes, Mitochondrial ; Genetic Variation ; Genetics, Population ; India ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {India has rich marine ornamental fish diversity with 400 fish species distributed in Gulf of Munnar/Palk Bay, Gulf of Kutch, and in reefs around Andaman &amp; Nicobar and Lakshadweep Islands. Marine ornamental fish identification at the field level is very difficult because of their high diversity and profound changes in appearance during their developmental stages and camouflage. To facilitate ornamental fish trading with ease and in compliance with the biodiversity act, DNA barcoding technique could be used to accurately identify species. In this study, DNA barcodes were generated for 31 species of commercially important marine ornamental fishes from India. The average genetic distance (K2P model) within species, genus, and family was 0.446, 13.08, and 20.09%, respectively. Intraspecific variation has increased several folds (15-20 times) after including conspecific sequences from different geographical locations. The presence of allopatric lineages/cryptic species was observed in the Indo-pacific region. The NJ tree constructed based on K2P values showed distinct clusters shared by congeneric species specific to populations.},
}
@article {pmid25703061,
year = {2015},
author = {Cristescu, ME},
title = {Genetic reconstructions of invasion history.},
journal = {Molecular ecology},
volume = {24},
number = {9},
pages = {2212-2225},
doi = {10.1111/mec.13117},
pmid = {25703061},
issn = {1365-294X},
mesh = {Animals ; *Biological Evolution ; Gene Flow ; Genetic Markers ; Genetics, Population/*methods/trends ; Hybridization, Genetic ; Inbreeding ; *Introduced Species ; Phylogeny ; Phylogeography ; Zooplankton/genetics ; },
abstract = {A diverse array of molecular markers and constantly evolving analytical approaches have been employed to reconstruct the invasion histories of the most notorious invasions. Detailed information on the source(s) of introduction, invasion route, type of vectors, number of independent introductions and pathways of secondary spread has been corroborated for a large number of biological invasions. In this review, I present the promises and limitations of current techniques while discussing future directions. Broad phylogeographic surveys of native and introduced populations have traced back invasion routes with surprising precision. These approaches often further clarify species boundaries and reveal complex patterns of genetic relationships with noninvasive relatives. Moreover, fine-scale analyses of population genetics or genomics allow deep inferences on the colonization dynamics across invaded ranges and can reveal the extent of gene flow among populations across various geographical scales, major demographic events such as genetic bottlenecks as well as other important evolutionary events such as hybridization with native taxa, inbreeding and selective sweeps. Genetic data have been often corroborated successfully with historical, geographical and ecological data to enable a comprehensive reconstruction of the invasion process. The advent of next-generation sequencing, along with the availability of extensive databases of repository sequences generated by barcoding projects opens the opportunity to broadly monitor biodiversity, to identify early invasions and to quantify failed invasions that would otherwise remain inconspicuous to the human eye.},
}
@article {pmid25701440,
year = {2015},
author = {Perié, L and Naik, SH},
title = {Toward defining a 'lineage'--The case for dendritic cells.},
journal = {Seminars in cell &amp; developmental biology},
volume = {41},
number = {},
pages = {3-8},
doi = {10.1016/j.semcdb.2015.02.004},
pmid = {25701440},
issn = {1096-3634},
mesh = {Animals ; Antigen Presentation/*immunology ; Cell Lineage/*immunology ; Dendritic Cells/*immunology/metabolism ; Humans ; Models, Immunological ; T-Lymphocytes/*immunology ; fms-Like Tyrosine Kinase 3/immunology/metabolism ; },
abstract = {The immune system consists of a heterogeneous ensemble of cell types that immunologists have tried to classify and order for decades. This classification has relied on varying criteria, resulting in major debates in the immunology community. Discovered in the late 1970s [1], dendritic cells (DCs) are no exception, and their membership to a distinct immune lineage is still vividly debated [2-6]. Here, we review recent work on the origin of DCs and discuss the possible definition of a separate 'DC lineage'.},
}
@article {pmid25700044,
year = {2015},
author = {Bergqvist, J and Forsman, O and Larsson, P and Näslund, J and Lilja, T and Engdahl, C and Lindström, A and Gylfe, &#xc5; and Ahlm, C and Evander, M and Bucht, G},
title = {Detection and isolation of Sindbis virus from mosquitoes captured during an outbreak in Sweden, 2013.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {15},
number = {2},
pages = {133-140},
doi = {10.1089/vbz.2014.1717},
pmid = {25700044},
issn = {1557-7759},
mesh = {Alphavirus Infections/*epidemiology/virology ; Animals ; Base Sequence ; Culicidae/*virology ; DNA Barcoding, Taxonomic ; *Disease Outbreaks ; Genome, Viral/*genetics ; Humans ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sindbis Virus/classification/genetics/*isolation &amp; purification ; Sweden/epidemiology ; },
abstract = {Mosquito-borne alphaviruses have the potential to cause large outbreaks throughout the world. Here we investigated the causative agent of an unexpected Sindbis virus (SINV) outbreak during August-September, 2013, in a previously nonendemic region of Sweden. Mosquitoes were collected using carbon dioxide-baited CDC traps at locations close to human cases. The mosquitoes were initially screened as large pools by SINV-specific quantitative RT-PCR, and the SINV-positive mosquitoes were species determined by single-nucleotide polymorphism (SNP) analysis, followed by sequencing the barcoding region of the cytochrome oxidase I gene. The proportion of the collected mosquitoes was determined by a metabarcoding strategy. By using novel strategies for PCR screening and genetic typing, a new SINV strain, Lövånger, was isolated from a pool of 1600 mosquitoes composed of Culex, Culiseta, and Aedes mosquitoes as determined by metabarcoding. The SINV-positive mosquito Culiseta morsitans was identified by SNP analysis and sequencing. After whole-genome sequencing and phylogenetic analysis, the SINV Lövånger isolate was shown to be most closely similar to recent Finnish SINV isolates. In conclusion, within a few weeks, we were able to detect and isolate a novel SINV strain and identify the mosquito vector during a sudden SINV outbreak.},
}
@article {pmid25699289,
year = {2014},
author = {Fox, EJ and Reid-Bayliss, KS and Emond, MJ and Loeb, LA},
title = {Accuracy of Next Generation Sequencing Platforms.},
journal = {Next generation, sequencing &amp; applications},
volume = {1},
number = {},
pages = {},
pmid = {25699289},
issn = {2469-9853},
support = {R01 CA102029/CA/NCI NIH HHS/United States ; P01 CA077852/CA/NCI NIH HHS/United States ; P01 AG001751/AG/NIA NIH HHS/United States ; R01 CA115802/CA/NCI NIH HHS/United States ; T32 AG000057/AG/NIA NIH HHS/United States ; R01 CA160674/CA/NCI NIH HHS/United States ; R33 CA181771/CA/NCI NIH HHS/United States ; T32 GM007266/GM/NIGMS NIH HHS/United States ; P30 AG013280/AG/NIA NIH HHS/United States ; },
abstract = {Next-generation DNA sequencing has revolutionized genomic studies and is driving the implementation of precision diagnostics. The ability of these technologies to disentangle sequence heterogeneity, however, is limited by their relatively high error rates. A Several single molecule barcoding strategies have been propose to reduce the overall error frequency. A Duplex Sequencing additionally exploits the fact that DNA is double-strand, with one strand reciprocally encoding the sequence information of its complement, and can eliminate nearly all sequencing errors by comparing the sequence of individually tagged amplicons derived from one strand of DNA with that of its complementary strand. This method reduces errors to fewer than one per ten million nucleotides sequenced.},
}
@article {pmid25697864,
year = {2015},
author = {Nzelu, CO and Cáceres, AG and Arrunátegui-Jiménez, MJ and Lañas-Rosas, MF and Yañez-Trujillano, HH and Luna-Caipo, DV and Holguín-Mauricci, CE and Katakura, K and Hashiguchi, Y and Kato, H},
title = {DNA barcoding for identification of sand fly species (Diptera: Psychodidae) from leishmaniasis-endemic areas of Peru.},
journal = {Acta tropica},
volume = {145},
number = {},
pages = {45-51},
doi = {10.1016/j.actatropica.2015.02.003},
pmid = {25697864},
issn = {1873-6254},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Disease Vectors ; Electron Transport Complex IV/genetics ; Endemic Diseases ; Humans ; Leishmaniasis/*parasitology/transmission ; Molecular Sequence Data ; Peru ; Phlebotomus/*classification/enzymology/*genetics ; },
abstract = {Phlebotomine sand flies are the only proven vectors of leishmaniases, a group of human and animal diseases. Accurate knowledge of sand fly species identification is essential in understanding the epidemiology of leishmaniasis and vector control in endemic areas. Classical identification of sand fly species based on morphological characteristics often remains difficult and requires taxonomic expertise. Here, we generated DNA barcodes of the cytochrome c oxidase subunit 1 (COI) gene using 159 adult specimens morphologically identified to be 19 species of sand flies, belonging to 6 subgenera/species groups circulating in Peru, including the vector species. Neighbor-joining (NJ) analysis based on Kimura 2-Parameter genetic distances formed non-overlapping clusters for all species. The levels of intraspecific genetic divergence ranged from 0 to 5.96%, whereas interspecific genetic divergence among different species ranged from 8.39 to 19.08%. The generated COI barcodes could discriminate between all the sand fly taxa. Besides its success in separating known species, we found that DNA barcoding is useful in revealing population differentiation and cryptic diversity, and thus promises to be a valuable tool for epidemiological studies of leishmaniasis.},
}
@article {pmid25693692,
year = {2016},
author = {Strohm, JH and Gwiazdowski, RA and Hanner, R},
title = {Mitogenome metadata: current trends and proposed standards.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3263-3269},
doi = {10.3109/19401736.2015.1015003},
pmid = {25693692},
issn = {2470-1408},
mesh = {Animals ; DNA, Mitochondrial/chemistry/*standards ; *Genome, Mitochondrial ; Lepidoptera/genetics ; Metadata/*standards ; Perciformes/genetics ; Polymorphism, Genetic ; Reference Standards ; Sequence Analysis, DNA/methods/*standards ; },
abstract = {Mitogenome metadata are descriptive terms about the sequence, and its specimen description that allow both to be digitally discoverable and interoperable. Here, we review a sampling of mitogenome metadata published in the journal Mitochondrial DNA between 2005 and 2014. Specifically, we have focused on a subset of metadata fields that are available for GenBank records, and specified by the Genomics Standards Consortium (GSC) and other biodiversity metadata standards; and we assessed their presence across three main categories: collection, biological and taxonomic information. To do this we reviewed 146 mitogenome manuscripts, and their associated GenBank records, and scored them for 13 metadata fields. We also explored the potential for mitogenome misidentification using their sequence diversity, and taxonomic metadata on the Barcode of Life Datasystems (BOLD). For this, we focused on all Lepidoptera and Perciformes mitogenomes included in the review, along with additional mitogenome sequence data mined from Genbank. Overall, we found that none of 146 mitogenome projects provided all the metadata we looked for; and only 17 projects provided at least one category of metadata across the three main categories. Comparisons using mtDNA sequences from BOLD, suggest that some mitogenomes may be misidentified. Lastly, we appreciate the research potential of mitogenomes announced through this journal; and we conclude with a suggestion of 13 metadata fields, available on GenBank, that if provided in a mitogenomes's GenBank record, would increase their research value.},
}
@article {pmid25693135,
year = {2015},
author = {Wang, B and Wei, X and Dong, J and Zhang, Q},
title = {Improved lower bounds of DNA tags based on a modified genetic algorithm.},
journal = {PloS one},
volume = {10},
number = {2},
pages = {e0110640},
pmid = {25693135},
issn = {1932-6203},
mesh = {*Algorithms ; Base Composition ; Base Pairing ; DNA/chemistry ; High-Throughput Nucleotide Sequencing/*methods ; Models, Genetic ; Sequence Analysis, DNA/*methods ; },
abstract = {The well-known massively parallel sequencing method is efficient and it can obtain sequence data from multiple individual samples. In order to ensure that sequencing, replication, and oligonucleotide synthesis errors do not result in tags (or barcodes) that are unrecoverable or confused, the tag sequences should be abundant and sufficiently different. Recently, many design methods have been proposed for correcting errors in data using error-correcting codes. The existing tag sets contain small tag sequences, so we used a modified genetic algorithm to improve the lower bound of the tag sets in this study. Compared with previous research, our algorithm is effective for designing sets of DNA tags. Moreover, the GC content determined by existing methods includes an imprecise range. Thus, we improved the GC content determination method to obtain tag sets that control the GC content in a more precise range. Finally, previous studies have only considered perfect self-complementarity. Thus, we considered the crossover between different tags and introduced an improved constraint into the design of tag sets.},
}
@article {pmid25689780,
year = {2015},
author = {Wu, L and Wang, Z and Fan, K and Zong, S and Cui, Y},
title = {A SERS-Assisted 3D Barcode Chip for High-Throughput Biosensing.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {11},
number = {23},
pages = {2798-2806},
doi = {10.1002/smll.201403474},
pmid = {25689780},
issn = {1613-6829},
mesh = {Equipment Design ; Equipment Failure Analysis ; Immunoassay/*instrumentation ; Microarray Analysis/*instrumentation ; Robotics/*instrumentation ; Staining and Labeling/*instrumentation ; Surface Plasmon Resonance/*instrumentation ; },
abstract = {A surface enhanced Raman scattering (SERS)-assisted 3D barcode chip has been developed for high-throughput biosensing. The 3D barcode is realized through joint 2D spatial encoding with the Raman spectroscopic encoding, which stores the SERS fingerprint information in the format of a 2D array. Here, the concept of SERS-assisted 3D barcode is demonstrated through multiplex immunoassay, where simultaneous detection of multiple targets in different samples has been achieved using a microfluidic platform. First, multiple proteins in different samples are spatially separated using a microfluidic patterned antibody barcode substrate, forming a 2D hybridization array. Then the SERS probes are used to identify and quantify the proteins. As different SERS probes are labeled with different Raman reporters, they could be employed as "SERS tags" to incorporate spectroscopic information into the 3D barcode. In this 3D barcode, the 2D spatial information helps to differentiate the samples and targets while the SERS information allows quantitative multiplex detection. It is found that the SERS-assisted 3D barcode chip can not only accomplish one-step multiplex detection within 30 min but also achieve an ultrasensitivity down to 10 fg mL(-1) (≈70 aM), which is expected to provide a promising tool for high-throughput biomedical applications.},
}
@article {pmid25686605,
year = {2015},
author = {Busch, K and Klapproth, K and Barile, M and Flossdorf, M and Holland-Letz, T and Schlenner, SM and Reth, M and Höfer, T and Rodewald, HR},
title = {Fundamental properties of unperturbed haematopoiesis from stem cells in vivo.},
journal = {Nature},
volume = {518},
number = {7540},
pages = {542-546},
pmid = {25686605},
issn = {1476-4687},
mesh = {Aging ; Animals ; Animals, Newborn ; Bone Marrow Transplantation ; Cell Lineage/*physiology ; Cell Proliferation ; Cell Tracking ; Female ; Fetus/cytology/embryology ; Fluorouracil ; *Hematopoiesis ; Hematopoietic Stem Cells/*cytology/metabolism ; Male ; Mice ; Receptor, TIE-2/metabolism ; Stem Cells/*cytology/metabolism ; },
abstract = {Haematopoietic stem cells (HSCs) are widely studied by HSC transplantation into immune- and blood-cell-depleted recipients. Single HSCs can rebuild the system after transplantation. Chromosomal marking, viral integration and barcoding of transplanted HSCs suggest that very low numbers of HSCs perpetuate a continuous stream of differentiating cells. However, the numbers of productive HSCs during normal haematopoiesis, and the flux of differentiating progeny remain unknown. Here we devise a mouse model allowing inducible genetic labelling of the most primitive Tie2(+) HSCs in bone marrow, and quantify label progression along haematopoietic development by limiting dilution analysis and data-driven modelling. During maintenance of the haematopoietic system, at least 30% or ∼5,000 HSCs are productive in the adult mouse after label induction. However, the time to approach equilibrium between labelled HSCs and their progeny is surprisingly long, a time scale that would exceed the mouse's life. Indeed, we find that adult haematopoiesis is largely sustained by previously designated 'short-term' stem cells downstream of HSCs that nearly fully self-renew, and receive rare but polyclonal HSC input. By contrast, in fetal and early postnatal life, HSCs are rapidly used to establish the immune and blood system. In the adult mouse, 5-fluoruracil-induced leukopenia enhances the output of HSCs and of downstream compartments, thus accelerating haematopoietic flux. Label tracing also identifies a strong lineage bias in adult mice, with several-hundred-fold larger myeloid than lymphoid output, which is only marginally accentuated with age. Finally, we show that transplantation imposes severe constraints on HSC engraftment, consistent with the previously observed oligoclonal HSC activity under these conditions. Thus, we uncover fundamental differences between the normal maintenance of the haematopoietic system, its regulation by challenge, and its re-establishment after transplantation. HSC fate mapping and its linked modelling provide a quantitative framework for studying in situ the regulation of haematopoiesis in health and disease.},
}
@article {pmid25686050,
year = {2015},
author = {Gao, Z and Gu, Y and Lv, Z and Yu, G and Zhou, J},
title = {Practical electronic information system and printed recording promote management accuracy in an early-stage small-scale non-automatic biobank.},
journal = {Biopreservation and biobanking},
volume = {13},
number = {1},
pages = {61-66},
doi = {10.1089/bio.2014.0102},
pmid = {25686050},
issn = {1947-5543},
mesh = {Biological Specimen Banks/*standards ; *Database Management Systems ; *Databases, Factual ; Humans ; Systems Integration ; },
abstract = {It is particularly necessary for biomedical researchers to obtain applicable biosamples accurately and efficiently, especially from a biobank with multiple-disease catalogs. To optimize the retrieval procedure, especially in the early stages of a non-automatic biobank, we developed a procedure that combined the electronic information system with a graphically designed printed recording system, which assisted in retrieving the samples quickly in a visualized way. In this procedure, we designed tables depending on the structure of equipment and registered the corresponding information in the tables layer by layer. Different samples from different types of diseases were first registered in the electronic system with the specific pre-allocation and barcodes. Then they were stored in the allocated position using their respective barcodes. In this way, the sample number and the location information in the electronic database were completely matched with the printed record. When the samples are needed, it is convenient to check the electronic information with the printed record. This procedure provides a convenient way to record the sample information during its lifecycle, and helps the administrator to double check information about the sample. The current solution offers an easy way for the transformation of a non-automatic biobank from the small-scale early-stage to the large-scale highly-automated level.},
}
@article {pmid25685029,
year = {2015},
author = {van der Bank, H and Greenfield, R},
title = {A pioneer survey and DNA barcoding of some commonly found gastropod molluscs on Robben Island.},
journal = {ZooKeys},
volume = {},
number = {481},
pages = {15-23},
pmid = {25685029},
issn = {1313-2989},
abstract = {Nineteen species of abundant gastropods were collected at Robben Island, including introduced dune snails and European brown garden snails. They were identified using morphology and DNA barcoding. It was expected that the species recorded would be similar to those from the Cape peninsula, South Africa, but we were surprised to find some exceptions: the very abundant invasive mussel species in South Africa, the South American bisexual mussel (Semimytilusalgosus), and the beaded topshells (Oxysteleimpervia) were not found on Robben Island. Possible explanations are presented for these differences.},
}
@article {pmid25685006,
year = {2015},
author = {García-Robledo, C and Staines, CL and Kress, WJ},
title = {A new species of bromeliad-feeding Cephaloleia Chevrolat (Coleoptera, Chrysomelidae, Cassidinae) from Costa Rica: evidence from DNA barcodes, larval and adult morphology and insect diets.},
journal = {ZooKeys},
volume = {},
number = {477},
pages = {143-155},
pmid = {25685006},
issn = {1313-2989},
abstract = {The Neotropical genus Cephaloleia Chevrolat (Coleoptera: Chrysomelidae: Cassidinae) includes 214 species distributed from the south of Mexico to Argentina. Cephaloleia beetles feed mostly on plants from the order Zingiberales. The interactions between Cephaloleia beetles and their Zingiberales host plants is proposed as one of the oldest and most conservative associations. Here we describe a new species of Cephaloleia (Cephaloleiakuprewiczae sp. n.) that feeds on two species of bromeliads (Pitcairniaarcuata and Pitcairniabrittoniana, Bromeliaceae: Pitcairnioideae). Cephaloleiakuprewiczae was previously described as Cephaloleiahistrionica. This study includes evidence from DNA barcodes (COI), larval and adult morphology and insect diets that separates Cephaloleiakuprewiczae from Cephaloleiahistrionica as a new species.},
}
@article {pmid25681938,
year = {2015},
author = {Reinhart, WF and Reifenberger, JG and Gupta, D and Muralidhar, A and Sheats, J and Cao, H and Dorfman, KD},
title = {Distribution of distances between DNA barcode labels in nanochannels close to the persistence length.},
journal = {The Journal of chemical physics},
volume = {142},
number = {6},
pages = {064902},
pmid = {25681938},
issn = {1089-7690},
support = {R01 HG006851/HG/NHGRI NIH HHS/United States ; R01-HG006851/HG/NHGRI NIH HHS/United States ; },
mesh = {Chromosome Mapping ; DNA, Bacterial/chemistry/*genetics ; Escherichia coli/*genetics ; Fluorescent Dyes/chemistry ; Genome, Bacterial/genetics ; Nanotechnology/*methods ; Probability ; },
abstract = {We obtained experimental extension data for barcoded E. coli genomic DNA molecules confined in nanochannels from 40 nm to 51 nm in width. The resulting data set consists of 1 627 779 measurements of the distance between fluorescent probes on 25 407 individual molecules. The probability density for the extension between labels is negatively skewed, and the magnitude of the skewness is relatively insensitive to the distance between labels. The two Odijk theories for DNA confinement bracket the mean extension and its variance, consistent with the scaling arguments underlying the theories. We also find that a harmonic approximation to the free energy, obtained directly from the probability density for the distance between barcode labels, leads to substantial quantitative error in the variance of the extension data. These results suggest that a theory for DNA confinement in such channels must account for the anharmonic nature of the free energy as a function of chain extension.},
}
@article {pmid25681158,
year = {2015},
author = {Mezger, A and Kühnemund, M and Nilsson, M and Herthnek, D},
title = {Highly specific DNA detection employing ligation on suspension bead array readout.},
journal = {New biotechnology},
volume = {32},
number = {5},
pages = {504-510},
doi = {10.1016/j.nbt.2015.01.011},
pmid = {25681158},
issn = {1876-4347},
mesh = {DNA/*analysis ; Ligation ; Limit of Detection ; Reproducibility of Results ; },
abstract = {We show for the first time that monomerized rolling circle amplification (RCA) products can be directly detected with the Luminex suspension bead array readout without the need of PCR amplification. Furthermore, using monomerized RCA products to guide ligation of the detection oligonucleotide (DO) to barcode sequences on the magnetic Luminex beads, combined with efficient washing and increased measurement temperature, yields a higher signal to noise ratio. As a proof-of-principle, we demonstrate detection of pathogenic DNA sequences with high reproducibility, sensitivity and a dynamic range over four orders of magnitude. Using padlock probes in combination with bead suspension arrays opens up the possibility for highly multiplexed DNA targeting and readout.},
}
@article {pmid25681145,
year = {2015},
author = {Heddergott, M and Müller, F and Frantz, AC},
title = {Prevalence and molecular identification of the sinus worm Skrjabingylus petrowi (Nematoda: Metastrongyloidea) from Martes spp. in Germany.},
journal = {Parasitology research},
volume = {114},
number = {6},
pages = {2053-2061},
pmid = {25681145},
issn = {1432-1955},
mesh = {Animals ; Base Sequence ; Female ; Germany/epidemiology ; Male ; Metastrongyloidea/genetics/*isolation &amp; purification ; Molecular Sequence Data ; Mustelidae/*parasitology ; Phylogeny ; Prevalence ; Sequence Analysis, DNA ; Strongylida Infections/epidemiology/parasitology/*veterinary ; },
abstract = {The nematodes of the genus Skrjabingylus (family Metastrongylidae) can parasitise the nasal and frontal sinus cavities of different carnivore species. Until recently, Skrjabingylus petrowi Bageanov &amp; Petrov, 1941, has mainly been described in pine martens (Martes martes Linnaeus, 1758) and sables (Martes zibellina Linnaeus, 1758) sampled in the European part of the former Soviet Union. Newer finds in the stone marten (Martes foina Erxleben, 1777) and from different parts of Europe suggest, however, that the species might have a broader host-species range than previously assumed and be geographically more widespread as well. Since most S. petrowi records have resulted from chance discoveries rather than systematic surveys, very little is known about the prevalence of S. petrowi in marten populations. Here, we report results of a 20-year extensive survey of fresh marten skulls, where we tested 1.059 marten carcasses originating from 248 localities in Germany for the presence of S. petrowi. We identified an infestation in only four M. martes individuals and one M. foina, despite using a reliable identification method. Based on the spicule lengths of the male nematodes, the parasites were identified as S. petrowi and genetic barcoding confirmed the identification of the samples. In a phylogenetic analysis, S. petrowi and Skrjabingylus nasicola (Leuckart, 1842), formed a sister clade to all the other members of the family Metastrongylidae. The low prevalence of S. petrowi is possibly due to its parasitising in the two marten species that are either not very common (M. martes) or predominantly live in urban habitat (M. foina).},
}
@article {pmid25678350,
year = {2015},
author = {Hafeez, MA and Shivaramaiah, S and Dorsey, KM and Ogedengbe, ME and El-Sherry, S and Whale, J and Cobean, J and Barta, JR},
title = {Simultaneous identification and DNA barcoding of six Eimeria species infecting turkeys using PCR primers targeting the mitochondrial cytochrome c oxidase subunit I (mtCOI) locus.},
journal = {Parasitology research},
volume = {114},
number = {5},
pages = {1761-1768},
pmid = {25678350},
issn = {1432-1955},
mesh = {Animals ; Chickens ; Coccidiosis/parasitology/*veterinary ; DNA/genetics ; *DNA Barcoding, Taxonomic ; DNA Primers/genetics ; Eimeria/*genetics ; Electron Transport Complex IV/*genetics ; Genotype ; Mitochondria/genetics ; Oocysts ; Polymerase Chain Reaction/veterinary ; Poultry Diseases/genetics/*parasitology ; Sequence Analysis, DNA ; Species Specificity ; *Turkeys ; },
abstract = {Species-specific PCR primers targeting the mitochondrial cytochrome c oxidase subunit I (mtCOI) locus were generated that allow for the specific identification of the most common Eimeria species infecting turkeys (i.e., Eimeria adenoeides, Eimeria meleagrimitis, Eimeria gallopavonis, Eimeria meleagridis, Eimeria dispersa, and Eimeria innocua). PCR reaction chemistries were optimized with respect to divalent cation (MgCl2) and dNTP concentrations, as well as PCR cycling conditions (particularly anneal temperature for primers). Genomic DNA samples from single oocyst-derived lines of six Eimeria species were tested to establish specificity and sensitivity of these newly designed primer pairs. A mixed 60-ng total DNA sample containing 10 ng of each of the six Eimeria species was used as DNA template to demonstrate specific amplification of the correct product using each of the species-specific primer pairs. Ten nanograms of each of the five non-target Eimeria species was pooled to provide a non-target, control DNA sample suitable to test the specificity of each primer pair. The amplifications of the COI region with species-specific primer pairs from pooled samples yielded products of expected sizes (209 to 1,012 bp) and no amplification of non-target Eimeria sp. DNA was detected using the non-target, control DNA samples. These primer pairs specific for Eimeria spp. of turkeys did not amplify any of the seven Eimeria species infecting chickens. The newly developed PCR primers can be used as a diagnostic tool capable of specifically identifying six turkey Eimeria species; additionally, sequencing of the PCR amplification products yields sequence-based genotyping data suitable for identification and molecular phylogenetics.},
}
@article {pmid25672218,
year = {2015},
author = {Dong, W and Xu, C and Li, C and Sun, J and Zuo, Y and Shi, S and Cheng, T and Guo, J and Zhou, S},
title = {ycf1, the most promising plastid DNA barcode of land plants.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {8348},
pmid = {25672218},
issn = {2045-2322},
mesh = {*DNA Barcoding, Taxonomic ; Embryophyta/*classification/*genetics ; *Genes, Plant ; Genome, Plant ; Plastids/*genetics ; Reproducibility of Results ; Trees/classification/genetics ; },
abstract = {A DNA barcode is a DNA fragment used to identify species. For land plants, DNA fragments of plastid genome could be the primary consideration. Unfortunately, most of the plastid candidate barcodes lack species-level resolution. The identification of DNA barcodes of high resolution at species level is critical to the success of DNA barcoding in plants. We searched the available plastid genomes for the most variable regions and tested the best candidates using both a large number of tree species and seven well-sampled plant groups. Two regions of the plastid gene ycf1, ycf1a and ycf1b, were the most variable loci that were better than existing plastid candidate barcodes and can serve as a barcode of land plants. Primers were designed for the amplification of these regions, and the PCR success of these primers ranged from 82.80% to 98.17%. Of 420 tree species, 357 species could be distinguished using ycf1b, which was slightly better than the combination of matK and rbcL. For the well-sampled representative plant groups, ycf1b generally performed better than any of the matK, rbcL and trnH-psbA. We concluded that ycf1a or ycf1b is the most variable plastid genome region and can serve as a core barcode of land plants.},
}
@article {pmid25671322,
year = {2015},
author = {Janssen, A and Kaiser, S and Meißner, K and Brenke, N and Menot, L and Martínez Arbizu, P},
title = {A reverse taxonomic approach to assess macrofaunal distribution patterns in abyssal Pacific polymetallic nodule fields.},
journal = {PloS one},
volume = {10},
number = {2},
pages = {e0117790},
pmid = {25671322},
issn = {1932-6203},
mesh = {Animals ; Aquatic Organisms/*classification ; Biodiversity ; Classification/*methods ; Minerals/chemistry ; Molecular Sequence Data ; Pacific Ocean ; },
abstract = {Heightened interest in the exploitation of deep seafloor minerals is raising questions on the consequences for the resident fauna. Assessing species ranges and determination of processes underlying current species distributions are prerequisites to conservation planning and predicting faunal responses to changing environmental conditions. The abyssal central Pacific nodule belt, located between the Clarion and Clipperton Fracture Zones (CCZ), is an area prospected for mining of polymetallic nodules. We examined variations in genetic diversity and broad-scale connectivity of isopods and polychaetes across the CCZ. Faunal assemblages were studied from two mining claims (the eastern German and French license areas) located 1300 km apart and influenced by different productivity regimes. Using a reverse taxonomy approach based on DNA barcoding, we tested to what extent distance and large-scale changes in environmental parameters lead to differentiation in two macrofaunal taxa exhibiting different functions and life-history patterns. A fragment of the mitochondrial gene Cytochrome Oxidase Subunit 1 (COI) was analyzed. At a 97% threshold the molecular operational taxonomic units (MOTUs) corresponded well to morphological species. Molecular analyses indicated high local and regional diversity mostly because of large numbers of singletons in the samples. Consequently, variation in composition of genotypic clusters between sites was exceedingly large partly due to paucity of deep-sea sampling and faunal patchiness. A higher proportion of wide-ranging species in polychaetes was contrasted with mostly restricted distributions in isopods. Remarkably, several cryptic lineages appeared to be sympatric and occurred in taxa with putatively good dispersal abilities, whereas some brooding lineages revealed broad distributions across the CCZ. Geographic distance could explain variation in faunal connectivity between regions and sites to some extent, while assumed dispersal capabilities were not as important.},
}
@article {pmid25668035,
year = {2015},
author = {Cowart, DA and Pinheiro, M and Mouchel, O and Maguer, M and Grall, J and Miné, J and Arnaud-Haond, S},
title = {Metabarcoding is powerful yet still blind: a comparative analysis of morphological and molecular surveys of seagrass communities.},
journal = {PloS one},
volume = {10},
number = {2},
pages = {e0117562},
pmid = {25668035},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; Biomarkers ; Cell Nucleus/genetics ; DNA/genetics ; DNA Barcoding, Taxonomic/methods ; France ; Geologic Sediments/analysis ; Mitochondria/genetics ; Molecular Sequence Data ; RNA, Ribosomal, 18S/genetics ; Reproducibility of Results ; Zosteraceae/*classification/*genetics ; },
abstract = {In the context of the sixth wave of extinction, reliable surveys of biodiversity are increasingly needed to infer the cause and consequences of species and community declines, identify early warning indicators of tipping points, and provide reliable impact assessments before engaging in activities with potential environmental hazards. DNA metabarcoding has emerged as having potential to provide speedy assessment of community structure from environmental samples. Here we tested the reliability of metabarcoding by comparing morphological and molecular inventories of invertebrate communities associated with seagrasses through estimates of alpha and beta diversity, as well as the identification of the most abundant taxa. Sediment samples were collected from six Zostera marina seagrass meadows across Brittany, France. Metabarcoding surveys were performed using both mitochondrial (Cytochrome Oxidase I) and nuclear (small subunit 18S ribosomal RNA) markers, and compared to morphological inventories compiled by a long-term benthic monitoring network. A sampling strategy was defined to enhance performance and accuracy of results by preventing the dominance of larger animals, boosting statistical support through replicates, and using two genes to compensate for taxonomic biases. Molecular barcodes proved powerful by revealing a remarkable level of diversity that vastly exceeded the morphological survey, while both surveys identified congruent differentiation of the meadows. However, despite the addition of individual barcodes of common species into taxonomic reference databases, the retrieval of only 36% of these species suggest that the remaining were either not present in the molecular samples or not detected by the molecular screening. This finding exemplifies the necessity of comprehensive and well-curated taxonomic reference libraries and multi-gene surveys. Overall, results offer methodological guidelines and support for metabarcoding as a powerful and repeatable method of characterizing communities, while also presenting suggestions for improvement, including implementation of pilot studies prior to performing full "blind" metabarcoding assessments to optimize sampling and amplification protocols.},
}
@article {pmid25663999,
year = {2014},
author = {Sun, Z and Du, Y and Cheng, L and Zhu, N},
title = {Identification of medicinal species and antifungal property of a Dong ethnic drug.},
journal = {International journal of clinical and experimental medicine},
volume = {7},
number = {12},
pages = {5004-5009},
pmid = {25663999},
issn = {1940-5901},
abstract = {OBJECTIVE: To identify the medicinal species in the Zi Hua Di Ding (ZHDD) prescription commonly used by the Dong ethnic people, and investigate the potential mechanism involved with the anti-fungal properties on Trichophyton rubrum.<br><br>METHODS: DNA barcode technique was used to identify the species in the ZHDD prescription. In vitro study was performed to investigate the antifungal properties of the identified Viola philippica on the T. rubrum. Microscopy was used to observe the growth of the T. rubrum.<br><br>RESULTS: The ZHDD prescription is a mixture of V. philippica and V. inconspicua, and its antifungal properties was superior to the single component. V. philippica could affect the surface and flexibility of hypha, and contribute to the generation of branches. In addition, it could damage the biofilm.<br><br>CONCLUSIONS: Using the DNA barcode technique, we identify the ZHDD prescription is a mixture of V. philippica and V. inconspicua, and its antifungal properties was superior to the single component. V. philippica could affect the growth and biofilm formation of T. rubrum.},
}
@article {pmid25662109,
year = {2015},
author = {Schütte, A and Stüben, PE},
title = {Molecular systematics and morphological identification of the cryptic species of the genus Acalles Schoenherr, 1825, with descriptions of new species (Coleoptera: Curculionidae: Cryptorhynchinae).},
journal = {Zootaxa},
volume = {3915},
number = {1},
pages = {1-51},
doi = {10.11646/zootaxa.3915.1.1},
pmid = {25662109},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Female ; Male ; Organ Size ; RNA, Ribosomal, 16S/genetics ; Weevils/*anatomy &amp; histology/*classification/genetics/growth &amp; development ; },
abstract = {Molecular systematics and morphological study of the monophyletic weevil genus Acalles Schoenherr, 1825 are presented. Based on the mitochondrial CO1 barcoding gene and 16S ribosomal RNA gene, we discuss three difficult species complexes in the framework of a molecular phylogenetic reconstruction of 37 of 47 Western Palaearctic Acalles species or subspecies: the A. echinatus, A. maraoensis and A. sierrae complexes. Two results are given: 1. An exclusive focus on morphological, exoskeletal methods reach their limits in the case of many cryptic Cryptorhynchinae. In these cases molecular analysis is indispensable to resolve species level questions. 2. By using a combination of phenotypic and genotypic characters it is not only possible to ascertain phylogenetic relationships, but also to uncover new morphological, non-intraspecifical characteristics. Digital photography with image stacking makes this possible: for the first time we present photo key for Acalles species, a reliable, less costly and quick method for identification alongside DNA barcoding. The following taxonomic changes are given: Coloracalles edoughensis Desbrochers, 1892 comb. nov. (formerly Acalles edoughensis) from North Africa and Spain change to Coloracalles Astrin &amp; Stüben, 2008 and Pseudodichromacalles xerampelinus Wollaston, 1864 comb. nov. from the Canarian Island Tenerife, Acalles bazaensis Stüben, 2001 syn. nov. is a junior synonym of Acalles sierrae H. Brisout, 1865. Two new species of Acalles s. str. , A. iblanensis Stüben sp. nov. from Morocco and A. vorsti Stüben sp. nov. from Spain (Mallorca), and a new species of the subgenus Origoacalles Stüben &amp; Astrin 2010, A. granulimaculosus Stüben sp. nov. from La Gomera, are described. Acalles temperei Péricart, 1987 stat. nov. is a subspecies of A. parvulus Boheman, 1837. A catalogue of all 43 (+4 incertae sedis) species of Acalles is presented. Finally and for the first time we compare 9 of 12 known North American so-called "Acalles" species with the Western Palaearctic species of Acalles surrounding the type species Curculio camelus Fabricius, 1792. The morphological and molecular analysis for the New World Acalles show that none of the species from the United States actually belong to the genus Acalles or one of the other genera of Western Palaearctic Cryptorhynchinae. There is one exception: Acalles costifer Le Conte, 1884, is transferred to the phylogenetically basal genus Acallocrates Reitter, 1913 as Acallocrates costifer (LeConte, 1884) comb. nov.},
}
@article {pmid25661634,
year = {2015},
author = {Gill, BA and Kondratieff, BC and Stark, BP and Sandberg, JB},
title = {The Banded-wing Moselia infuscata (Claassen) Phenotype from California and Oregon, U.S.A. (Plecoptera: Leuctridae).},
journal = {Zootaxa},
volume = {3911},
number = {4},
pages = {593-597},
doi = {10.11646/zootaxa.3911.4.9},
pmid = {25661634},
issn = {1175-5334},
mesh = {Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; California ; Female ; Insecta/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Male ; Oregon ; Organ Size ; Phylogeny ; },
abstract = {Moselia specimens from California and Oregon with a banded-wing phenotype were found to be indistinguishable morphologically from those of M. infuscata (Claassen) with typical wing pigment pattern. Preliminary DNA barcode data (Cytochrome c Oxidase subunit I [COI]), however, show significant genetic variation among four populations including three from northern California sites and one from southern Oregon. Although this genetic variation exceeded standard divergence thresholds often used to recognize distinct stream insect species, no new taxa are proposed at this time due to the preliminary nature of the data.},
}
@article {pmid25661584,
year = {2015},
author = {Ming, K and Kim, J and Biondi, MJ and Syed, A and Chen, K and Lam, A and Ostrowski, M and Rebbapragada, A and Feld, JJ and Chan, WC},
title = {Integrated quantum dot barcode smartphone optical device for wireless multiplexed diagnosis of infected patients.},
journal = {ACS nano},
volume = {9},
number = {3},
pages = {3060-3074},
doi = {10.1021/nn5072792},
pmid = {25661584},
issn = {1936-086X},
support = {MOP-93532//Canadian Institutes of Health Research/Canada ; },
mesh = {Fluorescent Dyes/chemistry ; HIV Infections/*diagnosis ; Hepatitis B/*diagnosis ; Humans ; *Optical Devices ; *Quantum Dots/chemistry ; *Smartphone ; *Wireless Technology ; },
abstract = {Inorganic nanoparticles are ideal precursors for engineering barcodes for rapidly detecting diseases. Despite advances in the chemical design of these barcodes, they have not advanced to clinical use because they lack sensitivity and are not cost-effective due to requirement of a large read-out system. Here we combined recent advances in quantum dot barcode technology with smartphones and isothermal amplification to engineer a simple and low-cost chip-based wireless multiplex diagnostic device. We characterized the analytical performance of this device and demonstrated that the device is capable of detecting down to 1000 viral genetic copies per milliliter, and this enabled the diagnosis of patients infected with HIV or hepatitis B. More importantly, the barcoding enabled us to detect multiple infectious pathogens simultaneously, in a single test, in less than 1 h. This multiplexing capability of the device enables the diagnosis of infections that are difficult to differentiate clinically due to common symptoms such as a fever or rash. The integration of quantum dot barcoding technology with a smartphone reader provides a capacity for global surveillance of infectious diseases and the potential to accelerate knowledge exchange transfer of emerging or exigent disease threats with healthcare and military organizations in real time.},
}
@article {pmid25661225,
year = {2015},
author = {Rakhshani, E and Starý, P and Hidalgo, NP and Čkrkić, J and Moghaddam, MG and Tomanović, S and Petrović, A and Tomanović, &#x17d;},
title = {Revision of the world Monoctonia Starý, parasitoids of gall aphids: taxonomy, distribution, host range, and phylogeny (Hymenoptera, Braconidae: Aphidiinae).},
journal = {Zootaxa},
volume = {3905},
number = {4},
pages = {474-488},
doi = {10.11646/zootaxa.3905.4.2},
pmid = {25661225},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Ecosystem ; Female ; Host Specificity ; Male ; Organ Size ; Phylogeny ; Wasps/*classification/*genetics/growth &amp; development/physiology ; },
abstract = {The present paper represents a contribution to the knowledge of the taxonomy of Monoctonia Starý aphid parasitoids obtained using the barcoding region of the mitochondrial COI gene. We discuss the phylogenetic position of the genus within the subtribe Monoctonina, redescribe known species, and describe Monoctonia japonica sp. n. from Japan in the association Pemphigus matsumurai Monzen/Populus maximowiczii. A key for species identification is provided. Also, we review and discuss the host records, origin, and geographical distribution of Monoctonia species. It is hypothesized that the genus Monoctonia evolved in Paleogene forests of the temperate (and subtropical) belt, most probably in the European part of the Mediterranean region, which is also the center of origin of their host plants.},
}
@article {pmid25661026,
year = {2015},
author = {Zhang, Y and Chen, HW},
title = {Four new species of the Stegana ornatipes species group (Diptera: Drosophilidae) from Yunnan, China, with DNA barcoding information.},
journal = {Zootaxa},
volume = {3905},
number = {1},
pages = {131-137},
doi = {10.11646/zootaxa.3905.1.8},
pmid = {25661026},
issn = {1175-5334},
mesh = {Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; China ; DNA Barcoding, Taxonomic ; Drosophilidae/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Female ; Male ; Molecular Sequence Data ; Organ Size ; Phylogeny ; },
abstract = {Fore new species of Stegana (Steganina) ornatipes species group are found from Yunnan, China: S. (S.) angustifoliacea sp. nov., S. (S.) crinata sp. nov., S. (S.) nigripes sp. nov. and S. (S.) polysphyra sp. nov. The DNA sequences of the mitochondrial COI gene with BOLD Process ID and GenBank accession numbers are provided for the Chinese species.},
}
@article {pmid25661009,
year = {2015},
author = {Xin, T and Li, X and Yao, H and Lin, Y and Ma, X and Cheng, R and Song, J and Ni, L and Fan, C and Chen, S},
title = {Survey of commercial Rhodiola products revealed species diversity and potential safety issues.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {8337},
pmid = {25661009},
issn = {2045-2322},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/analysis/*genetics ; Drugs, Chinese Herbal/*analysis ; Rhodiola/*genetics ; },
abstract = {The adulteration of herbal products is a threat to consumer safety. Here we surveyed the species composition of commercial Rhodiola products using DNA barcoding as a supervisory method. A Rhodiola dietary supplement DNA barcode database was successfully constructed using 82 voucher samples from 10 Rhodiola species. Based on the DNA barcoding standard operating procedure (SOP), we used this database to identify 100 Rhodiolae Crenulatae Radix et Rhizoma decoction piece samples that were purchased from drug stores and hospitals. The results showed that only 36 decoction piece sequences (40%) were authentic R. crenulata, which is recorded in Chinese Pharmacopeia, whereas the other samples were all adulterants and may indicate a potential safety issue. Among the adulterants, 35 sequences (38.9%) were authenticated as R. serrata, nine sequences (10%) were authenticated as R. rosea, which is documented in the United States Pharmacopeia, and the remaining samples were authenticated as other three Rhodiola species. This result indicates decoction pieces that are available in the market have complex origins and DNA barcoding is a convenient tool for market supervision.},
}
@article {pmid25658694,
year = {2015},
author = {Benzaquem, DC and Oliveira, C and Batista, Jda S and Zuanon, J and Porto, JI},
title = {DNA barcoding in pencilfishes (Lebiasinidae: Nannostomus) reveals cryptic diversity across the Brazilian Amazon.},
journal = {PloS one},
volume = {10},
number = {2},
pages = {e0112217},
pmid = {25658694},
issn = {1932-6203},
mesh = {Animals ; Brazil ; *DNA Barcoding, Taxonomic ; Fishes/*classification/*genetics ; *Genetic Variation ; },
abstract = {Nannostomus is comprised of 20 species. Popularly known as pencilfishes the vast majority of these species lives in the flooded forests of the Amazon basin and are popular in the ornamental trade. Among the lebiasinids, it is the only genus to have undergone more than one taxonomic revision. Even so, it still possesses poorly defined species. Here, we report the results of an application of DNA barcoding to the identification of pencilfishes and highlight the deeply divergent clades within four nominal species. We surveyed the sequence variation in the mtDNA cytochrome c oxidase subunit I gene among 110 individuals representing 14 nominal species that were collected from several rivers along the Amazon basin. The mean Kimura-2-parameter distances within species and genus were 2% and 19,0%, respectively. The deep lineage divergences detected in N. digrammus, N. trifasciatus, N. unifasciatus and N. eques suggest the existence of hidden diversity in Nannostomus species. For N. digrammus and N. trifasciatus, in particular, the estimated divergences in some lineages were so high that doubt about their conspecific status is raised.},
}
@article {pmid25657253,
year = {2015},
author = {Fan, HC and Fu, GK and Fodor, SP},
title = {Expression profiling. Combinatorial labeling of single cells for gene expression cytometry.},
journal = {Science (New York, N.Y.)},
volume = {347},
number = {6222},
pages = {1258367},
doi = {10.1126/science.1258367},
pmid = {25657253},
issn = {1095-9203},
mesh = {*Combinatorial Chemistry Techniques ; DNA Barcoding, Taxonomic/*methods ; DNA, Complementary/chemistry ; Flow Cytometry/*methods ; Gene Expression Profiling/*methods ; Hematopoiesis/genetics ; Humans ; Microspheres ; RNA, Messenger/*analysis/chemistry ; Single-Cell Analysis/*methods ; T-Lymphocytes ; },
abstract = {We present a technically simple approach for gene expression cytometry combining next-generation sequencing with stochastic barcoding of single cells. A combinatorial library of beads bearing cell- and molecular-barcoding capture probes is used to uniquely label transcripts and reconstruct the digital gene expression profile of thousands of individual cells in a single experiment without the need for robotics or automation. We applied the technology to dissect the human hematopoietic system and to characterize heterogeneous response to in vitro stimulation. High sensitivity is demonstrated by detection of low-abundance transcripts and rare cells. Under current implementation, the technique can analyze a few thousand cells simultaneously and can readily scale to 10,000s or 100,000s of cells.},
}
@article {pmid25656854,
year = {2015},
author = {von Beeren, C and Stoeckle, MY and Xia, J and Burke, G and Kronauer, DJ},
title = {Interbreeding among deeply divergent mitochondrial lineages in the American cockroach (Periplaneta americana).},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {8297},
pmid = {25656854},
issn = {2045-2322},
mesh = {Animals ; DNA Barcoding, Taxonomic ; *DNA, Mitochondrial ; *Genetic Variation ; Haplotypes ; *Inbreeding ; Periplaneta/*classification/*genetics ; Phenotype ; Phylogeny ; Phylogeography ; },
abstract = {DNA barcoding promises to be a useful tool to identify pest species assuming adequate representation of genetic variants in a reference library. Here we examined mitochondrial DNA barcodes in a global urban pest, the American cockroach (Periplaneta americana). Our sampling effort generated 284 cockroach specimens, most from New York City, plus 15 additional U.S. states and six other countries, enabling the first large-scale survey of P. americana barcode variation. Periplaneta americana barcode sequences (n = 247, including 24 GenBank records) formed a monophyletic lineage separate from other Periplaneta species. We found three distinct P. americana haplogroups with relatively small differences within (≤0.6%) and larger differences among groups (2.4%-4.7%). This could be interpreted as indicative of multiple cryptic species. However, nuclear DNA sequences (n = 77 specimens) revealed extensive gene flow among mitochondrial haplogroups, confirming a single species. This unusual genetic pattern likely reflects multiple introductions from genetically divergent source populations, followed by interbreeding in the invasive range. Our findings highlight the need for comprehensive reference databases in DNA barcoding studies, especially when dealing with invasive populations that might be derived from multiple genetically distinct source populations.},
}
@article {pmid25655460,
year = {2015},
author = {Frantine-Silva, W and Sofia, SH and Orsi, ML and Almeida, FS},
title = {DNA barcoding of freshwater ichthyoplankton in the Neotropics as a tool for ecological monitoring.},
journal = {Molecular ecology resources},
volume = {15},
number = {5},
pages = {1226-1237},
doi = {10.1111/1755-0998.12385},
pmid = {25655460},
issn = {1755-0998},
mesh = {Animals ; Biodiversity ; Brazil ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/*genetics ; Fishes/*classification/*genetics ; Fresh Water ; Larva/classification/genetics ; Molecular Sequence Data ; Rivers ; Sequence Analysis, DNA ; Zygote/classification ; },
abstract = {Quantifying and classifying ichthyoplankton is one of the most effective ways of monitoring the recruitment process in fishes. However, correctly identifying the fish based on morphological characters is extremely difficult, especially in the early stages of development. We examined ichthyoplankton from tributaries and reservoirs along the middle stretch of the Paranapanema River, one of the areas most impacted by hydroelectric projects in the Neotropics. Matching DNA sequences of the COI gene (628-648 bp) allowed us to identify 99.25% of 536 samples of eggs (293) and larvae (243) subjected to BOLD-IDS similarity analysis with a species-level threshold of 1.3%. The results revealed 37 species in 27 genera, 15 families and four orders, some 23.8% of documented fish species in the Paranapanema River. Molecular identification meant that we could include data from egg samples that accounted for about 30% of the species richness observed. The results in this study confirm the efficacy of DNA barcoding in identifying Neotropical ichthyoplankton and show how the data produced provide valuable information for preparing plans for conserving and managing inland waters.},
}
@article {pmid25655349,
year = {2015},
author = {Doña, J and Diaz-Real, J and Mironov, S and Bazaga, P and Serrano, D and Jovani, R},
title = {DNA barcoding and minibarcoding as a powerful tool for feather mite studies.},
journal = {Molecular ecology resources},
volume = {15},
number = {5},
pages = {1216-1225},
doi = {10.1111/1755-0998.12384},
pmid = {25655349},
issn = {1755-0998},
mesh = {Animals ; Birds ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/*genetics ; Feathers/parasitology ; Mites/*classification/*genetics ; Molecular Sequence Data ; Russia ; Sequence Analysis, DNA ; Spain ; },
abstract = {Feather mites (Astigmata: Analgoidea and Pterolichoidea) are among the most abundant and commonly occurring bird ectosymbionts. Basic questions on the ecology and evolution of feather mites remain unanswered because feather mite species identification is often only possible for adult males, and it is laborious even for specialized taxonomists, thus precluding large-scale identifications. Here, we tested DNA barcoding as a useful molecular tool to identify feather mites from passerine birds. Three hundred and sixty-one specimens of 72 species of feather mites from 68 species of European passerine birds from Russia and Spain were barcoded. The accuracy of barcoding and minibarcoding was tested. Moreover, threshold choice (a controversial issue in barcoding studies) was also explored in a new way, by calculating through simulations the effect of sampling effort (in species number and species composition) on threshold calculations. We found one 200-bp minibarcode region that showed the same accuracy as the full-length barcode (602 bp) and was surrounded by conserved regions potentially useful for group-specific degenerate primers. Species identification accuracy was perfect (100%) but decreased when singletons or species of the Proctophyllodes pinnatus group were included. In fact, barcoding confirmed previous taxonomic issues within the P. pinnatus group. Following an integrative taxonomy approach, we compared our barcode study with previous taxonomic knowledge on feather mites, discovering three new putative cryptic species and validating three previous morphologically different (but still undescribed) new species.},
}
@article {pmid25654664,
year = {2015},
author = {Jang, D and Shin, SY and Seo, DW and Joo, S and Huh, SJ},
title = {A smartphone-based system for the automated management of point-of-care test results in hospitals.},
journal = {Telemedicine journal and e-health : the official journal of the American Telemedicine Association},
volume = {21},
number = {4},
pages = {301-305},
doi = {10.1089/tmj.2014.0083},
pmid = {25654664},
issn = {1556-3669},
mesh = {Disease Management ; Emergency Service, Hospital/*organization &amp; administration ; Female ; HIV Infections/diagnosis/therapy ; Humans ; Male ; Medical Records Systems, Computerized/*organization &amp; administration ; *Mobile Applications ; *Outcome Assessment, Health Care ; Point-of-Care Systems/*organization &amp; administration ; Program Development ; Program Evaluation ; Republic of Korea ; Smartphone/statistics &amp; numerical data ; Telemedicine/*organization &amp; administration ; },
abstract = {OBJECTIVE: Managing test results is an important issue in hospitals because of the increasing use of point-of-care testing (POCT). Here, we propose a smartphone-based system for automatically managing POCT test results.<br><br>MATERIALS AND METHODS: We developed the system to provide convenience to the medical staffs. The system recognizes the patient identification or prescription number of the test by reading barcodes and provides a countdown to indicate when the results will be ready. When the countdown in finished, a picture of the test result is transferred to the electronic medical record server using the Health Level 7 protocol. Human immunodeficiency virus (HIV) kits were selected in this research because HIV is a life-threatening infectious virus, especially for the medical staff who treat undiagnosed patients. The performance of the system was verified from a survey of the users.<br><br>RESULTS: The performance of the system was tested at the emergency room (ER) for 10 months using commercially available POCT kits for detecting HIV. The survey showed that, in total, 80% and 0% of users reported positive or negative feedback, respectively. The staff also reported that the system reduced total processing time by approximately 32&#x2009;min, in addition to reducing workload.<br><br>CONCLUSIONS: The developed automated management system was successfully tested at an ER for 10 months. The survey results show that the system is effective and that medical staff members who used the system are satisfied with using the system at the ER.},
}
@article {pmid25652231,
year = {2015},
author = {Bellanger, JM and Moreau, PA and Corriol, G and Bidaud, A and Chalange, R and Dudova, Z and Richard, F},
title = {Plunging hands into the mushroom jar: a phylogenetic framework for Lyophyllaceae (Agaricales, Basidiomycota).},
journal = {Genetica},
volume = {143},
number = {2},
pages = {169-194},
pmid = {25652231},
issn = {1573-6857},
mesh = {Agaricales/*classification ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Fungal Proteins/genetics ; Genetic Markers ; *Phylogeny ; RNA Polymerase II/genetics ; RNA, Ribosomal, 5.8S/genetics ; },
abstract = {During the last two decades, the unprecedented development of molecular phylogenetic tools has propelled an opportunity to revisit the fungal kingdom under an evolutionary perspective. Mycology has been profoundly changed but a sustained effort to elucidate large sections of the astonishing fungal diversity is still needed. Here we fill this gap in the case of Lyophyllaceae, a species-rich and ecologically diversified family of mushrooms. Assembly and genealogical concordance multigene phylogenetic analysis of a large dataset that includes original, vouchered material from expert field mycologists reveal the phylogenetic topology of the family, from higher (generic) to lower (species) levels. A comparative analysis of the most widely used phylogenetic markers in Fungi indicates that the nuc rDNA region encompassing the internal transcribed spacers 1 and 2, along with the 5.8S rDNA (ITS) and portions of the genes for RNA polymerase II second largest subunit (RPB2) is the most performing combination to resolve the broadest range of taxa within Lyophyllaceae. Eleven distinct evolutionary lineages are identified, that display partial overlap with traditional genera as well as with the phylogenetic framework previously proposed for the family. Eighty phylogenetic species are delineated, which shed light on a large number of morphological concepts, including rare and poorly documented ones. Probing these novel phylogenetic species to the barcoding method of species limit delineation, indicates that the latter method fully resolves Lyophyllaceae species, except in one clade. This case study provides the first comprehensive phylogenetic overview of Lyophyllaceae, a necessary step towards a taxonomical, ecological and nomenclatural revision of this family of mushrooms. It also proposes a set of methodological guidelines that may be of relevance for future taxonomic works in other groups of Fungi.},
}
@article {pmid25647581,
year = {2015},
author = {Sinclair, L and Osman, OA and Bertilsson, S and Eiler, A},
title = {Microbial community composition and diversity via 16S rRNA gene amplicons: evaluating the illumina platform.},
journal = {PloS one},
volume = {10},
number = {2},
pages = {e0116955},
pmid = {25647581},
issn = {1932-6203},
mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Computational Biology ; DNA, Bacterial/*genetics ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {As new sequencing technologies become cheaper and older ones disappear, laboratories switch vendors and platforms. Validating the new setups is a crucial part of conducting rigorous scientific research. Here we report on the reliability and biases of performing bacterial 16S rRNA gene amplicon paired-end sequencing on the MiSeq Illumina platform. We designed a protocol using 50 barcode pairs to run samples in parallel and coded a pipeline to process the data. Sequencing the same sediment sample in 248 replicates as well as 70 samples from alkaline soda lakes, we evaluated the performance of the method with regards to estimates of alpha and beta diversity. Using different purification and DNA quantification procedures we always found up to 5-fold differences in the yield of sequences between individually barcodes samples. Using either a one-step or a two-step PCR preparation resulted in significantly different estimates in both alpha and beta diversity. Comparing with a previous method based on 454 pyrosequencing, we found that our Illumina protocol performed in a similar manner - with the exception for evenness estimates where correspondence between the methods was low. We further quantified the data loss at every processing step eventually accumulating to 50% of the raw reads. When evaluating different OTU clustering methods, we observed a stark contrast between the results of QIIME with default settings and the more recent UPARSE algorithm when it comes to the number of OTUs generated. Still, overall trends in alpha and beta diversity corresponded highly using both clustering methods. Our procedure performed well considering the precisions of alpha and beta diversity estimates, with insignificant effects of individual barcodes. Comparative analyses suggest that 454 and Illumina sequence data can be combined if the same PCR protocol and bioinformatic workflows are used for describing patterns in richness, beta-diversity and taxonomic composition.},
}
@article {pmid25646789,
year = {2015},
author = {Fields, AT and Abercrombie, DL and Eng, R and Feldheim, K and Chapman, DD},
title = {A novel mini-DNA barcoding assay to identify processed fins from internationally protected shark species.},
journal = {PloS one},
volume = {10},
number = {2},
pages = {e0114844},
pmid = {25646789},
issn = {1932-6203},
mesh = {*Animal Fins ; Animals ; *Conservation of Natural Resources ; DNA Barcoding, Taxonomic/*methods ; *Endangered Species ; *Food Handling ; Internationality ; Sequence Analysis, DNA ; Sharks/anatomy &amp; histology/*classification/*genetics ; },
abstract = {There is a growing need to identify shark products in trade, in part due to the recent listing of five commercially important species on the Appendices of the Convention on International Trade in Endangered Species (CITES; porbeagle, Lamna nasus, oceanic whitetip, Carcharhinus longimanus scalloped hammerhead, Sphyrna lewini, smooth hammerhead, S. zygaena and great hammerhead S. mokarran) in addition to three species listed in the early part of this century (whale, Rhincodon typus, basking, Cetorhinus maximus, and white, Carcharodon carcharias). Shark fins are traded internationally to supply the Asian dried seafood market, in which they are used to make the luxury dish shark fin soup. Shark fins usually enter international trade with their skin still intact and can be identified using morphological characters or standard DNA-barcoding approaches. Once they reach Asia and are traded in this region the skin is removed and they are treated with chemicals that eliminate many key diagnostic characters and degrade their DNA ("processed fins"). Here, we present a validated mini-barcode assay based on partial sequences of the cytochrome oxidase I gene that can reliably identify the processed fins of seven of the eight CITES listed shark species. We also demonstrate that the assay can even frequently identify the species or genus of origin of shark fin soup (31 out of 50 samples).},
}
@article {pmid25646458,
year = {2015},
author = {Leray, M and Knowlton, N},
title = {DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {112},
number = {7},
pages = {2076-2081},
pmid = {25646458},
issn = {1091-6490},
mesh = {*Biodiversity ; *DNA Barcoding, Taxonomic ; *Marine Biology ; Molecular Sequence Data ; },
abstract = {Documenting the diversity of marine life is challenging because many species are cryptic, small, and rare, and belong to poorly known groups. New sequencing technologies, especially when combined with standardized sampling, promise to make comprehensive biodiversity assessments and monitoring feasible on a large scale. We used this approach to characterize patterns of diversity on oyster reefs across a range of geographic scales comprising a temperate location [Virginia (VA)] and a subtropical location [Florida (FL)]. Eukaryotic organisms that colonized multilayered settlement surfaces (autonomous reef monitoring structures) over a 6-mo period were identified by cytochrome c oxidase subunit I barcoding (>2-mm mobile organisms) and metabarcoding (sessile and smaller mobile organisms). In a total area of ∼ 15.64 m(2) and volume of ∼ 0.09 m(3), 2,179 operational taxonomic units (OTUs) were recorded from 983,056 sequences. However, only 10.9% could be matched to reference barcodes in public databases, with only 8.2% matching barcodes with both genus and species names. Taxonomic coverage was broad, particularly for animals (22 phyla recorded), but 35.6% of OTUs detected via metabarcoding could not be confidently assigned to a taxonomic group. The smallest size fraction (500 to 106 μm) was the most diverse (more than two-thirds of OTUs). There was little taxonomic overlap between VA and FL, and samples separated by ∼ 2 m were significantly more similar than samples separated by ∼ 100 m. Ground-truthing with independent assessments of taxonomic composition indicated that both presence-absence information and relative abundance information are captured by metabarcoding data, suggesting considerable potential for ecological studies and environmental monitoring.},
}
@article {pmid25645694,
year = {2015},
author = {Lai, L and Ong, R and Li, J and Albani, S},
title = {A CD45-based barcoding approach to multiplex mass-cytometry (CyTOF).},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {87},
number = {4},
pages = {369-374},
pmid = {25645694},
issn = {1552-4930},
mesh = {Adult ; Antibodies/immunology ; Flow Cytometry/*methods ; Humans ; Leukocyte Common Antigens/*analysis/immunology ; Leukocytes, Mononuclear/cytology ; Mass Spectrometry/*methods ; Staining and Labeling ; },
abstract = {CyTOF enables the study of the immune system with a complexity, depth, and multidimensionality never achieved before. However, the full potential of using CyTOF can be limited by scarce cell samples. Barcoding strategies developed based on direct labeling of cells using maleimido-monoamide-DOTA (m-DOTA) provide a very useful tool. However, using m-DOTA has some inherent problems, mainly associated with signal intensity. This may be a source of uncertainty when samples are multiplexed. As an alternative or complementary approach to m-DOTA, conjugating an antibody, specific for a membrane protein present on most immune cells, with different isotopes could address the issues of stability and signal intensity needed for effective barcoding. We chose for this purpose CD45, and designed experiments to address different types of cultures and the ability to detect extra- and intra-cellular targets. We show here that our approach provides an useful alternative to m-DOTA in terms of sensitivity, specificity, flexibility, and user-friendliness. Our manuscript provides details to effectively barcode immune cells, overcoming limitations in current technology and enabling the use of CyTOF with scarce samples (for instance precious clinical samples).},
}
@article {pmid25644900,
year = {2015},
author = {Budischak, SA and Hoberg, EP and Abrams, A and Jolles, AE and Ezenwa, VO},
title = {A combined parasitological molecular approach for noninvasive characterization of parasitic nematode communities in wild hosts.},
journal = {Molecular ecology resources},
volume = {15},
number = {5},
pages = {1112-1119},
doi = {10.1111/1755-0998.12382},
pmid = {25644900},
issn = {1755-0998},
mesh = {Animals ; Animals, Wild ; Buffaloes/*parasitology ; DNA Barcoding, Taxonomic/*methods ; Helminthiasis/diagnosis/parasitology ; Helminthiasis, Animal/diagnosis/*parasitology ; Intestinal Diseases, Parasitic/diagnosis/parasitology/*veterinary ; Molecular Diagnostic Techniques/methods ; Molecular Sequence Data ; Nematoda/*classification/genetics/*isolation &amp; purification ; Nematode Infections/diagnosis/parasitology/*veterinary ; Parasite Load ; Selection Bias ; Sequence Analysis, DNA ; Specimen Handling ; },
abstract = {Most hosts are concurrently or sequentially infected with multiple parasites; thus, fully understanding interactions between individual parasite species and their hosts depends on accurate characterization of the parasite community. For parasitic nematodes, noninvasive methods for obtaining quantitative, species-specific infection data in wildlife are often unreliable. Consequently, characterization of gastrointestinal nematode communities of wild hosts has largely relied on lethal sampling to isolate and enumerate adult worms directly from the tissues of dead hosts. The necessity of lethal sampling severely restricts the host species that can be studied, the adequacy of sample sizes to assess diversity, the geographic scope of collections and the research questions that can be addressed. Focusing on gastrointestinal nematodes of wild African buffalo, we evaluated whether accurate characterization of nematode communities could be made using a noninvasive technique that combined conventional parasitological approaches with molecular barcoding. To establish the reliability of this new method, we compared estimates of gastrointestinal nematode abundance, prevalence, richness and community composition derived from lethal sampling with estimates derived from our noninvasive approach. Our noninvasive technique accurately estimated total and species-specific worm abundances, as well as worm prevalence and community composition when compared to the lethal sampling method. Importantly, the rate of parasite species discovery was similar for both methods, and only a modest number of barcoded larvae (n = 10) were needed to capture key aspects of parasite community composition. Overall, this new noninvasive strategy offers numerous advantages over lethal sampling methods for studying nematode-host interactions in wildlife and can readily be applied to a range of study systems.},
}
@article {pmid25644663,
year = {2015},
author = {Mitchell, A},
title = {Collecting in collections: a PCR strategy and primer set for DNA barcoding of decades-old dried museum specimens.},
journal = {Molecular ecology resources},
volume = {15},
number = {5},
pages = {1102-1111},
doi = {10.1111/1755-0998.12380},
pmid = {25644663},
issn = {1755-0998},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/*genetics ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/genetics ; Insecta/*classification/*genetics ; Molecular Sequence Data ; Museums ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA ; },
abstract = {Natural history museums are vastly underutilized as a source of material for DNA analysis because of perceptions about the limitations of DNA degradation in older specimens. Despite very few exceptions, most DNA barcoding projects, which aim to obtain sequence data from all species, generally use specimens collected specifically for that purpose, instead of the wealth of identified material in museums, constrained by the lack of suitable PCR methods. Any techniques that extend the utility of museum specimens for DNA analysis therefore are highly valuable. This study first tested the effects of specimen age and PCR amplicon size on PCR success rates in pinned insect specimens, then developed a PCR primer set and amplification strategy allowing greatly increased utilization of older museum specimens for DNA barcoding. PCR success rates compare favourably with the few published studies utilizing similar aged specimens, and this new strategy has the advantage of being easily automated for high-throughput laboratory workflows. The strategy uses hemi-nested, degenerate, M13-tailed PCR primers to amplify two overlapping amplicons, using two PCRs per amplicon (i.e. four PCRs per DNA sample). Initial PCR products are reamplified using an internal primer and a M13 primer. Together the two PCR amplicons yield 559 bp of the COI gene from Coleoptera, Lepidoptera, Diptera, Hemiptera, Odonata and presumably also other insects. BARCODE standard-compliant data were recovered from 67% (56 of 84) of specimens up to 25 years old, and 51% (102 of 197) of specimens up to 55 years old. Given the time, cost and specialist expertise required for fieldwork and identification, 'collecting in collections' is a viable alternative allowing researchers to capitalize on the knowledge captured by curation work in decades past.},
}
@article {pmid25638815,
year = {2015},
author = {Zorita, E and Cuscó, P and Filion, GJ},
title = {Starcode: sequence clustering based on all-pairs search.},
journal = {Bioinformatics (Oxford, England)},
volume = {31},
number = {12},
pages = {1913-1919},
pmid = {25638815},
issn = {1367-4811},
mesh = {*Algorithms ; *Cluster Analysis ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Sequence Analysis, DNA/*methods ; *Software ; },
abstract = {MOTIVATION: The increasing throughput of sequencing technologies offers new applications and challenges for computational biology. In many of those applications, sequencing errors need to be corrected. This is particularly important when sequencing reads from an unknown reference such as random DNA barcodes. In this case, error correction can be done by performing a pairwise comparison of all the barcodes, which is a computationally complex problem.<br><br>RESULTS: Here, we address this challenge and describe an exact algorithm to determine which pairs of sequences lie within a given Levenshtein distance. For error correction or redundancy reduction purposes, matched pairs are then merged into clusters of similar sequences. The efficiency of starcode is attributable to the poucet search, a novel implementation of the Needleman-Wunsch algorithm performed on the nodes of a trie. On the task of matching random barcodes, starcode outperforms sequence clustering algorithms in both speed and precision.<br><br>The C source code is available at http://github.com/gui11aume/starcode.},
}
@article {pmid25638289,
year = {2015},
author = {González, AD and Lotta, IA and García, LF and Moncada, LI and Matta, NE},
title = {Avian haemosporidians from Neotropical highlands: Evidence from morphological and molecular data.},
journal = {Parasitology international},
volume = {64},
number = {4},
pages = {48-59},
doi = {10.1016/j.parint.2015.01.007},
pmid = {25638289},
issn = {1873-0329},
mesh = {Animals ; Birds/*parasitology ; Colombia ; Cytochromes b/genetics ; Genetic Variation ; Haemosporida/*classification/*cytology/genetics/isolation &amp; purification ; Host-Parasite Interactions ; Phylogeny ; Plasmodium/*classification/*cytology/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; },
abstract = {Avian haemosporidian parasites have been scarcely studied in the Neotropical highlands despite the high avian diversity reported and the uniqueness of these ecosystems. The aims of this study were to examine Haemoproteus and Plasmodium diversity based on morphological and molecular data, as well as to explore the concordance between these two approaches, when identifying species. We sampled 1487 birds belonging to 166 species, in localities of the Colombian Andean region at elevations ranging from 2100 to 4000 m above sea level. Here, we report twelve morphological parasite species, of which five are undescribed. Thirty parasite cytochrome b lineages are reported, 17 of which for the first time. We provide morphological information and illustrations, as well as, cytochrome b lineages for six morphospecies: Haemoproteus columbae, Haemoproteus witti, Haemoproteus coatneyi, Haemoproteus vireonis, Plasmodium lutzi, and Plasmodium unalis. This is the first report to provide a linkage between morphology and a molecular lineage for H. witti. Cytochrome b gene proved to be useful for species determination as DNA barcoding. Differences in parasite composition between lowlands and highlands in Colombia suggest a replacement of avian Plasmodium fauna. Parasite lineages restricted to either Colombian resident or Nearctic migratory birds were found; but a single lineage common in both has not been recorded in Nearctic non-migratory birds. We generated valuable information by using both morphological and molecular data representing competent host-parasite relationships which are based on observation of gametocytes in circulation; and increased the taxon sampling of avian haemosporidian.},
}
@article {pmid26975140,
year = {2015},
author = {Lukhtanov, VA and Khruleva, OA},
title = {Taxonomic Position and Status of Arctic Gynaephora and Dicallomera Moths (Lepidoptera, Erebidae, Lymantriinae).},
journal = {Folia biologica},
volume = {63},
number = {4},
pages = {257-261},
doi = {10.3409/fb63_4.257},
pmid = {26975140},
issn = {0015-5497},
mesh = {Animal Distribution ; Animals ; Arctic Regions ; Moths/*classification/*genetics ; Phylogeny ; },
abstract = {We use analysis of mitochondrial DNA barcodes in combination with published data on morphology to rearrange the taxonomy of two arctic species, Gynaephora groenlandica and G. rossii. We demonstrate that (1) the taxon lugens Kozhanchikov, 1948 originally described as a distinct species is a subspecies of Gynaephora rossii, and (2) the taxon kusnezovi Lukhtanov et Khruliova, 1989 originally described as a distinct species in the genus Dicallomera is a subspecies of Gynaephora groenlandica. We also provide the first evidence for the occurrence of G. groenlandica in the Palearctic region (Wrangel Island).},
}
@article {pmid26988791,
year = {2014},
author = {Vieira, C and D'hondt, S and De Clerck, O and Payri, CE},
title = {Toward an inordinate fondness for stars, beetles and Lobophora? Species diversity of the genus Lobophora (Dictyotales, Phaeophyceae) in New Caledonia.},
journal = {Journal of phycology},
volume = {50},
number = {6},
pages = {1101-1119},
doi = {10.1111/jpy.12243},
pmid = {26988791},
issn = {1529-8817},
abstract = {Until the recent use of molecular markers, species diversity of Lobophora, an ecologically important brown algal genus with a worldwide distribution in temperate and tropical seas, has been critically underestimated. Using a DNA-based taxonomic approach, we re-examined diversity of the genus from New Caledonia in the Southwest Pacific Ocean. First, species were delineated using general mixed Yule coalescent-based and barcoding gap approaches applied to a mitochondrial cox3 data set. Results were subsequently confirmed using chloroplast psbA and rbcL data sets. Species delimitation analyses agreed well across markers and delimitation algorithms, with the barcoding gap approach being slightly more conservative. Analyses of the cox3 data set resulted in 31-39 molecular operational taxonomic units (MOTUs), four of which are previously described species (L. asiatica, L. crassa, L. nigrescens s.l., L. pachyventera). Of the remaining MOTUs for which we obtained a representative number of sequences and results are corroborated across analyses and genes, we described 10 species de novo: L. abaculusa, L. abscondita, L. densa, L. dimorpha, L. gibbera, L. hederacea, L. monticola, L. petila, L. rosacea, and L. undulata. Our study presents an excellent case of how a traditional morphology-based taxonomy fails to provide accurate estimates of algal diversity. Furthermore, the level of Lobophora diversity unveiled from a single locality in the Pacific Ocean raises important questions with respect to the global diversity of the genus, the distributions and range sizes of the individual species, as well as the mechanisms facilitating coexistence.},
}
@article {pmid26988778,
year = {2014},
author = {Saunders, GW},
title = {Long distance kelp rafting impacts seaweed biogeography in the Northeast Pacific: the kelp conveyor hypothesis.},
journal = {Journal of phycology},
volume = {50},
number = {6},
pages = {968-974},
doi = {10.1111/jpy.12237},
pmid = {26988778},
issn = {1529-8817},
abstract = {Routine DNA barcoding of the Haida Gwaii seaweed flora revealed "endemic species" attributed initially to this region's past as a glacial refugium. However, subsequent barcode records from central California rapidly eroded this list leaving species characterized by disjunct distributions (DD) between California and Haida Gwaii. This observation prompted a more detailed look at species for California and British Columbia and revealed that 33 of 180 DNA-barcoded genetic groups in common between these regions (~18%) predominantly displayed DD between California and northern British Columbia. A previous discovery that a red abalone shell found in Haida Gwaii (far north of its range) had a float-bearing kelp (Nereocystis luetkeana) holdfast attached to it prompted a closer consideration of the COI-5P barcode data in support of a "kelp conveyor hypothesis." The hypothesis posits that there has been a net migration of Californian species to northern British Columbia the vector being species growing on substrata carried along with kelp rafts on the winter Davidson Current.},
}
@article {pmid26988325,
year = {2014},
author = {Salomaki, ED and Kwandrans, J and Eloranta, P and Vis, ML},
title = {Molecular and morphological evidence for Sheathia gen. nov. (Batrachospermales, Rhodophyta) and three new species.},
journal = {Journal of phycology},
volume = {50},
number = {3},
pages = {526-542},
doi = {10.1111/jpy.12179},
pmid = {26988325},
issn = {1529-8817},
abstract = {The freshwater red algal genus Batrachospermum has been shown to be paraphyletic since the first molecular studies of the Batrachospermales. Previous research, along with this study, provides strong support for the clade Batrachospermum section Helminthoidea. This study has found that heterocortication, the presence of both cylindrical and bulbous cells on the main axis, is an underlying synapomorphy of this clade. Based on support from DNA sequences of the rbcL gene, the COI barcode region and the rDNA ITS 1 and 2, along with morphological studies, the new genus Sheathia is proposed. Seven heterocorticate species were recognized from the molecular clades. Sheathia boryana and S. exigua sp. nov. appear to be restricted to Europe, whereas S. confusa occurs in Europe and New Zealand. Sheathia involuta is widespread in the USA and reported for the first time from Europe. Sheathia americana sp. nov., has been collected in the USA and Canada, and S. heterocortica and S. grandis sp. nov. have been collected only in the USA. Sheathia confusa and S. grandis can be distinguished based on morphological characters, whereas DNA sequence data are required to conclusively distinguish the other species. Sheathia fluitans and S. carpoinvolucra also are placed within this genus based on the presence of heterocortication. These data also hint at greater diversity among non-heterocorticate Sheathia than is recognized by the single species name S. arcuata.},
}
@article {pmid26579387,
year = {2014},
author = {Long, P and Cui, Z and Wang, Y and Zhang, C and Zhang, N and Li, M and Xiao, P},
title = {Commercialized non-Camellia tea: traditional function and molecular identification.},
journal = {Acta pharmaceutica Sinica. B},
volume = {4},
number = {3},
pages = {227-237},
pmid = {26579387},
issn = {2211-3835},
abstract = {Non-Camellia tea is a part of the colorful Chinese tea culture, and is also widely used as beverage and medicine in folk for disease prevention and treatment. In this study, 37 samples were collected, including 33 kinds of non-Camellia teas and 4 kinds of teas (Camellia). Traditional functions of non-Camellia teas were investigated. Furthermore, non-Camellia teas of original plants were characterized and identified by molecular methods. Four candidate regions (rbcL, matK, ITS2, psbA-trnH) were amplified by polymerase chain reaction. In addition, DNA barcodes were used for the first time to discriminate the commercial non-Camellia tea and their adulterants, and to evaluate their safety. This study showed that BLASTN and the relevant phylogenetic tree are efficient tools for identification of the commercial non-Camellia tea and their adulterants. However, some sequences from original plants have not been found and there is a limitation of sequence number of original plants in GenBank. Submitting more original plant sequences to the GenBank will be helpful for evaluating the safety of non-Camellia teas.},
}
@article {pmid27275406,
year = {2014},
author = {Parkanyi, V and Ondruska, L and Vasicek, D and Slamecka, J},
title = {Multilevel D-loop PCR identification of hunting game.},
journal = {Applied &amp; translational genomics},
volume = {3},
number = {1},
pages = {1-7},
pmid = {27275406},
issn = {2212-0661},
abstract = {The control region of mtDNA (D-loop) was used for hair samples of the five hunting game species identification: red deer (Cervus elaphus), roe deer (Capreolus capreolus), fallow deer (Dama dama), mouflon (Ovis aries musimon), and wild boar (Sus scrofa). For D-loop multilevel PCR detection scheme was applied in six primers (CE CVZV 1 = 5'-GATCACGAGCTTGATCACCA-3'; CE CVZV 2 = 5'-AGGAGTGGGCGATTTTAGGT-3'; DD CVZV 3 = 5'-CGCGTGAAACCAACAACCCGC-3'; DD CVZV 4 = 5'-CCGGGTCGGGGCCTTAGACG-3'; SSW CVZV 5 = 5'-ACACGTGCGTACACGCGCATA-3'; SSW CVZV 6 = 5'-GGTGCCTGCT T TCGTAGCACG-3') designed to identify unknown biological samples of the hunting game animals. The PCR reaction volume was 25 μl at conditions 95 °C for 2 min, 94 °C for 30 s, 60 °C for 30 s, 72 °C for 30 s, 35 cycles, with last extension at 72 °C for 10 min. D-loop mtDNA amplicons of the game animals are characterized with specific PCR product sizes depending on species: red deer = 163 bp and 140 bp, fallow deer = 280 bp and 138 bp, roe deer = 303 bp, 280 bp, 160 bp and 138 bp, mouflon = 299 bp and 178 bp, wild boar = 137 bp and 229 bp.},
}
@article {pmid26988016,
year = {2014},
author = {Yang, EC and Peters, AF and Kawai, H and Stern, R and Hanyuda, T and Bárbara, I and Müller, DG and Strittmatter, M and van Reine, WF and Küpper, FC},
title = {Ligulate Desmarestia (Desmarestiales, Phaeophyceae) revisited: D. japonica sp. nov. and D. dudresnayi differ from D. ligulata.},
journal = {Journal of phycology},
volume = {50},
number = {1},
pages = {149-166},
doi = {10.1111/jpy.12148},
pmid = {26988016},
issn = {0022-3646},
abstract = {The phylogeny of ligulate and sulfuric-acid containing species of Desmarestia, occurring worldwide from polar to temperate regions, was revised using a multigenic and polyphasic approach. Sequence data, gametophyte characteristics, and sporophyte morphology support reducing a total of 16 taxa to four different species. (1) D. herbacea, containing broad-bladed and highly branched forms, has dioecious gametophytes. The three other species have monoecious gametophytes: (2) D. ligulata which is profusely branched and, except for one subspecies, narrow-bladed, (3) Japanese ligulate Desmarestia, here described as D. japonica sp. nov., which is morphologically similar to D. ligulata but genetically distant from all other ligulate taxa. This species may have conserved the morphology of original ligulate Desmarestia. (4) D. dudresnayi, including unbranched or little branched broad-bladed taxa. A figure of the holotype of D. dudresnayi, which was lost for decades, was relocated. The taxonomy is complemented by a comparison of internal transcribed spacer and cytochrome c oxidase subunit I (cox1) as potential barcode loci, with cox1 offering good resolution, reflecting species delimitations within the genus Desmarestia.},
}
@article {pmid26988015,
year = {2014},
author = {Bendif, el M and Probert, I and Carmichael, M and Romac, S and Hagino, K and de Vargas, C},
title = {Genetic delineation between and within the widespread coccolithophore morpho-species Emiliania huxleyi and Gephyrocapsa oceanica (Haptophyta).},
journal = {Journal of phycology},
volume = {50},
number = {1},
pages = {140-148},
doi = {10.1111/jpy.12147},
pmid = {26988015},
issn = {0022-3646},
abstract = {Emiliania huxleyi and Gephyrocapsa oceanica are abundant coccolithophore morpho-species that play key roles in ocean carbon cycling due to their importance as both primary producers and cal-cifiers. Global change processes such as ocean acidification impact these key calcifying species. The physiology of E. huxleyi, a developing model species, has been widely studied, but its genetic delineation from G. oceanica remains unclear due to a lack of resolution in classical genetic markers. Using nuclear (18S rDNA and 28S rDNA), mitochondrial (cox1, cox2, cox3, rpl16, and dam), and plastidial (16S rDNA, rbcL, tufA, and petA) DNA markers from 99 E. huxleyi and 44 G. oceanica strains, we conducted a multigene/multistrain survey to compare the suitability of different markers for resolving phylogenetic patterns within and between these two morpho-species. The nuclear genes tested did not provide sufficient resolution to discriminate between the two morpho-species that diverged only 291Kya. Typical patterns of incomplete lineage sorting were generated in phylogenetic analyses using plastidial genes. In contrast, full morpho-species delineation was achieved with mitochondrial markers and common intra-morpho-species phylogenetic patterns were observed despite differing rates of DNA substitution. Mitochondrial genes are thus promising barcodes for distinguishing these coccolithophore morpho-species, in particular in the context of environmental monitoring.},
}
@article {pmid27147879,
year = {2014},
author = {Weant, KA and Bailey, AM and Baker, SN},
title = {Strategies for reducing medication errors in the emergency department.},
journal = {Open access emergency medicine : OAEM},
volume = {6},
number = {},
pages = {45-55},
pmid = {27147879},
issn = {1179-1500},
abstract = {Medication errors are an all-too-common occurrence in emergency departments across the nation. This is largely secondary to a multitude of factors that create an almost ideal environment for medication errors to thrive. To limit and mitigate these errors, it is necessary to have a thorough knowledge of the medication-use process in the emergency department and develop strategies targeted at each individual step. Some of these strategies include medication-error analysis, computerized provider-order entry systems, automated dispensing cabinets, bar-coding systems, medication reconciliation, standardizing medication-use processes, education, and emergency-medicine clinical pharmacists. Special consideration also needs to be given to the development of strategies for the pediatric population, as they can be at an elevated risk of harm. Regardless of the strategies implemented, the prevention of medication errors begins and ends with the development of a culture that promotes the reporting of medication errors, and a systematic, nonpunitive approach to their elimination.},
}
@article {pmid26462823,
year = {2014},
author = {Campbell, AM and Lawrence, AJ and Hudspath, CB and Gruwell, ME},
title = {Molecular Identification of Diaspididae and Elucidation of Non-Native Species Using the Genes 28s and 16s.},
journal = {Insects},
volume = {5},
number = {3},
pages = {528-538},
pmid = {26462823},
issn = {2075-4450},
abstract = {Armored scale insects pose a serious threat to habitat conservation across the globe because they include some of the most potent invasive species in the world. They are such a serious concern because their basic morphology, small size, and polyphagous feeding habits often allow them to exist undetected by growers and quarantine experts. In order to provide a potential solution to the problem, we have attempted to elucidate the effectiveness of molecular identification techniques using ribosomal 28s and endosymbiotic 16s rRNA. Sequence data was obtained from many field-collected insects to test the feasibility of identification techniques. A protocol for quick species determination based on sequence data is provided.},
}
@article {pmid25946863,
year = {2014},
author = {Zhou, C and Wang, J and Wang, Y and Liang, Y},
title = {Identification of phage-induced genomic islands in the 13 Streptococcus pyogenes strains using genome barcodes.},
journal = {International journal of data mining and bioinformatics},
volume = {10},
number = {3},
pages = {269-284},
doi = {10.1504/ijdmb.2014.064524},
pmid = {25946863},
issn = {1748-5673},
mesh = {Algorithms ; Bacteriophages ; Cluster Analysis ; Computational Biology/*methods ; *DNA Barcoding, Taxonomic ; Genome, Bacterial ; *Genomic Islands ; Models, Statistical ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; Species Specificity ; Streptococcus pyogenes/*genetics ; },
abstract = {With the revolutionary invention of the high-throughput sequencing technique, the production of bacterial genomes is significantly sped up. The in silico characterisation of genomic islands (GIs) in the pathogenic bacterium becomes increasingly needed, due to the time consumption and the high cost of the experimental techniques. A GI can be computationally detected through the DNA composition. Barcode, a dimension reduction and visualisation technique of genomic DNA composition, was recently applied to detect different DNA compositions effectively. In this work, we proposed a Barcode-based technique to detect Phage-induced Genomic Islands (PGIs) in the 13 completely sequenced strains of Streptococcus pyogenes. Our experimental results showed that the detected PGIs are highly consistent with the known GIs, the novel PGIs are promising candidates for the clinical diagnosis of S. pyogenes.},
}
@article {pmid25927719,
year = {2014},
author = {Darwell, CT and al-Beidh, S and Cook, JM},
title = {Molecular species delimitation of a symbiotic fig-pollinating wasp species complex reveals extreme deviation from reciprocal partner specificity.},
journal = {BMC evolutionary biology},
volume = {14},
number = {},
pages = {189},
pmid = {25927719},
issn = {1471-2148},
mesh = {Animals ; Australia ; Cytochromes b/genetics ; Ecosystem ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Ficus/*genetics ; Molecular Sequence Data ; Phylogeny ; *Pollination ; Sequence Alignment ; Species Specificity ; Symbiosis/*genetics ; Wasps/*genetics/*physiology ; },
abstract = {BACKGROUND: Symbiotic relationships have contributed to major evolutionary innovations, the maintenance of fundamental ecosystem functions, and the generation and maintenance of biodiversity. However, the exact nature of host/symbiont associations, which has important consequences for their dynamics, is often poorly known due to limited understanding of symbiont taxonomy and species diversity. Among classical symbioses, figs and their pollinating wasps constitute a highly diverse keystone resource in tropical forest and savannah environments. Historically, they were considered to exemplify extreme reciprocal partner specificity (one-to-one host-symbiont species relationships), but recent work has revealed several more complex cases. However, there is a striking lack of studies with the specific aims of assessing symbiont diversity and how this varies across the geographic range of the host.<br><br>RESULTS: Here, we use molecular methods to investigate cryptic diversity in the pollinating wasps of a widespread Australian fig species. Standard barcoding genes and methods were not conclusive, but incorporation of phylogenetic analyses and a recently developed nuclear barcoding gene (ITS2), gave strong support for five pollinator species. Each pollinator species was most common in a different geographic region, emphasising the importance of wide geographic sampling to uncover diversity, and the scope for divergence in coevolutionary trajectories across the host plant range. In addition, most regions had multiple coexisting pollinators, raising the question of how they coexist in apparently similar or identical resource niches.<br><br>CONCLUSION: Our study offers a striking example of extreme deviation from reciprocal partner specificity over the full geographical range of a fig-wasp system. It also suggests that superficially identical species may be able to co-exist in a mutualistic setting albeit at different frequencies in relation to their fig host's range. We show that comprehensive sampling and molecular taxonomic techniques may be required to uncover the true structure of cryptic biodiversity underpinning intimate ecological interactions.},
}
@article {pmid27008509,
year = {2013},
author = {De Clerck, O and Guiry, MD and Leliaert, F and Samyn, Y and Verbruggen, H},
title = {Algal taxonomy: a road to nowhere?.},
journal = {Journal of phycology},
volume = {49},
number = {2},
pages = {215-225},
doi = {10.1111/jpy.12020},
pmid = {27008509},
issn = {0022-3646},
abstract = {The widespread view of taxonomy as an essentially retrogressive and outmoded science unable to cope with the current biodiversity crisis stimulated us to analyze the current status of cataloguing global algal diversity. Contrary to this largely pessimistic belief, species description rates of algae through time and trends in the number of active taxonomists, as revealed by the web resource AlgaeBase, show a much more positive picture. More species than ever before are being described by a large community of algal taxonomists. The lack of any decline in the rate at which new species and genera are described, however, is indicative of the large proportion of undiscovered diversity and bears heavily on any prediction of global algal species diversity and the time needed to catalogue it. The saturation of accumulation curves of higher taxa (family, order, and classes) on the other hand suggest that at these taxonomic levels most diversity has been discovered. This reasonably positive picture does not imply that algal taxonomy does not face serious challenges in the near future. The observed levels of cryptic diversity in algae, combined with the shift in methods used to characterize them, have resulted in a rampant uncertainty about the status of many older species. As a consequence, there is a tendency in phycology to move gradually away from traditional names to a more informal system whereby clade-, specimen- or strain-based identifiers are used to communicate biological information. Whether these informal names for species-level clades represent a temporary situation stimulated by the lag between species discovery and formal description, or an incipient alternative or parallel taxonomy, will be largely determined by how well we manage to integrate historical collections into modern taxonomic research. Additionally, there is a pressing need for a consensus about the organizational framework to manage the information about algal species names. An eventual strategy should preferably come out of an international working group that includes the various databases as well as the various phycological societies. In this strategy, phycologists should link up to major international initiatives that are currently being developed, such as the compulsory registration of taxonomic and nomenclatural acts and the introduction of Life Science Identifiers.},
}
@article {pmid27008390,
year = {2013},
author = {Kirkendale, L and Saunders, GW and Winberg, P},
title = {A Molecular Survey of Ulva (Chlorophyta) in Temperate Australia Reveals Enhanced Levels of Cosmopolitanism.},
journal = {Journal of phycology},
volume = {49},
number = {1},
pages = {69-81},
doi = {10.1111/jpy.12016},
pmid = {27008390},
issn = {0022-3646},
abstract = {The green algal genus Ulva includes a speciose group of marine macroalgae inhabiting shallow seas worldwide. Although algal blooms in Asia highlight the opportunistic nature of several "nuisance" species, recent research clearly reveals important positive benefits of Ulva. Applied research requires accurate, reliable, and rapid identification, however, identification of Ulva spp. has met with con-siderable difficulty. Consequently, many have turned to molecular markers to aid in taxonomy. Previous studies of plants and algae have relied heavily on ITS and rbcL. Recently, tufA has been presented as a suitable barcoding gene to facilitate species-level identification of green macroalgae and it is used here to explore the diversity of Ulva spp. in temperate Australia. Ninety Ulva specimens collected from 38 sites across five states were sequenced for this gene region with exemplars from each genetic group also sequenced for rbcL to test for congruence. Collections of Australian Ulva spp. were compared to samples from Asia and North America and exhibited trends consistent with recent studies in terms of species relationships. Results support an overwhelmingly cosmopolitan flora in temperate Australia that contrasts with other Australasian surveys of Ulva that report a greater number of endemics and new species. Four new records, as well as numerous range extensions for taxa already known from the country, are documented. Evidence for three nonindigenous Ulva species in temperate Australia is discussed.},
}
@article {pmid26438957,
year = {2013},
author = {Gonzalez-Vaquero, RA and Roig-Alsina, A},
title = {Revision of the species of the bee genus Caenohalictus (Hymenoptera: Halictidae) occurring in Argentinean Patagonia.},
journal = {Zootaxa},
volume = {3670},
number = {},
pages = {493-515},
doi = {10.11646/zootaxa.3670.4.5},
pmid = {26438957},
issn = {1175-5326},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Argentina ; Bees/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Body Size ; Female ; Male ; Organ Size ; Phylogeny ; },
abstract = {The species of the halictid bee genus Caenohalictus Cameron occurring in Argentinean Patagonia are revised. Eight species are recognized, one of them here described as new: Caenohalictus flammeus n. sp. The female of C. turquesa Rojas &amp; Toro 2000 is described for the first time. Pseudagapostemon babuarus Jörgensen 1912, based on the male holotype, is synonymized under Augochlora (Pseudaugochloropsis) thamyris Jörgensen 1912, based on the female lectotype. Lectotypes are designated for Augochlora (Pseudaugochloropsis) thamyris Jörgensen 1912 and Halictomorpha autumnalis Jörgensen 1912. Caenohalictus cyanopygus Rojas &amp; Toro 2000, C. galletue Rojas &amp; Toro 2000, C. iodurus (Vachal 1903), C. opaciceps (Friese 1916), and C. turquesa Rojas &amp; Toro 2000, all known from Chile, are cited for Argentina for the first time. Notes on the variation observed within species, images of diagnostic structures, a key to the species and distributional data are provided. In addition, DNA barcoding results for four species are briefly discussed.},
}
@article {pmid26312357,
year = {2013},
author = {Victor, BC and Alfaro, ME and Sorenson, L},
title = {Rediscovery of Sagittalarva inornata n. gen., n. comb. (Gilbert, 1890) (Perciformes: Labridae), a long-lost deepwater fish from the eastern Pacific Ocean: a case study of a forensic approach to taxonomy using DNA barcoding.},
journal = {Zootaxa},
volume = {3669},
number = {},
pages = {551-570},
doi = {10.11646/zootaxa.3669.4.8},
pmid = {26312357},
issn = {1175-5326},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Female ; Larva/anatomy &amp; histology/classification/genetics/physiology ; Male ; Pacific Ocean ; Perciformes/anatomy &amp; histology/*classification/*genetics/physiology ; Phylogeny ; Species Specificity ; },
abstract = {Some of the more valuable contributions of a standardized DNA sequence database (the DNA barcode) are matching specimens of different life stages and confirming the species identity of individuals from distant locations. These applications can facilitate the detective work required to solve difficult taxonomic problems. In this case, a match was made between the COI mtDNA sequence of an adult male wrasse recently caught at the tip of Baja California in Mexico in deep water (30-100m) and sequences from a series of unusual larvae collected about 3500 km to the south, in the open ocean over the Galápagos Rift hydrothermal vents in 1985. The Baja adults fit the recent description of Halichoeres raisneri Baldwin &amp; McCosker, 2001 from the Galápagos and Cocos Islands. However, another deepwater labrid is known from the same site and depth in Baja; it is the type locality for the century-old holotype and only specimen of the Cape Wrasse Pseudojulis inornatus Gilbert, 1890 (later as Pseudojuloides inornatus). Deepwater video images from the tip of Baja show wrasses identical to H. raisneri photographed in Galápagos but who also fit the description of Pseudojulis inornatus. This coincidence led to a closer investigation of the holotype with x-ray, which revealed unanticipated caniniform teeth (vs. incisiform in Pseudojuloides) and an error in the fin-ray count in the original description, both of which mistakenly separated Halichoeres raisneri. The two species now match in markings, meristics, and morphology as well as overlapping range and are therefore synonymized. Phenetic and phylogenetic trees using mtDNA and nuclear DNA sequences show the species is not close to any other lineage and does not group with the other julidine labrids of the New World or the Pseudojuloides or Halichoeres of the Indo-Pacific. The distinctive larval morphology, long, thin, and flattened with a sharply pointed black-tipped snout, resembles no other described labrid larvae and, without an available genus, the new genus Sagittalarva Victor, n. gen. and the new combination Sagittalarva inornata (Gilbert, 1890), n. gen., n. comb. are described.},
}
@article {pmid26287091,
year = {2013},
author = {Nakamori, T},
title = {A new species of Ceratophysella (Collembola: Hypogastruridae) from Japan, with notes on its DNA barcode and a key to Japanese species in the genus.},
journal = {Zootaxa},
volume = {3641},
number = {},
pages = {371-378},
doi = {10.11646/zootaxa.3641.4.3},
pmid = {26287091},
issn = {1175-5326},
mesh = {Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Arthropods/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Body Size ; DNA Barcoding, Taxonomic ; Japan ; Organ Size ; Phylogeny ; },
abstract = {Ceratophysella comosa sp. nov. was collected from ascomata of Ciborinia canielliae in Japan and the morphological and molecular characteristics of the species are described here. The species has 3 + 3 cephalic spines as in Ceratophysella loricata and Ceratophysella pilosa, but a plurichaetosis intermediate between C. loricata (absent) and C. pilosa (strong). The new species can be distinguished from these two species also by the number of setae on the first thorax segment and ventral tube. Partial DNA sequences of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene were used as DNA barcodes to distinguish species. Interspecific genetic distances of the gene were higher than the intraspecific distances between Ceratophysella species for which sequence data are available. An identification key of Japanese Ceratophysella is provided.},
}
@article {pmid26269853,
year = {2013},
author = {Dumont, HJ and Rietzler, AC and Kalapothakis, E},
title = {Micromoina arboricola n. gen., n. spec. (Crustacea: Cladocera), a new moinid living in a forest tree-hole in Minas Gerais, Brazil.},
journal = {Zootaxa},
volume = {3652},
number = {},
pages = {533-546},
doi = {10.11646/zootaxa.3652.5.3},
pmid = {26269853},
issn = {1175-5326},
mesh = {Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Brazil ; Cladocera/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Female ; Forests ; Male ; Organ Size ; Phylogeny ; },
abstract = {With a maximum size of ca 0.5 mm, Micromoina arboricola is among the smallest moinids known to date. It was discovered in a flooded treehole in a forest in the Medio Rio Doce Valley, Minas Gerais, Brazil, where it mainly feeds on particulate organic matter derived from the vinhatico tree . However, it is easily cultured in the lab on a diet of green algae plus yeast and pelleted fish food. Structurally, it is a miniature version of a moinid, distinguished by characters on the antennules (both sexes) and the postabdomen. The latter is peculiar in shape, in lacking a basal spine, and in having only three lateral plumose setae. A comparative investigation of the barcoding fragment of the COI gene in a number of moinids confirms the family Moinidae as composed of several genera, as well as the status of the new taxon.},
}
@article {pmid26266320,
year = {2013},
author = {Niedbała, W and Dabert, M},
title = {Madeira's ptyctimous mites (Acari, Oribatida).},
journal = {Zootaxa},
volume = {3664},
number = {},
pages = {571-585},
doi = {10.11646/zootaxa.3664.4.9},
pmid = {26266320},
issn = {1175-5326},
mesh = {Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Female ; Male ; Mites/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Molecular Sequence Data ; Organ Size ; Phylogeny ; },
abstract = {In the material recently collected in Madeira, 16 species of ptyctimous mites have been found. A new species of Austrophthiracarus rabacalensis Niedbala sp. nov. has been described. The presence of P. globosus and S. (R.) ortizi, reported earlier from Madeira has not been confirmed, but P. anonymus and P. montanus, so far not reported from this island, have been found. All 16 species identified in the material from Madeira studied occur in the Palaearctic Region; four of them are endemites, seven occur in western Palaearctic, four are panpalaearctic, while one is a semicosmopolitan. Morphological analysis has revealed a high similarity of two endemic species of Madeira with two European species: Steganacarus (Steganacarus) crassisetosus is similar to Steganacarus (Steganacarus) applicatus, while Steganacarus (Steganacarus) similis to Steganacarus (Steganacarus) spinosus. DNA-barcode analysis using COI and D2 28S rDNA sequences confirmed the species status of these four species. The phylogenetic analyses of COI amino acid data and D2 28S rDNA sequences suggest a closer relationship between S. (S.) crassisetosus and S. (S.) applicatus, pointing to a great genetic distance between S. (S.) spinosus and the other species of Steganacarus (Steganacarus).},
}
@article {pmid26266313,
year = {2013},
author = {Pillai, PM and Unnikrishnan, V},
title = {Morphology and molecular phylogeny of Macrobrachium snpurii, a new species of the genus Macrobrachium Bate, 1868 from Kerala, India.},
journal = {Zootaxa},
volume = {3664},
number = {},
pages = {434-444},
doi = {10.11646/zootaxa.3664.4.2},
pmid = {26266313},
issn = {1175-5326},
mesh = {Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Arthropod Proteins ; Body Size ; Female ; India ; Male ; Molecular Sequence Data ; Organ Size ; Palaemonidae/anatomy &amp; histology/*classification/*genetics/growth &amp; development ; *Phylogeny ; },
abstract = {Macrobrachium snpurii sp. nov., collected from the Karamana River, in the lower reaches of Western Ghats, is described and illustrated. DNA barcoding using Cytochrome B gene sequences has elucidated the taxonomic status of the new species and the NJ tree reveals that M. snpurii sp. nov., is phylogenetically close to M. idella idella. However, morphometric and meristic features of the species share certain characters with M. idella idella, M. patheinense and M. tratense, while it diverges remarkably from these three species in distinctive diagnostic characters: rostral formula 12-14/4 with 2 postorbital teeth; carapace smooth with distal end of rostrum directed upwards; chelae with 2 proximal denticles both in the movable and immovable fingers. A wide gap present in the distal part of the chelae, when fingers are closed. Movable finger, longer than the immovable and distal end of fingers inwardly hook-like; palm more pigmented than fingers and telson extends beyond the level of the outer lateral spine of uropodal exopod. A pair of plumose setae is present between the inner pair of movable spines of telson.},
}
@article {pmid26258217,
year = {2013},
author = {Bellis, G and Kim, HC and Kim, MS and Klein, TA and Lee, DK and Gopurenko, D},
title = {Three species of Culicoides Latreille (Diptera: Ceratopogonidae) newly recorded from the Republic of Korea.},
journal = {Zootaxa},
volume = {3718},
number = {},
pages = {171-182},
doi = {10.11646/zootaxa.3718.2.5},
pmid = {26258217},
issn = {1175-5326},
mesh = {Animal Distribution ; Animals ; Ceratopogonidae/*anatomy &amp; histology/*classification/genetics ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Phylogeny ; Republic of Korea ; Species Specificity ; },
abstract = {Light trap surveys of adult Culicoides Latreille in the Republic of Korea (ROK) resulted in the capture of three previously unreported species, C. nasuensis Kitaoka, C. pallidulus Yu and C. jacobsoni Macfie. These new records are supported by supplementary morphological descriptions and DNA barcodes (mitochondrial cytochrome oxidase I or COI). An updated checklist of species reported from the ROK is provided.},
}
@article {pmid26240915,
year = {2013},
author = {De Prins, J and De Prins, W and De Coninck, E and Kawahara, AY and Milton, MA and Hebert, PD},
title = {Taxonomic history and invasion biology of two Phyllonorycter leaf miners (Lepidoptera: Gracillariidae) with links to taxonomic and molecular datasets.},
journal = {Zootaxa},
volume = {3709},
number = {},
pages = {341-362},
doi = {10.11646/zootaxa.3709.4.3},
pmid = {26240915},
issn = {1175-5326},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Databases, Genetic ; Female ; Genetic Variation ; Host Specificity ; *Introduced Species ; Lepidoptera/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Male ; Organ Size ; Phylogeny ; Plant Diseases/parasitology ; Plant Leaves/parasitology ; Spain ; },
abstract = {This paper deals with two European species, Phyllonorycter mespilella (Hübner, 1805) and P. trifasciella (Haworth, 1828), that have colonized the subtropical Canary Islands. The Rosaceae leaf miner, P. mespilella, is recorded for the first time from Lanzarote and La Palma, while the Caprifoliaceae leaf miner, P. trifasciella, is recorded from Tenerife. We present the diagnoses of these species based on morphology, a preliminary DNA barcode (COI) library of congeneric and con-familial species, and discuss the taxonomic position of the colonizers within the blancardella and trifasciella species groups. The recent intensification of anthropogenic disturbance likely accounts for their range expansion, an event that may impact the relict flora present on the Canary Islands.},
}
@article {pmid26217836,
year = {2013},
author = {Ilgūnas, M and Palinauskas, V and Iezhova, TA and Valkiūnas, G},
title = {Molecular and morphological characterization of two avian malaria parasites (Haemosporida: Plasmodiidae), with description of Plasmodium homonucleophilum n. sp.},
journal = {Zootaxa},
volume = {3666},
number = {},
pages = {49-61},
doi = {10.11646/zootaxa.3666.1.5},
pmid = {26217836},
issn = {1175-5326},
mesh = {Animals ; Bird Diseases/*parasitology ; Cytochromes b/genetics ; Malaria, Avian/*parasitology ; Molecular Sequence Data ; Passeriformes/parasitology ; Phylogeny ; Plasmodium/*classification/*genetics/growth &amp; development/isolation &amp; purification ; Protozoan Proteins/genetics ; },
abstract = {Plasmodium hoionucleophilum n. sp. was described from the Common Grasshopper Warbler Locustella naevia based on the morphology of blood stages and partial sequences of the mitochondrial cytochrome b (cyt b) gene. This malaria parasite belongs to the subgenus Novyella; it can be readily distinguished from all described Novyella parasites due to two features, i. e. the strict adherence of its meronts to the nuclei of infected erythrocytes and the lack of such adherence in the case of gametocytes. We also found the lineage pLZFUS01 in Red-Backed Shrike Lanius collurio, identified this parasite and conclude that it belongs to Plasiodium relictum. Illustrations of blood stages of these two parasites are given. DNA lineages associated with P. hoionucleophilum (pSW2, GenBank KC342643) and P. relictum (pLZFUS01, GenBank KC342644) are reported and can be used for molecular identification of these malarial infections. Phylogenetic analysis determines DNA lineages closely related to both reported parasites and is in accordance with the parasites' morphological identification. This study contributes to barcoding of avian malaria parasites using partial sequences of cyt b gene.},
}
@article {pmid26171512,
year = {2013},
author = {Feller, KD and Cronin, TW and Ahyong, ST and Porter, ML},
title = {Morphological and molecular description of the late-stage larvae of Alima Leach, 1817 (Crustacea: Stomatopoda) from Lizard Island, Australia.},
journal = {Zootaxa},
volume = {3722},
number = {},
pages = {22-32},
doi = {10.11646/zootaxa.3722.1.2},
pmid = {26171512},
issn = {1175-5326},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Australia ; Body Size ; Crustacea/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Female ; Islands ; Male ; Molecular Sequence Data ; Phylogeny ; },
abstract = {Alima pacifica and A. orientalis are stomatopods commonly found at Lizard Island, Great Barrier Reef, Australia. There are currently no descriptions that link the larvae to the adult morphotype despite the frequent occurrence of the last larval stage of these two species. We used DNA barcoding of the cytochrome oxidase I (COI) gene to link the last stage larvae of A. pacifica and A. orientalis to the respective adult morphotype. Detailed morphological descriptions of the late larva of each species are provided and compared to other described last-stage Alima larvae. These data support previous studies that suggest paraphyly of the genus Alima.},
}
@article {pmid26146710,
year = {2013},
author = {Rubio, RM and Guerrero, JJ and Manuel, G and Ortiz, AS},
title = {DNA barcoding confirms the presence of Hydria cervinalis (Scopoli, 1763) in the Iberian Peninsula (Lepidoptera: Geometridae: Larentiinae).},
journal = {Zootaxa},
volume = {3702},
number = {},
pages = {97-99},
doi = {10.11646/zootaxa.3702.1.7},
pmid = {26146710},
issn = {1175-5326},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Female ; Genitalia, Female/anatomy &amp; histology ; Lepidoptera/anatomy &amp; histology/*classification/*genetics ; Phylogeny ; Spain ; },
}
@article {pmid26146702,
year = {2013},
author = {Gibbs, J and Packer, L and Dumesh, S and Danforth, BN},
title = {Revision and reclassification of Lasioglossum (Evylaeus), L. (Hemihalictus) and L. (Sphecodogastra) in eastern North America (Hymenoptera: Apoidea: Halictidae).},
journal = {Zootaxa},
volume = {3672},
number = {},
pages = {1-117},
doi = {10.11646/zootaxa.3672.1.1},
pmid = {26146702},
issn = {1175-5326},
mesh = {Animal Distribution ; Animals ; Bees/anatomy &amp; histology/*classification/genetics ; DNA Barcoding, Taxonomic ; Female ; Male ; North America ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The black species of weak-veined Lasioglossum (or Hemihalictus series) in eastern North America are revised to clarify their taxonomy and nomenclature and to facilitate identification. A subgeneric classification based upon available phylogenetic data is applied. Lasioglossum (Sphecodogastra) is applied more broadly than any previous usage to include many species typically classified as L. (Evylaeus). The subgenus L. (Evylaeus) is retained but applied narrowly in agreement with phylogenetic results. Lasioglossum (Hemihalictus) has historically been considered monotypic but is here applied to many species of L. (Dialictus) sensu lato (equivalent to the carinaless L. (Evylaeus) of some authors). Usage of L. (Dialictus) is restricted primarily to species with metallic integument. Additional subgeneric synonymies for extralimital taxa are formalized and discussed. Descriptions are provided for each species with a synonymic list, diagnosis, and notes on taxonomy and biology. The recently revised Onagraceae-specialist species of L. (Sphecodogastra) are given abbreviated treatments. Notes on available DNA barcode data are given, with diagnostic characters supplied for closely related spe-cies. One new species is described: L. (Sphecodogastra) seillean Gibbs and Packer and the males of L. fedorense (Crawford) and L. pectinatum (Robertson) are described for the first time. The following three new synonymies are proposed: Lasioglossum (Hemihalictus) sopinci (Crawford), senior subjective synonym of Evylaeus bradleyi Mitchell; Lasioglosum (Hemihalictus) macoupinense (Robertson), senior subjective synonym of Halictus divergens Lovell; and Lasioglossum (Hemihalictus) inconditum (Cockerell), senior subjective synonym of Halictus tracyi Cockerell. Lasioglossum inconditum is here considered to be distinct from the Palaearctic species L. rufitarse (Zetterstedt). A lectotype is designat-ed for Halictus quebecensis Crawford. We present the first record of L. lustrans (Cockerell) and L. swenki (Crawford) in Canada and the first record of L. lusorium (Cresson) east of the Mississippi River. Updated keys to species are provided for the fauna of eastern North America.},
}
@article {pmid26106783,
year = {2013},
author = {Gjershaug, JO and Staverløkk, A and Kleven, O and Ødegaard, F},
title = {Species status of Bombus monticola Smith (Hymenoptera: Apidae) supported by DNA barcoding.},
journal = {Zootaxa},
volume = {3716},
number = {},
pages = {431-440},
doi = {10.11646/zootaxa.3716.3.6},
pmid = {26106783},
issn = {1175-5326},
mesh = {Animal Distribution ; Animals ; Bees/anatomy &amp; histology/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Female ; Male ; Norway ; Phylogeny ; Species Specificity ; },
abstract = {Certain species of bumblebees are difficult to distinguish based on morphology alone due to a lack of diagnostic characters and extensive intraspecific variation in colour patterns. The discussion concerning whether Bombus lapponicus and Bombus monticola are the same species or not, seems to be ongoing. We present a study of 16 speciemens of B. monticola/B. lapponicus from Norway, identified with previously published morphological characters and with DNA barcoding. The results showed a match with the examination of the morphological characters and the DNA sequence data. These results confirm that B. lapponicus and B. monticola appear as separate species in Norway, which supports earlier conclusions based on both morphological differences and differences in cephalic marking pheromones in males. The wide sympatric range of the two taxa in Scandinavia also strongly support their species status.},
}
@article {pmid26106771,
year = {2013},
author = {Pogue, MG and Ouellette, GD and Harp, CE},
title = {A revision of the Schinia volupia (Fitch) species complex (Lepidoptera: Noctuidae: Heliothinae).},
journal = {Zootaxa},
volume = {3716},
number = {},
pages = {157-191},
doi = {10.11646/zootaxa.3716.2.3},
pmid = {26106771},
issn = {1175-5326},
mesh = {Animal Distribution ; Animals ; Female ; Genetic Variation ; Haplotypes ; Male ; Moths/*anatomy &amp; histology/*classification/genetics/physiology ; Phylogeny ; Species Specificity ; },
abstract = {DNA barcode analysis of cytochrome oxidase I (COI) could not differentiate between the species of the Schinia volupia (Fitch, 1868) complex including S. volupia, S. masoni Smith, S. fulleri (McElvare, 1961); S. sanrafaeli Opler, 2004; S. miniana (Grote, 1881); and S. biforma Smith, 1906. Genitalic characters could only differentiate S. biforma from the S. volupia complex. Based on forewing color and pattern, larval host plant utilization, and geographic distribution, S. volupia, S. sanrafaeli, S. fulleri, and S. miniana are recognized as valid species and S. masoni is considered a new synonym of S. volupia. Schinia volupia, S.fulleri, S. sanrafaeli, S. miniana, and S. biforma are diagnosed and described. A variety of adult images are presented to show the range of variation among these species. Male and female genitalia of all included taxa are illustrated. Host plant utilization is discussed and illustrated. Distribution maps for examined specimens are provided.},
}
@article {pmid26106770,
year = {2013},
author = {Timm, T and Arslan, N and Rüzgar, M and Martinsson, S and Erséus, C},
title = {Oligochaeta (Annelida) of the profundal of Lake Hazar (Turkey), with description of Potamothrix alatus hazaricus n. ssp.},
journal = {Zootaxa},
volume = {3716},
number = {},
pages = {144-156},
doi = {10.11646/zootaxa.3716.2.2},
pmid = {26106770},
issn = {1175-5326},
mesh = {Animal Distribution ; Animals ; Lakes ; Oligochaeta/*anatomy &amp; histology/*classification/genetics/physiology ; Phylogeny ; Species Specificity ; Turkey ; },
abstract = {Lake Hazar is an alkaline oligotrophic lake of tectonic origin, located in the Eastern Anatolia region in Turkey, 1248 a a.s.l. Its surface area is 80 km2, the average depth 93 m and maximum depth 205 m. The lake and its surroundings an under protection as a region of historical value. During the present study (2007-2012), samples were taken from 15 stations located at a depth of 2-200 m. Oligochaeta comprised 69% of the total invertebrate abundance. The profundal olgochaete fauna was found to consist of only three tubificid taxa, all of the subfamily Tubificinae. Potamothrix alatus hazaricus Timm &amp; Arslan, n. ssp. was dominating anywhere down to maximum depths while Psammoryctides barbatus (Grube) and Ilyodrilus(?) sp. occurred seldom. All three are new records for Lake Hazar. Potamothrix alatus hazaricus shares the "winged" body shape in its genital region with the nominal, brackish-water subspecies P. a. alatus Finogenova, 1972, and the lateral position of the spermathecal pores and the shape of the ventral chaetae with the freshwater subspecies P. a. paravanicus Poddubnaja &amp; Pataridze, 1989 known from Transcaucasian lakes. The mitochondrial COI barcoding gene suggests long separation between the two taxa, but the nuclear ITS region shows no variation. The generic position of Ilyodrilus (?) sp. remains obscure since its internal genitalia could not be studied.},
}
@article {pmid26046203,
year = {2013},
author = {Su, Y and Lu, J and Chen, H},
title = {The genus Leucophenga (Diptera, Drosophilidae), Part I: The abbreviata species group from the Oriental region with morphological and molecular evidence.},
journal = {Zootaxa},
volume = {3637},
number = {},
pages = {361-373},
doi = {10.11646/zootaxa.3637.3.8},
pmid = {26046203},
issn = {1175-5326},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology ; Animals ; Base Sequence ; Drosophilidae/anatomy &amp; histology/*classification/*genetics ; Ecosystem ; Electron Transport Complex IV/genetics ; Female ; Insect Proteins/genetics ; Male ; Molecular Sequence Data ; Phylogeny ; },
abstract = {A new species group, the abbreviata group is established within the genus Leucophenga based on one known and three new species, all of which are endemic to the Oriental region: L. abbreviata (de Meijere, 1911), L. brevivena sp. nov., L. sujuanae sp. nov. and L. zhenfangae sp. nov. A key to four species of the abbreviata group and the DNA barcoding are provided. Twenty-three mtDNA COI sequences belonging to the above species are analyzed; the molecular data are used as interactive evidence to evaluate the species boundaries defined by the morphological data.},
}
@article {pmid27011285,
year = {2012},
author = {Gulbransen, DJ and McGlathery, KJ and Marklund, M and Norris, JN and Gurgel, CF},
title = {GRACILARIA VERMICULOPHYLLA (RHODOPHYTA, GRACILARIALES) IN THE VIRGINIA COASTAL BAYS, USA: COX1 ANALYSIS REVEALS HIGH GENETIC RICHNESS OF AN INTRODUCED MACROALGA.},
journal = {Journal of phycology},
volume = {48},
number = {5},
pages = {1278-1283},
doi = {10.1111/j.1529-8817.2012.01218.x},
pmid = {27011285},
issn = {0022-3646},
abstract = {Gracilaria vermiculophylla (Ohmi) Papenfuss is an invasive alga that is native to Southeast Asia and has invaded many estuaries in North America and Europe. It is difficult to differentiate G. vermiculophylla from native forms using morphology and therefore molecular techniques are needed. In this study, we used three molecular markers (rbcL, cox2-cox3 spacer, cox1) to identify G. vermiculophylla at several locations in the western Atlantic. RbcL and cox2-cox3 spacer markers confirmed the presence of G. vermiculophylla on the east coast of the USA from Massachusetts to South Carolina. We used a 507 base pair region of cox1 mtDNA to (i) verify the widespread distribution of G. vermiculophylla in the Virginia (VA) coastal bays and (ii) determine the intraspecific diversity of these algae. Cox1 haplotype richness in the VA coastal bays was much higher than that previously found in other invaded locations, as well as some native locations. This difference is likely attributed to the more intensive sampling design used in this study, which was able to detect richness created by multiple, diverse introductions. On the basis of our results, we recommend that future studies take differences in sampling design into account when comparing haplotype richness and diversity between native and non-native studies in the literature.},
}
@article {pmid27011270,
year = {2012},
author = {Verbruggen, H and Schils, T},
title = {RHIPILIA COPPEJANSII, A NEW CORAL REEF-ASSOCIATED SPECIES FROM GUAM (BRYOPSIDALES, CHLOROPHYTA)(1).},
journal = {Journal of phycology},
volume = {48},
number = {5},
pages = {1090-1098},
doi = {10.1111/j.1529-8817.2012.01199.x},
pmid = {27011270},
issn = {0022-3646},
abstract = {The new species Rhipilia coppejansii is described from Guam. This species, which has the external appearance of a Chlorodesmis species, features tenacula upon microscopical examination, a diagnostic character of Rhipilia. This unique morphology, along with the tufA and rbcL data presented herein, set this species apart from others in the respective genera. Phylogenetic analyses show that the taxon is nested within the Rhipiliaceae. We discuss the diversity and possible adaptation of morphological types in the Udoteaceae and Rhipiliaceae.},
}
@article {pmid27008998,
year = {2012},
author = {Kucera, H and Saunders, GW},
title = {A SURVEY OF BANGIALES (RHODOPHYTA) BASED ON MULTIPLE MOLECULAR MARKERS REVEALS CRYPTIC DIVERSITY(1).},
journal = {Journal of phycology},
volume = {48},
number = {4},
pages = {869-882},
doi = {10.1111/j.1529-8817.2012.01193.x},
pmid = {27008998},
issn = {0022-3646},
abstract = {The Bangiales is a diverse order consisting of 28 species in Canada. Morphological simplicity and similarity among species has led to taxonomic confusion and the need for molecular techniques for species identification. This study is the first to employ the standardized DNA barcode marker COI-5P in a broad floristic survey of the Bangiales in Canadian marine waters. A total of 37 species were ultimately sequenced, 29 of which occurred in Canada. Molecular results led to the synonymization of Wildemania cuneiformis with W. amplissima, as well as the description of two new species: Porphyra corallicola sp. nov. and Pyropia peggicovensis sp. nov., and discovery of another five putative new species. Comparison of the performance of COI-5P as a species identification tool relative to rbcL (large subunit of ribulose-1,5-bisphosphate carboxylase oxygenase) and the UPA (universal plastid amplicon) revealed that, although each marker had strengths and weaknesses, the COI-5P showed the highest species-discriminatory power due to its high level of interspecific variation. The rbcL was further used to place the new species into a phylogenetic context, whereas UPA was not recommended for species identification in the Bangiales owing to within-individual heterogeneity between the two copies present in the plastid genomes in some lineages.},
}
@article {pmid25683426,
year = {2012},
author = {Ganopoulos, I and Madesis, P and Darzentas, N and Argiriou, A and Tsaftaris, A},
title = {Barcode High Resolution Melting (Bar-HRM) analysis for detection and quantification of PDO "Fava Santorinis" (Lathyrus clymenum) adulterants.},
journal = {Food chemistry},
volume = {133},
number = {2},
pages = {505-512},
doi = {10.1016/j.foodchem.2012.01.015},
pmid = {25683426},
issn = {1873-7072},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Chloroplast/*genetics ; DNA, Plant/*genetics ; Food Contamination/*analysis ; Genotype ; Lathyrus/chemistry/*classification/genetics ; },
abstract = {Legumes considered as one of the most important crops worldwide. Due to high price as a PDO product, commercial products of "Fava Santorinis" are often subjected to adulterations from other legume products coming from other Lathyrus or Vicia and Pisum species. Using plant DNA barcoding regions (trnL and rpoC) coupled with High Resolution Melting (Bar-HRM) we have developed a method allowing us to detect and authenticate PDO "Fava Santorinis". Bar-HRM proved to be a very sensitive tool able to genotype Lathyrus and its closed relative species and to detect admixtures, being sensitive enough to as low as 1:100 of non-"Fava Santorinis" in "Fava Santorinis" commercial products. In conclusion, Bar-HRM analysis can be a faster, with higher resolution and cost effectiveness alternative method to authenticate PDO "Fava Santorinis" and to quantitatively detect adulterations in "Fava Santorinis" with other relative commercial "Fava" food products.},
}
@article {pmid27011092,
year = {2012},
author = {Vis, ML and Necchi, O and Chiasson, WB and Entwisle, TJ},
title = {MOLECULAR PHYLOGENY OF THE GENUS KUMANOA (BATRACHOSPERMALES, RHODOPHYTA)(1).},
journal = {Journal of phycology},
volume = {48},
number = {3},
pages = {750-758},
doi = {10.1111/j.1529-8817.2012.01141.x},
pmid = {27011092},
issn = {0022-3646},
abstract = {Species belonging to the newly established genus Kumanoa were sampled from locations worldwide. DNA sequence data from the rbcL gene, cox1 barcode region, and universal plastid amplicon (UPA) were collected. The new sequence data for the rbcL were combined with the extensive batrachospermalean rbcL data available in GenBank. Single gene rbcL results showed the genus Kumanoa to be a well-supported clade, and there was high statistical support for many of the terminal nodes. However, with this gene alone, there was very little support for any of the internal nodes. Analysis of the concatenated data set (rbcL, cox1, and UPA) provided higher statistical support across the tree. The taxa K. vittata and K. amazonensis formed a basal grade, and both were on relatively long branches. Three new species are proposed, K. holtonii, K. gudjewga, and K. novaecaledonensis; K. procarpa var. americana is raised to species level. In addition, the synonymy of K. capensis and K. breviarticulata is proposed, with K. capensis having precedence. Five new combinations are made, bringing the total number of accepted species in Kumanoa to 31. The phylogenetic analyses did not reveal any interpretable biogeographic patterns within the genus (e.g., K. spermatiophora from the tropical oceanic island Maui, Hawaii, was sister to K. faroensis from temperate midcontinental Ohio in North America). Previously hypothesized relationships among groups of species were not substantiated in the phylogenetic analyses, and no intrageneric classification is recommended based on current knowledge.},
}
@article {pmid27009722,
year = {2012},
author = {Ciancia, M and Alberghina, J and Arata, PX and Benavides, H and Leliaert, F and Verbruggen, H and Estevez, JM},
title = {CHARACTERIZATION OF CELL WALL POLYSACCHARIDES OF THE COENCOCYTIC GREEN SEAWEED BRYOPSIS PLUMOSA (BRYOPSIDACEAE, CHLOROPHYTA) FROM THE ARGENTINE COAST(1).},
journal = {Journal of phycology},
volume = {48},
number = {2},
pages = {326-335},
doi = {10.1111/j.1529-8817.2012.01131.x},
pmid = {27009722},
issn = {0022-3646},
abstract = {Bryopsis sp. from a restricted area of the rocky shore of Mar del Plata (Argentina) on the Atlantic coast was identified as Bryopsis plumosa (Hudson) C. Agardh (Bryopsidales, Chlorophyta) based on morphological characters and rbcL and tufA DNA barcodes. To analyze the cell wall polysaccharides of this seaweed, the major room temperature (B1) and 90°C (X1) water extracts were studied. By linkage analysis and NMR spectroscopy, the structure of a sulfated galactan was determined, and putative sulfated rhamnan structures and furanosidic nonsulfated arabinan structures were also found. By anion exchange chromatography of X1, a fraction (F4), comprising a sulfated galactan as major structure was isolated. Structural analysis showed a linear backbone constituted of 3-linked β-d-galactose units, partially sulfated on C-6 and partially substituted with pyruvic acid forming an acetal linked to O-4 and O-6. This galactan has common structural features with those of green seaweeds of the genus Codium (Bryopsidales, Chlorophyta), but some important differences were also found. This is the first report about the structure of the water-soluble polysaccharides biosynthesized by seaweeds of the genus Bryopsis. These sulfated galactans and rhamnans were in situ localized mostly in two layers, one close to the plasma membrane and the other close to the apoplast, leaving a middle amorphous, unstained cell wall zone. In addition, fibrillar polysaccharides, comprising (1→3)-β-d-xylans and cellulose, were obtained by treatment of the residue from the water extractions with an LiCl/DMSO solution at high temperature. These polymers were also localized in a bilayer arrangement.},
}
@article {pmid27335662,
year = {2012},
author = {Sahu, SK and Thangaraj, M and Kathiresan, K},
title = {DNA Extraction Protocol for Plants with High Levels of Secondary Metabolites and Polysaccharides without Using Liquid Nitrogen and Phenol.},
journal = {ISRN molecular biology},
volume = {2012},
number = {},
pages = {205049},
pmid = {27335662},
issn = {2090-7907},
abstract = {Mangroves and salt marsh species are known to synthesize a wide spectrum of polysaccharides and polyphenols including flavonoids and other secondary metabolites which interfere with the extraction of pure genomic DNA. Although a plethora of plant DNA isolation protocols exist, extracting DNA from mangroves and salt marsh species is a challenging task. This study describes a rapid and reliable cetyl trimethylammonium bromide (CTAB) protocol suited specifically for extracting DNA from plants which are rich in polysaccharides and secondary metabolites, and the protocol also excludes the use of expensive liquid nitrogen and toxic phenols. Purity of extracted DNA was excellent as evident by A260/A280 ratio ranging from 1.78 to 1.84 and A260/A230 ratio was >2, which also suggested that the preparations were sufficiently free of proteins and polyphenolics/polysaccharide compounds. DNA concentration ranged from 8.8 to 9.9 μg μL(-1). The extracted DNA was amenable to RAPD, restriction digestion, and PCR amplification of plant barcode genes (matK and rbcl). The optimized method is suitable for both dry and fresh leaves. The success of this method in obtaining high-quality genomic DNA demonstrated the broad applicability of this method.},
}
@article {pmid26466628,
year = {2012},
author = {Jenkins, C and Chapman, TA and Micallef, JL and Reynolds, OL},
title = {Molecular Techniques for the Detection and Differentiation of Host and Parasitoid Species and the Implications for Fruit Fly Management.},
journal = {Insects},
volume = {3},
number = {3},
pages = {763-788},
pmid = {26466628},
issn = {2075-4450},
abstract = {Parasitoid detection and identification is a necessary step in the development and implementation of fruit fly biological control strategies employing parasitoid augmentive release. In recent years, DNA-based methods have been used to identify natural enemies of pest species where morphological differentiation is problematic. Molecular techniques also offer a considerable advantage over traditional morphological methods of fruit fly and parasitoid discrimination as well as within-host parasitoid identification, which currently relies on dissection of immature parasitoids from the host, or lengthy and labour-intensive rearing methods. Here we review recent research focusing on the use of molecular strategies for fruit fly and parasitoid detection and differentiation and discuss the implications of these studies on fruit fly management.},
}
@article {pmid26949752,
year = {2010},
author = {Sanketi, PR and Coughlan, JM},
title = {Anti-Blur Feedback for Visually Impaired Users of Smartphone Cameras.},
journal = {ASSETS. Annual ACM Conference on Assistive Technologies},
volume = {2010},
number = {},
pages = {233-234},
pmid = {26949752},
support = {R01 EY018210/EY/NEI NIH HHS/United States ; },
abstract = {A wide range of smartphone applications are emerging that employ image processing and computer vision algorithms to interpret the contents of images acquired by the phone's built-in camera, including applications that read product barcodes and recognize a variety of documents and other objects. However, almost all of these applications are designed for normally sighted users; a major barrier for visually impaired users (who might benefit greatly from such applications) is the difficulty of taking good-quality images. To overcome this barrier, this paper focuses on reducing the incidence of motion blur, caused by camera shake and other movements, which is a common cause of poor-quality, unusable images. We propose a simple technique for detecting camera shake, using the smartphone's built-in accelerometer (i.e. tilt sensor) to alert the user in real-time to any shake, providing feedback that enables him/her to hold the camera more steadily. A preliminary experiment with a blind iPhone user demonstrates the feasibility of the approach.},
}
@article {pmid26949757,
year = {2010},
author = {Tekin, E and Coughlan, JM},
title = {A Mobile Phone Application Enabling Visually Impaired Users to Find and Read Product Barcodes.},
journal = {Computers helping people with special needs : ... International Conference, ICCHP ... : proceedings. International Conference on Computers Helping People with Special Needs},
volume = {6180},
number = {},
pages = {290-295},
pmid = {26949757},
support = {R01 EY018890/EY/NEI NIH HHS/United States ; },
abstract = {While there are many barcode readers available for identifying products in a supermarket or at home on mobile phones (e.g., Red Laser iPhone app), such readers are inaccessible to blind or visually impaired persons because of their reliance on visual feedback from the user to center the barcode in the camera's field of view. We describe a mobile phone application that guides a visually impaired user to the barcode on a package in real-time using the phone's built-in video camera. Once the barcode is located by the system, the user is prompted with audio signals to bring the camera closer to the barcode until it can be resolved by the camera, which is then decoded and the corresponding product information read aloud using text-to-speech. Experiments with a blind volunteer demonstrate proof of concept of our system, which allowed the volunteer to locate barcodes which were then translated to product information that was announced to the user. We successfully tested a series of common products, as well as user-generated barcodes labeling household items that may not come with barcodes.},
}
@article {pmid26949755,
year = {2008},
author = {Manduchi, R and Coughlan, J and Ivanchenko, V},
title = {Search Strategies of Visually Impaired Persons using a Camera Phone Wayfinding System.},
journal = {Computers helping people with special needs : ... International Conference, ICCHP ... : proceedings. International Conference on Computers Helping People with Special Needs},
volume = {5105},
number = {},
pages = {1135-1140},
pmid = {26949755},
support = {R21 EY017003/EY/NEI NIH HHS/United States ; },
abstract = {We report new experiments conducted using a camera phone wayfinding system, which is designed to guide a visually impaired user to machine-readable signs (such as barcodes) labeled with special color markers. These experiments specifically investigate search strategies of such users detecting, localizing and touching color markers that have been mounted in various ways in different environments: in a corridor (either flush with the wall or mounted perpendicular to it) or in a large room with obstacles between the user and the markers. The results show that visually impaired users are able to reliably find color markers in all the conditions that we tested, using search strategies that vary depending on the environment in which they are placed.},
}
@article {pmid25636615,
year = {2015},
author = {Kukavica-Ibrulj, I and Levesque, RC},
title = {Essential genes in the infection model of Pseudomonas aeruginosa-PCR-based signature-tagged mutagenesis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1279},
number = {},
pages = {97-123},
doi = {10.1007/978-1-4939-2398-4_7},
pmid = {25636615},
issn = {1940-6029},
support = {//Canadian Institutes of Health Research/Canada ; },
mesh = {Animals ; Chromosome Mapping ; Cloning, Molecular ; Disease Models, Animal ; Electroporation ; Gene Knockout Techniques ; Gene Library ; *Genes, Bacterial ; *Genes, Essential ; Male ; Mutagenesis/*genetics ; Mutation ; Oligonucleotides/*metabolism ; Open Reading Frames/genetics ; Physical Chromosome Mapping ; Plasmids/metabolism ; Polymerase Chain Reaction/*methods ; Pseudomonas Infections/*microbiology ; Pseudomonas aeruginosa/*genetics ; Rats, Sprague-Dawley ; },
abstract = {PCR-based signature tagged mutagenesis is an "en masse" screening technique based upon unique oligonucleotide tags (molecular barcodes) for identification of genes that will diminish or enhance maintenance of an organism in a specific ecological niche or environment. PCR-based STM applied to Pseudomonas aeruginosa permitted the identification of genes essential for in vivo maintenance by transposon insertion and negative selection in a mixed population of bacterial mutants. The innovative adaptations and refinement of the technology presented here with P. aeruginosa STM mutants selected in the rat model of chronic lung infection have given critical information about genes essential for causing a chronic infection and a wealth of information about biological processes in vivo. The additional use of competitive index analysis for measurement of the level of virulence in vivo, microarray-based screening of selected prioritized STM mutants coupled to metabolomics analysis can now be attempted systematically on a genomic scale. PCR-based STM and combined whole-genome methods can also be applied to any organism having selectable phenotypes for screening.},
}
@article {pmid25636000,
year = {2015},
author = {Oba, Y and Ôhira, H and Murase, Y and Moriyama, A and Kumazawa, Y},
title = {DNA barcoding of Japanese click beetles (Coleoptera, Elateridae).},
journal = {PloS one},
volume = {10},
number = {1},
pages = {e0116612},
pmid = {25636000},
issn = {1932-6203},
mesh = {Animals ; Coleoptera/classification/*genetics ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Genes, Insect ; Insect Proteins/genetics ; Japan ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Click beetles (Coleoptera: Elateridae) represent one of the largest groups of beetle insects. Some click beetles in larval form, known as wireworms, are destructive agricultural pests. Morphological identification of click beetles is generally difficult and requires taxonomic expertise. This study reports on the DNA barcoding of Japanese click beetles to enable their rapid and accurate identification. We collected and assembled 762 cytochrome oxidase subunit I barcode sequences from 275 species, which cover approximately 75% of the common species found on the Japanese main island, Honshu. This barcode library also contains 20 out of the 21 potential pest species recorded in Japan. Our analysis shows that most morphologically identified species form distinct phylogenetic clusters separated from each other by large molecular distances. This supports the general usefulness of the DNA barcoding approach for quick and reliable identification of Japanese elaterid species for environmental impact assessment, agricultural pest control, and biodiversity analysis. On the other hand, the taxonomic boundary in dozens of species did not agree with the boundary of barcode index numbers (a criterion for sequence-based species delimitation). These findings urge taxonomic reinvestigation of these mismatched taxa.},
}
@article {pmid25632257,
year = {2015},
author = {Kirichenko, N and Huemer, P and Deutsch, H and Triberti, P and Rougerie, R and Lopez-Vaamonde, C},
title = {Integrative taxonomy reveals a new species of Callisto (Lepidoptera, Gracillariidae) in the Alps.},
journal = {ZooKeys},
volume = {},
number = {473},
pages = {157-176},
pmid = {25632257},
issn = {1313-2989},
abstract = {Europe has one of the best-known Lepidopteran faunas in the world, yet many species are still being discovered, especially in groups of small moths. Here we describe a new gracillariid species from the south-eastern Alps, Callistobasistrigella Huemer, Deutsch &amp; Triberti, sp. n. It shows differences from its sister species Callistocoffeella in morphology, the barcode region of the cytochrome c oxidase I gene and the nuclear gene histone H3. Both Callistobasistrigella and Callistocoffeella can co-occur in sympatry without evidence of admixture. Two Callistobasistrigella specimens show evidence of introgression. We highlight the importance of an integrative approach to delimit species, combining morphological and ecological data with mitochondrial and nuclear sequence data. Furthermore, in connection with this study, Ornixblandella Müller-Rutz, 1920, syn. n. is synonymized with Callistocoffeella (Zetterstedt, 1839).},
}
@article {pmid25632252,
year = {2015},
author = {Mally, R and Korycinska, A and Agassiz, DJ and Hall, J and Hodgetts, J and Nuss, M},
title = {Discovery of an unknown diversity of Leucinodes species damaging Solanaceae fruits in sub-Saharan Africa and moving in trade (Insecta, Lepidoptera, Pyraloidea).},
journal = {ZooKeys},
volume = {},
number = {472},
pages = {117-162},
pmid = {25632252},
issn = {1313-2989},
abstract = {The larvae of the Old World genera Leucinodes Guenée, 1854 and Sceliodes Guenée, 1854 are internal feeders in the fruits of Solanaceae, causing economic damage to cultivated plants like Solanummelongena and Solanumaethiopicum. In sub-Saharan Africa five nominal species of Leucinodes and one of Sceliodes occur. One of these species, the eggplant fruit and shoot borer Leucinodesorbonalis Guenée, 1854, is regarded as regularly intercepted from Africa and Asia in Europe, North and South America and is therefore a quarantine pest on these continents. We investigate the taxonomy of African Leucinodes and Sceliodes based on morphological characters in wing pattern, genitalia and larvae, as well as mitochondrial DNA, providing these data for identification of all life stages. The results suggest that both genera are congeneric, with Sceliodes syn. n. established as junior subjective synonym of Leucinodes. Leucinodesorbonalis is described from Asia and none of the samples investigated from Africa belong to this species. Instead, sub-Saharan Africa harbours a complex of eight endemic Leucinodes species. Among the former nominal species of Leucinodes (and Sceliodes) from Africa, only Leucinodeslaisalis (Walker, 1859), comb. n. (Sceliodes) is confirmed, with Leucinodestranslucidalis Gaede, 1917, syn. n. as a junior subjective synonym. The other African Leucinodes species were unknown to science and are described as new: Leucinodesafricensis sp. n., Leucinodesethiopica sp. n., Leucinodeskenyensis sp. n., Leucinodesmalawiensis sp. n., Leucinodespseudorbonalis sp. n., Leucinodesrimavallis sp. n. and Leucinodesugandensis sp. n. An identification key based on male genitalia is provided for the African Leucinodes species. Most imports of Leucinodes specimens from Africa into Europe refer to Leucinodesafricensis, which has been frequently imported with fruits during the last 50 years. In contrast, Leucinodeslaisalis has been much less frequently recorded, and Leucinodespseudorbonalis as well as Leucinodesrimavallis only very recently in fruit imports from Uganda. Accordingly, interceptions of Leucinodes from Africa into other continents will need to be re-investigated for their species identity and will likely require, at least in parts, revisions of the quarantine regulations. The following African taxa are excluded from Leucinodes: Hyperanalyta Strand, 1918, syn. rev. as revised synonym of Analyta Lederer, 1863; Analytaapicalis (Hampson, 1896), comb. n. (Leucinodes); Lygropiaaureomarginalis (Gaede, 1916), comb. n. (Leucinodes); Sylleptehemichionalis Mabille, 1900, comb. rev., Sylleptehemichionalisidalis Viette, 1958, comb. rev. and Sylleptevagans (Tutt, 1890), comb. n. (Aphytoceros). Deanolisiriocapna (Meyrick, 1938), comb. n. from Indonesia is originally described and misplaced in Sceliodes, and Leucinodescordalis (Doubleday, 1843), comb. n. (Margaritia) from New Zealand, Leucinodesraondry (Viette, 1981), comb. n. (Daraba) from Madagascar as well as Leucinodesgrisealis (Kenrick, 1912), comb. n. (Sceliodes) from New Guinea are transferred from Sceliodes to Leucinodes. While Leucinodes is now revised from Africa, it still needs further revision in Asia.},
}
@article {pmid25630694,
year = {2015},
author = {Kuhn, JA and Kristoffersen, R and Knudsen, R and Jakobsen, J and Marcogliese, DJ and Locke, SA and Primicerio, R and Amundsen, PA},
title = {Parasite communities of two three-spined stickleback populations in subarctic Norway--effects of a small spatial-scale host introduction.},
journal = {Parasitology research},
volume = {114},
number = {4},
pages = {1327-1339},
pmid = {25630694},
issn = {1432-1955},
mesh = {Animals ; Base Sequence ; Cestoda/genetics/*physiology ; Cestode Infections/epidemiology/parasitology/*veterinary ; Ecosystem ; Female ; Fish Diseases/*epidemiology/parasitology ; Lakes ; Male ; Molecular Sequence Data ; Norway/epidemiology ; Phylogeny ; Population Dynamics ; Sequence Analysis, DNA/veterinary ; Smegmamorpha/*parasitology ; Species Specificity ; Trematoda/genetics/*physiology ; Trematode Infections/epidemiology/parasitology/*veterinary ; },
abstract = {Co-introduction and colonization of parasites with the introduction of new host species into aquatic habitats may depend on the host specificity and dispersal capabilities of the parasites. We compared the metazoan parasite community of an introduced three-spined stickleback (Gasterosteus aculeatus) population with that of the nearby source population in subarctic Norway. As expected from a small spatial scale (5 km), the parasite component communities in the two lakes were highly similar. All identifiable allogenic parasite taxa (Diphyllobothrium dendriticum, Diphyllobothrium ditremum, Diphyllobothrium spp., Schistocephalus solidus, Apatemon sp. and Diplostomum spp.) were also observed in both lakes while inter-lake differences were driven by autogenic parasite taxa (Eubothrium spp., Crepidostomum spp., Nematoda spp., Proteocephalus sp. and Gyrodactylus arcuatus). Contrary to expectation, the total number of parasite taxa was higher in the introduced stickleback population (12) compared to that found in the source population (9) with three parasite taxa (Eubothrium spp., Crepidostomum spp., Nematoda spp.) only occurring in the introduced population. These parasites were uncommon however and normally restricted to salmonids. Sticklebacks from both populations were heavily infected, particularly with eye-infecting metacercariae. Sequences from the DNA barcode region of cytochrome oxidase 1 indicated that these include Diplostomum lineage 6, a member of the Diplostomum baeri complex and a member of the Strigeinae. Despite high similarity between the two component communities, quantitative inter-lake differences were found at the infracommunity level. At this scale, parasite intensity was significantly higher in the source population for the two autogenic stickleback specialists: G. arcuatus and Proteocephalus sp., assumed to be the autogenic stickleback specialist Proteocephalus filicollis. Parasite infracommunities within each lake also resembled each other significantly more than infracommunities between lakes, primarily driven by the allogenic cestode D. ditremum, as well as G. arcuatus and Proteocephalus sp. Overall, quantitative dissimilarities between the two parasite communities were possibly explained by inter-lake differences in the density of sticklebacks and intermediate hosts.},
}
@article {pmid25628863,
year = {2015},
author = {Kreuzinger, AJ and Fiedler, K and Letsch, H and Grill, A},
title = {Tracing the radiation of Maniola (Nymphalidae) butterflies: new insights from phylogeography hint at one single incompletely differentiated species complex.},
journal = {Ecology and evolution},
volume = {5},
number = {1},
pages = {46-58},
pmid = {25628863},
issn = {2045-7758},
support = {V 169/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {The use of DNA sequence data often leads to the recognition of cryptic species within putatively well-known taxa. The opposite case, detecting less diversity than originally described, has, however, far more rarely been documented. Maniola jurtina, the Meadow Brown butterfly, occurs all over Europe, whereas all other six species in the genus Maniola are restricted to the Mediterranean area. Among them, three are island endemics on Sardinia, Cyprus, and Chios, respectively. Maniola species are almost indistinguishable morphologically, and hybridization seems to occur occasionally. To clarify species boundaries and diversification history of the genus, we reconstructed the phylogeography and phylogeny of all seven species within Maniola analyzing 138 individuals from across its range using mitochondrial and nuclear genetic markers. Examination of variation in mitochondrial and nuclear DNA surprisingly revealed a case of taxonomic "oversplitting". The topology of the recovered phylogenetic tree is not consistent with accepted taxonomy, but rather reveals haplotype clades that are incongruent with nominal species boundaries: instead of seven species, we recognized only two major, yet incompletely segregated, lineages. Our results are consistent with the hypothesis that Maniola originated in Africa. We suggest that one lineage dispersed over the Strait of Gibraltar and the Iberian Peninsula to the west of Europe, while the other lineage spreads eastward through Asia Minor and over the Bosporus to Eastern Europe.},
}
@article {pmid25627334,
year = {2015},
author = {Lassmann, T},
title = {TagDust2: a generic method to extract reads from sequencing data.},
journal = {BMC bioinformatics},
volume = {16},
number = {},
pages = {24},
pmid = {25627334},
issn = {1471-2105},
mesh = {Computational Biology/*methods ; Electronic Data Processing ; Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Sequence Analysis, DNA/*methods ; *Software ; },
abstract = {BACKGROUND: Arguably the most basic step in the analysis of next generation sequencing data (NGS) involves the extraction of mappable reads from the raw reads produced by sequencing instruments. The presence of barcodes, adaptors and artifacts subject to sequencing errors makes this step non-trivial.<br><br>RESULTS: Here I present TagDust2, a generic approach utilizing a library of hidden Markov models (HMM) to accurately extract reads from a wide array of possible read architectures. TagDust2 extracts more reads of higher quality compared to other approaches. Processing of multiplexed single, paired end and libraries containing unique molecular identifiers is fully supported. Two additional post processing steps are included to exclude known contaminants and filter out low complexity sequences. Finally, TagDust2 can automatically detect the library type of sequenced data from a predefined selection.<br><br>CONCLUSION: Taken together TagDust2 is a feature rich, flexible and adaptive solution to go from raw to mappable NGS reads in a single step. The ability to recognize and record the contents of raw reads will help to automate and demystify the initial, and often poorly documented, steps in NGS data analysis pipelines. TagDust2 is freely available at: http://tagdust.sourceforge.net .},
}
@article {pmid25627196,
year = {2015},
author = {Zaiko, A and Martinez, JL and Schmidt-Petersen, J and Ribicic, D and Samuiloviene, A and Garcia-Vazquez, E},
title = {Metabarcoding approach for the ballast water surveillance--an advantageous solution or an awkward challenge?.},
journal = {Marine pollution bulletin},
volume = {92},
number = {1-2},
pages = {25-34},
doi = {10.1016/j.marpolbul.2015.01.008},
pmid = {25627196},
issn = {1879-3363},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Introduced Species ; Ribulose-Bisphosphate Carboxylase/genetics ; *Ships ; Temperature ; Water/*analysis ; Water Microbiology ; },
abstract = {Transfer of organisms with ships' ballast water is recognized as a major pathway of non-indigenous species introduction and addressed in a few recent legislative initiatives. Among other they imply scientific and technical research and monitoring to be conducted in a efficient and reliable way. The recent development of DNA barcoding and metabarcoding technologies opens new opportunities for biodiversity and biosecurity surveillance. In the current study, the performance of metabarcoding approach was assessed in comparison to the conventional (visual) observations, during the en route experimental ballast water survey. Opportunities and limitations of the molecular method were identified from taxonomical datasets rendered by two molecular markers of different degree of universality - the universal cytochrome oxydase sub-unit I gene and a fragment of RuBisCO gene. The cost-efficacy and possible improvements of these methods are discussed for the further successful development and implementation of the approach in ballast water control and NIS surveillance.},
}
@article {pmid25622433,
year = {2014},
author = {Crist, D},
title = {Barcoding 2.0: better patient monitoring, better patient safety.},
journal = {Health management technology},
volume = {35},
number = {10},
pages = {12-13},
pmid = {25622433},
issn = {1074-4770},
mesh = {Electronic Data Processing ; Hospitalization ; Humans ; *Monitoring, Physiologic ; *Patient Identification Systems ; *Patient Safety ; *Point-of-Care Systems ; United States ; },
}
@article {pmid25621335,
year = {2015},
author = {Fujisawa, T and Vogler, AP and Barraclough, TG},
title = {Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles.},
journal = {Proceedings. Biological sciences},
volume = {282},
number = {1799},
pages = {20142476},
pmid = {25621335},
issn = {1471-2954},
mesh = {Animals ; Coleoptera/*genetics ; DNA, Mitochondrial/chemistry ; *Evolution, Molecular ; Genetic Variation ; *Models, Genetic ; Multivariate Analysis ; Phylogeny ; Population Density ; Population Dynamics ; Sequence Analysis, DNA ; },
abstract = {Comparative analysis is a potentially powerful approach to study the effects of ecological traits on genetic variation and rate of evolution across species. However, the lack of suitable datasets means that comparative studies of correlates of genetic traits across an entire clade have been rare. Here, we use a large DNA-barcode dataset (5062 sequences) of water beetles to test the effects of species ecology and geographical distribution on genetic variation within species and rates of molecular evolution across species. We investigated species traits predicted to influence their genetic characteristics, such as surrogate measures of species population size, latitudinal distribution and habitat types, taking phylogeny into account. Genetic variation of cytochrome oxidase I in water beetles was positively correlated with occupancy (numbers of sites of species presence) and negatively with latitude, whereas substitution rates across species depended mainly on habitat types, and running water specialists had the highest rate. These results are consistent with theoretical predictions from nearly-neutral theories of evolution, and suggest that the comparative analysis using large databases can give insights into correlates of genetic variation and molecular evolution.},
}
@article {pmid25617768,
year = {2015},
author = {Ermakov, OA and Simonov, E and Surin, VL and Titov, SV and Brandler, OV and Ivanova, NV and Borisenko, AV},
title = {Implications of hybridization, NUMTs, and overlooked diversity for DNA Barcoding of Eurasian ground squirrels.},
journal = {PloS one},
volume = {10},
number = {1},
pages = {e0117201},
pmid = {25617768},
issn = {1932-6203},
mesh = {Animals ; Cell Nucleus/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Genetic Variation ; *Hybridization, Genetic ; Mitochondria/*genetics ; Pseudogenes/*genetics ; Sciuridae/*classification/*genetics ; },
abstract = {The utility of DNA Barcoding for species identification and discovery has catalyzed a concerted effort to build the global reference library; however, many animal groups of economical or conservational importance remain poorly represented. This study aims to contribute DNA barcode records for all ground squirrel species (Xerinae, Sciuridae, Rodentia) inhabiting Eurasia and to test efficiency of this approach for species discrimination. Cytochrome c oxidase subunit 1 (COI) gene sequences were obtained for 97 individuals representing 16 ground squirrel species of which 12 were correctly identified. Taxonomic allocation of some specimens within four species was complicated by geographically restricted mtDNA introgression. Exclusion of individuals with introgressed mtDNA allowed reaching a 91.6% identification success rate. Significant COI divergence (3.5-4.4%) was observed within the most widespread ground squirrel species (Spermophilus erythrogenys, S. pygmaeus, S. suslicus, Urocitellus undulatus), suggesting the presence of cryptic species. A single putative NUMT (nuclear mitochondrial pseudogene) sequence was recovered during molecular analysis; mitochondrial COI from this sample was amplified following re-extraction of DNA. Our data show high discrimination ability of 100 bp COI fragments for Eurasian ground squirrels (84.3%) with no incorrect assessments, underscoring the potential utility of the existing reference librariy for the development of diagnostic 'mini-barcodes'.},
}
@article {pmid25614792,
year = {2014},
author = {Ovalle, TM and Parsa, S and Hernández, MP and Becerra Lopez-Lavalle, LA},
title = {Reliable molecular identification of nine tropical whitefly species.},
journal = {Ecology and evolution},
volume = {4},
number = {19},
pages = {3778-3787},
pmid = {25614792},
issn = {2045-7758},
abstract = {The identification of whitefly species in adult stage is problematic. Morphological differentiation of pupae is one of the better methods for determining identity of species, but it may vary depending on the host plant on which they develop which can lead to misidentifications and erroneous naming of new species. Polymerase chain reaction (PCR) fragment amplified from the mitochondrial cytochrome oxidase I (COI) gene is often used for mitochondrial haplotype identification that can be associated with specific species. Our objective was to compare morphometric traits against DNA barcode sequences to develop and implement a diagnostic molecular kit based on a RFLP-PCR method using the COI gene for the rapid identification of whiteflies. This study will allow for the rapid diagnosis of the diverse community of whiteflies attacking plants of economic interest in Colombia. It also provides access to the COI sequence that can be used to develop predator conservation techniques by establishing which predators have a trophic linkage with the focal whitefly pest species.},
}
@article {pmid25613325,
year = {2015},
author = {Pompanon, F and Samadi, S},
title = {Next generation sequencing for characterizing biodiversity: promises and challenges.},
journal = {Genetica},
volume = {143},
number = {2},
pages = {133-138},
pmid = {25613325},
issn = {1573-6857},
mesh = {*Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Ecology/methods ; High-Throughput Nucleotide Sequencing/*methods ; Phylogeny ; },
abstract = {DNA barcoding approaches are used to describe biodiversity by analysing specimens or environmental samples in taxonomic, phylogenetic and ecological studies. While sharing data among these disciplines would be highly valuable, this remains difficult because of contradictory requirements. The properties making a DNA barcode efficient for specimen identification or species delimitation are hardly reconcilable with those required for a powerful analysis of degraded DNA from environmental samples. The use of next generation sequencing methods open up the way towards the development of new markers (e.g., multilocus barcodes) that would overcome such limitations. However, several challenges should be taken up for coordinating actions at the interface between taxonomy, ecology, molecular biology and bioinformatics in order to develop methods and protocols compatible with both taxonomic and ecological studies.},
}
@article {pmid25612936,
year = {2015},
author = {Těšitelová, T and Kotilínek, M and Jersáková, J and Joly, FX and Košnar, J and Tatarenko, I and Selosse, MA},
title = {Two widespread green Neottia species (Orchidaceae) show mycorrhizal preference for Sebacinales in various habitats and ontogenetic stages.},
journal = {Molecular ecology},
volume = {24},
number = {5},
pages = {1122-1134},
doi = {10.1111/mec.13088},
pmid = {25612936},
issn = {1365-294X},
mesh = {Basidiomycota/*classification ; Carbon Isotopes/analysis ; DNA Barcoding, Taxonomic ; Ecosystem ; Europe ; Molecular Sequence Data ; Mycorrhizae/*classification ; Nitrogen Isotopes/analysis ; Orchidaceae/*genetics/*microbiology ; Phylogeny ; Symbiosis ; },
abstract = {Plant dependence on fungal carbon (mycoheterotrophy) evolved repeatedly. In orchids, it is connected with a mycorrhizal shift from rhizoctonia to ectomycorrhizal fungi and a high natural (13)C and (15)N abundance. Some green relatives of mycoheterotrophic species show identical trends, but most of these remain unstudied, blurring our understanding of evolution to mycoheterotrophy. We analysed mycorrhizal associations and (13)C and (15)N biomass content in two green species, Neottia ovata and N. cordata (tribe Neottieae), from a genus comprising green and nongreen (mycoheterotrophic) species. Our study covered 41 European sites, including different meadow and forest habitats and orchid developmental stages. Fungal ITS barcoding and electron microscopy showed that both Neottia species associated mainly with nonectomycorrhizal Sebacinales Clade B, a group of rhizoctonia symbionts of green orchids, regardless of the habitat or growth stage. Few additional rhizoctonias from Ceratobasidiaceae and Tulasnellaceae, and ectomycorrhizal fungi were detected. Isotope abundances did not detect carbon gain from the ectomycorrhizal fungi, suggesting a usual nutrition of rhizoctonia-associated green orchids. Considering associations of related partially or fully mycoheterotrophic species such as Neottia camtschatea or N. nidus-avis with ectomycorrhizal Sebacinales Clade A, we propose that the genus Neottia displays a mycorrhizal preference for Sebacinales and that the association with nonectomycorrhizal Sebacinales Clade B is likely ancestral. Such a change in preference for mycorrhizal associates differing in ecology within the same fungal taxon is rare among orchids. Moreover, the existence of rhizoctonia-associated Neottia spp. challenges the shift to ectomycorrhizal fungi as an ancestral pre-adaptation to mycoheterotrophy in the whole Neottieae.},
}
@article {pmid25612231,
year = {2015},
author = {Zunder, ER and Finck, R and Behbehani, GK and Amir, el-AD and Krishnaswamy, S and Gonzalez, VD and Lorang, CG and Bjornson, Z and Spitzer, MH and Bodenmiller, B and Fantl, WJ and Pe'er, D and Nolan, GP},
title = {Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm.},
journal = {Nature protocols},
volume = {10},
number = {2},
pages = {316-333},
pmid = {25612231},
issn = {1750-2799},
support = {R33 CA183654/CA/NCI NIH HHS/United States ; HHSN268201000034C/HL/NHLBI NIH HHS/United States ; U19 AI057229/AI/NIAID NIH HHS/United States ; U19 AI100627/AI/NIAID NIH HHS/United States ; R01CA184968/CA/NCI NIH HHS/United States ; T32 GM007276/GM/NIGMS NIH HHS/United States ; N01-HV-00242/HV/NHLBI NIH HHS/United States ; T32 AI007328/AI/NIAID NIH HHS/United States ; 1 R33CA183654/CA/NCI NIH HHS/United States ; U54CA149145/CA/NCI NIH HHS/United States ; R01 AI073724/AI/NIAID NIH HHS/United States ; U54 CA149145/CA/NCI NIH HHS/United States ; 5R01AI07372405/AI/NIAID NIH HHS/United States ; R01 CA184968/CA/NCI NIH HHS/United States ; 1U19AI100627/AI/NIAID NIH HHS/United States ; },
mesh = {*Algorithms ; Flow Cytometry/*methods ; *Palladium ; Single-Cell Analysis/*methods ; Software ; Staining and Labeling/methods ; },
abstract = {Mass-tag cell barcoding (MCB) labels individual cell samples with unique combinatorial barcodes, after which they are pooled for processing and measurement as a single multiplexed sample. The MCB method eliminates variability between samples in antibody staining and instrument sensitivity, reduces antibody consumption and shortens instrument measurement time. Here we present an optimized MCB protocol. The use of palladium-based labeling reagents expands the number of measurement channels available for mass cytometry and reduces interference with lanthanide-based antibody measurement. An error-detecting combinatorial barcoding scheme allows cell doublets to be identified and removed from the analysis. A debarcoding algorithm that is single cell-based rather than population-based improves the accuracy and efficiency of sample deconvolution. This debarcoding algorithm has been packaged into software that allows rapid and unbiased sample deconvolution. The MCB procedure takes 3-4 h, not including sample acquisition time of ∼1 h per million cells.},
}
@article {pmid25611173,
year = {2015},
author = {Ruhsam, M and Rai, HS and Mathews, S and Ross, TG and Graham, SW and Raubeson, LA and Mei, W and Thomas, PI and Gardner, MF and Ennos, RA and Hollingsworth, PM},
title = {Does complete plastid genome sequencing improve species discrimination and phylogenetic resolution in Araucaria?.},
journal = {Molecular ecology resources},
volume = {15},
number = {5},
pages = {1067-1078},
doi = {10.1111/1755-0998.12375},
pmid = {25611173},
issn = {1755-0998},
support = {G0900740/MRC_/Medical Research Council/United Kingdom ; MR/K001744/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {DNA Barcoding, Taxonomic ; *Genome, Plastid ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Data ; Pacific Islands ; *Phylogeny ; Plastids/*genetics ; *Sequence Analysis, DNA ; Tracheophyta/*classification/*genetics ; },
abstract = {Obtaining accurate phylogenies and effective species discrimination using a small standardized set of plastid genes is challenging in evolutionarily young lineages. Complete plastid genome sequencing offers an increasingly easy-to-access source of characters that helps address this. The usefulness of this approach, however, depends on the extent to which plastid haplotypes track morphological species boundaries. We have tested the power of complete plastid genomes to discriminate among multiple accessions of 11 of 13 New Caledonian Araucaria species, an evolutionarily young lineage where the standard DNA barcoding approach has so far failed and phylogenetic relationships have remained elusive. Additionally, 11 nuclear gene regions were Sanger sequenced for all accessions to ascertain the success of species discrimination using a moderate number of nuclear genes. Overall, fewer than half of the New Caledonian Araucaria species with multiple accessions were monophyletic in the plastid or nuclear trees. However, the plastid data retrieved a phylogeny with a higher resolution compared to any previously published tree of this clade and supported the monophyly of about twice as many species and nodes compared to the nuclear data set. Modest gains in discrimination thus are possible, but using complete plastid genomes or a small number of nuclear genes in DNA barcoding may not substantially raise species discriminatory power in many evolutionarily young lineages. The big challenge therefore remains to develop techniques that allow routine access to large numbers of nuclear markers scaleable to thousands of individuals from phylogenetically disparate sample sets.},
}
@article {pmid25610342,
year = {2014},
author = {Shiraiwa, K and Cong, Q and Grishin, NV},
title = {A new Heraclides swallowtail (Lepidoptera, Papilionidae) from North America is recognized by the pattern on its neck.},
journal = {ZooKeys},
volume = {},
number = {468},
pages = {85-135},
pmid = {25610342},
issn = {1313-2989},
abstract = {Heraclidesrumiko Shiraiwa &amp; Grishin, sp. n. is described from southwestern United States, Mexico, and Central America (type locality: USA, Texas, Duval County). It is closely allied to Heraclidescresphontes (Cramer, 1777) and the two species are sympatric in central Texas. The new species is diagnosed by male genitalia and exhibits a nearly 3% difference from Heraclidescresphontes in the COI DNA barcode sequence of mitochondrial DNA. The two Heraclides species can usually be told apart by the shape and size of yellow spots on the neck, by the wing shape, and the details of wing patterns. "Western Giant Swallowtail" is proposed as the English name for Heraclidesrumiko. To stabilize nomenclature, neotype for Papiliocresphontes Cramer, 1777, an eastern United States species, is designated from Brooklyn, New York, USA; and lectotype for Papiliothoas Linnaeus, 1771 is designated from Suriname. We sequenced DNA barcodes and ID tags of nearly 400 Papilionini specimens completing coverage of all Heraclides species. Comparative analyses of DNA barcodes, genitalia, and facies suggest that Heraclidesoviedo (Gundlach, 1866), reinstated status, is a species-level taxon rather than a subspecies of Heraclidesthoas (Linnaeus, 1771); and Heraclidespallas (G. Gray, [1853]), reinstated status, with its subspecies HeraclidesPapiliobajaensis (J. Brown &amp; Faulkner, 1992), comb. n., and Heraclidesanchicayaensis Constantino, Le Crom &amp; Salazar, 2002, stat. n., are not conspecific with Heraclidesastyalus (Godart, 1819).},
}
@article {pmid25610340,
year = {2014},
author = {Riedel, A and Tänzler, R and Balke, M and Rahmadi, C and Suhardjono, YR},
title = {Ninety-eight new species of Trigonopterus weevils from Sundaland and the Lesser Sunda Islands.},
journal = {ZooKeys},
volume = {},
number = {467},
pages = {1-162},
pmid = {25610340},
issn = {1313-2989},
abstract = {The genus Trigonopterus Fauvel, 1862 is highly diverse in Melanesia. Only one species, Trigonopterusamphoralis Marshall, 1925 was so far recorded West of Wallace's Line (Eastern Sumatra). Based on focused field-work the fauna from Sundaland (Sumatra, Java, Bali, Palawan) and the Lesser Sunda Islands (Lombok, Sumbawa, Flores) is here revised. We redescribe Trigonopterusamphoralis Marshall and describe an additional 98 new species: Trigonopterusacuminatus sp. n., Trigonopterusaeneomicans sp. n., Trigonopterusalaspurwensis sp. n., Trigonopterusallopatricus sp. n., Trigonopterusallotopus sp. n., Trigonopterusangulicollis sp. n., Trigonopterusargopurensis sp. n., Trigonopterusarjunensis sp. n., Trigonopterusasper sp. n., Trigonopterusattenboroughi sp. n., Trigonopterusbaliensis sp. n., Trigonopterusbatukarensis sp. n., Trigonopterusbawangensis sp. n., Trigonopterusbinodulus sp. n., Trigonopterusbornensis sp. n., Trigonopteruscahyoi sp. n., Trigonopteruscostipennis sp. n., Trigonopteruscuprescens sp. n., Trigonopteruscupreus sp. n., Trigonopterusdacrycarpi sp. n., Trigonopterusdelapan sp. n., Trigonopterusdentipes sp. n., Trigonopterusdiengensis sp. n., Trigonopterusdimorphus sp. n., Trigonopterusdisruptus sp. n., Trigonopterusdua sp. n., Trigonopterusduabelas sp. n., Trigonopterusechinatus sp. n., Trigonopterusempat sp. n., Trigonopterusenam sp. n., Trigonopterusfissitarsis sp. n., Trigonopterusflorensis sp. n., Trigonopterusfoveatus sp. n., Trigonopterusfulgidus sp. n., Trigonopterusgedensis sp. n., Trigonopterushalimunensis sp. n., Trigonopterushonjensis sp. n., Trigonopterusijensis sp. n., Trigonopterusjavensis sp. n., Trigonopteruskalimantanensis sp. n., Trigonopteruskintamanensis sp. n., Trigonopterusklatakanensis sp. n., Trigonopteruslampungensis sp. n., Trigonopteruslatipes sp. n., Trigonopteruslima sp. n., Trigonopteruslombokensis sp. n., Trigonopterusmerubetirensis sp. n., Trigonopterusmesehensis sp. n., Trigonopterusmicans sp. n., Trigonopterusmisellus sp. n., Trigonopteruspalawanensis sp. n., Trigonopteruspangandaranensis sp. n., Trigonopterusparaflorensis sp. n., Trigonopteruspararugosus sp. n., Trigonopterusparasumbawensis sp. n., Trigonopteruspauxillus sp. n., Trigonopteruspayungensis sp. n., Trigonopterusporcatus sp. n., Trigonopteruspseudoflorensis sp. n., Trigonopteruspseudosumbawensis sp. n., Trigonopteruspunctatoseriatus sp. n., Trigonopterusranakensis sp. n., Trigonopterusrelictus sp. n., Trigonopterusrinjaniensis sp. n., Trigonopterusroensis sp. n., Trigonopterusrugosostriatus sp. n., Trigonopterusrugosus sp. n., Trigonopterusrutengensis sp. n., Trigonopterussaltator sp. n., Trigonopterussantubongensis sp. n., Trigonopterussasak sp. n., Trigonopterussatu sp. n., Trigonopterusschulzi sp. n., Trigonopterussebelas sp. n., Trigonopterussembilan sp. n., Trigonopterussepuluh sp. n., Trigonopterusseriatus sp. n., Trigonopterusserratifemur sp. n., Trigonopterussetifer sp. n., Trigonopterussilvestris sp. n., Trigonopterussingkawangensis sp. n., Trigonopterussingularis sp. n., Trigonopterussinuatus sp. n., Trigonopterussqualidus sp. n., Trigonopterussumatrensis sp. n., Trigonopterussumbawensis sp. n., Trigonopterussundaicus sp. n., Trigonopterussuturalis sp. n., Trigonopterussyarbis sp. n., Trigonopterustelagensis sp. n., Trigonopterustepalensis sp. n., Trigonopterustiga sp. n., Trigonopterustrigonopterus sp. n., Trigonopterustujuh sp. n., Trigonopterusujungkulonensis sp. n., Trigonopterusvariolosus sp. n., Trigonopterusvulcanicus sp. n., Trigonopteruswallacei sp. n.. All new species are authored by the taxonomist-in-charge, Alexander Riedel. Most species belong to the litter fauna of primary wet evergreen forests. This habitat has become highly fragmented in the study area and many of its remnants harbor endemic species. Conservation measures should be intensified, especially in smaller and less famous sites to minimize the number of species threatened by extinction.},
}
@article {pmid25609839,
year = {2015},
author = {Mei, HE and Leipold, MD and Schulz, AR and Chester, C and Maecker, HT},
title = {Barcoding of live human peripheral blood mononuclear cells for multiplexed mass cytometry.},
journal = {Journal of immunology (Baltimore, Md. : 1950)},
volume = {194},
number = {4},
pages = {2022-2031},
pmid = {25609839},
issn = {1550-6606},
support = {5U19AI090019/AI/NIAID NIH HHS/United States ; U19 AI057229/AI/NIAID NIH HHS/United States ; S10 RR027582/RR/NCRR NIH HHS/United States ; U19 AI090019/AI/NIAID NIH HHS/United States ; S10RR027582/RR/NCRR NIH HHS/United States ; 5U19AI057229/AI/NIAID NIH HHS/United States ; },
mesh = {Cell Separation/instrumentation/*methods ; Flow Cytometry/instrumentation/*methods ; Humans ; Immunophenotyping/*methods ; *Leukocyte Common Antigens ; *Leukocytes, Mononuclear ; Staining and Labeling/methods ; },
abstract = {Mass cytometry is developing as a means of multiparametric single-cell analysis. In this study, we present an approach to barcoding separate live human PBMC samples for combined preparation and acquisition on a cytometry by time of flight instrument. Using six different anti-CD45 Ab conjugates labeled with Pd104, Pd106, Pd108, Pd110, In113, and In115, respectively, we barcoded up to 20 samples with unique combinations of exactly three different CD45 Ab tags. Cell events carrying more than or less than three different tags were excluded from analyses during Boolean data deconvolution, allowing for precise sample assignment and the electronic removal of cell aggregates. Data from barcoded samples matched data from corresponding individually stained and acquired samples, at cell event recoveries similar to individual sample analyses. The approach greatly reduced technical noise and minimizes unwanted cell doublet events in mass cytometry data, and it reduces wet work and Ab consumption. It also eliminates sample-to-sample carryover and the requirement of instrument cleaning between samples, thereby effectively reducing overall instrument runtime. Hence, CD45 barcoding facilitates accuracy of mass cytometric immunophenotyping studies, thus supporting biomarker discovery efforts, and it should be applicable to fluorescence flow cytometry as well.},
}
@article {pmid25609565,
year = {2015},
author = {Durán, S and Novo, S and Duch, M and Gómez-Martínez, R and Fernández-Regúlez, M and San Paulo, A and Nogués, C and Esteve, J and Ibañez, E and Plaza, JA},
title = {Silicon-nanowire based attachment of silicon chips for mouse embryo labelling.},
journal = {Lab on a chip},
volume = {15},
number = {6},
pages = {1508-1514},
doi = {10.1039/c4lc01299b},
pmid = {25609565},
issn = {1473-0189},
mesh = {Animals ; Cell Adhesion ; Embryo, Mammalian/*cytology ; Kinetics ; Mice ; Microscopy, Electron, Scanning ; Nanotechnology/*instrumentation ; *Nanowires ; Silicon/*chemistry ; Staining and Labeling/*methods ; Volatilization ; Zona Pellucida/metabolism ; },
abstract = {The adhesion of small silicon chips to cells has many potential applications as direct interconnection of the cells to the external world can be accomplished. Hence, although some typical applications of silicon nanowires integrated into microsystems are focused on achieving a cell-on-a-chip strategy, we are interested in obtaining chip-on-a-cell systems. This paper reports the design, technological development and characterization of polysilicon barcodes featuring silicon nanowires as nanoscale attachment to identify and track living mouse embryos during their in vitro development. The chips are attached to the outer surface of the Zona Pellucida, the cover that surrounds oocytes and embryos, to avoid the direct contact between the chip and the embryo cell membrane. Two attachment methodologies, rolling and pushpin, which allow two entirely different levels of applied forces to attach the chips to living embryos, are evaluated. The former consists of rolling the mouse embryos over one barcode with the silicon nanowires facing upwards, while in the latter, the barcode is pushed against the embryo with a micropipette. The effect on in vitro embryo development and the retention rate related to the calculated applied forces are stated. Field emission scanning electron microscopy inspection, which allowed high-resolution imaging, also confirms the physical attachment of the nanowires with some of them piercing or wrapped by the Zona Pellucida and revealed extraordinary bent silicon nanowires.},
}
@article {pmid25606457,
year = {2014},
author = {Tembe, S and Shouche, Y and Ghate, HV},
title = {DNA barcoding of Pentatomomorpha bugs (Hemiptera: Heteroptera) from Western Ghats of India.},
journal = {Meta gene},
volume = {2},
number = {},
pages = {737-745},
pmid = {25606457},
issn = {2214-5400},
abstract = {Recent studies from East Asia and Canadian National Collection of Insects have established the utility of DNA barcoding technique in identification of true bugs. The present study is an expansion of the database by adding mitochondrial cytochrome c oxidase I (mtCOI) sequences from forty three species of indigenous true bugs of India. mtCOI gene analysis of infraorder Pentatomomorpha covering a total of seventy three species that belong to five superfamilies; Pentatomoidea, Coreoidea, Pyrrhocoroidea, Lygaeoidea and Aradoidea revealed more than 3% interspecific distances in all the taxa studied except for two cases which showed barcode sharing. Less than 2% intra-specific divergence was observed in 97% of the taxa analysed and the average interspecies genetic distance was about 29 times higher than the average intraspecies genetic divergence. Distinct sequence divergence pattern at generic level and NJ clustering analysis suggests that COI barcode is an excellent molecular marker for species level identification of unknown taxa; however it may not be useful for resolving deep levels of divergence. Species identification even at nymphal stage could be achieved confirming the efficacy of this technique.},
}
@article {pmid25606392,
year = {2014},
author = {Kowasupat, C and Panijpan, B and Laosinchai, P and Ruenwongsa, P and Phongdara, A and Wanna, W and Senapin, S and Phiwsaiya, K},
title = {Biodiversity of the Betta smaragdina (Teleostei: Perciformes) in the northeast region of Thailand as determined by mitochondrial COI and nuclear ITS1 gene sequences.},
journal = {Meta gene},
volume = {2},
number = {},
pages = {83-95},
pmid = {25606392},
issn = {2214-5400},
abstract = {In Thailand, there are currently five recognized species members of the bubble-nesting Betta genus, namely Betta splendens, B. smaragdina, B. imbellis, B. mahachaiensis and B. siamorientalis. In 2010, we indicated the possibility, based on COI barcoding evidence, that there might be two additional species, albeit cryptic, related to the type-locality B. smaragdina in some provinces in the northeast of Thailand. In the present study, after a more extensive survey of the northeast, and phylogenetic analyses based on COI and ITS1 sequences, the B. smaragdina group may be composed of at least 3 cryptic species members. The phylogenetic positions of these B. smaragdina group members in the bubble-nesting bettas' tree together with those of their congeners have been consolidated by better DNA sequence quality and phylogenetic analyses. With a better supported tree, the species statuses of B. siamorientalis and the Cambodian B. smaragdina-like fish, B. stiktos, are also confirmed.},
}
@article {pmid25605421,
year = {2015},
author = {Wienerroither, RM and Bjelland, O and Bachmann, L and Junge, C},
title = {Northernmost record of the little gulper shark Centrophorus uyato in the north-eastern Atlantic Ocean, with taxonomical notes on Centrophorus zeehaani.},
journal = {Journal of fish biology},
volume = {86},
number = {2},
pages = {834-844},
doi = {10.1111/jfb.12602},
pmid = {25605421},
issn = {1095-8649},
abstract = {A specimen of the little gulper shark Centrophorus uyato was collected in the Norwegian Sea off the coast of northern Norway, marking the northernmost record of the species in the eastern North Atlantic Ocean. Morphological characteristics collected from the specimen indicate a close relationship to the Australian species Centrophorus zeehaani. DNA barcoding analysis of the mitochondrial cytochrome oxidase subunit I (coI) gene for species of Centrophorus suggests conspecificity of C. uyato and C. zeehaani.},
}
@article {pmid25604341,
year = {2015},
author = {Guo, L and Sui, Z and Zhang, S and Ren, Y and Liu, Y},
title = {Comparison of potential diatom 'barcode' genes (the 18S rRNA gene and ITS, COI, rbcL) and their effectiveness in discriminating and determining species taxonomy in the Bacillariophyta.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {65},
number = {Pt 4},
pages = {1369-1380},
doi = {10.1099/ijs.0.000076},
pmid = {25604341},
issn = {1466-5034},
mesh = {Bayes Theorem ; *DNA Barcoding, Taxonomic ; DNA Primers ; DNA, Ribosomal Spacer/genetics ; Diatoms/*classification ; Electron Transport Complex IV/genetics ; Genes, Chloroplast ; Genes, Mitochondrial ; Genes, rRNA ; *Phylogeny ; Plastids/genetics ; RNA, Ribosomal, 18S/genetics ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Analysis, DNA ; },
abstract = {Diatoms form an enormous group of photoautotrophic micro-eukaryotes and play a crucial role in marine ecology. In this study, we evaluated typical genes to determine whether they were effective at different levels of diatom clustering analysis to assess the potential of these regions for barcoding taxa. Our test genes included nuclear rRNA genes (the nuclear small-subunit rRNA gene and the 5.8S rRNA gene+ITS-2), a mitochondrial gene (cytochrome c-oxidase subunit 1, COI), a chloroplast gene [ribulose-1,5-biphosphate carboxylase/oxygenase large subunit (rbcL)] and the universal plastid amplicon (UPA). Calculated genetic divergence was highest for the internal transcribed spacer (ITS; 5.8S+ITS-2) (p-distance of 1.569, 85.84% parsimony-informative sites) and COI (6.084, 82.14%), followed by the 18S rRNA gene (0.139, 57.69%), rbcL (0.120, 42.01%) and UPA (0.050, 14.97%), which indicated that ITS and COI were highly divergent compared with the other tested genes, and that their nucleotide compositions were variable within the whole group of diatoms. Bayesian inference (BI) analysis showed that the phylogenetic trees generated from each gene clustered diatoms at different phylogenetic levels. The 18S rRNA gene was better than the other genes in clustering higher diatom taxa, and both the 18S rRNA gene and rbcL performed well in clustering some lower taxa. The COI region was able to barcode species of some genera within the Bacillariophyceae. ITS was a potential marker for DNA based-taxonomy and DNA barcoding of Thalassiosirales, while species of Cyclotella, Skeletonema and Stephanodiscus gathered in separate clades, and were paraphyletic with those of Thalassiosira. Finally, UPA was too conserved to serve as a diatom barcode.},
}
@article {pmid25603604,
year = {2014},
author = {Shen, Q and Jiang, T and Li, N and Wang, J and Han, C and Zhang, J and Xu, J and Zhang, D and Li, F},
title = {[Study on tetrodotoxin detection and toxic puffer fish identification of roasted fish fillet at the retail in Beijing and Qingdao].},
journal = {Wei sheng yan jiu = Journal of hygiene research},
volume = {43},
number = {6},
pages = {944-952},
pmid = {25603604},
issn = {1000-8020},
mesh = {Animals ; Commerce ; DNA ; Fish Products/poisoning ; Poisons/*analysis/toxicity ; Polymerase Chain Reaction ; Tetraodontiformes/classification/*metabolism ; Tetrodotoxin/genetics/*toxicity ; Tissue Extracts/*analysis/toxicity ; },
abstract = {OBJECTIVE: The roasted fish fillet sample at the retail collected in Beijing and Qingdao were detected for TTX, and the TTX positive samples was analyzed for fish species identification.<br><br>METHODS: TTX was tested by EUSA method and the cytochrome c oxidase I (COI) genome of TTX-positive samples was extracted and identified by DNA barcode.<br><br>RESULTS: Totally, 90 samples were tested by EUSA and 58 (64.4%) samples were positive for TTX with the levels ranging from 0.10 mg/kg to 63.81 mg/kg. Among the TTX positive samples, 24 (41.3%) were identified containing toxic puffer fish and 21 (87.5%) were Lagocephalus lunaris, the highly toxic puffer fish.<br><br>CONCLUSION: Some roasted fish fillet samples obtained from the retail in two cities were positive for TTX and contained toxic puffer fish. Based on these results, we suggest that roasted fish fillet producers should prevent toxic puffer fish from mixing in the raw material and the I regulators should strengthen the TTX surveillance and product labeling supervision of roasted fish fillet.},
}
@article {pmid25602282,
year = {2015},
author = {Xu, S and Li, D and Li, J and Xiang, X and Jin, W and Huang, W and Jin, X and Huang, L},
title = {Evaluation of the DNA barcodes in Dendrobium (Orchidaceae) from mainland Asia.},
journal = {PloS one},
volume = {10},
number = {1},
pages = {e0115168},
pmid = {25602282},
issn = {1932-6203},
mesh = {Asia ; *DNA Barcoding, Taxonomic ; DNA, Intergenic ; DNA, Plant ; Dendrobium/*classification/*genetics ; *Evolution, Molecular ; Genes, Plant ; Genetic Variation ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {DNA barcoding has been proposed to be one of the most promising tools for accurate and rapid identification of taxa. However, few publications have evaluated the efficiency of DNA barcoding for the large genera of flowering plants. Dendrobium, one of the largest genera of flowering plants, contains many species that are important in horticulture, medicine and biodiversity conservation. Besides, Dendrobium is a notoriously difficult group to identify. DNA barcoding was expected to be a supplementary means for species identification, conservation and future studies in Dendrobium. We assessed the power of 11 candidate barcodes on the basis of 1,698 accessions of 184 Dendrobium species obtained primarily from mainland Asia. Our results indicated that five single barcodes, i.e., ITS, ITS2, matK, rbcL and trnH-psbA, can be easily amplified and sequenced with the currently established primers. Four barcodes, ITS, ITS2, ITS+matK, and ITS2+matK, have distinct barcoding gaps. ITS+matK was the optimal barcode based on all evaluation methods. Furthermore, the efficiency of ITS+matK was verified in four other large genera including Ficus, Lysimachia, Paphiopedilum, and Pedicularis in this study. Therefore, we tentatively recommend the combination of ITS+matK as a core DNA barcode for large flowering plant genera.},
}
@article {pmid25602160,
year = {2015},
author = {Sapkota, R and Nicolaisen, M},
title = {An improved high throughput sequencing method for studying oomycete communities.},
journal = {Journal of microbiological methods},
volume = {110},
number = {},
pages = {33-39},
doi = {10.1016/j.mimet.2015.01.013},
pmid = {25602160},
issn = {1872-8359},
mesh = {Aphanomyces/genetics ; DNA Barcoding, Taxonomic ; DNA Primers ; DNA, Ribosomal Spacer/genetics ; *Daucus carota ; Denmark ; Genetic Variation ; *High-Throughput Nucleotide Sequencing/methods ; Oomycetes/*classification/*genetics ; Peronospora/genetics ; Phytophthora/*classification/genetics ; Polymerase Chain Reaction/*methods ; Pythium/genetics ; Saprolegnia/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Species Specificity ; },
abstract = {Culture-independent studies using next generation sequencing have revolutionized microbial ecology, however, oomycete ecology in soils is severely lagging behind. The aim of this study was to improve and validate standard techniques for using high throughput sequencing as a tool for studying oomycete communities. The well-known primer sets ITS4, ITS6 and ITS7 were used in the study in a semi-nested PCR approach to target the internal transcribed spacer (ITS) 1 of ribosomal DNA in a next generation sequencing protocol. These primers have been used in similar studies before, but with limited success. We were able to increase the proportion of retrieved oomycete sequences dramatically mainly by increasing the annealing temperature during PCR. The optimized protocol was validated using three mock communities and the method was further evaluated using total DNA from 26 soil samples collected from different agricultural fields in Denmark, and 11 samples from carrot tissue with symptoms of Pythium infection. Sequence data from the Pythium and Phytophthora mock communities showed that our strategy successfully detected all included species. Taxonomic assignments of OTUs from 26 soil sample showed that 95% of the sequences could be assigned to oomycetes including Pythium, Aphanomyces, Peronospora, Saprolegnia and Phytophthora. A high proportion of oomycete reads was consistently present in all 26 soil samples showing the versatility of the strategy. A large diversity of Pythium species including pathogenic and saprophytic species were dominating in cultivated soil. Finally, we analyzed amplicons from carrots with symptoms of cavity spot. This resulted in 94% of the reads belonging to oomycetes with a dominance of species of Pythium that are known to be involved in causing cavity spot, thus demonstrating the usefulness of the method not only in soil DNA but also in a plant DNA background. In conclusion, we demonstrate a successful approach for pyrosequencing of oomycete communities using ITS1 as the barcode sequence with well-known primers for oomycete DNA amplification.},
}
@article {pmid25599890,
year = {2015},
author = {Galinsky, K and Valim, C and Salmier, A and de Thoisy, B and Musset, L and Legrand, E and Faust, A and Baniecki, ML and Ndiaye, D and Daniels, RF and Hartl, DL and Sabeti, PC and Wirth, DF and Volkman, SK and Neafsey, DE},
title = {COIL: a methodology for evaluating malarial complexity of infection using likelihood from single nucleotide polymorphism data.},
journal = {Malaria journal},
volume = {14},
number = {},
pages = {4},
pmid = {25599890},
issn = {1475-2875},
support = {R01 AI099105/AI/NIAID NIH HHS/United States ; R01 AI106734/AI/NIAID NIH HHS/United States ; },
mesh = {Computational Biology/*methods ; DNA, Protozoan/genetics ; Gene Frequency/genetics ; Genotype ; Humans ; Malaria/classification/*parasitology/physiopathology ; *Models, Statistical ; Plasmodium/*genetics ; Polymorphism, Single Nucleotide/*genetics ; Software ; },
abstract = {BACKGROUND: Complex malaria infections are defined as those containing more than one genetically distinct lineage of Plasmodium parasite. Complexity of infection (COI) is a useful parameter to estimate from patient blood samples because it is associated with clinical outcome, epidemiology and disease transmission rate. This manuscript describes a method for estimating COI using likelihood, called COIL, from a panel of bi-allelic genotyping assays.<br><br>METHODS: COIL assumes that distinct parasite lineages in complex infections are unrelated and that genotyped loci do not exhibit significant linkage disequilibrium. Using the population minor allele frequency (MAF) of the genotyped loci, COIL uses the binomial distribution to estimate the likelihood of a COI level given the prevalence of observed monomorphic or polymorphic genotypes within each sample.<br><br>RESULTS: COIL reliably estimates COI up to a level of three or five with at least 24 or 96 unlinked genotyped loci, respectively, as determined by in silico simulation and empirical validation. Evaluation of COI levels greater than five in patient samples may require a very large collection of genotype data, making sequencing a more cost-effective approach for evaluating COI under conditions when disease transmission is extremely high. Performance of the method is positively correlated with the MAF of the genotyped loci. COI estimates from existing SNP genotype datasets create a more detailed portrait of disease than analyses based simply on the number of polymorphic genotypes observed within samples.<br><br>CONCLUSIONS: The capacity to reliably estimate COI from a genome-wide panel of SNP genotypes provides a potentially more accurate alternative to methods relying on PCR amplification of a small number of loci for estimating COI. This approach will also increase the number of applications of SNP genotype data, providing additional motivation to employ SNP barcodes for studies of disease epidemiology or control measure efficacy. The COIL program is available for download from GitHub, and users may also upload their SNP genotype data to a web interface for simple and efficient determination of sample COI.},
}
@article {pmid25596347,
year = {2015},
author = {Vassou, SL and Kusuma, G and Parani, M},
title = {DNA barcoding for species identification from dried and powdered plant parts: a case study with authentication of the raw drug market samples of Sida cordifolia.},
journal = {Gene},
volume = {559},
number = {1},
pages = {86-93},
doi = {10.1016/j.gene.2015.01.025},
pmid = {25596347},
issn = {1879-0038},
mesh = {*DNA Barcoding, Taxonomic ; *Genes, Plant ; Malvaceae/*genetics ; Phytotherapy ; Plant Proteins/*genetics ; Plants, Medicinal/*genetics ; },
abstract = {The majority of the plant materials used in herbal medicine is procured from the markets in the form of dried or powdered plant parts. It is essential to use authentic plant materials to derive the benefits of herbal medicine. However, establishing the identity of these plant materials by conventional taxonomy is extremely difficult. Here we report a case study in which the species identification of the market samples of Sida cordifolia was done by DNA barcoding. As a prelude to species identification by DNA barcoding, 13 species of Sida were collected, and a reference DNA barcode library was developed using rbcL, matK, psbA-trnH and ITS2 markers. Based on the intra-species and inter-species divergence observed, psbA-trnH and ITS2 were found to be the best two-marker combination for species identification of the market samples. The study showed that none of the market samples belonged to the authentic species, S. cordifolia. Seventy-six per cent of the market samples belonged to other species of Sida. The predominant one was Sida acuta (36%) followed by S. spinosa (20%), S. alnifolia (12%), S. scabrida (4%) and S. ravii (4%). Such substitutions may not only fail to give the expected therapeutic effect, but may also give undesirable effects as in case of S. acuta which contains a 6-fold higher amount of ephedrine compared to the roots of S. cordifolia. The remaining 24% of the samples were from other genera such as Abutilon sp. (8%), Ixonanthes sp., Terminalia sp., Fagonia sp., and Tephrosia sp. (4% each). This observation is in contrast to the belief that medicinal plants are generally substituted or adulterated with closely related species. The current study strongly suggests that the raw drug market samples of herbal medicines need to be properly authenticated before use, and DNA barcoding has been found to be suitable for this purpose.},
}
@article {pmid25593348,
year = {2015},
author = {Schwach, F and Bushell, E and Gomes, AR and Anar, B and Girling, G and Herd, C and Rayner, JC and Billker, O},
title = {PlasmoGEM, a database supporting a community resource for large-scale experimental genetics in malaria parasites.},
journal = {Nucleic acids research},
volume = {43},
number = {Database issue},
pages = {D1176-82},
pmid = {25593348},
issn = {1362-4962},
support = {089085/Z/09/Z//Wellcome Trust/United Kingdom ; G0501670//Medical Research Council/United Kingdom ; },
mesh = {*Databases, Genetic ; Genetic Vectors ; Genome, Protozoan ; Genotype ; High-Throughput Nucleotide Sequencing ; Internet ; Mutation ; Plasmids ; Plasmodium/genetics ; Plasmodium berghei/*genetics ; Software ; },
abstract = {The Plasmodium Genetic Modification (PlasmoGEM) database (http://plasmogem.sanger.ac.uk) provides access to a resource of modular, versatile and adaptable vectors for genome modification of Plasmodium spp. parasites. PlasmoGEM currently consists of >2000 plasmids designed to modify the genome of Plasmodium berghei, a malaria parasite of rodents, which can be requested by non-profit research organisations free of charge. PlasmoGEM vectors are designed with long homology arms for efficient genome integration and carry gene specific barcodes to identify individual mutants. They can be used for a wide array of applications, including protein localisation, gene interaction studies and high-throughput genetic screens. The vector production pipeline is supported by a custom software suite that automates both the vector design process and quality control by full-length sequencing of the finished vectors. The PlasmoGEM web interface allows users to search a database of finished knock-out and gene tagging vectors, view details of their designs, download vector sequence in different formats and view available quality control data as well as suggested genotyping strategies. We also make gDNA library clones and intermediate vectors available for researchers to produce vectors for themselves.},
}
@article {pmid25593084,
year = {2015},
author = {Pedraza-Lara, C and Barrientos-Lozano, L and Rocha-Sánchez, AY and Zaldívar-Riverón, A},
title = {Montane and coastal species diversification in the economically important Mexican grasshopper genus Sphenarium (Orthoptera: Pyrgomorphidae).},
journal = {Molecular phylogenetics and evolution},
volume = {84},
number = {},
pages = {220-231},
doi = {10.1016/j.ympev.2015.01.001},
pmid = {25593084},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Genes, Insect ; Grasshoppers/anatomy &amp; histology/*classification ; Mexico ; Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The genus Sphenarium (Pyrgomorphidae) is a small group of grasshoppers endemic to México and Guatemala that are economically and culturally important both as a food source and as agricultural pests. However, its taxonomy has been largely neglected mainly due to its conserved interspecific external morphology and the considerable intraspecific variation in colour pattern of some taxa. Here we examined morphological as well as mitochondrial and nuclear DNA sequence data to assess the species boundaries and evolutionary history in Sphenarium. Our morphological identification and DNA sequence-based species delimitation, carried out with three different approaches (DNA barcoding, general mixed Yule-coalescent model, Bayesian species delimitation), all recovered a higher number of putative species of Sphenarium than previously recognised. We unambiguously delimit seven species, and between five and ten additional species depending on the data/method analysed. Phylogenetic relationships within the genus strongly support two main clades, one exclusively montane, the other coastal. Divergence time estimates suggest late Miocene to Pliocene ages for the origin and most of the early diversification events in the genus, which were probably influenced by the formation of the Trans-Mexican Volcanic Belt. A series of Pleistocene events could have led to the current species diversification in both montane and coastal regions. This study not only reveals an overlooked species richness for the most popular edible insect in Mexico, but also highlights the influence of the dynamic geological and climatic history of the region in shaping its current diversity.},
}
@article {pmid25589864,
year = {2014},
author = {Stur, E and Borkent, A},
title = {When DNA barcoding and morphology mesh: Ceratopogonidae diversity in Finnmark, Norway.},
journal = {ZooKeys},
volume = {},
number = {463},
pages = {95-131},
pmid = {25589864},
issn = {1313-2989},
abstract = {DNA barcoding in Ceratopogonidae has been restricted to interpreting the medically and veterinary important members of Culicoides Latreille. Here the technique is utilised, together with morphological study, to interpret all members of the family in a select area. Limited sampling from the county of Finnmark in northernmost Norway indicated the presence of 54 species, including 14 likely new to science, 16 new to Norway, and one new to Europe. No species were previously recorded from this county. Only 93 species were known for all of Norway before this survey, indicating how poorly studied the group is. We evaluate and discuss morphological characters commonly used in identification of biting midges and relate species diagnoses to released DNA barcode data from 223 specimens forming 58 barcode clusters in our dataset. DNA barcodes and morphology were congruent for all species, except in three morphological species where highly divergent barcode clusters indicate the possible presence of cryptic species.},
}
@article {pmid25589855,
year = {2014},
author = {Schwarzfeld, MD and Sperling, FA},
title = {Species delimitation using morphology, morphometrics, and molecules: definition of the Ophionscutellaris Thomson species group, with descriptions of six new species (Hymenoptera, Ichneumonidae).},
journal = {ZooKeys},
volume = {},
number = {462},
pages = {59-114},
pmid = {25589855},
issn = {1313-2989},
abstract = {The diverse genus Ophion is almost entirely undescribed in the Nearctic region. In this paper we define the Ophionscutellaris species group. This species group is well-supported by analysis of DNA (ITS2, COI, and 28S D2-D3) and morphology. It includes the Palearctic species Ophionscutellaris and the Nearctic species Ophionidoneus. An integrative analysis of DNA, geometric wing morphometrics, classical morphometrics and qualitative morphology indicates that this species group contains a minimum of seven species in North America, although the full diversity of the group has likely not been sampled. Ophionclave Schwarzfeld, sp. n., Ophionaureus Schwarzfeld, sp. n., Ophionbrevipunctatus Schwarzfeld, sp. n., Ophiondombroskii Schwarzfeld, sp. n., Ophionkeala Schwarzfeld, sp. n. and Ophionimportunus Schwarzfeld, sp. n. are described, and a key to the known Nearctic species of the Ophionscutellaris group is provided.},
}
@article {pmid25588628,
year = {2015},
author = {Schmidt, S and Schmid-Egger, C and Morinière, J and Haszprunar, G and Hebert, PD},
title = {DNA barcoding largely supports 250 years of classical taxonomy: identifications for Central European bees (Hymenoptera, Apoidea partim).},
journal = {Molecular ecology resources},
volume = {15},
number = {4},
pages = {985-1000},
doi = {10.1111/1755-0998.12363},
pmid = {25588628},
issn = {1755-0998},
mesh = {Animals ; Bees/anatomy &amp; histology/*classification/*genetics ; Classification/*methods ; DNA Barcoding, Taxonomic/*methods ; Germany ; Molecular Sequence Data ; Sequence Analysis, DNA ; },
abstract = {This study presents DNA barcode records for 4118 specimens representing 561 species of bees belonging to the six families of Apoidea (Andrenidae, Apidae, Colletidae, Halictidae, Megachilidae and Melittidae) found in Central Europe. These records provide fully compliant barcode sequences for 503 of the 571 bee species in the German fauna and partial sequences for 43 more. The barcode results are largely congruent with traditional taxonomy as only five closely allied pairs of species could not be discriminated by barcodes. As well, 90% of the species possessed sufficiently deep sequence divergence to be assigned to a different Barcode Index Number (BIN). In fact, 56 species (11%) were assigned to two or more BINs reflecting the high levels of intraspecific divergence among their component specimens. Fifty other species (9.7%) shared the same Barcode Index Number with one or more species, but most of these species belonged to a distinct barcode cluster within a particular BIN. The barcode data contributed to clarifying the status of nearly half the examined taxonomically problematic species of bees in the German fauna. Based on these results, the role of DNA barcoding as a tool for current and future taxonomic work is discussed.},
}
@article {pmid25583356,
year = {2015},
author = {Meiswinkel, R and De Bree, F and Bossers-De Vries, R and Elbers, AR},
title = {An unrecognized species of the Culicoides obsoletus complex feeding on livestock in The Netherlands.},
journal = {Veterinary parasitology},
volume = {207},
number = {3-4},
pages = {324-328},
doi = {10.1016/j.vetpar.2014.12.032},
pmid = {25583356},
issn = {1873-2550},
mesh = {Animals ; Ceratopogonidae/*classification/genetics ; Electron Transport Complex IV/genetics ; Female ; Livestock/*parasitology ; Netherlands ; *Phylogeny ; Sequence Homology ; Species Specificity ; Wings, Animal/anatomy &amp; histology ; },
abstract = {In studies on Culicoides attacking livestock in the Netherlands, we chanced upon a species of the Obsoletus complex that we do not recognize, but whose dark wing pattern is distinctive. Nine cytochrome c oxidase (CO1) sequences of our so-called 'dark obsoletus' support its status as a separate species, the sequences differing significantly from those representing Culicoides obsoletus (Meigen) (90-91% homology) and Culicoides scoticus Downes &amp; Kettle (87-88% homology). In the last decade, several research groups in Europe have encountered 'mystery species' related to C. obsoletus and in some instances have made their sequences for various genetic loci available in GenBank. These include a CO1 series submitted from Sweden in 2012 (annotated as 'obsoletus 01, 02, or 03 MA-2012') and of which some share a 99% identity with our sequences for 'dark obsoletus'. Without doubt, the series from the Netherlands, along with a portion of the Swedish submissions, together represent a single species ('dark obsoletus'). Whether this species is referable to the Russian Culicoides gornostaevae Mirzaeva recorded recently from Norway, Sweden and Poland, and based solely upon the external morphology of the male, is not clear. The presence in Western Europe of multiple undescribed species related to C. obsoletus means that the taxonomy of this important vector complex is not fully resolved; consequently, we know little about these cryptic species with regard to seasonality, geographic range and host preference. This is undesirable given that Culicoides-borne arboviruses causing disease in livestock are moving more regularly out of the tropics and spreading north into temperate latitudes.},
}
@article {pmid25583149,
year = {2015},
author = {Chabbert, CD and Adjalley, SH and Klaus, B and Fritsch, ES and Gupta, I and Pelechano, V and Steinmetz, LM},
title = {A high-throughput ChIP-Seq for large-scale chromatin studies.},
journal = {Molecular systems biology},
volume = {11},
number = {1},
pages = {777},
pmid = {25583149},
issn = {1744-4292},
mesh = {Acetylation ; Chromatin/chemistry/*genetics ; Chromatin Immunoprecipitation/*methods ; DNA, Fungal/genetics ; Databases, Genetic ; Gene Expression Profiling ; Genetic Association Studies ; Genetic Markers ; High-Throughput Nucleotide Sequencing/*methods ; Histones/genetics/metabolism ; Methylation ; Nucleosomes ; Reproducibility of Results ; Saccharomyces cerevisiae/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {We present a modified approach of chromatin immuno-precipitation followed by sequencing (ChIP-Seq), which relies on the direct ligation of molecular barcodes to chromatin fragments, thereby permitting experimental scale-up. With Bar-ChIP now enabling the concurrent profiling of multiple DNA-protein interactions, we report the simultaneous generation of 90 ChIP-Seq datasets without any robotic instrumentation. We demonstrate that application of Bar-ChIP to a panel of Saccharomyces cerevisiae chromatin-associated mutants provides a rapid and accurate genome-wide overview of their chromatin status. Additionally, we validate the utility of this technology to derive novel biological insights by identifying a role for the Rpd3S complex in maintaining H3K14 hypo-acetylation in gene bodies. We also report an association between the presence of intragenic H3K4 tri-methylation and the emergence of cryptic transcription in a Set2 mutant. Finally, we uncover a crosstalk between H3K14 acetylation and H3K4 methylation in this mutant. These results show that Bar-ChIP enables biological discovery through rapid chromatin profiling at single-nucleosome resolution for various conditions and protein modifications at once.},
}
@article {pmid25577880,
year = {2014},
author = {Wu, JS and Zhang, YS and Liu, W and Hou, BW and Tong, WJ and Zhang, L and Zhang, WM and Ding, XY},
title = {[DNA barcoding research and its application on medicinal plants of Bletilla H. G. Reichenbach].},
journal = {Yao xue xue bao = Acta pharmaceutica Sinica},
volume = {49},
number = {10},
pages = {1466-1474},
pmid = {25577880},
issn = {0513-4870},
mesh = {Base Sequence ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Orchidaceae/*classification ; Plants, Medicinal/*classification ; },
abstract = {To identify adulterants from medicinal plants of Bletilla H. G. Reichenbach, the suitable candidate DNA barcoding of Bletilla was evaluated. In this study, the internal transcribed spacer (ITS) of nuclear ribosomal DNA, the LFY homologous gene intron 2 and chloroplast ycfl gene were amplified and sequenced from forty-one samples. The intra-specific and inter-specific divergences of Bletilla were calculated, and the identification efficiency was assessed using Barcoding Gap, NJ tree by K2P distance and BLAST1 method. The result showed the intra-specific divergence of nrDNA ITS and ycJfl (0.022-0.106 and 0.017-0.106) were obviously higher than the inter-specific divergence (0-0.012 and 0-0.015), and four species of Bletilla were also accurately distinguished in NJ trees. Whereas, there was no Barcoding Gap on LFY homologous gene intron 2, thus it cannot effectively identify species of Bletilla. Using NJ tree of nrDNA ITS and ycfl gene, powdery medicine and the adulterants of Bletilla were successfully unidentified. In conclusion, nrDNA ITS and ycfl can be used as a potential DNA barcoding to identify the medicinal plants in Bletilla and its adulterants. There were only three basic differences on nrDNA ITS between "Jujing baiji" and Bletilla striata of Lu'an in Anhui province, and two basic differences in ycfl. Based on morphological and molecular data, "Jujing baiji" could be recognized as the species of Bletilla striata.},
}
@article {pmid25577384,
year = {2015},
author = {Bruno, F and Marinella, M and Santamaria, M},
title = {e-DNA meta-barcoding: from NGS raw data to taxonomic profiling.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1269},
number = {},
pages = {257-278},
doi = {10.1007/978-1-4939-2291-8_16},
pmid = {25577384},
issn = {1940-6029},
mesh = {Animals ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In recent years, thanks to the essential support provided by the Next-Generation Sequencing (NGS) technologies, Metagenomics is enabling the direct access to the taxonomic and functional composition of mixed microbial communities living in any environmental niche, without the prerequisite to isolate or culture the single organisms. This approach has already been successfully applied for the analysis of many habitats, such as water or soil natural environments, also characterized by extreme physical and chemical conditions, food supply chains, and animal organisms, including humans. A shotgun sequencing approach can lead to investigate both organisms and genes diversity. Anyway, if the purpose is limited to explore the taxonomic complexity, an amplicon-based approach, based on PCR-targeted sequencing of selected genetic species markers, commonly named "meta-barcodes", is desirable. Among the genomic regions most widely used for the discrimination of bacterial organisms, in some cases up to the species level, some hypervariable domains of the gene coding for the 16S rRNA occupy a prominent place. The amplification of a certain meta-barcode from a microbial community through the use of PCR primers able to work in the entire considered taxonomic group is the first task after the extraction of the total DNA. Generally, this step is followed by the high-throughput sequencing of the resulting amplicons libraries by means of a selected NGS platform. Finally, the interpretation of the huge amount of produced data requires appropriate bioinformatics tools and know-how in addition to efficient computational resources. Here a computational methodology suitable for the taxonomic characterization of 454 meta-barcode sequences is described in detail. In particular, a dataset covering the V1-V3 region belonging to the bacterial 16S rRNA coding gene and produced in the Human Microbiome Project (HMP) from a palatine tonsils sample is analyzed. The proposed exercise includes the basic steps to manage raw sequencing data, remove amplification and pyrosequencing errors, and finally map sequences on the taxonomy.},
}
@article {pmid25576160,
year = {2015},
author = {Masiulionis, VE and Cabello, MN and Seifert, KA and Rodrigues, A and Pagnocca, FC},
title = {Escovopsis trichodermoides sp. nov., isolated from a nest of the lower attine ant Mycocepurus goeldii.},
journal = {Antonie van Leeuwenhoek},
volume = {107},
number = {3},
pages = {731-740},
doi = {10.1007/s10482-014-0367-1},
pmid = {25576160},
issn = {1572-9699},
mesh = {Animals ; Ants ; Brazil ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Helminth/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; *Environmental Microbiology ; Hypocreales/*classification/cytology/genetics/*isolation &amp; purification ; Microbiological Techniques ; Microscopy ; Molecular Sequence Data ; Peptide Elongation Factor 1/genetics ; Phylogeny ; Sequence Analysis, DNA ; Spores, Fungal/cytology ; },
abstract = {Currently, five species are formally described in Escovopsis, a specialized mycoparasitic genus of fungus gardens of attine ants (Hymenoptera: Formicidae: tribe Attini). Four species were isolated from leaf-cutting ants in Brazil, including Escovopsis moelleri and Escovopsis microspora from nests of Acromyrmex subterraneus molestans, Escovopsis weberi from a nest of Atta sp. and Escovopsis lentecrescens from a nest of Acromyrmex subterraneus subterraneus. The fifth species, Escovopsis aspergilloides was isolated from a nest of the higher attine ant Trachymyrmex ruthae from Trinidad. Here, we describe a new species, Escovopsis trichodermoides isolated from a fungus garden of the lower attine ant Mycocepurus goeldii, which differs from the five other species by highly branched, trichoderma-like conidiophores lacking swollen vesicles, with reduced conidiogenous cells and distinctive conidia morphology. Phylogenetic analyses based on partial tef1 gene sequences support the distinctiveness of this species. A portion of the internal transcribed spacers of the nuclear rDNA was sequenced to serve as a DNA barcode. Future molecular and morphological studies in this group of fungi will certainly unravel the taxonomic diversity of Escovopsis associated with fungus-growing ants.},
}
@article {pmid25572526,
year = {2015},
author = {King, RA and Symondson, WO and Thomas, RJ},
title = {Molecular analysis of faecal samples from birds to identify potential crop pests and useful biocontrol agents in natural areas.},
journal = {Bulletin of entomological research},
volume = {105},
number = {3},
pages = {261-272},
doi = {10.1017/S0007485314000935},
pmid = {25572526},
issn = {1475-2670},
mesh = {Animals ; Base Sequence ; *Biological Control Agents ; Cloning, Molecular ; DNA/*genetics ; DNA Barcoding, Taxonomic ; DNA Primers/genetics ; Feces/*microbiology ; *Food Chain ; Insecta/*genetics ; Molecular Sequence Data ; Polymerase Chain Reaction/veterinary ; Sequence Analysis, DNA/veterinary ; Songbirds/*microbiology ; Species Specificity ; },
abstract = {Wild habitats adjoining farmland are potentially valuable sources of natural enemies, but also of pests. Here we tested the utility of birds as 'sampling devices', to identify the diversity of prey available to predators and particularly to screen for pests and natural enemies using natural ecosystems as refugia. Here we used PCR to amplify prey DNA from three sympatric songbirds foraging on small invertebrates in Phragmites reedbed ecosystems, namely the Reed Warbler (Acrocephalus scirpaceus), Sedge Warbler (Acrocephalus schoenobaenus) and Cetti's Warbler (Cettia cetti). A recently described general invertebrate primer pair was used for the first time to analyse diets. Amplicons were cloned and sequenced, then identified by reference to the Barcoding of Life Database and to our own sequences obtained from fresh invertebrates. Forty-five distinct prey DNA sequences were obtained from 11 faecal samples, of which 39 could be identified to species or genus. Targeting three warbler species ensured that species-specific differences in prey choice broadened the range of prey taken. Amongst the prey found in reedbeds were major pests (including the tomato moth Lacanobia oleracea) as well as many potentially valuable natural enemies including aphidophagous hoverflies and braconid wasps. Given the mobility of birds, this approach provides a practical way of sampling a whole habitat at once, providing growers with information on possible invasion by locally resident pests and the colonization potential of natural enemies from local natural habitats.},
}
@article {pmid25572242,
year = {2014},
author = {Srirama, R and Gurumurthy, BR and Senthilkumar, U and Ravikanth, G and Uma Shaanker, R and Shivanna, MB},
title = {Are mini DNA-barcodes sufficiently informative to resolve species identities? An in silico analysis using Phyllanthus.},
journal = {Journal of genetics},
volume = {93},
number = {3},
pages = {823-829},
pmid = {25572242},
issn = {0973-7731},
mesh = {Computer Simulation ; *DNA Barcoding, Taxonomic ; Phyllanthus/*genetics ; Sequence Analysis, DNA ; *Species Specificity ; },
}
@article {pmid25569601,
year = {2015},
author = {Santoferrara, LF and Tian, M and Alder, VA and McManus, GB},
title = {Discrimination of closely related species in tintinnid ciliates: new insights on crypticity and polymorphism in the genus Helicostomella.},
journal = {Protist},
volume = {166},
number = {1},
pages = {78-92},
doi = {10.1016/j.protis.2014.11.005},
pmid = {25569601},
issn = {1618-0941},
mesh = {Atlantic Ocean ; Ciliophora/*classification/cytology/*genetics ; Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; *Genetic Variation ; Microscopy ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 5.8S/genetics ; Seawater/parasitology ; Sequence Analysis, DNA ; },
abstract = {This study focuses on the utility of molecular markers for the discrimination of closely related species in tintinnid ciliates. We analyzed the ecologically important genus Helicostomella by sequencing part of the large-subunit rDNA (LSU rDNA) and the 5.8S rDNA combined with the internally transcribed spacer regions 1 and 2 (5.8S rDNA-ITS) from forty-five individuals collected in NW and SW Atlantic waters and after culturing. Although all described Helicostomella species represent a continuum of morphologies, forms with shorter or longer loricae would correspond to different species according to previous molecular data. Here we observed that long forms show both crypticity (i.e. two almost identical long forms with different DNA sequences) and polymorphism (i.e. some long forms develop significantly shorter loricae after culturing). Reviewing all available tintinnid sequences, we found that 1) three Helicostomella clusters are consistent with different species from a molecular perspective, although these clusters are neither clearly differentiated by their loricae nor unambiguously linked to described species, 2) Helicostomella is closely related (probably to the family or genus level) to four "Tintinnopsis-like" morphospecies, and 3) if considered separately, neither LSU rDNA nor 5.8S rDNA-ITS completely discriminate closely related species, thus supporting the use of multi-gene barcodes for tintinnids.},
}
@article {pmid25561859,
year = {2014},
author = {Phillips-Rodríguez, E and Powell, JA and Hallwachs, W and Janzen, DH},
title = {A synopsis of the genus Ethmia Hübner in Costa Rica: biology, distribution, and description of 22 new species (Lepidoptera, Gelechioidea, Depressariidae, Ethmiinae), with emphasis on the 42 species known from Área de Conservación Guanacaste.},
journal = {ZooKeys},
volume = {},
number = {461},
pages = {1-86},
pmid = {25561859},
issn = {1313-2989},
abstract = {We discuss 45 Costa Rican species of Ethmia Hübner, 1819, including 23 previously described: Ethmiadelliella (Fernald), Ethmiabittenella (Busck), Ethmiafestiva Busck, Ethmiascythropa Walsingham, Ethmiaperpulchra Walsingham, Ethmiaterpnota Walsingham, Ethmiaelutella Busck, Ethmiajanzeni Powell, Ethmiaungulatella Busck, Ethmiaexornata (Zeller), Ethmiaphylacis Walsingham, Ethmiamnesicosma Meyrick, Ethmiachemsaki Powell, Ethmiabaliostola Walsingham, Ethmiaduckworthi Powell, Ethmiasandra Powell, Ethmianigritaenia Powell, Ethmiacatapeltica Meyrick, Ethmialichyi Powell, Ethmiatransversella Busck, Ethmiasimilatella Busck, Ethmiahammella Busck, Ethmialinda Busck, and 22 new species: Ethmiablaineorum, Ethmiamillerorum, Ethmiadianemillerae, Ethmiaadrianforsythi, Ethmiastephenrumseyi, Ethmiaberndkerni, Ethmiadimauraorum, Ethmiabillalleni, Ethmiaehakernae, Ethmiahelenmillerae, Ethmiajohnpringlei, Ethmialaphamorum, Ethmiapetersterlingi, Ethmialesliesaulae, Ethmiaturnerorum, Ethmianormgershenzi, Ethmianicholsonorum, Ethmiahendersonorum, Ethmiarandyjonesi, Ethmiarandycurtisi, Ethmiamiriamschulmanae and Ethmiatilneyorum. We illustrate all species and their male and female genitalia, along with distribution maps of Costa Rican localities. Immature stages are illustrated for 11 species, and food plants are listed when known. Gesneriaceae is added as a new food plant family record for Ethmia. CO1 nucleotide sequences ("DNA barcodes") were obtained for 41 of the species.},
}
@article {pmid25561856,
year = {2014},
author = {Baldizzone, G and Nel, J and Landry, JF},
title = {Coleophoranepetellae Baldizzone &amp; Nel, a new species of the C.lixella group (Lepidoptera, Coleophoridae) from France and Italy.},
journal = {ZooKeys},
volume = {},
number = {459},
pages = {119-135},
pmid = {25561856},
issn = {1313-2989},
abstract = {Coleophoranepetellae Baldizzone &amp; Nel, sp. n. is described from the southern Alps (Italy and France). It belongs to the Coleophoralixella species group. Its host plants are Nepetanepetella L. (Lamiaceae) and an unidentified Poaceae. The fifth instar larva, its case, the adult habitus, and genitalia are illustrated. The species is compared to Coleophoranevadella Baldizzone, 1985, here newly confirmed from France and whose larvae feed on Nepetalatifolia DC. in the Eastern Pyrénées. DNA barcodes are shown to be distinct and congruent with morphological differences among species of the lixella group. Barcodes revealed that Coleophoratricolor Walsingham, 1889, formerly known only from Great Britain, is also present in France and Greece.},
}
@article {pmid25561842,
year = {2014},
author = {Carvalho-Batista, A and Negri, M and Pileggi, LG and Castilho, AL and Costa, RC and Mantelatto, FL},
title = {Inferring population connectivity across the range of distribution of the stiletto shrimp Artemesialonginaris Spence Bate, 1888 (Decapoda, Penaeidae) from DNA barcoding: implications for fishery management.},
journal = {ZooKeys},
volume = {},
number = {457},
pages = {271-288},
pmid = {25561842},
issn = {1313-2989},
abstract = {Artemesialonginaris is a marine shrimp endemic to the southwestern Atlantic and distributed from Atafona, Rio de Janeiro (Brazil) to Rawson, Chubut (Argentina). In recent years, this species has become an important target of the commercial fishery as a consequence of the decline in the fishery of more traditional and profitable marine shrimps. In addition, phenotypic variations have been documented in populations along its distribution. Therefore, investigations on the genetics of the fishing stocks are necessary for the development of sustainable management strategies and for understanding the possible sources of these variations. The mitochondrial gene Cytochrome Oxidase I (COI) was used to search for evidence of genetic structure among the populations of Artemesialonginaris and to analyze the phylogenetic relationships among them. A total of 60 specimens were collected from seven different localities, covering its geographical range. The final alignment showed 53 haplotypes (48 individuals and 5 shared), with no biogeographical pattern. The low genetic divergence found, with a non-significant FST value, also suggests the absence of population structure for this gene. These findings indicate a continuous gene flow among the populations analyzed, suggesting that the phenotypic variation is a consequence of different environmental conditions among the localities.},
}
@article {pmid25561355,
year = {2014},
author = {Eckert, EM and Fontaneto, D and Coci, M and Callieri, C},
title = {Does a barcoding gap exist in prokaryotes? Evidences from species delimitation in cyanobacteria.},
journal = {Life (Basel, Switzerland)},
volume = {5},
number = {1},
pages = {50-64},
pmid = {25561355},
issn = {2075-1729},
abstract = {The amount of information that is available on 16S rRNA sequences for prokaryotes thanks to high-throughput sequencing could allow a better understanding of diversity. Nevertheless, the application of predetermined threshold in genetic distances to identify units of diversity (Operative Taxonomic Units, OTUs) may provide biased results. Here we tests for the existence of a barcoding gap in several groups of Cyanobacteria, defining units of diversity according to clear differences between within-species and among-species genetic distances in 16S rRNA. The application of a tool developed for animal DNA taxonomy, the Automatic Barcode Gap Detector (ABGD), revealed that a barcoding gap could actually be found in almost half of the datasets that we tested. The identification of units of diversity through this method provided results that were not compatible with those obtained with the identification of OTUs with threshold of similarity in genetic distances of 97% or 99%. The main message of our results is a call for caution in the estimate of diversity from 16S sequences only, given that different subjective choices in the method to delimit units could provide different results.},
}
@article {pmid25555150,
year = {2015},
author = {Nitsche, F and Arndt, H},
title = {Comparison of similar Arctic and Antarctic morphotypes of heterotrophic protists regarding their genotypes and ecotypes.},
journal = {Protist},
volume = {166},
number = {1},
pages = {42-57},
doi = {10.1016/j.protis.2014.11.002},
pmid = {25555150},
issn = {1618-0941},
mesh = {Antarctic Regions ; Arctic Regions ; *Biota ; Cluster Analysis ; DNA, Algal/chemistry/genetics ; DNA, Plant/chemistry/genetics ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Ecotype ; Eukaryota/genetics/*isolation &amp; purification/ultrastructure ; *Genotype ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Water/parasitology ; },
abstract = {The polar regions offer the opportunity to study possible diversification processes of spatially and temporally separated populations. We focused our study on similar morphotypes/species (e. g. species with the same morphology) of heterotrophic flagellates and ciliates originating from both, Antarctic and Arctic waters: 38 populations of six choanoflagellate morphospecies (Acanthocorbis unguiculata, Helgoeca nana, Diaphanoeca grandis, Savillea micropora, Stephanoeca apheles, Salpingoeca tuba), four other flagellate morphospecies (Cafeteria roenbergensis, Podomonas magma, Procryptobia sorokini, Protaspis sp.) and three ciliate morphospecies (Holosticha sp., Uronema marinum, Pseudocohnilembus persalinus). We analysed similarities and differences regarding their genotypes (SSU rDNA) and for several species regarding morphotypes and autecology (temperature and salinity tolerance). Most of the investigated polar protists were psychrophilic and showed a high salinity tolerance. Morphologically well defined acanthoecid choanoflagellates isolated from both poles showed the lowest intraspecific diversity (< 0.5% p-distance). No intragenomic polymorphism of SSU rDNA within one individual and among clones from one population occurred. The way of dispersal for acanthoecid choanoflagellates still remains unclear. Even under extreme stress none of the examined cultures formed cysts. Single cell PCR appeared to be an appropriate method to investigate species not available as monoclonal cultures. As a prerequisite for barcoding, acanthoecid choanoflagellate species have a very low intraspecific variability regarding SSU rDNA. There was a clear correlation between autecological, morphological and molecular data sets, which may help interpreting molecular data from clone libraries or next generation sequencing.},
}
@article {pmid25553196,
year = {2014},
author = {Manneschi, C and Fanzio, P and Ala-Nissila, T and Angeli, E and Repetto, L and Firpo, G and Valbusa, U},
title = {Stretching of DNA confined in nanochannels with charged walls.},
journal = {Biomicrofluidics},
volume = {8},
number = {6},
pages = {064121},
pmid = {25553196},
issn = {1932-1058},
abstract = {There is currently a growing interest in control of stretching of DNA inside nanoconfined regions due to the possibility to analyze and manipulate single biomolecules for applications such as DNA mapping and barcoding, which are based on stretching the DNA in a linear fashion. In the present work, we couple Finite Element Methods and Monte Carlo simulations in order to study the conformation of DNA molecules confined in nanofluidic channels with neutral and charged walls. We find that the electrostatic forces become more and more important when lowering the ionic strength of the solution. The influence of the nanochannel cross section geometry is also studied by evaluating the DNA elongation in square, rectangular, and triangular channels. We demonstrate that coupling electrostatically interacting walls with a triangular geometry is an efficient way to stretch DNA molecules at the scale of hundreds of nanometers. The paper reports experimental observations of λ-DNA molecules in poly(dimethylsiloxane) nanochannels filled with solutions of different ionic strength. The results are in good agreement with the theoretical predictions, confirming the crucial role of the electrostatic repulsion of the constraining walls on the molecule stretching.},
}
@article {pmid25550390,
year = {2015},
author = {Mirhendi, H and Makimura, K and de Hoog, GS and Rezaei-Matehkolaei, A and Najafzadeh, MJ and Umeda, Y and Ahmadi, B},
title = {Translation elongation factor 1-α gene as a potential taxonomic and identification marker in dermatophytes.},
journal = {Medical mycology},
volume = {53},
number = {3},
pages = {215-224},
doi = {10.1093/mmy/myu088},
pmid = {25550390},
issn = {1460-2709},
mesh = {Arthrodermataceae/*classification/*genetics ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; *Genetic Variation ; Humans ; Molecular Sequence Data ; Peptide Elongation Factor 1/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Intra- and interspecies variations of the translation elongation factor 1-α (Tef-1α) gene were evaluated as a new identification marker in a wide range of dermatophytes, which included 167 strains of 30 species. An optimized pan-dermatophyte primer pair was designed, and the target was sequenced. Consensus sequences were used for multiple alignment and phylogenetic tree analysis and the levels of intra- and interspecific nucleotide polymorphism were assessed. Between species, the analyzed part of the Tef-1α gene varied in length from 709 to 769 nucleotides. Significant numbers of species including Trichophyton rubrum, T. tonsurans, T. schoenleinii, T. concentricum, T. violaceum, Epidermophyton floccosum, Microsporum ferrugineum, M. canis, M. audouinii, T. equinum, T. eriotrephon, and T. erinacei were invariant in Tef-1α and had sufficient barcoding distance with neighboring species. Although overall consistency was found between ITS phylogeny as the current molecular marker of dermatophytes and Tef-1α, a higher discriminatory power of Tef-1α appeared particularly useful in some clades of closely related species such as the A. vanbreuseghemii, T. rubrum, A. benhamiae, and A. otae complexes. Nevertheless, we stress that a single gene can not specify species borderlines among dermatophytes and multiple lines of evidence based on a multilocus inquiry may ascertain an incontrovertible evaluation of kinship.},
}
@article {pmid25548775,
year = {2014},
author = {Jiang, C and Cao, L and Yuan, Y and Chen, M and Jin, Y and Huang, L},
title = {Barcoding melting curve analysis for rapid, sensitive, and discriminating authentication of saffron (Crocus sativus L.) from its adulterants.},
journal = {BioMed research international},
volume = {2014},
number = {},
pages = {809037},
pmid = {25548775},
issn = {2314-6141},
mesh = {Crocus/classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Chloroplast/*genetics ; *Drug Contamination ; Humans ; },
abstract = {Saffron (Crocus sativus L.) is one of the most important and expensive medicinal spice products in the world. Because of its high market value and premium price, saffron is often adulterated through the incorporation of other materials, such as Carthamus tinctorius L. and Calendula officinalis L. flowers, Hemerocallis L. petals, Daucus carota L. fleshy root, Curcuma longa L. rhizomes, Zea may L., and Nelumbo nucifera Gaertn. stigmas. To develop a straightforward, nonsequencing method for rapid, sensitive, and discriminating detection of these adulterants in traded saffron, we report here the application of a barcoding melting curve analysis method (Bar-MCA) that uses the universal chloroplast plant DNA barcoding region trnH-psbA to identify adulterants. When amplified at DNA concentrations and annealing temperatures optimized for the curve analysis, peaks were formed at specific locations for saffron (81.92°C) and the adulterants: D. carota (81.60°C), C. tinctorius (80.10°C), C. officinalis (79.92°C), Dendranthema morifolium (Ramat.) Tzvel. (79.62°C), N. nucifera (80.58°C), Hemerocallis fulva (L.) L. (84.78°C), and Z. mays (84.33°C). The constructed melting curves for saffron and its adulterants have significantly different peak locations or shapes. In conclusion, Bar-MCA could be a faster and more cost-effective method to authenticate saffron and detect its adulterants.},
}
@article {pmid25547078,
year = {2015},
author = {Zhao, Y and Cao, Z and Cheng, J and Hu, L and Ma, J and Yang, Y and Wang, X and Zeng, J and Wang, T},
title = {Population identification of Sarcoptes hominis and Sarcoptes canis in China using DNA sequences.},
journal = {Parasitology research},
volume = {114},
number = {3},
pages = {1001-1010},
pmid = {25547078},
issn = {1432-1955},
mesh = {Animal Distribution ; Animals ; Australia ; China ; Cyclooxygenase 1/genetics ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/*genetics ; Humans ; *Phylogeny ; Sarcoptidae/*classification/*genetics ; United States ; },
abstract = {There has been no consistent conclusion on whether Sarcoptes mites parasitizing in humans and animals are the same species. To identify Sarcoptes (S.) hominis and S. canis in China, gDNA was extracted from individual mites (five from patients with scabies and five from dogs with mange) for amplification of rDNA ITS2, mtDNA 16S, and cox1 fragment sequences. Then, the sequences obtained were aligned with those from different hosts and geographical locations retrieved from GenBank and sequence analyses were conducted. Phylogenetic trees based on 317-bp mtDNA cox1 showed five distinctive branches (species) of Sarcoptes mites, four for S. hominis (S. hominis Chinese, S. nr. hominis Chinese, S. hominis Australian, and S. hominis Panamanian) and one for S. animal (S. animal). S. animal included mites from nine animal species, with S. canis China, S. canis Australia, and S. canis USA clustering as a subbranch. Further sequence divergence analysis revealed no overlap between intraspecific (≤ 2.6 %) and interspecific (2.6-10.5 %) divergences in 317-bp mtDNA cox1. However, overlap was detected between intra- and interspecific divergences in 311-bp rDNA ITS2 or 275-bp mtDNA 16S when the divergences exceeded 1.0 %, which resulted in failure in identification of Sarcoptes. The results showed that the 317-bp mtDNA cox1 could be used as a DNA barcode for molecular identification of Sarcoptes mites. In addition, geographical isolation was observed between S. hominis Chinese, S. hominis Australian, and S. hominis Panamanian, but not between all S. canis. S. canis and the other S. animal belonged to the same species.},
}
@article {pmid25545929,
year = {2014},
author = {Moser, W and Greter, H and Schindler, C and Allan, F and Ngandolo, BN and Moto, DD and Utzinger, J and Zinsstag, J},
title = {The spatial and seasonal distribution of Bulinus truncatus, Bulinus forskalii and Biomphalaria pfeifferi, the intermediate host snails of schistosomiasis, in N'Djamena, Chad.},
journal = {Geospatial health},
volume = {9},
number = {1},
pages = {109-118},
doi = {10.4081/gh.2014.9},
pmid = {25545929},
issn = {1970-7096},
mesh = {Animals ; *Bulinus/parasitology/physiology ; Chad/epidemiology ; DNA Barcoding, Taxonomic ; Disease Vectors ; Environment ; Geographic Information Systems ; Humans ; Schistosomiasis/transmission ; Seasons ; Spatio-Temporal Analysis ; },
abstract = {There is a paucity of epidemiological and malacological data pertaining to schistosomiasis in Chad. In view of a recently articulated elimination agenda, a deeper understanding of the spatio-temporal distribution of schistosomiasis intermediate host snails is pivotal. We conducted cross-sectional malacological surveys during the dry season (April/May 2013) and after the short rainy season (October 2013) in N'Djamena, the capital of Chad. Snails were identified at the genus and species level using morphological keys and molecular DNA barcoding approaches. Those belonging to Bulinus and Biomphalaria were examined for cercarial shedding. Snail habitats were characterised and their predictive potential for the presence of schistosomiasis intermediate host snails explored. Seasonal patterns were studied using geographical information system and kriging in order to interpolate snail abundance data to make predictions at non-sampled locations across N'Djamena. Overall, 413 Bulinus truncatus, 369 Bulinus forskalii and 108 Biomphalaria pfeifferi snails were collected and subjected to cercarial shedding. During the dry season, one Bu. truncatus of 119 snails collected shed Schistosoma spp. cercariae (0.84%), while S. mansoni was shed by one of 108 Bi. pfeifferi snails (0.93%). None of the snails collected after the rainy season shed Schistosoma spp. cercariae. The abundance of Bu. truncatus and Bu. forskalii showed an inverse U-shape relationship with the square term of conductivity, i.e. low abundance at the lowest and highest levels of conductivity and high abundance at intermediate levels. Bi. pfeifferi showed a negative, linear association with pH in the dry seasons. It is planned to link these intermediate host snail data to infection data in human populations with the goal to draw a predictive risk map that can be utilised for control and elimination of schistosomiasis in N'Djamena.},
}
@article {pmid25545675,
year = {2015},
author = {Kartzinel, TR and Pringle, RM},
title = {Molecular detection of invertebrate prey in vertebrate diets: trophic ecology of Caribbean island lizards.},
journal = {Molecular ecology resources},
volume = {15},
number = {4},
pages = {903-914},
doi = {10.1111/1755-0998.12366},
pmid = {25545675},
issn = {1755-0998},
mesh = {Animals ; Arthropods/*classification/*genetics ; Cluster Analysis ; DNA Primers/genetics ; DNA, Mitochondrial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Feces/*chemistry ; Food Chain ; Lizards/*physiology ; Molecular Sequence Data ; Phylogeny ; *Predatory Behavior ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; West Indies ; },
abstract = {Understanding community assembly and population dynamics frequently requires detailed knowledge of food web structure. For many consumers, obtaining precise information about diet composition has traditionally required sacrificing animals or other highly invasive procedures, generating tension between maintaining intact study populations and knowing what they eat. We developed 16S mitochondrial DNA sequencing methods to identify arthropods in the diets of generalist vertebrate predators without requiring a blocking primer. We demonstrate the utility of these methods for a common Caribbean lizard that has been intensively studied in the context of small island food webs: Anolis sagrei (a semi-arboreal 'trunk-ground' anole ecomorph). Novel PCR primers were identified in silico and tested in vitro. Illumina sequencing successfully characterized the arthropod component of 168 faecal DNA samples collected during three field trips spanning 12 months, revealing 217 molecular operational taxonomic units (mOTUs) from at least nine arthropod orders (including Araneae, Blattodea, Coleoptera, Hemiptera, Hymenoptera, Isoptera, Lepidoptera and Orthoptera). Three mOTUs (one beetle, one cockroach and one ant) were particularly frequent, occurring in ≥50% of samples, but the majority of mOTUs were infrequent (180, or 83%, occurred in ≤5% of samples). Species accumulation curves showed that dietary richness and composition were similar between size-dimorphic sexes; however, female lizards had greater per-sample dietary richness than males. Overall diet composition (but not richness) was significantly different across seasons, and we found more pronounced interindividual variation in December than in May. These methods will be generally useful in characterizing the diets of diverse insectivorous vertebrates.},
}
@article {pmid25544958,
year = {2014},
author = {Kaygorodova, IA and Mandzyak, N and Petryaeva, E and Pronin, NM},
title = {Genetic diversity of freshwater leeches in Lake Gusinoe (eastern Siberia, Russia).},
journal = {TheScientificWorldJournal},
volume = {2014},
number = {},
pages = {619127},
pmid = {25544958},
issn = {1537-744X},
mesh = {Animals ; *Genetic Variation ; *Lakes ; Leeches/*classification/*genetics ; *Phylogeny ; Siberia ; },
abstract = {The study of leeches from Lake Gusinoe and its adjacent area offered us the possibility to determine species diversity. As a result, an updated species list of the Gusinoe Hirudinea fauna (Annelida, Clitellata) has been compiled. There are two orders and three families of leeches in the Gusinoe area: order Rhynchobdellida (families Glossiphoniidae and Piscicolidae) and order Arhynchobdellida (family Erpobdellidae). In total, 6 leech species belonging to 6 genera have been identified. Of these, 3 taxa belonging to the family Glossiphoniidae (Alboglossiphonia heteroclita f. papillosa, Hemiclepsis marginata, and Helobdella stagnalis) and representatives of 3 unidentified species (Glossiphonia sp., Piscicola sp., and Erpobdella sp.) have been recorded. The checklist gives a contemporary overview of the species composition of leeches and information on their hosts or substrates. The validity of morphological identification of each taxon has been verified by phylogenetic approach with a molecular marker adopted for a DNA barcoding of most invertebrates.},
}
@article {pmid25544627,
year = {2014},
author = {Blagoev, GA and Dondale, CD},
title = {A new species of Alopecosa (Araneae: Lycosidae) from Canada: a morphological description supported by DNA barcoding of 19 congeners.},
journal = {Zootaxa},
volume = {3894},
number = {},
pages = {152-160},
doi = {10.11646/zootaxa.3894.1.12},
pmid = {25544627},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; DNA Barcoding, Taxonomic ; Ecosystem ; Female ; Male ; Organ Size ; Phylogeny ; Spiders/anatomy &amp; histology/*classification/*genetics/growth &amp; development ; },
abstract = {A new species, Alopecosa koponeni sp. n., is described from the Arctic part of Manitoba. Individuals of A. koponeni most resemble those of A. pictilis (Emerton, 1885), but are smaller than the latter and differ in the epiginum and in colour pattern in both sexes. DNA barcode results show an interspecific distance of 0.93 between A. koponeni sp. n. and A. pictilis, a shallow genetic divergence that suggests a recent separation.},
}
@article {pmid25544622,
year = {2014},
author = {Fet, V and Graham, MR and Webber, MM and Blagoev, G},
title = {Two new species of Euscorpius (Scorpiones: Euscorpiidae) from Bulgaria, Serbia, and Greece.},
journal = {Zootaxa},
volume = {3894},
number = {},
pages = {83-105},
doi = {10.11646/zootaxa.3894.1.7},
pmid = {25544622},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Bulgaria ; Female ; Greece ; Male ; Organ Size ; Scorpions/anatomy &amp; histology/*classification/growth &amp; development ; Serbia ; },
abstract = {Two new species of Euscorpius Thorell, 1876 (subgenus Euscorpius s.str.) (Scorpiones: Euscorpiidae) are described based on morphology and the COI DNA barcoding marker: E. deltshevi sp. n. from northern Bulgaria and neighbouring Serbia (formerly reported as E. carpathicus) and E. solegladi sp. n. from southwestern Bulgaria and neighbouring Greece (formerly reported as E. hadzii).},
}
@article {pmid25544520,
year = {2014},
author = {Yoon, TJ and Kim, JK},
title = {Taxonomy of Eumenes punctatus-complex (Hymenoptera: Vespidae: Eumeninae) from Korea with DNA barcoding and key to Far Eastern species of the genus Eumenes Latreille, 1802.},
journal = {Zootaxa},
volume = {3893},
number = {2},
pages = {232-242},
doi = {10.11646/zootaxa.3893.2.4},
pmid = {25544520},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Female ; Male ; Organ Size ; Republic of Korea ; Wasps/anatomy &amp; histology/*classification/growth &amp; development ; },
abstract = {Based on DNA barcoding analysis and morphological comparison, new synonymy is proposed for Eumenes punctatus de Saussure, 1852 =E. asioboreus Kim &amp; Sk. Yamane, 2001, syn. nov. Independent status of the Far Eastern species E. rubrofemoratus Giordani Soika, 1941 from the transpalearctic E. coarctatus (Linnaeus, 1758) is supported, suggesting their recent origin with comparatively low genetic divergence. A revised key to the Far Eastern species of the genus Eumenes is provided. Distribution of E. quadratus Smith, 1852 is corrected and E. rubrofemoratus Giordani Soika, 1941 is newly recorded from South Korea. For future taxonomic comprehension of the Far Eastern Eumenes, problematic species pairs requiring additional molecular tests are hereby suggested and discussed.},
}
@article {pmid25544100,
year = {2014},
author = {Sarvašová, A and Kočišová, A and Halán, M and Delécolle, JC and Mathieu, B},
title = {Morphological and molecular analysis of the genus Culicoides (Diptera: Ceratopogonidae) in Slovakia with five new records.},
journal = {Zootaxa},
volume = {3872},
number = {5},
pages = {541-560},
doi = {10.11646/zootaxa.3872.5.6},
pmid = {25544100},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Body Size ; Ceratopogonidae/anatomy &amp; histology/*classification/*genetics/growth &amp; development ; Ecosystem ; Female ; Male ; Molecular Sequence Data ; Organ Size ; Phylogeny ; Slovakia ; Wings, Animal/anatomy &amp; histology/growth &amp; development ; },
abstract = {The biodiversity of Culicoides from eastern Slovakia was investigated by light trapping. An integrative taxonomy approach combining DNA barcode sequence and morphological analyses was used to accurately identify specimens. Five species were newly recorded from Slovakia: Culicoides picturatus Kremer &amp; Deduit, C. gejgelensis Dzhafarov, C. clastrieri Callot et al., C. griseidorsum Kieffer and C. odiatus Austen. The checklist of the Culicoides species recorded from SK has been updated to 63 species and barcode sequence data is provided for 8 species not previously available on GenBank. Conflict between results from molecular and morphological analyses resulted in the discovery of some potentially new cryptic species and the inability of DNA barcodes to distinguish C. festivipennis Kieffer from C. clastrieri, C. salinarius Kieffer from C. manchuriensis Tokunaga and C. pallidicornis Kieffer from C. subfasciipennis Kieffer. These conflicts suggest further study is required to clarify the status of these species.},
}
@article {pmid25544088,
year = {2014},
author = {Makarchenko, EA and Semenchenko, AA},
title = {Morphological redescription and DNA barcoding of Linevitshia prima Makarchenko, 1987 (Diptera: Chironomidae: Diamesinae) from Amur River basin (Russian Far East), with notes on systematics of the genus.},
journal = {Zootaxa},
volume = {3872},
number = {4},
pages = {355-364},
doi = {10.11646/zootaxa.3872.4.2},
pmid = {25544088},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Chironomidae/anatomy &amp; histology/*classification/*genetics/growth &amp; development ; DNA Barcoding, Taxonomic ; Ecosystem ; Female ; Larva/anatomy &amp; histology/classification/genetics/growth &amp; development ; Male ; Organ Size ; Pupa/anatomy &amp; histology/classification/genetics/growth &amp; development ; Russia ; },
abstract = {Additions and corrections to the diagnosis of the genus Linevitshia for male adult, pupa and larva are given, and systematic position of the genus is discussed. Illustrated redescription of adult male and first description of 4[th] instar larva of L. prima Makarchenko from Amur River basin are provided. Comparison of data based on a new material with those of L. yezoensis Endo showed that the latter name is a junior synonym of L. prima. The species-specificity of L. prima COI sequences is analyzed and the sequences are presented as diagnostic characters-molecular markers of L. prima.},
}
@article {pmid25544070,
year = {2014},
author = {Rightmyer, MG and Kono, Y and Kohn, JR and Hung, KL},
title = {A new species of Triepeolus (Hymenoptera: Apidae), with comments on T. utahensis (Cockerell) and T. melanarius Rightmyer.},
journal = {Zootaxa},
volume = {3872},
number = {1},
pages = {48-56},
doi = {10.11646/zootaxa.3872.1.4},
pmid = {25544070},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Bees/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Body Size ; Ecosystem ; Female ; Male ; Organ Size ; Phylogeny ; },
abstract = {Triepeolus matildae Rightmyer, sp. nov., from Mexico (Baja California) and USA (California) is described and both genders are differentiated from the closely related species T. utahensis (Cockerell) using morphological characters. The synonymy of T. utahensis and T. heterurus was established in Rightmyer (2008); however, the younger name was used in that treatment, an error that is corrected herein. Males of both T. matildae and T. utahensis are additionally differentiated from T. melanarius Rightmyer, which is morphologically similar in that gender only. DNA barcoding evidence supporting the recognition of the new species is additionally presented.},
}
@article {pmid25543945,
year = {2014},
author = {Kehlmaier, C},
title = {A new Lampromyia Macquart from Europe (Diptera: Vermileonidae).},
journal = {Zootaxa},
volume = {3887},
number = {4},
pages = {481-493},
doi = {10.11646/zootaxa.3887.4.6},
pmid = {25543945},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Diptera/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Ecosystem ; Europe ; Female ; Male ; Organ Size ; Phylogeny ; },
abstract = {Lampromyia bellasiciliae sp. n. is described from Sicily, Italy. The new species belongs to the pallida subgroup and is differentiated from related taxa in a dichotomous identification key. DNA barcodes for eight of the currently recognised ten Palaearctic species of Lampromyia are provided, and the calculated genetic distances between the taxa and species groups/subgroups are discussed. New distributional data for additional species of Lampromyia are presented and the occurrence of the Palaearctic taxa is depicted in a distribution map.},
}
@article {pmid25543933,
year = {2014},
author = {Görföl, T and Csorba, G and Eger, JL and Son, NT and Francis, CM},
title = {Canines make the difference: a new species of Hypsugo (Chiroptera: Vespertilionidae) from Laos and Vietnam.},
journal = {Zootaxa},
volume = {3887},
number = {2},
pages = {239-250},
doi = {10.11646/zootaxa.3887.2.6},
pmid = {25543933},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; Chiroptera/*anatomy &amp; histology/*classification/physiology ; Cuspid/*anatomy &amp; histology ; Laos ; Species Specificity ; Vietnam ; },
abstract = {Hypsugo was regarded as a subgenus of Pipistrellus by many authors, but its generic distinctiveness is now widely accepted. According to recent taxonomic arrangements, nine species are known to occur in Southeast Asia. During the investigation of material recently collected from Lao PDR and Vietnam we identified an additional species and hence describe it here as Hypsugo dolichodon n. sp. It resembles H. pulveratus, but is larger with conspicuously long canines and differs considerably in the DNA barcode gene sequence.},
}
@article {pmid25543914,
year = {2016},
author = {Huang, Z and Yang, C and Ke, D},
title = {DNA barcoding and molecular phylogeny in Ranidae.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4003-4007},
doi = {10.3109/19401736.2014.989522},
pmid = {25543914},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; *Phylogeny ; Ranidae/classification/*genetics ; },
abstract = {The family Ranidae has the widest distribution compared with other frog family. The phylogeny of the Ranidae is still a matter of dispute. In the present study, we analyzed the COI barcodes of 29 species from six genera belonging to the family Ranidae. Twenty-seven species (93.10% of all the species) were correctly identified by their DNA barcodes. Pelophylax lessonae and Pelophylax ridibundus shared the same one barcode sequence. Kimura two-parameter distances were calculated between barcodes. Pair-wise comparisons among-species were distributed from 0.16% (between Pelophylax lessonae and Pelophylax esculenta) to 29.13% (between Rana warszewitschii and Rana dybowskii). The average genetic distance between species was 28 times higher than the average genetic distance within species. The neighbor-joining method was used to construct a phylogenetic tree, which grouped all the genera into two divergent clades. The results indicated that some currently recognized genera of Ranidae may not be monophyletic. COI gene data supported the hypothesis of polyphyly for Rana, Amolops, Babina, and Hylarana. DNA barcoding is an effective molecular tool for Ranidae species identification and phylogenetic inference.},
}
@article {pmid25543856,
year = {2015},
author = {Rane, TD and Zec, HC and Wang, TH},
title = {A barcode-free combinatorial screening platform for matrix metalloproteinase screening.},
journal = {Analytical chemistry},
volume = {87},
number = {3},
pages = {1950-1956},
pmid = {25543856},
issn = {1520-6882},
support = {R01 CA155305/CA/NCI NIH HHS/United States ; R21 CA173390/CA/NCI NIH HHS/United States ; R01CA155305/CA/NCI NIH HHS/United States ; R21CA173390/CA/NCI NIH HHS/United States ; },
mesh = {Enzyme Assays/*instrumentation ; Equipment Design ; Matrix Metalloproteinases/analysis/*metabolism ; Microfluidic Analytical Techniques/*instrumentation ; },
abstract = {Application of droplet microfluidics to combinatorial screening applications remains elusive because of the need for composition-identifying unique barcodes. Here we propose a barcode-free continuous flow droplet microfluidic platform to suit the requirements of combinatorial screening applications. We demonstrate robust and repeatable functioning of this platform with matrix metalloproteinase activity screening as a sample application.},
}
@article {pmid25543808,
year = {2014},
author = {Lis, JA and Lis, B and Ziaja, DJ and Dobosz, R},
title = {Description and DNA barcoding of Ochetostethomorpha secunda, a new species of the South African endemic burrower bug genus (Hemiptera: Heteroptera: Cydnidae) from Namibia.},
journal = {Zootaxa},
volume = {3884},
number = {6},
pages = {561-566},
doi = {10.11646/zootaxa.3884.6.4},
pmid = {25543808},
issn = {1175-5334},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Female ; Heteroptera/anatomy &amp; histology/*classification/*genetics/physiology ; Male ; Molecular Sequence Data ; Namibia ; },
abstract = {Ochetostethomorpha secunda sp. nov. from Namibia, the second species of the South African endemic genus is described, illustrated, and compared with O. nollothensis Schumacher, 1913. The new species is the third of the subfamily Sehirinae known from Namibia. Moreover, a DNA barcode sequence was generated for this new species (827 bp of cytochrome oxidase I) and was deposited in GenBank.},
}
@article {pmid25543775,
year = {2014},
author = {Sim, KA and Buddle, CM and Wheeler, TA},
title = {Species boundaries of Pardosa concinna and P. lapponica (Araneae: Lycosidae) in the northern Nearctic: morphology and DNA barcodes.},
journal = {Zootaxa},
volume = {3884},
number = {2},
pages = {169-178},
doi = {10.11646/zootaxa.3884.2.5},
pmid = {25543775},
issn = {1175-5334},
mesh = {*Animal Distribution ; Animals ; Canada ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Female ; Haplotypes ; Male ; Phylogeny ; Species Specificity ; Spiders/*anatomy &amp; histology/*classification/genetics/physiology ; },
abstract = {The Holarctic Pardosa lapponica (Thorell, 1872) and the Nearctic P. concinna (Thorell, 1877) are the only North American members of the Pardosa lapponica species-group. The morphological similarity between the two species raises the question of whether or not they should be treated as separate species. To examine the boundary between P. lapponica and P. concinna, morphological and genetic variation within and between the species was analysed. Copulatory organ characters of Nearctic specimens were analysed to determine if additional diagnostic characters exist, and the mtDNA COI region was sequenced to look for species-specific variation. Morphometric analysis of copulatory characters in females (e.g. length of median septum) and males (e.g. embolus length) of both species did not reveal diagnostic characters other than the terminal apophysis. No species-specific genetic patterns were found between the two species. The interspecific similarities in morphology and low genetic divergence between Nearctic specimens of P. lapponica and P. concinna contrasts with high genetic divergence between Palearctic and Nearctic specimens of P. lapponica. The results suggest a comprehensive taxonomic revision is necessary for the P. lapponica species-group.},
}
@article {pmid25541991,
year = {2014},
author = {Huemer, P and Mutanen, M and Sefc, KM and Hebert, PD},
title = {Testing DNA barcode performance in 1000 species of European lepidoptera: large geographic distances have small genetic impacts.},
journal = {PloS one},
volume = {9},
number = {12},
pages = {e115774},
pmid = {25541991},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; *Geography ; Lepidoptera/*classification ; },
abstract = {This study examines the performance of DNA barcodes (mt cytochrome c oxidase 1 gene) in the identification of 1004 species of Lepidoptera shared by two localities (Finland, Austria) that are 1600 km apart. Maximum intraspecific distances for the pooled data were less than 2% for 880 species (87.6%), while deeper divergence was detected in 124 species. Despite such variation, the overall DNA barcode library possessed diagnostic COI sequences for 98.8% of the taxa. Because a reference library based on Finnish specimens was highly effective in identifying specimens from Austria, we conclude that barcode libraries based on regional sampling can often be effective for a much larger area. Moreover, dispersal ability (poor, good) and distribution patterns (disjunct, fragmented, continuous, migratory) had little impact on levels of intraspecific geographic divergence. Furthermore, the present study revealed that, despite the intensity of past taxonomic work on European Lepidoptera, nearly 20% of the species shared by Austria and Finland require further work to clarify their status. Particularly discordant BIN (Barcode Index Number) cases should be checked to ascertain possible explanatory factors such as incorrect taxonomy, hybridization, introgression, and Wolbachia infections.},
}
@article {pmid25541974,
year = {2014},
author = {Miller, JA and Miller, JH and Pham, DS and Beentjes, KK},
title = {Cyberdiversity: improving the informatic value of diverse tropical arthropod inventories.},
journal = {PloS one},
volume = {9},
number = {12},
pages = {e115750},
pmid = {25541974},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic ; Informatics/*methods ; Internet ; Spiders/*classification ; *Tropical Climate ; },
abstract = {In an era of biodiversity crisis, arthropods have great potential to inform conservation assessment and test hypotheses about community assembly. This is because their relatively narrow geographic distributions and high diversity offer high-resolution data on landscape-scale patterns of biodiversity. However, a major impediment to the more widespread application of arthropod data to a range of scientific and policy questions is the poor state of modern arthropod taxonomy, especially in the tropics. Inventories of spiders and other megadiverse arthropods from tropical forests are dominated by undescribed species. Such studies typically organize their data using morphospecies codes, which make it difficult for data from independent inventories to be compared and combined. To combat this shortcoming, we offer cyberdiversity, an online community-based approach for reconciling results of independent inventory studies where current taxonomic knowledge is incomplete. Participating scientists can upload images and DNA barcode sequences to dedicated databases and submit occurrence data and links to a web site (www.digitalSpiders.org). Taxonomic determinations can be shared with a crowdsourcing comments feature, and researchers can discover specimens of interest available for loan and request aliquots of genomic DNA extract. To demonstrate the value of the cyberdiversity framework, we reconcile data from three rapid structured inventories of spiders conducted in Vietnam with an independent inventory (Doi Inthanon, Thailand) using online image libraries. Species richness and inventory completeness were assessed using non-parametric estimators. Community similarity was evaluated using a novel index based on the Jaccard replacing observed with estimated values to correct for unobserved species. We use a distance-decay framework to demonstrate a rudimentary model of landscape-scale changes in community composition that will become increasingly informative as additional inventories participate. With broader adoption of the cyberdiversity approach, networks of information-sharing taxonomists can more efficiently and effectively address taxonomic impediments while elucidating landscape scale patterns of biodiversity.},
}
@article {pmid25535946,
year = {2015},
author = {Harrup, LE and Bellis, GA and Balenghien, T and Garros, C},
title = {Culicoides Latreille (Diptera: Ceratopogonidae) taxonomy: current challenges and future directions.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {30},
number = {},
pages = {249-266},
pmid = {25535946},
issn = {1567-7257},
mesh = {Animals ; Biological Evolution ; *Ceratopogonidae/anatomy &amp; histology/classification/genetics ; Genome, Insect/genetics ; Genomics ; Phylogeny ; Wings, Animal/anatomy &amp; histology ; },
abstract = {Culicoides Latreille biting midges (Diptera: Ceratopogonidae) cause a significant biting nuisance to humans, livestock and equines, and are the biological vectors of a range of internationally important pathogens of both veterinary and medical importance. Despite their economic significance, the delimitation and identification of species and evolutionary relationships between species within this genus remains at best problematic. To date no phylogenetic study has attempted to validate the subgeneric classification of the genus and the monophyly of many of the subgenera remains doubtful. Many informal species groupings are also known to exist but few are adequately described, further complicating accurate identification. Recent contributions to Culicoides taxonomy at the species level have revealed a high correlation between morphological and molecular analyses although molecular analyses are revealing the existence of cryptic species. This review considers the methods for studying the systematics of Culicoides using both morphological and genetic techniques, with a view to understanding the factors limiting our current understanding of Culicoides biology and hence arbovirus epidemiology. In addition, we examine the global status of Culicoides identification, highlighting areas that are poorly addressed, including the potential implementation of emerging technologies.},
}
@article {pmid25535487,
year = {2014},
author = {Salmela, J and Kaunisto, KM and Vahtera, V},
title = {Unveiling of a cryptic Dicranomyia (Idiopyga) from northern Finland using integrative approach (Diptera, Limoniidae).},
journal = {Biodiversity data journal},
volume = {},
number = {2},
pages = {e4238},
pmid = {25535487},
issn = {1314-2828},
abstract = {The subgenus Idiopyga Savchenko, 1987 is a northern hemisphere group of short-palped crane flies (Diptera, Limoniidae). In the current article we describe a new species, Dicranomyia (I.) boreobaltica Salmela sp.n., and redescribe the male and female post-abdomen of a closely related species, D. (I.) intricata Alexander. A standard DNA barcoding fragment of 5' region of the cytochrome c oxidase I (COI) gene of the new species is presented, whilst the K2P minimum distances between the new species and 10 other species of the subgenus were found to range from 5.1 to 15.7 % (mean 11.2 %). Phylogenetic analyses (parsimony and maximum likelihood) based on COI sequences support the identity of the new species and its close relationship with D. (I.) intricata and D. (I.) esbeni (Nielsen). The new species is known from the northern Baltic area of Finland. The new species has been mostly collected from Baltic coastal meadows but an additional relict population is known from a calcareous rich fen that was estimated to have been at sea level circa 600-700 years ago. Dicranomyia (I.) intricata (syn. D.suecica Nielsen) is a Holarctic species, occurring in the north boreal and subarctic vegetation zones in Fennoscandia.},
}
@article {pmid25532760,
year = {2014},
author = {Nguyen, LV and Cox, CL and Eirew, P and Knapp, DJ and Pellacani, D and Kannan, N and Carles, A and Moksa, M and Balani, S and Shah, S and Hirst, M and Aparicio, S and Eaves, CJ},
title = {DNA barcoding reveals diverse growth kinetics of human breast tumour subclones in serially passaged xenografts.},
journal = {Nature communications},
volume = {5},
number = {},
pages = {5871},
pmid = {25532760},
issn = {2041-1723},
support = {//Canadian Institutes of Health Research/Canada ; },
mesh = {Animals ; Breast Neoplasms/*genetics/physiopathology ; Cell Line, Tumor ; *Cell Proliferation ; Clone Cells ; DNA Barcoding, Taxonomic ; Female ; Humans ; Kinetics ; Mice ; Neoplasm Transplantation ; Tumor Cells, Cultured ; },
abstract = {Genomic and phenotypic analyses indicate extensive intra- as well as intertumoral heterogeneity in primary human malignant cell populations despite their clonal origin. Cellular DNA barcoding offers a powerful and unbiased alternative to track the number and size of multiple subclones within a single human tumour xenograft and their response to continued in vivo passaging. Using this approach we find clone-initiating cell frequencies that vary from ~1/10 to ~1/10,000 cells transplanted for two human breast cancer cell lines and breast cancer xenografts derived from three different patients. For the cell lines, these frequencies are negatively affected in transplants of more than 20,000 cells. Serial transplants reveal five clonal growth patterns (unchanging, expanding, diminishing, fluctuating or of delayed onset), whose predominance is highly variable both between and within original samples. This study thus demonstrates the high growth potential and diverse growth properties of xenografted human breast cancer cells.},
}
@article {pmid25531885,
year = {2014},
author = {Huang, Q and Duan, Z and Yang, J and Ma, X and Zhan, R and Xu, H and Chen, W},
title = {SNP typing for germplasm identification of Amomum villosum Lour. Based on DNA barcoding markers.},
journal = {PloS one},
volume = {9},
number = {12},
pages = {e114940},
pmid = {25531885},
issn = {1932-6203},
mesh = {Amomum/*genetics ; Base Sequence ; Cytoplasm/metabolism ; DNA Barcoding, Taxonomic ; DNA, Plant/metabolism ; Discriminant Analysis ; Genetic Markers ; Genotype ; Phylogeny ; Plant Proteins/classification/genetics ; *Polymorphism, Single Nucleotide ; },
abstract = {Amomum villosum Lour., produced from Yangchun, Guangdong Province, China, is a Daodi medicinal material of Amomi Fructus in traditional Chinese medicine. This herb germplasm should be accurately identified and collected to ensure its quality and safety in medication. In the present study, single nucleotide polymorphism typing method was evaluated on the basis of DNA barcoding markers to identify the germplasm of Amomi Fructus. Genomic DNA was extracted from the leaves of 29 landraces representing three Amomum species (A. villosum Lour., A. xanthioides Wall. ex Baker and A. longiligulare T. L. Wu) by using the CTAB method. Six barcoding markers (ITS, ITS2, LSU D1-D3, matK, rbcL and trnH-psbA) were PCR amplified and sequenced; SNP typing and phylogenetic analysis were performed to differentiate the landraces. Results showed that high-quality bidirectional sequences were acquired for five candidate regions (ITS, ITS2, LSU D1-D3, matK, and rbcL) except trnH-psbA. Three ribosomal regions, namely, ITS, ITS2, and LSU D1-D3, contained more SNP genotypes (STs) than the plastid genes rbcL and matK. In the 29 specimens, 19 STs were detected from the combination of four regions (ITS, LSU D1-D3, rbcL, and matK). Phylogenetic analysis results further revealed two clades. Minimum-spanning tree demonstrated the existence of two main groups: group I was consisting of 9 STs (ST1-8 and ST11) of A. villosum Lour., and group II was composed of 3 STs (ST16-18) of A. longiligulare T.L. Wu. Our results suggested that ITS and LSU D1-D3 should be incorporated with the core barcodes rbcL and matK. The four combined regions could be used as a multiregional DNA barcode to precisely differentiate the Amomi Fructus landraces in different producing areas.},
}
@article {pmid25526752,
year = {2014},
author = {Dong, W and Liu, H and Xu, C and Zuo, Y and Chen, Z and Zhou, S},
title = {A chloroplast genomic strategy for designing taxon specific DNA mini-barcodes: a case study on ginsengs.},
journal = {BMC genetics},
volume = {15},
number = {},
pages = {138},
pmid = {25526752},
issn = {1471-2156},
mesh = {DNA Barcoding, Taxonomic ; Genes, Plant ; Genetic Markers ; *Genome, Chloroplast ; Panax/*genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Universal conventional DNA barcodes will become more and more popular in biological material identifications. However, in many cases such as processed medicines or canned food, the universal conventional barcodes are unnecessary and/or inapplicable due to DNA degradation. DNA mini-barcode is a solution for such specific purposes. Here we exemplify how to develop the best mini-barcodes for specific taxa using the ginseng genus (Panax) as an example.<br><br>RESULTS: The chloroplast genome of P. notoginseng was sequenced. The genome was compared with that of P. ginseng. Regions of the highest variability were sought out. The shortest lengths which had the same discrimination powers of conventional lengths were considered the best mini-barcodes. The results showed that the chloroplast genome of P. notoginseng is 156,387 bp. There are only 464 (0.30%) substitutions between the two genomes. The intron of rps16 and two regions of the coding gene ycf1, ycf1a and ycf1b, evolved the quickest and served as candidate regions. The mini-barcodes of Panax turned out to be 60 bp for ycf1a at a discrimination power of 91.67%, 100 bp for ycf1b at 100%, and 280 bp for rps16 at 83.33%.<br><br>CONCLUSIONS: The strategy by searching the whole chloroplast genomes, identifying the most variable regions, shortening the focal regions for mini-barcodes are believed to be efficient in developing taxon-specific DNA mini-barcodes. The best DNA mini-barcodes are guaranteed to be found following this strategy.},
}
@article {pmid25525788,
year = {2014},
author = {Wu, G and Webby, RJ},
title = {Barcoding influenza virus to decode transmission.},
journal = {Cell host &amp; microbe},
volume = {16},
number = {5},
pages = {559-561},
doi = {10.1016/j.chom.2014.10.016},
pmid = {25525788},
issn = {1934-6069},
mesh = {Animals ; Humans ; Influenza A virus/*pathogenicity ; Influenza, Human/*transmission ; Male ; Orthomyxoviridae Infections/*transmission ; },
abstract = {How much population diversity is transmitted during influenza virus infection? In this issue of Cell Host &amp; Microbe, Varble et al. (2014) report a method of tagging influenza viruses with a unique genetic "barcode" that allows them to be traced through transmission and growth chains, providing a leap forward for the field.},
}
@article {pmid25524896,
year = {2015},
author = {Yoon, H and Leitner, T},
title = {PrimerDesign-M: a multiple-alignment based multiple-primer design tool for walking across variable genomes.},
journal = {Bioinformatics (Oxford, England)},
volume = {31},
number = {9},
pages = {1472-1474},
pmid = {25524896},
issn = {1367-4811},
support = {R01 AI087520/AI/NIAID NIH HHS/United States ; R01AI087520/AI/NIAID NIH HHS/United States ; Y1-AI-8309/AI/NIAID NIH HHS/United States ; },
mesh = {DNA Primers/*chemistry ; Genome, Viral ; Genomics/methods ; HIV-1/genetics ; *Sequence Alignment ; *Sequence Analysis, DNA ; *Software ; },
abstract = {SUMMARY: Analyses of entire viral genomes or mtDNA requires comprehensive design of many primers across their genomes. Furthermore, simultaneous optimization of several DNA primer design criteria may improve overall experimental efficiency and downstream bioinformatic processing. To achieve these goals, we developed PrimerDesign-M. It includes several options for multiple-primer design, allowing researchers to efficiently design walking primers that cover long DNA targets, such as entire HIV-1 genomes, and that optimizes primers simultaneously informed by genetic diversity in multiple alignments and experimental design constraints given by the user. PrimerDesign-M can also design primers that include DNA barcodes and minimize primer dimerization. PrimerDesign-M finds optimal primers for highly variable DNA targets and facilitates design flexibility by suggesting alternative designs to adapt to experimental conditions.<br><br>PrimerDesign-M is available as a webtool at http://www.hiv.lanl.gov/content/sequence/PRIMER_DESIGN/primer_design.html<br><br>CONTACT: tkl@lanl.gov or seq-info@lanl.gov.},
}
@article {pmid25524367,
year = {2015},
author = {Mutanen, M and Kekkonen, M and Prosser, SW and Hebert, PD and Kaila, L},
title = {One species in eight: DNA barcodes from type specimens resolve a taxonomic quagmire.},
journal = {Molecular ecology resources},
volume = {15},
number = {4},
pages = {967-984},
pmid = {25524367},
issn = {1755-0998},
mesh = {Animals ; Computational Biology/*methods ; DNA/*genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Haplotypes ; Lepidoptera/anatomy &amp; histology/*classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {Each holotype specimen provides the only objective link to a particular Linnean binomen. Sequence information from them is increasingly valuable due to the growing usage of DNA barcodes in taxonomy. As type specimens are often old, it may only be possible to recover fragmentary sequence information from them. We tested the efficacy of short sequences from type specimens in the resolution of a challenging taxonomic puzzle: the Elachista dispunctella complex which includes 64 described species with minuscule morphological differences. We applied a multistep procedure to resolve the taxonomy of this species complex. First, we sequenced a large number of newly collected specimens and as many holotypes as possible. Second, we used all >400 bp examine species boundaries. We employed three unsupervised methods (BIN, ABGD, GMYC) with specified criteria on how to handle discordant results and examined diagnostic bases from each delineated putative species (operational taxonomic units, OTUs). Third, we evaluated the morphological characters of each OTU. Finally, we associated short barcodes from types with the delineated OTUs. In this step, we employed various supervised methods, including distance-based, tree-based and character-based. We recovered 658 bp barcode sequences from 194 of 215 fresh specimens and recovered an average of 141 bp from 33 of 42 holotypes. We observed strong congruence among all methods and good correspondence with morphology. We demonstrate potential pitfalls with tree-, distance- and character-based approaches when associating sequences of varied length. Our results suggest that sequences as short as 56 bp can often provide valuable taxonomic information. The results support significant taxonomic oversplitting of species in the Elachista dispunctella complex.},
}
@article {pmid25523342,
year = {2015},
author = {Xia, K and Feng, X and Tong, Y and Wei, GW},
title = {Persistent homology for the quantitative prediction of fullerene stability.},
journal = {Journal of computational chemistry},
volume = {36},
number = {6},
pages = {408-422},
pmid = {25523342},
issn = {1096-987X},
support = {R01 GM090208/GM/NIGMS NIH HHS/United States ; R01GM-090208/GM/NIGMS NIH HHS/United States ; },
mesh = {Fullerenes/*chemistry ; Isomerism ; *Models, Molecular ; Molecular Conformation ; Quantum Theory ; Thermodynamics ; },
abstract = {Persistent homology is a relatively new tool often used for qualitative analysis of intrinsic topological features in images and data originated from scientific and engineering applications. In this article, we report novel quantitative predictions of the energy and stability of fullerene molecules, the very first attempt in using persistent homology in this context. The ground-state structures of a series of small fullerene molecules are first investigated with the standard Vietoris-Rips complex. We decipher all the barcodes, including both short-lived local bars and long-lived global bars arising from topological invariants, and associate them with fullerene structural details. Using accumulated bar lengths, we build quantitative models to correlate local and global Betti-2 bars, respectively with the heat of formation and total curvature energies of fullerenes. It is found that the heat of formation energy is related to the local hexagonal cavities of small fullerenes, while the total curvature energies of fullerene isomers are associated with their sphericities, which are measured by the lengths of their long-lived Betti-2 bars. Excellent correlation coefficients (>0.94) between persistent homology predictions and those of quantum or curvature analysis have been observed. A correlation matrix based filtration is introduced to further verify our findings.},
}
@article {pmid25522875,
year = {2015},
author = {Dan, S and Kang, B and Duan, X and Wang, YJ},
title = {A cell-free system toward deciphering the post-translational modification barcodes of Oct4 in different cellular contexts.},
journal = {Biochemical and biophysical research communications},
volume = {456},
number = {3},
pages = {714-720},
doi = {10.1016/j.bbrc.2014.12.043},
pmid = {25522875},
issn = {1090-2104},
mesh = {Amino Acid Sequence ; Cell-Free System ; Escherichia coli ; Humans ; Metabolic Networks and Pathways ; Molecular Sequence Data ; Octamer Transcription Factor-3/biosynthesis/genetics/*metabolism ; Phosphorylation ; Protein Biosynthesis ; Protein Kinases/metabolism ; *Protein Processing, Post-Translational ; Recombinant Proteins/biosynthesis/genetics/metabolism ; },
abstract = {The octamer-binding transcription factor 4 (Oct4) is essential for maintaining the self-renewal and pluripotency of embryonic stem cells (ESCs). Post-translational modifications (PTMs) of Oct4 critically control its structure, function and intracellular localization. However, determination of Oct4 PTM profiles has largely been restricted by the quantity and purity of the Oct4 protein samples required for mass spectrometric analyses. In this study, by incubating the Escherichia coli-derived His-tagged Oct4 proteins with the whole cell lysates of a variety of human cells followed by retrieving the reacted Oct4 proteins with the Ni-NTA beads, we developed a labor- and cost-effective in vitro PTM method that allowed for mass spectrometric determination of the phosphorylation profiles of Oct4 proteins exposed to various cell-free systems. A number of Oct4 phosphorylation sites that were commonly present in all the cell-free systems or specifically present in a particular cellular context were identified, indicating that Oct4 is controlled by both common and distinct PTM regulatory pathways. Our work provided a proof-of-concept that such a cell-free system-based in vitro PTM approach can be applied to systematically map out the physiologically-relevant PTM sites in Oct4 proteins, which opened up an avenue to fully decipher the Oct4 PTM barcodes in various cellular contexts.},
}
@article {pmid25522780,
year = {2015},
author = {Assad, ON and Di Fiori, N and Squires, AH and Meller, A},
title = {Two color DNA barcode detection in photoluminescence suppressed silicon nitride nanopores.},
journal = {Nano letters},
volume = {15},
number = {1},
pages = {745-752},
pmid = {25522780},
issn = {1530-6992},
support = {R01 HG005871/HG/NHGRI NIH HHS/United States ; R01HG-005871/HG/NHGRI NIH HHS/United States ; },
mesh = {DNA/*chemistry ; *Luminescent Measurements ; *Membranes, Artificial ; *Nanopores ; Signal-To-Noise Ratio ; },
abstract = {Optical sensing of solid-state nanopores is a relatively new approach that can enable high-throughput, multicolor readout from a collection of nanopores. It is therefore highly attractive for applications such as nanopore-based DNA sequencing and genotyping using DNA barcodes. However, to date optical readout has been plagued by the need to achieve sufficiently high signal-to-noise ratio (SNR) for single fluorophore sensing, while still maintaining millisecond resolution. One of the main factors degrading the optical SNR in solid-state nanopores is the high photoluminescence (PL) background emanating from the silicon nitride (SiNx) membrane in which pores are commonly fabricated. Focusing on the optical properties of SiNx nanopores we show that the local membrane PL intensity is substantially reduced, and its spectrum is shifted toward shorter wavelengths with increasing e-beam dose. This phenomenon, which is correlated with a marked photocurrent enhancement in these nanopores, is utilized to perform for the first time single molecule fluorescence detection using both green and red laser excitations. Specifically, the reduction in PL and the concurrent measurement of the nanopore photocurrent enhancement allow us to maximize the background suppression and to detect a dual color, five-unit DNA barcode with high SNR levels.},
}
@article {pmid25512849,
year = {2014},
author = {Arroyave, J and Stiassny, ML},
title = {DNA barcoding reveals novel insights into pterygophagy and prey selection in distichodontid fishes (Characiformes: Distichodontidae).},
journal = {Ecology and evolution},
volume = {4},
number = {23},
pages = {4534-4542},
pmid = {25512849},
issn = {2045-7758},
abstract = {DNA barcoding was used to investigate dietary habits and prey selection in members of the African-endemic family Distichodontidae noteworthy for displaying highly specialized ectoparasitic fin-eating behaviors (pterygophagy). Fin fragments recovered from the stomachs of representatives of three putatively pterygophagous distichodontid genera (Phago, Eugnathichthys, and Ichthyborus) were sequenced for the mitochondrial gene co1. DNA barcodes (co1 sequences) were then used to identify prey items in order to determine whether pterygophagous distichodontids are opportunistic generalists or strict specialists with regard to prey selection and, whether as previously proposed, aggressive mimicry is used as a strategy for successful pterygophagy. Our findings do not support the hypothesis of aggressive mimicry suggesting instead that, despite the possession of highly specialized trophic anatomies, fin-eating distichodontids are opportunistic generalists, preying on fishes from a wide phylogenetic spectrum and to the extent of engaging in cannibalism. This study demonstrates how DNA barcoding can be used to shed light on evolutionary and ecological aspects of highly specialized ectoparasitic fin-eating behaviors by enabling the identification of prey species from small pieces of fins found in fish stomachs.},
}
@article {pmid25510397,
year = {2015},
author = {Kundu, S and Ghosh, SK},
title = {Trend of different molecular markers in the last decades for studying human migrations.},
journal = {Gene},
volume = {556},
number = {2},
pages = {81-90},
doi = {10.1016/j.gene.2014.12.023},
pmid = {25510397},
issn = {1879-0038},
mesh = {Animals ; Chromosomes, Human, Y/*genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genetic Markers ; Genetic Variation ; *Human Migration ; Humans ; Phylogeography ; Selection, Genetic ; Sequence Analysis, DNA/economics/*methods ; },
abstract = {Anatomically modern humans are known to have widely migrated throughout history. Different scientific evidences suggest that the entire human population descended from just several thousand African migrants. About 85,000 years ago, the first wave of human migration was out of Africa, that followed the coasts through the Middle East, into Southern Asia via Sri Lanka, and in due course around Indonesia and into Australia. Another wave of migration between 40,000 and 12,000 years ago brought humans northward into Europe. However, the frozen north limited human expansion in Europe, and created a land bridge, "Bering land bridge", connecting Asia with North America about 25,000 years ago. Although fossil data give the most direct information about our past, it has certain anomalies. So, molecular archeologists are now using different molecular markers to trace the "most recent common ancestor" and also the migration pattern of modern humans. In this study, we have studied the trend of molecular markers and also the methodologies implemented in the last decades (2003-2014). From our observation, we can say that D-loop region of mtDNA and Y chromosome based markers are predominant. Nevertheless, mtDNA, especially the D-loop region, has some unique features, which makes it a more effective marker for tracing prehistoric footprints of modern human populations. Although, natural selection should also be taken into account in studying mtDNA based human migration. As per technology is concerned, Sanger sequencing is the major technique that is being used in almost all studies. But, the emergence of different cost-effective-and-easy-to-handle NGS platforms has increased its popularity over Sanger sequencing in studying human migration.},
}
@article {pmid25505841,
year = {2014},
author = {Vivas, CV and Moraes, RC and Alves-Araújo, A and Alves, M and Mariano-Neto, E and van den Berg, C and Gaiotto, FA},
title = {DNA barcoding in Atlantic Forest plants: What is the best marker for Sapotaceae species identification?.},
journal = {Genetics and molecular biology},
volume = {37},
number = {4},
pages = {662-670},
pmid = {25505841},
issn = {1415-4757},
abstract = {The Atlantic Forest is a phytogeographic domain with a high rate of endemism and large species diversity. The Sapotaceae is a botanical family for which species identification in the Atlantic Forest is difficult. An approach that facilitates species identification in the Sapotaceae is urgently needed because this family includes threatened species and valuable timber species. In this context, DNA barcoding could provide an important tool for identifying species in the Atlantic Forest. In this work, we evaluated four plant barcode markers (matK, rbcL, trnH-psbA and the nuclear ribosomal internal transcribed spacer region - ITS) in 80 samples from 26 species of Sapotaceae that occur in the Atlantic Forest. ITS yielded the highest average interspecific distance (0.122), followed by trnH-psbA (0.019), matK (0.008) and rbcL (0.002). For species discrimination, ITS provided the best results, followed by matK, trnH-psbA and rbcL. Furthermore, the combined analysis of two, three or four markers did not result in higher rates of discrimination than obtained with ITS alone. These results indicate that the ITS region is the best option for molecular identification of Sapotaceae species from the Atlantic Forest.},
}
@article {pmid25505839,
year = {2014},
author = {Paim, FG and Brandão, JH and Sampaio, I and de Mello Affonso, PR and Diniz, D},
title = {Genetic identification of bucktooth parrotfish Sparisoma radians (Valenciennes, 1840) (Labridae, Scarinae) by chromosomal and molecular markers.},
journal = {Genetics and molecular biology},
volume = {37},
number = {4},
pages = {646-651},
pmid = {25505839},
issn = {1415-4757},
abstract = {Parrotfishes (Labridae, Scarinae) comprise a large marine fish group of difficult identification, particularly during juvenile phase when the typical morphology and coloration of adults are absent. Therefore, the goal of this study was to test cytogenetic markers and DNA barcoding in the identification of bucktooth parrtotfish Sparisoma radians from the northeastern coast of Brazil. Sequencing of cytochrome c oxidase subunit I (COI) confirmed all studied samples as S. radians, and all showed high similarity (99-100%) with Caribbean populations. The karyotype of this species was divergent from most marine Perciformes, being composed of 2n = 46 chromosomes. These consisted of a large number of metacentric and submetacentric pairs with small amounts of heterochromatin and GC-rich single nucleolar organizer regions (NORs) not syntenic to 5S rDNA clusters. These are the first data about DNA barcoding in parrotfish from the Brazilian province and the first refined chromosomal analysis in Scarinae, providing useful data to a reliable genetic identification of S. radians.},
}
@article {pmid25502890,
year = {2014},
author = {Cabral, V and Znaidi, S and Walker, LA and Martin-Yken, H and Dague, E and Legrand, M and Lee, K and Chauvel, M and Firon, A and Rossignol, T and Richard, ML and Munro, CA and Bachellier-Bassi, S and d'Enfert, C},
title = {Targeted changes of the cell wall proteome influence Candida albicans ability to form single- and multi-strain biofilms.},
journal = {PLoS pathogens},
volume = {10},
number = {12},
pages = {e1004542},
pmid = {25502890},
issn = {1553-7374},
support = {//Wellcome Trust/United Kingdom ; WT088858MA//Wellcome Trust/United Kingdom ; G0400284//Medical Research Council/United Kingdom ; },
mesh = {Biofilms/*growth &amp; development ; Candida albicans/cytology/*physiology ; Cell Adhesion/physiology ; Cell Wall/*physiology ; Fungal Proteins/genetics/*physiology ; Gene Expression Regulation, Fungal/physiology ; Phenotype ; Proteome/genetics/*physiology ; Shear Strength/physiology ; Transcriptome/physiology ; },
abstract = {Biofilm formation is an important virulence trait of the pathogenic yeast Candida albicans. We have combined gene overexpression, strain barcoding and microarray profiling to screen a library of 531 C. albicans conditional overexpression strains (∼10% of the genome) for genes affecting biofilm development in mixed-population experiments. The overexpression of 16 genes increased strain occupancy within a multi-strain biofilm, whereas overexpression of 4 genes decreased it. The set of 16 genes was significantly enriched for those encoding predicted glycosylphosphatidylinositol (GPI)-modified proteins, namely Ihd1/Pga36, Phr2, Pga15, Pga19, Pga22, Pga32, Pga37, Pga42 and Pga59; eight of which have been classified as pathogen-specific. Validation experiments using either individually- or competitively-grown overexpression strains revealed that the contribution of these genes to biofilm formation was variable and stage-specific. Deeper functional analysis of PGA59 and PGA22 at a single-cell resolution using atomic force microscopy showed that overexpression of either gene increased C. albicans ability to adhere to an abiotic substrate. However, unlike PGA59, PGA22 overexpression led to cell cluster formation that resulted in increased sensitivity to shear forces and decreased ability to form a single-strain biofilm. Within the multi-strain environment provided by the PGA22-non overexpressing cells, PGA22-overexpressing cells were protected from shear forces and fitter for biofilm development. Ultrastructural analysis, genome-wide transcript profiling and phenotypic analyses in a heterologous context suggested that PGA22 affects cell adherence through alteration of cell wall structure and/or function. Taken together, our findings reveal that several novel predicted GPI-modified proteins contribute to the cooperative behaviour between biofilm cells and are important participants during C. albicans biofilm formation. Moreover, they illustrate the power of using signature tagging in conjunction with gene overexpression for the identification of novel genes involved in processes pertaining to C. albicans virulence.},
}
@article {pmid25501246,
year = {2014},
author = {Naeem, A and Khan, AA and Cheema, HM and Khan, IA and Buerkert, A},
title = {DNA barcoding for species identification in the Palmae family.},
journal = {Genetics and molecular research : GMR},
volume = {13},
number = {4},
pages = {10341-10348},
doi = {10.4238/2014.December.4.29},
pmid = {25501246},
issn = {1676-5680},
mesh = {Arecaceae/*genetics ; DNA/genetics ; *DNA Barcoding, Taxonomic ; Endoribonucleases/*genetics ; Genetic Variation ; Nucleotidyltransferases/*genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; Species Specificity ; },
abstract = {DNA barcoding is a promising tool for species identification at the molecular level. The barcoding system is well established for species differentiation in animals, while it is less common in plants. We evaluated 2 barcoding regions, maturase K (matK) and ribulose bisphosphate carboxylase (rbcL), to compare species of Palmae according to amplification success, discrimination power, and inter- and intra-specific divergence. Both regions appear to have potential to discriminate most species of Palmae, but 2 species, Phoenix dactylifera and Phoenix sylvestris, did not show variation in the nucleotides of the barcode genes. P. sylvestris is said to be the sister species of P. dactilyfera according to its morphological and genetic proximity to the cultivated date palm. Thus, the status of these 2 species needs to be re-evaluated considering more genes as barcodes. Furthermore, rbcL has a higher discrimination power (90%) than matK (66.6%) and can thus be potentially used as a standard barcode to discriminate the species of Palmae.},
}
@article {pmid25499083,
year = {2014},
author = {Ergunay, K and Kasap, OE and Orsten, S and Oter, K and Gunay, F and Yoldar, AZ and Dincer, E and Alten, B and Ozkul, A},
title = {Phlebovirus and Leishmania detection in sandflies from eastern Thrace and northern Cyprus.},
journal = {Parasites &amp; vectors},
volume = {7},
number = {},
pages = {575},
pmid = {25499083},
issn = {1756-3305},
mesh = {Animals ; Cyprus ; Insect Vectors/*parasitology/*virology ; Leishmania/classification/genetics/*isolation &amp; purification ; Molecular Sequence Data ; Phlebotomus/*parasitology/*virology ; Phlebovirus/classification/genetics/*isolation &amp; purification ; Phylogeny ; Turkey ; },
abstract = {BACKGROUND: Phlebotomine sandflies are vectors of several pathogens with significant impact for public health. This study was conducted to investigate and characterize phlebovirus and Leishmania infections in vector sandflies collected in the eastern Thrace region in Turkey and Northern Cyprus, where previous data indicate activity of these agents.<br><br>METHODS: Field sampling of sandflies was performed at 4 locations in Edirne and Tekirdag provinces of eastern Thrace and at 17 locations in Lefkosa, Girne, Magosa and Guzelyurt provinces of northern Cyprus. In sandfly pools, phlebovirus RNA and Leishmania DNA were screened via a generic polymerase chain reaction (PCR) and kinetoplast minicircle PCR, respectively. Selected sandfly specimens unsuitable for pathogen detection were identified to species level. Cytochrome oxidase 1 gene region was used for DNA barcoding of selected specimens and pathogen positive pools. Positive amplicons were cloned and characterized by sequencing.<br><br>RESULTS: A total of 2690 sandflies, collected from Eastern Thrace (15.4%) and Northern Cyprus (84.6%) were evaluated. Morphological examination of 780 specimens from Cyprus exhibited Phlebotomus perfiliewi sensu lato (72.6%), Phlebotomus tobbi (19.7%), Phlebotomus papatasi (2.8%), Laroussius sp. (1.6%) and Sergentomyia azizi (1.6%), Sergentomyia sp. (0.9%), Sergentomyia minuta (0.5%) and Phleobotomus jacusieli (0.1%) species. Pathogen screening was performed in 1910 specimens distributed in 195 pools. In eight pools of P.tobbi sandflies collected in Cyprus, Leishmania infantum DNA was demonstrated. Toscana virus (TOSV) genotype A sequences were identified in two pools of P. perfiliewi s.l. and one pool of P.tobbi sandflies from Cyprus. Co-infection of TOSV and Leishmania infantum was characterized in a P.tobbi pool. Sequences belonging to novel phleboviruses are revealed in three P. perfiliewi s.l. pools. One sequence, provisionally named Edirne virus, identified in Edirne province in eastern Thrace, demonstrated the highest rate of genomic similarity to Adria and Salehabad viruses. Furthermore, Girne 1 and Girne 2 viruses, identified in Girne province, revealed similarities to TOSV and Sandfly Fever Sicilian virus and related strains, respectively.<br><br>CONCLUSIONS: Activity of TOSV genotype A strains in Cyprus and co-infection of sandfly vectors with L. infantum was documented for the first time. Novel phlebovirus strains of unknown medical significance was identified in sampling regions.},
}
@article {pmid25498759,
year = {2014},
author = {Chan, A and Chiang, LP and Hapuarachchi, HC and Tan, CH and Pang, SC and Lee, R and Lee, KS and Ng, LC and Lam-Phua, SG},
title = {DNA barcoding: complementing morphological identification of mosquito species in Singapore.},
journal = {Parasites &amp; vectors},
volume = {7},
number = {},
pages = {569},
pmid = {25498759},
issn = {1756-3305},
mesh = {Animal Distribution ; Animals ; Culicidae/classification/*genetics/physiology ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics/metabolism ; Gene Expression Regulation, Enzymologic ; Mitochondria/enzymology ; Phylogeny ; Singapore ; },
abstract = {BACKGROUND: Taxonomy that utilizes morphological characteristics has been the gold standard method to identify mosquito species. However, morphological identification is challenging when the expertise is limited and external characters are damaged because of improper specimen handling. Therefore, we explored the applicability of mitochondrial cytochrome C oxidase subunit 1 (COI) gene-based DNA barcoding as an alternative tool to identify mosquito species. In the present study, we compared the morphological identification of mosquito specimens with their differentiation based on COI barcode, in order to establish a more reliable identification system for mosquito species found in Singapore.<br><br>METHODS: We analysed 128 adult mosquito specimens, belonging to 45 species of 13 genera. Phylogenetic trees were constructed for Aedes, Anopheles, Culex and other genera of mosquitoes and the distinctive clustering of different species was compared with their taxonomic identity.<br><br>RESULTS: The COI-based DNA barcoding achieved a 100% success rate in identifying the mosquito species. We also report COI barcode sequences of 16 mosquito species which were not available previously in sequence databases.<br><br>CONCLUSIONS: Our study utilised for the first time DNA barcoding to identify mosquito species in Singapore. COI-based DNA barcoding is a useful tool to complement taxonomy-based identification of mosquito species.},
}
@article {pmid25497983,
year = {2015},
author = {Huang, L and Zheng, L and Chen, Y and Xue, F and Cheng, L and Adeloju, SB and Chen, W},
title = {A novel GMO biosensor for rapid ultrasensitive and simultaneous detection of multiple DNA components in GMO products.},
journal = {Biosensors &amp; bioelectronics},
volume = {66},
number = {},
pages = {431-437},
doi = {10.1016/j.bios.2014.12.005},
pmid = {25497983},
issn = {1873-4235},
mesh = {Biosensing Techniques/*methods/statistics &amp; numerical data ; DNA Probes ; DNA, Recombinant/*analysis/*genetics ; Food Technology ; *Food, Genetically Modified ; Gold ; Metal Nanoparticles ; Nucleic Acid Amplification Techniques ; Organisms, Genetically Modified/*genetics ; Oxidation-Reduction ; },
abstract = {Since the introduction of genetically modified organisms (GMOs), there has been on-going and continuous concern and debates on the commercialization of products derived from GMOs. There is an urgent need for development of highly efficient analytical methods for rapid and high throughput screening of GMOs components, as required for appropriate labeling of GMO-derived foods, as well as for on-site inspection and import/export quarantine. In this study, we describe, for the first time, a multi-labeling based electrochemical biosensor for simultaneous detection of multiple DNA components of GMO products on the same sensing interface. Two-round signal amplification was applied by using both an exonuclease enzyme catalytic reaction and gold nanoparticle-based bio-barcode related strategies, respectively. Simultaneous multiple detections of different DNA components of GMOs were successfully achieved with satisfied sensitivity using this electrochemical biosensor. Furthermore, the robustness and effectiveness of the proposed approach was successfully demonstrated by application to various GMO products, including locally obtained and confirmed commercial GMO seeds and transgenetic plants. The proposed electrochemical biosensor demonstrated unique merits that promise to gain more interest in its use for rapid and on-site simultaneous multiple screening of different components of GMO products.},
}
@article {pmid25495290,
year = {2014},
author = {Little, DP},
title = {Authentication of Ginkgo biloba herbal dietary supplements using DNA barcoding.},
journal = {Genome},
volume = {57},
number = {9},
pages = {513-516},
doi = {10.1139/gen-2014-0130},
pmid = {25495290},
issn = {1480-3321},
mesh = {DNA Barcoding, Taxonomic/*methods ; *Dietary Supplements ; Ginkgo biloba/classification/*genetics ; },
abstract = {Ginkgo biloba L. (known as ginkgo or maidenhair tree) is a phylogenetically isolated, charismatic, gymnosperm tree. Herbal dietary supplements, prepared from G. biloba leaves, are consumed to boost cognitive capacity via improved blood perfusion and mitochondrial function. A novel DNA mini-barcode assay was designed and validated for the authentication of G. biloba in herbal dietary supplements (n = 22; sensitivity = 1.00, 95% CI = 0.59-1.00; specificity = 1.00, 95% CI = 0.64-1.00). This assay was further used to estimate the frequency of mislabeled ginkgo herbal dietary supplements on the market in the United States of America: DNA amenable to PCR could not be extracted from three (7.5%) of the 40 supplements sampled, 31 of 37 (83.8%) assayable supplements contained identifiable G. biloba DNA, and six supplements (16.2%) contained fillers without any detectable G. biloba DNA. It is hoped that this assay will be used by supplement manufacturers to ensure that their supplements contain G. biloba.},
}
@article {pmid25492984,
year = {2014},
author = {Houbraken, J and Visagie, CM and Meijer, M and Frisvad, JC and Busby, PE and Pitt, JI and Seifert, KA and Louis-Seize, G and Demirel, R and Yilmaz, N and Jacobs, K and Christensen, M and Samson, RA},
title = {A taxonomic and phylogenetic revision of Penicillium section Aspergilloides.},
journal = {Studies in mycology},
volume = {78},
number = {},
pages = {373-451},
pmid = {25492984},
issn = {0166-0616},
abstract = {Species belonging to Penicillium section Aspergilloides have a world-wide distribution with P. glabrum, P. spinulosum and P. thomii the most well-known species of this section. These species occur commonly and can be isolated from many substrates including soil, food, bark and indoor environments. The taxonomy of these species has been investigated several times using various techniques, but species delimitation remains difficult. In the present study, 349 strains belonging to section Aspergilloides were subjected to multilocus molecular phylogenetic analyses using partial β-tubulin (BenA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) sequences. Section Aspergilloides is subdivided into 12 clades and 51 species. Twenty-five species are described here as new and P. yezoense, a species originally described without a Latin diagnosis, is validated. Species belonging to section Aspergilloides are phenotypically similar and most have monoverticillate conidiophores and grow moderately or quickly on agar media. The most important characters to distinguish these species were colony sizes on agar media, growth at 30 °C, ornamentation and shape of conidia, sclerotium production and stipe roughness.},
}
@article {pmid25492983,
year = {2014},
author = {Yilmaz, N and Visagie, CM and Houbraken, J and Frisvad, JC and Samson, RA},
title = {Polyphasic taxonomy of the genus Talaromyces.},
journal = {Studies in mycology},
volume = {78},
number = {},
pages = {175-341},
pmid = {25492983},
issn = {0166-0616},
abstract = {The genus Talaromyces was described by Benjamin in 1955 as a sexual state of Penicillium that produces soft walled ascomata covered with interwoven hyphae. Phylogenetic information revealed that Penicillium subgenus Biverticillium and Talaromyces form a monophyletic clade distinct from the other Penicillium subgenera. Subsequently, in combination with the recent adoption of the one fungus one name concept, Penicillium subgenus Biverticillium was transferred to Talaromyces. At the time, the new combinations were made based only on phylogenetic information. As such, the aim of this study was to provide a monograph on Talaromyces applying a polyphasic species concept, including morphological, molecular and physiological characters. Based on an ITS, BenA and RPB2 multigene phylogeny, we propose a new sectional classification for the genus, placing the 88 accepted species into seven sections, named sections Bacillispori, Helici, Islandici, Purpurei, Subinflati, Talaromyces and Trachyspermi. We provide morphological descriptions for each of these species, as well as notes on their identification using morphology and DNA sequences. For molecular identification, BenA is proposed as a secondary molecular marker to the accepted ITS barcode for fungi.},
}
@article {pmid25492981,
year = {2014},
author = {Visagie, CM and Hirooka, Y and Tanney, JB and Whitfield, E and Mwange, K and Meijer, M and Amend, AS and Seifert, KA and Samson, RA},
title = {Aspergillus, Penicillium and Talaromyces isolated from house dust samples collected around the world.},
journal = {Studies in mycology},
volume = {78},
number = {},
pages = {63-139},
pmid = {25492981},
issn = {0166-0616},
abstract = {As part of a worldwide survey of the indoor mycobiota, dust was collected from nine countries. Analyses of dust samples included the culture-dependent dilution-to-extinction method and the culture-independent 454-pyrosequencing. Of the 7 904 isolates, 2 717 isolates were identified as belonging to Aspergillus, Penicillium and Talaromyces. The aim of this study was to identify isolates to species level and describe the new species found. Secondly, we wanted to create a reliable reference sequence database to be used for next-generation sequencing projects. Isolates represented 59 Aspergillus species, including eight undescribed species, 49 Penicillium species of which seven were undescribed and 18 Talaromyces species including three described here as new. In total, 568 ITS barcodes were generated, and 391 β-tubulin and 507 calmodulin sequences, which serve as alternative identification markers.},
}
@article {pmid25492543,
year = {2016},
author = {Feroz Khan, K and Sanker, G and Prasanna Kumar, C},
title = {Linking eggs and adults of Argulus spp. using mitochondrial DNA barcodes.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {3927-3931},
doi = {10.3109/19401736.2014.987269},
pmid = {25492543},
issn = {2470-1408},
mesh = {Animals ; Arguloida/classification/*genetics/growth &amp; development ; Cluster Analysis ; DNA/isolation &amp; purification/metabolism ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*chemistry/isolation &amp; purification/metabolism ; Databases, Genetic ; Electron Transport Complex IV/chemistry/genetics ; Genome, Mitochondrial ; Goldfish/genetics/parasitology ; Ovum/metabolism ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {We have created barcode library for common Argulus spp. infecting Carassius auratus, which could also be used to identify premature forms of Argulus spp. even by non-professionals. Infected C. auratus was examined and purchased from ornamental fish-trading centers and the adult life stage of Argulus spp. was identified and DNA barcoded. The eggs of Argulus spp. were collected using bottle implants. The collected eggs are barcoded and precisely identified by matching with the adult sequences. Four species of adult Argulus spp. were identified, namely Argulus japonicus, Argulus indicus, Argulus siamensis, and Argulus foliaceus. Precise identification of egg samples was done by two different analyses, namely (i) BLAST analysis and (ii) phylogenetic clustering of adults and eggs. All egg samples including the control were precisely identified by BLAST analysis and the results are consistent with phylogenetic clustering of adult and egg's DNA barcodes. In order to establish the DNA barcode technology for the identification of all Argulus spp and its premature forms, the development of full-fledged barcode library that includes all species of this genus is very important for the benefit of ornamental fish industries.},
}
@article {pmid25492536,
year = {2016},
author = {Khedkar, GD and Abhayankar, SB and Nalage, D and Ahmed, SN and Khedkar, CD},
title = {DNA barcode based wildlife forensics for resolving the origin of claw samples using a novel primer cocktail.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {3932-3935},
doi = {10.3109/19401736.2014.987270},
pmid = {25492536},
issn = {2470-1408},
mesh = {Animals ; Conservation of Natural Resources ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/*metabolism ; DNA, Mitochondrial/genetics/metabolism ; Electron Transport Complex IV/chemistry/genetics/metabolism ; Felidae/*genetics ; Forensic Sciences ; Genome, Mitochondrial ; Haplotypes ; Hoof and Claw/*metabolism ; },
abstract = {Excessive wildlife hunting for commercial purposes can have negative impacts on biodiversity and may result in species extinction. To ensure compliance with legal statutes, forensic identification approaches relying on molecular markers may be used to identify the species of origin of animal material from hairs, claw, blood, bone, or meat. Using this approach, DNA sequences from the COI "barcoding" gene have been used to identify material from a number of domesticated animal species. However, many wild species of carnivores still present great challenges in generating COI barcodes using standard "universal" primer pairs. In the work presented here, the mitochondrial COI gene was successfully amplified using a novel primer cocktail, and the products were sequenced to determine the species of twenty one unknown samples of claw material collected as part of forensic wildlife case investigations. Sixteen of the unknown samples were recognized to have originated from either Panthera leo or P. pardus individuals. The remaining five samples could be identified only to the family level due to the absence of reference animal sequences. This is the first report on the use of COI sequences for the identification of P. pardus and P. leo from claw samples as part of forensic investigations in India. The study also highlights the need for adequate reference material to aid in the resolution of suspected cases of illegal wildlife harvesting.},
}
@article {pmid25492149,
year = {2014},
author = {An, C and Sun, Y and Chen, B and Fan, S and Huo, L and She, J and Lyu, W},
title = {[Identification on host animals for plague by DNA barcoding technology in Shaanxi province].},
journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi},
volume = {35},
number = {9},
pages = {1042-1045},
pmid = {25492149},
issn = {0254-6450},
abstract = {OBJECTIVE: To apply the DNA barcoding technology for identification on host animal and to establish the host animal DNA bar code database on natural foci of plague in Shaanxi.<br><br>METHODS: 139 host animals belonging to 3 orders, 6 families and 12 genera and 62 residues belonging to 7 species from 8 different parts of the province, were detected. DNA barcoding technology was used to analyze the DNA CO I gene sequence on the natural foci of plague in Dingbian county.<br><br>RESULTS: The intra-specific genetic distance was less than 2% while the inter-specific distance ranged from 8.9% to 15.1%. Fourteen major clusters were apparently showed on a Neighbor-Joining tree. Residue samples could be detected regarding the objective gene. Alashan ground squirrel was previously noticed to carry 14 major clusters, which were previously mistakenly named as Citellus dauricus in Dingbian county.<br><br>CONCLUSION: DNA barcoding technology could overcome the shortcomings caused by the morphological identification so could be used to identify the host animal and residues in the natural focus of plague.},
}
@article {pmid25490869,
year = {2015},
author = {Van Steenkiste, N and Locke, SA and Castelin, M and Marcogliese, DJ and Abbott, CL},
title = {New primers for DNA barcoding of digeneans and cestodes (Platyhelminthes).},
journal = {Molecular ecology resources},
volume = {15},
number = {4},
pages = {945-952},
doi = {10.1111/1755-0998.12358},
pmid = {25490869},
issn = {1755-0998},
mesh = {Animals ; Cestoda/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/*genetics ; DNA, Helminth/chemistry/genetics ; Electron Transport Complex IV/genetics ; Molecular Sequence Data ; Sequence Analysis, DNA ; Trematoda/*classification/*genetics ; },
abstract = {Digeneans and cestodes are species-rich taxa and can seriously impact human health, fisheries, aqua- and agriculture, and wildlife conservation and management. DNA barcoding using the COI Folmer region could be applied for species detection and identification, but both 'universal' and taxon-specific COI primers fail to amplify in many flatworm taxa. We found that high levels of nucleotide variation at priming sites made it unrealistic to design primers targeting all flatworms. We developed new degenerate primers that enabled acquisition of the COI barcode region from 100% of specimens tested (n = 46), representing 23 families of digeneans and 6 orders of cestodes. This high success rate represents an improvement over existing methods. Primers and methods provided here are critical pieces towards redressing the current paucity of COI barcodes for these taxa in public databases.},
}
@article {pmid25487342,
year = {2015},
author = {Rohland, N and Harney, E and Mallick, S and Nordenfelt, S and Reich, D},
title = {Partial uracil-DNA-glycosylase treatment for screening of ancient DNA.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {370},
number = {1660},
pages = {20130624},
pmid = {25487342},
issn = {1471-2970},
mesh = {Base Sequence ; DNA/*genetics/history ; DNA Barcoding, Taxonomic/methods ; *Fossils ; *Gene Library ; Genetic Testing/*methods ; Genetics, Population/methods ; History, Ancient ; Humans ; Molecular Sequence Data ; Sequence Analysis, DNA/*methods ; Uracil-DNA Glycosidase/*chemistry ; },
abstract = {The challenge of sequencing ancient DNA has led to the development of specialized laboratory protocols that have focused on reducing contamination and maximizing the number of molecules that are extracted from ancient remains. Despite the fact that success in ancient DNA studies is typically obtained by screening many samples to identify a promising subset, ancient DNA protocols have not, in general, focused on reducing the time required to screen samples. We present an adaptation of a popular ancient library preparation method that makes screening more efficient. First, the DNA extract is treated using a protocol that causes characteristic ancient DNA damage to be restricted to the terminal nucleotides, while nearly eliminating it in the interior of the DNA molecules, allowing a single library to be used both to test for ancient DNA authenticity and to carry out population genetic analysis. Second, the DNA molecules are ligated to a unique pair of barcodes, which eliminates undetected cross-contamination from this step onwards. Third, the barcoded library molecules include incomplete adapters of short length that can increase the specificity of hybridization-based genomic target enrichment. The adapters are completed just before sequencing, so the same DNA library can be used in multiple experiments, and the sequences distinguished. We demonstrate this protocol on 60 ancient human samples.},
}
@article {pmid25487333,
year = {2015},
author = {Parducci, L and Väliranta, M and Salonen, JS and Ronkainen, T and Matetovici, I and Fontana, SL and Eskola, T and Sarala, P and Suyama, Y},
title = {Proxy comparison in ancient peat sediments: pollen, macrofossil and plant DNA.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {370},
number = {1660},
pages = {20130382},
pmid = {25487333},
issn = {1471-2970},
mesh = {Base Sequence ; DNA, Plant/classification/*genetics/history ; Finland ; *Fossils ; Geologic Sediments/*chemistry ; History, Ancient ; Molecular Sequence Data ; Multiplex Polymerase Chain Reaction ; Pollen/*genetics ; Russia ; Sequence Analysis, DNA/methods ; Soil/*chemistry ; },
abstract = {We compared DNA, pollen and macrofossil data obtained from Weichselian interstadial (age more than 40 kyr) and Holocene (maximum age 8400 cal yr BP) peat sediments from northern Europe and used them to reconstruct contemporary floristic compositions at two sites. The majority of the samples provided plant DNA sequences of good quality with success amplification rates depending on age. DNA and sequencing analysis provided five plant taxa from the older site and nine taxa from the younger site, corresponding to 7% and 15% of the total number of taxa identified by the three proxies together. At both sites, pollen analysis detected the largest (54) and DNA the lowest (10) number of taxa, but five of the DNA taxa were not detected by pollen and macrofossils. The finding of a larger overlap between DNA and pollen than between DNA and macrofossils proxies seems to go against our previous suggestion based on lacustrine sediments that DNA originates principally from plant tissues and less from pollen. At both sites, we also detected Quercus spp. DNA, but few pollen grains were found in the record, and these are normally interpreted as long-distance dispersal. We confirm that in palaeoecological investigations, sedimentary DNA analysis is less comprehensive than classical morphological analysis, but is a complementary and important tool to obtain a more complete picture of past flora.},
}
@article {pmid25487126,
year = {2014},
author = {Witsenburg, F and Schneider, F and Christe, P},
title = {Epidemiological traits of the malaria-like parasite Polychromophilus murinus in the Daubenton's bat Myotis daubentonii.},
journal = {Parasites &amp; vectors},
volume = {7},
number = {},
pages = {566},
pmid = {25487126},
issn = {1756-3305},
mesh = {Aging ; Animals ; *Chiroptera ; Female ; Haemosporida/*classification ; Male ; Protozoan Infections, Animal/epidemiology/*parasitology ; Risk Factors ; Switzerland/epidemiology ; },
abstract = {BACKGROUND: The great diversity of bat haemosporidians is being uncovered with the help of molecular tools. Yet most of these studies provide only snapshots in time of the parasites discovered. Polychromophilus murinus, a malaria-like blood parasite, specialised on temperate-zone bats is a species that is being 'rediscovered'. This study describes the infection dynamics over time and between host sex and age classes.<br><br>METHODS: For three years we followed the members of three breeding colonies of Myotis daubentonii in Western Switzerland and screened them for the prevalence and parasitemia of P. murinus using both molecular tools and traditional microscopy. In order to identify more susceptible classes of hosts, we measured, sexed and aged all individuals. During one year, we additionally measured body temperature and haematocrit values.<br><br>RESULTS: Juvenile bats demonstrated much higher parasitemia than any other age class sampled, suggesting that first exposure to the parasite is very early in life during which infections are also at their most intense. Moreover, in subadults there was a clear negative correlation between body condition and intensity of infection, whereas a weak positive correlation was observed in adults. Neither body temperature, nor haematocrit, two proxies used for pathology, could be linked to intensities of infection.<br><br>CONCLUSION: If both weaker condition and younger age are associated with higher infection intensity, then the highest selection pressure exerted by P. murinus should be at the juvenile stage. Confusion over the identities and nomenclature of malarial-like parasites requires that molecular barcodes are coupled to accurate morphological descriptions.},
}
@article {pmid25476018,
year = {2015},
author = {Novak, M and Kraševec, N and Skočaj, M and Maček, P and Anderluh, G and Sepčić, K},
title = {Fungal aegerolysin-like proteins: distribution, activities, and applications.},
journal = {Applied microbiology and biotechnology},
volume = {99},
number = {2},
pages = {601-610},
doi = {10.1007/s00253-014-6239-9},
pmid = {25476018},
issn = {1432-0614},
mesh = {Agaricales/*metabolism ; Fungal Proteins/*biosynthesis/genetics ; Genetic Markers ; Hemolysin Proteins/*biosynthesis/genetics ; Promoter Regions, Genetic ; },
abstract = {The aegerolysin protein family (from aegerolysin of the mushroom Agrocybe aegerita) comprises proteins of ∼15-20 kDa from various eukaryotic and bacterial taxa. Aegerolysins are inconsistently distributed among fungal species, and variable numbers of homologs have been reported for species within the same genus. As such noncore proteins, without a member of a protein family in each of the sequenced fungi, they can give insight into different species-specific processes. Some aegerolysins have been reported to be hemolytically active against mammalian erythrocytes. However, some function as bi-component proteins that have membrane activity in concert with another protein that contains a membrane attack complex/perforin domain. The function of most of aegerolysins is unknown, although some have been suggested to have a role in development of the organism. Potential biotechnological applications of aegerolysins are already evident, despite the limited scientific knowledge available at present. Some mushroom aegerolysins, for example, can be used as markers to detect and label specific membrane lipids. Others can be used as biomarkers of fungal exposure, where their genes can serve as targets for detection of fungi and their progression during infectious diseases. Antibodies against aegerolysins can also be raised as immuno-diagnostic tools. Aegerolysins have been shown to serve as a species determination tool for fungal phytopathogen isolates in terms of some closely related species, where commonly used internal transcribed spacer barcoding has failed. Moreover, strong promoters that regulate aegerolysin genes can promote secretion of heterologous proteins from fungi and have been successfully applied in simultaneous multi-gene expression techniques.},
}
@article {pmid25473326,
year = {2014},
author = {Fernandez-Triana, JL and Penev, L and Ratnasingham, S and Smith, MA and Sones, J and Telfer, A and deWaard, JR and Hebert, PD},
title = {Streamlining the use of BOLD specimen data to record species distributions: a case study with ten Nearctic species of Microgastrinae (Hymenoptera: Braconidae).},
journal = {Biodiversity data journal},
volume = {},
number = {2},
pages = {e4153},
pmid = {25473326},
issn = {1314-2828},
abstract = {The Barcode of Life Data Systems (BOLD) is designed to support the generation and application of DNA barcode data, but it also provides a unique source of data with potential for many research uses. This paper explores the streamlining of BOLD specimen data to record species distributions - and its fast publication using the Biodiversity Data Journal (BDJ), and its authoring platform, the Pensoft Writing Tool (PWT). We selected a sample of 630 specimens and 10 species of a highly diverse group of parasitoid wasps (Hymenoptera: Braconidae, Microgastrinae) from the Nearctic region and used the information in BOLD to uncover a significant number of new records (of locality, provinces, territories and states). By converting specimen information (such as locality, collection date, collector, voucher depository) from the BOLD platform to the Excel template provided by the PWT, it is possible to quickly upload and generate long lists of "Material Examined" for papers discussing taxonomy, ecology and/or new distribution records of species. For the vast majority of publications including DNA barcodes, the generation and publication of ancillary data associated with the barcoded material is seldom highlighted and often disregarded, and the analysis of those data sets to uncover new distribution patterns of species has rarely been explored, even though many BOLD records represent new and/or significant discoveries. The introduction of journals specializing in - and streamlining - the release of these datasets, such as the BDJ, should facilitate thorough analysis of these records, as shown in this paper.},
}
@article {pmid25472605,
year = {2015},
author = {Mahajan, V and Sharma, N and Kumar, S and Bhardwaj, V and Ali, A and Khajuria, RK and Bedi, YS and Vishwakarma, RA and Gandhi, SG},
title = {Production of rohitukine in leaves and seeds of Dysoxylum binectariferum: an alternate renewable resource.},
journal = {Pharmaceutical biology},
volume = {53},
number = {3},
pages = {446-450},
doi = {10.3109/13880209.2014.923006},
pmid = {25472605},
issn = {1744-5116},
mesh = {Chromones/*isolation &amp; purification/metabolism ; *Meliaceae/metabolism ; Piperidines/*isolation &amp; purification/metabolism ; Plant Extracts/*isolation &amp; purification/metabolism ; Plant Leaves/*chemistry/metabolism ; Seeds/*chemistry/metabolism ; },
abstract = {CONTEXT: Rohitukine is an important precursor for the synthesis of potential anticancer drugs flavopiridol (Sanofi-Aventis) and P-276-00 (Piramal Healthcare Limited, Mumbai, India). Trunk bark of Dysoxylum binectariferum (Roxb.) Hook. f. ex Bedd. (Meliaceae) is the widely used source for isolation of rohitukine. However, removal of trunk bark threatens the survival of the tree.<br><br>OBJECTIVE: To investigate the amount of rohitukine accumulated in other tissues of D. binectariferum.<br><br>MATERIALS AND METHODS: Rohitukine standard was isolated from leaves of D. binectariferum. Its purity was ascertained using HR-MS and NMR. Crude extracts were prepared from different tissues of D. binectariferum. Rohitukine content in all the tissues was quantified by HPLC.<br><br>RESULTS: Rohitukine accumulates in a significant amount in seeds, trunk bark, leaves, twigs, and fruits of D. binectariferum. Seeds have the highest rohitukine content (2.42%, dry weight) followed by trunk bark (1.34%, dry weight), leaves (1.064%, dry weight), twigs (0.844% dry weight), and fruits (0.4559% dry weight).<br><br>DISCUSSION AND CONCLUSION: Seeds and leaves of D. binectariferum could be used as alternate renewable sources for isolation of rohitukine.},
}
@article {pmid25471442,
year = {2016},
author = {Chee, SY and Mohd Nor, SA},
title = {DNA barcoding reveals neritid diversity (Mollusca: Gastropoda) diversity in Malaysian waters.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {3},
pages = {2282-2284},
doi = {10.3109/19401736.2014.987237},
pmid = {25471442},
issn = {2470-1408},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/classification/genetics/metabolism ; *Genetic Variation ; *Genome, Mitochondrial ; Malaysia ; Mollusca/classification/*genetics ; Phylogeny ; },
abstract = {This is the first study to identify and determine the phylogenetics of neritids found in Malaysia. In total, twelve species from the family Neritidae were recorded. Ten species were from the genus Nerita and two species were from the genus Neritina. DNA barcodes were successfully assigned to each species. Although some of these species were previously reported in the region, three are only presently reported in this study. The dendrogram showed Nerita and Neritina strongly supported in their respective monophyletic clades. Phylogenetic positions of some species appeared unstable in the trees. This could be due to the differences in a small number of nucleotides, thus minimizing genetic variation between each specimen and species.},
}
@article {pmid25471105,
year = {2014},
author = {Scolari, F and Gomulski, LM and Gabrieli, P and Manni, M and Savini, G and Gasperi, G and Malacrida, AR},
title = {How functional genomics will impact fruit fly pest control: the example of the Mediterranean fruit fly, Ceratitis capitata.},
journal = {BMC genetics},
volume = {15 Suppl 2},
number = {Suppl 2},
pages = {S11},
pmid = {25471105},
issn = {1471-2156},
mesh = {Animals ; Animals, Genetically Modified ; Ceratitis capitata/embryology/*genetics/metabolism ; Embryonic Development/genetics ; Female ; *Genomics/methods ; Male ; *Pest Control, Biological ; Reproduction ; Sexual Behavior, Animal ; Sexual Maturation/genetics ; },
abstract = {The highly invasive agricultural insect pest Ceratitis capitata (Diptera: Tephritidae) is the most thoroughly studied tephritid fruit fly at the genetic and molecular levels. It has become a model for the analysis of fruit fly invasions and for the development of area-wide integrated pest management (AW-IPM) programmes based on the environmentally-friendly Sterile Insect Technique (SIT). Extensive transcriptome resources and the recently released genome sequence are making it possible to unravel several aspects of the medfly reproductive biology and behaviour, opening new opportunities for comparative genomics and barcoding for species identification. New genes, promotors and regulatory sequences are becoming available for the development/improvement of highly competitive sexing strains, for the monitoring of sterile males released in the field and for determining the mating status of wild females. The tools developed in this species have been transferred to other tephritids that are also the subject of SIT programmes.},
}
@article {pmid25470961,
year = {2014},
author = {Yi, F and Han, FM and Peng, Y},
title = {[Molecular identification of 15 species of Ilex genus based on ITS sequence analysis ].},
journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials},
volume = {37},
number = {6},
pages = {974-976},
pmid = {25470961},
issn = {1001-4454},
mesh = {DNA Barcoding, Taxonomic ; DNA Primers ; DNA, Plant/genetics ; Ilex/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {OBJECTIVE: To establish molecular method for identification of Ilex plants using the internal transcribed spacer(ITS) bar- code.<br><br>METHODS: DNA was extracted using centrifugal columnar kits. The ITS sequences of all experimental samples were amplified and sequenced using a pair of universal primers. The alignment and the phylogenetic tree were performed in MEGA5. 0.<br><br>RESULTS: The length of ITS sequence in each species was 759 bp,in which there were 216 sites discrepancy.<br><br>CONCLUSION: DNA barcoding technology based on ITS sequence can be used to identify plants of Ilex genus.},
}
@article {pmid25469559,
year = {2015},
author = {Hendrich, L and Morinière, J and Haszprunar, G and Hebert, PD and Hausmann, A and Köhler, F and Balke, M},
title = {A comprehensive DNA barcode database for Central European beetles with a focus on Germany: adding more than 3500 identified species to BOLD.},
journal = {Molecular ecology resources},
volume = {15},
number = {4},
pages = {795-818},
doi = {10.1111/1755-0998.12354},
pmid = {25469559},
issn = {1755-0998},
mesh = {Animals ; Coleoptera/*classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry/genetics ; *Databases, Nucleic Acid ; Germany ; Molecular Sequence Data ; Sequence Analysis, DNA ; },
abstract = {Beetles are the most diverse group of animals and are crucial for ecosystem functioning. In many countries, they are well established for environmental impact assessment, but even in the well-studied Central European fauna, species identification can be very difficult. A comprehensive and taxonomically well-curated DNA barcode library could remedy this deficit and could also link hundreds of years of traditional knowledge with next generation sequencing technology. However, such a beetle library is missing to date. This study provides the globally largest DNA barcode reference library for Coleoptera for 15 948 individuals belonging to 3514 well-identified species (53% of the German fauna) with representatives from 97 of 103 families (94%). This study is the first comprehensive regional test of the efficiency of DNA barcoding for beetles with a focus on Germany. Sequences ≥500 bp were recovered from 63% of the specimens analysed (15 948 of 25 294) with short sequences from another 997 specimens. Whereas most specimens (92.2%) could be unambiguously assigned to a single known species by sequence diversity at CO1, 1089 specimens (6.8%) were assigned to more than one Barcode Index Number (BIN), creating 395 BINs which need further study to ascertain if they represent cryptic species, mitochondrial introgression, or simply regional variation in widespread species. We found 409 specimens (2.6%) that shared a BIN assignment with another species, most involving a pair of closely allied species as 43 BINs were involved. Most of these taxa were separated by barcodes although sequence divergences were low. Only 155 specimens (0.97%) show identical or overlapping clusters.},
}
@article {pmid25469426,
year = {2015},
author = {Yan, LJ and Liu, J and Möller, M and Zhang, L and Zhang, XM and Li, DZ and Gao, LM},
title = {DNA barcoding of Rhododendron (Ericaceae), the largest Chinese plant genus in biodiversity hotspots of the Himalaya-Hengduan Mountains.},
journal = {Molecular ecology resources},
volume = {15},
number = {4},
pages = {932-944},
doi = {10.1111/1755-0998.12353},
pmid = {25469426},
issn = {1755-0998},
mesh = {*Biodiversity ; China ; Cluster Analysis ; Computational Biology/methods ; *DNA Barcoding, Taxonomic ; DNA, Plant/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/genetics ; Rhododendron/*classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {The Himalaya-Hengduan Mountains encompass two global biodiversity hotspots with high levels of biodiversity and endemism. This area is one of the diversification centres of the genus Rhododendron, which is recognized as one of the most taxonomically challenging plant taxa due to recent adaptive radiations and rampant hybridization. In this study, four DNA barcodes were evaluated on 531 samples representing 173 species of seven sections of four subgenera in Rhododendron, with a high sampling density from the Himalaya-Hengduan Mountains employing three analytical methods. The varied approaches (nj, pwg and blast) had different species identification powers with blast performing best. With the pwg analysis, the discrimination rates for single barcodes varied from 12.21% to 25.19% with ITS < rbcL < matK < psbA-trnH. Combinations of ITS + psbA-trnH + matK and the four barcodes showed the highest discrimination ability (both 41.98%) among all possible combinations. As a single barcode, psbA-trnH performed best with a relatively high performance (25.19%). Overall, the three-marker combination of ITS + psbA-trnH + matK was found to be the best DNA barcode for identifying Rhododendron species. The relatively low discriminative efficiency of DNA barcoding in this genus (~42%) may possibly be attributable to too low sequence divergences as a result of a long generation time of Rhododendron and complex speciation patterns involving recent radiations and hybridizations. Taking the morphology, distribution range and habitat of the species into account, DNA barcoding provided additional information for species identification and delivered a preliminary assessment of biodiversity for the large genus Rhododendron in the biodiversity hotspots of the Himalaya-Hengduan Mountains.},
}
@article {pmid25468359,
year = {2015},
author = {Kress, WJ and García-Robledo, C and Uriarte, M and Erickson, DL},
title = {DNA barcodes for ecology, evolution, and conservation.},
journal = {Trends in ecology &amp; evolution},
volume = {30},
number = {1},
pages = {25-35},
doi = {10.1016/j.tree.2014.10.008},
pmid = {25468359},
issn = {1872-8383},
mesh = {Biodiversity ; Biological Evolution ; Conservation of Natural Resources ; *DNA Barcoding, Taxonomic ; Ecology ; Phylogeny ; },
abstract = {The use of DNA barcodes, which are short gene sequences taken from a standardized portion of the genome and used to identify species, is entering a new phase of application as more and more investigations employ these genetic markers to address questions relating to the ecology and evolution of natural systems. The suite of DNA barcode markers now applied to specific taxonomic groups of organisms are proving invaluable for understanding species boundaries, community ecology, functional trait evolution, trophic interactions, and the conservation of biodiversity. The application of next-generation sequencing (NGS) technology will greatly expand the versatility of DNA barcodes across the Tree of Life, habitats, and geographies as new methodologies are explored and developed.},
}
@article {pmid25465795,
year = {2015},
author = {An, JH and Choi, DK and Lee, KJ and Choi, JW},
title = {Surface-enhanced Raman spectroscopy detection of dopamine by DNA Targeting amplification assay in Parkisons's model.},
journal = {Biosensors &amp; bioelectronics},
volume = {67},
number = {},
pages = {739-746},
doi = {10.1016/j.bios.2014.10.049},
pmid = {25465795},
issn = {1873-4235},
mesh = {Animals ; *Biosensing Techniques ; Corpus Striatum ; DNA/chemistry/genetics ; Disease Models, Animal ; Dopamine/genetics/*isolation &amp; purification ; Gold/chemistry ; Humans ; Mice ; Nucleic Acid Amplification Techniques ; Parkinson Disease/*diagnosis/genetics ; Parkinsonian Disorders/*diagnosis/genetics ; Spectrum Analysis, Raman ; },
abstract = {Dopamine is a potent neuromodulator in the brain that influences a variety of motivated behaviors and is involved in several neurologic diseases. We evaluated a bio-barcode amplification assay for its ability to detect dopamine in a mouse model with and without prior administration of the neurotoxin 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine (MPTP). Our approach uses a combination of DNA barcodes and bead-based immunoassays for detecting neurotransmitters with surface-enhanced Raman spectroscopy (SERS). This method relies on a gold nanoplate with adsorbed antibodies and gold nanoparticles that are encoded with DNA and antibodies that can sandwich the target protein captured by the nanoparticle-bound antibodies. C57BL/6 mice were infused intranasally with MPTP (25mg/kg/day) over 7 consecutive days. At 7 and 21 days after the last administration of MPTP, dopamine was found by western blot analysis to have decreased in the midbrain by 37.44% and 92.95%, respectively. Furthermore, the Raman intensity of dopamine in the midbrains of MPTP-treated mice decreased by 56.77% and 61.12% on days 7 and 21, respectively. Our results demonstrate that the concentration of dopamine in midbrain and striatum of MPTP-treated mice can be easily detected using the bio-barcode assay, which is a rapid, high-throughput screening tool for detecting neurotransmitters.},
}
@article {pmid25461531,
year = {2014},
author = {Ho, T and Tzanetakis, IE},
title = {Development of a virus detection and discovery pipeline using next generation sequencing.},
journal = {Virology},
volume = {471-473},
number = {},
pages = {54-60},
doi = {10.1016/j.virol.2014.09.019},
pmid = {25461531},
issn = {1096-0341},
mesh = {Algorithms ; Animals ; Base Sequence ; DNA Barcoding, Taxonomic ; DNA, Viral/classification/genetics ; Insect Viruses/classification/*genetics/*isolation &amp; purification ; Nucleic Acid Amplification Techniques/*methods/*trends ; Phylogeny ; Plant Viruses/classification/*genetics/*isolation &amp; purification ; RNA, Viral/classification/genetics ; Software ; },
abstract = {Next generation sequencing (NGS) has revolutionized virus discovery. Notwithstanding, a vertical pipeline, from sample preparation to data analysis, has not been available to the plant virology community. We developed a degenerate oligonucleotide primed RT-PCR method with multiple barcodes for NGS, and constructed VirFind, a bioinformatics tool specifically for virus detection and discovery able to: (i) map and filter out host reads, (ii) deliver files of virus reads with taxonomic information and corresponding Blastn and Blastx reports, and (iii) perform conserved domain search for reads of unknown origin. The pipeline was used to process more than 30 samples resulting in the detection of all viruses known to infect the processed samples, the extension of the genomic sequences of others, and the discovery of several novel viruses. VirFind was tested by four external users with datasets from plants or insects, demonstrating its potential as a universal virus detection and discovery tool.},
}
@article {pmid25457632,
year = {2015},
author = {Ferri, G and Corradini, B and Ferrari, F and Santunione, AL and Palazzoli, F and Alu', M},
title = {Forensic botany II, DNA barcode for land plants: Which markers after the international agreement?.},
journal = {Forensic science international. Genetics},
volume = {15},
number = {},
pages = {131-136},
doi = {10.1016/j.fsigen.2014.10.005},
pmid = {25457632},
issn = {1878-0326},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; *Genetic Markers ; Plants/*genetics ; },
abstract = {The ambitious idea of using a short piece of DNA for large-scale species identification (DNA barcoding) is already a powerful tool for scientists and the application of this standard technique seems promising in a range of fields including forensic genetics. While DNA barcoding enjoyed a remarkable success for animal identification through cytochrome c oxidase I (COI) analysis, the attempts to identify a single barcode for plants remained a vain hope for a longtime. From the beginning, the Consortium for the Barcode of Life (CBOL) showed a lack of agreement on a core plant barcode, reflecting the diversity of viewpoints. Different research groups advocated various markers with divergent set of criteria until the recent publication by the CBOL-Plant Working Group. After a four-year effort, in 2009 the International Team concluded to agree on standard markers promoting a multilocus solution (rbcL and matK), with 70-75% of discrimination to the species level. In 2009 our group firstly proposed the broad application of DNA barcoding principles as a tool for identification of trace botanical evidence through the analysis of two chloroplast loci (trnH-psbA and trnL-trnF) in plant species belonging to local flora. Difficulties and drawbacks that were encountered included a poor coverage of species in specific databases and the lack of authenticated reference sequences for the selected markers. Successful preliminary results were obtained providing an approach to progressively identify unknown plant specimens to a given taxonomic rank, usable by any non-specialist botanist or in case of a shortage of taxonomic expertise. Now we considered mandatory to update and to compare our previous findings with the new selected plastid markers (matK+rbcL), taking into account forensic requirements. Features of all the four loci (the two previously analyzed trnH-psbA+trnL-trnF and matK+rbcL) were compared singly and in multilocus solutions to assess the most suitable combination for forensic botany. Based on obtained results, we recommend the adoption of a two-locus combination with rbcL+trnH-psbA plastid markers, which currently best satisfies forensic needs for botanical species identification.},
}
@article {pmid25456074,
year = {2014},
author = {Varble, A and Albrecht, RA and Backes, S and Crumiller, M and Bouvier, NM and Sachs, D and García-Sastre, A and tenOever, BR},
title = {Influenza A virus transmission bottlenecks are defined by infection route and recipient host.},
journal = {Cell host &amp; microbe},
volume = {16},
number = {5},
pages = {691-700},
pmid = {25456074},
issn = {1934-6069},
support = {HHSN272201400008C/AI/NIAID NIH HHS/United States ; R01 AI093571/AI/NIAID NIH HHS/United States ; HHSN266200700010C//PHS HHS/United States ; R01 A1093571//PHS HHS/United States ; HHSN266200700010C/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Cell Line, Tumor ; DNA Barcoding, Taxonomic ; Disease Transmission, Infectious/veterinary ; Dogs ; Ferrets ; Genome, Viral ; Guinea Pigs ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions ; Humans ; Influenza A virus/genetics/*pathogenicity ; Influenza, Human/*transmission ; Madin Darby Canine Kidney Cells ; Male ; Orthomyxoviridae Infections/*transmission ; },
abstract = {Despite its global relevance, our understanding of how influenza A virus transmission impacts the overall population dynamics of this RNA virus remains incomplete. To define this dynamic, we inserted neutral barcodes into the influenza A virus genome to generate a population of viruses that can be individually tracked during transmission events. We find that physiological bottlenecks differ dramatically based on the infection route and level of adaptation required for efficient replication. Strong genetic pressures are responsible for bottlenecks during adaptation across different host species, whereas transmission between susceptible hosts results in bottlenecks that are not genetically driven and occur at the level of the recipient. Additionally, the infection route significantly influences the bottleneck stringency, with aerosol transmission imposing greater selection than direct contact. These transmission constraints have implications in understanding the global migration of virus populations and provide a clearer perspective on the emergence of pandemic strains.},
}
@article {pmid25454249,
year = {2015},
author = {Piñol, J and Mir, G and Gomez-Polo, P and Agustí, N},
title = {Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods.},
journal = {Molecular ecology resources},
volume = {15},
number = {4},
pages = {819-830},
doi = {10.1111/1755-0998.12355},
pmid = {25454249},
issn = {1755-0998},
mesh = {Animals ; Arthropods/*classification/*genetics ; *Base Pair Mismatch ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/*genetics ; Diagnostic Errors ; High-Throughput Nucleotide Sequencing/*methods ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA ; },
abstract = {The quantification of the biological diversity in environmental samples using high-throughput DNA sequencing is hindered by the PCR bias caused by variable primer-template mismatches of the individual species. In some dietary studies, there is the added problem that samples are enriched with predator DNA, so often a predator-specific blocking oligonucleotide is used to alleviate the problem. However, specific blocking oligonucleotides could coblock nontarget species to some degree. Here, we accurately estimate the extent of the PCR biases induced by universal and blocking primers on a mock community prepared with DNA of twelve species of terrestrial arthropods. We also compare universal and blocking primer biases with those induced by variable annealing temperature and number of PCR cycles. The results show that reads of all species were recovered after PCR enrichment at our control conditions (no blocking oligonucleotide, 45 °C annealing temperature and 40 cycles) and high-throughput sequencing. They also show that the four factors considered biased the final proportions of the species to some degree. Among these factors, the number of primer-template mismatches of each species had a disproportionate effect (up to five orders of magnitude) on the amplification efficiency. In particular, the number of primer-template mismatches explained most of the variation (~3/4) in the amplification efficiency of the species. The effect of blocking oligonucleotide concentration on nontarget species relative abundance was also significant, but less important (below one order of magnitude). Considering the results reported here, the quantitative potential of the technique is limited, and only qualitative results (the species list) are reliable, at least when targeting the barcoding COI region.},
}
@article {pmid25447914,
year = {2015},
author = {Dhar, B and Ghosh, SK},
title = {Genetic assessment of ornamental fish species from North East India.},
journal = {Gene},
volume = {555},
number = {2},
pages = {382-392},
doi = {10.1016/j.gene.2014.11.037},
pmid = {25447914},
issn = {1879-0038},
mesh = {Animals ; Biodiversity ; Cluster Analysis ; Computational Biology/methods ; Conservation of Natural Resources ; DNA Barcoding, Taxonomic ; Endangered Species ; Fishes/classification/*genetics ; Genetic Markers ; India ; Species Specificity ; },
abstract = {Ornamental fishes are traded with multiple names from various parts around the world, including North East India. Most are collected from the wild, due to lack of species-specific culture or breeding, and therefore, such unmanaged collection of the wild and endemic species could lead to severe threats to biodiversity. Despite many regulatory policies, trade of threatened species, including the IUCN listed species have been largely uncontrolled, due to species identification problems arising from the utilization of multiple trade names. So, the development of species-specific DNA marker is indispensable where DNA Barcoding is proved to be helpful in species identification. Here, we investigated, through DNA Barcoding and morphological assessment, the identification of 128 ornamental fish specimens exported from NE India from different exporters. The generated sequences were subjected to similarity match in BOLD-IDS as well as BLASTN, and analysed using MEGA5.2 for species identification through Neighbour-Joining (NJ) clustering, and K2P distance based approach. The analysis revealed straightforward identification of 84 specimens into 35 species, while 44 specimens were difficult to distinguish based on CO1 barcode alone. However, these cases were resolved through morphology, NJ and distanced based method and found to be belonging to 16 species. Among the 51 identified species, 14 species represented multiple trade names; 17 species belonged to threatened category. Species-level identification through DNA Barcoding along with traditional morphotaxonomy reflects its efficacy in regulating ornamental fish trade and therefore, appeals for their conservation in nature. The use of trade names rather than the zoological name created the passage for trafficking of the threatened species and demands immediate attention for sustaining wildlife conservation.},
}
@article {pmid25447202,
year = {2014},
author = {Ondrejicka, DA and Locke, SA and Morey, K and Borisenko, AV and Hanner, RH},
title = {Status and prospects of DNA barcoding in medically important parasites and vectors.},
journal = {Trends in parasitology},
volume = {30},
number = {12},
pages = {582-591},
doi = {10.1016/j.pt.2014.09.003},
pmid = {25447202},
issn = {1471-5007},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Disease Vectors ; Humans ; Parasites/*genetics ; Parasitology/*methods/trends ; },
abstract = {For over 10 years, DNA barcoding has been used to identify specimens and discern species. Its potential benefits in parasitology were recognized early, but its utility and uptake remain unclear. Here we review studies using DNA barcoding in parasites and vectors affecting humans and find that the technique is accurate (accords with author identifications based on morphology or other markers) in 94-95% of cases, although aspects of DNA barcoding (vouchering, marker implicated) have often been misunderstood. In a newly compiled checklist of parasites, vectors, and hazards, barcodes are available for 43% of all 1403 species and for more than half of 429 species of greater medical importance. This is encouraging coverage that would improve with an active campaign targeting parasites and vectors.},
}
@article {pmid25446712,
year = {2015},
author = {Li, X and Liao, B and Chen, H},
title = {A new technique for generating pathogenic barcodes in breast cancer susceptibility analysis.},
journal = {Journal of theoretical biology},
volume = {366},
number = {},
pages = {84-90},
doi = {10.1016/j.jtbi.2014.11.005},
pmid = {25446712},
issn = {1095-8541},
mesh = {Algorithms ; Breast Neoplasms/*genetics/pathology ; *Databases, Genetic ; Entropy ; Female ; *Genetic Predisposition to Disease ; Humans ; Odds Ratio ; Polymorphism, Single Nucleotide/genetics ; Risk Factors ; },
abstract = {Complex diseases usually involve complex interactions between multiple loci. The artificial intelligent algorithm is a plausible strategy to evade combinatorial explosion. However, the randomness of solution of this algorithm loses decreases the confidence of biological researchers on this algorithm. Meanwhile, the lack of an efficient and effective measure to profile the distribution of cases and controls impedes the discovery of pathogenic epistasis. Here we present an efficient method called maximum dissimilarity-minimum entropy (MDME) to analyze breast cancer single-nucleotide polymorphism (SNP) data. The method searches risky barcodes, which to increase the odds ratio and relative risk of the breast cancer. This method based on the hypothesis that if a specific barcode is associated with a disease, then the barcode permits distinction of cases from controls and more importantly it shows a relative consistent pattern in cases. An analysis based on simulated dataset explains the necessity of minimum entropy. Experimental results show that our method can find the most risky barcode that contributes to breast cancer susceptibility. Our method may also mine several pathogenic barcodes that condition the different subtypes of cancer.},
}
@article {pmid25446171,
year = {2015},
author = {Gunay, F and Alten, B and Simsek, F and Aldemir, A and Linton, YM},
title = {Barcoding Turkish Culex mosquitoes to facilitate arbovirus vector incrimination studies reveals hidden diversity and new potential vectors.},
journal = {Acta tropica},
volume = {143},
number = {},
pages = {112-120},
doi = {10.1016/j.actatropica.2014.10.013},
pmid = {25446171},
issn = {1873-6254},
mesh = {Animals ; Arboviruses/*isolation &amp; purification ; Culex/*genetics/*virology ; DNA Barcoding, Taxonomic/*methods ; Insect Vectors/*virology ; Polymerase Chain Reaction ; Species Specificity ; Turkey ; West Nile virus/isolation &amp; purification ; },
abstract = {As a precursor to planned arboviral vector incrimination studies, an integrated systematics approach was adopted using morphology and DNA barcoding to examine the Culex fauna present in Turkey. The mitochondrial COI gene (658bp) were sequenced from 185 specimens collected across 11 Turkish provinces, as well as from colony material. Although by morphology only 9 species were recognised, DNA barcoding recovered 13 distinct species including: Cx. (Barraudius) modestus, Cx. (Culex) laticinctus, Cx. (Cux.) mimeticus, Cx. (Cux.) perexiguus, Cx. (Cux.) pipiens, Cx. (Cux.) pipiens form molestus, Cx. (Cux.) quinquefasciatus, Cx. (Cux.) theileri, Cx. (Cux.) torrentium, Cx. (Cux.) tritaeniorhynchus and Cx. (Maillotia) hortensis. The taxon formerly identified as Cx. (Neoculex) territans was shown to comprise two distinct species, neither of which correspond to Cx. territans s.s. These include Cx. (Neo.) impudicus and another uncertain species, which may be Cx. (Neo.) europaeus or Cx. (Neo.) martinii (herein=Cx. (Neo.) sp. 1). Detailed examination of the Pipiens Group revealed Cx. pipiens, Cx. pipiens f. molestus and the widespread presence of the highly efficient West Nile virus vector Cx. quinquefasciatus for the first time. Four new country records are reported, increasing the Culex of Turkey to 15 recognised species and Cx. pipiens f. molestus. A new taxonomic checklist is provided, annotated with respective vector competencies for transmission of arboviruses.},
}
@article {pmid25445650,
year = {2014},
author = {Depaquit, J},
title = {Molecular systematics applied to Phlebotomine sandflies: review and perspectives.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {28},
number = {},
pages = {744-756},
doi = {10.1016/j.meegid.2014.10.027},
pmid = {25445650},
issn = {1567-7257},
mesh = {Animals ; DNA, Mitochondrial ; Genes, Insect ; Insect Vectors ; Leishmaniasis ; Phylogeny ; Psychodidae/*classification/*genetics ; },
abstract = {A review of the literature related to the molecular systematics of the Phlebotomine sandflies (Diptera, Psychodidae) is proposed. It shows that molecular systematics is more frequently used to perform evolutionary systematics than to help in the field of alpha taxonomy. On more than 900 living species and subspecies described, 180 (about 20%) have been processed for molecular systematics. The countries of origin where the sandflies processed come from are endemic for leishmaniases and the ratio of species sampled for molecular systematics studies is high for vector groups and low for species not involved in the transmission of leishmaniasis. The main studies focused on intraspecific topics, others on closely related species, and a few compared genera of sandflies. Mitochondrial markers (more than 50% of the markers studied) are preferred to non mitochondrial markers. The use of mtDNA markers alone to explore phylogenetic relationships is considered as dangerous, especially concerning closely related species.},
}
@article {pmid25444539,
year = {2014},
author = {Hu, N and Wei, F and Lv, X and Wu, L and Dong, XY and Chen, H},
title = {Profiling of triacylglycerols in plant oils by high-performance liquid chromatography-atmosphere pressure chemical ionization mass spectrometry using a novel mixed-mode column.},
journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences},
volume = {972},
number = {},
pages = {65-72},
doi = {10.1016/j.jchromb.2014.09.039},
pmid = {25444539},
issn = {1873-376X},
mesh = {Atmospheric Pressure ; Chromatography, High Pressure Liquid/*methods ; Hydrophobic and Hydrophilic Interactions ; Mass Spectrometry/*methods ; Plant Oils/*chemistry ; Principal Component Analysis ; Reproducibility of Results ; Triglycerides/*chemistry ; },
abstract = {In this investigation, a rapid and high-throughput method for profiling of TAGs in plant oils by liquid chromatography using a single column coupled with atmospheric pressure chemical ionization (APCI) mass spectrometry was reported. A novel mixed-mode phenyl-hexyl chromatographic column was employed in this separation system. The phenyl-hexyl column could provide hydrophobic interactions as well as π-π interactions. Compared with two traditionally columns used in TAG separation - the C18 column and silver-ion column, this column exhibited much higher selectivity for the separation of TAGs with great efficiency and rapid speed. By comparison with a novel mix-mode column (Ag-HiSep OTS column), which can also provide both hydrophobic interactions as well as π-π interactions for the separation of TAGs, phenyl-hexyl column exhibited excellent stability. LC method using phenyl-hexyl column coupled with APCI-MS was successfully applied for the profiling of TAGs in soybean oils, peanut oils, corn oils, and sesame oils. 29 TAGs in peanut oils, 22 TAGs in soybean oils, 19 TAGs in corn oils, and 19 TAGs in sesame oils were determined and quantified. The LC-MS data was analyzed by barcodes and principal component analysis (PCA). The resulting barcodes constitute a simple tool to display differences between different plant oils. Results of PCA also enabled a clear identification of different plant oils. This method provided an efficient and convenient chromatographic technology for the fast characterization and quantification of complex TAGs in plant oils at high selectivity. It has great potential as a routine analytical method for analysis of edible oil quality and authenticity control.},
}
@article {pmid25444445,
year = {2014},
author = {Chao, Z and Zeng, W and Liao, J and Liu, L and Liang, Z and Li, X},
title = {DNA barcoding Chinese medicinal Bupleurum.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {21},
number = {13},
pages = {1767-1773},
doi = {10.1016/j.phymed.2014.09.001},
pmid = {25444445},
issn = {1618-095X},
mesh = {Bupleurum/*classification/genetics ; China ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Genes, Chloroplast ; Plants, Medicinal/*classification/genetics ; },
abstract = {We tested 4 markers, namely nuclear internal transcribed spacer 2 (ITS2), psbA-trnH, matK, and rbcL, to evaluate these candidate DNA barcodes for distinguishing Bupleuri radix (Chaihu) from its adulterants. 51 plant samples of Bupleurum representing 19 species were collected from different areas in China. Amplification and sequencing were attempted for all the 4 candidate barcode regions, whose validity was assessed in terms of the success rate of PCR amplification and sequencing, differential intra- and inter-specific divergences, DNA barcoding gap and the ability to discriminate species. The results showed that ITS2 had the best performance in identifying Bupleurum with an identification efficiency of 73.68%, which, after combining with psbA-trnH, increased to 83.33%. We further evaluated the efficiency of ITS2 for discriminating the species of Bupleurum using a large database from GenBank, which archived data of 223 samples from 74 species, and ITS2 successfully discriminated 64.13% of the samples at the species level. In conclusion, the ITS2 can serve as a potentially useful barcode for Bupleurum species, with psbA-trnH as a supplementary locus.},
}
@article {pmid25441303,
year = {2015},
author = {Valverde-Barrantes, OJ and Smemo, KA and Feinstein, LM and Kershner, MW and Blackwood, CB},
title = {Aggregated and complementary: symmetric proliferation, overyielding, and mass effects explain fine-root biomass in soil patches in a diverse temperate deciduous forest landscape.},
journal = {The New phytologist},
volume = {205},
number = {2},
pages = {731-742},
doi = {10.1111/nph.13179},
pmid = {25441303},
issn = {1469-8137},
mesh = {Biomass ; Ecosystem ; *Forests ; Ohio ; Plant Roots/*physiology ; Soil ; Species Specificity ; Trees/*physiology ; },
abstract = {Few studies describe root distributions at the species level in diverse forests, although belowground species interactions and traits are often assumed to affect fine-root biomass (FRB). We used molecular barcoding to study how FRB of trees relates to soil characteristics, species identity, root diversity, and root traits, and how these relationships are affected by proximity to ecotones in a temperate forest landscape. We found that soil patch root biomass increased in response to soil resources across all species, and there was little belowground vertical or horizontal spatial segregation among species. Root traits and species relative abundance did not explain significant variation in FRB after correcting for soil fertility. A positive relationship between phylogenetic diversity and FRB indicated significant belowground overyielding attributable to local root diversity. Finally, variation in FRB explained by soil fertility and diversity was reduced near ecotones, but only because of a reduction in biomass in periodically anoxic areas. These results suggest that symmetric responses to soil properties are coupled with complementary species traits and interactions to explain variation in FRB among soil patches. In addition, landscape-level dispersal among habitats and across ecotones helps explain variation in the strength of these relationships in complex landscapes.},
}
@article {pmid25434821,
year = {2015},
author = {Klauke, K and Broekhuis, MJC and Weersing, E and Dethmers-Ausema, A and Ritsema, M and González, MV and Zwart, E and Bystrykh, LV and de Haan, G},
title = {Tracing dynamics and clonal heterogeneity of Cbx7-induced leukemic stem cells by cellular barcoding.},
journal = {Stem cell reports},
volume = {4},
number = {1},
pages = {74-89},
pmid = {25434821},
issn = {2213-6711},
mesh = {Animals ; Bone Marrow Cells/metabolism/pathology ; Cell Transformation, Neoplastic/genetics ; Clonal Evolution/*genetics ; Cluster Analysis ; Disease Models, Animal ; Disease Progression ; Gene Expression ; Gene Expression Profiling ; Immunophenotyping ; Leukemia/*genetics/pathology ; Mice ; Neoplastic Stem Cells/*metabolism/pathology ; Phenotype ; Polycomb Repressive Complex 1/*genetics ; },
abstract = {Accurate monitoring of tumor dynamics and leukemic stem cell (LSC) heterogeneity is important for the development of personalized cancer therapies. In this study, we experimentally induced distinct types of leukemia in mice by enforced expression of Cbx7. Simultaneous cellular barcoding allowed for thorough analysis of leukemias at the clonal level and revealed high and unpredictable tumor complexity. Multiple LSC clones with distinct leukemic properties coexisted. Some of these clones remained dormant but bore leukemic potential, as they progressed to full-blown leukemia after challenge. LSC clones could retain multilineage differentiation capacities, where one clone induced phenotypically distinct leukemias. Beyond a detailed insight into CBX7-driven leukemic biology, our model is of general relevance for the understanding of tumor dynamics and clonal evolution.},
}
@article {pmid25431824,
year = {2016},
author = {Kvist, S},
title = {Does a global DNA barcoding gap exist in Annelida?.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {3},
pages = {2241-2252},
doi = {10.3109/19401736.2014.984166},
pmid = {25431824},
issn = {2470-1408},
mesh = {Animals ; Annelida/*genetics ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Electron Transport Complex IV/chemistry/genetics/metabolism ; Mitochondria/genetics ; },
abstract = {Accurate identification of unknown specimens by means of DNA barcoding is contingent on the presence of a DNA barcoding gap, among other factors, as its absence may result in dubious specimen identifications - false negatives or positives. Whereas the utility of DNA barcoding would be greatly reduced in the absence of a distinct and sufficiently sized barcoding gap, the limits of intraspecific and interspecific distances are seldom thoroughly inspected across comprehensive sampling. The present study aims to illuminate this aspect of barcoding in a comprehensive manner for the animal phylum Annelida. All cytochrome c oxidase subunit I sequences (cox1 gene; the chosen region for zoological DNA barcoding) present in GenBank for Annelida, as well as for "Polychaeta", "Oligochaeta", and Hirudinea separately, were downloaded and curated for length, coverage and potential contaminations. The final datasets consisted of 9782 (Annelida), 5545 ("Polychaeta"), 3639 ("Oligochaeta"), and 598 (Hirudinea) cox1 sequences and these were either (i) used as is in an automated global barcoding gap detection analysis or (ii) further analyzed for genetic distances, separated into bins containing intraspecific and interspecific comparisons and plotted in a graph to visualize any potential global barcoding gap. Over 70 million pairwise genetic comparisons were made and results suggest that although there is a tendency towards separation, no distinct or sufficiently sized global barcoding gap exists in either of the datasets rendering future barcoding efforts at risk of erroneous specimen identifications (but local barcoding gaps may still exist allowing for the identification of specimens at lower taxonomic ranks). This seems to be especially true for earthworm taxa, which account for fully 35% of the total number of interspecific comparisons that show 0% divergence.},
}
@article {pmid25431817,
year = {2016},
author = {Jose, D and Rozario, JV and Benjamin, D and Harikrishnan, M},
title = {Morphological and molecular description for Glyphocrangon investigatoris Wood-Mason &amp; Alcock, 1891 emphasizing its phylogenetic relationship.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {3},
pages = {2053-2057},
doi = {10.3109/19401736.2014.982554},
pmid = {25431817},
issn = {2470-1408},
mesh = {Animals ; Decapoda/*anatomy &amp; histology/*genetics ; Female ; Geography ; *Phylogeny ; Species Specificity ; },
abstract = {Genus Glyphocrangon, the only representative of Family Glyphocrangonidae, comprises about 89 species. According to previous records, this species is known to inhabit a depth range of 145-410 fathoms in Bay of Bengal. A thorough scrutiny of literature revealed a detailed morphological description of G. investigatoris and little molecular database. As part of an exploratory research survey conducted in Bay of Bengal, specimens of this species were collected from trawl catches off Paradeep, Orissa. In our present study, an attempt was made to develop its DNA barcode based on mitochondrial Cytochrome oxidase subunit I (mtCOI) and to establish its phylogenetic relationship with other species of genus Glyphocrangon. The developed mtCOI sequences of G. investigatoris exhibited its genetic identity favoring its morphological description.},
}
@article {pmid25431472,
year = {2015},
author = {Yu, J and Walther, G and Van Diepeningen, AD and Gerrits Van Den Ende, AH and Li, RY and Moussa, TA and Almaghrabi, OA and De Hoog, GS},
title = {DNA barcoding of clinically relevant Cunninghamella species.},
journal = {Medical mycology},
volume = {53},
number = {2},
pages = {99-106},
doi = {10.1093/mmy/myu079},
pmid = {25431472},
issn = {1460-2709},
mesh = {Cluster Analysis ; Cunninghamella/*classification/*genetics/isolation &amp; purification ; *DNA Barcoding, Taxonomic ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Humans ; Molecular Sequence Data ; Mucormycosis/microbiology ; Peptide Elongation Factor 1/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Mucormycosis caused, in part, by representatives of the genus Cunninghamella is a severe infection with high mortality in patients with impaired immunity. Several species have been described in the literature as etiologic agents. A DNA barcoding study using ITS rDNA and tef-1α provided concordance of molecular data with conventional characters. The currently accepted Cunninghamella species were well supported in phylogenetic trees of both markers except for C. septata with ITS that clustered in the C. echinulata clade. Sequence variability was distinctly higher for the ITS than for tef-1α. Intraspecific ITS variability of some of the species exceeded that between some closely related species, but the marker remained applicable for species identification. The most variable species for both markers was C. echinulata. Cunninghamella bertholletiae is the main pathogenic species; infections by C. blakesleeana, C. echinulata, and C. elegans are highly exceptional.},
}
@article {pmid25425941,
year = {2014},
author = {Fernandez-Triana, JL and Whitfield, JB and Smith, MA and Hallwachs, W and Janzen, DH},
title = {First record of the genus Venanus (Hymenoptera: Braconidae: Microgastrinae) in Mesoamerica, with the description of two new species from Costa Rica.},
journal = {Biodiversity data journal},
volume = {},
number = {2},
pages = {e4167},
pmid = {25425941},
issn = {1314-2828},
abstract = {The New World genus Venanus (Hymenoptera: Braconidae: Microgastrinae) is a small group of parasitoid wasps that includes two Nearctic and seven Neotropical species. Here two additional species, authored by Fernández-Triana &amp; Whitfield, are described from Costa Rica: V.johnnyrosalesi sp. n. from Area de Conservación Guanacaste (ACG) and V.randallgarciai sp. n. from Area de Conservación Cordillera Volcanica Central. They represent the first record of the genus for Mesoamerica. A previous key to all known Venanus (Whitfield et al. 2011) is modified to include the new species. The Costa Rican species were collected at altitudes of 1,400-1,460 m, but nothing is known of their biology. DNA barcodes were obtained for both species and are included as part of the description along with extensive photos. This paper is part of a series inventorying the diversity of Microgastrinae in ACG.},
}
@article {pmid25425095,
year = {2015},
author = {Seethapathy, GS and Ganesh, D and Santhosh Kumar, JU and Senthilkumar, U and Newmaster, SG and Ragupathy, S and Uma Shaanker, R and Ravikanth, G},
title = {Assessing product adulteration in natural health products for laxative yielding plants, Cassia, Senna, and Chamaecrista, in Southern India using DNA barcoding.},
journal = {International journal of legal medicine},
volume = {129},
number = {4},
pages = {693-700},
pmid = {25425095},
issn = {1437-1596},
mesh = {Cassia/*genetics ; Chamaecrista/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Plant ; *Drug Contamination ; Humans ; India ; Laxatives ; *Phytotherapy ; Plants, Medicinal/genetics ; Quality Control ; Senna Plant/*genetics ; Sequence Analysis, DNA ; },
abstract = {Medicinal plants such as Cassia, Senna, and Chamaecrista (belonging to the family Fabaceae) are well known for their laxative properties. They are extensively used within indigenous health care systems in India and several other countries. India exports over 5000 metric tonnes per year of these specific herbal products, and the demand for natural health product market is growing at approximately 10-15% annually. The raw plant material used as active ingredients is almost exclusively sourced from wild populations. Consequently, it is widely suspected that the commercial herbal products claiming to contain these species may be adulterated or contaminated. In this study, we have attempted to assess product authentication and the extent of adulteration in the herbal trade of these species using DNA barcoding. Our method includes four common DNA barcode regions: ITS, matK, rbcL, and psbA-trnH. Analysis of market samples revealed considerable adulteration of herbal products: 50% in the case of Senna auriculata, 37% in Senna tora, and 8% in Senna alexandrina. All herbal products containing Cassia fistula were authentic, while the species under the genus Chamaecrista were not in trade. Our results confirm the suspicion that there is rampant herbal product adulteration in Indian markets. DNA barcodes such as that demonstrated in this study could be effectively used as a regulatory tool to control the adulteration of herbal products and contribute to restoring quality assurance and consumer confidence in natural health products.},
}
@article {pmid25424838,
year = {2015},
author = {Hoffmann, GS and Johannesen, J and Griebeler, EM},
title = {Species cross-amplification, identification and genetic variation of 17 species of deer (Cervidae) with microsatellite and mitochondrial DNA from antlers.},
journal = {Molecular biology reports},
volume = {42},
number = {6},
pages = {1059-1067},
pmid = {25424838},
issn = {1573-4978},
mesh = {Animals ; Antlers/*metabolism ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Deer/classification/*genetics ; *Genetic Variation ; Genotype ; Male ; Microsatellite Repeats/*genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/classification/genetics ; Species Specificity ; },
abstract = {Strong anthropogenic impact has caused 28 of the currently recognized 55 species of deer (Cervidae) to be listed on the IUCN Red List. Particular threats to vulnerable species include habitat deterioration and hybridization with alien, introduced species. The scarcity of many species has severely hampered genetic analyses of their populations, including the detection of loci for cross-species amplification. Because deer antlers are shed and re-grown annually, antlers offer the possibility for non-invasive genetic sampling of large individual numbers, and may provide material for reference genotyping from historical samples stored in zoos, museums and trophy collections of rare and extinct species/populations. In this paper, we report cross-species amplification of 19 nuclear microsatellite loci and the amplification of 16S mtDNA for barcoding from nearly a third of all deer species worldwide based on high quality DNA extracted from antler bone up to 40 years old. Phylogenetic analysis based on mtDNA of seventeen species and five subspecies corroborate previously published phylogenetic data, thus confirming the specific resolution of the DNA extraction methodology.},
}
@article {pmid25422545,
year = {2014},
author = {Chao, Z and Liao, J and Liang, Z and Huang, S and Zhang, L and Li, J},
title = {Cytochrome C oxidase subunit I barcodes provide an efficient tool for Jinqian Baihua She (Bungarus parvus) authentication.},
journal = {Pharmacognosy magazine},
volume = {10},
number = {40},
pages = {449-457},
pmid = {25422545},
issn = {0973-1296},
abstract = {OBJECTIVE: To test the feasibility of DNA barcoding for accurate identification of Jinqian Baihua She and its adulterants.<br><br>MATERIALS AND METHODS: Standard cytochrome C oxidase subunit I (COI) gene fragments were sequenced for DNA barcoding of 39 samples from 9 snake species, including Bungarus multicinctus, the officially recognized origin animal by Chinese Pharmacopoeia, and other 8 adulterate species. The aligned sequences, 658 base pairs in length, were analyzed for divergence using the Kimura-2-parameter (K2P) distance model with MEGA5.0.<br><br>RESULTS: The mean intraspecific K2P distance was 0.0103 and the average interspecific genetic distance was 0.2178 in B. multicinctus, far greater than the minimal interspecific genetic distance of 0.027 recommended for species identification. A neighbor-joining (NJ) tree was constructed, in which each species formed a monophyletic clade with bootstrap supports of 100%. All the data were submitted to Barcode of Life Data system version 3.0 (BOLD, http://www.barcodinglife.org) under the project title "DNA barcoding Bungarus multicinctus and its adulterants". Ten samples of commercially available crude drugs of JBS were identified using the identification engine provided by BOLD. All the samples were clearly identified at the species level, among which five were found to be the adulterants and identified as Dinodon rufozonatum.<br><br>CONCLUSION: DNA barcoding using the standard COI gene fragments provides an effective and accurate means for JBS identification and authentication.},
}
@article {pmid25422535,
year = {2014},
author = {Zhou, J and Wang, W and Liu, M and Liu, Z},
title = {Molecular authentication of the traditional medicinal plant Peucedanum praeruptorum and its substitutes and adulterants by DNA - barcoding technique.},
journal = {Pharmacognosy magazine},
volume = {10},
number = {40},
pages = {385-390},
pmid = {25422535},
issn = {0973-1296},
abstract = {BACKGROUND: Peucedanum praeruptorum L., a traditional Chinese medicine known as Qian-hu, is commonly used for dispelling wind-heat and expectorant and loss of energy. However, due to similar morphological characters and high market demand, there are many substitutes and adulterants of P. praeruptorum. DNA barcoding is an approach to identify species based on sequences from a short, standardized DNA region.<br><br>OBJECTIVE: To authenticate P. praeruptorum from its substitutes and adulterants.<br><br>MATERIALS AND METHODS: The differential identification of P. praeruptorum and 13 regional substitutes and 23 adulterants was investigated by means of DNA sequence analysis of internal transcribed spacer (ITS) region of the nuclear ribosomal DNA (nrDNA), a bootstrap neighbor-joining (NJ) tree according to Kimura's 2-parameter method was also calculated.<br><br>RESULTS: The data showed that P. praeruptorum, its substitutes and adulterants could be easily distinguished at the DNA level, while almost all species were well resolved, and successfully identified on the NJ tree.<br><br>CONCLUSION: The ITS sequence can be used for the identification of P. praeruptorum and to distinguish it from common substitutes and adulterants.},
}
@article {pmid25417731,
year = {2015},
author = {Chaves, BR and Chaves, AV and Nascimento, AC and Chevitarese, J and Vasconcelos, MF and Santos, FR},
title = {Barcoding Neotropical birds: assessing the impact of nonmonophyly in a highly diverse group.},
journal = {Molecular ecology resources},
volume = {15},
number = {4},
pages = {921-931},
doi = {10.1111/1755-0998.12344},
pmid = {25417731},
issn = {1755-0998},
mesh = {Animals ; Birds/*classification/*genetics ; Brazil ; DNA Barcoding, Taxonomic/*methods ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {In this study, we verified the power of DNA barcodes to discriminate Neotropical birds using Bayesian tree reconstructions of a total of 7404 COI sequences from 1521 species, including 55 Brazilian species with no previous barcode data. We found that 10.4% of species were nonmonophyletic, most likely due to inaccurate taxonomy, incomplete lineage sorting or hybridization. At least 0.5% of the sequences (2.5% of the sampled species) retrieved from GenBank were associated with database errors (poor-quality sequences, NuMTs, misidentification or unnoticed hybridization). Paraphyletic species (5.8% of the total) can be related to rapid speciation events leading to nonreciprocal monophyly between recently diverged sister species, or to absence of synapomorphies in the small COI region analysed. We also performed two series of genetic distance calculations under the K2P model for intraspecific and interspecific comparisons: the first included all COI sequences, and the second included only monophyletic taxa observed in the Bayesian trees. As expected, the mean and median pairwise distances were smaller for intraspecific than for interspecific comparisons. However, there was no precise 'barcode gap', which was shown to be larger in the monophyletic taxon data set than for the data from all species, as expected. Our results indicated that although database errors may explain some of the difficulties in the species discrimination of Neotropical birds, distance-based barcode assignment may also be compromised because of the high diversity of bird species and more complex speciation events in the Neotropics.},
}
@article {pmid25415202,
year = {2014},
author = {Vidergar, N and Toplak, N and Kuntner, M},
title = {Streamlining DNA barcoding protocols: automated DNA extraction and a new cox1 primer in arachnid systematics.},
journal = {PloS one},
volume = {9},
number = {11},
pages = {e113030},
pmid = {25415202},
issn = {1932-6203},
mesh = {Animals ; Arachnida/classification/*genetics ; Base Sequence ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; DNA, Mitochondrial/chemistry/*genetics/isolation &amp; purification ; Electron Transport Complex IV/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/methods ; Reproducibility of Results ; Sequence Homology, Nucleic Acid ; Spiders/classification/genetics ; },
abstract = {BACKGROUND: DNA barcoding is a popular tool in taxonomic and phylogenetic studies, but for most animal lineages protocols for obtaining the barcoding sequences--mitochondrial cytochrome C oxidase subunit I (cox1 AKA CO1)--are not standardized. Our aim was to explore an optimal strategy for arachnids, focusing on the species-richest lineage, spiders by (1) improving an automated DNA extraction protocol, (2) testing the performance of commonly used primer combinations, and (3) developing a new cox1 primer suitable for more efficient alignment and phylogenetic analyses.<br><br>METHODOLOGY: We used exemplars of 15 species from all major spider clades, processed a range of spider tissues of varying size and quality, optimized genomic DNA extraction using the MagMAX Express magnetic particle processor-an automated high throughput DNA extraction system-and tested cox1 amplification protocols emphasizing the standard barcoding region using ten routinely employed primer pairs.<br><br>RESULTS: The best results were obtained with the commonly used Folmer primers (LCO1490/HCO2198) that capture the standard barcode region, and with the C1-J-2183/C1-N-2776 primer pair that amplifies its extension. However, C1-J-2183 is designed too close to HCO2198 for well-interpreted, continuous sequence data, and in practice the resulting sequences from the two primer pairs rarely overlap. We therefore designed a new forward primer C1-J-2123 60 base pairs upstream of the C1-J-2183 binding site. The success rate of this new primer (93%) matched that of C1-J-2183.<br><br>CONCLUSIONS: The use of C1-J-2123 allows full, indel-free overlap of sequences obtained with the standard Folmer primers and with C1-J-2123 primer pair. Our preliminary tests suggest that in addition to spiders, C1-J-2123 will also perform in other arachnids and several other invertebrates. We provide optimal PCR protocols for these primer sets, and recommend using them for systematic efforts beyond DNA barcoding.},
}
@article {pmid25414723,
year = {2014},
author = {Erickson, DL and Jones, FA and Swenson, NG and Pei, N and Bourg, NA and Chen, W and Davies, SJ and Ge, XJ and Hao, Z and Howe, RW and Huang, CL and Larson, AJ and Lum, SK and Lutz, JA and Ma, K and Meegaskumbura, M and Mi, X and Parker, JD and Fang-Sun, I and Wright, SJ and Wolf, AT and Ye, W and Xing, D and Zimmerman, JK and Kress, WJ},
title = {Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach.},
journal = {Frontiers in genetics},
volume = {5},
number = {},
pages = {358},
pmid = {25414723},
issn = {1664-8021},
abstract = {Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of phylogenetic diversity in the mega-phylogeny were more consistent, thereby removing a potential source of bias at the plot-level, and demonstrating the value of assessing phylogenetic relationships simultaneously within a mega-phylogeny. An unexpected result of the comparisons among plots based on the mega-phylogeny was that the communities in the ForestGEO plots in general appear to be assemblages of more closely related species than expected by chance, and that differentiation among communities is very low, suggesting deep floristic connections among communities and new avenues for future analyses in community ecology.},
}
@article {pmid25414325,
year = {2015},
author = {Yoon, JK and Ahn, J and Kim, HS and Han, SM and Jang, H and Lee, MG and Lee, JH and Bang, D},
title = {microDuMIP: target-enrichment technique for microarray-based duplex molecular inversion probes.},
journal = {Nucleic acids research},
volume = {43},
number = {5},
pages = {e28},
pmid = {25414325},
issn = {1362-4962},
mesh = {DNA, Single-Stranded/*genetics ; Exome/genetics ; *Molecular Probe Techniques ; Oligonucleotide Array Sequence Analysis/*methods ; Oligonucleotide Probes/*genetics ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; },
abstract = {Molecular inversion probe (MIP)-based capture is a scalable and effective target-enrichment technology that can use synthetic single-stranded oligonucleotides as probes. Unlike the straightforward use of synthetic oligonucleotides for low-throughput target capture, high-throughput MIP capture has required laborious protocols to generate thousands of single-stranded probes from DNA microarray because of multiple enzymatic steps, gel purifications and extensive PCR amplifications. Here, we developed a simple and efficient microarray-based MIP preparation protocol using only one enzyme with double-stranded probes and improved target capture yields by designing probes with overlapping targets and unique barcodes. To test our strategy, we produced 11 510 microarray-based duplex MIPs (microDuMIPs) and captured 3554 exons of 228 genes in a HapMap genomic DNA sample (NA12878). Under our protocol, capture performance and precision of calling were compatible to conventional MIP capture methods, yet overlapping targets and unique barcodes allowed us to precisely genotype with as little as 50 ng of input genomic DNA without library preparation. microDuMIP method is simpler and cheaper, allowing broader applications and accurate target sequencing with a scalable number of targets.},
}
@article {pmid25413618,
year = {2014},
author = {Justi, SA and Dale, C and Galvão, C},
title = {DNA barcoding does not separate South American Triatoma (Hemiptera: Reduviidae), Chagas Disease vectors.},
journal = {Parasites &amp; vectors},
volume = {7},
number = {},
pages = {519},
pmid = {25413618},
issn = {1756-3305},
mesh = {Animals ; Chagas Disease/*transmission ; DNA/*genetics ; DNA Barcoding, Taxonomic/*methods ; Insect Vectors/*genetics ; Reduviidae/*genetics ; Species Specificity ; },
abstract = {BACKGROUND: DNA barcoding assumes that a biological entity is completely separated from its closest relatives by a barcoding gap, which means that intraspecific genetic distance (from COI sequences) should never be greater than interspecific distances. We investigated the applicability of this strategy in identifying species of the genus Triatoma from South America.<br><br>FINDINGS: We calculated intra and interspecific Kimura-2-parameter distances between species from the infestans, matogrossensis, sordida and rubrovaria subcomplexes. In every subcomplex examined we observed at least one intraspecific distance greater than interspecific distances.<br><br>CONCLUSIONS: Although DNA barcoding is a straightforward approach, it was not applicable for identifying Southern American Triatoma species, which may have diverged recently. Thus, caution should be taken in identifying vector species using this approach, especially in groups where accurate identification of taxa is fundamentally linked to public health issues.},
}
@article {pmid25412510,
year = {2014},
author = {Kajtoch, &#x141;},
title = {A DNA metabarcoding study of a polyphagous beetle dietary diversity: the utility of barcodes and sequencing techniques.},
journal = {Folia biologica},
volume = {62},
number = {3},
pages = {223-234},
doi = {10.3409/fb62_3.223},
pmid = {25412510},
issn = {0015-5497},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Diet ; *Feeding Behavior ; Nucleic Acid Amplification Techniques/*methods ; Plants/*genetics ; Weevils/*physiology ; },
abstract = {Recently developed techniques of DNA barcoding and next-generation sequencing (NGS) overcome previous limitations of evaluation of animal diet composition and together are promising method in molecular ecology. The objective was to compare standard ABI Sanger sequencing with new high throughput sequencing (Illumina MiSeq) technique and the two selected plant barcodes (rbcL gene and trnL intron) in terms of the identification of host plant composition for the selected beetle species--the Centricnemus leucogrammus weevil. A comparison of two sequencing techniques showed that NGS (in this case Illumina) gave more exhaustive results than the Sanger method. Moreover, it was proven that a two-locus barcoding systems (rbcL and trnL) is sufficient for host plant identification from DNA isolated from insect bodies, at least at the genus level. A comparison of host plant composition among distant populations revealed that the studied species did not feed uniformly across its range. This probably reveals an ecological adaptation of geographically and genetically isolated populations. These findings, beside broadening basic knowledge on the use of barcoding and sequencing techniques for host plant identifications in insect populations, can have implications for conservation studies and strategies for rare and endangered species.},
}
@article {pmid25411954,
year = {2014},
author = {Gargiulo, G and Serresi, M and Cesaroni, M and Hulsman, D and van Lohuizen, M},
title = {In vivo shRNA screens in solid tumors.},
journal = {Nature protocols},
volume = {9},
number = {12},
pages = {2880-2902},
pmid = {25411954},
issn = {1750-2799},
mesh = {Adenocarcinoma/genetics ; Adenocarcinoma of Lung ; Animals ; Clustered Regularly Interspaced Short Palindromic Repeats ; Female ; Gene Library ; Gene Targeting/*methods ; *Genetic Techniques ; Heterografts ; Humans ; Lung Neoplasms/genetics ; Male ; Mice, Inbred BALB C ; Neoplasms, Experimental/*genetics ; Oncogenes ; RNA Interference ; RNA, Small Interfering/*genetics ; Transfection ; },
abstract = {Loss-of-function (LOF) experiments targeting multiple genes during tumorigenesis can be implemented using pooled shRNA libraries. RNAi screens in animal models rely on the use of multiple shRNAs to simultaneously disrupt gene function, as well as to serve as barcodes for cell fate outcomes during tumorigenesis. Here we provide a protocol for performing RNAi screens in orthotopic mouse tumor models, referring to glioma and lung adenocarcinoma as specific examples. The protocol aims to provide guidelines for applying RNAi to a diverse spectrum of solid tumors and to highlight crucial considerations when designing and performing these studies. It covers shRNA library assembly and packaging into lentiviral particles, and transduction into tumor-initiating cells (TICs), followed by in vivo transplantation, tumor DNA recovery, sequencing and analysis. Depending on the target genes and tumor model, tumor suppressors and oncogenes can be identified or biological pathways can be dissected in 6-9 weeks.},
}
@article {pmid25411428,
year = {2015},
author = {Łyszkiewicz, M and Ziętara, N and Föhse, L and Puchałka, J and Diestelhorst, J and Witzlau, K and Prinz, I and Schambach, A and Krueger, A},
title = {Limited niche availability suppresses murine intrathymic dendritic-cell development from noncommitted progenitors.},
journal = {Blood},
volume = {125},
number = {3},
pages = {457-464},
doi = {10.1182/blood-2014-07-592667},
pmid = {25411428},
issn = {1528-0020},
mesh = {Animals ; Cell Differentiation ; Cell Lineage ; Cells, Cultured ; Dendritic Cells/cytology/*immunology ; Flow Cytometry ; Mice ; Mice, Inbred C57BL ; Myeloid Cells/cytology/*immunology ; Stem Cell Niche/*immunology ; Stem Cells/cytology/*immunology ; T-Lymphocytes/cytology/*immunology ; Thymus Gland/cytology/*immunology ; },
abstract = {The origins of dendritic cells (DCs) and other myeloid cells in the thymus have remained controversial. In this study, we assessed developmental relationships between thymic dendritic cells and thymocytes, employing retrovirus-based cellular barcoding and reporter mice, as well as intrathymic transfers coupled with DC depletion. We demonstrated that a subset of early T-lineage progenitors expressed CX3CR1, a bona fide marker for DC progenitors. However, intrathymic transfers into nonmanipulated mice, as well as retroviral barcoding, indicated that thymic dendritic cells and thymocytes were largely of distinct developmental origin. In contrast, intrathymic transfers after in vivo depletion of DCs resulted in intrathymic development of non-T-lineage cells. In conclusion, our data support a model in which the adoption of T-lineage fate by noncommitted progenitors at steady state is enforced by signals from the thymic microenvironment unless niches promoting alternative lineage fates become available.},
}
@article {pmid25406744,
year = {2014},
author = {Heffelfinger, C and Fragoso, CA and Moreno, MA and Overton, JD and Mottinger, JP and Zhao, H and Tohme, J and Dellaporta, SL},
title = {Flexible and scalable genotyping-by-sequencing strategies for population studies.},
journal = {BMC genomics},
volume = {15},
number = {1},
pages = {979},
pmid = {25406744},
issn = {1471-2164},
support = {R01 GM59507/GM/NIGMS NIH HHS/United States ; S10 RR029676/RR/NCRR NIH HHS/United States ; T15 LM007056/LM/NLM NIH HHS/United States ; RR19895/RR/NCRR NIH HHS/United States ; S10 RR019895/RR/NCRR NIH HHS/United States ; UL1 TR000142/TR/NCATS NIH HHS/United States ; RR029676-01/RR/NCRR NIH HHS/United States ; R01 GM059507/GM/NIGMS NIH HHS/United States ; },
mesh = {Base Composition/genetics ; Base Pairing/genetics ; Computer Simulation ; Crosses, Genetic ; Databases, Genetic ; Genetics, Population ; Genomics ; Genotyping Techniques/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Methylation ; Oryza/*genetics ; Quantitative Trait, Heritable ; Reproducibility of Results ; Restriction Mapping ; Zea mays/*genetics ; },
abstract = {BACKGROUND: Many areas critical to agricultural production and research, such as the breeding and trait mapping in plants and livestock, require robust and scalable genotyping platforms. Genotyping-by-sequencing (GBS) is a one such method highly suited to non-human organisms. In the GBS protocol, genomic DNA is fractionated via restriction digest, then reduced representation is achieved through size selection. Since many restriction sites are conserved across a species, the sequenced portion of the genome is highly consistent within a population. This makes the GBS protocol highly suited for experiments that require surveying large numbers of markers within a population, such as those involving genetic mapping, breeding, and population genomics. We have modified the GBS technology in a number of ways. Custom, enzyme specific adaptors have been replaced with standard Illumina adaptors compatible with blunt-end restriction enzymes. Multiplexing is achieved through a dual barcoding system, and bead-based library preparation protocols allows for in-solution size selection and eliminates the need for columns and gels.<br><br>RESULTS: A panel of eight restriction enzymes was selected for testing on B73 maize and Nipponbare rice genomic DNA. Quality of the data was demonstrated by identifying that the vast majority of reads from each enzyme aligned to restriction sites predicted in silico. The link between enzyme parameters and experimental outcome was demonstrated by showing that the sequenced portion of the genome was adaptable by selecting enzymes based on motif length, complexity, and methylation sensitivity. The utility of the new GBS protocol was demonstrated by correctly mapping several in a maize F2 population resulting from a B73&#xd7;Country Gentleman test cross.<br><br>CONCLUSIONS: This technology is readily adaptable to different genomes, highly amenable to multiplexing and compatible with over forty commercially available restriction enzymes. These advancements represent a major improvement in genotyping technology by providing a highly flexible and scalable GBS that is readily implemented for studies on genome-wide variation.},
}
@article {pmid25399432,
year = {2014},
author = {Starý, P and Kavallieratos, NG and Petrović, A and Žikić, V and Rakhshani, E and Tomanović, S and Tomanović, &#x17d; and Havelka, J},
title = {Interference of field evidence, morphology, and DNA analyses of three related Lysiphlebus aphid parasitoids (Hymenoptera: Braconidae: Aphidiinae).},
journal = {Journal of insect science (Online)},
volume = {14},
number = {},
pages = {171},
pmid = {25399432},
issn = {1536-2442},
mesh = {Animals ; Aphids/*parasitology ; Czech Republic ; DNA Barcoding, Taxonomic ; Ecosystem ; Female ; *Host Specificity ; Wasps/anatomy &amp; histology/*genetics ; },
abstract = {This study provides evidence on integrating the morphological, field, and laboratory data, and application of the cytochrome oxidase subunit I (COI) barcoding gene to the three asexual or sexual Lysiphlebus spp., i.e., Lysiphlebus cardui (Marshall), Lysiphlebus confusus Tremblay and Eady and Lysiphlebus fabarum (Marshall) (Hymenoptera: Braconidae: Aphidiinae). New aphid- invasive plant association, Aphis fabae Scopoli (Hemipreta: Aphididae) on Impatiens glandulifera Royle, has been used in the same model area in the Czech Republic under the same sampling and rearing method for several consecutive years and throughout the season. For molecular identification of these three species, we used DNA sequences of the barcoding region of the mitochondrial COI gene. Although our results confirmed ecological and morphological differences among L. cardui, L. confusus, and L. fabarum, genetic analysis on the basis of COI mitochondrial barcoding gene does not support species status of the mentioned Lysiphlebus taxa. The level of morphological differentiation in these Lysiphlebus Förster species is in accordance with the usual species variability within subfamily Aphidiinae. However, it should be examined how appearance of asexual lineages affects the morphological or genetical variability.},
}
@article {pmid25393430,
year = {2014},
author = {Zhao, Y and Shang, L and Cheng, Y and Gu, Z},
title = {Spherical colloidal photonic crystals.},
journal = {Accounts of chemical research},
volume = {47},
number = {12},
pages = {3632-3642},
doi = {10.1021/ar500317s},
pmid = {25393430},
issn = {1520-4898},
mesh = {Clinical Laboratory Techniques ; Colloids/*chemistry ; Crystallization ; Nanoparticles/chemistry ; *Optics and Photonics ; Particle Size ; },
abstract = {CONSPECTUS: Colloidal photonic crystals (PhCs), periodically arranged monodisperse nanoparticles, have emerged as one of the most promising materials for light manipulation because of their photonic band gaps (PBGs), which affect photons in a manner similar to the effect of semiconductor energy band gaps on electrons. The PBGs arise due to the periodic modulation of the refractive index between the building nanoparticles and the surrounding medium in space with subwavelength period. This leads to light with certain wavelengths or frequencies located in the PBG being prohibited from propagating. Because of this special property, the fabrication and application of colloidal PhCs have attracted increasing interest from researchers. The most simple and economical method for fabrication of colloidal PhCs is the bottom-up approach of nanoparticle self-assembly. Common colloidal PhCs from this approach in nature are gem opals, which are made from the ordered assembly and deposition of spherical silica nanoparticles after years of siliceous sedimentation and compression. Besides naturally occurring opals, a variety of manmade colloidal PhCs with thin film or bulk morphology have also been developed. In principle, because of the effect of Bragg diffraction, these PhC materials show different structural colors when observed from different angles, resulting in brilliant colors and important applications. However, this angle dependence is disadvantageous for the construction of some optical materials and devices in which wide viewing angles are desired. Recently, a series of colloidal PhC materials with spherical macroscopic morphology have been created. Because of their spherical symmetry, the PBGs of spherical colloidal PhCs are independent of rotation under illumination of the surface at a fixed incident angle of the light, broadening the perspective of their applications. Based on droplet templates containing colloidal nanoparticles, these spherical colloidal PhCs can be generated by evaporation-induced nanoparticle crystallization or polymerization of ordered nanoparticle crystallization arrays. In particular, because microfluidics was used for the generation of the droplet templates, the development of spherical colloidal PhCs has progressed significantly. These new strategies not only ensure monodispersity, but also increase the structural and functional diversity of the PhC beads, paving the way for the development of advanced optoelectronic devices. In this Account, we present the research progress on spherical colloidal PhCs, including their design, preparation, and potential applications. We outline various types of spherical colloidal PhCs, such as close-packed, non-close-packed, inverse opal, biphasic or multiphasic Janus structured, and core-shell structured geometries. Based on their unique optical properties, applications of the spherical colloidal PhCs for displays, sensors, barcodes, and cell culture microcarriers are presented. Future developments of the spherical colloidal PhC materials are also envisioned.},
}
@article {pmid25392800,
year = {2014},
author = {Karp, DS and Judson, S and Daily, GC and Hadly, EA},
title = {Molecular diagnosis of bird-mediated pest consumption in tropical farmland.},
journal = {SpringerPlus},
volume = {3},
number = {},
pages = {630},
pmid = {25392800},
issn = {2193-1801},
abstract = {Biodiversity loss will likely have surprising and dramatic consequences for human wellbeing. Identifying species that benefit society represents a critical first step towards predicting the consequences of biodiversity loss. Though natural predators prevent billions of dollars in agricultural pest damage annually, characterizing which predators consume pests has proven challenging. Emerging molecular techniques may illuminate these interactions. In the countryside of Costa Rica, we identified avian predators of coffee's most damaging insect pest, the coffee berry borer beetle (Coleoptera:Scolytidae Hypothenemus hampeii), by assaying 1430 fecal samples of 108 bird species for borer DNA. While feeding trials confirmed the efficacy of our approach, detection rates were low. Nevertheless, we identified six species that consume the borer. These species had narrow diet breadths, thin bills, and short wings; traits shared with borer predators in other systems. Borer predators were not threatened; therefore, safeguarding pest control necessitates managing species beyond those at risk of regional extinction by maintaining populations in farmland habitats. Generally, our results demonstrate potential for pairing molecular methods with ecological analyses to yield novel insights into species interactions.},
}
@article {pmid25391846,
year = {2015},
author = {Erpenbeck, D and Aryasari, R and Hooper, JN and Wörheide, G},
title = {A mitochondrial intron in a verongid sponge.},
journal = {Journal of molecular evolution},
volume = {80},
number = {1},
pages = {13-17},
pmid = {25391846},
issn = {1432-1432},
mesh = {Animals ; Genome, Mitochondrial ; Introns/*genetics ; Mitochondria/*genetics ; Phylogeny ; Porifera/classification/*genetics ; },
abstract = {We discovered for the first time a mitochondrial intron in a non-tetillid demosponge, which sheds new light on the interpretation of mitochondrial intron evolution among non-bilaterian animals and has consequences for phylogenetic and DNA barcoding studies. The newly discovered class 1 intron of Aplysinella rhax (Verongida) CO1 has an ORF for a putative LAGLIDADG-type and resembles other sponge and cnidarian mitochondrial introns. Our analysis of the Aplysinella rhax intron underlines that the patchy distribution of introns in sponges is caused by a combination of horizontal and vertical transmission. Further implications for CO1 phylogenetic and barcoding projects are discussed.},
}
@article {pmid25388264,
year = {2015},
author = {Haddon, DJ and Jarrell, JA and Hughes, MR and Snyder, K and McNagny, KM and Kattah, MG and Utz, PJ},
title = {Measurement of mast cell surface molecules by high-throughput immunophenotyping using transcription (HIT).},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1220},
number = {},
pages = {381-400},
doi = {10.1007/978-1-4939-1568-2_24},
pmid = {25388264},
issn = {1940-6029},
support = {2 OR-92141//Canadian Institutes of Health Research/Canada ; 268201000034C//PHS HHS/United States ; 5 U19-AI082719/AI/NIAID NIH HHS/United States ; },
mesh = {Antigens, Surface/metabolism ; Base Sequence ; Cell Line, Tumor ; Cytokines/metabolism ; Flow Cytometry ; Humans ; Immunophenotyping/*methods ; Mast Cells/cytology/immunology/*metabolism ; Nucleic Acid Hybridization ; Oligonucleotides/biosynthesis/genetics ; Staining and Labeling ; Transcription Factors/metabolism ; *Transcription, Genetic ; },
abstract = {Here we describe the application of a highly multiplexed proteomic assay, called HIT (high-throughput immunophenotyping using transcription), to analyze human mast cell surface antigens at rest and during stimulation. HIT allows analysis of up to 100 analytes, including surface antigens and intracellular phosphoproteins, transcription factors, and cytokines, in a single experiment. Briefly, anti-mouse monovalent Fab fragments are covalently conjugated with barcoded oligonucleotides to generate a panel of conjugates. The oligonucleotide-Fab fragment conjugates are bound to monoclonal primary antibodies, creating a cocktail of up to 48 unique barcoded primary antibodies. As few as 100,000 mast cells are stained with the cocktail and the barcodes of the bound primary antibodies are amplified by in vitro transcription with fluorescently labeled NTPs. The resulting barcoded transcripts are quantified using a microarray spotted with oligonucleotides that are complementary to the barcoded transcripts. Differences in levels of the barcoded transcripts correlate well with actual protein levels and are capable of detecting stimulation-dependent changes in protein levels. HIT is an invaluable, broad-spectrum approach for characterizing mast cell surface antigens, signaling molecules, transcription factors, and cytokines.},
}
@article {pmid25386879,
year = {2014},
author = {Muscarella, R and Uriarte, M and Erickson, DL and Swenson, NG and Zimmerman, JK and Kress, WJ},
title = {A well-resolved phylogeny of the trees of Puerto Rico based on DNA barcode sequence data.},
journal = {PloS one},
volume = {9},
number = {11},
pages = {e112843},
pmid = {25386879},
issn = {1932-6203},
mesh = {DNA Barcoding, Taxonomic/*methods ; Forests ; *Phylogeny ; Puerto Rico ; Trees/classification/*genetics ; },
abstract = {BACKGROUND: The use of phylogenetic information in community ecology and conservation has grown in recent years. Two key issues for community phylogenetics studies, however, are (i) low terminal phylogenetic resolution and (ii) arbitrarily defined species pools.<br><br>We used three DNA barcodes (plastid DNA regions rbcL, matK, and trnH-psbA) to infer a phylogeny for 527 native and naturalized trees of Puerto Rico, representing the vast majority of the entire tree flora of the island (89%). We used a maximum likelihood (ML) approach with and without a constraint tree that enforced monophyly of recognized plant orders. Based on 50% consensus trees, the ML analyses improved phylogenetic resolution relative to a comparable phylogeny generated with Phylomatic (proportion of internal nodes resolved: constrained ML&#x200a;=&#x200a;74%, unconstrained ML&#x200a;=&#x200a;68%, Phylomatic&#x200a;=&#x200a;52%). We quantified the phylogenetic composition of 15 protected forests in Puerto Rico using the constrained ML and Phylomatic phylogenies. We found some evidence that tree communities in areas of high water stress were relatively phylogenetically clustered. Reducing the scale at which the species pool was defined (from island to soil types) changed some of our results depending on which phylogeny (ML vs. Phylomatic) was used. Overall, the increased terminal resolution provided by the ML phylogeny revealed additional patterns that were not observed with a less-resolved phylogeny.<br><br>CONCLUSIONS/SIGNIFICANCE: With the DNA barcode phylogeny presented here (based on an island-wide species pool), we show that a more fully resolved phylogeny increases power to detect nonrandom patterns of community composition in several Puerto Rican tree communities. Especially if combined with additional information on species functional traits and geographic distributions, this phylogeny will (i) facilitate stronger inferences about the role of historical processes in governing the assembly and composition of Puerto Rican forests, (ii) provide insight into Caribbean biogeography, and (iii) aid in incorporating evolutionary history into conservation planning.},
}
@article {pmid25377225,
year = {2014},
author = {Frausto, RF and Wang, C and Aldave, AJ},
title = {Transcriptome analysis of the human corneal endothelium.},
journal = {Investigative ophthalmology &amp; visual science},
volume = {55},
number = {12},
pages = {7821-7830},
pmid = {25377225},
issn = {1552-5783},
support = {P30 EY000331/EY/NEI NIH HHS/United States ; R01 EY022082/EY/NEI NIH HHS/United States ; },
mesh = {Adult ; Corneal Dystrophies, Hereditary/*genetics/metabolism ; Endothelium, Corneal/*metabolism ; Eye Proteins/*genetics/metabolism ; Fuchs' Endothelial Dystrophy/*genetics/metabolism ; Gene Expression Profiling ; Humans ; Oligonucleotide Array Sequence Analysis ; RNA, Messenger/metabolism ; Transcriptome ; },
abstract = {PURPOSE: To comprehensively characterize human corneal endothelial cell (HCEnC) gene expression and age-dependent differential gene expression and to identify expressed genes mapped to chromosomal loci associated with the corneal endothelial dystrophies posterior polymorphous corneal dystrophy (PPCD)1, Fuchs endothelial corneal dystrophy (FECD)4, and X-linked endothelial dystrophy (XECD).<br><br>METHODS: Total RNA was isolated from ex vivo corneal endothelium obtained from six pediatric and five adult donor corneas. Complementary DNA was hybridized to the Affymetrix GeneChip 1.1ST array. Data analysis was performed using Partek Genomics Suite software, and differentially expressed genes were validated by digital molecular barcoding technology.<br><br>RESULTS: Transcripts corresponding to 12,596 genes were identified in HCEnC. Nine genes displayed the most significant differential expression between pediatric and adult HCEnC: CAPN6, HIST1H3A, HIST1H4E, and HSPA2 were expressed at higher levels in pediatric HCEnC, while ITGBL1, NALCN, PREX2, TAC1, and TMOD1 were expressed at higher levels in adult HCEnC. Analysis of the PPCD1, FECD4 and XECD loci demonstrated transcription of 53/95 protein-coding genes in the PPCD1 locus, 27/40 in the FECD4 locus, and 35/68 in the XECD locus.<br><br>CONCLUSIONS: An analysis of the HCEnC transcriptome reveals the expression of almost 13,000 genes, with less than 1% mapped to chromosomal loci associated with PPCD1, FECD4, and XECD. At least nine genes demonstrated significant differential expression between pediatric and adult HCEnC, defining specific functional properties distinct to each age group. These data will serve as a resource for vision scientists investigating HCEnC gene expression and can be used to focus the search for the genetic basis of the corneal endothelial dystrophies for which the genetic basis remains unknown.},
}
@article {pmid25376582,
year = {2015},
author = {Lv, W and Wei, X and Guo, R and Liu, Q and Zheng, Y and Chang, J and Bai, T and Li, H and Zhang, J and Song, Z and Cram, DS and Liang, D and Wu, L},
title = {Noninvasive prenatal testing for Wilson disease by use of circulating single-molecule amplification and resequencing technology (cSMART).},
journal = {Clinical chemistry},
volume = {61},
number = {1},
pages = {172-181},
doi = {10.1373/clinchem.2014.229328},
pmid = {25376582},
issn = {1530-8561},
mesh = {Adenosine Triphosphatases/genetics ; Alleles ; Cation Transport Proteins/genetics ; Copper-Transporting ATPases ; *DNA/blood/genetics ; DNA Mutational Analysis/*methods ; DNA Probes ; Female ; Gestational Age ; Hepatolenticular Degeneration/*blood/embryology/*genetics ; Heterozygote ; Homozygote ; Humans ; Male ; Molecular Diagnostic Techniques/instrumentation/*methods ; Pregnancy ; Prenatal Diagnosis/instrumentation/*methods ; },
abstract = {BACKGROUND: Noninvasive prenatal testing (NIPT) for monogenic diseases by use of PCR-based strategies requires precise quantification of mutant fetal alleles circulating in the maternal plasma. The study describes the development and validation of a novel assay termed circulating single-molecule amplification and resequencing technology (cSMART) for counting single allelic molecules in plasma. Here we demonstrate the suitability of cSMART for NIPT, with Wilson Disease (WD) as proof of concept.<br><br>METHODS: We used Sanger and whole-exome sequencing to identify familial ATP7B (ATPase, Cu(++) transporting, &#x3b2; polypeptide) gene mutations. For cSMART, single molecules were tagged with unique barcodes and circularized, and alleles were targeted and replicated by inverse PCR. The unique single allelic molecules were identified by sequencing and counted, and the percentage of mutant alleles in the original maternal plasma sample was used to determine fetal genotypes.<br><br>RESULTS: Four families with WD pedigrees consented to the study. Using Sanger and whole-exome sequencing, we mapped the pathogenic ATP7B mutations in each pedigree and confirmed the proband's original diagnosis of WD. After validation of cSMART with defined plasma models mimicking fetal inheritance of paternal, maternal, or both parental mutant alleles, we retrospectively showed in second pregnancies that the fetal genotypes assigned by invasive testing and NIPT were concordant.<br><br>CONCLUSIONS: We developed a reliable and accurate NIPT assay that correctly diagnosed the fetal genotypes in 4 pregnancies at risk for WD. This novel technology has potential as a universal strategy for NIPT of other monogenic disorders, since it requires only knowledge of the parental pathogenic mutations.},
}
@article {pmid25373757,
year = {2015},
author = {Maughan, PJ and Udall, JA and Jellen, EN},
title = {Genomic reduction assisted single nucleotide polymorphism discovery using 454-pyrosequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1245},
number = {},
pages = {169-182},
doi = {10.1007/978-1-4939-1966-6_13},
pmid = {25373757},
issn = {1940-6029},
mesh = {Biotin/metabolism ; Chromatography, Gel ; DNA Barcoding, Taxonomic ; Genomics/*methods ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide/*genetics ; Restriction Mapping ; Sequence Analysis, DNA/*methods ; Streptavidin/metabolism ; },
abstract = {We report the development of a simple genomic reduction protocol based on 454-pyrosequencing technology that discovers large numbers of single nucleotide polymorphisms (SNP) from pooled DNA samples. The method is based on the conservation of restriction endonuclease sites across samples and biotin separation for genomic reduction and the addition of multiplex identifier (MID) barcodes to each of the pooled samples to allow for postsequencing deconvolution of the pooled DNA fragments and SNP discovery.},
}
@article {pmid25373752,
year = {2015},
author = {de Vere, N and Rich, TC and Trinder, SA and Long, C},
title = {DNA barcoding for plants.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1245},
number = {},
pages = {101-118},
doi = {10.1007/978-1-4939-1966-6_8},
pmid = {25373752},
issn = {1940-6029},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/isolation &amp; purification ; Electrophoresis, Agar Gel ; Information Systems ; Plants/classification/*genetics ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; Specimen Handling ; Terminology as Topic ; },
abstract = {DNA barcoding uses specific regions of DNA in order to identify species. Initiatives are taking place around the world to generate DNA barcodes for all groups of living organisms and to make these data publically available in order to help understand, conserve, and utilize the world's biodiversity. For land plants the core DNA barcode markers are two sections of coding regions within the chloroplast, part of the genes, rbcL and matK. In order to create high quality databases, each plant that is DNA barcoded needs to have a herbarium voucher that accompanies the rbcL and matK DNA sequences. The quality of the DNA sequences, the primers used, and trace files should also be accessible to users of the data. Multiple individuals should be DNA barcoded for each species in order to check for errors and allow for intraspecific variation. The world's herbaria provide a rich resource of already preserved and identified material and these can be used for DNA barcoding as well as by collecting fresh samples from the wild. These protocols describe the whole DNA barcoding process, from the collection of plant material from the wild or from the herbarium, how to extract and amplify the DNA, and how to check the quality of the data after sequencing.},
}
@article {pmid25373226,
year = {2014},
author = {Li, M and Liu, Q and Xi, L and Liu, Y and Zhu, G and Zhao, Y and Bu, W},
title = {Testing the potential of proposed DNA barcoding markers in Nezara virudula and Nezara antennata when geographic variation and closely related species were considered.},
journal = {Journal of insect science (Online)},
volume = {14},
number = {},
pages = {79},
pmid = {25373226},
issn = {1536-2442},
mesh = {Animals ; Cytochromes b/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Hemiptera/*genetics ; Phylogeography ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {The COI gene as the core of the DNA barcoding system for animals has received significant attention. The observed wide overlap between intraand interspecific sequence variability has led researchers to envisage the primary COI-based method. The sequences of 16S rDNA, COI, and Cyt b genes of Nezara virudula (L.) (Hemiptera: Pentatomidae) from 13 countries and the same sequences of N. antennata Scott were chosen as molecular markers to analyze the intraand interspecific relationships between the closely related species in this study. The results support that Cyt b gene may be a good candidate alongside COI, when the combined factors of geographic variation and closely related species are taken into account.},
}
@article {pmid25373224,
year = {2014},
author = {Farinha, A and Dourado, CG and Centeio, N and Oliveira, AR and Dias, D and Rebelo, MT},
title = {Small bait traps as accurate predictors of dipteran early colonizers in forensic studies.},
journal = {Journal of insect science (Online)},
volume = {14},
number = {},
pages = {77},
pmid = {25373224},
issn = {1536-2442},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic ; *Diptera ; Forensic Sciences/*instrumentation ; },
abstract = {Insect carrion communities vary among habitats and over time. Concerning the dipteran early colonizers of carrion, the use of small bait traps should be accurate because the odors emitted from meat baits should contain many of the volatile organic compounds emitted from the freshly dead mammals. In addition, this kind of trap is easy to replicate and set in position in a given habitat. In the present study, small bait preferences of early Diptera carrion colonizers were examined in an urban biotope. Specifically, three baits were compared (pork muscle, pork liver, and fish flavored cat food) in respect to the number of specimens and species captured and the presence or absence of oviposition at high and low environmental temperatures. A total of 2371 specimens were trapped, primarily belonging to three insect orders, Diptera, Coleoptera, and Hymenoptera. Diptera was the predominant order, with blowflies (Calliphoridae) being the most representative family, followed by filth flies (Muscidae). The pork muscle bait was responsible for the highest number of captures and the highest diversity. The community of Diptera collected with the most efficient bait, pork muscle, was compared with the carrion communities reported in the literature from the Iberian Peninsula. Similar taxonomic species composition was found regarding Calliphoridae species. A specimen from all species morphologically identified were also identified at a molecular level using the cytochrome c oxidase I (COI) barcode region, and the sequences were submitted to online databases.},
}
@article {pmid25372406,
year = {2014},
author = {Hua, GK and Bertier, L and Soltaninejad, S and Höfte, M},
title = {Cropping systems and cultural practices determine the Rhizoctonia anastomosis groups associated with Brassica spp. in Vietnam.},
journal = {PloS one},
volume = {9},
number = {11},
pages = {e111750},
pmid = {25372406},
issn = {1932-6203},
mesh = {Brassica/*microbiology ; DNA, Intergenic ; Geography ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Plant Diseases/microbiology ; Plant Leaves/microbiology ; Rhizoctonia/*classification/genetics ; Vietnam ; },
abstract = {Ninety seven Rhizoctonia isolates were collected from different Brassica species with typical Rhizoctonia symptoms in different provinces of Vietnam. The isolates were identified using staining of nuclei and sequencing of the rDNA-ITS barcoding gene. The majority of the isolates were multinucleate R. solani and four isolates were binucleate Rhizoctonia belonging to anastomosis groups (AGs) AG-A and a new subgroup of A-F that we introduce here as AG-Fc on the basis of differences in rDNA-ITS sequence. The most prevalent multinucleate AG was AG 1-IA (45.4% of isolates), followed by AG 1-ID (17.5%), AG 1-IB (13.4%), AG 4-HGI (12.4%), AG 2-2 (5.2%), AG 7 (1.0%) and an unknown AG related to AG 1-IA and AG 1-IE that we introduce here as AG 1-IG (1.0%) on the basis of differences in rDNA-ITS sequence. AG 1-IA and AG 1-ID have not been reported before on Brassica spp. Pathogenicity tests revealed that isolates from all AGs, except AG-A, induced symptoms on detached leaves of several cabbage species. In in vitro tests on white cabbage and Chinese cabbage, both hosts were severely infected by AG 1-IB, AG 2-2, AG 4-HGI, AG 1-IG and AG-Fc isolates, while under greenhouse conditions, only AG 4-HGI, AG 2-2 and AG-Fc isolates could cause severe disease symptoms. The occurrence of the different AGs seems to be correlated with the cropping systems and cultural practices in different sampling areas suggesting that agricultural practices determine the AGs associated with Brassica plants in Vietnam.},
}
@article {pmid25366863,
year = {2014},
author = {Shaw, J and Shafer, HL and Leonard, OR and Kovach, MJ and Schorr, M and Morris, AB},
title = {Chloroplast DNA sequence utility for the lowest phylogenetic and phylogeographic inferences in angiosperms: the tortoise and the hare IV.},
journal = {American journal of botany},
volume = {101},
number = {11},
pages = {1987-2004},
doi = {10.3732/ajb.1400398},
pmid = {25366863},
issn = {1537-2197},
mesh = {Animals ; Chloroplasts/genetics ; DNA, Chloroplast/chemistry/*genetics ; Hares ; Introns/genetics ; Magnoliopsida/*genetics ; Phylogeography ; },
abstract = {PREMISE OF THE STUDY: Noncoding chloroplast DNA (NC-cpDNA) sequences are the staple data source of low-level phylogeographic and phylogenetic studies of angiosperms. We followed up on previous papers (tortoise and hare II and III) that sought to identify the most consistently variable regions of NC-cpDNA. We used an exhaustive literature review and newly available whole plastome data to assess applicability of previous conclusions at low taxonomic levels.<br><br>METHODS: We aligned complete plastomes of 25 species pairs from across angiosperms, comparing the number of genetic differences found in 107 NC-cpDNA regions and matK. We surveyed Web of Science for the plant phylogeographic literature between 2007 and 2013 to assess how NC-cpDNA has been used at the intraspecific level.<br><br>KEY RESULTS: Several regions are consistently the most variable across angiosperm lineages: ndhF-rpl32, rpl32-trnL((UAG)), ndhC-trnV((UAC)), 5'rps16-trnQ((UUG)), psbE-petL, trnT((GGU))-psbD, petA-psbJ, and rpl16 intron. However, there is no universally best region. The average number of regions applied to low-level studies is &#x223c;2.5, which may be too little to access the full discriminating power of this genome.<br><br>CONCLUSIONS: Plastome sequences have been used successfully at lower and lower taxonomic levels. Our findings corroborate earlier works, suggesting that there are regions that are most likely to be the most variable. However, while NC-cpDNA sequences are commonly used in plant phylogeographic studies, few of the most variable regions are applied in that context. Furthermore, it appears that in most studies too few NC-cpDNAs are used to access the discriminating power of the cpDNA genome.},
}
@article {pmid25366769,
year = {2014},
author = {Freitas, MT and Gomes-Júnior, PP and Batista, MV and Leal-Balbino, TC and Araujo, AL and Balbino, VQ},
title = {Novel DNA extraction assay for molecular identification of Aedes spp eggs.},
journal = {Genetics and molecular research : GMR},
volume = {13},
number = {4},
pages = {8776-8782},
doi = {10.4238/2014.October.27.19},
pmid = {25366769},
issn = {1676-5680},
mesh = {Aedes/classification/*genetics/virology ; Animals ; Base Sequence ; DNA/chemistry/*genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/chemistry/genetics ; Dengue Virus/physiology ; Female ; Host-Pathogen Interactions ; Insect Vectors/classification/genetics/virology ; Molecular Sequence Data ; Ovum/cytology/*metabolism ; Reproducibility of Results ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Species Specificity ; },
abstract = {Aedes aegypti and A. albopictus represent the two most important species of mosquitoes in relation to dengue virus transmission both in the Americas and Asia. However, the study of theses species generally requires the establishment of a colony for the larvae to hatch, or waiting for the adult development to perform its taxonomic classification, which is time consuming. Thus, the establishment of new methods aimed at obtaining DNA directly from the mosquito eggs is relevant. Accordingly, we compared a new approach based on Chelex(®) 100 resin with the standard STE method to extract DNA from the eggs of Aedes spp to molecularly identify these vectors. The Chelex(®) 100 resin approach was very efficient, as satisfactory amounts of DNA were obtained, making it possible to amplify and sequence a mitochondrial DNA barcode region widely used to identify species. The STE protocol yielded substantial amounts of DNA, but the 260/280 optical density ratio indicated a low quality, precluding amplification. This new method proved quite effective in obtaining DNA from even a single mosquito egg, and it can thus be applied in population genetic studies of various vector insects to enhance monitoring programs.},
}
@article {pmid25366764,
year = {2014},
author = {Marghali, S and Zitouna, N and Gharbi, M and Fadhlaoui, I and Trifi-Farah, N},
title = {Evolution of rbcL among Lathyrus and Kupicha's classification.},
journal = {Genetics and molecular research : GMR},
volume = {13},
number = {4},
pages = {8729-8739},
doi = {10.4238/2014.October.27.14},
pmid = {25366764},
issn = {1676-5680},
mesh = {Classification/methods ; *Evolution, Molecular ; Lathyrus/classification/*genetics ; Phylogeny ; Ribulose-Bisphosphate Carboxylase/*genetics ; },
abstract = {Phylogenetic relationships in the Lathyrus genus were examined using cpDNA data, particularly data attributed to the "barcode" rbcL gene to construct a possible evolutionary scenario. Plant barcoding can be used to differentiate between species within a genus and to conserve DNA within the same species. We assessed the phylogeny of 29 species of Lathyrus using maximum parsimony, maximum likelihood and unweighted pair-group method and arithmetic mean. The classifications did not agree with current morphological and basic Lathyrus classification. Lathyrus belinensis is a new species that was not described by Kupicha; according to rbcL analysis, the species belongs in the Lathyrus genus. Additionally, the genus Lathyrus has undergone a rapid population expansion as indicated by neutral selection indices.},
}
@article {pmid25365514,
year = {2014},
author = {Yang, Y and Dang, Y and Li, Q and Lu, J and Li, X and Wang, Y},
title = {Complete chloroplast genome sequence of poisonous and medicinal plant Datura stramonium: organizations and implications for genetic engineering.},
journal = {PloS one},
volume = {9},
number = {11},
pages = {e110656},
pmid = {25365514},
issn = {1932-6203},
mesh = {Base Composition ; Codon ; Computational Biology ; Datura stramonium/classification/*genetics ; Genetic Engineering ; *Genome, Chloroplast ; Genomics ; Microsatellite Repeats ; Molecular Sequence Annotation ; Phylogeny ; Plants, Medicinal/classification/*genetics ; Plants, Toxic/classification/*genetics ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; },
abstract = {Datura stramonium is a widely used poisonous plant with great medicinal and economic value. Its chloroplast (cp) genome is 155,871 bp in length with a typical quadripartite structure of the large (LSC, 86,302 bp) and small (SSC, 18,367 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 25,601 bp). The genome contains 113 unique genes, including 80 protein-coding genes, 29 tRNAs and four rRNAs. A total of 11 forward, 9 palindromic and 13 tandem repeats were detected in the D. stramonium cp genome. Most simple sequence repeats (SSR) are AT-rich and are less abundant in coding regions than in non-coding regions. Both SSRs and GC content were unevenly distributed in the entire cp genome. All preferred synonymous codons were found to use A/T ending codons. The difference in GC contents of entire genomes and of the three-codon positions suggests that the D. stramonium cp genome might possess different genomic organization, in part due to different mutational pressures. The five most divergent coding regions and four non-coding regions (trnH-psbA, rps4-trnS, ndhD-ccsA, and ndhI-ndhG) were identified using whole plastome alignment, which can be used to develop molecular markers for phylogenetics and barcoding studies within the Solanaceae. Phylogenetic analysis based on 68 protein-coding genes supported Datura as a sister to Solanum. This study provides valuable information for phylogenetic and cp genetic engineering studies of this poisonous and medicinal plant.},
}
@article {pmid25361832,
year = {2015},
author = {Park, MS and Fong, JJ and Oh, SY and Houbraken, J and Sohn, JH and Hong, SB and Lim, YW},
title = {Penicillium jejuense sp. nov., isolated from the marine environments of Jeju Island, Korea.},
journal = {Mycologia},
volume = {107},
number = {1},
pages = {209-216},
doi = {10.3852/14-180},
pmid = {25361832},
issn = {0027-5514},
mesh = {DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Molecular Sequence Data ; Penicillium/*classification/genetics/growth &amp; development/*isolation &amp; purification ; Phylogeny ; Republic of Korea ; Seawater/*microbiology ; Spores, Fungal/classification/genetics/growth &amp; development/isolation &amp; purification ; },
abstract = {Three strains of an unidentified Penicillium species were isolated during a fungal diversity survey of marine environments in Korea. These strains are described here as a new species following a multigene phylogenetic analyses of nuc rDNA internal transcribed spacer barcodes (ITS1-5.8S-ITS2), genes for β-tubulin, calmodulin and RNA polymerase II second largest subunit, and observation of macro-and micromorphological characters. Phylogenetic analyses revealed that the three strains formed a strongly supported monophyletic group distinct from previously reported species of section Aspergilloides. Morphologically this species can be distinguished from its sister species, P. crocicola, by the reverse color on Czapek yeast autolysate agar, abundant production of sclerotia on malt extract agar and colony characters on yeast extract sucrose agar. We name this new species P. jejuense, after the locality where it was discovered. At 25 C for 7 d, P. jejuense colonies grew to 55-60 mm on CYA, 45-48 mm on MEA, 48-52 mm on YES and 23-26 mm on CREA. Conidia (2.2-3.4 × 2.0-2.6 μm) and sclerotia (160-340 × 125-210 μm) were globose to ellipsoidal.},
}
@article {pmid25360280,
year = {2014},
author = {Liu, XF and Yang, CH and Han, HL and Ward, RD and Zhang, AB},
title = {Identifying species of moths (Lepidoptera) from Baihua Mountain, Beijing, China, using DNA barcodes.},
journal = {Ecology and evolution},
volume = {4},
number = {12},
pages = {2472-2487},
pmid = {25360280},
issn = {2045-7758},
abstract = {DNA barcoding has become a promising means for the identification of organisms of all life-history stages. Currently, distance-based and tree-based methods are most widely used to define species boundaries and uncover cryptic species. However, there is no universal threshold of genetic distance values that can be used to distinguish taxonomic groups. Alternatively, DNA barcoding can deploy a "character-based" method, whereby species are identified through the discrete nucleotide substitutions. Our research focuses on the delimitation of moth species using DNA-barcoding methods. We analyzed 393 Lepidopteran specimens belonging to 80 morphologically recognized species with a standard cytochrome c oxidase subunit I (COI) sequencing approach, and deployed tree-based, distance-based, and diagnostic character-based methods to identify the taxa. The tree-based method divided the 393 specimens into 79 taxa (species), and the distance-based method divided them into 84 taxa (species). Although the diagnostic character-based method found only 39 so-identifiable species in the 80 species, with a reduction in sample size the accuracy rate substantially improved. For example, in the Arctiidae subset, all 12 species had diagnostics characteristics. Compared with traditional morphological method, molecular taxonomy performed well. All three methods enable the rapid delimitation of species, although they have different characteristics and different strengths. The tree-based and distance-based methods can be used for accurate species identification and biodiversity studies in large data sets, while the character-based method performs well in small data sets and can also be used as the foundation of species-specific biochips.},
}
@article {pmid25360247,
year = {2014},
author = {Harrison, HB and Feldheim, KA and Jones, GP and Ma, K and Mansour, H and Perumal, S and Williamson, DH and Berumen, ML},
title = {Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae).},
journal = {Ecology and evolution},
volume = {4},
number = {11},
pages = {2046-2057},
pmid = {25360247},
issn = {2045-7758},
abstract = {Microsatellites are often considered ideal markers to investigate ecological processes in animal populations. They are regularly used as genetic barcodes to identify species, individuals, and infer familial relationships. However, such applications are highly sensitive the number and diversity of microsatellite markers, which are also prone to error. Here, we propose a novel framework to assess the suitability of microsatellite datasets for parentage analysis and species discrimination in two closely related species of coral reef fish, Plectropomus leopardus and P. maculatus (Serranidae). Coral trout are important fisheries species throughout the Indo-Pacific region and have been shown to hybridize in parts of the Great Barrier Reef, Australia. We first describe the development of 25 microsatellite loci and their integration to three multiplex PCRs that co-amplify in both species. Using simulations, we demonstrate that the complete suite of markers provides appropriate power to discriminate between species, detect hybrid individuals, and resolve parent-offspring relationships in natural populations, with over 99.6% accuracy in parent-offspring assignments. The markers were also tested on seven additional species within the Plectropomus genus with polymorphism in 28-96% of loci. The multiplex PCRs developed here provide a reliable and cost-effective strategy to investigate evolutionary and ecological dynamics and will be broadly applicable in studies of wild populations and aquaculture brood stocks for these closely related fish species.},
}
@article {pmid25359889,
year = {2015},
author = {Skums, P and Artyomenko, A and Glebova, O and Ramachandran, S and Mandoiu, I and Campo, DS and Dimitrova, Z and Zelikovsky, A and Khudyakov, Y},
title = {Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling.},
journal = {Bioinformatics (Oxford, England)},
volume = {31},
number = {5},
pages = {682-690},
doi = {10.1093/bioinformatics/btu726},
pmid = {25359889},
issn = {1367-4811},
mesh = {*Algorithms ; Computational Biology/*methods ; DNA, Viral/*genetics ; Genetic Variation ; *Genome, Viral ; Hepacivirus/classification/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Sequence Analysis, DNA/*methods ; Viruses/*classification/*genetics ; },
abstract = {MOTIVATION: Next-generation sequencing (NGS) allows for analyzing a large number of viral sequences from infected patients, providing an opportunity to implement large-scale molecular surveillance of viral diseases. However, despite improvements in technology, traditional protocols for NGS of large numbers of samples are still highly cost and labor intensive. One of the possible cost-effective alternatives is combinatorial pooling. Although a number of pooling strategies for consensus sequencing of DNA samples and detection of SNPs have been proposed, these strategies cannot be applied to sequencing of highly heterogeneous viral populations.<br><br>RESULTS: We developed a cost-effective and reliable protocol for sequencing of viral samples, that combines NGS using barcoding and combinatorial pooling and a computational framework including algorithms for optimal virus-specific pools design and deconvolution of individual samples from sequenced pools. Evaluation of the framework on experimental and simulated data for hepatitis C virus showed that it substantially reduces the sequencing costs and allows deconvolution of viral populations with a high accuracy.<br><br>The source code and experimental data sets are available at http://alan.cs.gsu.edu/NGS/?q=content/pooling.},
}
@article {pmid25356840,
year = {2014},
author = {Handy, SM and Chizhikov, V and Yakes, BJ and Paul, SZ and Deeds, JR and Mossoba, MM},
title = {Microarray chip development using infrared imaging for the identification of catfish species.},
journal = {Applied spectroscopy},
volume = {68},
number = {12},
pages = {1365-1373},
doi = {10.1366/14-07505},
pmid = {25356840},
issn = {1943-3530},
mesh = {Animals ; Catfishes/*classification/*genetics ; DNA/analysis/*genetics ; Equipment Design ; Equipment Failure Analysis ; Oligonucleotide Array Sequence Analysis/*instrumentation ; Reproducibility of Results ; Sensitivity and Specificity ; Species Specificity ; Spectrophotometry, Infrared/*instrumentation ; },
abstract = {Several families of catfish species are extensively aquacultured around the world; however, only those from the family Ictaluridae can be labeled as catfish in the United States. Non-Ictalurid catfish species that are marketed as "catfish" in the USA are considered misbranded. Misbranding in general has led to an increased interest in developing deoxyribonucleic acid (DNA)-based methods such as DNA barcoding, polymerase chain reaction restriction fragment length polymorphism, and DNA microarrays with fluorescence detection for the identification of fish species. In this proof-of-concept study, DNA microarrays coupled with a newly developed mid-infrared imaging detection method were applied to the identification of seven species of catfish for the first time. Species-specific DNA probes targeting three regions per species of the cytochrome c oxidase 1 (barcoding) gene were developed and printed as microarrays on glass slides. Deoxyribonucleic acid targets labeled with biotin were hybridized to their complementary probes using a strategy that allowed the selective formation of a silver layer on hybridized spots needed for detection. Using this three-probe format, the seven species were all identified correctly, even when a limited number of false positive spots were observed. Raman spectroscopy was employed to further characterize the arrays.},
}
@article {pmid25353316,
year = {2015},
author = {Lin, G and Makarov, D and Medina-Sánchez, M and Guix, M and Baraban, L and Cuniberti, G and Schmidt, OG},
title = {Magnetofluidic platform for multidimensional magnetic and optical barcoding of droplets.},
journal = {Lab on a chip},
volume = {15},
number = {1},
pages = {216-224},
doi = {10.1039/c4lc01160k},
pmid = {25353316},
issn = {1473-0189},
mesh = {Electronic Data Processing ; Equipment Design ; *Magnetic Phenomena ; Magnetite Nanoparticles/chemistry ; Microfluidic Analytical Techniques/*instrumentation/*methods ; },
abstract = {We present a concept of multidimensional magnetic and optical barcoding of droplets based on a magnetofluidic platform. The platform comprises multiple functional areas, such as an encoding area, an encoded droplet pool and a magnetic decoding area with integrated giant magnetoresistive (GMR) sensors. To prove this concept, penicillin functionalized with fluorescent dyes is coencapsulated with magnetic nanoparticles into droplets. While fluorescent dyes are used as conventional optical barcodes which are decoded with an optical decoding setup, an additional dimensionality of barcodes is created by using magnetic nanoparticles as magnetic barcodes for individual droplets and integrated micro-patterned GMR sensors as the corresponding magnetic decoding devices. The strategy of incorporating a magnetic encoding scheme provides a dynamic range of ~40 dB in addition to that of the optical method. When combined with magnetic barcodes, the encoding capacity can be increased by more than 1 order of magnitude compared with using only optical barcodes, that is, the magnetic platform provides more than 10 unique magnetic codes in addition to each optical barcode. Besides being a unique magnetic functional element for droplet microfluidics, the platform is capable of on-demand facile magnetic encoding and real-time decoding of droplets which paves the way for the development of novel non-optical encoding schemes for highly multiplexed droplet-based biological assays.},
}
@article {pmid25349513,
year = {2014},
author = {Back, J and Lee, W},
title = {A new genus (Copepoda, Harpacticoida, Laophontidae) from Jeju Island of Korea.},
journal = {ZooKeys},
volume = {},
number = {447},
pages = {1-20},
pmid = {25349513},
issn = {1313-2989},
abstract = {A survey on the harpacticoid copepods from an intertidal zone in Hyeopjae sandy beach, Jeju Island, Korea, resulted in the discovery of an unusual laophontid, Jejulaophontehyeopjaeensis sp. n., which cannot be placed in any extant genus within the family. To accommodate the species, a new genus of the family Laophontidae T. Scott, 1905 is proposed and fully described here. The new species is closely related to the lineage of the five primitive genera, Carraroenia McCormack, 2006, Coullia Hamond, 1973, Hemilaophonte Jakubisiak 1933, Psammoplatypus Lee &amp; Huys, 1999, and Robustunguis Fiers, 1992 (the CCHPR-lineage) by the reduced P2 endopod, ovate shape of the female P5 exopod and sexual dimorphism in the P3 endopod. However, it displays discrepancies from the species of the CCHPR-lineage in the presence of an inner seta on P3 and P4 exp-2, four setae on P4 enp-2, and an inner seta on P3 and P4 enp-2 in the female. Furthermore, no other species within the family Laophontidae has three setae on P2 exp-3 and a seta on P2 enp-2 at the same time. The new species has sexual dimorphism in the antennule, genital segmentation and the legs from P2 to P5. The terminal seta on the second endopodal segment of P2 in the male is longer than that in the female. The endopod of P3 is 3-segmented and displays a short inner apophysis on the second segment in the male. The outer setae on the exopod of P3 and P4 are distinctly thicker and stronger in the male than in the female. Mitochondrial cytochrome oxidase subunit I (mtCOI) sequencing of the new species has been realized in order to be used in future phylogenetic analysis.},
}
@article {pmid25349512,
year = {2014},
author = {Fernández-Triana, JL and Janzen, DH and Hallwachs, W and Whitfield, JB and Smith, MA and Kula, R},
title = {Revision of the genus Pseudapanteles (Hymenoptera, Braconidae, Microgastrinae), with emphasis on the species in Area de Conservación Guanacaste, northwestern Costa Rica.},
journal = {ZooKeys},
volume = {},
number = {446},
pages = {1-82},
pmid = {25349512},
issn = {1313-2989},
abstract = {Pseudapanteles is a moderately diverse genus of Microgastrinae parasitoid wasps (Hymenoptera: Braconidae), endemic to the New World and with the vast majority of its species (including many undescribed) in the Neotropical region. We describe here 25 new species from Area de Conservación Guanacaste (ACG), northwestern Costa Rica, based on 400 studied specimens. A key to all 36 known species of Pseudapanteles is provided (except for Pseudapantelesbrunneus, only known from a single male), and species are placed in three newly created species-groups. Host records are known for only 25% of the species; most are solitary parasitoids of the caterpillars of several families of small Lepidoptera (Crambidae, Elachistidae, Gelechiidae, Incurvariidae, Sesiidae, Tineidae). DNA barcodes (part of the CO1 gene) were obtained for 30 species (83%), and provide a start for future study of the genus beyond ACG. Brief descriptions (generated by Lucid 3.5 software) and extensive illustrations are provided for all species. The following new taxonomic and nomenclatural acts are proposed: Pseudapantelesmoerens (Nixon, 1965), comb. n., Pseudapantelesbrunneus Ashmead, 1900, comb. rev., a lectotype is designated for Pseudapantelesruficollis (Cameron, 1911), and the following 25 species nova of Pseudapanteles (all authored by Fernández-Triana and Whitfield): alfiopivai, alvaroumanai, analorenaguevarae, carlosespinachi, carlosrodriguezi, christianafigueresae, hernanbravoi, jorgerodriguezi, josefigueresi, laurachinchillae, luisguillermosolisi, margaritapenonae, mariobozai, mariocarvajali, maureenballesteroae, munifigueresae, oscarariasi, ottonsolisi, pedroleoni, raulsolorzanoi, renecastroi, rodrigogamezi, rosemarykarpinskiae, soniapicadoae, teofilodelatorrei.},
}
@article {pmid25349505,
year = {2014},
author = {Lee, S and Kim, K and Lee, W},
title = {A new species of Harpacticella Sars, 1908 (Copepoda, Harpacticoida), from a tidal pool on Jeju Island, Korea.},
journal = {ZooKeys},
volume = {},
number = {445},
pages = {13-30},
pmid = {25349505},
issn = {1313-2989},
abstract = {A new species of the genus Harpacticella Sars, 1908 is described from a tidal pool on Jeju Island, Korea. Harpacticellajejuensis sp. n. is closely related to Harpacticellaitoi Chang &amp; Kim, 1991, with regard to the structure of P1 exp-1 and enp-1, the length of P1 exp-1 and exp-2, and the setal number of the P5 exopod in males. However, the new species is clearly distinguishable from Harpacticellaitoi by the combined following characters: six setae on the P5 exopod in females, one naked seta on the inner margin of P1 exp-2, the short endopod of P1 compared to the exopod, and a naked long seta on the proximal inner margin of the P5 exopod of males. The mtCOI partial sequence is provided as a DNA barcode for the new species.},
}
@article {pmid25349123,
year = {2015},
author = {Atkuri, KR and Stevens, JC and Neubert, H},
title = {Mass cytometry: a highly multiplexed single-cell technology for advancing drug development.},
journal = {Drug metabolism and disposition: the biological fate of chemicals},
volume = {43},
number = {2},
pages = {227-233},
doi = {10.1124/dmd.114.060798},
pmid = {25349123},
issn = {1521-009X},
mesh = {Animals ; Biomarkers/analysis ; Drug Discovery/methods/trends ; Drug Evaluation, Preclinical/*methods/trends ; Flow Cytometry ; Fluorescent Antibody Technique ; Humans ; Metals, Rare Earth/analysis ; Pharmacokinetics ; *Single-Cell Analysis/instrumentation ; Spectrophotometry, Atomic ; },
abstract = {Advanced single-cell analysis technologies (e.g., mass cytometry) that help in multiplexing cellular measurements in limited-volume primary samples are critical in bridging discovery efforts to successful drug approval. Mass cytometry is the state-of-the-art technology in multiparametric single-cell analysis. Mass cytometers (also known as cytometry by time-of-flight or CyTOF) combine the cellular analysis principles of traditional fluorescence-based flow cytometry with the selectivity and quantitative power of inductively coupled plasma-mass spectrometry. Standard flow cytometry is limited in the number of parameters that can be measured owing to the overlap in signal when detecting fluorescently labeled antibodies. Mass cytometry uses antibodies tagged to stable isotopes of rare earth metals, which requires minimal signal compensation between the different metal tags. This unique feature enables researchers to seamlessly multiplex up to 40 independent measurements on single cells. In this overview we first present an overview of mass cytometry and compare it with traditional flow cytometry. We then discuss the emerging and potential applications of CyTOF technology in the pharmaceutical industry, including quantitative and qualitative deep profiling of immune cells and their applications in assessing drug immunogenicity, extensive mapping of signaling networks in single cells, cell surface receptor quantification and multiplexed internalization kinetics, multiplexing sample analysis by barcoding, and establishing cell ontologies on the basis of phenotype and/or function. We end with a discussion of the anticipated impact of this technology on drug development lifecycle with special emphasis on the utility of mass cytometry in deciphering a drug's pharmacokinetics and pharmacodynamics relationship.},
}
@article {pmid25349100,
year = {2014},
author = {Lai, J and Zhang, Y and Pasquale, N and Lee, KB},
title = {An upconversion nanoparticle with orthogonal emissions using dual NIR excitations for controlled two-way photoswitching.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {53},
number = {52},
pages = {14419-14423},
pmid = {25349100},
issn = {1521-3773},
support = {DP2 OD006462/OD/NIH HHS/United States ; R21 NS085569/NS/NINDS NIH HHS/United States ; 1R21NS085569-01/NS/NINDS NIH HHS/United States ; 1DP20D006462-01/DP/NCCDPHP CDC HHS/United States ; },
mesh = {Infrared Rays ; Lasers ; Luminescent Measurements ; Nanoparticles/*chemistry ; Pyrans/chemistry ; Spiro Compounds/chemistry ; },
abstract = {Developing multicolor upconversion nanoparticles (UCNPs) with the capability of regulating their emission wavelengths in the UV to visible range in response to external stimuli can offer more dynamic platforms for applications in high-resolution bioimaging, multicolor barcoding, and driving multiple important photochemical reactions, such as photoswitching. Here, we have rationally designed single-crystal core-shell-structured UCNPs which are capable of orthogonal UV and visible emissions in response to two distinct NIR excitations at 808 and 980 nm. The orthogonal excitation-emission properties of such UCNPs, as well as their ability to utilize low-power excitation, which attenuates any local heating from the lasers, endows the UCNPs with great potential for applications in materials and biological settings. As a proof of concept, the use of this UCNP for the efficient regulation of the two-way photoswitching of spiropyran by using dual wavelengths of NIR irradiation has been demonstrated.},
}
@article {pmid25345460,
year = {2014},
author = {He, L and Sok, D and Azadnia, P and Hsueh, J and Landais, E and Simek, M and Koff, WC and Poignard, P and Burton, DR and Zhu, J},
title = {Toward a more accurate view of human B-cell repertoire by next-generation sequencing, unbiased repertoire capture and single-molecule barcoding.},
journal = {Scientific reports},
volume = {4},
number = {},
pages = {6778},
pmid = {25345460},
issn = {2045-2322},
support = {UM1 AI100663/AI/NIAID NIH HHS/United States ; },
mesh = {Antibodies/classification/*genetics/immunology ; Antibodies, Neutralizing ; Antibody Formation/*genetics/immunology ; B-Lymphocytes/immunology/*metabolism ; DNA Barcoding, Taxonomic ; HIV Infections/genetics/immunology ; HIV-1/immunology ; High-Throughput Nucleotide Sequencing/methods/standards ; Humans ; Immunoglobulin Heavy Chains/classification/genetics ; Immunoglobulin Light Chains/classification/genetics ; Phylogeny ; Polymerase Chain Reaction/methods ; Reproducibility of Results ; Somatic Hypermutation, Immunoglobulin ; },
abstract = {B-cell repertoire analysis using next-generation sequencing has become a valuable tool for interrogating the genetic record of humoral response to infection. However, key obstacles such as low throughput, short read length, high error rate, and undetermined bias of multiplex PCR method have hindered broader application of this technology. In this study, we report several technical advances in antibody repertoire sequencing. We first demonstrated the ability to sequence antibody variable domains using the Ion Torrent PGM platform. As a test case, we analyzed the PGT121 class of antibodies from IAVI donor 17, an HIV-1-infected individual. We then obtained "unbiased" antibody repertoires by sequencing the 5'-RACE PCR products of B-cell transcripts from IAVI donor 17 and two HIV-1-uninfected individuals. We also quantified the bias of previously published gene-specific primers by comparing the repertoires generated by 5'-RACE PCR and multiplex PCR. We further developed a single-molecule barcoding strategy to reduce PCR-based amplification noise. Lastly, we evaluated several new PGM technologies in the context of antibody sequencing. We expect that, based upon long-read and high-fidelity next-generation sequencing technologies, the unbiased analysis will provide a more accurate view of the overall antibody repertoire while the barcoding strategy will facilitate high-resolution analysis of individual antibody families.},
}
@article {pmid25342243,
year = {2015},
author = {Dabert, M and Coulson, SJ and Gwiazdowicz, DJ and Moe, B and Hanssen, SA and Biersma, EM and Pilskog, HE and Dabert, J},
title = {Differences in speciation progress in feather mites (Analgoidea) inhabiting the same host: the case of Zachvatkinia and Alloptes living on arctic and long-tailed skuas.},
journal = {Experimental &amp; applied acarology},
volume = {65},
number = {2},
pages = {163-179},
pmid = {25342243},
issn = {1572-9702},
mesh = {Animals ; Birds/*parasitology ; DNA Barcoding, Taxonomic ; Feathers/parasitology ; Female ; Gene Flow ; *Genetic Speciation ; Haplotypes ; Host Specificity ; Host-Pathogen Interactions ; Male ; Mites/anatomy &amp; histology/*genetics/physiology ; Molecular Sequence Data ; Phylogeny ; },
abstract = {Recent molecular phylogenetic analyses have revealed that some apparently oligoxenous feather mite species are in fact monoxenous cryptic species with little morphological differentiation. In this study we analyzed two species, Zachvatkinia isolata (Avenzoariidae) and Alloptes (Sternalloptes) stercorarii (Alloptidae) which prefer different parts of the plumage of two sister species of birds: arctic skua (Stercorarius parasiticus) and long-tailed skua (S. longicaudus) breeding on tundra in the High Arctic archipelago of Svalbard. Given that there are no reports about hybridization events between the host species, we expected that both skuas would have a species-specific acarofauna. The genetic distances among DNA-barcode sequences (COI and 28S rDNA), phylogenetic tree topologies, and haplotype networks of the COI sequences of mites suggested extensive gene flow in Z. isolata between and within populations inhabiting both skua species, whereas the Alloptes populations were host specific and sufficiently genetically separated as to warrant species-level status. The discrepancy in the genetic structure of Alloptes and Zachvatkinia populations suggests frequent but transient contacts between the two skua species in which the probability of mite exchange is much higher for Zachvatkinia, which is present in high numbers and inhabits exposed parts of primary flight feathers, than for the less abundant Alloptes that lives primarily in more protected and inaccessible parts of the plumage. We discuss the possible nature of these contacts between host species and the area(s) where they might take place. The star-like structures in the haplotype network as well as high haplotype diversity and low nucleotide diversity observed in Z. isolata are concordant with the known dispersal strategy of feather mites: vertical colonization of new host individuals followed by rapid growth of founder populations.},
}
@article {pmid25341815,
year = {2014},
author = {Xie, L and Wang, YW and Guan, SY and Xie, LJ and Long, X and Sun, CY},
title = {Prospects and Problems for Identification of Poisonous Plants in China using DNA Barcodes.},
journal = {Biomedical and environmental sciences : BES},
volume = {27},
number = {10},
pages = {794-806},
doi = {10.3967/bes2014.115},
pmid = {25341815},
issn = {0895-3988},
mesh = {China ; DNA Barcoding, Taxonomic/*standards ; DNA Primers/genetics ; DNA, Intergenic/*genetics ; Plant Proteins/*genetics ; Plants, Toxic/*classification/*genetics ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {OBJECTIVE: Poisonous plants are a deadly threat to public health in China. The traditional clinical diagnosis of the toxic plants is inefficient, fallible, and dependent upon experts. In this study, we tested the performance of DNA barcodes for identification of the most threatening poisonous plants in China.<br><br>METHODS: Seventy-four accessions of 27 toxic plant species in 22 genera and 17 families were sampled and three DNA barcodes (matK, rbcL, and ITS) were amplified, sequenced and tested. Three methods, Blast, pairwise global alignment (PWG) distance, and Tree-Building were tested for discrimination power.<br><br>RESULTS: The primer universality of all the three markers was high. Except in the case of ITS for Hemerocallis minor, the three barcodes were successfully generated from all the selected species. Among the three methods applied, Blast showed the lowest discrimination rate, whereas PWG Distance and Tree-Building methods were equally effective. The ITS barcode showed highest discrimination rates using the PWG Distance and Tree-Building methods. When the barcodes were combined, discrimination rates were increased for the Blast method.<br><br>CONCLUSION: DNA barcoding technique provides us a fast tool for clinical identification of poisonous plants in China. We suggest matK, rbcL, ITS used in combination as DNA barcodes for authentication of poisonous plants.},
}
@article {pmid25338970,
year = {2015},
author = {Ralf, A and van Oven, M and Zhong, K and Kayser, M},
title = {Simultaneous analysis of hundreds of Y-chromosomal SNPs for high-resolution paternal lineage classification using targeted semiconductor sequencing.},
journal = {Human mutation},
volume = {36},
number = {1},
pages = {151-159},
doi = {10.1002/humu.22713},
pmid = {25338970},
issn = {1098-1004},
mesh = {Chromosomes, Human, Y/*genetics ; Haplotypes ; Humans ; Male ; *Polymorphism, Single Nucleotide ; Sensitivity and Specificity ; Sequence Analysis, DNA/economics/instrumentation/*methods ; Software ; },
abstract = {SNPs from the non-recombining part of the human Y chromosome (Y-SNPs) are informative to classify paternal lineages in forensic, genealogical, anthropological, and evolutionary studies. Although thousands of Y-SNPs were identified thus far, previous Y-SNP multiplex tools target only dozens of markers simultaneously, thereby restricting the provided Y-haplogroup resolution and limiting their applications. Here, we overcome this shortcoming by introducing a high-resolution multiplex tool for parallel genotyping-by-sequencing of 530 Y-SNPs using the Ion Torrent PGM platform, which allows classification of 432 worldwide Y haplogroups. Contrary to previous Y-SNP multiplex tools, our approach covers branches of the entire Y tree, thereby maximizing the paternal lineage classification obtainable. We used a default DNA input amount of 10 ng per reaction but preliminary sensitivity testing revealed positive results from as little as 100 pg input DNA. Furthermore, we demonstrate that sample pooling using barcodes is feasible, allowing increased throughput for lower per-sample costs. In addition to the wetlab protocol, we provide a software tool for automated data quality control and haplogroup classification. The unique combination of ultra-high marker density and high sensitivity achievable from low amounts of potentially degraded DNA makes this new multiplex tool suitable for a wide range of Y-chromosome applications.},
}
@article {pmid25337468,
year = {2014},
author = {Mashinchian, O and Johari-Ahar, M and Ghaemi, B and Rashidi, M and Barar, J and Omidi, Y},
title = {Impacts of quantum dots in molecular detection and bioimaging of cancer.},
journal = {BioImpacts : BI},
volume = {4},
number = {3},
pages = {149-166},
pmid = {25337468},
issn = {2228-5652},
abstract = {INTRODUCTION: A number of assays have so far been exploited for detection of cancer biomarkers in various malignancies. However, the expression of cancer biomarker(s) appears to be extremely low, therefore accurate detection demands sensitive optical imaging probes. While optical detection using conventional fluorophores often fail due to photobleaching problems, quantum dots (QDs) offer stable optical imaging in vitro and in vivo.<br><br>METHODS: In this review, we briefly overview the impacts of QDs in biology and its applications in bioimaging of malignancies. We will also delineate the existing obstacles for early detection of cancer and the intensifying use of QDs in advancement of diagnostic devices.<br><br>RESULTS: Of the QDs, unlike the II-VI type QDs (e.g., cadmium (Cd), selenium (Se) or tellurium (Te)) that possess inherent cytotoxicity, the I-III-VI 2 type QDs (e.g., AgInS2, CuInS2, ZnS-AgInS2) appear to be less toxic bioimaging agents with better control of band-gap energies. As highly-sensitive bioimaging probes, advanced hybrid QDs (e.g., QD-QD, fluorochrome-QD conjugates used for sensing through fluorescence resonance energy transfer (FRET), quenching, and barcoding techniques) have also been harnessed for the detection of biomarkers and the monitoring of delivery of drugs/genes to the target sites. Antibody-QD (Ab-QD) and aptamer- QD (Ap-QD) bioconjugates, once target the relevant biomarker, can provide highly stable photoluminescence (PL) at the target sites. In addition to their potential as nanobiosensors, the bioconjugates of QDs with homing devices have successfully been used for the development of smart nanosystems (NSs) providing targeted bioimaging and photodynamic therapy (PDT).<br><br>CONCLUSION: Having possessed great deal of photonic characteristics, QDs can be used for development of seamless multifunctional nanomedicines, theranostics and nanobiosensors.},
}
@article {pmid25336337,
year = {2014},
author = {Miller, AC and Woeste, KE and Anagnostakis, SL and Jacobs, DF},
title = {Exploration of a rare population of Chinese chestnut in North America: stand dynamics, health and genetic relationships.},
journal = {AoB PLANTS},
volume = {6},
number = {},
pages = {},
pmid = {25336337},
issn = {2041-2851},
abstract = {With the transport of plants around the globe, exotic species can readily spread disease to their native relatives; however, they can also provide genetic resistance to those relatives through hybrid breeding programmes. American chestnut (Castanea dentata) was an abundant tree species in North America until its decimation by introduced chestnut blight. To restore chestnut in North America, efforts are ongoing to test putative blight-resistant hybrids of Castanea dentata and Chinese chestnut (Castanea mollissima), but little is known about the ecology of C. mollissima. In a forest in northeastern USA in which C. mollissima has become established, we explored questions of stand dynamics, health and genetic relationships of C. mollissima offspring to an adjacent parent orchard. We found that C. mollissima was adapted and randomly distributed among native species in this relatively young forest. The genetics of the C. mollissima population compared with its parents indicated little effect of selection pressure as each of the parent trees contributed at least one offspring. The ease with which this exotic species proliferated calls to question why C. mollissima is rare elsewhere in forests of North America. It is likely that a time window of low animal predation allowed seedlings to establish, and the shallow soil at this site limited the maximum forest canopy height, permitting the characteristically short-statured C. mollissima to avoid suppression. Our results indicate that because C. mollissima exhibited pioneer species characteristics, hybrids between C. mollissima and C. dentata have the potential to be successful pioneer species of future forests in North America, and we challenge the paradigm that exotic tree species are wholly detrimental to native biodiversity. We contend that exotic tree species should be assessed not only by their level of threat to native species, but also by their potential positive impacts on ecosystems via hybrid breeding programmes.},
}
@article {pmid25333869,
year = {2014},
author = {Vaughn, JN and Chaluvadi, SR and Tushar, and Rangan, L and Bennetzen, JL},
title = {Whole plastome sequences from five ginger species facilitate marker development and define limits to barcode methodology.},
journal = {PloS one},
volume = {9},
number = {10},
pages = {e108581},
pmid = {25333869},
issn = {1932-6203},
mesh = {Chloroplasts/genetics ; DNA, Plant/analysis ; *Genome, Chloroplast ; Zingiber officinale/classification/*genetics ; High-Throughput Nucleotide Sequencing ; Microsatellite Repeats ; Molecular Sequence Annotation ; Phylogeny ; Plant Proteins/chemistry/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Plants from the Zingiberaceae family are a key source of spices and herbal medicines. Species identification within this group is critical in the search for known and possibly novel bioactive compounds. To facilitate precise characterization of this group, we have sequenced chloroplast genomes from species representing five major groups within Zingiberaceae. Generally, the structure of these genomes is similar to the basal angiosperm excepting an expansion of 3 kb associated with the inverted repeat A region. Portions of this expansion appear to be shared across the entire Zingiberales order, which includes gingers and bananas. We used whole plastome alignment information to develop DNA barcodes that would maximize the ability to differentiate species within the Zingiberaceae. Our computation pipeline identified regions of high variability that were flanked by highly conserved regions used for primer design. This approach yielded hitherto unexploited regions of variability. These theoretically optimal barcodes were tested on a range of species throughout the family and were found to amplify and differentiate genera and, in some cases, species. Still, though these barcodes were specifically optimized for the Zingiberaceae, our data support the emerging consensus that whole plastome sequences are needed for robust species identification and phylogenetics within this family.},
}
@article {pmid25331055,
year = {2015},
author = {Zhao, Y and Cheng, Y and Shang, L and Wang, J and Xie, Z and Gu, Z},
title = {Microfluidic synthesis of barcode particles for multiplex assays.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {11},
number = {2},
pages = {151-174},
doi = {10.1002/smll.201401600},
pmid = {25331055},
issn = {1613-6829},
mesh = {*Electronic Data Processing ; High-Throughput Screening Assays ; *Microfluidics ; },
abstract = {The increasing use of high-throughput assays in biomedical applications, including drug discovery and clinical diagnostics, demands effective strategies for multiplexing. One promising strategy is the use of barcode particles that encode information about their specific compositions and enable simple identification. Various encoding mechanisms, including spectroscopic, graphical, electronic, and physical encoding, have been proposed for the provision of sufficient identification codes for the barcode particles. These particles are synthesized in various ways. Microfluidics is an effective approach that has created exciting avenues of scientific research in barcode particle synthesis. The resultant particles have found important application in the detection of multiple biological species as they have properties of high flexibility, fast reaction times, less reagent consumption, and good repeatability. In this paper, research progress in the microfluidic synthesis of barcode particles for multiplex assays is discussed. After introducing the general developing strategies of the barcode particles, the focus is on studies of microfluidics, including their design, fabrication, and application in the generation of barcode particles. Applications of the achieved barcode particles in multiplex assays will be described and emphasized. The prospects for future development of these barcode particles are also presented.},
}
@article {pmid25329378,
year = {2014},
author = {Brozynska, M and Furtado, A and Henry, RJ},
title = {Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.},
journal = {PloS one},
volume = {9},
number = {10},
pages = {e110387},
pmid = {25329378},
issn = {1932-6203},
mesh = {Base Sequence ; Contig Mapping ; DNA Barcoding, Taxonomic/*methods ; Genome, Chloroplast/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; INDEL Mutation/genetics ; Molecular Sequence Data ; Oryza/*genetics ; Polymorphism, Single Nucleotide/genetics ; },
abstract = {Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina) and Ion Torrent (Life Technology) sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare). Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels) between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.},
}
@article {pmid25329278,
year = {2016},
author = {Asis, AM and Destura, I and Santos, MD},
title = {Species composition of by-catch from milkfish (Chanos chanos) fry fishery in selected sites in the Philippines as determined by DNA barcodes.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {3},
pages = {1981-1985},
doi = {10.3109/19401736.2014.971314},
pmid = {25329278},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; *Fisheries ; Fishes/*classification/*genetics ; Models, Theoretical ; Philippines ; Phylogeny ; Species Specificity ; },
abstract = {Milkfish fry fishery, an important industry in the Philippines, uses non-selective fishing gears and push nets in coastal areas which lead to the capture of other non-targeted juvenile aquatic species. Unfortunately, information on the amount and the identity of by-catch species is lacking thus the extent of impact of the fry fishery is not known. In this study, the species composition of milkfish fry fishery by-catch sampled from selected coastal areas that are known to be fry collection sites in the country were identified and assessed through the use of DNA barcoding. Analyses revealed that by-catch fish species of the milkfish fry industry included Black Tiger shrimp (Peneaus monodon), Tarpon (Megalops cyprinoides), Glass perchlets (Ambasis gymnocephalus and Ambasis buruensis), Ladyfish (Elops hawaiensis), Snapper (Lutjanus fulviflamma), Cardinal fishes (Apogon hyalosoma and Sphaeramia orbicularis), Whipfin siver biddy (Gerres filamentosus), Mullet (Liza sp.), Anchovy (Encrasicholina heteroloba), and Tiger perch (Terapon jarbua), almost all of which are potential marketable food fish and culture species. The results of the study provide preliminary information, as well as awareness, on the species composition of milkfish fry by-catch.},
}
@article {pmid25324846,
year = {2014},
author = {He, J and Zhao, X and Laroche, A and Lu, ZX and Liu, H and Li, Z},
title = {Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding.},
journal = {Frontiers in plant science},
volume = {5},
number = {},
pages = {484},
pmid = {25324846},
issn = {1664-462X},
abstract = {Marker-assisted selection (MAS) refers to the use of molecular markers to assist phenotypic selections in crop improvement. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra-throughput sequences to revolutionize plant genotyping and breeding. To further broaden NGS usages to large crop genomes such as maize and wheat, genotyping-by-sequencing (GBS) has been developed and applied in sequencing multiplexed samples that combine molecular marker discovery and genotyping. GBS is a novel application of NGS protocols for discovering and genotyping SNPs in crop genomes and populations. The GBS approach includes the digestion of genomic DNA with restriction enzymes followed by the ligation of barcode adapter, PCR amplification and sequencing of the amplified DNA pool on a single lane of flow cells. Bioinformatic pipelines are needed to analyze and interpret GBS datasets. As an ultimate MAS tool and a cost-effective technique, GBS has been successfully used in implementing genome-wide association study (GWAS), genomic diversity study, genetic linkage analysis, molecular marker discovery and genomic selection under a large scale of plant breeding programs.},
}
@article {pmid25306350,
year = {2015},
author = {Bruni, I and Galimberti, A and Caridi, L and Scaccabarozzi, D and De Mattia, F and Casiraghi, M and Labra, M},
title = {A DNA barcoding approach to identify plant species in multiflower honey.},
journal = {Food chemistry},
volume = {170},
number = {},
pages = {308-315},
doi = {10.1016/j.foodchem.2014.08.060},
pmid = {25306350},
issn = {1873-7072},
mesh = {DNA Barcoding, Taxonomic/*methods ; Genes, Plant ; Honey/*analysis ; Plants/*genetics ; },
abstract = {The purpose of this study was to test the ability of DNA barcoding to identify the plant origins of processed honey. Four multifloral honeys produced at different sites in a floristically rich area in the northern Italian Alps were examined by using the rbcL and trnH-psbA plastid regions as barcode markers. An extensive reference database of barcode sequences was generated for the local flora to determine the taxonomic composition of honey. Thirty-nine plant species were identified in the four honey samples, each of which originated from a mix of common plants belonging to Castanea, Quercus, Fagus and several herbaceous taxa. Interestingly, at least one endemic plant was found in all four honey samples, providing a clear signature for the geographic identity of these products. DNA of the toxic plant Atropa belladonna was detected in one sample, illustrating the usefulness of DNA barcoding for evaluating the safety of honey.},
}
@article {pmid25296114,
year = {2014},
author = {Galimberti, A and De Mattia, F and Bruni, I and Scaccabarozzi, D and Sandionigi, A and Barbuto, M and Casiraghi, M and Labra, M},
title = {A DNA barcoding approach to characterize pollen collected by honeybees.},
journal = {PloS one},
volume = {9},
number = {10},
pages = {e109363},
pmid = {25296114},
issn = {1932-6203},
mesh = {Animals ; Bees/*physiology ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Molecular Sequence Data ; Plants/*classification/genetics ; Pollen/chemistry/*genetics ; Pollination ; Sequence Analysis, DNA ; },
abstract = {In the present study, we investigated DNA barcoding effectiveness to characterize honeybee pollen pellets, a food supplement largely used for human nutrition due to its therapeutic properties. We collected pollen pellets using modified beehives placed in three zones within an alpine protected area (Grigna Settentrionale Regional Park, Italy). A DNA barcoding reference database, including rbcL and trnH-psbA sequences from 693 plant species (104 sequenced in this study) was assembled. The database was used to identify pollen collected from the hives. Fifty-two plant species were identified at the molecular level. Results suggested rbcL alone could not distinguish among congeneric plants; however, psbA-trnH identified most of the pollen samples at the species level. Substantial variability in pollen composition was observed between the highest elevation locality (Alpe Moconodeno), characterized by arid grasslands and a rocky substrate, and the other two sites (Cornisella and Ortanella) at lower altitudes. Pollen from Ortanella and Cornisella showed the presence of typical deciduous forest species; however in samples collected at Ortanella, pollen of the invasive Lonicera japonica, and the ornamental Pelargonium x hortorum were observed. Our results indicated pollen composition was largely influenced by floristic local biodiversity, plant phenology, and the presence of alien flowering species. Therefore, pollen molecular characterization based on DNA barcoding might serve useful to beekeepers in obtaining honeybee products with specific nutritional or therapeutic characteristics desired by food market demands.},
}
@article {pmid25293875,
year = {2015},
author = {Terrat, S and Dequiedt, S and Horrigue, W and Lelievre, M and Cruaud, C and Saby, NP and Jolivet, C and Arrouays, D and Maron, PA and Ranjard, L and Chemidlin Prévost-Bouré, N},
title = {Improving soil bacterial taxa-area relationships assessment using DNA meta-barcoding.},
journal = {Heredity},
volume = {114},
number = {5},
pages = {468-475},
pmid = {25293875},
issn = {1365-2540},
mesh = {Bacteria/*classification/genetics ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA Fingerprinting ; DNA, Bacterial/genetics ; France ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; },
abstract = {The evaluation of the taxa-area relationship (TAR) with molecular fingerprinting data demonstrated the spatial structuration of soil microorganisms and provided insights into the processes shaping their diversity. The increasing use of massive sequencing technologies in biodiversity investigations has now raised the question of the advantages of such technologies over the fingerprinting approach for elucidation of the determinism of soil microbial community assembly in broad-scale biogeographic studies. Our objectives in this study were to compare DNA fingerprinting and meta-barcoding approaches for evaluating soil bacterial TAR and the determinism of soil bacterial community assembly on a broad scale. This comparison was performed on 392 soil samples from four French geographic regions with different levels of environmental heterogeneity. Both molecular approaches demonstrated a TAR with a significant slope but, because of its more sensitive description of soil bacterial community richness, meta-barcoding provided significantly higher and more accurate estimates of turnover rates. Both approaches were useful in evidencing the processes shaping bacterial diversity variations on a broad scale. When different taxonomic resolutions were considered for meta-barcoding data, they significantly influenced the estimation of turnover rates but not the relative importance of each component process. Altogether, DNA meta-barcoding provides a more accurate evaluation of the TAR and may lead to re-examination of the processes shaping soil bacterial community assembly. This should provide new insights into soil microbial ecology in the context of sustainable use of soil resources.},
}
@article {pmid25286434,
year = {2014},
author = {Morinière, J and Hendrich, L and Hausmann, A and Hebert, P and Haszprunar, G and Gruppe, A},
title = {Barcoding Fauna Bavarica: 78% of the Neuropterida fauna barcoded!.},
journal = {PloS one},
volume = {9},
number = {10},
pages = {e109719},
pmid = {25286434},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; *DNA Barcoding, Taxonomic ; Europe ; Insecta/*classification/*genetics ; },
abstract = {This publication provides the first comprehensive DNA barcode data set for the Neuropterida of Central Europe, including 80 of the 102 species (78%) recorded from Bavaria (Germany) and three other species from nearby regions (Austria, France and the UK). Although the 286 specimens analyzed had a heterogeneous conservation history (60% dried; 30% in 80% EtOH; 10% fresh specimens in 95% EtOH), 237 (83%) generated a DNA barcode. Eleven species (13%) shared a BIN, but three of these taxa could be discriminated through barcodes. Four pairs of closely allied species shared barcodes including Chrysoperla pallida Henry et al., 2002 and C. lucasina Lacroix, 1912; Wesmaelius concinnus (Stephens, 1836) and W. quadrifasciatus (Reuter, 1894); Hemerobius handschini Tjeder, 1957 and H. nitidulus Fabricius, 1777; and H. atrifrons McLachlan, 1868 and H. contumax Tjeder, 1932. Further studies are needed to test the possible synonymy of these species pairs or to determine if other genetic markers permit their discrimination. Our data highlight five cases of potential cryptic diversity within Bavarian Neuropterida: Nineta flava (Scopoli, 1763), Sympherobius pygmaeus (Rambur, 1842), Sisyra nigra (Retzius, 1783), Semidalis aleyrodiformis (Stephens, 1836) and Coniopteryx pygmaea Enderlein, 1906 are each split into two or three BINs. The present DNA barcode library not only allows the identification of adult and larval stages, but also provides valuable information for alpha-taxonomy, and for ecological and evolutionary research.},
}
@article {pmid25284671,
year = {2014},
author = {Johnson, JW and Struthers, CD and Wilmer, JW},
title = {Parapercis nigrodorsalis (Perciformes: Pinguipedidae), a new species of sandperch from northern New Zealand and the Norfolk Ridge, Tasman Sea and remarks on P. binivirgata (Waite, 1904).},
journal = {Zootaxa},
volume = {3856},
number = {4},
pages = {484-500},
doi = {10.11646/zootaxa.3856.4.2},
pmid = {25284671},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Ecosystem ; Female ; Male ; New Zealand ; Organ Size ; Perciformes/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Phylogeny ; },
abstract = {A new species of pinguipedid fish, Parapercis nigrodorsalis, is described from 17 specimens collected off the North Island of New Zealand and Wanganella Bank, Norfolk Ridge, Tasman Sea, in depths of 56-280 m. The species has also been photographed underwater off the Poor Knights Islands Reserve and Burgess Island, Mokohinau Group, in New Zealand. It is most similar to Parapercis binivirgata (Waite, 1904) in morphology, coloration and meristic values, but is unique among the genus in having a combination of dorsal-fin rays V, 23, anal-fin rays I, 19, lateral-line scales 57-63, vomer with 1-2 irregular rows of robust conical teeth, palatines with 1-2 rows of small teeth, angle of subopercle smooth, 10 abdominal and 22 caudal vertebrae, and coloration, including seven broad reddish-brown bands on the upper body between the spinous dorsal-fin and the caudal peduncle, most bands bifurcated into close-set double bars with black smudge-like blotches below, and membrane of the spinous dorsal fin black. Comparison of the mitochondrial cytochrome c oxidase subunit 1 (CO 1) genetic marker utilised in DNA barcoding produced a genetic divergence of 5.38% and 7.63% between the new species and its two closest sampled congeners. The holotype of P. binivirgata is identified from two specimens previously regarded as syntypes, some revisions are made to meristic data in the original description of the latter, and a detailed description of the revised geographic range of P. binivirgata is provided.},
}
@article {pmid25284579,
year = {2014},
author = {Simard, C and Cloutier, M and Néron, S},
title = {Rapid determination of IL-6 specific activity by flow cytometry.},
journal = {Journal of immunological methods},
volume = {415},
number = {},
pages = {63-65},
doi = {10.1016/j.jim.2014.09.005},
pmid = {25284579},
issn = {1872-7905},
mesh = {Animals ; Carbocyanines ; Cell Line, Tumor ; Dose-Response Relationship, Immunologic ; Flow Cytometry/*methods/standards ; Fluorescent Dyes ; Gene Expression ; Interleukin-6/*analysis/pharmacology ; Mice ; Myeloid Cells/cytology/*drug effects/immunology ; STAT3 Transcription Factor/genetics/immunology ; },
abstract = {Current methods to measure the specific activity of cytokines are based on the time-consuming determination of the growth curve of a sensitive cell line. Here, we present a faster alternative based on flow cytometry, by determining the dose-response curve of cellular response to a cytokine. By using World Health Organization (WHO) cytokine standards, rapid determination of cytokine specific activity is now possible, as it takes only a few hours to achieve, in comparison to days with the classical method thus allowing laboratories to rapidly and easily assess the potency of their cytokines.},
}
@article {pmid25284399,
year = {2014},
author = {Gao, Q and Chen, H},
title = {The genera Luzonimyia and Pararhinoleucophenga from China (Diptera: Drosophilidae), with DNA barcoding information.},
journal = {Zootaxa},
volume = {3852},
number = {2},
pages = {294-300},
doi = {10.11646/zootaxa.3852.2.8},
pmid = {25284399},
issn = {1175-5334},
mesh = {Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; China ; DNA Barcoding, Taxonomic ; Drosophilidae/anatomy &amp; histology/*classification/*genetics/growth &amp; development ; Electron Transport Complex IV/genetics ; Female ; Insect Proteins/genetics ; Male ; Molecular Sequence Data ; Organ Size ; Phylogeny ; },
abstract = {Four new species are described from Yunnan, China, which belong to two different genera within the subfamily Steganinae: Luzonimyia hirsutina sp. nov., Luzonimyia setocauda sp. nov., Pararhinoleucophenga amnicola sp. nov. and Pararhinoleucophenga sylvatica sp. nov. The DNA sequences and GenBank accession numbers of the mitochondrial COI gene among Chinese species are provided.},
}
@article {pmid25283944,
year = {2014},
author = {Grebennikov, VV and Pham, HT},
title = {First record of Otibazo (Coleoptera: Curculionidae: Molytinae) outside of Japan, with description of a new species from Vietnam.},
journal = {Zootaxa},
volume = {3869},
number = {5},
pages = {597-600},
doi = {10.11646/zootaxa.3869.5.11},
pmid = {25283944},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Female ; Japan ; Male ; Organ Size ; Vietnam ; Weevils/anatomy &amp; histology/*classification/genetics/growth &amp; development ; },
abstract = {A new species of wingless leaf litter weevil, Otibazo polyphemus sp. n., is described from Tam Dao, northern Vietnam. This is the fourth named species in the genus, with its three other species known only from Japan. Habitus and genitalia of the male holotype are illustrated and DNA barcoding data are provided.},
}
@article {pmid25283910,
year = {2014},
author = {Kehlmaier, C and Gharali, B and Majnon Jahromi, B},
title = {A new Corononcodes Speiser from the Palaearctic Region, with a key to species (Diptera: Acroceridae).},
journal = {Zootaxa},
volume = {3869},
number = {2},
pages = {171-179},
doi = {10.11646/zootaxa.3869.2.7},
pmid = {25283910},
issn = {1175-5334},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Diptera/*anatomy &amp; histology/*classification/genetics ; Female ; Iran ; Male ; Spain ; },
abstract = {Corononcodes ziegleri spec. nov. is described and illustrated based on material from Iran. The species represents the second Palaearctic representative of this panopine genus. In addition, C. siculus Bezzi is recorded from Fuerteventura (Canary Islands, Spain) for the first time. An identification key to the Palaearctic species of Corononcodes is presented. Additional faunistic records for the Iranian fauna comprise Acrocera orbiculus (Fabricius) and an apparently undescribed species of Ogcodes Latreille. DNA-barcodes for all Iranian taxa are provided.},
}
@article {pmid25283651,
year = {2014},
author = {Heinold, BD and Gill, BA and Belcher, TP and Verdone, CJ},
title = {Discovery of new populations and DNA barcoding of the Arapahoe snowfly Arsapnia arapahoe (Plecoptera: Capniidae).},
journal = {Zootaxa},
volume = {3866},
number = {1},
pages = {131-137},
doi = {10.11646/zootaxa.3866.1.7},
pmid = {25283651},
issn = {1175-5334},
mesh = {Animal Distribution ; Animals ; DNA Barcoding, Taxonomic ; Ecosystem ; Female ; Insecta/*classification/*genetics ; Male ; },
abstract = {The Arapahoe Snowfly, Arsapnia arapahoe (Nelson &amp; Kondratieff)was recently discovered in six different first-order streams outside of the Cache la Poudre River Basin where it was previously considered endemic. Specimens of A. arapahoe were always collected in much lower relative abundance, 1.09% (±2.3SD), than other sympatric adult capniids. The first mitochondrial deoxyribonucleic acid (DNA) barcodes for A. arapahoe and A. coyote (Nelson &amp; Baumann) are presented and compared with those of A. decepta. DNA barcoding was not able to differentiate between A. arapahoe and A. decepta Banks but it was able to indicate that A. coyote is specifically distinct.},
}
@article {pmid25281214,
year = {2014},
author = {Andersen, JC and Mills, NJ},
title = {iMSAT: a novel approach to the development of microsatellite loci using barcoded Illumina libraries.},
journal = {BMC genomics},
volume = {15},
number = {1},
pages = {858},
pmid = {25281214},
issn = {1471-2164},
support = {S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; S10RR029668/RR/NCRR NIH HHS/United States ; S10RR027303/RR/NCRR NIH HHS/United States ; },
mesh = {Animals ; Aphids/classification/*genetics ; Chromosome Mapping ; Computational Biology/*methods ; DNA Barcoding, Taxonomic ; Databases, Genetic ; Female ; Genome ; *Microsatellite Repeats ; *Software ; Wasps/classification/*genetics ; },
abstract = {BACKGROUND: Illumina sequencing with its high number of reads and low per base pair cost is an attractive technology for development of molecular resources for non-model organisms. While many software packages have been developed to identify short tandem repeats (STRs) from next-generation sequencing data, these methods do not inform the investigator as to whether or not candidate loci are polymorphic in their target populations.<br><br>RESULTS: We provide a python program iMSAT that uses the polymorphism data obtained from mapping individual Illumina sequence reads onto a reference genome to identify polymorphic STRs. Using this approach, we identified 9,119 candidate polymorphic STRs for use with the parasitoid wasp Trioxys pallidus and 2,378 candidate polymorphic STRs for use with the aphid Chromaphis juglandicola. For both organisms we selected 20 candidate tri-nucleotide STRs for validation. Using fluorescent-labeled oligonucleotide primers, we genotyped 91 female T. pallidus collected in nine localities and 46 female C. juglandicola collected in 4 localities and found 15 of the examined markers to be polymorphic for T. pallidus and 12 of the examined markers to be polymorphic for C. juglandicola.<br><br>CONCLUSIONS: We present a novel approach that uses standard Illumina barcoding primers and a single Illumina HiSeq run to target polymorphic STR fragments to develop and test STR markers. We validate this approach using the parasitoid wasp T. pallidus and its aphid host C. juglandicola. This approach, which would also be compatible with 454 Sequencing, allowed us to quickly identify markers with known variability. Accordingly, our method constitutes a significant improvement over existing STR identification software packages.},
}
@article {pmid25280636,
year = {2015},
author = {Hanelt, B and Schmidt-Rhaesa, A and Bolek, MG},
title = {Cryptic species of hairworm parasites revealed by molecular data and crowdsourcing of specimen collections.},
journal = {Molecular phylogenetics and evolution},
volume = {82 Pt A},
number = {},
pages = {211-218},
doi = {10.1016/j.ympev.2014.09.010},
pmid = {25280636},
issn = {1095-9513},
support = {1P20RR18754/RR/NCRR NIH HHS/United States ; },
mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Crowdsourcing ; DNA, Helminth/genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics ; Genetics, Population/methods ; Helminths/*classification ; Likelihood Functions ; Models, Genetic ; Parasites/classification ; *Phylogeny ; Sequence Analysis, DNA ; United States ; },
abstract = {Recognizing cryptic species promotes a better understanding of biodiversity, systematics, evolutionary biology, and biogeography. When cryptic species are disease-causing organisms, such as parasites, their correct recognition has important implications for the study of epidemiology, disease ecology, and host-parasite relationships. Freshwater nematomorphs (Nematomorpha: Gordiida) or hairworms, are an enigmatic yet fascinating group of parasites that are known to manipulate host behavior to aid transition from the parasitic phase, within terrestrial insects, to the free-living aquatic stage. Hairworm taxonomy has been hampered by a paucity of informative diagnostic characters and it has long been suspected that this group contains numerous cryptic species. Study of single hairworm species over large geographical areas has been difficult due to extremely rare encounters and unreliable methods of collecting adult worms. Here we report that by using crowdsourcing, citizen scientists have collected and submitted samples of Gordius cf. robustus from throughout its range in North America making its genetic study possible. Combined with our own collections, we examined samples from 28 localities within the USA; despite the collection of numerous hairworms from Canada and Mexico, G. cf. robustus were not collected outside of the contiguous United States. Mitochondrial CO1 genetic distances revealed that specimens grouped into 8 clades separated by 8-24.3%. In addition, molecular evidence from mitochondrial (CO1 and cytB) and nuclear (partial 28S, ITS1, 5.8S and ITS2) DNA suggests that these 8 clades are distinct species and that this group of species is paraphyletic, since the North American species G. attoni and the European species G. aquaticus and G. balticus group among the G. robustus lineages. Furthermore, there was a significant correlation between genetic (CO1) and geographic distance between the 8 Gordius species. This study demonstrates the value of involving the general public in biodiversity studies and highlights the feasibility of using the mitochondrial CO1 gene as a taxonomic marker for genetic barcoding and species identification within the phylum Nematomorpha.},
}
@article {pmid25277098,
year = {2015},
author = {Danaher, P and White, RL and Hanson, EK and Ballantyne, J},
title = {Facile semi-automated forensic body fluid identification by multiplex solution hybridization of NanoString® barcode probes to specific mRNA targets.},
journal = {Forensic science international. Genetics},
volume = {14},
number = {},
pages = {18-30},
doi = {10.1016/j.fsigen.2014.09.005},
pmid = {25277098},
issn = {1878-0326},
mesh = {*Automation ; Body Fluids/*metabolism ; *Forensic Genetics ; Humans ; *Nucleic Acid Hybridization ; *Oligonucleotide Probes ; RNA, Messenger/*genetics/isolation &amp; purification ; },
abstract = {A DNA profile from the perpetrator does not reveal, per se, the circumstances by which it was transferred. Body fluid identification by mRNA profiling may allow extraction of contextual 'activity level' information from forensic samples. Here we describe the development of a prototype multiplex digital gene expression (DGE) method for forensic body fluid/tissue identification based upon solution hybridization of color-coded NanoString(®) probes to 23 mRNA targets. The method identifies peripheral blood, semen, saliva, vaginal secretions, menstrual blood and skin. We showed that a simple 5 min room temperature cellular lysis protocol gave equivalent results to standard RNA isolation from the same source material, greatly enhancing the ease-of-use of this method in forensic sample processing. We first describe a model for gene expression in a sample from a single body fluid and then extend that model to mixtures of body fluids. We then describe calculation of maximum likelihood estimates (MLEs) of body fluid quantities in a sample, and we describe the use of likelihood ratios to test for the presence of each body fluid in a sample. Known single source samples of blood, semen, vaginal secretions, menstrual blood and skin all demonstrated the expected tissue-specific gene expression for at least two of the chosen biomarkers. Saliva samples were more problematic, with their previously identified characteristic genes exhibiting poor specificity. Nonetheless the most specific saliva biomarker, HTN3, was expressed at a higher level in saliva than in any of the other tissues. Crucially, our algorithm produced zero false positives across this study's 89 unique samples. As a preliminary indication of the ability of the method to discern admixtures of body fluids, five mixtures were prepared. The identities of the component fluids were evident from the gene expression profiles of four of the five mixtures. Further optimization of the biomarker 'CodeSet' will be required before it can be used in casework, particularly with respect to increasing the signal-to-noise ratio of the saliva biomarkers. With suitable modifications, this simplified protocol with minimal hands on requirement should facilitate routine use of mRNA profiling in casework laboratories.},
}
@article {pmid25276506,
year = {2014},
author = {Mahé, F and Rognes, T and Quince, C and de Vargas, C and Dunthorn, M},
title = {Swarm: robust and fast clustering method for amplicon-based studies.},
journal = {PeerJ},
volume = {2},
number = {},
pages = {e593},
pmid = {25276506},
issn = {2167-8359},
abstract = {Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters' internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units.},
}
@article {pmid25274027,
year = {2014},
author = {Behbehani, GK and Thom, C and Zunder, ER and Finck, R and Gaudilliere, B and Fragiadakis, GK and Fantl, WJ and Nolan, GP},
title = {Transient partial permeabilization with saponin enables cellular barcoding prior to surface marker staining.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {85},
number = {12},
pages = {1011-1019},
pmid = {25274027},
issn = {1552-4930},
support = {R01 CA130826/CA/NCI NIH HHS/United States ; U54CA149145/CA/NCI NIH HHS/United States ; 1R01CA130826/CA/NCI NIH HHS/United States ; U54 CA149145/CA/NCI NIH HHS/United States ; HHSN272200700038C/AI/NIAID NIH HHS/United States ; P01 CA034233/CA/NCI NIH HHS/United States ; 272200700038C//PHS HHS/United States ; HHSN268201000034C/HL/NHLBI NIH HHS/United States ; U19 AI057229/AI/NIAID NIH HHS/United States ; N01-HV-00242/HV/NHLBI NIH HHS/United States ; T32 AI007328/AI/NIAID NIH HHS/United States ; },
mesh = {Cytophotometry/*methods ; High-Throughput Screening Assays/*methods ; Humans ; Jurkat Cells ; Optical Imaging/*methods ; *Saponins ; U937 Cells ; },
abstract = {Fluorescent cellular barcoding and mass-tag cellular barcoding are cytometric methods that enable high sample throughput, minimize inter-sample variation, and reduce reagent consumption. Previously employed barcoding protocols require that barcoding be performed after surface marker staining, complicating combining the technique with measurement of alcohol-sensitive surface epitopes. This report describes a method of barcoding fixed cells after a transient partial permeabilization with 0.02% saponin that results in efficient and consistent barcode staining with fluorescent or mass-tagged reagents while preserving surface marker staining. This approach simplifies barcoding protocols and allows direct comparison of surface marker staining of multiple samples without concern for variations in the antibody cocktail volume, antigen-antibody ratio, or machine sensitivity. Using this protocol, cellular barcoding can be used to reliably detect subtle differences in surface marker expression.},
}
@article {pmid25270225,
year = {2015},
author = {Keller, A and Danner, N and Grimmer, G and Ankenbrand, M and von der Ohe, K and von der Ohe, W and Rost, S and Härtel, S and Steffan-Dewenter, I},
title = {Evaluating multiplexed next-generation sequencing as a method in palynology for mixed pollen samples.},
journal = {Plant biology (Stuttgart, Germany)},
volume = {17},
number = {2},
pages = {558-566},
doi = {10.1111/plb.12251},
pmid = {25270225},
issn = {1438-8677},
mesh = {Animals ; Bees ; DNA Barcoding, Taxonomic/*methods ; Databases, Genetic ; Germany ; High-Throughput Nucleotide Sequencing/*methods ; Pollen/*classification/*genetics ; Workflow ; },
abstract = {The identification of pollen plays an important role in ecology, palaeo-climatology, honey quality control and other areas. Currently, expert knowledge and reference collections are essential to identify pollen origin through light microscopy. Pollen identification through molecular sequencing and DNA barcoding has been proposed as an alternative approach, but the assessment of mixed pollen samples originating from multiple plant species is still a tedious and error-prone task. Next-generation sequencing has been proposed to avoid this hindrance. In this study we assessed mixed pollen probes through next-generation sequencing of amplicons from the highly variable, species-specific internal transcribed spacer 2 region of nuclear ribosomal DNA. Further, we developed a bioinformatic workflow to analyse these high-throughput data with a newly created reference database. To evaluate the feasibility, we compared results from classical identification based on light microscopy from the same samples with our sequencing results. We assessed in total 16 mixed pollen samples, 14 originated from honeybee colonies and two from solitary bee nests. The sequencing technique resulted in higher taxon richness (deeper assignments and more identified taxa) compared to light microscopy. Abundance estimations from sequencing data were significantly correlated with counted abundances through light microscopy. Simulation analyses of taxon specificity and sensitivity indicate that 96% of taxa present in the database are correctly identifiable at the genus level and 70% at the species level. Next-generation sequencing thus presents a useful and efficient workflow to identify pollen at the genus and species level without requiring specialised palynological expert knowledge.},
}
@article {pmid25270047,
year = {2015},
author = {Zimmermann, J and Glöckner, G and Jahn, R and Enke, N and Gemeinholzer, B},
title = {Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies.},
journal = {Molecular ecology resources},
volume = {15},
number = {3},
pages = {526-542},
doi = {10.1111/1755-0998.12336},
pmid = {25270047},
issn = {1755-0998},
mesh = {Algorithms ; Biodiversity ; *Cytological Techniques ; DNA Barcoding, Taxonomic/*methods ; Diatoms/*classification/cytology/genetics/*isolation &amp; purification ; Fresh Water/*microbiology ; Genetic Variation ; Microscopy/*methods ; Molecular Sequence Data ; Rivers/microbiology ; Sequence Analysis, DNA ; Water Quality/standards ; Workflow ; },
abstract = {Diatoms are frequently used for water quality assessments; however, identification to species level is difficult, time-consuming and needs in-depth knowledge of the organisms under investigation, as nonhomoplastic species-specific morphological characters are scarce. We here investigate how identification methods based on DNA (metabarcoding using NGS platforms) perform in comparison to morphological diatom identification and propose a workflow to optimize diatom fresh water quality assessments. Diatom diversity at seven different sites along the course of the river system Odra and Lusatian Neisse from the source to the mouth is analysed with DNA and morphological methods, which are compared. The NGS technology almost always leads to a higher number of identified taxa (270 via NGS vs. 103 by light microscopy LM), whose presence could subsequently be verified by LM. The sequence-based approach allows for a much more graduated insight into the taxonomic diversity of the environmental samples. Taxa retrieval varies considerably throughout the river system, depending on species occurrences and the taxonomic depth of the reference databases. Mostly rare taxa from oligotrophic parts of the river systems are less well represented in the reference database used. A workflow for DNA-based NGS diatom identification is presented. 28 000 diatom sequences were evaluated. Our findings provide evidence that metabarcoding of diatoms via NGS sequencing of the V4 region (18S) has a great potential for water quality assessments and could complement and maybe even improve the identification via light microscopy.},
}
@article {pmid25265556,
year = {2014},
author = {Zimmermann, J and Abarca, N and Enke, N and Skibbe, O and Kusber, WH and Jahn, R},
title = {Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research.},
journal = {PloS one},
volume = {9},
number = {9},
pages = {e108793},
pmid = {25265556},
issn = {1932-6203},
mesh = {Base Pairing/genetics ; Base Sequence ; Berlin ; DNA Barcoding, Taxonomic/*methods ; Diatoms/*classification/genetics/ultrastructure ; Ecosystem ; *Environment ; *Gene Library ; Molecular Sequence Data ; Phylogeny ; Reference Standards ; *Research ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Terminology as Topic ; },
abstract = {DNA barcoding uses a short fragment of a DNA sequence to identify a taxon. After obtaining the target sequence it is compared to reference sequences stored in a database to assign an organism name to it. The quality of data in the reference database is the key to the success of the analysis. In the here presented study, multiple types of data have been combined and critically examined in order to create best practice guidelines for taxonomic reference libraries for environmental barcoding. 70 unialgal diatom strains from Berlin waters have been established and cultured to obtain morphological and molecular data. The strains were sequenced for 18S V4 rDNA (the pre-Barcode for protists) as well as rbcL data, and identified by microscopy. LM and for some strains also SEM pictures were taken and physical vouchers deposited at the BGBM. 37 freshwater taxa from 15 naviculoid diatom genera were identified. Four taxa from the genera Amphora, Mayamaea, Planothidium and Stauroneis are described here as new. Names, molecular, morphological and habitat data as well as additional images of living cells are also available electronically in the AlgaTerra Information System. All reference sequences (or reference barcodes) presented here are linked to voucher specimens in order to provide a complete chain of evidence back to the formal taxonomic literature.},
}
@article {pmid25264574,
year = {2016},
author = {Sarwat, M and Yamdagni, MM},
title = {DNA barcoding, microarrays and next generation sequencing: recent tools for genetic diversity estimation and authentication of medicinal plants.},
journal = {Critical reviews in biotechnology},
volume = {36},
number = {2},
pages = {191-203},
doi = {10.3109/07388551.2014.947563},
pmid = {25264574},
issn = {1549-7801},
mesh = {*DNA Barcoding, Taxonomic ; Genetic Variation ; *High-Throughput Nucleotide Sequencing ; *Oligonucleotide Array Sequence Analysis ; *Plants, Medicinal/classification/genetics ; },
abstract = {DNA barcoding, microarray technology and next generation sequencing have emerged as promising tools for the elucidation of plant genetic diversity and its conservation. They are proving to be immensely helpful in authenticating the useful medicinal plants for herbal drug preparations. These newer versions of molecular markers utilize short genetic markers in the genome to characterize the organism to a particular species. This has the potential not only to classify the known and yet unknown species but also has a promising future to link the medicinally important plants according to their properties. The newer trends being followed in DNA chips and barcoding pave the way for a future with many different possibilities. Several of these possibilities might be: characterization of unknown species in a considerably less time than usual, identification of newer medicinal properties possessed by the species and also updating the data of the already existing but unnoticed properties. This can assist us to cure many different diseases and will also generate novel opportunities in medicinal drug delivery and targeting.},
}
@article {pmid25264390,
year = {2014},
author = {Crous, PW and Shivas, RG and Quaedvlieg, W and van der Bank, M and Zhang, Y and Summerell, BA and Guarro, J and Wingfield, MJ and Wood, AR and Alfenas, AC and Braun, U and Cano-Lira, JF and García, D and Marin-Felix, Y and Alvarado, P and Andrade, JP and Armengol, J and Assefa, A and den Breeÿen, A and Camele, I and Cheewangkoon, R and De Souza, JT and Duong, TA and Esteve-Raventós, F and Fournier, J and Frisullo, S and García-Jiménez, J and Gardiennet, A and Gené, J and Hernández-Restrepo, M and Hirooka, Y and Hospenthal, DR and King, A and Lechat, C and Lombard, L and Mang, SM and Marbach, PA and Marincowitz, S and Marin-Felix, Y and Montaño-Mata, NJ and Moreno, G and Perez, CA and Pérez Sierra, AM and Robertson, JL and Roux, J and Rubio, E and Schumacher, RK and Stchigel, AM and Sutton, DA and Tan, YP and Thompson, EH and van der Linde, E and Walker, AK and Walker, DM and Wickes, BL and Wong, PT and Groenewald, JZ},
title = {Fungal Planet description sheets: 214-280.},
journal = {Persoonia},
volume = {32},
number = {},
pages = {184-306},
pmid = {25264390},
issn = {0031-5850},
abstract = {Novel species of microfungi described in the present study include the following from South Africa: Cercosporella dolichandrae from Dolichandra unguiscati, Seiridium podocarpi from Podocarpus latifolius, Pseudocercospora parapseudarthriae from Pseudarthria hookeri, Neodevriesia coryneliae from Corynelia uberata on leaves of Afrocarpus falcatus, Ramichloridium eucleae from Euclea undulata and Stachybotrys aloeticola from Aloe sp. (South Africa), as novel member of the Stachybotriaceae fam. nov. Several species were also described from Zambia, and these include Chaetomella zambiensis on unknown Fabaceae, Schizoparme pseudogranati from Terminalia stuhlmannii, Diaporthe isoberliniae from Isoberlinia angolensis, Peyronellaea combreti from Combretum mossambiciensis, Zasmidium rothmanniae and Phaeococcomyces rothmanniae from Rothmannia engleriana, Diaporthe vangueriae from Vangueria infausta and Diaporthe parapterocarpi from Pterocarpus brenanii. Novel species from the Netherlands include: Stagonospora trichophoricola, Keissleriella trichophoricola and Dinemasporium trichophoricola from Trichophorum cespitosum, Phaeosphaeria poae, Keissleriella poagena, Phaeosphaeria poagena, Parastagonospora poagena and Pyrenochaetopsis poae from Poa sp., Septoriella oudemansii from Phragmites australis and Dendryphion europaeum from Hedera helix (Germany) and Heracleum sphondylium (the Netherlands). Novel species from Australia include: Anungitea eucalyptorum from Eucalyptus leaf litter, Beltraniopsis neolitseae and Acrodontium neolitseae from Neolitsea australiensis, Beltraniella endiandrae from Endiandra introrsa, Phaeophleospora parsoniae from Parsonia straminea, Penicillifer martinii from Cynodon dactylon, Ochroconis macrozamiae from Macrozamia leaf litter, Triposporium cycadicola, Circinotrichum cycadis, Cladosporium cycadicola and Acrocalymma cycadis from Cycas spp. Furthermore, Vermiculariopsiella dichapetali is described from Dichapetalum rhodesicum (Botswana), Ophiognomonia acadiensis from Picea rubens (Canada), Setophoma vernoniae from Vernonia polyanthes and Penicillium restingae from soil (Brazil), Pseudolachnella guaviyunis from Myrcianthes pungens (Uruguay) and Pseudocercospora neriicola from Nerium oleander (Italy). Novelties from Spain include: Dendryphiella eucalyptorum from Eucalyptus globulus, Conioscypha minutispora from dead wood, Diplogelasinospora moalensis and Pseudoneurospora canariensis from soil and Inocybe lanatopurpurea from reforested woodland of Pinus spp. Novelties from France include: Kellermania triseptata from Agave angustifolia, Zetiasplozna acaciae from Acacia melanoxylon, Pyrenochaeta pinicola from Pinus sp. and Pseudonectria rusci from Ruscus aculeatus. New species from China include: Dematiocladium celtidicola from Celtis bungeana, Beltrania pseudorhombica, Chaetopsina beijingensis and Toxicocladosporium pini from Pinus spp. and Setophaeosphaeria badalingensis from Hemerocallis fulva. Novel genera of Ascomycetes include Alfaria from Cyperus esculentus (Spain), Rinaldiella from a contaminated human lesion (Georgia), Hyalocladosporiella from Tectona grandis (Brazil), Pseudoacremonium from Saccharum spontaneum and Melnikomyces from leaf litter (Vietnam), Annellosympodiella from Juniperus procera (Ethiopia), Neoceratosperma from Eucalyptus leaves (Thailand), Ramopenidiella from Cycas calcicola (Australia), Cephalotrichiella from air in the Netherlands, Neocamarosporium from Mesembryanthemum sp. and Acervuloseptoria from Ziziphus mucronata (South Africa) and Setophaeosphaeria from Hemerocallis fulva (China). Several novel combinations are also introduced, namely for Phaeosphaeria setosa as Setophaeosphaeria setosa, Phoma heteroderae as Peyronellaea heteroderae and Phyllosticta maydis as Peyronellaea maydis. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.},
}
@article {pmid25263402,
year = {2014},
author = {Twyford, AD},
title = {Testing evolutionary hypotheses for DNA barcoding failure in willows.},
journal = {Molecular ecology},
volume = {23},
number = {19},
pages = {4674-4676},
doi = {10.1111/mec.12892},
pmid = {25263402},
issn = {1365-294X},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Chloroplast/*genetics ; *Haplotypes ; Salix/*genetics ; },
abstract = {The goal of DNA barcoding is to enable the rapid identification of taxa from short diagnostic DNA sequence profiles. But how feasible is this objective when many evolutionary processes, such as hybridization and selective sweeps, cause alleles to be shared among related taxa? In this issue of Molecular Ecology, Percy et al. (2014) test the full suite of seven candidate plant barcoding loci in a broad geographic sample of willow species. They show exceptional plastid haplotype sharing between species across continents, with most taxa not possessing a unique barcode sequence. Using population genetic and molecular dating analyses, they implicate hybridization and selective sweeps, but not incomplete lineage sorting, as the historical processes causing widespread haplotype sharing among willow taxa. This study represents an exceptional case of how poorly barcoding can perform, and highlights methodological issues using universal organellar regions for species identification.},
}
@article {pmid25263329,
year = {2014},
author = {Dezfouli, M and Vickovic, S and Iglesias, MJ and Schwenk, JM and Ahmadian, A},
title = {Parallel barcoding of antibodies for DNA-assisted proteomics.},
journal = {Proteomics},
volume = {14},
number = {21-22},
pages = {2432-2436},
doi = {10.1002/pmic.201400215},
pmid = {25263329},
issn = {1615-9861},
mesh = {Antibodies/*chemistry ; Blood Proteins/*analysis ; DNA/*chemistry ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Immunoassay/methods ; Immunoconjugates/chemistry ; Immunomagnetic Separation/methods ; Polymerase Chain Reaction/methods ; Proteomics/*methods ; },
abstract = {DNA-assisted proteomics technologies enable ultra-sensitive measurements in multiplex format using DNA-barcoded affinity reagents. Although numerous antibodies are available, nowadays targeting nearly the complete human proteome, the majority is not accessible at the quantity, concentration, or purity recommended for most bio-conjugation protocols. Here, we introduce a magnetic bead-assisted DNA-barcoding approach, applicable for several antibodies in parallel, as well as reducing required reagents quantities up to a thousand-fold. The success of DNA-barcoding and retained functionality of antibodies were demonstrated in sandwich immunoassays and standard quantitative Immuno-PCR assays. Specific DNA-barcoding of antibodies for multiplex applications was presented on suspension bead arrays with read-out on a massively parallel sequencing platform in a procedure denoted Immuno-Sequencing. Conclusively, human plasma samples were analyzed to indicate the functionality of barcoded antibodies in intended proteomics applications.},
}
@article {pmid25260907,
year = {2014},
author = {Blundell, JR and Levy, SF},
title = {Beyond genome sequencing: lineage tracking with barcodes to study the dynamics of evolution, infection, and cancer.},
journal = {Genomics},
volume = {104},
number = {6 Pt A},
pages = {417-430},
doi = {10.1016/j.ygeno.2014.09.005},
pmid = {25260907},
issn = {1089-8646},
support = {R01 HG003328/HG/NHGRI NIH HHS/United States ; R25 GM067110/GM/NIGMS NIH HHS/United States ; },
mesh = {Cell Lineage/*genetics ; *DNA Barcoding, Taxonomic ; Drug Resistance/genetics ; *Evolution, Molecular ; *Genome ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Infections/*genetics ; Mutation ; Neoplasms/*genetics ; },
abstract = {Evolving cellular communities, such as the gut microbiome, pathogenic infections, and cancer, consist of large populations of ~10(7)-10(14) cells. Because of their large population sizes, adaptation within these populations can be driven by many beneficial mutations that never rise above extremely low frequencies. Genome sequencing methods such as clonal, single cell, or whole population sequencing are poorly suited to detect these rare beneficial lineages, and, more generally, to characterize which mutations are most important to the population dynamics. Here, we introduce an alternative approach: high-resolution lineage tracking with DNA barcodes. In contrast to whole genome sequencing, lineage tracking can detect a beneficial mutation at an extremely low frequency within the population, and estimate its time of occurrence and fitness effect. Many lineage trajectories can be observed in parallel, allowing one to observe the population dynamics in exquisite detail. We describe some of the technical and analytical challenges to lineage tracking with DNA barcodes and discuss its applications to studies of evolution, infectious disease and cancer.},
}
@article {pmid25259794,
year = {2014},
author = {Nithaniyal, S and Newmaster, SG and Ragupathy, S and Krishnamoorthy, D and Vassou, SL and Parani, M},
title = {DNA barcode authentication of wood samples of threatened and commercial timber trees within the tropical dry evergreen forest of India.},
journal = {PloS one},
volume = {9},
number = {9},
pages = {e107669},
pmid = {25259794},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic ; *Endangered Species ; *Forests ; Genetic Markers ; Geography ; India ; Phylogeny ; Species Specificity ; Trees/*classification/genetics ; *Tropical Climate ; Wood/*classification/genetics ; },
abstract = {BACKGROUND: India is rich with biodiversity, which includes a large number of endemic, rare and threatened plant species. Previous studies have used DNA barcoding to inventory species for applications in biodiversity monitoring, conservation impact assessment, monitoring of illegal trading, authentication of traded medicinal plants etc. This is the first tropical dry evergreen forest (TDEF) barcode study in the World and the first attempt to assemble a reference barcode library for the trees of India as part of a larger project initiated by this research group.<br><br>We sampled 429 trees representing 143 tropical dry evergreen forest (TDEF) species, which included 16 threatened species. DNA barcoding was completed using rbcL and matK markers. The tiered approach (1st tier rbcL; 2nd tier matK) correctly identified 136 out of 143 species (95%). This high level of species resolution was largely due to the fact that the tree species were taxonomically diverse in the TDEF. Ability to resolve taxonomically diverse tree species of TDEF was comparable among the best match method, the phylogenetic method, and the characteristic attribute organization system method.<br><br>CONCLUSIONS: We demonstrated the utility of the TDEF reference barcode library to authenticate wood samples from timber operations in the TDEF. This pilot research study will enable more comprehensive surveys of the illegal timber trade of threatened species in the TDEF. This TDEF reference barcode library also contains trees that have medicinal properties, which could be used to monitor unsustainable and indiscriminate collection of plants from the wild for their medicinal value.},
}
@article {pmid25256349,
year = {2015},
author = {Silva, TL and Godinho, R and Castro, D and Abáigar, T and Brito, JC and Alves, PC},
title = {Genetic identification of endangered North African ungulates using noninvasive sampling.},
journal = {Molecular ecology resources},
volume = {15},
number = {3},
pages = {652-661},
doi = {10.1111/1755-0998.12335},
pmid = {25256349},
issn = {1755-0998},
mesh = {Africa, Northern ; Animals ; Caseins/genetics ; Costs and Cost Analysis ; Cytochromes b/genetics ; DNA/chemistry/genetics/isolation &amp; purification ; DNA Fingerprinting/*methods ; Genetic Variation ; Mammals/*classification/*genetics ; Molecular Sequence Data ; Reproducibility of Results ; Sequence Analysis, DNA ; },
abstract = {North African ungulates include several threatened and emblematic species, yet are poorly studied mainly due to their remoteness and elusiveness. Noninvasive sampling provides a useful approach to obtain ecological and genetic information essential to guide conservation actions. The very first and most important step in conservation planning is to accurately identify species, and molecular genetics has been proved to be a useful tool. Several molecular genetics protocols are available for species identification, even for samples with poor quality DNA, such as faeces, hairs or bones. Most of these protocols use mitochondrial DNA for barcoding despite this marker being especially prone to problems, including mtDNA introgression, nuclear insert copies, high intraspecific diversity or heteroplasmy. In this work, we developed a molecular method based on polymorphisms in small fragments of the mitochondrial cytochrome b (cytb, mtDNA) and the nuclear kappa casein genes (KCAS, nDNA) for identifying endangered North African ungulates. These fragments revealed polymorphisms, including species-specific variation, which allowed species identification of nine ungulate species that co-occur in North Africa. The method was validated across more than 400 samples, including different types of noninvasive samples collected in the field. The simplicity, high reliability and relative low cost of the described method make it a promising tool to improve ecological studies of the North African ungulates and consequently, the implementation of more efficient management and conservation plans for these endangered ungulates.},
}
@article {pmid25255319,
year = {2014},
author = {Pentinsaari, M and Hebert, PD and Mutanen, M},
title = {Barcoding beetles: a regional survey of 1872 species reveals high identification success and unusually deep interspecific divergences.},
journal = {PloS one},
volume = {9},
number = {9},
pages = {e108651},
pmid = {25255319},
issn = {1932-6203},
mesh = {Animals ; Base Composition ; Biodiversity ; Coleoptera/*classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; Evolution, Molecular ; Genetic Variation ; Haplotypes ; },
abstract = {With 400 K described species, beetles (Insecta: Coleoptera) represent the most diverse order in the animal kingdom. Although the study of their diversity currently represents a major challenge, DNA barcodes may provide a functional, standardized tool for their identification. To evaluate this possibility, we performed the first comprehensive test of the effectiveness of DNA barcodes as a tool for beetle identification by sequencing the COI barcode region from 1872 North European species. We examined intraspecific divergences, identification success and the effects of sample size on variation observed within and between species. A high proportion (98.3%) of these species possessed distinctive barcode sequence arrays. Moreover, the sequence divergences between nearest neighbor species were considerably higher than those reported for the only other insect order, Lepidoptera, which has seen intensive analysis (11.99% vs up to 5.80% mean NN divergence). Although maximum intraspecific divergence increased and average divergence between nearest neighbors decreased with increasing sampling effort, these trends rarely hampered identification by DNA barcodes due to deep sequence divergences between most species. The Barcode Index Number system in BOLD coincided strongly with known species boundaries with perfect matches between species and BINs in 92.1% of all cases. In addition, DNA barcode analysis revealed the likely occurrence of about 20 overlooked species. The current results indicate that DNA barcodes distinguish species of beetles remarkably well, establishing their potential to provide an effective identification tool for this order and to accelerate the discovery of new beetle species.},
}
@article {pmid25253712,
year = {2014},
author = {Vislobokov, NA and Galinskaya, TV and Degtjareva, GV and Valiejo-Roman, CM and Samigullin, TH and Kuznetsov, AN and Sokoloff, DD},
title = {Pollination of Vietnamese Aspidistra xuansonensis (Asparagaceae) by female Cecidomyiidi flies: larvae of pollinator feed on fertile pollen in anthers of anthetic bisexual flowers.},
journal = {American journal of botany},
volume = {101},
number = {9},
pages = {1519-1531},
doi = {10.3732/ajb.1400359},
pmid = {25253712},
issn = {1537-2197},
mesh = {Animals ; Ants ; *Diptera ; Female ; *Flowers ; *Larva ; Liliaceae/*physiology ; Oviposition ; *Pollen ; *Pollination ; Reproduction ; Vietnam ; },
abstract = {UNLABELLED: •<br><br>PREMISE OF THE STUDY: Aspidistra is a species-rich, herbaceous monocot genus of tropical Southeast Asia. Most species are recently discovered and apparently endangered, though virtually nothing is known about their biology. Species of the genus are primarily distinguished using flower morphology, which is enormously diverse. However, the pollination process has not been directly observed in the center of diversity of the genus (N Vietnam and S China). Indirect and partly direct data on the only widely cultivated species of the genus (A. elatior) placed it among angiosperms with the most unusual pollination biology, though these data are highly controversial, suggesting pollen transfer by mollusks, crustaceans, flies, or possibly tiny soil invertebrates such as collembolans.&#x2022;<br><br>METHODS: Pollination of Aspidistra xuansonensis in the center of diversity of the genus was studied using visual observations and videos and light and scanning electron microscopy investigation of flowers and their pollinators. Pollinators and their larvae were molecularly barcoded.&#x2022;<br><br>KEY RESULTS: Aspidistra xuansonensis is pollinated by female cecidomyiid flies (gall midges). They oviposit on anthers, and larvae develop among the pollen mass. Molecular barcoding proved taxonomic identity of the larvae and the flies. The larvae neither damage floral parts nor cause gall formation, but feed on pollen grains by sucking out their content. The larvae move out of the flowers before decomposition starts. Carebara ants steal developing larvae from flowers but do not contribute to pollination.&#x2022;<br><br>CONCLUSIONS: More than one kind of myiophily is present in Aspidistra. Brood site pollination was documented for the first time in Aspidistra. The pollination system of A. xuansonensis differs from other kinds of brood site pollination in the exit of the larvae prior to the decomposition of floral parts.},
}
@article {pmid25252978,
year = {2014},
author = {Gu, L and Li, C and Aach, J and Hill, DE and Vidal, M and Church, GM},
title = {Multiplex single-molecule interaction profiling of DNA-barcoded proteins.},
journal = {Nature},
volume = {515},
number = {7528},
pages = {554-557},
pmid = {25252978},
issn = {1476-4687},
support = {R01 HG001715/HG/NHGRI NIH HHS/United States ; U01 HG001715/HG/NHGRI NIH HHS/United States ; U41 HG001715/HG/NHGRI NIH HHS/United States ; HG001715/HG/NHGRI NIH HHS/United States ; },
mesh = {DNA/*chemistry ; DNA, Complementary/chemistry ; Gene Expression Profiling/*methods ; Immunoprecipitation ; Nucleic Acid Amplification Techniques ; Peptide Library ; RNA, Messenger/chemistry ; },
abstract = {In contrast with advances in massively parallel DNA sequencing, high-throughput protein analyses are often limited by ensemble measurements, individual analyte purification and hence compromised quality and cost-effectiveness. Single-molecule protein detection using optical methods is limited by the number of spectrally non-overlapping chromophores. Here we introduce a single-molecular-interaction sequencing (SMI-seq) technology for parallel protein interaction profiling leveraging single-molecule advantages. DNA barcodes are attached to proteins collectively via ribosome display or individually via enzymatic conjugation. Barcoded proteins are assayed en masse in aqueous solution and subsequently immobilized in a polyacrylamide thin film to construct a random single-molecule array, where barcoding DNAs are amplified into in situ polymerase colonies (polonies) and analysed by DNA sequencing. This method allows precise quantification of various proteins with a theoretical maximum array density of over one million polonies per square millimetre. Furthermore, protein interactions can be measured on the basis of the statistics of colocalized polonies arising from barcoding DNAs of interacting proteins. Two demanding applications, G-protein coupled receptor and antibody-binding profiling, are demonstrated. SMI-seq enables 'library versus library' screening in a one-pot assay, simultaneously interrogating molecular binding affinity and specificity.},
}
@article {pmid25251413,
year = {2014},
author = {Ferreira-Paim, K and Ferreira, TB and Andrade-Silva, L and Mora, DJ and Springer, DJ and Heitman, J and Fonseca, FM and Matos, D and Melhem, MS and Silva-Vergara, ML},
title = {Phylogenetic analysis of phenotypically characterized Cryptococcus laurentii isolates reveals high frequency of cryptic species.},
journal = {PloS one},
volume = {9},
number = {9},
pages = {e108633},
pmid = {25251413},
issn = {1932-6203},
mesh = {Cryptococcus/*classification ; Haplotypes ; *Phylogeny ; Species Specificity ; },
abstract = {BACKGROUND: Although Cryptococcus laurentii has been considered saprophytic and its taxonomy is still being described, several cases of human infections have already reported. This study aimed to evaluate molecular aspects of C. laurentii isolates from Brazil, Botswana, Canada, and the United States.<br><br>METHODS: In this study, 100 phenotypically identified C. laurentii isolates were evaluated by sequencing the 18S nuclear ribosomal small subunit rRNA gene (18S-SSU), D1/D2 region of 28S nuclear ribosomal large subunit rRNA gene (28S-LSU), and the internal transcribed spacer (ITS) of the ribosomal region.<br><br>RESULTS: BLAST searches using 550-bp, 650-bp, and 550-bp sequenced amplicons obtained from the 18S-SSU, 28S-LSU, and the ITS region led to the identification of 75 C. laurentii strains that shared 99-100% identity with C. laurentii CBS 139. A total of nine isolates shared 99% identity with both Bullera sp. VY-68 and C. laurentii RY1. One isolate shared 99% identity with Cryptococcus rajasthanensis CBS 10406, and eight isolates shared 100% identity with Cryptococcus sp. APSS 862 according to the 28S-LSU and ITS regions and designated as Cryptococcus aspenensis sp. nov. (CBS 13867). While 16 isolates shared 99% identity with Cryptococcus flavescens CBS 942 according to the 18S-SSU sequence, only six were confirmed using the 28S-LSU and ITS region sequences. The remaining 10 shared 99% identity with Cryptococcus terrestris CBS 10810, which was recently described in Brazil. Through concatenated sequence analyses, seven sequence types in C. laurentii, three in C. flavescens, one in C. terrestris, and one in the C. aspenensis sp. nov. were identified.<br><br>CONCLUSIONS: Sequencing permitted the characterization of 75% of the environmental C. laurentii isolates from different geographical areas and the identification of seven haplotypes of this species. Among sequenced regions, the increased variability of the ITS region in comparison to the 18S-SSU and 28S-LSU regions reinforces its applicability as a DNA barcode.},
}
@article {pmid25250663,
year = {2014},
author = {Salvi, D and Macali, A and Mariottini, P},
title = {Molecular phylogenetics and systematics of the bivalve family Ostreidae based on rRNA sequence-structure models and multilocus species tree.},
journal = {PloS one},
volume = {9},
number = {9},
pages = {e108696},
pmid = {25250663},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; Bivalvia/*classification/genetics ; DNA Barcoding, Taxonomic ; Likelihood Functions ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Phylogeny ; RNA, Ribosomal/chemistry/*genetics ; Species Specificity ; },
abstract = {The bivalve family Ostreidae has a worldwide distribution and includes species of high economic importance. Phylogenetics and systematic of oysters based on morphology have proved difficult because of their high phenotypic plasticity. In this study we explore the phylogenetic information of the DNA sequence and secondary structure of the nuclear, fast-evolving, ITS2 rRNA and the mitochondrial 16S rRNA genes from the Ostreidae and we implemented a multi-locus framework based on four loci for oyster phylogenetics and systematics. Sequence-structure rRNA models aid sequence alignment and improved accuracy and nodal support of phylogenetic trees. In agreement with previous molecular studies, our phylogenetic results indicate that none of the currently recognized subfamilies, Crassostreinae, Ostreinae, and Lophinae, is monophyletic. Single gene trees based on Maximum likelihood (ML) and Bayesian (BA) methods and on sequence-structure ML were congruent with multilocus trees based on a concatenated (ML and BA) and coalescent based (BA) approaches and consistently supported three main clades: (i) Crassostrea, (ii) Saccostrea, and (iii) an Ostreinae-Lophinae lineage. Therefore, the subfamily Crassostreinae (including Crassostrea), Saccostreinae subfam. nov. (including Saccostrea and tentatively Striostrea) and Ostreinae (including Ostreinae and Lophinae taxa) are recognized [corrected]. Based on phylogenetic and biogeographical evidence the Asian species of Crassostrea from the Pacific Ocean are assigned to Magallana gen. nov., whereas an integrative taxonomic revision is required for the genera Ostrea and Dendostrea. This study pointed out the suitability of the ITS2 marker for DNA barcoding of oyster and the relevance of using sequence-structure rRNA models and features of the ITS2 folding in molecular phylogenetics and taxonomy. The multilocus approach allowed inferring a robust phylogeny of Ostreidae providing a broad molecular perspective on their systematics.},
}
@article {pmid25250216,
year = {2014},
author = {Wares, JP},
title = {Mitochondrial cytochrome b sequence data are not an improvement for species identification in scleractinian corals.},
journal = {PeerJ},
volume = {2},
number = {},
pages = {e564},
pmid = {25250216},
issn = {2167-8359},
abstract = {There are well-known difficulties in using the cytochrome oxidase I (COI) mitochondrial gene region for population genetics and DNA barcoding in corals. A recent study of species divergence in the endemic Caribbean genus Agaricia reinforced such knowledge. However, the growing availability of whole mitochondrial genomes may help indicate more promising gene regions for species delineation. I assembled the whole mitochondrial genome for Agaricia fragilis from Illumina single-end 250 bp reads and compared this sequence to that of the congener A. humilis. Although these data suggest that the cytochrome b (CYB) gene region is more promising, comparison of available CYB sequence data from scleractinian and other reef-building corals indicates that multilocus approaches are still probably necessary for phylogenetic and population genetic analysis of recently-diverged coral taxa.},
}
@article {pmid25246939,
year = {2014},
author = {Zheng, S and Liu, D and Ren, W and Fu, J and Huang, L and Chen, S},
title = {Integrated analysis for identifying radix astragali and its adulterants based on DNA barcoding.},
journal = {Evidence-based complementary and alternative medicine : eCAM},
volume = {2014},
number = {},
pages = {843923},
pmid = {25246939},
issn = {1741-427X},
abstract = {Radix Astragali is a popular herb used in traditional Chinese medicine for its proimmune and antidiabetic properties. However, methods are needed to help distinguish Radix Astragali from its varied adulterants. DNA barcoding is a widely applicable molecular method used to identify medicinal plants. Yet, its use has been hampered by genetic distance, base variation, and limitations of the bio-NJ tree. Herein, we report the validation of an integrated analysis method for plant species identification using DNA barcoding that focuses on genetic distance, identification efficiency, inter- and intraspecific variation, and barcoding gap. We collected 478 sequences from six candidate DNA barcodes (ITS2, ITS, psbA-trnH, rbcL, matK, and COI) from 29 species of Radix Astragali and adulterants. The internal transcribed spacer (ITS) sequence was demonstrated as the optimal barcode for identifying Radix Astragali and its adulterants. This new analysis method is helpful in identifying Radix Astragali and expedites the utilization and data mining of DNA barcoding.},
}
@article {pmid25244750,
year = {2014},
author = {Song, M and Zhang, YQ and Lin, YH and Tu, Y and Ma, XX and Sun, W and Xiang, L and Jiao, WJ and Liu, X},
title = {[Identification of plantaginis semen based on ITS2 and psbA-trnH sequences].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {39},
number = {12},
pages = {2227-2232},
pmid = {25244750},
issn = {1001-5302},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Drug Contamination/prevention &amp; control ; Drugs, Chinese Herbal/chemistry/*classification ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/*genetics ; Plantago/*classification/*genetics ; Quality Control ; Seeds/classification/genetics ; },
abstract = {In order to evaluate the efficiency of ITS2 and psbA-trnH sequences used as DNA barcodes to distinguish Plantaginis Semen from its adulterants, we collected 71 samples of Plantaginis Semen and its adulterants. The ITS2 and psbA-trnH sequences were aligned through Clustal W, and the genetic distances were calculated by kimura 2-parameter (K2P) model and the Neighbor-Joining (NJ) phylogenetic trees were constructed using MEGA 5.1. The results indicated that the ITS2 sequence lengths of Plantago asiatica and P. depressa were 199 bp and 200 bp, respectively; the maximum intra-specific K2P distance were lower than the minimum inter-specific K2P distance; the NJ tree based on ITS2 sequence indicated that Plantaginis Semen and its adulterants could be distinguished clearly. The sequence lengths of psbA-trnH of both P. asiatica and P. depressa were 340 bp; the maximum intra-specific K2P distances were lower than the minimum inter-specific K2P distance; the NJ tree based on psbA-trnH sequence showed that Plantaginis Semen can be distinguished clearly from its adulterants except for P. major. Therefore, ITS2 sequences can be used as an ideal DNA barcode to distinguish Plantaginis Semen from its adulterants.},
}
@article {pmid25244749,
year = {2014},
author = {Zhang, YQ and Shi, Y and Song, M and Lin, YH and Ma, XX and Sun, W and Xiang, L and Liu, X},
title = {[Identification of pyrrosiae folium and its adulterants based on psbA-trnH sequence].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {39},
number = {12},
pages = {2222-2226},
pmid = {25244749},
issn = {1001-5302},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/genetics ; Drug Contamination/prevention &amp; control ; Drugs, Chinese Herbal/chemistry/*classification ; Ferns/*classification/*genetics ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/*genetics ; Quality Control ; },
abstract = {In this study, the psbA-trnH sequence as DNA barcode was used to evaluate the accuracy and stability for identification pteridophyte medicinal material Pyrrosiae Foliumas from adulterants. Genomic DNA from 106 samples were extracted successfully. The Kimura 2-Parameter (K2P) distances and ML tree were calculated using software MEGA 6.0. The intra-specific genetic distances of 3 original plants were lower than inter-specific genetic distances of adulterants. The ML tree indicated that Pyrrosiae Folium can be distinguished from its adulterants obviously. Therefore, the psbA-trnH sequence as a barcode of the pteridophyte, can accurately and stably distinguish Pyrrosiae Folium from its adulterants.},
}
@article {pmid25244748,
year = {2014},
author = {Wang, GP and Fan, CZ and Zhu, J and Li, XJ},
title = {[Identification of original plants of uyghur medicinal materials fructus elaeagni using morphological characteristics and DNA barcode].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {39},
number = {12},
pages = {2216-2221},
pmid = {25244748},
issn = {1001-5302},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Drug Contamination/prevention &amp; control ; Drugs, Chinese Herbal/chemistry/*classification ; Elaeagnaceae/anatomy &amp; histology/*classification/*genetics ; Fruit/anatomy &amp; histology/classification/genetics ; Molecular Sequence Data ; Phylogeny ; Quality Control ; },
abstract = {Morphology and molecular identification technology were used to identify 3 original plants of Fructus Elaeagni which was commonly used in Uygur medicine. Leaves, flowers and fruits from different areas were selected randomly for morphology research. ITS2 sequence as DNA barcode was used to identify 17 samples of Fructus Elaeagni. The genetic distances were computed by kimura 2-parameter (K2P) model, and the Neighbor-Joining (NJ) and Maximum Likelihood phylogenetic trees were constructed using MEGA5.0. The results showed that Elaeagnus angustifolia, E. oxycarpa and E. angustifolia var. orientalis cannot be distinguished by morphological characteristics of leaves, flowers and fruits. The sequence length of ITS2 ranged from 220 to 223 bp, the average GC content was 61.9%. The haplotype numbers of E. angustifolia, E. oxycarpa and E. angustifolia var. orientals were 4, 3, 3, respectively. The results from the NJ tree and ML tree showed that the 3 original species of Fructus Elaeagni cannot be distinguished obviously. Therefore, 3 species maybe have the same origin, and can be used as the original plant of Uygur medicineal material Fructus Elaeagni. However, further evidence of chemical components and pharmacological effect were needed.},
}
@article {pmid25244747,
year = {2014},
author = {Jia, J and Zhang, HY and Chen, J and Liu, D and Yao, H and Qian, QN and Zhang, H},
title = {[Molecular identification of Manis pentadactyla using DNA barcoding].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {39},
number = {12},
pages = {2212-2215},
pmid = {25244747},
issn = {1001-5302},
mesh = {Animals ; Cattle ; DNA Barcoding, Taxonomic/*methods ; Drug Contamination/prevention &amp; control ; Electron Transport Complex IV/genetics ; Mammals/*classification/*genetics ; Medicine, Chinese Traditional ; Molecular Sequence Data ; Phylogeny ; Quality Control ; Sheep ; Swine ; },
abstract = {The COI gene as DNA barcode was used to identify the Manis pentadactyla and its adulterants in order to provide a scientific basis for the molecular identification of M. pentadactyla. Genomic DNA was extracted from experimental samples using the DNA extraction kit. The COI genes were amplified using polymerase chain reaction (PCR) and sequenced bi-directionally. Obtained sequences were assembled using the CodonCode Aligner. The neighbor-joining (NJ) tree was constructed by MEGA 6.0. The results indicated that COI sequences were successfully amplified and NJ trees results indicated that M. pentadactyla and its adulterants can be easily identification. Therefore, the COI gene is an efficient barcode for identification of M. pentadactyla and its adulterants,which will provide a new technique for the market supervision.},
}
@article {pmid25244746,
year = {2014},
author = {Zhang, HY and Chen, J and Jia, J and Liu, D and Shi, LC and Zhang, H and Song, JY and Yao, H},
title = {[Identification of Scolopendra subspinipes mutilans and its adulterants using DNA barcode].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {39},
number = {12},
pages = {2208-2211},
pmid = {25244746},
issn = {1001-5302},
mesh = {Animals ; Arthropod Proteins/*genetics ; DNA Barcoding, Taxonomic/*methods ; Drug Contamination/prevention &amp; control ; Electron Transport Complex IV/*genetics ; Medicine, Chinese Traditional ; Molecular Sequence Data ; Phylogeny ; Quality Control ; Scorpions/*classification/enzymology/*genetics ; },
abstract = {In this study, the COI barcode was used to identify the Scolopendra medicinal materials and its adulterants in order to provide a new method for the identification of Scolopendra. Genomic DNA was extracted from the experimental samples. The COI sequences were amplified and sequenced bi-directionally. Sequence alignment and NJ tree construction was carried out by MEGA6.0 software. The results showed that the COI sequences can be obtained from all experimental samples. The average inter-specific K2P distance of Scolopendra was 0.222 and the minimum inter-specific distance was 0.190. All the Scolopendra subspinipes mutilans medicinal samples clustered into a clade in the NJ tree and can be distinguished from its adulterants. In a conclusion, COI can be used to correctly identify Scolopendra medicinal materials, and it will be a potential DNA barcode for identifying other animal medicinal materials.},
}
@article {pmid25244745,
year = {2014},
author = {Chen, J and Jia, J and Xu, XL and Xin, TY and Zhang, HY and Shi, LC and Yao, H and Liu, D and Wu, ZH},
title = {[Identification of Placenta hominis and its adulterants using COI barcode].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {39},
number = {12},
pages = {2204-2207},
pmid = {25244745},
issn = {1001-5302},
mesh = {Animals ; Cattle ; DNA Barcoding, Taxonomic/*methods ; Drug Contamination/prevention &amp; control ; Electron Transport Complex IV/*genetics ; Female ; Humans ; Medicine, Chinese Traditional ; Molecular Sequence Data ; Phylogeny ; Placenta/*chemistry/*enzymology ; Pregnancy ; Quality Control ; Sheep ; Swine ; },
abstract = {In order to provide a new method for the identification of Placenta hominis, the COI barcode has been employed to identify the P. hominis medicinal materials and its adulterants. Genomic DNA was extracted from the experimental samples. The COI sequences were amplified and sequenced bi-directionally. Sequence assembly and consensus sequence generation were performed using the CodonCode Aligner. NJ tree was constructed by MEGA6.0 software. COI sequences can be successfully obtained from all experimental samples. The intra-specific variation and inter-specific divergence were calculated. The average intra-specific K2P distance of P. hominis was 0.001 and the maximum intra-specific distance was 0.008. The cluster dendrogram constructed can be seen that the same genus is together, and distinguished from its adulterants. It is concluded that P. hominis and its adulterants can be correctly identified by DNA barcoding method.},
}
@article {pmid25244744,
year = {2014},
author = {Shi, YH and Sun, W and Fang, GH and Zheng, RB and Xu, WL and Huang, XD and Weng, SQ and Li, CY and Chen, SL},
title = {[Identification of herbal tea ingredient Plumeria rubra and its adulterants using DNA barcoding].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {39},
number = {12},
pages = {2199-2203},
pmid = {25244744},
issn = {1001-5302},
mesh = {Apocynaceae/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Drug Contamination/prevention &amp; control ; Drugs, Chinese Herbal/chemistry/*classification ; Flowers/chemistry/classification ; Molecular Sequence Data ; Phylogeny ; Quality Control ; },
abstract = {ITS2 sequence was used as a barcode to identify herbal tea ingredient Plumeria rubra and its adulterants. Genomic DNAs from forty eight samples were extracted, the ITS2 sequences were amplified and sequenced bi-direstionlly, and then assembled and obtained using CodonCode Aligner. The sequences were aligned using ClustalW, the genetic distances were computed by kimura 2-parameter (K2P) model and the Neighbor-joining (NJ) phylogenetic trees were constructed using MEGA5.0. Results showed that the length of ITS2 sequence of P. rubra were 244 bp. The intra-specific genetic distances (0-0. 016 6) were much smaller than inter-specific ones between P. rubra and its adulterants(0.320 8-0.650 4). The NJ tree indicated that P. rubra and its adulterants could be distinguished clearly. Therefore, Using ITS2 barcode can accurately andeffectively distinguish herbal tea ingredient P. rubra from its adulterants, which providesa new molecular method to identify P. rubra and ensure its safety in use.},
}
@article {pmid25244743,
year = {2014},
author = {Yu, YD and Shi, LC and Ma, XC and Sun, W and Ye, M and Xiang, L},
title = {[Identification of atractylodis macrocephalae rhizoma and atractylodis rhizoma from their adulterants using DNA barcoding].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {39},
number = {12},
pages = {2194-2198},
pmid = {25244743},
issn = {1001-5302},
mesh = {Atractylodes/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Drug Contamination/prevention &amp; control ; Drugs, Chinese Herbal/chemistry/*classification ; Molecular Sequence Data ; Phylogeny ; Quality Control ; Rhizome/classification/genetics ; },
abstract = {Atractylodis Macrocephalae Rhizoma and Atractylodis Rhizoma were widely used in strengthening spleen under different disease conditions, and were easily and often misused each other. Therefore, DNA barcode was used to distinguish Atractylodis Macrocephalae Rhizoma and Atractylodis Rhizoma from their adulterants to ensure the safe use. The sequence lengths of ITS2 of Atractylodes macrocephala, Atractylodis Rhizoma (A. lancea, A. japonica and A. coreana) were both 229 bp. Among the ITS2 sequences of A. macrocephala, only one G/C transversion was detected at site 98, and the average GC content was 69.42%. No variable site was detected in the ITS2 sequences of A. lancea. The maximum K2P intraspecific genetic distances of both A. japonica and A. coreana were 0.013. The maximum K2P intraspecific genetic distances of A. macrocephala, A. lancea, A. japonica and A. coreana were less than the minimum interspecific genetic distance of adulterants. The ITS2 sequences in each of these polytypic species were separated into pairs of divergent clusters in the NJ tree. DNA barcoding could be used as a fast and accurate identification method to distinguish Atractylodis Macrocephalae Rhizoma, Atractylodis Rhizoma, from their adulterants to ensure its safe use.},
}
@article {pmid25244742,
year = {2014},
author = {Ma, XX and Sun, W and Ren, WC and Xiang, L and Zhao, B and Zhang, YQ and Song, M and Mu, ZJ and Chen, SL},
title = {[Identification of cattail pollen (puhuang), pine pollen (songhuafen) and its adulterants by ITS2 sequence].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {39},
number = {12},
pages = {2189-2193},
pmid = {25244742},
issn = {1001-5302},
mesh = {China ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; DNA, Ribosomal Spacer/*genetics ; Drug Contamination/prevention &amp; control ; Drugs, Chinese Herbal/chemistry/*classification ; Molecular Sequence Data ; Phylogeny ; Pinus/*classification/genetics ; Pollen/classification/genetics ; Quality Control ; Typhaceae/*classification/genetics ; },
abstract = {DNA barcoding method was conducted for the authentication of pollen materials due to difficulty of discriminating pollen materials bearing morphological similarity. In this study, a specific focus was to identify cattail pollen (Puhuang) and pine pollen (Songhuafen) samples from their adulterants which are frequently mixed-together. Regions of the internal transcribed spacer (ITS2) from 60 samples were sequenced, and new primers for cattail pollen were designed according to the sequence information. The results from the NJ trees showed that the species of pine pollen, Puhuang and their adulterants can be classified as obvious monophyly. Therefore, we propose to adapt DNA barcoding methodology to accurately distinguish cattail pollen, pine pollen and their adulterant materials. It is a great help for drug regulatory agency to supervise the quality of medicinal materials.},
}
@article {pmid25244741,
year = {2014},
author = {Ren, WC and Ma, XX and Yu, JL and Ma, W and Sun, W},
title = {[Identification of cimicifugae rhizoma and its adulterants using ITS2 sequence].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {39},
number = {12},
pages = {2184-2188},
pmid = {25244741},
issn = {1001-5302},
mesh = {Base Sequence ; China ; Cimicifuga/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; DNA, Ribosomal Spacer/*genetics ; Drug Contamination/prevention &amp; control ; Drugs, Chinese Herbal/chemistry/*classification ; Molecular Sequence Data ; Phylogeny ; Quality Control ; Rhizome/classification/genetics ; },
abstract = {In order to identify Cimicifugae Rhizoma from its adulterants and to ensure its safe use, the internal transcribed spacer 2 (ITS2) sequence of Cimicifugae Rhizoma and its adulterants were amplified and bidirectionally sequenced by DNA barcoding technology. Sequence assembly and consensus sequence generation were performed by the CodonCode Aligner V3.7.1. The genetic distances were computed by MEGA 5.0. Identification analyses were performed using neighbor-joining (NJ) methods. The length of ITS2 sequence of the three origin plants of Cimicifugae Rhizoma include Cimicifuga heracleifolia, C. foetida, C. dahurica was 217, 219 and 219 bp, respectively. Their intraspecific genetic distance was much lower than the interspecific genetic distance with their closely related species. The NJ tree of ITS2 indicated that the three origin plants of Cimicifugae Rhizoma formed a monophyletic clade, Cimicifugae Rhizoma and its adulterants could be distinguished clearly. The authors proposed that ITS2 sequence was suitable for the authentication of Cimicifugae Rhizoma and its adulterants.},
}
@article {pmid25244739,
year = {2014},
author = {Shi, LC and Chen, J and Xiang, L and Song, JY and Yao, H},
title = {[DNA barcoding identification between arisaematis rhizoma and its adulterants based on ITS2 sequences].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {39},
number = {12},
pages = {2176-2179},
pmid = {25244739},
issn = {1001-5302},
mesh = {Arisaema/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; DNA, Ribosomal Spacer/*genetics ; Drug Contamination/prevention &amp; control ; Drugs, Chinese Herbal/chemistry/*classification ; Molecular Sequence Data ; Phylogeny ; Quality Control ; Rhizome/classification/genetics ; },
abstract = {Fifty-eight samples belonging to 7 species of Arisaematis Rhizoma and its adulterants were collected. The ITS2 locus was employed as a DNA barcode and amplified, sequenced and assembled for all of the collected samples. Then, ITS2 sequences have been annotated using HMM-based method. The intra- and inter-specific variations were calculated and NJ tree was constructed using MEGA 6.0 software. The results showed that inter-specific K2P distances were significantly larger than intra-specific distances for all of the three origin species of Arisaematis Rhizoma. Furthermore, three origin species, Arisaema amurense, A. erubescens and A. heterophyllum, can be respectively formed to be a single branch with high bootstrap values. It is concluded that ITS2 can be used to correctly identify Arisaematis Rhizoma from its adulterants and the application of ITS2 in the identification of traditional Chinese medicine has an important prospective.},
}
@article {pmid25244738,
year = {2014},
author = {Ma, XC and Yao, H and Wu, L and Xiang, L and Chen, XC and Song, JY},
title = {[Molecular identification of aucklandiae radix, vladimiriae radix, inulae radix, aristolochiae radix and kadsurae radix using ITS2 barcode].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {39},
number = {12},
pages = {2169-2175},
pmid = {25244738},
issn = {1001-5302},
mesh = {Aristolochia/classification/genetics ; Base Sequence ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; DNA, Ribosomal Spacer/*genetics ; Drugs, Chinese Herbal/chemistry/*classification ; Molecular Sequence Data ; Phylogeny ; Plants, Medicinal/*classification/genetics ; Quality Control ; },
abstract = {In order to identify Aucklandiae Radix, Vladimiriae Radix, Inulae Radix, Aristolochiae Radix and Kadsurae Radix using ITS2 barcodes, genomic DNA from sixty samples was extracted and the ITS2 (internal transcribed spacer) regions were amplified and sequenced. The genetic distances were computed using MEGA 5.0 in accordance with the kimura 2-parameter (K2P) model and the neighbor-joining (NJ) phylogenetic tree was constructed. The results indicated that for Aucklandiae Radix (Aucklandia lappa), Vladimiriae Radix (Vladimiria souliei and V. souliei var. cinerea), Inulae Radix (Inula helenium), Aristolochiae Radix (Aristolochia debilis) and Kadsurae Radix (Kadsura longipedunculata), the intra-specific variation was smaller than inter-specific one. There are 162 variable sites among 272 bp after alignment of all ITS2 sequence haplotypes. For each species, the intra-specific genetic distances were also smaller than inter-specific one. Furthermore, the NJ tree strongly supported that Aucklandiae Radix, Vladimiriae Radix, Inulae Radix, Aristolochiae Radix and Kadsurae Radix can be differentiated. At the same time, V. souliei (Dolomiaea souliei) and V. souliei var. cinerea(D. souliei var. cinerea) belonging to Vladimiriae Radix were clearly identified. In conclusion, ITS2 barcode could be used to identify Aucklandiae Radix, Vladimiriae Radix, Inulae Radix, Aristolochiae Radix and Kadsurae Radix. Our study may provide a scientific foundation for clinical safe use of the traditional Chinese medicines.},
}
@article {pmid25244737,
year = {2014},
author = {Zhao, S and Pang, XH and Song, JY and Chen, SL},
title = {[Identification of albiziae cortex, albiziae flos and their adulterants using ITS2 barcoding].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {39},
number = {12},
pages = {2164-2168},
pmid = {25244737},
issn = {1001-5302},
mesh = {Albizzia/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; DNA, Ribosomal Spacer/*genetics ; Drugs, Chinese Herbal/chemistry/*classification ; Flowers/classification/genetics ; Molecular Sequence Data ; Phylogeny ; Quality Control ; },
abstract = {The ITS2 barcode was used to accurately identify Albiziae Cortex, Albiziae Flos and their adulterants in this study. A total of46 samples from Albiziae Cortex, Albiziae Flos and their adulterants were collected. The ITS2 regions were amplified and sequenced. Sequences were assembled using the CodonCode Aligner. The genetic distances of ITS2 region were calculated using MEGA 5.0. BLAST1, nearest distance and phylogenetic tree (NJ-tree) methods were used to assess the identification efficiency of the ITS2 barcode. The results revealed that the intraspecific genetic distances of Albizia julibrissin were lower than the interspecific genetic distances between A. julibrissin and its adulterants. The identification efficiency of ITS2 barcode using BLAST1 was 100%. The NJ-tree showed that A. julibrissin and their adulterants can be easily differentiated according to their monophyly. The ITS2 barcode is suitable to be as a barcode to identify Albiziae Cortex, Albiziae Flos and their adulterants.},
}
@article {pmid25244735,
year = {2014},
author = {Shi, LC and Yao, H and Xie, LF and Zhu, YJ and Song, JY and Zhang, H and Chen, SL},
title = {[Integrated DNA barcoding database for identifying Chinese animal medicine].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {39},
number = {12},
pages = {2155-2159},
pmid = {25244735},
issn = {1001-5302},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; *Databases, Nucleic Acid ; Eukaryota/*classification/genetics ; *Medicine, Chinese Traditional ; },
abstract = {In order to construct an integrated DNA barcoding database for identifying Chinese animal medicine, the authors and their cooperators have completed a lot of researches for identifying Chinese animal medicines using DNA barcoding technology. Sequences from GenBank have been analyzed simultaneously. Three different methods, BLAST, barcoding gap and Tree building, have been used to confirm the reliabilities of barcode records in the database. The integrated DNA barcoding database for identifying Chinese animal medicine has been constructed using three different parts: specimen, sequence and literature information. This database contained about 800 animal medicines and the adulterants and closely related species. Unknown specimens can be identified by pasting their sequence record into the window on the ID page of species identification system for traditional Chinese medicine (www. tcmbarcode. cn). The integrated DNA barcoding database for identifying Chinese animal medicine is significantly important for animal species identification, rare and endangered species conservation and sustainable utilization of animal resources.},
}
@article {pmid25238110,
year = {2016},
author = {Alcantara, SG and Yambot, AV},
title = {DNA barcoding of commercially important Grouper species (Perciformes, Serranidae) in the Philippines.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {3837-3845},
doi = {10.3109/19401736.2014.958672},
pmid = {25238110},
issn = {2470-1408},
mesh = {Animals ; Bass/*classification/genetics ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Electron Transport Complex IV/genetics ; Endangered Species ; Gene Frequency ; Geography ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Fish identification is generally challenging because of their unpronounced and overlapping morphological characters which is true in grouper species. In the Philippines, an updated, reliable and accurate inventory of this high value commercial groupers has not been carried out previously. Using molecular tools in the identification and inventory of fish species in the country is confined to few laboratories and experts in the country. In this study, 27 species of the Serranidae family were identified from the grouper samples collected from major fish landing sites and markets in the Philippines. The grouper species were molecularly identified using the cytochrome c oxidase I (COI) sequences for DNA barcoding. The accuracy of the inferred species-level taxonomy based on COI is supported with high similarity search (98-100%) both in BOLD and BLAST, well-distributed genetic distance values and cohesive clustering in the Neighbor-Joining Tree. Aside from reinforcing the classical methodology of grouper identification in the country, this pioneering study on molecular identification of Philippine groupers constitutes a significant contribution to the DNA barcode library of Philippine marine fishes and to the global barcode entries in general, which can be used when dealing with grouper taxonomy, biodiversity, stock assessment and trade. The results reveal the different localities where the grouper species can be possibly sourced out in the country for trade and aquaculture purposes. Several of the grouper species are included in the IUCN Red List of Threatened Species. As a tool for conservation ecology, this study signals the implementation of sustainable fisheries management regulation to protect in particular those which are listed under the IUCN.},
}
@article {pmid25233044,
year = {2014},
author = {Zhou, Z and Li, T and Huang, H and Chen, Y and Liu, F and Huang, C and Li, N},
title = {A dual amplification strategy for DNA detection combining bio-barcode assay and metal-enhanced fluorescence modality.},
journal = {Chemical communications (Cambridge, England)},
volume = {50},
number = {87},
pages = {13373-13376},
doi = {10.1039/c4cc05554c},
pmid = {25233044},
issn = {1364-548X},
mesh = {Biosensing Techniques/*methods ; DNA/*analysis/chemistry ; *Fluorescence ; Metal Nanoparticles/chemistry ; Silver/*chemistry ; },
abstract = {Silver-enhanced fluorescence was coupled with a bio-barcode assay to facilitate a dual amplification assay to demonstrate a non-enzymatic approach for simple and sensitive detection of DNA. In the assay design, magnetic nanoparticles seeded with silver nanoparticles were modified with the capture DNA, and silver nanoparticles were modified with the binding of ssDNA and the fluorescently labeled barcode dsDNA. Upon introduction of the target DNA, a sandwich structure was formed because of the hybridization reaction. By simple magnetic separation, silver-enhanced fluorescence of barcode DNAs could be readily measured without the need of a further step to liberate barcode DNAs from silver nanoparticles, endowing the method with simplicity and high sensitivity with a detection limit of 1 pM.},
}
@article {pmid25232993,
year = {2014},
author = {Yue, Q and Wu, K and Qiu, D and Hu, J and Liu, D and Wei, X and Chen, J and Cook, CE},
title = {A formal re-description of the cockroach Hebardina concinna anchored on DNA Barcodes confirms wing polymorphism and identifies morphological characters for field identification.},
journal = {PloS one},
volume = {9},
number = {9},
pages = {e106789},
pmid = {25232993},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Cockroaches/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genitalia, Male/*anatomy &amp; histology ; Male ; Mitochondria/genetics ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Wings, Animal/anatomy &amp; histology ; },
abstract = {BACKGROUND: Hebardina concinna is a domestic pest and potential vector of pathogens throughout East and Southeast Asia, yet identification of this species has been difficult due to a lack of diagnostic morphological characters, and to uncertainty in the relationship between macroptyrous (long-winged) and brachypterous (small-winged) morphotypes. In insects male genital structures are typically species-specific and are frequently used to identify species. However, male genital structures in H. concinna had not previously been described, in part due to difficulty in identifying conspecifics.<br><br>METHODS/PRINCIPAL FINDINGS: We collected 15 putative H. concinna individuals, from Chinese populations, of both wing morphotypes and both sexes and then generated mitochondrial COI (the standard barcode region) and COII sequences from five of these individuals. These confirmed that both morphotypes of both sexes are the same species. We then dissected male genitalia and compared genital structures from macropterous and brachypterous individuals, which we showed to be identical, and present here for the first time a detailed description of H. concinna male genital structures. We also present a complete re-description of the morphological characters of this species, including both wing morphs.<br><br>CONCLUSIONS/SIGNIFICANCE: This work describes a practical application of DNA barcoding to confirm that putatively polymorphic insects are conspecific and then to identify species-specific characters that can be used in the field to identify individuals and to obviate the delay and cost of returning samples to a laboratory for DNA sequencing.},
}
@article {pmid25229871,
year = {2015},
author = {Willows-Munro, S and Schoeman, MC},
title = {Influence of killing method on Lepidoptera DNA barcode recovery.},
journal = {Molecular ecology resources},
volume = {15},
number = {3},
pages = {613-618},
doi = {10.1111/1755-0998.12331},
pmid = {25229871},
issn = {1755-0998},
mesh = {Animals ; DNA/chemistry/*genetics/*isolation &amp; purification ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Entomology/*methods/standards ; Lepidoptera/*classification/*genetics ; Molecular Biology/*methods/standards ; Molecular Sequence Data ; Sequence Analysis, DNA ; },
abstract = {The global DNA barcoding initiative has revolutionized the field of biodiversity research. Such large-scale sequencing projects require the collection of large numbers of specimens, which need to be killed and preserved in a way that is both DNA-friendly and which will keep voucher specimens in good condition for later study. Factors such as time since collection, correct storage (exposure to free water and heat) and DNA extraction protocol are known to play a role in the success of downstream molecular applications. Limited data are available on the most efficient, DNA-friendly protocol for killing. In this study, we evaluate the quality of DNA barcode (cytochrome oxidase I) sequences amplified from DNA extracted from specimens collected using three different killing methods (ethyl acetate, cyanide and freezing). Previous studies have suggested that chemicals, such as ethyl acetate and formaldehyde, degraded DNA and as such may not be appropriate for the collection of insects for DNA-based research. All Lepidoptera collected produced DNA barcodes of good quality, and our study found no clear difference in nucleotide signal strength, probability of incorrect base calling and phylogenetic utility among the three different treatment groups. Our findings suggest that ethyl acetate, cyanide and freezing can all be used to collect specimens for DNA analysis.},
}
@article {pmid25229704,
year = {2014},
author = {Lutomiah, J and Omondi, D and Masiga, D and Mutai, C and Mireji, PO and Ongus, J and Linthicum, KJ and Sang, R},
title = {Blood meal analysis and virus detection in blood-fed mosquitoes collected during the 2006-2007 Rift Valley fever outbreak in Kenya.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {14},
number = {9},
pages = {656-664},
pmid = {25229704},
issn = {1557-7759},
mesh = {Animals ; Cattle ; Cattle Diseases/*epidemiology/virology ; Culicidae/*virology ; Disease Outbreaks/*veterinary ; Goats ; Humans ; Insect Vectors/*virology ; Kenya/epidemiology ; RNA, Viral/blood ; Rift Valley Fever/*epidemiology/virology ; Rift Valley fever virus/genetics/*immunology/isolation &amp; purification ; Sheep ; },
abstract = {BACKGROUND: Rift Valley fever (RVF) is a zoonosis of domestic ruminants in Africa. Blood-fed mosquitoes collected during the 2006-2007 RVF outbreak in Kenya were analyzed to determine the virus infection status and animal source of the blood meals.<br><br>MATERIALS AND METHODS: Blood meals from individual mosquito abdomens were screened for viruses using Vero cells and RT-PCR. DNA was also extracted and the cytochrome c oxidase 1 (CO1) and cytochrome b (cytb) genes amplified by PCR. Purified amplicons were sequenced and queried in GenBank and Barcode of Life Database (BOLD) to identify the putative blood meal sources.<br><br>RESULTS: The predominant species in Garissa were Aedes ochraceus, (n=561, 76%) and Ae. mcintoshi, (n=176, 24%), and Mansonia uniformis, (n=24, 72.7%) in Baringo. Ae. ochraceus fed on goats (37.6%), cattle (16.4%), donkeys (10.7%), sheep (5.9%), and humans (5.3%). Ae. mcintoshi fed on the same animals in almost equal proportions. RVFV was isolated from Ae. ochraceus that had fed on sheep (4), goats (3), human (1), cattle (1), and unidentified host (1), with infection and dissemination rates of 1.8% (10/561) and 50% (5/10), respectively, and 0.56% (1/176) and 100% (1/1) in Ae. mcintoshi. In Baringo, Ma. uniformis fed on sheep (38%), frogs (13%), duikers (8%), cattle (4%), goats (4%), and unidentified hosts (29%), with infection and dissemination rates of 25% (6/24) and 83.3% (5/6), respectively. Ndumu virus (NDUV) was also isolated from Ae. ochraceus with infection and dissemination rates of 2.3% (13/561) and 76.9% (10/13), and Ae. mcintoshi, 2.8% (5/176) and 80% (4/5), respectively. Ten of the infected Ae. ochraceus had fed on goats, sheep (1), and unidentified hosts (2), and Ae. mcintoshi on goats (3), camel (1), and donkey (1).<br><br>CONCLUSION: This study has demonstrated that RVFV and NDUV were concurrently circulating during the outbreak, and sheep and goats were the main amplifiers of these viruses respectively.},
}
@article {pmid25229424,
year = {2014},
author = {Obase, K and Douhan, GW and Matsuda, Y and Smith, ME},
title = {Culturable fungal assemblages growing within Cenococcum sclerotia in forest soils.},
journal = {FEMS microbiology ecology},
volume = {90},
number = {3},
pages = {708-717},
doi = {10.1111/1574-6941.12428},
pmid = {25229424},
issn = {1574-6941},
mesh = {Ascomycota/*classification/genetics/isolation &amp; purification ; Basidiomycota/classification/genetics/isolation &amp; purification ; Biodiversity ; DNA, Ribosomal Spacer/genetics ; *Forests ; *Mycorrhizae ; Sequence Analysis, DNA ; *Soil Microbiology ; Trees/*microbiology ; },
abstract = {The ectomycorrhizal fungus Cenococcum geophilum (Ascomycota, Dothideomycetes) forms black, round to irregular sclerotia in forest soils. Fungi that colonize the sclerotia appear to affect sclerotia viability and may play an important role in the life history of Cenococcum. Some of the fungi could also affect nutrient cycling by decomposing Cenococcum sclerotia, which are melanized and recalcitrant to decay. We used a culture-based method to document the fungal communities growing inside surface-sterilized sclerotia that were collected from forest soils. Cenococcum was successfully isolated from 297 of 971 sclerotia whereas 427 sclerotia hosted fungi other than Cenococcum. DNA barcoding of the internal transcribed spacer rDNA followed by grouping at 97% sequence similarity yielded 85 operational taxonomic units (OTUs) that consisted primarily of Ascomycota (e.g. Chaetothyriales, Eurotiales, Helotiales, Pleosporales) and a few Basidiomycota and Mucoromycotina. Although most fungal OTUs were infrequently cultured, several OTUs such as members of Asterostroma, Cladophialophora, Oidiodendron, and Pleosporales were common and found across many sites. Our results suggest that Cenococcum sclerotia act as a substrate for diverse fungi. The occurrence of several OTUs in sclerotia across many sites suggests that these fungi may be active parasites of Cenococcum sclerotia or may preferentially use sclerotia as a nutrient source.},
}
@article {pmid25226019,
year = {2014},
author = {Sanschagrin, S and Yergeau, E},
title = {Next-generation sequencing of 16S ribosomal RNA gene amplicons.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {90},
pages = {},
pmid = {25226019},
issn = {1940-087X},
mesh = {*Environmental Microbiology ; RNA, Bacterial/chemistry/genetics ; RNA, Ribosomal, 16S/chemistry/genetics ; Sequence Analysis, RNA/*methods ; },
abstract = {One of the major questions in microbial ecology is "who is there?" This question can be answered using various tools, but one of the long-lasting gold standards is to sequence 16S ribosomal RNA (rRNA) gene amplicons generated by domain-level PCR reactions amplifying from genomic DNA. Traditionally, this was performed by cloning and Sanger (capillary electrophoresis) sequencing of PCR amplicons. The advent of next-generation sequencing has tremendously simplified and increased the sequencing depth for 16S rRNA gene sequencing. The introduction of benchtop sequencers now allows small labs to perform their 16S rRNA sequencing in-house in a matter of days. Here, an approach for 16S rRNA gene amplicon sequencing using a benchtop next-generation sequencer is detailed. The environmental DNA is first amplified by PCR using primers that contain sequencing adapters and barcodes. They are then coupled to spherical particles via emulsion PCR. The particles are loaded on a disposable chip and the chip is inserted in the sequencing machine after which the sequencing is performed. The sequences are retrieved in fastq format, filtered and the barcodes are used to establish the sample membership of the reads. The filtered and binned reads are then further analyzed using publically available tools. An example analysis where the reads were classified with a taxonomy-finding algorithm within the software package Mothur is given. The method outlined here is simple, inexpensive and straightforward and should help smaller labs to take advantage from the ongoing genomic revolution.},
}
@article {pmid25225631,
year = {2014},
author = {Byers, C and Maughan, PJ and Clouse, J and Stewart, JR},
title = {Microsatellite primers in Agave utahensis (Asparagaceae), a keystone species in the Mojave Desert and Colorado Plateau.},
journal = {Applications in plant sciences},
volume = {2},
number = {9},
pages = {},
pmid = {25225631},
issn = {2168-0450},
abstract = {PREMISE OF THE STUDY: Utah agave (Agave utahensis) and its putative subspecies, A. utahensis subsp. kaibabensis and A. utahensis subsp. utahensis, are keystone species of the Mojave Desert and Colorado Plateau in the southwestern United States. Here we developed microsatellite markers to study population structure and genetic diversity of the two subspecies of A. utahensis. •<br><br>METHODS AND RESULTS: We analyzed 22,386 454-pyrosequencing large contigs (>400 bp), derived from a genome reduction experiment consisting of A. utahensis accessions, for putative microsatellites. The use of unique multiplex barcodes for each of the Agave accessions allowed for the identification of putatively polymorphic microsatellites based solely on sequence alignment analysis. We report the characteristics of 11 polymorphic microsatellite loci based on a panel of 104 individuals from the two subspecies. The number of alleles per locus varied from three to eight, with an average of 5.5 alleles per locus. Observed and expected heterozygosity values ranged from 0.038 to 0.777 and 0.038 to 0.707, respectively. &#x2022;<br><br>CONCLUSIONS: The microsatellites identified here will be invaluable for future studies of population structure, polyploidy, and genetic diversity across the species.},
}
@article {pmid25222272,
year = {2014},
author = {Landi, M and Dimech, M and Arculeo, M and Biondo, G and Martins, R and Carneiro, M and Carvalho, GR and Lo Brutto, S and Costa, FO},
title = {DNA barcoding for species assignment: the case of Mediterranean marine fishes.},
journal = {PloS one},
volume = {9},
number = {9},
pages = {e106135},
pmid = {25222272},
issn = {1932-6203},
mesh = {Animals ; Classification/methods ; DNA Barcoding, Taxonomic/*methods ; Fishes/classification/*genetics ; Mediterranean Sea ; Phylogeny ; Species Specificity ; },
abstract = {BACKGROUND: DNA barcoding enhances the prospects for species-level identifications globally using a standardized and authenticated DNA-based approach. Reference libraries comprising validated DNA barcodes (COI) constitute robust datasets for testing query sequences, providing considerable utility to identify marine fish and other organisms. Here we test the feasibility of using DNA barcoding to assign species to tissue samples from fish collected in the central Mediterranean Sea, a major contributor to the European marine ichthyofaunal diversity.<br><br>A dataset of 1278 DNA barcodes, representing 218 marine fish species, was used to test the utility of DNA barcodes to assign species from query sequences. We tested query sequences against 1) a reference library of ranked DNA barcodes from the neighbouring North East Atlantic, and 2) the public databases BOLD and GenBank. In the first case, a reference library comprising DNA barcodes with reliability grades for 146 fish species was used as diagnostic dataset to screen 486 query DNA sequences from fish specimens collected in the central basin of the Mediterranean Sea. Of all query sequences suitable for comparisons 98% were unambiguously confirmed through complete match with reference DNA barcodes. In the second case, it was possible to assign species to 83% (BOLD-IDS) and 72% (GenBank) of the sequences from the Mediterranean. Relatively high intraspecific genetic distances were found in 7 species (2.2%-18.74%), most of them of high commercial relevance, suggesting possible cryptic species.<br><br>CONCLUSION/SIGNIFICANCE: We emphasize the discriminatory power of COI barcodes and their application to cases requiring species level resolution starting from query sequences. Results highlight the value of public reference libraries of reliability grade-annotated DNA barcodes, to identify species from different geographical origins. The ability to assign species with high precision from DNA samples of disparate quality and origin has major utility in several fields, from fisheries and conservation programs to control of fish products authenticity.},
}
@article {pmid25222240,
year = {2014},
author = {Huang, ZH and Ke, DH},
title = {DNA barcoding and evolutionary relationships of the Phasianidae family in China.},
journal = {Genetics and molecular research : GMR},
volume = {13},
number = {3},
pages = {7411-7419},
doi = {10.4238/2014.September.12.7},
pmid = {25222240},
issn = {1676-5680},
mesh = {Animals ; Birds/*classification/*genetics ; China ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; Genotype ; Phylogeny ; },
abstract = {A DNA barcode is a short sequence of standardized genomic region that is specific to a species. According to studies of bird species, the 694-bp sequence of the mitochondrial gene encoding cytochrome c oxidase 1 (COI) is extremely useful for species identification and phylogeny. In the present study, we analyzed the COI barcodes of 31 species from 18 genera belonging to the Phasianidae family in China. Kimura two-parameter (K2P) distances were calculated between barcodes. We found that the average genetic distance between congeneric species was 24 times higher compared to the average genetic distance within species. Each bird species had a barcode that was distinct to all other bird species. The neighbor-joining method was used to construct a phylogenetic tree, which grouped all of the genera into 2 divergent clades. In conclusion, DNA barcoding is an effective molecular tool for Phasianidae species identification and phylogenetic inference.},
}
@article {pmid25213249,
year = {2014},
author = {Lefrançois, P and Gallagher, JE and Snyder, M},
title = {Global analysis of transcription factor-binding sites in yeast using ChIP-Seq.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1205},
number = {},
pages = {231-255},
pmid = {25213249},
issn = {1940-6029},
support = {T32 HG000044/HG/NHGRI NIH HHS/United States ; },
mesh = {Binding Sites ; Chromatin Immunoprecipitation/*methods ; DNA, Fungal/chemistry/*genetics/metabolism ; Fungal Proteins/*metabolism ; Gene Library ; Genomics/methods ; High-Throughput Nucleotide Sequencing/*methods ; Protein Binding ; Sequence Analysis, DNA/*methods ; Transcription Factors/*metabolism ; Yeasts/chemistry/*genetics/metabolism ; },
abstract = {Transcription factors influence gene expression through their ability to bind DNA at specific regulatory elements. Specific DNA-protein interactions can be isolated through the chromatin immunoprecipitation (ChIP) procedure, in which DNA fragments bound by the protein of interest are recovered. ChIP is followed by high-throughput DNA sequencing (Seq) to determine the genomic provenance of ChIP DNA fragments and their relative abundance in the sample. This chapter describes a ChIP-Seq strategy adapted for budding yeast to enable the genome-wide characterization of binding sites of transcription factors (TFs) and other DNA-binding proteins in an efficient and cost-effective way.Yeast strains with epitope-tagged TFs are most commonly used for ChIP-Seq, along with their matching untagged control strains. The initial step of ChIP involves the cross-linking of DNA and proteins. Next, yeast cells are lysed and sonicated to shear chromatin into smaller fragments. An antibody against an epitope-tagged TF is used to pull down chromatin complexes containing DNA and the TF of interest. DNA is then purified and proteins degraded. Specific barcoded adapters for multiplex DNA sequencing are ligated to ChIP DNA. Short DNA sequence reads (28-36 base pairs) are parsed according to the barcode and aligned against the yeast reference genome, thus generating a nucleotide-resolution map of transcription factor-binding sites and their occupancy.},
}
@article {pmid25211345,
year = {2014},
author = {Hsu, CM and de Palmas, S and Kuo, CY and Denis, V and Chen, CA},
title = {Identification of scleractinian coral recruits using fluorescent censusing and DNA barcoding techniques.},
journal = {PloS one},
volume = {9},
number = {9},
pages = {e107366},
pmid = {25211345},
issn = {1932-6203},
mesh = {Animal Distribution ; Animals ; Anthozoa/*classification/genetics ; Coral Reefs ; DNA Barcoding, Taxonomic ; Genes, Mitochondrial ; Molecular Typing ; Optical Imaging ; Phylogeny ; Taiwan ; },
abstract = {The identification of coral recruits has been problematic due to a lack of definitive morphological characters being available for higher taxonomic resolution. In this study, we tested whether fluorescent detection of coral recruits used in combinations of different DNA-barcoding markers (cytochrome oxidase I gene [COI], open reading frame [ORF], and nuclear Pax-C intron [PaxC]) could be useful for increasing the resolution of coral spat identification in ecological studies. One hundred and fifty settlement plates were emplaced at nine sites on the fringing reefs of Kenting National Park in southern Taiwan between April 2011 and September 2012. A total of 248 living coral spats and juveniles (with basal areas ranging from 0.21 to 134.57 mm(2)) were detected on the plates with the aid of fluorescent light and collected for molecular analyses. Using the COI DNA barcoding technique, 90.3% (224/248) of coral spats were successfully identified into six genera, including Acropora, Isopora, Montipora, Pocillopora, Porites, and Pavona. PaxC further separated I. cuneata and I. palifera of Isopora from Acropora, and ORF successfully identified the species of Pocillopora (except P. meandrina and P. eydouxi). Moreover, other cnidarian species such as actinarians, zoanthids, and Millepora species were visually found using fluorescence and identified by COI DNA barcoding. This combination of existing approaches greatly improved the taxonomic resolution of early coral life stages, which to date has been mainly limited to the family level based on skeletal identification. Overall, this study suggests important improvements for the identification of coral recruits in ecological studies.},
}
@article {pmid25209199,
year = {2014},
author = {Deagle, BE and Jarman, SN and Coissac, E and Pompanon, F and Taberlet, P},
title = {DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match.},
journal = {Biology letters},
volume = {10},
number = {9},
pages = {},
pmid = {25209199},
issn = {1744-957X},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Electron Transport Complex IV/*genetics ; Sequence Analysis, DNA/methods ; Species Specificity ; },
abstract = {DNA metabarcoding enables efficient characterization of species composition in environmental DNA or bulk biodiversity samples, and this approach is making significant and unique contributions in the field of ecology. In metabarcoding of animals, the cytochrome c oxidase subunit I (COI) gene is frequently used as the marker of choice because no other genetic region can be found in taxonomically verified databases with sequences covering so many taxa. However, the accuracy of metabarcoding datasets is dependent on recovery of the targeted taxa using conserved amplification primers. We argue that COI does not contain suitably conserved regions for most amplicon-based metabarcoding applications. Marker selection deserves increased scrutiny and available marker choices should be broadened in order to maximize potential in this exciting field of research.},
}
@article {pmid25207152,
year = {2013},
author = {Sahin, S and Atabey, C and Simşek, M and Naderi, S},
title = {Spinal textiloma (gossypiboma): a report of three cases misdiagnosed as tumour.},
journal = {Balkan medical journal},
volume = {30},
number = {4},
pages = {422-428},
pmid = {25207152},
issn = {2146-3123},
abstract = {BACKGROUND: Textile products commonly used in surgery (e.g., sponges or gauze) have been known to cause complications after spinal surgery. Associated complications usually arise months or even years after the primary surgery. In case of spine surgery, these bodies are often detected during neuroradiological evaluations to investigate reported back pain; however, this complication often remains asymptomatic.<br><br>AIMS: The research is intended to increase awareness among both spinal surgeons and neuroradiologists of this potential complication.<br><br>STUDY DESIGN: Retrospective study.<br><br>METHODS: This study is a retrospective case series of three patients with retained surgical textile products who had been misdiagnosed with spinal tumour. The medical records of the patients were reviewed and demographic data, clinical aspects, initial diagnosis, surgical procedures, time interval between previous operation and onset of symptoms, laboratory findings, radiological findings, treatment, and outcome were analysed.<br><br>RESULTS: The three patients included two women and one man aged between 64 and 67 years. All patients had a previous surgery for lumbar disc herniation. The time from the previous surgical procedures to presentation ranged from 3 to 17 years. All patients presented with non-specific lower back pain and/or radiculopathy without clinical findings of infection. Laboratory parameters were otherwise normal. All three cases had been misdiagnosed as a spinal tumor based on magnetic resonance imaging findings. During new surgical procedures, gauze bandages, i.e., surgical textiles left during a previous operation, were found.<br><br>CONCLUSION: Textiloma is an important and rarely mentioned potential neurosurgical complication that may remain asymptomatic for years. They are more common in obese patients, after emergency surgery, and with unplanned changes in surgical procedure such as bleeding and unintended neurosurgical complications. Neuroradiological findings are variable and non-specific; thus, patients could be misdiagnosed with a spinal tumor or abscess. Likewise, in patients with a history of spinal surgery, spinal abscesses, haematomas, hypertrophic scars, fibrosarcomas, rhabdomyosarcomas, and schwannomas should definitely be considered in the differential diagnosis and considered when planning diagnostic procedures. Appropriate antibiotic therapy is recommended when a suppurative complication is present or suspected. Textiloma is a medico-legal complication that can be prevented by the education of surgical staff, the counting method (preoperatively, at closure, and at the end), and use of products with radiopaque barcodes.},
}
@article {pmid25204516,
year = {2014},
author = {Kreisinger, J and Cížková, D and Vohánka, J and Piálek, J},
title = {Gastrointestinal microbiota of wild and inbred individuals of two house mouse subspecies assessed using high-throughput parallel pyrosequencing.},
journal = {Molecular ecology},
volume = {23},
number = {20},
pages = {5048-5060},
doi = {10.1111/mec.12909},
pmid = {25204516},
issn = {1365-294X},
mesh = {Animals ; Animals, Wild/microbiology ; Bacteria/classification ; DNA Barcoding, Taxonomic ; Gastrointestinal Tract/*microbiology ; *Genetic Variation ; Metagenome ; Mice ; Mice, Inbred Strains/*microbiology ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The effects of gastrointestinal tract microbiota (GTM) on host physiology and health have been the subject of considerable interest in recent years. While a variety of captive bred species have been used in experiments, the extent to which GTM of captive and/or inbred individuals resembles natural composition and variation in wild populations is poorly understood. Using 454 pyrosequencing, we performed 16S rDNA GTM barcoding for 30 wild house mice (Mus musculus) and wild-derived inbred strain mice belonging to two subspecies (M. m. musculus and M. m. domesticus). Sequenced individuals were selected according to a 2 × 2 experimental design: wild (14) vs. inbred origin (16) and M. m. musculus (15) vs. M. m. domesticus (15). We compared alpha diversity (i.e. number of operational taxonomic units - OTUs), beta diversity (i.e. interindividual variability) and microbiota composition across the four groups. We found no difference between M. m. musculus and M. m. domesticus subspecies, suggesting low effect of genetic differentiation between these two subspecies on GTM structure. Both inbred and wild populations showed the same level of microbial alpha and beta diversity; however, we found strong differentiation in microbiota composition between wild and inbred populations. Relative abundance of ~ 16% of OTUs differed significantly between wild and inbred individuals. As laboratory mice represent the most abundant model for studying the effects of gut microbiota on host metabolism, immunity and neurology, we suggest that the distinctness of laboratory-kept mouse microbiota, which differs from wild mouse microbiota, needs to be considered in future biomedical research.},
}
@article {pmid25203616,
year = {2014},
author = {Raupach, MJ and Hendrich, L and Küchler, SM and Deister, F and Morinière, J and Gossner, MM},
title = {Building-up of a DNA barcode library for true bugs (insecta: hemiptera: heteroptera) of Germany reveals taxonomic uncertainties and surprises.},
journal = {PloS one},
volume = {9},
number = {9},
pages = {e106940},
pmid = {25203616},
issn = {1932-6203},
mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic/methods ; Gene Library ; Genes, Insect/genetics ; Germany ; Hemiptera/*genetics ; Heteroptera/*genetics ; Phylogeny ; },
abstract = {During the last few years, DNA barcoding has become an efficient method for the identification of species. In the case of insects, most published DNA barcoding studies focus on species of the Ephemeroptera, Trichoptera, Hymenoptera and especially Lepidoptera. In this study we test the efficiency of DNA barcoding for true bugs (Hemiptera: Heteroptera), an ecological and economical highly important as well as morphologically diverse insect taxon. As part of our study we analyzed DNA barcodes for 1742 specimens of 457 species, comprising 39 families of the Heteroptera. We found low nucleotide distances with a minimum pairwise K2P distance <2.2% within 21 species pairs (39 species). For ten of these species pairs (18 species), minimum pairwise distances were zero. In contrast to this, deep intraspecific sequence divergences with maximum pairwise distances >2.2% were detected for 16 traditionally recognized and valid species. With a successful identification rate of 91.5% (418 species) our study emphasizes the use of DNA barcodes for the identification of true bugs and represents an important step in building-up a comprehensive barcode library for true bugs in Germany and Central Europe as well. Our study also highlights the urgent necessity of taxonomic revisions for various taxa of the Heteroptera, with a special focus on various species of the Miridae. In this context we found evidence for on-going hybridization events within various taxonomically challenging genera (e.g. Nabis Latreille, 1802 (Nabidae), Lygus Hahn, 1833 (Miridae), Phytocoris Fallén, 1814 (Miridae)) as well as the putative existence of cryptic species (e.g. Aneurus avenius (Duffour, 1833) (Aradidae) or Orius niger (Wolff, 1811) (Anthocoridae)).},
}
@article {pmid25202604,
year = {2014},
author = {Avanesyan, A},
title = {Plant DNA detection from grasshopper guts: A step-by-step protocol, from tissue preparation to obtaining plant DNA sequences.},
journal = {Applications in plant sciences},
volume = {2},
number = {2},
pages = {},
pmid = {25202604},
issn = {2168-0450},
abstract = {PREMISE OF THE STUDY: A PCR-based method of identifying ingested plant DNA in gut contents of Melanoplus grasshoppers was developed. Although previous investigations have focused on a variety of insects, there are no protocols available for plant DNA detection developed for grasshoppers, agricultural pests that significantly influence plant community composition. •<br><br>METHODS AND RESULTS: The developed protocol successfully used the noncoding region of the chloroplast trnL (UAA) gene and was tested in several feeding experiments. Plant DNA was obtained at seven time points post-ingestion from whole guts and separate gut sections, and was detectable up to 12 h post-ingestion in nymphs and 22 h post-ingestion in adult grasshoppers. &#x2022;<br><br>CONCLUSIONS: The proposed protocol is an effective, relatively quick, and low-cost method of detecting plant DNA from the grasshopper gut and its different sections. This has important applications, from exploring plant "movement" during food consumption, to detecting plant-insect interactions.},
}
@article {pmid25197209,
year = {2014},
author = {Allegrucci, G and Rampini, M and Di Russo, C and Lana, E and Cocchi, S and Sbordoni, V},
title = {Phylogeography and systematics of the westernmost Italian Dolichopoda species (Orthoptera, Rhaphidophoridae).},
journal = {ZooKeys},
volume = {},
number = {437},
pages = {1-23},
pmid = {25197209},
issn = {1313-2989},
abstract = {The genus Dolichopoda (Orthoptera; Rhaphidopohoridae) is present in Italy with 9 species distributed from northwestern Italy (Piedmont and Liguria) to the southernmost Apennines (Calabria), occurring also in the Tyrrhenian coastal areas and in Sardinia. Three morphologically very close taxa have been described in Piedmont and Liguria, i.e., D. ligustica ligustica, D. ligustica septentrionalis and D. azami azami. To investigate the delimitation of the northwestern species of Dolichopoda, we performed both morphological and molecular analyses. Morphological analysis was carried out by considering diagnostic characters generally used to distinguish different taxa, as the shape of epiphallus in males and the subgenital fig in females. Molecular analysis was performed by sequencing three mitochondrial genes, 12S rRNA, 16S rRNA, partially sequenced and the entire gene of COI. Results from both morphological and molecular analyses highlighted a very homogeneous group of populations, although genetically structured. Three haplogroups geographically distributed could be distinguished and based on these results we suggest a new taxonomic arrangement. All populations, due to the priority of description, should be assigned to D. azami azami Saulcy, 1893 and to preserve the names ligustica and septentrionalis, corresponding to different genetic haplogroups, we assign them to D. azami ligustica stat. n. Baccetti &amp; Capra, 1959 and to D. azami septentrionalis stat. n. Baccetti &amp; Capra, 1959.},
}
@article {pmid25195439,
year = {2014},
author = {Etzler, FE and Wanner, KW and Morales-Rodriguez, A and Ivie, MA},
title = {DNA barcoding to improve the species-level management of wireworms (Coleoptera: Elateridae).},
journal = {Journal of economic entomology},
volume = {107},
number = {4},
pages = {1476-1485},
doi = {10.1603/ec13312},
pmid = {25195439},
issn = {0022-0493},
mesh = {Animals ; Coleoptera/classification/*genetics ; *DNA Barcoding, Taxonomic ; Insect Control ; Larva ; },
abstract = {Economically important species of wireworms (Coleoptera: Elateridae) were successfully associated with adults using cytochrome oxidase I (COI) barcoding, proving the usefulness of this technique to associate life stages in taxonomically difficult pest groups. Previously unrecognized and morphologically difficult, even indistinguishable, pest larvae were shown to be identifiable using this technique. This is a critical step toward discovering effective species-based integrated pest management strategies for this resurgent pest group following the loss of Lindane seed treatments. Three new adult-larval associations were discovered for Hadromorphus callidus (Brown), Hemicrepidius carbonatus (LeConte) and Metanomus insidiosus (LeConte). Hypnoidus bicolor (Eschscholtz) was shown to comprise multiple divergent lineages at a level usually considered different species, indicating that the population structure of some pest species requires more investigation. The status of the prairie grain wireworm, Selatosomus destructor (Brown), as a full species or as a subspecies of Selatosomus aeripennis (Kirby) is called into question.},
}
@article {pmid25189742,
year = {2015},
author = {Brendel, C and Goebel, B and Daniela, A and Brugman, M and Kneissl, S and Schwäble, J and Kaufmann, KB and Müller-Kuller, U and Kunkel, H and Chen-Wichmann, L and Abel, T and Serve, H and Bystrykh, L and Buchholz, CJ and Grez, M},
title = {CD133-targeted gene transfer into long-term repopulating hematopoietic stem cells.},
journal = {Molecular therapy : the journal of the American Society of Gene Therapy},
volume = {23},
number = {1},
pages = {63-70},
pmid = {25189742},
issn = {1525-0024},
mesh = {AC133 Antigen ; Animals ; Antigens, CD/*genetics/immunology ; Antigens, CD34/genetics/immunology ; Gene Expression ; Genetic Therapy/*methods ; Genetic Vectors ; Glycoproteins/*genetics/immunology ; Granulomatous Disease, Chronic/genetics/immunology/pathology/therapy ; Green Fluorescent Proteins/genetics/metabolism ; Hematopoietic Stem Cells/*immunology/pathology ; Humans ; Lentivirus/*genetics ; Leukocytes, Mononuclear/cytology/immunology ; Membrane Glycoproteins/genetics/metabolism ; Mice ; Peptides/*genetics/immunology ; Primary Cell Culture ; Transduction, Genetic ; Vesicular stomatitis Indiana virus/genetics ; Viral Envelope Proteins/genetics/metabolism ; },
abstract = {Gene therapy for hematological disorders relies on the genetic modification of CD34(+) cells, a heterogeneous cell population containing about 0.01% long-term repopulating cells. Here, we show that the lentiviral vector CD133-LV, which uses a surface marker on human primitive hematopoietic stem cells (HSCs) as entry receptor, transfers genes preferentially into cells with high engraftment capability. Transduction of unstimulated CD34(+) cells with CD133-LV resulted in gene marking of cells with competitive proliferative advantage in vitro and in immunodeficient mice. The CD133-LV-transduced population contained significantly more cells with repopulating capacity than cells transduced with vesicular stomatitis virus (VSV)-LV, a lentiviral vector pseudotyped with the vesicular stomatitis virus G protein. Upon transfer of a barcode library, CD133-LV-transduced cells sustained gene marking in vivo for a prolonged period of time with a 6.7-fold higher recovery of barcodes compared to transduced control cells. Moreover, CD133-LV-transduced cells were capable of repopulating secondary recipients. Lastly, we show that this targeting strategy can be used for transfer of a therapeutic gene into CD34(+) cells obtained from patients suffering of X-linked chronic granulomatous disease. In conclusion, direct gene transfer into CD133(+) cells allows for sustained long-term engraftment of gene corrected cells.},
}
@article {pmid25187125,
year = {2015},
author = {Wang, XC and Liu, C and Huang, L and Bengtsson-Palme, J and Chen, H and Zhang, JH and Cai, D and Li, JQ},
title = {ITS1: a DNA barcode better than ITS2 in eukaryotes?.},
journal = {Molecular ecology resources},
volume = {15},
number = {3},
pages = {573-586},
doi = {10.1111/1755-0998.12325},
pmid = {25187125},
issn = {1755-0998},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/chemistry/*genetics ; Eukaryota/*classification/*genetics ; Molecular Sequence Data ; Sequence Analysis, DNA ; },
abstract = {A DNA barcode is a short piece of DNA sequence used for species determination and discovery. The internal transcribed spacer (ITS/ITS2) region has been proposed as the standard DNA barcode for fungi and seed plants and has been widely used in DNA barcoding analyses for other biological groups, for example algae, protists and animals. The ITS region consists of both ITS1 and ITS2 regions. Here, a large-scale meta-analysis was carried out to compare ITS1 and ITS2 from three aspects: PCR amplification, DNA sequencing and species discrimination, in terms of the presence of DNA barcoding gaps, species discrimination efficiency, sequence length distribution, GC content distribution and primer universality. In total, 85 345 sequence pairs in 10 major groups of eukaryotes, including ascomycetes, basidiomycetes, liverworts, mosses, ferns, gymnosperms, monocotyledons, eudicotyledons, insects and fishes, covering 611 families, 3694 genera, and 19 060 species, were analysed. Using similarity-based methods, we calculated species discrimination efficiencies for ITS1 and ITS2 in all major groups, families and genera. Using Fisher's exact test, we found that ITS1 has significantly higher efficiencies than ITS2 in 17 of the 47 families and 20 of the 49 genera, which are sample-rich. By in silico PCR amplification evaluation, primer universality of the extensively applied ITS1 primers was found superior to that of ITS2 primers. Additionally, shorter length of amplification product and lower GC content was discovered to be two other advantages of ITS1 for sequencing. In summary, ITS1 represents a better DNA barcode than ITS2 for eukaryotic species.},
}
@article {pmid25186809,
year = {2015},
author = {Knebelsberger, T and Dunz, AR and Neumann, D and Geiger, MF},
title = {Molecular diversity of Germany's freshwater fishes and lampreys assessed by DNA barcoding.},
journal = {Molecular ecology resources},
volume = {15},
number = {3},
pages = {562-572},
doi = {10.1111/1755-0998.12322},
pmid = {25186809},
issn = {1755-0998},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/genetics ; Fishes/*classification/*genetics ; *Fresh Water ; Germany ; Lampreys/*classification/*genetics ; Molecular Sequence Data ; Phylogeography ; Sequence Analysis, DNA ; },
abstract = {This study represents the first comprehensive molecular assessment of freshwater fishes and lampreys from Germany. We analysed COI sequences for almost 80% of the species mentioned in the current German Red List. In total, 1056 DNA barcodes belonging to 92 species from all major drainages were used to (i) build a reliable DNA barcode reference library, (ii) test for phylogeographic patterns, (iii) check for the presence of barcode gaps between species and (iv) evaluate the performance of the barcode index number (BIN) system, available on the Barcode of Life Data Systems. For over 78% of all analysed species, DNA barcodes are a reliable means for identification, indicated by the presence of barcode gaps. An overlap between intra- and interspecific genetic distances was present in 19 species, six of which belong to the genus Coregonus. The Neighbour-Joining phenogram showed 60 nonoverlapping species clusters and three singleton species, which were related to 63 separate BIN numbers. Furthermore, Barbatula barbatula, Leucaspius delineatus, Phoxinus phoxinus and Squalius cephalus exhibited remarkable levels of cryptic diversity. In contrast, 11 clusters showed haplotype sharing, or low levels of divergence between species, hindering reliable identification. The analysis of our barcode library together with public data resulted in 89 BINs, of which 56% showed taxonomic conflicts. Most of these conflicts were caused by the use of synonymies, inadequate taxonomy or misidentifications. Moreover, our study increased the number of potential alien species in Germany from 14 to 21 and is therefore a valuable groundwork for further faunistic investigations.},
}
@article {pmid25186335,
year = {2016},
author = {Yu, Z and Li, Q and Kong, L},
title = {New insight into the phylogeny of Sinonovacula (Bivalvia: Solecurtidae) revealed by comprehensive DNA barcoding analyses of two mitochondrial genes.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1554-1557},
doi = {10.3109/19401736.2014.953135},
pmid = {25186335},
issn = {2470-1408},
mesh = {Animals ; Bivalvia/*genetics ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*chemistry ; *Genes, Mitochondrial ; Genetic Variation ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The present study was undertaken to clarify the genetic relationships of Sinonovacula through comprehensive DNA barcoding analyses of COI and 16S rRNA genes. For both genes, the K2P distances between individuals of Sinonovacula and individuals of other genera belonging to Tellinoidea were much bigger than those between Sinonovacula and genera of Solenoidea. On the Bayesian tree of combined data, Sinonovacula and Cultellus formed a well supports monophylic clade. An extremely high matching rate of CAs between Sinonovacula and the reference family Cultellidae was found. Thus, we suggest transferring Sinonovacula from Solecurtidae to Cultellidae, as a sister group of Cultellus.},
}
@article {pmid25180800,
year = {2015},
author = {Castellarnau, M and Szeto, GL and Su, HW and Tokatlian, T and Love, JC and Irvine, DJ and Voldman, J},
title = {Stochastic particle barcoding for single-cell tracking and multiparametric analysis.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {11},
number = {4},
pages = {489-498},
pmid = {25180800},
issn = {1613-6829},
support = {1F32CA180586/CA/NCI NIH HHS/United States ; P30 CA014051/CA/NCI NIH HHS/United States ; P30-CA14051/CA/NCI NIH HHS/United States ; F32 CA180586/CA/NCI NIH HHS/United States ; /HHMI_/Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; Cell Line, Tumor ; Cell Survival ; Cell Tracking/*methods ; Humans ; Image Processing, Computer-Assisted ; Macromolecular Substances/metabolism ; Mice ; Models, Theoretical ; Nucleic Acids/metabolism ; Polyethylene Glycols/chemistry ; Stochastic Processes ; },
abstract = {This study presents stochastic particle barcoding (SPB), a method for tracking cell identity across bioanalytical platforms. In this approach, single cells or small collections of cells are co-encapsulated within an enzymatically-degradable hydrogel block along with a random collection of fluorescent beads, whose number, color, and position encode the identity of the cell, enabling samples to be transferred in bulk between single-cell assay platforms without losing the identity of individual cells. The application of SPB is demonstrated for transferring cells from a subnanoliter protein secretion/phenotyping array platform into a microtiter plate, with re-identification accuracies in the plate assay of 96±2%. Encapsulated cells are recovered by digesting the hydrogel, allowing subsequent genotyping and phenotyping of cell lysates. Finally, a model scaling is developed to illustrate how different parameters affect the accuracy of SPB and to motivate scaling of the method to thousands of unique blocks.},
}
@article {pmid25175416,
year = {2014},
author = {Cristescu, ME},
title = {From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity.},
journal = {Trends in ecology &amp; evolution},
volume = {29},
number = {10},
pages = {566-571},
doi = {10.1016/j.tree.2014.08.001},
pmid = {25175416},
issn = {1872-8383},
mesh = {*Biodiversity ; Biota/genetics ; Computational Biology ; DNA/analysis/genetics ; *DNA Barcoding, Taxonomic ; *Electronic Data Processing ; Species Specificity ; },
abstract = {DNA-based species identification, known as barcoding, transformed the traditional approach to the study of biodiversity science. The field is transitioning from barcoding individuals to metabarcoding communities. This revolution involves new sequencing technologies, bioinformatics pipelines, computational infrastructure, and experimental designs. In this dynamic genomics landscape, metabarcoding studies remain insular and biodiversity estimates depend on the particular methods used. In this opinion article, I discuss the need for a coordinated advancement of DNA-based species identification that integrates taxonomic and barcoding information. Such an approach would facilitate access to almost 3 centuries of taxonomic knowledge and 1 decade of building repository barcodes. Conservation projects are time sensitive, research funding is becoming restricted, and informed decisions depend on our ability to embrace integrative approaches to biodiversity science.},
}
@article {pmid25174103,
year = {2014},
author = {Liu, YM and Jin, LN and Xiong, YX and Wu, L and Chen, KL},
title = {[Molecular identification of Hibiscus syriacus and its adulterants using ITS2 barcode].},
journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials},
volume = {37},
number = {3},
pages = {408-410},
pmid = {25174103},
issn = {1001-4454},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; DNA, Ribosomal Spacer/*genetics ; Drug Contamination/prevention &amp; control ; Drugs, Chinese Herbal/chemistry/*classification ; Flowers/classification/genetics ; Hibiscus/classification/*genetics ; Molecular Sequence Data ; Phylogeny ; Plant Leaves/classification/genetics ; Quality Control ; },
abstract = {OBJECTIVE: To identify Hibiscus syriacus and its adulterants using DNA barcoding technique.<br><br>METHODS: Nine samples of five species were PCR amplified and sequenced, and twelve samples were downloaded from the GenBank. The intra-specific and interspecific K2P distances were calculated, and neighbor-joining(NJ) tree was constructed by MEGA 5.0.<br><br>RESULTS: The results showed the intra-specific genetic distances of Hibiscus syriacus were ranged from 0.009 to 0.056, which were far lower than inter-specific genetic distances between Hibiscus syriacus and its adulterants (0.236 - 0.301). Variable sites within Hibiscus syriacus ranged from 2 to 9 which were far less than the adulterants (45 - 52); Different samples of Hibiscus syriacus were gathered together and could be distinguished from its adulterants by NJ tree.<br><br>CONCLUSION: ITS2 can discriminate Hibiscus syriacus from its adulterants correctly. The ITS2 region is an efficient barcode for authentication of Hibiscus syriacus and its adulterants.},
}
@article {pmid25170185,
year = {2014},
author = {Kruckenhauser, L and Duda, M and Bartel, D and Sattmann, H and Harl, J and Kirchner, S and Haring, E},
title = {Paraphyly and budding speciation in the hairy snail (Pulmonata, Hygromiidae).},
journal = {Zoologica scripta},
volume = {43},
number = {3},
pages = {273-288},
pmid = {25170185},
issn = {0300-3256},
support = {P 19592/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Delimitation of species is often complicated by discordance of morphological and genetic data. This may be caused by the existence of cryptic or polymorphic species. The latter case is particularly true for certain snail species showing an exceptionally high intraspecific genetic diversity. The present investigation deals with the Trochulus hispidus complex, which has a complicated taxonomy. Our analyses of the COI sequence revealed that individuals showing a T. hispidus phenotype are distributed in nine highly differentiated mitochondrial clades (showing p-distances up to 19%). The results of a parallel morphometric investigation did not reveal any differentiation between these clades, although the overall variability is quite high. The phylogenetic analyses based on 12S, 16S and COI sequences show that the T. hispidus complex is paraphyletic with respect to several other morphologically well-defined Trochulus species (T. clandestinus, T. villosus, T. villosulus and T. striolatus) which form well-supported monophyletic groups. The nc marker sequence (5.8S-ITS2-28S) shows only a clear separation of T. o. oreinos and T. o. scheerpeltzi, and a weakly supported separation of T. clandestinus, whereas all other species and the clades of the T. hispidus complex appear within one homogeneous group. The paraphyly of the T. hispidus complex reflects its complicated history, which was probably driven by geographic isolation in different glacial refugia and budding speciation. At our present state of knowledge, it cannot be excluded that several cryptic species are embedded within the T. hispidus complex. However, the lack of morphological differentiation of the T. hispidus mitochondrial clades does not provide any hints in this direction. Thus, we currently do not recommend any taxonomic changes. The results of the current investigation exemplify the limitations of barcoding attempts in highly diverse species such as T. hispidus.},
}
@article {pmid25158042,
year = {2015},
author = {Chen, J and Zhao, J and Erickson, DL and Xia, N and Kress, WJ},
title = {Testing DNA barcodes in closely related species of Curcuma (Zingiberaceae) from Myanmar and China.},
journal = {Molecular ecology resources},
volume = {15},
number = {2},
pages = {337-348},
doi = {10.1111/1755-0998.12319},
pmid = {25158042},
issn = {1755-0998},
mesh = {China ; Curcuma/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Chloroplast/chemistry/genetics ; DNA, Plant/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Genotype ; Molecular Sequence Data ; Myanmar ; Sequence Analysis, DNA ; },
abstract = {The genus Curcuma L. is commonly used as spices, medicines, dyes and ornamentals. Owing to its economic significance and lack of clear-cut morphological differences between species, this genus is an ideal case for developing DNA barcodes. In this study, four chloroplast DNA regions (matK, rbcL, trnH-psbA and trnL-F) and one nuclear region (ITS2) were generated for 44 Curcuma species and five species from closely related genera, represented by 96 samples. PCR amplification success rate, intra- and inter-specific genetic distance variation and the correct identification percentage were taken into account to assess candidate barcode regions. PCR and sequence success rate were high in matK (89.7%), rbcL (100%), trnH-psbA (100%), trnL-F (95.7%) and ITS2 (82.6%) regions. The results further showed that four candidate chloroplast barcoding regions (matK, rbcL, trnH-psbA and trnL-F) yield no barcode gaps, indicating that the genus Curcuma represents a challenging group for DNA barcoding. The ITS2 region presented large interspecific variation and provided the highest correct identification rates (46.7%) based on BLASTClust method among the five regions. However, the ITS2 only provided 7.9% based on NJ tree method. An increase in discriminatory power needs the development of more variable markers.},
}
@article {pmid25154542,
year = {2014},
author = {Ferreira, MU and Rodrigues, PT},
title = {Tracking malaria parasites in the eradication era.},
journal = {Trends in parasitology},
volume = {30},
number = {10},
pages = {465-466},
doi = {10.1016/j.pt.2014.08.003},
pmid = {25154542},
issn = {1471-5007},
mesh = {Animals ; DNA Barcoding, Taxonomic/standards ; Genetic Variation ; Genome, Protozoan/genetics ; Malaria/*parasitology ; Plasmodium falciparum/classification/*genetics ; },
abstract = {As more endemic countries enter the elimination phase, the detection of sporadic malaria infections or outbreaks elicits many questions: (i) are the infections locally acquired or imported? (ii) If imported, where do they come from? (iii) Do outbreak strains have a single or multiple geographic origins? New molecular barcoding methods provide ways to analyze clinical malaria parasite samples and answer these and other crucial questions.},
}
@article {pmid25150612,
year = {2014},
author = {Weber, AA and Pawlowski, J},
title = {Wide occurrence of SSU rDNA intragenomic polymorphism in foraminifera and its implications for molecular species identification.},
journal = {Protist},
volume = {165},
number = {5},
pages = {645-661},
doi = {10.1016/j.protis.2014.07.006},
pmid = {25150612},
issn = {1618-0941},
mesh = {Cluster Analysis ; DNA, Protozoan/chemistry/*genetics ; DNA, Ribosomal/chemistry/*genetics ; Foraminifera/*classification/*genetics ; *Genetic Variation ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA ; },
abstract = {Ribosomal DNA is commonly used as a marker for protist phylogeny and taxonomy because of its ubiquity and its expected species specificity thanks to the mechanism of concerted evolution. However, numerous studies reported the occurrence of intragenomic (intra-individual) polymorphism in various protists and particularly in Foraminifera. To infer to what extent the SSU rDNA intragenomic variability occurs in Foraminifera, we studied 16 foraminiferal species belonging to single-chambered monothalamids and multi-chambered Globothalamea, with one to six individuals per species. We performed single-cell DNA extractions and PCRs of a 600bp fragment of SSU rDNA, and sequenced 9 to 23 clones per individual for a total of 818 sequences. We found intragenomic variability in almost all species, even after excluding singleton mutations. Intra-individual sequence divergence ranged from 0 to 5.15% and was higher than 1% in 11 species. Variability was usually located at the end of stem-loop structures and included compensatory single nucleotide polymorphisms and expansion segments polymorphisms. However, the polymorphisms did not change the secondary structure of the rRNA. Our results suggest a non-concerted evolution of rRNA genes in Foraminifera. The origin of this variability and its implications for species identification in environmental DNA studies are discussed.},
}
@article {pmid25149069,
year = {2014},
author = {Yourstone, SM and Lundberg, DS and Dangl, JL and Jones, CD},
title = {MT-Toolbox: improved amplicon sequencing using molecule tags.},
journal = {BMC bioinformatics},
volume = {15},
number = {1},
pages = {284},
pmid = {25149069},
issn = {1471-2105},
support = {T32 GM067553/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; T32 GM067553-06/GM/NIGMS NIH HHS/United States ; },
mesh = {Computer Graphics ; DNA/*genetics ; Metagenomics ; Oligonucleotides/genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; *Software ; Time Factors ; User-Computer Interface ; },
abstract = {BACKGROUND: Short oligonucleotides can be used as markers to tag and track DNA sequences. For example, barcoding techniques (i.e. Multiplex Identifiers or Indexing) use short oligonucleotides to distinguish between reads from different DNA samples pooled for high-throughput sequencing. A similar technique called molecule tagging uses the same principles but is applied to individual DNA template molecules. Each template molecule is tagged with a unique oligonucleotide prior to polymerase chain reaction. The resulting amplicon sequences can be traced back to their original templates by their oligonucleotide tag. Consensus building from sequences sharing the same tag enables inference of original template molecules thereby reducing effects of sequencing error and polymerase chain reaction bias. Several independent groups have developed similar protocols for molecule tagging; however, user-friendly software for build consensus sequences from molecule tagged reads is not readily available or is highly specific for a particular protocol.<br><br>RESULTS: MT-Toolbox recognizes oligonucleotide tags in amplicons and infers the correct template sequence. On a set of molecule tagged test reads, MT-Toolbox generates sequences having on average 0.00047 errors per base. MT-Toolbox includes a graphical user interface, command line interface, and options for speed and accuracy maximization. It can be run in serial on a standard personal computer or in parallel on a Load Sharing Facility based cluster system. An optional plugin provides features for common 16S metagenome profiling analysis such as chimera filtering, building operational taxonomic units, contaminant removal, and taxonomy assignments.<br><br>CONCLUSIONS: MT-Toolbox provides an accessible, user-friendly environment for analysis of molecule tagged reads thereby reducing technical errors and polymerase chain reaction bias. These improvements reduce noise and allow for greater precision in single amplicon sequencing experiments.},
}
@article {pmid25147310,
year = {2014},
author = {Ojeda, DI and Santos-Guerra, A and Oliva-Tejera, F and Jaen-Molina, R and Caujapé-Castells, J and Marrero-Rodríguez, A and Cronk, Q},
title = {DNA barcodes successfully identified Macaronesian Lotus (Leguminosae) species within early diverged lineages of Cape Verde and mainland Africa.},
journal = {AoB PLANTS},
volume = {6},
number = {},
pages = {},
pmid = {25147310},
issn = {2041-2851},
abstract = {Plant DNA barcoding currently relies on the application of a two-locus combination, matK + rbcL. Despite the universality of these two gene regions across plants, it is suspected that this combination might not have sufficient variation to discriminate closely related species. In this study, we tested the performance of this two-locus plant barcode along with the additional plastid regions trnH-psbA, rpoC1 and rpoB and the nuclear region internal transcribed spacer (nrITS) in a group of 38 species of Lotus from the Macaronesian region. The group has radiated into the five archipelagos within this region from mid-Miocene to early Pleistocene, and thus provides both early divergent and recent radiations that pose a particularly difficult challenge for barcoding. The group also has 10 species considered under different levels of conservation concern. We found different levels of species discrimination depending on the age of the lineages. We obtained 100 % of the species identification from mainland Africa and Cape Verde when all six regions were combined. These lineages radiated >4.5 Mya; however, in the most recent radiations from the end of the Pliocene to the mid-Pleistocene (3.5-1.5 Mya), only 30 % of the species were identified. Of the regions examined, the intergenic region trnH-psbA was the most variable and had the greatest discriminatory power (18 %) of the plastid regions when analysed alone. The nrITS region was the best region when analysed alone with a discriminatory power of 26 % of the species. Overall, we identified 52 % of the species and 30 % of the endangered or threatened species within this group when all six regions were combined. Our results are consistent with those of other studies that indicate that additional approaches to barcoding will be needed in recently evolved groups, such as the inclusion of faster evolving regions from the nuclear genome.},
}
@article {pmid25143182,
year = {2015},
author = {Versteirt, V and Nagy, ZT and Roelants, P and Denis, L and Breman, FC and Damiens, D and Dekoninck, W and Backeljau, T and Coosemans, M and Van Bortel, W},
title = {Identification of Belgian mosquito species (Diptera: Culicidae) by DNA barcoding.},
journal = {Molecular ecology resources},
volume = {15},
number = {2},
pages = {449-457},
doi = {10.1111/1755-0998.12318},
pmid = {25143182},
issn = {1755-0998},
mesh = {Animals ; Belgium ; Culicidae/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; *Genetic Variation ; Molecular Sequence Data ; Sequence Analysis, DNA ; },
abstract = {Since its introduction in 2003, DNA barcoding has proven to be a promising method for the identification of many taxa, including mosquitoes (Diptera: Culicidae). Many mosquito species are potential vectors of pathogens, and correct identification in all life stages is essential for effective mosquito monitoring and control. To use DNA barcoding for species identification, a reliable and comprehensive reference database of verified DNA sequences is required. Hence, DNA sequence diversity of mosquitoes in Belgium was assessed using a 658 bp fragment of the mitochondrial cytochrome oxidase I (COI) gene, and a reference data set was established. Most species appeared as well-supported clusters. Intraspecific Kimura 2-parameter (K2P) distances averaged 0.7%, and the maximum observed K2P distance was 6.2% for Aedes koreicus. A small overlap between intra- and interspecific K2P distances for congeneric sequences was observed. Overall, the identification success using best match and the best close match criteria were high, that is above 98%. No clear genetic division was found between the closely related species Aedes annulipes and Aedes cantans, which can be confused using morphological identification only. The members of the Anopheles maculipennis complex, that is Anopheles maculipennis s.s. and An. messeae, were weakly supported as monophyletic taxa. This study showed that DNA barcoding offers a reliable framework for mosquito species identification in Belgium except for some closely related species.},
}
@article {pmid25133638,
year = {2014},
author = {Nanjappa, D and Audic, S and Romac, S and Kooistra, WH and Zingone, A},
title = {Assessment of species diversity and distribution of an ancient diatom lineage using a DNA metabarcoding approach.},
journal = {PloS one},
volume = {9},
number = {8},
pages = {e103810},
pmid = {25133638},
issn = {1932-6203},
mesh = {DNA Barcoding, Taxonomic ; DNA, Ribosomal/genetics ; Diatoms/classification/*genetics ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Seawater ; },
abstract = {BACKGROUND: Continuous efforts to estimate actual diversity and to trace the species distribution and ranges in the natural environments have gone in equal pace with advancements of the technologies in the study of microbial species diversity from microscopic observations to DNA-based barcoding. DNA metabarcoding based on Next Generation Sequencing (NGS) constitutes the latest advancement in these efforts. Here we use NGS data from different sites to investigate the geographic range of six species of the diatom family Leptocylindraceae and to identify possible new taxa within the family.<br><br>We analysed the V4 and V9 regions of the nuclear-encoded SSU rDNA gene region in the NGS database of the European ERA-Biodiversa project BioMarKs, collected in plankton and sediments at six coastal sites in European coastal waters, as well as environmental sequences from the NCBI database. All species known in the family Leptocylindraceae were detected in both datasets, but the much larger Illumina V9 dataset showed a higher species coverage at the various sites than the 454 V4 dataset. Sequences identical or similar to the references of Leptocylindrus aporus, L. convexus, L. danicus/hargravesii and Tenuicylindrus belgicus were found in the Mediterranean Sea, North Atlantic Ocean and Black Sea as well as at locations outside Europe. Instead, sequences identical or close to that of L. minimus were found in the North Atlantic Ocean and the Black Sea but not in the Mediterranean Sea, while sequences belonging to a yet undescribed taxon were encountered only in Oslo Fjord and Baffin Bay.<br><br>CONCLUSIONS/SIGNIFICANCE: Identification of Leptocylindraceae species in NGS datasets has expanded our knowledge of the species biogeographic distribution and of the overall diversity of this diatom family. Individual species appear to be widespread, but not all of them are found everywhere. Despite the sequencing depth allowed by NGS and the wide geographic area covered by this study, the diversity of this ancient diatom family appears to be low, at least at the level of the marker used in this study.},
}
@article {pmid25133520,
year = {2014},
author = {Tabanca, N and Gao, Z and Demirci, B and Techen, N and Wedge, DE and Ali, A and Sampson, BJ and Werle, C and Bernier, UR and Khan, IA and Baser, KH},
title = {Molecular and phytochemical investigation of Angelica dahurica and Angelica pubescentis essential oils and their biological activity against Aedes aegypti, Stephanitis pyrioides, and Colletotrichum species.},
journal = {Journal of agricultural and food chemistry},
volume = {62},
number = {35},
pages = {8848-8857},
doi = {10.1021/jf5024752},
pmid = {25133520},
issn = {1520-5118},
support = {300 212 193G//PHS HHS/United States ; },
mesh = {Aedes/drug effects/growth &amp; development ; Angelica/*chemistry ; Animals ; Antifungal Agents/*chemistry/*pharmacology ; Colletotrichum/drug effects ; Heteroptera/drug effects ; Insecticides/*chemistry/*pharmacology ; Larva/drug effects/growth &amp; development ; Oils, Volatile/*chemistry/*pharmacology ; Plant Oils/chemistry/pharmacology ; },
abstract = {In this study, Angelica dahurica and Angelica pubescentis root essential oils were investigated as pest management perspectives, and root samples were also analyzed genetically using the nuclear ribosomal internal transcribed spacer (ITS) region as a DNA barcode marker. A. pubescentis root essential oil demonstrated weak antifungal activity against Colletotrichum acutatum, Colletotrichum fragariae, and Colletotrichum gloeosporioides, whereas A. dahurica root essential oil did not show antifungal activity. Conversely, A. dahurica root essential oil demonstrated better biting deterrent and insecticidal activity against yellow fever mosquito, Aedes aegypti, and azalea lace bugs, Stephanitis pyrioides, than A. pubescentis root oil. The major compounds in the A. dahurica oil were found as α-pinene (46.3%), sabinene (9.3%), myrcene (5.5%), 1-dodecanol (5.2%), and terpinen-4-ol (4.9%). α-Pinene (37.6%), p-cymene (11.6%), limonene (8.7%), and cryptone (6.7%) were the major compounds found in the A. pubescentis oil. In mosquito bioassays, 1-dodecanol and 1-tridecanol showed antibiting deterrent activity similar to the positive control DEET (N,N-diethyl-3-methylbenzamide) at 25 nmol/cm(2) against Ae. aegypti, whereas only 1-tridecanol showed repellent activity in human-based cloth patch bioassay with minimum effective dosages (MED) of 0.086 ± 0.089 mg/cm(2) (DEET = 0.007 ± 0.003 mg/cm(2)). In larval bioassays, 1-tridecanol was more toxic with an LC50 value of 2.1 ppm than 1-dodecanol having an LC50 value of 5.2 ppm against 1-day-old Ae. aegypti larvae. 1-Dodecanol and 1-tridecanol could be useful for the natural mosquito control agents.},
}
@article {pmid25132566,
year = {2014},
author = {Zhao, YE and Cheng, J and Hu, L and Ma, JX},
title = {Molecular identification and phylogenetic study of Demodex caprae.},
journal = {Parasitology research},
volume = {113},
number = {10},
pages = {3601-3608},
pmid = {25132566},
issn = {1432-1955},
mesh = {Animals ; Base Sequence ; China ; Cyclooxygenase 1/*genetics ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry/genetics ; Dogs ; Female ; Mite Infestations/parasitology/*veterinary ; Mites/*classification/genetics ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; Ovum ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {The DNA barcode has been widely used in species identification and phylogenetic analysis since 2003, but there have been no reports in Demodex. In this study, to obtain an appropriate DNA barcode for Demodex, molecular identification of Demodex caprae based on mitochondrial cox1 was conducted. Firstly, individual adults and eggs of D. caprae were obtained for genomic DNA (gDNA) extraction; Secondly, mitochondrial cox1 fragment was amplified, cloned, and sequenced; Thirdly, cox1 fragments of D. caprae were aligned with those of other Demodex retrieved from GenBank; Finally, the intra- and inter-specific divergences were computed and the phylogenetic trees were reconstructed to analyze phylogenetic relationship in Demodex. Results obtained from seven 429-bp fragments of D. caprae showed that sequence identities were above 99.1% among three adults and four eggs. The intraspecific divergences in D. caprae, Demodex folliculorum, Demodex brevis, and Demodex canis were 0.0-0.9, 0.5-0.9, 0.0-0.2, and 0.0-0.5%, respectively, while the interspecific divergences between D. caprae and D. folliculorum, D. canis, and D. brevis were 20.3-20.9, 21.8-23.0, and 25.0-25.3, respectively. The interspecific divergences were 10 times higher than intraspecific ones, indicating considerable barcoding gap. Furthermore, the phylogenetic trees showed that four Demodex species gathered separately, representing independent species; and Demodex folliculorum gathered with canine Demodex, D. caprae, and D. brevis in sequence. In conclusion, the selected 429-bp mitochondrial cox1 gene is an appropriate DNA barcode for molecular classification, identification, and phylogenetic analysis of Demodex. D. caprae is an independent species and D. folliculorum is closer to D. canis than to D. caprae or D. brevis.},
}
@article {pmid25130907,
year = {2014},
author = {Khaund, P and Joshi, SR},
title = {DNA barcoding of wild edible mushrooms consumed by the ethnic tribes of India.},
journal = {Gene},
volume = {550},
number = {1},
pages = {123-130},
doi = {10.1016/j.gene.2014.08.027},
pmid = {25130907},
issn = {1879-0038},
mesh = {Agaricales/classification/*genetics/ultrastructure ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; *Ethnicity ; *Food ; Fungal Proteins/genetics ; Humans ; India ; Microscopy, Electron, Scanning ; Molecular Sequence Data ; Phylogeny ; Protein Subunits/genetics ; RNA Polymerase II/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Wild edible mushrooms are consumed by the tribes of Meghalaya in the North-Eastern region of India, as part of their ethnic cuisine because of their favored organoleptic characteristics and traditionally known health benefits. Majority of these mushrooms have not yet been characterized in detail and are slowly shrinking in their natural habitats owing to anthropogenic factors and climate change. In the present study, representative specimens of ten morphologically distinct groups of wild edible mushrooms available in the traditional markets and their respective forest habitats, were subjected to multi-loci molecular characterization using SSU, ITS, RPB1 and RPB2 markers. The species identities inferred for the ten mushroom types using the SSU marker matched their morphological description in the case of four morphological groups only whereas the ITS marker successfully resolved the species identity for nine out of the ten mushroom groups under study. Both the protein coding gene markers RPB1 and RPB2 successfully resolved the species identity for three out of the ten morphologically distinct groups. Finally the most likely identity of the wild edible mushrooms under study has been suggested by matching their unique morphological characteristics with the generated DNA barcoding data. The present molecular characterization reveals the ten widely consumed wild mushroom types of Meghalaya, India to be Gomphus floccosus, Lactarius deliciosus, Lactarius volemus, Cantharellus cibarius, Tricholoma viridiolivaceum, Inocybe aff. sphaerospora, Laccaria vinaceoavellanea, Albatrellus ellisii, Ramaria maculatipes and Clavulina cristata. The final species identity generated by the ITS marker matched more accurately with the morphological characteristics/appearance of the specimens indicating the ITS region as a reliable barcode for identifying wild edible mushrooms.},
}
@article {pmid25124146,
year = {2014},
author = {Põlme, S and Bahram, M and Kõljalg, U and Tedersoo, L},
title = {Global biogeography of Alnus-associated Frankia actinobacteria.},
journal = {The New phytologist},
volume = {204},
number = {4},
pages = {979-988},
doi = {10.1111/nph.12962},
pmid = {25124146},
issn = {1469-8137},
mesh = {Alnus/genetics/*microbiology ; Biological Evolution ; Frankia/classification/*genetics ; Oxidoreductases/genetics ; *Phylogeny ; Phylogeography ; Symbiosis/genetics ; },
abstract = {Macroecological patterns of microbes have received relatively little attention until recently. This study aimed to disentangle the determinants of the global biogeographic community of Alnus-associated actinobacteria belonging to the Frankia alni complex. By determining a global sequence similarity threshold for the nitrogenase reductase (nifH) gene, we separated Frankia into operational taxonomic units (OTUs) and tested the relative effects of Alnus phylogeny, geographic relatedness, and climatic and edaphic variables on community composition at the global scale. Based on the optimal nifH gene sequence similarity threshold of 99.3%, we distinguished 43 Frankia OTUs from root systems of 22 Alnus species on four continents. Host phylogeny was the main determinant of Frankia OTU-based community composition, but there was no effect on the phylogenetic structure of Frankia. Biogeographic analyses revealed the strongest cross-continental links over the Beringian land bridge. Despite the facultative symbiotic nature of Frankia, phylogenetic relations among Alnus species play a prominent role in structuring root-associated Frankia communities and their biogeographic patterns. Our results suggest that Alnus species exert strong phylogenetically determined selection pressure on compatible Actinobacteria.},
}
@article {pmid25123930,
year = {2014},
author = {GilArriortua, M and Saloña Bordas, MI and Köhnemann, S and Pfeiffer, H and de Pancorbo, MM},
title = {Molecular differentiation of Central European blowfly species (Diptera, Calliphoridae) using mitochondrial and nuclear genetic markers.},
journal = {Forensic science international},
volume = {242},
number = {},
pages = {274-282},
doi = {10.1016/j.forsciint.2014.07.018},
pmid = {25123930},
issn = {1872-6283},
mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics ; Diptera/*genetics ; Electron Transport Complex IV/genetics ; *Genetic Markers ; Phylogeny ; RNA, Nuclear/genetics ; Sequence Analysis, DNA ; },
abstract = {A challenging step in medical, veterinary and forensic entomology casework is the rapid and accurate identification of insects to estimate the period of insect activity (PIA), which usually approximates the post-mortem interval (PMI). The morphological identification of insect evidence is hampered by species similarities, especially at the early larval stages. However, DNA-based species identification is more accurate and reliable. In this study, we improved the suitability and efficacy of the standard mitochondrial cytochrome c oxidase subunit I (COI) barcode region of 658 bp combined with an additional region of 616 bp of the same gene. We also tested the usefulness of other mitochondrial and nuclear loci, such as the non-coding region included in mitochondrial Cyt-b-tRNA(ser)-ND1 (495-496 bp) and the second internal transcribed spacer (ITS2) region of nuclear ribosomal DNA (rDNA) (310-337 bp). We classified a total of 54 specimens from five blowfly species belonging to three Calliphoridae genera commonly found in Central Europe: Phormia (P. regina), Calliphora (C. vicina) and Lucilia (L. sericata, L. ampullacea and L. caesar). Additionally included were the Cyt-b (307 bp) sequences for P. regina species and GenBank recorded information about the studied loci for select species. The results revealed the robustness of COI (616 bp) and ITS2 (310-337 bp) as diagnostic tools to be added to the widely established COI barcode (658 bp). Their higher discriminatory power allows for more precise and reliable identifications, even within more complex genera (Lucilia). This work also contributes new nucleotide sequences that are useful for accurate species diagnosis and new sequence data of Calliphoridae interspecific variability in the European Westphalia region (Germany).},
}
@article {pmid25121832,
year = {2016},
author = {Turanov, SV and Kartavtsev, YP and Lipinsky, VV and Zemnukhov, VV and Balanov, AA and Lee, YH and Jeong, D},
title = {DNA-barcoding of perch-like fishes (Actinopterygii: Perciformes) from far-eastern seas of Russia with taxonomic remarks for some groups.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1188-1209},
doi = {10.3109/19401736.2014.945525},
pmid = {25121832},
issn = {2470-1408},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Genetic Markers ; Perches/*classification/*genetics ; Siberia ; },
abstract = {The analysis of variation among 203 nucleotide sequences of Co-1 gene (DNA-barcode) for 45 species, 31 genera and 7 families of the order Perciformes from the Far Eastern seas of Russia has been performed. As a result, 42 species (93.3%) can be unambiguously identified using molecular DNA-barcode at Co-1, whereas more variable markers are required for other species (6.7%): Stichaeus grigorjewi, S. nozawae, and Lumpenus sagitta. The latter includes as well 2 morphologically distinct (by number of vertebrae) but genetically unresolved species, L. sagitta (Sea of Okhotsk) and L. fabricii (Bering Sea). In addition, within this genus morphologically poorly characterized but genetically well-distinguished cryptic species has been detected. Amphi-Pacific distribution is in question relative to L. sagitta. Cryptic diversity was observed in the genus Ammodytes.},
}
@article {pmid25120558,
year = {2014},
author = {Dittami, SM and Barbeyron, T and Boyen, C and Cambefort, J and Collet, G and Delage, L and Gobet, A and Groisillier, A and Leblanc, C and Michel, G and Scornet, D and Siegel, A and Tapia, JE and Tonon, T},
title = {Genome and metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae.},
journal = {Frontiers in genetics},
volume = {5},
number = {},
pages = {241},
pmid = {25120558},
issn = {1664-8021},
abstract = {Rhizobiales and related orders of Alphaproteobacteria comprise several genera of nodule-inducing symbiotic bacteria associated with plant roots. Here we describe the genome and the metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a member of a new candidate genus closely related to Rhizobiales and found in association with cultures of the filamentous brown algal model Ectocarpus. The "Ca. P. ectocarpi" genome encodes numerous metabolic pathways that may be relevant for this bacterium to interact with algae. Notably, it possesses a large set of glycoside hydrolases and transporters, which may serve to process and assimilate algal metabolites. It also harbors several proteins likely to be involved in the synthesis of algal hormones such as auxins and cytokinins, as well as the vitamins pyridoxine, biotin, and thiamine. As of today, "Ca. P. ectocarpi" has not been successfully cultured, and identical 16S rDNA sequences have been found exclusively associated with Ectocarpus. However, related sequences (≥97% identity) have also been detected free-living and in a Fucus vesiculosus microbiome barcoding project, indicating that the candidate genus "Phaeomarinobacter" may comprise several species, which may colonize different niches.},
}
@article {pmid25119900,
year = {2014},
author = {André, A and Quillévéré, F and Morard, R and Ujiié, Y and Escarguel, G and de Vargas, C and de Garidel-Thoron, T and Douady, CJ},
title = {SSU rDNA divergence in planktonic foraminifera: molecular taxonomy and biogeographic implications.},
journal = {PloS one},
volume = {9},
number = {8},
pages = {e104641},
pmid = {25119900},
issn = {1932-6203},
mesh = {Base Sequence ; *Evolution, Molecular ; Foraminifera/*classification/*genetics ; *Genetic Variation ; Marine Biology/methods ; Models, Genetic ; Molecular Sequence Data ; Paleontology/methods ; Phylogeography ; Plankton/classification/*genetics ; Ribosome Subunits, Small/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The use of planktonic foraminifera in paleoceanography requires taxonomic consistency and precise assessment of the species biogeography. Yet, ribosomal small subunit (SSUr) DNA analyses have revealed that most of the modern morpho-species of planktonic foraminifera are composed of a complex of several distinct genetic types that may correspond to cryptic or pseudo-cryptic species. These genetic types are usually delimitated using partial sequences located at the 3'end of the SSUrDNA, but typically based on empirical delimitation. Here, we first use patristic genetic distances calculated within and among genetic types of the most common morpho-species to show that intra-type and inter-type genetic distances within morpho-species may significantly overlap, suggesting that genetic types have been sometimes inconsistently defined. We further apply two quantitative and independent methods, ABGD (Automatic Barcode Gap Detection) and GMYC (General Mixed Yule Coalescent) to a dataset of published and newly obtained partial SSU rDNA for a more objective assessment of the species status of these genetic types. Results of these complementary approaches are highly congruent and lead to a molecular taxonomy that ranks 49 genetic types of planktonic foraminifera as genuine (pseudo)cryptic species. Our results advocate for a standardized sequencing procedure allowing homogenous delimitations of (pseudo)cryptic species. On the ground of this revised taxonomic framework, we finally provide an integrative taxonomy synthesizing geographic, ecological and morphological differentiations that can occur among the genuine (pseudo)cryptic species. Due to molecular, environmental or morphological data scarcities, many aspects of our proposed integrative taxonomy are not yet fully resolved. On the other hand, our study opens up the potential for a correct interpretation of environmental sequence datasets.},
}
@article {pmid25119899,
year = {2014},
author = {Burg, NA and Pradhan, A and Gonzalez, RM and Morban, EZ and Zhen, EW and Sakchoowong, W and Lohman, DJ},
title = {Inferring the provenance of an alien species with DNA barcodes: the neotropical butterfly Dryas iulia in Thailand.},
journal = {PloS one},
volume = {9},
number = {8},
pages = {e104076},
pmid = {25119899},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Biodiversity ; Butterflies/classification/*genetics ; DNA Barcoding, Taxonomic ; *Introduced Species ; Larva/genetics/physiology ; Molecular Sequence Data ; Sequence Analysis, DNA ; Thailand ; },
abstract = {The Neotropical butterfly Dryas iulia has been collected from several locations in Thailand and Malaysia since 2007, and has been observed breeding in the wild, using introduced Passiflora foetida as a larval host plant. The butterfly is bred by a butterfly house in Phuket, Thailand, for release at weddings and Buddhist ceremonies, and we hypothesized that this butterfly house was the source of wild, Thai individuals. We compared wing patterns and COI barcodes from two, wild Thai populations with individuals obtained from this butterfly house. All Thai individuals resemble the subspecies D. iulia modesta, and barcodes from wild and captive Thai specimens were identical. This unique, Thai barcode was not found in any of the 30 specimens sampled from the wild in the species' native range, but is most similar to specimens from Costa Rica, where many exporting butterfly farms are located. These data implicate the butterfly house as the source of Thailand's wild D. iulia populations, which are currently so widespread that eradication efforts are unlikely to be successful.},
}
@article {pmid25117374,
year = {2014},
author = {Al-Qurainy, F and Khan, S and Nadeem, M and Tarroum, M and Al-Ameri, A},
title = {Selection of DNA barcoding loci and phylogenetic study of a medicinal and endemic plant, Plectranthus asirensis J.R.I. Wood from Saudi Arabia.},
journal = {Genetics and molecular research : GMR},
volume = {13},
number = {3},
pages = {6184-6190},
doi = {10.4238/2014.August.7.31},
pmid = {25117374},
issn = {1676-5680},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Chloroplast/genetics ; DNA, Intergenic ; DNA, Plant ; Molecular Sequence Data ; Phenotype ; *Phylogeny ; Plants, Medicinal ; Plectranthus/*classification/*genetics ; Quantitative Trait Loci ; RNA, Ribosomal, 5.8S/genetics ; Saudi Arabia ; *Wood ; },
abstract = {Genuine medicinal plant materials are very important for potential crude drug production, which can be used to cure many human diseases. DNA barcoding of medicinal plants is an effective way to identify adulterated or contaminated market materials, but it can be quite challenging to generate barcodes and analyze the data to determine discrimination power. The molecular phylogeny of a plant species infers its relationship to other species. We screened the various loci of the nuclear and chloroplast genome for the barcoding of Plectranthus asirensis, an endemic plant of Saudi Arabia. The chloroplast genome loci such as rps16 and rpoB showed maximum similarity to taxa of the same and other genera via BLAST of the National Center for Biotechnology Information (NCBI) GenBank database; hence, they are less preferable for the development of a DNA barcode. However, nrDNA-ITS and chloroplast loci rbcL and rpoC1 showed less similarity via BLAST of the NCBI GenBank database; therefore, they could be used for DNA barcoding for this species.},
}
@article {pmid25116917,
year = {2014},
author = {Collins, RA and Cruickshank, RH},
title = {Known knowns, known unknowns, unknown unknowns and unknown knowns in DNA barcoding: a comment on Dowton et al.},
journal = {Systematic biology},
volume = {63},
number = {6},
pages = {1005-1009},
doi = {10.1093/sysbio/syu060},
pmid = {25116917},
issn = {1076-836X},
mesh = {Classification/*methods ; DNA Barcoding, Taxonomic/*standards ; *Phylogeny ; },
}
@article {pmid25116625,
year = {2014},
author = {Bast, F and Bhushan, S and John, AA},
title = {DNA barcoding of a new record of epi-endophytic green algae Ulvella leptochaete (Ulvellaceae, Chlorophyta) in India.},
journal = {Journal of biosciences},
volume = {39},
number = {4},
pages = {711-716},
pmid = {25116625},
issn = {0973-7138},
mesh = {Chlorophyta/*classification/*genetics/microbiology ; DNA Barcoding, Taxonomic/*methods ; DNA, Intergenic/genetics ; India ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; Rhodophyta/microbiology ; Species Specificity ; },
abstract = {Epi-endophytic green algae comprise one of the most diverse and phylogenetically primitive groups of green algae and are considered to be ubiquitous in the world's oceans; however, no reports of these algae exist from India. Here we report the serendipitous discovery of Ulvella growing on intertidal green algae Cladophora glomerata and benthic red algae Laurencia obtusa collected from India. DNA barcodes at nuclear ribosomal DNA Internal Transcriber Spacer (nrDNA ITS) 1 and 2 regions for Indian isolates from the west and east coasts have been generated for the first time. Based on morphology and DNA barcoding, isolates were identified as Ulvella leptochaete. Phylogenetic reconstruction of concatenated dataset using Maximum Likelihood method differentiated Indian isolates from other accessions of this alga available in Genbank, albeit with low bootstrap support. Monophyly of Ulvella leptochaete was obvious in both of our phylogenetic analyses. With this first report of epi-endophytic algae from Indian territorial waters, the dire need to catalogue its cryptic diversity is highlighted and avenues of future research are discussed.},
}
@article {pmid25115915,
year = {2015},
author = {Borisjuk, N and Chu, P and Gutierrez, R and Zhang, H and Acosta, K and Friesen, N and Sree, KS and Garcia, C and Appenroth, KJ and Lam, E},
title = {Assessment, validation and deployment strategy of a two-barcode protocol for facile genotyping of duckweed species.},
journal = {Plant biology (Stuttgart, Germany)},
volume = {17 Suppl 1},
number = {},
pages = {42-49},
doi = {10.1111/plb.12229},
pmid = {25115915},
issn = {1438-8677},
mesh = {Araceae/*genetics ; Base Sequence ; Bayes Theorem ; DNA Barcoding, Taxonomic/*methods ; DNA, Intergenic/genetics ; Databases, Genetic ; Genotyping Techniques/*methods ; Phylogeny ; Reproducibility of Results ; Species Specificity ; },
abstract = {Lemnaceae, commonly called duckweeds, comprise a diverse group of floating aquatic plants that have previously been classified into 37 species based on morphological and physiological criteria. In addition to their unique evolutionary position among angiosperms and their applications in biomonitoring, the potential of duckweeds as a novel sustainable crop for fuel and feed has recently increased interest in the study of their biodiversity and systematics. However, due to their small size and abbreviated structure, accurate typing of duckweeds based on morphology can be challenging. In the past decade, attempts to employ molecular barcoding techniques for species assignment have produced promising results; however, they have yet to be codified into a simple and quantitative protocol. A study that compiles and compares the barcode sequences within all known species of this family would help to establish the fidelity and limits of this DNA-based approach. In this work, we compared the level of conservation between over 100 strains of duckweed for two intergenic barcode sequences derived from the plastid genome. By using over 300 sequences publicly available in the NCBI database, we determined the utility of each of these two barcodes for duckweed species identification. Through sequencing of these barcodes from additional accessions, 30 of the 37 known species of duckweed could be identified with varying levels of confidence using this approach. From our analyses using this reference dataset, we also confirmed two instances where mis-assignment of species has likely occurred. Potential strategies for further improving the scope of this technology are discussed.},
}
@article {pmid25111057,
year = {2014},
author = {Pardo, C and Lopez, L and Peña, V and Hernández-Kantún, J and Le Gall, L and Bárbara, I and Barreiro, R},
title = {A multilocus species delimitation reveals a striking number of species of coralline algae forming Maerl in the OSPAR maritime area.},
journal = {PloS one},
volume = {9},
number = {8},
pages = {e104073},
pmid = {25111057},
issn = {1932-6203},
mesh = {Atlantic Ocean ; *Conservation of Natural Resources ; DNA Barcoding, Taxonomic ; Genetic Loci/*genetics ; Phylogeny ; Rhodophyta/*classification/*genetics ; },
abstract = {Maerl beds are sensitive biogenic habitats built by an accumulation of loose-lying, non-geniculate coralline algae. While these habitats are considered hot-spots of marine biodiversity, the number and distribution of maerl-forming species is uncertain because homoplasy and plasticity of morphological characters are common. As a result, species discrimination based on morphological features is notoriously challenging, making these coralline algae the ideal candidates for a DNA barcoding study. Here, mitochondrial (COI-5P DNA barcode fragment) and plastidial (psbA gene) sequence data were used in a two-step approach to delimit species in 224 collections of maerl sampled from Svalbard (78°96'N) to the Canary Islands (28°64'N) that represented 10 morphospecies from four genera and two families. First, the COI-5P dataset was analyzed with two methods based on distinct criteria (ABGD and GMYC) to delineate 16 primary species hypotheses (PSHs) arranged into four major lineages. Second, chloroplast (psbA) sequence data served to consolidate these PSHs into 13 secondary species hypotheses (SSHs) that showed biologically plausible ranges. Using several lines of evidence (e.g. morphological characters, known species distributions, sequences from type and topotype material), six SSHs were assigned to available species names that included the geographically widespread Phymatolithon calcareum, Lithothamnion corallioides, and L. glaciale; possible identities of other SSHs are discussed. Concordance between SSHs and morphospecies was minimal, highlighting the convenience of DNA barcoding for an accurate identification of maerl specimens. Our survey indicated that a majority of maerl forming species have small distribution ranges and revealed a gradual replacement of species with latitude.},
}
@article {pmid25109631,
year = {2016},
author = {Yu, H and Kong, L and Li, Q},
title = {Evaluation of the efficacy of twelve mitochondrial protein-coding genes as barcodes for mollusk DNA barcoding.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1336-1339},
doi = {10.3109/19401736.2014.945579},
pmid = {25109631},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods/standards ; Mitochondrial Proteins/*genetics ; Mytilus/classification/*genetics ; },
abstract = {In this study, we evaluated the efficacy of 12 mitochondrial protein-coding genes from 238 mitochondrial genomes of 140 molluscan species as potential DNA barcodes for mollusks. Three barcoding methods (distance, monophyly and character-based methods) were used in species identification. The species recovery rates based on genetic distances for the 12 genes ranged from 70.83 to 83.33%. There were no significant differences in intra- or interspecific variability among the 12 genes. The monophyly and character-based methods provided higher resolution than the distance-based method in species delimitation. Especially in closely related taxa, the character-based method showed some advantages. The results suggested that besides the standard COI barcode, other 11 mitochondrial protein-coding genes could also be potentially used as a molecular diagnostic for molluscan species discrimination. Our results also showed that the combination of mitochondrial genes did not enhance the efficacy for species identification and a single mitochondrial gene would be fully competent.},
}
@article {pmid25109627,
year = {2016},
author = {Rice, LM and Reis, AH and Wangh, LJ},
title = {Virtual Barcoding using LATE-PCR and Lights-On/Lights-Off probes: identification of nematode species in a closed-tube reaction.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1358-1363},
doi = {10.3109/19401736.2014.947581},
pmid = {25109627},
issn = {2470-1408},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Fluorescent Dyes/*chemistry ; Genes, Mitochondrial ; Genome, Helminth ; Nematoda/classification/*genetics ; Polymerase Chain Reaction/methods ; },
abstract = {The present study describes a rapid, universal, easy-to-use, closed-tube, non-sequencing method that should also be able to uniquely identify almost any animal species on earth. The approach, called Virtual Barcoding, is illustrated using five species of nematodes from three genera. Linear-After-The-Exponential (LATE) PCR was used to amplify a portion of the CO1 gene for each of five commercially available, beneficial species of soil nematodes. A set of ten low temperature Lights-On/Lights-Off consensus probes were included in the reaction mixture and were used at end-point to coat the accumulated single-stranded amplicon by dropping the temperature. Because each of the probes is mis-match tolerant, the temperature at which it hybridizes to its complementary region within the target is sequence dependent. As anticipated, each species had its own unique fluorescent signature in either three different colors, or a single color depending on which fluorophores were used to label the Lights-On probes. Each fluorescent signature was then mathematically converted to a species-specific Virtual Barcode.},
}
@article {pmid25109295,
year = {2014},
author = {Andersen, JD and Pereira, V and Pietroni, C and Mikkelsen, M and Johansen, P and Børsting, C and Morling, N},
title = {Next-generation sequencing of multiple individuals per barcoded library by deconvolution of sequenced amplicons using endonuclease fragment analysis.},
journal = {BioTechniques},
volume = {57},
number = {2},
pages = {91-94},
doi = {10.2144/000114200},
pmid = {25109295},
issn = {1940-9818},
mesh = {DNA/genetics ; DNA Barcoding, Taxonomic ; Endonucleases/*genetics ; Genotyping Techniques/methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Receptor, Melanocortin, Type 1/*genetics ; },
abstract = {The simultaneous sequencing of samples from multiple individuals increases the efficiency of next-generation sequencing (NGS) while also reducing costs. Here we describe a novel and simple approach for sequencing DNA from multiple individuals per barcode. Our strategy relies on the endonuclease digestion of PCR amplicons prior to library preparation, creating a specific fragment pattern for each individual that can be resolved after sequencing. By using both barcodes and restriction fragment patterns, we demonstrate the ability to sequence the human melanocortin 1 receptor (MC1R) genes from 72 individuals using only 24 barcoded libraries.},
}
@article {pmid25107691,
year = {2015},
author = {Yu, Z and Li, Q and Kong, L and Yu, H},
title = {Utility of DNA barcoding for Tellinoidea: a comparison of distance, coalescent and character-based methods on multiple genes.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {17},
number = {1},
pages = {55-65},
pmid = {25107691},
issn = {1436-2236},
mesh = {Animals ; Bivalvia/*genetics ; DNA Barcoding, Taxonomic/*methods/*standards ; Electron Transport Complex IV/genetics ; Models, Genetic ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; },
abstract = {DNA barcoding has become a promising tool for rapid species identification using a short fragment of mitochondrial gene. Currently, an increasing number of analytical methods are available to assign DNA barcodes to taxa. The methods can be broadly divided into three main categories: (i) distance-based methods (the classical approach and the automatic barcode gap discovery (ABGD) approach), (ii) coalescent-based methods (the monophyly-based method and the general mixed Yule coalescent (GMYC) model) and (iii) the character-based method (CAOS). This study is set out to evaluate the availability of each method in barcoding Tellinoidea on the cytomchrome c oxidase subunit I (COI) and the 16 small-subunit ribosomal DNA (16S rDNA) genes. As a result, the character-based method was found to be the best in all cases, especially on a genus level. For distance-based methods, the elaborate one gained a success equal or greater than the basic one. The traditional coalescent-based method nicely delimited all of the tellinoideans on a species level. The GMYC model, which is the most radical, clearly inflated the number of species units by 34.6 % for COI gene and by 58.8 % for 16S gene. Thus, we conclude that CAOS better approximates a real barcode, and suggest the use of the ABGD method and the monophyly-based method for primary partitions. Additionally, COI gene may be more suitable as a standard barcode marker than 16S gene, particularly for tree-based methods.},
}
@article {pmid25103425,
year = {2016},
author = {Yang, P and Zhou, H and Qian, J and Xu, H and Shao, Q and Li, Y and Yao, H},
title = {The complete chloroplast genome sequence of Dendrobium officinale.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1262-1264},
doi = {10.3109/19401736.2014.945547},
pmid = {25103425},
issn = {2470-1408},
mesh = {Base Composition/genetics ; Base Sequence ; China ; Chloroplasts/*genetics ; Chromosome Mapping ; DNA, Chloroplast/*genetics ; Dendrobium/*genetics ; Gene Order/genetics ; Genes, Plant/genetics ; Genome Size/genetics ; Genome, Chloroplast/*genetics ; Genome, Plant/*genetics ; Inverted Repeat Sequences/genetics ; Medicine, Chinese Traditional ; Plant Leaves/genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; },
abstract = {The complete chloroplast sequence of Dendrobium officinale, an endangered and economically important traditional Chinese medicine, was reported and characterized. The genome size is 152,018 bp, with 37.5% GC content. A pair of inverted repeats (IRs) of 26,284 bp are separated by a large single-copy region (LSC, 84,944 bp) and a small single-copy region (SSC, 14,506 bp). The complete cp DNA contains 83 protein-coding genes, 39 tRNA genes and 8 rRNA genes. Fourteen genes contained one or two introns.},
}
@article {pmid25099936,
year = {2014},
author = {Ashfaq, M and Hebert, PD and Mirza, MS and Khan, AM and Mansoor, S and Shah, GS and Zafar, Y},
title = {DNA barcoding of Bemisia tabaci complex (Hemiptera: Aleyrodidae) reveals southerly expansion of the dominant whitefly species on cotton in Pakistan.},
journal = {PloS one},
volume = {9},
number = {8},
pages = {e104485},
pmid = {25099936},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Gossypium/*parasitology ; Hemiptera/*genetics ; Pakistan ; *Phylogeny ; },
abstract = {BACKGROUND: Although whiteflies (Bemisia tabaci complex) are an important pest of cotton in Pakistan, its taxonomic diversity is poorly understood. As DNA barcoding is an effective tool for resolving species complexes and analyzing species distributions, we used this approach to analyze genetic diversity in the B. tabaci complex and map the distribution of B. tabaci lineages in cotton growing areas of Pakistan.<br><br>METHODS/PRINCIPAL FINDINGS: Sequence diversity in the DNA barcode region (mtCOI-5') was examined in 593 whiteflies from Pakistan to determine the number of whitefly species and their distributions in the cotton-growing areas of Punjab and Sindh provinces. These new records were integrated with another 173 barcode sequences for B. tabaci, most from India, to better understand regional whitefly diversity. The Barcode Index Number (BIN) System assigned the 766 sequences to 15 BINs, including nine from Pakistan. Representative specimens of each Pakistan BIN were analyzed for mtCOI-3' to allow their assignment to one of the putative species in the B. tabaci complex recognized on the basis of sequence variation in this gene region. This analysis revealed the presence of Asia II 1, Middle East-Asia Minor 1, Asia 1, Asia II 5, Asia II 7, and a new lineage "Pakistan". The first two taxa were found in both Punjab and Sindh, but Asia 1 was only detected in Sindh, while Asia II 5, Asia II 7 and "Pakistan" were only present in Punjab. The haplotype networks showed that most haplotypes of Asia II 1, a species implicated in transmission of the cotton leaf curl virus, occurred in both India and Pakistan.<br><br>CONCLUSIONS: DNA barcodes successfully discriminated cryptic species in B. tabaci complex. The dominant haplotypes in the B. tabaci complex were shared by India and Pakistan. Asia II 1 was previously restricted to Punjab, but is now the dominant lineage in southern Sindh; its southward spread may have serious implications for cotton plantations in this region.},
}
@article {pmid25099007,
year = {2014},
author = {Buschmann, T and Zhang, R and Brash, DE and Bystrykh, LV},
title = {Enhancing the detection of barcoded reads in high throughput DNA sequencing data by controlling the false discovery rate.},
journal = {BMC bioinformatics},
volume = {15},
number = {1},
pages = {264},
pmid = {25099007},
issn = {1471-2105},
support = {UL1 TR000142/TR/NCATS NIH HHS/United States ; },
mesh = {Animals ; DNA/*genetics ; DNA Contamination ; DNA Primers/genetics ; False Positive Reactions ; Genome/genetics ; High-Throughput Nucleotide Sequencing/*methods/standards ; Mice ; Reference Standards ; Sequence Analysis, DNA/*methods/standards ; Sodium-Potassium-Exchanging ATPase/genetics ; },
abstract = {BACKGROUND: DNA barcodes are short unique sequences used to label DNA or RNA-derived samples in multiplexed deep sequencing experiments. During the demultiplexing step, barcodes must be detected and their position identified. In some cases (e.g., with PacBio SMRT), the position of the barcode and DNA context is not well defined. Many reads start inside the genomic insert so that adjacent primers might be missed. The matter is further complicated by coincidental similarities between barcode sequences and reference DNA. Therefore, a robust strategy is required in order to detect barcoded reads and avoid a large number of false positives or negatives.For mass inference problems such as this one, false discovery rate (FDR) methods are powerful and balanced solutions. Since existing FDR methods cannot be applied to this particular problem, we present an adapted FDR method that is suitable for the detection of barcoded reads as well as suggest possible improvements.<br><br>RESULTS: In our analysis, barcode sequences showed high rates of coincidental similarities with the Mus musculus reference DNA. This problem became more acute when the length of the barcode sequence decreased and the number of barcodes in the set increased. The method presented in this paper controls the tail area-based false discovery rate to distinguish between barcoded and unbarcoded reads. This method helps to establish the highest acceptable minimal distance between reads and barcode sequences. In a proof of concept experiment we correctly detected barcodes in 83% of the reads with a precision of 89%. Sensitivity improved to 99% at 99% precision when the adjacent primer sequence was incorporated in the analysis. The analysis was further improved using a paired end strategy. Following an analysis of the data for sequence variants induced in the Atp1a1 gene of C57BL/6 murine melanocytes by ultraviolet light and conferring resistance to ouabain, we found no evidence of cross-contamination of DNA material between samples.<br><br>CONCLUSION: Our method offers a proper quantitative treatment of the problem of detecting barcoded reads in a noisy sequencing environment. It is based on the false discovery rate statistics that allows a proper trade-off between sensitivity and precision to be chosen.},
}
@article {pmid25093850,
year = {2014},
author = {Schoelinck, C and Hinsinger, DD and Dettaï, A and Cruaud, C and Justine, JL},
title = {A phylogenetic re-analysis of groupers with applications for ciguatera fish poisoning.},
journal = {PloS one},
volume = {9},
number = {8},
pages = {e98198},
pmid = {25093850},
issn = {1932-6203},
mesh = {Animals ; Bayes Theorem ; Ciguatera Poisoning/*genetics ; Electron Transport Complex IV/genetics ; Fishes/*classification ; Genetic Markers ; *Phylogeny ; Species Specificity ; },
abstract = {BACKGROUND: Ciguatera fish poisoning (CFP) is a significant public health problem due to dinoflagellates. It is responsible for one of the highest reported incidence of seafood-borne illness and Groupers are commonly reported as a source of CFP due to their position in the food chain. With the role of recent climate change on harmful algal blooms, CFP cases might become more frequent and more geographically widespread. Since there is no appropriate treatment for CFP, the most efficient solution is to regulate fish consumption. Such a strategy can only work if the fish sold are correctly identified, and it has been repeatedly shown that misidentifications and species substitutions occur in fish markets.<br><br>METHODS: We provide here both a DNA-barcoding reference for groupers, and a new phylogenetic reconstruction based on five genes and a comprehensive taxonomical sampling. We analyse the correlation between geographic range of species and their susceptibility to ciguatera accumulation, and the co-occurrence of ciguatoxins in closely related species, using both character mapping and statistical methods.<br><br>RESULTS: Misidentifications were encountered in public databases, precluding accurate species identifications. Epinephelinae now includes only twelve genera (vs. 15 previously). Comparisons with the ciguatera incidences show that in some genera most species are ciguateric, but statistical tests display only a moderate correlation with the phylogeny. Atlantic species were rarely contaminated, with ciguatera occurrences being restricted to the South Pacific.<br><br>CONCLUSIONS: The recent changes in classification based on the reanalyses of the relationships within Epinephelidae have an impact on the interpretation of the ciguatera distribution in the genera. In this context and to improve the monitoring of fish trade and safety, we need to obtain extensive data on contamination at the species level. Accurate species identifications through DNA barcoding are thus an essential tool in controlling CFP since meal remnants in CFP cases can be easily identified with molecular tools.},
}
@article {pmid25093815,
year = {2014},
author = {Leasi, F and Norenburg, JL},
title = {The necessity of DNA taxonomy to reveal cryptic diversity and spatial distribution of meiofauna, with a focus on Nemertea.},
journal = {PloS one},
volume = {9},
number = {8},
pages = {e104385},
pmid = {25093815},
issn = {1932-6203},
mesh = {Animals ; Aquatic Organisms/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Panama ; Phylogeny ; Phylogeography ; *Spatial Analysis ; },
abstract = {Meiofauna represent one of the most abundant and diverse communities in marine benthic ecosystems. However, an accurate assessment of diversity at the level of species has been and remains challenging for these microscopic organisms. Therefore, for many taxa, especially the soft body forms such as nemerteans, which often lack clear diagnostic morphological traits, DNA taxonomy is an effective means to assess species diversity. Morphological taxonomy of Nemertea is well documented as complicated by scarcity of unambiguous character states and compromised by diagnoses of a majority of species (and higher clades) being inadequate or based on ambiguous characters and character states. Therefore, recent studies have advocated for the primacy of molecular tools to solve the taxonomy of this group. DNA taxonomy uncovers possible hidden cryptic species, provides a coherent means to systematize taxa in definite clades, and also reveals possible biogeographic patterns. Here, we analyze diversity of nemertean species by considering the barcode region of the mitochondrial gene Cytochrome Oxidase subunit I (COI) and different species delineation approaches in order to infer evolutionarily significant units. In the aim to uncover actual diversity of meiofaunal nemerteans across different sites in Central America, COI sequences were obtained for specimens assigned here to the genera Cephalothrix, Ototyphlonemertes, and Tetrastemma-like worms, each commonly encountered in our sampling. Additional genetic, taxonomic, and geographic data of other specimens belonging to these genera were added from GenBank. Results are consistent across different DNA taxonomy approaches, and revealed (i) the presence of several hidden cryptic species and (ii) numerous potential misidentifications due to traditional taxonomy. (iii) We additionally test a possible biogeographic pattern of taxonomic units revealed by this study, and, except for a few cases, the putative species seem not to be widely distributed, in contrast to what traditional taxonomy would suggest for the recognized morphotypes.},
}
@article {pmid25093586,
year = {2014},
author = {Zhou, WW and Zhang, BL and Chen, HM and Jin, JQ and Yang, JX and Wang, YY and Jiang, K and Murphy, RW and Zhang, YP and Che, J},
title = {DNA barcodes and species distribution models evaluate threats of global climate changes to genetic diversity: a case study from Nanorana parkeri (Anura: Dicroglossidae).},
journal = {PloS one},
volume = {9},
number = {8},
pages = {e103899},
pmid = {25093586},
issn = {1932-6203},
mesh = {Animals ; Anura/*genetics ; Base Sequence ; *Climate Change ; *DNA Barcoding, Taxonomic ; Demography ; Genetic Speciation ; *Genetic Variation ; Geography ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Anthropogenic global climate changes are one of the greatest threats to biodiversity. Distribution modeling can predict the effects of climate changes and potentially their effects on genetic diversity. DNA barcoding quickly identifies patterns of genetic diversity. As a case study, we use DNA barcodes and distribution models to predict threats under climate changes in the frog Nanorana parkeri, which is endemic to the Qinghai-Tibetan Plateau. Barcoding identifies major lineages W and E. Lineage W has a single origin in a refugium and Lineage E derives from three refugia. All refugia locate in river valleys and each greatly contributes to the current level of intraspecific genetic diversity. Species distribution models suggest that global climate changes will greatly influence N. parkeri, especially in the level of genetic diversity, because two former refugia will fail to provide suitable habitat. Our pipeline provides a novel application of DNA barcoding and has important implications for the conservation of biodiversity in southern areas of the Qinghai-Tibetan Plateau.},
}
@article {pmid25093034,
year = {2014},
author = {Hope, PR and Bohmann, K and Gilbert, MTP and Zepeda-Mendoza, ML and Razgour, O and Jones, G},
title = {Second generation sequencing and morphological faecal analysis reveal unexpected foraging behaviour by Myotis nattereri (Chiroptera, Vespertilionidae) in winter.},
journal = {Frontiers in zoology},
volume = {11},
number = {},
pages = {39},
pmid = {25093034},
issn = {1742-9994},
abstract = {BACKGROUND: Temperate winters produce extreme energetic challenges for small insectivorous mammals. Some bat species inhabiting locations with mild temperate winters forage during brief inter-torpor normothermic periods of activity. However, the winter diet of bats in mild temperate locations is studied infrequently. Although microscopic analyses of faeces have traditionally been used to characterise bat diet, recently the coupling of PCR with second generation sequencing has offered the potential to further advance our understanding of animal dietary composition and foraging behaviour by allowing identification of a much greater proportion of prey items often with increased taxonomic resolution. We used morphological analysis and Illumina-based second generation sequencing to study the winter diet of Natterer's bat (Myotis nattereri) and compared the results obtained from these two approaches. For the first time, we demonstrate the applicability of the Illumina MiSeq platform as a data generation source for bat dietary analyses.<br><br>RESULTS: Faecal pellets collected from a hibernation site in southern England during two winters (December-March 2009-10 and 2010-11), indicated that M. nattereri forages throughout winter at least in a location with a mild winter climate. Through morphological analysis, arthropod fragments from seven taxonomic orders were identified. A high proportion of these was non-volant (67.9% of faecal pellets) and unexpectedly included many lepidopteran larvae. Molecular analysis identified 43 prey species from six taxonomic orders and confirmed the frequent presence of lepidopteran species that overwinter as larvae.<br><br>CONCLUSIONS: The winter diet of M. nattereri is substantially different from other times of the year confirming that this species has a wide and adaptable dietary niche. Comparison of DNA derived from the prey to an extensive reference dataset of potential prey barcode sequences permitted fine scale taxonomic resolution of prey species. The high occurrence of non-volant prey suggests that gleaning allows prey capture at low ambient temperatures when the abundance of flying insects may be substantially reduced. Interesting questions arise as to how M. nattereri might successfully locate and capture some of the non-volant prey species encountered in its faeces. The consumption of lepidopteran larvae such as cutworms suggests that M. nattereri eats agricultural pest species.},
}
@article {pmid25090397,
year = {2016},
author = {Wang, X and Xu, G and Liu, C and Huang, L and Zhao, B and Ren, X and Fu, X and Ren, G and Liu, S},
title = {Development of deft amplification refractory mutation sequencing system (ARMSS) for discriminating Pilos antler based on a short cytochrome b (Cytb) gene.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1332-1335},
doi = {10.3109/19401736.2014.945578},
pmid = {25090397},
issn = {2470-1408},
mesh = {Animals ; Antlers/*chemistry ; Artiodactyla/genetics ; Base Sequence ; Cytochrome b Group/*genetics ; DNA Barcoding, Taxonomic/*methods ; Medicine, Chinese Traditional ; Molecular Sequence Data ; *Mutation ; Nucleic Acid Amplification Techniques/*methods ; },
abstract = {Pilos antler (Lu-Rong in Chinese) is a famous traditional medicine in China. Many adulterants have been discovered in Chinese markets in recent years. However, few DNA-based methods are effective for discrimination of this DNA-degraded animal medicine. Here, novel and deft amplification refractory mutation sequencing system (ARMSS), integrating the advantages of the amplification refractory mutation system (ARMS) and the short DNA barcode, was first developed to discriminate Pilos antler from its adulterants. We aimed to provide a new sight and inspiration for deft detection. The results showed that developed ARMS achieved strong specificity and high sensitivity in rapid identification, while the short Cytb gene was of excellent identification power in terms of accurate identification, which suggested that ARMSS successfully integrated the advantages of the ARMS and short DNA barcode, and that it was useful for deft detection. Our study determined that the deft ARMSS could be the well candidate for discrimination of Pilos antler, as well as be a valuable tool for deft identification of Chinese medicine.},
}
@article {pmid25087935,
year = {2014},
author = {Chen, S and Pang, X and Song, J and Shi, L and Yao, H and Han, J and Leon, C},
title = {A renaissance in herbal medicine identification: from morphology to DNA.},
journal = {Biotechnology advances},
volume = {32},
number = {7},
pages = {1237-1244},
doi = {10.1016/j.biotechadv.2014.07.004},
pmid = {25087935},
issn = {1873-1899},
mesh = {*DNA Barcoding, Taxonomic ; *DNA, Plant/analysis/genetics ; Herbal Medicine/*standards ; *Plants, Medicinal/classification/genetics ; },
abstract = {Numerous adverse reactions have arisen following the use of inaccurately identified medicinal plant ingredients, resulting in conditions such as aristolochic acid nephropathy and herb-induced poisoning. This problem has prompted increased global concern over the safety of herbal medicines. DNA barcoding, a technique aiming at detecting species-specific differences in a short region of DNA, provides a powerful new tool for addressing this problem. A preliminary system for DNA barcoding herbal materials has been established based on a two-locus combination of ITS2+psbA-trnH barcodes. There are 78,847 sequences belonging to 23,262 species in the system, which include more than 95% of crude herbal drugs in pharmacopeia, such as those of China, Japan, Korea, India, USA, and Europe. The system has been widely used in traditional herbal medicine enterprises. This review summarizes recent key advances in the DNA barcoding of medicinal plant ingredients (herbal materia medica) as a contribution towards safe and efficacious herbal medicines.},
}
@article {pmid25086649,
year = {2014},
author = {Pollen, AA and Nowakowski, TJ and Shuga, J and Wang, X and Leyrat, AA and Lui, JH and Li, N and Szpankowski, L and Fowler, B and Chen, P and Ramalingam, N and Sun, G and Thu, M and Norris, M and Lebofsky, R and Toppani, D and Kemp, DW and Wong, M and Clerkson, B and Jones, BN and Wu, S and Knutsson, L and Alvarado, B and Wang, J and Weaver, LS and May, AP and Jones, RC and Unger, MA and Kriegstein, AR and West, JA},
title = {Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex.},
journal = {Nature biotechnology},
volume = {32},
number = {10},
pages = {1053-1058},
pmid = {25086649},
issn = {1546-1696},
support = {R01 NS072630/NS/NINDS NIH HHS/United States ; R01 NS075998/NS/NINDS NIH HHS/United States ; R01NS075998/NS/NINDS NIH HHS/United States ; R01NS072630/NS/NINDS NIH HHS/United States ; },
mesh = {Animals ; Cerebral Cortex/*growth &amp; development/metabolism ; Computational Biology/*methods ; Equipment Design ; Gene Expression Profiling/*methods ; Humans ; Mice ; Microfluidic Analytical Techniques ; RNA, Messenger/*analysis/genetics/metabolism ; Sequence Analysis, RNA/*methods ; Signal Transduction/*genetics/physiology ; },
abstract = {Large-scale surveys of single-cell gene expression have the potential to reveal rare cell populations and lineage relationships but require efficient methods for cell capture and mRNA sequencing. Although cellular barcoding strategies allow parallel sequencing of single cells at ultra-low depths, the limitations of shallow sequencing have not been investigated directly. By capturing 301 single cells from 11 populations using microfluidics and analyzing single-cell transcriptomes across downsampled sequencing depths, we demonstrate that shallow single-cell mRNA sequencing (~50,000 reads per cell) is sufficient for unbiased cell-type classification and biomarker identification. In the developing cortex, we identify diverse cell types, including multiple progenitor and neuronal subtypes, and we identify EGR1 and FOS as previously unreported candidate targets of Notch signaling in human but not mouse radial glia. Our strategy establishes an efficient method for unbiased analysis and comparison of cell populations from heterogeneous tissue by microfluidic single-cell capture and low-coverage sequencing of many cells.},
}
@article {pmid25084993,
year = {2014},
author = {Oba, Y and Schultz, DT},
title = {Eco-evo bioluminescence on land and in the sea.},
journal = {Advances in biochemical engineering/biotechnology},
volume = {144},
number = {},
pages = {3-36},
doi = {10.1007/978-3-662-43385-0_1},
pmid = {25084993},
issn = {0724-6145},
mesh = {Animals ; *Aquatic Organisms ; *Biological Evolution ; *Ecological and Environmental Phenomena ; *Luminescence ; },
abstract = {This review discusses the evolution of bioluminescence organisms that inhabit various environments based on the current understanding of their unique ecologies and biochemistries. As shown here, however, there are still many unanswered questions regarding the functions and mechanisms of bioluminescence, which should be investigated in further studies. To facilitate future research in this field, we introduce our recent attempt, the bioluminescent organism DNA barcode initiative. This genetic reference library will provide resources for other scientists to efficiently identify unstudied bioluminescent organisms, focus their biochemical and genetic research goals, and will generally promote bioluminescence as a field of scientific study.},
}
@article {pmid25084126,
year = {2014},
author = {Keller, A and Horn, H and Förster, F and Schultz, J},
title = {Computational integration of genomic traits into 16S rDNA microbiota sequencing studies.},
journal = {Gene},
volume = {549},
number = {1},
pages = {186-191},
doi = {10.1016/j.gene.2014.07.066},
pmid = {25084126},
issn = {1879-0038},
mesh = {Bacteria/classification/*genetics ; Computational Biology/*methods ; DNA Barcoding, Taxonomic ; DNA, Bacterial/*genetics ; DNA, Ribosomal/*genetics ; Genetic Markers ; Genome, Bacterial ; Genomics ; Metagenomics ; Microbiota/*genetics ; Multigene Family ; RNA, Ribosomal, 16S/*genetics ; Reproducibility of Results ; },
abstract = {Molecular sequencing techniques help to understand microbial biodiversity with regard to species richness, assembly structure and function. In this context, available methods are barcoding, metabarcoding, genomics and metagenomics. The first two are restricted to taxonomic assignments, whilst genomics only refers to functional capabilities of a single organism. Metagenomics by contrast yields information about organismal and functional diversity of a community. However currently it is very demanding regarding labour and costs and thus not applicable to most laboratories. Here, we show in a proof-of-concept that computational approaches are able to retain functional information about microbial communities assessed through 16S rDNA (meta)barcoding by referring to reference genomes. We developed an automatic pipeline to show that such integration may infer preliminary or supplementary genomic content of a community. We applied it to two biological datasets and delineated significantly overrepresented protein families between communities. The script alongside supporting data is available at http://bioapps.biozentrum.uni-wuerzburg.de.},
}
@article {pmid25083414,
year = {2014},
author = {Crous, PW and Giraldo, A and Hawksworth, DL and Robert, V and Kirk, PM and Guarro, J and Robbertse, B and Schoch, CL and Damm, U and Trakunyingcharoen, T and Groenewald, JZ},
title = {The Genera of Fungi: fixing the application of type species of generic names.},
journal = {IMA fungus},
volume = {5},
number = {1},
pages = {141-160},
pmid = {25083414},
issn = {2210-6340},
abstract = {To ensure a stable platform for fungal taxonomy, it is of paramount importance that the genetic application of generic names be based on their DNA sequence data, and wherever possible, not morphology or ecology alone. To facilitate this process, a new database, accessible at www.GeneraofFungi.org (GoF) was established, which will allow deposition of metadata linked to holo-, lecto-, neo- or epitype specimens, cultures and DNA sequence data of the type species of genera. Although there are presently more than 18 000 fungal genera described, we aim to initially focus on the subset of names that have been placed on the "Without-prejudice List of Protected Generic Names of Fungi" (see IMA Fungus 4(2): 381-443, 2013). To enable the global mycological community to keep track of typification events and avoid duplication, special MycoBank Typification identfiers (MBT) will be issued upon deposit of metadata in MycoBank. MycoBank is linked to GoF, thus deposited metadata of generic type species will be displayed in GoF (and vice versa), but will also be linked to Index Fungorum (IF) and the curated RefSeq Targeted Loci (RTL) database in GenBank at the National Center for Biotechnology Information (NCBI). This initial paper focuses on eight genera of appendaged coelomycetes, the type species of which are neo- or epitypified here: Bartalinia (Bartalinia robillardoides; Amphisphaeriaceae, Xylariales), Chaetospermum (Chaetospermum chaetosporum, incertae sedis, Sebacinales), Coniella (Coniella fragariae, Schizoparmaceae, Diaporthales), Crinitospora (Crinitospora pulchra, Melanconidaceae, Diaporthales), Eleutheromyces (Eleutheromyces subulatus, Helotiales), Kellermania (Kellermania yuccigena, Planistromataceae, Botryosphaeriales), Mastigosporium (Mastigosporium album, Helotiales), and Mycotribulus (Mycotribulus mirabilis, Agaricales). Authors interested in contributing accounts of individual genera to larger multi-authored papers to be published in IMA Fungus, should contact the associate editors listed below for the major groups of fungi on the List of Protected Generic Names for Fungi.},
}
@article {pmid25082040,
year = {2014},
author = {Haszprunar, G and Spies, M},
title = {An integrative approach to the taxonomy of the crown-of-thorns starfish species group (Asteroidea: Acanthaster): A review of names and comparison to recent molecular data.},
journal = {Zootaxa},
volume = {3841},
number = {2},
pages = {271-284},
doi = {10.11646/zootaxa.3841.2.6},
pmid = {25082040},
issn = {1175-5334},
mesh = {Animals ; Names ; Starfish/*classification ; },
abstract = {The scientific names published for species and subspecies in the genus Acanthaster Gervais (Asteroidea: Valvatida: Acanthasteridae) are reviewed, with particular attention to the A. planci species group (crown-of-thorn starfish, COTS). Several problems with earlier nomenclatural and bibliographic data are resolved. The available name for the type species of Acanthaster in the original combination is Asterias echinites Ellis &amp; Solander in Watt, 1786; the often-cited "Asterias echinus" and "Acanthaster echinus" are incorrect subsequent spellings, therefore unavailable. The scientific names and taxonomic concepts for species and subspecies in Acanthaster are compared to recently published, robust COI-barcoding clades. Two of four clades in the A. planci group can be named unequivocally, a third requires a neotype designation to decide which of two available names will be valid, and the fourth clade necessitates a new species description and name. The References section includes annotations explaining bibliographical data important to the nomenclatural evaluations. Many hyperlinks interspersed with the paper's texts offer quick access to digital versions of the respective references.},
}
@article {pmid25081766,
year = {2014},
author = {Grebennikov, VV},
title = {DNA barcode and phylogeography of six new high altitude wingless Niphadomimus (Coleoptera: Curculionidae: Molytinae) from Southwest China.},
journal = {Zootaxa},
volume = {3838},
number = {2},
pages = {151-173},
doi = {10.11646/zootaxa.3838.2.1},
pmid = {25081766},
issn = {1175-5334},
mesh = {Altitude ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; China ; DNA Barcoding, Taxonomic ; Ecosystem ; Female ; Male ; Organ Size ; *Phylogeny ; Phylogeography ; Weevils/anatomy &amp; histology/*classification/*genetics/growth &amp; development ; },
abstract = {The genus Niphadomimus Zherikhin, 1987 is taxonomically revised herein. In addition to the two recorded Nepalese species, N. nigriventris Zherikhin and N. niger Zherikhin, known only from the holotypes, two additional specimens of N. nigriventris are reported and six new species from China represented by 96 specimens are described and illustrated. These are: N. alcyone sp. n. (Sichuan), N. celaeno sp. n. (Yunnan), N. electra sp. n. (Yunnan), N. maia sp. n. (Yunnan), N. merope sp. n. (Shaanxi) and N. sterope sp. n. (Sichuan). All known Niphadomimus species are apterous inhabitants of the leaf litter in the upper Rhododendron-dominated forest zone between 2000 and 4114 m. Phylogenetic analyses using DNA barcodes of six new species and representatives of 13 other Molytinae genera with available DNA data (A.) corroborates Niphadomimus monophyly; (B.) strongly argues for the sister-group relationship between N. merope sp. n. from the Qinling Mt. Range and the rest of the species distributed in the Hengduan mountains; (C.) in two among four analyses weakly relates the genus with the East Palaearctic Leiosoma. The tribe Typoderini could not be shown as monophyletic, which may be due to insufficient signal content of the cox1 marker at the tribal level. The detected phylogeographic pattern of Niphadomimus is compared with that of similarly distributed or closely related clades. Temporal DNA analysis estimates the N. merope sp. n. split at 6-11 MY, while the diversification of the Hengduan clade dates between 5.5 MY and 3.6 MY, i.e. well before the onset of the Quaternary climate fluctuations.},
}
@article {pmid25081435,
year = {2014},
author = {Oberhummer, E and Barten, C and Schweizer, M and Das, I and Haas, A and Hertwig, ST},
title = {Description of the tadpoles of three rare species of megophryid frogs (Amphibia: Anura: Megophryidae) from Gunung Mulu, Sarawak, Malaysia.},
journal = {Zootaxa},
volume = {3835},
number = {1},
pages = {59-79},
doi = {10.11646/zootaxa.3835.1.3},
pmid = {25081435},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Anura/anatomy &amp; histology/classification/genetics/*growth &amp; development ; Body Size ; Female ; Larva/anatomy &amp; histology/classification/genetics/growth &amp; development ; Malaysia ; Male ; Molecular Sequence Data ; Organ Size ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The megophryid frogs Leptobrachella brevicrus, Leptolalax dringi and Megophrys dringi are species exclusively known from highly localised areas in isolated mountain ranges on Borneo. The tadpoles and adults in this study were collected at the shared type locality for the three species in Gunung Mulu National Park, Sarawak, Malaysia (Borneo). The species identities of larvae were determined via comparison to syntopic adults using DNA barcoding techniques based on partial 16S rRNA mitochondrial gene sequences. The genetic data supported the status of the three taxa as valid species. Descriptions of colouration in life and after preservation, external morphological features, morphometric measurements and ecological notes in comparison to congeneric species are supplied. The tadpoles of L. brevicrus and L. dringi show similar adaptations to a fossorial lifestyle. These include an elongated, vermiform body, a relatively long tail and small eyes. Both were found in the gravel beds of a small mountain stream. In contrast, the larvae of M. dringi are adapted to occupying and feeding at the surface of pools within the stream.},
}
@article {pmid25081151,
year = {2014},
author = {Powers, TO and Bernard, EC and Harris, T and Higgins, R and Olson, M and Lodema, M and Mullin, P and Sutton, L and Powers, KS},
title = {COI haplotype groups in Mesocriconema (Nematoda: Criconematidae) and their morphospecies associations.},
journal = {Zootaxa},
volume = {3827},
number = {2},
pages = {101-146},
doi = {10.11646/zootaxa.3827.2.1},
pmid = {25081151},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Electron Transport Complex IV/*genetics ; Female ; Haplotypes ; Helminth Proteins/*genetics ; Male ; Molecular Sequence Data ; Nematoda/anatomy &amp; histology/*classification/*genetics/growth &amp; development ; Phylogeny ; },
abstract = {Without applying an a priori bias for species boundaries, specimen identities in the plant-parasitic nematode genus Mesocriconema were evaluated by examining mitochondrial COI nucleotide sequences, morphology, and biogeography. A total of 242 specimens that morphologically conformed to the genus were individually photographed, measured, and amplified by a PCR primer set to preserve the linkage between specimen morphology and a specific DNA barcode sequence. Specimens were extracted from soil samples representing 45 locations across 23 ecoregions in North America. Dendrograms constructed by neighbor-joining, maximum likelihood, and Bayesian Inference using a 721-bp COI barcode were used to group COI haplotypes. Each tree-building approach resulted in 24 major haplotype groups within the dataset. The distinctiveness of these groups was evaluated by node support, genetic distance, absence of intermediates, and several measures of distinctiveness included in software used for the exploration of species boundaries. Five of the 24 COI haplotype groups corresponded to morphologically characterized, Linnaean species. Morphospecies conforming to M. discus, Discocriconemella inarata, M. rusticum, M. onoense, and M. kirjanovae were represented by groups composed of multiple closely related or identical COI haplotypes. In other cases, morphospecies names could be equally applied to multiple haplotype groups that were genetically distant from each other. Identification based on morphology alone resulted in M. curvatum and M. ornatum species designations applied to seven and three groups, respectively. Morphological characters typically used for species level identification were demonstrably variable within haplotype groups, suggesting caution in assigning species names based on published compendia that solely consider morphological characters. Morphospecies classified as M. xenoplax formed a monophyletic group composed of seven genetically distinct COI subgroups. The species Discocriconemella inarata is transferred to Mesocriconema inaratum based on its phylogenetic position on the COI tree as well as previous phylogenetic analyses using 18S, ITS1, and cytochrome b nucleotide sequences. This study indicates that some of the species considered cosmopolitan in their distribution are actually multispecies polyphyletic groupings and an accurate assessment of Mesocriconema species distributions will benefit from molecular determination of haplotype relationships. The groups revealed by COI analysis should provide a useful framework for the evaluation of additional Mesocriconema species and will improve the reliability of designating taxonomic units in studies of nematode biodiversity.},
}
@article {pmid25081059,
year = {2014},
author = {Doody, KM and Bottini, N},
title = {"PEST control": regulation of molecular barcodes by tyrosine phosphatases.},
journal = {Cell research},
volume = {24},
number = {9},
pages = {1027-1028},
pmid = {25081059},
issn = {1748-7838},
mesh = {*Catalytic Domain ; Female ; Humans ; Protein Tyrosine Phosphatases, Non-Receptor/*chemistry/*metabolism ; Receptor, ErbB-2/*metabolism ; *Ubiquitination ; },
abstract = {The emerging concept of "molecular barcodes" refers to the dynamic combination of post-translational modifications, often of different nature (e.g., phosphorylation and ubiquitination) that gives rise to multiple forms of a protein which can relay distinct signals throughout a cell. In a recent Cell Research paper by Wang et al., the authors report that a PEST domain-containing tyrosine phosphatase, PTPN18, is able to regulate both phosphorylation and ubiquitination of the HER2 oncogene, barcoding HER2 for increased proteasomal degradation rather than for intracellular trafficking.},
}
@article {pmid25081058,
year = {2014},
author = {Wang, HM and Xu, YF and Ning, SL and Yang, DX and Li, Y and Du, YJ and Yang, F and Zhang, Y and Liang, N and Yao, W and Zhang, LL and Gu, LC and Gao, CJ and Pang, Q and Chen, YX and Xiao, KH and Ma, R and Yu, X and Sun, JP},
title = {The catalytic region and PEST domain of PTPN18 distinctly regulate the HER2 phosphorylation and ubiquitination barcodes.},
journal = {Cell research},
volume = {24},
number = {9},
pages = {1067-1090},
pmid = {25081058},
issn = {1748-7838},
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Breast Neoplasms/metabolism/pathology ; *Catalytic Domain ; Cell Line, Tumor ; Crystallography, X-Ray ; Female ; Humans ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Lysine/metabolism ; Lysosomes/metabolism ; Models, Biological ; Molecular Sequence Data ; Neoplasm Staging ; Peptides/metabolism ; Phosphorylation ; Phosphotyrosine/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Protein Tyrosine Phosphatases, Non-Receptor/*chemistry/*metabolism ; Proteolysis ; Receptor, ErbB-2/*metabolism ; Signal Transduction ; Structure-Activity Relationship ; Substrate Specificity ; *Ubiquitination ; beta-Transducin Repeat-Containing Proteins/metabolism ; },
abstract = {The tyrosine phosphorylation barcode encoded in C-terminus of HER2 and its ubiquitination regulate diverse HER2 functions. PTPN18 was reported as a HER2 phosphatase; however, the exact mechanism by which it defines HER2 signaling is not fully understood. Here, we demonstrate that PTPN18 regulates HER2-mediated cellular functions through defining both its phosphorylation and ubiquitination barcodes. Enzymologic characterization and three crystal structures of PTPN18 in complex with HER2 phospho-peptides revealed the molecular basis for the recognition between PTPN18 and specific HER2 phosphorylation sites, which assumes two distinct conformations. Unique structural properties of PTPN18 contribute to the regulation of sub-cellular phosphorylation networks downstream of HER2, which are required for inhibition of HER2-mediated cell growth and migration. Whereas the catalytic domain of PTPN18 blocks lysosomal routing and delays the degradation of HER2 by dephosphorylation of HER2 on pY(1112), the PEST domain of PTPN18 promotes K48-linked HER2 ubiquitination and its rapid destruction via the proteasome pathway and an HER2 negative feedback loop. In agreement with the negative regulatory role of PTPN18 in HER2 signaling, the HER2/PTPN18 ratio was correlated with breast cancer stage. Taken together, our study presents a structural basis for selective HER2 dephosphorylation, a previously uncharacterized mechanism for HER2 degradation and a novel function for the PTPN18 PEST domain. The new regulatory role of the PEST domain in the ubiquitination pathway will broaden our understanding of the functions of other important PEST domain-containing phosphatases, such as LYP and PTPN12.},
}
@article {pmid25079858,
year = {2014},
author = {Picelli, S and Björklund, AK and Reinius, B and Sagasser, S and Winberg, G and Sandberg, R},
title = {Tn5 transposase and tagmentation procedures for massively scaled sequencing projects.},
journal = {Genome research},
volume = {24},
number = {12},
pages = {2033-2040},
pmid = {25079858},
issn = {1549-5469},
support = {243066/ERC_/European Research Council/International ; },
mesh = {DNA, Complementary ; Gene Expression ; *Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Recombinant Proteins ; Saccharomyces cerevisiae/genetics/metabolism ; Sequence Analysis, RNA ; Single-Cell Analysis ; Transposases/genetics/*metabolism ; },
abstract = {Massively parallel DNA sequencing of thousands of samples in a single machine-run is now possible, but the preparation of the individual sequencing libraries is expensive and time-consuming. Tagmentation-based library construction, using the Tn5 transposase, is efficient for generating sequencing libraries but currently relies on undisclosed reagents, which severely limits development of novel applications and the execution of large-scale projects. Here, we present simple and robust procedures for Tn5 transposase production and optimized reaction conditions for tagmentation-based sequencing library construction. We further show how molecular crowding agents both modulate library lengths and enable efficient tagmentation from subpicogram amounts of cDNA. The comparison of single-cell RNA-sequencing libraries generated using produced and commercial Tn5 demonstrated equal performances in terms of gene detection and library characteristics. Finally, because naked Tn5 can be annealed to any oligonucleotide of choice, for example, molecular barcodes in single-cell assays or methylated oligonucleotides for bisulfite sequencing, custom Tn5 production and tagmentation enable innovation in sequencing-based applications.},
}
@article {pmid25079766,
year = {2014},
author = {Maximino, C and da Silva, AW and Araújo, J and Lima, MG and Miranda, V and Puty, B and Benzecry, R and Picanço-Diniz, DL and Gouveia, A and Oliveira, KR and Herculano, AM},
title = {Fingerprinting of psychoactive drugs in zebrafish anxiety-like behaviors.},
journal = {PloS one},
volume = {9},
number = {7},
pages = {e103943},
pmid = {25079766},
issn = {1932-6203},
mesh = {Animals ; Anti-Anxiety Agents/*pharmacology ; Anxiety/*drug therapy ; Buspirone/pharmacology ; Caffeine/pharmacology ; Diazepam/pharmacology ; Drug Evaluation, Preclinical ; Freezing Reaction, Cataleptic/drug effects ; Serotonin/metabolism ; Swimming ; Zebrafish ; },
abstract = {A major hindrance for the development of psychiatric drugs is the prediction of how treatments can alter complex behaviors in assays which have good throughput and physiological complexity. Here we report the development of a medium-throughput screen for drugs which alter anxiety-like behavior in adult zebrafish. The observed phenotypes were clustered according to shared behavioral effects. This barcoding procedure revealed conserved functions of anxiolytic, anxiogenic and psychomotor stimulating drugs and predicted effects of poorly characterized compounds on anxiety. Moreover, anxiolytic drugs all decreased, while anxiogenic drugs increased, serotonin turnover. These results underscore the power of behavioral profiling in adult zebrafish as an approach which combines throughput and physiological complexity in the pharmacological dissection of complex behaviors.},
}
@article {pmid25078790,
year = {2014},
author = {Teng, JE and Thomson, DR and Lascher, JS and Raymond, M and Ivers, LC},
title = {Using Mobile Health (mHealth) and geospatial mapping technology in a mass campaign for reactive oral cholera vaccination in rural Haiti.},
journal = {PLoS neglected tropical diseases},
volume = {8},
number = {7},
pages = {e3050},
pmid = {25078790},
issn = {1935-2735},
support = {R01 AI099243/AI/NIAID NIH HHS/United States ; R01 HD057627/HD/NICHD NIH HHS/United States ; R01AI099243/AI/NIAID NIH HHS/United States ; R01HD057627/HD/NICHD NIH HHS/United States ; },
mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; Cholera/*epidemiology/immunology/*prevention &amp; control ; Cholera Vaccines/*administration &amp; dosage ; Female ; Haiti/epidemiology ; Humans ; Infant ; Male ; Middle Aged ; Rural Population ; Telemedicine/*organization &amp; administration ; Vaccination/*methods/*statistics &amp; numerical data ; Young Adult ; },
abstract = {BACKGROUND: In mass vaccination campaigns, large volumes of data must be managed efficiently and accurately. In a reactive oral cholera vaccination (OCV) campaign in rural Haiti during an ongoing epidemic, we used a mobile health (mHealth) system to manage data on 50,000 participants in two isolated communities.<br><br>METHODS: Data were collected using 7-inch tablets. Teams pre-registered and distributed vaccine cards with unique barcodes to vaccine-eligible residents during a census in February 2012. First stored on devices, data were uploaded nightly via Wi-fi to a web-hosted database. During the vaccination campaign between April and June 2012, residents presented their cards at vaccination posts and their barcodes were scanned. Vaccinee data from the census were pre-loaded on tablets to autopopulate the electronic form. Nightly analysis of the day's community coverage informed the following day's vaccination strategy. We generated case-finding reports allowing us to identify those who had not yet been vaccinated.<br><br>RESULTS: During 40 days of vaccination, we collected approximately 1.9 million pieces of data. A total of 45,417 people received at least one OCV dose; of those, 90.8% were documented to have received 2 doses. Though mHealth required up-front financial investment and training, it reduced the need for paper registries and manual data entry, which would have been costly, time-consuming, and is known to increase error. Using Global Positioning System coordinates, we mapped vaccine posts, population size, and vaccine coverage to understand the reach of the campaign. The hardware and software were usable by high school-educated staff.<br><br>CONCLUSION: The use of mHealth technology in an OCV campaign in rural Haiti allowed timely creation of an electronic registry with population-level census data, and a targeted vaccination strategy in a dispersed rural population receiving a two-dose vaccine regimen. The use of mHealth should be strongly considered in mass vaccination campaigns in future initiatives.},
}
@article {pmid25078035,
year = {2014},
author = {Hoop, M and Paunescu, D and Stoessel, PR and Eichenseher, F and Stark, WJ and Grass, RN},
title = {PCR quantification of SiO2 particle uptake in cells in the ppb and ppm range via silica encapsulated DNA barcodes.},
journal = {Chemical communications (Cambridge, England)},
volume = {50},
number = {73},
pages = {10707-10709},
doi = {10.1039/c4cc04480k},
pmid = {25078035},
issn = {1364-548X},
mesh = {Cell Line, Tumor ; DNA Probes/*chemistry/*metabolism ; Humans ; Microscopy, Confocal ; Nanoparticles/*analysis/chemistry/*metabolism ; Particle Size ; *Polymerase Chain Reaction ; Silicon Dioxide/*analysis/chemistry/*metabolism ; },
abstract = {There is a strong interest in studying the cellular uptake of silica nanoparticles, particularly at medically relevant concentrations (ppb-ppm range) to understand their toxicology. At present, uptake analysis at these exposure levels is impeded by the high silica background concentration. Here we describe the use of DNA encapsulated within silica particles as a tool to quantify silica nanoparticles in in vitro cell-uptake experiments at low concentrations (down to 10 fg cell(-1)).},
}
@article {pmid25076805,
year = {2014},
author = {Hametner, C and Stocker-Wörgötter, E and Grube, M},
title = {New insights into diversity and selectivity of trentepohlialean lichen photobionts from the extratropics.},
journal = {Symbiosis (Philadelphia, Pa.)},
volume = {63},
number = {1},
pages = {31-40},
pmid = {25076805},
issn = {0334-5114},
abstract = {Aerial green algae of Trentepohliaceae can form conspicuous free-living colonies, be parasites of plants or photobionts of lichen-forming ascomycetes. So far, their diversity in temperate regions is still poorly known as it has been mostly studied by phenotypic approaches only. We present new insights in the phylogenetic relationships of lichenized representatives from temperate and Mediterranean parts of Europe by analysis of 18S rRNA and rbcL gene fragments, and nuclear ITS sequence data. For this purpose we isolated the trentepohlialean photobionts from lichens representing different genera. Algal cultures from lichenized and free-living Trentepohliaceae were used to design new primers for amplification of the marker loci. We constructed a phylogenetic hypothesis to reveal the phylogenetic placements of lichenized lineages with 18S rRNA and rbcL sequences. ITS variation among the clades was substantial and did not allow including them in the general phylogenetic assessment, yet ITS appears to be a promising marker for DNA-barcoding approaches. Specific algae were found in particular lichen but the overall diversity of photobionts was limited. The multilocus tree does not support the current morphological classification of genera in Trentepohliaceae, suggesting that morphology is more variable than previously thought in this group of algae.},
}
@article {pmid25074903,
year = {2014},
author = {Spence, ML and Storrs, KR and Arnold, DH},
title = {Why the long face? The importance of vertical image structure for biological "barcodes" underlying face recognition.},
journal = {Journal of vision},
volume = {14},
number = {8},
pages = {25},
doi = {10.1167/14.8.25},
pmid = {25074903},
issn = {1534-7362},
mesh = {Adolescent ; Adult ; *Face ; Female ; Humans ; Male ; Pattern Recognition, Visual/*physiology ; Recognition, Psychology/*physiology ; Young Adult ; },
abstract = {Humans are experts at face recognition. The mechanisms underlying this complex capacity are not fully understood. Recently, it has been proposed that face recognition is supported by a coarse-scale analysis of visual information contained in horizontal bands of contrast distributed along the vertical image axis-a biological facial "barcode" (Dakin &amp; Watt, 2009). A critical prediction of the facial barcode hypothesis is that the distribution of image contrast along the vertical axis will be more important for face recognition than image distributions along the horizontal axis. Using a novel paradigm involving dynamic image distortions, a series of experiments are presented examining famous face recognition impairments from selectively disrupting image distributions along the vertical or horizontal image axes. Results show that disrupting the image distribution along the vertical image axis is more disruptive for recognition than matched distortions along the horizontal axis. Consistent with the facial barcode hypothesis, these results suggest that human face recognition relies disproportionately on appropriately scaled distributions of image contrast along the vertical image axis.},
}
@article {pmid25071381,
year = {2014},
author = {Lee, WD and Lee, H and Fong, JJ and Oh, SY and Park, MS and Quan, Y and Jung, PE and Lim, YW},
title = {A checklist of the basidiomycetous macrofungi and a record of five new species from mt. Oseo in Korea.},
journal = {Mycobiology},
volume = {42},
number = {2},
pages = {132-139},
pmid = {25071381},
issn = {1229-8093},
abstract = {Basidiomycetous macrofungi play important roles in maintaining forest ecosystems via carbon cycling and the mobilization of nitrogen and phosphorus. To understand the impact of human activity on macrofungi, an ongoing project at the Korea National Arboretum is focused on surveying the macrofungi in unexploited areas. Mt. Oseo was targeted in this survey because the number of visitors to this destination has been steadily increasing, and management and conservation plans for this destination are urgently required. Through 5 field surveys of Mt. Oseo from April to October 2012, 116 specimens of basidiomycetous macrofungi were collected and classified. The specimens were identified to the species level by analyzing their morphological characteristics and their DNA sequence data. A total of 80 species belonging to 57 genera and 25 families were identified. To the best of our knowledge, this is the first study to identify five of these species-Artomyces microsporus, Hymenopellis raphanipes, Pholiota abietis, Phylloporus brunneiceps, and Sirobasidium magnum-in Korea.},
}
@article {pmid25071377,
year = {2014},
author = {Kim, H and You, YH and Yoon, H and Seo, Y and Kim, YE and Choo, YS and Lee, IJ and Shin, JH and Kim, JG},
title = {Culturable fungal endophytes isolated from the roots of coastal plants inhabiting korean East coast.},
journal = {Mycobiology},
volume = {42},
number = {2},
pages = {100-108},
pmid = {25071377},
issn = {1229-8093},
abstract = {Twelve plant species were collected from the east coast of Korea to identify culturable endophytes present in their roots. The fungal internal transcribe spacer (ITS) region (ITS1-5.8SrRNA-ITS2) was used as a DNA barcode for identification of fungi. A total of 194 fungal strains were identified and categorized into 31 genera. The genus Penicillium accounted for the largest number of strains, followed by the genus Aspergillus. Furthermore, using 5 statistical methods, the diversity indices of the fungi were calculated at the genus level. After comprehensive evaluation, the endophytic fungal group from Phragmites australis ranked highest in diversity analyses. Several strains responsible for plant growth and survival (Penicillium citrinum, P. funiculosum, P. janthinellum, P. restrictum, and P. simplicissimum), were also identified. This study provides basic data on the sheds light on the symbiotic relationship between coastal plants and fungi.},
}
@article {pmid25069164,
year = {2014},
author = {He, Y and Wan, F and Xiong, L and Li, DM and Peng, C},
title = {Identification of two chemotypes of Pogostemon cablin (Blanco) Benth. through DNA barcodes.},
journal = {Zeitschrift fur Naturforschung. C, Journal of biosciences},
volume = {69},
number = {5-6},
pages = {253-258},
doi = {10.5560/znc.2013-0180},
pmid = {25069164},
issn = {0939-5075},
mesh = {Base Sequence ; *DNA Barcoding, Taxonomic ; DNA Primers ; DNA, Plant/*genetics ; Lamiaceae/*classification/genetics ; Polymerase Chain Reaction ; },
abstract = {Pogostemon cablin (Blanco) Benth. is an important medicinal plant in Traditional Chinese Medicine (TCM). Because of differences in the chemical composition, this species has been classified into two major chemotypes, i. e. the patchouliol-type and the pogostone-type; however, no quick and effective method is presently available for the precise identification of these two chemotypes. DNA barcoding, using a standardized DNA fragment, is a promising molecular diagnostic method for species identification. We have established a reliable and quick method for the identification of the P. cablin chemotypes. Of five potential barcodes [rbcL, psbA-trnH, rpoB, ITS (internal transcibed spacer), and ndhJ], tested among 103 samples, ITS was the best candidate, as comparative studies between patchouliol-type and pogostone-type P. cablin revealed that ITS had more variable regions among these five barcodes. We suggest that ITS can serve as the most suitable barcode for differentiating between the chemotypes of P. cablin.},
}
@article {pmid25065134,
year = {2014},
author = {Glowska, E and Dragun-Damian, A and Broda, L and Dabert, J and Dabert, M},
title = {DNA barcodes reveal female dimorphism in syringophilid mites (Actinotrichida: Prostigmata: Cheyletoidea): Stibarokris phoeniconaias and Ciconichenophilus phoeniconaias are conspecific.},
journal = {Folia parasitologica},
volume = {61},
number = {3},
pages = {272-276},
doi = {10.14411/fp.2014.030},
pmid = {25065134},
issn = {0015-5683},
mesh = {Animals ; Bird Diseases/parasitology ; Birds ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics/metabolism ; Female ; Male ; Mite Infestations/parasitology/veterinary ; Mites/*classification/*genetics ; RNA, Ribosomal, 28S/genetics ; Sex Factors ; Species Specificity ; },
abstract = {Here we present the first evidence of female dimorphism in ectoparasitic quill mites of the family Syringophilidae (Actinotrichida: Prostigmata: Cheyletoidea). Stibarokris phoeniconaias Skoracki et OConnor, 2010 and Ciconichenophilus phoeniconaias Skoracki et OConnor, 2010 so far have been treated as two distinct species cohabiting inside the quills of feathers of the lesser flamingo Phoeniconaias minor (Geoffroy Saint-Hilaire) and the American flamingo Phoenicopterus ruber Linnaeus. Although females of these species differ morphologically by the extent of body sclerotisation, presence/absence of lateral hypostomal teeth, and shape of dorsal setae, their important common features are the lack of leg setae vs II, and both stylophore and peritremes shape. Here, we apply the DNA barcode markers to test whether the differences between S. phoeniconaias and C. phoeniconaias have a genetic basis, indicating that they really are distinct taxa, or whether they just represent two morphs of a single species. All analysed sequences (616 bp for COI and 1159 bp for 28S rDNA) obtained for specimens representing females of both studied taxa as well as male, tritonymph, protonymph and larva of S. phoeniconaias were identical, which indicates that S. phoeniconaias and C. phoeniconaias are conspecific. The formal taxonomic consequence of our results is denial of the genus status of Ciconichenophilus Skoracki et OConnor, 2010 and species status of C. phoeniconaias, and recommendation that they should be treated as junior synonyms of Stibarokris Kethley, 1970 and S. phoeniconaias, respectively.},
}
@article {pmid25065127,
year = {2014},
author = {Bueno-Silva, M and Boeger, WA},
title = {Neotropical Monogenoidea. 58. Three new species of Gyrodactylus (Gyrodactylidae) from Scleromystax spp. (Callichthyidae) and the proposal of COII gene as an additional fragment for barcoding gyrodactylids.},
journal = {Folia parasitologica},
volume = {61},
number = {3},
pages = {213-222},
doi = {10.14411/fp.2014.028},
pmid = {25065127},
issn = {0015-5683},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics/*metabolism ; Fish Diseases/*parasitology ; Fishes ; *Genetic Markers ; Male ; Species Specificity ; Trematoda/classification/*enzymology/*genetics ; Trematode Infections/parasitology/veterinary ; },
abstract = {Based on molecular markers (COII and ITS1-ITS2) and morphological data, we describe three new Neotropical species of Gyrodactylus von Nordmann, 1832 from Scleromystax barbatus (Quoy et Gaimard) and Scleromystax macropterus (Regan) from southern Brazil. The three new species can be distinguished from each other by sequences of both molecular markers and morphology of hooks and anchors. Gyrodactylus bueni sp. n. is characterised by having hook with shaft curved, heel straight, shelf straight, toe pointed, anchor with superficial root slender, elongate and male copulatory organ armed with two rows of spinelets. Gyrodactylus major sp. n. presents hook with shaft, point curved, proximal shaft straight, heel convex, shelf convex, toe concave, anchor with superficial root robust and male copulatory organ armed with two rows of spinelets. Gyrodactylus scleromystaci sp. n. presents hook with shaft, point recurved, heel convex, shelf convex, toe pointed, anchor with superficial root curved and male copulatory organ armed with two rows of spinelets. These species appear to be closely related to other species of Gyrodactylus known from other species of Callichthyidae. These new species, however, differ by the comparative morphology of the haptoral hard structures and molecular data. Comparative analysis of sequences from these species of Gyrodactylus suggests that the COII gene may represent an important marker for the taxonomy of species of Gyrodactylidae and, perhaps, for species of other lineages of Monogenoidea.},
}
@article {pmid25062640,
year = {2014},
author = {Bystrykh, LV and de Haan, G and Verovskaya, E},
title = {Barcoded vector libraries and retroviral or lentiviral barcoding of hematopoietic stem cells.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1185},
number = {},
pages = {345-360},
doi = {10.1007/978-1-4939-1133-2_23},
pmid = {25062640},
issn = {1940-6029},
mesh = {Cell Proliferation ; Clone Cells/cytology/metabolism ; DNA Barcoding, Taxonomic ; Escherichia coli/genetics ; *Gene Library ; Genetic Vectors/*genetics ; HEK293 Cells ; Hematopoietic Stem Cells/*cytology/*metabolism ; Humans ; Lentivirus/*genetics ; Sequence Analysis, DNA ; Transduction, Genetic ; Transformation, Genetic ; },
abstract = {Cellular barcoding is a relatively recent technique aimed at clonal analysis of a proliferating cell population of any kind. The method was shown to be particularly successful in monitoring clonal contributions of hematopoietic stem cells (HSCs). An essential step of the method is retroviral or lentiviral labeling of the hematopoietic cells. The unique feature of the method is the generation of a vector library containing specific artificial DNA tags, generally known as barcodes. The library must satisfy multiple essential requirements. Importantly, considering the number of possible variations within the barcode sequence, the actual size of the barcoded vector library, and the number of clonogenic (stem) cells in the given experiment should be in ratios far from saturation. Excessive bias in barcodes frequencies must be avoided, and the library size must be assessed prior to the sequencing analysis. The final sequencing results must undergo statistical filtering. If all requirements are met, the method ensures profound sensitivity and accuracy for monitoring of the clonal fluctuations in a wide range of biological experiments.},
}
@article {pmid25061844,
year = {2014},
author = {Franzini, RM and Samain, F and Abd Elrahman, M and Mikutis, G and Nauer, A and Zimmermann, M and Scheuermann, J and Hall, J and Neri, D},
title = {Systematic evaluation and optimization of modification reactions of oligonucleotides with amines and carboxylic acids for the synthesis of DNA-encoded chemical libraries.},
journal = {Bioconjugate chemistry},
volume = {25},
number = {8},
pages = {1453-1461},
doi = {10.1021/bc500212n},
pmid = {25061844},
issn = {1520-4812},
mesh = {Aldehydes/chemistry ; Amination ; Amines/*chemistry ; Carboxylic Acids/*chemistry ; Chemistry Techniques, Synthetic ; DNA/*chemistry ; Ion Exchange Resins/chemistry ; Oligonucleotides/*chemistry ; Oxidation-Reduction ; Small Molecule Libraries/*chemical synthesis/*chemistry ; },
abstract = {DNA-encoded chemical libraries are collections of small molecules, attached to DNA fragments serving as identification barcodes, which can be screened against multiple protein targets, thus facilitating the drug discovery process. The preparation of large DNA-encoded chemical libraries crucially depends on the availability of robust synthetic methods, which enable the efficient conjugation to oligonucleotides of structurally diverse building blocks, sharing a common reactive group. Reactions of DNA derivatives with amines and/or carboxylic acids are particularly attractive for the synthesis of encoded libraries, in view of the very large number of building blocks that are commercially available. However, systematic studies on these reactions in the presence of DNA have not been reported so far. We first investigated conditions for the coupling of primary amines to oligonucleotides, using either a nucleophilic attack on chloroacetamide derivatives or a reductive amination on aldehyde-modified DNA. While both methods could be used for the production of secondary amines, the reductive amination approach was generally associated with higher yields and better purity. In a second endeavor, we optimized conditions for the coupling of a diverse set of 501 carboxylic acids to DNA derivatives, carrying primary and secondary amine functions. The coupling efficiency was generally higher for primary amines, compared to secondary amine substituents, but varied considerably depending on the structure of the acids and on the synthetic methods used. Optimal reaction conditions could be found for certain sets of compounds (with conversions >80%), but multiple reaction schemes are needed when assembling large libraries with highly diverse building blocks. The reactions and experimental conditions presented in this article should facilitate the synthesis of future DNA-encoded chemical libraries, while outlining the synthetic challenges that remain to be overcome.},
}
@article {pmid25061381,
year = {2014},
author = {Schmidt, BC and Anweiler, GG},
title = {Taxonomy and biogeography of the Nearctic Raphia Hübner (Lepidoptera, Noctuidae, Raphiinae).},
journal = {ZooKeys},
volume = {},
number = {421},
pages = {91-113},
pmid = {25061381},
issn = {1313-2989},
abstract = {The taxonomic status and biogeography of the North American Raphia species is reviewed using adult morphology, larval host plants, geographic phenotypic variation, and variation of mtDNA COI barcode sequences. Lack of diagnostic morphological differences, combined with relatively low mtDNA barcode divergences and clinal phenotypic variation in key geographic regions indicate that the six previously recognized species of North American Raphia are best interpreted as parapatric subspecies. Raphia frater abrupta Grote, stat. n., R. f. coloradensis Putnam-Cramer, stat. r., R. f. piazzi Hill, stat. n., and R. f. elbea Smith, stat. n., are accordingly revised to subspecies of R. frater Grote. Type locality restrictions are provided for Raphia abrupta and Raphia frater and a neotype is designated for Raphia frater var. coloradensis.},
}
@article {pmid25061379,
year = {2014},
author = {Chacón, IA and Janzen, DH and Hallwachs, W},
title = {Four new species of Symmerista Hübner, 1816 (Notodontidae, Nystaleinae) from Costa Rica.},
journal = {ZooKeys},
volume = {},
number = {421},
pages = {39-63},
pmid = {25061379},
issn = {1313-2989},
abstract = {The genus Symmerista Hübner (Notodontidae, Nystaleinae) is reviewed for Costa Rica, based on 49 wild-caught specimens. Four species are newly described: Symmerista luisdiegogomezi Chacón, Symmerista inbioi Chacón, Symmerista minaei Chacón and Symmerista aura Chacón. All are from the cloud forests of the Talamanca moutain range, southern Costa Rica. Photographs of the adults, male and female genitalia, and barcodes are also provided. The species Symmerista tlotzin Schaus (1892) is removed from Symmerista and assigned to the genus Elymiotis Walker as a new combination.},
}
@article {pmid25061377,
year = {2014},
author = {Sullivan, JB},
title = {The Phyllodonta latrata (Guenée) species group in Costa Rica (Geometridae, Ennominae).},
journal = {ZooKeys},
volume = {},
number = {421},
pages = {3-19},
pmid = {25061377},
issn = {1313-2989},
abstract = {Historically, the name Phyllodonta latrata (Guenée) has been applied to what is a complex of three undescribed species in Costa Rica. They are very similar in maculation, but can be differentiated by genitalic characters and barcodes. P. alajuela Sullivan, sp. n. occurs at lower altitudes in the northwestern part of Costa Rica whereas P. intermediata Sullivan, sp. n. and P. esperanza Sullivan, sp. n. are found at partially overlapping altitudes in the central mountain ranges.},
}
@article {pmid25058465,
year = {2014},
author = {Ergunay, K and Gunay, F and Erisoz Kasap, O and Oter, K and Gargari, S and Karaoglu, T and Tezcan, S and Cabalar, M and Yildirim, Y and Emekdas, G and Alten, B and Ozkul, A},
title = {Serological, molecular and entomological surveillance demonstrates widespread circulation of West Nile virus in Turkey.},
journal = {PLoS neglected tropical diseases},
volume = {8},
number = {7},
pages = {e3028},
pmid = {25058465},
issn = {1935-2735},
mesh = {Animals ; Birds/*virology ; Culicidae/*virology ; Horses/virology ; Humans ; Molecular Sequence Data ; Public Health Surveillance ; Turkey/epidemiology ; *West Nile Fever/epidemiology/veterinary/virology ; *West Nile virus ; },
abstract = {West Nile virus (WNV), a mosquito-borne flavivirus with significant impact on human and animal health, has recently demonstrated an expanded zone of activity globally. The aim of this study is to investigate the frequency and distribution of WNV infections in potential vectors and several mammal and avian species in Turkey, where previous data indicate viral circulation. The study was conducted in 15 provinces across Turkey during 2011-2013. In addition, the entomological study was extended to 4 districts of the Turkish Republic of Northern Cyprus. WNV exposure was determined in humans, horses, sheep and ducks from Mersin, Sanliurfa, Van and Kars provinces of Turkey, via the detection of neutralizing antibodies. WNV RNA was sought in human and equine samples from Mersin, Adana and Mugla provinces. Field-collected mosquitoes from 92 sites at 46 locations were characterized morphologically and evaluated for viral RNA. Neutralizing antibodies were identified in 10.5% of the 1180 samples studied and detected in all species evaluated. Viral nucleic acids were observed in 5.9% of 522 samples but only in horses. A total of 2642 mosquito specimens belonging to 15 species were captured, where Ochlerotatus caspius (52.4%), Culex pipiens sensu lato (24.2%) comprise the most frequent species. WNV RNA was detected in 4 mosquito pools (1.9%), that comprise Oc. caspius Cx. pipiens s.l. and DNA barcoding revealed the presence of Cx. quinquefasciatus and Cx. perexiguus mosquitoes in infected Culex pools. All WNV partial sequences were characterized as lineage 1 clade 1a. These findings indicate a widespread WNV activity in Turkey, in Eastern Thrace and Mediterranean-Aegean regions as well as Southeastern and Northeastern Anatolia.},
}
@article {pmid25057250,
year = {2014},
author = {Ramaraj, P and Selvakumar, C and Ganesh, A and Janarthanan, S},
title = {Report on the occurrence of synanthropic derived form of Chrysomyamegacephala (Diptera: Calliphoridae) from Royapuram fishing harbour, Chennai, Tamil Nadu, India.},
journal = {Biodiversity data journal},
volume = {},
number = {2},
pages = {e1111},
pmid = {25057250},
issn = {1314-2828},
abstract = {The occurrence of dipteran fly, Chrysomyamegacephala (Fabricius, 1794) is reported for the first time from Royapuram fishing harbour (Chennai), Tamil Nadu, South East India. The fully grown third instar larvae of Chrysomyamegacephala were collected from decaying fishes near Royapuram fishing harbour. This site is found to be the regular breeding site for Chrysomyamegacephala. Larvae were reared under laboratory condition and freshly emerged adult flies from pupae were collected and identified by morphological features and molecular tools. Molecular identification through generation of DNA barcoding using mitochondrial COI gene of Chrysomyamegacephala is appended.},
}
@article {pmid25056834,
year = {2014},
author = {Spurgeon, BE and Aburima, A and Oberprieler, NG and Taskén, K and Naseem, KM},
title = {Multiplexed phosphospecific flow cytometry enables large-scale signaling profiling and drug screening in blood platelets.},
journal = {Journal of thrombosis and haemostasis : JTH},
volume = {12},
number = {10},
pages = {1733-1743},
doi = {10.1111/jth.12670},
pmid = {25056834},
issn = {1538-7836},
mesh = {Animals ; Antibodies/chemistry ; Blood Platelets/*drug effects ; Cell Adhesion Molecules/metabolism ; Cyclic AMP/metabolism ; Cyclic AMP-Dependent Protein Kinases/metabolism ; Drug Design ; *Drug Evaluation, Preclinical ; Electrophoresis ; *Flow Cytometry ; Fluorescent Dyes/chemistry ; Humans ; Mice ; Microfilament Proteins/metabolism ; Phosphoproteins/metabolism ; Phosphorylation ; Platelet Aggregation ; Platelet Aggregation Inhibitors/chemistry ; Prostaglandins/chemistry ; Signal Transduction ; Vasodilator-Stimulated Phosphoprotein ; },
abstract = {BACKGROUND: Dissecting the signaling events that contribute to platelet activation will increase our understanding of platelet function and aid in the development of new antiplatelet agents. However, high-throughput methodology for the quantitative analysis of platelet signaling events is still lacking.<br><br>OBJECTIVE: To develop a high-throughput assay for the analysis of platelet signaling events in whole blood.<br><br>METHODS AND RESULTS: We developed a fluorescent barcoding protocol to facilitate multiplexing and enable large-scale signaling profiling in platelets in whole blood. The methodology allowed simultaneous staining and acquisition of 24-96 samples in a single analysis tube with a standard flow cytometer. This approach significantly reduced experimental numbers, data acquisition time, and antibody consumption, while providing automated statistically rich quantitative data on signaling events. Using vasodilator-stimulated phosphoprotein (VASP), an established marker of platelet inhibition and antiplatelet drug therapy, we demonstrated that the assay could detect subtle changes in phosphoVASP-Ser157/239 in response to cAMP-elevating agents of varying potency and known modulators of the cAMP signaling cascade. The assay could be used with washed platelets or whole blood, analyzed immediately or frozen, without any significant change in assay performance. To demonstrate the usefulness of the assay as a drug discovery platform, we examined a prostaglandin screening library. Our screen of 70 prostaglandin derivatives revealed three previously uncharacterized lipids that stimulated phosphorylation of VASP-Ser157. Follow-up analyses demonstrated that these agents elevated intraplatelet cAMP and inhibited collagen-induced platelet aggregation.<br><br>CONCLUSIONS: This novel method enables rapid, large-scale quantitative signaling profiling and compound screening in human platelets present in whole blood.},
}
@article {pmid25050928,
year = {2014},
author = {Ponce de León, JL and León, G and Rodríguez, R and Metcalfe, CJ and Hernández, D and Casane, D and García-Machado, E},
title = {Phylogeography of Cuban Rivulus: evidence for allopatric speciation and secondary dispersal across a marine barrier.},
journal = {Molecular phylogenetics and evolution},
volume = {79},
number = {},
pages = {404-414},
doi = {10.1016/j.ympev.2014.07.007},
pmid = {25050928},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Cell Nucleus/genetics ; Cuba ; Cyprinodontiformes/anatomy &amp; histology/*classification/genetics ; DNA, Mitochondrial/genetics ; Female ; *Genetic Speciation ; Genetic Variation ; Haplotypes ; Likelihood Functions ; Male ; Models, Genetic ; *Phylogeny ; Phylogeography ; Pigmentation ; Sequence Analysis, DNA ; },
abstract = {The genus Rivulus is currently comprised of two species, R. cylindraceus and R. insulaepinorum, which are endemic to Cuba. However, the taxonomic status of the latter species remains dubious because of the poor quality of the original description. In addition, a recent barcoding survey suggests that the two species may be conspecific. The aim of this study was to test the hypothesis that the two species represent a single evolutionary clade. To delimit the species and their evolutionary history, we used a combination of molecular phylogenetic analyses, with both mitochondrial and nuclear sequences, tests of phylogeographic hypotheses, combined with morphological measurements and information on known dispersal barriers and species distribution. None of the data sets support R. insulaepinorum and R. cylindraceus as separate taxa. However, a new species, restricted to the northwestern part of the main island, was identified by phylogenetic analyses, body colour pattern and geographical distribution. The evolutionary distance between the two lineages (cytb, d=15%; CAM-4, d=2.5%) indicates a long period of divergence. Phylogeographic analyses shed light on the dispersal history of R. cylindraceus, which probably originated on the Isla de la Juventud. They also suggest that each lineage had contrasting histories; Rivulus sp. is restricted to a relatively small geographic area whereas R. cylindraceus has dispersed considerably and more than once from its centre of origin, probably facilitated by sea level fluctuations. These results strengthen previous findings, i.e. that the diversity of Cuban freshwater fishes is far from well-known and deserves more in-depth studies, and that vicariance and dispersal events have resulted in a complex biogeographical landscape which has had a significant impact on the freshwater fishes of the Caribbean islands.},
}
@article {pmid25048292,
year = {2014},
author = {Mahadani, P and Ghosh, SK},
title = {Utility of indels for species-level identification of a biologically complex plant group: a study with intergenic spacer in Citrus.},
journal = {Molecular biology reports},
volume = {41},
number = {11},
pages = {7217-7222},
pmid = {25048292},
issn = {1573-4978},
mesh = {Base Sequence ; Citrus/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; DNA, Chloroplast/*genetics ; DNA, Intergenic/*genetics ; INDEL Mutation/*genetics ; India ; Molecular Sequence Data ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The Consortium of Barcode of Life plant working group proposed to use the defined portion of plastid genes rbcL and matK either singly or in combination as the standard DNA barcode for plants. But DNA barcode based identification of biologically complex plant groups are always a challenging task due to the occurrence of natural hybridization. Here, we examined the use of indels polymorphism in trnH-psbA and trnL-trnF sequences for rapid species identification of citrus. DNA from young leaves of selected citrus species were isolated and matK gene (~800 bp) and trnH-psbA spacer (~450 bp) of Chloroplast DNA was amplified for species level identification. The sequences within the group taxa of Citrus were aligned using the ClustalX program. With few obvious misalignments were corrected manually using the similarity criterion. We identified a 54 bp inverted repeat or palindrome sequence (27-80 regions) and 6 multi residues indel coding regions. Large inverted repeats in cpDNA provided authentication at the higher taxonomic levels. These diagnostics indel marker from trnH-psbA were successful in identifying different species (5 out of 7) within the studied Citrus except Citrus limon and Citrus medica. These two closely related species are distinguished through the 6 bp deletion in trnL-trnF. This study demonstrated that the indel polymorphism based approach easily characterizes the Citrus species and the same may be applied in other complex groups. Likewise other indels occurring intergenic spacer of chloroplast regions may be tested for rapid identification of other secondary citrus species.},
}
@article {pmid25042453,
year = {2014},
author = {Zhang, Y and Li, L and Yan, TL and Liu, Q},
title = {Complete chloroplast genome sequences of Praxelis (Eupatorium catarium Veldkamp), an important invasive species.},
journal = {Gene},
volume = {549},
number = {1},
pages = {58-69},
doi = {10.1016/j.gene.2014.07.041},
pmid = {25042453},
issn = {1879-0038},
mesh = {Asteraceae/classification/genetics ; Chloroplast Proteins/*genetics/metabolism ; DNA, Chloroplast/genetics ; Eupatorium/*classification/*genetics/metabolism ; Evolution, Molecular ; Genes, Plant ; *Genome, Chloroplast ; Genome, Plant ; Microsatellite Repeats ; Phylogeny ; Plant Leaves/genetics ; },
abstract = {Praxelis (Eupatorium catarium Veldkamp) is a new hazardous invasive plant species that has caused serious economic losses and environmental damage in the Northern hemisphere tropical and subtropical regions. Although previous studies focused on detecting the biological characteristics of this plant to prevent its expansion, little effort has been made to understand the impact of Praxelis on the ecosystem in an evolutionary process. The genetic information of Praxelis is required for further phylogenetic identification and evolutionary studies. Here, we report the complete Praxelis chloroplast (cp) genome sequence. The Praxelis chloroplast genome is 151,410 bp in length including a small single-copy region (18,547 bp) and a large single-copy region (85,311 bp) separated by a pair of inverted repeats (IRs; 23,776 bp). The genome contains 85 unique and 18 duplicated genes in the IR region. The gene content and organization are similar to other Asteraceae tribe cp genomes. We also analyzed the whole cp genome sequence, repeat structure, codon usage, contraction of the IR and gene structure/organization features between native and invasive Asteraceae plants, in order to understand the evolution of organelle genomes between native and invasive Asteraceae. Comparative analysis identified the 14 markers containing greater than 2% parsimony-informative characters, indicating that they are potential informative markers for barcoding and phylogenetic analysis. Moreover, a sister relationship between Praxelis and seven other species in Asteraceae was found based on phylogenetic analysis of 28 protein-coding sequences. Complete cp genome information is useful for plant phylogenetic and evolutionary studies within this invasive species and also within the Asteraceae family.},
}
@article {pmid25042335,
year = {2015},
author = {Čandek, K and Kuntner, M},
title = {DNA barcoding gap: reliable species identification over morphological and geographical scales.},
journal = {Molecular ecology resources},
volume = {15},
number = {2},
pages = {268-277},
doi = {10.1111/1755-0998.12304},
pmid = {25042335},
issn = {1755-0998},
mesh = {Anatomy, Comparative ; Animals ; DNA Barcoding, Taxonomic/*methods ; Phylogeography ; Spiders/anatomy &amp; histology/*classification/*genetics ; *Statistics as Topic ; },
abstract = {The philosophical basis and utility of DNA barcoding have been a subject of numerous debates. While most literature embraces it, some studies continue to question its use in dipterans, butterflies and marine gastropods. Here, we explore the utility of DNA barcoding in identifying spider species that vary in taxonomic affiliation, morphological diagnosibility and geographic distribution. Our first test searched for a 'barcoding gap' by comparing intra- and interspecific means, medians and overlap in more than 75,000 computed Kimura 2-parameter (K2P) genetic distances in three families. Our second test compared K2P distances of congeneric species with high vs. low morphological distinctness in 20 genera of 11 families. Our third test explored the effect of enlarging geographical sampling area at a continental scale on genetic variability in DNA barcodes within 20 species of nine families. Our results generally point towards a high utility of DNA barcodes in identifying spider species. However, the size of the barcoding gap strongly depends on taxonomic groups and practices. It is becoming critical to define the barcoding gap statistically more consistently and to document its variation over taxonomic scales. Our results support models of independent patterns of morphological and molecular evolution by showing that DNA barcodes are effective in species identification regardless of their morphological diagnosibility. We also show that DNA barcodes represent an effective tool for identifying spider species over geographic scales, yet their variation contains useful biogeographic information.},
}
@article {pmid25042073,
year = {2015},
author = {Srivathsan, A and Sha, JC and Vogler, AP and Meier, R},
title = {Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey (Pygathrix nemaeus).},
journal = {Molecular ecology resources},
volume = {15},
number = {2},
pages = {250-261},
doi = {10.1111/1755-0998.12302},
pmid = {25042073},
issn = {1755-0998},
mesh = {Animals ; Cercopithecidae/*physiology ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*analysis/*genetics/isolation &amp; purification ; *Diet ; Feces/chemistry ; *Feeding Behavior ; Metagenomics/*methods ; Molecular Sequence Data ; Plants/classification/genetics ; Sequence Analysis, DNA ; },
abstract = {Faecal samples are of great value as a non-invasive means to gather information on the genetics, distribution, demography, diet and parasite infestation of endangered species. Direct shotgun sequencing of faecal DNA could give information on these simultaneously, but this approach is largely untested. Here, we used two faecal samples to characterize the diet of two red-shanked doucs langurs (Pygathrix nemaeus) that were fed known foliage, fruits, vegetables and cereals. Illumina HiSeq produced ~74 and 67 million paired reads for these samples, of which ~ 10,000 (0.014%) and ~ 44,000 (0.066%), respectively, were of chloroplast origin. Sequences were matched against a database of available chloroplast 'barcodes' for angiosperms. The results were compared with 'metabarcoding' using PCR amplification of the P6 loop of trnL. Metagenomics identified seven and nine of the likely 16 diet plants while six and five were identified by metabarcoding. Metabarcoding produced thousands of reads consistent with the known diet, but the barcodes were too short to identify several plant species to genus. Metagenomics utilized multiple, longer barcodes that combined had greater power of identification. However, rare diet items were not recovered. Read numbers for diet species in metagenomic and metabarcoding data were correlated, indicating that both are useful for determining relative sequence abundance. Metagenomic reads were uniformly distributed across the chloroplast genomes; thus, if chloroplast genomes were used as reference, the precision of identifications and species recovery would improve further. Metagenomics also recovered the host mitochondrial genome and numerous intestinal parasite sequences in addition to generating data useful for characterizing the microbiome.},
}
@article {pmid25040425,
year = {2014},
author = {Lee, MY and Munroe, TA and Shao, KT},
title = {Description of a new cryptic, shallow-water tonguefish (Pleuronectiformes: Cynoglossidae: Symphurus) from the western North Pacific Ocean.},
journal = {Journal of fish biology},
volume = {85},
number = {3},
pages = {563-585},
doi = {10.1111/jfb.12440},
pmid = {25040425},
issn = {1095-8649},
mesh = {Animal Fins ; Animals ; Female ; Flatfishes/anatomy &amp; histology/*classification/genetics ; Japan ; Male ; Pacific Ocean ; Pigmentation ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Taiwan ; },
abstract = {Combined results based on morphological characters and analyses of partial sequences of the 16s rRNA and coI genes confirm the validity of a new, cryptic, symphurine tonguefish from the western North Pacific Ocean. Symphurus leucochilus n. sp., a diminutive species reaching sizes to c. 67 mm standard length, is described from nine specimens that were collected from fish-landing ports and from trawls made at c. 150 m off Taiwan and Japan. Symphurus leucochilus shares many similar features with those of Symphurus microrhynchus and that of several undescribed species that are morphologically similar to S. microrhynchus. Symphurus leucochilus has also been misidentified as Symphurus orientalis in fish collections because of shared similarities in some aspects of their morphology. The new species differs from all congeners by the following combination of meristic, morphological and pigmentation features: a predominant 1-2-2-2-2 pattern of interdigitation of proximal dorsal-fin pterygiophores and neural spines; 12 caudal-fin rays; 89-92 dorsal-fin rays; 76-80 anal-fin rays; 49-51 total vertebrae; four hypurals; 75-83 longitudinal scale rows; 32-35 transverse scales; 15-17 scale rows on the head posterior to the lower orbit; absence of a fleshy ridge on the ocular-side lower jaw and a membranous connection between the anterior nostril and lower part of the eye; a narrow interorbital space and dorsal-fin origin anterior to the vertical through the anterior margin of the upper eye; absence of both dermal spots at bases of anterior dorsal-fin rays and melanophores on the isthmus; uniformly yellow to light-brown ocular-side colouration without bands; dorsal and anal fins with alternating series of dark rectangular blotches and unpigmented areas; a uniform white blind side and a bluish-black peritoneum. Despite overall similarities in morphology between S. leucochilus and S. orientalis, as well as between two of the nominal species morphologically similar to S. microrhynchus, analyses of partial 16s rRNA and coI gene sequences show that S. leucochilus, S. orientalis and the two other nominal species represent three distinct lineages within the genus Symphurus.},
}
@article {pmid25031181,
year = {2014},
author = {Gardner, KM and Brown, P and Cooke, TF and Cann, S and Costa, F and Bustamante, C and Velasco, R and Troggio, M and Myles, S},
title = {Fast and cost-effective genetic mapping in apple using next-generation sequencing.},
journal = {G3 (Bethesda, Md.)},
volume = {4},
number = {9},
pages = {1681-1687},
pmid = {25031181},
issn = {2160-1836},
support = {T32 HG000044/HG/NHGRI NIH HHS/United States ; },
mesh = {Chromosome Mapping/*methods ; Color ; DNA, Plant/*genetics ; Fruit ; Genetic Linkage ; Genome, Plant ; Malus/*genetics ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Sequence Analysis, DNA/*methods ; },
abstract = {Next-generation DNA sequencing (NGS) produces vast amounts of DNA sequence data, but it is not specifically designed to generate data suitable for genetic mapping. Recently developed DNA library preparation methods for NGS have helped solve this problem, however, by combining the use of reduced representation libraries with DNA sample barcoding to generate genome-wide genotype data from a common set of genetic markers across a large number of samples. Here we use such a method, called genotyping-by-sequencing (GBS), to produce a data set for genetic mapping in an F1 population of apples (Malus × domestica) segregating for skin color. We show that GBS produces a relatively large, but extremely sparse, genotype matrix: over 270,000 SNPs were discovered but most SNPs have too much missing data across samples to be useful for genetic mapping. After filtering for genotype quality and missing data, only 6% of the 85 million DNA sequence reads contributed to useful genotype calls. Despite this limitation, using existing software and a set of simple heuristics, we generated a final genotype matrix containing 3967 SNPs from 89 DNA samples from a single lane of Illumina HiSeq and used it to create a saturated genetic linkage map and to identify a known QTL underlying apple skin color. We therefore demonstrate that GBS is a cost-effective method for generating genome-wide SNP data suitable for genetic mapping in a highly diverse and heterozygous agricultural species. We anticipate future improvements to the GBS analysis pipeline presented here that will enhance the utility of next-generation DNA sequence data for the purposes of genetic mapping across diverse species.},
}
@article {pmid25026655,
year = {2014},
author = {Mastrangelo, T and Paulo, DF and Bergamo, LW and Morais, EG and Silva, M and Bezerra-Silva, G and Azeredo-Espin, AM},
title = {Detection and genetic diversity of a heliothine invader (Lepidoptera: Noctuidae) from north and northeast of Brazil.},
journal = {Journal of economic entomology},
volume = {107},
number = {3},
pages = {970-980},
doi = {10.1603/ec13403},
pmid = {25026655},
issn = {0022-0493},
mesh = {Animals ; Brazil ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics/metabolism ; *Genetic Variation ; Insect Proteins/*genetics/metabolism ; Larva/genetics/growth &amp; development/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Molecular Sequence Data ; Moths/*classification/genetics/growth &amp; development/*physiology ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; },
abstract = {The cotton bollworm, Helicoverpa armigera (Hübner), was recently introduced in Brazil. During the 2012-2013 harvest, producers reported reduced yields up to 35% on major crops. The economic losses reached US$ 1 billion only in western Bahia, triggering a phytosanitary crisis. The deficiencies in existing taxonomic keys to deal with the morphologically indistinct larvae of H. armigera and the native Helicoverpa zea (Boddie) constrained the detection of new incursions of this heliothine invader. This study explored the identity of heliothine larvae that were found infesting soybean- and corn-growing areas from Roraima state, northern Brazil, through sequences of the mitochondrial cytochrome c oxidase subunit I gene. The inter- and intraspecies sequence variations of DNA barcodes in H. armigera and H. zea were analyzed. The genetic diversity and population structure of the specimens from Roraima and two populations from Piauí and Bahia states, northeastern Brazil, were assessed by adding the cytochrome c oxidase subunit II gene to the analysis. Owing to the lack of studies on genetic introgression for the two species, the suitability of using three different nuclear genes to distinguish the two species was also investigated. The results showed strong evidence that the heliothine larvae from north and northeast of Brazil are conspecific with H. armigera, suggesting that this invasive moth has already crossed the Amazon basin. Surveys in the north of South America should start as soon as possible to monitor the entry or spread of this moth in the Caribbean, Central America, and the United States.},
}
@article {pmid25025532,
year = {2014},
author = {Sakamoto, JM and Goddard, J and Rasgon, JL},
title = {Population and demographic structure of Ixodes scapularis Say in the eastern United States.},
journal = {PloS one},
volume = {9},
number = {7},
pages = {e101389},
pmid = {25025532},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; DNA, Mitochondrial ; Evolution, Molecular ; Female ; Genetic Variation ; Genetics, Population ; Geography ; Haplotypes ; Ixodes/classification/*genetics ; Phylogeny ; Population Dynamics ; RNA, Ribosomal, 16S ; United States ; },
abstract = {INTRODUCTION: The most significant vector of tick-borne pathogens in the United States is Ixodes scapularis Say (the blacklegged tick). Previous studies have identified significant genetic, behavioral and morphological differences between northern vs. southern populations of this tick. Because tick-borne pathogens are dependent on their vectors for transmission, a baseline understanding of the vector population structure is crucial to determining the risks and epidemiology of pathogen transmission.<br><br>METHODS: We investigated population genetic variation of I. scapularis populations in the eastern United States using a multilocus approach. We sequenced and analyzed the mitochondrial COI and 16S genes and three nuclear genes (serpin2, ixoderin B and lysozyme) from wild specimens.<br><br>RESULTS: We identified a deep divergence (3-7%) in I. scapularis COI gene sequences from some southern specimens, suggesting we had sampled a different Ixodes species. Analysis of mitochondrial 16S rRNA sequences did not support this hypothesis and indicated that all specimens were I. scapularis. Phylogenetic analysis and analysis of molecular variance (AMOVA) supported significant differences between northern vs. southern populations. Demographic analysis suggested that northern populations had experienced a bottleneck/expansion event sometime in the past, possibly associated with Pleistocene glaciation events.<br><br>CONCLUSIONS: Similar to other studies, our data support the division of northern vs. southern I. scapularis genetic lineages, likely due to differences in the demographic histories between these geographic regions. The deep divergence identified in some COI gene sequences highlights a potential hazard of relying solely on COI for species identification ("barcoding") and population genetics in this important vector arthropod.},
}
@article {pmid25019088,
year = {2014},
author = {Silverio, MS and Rodovalho, Vde R and Bonetti, AM and de Oliveira, GC and Cuadros-Orellana, S and Ueira-Vieira, C and Rodrigues dos Santos, A},
title = {Preliminary characterization of mitochondrial genome of Melipona scutellaris, a Brazilian stingless bee.},
journal = {BioMed research international},
volume = {2014},
number = {},
pages = {927546},
pmid = {25019088},
issn = {2314-6141},
mesh = {Animals ; Bees/*classification/*genetics ; Biological Evolution ; Brazil ; Chromosome Mapping/*methods ; Genome, Mitochondrial/*genetics ; Mitochondrial Proteins/*genetics ; Open Reading Frames/*genetics ; Pilot Projects ; Species Specificity ; },
abstract = {Bees are manufacturers of relevant economical products and have a pollinator role fundamental to ecosystems. Traditionally, studies focused on the genus Melipona have been mostly based on behavioral, and social organization and ecological aspects. Only recently the evolutionary history of this genus has been assessed using molecular markers, including mitochondrial genes. Even though these studies have shed light on the evolutionary history of the Melipona genus, a more accurate picture may emerge when full nuclear and mitochondrial genomes of Melipona species become available. Here we present the assembly, annotation, and characterization of a draft mitochondrial genome of the Brazilian stingless bee Melipona scutellaris using Melipona bicolor as a reference organism. Using Illumina MiSeq data, we achieved the annotation of all protein coding genes, as well as the genes for the two ribosomal subunits (16S and 12S) and transfer RNA genes as well. Using the COI sequence as a DNA barcode, we found that M. cramptoni is the closest species to M. scutellaris.},
}
@article {pmid25017375,
year = {2014},
author = {Bilia, AR},
title = {Science meets regulation.},
journal = {Journal of ethnopharmacology},
volume = {158 Pt B},
number = {},
pages = {487-494},
doi = {10.1016/j.jep.2014.06.036},
pmid = {25017375},
issn = {1872-7573},
mesh = {Chemistry Techniques, Analytical/*methods ; European Union ; Humans ; *Legislation, Drug ; *Pharmacopoeias as Topic ; Plant Preparations/analysis/*standards ; Quality Control ; },
abstract = {The European Pharmacopoeia (Ph. Eur.) is a standard reference for both European and non-European countries and defines requirements for the qualitative and quantitative composition of medicines. Herbal drug (HD) monographs state which aspects have to be considered for quality assurance through the relevant chapters "Definition", "Characters", "Identification", "Tests", and "Assay". Identification of botanical material is achieved by macroscopic and microscopic morphology, generally examined by a trained expert. Content or assay is the most difficult area of quality control to perform, since in most herbal drugs the active constituents are unknown and markers should be used which cannot be really related to the quality. The other critical points are represented by the purity tests, in particular some tests such as heavy metals, aflatoxins and pesticides are laborious and time intensive, requiring a significant investment in equipment, materials, and maintenance.<br><br>MATERIAL AND METHODS: A literature survey concerning alternative and/or complementary tools for quality control of botanicals has been performed by searching the scientific databases Pubmed, SciFinder, Scopus and Web of Science.<br><br>RESULTS: Diverse analytical methods including DNA fingerprinting, Nuclear Magnetic Resonance (NMR), Near Infra Red (NIR) and (bio)sensors have been reported in the literature to evaluate the quality of botanical products. Identification of plants at the species level can be successfully based on genome-based methods, using DNA barcodes, the nucleotide sequence of a short DNA fragment. NMR can provide direct NMR fingerprint determination (complete assignment of the signals by 1D and 2D experiments), quantitative NMR and chemometric analysis (the metabolite fingerprint is based on the distribution of intensity in the NMR spectrum to provide sample classification). NIR spectroscopy is a fast qualitative and quantitative analytical method, getting knowledge about plant species and/or its geographic origin. Finally, the development of chemical and biological sensors is currently one of the most active areas of analytical research. Immobilization of specific enzymes led to recognize definite class of compounds such as cysteine sulfoxides, glucosinolates, cyanogenic glycosides, and polyphenols. Other recognition elements are nucleic acids to evaluate the ability of different molecules to bind DNA. Sensors have also been developed for the detection of heavy metals in botanicals. Moreover, the analysis of mycotoxins and pesticides, could represent another field of possible application.<br><br>CONCLUSIONS: These alternative/complementary analytical methods represent tools which appear to be an analyst's dream: they are able to give rapid analysis responses; to operate directly on complex matrices, in many cases; to be selective and sensitive enough for the required application; to be portable and sometimes also disposable; and to have fast analysis times.},
}
@article {pmid25013183,
year = {2014},
author = {Deakin, CT and Deakin, JJ and Ginn, SL and Young, P and Humphreys, D and Suter, CM and Alexander, IE and Hallwirth, CV},
title = {Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence.},
journal = {Nucleic acids research},
volume = {42},
number = {16},
pages = {e129},
pmid = {25013183},
issn = {1362-4962},
mesh = {Artifacts ; *Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; *Plasmids ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; },
abstract = {Barcoded vectors are promising tools for investigating clonal diversity and dynamics in hematopoietic gene therapy. Analysis of clones marked with barcoded vectors requires accurate identification of potentially large numbers of individually rare barcodes, when the exact number, sequence identity and abundance are unknown. This is an inherently challenging application, and the feasibility of using contemporary next-generation sequencing technologies is unresolved. To explore this potential application empirically, without prior assumptions, we sequenced barcode libraries of known complexity. Libraries containing 1, 10 and 100 Sanger-sequenced barcodes were sequenced using an Illumina platform, with a 100-barcode library also sequenced using a SOLiD platform. Libraries containing 1 and 10 barcodes were distinguished from false barcodes generated by sequencing error by a several log-fold difference in abundance. In 100-barcode libraries, however, expected and false barcodes overlapped and could not be resolved by bioinformatic filtering and clustering strategies. In independent sequencing runs multiple false-positive barcodes appeared to be represented at higher abundance than known barcodes, despite their confirmed absence from the original library. Such errors, which potentially impact barcoding studies in an application-dependent manner, are consistent with the existence of both stochastic and systematic error, the mechanism of which is yet to be fully resolved.},
}
@article {pmid25013180,
year = {2014},
author = {Nilsson, AN and Emilsson, G and Nyberg, LK and Noble, C and Stadler, LS and Fritzsche, J and Moore, ER and Tegenfeldt, JO and Ambjörnsson, T and Westerlund, F},
title = {Competitive binding-based optical DNA mapping for fast identification of bacteria--multi-ligand transfer matrix theory and experimental applications on Escherichia coli.},
journal = {Nucleic acids research},
volume = {42},
number = {15},
pages = {e118},
pmid = {25013180},
issn = {1362-4962},
mesh = {Anti-Bacterial Agents ; Benzoxazoles ; Binding, Competitive ; DNA Barcoding, Taxonomic/*methods ; DNA, Bacterial/chemistry ; Escherichia coli/*classification/genetics ; Fluorescent Dyes ; Ligands ; Nanotechnology ; Netropsin ; Quinolinium Compounds ; },
abstract = {We demonstrate a single DNA molecule optical mapping assay able to resolve a specific Escherichia coli strain from other strains. The assay is based on competitive binding of the fluorescent dye YOYO-1 and the AT-specific antibiotic netropsin. The optical map is visualized by stretching the DNA molecules in nanofluidic channels. We optimize the experimental conditions to obtain reproducible barcodes containing as much information as possible. We implement a multi-ligand transfer matrix method for calculating theoretical barcodes from known DNA sequences. Our method extends previous theoretical approaches for competitive binding of two types of ligands to many types of ligands and introduces a recursive approach that allows long barcodes to be calculated with standard computer floating point formats. The identification of a specific E. coli strain (CCUG 10979) is based on mapping of 50-160 kilobasepair experimental DNA fragments onto the theoretical genome using the developed theory. Our identification protocol introduces two theoretical constructs: a P-value for a best experiment-theory match and an information score threshold. The developed methods provide a novel optical mapping toolbox for identification of bacterial species and strains. The protocol does not require cultivation of bacteria or DNA amplification, which allows for ultra-fast identification of bacterial pathogens.},
}
@article {pmid25013177,
year = {2014},
author = {Peikon, ID and Gizatullina, DI and Zador, AM},
title = {In vivo generation of DNA sequence diversity for cellular barcoding.},
journal = {Nucleic acids research},
volume = {42},
number = {16},
pages = {e127},
pmid = {25013177},
issn = {1362-4962},
support = {1R01DA036913-01/DA/NIDA NIH HHS/United States ; 5R01NS073129-04/NS/NINDS NIH HHS/United States ; },
mesh = {DNA Shuffling ; Escherichia coli/genetics ; Genetic Variation ; High-Throughput Nucleotide Sequencing/*methods ; Integrases ; Recombinases ; Sequence Analysis, DNA/*methods ; },
abstract = {Heterogeneity is a ubiquitous feature of biological systems. A complete understanding of such systems requires a method for uniquely identifying and tracking individual components and their interactions with each other. We have developed a novel method of uniquely tagging individual cells in vivo with a genetic 'barcode' that can be recovered by DNA sequencing. Our method is a two-component system comprised of a genetic barcode cassette whose fragments are shuffled by Rci, a site-specific DNA invertase. The system is highly scalable, with the potential to generate theoretical diversities in the billions. We demonstrate the feasibility of this technique in Escherichia coli. Currently, this method could be employed to track the dynamics of populations of microbes through various bottlenecks. Advances of this method should prove useful in tracking interactions of cells within a network, and/or heterogeneity within complex biological samples.},
}
@article {pmid25009417,
year = {2014},
author = {Wesener, T and Le, DM and Loria, SF},
title = {Integrative revision of the giant pill-millipede genus Sphaeromimus from Madagascar, with the description of seven new species (Diplopoda, Sphaerotheriida, Arthrosphaeridae).},
journal = {ZooKeys},
volume = {},
number = {414},
pages = {67-107},
pmid = {25009417},
issn = {1313-2989},
abstract = {The Malagasy giant pill-millipede genus Sphaeromimus de Saussure &amp; Zehntner, 1902 is revised. Seven new species, S. titanus sp. n., S. vatovavy sp. n., S. lavasoa sp. n., S. andohahela sp. n., S. ivohibe sp. n., S. saintelucei sp. n., and S. andrahomana sp. n. were discovered, in one case with the help of sequence data, in the rainforests of southeastern Madagascar. The species are described using light- and scanning electron microscopy. A key to all 10 species of the genus is presented. All but one (S. andohahela) of the newly discovered species are microendemics each occurring in isolated forest fragments. The mitochondrial COI barcoding gene was amplified and sequenced for 18 Sphaeromimus specimens, and a dataset containing COI sequences of 28 specimens representing all Sphaeromimus species (except S. vatovavy) was analyzed. All species are genetically monophyletic. Interspecific uncorrected genetic distances were moderate (4-10%) to high (18-25%), whereas intraspecific variation is low (0-3.5%). Sequence data allowed the correct identification of three colour morphs of S. musicus, as well as the identity of a cave specimen, which although aberrant in its morphology and colouration, was genetically identical to the holotype of S. andrahoma.},
}
@article {pmid25005355,
year = {2014},
author = {Bertrand, C and Janzen, DH and Hallwachs, W and Burns, JM and Gibson, JF and Shokralla, S and Hajibabaei, M},
title = {Mitochondrial and nuclear phylogenetic analysis with Sanger and next-generation sequencing shows that, in Área de Conservación Guanacaste, northwestern Costa Rica, the skipper butterfly named Urbanus belli (family Hesperiidae) comprises three morphologically cryptic species.},
journal = {BMC evolutionary biology},
volume = {14},
number = {},
pages = {153},
pmid = {25005355},
issn = {1471-2148},
mesh = {Animals ; Butterflies/*classification/*genetics/microbiology ; Cell Nucleus/genetics ; Costa Rica ; DNA, Ribosomal Spacer/genetics ; High-Throughput Nucleotide Sequencing ; Mitochondria/genetics ; Phylogeny ; Wolbachia/genetics ; },
abstract = {BACKGROUND: Skipper butterflies (Hesperiidae) are a relatively well-studied family of Lepidoptera. However, a combination of DNA barcodes, morphology, and natural history data has revealed several cryptic species complexes within them. Here, we investigate three DNA barcode lineages of what has been identified as Urbanus belli (Hesperiidae, Eudaminae) in Área de Conservación Guanacaste (ACG), northwestern Costa Rica.<br><br>RESULTS: Although no morphological traits appear to distinguish among the three, congruent nuclear and mitochondrial lineage patterns show that "Urbanus belli" in ACG is a complex of three sympatric species. A single strain of Wolbachia present in two of the three cryptic species indicates that Urbanus segnestami Burns (formerly Urbanus belliDHJ01), Urbanus bernikerni Burns (formerly Urbanus belliDHJ02), and Urbanus ehakernae Burns (formerly Urbanus belliDHJ03) may be biologically separated by Wolbachia, as well as by their genetics. Use of parallel sequencing through 454-pyrosequencing improved the utility of ITS2 as a phylogenetic marker and permitted examination of the intra- and interlineage relationships of ITS2 variants within the species complex. Interlineage, intralineage and intragenomic compensatory base pair changes were discovered in the secondary structure of ITS2.<br><br>CONCLUSION: These findings corroborate the existence of three cryptic species. Our confirmation of a novel cryptic species complex, initially suggested by DNA barcode lineages, argues for using a multi-marker approach coupled with next-generation sequencing for exploration of other suspected species complexes.},
}
@article {pmid25004106,
year = {2014},
author = {Foottit, RG and Maw, E and Hebert, PD},
title = {DNA barcodes for Nearctic Auchenorrhyncha (Insecta: Hemiptera).},
journal = {PloS one},
volume = {9},
number = {7},
pages = {e101385},
pmid = {25004106},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; Evolution, Molecular ; Genes, Insect ; Genetic Variation ; Hemiptera/*classification/*genetics ; },
abstract = {BACKGROUND: Many studies have shown the suitability of sequence variation in the 5' region of the mitochondrial cytochrome c oxidase I (COI) gene as a DNA barcode for the identification of species in a wide range of animal groups. We examined 471 species in 147 genera of Hemiptera: Auchenorrhyncha drawn from specimens in the Canadian National Collection of Insects to assess the effectiveness of DNA barcoding in this group.<br><br>Analysis of the COI gene revealed less than 2% intra-specific divergence in 93% of the taxa examined, while minimum interspecific distances exceeded 2% in 70% of congeneric species pairs. Although most species are characterized by a distinct sequence cluster, sequences for members of many groups of closely related species either shared sequences or showed close similarity, with 25% of species separated from their nearest neighbor by less than 1%.<br><br>CONCLUSIONS/SIGNIFICANCE: This study, although preliminary, provides DNA barcodes for about 8% of the species of this hemipteran suborder found in North America north of Mexico. Barcodes can enable the identification of many species of Auchenorrhyncha, but members of some species groups cannot be discriminated. Future use of DNA barcodes in regulatory, pest management, and environmental applications will be possible as the barcode library for Auchenorrhyncha expands to include more species and broader geographic coverage.},
}
@article {pmid24997861,
year = {2014},
author = {Nguyen, UT and Bittova, L and Müller, MM and Fierz, B and David, Y and Houck-Loomis, B and Feng, V and Dann, GP and Muir, TW},
title = {Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries.},
journal = {Nature methods},
volume = {11},
number = {8},
pages = {834-840},
pmid = {24997861},
issn = {1548-7105},
support = {R01 GM107047/GM/NIGMS NIH HHS/United States ; R37 GM086868/GM/NIGMS NIH HHS/United States ; R37-GM086868/GM/NIGMS NIH HHS/United States ; },
mesh = {Chromatin/*chemistry ; Chromatin Immunoprecipitation ; *DNA Barcoding, Taxonomic ; Nucleosomes/chemistry ; },
abstract = {Elucidating the molecular details of how chromatin-associated factors deposit, remove and recognize histone post-translational modification (PTM) signatures remains a daunting task in the epigenetics field. We introduce a versatile platform that greatly accelerates biochemical investigations into chromatin recognition and signaling. This technology is based on the streamlined semisynthesis of DNA-barcoded nucleosome libraries with distinct combinations of PTMs. Chromatin immunoprecipitation of these libraries, once they have been treated with purified chromatin effectors or the combined chromatin recognizing and modifying activities of the nuclear proteome, is followed by multiplexed DNA-barcode sequencing. This ultrasensitive workflow allowed us to collect thousands of biochemical data points revealing the binding preferences of various nuclear factors for PTM patterns and how preexisting PTMs, alone or synergistically, affect further PTM deposition via cross-talk mechanisms. We anticipate that the high throughput and sensitivity of the technology will help accelerate the decryption of the diverse molecular controls that operate at the level of chromatin.},
}
@article {pmid24996012,
year = {2014},
author = {Naik, SH and Schumacher, TN and Perié, L},
title = {Cellular barcoding: a technical appraisal.},
journal = {Experimental hematology},
volume = {42},
number = {8},
pages = {598-608},
doi = {10.1016/j.exphem.2014.05.003},
pmid = {24996012},
issn = {1873-2399},
mesh = {Animals ; *Cell Lineage ; Cell Separation ; Cell Tracking/*methods ; Hematopoiesis ; Humans ; },
abstract = {Cellular barcoding involves the tagging of individual cells of interest with unique genetic heritable identifiers or barcodes and is emerging as a powerful tool to address individual cell fates on a large scale. However, as with many new technologies, diverse technical and analytical challenges have emerged. Here, we review those challenges and highlight both the power and limitations of cellular barcoding. We then illustrate the contribution of cellular barcoding to the understanding of hematopoiesis and outline the future potential of this technology.},
}
@article {pmid24995947,
year = {2015},
author = {Wang, W and Messing, J},
title = {Status of duckweed genomics and transcriptomics.},
journal = {Plant biology (Stuttgart, Germany)},
volume = {17 Suppl 1},
number = {},
pages = {10-15},
doi = {10.1111/plb.12201},
pmid = {24995947},
issn = {1438-8677},
mesh = {Araceae/anatomy &amp; histology/*genetics/growth &amp; development ; DNA Barcoding, Taxonomic ; Gene Expression Profiling/*methods ; Genome, Plant ; Genomics/*methods ; Organelles/genetics ; },
abstract = {Duckweeds belong to the smallest flowering plants that undergo fast vegetative growth in an aquatic environment. They are commonly used in wastewater treatment and animal feed. Whereas duckweeds have been studied at the biochemical level, their reduced morphology and wide environmental adaption had not been subjected to molecular analysis until recently. Here, we review the progress that has been made in using a DNA barcode system and the sequences of chloroplast and mitochondrial genomes to identify duckweed species at the species or population level. We also review analysis of the nuclear genome sequence of Spirodela that provides new insights into fundamental biological questions. Indeed, reduced gene families and missing genes are consistent with its compact morphogenesis, aquatic floating and suppression of juvenile-to-adult transition. Furthermore, deep RNA sequencing of Spirodela at the onset of dormancy and Landoltia in exposure of nutrient deficiency illustrate the molecular network for environmental adaption and stress response, constituting major progress towards a post-genome sequencing phase, where further functional genomic details can be explored. Rapid advances in sequencing technologies could continue to promote a proliferation of genome sequences for additional ecotypes as well as for other duckweed species.},
}
@article {pmid24992018,
year = {2014},
author = {Anderson, MP and Dubnicka, SR},
title = {A sequential naïve Bayes classifier for DNA barcodes.},
journal = {Statistical applications in genetics and molecular biology},
volume = {13},
number = {4},
pages = {423-434},
doi = {10.1515/sagmb-2013-0025},
pmid = {24992018},
issn = {1544-6115},
mesh = {Bayes Theorem ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*genetics ; *Models, Genetic ; },
abstract = {DNA barcodes are short strands of 255-700 nucleotide bases taken from the cytochrome c oxidase subunit 1 (COI) region of the mitochondrial DNA. It has been proposed that these barcodes may be used as a method of differentiating between biological species. Current methods of species classification utilize distance measures that are heavily dependent on both evolutionary model assumptions as well as a clearly defined "gap" between intra- and interspecies variation. Such distance measures fail to measure classification uncertainty or to indicate how much of the barcode is necessary for classification. We propose a sequential naïve Bayes classifier for species classification to address these limitations. The proposed method is shown to provide accurate species-level classification on real and simulated data. The method proposed here quantifies the uncertainty of each classification and addresses how much of the barcode is necessary.},
}
@article {pmid24991801,
year = {2014},
author = {Khedkar, GD and Jamdade, R and Naik, S and David, L and Haymer, D},
title = {DNA barcodes for the fishes of the Narmada, one of India's longest rivers.},
journal = {PloS one},
volume = {9},
number = {7},
pages = {e101460},
pmid = {24991801},
issn = {1932-6203},
mesh = {Animals ; Computational Biology ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Fishes/classification/*genetics ; Genetic Variation ; India ; Phylogeny ; Rivers ; Sequence Analysis, DNA ; },
abstract = {This study describes the species diversity of fishes of the Narmada River in India. A total of 820 fish specimens were collected from 17 sampling locations across the whole river basin. Fish were taxonomically classified into one of 90 possible species based on morphological characters, and then DNA barcoding was employed using COI gene sequences as a supplemental identification method. A total of 314 different COI sequences were generated, and specimens were confirmed to belong to 85 species representing 63 genera, 34 families and 10 orders. Findings of this study include the identification of five putative cryptic or sibling species and 43 species not previously known from the Narmada River basin. Five species are endemic to India and three are introduced species that had not been previously reported to occur in the Narmada River. Conversely, 43 species previously reported to occur in the Narmada were not found. Genetic diversity and distance values were generated for all of the species within genera, families and orders using Kimura's 2 parameter distance model followed by the construction of a Neighbor Joining tree. High resolution clusters generated in NJ trees aided the groupings of species corresponding to their genera and families which are in confirmation to the values generated by Automatic Barcode Gap Discovery bioinformatics platform. This aided to decide a threshold value for the discrimination of species boundary from the Narmada River. This study provides an important validation of the use of DNA barcode sequences for monitoring species diversity and changes within complex ecosystems such as the Narmada River.},
}
@article {pmid24990044,
year = {2014},
author = {Khalaji-Pirbalouty, V and Raupach, MJ},
title = {A new species of Cymodoce Leach, 1814 (Crustacea: Isopoda: Sphaeromatidae) based on morphological and molecular data, with a key to the Northern Indian Ocean species.},
journal = {Zootaxa},
volume = {3826},
number = {1},
pages = {230-254},
doi = {10.11646/zootaxa.3826.1.7},
pmid = {24990044},
issn = {1175-5334},
mesh = {Animals ; Female ; Indian Ocean ; Isopoda/*anatomy &amp; histology/*classification ; Male ; },
abstract = {Cymodoce waegelei sp. nov. is described from the subtidal zone of the Iranian coasts of the Persian Gulf using both morphological and molecular data. C. waegelei sp. nov. is most similar to C. tribullis Harrison &amp; Holdich, 1984 from Australia, Vietnam and Singapore. Analysis of DNA barcodes and nuclear 28S rDNA: D8 expansion segments clearly support the existence of two distinct species. Cymodoce waegelei sp. nov morphologically differs from C. tribullis by lacking two continuous rows of tubercles on the pereonites 3 and 4. Moreover, the pleotelson has numerous scattered tubercles between two large prominent bosses, and small lateral tubercles rather than two prominent tubercles in C. tribullis. Based on our results we redescribe Cymodoce tribullis using specimens sampled from the type locality, Magnetic Island, Queensland. Cymodoce lirella Schotte &amp; Kensley, 2005 from the Seychelles is placed in synonymy with C. tribullis Harrison &amp; Holdich 1984. Furthermore we provide a key to the northern Indian Ocean species of this genus.},
}
@article {pmid24988408,
year = {2014},
author = {Stoeckle, MY and Thaler, DS},
title = {DNA barcoding works in practice but not in (neutral) theory.},
journal = {PloS one},
volume = {9},
number = {7},
pages = {e100755},
pmid = {24988408},
issn = {1932-6203},
mesh = {Animals ; Birds/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; *Evolution, Molecular ; },
abstract = {BACKGROUND: DNA barcode differences within animal species are usually much less than differences among species, making it generally straightforward to match unknowns to a reference library. Here we aim to better understand the evolutionary mechanisms underlying this usual "barcode gap" pattern. We employ avian barcode libraries to test a central prediction of neutral theory, namely, intraspecific variation equals 2 Nµ, where N is population size and µ is mutations per site per generation. Birds are uniquely suited for this task: they have the best-known species limits, are well represented in barcode libraries, and, most critically, are the only large group with documented census population sizes. In addition, we ask if mitochondrial molecular clock measurements conform to neutral theory prediction of clock rate equals µ.<br><br>RESULTS: Intraspecific COI barcode variation was uniformly low regardless of census population size (n&#x200a;=&#x200a;142 species in 15 families). Apparent outliers reflected lumping of reproductively isolated populations or hybrid lineages. Re-analysis of a published survey of cytochrome b variation in diverse birds (n&#x200a;=&#x200a;93 species in 39 families) further confirmed uniformly low intraspecific variation. Hybridization/gene flow among species/populations was the main limitation to DNA barcode identification.<br><br>CONCLUSIONS/SIGNIFICANCE: To our knowledge, this is the first large study of animal mitochondrial diversity using actual census population sizes and the first to test outliers for population structure. Our finding of universally low intraspecific variation contradicts a central prediction of neutral theory and is not readily accounted for by commonly proposed ad hoc modifications. We argue that the weight of evidence-low intraspecific variation and the molecular clock-indicates neutral evolution plays a minor role in mitochondrial sequence evolution. As an alternate paradigm consistent with empirical data, we propose extreme purifying selection, including at synonymous sites, limits variation within species and continuous adaptive selection drives the molecular clock.},
}
@article {pmid24987846,
year = {2014},
author = {Rougerie, R and Kitching, IJ and Haxaire, J and Miller, SE and Hausmann, A and Hebert, PD},
title = {Australian Sphingidae--DNA barcodes challenge current species boundaries and distributions.},
journal = {PloS one},
volume = {9},
number = {7},
pages = {e101108},
pmid = {24987846},
issn = {1932-6203},
mesh = {Animals ; Australia ; DNA Barcoding, Taxonomic/*methods ; Lepidoptera/*classification/*genetics ; },
abstract = {MAIN OBJECTIVE: We examine the extent of taxonomic and biogeographical uncertainty in a well-studied group of Australian Lepidoptera, the hawkmoths (Sphingidae).<br><br>METHODS: We analysed the diversity of Australian sphingids through the comparative analysis of their DNA barcodes, supplemented by morphological re-examinations and sequence information from a nuclear marker in selected cases. The results from the analysis of Australian sphingids were placed in a broader context by including conspecifics and closely related taxa from outside Australia to test taxonomic boundaries.<br><br>RESULTS: Our results led to the discovery of six new species in Australia, one case of erroneously synonymized species, and three cases of synonymy. As a result, we establish the occurrence of 75 species of hawkmoths on the continent. The analysis of records from outside Australia also challenges the validity of current taxonomic boundaries in as many as 18 species, including Agrius convolvuli (Linnaeus, 1758), a common species that has gained adoption as a model system. Our work has revealed a higher level of endemism than previously recognized. Most (90%) Australian sphingids are endemic to the continent (45%) or to Australia, the Pacific Islands and the Papuan and Wallacean regions (45%). Only seven species (10%) have ranges that extend beyond this major biogeographical boundary toward SE Asia and other regions of the Old World.<br><br>MAIN CONCLUSIONS: This study has established that overlooked cryptic diversity and inaccurate species delineation produced significant misconceptions concerning diversity and distribution patterns in a group of insects that is considered well known taxonomically. Because DNA barcoding represents a straightforward way to test taxonomic boundaries, its implementation can improve the accuracy of primary diversity data in biogeography and conservation studies.},
}
@article {pmid24987576,
year = {2014},
author = {Blanco-Bercial, L and Cornils, A and Copley, N and Bucklin, A},
title = {DNA barcoding of marine copepods: assessment of analytical approaches to species identification.},
journal = {PLoS currents},
volume = {6},
number = {},
pages = {},
pmid = {24987576},
issn = {2157-3999},
abstract = {More than 2,500 species of copepods (Class Maxillopoda; Subclass Copepoda) occur in the marine planktonic environment. The exceptional morphological conservation of the group, with numerous sibling species groups, makes the identification of species challenging, even for expert taxonomists. Molecular approaches to species identification have allowed rapid detection, discrimination, and identification of species based on DNA sequencing of single specimens and environmental samples. Despite the recent development of diverse genetic and genomic markers, the barcode region of the mitochondrial cytochrome c oxidase subunit I (COI) gene remains a useful and - in some cases - unequaled diagnostic character for species-level identification of copepods. This study reports 800 new barcode sequences for 63 copepod species not included in any previous study and examines the reliability and resolution of diverse statistical approaches to species identification based upon a dataset of 1,381 barcode sequences for 195 copepod species. We explore the impact of missing data (i.e., species not represented in the barcode database) on the accuracy and reliability of species identifications. Among the tested approaches, the best close match analysis resulted in accurate identification of all individuals to species, with no errors (false positives), and out-performed automated tree-based or BLAST based analyses. This comparative analysis yields new understanding of the strengths and weaknesses of DNA barcoding and confirms the value of DNA barcodes for species identification of copepods, including both individual specimens and bulk samples. Continued integrative morphological-molecular taxonomic analysis is needed to produce a taxonomically-comprehensive database of barcode sequences for all species of marine copepods.},
}
@article {pmid24984714,
year = {2014},
author = {Zarrei, M and Stefanović, S and Dickinson, TA},
title = {Reticulate evolution in North American black-fruited hawthorns (Crataegus section Douglasia; Rosaceae): evidence from nuclear ITS2 and plastid sequences.},
journal = {Annals of botany},
volume = {114},
number = {2},
pages = {253-269},
pmid = {24984714},
issn = {1095-8290},
mesh = {Base Sequence ; *Biological Evolution ; Cell Nucleus/*genetics ; Crataegus/*genetics ; DNA, Ribosomal Spacer/*genetics ; Fruit/*genetics ; Genetic Variation ; Hybridization, Genetic ; Models, Biological ; North America ; Nucleic Acid Conformation ; Phylogeny ; Plastids/*genetics ; Polyploidy ; Species Specificity ; },
abstract = {BACKGROUND AND AIMS: The taxonomic complexity of Crataegus (hawthorn; Rosaceae, Maleae), especially in North America, has been attributed by some to hybridization in combination with gametophytic apomixis and polyploidization, whereas others have considered the roles of hybridization and apomixis to be minimal. Study of the chemical composition and therapeutic value of hawthorn extracts requires reproducible differentiation of entities that may be difficult to distinguish by morphology alone. This study sought to address this by using the nuclear ribosomal spacer region ITS2 as a supplementary DNA barcode; however, a lack of success prompted an investigation to discover why this locus gave unsatisfactory results.<br><br>METHODS: ITS2 was extensively cloned so as to document inter- and intraindividual variation in this locus, using hawthorns of western North America where the genus Crataegus is represented by only two widely divergent groups, the red-fruited section Coccineae and the black-fruited section Douglasia. Additional sequence data from selected loci on the plastid genome were obtained to enhance further the interpretation of the ITS2 results.<br><br>KEY RESULTS: In the ITS2 gene tree, ribotypes from western North American hawthorns are found in two clades. Ribotypes from diploid members of section Douglasia occur in one clade (with representatives of the east-Asian section Sanguineae). The other clade comprises those from diploid and polyploid members of section Coccineae. Both clades contribute ribotypes to polyploid Douglasia. Data from four plastid-derived intergenic spacers demonstrate the maternal parentage of these allopolyploids.<br><br>CONCLUSIONS: Repeated hybridization between species of section Douglasia and western North American members of section Coccineae involving the fertilization of unreduced female gametes explains the observed distribution of ribotypes and accounts for the phenetic intermediacy of many members of section Douglasia.},
}
@article {pmid24984000,
year = {2014},
author = {Clark, MA and Goheen, MM and Spidale, NA and Kasthuri, RS and Fulford, A and Cerami, C},
title = {RBC barcoding allows for the study of erythrocyte population dynamics and P. falciparum merozoite invasion.},
journal = {PloS one},
volume = {9},
number = {7},
pages = {e101041},
pmid = {24984000},
issn = {1932-6203},
support = {CA16086-36/CA/NCI NIH HHS/United States ; P30 CA016086/CA/NCI NIH HHS/United States ; U01 HD061235/HD/NICHD NIH HHS/United States ; U01HD061235/HD/NICHD NIH HHS/United States ; P30CA06086./CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Erythrocytes/*parasitology ; Flow Cytometry ; Humans ; Plasmodium falciparum/*physiology ; },
abstract = {Plasmodium falciparum invasion of host erythrocytes is essential for the propagation of the blood stage of malaria infection. Additionally, the brief extracellular merozoite stage of P. falciparum represents one of the rare windows during which the parasite is directly exposed to the host immune response. Therefore, efficient invasion of the host erythrocyte is necessary not only for productive host erythrocyte infection, but also for evasion of the immune response. Host traits, such as hemoglobinopathies and differential expression of erythrocyte invasion ligands, can protect individuals from malaria by impeding parasite erythrocyte invasion. Here we combine RBC barcoding with flow cytometry to study P. falciparum invasion. This novel high-throughput method allows for the (i) direct comparison of P. falciparum invasion into different erythrocyte populations and (ii) assessment of the impact of changing erythrocyte population dynamics on P. falciparum invasion.},
}
@article {pmid24981896,
year = {2014},
author = {Bartling, CM and Hester, ME and Bartz, J and Heizer, E and Faith, SA},
title = {Next-generation sequencing approach to epigenetic-based tissue source attribution.},
journal = {Electrophoresis},
volume = {35},
number = {21-22},
pages = {3096-3101},
doi = {10.1002/elps.201400087},
pmid = {24981896},
issn = {1522-2683},
mesh = {Body Fluids/chemistry ; DNA Methylation/*genetics ; Epigenesis, Genetic/*genetics ; Forensic Genetics/*methods ; Genetic Markers/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Organ Specificity ; },
abstract = {The ability to determine the tissue source of biological materials from evidence samples can be highly informative for interpreting forensic data. In this study, a previously published CE-based method to probe locus-specific DNA methylation was modified to accommodate detection using next-generation sequencing (NGS) to perform tissue source attribution. DNA samples (1 ng) from each of four different tissue types were digested with the methylation sensitive restriction endonuclease Hha1 and PCR was used to amplify an optimized subset of ten methylated loci, including positive and negative control loci. The products were prepared as NGS libraries, pooled in a multiplex assay with sample-specific barcodes, sequenced with an Illumina MiSeq, and analyzed using a k-Nearest Neighbor algorithm. With this initial effort a concordance rate of 15/16 was demonstrated from samples of varying types: semen, saliva, skin epidermis, and blood. This method also was designed to be compatible with the workflows published to date for NGS of STRs. Thus, the methylation approach described here is highly accurate and upon further validation and testing may be potentially used in practice as a confirmatory test in conjunction with other NGS protocols used in forensic laboratories.},
}
@article {pmid24978689,
year = {2014},
author = {Wang, P and Tian, C and Li, X and Mao, C},
title = {Assembly of barcode-like nucleic acid nanostructures.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {10},
number = {19},
pages = {3923-3926},
doi = {10.1002/smll.201400942},
pmid = {24978689},
issn = {1613-6829},
mesh = {Biosensing Techniques ; DNA/chemistry ; *Electronic Data Processing ; Microscopy, Atomic Force ; Nanostructures/*chemistry ; Nanotechnology ; Nucleic Acid Conformation ; Nucleic Acids/*chemistry ; RNA/chemistry ; Software ; },
abstract = {Barcode-like (BC) nanopatterns from programmed self-assembly of nucleic acids (DNA and RNA) are reported. BC nanostructures are generated by the introduction of open spaces at selected sites to an otherwise closely packed, plain, rectangle nucleic acid nanostructure. This strategy is applied to nanostructures assembled from both origami approach and single stranded tile approach.},
}
@article {pmid24974777,
year = {2015},
author = {Mora, CA and Paunescu, D and Grass, RN and Stark, WJ},
title = {Silica particles with encapsulated DNA as trophic tracers.},
journal = {Molecular ecology resources},
volume = {15},
number = {2},
pages = {231-241},
doi = {10.1111/1755-0998.12299},
pmid = {24974777},
issn = {1755-0998},
mesh = {Animals ; Arthropods/physiology ; DNA/*genetics/*isolation &amp; purification ; Diptera/physiology ; *Ecosystem ; Food Chain ; *Nanoparticles ; Pollination ; *Silicon Dioxide ; Staining and Labeling/*methods ; },
abstract = {Ecological networks such as food webs are extremely complex and can provide important information about the robustness and productivity of an ecosystem. In most cases, it is not feasible to observe trophic interactions between predators and prey directly and with the available methods, it is difficult to quantify the connections between them. Here, we show that submicron-sized silica particles (100-150 nm) with encapsulated DNA (SPED) enable accurate food and organism labelling and quantification of specific animal-to-animal transfer over more than one trophic level. We found that SPED were readily transferable and quantifiable from the bottom to the top of a two-level food chain of arthropods. SPED were taken up in the gut system and remained persistent in an animal over several days. When uniquely labelled SPED were applied at predefined ratios, we found that information about their relative abundance was reliably conserved after trophic level transfer and over time. SPED were also applied to investigate the flower preference of fly pollinators and proved to be a fast and accurate analysis method. SPED combine attributes of DNA barcoding and stable isotope analysis such as unique labelling, quantification via real-time PCR and exact backtracking to the tracer source. This improves and simplifies the analysis and monitoring of ecological networks.},
}
@article {pmid24974586,
year = {2014},
author = {Tekiner, H},
title = {Pharmacy in Turkey: past, present, and future.},
journal = {Die Pharmazie},
volume = {69},
number = {6},
pages = {477-480},
pmid = {24974586},
issn = {0031-7144},
mesh = {Drug Costs ; Education, Pharmacy/history ; *History of Pharmacy ; History, 20th Century ; History, 21st Century ; History, Medieval ; Hospitals/history ; Humans ; Legislation, Pharmacy ; Pharmacies/economics/history ; Pharmacy/*trends ; Turkey ; },
abstract = {Pharmacy in Turkey underwent a radical change within the last decade. Introduction of the Health Transformation Program in 2003 has had a significant impact on Turkey's pharmacy system in accordance with objectives of the program to establish new pricing regulations for pharmaceuticals based on reference prices, and to develop better computer based health information/record systems. In this context, Pharmaceutical Tracking (Track-and-Trace) System using two dimensional matrix barcodes was initiated to prevent not only drug counterfeiting, but also fraud against the medical insurance system and off-record transactions within the pharmaceutical sector; and the process of recording prescriptions in an electronic format was launched. Some other improvements have also been made with respect to pharmacy education, law and practice. In contrast with all these positive outcomes, Turkish pharmacy sector is currently in a deep financial struggle. This paper aims to provide a brief overview of the recent developments in Turkish pharmacy system and to discuss future roles and challenges of the profession.},
}
@article {pmid24971797,
year = {2014},
author = {Palhares, RM and Drummond, MG and Brasil, BS and Krettli, AU and Oliveira, GC and Brandão, MG},
title = {The use of an integrated molecular-, chemical- and biological-based approach for promoting the better use and conservation of medicinal species: a case study of Brazilian quinas.},
journal = {Journal of ethnopharmacology},
volume = {155},
number = {1},
pages = {815-822},
doi = {10.1016/j.jep.2014.06.040},
pmid = {24971797},
issn = {1872-7573},
mesh = {Antimalarials/chemistry/economics/isolation &amp; purification ; Base Sequence ; Brazil ; Cinchona/*chemistry/genetics ; Commerce ; *Conservation of Natural Resources ; DNA Barcoding, Taxonomic ; Ethnopharmacology ; Humans ; Medicine, Traditional/economics/*methods ; Plant Bark ; Plant Extracts/chemistry/economics/pharmacology ; Plants, Medicinal/*chemistry/genetics ; },
abstract = {Quina is a popular name originally attributed to Cinchona pubescens Vahl (=Cinchona succirubra) and Cinchona. calisaya Wedd., species native from Peru that have the antimalarial alkaloid quinine. In Brazil, bitter barks substitutes for the Peruvian species began to be used centuries ago, and they still are sold in popular markets. To assess the authenticity and the conditions on which samples of quinas have been commercialized, using the DNA barcode, chemical and biological assays.<br><br>MATERIALS AND METHODS: Starting with 28 samples of barks acquired on a popular market, 23 had their DNA extracted successfully. The regions matK and rbcL were amplified and sequenced for 15 and 23 samples, respectively. Phytochemical analyses were performed by chromatographic methods, and biological essays were done by antimalarial tests in vitro.<br><br>RESULTS: The identified species belonged to six different families, many of them endangered or with no correlation with use in traditional medicine as a Brazilian quina. The absence of typical bitter chemical substances indicated that barks have been collected from other species or from very young trees. The results of biological essays confirm the lack of standardization of the sold materials.<br><br>CONCLUSION: The integrated approaches proved to be efficient to evaluate medicinal plants sold in popular markets and can be useful for promoting their better use and conservation.},
}
@article {pmid24965753,
year = {2014},
author = {Tan, YC and Kongpachith, S and Blum, LK and Ju, CH and Lahey, LJ and Lu, DR and Cai, X and Wagner, CA and Lindstrom, TM and Sokolove, J and Robinson, WH},
title = {Barcode-enabled sequencing of plasmablast antibody repertoires in rheumatoid arthritis.},
journal = {Arthritis &amp; rheumatology (Hoboken, N.J.)},
volume = {66},
number = {10},
pages = {2706-2715},
pmid = {24965753},
issn = {2326-5205},
support = {R01 AR063676/AR/NIAMS NIH HHS/United States ; T32 AI007290/AI/NIAID NIH HHS/United States ; R01-AR-063676/AR/NIAMS NIH HHS/United States ; U19 AI110491/AI/NIAID NIH HHS/United States ; T32 AR050942/AR/NIAMS NIH HHS/United States ; U01-AI-101981/AI/NIAID NIH HHS/United States ; U01 AI101981/AI/NIAID NIH HHS/United States ; N01-HV-00242/HV/NHLBI NIH HHS/United States ; },
mesh = {Arthritis, Rheumatoid/blood/genetics/*immunology ; Autoantibodies/*blood ; B-Lymphocytes/*immunology ; *DNA Barcoding, Taxonomic ; Epitopes/genetics ; Humans ; Plasma Cells/*immunology ; },
abstract = {OBJECTIVE: A hallmark of rheumatoid arthritis (RA) is the production of autoantibodies, including anti-citrullinated protein antibodies (ACPAs). Nevertheless, the specific targets of these autoantibodies remain incompletely defined. During an immune response, B cells specific for the inciting antigen(s) are activated and differentiate into plasmablasts, which are released into the blood. We undertook this study to sequence the plasmablast antibody repertoire to define the targets of the active immune response in RA.<br><br>METHODS: We developed a novel DNA barcoding method to sequence the cognate heavy- and light-chain pairs of antibodies expressed by individual blood plasmablasts in RA. The method uses a universal 5' adapter that enables full-length sequencing of the antibodies' variable regions and recombinant expression of the paired antibody chains. The sequence data sets were bioinformatically analyzed to generate phylogenetic trees that identify clonal families of antibodies sharing heavy- and light-chain VJ sequences. Representative antibodies were expressed, and their binding properties were characterized using anti-cyclic citrullinated peptide 2 (anti-CCP-2) enzyme-linked immunosorbent assay (ELISA) and antigen microarrays.<br><br>RESULTS: We used our sequencing method to generate phylogenetic trees representing the antibody repertoires of peripheral blood plasmablasts from 4 individuals with anti-CCP+ RA, and recombinantly expressed 14 antibodies that were either "singleton" antibodies or representative of clonal antibody families. Anti-CCP-2 ELISA identified 4 ACPAs, and antigen microarray analysis identified ACPAs that differentially targeted epitopes on &#x3b1;-enolase, citrullinated fibrinogen, and citrullinated histone H2B.<br><br>CONCLUSION: Our data provide evidence that autoantibodies targeting &#x3b1;-enolase, citrullinated fibrinogen, and citrullinated histone H2B are produced by the ongoing activated B cell response in, and thus may contribute to the pathogenesis of, RA.},
}
@article {pmid24963726,
year = {2014},
author = {Loh, WK and Bond, P and Ashton, KJ and Roberts, DT and Tibbetts, IR},
title = {DNA barcoding of freshwater fishes and the development of a quantitative qPCR assay for the species-specific detection and quantification of fish larvae from plankton samples.},
journal = {Journal of fish biology},
volume = {85},
number = {2},
pages = {307-328},
doi = {10.1111/jfb.12422},
pmid = {24963726},
issn = {1095-8649},
mesh = {Animals ; Base Sequence ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Fishes/*genetics ; Lakes ; Larva/genetics ; Molecular Sequence Data ; Phylogeny ; *Plankton ; Polymerase Chain Reaction/*methods ; Queensland ; Species Specificity ; },
abstract = {The barcoding of mitochondrial cytochrome c oxidase subunit 1 (coI) gene was amplified and sequenced from 16 species of freshwater fishes found in Lake Wivenhoe (south-eastern Queensland, Australia) to support monitoring of reservoir fish populations, ecosystem function and water health. In this study, 630-650 bp sequences of the coI barcoding gene from 100 specimens representing 15 genera, 13 families and two subclasses of fishes allowed 14 of the 16 species to be identified and differentiated. The mean ± s.e. Kimura 2 parameter divergence within and between species was 0.52 ± 0.10 and 23.8 ± 2.20% respectively, indicating that barcodes can be used to discriminate most of the fish species accurately. The two terapontids, Amniataba percoides and Leiopotherapon unicolor, however, shared coI DNA sequences and could not be differentiated using this gene. A barcoding database was established and a qPCR assay was developed using coI sequences to identify and quantify proportional abundances of fish species in ichthyoplankton samples from Lake Wivenhoe. These methods provide a viable alternative to the time-consuming process of manually enumerating and identifying ichthyoplankton samples.},
}
@article {pmid24961287,
year = {2015},
author = {Yuan, QJ and Zhang, B and Jiang, D and Zhang, WJ and Lin, TY and Wang, NH and Chiou, SJ and Huang, LQ},
title = {Identification of species and materia medica within Angelica L. (Umbelliferae) based on phylogeny inferred from DNA barcodes.},
journal = {Molecular ecology resources},
volume = {15},
number = {2},
pages = {358-371},
pmid = {24961287},
issn = {1755-0998},
mesh = {Angelica/*classification/*genetics ; China ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Levisticum/classification/genetics ; Materia Medica/*isolation &amp; purification ; Molecular Sequence Data ; *Phylogeny ; Plants, Medicinal/*classification/*genetics ; Sequence Analysis, DNA ; Temperature ; },
abstract = {DNA barcodes have been increasingly used in authentication of medicinal plants, while their wide application in materia medica is limited in their accuracy due to incomplete sampling of species and absence of identification for materia medica. In this study, 95 leaf accessions of 23 species (including one variety) and materia medica of three Pharmacopoeia-recorded species of Angelica in China were collected to evaluate the effectiveness of four DNA barcodes (rbcL, matK, trnH-psbA and ITS). Our results showed that ITS provided the best discriminatory power by resolving 17 species as monophyletic lineages without shared alleles and exhibited the largest barcoding gap among the four single barcodes. The phylogenetic analysis of ITS showed that Levisticum officinale and Angelica sinensis were sister taxa, which indicates that L. officinale should be considered as a species of Angelica. The combination of ITS + rbcL + matK + trnH-psbA performed slight better discriminatory power than ITS, recovering 23 species without shared alleles and 19 species as monophyletic clades in ML tree. Authentication of materia medica using ITS revealed that the decoction pieces of A. sinensis and A. biserrata were partially adulterated with those of L. officinale, and the temperature around 80 °C processing A. dahurica decoction pieces obviously reduced the efficiency of PCR and sequencing. The examination of two cultivated varieties of A. dahurica from different localities indicated that the four DNA barcodes are inefficient for discriminating geographical authenticity of conspecific materia medica. This study provides an empirical paradigm in identification of medicinal plants and their materia medica using DNA barcodes.},
}
@article {pmid24958950,
year = {2014},
author = {Cohen, MR and Smetzer, JL},
title = {Mislabeling event with batched drugs: unintended consequences of practice change; morse code imprint; multiple barcodes cause confusion.},
journal = {Hospital pharmacy},
volume = {49},
number = {5},
pages = {415-418},
doi = {10.1310/hpj4905-415},
pmid = {24958950},
issn = {0018-5787},
abstract = {These medication errors have occurred in health care facilities at least once. They will happen again-perhaps where you work. Through education and alertness of personnel and procedural safeguards, they can be avoided. You should consider publishing accounts of errors in your newsletters and/or presenting them at your inservice training programs. Your assistance is required to continue this feature. The reports described here were received through the Institute for Safe Medication Practices (ISMP) Medication Errors Reporting Program. Any reports published by ISMP will be anonymous. Comments are also invited; the writers' names will be published if desired. ISMP may be contacted at the address shown below. Errors, close calls, or hazardous conditions may be reported directly to ISMP through the ISMP Web site (www.ismp.org), by calling 800-FAIL-SAFE, or via e-mail at ismpinfo@ismp.org. ISMP guarantees the confidentiality and security of the information received and respects reporters' wishes as to the level of detail included in publications.},
}
@article {pmid24956815,
year = {2013},
author = {Xiong, YX and Wu, L and Liu, YM and Chen, KL and Xiong, YX and Wu, L and Liu, YM and Chen, KL},
title = {[Identification of Peucedani Radix and its adulterants by DNA barcoding technique].},
journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials},
volume = {36},
number = {11},
pages = {1762-1765},
pmid = {24956815},
issn = {1001-4454},
mesh = {Apiaceae/classification/*genetics ; Base Sequence ; *DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; DNA, Ribosomal Spacer/*genetics ; *Drug Contamination ; Molecular Sequence Data ; Phylogeny ; Plant Roots/genetics ; Plants, Medicinal/classification/genetics ; Polymerase Chain Reaction ; Quality Control ; Species Specificity ; },
abstract = {OBJECTIVE: To identify Peucedani Radix and its adulterants using DNA barcoding technique.<br><br>METHODS: Total genomic DNA was isolated from Peucedani Radix and its adulterants. Nuclear DNA ITS2 sequences were amplified and purified PCR products were sequenced. Sequence assembly and consensus sequence generation were performed using the CodonCode Aligner V3.0. The Kimura 2-Parameter(K2P) distances were calculated using software MEGA 4. 0. Identification analyses were performed using BLAST1, Nearest Distance and Neighbor-Joining (NJ) methods, and the secondary structure of the ITS2 sequence differences between species were analyzed.<br><br>RESULTS: Different samples of Peucedani Radix were gathered together and distinguished from its adulterants by NJ tree. The ITS2 secondary structure showed that Peucedani Radix could be differentiated obviously from its adulterants.<br><br>CONCLUSION: ITS2 sequence is able to identify Peucedani Radix and its adulterants correctly, which provides a scientific basis for fast and accurate identification of the herb.},
}
@article {pmid24956810,
year = {2013},
author = {Liao, J and Chao, Z and Zhang, L},
title = {[Identification of common medicinal snakes in medicated liquor of Guangdong by COI barcode sequence].},
journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials},
volume = {36},
number = {11},
pages = {1740-1742},
pmid = {24956810},
issn = {1001-4454},
mesh = {Animals ; Base Sequence ; China ; *DNA Barcoding, Taxonomic ; DNA Primers ; DNA, Ribosomal Spacer ; Electron Transport Complex IV/*genetics ; *Materia Medica ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Snakes/classification/*genetics ; Species Specificity ; Wine ; },
abstract = {OBJECTIVE: To identify the common snakes in medicated liquor of Guangdong using COI barcode sequence,and to test the feasibility.<br><br>METHODS: The COI barcode sequences of collected medicinal snakes were amplified and sequenced. The sequences combined with the data from GenBank were analyzed for divergence and building a neighbor-joining(NJ) tree with MEGA 5.0.<br><br>RESULTS: The genetic distance and NJ tree demonstrated that there were 241 variable sites in these species, and the average (A + T) content of 56.2% was higher than the average (G + C) content of 43.7%. The maximum interspecific genetic distance was 0.2568, and the minimum was 0. 1519. In the NJ tree,each species formed a monophyletic clade with bootstrap supports of 100%.<br><br>CONCLUSION: DNA barcoding identification method based on the COI sequence is accurate and can be applied to identify the common medicinal snakes.},
}
@article {pmid24955105,
year = {2014},
author = {Chuang, LY and Lane, HY and Lin, YD and Lin, MT and Yang, CH and Chang, HW},
title = {Identification of SNP barcode biomarkers for genes associated with facial emotion perception using particle swarm optimization algorithm.},
journal = {Annals of general psychiatry},
volume = {13},
number = {},
pages = {15},
pmid = {24955105},
issn = {1744-859X},
abstract = {BACKGROUND: Facial emotion perception (FEP) can affect social function. We previously reported that parts of five tested single-nucleotide polymorphisms (SNPs) in the MET and AKT1 genes may individually affect FEP performance. However, the effects of SNP-SNP interactions on FEP performance remain unclear.<br><br>METHODS: This study compared patients with high and low FEP performances (n&#x2009;=&#x2009;89 and 93, respectively). A particle swarm optimization (PSO) algorithm was used to identify the best SNP barcodes (i.e., the SNP combinations and genotypes that revealed the largest differences between the high and low FEP groups).<br><br>RESULTS: The analyses of individual SNPs showed no significant differences between the high and low FEP groups. However, comparisons of multiple SNP-SNP interactions involving different combinations of two to five SNPs showed that the best PSO-generated SNP barcodes were significantly associated with high FEP score. The analyses of the joint effects of the best SNP barcodes for two to five interacting SNPs also showed that the best SNP barcodes had significantly higher odds ratios (2.119 to 3.138; P&#x2009;<&#x2009;0.05) compared to other SNP barcodes. In conclusion, the proposed PSO algorithm effectively identifies the best SNP barcodes that have the strongest associations with FEP performance.<br><br>CONCLUSIONS: This study also proposes a computational methodology for analyzing complex SNP-SNP interactions in social cognition domains such as recognition of facial emotion.},
}
@article {pmid24955007,
year = {2014},
author = {Ajmal Ali, M and Gyulai, G and Hidvégi, N and Kerti, B and Al Hemaid, FM and Pandey, AK and Lee, J},
title = {The changing epitome of species identification - DNA barcoding.},
journal = {Saudi journal of biological sciences},
volume = {21},
number = {3},
pages = {204-231},
pmid = {24955007},
issn = {1319-562X},
abstract = {The discipline taxonomy (the science of naming and classifying organisms, the original bioinformatics and a basis for all biology) is fundamentally important in ensuring the quality of life of future human generation on the earth; yet over the past few decades, the teaching and research funding in taxonomy have declined because of its classical way of practice which lead the discipline many a times to a subject of opinion, and this ultimately gave birth to several problems and challenges, and therefore the taxonomist became an endangered race in the era of genomics. Now taxonomy suddenly became fashionable again due to revolutionary approaches in taxonomy called DNA barcoding (a novel technology to provide rapid, accurate, and automated species identifications using short orthologous DNA sequences). In DNA barcoding, complete data set can be obtained from a single specimen irrespective to morphological or life stage characters. The core idea of DNA barcoding is based on the fact that the highly conserved stretches of DNA, either coding or non coding regions, vary at very minor degree during the evolution within the species. Sequences suggested to be useful in DNA barcoding include cytoplasmic mitochondrial DNA (e.g. cox1) and chloroplast DNA (e.g. rbcL, trnL-F, matK, ndhF, and atpB rbcL), and nuclear DNA (ITS, and house keeping genes e.g. gapdh). The plant DNA barcoding is now transitioning the epitome of species identification; and thus, ultimately helping in the molecularization of taxonomy, a need of the hour. The 'DNA barcodes' show promise in providing a practical, standardized, species-level identification tool that can be used for biodiversity assessment, life history and ecological studies, forensic analysis, and many more.},
}
@article {pmid24954855,
year = {2014},
author = {Li, X and Baker-Andresen, D and Zhao, Q and Marshall, V and Bredy, TW},
title = {Methyl CpG binding domain ultra-sequencing: a novel method for identifying inter-individual and cell-type-specific variation in DNA methylation.},
journal = {Genes, brain, and behavior},
volume = {13},
number = {7},
pages = {721-731},
doi = {10.1111/gbb.12150},
pmid = {24954855},
issn = {1601-183X},
mesh = {Animals ; *CpG Islands ; *DNA Methylation ; Genetic Variation ; Male ; Mice ; Mice, Inbred C57BL ; Neurons/metabolism ; Organ Specificity ; Prefrontal Cortex/cytology/metabolism ; Sequence Analysis, DNA/*methods ; },
abstract = {Experience-dependent changes in DNA methylation can exert profound effects on neuronal function and behaviour. A single learning event can induce a variety of DNA modifications within the neuronal genome, some of which may be common to all individuals experiencing the event, whereas others may occur in a subset of individuals. Variations in experience-induced DNA methylation may subsequently confer increased vulnerability or resilience to the development of neuropsychiatric disorders. However, the detection of experience-dependent changes in DNA methylation in the brain has been hindered by the interrogation of heterogeneous cell populations, regional differences in epigenetic states and the use of pooled tissue obtained from multiple individuals. Methyl CpG Binding Domain Ultra-Sequencing (MBD Ultra-Seq) overcomes current limitations on genome-wide epigenetic profiling by incorporating fluorescence-activated cell sorting and sample-specific barcoding to examine cell-type-specific CpG methylation in discrete brain regions of individuals. We demonstrate the value of this method by characterizing differences in 5-methylcytosine (5mC) in neurons and non-neurons of the ventromedial prefrontal cortex of individual adult C57BL/6 mice, using as little as 50 ng of genomic DNA per sample. We find that the neuronal methylome is characterized by greater CpG methylation as well as the enrichment of 5mC within intergenic loci. In conclusion, MBD Ultra-Seq is a robust method for detecting DNA methylation in neurons derived from discrete brain regions of individual animals. This protocol will facilitate the detection of experience-dependent changes in DNA methylation in a variety of behavioural paradigms and help identify aberrant experience-induced DNA methylation that may underlie risk and resiliency to neuropsychiatric disease.},
}
@article {pmid24947032,
year = {2014},
author = {Gui, H and Bao, JY and Tang, CS and So, MT and Ngo, DN and Tran, AQ and Bui, DH and Pham, DH and Nguyen, TL and Tong, A and Lok, S and Sham, PC and Tam, PK and Cherny, SS and Garcia-Barcelo, MM},
title = {Targeted next-generation sequencing on Hirschsprung disease: a pilot study exploits DNA pooling.},
journal = {Annals of human genetics},
volume = {78},
number = {5},
pages = {381-387},
doi = {10.1111/ahg.12076},
pmid = {24947032},
issn = {1469-1809},
mesh = {Asian People/*genetics ; Enteric Nervous System/physiology ; Female ; Genotyping Techniques/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Hirschsprung Disease/*genetics ; Humans ; Male ; Pilot Projects ; Polymorphism, Single Nucleotide/genetics ; Sensitivity and Specificity ; Signal Transduction/*genetics/physiology ; },
abstract = {To adopt an efficient approach of identifying rare variants possibly related to Hirschsprung disease (HSCR), a pilot study was set up to evaluate the performance of a newly designed protocol for next generation targeted resquencing. In total, 20 Chinese HSCR patients and 20 Chinese sex-matched individuals with no HSCR were included, for which coding sequences (CDS) of 62 genes known to be in signaling pathways relevant to enteric nervous system development were selected for capture and sequencing. Blood DNAs from eight pools of five cases or controls were enriched by PCR-based RainDance technology (RDT) and then sequenced on a 454 FLX platform. As technical validation, five patients from case Pool-3 were also independently enriched by RDT, indexed with barcode and sequenced with sufficient coverage. Assessment for CDS single nucleotide variants showed DNA pooling performed well (specificity/sensitivity at 98.4%/83.7%) at the common variant level; but relatively worse (specificity/sensitivity at 65.5%/61.3%) at the rare variant level. Further Sanger sequencing only validated five out of 12 rare damaging variants likely involved in HSCR. Hence more improvement at variant detection and sequencing technology is needed to realize the potential of DNA pooling for large-scale resequencing projects.},
}
@article {pmid24945930,
year = {2014},
author = {Tekle, YI},
title = {DNA barcoding in amoebozoa and challenges: the example of Cochliopodium.},
journal = {Protist},
volume = {165},
number = {4},
pages = {473-484},
doi = {10.1016/j.protis.2014.05.002},
pmid = {24945930},
issn = {1618-0941},
mesh = {Amoebozoa/drug effects/enzymology/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Genetic Variation/genetics ; Retrospective Studies ; },
abstract = {The diversity of microbial eukaryotes in general and amoeboid lineages in particular is poorly documented. Even though amoeboid lineages are among the most abundant microbes, taxonomic progress in the group has been hindered by the limitations of traditional taxonomy and technical difficultly in studying them. Studies using molecular approaches such as DNA barcoding with cytochrome oxidase I (COI) gene are slowly trickling in for Amoebozoa, and they hopefully will aid in unveiling the true diversity of the group. In this study a retrospective approach is used to test the utility of COI gene in a scale-bearing amoeba, Cochliopodium, which is morphologically well defined. A total of 126 COI sequences and 62 unique haplotypes were generated from 9 Cochliopodium species. Extensive analyses exploring effects of sequence evolution models and length of sequence on genetic diversity computations were conducted. The findings show that COI is a promising marker for Cochliopodium, except in one case where it failed to delineate two morphologically well-defined cochliopodiums. Two species delimitation approaches also recognize 8 genetic lineages out of 9 species examined. The taxonomic implications of these findings and factors that may confound COI as a barcode marker in Cochliopodium and other amoebae are discussed.},
}
@article {pmid24944007,
year = {2014},
author = {Percy, DM and Argus, GW and Cronk, QC and Fazekas, AJ and Kesanakurti, PR and Burgess, KS and Husband, BC and Newmaster, SG and Barrett, SC and Graham, SW},
title = {Understanding the spectacular failure of DNA barcoding in willows (Salix): does this result from a trans-specific selective sweep?.},
journal = {Molecular ecology},
volume = {23},
number = {19},
pages = {4737-4756},
doi = {10.1111/mec.12837},
pmid = {24944007},
issn = {1365-294X},
mesh = {Bayes Theorem ; *DNA Barcoding, Taxonomic ; DNA, Chloroplast/*genetics ; DNA, Plant/genetics ; Genetic Markers ; *Haplotypes ; Hybridization, Genetic ; Molecular Sequence Data ; North America ; Salix/*genetics ; },
abstract = {Willows (Salix: Salicaceae) form a major ecological component of Holarctic floras and consequently are an obvious target for a DNA-based identification system. We surveyed two to seven plastid genome regions (~3.8 kb; ~3% of the genome) from 71 Salix species across all five subgenera, to assess their performance as DNA barcode markers. Although Salix has a relatively high level of interspecific hybridization, this may not sufficiently explain the near complete failure of barcoding that we observed: only one species had a unique barcode. We recovered 39 unique haplotypes, from more than 500 specimens, that could be partitioned into six major haplotype groups. A unique variant of group I (haplotype 1*) was shared by 53 species in three of five Salix subgenera. This unusual pattern of haplotype sharing across infrageneric taxa is suggestive of either a massive nonrandom coalescence failure (incomplete lineage sorting), or of repeated plastid capture events, possibly including a historical selective sweep of haplotype 1* across taxonomic sections. The former is unlikely as molecular dating indicates that haplotype 1* originated recently and is nested in the oldest major haplotype group in the genus. Further, we detected significant non-neutrality in the frequency spectrum of mutations in group I, but not outside group I, and demonstrated a striking absence of geographical (isolation by distance) effects in the haplotype distributions of this group. The most likely explanation for the patterns we observed involves recent repeated plastid capture events, aided by widespread hybridization and long-range seed dispersal, but primarily propelled by one or more trans-species selective sweeps.},
}
@article {pmid24943442,
year = {2014},
author = {Hall, KA and Ekins, MG and Hooper, JN},
title = {Two new desma-less species of Theonella Gray, 1868 (Demospongiae: Astrophorida: Theonellidae), from the Great Barrier Reef, Australia,and a re-evaluation of one species assigned previously to Dercitus Gray, 1867.},
journal = {Zootaxa},
volume = {},
number = {3814},
pages = {451-477},
doi = {10.11646/zootaxa.3814.4.1},
pmid = {24943442},
issn = {1175-5326},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology ; Animals ; Australia ; Biological Evolution ; DNA, Mitochondrial/genetics ; Ecosystem ; Molecular Sequence Data ; Phylogeny ; Porifera/anatomy &amp; histology/*classification/genetics ; },
abstract = {Extensive surveys of the biodiversity on the seafloor of the inter-reef regions of the Great Barrier Reef, Australia, have resulted in the collection of large numbers of sponges, many of which are likely new to science. Identification of these sponges, however, was made difficult by the absence in some specimens of key diagnostic characters, such as megascleres. We used an integrated approach to the taxonomy of these sponges, incorporating morphological examination by SEM, analysis of DNA sequence data (using the COI barcoding fragment of mtDNA) and preliminary studies of the chemistry of the sponges, to describe the new species, which were found to contain no native spicules other than acanthose microrhabds. Here, we propose two new species of Theonella Gray, 1868: Theonella deliqua n. sp. (found in association with a single unidentified species of siliquariid mollusc) and Theonella maricae n. sp. from the Great Barrier Reef. Further, we propose the new combination of Theonella xantha (Sutcliffe, Hooper and Pitcher 2010) n. comb. for another microrhabd-only-bearing species. On the basis of our gene trees, we recognise Theonella (and Theonellidae Lendenfeld, 1903) within Astrophorida Sollas, 1887. We discuss the potential for chemotaxonomic and DNA-based insights into the origins and radiation of species of Theonella and explore the evolutionary significance of the reduced morphology of the three additional species recognised here.},
}
@article {pmid24943438,
year = {2014},
author = {Mortelmans, J and Tomasovic, G and Nagy, ZT},
title = {A remarkable new species of Paraphamartania Engel from Portugal (Diptera, Asilidae).},
journal = {Zootaxa},
volume = {},
number = {3814},
pages = {409-418},
doi = {10.11646/zootaxa.3814.3.8},
pmid = {24943438},
issn = {1175-5326},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology ; Animals ; Diptera/anatomy &amp; histology/*classification/genetics ; Ecosystem ; Female ; Male ; Molecular Sequence Data ; Portugal ; },
abstract = {Paraphamartania marvaoensis sp. nov. is described based on three male and one female specimens from Marvão, Portugal. The discovery of this new species of Paraphamartania is of great significance since it shows the occurrence of a second species of Paraphamartania in the western Mediterranean. High resolution pictures of type material of all three species of Paraphamartania are provided together with a key to these three species. DNA barcodes of this new species are provided, so future workers are able to study relationships of Paraphamartania.},
}
@article {pmid24942183,
year = {2014},
author = {Novo, S and Morató, R and Penon, O and Duran, S and Barrios, L and Nogués, C and Plaza, JA and Pérez-García, L and Mogas, T and Ibáñez, E},
title = {Identification of bovine embryos cultured in groups by attachment of barcodes to the zona pellucida.},
journal = {Reproduction, fertility, and development},
volume = {26},
number = {5},
pages = {645-652},
doi = {10.1071/RD13066},
pmid = {24942183},
issn = {1448-5990},
mesh = {Animals ; Cattle ; Cryopreservation ; *Embryo Culture Techniques ; *Embryonic Development ; Female ; Vitrification ; *Zona Pellucida ; },
abstract = {The low number of oocytes collected from unstimulated donors by ovum pick-up means that embryos produced from each individual female have to be cultured individually or in very small groups. However, it has been demonstrated that single-embryo culture is less efficient than embryo culture in groups. To overcome this limitation, we developed a direct embryo-tagging system, which allows the collective culture of embryos from different origins whilst preserving their pedigree. Presumptive bovine zygotes were tagged with eight wheat-germ agglutinin biofunctionalised polysilicon barcodes attached to the outer surface of the zona pellucida (ZP). Four different barcodes were used to encode groups of 20-25 embryos, which were then cultured in the same drop. Cleavage, Day-7 and Day-8 blastocysts and barcode retention rates were assessed. In addition, Day-7 blastocysts were vitrified and warmed. Barcode attachment to the ZP of bovine embryos affected neither in vitro embryo development nor post-warming survival of the tagged embryos. All the embryos maintained barcodes attached until Day 8 of culture (3.63±0.37 barcodes per embryo) and could be identified. In conclusion, identification of embryos by barcodes attached to the ZP is feasible and will allow the culture of embryos from different donors in the same drop.},
}
@article {pmid24940050,
year = {2014},
author = {McCann, JC and Wickersham, TA and Loor, JJ},
title = {High-throughput Methods Redefine the Rumen Microbiome and Its Relationship with Nutrition and Metabolism.},
journal = {Bioinformatics and biology insights},
volume = {8},
number = {},
pages = {109-125},
pmid = {24940050},
issn = {1177-9322},
abstract = {Diversity in the forestomach microbiome is one of the key features of ruminant animals. The diverse microbial community adapts to a wide array of dietary feedstuffs and management strategies. Understanding rumen microbiome composition, adaptation, and function has global implications ranging from climatology to applied animal production. Classical knowledge of rumen microbiology was based on anaerobic, culture-dependent methods. Next-generation sequencing and other molecular techniques have uncovered novel features of the rumen microbiome. For instance, pyrosequencing of the 16S ribosomal RNA gene has revealed the taxonomic identity of bacteria and archaea to the genus level, and when complemented with barcoding adds multiple samples to a single run. Whole genome shotgun sequencing generates true metagenomic sequences to predict the functional capability of a microbiome, and can also be used to construct genomes of isolated organisms. Integration of high-throughput data describing the rumen microbiome with classic fermentation and animal performance parameters has produced meaningful advances and opened additional areas for study. In this review, we highlight recent studies of the rumen microbiome in the context of cattle production focusing on nutrition, rumen development, animal efficiency, and microbial function.},
}
@article {pmid24938090,
year = {2016},
author = {Huang, Z and Yang, C and Ke, D},
title = {DNA barcoding and phylogenetic relationships in Anatidae.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1042-1044},
doi = {10.3109/19401736.2014.926545},
pmid = {24938090},
issn = {2470-1408},
mesh = {Animals ; Avian Proteins/*genetics ; Birds/classification/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; *Phylogeny ; Species Specificity ; },
abstract = {Mitochondrial cytochrome c oxidase subunit I (COI) has been used as a powerful marker in a variety of phylogenetic studies. According to studies of bird species, the 694-bp sequence of the mitochondrial gene encoding COI is extremely useful for species identification and phylogeny. In the present study, we analyzed the COI barcodes of 79 species from 26 genera belonging to the Anatidae family. Sixty-six species (83.54%) of the species were identified correctly from their DNA barcodes. The remaining 13 species shared barcodes sequences with closely related species. Kimura two-parameter (K2P) distances were calculated between barcodes. The average genetic distance between species was 41 times higher compared to the average genetic distance within species. Neighbor-joining method was used to construct a phylogenetic tree, which grouped all of the genera into three divergent clades. Dendrocygna and Nomonyx + Oxyura were identified as early offshoots of the Anatidae. All the remaining taxa fell into two clades that correspond to the two subfamilies Anserinae and Anatiane. Based on our results, DNA barcoding is an effective molecular tool for Anatidae species identification and phylogenetic inference.},
}
@article {pmid24937469,
year = {2014},
author = {Ferreira, M and Kavalco, KF and de Almeida-Toledo, LF and Garcia, C},
title = {Cryptic diversity between two Imparfinis species (Siluriformes, Heptapteridae) by cytogenetic analysis and DNA barcoding.},
journal = {Zebrafish},
volume = {11},
number = {4},
pages = {306-317},
doi = {10.1089/zeb.2014.0981},
pmid = {24937469},
issn = {1557-8542},
mesh = {Animals ; Biological Evolution ; Brazil ; Catfishes/*classification/*genetics ; Cytogenetic Analysis ; DNA Barcoding, Taxonomic ; Female ; *Genetic Variation ; *Karyotype ; Male ; },
abstract = {Five Imparfinis mirini and one Imparfinis minutus populations were studied using basic cytogenetic and molecular techniques. Cytogenetic analysis showed that I. mirini individuals presented the same diploid number 2n=58 (FN=116). However, they presented two distinct karyomorphs: karyomorph A (36m+18sm+4st) for the Mogi-Guaçu and Paranapanema basin populations, and karyomorph B (42m+12sm+4st) for the Tietê basin populations. I. minutus populations from the Paraíba do Sul basin presented a karyotype identical to karyomorph A of I. mirini. C-banding also presented distinct patterns, with a greater amount of heterochromatin, most of which was pericentromeric and interstitial for karyomorph A I. mirini and I. minutus. There was a minor amount of heterochromatin in karyomorph B, most of which was terminal and interstitial. Simple and interstitial nucleoli organizer regions were located in the biggest metacentric pair of the complement in all populations with GC-rich nature, and this location was confirmed by the fluorescent in situ hybridization technique with 18S ribosomal DNA with 5S rDNA synteny. In molecular analysis by DNA barcoding, two other populations from the Tietê basin were added. The phylogram showed that the populations were more related to the intrabasin. Cytogenetic resemblance among specimens from distinct basins may be the result of either recent convergence or ancestral feature retention not followed by mutations in mitochondrial DNA.},
}
@article {pmid24935524,
year = {2015},
author = {Hubert, N and Espiau, B and Meyer, C and Planes, S},
title = {Identifying the ichthyoplankton of a coral reef using DNA barcodes.},
journal = {Molecular ecology resources},
volume = {15},
number = {1},
pages = {57-67},
doi = {10.1111/1755-0998.12293},
pmid = {24935524},
issn = {1755-0998},
mesh = {Animals ; *Biota ; *Coral Reefs ; *DNA Barcoding, Taxonomic ; Fishes/*classification/*genetics ; Larva/classification/genetics ; },
abstract = {Marine fishes exhibit spectacular phenotypic changes during their ontogeny, and the identification of their early stages is challenging due to the paucity of diagnostic morphological characters at the species level. Meanwhile, the importance of early life stages in dispersal and connectivity has recently experienced an increasing interest in conservation programmes for coral reef fishes. This study aims at assessing the effectiveness of DNA barcoding for the automated identification of coral reef fish larvae through large-scale ecosystemic sampling. Fish larvae were mainly collected using bongo nets and light traps around Moorea between September 2008 and August 2010 in 10 sites distributed in open waters. Fish larvae ranged from 2 to 100 mm of total length, with the most abundant individuals being <5 mm. Among the 505 individuals DNA barcoded, 373 larvae (i.e. 75%) were identified to the species level. A total of 106 species were detected, among which 11 corresponded to pelagic and bathypelagic species, while 95 corresponded to species observed at the adult stage on neighbouring reefs. This study highlights the benefits and pitfalls of using standardized molecular systems for species identification and illustrates the new possibilities enabled by DNA barcoding for future work on coral reef fish larval ecology.},
}
@article {pmid24933453,
year = {2014},
author = {Op De Beeck, M and Lievens, B and Busschaert, P and Declerck, S and Vangronsveld, J and Colpaert, JV},
title = {Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies.},
journal = {PloS one},
volume = {9},
number = {6},
pages = {e97629},
pmid = {24933453},
issn = {1932-6203},
mesh = {Belgium ; Computer Simulation ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/*genetics ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/*genetics ; Fungi/classification/genetics/*isolation &amp; purification ; Polymerase Chain Reaction ; Reproducibility of Results ; Soil Microbiology ; },
abstract = {Current metabarcoding studies aiming to characterize microbial communities generally rely on the amplification and sequencing of relatively short DNA regions. For fungi, the internal transcribed spacer (ITS) region in the ribosomal RNA (rRNA) operon has been accepted as the formal fungal barcode. Despite an increasing number of fungal metabarcoding studies, the amplification efficiency of primers is generally not tested prior to their application in metabarcoding studies. Some of the challenges that metabarcoding primers should overcome efficiently are the amplification of target DNA strands in samples rich in non-target DNA and environmental pollutants, such as humic acids, that may have been co-extracted with DNA. In the current study, three selected primer pairs were tested for their suitability as fungal metabarcoding primers. The selected primer pairs include two primer pairs that have been frequently used in fungal metabarcoding studies (ITS1F/ITS2 and ITS3/ITS4) and a primer pair (ITS86F/ITS4) that has been shown to efficiently amplify the ITS2 region of a broad range of fungal taxa in environmental soil samples. The selected primer pairs were evaluated in a 454 amplicon pyrosequencing experiment, real-time PCR (qPCR) experiments and in silico analyses. Results indicate that experimental evaluation of primers provides valuable information that could aid in the selection of suitable primers for fungal metabarcoding studies. Furthermore, we show that the ITS86F/ITS4 primer pair outperforms other primer pairs tested in terms of in silico primer efficiency, PCR efficiency, coverage, number of reads and number of species-level operational taxonomic units (OTUs) obtained. These traits push the ITS86F/ITS4 primer pair forward as highly suitable for studying fungal diversity and community structures using DNA metabarcoding.},
}
@article {pmid24933158,
year = {2014},
author = {Casini, A and Christodoulou, G and Freemont, PS and Baldwin, GS and Ellis, T and MacDonald, JT},
title = {R2oDNA designer: computational design of biologically neutral synthetic DNA sequences.},
journal = {ACS synthetic biology},
volume = {3},
number = {8},
pages = {525-528},
doi = {10.1021/sb4001323},
pmid = {24933158},
issn = {2161-5063},
mesh = {DNA/*chemistry/*genetics ; Genome ; Monte Carlo Method ; *Software ; Stochastic Processes ; User-Computer Interface ; },
abstract = {R2oDNA Designer is a web application that stochastically generates orthogonal sets of synthetic DNA sequences designed to be biologically neutral. Biologically neutral sequences may be used for directing efficient DNA assembly by overlap-directed methods, as a negative control for functional DNA, as barcodes, or potentially as spacer regions to insulate biological parts from local context. The software creates optimized sequences using a Monte Carlo simulated annealing approach followed by the elimination of sequences homologous to host genomes and commonly used biological parts. An orthogonal set is finally determined by using a network elimination algorithm. Design constraints can be defined using either a web-based graphical user interface (GUI) or uploading a file containing a set of text commands.},
}
@article {pmid24932001,
year = {2014},
author = {Mangul, S and Wu, NC and Mancuso, N and Zelikovsky, A and Sun, R and Eskin, E},
title = {Accurate viral population assembly from ultra-deep sequencing data.},
journal = {Bioinformatics (Oxford, England)},
volume = {30},
number = {12},
pages = {i329-37},
pmid = {24932001},
issn = {1367-4811},
support = {R01-GM083198/GM/NIGMS NIH HHS/United States ; R01 MH101782/MH/NIMH NIH HHS/United States ; P01- HL30568/HL/NHLBI NIH HHS/United States ; U01-DA024417/DA/NIDA NIH HHS/United States ; K25 HL080079/HL/NHLBI NIH HHS/United States ; P01 HL028481/HL/NHLBI NIH HHS/United States ; U01 DA024417/DA/NIDA NIH HHS/United States ; R01-MH101782/MH/NIMH NIH HHS/United States ; K25-HL080079/HL/NHLBI NIH HHS/United States ; R01 ES022282/ES/NIEHS NIH HHS/United States ; P01 HL030568/HL/NHLBI NIH HHS/United States ; R01 GM083198/GM/NIGMS NIH HHS/United States ; R01-ES022282/ES/NIEHS NIH HHS/United States ; P01-HL28481/HL/NHLBI NIH HHS/United States ; P30 CA016042/CA/NCI NIH HHS/United States ; P30 AI028697/AI/NIAID NIH HHS/United States ; },
mesh = {*Algorithms ; *Genome, Viral ; Genomics/methods ; HIV/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Sequence Analysis, DNA ; Software ; },
abstract = {MOTIVATION: Next-generation sequencing technologies sequence viruses with ultra-deep coverage, thus promising to revolutionize our understanding of the underlying diversity of viral populations. While the sequencing coverage is high enough that even rare viral variants are sequenced, the presence of sequencing errors makes it difficult to distinguish between rare variants and sequencing errors.<br><br>RESULTS: In this article, we present a method to overcome the limitations of sequencing technologies and assemble a diverse viral population that allows for the detection of previously undiscovered rare variants. The proposed method consists of a high-fidelity sequencing protocol and an accurate viral population assembly method, referred to as Viral Genome Assembler (VGA). The proposed protocol is able to eliminate sequencing errors by using individual barcodes attached to the sequencing fragments. Highly accurate data in combination with deep coverage allow VGA to assemble rare variants. VGA uses an expectation-maximization algorithm to estimate abundances of the assembled viral variants in the population. RESULTS on both synthetic and real datasets show that our method is able to accurately assemble an HIV viral population and detect rare variants previously undetectable due to sequencing errors. VGA outperforms state-of-the-art methods for genome-wide viral assembly. Furthermore, our method is the first viral assembly method that scales to millions of sequencing reads.<br><br>AVAILABILITY: Our tool VGA is freely available at http://genetics.cs.ucla.edu/vga/},
}
@article {pmid24929135,
year = {2014},
author = {Blasco-Costa, I and Faltýnková, A and Georgieva, S and Skírnisson, K and Scholz, T and Kostadinova, A},
title = {Fish pathogens near the Arctic Circle: molecular, morphological and ecological evidence for unexpected diversity of Diplostomum (Digenea: Diplostomidae) in Iceland.},
journal = {International journal for parasitology},
volume = {44},
number = {10},
pages = {703-715},
doi = {10.1016/j.ijpara.2014.04.009},
pmid = {24929135},
issn = {1879-0135},
mesh = {Animals ; Arctic Regions ; Biodiversity ; DNA, Helminth/genetics ; Ecosystem ; Fish Diseases/epidemiology/*parasitology ; Fishes ; Genetic Variation ; Iceland/epidemiology ; Phylogeny ; Trematoda/*classification/genetics ; Trematode Infections/epidemiology/parasitology/*veterinary ; },
abstract = {Host-parasite systems at high latitudes are promising model systems for detecting and predicting the impact of accelerated environmental change. A major challenge is the lack of baselines for the diversity and distribution of parasites in Arctic wildlife, especially in the freshwater environment. Here we present the first known estimates of the species diversity and host associations of Diplostomum spp. in sub-Arctic freshwater ecosystems of the Palaearctic. Our analyses integrating different analytical approaches, phylogenies based on mitochondrial and nuclear DNA, estimates of genetic divergence, character-based barcoding, morphological examination, precise detection of microhabitat specialisation and host use, led to the discovery of one described and five putative new species that complete their life-cycles within a fairly narrow geographic area in Iceland. This increases the species richness of Diplostomum in Iceland by 200% and raises the number of molecularly characterised species from the Palaearctic to 17 species. Our results suggest that the diversity of Diplostomum spp. is underestimated globally in the high latitude ecosystems and call for a cautionary approach to pathogen identification in developing the much needed baselines of pathogen diversity that may help detect effects of climate change in the freshwater environment of the sub-Arctic.},
}
@article {pmid24927410,
year = {2014},
author = {Dhami, MK and Kumarasinghe, L},
title = {A HRM real-time PCR assay for rapid and specific identification of the emerging pest spotted-wing drosophila (Drosophila suzukii).},
journal = {PloS one},
volume = {9},
number = {6},
pages = {e98934},
pmid = {24927410},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Drosophila/classification/*genetics ; New Zealand ; Pest Control/*methods ; Real-Time Polymerase Chain Reaction/*methods ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Homology, Nucleic Acid ; Species Specificity ; Time Factors ; },
abstract = {Spotted wing drosophila (Drosophila suzukii) is an emerging pest that began spreading in 2008 and its distribution now includes 13 countries across two continents. Countries where it is established have reported significant economic losses of fresh produce, such as cherries due to this species of fly. At larval stages, it is impossible to identify due to its striking similarities with other cosmopolitan and harmless drosophilids. Molecular methods allow identification but the current technique of DNA barcoding is time consuming. We developed and validated a rapid, highly sensitive and specific assay based on real-time PCR and high resolution melt (HRM) analysis using EvaGreen DNA intercalating dye chemistry. Performance characteristics of this qualitative assay, validation and applicability in a New Zealand quarantine framework are discussed. Application of this robust and independently validated assay across the spectrum of key food production and border protection industries will allow us to reduce the further spread of this damaging species worldwide.},
}
@article {pmid24926290,
year = {2014},
author = {Koch, C and Harnisch, F and Schröder, U and Müller, S},
title = {Cytometric fingerprints: evaluation of new tools for analyzing microbial community dynamics.},
journal = {Frontiers in microbiology},
volume = {5},
number = {},
pages = {273},
pmid = {24926290},
issn = {1664-302X},
abstract = {Optical characteristics of individual bacterial cells of natural communities can be measured with flow cytometry (FCM) in high throughput. The resulting data are visualized in cytometric histograms. These histograms represent individual cytometric fingerprints of microbial communities, e.g., at certain time points or microenvironmental conditions. Up to now four tools for analyzing the variation in these cytometric fingerprints are available but have not yet been systematically compared regarding application: Dalmatian Plot, Cytometric Histogram Image Comparison (CHIC), Cytometric Barcoding (CyBar), and FlowFP. In this article these tools were evaluated concerning (i) the required experience of the operator in handling cytometric data sets, (ii) the detection level of changes, (iii) time demand for analysis, and (iv) software requirements. As an illustrative example, FCM was used to characterize the microbial community structure of electroactive microbial biofilms. Their cytometric fingerprints were determined, analyzed with all four tools, and correlated to experimental and functional parameters. The source of inoculum (four different types of wastewater samples) showed the strongest influence on the microbial community structure and biofilm performance while the choice of substrate (acetate or lactate) had no significant effect in the present study. All four evaluation tools were found suitable to monitor structural changes of natural microbial communities. The Dalmatian Plot was shown to be most sensitive to operator impact but nevertheless provided an overview on community shifts. CHIC, CyBar, and FlowFP showed less operator dependence and gave highly resolved information on community structure variation on different detection levels. In conclusion, experimental and productivity parameters correlated with the biofilm structures and practical process integration details were available from cytometric fingerprint analysis.},
}
@article {pmid24925925,
year = {2014},
author = {Chan, YL and Schanzenbach, D and Hickerson, MJ},
title = {Detecting concerted demographic response across community assemblages using hierarchical approximate Bayesian computation.},
journal = {Molecular biology and evolution},
volume = {31},
number = {9},
pages = {2501-2515},
pmid = {24925925},
issn = {1537-1719},
support = {P20 GM103466/GM/NIGMS NIH HHS/United States ; P20 RR016467/RR/NCRR NIH HHS/United States ; 8 P20 GM 103466-11/GM/NIGMS NIH HHS/United States ; 5P20RR016467-11/RR/NCRR NIH HHS/United States ; },
mesh = {Adaptation, Biological ; Animals ; Australia ; Bayes Theorem ; Birds/classification/*genetics ; Computational Biology/*methods ; Computer Simulation ; Models, Statistical ; Phylogeny ; Phylogeography ; Population Density ; },
abstract = {Methods that integrate population-level sampling from multiple taxa into a single community-level analysis are an essential addition to the comparative phylogeographic toolkit. Detecting how species within communities have demographically tracked each other in space and time is important for understanding the effects of future climate and landscape changes and the resulting acceleration of extinctions, biological invasions, and potential surges in adaptive evolution. Here, we present a statistical framework for such an analysis based on hierarchical approximate Bayesian computation (hABC) with the goal of detecting concerted demographic histories across an ecological assemblage. Our method combines population genetic data sets from multiple taxa into a single analysis to estimate: 1) the proportion of a community sample that demographically expanded in a temporally clustered pulse and 2) when the pulse occurred. To validate the accuracy and utility of this new approach, we use simulation cross-validation experiments and subsequently analyze an empirical data set of 32 avian populations from Australia that are hypothesized to have expanded from smaller refugia populations in the late Pleistocene. The method can accommodate data set heterogeneity such as variability in effective population size, mutation rates, and sample sizes across species and exploits the statistical strength from the simultaneous analysis of multiple species. This hABC framework used in a multitaxa demographic context can increase our understanding of the impact of historical climate change by determining what proportion of the community responded in concert or independently and can be used with a wide variety of comparative phylogeographic data sets as biota-wide DNA barcoding data sets accumulate.},
}
@article {pmid24925024,
year = {2014},
author = {Decaup, E and Duault, C and Bezombes, C and Poupot, M and Savina, A and Olive, D and Fournié, JJ},
title = {Phosphoantigens and butyrophilin 3A1 induce similar intracellular activation signaling in human TCRVγ9+ γδ T lymphocytes.},
journal = {Immunology letters},
volume = {161},
number = {1},
pages = {133-137},
doi = {10.1016/j.imlet.2014.05.011},
pmid = {24925024},
issn = {1879-0542},
mesh = {Antibodies, Monoclonal/pharmacology ; Antigens, CD/*metabolism ; Antigens, Surface/metabolism ; Butyrophilins ; Cell Line ; Humans ; Immunophenotyping ; *Lymphocyte Activation ; Phosphoproteins/*immunology ; Receptors, Antigen, T-Cell, gamma-delta/*metabolism ; *Signal Transduction/drug effects ; T-Lymphocyte Subsets/drug effects/*immunology/*metabolism ; },
abstract = {Human γδ cells expressing TCRVγ9 are T lymphocytes with great potential for cancer immunotherapy and unconventional pattern of antigen specificity. These HLA-unrestricted lymphocytes are specifically reactive to non-peptide metabolites (phosphoantigens) and to the butyrophilin 3A (BTN3A/CD277) protein. Whether recognition of such highly different structures trigger the same activation signaling pathway remains unclear, however. Here we combined fluorescent cell barcoding and phosphoflow analysis of TCRVγ9(+) T lymphocytes to compare simultaneously the level of several signaling phosphoproteins after activation by phosphoantigen (BrHPP) or by anti-BTN3A (monoclonal antibody 20.1). This approach shows that the same pathways involving ZAP70, PLCγ2, Akt, NFκB p65, MAPK p38 and Erk1, were induced by either of these stimuli. These data strongly suggest the TCRVγ9(+) T lymphocytes detect phosphoantigens and butyrophilin A3 by the same recognition process.},
}
@article {pmid24921655,
year = {2014},
author = {Helyar, SJ and Lloyd, HA and de Bruyn, M and Leake, J and Bennett, N and Carvalho, GR},
title = {Fish product mislabelling: failings of traceability in the production chain and implications for illegal, unreported and unregulated (IUU) fishing.},
journal = {PloS one},
volume = {9},
number = {6},
pages = {e98691},
pmid = {24921655},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Fish Products/economics/*standards ; Fishes/genetics ; Food Labeling/legislation &amp; jurisprudence/*methods ; United Kingdom ; },
abstract = {Increasing consumer demand for seafood, combined with concern over the health of our oceans, has led to many initiatives aimed at tackling destructive fishing practices and promoting the sustainability of fisheries. An important global threat to sustainable fisheries is Illegal, Unreported and Unregulated (IUU) fishing, and there is now an increased emphasis on the use of trade measures to prevent IUU-sourced fish and fish products from entering the international market. Initiatives encompass new legislation in the European Union requiring the inclusion of species names on catch labels throughout the distribution chain. Such certification measures do not, however, guarantee accuracy of species designation. Using two DNA-based methods to compare species descriptions with molecular ID, we examined 386 samples of white fish, or products labelled as primarily containing white fish, from major UK supermarket chains. Species specific real-time PCR probes were used for cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) to provide a highly sensitive and species-specific test for the major species of white fish sold in the UK. Additionally, fish-specific primers were used to sequence the forensically validated barcoding gene, mitochondrial cytochrome oxidase I (COI). Overall levels of congruence between product label and genetic species identification were high, with 94.34% of samples correctly labelled, though a significant proportion in terms of potential volume, were mislabelled. Substitution was usually for a cheaper alternative and, in one case, extended to a tropical species. To our knowledge, this is the first published study encompassing a large-scale assessment of UK retailers, and if representative, indicates a potentially significant incidence of incorrect product designation.},
}
@article {pmid24919645,
year = {2014},
author = {Wang, Y and Wen, Z and Shen, J and Cheng, W and Li, J and Qin, X and Ma, D and Shi, Y},
title = {Comparison of the performance of Ion Torrent chips in noninvasive prenatal trisomy detection.},
journal = {Journal of human genetics},
volume = {59},
number = {7},
pages = {393-396},
pmid = {24919645},
issn = {1435-232X},
mesh = {Female ; Humans ; Karyotyping ; Oligonucleotide Array Sequence Analysis/*methods/standards ; Pregnancy ; Prenatal Diagnosis/*methods/standards ; Reproducibility of Results ; Trisomy/*diagnosis/genetics ; },
abstract = {Semiconductor high-throughput sequencing, represented by Ion Torrent PGM/Proton, proves to be feasible in the noninvasive prenatal diagnosis of fetal aneuploidies. It is commendable that, with less data and relevant cost also, an accurate result can be achieved owing to the high sensitivity and specificity of such kind of technology. We conducted a comparative analysis of the performance of four different Ion chips in detecting fetal chromosomal aneuploidies. Eight maternal plasma DNA samples, including four pregnancies with normal fetuses and four with trisomy 21 fetuses, were sequenced on Ion Torrent 314/316/318/PI chips, respectively. Results such as read mapped ratio, correlation coefficient and phred quality score were calculated and parallelly compared. All samples were correctly classified even with low-throughput chip, and, among the four chips, the 316 chip had the highest read mapped ratio, correlation coefficient, mean read length and phred quality score. All chips were well consistent with each other. Our results showed that all Ion chips are applicable in noninvasive prenatal fetal aneuploidy diagnosis. We recommend researchers or clinicians to use the appropriate chip with barcoding technology on the basis of the sample number.},
}
@article {pmid24919404,
year = {2015},
author = {Jaén-Molina, R and Marrero-Rodríguez, &#xc1; and Reyes-Betancort, JA and Santos-Guerra, A and Naranjo-Suárez, J and Caujapé-Castells, J},
title = {Molecular taxonomic identification in the absence of a 'barcoding gap': a test with the endemic flora of the Canarian oceanic hotspot.},
journal = {Molecular ecology resources},
volume = {15},
number = {1},
pages = {42-56},
doi = {10.1111/1755-0998.12292},
pmid = {24919404},
issn = {1755-0998},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Chloroplast/genetics ; DNA, Plant/genetics ; *Genetics, Population ; Magnoliopsida/*classification/*genetics ; Spain ; },
abstract = {We use a comprehensive subset of Canarian angiosperms corresponding to 23 families, 35 genera and 60 Canarian endemic taxa to test whether this flora is suitable to taxonomic identification with the two proposed plant DNA barcode sequences and whether these sequences may reveal the existence of cryptic species overlooked by morphology. The rate of discrimination success between the insular congeneric samples using the rbcL+matK combination and a 'character-based' approach (where we use only the combination of nucleotide positions in an alignment that allows unambiguous species identification) is higher (82.29%) than that obtained with the 'distance-based' approach (80.20%) used by the CBOL Plant Working Group in 2009 and also when compared with tests conducted in other floras. This suggests that the molecular identification of the Canarian endemic flora can be achieved as successfully as in other floras where the incidence of radiation is not as relevant. The facts that (i) a distance-based criterion was unable to discriminate between congeneric and conspecific comparisons and (ii) only the character-based discrimination criterion resolved cases that the distance-based criterion did not, further support the use of a character discrimination approach for a more efficient DNA barcoding of floras from oceanic islands like the Canaries. Thus, a barcoding gap seems not to be necessary for the correct molecular characterization of the Canarian flora. DNA barcodes also suggest the possible existence of cryptic taxa to be further investigated by morphology and that the current taxonomic status of some of the taxa analysed may need revision.},
}
@article {pmid24917876,
year = {2014},
author = {Sun, C and McAndrew, T and Smith, BC and Chen, Z and Frimer, M and Burk, RD},
title = {Characterization of HPV DNA methylation of contiguous CpG sites by bisulfite treatment and massively parallel sequencing-the FRAGMENT approach.},
journal = {Frontiers in genetics},
volume = {5},
number = {},
pages = {150},
pmid = {24917876},
issn = {1664-8021},
support = {P30 AI051519/AI/NIAID NIH HHS/United States ; P30 CA013330/CA/NCI NIH HHS/United States ; R01 CA078527/CA/NCI NIH HHS/United States ; U01 CA078527/CA/NCI NIH HHS/United States ; },
abstract = {Invasive cervix cancer (ICC) is the third most common malignant tumor in women and human papillomavirus 16 (HPV16) causes more than 50% of ICC. DNA methylation is a covalent modification predominantly occurring at CpG dinucleotides and increased methylation across the HPV16 genome is strongly associated with ICC development. Next generation (Next Gen) sequencing has been proposed as a novel approach to determine DNA methylation. However, utilization of this method to survey CpG methylation in the HPV16 genome is not well described. Moreover, it provides additional information on methylation "haplotypes." In the current study, we chose 12 random samples, amplified multiple segments in the HPV16 bisulfite treated genome with specific barcodes, inspected the methylation ratio at 31 CpG sites for all samples using Illumina sequencing, and compared the results with quantitative pyrosequencing. Most of the CpG sites were highly consistent between the two approaches (overall correlation, r = 0.92), thus verifying that Next Gen sequencing is an accurate and convenient method to survey HPV16 methylation and thus can be used in clinical samples for risk assessment. Moreover, the CpG methylation patterns (methylation haplotypes) in single molecules identified an excess of complete-and non-methylated molecules and a substantial amount of partial-methylated ones, thus indicating a complex dynamic for the mechanisms of HPV16 CpG methylation. In summary, the advantages of Next Gen sequencing compared to pyrosequencing for HPV genome methylation analyses include higher throughput, increased resolution, and improved efficiency of time and resources.},
}
@article {pmid24915194,
year = {2014},
author = {Serrao, NR and Steinke, D and Hanner, RH},
title = {Calibrating snakehead diversity with DNA barcodes: expanding taxonomic coverage to enable identification of potential and established invasive species.},
journal = {PloS one},
volume = {9},
number = {6},
pages = {e99546},
pmid = {24915194},
issn = {1932-6203},
mesh = {Animals ; Calibration ; *DNA Barcoding, Taxonomic ; Fishes/*classification/*genetics ; *Genetic Variation ; Haplotypes ; *Introduced Species ; Phenotype ; Phylogeny ; Reference Standards ; Species Specificity ; },
abstract = {Detecting and documenting the occurrence of invasive species outside their native range requires tools to support their identification. This can be challenging for taxa with diverse life stages and/or problematic or unresolved morphological taxonomies. DNA barcoding provides a potent method for identifying invasive species, as it allows for species identification at all life stages, including fragmentary remains. It also provides an efficient interim taxonomic framework for quantifying cryptic genetic diversity by parsing barcode sequences into discontinuous haplogroup clusters (typical of reproductively isolated species) and labelling them with unique alphanumeric identifiers. Snakehead fishes are a diverse group of opportunistic predators endemic to Asia and Africa that may potentially pose significant threats as aquatic invasive species. At least three snakehead species (Channa argus, C. maculata, and C. marulius) are thought to have entered North America through the aquarium and live-food fish markets, and have established populations, yet their origins remain unclear. The objectives of this study were to assemble a library of DNA barcode sequences derived from expert identified reference specimens in order to determine the identity and aid invasion pathway analysis of the non-indigenous species found in North America using DNA barcodes. Sequences were obtained from 121 tissue samples representing 25 species and combined with public records from GenBank for a total of 36 putative species, which then partitioned into 49 discrete haplogroups. Multiple divergent clusters were observed within C. gachua, C. marulius, C. punctata and C. striata suggesting the potential presence of cryptic species diversity within these lineages. Our findings demonstrate that DNA barcoding is a valuable tool for species identification in challenging and under-studied taxonomic groups such as snakeheads, and provides a useful framework for inferring invasion pathway analysis.},
}
@article {pmid24911683,
year = {2014},
author = {Reyes, I and Rollins, T and Mahnke, A and Kadolph, C and Minor, G and Keifer, M},
title = {Farm Mapping to Assist, Protect, and Prepare Emergency Responders: Farm MAPPER.},
journal = {Journal of agromedicine},
volume = {19},
number = {2},
pages = {90-95},
doi = {10.1080/1059924X.2014.888024},
pmid = {24911683},
issn = {1545-0813},
mesh = {*Agriculture ; *Emergency Responders ; Firefighters ; Humans ; *Internet ; },
abstract = {Responders such as firefighters and emergency medical technicians who respond to farm emergencies often face complex and unknown environments. They may encounter hazards such as fuels, solvents, pesticides, caustics, and exploding gas storage cylinders. Responders may be unaware of dirt roads within the farm that can expedite their arrival at critical sites or snow-covered manure pits that act as hidden hazards. A response to a farm, unless guided by someone familiar with the operation, may present a risk to responders and post a challenge in locating the victim. This project explored the use of a Web-based farm-mapping application optimized for tablets and accessible via easily accessible on-site matrix barcodes, or quick response codes (QR codes), to provide emergency responders with hazard and resource information to agricultural operations. Secured portals were developed for both farmers and responders, allowing both parties to populate and customize farm maps with icons. Data were stored online and linked to QR codes attached to mailbox posts where emergency responders may read them with a mobile device. Mock responses were conducted on dairy farms to test QR code linking efficacy, Web site security, and field usability. Findings from farmer usability tests showed willingness to enter data as well as ease of Web site navigation and data entry even with farmers who had limited computer knowledge. Usability tests with emergency responders showed ease of QR code connectivity to the farm maps and ease of Web site navigation. Further research is needed to improve data security as well as assess the program's applicability to nonfarm environments and integration with existing emergency response systems. The next phases of this project will expand the program for regional and national use, develop QR code-linked, Web-based extrication guidance for farm machinery for victim entrapment rescue, and create QR code-linked online training videos and materials for limited English proficient immigrant farm workers.},
}
@article {pmid24911009,
year = {2014},
author = {Lam, KN and Hall, MW and Engel, K and Vey, G and Cheng, J and Neufeld, JD and Charles, TC},
title = {Evaluation of a pooled strategy for high-throughput sequencing of cosmid clones from metagenomic libraries.},
journal = {PloS one},
volume = {9},
number = {6},
pages = {e98968},
pmid = {24911009},
issn = {1932-6203},
support = {//Canadian Institutes of Health Research/Canada ; },
mesh = {Cloning, Molecular ; Cosmids/*genetics ; *Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Metagenomics ; Sequence Analysis, DNA/*methods ; },
abstract = {High-throughput sequencing methods have been instrumental in the growing field of metagenomics, with technological improvements enabling greater throughput at decreased costs. Nonetheless, the economy of high-throughput sequencing cannot be fully leveraged in the subdiscipline of functional metagenomics. In this area of research, environmental DNA is typically cloned to generate large-insert libraries from which individual clones are isolated, based on specific activities of interest. Sequence data are required for complete characterization of such clones, but the sequencing of a large set of clones requires individual barcode-based sample preparation; this can become costly, as the cost of clone barcoding scales linearly with the number of clones processed, and thus sequencing a large number of metagenomic clones often remains cost-prohibitive. We investigated a hybrid Sanger/Illumina pooled sequencing strategy that omits barcoding altogether, and we evaluated this strategy by comparing the pooled sequencing results to reference sequence data obtained from traditional barcode-based sequencing of the same set of clones. Using identity and coverage metrics in our evaluation, we show that pooled sequencing can generate high-quality sequence data, without producing problematic chimeras. Though caveats of a pooled strategy exist and further optimization of the method is required to improve recovery of complete clone sequences and to avoid circumstances that generate unrecoverable clone sequences, our results demonstrate that pooled sequencing represents an effective and low-cost alternative for sequencing large sets of metagenomic clones.},
}
@article {pmid24901064,
year = {2014},
author = {Duong, B and Liu, H and Ma, L and Su, M},
title = {Covert thermal barcodes based on phase change nanoparticles.},
journal = {Scientific reports},
volume = {4},
number = {},
pages = {5170},
pmid = {24901064},
issn = {2045-2322},
abstract = {An unmet need is to develop covert barcodes that can be used to track-trace objects, and authenticate documents. This paper describes a new nanoparticle-based covert barcode system, in which a selected panel of solid-to-liquid phase change nanoparticles with discrete and sharp melting peaks is added in a variety of objects such as explosive derivative, drug, polymer, and ink. This method has high labeling capacity owing to the small sizes of nanoparticles, sharp melting peaks, and large scan range of thermal analysis. The thermal barcode can enhance forensic investigation by its technical readiness, structural covertness, and robustness.},
}
@article {pmid24899857,
year = {2014},
author = {Karanovic, T and Kim, K and Lee, W},
title = {Morphological and molecular affinities of two East Asian species of Stenhelia (Crustacea, Copepoda, Harpacticoida).},
journal = {ZooKeys},
volume = {},
number = {411},
pages = {105-143},
pmid = {24899857},
issn = {1313-2989},
abstract = {Definition of monophyletic supraspecific units in the harpacticoid subfamily Stenheliinae Brady, 1880 has been considered problematic and hindered by the lack of molecular or morphology based phylogenies, as well as by incomplete original descriptions of many species. Presence of a modified seta on the fifth leg endopod has been suggested recently as a synapomorphy of eight species comprising the redefined genus Stenhelia Boeck, 1865, although its presence was not known in S. pubescens Chislenko, 1978. We redescribe this species in detail here, based on our freshly collected topotypes from the Russian Far East. The other species redescribed in this paper was collected from the southern coast of South Korea and identified as the Chinese S. taiae Mu &amp; Huys, 2002, which represents its second record ever and the first one in Korea. A fragment of the mtCOI gene was successfully PCR-amplified from two specimens of each species, which represents the first molecular data for this genus, and from additional 19 specimens belonging to six different species of other stenheliins from Korea and Russia. Reconstructed phylogenies confirm previously postulated monophyly of Stenhelia and polyphyly of the closely related genus Delavalia Brady, 1869. Average pairwise maximum likelihood distances between S. pubescens and S. taiae are only slightly above 10%, suggesting a very close relationship despite numerous newly discovered micro-morphological differences and despite macro-morphological similarities being probable plesiomorphies.},
}
@article {pmid24899845,
year = {2014},
author = {Baldwin, CC and Robertson, DR},
title = {A new Liopropoma sea bass (Serranidae, Epinephelinae, Liopropomini) from deep reefs off Curaçao, southern Caribbean, with comments on depth distributions of western Atlantic liopropomins.},
journal = {ZooKeys},
volume = {},
number = {409},
pages = {71-92},
pmid = {24899845},
issn = {1313-2989},
abstract = {Collecting reef-fish specimens using a manned submersible diving to 300 m off Curaçao, southern Caribbean, is resulting in the discovery of numerous new fish species. The new Liopropoma sea bass described here differs from other western Atlantic members of the genus in having VIII, 13 dorsal-fin rays; a moderately indented dorsal-fin margin; a yellow-orange stripe along the entire upper lip; a series of approximately 13 white, chevron-shaped markings on the ventral portion of the trunk; and a reddish-black blotch on the tip of the lower caudal-fin lobe. The new species, with predominantly yellow body and fins, closely resembles the other two "golden basses" found together with it at Curaçao: L. aberrans and L. olneyi. It also shares morphological features with the other western Atlantic liopropomin genus, Bathyanthias. Preliminary phylogenetic data suggest that western Atlantic liopropomins, including Bathyanthias, are monophyletic with respect to Indo-Pacific Liopropoma, and that Bathyanthias is nested within Liopropoma, indicating a need for further study of the generic limits of Liopropoma. The phylogenetic data also suggest that western Atlantic liopropomins comprise three monophyletic clades that have overlapping depth distributions but different depth maxima (3-135 m, 30-150 m, 133-411 m). The new species has the deepest depth range (182-241 m) of any known western Atlantic Liopropoma species. Both allopatric and depth-mediated ecological speciation may have contributed to the evolution of western Atlantic Liopropomini.},
}
@article {pmid24896814,
year = {2014},
author = {Coeur d'Acier, A and Cruaud, A and Artige, E and Genson, G and Clamens, AL and Pierre, E and Hudaverdian, S and Simon, JC and Jousselin, E and Rasplus, JY},
title = {DNA barcoding and the associated PhylAphidB@se website for the identification of European aphids (Insecta: Hemiptera: Aphididae).},
journal = {PloS one},
volume = {9},
number = {6},
pages = {e97620},
pmid = {24896814},
issn = {1932-6203},
mesh = {Animals ; Aphids/*genetics ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Europe ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {UNLABELLED: Aphids constitute a diverse group of plant-feeding insects and are among the most important crop pests in temperate regions. Their morphological identification is time-consuming and requires specific knowledge, training and skills that may take years to acquire. We assessed the advantages and limits of DNA barcoding with the standard COI barcode fragment for the identification of European aphids. We constructed a large reference dataset of barcodes from 1020 specimens belonging to 274 species and 87 genera sampled throughout Europe and set up a database-driven website allowing species identification from query sequences.<br><br>RESULTS: In this unbiased sampling of the taxonomic diversity of European aphids, intraspecific divergence ranged from 0.0% to 3.9%, with a mean value of 0.29%, whereas mean congeneric divergence was 6.4%, ranging from 0.0% to 15%. Neighbor-joining analysis generated a tree in which most species clustered in distinct genetic units. Most of the species with undifferentiated or overlapping barcodes belonged to the genus Aphis or, to a lesser extent, the genera Brachycaudus, Dysaphis and Macrosiphum. The taxa involved were always morphologically similar or closely related and belonged to species groups known to present taxonomic difficulties.<br><br>CONCLUSIONS: These data confirm that COI barcoding is a useful identification tool for aphids. Barcode identification is straightforward and reliable for 80% of species, including some difficult to distinguish on the basis of morphological characters alone. Unsurprisingly, barcodes often failed to distinguish between species from groups for which classical taxonomy has also reached its limits, leading to endless revisions and discussions about species and subspecies definitions. In such cases, the development of an effective procedure for the accurate identification of aphid specimens continues to pose a difficult challenge.},
}
@article {pmid24892414,
year = {2014},
author = {Ruano-Fajardo, G and Rovito, SM and Ladle, RJ},
title = {Bromeliad selection by two salamander species in a harsh environment.},
journal = {PloS one},
volume = {9},
number = {6},
pages = {e98474},
pmid = {24892414},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Ecosystem ; Hydrogen-Ion Concentration ; Temperature ; Caudata/classification/*genetics ; },
abstract = {Bromeliad phytotelmata are frequently used by several Neotropical amphibian taxa, possibly due to their high humidity, microclimatic stability, and role as a refuge from predators. Indeed, the ability of phytotelmata to buffer against adverse environmental conditions may be instrumental in allowing some amphibian species to survive during periods of environmental change or to colonize sub-optimal habitats. Association between bromeliad traits and salamanders has not been studied at a fine scale, despite the intimate association of many salamander species with bromeliads. Here, we identify microhabitat characteristics of epiphytic bromeliads used by two species of the Bolitoglossa morio group (B. morio and B. pacaya) in forest disturbed by volcanic activity in Guatemala. Specifically, we measured multiple variables for bromeliads (height and position in tree, phytotelma water temperature and pH, canopy cover, phytotelma size, leaf size, and tree diameter at breast height), as well as salamander size. We employed a DNA barcoding approach to identify salamanders. We found that B. morio and B. pacaya occurred in microsympatry in bromeliads and that phytotelmata size and temperature of bromeliad microhabitat were the most important factors associated with the presence of salamanders. Moreover, phytotelmata with higher pH contained larger salamanders, suggesting that larger salamanders or aggregated individuals might modify pH. These results show that bromeliad selection is nonrandom with respect to microhabitat characteristics, and provide insight into the relationship between salamanders and this unique arboreal environment.},
}
@article {pmid24888892,
year = {2014},
author = {Lentendu, G and Wubet, T and Chatzinotas, A and Wilhelm, C and Buscot, F and Schlegel, M},
title = {Effects of long-term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach.},
journal = {Molecular ecology},
volume = {23},
number = {13},
pages = {3341-3355},
doi = {10.1111/mec.12819},
pmid = {24888892},
issn = {1365-294X},
mesh = {*Biodiversity ; Cercozoa/classification/genetics ; Chrysophyta/classification/genetics ; DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; *Fertilizers ; Fungi/classification/genetics ; Kinetoplastida/classification/genetics ; Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 23S/genetics ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {To understand the fine-scale effects of changes in nutrient availability on eukaryotic soil microorganisms communities, a multiple barcoding approach was used to analyse soil samples from four different treatments in a long-term fertilization experiment. We performed PCR amplification on soil DNA with primer pairs specifically targeting the 18S rRNA genes of all eukaryotes and three protist groups (Cercozoa, Chrysophyceae-Synurophyceae and Kinetoplastida) as well as the ITS gene of fungi and the 23S plastid rRNA gene of photoautotrophic microorganisms. Amplicons were pyrosequenced, and a total of 88,706 quality filtered reads were clustered into 1232 operational taxonomic units (OTU) across the six data sets. Comparisons of the taxonomic coverage achieved based on overlapping assignment of OTUs revealed that half of the eukaryotic taxa identified were missed by the universal eukaryotic barcoding marker. There were only little differences in OTU richness observed between organic- (farmyard manure), mineral- and nonfertilized soils. However, the community compositions appeared to be strongly structured by organic fertilization in all data sets other than that generated using the universal eukaryotic 18S rRNA gene primers, whereas mineral fertilization had only a minor effect. In addition, a co-occurrence based network analysis revealed complex potential interaction patterns between OTUs from different trophic levels, for example between fungivorous flagellates and fungi. Our results demonstrate that changes in pH, moisture and organic nutrients availability caused shifts in the composition of eukaryotic microbial communities at multiple trophic levels.},
}
@article {pmid24887104,
year = {2014},
author = {Nikinmaa, M},
title = {What is biodiversity? Stepping forward from barcoding to understanding biological differences.},
journal = {Marine genomics},
volume = {17},
number = {},
pages = {65-67},
doi = {10.1016/j.margen.2014.05.007},
pmid = {24887104},
issn = {1876-7478},
mesh = {*Biodiversity ; *Biological Evolution ; Classification/*methods ; DNA Barcoding, Taxonomic/trends ; Physiology, Comparative/methods/*trends ; Selection, Genetic ; },
abstract = {This opinion paper gives personal views of the direction that cataloguing biodiversity should be going in. Although molecular taxonomy enables rapid and high throughput identification of species, it needs to be anchored to traditional taxonomy, because without information of actual biological properties of species, DNA barcoding just reports differences in selected DNA sequences, which need not have anything to do with the biological properties of the organisms, and the reasons for the development of the species. Since functional differences are the most common reason behind species differences, the future of cataloguing biodiversity and biodiversity research is, in my opinion, in trying to integrate genomic research to comparative physiology in order to be able to evaluate which functional properties have likely been important in generating biodiversity. This task is overwhelming, and requires forgetting the traditional disciplines. Further, major problems associated with the present-day treatment of genomic data are presented from my viewpoint.},
}
@article {pmid24886633,
year = {2014},
author = {Porter, SN and Baker, LC and Mittelman, D and Porteus, MH},
title = {Lentiviral and targeted cellular barcoding reveals ongoing clonal dynamics of cell lines in vitro and in vivo.},
journal = {Genome biology},
volume = {15},
number = {5},
pages = {R75},
pmid = {24886633},
issn = {1474-760X},
mesh = {3T3 Cells ; Animals ; Cell Culture Techniques ; Cell Line, Tumor ; Cell Tracking/*methods ; *Clonal Evolution ; Clone Cells/cytology ; DNA Barcoding, Taxonomic/*methods ; HEK293 Cells ; HeLa Cells ; Humans ; In Vitro Techniques ; K562 Cells ; Lentivirus/*physiology ; Mice ; Transduction, Genetic ; Transplantation, Heterologous ; },
abstract = {BACKGROUND: Cell lines are often regarded as clonal, even though this simplifies what is known about mutagenesis, transformation and other processes that destabilize them over time. Monitoring these clonal dynamics is important for multiple areas of biomedical research, including stem cell and cancer biology. Tracking the contributions of individual cells to large populations, however, has been constrained by limitations in sensitivity and complexity.<br><br>RESULTS: We utilize cellular barcoding methods to simultaneously track the clonal contributions of tens of thousands of cells. We demonstrate that even with optimal culturing conditions, common cell lines including HeLa, K562 and HEK-293 T exhibit ongoing clonal dynamics. Starting a population with a single clone diminishes but does not eradicate this phenomenon. Next, we compare lentiviral and zinc-finger nuclease barcode insertion approaches, finding that the zinc-finger nuclease protocol surprisingly results in reduced clonal diversity. We also document the expected reduction in clonal complexity when cells are challenged with genotoxic stress. Finally, we demonstrate that xenografts maintain clonal diversity to a greater extent than in vitro culturing of the human non-small-cell lung cancer cell line HCC827.<br><br>CONCLUSIONS: We demonstrate the feasibility of tracking and quantifying the clonal dynamics of entire cell populations within multiple cultured cell lines. Our results suggest that cell heterogeneity should be considered in the design and interpretation of in vitro culture experiments. Aside from clonal cell lines, we propose that cellular barcoding could prove valuable in modeling the clonal behavior of heterogeneous cell populations over time, including tumor populations treated with chemotherapeutic agents.},
}
@article {pmid24885602,
year = {2014},
author = {Ford, E and Nikopoulou, C and Kokkalis, A and Thanos, D},
title = {A method for generating highly multiplexed ChIP-seq libraries.},
journal = {BMC research notes},
volume = {7},
number = {},
pages = {312},
pmid = {24885602},
issn = {1756-0500},
mesh = {*Chromatin Immunoprecipitation ; },
abstract = {BACKGROUND: The barcoding of next generation sequencing libraries has become an essential part of the experimental design. Barcoding not only allows the sequencing of more than one sample per lane, but also reduces technical bias. However, current barcoding strategies impose significant limitations and/or technical barriers in their implementation for ChIP-sequencing.<br><br>FINDINGS: Converting Y-shaped sequencing adapters to double stranded DNA prior to agarose gel size selection reduces adapter dimer contamination and quantitating the number of cycles required for amplification of the library with qPCR prior to library amplification eliminates library over-amplification.<br><br>CONCLUSIONS: We describe an efficient and cost effective method for making barcoded ChIP-seq libraries for sequencing on the Illumina platform.},
}
@article {pmid24885485,
year = {2014},
author = {Doerder, FP},
title = {Abandoning sex: multiple origins of asexuality in the ciliate Tetrahymena.},
journal = {BMC evolutionary biology},
volume = {14},
number = {},
pages = {112},
pmid = {24885485},
issn = {1471-2148},
mesh = {Cell Nucleus/genetics ; Conjugation, Genetic ; Cyclooxygenase 1/genetics ; DNA, Protozoan/genetics ; Phylogeny ; Reproduction ; Reproduction, Asexual ; Tetrahymena/*classification/cytology/genetics/*physiology ; Tetrahymena thermophila/cytology/genetics ; },
abstract = {BACKGROUND: By segregating somatic and germinal functions into large, compound macronuclei and small diploid micronuclei, respectively, ciliates can explore sexuality in ways other eukaryotes cannot. Sex, for instance, is not for reproduction but for nuclear replacement in the two cells temporarily joined in conjugation. With equal contributions from both conjugants, there is no cost of sex which theory predicts should favor asexuality. Yet ciliate asexuality is rare. The exceptional Tetrahymena has abandoned sex through loss of the micronucleus; its amicronucleates are abundant in nature where they reproduce by binary fission but never form conjugating pairs. A possible reason for their abundance is that the Tetrahymena macronucleus does not accumulate mutations as proposed by Muller's ratchet. As such, Tetrahymena amicronucleates have the potential to be very old. This study used cytochrome oxidase-1 barcodes to determine the phylogenetic origin and relative age of amicronucleates isolated from nature.<br><br>RESULTS: Amicronucleates constituted 25% of Tetrahymena-like wild isolates. Of the 244 amicronucleates examined for cox1 barcodes, 237 belonged to Tetrahymena, seven to other genera. Sixty percent originated from 12 named species or barcoded strains, including the model Tetrahymena thermophila, while the remaining 40% represent 19 putative new species, eight of which have micronucleate counterparts and 11 of which are known only as amicronucleates. In some instances, cox1 haplotypes were shared among micronucleate and amicronucleates collected from the same source. Phylogenetic analysis showed that most amicronucleates belong to the "borealis" clade in which mating type is determined by gene rearrangement. Some amicronucleate species were clustered on the SSU phylogenetic tree and had longer branch lengths, indicating more ancient origin.<br><br>CONCLUSIONS: Naturally occurring Tetrahymena amicronucleates have multiple origins, arising from numerous species. Likely many more new species remain to be discovered. Shared haplotypes indicate that some are of contemporary origin, while phylogeny indicates that others may be millions of years old. The apparent success of amicronucleate Tetrahymena may be because macronuclear assortment and recombination allow them to avoid Muller's ratchet, incorporate beneficial mutations, and evolve independently of sex. The inability of amicronucleates to mate may be the result of error(s) in mating type gene rearrangement.},
}
@article {pmid24878840,
year = {2014},
author = {Cho, M and Chung, S and Jung, JH and Rhie, GE and Jeon, JH and Seo, TS},
title = {Combination of biobarcode assay with on-chip capillary electrophoresis for ultrasensitive and multiplex biological agent detection.},
journal = {Biosensors &amp; bioelectronics},
volume = {61},
number = {},
pages = {172-176},
doi = {10.1016/j.bios.2014.05.018},
pmid = {24878840},
issn = {1873-4235},
mesh = {Bacillus anthracis/genetics/isolation &amp; purification ; Bacterial Infections/diagnosis/microbiology ; Biosensing Techniques/*instrumentation ; Bioterrorism ; Botulinum Toxins, Type A/genetics/isolation &amp; purification ; DNA, Bacterial/genetics/*isolation &amp; purification ; DNA, Viral/genetics/*isolation &amp; purification ; Electrophoresis, Capillary/*instrumentation ; Equipment Design ; Francisella tularensis/genetics/isolation &amp; purification ; Humans ; Oligonucleotide Array Sequence Analysis ; Polymerase Chain Reaction ; Vaccinia/diagnosis/genetics ; Vaccinia virus/genetics/isolation &amp; purification ; Yersinia pestis/genetics/isolation &amp; purification ; },
abstract = {Early diagnosis of biological agents is of paramount importance to prevent the casualties and fatal disease in human during bioterrorism or biological warfare. In this study, we reported an efficient and sensitive multiplex biological agent detection method based on the DNA biobarcode assay and the micro-capillary electrophoresis (μCE) technology. Monoplex as well as multiplex pathogen identification was performed using five targets including Bacillus anthracis, Francisella tularensis, Yersinia pestis, Vaccinia virus and Botulinum toxin A. Through the DNA biobarcode assay process, the magnetic microparticle-pathogen-polystyrene microbead complexes were formed, and the FAM labeled single stranded barcode DNA could be released from the complexes upon denaturation. Different lengths of a barcode DNA were designed to designate each pathogen, so that the specific peak elution time in the capillary electrophoresis on a chip allows us to distinguish the target with high accuracy within 3 min. We improved the assignment accuracy of the peak in the electropherogram by adding two bracket ladders. Owing to the abundant amount of barcode DNAs, the presence of B. anthracis, F. tularensis, Y. pestis, Vaccinia virus was confirmed with a limit of detection of 50CFU/mL, while Botulinum toxin A was analyzed even at a concentration of 12.5 ag/mL. Multiple pathogen detection was also successfully conducted in a phosphate buffered saline (PBS) as well as a serum medium with background of other pathogens. Thus, our analytical platform based on the biobarcode assay and on-chip CE analysis provides rapid, sensitive, multiplex, and accurate biological agent identification.},
}
@article {pmid24878569,
year = {2014},
author = {Castro Paz, FP and Batista, Jda S and Porto, JI},
title = {DNA barcodes of Rosy Tetras and allied species (Characiformes: Characidae: Hyphessobrycon) from the Brazilian Amazon basin.},
journal = {PloS one},
volume = {9},
number = {5},
pages = {e98603},
pmid = {24878569},
issn = {1932-6203},
mesh = {Animals ; Brazil ; Characidae/*genetics ; Characiformes/*genetics ; DNA/genetics ; DNA Barcoding, Taxonomic/methods ; Fishes/*genetics ; Fresh Water ; Phylogeny ; Rivers ; },
abstract = {DNA barcoding can be an effective tool for fast and accurate species-level identification based on sequencing of the mitochondrial cytochrome c oxidase subunit (COI) gene. The diversity of this fragment can be used to estimate the richness of the respective species. In this study, we explored the use of DNA barcoding in a group of ornamental freshwater fish of the genus Hyphessobrycon. We sequenced the COI from 10 species of Hyphessobrycon belonging to the "Rosy Tetra Clade" collected from the Amazon and Negro River basins and combined our results with published data. The average conspecific and congeneric Kimura 2-parameter distances were 2.3% and 19.3%, respectively. Six of the 10 species were easily distinguishable by DNA barcoding (H. bentosi, H. copelandi, H. eques, H. epicharis, H. pulchrippinis, and H. sweglesi), whereas the remaining species (H. erythrostigma, H. pyrrhonotus, H. rosaceus and H. socolofi) lacked reciprocal monophyly. Although the COI gene was not fully diagnostic, the discovery of distinct evolutionary units in certain Hyphessobrycon species under the same specific epithet as well as haplotype sharing between different species suggest that DNA barcoding is useful for species identification in this speciose genus.},
}
@article {pmid24878503,
year = {2014},
author = {Silva, Edos S and de Abreu, CB and Orlando, TC and Wisniewski, C and dos Santos-Wisniewski, MJ},
title = {Alona iheringula Sinev &amp; Kotov, 2004 (Crustacea, Anomopoda, Chydoridae, Aloninae): life cycle and DNA barcode with implications for the taxonomy of the Aloninae subfamily.},
journal = {PloS one},
volume = {9},
number = {5},
pages = {e97050},
pmid = {24878503},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; Cladocera/*classification/enzymology/genetics/*growth &amp; development ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; *Life Cycle Stages ; },
abstract = {Knowledge of reproductive rates and life cycle of the Cladocera species is essential for population dynamic studies, secondary production and food webs, as well as the management and preservation of aquatic ecosystems. The present study aimed to understand the life cycle and growth of Alona iheringula Kotov &amp; Sinev, 2004 (Crustacea, Anomopoda, Chydoridae), a Neotropical species, as well as its DNA barcoding, providing new information on the Aloninae taxonomy. The specimens were collected in the dammed portion of the Cabo Verde River (21°26'05″ S and 46°10'57″ W), in the Furnas Reservoir, Minas Gerais State, Brazil. Forty neonates were observed individually two or three times a day under controlled temperature (25±1°C), photoperiod (12 h light/12 h dark) and feeding (Pseudokirchneriella subcapitata at a concentration of 105 cells.mL-1 and a mixed suspension of yeast and fish feed in equal proportion). Individual body growth was measured daily under optical microscope using a micrometric grid and 40× magnification. The species had a mean size of 413(±29) µm, a maximum size of 510 µm and reached maturity at 3.24(±0.69) days of age. Mean fecundity was 2 eggs per female per brood and the mean number of eggs produced per female during the entire life cycle was 47.6(±6.3) eggs per female. The embryonic development time was 1.79(±0.23) days and the maximum longevity was 54 days. The species had eight instars throughout its life cycle and four instars between neonate and primipara stage. The present study using molecular data (a 461 bp smaller COI fragment) demonstrated a deep divergence in the Aloninae subfamily.},
}
@article {pmid24874264,
year = {2014},
author = {Ramírez, R and Bakke, TA and Harris, PD},
title = {Same barcode, different biology: differential patterns of infectivity, specificity and pathogenicity in two almost identical parasite strains.},
journal = {International journal for parasitology},
volume = {44},
number = {8},
pages = {543-549},
doi = {10.1016/j.ijpara.2014.04.003},
pmid = {24874264},
issn = {1879-0135},
mesh = {Animals ; Fish Diseases/parasitology ; Platyhelminths/*genetics/growth &amp; development/isolation &amp; purification/*physiology ; Polymorphism, Single Nucleotide ; Reproduction ; Salmo salar/*parasitology ; Sequence Analysis, DNA ; Survival Analysis ; Trout/*parasitology ; },
abstract = {Two Norwegian isolates of the monogenean Gyrodactylus salaris Malmberg, 1957 with identical cytochrome c oxidase subunit I barcodes from different hosts, show highly divergent biological and behavioural characteristics. The Lierelva parasite strain, typically infecting Atlantic salmon, Salmo salar L., grew exponentially on Atlantic salmon, but the Pålsbufjorden parasite strain, commonly infecting Arctic charr, Salvelinus alpinus L., grew slowly on both hosts and was non-pathogenic to Atlantic salmon. Both parasite strains reproduced successfully on Arctic charr, but the Atlantic salmon-infecting Lierelva strain grew faster on both hosts. Experiments with isolated worms revealed differences in reproductive rates which may account for the observed population differences. Atlantic salmon parasites consistently gave birth at an earlier age than the Arctic charr parasites, with the differential increasing from 1 day for the first birth up to 2-4 days for the third birth. Arctic charr-infecting parasites were more active on Atlantic salmon than salmon parasites on Arctic charr, a behavioural strategy leading to enhanced G. salaris mortality. Sequencing of 10 kb of nuclear genomic markers revealed only four single nucleotide polymorphisms, confirming that isolates of G. salaris with differences in fitness traits influencing establishment, fecundity and behaviour may be remarkably similar at a molecular level. The framework for reporting and control of G. salaris requires re-appraisal in light of the discovery of variants with such divergent biology.},
}
@article {pmid24872031,
year = {2014},
author = {Nguyen, SN and Yang, JX and Le, TN and Nguyen, LT and Orlov, NL and Hoang, CV and Nguyen, TQ and Jin, JQ and Rao, DQ and Hoang, TN and Che, J and Murphy, RW and Zhang, YP},
title = {DNA barcoding of Vietnamese bent-toed geckos (Squamata: Gekkonidae: Cyrtodactylus) and the description of a new species.},
journal = {Zootaxa},
volume = {3784},
number = {},
pages = {48-66},
doi = {10.11646/zootaxa.3784.1.2},
pmid = {24872031},
issn = {1175-5326},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology ; Animals ; China ; DNA Barcoding, Taxonomic ; Ecosystem ; Female ; Genetic Drift ; Laos ; Lizards/anatomy &amp; histology/*classification/*genetics ; Male ; Molecular Sequence Data ; Phylogeny ; Vietnam ; },
abstract = {Species of bent-toed gecko (Cyrtodactylus) in Vietnam have been described at a rate of nearly four species per year since 2007 mostly based on morphological data. A tool that guides species delimitation will accelerate the rate of documentation, and at a time when the recognition of species greatly benefits conservation. We use DNA barcoding using COI (550 bp) to re-examine the levels of genetic divergence and taxonomic status of 21 described species of Vietnamese bent-toed geckos. Tree-based analyses resolve all sampled species and identify potential undescribed taxa. Kimura 2-parameter genetic distances between the described species average 21.0±4.2% and range from 4.3% to 28.7%. Further, our analyses discover two potentially new species from Vietnam, two from Laos and one from China. Herein we describe the new species Cyrtodactylus puhuensis sp. nov. from Vietnam on the basis of both genetics and morphology. Genetically, it differs from the remaining species by an average K2P distance of 24.0±1.8%. Morphologically, the new species is diagnosed by its medium-size (snout-vent length 79.24 mm and tail length 82.59 mm, for the single known individual), in having a series of moderately enlarged transverse subcaudals and a series of moderately enlarged femoral scales that extend from precloacal scales, in possessing femoral scales without pores, with males having five precloacal pores, and in exhibiting 8 supralabials, 10 infralabials, 23 narrow subdigital lamellae on its fourth toe, and 36 transverse ventrals.},
}
@article {pmid24871849,
year = {2014},
author = {Niu, ZQ and Zhu, CD and Kuhlmann, M},
title = {Bees of the Colletes flavicornis-group from China with description of one new species (Hymenoptera: Apoidea: Colletidae).},
journal = {Zootaxa},
volume = {3780},
number = {},
pages = {534-546},
doi = {10.11646/zootaxa.3780.3.5},
pmid = {24871849},
issn = {1175-5326},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Bees/anatomy &amp; histology/*classification/growth &amp; development ; Body Size ; China ; Female ; Male ; Molecular Sequence Data ; Phylogeny ; },
abstract = {Two species of the Colletes flavicornis-group from China are treated in this paper. C. vestitus sp. n. from Xinjiang is illustrated and described, and C. popovi Noskiewicz, 1936 is illustrated and redescribed. Both sexes of the two species are in addition characterized by DNA barcodes. The type specimens of the new species are deposited in the Insect Collection of Institute of Zoology, Chinese Academy of Sciences, Beijing, China.},
}
@article {pmid24871830,
year = {2014},
author = {Kehlmaier, C and Almeida, JM},
title = {New host records for European Acroceridae (Diptera), with discussion of species limits of Acrocera orbiculus (Fabricius) based on DNA-barcoding.},
journal = {Zootaxa},
volume = {3780},
number = {},
pages = {135-152},
doi = {10.11646/zootaxa.3780.1.5},
pmid = {24871830},
issn = {1175-5326},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Diptera/*classification/genetics/growth &amp; development/*physiology ; Female ; *Host Specificity ; Male ; Molecular Sequence Data ; Phylogeny ; Spiders/*parasitology ; },
abstract = {New European host records for the Acroceridae species Acrocera orbiculus (Fabricius) and Ogcodes reginae Trojan are reported. Acrocera orbiculus was reared from Amaurobius erberi (Keyserling), and O. reginae from Clubiona leucaspis (Simon) and Evarcha jucunda (Lucas). Where possible, DNA-barcodes are presented for reared endoparasitoids and their host specimens. Based on mitochondrial COI, the intraspecific genetic variability of 15 western Palaearctic A. orbiculus is discussed. Maximum likelihood analysis reveals two clades, though they have low statistical support and no distinct barcoding gap. Therefore, we consider all barcoded specimens of A. orbiculus to be a single biological species with a high degree of phenotypic plasticity regarding body size and coloration. Based on molecular and morphological evidence, Paracrocera kaszabi Majer, Paracrocera manevali Séguy and Paracrocera minuscula Séguy are placed in synonymy with A. orbiculus. The male of the Canary Islands endemic Acrocera cabrerae Frey is described for the first time.},
}
@article {pmid24871504,
year = {2014},
author = {Chang, CH and Chuang, SC and Wu, JH and Chen, JH},
title = {New species of earthworms belonging to the Metaphire formosae species group (Clitellata: Megascolecidae) in Taiwan.},
journal = {Zootaxa},
volume = {3774},
number = {},
pages = {324-332},
doi = {10.11646/zootaxa.3774.4.2},
pmid = {24871504},
issn = {1175-5326},
mesh = {Animals ; DNA/analysis/genetics ; DNA Barcoding, Taxonomic ; Female ; Male ; *Oligochaeta/anatomy &amp; histology/classification/genetics ; Taiwan ; },
abstract = {The Metaphire formosae species group is a member of the Pheretima complex of the family Megascolecidae. It is composed of 12 nominal taxa, Metaphire bununa Tsai et al., 2000, Metaphire feijani Chang &amp; Chen, 2004, Metaphire formosae (Michaelsen, 1922), Metaphire glareosa Tsai et al., 2000, Metaphire nanaoensis Chang &amp; Chen, 2005, Metaphire paiwanna paiwanna Tsai et al., 2000, Metaphire paiwanna hengchunensis (James et al., 2005), Metaphire paiwanna liliumfordi Tsai et al., 2000, Metaphire tahanmonta Chang &amp; Chen, 2005, Metaphire taiwanensis Tsai et al., 2004, Metaphire trutina Tsai et al., 2003, and Metaphire yuhsi (Tsai, 1964). In this study, we describe a new species, Metaphire tengjhihensis sp. nov., and two new subspecies, Metaphire nanaoensis truku ssp. nov. and Metaphire taiwanensis tsaii ssp. nov., belonging to this species group. DNA barcodes (partial sequences of the mitochondrial cytochrome c oxidase subunit 1, COI) from type specimens of M. feijani, M. tengjhihensis sp. nov., M. nanaoensis truku ssp. nov., M. tahanmonta and M. taiwanensis tsaii ssp. nov. have been deposited in GenBank in previous studies and are explicitly linked to the type specimens for the first time, enabling unambiguous identification using both morphology and DNA barcodes. Finally, we comment on the systematics of the M. formosae species group and suggest an integrative taxonomic approach that combines morphology and DNA barcodes for future descriptions of new species of Amynthas and Metaphire.},
}
@article {pmid24871224,
year = {2014},
author = {Kitano, YF and Benzoni, F and Arrigoni, R and Shirayama, Y and Wallace, CC and Fukami, H},
title = {A phylogeny of the family Poritidae (Cnidaria, Scleractinia) based on molecular and morphological analyses.},
journal = {PloS one},
volume = {9},
number = {5},
pages = {e98406},
pmid = {24871224},
issn = {1932-6203},
mesh = {Animals ; Anthozoa/*anatomy &amp; histology/*classification/*genetics ; Base Sequence ; Body Weights and Measures ; Cluster Analysis ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Extremities/anatomy &amp; histology ; Indian Ocean ; Japan ; Malaysia ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The family Poritidae formerly included 6 genera: Alveopora, Goniopora, Machadoporites, Porites, Poritipora, and Stylaraea. Morphologically, the genera can be differentiated based on the number of tentacles, the number of septa and their arrangement, the length of the polyp column, and the diameter of the corallites. However, the phylogenetic relationships within and between the genera are unknown or contentious. On the one hand, Alveopora has been transferred to the Acroporidae recently because it was shown to be more closely related to this family than to the Poritidae by previous molecular studies. On the other hand, Goniopora is morphologically similar to 2 recently described genera, Machadoporites and Poritipora, particularly with regard to the number of septa (approximately 24), but they have not yet been investigated at the molecular level. In this study, we analyzed 93 samples from all 5 poritid genera and Alveopora using 2 genetic markers (the barcoding region of the mitochondrial COI and the ITS region of the nuclear rDNA) to investigate their phylogenetic relationships and to revise their taxonomy. The reconstructed molecular trees confirmed that Alveopora is genetically distant from all poritid genera but closely related to the family Acroporidae, whereas the other genera are genetically closely related. The molecular trees also revealed that Machadoporites and Poritipora were indistinguishable from Goniopora. However, Goniopora stutchburyi was genetically isolated from the other congeneric species and formed a sister group to Goniopora together with Porites and Stylaraea, thus suggesting that 24 septa could be an ancestral feature in the Poritidae. Based on these data, we move G. stutchburyi into a new genus, Bernardpora gen. nov., whereas Machadoporites and Poritipora are merged with Goniopora.},
}
@article {pmid24871192,
year = {2014},
author = {Pillai, PM and Unnikrishnan, V and Kumar, US},
title = {Description, DNA barcode and phylogeny of a new species, Macrobrachium abrahami (Decapoda: Palaemonidae) from Kerala, India.},
journal = {Zootaxa},
volume = {3768},
number = {},
pages = {546-556},
doi = {10.11646/zootaxa.3768.5.2},
pmid = {24871192},
issn = {1175-5326},
mesh = {Animals ; Base Sequence ; DNA/genetics ; *DNA Barcoding, Taxonomic ; Demography ; Genetic Variation ; India ; Molecular Sequence Data ; Palaemonidae/anatomy &amp; histology/*classification/*genetics/physiology ; *Phylogeny ; Species Specificity ; },
abstract = {Macrobrachium abrahami, new species is described from Vamanapuram River, Kerala, South India. DNA bar-coding using Cytochrome B gene sequences has elucidated the taxonomic status of the new species and the ML tree reveals that M. abrahami sp. nov., is phylogenetically close to M. prabhakarani, but morphologically more similar to M. scabriculum. However, the species shares certain morphological characters with M. scabriculum, M. prabhakarani and M. lanatum, but differs remarkably from these three species in distinctive diagnostic characters: rostrum moderately long, convex, distal end directed upwards, rostral formula 12-15/2-3 with 5-6 postorbital teeth, and carapace glabrous. In larger second chelate leg, fingers stout, pubescence restricted to their base; proximal half of cutting edge with fifteen denticles. In smaller second chelate leg, cutting edge of both fingers carry six small denticles situated proximally, distal one comparatively larger. Delicate setae are seen throughout the palm. A row of dark chromatophores is present along the posterio-dorsal margin of uropodal exopods and endopods, close to the base of uropodal setae. The thickness of each band of the row is almost equal to the thickness of uropodal setae.},
}
@article {pmid24871188,
year = {2014},
author = {Sihvonen, P and Skou, P and Flamigni, C and Fiumi, G and Hausmann, A},
title = {Revision of the Hylaea fasciaria (Linnaeus, 1758) species group in the western Palaearctic (Lepidoptera: Geometridae, Ennominae).},
journal = {Zootaxa},
volume = {3768},
number = {},
pages = {469-486},
doi = {10.11646/zootaxa.3768.4.5},
pmid = {24871188},
issn = {1175-5326},
mesh = {Animals ; Asia, Central ; Asia, Northern ; DNA/genetics ; DNA Barcoding, Taxonomic ; Demography ; Ecosystem ; Europe ; Female ; Male ; Middle East ; Moths/*anatomy &amp; histology/*classification/genetics ; Phylogeny ; Species Specificity ; },
abstract = {The Palaearctic Hylaea fasciaria (Linnaeus, 1758) species group is revised (Lepidoptera: Geometridae, Ennominae). Four taxa are considered valid at species level: H. fasciaria (Linnaeus, 1758), H. pinicolaria (Bellier, 1861), H. compararia (Staudinger, 1894) and one new species, H. mediterranea, from Italy: Sicily, Calabria and Molise. The following taxonomic changes are proposed: Ellopia cedricola Wehrli, 1919, from Turkey is downgraded to subspecies of Hylaea fasciaria (Linnaeus, 1758) (revised status), Hylaea fasciaria cleui Leraut, 1993, from France is downgraded from subspecies to synonymy with H. fasciaria fasciaria (Linnaeus, 1758) (new synonymy) and Ellopia compararia Staudinger, 1894, from Algeria is raised from subspecies of Hylaea fasciaria (Linnaeus, 1758) to species status (revised status). Hemithea squalidaria O. G. Costa, 1848 from southern Italy was placed in the genus Hylaea, but it is reverted to its original combination as its taxonomic status is uncertain. Adults, male and female genitalia and distribution maps are illustrated for all species. DNA barcodes are presented for most taxa studied.},
}
@article {pmid24870083,
year = {2014},
author = {Vincent, B and Hajibabaei, M and Rougerie, R},
title = {A striking new genus and species of tiger-moth (Lepidoptera: Erebidae, Arctiinae, Arctiini) from the Caribbean, with molecular and morphological analysis of its systematic placement.},
journal = {Zootaxa},
volume = {3760},
number = {},
pages = {289-300},
doi = {10.11646/zootaxa.3760.2.8},
pmid = {24870083},
issn = {1175-5326},
mesh = {Animals ; Demography ; Dominican Republic ; Female ; Male ; Moths/*anatomy &amp; histology/*classification/physiology ; Phylogeny ; Species Specificity ; },
abstract = {Westindia Vincent, a new genus, is proposed for W. haxairei Vincent, a new species of Neotropical tiger-moth described from Dominican Republic. Habitus, male and female genitalia are described and figured. The systematic position of the new genus within Arctiinae is discussed in light of a comparative morphology and a molecular phylogeny derived from the DNA barcode fragment of the mitochondrial COI gene and of the D2 region of the 28S rDNA gene.},
}
@article {pmid24869876,
year = {2014},
author = {Kullander, SO and Karlsson, M and Karlsson, M and Norén, M},
title = {Chalinochromis cyanophleps, a new species of cichlid fish (Teleostei: Cichlidae) from Lake Tanganyika.},
journal = {Zootaxa},
volume = {3790},
number = {},
pages = {425-438},
doi = {10.11646/zootaxa.3790.3.2},
pmid = {24869876},
issn = {1175-5326},
mesh = {Animals ; *Biodiversity ; Cichlids/*anatomy &amp; histology/classification/genetics ; DNA Barcoding, Taxonomic ; *Ecosystem ; Female ; Lakes ; Male ; Tanzania ; },
abstract = {Chalinochromis cyanophleps is described from nine specimens, the largest 129 mm SL, from Namansi. It differs from other species of Chalinochromis in plain trunk colouration, absence of black stripes on the head, relatively narrow lips, presence of tricuspid jaw teeth, and presence of five rather than four dentary lateralis foramina. The blue iridescent stripe below the eye is shared with other lamprologin cichlids, but is broader and more conspicuous in C. cyanophleps. Chalinochromis cyanophleps occurs at depths between 6 and 45 m in rocky habitats along the Tanzanian coast of Lake Tanganyika, from Mvuna Island south to Kalala Island, a stretch of about 90 km. Field observations were made of specimens up to 18 cm total length. The COI DNA barcode sequence differs by 1.8% from that of C. popelini.},
}
@article {pmid24869835,
year = {2014},
author = {Vences, M and Lima, A and Miralles, A and Glaw, F},
title = {DNA barcoding assessment of genetic variation in two widespread skinks from Madagascar, Trachylepis elegans and T. gravenhorstii (Squamata: Scincidae).},
journal = {Zootaxa},
volume = {3755},
number = {},
pages = {477-484},
doi = {10.11646/zootaxa.3755.5.7},
pmid = {24869835},
issn = {1175-5326},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Demography ; *Genetic Variation ; Lizards/*genetics/*physiology ; Madagascar ; Phylogeny ; Species Specificity ; },
abstract = {Trachylepis elegans and T. gravenhorstii are two of the most widespread reptiles in Madagascar, inhabiting a wide variety of habitats. Previous studies have indicated a considerable mitochondrial DNA (mtDNA) variation within these species, but the geographic distribution of the major haplotype lineages is poorly known. Herein we analyse the phylogeography of these lizards based on 107 sequences of the mitochondrial cytochrome oxidase subunit I gene, 101 of which newly determined. As in previous mtDNA assessments, T. elegans and T. gravenhorstii were not reciprocally monophyletic, although recent analyses including nuclear markers indicated their probable monophyly, respectively. The main lineages within T. gravenhorstii were found in strict allopatry and could be divided into a subclade of roughly northern and eastern distribution (lineages 1 and 2) and a subclade of roughly southern and western distribution (lineages 3, 4a, 4b, and 5, plus T. elegans). Our data serve to identify more precisely the probable contact zones among T. gravenhorstii lineages. The two main mtDNA clades (represented by lineages 2 and 3, respectively) can be expected to come into close contact in the area of the upper Mangoro river and Alaotra Lake, and (lineages 2 and 4a) in the Southern Central East between Mananjary and Ranomafana. Future studies intensively sampling these contact zones have the potential to assess hybridization and admixture among these lineages, and to test whether they are deep conspecific lineages of T. gravenhorstii as currently understood, or might represent distinct species.},
}
@article {pmid24869539,
year = {2014},
author = {Soon, V and Budrys, E and Orlovskytė, S and Paukkunen, J and Odegaard, F and Ljubomirov, T and Saarma, U},
title = {Testing the validity of Northern European species in the Chrysis ignita species group (Hymenoptera: Chrysididae) with DNA barcoding.},
journal = {Zootaxa},
volume = {3786},
number = {},
pages = {301-330},
doi = {10.11646/zootaxa.3786.3.4},
pmid = {24869539},
issn = {1175-5326},
mesh = {Animal Distribution ; Animals ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Ecosystem ; Europe ; Female ; Hymenoptera/*classification/*genetics ; Male ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Containing more than a hundred species, the Chrysis ignita species group is the largest and one of the most taxonomically challenging groups in its genus. It has not been possible to resolve the taxonomy of the group using traditional methods due to the lack of robust diagnostic morphological characters. Here we present the results of a molecular analysis designed to delimit species in the Chrysis ignita group for the first time; using mitochondrial sequence data for 364 in-group specimens consisting of all 18 species known to occur in Northern Europe. Two mitochondrial loci were analysed: a COI gene fragment, and a continuous DNA sequence consisting of 16S rRNA, tRNA[Val], 12S rRNA and ND4. Two approaches were employed for delimiting species: (1) genetic distance analysis based on the standard COI barcode sequences and; (2) phylogenetic analysis of the COI fragment together with rRNA genes. Both analyses yielded trees with similar topology, but support values for nodes were higher using the second approach. Fifteen species were distinguished in all analyses: Chrysis angustula Schenck, 1856, C. brevitarsis Thomson, 1870, C. clarinicollis Linsenmaier, 1951, C. corusca Valkeila, 1971, C. fulgida Linnaeus, 1761, C. ignita (Linnaeus, 1758), C. impressa Schenck, 1856, C. iris Christ, 1791, C. leptomandibularis Niehuis, 2000, C. longula Abeille de Perrin, 1879, C. ruddii Shuckard, 1837, C. schencki Linsenmaier, 1968, C. subcoriacea Linsenmaier, 1959, C. terminata Dahlbom, 1854 and C. vanlithi Linsenmaier, 1959. The specific status of C. mediata Linsenmaier, 1951 and C. solida Haupt, 1957 was not resolved. Included unidentified specimens grouped in three clusters, two of which are distinctly delimited and apparently represent cryptic species. The specific status of the unidentified samples in the third cluster remained unclear. Moreover, our data suggest the existence of additional cryptic species currently lumped under the names C. pseudobrevitarsis Linsenmaier, 1951 and C. schencki Linsenmaier, 1968. In conclusion, our results derived from analysis of mitochondrial loci strongly support the specific status of the majority of currently recognised species in the Chrysis ignita species group, and suggest the existence of additional cryptic species in Northern Europe. Thus, considering the difficulties that often arise during species determination based on morphological characters, the mtDNA loci used here appear highly suitable for assisting species delimitation in this group as well as identification of specimens.},
}
@article {pmid24859078,
year = {2015},
author = {Jelacic, S and Bowdle, A and Nair, BG and Kusulos, D and Bower, L and Togashi, K},
title = {A System for Anesthesia Drug Administration Using Barcode Technology: The Codonics Safe Label System and Smart Anesthesia Manager.},
journal = {Anesthesia and analgesia},
volume = {121},
number = {2},
pages = {410-421},
doi = {10.1213/ANE.0000000000000256},
pmid = {24859078},
issn = {1526-7598},
mesh = {*Anesthesia/adverse effects/methods/standards ; *Anesthesia Department, Hospital/methods/standards ; Anesthetics/*administration &amp; dosage/adverse effects/standards ; Drug Labeling/*instrumentation/methods/standards ; Equipment Design ; Equipment Failure ; Guideline Adherence ; Humans ; Materials Testing ; Medication Errors/*prevention &amp; control ; *Medication Systems, Hospital/standards ; *Pharmacy Service, Hospital/methods/standards ; Practice Guidelines as Topic ; Software Design ; Treatment Outcome ; },
abstract = {BACKGROUND: Many anesthetic drug errors result from vial or syringe swaps. Scanning the barcodes on vials before drug preparation, creating syringe labels that include barcodes, and scanning the syringe label barcodes before drug administration may help to prevent errors. In contrast, making syringe labels by hand that comply with the recommendations of regulatory agencies and standards-setting bodies is tedious and time consuming. A computerized system that uses vial barcodes and generates barcoded syringe labels could address both safety issues and labeling recommendations.<br><br>METHODS: We measured compliance of syringe labels in multiple operating rooms (ORs) with the recommendations of regulatory agencies and standards-setting bodies before and after the introduction of the Codonics Safe Label System (SLS). The Codonics SLS was then combined with Smart Anesthesia Manager software to create an anesthesia barcode drug administration system, which allowed us to measure the rate of scanning syringe label barcodes at the time of drug administration in 2 cardiothoracic ORs before and after introducing a coffee card incentive. Twelve attending cardiothoracic anesthesiologists and the OR satellite pharmacy participated.<br><br>RESULTS: The use of the Codonics SLS drug labeling system resulted in >75% compliant syringe labels (95% confidence interval, 75%-98%). All syringe labels made using the Codonics SLS system were compliant. The average rate of scanning barcodes on syringe labels using Smart Anesthesia Manager was 25% (730 of 2976) over 13 weeks but increased to 58% (956 of 1645) over 8 weeks after introduction of a simple (coffee card) incentive (P < 0.001).<br><br>CONCLUSIONS: An anesthesia barcode drug administration system resulted in a moderate rate of scanning syringe label barcodes at the time of drug administration. Further, adaptation of the system will be required to achieve a higher utilization rate.},
}
@article {pmid24857374,
year = {2016},
author = {Cao, S and Guo, L and Luo, H and Yuan, H and Chen, S and Zheng, J and Lin, R},
title = {Application of COI barcode sequence for the identification of snake medicine (Zaocys).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {1},
pages = {483-489},
doi = {10.3109/19401736.2014.905828},
pmid = {24857374},
issn = {2470-1408},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Medicine, Chinese Traditional ; Phylogeny ; Snakes/*genetics ; Species Specificity ; },
abstract = {Counterfeits in the medicine market make the authentication of snakes used for Chinese medicine a challenge to Chinese drug regulatory control agencies. This paper explores existing methods that can be used to quickly and accurately distinguish Zaocys (Z. dhumnades) from its counterfeits for routine identification of snake meats in food and drug control laboratories. In this research, the Cytochrome Oxidase I (COI) fragments of 51 samples from 17 species of snakes were amplified using Polymerase Chain Reaction (PCR) and sequenced. The inter- and intra-specific variations of COI sequences were analyzed and compared based on Kimura-2-parameter (K-2P) distances; the minimal interspecific K-2P distance was 0.0934, which was bigger than the maximum intraspecific K-2P distance in Z. dhumnades (0.0523), indicating that Zaocys can be separated from its counterfeits. The Neighbor-Joining (N-J) tree of the snakes was constructed and the results show that snakes of the same species cluster with 100% bootstrap values. Since the Zaocys and its counterfeits are of different species, they can be distinguished using the N-J tree method. Another 10 samples of Zaocys from markets and drug stores were identified at the species level, among which 5 samples were proven to be the counterfeits--Ptyas korros.},
}
@article {pmid24855447,
year = {2014},
author = {Ito, Y and Tanaka, N and Pooma, R and Tanaka, N},
title = {DNA barcoding reveals a new record of Potamogeton distinctus (Potamogetonaceae) and its natural hybrids, P. distinctus x P. nodosus and P. distinctus x P. wrightii) (P. x malainoides) from Myanmar.},
journal = {Biodiversity data journal},
volume = {},
number = {2},
pages = {e1073},
pmid = {24855447},
issn = {1314-2828},
abstract = {Indo-China floristic region is among the 34 richest floristic regions of the world, and its plant diversity is still under investigation. Here we report a new record of an aquatic plant, Potamogetondistinctus, from Myanmar, a part of the region, that is detected by means of DNA barcoding method. The molecular method further identified the other specimens as hybrids of Potamogeton: one is Potamogeton×malainoides (Potamogetondistinctus × Potamogetonwrightii), and the other is Potamogetondistinctus × Potamogetonnodosus. The first of these was thus far genetically confirmed in China, but the parental combination of the hybrid in Myanmar was reciprocal to those reported from China. The second hybrid was also recorded from China, but the maternal lineage was revealed for the first time, in this case it was Potamogetondistinctus. The present study showed that 1) nrITS is useful to distinguish closely related Potamogeton species as well as hybrids among them and 2) atpB-rbcL has higher utility than other frequently used plastid DNA markers. We thus propose nrITS and atpB-rbcL as DNA barcoding markers for future Potamogeton studies.},
}
@article {pmid24854031,
year = {2014},
author = {Zheng, S and Jiang, X and Wu, L and Wang, Z and Huang, L},
title = {Chemical and genetic discrimination of Cistanches Herba based on UPLC-QTOF/MS and DNA barcoding.},
journal = {PloS one},
volume = {9},
number = {5},
pages = {e98061},
pmid = {24854031},
issn = {1932-6203},
mesh = {Chromatography, Liquid ; Cistanche/*chemistry/*genetics ; *DNA Barcoding, Taxonomic ; Mass Spectrometry/*methods ; Polymerase Chain Reaction ; Principal Component Analysis ; },
abstract = {Cistanches Herba (Rou Cong Rong), known as "Ginseng of the desert", has a striking curative effect on strength and nourishment, especially in kidney reinforcement to strengthen yang. However, the two plant origins of Cistanches Herba, Cistanche deserticola and Cistanche tubulosa, vary in terms of pharmacological action and chemical components. To discriminate the plant origin of Cistanches Herba, a combined method system of chemical and genetic--UPLC-QTOF/MS technology and DNA barcoding--were firstly employed in this study. The results indicated that three potential marker compounds (isomer of campneoside II, cistanoside C, and cistanoside A) were obtained to discriminate the two origins by PCA and OPLS-DA analyses. DNA barcoding enabled to differentiate two origins accurately. NJ tree showed that two origins clustered into two clades. Our findings demonstrate that the two origins of Cistanches Herba possess different chemical compositions and genetic variation. This is the first reported evaluation of two origins of Cistanches Herba, and the finding will facilitate quality control and its clinical application.},
}
@article {pmid24845432,
year = {2013},
author = {Miranda, LB and Wyatt, K and Johnston, I and Milljanic, M and Chaffey, J},
title = {"Proof of concept" pilot study: bioprocess chain of custody and bioresource sample management temperature observations. Sample level temperature trends and stability data obtained via utilization of bluechiip(®) temperature tracking technology.},
journal = {Biopreservation and biobanking},
volume = {11},
number = {2},
pages = {115-121},
doi = {10.1089/bio.2012.0059},
pmid = {24845432},
issn = {1947-5543},
mesh = {*Biological Specimen Banks ; Cryopreservation/*methods ; Humans ; Pilot Projects ; Reproducibility of Results ; *Temperature ; },
abstract = {BACKGROUND: Preservation and optimization of biosample integrity to foster relevant research results and outcomes is a guiding principle of sample management. Tracking pre-analytical biospecimen lifecycle variables and bioprocessing chain of custody data enables documentation of adherence to best, regulatory and quality biobanking practices. Knowledge of individual sample and sample set temperature variability is believed to enhance delineation of artifacts during downstream analysis. Analysis of temperature responses may elucidate understanding of temperature trends which can aid downstream interpretation and provide an empirical foundation for "fit for purpose" sample management protocols and evidence-based biobanking practices. Bluechiip and the American Type Culture Collection (ATCC) conducted a pilot to test the bluechiip technology(®) performance and validate key proofs of concept for tracking temperature of biological samples.<br><br>METHODS: One hundred six (106) Corning(&#xae;) cryovials with bluechiip(&#xae;) buttons and one hundred six (106) standard Corning(&#xae;) cryovials labeled with 1-dimensional (1D) barcoded labels were evaluated. Identifiers were tracked and temperature data recorded in corresponding environments ranging from -192&#xb0;C to +57&#xb0;.<br><br>RESULTS: Nine of ten proof of concepts, defined in collaboration with ATCC successfully demonstrated functional capabilities of the bluechiip(&#xae;) technology. Bar-code label read performance was compared, producing evidence demonstrating a high rate of failure on the bar-code arm.<br><br>CONCLUSION: Temperature data collected heightened observations of sample temperature variability. Prevalence of bar-code label read failure and issues affecting reliability of barcode performance may be under-reported and unrecognized in sample management practice, particularly when the temperatures are lower than -60&#xb0;C. It appears the bluechiip(&#xae;) tracking technology may offer increased reliability over one-dimensional (1D) bar-coding technology; however while promising these findings require validation in future trials, including two-dimensional (2D) bar-coding technologies.},
}
@article {pmid24843929,
year = {2013},
author = {Conflitti, IM and Pruess, KP and Cywinska, A and Powers, TO and Currie, DC},
title = {DNA barcoding distinguishes pest species of the black fly genus Cnephia (Diptera: Simuliidae).},
journal = {Journal of medical entomology},
volume = {50},
number = {6},
pages = {1250-1260},
doi = {10.1603/me13063},
pmid = {24843929},
issn = {0022-2585},
mesh = {Animals ; Bayes Theorem ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics/metabolism ; Europe ; Insect Control/*methods ; Insect Proteins/genetics/metabolism ; Larva/genetics/growth &amp; development/metabolism ; Molecular Sequence Data ; North America ; Phylogeny ; Polymerase Chain Reaction ; Pupa/genetics/growth &amp; development/metabolism ; Sequence Analysis, DNA ; Simuliidae/*classification/*genetics/growth &amp; development ; },
abstract = {Accurate species identification is essential for cost-effective pest control strategies. We tested the utility of COI barcodes for identifying members of the black fly genus Cnephia Enderlein (Diptera: Simuliidae). Our efforts focus on four Nearctic Cnephia species-Cnephia dacotensis (Dyar &amp; Shannon), Cnephia eremities Shewell, Cnephia ornithophilia (Davies, Peterson &amp; Wood), and Cnephia pecuarum (Riley)--the latter two being current or potential targets of biological control programs. We also analyzed one Palearctic species, Cnephia pallipes (Fries). Although Cnephia adults can be identified anatomically to species, control programs target the larval stage, which is difficult or impossible to distinguish morphologically. By using neighbor-joining, maximum parsimony, and Bayesian methods, we found that COI barcodes successfully identified three Nearctic Cnephia species, but not C. pecuarum. The Palearctic C. pallipes was also successfully identified. Despite nonmonophyly of C. pecuarum, we show that data from COI barcoding, in combination with geographical and ecological information, can be used to distinguish all four Nearctic species. Finally, we discussed 1) possible reasons for paraphyly in C. pecuarum, 2) topological concordance to previously reported chromosomal dendrograms, and 3) evolution of diverse feeding strategies within the genus Cnephia.},
}
@article {pmid24843290,
year = {2014},
author = {Christensen, KI and Zarrei, M and Kuzmina, M and Talent, N and Lin, C and Dickinson, TA},
title = {Crataegus ×ninae-celottiae and C. ×cogswellii (Rosaceae, Maleae), two spontaneously formed intersectional nothospecies.},
journal = {PhytoKeys},
volume = {},
number = {36},
pages = {1-26},
pmid = {24843290},
issn = {1314-2011},
abstract = {Crataegus monogyna Jacq. is naturalized in North America, where it has hybridized with native diploid hawthorns at least twice. We provide names for the two nothospecies (as well as for the corresponding nothosections and nothoseries), referring to existing documentation in the literature for nothosp. nov. Crataegus ×ninae-celottiae K.I. Chr. &amp; T.A. Dickinson (C. monogyna × C. punctata Jacq.). New data are provided to further document nothosp. nov. Crataegus ×cogswellii K.I. Chr. &amp; T.A. Dickinson (C. monogyna × C. suksdorfii (Sarg.) Kruschke). In both cases, the striking differences in leaf shape between most New World hawthorns and Old World section Crataegus, and the intermediacy of the hybrids, account for the relative ease with which these hybrids can be recognized. Finally, new sequence data from ITS2 and chloroplast DNA barcoding loci confirm the genetic relationships between the two nothospecies and their respective parents.},
}
@article {pmid24843281,
year = {2014},
author = {Li, NN and Toda, MJ and Fu, Z and Chen, JM and Li, SH and Gao, JJ},
title = {Taxonomy of the Colocasiomyia gigantea species group (Diptera, Drosophilidae), with descriptions of four new species from Yunnan, China.},
journal = {ZooKeys},
volume = {},
number = {406},
pages = {41-64},
pmid = {24843281},
issn = {1313-2989},
abstract = {Species of the genus Colocasiomyia de Meijere feed/breed on inflorescences/infructescences of the plants from the families Araceae, Arecaceae and Magnoliaceae. Although most of them utilize plants from the subfamily Aroideae of Araceae, three species of the recently established C. gigantea species group make use of plants of the subfamily Monsteroideae. We describe four new species of the gigantea group found from Yunnan, China: Colocasiomyia longifilamentata Li &amp; Gao, sp. n., C. longivalva Li &amp; Gao, sp. n., C. hailini Li &amp; Gao, sp. n., and C. yini Li &amp; Gao, sp. n. The species delimitation is proved in virtue of not only morphology but also DNA barcodes, i.e., sequences of the partial mitochondrial COI (cytochrome c oxidase subunit I) gene. Some nucleotide sites with fixed status in the alignment of the COI sequences (658 sites in length) are used as "pure" molecular diagnostic characters to delineate species in the gigantea group.},
}
@article {pmid24843272,
year = {2014},
author = {Huemer, P and Karsholt, O and Mutanen, M},
title = {DNA barcoding as a screening tool for cryptic diversity: an example from Caryocolum, with description of a new species (Lepidoptera, Gelechiidae).},
journal = {ZooKeys},
volume = {},
number = {404},
pages = {91-111},
pmid = {24843272},
issn = {1313-2989},
abstract = {We explore the potential value of DNA barcode divergence for species delimitation in the genus Caryocolum Gregor &amp; Povolný, 1954 (Lepidoptera, Gelechiidae), based on data from 44 European species (including 4 subspecies). Low intraspecific divergence of the DNA barcodes of the mtCOI (cytochrome c oxidase 1) gene and/or distinct barcode gaps to the nearest neighbor support species status for all examined nominal taxa. However, in 8 taxa we observed deep splits with a maximum intraspecific barcode divergence beyond a threshold of 3%, thus indicating possible cryptic diversity. The taxonomy of these taxa has to be re-assessed in the future. We investigated one such deep split in Caryocolum amaurella (Hering, 1924) and found it in congruence with yet unrecognized diagnostic morphological characters and specific host-plants. The integrative species delineation leads to the description of Caryocolum crypticum sp. n. from northern Italy, Switzerland and Greece. The new species and the hitherto intermixed closest relative C. amaurella are described in detail and adults and genitalia of both species are illustrated and a lectotype of C. amaurella is designated; a diagnostic comparison of the closely related C. iranicum Huemer, 1989, is added.},
}
@article {pmid24843256,
year = {2014},
author = {Neumeyer, R and Baur, H and Guex, GD and Praz, C},
title = {A new species of the paper wasp genus Polistes (Hymenoptera, Vespidae, Polistinae) in Europe revealed by morphometrics and molecular analyses.},
journal = {ZooKeys},
volume = {},
number = {400},
pages = {67-118},
pmid = {24843256},
issn = {1313-2989},
abstract = {We combine multivariate ratio analysis (MRA) of body measurements and analyses of mitochondrial and nuclear data to examine the status of several species of European paper wasps (Polistes Latreille, 1802) closely related to P. gallicus. Our analyses unambiguously reveal the presence of a cryptic species in Europe, as two distinct species can be recognized in what has hitherto been considered Polistes bischoffi Weyrauch, 1937. One species is almost as light coloured as P. gallicus, and is mainly recorded from Southern Europe and Western Asia. The other species is darker and has a more northern distribution in Central Europe. Both species occur syntopically in Switzerland. Given that the lost lectotype of P. bischoffi originated from Sardinia, we selected a female of the southern species as a neotype. The northern species is described as P. helveticus sp. n. here. We also provide a redescription of P. bischoffi rev. stat. and an identification key including three more closely related species, P. biglumis, P. gallicus and P. hellenicus.},
}
@article {pmid24841434,
year = {2016},
author = {Asis, AM and Lacsamana, JK and Santos, MD},
title = {Illegal trade of regulated and protected aquatic species in the Philippines detected by DNA barcoding.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {1},
pages = {659-666},
doi = {10.3109/19401736.2014.913138},
pmid = {24841434},
issn = {2470-1408},
mesh = {Anguilla/genetics ; Animals ; *Conservation of Natural Resources ; DNA/*genetics ; DNA Barcoding, Taxonomic/*methods ; Eels/genetics ; Endangered Species ; Fisheries/*legislation &amp; jurisprudence ; Sharks/genetics ; Skates, Fish/genetics ; },
abstract = {Illegal trade has greatly affected marine fish stocks, decreasing fish populations worldwide. Despite having a number of aquatic species being regulated, illegal trade still persists through the transport of dried or processed products and juvenile species trafficking. In this regard, accurate species identification of illegally traded marine fish stocks by DNA barcoding is deemed to be a more efficient method in regulating and monitoring trade than by morphological means which is very difficult due to the absence of key morphological characters in juveniles and processed products. Here, live juvenile eels (elvers) and dried products of sharks and rays confiscated for illegal trade were identified. Twenty out of 23 (87%) randomly selected "elvers" were identified as Anguilla bicolor pacifica and 3 (13%) samples as Anguilla marmorata. On the other hand, 4 out of 11 (36%) of the randomly selected dried samples of sharks and rays were Manta birostris. The rest of the samples were identified as Alopias pelagicus, Taeniura meyeni, Carcharhinus falciformis, Himantura fai and Mobula japonica. These results confirm that wild juvenile eels and species of manta rays are still being caught in the country regardless of its protected status under Philippine and international laws. It is evident that the illegal trade of protected aquatic species is happening in the guise of dried or processed products thus the need to put emphasis on strengthening conservation measures. This study aims to underscore the importance of accurate species identification in such cases of illegal trade and the effectivity of DNA barcoding as a tool to do this.},
}
@article {pmid24838015,
year = {2015},
author = {Li, J and Zheng, X and Cai, Y and Zhang, X and Yang, M and Yue, B and Li, J},
title = {DNA barcoding of Murinae (Rodentia: Muridae) and Arvicolinae (Rodentia: Cricetidae) distributed in China.},
journal = {Molecular ecology resources},
volume = {15},
number = {1},
pages = {153-167},
doi = {10.1111/1755-0998.12279},
pmid = {24838015},
issn = {1755-0998},
mesh = {Animals ; Arvicolinae/*classification/*genetics ; China ; Computational Biology ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Murinae/*classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {Identification of rodents is very difficult mainly due to high similarities in morphology and controversial taxonomy. In this study, mitochondrial cytochrome oxidase subunit I (COI) was used as DNA barcode to identify the Murinae and Arvicolinae species distributed in China and to facilitate the systematics studies of Rodentia. In total, 242 sequences (31 species, 11 genera) from Murinae and 130 sequences (23 species, 6 genera) from Arvicolinae were investigated, of which 90 individuals were novel. Genetic distance, threshold method, tree-based method, online BLAST and BLOG were employed to analyse the data sets. There was no obvious barcode gap. The average K2P distance within species and genera was 2.10% and 12.61% in Murinae, and 2.86% and 11.80% in Arvicolinae, respectively. The optimal threshold was 5.62% for Murinae and 3.34% for Arvicolinae. All phylogenetic trees exhibited similar topology and could distinguish 90.32% of surveyed species in Murinae and 82.60% in Arvicolinae with high support values. BLAST analyses yielded similar results with identification success rates of 92.15% and 93.85% for Murinae and Arvicolinae, respectively. BLOG successfully authenticated 100% of detected species except Leopoldamys edwardsi based on the latest taxonomic revision. Our results support the species status of recently recognized Micromys erythrotis, Eothenomys tarquinius and E. hintoni and confirm the important roles of comprehensive taxonomy and accurate morphological identification in DNA barcoding studies. We believe that, when proper analytic methods are applied or combined, DNA barcoding could serve as an accurate and effective species identification approach for Murinae and Arvicolinae based on a proper taxonomic framework.},
}
@article {pmid24836940,
year = {2014},
author = {Moravec, F and Justine, JL},
title = {Philometrids (Nematoda: Philometridae) in carangid and serranid fishes off New Caledonia, including three new species.},
journal = {Parasite (Paris, France)},
volume = {21},
number = {},
pages = {21},
pmid = {24836940},
issn = {1776-1042},
mesh = {Animals ; Base Sequence ; Dracunculoidea/classification/growth &amp; development/*isolation &amp; purification ; Female ; Fish Diseases/*parasitology ; Fishes/genetics/*parasitology ; Helminthiasis/parasitology ; Intestinal Diseases/parasitology/veterinary ; Intestinal Diseases, Parasitic ; Larva ; Male ; Molecular Sequence Data ; New Caledonia ; Ovary/parasitology ; Pacific Ocean ; Perciformes/genetics/parasitology ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Sex Characteristics ; Species Specificity ; Spirurida Infections/parasitology/*veterinary ; },
abstract = {A recent examination of newly obtained specimens of philometrid nematodes (Philometridae) parasitising carangid and serranid fishes off New Caledonia, South Pacific, revealed the presence of several nematodes of the genus Philometra Costa, 1845, including three new species: P. austropacifica n. sp. (males and females) from the ovary of Alepes vari (Carangidae), P. piscaria n. sp. (males) from the ovary of Epinephelus coioides (Serranidae), and P. selaris n. sp. (males) probably from the abdominal cavity (found in washings) of Selar crumenophthalmus (Carangidae). The new species are characterised mainly by the length and structure of the spicules and gubernaculum, body size, their location in the host and the type of host. Philometra austropacifica n. sp. is the first known nominal gonad-infecting species of Philometra parasitising a carangid fish. In addition, the gravid female of P. fasciati Moravec &amp; Justine, 2008 from the ovary of Epinephelus fasciatus (Serranidae) is described for the first time. Carangid host fish were identified by both morphology and DNA barcoding.},
}
@article {pmid24836713,
year = {2014},
author = {Scott, AC and Ludlow, CL and Cromie, GA and Dudley, AM},
title = {BEST: barcode enabled sequencing of tetrads.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {87},
pages = {},
pmid = {24836713},
issn = {1940-087X},
support = {K22 HG002908/HG/NHGRI NIH HHS/United States ; },
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/genetics ; Diploidy ; Flow Cytometry/instrumentation/methods ; Haploidy ; High-Throughput Nucleotide Sequencing/instrumentation/*methods ; Meiosis/genetics ; Saccharomyces cerevisiae/chemistry/*genetics ; },
abstract = {Tetrad analysis is a valuable tool for yeast genetics, but the laborious manual nature of the process has hindered its application on large scales. Barcode Enabled Sequencing of Tetrads (BEST)1 replaces the manual processes of isolating, disrupting and spacing tetrads. BEST isolates tetrads by virtue of a sporulation-specific GFP fusion protein that permits fluorescence-activated cell sorting of tetrads directly onto agar plates, where the ascus is enzymatically digested and the spores are disrupted and randomly arrayed by glass bead plating. The haploid colonies are then assigned sister spore relationships, i.e. information about which spores originated from the same tetrad, using molecular barcodes read during genotyping. By removing the bottleneck of manual dissection, hundreds or even thousands of tetrads can be isolated in minutes. Here we present a detailed description of the experimental procedures required to perform BEST in the yeast Saccharomyces cerevisiae, starting with a heterozygous diploid strain through the isolation of colonies derived from the haploid meiotic progeny.},
}
@article {pmid24835790,
year = {2014},
author = {Martin, JW and Chilton-MacNeill, S and Koti, M and van Wijnen, AJ and Squire, JA and Zielenska, M},
title = {Digital expression profiling identifies RUNX2, CDC5L, MDM2, RECQL4, and CDK4 as potential predictive biomarkers for neo-adjuvant chemotherapy response in paediatric osteosarcoma.},
journal = {PloS one},
volume = {9},
number = {5},
pages = {e95843},
pmid = {24835790},
issn = {1932-6203},
support = {R01 AR049069/AR/NIAMS NIH HHS/United States ; CCRI-020247/CAPMC/CIHR/Canada ; },
mesh = {Adolescent ; Cell Cycle Proteins/genetics ; Child ; Core Binding Factor Alpha 1 Subunit/genetics ; Cyclin-Dependent Kinase 4/genetics ; Drug Therapy/*methods ; Female ; Gene Expression Profiling/methods ; Gene Expression Regulation, Neoplastic/*genetics ; Gene Regulatory Networks/*genetics ; Genetic Markers/*genetics ; Humans ; Male ; Neoadjuvant Therapy/*methods ; Osteosarcoma/*drug therapy/*genetics ; Proto-Oncogene Proteins c-mdm2/genetics ; RNA-Binding Proteins/genetics ; RecQ Helicases/genetics ; Treatment Outcome ; },
abstract = {Osteosarcoma is the most common malignancy of bone, and occurs most frequently in children and adolescents. Currently, the most reliable technique for determining a patients' prognosis is measurement of histopathologic tumor necrosis following pre-operative neo-adjuvant chemotherapy. Unfavourable prognosis is indicated by less than 90% estimated necrosis of the tumor. Neither genetic testing nor molecular biomarkers for diagnosis and prognosis have been described for osteosarcomas. We used the novel nanoString mRNA digital expression analysis system to analyse gene expression in 32 patients with sporadic paediatric osteosarcoma. This system used specific molecular barcodes to quantify expression of a set of 17 genes associated with osteosarcoma tumorigenesis. Five genes, from this panel, which encoded the bone differentiation regulator RUNX2, the cell cycle regulator CDC5L, the TP53 transcriptional inactivator MDM2, the DNA helicase RECQL4, and the cyclin-dependent kinase gene CDK4, were differentially expressed in tumors that responded poorly to neo-adjuvant chemotherapy. Analysis of the signalling relationships of these genes, as well as other expression markers of osteosarcoma, indicated that gene networks linked to RB1, TP53, PI3K, PTEN/Akt, myc and RECQL4 are associated with osteosarcoma. The discovery of these networks provides a basis for further experimental studies of role of the five genes (RUNX2, CDC5L, MDM2, RECQL4, and CDK4) in differential response to chemotherapy.},
}
@article {pmid24835119,
year = {2015},
author = {Saitoh, T and Sugita, N and Someya, S and Iwami, Y and Kobayashi, S and Kamigaichi, H and Higuchi, A and Asai, S and Yamamoto, Y and Nishiumi, I},
title = {DNA barcoding reveals 24 distinct lineages as cryptic bird species candidates in and around the Japanese Archipelago.},
journal = {Molecular ecology resources},
volume = {15},
number = {1},
pages = {177-186},
doi = {10.1111/1755-0998.12282},
pmid = {24835119},
issn = {1755-0998},
mesh = {Animals ; Birds/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Islands ; Japan ; Mitochondria/enzymology/genetics ; },
abstract = {DNA barcoding using a partial region (648 bp) of the cytochrome c oxidase I (COI) gene is a powerful tool for species identification and has revealed many cryptic species in various animal taxa. In birds, cryptic species are likely to occur in insular regions like the Japanese Archipelago due to the prevention of gene flow by sea barriers. Using COI sequences of 234 of the 251 Japanese-breeding bird species, we established a DNA barcoding library for species identification and estimated the number of cryptic species candidates. A total of 226 species (96.6%) had unique COI sequences with large genetic divergence among the closest species based on neighbour-joining clusters, genetic distance criterion and diagnostic substitutions. Eleven cryptic species candidates were detected, with distinct intraspecific deep genetic divergences, nine lineages of which were geographically separated by islands and straits within the Japanese Archipelago. To identify Japan-specific cryptic species from trans-Paleartic birds, we investigated the genetic structure of 142 shared species over an extended region covering Japan and Eurasia; 19 of these species formed two or more clades with high bootstrap values. Excluding six duplicated species from the total of 11 species within the Japanese Archipelago and 19 trans-Paleartic species, we identified 24 species that were cryptic species candidates within and surrounding the Japanese Archipelago. Repeated sea level changes during the glacial and interglacial periods may be responsible for the deep genetic divergences of Japanese birds in this insular region, which has led to inconsistencies in traditional taxonomies based on morphology.},
}
@article {pmid24832008,
year = {2014},
author = {Srinivasan, R and Jambulingam, P and Kumar, NP},
title = {Sergentomyia (Neophlebotomus) monticola, a new species of sand fly (Diptera: Psychodidae) from the Western Ghats, Thiruvananthapuram District, Kerala, India.},
journal = {Acta tropica},
volume = {137},
number = {},
pages = {74-79},
doi = {10.1016/j.actatropica.2014.04.023},
pmid = {24832008},
issn = {1873-6254},
mesh = {Animals ; *Biometry ; *DNA Barcoding, Taxonomic ; Female ; India ; Male ; *Microscopy ; Psychodidae/anatomy &amp; histology/*classification/genetics/*growth &amp; development ; },
abstract = {Sergentomyia (Neophlebotomus) monticola, a new species of sand fly (Diptera: Psychodidae), from the Kani tribal settlements, Thiruvananthapuram District, Kerala, southern India was described. These settlements were located in the Western Ghats, which is one of the 25 biodiversity hotspots in the world. Morphological characters of male and female specimens of Sergentomyia (Neophlebotomus) monticola were described with illustrations and its taxonomic position is defined within the genus. The DNA barcode analysis showed that both male and female specimens of the species were belonging to a single taxonomic category. The genetic distance with the most similar taxonomic neighbour was 14.61%, which confirms its distinctness from its congeners. Voucher specimens of the new species were deposited at the museum, Vector Control Research Centre (Indian Council of Medical Research), Puducherry, India, Zoological Survey of India, India and Smithsonian National Museum of Natural History (NMNH), Washington, D.C., USA.},
}
@article {pmid24827460,
year = {2014},
author = {Ashfaq, M and Hebert, PD and Mirza, JH and Khan, AM and Zafar, Y and Mirza, MS},
title = {Analyzing mosquito (Diptera: culicidae) diversity in Pakistan by DNA barcoding.},
journal = {PloS one},
volume = {9},
number = {5},
pages = {e97268},
pmid = {24827460},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; Culicidae/*genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/genetics ; Dengue/genetics ; Disease Vectors ; Genetic Variation/*genetics ; Haplotypes/genetics ; Insect Vectors/genetics ; Pakistan ; Phylogeography/methods ; },
abstract = {BACKGROUND: Although they are important disease vectors mosquito biodiversity in Pakistan is poorly known. Recent epidemics of dengue fever have revealed the need for more detailed understanding of the diversity and distributions of mosquito species in this region. DNA barcoding improves the accuracy of mosquito inventories because morphological differences between many species are subtle, leading to misidentifications.<br><br>Sequence variation in the barcode region of the mitochondrial COI gene was used to identify mosquito species, reveal genetic diversity, and map the distribution of the dengue-vector species in Pakistan. Analysis of 1684 mosquitoes from 491 sites in Punjab and Khyber Pakhtunkhwa during 2010-2013 revealed 32 species with the assemblage dominated by Culex quinquefasciatus (61% of the collection). The genus Aedes (Stegomyia) comprised 15% of the specimens, and was represented by six taxa with the two dengue vector species, Ae. albopictus and Ae. aegypti, dominant and broadly distributed. Anopheles made up another 6% of the catch with An. subpictus dominating. Barcode sequence divergence in conspecific specimens ranged from 0-2.4%, while congeneric species showed from 2.3-17.8% divergence. A global haplotype analysis of disease-vectors showed the presence of multiple haplotypes, although a single haplotype of each dengue-vector species was dominant in most countries. Geographic distribution of Ae. aegypti and Ae. albopictus showed the later species was dominant and found in both rural and urban environments.<br><br>CONCLUSIONS: As the first DNA-based analysis of mosquitoes in Pakistan, this study has begun the construction of a barcode reference library for the mosquitoes of this region. Levels of genetic diversity varied among species. Because of its capacity to differentiate species, even those with subtle morphological differences, DNA barcoding aids accurate tracking of vector populations.},
}
@article {pmid24827102,
year = {2014},
author = {Rukke, BA and Cholidis, S and Johnsen, A and Ottesen, P},
title = {Confirming Hypoderma tarandi (Diptera: Oestridae) human ophthalmomyiasis by larval DNA barcoding.},
journal = {Acta parasitologica},
volume = {59},
number = {2},
pages = {301-304},
doi = {10.2478/s11686-014-0242-2},
pmid = {24827102},
issn = {1896-1851},
mesh = {Animals ; Child ; *DNA Barcoding, Taxonomic ; Diptera/classification/genetics/*growth &amp; development ; Electron Transport Complex IV/genetics ; Eye Diseases/*diagnosis/*parasitology ; Humans ; Male ; Molecular Sequence Data ; Myiasis/*diagnosis/*parasitology ; Norway ; Sequence Analysis, DNA ; },
abstract = {DNA barcoding is a practical tool for species identification, when morphological classification of an organism is difficult. Herein we describe the utilisation of this technique in a case of ophthalmomyiasis interna. A 12-year-old boy was infested during a summer holiday in northern Norway, while visiting an area populated with reindeer. Following medical examination, a Diptera larva was surgically removed from the boy's eye and tentatively identified from its morphological traits as Hypoderma tarandi (L.) (Diptera: Oestridae). Ultimately, DNA barcoding confirmed this impression. The larval cytochrome c oxidase subunit 1 (COI) DNA sequence was matched with both profiles of five adult H. tarandi from the same region where the boy was infested, and other established profiles of H. tarandi in the Barcode of Life Data Systems (BOLD) identification engine.},
}
@article {pmid24825118,
year = {2014},
author = {Baldwin, CC and Johnson, GD},
title = {Connectivity across the Caribbean Sea: DNA barcoding and morphology unite an enigmatic fish larva from the Florida straits with a new species of sea bass from deep reefs off Curaçao.},
journal = {PloS one},
volume = {9},
number = {5},
pages = {e97661},
pmid = {24825118},
issn = {1932-6203},
mesh = {Alcian Blue ; *Animal Distribution ; Animal Fins/anatomy &amp; histology ; Animals ; Anthraquinones ; Bass/*anatomy &amp; histology/*genetics ; Classification/methods ; Cluster Analysis ; *Coral Reefs ; DNA Barcoding, Taxonomic ; Florida ; Histological Techniques ; Larva/anatomy &amp; histology ; Netherlands Antilles ; Photomicrography ; *Phylogeny ; Skin Pigmentation/physiology ; Species Specificity ; },
abstract = {Integrative taxonomy, in which multiple disciplines are combined to address questions related to biological species diversity, is a valuable tool for identifying pelagic marine fish larvae and recognizing the existence of new fish species. Here we combine data from DNA barcoding, comparative morphology, and analysis of color patterns to identify an unusual fish larva from the Florida Straits and demonstrate that it is the pelagic larval phase of a previously undescribed species of Liopropoma sea bass from deep reefs off Curaçao, southern Caribbean. The larva is unique among larvae of the teleost family Serranidae, Tribe Liopropomini, in having seven elongate dorsal-fin spines. Adults of the new species are similar to the golden bass, Liopropoma aberrans, with which they have been confused, but they are distinct genetically and morphologically. The new species differs from all other western Atlantic liopropomins in having IX, 11 dorsal-fin rays and in having a unique color pattern-most notably the predominance of yellow pigment on the dorsal portion of the trunk, a pale to white body ventrally, and yellow spots scattered across both the dorsal and ventral portions of the trunk. Exploration of deep reefs to 300 m using a manned submersible off Curaçao is resulting in the discovery of numerous new fish species, improving our genetic databases, and greatly enhancing our understanding of deep-reef fish diversity in the southern Caribbean. Oh the mother and child reunion is only a moment away. Paul Simon.},
}
@article {pmid24816169,
year = {2014},
author = {Wong, WH and Tay, YC and Puniamoorthy, J and Balke, M and Cranston, PS and Meier, R},
title = {'Direct PCR' optimization yields a rapid, cost-effective, nondestructive and efficient method for obtaining DNA barcodes without DNA extraction.},
journal = {Molecular ecology resources},
volume = {14},
number = {6},
pages = {1271-1280},
doi = {10.1111/1755-0998.12275},
pmid = {24816169},
issn = {1755-0998},
mesh = {Animals ; Chironomidae/*classification/*genetics ; Costs and Cost Analysis ; DNA Barcoding, Taxonomic/economics/*methods ; Larva/classification/genetics ; Molecular Sequence Data ; Polymerase Chain Reaction/economics/*methods ; Sequence Analysis, DNA ; Time Factors ; },
abstract = {Macroinvertebrates that are collected in large numbers pose major problems in basic and applied biodiversity research: identification to species via morphology is often difficult, slow and/or expensive. DNA barcodes are an attractive alternative or complementary source of information. Unfortunately, obtaining DNA barcodes from specimens requires many steps and thus time and money. Here, we promote a short cut to DNA barcoding, that is, a nondestructive PCR method that skips DNA extraction ('direct PCR') and that can be used for a broad range of invertebrate taxa. We demonstrate how direct PCR can be optimized for the larvae and adults of nonbiting midges (Diptera: Chironomidae), a typical invertebrate group that is abundant, contains important bioindicator species, but is difficult to identify based on morphological features. After optimization, direct PCR yields high PCR success rates (>90%), preserves delicate morphological features (e.g. details of genitalia, and larval head capsules) while allowing for the recovery of genomic DNA. We also document that direct PCR can be successfully optimized for a wide range of other invertebrate taxa that need routine barcoding (flies: Culicidae, Drosophilidae, Dolichopodidae, Sepsidae; sea stars: Oreasteridae). Key for obtaining high PCR success rates is optimizing (i) tissue quantity, (ii) body part, (iii) primer pair and (iv) type of Taq polymerase. Unfortunately, not all invertebrates appear suitable because direct PCR has low success rates for other taxa that were tested (e.g. Coleoptera: Dytiscidae, Copepoda, Hymenoptera: Formicidae and Odonata). It appears that the technique is less successful for heavily sclerotized insects and/or those with many exocrine glands.},
}
@article {pmid24813673,
year = {2014},
author = {Halem, ZM and Ross, DJ and Cox, RL},
title = {Evidence for intraspecific endocrine disruption of Geukensia demissa (Atlantic ribbed mussel) in an urban watershed.},
journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology},
volume = {175},
number = {},
pages = {1-6},
doi = {10.1016/j.cbpa.2014.04.016},
pmid = {24813673},
issn = {1531-4332},
mesh = {Animals ; Endocrine Disruptors/chemistry ; Environmental Monitoring ; Estradiol/*blood ; Female ; Male ; Mytilidae/*drug effects/physiology ; Progesterone/*blood ; Rivers ; Testosterone/*blood ; Urbanization ; Water Pollutants, Chemical ; },
abstract = {Populations undergo physiological adaptations in response to environmental stressors. Our 5-year bio-monitoring study of the Bronx River Estuary demonstrates comparatively low dissolved oxygen concentrations in this urbanized watershed. Additionally, our current results establish altered hormonal levels, resulting from endocrine disruption, in Geukensia demissa (Atlantic ribbed mussel) from the Bronx River Estuary. No studies have yet investigated a correlation between low dissolved oxygen and endocrine disruption in field-collected bivalves. Testosterone, estradiol, and progesterone levels were collected from male and female mussels in the oxygen depleted Bronx River and well-oxygenated Greenwich Cove. Bronx River mussels exhibited higher testosterone levels and lower estradiol levels than Greenwich Cove mussels. The resulting abnormal hormonal ratio seems to indicate that environmental conditions in the Bronx River facilitate an allosteric inhibition of the cytochrome P450 aromatase enzyme, which aids conversion of testosterone to estradiol. Low progesterone levels suggest that Bronx River mussels are experiencing a delay in sexual maturation, and morphometric data show a stalling of shell and tissue growth. To confirm that the mussels collected from both sites are the same species, the universal mitochondrial cytochrome c oxidase subunit I gene was analyzed, through DNA barcoding. Minimal sequential heterogeneity confirmed the mussels are the same species. Such findings suggest intraspecific divergence in various endocrine processes, resulting from environmentally induced stress.},
}
@article {pmid24813242,
year = {2014},
author = {Elliott, TL and Jonathan Davies, T},
title = {Challenges to barcoding an entire flora.},
journal = {Molecular ecology resources},
volume = {14},
number = {5},
pages = {883-891},
doi = {10.1111/1755-0998.12277},
pmid = {24813242},
issn = {1755-0998},
mesh = {DNA Barcoding, Taxonomic/*methods ; *Environmental Microbiology ; *Microbiota ; Molecular Sequence Data ; Quebec ; Sequence Analysis, DNA ; },
abstract = {DNA barcodes are species-specific genetic markers that allow taxonomic identification of biological samples. The promise of DNA barcoding as a rapid molecular tool for conducting biodiversity inventories has catalysed renewed efforts to document and catalogue the diversity of life, parallel to the large-scale sampling conducted by Victorian naturalists. The unique contribution of DNA barcode data is in its ability to identify biotic material that would be impossible to classify using traditional taxonomic keys. However, the utility of DNA barcoding relies upon the construction of accurate barcode libraries that provide a reference database to match to unidentified samples. Whilst there has been much debate in the literature over the choice and efficacy of barcode markers, there has been little consideration of the practicalities of generating comprehensive barcode reference libraries for species-rich floras. Here, we discuss several challenges to the generation of such libraries and present a case study from a regional biodiversity hotspot in southern Quebec. We suggest that the key challenges include (i) collection of specimens for rare or ephemeral species, (ii) limited access to taxonomic expertise necessary for reliable identification of reference specimens and (iii) molecular challenges in amplifying and matching barcode data. To be most effective, we recommend that sampling must be both flexible and opportunistic and conducted across the entire growing season by expert taxonomists. We emphasize that the success of the global barcoding initiative will depend upon the close collaboration of taxonomists, plant collectors, and molecular biologists.},
}
@article {pmid24808136,
year = {2014},
author = {Gibson, J and Shokralla, S and Porter, TM and King, I and van Konynenburg, S and Janzen, DH and Hallwachs, W and Hajibabaei, M},
title = {Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {111},
number = {22},
pages = {8007-8012},
pmid = {24808136},
issn = {1091-6490},
mesh = {Animals ; Arthropods/*chemistry ; *Biodiversity ; Costa Rica ; DNA Barcoding, Taxonomic/methods ; Ecological Parameter Monitoring/*methods ; Ecosystem ; Electron Transport Complex IV/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {Conventional assessments of ecosystem sample composition are based on morphology-based or DNA barcode identification of individuals. Both approaches are costly and time-consuming, especially when applied to the large number of specimens and taxa commonly included in ecological investigations. Next-generation sequencing approaches can overcome the bottleneck of individual specimen isolation and identification by simultaneously sequencing specimens of all taxa in a bulk mixture. Here we apply multiple parallel amplification primers, multiple DNA barcode markers, 454-pyrosequencing, and Illumina MiSeq sequencing to the same sample to maximize recovery of the arthropod macrobiome and the bacterial and other microbial microbiome of a bulk arthropod sample. We validate this method with a complex sample containing 1,066 morphologically distinguishable arthropods from a tropical terrestrial ecosystem with high taxonomic diversity. Multiamplicon next-generation DNA barcoding was able to recover sequences corresponding to 91% of the distinguishable individuals in a bulk environmental sample, as well as many species present as undistinguishable tissue. 454-pyrosequencing was able to recover 10 more families of arthropods and 30 more species than did conventional Sanger sequencing of each individual specimen. The use of other loci (16S and 18S ribosomal DNA gene regions) also added the detection of species of microbes associated with these terrestrial arthropods. This method greatly decreases the time and money necessary to perform DNA-based comparisons of biodiversity among ecosystem samples. This methodology opens the door to much cheaper and increased capacity for ecological and evolutionary studies applicable to a wide range of socio-economic issues, as well as a basic understanding of how the world works.},
}
@article {pmid24807349,
year = {2014},
author = {Bastonini, E and Jeznach, M and Field, M and Juszczyk, K and Corfield, E and Dezfouli, M and Ahmat, N and Smith, A and Womersley, H and Jordan, P and Ramadass, A and Akoulitchev, A and Goding, CR},
title = {Chromatin barcodes as biomarkers for melanoma.},
journal = {Pigment cell &amp; melanoma research},
volume = {27},
number = {5},
pages = {788-800},
doi = {10.1111/pcmr.12258},
pmid = {24807349},
issn = {1755-148X},
mesh = {Adult ; Aged ; Algorithms ; Biomarkers, Tumor/*metabolism ; Cell Line, Tumor ; Chromatin/*chemistry ; Computational Biology ; Epigenesis, Genetic ; Female ; Gene Expression Regulation, Neoplastic ; Genetic Markers ; Humans ; Male ; Melanoma/*blood/diagnosis/*metabolism ; Microphthalmia-Associated Transcription Factor/*metabolism ; Middle Aged ; Multivariate Analysis ; Reproducibility of Results ; Skin Neoplasms/*blood/diagnosis/*metabolism ; },
abstract = {The major barrier to effective cancer therapy is the presence of genetic and phenotypic heterogeneity within cancer cell populations that provides a reservoir of therapeutically resistant cells. As the degree of heterogeneity present within tumours will be proportional to tumour burden, the development of rapid, robust, accurate and sensitive biomarkers for cancer progression that could detect clinically occult disease before substantial heterogeneity develops would provide a major therapeutic benefit. Here, we explore the application of chromatin conformation capture technology to generate a diagnostic epigenetic barcode for melanoma. The results indicate that binary states from chromatin conformations at 15 loci within five genes can be used to provide rapid, non-invasive multivariate test for the presence of melanoma using as little as 200 μl of patient blood.},
}
@article {pmid24806292,
year = {2014},
author = {Voglmayr, H and Montes-Borrego, M and Landa, BB},
title = {Disentangling Peronospora on Papaver: phylogenetics, taxonomy, nomenclature and host range of downy mildew of opium poppy (Papaver somniferum) and related species.},
journal = {PloS one},
volume = {9},
number = {5},
pages = {e96838},
pmid = {24806292},
issn = {1932-6203},
support = {P 22739/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {DNA, Fungal/genetics ; DNA, Ribosomal Spacer/*genetics ; Host Specificity/genetics ; Opium ; Papaver/*genetics/microbiology ; Peronospora/classification/*genetics/pathogenicity ; *Phylogeny ; Plant Diseases/genetics/microbiology ; },
abstract = {Based on sequence data from ITS rDNA, cox1 and cox2, six Peronospora species are recognised as phylogenetically distinct on various Papaver species. The host ranges of the four already described species P. arborescens, P. argemones, P. cristata and P. meconopsidis are clarified. Based on sequence data and morphology, two new species, P. apula and P. somniferi, are described from Papaver apulum and P. somniferum, respectively. The second Peronospora species parasitizing Papaver somniferum, that was only recently recorded as Peronospora cristata from Tasmania, is shown to represent a distinct taxon, P. meconopsidis, originally described from Meconopsis cambrica. It is shown that P. meconopsidis on Papaver somniferum is also present and widespread in Europe and Asia, but has been overlooked due to confusion with P. somniferi and due to less prominent, localized disease symptoms. Oospores are reported for the first time for P. meconopsidis from Asian collections on Papaver somniferum. Morphological descriptions, illustrations and a key are provided for all described Peronospora species on Papaver. cox1 and cox2 sequence data are confirmed as equally good barcoding loci for reliable Peronospora species identification, whereas ITS rDNA does sometimes not resolve species boundaries. Molecular phylogenetic data reveal high host specificity of Peronospora on Papaver, which has the important phytopathological implication that wild Papaver spp. cannot play any role as primary inoculum source for downy mildew epidemics in cultivated opium poppy crops.},
}
@article {pmid24806079,
year = {2014},
author = {Alonso, H and Granadeiro, JP and Waap, S and Xavier, J and Symondson, WO and Ramos, JA and Catry, P},
title = {An holistic ecological analysis of the diet of Cory's shearwaters using prey morphological characters and DNA barcoding.},
journal = {Molecular ecology},
volume = {23},
number = {15},
pages = {3719-3733},
doi = {10.1111/mec.12785},
pmid = {24806079},
issn = {1365-294X},
mesh = {Africa ; Animals ; Birds/*physiology ; Cephalopoda/classification ; *DNA Barcoding, Taxonomic ; *Diet ; Ecosystem ; Female ; Fishes/classification ; *Food Chain ; Gastrointestinal Contents ; Islands ; Male ; Molecular Sequence Data ; Phylogeny ; Predatory Behavior ; RNA, Ribosomal, 16S/genetics ; Seasons ; },
abstract = {Knowledge of the dietary choices and trophic niches of organisms is the key to understanding their roles in ecosystems. In seabird diet studies, prey identification is a difficult challenge, often yielding results with technique-specific biases. Additionally, sampling efforts are often not extensive enough to reveal intrapopulational variation. Immature animals, which may constitute up to 50% of a population, may occupy a significantly different trophic niche to more experienced birds, but this remains largely unexplored. We investigated the diet of Cory's shearwater (Calonectris diomedea) from Selvagem Grande, an island located off the northwest African coast, collecting a total of 698 regurgitate samples over three consecutive breeding seasons. The diet was assessed using two complementary approaches for prey identification: conventional morphological analysis (using fish vertebrae, otoliths and cephalopod beaks) and DNA barcoding of the 16S rRNA mitochondrial gene, in cases where a positive identification could not be retrieved. Species assignments employed BLAST and distance-based methods, as well as direct optimization of the tree length based on unaligned sequences in POY. This method resulted in robust tree estimates and species assignments, showing its potential for DNA barcoding of stomach contents using hypervariable markers such as the 16S. The molecular approach increased taxonomic resolution and revealed an additional 17 taxa. Diet differed significantly according to breeding status, sex, breeding phase (prelaying and chick rearing) and year. Such direct evidence of trophic segregation within the same population has rarely been shown in seabirds and highlights the importance of including such variables in ecosystem-based management approaches.},
}
@article {pmid24802796,
year = {2014},
author = {Kalivas, A and Ganopoulos, I and Xanthopoulou, A and Chatzopoulou, P and Tsaftaris, A and Madesis, P},
title = {DNA barcode ITS2 coupled with high resolution melting (HRM) analysis for taxonomic identification of Sideritis species growing in Greece.},
journal = {Molecular biology reports},
volume = {41},
number = {8},
pages = {5147-5155},
pmid = {24802796},
issn = {1573-4978},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Genetic Markers ; Genotyping Techniques/*methods ; Greece ; Molecular Sequence Data ; Phylogeny ; Phylogeography ; Real-Time Polymerase Chain Reaction ; Sequence Alignment ; Sideritis/*classification/*genetics ; },
abstract = {Identification of genotypes in Sideritis is complicated owing to the morphological similarity and common occurrence of natural hybridisation within Sideritis species. Species- and genotype-specific DNA markers are very useful for plant identification, breeding and preservation programs. Herein, a real-time polymerase chain reaction (PCR) of ITS2 barcode region coupled with high resolution melting-curve (HRM) analysis was evaluated for an accurate, rapid and sensitive tool for species identification focusing on seven Sideritis species growing in Greece. The HRM assay developed in this study is a rapid and straightforward method for the identification and discrimination of the investigated Sideritis species. This assay is simple compared to other genotyping methods as it does not require DNA sequencing or post-PCR processing. Therefore, this method offers a new alternative for rapid detection of Sideritis species.},
}
@article {pmid24796530,
year = {2015},
author = {Vartak, VR and Narasimmalu, R and Annam, PK and Singh, DP and Lakra, WS},
title = {DNA barcoding detected improper labelling and supersession of crab food served by restaurants in India.},
journal = {Journal of the science of food and agriculture},
volume = {95},
number = {2},
pages = {359-366},
doi = {10.1002/jsfa.6728},
pmid = {24796530},
issn = {1097-0010},
mesh = {Animals ; Brachyura/*genetics ; DNA/*analysis ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; *Food Labeling ; Humans ; India ; Phylogeny ; *Restaurants ; *Shellfish ; Species Specificity ; },
abstract = {BACKGROUND: Detection of improper labelling of raw and processed seafood is of global importance for reducing commercial fraud and enhancing food safety. Crabs are crustaceans with intricate morphological as well as genetic divergence among species and are popular as seafood in restaurants. Owing to the high number of crab species available, it can be difficult to identify those included in particular food dishes, thus increasing the chance of supersession. DNA barcoding is an advanced technology for detecting improper food labelling and has been used successfully to authenticate seafood.<br><br>RESULTS: This study identified 11 edible crab species from India by classical taxonomy and developed molecular barcodes with the cytochrome c oxidase I (COI) gene. These barcodes were used as reference barcodes for detecting any improper labelling of 50 restaurant crab samples. Neighbour-joining tree analysis with COI barcodes showed distinct clusters of restaurant samples with respective reference species. The study demonstrated 100% improper labelling of restaurant samples to cover up acts of inferior crab supersession.<br><br>CONCLUSION: DNA barcoding successfully identified 11 edible crabs in accordance with classical taxonomy and discerned improper crab food labelling in restaurants of India.},
}
@article {pmid24791482,
year = {2013},
author = {Hou, DY and Song, JY and Shi, LC and Yang, P and Chen, SL and Yao, H},
title = {[Molecular identification of Cynomorii herba using ITS2 DNA barcoding].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {38},
number = {23},
pages = {4028-4032},
pmid = {24791482},
issn = {1001-5302},
mesh = {Cynomorium/*classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Intergenic/*genetics ; DNA, Plant/*genetics ; Polymerase Chain Reaction ; },
abstract = {OBJECTIVE: To identify the Cynomorii Herba and its analogues species using DNA barcoding technique.<br><br>METHOD: Total genomic DNA extracted from all materials using the DNA extraction kit. The internal transcribed spacer 2 (ITS2) regions were amplified using polymerase chain reaction (PCR), and purified PCR products were sequenced bi-directionally. Sequence assembly and consensus sequence generation were performed using the CodonCode Aligner 3.7.1. The Kimura 2-Parameter (K2P) distances and GC content were computed using MEGA 5. 0. Species identification analyses were conducted through the species identification system for traditional Chinese medicine and neighbor-joining (NJ) trees.<br><br>RESULT: The ITS2 sequence lengths of Cynomorii Herba were 229 bp. The average intra-specific genetic distances of Cynomorii Herba were 0.003. The average inter-specific genetic distances between Cynomorii Herba and its adulterants species were 0.760. The results showed that the minimum inter-specific divergence is larger than the maximum intra-specific divergence. The species identification system for traditional Chinese medicine and NJ trees results indicated that Cynomorii Herba and its adulterants species can be easily identification.<br><br>CONCLUSION: The ITS2 region is an efficient barcode for identification of Cynomorii Herba, which provide a new technique to ensure clinical safety in utilization of traditional Chinese medicine.},
}
@article {pmid24782130,
year = {2014},
author = {Purushothaman, N and Newmaster, SG and Ragupathy, S and Stalin, N and Suresh, D and Arunraj, DR and Gnanasekaran, G and Vassou, SL and Narasimhan, D and Parani, M},
title = {A tiered barcode authentication tool to differentiate medicinal Cassia species in India.},
journal = {Genetics and molecular research : GMR},
volume = {13},
number = {2},
pages = {2959-2968},
doi = {10.4238/2014.April.16.4},
pmid = {24782130},
issn = {1676-5680},
mesh = {Cassia ; Chloroplasts/genetics ; *DNA Barcoding, Taxonomic ; DNA, Chloroplast/*genetics ; Genetic Markers/*genetics ; India ; Plants, Medicinal/*genetics ; Sequence Analysis, DNA ; },
abstract = {DNA barcoding is a desirable tool for medicinal product authentication. DNA barcoding is a method for species identification using short DNA sequences that are conserved within species, but variable between species. Unlike animals, there is no single universal DNA barcode locus for plants. Coding markers, matK and rbcL, and noncoding markers, trnH-psbA (chloroplast) and ITS2 (nuclear), have been reported to be suitable for the DNA barcoding of plants with varying degree of success. Sixty-four accessions from 20 species of the medicinal plant Cassia were collected, and analyzed for these 4 DNA barcoding markers. PCR amplification was 100% successful for all 4 markers, while intra-species divergence was 0 for all 4 Cassia species in which multiple accessions were studied. Assuming 1.0% divergence as the minimum requirement for discriminating 2 species, the 4 markers could only differentiate 15 to 65% of the species studied when used separately. Adding indels to the divergence increased the percentage of species discrimination by trnH-psbA to 90%. In 2-locus barcoding, while matK+rbcL (which is recommended by Consortium for the Barcoding of Life) discriminated 90% of the species, the other combinations of matK+ITS and rbcL+trnH-psbA showed 100% species discrimination. However, matK is plagued with primer issues. The combination of rbcL+trnH-psbA provided the most accurate (100% species ID) and efficient tiered DNA barcoding tool for the authentication of Cassia medicinal products.},
}
@article {pmid24781022,
year = {2014},
author = {Routtu, J and Grunberg, D and Izhar, R and Dagan, Y and Guttel, Y and Ucko, M and Ben-Ami, F},
title = {Selective and universal primers for trematode barcoding in freshwater snails.},
journal = {Parasitology research},
volume = {113},
number = {7},
pages = {2535-2540},
pmid = {24781022},
issn = {1432-1955},
mesh = {Animals ; DNA Barcoding, Taxonomic/methods ; DNA Primers/*genetics ; Fresh Water ; Genes, rRNA ; Israel ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Helminth/*genetics ; RNA, Ribosomal, 18S/drug effects/*genetics ; Snails/*parasitology ; Trematoda/*classification/genetics ; },
abstract = {Trematodes are significant pathogens of high medical, veterinary, and environmental importance. They are hard to isolate from their intermediate hosts, and their early life stages are difficult to identify morphologically. Therefore, primers were developed for trematodes to create a species barcoding system and allow selective PCR amplification in mixed samples. The specific oligonucleotide primer was universal for trematodes that infected several freshwater snail species in Israel. The diagnostic tool is based on the 18S rDNA gene. In contrast to morphological identification, trematode barcoding is rapid as it is based on a sequence of only 800 bp, and it classifies species accurately due to high polymorphism between conserved areas.},
}
@article {pmid24771579,
year = {2014},
author = {Chen, L and Man, H and Jia, H},
title = {On scanning linear barcodes from out-of-focus blurred images: a spatial domain dynamic template matching approach.},
journal = {IEEE transactions on image processing : a publication of the IEEE Signal Processing Society},
volume = {23},
number = {6},
pages = {2637-2650},
doi = {10.1109/TIP.2014.2319579},
pmid = {24771579},
issn = {1941-0042},
abstract = {Because of the lack of disciplined and efficient mechanisms, most modern area charge-coupled device-based barcode scanning technologies are not capable of handling out-of-focus (OOF) image blur and rely heavily on camera systems for capturing good quality, well-focused barcode images. In this paper, we present a novel linear barcode scanning system based on a dynamic template matching scheme. The proposed system works entirely in the spatial domain, and is capable of reading linear barcodes from low-resolution images containing severe OOF blur. This paper treats linear barcode scanning under the perspective of deformed binary waveform analysis and classification. A directed graphical model is designed to characterize the relationship between the blurred barcode waveform and its corresponding symbol value at any specific blur level. Under this model, linear barcode scanning is cast to find the optimal state sequence associated with the deformed barcode waveform segments. A dynamic programming-based inference algorithm is designed to retrieve the optimal state sequence, enabling real-time decoding on mobile devices of limited processing power.},
}
@article {pmid24765568,
year = {2014},
author = {Davies, SW and Meyer, E and Guermond, SM and Matz, MV},
title = {A cross-ocean comparison of responses to settlement cues in reef-building corals.},
journal = {PeerJ},
volume = {2},
number = {},
pages = {e333},
pmid = {24765568},
issn = {2167-8359},
abstract = {Caribbean coral reefs have deteriorated substantially over the past 30 years, which is broadly attributable to the effects of global climate change. In the same time, Indo-Pacific reefs maintain higher coral cover and typically recover rapidly after disturbances. This difference in reef resilience is largely due to much higher coral recruitment rates in the Pacific. We hypothesized that the lack of Caribbean recruitment might be explained by diminishing quality of settlement cues and/or impaired sensitivity of Caribbean coral larvae to those cues, relative to the Pacific. To evaluate this hypothesis, we assembled a collection of bulk samples of reef encrusting communities, mostly consisting of crustose coralline algae (CCA), from various reefs around the world and tested them as settlement cues for several coral species originating from different ocean provinces. Cue samples were meta-barcoded to evaluate their taxonomic diversity. We observed no systematic differences either in cue potency or in strength of larval responses depending on the ocean province, and no preference of coral larvae towards cues from the same ocean. Instead, we detected significant differences in cue preferences among coral species, even for corals originating from the same reef. We conclude that the region-wide disruption of the settlement process is unlikely to be the major cause of Caribbean reef loss. However, due to their high sensitivity to the effects of climate change, shifts in the composition of CCA-associated communities, combined with pronounced differences in cue preferences among coral species, could substantially influence future coral community structure.},
}
@article {pmid24761620,
year = {2014},
author = {Feng, SS and Zheng, SH and Li, YK and Huang, LF},
title = {[Identification of radix et rhizoma clematidis and its adulterants using DNA barcoding].},
journal = {Yao xue xue bao = Acta pharmaceutica Sinica},
volume = {49},
number = {2},
pages = {260-266},
pmid = {24761620},
issn = {0513-4870},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; Drug Contamination ; Nucleic Acid Amplification Techniques/methods ; Plant Roots/genetics ; Plants, Medicinal/classification/*genetics ; Ranunculaceae/classification/*genetics ; Rhizome/genetics ; Species Specificity ; },
abstract = {This study provides the candidate sequences in the identification of Radix et Rhizoma Clematidis and its adulterants using DNA barcoding. We amplified and sequenced the region psbA-trnH, with the data of 284 sequences from GenBank, the differential intra- and inter-specific divergences, genetic distance, barcoding gap were used to evaluate five barcodes, and the identification efficiency was assessed using BLAST1 and Nearest Distance methods. The results showed that psbA-trnH barcodes performed high identification efficiency and inter-specific divergences among the five different DNA barcodes. Analysis of the barcoding gap and NJ tree showed psbA-trnH was superior to other barcodes. Based on the identification and PCR amplification efficiency, psbA-trnH can be the ideal barcode to identify Radix et Rhizoma Clematidis and its adulterants accurately.},
}
@article {pmid24761043,
year = {2013},
author = {Crous, PW and Wingfield, MJ and Guarro, J and Cheewangkoon, R and van der Bank, M and Swart, WJ and Stchigel, AM and Cano-Lira, JF and Roux, J and Madrid, H and Damm, U and Wood, AR and Shuttleworth, LA and Hodges, CS and Munster, M and de Jesús Yáñez-Morales, M and Zúñiga-Estrada, L and Cruywagen, EM and de Hoog, GS and Silvera, C and Najafzadeh, J and Davison, EM and Davison, PJ and Barrett, MD and Barrett, RL and Manamgoda, DS and Minnis, AM and Kleczewski, NM and Flory, SL and Castlebury, LA and Clay, K and Hyde, KD and Maússe-Sitoe, SN and Chen, S and Lechat, C and Hairaud, M and Lesage-Meessen, L and Pawłowska, J and Wilk, M and Sliwińska-Wyrzychowska, A and Mętrak, M and Wrzosek, M and Pavlic-Zupanc, D and Maleme, HM and Slippers, B and Mac Cormack, WP and Archuby, DI and Grünwald, NJ and Tellería, MT and Dueñas, M and Martín, MP and Marincowitz, S and de Beer, ZW and Perez, CA and Gené, J and Marin-Felix, Y and Groenewald, JZ},
title = {Fungal Planet description sheets: 154-213.},
journal = {Persoonia},
volume = {31},
number = {},
pages = {188-296},
pmid = {24761043},
issn = {0031-5850},
abstract = {Novel species of microfungi described in the present study include the following from South Africa: Camarosporium aloes, Phaeococcomyces aloes and Phoma aloes from Aloe, C. psoraleae, Diaporthe psoraleae and D. psoraleae-pinnatae from Psoralea, Colletotrichum euphorbiae from Euphorbia, Coniothyrium prosopidis and Peyronellaea prosopidis from Prosopis, Diaporthe cassines from Cassine, D. diospyricola from Diospyros, Diaporthe maytenicola from Maytenus, Harknessia proteae from Protea, Neofusicoccum ursorum and N. cryptoaustrale from Eucalyptus, Ochrocladosporium adansoniae from Adansonia, Pilidium pseudoconcavum from Greyia radlkoferi, Stagonospora pseudopaludosa from Phragmites and Toxicocladosporium ficiniae from Ficinia. Several species were also described from Thailand, namely: Chaetopsina pini and C. pinicola from Pinus spp., Myrmecridium thailandicum from reed litter, Passalora pseudotithoniae from Tithonia, Pallidocercospora ventilago from Ventilago, Pyricularia bothriochloae from Bothriochloa and Sphaerulina rhododendricola from Rhododendron. Novelties from Spain include Cladophialophora multiseptata, Knufia tsunedae and Pleuroascus rectipilus from soil and Cyphellophora catalaunica from river sediments. Species from the USA include Bipolaris drechsleri from Microstegium, Calonectria blephiliae from Blephilia, Kellermania macrospora (epitype) and K. pseudoyuccigena from Yucca. Three new species are described from Mexico, namely Neophaeosphaeria agaves and K. agaves from Agave and Phytophthora ipomoeae from Ipomoea. Other African species include Calonectria mossambicensis from Eucalyptus (Mozambique), Harzia cameroonensis from an unknown creeper (Cameroon), Mastigosporella anisophylleae from Anisophyllea (Zambia) and Teratosphaeria terminaliae from Terminalia (Zimbabwe). Species from Europe include Auxarthron longisporum from forest soil (Portugal), Discosia pseudoartocreas from Tilia (Austria), Paraconiothyrium polonense and P. lycopodinum from Lycopodium (Poland) and Stachybotrys oleronensis from Iris (France). Two species of Chrysosporium are described from Antarctica, namely C. magnasporum and C. oceanitesii. Finally, Licea xanthospora is described from Australia, Hypochnicium huinayensis from Chile and Custingophora blanchettei from Uruguay. Novel genera of Ascomycetes include Neomycosphaerella from Pseudopentameris macrantha (South Africa), and Paramycosphaerella from Brachystegia sp. (Zimbabwe). Novel hyphomycete genera include Pseudocatenomycopsis from Rothmannia (Zambia), Neopseudocercospora from Terminalia (Zambia) and Neodeightoniella from Phragmites (South Africa), while Dimorphiopsis from Brachystegia (Zambia) represents a novel coelomycetous genus. Furthermore, Alanphillipsia is introduced as a new genus in the Botryosphaeriaceae with four species, A. aloes, A. aloeigena and A. aloetica from Aloe spp. and A. euphorbiae from Euphorbia sp. (South Africa). A new combination is also proposed for Brachysporium torulosum (Deightoniella black tip of banana) as Corynespora torulosa. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.},
}
@article {pmid24761041,
year = {2013},
author = {Morgado, LN and Noordeloos, ME and Lamoureux, Y and Geml, J},
title = {Multi-gene phylogenetic analyses reveal species limits, phylogeographic patterns, and evolutionary histories of key morphological traits in Entoloma (Agaricales, Basidiomycota).},
journal = {Persoonia},
volume = {31},
number = {},
pages = {159-178},
pmid = {24761041},
issn = {0031-5850},
abstract = {Species from Entoloma subg. Entoloma are commonly recorded from both the Northern and Southern Hemispheres and, according to literature, most of them have at least Nearctic-Palearctic distributions. However, these records are based on morphological analysis, and studies relating morphology, molecular data and geographical distribution have not been reported. In this study, we used phylogenetic species recognition criteria through gene genealogical concordance (based on nuclear ITS, LSU, rpb2 and mitochondrial SSU) to answer specific questions considering species limits in Entoloma subg. Entoloma and their geographic distribution in Europe, North America and Australasia. The studied morphotaxa belong to sect. Entoloma, namely species like the notorious poisonous E. sinuatum (E. lividum auct.), E. prunuloides (type-species of sect. Entoloma), E. nitidum and the red-listed E. bloxamii. With a few exceptions, our results reveal strong phylogeographical partitions that were previously not known. For example, no collection from Australasia proved to be conspecific with the Northern Hemisphere specimens. Almost all North American collections represent distinct and sister taxa to the European ones. And even within Europe, new lineages were uncovered for the red-listed E. bloxamii, which were previously unknown due to a broad morphological species concept. Our results clearly demonstrate the power of the phylogenetic species concept to reveal evolutionary units, to redefine the morphological limits of the species addressed and to provide insights into the evolutionary history of key morphological characters for Entoloma systematics. New taxa are described, and new combinations are made, including E. fumosobrunneum, E. pseudoprunuloides, E. ochreoprunuloides and E. caesiolamellatum. Epitypes are selected for E. prunuloides and E. bloxamii. In addition, complete descriptions are given of some other taxa used in this study for which modern descriptions are lacking, viz. E. subsinuatum, E. whiteae, E. flavifolium, E. luridum, E. bloxamii, E. madidum, E. corneri, E. callidermum and E. coeruleoviride.},
}
@article {pmid24755838,
year = {2014},
author = {Stein, ED and Martinez, MC and Stiles, S and Miller, PE and Zakharov, EV},
title = {Is DNA barcoding actually cheaper and faster than traditional morphological methods: results from a survey of freshwater bioassessment efforts in the United States?.},
journal = {PloS one},
volume = {9},
number = {4},
pages = {e95525},
pmid = {24755838},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; Cost-Benefit Analysis ; *DNA Barcoding, Taxonomic/economics/methods ; *Environmental Monitoring/economics/methods ; *Fresh Water ; United States ; },
abstract = {Taxonomic identification accounts for a substantial portion of cost associated with bioassessment programs across the United States. New analytical approaches, such as DNA barcoding have been promoted as a way to reduce monitoring costs and improve efficiency, yet this assumption has not been thoroughly evaluated. We address this question by comparing costs for traditional morphology-based bioassessment, the standard Sanger sequencing-based DNA barcoding approach, and emerging next-generation (NGS) molecular methods. Market demand for molecular approaches is also assessed through a survey of the level of freshwater bioassessment effort in the United States across multiple habitat types (lakes, streams, wetlands) and indicators (benthic invertebrates, fish, algae). All state and regional level programs administered by public agencies and reported via agency web sites were included in the survey. Costs were based on surveys of labs and programs willing to provide such information. More than 19,500 sites are sampled annually across the United States, with the majority of effort occurring in streams. Benthic invertebrates are the most commonly used indicator, but algae and fish comprise between 35% and 21% of total sampling effort, respectively. We estimate that between $104 and $193 million is spent annually on routine freshwater bioassessment in the United States. Approximately 30% of the bioassessment costs are comprised of the cost to conduct traditional morphology-based taxonomy. Current barcoding costs using Sanger sequencing are between 1.7 and 3.4 times as expensive as traditional taxonomic approaches, excluding the cost of field sampling (which is common to both approaches). However, the cost of NGS methods are comparable (or slightly less expensive) than traditional methods depending on the indicator. The promise of barcoding as a cheaper alternative to current practices is not yet realized, although molecular methods may provide other benefits, such as a faster sample processing and increased taxonomic resolution.},
}
@article {pmid24751335,
year = {2014},
author = {Hyde, JR and Underkoffler, KE and Sundberg, MA},
title = {DNA barcoding provides support for a cryptic species complex within the globally distributed and fishery important opah (Lampris guttatus).},
journal = {Molecular ecology resources},
volume = {14},
number = {6},
pages = {1239-1247},
doi = {10.1111/1755-0998.12268},
pmid = {24751335},
issn = {1755-0998},
mesh = {Animals ; Cluster Analysis ; Cytochromes b/genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Fishes/anatomy &amp; histology/*classification/*genetics ; Genes, RAG-1/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The cornerstone of fisheries management relies on a solid taxonomic base and an understanding of how animals can be grouped into coherent management units. Surprisingly, little is known about the basic biology and ecology of opah (Lampris guttatus), a globally distributed species that is commercially exploited and regionally common in the North Pacific. Recent efforts to collect life history data on this species uncovered evidence of two North Pacific morphotypes. Sequencing of the mitochondrial cytochrome c oxidase I gene (655 bp) for these morphotypes and other specimens collected worldwide (n = 480) produced five strongly diverged and well-supported clades. Additional sequence data from the cytochrome b gene (1141 bp) as well as the nuclear recombination activating gene 1 (1323 bp) corroborated these results, suggesting these five clades probably represent separate species. Our conclusion that opah is a complex of five separate species has implications for management and indicates a need to gather additional data on these poorly understood fishes.},
}
@article {pmid24743320,
year = {2014},
author = {Layton, KK and Martel, AL and Hebert, PD},
title = {Patterns of DNA barcode variation in Canadian marine molluscs.},
journal = {PloS one},
volume = {9},
number = {4},
pages = {e95003},
pmid = {24743320},
issn = {1932-6203},
mesh = {Animals ; Aquatic Organisms/*classification/*genetics ; Canada ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Mollusca/*classification/*genetics ; },
abstract = {BACKGROUND: Molluscs are the most diverse marine phylum and this high diversity has resulted in considerable taxonomic problems. Because the number of species in Canadian oceans remains uncertain, there is a need to incorporate molecular methods into species identifications. A 648 base pair segment of the cytochrome c oxidase subunit I gene has proven useful for the identification and discovery of species in many animal lineages. While the utility of DNA barcoding in molluscs has been demonstrated in other studies, this is the first effort to construct a DNA barcode registry for marine molluscs across such a large geographic area.<br><br>This study examines patterns of DNA barcode variation in 227 species of Canadian marine molluscs. Intraspecific sequence divergences ranged from 0-26.4% and a barcode gap existed for most taxa. Eleven cases of relatively deep (>2%) intraspecific divergence were detected, suggesting the possible presence of overlooked species. Structural variation was detected in COI with indels found in 37 species, mostly bivalves. Some indels were present in divergent lineages, primarily in the region of the first external loop, suggesting certain areas are hotspots for change. Lastly, mean GC content varied substantially among orders (24.5%-46.5%), and showed a significant positive correlation with nearest neighbour distances.<br><br>CONCLUSIONS/SIGNIFICANCE: DNA barcoding is an effective tool for the identification of Canadian marine molluscs and for revealing possible cases of overlooked species. Some species with deep intraspecific divergence showed a biogeographic partition between lineages on the Atlantic, Arctic and Pacific coasts, suggesting the role of Pleistocene glaciations in the subdivision of their populations. Indels were prevalent in the barcode region of the COI gene in bivalves and gastropods. This study highlights the efficacy of DNA barcoding for providing insights into sequence variation across a broad taxonomic group on a large geographic scale.},
}
@article {pmid24742477,
year = {2014},
author = {Lovric, S and Fang, H and Vega-Warner, V and Sadowski, CE and Gee, HY and Halbritter, J and Ashraf, S and Saisawat, P and Soliman, NA and Kari, JA and Otto, EA and Hildebrandt, F and , },
title = {Rapid detection of monogenic causes of childhood-onset steroid-resistant nephrotic syndrome.},
journal = {Clinical journal of the American Society of Nephrology : CJASN},
volume = {9},
number = {6},
pages = {1109-1116},
pmid = {24742477},
issn = {1555-905X},
support = {R01 DK076683/DK/NIDDK NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; DK076683/DK/NIDDK NIH HHS/United States ; },
mesh = {Adult ; Age of Onset ; Child, Preschool ; DNA Mutational Analysis/economics/*methods ; Drug Resistance/*genetics ; Female ; Genetic Testing/economics/*methods ; High-Throughput Nucleotide Sequencing/economics ; Humans ; Infant ; Infant, Newborn ; Laminin/genetics ; Male ; Membrane Proteins/genetics ; Nephrotic Syndrome/drug therapy/epidemiology/*genetics ; Phosphoinositide Phospholipase C/genetics ; Steroids/therapeutic use ; },
abstract = {BACKGROUND AND OBJECTIVES: In steroid-resistant nephrotic syndrome (SRNS), >21 single-gene causes are known. However, mutation analysis of all known SRNS genes is time and cost intensive. This report describes a new high-throughput method of mutation analysis using a PCR-based microfluidic technology that allows rapid simultaneous mutation analysis of 21 single-gene causes of SRNS in a large number of individuals.<br><br>This study screened individuals with SRNS; samples were submitted for mutation analysis from international sources between 1996 and 2012. For proof of principle, a pilot cohort of 48 individuals who harbored known mutations in known SRNS genes was evaluated. After improvements to the method, 48 individuals with an unknown cause of SRNS were then examined in a subsequent diagnostic study. The analysis included 16 recessive SRNS genes and 5 dominant SRNS genes. A 10-fold primer multiplexing was applied, allowing PCR-based amplification of 474 amplicons in 21 genes for 48 DNA samples simultaneously. Forty-eight individuals were indexed in a barcode PCR, and high-throughput sequencing was performed. All disease-causing variants were confirmed via Sanger sequencing.<br><br>RESULTS: The pilot study identified the genetic cause of disease in 42 of 48 (87.5%) of the affected individuals. The diagnostic study detected the genetic cause of disease in 16 of 48 (33%) of the affected individuals with a previously unknown cause of SRNS. Seven novel disease-causing mutations in PLCE1 (n=5), NPHS1 (n=1), and LAMB2 (n=1) were identified in <3 weeks. Use of this method could reduce costs to 1/29th of the cost of Sanger sequencing.<br><br>CONCLUSION: This highly parallel approach allows rapid (<3 weeks) mutation analysis of 21 genes known to cause SRNS at a greatly reduced cost (1/29th) compared with traditional mutation analysis techniques. It detects mutations in about 33% of childhood-onset SRNS cases.},
}
@article {pmid24739436,
year = {2014},
author = {Rimet, F and Trobajo, R and Mann, DG and Kermarrec, L and Franc, A and Domaizon, I and Bouchez, A},
title = {When is sampling complete? The effects of geographical range and marker choice on perceived diversity in Nitzschia palea (Bacillariophyta).},
journal = {Protist},
volume = {165},
number = {3},
pages = {245-259},
doi = {10.1016/j.protis.2014.03.005},
pmid = {24739436},
issn = {1618-0941},
mesh = {*Biodiversity ; DNA, Ribosomal/genetics ; Diatoms/classification/*genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; *Genetic Markers ; Geography ; Phylogeny ; Phylogeography ; },
abstract = {DNA barcoding, being developed for biomonitoring, requires a database of reference sequences and knowledge of how much sequences can deviate before they are assigned to separate species. The molecular hunt for hidden species also raises the question of species definitions. We examined whether there are objective criteria for sequence-based species delimitation in diatoms, using Nitzschia palea, an important monophyletic indicator species already known to contain cryptic diversity. Strains from a wide geographical range were sequenced for 28S rRNA, COI and rbcL. Homogeneity indices and the Chao index failed to objectively select a precise number of species existing in N. palea as well as an evolutionary method based on coalescence theory. COI always gave higher diversity estimations than 28S rRNA or rbcL. Mating data did not provide a precise calibration of molecular species thresholds. Rarefaction curves indicated that further MOTUs would be detected with more isolates than we sampled (81 clones, 42 localities). Although some genotypes had intercontinental distributions, there was a positive relationship between genetic and geographical distance, suggesting even higher richness than we assessed, given that many regions were not sampled. Overall, no objective criteria were found for species separation; instead barcoding will need a consensual approach to molecular species limits.},
}
@article {pmid24739357,
year = {2014},
author = {Liu, J and Shi, L and Han, J and Li, G and Lu, H and Hou, J and Zhou, X and Meng, F and Downie, SR},
title = {Identification of species in the angiosperm family Apiaceae using DNA barcodes.},
journal = {Molecular ecology resources},
volume = {14},
number = {6},
pages = {1231-1238},
doi = {10.1111/1755-0998.12262},
pmid = {24739357},
issn = {1755-0998},
mesh = {Apiaceae/*classification/*genetics ; China ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Molecular Sequence Data ; Plant Proteins/genetics ; Plants ; Sequence Analysis, DNA ; },
abstract = {Apiaceae (Umbelliferae) is a large angiosperm family that includes many medicinally important species. The ability to identify these species and their adulterants is important, yet difficult to do so because of their subtle fruit morphological differences and often lack of diagnostic features in preserved specimens. Moreover, dried roots are often the official medical organs, making visual identification to species almost impossible. DNA barcoding has been proposed as a powerful taxonomic tool for species identification. The Consortium for the Barcode of Life (CBOL) Plant Working Group has recommended the combination of rbcL+matK as the core plant barcode. Recently, the China Plant BOL Group proposed that the nuclear ribosomal DNA internal transcribed spacer (ITS), as well as a subset of this marker (ITS2), be incorporated alongside rbcL+matK into the core barcode for seed plants, particularly angiosperms. In this study, we assess the effectiveness of these four markers plus psbA-trnH as Apiaceae barcodes. A total of 6032 sequences representing 1957 species in 385 diverse genera were sampled, of which 211 sequences from 50 individuals (representing seven species) were newly obtained. Of these five markers, ITS and ITS2 showed superior results in intra- and interspecific divergence and DNA barcoding gap assessments. For the matched data set (173 samples representing 45 species in five genera), the ITS locus had the highest identification efficiency (73.3%), yet ITS2 also performed relatively well with 66.7% identification efficiency. The identification efficiency increased to 82.2% when using an ITS+psbA-trnH marker combination (ITS2+psbA-trnH was 80%), which was significantly higher than that of rbcL+matK (40%). For the full sample data set (3052 ITS sequences, 3732 ITS2 sequences, 1011 psbA-trnH sequences, 567 matK sequences and 566 rbcL sequences), ITS, ITS2, psbA-trnH, matK and rbcL had 70.0%, 64.3%, 49.5%, 38.6% and 32.1% discrimination abilities, respectively. These results confirm that ITS or its subset ITS2 be incorporated into the core barcode for Apiaceae and that the combination of ITS/ITS2+psbA-trnH has much potential value as a powerful, standard DNA barcode for Apiaceae identification.},
}
@article {pmid24735443,
year = {2014},
author = {Ellinger, B and Silber, J and Prashar, A and Landskron, J and Weber, J and Rehermann, S and Müller, FJ and Smith, S and Wrigley, S and Taskén, K and Gribbon, P and Labes, A and Imhoff, JF},
title = {A phenotypic screening approach to identify anticancer compounds derived from marine fungi.},
journal = {Assay and drug development technologies},
volume = {12},
number = {3},
pages = {162-175},
pmid = {24735443},
issn = {1557-8127},
mesh = {Antineoplastic Agents/*administration &amp; dosage/chemistry ; Biological Products/*administration &amp; dosage/chemistry ; Cell Line, Tumor ; Cell Survival/drug effects ; Drug Screening Assays, Antitumor/*methods ; Fungi/*chemistry ; Humans ; Neoplasms, Experimental/*drug therapy/*pathology ; Treatment Outcome ; Water Microbiology ; },
abstract = {This study covers the isolation, testing, and identification of natural products with anticancer properties. Secondary metabolites were isolated from fungal strains originating from a variety of marine habitats. Strain culture protocols were optimized with respect to growth media composition and fermentation conditions. From these producers, isolated compounds were screened for their effect on the viability and proliferation of a subset of the NCI60 panel of cancer cell lines. Active compounds of interest were identified and selected for detailed assessments and structural elucidation using nuclear magnetic resonance. This revealed the majority of fungal-derived compounds represented known anticancer chemotypes, confirming the integrity of the process and the ability to identify suitable compounds. Examination of effects of selected compounds on cancer-associated cell signaling pathways used phospho flow cytometry in combination with 3D fluorescent cell barcoding. In parallel, the study addressed the logistical aspects of maintaining multiple cancer cell lines in culture simultaneously. A potential solution involving microbead-based cell culture was investigated (BioLevitator, Hamilton). Selected cell lines were cultured in microbead and 2D methods and cell viability tests showed comparable compound inhibition in both methods (R2=0.95). In a further technology assessment, an image-based assay system was investigated for its utility as a possible complement to ATP-based detection for quantifying cell growth and viability in a label-free manner.},
}
@article {pmid24734911,
year = {2014},
author = {Pawlowski, J and Esling, P and Lejzerowicz, F and Cedhagen, T and Wilding, TA},
title = {Environmental monitoring through protist next-generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities.},
journal = {Molecular ecology resources},
volume = {14},
number = {6},
pages = {1129-1140},
doi = {10.1111/1755-0998.12261},
pmid = {24734911},
issn = {1755-0998},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Environmental Monitoring/*methods ; *Fisheries ; Foraminifera/*classification/*genetics ; Geologic Sediments/*parasitology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Salmon/growth &amp; development ; Scotland ; },
abstract = {The measurement of species diversity represents a powerful tool for assessing the impacts of human activities on marine ecosystems. Traditionally, the impact of fish farming on the coastal environment is evaluated by monitoring the dynamics of macrobenthic infaunal populations. However, taxonomic sorting and morphology-based identification of the macrobenthos demand highly trained specialists and are extremely time-consuming and costly, making it unsuitable for large-scale biomonitoring efforts involving numerous samples. Here, we propose to alleviate this laborious task by developing protist metabarcoding tools based on next-generation sequencing (NGS) of environmental DNA and RNA extracted from sediment samples. In this study, we analysed the response of benthic foraminiferal communities to the variation of environmental gradients associated with salmon farms in Scotland. We investigated the foraminiferal diversity based on ribosomal minibarcode sequences generated by the Illumina NGS technology. We compared the molecular data with morphospecies counts and with environmental gradients, including distance to cages and redox used as a proxy for sediment oxygenation. Our study revealed high variations between foraminiferal communities collected in the vicinity of fish farms and at distant locations. We found evidence for species richness decrease in impacted sites, especially visible in the RNA data. We also detected some candidate bioindicator foraminiferal species. Based on this proof-of-concept study, we conclude that NGS metabarcoding using foraminifera and other protists has potential to become a new tool for surveying the impact of aquaculture and other industrial activities in the marine environment.},
}
@article {pmid24732455,
year = {2014},
author = {Wu, B and Zhong, GY and Yue, JQ and Yang, RT and Li, C and Li, YJ and Zhong, Y and Wang, X and Jiang, B and Zeng, JW and Zhang, L and Yan, ST and Bei, XJ and Zhou, DG},
title = {Identification of pummelo cultivars by using a panel of 25 selected SNPs and 12 DNA segments.},
journal = {PloS one},
volume = {9},
number = {4},
pages = {e94506},
pmid = {24732455},
issn = {1932-6203},
mesh = {Base Sequence ; Citrus/*genetics ; DNA, Plant/*genetics ; *Ecotype ; Genetic Variation ; Genotyping Techniques ; Haplotypes/genetics ; Nucleic Acid Denaturation/genetics ; Nucleotides/genetics ; Polymorphism, Single Nucleotide/*genetics ; Population Dynamics ; },
abstract = {Pummelo cultivars are usually difficult to identify morphologically, especially when fruits are unavailable. The problem was addressed in this study with the use of two methods: high resolution melting analysis of SNPs and sequencing of DNA segments. In the first method, a set of 25 SNPs with high polymorphic information content were selected from SNPs predicted by analyzing ESTs and sequenced DNA segments. High resolution melting analysis was then used to genotype 260 accessions including 55 from Myanmar, and 178 different genotypes were thus identified. A total of 99 cultivars were assigned to 86 different genotypes since the known somatic mutants were identical to their original genotypes at the analyzed SNP loci. The Myanmar samples were genotypically different from each other and from all other samples, indicating they were derived from sexual propagation. Statistical analysis showed that the set of SNPs was powerful enough for identifying at least 1000 pummelo genotypes, though the discrimination power varied in different pummelo groups and populations. In the second method, 12 genomic DNA segments of 24 representative pummelo accessions were sequenced. Analysis of the sequences revealed the existence of a high haplotype polymorphism in pummelo, and statistical analysis showed that the segments could be used as genetic barcodes that should be informative enough to allow reliable identification of 1200 pummelo cultivars. The high level of haplotype diversity and an apparent population structure shown by DNA segments and by SNP genotypes, respectively, were discussed in relation to the origin and domestication of the pummelo species.},
}
@article {pmid24728520,
year = {2014},
author = {Ferreira, KA and Fajardo, EF and Baptista, RP and Macedo, AM and Lages-Silva, E and Ramírez, LE and Pedrosa, AL},
title = {Species-specific markers for the differential diagnosis of Trypanosoma cruzi and Trypanosoma rangeli and polymorphisms detection in Trypanosoma rangeli.},
journal = {Parasitology research},
volume = {113},
number = {6},
pages = {2199-2207},
pmid = {24728520},
issn = {1432-1955},
mesh = {Base Sequence ; Cloning, Molecular ; DNA, Protozoan/genetics ; Genetic Markers ; Humans ; Microsatellite Repeats ; Molecular Sequence Data ; Polymerase Chain Reaction/methods ; Polymorphism, Genetic ; Species Specificity ; Trypanosoma cruzi/classification/*genetics ; Trypanosoma rangeli/classification/*genetics ; Trypanosomiasis/diagnosis/*parasitology ; },
abstract = {Trypanosoma cruzi and Trypanosoma rangeli are kinetoplastid parasites which are able to infect humans in Central and South America. Misdiagnosis between these trypanosomes can be avoided by targeting barcoding sequences or genes of each organism. This work aims to analyze the feasibility of using species-specific markers for identification of intraspecific polymorphisms and as target for diagnostic methods by PCR. Accordingly, primers which are able to specifically detect T. cruzi or T. rangeli genomic DNA were characterized. The use of intergenic regions, generally divergent in the trypanosomatids, and the serine carboxypeptidase gene were successful. Using T. rangeli genomic sequences for the identification of group-specific polymorphisms and a polymorphic AT(n) dinucleotide repeat permitted the classification of the strains into two groups, which are entirely coincident with T. rangeli main lineages, KP1 (+) and KP1 (-), previously determined by kinetoplast DNA (kDNA) characterization. The sequences analyzed totalize 622 bp (382 bp represent a hypothetical protein sequence, and 240 bp represent an anonymous sequence), and of these, 581 (93.3%) are conserved sites and 41 bp (6.7%) are polymorphic, with 9 transitions (21.9%), 2 transversions (4.9%), and 30 (73.2%) insertion/deletion events. Taken together, the species-specific markers analyzed may be useful for the development of new strategies for the accurate diagnosis of infections. Furthermore, the identification of T. rangeli polymorphisms has a direct impact in the understanding of the population structure of this parasite.},
}
@article {pmid24728464,
year = {2014},
author = {Lee, J and Bisso, PW and Srinivas, RL and Kim, JJ and Swiston, AJ and Doyle, PS},
title = {Universal process-inert encoding architecture for polymer microparticles.},
journal = {Nature materials},
volume = {13},
number = {5},
pages = {524-529},
doi = {10.1038/nmat3938},
pmid = {24728464},
issn = {1476-4660},
support = {T32 GM08334/GM/NIGMS NIH HHS/United States ; },
mesh = {Biocompatible Materials/chemistry ; Chemical Engineering ; Drug Packaging ; Electrochemical Techniques ; Hot Temperature ; Magnetic Fields ; Metal Nanoparticles/chemistry ; Metals, Rare Earth/chemistry ; MicroRNAs/analysis ; Nanoparticles/chemistry ; Particle Size ; Polymers/chemical synthesis/*chemistry ; },
abstract = {Polymer microparticles with unique, decodable identities are versatile information carriers with a small footprint. Widespread incorporation into industrial processes, however, is limited by a trade-off between encoding density, scalability and decoding robustness in diverse physicochemical environments. Here, we report an encoding strategy that combines spatial patterning with rare-earth upconversion nanocrystals, single-wavelength near-infrared excitation and portable CCD (charge-coupled device)-based decoding to distinguish particles synthesized by means of flow lithography. This architecture exhibits large, exponentially scalable encoding capacities (>10(6) particles), an ultralow decoding false-alarm rate (<10(-9)), the ability to manipulate particles by applying magnetic fields, and pronounced insensitivity to both particle chemistry and harsh processing conditions. We demonstrate quantitative agreement between observed and predicted decoding for a range of practical applications with orthogonal requirements, including covert multiparticle barcoding of pharmaceutical packaging (refractive-index matching), multiplexed microRNA detection (biocompatibility) and embedded labelling of high-temperature-cast objects (temperature resistance).},
}
@article {pmid24727800,
year = {2014},
author = {Félix, MA and Braendle, C and Cutter, AD},
title = {A streamlined system for species diagnosis in Caenorhabditis (Nematoda: Rhabditidae) with name designations for 15 distinct biological species.},
journal = {PloS one},
volume = {9},
number = {4},
pages = {e94723},
pmid = {24727800},
issn = {1932-6203},
mesh = {Animals ; Caenorhabditis/*classification/*genetics ; Crosses, Genetic ; DNA, Intergenic ; Evolution, Molecular ; Phylogeny ; Reproductive Isolation ; },
abstract = {The rapid pace of species discovery outstrips the rate of species description in many taxa. This problem is especially acute for Caenorhabditis nematodes, where the naming of distinct species would greatly improve their visibility and usage for biological research, given the thousands of scientists studying Caenorhabditis. Species description and naming has been hampered in Caenorhabditis, in part due to the presence of morphologically cryptic species despite complete biological reproductive isolation and often enormous molecular divergence. With the aim of expediting species designations, here we propose and apply a revised framework for species diagnosis and description in this group. Our solution prioritizes reproductive isolation over traditional morphological characters as the key feature in delineating and diagnosing new species, reflecting both practical considerations and conceptual justifications. DNA sequence divergence criteria help prioritize crosses for establishing patterns of reproductive isolation among the many species of Caenorhabditis known to science, such as with the ribosomal internal transcribed spacer-2 (ITS2) DNA barcode. By adopting this approach, we provide new species name designations for 15 distinct biological species, thus increasing the number of named Caenorhabditis species in laboratory culture by nearly 3-fold. We anticipate that the improved accessibility of these species to the research community will expand the opportunities for study and accelerate our understanding of diverse biological phenomena.},
}
@article {pmid24725375,
year = {2014},
author = {Wang, YJ and Li, ZH and Zhang, SF and Varadínová, Z and Jiang, F and Kučerová, Z and Stejskal, V and Opit, G and Cao, Y and Li, FJ},
title = {DNA barcoding of five common stored-product pest species of genus Cryptolestes (Coleoptera: Laemophloeidae).},
journal = {Bulletin of entomological research},
volume = {104},
number = {5},
pages = {671-678},
doi = {10.1017/S0007485314000224},
pmid = {24725375},
issn = {1475-2670},
mesh = {Animals ; Classification/methods ; Coleoptera/*genetics ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry ; Genetic Variation ; Haplotypes ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Several species of the genus Cryptolestes Ganglbauer, 1899 (Coleoptera: Laemophloeidae) are commonly found in stored products. In this study, five species of Cryptolestes, with almost worldwide distribution, were obtained from laboratories in China, Czech Republic and the USA: Cryptolestes ferrugineus (Stephens, 1831), Cryptolestes pusillus (Schönherr, 1817), Cryptolestes turcicus (Grouvelle, 1876), Cryptolestes pusilloides (Steel &amp; Howe, 1952) and Cryptolestes capensis (Waltl, 1834). Molecular identification based on a 658 bp fragment from the mitochondrial DNA cytochrome c oxidase subunit I (COI) was adopted to overcome some problems of morphological identification of Cryptolestes species. The utility of COI sequences as DNA barcodes in discriminating the five Cryptolestes species was evaluated on adults and larvae by analysing Kimura 2-parameter distances, phylogenetic tree and haplotype networks. The results showed that molecular approaches based on DNA barcodes were able to accurately identify these species. This is the first study using DNA barcoding to identify Cryptolestes species and the gathered DNA sequences will complement the biological barcode database.},
}
@article {pmid24724934,
year = {2016},
author = {Khedkar, T and Sharma, R and Tiknaik, A and Khedkar, G and Naikwade, BS and Ron, TB and Haymer, D},
title = {DNA barcoding using skin exuviates can improve identification and biodiversity studies of snakes.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {1},
pages = {499-507},
doi = {10.3109/19401736.2014.905830},
pmid = {24724934},
issn = {2470-1408},
mesh = {Animals ; Biodiversity ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Endangered Species ; India ; Phylogeny ; *Skin ; Snakes/*genetics ; },
abstract = {Snakes represent a taxonomically underdeveloped group of animals in India with a lack of experts and incomplete taxonomic descriptions being the main deterrents to advances in this area. Molecular taxonomic approaches using DNA barcoding could aid in snake identification as well as studies of biodiversity. Here a non-invasive sampling method using DNA barcoding is tested using skin exuviates. Taxonomically authenticated samples were collected and tested for validation and comparisons to unknown snake exuviate samples. This approach was also used to construct the first comprehensive study targeting the snake species from Maharashtra state in India. A total of 92 skin exuviate samples were collected and tested for this study. Of these, 81 samples were successfully DNA barcoded and compared with unknown samples for assignment of taxonomic identity. Good quality DNA was obtained irrespective of age and quality of the exuviate material, and all unknown samples were successfully identified. A total of 23 species of snakes were identified, six of which were in the list of Endangered species (Red Data Book). Intra- and inter-specific distance values were also calculated, and these were sufficient to allow discrimination among species and between species without ambiguity in most cases. Two samples were suspected to represent cryptic species based on deep K2P divergence values (>3%), and one sample could be identified to the genus level only. Eleven samples failed to amplify COI sequences, suggesting the need for alternative PCR primer pairs. This study clearly documents how snake skin exuviates can be used for DNA barcoding, estimates of diversity and population genetic structuring in a noninvasive manner.},
}
@article {pmid24721333,
year = {2014},
author = {Weitschek, E and Fiscon, G and Felici, G},
title = {Supervised DNA Barcodes species classification: analysis, comparisons and results.},
journal = {BioData mining},
volume = {7},
number = {1},
pages = {4},
pmid = {24721333},
issn = {1756-0381},
abstract = {BACKGROUND: Specific fragments, coming from short portions of DNA (e.g., mitochondrial, nuclear, and plastid sequences), have been defined as DNA Barcode and can be used as markers for organisms of the main life kingdoms. Species classification with DNA Barcode sequences has been proven effective on different organisms. Indeed, specific gene regions have been identified as Barcode: COI in animals, rbcL and matK in plants, and ITS in fungi. The classification problem assigns an unknown specimen to a known species by analyzing its Barcode. This task has to be supported with reliable methods and algorithms.<br><br>METHODS: In this work the efficacy of supervised machine learning methods to classify species with DNA Barcode sequences is shown. The Weka software suite, which includes a collection of supervised classification methods, is adopted to address the task of DNA Barcode analysis. Classifier families are tested on synthetic and empirical datasets belonging to the animal, fungus, and plant kingdoms. In particular, the function-based method Support Vector Machines (SVM), the rule-based RIPPER, the decision tree C4.5, and the Na&#xef;ve Bayes method are considered. Additionally, the classification results are compared with respect to ad-hoc and well-established DNA Barcode classification methods.<br><br>RESULTS: A software that converts the DNA Barcode FASTA sequences to the Weka format is released, to adapt different input formats and to allow the execution of the classification procedure. The analysis of results on synthetic and real datasets shows that SVM and Na&#xef;ve Bayes outperform on average the other considered classifiers, although they do not provide a human interpretable classification model. Rule-based methods have slightly inferior classification performances, but deliver the species specific positions and nucleotide assignments. On synthetic data the supervised machine learning methods obtain superior classification performances with respect to the traditional DNA Barcode classification methods. On empirical data their classification performances are at a comparable level to the other methods.<br><br>CONCLUSIONS: The classification analysis shows that supervised machine learning methods are promising candidates for handling with success the DNA Barcoding species classification problem, obtaining excellent performances. To conclude, a powerful tool to perform species identification is now available to the DNA Barcoding community.},
}
@article {pmid24720350,
year = {2014},
author = {Rangnekar, A and LaBean, TH},
title = {Building DNA nanostructures for molecular computation, templated assembly, and biological applications.},
journal = {Accounts of chemical research},
volume = {47},
number = {6},
pages = {1778-1788},
doi = {10.1021/ar500023b},
pmid = {24720350},
issn = {1520-4898},
mesh = {Base Sequence ; *Biosensing Techniques ; *Computers, Molecular ; DNA/*chemistry ; DNA, Single-Stranded/chemistry ; Humans ; Nanostructures/*chemistry ; Nanotechnology/*methods ; Nanowires ; },
abstract = {CONSPECTUS: DNA is a critical biomolecule well-known for its roles in biology and genetics. Moreover, its double-helical structure and the Watson-Crick pairing of its bases make DNA structurally predictable. This predictability enables design and synthesis of artificial DNA nanostructures by suitable programming of the base sequences of DNA strands. Since the advent of the field of DNA nanotechnology in 1982, a variety of DNA nanostructures have been designed and used for numerous applications. In this Account, we discuss the progress made by our lab which has contributed toward the overall advancement of the field. Tile-based DNA nanostructures are an integral part of structural DNA nanotechnology. These structures are formed using several short, chemically synthesized DNA strands by programming their base sequences so that they self-assemble into desired constructs. Design and assembly of several DNA tiles will be discussed in this Account. Tiles include, for example, TX tiles with three parallel, coplanar duplexes, 4 × 4 cross-tiles with four arms, and weave-tiles with weave-like architecture. Another category of tiles we will present involve multiple parallel duplexes that assemble to form closed tubular structures. All of these tile types have been used to form micrometer-scale one- and two-dimensional arrays and lattices. Origami-based structures constitute another category where a long single-stranded DNA scaffold is folded into desired shapes by association with multiple short staple strands. This Account will describe the efforts by our lab in devising new strategies to improve the maximum size of origami structures. The various DNA nanostructures detailed here have been used in a wide variety of different applications. This Account will discuss the use of DNA tiles for logical computation, encoding information as molecular barcodes, and functionalization for patterning of other nanoscale organic and inorganic materials. Consequently, we have used DNA nanostructures for templating metallic nanowires as well as for programmed assembly of proteins and nanoparticles with controlled spacings. Among other applications, we have used DNA nanotechnology in biosensors that detect target DNA sequences and to affect cell surface receptor clustering for communicating with a cell signaling pathway. We used DNA weave-tiles to control the spacing between thrombin-binding aptamers which resulted in very high antithrombin and anticoagulant activity of the construct. We believe that the tremendous progress in DNA nanotechnology over the past three decades will open even more research avenues in the near future for applications in a wide variety of disciplines including electronics, photonics, biomedical engineering, biosensing, therapeutics, and nucleic-acid-based drug delivery.},
}
@article {pmid24719117,
year = {2014},
author = {Kakkar, V and Meister-Broekema, M and Minoia, M and Carra, S and Kampinga, HH},
title = {Barcoding heat shock proteins to human diseases: looking beyond the heat shock response.},
journal = {Disease models &amp; mechanisms},
volume = {7},
number = {4},
pages = {421-434},
pmid = {24719117},
issn = {1754-8411},
mesh = {Animals ; *Disease ; Heat-Shock Proteins/*metabolism ; *Heat-Shock Response ; Humans ; Proteostasis Deficiencies/metabolism/pathology ; },
abstract = {There are numerous human diseases that are associated with protein misfolding and the formation of toxic protein aggregates. Activating the heat shock response (HSR)--and thus generally restoring the disturbed protein homeostasis associated with such diseases--has often been suggested as a therapeutic strategy. However, most data on activating the HSR or its downstream targets in mouse models of diseases associated with aggregate formation have been rather disappointing. The human chaperonome consists of many more heat shock proteins (HSPs) that are not regulated by the HSR, however, and researchers are now focusing on these as potential therapeutic targets. In this Review, we summarize the existing literature on a set of aggregation diseases and propose that each of them can be characterized or 'barcoded' by a different set of HSPs that can rescue specific types of aggregation. Some of these 'non-canonical' HSPs have demonstrated effectiveness in vivo, in mouse models of protein-aggregation disease. Interestingly, several of these HSPs also cause diseases when mutated--so-called chaperonopathies--which are also discussed in this Review.},
}
@article {pmid24715783,
year = {2014},
author = {Liew, TS and Vermeulen, JJ and Marzuki, ME and Schilthuizen, M},
title = {A cybertaxonomic revision of the micro-landsnail genus Plectostoma Adam (Mollusca, Caenogastropoda, Diplommatinidae), from Peninsular Malaysia, Sumatra and Indochina.},
journal = {ZooKeys},
volume = {},
number = {393},
pages = {1-107},
pmid = {24715783},
issn = {1313-2989},
abstract = {Plectostoma is a micro land snail restricted to limestone outcrops in Southeast Asia. Plectostoma was previously classified as a subgenus of Opisthostoma because of the deviation from regular coiling in many species in both taxa. This paper is the first of a two-part revision of the genus Plectostoma, and includes all non-Borneo species. In the present paper, we examined 214 collection samples of 31 species, and obtained 62 references, 290 pictures, and 155 3D-models of 29 Plectostoma species and 51 COI sequences of 19 species. To work with such a variety of taxonomic data, and then to represent it in an integrated, scaleable and accessible manner, we adopted up-to-date cybertaxonomic tools. All the taxonomic information, such as references, classification, species descriptions, specimen images, genetic data, and distribution data, were tagged and linked with cyber tools and web servers (e.g. Lifedesks, Google Earth, and Barcoding of Life Database). We elevated Plectostoma from subgenus to genus level based on morphological, ecological and genetic evidence. We revised the existing 21 Plectostoma species and described 10 new species, namely, P. dindingensis sp. n., P. mengaburensis sp. n., P. whitteni sp. n., P. kayiani sp. n., P. davisoni sp. n., P. relauensis sp. n., P. kubuensis sp. n., P. tohchinyawi sp. n., P. tenggekensis sp. n., and P. ikanensis sp. n. All the synthesised, semantic-tagged, and linked taxonomic information is made freely and publicly available online.},
}
@article {pmid24711065,
year = {2014},
author = {Lewandowski, M and Skoracka, A and Szydło, W and Kozak, M and Druciarek, T and Griffiths, DA},
title = {Genetic and morphological diversity of Trisetacus species (Eriophyoidea: Phytoptidae) associated with coniferous trees in Poland: phylogeny, barcoding, host and habitat specialization.},
journal = {Experimental &amp; applied acarology},
volume = {63},
number = {4},
pages = {497-520},
pmid = {24711065},
issn = {1572-9702},
mesh = {Acari/*genetics/ultrastructure ; Amino Acid Sequence ; Animals ; Base Sequence ; DNA/chemistry/genetics ; Discriminant Analysis ; Electron Transport Complex IV/chemistry/genetics ; Female ; Genetic Variation/*genetics ; Microscopy, Phase-Contrast ; Molecular Sequence Data ; *Phylogeny ; Poland ; Polymerase Chain Reaction ; RNA, Ribosomal, 28S/chemistry/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Tracheophyta/*parasitology ; },
abstract = {Eriophyoid species belonging to the genus Trisetacus are economically important as pests of conifers. A narrow host specialization to conifers and some unique morphological characteristics have made these mites interesting subjects for scientific inquiry. In this study, we assessed morphological and genetic variation of seven Trisetacus species originating from six coniferous hosts in Poland by morphometric analysis and molecular sequencing of the mitochondrial cytochrome oxidase subunit I gene and the nuclear D2 region of 28S rDNA. The results confirmed the monophyly of the genus Trisetacus as well as the monophyly of five of the seven species studied. Both DNA sequences were effective in discriminating between six of the seven species tested. Host-dependent genetic and morphological variation in T. silvestris and T. relocatus, and habitat-dependent genetic and morphological variation in T. juniperinus were detected, suggesting the existence of races or even distinct species within these Trisetacus taxa. This is the first molecular phylogenetic analysis of the Trisetacus species. The findings presented here will stimulate further investigations on the evolutionary relationships of Trisetacus as well as the entire Phytoptidae family.},
}
@article {pmid24708138,
year = {2016},
author = {Khedkar, GD and Tiknaik, AD and Shinde, RN and Kalyankar, AD and Ron, TB and Haymer, D},
title = {High rates of substitution of the native catfish Clarias batrachus by Clarias gariepinus in India.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {1},
pages = {569-574},
doi = {10.3109/19401736.2014.905863},
pmid = {24708138},
issn = {2470-1408},
mesh = {Animals ; Base Sequence ; Catfishes/*genetics ; Geography ; India ; Phylogeny ; },
abstract = {The clariid catfish, Clarias batrachus commonly known as Magur, has declined drastically from natural habitats in India during the last decade. This fish is highly preferred fish by Indian consumers and has high market demand. As a result traders often substitute C. batrachus with a morphologically similar but supposedly banned exotic catfish, C. gariepinus, in India. This study uses rigorous morphological comparisons confirmed by DNA barcode analysis to examine the level of substitution of C. batracus by C. gariepinus in India. Our results indicate that up to 99% (in many cases) of the market samples sold as Magur or C. batrachus were in fact C. gariepinus.},
}
@article {pmid24708137,
year = {2016},
author = {Turčinavičienė, J and Radzevičiūtė, R and Budrienė, A and Budrys, E},
title = {Species identification and genetic differentiation of European cavity-nesting wasps (Hymenoptera: Vespidae, Pompilidae, Crabronidae) inferred from DNA barcoding data.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {1},
pages = {476-482},
doi = {10.3109/19401736.2014.905827},
pmid = {24708137},
issn = {2470-1408},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Ecosystem ; Genetic Drift ; *Genetic Variation ; Sequence Analysis, DNA ; Species Specificity ; Wasps/*genetics ; },
abstract = {Solitary trap-nesting wasps are prospective bioindicators of anthropogenic pressures on natural ecosystems and one of the surrogate taxa for biodiversity assessments. The implementation of these studies is taxonomy-based and relies on accurate identification of species. The identification of larval stages of cavity-nesting Hymenoptera, collected using trap-nests, is complicated or impossible before the post-hibernation hatching of adults. DNA barcoding may allow the identification of the trap-nesting Hymenoptera species immediately after collection of the trap-nests, using larvae or dead specimens as sources of DNA. Using the standard barcoding sequence, we identified 33 wasp species from the families Vespidae, Pompilidae and Crabronidae, inhabiting trap-nests in Europe. Within-species and between-species genetic distances were estimated to evaluate the differences of intraspecific and interspecific genetic diversity. Genetic distances between related species indicated an obvious "barcoding gap". Neighbour-joining analysis revealed that groups corresponding to taxa of genus level are cohesive as well. COI barcode approach was confirmed as a valuable tool for taxonomy-based biodiversity studies of the trap-nesting Hymenoptera.},
}
@article {pmid24708133,
year = {2016},
author = {Botero-Castro, F and Delsuc, F and Douzery, EJ},
title = {Thrice better than once: quality control guidelines to validate new mitogenomes.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {1},
pages = {449-454},
doi = {10.3109/19401736.2014.900666},
pmid = {24708133},
issn = {2470-1408},
mesh = {Animals ; Chiroptera/*genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; *Genome, Mitochondrial ; Phylogeny ; Quality Control ; Sequence Analysis, DNA ; },
abstract = {Mitogenomic data are increasingly used in evolutionary biology and ecology, stressing the importance for double checking the authenticity of DNA sequences. For example, Szcześniak et al. (2013) recently published the mitochondrial genome of a bat, the Leschenault's rousette (Rousettus leschenaultii). Here we show using straightforward phylogenetic analyses of available chiropteran sequence data that the taxonomic attribution of the reported mitogenome is erroneous. The purportedly-new complete mitochondrial genome likely belongs to the Egyptian fruit bat (R. aegyptiacus) for which a reference sequence already exists. We propose that future articles reporting complete mitochondrial genome sequences should mandatorily include maximum likelihood trees inferred from (i) the standard barcoding marker for the taxon under focus, which would benefit from the massive data available in public databases, and (ii) the available mitogenomes of closely related species. We also strongly advise these trees be presented as phylograms so that all pertinent phylogenetic information is displayed in the form of a topology and its associated branch lengths. Along with compulsory information on the geographical location and origin of the specimen, these new standards should help avoiding the publication of taxonomically misidentified mitogenomes that might end up as reference sequences in public databases and re-used in subsequent meta-analyses.},
}
@article {pmid24703835,
year = {2014},
author = {Boero, F and Bernardi, G},
title = {Phenotypic vs genotypic approaches to biodiversity, from conflict to alliance.},
journal = {Marine genomics},
volume = {17},
number = {},
pages = {63-64},
doi = {10.1016/j.margen.2014.03.005},
pmid = {24703835},
issn = {1876-7478},
mesh = {*Biodiversity ; Classification/*methods ; DNA Barcoding, Taxonomic/methods/*trends ; *Genotype ; *Phenotype ; Species Specificity ; },
abstract = {Taxonomy has traditionally been based on morphological characters. Such a "phenotypic taxonomy" has steadily been replaced by the advent of molecular approaches, culminating with the rapid sequencing of genetic barcodes. The convenience of barcoding and its relative ease has relegated "phenotypic taxonomy" to a historical status. The use of genetics is undeniably powerful. It has relatively few biases and DNA can be extracted from challenging groups, where forms are fragile, such as jellyfish, or where early life stages are difficult to connect with adult forms. The problem is that resources are finite, and the rise of one powerful method came with the demise of traditional taxonomy. In addition, genetic methods may be very sophisticated, requiring acute expertise to master its techniques. These two points in combination have resulted in less funding and attraction for traditional approaches. This is doubly unfortunate because, first we are quickly losing experts in organisms that have incredibly complex lifestyles, and second because in order to fully appreciate a molecular taxonomy, one needs to understand the organisms. In a time of rapid loss of biodiversity, time is ripe for traditional and molecular taxonomists to unite in order to better appreciate and understand the complexity of life forms.},
}
@article {pmid24702997,
year = {2014},
author = {Wu, C and Li, B and Lu, R and Koelle, SJ and Yang, Y and Jares, A and Krouse, AE and Metzger, M and Liang, F and Loré, K and Wu, CO and Donahue, RE and Chen, ISY and Weissman, I and Dunbar, CE},
title = {Clonal tracking of rhesus macaque hematopoiesis highlights a distinct lineage origin for natural killer cells.},
journal = {Cell stem cell},
volume = {14},
number = {4},
pages = {486-499},
pmid = {24702997},
issn = {1875-9777},
support = {R00 HL113104/HL/NHLBI NIH HHS/United States ; U01 HL099995/HL/NHLBI NIH HHS/United States ; U01 HL099999/HL/NHLBI NIH HHS/United States ; NIH-K99-HL11304/HL/NHLBI NIH HHS/United States ; NIH-UO1-HL099999/HL/NHLBI NIH HHS/United States ; ZIA HL002339-18//Intramural NIH HHS/United States ; R01 CA086065/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Antigens, CD34/metabolism ; *Cell Differentiation ; *Cell Lineage ; *Cell Tracking ; Cells, Cultured ; Genetic Vectors ; Hematopoiesis/*physiology ; Hematopoietic Stem Cells/*cytology/metabolism ; Humans ; Killer Cells, Natural/*cytology/metabolism ; Lymphocytes/*cytology/metabolism ; Macaca mulatta ; Myeloid Cells/*cytology/metabolism ; },
abstract = {Analysis of hematopoietic stem cell function in nonhuman primates provides insights that are relevant for human biology and therapeutic strategies. In this study, we applied quantitative genetic barcoding to track the clonal output of transplanted autologous rhesus macaque hematopoietic stem and progenitor cells over a time period of up to 9.5 months. We found that unilineage short-term progenitors reconstituted myeloid and lymphoid lineages at 1 month but were supplanted over time by multilineage clones, initially myeloid restricted, then myeloid-B clones, and then stable myeloid-B-T multilineage, long-term repopulating clones. Surprisingly, reconstitution of the natural killer (NK) cell lineage, and particularly the major CD16(+)/CD56(-) peripheral blood NK compartment, showed limited clonal overlap with T, B, or myeloid lineages, and therefore appears to be ontologically distinct. Thus, in addition to providing insights into clonal behavior over time, our analysis suggests an unexpected paradigm for the relationship between NK cells and other hematopoietic lineages in primates.},
}
@article {pmid24700576,
year = {2014},
author = {Smurthwaite, CA and Hilton, BJ and O'Hanlon, R and Stolp, ZD and Hancock, BM and Abbadessa, D and Stotland, A and Sklar, LA and Wolkowicz, R},
title = {Fluorescent genetic barcoding in mammalian cells for enhanced multiplexing capabilities in flow cytometry.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {85},
number = {1},
pages = {105-113},
doi = {10.1002/cyto.a.22406},
pmid = {24700576},
issn = {1552-4930},
mesh = {Animals ; Cell Line ; Flow Cytometry/*methods ; Fluorescent Dyes/chemistry ; Green Fluorescent Proteins/chemistry/*genetics ; Humans ; Lasers ; },
abstract = {The discovery of the green fluorescent protein from Aequorea victoria has revolutionized the field of cell and molecular biology. Since its discovery a growing panel of fluorescent proteins, fluorophores and fluorescent-coupled staining methodologies, have expanded the analytical capabilities of flow cytometry. Here, we exploit the power of genetic engineering to barcode individual cells with genes encoding fluorescent proteins. For genetic engineering, we utilize retroviral technology, which allows for the expression of ectopic genetic information in a stable manner in mammalian cells. We have genetically barcoded both adherent and nonadherent cells with different fluorescent proteins. Multiplexing power was increased by combining both the number of distinct fluorescent proteins, and the fluorescence intensity in each channel. Moreover, retroviral expression has proven to be stable for at least a 6-month period, which is critical for applications such as biological screens. We have shown the applicability of fluorescent barcoded multiplexing to cell-based assays that rely themselves on genetic barcoding, or on classical staining protocols. Fluorescent genetic barcoding gives the cell an inherited characteristic that distinguishes it from its counterpart. Once cell lines are developed, no further manipulation or staining is required, decreasing time, nonspecific background associated with staining protocols, and cost. The increasing number of discovered and/or engineered fluorescent proteins with unique absorbance/emission spectra, combined with the growing number of detection devices and lasers, increases multiplexing versatility, making fluorescent genetic barcoding a powerful tool for flow cytometry-based analysis.},
}
@article {pmid24699540,
year = {2014},
author = {Wynns, JT and Lange, CB},
title = {A comparison of 16 DNA regions for use as phylogenetic markers in the pleurocarpous moss genus Plagiothecium (Hypnales).},
journal = {American journal of botany},
volume = {101},
number = {4},
pages = {652-669},
doi = {10.3732/ajb.1300269},
pmid = {24699540},
issn = {1537-2197},
mesh = {Bryopsida/*genetics ; Chloroplast Proteins/*genetics ; DNA Barcoding, Taxonomic ; DNA, Intergenic/genetics ; DNA, Plant/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; },
abstract = {PREMISE OF THE STUDY: Within the Hypnales-the most derived and species-rich order of pleurocarpous mosses - phylogenies at or below the family level often show poor resolution. In preparation for a phylogeny of the genus Plagiothecium, we wished to identify the DNA markers best suited for evolutionary reconstruction in this group of hypnalean pleurocarps.<br><br>METHODS: For each of 25 collections of Plagiothecium and associated taxa, 16 DNA regions were sequenced: nuclear ITS and 26S, and plastid rps4, rps4-trnL, trnL-F, trnK (matK)-psbA, psbA-trnH, trnM-V, trnD-T, rbcL, atpB-rbcL, psbT-H, rpoC1 exon 2 (partial), the trnG intron, the rpl16 intron and the plastid ribosomal spacer DNA (cpITS). Each region was evaluated on the basis of its ability to resolve clades, the amount of homoplasy present in the data set, and the relative ease of obtaining the data. Descriptive statistics for each region are given.<br><br>KEY RESULTS: Under-utilized plastid markers for bryophytes such as trnK-psbA, rps4-trnL, and trnD-T outperformed more traditional markers such as trnL-F and rps4. Individual plastid topologies were similar, suggesting that only a limited amount of plastid data are needed to recover a backbone phylogeny. Adding a small amount of nuclear ribosomal data to a large plastid matrix restructured the recovered topology, emphasizing the importance of sampling multiple genomes and the need for new low-copy nuclear markers in bryophyte systematics.<br><br>CONCLUSIONS: Future genus-level phylogenies of pleurocarpous mosses should target under-utilized plastid markers such as trnK-psbA and rps4-trnL in conjunction with low-copy nuclear markers.},
}
@article {pmid24690386,
year = {2014},
author = {Jiang, F and Jin, Q and Liang, L and Zhang, AB and Li, ZH},
title = {Existence of species complex largely reduced barcoding success for invasive species of Tephritidae: a case study in Bactrocera spp.},
journal = {Molecular ecology resources},
volume = {14},
number = {6},
pages = {1114-1128},
doi = {10.1111/1755-0998.12259},
pmid = {24690386},
issn = {1755-0998},
mesh = {Animals ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; Introduced Species ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Tephritidae/*classification/*genetics ; },
abstract = {Fruit flies in the family Tephritidae are the economically important pests that have many species complexes. DNA barcoding has gradually been verified as an effective tool for identifying species in a wide range of taxonomic groups, and there are several publications on rapid and accurate identification of fruit flies based on this technique; however, comprehensive analyses of large and new taxa for the effectiveness of DNA barcoding for fruit flies identification have been rare. In this study, we evaluated the COI barcode sequences for the diagnosis of fruit flies using 1426 sequences for 73 species of Bactrocera distributed worldwide. Tree-based [neighbour-joining (NJ)]; distance-based, such as Best Match (BM), Best Close Match (BCM) and Minimum Distance (MD); and character-based methods were used to evaluate the barcoding success rates obtained with maintaining the species complex in the data set, treating a species complex as a single taxon unit, and removing the species complex. Our results indicate that the average divergence between species was 14.04% (0.00-25.16%), whereas within a species this was 0.81% (0.00-9.71%); the existence of species complexes largely reduced the barcoding success for Tephritidae, for example relatively low success rates (74.4% based on BM and BCM and 84.8% based on MD) were obtained when the sequences from species complexes were included in the analysis, whereas significantly higher success rates were achieved if the species complexes were treated as a single taxon or removed from the data set - BM (98.9%), BCM (98.5%) and MD (97.5%), or BM (98.1%), BCM (97.4%) and MD (98.2%).},
}
@article {pmid24690331,
year = {2014},
author = {Geiger, MF and Herder, F and Monaghan, MT and Almada, V and Barbieri, R and Bariche, M and Berrebi, P and Bohlen, J and Casal-Lopez, M and Delmastro, GB and Denys, GP and Dettai, A and Doadrio, I and Kalogianni, E and Kärst, H and Kottelat, M and Kovačić, M and Laporte, M and Lorenzoni, M and Marčić, Z and Özuluğ, M and Perdices, A and Perea, S and Persat, H and Porcelotti, S and Puzzi, C and Robalo, J and Šanda, R and Schneider, M and Šlechtová, V and Stoumboudi, M and Walter, S and Freyhof, J},
title = {Spatial heterogeneity in the Mediterranean Biodiversity Hotspot affects barcoding accuracy of its freshwater fishes.},
journal = {Molecular ecology resources},
volume = {14},
number = {6},
pages = {1210-1221},
doi = {10.1111/1755-0998.12257},
pmid = {24690331},
issn = {1755-0998},
mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Fishes/anatomy &amp; histology/*classification/*genetics ; Fresh Water ; Mediterranean Region ; Molecular Sequence Data ; Sequence Analysis, DNA ; *Spatial Analysis ; },
abstract = {Incomplete knowledge of biodiversity remains a stumbling block for conservation planning and even occurs within globally important Biodiversity Hotspots (BH). Although technical advances have boosted the power of molecular biodiversity assessments, the link between DNA sequences and species and the analytics to discriminate entities remain crucial. Here, we present an analysis of the first DNA barcode library for the freshwater fish fauna of the Mediterranean BH (526 spp.), with virtually complete species coverage (498 spp., 98% extant species). In order to build an identification system supporting conservation, we compared species determination by taxonomists to multiple clustering analyses of DNA barcodes for 3165 specimens. The congruence of barcode clusters with morphological determination was strongly dependent on the method of cluster delineation, but was highest with the general mixed Yule-coalescent (GMYC) model-based approach (83% of all species recovered as GMYC entity). Overall, genetic morphological discontinuities suggest the existence of up to 64 previously unrecognized candidate species. We found reduced identification accuracy when using the entire DNA-barcode database, compared with analyses on databases for individual river catchments. This scale effect has important implications for barcoding assessments and suggests that fairly simple identification pipelines provide sufficient resolution in local applications. We calculated Evolutionarily Distinct and Globally Endangered scores in order to identify candidate species for conservation priority and argue that the evolutionary content of barcode data can be used to detect priority species for future IUCN assessments. We show that large-scale barcoding inventories of complex biotas are feasible and contribute directly to the evaluation of conservation priorities.},
}
@article {pmid24690282,
year = {2014},
author = {Poole, H and Terlouw, DJ and Naunje, A and Mzembe, K and Stanton, M and Betson, M and Lalloo, DG and Stothard, JR},
title = {Schistosomiasis in pre-school-age children and their mothers in Chikhwawa district, Malawi with notes on characterization of schistosomes and snails.},
journal = {Parasites &amp; vectors},
volume = {7},
number = {},
pages = {153},
pmid = {24690282},
issn = {1756-3305},
support = {100890//Wellcome Trust/United Kingdom ; 101113//Wellcome Trust/United Kingdom ; },
mesh = {Adolescent ; Adult ; Aging ; Animals ; Anthelmintics/administration &amp; dosage/therapeutic use ; Child, Preschool ; Female ; Humans ; Infant ; Malawi/epidemiology ; Male ; Middle Aged ; Praziquantel/administration &amp; dosage/therapeutic use ; Prevalence ; Schistosoma/classification/*genetics ; Schistosomiasis/drug therapy/*epidemiology ; Snails/*classification/parasitology/physiology ; },
abstract = {BACKGROUND: To complement ongoing schistosomiasis control within national control programmes (NCPs) that administer praziquantel to school-age children, assessing the risk and extent of schistosomiasis in pre-school-age children (PSAC) is important.<br><br>METHODS: In June 2012, schistosomiasis in Chikhwawa district, Malawi was assessed across 12 villages examining pre-school-age children (PSAC) and their mothers by serological and parasitological diagnosis, as supplemented with urine-antigen and questionnaire-interview methods. Urinary tract morbidity was inferred by haematuria and albuminuria assays.<br><br>RESULTS: In total, 49.5% (CI&#x2089;&#x2085; 42.6-56.4) of 208 PSAC and 94.5% (CI&#x2089;&#x2085; 90.9-98.1) of 165 mothers were seropositive for schistosomiasis, in 2 villages seroprevalence exceeded 75% in PSAC. Egg-patent urogenital and intestinal schistosomiasis was observed; 17.7% (CI&#x2089;&#x2085; 12.4-23.2) of PSAC and 45.1% (CI&#x2089;&#x2085; 37.4-52.8) of mothers having active schistosomiasis by parasitological and urine-antigen testing combined. PSAC often had extensive daily water contact and many (~25%) had haematuria and albuminuria. As eggs with an atypical morphology of Schistosoma haematobium were observed, a general selection of schistosome eggs was characterized by DNA barcoding, finding Group I S. haematobium and Group IV and V S. mansoni. Malacological surveys encountered several populations of Bulinus globosus but failed to find Biomphalaria.<br><br>CONCLUSIONS: Both PSAC and their mothers appear to be at significant risk of schistosomiasis and should be considered for treatment within the NCP of Malawi.},
}
@article {pmid24689245,
year = {2013},
author = {Sun, ZY and Pang, XH},
title = {[Discussion on the botanical origin of Isatidis radix and Isatidis folium based on DNA barcoding].},
journal = {Yao xue xue bao = Acta pharmaceutica Sinica},
volume = {48},
number = {12},
pages = {1850-1855},
pmid = {24689245},
issn = {0513-4870},
mesh = {Chloroplasts/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/*genetics ; Genes, Plant/genetics ; Isatis/*classification/genetics ; Phylogeny ; Plant Leaves/genetics ; Plants, Medicinal/*classification/genetics ; Species Specificity ; },
abstract = {This paper aimed to investigate the botanical origins of Isatidis Radix and Isatidis Folium, and clarify the confusion of its classification. The second internal transcribed spacer (ITS2) of ribosomal DNA, the chloroplast matK gene of 22 samples from some major production areas were amplified and sequenced. Sequence assembly and consensus sequence generation were performed using the CodonCode Aligner. Phylogenetic study was performed using MEGA 4.0 software in accordance with the Kimura 2-Parameter (K2P) model, and the phylogenetic tree was constructed using the neighbor-joining methods. The results showed that the length of ITS2 sequence of the botanical origins of Isatidis Radix and Isatidis Folium was 191 bp. The sequence showed that some samples had several SNP sites, and some samples had heterozygosis sites. In the NJ tree, based on ITS2 sequence, the studied samples were separated into two groups, and one of them was gathered with Isatis tinctoria L. The studied samples also were divided into two groups obviously based on the chloroplast matK gene. In conclusion, our results support that the botanical origins of Isatidis Radix and Isatidis Folium are Isatis indigotica Fortune, and Isatis indigotica and Isatis tinctoria are two distinct species. This study doesn't support the opinion about the combination of these two species in Flora of China.},
}
@article {pmid24688073,
year = {2014},
author = {Betson, M and Nejsum, P and Bendall, RP and Deb, RM and Stothard, JR},
title = {Molecular epidemiology of ascariasis: a global perspective on the transmission dynamics of Ascaris in people and pigs.},
journal = {The Journal of infectious diseases},
volume = {210},
number = {6},
pages = {932-941},
pmid = {24688073},
issn = {1537-6613},
support = {/WT_/Wellcome Trust/United Kingdom ; 085440/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Ascariasis/*epidemiology/veterinary ; Ascaris/genetics ; Cyclooxygenase 1/genetics ; DNA, Helminth/genetics ; Haplotypes/genetics ; Humans ; Microsatellite Repeats/genetics ; *Molecular Epidemiology ; Swine ; Swine Diseases/*epidemiology/parasitology ; Zoonoses/epidemiology/genetics/parasitology ; },
abstract = {BACKGROUND: The roundworm Ascaris lumbricoides infects 0.8 billion people worldwide, and Ascaris suum infects innumerable pigs across the globe. The extent of natural cross-transmission of Ascaris between pig and human hosts in different geographical settings is unknown, warranting investigation.<br><br>METHODS: Adult Ascaris organisms were obtained from humans and pigs in Europe, Africa, Asia, and Latin America. Barcodes were assigned to 536 parasites on the basis of sequence analysis of the mitochondrial cytochrome c oxidase I gene. Genotyping of 410 worms was also conducted using a panel of microsatellite markers. Phylogenetic, population genetic, and Bayesian assignment methods were used for analysis.<br><br>RESULTS: There was marked genetic segregation between worms originating from human hosts and those originating from pig hosts. However, human Ascaris infections in Europe were of pig origin, and there was evidence of cross-transmission between humans and pigs in Africa. Significant genetic differentiation exists between parasite populations from different countries, villages, and hosts.<br><br>CONCLUSIONS: In conducting an analysis of variation within Ascaris populations from pig and human hosts across the globe, we demonstrate that cross-transmission takes place in developing and developed countries, contingent upon epidemiological potential and local phylogeography. Our results provide novel insights into the transmission dynamics and speciation of Ascaris worms from humans and pigs that are of importance for control programs.},
}
@article {pmid24684058,
year = {2014},
author = {Stefan, LM and McCoy, KD and Mironov, S},
title = {A new species of the feather mite genus Rhinozachvatkinia (Acari: Avenzoariidae) from Calonectris shearwaters (Procellariiformes: Procellariidae): integrating morphological descriptions with DNA barcode data.},
journal = {Folia parasitologica},
volume = {61},
number = {1},
pages = {90-96},
pmid = {24684058},
issn = {0015-5683},
mesh = {Animals ; Bird Diseases/*parasitology ; Birds ; DNA/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Feathers ; Female ; Male ; Mite Infestations/parasitology/veterinary ; Mites/*classification/*genetics ; },
abstract = {Rhinozachvatkinia calonectris sp. n., a new species of the feather mite genus Rhinozachvatkinia Mironov, 1989 (Avenzoariidae: Bonnetellinae), is described from two species of shearwaters in the North-East of the Atlantic Ocean, Calonectris edwardsii (Oustalet) (type host) and Calonectris borealis (Cory) (Procellariiformes: Procellariidae). We completed the morphological description of this new feather mite species with sequence data on the mitochondrial cytochrome c oxidase subunit I gene fragment (COI). The full generic status of Rhinozachvatkinia, originally established as a subgenus of Zachvatkinia Dubinin, 1949, is formally fixed and its systematic relationships are briefly discussed.},
}
@article {pmid24682750,
year = {2014},
author = {da Silva, M and Ribeiro, ED and Matoso, DA and Sousa, LM and Hrbek, T and Py-Daniel, LR and Feldberg, E},
title = {Chromosomal polymorphism in two species of Hypancistrus (Siluriformes: Loricariidae): an integrative approach for understanding their biodiversity.},
journal = {Genetica},
volume = {142},
number = {2},
pages = {127-139},
pmid = {24682750},
issn = {1573-6857},
mesh = {Animals ; Catfishes/*classification/*genetics ; Chromosome Inversion ; Chromosomes/*genetics ; Cytogenetic Analysis ; DNA Barcoding, Taxonomic ; Diploidy ; Evolution, Molecular ; Female ; Genes, rRNA ; Genetic Variation ; Karyotype ; Male ; Phylogeny ; },
abstract = {Structural chromosome changes are widely described in different vertebrate groups and generate genetic, phenotypic and behavioral diversity. During the evolution of loricariids, several rearrangements (fissions, fusions, inversions) seem to have occurred. Hypancistrus, tribe Ancistrini, are highly demanded for fishkeeping around the world. In this tribe, the diploid chromosome number 2n = 52 is considered a synapomorphy, and paracentric-type inversions appear to be involved in the chromosomal evolution of the tribe. The present study investigated the karyotypes of H. zebra and H. cf. debilittera using cytogenetic, classical and molecular tools, as well as DNA barcoding. Data reveal that, although diploid number in both species corroborates the proposed synapomorphy for the tribe, there is a complex karyotype dynamics, reflected in the intense chromosomal polymorphism, resulting from rearrangements involving ribosomal regions (5S and 18S rDNA), which are suggested to be paracentric inversions. Besides, DNA barcode confirms reciprocal monophyletism between the species, validating the existence of two species, only. This scenario, coupled with genomic instability caused by exogenous sequences such as Rex-3 retrotransposons and the species' sedentary lifestyle, which helps the fast polymorphism fixation, may reflect different phenotypic color patterns in natural populations, as observed in H. cf. debilittera.},
}
@article {pmid24682414,
year = {2014},
author = {West, C and James, SA and Davey, RP and Dicks, J and Roberts, IN},
title = {Ribosomal DNA sequence heterogeneity reflects intraspecies phylogenies and predicts genome structure in two contrasting yeast species.},
journal = {Systematic biology},
volume = {63},
number = {4},
pages = {543-554},
pmid = {24682414},
issn = {1076-836X},
support = {BB/G00045X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {DNA, Fungal/genetics ; DNA, Ribosomal/*genetics ; *Genetic Heterogeneity ; Genetic Variation ; Genome, Fungal/*genetics ; *Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Saccharomyces/*classification/*genetics ; },
abstract = {The ribosomal RNA encapsulates a wealth of evolutionary information, including genetic variation that can be used to discriminate between organisms at a wide range of taxonomic levels. For example, the prokaryotic 16S rDNA sequence is very widely used both in phylogenetic studies and as a marker in metagenomic surveys and the internal transcribed spacer region, frequently used in plant phylogenetics, is now recognized as a fungal DNA barcode. However, this widespread use does not escape criticism, principally due to issues such as difficulties in classification of paralogous versus orthologous rDNA units and intragenomic variation, both of which may be significant barriers to accurate phylogenetic inference. We recently analyzed data sets from the Saccharomyces Genome Resequencing Project, characterizing rDNA sequence variation within multiple strains of the baker's yeast Saccharomyces cerevisiae and its nearest wild relative Saccharomyces paradoxus in unprecedented detail. Notably, both species possess single locus rDNA systems. Here, we use these new variation datasets to assess whether a more detailed characterization of the rDNA locus can alleviate the second of these phylogenetic issues, sequence heterogeneity, while controlling for the first. We demonstrate that a strong phylogenetic signal exists within both datasets and illustrate how they can be used, with existing methodology, to estimate intraspecies phylogenies of yeast strains consistent with those derived from whole-genome approaches. We also describe the use of partial Single Nucleotide Polymorphisms, a type of sequence variation found only in repetitive genomic regions, in identifying key evolutionary features such as genome hybridization events and show their consistency with whole-genome Structure analyses. We conclude that our approach can transform rDNA sequence heterogeneity from a problem to a useful source of evolutionary information, enabling the estimation of highly accurate phylogenies of closely related organisms, and discuss how it could be extended to future studies of multilocus rDNA systems. [concerted evolution; genome hydridisation; phylogenetic analysis; ribosomal DNA; whole genome sequencing; yeast].},
}
@article {pmid24682413,
year = {2014},
author = {Dowton, M and Meiklejohn, K and Cameron, SL and Wallman, J},
title = {A preliminary framework for DNA barcoding, incorporating the multispecies coalescent.},
journal = {Systematic biology},
volume = {63},
number = {4},
pages = {639-644},
doi = {10.1093/sysbio/syu028},
pmid = {24682413},
issn = {1076-836X},
mesh = {Classification/*methods ; DNA Barcoding, Taxonomic/*standards/trends ; Databases, Nucleic Acid ; *Phylogeny ; },
}
@article {pmid24681439,
year = {2014},
author = {Soldi, M and Bremang, M and Bonaldi, T},
title = {Biochemical systems approaches for the analysis of histone modification readout.},
journal = {Biochimica et biophysica acta},
volume = {1839},
number = {8},
pages = {657-668},
doi = {10.1016/j.bbagrm.2014.03.008},
pmid = {24681439},
issn = {0006-3002},
mesh = {Acetylation ; Animals ; Chromatin/chemistry/*metabolism ; Chromatin Immunoprecipitation/methods ; DNA/genetics/*metabolism ; DNA Methylation ; *Epigenesis, Genetic ; Histones/genetics/*metabolism ; Humans ; Mass Spectrometry/statistics &amp; numerical data ; Methylation ; *Protein Processing, Post-Translational ; Signal Transduction ; },
abstract = {Chromatin is the macromolecular nucleoprotein complex that governs the organization of genetic material in the nucleus of eukaryotic cells. In chromatin, DNA is packed with histone proteins into nucleosomes. Core histones are prototypes of hyper-modified proteins, being decorated by a large number of site-specific reversible and irreversible post-translational modifications (PTMs), which contribute to the maintenance and modulation of chromatin plasticity, gene activation, and a variety of other biological processes and disease states. The observations of the variety, frequency and co-occurrence of histone modifications in distinct patterns at specific genomic loci have led to the idea that hPTMs can create a molecular barcode, read by effector proteins that translate it into a specific transcriptional state, or process, on the underlying DNA. However, despite the fact that this histone-code hypothesis was proposed more than 10 years ago, the molecular details of its working mechanisms are only partially characterized. In particular, two questions deserve specific investigation: how the different modifications associate and synergize into patterns and how these PTM configurations are read and translated by multi-protein complexes into a specific functional outcome on the genome. Mass spectrometry (MS) has emerged as a versatile tool to investigate chromatin biology, useful for both identifying and validating hPTMs, and to dissect the molecular determinants of histone modification readout systems. We review here the MS techniques and the proteomics methods that have been developed to address these fundamental questions in epigenetics research, emphasizing approaches based on the proteomic dissection of distinct native chromatin regions, with a critical evaluation of their present challenges and future potential. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.},
}
@article {pmid24675822,
year = {2014},
author = {Idziak, D and Hazuka, I and Poliwczak, B and Wiszynska, A and Wolny, E and Hasterok, R},
title = {Insight into the karyotype evolution of brachypodium species using comparative chromosome barcoding.},
journal = {PloS one},
volume = {9},
number = {3},
pages = {e93503},
pmid = {24675822},
issn = {1932-6203},
mesh = {Biological Evolution ; *Brachypodium/classification/genetics ; Chromosomes, Artificial, Bacterial ; Chromosomes, Plant/*chemistry ; DNA Barcoding, Taxonomic ; DNA, Plant/classification/*genetics ; *Genome, Plant ; Genomic Library ; In Situ Hybridization, Fluorescence ; *Karyotype ; Karyotyping ; *Phylogeny ; Ploidies ; },
abstract = {Paleogenomic studies based on bioinformatic analyses of DNA sequences have enabled unprecedented insight into the evolution of grass genomes. They have revealed that nested chromosome fusions played an important role in the divergence of modern grasses. Nowadays, studies on karyotype evolution based on the sequence analysis can also be effectively complemented by the fine-scale cytomolecular approach. In this work, we studied the karyotype evolution of small genome grasses using BAC-FISH based comparative chromosome barcoding in four Brachypodium species: diploid B. distachyon (2n = 10) and B. sylvaticum (2n = 18), diploid (2n = 18) and allopolyploid (2n = 28) B. pinnatum as well as B. phoenicoides (2n = 28). Using BAC clones derived from the B. distachyon genomic libraries for the chromosomes Bd2 and Bd3, we identified the descending dysploidy events that were common for diploids with x = 9 and B. distachyon as well as two nested chromosome fusions that were specific only for B. distachyon. We suggest that dysploidy events that are shared by different lineages of the genus had already appeared in their common ancestor. We also show that additional structural rearrangements, such as translocations and duplications, contributed to increasing genome diversification in the species analysed. No chromosomes structured exactly like Bd2 and Bd3 were found in B. pinnatum (2n = 28) and B. phoenicoides. The structure of Bd2 and Bd3 homeologues belonging to the two genomes in the allopolyploids resembled the structure of their counterparts in the 2n = 18 diploids. These findings reinforce the hypothesis which excludes B. distachyon as a potential parent for Eurasian perennial Brachypodium allopolyploids. Our cytomolecular data elucidate some mechanisms of the descending dysploidy in monocots and enable reconstructions of the evolutionary events which shaped the extant karyotypes in both the genus Brachypodium and in grasses as a whole.},
}
@article {pmid24673652,
year = {2014},
author = {Qiu, F and McAlpine, JB and Lankin, DC and Burton, I and Karakach, T and Chen, SN and Pauli, GF},
title = {2D NMR barcoding and differential analysis of complex mixtures for chemical identification: the Actaea triterpenes.},
journal = {Analytical chemistry},
volume = {86},
number = {8},
pages = {3964-3972},
pmid = {24673652},
issn = {1520-6882},
support = {P50 AT000155/AT/NCCIH NIH HHS/United States ; RC2 AT005899/AT/NCCIH NIH HHS/United States ; },
mesh = {Actaea/*chemistry ; Complex Mixtures/*chemistry ; Electronic Data Processing/*methods ; Magnetic Resonance Spectroscopy/*methods ; Software ; Triterpenes/*chemistry ; },
abstract = {The interpretation of NMR spectroscopic information for structure elucidation involves decoding of complex resonance patterns that contain valuable molecular information (δ and J), which is not readily accessible otherwise. We introduce a new concept of 2D-NMR barcoding that uses clusters of fingerprint signals and their spatial relationships in the δ-δ coordinate space to facilitate the chemical identification of complex mixtures. Similar to widely used general barcoding technology, the structural information of individual compounds is encoded as a specifics pattern of their C,H correlation signals. Software-based recognition of these patterns enables the structural identification of the compounds and their discrimination in mixtures. Using the triterpenes from various Actaea (syn. Cimicifuga) species as a test case, heteronuclear multiple-bond correlation (HMBC) barcodes were generated on the basis of their structural subtypes from a statistical investigation of their δH and δC data in the literature. These reference barcodes allowed in silico identification of known triterpenes in enriched fractions obtained from an extract of A. racemosa (black cohosh). After dereplication, a differential analysis of heteronuclear single-quantum correlation (HSQC) spectra even allowed for the discovery of a new triterpene. The 2D barcoding concept has potential application in a natural product discovery project, allowing for the rapid dereplication of known compounds and as a tool in the search for structural novelty within compound classes with established barcodes.},
}
@article {pmid24673190,
year = {2014},
author = {Franzini, RM and Neri, D and Scheuermann, J},
title = {DNA-encoded chemical libraries: advancing beyond conventional small-molecule libraries.},
journal = {Accounts of chemical research},
volume = {47},
number = {4},
pages = {1247-1255},
doi = {10.1021/ar400284t},
pmid = {24673190},
issn = {1520-4898},
mesh = {Chemistry Techniques, Synthetic ; DNA/*chemistry ; *Drug Discovery ; Drug Evaluation, Preclinical/methods ; Small Molecule Libraries/*chemistry/economics/*pharmacology ; Structure-Activity Relationship ; Time Factors ; },
abstract = {DNA-encoded chemical libraries (DECLs) represent a promising tool in drug discovery. DECL technology allows the synthesis and screening of chemical libraries of unprecedented size at moderate costs. In analogy to phage-display technology, where large antibody libraries are displayed on the surface of filamentous phage and are genetically encoded in the phage genome, DECLs feature the display of individual small organic chemical moieties on DNA fragments serving as amplifiable identification barcodes. The DNA-tag facilitates the synthesis and allows the simultaneous screening of very large sets of compounds (up to billions of molecules), because the hit compounds can easily be identified and quantified by PCR-amplification of the DNA-barcode followed by high-throughput DNA sequencing. Several approaches have been used to generate DECLs, differing both in the methods used for library encoding and for the combinatorial assembly of chemical moieties. For example, DECLs can be used for fragment-based drug discovery, displaying a single molecule on DNA or two chemical moieties at the extremities of complementary DNA strands. DECLs can vary substantially in the chemical structures and the library size. While ultralarge libraries containing billions of compounds have been reported containing four or more sets of building blocks, also smaller libraries have been shown to be efficient for ligand discovery. In general, it has been found that the overall library size is a poor predictor for library performance and that the number and diversity of the building blocks are rather important indicators. Smaller libraries consisting of two to three sets of building blocks better fulfill the criteria of drug-likeness and often have higher quality. In this Account, we present advances in the DECL field from proof-of-principle studies to practical applications for drug discovery, both in industry and in academia. DECL technology can yield specific binders to a variety of target proteins and is likely to become a standard tool for pharmaceutical hit discovery, lead expansion, and Chemical Biology research. The introduction of new methodologies for library encoding and for compound synthesis in the presence of DNA is an exciting research field and will crucially contribute to the performance and the propagation of the technology.},
}
@article {pmid24667847,
year = {2014},
author = {Zahiri, R and Lafontaine, JD and Schmidt, BC and Dewaard, JR and Zakharov, EV and Hebert, PD},
title = {A transcontinental challenge--a test of DNA barcode performance for 1,541 species of Canadian Noctuoidea (Lepidoptera).},
journal = {PloS one},
volume = {9},
number = {3},
pages = {e92797},
pmid = {24667847},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Lepidoptera/*classification/*genetics ; Phylogeography ; },
abstract = {This study provides a first, comprehensive, diagnostic use of DNA barcodes for the Canadian fauna of noctuoids or "owlet" moths (Lepidoptera: Noctuoidea) based on vouchered records for 1,541 species (99.1% species coverage), and more than 30,000 sequences. When viewed from a Canada-wide perspective, DNA barcodes unambiguously discriminate 90% of the noctuoid species recognized through prior taxonomic study, and resolution reaches 95.6% when considered at a provincial scale. Barcode sharing is concentrated in certain lineages with 54% of the cases involving 1.8% of the genera. Deep intraspecific divergence exists in 7.7% of the species, but further studies are required to clarify whether these cases reflect an overlooked species complex or phylogeographic variation in a single species. Non-native species possess higher Nearest-Neighbour (NN) distances than native taxa, whereas generalist feeders have lower NN distances than those with more specialized feeding habits. We found high concordance between taxonomic names and sequence clusters delineated by the Barcode Index Number (BIN) system with 1,082 species (70%) assigned to a unique BIN. The cases of discordance involve both BIN mergers and BIN splits with 38 species falling into both categories, most likely reflecting bidirectional introgression. One fifth of the species are involved in a BIN merger reflecting the presence of 158 species sharing their barcode sequence with at least one other taxon, and 189 species with low, but diagnostic COI divergence. A very few cases (13) involved species whose members fell into both categories. Most of the remaining 140 species show a split into two or three BINs per species, while Virbia ferruginosa was divided into 16. The overall results confirm that DNA barcodes are effective for the identification of Canadian noctuoids. This study also affirms that BINs are a strong proxy for species, providing a pathway for a rapid, accurate estimation of animal diversity.},
}
@article {pmid24666885,
year = {2015},
author = {Papadopoulou, A and Chesters, D and Coronado, I and De la Cadena, G and Cardoso, A and Reyes, JC and Maes, JM and Rueda, RM and Gómez-Zurita, J},
title = {Automated DNA-based plant identification for large-scale biodiversity assessment.},
journal = {Molecular ecology resources},
volume = {15},
number = {1},
pages = {136-152},
doi = {10.1111/1755-0998.12256},
pmid = {24666885},
issn = {1755-0998},
mesh = {*Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/chemistry/*genetics ; Forests ; Molecular Sequence Data ; Nicaragua ; Phylogeny ; Plants/classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {Rapid degradation of tropical forests urges to improve our efficiency in large-scale biodiversity assessment. DNA barcoding can assist greatly in this task, but commonly used phenetic approaches for DNA-based identifications rely on the existence of comprehensive reference databases, which are infeasible for hyperdiverse tropical ecosystems. Alternatively, phylogenetic methods are more robust to sparse taxon sampling but time-consuming, while multiple alignment of species-diagnostic, typically length-variable, markers can be problematic across divergent taxa. We advocate the combination of phylogenetic and phenetic methods for taxonomic assignment of DNA-barcode sequences against incomplete reference databases such as GenBank, and we developed a pipeline to implement this approach on large-scale plant diversity projects. The pipeline workflow includes several steps: database construction and curation, query sequence clustering, sequence retrieval, distance calculation, multiple alignment and phylogenetic inference. We describe the strategies used to establish these steps and the optimization of parameters to fit the selected psbA-trnH marker. We tested the pipeline using infertile plant samples and herbivore diet sequences from the highly threatened Nicaraguan seasonally dry forest and exploiting a valuable purpose-built resource: a partial local reference database of plant psbA-trnH. The selected methodology proved efficient and reliable for high-throughput taxonomic assignment, and our results corroborate the advantage of applying 'strict' tree-based criteria to avoid false positives. The pipeline tools are distributed as the scripts suite 'BAGpipe' (pipeline for Biodiversity Assessment using GenBank data), which can be readily adjusted to the purposes of other projects and applied to sequence-based identification for any marker or taxon.},
}
@article {pmid24666563,
year = {2015},
author = {Li, X and Yang, Y and Henry, RJ and Rossetto, M and Wang, Y and Chen, S},
title = {Plant DNA barcoding: from gene to genome.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {90},
number = {1},
pages = {157-166},
doi = {10.1111/brv.12104},
pmid = {24666563},
issn = {1469-185X},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; Gene Expression Regulation, Plant ; *Genome, Plant ; Plants/*genetics ; },
abstract = {DNA barcoding is currently a widely used and effective tool that enables rapid and accurate identification of plant species; however, none of the available loci work across all species. Because single-locus DNA barcodes lack adequate variations in closely related taxa, recent barcoding studies have placed high emphasis on the use of whole-chloroplast genome sequences which are now more readily available as a consequence of improving sequencing technologies. While chloroplast genome sequencing can already deliver a reliable barcode for accurate plant identification it is not yet resource-effective and does not yet offer the speed of analysis provided by single-locus barcodes to unspecialized laboratory facilities. Here, we review the development of candidate barcodes and discuss the feasibility of using the chloroplast genome as a super-barcode. We advocate a new approach for DNA barcoding that, for selected groups of taxa, combines the best use of single-locus barcodes and super-barcodes for efficient plant identification. Specific barcodes might enhance our ability to distinguish closely related plants at the species and population levels.},
}
@article {pmid24660942,
year = {2014},
author = {Pihlstrøm, L and Rengmark, A and Bjørnarå, KA and Toft, M},
title = {Effective variant detection by targeted deep sequencing of DNA pools: an example from Parkinson's disease.},
journal = {Annals of human genetics},
volume = {78},
number = {3},
pages = {243-252},
doi = {10.1111/ahg.12060},
pmid = {24660942},
issn = {1469-1809},
mesh = {Computational Biology ; Data Collection/*methods ; Exons/*genetics ; Genetic Variation/*genetics ; Genetics, Medical/*methods/trends ; High-Throughput Nucleotide Sequencing/methods/trends ; Humans ; Parkinson Disease/*genetics ; },
abstract = {Next-generation sequencing technologies will dominate the next phase of discoveries in human genetics, but considerable costs may still represent a limitation for studies involving large sample sets. Targeted capture of genomic regions may be combined with deep sequencing of DNA pools to efficiently screen sample cohorts for disease-relevant mutations. We designed a 200 kb HaloPlex kit for PCR-based capture of all coding exons in 71 genes relevant to Parkinson's disease and other neurodegenerative disorders. DNA from 387 patients with Parkinson's disease was combined into 39 pools, each representing 10 individuals, before library preparation with barcoding and Illumina sequencing. In this study, we focused the analysis on six genes implicated in Mendelian Parkinson's disease, emphasizing quality metrics and evaluation of the method, including validation of variants against individual genotyping and Sanger sequencing. Our data showed 97% sensitivity to detect a single nonreference allele in pools, rising to 100% where pools achieved sequence depth above 80x for the relevant position. Pooled sequencing detected 18 rare nonsynonymous variants, of which 17 were validated by independent methods, corresponding to a specificity of 94%. We argue that this design represents an effective and reliable approach with possible applications for both complex and Mendelian genetics.},
}
@article {pmid24656809,
year = {2014},
author = {Zhang, RL and Zhang, B},
title = {Prospects of using DNA barcoding for species identification and evaluation of the accuracy of sequence databases for ticks (Acari: Ixodida).},
journal = {Ticks and tick-borne diseases},
volume = {5},
number = {3},
pages = {352-358},
doi = {10.1016/j.ttbdis.2014.01.001},
pmid = {24656809},
issn = {1877-9603},
mesh = {Animals ; DNA/chemistry/genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Mitochondrial Proteins/genetics ; Phylogeny ; Species Specificity ; Ticks/*classification/genetics ; },
abstract = {Ticks are important vectors of disease and parasites of livestock. Species identification of ticks has been traditionally based on morphological characters, which is usually limited by the condition of samples and little variation among specimens, so a rapid and reliable identification method is needed. DNA barcoding uses a standard fragment of the mitochondrial gene cytochrome oxidase c subunit I (COI) to identify species and has been successfully used in many taxa. In this study, we applied DNA barcoding to tick species. K2P distances showed that most interspecific divergences exceed 8%, while intraspecific distances were usually lower than 2%. However, intraspecific distances of 12 species were unexpectedly high. ABGD grouping results demonstrated that sequences of these species should be divided into 2 or more groups. And some exceptional clustering occurred among sequences of Hyalomma marginatum, Hy. truncatum, and Hy. dromedarii, Amblyomma testudinarium and A. pattoni, Rhipicephalus sanguineus and R. pumilio, Haemaphysalis parva and Ha. concinna, Ixodes asanumai and I. nipponensis. Additionally, 226 unnamed sequences were assigned to known species or constituted different groups, and K2P distances of all these groups were less than 2%. In conclusion, our study demonstrated that DNA barcoding is a useful tool for the identification of tick species, and further work is needed to reveal ambiguous species delimitation in some problematic genera.},
}
@article {pmid24651153,
year = {2014},
author = {Kim, J and Yun, JM and Jung, J and Song, H and Kim, JB and Ihee, H},
title = {Anti-counterfeit nanoscale fingerprints based on randomly distributed nanowires.},
journal = {Nanotechnology},
volume = {25},
number = {15},
pages = {155303},
doi = {10.1088/0957-4484/25/15/155303},
pmid = {24651153},
issn = {1361-6528},
abstract = {Counterfeiting is conducted in almost every industry, and the losses caused by it are growing as today's world trade continues to increase. In an attempt to provide an efficient method to fight such counterfeiting, we herein demonstrate anti-counterfeit nanoscale fingerprints generated by randomly distributed nanowires. Specifically, we prepare silver nanowires coated with fluorescent dyes and cast them onto the surface of transparent PET film. The resulting non-repeatable patterns characterized by the random location of the nanowires and their fluorescent colors provide unique barcodes suitable for anti-counterfeit purposes. Counterfeiting such a fingerprint pattern is impractical and expensive; the cost of replicating it would be higher than the value of the typical target item being protected. Fingerprint patterns can be visually authenticated in a simple and straightforward manner by using an optical microscope. The concept of generating unique patterns by randomness is not limited to the materials shown in this paper and should be readily applicable to other types of materials.},
}
@article {pmid24645923,
year = {2014},
author = {Zhang, Y and Zhang, L and Deng, R and Tian, J and Zong, Y and Jin, D and Liu, X},
title = {Multicolor barcoding in a single upconversion crystal.},
journal = {Journal of the American Chemical Society},
volume = {136},
number = {13},
pages = {4893-4896},
doi = {10.1021/ja5013646},
pmid = {24645923},
issn = {1520-5126},
mesh = {Color ; Fluorides/chemical synthesis/*chemistry ; Luminescence ; Luminescent Agents/chemical synthesis/*chemistry ; Nanoparticles/*chemistry/ultrastructure ; Yttrium/*chemistry ; },
abstract = {We report the synthesis of luminescent crystals based on hexagonal-phase NaYF4 upconversion microrods. The synthetic procedure involves an epitaxial end-on growth of upconversion nanocrystals comprising different lanthanide activators onto the NaYF4 microrods. This bottom-up method readily affords multicolor-banded crystals in gram quantity by varying the composition of the activators. Importantly, the end-on growth method using one-dimensional microrods as the template enables facile multicolor tuning in a single crystal, which is inaccessible in conventional upconversion nanoparticles. We demonstrate that these novel materials offer opportunities as optical barcodes for anticounterfeiting and multiplexed labeling applications.},
}
@article {pmid24641208,
year = {2014},
author = {Shokralla, S and Gibson, JF and Nikbakht, H and Janzen, DH and Hallwachs, W and Hajibabaei, M},
title = {Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens.},
journal = {Molecular ecology resources},
volume = {14},
number = {5},
pages = {892-901},
pmid = {24641208},
issn = {1755-0998},
mesh = {Animals ; Cost-Benefit Analysis ; Costa Rica ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Lepidoptera/classification/genetics ; Time Factors ; },
abstract = {DNA barcoding is an efficient method to identify specimens and to detect undescribed/cryptic species. Sanger sequencing of individual specimens is the standard approach in generating large-scale DNA barcode libraries and identifying unknowns. However, the Sanger sequencing technology is, in some respects, inferior to next-generation sequencers, which are capable of producing millions of sequence reads simultaneously. Additionally, direct Sanger sequencing of DNA barcode amplicons, as practiced in most DNA barcoding procedures, is hampered by the need for relatively high-target amplicon yield, coamplification of nuclear mitochondrial pseudogenes, confusion with sequences from intracellular endosymbiotic bacteria (e.g. Wolbachia) and instances of intraindividual variability (i.e. heteroplasmy). Any of these situations can lead to failed Sanger sequencing attempts or ambiguity of the generated DNA barcodes. Here, we demonstrate the potential application of next-generation sequencing platforms for parallel acquisition of DNA barcode sequences from hundreds of specimens simultaneously. To facilitate retrieval of sequences obtained from individual specimens, we tag individual specimens during PCR amplification using unique 10-mer oligonucleotides attached to DNA barcoding PCR primers. We employ 454 pyrosequencing to recover full-length DNA barcodes of 190 specimens using 12.5% capacity of a 454 sequencing run (i.e. two lanes of a 16 lane run). We obtained an average of 143 sequence reads for each individual specimen. The sequences produced are full-length DNA barcodes for all but one of the included specimens. In a subset of samples, we also detected Wolbachia, nontarget species, and heteroplasmic sequences. Next-generation sequencing is of great value because of its protocol simplicity, greatly reduced cost per barcode read, faster throughout and added information content.},
}
@article {pmid24639297,
year = {2014},
author = {Rodrigues, PT and Alves, JM and Santamaria, AM and Calzada, JE and Xayavong, M and Parise, M and da Silva, AJ and Ferreira, MU},
title = {Using mitochondrial genome sequences to track the origin of imported Plasmodium vivax infections diagnosed in the United States.},
journal = {The American journal of tropical medicine and hygiene},
volume = {90},
number = {6},
pages = {1102-1108},
pmid = {24639297},
issn = {1476-1645},
support = {R01 AI075416/AI/NIAID NIH HHS/United States ; R01 AI 075416/AI/NIAID NIH HHS/United States ; },
mesh = {Base Sequence ; Bayes Theorem ; Genome, Mitochondrial/*genetics ; Genome, Protozoan/genetics ; Haplotypes ; Humans ; Malaria, Vivax/*epidemiology/parasitology ; Molecular Sequence Data ; Phylogeny ; Plasmodium vivax/genetics/*isolation &amp; purification ; *Population Surveillance ; Sequence Analysis, DNA ; Species Specificity ; Travel ; United States/epidemiology ; },
abstract = {Although the geographic origin of malaria cases imported into the United States can often be inferred from travel histories, these histories may be lacking or incomplete. We hypothesized that mitochondrial haplotypes could provide region-specific molecular barcodes for tracing the origin of imported Plasmodium vivax infections. An analysis of 348 mitochondrial genomes from worldwide parasites and new sequences from 69 imported malaria cases diagnosed across the United States allowed for a geographic assignment of most infections originating from the Americas, southeast Asia, east Asia, and Melanesia. However, mitochondrial lineages from Africa, south Asia, central Asia, and the Middle East, which altogether contribute the vast majority of imported malaria cases in the United States, were closely related to each other and could not be reliably assigned to their geographic origins. More mitochondrial genomes are required to characterize molecular barcodes of P. vivax from these regions.},
}
@article {pmid24637013,
year = {2014},
author = {Coll, F and Preston, M and Guerra-Assunção, JA and Hill-Cawthorn, G and Harris, D and Perdigão, J and Viveiros, M and Portugal, I and Drobniewski, F and Gagneux, S and Glynn, JR and Pain, A and Parkhill, J and McNerney, R and Martin, N and Clark, TG},
title = {PolyTB: a genomic variation map for Mycobacterium tuberculosis.},
journal = {Tuberculosis (Edinburgh, Scotland)},
volume = {94},
number = {3},
pages = {346-354},
pmid = {24637013},
issn = {1873-281X},
support = {098610//Wellcome Trust/United Kingdom ; },
mesh = {Chromosome Mapping ; Databases, Factual ; Gene Deletion ; Genetic Variation/genetics ; Genome, Bacterial/*genetics ; Humans ; Mycobacterium tuberculosis/*genetics ; Polymorphism, Genetic/genetics ; Tuberculosis/*genetics ; },
abstract = {Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) is the second major cause of death from an infectious disease worldwide. Recent advances in DNA sequencing are leading to the ability to generate whole genome information in clinical isolates of M. tuberculosis complex (MTBC). The identification of informative genetic variants such as phylogenetic markers and those associated with drug resistance or virulence will help barcode Mtb in the context of epidemiological, diagnostic and clinical studies. Mtb genomic datasets are increasingly available as raw sequences, which are potentially difficult and computer intensive to process, and compare across studies. Here we have processed the raw sequence data (>1500 isolates, eight studies) to compile a catalogue of SNPs (n = 74,039, 63% non-synonymous, 51.1% in more than one isolate, i.e. non-private), small indels (n = 4810) and larger structural variants (n = 800). We have developed the PolyTB web-based tool (http://pathogenseq.lshtm.ac.uk/polytb) to visualise the resulting variation and important meta-data (e.g. in silico inferred strain-types, location) within geographical map and phylogenetic views. This resource will allow researchers to identify polymorphisms within candidate genes of interest, as well as examine the genomic diversity and distribution of strains. PolyTB source code is freely available to researchers wishing to develop similar tools for their pathogen of interest.},
}
@article {pmid24634170,
year = {2014},
author = {Al-Qurainy, F and Khan, S and Nadeem, M and Tarroum, M and Gaafar, AR},
title = {Selection of DNA barcoding loci for Nepeta deflersiana Schweinf. ex Hedge from chloroplast and nuclear DNA genomes.},
journal = {Genetics and molecular research : GMR},
volume = {13},
number = {1},
pages = {1144-1151},
doi = {10.4238/2014.February.21.3},
pmid = {24634170},
issn = {1676-5680},
mesh = {DNA Barcoding, Taxonomic/*methods ; Evolution, Molecular ; Genetic Markers ; Genome, Chloroplast ; Genome, Plant ; Molecular Sequence Data ; Nepeta/classification/*genetics ; Phylogeny ; Plant Leaves/genetics ; Sequence Analysis, DNA ; },
abstract = {Molecular markers, mainly DNA-based are potential tools for DNA barcoding and phylogenetic study. The plant species belonging to the Nepeta genus have important medicinal value because of the presence of nepetalactones, and they have been used to treat human diseases. We amplified nuclear and chloroplast gene loci to develop a DNA barcode and phylogenetic study of Nepeta deflersiana. Among the studied loci, psbA-trnH and rps16 showed less identity within the genus than the other loci using the Basic Local Alignment Search Tool of the National Center for Biotechnology Information GenBank database. These loci can be used for the development of a DNA barcode to identify and preserve the identity of this species. We also constructed the phylogram of N. deflersiana and other Nepeta species retrieved from the GenBank database (nonredundant DNA-internal transcribed spacer). N. deflersiana was placed in the same clade as N. insaurica with a 99% bootstrap value.},
}
@article {pmid24634112,
year = {2014},
author = {Wilson, JJ and Sing, KW and Halim, MR and Ramli, R and Hashim, R and Sofian-Azirun, M},
title = {Utility of DNA barcoding for rapid and accurate assessment of bat diversity in Malaysia in the absence of formally described species.},
journal = {Genetics and molecular research : GMR},
volume = {13},
number = {1},
pages = {920-925},
doi = {10.4238/2014.February.19.2},
pmid = {24634112},
issn = {1676-5680},
mesh = {Animals ; *Biodiversity ; Chiroptera/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Evolution, Molecular ; Malaysia ; Phylogeny ; },
abstract = {Bats are important flagship species for biodiversity research; however, diversity in Southeast Asia is considerably underestimated in the current checklists and field guides. Incorporation of DNA barcoding into surveys has revealed numerous species-level taxa overlooked by conventional methods. Inclusion of these taxa in inventories provides a more informative record of diversity, but is problematic as these species lack formal description. We investigated how frequently documented, but undescribed, bat taxa are encountered in Peninsular Malaysia. We discuss whether a barcode library provides a means of recognizing and recording these taxa across biodiversity inventories. Tissue was sampled from bats trapped at Pasir Raja, Dungun Terengganu, Peninsular Malaysia. The DNA was extracted and the COI barcode region amplified and sequenced. We identified 9 species-level taxa within our samples, based on analysis of the DNA barcodes. Six specimens matched to four previously documented taxa considered candidate species but currently lacking formal taxonomic status. This study confirms the high diversity of bats within Peninsular Malaysia (9 species in 13 samples) and demonstrates how DNA barcoding allows for inventory and documentation of known taxa lacking formal taxonomic status.},
}
@article {pmid24627185,
year = {2014},
author = {Adams, M and Raadik, TA and Burridge, CP and Georges, A},
title = {Global biodiversity assessment and hyper-cryptic species complexes: more than one species of elephant in the room?.},
journal = {Systematic biology},
volume = {63},
number = {4},
pages = {518-533},
doi = {10.1093/sysbio/syu017},
pmid = {24627185},
issn = {1076-836X},
mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/standards ; Genes, Mitochondrial/genetics ; Isoenzymes/metabolism ; Molecular Sequence Data ; Osmeriformes/anatomy &amp; histology/*classification/genetics ; Phylogeny ; Species Specificity ; },
abstract = {Several recent estimates of global biodiversity have concluded that the total number of species on Earth lies near the lower end of the wide range touted in previous decades. However, none of these recent estimates formally explore the real "elephant in the room", namely, what proportion of species are taxonomically invisible to conventional assessments, and thus, as undiagnosed cryptic species, remain uncountable until revealed by multi-gene molecular assessments. Here we explore the significance and extent of so-called "hyper-cryptic" species complexes, using the Australian freshwater fish Galaxias olidus as a proxy for any organism whose taxonomy ought to be largely finalized when compared to those in little-studied or morphologically undifferentiated groups. Our comprehensive allozyme (838 fish for 54 putative loci), mtDNA (557 fish for 605 bp of cytb), and morphological (1963-3389 vouchers for 17-58 characters) assessment of this species across its broad geographic range revealed a 1500% increase in species-level biodiversity, and suggested that additional taxa may remain undiscovered. Importantly, while all 15 candidate species were morphologically diagnosable a posteriori from one another, single-gene DNA barcoding proved largely unsuccessful as an a priori method for species identification. These results lead us to draw two strong inferences of relevance to estimates of global biodiversity. First, hyper-cryptic complexes are likely to be common in many organismal groups. Second, no assessment of species numbers can be considered "best practice" in the molecular age unless it explicitly includes estimates of the extent of cryptic and hyper-cryptic biodiversity. [Galaxiidae; global estimates; hyper-diverse; mountain galaxias; species counts; species richness.].},
}
@article {pmid24624021,
year = {2014},
author = {Fernández-Triana, JL and Whitfield, JB and Rodriguez, JJ and Smith, MA and Janzen, DH and Hallwachs, WD and Hajibabaei, M and Burns, JM and Solis, MA and Brown, J and Cardinal, S and Goulet, H and Hebert, PD},
title = {Review of Apanteles sensu stricto (Hymenoptera, Braconidae, Microgastrinae) from Area de Conservación Guanacaste, northwestern Costa Rica, with keys to all described species from Mesoamerica.},
journal = {ZooKeys},
volume = {},
number = {383},
pages = {1-565},
pmid = {24624021},
issn = {1313-2989},
abstract = {More than half a million specimens of wild-caught Lepidoptera caterpillars have been reared for their parasitoids, identified, and DNA barcoded over a period of 34 years (and ongoing) from Area de Conservación de Guanacaste (ACG), northwestern Costa Rica. This provides the world's best location-based dataset for studying the taxonomy and host relationships of caterpillar parasitoids. Among Hymenoptera, Microgastrinae (Braconidae) is the most diverse and commonly encountered parasitoid subfamily, with many hundreds of species delineated to date, almost all undescribed. Here, we reassess the limits of the genus Apanteles sensu stricto, describe 186 new species from 3,200+ parasitized caterpillars of hundreds of ACG Lepidoptera species, and provide keys to all 205 described Apanteles from Mesoamerica - including 19 previously described species in addition to the new species. The Mesoamerican Apanteles are assigned to 32 species-groups, all but two of which are newly defined. Taxonomic keys are presented in two formats: traditional dichotomous print versions and links to electronic interactive versions (software Lucid 3.5). Numerous illustrations, computer-generated descriptions, distributional information, wasp biology, and DNA barcodes (where available) are presented for every species. All morphological terms are detailed and linked to the Hymenoptera Anatomy Ontology website. DNA barcodes (a standard fragment of the cytochrome c oxidase I (COI) mitochondrial gene), information on wasp biology (host records, solitary/gregariousness of wasp larvae), ratios of morphological features, and wasp microecological distributions were used to help clarify boundaries between morphologically cryptic species within species-complexes. Because of the high accuracy of host identification for about 80% of the wasp species studied, it was possible to analyze host relationships at a regional level. The ACG species of Apanteles attack mainly species of Hesperiidae, Elachistidae and Crambidae (Lepidoptera). About 90% of the wasp species with known host records seem to be monophagous or oligophagous at some level, parasitizing just one host family and commonly, just one species of caterpillar. Only 15 species (9%) parasitize species in more than one family, and some of these cases are likely to be found to be species complexes. We have used several information sources and techniques (traditional taxonomy, molecular, software-based, biology, and geography) to accelerate the process of finding and describing these new species in a hyperdiverse group such as Apanteles. The following new taxonomic and nomenclatural acts are proposed. Four species previously considered to be Apanteles are transferred to other microgastrine genera: Dolichogenidea hedyleptae (Muesebeck, 1958), comb. n., Dolichogenidea politiventris (Muesebeck, 1958), comb. n., Rhygoplitis sanctivincenti (Ashmead, 1900), comb. n., and Illidops scutellaris (Muesebeck, 1921), comb. rev. One European species that is a secondary homonym to a Mesoamerican species is removed from Apanteles and transferred to another genus: Iconella albinervis (Tobias, 1964), stat. rev. The name Apanteles albinervican Shenefelt, 1972, is an invalid replacement name for Apanteles albinervis (Cameron, 1904), stat. rev., and thus the later name is reinstated as valid. The following 186 species, all in Apanteles and all authored by Fernández-Triana, are described as species nova: adelinamoralesae, adrianachavarriae, adrianaguilarae, adrianguadamuzi, aichagirardae, aidalopezae, albanjimenezi, alejandromasisi, alejandromorai, minorcarmonai, alvarougaldei, federicomatarritai, anabellecordobae, rostermoragai, anamarencoae, anamartinesae, anapiedrae, anariasae, andreacalvoae, angelsolisi, arielopezi, bernardoespinozai, bernyapui, bettymarchenae, bienvenidachavarriae, calixtomoragai, carloscastilloi, carlosguadamuzi, eliethcantillanoae, carlosrodriguezi, carlosviquezi, carloszunigai, carolinacanoae, christianzunigai, cinthiabarrantesae, ciriloumanai, cristianalemani, cynthiacorderoae, deifiliadavilae, dickyui, didiguadamuzi, diegoalpizari, diegotorresi, diniamartinezae, duniagarciae, duvalierbricenoi, edgarjimenezi, edithlopezae, eduardoramirezi, edwinapui, eldarayae, erickduartei, esthercentenoae, eugeniaphilipsae, eulogiosequeira, felipechavarriai, felixcarmonai, fernandochavarriai, flormoralesae, franciscopizarroi, franciscoramirezi, freddyquesadai, freddysalazari, gabrielagutierrezae, garygibsoni, gerardobandoi, gerardosandovali, gladysrojasae, glenriverai, gloriasihezarae, guadaluperodriguezae, guillermopereirai, juanmatai, harryramirezi, hectorsolisi, humbertolopezi, inesolisae, irenecarrilloae, isaacbermudezi, isidrochaconi, isidrovillegasi, ivonnetranae, jairomoyai, javiercontrerasi, javierobandoi, javiersihezari, jesusbrenesi, jesusugaldei, jimmychevezi, johanvargasi, jorgecortesi, jorgehernandezi, josecalvoi, josecortesi, josediazi, josejaramilloi, josemonteroi, joseperezi, joserasi, juanapui, juancarrilloi, juangazoi, juanhernandezi, juanlopezi, juanvictori, juliodiazi, juniorlopezi, keineraragoni, laurahuberae, laurenmoralesae, leninguadamuzi, leonelgarayi, lilliammenae, lisabearssae, luciariosae, luisbrizuelai, luiscanalesi, luiscantillanoi, luisgarciai, luisgaritai, luishernandezi, luislopezi, luisvargasi, manuelarayai, manuelpereirai, manuelriosi, manuelzumbadoi, marcobustosi, marcogonzalezi, marcovenicioi, mariachavarriae mariaguevarae, marialuisariasae, mariamendezae, marianopereirai, mariatorrentesae, sigifredomarini, marisolarroyoae, marisolnavarroae, marvinmendozai, mauriciogurdiani, milenagutierrezae, monicachavarriae, oscarchavesi, osvaldoespinozai, pablotranai, pabloumanai, pablovasquezi, paulaixcamparijae, luzmariaromeroae, petronariosae, randallgarciai, randallmartinezi, raulacevedoi, raulsolorsanoi, wadyobandoi, ricardocaleroi, robertmontanoi, robertoespinozai, robertovargasi, rodrigogamezi, rogerblancoi, rolandoramosi, rolandovegai, ronaldcastroi, ronaldgutierrezi, ronaldmurilloi, ronaldnavarroi, ronaldquirosi, ronaldzunigai, rosibelelizondoae, ruthfrancoae, sergiocascantei, sergioriosi, tiboshartae, vannesabrenesae, minornavarroi, victorbarrantesi, waldymedinai, wilbertharayai, williamcamposi, yeissonchavesi, yilbertalvaradoi, yolandarojasae, hazelcambroneroae, zeneidabolanosae.},
}
@article {pmid24624015,
year = {2014},
author = {Winterbottom, R and Hanner, RH and Burridge, M and Zur, M},
title = {A cornucopia of cryptic species - a DNA barcode analysis of the gobiid fish genus Trimma (Percomorpha, Gobiiformes).},
journal = {ZooKeys},
volume = {},
number = {381},
pages = {79-111},
pmid = {24624015},
issn = {1313-2989},
abstract = {A genetic analysis of partial mitochondrial 5' cytochrome c oxidase I gene (DNA barcode) sequences of 473 specimens assigned to 52 morphological species (including four known, but not formally named, species) of the gobiid genus Trimma revealed the presence of 94 genetic lineages. Each lineage was separated by > 2% sequence divergence. Thus there were an additional 42 haplogroups recognizable as provisional candidate species given that a value of > 2% difference is typical of different species of fishes. Such a high degree of apparently different cryptic species is, in our experience, virtually unprecedented among vertebrates. These results have precipitated further morphological research in a few cases, which has uncovered subtle differences independently corroborating the genetic results. However, such efforts are limited by the dearth of traditional systematists available to undertake the necessary time-consuming, and highly detailed, morphological research. In some cases, the genetic results we present are consistent with, and confirm, minor taxonomic distinctions based on morphology and/or colour pattern. In other instances, what had been recognized as a single species consists of several genetic lineages - up to eight in, for example, what we have identified based on morphology as Trimma okinawae. The increase from 52 to 94 potential species in our sampling raises the predicted total number of species in this genus from about 110 to nearly 200 (versus the 73 valid described species currently recognized).},
}
@article {pmid24620934,
year = {2014},
author = {Yang, JB and Li, DZ and Li, HT},
title = {Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs.},
journal = {Molecular ecology resources},
volume = {14},
number = {5},
pages = {1024-1031},
doi = {10.1111/1755-0998.12251},
pmid = {24620934},
issn = {1755-0998},
mesh = {DNA Primers/*genetics ; DNA, Chloroplast/*chemistry/*genetics ; *Genome, Chloroplast ; Magnoliopsida/*genetics ; Molecular Sequence Data ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/*methods ; },
abstract = {Chloroplast genomes supply indispensable information that helps improve the phylogenetic resolution and even as organelle-scale barcodes. Next-generation sequencing technologies have helped promote sequencing of complete chloroplast genomes, but compared with the number of angiosperms, relatively few chloroplast genomes have been sequenced. There are two major reasons for the paucity of completely sequenced chloroplast genomes: (i) massive amounts of fresh leaves are needed for chloroplast sequencing and (ii) there are considerable gaps in the sequenced chloroplast genomes of many plants because of the difficulty of isolating high-quality chloroplast DNA, preventing complete chloroplast genomes from being assembled. To overcome these obstacles, all known angiosperm chloroplast genomes available to date were analysed, and then we designed nine universal primer pairs corresponding to the highly conserved regions. Using these primers, angiosperm whole chloroplast genomes can be amplified using long-range PCR and sequenced using next-generation sequencing methods. The primers showed high universality, which was tested using 24 species representing major clades of angiosperms. To validate the functionality of the primers, eight species representing major groups of angiosperms, that is, early-diverging angiosperms, magnoliids, monocots, Saxifragales, fabids, malvids and asterids, were sequenced and assembled their complete chloroplast genomes. In our trials, only 100 mg of fresh leaves was used. The results show that the universal primer set provided an easy, effective and feasible approach for sequencing whole chloroplast genomes in angiosperms. The designed universal primer pairs provide a possibility to accelerate genome-scale data acquisition and will therefore magnify the phylogenetic resolution and species identification in angiosperms.},
}
@article {pmid24619863,
year = {2015},
author = {Mathenge, CW and Riegler, M and Beattie, GA and Spooner-Hart, RN and Holford, P},
title = {Genetic variation amongst biotypes of Dactylopius tomentosus.},
journal = {Insect science},
volume = {22},
number = {3},
pages = {360-374},
doi = {10.1111/1744-7917.12120},
pmid = {24619863},
issn = {1744-7917},
mesh = {Animals ; Biological Control Agents ; Cactaceae/classification/*parasitology ; DNA, Bacterial/genetics ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial ; Genetic Variation ; Hemiptera/*genetics/*microbiology ; Host-Parasite Interactions ; Phylogeny ; Wolbachia/genetics ; },
abstract = {The tomentose cochineal scale insect, Dactylopius tomentosus (Lamarck) (Hemiptera: Dactylopiidae), is an important biological control agent against invasive species of Cylindropuntia (Caryophyllales: Cactaceae). Recent studies have demonstrated that this scale is composed of host-affiliated biotypes with differential host specificity and fitness on particular host species. We investigated genetic variation and phylogenetic relationships among D. tomentosus biotypes and provenances to examine the possibility that genetic diversity may be related to their host-use pattern, and whether their phylogenetic relationships would give insights into taxonomic relatedness of their host plants. Nucleotide sequence comparison was accomplished using sequences of the mitochondrial cytochrome c oxidase I (COI) gene. Sequences of individuals from the same host plant within a region were identical and characterized by a unique haplotype. Individuals belonging to the same biotype but from different regions had similar haplotypes. However, haplotypes were not shared between different biotypes. Phylogenetic analysis grouped the monophyletic D. tomentosus into 3 well-resolved clades of biotypes. The phylogenetic relationships and clustering of biotypes corresponded with known taxonomic relatedness of their hosts. Two biotypes, Fulgida and Mamillata, tested positive for Wolbachia (α-Proteobacteria), a common endosymbiont of insects. The Wolbachia sequences were serendipitously detected by using insect-specific COI DNA barcoding primers and are most similar to Wolbachia Supergroup F strains. This study is the first molecular characterization of cochineal biotypes that, together with Wolbachia sequences, contribute to the better identification of the biotypes of cochineal insects and to the biological control of cacti using host-specific biotypes of the scale.},
}
@article {pmid24618145,
year = {2014},
author = {Knebelsberger, T and Landi, M and Neumann, H and Kloppmann, M and Sell, AF and Campbell, PD and Laakmann, S and Raupach, MJ and Carvalho, GR and Costa, FO},
title = {A reliable DNA barcode reference library for the identification of the North European shelf fish fauna.},
journal = {Molecular ecology resources},
volume = {14},
number = {5},
pages = {1060-1071},
doi = {10.1111/1755-0998.12238},
pmid = {24618145},
issn = {1755-0998},
mesh = {Animals ; *Biodiversity ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; *Databases as Topic ; *Databases, Nucleic Acid ; Electron Transport Complex IV/genetics ; Fishes/*classification/*genetics ; Molecular Sequence Data ; North Sea ; Sequence Analysis, DNA/*methods ; },
abstract = {Valid fish species identification is an essential step both for fundamental science and fisheries management. The traditional identification is mainly based on external morphological diagnostic characters, leading to inconsistent results in many cases. Here, we provide a sequence reference library based on mitochondrial cytochrome c oxidase subunit I (COI) for a valid identification of 93 North Atlantic fish species originating from the North Sea and adjacent waters, including many commercially exploited species. Neighbour-joining analysis based on K2P genetic distances formed nonoverlapping clusters for all species with a ≥99% bootstrap support each. Identification was successful for 100% of the species as the minimum genetic distance to the nearest neighbour always exceeded the maximum intraspecific distance. A barcoding gap was apparent for the whole data set. Within-species distances ranged from 0 to 2.35%, while interspecific distances varied between 3.15 and 28.09%. Distances between congeners were on average 51-fold higher than those within species. The validation of the sequence library by applying BOLDs barcode index number (BIN) analysis tool and a ranking system demonstrated high taxonomic reliability of the DNA barcodes for 85% of the investigated fish species. Thus, the sequence library presented here can be confidently used as a benchmark for identification of at least two-thirds of the typical fish species recorded for the North Sea.},
}
@article {pmid24618119,
year = {2014},
author = {Mharakurwa, S and Daniels, R and Scott, A and Wirth, DF and Thuma, P and Volkman, SK},
title = {Pre-amplification methods for tracking low-grade Plasmodium falciparum populations during scaled-up interventions in Southern Zambia.},
journal = {Malaria journal},
volume = {13},
number = {},
pages = {89},
pmid = {24618119},
issn = {1475-2875},
support = {U19 AI089680/AI/NIAID NIH HHS/United States ; },
mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; Cross-Sectional Studies ; DNA, Protozoan/genetics/*isolation &amp; purification ; Desiccation ; Female ; Genotype ; Humans ; Infant ; Infant, Newborn ; Malaria, Falciparum/*diagnosis/*epidemiology/parasitology ; Male ; Middle Aged ; Nucleic Acid Amplification Techniques/*methods ; Parasitology/*methods ; Plasmodium falciparum/genetics/*isolation &amp; purification ; Polymorphism, Single Nucleotide ; Prospective Studies ; Specimen Handling/*methods ; Young Adult ; Zambia/epidemiology ; },
abstract = {BACKGROUND: Malaria is receding in many endemic countries with intervention scale -up against the disease. However, this resilient scourge may persist in low-grade submicroscopic infections among semi-immune members of the population, and be poised for possible resurgence, creating challenges for detection and assessment of intervention impact. Parasite genotyping methods, such as the molecular barcode, can identify specific malaria parasite types being transmitted and allow tracking and evaluation of parasite population structure changes as interventions are applied. This current study demonstrates application of pre-amplification methods for successful detection and genotyping of residual Plasmodium falciparum infections during a dramatic malarial decline.<br><br>METHODS: The study was a prospective cross-sectional design and based on a 2,000 sq km vicinity of Macha Mission Hospital in southern Zambia. Willing and predominantly asymptomatic residents of all ages were screened for malaria by microscopy during the 2005 and 2008 transmission seasons, with simultaneous collection of dried blood spots (DBS) on filter paper, and extraction of Plasmodium falciparum DNA was performed. Plasmodium falciparum infections were genotyped using a 24 SNP-based molecular barcode assay using real-time PCR. Submicroscopic parasitaemia samples were subjected to pre-amplification using TaqMan PreAmp Master Mix following the manufacturer's instructions before SNP barcode analysis.<br><br>RESULTS: There was a dramatic decline of malaria between 2005 and 2008, and the geometric mean parasite density (95% CI) fell from 704/&#x3bc;L (390-1,271) in 2005 to 39/&#x3bc;L (23-68) in 2008, culminating in a large proportion of submicroscopic infections of which 90% failed to yield ample DNA for standard molecular characterization among 2008 samples. Pre-amplification enabled successful detection and genotyping of 74% of these low-grade reservoir infections, overall, compared to 54% that were detectable before pre-amplification (p <0.0005, n = 84). Furthermore, nine samples negative for parasites by microscopy and standard quantitative PCR amplification were positive after pre-amplification.<br><br>CONCLUSIONS: Pre-amplification allows analysis of an otherwise undetectable parasite population and may be instrumental for parasites identification, tracking and assessing the impact of interventions on parasite populations during malaria control and elimination programmes when parasitaemia is expected to decline to submicroscopic levels.},
}
@article {pmid24616562,
year = {2014},
author = {Pratheepa, M and Jalali, SK and Arokiaraj, RS and Venkatesan, T and Nagesh, M and Panda, M and Pattar, S},
title = {Insect barcode information system.},
journal = {Bioinformation},
volume = {10},
number = {2},
pages = {98-100},
pmid = {24616562},
issn = {0973-2063},
abstract = {UNLABELLED: Insect Barcode Information System called as Insect Barcode Informática (IBIn) is an online database resource developed by the National Bureau of Agriculturally Important Insects, Bangalore. This database provides acquisition, storage, analysis and publication of DNA barcode records of agriculturally important insects, for researchers specifically in India and other countries. It bridges a gap in bioinformatics by integrating molecular, morphological and distribution details of agriculturally important insects. IBIn was developed using PHP/My SQL by using relational database management concept. This database is based on the client- server architecture, where many clients can access data simultaneously. IBIn is freely available on-line and is user-friendly. IBIn allows the registered users to input new information, search and view information related to DNA barcode of agriculturally important insects.This paper provides a current status of insect barcode in India and brief introduction about the database IBIn.<br><br>AVAILABILITY: http://www.nabg-nbaii.res.in/barcode.},
}
@article {pmid24616294,
year = {2014},
author = {Zhang, Q and Lee, YH and Phang, IY and Lee, CK and Ling, XY},
title = {Hierarchical 3D SERS substrates fabricated by integrating photolithographic microstructures and self-assembly of silver nanoparticles.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {10},
number = {13},
pages = {2703-2711},
doi = {10.1002/smll.201303773},
pmid = {24616294},
issn = {1613-6829},
abstract = {Most of the surface-enhanced Raman scattering (SERS) substrates are 2D planar systems, which limits the SERS active area to a single Cartesian plane. Here, we fabricate 3D SERS substrates with the aim to break the traditional 2D SERS active area limitation, and to extend the SERS hotspots into the third dimension along the z-axis. Our 3D SERS substrates are tailored with increased SERS hotspots in the z-direction from tens of nanometers to tens of micrometers, increasing the hotspots in the z-direction by at least an order of magnitude larger than the confocal volume (~1 μm) of most Raman spectrometers. Various hierarchical 3D SERS-active microstructures are fabricated by combining 3D laser photolithography with Langmuir-Blodgett nanoparticle assembly. 3D laser photolithography creates microstructured platforms required to extend the SERS-active area into 3D, and the self-assembly of Ag nanoparticles ensures homogeneous coating of SERS-active Ag nanoparticles over the entire microstructured platforms. Large-area 3D Raman imaging demonstrates that homogeneous signals can be collected throughout the entire 3D SERS substrates. We vary the morphology, height, and inclination angles of the 3D microstructures, where the inclination angle is found to exhibit strong influence on the SERS signals. We also demonstrate a potential application of this hierarchical 3D SERS substrate in information tagging, storage and encryption as SERS micro-barcodes, where multiple micro-barcodes can be created within a single set of microstructures.},
}
@article {pmid24615960,
year = {2014},
author = {Chung, S and Cho, M and Hwan Jung, J and Seok Seo, T},
title = {Highly sensitive detection of cancer cells based on the DNA barcode assay and microcapillary electrophoretic analysis.},
journal = {Electrophoresis},
volume = {35},
number = {10},
pages = {1504-1508},
doi = {10.1002/elps.201400001},
pmid = {24615960},
issn = {1522-2683},
mesh = {Cell Line, Tumor ; *DNA Barcoding, Taxonomic ; Electrophoresis, Capillary/*methods ; Humans ; Neoplasms/*diagnosis/genetics/pathology ; },
abstract = {Considering rarity of circulating tumor cells (CTCs) in human blood, the development of highly sensitive detection techniques for cancer cells is crucial for prediction, diagnosis, and prognosis of cancers. In this study, we propose an advanced cellular detection method by combining a biobarcode assay and microcapillary electrophoresis (μCE) technology. While the DNA biobarcode assay can provide ultrasensitive and multiplex detection platforms, the μCE chip can analyze barcode DNAs with high speed and accuracy according to the DNA size. We designed the barcode DNA size as 20 bp for indicating the expression of epithelial cell adhesion molecules (EpCAM) biomarkers and 30 bp for assigning CDX2 expression which is specific for colorectal cancer cells with addition to two bracket ladders (15 and 45 bp). Using MCF-7 (breast cancer) and SW620 (colorectal cancer) as models, we conducted a biobarcode assay and analyzed the resultant biobarcode DNA on the μCE chip. We could detect the 20 bp CE peak in the electropherogram even with ten MCF-7 and SW620 cells in a volume of 200 μL, thereby demonstrating the highly sensitive detection of cancer cells. We furthermore identified the type of colorectal cancer by observing two positive peaks (20 bp for EpCAM and 30 bp for CDX2) in the μCE analysis.},
}
@article {pmid24615105,
year = {2014},
author = {Enan, MR and Ahamed, A},
title = {DNA barcoding based on plastid matK and RNA polymerase for assessing the genetic identity of date (Phoenix dactylifera L.) cultivars.},
journal = {Genetics and molecular research : GMR},
volume = {13},
number = {2},
pages = {3527-3536},
doi = {10.4238/2014.February.14.2},
pmid = {24615105},
issn = {1676-5680},
mesh = {Chloroplasts/genetics ; DNA/genetics ; *DNA Barcoding, Taxonomic ; DNA-Directed RNA Polymerases/*genetics ; *Genetic Markers ; Genetic Variation ; Phoeniceae/*genetics ; Plant Proteins/genetics ; Plants/genetics ; Plastids ; Species Specificity ; },
abstract = {The cultivated date palm is the most agriculturally important species of the Arecaceae family. The standard chloroplast DNA barcode for land plants recommended by the Consortium for the Barcode of Life plant working group needs to be evaluated for a wide range of plant species. Therefore, we assessed the potential of the matK and rpoC1 markers for the authentication of date cultivars. There is not one universal method to authenticate date cultivars. In this study, 11 different date cultivars were sequenced and analyzed for matK and rpoC1 genes by using bioinformatic tools to establish a cultivar-specific molecular monogram. The chloroplast matK marker was more informative than the rpoC1 chloroplast DNA markers. Phylogenetic trees were constructed on the basis of the matK and rpoC1 sequences, and the results suggested that matK alone or in combination with rpoC1 can be used for determining the levels of genetic variation and for barcoding.},
}
@article {pmid24612741,
year = {2014},
author = {Vinitha, MR and Kumar, US and Aishwarya, K and Sabu, M and Thomas, G},
title = {Prospects for discriminating Zingiberaceae species in India using DNA barcodes.},
journal = {Journal of integrative plant biology},
volume = {56},
number = {8},
pages = {760-773},
doi = {10.1111/jipb.12189},
pmid = {24612741},
issn = {1744-7909},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer ; Genome, Plastid ; India ; Sequence Analysis, DNA ; Zingiberaceae/*classification/genetics ; },
abstract = {We evaluated nine plastid (matK, rbcL, rpoC1, rpoB, rpl36-rps8, ndhJ, trnL-F, trnH-psbA, accD) and two nuclear (ITS and ITS2) barcode loci in family Zingiberaceae by analyzing 60 accessions of 20 species belonging to seven genera from India. Bidirectional sequences were recovered for every plastid locus by direct sequencing of polymerase chain reaction (PCR) amplicons in all the accessions tested. However, only 35 (58%) and 40 accessions (66%) yielded ITS and ITS2 sequences, respectively, by direct sequencing. In different bioinformatics analyses, matK and rbcL consistently resolved 15 species (75%) into monophyletic groups and five species into two paraphyletic groups. The 173 ITS sequences, including 138 cloned sequences from 23 accessions, discriminated only 12 species (60%), and the remaining species were entered into three paraphyletic groups. Phylogenetic and genealogic analyses of plastid and ITS sequences imply the possible occurrence of natural hybridizations in the evolutionary past in giving rise to species paraphyly and intragenomic ITS heterogeneity in the species tested. The results support using matK and rbcL loci for barcoding Zingiberaceae members and highlight the poor utility of ITS and the highly regarded ITS2 in barcoding this family, and also caution against proposing ITS loci for barcoding taxa based on limited sampling.},
}
@article {pmid24611571,
year = {2014},
author = {Zhang, G and Chen, J and Yang, Y and Liu, N and Jiang, W and Gu, S and Wang, X and Wang, Z},
title = {Utility of DNA barcoding in distinguishing species of the family Taeniidae.},
journal = {The Journal of parasitology},
volume = {100},
number = {4},
pages = {542-546},
doi = {10.1645/13-224.1},
pmid = {24611571},
issn = {1937-2345},
mesh = {Animals ; Cestoda/*classification/genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/methods/*standards ; Electron Transport Complex IV/genetics ; Haplotypes ; },
abstract = {The family Taeniidae comprises many parasitic species, which cause serious zoonoses. However, effective identification of Taeniidae species is a long-standing problem, especially in samples from wild hosts with mixed infections of different Taeniidae species. DNA barcoding analysis of small fragments of the cytochrome c oxidase subunit I (COI) gene has been confirmed as an effective and useful method for identifying Taenia species. We therefore performed DNA barcoding analysis using a 351-bp region of the COI gene to identify 27 taeniid species including 9 in the genus Echinococcus, 2 in Hydatigera, 15 in Taenia, and 1 in Versteria. A total of 484 COI sequences were used to calculate genetic divergence expressed by the Kimura 2-parameter (K2P) distance. The mean intra-specific K2P distance in the family Taeniidae was 0.71 ± 0.17% (±SE), while inter-specific divergences were considerably higher. We found that, generally, a 2.0% optimal barcoding threshold could be set to distinguish taeniid species. Taenia polyacantha and Hydatigera taeniaeformis were the only 2 false-positive species identification cases in this study for their intra-specific divergences above the 2.0% optimal threshold. Their high intra-specific divergences coincided with fact that cryptic divergences exist in these 2 species, to which new taxa were recommended. On the other hand, sister species T. asiatica and T. saginata showed a 2.48 ± 0.83% inter-specific divergence, which was the smallest among all the taeniid species. Although fitting the 2.0% optimal species barcoding threshold, the close genetic relationship between T. asiatica and T. saginata implies that longer mitochondrial DNA sequences like the complete COI sequence are needed to strictly distinguish them. Therefore, we concluded that the barcoding technique based on a 351-bp region of the COI gene is able to distinguish taeniid species except for cryptic T. polyacantha and H. taeniaeformis and should be carefully used in distinguishing the closely related species T. asiatica and T. saginata .},
}
@article {pmid24609003,
year = {2014},
author = {Resch, MC and Shrubovych, J and Bartel, D and Szucsich, NU and Timelthaler, G and Bu, Y and Walzl, M and Pass, G},
title = {Where taxonomy based on subtle morphological differences is perfectly mirrored by huge genetic distances: DNA barcoding in Protura (Hexapoda).},
journal = {PloS one},
volume = {9},
number = {3},
pages = {e90653},
pmid = {24609003},
issn = {1932-6203},
support = {P 23251/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Animals ; Arthropods/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal/genetics ; Phylogeny ; },
abstract = {BACKGROUND: Protura is a group of tiny, primarily wingless hexapods living in soil habitats. Presently about 800 valid species are known. Diagnostic characters are very inconspicuous and difficult to recognize. Therefore taxonomic work constitutes an extraordinary challenge which requires special skills and experience. Aim of the present pilot project was to examine if DNA barcoding can be a useful additional approach for delimiting and determining proturan species.<br><br>The study was performed on 103 proturan specimens, collected primarily in Austria, with additional samples from China and Japan. The animals were examined with two markers, the DNA barcoding region of the mitochondrial COI gene and a fragment of the nuclear 28S rDNA (Divergent Domain 2 and 3). Due to the minuteness of Protura a modified non-destructive DNA-extraction method was used which enables subsequent species determination. Both markers separated the examined proturans into highly congruent well supported clusters. Species determination was performed without knowledge of the results of the molecular analyses. The investigated specimens comprise a total of 16 species belonging to 8 genera. Remarkably, morphological determination in all species exactly mirrors molecular clusters. The investigation revealed unusually huge genetic COI distances among the investigated proturans, both maximal intraspecific distances (0-21.3%), as well as maximal congeneric interspecifical distances (up to 44.7%).<br><br>CONCLUSIONS: The study clearly demonstrates that the tricky morphological taxonomy in Protura has a solid biological background and that accurate species delimitation is possible using both markers, COI and 28S rDNA. The fact that both molecular and morphological analyses can be performed on the same individual will be of great importance for the description of new species and offers a valuable new tool for biological and ecological studies, in which proturans have generally remained undetermined at species level.},
}
@article {pmid24603705,
year = {2014},
author = {Lawton, RJ and de Nys, R and Skinner, S and Paul, NA},
title = {Isolation and identification of oedogonium species and strains for biomass applications.},
journal = {PloS one},
volume = {9},
number = {3},
pages = {e90223},
pmid = {24603705},
issn = {1932-6203},
mesh = {Australia ; *Biomass ; Chlorophyta/classification/genetics/*growth &amp; development ; DNA, Algal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Fresh Water/*microbiology ; Geography ; Microalgae ; Molecular Sequence Data ; Phylogeny ; Phytoplankton/classification/genetics/*isolation &amp; purification ; RNA, Ribosomal, 28S/genetics ; RNA, Ribosomal, 5.8S/genetics ; Seasons ; Sequence Analysis, DNA ; Species Specificity ; Temperature ; },
abstract = {Freshwater macroalgae from the genus Oedogonium have recently been targeted for biomass applications; however, strains of Oedogonium for domestication have not yet been identified. Therefore, the objective of this study was to compare the performance of isolates of Oedogonium collected from multiple geographic locations under varying environmental conditions. We collected and identified wild-type isolates of Oedogonium from three geographic locations in Eastern Australia, then measured the growth of these isolates under a range of temperature treatments corresponding to ambient conditions in each geographic location. Our sampling identified 11 isolates of Oedogonium that could be successfully maintained under culture conditions. It was not possible to identify most isolates to species level using DNA barcoding techniques or taxonomic keys. However, there were considerable genetic and morphological differences between isolates, strongly supporting each being an identifiable species. Specific growth rates of species were high (>26% day-1) under 7 of the 9 temperature treatments (average tested temperature range: 20.9-27.7°C). However, the variable growth rates of species under lower temperature treatments demonstrated that some were better able to tolerate lower temperatures. There was evidence for local adaptation under lower temperature treatments (winter conditions), but not under higher temperature treatments (summer conditions). The high growth rates we recorded across multiple temperature treatments for the majority of species confirm the suitability of this diverse genus for biomass applications and the domestication of Oedogonium.},
}
@article {pmid24603433,
year = {2014},
author = {Aylagas, E and Borja, A and Rodríguez-Ezpeleta, N},
title = {Environmental status assessment using DNA metabarcoding: towards a genetics based Marine Biotic Index (gAMBI).},
journal = {PloS one},
volume = {9},
number = {3},
pages = {e90529},
pmid = {24603433},
issn = {1932-6203},
mesh = {Animals ; Aquatic Organisms/*classification/*genetics ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Databases, Genetic ; },
abstract = {Marine ecosystem protection and conservation initiatives rely on the assessment of ecological integrity and health status of marine environments. The AZTI's Marine Biotic Index (AMBI), which consists on using macroinvertebrate diversity as indicator of ecosystem health, is used worldwide for this purpose. Yet, this index requires taxonomic assignment of specimens, which typically involves a time and resource consuming visual identification of each sample. DNA barcoding or metabarcoding are potential harmonized, faster and cheaper alternatives for species identification, although the suitability of these methods for easing the implementation of the AMBI is yet to be evaluated. Here, we analyze the requirements for the implementation of a genetics based AMBI (gAMBI), and show, using available sequence data, that information about presence/absence of the most frequently occurring species provides accurate AMBI values. Our results set the basics for the implementation of the gAMBI, which has direct implications for a faster and cheaper marine monitoring and health status assessment.},
}
@article {pmid24594991,
year = {2014},
author = {Huynen, L and Lambert, DM},
title = {Complex species status for extinct moa (Aves: Dinornithiformes) from the genus Euryapteryx.},
journal = {PloS one},
volume = {9},
number = {3},
pages = {e90212},
pmid = {24594991},
issn = {1932-6203},
mesh = {Animals ; Birds/*genetics ; *Extinction, Biological ; Humans ; Molecular Sequence Data ; },
abstract = {The exact species status of New Zealand's extinct moa remains unknown. In particular, moa belonging to the genus Euryapteryx have been difficult to classify. We use the DNA barcoding sequence on a range of Euryapteryx samples in an attempt to resolve the species status for this genus. We obtained mitochondrial control region and the barcoding region from Cytochrome Oxidase Subunit I (COI) from a number of new moa samples and use available sequences from previous moa phylogenies and eggshell data to try and clarify the species status of Euryapteryx. Using the COI barcoding region we show that species status in Euryapteryx is complex with no clear separation between various individuals. Eggshell, soil, and bone data suggests that a Euryapteryx subspecies likely exists on New Zealand's North Island and can be characterized by a single mitochondrial control region SNP. COI divergences between Euryapteryx individuals from the south of New Zealand's South Island and those from the Far North of the North Island exceed 1.6% and are likely to represent separate species. Individuals from other areas of New Zealand were unable to be clearly separated based on COI differences possibly as a result of repeated hybridisation events. Despite the accuracy of the COI barcoding region to determine species status in birds, including that for the other moa genera, for moa from the genus Euryapteryx, COI barcoding fails to provide a clear result, possibly as a consequence of repeated hybridisation events between these moa. A single control region SNP was identified however that segregates with the two general morphological variants determined for Euryapteryx; a smaller subspecies restricted to the North Island of New Zealand, and a larger subspecies, found on both New Zealand's North and South Island.},
}
@article {pmid24594033,
year = {2014},
author = {Cheng, Y and Zhu, C and Xie, Z and Gu, H and Tian, T and Zhao, Y and Gu, Z},
title = {Anisotropic colloidal crystal particles from microfluidics.},
journal = {Journal of colloid and interface science},
volume = {421},
number = {},
pages = {64-70},
doi = {10.1016/j.jcis.2014.01.041},
pmid = {24594033},
issn = {1095-7103},
mesh = {Base Sequence ; Colloids/*chemistry ; Crystallization ; DNA/chemistry ; *Microfluidics ; },
abstract = {Anisotropic colloidal crystal particles (CCPs) have showed their great potential in biotechnology and structural materials due to their anisotropic shapes and tunable optical property. However, their controllable generation is still a challenge. Here, a novel microfluidic approach is developed to generate anisotropic CCPs. The microfluidic device is composed of an injection capillary and a collection capillary with available size and shape. Based on the device, the anisotropic particles with non-close-packed colloidal crystal structures are achieved by photo-polymerizing droplet templates in a confined collection capillary with different shapes and sizes. Moreover, anisotropic close-packed CCPs can be made from non-close-packed CCPs through a thermal process. It is demonstrated that the anisotropic CCPs in different sizes, structural colors and shapes (rods, cuboids and disks) can be generated. These distinguishable features of resultant particles make them ideal barcodes for high-throughput bioassays. In order to prove it, DNA multiplex detection is carried out. The experimental results indicate that achieved particles have a great encoding capacity and are highly practical for multiplex coding bioassays. Therefore, we believe that the anisotropic CCPs would be highly promising barcodes in biomedical applications, including high-throughput bioassays and cell culture research where multiplexing is needed.},
}
@article {pmid24589749,
year = {2014},
author = {Lu, DR and Tan, YC and Kongpachith, S and Cai, X and Stein, EA and Lindstrom, TM and Sokolove, J and Robinson, WH},
title = {Identifying functional anti-Staphylococcus aureus antibodies by sequencing antibody repertoires of patient plasmablasts.},
journal = {Clinical immunology (Orlando, Fla.)},
volume = {152},
number = {1-2},
pages = {77-89},
pmid = {24589749},
issn = {1521-7035},
support = {R01 AR063676/AR/NIAMS NIH HHS/United States ; RC1 AR058713/AR/NIAMS NIH HHS/United States ; T32 AI007290/AI/NIAID NIH HHS/United States ; N01-HV-00242/HV/NHLBI NIH HHS/United States ; },
mesh = {3T3 Cells ; Adhesins, Bacterial/immunology ; Animals ; Antibodies, Bacterial/*immunology ; Antibody Formation/immunology ; Base Sequence ; DNA Barcoding, Taxonomic ; Humans ; Immunoglobulin Heavy Chains/*genetics/immunology ; Immunoglobulin Light Chains/*genetics/immunology ; Mice ; Neutrophils/immunology ; Phagocytosis/immunology ; Recombinant Proteins/immunology ; Sequence Analysis, DNA/methods ; Staphylococcal Infections/*immunology ; Staphylococcus aureus/*immunology ; },
abstract = {Infection by Staphylococcus aureus is on the rise, and there is a need for a better understanding of host immune responses that combat S. aureus. Here we use DNA barcoding to enable deep sequencing of the paired heavy- and light-chain immunoglobulin genes expressed by individual plasmablasts derived from S. aureus-infected humans. Bioinformatic analysis of the antibody repertoires revealed clonal families of heavy-chain sequences and enabled rational selection of antibodies for recombinant expression. Of the ten recombinant antibodies produced, seven bound to S. aureus, of which four promoted opsonophagocytosis of S. aureus. Five of the antibodies bound to known S. aureus cell-surface antigens, including fibronectin-binding protein A. Fibronectin-binding protein A-specific antibodies were isolated from two independent S. aureus-infected patients and mediated neutrophil killing of S. aureus in in vitro assays. Thus, our DNA barcoding approach enabled efficient identification of antibodies involved in protective host antibody responses against S. aureus.},
}
@article {pmid24589289,
year = {2014},
author = {Lv, J and Wu, S and Zhang, Y and Chen, Y and Feng, C and Yuan, X and Jia, G and Deng, J and Wang, C and Wang, Q and Mei, L and Lin, X},
title = {Assessment of four DNA fragments (COI, 16S rDNA, ITS2, 12S rDNA) for species identification of the Ixodida (Acari: Ixodida).},
journal = {Parasites &amp; vectors},
volume = {7},
number = {},
pages = {93},
pmid = {24589289},
issn = {1756-3305},
mesh = {Animals ; Base Sequence ; *DNA Barcoding, Taxonomic ; DNA Primers/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Electron Transport Complex IV/*genetics ; Genetic Markers/genetics ; Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; Ticks/*classification/genetics ; },
abstract = {BACKGROUND: The 5' region of cytochrome oxidase I (COI) is the standard marker for DNA barcoding. However, COI has proved to be of limited use in identifying some species, and for some taxa, the coding sequence is not efficiently amplified by PCR. These deficiencies lead to uncertainty as to whether COI is the most suitable barcoding fragment for species identification of ticks.<br><br>METHODS: In this study, we directly compared the relative effectiveness of COI, 16S ribosomal DNA (rDNA), nuclear ribosomal internal transcribed spacer 2 (ITS2) and 12S rDNA for tick species identification. A total of 307 sequences from 84 specimens representing eight tick species were acquired by PCR. Besides the 1,834 published sequences of 189 tick species from GenBank and the Barcode of Life Database, 430 unpublished sequences representing 59 tick species were also successfully screened by Bayesian analyses. Thereafter, the performance of the four DNA markers to identify tick species was evaluated by identification success rates given by these markers using nearest neighbour (NN), BLASTn, liberal tree-based or liberal tree-based (+threshold) methods.<br><br>RESULTS: Genetic divergence analyses showed that the intra-specific divergence of each marker was much lower than the inter-specific divergence. Our results indicated that the rates of correct sequence identification for all four markers (COI, 16S rDNA, ITS2, 12S rDNA) were very high (> 96%) when using the NN methodology. We also found that COI was not significantly better than the other markers in terms of its rate of correct sequence identification. Overall, BLASTn and NN methods produced higher rates of correct species identification than that produced by the liberal tree-based methods (+threshold or otherwise).<br><br>CONCLUSIONS: As the standard DNA barcode, COI should be the first choice for tick species identification, while 16S rDNA, ITS2, and 12S rDNA could be used when COI does not produce reliable results. Besides, NN and BLASTn are efficient methods for species identification of ticks.},
}
@article {pmid24587752,
year = {2014},
author = {Avin, FA and Bhassu, S and Tan, YS and Shahbazi, P and Vikineswary, S},
title = {Molecular divergence and species delimitation of the cultivated oyster mushrooms: integration of IGS1 and ITS.},
journal = {TheScientificWorldJournal},
volume = {2014},
number = {},
pages = {793414},
pmid = {24587752},
issn = {1537-744X},
mesh = {Binding Sites/physiology ; *Evolution, Molecular ; *Phylogeny ; Pleurotus/*classification/*genetics/metabolism ; Species Specificity ; },
abstract = {Identification of edible mushrooms particularly Pleurotus genus has been restricted due to various obstacles. The present study attempted to use the combination of two variable regions of IGS1 and ITS for classifying the economically cultivated Pleurotus species. Integration of the two regions proved a high ability that not only could clearly distinguish the species but also served sufficient intraspecies variation. Phylogenetic tree (IGS1+ITS) showed seven distinct clades, each clade belonging to a separate species group. Moreover, the species differentiation was tested by AMOVA and the results were reconfirmed by presenting appropriate amounts of divergence (91.82% among and 8.18% within the species). In spite of achieving a proper classification of species by combination of IGS1 and ITS sequences, the phylogenetic tree showed the misclassification of the species of P. nebrodensis and P. eryngii var. ferulae with other strains of P. eryngii. However, the constructed median joining (MJ) network could not only differentiate between these species but also offer a profound perception of the species' evolutionary process. Eventually, due to the sufficient variation among and within species, distinct sequences, simple amplification, and location between ideal conserved ribosomal genes, the integration of IGS1 and ITS sequences is recommended as a desirable DNA barcode.},
}
@article {pmid24586623,
year = {2014},
author = {Su, Y and Tang, WX and Gao, X and Yu, F and Dai, ZY and Zhao, JD and Lu, Y and Ji, F and Huang, SS and Yuan, YY and Han, MY and Song, YS and Zhu, YH and Kang, DY and Han, DY and Dai, P},
title = {A novel mutation in the TECTA gene in a Chinese family with autosomal dominant nonsyndromic hearing loss.},
journal = {PloS one},
volume = {9},
number = {2},
pages = {e89240},
pmid = {24586623},
issn = {1932-6203},
mesh = {Asian People/genetics ; Audiometry, Pure-Tone ; China ; DNA Mutational Analysis ; Deafness/*genetics/physiopathology ; Extracellular Matrix Proteins/*genetics ; Female ; GPI-Linked Proteins/genetics ; Humans ; Male ; *Mutation ; Pedigree ; Pregnancy ; Prenatal Diagnosis ; },
abstract = {TECTA-related deafness can be inherited as autosomal-dominant nonsyndromic deafness (designated DFNA) or as the autosomal-recessive version. The α-tectorin protein, which is encoded by the TECTA gene, is one of the major components of the tectorial membrane in the inner ear. Using targeted DNA capture and massively parallel sequencing (MPS), we screened 42 genes known to be responsible for human deafness in a Chinese family (Family 3187) in which common deafness mutations had been ruled out as the cause, and identified a novel mutation, c.257-262CCTTTC>GCT (p. Ser86Cys; p. Pro88del) in exon 3 of the TECTA gene in the proband and his extended family. All affected individuals in this family had moderate down-sloping hearing loss across all frequencies. To our knowledge, this is the second TECTA mutation identified in Chinese population. This study demonstrates that targeted genomic capture, MPS, and barcode technology might broaden the availability of genetic testing for individuals with undiagnosed DFNA.},
}
@article {pmid24581441,
year = {2014},
author = {Brdlik, CM and Niu, W and Snyder, M},
title = {Chromatin immunoprecipitation and multiplex sequencing (ChIP-Seq) to identify global transcription factor binding sites in the nematode Caenorhabditis elegans.},
journal = {Methods in enzymology},
volume = {539},
number = {},
pages = {89-111},
doi = {10.1016/B978-0-12-420120-0.00007-4},
pmid = {24581441},
issn = {1557-7988},
mesh = {Animals ; Base Sequence ; Binding Sites ; Caenorhabditis elegans/genetics/*metabolism ; Caenorhabditis elegans Proteins/isolation &amp; purification/*metabolism ; Chromatin Immunoprecipitation ; DNA, Helminth/genetics/isolation &amp; purification/metabolism ; Multiplex Polymerase Chain Reaction ; Protein Binding ; Sequence Analysis, DNA ; Transcription Factors/isolation &amp; purification/*metabolism ; },
abstract = {The global identification of transcription factor (TF) binding sites is a critical step in the elucidation of the functional elements of the genome. Several methods have been developed that map TF binding in human cells, yeast, and other model organisms. These methods make use of chromatin immunoprecipitation, or ChIP, and take advantage of the fact that formaldehyde fixation of living cells can be used to cross-link DNA sequences to the TFs that bind them in vivo. In ChIP, the cross-linked TF-DNA complexes are sheared by sonication, size fractionated, and incubated with antibody specific to the TF of interest to generate a library of TF-bound DNA sequences. ChIP-chip was the first technology developed to globally identify TF-bound DNA sequences and involves subsequent hybridization of the ChIP DNA to oligonucleotide microarrays. However, ChIP-chip proved to be costly, labor-intensive, and limited by the fixed number of probes available on the microarray chip. ChIP-Seq combines ChIP with massively parallel high-throughput sequencing (see Explanatory Chapter: Next Generation Sequencing) and has demonstrated vast improvement over ChIP-chip with respect to time and cost, signal-to-noise ratio, and resolution. In particular, multiplex sequencing can be used to achieve a higher throughput in ChIP-Seq analyses involving organisms with genomes of lower complexity than that of human (Lefrançois et al., 2009) and thereby reduce the cost and amount of time needed for each result. The multiplex ChIP-Seq method described in this section has been developed for Caenorhabditis elegans, but is easily adaptable for other organisms.},
}
@article {pmid24581354,
year = {2013},
author = {Augot, D and Ninio, C and Akhoundi, M and Lehrter, V and Couloux, A and Jouet, D and Depaquit, J},
title = {Characterization of two cryptic species, Culicoides stigma and C.parroti (Diptera: Ceratopogonidae), based on barcode regions and morphology.},
journal = {Journal of vector ecology : journal of the Society for Vector Ecology},
volume = {38},
number = {2},
pages = {260-265},
doi = {10.1111/j.1948-7134.2013.12039.x},
pmid = {24581354},
issn = {1948-7134},
mesh = {Animals ; Ceratopogonidae/classification/*genetics ; DNA, Mitochondrial/genetics ; Diptera/classification/genetics ; France ; Insect Vectors/genetics ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {Biting midges of the genus Culicoides (Diptera: Ceratopogonidae) are insect vectors of economically important veterinary diseases such as African horse sickness, bluetongue, and Schmallenberg virus. The identification of Culicoides based on morphological features can be difficult. Three species of biting midges, Culicoides nubeculosus, C. stigma, and C. parroti have emerged in the laboratory from mud collected around watering troughs on a farm in northern France. Emerging Culicoides were characterized morphologically and molecularly using molecular markers. The closely related species C. stigma and C.parroti showed highly divergent sequences for both mitochondrial (cytochrome B and cytochrome oxidase I) and ribosomal DNA first internal transcribed spacer. A RFLP based on a single restriction using the same enzyme (HaeIII) for both cytochrome C oxidase I and cytochrome B is proposed to identify these species.},
}
@article {pmid24580860,
year = {2014},
author = {Torres, CR and Ogawa, LM and Gillingham, MA and Ferrari, B and van Tuinen, M},
title = {A multi-locus inference of the evolutionary diversification of extant flamingos (Phoenicopteridae).},
journal = {BMC evolutionary biology},
volume = {14},
number = {1},
pages = {36},
pmid = {24580860},
issn = {1471-2148},
mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Birds/anatomy &amp; histology/*classification/*genetics/physiology ; Cell Nucleus/genetics ; Evolution, Molecular ; *Fossils ; Genetic Variation ; Multilocus Sequence Typing ; *Phylogeography ; },
abstract = {BACKGROUND: Modern flamingos (Phoenicopteridae) occupy a highly specialized ecology unique among birds and represent a potentially powerful model system for informing the mechanisms by which a lineage of birds adapts and radiates. However, despite a rich fossil record and well-studied feeding morphology, molecular investigations of the evolutionary progression among modern flamingos have been limited. Here, using three mitochondrial (mtDNA) markers, we present the first DNA sequence-based study of population genetic variation in the widely distributed Chilean Flamingo and, using two mtDNA and 10 nuclear (nDNA) markers, recover the species tree and divergence time estimates for the six extant species of flamingos. Phylogenetic analyses include likelihood and Bayesian frameworks and account for potential gene tree discordance. Analyses of divergence times are fossil calibrated at the divergence of Mirandornithes (flamingos + grebes) and the divergence of crown grebes.<br><br>RESULTS: mtDNA sequences confirmed the presence of a single metapopulation represented by two minimally varying mtDNA barcodes in Chilean flamingos. Likelihood and Bayesian methods recovered identical phylogenies with flamingos falling into shallow-keeled (comprising the Greater, American and Chilean Flamingos) and deep-keeled (comprising the Lesser, Andean and James's Flamingos) sub-clades. The initial divergence among flamingos occurred at or shortly after the Mio-Pliocene boundary (6-3 Ma) followed by quick consecutive divergences throughout the Plio-Pleistocene. There is significant incongruence between the ages recovered by the mtDNA and nDNA datasets, likely due to mutational saturation occurring in the mtDNA loci.<br><br>CONCLUSION: The finding of a single metapopulation in the widespread Chilean Flamingo confirms similar findings in other widespread flamingo species. The robust species phylogeny is congruent with previous classifications of flamingos based on feeding morphology. Modern phoenicopterids likely originated in the New World with each sub-clade dispersing across the Atlantic at least once. Our divergence time estimates place flamingos among the youngest families of birds, counter to the classical notion of flamingos as among the oldest based on biogeography and the fossil record. Finally, we designate 'Phoeniconaias' as a junior synonym of 'Phoenicoparrus' and redefine the latter genus as containing all flamingos more closely related to Phoenicoparrus andinus than Phoenicopterus roseus.},
}
@article {pmid24579851,
year = {2014},
author = {Fu, GK and Wilhelmy, J and Stern, D and Fan, HC and Fodor, SP},
title = {Digital encoding of cellular mRNAs enabling precise and absolute gene expression measurement by single-molecule counting.},
journal = {Analytical chemistry},
volume = {86},
number = {6},
pages = {2867-2870},
pmid = {24579851},
issn = {1520-6882},
support = {R43 HG007129/HG/NHGRI NIH HHS/United States ; R43 HG007130/HG/NHGRI NIH HHS/United States ; R43HG007130/HG/NHGRI NIH HHS/United States ; R43HG007129/HG/NHGRI NIH HHS/United States ; },
mesh = {*Gene Expression ; Polymerase Chain Reaction ; RNA, Messenger/*genetics ; },
abstract = {We present a new approach for the sensitive detection and accurate quantitation of messenger ribonucleic acid (mRNA) gene transcripts in single cells. First, the entire population of mRNAs is encoded with molecular barcodes during reverse transcription. After amplification of the gene targets of interest, molecular barcodes are counted by sequencing or scored on a simple hybridization detector to reveal the number of molecules in the starting sample. Since absolute quantities are measured, calibration to standards is unnecessary, and many of the relative quantitation challenges such as polymerase chain reaction (PCR) bias are avoided. We apply the method to gene expression analysis of minute sample quantities and demonstrate precise measurements with sensitivity down to sub single-cell levels. The method is an easy, single-tube, end point assay utilizing standard thermal cyclers and PCR reagents. Accurate and precise measurements are obtained without any need for cycle-to-cycle intensity-based real-time monitoring or physical partitioning into multiple reactions (e.g., digital PCR). Further, since all mRNA molecules are encoded with molecular barcodes, amplification can be used to generate more material for multiple measurements and technical replicates can be carried out on limited samples. The method is particularly useful for small sample quantities, such as single-cell experiments. Digital encoding of cellular content preserves true abundance levels and overcomes distortions introduced by amplification.},
}
@article {pmid24578530,
year = {2014},
author = {Lee, JH and Daugharthy, ER and Scheiman, J and Kalhor, R and Yang, JL and Ferrante, TC and Terry, R and Jeanty, SS and Li, C and Amamoto, R and Peters, DT and Turczyk, BM and Marblestone, AH and Inverso, SA and Bernard, A and Mali, P and Rios, X and Aach, J and Church, GM},
title = {Highly multiplexed subcellular RNA sequencing in situ.},
journal = {Science (New York, N.Y.)},
volume = {343},
number = {6177},
pages = {1360-1363},
pmid = {24578530},
issn = {1095-9203},
support = {MH098977/MH/NIMH NIH HHS/United States ; P50 HG005550/HG/NHGRI NIH HHS/United States ; U01 MH098977/MH/NIMH NIH HHS/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; RC2 HL102815/HL/NHLBI NIH HHS/United States ; T32 GM080177/GM/NIGMS NIH HHS/United States ; GM080177/GM/NIGMS NIH HHS/United States ; RC2HL102815/HL/NHLBI NIH HHS/United States ; },
mesh = {Base Sequence ; Cell Line ; Cells, Cultured ; DNA, Complementary ; Fluorescence ; Gene Expression Profiling/*methods ; Humans ; Induced Pluripotent Stem Cells ; RNA, Messenger/genetics/metabolism ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis ; Transcription Initiation Site ; *Transcriptome ; Wound Healing ; },
abstract = {Understanding the spatial organization of gene expression with single-nucleotide resolution requires localizing the sequences of expressed RNA transcripts within a cell in situ. Here, we describe fluorescent in situ RNA sequencing (FISSEQ), in which stably cross-linked complementary DNA (cDNA) amplicons are sequenced within a biological sample. Using 30-base reads from 8102 genes in situ, we examined RNA expression and localization in human primary fibroblasts with a simulated wound-healing assay. FISSEQ is compatible with tissue sections and whole-mount embryos and reduces the limitations of optical resolution and noisy signals on single-molecule detection. Our platform enables massively parallel detection of genetic elements, including gene transcripts and molecular barcodes, and can be used to investigate cellular phenotype, gene regulation, and environment in situ.},
}
@article {pmid24574857,
year = {2014},
author = {Cong, Q and Grishin, NV},
title = {A new Hermeuptychia (Lepidoptera, Nymphalidae, Satyrinae) is sympatric and synchronic with H. sosybius in southeast US coastal plains, while another new Hermeuptychia species - not hermes - inhabits south Texas and northeast Mexico.},
journal = {ZooKeys},
volume = {},
number = {379},
pages = {43-91},
pmid = {24574857},
issn = {1313-2989},
abstract = {Hermeuptychia intricata Grishin, sp. n. is described from the Brazos Bend State Park in Texas, United States, where it flies synchronously with Hermeuptychia sosybius (Fabricius, 1793). The two species differ strongly in both male and female genitalia and exhibit 3.5% difference in the COI barcode sequence of mitochondrial DNA. Setting such significant genitalic and genotypic differences aside, we were not able to find reliable wing pattern characters to tell a difference between the two species. This superficial similarity may explain why H. intricata, only distantly related to H. sosybius, has remained unnoticed until now, despite being widely distributed in the coastal plains from South Carolina to Texas, USA (and possibly to Costa Rica). Obscuring the presence of a cryptic species even further, wing patterns are variable in both butterflies and ventral eyespots vary from large to almost absent. To avoid confusion with the new species, neotype for Papilio sosybius Fabricius, 1793, a common butterfly that occurs across northeast US, is designated from Savannah, Georgia, USA. It secures the universally accepted traditional usage of this name. Furthermore, we find that DNA barcodes of Hermeuptychia specimens from the US, even those from extreme south Texas, are at least 4% different from those of H. hermes (Fabricius, 1775)-type locality Brazil: Rio de Janeiro-and suggest that the name H. hermes should not be used for USA populations, but rather reserved for the South American species. This conclusion is further supported by comparison of male genitalia. However, facies, genitalia and 2.1% different DNA barcodes set Hermeuptychia populations in the lower Rio Grande Valley of Texas apart from H. sosybius. These southern populations, also found in northeastern Mexico, are described here as Hermeuptychia hermybius Grishin, sp. n. (type locality Texas: Cameron County). While being phylogenetically closer to H. sosybius than to any other Hermeuptychia species, H. hermybius can usually be recognized by wing patterns, such as the size of eyespots and the shape of brown lines on hindwing. "Intricate Satyr" and "South Texas Satyr" are proposed as the English names for H. intricata and H. hermybius, respectively.},
}
@article {pmid24569823,
year = {2014},
author = {Blin, A and Cissé, I and Bockelmann, U},
title = {Electronic hybridization detection in microarray format and DNA genotyping.},
journal = {Scientific reports},
volume = {4},
number = {},
pages = {4194},
pmid = {24569823},
issn = {2045-2322},
mesh = {Base Sequence ; Conductometry/*instrumentation ; DNA/*genetics ; DNA Mutational Analysis/*instrumentation ; Equipment Design ; Equipment Failure Analysis ; Genotype ; In Situ Hybridization/*instrumentation ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis/*instrumentation ; Sequence Analysis, DNA/*instrumentation ; *Transistors, Electronic ; },
abstract = {We describe an approach to substituting a fluorescence microarray with a surface made of an arrangement of electrolyte-gated field effect transistors. This was achieved using a dedicated blocking of non-specific interactions and comparing threshold voltage shifts of transistors exhibiting probe molecules of different base sequence. We apply the approach to detection of the 35delG mutation, which is related to non-syndromic deafness and is one of the most frequent mutations in humans. The process involves barcode sequences that are generated by Tas-PCR, a newly developed replication reaction using polymerase blocking. The barcodes are recognized by hybridization to surface attached probes and are directly detected by the semiconductor device.},
}
@article {pmid24569571,
year = {2014},
author = {Lee, H and Park, JE and Nam, JM},
title = {Bio-barcode gel assay for microRNA.},
journal = {Nature communications},
volume = {5},
number = {},
pages = {3367},
doi = {10.1038/ncomms4367},
pmid = {24569571},
issn = {2041-1723},
mesh = {Base Sequence ; Cell Line, Tumor ; DNA Probes/chemistry/*genetics ; Electrophoresis, Polyacrylamide Gel/*methods ; Gene Expression Profiling/methods ; *Gene Expression Regulation, Neoplastic ; Gold/chemistry ; Humans ; Metal Nanoparticles/chemistry ; MicroRNAs/*genetics/metabolism ; Potassium Cyanide/chemistry ; Reproducibility of Results ; Reverse Transcriptase Polymerase Chain Reaction ; },
abstract = {MicroRNA has been identified as a potential biomarker because expression level of microRNA is correlated with various cancers. Its detection at low concentrations would be highly beneficial for cancer diagnosis. Here, we develop a new type of a DNA-modified gold nanoparticle-based bio-barcode assay that uses a conventional gel electrophoresis platform and potassium cyanide chemistry and show this assay can detect microRNA at aM levels without enzymatic amplification. It is also shown that single-base-mismatched microRNA can be differentiated from perfectly matched microRNA and the multiplexed detection of various combinations of microRNA sequences is possible with this approach. Finally, differently expressed microRNA levels are selectively detected from cancer cells using the bio-barcode gel assay, and the results are compared with conventional polymerase chain reaction-based results. The method and results shown herein pave the way for practical use of a conventional gel electrophoresis for detecting biomolecules of interest even at aM level without polymerase chain reaction amplification.},
}
@article {pmid24569351,
year = {2014},
author = {Kielpinski, LJ and Vinther, J},
title = {Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility.},
journal = {Nucleic acids research},
volume = {42},
number = {8},
pages = {e70},
pmid = {24569351},
issn = {1362-4962},
mesh = {High-Throughput Nucleotide Sequencing/*methods ; *Hydroxyl Radical ; Models, Molecular ; Nucleic Acid Conformation ; RNA/*chemistry/isolation &amp; purification ; RNA, Ribosomal, 16S/chemistry/isolation &amp; purification ; Reverse Transcription ; Ribonuclease P/biosynthesis/genetics ; Sequence Analysis, RNA/*methods ; },
abstract = {Hydroxyl Radical Footprinting (HRF) is a tried-and-tested method for analysis of the tertiary structure of RNA and for identification of protein footprints on RNA. The hydroxyl radical reaction breaks accessible parts of the RNA backbone, thereby allowing ribose accessibility to be determined by detection of reverse transcriptase termination sites. Current methods for HRF rely on reverse transcription of a single primer and detection by fluorescent fragments by capillary electrophoresis. Here, we describe an accurate and efficient massive parallel-sequencing-based method for probing RNA accessibility with hydroxyl radicals, called HRF-Seq. Using random priming and a novel barcoding scheme, we show that HRF-Seq dramatically increases the throughput of HRF experiments and facilitates the parallel analysis of multiple RNAs or experimental conditions. Moreover, we demonstrate that HRF-Seq data for the Escherichia coli 16S rRNA correlates well with the ribose accessible surface area as determined by X-ray crystallography and have a resolution that readily allows the difference in accessibility caused by exposure of one side of RNA helices to be observed.},
}
@article {pmid24568212,
year = {2014},
author = {Puddu, M and Paunescu, D and Stark, WJ and Grass, RN},
title = {Magnetically recoverable, thermostable, hydrophobic DNA/silica encapsulates and their application as invisible oil tags.},
journal = {ACS nano},
volume = {8},
number = {3},
pages = {2677-2685},
doi = {10.1021/nn4063853},
pmid = {24568212},
issn = {1936-086X},
mesh = {Adsorption ; Base Sequence ; Capsules ; DNA/*chemistry/genetics ; Ferric Compounds/chemistry ; *Hydrophobic and Hydrophilic Interactions ; Magnets/*chemistry ; Nanoparticles/chemistry ; Oils/*chemistry ; Silicon Dioxide/*chemistry ; Surface Properties ; *Temperature ; },
abstract = {A method to encapsulate DNA in heat-resistant and inert magnetic particles was developed. An inexpensive synthesis technique based on co-precipitation was utilized to produce Fe2O3 nanoparticles, which were further functionalized with ammonium groups. DNA was adsorbed on this magnetic support, and the DNA/magnet nanocluster was surface coated with a dense silica layer by sol-gel chemistry. The materials were further surface modified with hexyltrimethoxysilane to achieve particle dispersibility in hydrophobic liquids. The hydrodynamic particle sizes were evaluated by analytical disc centrifugation, and the magnetic properties were investigated by vibrating sample magnetometry. The obtained nanoengineered encapsulates showed good dispersion abilities in various nonaqueous fluids and did not affect the optical properties of the hydrophobic dispersant when present at concentrations lower than 10(3) μg/L. Upon magnetic separation and particle dissolution, the DNA could be recovered unharmed and was analyzed by quantitative real-time PCR and Sanger sequencing. DNA encapsulated within the magnetic particles was stable for 2 years in decalin at room temperature, and the stability was further tested at elevated temperatures. The new magnetic DNA/silica encapsulates were utilized to developed a low-cost platform for the tracing/tagging of oils and oil-derived products, requiring 1 μg/L=1 ppb levels of the taggant and allowing quantification of taggant concentration on a logarithmic scale. The procedure was tested for the barcoding of a fuel (gasoline), a cosmetic oil (bergamot oil), and a food grade oil (extra virgin olive oil), being able to verify the authenticity of the products.},
}
@article {pmid24567825,
year = {2013},
author = {Collin, H and Burri, R and Comtesse, F and Fumagalli, L},
title = {Combining molecular evolution and environmental genomics to unravel adaptive processes of MHC class IIB diversity in European minnows (Phoxinus phoxinus).},
journal = {Ecology and evolution},
volume = {3},
number = {8},
pages = {2568-2585},
pmid = {24567825},
issn = {2045-7758},
abstract = {Host-pathogen interactions are a major evolutionary force promoting local adaptation. Genes of the major histocompatibility complex (MHC) represent unique candidates to investigate evolutionary processes driving local adaptation to parasite communities. The present study aimed at identifying the relative roles of neutral and adaptive processes driving the evolution of MHC class IIB (MHCIIB) genes in natural populations of European minnows (Phoxinus phoxinus). To this end, we isolated and genotyped exon 2 of two MHCIIB gene duplicates (DAB1 and DAB3) and 1'665 amplified fragment length polymorphism (AFLP) markers in nine populations, and characterized local bacterial communities by 16S rDNA barcoding using 454 amplicon sequencing. Both MHCIIB loci exhibited signs of historical balancing selection. Whereas genetic differentiation exceeded that of neutral markers at both loci, the populations' genetic diversities were positively correlated with local pathogen diversities only at DAB3. Overall, our results suggest pathogen-mediated local adaptation in European minnows at both MHCIIB loci. While at DAB1 selection appears to favor different alleles among populations, this is only partially the case in DAB3, which appears to be locally adapted to pathogen communities in terms of genetic diversity. These results provide new insights into the importance of host-pathogen interactions in driving local adaptation in the European minnow, and highlight that the importance of adaptive processes driving MHCIIB gene evolution may differ among duplicates within species, presumably as a consequence of alternative selective regimes or different genomic context. Using next-generation sequencing, the present manuscript identifies the relative roles of neutral and adaptive processes driving the evolution of MHC class IIB (MHCIIB) genes in natural populations of a cyprinid fish: the European minnow (Phoxinus phoxinus). We highlight that the relative importance of neutral versus adaptive processes in shaping immune competence may differ between duplicates as a consequence of alternative selective regimes or different genomic contexts.},
}
@article {pmid24564791,
year = {2014},
author = {Palla, P and Frau, G and Vargiu, L and Rodriguez-Tomé, P},
title = {QTREDS: a Ruby on Rails-based platform for omics laboratories.},
journal = {BMC bioinformatics},
volume = {15 Suppl 1},
number = {Suppl 1},
pages = {S13},
pmid = {24564791},
issn = {1471-2105},
mesh = {*Computational Biology ; Humans ; Information Systems ; Internet ; Software ; *User-Computer Interface ; Workflow ; },
abstract = {BACKGROUND: In recent years, the experimental aspects of the laboratory activities have been growing in complexity in terms of amount and diversity of data produced, equipment used, of computer-based workflows needed to process and analyze the raw data generated. To enhance the level of quality control over the laboratory activities and efficiently handle the large amounts of data produced, a Laboratory Management Information System (LIMS) is highly-recommended. A LIMS is a complex software platform that helps researchers to have a complete knowledge of the laboratory activities at each step encouraging them to adopt good laboratory practices.<br><br>RESULTS: We have designed and implemented Quality and TRacEability Data System--QTREDS, a software platform born to address the specific needs of the CRS4 Sequencing and Genotyping Platform (CSGP). The system written in the Ruby programming language and developed using the Rails framework is based on four main functional blocks: a sample handler, a workflow generator, an inventory management system and a user management system. The wizard-based sample handler allows to manage one or multiple samples at a time, tracking the path of each sample and providing a full chain of custody. The workflow generator encapsulates a user-friendly JavaScript-based visual tool that allows users to design customized workflows even for those without a technical background. With the inventory management system, reagents, laboratory glassware and consumables can be easily added through their barcodes and minimum stock levels can be controlled to avoid shortages of essential laboratory supplies. QTREDS provides a system for privileges management and authorizations to create different user roles, each with a well-defined access profile.<br><br>CONCLUSIONS: Tracking and monitoring all the phases of the laboratory activities can help to identify and troubleshoot problems more quickly, reducing the risk of process failures and their related costs. QTREDS was designed to address the specific needs of the CSGP laboratory, where it has been successfully used for over a year, but thanks to its flexibility it can be easily adapted to other "omics" laboratories. The software is freely available for academic users from http://qtreds.crs4.it.},
}
@article {pmid24563831,
year = {2013},
author = {Crous, PW and Quaedvlieg, W and Sarpkaya, K and Can, C and Erkılıç, A},
title = {Septoria-like pathogens causing leaf and fruit spot of pistachio.},
journal = {IMA fungus},
volume = {4},
number = {2},
pages = {187-199},
pmid = {24563831},
issn = {2210-6340},
abstract = {Several species of Septoria are associated with leaf and fruit spot of pistachio (Pistacia vera), though their identity has always been confused, making identification problematic. The present study elucidates the taxonomy of the Septoria spp. associated with pistachio, and distinguishes four species associated with this host genus. Partial nucleotide sequence data for five gene loci, ITS, LSU, EF-1α, RPB2 and Btub were generated for a subset of isolates. Cylindroseptoria pistaciae, which is associated with leaf spots of Pistacia lentiscus in Spain, is characterised by pycnidial conidiomata that give rise to cylindrical, aseptate conidia. Two species of Septoria s. str. are also recognised on pistachio, S. pistaciarum, and S. pistaciae. The latter is part of the S. protearum species complex, and appears to be a wide host range pathogen occurring on hosts in several different plant families. Septoria pistacina, a major pathogen of pistachio in Turkey, is shown to belong to Pseudocercospora, and not Septoria as earlier suspected. Other than for its pycnidial conidiomata, it is a typical species of Pseudocercospora based on its smooth, pigmented conidiogenous cells and septate conidia. This phenomenon has also been observed in Pallidocercospora, and seriously questions the value of conidiomatal structure at generic level, which has traditionally been used to separate hyphomycetous from coelomycetous ascomycetes. Other than DNA barcodes to facilitate the molecular identification of these taxa occurring on pistachio, a key is also provided to distinguish species based on morphology.},
}
@article {pmid24558808,
year = {2013},
author = {Sati, J and Sah, S and Pandey, H and Ali, S and Sahoo, PK and Pande, V and Baratz, A},
title = {Phylogenetic relationship and molecular identification of five Indian Mahseer species using COIsequence.},
journal = {Journal of environmental biology},
volume = {34},
number = {5},
pages = {933-939},
pmid = {24558808},
issn = {0254-8704},
mesh = {Animals ; Base Sequence ; Cyprinidae/*classification/*genetics/metabolism ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics/metabolism ; Fish Proteins/genetics/metabolism ; *Genetic Variation ; India ; Mitochondrial Proteins/genetics/metabolism ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; },
abstract = {This study examined the phylogenetic relationship and identification of five Mahseer species (Tor putitoro, Tor tor, Tor khudree, Tor chelynoides and Neolissochilus hexogonolopis) using partial sequencing of a Cytochrome Oxidase I (COl) DNA barcodes. The sequence analysis data showed that 134 (21.61%) sites out of 628 sites were variable without insertion or deletion. Rate of transition (70.5%) were higher than transversion (29.41%). There was a high inter-species divergence (range 4.1% to 12.2%) in Mahseer species as compared to intra-specific sequence divergence (1.7% for T. putitora, 1.2% for T tor, 1.4% for T. khudree, 3.0% for T chelynoides, 0.26 % for N. hexagonolopis). The phylogenetic tree, constructed by maximum parsimony, maximum likelihood and unweighted pair group average methods revealed similar results suggesting that T. putitoro, T. tor and T. khudree had a close relationship to each other while maximum divergence was observed in T. chelynoides, which was also confirmed by the genetic distance data. The results indicate that COl sequencing or bar-coding is useful in unravelling phylogenetic relationship and identification of Mahseer species.},
}
@article {pmid24558577,
year = {2014},
author = {Jo, H and Gim, JA and Jeong, KS and Kim, HS and Joo, GJ},
title = {Application of DNA barcoding for identification of freshwater carnivorous fish diets: Is number of prey items dependent on size class for Micropterus salmoides?.},
journal = {Ecology and evolution},
volume = {4},
number = {2},
pages = {219-229},
pmid = {24558577},
issn = {2045-7758},
abstract = {Understanding predator-prey interactions is a major challenge in ecological studies. In particular, the accurate identification of prey is a fundamental requirement in elucidating food-web structure. This study took a molecular approach in determining the species identity of consumed prey items of a freshwater carnivorous fish (largemouth bass, Micropterus salmoides), according to their size class. Thirty randomly selected gut samples were categorized into three size classes, based on the total length of the bass. Using the universal primer for the mtDNA cytochrome oxidase I (COI) region, polymerase chain reaction (PCR) amplification was performed on unidentified gut contents and then sequenced after cloning. Two gut samples were completely empty, and DNA materials from 27 of 28 gut samples were successfully amplified by PCR (success rate: 96.4%). Sequence database navigation yielded a total of 308 clones, containing DNA from 26 prey items. They comprised four phyla, including seven classes, 12 orders, and 12 families based on BLAST and BOLD database searches. The results indicate that largemouth bass show selective preferences in prey item consumption as they mature. These results corroborate a hypothesis, presence of ontogenetic diet shift, derived through other methodological approaches. Despite the practical limitations inherent in DNA barcoding analysis, high-resolution (i.e., species level) identification was possible, and the predation patterns of predators of different sizes were identifiable. The utilization of this method is strongly recommended for determining specific predator-prey relationships in complex freshwater ecosystems.},
}
@article {pmid24555538,
year = {2014},
author = {Liu, B and Zhang, X and Huang, H and Zhang, Y and Zhou, F and Wang, G},
title = {A novel molecular typing method of Mycobacteria based on DNA barcoding visualization.},
journal = {Journal of clinical bioinformatics},
volume = {4},
number = {1},
pages = {4},
pmid = {24555538},
issn = {2043-9113},
abstract = {Different subtypes of Mycobacterium tuberculosis (MTB) may induce diverse severe human infections, and some of their symptoms are similar to other pathogenes, e.g. Nontuberculosis mycobacteria (NTM). So determination of mycobacterium subtypes facilitates the effective control of MTB infection and proliferation. This study exploits a novel DNA barcoding visualization method for molecular typing of 17 mycobacteria genomes published in the NCBI prokaryotic genome database. Three mycobacterium genes (Rv0279c, Rv3508 and Rv3514) from the PE/PPE family of MT Band were detected to best represent the inter-strain pathogenetic variations. An accurate and fast MTB substrain typing method was proposed based on the combination of the aforementioned three biomarker genes and the 16S rRNA gene. The protocol of establishing a bacterial substrain typing system used in this study may also be applied to the other pathogenes.},
}
@article {pmid24555467,
year = {2014},
author = {Christa, G and Händeler, K and Schäberle, TF and König, GM and Wägele, H},
title = {Identification of sequestered chloroplasts in photosynthetic and non-photosynthetic sacoglossan sea slugs (Mollusca, Gastropoda).},
journal = {Frontiers in zoology},
volume = {11},
number = {1},
pages = {15},
pmid = {24555467},
issn = {1742-9994},
abstract = {BACKGROUND: Sacoglossan sea slugs are well known for their unique ability among metazoans to incorporate functional chloroplasts (kleptoplasty) in digestive glandular cells, enabling the slugs to use these as energy source when starved for weeks and months. However, members assigned to the shelled Oxynoacea and Limapontioidea (often with dorsal processes) are in general not able to keep the incorporated chloroplasts functional. Since obviously no algal genes are present within three (out of six known) species with chloroplast retention of several months, other factors enabling functional kleptoplasty have to be considered. Certainly, the origin of the chloroplasts is important, however, food source of most of the about 300 described species is not known so far. Therefore, a deduction of specific algal food source as a factor to perform functional kleptoplasty was still missing.<br><br>RESULTS: We investigated the food sources of 26 sacoglossan species, freshly collected from the field, by applying the chloroplast marker genes tufA and rbcL and compared our results with literature data of species known for their retention capability. For the majority of the investigated species, especially for the genus Thuridilla, we were able to identify food sources for the first time. Furthermore, published data based on feeding observations were confirmed and enlarged by the molecular methods. We also found that certain chloroplasts are most likely essential for establishing functional kleptoplasty.<br><br>CONCLUSIONS: Applying DNA-Barcoding appeared to be very efficient and allowed a detailed insight into sacoglossan food sources. We favor rbcL for future analyses, but tufA might be used additionally in ambiguous cases. We narrowed down the algal species that seem to be essential for long-term-functional photosynthesis: Halimeda, Caulerpa, Penicillus, Avrainvillea, Acetabularia and Vaucheria. None of these were found in Thuridilla, the only plakobranchoidean genus without long-term retention forms. The chloroplast type, however, does not solely determine functional kleptoplasty; members of no-retention genera, such as Cylindrobulla or Volvatella, feed on the same algae as e.g., the long-term-retention forms Plakobranchus ocellatus or Elysia crispata, respectively. Evolutionary benefits of functional kleptoplasty are still questionable, since a polyphagous life style would render slugs more independent of specific food sources and their abundance.},
}
@article {pmid24548270,
year = {2014},
author = {Lawrence, AL and Brown, GK and Peters, B and Spielman, DS and Morin-Adeline, V and Šlapeta, J},
title = {High phylogenetic diversity of the cat flea (Ctenocephalides felis) at two mitochondrial DNA markers.},
journal = {Medical and veterinary entomology},
volume = {28},
number = {3},
pages = {330-336},
doi = {10.1111/mve.12051},
pmid = {24548270},
issn = {1365-2915},
mesh = {Animals ; Australia ; Ctenocephalides/*genetics ; Electron Transport Complex IV/genetics ; Genetic Markers/genetics ; *Genetic Variation ; Insect Proteins/*genetics ; Mitochondrial Proteins/*genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA/veterinary ; },
abstract = {The cat flea, Ctenocephalides felis (Siphonaptera: Pulicidae) (Bouché), is the most common flea species found on cats and dogs worldwide. We investigated the genetic identity of the cosmopolitan subspecies C. felis felis and evaluated diversity of cat fleas from Australia, Fiji, Thailand and Seychelles using mtDNA sequences from cytochrome c oxidase subunit I (cox1) and II (cox2) genes. Both cox1 and cox2 confirmed the high phylogenetic diversity and paraphyletic origin of C. felis felis. The African subspecies C. felis strongylus (Jordan) is nested within the paraphyletic C. felis felis. The south East Asian subspecies C. felis orientis (Jordan) is monophyletic and is supported by morphology. We confirm that Australian cat fleas belong to C. felis felis and show that in Australia they form two distinct phylogenetic clades, one common with fleas from Fiji. Using a barcoding approach, we recognize two putative species within C. felis (C. felis and C. orientis). Nucleotide diversity was higher in cox1 but COX2 outperformed COX1 in amino acid diversity. COX2 amino acid sequences resolve all phylogenetic clades and provide an additional phylogenetic signal. Both cox1 and cox2 resolved identical phylogeny and are suitable for population structure studies of Ctenocephalides species.},
}
@article {pmid24533348,
year = {2013},
author = {Chagas, CR and Valkiūnas, G and Nery, CV and Henrique, PC and Gonzalez, IH and Monteiro, EF and Guimarães, Lde O and Romano, CM and Kirchgatter, K},
title = {Plasmodium (Novyella) nucleophilum from an Egyptian Goose in São Paulo Zoo, Brazil: microscopic confirmation and molecular characterization.},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {2},
number = {},
pages = {286-291},
pmid = {24533348},
issn = {2213-2244},
abstract = {Plasmodium (Novyella) nucleophilum was identified using microscopy and PCR, in an Egyptian Goose (Alopochen aegyptiacus) that died in São Paulo Zoo, Brazil. This parasite is characterized by elongated gametocytes, small meronts with scant cytoplasm, less than eight merozoites and mainly for having all the stages appressed to the nuclei of infected erythrocytes. Additionally, Plasmodium (Haemamoeba) sp. was identified by microscopy in the same blood sample. The latter parasite lacks nucleophilic blood stages and is characterized by large roundish trophozoites, each with a large prominent centrally collated vacuole. This co-infection was not confirmed by PCR amplification of the mitochondrial cytochrome b (cytb) gene and sequencing; only one Plasmodium sp. cytb sequence was detected in the blood sample. Since parasitemia of P. nucleophilum (2.4%) was much higher than that of P. (Haemamoeba) sp. (0.2%), PCR may have favored the amplification of the cytb sequence of the former. Phylogenetic analysis is in agreement with this conclusion because the reported cytb sequence was positioned in the same branch of sequences of several Novyella species. This is the first assignment of the mitochondrial cytb gene sequence to P. nucleophilum. The P. (Haemamoeba) parasite is particularly similar to Plasmodium (Haemamoeba) tejerai, because its advanced trophozoites and young erythrocytic meronts possess a large vacuole with prominent pigment granules arranged around it, the characteristic features of development in this species. For definitive identification of P. (Haemamoeba) species, mature meronts and gametocytes are required; however, these were absent from the thin blood smear. Representative images of the blood stages of P. nucleophilum and P. (Haemamoeba) sp. are provided. Together with microscopy data, the P. nucleophilum cytb sequence will assist in molecular identification (barcoding) of this Plasmodium species in other birds.},
}
@article {pmid24529707,
year = {2014},
author = {Decourty, L and Doyen, A and Malabat, C and Frachon, E and Rispal, D and Séraphin, B and Feuerbach, F and Jacquier, A and Saveanu, C},
title = {Long open reading frame transcripts escape nonsense-mediated mRNA decay in yeast.},
journal = {Cell reports},
volume = {6},
number = {4},
pages = {593-598},
doi = {10.1016/j.celrep.2014.01.025},
pmid = {24529707},
issn = {2211-1247},
mesh = {*3' Untranslated Regions ; Gene Expression Regulation, Fungal ; *Nonsense Mediated mRNA Decay ; *Open Reading Frames ; RNA Helicases/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; },
abstract = {Nonsense-mediated mRNA decay (NMD) destabilizes eukaryotic transcripts with long 3' UTRs. To investigate whether other transcript features affect NMD, we generated yeast strains expressing chromosomal-derived mRNAs with 979 different promoter and open reading frame (ORF) regions and with the same long, destabilizing 3' UTR. We developed a barcode-based DNA microarray strategy to compare the levels of each reporter mRNA in strains with or without active NMD. The size of the coding region had a significant negative effect on NMD efficiency. This effect was not specific to the tested 3' UTR because two other different NMD reporters became less sensitive to NMD when ORF length was increased. Inefficient NMD was not due to a lack of association of Upf1 to long ORF transcripts. In conclusion, in addition to a long 3' UTR, short translation length is an important feature of NMD substrates in yeast.},
}
@article {pmid24525048,
year = {2014},
author = {Tan, YC and Blum, LK and Kongpachith, S and Ju, CH and Cai, X and Lindstrom, TM and Sokolove, J and Robinson, WH},
title = {High-throughput sequencing of natively paired antibody chains provides evidence for original antigenic sin shaping the antibody response to influenza vaccination.},
journal = {Clinical immunology (Orlando, Fla.)},
volume = {151},
number = {1},
pages = {55-65},
pmid = {24525048},
issn = {1521-7035},
support = {R01 AR063676/AR/NIAMS NIH HHS/United States ; T32 AI007290/AI/NIAID NIH HHS/United States ; RC1 AR058713/AR/NIAMS NIH HHS/United States ; U19 AI057229/AI/NIAID NIH HHS/United States ; N01-HV-00242/HV/NHLBI NIH HHS/United States ; T32 AR050942/AR/NIAMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Antibodies, Neutralizing/biosynthesis/*immunology ; Antibodies, Viral/biosynthesis/*immunology ; Antigens, Viral/immunology ; B-Lymphocytes/immunology ; Hemagglutinins, Viral/immunology ; High-Throughput Nucleotide Sequencing ; Humans ; Immunoglobulin G/biosynthesis/*immunology ; Immunoglobulin Heavy Chains/biosynthesis/*immunology ; Immunoglobulin Light Chains/biosynthesis/*immunology ; Immunologic Memory ; Influenza A Virus, H1N2 Subtype/immunology ; Influenza A Virus, H3N2 Subtype/immunology ; Influenza Vaccines/*immunology ; Influenza, Human/immunology/*prevention &amp; control ; Molecular Sequence Data ; Molecular Typing ; Vaccination ; Vaccines, Subunit ; },
abstract = {We developed a DNA barcoding method to enable high-throughput sequencing of the cognate heavy- and light-chain pairs of the antibodies expressed by individual B cells. We used this approach to elucidate the plasmablast antibody response to influenza vaccination. We show that >75% of the rationally selected plasmablast antibodies bind and neutralize influenza, and that antibodies from clonal families, defined by sharing both heavy-chain VJ and light-chain VJ sequence usage, do so most effectively. Vaccine-induced heavy-chain VJ regions contained on average >20 nucleotide mutations as compared to their predicted germline gene sequences, and some vaccine-induced antibodies exhibited higher binding affinities for hemagglutinins derived from prior years' seasonal influenza as compared to their affinities for the immunization strains. Our results show that influenza vaccination induces the recall of memory B cells that express antibodies that previously underwent affinity maturation against prior years' seasonal influenza, suggesting that 'original antigenic sin' shapes the antibody response to influenza vaccination.},
}
@article {pmid24523650,
year = {2014},
author = {Bast, F and Rani, P and Meena, D},
title = {Chloroplast DNA phylogeography of holy basil (Ocimum tenuiflorum) in Indian subcontinent.},
journal = {TheScientificWorldJournal},
volume = {2014},
number = {},
pages = {847482},
pmid = {24523650},
issn = {1537-744X},
mesh = {*DNA, Chloroplast ; India ; Ocimum basilicum/*classification/*genetics ; *Phylogeny ; *Phylogeography ; },
abstract = {Ocimum tenuiflorum L., holy basil "Tulsi", is an important medicinal plant that is being grown and traditionally revered throughout Indian Subcontinent for thousands of years; however, DNA sequence-based genetic diversity of this aromatic herb is not yet known. In this report, we present our studies on the phylogeography of this species using trnL-trnF intergenic spacer of plastid genome as the DNA barcode for isolates from Indian subcontinent. Our pairwise distance analyses indicated that genetic heterogeneity of isolates remained quite low, with overall mean nucleotide p-distance of 5 × 10(-4). However, our sensitive phylogenetic analysis using maximum likelihood framework was able to reveal subtle intraspecific molecular evolution of this species within the subcontinent. All isolates except that from North-Central India formed a distinct phylogenetic clade, notwithstanding low bootstrap support and collapse of the clade in Bayesian Inference. North-Central isolates occupied more basal position compared to other isolates, which is suggestive of its evolutionarily primitive status. Indian isolates formed a monophyletic and well-supported clade within O. tenuiflorum clade, which indicates a distinct haplotype. Given the vast geographical area of more than 3 million km(2) encompassing many exclusive biogeographical and ecological zones, relatively low rate of evolution of this herb at this locus in India is particularly interesting.},
}
@article {pmid24522727,
year = {2014},
author = {Chakraborty, C and Doss, CG and Patra, BC and Bandyopadhyay, S},
title = {DNA barcoding to map the microbial communities: current advances and future directions.},
journal = {Applied microbiology and biotechnology},
volume = {98},
number = {8},
pages = {3425-3436},
doi = {10.1007/s00253-014-5550-9},
pmid = {24522727},
issn = {1432-0614},
mesh = {*Biota ; DNA Barcoding, Taxonomic/*methods ; Eukaryota/*classification ; Prokaryotic Cells/*classification ; },
abstract = {During the last two decades, the DNA barcode development towards microbial community has increased dramatically. DNA barcode development is related to error-free and quick species identification which aid in understanding the microbial biodiversity, as well as the diseases related to microbial species. Here, we seek to evaluate the so-called barcoding initiatives for the microbial communities and the emerging trends in this field. In this paper, we describe the development of DNA marker-based DNA barcoding system, comparison between routine species identification and DNA barcode, and microbial biodiversity and DNA barcode for microbial communities. Two major topics, such as the molecular diversity of viruses and barcode for viruses have been discussed at the same time. We demonstrate the current status and the maker of DNA barcode for bacteria, algae, fungi, and protozoa. Furthermore, we argue about the promises, limitations, and present and future challenges of microbial barcode development.},
}
@article {pmid24522142,
year = {2013},
author = {Kumari, S and Das, S and Mahapatra, N},
title = {Anopheles subpictus B and its role in transmission of malaria in Odisha, India.},
journal = {Tropical biomedicine},
volume = {30},
number = {4},
pages = {710-717},
pmid = {24522142},
issn = {2521-9855},
mesh = {Animals ; Anopheles/classification/genetics/*growth &amp; development/*parasitology ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; India/epidemiology ; *Insect Vectors ; Malaria/epidemiology/*transmission ; Plasmodium/*isolation &amp; purification ; Sporozoites ; },
abstract = {Odisha state is highly endemic for malaria and among several Anopheline species found in the state, Anopheles subpictus is known to be one of the most prevalent species. An. subpictus complex consists of four sibling species i,e A,B,C and D. However, no work has been conducted on prevalence of sibling species of An. subpictus in Odisha. Hence attempt was made to study the prevalence of sibling species of An. subpictus and their role in transmission of malaria in four districts i,e Angul, Khurda, Cuttack and Puri of Odisha using Mitochondrial Gene, Cytochrome C Oxidase subunit I (COI) known as DNA barcode. The sibling species B of An. subpictus with sporozoite were reported for the first time in Odisha.},
}
@article {pmid24508463,
year = {2014},
author = {Perié, L and Hodgkin, PD and Naik, SH and Schumacher, TN and de Boer, RJ and Duffy, KR},
title = {Determining lineage pathways from cellular barcoding experiments.},
journal = {Cell reports},
volume = {6},
number = {4},
pages = {617-624},
doi = {10.1016/j.celrep.2014.01.016},
pmid = {24508463},
issn = {2211-1247},
mesh = {Animals ; *Cell Lineage ; Hematopoiesis ; Hematopoietic Stem Cells/*cytology ; Mice ; *Models, Biological ; },
abstract = {Cellular barcoding and other single-cell lineage-tracing strategies form experimental methodologies for analysis of in vivo cell fate that have been instrumental in several significant recent discoveries. Due to the highly nonlinear nature of proliferation and differentiation, interrogation of the resulting data for evaluation of potential lineage pathways requires a new quantitative framework complete with appropriate statistical tests. Here, we develop such a framework, illustrating its utility by analyzing data from barcoded multipotent cells of the blood system. This application demonstrates that the data require additional paths beyond those found in the classical model, which leads us to propose that hematopoietic differentiation follows a loss of potential mechanism and to suggest further experiments to test this deduction. Our quantitative framework can evaluate the compatibility of lineage trees with barcoded data from any proliferating and differentiating cell system.},
}
@article {pmid24507442,
year = {2014},
author = {Quail, MA and Smith, M and Jackson, D and Leonard, S and Skelly, T and Swerdlow, HP and Gu, Y and Ellis, P},
title = {SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing.},
journal = {BMC genomics},
volume = {15},
number = {1},
pages = {110},
pmid = {24507442},
issn = {1471-2164},
support = {/WT_/Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; },
mesh = {DNA/chemistry/metabolism ; DNA Contamination ; Gene Library ; High-Throughput Nucleotide Sequencing ; Humans ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: A minor but significant fraction of samples subjected to next-generation sequencing methods are either mixed-up or cross-contaminated. These events can lead to false or inconclusive results. We have therefore developed SASI-Seq; a process whereby a set of uniquely barcoded DNA fragments are added to samples destined for sequencing. From the final sequencing data, one can verify that all the reads derive from the original sample(s) and not from contaminants or other samples.<br><br>RESULTS: By adding a mixture of three uniquely barcoded amplicons, of different sizes spanning the range of insert sizes one would normally use for Illumina sequencing, at a spike-in level of approximately 0.1%, we demonstrate that these fragments remain intimately associated with the sample. They can be detected following even the tightest size selection regimes or exome enrichment and can report the occurrence of sample mix-ups and cross-contamination.As a consequence of this work, we have designed a set of 384 eleven-base Illumina barcode sequences that are at least 5 changes apart from each other, allowing for single-error correction and very low levels of barcode misallocation due to sequencing error.<br><br>CONCLUSION: SASI-Seq is a simple, inexpensive and flexible tool that enables sample assurance, allows deconvolution of sample mix-ups and reports levels of cross-contamination between samples throughout NGS workflows.},
}
@article {pmid24502833,
year = {2014},
author = {Lammers, Y and Peelen, T and Vos, RA and Gravendeel, B},
title = {The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data.},
journal = {BMC bioinformatics},
volume = {15},
number = {},
pages = {44},
pmid = {24502833},
issn = {1471-2105},
mesh = {Classification/*methods ; DNA Barcoding, Taxonomic/*methods ; *Databases, Nucleic Acid ; Drugs, Chinese Herbal/classification ; Endangered Species/legislation &amp; jurisprudence ; Internationality ; Medicine, Chinese Traditional ; *Software ; },
abstract = {BACKGROUND: Mixtures of internationally traded organic substances can contain parts of species protected by the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). These mixtures often raise the suspicion of border control and customs offices, which can lead to confiscation, for example in the case of Traditional Chinese medicines (TCMs). High-throughput sequencing of DNA barcoding markers obtained from such samples provides insight into species constituents of mixtures, but manual cross-referencing of results against the CITES appendices is labor intensive. Matching DNA barcodes against NCBI GenBank using BLAST may yield misleading results both as false positives, due to incorrectly annotated sequences, and false negatives, due to spurious taxonomic re-assignment. Incongruence between the taxonomies of CITES and NCBI GenBank can result in erroneous estimates of illegal trade.<br><br>RESULTS: The HTS barcode checker pipeline is an application for automated processing of sets of 'next generation' barcode sequences to determine whether these contain DNA barcodes obtained from species listed on the CITES appendices. This analytical pipeline builds upon and extends existing open-source applications for BLAST matching against the NCBI GenBank reference database and for taxonomic name reconciliation. In a single operation, reads are converted into taxonomic identifications matched with names on the CITES appendices. By inclusion of a blacklist and additional names databases, the HTS barcode checker pipeline prevents false positives and resolves taxonomic heterogeneity.<br><br>CONCLUSIONS: The HTS barcode checker pipeline can detect and correctly identify DNA barcodes of CITES-protected species from reads obtained from TCM samples in just a few minutes. The pipeline facilitates and improves molecular monitoring of trade in endangered species, and can aid in safeguarding these species from extinction in the wild. The HTS barcode checker pipeline is available at https://github.com/naturalis/HTS-barcode-checker.},
}
@article {pmid24499562,
year = {2013},
author = {Ruiz-Lopez, F and Wilkerson, RC and Ponsonby, DJ and Herrera, M and Sallum, MA and Velez, ID and Quiñones, ML and Flores-Mendoza, C and Chadee, DD and Alarcon, J and Alarcon-Ormasa, J and Linton, YM},
title = {Systematics of the oswaldoi complex (Anopheles, Nyssorhynchus) in South America.},
journal = {Parasites &amp; vectors},
volume = {6},
number = {1},
pages = {324},
pmid = {24499562},
issn = {1756-3305},
support = {2R01AI054139/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Anopheles/*classification/genetics ; Cluster Analysis ; DNA, Ribosomal Spacer/chemistry/genetics ; Electron Transport Complex IV/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; South America ; },
abstract = {BACKGROUND: Effective malaria control relies on accurate identification of those Anopheles mosquitoes responsible for the transmission of Plasmodium parasites. Anopheles oswaldoi s.l. has been incriminated as a malaria vector in Colombia and some localities in Brazil, but not ubiquitously throughout its Neotropical range. This evidence together with variable morphological characters and genetic differences supports that An. oswaldoi s.l. compromises a species complex. The recent fully integrated redescription of An. oswaldoi s.s. provides a solid taxonomic foundation from which to molecularly determine other members of the complex.<br><br>METHODS: DNA sequences of the Second Internal Transcribed Spacer (ITS2 - rDNA) (n = 192) and the barcoding region of the Cytochrome Oxidase I gene (COI - mtDNA) (n = 110) were generated from 255 specimens of An. oswaldoi s.l. from 33 localities: Brazil (8 localities, including the lectotype series of An. oswaldoi), Ecuador (4), Colombia (17), Trinidad and Tobago (1), and Peru (3). COI sequences were analyzed employing the Kimura-two-parameter model (K2P), Bayesian analysis (MrBayes), Mixed Yule-Coalescent model (MYC, for delimitation of clusters) and TCS genealogies.<br><br>RESULTS: Separate and combined analysis of the COI and ITS2 data sets unequivocally supported four separate species: two previously determined (An. oswaldoi s.s. and An. oswaldoi B) and two newly designated species in the Oswaldoi Complex (An. oswaldoi A and An. sp. nr. konderi). The COI intra- and inter-specific genetic distances for the four taxa were non-overlapping, averaging 0.012 (0.007 to 0.020) and 0.052 (0.038 to 0.064), respectively. The concurring four clusters delineated by MrBayes and MYC, and four independent TCS networks, strongly confirmed their separate species status. In addition, An. konderi of Sallum should be regarded as unique with respect to the above. Despite initially being included as an outgroup taxon, this species falls well within the examined taxa, suggesting a combined analysis of these taxa would be most appropriate.<br><br>CONCLUSIONS: Through novel data and retrospective comparison of available COI and ITS2 DNA sequences, evidence is shown to support the separate species status of An. oswaldoi s.s., An. oswaldoi A and An. oswaldoi B, and at least two species in the closely related An. konderi complex (An. sp. nr. konderi, An. konderi of Sallum). Although An. oswaldoi s.s. has never been implicated in malaria transmission, An. oswaldoi B is a confirmed vector and the new species An. oswaldoi A and An. sp. nr. konderi are circumstantially implicated, most likely acting as secondary vectors.},
}
@article {pmid24498739,
year = {2013},
author = {Mech, AM and Asaro, C and Cram, MM and Coyle, DR and Gullan, PJ and Cook, LG and Gandhi, KJ},
title = {Matsucoccus macrocicatrices (Hemiptera: Matsucoccidae): first report, distribution, and association with symptomatic eastern white pine in the southeastern United States.},
journal = {Journal of economic entomology},
volume = {106},
number = {6},
pages = {2391-2398},
doi = {10.1603/ec13251},
pmid = {24498739},
issn = {0022-0493},
mesh = {Animals ; Appalachian Region ; Colony Count, Microbial ; Food Chain ; Forestry ; Fungi/classification/*physiology ; Genes, Insect ; Geography ; Hemiptera/classification/genetics/*physiology ; Molecular Sequence Data ; Pinus/growth &amp; development/*microbiology/*physiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/genetics/metabolism ; RNA, Ribosomal, 28S/genetics/metabolism ; Southeastern United States ; Symbiosis ; },
abstract = {We provide the first report of Matsucoccus macrocicatrices Richards (Hemiptera: Matsucoccidae) feeding and reproducing on eastern white pine, Pinus strobus L., in the southeastern United States. Until now, M. macrocicatrices had been reported only from the Canadian Atlantic Maritimes, New Hampshire, and Massachusetts. Entomological holdings of 27 major museums in eastern North America have no historical records for M. macrocicatrices from the southeastern region. However, our field surveys and molecular analyses (DNA barcoding) have resulted in the collection and positive identification of M. macrocicatrices in Georgia, North Carolina, South Carolina, Tennessee, Virginia, and West Virginia In addition to the new geographic range, M. macrocicatrices is also being associated with dieback and mortality of all diameter classes of P. strobus leading to concern about a potential shift from its historically nonpestiferous presence on the host tree. On P. strobus, M. macrocicatrices was found embedded in cankers or present on top of the bark with necrotic tissue under their feeding area, indicating that they may be creating wounds for opportunistic pathogenic fungi to infest. Further, we found M. macrocicatrices living outside of the epiphytic mats of its symbiotic fungus, Septobasidium pinicola Snell. This study shows that M. macrocicatrices is now widespread in the southeastern United States, with implications for the future survival and regeneration of P. strobus in eastern North America.},
}
@article {pmid24498724,
year = {2013},
author = {Evangelista, D and Buss, L and Ware, JL},
title = {Using DNA barcodes to confirm the presence of a new invasive cockroach pest in New York City.},
journal = {Journal of economic entomology},
volume = {106},
number = {6},
pages = {2275-2279},
doi = {10.1603/ec13402},
pmid = {24498724},
issn = {0022-0493},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics/metabolism ; Female ; *Introduced Species ; Male ; New York City ; Periplaneta/anatomy &amp; histology/*classification/*genetics ; Polymerase Chain Reaction ; },
abstract = {Recently, specimens of a Periplaneta sp. were discovered in New York, NY, that did not match the typical morphology of Periplaneta americana L., the ubiquitous American cockroach. Here, we used DNA barcoding and morphological identification to confirm that this newly invasive pest species was indeed Periplaneta japonica Karny, 1908. We discuss this recent invasion in light of known life history traits of this species, with specific predictions for its impact in the urban northeastern United States.},
}
@article {pmid24495171,
year = {2014},
author = {Song, T and Liu, J and Li, W and Li, Y and Yang, Q and Gong, X and Xuan, L and Chang, J},
title = {Self-healing encapsulation strategy for preparing highly stable, functionalized quantum-dot barcodes.},
journal = {ACS applied materials &amp; interfaces},
volume = {6},
number = {4},
pages = {2745-2752},
doi = {10.1021/am405285u},
pmid = {24495171},
issn = {1944-8252},
mesh = {*Electronic Data Processing ; Hydrogen-Ion Concentration ; Microscopy, Electron, Scanning ; Microspheres ; Polystyrenes/chemistry ; *Quantum Dots ; Spectrometry, Fluorescence ; alpha-Fetoproteins/analysis ; },
abstract = {Quantum dot (QD) barcodes are becoming an urgent requirement for researchers and clinicians to obtain high-density information in multiplexed suspension (bead-based) assay. However, how to improve the stability of quantum dot barcodes is a longstanding issue. Here, we present a new self-healing encapsulation strategy to generate functionalized uniform quantum dots barcodes with high physical and chemical stability. This efficient and facile strategy could make porous polymer microspheres self-heal to encapsulate QDs via the thermal motion and interaction of the molecular chains. Consequently, the new strategy solved especially the QDs leakage problem and improved the chemical stability under different pH physiological conditions as well as the longtime storage stability. In the meantime, the encoding capacity and the spatial distribution uniformity of quantum dots could be also improved. Furthermore, immunofluorescence assays for alpha fetoprotein (AFP) detections indicated that carboxyl groups on the surface of QD-encoded microspheres could facilitate efficient attachment of biomacromolecules.},
}
@article {pmid24493965,
year = {2014},
author = {Hosoishi, S and Ogata, K},
title = {Description and DNA barcoding of Crematogaster fraxatrix Forel, 1911 and two new closely related species from Cambodia and Indonesia (Hymenoptera, Formicidae).},
journal = {ZooKeys},
volume = {},
number = {374},
pages = {57-68},
pmid = {24493965},
issn = {1313-2989},
abstract = {Crematogaster fraxatrix Forel, 1911 and two new species, C. chhangi sp. n. and C. simboloni sp. n., are described from Cambodia and Indonesia, respectively. DNA sequences were generated for C. fraxarix and the two newly described species using 3 amplications of two regions of the mitochondrial gene COI with a total of 1129 bp. The mean interspecific divergences are 9.4% and 23.5% for C. fraxatrix vs. C. chhangi, C. simboloni, respectively. DNA sequences reveal that C. simboloni is found to be genetically distinct from the other two species, but C. chhangi is not distinct from C. fraxatrix.},
}
@article {pmid24493939,
year = {2013},
author = {Park, MS and Fong, JJ and Lee, H and Oh, SY and Jung, PE and Min, YJ and Seok, SJ and Lim, YW},
title = {Delimitation of russula subgenus amoenula in Korea using three molecular markers.},
journal = {Mycobiology},
volume = {41},
number = {4},
pages = {191-201},
pmid = {24493939},
issn = {1229-8093},
abstract = {Distinguishing individual Russula species has been difficult due to extensive phenotypic plasticity and obscure morphological and anatomical discontinuities. Due to highly similar macroscopic features, such as the presence of a red-cap, species identification within the Russula subgenus Amoenula is particularly difficult. Three species of the subgenus Amoneula have been reported in Korea. We used a combination of morphology and three molecular markers, the internal transcribed spacer (ITS), 28S nuclear ribosomal large subunit (LSU), and RNA polymerase II gene (RPB2), for identification and study of the genetic diversity of Russula subgenus Amoenula in Korea. We identified only two species in Korea (R. mariae and R. violeipes); these two species were indistinguishable according to morphology and LSU, but were found to be reciprocally monophyletic species using ITS and RPB2. The markers, ITS, LSU, and RPB2, have been tested in the past for use as DNA barcoding markers, and findings of our study suggest that ITS and RPB2 had the best performance for the Russula subgenus Amoneula.},
}
@article {pmid24491100,
year = {2015},
author = {Yang, C and Xiao, Z and Zou, Y and Zhang, X and Yang, B and Hao, Y and Moermond, T and Yue, B},
title = {DNA barcoding revises a misidentification on musk deer.},
journal = {Mitochondrial DNA},
volume = {26},
number = {4},
pages = {605-612},
doi = {10.3109/19401736.2014.880887},
pmid = {24491100},
issn = {1940-1744},
mesh = {Animals ; Base Sequence ; China ; Classification/methods ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*chemistry ; Deer/classification/*genetics ; Endangered Species ; Female ; Haplotypes ; Male ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Species Specificity ; },
abstract = {As an endangered animal group in China, musk deer (genus Moschus) have attracted the attention of deer biologists and wildlife conservationists. Clarifying the taxonomic status and distribution of musk deer species is important to determine the conservation status for each species and establish appropriate conservation strategies. There remains some uncertainty about the species determination of the musk deer in the Guandi Forest District of Shanxi Province, China. The musk deer in Shanxi would appear to represent an extension of the geographical distribution of either the Forest Musk Deer from the southwest or the Siberian Musk Deer from the northeast, or possibly both. The musk deer population in Shanxi Province provides an interesting and significant case to test the value of applying molecular methods to make a genetic species identification. In order to clarify the species status of the Shanxi musk deer, we sequenced 627 bp of the COI gene and ≈723 bp of the D-loop gene in 12 musk deer samples collected from the Guandi Forest District, and the two reference samples collected from Sichuan. Genetic analyses from the data suggest that all of the samples from the Guandi Forest District are M. berezovskii rather than M. moschiferus. It is most likely that the most previous studies had wrong species identification. And it is the first time we use DNA barcoding to prove that Shanxi is a new distribution of M. berezovskii.},
}
@article {pmid24490937,
year = {2014},
author = {Bineesh, KK and Akhilesh, KV and Gomon, MF and Abdussamad, EM and Pillai, NG and Gopalakrishnan, A},
title = {Redescription of Chlorophthalmus corniger, a senior synonym of Chlorophthalmus bicornis (Family: Chlorophthalmidae).},
journal = {Journal of fish biology},
volume = {84},
number = {2},
pages = {513-522},
doi = {10.1111/jfb.12305},
pmid = {24490937},
issn = {1095-8649},
mesh = {Animal Fins ; Animals ; Cypriniformes/anatomy &amp; histology/*classification ; DNA Barcoding, Taxonomic ; Indian Ocean ; Pigmentation ; },
abstract = {Chlorophthalmus corniger is redescribed on the basis of recently collected specimens. The species is redefined as a species of Chlorophthalmus with the lower jaw terminating in a distinctly projecting horizontal plate with strong, spine-like processes directed forward from the plate's corners; body silvery grey, with numerous minute black spots and traces of broad darker crossbars; base of anterior dorsal fin spines and distal parts of dorsal fins black; adipose fin tiny with numerous black spots; caudal fin black; 3·5 scales above lateral line; three rows of cheek scales; head very large, 34·3-40·1% standard length (LS); eye large, 29·8-40·8% head length (LH); pectoral fin long, extending to beyond dorsal fin base, 21·7-26·2% LS . Chlorophthalmus bicornis is a junior synonym of C. corniger based on the examination of the type series of both species. It is confined to the northern half of the Indian Ocean, reliably recorded from Somalia and the Gulf of Aden to southern Java, Indonesia, at depths between 200 and 500 m. A lectotype and three paralectotypes were designated for C. corniger. DNA barcodes for Indian species of Chlorophthalmus were generated.},
}
@article {pmid24486879,
year = {2014},
author = {Tarcz, S and Rautian, M and Potekhin, A and Sawka, N and Beliavskaya, A and Kiselev, A and Nekrasova, I and Przyboś, E},
title = {Paramecium putrinum (Ciliophora, Protozoa): the first insight into the variation of two DNA fragments - molecular support for the existence of cryptic species.},
journal = {Molecular phylogenetics and evolution},
volume = {73},
number = {},
pages = {140-145},
doi = {10.1016/j.ympev.2014.01.019},
pmid = {24486879},
issn = {1095-9513},
mesh = {DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Genome/genetics ; Haplotypes/genetics ; Paramecium/*classification/*genetics ; *Phylogeny ; Polymorphism, Genetic/*genetics ; Sequence Analysis, DNA ; },
abstract = {Paramecium putrinum (Claparede &amp; Lachmann 1858) is one of the smallest (80-140 μm long) species of the genus Paramecium. Although it commonly occurs in freshwater reservoirs, no molecular studies of P. putrinum have been conducted to date. Herein we present an assessment of molecular variation in 27 strains collected from widely separated populations by using two selected DNA fragments (ITS1-5.8S-ITS2-5'LSU rDNA and COI mtDNA). Both the trees and haplotype networks reconstructed for both genome fragments show that the studied strains of P. putrinum form five main haplogroups. The mean distance between the studied strains is p-distance=0.007/0.068 (rDNA/COI) and exhibits similar variability as that between P. bursaria syngens. Based on these data, one could hypothesize that the clusters revealed in the present study may correspond to previously reported syngens and that there are at least five cryptic species within P. putrinum.},
}
@article {pmid24484887,
year = {2014},
author = {Techen, N and Parveen, I and Pan, Z and Khan, IA},
title = {DNA barcoding of medicinal plant material for identification.},
journal = {Current opinion in biotechnology},
volume = {25},
number = {},
pages = {103-110},
doi = {10.1016/j.copbio.2013.09.010},
pmid = {24484887},
issn = {1879-0429},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*analysis/genetics ; Genetic Loci ; High-Throughput Nucleotide Sequencing ; Plants, Medicinal/*genetics ; Sequence Analysis, DNA ; },
abstract = {Because of the increasing demand for herbal remedies and for authentication of the source material, it is vital to provide a single database containing information about authentic plant materials and their potential adulterants. The database should provide DNA barcodes for data retrieval and similarity search. In order to obtain such barcodes, several molecular methods have been applied to develop markers that aid with the authentication and identification of medicinal plant materials. In this review, we discuss the genomic regions and molecular methods selected to provide barcodes, available databases and the potential future of barcoding using next generation sequencing.},
}
@article {pmid24479510,
year = {2014},
author = {Fan, L and Hui, JH and Yu, ZG and Chu, KH},
title = {VIP Barcoding: composition vector-based software for rapid species identification based on DNA barcoding.},
journal = {Molecular ecology resources},
volume = {14},
number = {4},
pages = {871-881},
doi = {10.1111/1755-0998.12235},
pmid = {24479510},
issn = {1755-0998},
mesh = {Algorithms ; Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; Multilocus Sequence Typing/methods ; Sensitivity and Specificity ; *Software ; },
abstract = {Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/.},
}
@article {pmid24479435,
year = {2014},
author = {Kekkonen, M and Hebert, PD},
title = {DNA barcode-based delineation of putative species: efficient start for taxonomic workflows.},
journal = {Molecular ecology resources},
volume = {14},
number = {4},
pages = {706-715},
pmid = {24479435},
issn = {1755-0998},
mesh = {Animals ; Cluster Analysis ; Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; Molecular Sequence Data ; Moths/*classification/*genetics ; Sequence Analysis, DNA ; Workflow ; },
abstract = {The analysis of DNA barcode sequences with varying techniques for cluster recognition provides an efficient approach for recognizing putative species (operational taxonomic units, OTUs). This approach accelerates and improves taxonomic workflows by exposing cryptic species and decreasing the risk of synonymy. This study tested the congruence of OTUs resulting from the application of three analytical methods (ABGD, BIN, GMYC) to sequence data for Australian hypertrophine moths. OTUs supported by all three approaches were viewed as robust, but 20% of the OTUs were only recognized by one or two of the methods. These OTUs were examined for three criteria to clarify their status. Monophyly and diagnostic nucleotides were both uninformative, but information on ranges was useful as sympatric sister OTUs were viewed as distinct, while allopatric OTUs were merged. This approach revealed 124 OTUs of Hypertrophinae, a more than twofold increase from the currently recognized 51 species. Because this analytical protocol is both fast and repeatable, it provides a valuable tool for establishing a basic understanding of species boundaries that can be validated with subsequent studies.},
}
@article {pmid24476916,
year = {2014},
author = {Cornils, K and Thielecke, L and Hüser, S and Forgber, M and Thomaschewski, M and Kleist, N and Hussein, K and Riecken, K and Volz, T and Gerdes, S and Glauche, I and Dahl, A and Dandri, M and Roeder, I and Fehse, B},
title = {Multiplexing clonality: combining RGB marking and genetic barcoding.},
journal = {Nucleic acids research},
volume = {42},
number = {7},
pages = {e56},
pmid = {24476916},
issn = {1362-4962},
mesh = {Animals ; Cells, Cultured ; Clone Cells ; Female ; Genetic Vectors ; HEK293 Cells ; Humans ; Leukemia/genetics ; Liver Regeneration ; Luminescent Proteins/genetics ; Male ; Mice ; Mice, Inbred BALB C ; Polymerase Chain Reaction ; Receptor, trkA/genetics ; Sequence Analysis, DNA ; Single-Cell Analysis/*methods ; Transduction, Genetic ; },
abstract = {RGB marking and DNA barcoding are two cutting-edge technologies in the field of clonal cell marking. To combine the virtues of both approaches, we equipped LeGO vectors encoding red, green or blue fluorescent proteins with complex DNA barcodes carrying color-specific signatures. For these vectors, we generated highly complex plasmid libraries that were used for the production of barcoded lentiviral vector particles. In proof-of-principle experiments, we used barcoded vectors for RGB marking of cell lines and primary murine hepatocytes. We applied single-cell polymerase chain reaction to decipher barcode signatures of individual RGB-marked cells expressing defined color hues. This enabled us to prove clonal identity of cells with one and the same RGB color. Also, we made use of barcoded vectors to investigate clonal development of leukemia induced by ectopic oncogene expression in murine hematopoietic cells. In conclusion, by combining RGB marking and DNA barcoding, we have established a novel technique for the unambiguous genetic marking of individual cells in the context of normal regeneration as well as malignant outgrowth. Moreover, the introduction of color-specific signatures in barcodes will facilitate studies on the impact of different variables (e.g. vector type, transgenes, culture conditions) in the context of competitive repopulation studies.},
}
@article {pmid24475157,
year = {2014},
author = {Stampar, SN and Maronna, MM and Kitahara, MV and Reimer, JD and Morandini, AC},
title = {Fast-evolving mitochondrial DNA in Ceriantharia: a reflection of hexacorallia paraphyly?.},
journal = {PloS one},
volume = {9},
number = {1},
pages = {e86612},
pmid = {24475157},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/genetics ; *Evolution, Molecular ; *Genetic Variation ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Sea Anemones/*classification/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The low evolutionary rate of mitochondrial genes in Anthozoa has challenged their utility for phylogenetic and systematic purposes, especially for DNA barcoding. However, the evolutionary rate of Ceriantharia, one of the most enigmatic "orders" within Anthozoa, has never been specifically examined. In this study, the divergence of mitochondrial DNA of Ceriantharia was compared to members of other Anthozoa and Medusozoa groups. In addition, nuclear markers were used to check the relative phylogenetic position of Ceriantharia in relation to other Cnidaria members. The results demonstrated a pattern of divergence of mitochondrial DNA completely different from those estimated for other anthozoans, and phylogenetic analyses indicate that Ceriantharia is not included within hexacorallians in most performed analyses. Thus, we propose that the Ceriantharia should be addressed as a separate clade.},
}
@article {pmid24474037,
year = {2014},
author = {Dimitrov, D and Zehtindjiev, P and Bensch, S and Ilieva, M and Iezhova, T and Valkiūnas, G},
title = {Two new species of Haemoproteus Kruse, 1890 (Haemosporida, Haemoproteidae) from European birds, with emphasis on DNA barcoding for detection of haemosporidians in wildlife.},
journal = {Systematic parasitology},
volume = {87},
number = {2},
pages = {135-151},
pmid = {24474037},
issn = {1573-5192},
mesh = {Animals ; Birds/*parasitology ; Bulgaria ; Cytochromes b/genetics ; DNA Barcoding, Taxonomic/*standards ; *Haemosporida/classification/cytology/genetics ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; },
abstract = {Two new species of Haemoproteus Kruse, 1890 (Haemosporida, Haemoproteidae) are described: Haemoproteus (Parahaemoproteus) homovelans n. sp. from Grey-faced Woodpecker, Picus canus Gmelin, and Haemoproteus (Parahaemoproteus) concavocentralis n. sp. recorded in Hawfinch, Coccothraustes coccothraustes (Linnaeus), both sampled in Bulgaria. The morphology of the gametocytes and their host-cells are described and mitochondrial cytochrome b (cyt b) gene sequences are generated. Haemoproteus homovelans possesses circumnuclear gametocytes lacking volutin granules. This parasite is particularly similar to Haemoproteus velans Coatney &amp; Roudabush, 1937 also possessing circumnuclear gametocytes that are, however, overfilled with volutin. Haemoproteus concavocentralis can be readily distinguished from all described avian haemoproteids due to the presence of an unfilled concave space between the central part of advanced gametocytes and erythrocyte nucleus. Bayesian phylogenetic analyses of 40 haemosporidian cyt b lineages showed close relationships of H. concavocentralis (hHAWF2) with a group of Haemoproteus spp. possessing gametocytes that are pale-stained with Giemsa. The lineage hPICAN02 of H. homovelans clustered with parasites infecting non-passerine birds. Phylogenetic analyses support the current subgeneric classification of the avian haemoproteids and suggest that cyt b lineage hPIPUB01 (GenBank EU254552) has been incorrectly assigned to Haemoproteus picae Coatney &amp; Roudabush, 1937, a common parasite of corvid birds (Passeriformes). This study emphasises the importance of combining molecular techniques and light microscopy in the identification and field studies of avian haemosporidian parasites. Future development of barcodes for molecular identification of haemoproteids will allow better diagnostics of these infections, particularly in veterinary studies addressing insufficiently investigated tissue pathology caused by these parasites.},
}
@article {pmid24473810,
year = {2013},
author = {Laurito, M and Oliveira, TM and Almirón, WR and Sallum, MA},
title = {COI barcode versus morphological identification of Culex (Culex) (Diptera: Culicidae) species: a case study using samples from Argentina and Brazil.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {108 Suppl 1},
number = {Suppl 1},
pages = {110-122},
pmid = {24473810},
issn = {1678-8060},
mesh = {Algorithms ; Animal Identification Systems/*statistics &amp; numerical data ; Animals ; Argentina ; Brazil ; Classification/*methods ; Cluster Analysis ; Culex/*anatomy &amp; histology/classification/*genetics ; DNA Barcoding, Taxonomic/*statistics &amp; numerical data ; Electron Transport Complex IV/*genetics ; Polymerase Chain Reaction ; },
abstract = {Sequences of the cytochrome c oxidase subunit I (COI) mitochondrial gene from adults of 22 Culex (Culex) species from Argentina and Brazil were employed to assess species identification and to test the usefulness of COI for barcoding using the best close match (BCM) algorithm. A pairwise Kimura two-parameter distance matrix including the mean intra and interspecific distances for 71 COI barcode sequences was constructed. Of the 12 COI lineages recovered in the Neighbour-joining topology, five confirmed recognised morphological species (Cx. acharistus, Cx. chidesteri, Cx. dolosus, Cx. lygrus and Cx. saltanensis) with intraspecific divergences lower than 1.75%. Cx. bilineatus is formally resurrected from the synonymy of Cx. dolosus. Cx. maxi , Cx. surinamensis and the Coronator group species included were clustered into an unresolved lineage. The intraspecific distance of Cx. pipiens (3%) was almost twice the interspecific between it and Cx. quinquefasciatus (1.6%). Regarding the BCM criteria, the COI barcode successfully identified 69% of all species. The rest of the sequences, approximately 10%, 18% and 3%, remained as ambiguously, mis and unidentified, respectively. The COI barcode does not contain enough information to distinguish Culex (Cux.) species.},
}
@article {pmid24473809,
year = {2013},
author = {Linton, YM and Pecor, JE and Porter, CH and Mitchell, LB and Garzón-Moreno, A and Foley, DH and Pecor, DB and Wilkerson, RC},
title = {Mosquitoes of eastern Amazonian Ecuador: biodiversity, bionomics and barcodes.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {108 Suppl 1},
number = {Suppl 1},
pages = {100-109},
pmid = {24473809},
issn = {1678-8060},
mesh = {Animals ; *Biodiversity ; Culicidae/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; Ecology/*classification ; Ecuador ; Electron Transport Complex IV/*genetics ; Oviposition ; Polymerase Chain Reaction ; Rainforest ; },
abstract = {Two snapshot surveys to establish the diversity and ecological preferences of mosquitoes (Diptera: Culicidae) in the terra firme primary rain forest surrounding the Tiputini Biodiversity Station in the UNESCO Yasuní Biosphere Reserve of eastern Amazonian Ecuador were carried out in November 1998 and May 1999. The mosquito fauna of this region is poorly known; the focus of this study was to obtain high quality link-reared specimens that could be used to unequivocally confirm species level diversity through integrated systematic study of all life stages and DNA sequences. A total of 2,284 specimens were preserved; 1,671 specimens were link-reared with associated immature exuviae, all but 108 of which are slide mounted. This study identified 68 unique taxa belonging to 17 genera and 27 subgenera. Of these, 12 are new to science and 37 comprise new country records. DNA barcodes [658-bp of the mtDNA cytochrome c oxidase (COI) I gene] are presented for 58 individuals representing 20 species and nine genera. DNA barcoding proved useful in uncovering and confirming new species and we advocate an integrated systematics approach to biodiversity studies in future. Associated bionomics of all species collected are discussed. An updated systematic checklist of the mosquitoes of Ecuador (n=179) is presented for the first time in 60 years.},
}
@article {pmid24471981,
year = {2014},
author = {Zhukovskyi, M and Sanchez-Botero, L and McDonald, MP and Hinestroza, J and Kuno, M},
title = {Nanowire-functionalized cotton textiles.},
journal = {ACS applied materials &amp; interfaces},
volume = {6},
number = {4},
pages = {2262-2269},
doi = {10.1021/am4052602},
pmid = {24471981},
issn = {1944-8252},
abstract = {We show the general functionalization of cotton fabrics using solution-synthesized CdSe and CdTe nanowires (NWs). Conformal coatings onto individual cotton fibers have been achieved through various physical and chemical approaches. Some involve the electrostatic attraction of NWs to cotton charged positively with a Van de Graaff generator or via 2,3-epoxypropyltrimethylammonium chloride treatments. Resulting NW-functionalized textiles consist of dense, conformal coatings and have been characterized for their UV-visible absorption as well as Raman activity. We demonstrate potential uses of these functionalized textiles through two proof-of-concept applications. The first entails barcoding cotton using the unique Raman signature of the NWs. We also demonstrate the surface-enhancement of their Raman signatures using codeposited Au. A second demonstration takes advantage of the photoconductive nature of semiconductor NWs to create cotton-based photodetectors. Apart from these illustrations, NW-functionalized cotton textiles may possess other uses in the realm of medical, anticounterfeiting, and photocatalytic applications.},
}
@article {pmid24470287,
year = {2014},
author = {Hyun, DC and Levinson, NS and Jeong, U and Xia, Y},
title = {Emerging applications of phase-change materials (PCMs): teaching an old dog new tricks.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {53},
number = {15},
pages = {3780-3795},
doi = {10.1002/anie.201305201},
pmid = {24470287},
issn = {1521-3773},
support = {DP1 OD000798/OD/NIH HHS/United States ; },
mesh = {Drug Delivery Systems ; Equipment Design/*instrumentation ; Technology/*instrumentation/methods ; },
abstract = {The nebulous term phase-change material (PCM) simply refers to any substance that has a large heat of fusion and a sharp melting point. PCMs have been used for many years in commercial applications, mainly for heat management purposes. However, these fascinating materials have recently been rediscovered and applied to a broad range of technologies, such as smart drug delivery, information storage, barcoding, and detection. With the hope of kindling interest in this incredibly versatile range of materials, this Review presents an array of aspects related to the compositions, preparations, and emerging applications of PCMs.},
}
@article {pmid24467909,
year = {2014},
author = {Poirier, P and Meloni, D and Nourrisson, C and Wawrzyniak, I and Viscogliosi, E and Livrelli, V and Delbac, F},
title = {Molecular subtyping of Blastocystis spp. using a new rDNA marker from the mitochondria-like organelle genome.},
journal = {Parasitology},
volume = {141},
number = {5},
pages = {670-681},
doi = {10.1017/S0031182013001996},
pmid = {24467909},
issn = {1469-8161},
mesh = {Animals ; Base Sequence ; Blastocystis/*classification/genetics/isolation &amp; purification ; Blastocystis Infections/*parasitology ; Coinfection ; DNA Barcoding, Taxonomic ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genetic Markers/genetics ; Genome, Protozoan/*genetics ; Genotype ; Humans ; Mitochondria/genetics ; Molecular Sequence Data ; Molecular Typing ; Organelles/genetics ; Phylogeny ; *Polymorphism, Genetic ; RNA, Ribosomal, 18S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Blastocystis spp. are common anaerobic intestinal protozoa found in both human and animals. They are characterized by a high genetic diversity with at least 17 subtypes (STs) that have been described on the basis of a 600 bp 'barcoding region' from the 18S rDNA gene. However, analysis of the recently sequenced genome of a Blastocystis ST7 isolate (strain B) revealed the presence of multiple variable copies of the 18S rDNA gene, with 17 completely assembled copies. Comparison of the barcoding region from these 17 copies allowed us to classify the 18S rDNA sequences into 6 clusters, each cluster containing identical sequences. Surprisingly, 4 of these clusters had the highest homology with 18S rDNA sequences from 2 other Blastocystis ST7 isolates referred as QQ98-4 and H. These results suggest that the 18S rDNA gene is not the marker of choice to discriminate between strains within STs. In the present study, we identified a single-copy subtyping rDNA marker in the genome of the mitochondria-like organelles (MLOs). Using a partial sequence of the MLO rDNA, we successfully subtyped 66 isolates from both human and animals belonging to Blastocystis ST1 to ST10. Our results also indicate that this mitochondrial marker could be useful to detect co-infections by different isolates of a same ST.},
}
@article {pmid24465470,
year = {2014},
author = {Gutiérrez-Aguirre, MA and Cervantes-Martínez, A and Elías-Gutiérrez, M},
title = {An example of how barcodes can clarify cryptic species: the case of the calanoid copepod Mastigodiaptomus albuquerquensis (Herrick).},
journal = {PloS one},
volume = {9},
number = {1},
pages = {e85019},
pmid = {24465470},
issn = {1932-6203},
mesh = {Altitude ; Animal Distribution ; Animals ; Copepoda/*classification/*genetics/ultrastructure ; DNA Barcoding, Taxonomic/*statistics &amp; numerical data ; Female ; Genetic Markers ; Genetic Variation ; Lakes ; Male ; Mexico ; *Phylogeny ; },
abstract = {BACKGROUND: The freshwater calanoid Mastigodiaptomus is a genus with high richness in the Americas and is composed of nine species, seven recorded in Mexico and four that are apparently endemic to small areas. Mastigodiaptomus albuquerquensis is a common, widely distributed species ranging from the southern USA to Central America. This species can be easily identified by a notable butterfly-like sclerotization on the basis of the right fifth leg of males. Nevertheless, morphological differences observed among populations throughout this species distributional range have led to the description of several related species or subspecies, such as M. albuquerquensis patzcuarensis from Lake Pátzcuaro in the Central Plateau of Mexico.<br><br>METHODS: Genetic results based on barcodes, morphology based on scanning electron and light microscopy images, and morphometric analyses were used to describe cryptic species within the M. albuquerquensis complex.<br><br>RESULTS: The morphological analyses coincided partially with the genetic markers, suggesting the existence of at least two sibling species: M. albuquerquensis s. str. and M. patzcuarensis. A third species was genetically separated but was morphologically indistinguishable from the M. patzcuarensis group.<br><br>CONCLUSIONS: Hidden diversity has been a major problem in establishing real patterns of species distribution and genetic acquisition from megadiverse hotspots such as Mexico, where the Nearctic and the Neotropical regions of the Americas meet. Barcodes can help taxonomists to reveal and formally name these new species. Here, we describe two of three potential species highlighted by the use of barcodes: M. albuquerquensis s. str. in the northern semi-desert and M. patzcuarensis on the Central Plateau at more than 2000 m above sea level.},
}
@article {pmid24464997,
year = {2014},
author = {LaFave, MC and Varshney, GK and Gildea, DE and Wolfsberg, TG and Baxevanis, AD and Burgess, SM},
title = {MLV integration site selection is driven by strong enhancers and active promoters.},
journal = {Nucleic acids research},
volume = {42},
number = {7},
pages = {4257-4269},
pmid = {24464997},
issn = {1362-4962},
support = {//Intramural NIH HHS/United States ; },
mesh = {*Attachment Sites, Microbiological ; Cell Line, Tumor ; *Enhancer Elements, Genetic ; Humans ; K562 Cells ; Moloney murine leukemia virus/*physiology ; *Promoter Regions, Genetic ; *Virus Integration ; },
abstract = {Retroviruses integrate into the host genome in patterns specific to each virus. Understanding the causes of these patterns can provide insight into viral integration mechanisms, pathology and genome evolution, and is critical to the development of safe gene therapy vectors. We generated murine leukemia virus integrations in human HepG2 and K562 cells and subjected them to second-generation sequencing, using a DNA barcoding technique that allowed us to quantify independent integration events. We characterized >3,700,000 unique integration events in two ENCODE-characterized cell lines. We find that integrations were most highly enriched in a subset of strong enhancers and active promoters. In both cell types, approximately half the integrations were found in <2% of the genome, demonstrating genomic influences even narrower than previously believed. The integration pattern of murine leukemia virus appears to be largely driven by regions that have high enrichment for multiple marks of active chromatin; the combination of histone marks present was sufficient to explain why some strong enhancers were more prone to integration than others. The approach we used is applicable to analyzing the integration pattern of any exogenous element and could be a valuable preclinical screen to evaluate the safety of gene therapy vectors.},
}
@article {pmid24462779,
year = {2014},
author = {Penon, O and Siapkas, D and Novo, S and Durán, S and Oncins, G and Errachid, A and Barrios, L and Nogués, C and Duch, M and Plaza, JA and Pérez-García, L},
title = {Optimized immobilization of lectins using self-assembled monolayers on polysilicon encoded materials for cell tagging.},
journal = {Colloids and surfaces. B, Biointerfaces},
volume = {116},
number = {},
pages = {104-113},
doi = {10.1016/j.colsurfb.2013.12.053},
pmid = {24462779},
issn = {1873-4367},
mesh = {Animals ; Cell Adhesion ; Cell Membrane/chemistry ; Lectins/*chemistry ; Mice ; Polymers/chemical synthesis/*chemistry ; Silicon/*chemistry ; Surface Properties ; },
abstract = {Self-assembled monolayers (SAMs) have been used for the preparation of functional microtools consisting of encoded polysilicon barcodes biofunctionalized with proteins of the lectin family. These hybrid microtools exploit the lectins ability for recognizing specific carbohydrates of the cell membrane to give an efficient system for cell tagging. This work describes how the control of the methodology for SAM formation on polysilicon surfaces followed by lectin immobilization has a crucial influence on the microtool biofunction. Several parameters (silanization time, silane molar concentration, type of solvent or deposition methodology) have been studied to establish optimal function. Furthermore, silanes incorporating different terminal groups, such as aldehyde, activated ester or epoxide groups were tested in order to analyze their chemical coupling with the biomolecules, as well as their influence on the biofunctionality of the immobilized protein. Two different lectins - wheat germ agglutinin (WGA) and phytohemagglutinin (PHA-L) - were immobilized, because they have different and specific cell recognition behaviour and exhibit different cell toxicity. In this way we can assess the effect of intrinsic bulk toxicity with that of the cell compatibility once immobilized as well as the importance of cell affinity. A variety of nanometrical techniques were used to characterize the active surfaces, and lectin immobilization was quantified using ultraviolet-visible absorption spectroscopy (UV-vis) and optical waveguide light mode spectroscopy (OWLS). Once the best protocol was found, WGA and PHA were immobilized on polysilicon coded barcodes, and these microtools showed excellent cell tagging on living mouse embryos when WGA was used.},
}
@article {pmid24460871,
year = {2014},
author = {Clarke, AC and Prost, S and Stanton, JA and White, WT and Kaplan, ME and Matisoo-Smith, EA and , },
title = {From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes.},
journal = {BMC genomics},
volume = {15},
number = {},
pages = {68},
pmid = {24460871},
issn = {1471-2164},
mesh = {Computational Biology/*methods ; DNA, Mitochondrial/*analysis/isolation &amp; purification ; *Genome, Mitochondrial ; *High-Throughput Nucleotide Sequencing ; Humans ; Mitochondria/*genetics ; Polymerase Chain Reaction ; Specimen Handling ; },
abstract = {BACKGROUND: Next-generation DNA sequencing (NGS) technologies have made huge impacts in many fields of biological research, but especially in evolutionary biology. One area where NGS has shown potential is for high-throughput sequencing of complete mtDNA genomes (of humans and other animals). Despite the increasing use of NGS technologies and a better appreciation of their importance in answering biological questions, there remain significant obstacles to the successful implementation of NGS-based projects, especially for new users.<br><br>RESULTS: Here we present an 'A to Z' protocol for obtaining complete human mitochondrial (mtDNA) genomes - from DNA extraction to consensus sequence. Although designed for use on humans, this protocol could also be used to sequence small, organellar genomes from other species, and also nuclear loci. This protocol includes DNA extraction, PCR amplification, fragmentation of PCR products, barcoding of fragments, sequencing using the 454 GS FLX platform, and a complete bioinformatics pipeline (primer removal, reference-based mapping, output of coverage plots and SNP calling).<br><br>CONCLUSIONS: All steps in this protocol are designed to be straightforward to implement, especially for researchers who are undertaking next-generation sequencing for the first time. The molecular steps are scalable to large numbers (hundreds) of individuals and all steps post-DNA extraction can be carried out in 96-well plate format. Also, the protocol has been assembled so that individual 'modules' can be swapped out to suit available resources.},
}
@article {pmid24458480,
year = {2014},
author = {Yang, GX and Zhuang, HS and Chen, HY and Ping, XY and Bu, D},
title = {A sensitive immunosorbent bio-barcode assay based on real-time immuno-PCR for detecting 3,4,3',4'-tetrachlorobiphenyl.},
journal = {Analytical and bioanalytical chemistry},
volume = {406},
number = {6},
pages = {1693-1700},
doi = {10.1007/s00216-013-7583-9},
pmid = {24458480},
issn = {1618-2650},
mesh = {Animals ; Antibodies, Anti-Idiotypic/chemistry/immunology ; Antibodies, Immobilized/chemistry/immunology ; DNA/chemistry ; Environmental Monitoring/*methods ; Gold/*chemistry ; Immunoassay/methods ; Immunoglobulin G/immunology ; Immunosorbents/chemistry ; Limit of Detection ; Nanoparticles/*chemistry ; Perciformes/metabolism ; Polychlorinated Biphenyls/*analysis ; Rabbits ; Real-Time Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; Sulfhydryl Compounds/chemistry ; Water Pollutants, Chemical/*analysis ; },
abstract = {A functionalized gold-nanoparticle bio-barcode assay, based on real-time immuno-PCR (IPCR), was designed for the determination of 3,4,3',4'-tetrachlorobiphenyl (PCB77). 15 nm gold nanoparticles were synthesized, and modified with thiol-capped DNA and goat anti-rabbit IgG. The nanoparticle probes were used to replace antibody-DNA conjugate in the IPCR, and were fixed on the PCR tube wall via the immune reaction. Real-time PCR was performed to quantify the DNA signal directly. Under optimized conditions, the new method was used to detect PCB77 with a linearity range from 5 pg L(-1) to 10 ng L(-1), and the limit of detection (LOD) was 1.72 pg L(-1). Real samples of Larimichthys polyactis, collected from the East China Sea, were analyzed. Recovery was from 82 % to 112 %, and the coefficient of variation (CV) was acceptable. The results were compared with GC-ECD, revealing that the method would be acceptable for providing rapid, semi-quantitative, and reliable test results for making environmental decisions.},
}
@article {pmid24454877,
year = {2014},
author = {Contreras Gutiérrez, MA and Vivero, RJ and Vélez, ID and Porter, CH and Uribe, S},
title = {DNA barcoding for the identification of sand fly species (Diptera, Psychodidae, Phlebotominae) in Colombia.},
journal = {PloS one},
volume = {9},
number = {1},
pages = {e85496},
pmid = {24454877},
issn = {1932-6203},
mesh = {Animals ; Colombia ; *DNA Barcoding, Taxonomic ; Diptera/classification/*genetics ; Electron Transport Complex IV/genetics ; Species Specificity ; },
abstract = {Sand flies include a group of insects that are of medical importance and that vary in geographic distribution, ecology, and pathogen transmission. Approximately 163 species of sand flies have been reported in Colombia. Surveillance of the presence of sand fly species and the actualization of species distribution are important for predicting risks for and monitoring the expansion of diseases which sand flies can transmit. Currently, the identification of phlebotomine sand flies is based on morphological characters. However, morphological identification requires considerable skills and taxonomic expertise. In addition, significant morphological similarity between some species, especially among females, may cause difficulties during the identification process. DNA-based approaches have become increasingly useful and promising tools for estimating sand fly diversity and for ensuring the rapid and accurate identification of species. A partial sequence of the mitochondrial cytochrome oxidase gene subunit I (COI) is currently being used to differentiate species in different animal taxa, including insects, and it is referred as a barcoding sequence. The present study explored the utility of the DNA barcode approach for the identification of phlebotomine sand flies in Colombia. We sequenced 700 bp of the COI gene from 36 species collected from different geographic localities. The COI barcode sequence divergence within a single species was <2% in most cases, whereas this divergence ranged from 9% to 26.6% among different species. These results indicated that the barcoding gene correctly discriminated among the previously morphologically identified species with an efficacy of nearly 100%. Analyses of the generated sequences indicated that the observed species groupings were consistent with the morphological identifications. In conclusion, the barcoding gene was useful for species discrimination in sand flies from Colombia.},
}
@article {pmid24453567,
year = {2013},
author = {Vanhove, MP and Tessens, B and Schoelinck, C and Jondelius, U and Littlewood, DT and Artois, T and Huyse, T},
title = {Problematic barcoding in flatworms: A case-study on monogeneans and rhabdocoels (Platyhelminthes).},
journal = {ZooKeys},
volume = {},
number = {365},
pages = {355-379},
pmid = {24453567},
issn = {1313-2989},
abstract = {Some taxonomic groups are less amenable to mitochondrial DNA barcoding than others. Due to the paucity of molecular information of understudied groups and the huge molecular diversity within flatworms, primer design has been hampered. Indeed, all attempts to develop universal flatworm-specific COI markers have failed so far. We demonstrate how high molecular variability and contamination problems limit the possibilities for barcoding using standard COI-based protocols in flatworms. As a consequence, molecular identification methods often rely on other widely applicable markers. In the case of Monogenea, a very diverse group of platyhelminth parasites, and Rhabdocoela, representing one-fourth of all free-living flatworm taxa, this has led to a relatively high availability of nuclear ITS and 18S/28S rDNA sequences on GenBank. In a comparison of the effectiveness in species assignment we conclude that mitochondrial and nuclear ribosomal markers perform equally well. In case intraspecific information is needed, rDNA sequences can guide the selection of the appropriate (i.e. taxon-specific) COI primers if available.},
}
@article {pmid24453566,
year = {2013},
author = {Van Der Bank, H and Herbert, D and Greenfield, R and Yessoufou, K},
title = {Revisiting species delimitation within the genus Oxystele using DNA barcoding approach.},
journal = {ZooKeys},
volume = {},
number = {365},
pages = {337-354},
pmid = {24453566},
issn = {1313-2989},
abstract = {The genus Oxystele, a member of the highly diverse marine gastropod superfamily Trochoidea, is endemic to southern Africa. Members of the genus include some of the most abundant molluscs on southern African shores and are important components of littoral biodiversity in rocky intertidal habitats. Species delimitation within the genus is still controversial, especially regarding the complex O. impervia / O. variegata. Here, we assessed species boundaries within the genus using DNA barcoding and phylogenetic tree reconstruction. We analysed 56 specimens using the mitochondrial gene COI. Our analysis delimits five molecular operational taxonomic units (MOTUs), and distinguishes O. impervia from O. variegata. However, we reveal important discrepancies between MOTUs and morphology-based species identification and discuss alternative hypotheses that can account for this. Finally, we indicate the need for future study that includes additional genes, and the combination of both morphology and genetic techniques (e.g. AFLP or microsatellites) to get deeper insight into species delimitation within the genus.},
}
@article {pmid24453565,
year = {2013},
author = {Sonet, G and Jordaens, K and Nagy, ZT and Breman, FC and De Meyer, M and Backeljau, T and Virgilio, M},
title = {Adhoc: an R package to calculate ad hoc distance thresholds for DNA barcoding identification.},
journal = {ZooKeys},
volume = {},
number = {365},
pages = {329-336},
pmid = {24453565},
issn = {1313-2989},
abstract = {Identification by DNA barcoding is more likely to be erroneous when it is based on a large distance between the query (the barcode sequence of the specimen to identify) and its best match in a reference barcode library. The number of such false positive identifications can be decreased by setting a distance threshold above which identification has to be rejected. To this end, we proposed recently to use an ad hoc distance threshold producing identifications with an estimated relative error probability that can be fixed by the user (e.g. 5%). Here we introduce two R functions that automate the calculation of ad hoc distance thresholds for reference libraries of DNA barcodes. The scripts of both functions, a user manual and an example file are available on the JEMU website (http://jemu.myspecies.info/computer-programs) as well as on the comprehensive R archive network (CRAN, http://cran.r-project.org).},
}
@article {pmid24453564,
year = {2013},
author = {Sonet, G and Jordaens, K and Braet, Y and Bourguignon, L and Dupont, E and Backeljau, T and De Meyer, M and Desmyter, S},
title = {Utility of GenBank and the Barcode of Life Data Systems (BOLD) for the identification of forensically important Diptera from Belgium and France.},
journal = {ZooKeys},
volume = {},
number = {365},
pages = {307-328},
pmid = {24453564},
issn = {1313-2989},
abstract = {Fly larvae living on dead corpses can be used to estimate post-mortem intervals. The identification of these flies is decisive in forensic casework and can be facilitated by using DNA barcodes provided that a representative and comprehensive reference library of DNA barcodes is available. We constructed a local (Belgium and France) reference library of 85 sequences of the COI DNA barcode fragment (mitochondrial cytochrome c oxidase subunit I gene), from 16 fly species of forensic interest (Calliphoridae, Muscidae, Fanniidae). This library was then used to evaluate the ability of two public libraries (GenBank and the Barcode of Life Data Systems - BOLD) to identify specimens from Belgian and French forensic cases. The public libraries indeed allow a correct identification of most specimens. Yet, some of the identifications remain ambiguous and some forensically important fly species are not, or insufficiently, represented in the reference libraries. Several search options offered by GenBank and BOLD can be used to further improve the identifications obtained from both libraries using DNA barcodes.},
}
@article {pmid24453563,
year = {2013},
author = {Smit, J and Reijnen, B and Stokvis, F},
title = {Half of the European fruit fly species barcoded (Diptera, Tephritidae); a feasibility test for molecular identification.},
journal = {ZooKeys},
volume = {},
number = {365},
pages = {279-305},
pmid = {24453563},
issn = {1313-2989},
abstract = {A FEASIBILITY TEST OF MOLECULAR IDENTIFICATION OF EUROPEAN FRUIT FLIES (DIPTERA: Tephritidae) based on COI barcode sequences has been executed. A dataset containing 555 sequences of 135 ingroup species from three subfamilies and 42 genera and one single outgroup species has been analysed. 73.3% of all included species could be identified based on their COI barcode gene, based on similarity and distances. The low success rate is caused by singletons as well as some problematic groups: several species groups within the genus Terellia and especially the genus Urophora. With slightly more than 100 sequences - almost 20% of the total - this genus alone constitutes the larger part of the failure for molecular identification for this dataset. Deleting the singletons and Urophora results in a success-rate of 87.1% of all queries and 93.23% of the not discarded queries as correctly identified. Urophora is of special interest due to its economic importance as beneficial species for weed control, therefore it is desirable to have alternative markers for molecular identification. We demonstrate that the success of DNA barcoding for identification purposes strongly depends on the contents of the database used to BLAST against. Especially the necessity of including multiple specimens per species of geographically distinct populations and different ecologies for the understanding of the intra- versus interspecific variation is demonstrated. Furthermore thresholds and the distinction between true and false positives and negatives should not only be used to increase the reliability of the success of molecular identification but also to point out problematic groups, which should then be flagged in the reference database suggesting alternative methods for identification.},
}
@article {pmid24453562,
year = {2013},
author = {Nagy, ZT and Sonet, G and Mortelmans, J and Vandewynkel, C and Grootaert, P},
title = {Using DNA barcodes for assessing diversity in the family Hybotidae (Diptera, Empidoidea).},
journal = {ZooKeys},
volume = {},
number = {365},
pages = {263-278},
pmid = {24453562},
issn = {1313-2989},
abstract = {Empidoidea is one of the largest extant lineages of flies, but phylogenetic relationships among species of this group are poorly investigated and global diversity remains scarcely assessed. In this context, one of the most enigmatic empidoid families is Hybotidae. Within the framework of a pilot study, we barcoded 339 specimens of Old World hybotids belonging to 164 species and 22 genera (plus two Empis as outgroups) and attempted to evaluate whether patterns of intra- and interspecific divergences match the current taxonomy. We used a large sampling of diverse Hybotidae. The material came from the Palaearctic (Belgium, France, Portugal and Russian Caucasus), the Afrotropic (Democratic Republic of the Congo) and the Oriental realms (Singapore and Thailand). Thereby, we optimized lab protocols for barcoding hybotids. Although DNA barcodes generally well distinguished recognized taxa, the study also revealed a number of unexpected phenomena: e.g., undescribed taxa found within morphologically very similar or identical specimens, especially when geographic distance was large; some morphologically distinct species showed no genetic divergence; or different pattern of intraspecific divergence between populations or closely related species. Using COI sequences and simple Neighbour-Joining tree reconstructions, the monophyly of many species- and genus-level taxa was well supported, but more inclusive taxonomical levels did not receive significant bootstrap support. We conclude that in hybotids DNA barcoding might be well used to identify species, when two main constraints are considered. First, incomplete barcoding libraries hinder efficient (correct) identification. Therefore, extra efforts are needed to increase the representation of hybotids in these databases. Second, the spatial scale of sampling has to be taken into account, and especially for widespread species or species complexes with unclear taxonomy, an integrative approach has to be used to clarify species boundaries and identities.},
}
@article {pmid24453561,
year = {2013},
author = {Miller, JA and Beentjes, KK and van Helsdingen, P and Ijland, S},
title = {Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol.},
journal = {ZooKeys},
volume = {},
number = {365},
pages = {245-261},
pmid = {24453561},
issn = {1313-2989},
abstract = {We report initial results from an ongoing effort to build a library of DNA barcode sequences for Dutch spiders and investigate the utility of museum collections as a source of specimens for barcoding spiders. Source material for the library comes from a combination of specimens freshly collected in the field specifically for this project and museum specimens collected in the past. For the museum specimens, we focus on 31 species that have been frequently collected over the past several decades. A series of progressively older specimens representing these 31 species were selected for DNA barcoding. Based on the pattern of sequencing successes and failures, we find that smaller-bodied species expire before larger-bodied species as tissue sources for single-PCR standard DNA barcoding. Body size and age of oldest successful DNA barcode are significantly correlated after factoring out phylogenetic effects using independent contrasts analysis. We found some evidence that extracted DNA concentration is correlated with body size and inversely correlated with time since collection, but these relationships are neither strong nor consistent. DNA was extracted from all specimens using standard destructive techniques involving the removal and grinding of tissue. A subset of specimens was selected to evaluate nondestructive extraction. Nondestructive extractions significantly extended the DNA barcoding shelf life of museum specimens, especially small-bodied species, and yielded higher DNA concentrations compared to destructive extractions. All primary data are publically available through a Dryad archive and the Barcode of Life database.},
}
@article {pmid24453560,
year = {2013},
author = {Marescaux, J and Van Doninck, K},
title = {Using DNA barcoding to differentiate invasive Dreissena species (Mollusca, Bivalvia).},
journal = {ZooKeys},
volume = {},
number = {365},
pages = {235-244},
pmid = {24453560},
issn = {1313-2989},
abstract = {The zebra mussel (Dreissena polymorpha) and the quagga mussel (Dreissena rostriformis bugensis) are considered as the most competitive invaders in freshwaters of Europe and North America. Although shell characteristics exist to differentiate both species, phenotypic plasticity in the genus Dreissena does not always allow a clear identification. Therefore, the need to find an accurate identification method is essential. DNA barcoding has been proven to be an adequate procedure to discriminate species. The cytochrome c oxidase subunit I mitochondrial gene (COI) is considered as the standard barcode for animals. We tested the use of this gene as an efficient DNA barcode and found that it allow rapid and accurate identification of adult Dreissena individuals.},
}
@article {pmid24453559,
year = {2013},
author = {Mankga, LT and Yessoufou, K and Moteetee, AM and Daru, BH and van der Bank, M},
title = {Efficacy of the core DNA barcodes in identifying processed and poorly conserved plant materials commonly used in South African traditional medicine.},
journal = {ZooKeys},
volume = {},
number = {365},
pages = {215-233},
pmid = {24453559},
issn = {1313-2989},
abstract = {Medicinal plants cover a broad range of taxa, which may be phylogenetically less related but morphologically very similar. Such morphological similarity between species may lead to misidentification and inappropriate use. Also the substitution of a medicinal plant by a cheaper alternative (e.g. other non-medicinal plant species), either due to misidentification, or deliberately to cheat consumers, is an issue of growing concern. In this study, we used DNA barcoding to identify commonly used medicinal plants in South Africa. Using the core plant barcodes, matK and rbcLa, obtained from processed and poorly conserved materials sold at the muthi traditional medicine market, we tested efficacy of the barcodes in species discrimination. Based on genetic divergence, PCR amplification efficiency and BLAST algorithm, we revealed varied discriminatory potentials for the DNA barcodes. In general, the barcodes exhibited high discriminatory power, indicating their effectiveness in verifying the identity of the most common plant species traded in South African medicinal markets. BLAST algorithm successfully matched 61% of the queries against a reference database, suggesting that most of the information supplied by sellers at traditional medicinal markets in South Africa is correct. Our findings reinforce the utility of DNA barcoding technique in limiting false identification that can harm public health.},
}
@article {pmid24453558,
year = {2013},
author = {Laiou, A and Mandolini, LA and Piredda, R and Bellarosa, R and Simeone, MC},
title = {DNA barcoding as a complementary tool for conservation and valorisation of forest resources.},
journal = {ZooKeys},
volume = {},
number = {365},
pages = {197-213},
pmid = {24453558},
issn = {1313-2989},
abstract = {Since the pre-historic era, humans have been using forests as a food, drugs and handcraft reservoir. Today, the use of botanical raw material to produce pharmaceuticals, herbal remedies, teas, spirits, cosmetics, sweets, dietary supplements, special industrial compounds and crude materials constitute an important global resource in terms of healthcare and economy. In recent years, DNA barcoding has been suggested as a useful molecular technique to complement traditional taxonomic expertise for fast species identification and biodiversity inventories. In this study, in situ application of DNA barcodes was tested on a selected group of forest tree species with the aim of contributing to the identification, conservation and trade control of these valuable plant resources. The "core barcode" for land plants (rbcL, matK, and trnH-psbA) was tested on 68 tree specimens (24 taxa). Universality of the method, ease of data retrieval and correct species assignment using sequence character states, presence of DNA barcoding gaps and GenBank discrimination assessment were evaluated. The markers showed different prospects of reliable applicability. RbcL and trnH-psbA displayed 100% amplification and sequencing success, while matK did not amplify in some plant groups. The majority of species had a single haplotype. The trnH-psbA region showed the highest genetic variability, but in most cases the high intraspecific sequence divergence revealed the absence of a clear DNA barcoding gap. We also faced an important limitation because the taxonomic coverage of the public reference database is incomplete. Overall, species identification success was 66.7%. This work illustrates current limitations in the applicability of DNA barcoding to taxonomic forest surveys. These difficulties urge for an improvement of technical protocols and an increase of the number of sequences and taxa in public databases.},
}
@article {pmid24453557,
year = {2013},
author = {Laiho, J and Ståhls, G},
title = {DNA barcodes identify Central Asian Colias butterflies (Lepidoptera, Pieridae).},
journal = {ZooKeys},
volume = {},
number = {365},
pages = {175-196},
pmid = {24453557},
issn = {1313-2989},
abstract = {A majority of the known Colias species (Lepidoptera: Pieridae, Coliadinae) occur in the mountainous regions of Central-Asia, vast areas that are hard to access, rendering the knowledge of many species limited due to the lack of extensive sampling. Two gene regions, the mitochondrial COI 'barcode' region and the nuclear ribosomal protein RpS2 gene region were used for exploring the utility of these DNA markers for species identification. A comprehensive sampling of COI barcodes for Central Asian Colias butterflies showed that the barcodes facilitated identification of most of the included species. Phylogenetic reconstruction based on parsimony and Neighbour-Joining recovered most species as monophyletic entities. For the RpS2 gene region species-specific sequences were registered for some of the included Colias spp. Nevertheless, this gene region was not deemed useful as additional molecular 'barcode'. A parsimony analysis of the combined COI and RpS2 data did not support the current subgeneric classification based on morphological characteristics.},
}
@article {pmid24453556,
year = {2013},
author = {Jordaens, K and Sonet, G and Braet, Y and De Meyer, M and Backeljau, T and Goovaerts, F and Bourguignon, L and Desmyter, S},
title = {DNA barcoding and the differentiation between North American and West European Phormia regina (Diptera, Calliphoridae, Chrysomyinae).},
journal = {ZooKeys},
volume = {},
number = {365},
pages = {149-174},
pmid = {24453556},
issn = {1313-2989},
abstract = {Phormia regina (the black fly) is a common Holarctic blow fly species which serves as a primary indicator taxon to estimate minimal post mortem intervals. It is also a major research model in physiological and neurological studies on insect feeding. Previous studies have shown a sequence divergence of up to 4.3% in the mitochondrial COI gene between W European and N American P. regina populations. Here, we DNA barcoded P. regina specimens from six N American and 17 W European populations and confirmed a mean sequence divergence of ca. 4% between the populations of the two continents, while sequence divergence within each continent was a ten-fold lower. Comparable mean mtDNA sequence divergences were observed for COII (3.7%) and cyt b (5.3%), but mean divergence was lower for 16S (0.4-0.6%). Intercontinental divergence at nuclear DNA was very low (≤ 0.1% for both 28S and ITS2), and we did not detect any morphological differentiation between N American and W European specimens. Therefore, we consider the strong differentiation at COI, COII and cyt b as intraspecific mtDNA sequence divergence that should be taken into account when using P. regina in forensic casework or experimental research.},
}
@article {pmid24453555,
year = {2013},
author = {Gere, J and Yessoufou, K and Daru, BH and Mankga, LT and Maurin, O and van der Bank, M},
title = {Incorporating trnH-psbA to the core DNA barcodes improves significantly species discrimination within southern African Combretaceae.},
journal = {ZooKeys},
volume = {},
number = {365},
pages = {129-147},
pmid = {24453555},
issn = {1313-2989},
abstract = {Recent studies indicate that the discriminatory power of the core DNA barcodes (rbcLa + matK) for land plants may have been overestimated since their performance have been tested only on few closely related species. In this study we focused mainly on how the addition of complementary barcodes (nrITS and trnH-psbA) to the core barcodes will affect the performance of the core barcodes in discriminating closely related species from family to section levels. In general, we found that the core barcodes performed poorly compared to the various combinations tested. Using multiple criteria, we finally advocated for the use of the core + trnH-psbA as potential DNA barcode for the family Combretaceae at least in southern Africa. Our results also indicate that the success of DNA barcoding in discriminating closely related species may be related to evolutionary and possibly the biogeographic histories of the taxonomic group tested.},
}
@article {pmid24453554,
year = {2013},
author = {Cox, K and Thomaes, A and Antonini, G and Zilioli, M and De Gelas, K and Harvey, D and Solano, E and Audisio, P and McKeown, N and Shaw, P and Minetti, R and Bartolozzi, L and Mergeay, J},
title = {Testing the performance of a fragment of the COI gene to identify western Palaearctic stag beetle species (Coleoptera, Lucanidae).},
journal = {ZooKeys},
volume = {},
number = {365},
pages = {105-126},
pmid = {24453554},
issn = {1313-2989},
abstract = {Lucanidae) remains challenging, mainly due to the sexual dimorphism and the strong allometry in males. Such conjecture confounds taxonomic based conservation efforts that are urgently needed due to numerous threats to stag beetle biodiversity. Molecular tools could help solve the problem of identification of the different recognized taxa in the "Lucanus cervus complex" and in some related Palaearctic species. We investigated the potential use of a 670 bp region at the 3' end of the mitochondrial cytochrome c oxidase subunit I gene (COI) for barcoding purposes (different from the standard COI barcoding region). Well resolved species and subspecies were L. tetraodon, L. cervusakbesianus, L. c. laticornis, as well as the two eastern Asian outgroup taxa L. formosanus and L. hermani. Conversely, certain taxa could not be distinguished from each other based on K2P-distances and tree topologies: L. c. fabiani / L. (P.) barbarossa, L. c. judaicus / an unknown Lucanus species, L. c. cervus / L. c. turcicus / L. c. pentaphyllus / L. (P.) macrophyllus / L. ibericus. The relative roles of phenotypic plasticity, recurrent hybridisation and incomplete lineage sorting underlying taxonomic and phylogenetic discordances are discussed.},
}
@article {pmid24453553,
year = {2013},
author = {Breugelmans, K and Jordaens, K and Adriaens, E and Remon, JP and Cardona, JQ and Backeljau, T},
title = {DNA barcodes and phylogenetic affinities of the terrestrial slugs Arion gilvus and A. ponsi (Gastropoda, Pulmonata, Arionidae).},
journal = {ZooKeys},
volume = {},
number = {365},
pages = {83-104},
pmid = {24453553},
issn = {1313-2989},
abstract = {The Iberian Peninsula is a region with a high endemicity of species of the terrestrial slug subgenus Mesarion. Many of these species have been described mainly on subtle differences in their proximal genitalia. It therefore remains to be investigated 1) whether these locally diverged taxa also represent different species under a phylogenetic species concept as has been shown for other Mesarion species outside the Iberian Peninsula, and 2) how these taxa are phylogenetically related. Here, we analysed DNA sequence data of two mitochondrial (COI and 16S) genes, and of the nuclear ITS1 region, to explore the phylogenetic affinities of two of these endemic taxa, viz. Arion gilvus Torres Mínguez, 1925 and A. ponsi Quintana Cardona, 2007. We also evaluated the use of these DNA sequence data as DNA barcodes for both species. Our results showed that ITS did not allow to differentiate among most of the Mesarion molecular operational taxonomic units (MOTUs) / morphospecies in Mesarion. Yet, the overall mean p-distance among the Mesarion MOTUs / morphospecies for both mtDNA fragments (16.7% for COI, 13% for 16S) was comparable to that between A. ponsi and its closest relative A. molinae (COI: 14.2%; 16S: 16.2%) and to that between A. gilvus and its closest relative A. urbiae (COI: 14.4%; 16S: 13.4%). Hence, with respect to mtDNA divergence, both A. ponsi and A. gilvus, behave as other Mesarion species or putative species-level MOTUs and thus are confirmed as distinct 'species'.},
}
@article {pmid24453552,
year = {2013},
author = {Ballardini, M and Mercuri, A and Littardi, C and Abbas, S and Couderc, M and Ludeña, B and Pintaud, JC},
title = {The chloroplast DNA locus psbZ-trnfM as a potential barcode marker in Phoenix L. (Arecaceae).},
journal = {ZooKeys},
volume = {},
number = {365},
pages = {71-82},
pmid = {24453552},
issn = {1313-2989},
abstract = {The genus Phoenix (Arecaceae) comprises 14 species distributed from Cape Verde Islands to SE Asia. It includes the economically important species Phoenix dactylifera. The paucity of differential morphological and anatomical useful characters, and interspecific hybridization, make identification of Phoenix species difficult. In this context, the development of reliable DNA markers for species and hybrid identification would be of great utility. Previous studies identified a 12 bp polymorphic chloroplast minisatellite in the trnG (GCC)-trnfM (CAU) spacer, and showed its potential for species identification in Phoenix. In this work, in order to develop an efficient DNA barcode marker for Phoenix, a longer cpDNA region (700 bp) comprising the mentioned minisatellite, and located between the psbZ and trnfM (CAU) genes, was sequenced. One hundred and thirty-six individuals, representing all Phoenix species except P. andamanensis,were analysed. The minisatellite showed 2-7 repetitions of the 12 bp motif, with 1-3 out of seven haplotypes per species. Phoenix reclinata and P. canariensis had species-specific haplotypes. Additional polymorphisms were found in the flanking regions of the minisatellite, including substitutions, indels and homopolymers. All this information allowed us to identify unambiguously eight out of the 13 species, and overall 80% of the individuals sampled. Phoenix rupicola and P. theophrasti had the same haplotype, and so had P. atlantica, P. dactylifera, and P. sylvestris (the "date palm complex" sensu Pintaud et al. 2013). For these species, additional molecular markers will be required for their unambiguous identification. The psbZ-trnfM (CAU) region therefore could be considered as a good basis for the establishment of a DNA barcoding system in Phoenix, and is potentially useful for the identification of the female parent in Phoenix hybrids.},
}
@article {pmid24453550,
year = {2013},
author = {Ardura, A and Planes, S and Garcia-Vazquez, E},
title = {Applications of DNA barcoding to fish landings: authentication and diversity assessment.},
journal = {ZooKeys},
volume = {},
number = {365},
pages = {49-65},
pmid = {24453550},
issn = {1313-2989},
abstract = {DNA barcoding methodologies are being increasingly applied not only for scientific purposes but also for diverse real-life uses. Fisheries assessment is a potential niche for DNA barcoding, which serves for species authentication and may also be used for estimating within-population genetic diversity of exploited fish. Analysis of single-sequence barcodes has been proposed as a shortcut for measuring diversity in addition to the original purpose of species identification. Here we explore the relative utility of different mitochondrial sequences (12S rDNA, COI, cyt b, and D-Loop) for application as barcodes in fisheries sciences, using as case studies two marine and two freshwater catches of contrasting diversity levels. Ambiguous catch identification from COI and cyt b was observed. In some cases this could be attributed to duplicated names in databases, but in others it could be due to mitochondrial introgression between closely related species that may obscure species assignation from mtDNA. This last problem could be solved using a combination of mitochondrial and nuclear genes. We suggest to simultaneously analyze one conserved and one more polymorphic gene to identify species and assess diversity in fish catches.},
}
@article {pmid24453549,
year = {2013},
author = {Aliabadian, M and Beentjes, KK and Roselaar, CS and van Brandwijk, H and Nijman, V and Vonk, R},
title = {DNA barcoding of Dutch birds.},
journal = {ZooKeys},
volume = {},
number = {365},
pages = {25-48},
pmid = {24453549},
issn = {1313-2989},
abstract = {The mitochondrial cytochrome c oxidase subunit I (COI) can serve as a fast and accurate marker for the identification of animal species, and has been applied in a number of studies on birds. We here sequenced the COI gene for 387 individuals of 147 species of birds from the Netherlands, with 83 species being represented by > 2 sequences. The Netherlands occupies a small geographic area and 95% of all samples were collected within a 50 km radius from one another. The intraspecific divergences averaged 0.29% among this assemblage, but most values were lower; the interspecific divergences averaged 9.54%. In all, 95% of species were represented by a unique barcode, with 6 species of gulls and skua (Larus and Stercorarius) having at least one shared barcode. This is best explained by these species representing recent radiations with ongoing hybridization. In contrast, one species, the Lesser Whitethroat Sylvia curruca showed deep divergences, averaging 5.76% and up to 8.68% between individuals. These possibly represent two distinct taxa, S. curruca and S. blythi, both clearly separated in a haplotype network analysis. Our study adds to a growing body of DNA barcodes that have become available for birds, and shows that a DNA barcoding approach enables to identify known Dutch bird species with a very high resolution. In addition some species were flagged up for further detailed taxonomic investigation, illustrating that even in ornithologically well-known areas such as the Netherlands, more is to be learned about the birds that are present.},
}
@article {pmid24453548,
year = {2013},
author = {Alfonsi, E and Méheust, E and Fuchs, S and Carpentier, FG and Quillivic, Y and Viricel, A and Hassani, S and Jung, JL},
title = {The use of DNA barcoding to monitor the marine mammal biodiversity along the French Atlantic coast.},
journal = {ZooKeys},
volume = {},
number = {365},
pages = {5-24},
pmid = {24453548},
issn = {1313-2989},
abstract = {In the last ten years, 14 species of cetaceans and five species of pinnipeds stranded along the Atlantic coast of Brittany in the North West of France. All species included, an average of 150 animals strand each year in this area. Based on reports from the stranding network operating along this coast, the most common stranding events comprise six cetacean species (Delphinus delphis, Tursiops truncatus, Stenella coeruleoalba, Globicephala melas, Grampus griseus, Phocoena phocoena)and one pinniped species (Halichoerus grypus). Rare stranding events include deep-diving or exotic species, such as arctic seals. In this study, our aim was to determine the potential contribution of DNA barcoding to the monitoring of marine mammal biodiversity as performed by the stranding network. We sequenced more than 500 bp of the 5' end of the mitochondrial COI gene of 89 animals of 15 different species (12 cetaceans, and three pinnipeds). Except for members of the Delphininae, all species were unambiguously discriminated on the basis of their COI sequences. We then applied DNA barcoding to identify some "undetermined" samples. With again the exception of the Delphininae, this was successful using the BOLD identification engine. For samples of the Delphininae, we sequenced a portion of the mitochondrial control region (MCR), and using a non-metric multidimentional scaling plot and posterior probability calculations we were able to determine putatively each species. We then showed, in the case of the harbour porpoise, that COI polymorphisms, although being lower than MCR ones, could also be used to assess intraspecific variability. All these results show that the use of DNA barcoding in conjunction with a stranding network could clearly increase the accuracy of the monitoring of marine mammal biodiversity.},
}
@article {pmid24453544,
year = {2013},
author = {Tate, AE and Riddle, RR and Soleglad, ME and Graham, MR},
title = {Pseudouroctonus peccatum, a new scorpion from the Spring Mountains near "Sin City," Nevada (Scorpiones, Vaejovidae).},
journal = {ZooKeys},
volume = {},
number = {364},
pages = {29-45},
pmid = {24453544},
issn = {1313-2989},
abstract = {A new scorpion species is described from the Spring Mountain Range near Las Vegas, Nevada. The new species appears to be geographically isolated from other closely related species of Uroctonites Williams &amp; Savaryand Pseudouroctonus Stahnke. We tentatively place the new species in Pseudouroctonus and provide detailed descriptions and illustrations of type material. We compare the new species to 17 congeneric taxa, briefly discuss the taxonomic history of Pseudouroctonus, and provide DNA barcodes for two paratypes to assist ongoing research on the systematics of family Vaejovidae.},
}
@article {pmid24451208,
year = {2014},
author = {Mueller, RC and Paula, FS and Mirza, BS and Rodrigues, JL and Nüsslein, K and Bohannan, BJ},
title = {Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest.},
journal = {The ISME journal},
volume = {8},
number = {7},
pages = {1548-1550},
pmid = {24451208},
issn = {1751-7370},
mesh = {Brazil ; *Conservation of Natural Resources ; DNA Barcoding, Taxonomic ; DNA, Fungal/*genetics ; DNA, Ribosomal/*genetics ; Ecosystem ; Fungi/classification/*genetics ; Phylogeny ; Plant Roots/classification/genetics/*microbiology ; *Soil Microbiology ; Trees/classification/genetics/microbiology ; Tropical Climate ; },
abstract = {Understanding the interactions among microbial communities, plant communities and soil properties following deforestation could provide insights into the long-term effects of land-use change on ecosystem functions, and may help identify approaches that promote the recovery of degraded sites. We combined high-throughput sequencing of fungal rDNA and molecular barcoding of plant roots to estimate fungal and plant community composition in soil sampled across a chronosequence of deforestation. We found significant effects of land-use change on fungal community composition, which was more closely correlated to plant community composition than to changes in soil properties or geographic distance, providing evidence for strong links between above- and below-ground communities in tropical forests.},
}
@article {pmid24451012,
year = {2013},
author = {Links, MG and Chaban, B and Hemmingsen, SM and Muirhead, K and Hill, JE},
title = {mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences.},
journal = {Microbiome},
volume = {1},
number = {1},
pages = {23},
pmid = {24451012},
issn = {2049-2618},
abstract = {BACKGROUND: Formation of operational taxonomic units (OTU) is a common approach to data aggregation in microbial ecology studies based on amplification and sequencing of individual gene targets. The de novo assembly of OTU sequences has been recently demonstrated as an alternative to widely used clustering methods, providing robust information from experimental data alone, without any reliance on an external reference database.<br><br>RESULTS: Here we introduce mPUMA (microbial Profiling Using Metagenomic Assembly, http://mpuma.sourceforge.net), a software package for identification and analysis of protein-coding barcode sequence data. It was developed originally for Cpn60 universal target sequences (also known as GroEL or Hsp60). Using an unattended process that is independent of external reference sequences, mPUMA forms OTUs by DNA sequence assembly and is capable of tracking OTU abundance. mPUMA processes microbial profiles both in terms of the direct DNA sequence as well as in the translated amino acid sequence for protein coding barcodes. By forming OTUs and calculating abundance through an assembly approach, mPUMA is capable of generating inputs for several popular microbiota analysis tools. Using SFF data from sequencing of a synthetic community of Cpn60 sequences derived from the human vaginal microbiome, we demonstrate that mPUMA can faithfully reconstruct all expected OTU sequences and produce compositional profiles consistent with actual community structure.<br><br>CONCLUSIONS: mPUMA enables analysis of microbial communities while empowering the discovery of novel organisms through OTU assembly.},
}
@article {pmid24450943,
year = {2014},
author = {Galindo, LA and Puillandre, N and Strong, EE and Bouchet, P},
title = {Using microwaves to prepare gastropods for DNA barcoding.},
journal = {Molecular ecology resources},
volume = {14},
number = {4},
pages = {700-705},
doi = {10.1111/1755-0998.12231},
pmid = {24450943},
issn = {1755-0998},
mesh = {Animals ; DNA/*isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Gastropoda/classification/*genetics ; *Microwaves ; Molecular Sequence Data ; Sequence Analysis, DNA ; },
abstract = {Extracting DNA from gastropods presents particular difficulties due to the capacity of the living animal to retract into the shell, resulting in poor penetration of the ethanol into the tissues. Because the shell is essential to establish the link between sequences and traditional taxonomic identity, cracking the shell to facilitate fixation is not ideal. Several methods are currently in routine use to overcome this difficulty, including chemical relaxation, drilling the shell and boiling. Most of these methods are time-consuming, may be safety hazards and constitute a bottleneck in the preparation of large numbers of specimens in the field. We have experimented with a method traditionally used to clean shells that involves placing the living gastropods in a microwave (MW) oven; the electromagnetic radiation very quickly heats both the animal and the water trapped inside the shell, resulting in separation of the muscles that anchor the animal to the shell. Done properly, the body can be removed intact from the shell and the shell voucher is preserved undamaged. To test the method, the bodies of live-collected specimens from two gastropod species were separated from their shell by microwaving and by anesthetizing/drilling. After identical extraction and PCR procedures, the gels showed no difference in DNA quantity or quality, and the resulting sequences are identical within species. The method was then implemented on a large scale during expeditions, resulting in higher percentage of DNA extraction success. The MWs are also effective for quickly and easily removing other molluscs from their shells, that is, bivalves and scaphopods. Workflows implementing the MW technique show a three- to fivefold increase in productivity compared with other methods.},
}
@article {pmid24449902,
year = {2014},
author = {Wirta, HK and Hebert, PD and Kaartinen, R and Prosser, SW and Várkonyi, G and Roslin, T},
title = {Complementary molecular information changes our perception of food web structure.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {111},
number = {5},
pages = {1885-1890},
pmid = {24449902},
issn = {1091-6490},
mesh = {Animals ; DNA/*genetics ; *Food Chain ; Geography ; Greenland ; Host-Parasite Interactions/genetics ; Lepidoptera/genetics ; Molecular Sequence Data ; *Perception ; },
abstract = {How networks of ecological interactions are structured has a major impact on their functioning. However, accurately resolving both the nodes of the webs and the links between them is fraught with difficulties. We ask whether the new resolution conferred by molecular information changes perceptions of network structure. To probe a network of antagonistic interactions in the High Arctic, we use two complementary sources of molecular data: parasitoid DNA sequenced from the tissues of their hosts and host DNA sequenced from the gut of adult parasitoids. The information added by molecular analysis radically changes the properties of interaction structure. Overall, three times as many interaction types were revealed by combining molecular information from parasitoids and hosts with rearing data, versus rearing data alone. At the species level, our results alter the perceived host specificity of parasitoids, the parasitoid load of host species, and the web-wide role of predators with a cryptic lifestyle. As the northernmost network of host-parasitoid interactions quantified, our data point exerts high leverage on global comparisons of food web structure. However, how we view its structure will depend on what information we use: compared with variation among networks quantified at other sites, the properties of our web vary as much or much more depending on the techniques used to reconstruct it. We thus urge ecologists to combine multiple pieces of evidence in assessing the structure of interaction webs, and suggest that current perceptions of interaction structure may be strongly affected by the methods used to construct them.},
}
@article {pmid24449890,
year = {2014},
author = {Fu, GK and Xu, W and Wilhelmy, J and Mindrinos, MN and Davis, RW and Xiao, W and Fodor, SP},
title = {Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {111},
number = {5},
pages = {1891-1896},
pmid = {24449890},
issn = {1091-6490},
support = {R43 HG007130/HG/NHGRI NIH HHS/United States ; R24 GM102656/GM/NIGMS NIH HHS/United States ; P01 HG000205/HG/NHGRI NIH HHS/United States ; R43HG007130/HG/NHGRI NIH HHS/United States ; P01-HG00205/HG/NHGRI NIH HHS/United States ; R24-GM102656/GM/NIGMS NIH HHS/United States ; R43HG007129/HG/NHGRI NIH HHS/United States ; R43 HG007129/HG/NHGRI NIH HHS/United States ; },
mesh = {DNA, Complementary/*genetics ; *Gene Library ; Humans ; Polymerase Chain Reaction ; RNA, Messenger/genetics/metabolism ; Reproducibility of Results ; *Sequence Analysis, RNA ; },
abstract = {We present a simple molecular indexing method for quantitative targeted RNA sequencing, in which mRNAs of interest are selectively captured from complex cDNA libraries and sequenced to determine their absolute concentrations. cDNA fragments are individually labeled so that each molecule can be tracked from the original sample through the library preparation and sequencing process. Multiple copies of cDNA fragments of identical sequence become distinct through labeling, and replicate clones created during PCR amplification steps can be identified and assigned to their distinct parent molecules. Selective capture enables efficient use of sequencing for deep sampling and for the absolute quantitation of rare or transient transcripts that would otherwise escape detection by standard sequencing methods. We have also constructed a set of synthetic barcoded RNA molecules, which can be introduced as controls into the sample preparation mix and used to monitor the efficiency of library construction. The quantitative targeted sequencing revealed extremely low efficiency in standard library preparations, which were further confirmed by using synthetic barcoded RNA molecules. This finding shows that standard library preparation methods result in the loss of rare transcripts and highlights the need for monitoring library efficiency and for developing more efficient sample preparation methods.},
}
@article {pmid24444052,
year = {2014},
author = {Links, MG and Demeke, T and Gräfenhan, T and Hill, JE and Hemmingsen, SM and Dumonceaux, TJ},
title = {Simultaneous profiling of seed-associated bacteria and fungi reveals antagonistic interactions between microorganisms within a shared epiphytic microbiome on Triticum and Brassica seeds.},
journal = {The New phytologist},
volume = {202},
number = {2},
pages = {542-553},
pmid = {24444052},
issn = {1469-8137},
mesh = {Alternaria/genetics ; Bacteria/genetics/*isolation &amp; purification ; Brassica/*microbiology ; Chaperonin 60/genetics ; Ecosystem ; Fungi/genetics/*isolation &amp; purification ; *Microbial Interactions ; *Microbiota ; Pantoea/genetics ; Seeds/*microbiology ; Triticum/*microbiology ; },
abstract = {In order to address the hypothesis that seeds from ecologically and geographically diverse plants harbor characteristic epiphytic microbiota, we characterized the bacterial and fungal microbiota associated with Triticum and Brassica seed surfaces. The total microbial complement was determined by amplification and sequencing of a fragment of chaperonin 60 (cpn60). Specific microorganisms were quantified by qPCR. Bacteria and fungi corresponding to operational taxonomic units (OTU) that were identified in the sequencing study were isolated and their interactions examined. A total of 5477 OTU were observed from seed washes. Neither total epiphytic bacterial load nor community richness/evenness was significantly different between the seed types; 578 OTU were shared among all samples at a variety of abundances. Hierarchical clustering revealed that 203 were significantly different in abundance on Triticum seeds compared with Brassica. Microorganisms isolated from seeds showed 99-100% identity between the cpn60 sequences of the isolates and the OTU sequences from this shared microbiome. Bacterial strains identified as Pantoea agglomerans had antagonistic properties toward one of the fungal isolates (Alternaria sp.), providing a possible explanation for their reciprocal abundances on both Triticum and Brassica seeds. cpn60 enabled the simultaneous profiling of bacterial and fungal microbiota and revealed a core seed-associated microbiota shared between diverse plant genera.},
}
@article {pmid24440600,
year = {2014},
author = {Nguyen, LV and Makarem, M and Carles, A and Moksa, M and Kannan, N and Pandoh, P and Eirew, P and Osako, T and Kardel, M and Cheung, AM and Kennedy, W and Tse, K and Zeng, T and Zhao, Y and Humphries, RK and Aparicio, S and Eaves, CJ and Hirst, M},
title = {Clonal analysis via barcoding reveals diverse growth and differentiation of transplanted mouse and human mammary stem cells.},
journal = {Cell stem cell},
volume = {14},
number = {2},
pages = {253-263},
doi = {10.1016/j.stem.2013.12.011},
pmid = {24440600},
issn = {1875-9777},
support = {//Canadian Institutes of Health Research/Canada ; },
mesh = {Animals ; Cell Culture Techniques/*methods ; *Cell Differentiation ; Cell Lineage ; Cell Proliferation ; Cell Size ; Clone Cells ; Epithelial Cells/cytology/transplantation ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Mammary Glands, Animal/*cytology ; Mammary Glands, Human/*cytology ; Mice ; Regeneration ; *Stem Cell Transplantation ; Stem Cells/*cytology ; },
abstract = {Cellular barcoding offers a powerful approach to characterize the growth and differentiation activity of large numbers of cotransplanted stem cells. Here, we describe a lentiviral genomic-barcoding and analysis strategy and its use to compare the clonal outputs of transplants of purified mouse and human basal mammary epithelial cells. We found that both sources of transplanted cells produced many bilineage mammary epithelial clones in primary recipients, although primary clones containing only one detectable mammary lineage were also common. Interestingly, regardless of the species of origin, many clones evident in secondary recipients were not detected in the primary hosts, and others that were changed from appearing luminal-restricted to appearing bilineage. This barcoding methodology has thus revealed conservation between mice and humans of a previously unknown diversity in the growth and differentiation activities of their basal mammary epithelial cells stimulated to grow in transplanted hosts.},
}
@article {pmid24435020,
year = {2014},
author = {Adachi, K and Enoki, T and Kawano, Y and Veraz, M and Nakai, H},
title = {Drawing a high-resolution functional map of adeno-associated virus capsid by massively parallel sequencing.},
journal = {Nature communications},
volume = {5},
number = {},
pages = {3075},
pmid = {24435020},
issn = {2041-1723},
support = {P41 RR006009/RR/NCRR NIH HHS/United States ; R01 DK078388/DK/NIDDK NIH HHS/United States ; P41 RR06009/RR/NCRR NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Capsid/*chemistry/physiology ; Cell Line ; DNA Barcoding, Taxonomic/*methods ; DNA, Viral/genetics ; Dependovirus/*chemistry/*genetics ; Genetic Therapy ; Genetic Vectors/*chemistry/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Homeodomain Proteins/genetics ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Molecular Sequence Data ; Mutation/genetics ; Phenotype ; },
abstract = {Adeno-associated virus (AAV) capsid engineering is an emerging approach to advance gene therapy. However, a systematic analysis on how each capsid amino acid contributes to multiple functions remains challenging. Here we show proof-of-principle and successful application of a novel approach, termed AAV Barcode-Seq, that allows us to characterize phenotypes of hundreds of different AAV strains in a high-throughput manner and therefore overcomes technical difficulties in the systematic analysis. In this approach, we generate DNA barcode-tagged AAV libraries and determine a spectrum of phenotypes of each AAV strain by Illumina barcode sequencing. By applying this method to AAV capsid mutant libraries tagged with DNA barcodes, we can draw a high-resolution map of AAV capsid amino acids important for the structural integrity and functions including receptor binding, tropism, neutralization and blood clearance. Thus, Barcode-Seq provides a new tool to generate a valuable resource for virus and gene therapy research.},
}
@article {pmid24433674,
year = {2014},
author = {Jargeat, P and Chaumeton, JP and Navaud, O and Vizzini, A and Gryta, H},
title = {The Paxillus involutus (Boletales, Paxillaceae) complex in Europe: genetic diversity and morphological description of the new species Paxillus cuprinus, typification of P. involutus s.s., and synthesis of species boundaries.},
journal = {Fungal biology},
volume = {118},
number = {1},
pages = {12-31},
doi = {10.1016/j.funbio.2013.10.008},
pmid = {24433674},
issn = {1878-6146},
mesh = {Basidiomycota/*classification/genetics ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; France ; Fungal Proteins/genetics ; *Genetic Variation ; Italy ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Paxillus involutus is a model species for ecological or physiological studies of ectomycorrhizal agaricomycetes. Three to six groups or species linked to it have been ecologically and morphologically distinguished. Phylogenetic studies have revealed the existence of four species in Europe: Paxillus ammoniavirescens, Paxillus obscurisporus, P. involutus, and a fourth as yet not described species. We studied 47 collections from 24 French and Italian locations, supplemented with GenBank data, in order to genetically and taxonomically delineate these species. Phylogenetic analyses of three nuclear DNA regions (rDNA internal transcribed spacer (ITS), tef1-α, and gpd) confirmed the four European species. Morphology, culture, and ecology features allowed us to delineate species boundaries and to describe the fourth species we named Paxillus cuprinus since it turns coppery with age. As there is no existing original herbarium specimen for P. involutus, one of our collections was chosen as the epitype. The low genetic diversity found in P. cuprinus correlates with stable morphological traits (basidiome colour, ovoid-amygdaliform spores with an apical constriction) and with ecological preferences (association with Betulaceae in open and temperate areas). In contrast, P. ammoniavirescens is characterized by a high genetic diversity and a high variation of its morphological and ecological features.},
}
@article {pmid24432382,
year = {2013},
author = {Gao, T and Ma, X and Zhu, X},
title = {Use of the psbA-trnH region to authenticate medicinal species of Fabaceae.},
journal = {Biological &amp; pharmaceutical bulletin},
volume = {36},
number = {12},
pages = {1975-1979},
doi = {10.1248/bpb.b13-00611},
pmid = {24432382},
issn = {1347-5215},
mesh = {DNA Barcoding, Taxonomic ; DNA, Intergenic/genetics ; DNA, Plant/*genetics ; Fabaceae/*genetics ; Plants, Medicinal/genetics ; Sequence Analysis, DNA ; },
abstract = {Fabaceae is a huge family that contains a large number of medicinal plants, many of which are commonly used in Chinese traditional medicine. However, traditional taxonomy has not been able to meet the complicated demands of species discrimination within Fabaceae. Thus, we employed a famous DNA barcode, the psbA-trnH region, to discriminate commonly used medicinal species of the family Fabaceae. Here, the psbA-trnH regions derived from 152 samples were amplified. These samples represented 104 Fabaceae medicinal species from 60 genera, including 25 authentic Fabaceae species listed in the Chinese pharmacopoeia and common adulterant species. The results indicate that the psbA-trnH region performed well in terms of its universality and high variability in length and composition. Species discriminative power analysis of the psbA-trnH region showed that 91.3% of species could be identified successfully by the BLAST1 method in conjunction with the nearest distance method. And, the species resolution rate of the TaxonGap method exceeded 93%. The results provide support for the use of the psbA-trnH plastid region as a sensitive marker to the authentication of Fabaceae medicinal plants.},
}
@article {pmid24431113,
year = {2014},
author = {Ullal, AV and Peterson, V and Agasti, SS and Tuang, S and Juric, D and Castro, CM and Weissleder, R},
title = {Cancer cell profiling by barcoding allows multiplexed protein analysis in fine-needle aspirates.},
journal = {Science translational medicine},
volume = {6},
number = {219},
pages = {219ra9},
pmid = {24431113},
issn = {1946-6242},
support = {R33 CA202064/CA/NCI NIH HHS/United States ; U54 CA151884/CA/NCI NIH HHS/United States ; },
mesh = {Antibodies/immunology ; Biopsy, Fine-Needle ; Cell Line, Tumor ; DNA/metabolism ; Humans ; Neoplasm Proteins/*analysis/metabolism ; Neoplasms/*metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; Phosphoinositide-3 Kinase Inhibitors ; Protein Array Analysis/*methods ; Protein Kinase Inhibitors/pharmacology ; Reproducibility of Results ; Signal Transduction/drug effects ; Single-Cell Analysis ; },
abstract = {Immunohistochemistry-based clinical diagnoses require invasive core biopsies and use a limited number of protein stains to identify and classify cancers. We introduce a technology that allows analysis of hundreds of proteins from minimally invasive fine-needle aspirates (FNAs), which contain much smaller numbers of cells than core biopsies. The method capitalizes on DNA-barcoded antibody sensing, where barcodes can be photocleaved and digitally detected without any amplification steps. After extensive benchmarking in cell lines, this method showed high reproducibility and achieved single-cell sensitivity. We used this approach to profile ~90 proteins in cells from FNAs and subsequently map patient heterogeneity at the protein level. Additionally, we demonstrate how the method could be used as a clinical tool to identify pathway responses to molecularly targeted drugs and to predict drug response in patient samples. This technique combines specificity with ease of use to offer a new tool for understanding human cancers and designing future clinical trials.},
}
@article {pmid24431108,
year = {2014},
author = {Gökmen-Polar, Y and Badve, S},
title = {Multiplexed protein analysis.},
journal = {Science translational medicine},
volume = {6},
number = {219},
pages = {219fs3},
doi = {10.1126/scitranslmed.3008407},
pmid = {24431108},
issn = {1946-6242},
mesh = {Animals ; Biomarkers, Tumor/analysis ; DNA Barcoding, Taxonomic ; Humans ; *Proteomics ; *Tissue Array Analysis ; Translational Research, Biomedical ; },
abstract = {Multiplexed protein analysis using an antibody-DNA barcoding approach could accelerate early detection and monitoring of cancer biomarkers in patient samples (Ullal et al., this issue).},
}
@article {pmid24429975,
year = {2014},
author = {Hoffmann, K and Behnke, T and Grabolle, M and Resch-Genger, U},
title = {Nanoparticle-encapsulated vis- and NIR-emissive fluorophores with different fluorescence decay kinetics for lifetime multiplexing.},
journal = {Analytical and bioanalytical chemistry},
volume = {406},
number = {14},
pages = {3315-3322},
doi = {10.1007/s00216-013-7597-3},
pmid = {24429975},
issn = {1618-2650},
mesh = {3T3 Cells ; Animals ; Cytological Techniques ; Flow Cytometry ; Fluorescent Dyes/*chemistry ; Mice ; Nanoparticles/*chemistry ; *Nanotechnology ; Polymers/chemistry ; *Spectrometry, Fluorescence ; *Spectroscopy, Near-Infrared ; Staining and Labeling ; User-Computer Interface ; },
abstract = {Bioanalytical, clinical, and security applications increasingly require simple, efficient, and versatile strategies to measure an ever increasing number of analytes or events in parallel in a broad variety of detection formats as well as in conjunction with chromatographic separation techniques or flow cytometry. An attractive alternative to common optical multiplexing and encoding methods utilizing spectral multiplexing/color encoding and intensity encoding is lifetime multiplexing, which relies on the discrimination between different fluorescent reporters based on their fluorescence decay kinetics. Here, we propose a platform of surface-functionalizable polymeric nanoparticles stained with fluorophores differing in their fluorescence lifetimes as a new multiplexing and encoding approach. Proof-of-concept measurements with different sets of lifetime-encoded polystyrene nanoparticles are presented, obtained via staining of preformed particles with visible (vis)- and near-infrared (NIR)-emissive organic dyes, which display very similar absorption and emission spectra to enable excitation and detection at the same wavelengths, yet sufficiently different fluorescence decay kinetics in suspension, thereby minimizing instrumentation costs. Data analysis was performed with a linear combination approach in the lifetime domain. Our results and first cell experiments with these reporter sets underline the suitability of our multiplexing strategy for the discrimination between and the quantification of different labels. This simple and versatile concept can be extended to all types of fluorophores, thereby expanding the accessible time scale, and can be used, e.g., for the design of labels and targeted probes for fluorescence assays and molecular imaging, cellular imaging studies, and barcoding applications, also in conjunction with spectral and intensity encoding.},
}
@article {pmid24419666,
year = {2014},
author = {Salinas, C and Cubillos, JC and Gómez, R and Trujillo, F and Caballero, S},
title = {"Pig in a poke (gato por liebre)": the "mota" (Calophysus macropterus) fishery, molecular evidence of commercialization in Colombia and toxicological analyses.},
journal = {EcoHealth},
volume = {11},
number = {2},
pages = {197-206},
pmid = {24419666},
issn = {1612-9210},
mesh = {Animals ; Catfishes/genetics/*metabolism ; Colombia ; DNA Barcoding, Taxonomic ; Extinction, Biological ; Fisheries/methods/*standards ; Food Contamination/*analysis ; Humans ; Mercury/*analysis ; Rivers/chemistry ; Water Pollutants, Chemical/*analysis ; },
abstract = {Overfishing has affected the population abundance trends of many commercial fish species. In the Amazon, the fishery of a catfish commonly known as "mota" or "piracatinga" (Calophysus macropterus) has become an important economic activity in the region as this species has replaced a number of other overexploited great catfish species in the markets. Due to this high exploitation, ways in which to increase captures have been identified. One strategy is to use decomposing animal carcasses as bait. Such strategy has increased the hunting pressure on endangered species such as caimans and river dolphins. We investigated which catfish species are currently commercialized in Colombian fish markets using DNA barcoding, and measured mercury concentration in the tissues of fish molecularly identified as C. macropterus. We collected 86 fish samples in markets of four Colombian cities. Sixty-eight of these were identified molecularly as C.macropterus. The mercury concentration of 29 such samples was analyzed. Samples presented total Hg concentrations higher than the limit for human consumption established by the WHO (0.5 μg/g). These results are worrisome and suggest that (1) C. macropterus is a widely used fish species for human consumption in Colombia and (2) C. macropterus has high concentrations of total Hg, making its consumption a public health risk. Results presented here suggest that C. macropterus has replaced capaz in most Colombian markets. This fishery threatens wild species of river dolphins and caimans, and is also a public health risk given the high mercury levels we found in a subsample of these fishes.},
}
@article {pmid24416210,
year = {2014},
author = {de Boer, HJ and Ouarghidi, A and Martin, G and Abbad, A and Kool, A},
title = {DNA barcoding reveals limited accuracy of identifications based on folk taxonomy.},
journal = {PloS one},
volume = {9},
number = {1},
pages = {e84291},
pmid = {24416210},
issn = {1932-6203},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic/*methods ; *Medicine, Traditional ; Pharmacopoeias as Topic ; Plant Roots/genetics ; Plants, Medicinal/*classification/genetics ; },
abstract = {BACKGROUND: The trade of plant roots as traditional medicine is an important source of income for many people around the world. Destructive harvesting practices threaten the existence of some plant species. Harvesters of medicinal roots identify the collected species according to their own folk taxonomies, but once the dried or powdered roots enter the chain of commercialization, accurate identification becomes more challenging.<br><br>METHODOLOGY: A survey of morphological diversity among four root products traded in the medina of Marrakech was conducted. Fifty-one root samples were selected for molecular identification using DNA barcoding using three markers, trnH-psbA, rpoC1, and ITS. Sequences were searched using BLAST against a tailored reference database of Moroccan medicinal plants and their closest relatives submitted to NCBI GenBank.<br><br>PRINCIPAL FINDINGS: Combining psbA-trnH, rpoC1, and ITS allowed the majority of the market samples to be identified to species level. Few of the species level barcoding identifications matched the scientific names given in the literature, including the most authoritative and widely cited pharmacopeia.<br><br>CONCLUSIONS/SIGNIFICANCE: The four root complexes selected from the medicinal plant products traded in Marrakech all comprise more than one species, but not those previously asserted. The findings have major implications for the monitoring of trade in endangered plant species as morphology-based species identifications alone may not be accurate. As a result, trade in certain species may be overestimated, whereas the commercialization of other species may not be recorded at all.},
}
@article {pmid24415470,
year = {2014},
author = {Drábková, LZ},
title = {DNA extraction from herbarium specimens.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1115},
number = {},
pages = {69-84},
doi = {10.1007/978-1-62703-767-9_4},
pmid = {24415470},
issn = {1940-6029},
mesh = {Cetrimonium ; Cetrimonium Compounds/chemistry ; Chemical Fractionation/*methods ; DNA, Plant/chemistry/genetics/*isolation &amp; purification ; Filtration ; Microsatellite Repeats ; Nitric Acid/chemistry ; Plant Leaves/chemistry ; Plants/*chemistry ; Seeds/chemistry ; Species Specificity ; *Tissue Preservation ; },
abstract = {With the expansion of molecular techniques, the historical collections have become widely used. Studying plant DNA using modern molecular techniques such as DNA sequencing plays an important role in understanding evolutionary relationships, identification through DNA barcoding, conservation status, and many other aspects of plant biology. Enormous herbarium collections are an important source of material especially for specimens from areas difficult to access or from taxa that are now extinct. The ability to utilize these specimens greatly enhances the research. However, the process of extracting DNA from herbarium specimens is often fraught with difficulty related to such variables as plant chemistry, drying method of the specimen, and chemical treatment of the specimen. Although many methods have been developed for extraction of DNA from herbarium specimens, the most frequently used are modified CTAB and DNeasy Plant Mini Kit protocols. Nine selected protocols in this chapter have been successfully used for high-quality DNA extraction from different kinds of plant herbarium tissues. These methods differ primarily with respect to their requirements for input material (from algae to vascular plants), type of the plant tissue (leaves with incrustations, sclerenchyma strands, mucilaginous tissues, needles, seeds), and further possible applications (PCR-based methods or microsatellites, AFLP).},
}
@article {pmid24410716,
year = {2014},
author = {Nightingale, MJ and Brazier, AM and McArthur, K and Jones, J and Cardigan, R and Lodge, L and Maclennan, S and , },
title = {The development and evaluation of options for improving future U.K. blood component labelling--outcome of the 2013 U.K. hospital survey.},
journal = {Transfusion medicine (Oxford, England)},
volume = {24},
number = {2},
pages = {89-98},
doi = {10.1111/tme.12098},
pmid = {24410716},
issn = {1365-3148},
mesh = {*Blood Component Transfusion ; *Data Collection ; Female ; *Hospitals ; Humans ; Male ; *Product Labeling ; United Kingdom ; },
abstract = {BACKGROUND/OBJECTIVES: U.K. blood component labels have evolved to accommodate a plethora of information. Concern has, however, been expressed that current U.K. labelling is too 'cluttered', detracting from the clarity of critical information. This prompted a holistic review of labelling and available information technology (IT) with the aim of improving the situation.<br><br>METHODS/MATERIALS: A survey was circulated requiring U.K. hospital participants to rank each item of information on the label according to its 'criticality' and assess three novel 'future' and one 'transition' prototype labels. Prototypes were based on applicable regulatory standards, best practice guidance, international benchmark data and U.K. expert input. The prototypes support steps towards 'full face' label printing and utilise 2D and quick response (QR) barcodes.<br><br>RESULTS: Two-hundred eleven completed surveys were received identifying 110 contributing hospitals with 41% from clinical staff, 37% from transfusion laboratory staff and 22% from transfusion practitioners. There was excellent agreement between the three groups on the critical information, i.e., blood group, expiry date, blood component name, unique donation identification number (DIN) and blood component volume but far less on the other information, especially the various warning messages. Of the 'future' labels, option 3 (closest to the current 'quadrant model') was most popular. Option 1, with its additional inverted section replicating critical information was least popular and prompted significant safety concerns.<br><br>CONCLUSION: The prototype labels correctly identified the critical items of information and extensive comments confirmed that this was more prominently and clearly displayed. Laboratory staff commented that the transition label was essential to enable IT systems to be adapted.},
}
@article {pmid24409929,
year = {2015},
author = {Chakraborty, M and Ghosh, SK},
title = {Unraveling the sequence information in COI barcode to achieve higher taxon assignment based on Indian freshwater fishes.},
journal = {Mitochondrial DNA},
volume = {26},
number = {2},
pages = {175-177},
doi = {10.3109/19401736.2013.855923},
pmid = {24409929},
issn = {1940-1744},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Fishes/*classification/*genetics ; *Genes, Mitochondrial ; },
abstract = {Efficacy of cytochrome c oxidase subunit I (COI) DNA barcode in higher taxon assignment is still under debate in spite of several attempts, using the conventional DNA barcoding methods, to assign higher taxa. Here we try to understand whether nucleotide and amino acid sequence in COI gene carry sufficient information to assign species to their higher taxonomic rank, using 160 species of Indian freshwater fishes. Our results reveal that with increase in the taxonomic rank, sequence conservation decreases for both nucleotides and amino acids. Order level exhibits lowest conservation with 50% of the nucleotides and amino acids being conserved. Among the variable sites, 30-50% were found to carry high information content within an order, while it was 70-80% within a family and 80-99% within a genus. High information content shows sites with almost conserved sequence but varying at one or two locations, which can be due to variations at species or population level. Thus, the potential of COI gene in higher taxon assignment is revealed with validation of ample inherent signals latent in the gene.},
}
@article {pmid24409805,
year = {2013},
author = {Zhang, L and Qian, J and Hu, L and Chen, Y},
title = {[Quality improvement and performance evaluation of Monitoring and Tracking Medical Materials Lot Number].},
journal = {Zhongguo yi liao qi xie za zhi = Chinese journal of medical instrumentation},
volume = {37},
number = {5},
pages = {386-388},
pmid = {24409805},
issn = {1671-7104},
mesh = {Hospital Distribution Systems/*organization &amp; administration ; *Materials Management, Hospital ; Quality Control ; },
abstract = {With various increasing health sector's demand of medical materials, monitoring and tracking medical materials lot number has become the most important thing of hospital's medical materials management. This paper discussed and researched deeply the actual operation problem through data analysis and charts comparison, put forward realizing barcodes wireless scanning, and synchronizing information in local area network, so to improve the barcode input accuracy. Achieve the ultimate goal of completing medical materials lot number traceability.},
}
@article {pmid24404030,
year = {2013},
author = {Zhang, Y and Qiao, L and Ren, Y and Wang, X and Gao, M and Tang, Y and Jeff Xi, J and Fu, TM and Jiang, X},
title = {Two dimensional barcode-inspired automatic analysis for arrayed microfluidic immunoassays.},
journal = {Biomicrofluidics},
volume = {7},
number = {3},
pages = {34110},
pmid = {24404030},
issn = {1932-1058},
abstract = {The usability of many high-throughput lab-on-a-chip devices in point-of-care applications is currently limited by the manual data acquisition and analysis process, which are labor intensive and time consuming. Based on our original design in the biochemical reactions, we proposed here a universal approach to perform automatic, fast, and robust analysis for high-throughput array-based microfluidic immunoassays. Inspired by two-dimensional (2D) barcodes, we incorporated asymmetric function patterns into a microfluidic array. These function patterns provide quantitative information on the characteristic dimensions of the microfluidic array, as well as mark its orientation and origin of coordinates. We used a computer program to perform automatic analysis for a high-throughput antigen/antibody interaction experiment in 10 s, which was more than 500 times faster than conventional manual processing. Our method is broadly applicable to many other microchannel-based immunoassays.},
}
@article {pmid24401328,
year = {2014},
author = {Dauphin, B and Vieu, J and Grant, JR},
title = {Molecular phylogenetics supports widespread cryptic species in moonworts (Botrychium s.s., Ophioglossaceae).},
journal = {American journal of botany},
volume = {101},
number = {1},
pages = {128-140},
doi = {10.3732/ajb.1300154},
pmid = {24401328},
issn = {1537-2197},
mesh = {Base Sequence ; Bayes Theorem ; DNA, Chloroplast/genetics ; Databases, Genetic ; Likelihood Functions ; *Phylogeny ; Plastids/genetics ; Sequence Analysis, DNA ; Species Specificity ; Tracheophyta/*genetics ; },
abstract = {PREMISE OF THE STUDY: Previous phylogenetic studies of moonworts (Botrychium sensu stricto (s.s.)) included few taxa from outside of North America. This low geographical representation limited interpretations of relationships of this group rich in cryptic species. With 18 out of 30 species in the genus being polyploid, understanding their evolutionary history remains a major challenge.<br><br>METHODS: A new molecular phylogeny was reconstructed using Maximum Likelihood (ML) and Bayesian Inference (BI) analyses based on multiple accessions of the most wide-ranging Arctic taxa of Botrychium in North America and Europe using three noncoding plastid DNA regions (psbA-trnH(GUG), trnL(UAA)-trnF(GAA) intergenic spacer, and rpL16 intron).<br><br>KEY RESULTS: The new phylogeny confirms the identity of several recently described species and proposed new taxa. Nine subclades are newly identified within the two major clades in Botrychium s.s.: Lanceolatum and Lunaria. Chloroplast DNA was variable enough to separate morphologically cryptic species in the Lunaria clade. On the contrary, much less variation is seen within the morphologically variable Lanceolatum clade despite sampling over the same broad geographic range. The chloroplast region psbA-trnH(GUG) is identified as an efficient DNA barcode for the identification of cryptic taxa in Botrychium s.s.<br><br>CONCLUSIONS: The combined increase in species representation, samples from throughout the geographic range of each species, and sequencing of multiple plastid DNA regions supports morphologically cryptic species in Botrychium s.s.},
}
@article {pmid24396312,
year = {2013},
author = {Song, LM and Munian, K and Abd Rashid, Z and Bhassu, S},
title = {Characterisation of Asian snakehead murrel Channa striata (Channidae) in Malaysia: an insight into molecular data and morphological approach.},
journal = {TheScientificWorldJournal},
volume = {2013},
number = {},
pages = {917506},
pmid = {24396312},
issn = {1537-744X},
mesh = {Animals ; Base Sequence ; DNA Primers ; Electron Transport Complex IV/genetics ; Fishes/*classification/genetics ; Genetic Markers ; Malaysia ; Polymerase Chain Reaction ; Species Specificity ; },
abstract = {Conservation is imperative for the Asian snakeheads Channa striata, as the species has been overfished due to its high market demand. Using maternal markers (mitochondrial cytochrome c oxidase subunit 1 gene (COI)), we discovered that evolutionary forces that drove population divergence did not show any match between the genetic and morphological divergence pattern. However, there is evidence of incomplete divergence patterns between the Borneo population and the populations from Peninsular Malaysia. This supports the claim of historical coalescence of C. striata during Pleistocene glaciations. Ecological heterogeneity caused high phenotypic variance and was not correlated with genetic variance among the populations. Spatial conservation assessments are required to manage different stock units. Results on DNA barcoding show no evidence of cryptic species in C. striata in Malaysia. The newly obtained sequences add to the database of freshwater fish DNA barcodes and in future will provide information relevant to identification of species.},
}
@article {pmid24391893,
year = {2013},
author = {Jiang, W and Zhu, J and Song, C and Li, X and Yang, Y and Yu, W},
title = {Molecular phylogeny of the butterfly genus Polytremis (Hesperiidae, Hesperiinae, Baorini) in China.},
journal = {PloS one},
volume = {8},
number = {12},
pages = {e84098},
pmid = {24391893},
issn = {1932-6203},
mesh = {Animals ; Butterflies/*genetics ; Cell Nucleus/*genetics ; China ; DNA, Intergenic/genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; *Evolution, Molecular ; Genetic Variation ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The genus Polytremis, restricted to the continental part of the southeastern Palaearctic and northern Oriental regions, is one of the largest and most diverse lineages of the tribe Baorini. Previous studies on the genus were focused mainly on morphological classification and identification of new species. Due to the lack of effective and homologous traits of morphology, there were many challenges in the traditional classification. In this report, we reconstruct the phylogeny to provide a solid framework for these studies and to test the traditional limits and relationships of taxa.<br><br>We sequenced a mitochondrial and three nuclear gene fragments, coupled with an evaluation of traditional morphological characters, to determine the phylogenetic relationships for a total of 15 species representing all major species groups of the Polytremis genus in China, and to elucidate their taxonomic status.<br><br>CONCLUSIONS AND SIGNIFICANCE: Analysis of mitochrondial and nuclear DNA showed considerable congruent phylogenetic signal in topology at the inter-species level. We found strong support for the monophyly of Polytremis and some clades were recognized with morphological data. Thus, the COI sequence in our study could be used as a DNA barcode to identify almost all members of the genus. However, incongruences of phylogenetic analyses occurred: in contrast to the phylogenetic trees of mitochondrial COI, it was not possible for nuclear rDNA to discriminate P. gotama from P. caerulescens, suggesting a possible recent separation of these two species. Additionally, P. theca was the only species with a greater intra-specific genetic distance compared to some inter-specific genetic distances in this study and some problems associated with the cryptic diversity of the species are discussed. The results of this study will helpful to reveal the causes of the high degree of diversity of butterflies, and possibly other groups of insects in China.},
}
@article {pmid24388609,
year = {2014},
author = {Pollock, JD and Wu, DY and Satterlee, JS},
title = {Molecular neuroanatomy: a generation of progress.},
journal = {Trends in neurosciences},
volume = {37},
number = {2},
pages = {106-123},
pmid = {24388609},
issn = {1878-108X},
support = {Z99 DA999999//Intramural NIH HHS/United States ; },
mesh = {Animals ; Humans ; Molecular Biology/*methods/*trends ; Neuroanatomy/*methods/*trends ; },
abstract = {The neuroscience research landscape has changed dramatically over the past decade. Specifically, an impressive array of new tools and technologies have been generated, including but not limited to: brain gene expression atlases, genetically encoded proteins to monitor and manipulate neuronal activity, and new methods for imaging and mapping circuits. However, despite these technological advances, several significant challenges must be overcome to enable a better understanding of brain function and to develop cell type-targeted therapeutics to treat brain disorders. This review provides an overview of some of the tools and technologies currently being used to advance the field of molecular neuroanatomy, and also discusses emerging technologies that may enable neuroscientists to address these crucial scientific challenges over the coming decade.},
}
@article {pmid24386128,
year = {2013},
author = {Mir, K and Neuhaus, K and Bossert, M and Schober, S},
title = {Short barcodes for next generation sequencing.},
journal = {PloS one},
volume = {8},
number = {12},
pages = {e82933},
pmid = {24386128},
issn = {1932-6203},
mesh = {DNA/*chemistry ; High-Throughput Nucleotide Sequencing/*methods ; Sequence Analysis, DNA ; },
abstract = {We consider the design and evaluation of short barcodes, with a length between six and eight nucleotides, used for parallel sequencing on platforms where substitution errors dominate. Such codes should have not only good error correction properties but also the code words should fulfil certain biological constraints (experimental parameters). We compare published barcodes with codes obtained by two new constructions methods, one based on the currently best known linear codes and a simple randomized construction method. The evaluation done is with respect to the error correction capabilities, barcode size and their experimental parameters and fundamental bounds on the code size and their distance properties. We provide a list of codes for lengths between six and eight nucleotides, where for length eight, two substitution errors can be corrected. In fact, no code with larger minimum distance can exist.},
}
@article {pmid24382328,
year = {2014},
author = {Hulin, M and Wheals, A},
title = {Rapid identification of Zygosaccharomyces with genus-specific primers.},
journal = {International journal of food microbiology},
volume = {173},
number = {},
pages = {9-13},
doi = {10.1016/j.ijfoodmicro.2013.12.009},
pmid = {24382328},
issn = {1879-3460},
mesh = {DNA Primers/*standards ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/genetics ; Fermentation ; Food Microbiology/*methods ; Sensitivity and Specificity ; Species Specificity ; Zygosaccharomyces/*genetics/growth &amp; development/isolation &amp; purification ; },
abstract = {There has been a recent and rapid increase in the number of species of the genus Zygosaccharomyces which now comprises Z. bailii, Z. bisporus, Z. gambellarensis, Z. kombuchaensis, Z. lentus, Z. machadoi, Z. mellis, Z. parabaillii, Z. pseudobailii, Z. pseudorouxii, Z. rouxii, Z. sapae, and Z. siamensis. Z. pseudorouxii is an unofficial name given to isolates closely related to the newly-described species Z. sapae. The Zygosaccharomyces genus contains species that are important as food and beverage spoilage organisms and others are associated with fermentations and sweet foodstuffs, such as honey. Their economic significance means that the ability to identify them rapidly is of significant importance. Although Z. rouxii and Z. bailii have been genome-sequenced the extent of sequence data for the others, especially the newly-discovered species, is sometimes extremely limited which makes identification slow. However, parts of the ITS1/5.8S/ITS2 rDNA region contain sequences of sufficient similarity within the genus and of sufficient difference with outgroups, to be potential regions for the design of genus-wide specific primers. We report here the development of genus-specific primers that can detect all the major Zygosaccharomyces species including all those associated with foods; the rare and localised species Z. machadoi and Z. gambellarensis are not detected. The size of the single amplicon produced varies between species and in some cases is sufficiently different to assign provisional species identification. Sequence data from rDNA regions are available for virtually all described yeast species in all genera, thus, prior to having sufficient sequence data from structural genes, rDNA regions may provide more generally suitable candidates for both genus-specific and species-specific primer design.},
}
@article {pmid24378233,
year = {2014},
author = {Chakraborty, M and Ghosh, SK},
title = {An assessment of the DNA barcodes of Indian freshwater fishes.},
journal = {Gene},
volume = {537},
number = {1},
pages = {20-28},
doi = {10.1016/j.gene.2013.12.047},
pmid = {24378233},
issn = {1879-0038},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Fishes/*classification/*genetics ; Fresh Water ; India ; Molecular Sequence Data ; },
abstract = {Freshwater fishes in India are poorly known and plagued by many unresolved cryptic species complexes that masks some latent and endemic species. Limitations in traditional taxonomy have resulted in this crypticism. Hence, molecular approaches like DNA barcoding, are needed to diagnose these latent species. We have analyzed 1383 barcode sequences of 175 Indian freshwater fish species available in the databases, of which 172 sequences of 70 species were generated. The congeneric and conspecific genetic divergences were calculated using Kimura's 2 parameter distance model followed by the construction of a Neighbor Joining tree using the MEGA 5.1. DNA barcoding principle at its first hand approach, led to the straightforward identification of 82% of the studied species with 2.9% (S.E=0.2) divergence between the nearest congeners. However, after validating some cases of synonymy and mislabeled sequences, 5% more species were found to be valid. Sequences submitted to the database under different names were found to represent single species. On the other hand, some sequences of the species like Barilius barna, Barilius bendelisis and Labeo bata were submitted to the database under a single name but were found to represent either some unexplored species or latent species. Overall, 87% of the available Indian freshwater fish barcodes were diagnosed as true species in parity with the existing checklist and can act as reference barcode for the particular taxa. For the remaining 13% (21 species) the correct species name was difficult to assign as they depicted some erroneous identification and cryptic species complex. Thus, these barcodes will need further assay and inclusion of barcodes of more specimens from same and sister species.},
}
@article {pmid24376533,
year = {2013},
author = {Huang, J and Zhang, A and Mao, S and Huang, Y},
title = {DNA barcoding and species boundary delimitation of selected species of Chinese Acridoidea (Orthoptera: Caelifera).},
journal = {PloS one},
volume = {8},
number = {12},
pages = {e82400},
pmid = {24376533},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; China ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Genetic Variation ; Haplotypes/genetics ; Molecular Sequence Data ; Orthoptera/*classification ; *Phylogeny ; Sequence Alignment ; Species Specificity ; },
abstract = {We tested the performance of DNA barcoding in Acridoidea and attempted to solve species boundary delimitation problems in selected groups using COI barcodes. Three analysis methods were applied to reconstruct the phylogeny. K2P distances were used to assess the overlap range between intraspecific variation and interspecific divergence. "Best match (BM)", "best close match (BCM)", "all species barcodes (ASB)" and "back-propagation neural networks (BP-based method)" were utilized to test the success rate of species identification. Phylogenetic species concept and network analysis were employed to delimitate the species boundary in eight selected species groups. The results demonstrated that the COI barcode region performed better in phylogenetic reconstruction at genus and species levels than at higher-levels, but showed a little improvement in resolving the higher-level relationships when the third base data or both first and third base data were excluded. Most overlaps and incorrect identifications may be due to imperfect taxonomy, indicating the critical role of taxonomic revision in DNA barcoding study. Species boundary delimitation confirmed the presence of oversplitting in six species groups and suggested that each group should be treated as a single species.},
}
@article {pmid24373187,
year = {2014},
author = {Bryson, RW},
title = {Bacterial endosymbiont infections in 'living fossils': a case study of North American vaejovid scorpions.},
journal = {Molecular ecology resources},
volume = {14},
number = {4},
pages = {789-793},
doi = {10.1111/1755-0998.12220},
pmid = {24373187},
issn = {1755-0998},
mesh = {Animals ; Bacteria/genetics/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; DNA Primers/genetics ; Genetic Testing/methods ; Scorpions/*microbiology ; *Symbiosis ; },
abstract = {Bacterial endosymbionts are common among arthropods, and maternally inherited forms can affect the reproductive and behavioural traits of their arthropod hosts. The prevalence of bacterial endosymbionts and their role in scorpion evolution have rarely been investigated. In this study, 61 samples from 40 species of scorpion in the family Vaejovidae were screened for the presence of the bacterial endosymbionts Cardinium, Rickettsia, Spiroplasma and Wolbachia. No samples were infected by these bacteria. However, one primer pair specifically designed to amplify Rickettsia amplified nontarget genes of other taxa. Similar off-target amplification using another endosymbiont-specific primer was also found during preliminary screenings. Results caution against the overreliance on previously published screening primers to detect bacterial endosymbionts in host taxa and suggest that primer specificity may be higher in primers targeting nuclear rather than mitochondrial genes.},
}
@article {pmid24372711,
year = {2014},
author = {Roy, V and Constantino, R and Chassany, V and Giusti-Miller, S and Diouf, M and Mora, P and Harry, M},
title = {Species delimitation and phylogeny in the genus Nasutitermes (Termitidae: Nasutitermitinae) in French Guiana.},
journal = {Molecular ecology},
volume = {23},
number = {4},
pages = {902-920},
doi = {10.1111/mec.12641},
pmid = {24372711},
issn = {1365-294X},
mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics ; French Guiana ; *Genetic Speciation ; Isoptera/*classification/genetics ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; },
abstract = {Species delimitation and identification can be arduous for taxa whose morphologic characters are easily confused, which can hamper global biodiversity assessments and pest species management. Exploratory methods of species delimitation that use DNA sequence as their primary information source to establish group membership and estimate putative species boundaries are useful approaches, complementary to traditional taxonomy. Termites of the genus Nasutitermes make interesting models for the application of such methods. They are dominant in Neotropical primary forests but also represent major agricultural and structural pests. Despite the prevalence, pivotal ecological role and economical impact of this group, the taxonomy of Nasutitermes species mainly depends on unreliable characters of soldier external morphology. Here, we generated robust species hypotheses for 79 Nasutitermes colonies sampled throughout French Guiana without any a priori knowledge of species affiliation. Sequence analysis of the mitochondrial cytochrome oxidase II gene was coupled with exploratory species-delimitation tools, using the automatic barcode gap discovery method (ABGD) and a generalized mixed Yule-coalescent model (GMYC) to propose primary species hypotheses (PSHs). PSHs were revaluated using phylogenetic analyses of two more loci (mitochondrial 16S rDNA and nuclear internal transcribed spacer 2) leading to 16 retained secondary species hypotheses (RSSH). Seven RSSHs, represented by 44/79 of the sampled colonies, were morphologically affiliated to species recognized as pests in the Neotropics, where they represent a real invasive pest potential in the context of growing ecosystem anthropization. Multigenic phylogenies based on combined alignments (1426-1784 bp) were also reconstructed to identify ancestral ecological niches and major-pest lineages, revealing that Guyanese pest species do not form monophyletic groups.},
}
@article {pmid24366109,
year = {2014},
author = {Phillips, RD and Scaccabarozzi, D and Retter, BA and Hayes, C and Brown, GR and Dixon, KW and Peakall, R},
title = {Caught in the act: pollination of sexually deceptive trap-flowers by fungus gnats in Pterostylis (Orchidaceae).},
journal = {Annals of botany},
volume = {113},
number = {4},
pages = {629-641},
pmid = {24366109},
issn = {1095-8290},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Diptera/classification/genetics/*physiology ; Flowers/physiology ; Fruit/physiology ; Fungi ; Male ; Orchidaceae/*physiology ; Pollen/physiology ; Pollination ; Reproduction ; Species Specificity ; },
abstract = {BACKGROUND AND AIMS: Pterostylis is an Australasian terrestrial orchid genus of more than 400 species, most of which use a motile, touch-sensitive labellum to trap dipteran pollinators. Despite studies dating back to 1872, the mechanism of pollinator attraction has remained elusive. This study tested whether the fungus gnat-pollinated Pterostylis sanguinea secures pollination by sexual deception.<br><br>METHODS: The literature was used to establish criteria for confirming sexual deception as a pollination strategy. Observations and video recordings allowed quantification of each step of the pollination process. Each floral visitor was sexed and DNA barcoding was used to evaluate the degree of pollinator specificity. Following observations that attraction to the flowers is by chemical cues, experimental dissection of flowers was used to determine the source of the sexual attractant and the effect of labellum orientation on sexual attraction. Fruit set was quantified for 19 populations to test for a relationship with plant density and population size.<br><br>KEY RESULTS: A single species of male gnat (Mycetophilidae) visited and pollinated the rewardless flowers. The gnats often showed probing copulatory behaviour on the labellum, leading to its triggering and the temporary entrapment of the gnat in the flower. Pollen deposition and removal occurred as the gnat escaped from the flower via the reproductive structures. The labellum was the sole source of the chemical attractant. Gnats always alighted on the labellum facing upwards, but when it was rotated 180 &#xb0; they attempted copulation less frequently. Pollination rate showed no relationship with orchid population size or plant density.<br><br>CONCLUSIONS: This study confirms for the first time that highly specific pollination by fungus gnats is achieved by sexual deception in Pterostylis. It is predicted that sexual deception will be widespread in the genus, although the diversity of floral forms suggests that other mechanisms may also operate.},
}
@article {pmid24363983,
year = {2013},
author = {Devi, KD and Punyarani, K and Singh, NS and Devi, HS},
title = {An efficient protocol for total DNA extraction from the members of order Zingiberales- suitable for diverse PCR based downstream applications.},
journal = {SpringerPlus},
volume = {2},
number = {},
pages = {669},
pmid = {24363983},
issn = {2193-1801},
abstract = {Different protocols are usually used for extracting total deoxyribonucleic acid (DNA) from different plant species of same order and DNA of the associated viruses. Here, we describe a rapid, efficient and universal protocol for isolating total DNA from the members of Zingiberales which harbor a high amount of polysaccharides and secondary metabolites. DNA isolated with this protocol was successfully used for PCR based downstream applications viz. random amplified polymorphic DNA (RAPD), Inter-simple sequence repeats (ISSR), DNA barcoding gene (Internal transcribed spacer and trnl-f) amplification and detection of the viruses.},
}
@article {pmid24363574,
year = {2013},
author = {Dehling, JM and Sinsch, U},
title = {Diversity of Ptychadena in Rwanda and taxonomic status of P. chrysogaster Laurent, 1954 (Amphibia, Anura, Ptychadenidae).},
journal = {ZooKeys},
volume = {},
number = {356},
pages = {69-102},
pmid = {24363574},
issn = {1313-2989},
abstract = {We assess the diversity of Ptychadena species in Rwanda based on re-examination of voucher specimens in museum collections and our own data from recent assessment of the species composition of amphibian communities in Rwanda. We recognize five species which we allocate to the following available names: P. anchietae, P. chrysogaster, P. nilotica, P. porosissima, and P. uzungwensis. We did not find evidence for the presence of P. grandisonae and P. oxyrhynchus which have been listed for the country. The five species can be distinguished by quantitative morphometrics (discriminant analysis, success rate: 100 %) and a number of qualitative characters of external morphology. We provide an identification key to the Rwandan species and describe the morphology of each species in detail. The taxonomic status and the phylogenetic position of Ptychadena chrysogaster are further assessed based on the partial sequence of the mitochondrial 16S rRNA. The species differs genetically from available homologous sequences from congeners by an uncorrected p distance of at least 4.2 % and appears to be most closely related to specimens assigned to P. porosissima, P. mahnerti, "P. aff. uzungwensis" and "P. aff. bibroni".},
}
@article {pmid24363568,
year = {2013},
author = {Rota, J and Miller, SE},
title = {A new genus of metalmark moths (Lepidoptera, Choreutidae) with Afrotropical and Australasian distribution.},
journal = {ZooKeys},
volume = {},
number = {355},
pages = {29-47},
pmid = {24363568},
issn = {1313-2989},
abstract = {Niveas Rota, new genus, and its two new species, N. agassizi Rota, new species, and N. kone Rota, new species, are described and illustrated. Niveas is assigned to the subfamily Choreutinae based on morphological and molecular data. Niveas agassizi is currently known only from Kenya and only from female specimens. Niveas kone has been found on the Solomon Islands and in Papua New Guinea (PNG). In PNG, larvae of this species have been reared from several species of Ficus (Moraceae). The two species are superficially quite dissimilar from each other. However, they share features in wing pattern and venation, as well as female genitalia, and the molecular data strongly support the monophyly of Niveas.},
}
@article {pmid24358363,
year = {2013},
author = {Hausmann, A and Godfray, HC and Huemer, P and Mutanen, M and Rougerie, R and van Nieukerken, EJ and Ratnasingham, S and Hebert, PD},
title = {Genetic patterns in European geometrid moths revealed by the Barcode Index Number (BIN) system.},
journal = {PloS one},
volume = {8},
number = {12},
pages = {e84518},
pmid = {24358363},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; *DNA Barcoding, Taxonomic ; Europe ; Female ; Male ; Moths/*classification/*genetics ; },
abstract = {BACKGROUND: The geometrid moths of Europe are one of the best investigated insect groups in traditional taxonomy making them an ideal model group to test the accuracy of the Barcode Index Number (BIN) system of BOLD (Barcode of Life Datasystems), a method that supports automated, rapid species delineation and identification.<br><br>This study provides a DNA barcode library for 219 of the 249 European geometrid moth species (88%) in five selected subfamilies. The data set includes COI sequences for 2130 specimens. Most species (93%) were found to possess diagnostic barcode sequences at the European level while only three species pairs (3%) were genetically indistinguishable in areas of sympatry. As a consequence, 97% of the European species we examined were unequivocally discriminated by barcodes within their natural areas of distribution. We found a 1:1 correspondence between BINs and traditionally recognized species for 67% of these species. Another 17% of the species (15 pairs, three triads) shared BINs, while specimens from the remaining species (18%) were divided among two or more BINs. Five of these species are mixtures, both sharing and splitting BINs. For 82% of the species with two or more BINs, the genetic splits involved allopatric populations, many of which have previously been hypothesized to represent distinct species or subspecies.<br><br>CONCLUSIONS/SIGNIFICANCE: This study confirms the effectiveness of DNA barcoding as a tool for species identification and illustrates the potential of the BIN system to characterize formal genetic units independently of an existing classification. This suggests the system can be used to efficiently assess the biodiversity of large, poorly known assemblages of organisms. For the moths examined in this study, cases of discordance between traditionally recognized species and BINs arose from several causes including overlooked species, synonymy, and cases where DNA barcodes revealed regional variation of uncertain taxonomic significance.},
}
@article {pmid24358258,
year = {2013},
author = {Bowser, AK and Diamond, AW and Addison, JA},
title = {From puffins to plankton: a DNA-based analysis of a seabird food chain in the northern Gulf of Maine.},
journal = {PloS one},
volume = {8},
number = {12},
pages = {e83152},
pmid = {24358258},
issn = {1932-6203},
mesh = {Animals ; Charadriiformes/*genetics ; DNA/*analysis ; DNA Barcoding, Taxonomic ; Diet ; Electron Transport Complex IV/analysis/genetics ; Fishes/genetics ; *Food Chain ; Gastrointestinal Contents/chemistry ; High-Throughput Nucleotide Sequencing ; Maine ; Plankton/*genetics ; RNA, Ribosomal, 16S/analysis/genetics ; },
abstract = {The predator-prey interactions within food chains are used to both characterize and understand ecosystems. Conventional methods of constructing food chains from visual identification of prey in predator diet can suffer from poor taxonomic resolution, misidentification, and bias against small or completely digestible prey. Next-generation sequencing (NGS) technology has become a powerful tool for diet reconstruction through barcoding of DNA in stomach content or fecal samples. Here we use multi-locus (16S and CO1) next-generation sequencing of DNA barcodes on the feces of Atlantic puffin (Fratercula arctica) chicks (n=65) and adults (n=64) and the stomach contents of their main prey, Atlantic herring (Clupea harengus, n=44) to investigate a previously studied food chain. We compared conventional and molecular-derived chick diet, tested the similarity between the diets of puffin adults and chicks, and determined whether herring prey can be detected in puffin diet samples. There was high variability in the coverage of prey groups between 16S and CO1 markers. We identified more unique prey with our 16S compared to CO1 barcoding markers (51 and 39 taxa respectively) with only 12 taxa identified by both genes. We found no significant difference between the 16S-identified diets of puffin adults (n=17) and chicks (n=41). Our molecular method is more taxonomically resolved and detected chick prey at higher frequencies than conventional field observations. Many likely planktonic prey of herring were detected in feces from puffin adults and chicks, highlighting the impact secondary consumption may have on the interpretation of molecular dietary analysis. This study represents the first simultaneous molecular investigation into the diet of multiple components of a food chain and highlights the utility of a multi-locus approach to diet reconstruction that is broadly applicable to food web analysis.},
}
@article {pmid24357310,
year = {2013},
author = {Harris, SE and Bellino, M},
title = {IBI* series winner. DNA barcoding from NYC to Belize.},
journal = {Science (New York, N.Y.)},
volume = {342},
number = {6165},
pages = {1462-1463},
doi = {10.1126/science.1230006},
pmid = {24357310},
issn = {1095-9203},
mesh = {Animals ; Belize ; *Biodiversity ; Biology/*education ; Curriculum ; DNA Barcoding, Taxonomic/*statistics &amp; numerical data ; Fish Products/classification ; Fishes/classification ; New York ; Research/*education ; Universities ; },
}
@article {pmid24348895,
year = {2013},
author = {Saarela, JM and Sokoloff, PC and Gillespie, LJ and Consaul, LL and Bull, RD},
title = {DNA barcoding the Canadian Arctic flora: core plastid barcodes (rbcL + matK) for 490 vascular plant species.},
journal = {PloS one},
volume = {8},
number = {10},
pages = {e77982},
pmid = {24348895},
issn = {1932-6203},
mesh = {Arctic Regions ; Biodiversity ; Canada ; *DNA Barcoding, Taxonomic ; Genetic Variation ; Haplotypes ; Plants/classification/*genetics ; Plastids/*genetics ; Ribulose-Bisphosphate Carboxylase/chemistry/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Accurate identification of Arctic plant species is critical for understanding potential climate-induced changes in their diversity and distributions. To facilitate rapid identification we generated DNA barcodes for the core plastid barcode loci (rbcL and matK) for 490 vascular plant species, representing nearly half of the Canadian Arctic flora and 93% of the flora of the Canadian Arctic Archipelago. Sequence recovery was higher for rbcL than matK (93% and 81%), and rbcL was easier to recover than matK from herbarium specimens (92% and 77%). Distance-based and sequence-similarity analyses of combined rbcL + matK data discriminate 97% of genera, 56% of species, and 7% of infraspecific taxa. There is a significant negative correlation between the number of species sampled per genus and the percent species resolution per genus. We characterize barcode variation in detail in the ten largest genera sampled (Carex, Draba, Festuca, Pedicularis, Poa, Potentilla, Puccinellia, Ranunculus, Salix, and Saxifraga) in the context of their phylogenetic relationships and taxonomy. Discrimination with the core barcode loci in these genera ranges from 0% in Salix to 85% in Carex. Haplotype variation in multiple genera does not correspond to species boundaries, including Taraxacum, in which the distribution of plastid haplotypes among Arctic species is consistent with plastid variation documented in non-Arctic species. Introgression of Poa glauca plastid DNA into multiple individuals of P. hartzii is problematic for identification of these species with DNA barcodes. Of three supplementary barcode loci (psbA-trnH, psbK-psbI, atpF-atpH) collected for a subset of Poa and Puccinellia species, only atpF-atpH improved discrimination in Puccinellia, compared with rbcL and matK. Variation in matK in Vaccinium uliginosum and rbcL in Saxifraga oppositifolia corresponds to variation in other loci used to characterize the phylogeographic histories of these Arctic-alpine species.},
}
@article {pmid24343640,
year = {2014},
author = {Lücking, R and Lawrey, JD and Gillevet, PM and Sikaroodi, M and Dal-Forno, M and Berger, SA},
title = {Multiple ITS haplotypes in the genome of the lichenized basidiomycete Cora inversa (Hygrophoraceae): fact or artifact?.},
journal = {Journal of molecular evolution},
volume = {78},
number = {2},
pages = {148-162},
pmid = {24343640},
issn = {1432-1432},
mesh = {Basidiomycota/classification/*genetics ; Biodiversity ; *DNA, Ribosomal Spacer ; Evolution, Molecular ; Genetic Variation ; *Genome, Fungal ; *Haplotypes ; Mutagenesis, Insertional ; },
abstract = {The internal transcribed spacer region (ITS) of the nuclear rDNA cistron represents the barcoding locus for Fungi. Intragenomic variation of this multicopy gene can interfere with accurate phylogenetic reconstruction of biological entities. We investigated the amount and nature of this variation for the lichenized fungus Cora inversa in the Hygrophoraceae (Basidiomycota: Agaricales), analyzing base call and length variation in ITS1 454 pyrosequencing data of three samples of the target mycobiont, for a total of 16,665 reads obtained from three separate repeats of the same samples under different conditions. Using multiple fixed alignment methods (PaPaRa) and maximum likelihood phylogenetic analysis (RAxML), we assessed phylogenetic relationships of the obtained reads, together with Sanger ITS sequences from the same samples. Phylogenetic analysis showed that all ITS1 reads belonged to a single species, C. inversa. Pyrosequencing data showed 266 insertion sites in addition to the 325 sites expected from Sanger sequences, for a total of 15,654 insertions (0.94 insertions per read). An additional 3,279 substitutions relative to the Sanger sequences were detected in the dataset, out of 5,461,125 bases to be called. Up to 99.3% of the observed indels in the dataset could be interpreted as 454 pyrosequencing errors, approximately 65% corresponding to incorrectly recovered homopolymer segments, and 35% to carry-forward-incomplete-extension errors. Comparison of automated clustering and alignment-based phylogenetic analysis demonstrated that clustering of these reads produced a 35-fold overestimation of biological diversity in the dataset at the 95% similarity threshold level, whereas phylogenetic analysis using a maximum likelihood approach accurately recovered a single biological entity. We conclude that variation detected in 454 pyrosequencing data must be interpreted with great care and that a combination of a sufficiently large number of reads per taxon, a set of Sanger references for the same taxon, and at least two runs under different emulsion PCR and sequencing conditions, are necessary to reliably separate biological variation from 454 sequencing errors. Our study shows that clustering methods are highly sensitive to artifactual sequence variation and inadequate to properly recover biological diversity in a dataset, if sequencing errors are substantial and not removed prior to clustering analysis.},
}
@article {pmid24343362,
year = {2013},
author = {Little, DP and Jeanson, ML},
title = {DNA barcode authentication of saw palmetto herbal dietary supplements.},
journal = {Scientific reports},
volume = {3},
number = {},
pages = {3518},
pmid = {24343362},
issn = {2045-2322},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant ; *Dietary Supplements/standards ; Fruit/genetics ; Genetic Markers ; Genetic Variation ; *Plant Extracts/standards ; Serenoa/*classification/*genetics ; },
abstract = {Herbal dietary supplements made from saw palmetto (Serenoa repens; Arecaceae) fruit are commonly consumed to ameliorate benign prostate hyperplasia. A novel DNA mini-barcode assay to accurately identify [specificity = 1.00 (95% confidence interval = 0.74-1.00); sensitivity = 1.00 (95% confidence interval = 0.66-1.00); n = 31] saw palmetto dietary supplements was designed from a DNA barcode reference library created for this purpose. The mini-barcodes were used to estimate the frequency of mislabeled saw palmetto herbal dietary supplements on the market in the United States of America. Of the 37 supplements examined, amplifiable DNA could be extracted from 34 (92%). Mini-barcode analysis of these supplements demonstrated that 29 (85%) contain saw palmetto and that 2 (6%) supplements contain related species that cannot be legally sold as herbal dietary supplements in the United States of America. The identity of 3 (9%) supplements could not be conclusively determined.},
}
@article {pmid24342484,
year = {2013},
author = {Malloch, L and Kadivar, K and Putz, J and Levett, PN and Tang, J and Hatchette, TF and Kadkhoda, K and Ng, D and Ho, J and Kim, J},
title = {Comparative evaluation of the Bio-Rad Geenius HIV-1/2 Confirmatory Assay and the Bio-Rad Multispot HIV-1/2 Rapid Test as an alternative differentiation assay for CLSI M53 algorithm-I.},
journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology},
volume = {58 Suppl 1},
number = {},
pages = {e85-91},
doi = {10.1016/j.jcv.2013.08.008},
pmid = {24342484},
issn = {1873-5967},
mesh = {Algorithms ; Clinical Laboratory Techniques/*methods ; Diagnostic Tests, Routine/*methods ; HIV Antibodies/*blood ; HIV Infections/*diagnosis/*virology ; HIV-1/*classification/immunology ; HIV-2/*classification/immunology ; Humans ; Immunoassay/methods ; Predictive Value of Tests ; Sensitivity and Specificity ; Virology/methods ; },
abstract = {INTRODUCTION: The CLSI-M53-A, Criteria for Laboratory Testing and Diagnosis of Human Immunodeficiency Virus (HIV) Infection; Approved Guideline includes an algorithm in which samples that are reactive on a 4th generation EIA screen proceed to a supplemental assay that is able to confirm and differentiate between antibodies to HIV-1 and HIV-2. The recently CE-marked Bio-Rad Geenius HIV-1/2 Confirmatory Assay was evaluated as an alternative to the FDA-approved Bio-Rad Multispot HIV-1/HIV-2 Rapid Test which has been previously validated for use in this new algorithm.<br><br>METHODS: This study used reference samples submitted to the Canadian - NLHRS and samples from commercial sources. Data was tabulated in 2&#xd7;2 tables for statistical analysis; sensitivity, specificity, predictive values, kappa and likelihood ratios.<br><br>RESULTS: The overall performance of the Geenius and Multispot was very high; sensitivity (100%, 100%), specificity (96.3%, 99.1%), positive (45.3, 181) and negative (0, 0) likelihood ratios respectively, high kappa (0.96) and low bias index (0.0068). The ability to differentiate HIV-1 (99.2%, 100%) and HIV-2 (98.1%, 98.1%) Ab was also very high.<br><br>CONCLUSION: The Bio-Rad Geenius HIV-1/2 Confirmatory Assay is a suitable alternative to the validated Multispot for use in the second stage of CLSI M53 algorithm-I. The Geenius has additional features including traceability and sample and cassette barcoding that improve the quality management/assurance of HIV testing. It is anticipated that the CLSI M53 guideline and assays such as the Geenius will reduce the number of indeterminate test results previously associated with the HIV-1 WB and improve the ability to differentiate HIV-2 infections.},
}
@article {pmid24340028,
year = {2013},
author = {Kazi, MA and Reddy, CR and Jha, B},
title = {Molecular phylogeny and barcoding of Caulerpa (Bryopsidales) based on the tufA, rbcL, 18S rDNA and ITS rDNA genes.},
journal = {PloS one},
volume = {8},
number = {12},
pages = {e82438},
pmid = {24340028},
issn = {1932-6203},
mesh = {Caulerpa/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; DNA, Ribosomal/*genetics ; Mitochondrial Proteins/*genetics ; Peptide Elongation Factor Tu/*genetics ; *Phylogeny ; RNA, Plant/*genetics ; RNA, Ribosomal, 18S/*genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; },
abstract = {The biodiversity assessment of different taxa of the genus Caulerpa is of interest from the context of morphological plasticity, invasive potential of some species and biotechnological and pharmacological applications. The present study investigated the identification and molecular phylogeny of different species of Caulerpa occurring along the Indian coast inferred from tufA, rbcL, 18S rDNA and ITS rDNA nucleotide sequences. Molecular data confirmed the identification of 10 distinct Caulerpa species: C. veravalensis, C. verticillata, C. racemosa, C. microphysa, C. taxifolia, C. sertularioides, C. scalpelliformis, C. serrulata, C. peltata and C. mexicana. All datasets significantly supported the sister relationship between C. veravalensis and C. racemosa var. cylindracea. It was also concluded from the results that the specimen identified previously as C. microphysa and C. lentillifera could not be considered as separate species. The molecular data revealed the presence of multiple lineages for C. racemosa which can be resolved into separate species. All four markers were used to ascertain their utility for DNA barcoding. The tufA gene proved a better marker with monophyletic association as the main criteria for identification at the species level. The results also support the use of 18S rDNA insertion sequences to delineate the Caulerpa species through character-based barcoding. The ITS rDNA (5.8S-ITS2) phylogenetic analysis also served as another supporting tool. Further, more sequences from additional Caulerpa specimens will need to be analysed in order to support the role of these two markers (ITS rDNA and 18S insertion sequence) in identification of Caulerpa species. The present study revealed the phylogeny of Caulerpa as complete as possible using the currently available data, which is the first comprehensive report illustrating the molecular phylogeny and barcoding of the genus Caulerpa from Indian waters.},
}
@article {pmid24339363,
year = {2014},
author = {Zhou, QS and Xi, YQ and Yu, F and Zhang, X and Li, XJ and Liu, CL and Niu, ZQ and Zhu, CD and Qiao, GX and Zhang, YZ},
title = {Application of DNA barcoding to the identification of Hymenoptera parasitoids from the soybean aphid (Aphis glycines) in China.},
journal = {Insect science},
volume = {21},
number = {3},
pages = {363-373},
doi = {10.1111/1744-7917.12095},
pmid = {24339363},
issn = {1744-7917},
mesh = {Animals ; Cell Nucleus/genetics ; China ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Hymenoptera/*classification/genetics/*physiology ; Sequence Analysis, DNA ; Glycine max/*parasitology ; },
abstract = {Aphis glycines Matsumura is an important pest of soybean in Asia and North America. Hymenoptera parasitoids play a key role in the control of the soybean aphid. The correct identification of parasitoids is a critical step that precedes the assessment of their potential biological control agents. Accurate identification of the majority of the species attacking the soybean aphid often requires elaborate specimen preparation and expert taxonomic knowledge. In this study, we facilitated the identification of soybean aphid parasitoids by applying a DNA barcoding approach following a preliminary morphological identification. We generated DNA sequence data from the mitochondrial COI gene and the D2 region of 28S rDNA to assess the genetic variation within and between parasitoid species emerging from the soybean aphid in China. Fifteen Hymenoptera parasitoid species belonging to 10 genera of five families were identified with little intra-specific variation (0.09% ± 0.06% for 28S and 0.36% ± 0.18% for COI) and large inter-specific divergence (30.46% ± 3.42% for 28S and 20.4% ± 1.20% for COI).},
}
@article {pmid24338354,
year = {2014},
author = {Preston, MD and Assefa, SA and Ocholla, H and Sutherland, CJ and Borrmann, S and Nzila, A and Michon, P and Hien, TT and Bousema, T and Drakeley, CJ and Zongo, I and Ouédraogo, JB and Djimde, AA and Doumbo, OK and Nosten, F and Fairhurst, RM and Conway, DJ and Roper, C and Clark, TG},
title = {PlasmoView: a web-based resource to visualise global Plasmodium falciparum genomic variation.},
journal = {The Journal of infectious diseases},
volume = {209},
number = {11},
pages = {1808-1815},
pmid = {24338354},
issn = {1537-6613},
support = {WT084289MA/WT_/Wellcome Trust/United Kingdom ; 101113/WT_/Wellcome Trust/United Kingdom ; /ImNIH/Intramural NIH HHS/United States ; TGC MR/J005398/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Base Sequence ; DNA, Protozoan/genetics ; Genome, Protozoan/*genetics ; Humans ; *Internet ; Malaria, Falciparum/epidemiology/*parasitology ; Molecular Sequence Annotation ; Plasmodium falciparum/*genetics ; Polymorphism, Single Nucleotide/*genetics ; },
abstract = {Malaria is a global public health challenge, with drug resistance a major barrier to disease control and elimination. To meet the urgent need for better treatments and vaccines, a deeper knowledge of Plasmodium biology and malaria epidemiology is required. An improved understanding of the genomic variation of malaria parasites, especially the most virulent Plasmodium falciparum (Pf) species, has the potential to yield new insights in these areas. High-throughput sequencing and genotyping is generating large amounts of genomic data across multiple parasite populations. The resulting ability to identify informative variants, particularly single-nucleotide polymorphisms (SNPs), will lead to the discovery of intra- and inter-population differences and thus enable the development of genetic barcodes for diagnostic assays and clinical studies. Knowledge of genetic variability underlying drug resistance and other differential phenotypes will also facilitate the identification of novel mutations and contribute to surveillance and stratified medicine applications. The PlasmoView interactive web-browsing tool enables the research community to visualise genomic variation and annotation (eg, biological function) in a geographic setting. The first release contains over 600,000 high-quality SNPs in 631 Pf isolates from laboratory strains and four malaria-endemic regions (West Africa, East Africa, Southeast Asia and Oceania).},
}
@article {pmid24336133,
year = {2013},
author = {, },
title = {Progress in immunization information systems - United States, 2012.},
journal = {MMWR. Morbidity and mortality weekly report},
volume = {62},
number = {49},
pages = {1005-1008},
pmid = {24336133},
issn = {1545-861X},
mesh = {Adult ; Child, Preschool ; Healthy People Programs ; Humans ; Immunization/*statistics &amp; numerical data ; Immunization Programs/*statistics &amp; numerical data ; Infant ; Information Systems/*trends ; Medical Records/statistics &amp; numerical data ; United States ; Vaccines/*administration &amp; dosage/supply &amp; distribution ; },
abstract = {Immunization information systems (IIS) are confidential, computerized, population-based systems that collect and consolidate vaccination data from vaccination providers that can be used in designing and sustaining effective immunization strategies. To monitor progress toward achieving IIS program goals, CDC annually surveys immunization program grantees using the IIS Annual Report (IISAR). Results from the 2012 IISAR, completed by 54 of 56 grantees, indicate that 86% (19.5 million) of U.S. children aged <6 years, and 25% (57.8 million) of U.S. adults participated in IIS. Eight of 12 minimum functional standards for IIS published by the National Vaccine Advisory Committee (NVAC) have been met by ≥90% of grantees. During 2011-2012, progress was also made in meeting three additional functional standards, including the presence of core data element fields, timeliness of vaccine records, and Health Level 7 (HL7) messaging, and will be monitored in new functional standards for IIS published in 2013. Several new and ongoing initiatives, including interoperability between IIS and electronic health records (i.e., ensuring systems can work together and exchange information), the use of IIS to support vaccine ordering and inventory management, the use of two-dimensional barcodes to record vaccination information, and collaboration with pharmacies, federal agencies, and other adult vaccination providers, will support further progress in meeting functional standards and enhance reporting of adult vaccinations to IIS.},
}
@article {pmid24327775,
year = {2013},
author = {Gou, H and Guan, G and Ma, M and Liu, A and Liu, Z and Xu, Z and Ren, Q and Li, Y and Yang, J and Chen, Z and Yin, H and Luo, J},
title = {Phylogenetic analysis of ruminant Theileria spp. from China based on 28S ribosomal RNA gene.},
journal = {The Korean journal of parasitology},
volume = {51},
number = {5},
pages = {511-517},
pmid = {24327775},
issn = {1738-0006},
mesh = {Animals ; Base Sequence ; China ; DNA, Ribosomal/chemistry/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 28S/genetics ; Ruminants ; Sequence Alignment ; Sequence Analysis, DNA/veterinary ; Theileria/*classification/genetics/isolation &amp; purification ; Theileriasis/*parasitology ; },
abstract = {Species identification using DNA sequences is the basis for DNA taxonomy. In this study, we sequenced the ribosomal large-subunit RNA gene sequences (3,037-3,061 bp) in length of 13 Chinese Theileria stocks that were infective to cattle and sheep. The complete 28S rRNA gene is relatively difficult to amplify and its conserved region is not important for phylogenetic study. Therefore, we selected the D2-D3 region from the complete 28S rRNA sequences for phylogenetic analysis. Our analyses of 28S rRNA gene sequences showed that the 28S rRNA was useful as a phylogenetic marker for analyzing the relationships among Theileria spp. in ruminants. In addition, the D2-D3 region was a short segment that could be used instead of the whole 28S rRNA sequence during the phylogenetic analysis of Theileria, and it may be an ideal DNA barcode.},
}
@article {pmid24324859,
year = {2013},
author = {Ando, H and Setsuko, S and Horikoshi, K and Suzuki, H and Umehara, S and Inoue-Murayama, M and Isagi, Y},
title = {Diet analysis by next-generation sequencing indicates the frequent consumption of introduced plants by the critically endangered red-headed wood pigeon (Columba janthina nitens) in oceanic island habitats.},
journal = {Ecology and evolution},
volume = {3},
number = {12},
pages = {4057-4069},
pmid = {24324859},
issn = {2045-7758},
abstract = {Oceanic island ecosystems are vulnerable to the introduction of alien species, and they provide a habitat for many endangered species. Knowing the diet of an endangered animal is important for appropriate nature restoration efforts on oceanic islands because introduced species may be a major component of the diets of some endangered species. DNA barcoding techniques together with next-generation sequencing may provide more detailed information on animal diets than other traditional methods. We performed a diet analysis using 48 fecal samples from the critically endangered red-headed wood pigeon that is endemic to the Ogasawara Islands based on chloroplast trnL P6 loop sequences. The frequency of each detected plant taxa was compared with a microhistological analysis of the same sample set. The DNA barcoding approach detected a much larger number of plants than the microhistological analysis. Plants that were difficult to identify by microhistological analysis after being digested in the pigeon stomachs were frequently identified only by DNA barcoding. The results of the barcoding analysis indicated the frequent consumption of introduced species, in addition to several native species, by the red-headed wood pigeon. The rapid eradication of specific introduced species may reduce the food resources available to this endangered bird; thus, balancing eradication efforts with the restoration of native food plants should be considered. Although some technical problems still exist, the trnL approach to next-generation sequencing may contribute to a better understanding of oceanic island ecosystems and their conservation.},
}
@article {pmid24314114,
year = {2014},
author = {Bhattacharjee, MJ and Ghosh, SK},
title = {Design of mini-barcode for catfishes for assessment of archival biodiversity.},
journal = {Molecular ecology resources},
volume = {14},
number = {3},
pages = {469-477},
doi = {10.1111/1755-0998.12198},
pmid = {24314114},
issn = {1755-0998},
mesh = {Animals ; *Biodiversity ; Catfishes/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Electron Transport Complex IV/genetics ; Fish Proteins/genetics ; Molecular Sequence Data ; Phylogeny ; },
abstract = {Recovery of DNA barcode sequences is often challenging from the archived specimens. However, short fragments of DNA may be recovered, which would significantly improve many unresolved taxonomic conflicts. Here, we designed a mini-barcode for catfishes comprising several species and many cryptic taxa. We analysed a data set of 3048 publicly available COI barcode sequences representing 547 worldwide catfish species and performed 152 628 interspecies comparisons. A significantly more positively correlated interspecies distance was detected with transversion (0.78, P < 0.001) than with transition (0.70, P < 0.001). This suggested that transversions were better diagnostics for species identification. In the aligned data set, two transversion-rich fragments (53 bp and 119 bp) were identified. Transition/transversion bias value was 1.04 in 53-bp fragment, 1.23 in 119-bp fragment and 1.50 in full-length barcode. The interspecies distance with full-length barcode was 0.212 ± 0.037, while that with 53-bp and 119-bp fragments was 0.325 ± 0.039 and 0.218 ± 0.045, respectively. Survey of 53-bp fragment showed a possibility of only 1144 barcodes, while that of 119-bp fragment showed >4 million barcodes. Thus, the 119-bp fragment is a viable mini-barcode for catfishes comprising >3000 extant species. Experiment with 82 archived catfishes showed successful recovery of this mini-barcode using the designed primer. The mini-barcode sequences showed species-specific similarity in the range of 98-100% with the global database. Therefore, survey of a transversion-rich fragment within the full-length barcode would be an ideal approach of mini-barcode design for biodiversity assessment.},
}
@article {pmid24312258,
year = {2013},
author = {Little, DP and Knopf, P and Schulz, C},
title = {DNA barcode identification of Podocarpaceae--the second largest conifer family.},
journal = {PloS one},
volume = {8},
number = {11},
pages = {e81008},
pmid = {24312258},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Genetic Variation ; Phylogeny ; Species Specificity ; Tracheophyta/*classification/*genetics ; },
abstract = {We have generated matK, rbcL, and nrITS2 DNA barcodes for 320 specimens representing all 18 extant genera of the conifer family Podocarpaceae. The sample includes 145 of the 198 recognized species. Comparative analyses of sequence quality and species discrimination were conducted on the 159 individuals from which all three markers were recovered (representing 15 genera and 97 species). The vast majority of sequences were of high quality (B 30 = 0.596-0.989). Even the lowest quality sequences exceeded the minimum requirements of the BARCODE data standard. In the few instances that low quality sequences were generated, the responsible mechanism could not be discerned. There were no statistically significant differences in the discriminatory power of markers or marker combinations (p = 0.05). The discriminatory power of the barcode markers individually and in combination is low (56.7% of species at maximum). In some instances, species discrimination failed in spite of ostensibly useful variation being present (genotypes were shared among species), but in many cases there was simply an absence of sequence variation. Barcode gaps (maximum intraspecific p-distance > minimum interspecific p-distance) were observed in 50.5% of species when all three markers were considered simultaneously. The presence of a barcode gap was not predictive of discrimination success (p = 0.02) and there was no statistically significant difference in the frequency of barcode gaps among markers (p = 0.05). In addition, there was no correlation between number of individuals sampled per species and the presence of a barcode gap (p = 0.27).},
}
@article {pmid24307551,
year = {2014},
author = {Patel, A and Schwab, R and Liu, YT and Bafna, V},
title = {Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations.},
journal = {Genome research},
volume = {24},
number = {2},
pages = {318-328},
pmid = {24307551},
issn = {1549-5469},
support = {U54 HL108460/HL/NHLBI NIH HHS/United States ; R01 HG004962/HG/NHGRI NIH HHS/United States ; P30 CA023100/CA/NCI NIH HHS/United States ; R01 GM114362/GM/NIGMS NIH HHS/United States ; 5R01-HG004962/HG/NHGRI NIH HHS/United States ; },
mesh = {Algorithms ; Chromosome Aberrations ; *Chromosome Breakpoints ; Cyclin-Dependent Kinase Inhibitor p16/*genetics ; Exome/genetics ; Genome, Human ; Genomic Structural Variation/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; MCF-7 Cells ; Neoplasms/*genetics ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Sequence Deletion/genetics ; Translocation, Genetic ; },
abstract = {Deletion of tumor-suppressor genes as well as other genomic rearrangements pervade cancer genomes across numerous types of solid tumor and hematologic malignancies. However, even for a specific rearrangement, the breakpoints may vary between individuals, such as the recurrent CDKN2A deletion. Characterizing the exact breakpoints for structural variants (SVs) is useful for designating patient-specific tumor biomarkers. We propose AmBre (Amplification of Breakpoints), a method to target SV breakpoints occurring in samples composed of heterogeneous tumor and germline DNA. Additionally, AmBre validates SVs called by whole-exome/genome sequencing and hybridization arrays. AmBre involves a PCR-based approach to amplify the DNA segment containing an SV's breakpoint and then confirms breakpoints using sequencing by Pacific Biosciences RS. To amplify breakpoints with PCR, primers tiling specified target regions are carefully selected with a simulated annealing algorithm to minimize off-target amplification and maximize efficiency at capturing all possible breakpoints within the target regions. To confirm correct amplification and obtain breakpoints, PCR amplicons are combined without barcoding and simultaneously long-read sequenced using a single SMRT cell. Our algorithm efficiently separates reads based on breakpoints. Each read group supporting the same breakpoint corresponds with an amplicon and a consensus amplicon sequence is called. AmBre was used to discover CDKN2A deletion breakpoints in cancer cell lines: A549, CEM, Detroit562, MOLT4, MCF7, and T98G. Also, we successfully assayed RUNX1-RUNX1T1 reciprocal translocations by finding both breakpoints in the Kasumi-1 cell line. AmBre successfully targets SVs where DNA harboring the breakpoints are present in 1:1000 mixtures.},
}
@article {pmid24304095,
year = {2014},
author = {Anderson, EC and Skaug, HJ and Barshis, DJ},
title = {Next-generation sequencing for molecular ecology: a caveat regarding pooled samples.},
journal = {Molecular ecology},
volume = {23},
number = {3},
pages = {502-512},
doi = {10.1111/mec.12609},
pmid = {24304095},
issn = {1365-294X},
mesh = {Alleles ; Animals ; Fishes/*genetics ; *Genetics, Population ; High-Throughput Nucleotide Sequencing/*methods ; *Models, Genetic ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/*methods ; },
abstract = {We develop a model based on the Dirichlet-compound multinomial distribution (CMD) and Ewens sampling formula to predict the fraction of SNP loci that will appear fixed for alternate alleles between two pooled samples drawn from the same underlying population. We apply this model to next-generation sequencing (NGS) data from Baltic Sea herring recently published by (Corander et al., 2013, Molecular Ecology, 2931-2940), and show that there are many more fixed loci than expected in the absence of genetic structure. However, we show through coalescent simulations that the degree of population structure required to explain the fraction of alternatively fixed SNPs is extraordinarily high and that the surplus of fixed loci is more likely a consequence of limited representation of individual gene copies in the pooled samples, than it is of population structure. Our analysis signals that the use of NGS on pooled samples to identify divergent SNPs warrants caution. With pooled samples, it is hard to diagnose when an NGS experiment has gone awry; especially when NGS data on pooled samples are of low read depth with a limited number of individuals, it may be worthwhile to temper claims of unexpected population differentiation from pooled samples, pending verification with more reliable methods or stricter adherence to recommended sampling designs for pooled sequencing e.g. Futschik &amp; Schlötterer 2010, Genetics, 186, 207; Gautier et al., 2013a, Molecular Ecology, 3766-3779). Analysis of the data and diagnosis of problems is easier and more reliable (and can be less costly) with individually barcoded samples. Consequently, for some scenarios, individual barcoding may be preferable to pooling of samples.},
}
@article {pmid24301941,
year = {2013},
author = {Noikotr, K and Chaveerach, A and Pinthong, K and Tanomtong, A and Sudmoon, R and Tanee, T},
title = {RAPD and barcode analyses of groupers of the genus Epinephelus.},
journal = {Genetics and molecular research : GMR},
volume = {12},
number = {4},
pages = {5721-5732},
doi = {10.4238/2013.November.18.21},
pmid = {24301941},
issn = {1676-5680},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Fish Proteins/genetics ; *Genetic Variation ; Perciformes/classification/*genetics ; Phylogeny ; Random Amplified Polymorphic DNA Technique ; },
abstract = {The diversity of Epinephelus species was investigated throughout Thailand. Random amplified polymorphic DNA successfully produced 1300 bands that were phylogenetically informative and used to construct cladograms. Values of pairwise genetic similarity (S) within species ranged from 0.65 in E. erythrurus to 0.99 in E. malabaricus. The interspecific values of S ranged from 0.23 between E. malabaricus and E. bleekeri to 0.66 between E. coeruleopunctatus and E. erythrurus. The intraspecific nucleotide variation ranged from 0.037 to 0.159 in the mitochondrially encoded 16S RNA (MT-RNR2) region and from 0.003 to 0.157 for the mitochondrially encoded cytochrome c oxidase I (MT-CO1) region. All sequences were submitted individually to GenBank. The barcode sequences of Thai species of Epinephelus were aligned to the same species found in GenBank. For the MT-RNR2 gene region, intraspecific nucleotide variation ranged from 0.000 to 0.121, and interspecific nucleotide variation ranged from 0.003 to 0.146. For the MT-CO1 gene region, intraspecific nucleotide variation ranged from 0.000 to 0.140, and interspecific nucleotide variation ranged from 0.000 to 0.166. The MT-RNR2 data indicate that some species, including E. bleekeri from India and E. malabaricus from Thailand are not monophyletic. Additionally, the MT-CO1 data indicated that E. bleekeri, E. quoyanus and E. coeruleopunctatus are not monophyletic. The sequences of E. lanceolatus from each country are highly conserved, with genetic distances ranging from 0.000 to 0.003. Another important result from this study is that the barcode sequence from Thai E. erythrurus was previously not present in the GenBank.},
}
@article {pmid24299419,
year = {2014},
author = {Hernández-Triana, LM and Prosser, SW and Rodríguez-Perez, MA and Chaverri, LG and Hebert, PD and Gregory, TR},
title = {Recovery of DNA barcodes from blackfly museum specimens (Diptera: Simuliidae) using primer sets that target a variety of sequence lengths.},
journal = {Molecular ecology resources},
volume = {14},
number = {3},
pages = {508-518},
doi = {10.1111/1755-0998.12208},
pmid = {24299419},
issn = {1755-0998},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/*genetics ; Electron Transport Complex IV/genetics ; Insect Proteins/genetics ; Molecular Sequence Data ; Museums ; Phylogeny ; Simuliidae/*classification/enzymology/*genetics ; },
abstract = {In this study, we evaluated the efficacy of various primers for the purpose of DNA barcoding old, pinned museum specimens of blackflies (Diptera: Simuliidae). We analysed 271 pinned specimens representing two genera and at least 36 species. Due to the age of our material, we targeted overlapping DNA fragments ranging in size from 94 to 407 bp. We were able to recover valid sequences from 215 specimens, of which 18% had 500- to 658-bp barcodes, 36% had 201- to 499-bp barcodes and 46% had 65- to 200-bp barcodes. Our study demonstrates the importance of choosing suitable primers when dealing with older specimens and shows that even very short sequences can be diagnostically informative provided that an appropriate gene region is used. Our study also highlights the lack of knowledge surrounding blackfly taxonomy, and we briefly discuss the need for further phylogenetic studies in this socioeconomically important family of insects.},
}
@article {pmid24298902,
year = {2013},
author = {Nicolè, S and Barcaccia, G and Erickson, DL and Kress, JW and Lucchin, M},
title = {The coding region of the UFGT gene is a source of diagnostic SNP markers that allow single-locus DNA genotyping for the assessment of cultivar identity and ancestry in grapevine (Vitis vinifera L.).},
journal = {BMC research notes},
volume = {6},
number = {},
pages = {502},
pmid = {24298902},
issn = {1756-0500},
mesh = {Base Sequence ; DNA Primers ; Glucosyltransferases/*genetics ; Molecular Sequence Data ; *Polymorphism, Single Nucleotide ; Vitis/*genetics ; },
abstract = {BACKGROUND: Vitis vinifera L. is one of society's most important agricultural crops with a broad genetic variability. The difficulty in recognizing grapevine genotypes based on ampelographic traits and secondary metabolites prompted the development of molecular markers suitable for achieving variety genetic identification.<br><br>FINDINGS: Here, we propose a comparison between a multi-locus barcoding approach based on six chloroplast markers and a single-copy nuclear gene sequencing method using five coding regions combined with a character-based system with the aim of reconstructing cultivar-specific haplotypes and genotypes to be exploited for the molecular characterization of 157 V. vinifera accessions. The analysis of the chloroplast target regions proved the inadequacy of the DNA barcoding approach at the subspecies level, and hence further DNA genotyping analyses were targeted on the sequences of five nuclear single-copy genes amplified across all of the accessions. The sequencing of the coding region of the UFGT nuclear gene (UDP-glucose: flavonoid 3-0-glucosyltransferase, the key enzyme for the accumulation of anthocyanins in berry skins) enabled the discovery of discriminant SNPs (1/34 bp) and the reconstruction of 130 V. vinifera distinct genotypes. Most of the genotypes proved to be cultivar-specific, and only few genotypes were shared by more, although strictly related, cultivars.<br><br>CONCLUSION: On the whole, this technique was successful for inferring SNP-based genotypes of grapevine accessions suitable for assessing the genetic identity and ancestry of international cultivars and also useful for corroborating some hypotheses regarding the origin of local varieties, suggesting several issues of misidentification (synonymy/homonymy).},
}
@article {pmid24295915,
year = {2013},
author = {Harder, CB and Læssøe, T and Frøslev, TG and Ekelund, F and Rosendahl, S and Kjøller, R},
title = {A three-gene phylogeny of the Mycena pura complex reveals 11 phylogenetic species and shows ITS to be unreliable for species identification.},
journal = {Fungal biology},
volume = {117},
number = {11-12},
pages = {764-775},
doi = {10.1016/j.funbio.2013.09.004},
pmid = {24295915},
issn = {1878-6146},
mesh = {Agaricales/*classification/*genetics ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/*genetics ; Genetic Variation ; Molecular Sequence Data ; Peptide Elongation Factor 1/*genetics ; *Phylogeny ; RNA Polymerase II/*genetics ; Sequence Analysis, DNA ; },
abstract = {Phylogenetic analyses of Mycena sect. Calodontes using ITS previously suggested ten cryptic monophyletic ITS lineages within the Mycena pura morphospecies. Here, we compare ITS data (645 bp incl. gaps) from 46 different fruit bodies that represent the previously described ITS diversity with partial tEF-1-α (423 bp) and RNA polymerase II (RPB1) (492 bp) sequence data to test the genealogical concordance. While neither of the markers were in complete topological agreement, the branches differing between the tEF and RPB1 trees had a low bootstrap (<50) support, and the partition homogeneity incongruence length difference (ILD) tests were not significant. ILD tests revealed significant discordances between ITS and the tEF and RPB1 markers in several lineages. And our analyses suggested recombination between ITS1 and ITS2, most pronounced in one phylospecies that was identical in tEF and RPB1. Based on the agreement between tEF and RPB1, we defined 11 mutually concordant terminal clades as phylospecies inside the M. pura morphospecies; most of them cryptic. While neither of the markers showed an unequivocal barcoding gap between inter- and intraspecific diversity, the overlap was most pronounced for ITS (intraspecific diversity 0-3.5 %, interspecific diversity 0.4 %-8.8 %). A clustering analysis on tEF separated at a 1.5 % level returned all phylogenetic species as Operational Taxonomic Units (OTUs), while ITS at both a 1.5 % level and at a 3 % threshold level not only underestimated diversity as found by the tEF and RPB1, but also identified an OTU which was not a phylogenetic species. Thus, our investigation does not support the universal suitability of ITS for species recognition in particular, and emphasises the general limitation of single gene analyses combined with single percentage separation values.},
}
@article {pmid24286499,
year = {2014},
author = {Little, DP},
title = {A DNA mini-barcode for land plants.},
journal = {Molecular ecology resources},
volume = {14},
number = {3},
pages = {437-446},
doi = {10.1111/1755-0998.12194},
pmid = {24286499},
issn = {1755-0998},
mesh = {DNA Barcoding, Taxonomic/instrumentation/*methods ; DNA Primers/genetics ; DNA, Plant/*genetics ; Embryophyta/*classification/*genetics ; Molecular Sequence Data ; Polymerase Chain Reaction/instrumentation/*methods ; },
abstract = {Small portions of the barcode region - mini-barcodes - may be used in place of full-length barcodes to overcome DNA degradation for samples with poor DNA preservation. 591,491,286 rbcL mini-barcode primer combinations were electronically evaluated for PCR universality, and two novel highly universal sets of priming sites were identified. Novel and published rbcL mini-barcode primers were evaluated for PCR amplification [determined with a validated electronic simulation (n = 2765) and empirically (n = 188)], Sanger sequence quality [determined empirically (n = 188)], and taxonomic discrimination [determined empirically (n = 30,472)]. PCR amplification for all mini-barcodes, as estimated by validated electronic simulation, was successful for 90.2-99.8% of species. Overall Sanger sequence quality for mini-barcodes was very low - the best mini-barcode tested produced sequences of adequate quality (B20 ≥ 0.5) for 74.5% of samples. The majority of mini-barcodes provide correct identifications of families in excess of 70.1% of the time. Discriminatory power noticeably decreased at lower taxonomic levels. At the species level, the discriminatory power of the best mini-barcode was less than 38.2%. For samples believed to contain DNA from only one species, an investigator should attempt to sequence, in decreasing order of utility and probability of success, mini-barcodes F (rbcL1/rbcLB), D (F52/R193) and K (F517/R604). For samples believed to contain DNA from more than one species, an investigator should amplify and sequence mini-barcode D (F52/R193).},
}
@article {pmid24282514,
year = {2013},
author = {Wilson, JJ and Sing, KW and Sofian-Azirun, M},
title = {Building a DNA barcode reference library for the true butterflies (Lepidoptera) of Peninsula Malaysia: what about the subspecies?.},
journal = {PloS one},
volume = {8},
number = {11},
pages = {e79969},
pmid = {24282514},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; Butterflies/anatomy &amp; histology/*genetics ; *DNA Barcoding, Taxonomic ; *Databases, Genetic ; Malaysia ; Species Specificity ; },
abstract = {The objective of this study was to build a DNA barcode reference library for the true butterflies of Peninsula Malaysia and assess the value of attaching subspecies names to DNA barcode records. A new DNA barcode library was constructed with butterflies from the Museum of Zoology, University of Malaya collection. The library was analysed in conjunction with publicly available DNA barcodes from other Asia-Pacific localities to test the ability of the DNA barcodes to discriminate species and subspecies. Analyses confirmed the capacity of the new DNA barcode reference library to distinguish the vast majority of species (92%) and revealed that most subspecies possessed unique DNA barcodes (84%). In some cases conspecific subspecies exhibited genetic distances between their DNA barcodes that are typically seen between species, and these were often taxa that have previously been regarded as full species. Subspecies designations as shorthand for geographically and morphologically differentiated groups provide a useful heuristic for assessing how such groups correlate with clustering patterns of DNA barcodes, especially as the number of DNA barcodes per species in reference libraries increases. Our study demonstrates the value in attaching subspecies names to DNA barcode records as they can reveal a history of taxonomic concepts and expose important units of biodiversity.},
}
@article {pmid24280211,
year = {2014},
author = {Hamilton, CA and Hendrixson, BE and Brewer, MS and Bond, JE},
title = {An evaluation of sampling effects on multiple DNA barcoding methods leads to an integrative approach for delimiting species: a case study of the North American tarantula genus Aphonopelma (Araneae, Mygalomorphae, Theraphosidae).},
journal = {Molecular phylogenetics and evolution},
volume = {71},
number = {},
pages = {79-93},
doi = {10.1016/j.ympev.2013.11.007},
pmid = {24280211},
issn = {1095-9513},
mesh = {Animals ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; *Phylogeny ; Sequence Analysis, DNA ; Spiders/*genetics ; United States ; },
abstract = {The North American tarantula genus Aphonopelma provides one of the greatest challenges to species delimitation and downstream identification in spiders because traditional morphological characters appear ineffective for evaluating limits of intra- and interspecific variation in the group. We evaluated the efficacy of numerous molecular-based approaches to species delimitation within Aphonopelma based upon the most extensive sampling of theraphosids to date, while also investigating the sensitivity of randomized taxon sampling on the reproducibility of species boundaries. Mitochondrial DNA (cytochrome c oxidase subunit I) sequences were sampled from 682 specimens spanning the genetic, taxonomic, and geographic breadth of the genus within the United States. The effects of random taxon sampling compared traditional Neighbor-Joining with three modern quantitative species delimitation approaches (ABGD, P ID(Liberal), and GMYC). Our findings reveal remarkable consistency and congruence across various approaches and sampling regimes, while highlighting highly divergent outcomes in GMYC. Our investigation allowed us to integrate methodologies into an efficient, consistent, and more effective general methodological workflow for estimating species boundaries within the mygalomorph spider genus Aphonopelma. Taken alone, these approaches are not particularly useful - especially in the absence of prior knowledge of the focal taxa. Only through the incorporation of multiple lines of evidence, employed in a hypothesis-testing framework, can the identification and delimitation of confident species boundaries be determined. A key point in studying closely related species, and perhaps one of the most important aspects of DNA barcoding, is to combine a sampling strategy that broadly identifies the extent of genetic diversity across the distributions of the species of interest and incorporates previous knowledge into the "species equation" (morphology, molecules, and natural history).},
}
@article {pmid24279427,
year = {2013},
author = {Blagoev, GA and Nikolova, NI and Sobel, CN and Hebert, PD and Adamowicz, SJ},
title = {Spiders (Araneae) of Churchill, Manitoba: DNA barcodes and morphology reveal high species diversity and new Canadian records.},
journal = {BMC ecology},
volume = {13},
number = {},
pages = {44},
pmid = {24279427},
issn = {1472-6785},
mesh = {Animals ; Arctic Regions ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Gene Library ; Genes, Mitochondrial ; Male ; Manitoba ; *Phylogeny ; Spiders/anatomy &amp; histology/*classification/genetics ; },
abstract = {BACKGROUND: Arctic ecosystems, especially those near transition zones, are expected to be strongly impacted by climate change. Because it is positioned on the ecotone between tundra and boreal forest, the Churchill area is a strategic locality for the analysis of shifts in faunal composition. This fact has motivated the effort to develop a comprehensive biodiversity inventory for the Churchill region by coupling DNA barcoding with morphological studies. The present study represents one element of this effort; it focuses on analysis of the spider fauna at Churchill.<br><br>RESULTS: 198 species were detected among 2704 spiders analyzed, tripling the count for the Churchill region. Estimates of overall diversity suggest that another 10-20 species await detection. Most species displayed little intraspecific sequence variation (maximum <1%) in the barcode region of the cytochrome c oxidase subunit I (COI) gene, but four species showed considerably higher values (maximum = 4.1-6.2%), suggesting cryptic species. All recognized species possessed a distinct haplotype array at COI with nearest-neighbour interspecific distances averaging 8.57%. Three species new to Canada were detected: Robertus lyrifer (Theridiidae), Baryphyma trifrons (Linyphiidae), and Satilatlas monticola (Linyphiidae). The first two species may represent human-mediated introductions linked to the port in Churchill, but the other species represents a range extension from the USA. The first description of the female of S. monticola was also presented. As well, one probable new species of Alopecosa (Lycosidae) was recognized.<br><br>CONCLUSIONS: This study provides the first comprehensive DNA barcode reference library for the spider fauna of any region. Few cryptic species of spiders were detected, a result contrasting with the prevalence of undescribed species in several other terrestrial arthropod groups at Churchill. Because most (97.5%) sequence clusters at COI corresponded with a named taxon, DNA barcoding reliably identifies spiders in the Churchill fauna. The capacity of DNA barcoding to enable the identification of otherwise taxonomically ambiguous specimens (juveniles, females) also represents a major advance for future monitoring efforts on this group.},
}
@article {pmid24278118,
year = {2013},
author = {Justine, JL and Rahmouni, C and Gey, D and Schoelinck, C and Hoberg, EP},
title = {The monogenean which lost its clamps.},
journal = {PloS one},
volume = {8},
number = {11},
pages = {e79155},
pmid = {24278118},
issn = {1932-6203},
mesh = {Animals ; Biological Evolution ; DNA, Ribosomal/genetics ; Fish Diseases/*physiopathology ; Trematoda/*pathogenicity ; Trematode Infections ; },
abstract = {Ectoparasites face a daily challenge: to remain attached to their hosts. Polyopisthocotylean monogeneans usually attach to the surface of fish gills using highly specialized structures, the sclerotized clamps. In the original description of the protomicrocotylid species Lethacotyle fijiensis, described 60 years ago, the clamps were considered to be absent but few specimens were available and this observation was later questioned. In addition, genera within the family Protomicrocotylidae have either clamps of the "gastrocotylid" or the "microcotylid" types; this puzzled systematists because these clamp types are characteristic of distinct, major groups. Discovery of another, new, species of the genus Lethacotyle, has allowed us to explore the nature of the attachment structures in protomicrocotylids. Lethacotyle vera n. sp. is described from the gills of the carangid Caranx papuensis off New Caledonia. It is distinguished from Lethacotyle fijiensis, the only other species of the genus, by the length of the male copulatory spines. Sequences of 28S rDNA were used to build a tree, in which Lethacotyle vera grouped with other protomicrocotylids. The identity of the host fish was confirmed with COI barcodes. We observed that protomicrocotylids have specialized structures associated with their attachment organ, such as lateral flaps and transverse striations, which are not known in other monogeneans. We thus hypothesized that the clamps in protomicrocotylids were sequentially lost during evolution, coinciding with the development of other attachment structures. To test the hypothesis, we calculated the surfaces of clamps and body in 120 species of gastrocotylinean monogeneans, based on published descriptions. The ratio of clamp surface: body surface was the lowest in protomicrocotylids. We conclude that clamps in protomicrocotylids are vestigial organs, and that occurrence of "gastrocotylid" and simpler "microcotylid" clamps within the same family are steps in an evolutionary sequence, leading to the absence of these attributes in species of Lethacotyle.},
}
@article {pmid24274093,
year = {2015},
author = {Quilang, JP and Yu, SC},
title = {DNA barcoding of commercially important catfishes in the Philippines.},
journal = {Mitochondrial DNA},
volume = {26},
number = {3},
pages = {435-444},
doi = {10.3109/19401736.2013.855897},
pmid = {24274093},
issn = {1940-1744},
mesh = {Animals ; Catfishes/classification/*genetics ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/analysis/*genetics/metabolism ; Electron Transport Complex IV/genetics ; Genetic Variation ; Philippines ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {Many species of catfish are important resources for human consumption, for sport fishing and for use in aquarium industry. In the Philippines, some species are cultivated and some are caught in the wild for food and a few introduced species have become invasive. In this study, DNA barcoding using the mitochondrial cytochrome c oxidase I (COI) gene was done on commercially and economically important Philippine catfishes. A total of 75 specimens belonging to 11 species and 5 families were DNA barcoded. The genetic distances were computed and Neighbor-Joining (NJ) trees were constructed based on the Kimura 2-Parameter (K2P) method. The average K2P distances within species, genus, family and order were 0.2, 8.2, 12.7 and 21.9%, respectively. COI sequences clustered according to their species designation for 7 of the 11 catfishes. DNA barcoding was not able to discriminate between Arius dispar and A. manillensis and between Pterygoplichthys disjunctivus and P. pardalis. The morphological characters that are used to distinguish between these species do not complement molecular identification through DNA barcoding. DNA barcoding also showed that Clarias batrachus from the Philippines is different from the species found in India and Thailand, which supports earlier suggestions based on morphology that those found in India should be designated as C. magur and those in mainland Southeast Asia as C. aff. batrachus "Indochina". This study has shown that DNA barcoding can be used for species delineation and for tagging some species for further taxonomic investigation, which has implications on proper management and conservation strategies.},
}
@article {pmid24270072,
year = {2014},
author = {Estrada-Bárcenas, DA and Vite-Garín, T and Navarro-Barranco, H and de la Torre-Arciniega, R and Pérez-Mejía, A and Rodríguez-Arellanes, G and Ramirez, JA and Humberto Sahaza, J and Taylor, ML and Toriello, C},
title = {Genetic diversity of Histoplasma and Sporothrix complexes based on sequences of their ITS1-5.8S-ITS2 regions from the BOLD System.},
journal = {Revista iberoamericana de micologia},
volume = {31},
number = {1},
pages = {90-94},
doi = {10.1016/j.riam.2013.10.003},
pmid = {24270072},
issn = {2173-9188},
mesh = {DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; *DNA, Ribosomal Spacer ; *Databases, Genetic ; Genetic Variation ; Histoplasma/classification/*genetics/isolation &amp; purification ; Histoplasmosis/diagnosis/microbiology ; Humans ; *Molecular Diagnostic Techniques ; Mycological Typing Techniques/*methods ; Sporothrix/classification/*genetics/isolation &amp; purification ; Sporotrichosis/diagnosis/microbiology ; },
abstract = {High sensitivity and specificity of molecular biology techniques have proven usefulness for the detection, identification and typing of different pathogens. The ITS (Internal Transcribed Spacer) regions of the ribosomal DNA are highly conserved non-coding regions, and have been widely used in different studies including the determination of the genetic diversity of human fungal pathogens. This article wants to contribute to the understanding of the intra- and interspecific genetic diversity of isolates of the Histoplasma capsulatum and Sporothrix schenckii species complexes by an analysis of the available sequences of the ITS regions from different sequence databases. ITS1-5.8S-ITS2 sequences of each fungus, either deposited in GenBank, or from our research groups (registered in the Fungi Barcode of Life Database), were analyzed using the maximum likelihood (ML) method. ML analysis of the ITS sequences discriminated isolates from distant geographic origins and particular wild hosts, depending on the fungal species analyzed. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012).},
}
@article {pmid24267156,
year = {2014},
author = {Kim, HM and Oh, SH and Bhandari, GS and Kim, CS and Park, CW},
title = {DNA barcoding of Orchidaceae in Korea.},
journal = {Molecular ecology resources},
volume = {14},
number = {3},
pages = {499-507},
doi = {10.1111/1755-0998.12207},
pmid = {24267156},
issn = {1755-0998},
mesh = {DNA Barcoding, Taxonomic ; Genetic Variation ; Molecular Sequence Data ; Orchidaceae/*classification/*genetics ; Phylogeny ; Plant Proteins/genetics ; Republic of Korea ; },
abstract = {Species of Orchidaceae are under severe threat of extinction mainly due to overcollection and habitat destruction; accurate identification of orchid species is critical in conservation biology and sustainable utilization of orchids as plant resources. We examined 647 sequences of the cpDNA regions rbcL, matK, atpF-atpH IGS, psbK-psbI IGS and trnH-psbA IGS from 89 orchid species (95 taxa) and four outgroup taxa to develop an efficient DNA barcode for Orchidaceae in Korea. The five cpDNA barcode regions were successfully amplified and sequenced for all chlorophyllous taxa, but the amplification and sequencing of the same regions in achlorophyllous taxa produced variable results. psbK-psbI IGS showed the highest mean interspecific K2P distance (0.1192), followed by matK (0.0803), atpF-atpH IGS (0.0648), trnH-psbA IGS (0.0460) and rbcL (0.0248). The degree of species resolution for individual barcode regions ranged from 60.5% (rbcL) to 83.5% (trnH-psbA IGS). The degree of species resolution was significantly enhanced in multiregion combinations of the five barcode regions. Of the 26 possible combinations of the five regions, six provided the highest degree of species resolution (98.8%). Among these, a combination of atpF-atpH IGS, psbK-psbI IGS and trnH-psbA IGS, which comprises the least number of DNA regions, is the best option for barcoding of the Korean orchid species.},
}
@article {pmid24266787,
year = {2013},
author = {Hu, Y and Wang, J and Li, C and Wang, Q and Wang, H and Zhu, J and Yang, Y},
title = {Janus photonic crystal microspheres: centrifugation-assisted generation and reversible optical property.},
journal = {Langmuir : the ACS journal of surfaces and colloids},
volume = {29},
number = {50},
pages = {15529-15534},
doi = {10.1021/la404082y},
pmid = {24266787},
issn = {1520-5827},
abstract = {A new strategy to prepare core/shell Janus photonic crystal (PC) microspheres with reversible optical spectrum property is demonstrated. The microfluidic technique was employed to generate the uniform core/shell PC microspheres containing nanogels aqueous suspension. Under centrifugal force, the nanogel particles homogeneously dispersed in the core of microspheres would aggregate in the half of the microspheres, leading to Janus PC microspheres with varied reflection spectra at the different side of the spheres. More interestingly, such Janus structure of PC microspheres and their reflection spectrum were significantly reversible when the centrifugation was employed and removed alternatively. In addition, due to the soft and thermal-responsive nature of the building blocks (e.g., nanogels), Janus structures and optical properties of the PC microspheres are highly influenced by the temperature, centrifugal speed, and time, providing the other parameters on the manipulation of properties of the PC microspheres. This strategy provides a new concept for the preparation of Janus PC microspheres with tunable structures and optical properties, which will find potential applications in the field of sensors, optical devices, barcodes, etc.},
}
@article {pmid24260209,
year = {2013},
author = {Liu, SY and Chan, CL and Lin, O and Hu, CS and Chen, CA},
title = {DNA barcoding of shark meats identify species composition and CITES-listed species from the markets in Taiwan.},
journal = {PloS one},
volume = {8},
number = {11},
pages = {e79373},
pmid = {24260209},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Meat ; Phylogeny ; Sharks/classification/*genetics ; Taiwan ; },
abstract = {BACKGROUND: An increasing awareness of the vulnerability of sharks to exploitation by shark finning has contributed to a growing concern about an unsustainable shark fishery. Taiwan's fleet has the 4th largest shark catch in the world, accounting for almost 6% of the global figures. Revealing the diversity of sharks consumed by Taiwanese is important in designing conservation plans. However, fins make up less than 5% of the total body weight of a shark, and their bodies are sold as filets in the market, making it difficult or impossible to identify species using morphological traits.<br><br>METHODS: In the present study, we adopted a DNA barcoding technique using a 391-bp fragment of the mitochondrial cytochrome oxidase I (COI) gene to examine the diversity of shark filets and fins collected from markets and restaurants island-wide in Taiwan.<br><br>RESULTS: Amongst the 548 tissue samples collected and sequenced, 20 major clusters were apparent by phylogenetic analyses, each of them containing individuals belonging to the same species (most with more than 95% bootstrap values), corresponding to 20 species of sharks. Additionally, Alopias pelagicus, Carcharhinus falciformis, Isurus oxyrinchus, and Prionace glauca consisted of 80% of the samples we collected, indicating that these species might be heavily consumed in Taiwan. Approximately 5% of the tissue samples used in this study were identified as species listed in CITES Appendix II, including two species of Sphyrna, C. longimanus and Carcharodon carcharias.<br><br>CONCLUSION: DNA barcoding provides an alternative method for understanding shark species composition when species-specific data is unavailable. Considering the global population decline, stock assessments of Appendix II species and highly consumed species are needed to accomplish the ultimate goal of shark conservation.},
}
@article {pmid24257329,
year = {2014},
author = {Guo, Z and Li, W and Peng, M and Duo, H and Shen, X and Fu, Y and Irie, T and Gan, T and Kirino, Y and Nasu, T and Horii, Y and Nonaka, N},
title = {Epidemiological study and control trial of taeniid cestode infection in farm dogs in Qinghai Province, China.},
journal = {The Journal of veterinary medical science},
volume = {76},
number = {3},
pages = {395-400},
pmid = {24257329},
issn = {1347-7439},
mesh = {Agriculture ; Animals ; China/epidemiology ; DNA Primers/genetics ; Dog Diseases/drug therapy/*epidemiology/*parasitology ; Dogs ; Feces/parasitology ; Ovum ; Polymerase Chain Reaction/veterinary ; Praziquantel ; Prevalence ; Surveys and Questionnaires ; Taenia/*genetics ; Taeniasis/drug therapy/epidemiology/*veterinary ; },
abstract = {An epidemiological study and control trial were conducted to assess taeniid infection in farm dogs in Qinghai Province, China. To improve egg detection by fecal examination, a deworming step with praziquantel was incorporated into the sampling methodology. As a result, a marked increase in the number of egg-positive samples was observed in samples collected at 24 hr after deworming. Then, the fecal examination and barcoding of egg DNA were performed to assess the prevalence of taeniid species in dogs from Xinghai, Haiyan, Gangcha and Chengduo counties. Analysis of 277 dog feces revealed that taeniid cestodes, including Taenia spp. and Echinococcus granulosus, were highly prevalent in Xinghai (34.4%), but eggs were not found in Haiyan where a control trial on canine echinococcosis had been conducted 20 years previously. A control trial involving the administration of 5-10 mg/kg praziquantel to 90 farm dogs at 45-day intervals was conducted in Xinghai. The prevalence of taeniid cestodes in the dogs was reduced to 9.6% and 4.9% after one and two years, respectively, indicating that some dogs were not administered praziquantel properly. A questionnaire survey of farmers in Xinghai and Haiyan revealed that most farmers in Xinghai were not familiar with echinococcosis or the transmission route of the disease, while most farmers in Haiyan had a more thorough understanding of the disease. The findings implied that a program for educating local farmers would be important for efficiently controlling canine taeniid infection in the region.},
}
@article {pmid24252700,
year = {2014},
author = {Pereira, JA and Quach, S and Hamid, JS and Quan, SD and Diniz, AJ and Van Exan, R and Malawski, J and Finkelstein, M and Samanani, S and Kwong, JC and , },
title = {The integration of barcode scanning technology into Canadian public health immunization settings.},
journal = {Vaccine},
volume = {32},
number = {23},
pages = {2748-2755},
doi = {10.1016/j.vaccine.2013.11.015},
pmid = {24252700},
issn = {1873-2518},
support = {//Canadian Institutes of Health Research/Canada ; },
mesh = {Canada ; Electronic Data Processing/instrumentation/*methods ; Electronic Health Records ; Feasibility Studies ; Humans ; *Immunization Programs ; Vaccination/*standards ; },
abstract = {BACKGROUND: As part of a series of feasibility studies following the development of Canadian vaccine barcode standards, we compared barcode scanning with manual methods for entering vaccine data into electronic client immunization records in public health settings.<br><br>METHODS: Two software vendors incorporated barcode scanning functionality into their systems so that Algoma Public Health (APH) in Ontario and four First Nations (FN) communities in Alberta could participate in our study. We compared the recording of client immunization data (vaccine name, lot number, expiry date) using barcode scanning of vaccine vials vs. pre-existing methods of entering vaccine information into the systems. We employed time and motion methodology to evaluate time required for data recording, record audits to assess data quality, and qualitative analysis of immunization staff interviews to gauge user perceptions.<br><br>RESULTS: We conducted both studies between July and November 2012, with 628 (282 barcoded) vials processed for the APH study, and 749 (408 barcoded) vials for the study in FN communities. Barcode scanning led to significantly fewer immunization record errors than using drop-down menus (APH study: 0% vs. 1.7%; p=0.04) or typing in vaccine data (FN study: 0% vs. 5.6%; p<0.001). There was no significant difference in time to enter vaccine data between scanning and using drop-down menus (27.6s vs. 26.3s; p=0.39), but scanning was significantly faster than typing data into the record (30.3s vs. 41.3s; p<0.001). Seventeen immunization nurses were interviewed; all noted improved record accuracy with scanning, but the majority felt that a more sensitive scanner was needed to reduce the occasional failures to read the 2D barcodes on some vaccines.<br><br>CONCLUSION: Entering vaccine data into immunization records through barcode scanning led to improved data quality, and was generally well received. Further work is needed to improve barcode readability, particularly for unit-dose vials.},
}
@article {pmid24245977,
year = {2014},
author = {Bock, DG and Kane, NC and Ebert, DP and Rieseberg, LH},
title = {Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke.},
journal = {The New phytologist},
volume = {201},
number = {3},
pages = {1021-1030},
doi = {10.1111/nph.12560},
pmid = {24245977},
issn = {1469-8137},
mesh = {*Biological Evolution ; Crops, Agricultural/*genetics ; DNA, Ribosomal/genetics ; Genome, Plant/*genetics ; Geography ; Haplotypes/genetics ; Helianthus/*genetics ; Likelihood Functions ; Phylogeny ; Plant Tubers/*genetics ; Polymorphism, Genetic ; },
abstract = {The perennial sunflower Helianthus tuberosus, known as Jerusalem Artichoke or Sunchoke, was cultivated in eastern North America before European contact. As such, it represents one of the few taxa that can support an independent origin of domestication in this region. Its tubers were adopted as a source of food and forage when the species was transferred to the Old World in the early 1600s, and are still used today. Despite the cultural and economic importance of this tuber crop species, its origin is debated. Competing hypotheses implicate the occurrence of polyploidization with or without hybridization, and list the annual sunflower H. annuus and five distantly related perennial sunflower species as potential parents. Here, we test these scenarios by skimming the genomes of diverse populations of Jerusalem Artichoke and its putative progenitors. We identify relationships among Helianthus taxa using complete plastomes (151 551 bp), partial mitochondrial genomes (196 853 bp) and 35S (8196 bp) and 5S (514 bp) ribosomal DNA. Our results refute the possibility that Jerusalem Artichoke is of H. annuus ancestry. We provide the first genetic evidence that this species originated recursively from perennial sunflowers of central-eastern North America via hybridization between tetraploid Hairy Sunflower and diploid Sawtooth Sunflower.},
}
@article {pmid24244670,
year = {2013},
author = {Müller, L and Gonçalves, GL and Cordeiro-Estrela, P and Marinho, JR and Althoff, SL and Testoni, AF and González, EM and Freitas, TR},
title = {DNA barcoding of sigmodontine rodents: identifying wildlife reservoirs of zoonoses.},
journal = {PloS one},
volume = {8},
number = {11},
pages = {e80282},
pmid = {24244670},
issn = {1932-6203},
mesh = {Animals ; Animals, Wild/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; Phylogeny ; Zoonoses/classification/*genetics ; },
abstract = {Species identification through DNA barcoding is a tool to be added to taxonomic procedures, once it has been validated. Applying barcoding techniques in public health would aid in the identification and correct delimitation of the distribution of rodents from the subfamily Sigmodontinae. These rodents are reservoirs of etiological agents of zoonoses including arenaviruses, hantaviruses, Chagas disease and leishmaniasis. In this study we compared distance-based and probabilistic phylogenetic inference methods to evaluate the performance of cytochrome c oxidase subunit I (COI) in sigmodontine identification. A total of 130 sequences from 21 field-trapped species (13 genera), mainly from southern Brazil, were generated and analyzed, together with 58 GenBank sequences (24 species; 10 genera). Preliminary analysis revealed a 9.5% rate of misidentifications in the field, mainly of juveniles, which were reclassified after examination of external morphological characters and chromosome numbers. Distance and model-based methods of tree reconstruction retrieved similar topologies and monophyly for most species. Kernel density estimation of the distance distribution showed a clear barcoding gap with overlapping of intraspecific and interspecific densities < 1% and 21 species with mean intraspecific distance < 2%. Five species that are reservoirs of hantaviruses could be identified through DNA barcodes. Additionally, we provide information for the description of a putative new species, as well as the first COI sequence of the recently described genus Drymoreomys. The data also indicated an expansion of the distribution of Calomys tener. We emphasize that DNA barcoding should be used in combination with other taxonomic and systematic procedures in an integrative framework and based on properly identified museum collections, to improve identification procedures, especially in epidemiological surveillance and ecological assessments.},
}
@article {pmid24244283,
year = {2013},
author = {Chapple, DG and Ritchie, PA},
title = {A retrospective approach to testing the DNA barcoding method.},
journal = {PloS one},
volume = {8},
number = {11},
pages = {e77882},
pmid = {24244283},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Lizards/*classification/*genetics ; New Zealand ; *Phylogeny ; Species Specificity ; },
abstract = {A decade ago, DNA barcoding was proposed as a standardised method for identifying existing species and speeding the discovery of new species. Yet, despite its numerous successes across a range of taxa, its frequent failures have brought into question its accuracy as a short-cut taxonomic method. We use a retrospective approach, applying the method to the classification of New Zealand skinks as it stood in 1977 (primarily based upon morphological characters), and compare it to the current taxonomy reached using both morphological and molecular approaches. For the 1977 dataset, DNA barcoding had moderate-high success in identifying specimens (78-98%), and correctly flagging specimens that have since been confirmed as distinct taxa (77-100%). But most matching methods failed to detect the species complexes that were present in 1977. For the current dataset, there was moderate-high success in identifying specimens (53-99%). For both datasets, the capacity to discover new species was dependent on the methodological approach used. Species delimitation in New Zealand skinks was hindered by the absence of either a local or global barcoding gap, a result of recent speciation events and hybridisation. Whilst DNA barcoding is potentially useful for specimen identification and species discovery in New Zealand skinks, its error rate could hinder the progress of documenting biodiversity in this group. We suggest that integrated taxonomic approaches are more effective at discovering and describing biodiversity.},
}
@article {pmid24243955,
year = {2013},
author = {Lou, DI and Hussmann, JA and McBee, RM and Acevedo, A and Andino, R and Press, WH and Sawyer, SL},
title = {High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {110},
number = {49},
pages = {19872-19877},
pmid = {24243955},
issn = {1091-6490},
support = {R01 GM093086/GM/NIGMS NIH HHS/United States ; R01 AI036178/AI/NIAID NIH HHS/United States ; F30 CA171715/CA/NCI NIH HHS/United States ; GM52319/GM/NIGMS NIH HHS/United States ; GM24110/GM/NIGMS NIH HHS/United States ; GM60987/GM/NIGMS NIH HHS/United States ; P01 AI091575/AI/NIAID NIH HHS/United States ; },
mesh = {Computational Biology/*methods ; DNA, Circular/*genetics ; Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; *Research Design ; },
abstract = {A major limitation of high-throughput DNA sequencing is the high rate of erroneous base calls produced. For instance, Illumina sequencing machines produce errors at a rate of ~0.1-1 × 10(-2) per base sequenced. These technologies typically produce billions of base calls per experiment, translating to millions of errors. We have developed a unique library preparation strategy, "circle sequencing," which allows for robust downstream computational correction of these errors. In this strategy, DNA templates are circularized, copied multiple times in tandem with a rolling circle polymerase, and then sequenced on any high-throughput sequencing machine. Each read produced is computationally processed to obtain a consensus sequence of all linked copies of the original molecule. Physically linking the copies ensures that each copy is independently derived from the original molecule and allows for efficient formation of consensus sequences. The circle-sequencing protocol precedes standard library preparations and is therefore suitable for a broad range of sequencing applications. We tested our method using the Illumina MiSeq platform and obtained errors in our processed sequencing reads at a rate as low as 7.6 × 10(-6) per base sequenced, dramatically improving the error rate of Illumina sequencing and putting error on par with low-throughput, but highly accurate, Sanger sequencing. Circle sequencing also had substantially higher efficiency and lower cost than existing barcode-based schemes for correcting sequencing errors.},
}
@article {pmid24243860,
year = {2014},
author = {Simard, C and Cloutier, M and Néron, S},
title = {Feasibility study: phosphospecific flow cytometry enabling rapid functional analysis of bone marrow samples from patients with multiple myeloma.},
journal = {Cytometry. Part B, Clinical cytometry},
volume = {86},
number = {2},
pages = {139-144},
doi = {10.1002/cyto.b.21142},
pmid = {24243860},
issn = {1552-4957},
mesh = {Bone Marrow/*pathology ; Feasibility Studies ; Flow Cytometry/*methods ; Humans ; Multiple Myeloma/*diagnosis/*metabolism/pathology ; Phosphorylation ; STAT3 Transcription Factor/metabolism ; Signal Transduction ; },
abstract = {BACKGROUND: Multiple myeloma (MM) is an incurable cancer accounting for about 2% of cancer deaths. Its diagnosis is based on a combination of criteria, which are not always easily measurable. Flow cytometry now allows multiplex analysis of intracellular signaling at the single cell level. We investigated the feasibility of using intracellular protein phosphorylation analysis by flow cytometry on primary plasma cells from bone marrow and its usefulness in MM diagnosis.<br><br>METHODS: Cells from frozen bone marrow of five MM patients and four normal donors were stimulated with LPS, IL-6, IL-21, IFN&#x3b1; and TNF&#x3b1;. Cells were stained by fluorescent cell barcoding to allow multiplex analysis. Staining with antibodies against phosphorylated NFkB-p65, Stat1, Stat3, and p38 were used to identify cellular responses following stimulation.<br><br>RESULTS: Activation profiles of MM and normal plasma cells have been established. MM cells showed heterogeneous response profiles while normal cells responses were homogeneous between donors. We also noticed that many MM samples seemed to show elevated basal level of Stat3 phosphorylation. These results suggest that different response profiles in primary MM cells might correspond to different subtypes of the disease. Thus, we provide an example of how these results may be used as a criterion for MM subtypes classification.<br><br>CONCLUSIONS: We demonstrate that flow cytometry can be used to study signaling pathways in primary MM cells. The heterogeneity observed in MM cells from different patients can prove valuable for MM characterization and represents an interesting avenue for future research in MM diagnosis.},
}
@article {pmid24240685,
year = {2014},
author = {Yan, S and Qiu, L and Ma, K and Zhang, X and Zhao, Y and Zhang, J and Li, X and Hao, X and Li, Z},
title = {FATS is an E2-independent ubiquitin ligase that stabilizes p53 and promotes its activation in response to DNA damage.},
journal = {Oncogene},
volume = {33},
number = {47},
pages = {5424-5433},
doi = {10.1038/onc.2013.494},
pmid = {24240685},
issn = {1476-5594},
mesh = {Cell Line ; Cytoskeletal Proteins/genetics/*metabolism ; *DNA Damage ; Humans ; Protein Stability ; Protein Structure, Tertiary ; Proto-Oncogene Proteins c-mdm2/metabolism ; Tumor Suppressor Protein p53/genetics/*metabolism ; Ubiquitination ; },
abstract = {Ubiquitin linkage is critical in directing the cellular fate of a ubiquitinated protein. Although K48-linked polyubiquitination of p53 leads to its degradation, whether K48-independent ubiquitin linkages are involved in p53 activation remains unknown. Here, we show that FATS acts as a p53 activator by inhibiting Mdm2 binding to p53 and stimulating non-proteolytic polyubiquitination of p53. Knockdown of FATS impairs p53 stabilization and activation in response to DNA damage. Furthermore, the NH2-terminal domain of FATS is sufficient to exhibit ubiquitin ligase (E3) activity and assemble ubiquitin polymers through K11-, K29- and K63-linkages, independently of the ubiquitin-conjugating enzyme (E2). FATS promotes p53-dependent transcription of p21, leading to robust checkpoint response. The E3 activity of FATS is required for promoting p53 stability and activation in response to DNA damage. Our findings reveal K48-linkage-independent non-linear polyubiquitination of p53 as a new barcode for p53 activation.},
}
@article {pmid24229463,
year = {2013},
author = {Edmunds, SC and Hunter, CI and Smith, V and Stoev, P and Penev, L},
title = {Biodiversity research in the "big data" era: GigaScience and Pensoft work together to publish the most data-rich species description.},
journal = {GigaScience},
volume = {2},
number = {1},
pages = {14},
pmid = {24229463},
issn = {2047-217X},
abstract = {With the publication of the first eukaryotic species description, combining transcriptomic, DNA barcoding, and micro-CT imaging data, GigaScience and Pensoft demonstrate how classical taxonomic description of a new species can be enhanced by applying new generation molecular methods, and novel computing and imaging technologies. This 'holistic' approach in taxonomic description of a new species of cave-dwelling centipede is published in the Biodiversity Data Journal (BDJ), with coordinated data release in the GigaScience GigaDB database.},
}
@article {pmid24228342,
year = {2013},
author = {Kar, S and Basu, R},
title = {Increasing productivity by reducing average length of stay (ALOS) in Apollo Gleneagles Hospitals, Kolkata, India.},
journal = {World hospitals and health services : the official journal of the International Hospital Federation},
volume = {49},
number = {2},
pages = {16-17},
pmid = {24228342},
issn = {1029-0540},
mesh = {Cost Savings ; *Efficiency, Organizational/economics ; *Hospitals ; Humans ; India ; Length of Stay/*trends ; Organizational Case Studies ; Total Quality Management/methods ; },
abstract = {Reduction of ALOS in the hospital through streamlined processes with validation for standardized work such as clinical pathways. The implementation of barcoding and streamlining laboratories with interface solutions has reduced the cycle time for the diagnostic areas. The long standing cases over seven days provided a trigger for the Medical Board, which helped in multidisciplinary care of these patients. Cohort of patients in respective wards according to discipline for almost 80% of patients have improved nursing and other paramedical services and had a definite impact on ALOS and other outcomes. Finally, the organization had a benefit of nearly USD 0.9 million for a period of nine months during this study. The organization has carried on with the benefits of the ALOS reduction and currently has reduced ALOS to 4.5 days.},
}
@article {pmid24227078,
year = {2014},
author = {Novo, S and Nogués, C and Penon, O and Barrios, L and Santaló, J and Gómez-Martínez, R and Esteve, J and Errachid, A and Plaza, JA and Pérez-García, L and Ibáñez, E},
title = {Barcode tagging of human oocytes and embryos to prevent mix-ups in assisted reproduction technologies.},
journal = {Human reproduction (Oxford, England)},
volume = {29},
number = {1},
pages = {18-28},
doi = {10.1093/humrep/det409},
pmid = {24227078},
issn = {1460-2350},
mesh = {Blastocyst ; Embryo Transfer ; Embryo, Mammalian/*metabolism ; Embryonic Development ; Humans ; Oocytes/*cytology ; Reproductive Techniques, Assisted/*standards ; Silicon/metabolism ; Vitrification ; *Wheat Germ Agglutinins/metabolism ; Zona Pellucida/metabolism ; },
abstract = {STUDY QUESTION: Is the attachment of biofunctionalized polysilicon barcodes to the outer surface of the zona pellucida an effective approach for the direct tagging and identification of human oocytes and embryos during assisted reproduction technologies (ARTs)?<br><br>SUMMARY ANSWER: The direct tagging system based on lectin-biofunctionalized polysilicon barcodes of micrometric dimensions is simple, safe and highly efficient, allowing the identification of human oocytes and embryos during the various procedures typically conducted during an assisted reproduction cycle.<br><br>WHAT IS KNOWN ALREADY: Measures to prevent mismatching errors (mix-ups) of the reproductive samples are currently in place in fertility clinics, but none of them are totally effective and several mix-up cases have been reported worldwide. Using a mouse model, our group has previously developed an effective direct embryo tagging system which does not interfere with the in vitro and in vivo development of the tagged embryos. This system has now been tested in human oocytes and embryos.<br><br>STUDY DESIGN, SIZE, DURATION: Fresh immature and mature fertilization-failed oocytes (n = 21) and cryopreserved day 1 embryos produced by in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI) (n = 205) were donated by patients (n = 76) undergoing ARTs. In vitro development rates, embryo quality and post-vitrification survival were compared between tagged (n = 106) and non-tagged (control) embryos (n = 99). Barcode retention and identification rates were also calculated, both for embryos and for oocytes subjected to a simulated ICSI and parthenogenetic activation. Experiments were conducted from January 2012 to January 2013.<br><br>Barcodes were fabricated in polysilicon and biofunctionalizated with wheat germ agglutinin lectin. Embryos were tagged with 10 barcodes and cultured in vitro until the blastocyst stage, when they were either differentially stained with propidium iodide and Hoechst or vitrified using the Cryotop method. Embryo quality was also analyzed by embryo grading and time-lapse monitoring. Injected oocytes were parthenogenetically activated using ionomycin and 6-dimethylaminopurine.<br><br>Blastocyst development rates of tagged (27/58) and non-tagged embryos (24/51) were equivalent, and no significant differences in the timing of key morphokinetic parameters and the number of inner cell mass cells were detected between the two groups (tagged: 24.7 &#xb1; 2.5; non-tagged: 22.3 &#xb1; 1.9), indicating that preimplantation embryo potential and quality are not affected by the barcodes. Similarly, re-expansion rates of vitrified-warmed tagged (19/21) and non-tagged (16/19) blastocysts were similar. Global identification rates of 96.9 and 89.5% were obtained in fresh (mean barcode retention: 9.22 &#xb1; 0.13) and vitrified-warmed (mean barcode retention: 7.79 &#xb1; 0.35) tagged embryos, respectively, when simulating an automatic barcode reading process, though these rates were increased to 100% just by rotating the embryos during barcode reading. Only one of the oocytes lost one barcode during intracytoplasmic injection (100% identification rate) and all oocytes retained all the barcodes after parthenogenetic activation.<br><br>Although the direct embryo tagging system developed is effective, it only allows the identification and traceability of oocytes destined for ICSI and embryos. Thus, the traceability of all reproductive samples (oocytes destined for IVF and sperm) is not yet ensured.<br><br>The direct embryo tagging system developed here provides fertility clinics with a novel tool to reduce the risk of mix-ups in human ARTs. The system can also be useful in research studies that require the individual identification of oocytes or embryos and their individual tracking.<br><br>This study was supported by the Sociedad Espa&#xf1;ola de Fertilidad, the Spanish Ministry of Education and Science (TEC2011-29140-C03) and the Generalitat de Catalunya (2009SGR-00282 and 2009SGR-00158). The authors do not have any competing interests.},
}
@article {pmid24223951,
year = {2013},
author = {de Groot, GA and During, H},
title = {Fern spore longevity in saline water: can sea bottom sediments maintain a viable spore bank?.},
journal = {PloS one},
volume = {8},
number = {11},
pages = {e79470},
pmid = {24223951},
issn = {1932-6203},
mesh = {Ferns/cytology/*drug effects/*physiology ; Geologic Sediments/*chemistry ; Germ Cells, Plant/drug effects ; Germination/drug effects ; Longevity/drug effects ; Salinity ; Salts/*pharmacology ; Spores/*drug effects/*physiology ; Water/*chemistry ; },
abstract = {Freshwater and marine sediments often harbor reservoirs of plant diaspores, from which germination and establishment may occur whenever the sediment falls dry. Therewith, they form valuable records of historical inter- and intraspecific diversity, and are increasingly exploited to facilitate diversity establishment in new or restored nature areas. Yet, while ferns may constitute a considerable part of a vegetation's diversity and sediments are known to contain fern spores, little is known about their longevity, which may suffer from inundation and--in sea bottoms--salt stress. We tested the potential of ferns to establish from a sea or lake bottom, using experimental studies on spore survival and gametophyte formation, as well as a spore bank analysis on sediments from a former Dutch inland sea. Our experimental results revealed clear differences among species. For Asplenium scolopendrium and Gymnocarpium dryopteris, spore germination was not affected by inundated storage alone, but decreased with rising salt concentrations. In contrast, for Asplenium trichomanes subsp. quadrivalens germination decreased following inundation, but not in response to salt. Germination rates decreased with time of storage in saline water. Smaller and less viable gametophytes were produced when saline storage lasted for a year. Effects on germination and gametophyte development clearly differed among genotypes of A. scolopendrium. Spore bank analyses detected no viable spores in marine sediment layers. Only two very small gametophytes (identified as Thelypteris palustris via DNA barcoding) emerged from freshwater sediments. Both died before maturation. We conclude that marine, and likely even freshwater sediments, will generally be of little value for long-term storage of fern diversity. The development of any fern vegetation on a former sea floor will depend heavily on the deposition of spores onto the drained land by natural or artificial means of dispersal.},
}
@article {pmid24223896,
year = {2013},
author = {Kulsantiwong, J and Prasopdee, S and Ruangsittichai, J and Ruangjirachuporn, W and Boonmars, T and Viyanant, V and Pierossi, P and Hebert, PD and Tesana, S},
title = {DNA barcode identification of freshwater snails in the family Bithyniidae from Thailand.},
journal = {PloS one},
volume = {8},
number = {11},
pages = {e79144},
pmid = {24223896},
issn = {1932-6203},
mesh = {Animal Shells/anatomy &amp; histology ; Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/chemistry/*genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Gastropoda/classification/genetics ; Genetic Variation ; Geography ; Phylogeny ; Sequence Analysis, DNA ; Snails/anatomy &amp; histology/classification/*genetics ; Species Specificity ; Thailand ; },
abstract = {Freshwater snails in the family Bithyniidae are the first intermediate host for Southeast Asian liver fluke (Opisthorchis viverrini), the causative agent of opisthorchiasis. Unfortunately, the subtle morphological characters that differentiate species in this group are not easily discerned by non-specialists. This is a serious matter because the identification of bithyniid species is a fundamental prerequisite for better understanding of the epidemiology of this disease. Because DNA barcoding, the analysis of sequence diversity in the 5' region of the mitochondrial COI gene, has shown strong performance in other taxonomic groups, we decided to test its capacity to resolve 10 species/ subspecies of bithyniids from Thailand. Our analysis of 217 specimens indicated that COI sequences delivered species-level identification for 9 of 10 currently recognized species. The mean intraspecific divergence of COI was 2.3% (range 0-9.2 %), whereas sequence divergences between congeneric species averaged 8.7% (range 0-22.2 %). Although our results indicate that DNA barcoding can differentiate species of these medically-important snails, we also detected evidence for the presence of one overlooked species and one possible case of synonymy.},
}
@article {pmid24223279,
year = {2013},
author = {Stålstedt, J and Bergsten, J and Ronquist, F},
title = {"Forms" of water mites (Acari: Hydrachnidia): intraspecific variation or valid species?.},
journal = {Ecology and evolution},
volume = {3},
number = {10},
pages = {3415-3435},
pmid = {24223279},
issn = {2045-7758},
abstract = {In many groups of organisms, especially in the older literature, it has been common practice to recognize sympatrically occurring phenotypic variants of a species as "forms". However, what these forms really represent often remains unclear, especially in poorly studied groups. With new algorithms for DNA-based species delimitation, the status of forms can be explicitly tested with molecular data. In this study, we test a number of what is now recognized as valid species of water mites (Hydrachnidia), but have in the past been treated as forms sympatrically occurring with their nominate species. We also test a form without prior taxonomical status, using DNA and morphometrics. The barcoding fragment of COI, nuclear 28S and quantitative analyses of morphological data were used to test whether these taxa merit species status, as suggested by several taxonomists. Our results confirm valid species. Genetic distances between the form and nominate species (Piona dispersa and Piona variabilis, COI 11%), as well as likelihood ratio tests under the general mixed-Yule coalescent model, supported that these are separately evolving lineages as defined by the unified species concept. In addition, they can be diagnosed with morphological characters. The study also reveals that some taxa genetically represent more than one species. We propose that P. dispersa are recognized as valid taxa at the species level. Unionicola minor (which may consist of several species), Piona stjordalensis, P. imminuta s. lat., and P. rotundoides are confirmed as species using this model. The results also imply that future studies of other water mite species complexes are likely to reveal many more genetically and morphologically distinct species.},
}
@article {pmid24223136,
year = {2013},
author = {Ritter, S and Michalski, SG and Settele, J and Wiemers, M and Fric, ZF and Sielezniew, M and Šašić, M and Rozier, Y and Durka, W},
title = {Wolbachia infections mimic cryptic speciation in two parasitic butterfly species, Phengaris teleius and P. nausithous (Lepidoptera: Lycaenidae).},
journal = {PloS one},
volume = {8},
number = {11},
pages = {e78107},
pmid = {24223136},
issn = {1932-6203},
mesh = {Animals ; Ants/parasitology ; Asia ; Butterflies/classification/*genetics ; Cell Nucleus/genetics ; Electron Transport Complex IV/classification/*genetics ; Europe ; Female ; Genetic Markers ; *Genetic Speciation ; Genetic Variation ; *Genome, Mitochondrial ; Insect Proteins/classification/*genetics ; Microsatellite Repeats ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Symbiosis ; Wolbachia/*physiology ; },
abstract = {Deep mitochondrial divergence within species may result from cryptic speciation, from phylogeographic isolation or from endosymbiotic bacteria like Wolbachia that manipulate host reproduction. Phengaris butterflies are social parasites that spend most of their life in close relationship with ants. Previously, cryptic speciation has been hypothesised for two Phengaris species based on divergent mtDNA sequences. Since Phengaris species are highly endangered, the existence of cryptic species would have drastic consequences for conservation and management. We tested for cryptic speciation and alternative scenarios in P. teleius and P. nausithous based on a comprehensive sample across their Palaearctic ranges using COI gene sequences, nuclear microsatellites and tests for Wolbachia. In both species a deep mitochondrial split occurring 0.65-1.97 myrs ago was observed that did not correspond with microsatellite data but was concordant with Wolbachia infection. Haplotypes previously attributed to cryptic species were part of the Wolbachia-infected clades. In both species remaining phylogeographic structure was largely consistent between mitochondrial and nuclear genomes. In P. teleius several mitochondrial and nuclear groups were observed in East Asia while a single haplogroup and nuclear cluster prevailed across continental Eurasia. Neutrality tests suggested rapid demographic expansion into that area. In contrast, P. nausithous had several mitochondrial and nuclear groups in Europe, suggesting a complex phylogeographic history in the western part of the species range. We conclude that deep intraspecific divergences found in DNA barcode studies do not necessarily need to represent cryptic speciation but instead can be due to both infection by Wolbachia and phylogeographic structure.},
}
@article {pmid24215491,
year = {2014},
author = {Engdahl, C and Larsson, P and Näslund, J and Bravo, M and Evander, M and Lundström, JO and Ahlm, C and Bucht, G},
title = {Identification of Swedish mosquitoes based on molecular barcoding of the COI gene and SNP analysis.},
journal = {Molecular ecology resources},
volume = {14},
number = {3},
pages = {478-488},
doi = {10.1111/1755-0998.12202},
pmid = {24215491},
issn = {1755-0998},
mesh = {Animals ; Culicidae/*classification/enzymology/genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Insect Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; *Polymorphism, Single Nucleotide ; Sweden ; },
abstract = {Mosquito-borne infectious diseases are emerging in many regions of the world. Consequently, surveillance of mosquitoes and concomitant infectious agents is of great importance for prediction and prevention of mosquito-borne infectious diseases. Currently, morphological identification of mosquitoes is the traditional procedure. However, sequencing of specified genes or standard genomic regions, DNA barcoding, has recently been suggested as a global standard for identification and classification of many different species. Our aim was to develop a genetic method to identify mosquitoes and to study their relationship. Mosquitoes were captured at collection sites in northern Sweden and identified morphologically before the cytochrome c oxidase subunit I (COI) gene sequences of 14 of the most common mosquito species were determined. The sequences obtained were then used for phylogenetic placement, for validation and benchmarking of phenetic classifications and finally to develop a hierarchical PCR-based typing scheme based on single nucleotide polymorphism sites (SNPs) to enable rapid genetic identification, circumventing the need for morphological characterization. The results showed that exact phylogenetic relationships between mosquito taxa were preserved at shorter evolutionary distances, but at deeper levels, they could not be inferred with confidence using COI gene sequence data alone. Fourteen of the most common mosquito species in Sweden were identified by the SNP/PCR-based typing scheme, demonstrating that genetic typing using SNPs of the COI gene is a useful method for identification of mosquitoes with potential for worldwide application.},
}
@article {pmid24211463,
year = {2014},
author = {Zhou, W and Su, J and Chai, Y and Yuan, R and Xiang, Y},
title = {Naked eye detection of trace cancer biomarkers based on biobarcode and enzyme-assisted DNA recycling hybrid amplifications.},
journal = {Biosensors &amp; bioelectronics},
volume = {53},
number = {},
pages = {494-498},
doi = {10.1016/j.bios.2013.10.020},
pmid = {24211463},
issn = {1873-4235},
mesh = {Biomarkers, Tumor/blood/*isolation &amp; purification ; Biosensing Techniques/*methods ; Carcinoembryonic Antigen/blood/*isolation &amp; purification ; Colorimetry ; DNA/chemistry ; G-Quadruplexes ; Humans ; Neoplasms/*blood/diagnosis ; Nucleic Acid Hybridization ; Peroxidase/chemistry ; },
abstract = {Naked eye-based detection has received increasing research interest due to the simplicity nature of this type of assay. However, improving the sensitivity of the naked eye detection method for the monitoring of trace amount of target molecules remains a major challenge. Herein, we describe a biobarcode and an enzyme-assisted DNA recycling hybrid amplification strategy for naked eye detection of sub-picomolar carcinoembryonic antigen (CEA), a cancer biomarker. The presence of CEA and the corresponding antibodies results in the formation of immunocomplexes and the capture of the biobarcodes in a microplate. The massive barcode DNAs released from the biobarcodes hybridize with the G-quadruplex inactive hairpin DNA probes and form catalytic nicking sites for N.BstNBI endonuclease, which cleaves the barcode DNA/hairpin partial dsDNA, releases the G-quadruplex active sequences and recycles the barcode DNA. Due to the barcode DNA recycling process, numerous G-quadruplex active sequences are generated and associate with hemin to form peroxidase mimicking enzymes, which convert colorless ABTS(2-) to green color intensified ABTS(•-) to achieve naked eye detection of CEA down to 0.025 ng mL(-1) (0.14 pM). The naked eye detection strategy reported herein can be applied also to complicated serum sample matrix, making this approach hold great promise for point-of-care diagnostic applications.},
}
@article {pmid24204702,
year = {2013},
author = {Tanabe, AS and Toju, H},
title = {Two new computational methods for universal DNA barcoding: a benchmark using barcode sequences of bacteria, archaea, animals, fungi, and land plants.},
journal = {PloS one},
volume = {8},
number = {10},
pages = {e76910},
pmid = {24204702},
issn = {1932-6203},
mesh = {Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Benchmarking/*methods ; Computational Biology/*methods ; DNA/analysis/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Embryophyta/classification/genetics ; Fungi/classification/genetics ; Genes, Chloroplast/genetics ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; },
abstract = {Taxonomic identification of biological specimens based on DNA sequence information (a.k.a. DNA barcoding) is becoming increasingly common in biodiversity science. Although several methods have been proposed, many of them are not universally applicable due to the need for prerequisite phylogenetic/machine-learning analyses, the need for huge computational resources, or the lack of a firm theoretical background. Here, we propose two new computational methods of DNA barcoding and show a benchmark for bacterial/archeal 16S, animal COX1, fungal internal transcribed spacer, and three plant chloroplast (rbcL, matK, and trnH-psbA) barcode loci that can be used to compare the performance of existing and new methods. The benchmark was performed under two alternative situations: query sequences were available in the corresponding reference sequence databases in one, but were not available in the other. In the former situation, the commonly used "1-nearest-neighbor" (1-NN) method, which assigns the taxonomic information of the most similar sequences in a reference database (i.e., BLAST-top-hit reference sequence) to a query, displays the highest rate and highest precision of successful taxonomic identification. However, in the latter situation, the 1-NN method produced extremely high rates of misidentification for all the barcode loci examined. In contrast, one of our new methods, the query-centric auto-k-nearest-neighbor (QCauto) method, consistently produced low rates of misidentification for all the loci examined in both situations. These results indicate that the 1-NN method is most suitable if the reference sequences of all potentially observable species are available in databases; otherwise, the QCauto method returns the most reliable identification results. The benchmark results also indicated that the taxon coverage of reference sequences is far from complete for genus or species level identification in all the barcode loci examined. Therefore, we need to accelerate the registration of reference barcode sequences to apply high-throughput DNA barcoding to genus or species level identification in biodiversity research.},
}
@article {pmid24203863,
year = {2014},
author = {Fišer Pečnikar, &#x17d; and Buzan, EV},
title = {20 years since the introduction of DNA barcoding: from theory to application.},
journal = {Journal of applied genetics},
volume = {55},
number = {1},
pages = {43-52},
pmid = {24203863},
issn = {2190-3883},
mesh = {Animals ; Biodiversity ; Conservation of Natural Resources ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Endoribonucleases/genetics ; Fungi/*genetics ; Genetic Markers/genetics ; Genetic Variation ; Mitochondrial Proteins/genetics ; Nucleotidyltransferases/genetics ; Plant Proteins/genetics ; Plants/*genetics ; Public Health ; Ribulose-Bisphosphate Carboxylase/genetics ; },
abstract = {Traditionally, taxonomic identification has relied upon morphological characters. In the last two decades, molecular tools based on DNA sequences of short standardised gene fragments, termed DNA barcodes, have been developed for species discrimination. The most common DNA barcode used in animals is a fragment of the cytochrome c oxidase (COI) mitochondrial gene, while for plants, two chloroplast gene fragments from the RuBisCo large subunit (rbcL) and maturase K (matK) genes are widely used. Information gathered from DNA barcodes can be used beyond taxonomic studies and will have far-reaching implications across many fields of biology, including ecology (rapid biodiversity assessment and food chain analysis), conservation biology (monitoring of protected species), biosecurity (early identification of invasive pest species), medicine (identification of medically important pathogens and their vectors) and pharmacology (identification of active compounds). However, it is important that the limitations of DNA barcoding are understood and techniques continually adapted and improved as this young science matures.},
}
@article {pmid24201005,
year = {2014},
author = {Zhu, W and Su, X and Gao, X and Dai, Z and Zou, X},
title = {A label-free and PCR-free electrochemical assay for multiplexed microRNA profiles by ligase chain reaction coupling with quantum dots barcodes.},
journal = {Biosensors &amp; bioelectronics},
volume = {53},
number = {},
pages = {414-419},
doi = {10.1016/j.bios.2013.10.023},
pmid = {24201005},
issn = {1873-4235},
mesh = {Biosensing Techniques/*methods ; Humans ; Ligase Chain Reaction/*methods ; Limit of Detection ; MicroRNAs/genetics/*isolation &amp; purification ; Quantum Dots/chemistry ; },
abstract = {The profiling of microRNAs (miRNAs) is greatly significant for cellular events or disease diagnosis. Electrochemical methods for miRNAs analysis mostly can only measure one kind of miRNA, which is unambiguous to indicate the disease type and state. Here a label-free and PCR-free electrochemical method is presented for multiplexed evaluation of miRNAs in a single-tube experiment. The method is based on the combination of the high base-mismatch selectivity of ligase chain reaction (LCR) and the remarkable voltammetric signature of electrochemical QDs barcodes. Two reporting probes of RP1 and RP2 were labeled with PbS and CdS quantum dots (QDs) to prepare PbS-RP1 and CdS-RP2 conjugates, and two capture probes of CP1 and CP2 were co-immobilized on magnetic beads (MBs) to fabricate MB-CP1CP2 conjugate. The miRNAs samples were simply incubated with MB-CP1CP2, PbS-RP1, and CdS-RP2 conjugates, and then added with T4 DNA ligase. After release of the disjoined QDs barcodes from the MB-conjugates, two target miRNAs of miR-155 and miR-27b were simultaneously detected by square wave voltammetry with linear ranges of 50 fM-30 pM and 50 fM-1050 pM, and limits of detection (LODs) of 12 fM and 31 fM (S/N=3). The method fulfilled the assay in less than 70 min, and showed acceptable testing recoveries for the determination of miRNAs in biological matrix. Currently there are rare reports about electrochemical multiplexed quantification of miRNAs. The method is likely to provide a new platform for identification of multiple miRNAs in a simple way.},
}
@article {pmid24200838,
year = {2014},
author = {Crainey, JL and Mattos-Glória, A and Hamada, N and Luz, SL},
title = {New tools and insights to assist with the molecular identification of Simulium guianense s.l., main Onchocerca volvulus vector within the highland areas of the Amazonia onchocerciasis focus.},
journal = {Acta tropica},
volume = {131},
number = {},
pages = {47-55},
doi = {10.1016/j.actatropica.2013.10.019},
pmid = {24200838},
issn = {1873-6254},
mesh = {Animal Distribution ; Animals ; Brazil/epidemiology ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/*classification/genetics ; Electron Transport Complex IV/classification/genetics ; *Genetic Speciation ; Humans ; Insect Proteins/classification/genetics ; *Insect Vectors ; Mitochondrial Proteins/classification/genetics ; Onchocerca volvulus/physiology ; Onchocerciasis/epidemiology/parasitology/transmission ; *Phylogeny ; Polymorphism, Single Nucleotide ; Ribosomes/genetics ; Simuliidae/*classification/genetics/parasitology ; },
abstract = {Following the success of the Onchocerciasis Elimination Programme for the Americas (OEPA), there is now just one Latin American onchocerciasis focus where onchocerciasis transmission is described as 'on-going:' the Amazonia Onchocerciasis focus. In the hyperendemic highland areas of the Amazonia focus, Simulium guianense s.l. Wise are the most important vectors of the disease. Populations of S. guianense s.l. are, however, known to vary in their cytogenetics and in a range of behaviours, including in their biting habits. In the hypoendemic lowland areas of the Amazonia focus, for example, S. guianense s.l. are generally regarded as zoophilic and consequently unimportant to disease transmission. Robust tools, to discriminate among various populations of S. guianense s.l. have, however, not yet been developed. In the work reported here, we have assessed the utility of a ribosomal DNA sequence fragment spanning the nuclear ribosomal ITS-1, ITS-2 and 5.8S sequence regions and a ∼850 nucleotide portion of the mitochondrial cytochrome oxidase gene (CO1) for species-level identification and for resolving the within species substructuring. We report here how we have generated 78 CO1 sequences from a rich set of both zoophilic and anthropophilic populations of S. guianense s.l. that were collected from eight sites that are broadly distributed across Brazil. Consistent with previous findings, our analysis supports the genetic isolation of Simulium litobranchium from S. guianense s.l. In contrast with previous findings, however, our results did not provide support for the divergence of the two species prior to the radiation of S. guianense s.l. In our analysis of the S. guianense s.l. ribosomal DNA sequence trace files we generated, we provide clear evidence of multiple within-specimen single nucleotide polymorphisms and indels suggesting that S. guianense s.l. ribosomal DNA is not a good target for conventional DNA barcoding. This is the first report of S. guianense s.l. within individual ribosomal DNA variation and thus the first evidence that the species is not subject to the normal effects of concerted evolution. Collectively, these data illustrate the need for diverse sampling in the development of robust molecular tools for vector identification and suggest that ribosomal DNA might be able to assist with resolving S. guianense s.l. species substructuring that C01 barcoding has hitherto failed to.},
}
@article {pmid24199866,
year = {2013},
author = {Nijman, V and Aliabadian, M},
title = {DNA barcoding as a tool for elucidating species delineation in wide-ranging species as illustrated by owls (Tytonidae and Strigidae).},
journal = {Zoological science},
volume = {30},
number = {11},
pages = {1005-1009},
doi = {10.2108/zsj.30.1005},
pmid = {24199866},
issn = {0289-0003},
mesh = {Animals ; Cyclooxygenase 1/genetics/metabolism ; DNA Barcoding, Taxonomic/*veterinary ; Demography ; Gene Expression Regulation, Enzymologic/physiology ; Phylogeny ; Species Specificity ; Strigiformes/*genetics ; },
abstract = {The mitochondrial cytochrome c-oxidase subunit I (cox1) can serve as a fast and accurate marker for the identification of animal species, and for the discovery of new species across the tree of life. Distinguishing species using this universal molecular marker, a technique known as DNA barcoding, relies on the identifying the gap between intra- and interspecific divergence. One of the difficulties could be wide-ranging, cosmopolitan species that show large amounts of morphological variation. The barn owl Tyto alba is a case in point. It occurs worldwide and varies morphologically, leading to the recognition of many subspecies or, more recently, species. We analysed data from the cox1 gene for 31 individuals of seven subspecies, and compared this with 214 sequences from 29 other owl species. Phylogenetic analysis of the T. alba samples gives very strong support for an Old World alba-clade (three subspecies) and a New World furcata-clade (four subspecies) that are genetically equidistant. The amount of intraspecific variation within each of these clades ranges from 0.66-0.99%, but variation among these clades ranges from 5.33-6.20%. Combined these data suggest that barn owl of the Old World is indeed best considered a separate species different from that of the New World. For combined dataset, sample size of owl species (n between 1 and 21 sequences) increased with geographic range size but we did not find significant relationships between interspecific divergence and sample size or between interspecific divergence and geographic range. For 21/24 species of owls with sample sizes of n ≥4 the maximum interspecific divergences was ≤ 3.00%. However, similar to those found in barn owls, the largest amount of divergence (3.23-4.09%) was present in two other wide-ranging species (Strix nebulosa and Aegolius funereus) raising the possibility of multiple species in other wide-ranging owls as well.},
}
@article {pmid24198709,
year = {2013},
author = {Diazgranados, M and Funk, VA},
title = {Utility of QR codes in biological collections.},
journal = {PhytoKeys},
volume = {},
number = {25},
pages = {21-34},
pmid = {24198709},
issn = {1314-2011},
abstract = {The popularity of QR codes for encoding information such as URIs has increased exponentially in step with the technological advances and availability of smartphones, digital tablets, and other electronic devices. We propose using QR codes on specimens in biological collections to facilitate linking vouchers' electronic information with their associated collections. QR codes can efficiently provide such links for connecting collections, photographs, maps, ecosystem notes, citations, and even GenBank sequences. QR codes have numerous advantages over barcodes, including their small size, superior security mechanisms, increased complexity and quantity of information, and low implementation cost. The scope of this paper is to initiate an academic discussion about using QR codes on specimens in biological collections.},
}
@article {pmid24198247,
year = {2014},
author = {Raabe, CA and Tang, TH and Brosius, J and Rozhdestvensky, TS},
title = {Biases in small RNA deep sequencing data.},
journal = {Nucleic acids research},
volume = {42},
number = {3},
pages = {1414-1426},
pmid = {24198247},
issn = {1362-4962},
mesh = {Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Polymerase Chain Reaction ; Precision Medicine ; RNA, Messenger/chemistry/metabolism ; RNA, Small Untranslated/chemistry/*metabolism ; Sequence Analysis, RNA/*methods ; },
abstract = {High-throughput RNA sequencing (RNA-seq) is considered a powerful tool for novel gene discovery and fine-tuned transcriptional profiling. The digital nature of RNA-seq is also believed to simplify meta-analysis and to reduce background noise associated with hybridization-based approaches. The development of multiplex sequencing enables efficient and economic parallel analysis of gene expression. In addition, RNA-seq is of particular value when low RNA expression or modest changes between samples are monitored. However, recent data uncovered severe bias in the sequencing of small non-protein coding RNA (small RNA-seq or sRNA-seq), such that the expression levels of some RNAs appeared to be artificially enhanced and others diminished or even undetectable. The use of different adapters and barcodes during ligation as well as complex RNA structures and modifications drastically influence cDNA synthesis efficacies and exemplify sources of bias in deep sequencing. In addition, variable specific RNA G/C-content is associated with unequal polymerase chain reaction amplification efficiencies. Given the central importance of RNA-seq to molecular biology and personalized medicine, we review recent findings that challenge small non-protein coding RNA-seq data and suggest approaches and precautions to overcome or minimize bias.},
}
@article {pmid24188728,
year = {2014},
author = {Cocuzza, GE and Cavalieri, V},
title = {Identification of aphids of Aphis frangulae-group living on Lamiaceae species through DNA barcode.},
journal = {Molecular ecology resources},
volume = {14},
number = {3},
pages = {447-457},
doi = {10.1111/1755-0998.12199},
pmid = {24188728},
issn = {1755-0998},
mesh = {Animals ; Aphids/*classification/*genetics/physiology ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Host Specificity ; Insect Proteins/genetics ; Lamiaceae/classification/*parasitology ; Phylogeny ; },
abstract = {The genus Aphis frangulae-group living on Lamiaceae includes several postulate species, which are morphologically indistinguishable. As a consequence, identification is possible only on the basis of the host plant or life cycle. This study tested the utility of a fragment (614 bp) of mitochondrial cytochrome oxidase 1 (COI) with the aim of identifying the species and/or to confirm the previous classification based on host plant and data reported in the literature. Although the general nucleotide variability found was rather low, the analysis enabled the separation and identification of all the specimens collected. In some cases, the lack of nucleotide variability among postulated taxa indicates the limits of identification based on biological traits. Consequently, based on the molecular analysis, the postulate species A. symphyti, A. stachydis and A. lamiorum should be regarded as synonymous of A. frangulae.},
}
@article {pmid24187846,
year = {2013},
author = {Li, XJ and Han, JP and Li, JX and Chen, XC and Zhang, LF and Li, J and Gu, ZW and Zhang, YQ},
title = {[Identification of Salvia shandongensis new species based on sequences of the plastid psbA-trnH intergenic region].},
journal = {Yao xue xue bao = Acta pharmaceutica Sinica},
volume = {48},
number = {8},
pages = {1338-1344},
pmid = {24187846},
issn = {0513-4870},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic ; DNA, Intergenic/*genetics ; DNA, Plant/*genetics ; Genetic Variation ; Phylogeny ; Plants, Medicinal/classification/*genetics ; Plastids/*genetics ; Salvia/classification/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {To identify Salvia shandongensis and its relatives at molecular level, the psbA-trnH intergenic region of three species including Salvia shandongensis, Salvia miltiorrhiza and S. miltiorrhiza f. alba were amplified and sequenced. Sequences were assembled with CodonCode Aligner. The K2P genetic distances between Salvia shandongensis and its relatives were calculated and UPGMA tree was performed by MEGA5.0. The results indicated that the lengths of psbA-trnH regions of Salvia shandongensis were about 391 bp, while the lengths of psbA-trnH regions of Salvia miltiorrhiza and S. miltiorrhiza f. alba were about 386 bp. The psbA-trnH sequences showed considerable variations between species and thus were revealed as a promising candidate for barcoding of Salvia shandongensis and its relatives. The intra-specific genetic distances of Salvia shandongensis were 0, while the intra-specific genetic distances of Salvia miltiorrhiza and S. miltiorrhiza f. alba were 0.002 and 0.001 respectively. Additionally, the genetic distance of Salvia shandongensis and Salvia miltiorrhiza ranged from 0.034 to 0.04, and the genetic distance of Salvia shandongensis and S. miltiorrhiza f. alba ranged from 0.005 to 0.008, the intra-specific genetic distances of Salvia shandongensis were much smaller than that of Salvia miltiorrhiza and S. miltiorrhiza f. alba; clustering results showed that there were obvious differences between Salvia shandongensis, Salvia miltiorrhiza and S. miltiorrhiza f. alba, which was consistent with morphological characteristics. This study not only firstly provides the scientific basis for establishing the taxonomy position in molecular level and revealing their genetic relationships of S. shandongensis, S. miltiorrhiza and S. miltiorrhiza f. alba; but also provides DNA molecular identification scientific basis for the development of new medicinal plant resources of Salvia shandongensis. Our results suggest that the psbA-trnH intergenic spacer region can be used as a barcoding to identify Salvia shandongensis, Salvia miltiorrhiza and S. miltiorrhiza f. alba.},
}
@article {pmid24185043,
year = {2014},
author = {Stefani, FO and Jones, RH and May, TW},
title = {Concordance of seven gene genealogies compared to phenotypic data reveals multiple cryptic species in Australian dermocyboid Cortinarius (Agaricales).},
journal = {Molecular phylogenetics and evolution},
volume = {71},
number = {},
pages = {249-260},
doi = {10.1016/j.ympev.2013.10.019},
pmid = {24185043},
issn = {1095-9513},
mesh = {Color ; Cortinarius/classification/cytology/*genetics ; DNA, Fungal/genetics ; Phenotype ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {This study aims to delimit species of Australian dermocyboid fungi (Cortinarius, Agaricales) using genealogical concordance on well-characterised phenotypic species and to assess the utility of seven loci for DNA barcoding Australian Cortinarius taxa. Eighty-six collections of dermocyboid Cortinarius were sampled from across southern Australia. Phenotypic species were first recognised by performing clustering analyses on a comprehensive phenotypic dataset including morphological, colour and pigment data. Then phylogenetic species were delimited from the concordance of seven locus genealogies (ITS, nLSU, gpd, mcm7, rpb1, rpb2 and tef1). Seventeen phenotypic species were recognised while the concordance of gene genealogies recovered 35 phylogenetic species. All loci except for LSU recovered most phylogenetic species, although only rpb1 correctly identified all phylogenetic species. The ITS region is confirmed as an effective barcode for Cortinarius and a standard pairwise distance threshold of 2.0% is proposed to DNA barcode Australian Cortinarius taxa. Australian dermocyboid fungi belong in separate clades to the boreal clade Dermocybe, mostly in the clade Splendidi. This study provides a solid foundation for future ecological, taxonomic and systematic research on one of the most diverse genera of mushrooms worldwide.},
}
@article {pmid24184205,
year = {2013},
author = {Gérard, K and Guilloton, E and Arnaud-Haond, S and Aurelle, D and Bastrop, R and Chevaldonné, P and Derycke, S and Hanel, R and Lapègue, S and Lejeusne, C and Mousset, S and Ramšak, A and Remerie, T and Viard, F and Féral, JP and Chenuil, A},
title = {PCR survey of 50 introns in animals: cross-amplification of homologous EPIC loci in eight non-bilaterian, protostome and deuterostome phyla.},
journal = {Marine genomics},
volume = {12},
number = {},
pages = {1-8},
doi = {10.1016/j.margen.2013.10.001},
pmid = {24184205},
issn = {1876-7478},
mesh = {Animals ; DNA Primers ; Genetic Markers ; Introns/*genetics ; Invertebrates/classification/*genetics ; Nucleic Acid Amplification Techniques ; *Phylogeny ; Polymerase Chain Reaction ; },
abstract = {Exon Primed Intron Crossing (EPIC) markers provide molecular tools that are susceptible to be variable within species while remaining amplifiable by PCR using potentially universal primers. In this study we tested the possibility of obtaining PCR products from 50 EPIC markers on 23 species belonging to seven different phyla (Porifera, Cnidaria, Arthropoda, Nematoda, Mollusca, Annelida, Echinodermata) using 70 new primer pairs. A previous study had identified and tested those loci in a dozen species, including another phylum, Urochordata (Chenuil et al., 2010). Results were contrasted among species. The best results were achieved with the oyster (Mollusca) where 28 loci provided amplicons susceptible to contain an intron according to their size. This was however not the case with the other mollusk Crepidula fornicata, which seems to have undergone a reduction in intron number or intron size. In the Porifera, 13 loci appeared susceptible to contain an intron, a surprisingly high number for this phylum considering its phylogenetic distance with genomic data used to design the primers. For two cnidarian species, numerous loci (24) were obtained. Ecdysozoan phyla (arthropods and nematodes) proved less successful than others as expected considering reports of their rapid rate of genome evolution and the worst results were obtained for several arthropods. Some general patterns among phyla arose, and we discuss how the results of this EPIC survey may give new insights into genome evolution of the study species. This work confirms that this set of EPIC loci provides an easy-to-use toolbox to identify genetic markers potentially useful for population genetics, phylogeography or phylogenetic studies for a large panel of metazoan species. We then argue that obtaining diploid sequence genotypes for these loci became simple and affordable owing to Next-Generation Sequencing development. Species surveyed in this study belong to several genera (Acanthaster, Alvinocaris, Aplysina, Aurelia, Crepidula, Eunicella, Hediste, Hemimysis, Litoditis, Lophelia, Mesopodopsis, Mya, Ophiocten, Ophioderma, Ostrea, Pelagia, Platynereis, Rhizostoma, Rimicaris), two of them, belonging to the family Vesicomydae and Eunicidae, could not be determined at the genus level.},
}
@article {pmid24183013,
year = {2013},
author = {Fishell, G and Heintz, N},
title = {The neuron identity problem: form meets function.},
journal = {Neuron},
volume = {80},
number = {3},
pages = {602-612},
doi = {10.1016/j.neuron.2013.10.035},
pmid = {24183013},
issn = {1097-4199},
support = {R01MH095147/MH/NIMH NIH HHS/United States ; 5 P50 MH090963 P2/MH/NIMH NIH HHS/United States ; HSSN271200723701C//PHS HHS/United States ; R01NS081297/NS/NINDS NIH HHS/United States ; P0NS074972/NS/NINDS NIH HHS/United States ; P30 DA035756/DA/NIDA NIH HHS/United States ; RC2 DA028968/DA/NIDA NIH HHS/United States ; R01MH071679/MH/NIMH NIH HHS/United States ; P50 MH090963/MH/NIMH NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; P30 DA035756-01/DA/NIDA NIH HHS/United States ; },
mesh = {Animals ; Cell Differentiation/*physiology ; Humans ; Nervous System/*cytology ; Neurons/*classification/*metabolism ; },
abstract = {A complete understanding of nervous system function cannot be achieved without the identification of its component cell types. In this Perspective, we explore a series of related issues surrounding cell identity and how revolutionary methods for labeling and probing specific neuronal types have clarified this question. Specifically, we ask the following questions: what is the purpose of such diversity, how is it generated, how is it maintained, and, ultimately, how can one unambiguously identity one cell type from another? We suggest that each cell type can be defined by a unique and conserved molecular ground state that determines its capabilities. We believe that gaining an understanding of these molecular barcodes will advance our ability to explore brain function, enhance our understanding of the biochemical basis of CNS disorders, and aid in the development of novel therapeutic strategies.},
}
@article {pmid24173429,
year = {2013},
author = {Luo, JY and Yan, D and Song, JY and Zhang, D and Xing, XY and Han, YM and Yang, MH and Dong, XP and Peng, C and Chen, SL and Xiao, XH},
title = {A strategy for trade monitoring and substitution of the organs of threatened animals.},
journal = {Scientific reports},
volume = {3},
number = {},
pages = {3108},
pmid = {24173429},
issn = {2045-2322},
mesh = {*Animal Structures ; Animals ; Animals, Wild ; *Conservation of Natural Resources/methods ; DNA Barcoding, Taxonomic ; *Endangered Species ; Genetic Variation ; Phylogeny ; },
abstract = {The use of threatened animals as a source of traditional medicines is accelerating the extinction of such species and imposes great challenges to animal conservation. In this study, we propose a feasible strategy for the conservation of threatened medicinal animals that combines trade monitoring and the search for substitutes. First, DNA barcoding provides a powerful technique for monitoring the trade of animal species, which helps in restricting the excessive use and illegal trade of such species. Second, pharmacological tests have been adopted to evaluate the biological equivalence of threatened and domestic animals; based on such testing, potential substitutes are recommended. Based on a review of threatened animal species and their substitutes, we find that the search for substitutes deserves special attention; however, this work is far from complete. These results may be of great value for the conservation of threatened animals and maintaining the heritage of traditional medicine.},
}
@article {pmid24170674,
year = {2014},
author = {Metri, R and Jerath, G and Kailas, G and Gacche, N and Pal, A and Ramakrishnan, V},
title = {Structure-based barcoding of proteins.},
journal = {Protein science : a publication of the Protein Society},
volume = {23},
number = {1},
pages = {117-120},
pmid = {24170674},
issn = {1469-896X},
mesh = {Computational Biology/*methods ; Databases, Protein ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Proteins/*chemistry ; },
abstract = {A reduced representation in the format of a barcode has been developed to provide an overview of the topological nature of a given protein structure from 3D coordinate file. The molecular structure of a protein coordinate file from Protein Data Bank is first expressed in terms of an alpha-numero code and further converted to a barcode image. The barcode representation can be used to compare and contrast different proteins based on their structure. The utility of this method has been exemplified by comparing structural barcodes of proteins that belong to same fold family, and across different folds. In addition to this, we have attempted to provide an illustration to (i) the structural changes often seen in a given protein molecule upon interaction with ligands and (ii) Modifications in overall topology of a given protein during evolution. The program is fully downloadable from the website http://www.iitg.ac.in/probar/.},
}
@article {pmid24167421,
year = {2013},
author = {Landry, JF and Hebert, PD},
title = {Plutella australiana (Lepidoptera, Plutellidae), an overlooked diamondback moth revealed by DNA barcodes.},
journal = {ZooKeys},
volume = {},
number = {327},
pages = {43-63},
pmid = {24167421},
issn = {1313-2989},
abstract = {The genus Plutella was thought to be represented in Australia by a single introduced species, Plutella xylostella (Linnaeus), the diamondback moth. Its status as a major pest of cruciferous crops, and the difficulty in developing control strategies has motivated broad-ranging studies on its biology. Prior genetic work has generally supported the conclusion that populations of this migratory species are connected by substantial gene flow. However, the present study reveals the presence of two genetically divergent lineages of this taxonin Australia. One shows close genetic and morphological similarity with the nearly cosmopolitan Plutella xylostella. The second lineage possesses a similar external morphology, but marked sequence divergence in the barcode region of the cytochrome c oxidase I gene, coupled with clear differences in genitalia. As a consequence, members of this lineage are described as a new species, Plutella australiana Landry &amp; Hebert, which is broadly distributed in the eastern half of Australia.},
}
@article {pmid24167002,
year = {2013},
author = {Simard, C and Cloutier, M and Néron, S},
title = {Feasibility study: phospho-specific flow cytometry enabling rapid functional analysis of bone marrow samples from patients with multiple myeloma.},
journal = {Cytometry. Part B, Clinical cytometry},
volume = {},
number = {},
pages = {},
doi = {10.1002/cytob.21142},
pmid = {24167002},
issn = {1552-4957},
abstract = {Background: Multiple myeloma (MM) is an incurable cancer accounting for about 2% of cancer deaths. Its diagnosis is based on a combination of criteria, which are not always easily measurable. Flow cytometry now allows multiplex analysis of intracellular signaling at the single cell level. We investigated the feasibility of using intracellular protein phosphorylation analysis by flow cytometry on primary plasma cells from bone marrow and its usefulness in MM diagnosis. Methods: Cells from frozen bone marrow of five MM patients and four normal donors were stimulated with LPS, IL-6, IL-21, IFN? and TNF?. Cells were stained by fluorescent cell barcoding to allow multiplex analysis. Staining with antibodies against phosphorylated NFkB-p65, Stat1, Stat3 and p38 were used to identify cellular responses following stimulation. Results: Activation profile of MM and normal plasma cells have been established. MM cells showed heterogeneous response profiles while normal cells responses were homogeneous between donors. We also noticed that many MM samples seemed to show elevated basal level of Stat3 phosphorylation. These results suggest that different response profiles in primary MM cells might correspond to different subtypes of the disease. Thus, we provide an example of how these results may be used as a criterion for MM subtypes classification. Conclusions: We demonstrate that flow cytometry can be used to study signaling pathways in primary MM cells. The heterogeneity observed in MM cells from different patients can prove valuable for MM characterization and represents an interesting avenue for future research in MM diagnosis. © 2013 Clinical Cytometry Society.},
}
@article {pmid24165195,
year = {2014},
author = {Stoeck, T and Przybos, E and Dunthorn, M},
title = {The D1-D2 region of the large subunit ribosomal DNA as barcode for ciliates.},
journal = {Molecular ecology resources},
volume = {14},
number = {3},
pages = {458-468},
doi = {10.1111/1755-0998.12195},
pmid = {24165195},
issn = {1755-0998},
mesh = {Ciliophora/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/*genetics ; Genetic Markers ; Molecular Sequence Data ; Phylogeny ; Ribosome Subunits, Large/*genetics ; },
abstract = {Ciliates are a major evolutionary lineage within the alveolates, which are distributed in nearly all habitats on our planet and are an essential component for ecosystem function, processes and stability. Accurate identification of these unicellular eukaryotes through, for example, microscopy or mating type reactions is reserved to few specialists. To satisfy the demand for a DNA barcode for ciliates, which meets the standard criteria for DNA barcodes defined by the Consortium for the Barcode of Life (CBOL), we here evaluated the D1-D2 region of the ribosomal DNA large subunit (LSU-rDNA). Primer universality for the phylum Ciliophora was tested in silico with available database sequences as well as in the laboratory with 73 ciliate species, which represented nine of 12 ciliate classes. Primers tested in this study were successful for all tested classes. To test the ability of the D1-D2 region to resolve conspecific and congeneric sequence divergence, 63 Paramecium strains were sampled from 24 mating species. The average conspecific D1-D2 variation was 0.18%, whereas congeneric sequence divergence averaged 4.83%. In pairwise genetic distance analyses, we identified a D1-D2 sequence divergence of <0.6% as an ideal threshold to discriminate Paramecium species. Using this definition, only 3.8% of all conspecific and 3.9% of all congeneric sequence comparisons had the potential of false assignments. Neighbour-joining analyses inferred monophyly for all taxa but for two Paramecium octaurelia strains. Here, we present a protocol for easy DNA amplification of single cells and voucher deposition. In conclusion, the presented data pinpoint the D1-D2 region as an excellent candidate for an official CBOL barcode for ciliated protists.},
}
@article {pmid24164967,
year = {2013},
author = {Woodcock, TS and Boyle, EE and Roughley, RE and Kevan, PG and Labbee, RN and Smith, AB and Goulet, H and Steinke, D and Adamowicz, SJ},
title = {The diversity and biogeography of the Coleoptera of Churchill: insights from DNA barcoding.},
journal = {BMC ecology},
volume = {13},
number = {},
pages = {40},
pmid = {24164967},
issn = {1472-6785},
mesh = {Animals ; Arctic Regions ; *Biodiversity ; Coleoptera/*classification/genetics ; *DNA Barcoding, Taxonomic ; Gene Library ; Larva ; Manitoba ; *Phylogeny ; },
abstract = {BACKGROUND: Coleoptera is the most diverse order of insects (>300,000 described species), but its richness diminishes at increasing latitudes (e.g., ca. 7400 species recorded in Canada), particularly of phytophagous and detritivorous species. However, incomplete sampling of northern habitats and a lack of taxonomic study of some families limits our understanding of biodiversity patterns in the Coleoptera. We conducted an intensive biodiversity survey from 2006-2010 at Churchill, Manitoba, Canada in order to quantify beetle species diversity in this model region, and to prepare a barcode library of beetles for sub-arctic biodiversity and ecological research. We employed DNA barcoding to provide estimates of provisional species diversity, including for families currently lacking taxonomic expertise, and to examine the guild structure, habitat distribution, and biogeography of beetles in the Churchill region.<br><br>RESULTS: We obtained DNA barcodes from 3203 specimens representing 302 species or provisional species (the latter quantitatively defined on the basis of Molecular Operational Taxonomic Units, MOTUs) in 31 families of Coleoptera. Of the 184 taxa identified to the level of a Linnaean species name, 170 (92.4%) corresponded to a single MOTU, four (2.2%) represented closely related sibling species pairs within a single MOTU, and ten (5.4%) were divided into two or more MOTUs suggestive of cryptic species. The most diverse families were the Dytiscidae (63 spp.), Staphylinidae (54 spp.), and Carabidae (52 spp.), although the accumulation curve for Staphylinidae suggests that considerable additional diversity remains to be sampled in this family. Most of the species present are predatory, with phytophagous, mycophagous, and saprophagous guilds being represented by fewer species. Most named species of Carabidae and Dytiscidae showed a significant bias toward open habitats (wet or dry). Forest habitats, particularly dry boreal forest, although limited in extent in the region, were undersampled.<br><br>CONCLUSIONS: We present an updated species list for this region as well as a species-level DNA barcode reference library. This resource will facilitate future work, such as biomonitoring and the study of the ecology and distribution of larvae.},
}
@article {pmid24164957,
year = {2014},
author = {Christina, VL and Annamalai, A},
title = {Nucleotide based validation of Ocimum species by evaluating three candidate barcodes of the chloroplast region.},
journal = {Molecular ecology resources},
volume = {14},
number = {1},
pages = {60-68},
doi = {10.1111/1755-0998.12167},
pmid = {24164957},
issn = {1755-0998},
mesh = {Cluster Analysis ; *DNA Barcoding, Taxonomic ; DNA, Chloroplast/chemistry/*genetics ; *Genetic Variation ; Molecular Sequence Data ; Ocimum/*classification/*genetics ; Phylogeny ; Plant Proteins/genetics ; Sequence Analysis, DNA ; },
abstract = {The genus Ocimum comprises of several medicinally important species which frequently fall prey to adulteration due to misidentification. A proficient method is hence required to solve the problems that exist in differentiating its various morphotypes. In plants, candidate DNA barcodes of the chloroplast and nuclear regions have proved to be a great success in the validation of several plant families. Hence, this study involves the use of the molecular-based DNA barcoding method to identify some of the most common and useful species of the genus Ocimum (Tulsi). Here, DNA amplification of three candidate barcodes of the chloroplast genome viz. matK, rbcL and psbA-trnH was performed, to access their ability to produce high sequence variability. The discrimination among species was performed using the Kimura 2-parameter and maximum composite likelihood methods. On analysing the sequence data, the psbA-trnH region proved to be the most suitable candidate barcode and gave an overall variation of 7.3% at the interspecies level. A clear differentiation was found at the species level, showing a maximum distance of 0.264 between dissimilar species. Also, phylogenetic analysis led to the successful identification of hybrids, while it failed to do so at the variety level. Hence, it can be inferred that DNA barcoding is ideal for species-level identification of the genus Ocimum.},
}
@article {pmid24164314,
year = {2014},
author = {Yin, HQ and Jia, MX and Shi, LJ and Liu, J and Wang, R and Lv, MM and Ma, YY and Zhao, X and Zhang, JG},
title = {Evaluation of a novel ultra-sensitive nanoparticle probe-based assay for ricin detection.},
journal = {Journal of immunotoxicology},
volume = {11},
number = {3},
pages = {291-295},
doi = {10.3109/1547691X.2013.847994},
pmid = {24164314},
issn = {1547-6901},
mesh = {Antibodies, Monoclonal/*metabolism ; Chemical Warfare Agents/*analysis ; DNA, Single-Stranded/*metabolism ; Gold/chemistry ; Humans ; Immunosorbent Techniques ; Magnetite Nanoparticles/chemistry/*statistics &amp; numerical data ; Observer Variation ; Ricin/*analysis/immunology ; Sensitivity and Specificity ; },
abstract = {A gold nanoparticle (GNP) probe-based assay (GNPA) modified from the bio-barcode assay (BCA) was developed for ultrasensitive detection of ricin, a potential biothreat agent. In the GNPA, a chain of ricin was captured by a GNP probe coated with polyclonal antibodies and single-stranded signal DNA. A magnetic microparticle (MMP) probe coated with ricin A chain monoclonal antibody was then added to form an immuno-complex. After being magnetically separated, the immuno-complex containing the single-stranded signal DNA was characterized by PCR and real-time PCR. A detection limit of 10(-2) fg/ml was determined for the ricin A chain; this is eight orders of magnitude more sensitive than that achieved with an ELISA and two orders more sensitive than that obtained with the BCA. The coefficients of variation (CV) of the intra- and inter-assay values ranged from 3.82-6.46%. The results here show that this novel assay is an ultrasensitive method for detection of ricin proteins and may be suitable for the ultrasensitive detection of other proteins.},
}
@article {pmid24161242,
year = {2013},
author = {Wijit, A and Saeung, A and Baimai, V and Otsuka, Y and Thongsahuan, S and Taai, K and Srisuka, W and Songsawatkiat, S and Sor-suwan, S and Hempolchom, C and Somboon, P and Choochote, W},
title = {DNA barcoding for the identification of eight species members of the Thai Hyrcanus Group and investigation of their stenogamous behavior.},
journal = {Comptes rendus biologies},
volume = {336},
number = {9},
pages = {449-456},
doi = {10.1016/j.crvi.2013.08.001},
pmid = {24161242},
issn = {1768-3238},
mesh = {Animals ; Anopheles/*classification/genetics/physiology ; Base Sequence ; DNA/*analysis ; DNA Primers ; Electrophoresis, Agar Gel ; Female ; Genes, Insect ; *Genetic Markers ; Genetic Variation ; Male ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Sexual Behavior, Animal ; Species Specificity ; },
abstract = {Eight species members of the Thai Hyrcanus Group were identified based on the intact morphology and molecular analysis (COI barcoding, 658 bp) of F1-progenies. Five iso-female lines of each species were pooled in order to establish stock colonies. A stenogamous colony of each species was investigated by making 200 and 300 newly emerged adult females and males co-habit in a 30 cm cubic cage for one week. After ovipositon, the spermathecae of females were examined for sperms. The results revealed that Anopheles argyropus, Anopheles crawfordi, Anopheles nitidus, Anopheles pursati, Anopheles sinensis, Anopheles nigerrimus, Anopheles paraliae and Anopheles peditaeniatus yielded insemination rates of 0%, 0%, 0%, 31%, 33%, 42%, 50% and 77%, respectively. Continuous selection to establish stenogamous colonies indicated that An. sinensis, An. pursati, An. nigerrimus, An. paraliae and An. peditaeniatus provided insemination rates of 33-34%, 27-31%, 42-58%, 43-57% and 61-86% in 1, 2, 5, 6 and 20 generations of passages, respectively.},
}
@article {pmid24147781,
year = {2014},
author = {Kohli, GS and Neilan, BA and Brown, MV and Hoppenrath, M and Murray, SA},
title = {Cob gene pyrosequencing enables characterization of benthic dinoflagellate diversity and biogeography.},
journal = {Environmental microbiology},
volume = {16},
number = {2},
pages = {467-485},
doi = {10.1111/1462-2920.12275},
pmid = {24147781},
issn = {1462-2920},
mesh = {Biodiversity ; Cytochromes b/*genetics ; DNA, Protozoan/genetics ; Dinoflagellida/*classification/genetics ; Likelihood Functions ; Papua New Guinea ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA/methods ; Western Australia ; },
abstract = {Dinoflagellates in marine benthic habitats living epiphytically on macroalgae are an important but highly understudied group of protists. Many produce toxins that can have severe economic impacts on marine-based economies, and improved monitoring tools are required to enhance the management of toxin-related hazards. We analysed the distribution and diversity of epibenthic dinoflagellates inhabiting eight sites in Cocos (Keeling) Islands, Papua New Guinea, and Broome and Exmouth, Western Australia. We used pyrosequencing approaches based on two DNA barcoding marker genes - 18S ribosomal RNA (rRNA) and mitochondrial cytochrome b (cob) - and compared these to an approach based on clone libraries (197 sequences) using the cob gene. Dinoflagellate sequences accounted for 133 [64 unique operational taxonomic units (OTU)] out of 10 529 18S rRNA gene sequences obtained from all samples. However, using the dinoflagellate specific assay targeting the cob gene marker, we obtained 9748 (1217 unique OTU) dinoflagellate sequences from the same environmental samples, providing the largest, to date, set of dinoflagellate cob gene sequences and reliable estimates of total dinoflagellate richness within the samples and biogeographic comparisons between samples. This study also reports the presence of potentially toxic species of the genera Gambierdiscus, Ostreopsis, Coolia, Prorocentrum and Amphidinium from the above-mentioned geographical regions.},
}
@article {pmid24146597,
year = {2013},
author = {Ghiglione, C and Alvaro, MC and Griffiths, HJ and Linse, K and Schiaparelli, S},
title = {Ross Sea Mollusca from the Latitudinal Gradient Program: R/V Italica 2004 Rauschert dredge samples.},
journal = {ZooKeys},
volume = {},
number = {341},
pages = {37-48},
pmid = {24146597},
issn = {1313-2989},
abstract = {Information regarding the molluscs in this dataset is based on the Rauschert dredge samples collected during the Latitudinal Gradient Program (LGP) on board the R/V "Italica" in the Ross Sea (Antarctica) in the austral summer 2004. A total of 18 epibenthic dredge deployments/samplings have been performed at four different locations at depths ranging from 84 to 515m by using a Rauschert dredge with a mesh size of 500μm. In total 8,359 specimens have been collected belonging to a total of 161 species. Considering this dataset in terms of occurrences, it corresponds to 505 discrete distributional records (incidence data). Of these, in order of abundance, 5,965 specimens were Gastropoda (accounting for 113 species), 1,323 were Bivalvia (accounting for 36 species), 949 were Aplacophora (accounting for 7 species), 74 specimens were Scaphopoda (3 species), 38 were Monoplacophora (1 species) and, finally, 10 specimens were Polyplacophora (1 species). This data set represents the first large-scale survey of benthic micro-molluscs for the area and provides important information about the distribution of several species, which have been seldom or never recorded before in the Ross Sea. All vouchers are permanently stored at the Italian National Antarctic Museum (MNA), Section of Genoa, enabling future comparison and crosschecking. This material is also currently under study, from a molecular point of view, by the barcoding project "BAMBi" (PNRA 2010/A1.10).},
}
@article {pmid24146582,
year = {2013},
author = {Bai, Y and Bu, Y},
title = {Hesperentomon yangi sp. n. from Jiangsu Province, Eastern China, with analyses of DNA barcodes (Protura, Acerentomata, Hesperentomidae).},
journal = {ZooKeys},
volume = {},
number = {338},
pages = {29-37},
pmid = {24146582},
issn = {1313-2989},
abstract = {Hesperentomon yangi sp. n. is described from eastern China. Its DNA barcodes are sequenced and compared to the similar species of the genus. Hesperentomon yangi sp. n. is characterized by 12 posterior setae on tergites II-VI, 8 posterior setae on sternites IV-VI (seta Pc absent), absence of seta sd4 on head, absence of seta P2a on tergite VII, 6 and 8 anterior setae on mesosternum and metasternum respectively, and few teeth on comb. It differs from Hesperentomon xiningense Bu &amp; Yin, 2007 and Hesperentomon nanshanensis Bu &amp; Yin, 2007 in the chaetotaxy of mesosternum and metanotum, maxillary gland, length and shape of some sensilla on foretarsus, as well as the body porotaxy. The genetic divergences of DNA barcodes sequences between Hesperentomon yangi sp. n., Hesperentomon xiningense and Hesperentomon nanshanensis are 24.1% on average, which is distinctly higher than the divergences between individuals of the new species (0.5%). Molecular data provide a solid evidence of the new species identified by the morphological characters.},
}
@article {pmid24143221,
year = {2013},
author = {Lawton, RJ and Mata, L and de Nys, R and Paul, NA},
title = {Algal bioremediation of waste waters from land-based aquaculture using ulva: selecting target species and strains.},
journal = {PloS one},
volume = {8},
number = {10},
pages = {e77344},
pmid = {24143221},
issn = {1932-6203},
mesh = {*Aquaculture ; Biodegradation, Environmental ; Species Specificity ; Ulva/growth &amp; development/*metabolism ; Wastewater/*microbiology ; },
abstract = {The optimised reduction of dissolved nutrient loads in aquaculture effluents through bioremediation requires selection of appropriate algal species and strains. The objective of the current study was to identify target species and strains from the macroalgal genus Ulva for bioremediation of land-based aquaculture facilities in Eastern Australia. We surveyed land-based aquaculture facilities and natural coastal environments across three geographic locations in Eastern Australia to determine which species of Ulva occur naturally in this region and conducted growth trials at three temperature treatments on a subset of samples from each location to determine whether local strains had superior performance under local environmental conditions. DNA barcoding using the markers ITS and tufA identified six species of Ulva, with U. ohnoi being the most common blade species and U. sp. 3 the most common filamentous species. Both species occurred at multiple land-based aquaculture facilities in Townsville and Brisbane and multiple strains of each species grew well in culture. Specific growth rates of U. ohnoi and U. sp. 3 were high (over 9% and 15% day(-1) respectively) across temperature treatments. Within species, strains of U. ohnoi had higher growth in temperatures corresponding to local conditions, suggesting that strains may be locally adapted. However, across all temperature treatments Townsville strains had the highest growth rates (11.2-20.4% day(-1)) and Sydney strains had the lowest growth rates (2.5-8.3% day(-1)). We also found significant differences in growth between strains of U. ohnoi collected from the same geographic location, highlighting the potential to isolate and cultivate fast growing strains. In contrast, there was no clearly identifiable competitive strain of filamentous Ulva, with multiple species and strains having variable performance. The fast growth rates and broad geographical distribution of U. ohnoi make this an ideal species to target for bioremediation activities at land-based aquaculture facilities in Eastern Australia.},
}
@article {pmid24133644,
year = {2013},
author = {Kurobe, T and Baxa, DV and Mioni, CE and Kudela, RM and Smythe, TR and Waller, S and Chapman, AD and Teh, SJ},
title = {Identification of harmful cyanobacteria in the Sacramento-San Joaquin Delta and Clear Lake, California by DNA barcoding.},
journal = {SpringerPlus},
volume = {2},
number = {},
pages = {491},
pmid = {24133644},
issn = {2193-1801},
abstract = {Accurate identification of cyanobacteria using traditional morphological taxonomy is challenging due to the magnitude of phenotypic plasticity among natural algal assemblages. In this study, molecular approach was utilized to facilitate the accurate identification of cyanobacteria in the Sacramento-San Joaquin Delta and in Clear Lake in Northern California where recurring blooms have been observed over the past decades. Algal samples were collected from both water bodies in 2011 and the samples containing diverse cyanobacteria as identified by morphological taxonomy were chosen for the molecular analysis. The 16S ribosomal RNA genes (16S rDNA) and the adjacent internal transcribed spacer (ITS) regions were amplified by PCR from the mixed algal samples using cyanobacteria generic primers. The obtained sequences were analyzed by similarity search (BLASTN) and phylogenetic analysis (16S rDNA) to differentiate species sharing significantly similar sequences. A total of 185 plasmid clones were obtained of which 77 were successfully identified to the species level: Aphanizomenon flos-aquae, Dolichospermum lemmermannii (taxonomic synonym: Anabaena lemmermannii), Limnoraphis robusta (taxonomic synonym: Lyngbya hieronymusii f. robusta) and Microcystis aeruginosa. To date, Dolichospermum and Limnoraphis found in Clear Lake have only been identified to the genus lavel by microscopy. During the course of this study, morphological identification and DNA barcoding confirmed A. flos-aquae as the predominant cyanobacterium in the Sacramento-San Joaquin Delta indicating a shift from M. aeruginosa that have dominated the blooms in the past decade. Lastly, the species-specific identification of Limnoraphis robusta in Clear Lake is another significant finding as this cyanobacterium has, thus far, only been reported in Lake Atitlan blooms in Guatemala.},
}
@article {pmid24130762,
year = {2013},
author = {Gu, G and Wang, T and Yang, Y and Xu, X and Wang, J},
title = {An improved SELEX-Seq strategy for characterizing DNA-binding specificity of transcription factor: NF-κB as an example.},
journal = {PloS one},
volume = {8},
number = {10},
pages = {e76109},
pmid = {24130762},
issn = {1932-6203},
mesh = {DNA/*metabolism ; Humans ; NF-kappa B/chemistry/genetics/*metabolism ; Protein Binding ; SELEX Aptamer Technique/methods ; Transcription Factors/chemistry/genetics/*metabolism ; },
abstract = {SELEX-Seq is now the optimal high-throughput technique for characterizing DNA-binding specificities of transcription factors. In this study, we introduced an improved EMSA-based SELEX-Seq strategy with several advantages. The improvements of this strategy included: (1) using a FAM-labeled probe to track protein-DNA complex in polyacrylamide gel for rapidly recovering the protein-bound dsDNA without relying on traditional radioactive labeling or ethidium bromide staining; (2) monitoring the specificity of SELEX selection by detecting a positive and negative sequence doped into the input DNAs used in each round with PCR amplification; (3) using nested PCR to ensure the specificity of PCR amplification of the selected DNAs after each round; (4) using the nucleotides added at the 5' end of the nested PCR primers as the split barcode to code DNAs from various rounds for multiplexing sequencing samples. The split barcode minimized selection times and thus greatly simplified the current SELEX-Seq procedure. The reliability of the strategy was demonstrated by performing a successful SELEX-Seq of a well-known transcription factor, NF-κB. Therefore, this study provided a useful SELEX-Seq strategy for characterizing DNA-binding specificities of transcription factors.},
}
@article {pmid24128146,
year = {2014},
author = {Bacci, G and Bazzicalupo, M and Benedetti, A and Mengoni, A},
title = {StreamingTrim 1.0: a Java software for dynamic trimming of 16S rRNA sequence data from metagenetic studies.},
journal = {Molecular ecology resources},
volume = {14},
number = {2},
pages = {426-434},
doi = {10.1111/1755-0998.12187},
pmid = {24128146},
issn = {1755-0998},
mesh = {Computational Biology/*methods ; Metagenomics/*methods ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Software ; },
abstract = {Next-generation sequencing technologies are extensively used in the field of molecular microbial ecology to describe taxonomic composition and to infer functionality of microbial communities. In particular, the so-called barcode or metagenetic applications that are based on PCR amplicon library sequencing are very popular at present. One of the problems, related to the utilization of the data of these libraries, is the analysis of reads quality and removal (trimming) of low-quality segments, while retaining sufficient information for subsequent analyses (e.g. taxonomic assignment). Here, we present StreamingTrim, a DNA reads trimming software, written in Java, with which researchers are able to analyse the quality of DNA sequences in fastq files and to search for low-quality zones in a very conservative way. This software has been developed with the aim to provide a tool capable of trimming amplicon library data, retaining as much as taxonomic information as possible. This software is equipped with a graphical user interface for a user-friendly usage. Moreover, from a computational point of view, StreamingTrim reads and analyses sequences one by one from an input fastq file, without keeping anything in memory, permitting to run the computation on a normal desktop PC or even a laptop. Trimmed sequences are saved in an output file, and a statistics summary is displayed that contains the mean and standard deviation of the length and quality of the whole sequence file. Compiled software, a manual and example data sets are available under the BSD-2-Clause License at the GitHub repository at https://github.com/GiBacci/StreamingTrim/.},
}
@article {pmid24124646,
year = {2013},
author = {Chen, Y and Ding, L and Liu, T and Ju, H},
title = {Arrayed profiling of multiple glycans on whole living cell surfaces.},
journal = {Analytical chemistry},
volume = {85},
number = {22},
pages = {11153-11158},
doi = {10.1021/ac403150n},
pmid = {24124646},
issn = {1520-6882},
mesh = {Cell Membrane/*metabolism ; Flow Cytometry ; Humans ; Lectins/*metabolism ; Oligonucleotide Array Sequence Analysis/*methods ; Polysaccharides/*analysis/metabolism ; Stomach Neoplasms/*metabolism ; },
abstract = {An array-based method for profiling and quantification of multiple glycans on whole living cell surfaces was developed through combining DNA encoding technology with DNA microarray. Using four kinds of lectins as the model to recognize four types of cell surface glycans, the specific barcode-lectin probes that contained the endonuclease cutting site were designed. The barcode-lectin probes had the DNA sequences complementary to four sequences immobilized on a DNA microarray, respectively. After the living cells were incubated with the mixture of four barcode-lectin probes, these probes could bind to cell surface through the specific interaction between the lectins and corresponding glycans. Thus, the glycans and their amounts could be profiled by releasing the barcodes from cell surface with endonuclease cleaving, binding the barcodes to DNA microarray with specific hybridization, and then producing the amplified fluorescence signal with hybridization chain reaction (HCR). The HCR was performed with two kinds of Cy5 labeled hairpins. The average amount of mannose, N-acetylgalactosamine, N-acetylglucosamine, and N-acetylneuraminic acid on BGC cell was obtained to be 6.8 × 10(7), 3.8 × 10(7), 2.1 × 10(8), and 1.1 × 10(7) moieties per cell, respectively. The proposed method possessed whole cell surface accessibility, powerful distinguishing capability, fast recognition kinetics, easy miniaturization, and high throughput without need of cell pretreatment or labeling. It could become a powerful tool for elucidation of the complex glycan-related biological processes.},
}
@article {pmid24124285,
year = {2013},
author = {Liu, Y and Wang, K and Liu, Z and Luo, K and Chen, S and Chen, K},
title = {Identification of medical plants of 24 Ardisia species from China using the matK genetic marker.},
journal = {Pharmacognosy magazine},
volume = {9},
number = {36},
pages = {331-337},
pmid = {24124285},
issn = {0973-1296},
abstract = {BACKGROUND: Ardisia is a group of famous herbs in China, which has been used as medical plants for more than 900 years. However, the species from the genus are so analogous that it is difficult to discriminate them just by morphological characteristics. DNA barcoding is a new technique that uses a short and standard fragment of DNA sequences to identify species.<br><br>OBJECTIVE: Choose a suitable DNA marker to authenticate Ardisia species.<br><br>MATERIALS AND METHODS: Four markers (psbA-trnH, internal transcribed spacer 2 [ITS2], rbcL, matK) were tested on 54 samples of 24 species from genus Ardisia. The success rates of polymerase chain reaction amplification and sequencing, differential intra- and inter-specific divergences, DNA barcoding gap and identification efficiency were used to evaluate the discrimination ability.<br><br>RESULTS: The results indicate that matK has the highest interspecific divergence and significant differences between inter- and intra-specific divergences, whereas psbA-trnH, ITS2 and rbcL have much lower divergence values. Matk possessed the highest species identification efficiency at 98.1% by basic local alignment search tool 1 [BLAST1], method and 91.7% by the nearest distance method.<br><br>CONCLUSION: The matK region is a promising DNA barcode for the genus Ardisia.},
}
@article {pmid24120035,
year = {2013},
author = {Newmaster, SG and Grguric, M and Shanmughanandhan, D and Ramalingam, S and Ragupathy, S},
title = {DNA barcoding detects contamination and substitution in North American herbal products.},
journal = {BMC medicine},
volume = {11},
number = {},
pages = {222},
pmid = {24120035},
issn = {1741-7015},
mesh = {Capsules/chemistry ; Chemistry, Pharmaceutical ; DNA Barcoding, Taxonomic/*methods ; *Drug Contamination ; North America ; Plant Extracts/*analysis/chemistry ; Plant Leaves/chemistry ; Powders/chemistry ; },
abstract = {BACKGROUND: Herbal products available to consumers in the marketplace may be contaminated or substituted with alternative plant species and fillers that are not listed on the labels. According to the World Health Organization, the adulteration of herbal products is a threat to consumer safety. Our research aimed to investigate herbal product integrity and authenticity with the goal of protecting consumers from health risks associated with product substitution and contamination.<br><br>METHODS: We used DNA barcoding to conduct a blind test of the authenticity for (i) 44 herbal products representing 12 companies and 30 different species of herbs, and (ii) 50 leaf samples collected from 42 herbal species. Our laboratory also assembled the first standard reference material (SRM) herbal barcode library from 100 herbal species of known provenance that were used to identify the unknown herbal products and leaf samples.<br><br>RESULTS: We recovered DNA barcodes from most herbal products (91%) and all leaf samples (100%), with 95% species resolution using a tiered approach (rbcL + ITS2). Most (59%) of the products tested contained DNA barcodes from plant species not listed on the labels. Although we were able to authenticate almost half (48%) of the products, one-third of these also contained contaminants and or fillers not listed on the label. Product substitution occurred in 30/44 of the products tested and only 2/12 companies had products without any substitution, contamination or fillers. Some of the contaminants we found pose serious health risks to consumers.<br><br>CONCLUSIONS: Most of the herbal products tested were of poor quality, including considerable product substitution, contamination and use of fillers. These activities dilute the effectiveness of otherwise useful remedies, lowering the perceived value of all related products because of a lack of consumer confidence in them. We suggest that the herbal industry should embrace DNA barcoding for authenticating herbal products through testing of raw materials used in manufacturing products. The use of an SRM DNA herbal barcode library for testing bulk materials could provide a method for 'best practices? in the manufacturing of herbal products. This would provide consumers with safe, high quality herbal products.},
}
@article {pmid24119263,
year = {2014},
author = {Dong, W and Cheng, T and Li, C and Xu, C and Long, P and Chen, C and Zhou, S},
title = {Discriminating plants using the DNA barcode rbcLb: an appraisal based on a large data set.},
journal = {Molecular ecology resources},
volume = {14},
number = {2},
pages = {336-343},
doi = {10.1111/1755-0998.12185},
pmid = {24119263},
issn = {1755-0998},
mesh = {Computational Biology ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; *Genetic Variation ; Genotyping Techniques/*methods ; Plants/*classification/*genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; },
abstract = {The ideal DNA barcode for plants remains to be discovered, and the candidate barcode rbcL has been met with considerable skepticism since its proposal. In fact, the variability within this gene has never been fully explored across all plant groups from algae to flowering plants, and its performance as a barcode has not been adequately tested. By analysing all of the rbcL sequences currently available in GenBank, we attempted to determine how well a region of rbcL performs as a barcode in species discrimination. We found that the rbcLb region was more variable than the frequently used rbcLa region. Both universal and plant group-specific primers were designed to amplify rbcLb, and the performance of rbcLa and rbcLb was tested in several ways. Using blast, both regions successfully identified all families and nearly all genera; however, the successful species identification rates varied significantly among plant groups, ranging from 24.58% to 85.50% for rbcLa and from 36.67% to 90.89% for rbcLb. Successful species discrimination ranged from 5.19% to 96.33% for rbcLa and from 22.09% to 98.43% for rbcLb in species-rich families, and from 0 to 88.73% for rbcLa and from 2.04% to 100% for rbcLb in species-rich genera. Both regions performed better for lower plants than for higher plants, although rbcLb performed significantly better than rbcLa overall, particularly for angiosperms. Considering the applicability across plants, easy and unambiguous alignment, high primer universality, high sequence quality and high species discrimination power for lower plants, we suggest rbcLb as a universal plant barcode.},
}
@article {pmid24119215,
year = {2014},
author = {S Alves, TL and Chauveau, O and Eggers, L and de Souza-Chies, TT},
title = {Species discrimination in Sisyrinchium (Iridaceae): assessment of DNA barcodes in a taxonomically challenging genus.},
journal = {Molecular ecology resources},
volume = {14},
number = {2},
pages = {324-335},
doi = {10.1111/1755-0998.12182},
pmid = {24119215},
issn = {1755-0998},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/chemistry/genetics ; Genes, Plant ; Iridaceae/*classification/*genetics ; Molecular Sequence Data ; Plastids/genetics ; Sequence Analysis, DNA ; },
abstract = {DNA barcoding aims to develop an efficient tool for species identification based on short and standardized DNA sequences. In this study, the DNA barcode paradigm was tested among the genera of the tribe Sisyrinchieae (Iridoideae). Sisyrinchium, with more than 77% of the species richness in the tribe, is a taxonomically complex genus. A total of 185 samples belonging to 98 species of Sisyrinchium, Olsynium, Orthrosanthus and Solenomelus were tested using matK, trnH-psbA and internal transcribed spacer (ITS). Candidate DNA barcodes were analysed either as single markers or in combination. Detection of a barcoding gap, similarity-based methods and tree-based analyses were used to assess the discrimination efficiency of DNA barcodes. The levels of species identification obtained from plastid barcodes were low and ranged from 17.35% to 20.41% for matK and 5.11% to 7.14% for trnH-psbA. The ITS provided better results with 30.61-38.78% of species identified. The analyses of the combined data sets did not result in a significant improvement in the discrimination rate. Among the tree-based methods, the best taxonomic resolution was obtained with Bayesian inference, particularly when the three data sets were combined. The study illustrates the difficulties for DNA barcoding to identify species in evolutionary complex lineages. Plastid markers are not recommended for barcoding Sisyrinchium due to the low discrimination power observed. ITS gave better results and may be used as a starting point for species identification.},
}
@article {pmid24119085,
year = {2014},
author = {Lees, DC and Kawahara, AY and Rougerie, R and Ohshima, I and Kawakita, A and Bouteleux, O and De Prins, J and Lopez-Vaamonde, C},
title = {DNA barcoding reveals a largely unknown fauna of Gracillariidae leaf-mining moths in the Neotropics.},
journal = {Molecular ecology resources},
volume = {14},
number = {2},
pages = {286-296},
doi = {10.1111/1755-0998.12178},
pmid = {24119085},
issn = {1755-0998},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Ecuador ; French Guiana ; Molecular Sequence Data ; Moths/*classification/*genetics ; Tropical Climate ; },
abstract = {Higher taxa often show increasing species richness towards tropical low latitudes, a pattern known as the latitudinal biodiversity gradient (LBG). A rare reverse LBG (with greater richness towards temperate high latitudes) is exhibited by Gracillariidae leaf-mining moths, in which most described species occur in northern temperate areas. We carried out the first assessment of gracillariid species diversity in two Neotropical regions to test whether the relatively low tropical species diversity of this family is genuine or caused by insufficient sampling and a strong taxonomic impediment. Field surveys in six French Guianan and one Ecuadorian site produced 516 gracillariid specimens that were DNA barcoded to facilitate identification and to match larvae inside leaf mines with adults. Species delineation from sequence data was approximated using Automatic Barcode Gap Discovery and Refined Single Linkage Analysis through the Barcode Index Number system, and the proportion of described/undescribed species was estimated after comparison with types of 83% of described species. Locally, alpha-diversity far exceeds that of any known temperate fauna, with as many as 108 candidate species (59.3% as singletons) collected at one site, and with an estimated species richness lower bound of 240 species. Strikingly, at least 85% of the species collected as adults were found to be undescribed. Our sampling represents the most thorough survey of gracillariid species diversity in the Neotropics to date and the results from both our molecular and morphological analyses indicate that the current reverse LBG seen in this group is an artefact of insufficient sampling and a strong description deficit in the Neotropics.},
}
@article {pmid24118979,
year = {2014},
author = {Krawczyk, K and Szczecińska, M and Sawicki, J},
title = {Evaluation of 11 single-locus and seven multilocus DNA barcodes in Lamium L. (Lamiaceae).},
journal = {Molecular ecology resources},
volume = {14},
number = {2},
pages = {272-285},
doi = {10.1111/1755-0998.12175},
pmid = {24118979},
issn = {1755-0998},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Chloroplast/chemistry/genetics ; DNA, Plant/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Genetic Variation ; Genotyping Techniques/*methods ; Lamiaceae/*classification/*genetics ; Molecular Sequence Data ; },
abstract = {The aim of this work was to evaluate the suitability of selected DNA regions in the barcoding of plants, based on the species belonging to the genus Lamium (Lamiaceae). For this purpose, nine chloroplast barcodes, that is, accD, matK, rbcL, rpoA, rpoB, rpoC1, rpoC2, trnH-psbA, trnL-trnF, as well as ITS nuclear region, and intron of mitochondrial nad5 gene were tested. Among the single-locus barcodes, most effective in the identification of Lamium species was the trnH-psbA spacer and matK gene. The high level of variability and resolving power was also observed in the case of rpoA and rpoC2 genes. Despite the high interspecies variability of ITS region, it turned out to be inapplicable in Lamium identification. An important disadvantage of ITS as a barcode is a limitation of its use in polyploid plants, samples contaminated with fungal material or samples with partially degraded DNA. We have also evaluated five-two-locus and two-three-locus barcode regions created from a combination of most effective single loci. The best-performing barcode combinations were matK + trnH-psbA and matK + rpoA. Both of them had equally high discriminative power to identify Lamium species.},
}
@article {pmid24118947,
year = {2014},
author = {Joly, S and Davies, TJ and Archambault, A and Bruneau, A and Derry, A and Kembel, SW and Peres-Neto, P and Vamosi, J and Wheeler, TA},
title = {Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead.},
journal = {Molecular ecology resources},
volume = {14},
number = {2},
pages = {221-232},
doi = {10.1111/1755-0998.12173},
pmid = {24118947},
issn = {1755-0998},
mesh = {*Biota ; DNA Barcoding, Taxonomic/*methods ; Ecology/*methods ; },
abstract = {Ten years after DNA barcoding was initially suggested as a tool to identify species, millions of barcode sequences from more than 1100 species are available in public databases. While several studies have reviewed the methods and potential applications of DNA barcoding, most have focused on species identification and discovery, and relatively few have addressed applications of DNA barcoding data to ecology. These data, and the associated information on the evolutionary histories of taxa that they can provide, offer great opportunities for ecologists to investigate questions that were previously difficult or impossible to address. We present an overview of potential uses of DNA barcoding relevant in the age of ecoinformatics, including applications in community ecology, species invasion, macroevolution, trait evolution, food webs and trophic interactions, metacommunities, and spatial ecology. We also outline some of the challenges and potential advances in DNA barcoding that lie ahead.},
}
@article {pmid24118115,
year = {2013},
author = {Fontaneto, D and Hortal, J},
title = {At least some protist species are not ubiquitous.},
journal = {Molecular ecology},
volume = {22},
number = {20},
pages = {5053-5055},
doi = {10.1111/mec.12507},
pmid = {24118115},
issn = {1365-294X},
mesh = {Amoeba/*genetics ; *Climate ; *Genetic Variation ; *Phylogeny ; },
abstract = {Body size is one of the main regulators of the ecological characteristics of living organisms, including their biogeography. The 'ubiquity hypothesis' for microorganisms states that they are widely distributed, if not cosmopolitan, due to their small size that allows passive dispersal, in contrast to large organisms that are limited by geographical barriers in their active dispersal. Such idea, summarized in the tenet 'Everything is everywhere, but the environment selects', has driven most of the research in biogeography for microscopic organisms in the last decades, spurring a debate on whether there are fundamental differences in the biogeography of small and large organisms or not (Fenchel &amp; Finlay 2004; Foissner 2008; Hortal 2011). The strong focus on the ubiquity hypothesis may have been often abused to provide a rationale for otherwise descriptive work on the spatial distribution of microscopic organisms; nevertheless, such focus also provides a framework to understand the mechanisms originating and maintaining biodiversity in space. The reliability of the analyses on unknown and understudied organisms is improving, and Heger et al. (2013) is a splendid example on small unicellular eukaryotes of what should be done to overcome the major problems and ambiguities that heated the debate on the ubiquity hypothesis.},
}
@article {pmid24117189,
year = {2015},
author = {Keith Barker, F and Oyler-McCance, S and Tomback, DF},
title = {Blood from a turnip: tissue origin of low-coverage shotgun sequencing libraries affects recovery of mitogenome sequences.},
journal = {Mitochondrial DNA},
volume = {26},
number = {3},
pages = {384-388},
doi = {10.3109/19401736.2013.840588},
pmid = {24117189},
issn = {1940-1744},
mesh = {Animals ; Brassica napus/*genetics ; DNA/*blood/isolation &amp; purification ; Databases, Genetic ; Gene Library ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Microsatellite Repeats/genetics ; Muscle, Skeletal/metabolism ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {Next generation sequencing methods allow rapid, economical accumulation of data that have many applications, even at relatively low levels of genome coverage. However, the utility of shotgun sequencing data sets for specific goals may vary depending on the biological nature of the samples sequenced. We show that the ability to assemble mitogenomes from three avian samples of two different tissue types varies widely. In particular, data with coverage typical of microsatellite development efforts (∼1×) from DNA extracted from avian blood failed to cover even 50% of the mitogenome, relative to at least 500-fold coverage from muscle-derived data. Researchers should consider possible applications of their data and select the tissue source for their work accordingly. Practitioners analyzing low-coverage shotgun sequencing data (including for microsatellite locus development) should consider the potential benefits of mitogenome assembly, including internal barcode verification of species identity, mitochondrial primer development, and phylogenetics.},
}
@article {pmid24112561,
year = {2014},
author = {Pramual, P and Adler, PH},
title = {DNA barcoding of tropical black flies (Diptera: Simuliidae) of Thailand.},
journal = {Molecular ecology resources},
volume = {14},
number = {2},
pages = {262-271},
doi = {10.1111/1755-0998.12174},
pmid = {24112561},
issn = {1755-0998},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Entomology/*methods ; Genetic Variation ; Genotyping Techniques/*methods ; Insect Proteins/genetics ; Molecular Sequence Data ; Simuliidae/*classification/*genetics ; Thailand ; Tropical Climate ; },
abstract = {The ecological and medical importance of black flies drives the need for rapid and reliable identification of these minute, structurally uniform insects. We assessed the efficiency of DNA barcoding for species identification of tropical black flies. A total of 351 cytochrome c oxidase subunit 1 sequences were obtained from 41 species in six subgenera of the genus Simulium in Thailand. Despite high intraspecific genetic divergence (mean = 2.00%, maximum = 9.27%), DNA barcodes provided 96% correct identification. Barcodes also differentiated cytoforms of selected species complexes, albeit with varying levels of success. Perfect differentiation was achieved for two cytoforms of Simulium feuerborni, and 91% correct identification was obtained for the Simulium angulistylum complex. Low success (33%), however, was obtained for the Simulium siamense complex. The differential efficiency of DNA barcodes to discriminate cytoforms was attributed to different levels of genetic structure and demographic histories of the taxa. DNA barcode trees were largely congruent with phylogenies based on previous molecular, chromosomal and morphological analyses, but revealed inconsistencies that will require further evaluation.},
}
@article {pmid24112538,
year = {2014},
author = {Porco, D and Skarżyński, D and Decaëns, T and Hebert, PD and Deharveng, L},
title = {Barcoding the Collembola of Churchill: a molecular taxonomic reassessment of species diversity in a sub-Arctic area.},
journal = {Molecular ecology resources},
volume = {14},
number = {2},
pages = {249-261},
doi = {10.1111/1755-0998.12172},
pmid = {24112538},
issn = {1755-0998},
mesh = {Animals ; Arctic Regions ; Arthropods/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; Entomology/*methods ; Genetic Variation ; Genotyping Techniques/*methods ; Manitoba ; Molecular Sequence Data ; },
abstract = {Although their functional importance in ecosystems is increasingly recognized, soil-dwelling micro-arthropods are usually poorly known in comparison with their above-ground counterparts. Collembola constitute a significant and species-rich component of the soil biodiversity, but it remains a woefully understudied group because of the taxonomic impediment. The ever-increasing use of molecular taxonomic tools, such as DNA barcoding, provides a possible solution. Here, we test the use of this approach through a diversity survey of Collembola from the vicinity of Churchill, Manitoba, Canada, and compare the results with previous surveys in the same area and in other sub-Arctic regions. The systematic barcoding campaign at Churchill revealed a diverse collembolan fauna consisting of 97 species-level MOTUs in six types of habitats. If all these MOTUs are confirmed as species, this richness would be far higher than prior records for Arctic Canada and could lead to reconsider the actual diversity of the group in Arctic environments.},
}
@article {pmid24112409,
year = {2013},
author = {Kõljalg, U and Nilsson, RH and Abarenkov, K and Tedersoo, L and Taylor, AF and Bahram, M and Bates, ST and Bruns, TD and Bengtsson-Palme, J and Callaghan, TM and Douglas, B and Drenkhan, T and Eberhardt, U and Dueñas, M and Grebenc, T and Griffith, GW and Hartmann, M and Kirk, PM and Kohout, P and Larsson, E and Lindahl, BD and Lücking, R and Martín, MP and Matheny, PB and Nguyen, NH and Niskanen, T and Oja, J and Peay, KG and Peintner, U and Peterson, M and Põldmaa, K and Saag, L and Saar, I and Schüßler, A and Scott, JA and Senés, C and Smith, ME and Suija, A and Taylor, DL and Telleria, MT and Weiss, M and Larsson, KH},
title = {Towards a unified paradigm for sequence-based identification of fungi.},
journal = {Molecular ecology},
volume = {22},
number = {21},
pages = {5271-5277},
doi = {10.1111/mec.12481},
pmid = {24112409},
issn = {1365-294X},
mesh = {DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; *Databases, Nucleic Acid ; Fungi/*classification/genetics ; Internet ; *Phylogeny ; },
abstract = {The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.},
}
@article {pmid24112240,
year = {2014},
author = {Silva, FL and Wiedenbrug, S},
title = {Integrating DNA barcodes and morphology for species delimitation in the Corynoneura group (Diptera: Chironomidae: Orthocladiinae).},
journal = {Bulletin of entomological research},
volume = {104},
number = {1},
pages = {65-78},
doi = {10.1017/S0007485313000515},
pmid = {24112240},
issn = {1475-2670},
mesh = {Animals ; Brazil ; Chironomidae/*anatomy &amp; histology/classification/*genetics ; Classification/*methods ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {In this study, we use DNA barcodes for species delimitation to solve taxonomic conflicts in 86 specimens of 14 species belonging to the Corynoneura group (Diptera: Chironomidae: Orthocladiinae), from the Atlantic Forest, Brazil. Molecular analysis of cytochrome c-oxidase subunit I (COI) gene sequences supported 14 cohesive species groups, of which two similar groups were subsequently associated with morphological variation at the pupal stage. Eleven species previously described based on morphological criteria were linked to DNA markers. Furthermore, there is the possibility that there may be cryptic species within the Corynoneura group, since one group of species presented internal grouping, although no morphological divergence was observed. Our results support DNA-barcoding as an excellent tool for species delimitation in groups where taxonomy by means of morphology is difficult or even impossible.},
}
@article {pmid24111803,
year = {2014},
author = {Meiser, A and Bálint, M and Schmitt, I},
title = {Meta-analysis of deep-sequenced fungal communities indicates limited taxon sharing between studies and the presence of biogeographic patterns.},
journal = {The New phytologist},
volume = {201},
number = {2},
pages = {623-635},
doi = {10.1111/nph.12532},
pmid = {24111803},
issn = {1469-8137},
mesh = {*Biodiversity ; DNA, Fungal/*chemistry ; DNA, Intergenic/chemistry ; Fungi/*classification/physiology ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Soil Microbiology ; },
abstract = {High-throughput amplicon sequencing gives new insights into fungal community ecology. Massively generated molecular data lead to the discovery of vast fungal diversity. However, it is unclear to what extent operational taxonomic units (OTUs) overlap among independent studies, because no comparative studies exist. We compared fungal diversity based on the internal transcribed spacer (ITS1) region among 10 published studies. Starting from the raw 454 pyrosequencing data, we used a uniform pipeline to prune the reads. We investigated fungal richness and taxonomic composition among phyllosphere and soil fungal communities, as well as biogeographic signals in the data. We did not find globally distributed OTUs, even when comparing fungal communities from similar habitats (phyllosphere or soil). This suggests that high local fungal diversity scales up to high global diversity. The most OTU-rich classes in the phyllosphere were Dothideomycetes (21%) and Sordariomycetes (14%), and in the soil were Sordariomycetes (13%) and Agaricomycetes (12%). The richness estimates suggest the presence of undiscovered fungal diversity even in deeply sequenced study systems. The small number of OTUs shared among studies indicates that globally distributed taxa and habitat generalists may be rare. Latitudinal diversity decline and distance decay relationships suggest the presence of biogeographic patterns similar to those in plants and animals.},
}
@article {pmid24111423,
year = {2013},
author = {Schreier, G and Schwarz, M and Modre-Osprian, R and Kastner, P and Scherr, D and Fruhwald, F},
title = {Design and evaluation of a multimodal mHealth based medication management system for patient self administration.},
journal = {Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference},
volume = {2013},
number = {},
pages = {7270-7273},
doi = {10.1109/EMBC.2013.6611236},
pmid = {24111423},
issn = {2694-0604},
mesh = {Adult ; Aged ; *Disease Management ; Equipment Design ; Female ; Humans ; Medication Adherence ; *Medication Systems ; Middle Aged ; Pharmaceutical Preparations ; Radio Waves ; Reminder Systems ; Self Administration ; Self Care ; Telemedicine/*instrumentation/methods ; Young Adult ; },
abstract = {The intake of prescribed medication presents a challenge, in particular for elderly people and in cases where a variety of medications have to be taken in accordance to a complex schedule. To support patients with this task, an mHealth-concept was developed and evaluated in the course of a clinical trial. The system used a multimodal user interface concept, i.e. both RFID tags and barcodes to identify and document the intake of medications. Results of the clinical study with 20 patients indicate that the multimodal mHealth concept utilizing barcode and RFID tags enabled easy-to-use medication management. Although further clinical evaluation is needed to assess whether such a tool can also enhance adherence, the system shows the potential for targeting the problem of medication management with mHealth methods.},
}
@article {pmid24104541,
year = {2013},
author = {Mutanen, M and Kaila, L and Tabell, J},
title = {Wide-ranging barcoding aids discovery of one-third increase of species richness in presumably well-investigated moths.},
journal = {Scientific reports},
volume = {3},
number = {},
pages = {2901},
pmid = {24104541},
issn = {2045-2322},
mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Moths/*classification/*genetics ; Phylogeny ; },
abstract = {Rapid development of broad regional and international DNA barcode libraries have brought new insights into the species diversity of many areas and groups. Many new species, even within well-investigated species groups, have been discovered based initially on differences in DNA barcodes. We barcoded 437 collection specimens belonging to 40 pre-identified Palearctic species of the Elachista bifasciella group of moths (Lepidoptera, Elachistidae). Although the study group has been a subject of several careful morphological taxonomic examinations, an unexpectedly high number of previously undetected putative species is revealed, resulting in a 34% rise in species number in the study area. The validity of putative new species was subsequently supported with diagnostic morphological traits. We show that DNA barcodes provide a powerful method of detecting potential new species even in taxonomic groups and geographic areas that have previously been under considerable morphological taxonomic scrutiny.},
}
@article {pmid24103324,
year = {2014},
author = {Yang, F and Shi, ZY and Bai, SL and Ward, RD and Zhang, AB},
title = {Comparative studies on species identification of Noctuoidea moths in two nature reserve conservation zones (Beijing, China) using DNA barcodes and thin-film biosensor chips.},
journal = {Molecular ecology resources},
volume = {14},
number = {1},
pages = {50-59},
doi = {10.1111/1755-0998.12165},
pmid = {24103324},
issn = {1755-0998},
mesh = {Animals ; Biosensing Techniques/*methods ; China ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/genetics ; Entomology/*methods ; Insect Proteins/genetics ; Lepidoptera/*classification/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Rapid and accurate identification of species is required for the biological control of pest Noctuoidea moths. DNA barcodes and thin-film biosensor chips are two molecular approaches that have gained wide attention. Here, we compare these two methods for the identification of a limited number of Noctuoidea moth species. Based on the commonly used mitochondrial gene cytochrome c oxidase I (the standard DNA barcode for animal species), 14 probes were designed and synthesized for 14 species shared by two national nature reserves in Beijing and Hebei, China. Probes ranged in length from 18 to 27 bp and were designed as mismatch probes to guarantee that there were at least three base differences between the probe and nontarget sequences. The results on the chip could be detected by the naked eye without needing special equipment. No cross-hybridizations were detected although we tested all probes on the 14 target and 24 nontarget Noctuoidea species. The neighbour-joining tree of the 38 species based on COI sequences gave 38 highly supported independent groups. Both DNA barcoding and thin-film biosensor chips, based on the COI gene, are able to accurately identify and discriminate the 14 targeted moth species in this study. Because of its speed, high accuracy and low cost, the thin-film biosensor chip is a very practical means of species identification. Now, a more comprehensive chip will be developed for the identification of additional Noctuoidea moths for pest control and ecological protection.},
}
@article {pmid24102670,
year = {2014},
author = {Gariepy, TD and Haye, T and Zhang, J},
title = {A molecular diagnostic tool for the preliminary assessment of host-parasitoid associations in biological control programmes for a new invasive pest.},
journal = {Molecular ecology},
volume = {23},
number = {15},
pages = {3912-3924},
doi = {10.1111/mec.12515},
pmid = {24102670},
issn = {1365-294X},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA Primers ; Hemiptera/genetics/*parasitology ; *Host-Parasite Interactions ; Hymenoptera/classification/genetics/*physiology ; Molecular Sequence Data ; Ovum/parasitology ; Pest Control, Biological ; Sensitivity and Specificity ; Species Specificity ; },
abstract = {Evaluation of host-parasitoid associations can be tenuous using conventional methods. Molecular techniques are well placed to identify trophic links and resolve host-parasitoid associations. Establishment of the highly invasive brown marmorated stink bug, Halyomorpha halys (Hemiptera: Pentatomidae), outside Asia has prompted interest in the use of egg parasitoids (Hymenoptera: Scelionidae) as biological control agents. However, little is known regarding their host ranges. To address this, a DNA barcoding approach was taken wherein general PCR primers for Scelionidae and Pentatomidae were developed to amplify and sequence >500-bp products within the DNA barcoding region of the cytochrome oxidase I (COI) gene that would permit the identification of key players in this association. Amplification of DNA from Pentatomidae and Scelionidae was consistent across a broad range of taxa within these families, and permitted the detection of Scelionidae eggs within H. halys 1 h following oviposition. In laboratory assays, amplification and sequencing of DNA from empty, parasitized eggs was successful for both host (100% success) and parasitoid (50% success). When applied to field-collected, empty egg masses, the primers permitted host identification in 50-100% of the eggs analysed, and yielded species-level identifications. Parasitoid identification success ranged from 33 to 67% among field-collected eggs, with genus-level identification for most specimens. The inability to obtain species-level identities for these individuals is due to the lack of coverage of this taxonomic group in public DNA sequence databases; this situation is likely to improve as more species are sequenced and recorded in these databases. These primers were able to detect and identify both pentatomid host and scelionid parasitoid in a hyperparasitized egg mass, thereby clarifying trophic links otherwise unresolved by conventional methodology.},
}
@article {pmid24101987,
year = {2013},
author = {Wang, Q and Jiang, ZF and Wang, NX and Niu, LM and Li, Z and Huang, DW},
title = {Host sex-specific parasites in a functionally dioecious fig: a preference way of adaptation to their hosts.},
journal = {Ecology and evolution},
volume = {3},
number = {9},
pages = {2976-2984},
pmid = {24101987},
issn = {2045-7758},
abstract = {Host-parasites interaction is a common phenomenon in nature. Diffusive coevolution might maintain stable cooperation in a fig-fig wasps system, in which the exploiter might diversify their genotype, phenotype, or behavior as a result of competition with pollinator, whereas the figs change flower syconia, fruits thickness, and syconia structure. In functionally dioecious Ficus auriculata, male figs and female figs contain two types of florets on separate plant, and share high similarities in outside morphology. Apocryptophagus (Sycophaginae, Chalcidoidea, Hymenoptera) is one of few groups of nonpollinating fig wasps that can reproduce within both male and female figs. On the basis of the morphology and DNA barcoding, evidence from partial sequences of mitochondrial cytochrome c oxidase I and nuclear internal transcribed spacer 2, we found that there are two nonsibling Apocryptophagus species living on male and female F. auriculata figs, respectively. We estimated that these two species diverged about 19.2 million years ago. Our study suggests that the host shift from Ficus variegate or Ficus prostrata fig species to male figs is a preference way for Apocryptophagus wasps to adapt to the separation of sexual function in diecious figs. Furthermore, to escape the disadvantage or sanction impact of the host, the exploiter Apocryptophagus wasps can preferably adapt to exploiting each sex of the figs, by changing their oviposition, niche shift, and habitat.},
}
@article {pmid24096738,
year = {2013},
author = {Ibanez, S and Manneville, O and Miquel, C and Taberlet, P and Valentini, A and Aubert, S and Coissac, E and Colace, MP and Duparc, Q and Lavorel, S and Moretti, M},
title = {Plant functional traits reveal the relative contribution of habitat and food preferences to the diet of grasshoppers.},
journal = {Oecologia},
volume = {173},
number = {4},
pages = {1459-1470},
pmid = {24096738},
issn = {1432-1939},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Diet ; *Ecosystem ; Female ; *Food Preferences ; *Grasshoppers ; *Herbivory ; Male ; Plants/*classification ; },
abstract = {Food preferences and food availability are two major determinants of the diet of generalist herbivores and of their spatial distribution. How do these factors interact and eventually lead to diet differentiation in co-occurring herbivores? We quantified the diet of four grasshopper species co-occurring in subalpine grasslands using DNA barcoding of the plants contained in the faeces of individuals sampled in the field. The food preferences of each grasshopper species were assessed by a choice (cafeteria) experiment from among 24 plant species common in five grassland plots, in which the four grasshoppers were collected, while the habitat was described by the relative abundance of plant species in the grassland plots. Plant species were characterised by their leaf economics spectrum (LES), quantifying their nutrient vs. structural tissue content. The grasshoppers' diet, described by the mean LES of the plants eaten, could be explained by their plant preferences but not by the available plants in their habitat. The diet differed significantly across four grasshopper species pairs out of six, which validates food preferences assessed in standardised conditions as indicators for diet partitioning in nature. In contrast, variation of the functional diversity (FD) for LES in the diet was mostly correlated to the FD of the available plants in the habitat, suggesting that diet mixing depends on the environment and is not an intrinsic property of the grasshopper species. This study sheds light on the mechanisms determining the feeding niche of herbivores, showing that food preferences influence niche position whereas habitat diversity affects niche breadth.},
}
@article {pmid24096607,
year = {2013},
author = {Shylla, JA and Ghatani, S and Tandon, V},
title = {Utility of divergent domains of 28S ribosomal RNA in species discrimination of paramphistomes (Trematoda: Digenea: Paramphistomoidea).},
journal = {Parasitology research},
volume = {112},
number = {12},
pages = {4239-4253},
pmid = {24096607},
issn = {1432-1955},
mesh = {Animals ; Base Sequence ; DNA, Helminth/genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/*genetics ; Sequence Analysis, DNA ; Species Specificity ; Trematoda/*classification/genetics ; },
abstract = {Among the digenetic trematodes, paramphistomes are known to be the causative agent of "amphistomiasis" or the stomach fluke disease of domestic and wild animals, mainly ruminants. The use of 28S (divergent domains) and 18S rRNA for phylogenetic inference is significantly warranted for these flukes since it is as yet limited to merely the exploration of the second internal transcribed spacer (ITS2) region. The present study intended to explore the divergent domains (D1-D3) of 28S rRNA and simultaneously equate the phylogenetic information with 18S rRNA in paramphistomes. Divergence of the 28S rRNA domains was evident amongst the divergent (D) domains, where D1 domain emerged as the most variable and D2, the most robust domain, since the latter could provide a higher resolution of the species. D2 was the only domain that comprised compensatory mutations in the helices of its structural constraints; this domain is thus well suited for species distinction and may be considered a potential DNA barcode complementary to mitochondrial DNA. 28S (D1 + D2 + D3) rRNA provided a significant resolution of the taxa corroborating with the taxonomy of these flukes and thus proved to be more robust as a phylogenetic marker for lower levels than 18S rRNA. Phylogenetic inferences of paramphitomes are still scarcely explored; additional data from other taxa belonging to this family may estimate better the biodiversity of these flukes.},
}
@article {pmid24089557,
year = {2013},
author = {Webster, B and Ott, M and Greene, WC},
title = {Evasion of superinfection exclusion and elimination of primary viral RNA by an adapted strain of hepatitis C virus.},
journal = {Journal of virology},
volume = {87},
number = {24},
pages = {13354-13369},
pmid = {24089557},
issn = {1098-5514},
support = {P30 AI027763/AI/NIAID NIH HHS/United States ; R56 AI085056/AI/NIAID NIH HHS/United States ; T32 AI060537/AI/NIAID NIH HHS/United States ; T32 A1060537-05//PHS HHS/United States ; },
mesh = {Cell Line ; Hepacivirus/classification/genetics/*physiology ; Hepatitis C/*virology ; Humans ; Mutation ; RNA, Viral/genetics/*metabolism ; Superinfection/*virology ; Viral Nonstructural Proteins/genetics/metabolism ; *Virus Replication ; },
abstract = {Cells that are productively infected by hepatitis C virus (HCV) are refractory to a second infection by HCV via a block in viral replication known as superinfection exclusion. The block occurs at a postentry step and likely involves translation or replication of the secondary viral RNA, but the mechanism is largely unknown. To characterize HCV superinfection exclusion, we selected for an HCV variant that could overcome the block. We produced a high-titer HC-J6/JFH1 (Jc1) viral genome with a fluorescent reporter inserted between NS5A and NS5B and used it to infect Huh7.5 cells containing a Jc1 replicon. With multiple passages of these infected cells, we isolated an HCV variant that can superinfect cells at high levels. Notably, the superinfectious virus rapidly cleared the primary replicon from superinfected cells. Viral competition experiments, using a novel strategy of sequence-barcoding viral strains, as well as superinfection of replicon cells demonstrated that mutations in E1, p7, NS5A, and the poly(U/UC) tract of the 3' untranslated region were important for superinfection. Furthermore, these mutations dramatically increased the infectivity of the virus in naive cells. Interestingly, viruses with a shorter poly(U/UC) and an NS5A domain II mutation were most effective in overcoming the postentry block. Neither of these changes affected viral RNA translation, indicating that the major barrier to postentry exclusion occurs at viral RNA replication. The evolution of the ability to superinfect after less than a month in culture and the concomitant exclusion of the primary replicon suggest that superinfection exclusion dramatically affects viral fitness and dynamics in vivo.},
}
@article {pmid24089097,
year = {2013},
author = {Sun, XQ and Bai, MM and Yao, H and Guo, JL and Li, MM and Hang, YY},
title = {DNA barcoding of populations of Fallopia multiflora, an indigenous herb in China.},
journal = {Genetics and molecular research : GMR},
volume = {12},
number = {3},
pages = {4078-4089},
doi = {10.4238/2013.September.27.9},
pmid = {24089097},
issn = {1676-5680},
mesh = {China ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; *Genes, Plant ; Genetic Loci ; Phylogeography ; Plants, Medicinal/*genetics ; Polygonaceae/classification/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Fallopia multiflora, locally known as Heshouwu, is one of the most important and widely used Chinese medicinal herbs. However, there is still considerable confusion concerning its different provenances. DNA barcoding is a recent aid to taxonomic identification and uses a short standardized DNA region to discriminate plant species. We assessed the applicability of 4 candidate DNA barcodes (matK, rbcL, psbA-trnH, and ITS2) to identify populations of F. multiflora. To our knowledge, this is the first attempt involving the plant kingdom to apply DNA barcoding at a level lower than species. Four DNA loci (matK, rbcL, psbA-trnH, and ITS2) of 105 samples, including the wild F. multiflora distributed in 17 provinces of China and 4 cultivated F. multiflora lines, were amplified by PCR and sequenced. The 4 loci were evaluated by PCR amplification for sequence quality, extent of genetic divergence, DNA barcoding gap, and the ability to discriminate between populations by BLAST1 and Nearest Distance. We found that psbA-trnH was the best barcode, with significant inter-population variability and best potential for identifying F. multiflora. The combination of loci gave better performance for distinguishing populations than a single locus. We recommend using matK + rbcL + psbA-trnH + ITS2 or psbA-trnH alone for this species. This research demonstrates the utility of DNA barcoding for geoherbalism identifications.},
}
@article {pmid24086124,
year = {2013},
author = {Salles, A and Billaudeau, C and Sergé, A and Bernard, AM and Phélipot, MC and Bertaux, N and Fallet, M and Grenot, P and Marguet, D and He, HT and Hamon, Y},
title = {Barcoding T cell calcium response diversity with methods for automated and accurate analysis of cell signals (MAAACS).},
journal = {PLoS computational biology},
volume = {9},
number = {9},
pages = {e1003245},
pmid = {24086124},
issn = {1553-7358},
mesh = {Animals ; COS Cells ; Calcium/*metabolism ; Chlorocebus aethiops ; Humans ; Molecular Probes ; *Signal Transduction ; *Software ; T-Lymphocytes/*metabolism ; },
abstract = {We introduce a series of experimental procedures enabling sensitive calcium monitoring in T cell populations by confocal video-microscopy. Tracking and post-acquisition analysis was performed using Methods for Automated and Accurate Analysis of Cell Signals (MAAACS), a fully customized program that associates a high throughput tracking algorithm, an intuitive reconnection routine and a statistical platform to provide, at a glance, the calcium barcode of a population of individual T-cells. Combined with a sensitive calcium probe, this method allowed us to unravel the heterogeneity in shape and intensity of the calcium response in T cell populations and especially in naive T cells, which display intracellular calcium oscillations upon stimulation by antigen presenting cells.},
}
@article {pmid24083972,
year = {2015},
author = {Kwak, HS and Choi, EH and Jang, KH and Ryu, SH and Kim, YS and Hwang, UW},
title = {Complete mitochondrial genome of Dendronephthya putteri (Octocorallia, Alcyonacea) and useful candidate for developing DNA barcode markers of Dendronephthya species.},
journal = {Mitochondrial DNA},
volume = {26},
number = {4},
pages = {627-628},
doi = {10.3109/19401736.2013.834435},
pmid = {24083972},
issn = {1940-1744},
mesh = {Animals ; Anthozoa/classification/*genetics ; Base Sequence ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*chemistry ; Endangered Species ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The mitochondrial genome of Dendronephthya putteri (Octocorallia, Alcyonacea) which is an endangered species was completely sequenced. It is 18,853 bp in length and identical to those of Dendronephthya species in its gene arrangement and genome organization. Nucleotide sequence comparison of the mitochondrial genomes of the two D. putteri individuals obtained from this study and the previously reported one (GenBank accession number JQ290079) showed that they are identical perfectly. We found useful candidate for DNA barcode markers for D. putteri species identification.},
}
@article {pmid24073641,
year = {2013},
author = {Jörger, KM and Schrödl, M},
title = {How to describe a cryptic species? Practical challenges of molecular taxonomy.},
journal = {Frontiers in zoology},
volume = {10},
number = {1},
pages = {59},
pmid = {24073641},
issn = {1742-9994},
abstract = {BACKGROUND: Molecular methods of species delineation are rapidly developing and widely considered as fast and efficient means to discover species and face the 'taxonomic impediment' in times of biodiversity crisis. So far, however, this form of DNA taxonomy frequently remains incomplete, lacking the final step of formal species description, thus enhancing rather than reducing impediments in taxonomy. DNA sequence information contributes valuable diagnostic characters and -at least for cryptic species - could even serve as the backbone of a taxonomic description. To this end solutions for a number of practical problems must be found, including a way in which molecular data can be presented to fulfill the formal requirements every description must meet. Multi-gene barcoding and a combined molecular species delineation approach recently revealed a radiation of at least 12 more or less cryptic species in the marine meiofaunal slug genus Pontohedyle (Acochlidia, Heterobranchia). All identified candidate species are well delimited by a consensus across different methods based on mitochondrial and nuclear markers.<br><br>RESULTS: The detailed microanatomical redescription of Pontohedyle verrucosa provided in the present paper does not reveal reliable characters for diagnosing even the two major clades identified within the genus on molecular data. We thus characterize three previously valid Pontohedyle species based on four genetic markers (mitochondrial cytochrome c oxidase subunit I, 16S rRNA, nuclear 28S and 18S rRNA) and formally describe nine cryptic new species (P. kepii sp. nov., P. joni sp. nov., P. neridae sp. nov., P. liliae sp. nov., P. wiggi sp. nov., P. wenzli sp. nov., P. peteryalli sp. nov., P. martynovi sp. nov., P. yurihookeri sp. nov.) applying molecular taxonomy, based on diagnostic nucleotides in DNA sequences of the four markers. Due to the minute size of the animals, entire specimens were used for extraction, consequently the holotype is a voucher of extracted DNA ('DNA-type'). We used the Character Attribute Organization System (CAOS) to determine diagnostic nucleotides, explore the dependence on input data and data processing, and aim for maximum traceability in our diagnoses for future research. Challenges, pitfalls and necessary considerations for applied DNA taxonomy are critically evaluated.<br><br>CONCLUSIONS: To describe cryptic species traditional lines of evidence in taxonomy need to be modified. DNA sequence information, for example, could even serve as the backbone of a taxonomic description. The present contribution demonstrates that few adaptations are needed to integrate into traditional taxonomy novel diagnoses based on molecular data. The taxonomic community is encouraged to join the discussion and develop a quality standard for molecular taxonomy, ideally in the form of an automated final step in molecular species delineation procedures.},
}
@article {pmid24072655,
year = {2013},
author = {Awan, AR and Umar, E and Zia ul Haq, M and Firyal, S},
title = {Molecular classification of Pakistani collared dove through DNA barcoding.},
journal = {Molecular biology reports},
volume = {40},
number = {11},
pages = {6329-6331},
pmid = {24072655},
issn = {1573-4978},
mesh = {Animals ; Columbidae/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial ; Molecular Sequence Data ; Phylogeny ; },
abstract = {Pakistan is bestowed by a diversified array of wild bird species including collared doves of which the taxonomy has been least studied and reported. DNA barcoding is a geno-taxonomic tool that has been used for characterization of bird species using mitochondrial cytochrome c oxidase I gene (COI). This study aimed to identify taxonomic order of Pakistani collared dove using DNA barcoding. Purposely herein, we present a phylogenetic analysis of Pakistani collared dove based on 650 base pairs of COI gene sequences. Analysis of phylogenetic tree revealed that Pakistani collared dove shared a common clade with Eurasian collared dove (Streptopelia decaocto) and African collared dove (Streptopelia roseogrisea) which indicated a super-species group in Streptopelia genus. This is the first report of molecular classification of Pakistani collared dove using DNA barcoding.},
}
@article {pmid24069303,
year = {2013},
author = {Egge, E and Bittner, L and Andersen, T and Audic, S and de Vargas, C and Edvardsen, B},
title = {454 pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: a test for marine haptophytes.},
journal = {PloS one},
volume = {8},
number = {9},
pages = {e74371},
pmid = {24069303},
issn = {1932-6203},
mesh = {*Biodiversity ; DNA, Complementary ; DNA, Ribosomal ; Haptophyta/*classification/*genetics ; *High-Throughput Nucleotide Sequencing/methods/standards ; *Metagenome ; Phylogeny ; },
abstract = {Next generation sequencing of ribosomal DNA is increasingly used to assess the diversity and structure of microbial communities. Here we test the ability of 454 pyrosequencing to detect the number of species present, and assess the relative abundance in terms of cell numbers and biomass of protists in the phylum Haptophyta. We used a mock community consisting of equal number of cells of 11 haptophyte species and compared targeting DNA and RNA/cDNA, and two different V4 SSU rDNA haptophyte-biased primer pairs. Further, we tested four different bioinformatic filtering methods to reduce errors in the resulting sequence dataset. With sequencing depth of 11000-20000 reads and targeting cDNA with Haptophyta specific primers Hap454 we detected all 11 species. A rarefaction analysis of expected number of species recovered as a function of sampling depth suggested that minimum 1400 reads were required here to recover all species in the mock community. Relative read abundance did not correlate to relative cell numbers. Although the species represented with the largest biomass was also proportionally most abundant among the reads, there was generally a weak correlation between proportional read abundance and proportional biomass of the different species, both with DNA and cDNA as template. The 454 sequencing generated considerable spurious diversity, and more with cDNA than DNA as template. With initial filtering based only on match with barcode and primer we observed 100-fold more operational taxonomic units (OTUs) at 99% similarity than the number of species present in the mock community. Filtering based on quality scores, or denoising with PyroNoise resulted in ten times more OTU99% than the number of species. Denoising with AmpliconNoise reduced the number of OTU99% to match the number of species present in the mock community. Based on our analyses, we propose a strategy to more accurately depict haptophyte diversity using 454 pyrosequencing.},
}
@article {pmid24069192,
year = {2013},
author = {Hawlitschek, O and Nagy, ZT and Berger, J and Glaw, F},
title = {Reliable DNA barcoding performance proved for species and island populations of comoran squamate reptiles.},
journal = {PloS one},
volume = {8},
number = {9},
pages = {e73368},
pmid = {24069192},
issn = {1932-6203},
mesh = {Animals ; *Bayes Theorem ; Comoros ; DNA Barcoding, Taxonomic/*methods ; Islands ; Reptiles/classification/*genetics ; },
abstract = {In the past decade, DNA barcoding became increasingly common as a method for species identification in biodiversity inventories and related studies. However, mainly due to technical obstacles, squamate reptiles have been the target of few barcoding studies. In this article, we present the results of a DNA barcoding study of squamates of the Comoros archipelago, a poorly studied group of oceanic islands close to and mostly colonized from Madagascar. The barcoding dataset presented here includes 27 of the 29 currently recognized squamate species of the Comoros, including 17 of the 18 endemic species. Some species considered endemic to the Comoros according to current taxonomy were found to cluster with non-Comoran lineages, probably due to poorly resolved taxonomy. All other species for which more than one barcode was obtained corresponded to distinct clusters useful for species identification by barcoding. In most species, even island populations could be distinguished using barcoding. Two cryptic species were identified using the DNA barcoding approach. The obtained barcoding topology, a Bayesian tree based on COI sequences of 5 genera, was compared with available multigene topologies, and in 3 cases, major incongruences between the two topologies became evident. Three of the multigene studies were initiated after initial screening of a preliminary version of the barcoding dataset presented here. We conclude that in the case of the squamates of the Comoros Islands, DNA barcoding has proven a very useful and efficient way of detecting isolated populations and promising starting points for subsequent research.},
}
@article {pmid24056366,
year = {2013},
author = {Olms, C and Klinke, T and Pirek, P and Hannak, WB},
title = {Randomized multi-centre study on the effect of training on tooth shade matching.},
journal = {Journal of dentistry},
volume = {41},
number = {12},
pages = {1259-1263},
doi = {10.1016/j.jdent.2013.09.002},
pmid = {24056366},
issn = {1879-176X},
mesh = {Adult ; Color Perception ; Dental Prosthesis Design/*instrumentation ; Double-Blind Method ; Education, Dental ; Female ; Humans ; Male ; Prosthesis Coloring/*instrumentation ; Prosthodontics/*education ; *Teaching Materials ; Young Adult ; },
abstract = {OBJECTIVES: The aim of this study was to find out whether Toothguide Trainer, TT, and Toothguide Training Box, TTB, show any training effects, independent of the shade guide chosen.<br><br>METHODS: Students from four dental schools (N=78) were included in this study. The participants were randomized into a study, 42 students (age range: 19-27 years; 69% female, 31% male) and a control group of 36 students (age range: 19-30 years; 57% female, 43% male). The study group started with a double blind introduction test, followed by the TT and TTB training, finishing with the final test. The control group only passed the introduction and - after a break - the final test. Eight randomly chosen samples, seven of the Vita classical and one of the 3D-Master colour scale, were marked by barcodes. Colour matching was arranged by the Vita classical scale.<br><br>RESULTS: The results of the pre- and final tests of both groups were combined. For every sample, the value &#x394;E was determined. The summation of all eight samples from the introduction and final tests offered a summarized &#x394;E value. The differences between introduction and final tests revealed the individual learning success. 47.6% of the study group showed statistically significant better results than the control group, 33% (p=0.031).<br><br>CONCLUSION: TT and TTB show a positive effect of training on tooth shade matching independent of the colour scale used.<br><br>CLINICAL SIGNIFICANCE: Visual shade taking is the most frequent clinical method for shade determination. To increase better results in visual colour matching, TT and TTB training is used. This is the first study examining the training effect of TT and TTB using Vita classical scale.},
}
@article {pmid24054573,
year = {2013},
author = {Loo, J and Lau, PM and Ho, HP and Kong, SK},
title = {An aptamer-based bio-barcode assay with isothermal recombinase polymerase amplification for cytochrome-c detection and anti-cancer drug screening.},
journal = {Talanta},
volume = {115},
number = {},
pages = {159-165},
doi = {10.1016/j.talanta.2013.04.051},
pmid = {24054573},
issn = {1873-3573},
mesh = {Antibodies/chemistry ; Antigens, Neoplasm/chemistry ; Antineoplastic Agents/*pharmacology ; Aptamers, Nucleotide/*chemistry ; Cell Death/drug effects ; Cell Line, Tumor ; Cytochromes c/*analysis/genetics ; Drug Screening Assays, Antitumor/*methods ; Fluorescent Dyes ; Gold/chemistry ; Humans ; Limit of Detection ; Magnets ; Metal Nanoparticles/chemistry ; Molecular Typing/*methods ; Nucleic Acid Amplification Techniques ; Recombinases/*chemistry/genetics ; },
abstract = {Based on a recently reported ultra-sensitive bio-barcode (BBC) assay, we have developed an aptamer-based bio-barcode (ABC) alternative to detect a cell death marker cytochrome-c (Cyto-c) and its subsequent application to screen anti-cancer drugs. Aptamer is a short single-stranded DNA selected from a synthetic DNA library by virtue of its high binding affinity and specificity to its target based on its unique 3D structure from the nucleotide sequence after folding. In the BBC assay, an antigen (Ag) in analytes is captured by a micro-magnetic particle (MMP) coated with capturing antibodies (Abs). Gold nanoparticles (NPs) with another recognition Ab against the same target and hundreds of identical DNA molecules of known sequence are subsequently added to allow the formation of sandwich structures ([MMP-Ab1]-Ag-[Ab2-NP-DNA]). After isolating the sandwiches by a magnetic field, the DNAs hybridized to their complementary DNAs covalently bound on the NPs are released from the sandwiches after heating. Acting as an Ag identification tag, these bio-barcode DNAs with known DNA sequence are then amplified by polymerase chain reaction (PCR) and detected by fluorescence. In our ABC assay, we employed a Cyto-c-specific aptamer to substitute both the recognition Ab and barcode DNAs on the NPs in the BBC assay; and a novel isothermal recombinase polymerase amplification for the time-consuming PCR. The detection limit of our ABC assay for the Cyto-c was found to be 10 ng/mL and this new assay can be completed within 3h. Several potential anti-cancer drugs have been tested in vitro for their efficacy to kill liver cancer with or without multi-drug resistance.},
}
@article {pmid24047183,
year = {2015},
author = {Viswambharan, D and Pavan-Kumar, A and Singh, DP and Jaiswar, AK and Chakraborty, SK and Nair, JR and Lakra, WS},
title = {DNA barcoding of gobiid fishes (Perciformes, Gobioidei).},
journal = {Mitochondrial DNA},
volume = {26},
number = {1},
pages = {15-19},
doi = {10.3109/19401736.2013.834438},
pmid = {24047183},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; *DNA Barcoding, Taxonomic ; Fishes/*classification/*genetics ; *Genes, Mitochondrial ; Genetic Variation ; Phylogeny ; },
abstract = {Gobiids constitute a major proportion of fish population in both tropical and temperate freshwater as well as marine ecosystem. Due to their small size, cryptic ecology and ambiguous morphological characters, gobiids diversity was not documented completely. In this study, DNA barcodes were generated for 11 species of gobiids, collected from the Ashtamudi Lake, India. The mitochondrial COI gene was amplified using universal primers and the resulted 650 bp amplicon was sequenced. The COI barcodes clearly distinguished all the species with high inter-specific genetic distance values than intra-specific values based on K2P (Kimura 2 Parameter) model. The average genetic distance (K2P model) within species, genus and family was 1.2%, 22.2% and 25.3%, respectively. In addition to barcode-based species identification system, Nucleotide Diagnostic (ND) characters specific for species were identified. The Neighbor-Joining tree revealed distinct clusters shared by the species of same genera.},
}
@article {pmid24047160,
year = {2015},
author = {Mohanty, M and Jayasankar, P and Sahoo, L and Das, P},
title = {A comparative study of COI and 16 S rRNA genes for DNA barcoding of cultivable carps in India.},
journal = {Mitochondrial DNA},
volume = {26},
number = {1},
pages = {79-87},
doi = {10.3109/19401736.2013.823172},
pmid = {24047160},
issn = {1940-1744},
mesh = {Animals ; Carps/*classification/*genetics ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Geography ; Haplotypes ; India ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; },
abstract = {The 5' region of the mitochondrial DNA gene cytochrome c oxidase subunit I (COI) is the standard marker for DNA barcoding. However, 16 S rRNA has also been advocated for DNA barcoding in many animal species. Herein, we directly compare the usefulness of COI and 16 S rRNA in discriminating six cultivable carp species: Labeo rohita, Catla catla, Cirrhinus mrigala, Labeo fimbriatus, Labeo bata and Cirrhinus reba from India. Analysis of partial sequences of these two gene fragments from 171 individuals indicated close genetic relationship between Catla catla and Labeo rohita. The results of the present study indicated COI to be more useful than 16 S rRNA for DNA barcoding of Indian carps.},
}
@article {pmid24042060,
year = {2014},
author = {Morales-Serna, FN and Pinacho-Pinacho, CD and Gómez, S and de León, GP},
title = {Diversity of sea lice (Copepoda: Caligidae) parasitic on marine fishes with commercial and aquaculture importance in Chamela Bay, Pacific coast of Mexico by using morphology and DNA barcoding, with description of a new species of Caligus.},
journal = {Parasitology international},
volume = {63},
number = {1},
pages = {69-79},
doi = {10.1016/j.parint.2013.09.005},
pmid = {24042060},
issn = {1873-0329},
mesh = {Animals ; Copepoda/classification/*genetics ; Ectoparasitic Infestations/epidemiology/parasitology/*veterinary ; Fish Diseases/epidemiology/*parasitology ; Fishes ; Mexico ; Pacific Ocean/epidemiology ; Species Specificity ; },
abstract = {The occurrence of parasitic copepods of the family Caligidae on wild and cultured marine fishes from Chamela Bay, on the Pacific coast of Mexico, is reported. A total of 16 species of Caligus and 1 species of Lepeophtheirus were found on 19 wild fish species. The description of Caligus chamelensis n. sp. parasitizing Kyphosus elegans is presented. Among the species of Caligus reported here, Caligus serratus is the most common since it was found infecting 11 fish species. On cultured fish, Lutjanus gutattus and L. peru, only one species of Caligus, C. sclerotinosus was collected. DNA barcodes [mitochondrial cytochrome c oxidase subunit I (COI) gene sequences] were obtained for the majority of the sea lice species herein reported. The molecular analyses support the recognition of the new species and suggest that neither Caligus nor Lepeophtheirus are monophyletic. COI is shown to be a good candidate for parasitic copepod species identification, although a more robust reference database is needed to expand our ability to accomplish a molecular identification.},
}
@article {pmid24041451,
year = {2015},
author = {Pavan-Kumar, A and Gireesh-Babu, P and Babu, PP and Jaiswar, AK and Prasad, KP and Chaudhari, A and Raje, SG and Chakraborty, SK and Krishna, G and Lakra, WS},
title = {DNA barcoding of elasmobranchs from Indian coast and its reliability in delineating geographically widespread specimens.},
journal = {Mitochondrial DNA},
volume = {26},
number = {1},
pages = {92-100},
doi = {10.3109/19401736.2013.823174},
pmid = {24041451},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; *DNA Barcoding, Taxonomic ; Elasmobranchii/*classification/*genetics ; Electron Transport Complex IV/chemistry/*genetics ; *Genes, Mitochondrial ; Genetic Variation ; India ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; },
abstract = {Identification of elasmobranchs by conventional taxonomy is difficult due to similarities in morphological characters. Species-specific molecular markers are good choice for identifying species irrespective of it's life stage. Recently, mitochondrial cytochrome c oxidase subunit I (COI) gene got global recognition as a barcode gene to discriminate all animals up-to species level. In this study, mitochondrial COI partial gene was used to develop DNA barcodes for 18 species of elasmobranchs (10 species of sharks and 8 species of rays). The COI barcodes clearly distinguished all the species with high interspecific distance values than intraspecific values. The average interspecific and intraspecific distance values are 8.6% and 0.3% for sharks, respectively and 12.4% and 0.63% for rays, respectively using K2P method. The Neighbor-Joining tree showed distinct clusters shared by the species of same genera. The COI barcodes were also used to estimate allopatric divergences for selected species across broad geographical locations and found that Sphyrna lewini, Aetobatus narinari and Neotrygon kuhlii have cryptic diversity.},
}
@article {pmid24040352,
year = {2013},
author = {Baselga, A and Gómez-Rodríguez, C and Novoa, F and Vogler, AP},
title = {Rare failures of DNA barcodes [corrected] to separate morphologically distinct species in a biodiversity survey of Iberian leaf beetles.},
journal = {PloS one},
volume = {8},
number = {9},
pages = {e74854},
pmid = {24040352},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; Coleoptera/*anatomy &amp; histology/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Female ; Genetic Speciation ; Genetic Variation ; Geography ; Likelihood Functions ; Male ; Phylogeny ; Plant Leaves/metabolism ; Portugal ; RNA, Ribosomal, 18S/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; Spain ; },
abstract = {During a survey of genetic and species diversity patterns of leaf beetle (Coleoptera: Chrysomelidae) assemblages across the Iberian Peninsula we found a broad congruence between morphologically delimited species and variation in the cytochrome oxidase (cox1) gene. However, one species pair each in the genera Longitarsus Berthold and Pachybrachis Chevrolat was inseparable using molecular methods, whereas diagnostic morphological characters (including male or female genitalia) unequivocally separated the named species. Parsimony haplotype networks and maximum likelihood trees built from cox1 showed high genetic structure within each species pair, but no correlation with the morphological types and neither with geographic distributions. This contrasted with all analysed congeneric species, which were recovered as monophyletic. A limited number of specimens were sequenced for the nuclear 18S rRNA gene, which showed no or very limited variation within the species pair and no separation of morphological types. These results suggest that processes of lineage sorting for either group are lagging behind the clear morphological and presumably reproductive separation. In the Iberian chrysomelids, incongruence between DNA-based and morphological delimitations is a rare exception, but the discovery of these species pairs may be useful as an evolutionary model for studying the process of speciation in this ecological and geographical setting. In addition, the study of biodiversity patterns based on DNA requires an evolutionary understanding of these incongruences and their potential causes.},
}
@article {pmid24034669,
year = {2014},
author = {Seraphim, N and Marín, MA and Freitas, AV and Silva-Brandão, KL},
title = {Morphological and molecular marker contributions to disentangling the cryptic Hermeuptychia hermes species complex (Nymphalidae: Satyrinae: Euptychiina).},
journal = {Molecular ecology resources},
volume = {14},
number = {1},
pages = {39-49},
doi = {10.1111/1755-0998.12161},
pmid = {24034669},
issn = {1755-0998},
mesh = {Americas ; Animal Structures/anatomy &amp; histology ; Animals ; Cluster Analysis ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/genetics ; Genitalia/anatomy &amp; histology ; Insect Proteins/genetics ; Lepidoptera/anatomy &amp; histology/*classification/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The genus Hermeuptychia is common and widespread through the Americas, from Argentina to the southern United States of America. All eight recognized species within Hermeuptychia are small and brown, with very similar interspecific external morphologies and intraspecifically variable ocelli patterns that render taxonomic identification based on morphology difficult. In our study, we surveyed variability within Hermeuptychia, and evaluated species boundaries based on molecular data (sequences of the 'barcode' mitochondrial DNA COI gene) and morphology (mainly male genitalia), using a phylogenetic approach. We found eight DNA-based and 12 morphological groups in our sampling. Species names were assigned based mainly on comparisons with male genitalia morphology descriptions corresponding to name-bearing type specimens. Morphological and DNA variability were highly congruent, with the exception of group H, the Hermeuptychia cucullina complex. Also, the barcode region showed a clear threshold for intra- and interspecific mean distances around 2%. Based on these results, we circumscribe the species boundaries in the genus Hermeuptychia and discuss conflicts between mitochondrial genes and classic morphological approaches for identifying and delimiting species. Our study revealed cryptic diversity within an ubiquitous genus of Neotropical butterflies.},
}
@article {pmid24034529,
year = {2014},
author = {Nunes, VL and Mendes, R and Marabuto, E and Novais, BM and Hertach, T and Quartau, JA and Seabra, SG and Paulo, OS and Simões, PC},
title = {Conflicting patterns of DNA barcoding and taxonomy in the cicada genus Tettigettalna from Southern Europe (Hemiptera: Cicadidae).},
journal = {Molecular ecology resources},
volume = {14},
number = {1},
pages = {27-38},
doi = {10.1111/1755-0998.12158},
pmid = {24034529},
issn = {1755-0998},
mesh = {Animals ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/genetics ; Europe ; Hemiptera/*classification/*genetics ; Insect Proteins/genetics ; Molecular Sequence Data ; Phylogeography ; Sequence Analysis, DNA ; },
abstract = {DNA barcodes have great potential to assist in species identification, especially when high taxonomical expertise is required. We investigated the utility of the 5' mitochondrial cytochrome c oxidase I (COI) region to discriminate between 13 European cicada species. These included all nine species currently recognized under the genus Tettigettalna, from which seven are endemic to the southern Iberian Peninsula. These cicadas have species-specific male calling songs but are morphologically very similar. Mean COI divergence between congeners ranged from 0.4% to 10.6%, but this gene was proven insufficient to determine species limits within genus Tettigettalna because a barcoding gap was absent for several of its species, that is, the highest intraspecific distance exceeded the lowest interspecific distance. The genetic data conflicted with current taxonomic classification for T. argentata and T. mariae. Neighbour-joining and Bayesian analyses revealed that T. argentata is geographically structured (clades North and South) and might constitute a species complex together with T. aneabi and T. mariae. The latter diverges very little from the southern clade of T. argentata and shares with it its most common haplotype. T. mariae is often in sympatry with T. argentata but it remains unclear whether introgression or incomplete lineage sorting may be responsible for the sharing of haplotypes. T. helianthemi and T. defauti also show high intraspecific variation that might signal hidden cryptic diversity. These taxonomic conflicts must be re-evaluated with further studies using additional genes and extensive morphological and acoustic analyses.},
}
@article {pmid24028345,
year = {2014},
author = {Clarke, LJ and Czechowski, P and Soubrier, J and Stevens, MI and Cooper, A},
title = {Modular tagging of amplicons using a single PCR for high-throughput sequencing.},
journal = {Molecular ecology resources},
volume = {14},
number = {1},
pages = {117-121},
doi = {10.1111/1755-0998.12162},
pmid = {24028345},
issn = {1755-0998},
mesh = {Animals ; DNA, Mitochondrial/chemistry/genetics ; DNA, Recombinant/*chemistry/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Insecta/*genetics ; Polymerase Chain Reaction/*methods ; Staining and Labeling/*methods ; },
abstract = {High-throughput sequencing (HTS) of PCR amplicons is becoming the method of choice to sequence one or several targeted loci for phylogenetic and DNA barcoding studies. Although the development of HTS has allowed rapid generation of massive amounts of DNA sequence data, preparing amplicons for HTS remains a rate-limiting step. For example, HTS platforms require platform-specific adapter sequences to be present at the 5' and 3' end of the DNA fragment to be sequenced. In addition, short multiplex identifier (MID) tags are typically added to allow multiple samples to be pooled in a single HTS run. Existing methods to incorporate HTS adapters and MID tags into PCR amplicons are either inefficient, requiring multiple enzymatic reactions and clean-up steps, or costly when applied to multiple samples or loci (fusion primers). We describe a method to amplify a target locus and add HTS adapters and MID tags via a linker sequence using a single PCR. We demonstrate our approach by generating reference sequence data for two mitochondrial loci (COI and 16S) for a diverse suite of insect taxa. Our approach provides a flexible, cost-effective and efficient method to prepare amplicons for HTS.},
}
@article {pmid24027345,
year = {2013},
author = {Walther, G and Pawłowska, J and Alastruey-Izquierdo, A and Wrzosek, M and Rodriguez-Tudela, JL and Dolatabadi, S and Chakrabarti, A and de Hoog, GS},
title = {DNA barcoding in Mucorales: an inventory of biodiversity.},
journal = {Persoonia},
volume = {30},
number = {},
pages = {11-47},
pmid = {24027345},
issn = {0031-5850},
abstract = {The order Mucorales comprises predominantly fast-growing saprotrophic fungi, some of which are used for the fermentation of foodstuffs but it also includes species known to cause infections in patients with severe immune or metabolic impairments. To inventory biodiversity in Mucorales ITS barcodes of 668 strains in 203 taxa were generated covering more than two thirds of the recognised species. Using the ITS sequences, Molecular Operational Taxonomic Units were defined by a similarity threshold of 99 %. An LSU sequence was generated for each unit as well. Analysis of the LSU sequences revealed that conventional phenotypic classifications of the Mucoraceae are highly artificial. The LSU- and ITS-based trees suggest that characters, such as rhizoids and sporangiola, traditionally used in mucoralean taxonomy are plesiomorphic traits. The ITS region turned out to be an appropriate barcoding marker in Mucorales. It could be sequenced directly in 82 % of the strains and its variability was sufficient to resolve most of the morphospecies. Molecular identification turned out to be problematic only for the species complexes of Mucor circinelloides, M. flavus, M. piriformis and Zygorhynchus moelleri. As many as 12 possibly undescribed species were detected. Intraspecific variability differed widely among mucorealean species ranging from 0 % in Backusella circina to 13.3 % in Cunninghamella echinulata. A high proportion of clinical strains was included for molecular identification. Clinical isolates of Cunninghamella elegans were identified molecularly for the first time. As a result of the phylogenetic analyses several taxonomic and nomenclatural changes became necessary. The genus Backusella was emended to include all species with transitorily recurved sporangiophores. Since this matched molecular data all Mucor species possessing this character were transferred to Backusella. The genus Zygorhynchus was shown to be polyphyletic based on ITS and LSU data. Consequently, Zygorhynchus was abandoned and all species were reclassified in Mucor. Our phylogenetic analyses showed, furthermore, that all non-thermophilic Rhizomucor species belong to Mucor. Accordingly, Rhizomucor endophyticus was transferred to Mucor and Rhizomucor chlamydosporus was synonymised with Mucor indicus. Lecto-, epi- or neotypes were designated for several taxa.},
}
@article {pmid24024093,
year = {2013},
author = {Panelli, S and Brambati, E and Bonacina, C and Feligini, M},
title = {Diversity of fungal flora in raw milk from the Italian Alps in relation to pasture altitude.},
journal = {SpringerPlus},
volume = {2},
number = {},
pages = {405},
pmid = {24024093},
issn = {2193-1801},
abstract = {The present paper explores the diversity of mycobiota inhabiting raw milk sampled at different altitudes (1400 m, 1800 m, 2200 m) from cows grazing Alpine pastures of Valle d'Aosta (North-Western Italian Alps). To this aim, multilocus sequencing was performed at barcodes commonly used for fungal identification (ITS1, D1/D2 domains of the 26S rRNA gene, and part of the β-tubulin gene). A total of 31 species were detected, most of them yeasts, followed by moulds and by 2 sequences of macroscopic fungi. Several yeasts and moulds were well-characterized inhabitants of the dairy environment, known to positively contribute to cheesemaking. Among these, Candida was the most represented genus with a tendency to cluster at the highest altitudes (6 over 8 observations at ≥ 1800 m), and Kluyveromyces marxianus the most abundant single species, retrieved at all altitudes. The environmental ascomycetous Atrotorquata lineata, never put in relation with food nor described outside North-America, was another species among those most frequently retrieved and was detected in 6 milks at 1400 and 1800 m. The remaining fungi, in general never reported in milk, were mostly environmental. Many of them resulted associated with plants as pathogens or symbionts. Finally, the highest sampled altitude yielded a significant fungal diversity (17 species). This work enlarges the knowledge of fungal consortia inhabiting raw milk and introduces microbial ecology among the altitude-dependent factors, in the composition of Alpine pastures, with the potential of shaping the properties of milks and cheeses, together with the already described physical, chemical and botanical variables.},
}
@article {pmid24024082,
year = {2013},
author = {Griffiths, AM and Miller, DD and Egan, A and Fox, J and Greenfield, A and Mariani, S},
title = {DNA barcoding unveils skate (Chondrichthyes: Rajidae) species diversity in 'ray' products sold across Ireland and the UK.},
journal = {PeerJ},
volume = {1},
number = {},
pages = {e129},
pmid = {24024082},
issn = {2167-8359},
abstract = {Skates are widely consumed across the globe, but many large species are subject to considerable concern regarding their conservation and management. Within Europe such issues have recently driven policy changes so that, for the first time, reports of skate landings now have to be made under species-specific names. Total allowable catches have also been established for many groups, which have been set to zero for a number of the most vulnerable species (e.g., Dipturus batis, Raja undulata and Rostoraja alba). Whilst accurate species identification has become an important issue for landings, the sale of skates is still usually made under a blanket term of "skate" or "ray". The matter of identifying species of skate is further complicated by their morphologically conservative nature and the fact that they are commercially valued for their wings. Thus, before sale their bodies are usually discarded (i.e., "winged") and often skinned, making morphological identification impossible. For the first time, DNA barcoding (of the mitochondrial COI gene) was applied to samples of skate wings from retail outlets across the British Isles, providing insight into which species are sold for consumption. A total of 98 wing samples were analysed, revealing that six species were sold; blonde ray (Raja brachyura), spotted ray (Raja montagui), thornback ray (Raja clavata), cuckoo ray (Leucoraja naevus) small-eyed ray (Raja microocellata) and shagreen ray (Leucoraja fullonica). Statistical testing demonstrated that there were significant differences in the species sold in the distinct retail groups which suggests complex drivers behind the patterns of sale in skates. The results also indicate that endangered species are not commonly being passed on to consumers. In addition, the practice of selling skate wings under ambiguous labels is highlighted as it makes it extremely difficult for consumers to exercise a right to avoid species of conservation concern. Interestingly, a single retailer chain labelled their wings as originating from three smaller-growing species (generally to be considered of lower conservation concern); of the six samples analysed from this company a third were mislabelled and originated from the thornback ray (a larger species that is currently undergoing population declines).},
}
@article {pmid24022383,
year = {2013},
author = {Stoeckle, MY and Coffran, C},
title = {TreeParser-aided Klee diagrams display taxonomic clusters in DNA barcode and nuclear gene datasets.},
journal = {Scientific reports},
volume = {3},
number = {},
pages = {2635},
pmid = {24022383},
issn = {2045-2322},
mesh = {Animals ; Birds/genetics ; Butterflies/genetics ; Cluster Analysis ; Computational Biology/methods ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Genomics/methods ; Internet ; *Phylogeny ; *Software ; },
abstract = {Indicator vector analysis of a nucleotide sequence alignment generates a compact heat map, called a Klee diagram, with potential insight into clustering patterns in evolution. However, so far this approach has examined only mitochondrial cytochrome c oxidase I (COI) DNA barcode sequences. To further explore, we developed TreeParser, a freely-available web-based program that sorts a sequence alignment according to a phylogenetic tree generated from the dataset. We applied TreeParser to nuclear gene and COI barcode alignments from birds and butterflies. Distinct blocks in the resulting Klee diagrams corresponded to species and higher-level taxonomic divisions in both groups, and this enabled graphic comparison of phylogenetic information in nuclear and mitochondrial genes. Our results demonstrate TreeParser-aided Klee diagrams objectively display taxonomic clusters in nucleotide sequence alignments. This approach may help establish taxonomy in poorly studied groups and investigate higher-level clustering which appears widespread but not well understood.},
}
@article {pmid24021095,
year = {2013},
author = {Scarpassa, VM and Alencar, RB},
title = {Molecular taxonomy of the two Leishmania vectors Lutzomyia umbratilis and Lutzomyia anduzei (Diptera: Psychodidae) from the Brazilian Amazon.},
journal = {Parasites &amp; vectors},
volume = {6},
number = {1},
pages = {258},
pmid = {24021095},
issn = {1756-3305},
mesh = {Animals ; Brazil ; *Disease Vectors ; Haplotypes ; Leishmania guyanensis/isolation &amp; purification ; Microscopy ; Molecular Sequence Data ; Phylogeny ; Psychodidae/anatomy &amp; histology/*classification/*genetics ; Sequence Analysis, DNA ; Sequence Homology ; },
abstract = {BACKGROUND: Lutzomyia umbratilis (a probable species complex) is the main vector of Leishmania guyanensis in the northern region of Brazil. Lutzomyia anduzei has been implicated as a secondary vector of this parasite. These species are closely related and exhibit high morphological similarity in the adult stage; therefore, they have been wrongly identified, both in the past and in the present. This shows the need for employing integrated taxonomy.<br><br>METHODS: With the aim of gathering information on the molecular taxonomy and evolutionary relationships of these two vectors, 118 sequences of 663 base pairs (barcode region of the mitochondrial DNA cytochrome oxidase I - COI) were generated from 72 L. umbratilis and 46 L. anduzei individuals captured, respectively, in six and five localities of the Brazilian Amazon. The efficiency of the barcode region to differentiate the L. umbratilis lineages I and II was also evaluated. The data were analyzed using the pairwise genetic distances matrix and the Neighbor-Joining (NJ) tree, both based on the Kimura Two Parameter (K2P) evolutionary model.<br><br>RESULTS: The analyses resulted in 67 haplotypes: 32 for L. umbratilis and 35 for L. anduzei. The mean intra-specific genetic distance was 0.008 (0.002 to 0.010 for L. umbratilis; 0.008 to 0.014 for L. anduzei), whereas the mean interspecific genetic distance was 0.044 (0.041 to 0.046), supporting the barcoding gap. Between the L. umbratilis lineages I and II, it was 0.009 to 0.010. The NJ tree analysis strongly supported monophyletic clades for both L. umbratilis and L. anduzei, whereas the L. umbratilis lineages I and II formed two poorly supported monophyletic subclades.<br><br>CONCLUSIONS: The barcode region clearly separated the two species and may therefore constitute a valuable tool in the identification of the sand fly vectors of Leishmania in endemic leishmaniasis areas. However, the barcode region had not enough power to separate the two lineages of L. umbratilis, likely reflecting incipient species that have not yet reached the status of distinct species.},
}
@article {pmid24021088,
year = {2013},
author = {Buschmann, T and Bystrykh, LV},
title = {Levenshtein error-correcting barcodes for multiplexed DNA sequencing.},
journal = {BMC bioinformatics},
volume = {14},
number = {},
pages = {272},
pmid = {24021088},
issn = {1471-2105},
mesh = {Algorithms ; DNA/analysis/*chemistry/genetics ; DNA Primers/chemistry/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Models, Genetic ; Nucleic Acid Amplification Techniques/*methods ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; Software ; },
abstract = {BACKGROUND: High-throughput sequencing technologies are improving in quality, capacity and costs, providing versatile applications in DNA and RNA research. For small genomes or fraction of larger genomes, DNA samples can be mixed and loaded together on the same sequencing track. This so-called multiplexing approach relies on a specific DNA tag or barcode that is attached to the sequencing or amplification primer and hence appears at the beginning of the sequence in every read. After sequencing, each sample read is identified on the basis of the respective barcode sequence.Alterations of DNA barcodes during synthesis, primer ligation, DNA amplification, or sequencing may lead to incorrect sample identification unless the error is revealed and corrected. This can be accomplished by implementing error correcting algorithms and codes. This barcoding strategy increases the total number of correctly identified samples, thus improving overall sequencing efficiency. Two popular sets of error-correcting codes are Hamming codes and Levenshtein codes.<br><br>RESULT: Levenshtein codes operate only on words of known length. Since a DNA sequence with an embedded barcode is essentially one continuous long word, application of the classical Levenshtein algorithm is problematic. In this paper we demonstrate the decreased error correction capability of Levenshtein codes in a DNA context and suggest an adaptation of Levenshtein codes that is proven of efficiently correcting nucleotide errors in DNA sequences. In our adaption we take the DNA context into account and redefine the word length whenever an insertion or deletion is revealed. In simulations we show the superior error correction capability of the new method compared to traditional Levenshtein and Hamming based codes in the presence of multiple errors.<br><br>CONCLUSION: We present an adaptation of Levenshtein codes to DNA contexts capable of correction of a pre-defined number of insertion, deletion, and substitution mutations. Our improved method is additionally capable of recovering the new length of the corrupted codeword and of correcting on average more random mutations than traditional Levenshtein or Hamming codes.As part of this work we prepared software for the flexible generation of DNA codes based on our new approach. To adapt codes to specific experimental conditions, the user can customize sequence filtering, the number of correctable mutations and barcode length for highest performance.},
}
@article {pmid24020964,
year = {2015},
author = {Yacoub, HA and Fathi, MM and Sadek, MA},
title = {Using cytochrome b gene of mtDNA as a DNA barcoding marker in chicken strains.},
journal = {Mitochondrial DNA},
volume = {26},
number = {2},
pages = {217-223},
doi = {10.3109/19401736.2013.825771},
pmid = {24020964},
issn = {1940-1744},
mesh = {Animals ; Chickens/*genetics ; Cytochromes b/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry ; Galliformes/genetics ; *Genes, Mitochondrial ; Phylogeny ; },
abstract = {This was the second study to apply using of a cytochrome b gene as barcoding tool in distinguishing among chicken strains. We performed polymerase chain reaction (PCR) amplification using universal primer to amplify around 415 bp fragment of cytochrome b gene of mtDNA. The tree reported that both Saudi chicken strains (black and dark brown) are closely related and it might be separated from same origin rather than bronze ones. The phylogenetic tree also, exploited that native chicken strains were closely related to cluster of Ceylon jungle fowl, black Minorca egg chicken and Fayoumi egg chicken. The genetic divergence between these populations or types of chickens in Saudi Arabia was low (0.02) and it was very low (0.011), when compared to other species of Gallus. We confirmed that short fragment of cyt-b gene as a universal DNA barcode region. It was much more accurate and efficient tool to discriminate inter-species than intra-species. Applying cyt-b of mtDNA was successfully distinguished among native strains and other species of Gallus as in a previous study. However, applying this thought on different species of farm animal species is recommended.},
}
@article {pmid24020880,
year = {2013},
author = {Lobo, J and Costa, PM and Teixeira, MA and Ferreira, MS and Costa, MH and Costa, FO},
title = {Enhanced primers for amplification of DNA barcodes from a broad range of marine metazoans.},
journal = {BMC ecology},
volume = {13},
number = {},
pages = {34},
pmid = {24020880},
issn = {1472-6785},
mesh = {Animals ; Aquatic Organisms/classification/genetics ; *DNA Barcoding, Taxonomic ; DNA Primers/*genetics ; Invertebrates/classification/*genetics ; Sequence Alignment ; },
abstract = {BACKGROUND: Building reference libraries of DNA barcodes is relatively straightforward when specifically designed primers are available to amplify the COI-5P region from a relatively narrow taxonomic group (e.g. single class or single order). DNA barcoding marine communities have been comparatively harder to accomplish due to the broad taxonomic diversity and lack of consistently efficient primers. Although some of the so-called "universal" primers have been relatively successful, they still fail to amplify COI-5P of many marine animal groups, while displaying random success even among species within each group. Here we propose a new pair of primers designed to enhance amplification of the COI-5P region in a wide range of marine organisms.<br><br>RESULTS: Amplification tests conducted on a wide range of marine animal taxa, rendered possible the first-time sequencing of DNA barcodes from eight separated phyla (Annelida, Arthropoda, Chordata, Cnidaria, Echinodermata, Mollusca, Nemertea and Platyhelminthes), comprising a total of 14 classes, 28 orders, 57 families, 68 genus and 76 species.<br><br>CONCLUSIONS: These primers demonstrated to be highly cost-effective, which is of key importance for DNA barcoding procedures, such as for building comprehensive DNA barcode libraries of marine communities, where the processing of a large numbers of specimens from a wide variety of marine taxa is compulsory.},
}
@article {pmid24014899,
year = {2013},
author = {Groenewald, JZ and Nakashima, C and Nishikawa, J and Shin, HD and Park, JH and Jama, AN and Groenewald, M and Braun, U and Crous, PW},
title = {Species concepts in Cercospora: spotting the weeds among the roses.},
journal = {Studies in mycology},
volume = {75},
number = {1},
pages = {115-170},
pmid = {24014899},
issn = {0166-0616},
abstract = {UNLABELLED: The genus Cercospora contains numerous important plant pathogenic fungi from a diverse range of hosts. Most species of Cercospora are known only from their morphological characters in vivo. Although the genus contains more than 5 000 names, very few cultures and associated DNA sequence data are available. In this study, 360 Cercospora isolates, obtained from 161 host species, 49 host families and 39 countries, were used to compile a molecular phylogeny. Partial sequences were derived from the internal transcribed spacer regions and intervening 5.8S nrRNA, actin, calmodulin, histone H3 and translation elongation factor 1-alpha genes. The resulting phylogenetic clades were evaluated for application of existing species names and five novel species are introduced. Eleven species are epi-, lecto- or neotypified in this study. Although existing species names were available for several clades, it was not always possible to apply North American or European names to African or Asian strains and vice versa. Some species were found to be limited to a specific host genus, whereas others were isolated from a wide host range. No single locus was found to be the ideal DNA barcode gene for the genus, and species identification needs to be based on a combination of gene loci and morphological characters. Additional primers were developed to supplement those previously published for amplification of the loci used in this study.<br><br>TAXONOMIC NOVELTIES: New species - Cercospora coniogrammes Crous &amp; R.G. Shivas, Cercospora delaireae C. Nakash., Crous, U. Braun &amp; H.D. Shin, Cercospora euphorbiae-sieboldianae C. Nakash., Crous, U. Braun &amp; H.D. Shin, Cercospora pileicola C. Nakash., Crous, U. Braun &amp; H.D. Shin, Cercospora vignigena C. Nakash., Crous, U. Braun &amp; H.D. Shin. Typifications: epitypifications - Cercospora alchemillicola U. Braun &amp; C.F. Hill, Cercospora althaeina Sacc., Cercospora armoraciae Sacc., Cercospora corchori Sawada, Cercospora mercurialis Pass., Cercospora olivascens Sacc., Cercospora violae Sacc.; neotypifications - Cercospora fagopyri N. Nakata &amp; S. Takim., Cercospora sojina Hara.},
}
@article {pmid24010710,
year = {2013},
author = {Nussinov, R and Ma, B and Tsai, CJ and Csermely, P},
title = {Allosteric conformational barcodes direct signaling in the cell.},
journal = {Structure (London, England : 1993)},
volume = {21},
number = {9},
pages = {1509-1521},
pmid = {24010710},
issn = {1878-4186},
support = {HHSN261200800001C/CA/NCI NIH HHS/United States ; HHSN261200800001E/CA/NCI NIH HHS/United States ; /ImNIH/Intramural NIH HHS/United States ; },
mesh = {Allosteric Regulation ; Animals ; Catalytic Domain ; Extracellular Signal-Regulated MAP Kinases/chemistry/metabolism ; Humans ; Intracellular Signaling Peptides and Proteins/*chemistry/metabolism ; Models, Molecular ; Phosphorylation ; Protein Interaction Maps ; Protein Processing, Post-Translational ; *Signal Transduction ; },
abstract = {The cellular network is highly interconnected. Pathways merge and diverge. They proceed through shared proteins and may change directions. How are cellular pathways controlled and their directions decided, coded, and read? These questions become particularly acute when we consider that a small number of pathways, such as signaling pathways that regulate cell fates, cell proliferation, and cell death in development, are extensively exploited. This review focuses on these signaling questions from the structural standpoint and discusses the literature in this light. All co-occurring allosteric events (including posttranslational modifications, pathogen binding, and gain-of-function mutations) collectively tag the protein functional site with a unique barcode. The barcode shape is read by an interacting molecule, which transmits the signal. A conformational barcode provides an intracellular address label, which selectively favors binding to one partner and quenches binding to others, and, in this way, determines the pathway direction, and, eventually, the cell's response and fate.},
}
@article {pmid24009730,
year = {2013},
author = {Yang, JB and Yang, SX and Li, HT and Yang, J and Li, DZ},
title = {Comparative chloroplast genomes of camellia species.},
journal = {PloS one},
volume = {8},
number = {8},
pages = {e73053},
pmid = {24009730},
issn = {1932-6203},
mesh = {Camellia/classification/*genetics ; Chloroplasts/*genetics ; Computational Biology ; Gene Order ; Genetic Variation ; *Genome, Chloroplast ; Genomics ; Molecular Sequence Data ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Camellia, comprising more than 200 species, is a valuable economic commodity due to its enormously popular commercial products: tea leaves, flowers, and high-quality edible oils. It is the largest and most important genus in the family Theaceae. However, phylogenetic resolution of the species has proven to be difficult. Consequently, the interspecies relationships of the genus Camellia are still hotly debated. Phylogenomics is an attractive avenue that can be used to reconstruct the tree of life, especially at low taxonomic levels.<br><br>Seven complete chloroplast (cp) genomes were sequenced from six species representing different subdivisions of the genus Camellia using Illumina sequencing technology. Four junctions between the single-copy segments and the inverted repeats were confirmed and genome assemblies were validated by PCR-based product sequencing using 123 pairs of primers covering preliminary cp genome assemblies. The length of the Camellia cp genome was found to be about 157kb, which contained 123 unique genes and 23 were duplicated in the IR regions. We determined that the complete Camellia cp genome was relatively well conserved, but contained enough genetic differences to provide useful phylogenetic information. Phylogenetic relationships were analyzed using seven complete cp genomes of six Camellia species. We also identified rapidly evolving regions of the cp genome that have the potential to be used for further species identification and phylogenetic resolution.<br><br>CONCLUSIONS/SIGNIFICANCE: In this study, we wanted to determine if analyzing completely sequenced cp genomes could help settle these controversies of interspecies relationships in Camellia. The results demonstrate that cp genome data are beneficial in resolving species definition because they indicate that organelle-based "barcodes", can be established for a species and then used to unmask interspecies phylogenetic relationships. It reveals that phylogenomics based on cp genomes is an effective approach for achieving phylogenetic resolution between Camellia species.},
}
@article {pmid24006393,
year = {2013},
author = {Kovarik, DN and Patterson, DG and Cohen, C and Sanders, EA and Peterson, KA and Porter, SG and Chowning, JT},
title = {Bioinformatics education in high school: implications for promoting science, technology, engineering, and mathematics careers.},
journal = {CBE life sciences education},
volume = {12},
number = {3},
pages = {441-459},
pmid = {24006393},
issn = {1931-7913},
mesh = {*Career Choice ; Computational Biology/*education ; Curriculum ; Data Collection ; Engineering/education ; Faculty/statistics &amp; numerical data ; Female ; Humans ; Male ; Mathematics/*education ; Professional Competence ; *Schools/statistics &amp; numerical data ; Science/*education ; Students/statistics &amp; numerical data ; Technology/*education ; },
abstract = {We investigated the effects of our Bio-ITEST teacher professional development model and bioinformatics curricula on cognitive traits (awareness, engagement, self-efficacy, and relevance) in high school teachers and students that are known to accompany a developing interest in science, technology, engineering, and mathematics (STEM) careers. The program included best practices in adult education and diverse resources to empower teachers to integrate STEM career information into their classrooms. The introductory unit, Using Bioinformatics: Genetic Testing, uses bioinformatics to teach basic concepts in genetics and molecular biology, and the advanced unit, Using Bioinformatics: Genetic Research, utilizes bioinformatics to study evolution and support student research with DNA barcoding. Pre-post surveys demonstrated significant growth (n = 24) among teachers in their preparation to teach the curricula and infuse career awareness into their classes, and these gains were sustained through the end of the academic year. Introductory unit students (n = 289) showed significant gains in awareness, relevance, and self-efficacy. While these students did not show significant gains in engagement, advanced unit students (n = 41) showed gains in all four cognitive areas. Lessons learned during Bio-ITEST are explored in the context of recommendations for other programs that wish to increase student interest in STEM careers.},
}
@article {pmid24004516,
year = {2013},
author = {Subedi, A and Kunwar, B and Choi, Y and Dai, Y and van Andel, T and Chaudhary, RP and de Boer, HJ and Gravendeel, B},
title = {Collection and trade of wild-harvested orchids in Nepal.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {9},
number = {1},
pages = {64},
pmid = {24004516},
issn = {1746-4269},
mesh = {DNA Barcoding, Taxonomic ; Medicine, Traditional ; Nepal ; *Orchidaceae/genetics/growth &amp; development ; Plants, Medicinal ; },
abstract = {BACKGROUND: Wild orchids are illegally harvested and traded in Nepal for use in local traditional medicine, horticulture, and international trade. This study aims to: 1) identify the diversity of species of wild orchids in trade in Nepal; 2) study the chain of commercialization from collector to client and/or export; 3) map traditional knowledge and medicinal use of orchids; and 4) integrate the collected data to propose a more sustainable approach to orchid conservation in Nepal.<br><br>METHODS: Trade, species diversity, and traditional use of wild-harvested orchids were documented during field surveys of markets and through interviews. Trade volumes and approximate income were estimated based on surveys and current market prices. Orchid material samples were identified to species level using a combination of morphology and DNA barcoding.<br><br>RESULTS: Orchid trade is a long tradition, and illegal export to China, India and Hong Kong is rife. Estimates show that 9.4 tons of wild orchids were illegally traded from the study sites during 2008/2009. A total of 60 species of wild orchids were reported to be used in traditional medicinal practices to cure at least 38 different ailments, including energizers, aphrodisiacs and treatments of burnt skin, fractured or dislocated bones, headaches, fever and wounds. DNA barcoding successfully identified orchid material to species level that remained sterile after culturing.<br><br>CONCLUSIONS: Collection of wild orchids was found to be widespread in Nepal, but illegal trade is threatening many species in the wild. Establishment of small-scale sustainable orchid breeding enterprises could be a valuable alternative for the production of medicinal orchids for local communities. Critically endangered species should be placed on CITES Appendix I to provide extra protection to those species. DNA barcoding is an effective method for species identification and monitoring of illegal cross-border trade.},
}
@article {pmid24003196,
year = {2013},
author = {Dunham, JP and Friesen, ML},
title = {A cost-effective method for high-throughput construction of illumina sequencing libraries.},
journal = {Cold Spring Harbor protocols},
volume = {2013},
number = {9},
pages = {820-834},
pmid = {24003196},
issn = {1559-6095},
support = {R01 GM098741/GM/NIGMS NIH HHS/United States ; R01 GM102227/GM/NIGMS NIH HHS/United States ; GM102227/GM/NIGMS NIH HHS/United States ; GM098741/GM/NIGMS NIH HHS/United States ; },
mesh = {Costs and Cost Analysis ; *Gene Library ; High-Throughput Nucleotide Sequencing/*economics/*methods ; Time Factors ; },
abstract = {Despite the plummeting cost of next-generation sequencing, the preparation of sequencing libraries using commercially available kits still remains expensive. The cost can be prohibitive for large-scale comparative or experimental studies, where hundreds to thousands of samples need to be analyzed. The increasing use of multiplexing dozens to hundreds of samples underscores the urgent need to develop a cost-effective and time-efficient high-throughput method for library preparation. By optimizing and scaling down the steps in library construction and using commonly available reagents, the protocol described here allows for the preparation of DNA libraries in a 96-well format using no specialized equipment and at a substantial savings in both reagent cost and personnel hours. Utilizing this optimized high-throughput format results in a 10-fold cost reduction, compared to commercially available kits, making per library or pooled sample costs ∼$12.60-14.90 for individually prepared libraries and ∼$8.60-10.60 for pooled libraries with individual barcodes; both techniques allow for up to 144 samples to be pooled on a single lane with the barcodes tested herein.},
}
@article {pmid23996313,
year = {2013},
author = {Urbański, DF and Małolepszy, A and Stougaard, J and Andersen, SU},
title = {High-throughput and targeted genotyping of Lotus japonicus LORE1 insertion mutants.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1069},
number = {},
pages = {119-146},
doi = {10.1007/978-1-62703-613-9_10},
pmid = {23996313},
issn = {1940-6029},
mesh = {Computational Biology/methods ; Gene Targeting ; Genotyping Techniques/*methods ; High-Throughput Screening Assays/*methods ; Lotus/*genetics ; *Mutagenesis, Insertional ; Mutation ; Reproducibility of Results ; *Retroelements ; },
abstract = {The Lotus Retrotransposon 1 (LORE1) is used for genome-wide mutagenesis of the model legume Lotus japonicus. Characterization of the LORE1 insertion sites in individual mutant lines is critical for development and use of the resource. Here we present guidelines for use of the LORE1 reverse genetics resource and provide detailed protocols for insertion site identification and validation. For high-throughput identification of insertions in up to 9,216 pooled lines, the FSTpoolit protocol takes advantage of Splinkerette adapters, molecular barcoding, 2D pooling, Illumina sequencing, and automated data analysis using the freely available FSTpoolit software. Complementing the high-throughput approach, we describe a simplified sequence-specific amplification polymorphism (SSAP) protocol well suited for quick identification of insertion sites in a limited number of lines. Both the FSTpoolit and simplified SSAP protocols are generally applicable to insertion site identification in any insertional mutagenesis setup.},
}
@article {pmid23995318,
year = {2013},
author = {Paramasivan, R and Dhananjeyan, KJ and Pandian, RS},
title = {A preliminary report on DNA barcoding and phylogenetic relationships of certain public health important mosquito species recorded in rural areas of south India.},
journal = {Journal of vector borne diseases},
volume = {50},
number = {2},
pages = {144-146},
pmid = {23995318},
issn = {0972-9062},
mesh = {Animals ; Cluster Analysis ; Culicidae/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Genotype ; India ; *Insect Vectors ; *Phylogeny ; Polymerase Chain Reaction ; },
}
@article {pmid23994277,
year = {2014},
author = {Li, Y and Zeng, Y and Mao, Y and Lei, C and Zhang, S},
title = {Proximity-dependent isothermal cycle amplification for small-molecule detection based on surface enhanced Raman scattering.},
journal = {Biosensors &amp; bioelectronics},
volume = {51},
number = {},
pages = {304-309},
doi = {10.1016/j.bios.2013.07.055},
pmid = {23994277},
issn = {1873-4235},
mesh = {Aptamers, Nucleotide/chemistry ; Cocaine/*blood ; Gold/*chemistry ; Humans ; Illicit Drugs/*blood ; Limit of Detection ; Nanoparticles/chemistry ; Reproducibility of Results ; Spectrum Analysis, Raman/*methods ; Substance Abuse Detection/*methods ; },
abstract = {A novel proximity-dependent isothermal cycle amplification (PDICA) strategy has been proposed and successfully used for the determination of cocaine coupled with surface enhanced Raman scattering (SERS). For enhancing the SERS signal, Raman dye molecules modified bio-barcode DNA and gold nanoparticles (AuNPs) are used to prepare the Raman probes. Magnetic beads (MBs) are used as the carrier of amplification template and signal output products for circumventing the problem of high background induced by excess bio-barcode DNA. In the presence of target molecules, two label-free proximity probes can hybridize with each other and subsequently opens the hairpin connector-probe to perform the PDICA reaction including the target recycling amplification and strand-displacement amplification. As a result, abundant AuNPs Raman probes can be anchored on the surface of MBs and a low detection limit of 0.1 nM for cocaine is obtained. This assay also exhibits an excellent selectivity and has been successfully performed in human serum, which confirms the reliability and practicality of this protocol.},
}
@article {pmid23983642,
year = {2013},
author = {Lin, CY and Pan, TS and Ting, CC and Liang, SS and Huang, SH and Liu, HY and Ko, EC and Wu, CW and Tang, JY and Chen, PH},
title = {Cytochrome p450 metabolism of betel quid-derived compounds: implications for the development of prevention strategies for oral and pharyngeal cancers.},
journal = {TheScientificWorldJournal},
volume = {2013},
number = {},
pages = {618032},
pmid = {23983642},
issn = {1537-744X},
mesh = {Areca/*chemistry ; Carcinogens/toxicity ; Cytochrome P-450 Enzyme System/*metabolism ; Humans ; Mouth Neoplasms/chemically induced/*prevention &amp; control ; Pharyngeal Neoplasms/chemically induced/*prevention &amp; control ; Taiwan ; },
abstract = {Betel quid (BQ) products, with or without tobacco, have been classified by the International Agency for Research on Cancer (IARC) as group I human carcinogens that are associated with an elevated risk of oral potentially malignant disorders (OPMDs) and cancers of the oral cavity and pharynx. There are estimated 600 million BQ users worldwide. In Taiwan alone there are 2 million habitual users (approximately 10% of the population). Oral and pharyngeal cancers result from interactions between genes and environmental factors (BQ exposure). Cytochrome p450 (CYP) families are implicated in the metabolic activation of BQ- and areca nut-specific nitrosamines. In this review, we summarize the current knowledge base regarding CYP genetic variants and related oral disorders. In clinical applications, we focus on cancers of the oral cavity and pharynx and OPMDs associated with CYP gene polymorphisms, including CYP1A1, CYP2A6, CYP2E1, and CYP26B1. Our discussion of CYP polymorphisms provides insight into the importance of screening tests in OPMDs patients for the prevention of oral and pharyngeal cancers. Future studies will establish a strong foundation for the development of chemoprevention strategies, polymorphism-based clinical diagnostic tools (e.g., specific single-nucleotide polymorphism (SNP) "barcodes"), and effective treatments for BQ-related oral disorders.},
}
@article {pmid23978265,
year = {2013},
author = {Tran, TN and Cui, J and Hartman, MR and Peng, S and Funabashi, H and Duan, F and Yang, D and March, JC and Lis, JT and Cui, H and Luo, D},
title = {A universal DNA-based protein detection system.},
journal = {Journal of the American Chemical Society},
volume = {135},
number = {38},
pages = {14008-14011},
pmid = {23978265},
issn = {1520-5126},
support = {DP2 OD007155/OD/NIH HHS/United States ; },
mesh = {DNA/*chemistry ; Fluorescent Dyes ; Horseradish Peroxidase/chemistry ; Immunoglobulin G/*chemistry ; In Situ Hybridization, Fluorescence ; Indicators and Reagents ; *Nanostructures ; Oligonucleotides/chemistry ; Proteins/*analysis/immunology ; Quantum Dots ; },
abstract = {Protein immune detection requires secondary antibodies which must be carefully selected in order to avoid interspecies cross-reactivity, and is therefore restricted by the limited availability of primary/secondary antibody pairs. Here we present a versatile DNA-based protein detection system using a universal adapter to interface between IgG antibodies and DNA-modified reporter molecules. As a demonstration of this capability, we successfully used DNA nano-barcodes, quantum dots, and horseradish peroxidase enzyme to detect multiple proteins using our DNA-based labeling system. Our system not only eliminates secondary antibodies but also serves as a novel method platform for protein detection with modularity, high capacity, and multiplexed capability.},
}
@article {pmid23977122,
year = {2013},
author = {Feng, J and Jiang, D and Shang, H and Dong, M and Wang, G and He, X and Zhao, C and Mao, K},
title = {Barcoding poplars (Populus L.) from western China.},
journal = {PloS one},
volume = {8},
number = {8},
pages = {e71710},
pmid = {23977122},
issn = {1932-6203},
mesh = {China ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; Genetic Loci/genetics ; Genetic Variation ; Plastids/genetics ; Populus/*classification/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND: Populus is an ecologically and economically important genus of trees, but distinguishing between wild species is relatively difficult due to extensive interspecific hybridization and introgression, and the high level of intraspecific morphological variation. The DNA barcoding approach is a potential solution to this problem.<br><br>Here, we tested the discrimination power of five chloroplast barcodes and one nuclear barcode (ITS) among 95 trees that represent 21 Populus species from western China. Among all single barcode candidates, the discrimination power is highest for the nuclear ITS, progressively lower for chloroplast barcodes matK (M), trnG-psbK (G) and psbK-psbI (P), and trnH-psbA (H) and rbcL (R); the discrimination efficiency of the nuclear ITS (I) is also higher than any two-, three-, or even the five-locus combination of chloroplast barcodes. Among the five combinations of a single chloroplast barcode plus the nuclear ITS, H+I and P+I differentiated the highest and lowest portion of species, respectively. The highest discrimination rate for the barcodes or barcode combinations examined here is 55.0% (H+I), and usually discrimination failures occurred among species from sympatric or parapatric areas.<br><br>CONCLUSIONS/SIGNIFICANCE: In this case study, we showed that when discriminating Populus species from western China, the nuclear ITS region represents a more promising barcode than any maternally inherited chloroplast region or combination of chloroplast regions. Meanwhile, combining the ITS region with chloroplast regions may improve the barcoding success rate and assist in detecting recent interspecific hybridizations. Failure to discriminate among several groups of Populus species from sympatric or parapatric areas may have been the result of incomplete lineage sorting, frequent interspecific hybridizations and introgressions. We agree with a previous proposal for constructing a tiered barcoding system in plants, especially for taxonomic groups that have complex evolutionary histories (e.g. Populus).},
}
@article {pmid23973380,
year = {2013},
author = {Šlapeta, J},
title = {Cryptosporidiosis and Cryptosporidium species in animals and humans: a thirty colour rainbow?.},
journal = {International journal for parasitology},
volume = {43},
number = {12-13},
pages = {957-970},
doi = {10.1016/j.ijpara.2013.07.005},
pmid = {23973380},
issn = {1879-0135},
mesh = {Animals ; Cryptosporidiosis/parasitology/transmission/*veterinary ; Cryptosporidium/*classification/genetics ; Genetic Markers ; Humans ; Zoonoses ; },
abstract = {Parasites of the genus Cryptosporidium (Apicomplexa) cause cryptosporidiosis in humans and animals worldwide. The species names used for Cryptosporidium spp. are confusing for parasitologists and even more so for non-specialists. Here, 30 named species of the genus Cryptosporidium are reviewed and proposed as valid. Molecular and experimental evidence suggests that humans and cattle are the hosts for 14 and 13 out of 30 named species, respectively. Two, four and eight named species are considered of major, moderate and minor public health significance, respectively. There are at least nine named species that are shared between humans and cattle. The aim of this review is to outline available species information together with the most commonly used genetic markers enabling the identification of named Cryptosporidium spp. Currently, 28 of 30 named species can be identified using the complete or partial ssrRNA, serving as a retrospective 'barcode'. Currently, the ssrRNA satisfies the implicit assumption that the reference databases used for comparison are sufficiently complete and applicable across the whole genus. However, due to unreliable annotation in public DNA repositories, the reference nucleotide entries and alignment of named Cryptosporidium spp. has been compiled. Despite its known limitations, ssrRNA remains the optimal marker for species identification.},
}
@article {pmid23967453,
year = {2013},
author = {Gugerli, F and Alvarez, N and Tinner, W},
title = {A deep dig––hindsight on Holocene vegetation composition from ancient environmental DNA.},
journal = {Molecular ecology},
volume = {22},
number = {13},
pages = {3433-3436},
doi = {10.1111/mec.12356},
pmid = {23967453},
issn = {1365-294X},
mesh = {Geologic Sediments/*analysis ; Lakes/*analysis ; Plants/*genetics ; Pollen/*chemistry ; },
abstract = {Want a glimpse at past vegetation? Studying pollen and other plant remains, which are preserved for example in lake sediments or mires for thousands of years, allows us to document regional occurrences of plant species over radiocarbon-dated time series. Such vegetation reconstructions derived from optical analyses of fossil samples are inherently incomplete because they only comprise taxa that contribute sufficient amounts of pollen, spores, macrofossil or other evidences. To complement optical analyses for paleoecological inference, molecular markers applied to ancient DNA (aDNA) may help in disclosing information hitherto inaccessible to biologists. Parducci et al. (2013) targeted aDNA from sediment cores of two lakes in the Scandes Mountains with generic primers in a meta-barcoding approach. When compared to palynological records from the same cores, respective taxon lists show remarkable differences in their compositions, but also in quantitative representation and in taxonomic resolution similar to a previous study (Jørgensen et al. 2012). While not free of assumptions that need critical and robust testing, notably the question of possible contamination, this study provides thrilling prospects to improve our knowledge about past vegetation composition, but also other organismic groups, stored as a biological treasure in the ground.},
}
@article {pmid23967149,
year = {2013},
author = {Kirchner, SM and Hiltunen, L and Döring, TF and Virtanen, E and Palohuhta, JP and Valkonen, JP},
title = {Seasonal phenology and species composition of the aphid fauna in a northern crop production area.},
journal = {PloS one},
volume = {8},
number = {8},
pages = {e71030},
pmid = {23967149},
issn = {1932-6203},
mesh = {Animals ; Aphids/*classification/physiology/virology ; *Biodiversity ; Climate ; Cluster Analysis ; *Crops, Agricultural ; Ecological Parameter Monitoring ; Finland ; Flight, Animal ; Geography ; Insect Vectors/classification/physiology/virology ; Plant Diseases/virology ; *Seasons ; },
abstract = {BACKGROUND: The species diversity of aphids and seasonal timing of their flight activity can have significant impacts on crop production, as aphid species differ in their ability to transmit plant viruses and flight timing affects virus epidemiology. The aim of the study was to characterise the species composition and phenology of aphid fauna in Finland in one of the northernmost intensive crop production areas of the world (latitude 64°).<br><br>Flight activity was monitored in four growing seasons (2007-010) using yellow pan traps (YPTs) placed in 4-8 seed potato fields and a Rothamsted suction trap. A total of 58,528 winged aphids were obtained, identified to 83 taxa based on morphology, and 34 species were additionally characterised by DNA barcoding. Seasonal flight activity patterns analysed based on YPT catch fell into three main phenology clusters. Monoecious taxa showed early or middle-season flight activity and belonged to species living on shrubs/trees or herbaceous plants, respectively. Heteroecious taxa occurred over the entire potato growing season (ca. 90 days). Abundance of aphids followed a clear 3-year cycle based on suction trap data covering a decade. Rhopalosiphum padi occurring at the end of the potato growing season was the most abundant species. The flight activity of Aphis fabae, the main vector of Potato virus Y in the region, and Aphis gossypii peaked in the beginning of potato growing season.<br><br>CONCLUSIONS/SIGNIFICANCE: Detailed information was obtained on phenology of a large number aphid species, of which many are agriculturally important pests acting as vectors of plant viruses. Aphis gossypii is known as a pest in greenhouses, but our study shows that it occurs also in the field, even far in the north. The novel information on aphid phenology and ecology has wide implications for prospective pest management, particularly in light of climate change.},
}
@article {pmid23965160,
year = {2013},
author = {Brodin, J and Krishnamoorthy, M and Athreya, G and Fischer, W and Hraber, P and Gleasner, C and Green, L and Korber, B and Leitner, T},
title = {A multiple-alignment based primer design algorithm for genetically highly variable DNA targets.},
journal = {BMC bioinformatics},
volume = {14},
number = {},
pages = {255},
pmid = {23965160},
issn = {1471-2105},
support = {R01 AI087520/AI/NIAID NIH HHS/United States ; AI087520/AI/NIAID NIH HHS/United States ; },
mesh = {*Algorithms ; DNA Primers/*genetics ; HIV Infections/virology ; HIV-1/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Models, Genetic ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA/*methods ; *Software ; },
abstract = {BACKGROUND: Primer design for highly variable DNA sequences is difficult, and experimental success requires attention to many interacting constraints. The advent of next-generation sequencing methods allows the investigation of rare variants otherwise hidden deep in large populations, but requires attention to population diversity and primer localization in relatively conserved regions, in addition to recognized constraints typically considered in primer design.<br><br>RESULTS: Design constraints include degenerate sites to maximize population coverage, matching of melting temperatures, optimizing de novo sequence length, finding optimal bio-barcodes to allow efficient downstream analyses, and minimizing risk of dimerization. To facilitate primer design addressing these and other constraints, we created a novel computer program (PrimerDesign) that automates this complex procedure. We show its powers and limitations and give examples of successful designs for the analysis of HIV-1 populations.<br><br>CONCLUSIONS: PrimerDesign is useful for researchers who want to design DNA primers and probes for analyzing highly variable DNA populations. It can be used to design primers for PCR, RT-PCR, Sanger sequencing, next-generation sequencing, and other experimental protocols targeting highly variable DNA samples.},
}
@article {pmid23962024,
year = {2013},
author = {Wong, KL and But, PP and Shaw, PC},
title = {Evaluation of seven DNA barcodes for differentiating closely related medicinal Gentiana species and their adulterants.},
journal = {Chinese medicine},
volume = {8},
number = {1},
pages = {16},
pmid = {23962024},
issn = {1749-8546},
abstract = {BACKGROUND: Species identification of living organisms by standard DNA sequences has been well-accepted. Consortium for the Barcode of Life (CBOL) recommends chloroplast regions rbcL and matK as the DNA barcodes for the land plants. This study aims to evaluate the feasibility and limitations of rbcL, matK, and 5 other commonly used regions as the DNA barcodes for the medicinal Gentiana and their adulterants, Gentiana. rhodantha and Podophyllum hexandrum.<br><br>METHODS: The species differentiation power of rbcL, matK, nuclear internal transcribed spacer (ITS) and 5S rRNA intergenic spacer, and chloroplast trnH-psbA, trnL-F and rpl36-rps8 intergenic spacers were tested in different medicinal Gentiana, including Gentiana scabra, Gentiana triflora, Gentiana manshurica and Gentiana rigescens, from common adulterants such as Gentiana rhodantha and Podophyllum hexandrum (a toxic herb producing podophyllotoxin).<br><br>RESULTS: All seven tested loci could be used to differentiate medicinal Gentiana species from their adulterants, and to distinguish Guanlongdan from Jianlongdan. In terms of general differentiation powers, rbcL and matK had no significant advantages over the other five loci. Only the 5S rRNA and trnL-F intergenic spacers were able to discriminate the closely related species G. triflora, G. scabra and G. manshurica.<br><br>CONCLUSION: The DNA barcodes rbcL and matK are useful in differentiation of closely related medicinal species of Gentiana, but had no significant advantages over the other five tested loci.},
}
@article {pmid23950998,
year = {2013},
author = {Kidwai, AS and Mushamiri, I and Niemann, GS and Brown, RN and Adkins, JN and Heffron, F},
title = {Diverse secreted effectors are required for Salmonella persistence in a mouse infection model.},
journal = {PloS one},
volume = {8},
number = {8},
pages = {e70753},
pmid = {23950998},
issn = {1932-6203},
support = {R01 AI022933/AI/NIAID NIH HHS/United States ; U01 GM094623/GM/NIGMS NIH HHS/United States ; R01 AI 022933/AI/NIAID NIH HHS/United States ; U01 GM 094623/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; Bacterial Secretion Systems ; Disease Models, Animal ; Genomic Islands/genetics ; Mice ; Protein Transport ; Salmonella Infections, Animal/*microbiology ; Salmonella typhimurium/*genetics/*pathogenicity ; Virulence/genetics ; Virulence Factors/genetics ; },
abstract = {Salmonella enterica serovar Typhimurium causes typhoid-like disease in mice and is a model of typhoid fever in humans. One of the hallmarks of typhoid is persistence, the ability of the bacteria to survive in the host weeks after infection. Virulence factors called effectors facilitate this process by direct transfer to the cytoplasm of infected cells thereby subverting cellular processes. Secretion of effectors to the cell cytoplasm takes place through multiple routes, including two separate type III secretion (T3SS) apparati as well as outer membrane vesicles. The two T3SS are encoded on separate pathogenicity islands, SPI-1 and -2, with SPI-1 more strongly associated with the intestinal phase of infection, and SPI-2 with the systemic phase. Both T3SS are required for persistence, but the effectors required have not been systematically evaluated. In this study, mutations in 48 described effectors were tested for persistence. We replaced each effector with a specific DNA barcode sequence by allelic exchange and co-infected with a wild-type reference to calculate the ratio of wild-type parent to mutant at different times after infection. The competitive index (CI) was determined by quantitative PCR in which primers that correspond to the barcode were used for amplification. Mutations in all but seven effectors reduced persistence demonstrating that most effectors were required. One exception was CigR, a recently discovered effector that is widely conserved throughout enteric bacteria. Deletion of cigR increased lethality, suggesting that it may be an anti-virulence factor. The fact that almost all Salmonella effectors are required for persistence argues against redundant functions. This is different from effector repertoires in other intracellular pathogens such as Legionella.},
}
@article {pmid23950690,
year = {2013},
author = {Fernández-Triana, JL and Cardinal, S and Whitfield, JB and Winnie Hallwachs, and Smith, MA and Janzenr, DH},
title = {A review of the New World species of the parasitoid wasp Iconella (Hymenoptera, Braconidae, Microgastrinae).},
journal = {ZooKeys},
volume = {},
number = {321},
pages = {65-87},
pmid = {23950690},
issn = {1313-2989},
abstract = {The New World species of Iconella (Hymenoptera: Braconidae, Microgastrinae) are revised. Iconella andydeansi Fernández-Triana, sp. n., Iconella canadensis Fernández-Triana, sp. n., and Iconella jayjayrodriguezae Fernández-Triana, sp. n., are described as new. Iconella isolata (Muesebeck, 1955), stat. r., previously considered as a subspecies of Iconella etiellae (Viereck, 1911), is here elevated to species rank. All species have different, well defined geographic distributions and hosts. Taxonomic keys are presented in two formats: traditional dichotomous hardcopy versions and links to electronic interactive versions (software Lucid 3.5). Numerous illustrations, computer-generated descriptions, distributional information, host records (mostly Lepidoptera: Crambidae and Pyralidae), and DNA barcodes (where available) are presented for every species. Phylogenetic analyses of the barcoding region of COI indicate the possibility that Iconella is not monophyletic and that the New World species may not form a monophyletic group; more data is needed to resolve this issue.},
}
@article {pmid23949672,
year = {2012},
author = {Giraldo, CE and Uribe, SI},
title = {Taxonomy of Mechanitis (f.) (Lepidoptera: Nymphalidae) from the west Colombian Andes: an integrative approach.},
journal = {Neotropical entomology},
volume = {41},
number = {6},
pages = {472-484},
pmid = {23949672},
issn = {1678-8052},
mesh = {Altitude ; Animals ; Colombia ; Female ; Lepidoptera/*anatomy &amp; histology/*classification ; Male ; },
abstract = {Species identification in the butterfly genus Mechanitis (F.) (Lepidoptera: Nymphalidae) becomes difficult when it is based only on wing color patterns, a common practice in butterfly taxonomy. Difficulties in Mechanitis taxonomy are related to the widespread mimicry and polymorphism among species belonging to this genus. Species recognition and inventories of Mechanitis genus in geographic areas as the Andean region of Colombia are of particular interest and the use of more than one character for taxonomic identification is desirable. In this study, we included morphological, ecological, and mitochondrial DNA data to identify the occurring species in this region. Species of Mechanitis were studied from ecological, morphological, and molecular perspectives considering host plant identification, oviposition behavior, and life cycles under laboratory conditions. Immature morphology, patterns of wing color, and genital structures of adults were also studied. The genetic barcoding region of the cytochrome oxidase I mitochondrial gene was sequenced and used to verify the limits between species previously defined by the other characters and to validate its usefulness for species delimitation in this particular genus. The integrative approach combining independent datasets successfully allowed species identification as compared to the approach based on a single dataset. Three well-differentiated species were found in the studied region, Mechanitis menapis (Hewitson), Mechanitis polymnia (Linnaeus), and Mechanitis lysimnia (Fabricius). New valuable characters that could improve taxonomic identification in this genus are considered.},
}
@article {pmid23949162,
year = {2012},
author = {Obasi, C and Etienne-Cummings, R and Lehmann, H and Lewin, JS and Asiyanbola, B},
title = {WITHDRAWN: Sponges and incorrect sponge count: Minor contributions to the process of detecting retained foreign bodies.},
journal = {Technology and health care : official journal of the European Society for Engineering and Medicine},
volume = {},
number = {},
pages = {},
doi = {10.3233/THC-2012-0688},
pmid = {23949162},
issn = {1878-7401},
abstract = {Ahead of Print article withdrawn by publisher. Background: Postoperative retained foreign bodies [RFBs] can be a serious event, but they are rare. The x-ray is the current gold standard to detect RFBs. There has been scant research on the process of detection as opposed to the consequence of RFBs. Surgical sponges incorporating automatic data identity capture technology (radiofrequency tags, barcodes) have been proposed to detect RFBs. Because resources in healthcare are scarce, careful consideration needs to be given to developing the right technology in order to maximize the process of RFB elimination. There have been few studies that identify factors contributing to the process of RFB detection. Study design: Our goal was to determine the frequency with which x-rays were ordered to detect abdominal surgery post operative RFBs and the indications for ordering them. We reviewed the Johns Hopkins Hospital's Department of Radiology database to retrospectively study the demographic and radiologic data on patients who underwent exploratory surgery for RFBs following abdominal procedures performed between April 2004 and April 2008. Results: Of the 13,335 portable abdominal x-rays taken during the period, 203 (1.5%) were ordered to assess patients for the presence of an RFB. Of these, 57 (28%) were taken because no RFB count was made (e.g., for emergency procedures), 57 (28%) were taken per procedure or protocol, 51 (25%) were taken because of an incorrect instrument count, and 39 (19%) were taken because of an incorrect sponge count. Of the 203 x-rays, 192 (95%) were negative for RFBs, 11 (5%) were positive or had suspicious findings, and of these 3 (2%) revealed more than 1 RFB. The 11 patients with positive or suspicious findings underwent exploratory procedures immediately during the same operation; of these, 8 (72%) actually had an RFB and 3 (28%) had a negative result at exploration. Conclusion: Multiple pathways lead to the decision to obtain X-rays for RFBs, of which sponges/Incorrect sponge counts make up only one in five. Therefore, technology that focuses on sponges alone may not majorly impact clinical outcome because x-rays will still be required in the majority of cases of suspected high risk.},
}
@article {pmid23946608,
year = {2013},
author = {Wang, GQ and Xu, JT and Xu, GY and Zhang, Y and Li, F and Suo, J},
title = {Predicting a novel pathogenicity island in Helicobacter pylori by genomic barcoding.},
journal = {World journal of gastroenterology},
volume = {19},
number = {30},
pages = {5006-5010},
pmid = {23946608},
issn = {2219-2840},
mesh = {Computational Biology ; *DNA Barcoding, Taxonomic ; DNA, Bacterial/*analysis ; Databases, Genetic ; Escherichia coli/genetics ; *Genome, Bacterial ; *Genomic Islands ; Genotype ; Helicobacter pylori/classification/*genetics/*pathogenicity ; Phenotype ; Virulence/genetics ; },
abstract = {AIM: To apply a new, integrated technique for visualizing bacterial genomes to identify novel pathogenicity islands in Helicobacter pylori (H. pylori).<br><br>METHODS: A genomic barcode imaging method (converting frequency matrices to grey-scale levels) was designed to visually distinguish origin-specific genomic regions in H. pylori. The complete genome sequences of the six H. pylori strains published in the National Center for Biotechnological Information prokaryotic genome database were scanned, and compared to the genome barcodes of Escherichia coli (E. coli) O157:H7 strain EDL933 and a random nucleotide sequence. The following criteria were applied to identify potential pathogenicity islands (PAIs): (1) barcode distance distinct from that of the general background; (2) length greater than 10000 continuous base pairs; and (3) containing genes with known virulence-related functions (as determined by PfamScan and Blast2GO).<br><br>RESULTS: Comparison of the barcode images generated for the 26695, HPAG1, J99, Shi470, G27 and P12 H. pylori genomes with those for the E. coli and random sequence controls revealed that H. pylori genomes contained fewer anomalous regions. Among the H. pylori-specific continuous anomalous regions (longer than 20 kbp in each strain's genome), two fit the criteria for identifying candidate PAIs. The bioinformatic-based functional analyses revealed that one of the two anomalous regions was the known pathogenicity island cag-PAI, this finding also served as proof-of-principle for the utility of the genomic barcoding approach for identifying PAIs, and characterized the other as a novel PAI, which was designated as tfs3-PAI. Furthermore, the cag-PAI and tfs3-PAI harbored genes encoding type IV secretion system proteins and were predicted to have potential for functional synergy.<br><br>CONCLUSION: Genomic barcode imaging represents an effective bioinformatic-based approach for scanning bacterial genomes, such as H. pylori, to identify candidate PAIs.},
}
@article {pmid23933277,
year = {2013},
author = {Chen, X and Liao, B and Song, J and Pang, X and Han, J and Chen, S},
title = {A fast SNP identification and analysis of intraspecific variation in the medicinal Panax species based on DNA barcoding.},
journal = {Gene},
volume = {530},
number = {1},
pages = {39-43},
doi = {10.1016/j.gene.2013.07.097},
pmid = {23933277},
issn = {1879-0038},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; Humans ; Medicine, Chinese Traditional ; Panax/classification/*genetics ; Polymorphism, Single Nucleotide/*genetics ; Species Specificity ; },
abstract = {Medicinal plants of the Panax genus belonging to Araliaceae family are well-known, rare plants used as tonics in traditional Chinese medicine and have been described in the Chinese Pharmacopoeia. Because of the high price and the huge human demand, these commercial products often contain adulterants. In this study, 377 sequences from four species were analyzed. Single nucleotide polymorphisms (SNPs) were detected and patterns of intragenomic variation in internal transcribed spacer 2 (ITS2) from the four Panax species were studied. Intraspecific variations were analyzed based on three typical DNA barcodings (ITS2, matK and psbA-trnH). Results from this study revealed that intraspecific genetic distances in Panax ginseng and Panax quinquefolius were quite low (0-0.002) and the multi-copy ITS2 could be considered a single locus in the genomes of these two species. Five stable SNPs were detected in ITS2 region to identify the Panax medicinal species. Considering the mixed powder of P. ginseng and P. quinquefolius, double peaks could be clearly examined at SNP positions and the height of the peaks could indicate the mixed ratio roughly. Our findings indicate that SNP-based molecular barcodes could be developed as a routine method for the identification of the Panax genus with closely related species and the mixed powder P. ginseng and P. quinquefolius.},
}
@article {pmid23933134,
year = {2013},
author = {Størvold, GL and Landskron, J and Strozynski, M and Arntzen, M&#xd8; and Koehler, CJ and Kalland, ME and Taskén, K and Thiede, B},
title = {Quantitative profiling of tyrosine phosphorylation revealed changes in the activity of the T cell receptor signaling pathway upon cisplatin-induced apoptosis.},
journal = {Journal of proteomics},
volume = {91},
number = {},
pages = {344-357},
doi = {10.1016/j.jprot.2013.07.019},
pmid = {23933134},
issn = {1876-7737},
mesh = {Antineoplastic Agents/chemistry ; *Apoptosis ; Cell Survival ; Cisplatin/*chemistry ; Gene Expression Profiling ; *Gene Expression Regulation, Neoplastic ; Humans ; Immunosuppressive Agents/chemistry ; Jurkat Cells ; Phosphorylation ; Phosphotyrosine/chemistry ; Proteomics ; Receptors, Antigen, T-Cell/*metabolism ; Signal Transduction ; T-Lymphocytes/cytology ; Tyrosine/*chemistry ; p38 Mitogen-Activated Protein Kinases/metabolism ; },
abstract = {UNLABELLED: In order to better understand the cellular responses to the chemotherapeutic drug cisplatin and the mechanisms leading to apoptosis and potential side effects, we performed a SILAC-based quantitative phosphotyrosine analysis of Jurkat T cells exposed to cisplatin. Signaling molecules in the T cell receptor (TCR) pathway were enriched among proteins displaying reduced phosphorylation levels. The results were verified by immunoblotting and/or phospho-flow cytometry for a selected set of proteins, including the tyrosine kinases Lck and Zap70, and downstream targets Itk, Plcγ1 and Erk. In contrast to the effects on the T cell signaling pathways, the dually phosphorylated form of p38α MAPK was increased in treated cells, and activation of this signaling pathway was verified by immunoblot analysis of phosphorylation levels of p38α MAPK and the downstream targets Atf2 and MAPKAPK2. Activation of the p38α MAPK signaling pathway has been suggested to be one of the main mechanisms by which cisplatin induces apoptosis. Our results indicate that cisplatin may reduce the activity of proteins involved in the TCR signaling pathway, which has an important role in regulating proliferation of T cells, and may contribute to explain previous observations where cisplatin has been reported to inhibit proliferation of T cells.<br><br>BIOLOGICAL SIGNIFICANCE: In this study, a quantitative phosphotyrosine analysis was performed to identify changes of the phosphoproteome during exposure of Jurkat T cells by cisplatin. The results of the phosphoproteome analysis were complemented with immunoblotting and temporal phospho-flow analysis. An initial activation of the p38&#x3b1; MAPK signaling pathway was detected at early time points of cisplatin treatment, a response previously suggested to be part of the mechanism by which cisplatin induces apoptosis. Furthermore, reduced phosphorylation levels of proteins involved in signaling downstream of the TCR during apoptosis were found by the phosphotyrosine proteome analysis. Our study can support to elucidate the mechanism behind the previously observed immunosuppressive effect of cisplatin.},
}
@article {pmid23931113,
year = {2013},
author = {Money, NP},
title = {Against the naming of fungi.},
journal = {Fungal biology},
volume = {117},
number = {7-8},
pages = {463-465},
doi = {10.1016/j.funbio.2013.05.007},
pmid = {23931113},
issn = {1878-6146},
mesh = {Classification/methods ; Fungi/*classification/genetics/growth &amp; development/*isolation &amp; purification ; Phylogeny ; *Terminology as Topic ; },
abstract = {The use of molecular bar-coding and consensus on nomenclatural practices has encouraged optimism about the future of fungal taxonomy and systematics. There are, however, profound deficiencies in our understanding of fungal diversity and broader problems with the taxonomic enterprise that deserve greater attention. For 250 years mycologists have tried to reconcile fungal diversity with the Linnean fantasy of a divine order throughout nature that included unambiguous species. This effort has failed and today's taxonomy rests on an unstable philosophical foundation. Rather than persisting with the present endeavour, it may be more fruitful to abandon the notion of fungal species pending further basic research. In the meantime, mycologists should consider tagging collections with digital codes and assigning these operational taxonomic units to higher taxonomic ranks whose objective reality is corroborated by strong phylogenetic evidence.},
}
@article {pmid23930011,
year = {2013},
author = {Mahadani, P and Sharma, GD and Ghosh, SK},
title = {Identification of ethnomedicinal plants (Rauvolfioideae: Apocynaceae) through DNA barcoding from northeast India.},
journal = {Pharmacognosy magazine},
volume = {9},
number = {35},
pages = {255-263},
pmid = {23930011},
issn = {0973-1296},
abstract = {BACKGROUND: DNA barcode-based molecular characterization is in practice for plants, but yet lacks total agreement considering the selection of marker. Plant species of subfamily Rauvolfioideae have long been used as herbal medicine by the majority of tribal people in Northeast (NE) India and at present holds mass effect on the society. Hence, there is an urgent need of correct taxonomic inventorization vis-à-vis species level molecular characterization of important medicinal plants.<br><br>OBJECTIVE: To test the efficiency of matK in species delineation like DNA barcoding in Rauvolfiadae (Apocynaceae).<br><br>MATERIALS AND METHODS: In this study, the core DNA barcode matK and trnH-psbA sequences are examined for differentiation of selected ethnomedicinal plants of Apocynaceae. DNA from young leaves of selected species was isolated, and matK gene (~800 bp) and trnH-psbA spacer (~450 bp) of Chloroplast DNA was amplified for species level identification.<br><br>RESULTS: The ~758 bp matK sequence in comparison to the trnH-psbA showed easy amplification, alignment, and high level of discrimination value among the medicinal Rauvolfioidae species. Intergenic spacer trnH-psbA is also exhibited persistent problem in obtaining constant bidirectional sequences. Partial matK sequences exhibited 3 indels in multiple of 3 at 5 end. Evidently, generated matK sequences are clustered cohesively, with their conspecific Genbank sequences. However, repeat structures with AT-rich regions, possessing indels in multiple of 3, could be utilized as qualitative molecular markers in further studies both at the intra-specific and shallow inter-specific levels like the intergenic spacers of CpDNA.<br><br>CONCLUSION: matK sequence information could help in correct species identification for medicinal plants of Rauvolfioideae.},
}
@article {pmid23929860,
year = {2013},
author = {Yang, CH and Lin, YD and Chuang, LY and Chang, HW},
title = {Evaluation of breast cancer susceptibility using improved genetic algorithms to generate genotype SNP barcodes.},
journal = {IEEE/ACM transactions on computational biology and bioinformatics},
volume = {10},
number = {2},
pages = {361-371},
doi = {10.1109/TCBB.2013.27},
pmid = {23929860},
issn = {1557-9964},
mesh = {*Algorithms ; Biomarkers, Tumor/genetics ; Breast Neoplasms/*genetics ; Computational Biology/*methods ; Databases, Genetic ; Electronic Data Processing ; Female ; Genetic Predisposition to Disease ; Genotype ; Humans ; *Models, Genetic ; Models, Statistical ; Polymorphism, Single Nucleotide ; Risk ; Signal Transduction/genetics ; },
abstract = {Genetic association is a challenging task for the identification and characterization of genes that increase the susceptibility to common complex multifactorial diseases. To fully execute genetic studies of complex diseases, modern geneticists face the challenge of detecting interactions between loci. A genetic algorithm (GA) is developed to detect the association of genotype frequencies of cancer cases and noncancer cases based on statistical analysis. An improved genetic algorithm (IGA) is proposed to improve the reliability of the GA method for high-dimensional SNP-SNP interactions. The strategy offers the top five results to the random population process, in which they guide the GA toward a significant search course. The IGA increases the likelihood of quickly detecting the maximum ratio difference between cancer cases and noncancer cases. The study systematically evaluates the joint effect of 23 SNP combinations of six steroid hormone metabolisms, and signaling-related genes involved in breast carcinogenesis pathways were systematically evaluated, with IGA successfully detecting significant ratio differences between breast cancer cases and noncancer cases. The possible breast cancer risks were subsequently analyzed by odds-ratio (OR) and risk-ratio analysis. The estimated OR of the best SNP barcode is significantly higher than 1 (between 1.15 and 7.01) for specific combinations of two to 13 SNPs. Analysis results support that the IGA provides higher ratio difference values than the GA between breast cancer cases and noncancer cases over 3-SNP to 13-SNP interactions. A more specific SNP-SNP interaction profile for the risk of breast cancer is also provided.},
}
@article {pmid23927075,
year = {2013},
author = {Xiang, L and Song, J and Xin, T and Zhu, Y and Shi, L and Xu, X and Pang, X and Yao, H and Li, W and Chen, S},
title = {DNA barcoding the commercial Chinese caterpillar fungus.},
journal = {FEMS microbiology letters},
volume = {347},
number = {2},
pages = {156-162},
doi = {10.1111/1574-6968.12233},
pmid = {23927075},
issn = {1574-6968},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Fungal/chemistry ; DNA, Ribosomal Spacer/genetics ; Genetic Variation ; Hypocreales/*genetics ; Moths/microbiology ; Phylogeny ; Species Specificity ; },
abstract = {Chinese caterpillar fungus (Ophiocordyceps sinensis) has been widely used as tonic in Asian medicine. Considering its curative effect and high cost, various counterfeit versions of O. sinensis have been introduced and are commercially available. These counterfeits have morphological characteristics that are difficult to distinguish based on morphology alone, thereby causing confusion and threatening its safe use. In this study, internal transcribed spacer (ITS) sequences as a DNA barcode were analyzed and assessed for rapid and accurate identification of 131 O. sinensis samples and 12 common counterfeits and closely related species. Results showed that sufficient ITS sequence differences, also known as 'barcode gaps', existed to distinguish between O. sinensis and counterfeit species. ITS sequence correctly identified 100% of the samples at the species and genus level using the Basic Local Alignment Search Tool 1 and the nearest distance method. Furthermore, O. sinensis, counterfeits, and closely related species can be successfully identified using tree-based methods including maximum parsimony, neighbor-joining, and maximum likelihood analysis. These results indicated that DNA barcoding could be used as a fast and accurate identification method to distinguish O. sinensis from counterfeits and closely related species to ensure its safe use.},
}
@article {pmid23921661,
year = {2013},
author = {Mogno, I and Kwasnieski, JC and Cohen, BA},
title = {Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants.},
journal = {Genome research},
volume = {23},
number = {11},
pages = {1908-1915},
pmid = {23921661},
issn = {1549-5469},
support = {R01 GM092910/GM/NIGMS NIH HHS/United States ; GM092910-02/GM/NIGMS NIH HHS/United States ; },
mesh = {Binding Sites/*genetics ; Cloning, Molecular ; DNA-Binding Proteins/genetics ; Databases, Genetic ; Gene Expression Regulation ; Genes, Reporter ; Genetic Variation ; Models, Molecular ; *Promoter Regions, Genetic ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Thermodynamics ; Transcription Factors/*genetics ; },
abstract = {Gene promoters typically contain multiple transcription factor binding sites (TFBSs), which may vary in affinity for their cognate transcription factors (TFs). One major challenge in studying cis-regulation is to understand how TFBS variants affect gene expression. We studied the in vivo effects of TFBS variants on cis-regulation using synthetic promoters coupled with a thermodynamic model of TF binding. We measured expression driven by each promoter with RNA-seq of transcribed sequence barcodes. This allowed reporter genes to be highly multiplexed and increased our statistical power to detect the effects of TFBS variants. We analyzed the effects of TFBS variants using a thermodynamic framework that models both TF-DNA interactions and TF-TF interactions. We found that this system accurately estimates the in vivo relative affinities of TFBSs and predicts unexpected interactions between several TFBSs. Our results reveal that binding site variants can have complex effects on gene expression due to differences in TFBS affinity for cognate TFs and differences in TFBS specificity for noncognate TFs.},
}
@article {pmid23920794,
year = {2013},
author = {Nakayama, M and Shimokawa, H},
title = {Evaluation of an electrocardiogram on QR code.},
journal = {Studies in health technology and informatics},
volume = {192},
number = {},
pages = {1020},
pmid = {23920794},
issn = {1879-8365},
mesh = {Computer Graphics ; Data Compression/*methods ; Data Display ; Diagnosis, Computer-Assisted/*methods ; Electrocardiography/classification/*methods ; Electronic Data Processing/*methods ; *Electronic Health Records ; Humans ; Information Storage and Retrieval/*methods ; *Mobile Applications ; Software Design ; },
abstract = {An electrocardiogram (ECG) is an indispensable tool to diagnose cardiac diseases, such as ischemic heart disease, myocarditis, arrhythmia, and cardiomyopathy. Since ECG patterns vary depend on patient status, it is also used to monitor patients during treatment and comparison with ECGs with previous results is important for accurate diagnosis. However, the comparison requires connection to ECG data server in a hospital and the availability of data connection among hospitals is limited. To improve the portability and availability of ECG data regardless of server connection, we here introduce conversion of ECG data into 2D barcodes as text data and decode of the QR code for drawing ECG with Google Chart API. Fourteen cardiologists and six general physicians evaluated the system using iPhone and iPad. Overall, they were satisfied with the system in usability and accuracy of decoded ECG compared to the original ECG. This new coding system may be useful in utilizing ECG data irrespective of server connections.},
}
@article {pmid23920610,
year = {2013},
author = {Samson, LL and Pape-Haugaard, LB and Søgaard, M and Schønheyder, HC and Hejlesen, OK},
title = {Exploring end users' system requirements for a handheld computer supporting both sepsis test workflow and current IT solutions.},
journal = {Studies in health technology and informatics},
volume = {192},
number = {},
pages = {524-528},
pmid = {23920610},
issn = {1879-8365},
mesh = {*Attitude of Health Personnel ; Computers, Handheld ; Denmark ; Humans ; Medical Informatics ; *Medical Order Entry Systems ; *Needs Assessment ; Norway ; Sepsis/*diagnosis/*therapy ; Technology Assessment, Biomedical/methods ; Telemedicine/*instrumentation/methods ; User-Computer Interface ; *Workflow ; },
abstract = {Sepsis is a systemic response associated with very high mortality. Early initiation of the correct antimicrobial therapy remains a cornerstone in the treatment of sepsis. Currently, a new microbiological test is under development, which aims to detect major, prevalent pathogens in positive blood cultures within an hour. Concurrently, a tablet-based data entry and reporting system will be developed to facilitate the workflow of the test. This study investigated the system requirements for the tablet-based data entry and reporting system in order to support the clinical workflow. By observing the workflow of the blood culture analysis and through interviews with medical laboratory technicians, four main system requirements were identified. The system requirements are; the ability to receive and send data to the laboratory information system, support for the use of barcodes, the ability to access a browser based instruction system, and communication of results between medical laboratory technicians and physicians. These system requirements will be used as a basis in the future development of the tablet-based data entry and reporting system.},
}
@article {pmid23920054,
year = {2013},
author = {Guardone, L and Deplazes, P and Macchioni, F and Magi, M and Mathis, A},
title = {Ribosomal and mitochondrial DNA analysis of Trichuridae nematodes of carnivores and small mammals.},
journal = {Veterinary parasitology},
volume = {197},
number = {1-2},
pages = {364-369},
doi = {10.1016/j.vetpar.2013.06.022},
pmid = {23920054},
issn = {1873-2550},
mesh = {Animals ; DNA, Helminth/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/*genetics ; Mammals/*parasitology ; Nematoda/*classification ; Nematode Infections/parasitology/*veterinary ; Phylogeny ; RNA, Helminth/genetics ; RNA, Ribosomal, 18S/*genetics ; Species Specificity ; },
abstract = {Several species of Trichuridae nematodes can infect dogs, cats and wild mammals. The diagnosis of these infections relies on the microscopic identification of eggs which are characterized by a similar "lemon" shape and polar plugs in all Trichuridae. Thus, morphological diagnosis to species level is challenging. The use of biomolecular diagnostic methods is desirable but very little genetic data are known from Trichuridae of carnivores and small mammals. The aim of this work was to genetically characterize several species of Trichuridae that can affect dogs, cats and wild mammals, as a basis to develop molecular diagnostic tests. Specimens (adult worms or eggs) of Eucoleus aerophilus (syn. Capillaria aerophila), Eucoleus boehmi (syn. Capillaria boehmi), Pearsonema plica (syn. Capillaria plica), Aonchotheca putorii (syn. Capillaria putorii), Calodium hepaticum (syn. Capillaria hepatica), Calodium splenaecum (syn. Capillaria splenaeca) and Trichuris vulpis were obtained from carcasses of red foxes, feces of dogs, the liver of a vole and from the spleen of Crocidura sp. Parts of the small subunit rRNA (18S rRNA) gene and of the mitochondrial cytochrome c oxidase subunit I (cox 1 mtDNA) gene were amplified from the above mentioned nematodes, yielding the first 18S rRNA gene sequences of all the capillariid nematodes and the first cox 1 mtDNA sequences of E. boehmi, P. plica, C. hepaticum, A. putorii and T. vulpis. The 18S rRNA gene is highly conserved among the different species and not suitable as a target for specific diagnostic oligonucleotides. However, these sequences contribute to a better understanding of the complex taxonomic relations among Trichuridae. Indeed, a dendrogram based on the 18S rRNA gene locus supports the latest taxonomic revision. Interspecies divergence was much higher at the cox 1 mtDNA gene locus, rendering it suitable for DNA barcoding and particularly valuable in resolving closely related species. Furthermore, the mitochondrial genetic markers defined in the present study are useful to develop Trichuridae species-specific primers.},
}
@article {pmid23919608,
year = {2013},
author = {Ergunay, K and Gunay, F and Oter, K and Kasap, OE and Orsten, S and Akkutay, AZ and Erdem, H and Ozkul, A and Alten, B},
title = {Arboviral surveillance of field-collected mosquitoes reveals circulation of West Nile virus lineage 1 strains in Eastern Thrace, Turkey.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {13},
number = {10},
pages = {744-752},
doi = {10.1089/vbz.2012.1288},
pmid = {23919608},
issn = {1557-7759},
mesh = {Animals ; Arboviruses/genetics/*isolation &amp; purification ; Base Sequence ; Cross-Sectional Studies ; Culicidae/*virology ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Epidemiological Monitoring ; Flavivirus/genetics/*isolation &amp; purification ; Genetic Variation ; Geography ; Insect Vectors/*virology ; Molecular Sequence Data ; Phlebovirus/genetics/*isolation &amp; purification ; Pilot Projects ; Sequence Alignment ; Sequence Analysis, RNA ; Species Specificity ; Turkey/epidemiology ; West Nile Fever/*epidemiology/transmission/virology ; West Nile virus/genetics/*isolation &amp; purification ; },
abstract = {INTRODUCTION: Arbovirus screening in invertebrate vectors is an important component of the vector-borne disease surveillance programs. Turkey has been shown to harbor medically important mosquito-borne arboviruses such as West Nile Virus (WNV). However, limited information about infections in vectors are currently available. This study was performed to provide preliminary data from Eastern Thrace region, Turkey, where no arbovirus vector surveillance has previously been performed.<br><br>MATERIALS AND METHODS: Mosquito sampling was undertaken at 23 sites in Edirne province during July, 2012. All specimens were identified morphologically, and selected individuals were subjected to DNA barcoding via cytochrome c oxidase I (COI) sequencing. Consensus PCR for Flavivirus, Alphavirus, and Phlebovirus genera and WNV-specific nested and real-time reverse transcription PCR were employed for mosquito pool screening and/or confirmation. Viral sequences detected in pools were characterized via sequencing.<br><br>RESULTS: A total of 9261 mosquitoes were captured and distributed into 232 pools from the following species: Ochlerotatus caspius (90.9%), Culex pipiens sensu lato (s.l.) (4.7%), Anopheles pseudopictus (3%), and Anopheles maculipennis s.l. (1.3%). Specimens morphologically classified as Cx. pipiens s.l. were identified as Cx. pipiens pipiens via barcoding. Thirty-seven mosquito pools (15.9%) were positive in pan-flavivirus and WNV-specific assays. Viral sequences in positive pools were characterized as WNV lineage 1 clade 1a and demonstrated 1-4% divergence. No flavivirus sequences other than WNV were detected in the mosquito pools. WNV infection rates in Oc. caspius and Cx. pipiens s.l. pools were 15.6% and 36.3%, respectively. Comparison of current and previously identified WNV sequences from Turkey revealed 94.00-96.34% similarity.<br><br>DISCUSSION: WNV RNA was identified for the first time in Cx. pipiens s.l. and Oc. caspius mosquitoes in Eastern Thrace, Turkey. Our findings indicate the circulation of WNV lineage 1 strains in potential vector species and provide an epidemiological link between WNV activity in mosquitoes and vertebrate infections.},
}
@article {pmid23919569,
year = {2013},
author = {Carew, ME and Pettigrove, VJ and Metzeling, L and Hoffmann, AA},
title = {Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species.},
journal = {Frontiers in zoology},
volume = {10},
number = {1},
pages = {45},
pmid = {23919569},
issn = {1742-9994},
abstract = {INTRODUCTION: Invertebrate communities are central to many environmental monitoring programs. In freshwater ecosystems, aquatic macroinvertebrates are collected, identified and then used to infer ecosystem condition. Yet the key step of species identification is often not taken, as it requires a high level of taxonomic expertise, which is lacking in most organizations, or species cannot be identified as they are morphologically cryptic or represent little known groups. Identifying species using DNA sequences can overcome many of these issues; with the power of next generation sequencing (NGS), using DNA sequences for routine monitoring becomes feasible.<br><br>RESULTS: In this study, we test if NGS can be used to identify species from field-collected samples in an important bioindicator group, the Chironomidae. We show that Cytochrome oxidase I (COI) and Cytochrome B (CytB) sequences provide accurate DNA barcodes for chironomid species. We then develop a NGS analysis pipeline to identifying species using megablast searches of high quality sequences generated using 454 pyrosequencing against comprehensive reference libraries of Sanger-sequenced voucher specimens. We find that 454 generated COI sequences successfully identified up to 96% of species in samples, but this increased up to 99% when combined with CytB sequences. Accurate identification depends on having at least five sequences for a species; below this level species not expected in samples were detected. Incorrect incorporation of some multiplex identifiers (MID's) used to tag samples was a likely cause, and most errors could be detected when using MID tags on forward and reverse primers. We also found a strong quantitative relationship between the number of 454 sequences and individuals showing that it may be possible to estimate the abundance of species from 454 pyrosequencing data.<br><br>CONCLUSIONS: Next generation sequencing using two genes was successful for identifying chironomid species. However, when detecting species from 454 pyrosequencing data sets it was critical to include known individuals for quality control and to establish thresholds for detecting species. The NGS approach developed here can lead to routine species-level diagnostic monitoring of aquatic ecosystems.},
}
@article {pmid23919425,
year = {2014},
author = {Jordal, BH and Kambestad, M},
title = {DNA barcoding of bark and ambrosia beetles reveals excessive NUMTs and consistent east-west divergence across Palearctic forests.},
journal = {Molecular ecology resources},
volume = {14},
number = {1},
pages = {7-17},
doi = {10.1111/1755-0998.12150},
pmid = {23919425},
issn = {1755-0998},
mesh = {Ambrosia/*parasitology ; Animals ; Arctic Regions ; *Biodiversity ; Cluster Analysis ; Coleoptera/*classification/*genetics ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/genetics ; Molecular Sequence Data ; North America ; *Phylogeography ; Sequence Analysis, DNA ; Trees ; },
abstract = {A comprehensive DNA barcoding library is very useful for rapid identification and detection of invasive pest species. We tested the performance of species identification in the economically most damaging group of wood-boring insects - the bark and ambrosia beetles - with particular focus on broad geographical sampling across the boreal Palearctic forests. Neighbour-joining and Bayesian analyses of cytochrome oxidase I (COI) sequences from 151 species in 40 genera revealed high congruence between morphology-based identification and sequence clusters. Inconsistencies with morphological identifications included the discovery of a likely cryptic Nearctic species of Dryocoetes autographus, the possible hybrid origin of shared mitochondrial haplotypes in Pityophthorus micrographus and P. pityographus, and a possible paraphyletic Xyleborinus saxeseni. The first record of Orthotomicus suturalis in North America was confirmed by DNA barcoding. The mitochondrial data also revealed consistent divergence across the Palearctic or Holarctic, confirmed in part by data from the large ribosomal subunit (28S). Some populations had considerable variation in the mitochondrial barcoding marker, but were invariant in the nuclear ribosomal marker. These findings must be viewed in light of the high number of nuclear insertions of mitochondrial DNA (NUMTs) detected in eight bark beetle species, suggesting the possible presence of additional cryptic NUMTs. The occurrence of paralogous COI copies, hybridization or cryptic speciation demands a stronger focus on data quality assessment in the construction of DNA barcoding databases.},
}
@article {pmid23919390,
year = {2013},
author = {Elías-Gutiérrez, M and León-Regagnon, V},
title = {DNA barcoding in Mexico: an introduction.},
journal = {Molecular ecology resources},
volume = {13},
number = {6},
pages = {1093-1096},
doi = {10.1111/1755-0998.12149},
pmid = {23919390},
issn = {1755-0998},
mesh = {Biodiversity ; Classification/methods ; DNA Barcoding, Taxonomic/*trends ; *Databases, Nucleic Acid ; Mexico ; Species Specificity ; },
abstract = {DNA barcoding has become an important current scientific trend to the understanding of the world biodiversity. In the case of mega-diverse hot spots like Mexico, this technique represents an important tool for taxonomists, allowing them to concentrate in highlighted species by the barcodes instead of analyzing entire sets of specimens. This tendency resulted in the creation of a national network named Mexican Barcode of Life (MEXBOL) which main goals are to train students, and to promote the interaction and collective work among researchers interested in this topic. As a result, the number of records in the Barcode of Life Database (BOLD) for some groups, such as the Mammalia, Actinopterygii, Polychaeta, Branchiopoda, Ostracoda, Maxillopoda, Nematoda, Pinophyta, Ascomycota and Basidiomycota place Mexico among the top ten countries in the generation of these data. This special number presents only few of the many interesting findings in this region of the world, after the use of this technique and its integration with other methodologies.},
}
@article {pmid23919139,
year = {2013},
author = {Kerr, KC and Dove, CJ},
title = {Delimiting shades of gray: phylogeography of the Northern Fulmar, Fulmarus glacialis.},
journal = {Ecology and evolution},
volume = {3},
number = {7},
pages = {1915-1930},
pmid = {23919139},
issn = {2045-7758},
abstract = {The Northern Fulmar (Fulmarus glacialis) is a common tube-nosed seabird with a disjunct Holarctic range. Taxonomic divisions within the Northern Fulmar have historically been muddled by geographical variation notably including highly polymorphic plumage. Recent molecular analyses (i.e., DNA barcoding) have suggested that genetic divergence between Atlantic and Pacific populations could be on par with those typically observed between species. We employ a multigene phylogenetic analysis to better explore the level of genetic divergence between these populations and to test an old hypothesis on the origin of the modern distribution of color morphs across their range. Additionally, we test whether mutations in the melanocortin-1 receptor gene (MC1R) are associated with dark plumage in the Northern Fulmar. We confirmed that mitochondrial lineages in the Atlantic and Pacific populations are highly divergent, but nuclear markers revealed incomplete lineage sorting. Genetic divergence between these populations is consistent with that observed between many species of Procellariiformes and we recommend elevating these two forms to separate species. We also find that MC1R variation is not associated with color morph but rather is better explained by geographical divergence.},
}
@article {pmid23918170,
year = {2014},
author = {Zivanovic, N and Jacobs, A and Bodenmiller, B},
title = {A practical guide to multiplexed mass cytometry.},
journal = {Current topics in microbiology and immunology},
volume = {377},
number = {},
pages = {95-109},
doi = {10.1007/82_2013_335},
pmid = {23918170},
issn = {0070-217X},
mesh = {Animals ; Cells/chemistry/*cytology ; Flow Cytometry/*methods ; Humans ; Mass Spectrometry/*methods ; Metals/chemistry ; Single-Cell Analysis/*methods ; Staining and Labeling/*methods ; },
abstract = {Recent advances in inductively coupled plasma mass spectrometry (ICP-MS) as applied in mass cytometry, enabled its broad applicability to life science research. Mass cytometry enables the high-dimensional characterization of cellular systems by simultaneously measuring dozens of metal isotope reporter labeled antibodies bound to cell components. With the ability to simultaneously interrogate an unprecedented number of molecular components on a per cell basis, it offers the possibility to gain better understanding of single cell biology in heterogeneous samples. To upscale this single cell information to screening approaches by mass cytometry, a cell-based multiplexing technique, called mass-tag cellular barcoding (MCB), was developed. MCB enables the simultaneous analysis of multiple cell samples by using n metal ion tags to multiplex up to 2 (n) samples. Different mass tag combinations are used to label individual cell samples with a unique mass barcode that allows multiple samples to be combined and immunostained together for a single analysis on the mass cytometer. Taken together, MCB enables increased sample throughput, reduces antibody consumption, and increases the overall data quality. In this chapter, we describe the MCB to array the samples in a 96-well format that allows for medium-scale profiling/screening experiments to be run on a standard mass cytometer.},
}
@article {pmid23915781,
year = {2013},
author = {Lima, L and Espinosa-Álvarez, O and Hamilton, PB and Neves, L and Takata, CS and Campaner, M and Attias, M and de Souza, W and Camargo, EP and Teixeira, MM},
title = {Trypanosoma livingstonei: a new species from African bats supports the bat seeding hypothesis for the Trypanosoma cruzi clade.},
journal = {Parasites &amp; vectors},
volume = {6},
number = {1},
pages = {221},
pmid = {23915781},
issn = {1756-3305},
mesh = {Animals ; Chiroptera/*parasitology ; DNA, Protozoan/genetics ; Disease Reservoirs/*parasitology ; Humans ; Mice ; Mice, Inbred BALB C ; Mozambique ; Phylogeny ; Protozoan Proteins/genetics ; RNA, Ribosomal/genetics ; Trypanosoma cruzi/*classification/genetics/*isolation &amp; purification/physiology ; Trypanosomiasis/*parasitology ; },
abstract = {BACKGROUND: Bat trypanosomes have been implicated in the evolutionary history of the T. cruzi clade, which comprises species from a wide geographic and host range in South America, Africa and Europe, including bat-restricted species and the generalist agents of human American trypanosomosis T. cruzi and T. rangeli.<br><br>METHODS: Trypanosomes from bats (Rhinolophus landeri and Hipposideros caffer) captured in Mozambique, southeast Africa, were isolated by hemoculture. Barcoding was carried out through the V7V8 region of Small Subunit (SSU) rRNA and Fluorescent Fragment Length barcoding (FFLB). Phylogenetic inferences were based on SSU rRNA, glyceraldehyde phosphate dehydrogenase (gGAPDH) and Spliced Leader (SL) genes. Morphological characterization included light, scanning and transmission electron microscopy.<br><br>RESULTS: New trypanosomes from bats clustered together forming a clade basal to a larger assemblage called the T. cruzi clade. Barcoding, phylogenetic analyses and genetic distances based on SSU rRNA and gGAPDH supported these trypanosomes as a new species, which we named Trypanosoma livingstonei n. sp. The large and highly polymorphic SL gene repeats of this species showed a copy of the 5S ribosomal RNA into the intergenic region. Unique morphological (large and broad blood trypomastigotes compatible to species of the subgenus Megatrypanum and cultures showing highly pleomorphic epimastigotes and long and slender trypomastigotes) and ultrastructural (cytostome and reservosomes) features and growth behaviour (when co-cultivated with HeLa cells at 37&#xb0;C differentiated into trypomastigotes resembling the blood forms and do not invaded the cells) complemented the description of this species.<br><br>CONCLUSION: Phylogenetic inferences supported the hypothesis that Trypanosoma livingstonei n. sp. diverged from a common ancestral bat trypanosome that evolved exclusively in Chiroptera or switched at independent opportunities to mammals of several orders forming the clade T. cruzi, hence, providing further support for the bat seeding hypothesis to explain the origin of T. cruzi and T. rangeli.},
}
@article {pmid23910579,
year = {2013},
author = {Ji, Y and Ashton, L and Pedley, SM and Edwards, DP and Tang, Y and Nakamura, A and Kitching, R and Dolman, PM and Woodcock, P and Edwards, FA and Larsen, TH and Hsu, WW and Benedick, S and Hamer, KC and Wilcove, DS and Bruce, C and Wang, X and Levi, T and Lott, M and Emerson, BC and Yu, DW},
title = {Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding.},
journal = {Ecology letters},
volume = {16},
number = {10},
pages = {1245-1257},
doi = {10.1111/ele.12162},
pmid = {23910579},
issn = {1461-0248},
mesh = {Animals ; Arthropods/physiology ; *Biodiversity ; Computational Biology ; Ecology/*methods ; *Electronic Data Processing ; Environmental Monitoring/*methods ; },
abstract = {To manage and conserve biodiversity, one must know what is being lost, where, and why, as well as which remedies are likely to be most effective. Metabarcoding technology can characterise the species compositions of mass samples of eukaryotes or of environmental DNA. Here, we validate metabarcoding by testing it against three high-quality standard data sets that were collected in Malaysia (tropical), China (subtropical) and the United Kingdom (temperate) and that comprised 55,813 arthropod and bird specimens identified to species level with the expenditure of 2,505 person-hours of taxonomic expertise. The metabarcode and standard data sets exhibit statistically correlated alpha- and beta-diversities, and the two data sets produce similar policy conclusions for two conservation applications: restoration ecology and systematic conservation planning. Compared with standard biodiversity data sets, metabarcoded samples are taxonomically more comprehensive, many times quicker to produce, less reliant on taxonomic expertise and auditable by third parties, which is essential for dispute resolution.},
}
@article {pmid23909138,
year = {2013},
author = {Lee, SR and Jeon, CS and Hwang, I and Chung, TD and Kim, HC},
title = {Simultaneous detection of SERS and fluorescence using a single excitation for microbead-based analysis.},
journal = {Journal of biomedical nanotechnology},
volume = {9},
number = {7},
pages = {1241-1244},
doi = {10.1166/jbn.2013.1517},
pmid = {23909138},
issn = {1550-7033},
mesh = {Microspheres ; Molecular Imaging/*methods ; *Molecular Probe Techniques ; Silver/*analysis/*chemistry ; Spectrometry, Fluorescence/*methods ; Spectrum Analysis, Raman/*methods ; },
abstract = {We demonstrate simultaneous detection of surface-enhanced Raman scattering (SERS) and fluorescence signals from a silver microbead. For the dual signal generation, silver microbeads with a diameter of 15 microm were functionalized with benzenethiol (BT) as a Raman tag and a cardiac troponin I (cTnI) antibody on their surface. SERS and fluorescence signals were obtained using a single argon laser source with 488 nm wavelength. The SERS signals from Raman tag can be used as identification indices for decoding a particular microbead, while the fluorescence signals provide the information about molecular interactions with a specific biomarker. With simultaneous detection of SERS and fluorescence signals using single excitation on the functionalized microbeads, we successfully showed the possibility of a simple barcoding strategy for multiplex analysis using suspension arrays.},
}
@article {pmid23902257,
year = {2013},
author = {Ng'endo, RN and Osiemo, ZB and Brandl, R},
title = {DNA barcodes for species identification in the hyperdiverse ant genus Pheidole (Formicidae: Myrmicinae).},
journal = {Journal of insect science (Online)},
volume = {13},
number = {},
pages = {27},
pmid = {23902257},
issn = {1536-2442},
mesh = {Animals ; Ants/*classification/genetics ; Brazil ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; },
abstract = {DNA sequencing is increasingly being used to assist in species identification in order to overcome taxonomic impediment. However, few studies attempt to compare the results of these molecular studies with a more traditional species delineation approach based on morphological characters. Mitochondrial DNA Cytochrome oxidase subunit 1 (CO1) gene was sequenced, measuring 636 base pairs, from 47 ants of the genus Pheidole (Formicidae: Myrmicinae) collected in the Brazilian Atlantic Forest to test whether the morphology-based assignment of individuals into species is supported by DNA-based species delimitation. Twenty morphospecies were identified, whereas the barcoding analysis identified 19 Molecular Operational Taxonomic Units (MOTUs). Fifteen out of the 19 DNA-based clusters allocated, using sequence divergence thresholds of 2% and 3%, matched with morphospecies. Both thresholds yielded the same number of MOTUs. Only one MOTU was successfully identified to species level using the CO1 sequences of Pheidole species already in the Genbank. The average pairwise sequence divergence for all 47 sequences was 19%, ranging between 0-25%. In some cases, however, morphology and molecular based methods differed in their assignment of individuals to morphospecies or MOTUs. The occurrence of distinct mitochondrial lineages within morphological species highlights groups for further detailed genetic and morphological studies, and therefore a pluralistic approach using several methods to understand the taxonomy of difficult lineages is advocated.},
}
@article {pmid23895393,
year = {2014},
author = {Sri Kumaran, N and Bragadeeswaran, S and Meenakshi, VK},
title = {Mitochondrial cytochrome oxidase I (COI) DNA sequencing of the ascidians Didemnum granulatum (JQ013198) and D. psammathodes (JN624758).},
journal = {Mitochondrial DNA},
volume = {25},
number = {2},
pages = {131-134},
doi = {10.3109/19401736.2013.779263},
pmid = {23895393},
issn = {1940-1744},
mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Genome, Mitochondrial ; Molecular Sequence Data ; Phylogeny ; Reproducibility of Results ; Sequence Analysis, DNA ; Species Specificity ; Urochordata/*genetics ; },
abstract = {Two colonial ascidians Didemnum granulatum and D. psammathodes were collected from Tuticorin coastal waters. These ascidians were sequenced at 603 and 576 bp region of the mitochondrial cytochrome oxidase subunit I gene (COI) for phylogenetic analysis. Barcode sequences were extracted via FASTA format from NCBI. The genetic distances of submitted DNA sequences were compared with related ascidian species. Didemnum granulatum (JQ013198) sequence shows maximum identical 99% with D. vexillum. Didemnum psammathodes (JN624758) sequence submitted at present shows maximum identical 100% with another D. psammathodes sequence which was already submitted in NCBI. The sequence also shows maximum identical 90-89% with D. vexillum. From the present study it is concluded that precise and accurate identification of ascidians could be performed using the barcode sequences of the mitochondrial DNA (in the COI gene).},
}
@article {pmid23892412,
year = {2013},
author = {Subirana, L and Péquin, B and Michely, S and Escande, ML and Meilland, J and Derelle, E and Marin, B and Piganeau, G and Desdevises, Y and Moreau, H and Grimsley, NH},
title = {Morphology, genome plasticity, and phylogeny in the genus ostreococcus reveal a cryptic species, O. mediterraneus sp. nov. (Mamiellales, Mamiellophyceae).},
journal = {Protist},
volume = {164},
number = {5},
pages = {643-659},
doi = {10.1016/j.protis.2013.06.002},
pmid = {23892412},
issn = {1618-0941},
mesh = {Base Sequence ; Chlorophyta/chemistry/*classification/genetics/*growth &amp; development ; DNA, Ribosomal Spacer/chemistry/genetics ; Genetic Variation ; *Genome ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Phylogeny ; Seawater/parasitology ; },
abstract = {Coastal marine waters in many regions worldwide support abundant populations of extremely small (1-3 μm diameter) unicellular eukaryotic green algae, dominant taxa including several species in the class Mamiellophyceae. Their diminutive size conceals surprising levels of genetic diversity and defies classical species' descriptions. We present a detailed analysis within the genus Ostreococcus and show that morphological characteristics cannot be used to describe diversity within this group. Karyotypic analyses of the best-characterized species O. tauri show it to carry two chromosomes that vary in size between individual clonal lines, probably an evolutionarily ancient feature that emerged before species' divergences within the Mamiellales. By using a culturing technique specifically adapted to members of the genus Ostreococcus, we purified >30 clonal lines of a new species, Ostreococcus mediterraneus sp. nov., previously known as Ostreococcus clade D, that has been overlooked in several studies based on PCR-amplification of genetic markers from environment-extracted DNA. Phylogenetic analyses of the S-adenosylmethionine synthetase gene, and of the complete small subunit ribosomal RNA gene, including detailed comparisons of predicted ITS2 (internal transcribed spacer 2) secondary structures, clearly support that this is a separate species. In addition, karyotypic analyses reveal that the chromosomal location of its ribosomal RNA gene cluster differs from other Ostreococcus clades.},
}
@article {pmid23891950,
year = {2013},
author = {Bourguignon, T and Šobotník, J and Hanus, R and Krasulová, J and Vrkoslav, V and Cvačka, J and Roisin, Y},
title = {Delineating species boundaries using an iterative taxonomic approach: the case of soldierless termites (Isoptera, Termitidae, Apicotermitinae).},
journal = {Molecular phylogenetics and evolution},
volume = {69},
number = {3},
pages = {694-703},
doi = {10.1016/j.ympev.2013.07.007},
pmid = {23891950},
issn = {1095-9513},
mesh = {Animals ; Classification/*methods ; DNA Barcoding, Taxonomic ; French Guiana ; Gas Chromatography-Mass Spectrometry ; *Genetic Speciation ; Hydrocarbons/chemistry ; Isoptera/anatomy &amp; histology/chemistry/*classification/genetics ; *Phylogeny ; Species Specificity ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {Species boundaries are traditionally inferred using morphological characters, although morphology sometimes fails to correctly delineate species. To overcome this limitation, researchers have widely taken advantage of alternative methods such as DNA barcoding or analysis of cuticular hydrocarbons (CHs) profiles, but rarely use them simultaneously in an iterative taxonomic approach. Here, we follow such an approach using morphology, DNA barcoding and CHs profiles to precisely discriminate species of soldierless termites, a diversified clade constituting about one-third of the Neotropical termite species richness, but poorly resolved taxonomically due to the paucity of useful characters. We sampled soldierless termites in various forest types of the Nouragues Nature Reserve, French Guiana. Our results show that morphological species determination generally matches DNA barcoding, which only suggests the existence of three cryptic species in the 31 morphological species. Among them, Longustitermes manni is the only species whose splitting is corroborated by ecological data, other widely distributed species being supported by DNA barcoding. On the contrary, although CHs profiles provide a certain taxonomic signal, they often suggest inconsistent groupings which are not supported by other methods. Overall, our data support DNA barcoding and morphology as two efficient methods to distinguish soldierless termite species.},
}
@article {pmid23886615,
year = {2014},
author = {Ramírez, JD and Sánchez, LV and Bautista, DC and Corredor, AF and Flórez, AC and Stensvold, CR},
title = {Blastocystis subtypes detected in humans and animals from Colombia.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {22},
number = {},
pages = {223-228},
doi = {10.1016/j.meegid.2013.07.020},
pmid = {23886615},
issn = {1567-7257},
mesh = {Animals ; Blastocystis/*classification/genetics/*isolation &amp; purification ; Blastocystis Infections/epidemiology/*parasitology/veterinary ; Cattle ; Colombia/epidemiology ; DNA, Bacterial/analysis/genetics ; Dogs ; Humans ; Molecular Epidemiology ; Phylogeny ; Prevalence ; Rats ; },
abstract = {Blastocystis is a common enteric protist colonizing probably more than 1 billion people along with a large variety of non-human hosts. This protist has been linked to symptoms and diseases such as abdominal pain, constipation, diarrhea, flatulence and irritable bowel syndrome (IBS). Remarkable genetic diversity has been observed, leading to the subdivision of the genus into multiple subtypes (ST), some of which are exclusively found in non-human hosts. The aim of this study was to determine the distribution of Blastocystis STs in different Colombian hosts. We obtained fecal samples positive for Blastocystis by microscopy from 277 humans, 52 birds, and 117 mammals (25 cattle, 40 opossums, 40 dogs, 10 rats and 2 howler monkeys). The samples were submitted to DNA extraction, PCR and sequencing using primers targeting the small subunit rRNA gene, and ST identification was performed according to DNA barcoding. We observed the occurrence of ST1 (34%) and ST2 (23%) and lower proportions of STs 3 (11.4%), 4 (0.8%), 6 (19.8%) and 8 (10.5%). Domesticated mammals shared the same STs as those usually seen in humans (ST1, ST2, ST3), while birds and marsupials had STs, which are usually rare in humans (ST6, ST8). Further studies implementing high-resolution molecular markers are necessary to understand the phylodynamics of Blastocystis transmission and the role of this stramenopile in health and disease in Colombian populations, and to expand on the phylogeographic differences observed so far with a view to exploring and understanding host-parasite co-evolution.},
}
@article {pmid23885897,
year = {2014},
author = {Reyes-Prieto, M and Oceguera-Figueroa, A and Snell, S and Negredo, A and Barba, E and Fernández, L and Moya, A and Latorre, A},
title = {DNA barcodes reveal the presence of the introduced freshwater leech Helobdella europaea in Spain.},
journal = {Mitochondrial DNA},
volume = {25},
number = {5},
pages = {387-393},
doi = {10.3109/19401736.2013.809426},
pmid = {23885897},
issn = {1940-1744},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Fresh Water ; Introduced Species ; Leeches/*classification/*genetics ; Phylogeography ; Spain ; },
abstract = {Abstract We report the finding of the freshwater leech Helobdella europaea in Spain for the first time. Three leech specimens were found attached to the European pond turtle Emys orbicularis. Helobdella europaea is not a blood feeder and, like all members of the genus, feeds on the hemolymph of aquatic invertebrates including snails and worms. Despite the fact that the original geographical distribution or source population of this species is unknown, the close relationship between H. europaea and leeches of the "triserialis" series (sensu Sawyer, 1986) suggests a New World origin. Given its ability to invade and persist in new environments, this leech has been described as a new species by local taxonomists resulting in some nomenclatural problems. The presence of this introduced organism in Spain may represent serious obstacles to the current efforts to preserve endemic fauna and the potential negative impacts of this species in European environments should be investigated.},
}
@article {pmid23884864,
year = {2013},
author = {López-Quintero, CA and Atanasova, L and Franco-Molano, AE and Gams, W and Komon-Zelazowska, M and Theelen, B and Müller, WH and Boekhout, T and Druzhinina, I},
title = {DNA barcoding survey of Trichoderma diversity in soil and litter of the Colombian lowland Amazonian rainforest reveals Trichoderma strigosellum sp. nov. and other species.},
journal = {Antonie van Leeuwenhoek},
volume = {104},
number = {5},
pages = {657-674},
pmid = {23884864},
issn = {1572-9699},
mesh = {*Biodiversity ; Cluster Analysis ; Colombia ; *DNA Barcoding, Taxonomic ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Haplotypes ; Microbiological Techniques ; Microscopy ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; *Soil Microbiology ; Trichoderma/*classification/cytology/*genetics/isolation &amp; purification ; },
abstract = {The diversity of Trichoderma (Hypocreales, Ascomycota) colonizing leaf litter as well as the rhizosphere of Garcinia macrophylla (Clusiaceae) was investigated in primary and secondary rain forests in Colombian Amazonia. DNA barcoding of 107 strains based on the internal transcribed spacers 1 and 2 (ITS1 and 2) of the ribosomal RNA gene cluster and the partial sequence of the translation elongation factor 1 alpha (tef1) gene revealed that the diversity of Trichoderma was dominated (71 %) by three common cosmopolitan species, namely Trichoderma harzianum sensu lato (41 %), Trichoderma spirale (17 %) and Trichoderma koningiopsis (13 %). Four ITS 1 and 2 phylotypes (13 strains) could not be identified with certainty. Multigene phylogenetic analysis and phenotype profiling of four strains with an ITS1 and 2 phylotype similar to Trichoderma strigosum revealed a new sister species of the latter that is described here as Trichoderma strigosellum sp. nov. Sequence similarity searches revealed that this species also occurs in soils of Malaysia and Cameroon, suggesting a pantropical distribution.},
}
@article {pmid23879661,
year = {2013},
author = {Lax, G and Simpson, AG},
title = {Combining molecular data with classical morphology for uncultured phagotrophic euglenids (Excavata): a single-cell approach.},
journal = {The Journal of eukaryotic microbiology},
volume = {60},
number = {6},
pages = {615-625},
doi = {10.1111/jeu.12068},
pmid = {23879661},
issn = {1550-7408},
mesh = {Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Euglenida/classification/*cytology/*genetics/isolation &amp; purification ; Fresh Water/*parasitology ; Genes, rRNA ; Geologic Sediments/*parasitology ; Microscopy ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; },
abstract = {Phagotrophic euglenids are one of the most diverse and important forms of heterotrophic flagellates in sediment systems, and are key to understanding the evolution of photosynthetic euglenids and 'primary osmotrophs', yet relatively little is known about their biodiversity and phylogenetic relationships. A wealth of light microscopy-based information is available, but little progress has been made in associating this with molecular sequence data. We established a protocol to obtain light microscopy data and molecular data from single euglenid cells isolated from environmental samples. Individual cells from freshwater and marine benthic samples were isolated and rinsed by micropipetting, documented using high-resolution photomicroscopy, then subjected to single-cell nested PCR using taxon-specific primers in combination with universal eukaryotic primers, generating > 75% or full-length SSU rDNA sequences. As a proof-of-principle eight individuals were characterised and subjected to phylogenetic analyses. Many of these cells were identified as Anisonema or Dinema, and grouped with existing sequences assigned to these taxa, and with a 'Peranema sp.' sequence that we could now clearly demonstrate was misidentified or misannotated. Another cell is Heteronema c.f. exaratum, the first 'skidding heteronemid' for which sequence data are available. This is not closely related to Heteronema scaphurum, and intriguingly, branches as the sister group to primary osmotrophs. A cell similar to Ploeotia vitrea (the type of this genus), shows no particular phylogenetic affinity to Ploeotia costata, the best studied Ploeotia species. Our experimental protocol provides a useful starting point for future analyses on euglenid biodiversity (including environmental sequence surveys), and their evolution and systematics.},
}
@article {pmid23876292,
year = {2013},
author = {Krug, PJ and Vendetti, JE and Rodriguez, AK and Retana, JN and Hirano, YM and Trowbridge, CD},
title = {Integrative species delimitation in photosynthetic sea slugs reveals twenty candidate species in three nominal taxa studied for drug discovery, plastid symbiosis or biological control.},
journal = {Molecular phylogenetics and evolution},
volume = {69},
number = {3},
pages = {1101-1119},
pmid = {23876292},
issn = {1095-9513},
support = {R25 GM061331/GM/NIGMS NIH HHS/United States ; GM 61331/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Bayes Theorem ; *Biological Control Agents ; Cell Nucleus/genetics ; Chlorophyta ; Chloroplasts/*genetics ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; *Drug Discovery ; Gastropoda/*classification/genetics/physiology ; Genes, Mitochondrial ; Haplotypes ; Models, Genetic ; *Photosynthesis ; *Phylogeny ; Sequence Analysis, DNA ; Symbiosis/genetics ; },
abstract = {DNA barcoding can highlight taxa in which conventional taxonomy underestimates species richness, identifying mitochondrial lineages that may correspond to unrecognized species. However, key assumptions of barcoding remain untested for many groups of soft-bodied marine invertebrates with poorly resolved taxonomy. Here, we applied an integrative approach for species delimitation to herbivorous sea slugs in clade Sacoglossa, in which unrecognized diversity may complicate studies of drug discovery, plastid endosymbiosis, and biological control. Using the mitochondrial barcoding COI gene and the nuclear histone 3 gene, we tested the hypothesis that three widely distributed "species" each comprised a complex of independently evolving lineages. Morphological and reproductive characters were then used to evaluate whether each lineage was distinguishable as a candidate species. The "circumtropical" Elysia ornata comprised a Caribbean species and four Indo-Pacific candidate species that are potential sources of kahalalides, anti-cancer compounds. The "monotypic" and highly photosynthetic Plakobranchus ocellatus, used for over 60 years to study chloroplast symbiosis, comprised 10 candidate species. Finally, six candidate species were distinguished in the Elysia tomentosa complex, including potential biological control agents for invasive green algae (Caulerpa spp.). We show that a candidate species approach developed for vertebrates effectively categorizes cryptic diversity in marine invertebrates, and that integrating threshold COI distances with non-molecular character data can delimit species even when common assumptions of DNA barcoding are violated.},
}
@article {pmid23874660,
year = {2013},
author = {Hebert, PD and Dewaard, JR and Zakharov, EV and Prosser, SW and Sones, JE and McKeown, JT and Mantle, B and La Salle, J},
title = {A DNA 'barcode blitz': rapid digitization and sequencing of a natural history collection.},
journal = {PloS one},
volume = {8},
number = {7},
pages = {e68535},
pmid = {23874660},
issn = {1932-6203},
mesh = {Animals ; Australia ; *Biological Specimen Banks ; DNA Barcoding, Taxonomic/*methods ; Feasibility Studies ; Information Storage and Retrieval/methods ; Insecta/*classification/genetics ; *Libraries, Digital ; Natural History/*methods ; Quality Control ; Sequence Analysis, DNA/*methods/standards ; Specimen Handling/methods ; Time Factors ; },
abstract = {DNA barcoding protocols require the linkage of each sequence record to a voucher specimen that has, whenever possible, been authoritatively identified. Natural history collections would seem an ideal resource for barcode library construction, but they have never seen large-scale analysis because of concerns linked to DNA degradation. The present study examines the strength of this barrier, carrying out a comprehensive analysis of moth and butterfly (Lepidoptera) species in the Australian National Insect Collection. Protocols were developed that enabled tissue samples, specimen data, and images to be assembled rapidly. Using these methods, a five-person team processed 41,650 specimens representing 12,699 species in 14 weeks. Subsequent molecular analysis took about six months, reflecting the need for multiple rounds of PCR as sequence recovery was impacted by age, body size, and collection protocols. Despite these variables and the fact that specimens averaged 30.4 years old, barcode records were obtained from 86% of the species. In fact, one or more barcode compliant sequences (>487 bp) were recovered from virtually all species represented by five or more individuals, even when the youngest was 50 years old. By assembling specimen images, distributional data, and DNA barcode sequences on a web-accessible informatics platform, this study has greatly advanced accessibility to information on thousands of species. Moreover, much of the specimen data became publically accessible within days of its acquisition, while most sequence results saw release within three months. As such, this study reveals the speed with which DNA barcode workflows can mobilize biodiversity data, often providing the first web-accessible information for a species. These results further suggest that existing collections can enable the rapid development of a comprehensive DNA barcode library for the most diverse compartment of terrestrial biodiversity - insects.},
}
@article {pmid23870888,
year = {2013},
author = {Di Pinto, A and Di Pinto, P and Terio, V and Bozzo, G and Bonerba, E and Ceci, E and Tantillo, G},
title = {DNA barcoding for detecting market substitution in salted cod fillets and battered cod chunks.},
journal = {Food chemistry},
volume = {141},
number = {3},
pages = {1757-1762},
doi = {10.1016/j.foodchem.2013.05.093},
pmid = {23870888},
issn = {1873-7072},
mesh = {Animals ; Consumer Product Safety ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Fish Products/*analysis ; Food Contamination/*analysis ; Food Handling ; Gadiformes/*classification/*genetics ; },
abstract = {The Italian Ministry of Agricultural, Food and Forestry Policies (MiPAAF) Decree dated 31 January 2008, which reports the Italian name for fish species of commercial interest, establishes that baccalà can be obtained exclusively from G. macrocephalus (Pacific cod) and G. morhua (Atlantic cod). This paper describes the COI-based DNA identification system to verify the substitution or misbranding of gadoid fish species and, consequently, its concordance with the labels on salted cod fillets shown as baccalà and on battered cod chunks labelled as bocconcini di baccalà. The analysis of interpretable sequences revealed that 55/65 dried salted cod fillet samples were detected as belonging to the family Gadidae, while 10/65 samples appeared to belong to the Lotidae family, while among battered cod chunks labelled as bocconcini di baccalà, the post-sequencing data analysis shows that the labels were completely wrong, with 28/40 samples from Pollachius virens and 12/40 samples from Brosme brosme. The substitution rate for products labelled on the market as baccalà in this study raises significant issues relating to food safety and consumer protection.},
}
@article {pmid23867856,
year = {2013},
author = {Wang, M and Zhao, HX and Wang, L and Wang, T and Yang, RW and Wang, XL and Zhou, YH and Ding, CB and Zhang, L},
title = {Potential use of DNA barcoding for the identification of Salvia based on cpDNA and nrDNA sequences.},
journal = {Gene},
volume = {528},
number = {2},
pages = {206-215},
doi = {10.1016/j.gene.2013.07.009},
pmid = {23867856},
issn = {1879-0038},
mesh = {Base Composition ; DNA Barcoding, Taxonomic ; DNA, Chloroplast/*genetics ; DNA, Intergenic/genetics ; DNA, Plant/genetics ; DNA, Ribosomal/*genetics ; Genes, Plant ; Genetic Loci ; Genetic Markers ; Genetic Variation ; Genome, Chloroplast ; Models, Genetic ; Salvia/*genetics ; Sequence Analysis, DNA ; Statistics, Nonparametric ; },
abstract = {An effective DNA marker for authenticating the genus Salvia was screened using seven DNA regions (rbcL, matK, trnL-F, and psbA-trnH from the chloroplast genome, and ITS, ITS1, and ITS2 from the nuclear genome) and three combinations (rbcL+matK, psbA-trnH+ITS1, and trnL-F+ITS1). The present study collected 232 sequences from 27 Salvia species through DNA sequencing and 77 sequences within the same taxa from the GenBank. The discriminatory capabilities of these regions were evaluated in terms of PCR amplification success, intraspecific and interspecific divergence, DNA barcoding gaps, and identification efficiency via a tree-based method. ITS1 was superior to the other marker for discriminating between species, with an accuracy of 81.48%. The three combinations did not increase species discrimination. Finally, we found that ITS1 is a powerful barcode for identifying Salvia species, especially Salvia miltiorrhiza.},
}
@article {pmid23865560,
year = {2013},
author = {Gathier, G and van der Niet, T and Peelen, T and van Vugt, RR and Eurlings, MC and Gravendeel, B},
title = {Forensic identification of CITES protected slimming cactus (Hoodia) using DNA barcoding.},
journal = {Journal of forensic sciences},
volume = {58},
number = {6},
pages = {1467-1471},
doi = {10.1111/1556-4029.12184},
pmid = {23865560},
issn = {1556-4029},
mesh = {Apocynaceae/*genetics ; *Commerce ; *Crime ; *DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/genetics ; *Endangered Species ; Humans ; Mass Spectrometry ; Phytotherapy ; Plant Stems ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Reproducibility of Results ; Sequence Analysis, DNA ; },
abstract = {Slimming cactus (Hoodia), found only in southwestern Africa, is a well-known herbal product for losing weight. Consequently, Hoodia extracts are sought-after worldwide despite a CITES Appendix II status. The failure to eradicate illegal trade is due to problems with detecting and identifying Hoodia using morphological and chemical characters. Our aim was to evaluate the potential of molecular identification of Hoodia based on DNA barcoding. Screening of nrITS1 and psbA-trnH DNA sequences from 26 accessions of Ceropegieae resulted in successful identification, while conventional chemical profiling using DLI-MS led to inaccurate detection and identification of Hoodia. The presence of Hoodia in herbal products was also successfully established using DNA sequences. A validation procedure of our DNA barcoding protocol demonstrated its robustness to changes in PCR conditions. We conclude that DNA barcoding is an effective tool for Hoodia detection and identification which can contribute to preventing illegal trade.},
}
@article {pmid23862147,
year = {2013},
author = {Hou, D and Song, J and Shi, L and Ma, X and Xin, T and Han, J and Xiao, W and Sun, Z and Cheng, R and Yao, H},
title = {Stability and accuracy assessment of identification of traditional Chinese materia medica using DNA barcoding: a case study on Flos Lonicerae Japonicae.},
journal = {BioMed research international},
volume = {2013},
number = {},
pages = {549037},
pmid = {23862147},
issn = {2314-6141},
mesh = {Base Sequence ; China ; DNA Barcoding, Taxonomic/*methods ; DNA, Intergenic/genetics ; DNA, Plant/genetics ; Flowers/*genetics ; Genetic Variation ; Lonicera/*genetics ; Materia Medica/*analysis ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Species Specificity ; },
abstract = {DNA barcoding is a novel molecular identification method that aids in identifying traditional Chinese materia medica using traditional identification techniques. However, further study is needed to assess the stability and accuracy of DNA barcoding. Flos Lonicerae Japonicae, a typical medicinal flower, is widely used in China, Korea, and other Southeast Asian countries. However, Flos Lonicerae Japonicae and its closely related species have been misused and traded at varying for a wide range of prices. Therefore, Flos Lonicerae Japonicae must be accurately identified. In this study, the ITS2 and psbA-trnH regions were amplified by polymerase chain reaction (PCR). Sequence assembly was performed using CodonCode Aligner V 3.5.4. The intra- versus inter-specific variations were assessed using six metrics and "barcoding gaps." Species identification was conducted using BLAST1 and neighbor-joining (NJ) trees. Results reveal that ITS2 and psbA-trnH exhibited an average intraspecific divergence of 0.001 and 0, respectively, as well as an average inter-specific divergence of 0.0331 and 0.0161. The identification efficiency of ITS2 and psbA-trnH evaluated using BLAST1 was 100%. Flos Lonicerae Japonicae was formed into one clade through the NJ trees. Therefore, Flos Lonicerae Japonicae can be stably and accurately identified through the ITS2 and psbA-trnH regions, respectively.},
}
@article {pmid23862106,
year = {2013},
author = {Merker, JD and O'Grady, N and Gojenola, L and Dao, M and Lenta, R and Yeakley, JM and Schrijver, I},
title = {Feasibility of using microbeads with holographic barcodes to track DNA specimens in the clinical molecular laboratory.},
journal = {PeerJ},
volume = {1},
number = {},
pages = {e91},
pmid = {23862106},
issn = {2167-8359},
abstract = {We demonstrate the feasibility of using glass microbeads with a holographic barcode identifier to track DNA specimens in the molecular pathology laboratory. These beads can be added to peripheral blood specimens and are carried through automated DNA extraction protocols that use magnetic glass particles. We found that an adequate number of microbeads are consistently carried over during genomic DNA extraction to allow specimen identification, that the beads do not interfere with the performance of several different molecular assays, and that the beads and genomic DNA remain stable when stored together under regular storage conditions in the molecular pathology laboratory. The beads function as an internal, easily readable specimen barcode. This approach may be useful for identifying DNA specimens and reducing errors associated with molecular laboratory testing.},
}
@article {pmid23861743,
year = {2013},
author = {Ratnasingham, S and Hebert, PD},
title = {A DNA-based registry for all animal species: the barcode index number (BIN) system.},
journal = {PloS one},
volume = {8},
number = {7},
pages = {e66213},
pmid = {23861743},
issn = {1932-6203},
mesh = {Algorithms ; Animals ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; Databases as Topic ; Lepidoptera/classification ; North America ; *Registries ; Species Specificity ; Time Factors ; },
abstract = {Because many animal species are undescribed, and because the identification of known species is often difficult, interim taxonomic nomenclature has often been used in biodiversity analysis. By assigning individuals to presumptive species, called operational taxonomic units (OTUs), these systems speed investigations into the patterning of biodiversity and enable studies that would otherwise be impossible. Although OTUs have conventionally been separated through their morphological divergence, DNA-based delineations are not only feasible, but have important advantages. OTU designation can be automated, data can be readily archived, and results can be easily compared among investigations. This study exploits these attributes to develop a persistent, species-level taxonomic registry for the animal kingdom based on the analysis of patterns of nucleotide variation in the barcode region of the cytochrome c oxidase I (COI) gene. It begins by examining the correspondence between groups of specimens identified to a species through prior taxonomic work and those inferred from the analysis of COI sequence variation using one new (RESL) and four established (ABGD, CROP, GMYC, jMOTU) algorithms. It subsequently describes the implementation, and structural attributes of the Barcode Index Number (BIN) system. Aside from a pragmatic role in biodiversity assessments, BINs will aid revisionary taxonomy by flagging possible cases of synonymy, and by collating geographical information, descriptive metadata, and images for specimens that are likely to belong to the same species, even if it is undescribed. More than 274,000 BIN web pages are now available, creating a biodiversity resource that is positioned for rapid growth.},
}
@article {pmid23859496,
year = {2013},
author = {Marcili, A and da Costa, AP and Soares, HS and Acosta, Ida C and de Lima, JT and Minervino, AH and Melo, AT and Aguiar, DM and Pacheco, RC and Gennari, SM},
title = {Isolation and phylogenetic relationships of bat trypanosomes from different biomes in Mato Grosso, Brazil.},
journal = {The Journal of parasitology},
volume = {99},
number = {6},
pages = {1071-1076},
doi = {10.1645/12-156.1},
pmid = {23859496},
issn = {1937-2345},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; Brazil/epidemiology ; Chiroptera/classification/*parasitology ; DNA Barcoding, Taxonomic ; DNA, Protozoan/chemistry ; DNA, Ribosomal/chemistry ; Ecosystem ; *Phylogeny ; Prevalence ; Trypanosoma/classification/genetics/*isolation &amp; purification ; Trypanosomiasis/epidemiology/parasitology/*veterinary ; },
abstract = {In the order Chiroptera, more than 30 trypanosome species belonging to the subgenera Herpetosoma, Schizotrypanum, Megatrypanum, and Trypanozoon have been described. The species Trypanosoma cruzi , Trypanosoma cruzi marinkellei, and Trypanosoma dionisii are the most common in bats and belong to the Schizotrypanum subgenus. Bats from 2 different biomes, Pantanal and Amazonia/Cerrado in the state of Mato Grosso, Brazil, were evaluated according to the presence of trypanosome parasites by means of hemoculture and PCR in primary samples (blood samples). A total of 211 bats from 20 different species were caught and the trypanosome prevalence, evaluated through hemoculture, was 9.0% (19), 15.5% (13), and 4.8% (6) in the municipalities of Confresa (Amazonia/Cerrado biome) and Poconé (Pantanal biome). Among the 123 primary samples obtained from the bats, only 3 (2.4%) were positive. Phylogenetic analysis using trypanosomatid barcoding (V7V8 region of SSU rDNA) identified all the isolates and primary samples as T. c. marinkellei. The sequences of the isolates were segregated according to the bat host genus or species and suggest that co-evolutionary patterns exist between hosts and parasites. Further studies in different Brazilian regions and biomes need to be conducted in order to gain real understanding of the diversity of trypanosomes in bats.},
}
@article {pmid23815444,
year = {2013},
author = {La Rosa, M and Fiannaca, A and Rizzo, R and Urso, A},
title = {Alignment-free analysis of barcode sequences by means of compression-based methods.},
journal = {BMC bioinformatics},
volume = {14 Suppl 7},
number = {Suppl 7},
pages = {S4},
pmid = {23815444},
issn = {1471-2105},
mesh = {Animals ; Computer Simulation ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial ; Humans ; *Phylogeny ; },
abstract = {BACKGROUND: The key idea of DNA barcode initiative is to identify, for each group of species belonging to different kingdoms of life, a short DNA sequence that can act as a true taxon barcode. DNA barcode represents a valuable type of information that can be integrated with ecological, genetic, and morphological data in order to obtain a more consistent taxonomy. Recent studies have shown that, for the animal kingdom, the mitochondrial gene cytochrome c oxidase I (COI), about 650 bp long, can be used as a barcode sequence for identification and taxonomic purposes of animals. In the present work we aims at introducing the use of an alignment-free approach in order to make taxonomic analysis of barcode sequences. Our approach is based on the use of two compression-based versions of non-computable Universal Similarity Metric (USM) class of distances. Our purpose is to justify the employ of USM also for the analysis of short DNA barcode sequences, showing how USM is able to correctly extract taxonomic information among those kind of sequences.<br><br>RESULTS: We downloaded from Barcode of Life Data System (BOLD) database 30 datasets of barcode sequences belonging to different animal species. We built phylogenetic trees of every dataset, according to compression-based and classic evolutionary methods, and compared them in terms of topology preservation. In the experimental tests, we obtained scores with a percentage of similarity between evolutionary and compression-based trees between 80% and 100% for the most of datasets (94%). Moreover we carried out experimental tests using simulated barcode datasets composed of 100, 150, 200 and 500 sequences, each simulation replicated 25-fold. In this case, mean similarity scores between evolutionary and compression-based trees span between 83% and 99% for all simulated datasets.<br><br>CONCLUSIONS: In the present work we aims at introducing the use of an alignment-free approach in order to make taxonomic analysis of barcode sequences. Our approach is based on the use of two compression-based versions of non-computable Universal Similarity Metric (USM) class of distances. This way we demonstrate the reliability of compression-based methods even for the analysis of short barcode sequences. Compression-based methods, with their strong theoretical assumptions, may then represent a valid alignment-free and parameter-free approach for barcode studies.},
}
@article {pmid23849725,
year = {2013},
author = {Borsa, P and Arlyza, IS and Chen, WJ and Durand, JD and Meekan, MG and Shen, KN},
title = {Resurrection of New Caledonian maskray Neotrygon trigonoides (Myliobatoidei: Dasyatidae) from synonymy with N. kuhlii, based on cytochrome-oxidase I gene sequences and spotting patterns.},
journal = {Comptes rendus biologies},
volume = {336},
number = {4},
pages = {221-232},
doi = {10.1016/j.crvi.2013.05.005},
pmid = {23849725},
issn = {1768-3238},
mesh = {Animals ; Base Sequence ; Color ; Coral Reefs ; DNA/genetics ; Indian Ocean ; New Caledonia ; Pacific Ocean ; Phylogeny ; Polymerase Chain Reaction ; Skates, Fish/anatomy &amp; histology/classification/*physiology ; Terminology as Topic ; },
abstract = {The maskray from New Caledonia, Neotrygon trigonoides Castelnau, 1873, has been recently synonymized with the blue-spotted maskray, N. kuhlii (Müller and Henle, 1841), a species with wide Indo-West Pacific distribution, but the reasons for this are unclear. Blue-spotted maskray specimens were collected from the Indian Ocean (Tanzania, Sumatra) and the Coral Triangle (Indonesia, Taiwan, and West Papua), and N. trigonoides specimens were collected from New Caledonia (Coral-Sea). Their partial COI gene sequences were generated to expand the available DNA-barcode database on this species, which currently comprises homologous sequences from Ningaloo Reef, the Coral Triangle and the Great Barrier Reef (Coral-Sea). Spotting patterns were also compared across regions. Haplotypes from the Coral-Sea formed a haplogroup phylogenetically distinct from all other haplotypes sampled in the Indo-West Pacific. No clear-cut geographic composition relative to DNA-barcodes or spotting patterns was apparent in N. kuhlii samples across the Indian Ocean and the Coral Triangle. The New Caledonian maskray had spotting patterns markedly different from all the other samples. This, added to a substantial level of net nucleotide divergence (2.6%) with typical N. kuhlii justifies considering the New Caledonian maskray as a separate species, for which we propose to resurrect the name Neotrygon trigonoides.},
}
@article {pmid23848937,
year = {2013},
author = {Geller, J and Meyer, C and Parker, M and Hawk, H},
title = {Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all-taxa biotic surveys.},
journal = {Molecular ecology resources},
volume = {13},
number = {5},
pages = {851-861},
doi = {10.1111/1755-0998.12138},
pmid = {23848937},
issn = {1755-0998},
mesh = {Animals ; Aquatic Organisms/*classification/genetics ; *Biota ; California ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Invertebrates/*classification/genetics ; Polymerase Chain Reaction/methods ; Polynesia ; United States ; },
abstract = {DNA barcoding is a powerful tool for species detection, identification and discovery. Metazoan DNA barcoding is primarily based upon a specific region of the cytochrome c oxidase subunit I gene that is PCR amplified by primers HCO2198 and LCO1490 ('Folmer primers') designed by Folmer et al. (Molecular Marine Biology and Biotechnology, 3, 1994, 294). Analysis of sequences published since 1994 has revealed mismatches in the Folmer primers to many metazoans. These sequences also show that an extremely high level of degeneracy would be necessary in updated Folmer primers to maintain broad taxonomic utility. In primers jgHCO2198 and jgLCO1490, we replaced most fully degenerated sites with inosine nucleotides that complement all four natural nucleotides and modified other sites to better match major marine invertebrate groups. The modified primers were used to amplify and sequence cytochrome c oxidase subunit I from 9105 specimens from Moorea, French Polynesia and San Francisco Bay, California, USA representing 23 phyla, 42 classes and 121 orders. The new primers, jgHCO2198 and jgLCO1490, are well suited for routine DNA barcoding, all-taxon surveys and metazoan metagenomics.},
}
@article {pmid23848578,
year = {2013},
author = {Françoso, E and Arias, MC},
title = {Cytochrome c oxidase I primers for corbiculate bees: DNA barcode and mini-barcode.},
journal = {Molecular ecology resources},
volume = {13},
number = {5},
pages = {844-850},
doi = {10.1111/1755-0998.12135},
pmid = {23848578},
issn = {1755-0998},
mesh = {Animals ; Bees/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Electron Transport Complex IV/*genetics ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {Bees (Apidae), of which there are more than 19 900 species, are extremely important for ecosystem services and economic purposes, so taxon identity is a major concern. The goal of this study was to optimize the DNA barcode technique based on the Cytochrome c oxidase (COI) mitochondrial gene region. This approach has previously been shown to be useful in resolving taxonomic inconsistencies and for species identification when morphological data are poor. Specifically, we designed and tested new primers and standardized PCR conditions to amplify the barcode region for bees, focusing on the corbiculate Apids. In addition, primers were designed to amplify small COI amplicons and tested with pinned specimens. Short barcode sequences were easily obtained for some Bombus century-old museum specimens and shown to be useful as mini-barcodes. The new primers and PCR conditions established in this study proved to be successful for the amplification of the barcode region for all species tested, regardless of the conditions of tissue preservation. We saw no evidence of Wolbachia or numts amplification by these primers, and so we suggest that these new primers are of broad value for corbiculate bee identification through DNA barcode.},
}
@article {pmid23848238,
year = {2014},
author = {Stoeck, T and Breiner, HW and Filker, S and Ostermaier, V and Kammerlander, B and Sonntag, B},
title = {A morphogenetic survey on ciliate plankton from a mountain lake pinpoints the necessity of lineage-specific barcode markers in microbial ecology.},
journal = {Environmental microbiology},
volume = {16},
number = {2},
pages = {430-444},
pmid = {23848238},
issn = {1462-2920},
mesh = {Austria ; Chlorophyll/analysis ; Chlorophyll A ; Ciliophora/classification/cytology/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Protozoan/genetics ; *Genes, rRNA ; Lakes/*microbiology ; Plankton/classification/cytology/genetics ; RNA, Ribosomal, 18S/genetics ; Water Microbiology ; },
abstract = {Analyses of high-throughput environmental sequencing data have become the 'gold-standard' to address fundamental questions of microbial diversity, ecology and biogeography. Findings that emerged from sequencing are, e.g. the discovery of the extensive 'rare microbial biosphere' and its potential function as a seed-bank. Even though applied since several years, results from high-throughput environmental sequencing have hardly been validated. We assessed how well pyrosequenced amplicons [the hypervariable eukaryotic V4 region of the small subunit ribosomal RNA (SSU rRNA) gene] reflected morphotype ciliate plankton. Moreover, we assessed if amplicon sequencing had the potential to detect the annual ciliate plankton stock. In both cases, we identified significant quantitative and qualitative differences. Our study makes evident that taxon abundance distributions inferred from amplicon data are highly biased and do not mirror actual morphotype abundances at all. Potential reasons included cell losses after fixation, cryptic morphotypes, resting stages, insufficient sequence data availability of morphologically described species and the unsatisfying resolution of the V4 SSU rRNA fragment for accurate taxonomic assignments. The latter two underline the necessity of barcoding initiatives for eukaryotic microbes to better and fully exploit environmental amplicon data sets, which then will also allow studying the potential of seed-bank taxa as a buffer for environmental changes.},
}
@article {pmid23847935,
year = {2013},
author = {Li, XL and Zhang, YY and Xu, YL and Zhao, CJ and Gu, YL and Li, L},
title = {[DNA barcoding of COI gene in some medicinal animals of Lacertilia].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {38},
number = {7},
pages = {951-956},
pmid = {23847935},
issn = {1001-5302},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Lizards/*classification/*genetics ; Medicine, Chinese Traditional ; Molecular Sequence Data ; Phylogeny ; Reptilian Proteins/*genetics ; Sequence Analysis, DNA ; },
abstract = {To identify some medicinal animals of Lacertilia, in total 59 individuals belonging to 12 species 7 genera 3 families, we used the universal barcoding primers to sequence these species, compared with other homologous sequences (564 bp) obtaining from the GenBank and finally constructed phylogenetic trees using Neighbor-joining, Maximum parsimony and Bayesian inference, respectively. As a result, the mean content of G + C (46.5%) was lower than that of A + T (53.5%). As calculated by Kimera-2-parameter model, the whole individuals mean distance for interspecies and intraspecies was 35. 5% and 1.7%, respectively. The mean distance for interspecies was 21 times as much as that for intraspecies. The mean distance for intraspecies of Gekko swinhonis, Hemidactylus frenatus and G. gecko was greater than 2%, respectively. Further analyses suggested that geographical groups of the three species might be of different subSpecies, even species. Of course, incorporating morphological characters and other unlinked genetic markers in future studies will offer further insights into the divergence. On the basis of phylogenetic trees constructed by COI, our results indicated that the taxonomy of the category (family, genus, and species) by DNA barcoding is consistent with morphological characters. Therefore, DNA barcoding is a useful tool for both identification and phylogeny of medicinal animals of Lacertilia, particularly for nonprofessor identifying authentication of Chinese crude drugs of these species.},
}
@article {pmid23847934,
year = {2013},
author = {Liu, XF and Liu, CS and Yang, YJ and Li, JD and Xu, J and Wu, LJ and Dai, D and Liu, J},
title = {[Research of DNA barcode of Teseudinis Carapax et Planstrum and its adulterants based on COI gene sequence].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {38},
number = {7},
pages = {947-950},
pmid = {23847934},
issn = {1001-5302},
mesh = {Animals ; Base Sequence ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Medicine, Chinese Traditional/*standards ; Molecular Sequence Data ; Phylogeny ; Quality Control ; Reptilian Proteins/*genetics ; Sequence Analysis, DNA ; Turtles/*classification/*genetics ; },
abstract = {OBJECTIVE: To use COI gene on the Mauremys reevesii and its adulterants by molecular identification. Search a rapid, accurate method of identification of Teseudinis Carapax et Planstrum and its adulterants.<br><br>METHOD: We collected 8 species of the authentic and adulterants of teseudinis carapax et planstrum in a nationwide then, extracted DNA, got the COI sequences. Use ContigExpress, Dnaman, Edit Sequence and Mega 5 to analyze the variable site and construct the N-J tree.<br><br>RESULT: Compare with the authentic Teseudinis Carapax et Planstrum, the adulterant exist lots of variable site. The N-J tree Indicates that the same genus belong together and each species belong to relatively independent branch.<br><br>CONCLUSION: Based on the COI gene, the technology of DNA bar code can be a excellent identification of Teseudinis Carapax et Planstrum and its adulterants.},
}
@article {pmid23847933,
year = {2013},
author = {Xie, JY and Li, JD and Huang, YS},
title = {[DNA barcoding application of mitochondrial COI gene sequence in medicinal fish of Culter (Pisces: Cyprinidae)].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {38},
number = {7},
pages = {943-946},
pmid = {23847933},
issn = {1001-5302},
mesh = {Animals ; China ; Cyprinidae/*classification/*genetics ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Fish Proteins/*genetics ; Medicine, Chinese Traditional ; Molecular Sequence Data ; Phylogeny ; },
abstract = {The sequence variation of medicinal fish of Culter (Pisces: Cyprinidae) was analyzed by using cytochrome c oxidase subunit I (COI) sequencing collected from different regions of the Yangtze River basin, and we examine whether barcoding of COI can be used to discriminate medicinal fish of Culter. The AT content in the COI region of medicinal fish of Culter was higher than that of GC, which was similar with other species of Cypriniformes. Ninty-six percent of nucleotide changes were observed at the 3rd codon position of COI sequence, but the amino acid compositions translated by COI sequences of all Culter fish stayed the same. It is suggested that most synonymous mutations might occur at the 3rd position. The average Kimura-2-parameter (K2P) distance within-species was lower than 1%, and the K2P distance of pairwise-species was 10 times as much as that of within-species. The phylogenetic tree estimated by Neighbour-joining method indicated that species within genera invariably clustered, and generally so did individuals within species. Individuals from operational taxonomic units designated as different Culter species, supporting morphological evidence for each of these being separate species. It is suggested that the COI barcoding can be used to identify medicinal fish species of Culter.},
}
@article {pmid23842669,
year = {2013},
author = {Cornara, L and Borghesi, B and Canali, C and Andrenacci, M and Basso, M and Federici, S and Labra, M},
title = {Smart drugs: green shuttle or real drug?.},
journal = {International journal of legal medicine},
volume = {127},
number = {6},
pages = {1109-1123},
pmid = {23842669},
issn = {1437-1596},
mesh = {Cannabinoids/*analysis ; DNA, Intergenic/genetics ; DNA, Plant/analysis/genetics ; Designer Drugs/*analysis ; Gas Chromatography-Mass Spectrometry ; Herbal Medicine ; Humans ; Illicit Drugs/*analysis ; Italy ; Microscopy, Electron, Scanning ; Plants/anatomy &amp; histology/*chemistry/genetics ; Ribulose-Bisphosphate Carboxylase/genetics ; Secologanin Tryptamine Alkaloids/*analysis ; Spectrometry, X-Ray Emission ; },
abstract = {We have combined morphological, molecular, and chemical techniques in order to identify the plant and chemical composition of some last-generation smart drugs, present on the market under the following names: Jungle Mistic Incense, B-52, Blendz, and Kratom 10x. Micromorphological analyses of botanical fragments allowed identification of epidermal cells, stomata, trichomes, starch, crystals, and pollen. DNA barcoding was carried out by the plastidial gene rbcL and the spacer trnH-psbA as universal markers. The combination of morphological and molecular data revealed a mixture of plants from different families, including aromatic species, viz., Lamiaceae and Turneraceae. GC-MS and LC-MS analyses on ethanol or methanol extracts showed the presence of synthetic cannabinoids, including JWH-250 in Jungle, JWH-122 in B-52, and JWH-073 and JWH-018 in Blendz. In Kratom 10x, only the indole alkaloid mitragynine was detected. All the identified synthetic cannabinoids, apart from mitragynine, are under the restriction of law in Italy (TU 309/90). Synthetic cannabinoid crystals were also identified by scanning electron microscopy and energy dispersive X-ray spectroscopy, which also detected other foreign organic chemicals, probably preservatives or antimycotics. In Kratom only leaf fragments from Mitragyna speciosa, containing the alkaloid mitragynine, were found. In the remaining products, aromatic plant species have mainly the role of hiding synthetic cannabinoids, thus acting as a "green shuttle" rather than as real drugs. Such a multidisciplinary approach is proposed as a method for the identification of herbal blends of uncertain composition, which are widely marketed in "headshops" and on the Internet, and represent a serious hazard to public health.},
}
@article {pmid23841619,
year = {2014},
author = {Chang, H and Liu, Q and Hao, D and Liu, Y and An, Y and Qian, L and Yang, X},
title = {DNA barcodes and molecular diagnostics for distinguishing introduced Xyleborus (Coleoptera: Scolytinae) species in China.},
journal = {Mitochondrial DNA},
volume = {25},
number = {1},
pages = {63-69},
doi = {10.3109/19401736.2013.779260},
pmid = {23841619},
issn = {1940-1744},
mesh = {Animals ; Base Sequence ; China ; Coleoptera/*genetics ; Commerce/instrumentation ; Computational Biology ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; *Genetic Variation ; *Introduced Species ; Molecular Sequence Data ; Sequence Analysis, DNA ; Wood/*parasitology ; },
abstract = {Members of the large and complex genus Xyleborus (Coleoptera: Scolytinae: Xyleborini) are the most commonly intercepted beetles associated with solid wood-packing materials at ports of entry in China. The accurate identification of species is critical in preventing the invasion of exotic insects. Considering the difficulties in morphological identification, genetic divergences of mitochondrial cytochrome c oxidase subunit I (COI) genes have been used in insect species identification. In this study, 32 Xyleborus and 2 outgroup species were collected from Jiangsu ports and selected to evaluate the effectiveness of DNA barcoding for Xyleborus species. The results showed that the mean interspecific divergence values (23.6%) were 15-fold higher than the observed intraspecific divergence (1.6%), except Xyleborus affinis. The results supported the inference that the barcode variation within species of insects is somewhat higher than interspecific ones. Thus, this study validated the effectiveness of barcoding for the identification of Xyleborus species.},
}
@article {pmid23840709,
year = {2013},
author = {Ge, H and Huang, X and Li, X and Chen, S and Zheng, J and Jiang, H and Zhang, C and Pan, X and Guo, J and Chen, F and Chen, N and Fang, Q and Jiang, H and Wang, W},
title = {Noninvasive prenatal detection for pathogenic CNVs: the application in α-thalassemia.},
journal = {PloS one},
volume = {8},
number = {6},
pages = {e67464},
pmid = {23840709},
issn = {1932-6203},
mesh = {DNA/*genetics ; DNA Copy Number Variations/*genetics ; Female ; Fetus ; Gene Deletion ; Heterozygote ; Homozygote ; Humans ; Male ; Polymorphism, Single Nucleotide/genetics ; Pregnancy ; Prenatal Diagnosis/methods ; Sequence Analysis, DNA/methods ; alpha-Globins/genetics ; alpha-Thalassemia/*diagnosis/*genetics ; beta-Globins/genetics ; },
abstract = {BACKGROUND: The discovery of cell free fetal DNA (cff-DNA) in maternal plasma has brought new insight for noninvasive prenatal diagnosis. Combining with the rapidly developed massively parallel sequencing technology, noninvasive prenatal detection of chromosome aneuploidy and single base variation has been successfully validated. However, few studies discussed the possibility of noninvasive pathogenic CNVs detection.<br><br>A novel algorithm for noninvasive prenatal detection of fetal pathogenic CNVs was firstly tested in 5 pairs of parents with heterozygote &#x3b1;-thalassemia of Southeast Asian (SEA) deletion using target region capture sequencing for maternal plasma. Capture probes were designed for &#x3b1;-globin (HBA) and &#x3b2;-globin (HBB) gene, as well as 4,525 SNPs selected from 22 automatic chromosomes. Mixed adaptors with 384 different barcodes were employed to construct maternal plasma DNA library for massively parallel sequencing. The signal of fetal CNVs was calculated using the relative copy ratio (RCR) of maternal plasma combined with the analysis of R-score and L-score by comparing with normal control. With mean of 101.93&#xd7; maternal plasma sequencing depth for the target region, the RCR value combined with further R-score and L-score analysis showed a possible homozygous deletion in the HBA gene region for one fetus, heterozygous deletion for two fetus and normal for the other two fetus, which was consistent with that of invasive prenatal diagnosis.<br><br>CONCLUSIONS/SIGNIFICANCE: Our study showed the feasibility to detect pathogenic CNVs using target region capture sequencing, which might greatly extend the scope of noninvasive prenatal diagnosis.},
}
@article {pmid23840661,
year = {2013},
author = {Nolan-Stevaux, O and Tedesco, D and Ragan, S and Makhanov, M and Chenchik, A and Ruefli-Brasse, A and Quon, K and Kassner, PD},
title = {Measurement of Cancer Cell Growth Heterogeneity through Lentiviral Barcoding Identifies Clonal Dominance as a Characteristic of In Vivo Tumor Engraftment.},
journal = {PloS one},
volume = {8},
number = {6},
pages = {e67316},
pmid = {23840661},
issn = {1932-6203},
mesh = {Animals ; Cell Proliferation ; *Cell Transformation, Neoplastic ; Clone Cells/pathology ; Female ; HCT116 Cells ; Humans ; Lentivirus/*genetics ; Mice ; RNA, Small Interfering/genetics ; Transduction, Genetic ; },
abstract = {Advances in the fields of cancer initiating cells and high-throughput in vivo shRNA screens have highlighted a need to observe the growth of tumor cells in cancer models at the clonal level. While in vivo cancer cell growth heterogeneity in xenografts has been described, it has yet to be measured. Here, we tested an approach to quantify the clonal growth heterogeneity of cancer cells in subcutaneous xenograft mouse models. Using a high-throughput sequencing method, we followed the fate in vitro and in vivo of ten thousand HCT-116 cells individually tagged with a unique barcode delivered by lentiviral transduction. While growth in vitro was less homogeneous than anticipated, we still find that 95% of the final cells derived from 80% of the original cells. In xenografts, however, 95% of the retrieved barcoded cells originated from only 6% of the initially injected cells, an effect we term "clonal dominance". We observed this clonal dominance in two additional xenograft models (MDA-MB-468 and A2780(cis)) and in two different host strains (NSG and Nude). By precisely and reproducibly quantifying clonal cancer cell growth in vivo, we find that a small subset of clones accounts for the vast majority of the descendant cells, even with HCT-116, a cell line reported to lack a tumor-initiating compartment. The stochastic in vivo selection process we describe has important implications for the fields of in vivo shRNA screening and tumor initiating cells.},
}
@article {pmid23837914,
year = {2013},
author = {Maccari, M and Gómez, A and Hontoria, F and Amat, F},
title = {Functional rare males in diploid parthenogenetic Artemia.},
journal = {Journal of evolutionary biology},
volume = {26},
number = {9},
pages = {1934-1948},
doi = {10.1111/jeb.12191},
pmid = {23837914},
issn = {1420-9101},
mesh = {Animal Distribution ; Animals ; Artemia/*genetics ; *Biological Evolution ; DNA Barcoding, Taxonomic ; *Diploidy ; Male ; Microsatellite Repeats/genetics ; Parthenogenesis/*genetics ; Reproduction/*genetics ; *Sex Characteristics ; Sex Ratio ; Species Specificity ; },
abstract = {Functional males that are produced occasionally in some asexual taxa - called 'rare males' - raise considerable evolutionary interest, as they might be involved in the origin of new parthenogenetic lineages. Diploid parthenogenetic Artemia produce rare males, which may retain the ability to mate with females of related sexual lineages. Here, we (i) describe the frequency of male progeny in populations of diploid parthenogenetic Artemia, (ii) characterize rare males morphologically, (iii) assess their reproductive role, using cross-mating experiments with sexual females of related species from Central Asia and characterize the F1 hybrid offspring viability and (iv) confirm genetically both the identity and functionality of rare males using DNA barcoding and microsatellite loci. Our result suggests that these males may have an evolutionary role through genetic exchange with related sexual species and that diploid parthenogenetic Artemia is a good model system to investigate the evolutionary transitions between sexual species and parthenogenetic strains.},
}
@article {pmid23837789,
year = {2013},
author = {Bowman, SK and Simon, MD and Deaton, AM and Tolstorukov, M and Borowsky, ML and Kingston, RE},
title = {Multiplexed Illumina sequencing libraries from picogram quantities of DNA.},
journal = {BMC genomics},
volume = {14},
number = {},
pages = {466},
pmid = {23837789},
issn = {1471-2164},
support = {R01 GM043901/GM/NIGMS NIH HHS/United States ; R37 GM048405/GM/NIGMS NIH HHS/United States ; },
mesh = {Chromatin Immunoprecipitation ; DNA/*genetics ; *Gene Library ; Sequence Analysis, DNA/*methods ; Time Factors ; },
abstract = {BACKGROUND: High throughput sequencing is frequently used to discover the location of regulatory interactions on chromatin. However, techniques that enrich DNA where regulatory activity takes place, such as chromatin immunoprecipitation (ChIP), often yield less DNA than optimal for sequencing library preparation. Existing protocols for picogram-scale libraries require concomitant fragmentation of DNA, pre-amplification, or long overnight steps.<br><br>RESULTS: We report a simple and fast library construction method that produces libraries from sub-nanogram quantities of DNA. This protocol yields conventional libraries with barcodes suitable for multiplexed sample analysis on the Illumina platform. We demonstrate the utility of this method by constructing a ChIP-seq library from 100 pg of ChIP DNA that demonstrates equivalent genomic coverage of target regions to a library produced from a larger scale experiment.<br><br>CONCLUSIONS: Application of this method allows whole genome studies from samples where material or yields are limiting.},
}
@article {pmid23837453,
year = {2013},
author = {Hoffmann, K and Behnke, T and Drescher, D and Kneipp, J and Resch-Genger, U},
title = {Near-infrared-emitting nanoparticles for lifetime-based multiplexed analysis and imaging of living cells.},
journal = {ACS nano},
volume = {7},
number = {8},
pages = {6674-6684},
doi = {10.1021/nn4029458},
pmid = {23837453},
issn = {1936-086X},
mesh = {3T3 Cells ; Absorption ; Animals ; Biological Assay ; Cell Line ; Coculture Techniques ; Culture Media/chemistry ; Fibroblasts/metabolism ; Fluorescent Dyes/chemistry ; Kinetics ; Macrophages/cytology/metabolism ; Mice ; Microscopy, Confocal ; Microscopy, Fluorescence ; Molecular Imaging ; Nanoparticles/*chemistry ; Nanotechnology/*methods ; Spectrophotometry ; Spectroscopy, Near-Infrared/*methods ; },
abstract = {The increase in information content from bioassays and bioimaging requires robust and efficient strategies for the detection of multiple analytes or targets in a single measurement, thereby addressing current health and security concerns. For fluorescence techniques, an attractive alternative to commonly performed spectral or color multiplexing presents lifetime multiplexing and the discrimination between different fluorophores based on their fluorescence decay kinetics. This strategy relies on fluorescent labels with sufficiently different lifetimes that are excitable at the same wavelength and detectable within the same spectral window. Here, we report on lifetime multiplexing and discrimination with a set of nanometer-sized particles loaded with near-infrared emissive organic fluorophores chosen to display very similar absorption and emission spectra, yet different fluorescence decay kinetics in suspension. Furthermore, as a first proof-of-concept, we describe bioimaging studies with 3T3 fibroblasts and J774 macrophages, incubated with mixtures of these reporters employing fluorescence lifetime imaging microscopy. These proof-of-concept measurements underline the potential of fluorescent nanoparticle reporters in fluorescence lifetime multiplexing, barcoding, and imaging for cellular studies, cell-based assays, and molecular imaging.},
}
@article {pmid23831017,
year = {2014},
author = {Ramírez, JD and Tapia-Calle, G and Muñoz-Cruz, G and Poveda, C and Rendón, LM and Hincapié, E and Guhl, F},
title = {Trypanosome species in neo-tropical bats: biological, evolutionary and epidemiological implications.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {22},
number = {},
pages = {250-256},
pmid = {23831017},
issn = {1567-7257},
mesh = {Animals ; Biological Evolution ; Chiroptera/*parasitology ; Colombia/epidemiology ; Ecology ; Phylogeny ; Prevalence ; Trypanosoma/classification/genetics/isolation &amp; purification ; Trypanosomiasis/epidemiology/*parasitology ; },
abstract = {Bats (Chiroptera) are the only mammals naturally able to fly. Due to this characteristic they play a relevant ecological role in the niches they inhabit. These mammals spread infectious diseases from enzootic to domestic foci. Rabbies, SARS, fungi, ebola and trypanosomes are the most common pathogens these animals may host. We conducted intensive sampling of bats from the phyllostomidae, vespertilionidae and emballonuridae families in six localities from Casanare department in eastern Colombia. Blood-EDTA samples were obtained and subsequently submitted to analyses of mitochondrial and nuclear genetic markers in order to conduct barcoding analyses to discriminate trypanosome species. The findings according to the congruence of the three molecular markers suggest the occurrence of Trypanosoma cruzi cruzi (51%), T. c. marinkellei (9%), T. dionisii (13%), T. rangeli (21%), T. evansi (4%) and T. theileri (2%) among 107 positive bat specimens. Regarding the T. cruzi DTUs, we observed the presence of TcI (60%), TcII (15%), TcIII (7%), TcIV (7%) and TcBAT (11%) being the first evidence to our concern of the foreseen genotype TcBAT in Colombia. These results allowed us to propose reliable hypotheses regarding the ecology and biology of the bats circulating in the area including the enigmatic question whether TcBAT should be considered a novel DTU. The epidemiological and evolutionary implications of these findings are herein discussed.},
}
@article {pmid23826345,
year = {2013},
author = {Gu, W and Song, J and Cao, Y and Sun, Q and Yao, H and Wu, Q and Chao, J and Zhou, J and Xue, W and Duan, J},
title = {Application of the ITS2 Region for Barcoding Medicinal Plants of Selaginellaceae in Pteridophyta.},
journal = {PloS one},
volume = {8},
number = {6},
pages = {e67818},
pmid = {23826345},
issn = {1932-6203},
mesh = {China ; Cluster Analysis ; *DNA Barcoding, Taxonomic/methods ; *DNA, Plant ; Haplotypes ; Nucleic Acid Conformation ; Plants, Medicinal/genetics ; Selaginellaceae/*genetics ; Tracheophyta/*genetics ; },
abstract = {BACKGROUND: Selaginellaceae is a family of nonseed plants with special evolutionary significance. Plants of the family Selaginellaceae are similarly shaped and easily confused, complicating identification via traditional methods. This study explored, for the first time, the use of the DNA barcode ITS2 to identify medicinal plants of the Selaginellaceae family.<br><br>In our study, 103 samples were collected from the main distribution areas in China; these samples represented 34 species and contained almost all of the medicinal plants of Selaginellaceae. The ITS2 region of the genome was amplified from these samples and sequenced using universal primers and reaction conditions. The success rates of the PCR amplification and sequencing were 100%. There was significant divergence between the interspecific and intraspecific genetic distances of the ITS2 regions, while the presence of a barcoding gap was obvious. Using the BLAST1 and nearest distance methods, our results proved that the ITS2 regions could successfully identify the species of all Selaginellaceae samples examined. In addition, the secondary structures of ITS2 in the helical regions displayed clear differences in stem loop number, size, position, and screw angle among the medicinal plants of Selaginellaceae. Furthermore, cluster analysis using the ITS2 barcode supported the relationship between the species of Selaginellaceae established by traditional morphological methods.<br><br>CONCLUSION: The ITS2 barcode can effectively identify medicinal plants of Selaginellaceae. The results provide a scientific basis for the precise identification of plants of the family Selaginellaceae and the reasonable development of these resources. This study may broaden the application of DNA barcoding in the medicinal plant field and benefit phylogenetic investigations.},
}
@article {pmid23821442,
year = {2013},
author = {Eminaga, S and Christodoulou, DC and Vigneault, F and Church, GM and Seidman, JG},
title = {Quantification of microRNA expression with next-generation sequencing.},
journal = {Current protocols in molecular biology},
volume = {Chapter 4},
number = {},
pages = {Unit 4.17},
pmid = {23821442},
issn = {1934-3647},
support = {1U01HL098166/HL/NHLBI NIH HHS/United States ; /CAPMC/CIHR/Canada ; U01 HL098166/HL/NHLBI NIH HHS/United States ; PL1 HL092552/HL/NHLBI NIH HHS/United States ; U54 PL1 HL092552/HL/NHLBI NIH HHS/United States ; R01 HL084553/HL/NHLBI NIH HHS/United States ; },
mesh = {Computational Biology/methods ; Gene Expression Profiling/*methods ; Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; MicroRNAs/*biosynthesis/genetics/isolation &amp; purification ; },
abstract = {Rapid advancement of next-generation sequencing technologies has made it possible to study expression profiles of microRNAs (miRNAs) comprehensively and efficiently. Multiplexing miRNA libraries by barcoding can significantly reduce sequencing cost per sample without compromising library quality. This unit provides a step-by-step protocol for isolating miRNAs and constructing multiplexed miRNA libraries. Also described is a custom computational pipeline for analyzing the multiplexed miRNA library sequencing reads generated by Illumina-based technology.},
}
@article {pmid23820953,
year = {2013},
author = {Li, Y and Qi, X and Ji, X and Guo, Y},
title = {Simultaneous electrochemical determination of two analytes based on nuclease-assisted target recycling amplification.},
journal = {Analytical and bioanalytical chemistry},
volume = {405},
number = {21},
pages = {6845-6851},
doi = {10.1007/s00216-013-7119-3},
pmid = {23820953},
issn = {1618-2650},
mesh = {Base Sequence ; Complex Mixtures/analysis ; Conductometry/*methods ; DNA/*analysis/chemistry/*genetics ; Deoxyribonucleases/*chemistry ; Molecular Sequence Data ; Nucleic Acid Amplification Techniques ; Sequence Analysis, DNA/*methods ; },
abstract = {In the present study, a method for simultaneous determination of two different DNAs is developed based on nuclease-assisted target recycling and nanoparticle amplification. The target recycling process is accomplished by taking advantage of the cleavage property of nicking endonuclease (NEase) for specific nucleotide sequences in duplex. In the presence of target DNA, the linker DNA in our detection system can hybridize with the target and be cleaved to form short fragments. Thus the target DNA is released and recognized by another linker DNA, activating the next round of cleavage reaction. On the other hand, two bio-barcode probes, a PbS nanoparticles (NPs)-DNA probe and a CdS NPs-DNA probe, are used for tracing two target DNAs to further amplify the detection signals. Based on a sensitive differential pulse anodic stripping voltammetry (DPASV) method for the simultaneous detection of Pb(2+) and Cd(2+) obtained by dissolving two probes, two different target DNAs are determined with high sensitivity and single-base mismatch selectivity.},
}
@article {pmid23816787,
year = {2013},
author = {Davis, MP and van Dongen, S and Abreu-Goodger, C and Bartonicek, N and Enright, AJ},
title = {Kraken: a set of tools for quality control and analysis of high-throughput sequence data.},
journal = {Methods (San Diego, Calif.)},
volume = {63},
number = {1},
pages = {41-49},
pmid = {23816787},
issn = {1095-9130},
support = {BB/01589X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Algorithms ; Electronic Data Processing ; *High-Throughput Screening Assays ; Humans ; *Quality Control ; Sequence Analysis, RNA/*methods ; *Software ; },
abstract = {New sequencing technologies pose significant challenges in terms of data complexity and magnitude. It is essential that efficient software is developed with performance that scales with this growth in sequence information. Here we present a comprehensive and integrated set of tools for the analysis of data from large scale sequencing experiments. It supports adapter detection and removal, demultiplexing of barcodes, paired-end data, a range of read architectures and the efficient removal of sequence redundancy. Sequences can be trimmed and filtered based on length, quality and complexity. Quality control plots track sequence length, composition and summary statistics with respect to genomic annotation. Several use cases have been integrated into a single streamlined pipeline, including both mRNA and small RNA sequencing experiments. This pipeline interfaces with existing tools for genomic mapping and differential expression analysis.},
}
@article {pmid23808976,
year = {2013},
author = {Oter, K and Gunay, F and Tuzer, E and Linton, YM and Bellini, R and Alten, B},
title = {First record of Stegomyia albopicta in Turkey determined by active ovitrap surveillance and DNA barcoding.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {13},
number = {10},
pages = {753-761},
doi = {10.1089/vbz.2012.1093},
pmid = {23808976},
issn = {1557-7759},
mesh = {Aedes/*genetics ; Animals ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/genetics ; Epidemiological Monitoring ; Insect Vectors/*genetics ; Ovum ; Phylogeny ; Turkey/epidemiology ; },
abstract = {Despite its confirmed establishment in neighboring Greece and Bulgaria, the presence of the Oriental invasive species Stegomyia albopicta (Skuse) (=Aedes albopictus) has never been confirmed in Turkey. Active surveillance for this container-breeding species was carried out using oviposition traps at 15 discrete sites in the towns of Ipsala (n=8 sites), Kesan (n=5) (Edirne District), and Malkara (n=2) (Tekirdag District) in the Thrace region of northwestern Turkey, from May 23 through November 10, 2011. Eggs collected were reared to the fourth larval instar and adult stages where possible to facilitate integrated morphological and molecular species identification. DNA barcodes (658 bp of the mitochondrial cytochrome c oxidase I [COI] gene) were compared with all four potentially invasive Stegomyia species: St. aegypti, St. albopicta, St. cretina, and St. japonica. Sequences generated for samples collected in Thrace Region were herein confirmed as St. albopicta, the first record of this vector species in Turkey. Eggs of St. albopicta were detected in two discrete localities: (1) In the grounds of a restaurant in Kesan (in week 36), and (2) in the customs area of the Turkish-Greek border at Ipsala (in weeks 32 and 38). Multiple detection of St. albopicta eggs indicates the possible establishment of the species in northwestern Turkey. Finding this important disease vector has implications for public health and requires the implementation of active vector monitoring programs and targeted vector suppression strategies to limit the spread of this invasive vector species in Turkey.},
}
@article {pmid23808689,
year = {2013},
author = {Ponton, D and Carassou, L and Raillard, S and Borsa, P},
title = {Geometric morphometrics as a tool for identifying emperor fish (Lethrinidae) larvae and juveniles.},
journal = {Journal of fish biology},
volume = {83},
number = {1},
pages = {14-27},
doi = {10.1111/jfb.12138},
pmid = {23808689},
issn = {1095-8649},
mesh = {Aging/physiology ; Animals ; Biometry ; Larva/anatomy &amp; histology/classification ; Principal Component Analysis ; Sea Bream/anatomy &amp; histology/*classification ; },
abstract = {The aim of this study was to evaluate the efficiency of geometric morphometrics for describing the body shape of fish larvae and juveniles, and identifying them to species, in comparison with traditional linear measurements. Species of emperor fishes (Perciformes: Lethrinidae, genus Lethrinus) were chosen as the model group, as the late larval and early juvenile stages in this genus are particularly difficult to identify. Forty-five individuals of different species of Lethrinus were collected from the south-western lagoon of New Caledonia between May 2005 and March 2006. The individuals were first identified to species by their partial cytochrome-b gene sequence. They were then morphologically characterized using eight linear measurements and 23 landmarks recorded on digital photographs. Except for a small proportion of individuals, geometric morphometrics gave better results to distinguish the different species than linear measurements. A 'leave one out' approach confirmed the nearly total discrimination of recently settled Lethrinus genivittatus and Lethrinus nebulosus, whereas traditional identification keys failed to distinguish them. Therefore, geometric morphometrics is a promising tool for identifying fish larvae and juveniles to species. An effective approach would require building image databases of voucher specimens associated with their DNA barcodes. These images could be downloaded by the operator and processed with the specimens to be identified.},
}
@article {pmid23806673,
year = {2013},
author = {Bourlat, SJ and Borja, A and Gilbert, J and Taylor, MI and Davies, N and Weisberg, SB and Griffith, JF and Lettieri, T and Field, D and Benzie, J and Glöckner, FO and Rodríguez-Ezpeleta, N and Faith, DP and Bean, TP and Obst, M},
title = {Genomics in marine monitoring: new opportunities for assessing marine health status.},
journal = {Marine pollution bulletin},
volume = {74},
number = {1},
pages = {19-31},
doi = {10.1016/j.marpolbul.2013.05.042},
pmid = {23806673},
issn = {1879-3363},
mesh = {Aquatic Organisms/*genetics ; Biodiversity ; Conservation of Natural Resources ; Ecosystem ; Environmental Monitoring/economics/*methods ; *Genomics ; },
abstract = {This viewpoint paper explores the potential of genomics technology to provide accurate, rapid, and cost efficient observations of the marine environment. The use of such approaches in next generation marine monitoring programs will help achieve the goals of marine legislation implemented world-wide. Genomic methods can yield faster results from monitoring, easier and more reliable taxonomic identification, as well as quicker and better assessment of the environmental status of marine waters. A summary of genomic methods that are ready or show high potential for integration into existing monitoring programs is provided (e.g. qPCR, SNP based methods, DNA barcoding, microarrays, metagenetics, metagenomics, transcriptomics). These approaches are mapped to existing indicators and descriptors and a series of case studies is presented to assess the cost and added value of these molecular techniques in comparison with traditional monitoring systems. Finally, guidelines and recommendations are suggested for how such methods can enter marine monitoring programs in a standardized manner.},
}
@article {pmid23806568,
year = {2013},
author = {Loaiza, JR and Scott, ME and Bermingham, E and Sanjur, OI and Rovira, JR and Dutari, LC and Linton, YM and Bickersmith, S and Conn, JE},
title = {Novel genetic diversity within Anopheles punctimacula s.l.: phylogenetic discrepancy between the Barcode cytochrome c oxidase I (COI) gene and the rDNA second internal transcribed spacer (ITS2).},
journal = {Acta tropica},
volume = {128},
number = {1},
pages = {61-69},
pmid = {23806568},
issn = {1873-6254},
support = {R01 AI054139/AI/NIAID NIH HHS/United States ; AI 2R0154139/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Anopheles/anatomy &amp; histology/*classification/*genetics ; Cluster Analysis ; Costa Rica ; DNA, Ribosomal Spacer/*genetics ; Electron Transport Complex IV/*genetics ; Female ; *Genetic Variation ; Microscopy ; Molecular Sequence Data ; Panama ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Anopheles punctimacula s.l. is a regional malaria vector in parts of Central America, but its role in transmission is controversial due to its unresolved taxonomic status. Two cryptic species, An. malefactor and An. calderoni, have been previously confused with this taxon, and evidence for further genetic differentiation has been proposed. In the present study we collected and morphologically identified adult female mosquitoes of An. punctimacula s.l. from 10 localities across Panama and one in Costa Rica. DNA sequences from three molecular regions, the three prime end of the mitochondrial cytochrome c oxidase I gene (3' COI), the Barcode region in the five prime end of the COI (5' COI), and the rDNA second internal transcribed spacer (ITS2) were used to test the hypothesis of new molecular lineages within An. punctimacula s.l. Phylogenetic analyses using the 3' COI depicted six highly supported molecular lineages (A-F), none of which was An. malefactor. In contrast, phylogenetic inference with the 5' COI demonstrated paraphyly. Tree topologies based on the combined COI regions and ITS2 sequence data supported the same six lineages as the 3' COI alone. As a whole this evidence suggests that An. punctimacula s.l. comprises two geographically isolated lineages, but it is not clear whether these are true species. The phylogenetic structure of the An. punctimacula cluster as well as that of other unknown lineages (C type I vs C type II; D vs E) appears to be driven by geographic partition, because members of these assemblages did not overlap spatially. We report An. malefactor for the first time in Costa Rica, but our data do not support the presence of An. calderoni in Panama.},
}
@article {pmid23805311,
year = {2013},
author = {Sipiczki, M and Pfliegler, WP and Holb, IJ},
title = {Metschnikowia Species Share a Pool of Diverse rRNA Genes Differing in Regions That Determine Hairpin-Loop Structures and Evolve by Reticulation.},
journal = {PloS one},
volume = {8},
number = {6},
pages = {e67384},
pmid = {23805311},
issn = {1932-6203},
mesh = {DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; *Databases, Nucleic Acid ; Metschnikowia/classification/*genetics ; *Nucleic Acid Conformation ; RNA, Fungal/*genetics ; RNA, Ribosomal/*genetics ; Species Specificity ; },
abstract = {Modern taxonomy of yeasts is mainly based on phylogenetic analysis of conserved DNA and protein sequences. By far the most frequently used sequences are those of the repeats of the chromosomal rDNA array. It is generally accepted that the rDNA repeats of a genome have identical sequences due to the phenomenon of sequence homogenisation and can thus be used for identification and barcoding of species. Here we show that the rDNA arrays of the type strains of Metschnikowia andauensis and M. fructicola are not homogenised. Both have arrays consisting of diverse repeats that differ from each other in the D1/D2 domains by up to 18 and 25 substitutions. The variable sites are concentrated in two regions that correspond to back-folding stretches of hairpin loops in the predicted secondary structure of the RNA molecules. The substitutions do not alter significantly the overall hairpin-loop structure due to wobble base pairing at sites of C-T transitions and compensatory mutations in the complementary strand of the hairpin stem. The phylogenetic and network analyses of the cloned sequences revealed that the repeats had not evolved in a vertical tree-like way but reticulation might have shaped the rDNA arrays of both strains. The neighbour-net analysis of all cloned sequences of the type strains and the database sequences of different strains further showed that these species share a continuous pool of diverse repeats that appear to evolve by reticulate evolution.},
}
@article {pmid23798894,
year = {2013},
author = {Blakemore, RJ},
title = {Earthworms newly from Mongolia (Oligochaeta, Lumbricidae, Eisenia).},
journal = {ZooKeys},
volume = {},
number = {285},
pages = {1-21},
pmid = {23798894},
issn = {1313-2989},
abstract = {Two new megadrile earthworms from the steppes, the first species wholly from Outer Mongolia, are ascribed to the partially parthenogenetic Eisenia nordenskioldi (Eisen, 1879) species-complex. Taxonomic justification of sympatric Eisenia nordenskioldi mongol and Eisenia nordenskioldi onon ssp. n. are supported by mtDNA COI barcodes. The unreliability of molecular differentiation based on voucher names compared to definitive types is again demonstrated, as pertains to the ultimate Eisenia andrei Bouché, 1972 synonym of the Eisenia fetida (Savigny, 1826) sibling species-complex composed of more than a dozen prior names. Similar species described from Northeast China [formerly Manchuria] and North Korea are briefly considered, albeit they are intermittently held in synonymy of cosmopolitan Aporrectodea rosea (Savigny, 1826) along with many other taxa including some exotic lumbricids initially found in India. Japanese and North American lumbricids are also mentioned. Distributions are discussed and an annotated checklist of all nine Siberian/sub-arctic Eisenia nordenskioldi ssp. is appended.},
}
@article {pmid23797804,
year = {2013},
author = {Hajiahmadi, Z and Talebi, M and Sayed-Tabatabaei, BE},
title = {Studying genetic variability of pomegranate (Punica granatum L.) based on chloroplast DNA and barcode genes.},
journal = {Molecular biotechnology},
volume = {55},
number = {3},
pages = {249-259},
pmid = {23797804},
issn = {1559-0305},
mesh = {Chloroplasts/*genetics ; DNA Barcoding, Taxonomic/*methods ; *DNA, Chloroplast ; Evolution, Molecular ; *Genes, Chloroplast ; Genes, Plant ; Genetic Variation ; Genotype ; Lythraceae/classification/*genetics ; Myrtus/genetics ; Phylogeny ; Plant Leaves/genetics ; Plants/genetics ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Chloroplast DNA has been used extensively to analyze plant phylogenies at different taxonomic levels because of its size, organization and sequence conservation. In the present research, two chloroplastic regions, petA–psaJ, trnC–trnD and four DNA barcodes (trnH–psbA, ITS, rbcL, matK), were used to introduce suitable regions for the assessment of genetic diversity among P. granatum L. genotypes. Analysis of psbE–petL in petA–psaJ region revealed 1,300 nucleotides with 4.29 % genetic diversity among genotypes, while trnC–petN in trnC–trnD region showed 1.8 % genetic diversity. Therefore, despite the results obtained from the study of other plants, the trnC–trnD region had a low potential for the evaluation of diversity among pomegranate genotypes. Analysis of DNA barcodes in pomegranate showed that trnH–psbA (genetic diversity 2.91 %) provides the highest intra-species variation, followed by ITS (genetic diversity 0.44 %). Eighteen genotypes from different geographical origins of Iran were used to investigate psbE–petL and trnH–psbA potential as novel barcodes to determine genetic polymorphism and characterize pomegranate genotypes. The results suggested that two regions, psbE–petL and trnH–psbA, were more suitable for determining intra-species relationships of pomegranate.},
}
@article {pmid23795700,
year = {2013},
author = {Prosser, S and Martínez-Arce, A and Elías-Gutiérrez, M},
title = {A new set of primers for COI amplification from freshwater microcrustaceans.},
journal = {Molecular ecology resources},
volume = {13},
number = {6},
pages = {1151-1155},
doi = {10.1111/1755-0998.12132},
pmid = {23795700},
issn = {1755-0998},
mesh = {Animals ; Biodiversity ; Crustacea/classification/*genetics ; *DNA Barcoding, Taxonomic ; *DNA Primers ; Electron Transport Complex IV/chemistry/classification/*genetics ; *Fresh Water ; Molecular Sequence Data ; Nucleic Acid Amplification Techniques ; },
abstract = {Despite the contribution of DNA barcoding towards understanding the biodiversity and distribution of species, the success of COI amplification has been quite variable when it comes to freshwater zooplankton (Elías-Gutiérrez &amp; Valdez-Moreno 2008; Jeffery et al. 2011). Some genera of microcrustaceans seem to be more difficult to amplify than others. For example, Macrothrix, Scapholeberis, Diaphanosoma and cyclopoids have yielded limited results. Among several possible reasons for the inability to barcode freshwater microcrustaceans is that there does not exist a specific set of primers for COI amplification. To this end, we developed a zooplankton - specific set of primers, which significantly increased average amplification success (20% increase). With these primers, we observed an overall success of over 70% for Sididae and Chydoridae, and more than 80% for Daphniidae, Moinidae, Bosminidae, Macrothricidae, Ilyocryptidae and Diaptomidae. We also demonstrate a simple alteration to a common specimen fixation method that increases the overall recovery of barcodes from freshwater zooplankton. Collectively, we believe our results will greatly aid the recovery of barcodes from these difficult groups.},
}
@article {pmid23794922,
year = {2013},
author = {Blakemore, RJ and Lee, S and Lee, W and Seo, HY},
title = {Two new Korean earthworms (Annelida, Oligochaeta, Megadrilacea, Megascolecidae).},
journal = {ZooKeys},
volume = {},
number = {307},
pages = {35-44},
pmid = {23794922},
issn = {1313-2989},
abstract = {Two Korean endemic pheretimoid Amynthas Kinberg, 1867 species belonging in family Megascolecidae s. stricto are sketched, dissected and described. Amynthas daeari Blakemore sp. n. has spermathecae in 6/7/8 complying with an Amynthas tokioensis spp-group, whilst Amynthas jinburi Blakemore sp. n. has spermathecal pores in 5 &amp; 6 strictly complying with Sims and Easton's (1972)Amynthas canaliculatus-group. A definitive COI gene barcode is provided for the holotype of Amynthas daeari but the age since collection or preservation of the Amynthas jinburi type in 2000 precluded its mtDNA extraction at this time.},
}
@article {pmid23794832,
year = {2013},
author = {Riedel, A and Sagata, K and Surbakti, S and Rene Tänzler, and Michael Balke, },
title = {One hundred and one new species of Trigonopterus weevils from New Guinea.},
journal = {ZooKeys},
volume = {},
number = {280},
pages = {1-150},
pmid = {23794832},
issn = {1313-2989},
abstract = {A species discovery and description pipeline to accelerate and improve taxonomy is outlined, relying on concise expert descriptions, combined with DNA sequencing, digital imaging, and automated wiki species page creation from the journal. One hundred and one new species of Trigonopterus Fauvel, 1862 are described to demonstrate the feasibility of this approach: Trigonopterus aeneipennis sp. n., Trigonopterus aeneus sp. n., Trigonopterus agathis sp. n., Trigonopterus agilis sp. n., Trigonopterus amplipennis sp. n., Trigonopterus ancoruncus sp. n., Trigonopterus angulatus sp. n., Trigonopterus angustus sp. n., Trigonopterus apicalis sp. n., Trigonopterus armatus sp. n., Trigonopterus ascendens sp. n., Trigonopterus augur sp. n., Trigonopterus balimensis sp. n., Trigonopterus basalis sp. n., Trigonopterus conformis sp. n., Trigonopterus constrictus sp. n., Trigonopterus costatus sp. n., Trigonopterus costicollis sp. n., Trigonopterus crassicornis sp. n., Trigonopterus cuneipennis sp. n., Trigonopterus cyclopensis sp. n., Trigonopterus dentirostris sp. n., Trigonopterus discoidalis sp. n., Trigonopterus dromedarius sp. n., Trigonopterus durus sp. n., Trigonopterus echinus sp. n., Trigonopterus edaphus sp. n., Trigonopterus eremitus sp. n., Trigonopterus euops sp. n., Trigonopterus ferrugineus sp. n., Trigonopterus fusiformis sp. n., Trigonopterus glaber sp. n., Trigonopterus gonatoceros sp. n., Trigonopterus granum sp. n., Trigonopterus helios sp. n., Trigonopterus hitoloorum sp. n., Trigonopterus imitatus sp. n., Trigonopterus inflatus sp. n., Trigonopterus insularis sp. n., Trigonopterus irregularis sp. n., Trigonopterus ixodiformis sp. n., Trigonopterus kanawiorum sp. n., Trigonopterus katayoi sp. n., Trigonopterus koveorum sp. n., Trigonopterus kurulu sp. n., Trigonopterus lekiorum sp. n., Trigonopterus lineatus sp. n., Trigonopterus lineellus sp. n., Trigonopterus maculatus sp. n., Trigonopterus mimicus sp. n., Trigonopterus monticola sp. n., Trigonopterus montivagus sp. n., Trigonopterus moreaorum sp. n., Trigonopterus myops sp. n., Trigonopterus nangiorum sp. n., Trigonopterus nothofagorum sp. n., Trigonopterus ovatus sp. n., Trigonopterus oviformis sp. n., Trigonopterus parumsquamosus sp. n., Trigonopterus parvulus sp. n., Trigonopterus phoenix sp. n., Trigonopterus plicicollis sp. n., Trigonopterus politoides sp. n., Trigonopterus pseudogranum sp. n., Trigonopterus pseudonasutus sp. n., Trigonopterus ptolycoides sp. n., Trigonopterus punctulatus sp. n., Trigonopterus ragaorum sp. n., Trigonopterus rhinoceros sp. n., Trigonopterus rhomboidalis sp. n., Trigonopterus rubiginosus sp. n., Trigonopterus rubripennis sp. n., Trigonopterus rufibasis sp. n., Trigonopterus scabrosus sp. n., Trigonopterus scissops sp. n., Trigonopterus scharfi sp. n., Trigonopterus signicollis sp. n., Trigonopterus simulans sp. n., Trigonopterus soiorum sp. n., T sordidus sp. n., Trigonopterus squamirostris sp. n., Trigonopterus striatus sp. n., Trigonopterus strigatus sp. n., Trigonopterus strombosceroides sp. n., Trigonopterus subglabratus sp. n., Trigonopterus sulcatus sp. n., Trigonopterus taenzleri sp. n., Trigonopterus talpa sp. n., Trigonopterus taurekaorum sp. n., Trigonopterus tialeorum sp. n., Trigonopterus tibialis sp. n., Trigonopterus tridentatus sp. n., Trigonopterus uniformis sp. n., Trigonopterus variabilis sp. n., Trigonopterus velaris sp. n., Trigonopterus verrucosus sp. n., Trigonopterus violaceus sp. n., Trigonopterus viridescens sp. n., Trigonopterus wamenaensis sp. n., Trigonopterus wariorum sp. n., Trigonopterus zygops sp. n.. All new species are authored by the taxonomist-in-charge, Alexander Riedel.},
}
@article {pmid23794827,
year = {2013},
author = {Hoare, RJ and van Nieukerken, EJ},
title = {Phylogeny and host-plant relationships of the Australian Myrtaceae leafmining moth genus Pectinivalva (Lepidoptera, Nepticulidae), with new subgenera and species.},
journal = {ZooKeys},
volume = {},
number = {278},
pages = {1-64},
pmid = {23794827},
issn = {1313-2989},
abstract = {The phylogeny of the mainly Australian nepticulid genus Pectinivalva Scoble, 1983 is investigated on the basis of morphology, and a division into three monophyletic subgenera is proposed on the basis of these results. These subgenera (Pectinivalva, Casanovula Hoare, subgen. n. and Menurella Hoare, subgen. n.) are described and diagnosed, the described species of Pectinivalva are assigned to them, and representative new species are described in each: Pectinivalva (Pectinivalva) mystaconota Hoare, sp. n., Pectinivalva (Casanovula) brevipalpa Hoare, sp. n., Pectinivalva (Casanovula) minotaurus Hoare, sp. n., Pectinivalva (Menurella) scotodes Hoare, sp. n., Pectinivalva (Menurella) acmenae Hoare, sp. n., Pectinivalva (Menurella) xenadelpha Van Nieukerken &amp; Hoare, sp. n., Pectinivalva (Menurella) quintiniae Hoare &amp; Van Nieukerken, sp. n., and Pectinivalva (Menurella) tribulatrix Van Nieukerken &amp; Hoare, sp. n. Pectinivalva (Menurella) quintiniae (from Quintinia verdonii, Paracryphiaceae) is the first known member of the genus with a host-plant not belonging to Myrtaceae. Pectinivalva (Menurella) xenadelpha from Mt Gunung Lumut, Kalimantan, Borneo, is the first pectinivalvine reported from outside Australia. Keys to the subgenera of Nepticulidae known from Australia, based on adults, male and female genitalia, and larvae, are presented. Host-plant relationships of Pectinivalva are discussed with relation to the phylogeny, and a list of known host-plants of Pectinivalva, including hosts of undescribed species, is presented. DNA barcodes are provided for most of the new and several unnamed species.},
}
@article {pmid23789643,
year = {2013},
author = {Ivanova, NV and Kuzmina, ML},
title = {Protocols for dry DNA storage and shipment at room temperature.},
journal = {Molecular ecology resources},
volume = {13},
number = {5},
pages = {890-898},
pmid = {23789643},
issn = {1755-0998},
mesh = {Animals ; DNA/*isolation &amp; purification ; *Desiccation ; Insecta/genetics ; Polymerase Chain Reaction ; Preservation, Biological/*methods ; Sequence Analysis, DNA ; Specimen Handling/*methods ; Temperature ; Time Factors ; },
abstract = {The globalization of DNA barcoding will require core analytical facilities to develop cost-effective, efficient protocols for the shipment and archival storage of DNA extracts and PCR products. We evaluated three dry-state DNA stabilization systems: commercial Biomatrica(®) DNAstable(®) plates, home-made trehalose and polyvinyl alcohol (PVA) plates on 96-well panels of insect DNA stored at 56 °C and at room temperature. Controls included unprotected samples that were stored dry at room temperature and at 56 °C, and diluted samples held at 4 °C and at -20 °C. PCR and selective sequencing were performed over a 4-year interval to test the condition of DNA extracts. Biomatrica(®) provided better protection of DNA at 56 °C and at room temperature than trehalose and PVA, especially for diluted samples. PVA was the second best protectant after Biomatrica(®) at room temperature, whereas trehalose was the second best protectant at 56 °C. In spite of lower PCR success, the DNA stored at -20 °C yielded longer sequence reads and stronger signal, indicating that temperature is a crucial factor for DNA quality which has to be considered especially for long-term storage. Although it is premature to advocate a transition to DNA storage at room temperature, dry storage provides an additional layer of security for frozen samples, protecting them from degradation in the event of freezer failure. All three forms of DNA preservation enable shipment of dry DNA and PCR products between barcoding facilities.},
}
@article {pmid23789612,
year = {2013},
author = {Ashfaq, M and Akhtar, S and Khan, AM and Adamowicz, SJ and Hebert, PD},
title = {DNA barcode analysis of butterfly species from Pakistan points towards regional endemism.},
journal = {Molecular ecology resources},
volume = {13},
number = {5},
pages = {832-843},
pmid = {23789612},
issn = {1755-0998},
mesh = {Animals ; Butterflies/*classification/*genetics ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/genetics ; Entomology/*methods ; Molecular Sequence Data ; Pakistan ; *Phylogeography ; Sequence Analysis, DNA ; },
abstract = {DNA barcodes were obtained for 81 butterfly species belonging to 52 genera from sites in north-central Pakistan to test the utility of barcoding for their identification and to gain a better understanding of regional barcode variation. These species represent 25% of the butterfly fauna of Pakistan and belong to five families, although the Nymphalidae were dominant, comprising 38% of the total specimens. Barcode analysis showed that maximum conspecific divergence was 1.6%, while there was 1.7-14.3% divergence from the nearest neighbour species. Barcode records for 55 species showed <2% sequence divergence to records in the Barcode of Life Data Systems (BOLD), but only 26 of these cases involved specimens from neighbouring India and Central Asia. Analysis revealed that most species showed little incremental sequence variation when specimens from other regions were considered, but a threefold increase was noted in a few cases. There was a clear gap between maximum intraspecific and minimum nearest neighbour distance for all 81 species. Neighbour-joining cluster analysis showed that members of each species formed a monophyletic cluster with strong bootstrap support. The barcode results revealed two provisional species that could not be clearly linked to known taxa, while 24 other species gained their first coverage. Future work should extend the barcode reference library to include all butterfly species from Pakistan as well as neighbouring countries to gain a better understanding of regional variation in barcode sequences in this topographically and climatically complex region.},
}
@article {pmid23789083,
year = {2013},
author = {Lindner, DL and Carlsen, T and Henrik Nilsson, R and Davey, M and Schumacher, T and Kauserud, H},
title = {Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi.},
journal = {Ecology and evolution},
volume = {3},
number = {6},
pages = {1751-1764},
pmid = {23789083},
issn = {2045-7758},
abstract = {The rDNA internal transcribed spacer (ITS) region has been accepted as a DNA barcoding marker for fungi and is widely used in phylogenetic studies; however, intragenomic ITS variability has been observed in a broad range of taxa, including prokaryotes, plants, animals, and fungi, and this variability has the potential to inflate species richness estimates in molecular investigations of environmental samples. In this study 454 amplicon pyrosequencing of the ITS1 region was applied to 99 phylogenetically diverse axenic single-spore cultures of fungi (Dikarya: Ascomycota and Basidiomycota) to investigate levels of intragenomic variation. Three species (one Basidiomycota and two Ascomycota), in addition to a positive control species known to contain ITS paralogs, displayed levels of molecular variation indicative of intragenomic variation; taxon inflation due to presumed intragenomic variation was ≈9%. Intragenomic variability in the ITS region appears to be widespread but relatively rare in fungi (≈3-5% of species investigated in this study), suggesting this problem may have minor impacts on species richness estimates relative to PCR and/or pyrosequencing errors. Our results indicate that 454 amplicon pyrosequencing represents a powerful tool for investigating levels of ITS intragenomic variability across taxa, which may be valuable for better understanding the fundamental mechanisms underlying concerted evolution of repetitive DNA regions.},
}
@article {pmid23788453,
year = {2013},
author = {Huang, X and Huang, G and Zhang, S and Sagiyama, K and Togao, O and Ma, X and Wang, Y and Li, Y and Soesbe, TC and Sumer, BD and Takahashi, M and Sherry, AD and Gao, J},
title = {Multi-chromatic pH-activatable 19F-MRI nanoprobes with binary ON/OFF pH transitions and chemical-shift barcodes.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {52},
number = {31},
pages = {8074-8078},
pmid = {23788453},
issn = {1521-3773},
support = {P41 EB015908/EB/NIBIB NIH HHS/United States ; R01EB013149/EB/NIBIB NIH HHS/United States ; P30 CA142543/CA/NCI NIH HHS/United States ; R01 CA129011/CA/NCI NIH HHS/United States ; U24 CA126608/CA/NCI NIH HHS/United States ; R01 EB013149/EB/NIBIB NIH HHS/United States ; R01CA129011/CA/NCI NIH HHS/United States ; },
mesh = {Contrast Media/chemistry ; Fluorine/chemistry ; Hydrogen-Ion Concentration ; *Magnetic Resonance Imaging ; Micelles ; Nanostructures/*chemistry ; Polymers/chemistry ; },
}
@article {pmid23787178,
year = {2013},
author = {Hou, DY and Song, JY and Yao, H and Han, JP and Pang, XH and Shi, LC and Wang, XC and Chen, SL},
title = {Molecular identification of Corni Fructus and its adulterants by ITS/ITS2 sequences.},
journal = {Chinese journal of natural medicines},
volume = {11},
number = {2},
pages = {121-127},
doi = {10.1016/S1875-5364(13)60038-2},
pmid = {23787178},
issn = {1875-5364},
mesh = {Base Sequence ; Cornus/*classification/*genetics ; DNA, Plant/*genetics ; DNA, Ribosomal Spacer/*genetics ; Drug Contamination ; Molecular Sequence Data ; Molecular Typing/*methods ; Phylogeny ; Species Specificity ; },
abstract = {UNLABELLED: The DNA barcoding method was used to accurately and rapidly identify Corni Fructus and its adulterants.<br><br>METHODS: Genomic DNA extracted from Corni Fructus and its adulterants were used as templates. The ITS (internal trascribed spacer) regions were amplified using polymerase chain reaction. Sequence assembly was performed using CodonCode Aligner V 3.5.4. Genetic distances were computed using MEGA V 5.0. Species identification was conducted using neighbor-joining (NJ) trees.<br><br>RESULTS: The ITS sequence length of Corni Fructus was 659 bp. The average intra-specific genetic distance of Corni Fructus was 0.005, markedly lower than the inter-specific genetic distance between Corni Fructus and its adulterants (0.357). The ITS2 sequence length of Corni Fructus was 250 bp. No variation was found among the different samples. The interspecific genetic distance of ITS2 between Corni Fructus and its adulterants was 0.571. NJ trees and BLAST results indicated that Corni Fructus and its adulterants can be easily differentiated with monophyly.<br><br>CONCLUSION: ITS/ITS2 regions can accurately and efficiently distinguish Corni Fructus and its adulterants. In addition, the results not only established the foundation for the clinical safety in the utilization of Corni Fructus, but also provided reference for molecular identification of other Chinese herbal medicine and Chinese herbal pieces.},
}
@article {pmid23784850,
year = {2013},
author = {Crothers, DM},
title = {Long-range mapping of DNA.},
journal = {Biopolymers},
volume = {99},
number = {12},
pages = {1019-1031},
doi = {10.1002/bip.22332},
pmid = {23784850},
issn = {1097-0282},
mesh = {*DNA ; *Sequence Analysis, DNA ; },
abstract = {Sequence-specific optical signals are used to establish long-range sequence order and identification for fragments hundreds of kilo bases in length.},
}
@article {pmid23777414,
year = {2014},
author = {Chen, JB and Chuang, LY and Lin, YD and Liou, CW and Lin, TK and Lee, WC and Cheng, BC and Chang, HW and Yang, CH},
title = {Genetic algorithm-generated SNP barcodes of the mitochondrial D-loop for chronic dialysis susceptibility.},
journal = {Mitochondrial DNA},
volume = {25},
number = {3},
pages = {231-237},
doi = {10.3109/19401736.2013.796513},
pmid = {23777414},
issn = {1940-1744},
mesh = {*Algorithms ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry/*genetics ; Epistasis, Genetic ; Genetic Predisposition to Disease ; Humans ; Models, Genetic ; Nucleic Acid Conformation ; *Polymorphism, Single Nucleotide ; *Renal Dialysis ; Renal Insufficiency, Chronic/*genetics/*therapy ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND AND AIMS: Single nucleotide polymorphism (SNP) interaction analysis can simultaneously evaluate the complex SNP interactions present in complex diseases. However, it is less commonly applied to evaluate the predisposition of chronic dialysis and its computational analysis remains challenging. In this study, we aimed to improve the analysis of SNP-SNP interactions within the mitochondrial D-loop in chronic dialysis.<br><br>MATERIAL &amp; METHOD: The SNP-SNP interactions between 77 reported SNPs within the mitochondrial D-loop in chronic dialysis study were evaluated in terms of SNP barcodes (different SNP combinations with their corresponding genotypes). We propose a genetic algorithm (GA) to generate SNP barcodes. The &#x3c7;(2) values were then calculated by the occurrences of the specific SNP barcodes and their non-specific combinations between cases and controls.<br><br>RESULTS: Each SNP barcode (2- to 7-SNP) with the highest value in the &#x3c7;(2) test was regarded as the best SNP barcode (11.304 to 23.310; p&#x2009;<&#x2009;0.001). The best GA-generated SNP barcodes (2- to 7-SNP) were significantly associated with chronic dialysis (odds ratio [OR]&#x2009;=&#x2009;1.998 to 3.139; p&#x2009;<&#x2009;0.001). The order of influence for SNPs was the same as the order of their OR values for chronic dialysis in terms of 2- to 7-SNP barcodes.<br><br>CONCLUSION: Taken together, we propose an effective algorithm to address the SNP-SNP interactions and demonstrated that many non-significant SNPs within the mitochondrial D-loop may play a role in jointed effects to chronic dialysis susceptibility.},
}
@article {pmid23773698,
year = {2013},
author = {Deiner, K and Knapp, RA and Boiano, DM and May, B},
title = {Increased accuracy of species lists developed for alpine lakes using morphology and cytochrome oxidase I for identification of specimens.},
journal = {Molecular ecology resources},
volume = {13},
number = {5},
pages = {820-831},
doi = {10.1111/1755-0998.12130},
pmid = {23773698},
issn = {1755-0998},
mesh = {Animals ; *Biota ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Invertebrates/anatomy &amp; histology/*classification/genetics ; *Lakes ; Molecular Sequence Data ; Sequence Analysis, DNA ; United States ; },
abstract = {The first step in many community ecology studies is to produce a species list from a sample of individuals. Community ecologists now have two viable ways of producing a species list: morphological and barcode identification. In this study, we compared the taxonomic resolution gained by a combined use of both methods and tested whether a change in taxonomic resolution significantly impacted richness estimates for benthic macroinvertebrates sampled from ten lakes in Sequoia National Park, USA. Across all lakes, 77 unique taxa were identified and 42% (32) were reliably identified to species using both barcode and morphological identification. Of the 32 identified to species, 63% (20) were identified solely by comparing the barcode sequence from cytochrome oxidase I to the Barcode of Life reference library. The increased resolution using a combined identification approach compared to identifications based solely on morphology resulted in a significant increase in estimated richness within a lake at the order, family, genus and species levels of taxonomy (P < 0.05). Additionally, young or damaged individuals that could not be identified using morphology were identified using their COI sequences to the genus or species level on average 75% of the time. Our results demonstrate that a combined identification approach improves accuracy of benthic macroinvertebrate species lists in alpine lakes and subsequent estimates of richness. We encourage the use of barcodes for identification purposes and specifically when morphology is insufficient, as in the case of damaged and early life stage specimens of benthic macroinvertebrates.},
}
@article {pmid23770574,
year = {2013},
author = {Alfellani, MA and Taner-Mulla, D and Jacob, AS and Imeede, CA and Yoshikawa, H and Stensvold, CR and Clark, CG},
title = {Genetic diversity of blastocystis in livestock and zoo animals.},
journal = {Protist},
volume = {164},
number = {4},
pages = {497-509},
doi = {10.1016/j.protis.2013.05.003},
pmid = {23770574},
issn = {1618-0941},
mesh = {Animals ; Animals, Zoo/*parasitology ; Blastocystis/classification/*genetics/*isolation &amp; purification/physiology ; Disease Reservoirs/*parasitology ; *Genetic Variation ; Host Specificity ; Humans ; Livestock/*parasitology ; Molecular Sequence Data ; Phylogeny ; },
abstract = {Blastocystis is a common unicellular anaerobic eukaryote that inhabits the large intestine of many animals worldwide, including humans. The finding of Blastocystis in faeces in mammals and birds has led to proposals of zoonotic potential and that these hosts may be the source of many human infections. Blastocystis is, however, a genetically diverse complex of many distinct organisms (termed subtypes; STs), and sampling to date has been limited, both geographically and in the range of hosts studied. In order to expand our understanding of host specificity of Blastocystis STs, 557 samples were examined from various non-primate animal hosts and from a variety of different countries in Africa, Asia and Europe. STs were identified using 'barcoding' of the small subunit rRNA gene using DNA extracted either from culture or directly from faeces. The host and geographic range of several STs has thereby been greatly expanded and the evidence suggests that livestock is not a major contributor to human infection. Two new STs were detected among the barcode sequences obtained; for these, and for three others where the data were incomplete, the corresponding genes were fully sequenced and phylogenetic analysis was undertaken.},
}
@article {pmid23767809,
year = {2013},
author = {Leray, M and Yang, JY and Meyer, CP and Mills, SC and Agudelo, N and Ranwez, V and Boehm, JT and Machida, RJ},
title = {A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents.},
journal = {Frontiers in zoology},
volume = {10},
number = {},
pages = {34},
pmid = {23767809},
issn = {1742-9994},
abstract = {INTRODUCTION: The PCR-based analysis of homologous genes has become one of the most powerful approaches for species detection and identification, particularly with the recent availability of Next Generation Sequencing platforms (NGS) making it possible to identify species composition from a broad range of environmental samples. Identifying species from these samples relies on the ability to match sequences with reference barcodes for taxonomic identification. Unfortunately, most studies of environmental samples have targeted ribosomal markers, despite the fact that the mitochondrial Cytochrome c Oxidase subunit I gene (COI) is by far the most widely available sequence region in public reference libraries. This is largely because the available versatile ("universal") COI primers target the 658 barcoding region, whose size is considered too large for many NGS applications. Moreover, traditional barcoding primers are known to be poorly conserved across some taxonomic groups.<br><br>RESULTS: We first design a new PCR primer within the highly variable mitochondrial COI region, the "mlCOIintF" primer. We then show that this newly designed forward primer combined with the "jgHCO2198" reverse primer to target a 313&#xa0;bp fragment performs well across metazoan diversity, with higher success rates than versatile primer sets traditionally used for DNA barcoding (i.e. LCO1490/HCO2198). Finally, we demonstrate how the shorter COI fragment coupled with an efficient bioinformatics pipeline can be used to characterize species diversity from environmental samples by pyrosequencing. We examine the gut contents of three species of planktivorous and benthivorous coral reef fish (family: Apogonidae and Holocentridae). After the removal of dubious COI sequences, we obtained a total of 334 prey Operational Taxonomic Units (OTUs) belonging to 14 phyla from 16 fish guts. Of these, 52.5% matched a reference barcode (>98% sequence similarity) and an additional 32% could be assigned to a higher taxonomic level using Bayesian assignment.<br><br>CONCLUSIONS: The molecular analysis of gut contents targeting the 313 COI fragment using the newly designed mlCOIintF primer in combination with the jgHCO2198 primer offers enormous promise for metazoan metabarcoding studies. We believe that this primer set will be a valuable asset for a range of applications from large-scale biodiversity assessments to food web studies.},
}
@article {pmid23756524,
year = {2013},
author = {Goswami, J and Davis, MC and Andersen, T and Alileche, A and Hampikian, G},
title = {Safeguarding forensic DNA reference samples with nullomer barcodes.},
journal = {Journal of forensic and legal medicine},
volume = {20},
number = {5},
pages = {513-519},
doi = {10.1016/j.jflm.2013.02.003},
pmid = {23756524},
issn = {1878-7487},
mesh = {*DNA Barcoding, Taxonomic ; *DNA Contamination ; DNA Fingerprinting ; DNA Primers ; Humans ; Laboratories ; Microsatellite Repeats ; Oligonucleotides ; Polymerase Chain Reaction ; *Quality Control ; Sequence Analysis, DNA ; *Specimen Handling ; },
abstract = {Unintended transfer of biological material containing DNA is a concern to all laboratories conducting PCR analysis. While forensic laboratories have protocols in place to reduce the possibility of contaminating casework samples, there is no way to detect when a reference sample is mislabeled as evidence, or contaminates a forensic sample. Thus there is public concern regarding the safeguarding of DNA submitted to crime labs. We demonstrate a method of introducing an internal amplification control to reference samples, in the form of a nullomer barcode which is based upon sequences absent or rare from publically accessible DNA databases. The detection of this barcode would indicate that the source of analyzed DNA was from a reference sample provided by an individual, and not from an evidence sample. We demonstrate that the nullomers can be added directly to collection devices (FTA paper) to allow tagging during the process of sample collection. We show that such nullomer oligonucleotides can be added to existing forensic typing and quantification kits, without affecting genotyping or quantification results. Finally, we show that even when diluted a million-fold and spilled on a knife, the nullomer tags can be clearly detected. These tags support the National Research Council of the National Academy recommendation that "Quality control procedures should be designed to identify mistakes, fraud, and bias" in forensic science (National Academy of Sciences, 2009).},
}
@article {pmid23753661,
year = {2013},
author = {Morrow, CC and Redmond, NE and Picton, BE and Thacker, RW and Collins, AG and Maggs, CA and Sigwart, JD and Allcock, AL},
title = {Molecular phylogenies support homoplasy of multiple morphological characters used in the taxonomy of Heteroscleromorpha (Porifera: Demospongiae).},
journal = {Integrative and comparative biology},
volume = {53},
number = {3},
pages = {428-446},
pmid = {23753661},
issn = {1557-7023},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; DNA Primers/genetics ; Electron Transport Complex IV/genetics ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Porifera/*anatomy &amp; histology/*classification/*genetics ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Sponge classification has long been based mainly on morphocladistic analyses but is now being greatly challenged by more than 12 years of accumulated analyses of molecular data analyses. The current study used phylogenetic hypotheses based on sequence data from 18S rRNA, 28S rRNA, and the CO1 barcoding fragment, combined with morphology to justify the resurrection of the order Axinellida Lévi, 1953. Axinellida occupies a key position in different morphologically derived topologies. The abandonment of Axinellida and the establishment of Halichondrida Vosmaer, 1887 sensu lato to contain Halichondriidae Gray, 1867, Axinellidae Carter, 1875, Bubaridae Topsent, 1894, Heteroxyidae Dendy, 1905, and a new family Dictyonellidae van Soest et al., 1990 was based on the conclusion that an axially condensed skeleton evolved independently in separate lineages in preference to the less parsimonious assumption that asters (star-shaped spicules), acanthostyles (club-shaped spicules with spines), and sigmata (C-shaped spicules) each evolved more than once. Our new molecular trees are congruent and contrast with the earlier, morphologically based, trees. The results show that axially condensed skeletons, asters, acanthostyles, and sigmata are all homoplasious characters. The unrecognized homoplasious nature of these characters explains much of the incongruence between molecular-based and morphology-based phylogenies. We use the molecular trees presented here as a basis for re-interpreting the morphological characters within Heteroscleromorpha. The implications for the classification of Heteroscleromorpha are discussed and a new order Biemnida ord. nov. is erected.},
}
@article {pmid23750303,
year = {2013},
author = {Kawano, T},
title = {Run-length encoding graphic rules, biochemically editable designs and steganographical numeric data embedment for DNA-based cryptographical coding system.},
journal = {Communicative &amp; integrative biology},
volume = {6},
number = {2},
pages = {e23478},
pmid = {23750303},
issn = {1942-0889},
abstract = {There have been a wide variety of approaches for handling the pieces of DNA as the "unplugged" tools for digital information storage and processing, including a series of studies applied to the security-related area, such as DNA-based digital barcodes, water marks and cryptography. In the present article, novel designs of artificial genes as the media for storing the digitally compressed data for images are proposed for bio-computing purpose while natural genes principally encode for proteins. Furthermore, the proposed system allows cryptographical application of DNA through biochemically editable designs with capacity for steganographical numeric data embedment. As a model case of image-coding DNA technique application, numerically and biochemically combined protocols are employed for ciphering the given "passwords" and/or secret numbers using DNA sequences. The "passwords" of interest were decomposed into single letters and translated into the font image coded on the separate DNA chains with both the coding regions in which the images are encoded based on the novel run-length encoding rule, and the non-coding regions designed for biochemical editing and the remodeling processes revealing the hidden orientation of letters composing the original "passwords." The latter processes require the molecular biological tools for digestion and ligation of the fragmented DNA molecules targeting at the polymerase chain reaction-engineered termini of the chains. Lastly, additional protocols for steganographical overwriting of the numeric data of interests over the image-coding DNA are also discussed.},
}
@article {pmid23749034,
year = {2013},
author = {Li, W and Guo, Z and Duo, H and Fu, Y and Peng, M and Shen, X and Tsukada, H and Irie, T and Nasu, T and Horii, Y and Nonaka, N},
title = {Survey on helminths in the small intestine of wild foxes in Qinghai, China.},
journal = {The Journal of veterinary medical science},
volume = {75},
number = {10},
pages = {1329-1333},
pmid = {23749034},
issn = {1347-7439},
mesh = {Animals ; Cestoda/*isolation &amp; purification ; Cestode Infections/epidemiology/parasitology/*veterinary ; China/epidemiology ; DNA, Helminth/chemistry/genetics ; Feces/parasitology ; Foxes/*parasitology ; Intestinal Diseases, Parasitic/epidemiology/*veterinary ; Parasite Egg Count/veterinary ; Polymerase Chain Reaction/veterinary ; Prevalence ; Zoonoses/epidemiology/*parasitology ; },
abstract = {The intestinal helminth fauna of Tibetan sand foxes (Vulpes ferrilata) and red foxes (Vulpes vulpes) inhabiting in Qinghai, China, was evaluated by conducting necropsy of hunted foxes and fecal egg examination of field-collected feces. In northeast and south Qinghai, 36 foxes were necropsied, and the species of foxes and the parasites detected were identified by the DNA barcoding. In 27 red foxes and 9 Tibetan sand foxes examined, Mesocestoides litteratus (total prevalence: 64%), Toxascaris leonina (50%), Taenia pisiformis (8%) and Taenia crassiceps (8%) were found in both species of foxes. Echinococcus shiquicus (8%) and Taenia multiceps (6%) were found only in Tibetan sand foxes. Echinococcus multilocularis (3%) and Alaria alata (8%) were found only in red foxes. In the fecal egg examination of the rectal feces, 100% of taeniid cestodes, 73% of Toxascaris and 27% of Mesocestoides worm-positive samples showed egg-positive, indicating that coprological survey for parasite eggs could only provide partial information of intestinal parasite fauna. For field-collected feces, molecular identification of feces origins and fecal egg examination were performed. In 15 Tibetan sand fox and 30 red fox feces, we found E. multilocularis eggs in one feces of Tibetan sand fox. The present study indicated that the upper intestinal helminth fauna of the two fox species in Qinghai does not differ significantly and both species would play an important role in the maintenance of taeniid cestodes.},
}
@article {pmid23747522,
year = {2013},
author = {Týč, J and Votýpka, J and Klepetková, H and Suláková, H and Jirků, M and Lukeš, J},
title = {Growing diversity of trypanosomatid parasites of flies (Diptera: Brachycera): frequent cosmopolitism and moderate host specificity.},
journal = {Molecular phylogenetics and evolution},
volume = {69},
number = {1},
pages = {255-264},
doi = {10.1016/j.ympev.2013.05.024},
pmid = {23747522},
issn = {1095-9513},
mesh = {Africa ; Animals ; Bayes Theorem ; Biological Evolution ; DNA, Protozoan/*classification/genetics ; Diptera/*parasitology ; Europe ; *Genetic Variation ; Host Specificity ; Latin America ; Models, Genetic ; *Phylogeny ; Phylogeography ; RNA, Ribosomal/*classification/genetics ; Sequence Analysis, DNA ; Trypanosomatina/*classification/genetics ; },
abstract = {Widely distributed, highly prevalent and speciose, trypanosomatid flagellates represent a convenient model to address topics such as host specificity, diversity and distribution of parasitic protists. Recent studies dealing with insect parasites of the class Kinetoplastea have been focused mainly on trypanosomatids from true bugs (Heteroptera), even though flies (Diptera, Brachycera) are also known as their frequent hosts. Phylogenetic position, host specificity and geographic distribution of trypanosomatids parasitizing dipteran hosts collected in nine countries on four continents (Bulgaria, Czech Republic, Ecuador, Ghana, Kenya, Madagascar, Mongolia, Papua New Guinea and Turkey) are presented. Spliced leader (SL) RNA gene repeats and small subunit (SSU) rRNA genes were PCR amplified from trypanosomatids infecting the gut of a total of forty fly specimens belonging to nine families. While SL RNA was mainly used for barcoding, SSU rRNA was utilized in phylogenetic analyses. Thirty-six different typing units (TUs) were revealed, of which 24 are described for the first time and represent potential new species. Multiple infections with several TUs are more common among brachyceran hosts than in true bugs, reaching one third of cases. When compared to trypanosomatids from heteropteran bugs, brachyceran flagellates are more host specific on the genus level. From seven previously recognized branches of monoxenous trypanosomatids, the Blastocrithidia and "jaculum" clades accommodate almost solely parasites of Heteroptera; two other clades (Herpetomonas and Angomonas) are formed primarily by flagellates found in dipteran hosts, with the most species-rich Leishmaniinae and the small Strigomonas and "collosoma" clades remaining promiscuous. Furthermore, two new clades of trypanosomatids from brachyceran flies emerged in this study. While flagellates from brachyceran hosts have moderate to higher host specificity, geographic distribution of at least some of them seems to be cosmopolitan. Moreover, the genus Angomonas, so far known only from South America, is present on other continents as well.},
}
@article {pmid23741330,
year = {2013},
author = {Jin, Q and Han, H and Hu, X and Li, X and Zhu, C and Ho, SY and Ward, RD and Zhang, AB},
title = {Quantifying species diversity with a DNA barcoding-based method: Tibetan moth species (Noctuidae) on the Qinghai-Tibetan Plateau.},
journal = {PloS one},
volume = {8},
number = {5},
pages = {e64428},
pmid = {23741330},
issn = {1932-6203},
mesh = {Animals ; Bayes Theorem ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*classification/genetics ; Female ; Humidity ; Male ; Moths/anatomy &amp; histology/*classification/genetics ; *Phylogeny ; Seasons ; Tibet ; },
abstract = {With the ongoing loss of biodiversity, there is a great need for fast and effective ways to assess species richness and diversity: DNA barcoding provides a powerful new tool for this. We investigated this approach by focusing on the Tibetan plateau, which is one of the world's top biodiversity hotspots. There have been few studies of its invertebrates, although they constitute the vast majority of the region's diversity. Here we investigated species diversity of the lepidopteran family Noctuidae, across different environmental gradients, using measurements based on traditional morphology as well as on DNA barcoding. The COI barcode showed an average interspecific K2P distance of 9.45±2.08%, which is about four times larger than the mean intraspecific distance (1.85±3.20%). Using six diversity indices, we did not detect any significant differences in estimated species diversity between measurements based on traditional morphology and on DNA barcoding. Furthermore, we found strong positive correlations between them, indicating that barcode-based measures of species diversity can serve as a good surrogate for morphology-based measures in most situations tested. Eastern communities were found to have significantly higher diversity than Western ones. Among 22 environmental factors tested, we found that three (precipitation of driest month, precipitation of driest quarter, and precipitation of coldest quarter) were significantly correlated with species diversity. Our results indicate that these factors could be the key ecological factors influencing the species diversity of the lepidopteran family Noctuidae on the Tibetan plateau.},
}
@article {pmid23736940,
year = {2013},
author = {Seo, SB and King, JL and Warshauer, DH and Davis, CP and Ge, J and Budowle, B},
title = {Single nucleotide polymorphism typing with massively parallel sequencing for human identification.},
journal = {International journal of legal medicine},
volume = {127},
number = {6},
pages = {1079-1086},
pmid = {23736940},
issn = {1437-1596},
mesh = {Alleles ; DNA/*genetics ; Feasibility Studies ; Female ; Forensic Genetics/instrumentation/*methods ; Gene Amplification ; Gene Library ; Genetic Carrier Screening ; Genetic Loci/genetics ; *Genotype ; Humans ; Male ; Polymorphism, Single Nucleotide/*genetics ; Sensitivity and Specificity ; *Sequence Analysis, DNA/instrumentation ; },
abstract = {The Ion AmpliSeq™ HID single nucleotide polymorphism (SNP) panel, a primer pool of 103 autosomal SNPs and 33 Y-SNPs, was evaluated using the Ion 314™ Chip on the Ion PGM™ Sequencer with four DNA samples. The study focused on the sequencing of DNA at three different initial target quantities, related interpretation issues, and concordance of results with another sequencing platform, i.e., Genome Analyzer IIx. With 10 ng of template DNA, all genotypes at the 136 SNPs were detected. With 1 ng of DNA, all SNPs were detected and one SNP locus in one sample showed extreme heterozygote imbalance on allele coverage. With 100 pg of DNA, an average of 1.6 SNP loci were not detected, and an average of 4.3 SNPs showed heterozygote imbalance. The average sequence coverage was 945-600× at autosomal SNPs and 465-209× at Y-SNPs for 10 ng-100 pg of DNA. The average heterozygote allele coverage ratio was 89.6-61.8 % for 10 ng-100 pg of DNA. At 10 ng of DNA, all genotypes of the 95 SNPs shared between the two different sequencing platforms were concordant except for one SNP, rs1029047. The error was due to the misalignment of a flanking homopolymer. Overall, the data support that genotyping a large battery of SNPs is feasible with massively parallel sequencing. With barcode systems, better allele balance, and specifically designed alignment software, a more comprehensive rapid genotyping and more cost-effective results may be obtained from multiple samples in one analysis than are possible with current typing and capillary electrophoresis systems.},
}
@article {pmid23730349,
year = {2013},
author = {Lee, JS and Zhao, H},
title = {On Estimation of Allele Frequencies via Next-Generation DNA Resequencing with Barcoding.},
journal = {Statistics in biosciences},
volume = {5},
number = {1},
pages = {26-53},
pmid = {23730349},
issn = {1867-1764},
support = {R01 GM059507/GM/NIGMS NIH HHS/United States ; S10 RR019895/RR/NCRR NIH HHS/United States ; T15 LM007056/LM/NLM NIH HHS/United States ; },
abstract = {Next Generation Sequencing (NGS) has revolutionized biomedical research in recent years. It is now commonly used to identify rare variants through re-sequencing individual genomes. Due to the cost of NGS, researchers have considered pooling samples as a cost-effective alternative to individual sequencing. In this article, we consider the estimation of allele frequencies of rare variants through the NGS technologies with pooled DNA samples with or without barcodes. We consider three methods for estimating allele frequencies from such data, including raw sequencing counts, inferred genotypes, and expected minor allele counts and compare their performance. Our simulation results suggest that the estimator based on inferred genotypes overall performs better than or as well as the other two estimators. When the sequencing coverage is low, biases and MSEs can be sensitive to the choice of the prior probabilities of genotypes for the estimators based on inferred genotypes and expected minor allele counts so that more accurate specification of prior probabilities is critical to lower biases and MSEs. Our study shows that the optimal number of barcodes in a pool is relatively robust to the frequencies of rare variants at a specific coverage depth. We provide general guidelines on using DNA pooling with barcoding for the estimation of allele frequencies of rare variants.},
}
@article {pmid23730179,
year = {2013},
author = {Crabo, LG and Davis, M and Hammond, P and Tomas Mustelin, and Jon Shepard, },
title = {Five new species and three new subspecies of Erebidae and Noctuidae (Insecta, Lepidoptera) from Northwestern North America, with notes on Chytolita Grote (Erebidae) and Hydraecia Guenée (Noctuidae).},
journal = {ZooKeys},
volume = {},
number = {264},
pages = {85-123},
pmid = {23730179},
issn = {1313-2989},
abstract = {Several taxonomic issues in the moth families Erebidae and Noctuidae are addressed for Northwestern North America. Drasteria parallelaCrabo &amp; Mustelin andCycnia oregonensis tristisCrabo in the Erebidae and Eudryas brevipennis bonneville Shepard &amp; Crabo, Resapamea diluvius Crabo, Resapamea angelika Crabo, Resapamea mammuthus Crabo, Fishia nigrescens Hammond &amp; Crabo, and Xestia perquiritata orcaCrabo &amp; Hammond in the Noctuidae are described as new. The following new synonyms are proposed: Chytolita petrealis Grote with Herminea morbidalis Guenée; Gortyna columbia Barnes &amp; Benjamin and Gortyna ximena Barnes &amp; Benjamin with Gortyna obliqua Harvey; and Hydroecia pallescens Smith with Hydroecia medialis Smith. The type locality of Gortyna intermedia Barnes &amp; Benjamin is restricted to Lundbreck, Municipality of Crowsnest Pass, Alberta, Canada.},
}
@article {pmid23730176,
year = {2013},
author = {Chacón, IA and Janzen, DH and Hallwachs, W and J Bolling Sullivan, and Hajibabaei, M},
title = {Cryptic species within cryptic moths: new species of Dunama Schaus (Notodontidae, Nystaleinae) in Costa Rica.},
journal = {ZooKeys},
volume = {},
number = {264},
pages = {11-45},
pmid = {23730176},
issn = {1313-2989},
abstract = {Based on almost 1,700 recently reared and wild-collected specimens, the genus Dunama Schaus (Notodontidae, Nystaelinae) in Costa Rica is reviewed. Eight species are recorded of which seven are newly described: Dunama jessiehillae Chacón, Dunama jessiebarronae Chacón, Dunama janewaldronae Chacón, Dunama jessiebancroftae Chacón, Dunama janecoxae Chacón, Dunama biosise Chacón, Dunama indereci Chacón. Dunama angulinea Schaus is redescribed and associated with its correct genitalia. Dunama tuna (Schaus), previously listed as ocurring in Costa Rica, is restricted to Colombia. Most species are described through their distinctive CO1 barcodes, genitalia and life histories. Dunama adults and caterpillars, their foodplants, and their parasites in Area de Conservación Guanacaste (ACG) in northwestern Costa Rica are described where known. Many life history stages are illustrated.},
}
@article {pmid23726715,
year = {2013},
author = {Elad, T and Belkin, S},
title = {Broad spectrum detection and "barcoding" of water pollutants by a genome-wide bacterial sensor array.},
journal = {Water research},
volume = {47},
number = {11},
pages = {3782-3790},
doi = {10.1016/j.watres.2013.04.011},
pmid = {23726715},
issn = {1879-2448},
mesh = {Artificial Intelligence ; Cluster Analysis ; Environmental Monitoring/*methods ; Escherichia coli/drug effects/*genetics ; Gene Expression/drug effects ; Genome, Bacterial/*drug effects ; Models, Theoretical ; Predictive Value of Tests ; Promoter Regions, Genetic ; Sensitivity and Specificity ; Water Pollutants, Chemical/analysis/*toxicity ; },
abstract = {An approach for the rapid detection and classification of a broad spectrum of water pollutants, based on a genome-wide reporter bacterial live cell array, is proposed and demonstrated. An array of ca. 2000 Escherichia coli fluorescent transcriptional reporters was exposed to 25 toxic compounds as well as to unpolluted water, and its responses were recorded after 3 h. The 25 toxic compounds represented 5 pollutant classes: genotoxicants, metals, detergents, alcohols, and monoaromatic hydrocarbons. Identifying unique gene expression patterns, a nearest neighbour-based model detected pollutant presence and predicted class attribution with an estimated accuracy of 87%. Sensitivity and positive predictive values varied among classes, being higher for pollutant classes that were defined by mode of action than for those defined by structure only. Sensitivity for unpolluted water was 0.90 and the positive predictive value was 0.79. All pollutant classes induced the transcription of a statistically significant proportion of membrane associated genes; in addition, the sets of genes responsive to genotoxicants, detergents and alcohols were enriched with genes involved in DNA repair, iron utilization and the translation machinery, respectively. Following further development, a methodology of the type described herein may be suitable for integration in water monitoring schemes in conjunction with existing analytical and biological detection techniques.},
}
@article {pmid23724665,
year = {2013},
author = {Chen, SL and Zhu, XX and Chen, XC and Niu, YY and Zhang, X and Song, JY and Luo, HM and Sun, C},
title = {[New technologies used for Panax genus research].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {38},
number = {5},
pages = {633-639},
pmid = {23724665},
issn = {1001-5302},
mesh = {Biotechnology/*methods ; Cloning, Molecular ; DNA Fingerprinting ; Ginsenosides/biosynthesis ; *Panax/enzymology/genetics/metabolism ; *Research Design ; },
abstract = {The authors reviewed the new technologies used for Panax genus research, including molecular identification technologies (especially for DNA barcoding), modern biotechnologies (e. g. the first generation and second generation sequencing technologies), and gene cloning and identification in this paper. These technologies have been successfully applied to species identification, transcriptome analysis, secondary metabolite biosynthetic pathway and the key enzyme function identification, indicating that the application of modern biotechnologies provide guarantee for the molecular identification of Panax genus. The application of modern biotechnologies also reveals the genetic information of transcriptome and functional genomics, and promotes the design of Panax plants genomic map. In summary, the application of the new technologies lay the foundation for clarifying the molecular mechanisms of ginsenoside biosynthesis and enforcing the in vitro synthesis of important natural products and new drugs in future.},
}
@article {pmid23721749,
year = {2013},
author = {Kvist, S},
title = {Barcoding in the dark? A critical view of the sufficiency of zoological DNA barcoding databases and a plea for broader integration of taxonomic knowledge.},
journal = {Molecular phylogenetics and evolution},
volume = {69},
number = {1},
pages = {39-45},
doi = {10.1016/j.ympev.2013.05.012},
pmid = {23721749},
issn = {1095-9513},
mesh = {Animals ; Biodiversity ; DNA/*classification/genetics ; DNA Barcoding, Taxonomic/*standards/statistics &amp; numerical data ; Databases, Nucleic Acid/standards/*supply &amp; distribution ; Fungi/*classification/genetics ; Guidelines as Topic ; *Phylogeny ; Plants/*classification/genetics ; Sequence Analysis, DNA ; },
abstract = {The functionality of standard zoological DNA barcoding practice (the identification of unknown specimens by comparison of COI sequences) is contingent on working barcode databases with sufficient taxonomic coverage. It has already been established that the main barcoding repositories, NCBI and BOLD, are devoid of data for many animal groups but the specific taxonomic coverage of the repositories across animal biodiversity remains unexplored. Here, I shed light on this mystery by contrasting the number of unique taxon labels in the two databases with the number of currently recognized species for each animal phylum. The numbers reveal an overall paucity of COI sequence data in the repositories (15.13% total coverage across the recognized biodiversity on Earth, and 20.76% average taxonomic coverage for each phylum) and, more importantly, bear witness to the idleness towards numerous phyla, rendering current barcoding efforts either ineffective or inaccurate. The importance of further integrating taxonomic expertise into barcoding practice is briefly discussed and some guidelines, previously mentioned in the barcoding literature, are suggested anew. Finally, the asserted values concerning the taxonomic coverage in barcoding databases for Animalia are contrasted with those of Plantae and Fungi.},
}
@article {pmid23719303,
year = {2013},
author = {Verovskaya, E and Broekhuis, MJ and Zwart, E and Ritsema, M and van Os, R and de Haan, G and Bystrykh, LV},
title = {Heterogeneity of young and aged murine hematopoietic stem cells revealed by quantitative clonal analysis using cellular barcoding.},
journal = {Blood},
volume = {122},
number = {4},
pages = {523-532},
doi = {10.1182/blood-2013-01-481135},
pmid = {23719303},
issn = {1528-0020},
mesh = {Age Factors ; Aging/*blood ; Animals ; *Blood Donors ; Cell Separation/methods ; Cell Tracking/*methods ; Cells, Cultured ; Cellular Senescence/*physiology ; Clonal Evolution/*physiology ; Clone Cells/cytology/physiology ; DNA Barcoding, Taxonomic/methods/statistics &amp; numerical data ; Hematopoietic Stem Cells/*cytology/physiology ; High-Throughput Nucleotide Sequencing ; Mice ; Mice, Inbred C57BL ; Models, Biological ; Molecular Typing/methods ; },
abstract = {The number of hematopoietic stem cells (HSCs) that contributes to blood formation and the dynamics of their clonal contribution is a matter of ongoing discussion. Here, we use cellular barcoding combined with multiplex high-throughput sequencing to provide a quantitative and sensitive analysis of clonal behavior of hundreds of young and old HSCs. The majority of transplanted clones steadily contributes to hematopoiesis in the long-term, although clonal output in granulocytes, T cells, and B cells is substantially different. Contributions of individual clones to blood are dynamically changing; most of the clones either expand or decline with time. Finally, we demonstrate that the pool of old HSCs is composed of multiple small clones, whereas the young HSC pool is dominated by fewer, but larger, clones.},
}
@article {pmid23719221,
year = {2013},
author = {Tamm, H and Põldmaa, K},
title = {Diversity, host associations, and phylogeography of temperate aurofusarin-producing Hypomyces/Cladobotryum including causal agents of cobweb disease of cultivated mushrooms.},
journal = {Fungal biology},
volume = {117},
number = {5},
pages = {348-367},
doi = {10.1016/j.funbio.2013.03.005},
pmid = {23719221},
issn = {1878-6146},
mesh = {Agaricales/*physiology ; Biodiversity ; Evolution, Molecular ; Fungal Proteins/genetics/metabolism ; Genetic Variation ; Host-Pathogen Interactions ; Hypocreales/classification/*genetics/isolation &amp; purification/*metabolism ; Molecular Sequence Data ; Naphthoquinones/*metabolism ; Phylogeny ; Plant Diseases ; Vegetables/*microbiology ; },
abstract = {Temperate species of Hypomyces and Cladobotryum that produce the red pigment aurofusarin are common on agaricoid and polyporoid basidiomata of species from five orders of Agaricomycetes. Several cause cobweb disease of commercially cultivated mushrooms resulting in serious losses. We sequenced rpb1, rpb2, tef1, and FG1093 regions in 90 wild strains and 30 strains from mushroom farms, isolated from Europe, North America, Africa, Asia, Australia, and New Zealand. Multigene analyses support the distinctness of five species but reveal Hypomyces rosellus to be paraphyletic, comprising several cryptic lineages. Hypomyces rosellus s. str. is characterised by wide dispersal and gene flow across Eurasia but does not occur in North America. Instead, the lineages from the West and the East Coast appear distinct, having given rise to species inhabiting the Southern Hemisphere. Our results reveal wide misuse of the name H. rosellus, especially for cobweb isolates. The majority of these belong to Hypomyces odoratus, including a weakly supported group of fungicide-resistant strains from Europe and North America sharing identical sequence data. New collections are presented for Cladobotryum rubrobrunnescens and Cladobotryum tenue as well as Cladobotryum multiseptatum and Hypomyces dactylarioides, all previously known only from their type material. The former species pair occurs in Europe and the latter in Australia and New Zealand. Separate lineages appear to be maintained by geographic isolation in North America and temperate Australasia but by host specialisation in the species occurring sympatrically in Europe and Asia. Both specialist and generalist host use strategies have evolved in the group. Although teleomorphs are known in most of the species and unnamed lineages, analyses of the five-gene regions suggest the prevalence of clonal reproduction in H. odoratus. This can be the reason for its success in mushroom farms, also facilitating the spread of fungicide resistance. While tef1 and rpb2 can be recommended for species delimitation, low variation, not exceeding 1 % in the whole ingroup, impeaches the use of ITS as a barcoding gene region in this group of fungi.},
}
@article {pmid23718854,
year = {2013},
author = {Frey, JE and Guillén, L and Frey, B and Samietz, J and Rull, J and Aluja, M},
title = {Developing diagnostic SNP panels for the identification of true fruit flies (Diptera: Tephritidae) within the limits of COI-based species delimitation.},
journal = {BMC evolutionary biology},
volume = {13},
number = {},
pages = {106},
pmid = {23718854},
issn = {1471-2148},
mesh = {Animals ; Base Sequence ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Insect Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Tephritidae/*classification/enzymology/*genetics ; },
abstract = {BACKGROUND: Rapid and reliable identification of quarantine pests is essential for plant inspection services to prevent introduction of invasive species. For insects, this may be a serious problem when dealing with morphologically similar cryptic species complexes and early developmental stages that lack distinctive characters useful for taxonomic identification. DNA based barcoding could solve many of these problems. The standard barcode fragment, an approx. 650 base pairs long sequence of the 5'end of the mitochondrial cytochrome oxidase I (COI), enables differentiation of a very wide range of arthropods. However, problems remain in some taxa, such as Tephritidae, where recent genetic differentiation among some of the described species hinders accurate molecular discrimination.<br><br>RESULTS: In order to explore the full species discrimination potential of COI, we sequenced the barcoding region of the COI gene of a range of economically important Tephritid species and complemented these data with all GenBank and BOLD entries for the systematic group available as of January 2012. We explored the limits of species delimitation of this barcode fragment among 193 putative Tephritid species and established operational taxonomic units (OTUs), between which discrimination is reliably possible. Furthermore, to enable future development of rapid diagnostic assays based on this sequence information, we characterized all single nucleotide polymorphisms (SNPs) and established "near-minimal" sets of SNPs that differentiate among all included OTUs with at least three and four SNPs, respectively.<br><br>CONCLUSIONS: We found that although several species cannot be differentiated based on the genetic diversity observed in COI and hence form composite OTUs, 85% of all OTUs correspond to described species. Because our SNP panels are developed based on all currently available sequence information and rely on a minimal pairwise difference of three SNPs, they are highly reliable and hence represent an important resource for developing taxon-specific diagnostic assays. For selected cases, possible explanations that may cause composite OTUs are discussed.},
}
@article {pmid23718836,
year = {2013},
author = {Gao, R and Zhang, G},
title = {Potential of DNA barcoding for detecting quarantine fungi.},
journal = {Phytopathology},
volume = {103},
number = {11},
pages = {1103-1107},
doi = {10.1094/PHYTO-12-12-0321-R},
pmid = {23718836},
issn = {0031-949X},
mesh = {Basidiomycota/genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Fungi/classification/genetics/*isolation &amp; purification ; Fusarium/genetics/isolation &amp; purification ; Phytophthora/genetics/isolation &amp; purification ; Quarantine ; Species Specificity ; },
abstract = {The detection of live quarantine pathogenic fungi plays an important role in guaranteeing regional biological safety. DNA barcoding, an emerging species identification technology, holds promise for the reliable, quick, and accurate detection of quarantine fungi. International standards for phytosanitary guidelines are urgently needed. The varieties of quarantine fungi listed for seven countries/regions, the currently applied detection methods, and the status of DNA barcoding for detecting quarantine fungi are summarized in this study. Two approaches have been proposed to apply DNA barcoding to fungal quarantine procedures: (i) to verify the reliability of known internal transcribed spacer (ITS)/cytochrome c oxidase subunit I (COI) data for use as barcodes, and (ii) to determine other barcodes for species that cannot be identified by ITS/COI. As a unique, standardizable, and universal species identification tool, DNA barcoding offers great potential for integrating detection methods used in various countries/regions and establishing international detection standards based on accepted DNA barcodes. Through international collaboration, interstate disputes can be eased and many problems related to routine quarantine detection methods can be solved for global trade.},
}
@article {pmid23718785,
year = {2013},
author = {Meganathan, PR and Dubey, B and Jogayya, KN and Haque, I},
title = {Identification of Indian crocodile species through DNA barcodes.},
journal = {Journal of forensic sciences},
volume = {58},
number = {4},
pages = {993-998},
doi = {10.1111/1556-4029.12129},
pmid = {23718785},
issn = {1556-4029},
mesh = {Alligators and Crocodiles/*genetics ; Animals ; Conservation of Natural Resources/legislation &amp; jurisprudence ; Crime/legislation &amp; jurisprudence ; DNA Barcoding, Taxonomic/*methods ; DNA Primers ; Electron Transport Complex IV/*genetics ; India ; Phylogeny ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The biodiversity of India includes three crocodile species, Crocodylus palustris, Crocodylus porosus, and Gavialis gangeticus, whose status is threatened due to bushmeat crisis and illegal hunting. The crocodilian conservation management requires novel techniques to help forensic analysts to reveal species identity. DNA barcoding is a species identification technique, where a partial cytochrome c oxidase subunit 1 gene is used as a marker for species identification. Herein, the DNA barcoding technique is evaluated for three Indian crocodiles by analyzing an approximately 750-bp barcode region. The alignment result shows interspecific variations between sequences for discrimination of the three Indian crocodiles leading to species identification. The phylogenetic analyses also substantiate the established crocodilian relationships, which add further advantage to use this DNA barcoding approach for Indian crocodiles. This study provides preliminary evidences for the use of DNA barcoding technique in the identification of Indian crocodile species.},
}
@article {pmid23711340,
year = {2013},
author = {Bergmann, T and Rach, J and Damm, S and Desalle, R and Schierwater, B and Hadrys, H},
title = {The potential of distance-based thresholds and character-based DNA barcoding for defining problematic taxonomic entities by CO1 and ND1.},
journal = {Molecular ecology resources},
volume = {13},
number = {6},
pages = {1069-1081},
doi = {10.1111/1755-0998.12125},
pmid = {23711340},
issn = {1755-0998},
mesh = {Classification/methods ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/chemistry/genetics ; Molecular Sequence Data ; NADH Dehydrogenase/chemistry/genetics ; Odonata/classification/*genetics ; Sequence Alignment ; Species Specificity ; },
abstract = {The mitochondrial CO1 gene (cytochrome c oxidase I) is a widely accepted metazoan barcode region. In insects, the mitochondrial NADH dehydrogenase subunit 1 (ND1) gene region has proved to be another suitable marker especially for the identification of lower level taxonomic entities such as populations and sister species. To evaluate the potential of distance-based thresholds and character-based DNA barcoding for the identification of problematic species-rich taxa, both markers, CO1 and ND1, were used as test parameters in odonates. We sequenced and compared gene fragments of CO1 and ND1 for 271 odonate individuals representing 51 species, 22 genera and eight families. Our data suggests that (i) the combination of the CO1 and ND1 fragment forms a better identifier than a single region alone; and (ii) the character-based approach provides higher resolution than the distance-based method in Odonata especially in closely related taxonomic entities.},
}
@article {pmid23709623,
year = {2013},
author = {Rubinstein, ND and Feldstein, T and Shenkar, N and Botero-Castro, F and Griggio, F and Mastrototaro, F and Delsuc, F and Douzery, EJ and Gissi, C and Huchon, D},
title = {Deep sequencing of mixed total DNA without barcodes allows efficient assembly of highly plastic ascidian mitochondrial genomes.},
journal = {Genome biology and evolution},
volume = {5},
number = {6},
pages = {1185-1199},
pmid = {23709623},
issn = {1759-6653},
mesh = {Animals ; Base Sequence ; Gene Order ; Gene Rearrangement ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*methods ; Molecular Sequence Data ; Phylogeny ; Urochordata/*genetics ; },
abstract = {Ascidians or sea squirts form a diverse group within chordates, which includes a few thousand members of marine sessile filter-feeding animals. Their mitochondrial genomes are characterized by particularly high evolutionary rates and rampant gene rearrangements. This extreme variability complicates standard polymerase chain reaction (PCR) based techniques for molecular characterization studies, and consequently only a few complete Ascidian mitochondrial genome sequences are available. Using the standard PCR and Sanger sequencing approach, we produced the mitochondrial genome of Ascidiella aspersa only after a great effort. In contrast, we produced five additional mitogenomes (Botrylloides aff. leachii, Halocynthia spinosa, Polycarpa mytiligera, Pyura gangelion, and Rhodosoma turcicum) with a novel strategy, consisting in sequencing the pooled total DNA samples of these five species using one Illumina HiSeq 2000 flow cell lane. Each mitogenome was efficiently assembled in a single contig using de novo transcriptome assembly, as de novo genome assembly generally performed poorly for this task. Each of the new six mitogenomes presents a different and novel gene order, showing that no syntenic block has been conserved at the ordinal level (in Stolidobranchia and in Phlebobranchia). Phylogenetic analyses support the paraphyly of both Ascidiacea and Phlebobranchia, with Thaliacea nested inside Phlebobranchia, although the deepest nodes of the Phlebobranchia-Thaliacea clade are not well resolved. The strategy described here thus provides a cost-effective approach to obtain complete mitogenomes characterized by a highly plastic gene order and a fast nucleotide/amino acid substitution rate.},
}
@article {pmid23705974,
year = {2013},
author = {Yosipof, A and Basch, H and Hoz, S},
title = {Nucleophilic and electrophilic reactions of polyynes catalyzed by an electric field: toward barcoding of carbon nanotubes like long homogeneous substrates.},
journal = {The journal of physical chemistry. A},
volume = {117},
number = {24},
pages = {5023-5027},
doi = {10.1021/jp402758u},
pmid = {23705974},
issn = {1520-5215},
abstract = {Computational studies at the B3LYP/6-31+G* level were carried out on the addition of pyridine to polyynes (C6-C18) and on the protonation of polyynes by methyl ammonium fluoride under electric fields of 2.5 and 5 MV/cm. The electric field in each case was oriented along the polyyne axis in a direction that enhances the reaction by stabilizing the incipient dipole. It was found that the reaction of pyridine addition is endothermic with a late transition state. The longer the polyynes and the stronger the field, the electric field catalysis was more efficient. Extrapolation of the data to long polyynes shows that at 1000 nm an electric field of 50 000 V/cm will reduce the barrier by 10 kcal/mol. This reduction is equivalent to 7 orders of magnitude in rate enhancement. A similar barrier reduction could be achieved with a 2.5 MV/cm field at a polyyne length of 20 nm. Protonation reactions were found to be much more affected by the electric field. A reduction of the reaction barrier by 10 kcal/mol using a 2.5 MV/cm electric field could be achieved at a polyyne length of 10 nm. Thus the electric field along the long axis of a substrate could induce a gradient of reactivity which could, in principle, enable the barcoding of substrates by using a sequence of reactants having different reactivities.},
}
@article {pmid23702155,
year = {2013},
author = {Gómez, G and Jaramillo, L and Correa, MM},
title = {Wing geometric morphometrics and molecular assessment of members in the Albitarsis Complex from Colombia.},
journal = {Molecular ecology resources},
volume = {13},
number = {6},
pages = {1082-1092},
doi = {10.1111/1755-0998.12126},
pmid = {23702155},
issn = {1755-0998},
mesh = {Animals ; Anopheles/anatomy &amp; histology/classification/*genetics ; Bayes Theorem ; Biodiversity ; Colombia ; Female ; Genetic Markers ; Molecular Sequence Data ; Phenotype ; Sequence Analysis, DNA ; Species Specificity ; Wings, Animal/*anatomy &amp; histology ; },
abstract = {Malaria parasites are transmitted to humans by female mosquitoes of the genus Anopheles. The Albitarsis Complex harbours at least eight species not readily differentiable by morphology. This complicates the determination of those species involved in malaria transmission and the implementation of targeted and effective vector control strategies. In Colombia, there is little information about the identity and distribution of the Albitarsis Complex members. In this work, COI DNA barcoding was used to assign specimens Anopheles albitarsis s.l. to any of the previously designated species of the Albitarsis Complex. Two molecular operational taxonomic units (MOTUs), differentially distributed in Colombia, were detected, A. albitarsis I in the NW and NE, and A. albitarsis F, E and NE Colombia. In contrast, nuclear white gene and ITS2 sequence analyses did not allow differentiating between the MOTUs. Wing landmark-based geometric morphometrics applied to explore intertaxa phenotypic heterogeneity showed a subtle but significant difference in size, while shape did not allow the separation of the MOTUs. In general, the multiple marker analysis was not supportive of the existence in Colombia of more than one species of the Albitarsis Complex.},
}
@article {pmid23695686,
year = {2013},
author = {Baselga, A and Fujisawa, T and Crampton-Platt, A and Bergsten, J and Foster, PG and Monaghan, MT and Vogler, AP},
title = {Whole-community DNA barcoding reveals a spatio-temporal continuum of biodiversity at species and genetic levels.},
journal = {Nature communications},
volume = {4},
number = {},
pages = {1892},
pmid = {23695686},
issn = {2041-1723},
mesh = {Animals ; Aquatic Organisms/genetics ; *Biodiversity ; Biota ; Coleoptera/*classification/*genetics ; Computer Simulation ; DNA Barcoding, Taxonomic/*methods ; Ecosystem ; Europe ; Fractals ; *Genetic Variation ; Haplotypes/genetics ; Molecular Sequence Data ; Mutation/genetics ; *Spatio-Temporal Analysis ; Species Specificity ; Time Factors ; },
abstract = {A correlation of species and genetic diversity has been proposed but not uniformly supported. Large-scale DNA barcoding provides qualitatively novel data to test for correlations across hierarchical levels (genes, genealogies and species), and may help to unveil the underlying processes. Here we analyse sequence variation in communities of aquatic beetles across Europe (>5,000 individuals) to test for self-similarity of beta diversity patterns at multiple hierarchical levels. We show that community similarity at all levels decreases exponentially with geographic distance, and initial similarity is correlated with the lineage age, consistent with a molecular clock. Log-log correlations between lineage age, number of lineages, and range sizes, reveal a fractal geometry in time and space, indicating a spatio-temporal continuum of biodiversity across scales. Simulations show that these findings mirror dispersal-constrained models of haplotype distributions. These novel macroecological patterns may be explained by neutral evolutionary processes, acting continuously over time to produce multi-scale regularities of biodiversity.},
}
@article {pmid23695493,
year = {2013},
author = {Wu, SJ and Chuang, LY and Lin, YD and Ho, WH and Chiang, FT and Yang, CH and Chang, HW},
title = {Particle swarm optimization algorithm for analyzing SNP-SNP interaction of renin-angiotensin system genes against hypertension.},
journal = {Molecular biology reports},
volume = {40},
number = {7},
pages = {4227-4233},
pmid = {23695493},
issn = {1573-4978},
mesh = {*Algorithms ; Computational Biology/*methods ; *Epistasis, Genetic ; Genetic Predisposition to Disease ; Genotype ; Humans ; Hypertension/*genetics ; Models, Biological ; Odds Ratio ; *Polymorphism, Single Nucleotide ; Renin-Angiotensin System/*genetics ; Reproducibility of Results ; },
abstract = {Most non-significant individual single nucleotide polymorphisms (SNPs) were undiscovered in hypertension association studies. Their possible SNP-SNP interactions were usually ignored and leaded to missing heritability. In present study, we proposed a particle swarm optimization (PSO) algorithm to analyze the SNP-SNP interaction associated with hypertension. Genotype dataset of eight SNPs of renin-angiotensin system genes for 130 non-hypertension and 313 hypertension subjects were included. Without SNP-SNP interaction, most individual SNPs were non-significant difference between the hypertension and non-hypertension groups. For SNP-SNP interaction, PSO can select the SNP combinations involving different SNP numbers, namely the best SNP barcodes, to show the maximum frequency difference between non-hypertension and hypertension groups. After computation, the best PSO-generated SNP barcodes were dominant in non-hypertension in terms of the occurrences of frequency differences between non-hypertension and hypertension groups. The OR values of the best SNP barcodes involving 2-8 SNPs were 0.705-0.334, suggesting that these SNP barcodes were protective against hypertension. In conclusion, this study demonstrated that non-significant SNPs may generate the joint effect in association study. Our proposed PSO algorithm is effective to identify the best protective SNP barcodes against hypertension.},
}
@article {pmid23694692,
year = {2013},
author = {Porter, TM and Golding, GB and King, C and Froese, D and Zazula, G and Poinar, HN},
title = {Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility.},
journal = {Molecular ecology resources},
volume = {13},
number = {5},
pages = {798-810},
doi = {10.1111/1755-0998.12124},
pmid = {23694692},
issn = {1755-0998},
mesh = {Animals ; *Biodiversity ; Chloroplast Proteins/genetics ; Cluster Analysis ; Electron Transport Complex IV/genetics ; *Fossils ; Introns ; Plants ; Prokaryotic Cells ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil ; },
abstract = {DNA sequencing of ancient permafrost samples can be used to reconstruct past plant, animal and bacterial communities. In this study, we assess the small-scale reproducibility of taxonomic composition obtained from sequencing four molecular markers (mitochondrial 12S ribosomal DNA (rDNA), prokaryote 16S rDNA, mitochondrial cox1 and chloroplast trnL intron) from two soil cores sampled 10 cm apart. In addition, sequenced control reactions were used to produce a contaminant library that was used to filter similar sequences from sample libraries. Contaminant filtering resulted in the removal of 1% of reads or 0.3% of operational taxonomic units. We found similar richness, overlap, abundance and taxonomic diversity from the 12S, 16S and trnL markers from each soil core. Jaccard dissimilarity across the two soil cores was highest for metazoan taxa detected by the 12S and cox1 markers. Taxonomic community distances were similar for each marker across the two soil cores when the chi-squared metric was used; however, the 12S and cox1 markers did not cluster well when the Goodall similarity metric was used. A comparison of plant macrofossil vs. read abundance corroborates previous work that suggests eastern Beringia was dominated by grasses and forbs during cold stages of the Pleistocene, a habitat that is restricted to isolated sites in the present-day Yukon.},
}
@article {pmid23681854,
year = {2013},
author = {Fujisawa, T and Barraclough, TG},
title = {Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and evaluation on simulated data sets.},
journal = {Systematic biology},
volume = {62},
number = {5},
pages = {707-724},
pmid = {23681854},
issn = {1076-836X},
support = {BB/G004250/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Algorithms ; Animals ; Classification/*methods ; Coleoptera/classification/genetics ; *Computer Simulation ; Models, Theoretical ; *Phylogeny ; Species Specificity ; },
abstract = {DNA barcoding-type studies assemble single-locus data from large samples of individuals and species, and have provided new kinds of data for evolutionary surveys of diversity. An important goal of many such studies is to delimit evolutionarily significant species units, especially in biodiversity surveys from environmental DNA samples. The Generalized Mixed Yule Coalescent (GMYC) method is a likelihood method for delimiting species by fitting within- and between-species branching models to reconstructed gene trees. Although the method has been widely used, it has not previously been described in detail or evaluated fully against simulations of alternative scenarios of true patterns of population variation and divergence between species. Here, we present important reformulations to the GMYC method as originally specified, and demonstrate its robustness to a range of departures from its simplifying assumptions. The main factor affecting the accuracy of delimitation is the mean population size of species relative to divergence times between them. Other departures from the model assumptions, such as varying population sizes among species, alternative scenarios for speciation and extinction, and population growth or subdivision within species, have relatively smaller effects. Our simulations demonstrate that support measures derived from the likelihood function provide a robust indication of when the model performs well and when it leads to inaccurate delimitations. Finally, the so-called single-threshold version of the method outperforms the multiple-threshold version of the method on simulated data: we argue that this might represent a fundamental limit due to the nature of evidence used to delimit species in this approach. Together with other studies comparing its performance relative to other methods, our findings support the robustness of GMYC as a tool for delimiting species when only single-locus information is available.},
}
@article {pmid23680306,
year = {2013},
author = {Rebijith, KB and Asokan, R and Kumar, NK and Krishna, V and Chaitanya, BN and Ramamurthy, VV},
title = {DNA barcoding and elucidation of cryptic aphid species (Hemiptera: Aphididae) in India.},
journal = {Bulletin of entomological research},
volume = {103},
number = {5},
pages = {601-610},
doi = {10.1017/S0007485313000278},
pmid = {23680306},
issn = {1475-2670},
mesh = {Animals ; Aphids/*classification/genetics ; *DNA Barcoding, Taxonomic ; India ; },
abstract = {Rapid, precise and timely identification of invasive pest insects such as aphids is important and a challenge worldwide due to their complex life cycles, parthenogenetic reproduction, sex and colour morphs. In this respect, DNA barcoding employing a 658 bp fragment of 5′ region of the mitochondrial cytochrome oxidase I (CO-I) gene is an effective tool in addressing the above. In the present study, we employed CO-I for discriminating 142 individuals representing 32 species of aphids from India. Sequence analyses revealed that the intraspecific and interspecific distances ranged from zero to 3.8% and 2.31 to 18.9%, respectively. In addition, the study also showed for the first time the prevalence of three cryptic species, namely Brevicoryne brassicae (Linnaeus), Hyperomyzus carduellinus (Theobald) and Brachycaudus helichrysi (Kaltenbach) from India. Our work has clearly demonstrated that DNA barcoding is an efficient and accurate method for identification of aphid species (including cryptic species), an approach that potentially could play an important role in formulating viable pest management strategies, more especially biocontrol.},
}
@article {pmid23674199,
year = {2013},
author = {Yang, CG and Xu, ZR and Lee, AP and Wang, JH},
title = {A microfluidic concentration-gradient droplet array generator for the production of multi-color nanoparticles.},
journal = {Lab on a chip},
volume = {13},
number = {14},
pages = {2815-2820},
doi = {10.1039/c3lc50254f},
pmid = {23674199},
issn = {1473-0189},
mesh = {Color ; Dimethylpolysiloxanes/chemistry ; Equipment Design ; Gold/*chemistry ; High-Throughput Screening Assays/instrumentation/*methods ; Metal Nanoparticles/*chemistry ; Microfluidic Analytical Techniques/*instrumentation/methods ; Particle Size ; Silver/*chemistry ; Surface Properties ; },
abstract = {A microfluidic concentration-gradient droplet array generator (CDrAG) with parallel multi-channels and multi-layers was developed with 64 outlet channels producing 33 droplet gradient concentrations. A droplet production rate of 5 × 10(4) min(-1) was obtained, and the RSD value of droplet diameters in 64 groups is 5.5% (n = 64). Using the concentration gradient droplet array as parallel microreactors, 33 Au/Ag ratio nanoparticles were synthesized. The absorption spectra of the Au/Ag nanoparticles shifted from the spectrum of pure gold to one of pure silver. This demonstrates the CDrAG platform's promising potential to produce specific nanoparticle barcodes for high-throughput screening in chemistry, biology and a broad range of life science applications.},
}
@article {pmid23672031,
year = {2013},
author = {Chen, SL and Yao, H and Han, JP and Xin, TY and Pang, XH and Shi, LC and Luo, K and Song, JY and Hou, DY and Shi, SM and Qian, ZZ},
title = {[Principles for molecular identification of traditional Chinese materia medica using DNA barcoding].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {38},
number = {2},
pages = {141-148},
pmid = {23672031},
issn = {1001-5302},
mesh = {Animals ; China ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/genetics ; Drugs, Chinese Herbal/*classification/isolation &amp; purification ; Electron Transport Complex IV/genetics ; Materia Medica/*classification/isolation &amp; purification ; Medicine, Chinese Traditional ; Plant Proteins/genetics ; Plants, Medicinal ; },
abstract = {Since the research of molecular identification of Chinese Materia Medica (CMM) using DNA barcode is rapidly developing and popularizing, the principle of this method is approved to be listed in the Supplement of the Pharmacopoeia of the People's Republic of China. Based on the study on comprehensive samples, the DNA barcoding systems have been established to identify CMM, i.e. ITS2 as a core barcode and psbA-trnH as a complementary locus for identification of planta medica, and COI as a core barcode and ITS2 as a complementary locus for identification of animal medica. This article introduced the principle of molecular identification of CMM using DNA barcoding and its drafting instructions. Furthermore, its application perspective was discussed.},
}
@article {pmid23668535,
year = {2013},
author = {Keskın, E and Atar, HH},
title = {DNA barcoding commercially important fish species of Turkey.},
journal = {Molecular ecology resources},
volume = {13},
number = {5},
pages = {788-797},
doi = {10.1111/1755-0998.12120},
pmid = {23668535},
issn = {1755-0998},
mesh = {Animals ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; Fishes/*classification/*genetics ; Genetic Variation ; Molecular Sequence Data ; Sequence Analysis, DNA ; Turkey ; },
abstract = {DNA barcoding was used in the identification of 89 commercially important freshwater and marine fish species found in Turkish ichthyofauna. A total of 1765 DNA barcodes using a 654-bp-long fragment of the mitochondrial cytochrome c oxidase subunit I gene were generated for 89 commercially important freshwater and marine fish species found in Turkish ichthyofauna. These species belong to 70 genera, 40 families and 19 orders from class Actinopterygii, and all were associated with a distinct DNA barcode. Nine and 12 of the COI barcode clusters represent the first species records submitted to the BOLD and GenBank databases, respectively. All COI barcodes (except sequences of first species records) were matched with reference sequences of expected species, according to morphological identification. Average nucleotide frequencies of the data set were calculated as T = 29.7%, C = 28.2%, A = 23.6% and G = 18.6%. Average pairwise genetic distance among individuals were estimated as 0.32%, 9.62%, 17,90% and 22.40% for conspecific, congeneric, confamilial and within order, respectively. Kimura 2-parameter genetic distance values were found to increase with taxonomic level. For most of the species analysed in our data set, there is a barcoding gap, and an overlap in the barcoding gap exists for only two genera. Neighbour-joining trees were drawn based on DNA barcodes and all the specimens clustered in agreement with their taxonomic classification at species level. Results of this study supported DNA barcoding as an efficient molecular tool for a better monitoring, conservation and management of fisheries.},
}
@article {pmid23667494,
year = {2013},
author = {Fiore-Donno, AM and Clissmann, F and Meyer, M and Schnittler, M and Cavalier-Smith, T},
title = {Two-gene phylogeny of bright-spored Myxomycetes (slime moulds, superorder Lucisporidia).},
journal = {PloS one},
volume = {8},
number = {5},
pages = {e62586},
pmid = {23667494},
issn = {1932-6203},
mesh = {Evolution, Molecular ; Genes, Protozoan/*genetics ; Introns/genetics ; Myxomycetes/cytology/*genetics ; Peptide Elongation Factor 1/genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; Spliceosomes/genetics ; Spores, Protozoan/cytology/*genetics ; },
abstract = {Myxomycetes, or plasmodial slime-moulds, are one of the largest groups in phylum Amoebozoa. Nonetheless, only ∼10% are in the database for the small subunit (SSU) ribosomal RNA gene, the most widely used gene for phylogenetics and barcoding. Most sequences belong to dark-spored Myxomycetes (order Fuscisporida); the 318 species of superorder Lucisporidia (bright-spored) are represented by only eleven genuine sequences. To compensate for this, we provide 66 new sequences, 37 SSU rRNA and 29 elongation factor 1-alpha (EF-1α), for 82% of the genera of Lucisporidia. Phylogenetic analyses of single- and two-gene alignments produce congruent topologies and reveal both morphological characters that have been overemphasised and those that have been overlooked in past classifications. Both classical orders, Liceida and Trichiida, and several families and genera are para/polyphyletic; some previously unrecognised clades emerge. We discuss possible evolutionary pathways. Our study fills a gap in the phylogeny of Amoebozoa and provides an extensive SSU rRNA sequence reference database for environmental sampling and barcoding. We report a new group I intron insertion site for Myxomycetes in one Licea.},
}
@article {pmid23666411,
year = {2013},
author = {Ludlow, CL and Scott, AC and Cromie, GA and Jeffery, EW and Sirr, A and May, P and Lin, J and Gilbert, TL and Hays, M and Dudley, AM},
title = {High-throughput tetrad analysis.},
journal = {Nature methods},
volume = {10},
number = {7},
pages = {671-675},
pmid = {23666411},
issn = {1548-7105},
support = {K22 HG002908/HG/NHGRI NIH HHS/United States ; },
mesh = {*Algorithms ; Chromosome Mapping/*methods ; DNA, Fungal/*genetics ; Genetic Markers/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Meiosis/*genetics ; Saccharomyces cerevisiae/*genetics ; },
abstract = {Tetrad analysis has been a gold-standard genetic technique for several decades. Unfortunately, the need to manually isolate, disrupt and space tetrads has relegated its application to small-scale studies and limited its integration with high-throughput DNA sequencing technologies. We have developed a rapid, high-throughput method, called barcode-enabled sequencing of tetrads (BEST), that uses (i) a meiosis-specific GFP fusion protein to isolate tetrads by FACS and (ii) molecular barcodes that are read during genotyping to identify spores derived from the same tetrad. Maintaining tetrad information allows accurate inference of missing genetic markers and full genotypes of missing (and presumably nonviable) individuals. An individual researcher was able to isolate over 3,000 yeast tetrads in 3 h, an output equivalent to that of almost 1 month of manual dissection. BEST is transferable to other microorganisms for which meiotic mapping is significantly more laborious.},
}
@article {pmid23664988,
year = {2013},
author = {O'Connor, AC and Kennedy, ED and Loomis, RJ and Haque, SN and Layton, CM and Williams, WW and Amoozegar, JB and Braun, FM and Honeycutt, AA and Weinbaum, C},
title = {Prospective cost-benefit analysis of a two-dimensional barcode for vaccine production, clinical documentation, and public health reporting and tracking.},
journal = {Vaccine},
volume = {31},
number = {31},
pages = {3179-3186},
doi = {10.1016/j.vaccine.2013.04.073},
pmid = {23664988},
issn = {1873-2518},
support = {GS10F0097L//PHS HHS/United States ; },
mesh = {Cost-Benefit Analysis ; Data Collection ; Documentation/*standards ; Drug Storage/methods/standards ; Electronic Data Processing/economics ; Humans ; Immunization Programs/*organization &amp; administration ; Product Labeling ; Prospective Studies ; Public Health ; Quality Control ; United States ; Vaccination ; Vaccines/*economics/standards ; },
abstract = {In the United States recording accurate vaccine lot numbers in immunization records is required by the National Childhood Vaccine Injury Act and is necessary for public health surveillance and implementation of vaccine product recalls. However, this information is often missing or inaccurate in records. The Food and Drug Administration (FDA) requires a linear barcode of the National Drug Code (NDC) on vaccine product labels as a medication verification measure, but lot number and expiration date must still be recorded by hand. Beginning in 2011, FDA permitted manufacturers to replace linear barcodes with two-dimensional (2D) barcodes on unit-of-use product labels. A 2D barcode can contain the NDC, expiration date, and lot number in a symbol small enough to fit on a unit-of-use label. All three data elements could be scanned into a patient record. To assess 2D barcodes' potential impacts, a mixed-methods approach of time-motion data analysis, interview and survey data collection, and cost-benefit analysis was employed. Analysis of a time-motion study conducted at 33 practices suggests scanning 2D-barcoded vaccines could reduce immunization documentation time by 36-39 s per dose. Data from an internet survey of primary care providers and local health officials indicate that 60% of pediatric practices, 54% of family medicine practices, and 39% of health departments would use the 2D barcode, with more indicating they would do so if they used electronic health records. Inclusive of manufacturer and immunization provider costs and benefits, we forecast lower-bound net benefits to be $310-334 million between 2011 and 2023 with a benefit-to-cost ratio of 3.1:1-3.2:1. Although we were unable to monetize benefits for expected improved immunization coverage, surveillance, or reduced medication errors, based on our findings, we expect that using 2D barcodes will lower vaccine documentation costs, facilitate data capture, and enhance immunization data quality.},
}
@article {pmid23663201,
year = {2013},
author = {Kim, SJ and Lee, KY and Ju, SJ},
title = {Nuclear mitochondrial pseudogenes in Austinograea alayseae hydrothermal vent crabs (Crustacea: Bythograeidae): effects on DNA barcoding.},
journal = {Molecular ecology resources},
volume = {13},
number = {5},
pages = {781-787},
doi = {10.1111/1755-0998.12119},
pmid = {23663201},
issn = {1755-0998},
mesh = {Animals ; Brachyura/*classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry/*genetics ; Electron Transport Complex IV/*genetics ; Hydrothermal Vents ; Molecular Sequence Data ; *Pseudogenes ; Sequence Analysis, DNA ; },
abstract = {Members of the brachyuran crab family, Bythograeidae, are among the most abundant and common crabs in vent fields. However, their identification based on morphological characteristics often leads to incorrect species recognition due to a lack of taxonomic factors and the existence of sibling (or cryptic) species. For these reasons, we used DNA barcoding for vent crabs using mitochondrial cytochrome c oxidase subunit 1 (CO1). However, several nuclear mitochondrial pseudogenes (Numts) were amplified from Austinograea alayseae Guinot, 1990, using universal primers (Folmer primers). The Numts were characterized in six haplotypes, with 13.58-14.11% sequence divergence from A. alayseae, a higher nonsynonymous substitution ratio than true CO1, and the formation of an independent clade in bythograeids. In a neighbour-joining tree, the origin of the Numts would be expected to incorporate into the nucleus at an ancestral node of Austinograea, and they mutated more slowly in the nucleus than CO1 in the mitochondria. This evolutionary process may have resulted in the higher binding affinity of Numts for the Folmer primers than CO1. In the present study, we performed long PCR for the amplification of CO1 in A. alayseae. We also present evidence that Numts can introduce serious ambiguity into DNA barcoding, including overestimating the number of species in bythograeids. These results may help in conducting taxonomic studies using mitochondrial genes from organisms living in hydrothermal vent fields.},
}
@article {pmid23661685,
year = {2013},
author = {Hahn, C and Bachmann, L and Chevreux, B},
title = {Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads--a baiting and iterative mapping approach.},
journal = {Nucleic acids research},
volume = {41},
number = {13},
pages = {e129},
pmid = {23661685},
issn = {1362-4962},
mesh = {Animals ; Chromosome Mapping ; Computer Simulation ; Electron Transport Complex IV/genetics ; Fishes/genetics ; *Genome, Mitochondrial ; Genomics/methods ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics ; Platyhelminths/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {We present an in silico approach for the reconstruction of complete mitochondrial genomes of non-model organisms directly from next-generation sequencing (NGS) data-mitochondrial baiting and iterative mapping (MITObim). The method is straightforward even if only (i) distantly related mitochondrial genomes or (ii) mitochondrial barcode sequences are available as starting-reference sequences or seeds, respectively. We demonstrate the efficiency of the approach in case studies using real NGS data sets of the two monogenean ectoparasites species Gyrodactylus thymalli and Gyrodactylus derjavinoides including their respective teleost hosts European grayling (Thymallus thymallus) and Rainbow trout (Oncorhynchus mykiss). MITObim appeared superior to existing tools in terms of accuracy, runtime and memory requirements and fully automatically recovered mitochondrial genomes exceeding 99.5% accuracy from total genomic DNA derived NGS data sets in <24 h using a standard desktop computer. The approach overcomes the limitations of traditional strategies for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information at hand and represents a fast and highly efficient in silico alternative to laborious conventional strategies relying on initial long-range PCR. We furthermore demonstrate the applicability of MITObim for metagenomic/pooled data sets using simulated data. MITObim is an easy to use tool even for biologists with modest bioinformatics experience. The software is made available as open source pipeline under the MIT license at https://github.com/chrishah/MITObim.},
}
@article {pmid23659114,
year = {2013},
author = {Polukonova, NV and Demin, AG and Miuge, NS},
title = {[Molecular criteria in insects systematics: bar-coding gene COI range of variability as a taxonomic criterion for genus, tribe, and subfamily, with Chironominae and Orthocladiinae midges (Chironomidae, Diptera) as a case study].},
journal = {Zhurnal obshchei biologii},
volume = {74},
number = {1},
pages = {66-76},
pmid = {23659114},
issn = {0044-4596},
mesh = {Amino Acids/*genetics ; Animals ; Biomarkers/analysis ; Chironomidae/*classification/*genetics ; DNA Barcoding, Taxonomic/*standards ; Electron Transport Complex IV/*classification/genetics ; Evolution, Molecular ; Genetic Variation ; Insect Proteins/*classification/genetics ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Contemporary systematics of insects is based mainly on morphological traits. However, their usage is limited both by high variability and complications in comparisons of remote taxa due to low number of common traits. In whole, this leads to a somewhat subjective view when elaborating the system. Unlike morphological ones, molecular traits of taxa, revealed by use of marker genes such as gene cytochrome-c-oxidase I (COI), are less variable and more uniform, which allows them to be used as a criterion of genus, tribe, and subfamily for a wide range of organisms. Application of molecular criteria appears to be all the more important when constructing the system for groups of organisms with high morphological and specific diversity, such as midges (Chironomidae, Diptera). Last years, the DNA-sequence of gene COI is becoming widely used for species identification as a bar-coding one. Its use as a criterion for taxa of super-species level is hampered by its high nucleotide variability. We established the bounds of COI nucleotide and aminoacid divergence between midge species of Chironominae subfamily belonging to the same genus, same tribe, different tribes, as well as between species of Chironominae and Orthocladiinae subfamilies. It is shown that the level of aminoacid divergence reflects molecular boundaries of genus and tribe better than nucleotide one. It can be stated that if the level of aminoacid divergence falls within the limits from 0 to 1.7% then a pair of species compared belongs to the same genus; if it falls within the limits from 1.7 to 4.0% then they belong to the same tribe; within the limits from 4.6 to 6.3%--to different tribes; if it exceeds 7.9%--to different subfamilies. The accuracy of identification when using these ranges turns out to be not less than 75%. In this regard, bounds of COI sequence aminoacid divergence may be used as taxonomic criteria for midge genus, tribe or subfamily.},
}
@article {pmid23656374,
year = {2013},
author = {Yao, AI and Fenton, TA and Owsley, K and Seitzer, P and Larsen, DJ and Sit, H and Lau, J and Nair, A and Tantiongloc, J and Tagkopoulos, I and Facciotti, MT},
title = {Promoter element arising from the fusion of standard BioBrick parts.},
journal = {ACS synthetic biology},
volume = {2},
number = {2},
pages = {111-120},
doi = {10.1021/sb300114d},
pmid = {23656374},
issn = {2161-5063},
mesh = {Base Sequence ; Binding Sites ; Humans ; Molecular Sequence Data ; *Promoter Regions, Genetic ; Ribosomes/genetics ; Transcription Initiation Site ; *Transcription, Genetic ; },
abstract = {We characterize the appearance of a constitutive promoter element in the commonly used cI repressor-encoding BioBrick BBa_C0051. We have termed this promoter element pKAT. Full pKAT activity is created by the ordered assembly of sequences in BBa_C0051 downstream of the cI gene encoding the 11 amino acid LVA proteolytic degradation tag, a BioBrick standard double-TAA stop codon, a genetic barcode, and part of the RFC10 SpeI-XbaI BioBrick scar. Placing BBa_C0051 or other pKAT containing parts upstream of other functional RNA coding elements in a polycistronic context may therefore lead to the unintended transcription of the downstream elements. The frequent reuse of pKAT or pKAT-like containing basic parts in the Registry of Biological Parts has resulted in approximately 5% of registry parts encoding at least one instance of a predicted pKAT promoter located directly upstream of a ribosome binding site and ATG start codon. This example highlights that even seemingly simple modifications of a part's sequence (in this case addition of degradation tags and barcodes) may be sufficient to unexpectedly change the contextual behavior of a part and reaffirms the inherent challenge in carefully characterizing the behavior of standardized biological parts across a broad range of reasonable use scenarios.},
}
@article {pmid23653119,
year = {2013},
author = {Satoh, K and Maeda, M and Umeda, Y and Sugamata, M and Makimura, K},
title = {Cryptococcus lacticolor sp. nov. and Rhodotorula oligophaga sp. nov., novel yeasts isolated from the nasal smear microbiota of Queensland koalas kept in Japanese zoological parks.},
journal = {Antonie van Leeuwenhoek},
volume = {104},
number = {1},
pages = {83-93},
doi = {10.1007/s10482-013-9928-y},
pmid = {23653119},
issn = {1572-9699},
mesh = {Animals ; Animals, Zoo/*microbiology ; Base Sequence ; Breeding ; Carrier State/microbiology ; Cryptococcosis/microbiology/transmission/veterinary ; Cryptococcus/classification/genetics/growth &amp; development/*isolation &amp; purification/metabolism/pathogenicity ; Cryptococcus neoformans/isolation &amp; purification ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; Female ; Fungi/isolation &amp; purification ; Japan ; Male ; Molecular Sequence Data ; Mycology/methods ; Nasal Cavity/*microbiology ; Phascolarctidae/*microbiology ; Phenotype ; Phylogeny ; Queensland ; Rhodotorula/classification/genetics/growth &amp; development/*isolation &amp; purification/metabolism/pathogenicity ; Species Specificity ; },
abstract = {A total of 515 yeast strains were isolated from the nasal smears of Queensland koalas and their breeding environments in Japanese zoological parks between 2005 and 2012. The most frequent species in the basidiomycetous yeast biota isolated from koala nasal passages was Cryptococcus neoformans, followed by Rhodotorula minuta. R. minuta was the most frequent species in the breeding environments, while C. neoformans was rare. Seven strains representing two novel yeast species were identified. Analyses of the 26S rDNA (LSU) D1/D2 domain and nuclear ribosomal DNA internal transcribed spacer region sequences indicated that these strains represent new species with close phylogenetic relationships to Cryptococcus and Rhodotorula. A sexual state was not found for either of these two novel yeasts. Key phenotypic characters confirmed that these strains could be placed in Cryptococcus and Rhodotorula. The names Cryptococcus lacticolor sp. nov. (type strain TIMM 10013(T) = JCM 15449(T) = CBS 10915(T) = DSM 21093(T), DDBJ/EMBL/Genbank Accession No.; AB375774 (ITS) and AB375775 (26S rDNA D1/D2 region), MycoBank ID; MB 802688, Fungal Barcoding Database ID; 3174), and Rhodotorula oligophaga sp. nov. (type strain TIMM 10017(T) = JCM 18398(T) = CBS 12623(T) = DSM 25814(T), DDBJ/EMBL/Genbank Accession No.; AB702967 (ITS) and AB702967 (26S rDNA D1/D2 region), MycoBank ID; MB 802689, Fungal Barcoding Database ID; 3175) are proposed for these new species.},
}
@article {pmid23652200,
year = {2013},
author = {Hooper, JN and Hall, KA and Ekins, M and Erpenbeck, D and Wörheide, G and Jolley-Rogers, G},
title = {Managing and sharing the escalating number of sponge "unknowns": the SpongeMaps project.},
journal = {Integrative and comparative biology},
volume = {53},
number = {3},
pages = {473-481},
doi = {10.1093/icb/ict038},
pmid = {23652200},
issn = {1557-7023},
mesh = {Animals ; *Biodiversity ; Classification/*methods ; Computational Biology/*methods/trends ; DNA Barcoding, Taxonomic ; Geographic Information Systems ; Geographic Mapping ; Porifera/*chemistry/*classification/*genetics ; *Software ; Species Specificity ; },
abstract = {Contemporary collections of sponges in the Indo-west Pacific have escalated substantially due to pharmaceutical discovery, national bioregional planning, and compliance with international conventions on the seabed and its marine genetic resources beyond national jurisdictions. These partially processed operational taxonomic unit (OTU) collections now vastly outweigh the expertise available to make them better "known" via complete taxonomy, yet for many bioregions they represent the most significant body of currently available knowledge. Increasing numbers of cryptic species, previously undetected morphologically, are now being discovered by molecular and chemical analyses. The uncoordinated and fragmented nature of many previous collections, however, means that knowledge and expertise gained from a particular project are often lost to future projects without a biodiversity informatics legacy. Integrating these diverse data (GIS; OTUs; images; molecular, chemical, and other datasets) required a two-way iterative process so far unavailable for sponges with existing biodiversity informatics tools. SpongeMaps arose from the initial need for online collaboration to integrate morphometric data with molecular barcodes, including the Porifera Tree of Life (PorTol) project. It provides interrogation of existing data to better process new collections; capacity to create new OTUs; publication of online pages for individual species, so as to interpret GIS and other data for online biodiversity databases and services; and automatic links to external datasets for taxonomic hierarchy, specimen GIS and mapping, DNA sequence data, chemical structures, and images.},
}
@article {pmid23650486,
year = {2013},
author = {Hayakawa, M and Uchimura, Y and Omae, K and Waki, K and Fujita, H and Ohe, K},
title = {A smartphone-based medication self-management system with realtime medication monitoring.},
journal = {Applied clinical informatics},
volume = {4},
number = {1},
pages = {37-52},
pmid = {23650486},
issn = {1869-0327},
mesh = {Adult ; Aged ; Aged, 80 and over ; *Cell Phone ; Drug Administration Schedule ; Drug Monitoring/*instrumentation/methods ; Drug Storage ; Feasibility Studies ; Female ; Humans ; Male ; *Medication Adherence/psychology ; Middle Aged ; *Mobile Applications ; Reminder Systems/*instrumentation ; Self Report ; Time Factors ; Wireless Technology ; },
abstract = {BACKGROUND: Most patients cannot remember their entire medication regimen and occasionally forget to take their medication.<br><br>OBJECTIVES: The objective of the study was to design, develop, and demonstrate the feasibility of a new type of medication self-management system using smartphones with real-time medication monitoring.<br><br>METHODS: We designed and developed a smartphone-based medication self-management system (SMSS) based on interviews of 116 patients. The system offered patients two main functions by means of smartphones: (1) storage and provision of an accurate, portable medication history and medication-taking records of patients; and (2) provision of a reminder to take medication only when the patient has forgotten to take his/her medication. These functions were realized by two data input methods: (a) reading of prescription data represented in two-dimensional barcodes using the smartphone camera and getting the photographic images of the pills; and (b) real-time medication monitoring by novel user-friendly wireless pillboxes.<br><br>RESULTS: Interviews suggested that a pocket-sized pillbox was demanded to support patient's medication-taking outside the home and pillboxes for home use should be adaptable to the different means of pillbox storage. In accordance with the result, we designed and developed SMSS. Ten patients participated in the feasibility study. In 17 out of 47 cases (36.2%), patients took their medication upon being presented with reminders by the system. Correct medication-taking occurrence was improved using this system.<br><br>CONCLUSIONS: The SMSS is acceptable to patients and has the advantage of supporting ubiquitous medication self-management using a smartphone. We believe that the proposed system is feasible and provides an innovative solution to encourage medication self-management.},
}
@article {pmid23646946,
year = {2013},
author = {Chiesa, S and Filonzi, L and Vaghi, M and Papa, R and Marzano, FN},
title = {Molecular barcoding of an atypical cyprinid population assessed by cytochrome B gene sequencing.},
journal = {Zoological science},
volume = {30},
number = {5},
pages = {408-413},
doi = {10.2108/zsj.30.408},
pmid = {23646946},
issn = {0289-0003},
mesh = {Animals ; Cyprinidae/*genetics ; Cytochromes b/*genetics ; DNA Barcoding, Taxonomic/*methods ; Demography ; Italy ; Phylogeny ; },
abstract = {A fish population of the carp family Cyprinidae with atypical phenotypic characteristics was observed in one of the main catchments of the Pollino National Park, a valuable, protected area in southern Italy. In this area, the Italian roach Rutilus rubilio (Bonaparte, 1837), a native endemic fish of Tyrrhenean regions, has been introduced in sympatric conditions with Squalius squalus (Bonaparte, 1837) and Telestes muticellus (Bonaparte, 1837). A molecular investigation was carried out to assess the genetic identity of the population with a view to conservation. Direct sequencing of a cytochrome b gene fragment was performed based on 30 individuals of cyprinid fish with atypical phenotype, in addition to 30 S. squalus, 10 T. muticellus, and 30 R. rubilio pure individuals collected in different Italian regions, which served as reference samples. Multiple sequence alignments demonstrated that 50% of atypical-cyprinid haplotypes were maternally inherited from either S. squalus or R. rubilio. No contribution by T. muticellus was determined. Our results indicate an intergeneric hybridization event between S. squalus and R. rubilio, as a consequence of trans-introduction activities of alien species.},
}
@article {pmid23644244,
year = {2013},
author = {Hug, B},
title = {[Practical aspects of medication safety].},
journal = {Praxis},
volume = {102},
number = {10},
pages = {591-596},
doi = {10.1024/1661-8157/a001287},
pmid = {23644244},
issn = {1661-8157},
mesh = {Ambulatory Care/statistics &amp; numerical data ; Cross-Sectional Studies ; *Drug-Related Side Effects and Adverse Reactions ; Electronic Prescribing ; Hospitalization/statistics &amp; numerical data ; Humans ; Incidence ; Medical Order Entry Systems ; Medication Errors/prevention &amp; control/*statistics &amp; numerical data ; Switzerland ; },
abstract = {The incidence of adverse drug events (ADE) in hospitalized patients and ambulatory care is high. Next to human suffering they cause considerable additional cost and a prolonged length of stay. The reduction of ADE incidence is badly needed. Measures to reach this goal next to teaching are electronic prescribing tools with decision support, clinical pharmacists on ward rounds, therapeutic drug monitoring, smart infusion pumps and identification tools such as bar-coding and radio-frequency identification for patients, drugs and health professionals. Importantly, while integrating these technical tools, workflows of health professionals have to be considered and should be combined with a scientific analysis to uphold and ameliorate patient safety.},
}
@article {pmid23642457,
year = {2013},
author = {Grace, OM and Dzajic, A and Jäger, AK and Nyberg, NT and Önder, A and Rønsted, N},
title = {Monosaccharide analysis of succulent leaf tissue in Aloe.},
journal = {Phytochemistry},
volume = {93},
number = {},
pages = {79-87},
doi = {10.1016/j.phytochem.2013.03.015},
pmid = {23642457},
issn = {1873-3700},
mesh = {Aloe/*chemistry ; Gas Chromatography-Mass Spectrometry ; Monosaccharides/*analysis ; Multivariate Analysis ; Phylogeny ; Plant Leaves/*chemistry ; },
abstract = {INTRODUCTION: The succulent leaf mesophyll in Aloe species supports a burgeoning natural products industry, particularly in Africa. Comparative data necessary to prioritise species with economic potential have been lacking.<br><br>OBJECTIVE: To survey leaf mesophyll monosaccharide composition in the genus Aloe using a predictive phylogenetic approach.<br><br>METHODOLOGY: Monosaccharide composition was assessed in 31 species, representing the morphological and taxonomic diversity of Aloe sensu stricto. Leaf mesophyll polysaccharides were partially hydrolysed in a trifluoroacetic acid (TFA)-SilA assay. Oximes and trimethylsilyl ether products were detected by GC-MS. Constituent monosaccharides accounting for the greatest variation among species were identified by principal component analysis. Two plant DNA barcoding regions were sequenced in 28 of the sampled species and the resulting maximum likelihood tree was used to evaluate phylogenetic signal in monosaccharide composition throughout the genus.<br><br>RESULTS: Nineteen peaks (Rt=16.76-23.67 min) were identified in the GC-MS spectra. All samples were dominated by one constituent; glucose was the major monosaccharide in 19 species, mannose in eight species, and xylose in one species (Aloidendron pillansii). Three monosaccharides therefore account for 90% of the variation in leaf mesophyll in Aloe. Species which do not share this typical monosaccharide profile appear to group outside the core Aloe clade in the phylogeny.<br><br>CONCLUSION: Preliminary findings suggest that leaf mesophyll monosaccharide composition is conservative in Aloe. Characterisation of within-species variation and quantitative differences between species will be necessary to authenticate leaf mesophyll products, whereas unusual monosaccharide profiles could be diagnostic in some species. The common glucose-mannose-xylose profile identified in commercially important species is shared by many other Aloe species.},
}
@article {pmid23641326,
year = {2013},
author = {Bansal, D and Malla, S and Gudala, K and Tiwari, P},
title = {Anti-counterfeit technologies: a pharmaceutical industry perspective.},
journal = {Scientia pharmaceutica},
volume = {81},
number = {1},
pages = {1-13},
pmid = {23641326},
issn = {2218-0532},
abstract = {Growth of international free trade and inadequate drug regulation have led to the expansion of trade in counterfeit drugs worldwide. Technological protection is seen to be the best way to avoid this problem. Different technologies came into existence like overt, covert, and track and trace technologies. This review emphasises ideal technological characteristics, existing anti-counterfeit technologies, and their adoption in different countries. Developed countries like the USA have implemented RFID while the European trend is towards 2D barcodes. The Indian government is getting sensitised about the extent of the problem and has formulated rules mandating barcodes. Even the pharmaceutical companies have been employing these technologies in order to detain illegitimate drugs in their supply chain.},
}
@article {pmid23641116,
year = {2013},
author = {Dorfman, KD},
title = {The Fluid Mechanics of Genome Mapping.},
journal = {AIChE journal. American Institute of Chemical Engineers},
volume = {59},
number = {2},
pages = {346-354},
pmid = {23641116},
issn = {0001-1541},
support = {R01 HG005216/HG/NHGRI NIH HHS/United States ; },
}
@article {pmid23640878,
year = {2013},
author = {Ye, S and Xiao, J and Guo, Y and Zhang, S},
title = {Aptamer-based SERS assay of ATP and lysozyme by using primer self-generation.},
journal = {Chemistry (Weinheim an der Bergstrasse, Germany)},
volume = {19},
number = {25},
pages = {8111-8116},
doi = {10.1002/chem.201300126},
pmid = {23640878},
issn = {1521-3765},
mesh = {Adenosine Triphosphate/*analysis/chemistry/metabolism ; Aptamers, Nucleotide/*chemistry/metabolism ; Biosensing Techniques/methods ; DNA Primers/*chemistry ; Gold/chemistry ; Humans ; Magnetics ; Muramidase/*blood ; Nanoparticles/chemistry ; Nucleic Acid Conformation ; Spectrum Analysis, Raman/methods ; },
abstract = {A simple bifunctional surface-enhanced Raman scattering (SERS) assay based on primer self-generation strand-displacement polymerization (PS-SDP) is developed to detect small molecules or proteins in parallel. Triphosphate (ATP) and lysozyme are used as the models of small molecules and proteins. Compared to traditional bifunctional methods, the method possesses some remarkable features as follows: 1) by virtue of the simple PS-SDP reaction, a bifunctional aptamer assembly binding of trigger 1 and trigger 2 was used as a functional structure for the simultaneous sensing of ATP or lysozyme. 2) The concept of isothermal amplification bifunctional detection has been first introduced into SERS biosensing applications as a signal-amplification tool. 3) The problem of high background induced by excess bio-barcodes is circumvented by using magnetic beads (MBs) as the carrier of signal-output products and massive of hairpin DNA binding with SERS active bio-barcodes relied on Au nanoparticles (Au NPs), SERS signal is significantly enhanced. Overall, with multiple amplification steps and one magnetic-separation procedure, this flexible biosensing system exhibited not only high sensitivity and specificity, with the detection limits of ATP and lysozyme of 0.05 nM and 10 fM, respectively.},
}
@article {pmid23638077,
year = {2013},
author = {Osmundson, TW and Robert, VA and Schoch, CL and Baker, LJ and Smith, A and Robich, G and Mizzan, L and Garbelotto, MM},
title = {Filling gaps in biodiversity knowledge for macrofungi: contributions and assessment of an herbarium collection DNA barcode sequencing project.},
journal = {PloS one},
volume = {8},
number = {4},
pages = {e62419},
pmid = {23638077},
issn = {1932-6203},
support = {//Intramural NIH HHS/United States ; },
mesh = {Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/*genetics/isolation &amp; purification ; Databases, Nucleic Acid ; Fungi/*genetics ; Museums ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {Despite recent advances spearheaded by molecular approaches and novel technologies, species description and DNA sequence information are significantly lagging for fungi compared to many other groups of organisms. Large scale sequencing of vouchered herbarium material can aid in closing this gap. Here, we describe an effort to obtain broad ITS sequence coverage of the approximately 6000 macrofungal-species-rich herbarium of the Museum of Natural History in Venice, Italy. Our goals were to investigate issues related to large sequencing projects, develop heuristic methods for assessing the overall performance of such a project, and evaluate the prospects of such efforts to reduce the current gap in fungal biodiversity knowledge. The effort generated 1107 sequences submitted to GenBank, including 416 previously unrepresented taxa and 398 sequences exhibiting a best BLAST match to an unidentified environmental sequence. Specimen age and taxon affected sequencing success, and subsequent work on failed specimens showed that an ITS1 mini-barcode greatly increased sequencing success without greatly reducing the discriminating power of the barcode. Similarity comparisons and nonmetric multidimensional scaling ordinations based on pairwise distance matrices proved to be useful heuristic tools for validating the overall accuracy of specimen identifications, flagging potential misidentifications, and identifying taxa in need of additional species-level revision. Comparison of within- and among-species nucleotide variation showed a strong increase in species discriminating power at 1-2% dissimilarity, and identified potential barcoding issues (same sequence for different species and vice-versa). All sequences are linked to a vouchered specimen, and results from this study have already prompted revisions of species-sequence assignments in several taxa.},
}
@article {pmid23635529,
year = {2013},
author = {Pauciullo, A and Fleck, K and Lühken, G and Di Berardino, D and Erhardt, G},
title = {Dual-color high-resolution fiber-FISH analysis on lethal white syndrome carriers in sheep.},
journal = {Cytogenetic and genome research},
volume = {140},
number = {1},
pages = {46-54},
doi = {10.1159/000350786},
pmid = {23635529},
issn = {1424-859X},
mesh = {Animals ; Chromatin/genetics ; Chromosomes, Mammalian/*genetics/metabolism ; DNA Probes ; Female ; Gene Deletion ; *Heterozygote ; Hypopigmentation/*genetics/pathology ; In Situ Hybridization, Fluorescence/*methods ; Lymphocytes/cytology ; Male ; Metaphase ; Propidium/metabolism ; Receptor, Endothelin B/genetics/metabolism ; Sheep/genetics ; Sheep Diseases/genetics ; Sheep, Domestic/*genetics ; Syndrome ; },
abstract = {Molecular defects occurring in the endothelin receptor type-B (EDNRB) gene are known to be associated with pigmentary anomalies and intestinal aganglionosis in humans, rodents and horses. We carried out a cytogenetic investigation in 2 ewes heterozygous for the deletion of the EDNRB gene and in 2 more females as control. The RBA-banding showed that all 4 ewes were karyologically normal. EDNRB gene-specific probes were produced by PCR and cloning. The application of the R-banding and propidium iodide-staining fluorescent in situ hybridization allowed mapping the gene to OAR 10q22 and confirmed the heterozygous status of the ewes investigated for the EDNRB gene deletion. For the fine estimation of the gene length in sheep and for the correct sizing of the chromosomal gap, a dual-color FISH was applied to high-resolution DNA fibers in combination with digital imaging microscopy. The comparison of the DNA fiber barcodes indicated a chromosomal deletion larger than the EDNRB gene itself. The length of the gene, not known for sheep until now, was estimated to be ∼21 kb, whereas the microchromosomal deletion was ∼100 kb. EDNRB is located in a chromosomal region previously shown to be a fragile site. The applied method allowed locating the potential breakpoints, thus permitting further interesting prospective investigations also in the field of the fragile sites in sheep.},
}
@article {pmid23631370,
year = {2014},
author = {Lv, J and Wu, S and Zhang, Y and Zhang, T and Feng, C and Jia, G and Lin, X},
title = {Development of a DNA barcoding system for the Ixodida (Acari: Ixodida).},
journal = {Mitochondrial DNA},
volume = {25},
number = {2},
pages = {142-149},
doi = {10.3109/19401736.2013.792052},
pmid = {23631370},
issn = {1940-1744},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Genetic Variation ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Species Specificity ; Ticks/*genetics ; },
abstract = {To control the spread of tick-borne diseases, there is an urgent need to develop a reliable technique that can distinguish different species of ticks. DNA barcoding has been proved to be a powerful tool to identify species of arthropods, but this technique has not yet been developed for identifying ticks. Here, we screened and analyzed 1082 sequences of ticks from BOLD system and GenBank, consisting of 647 16S, 325 COI, and 110 18S. These sequences are reported in previous studies and considered to be correctly identified at the species level. Through the analyses of genetic divergences and neighbor-joining (NJ) phylogenetic relationships between the species of ticks, our results show that COI and 16S are reliable in discriminating species of ticks and the 18S could discriminate ticks at the genera level. New universal primers for 16S, 18S, and COI of ticks were designed and a DNA barcoding system for the Ixodida was developed. To assess the performance of this system, 57 specimens of ticks were collected within China. Our results show that DNA barcoding system could correctly identify the species of specimens in adult and subadult stages. This system would assist non-taxonomists to conveniently identify the species of Ixodida based on DNA sequences rather than morphological traits. However, there are still serious deficiencies in the information of 16S and COI of some species of ticks, and additional research is needed to resolve this problem.},
}
@article {pmid23629416,
year = {2013},
author = {Nolan, G},
title = {Inner-outer beauty: DNA-binding surface tags as cellular barcodes.},
journal = {Nature methods},
volume = {10},
number = {5},
pages = {399-401},
pmid = {23629416},
issn = {1548-7105},
mesh = {*DNA Barcoding, Taxonomic ; },
}
@article {pmid23621023,
year = {2013},
author = {An, JH and Oh, BK and Choi, JW},
title = {Detection of tyrosine hydroxylase in dopaminergic neuron cell using gold nanoparticles-based barcode DNA.},
journal = {Journal of biomedical nanotechnology},
volume = {9},
number = {4},
pages = {639-643},
doi = {10.1166/jbn.2013.1525},
pmid = {23621023},
issn = {1550-7033},
mesh = {Cell Line, Tumor ; Dopaminergic Neurons/*enzymology ; Electrophoresis, Agar Gel ; Gold/*chemistry ; Humans ; Metal Nanoparticles/*chemistry/ultrastructure ; Microscopy, Fluorescence ; Sequence Analysis, DNA/*methods ; Tyrosine 3-Monooxygenase/genetics/*metabolism ; },
abstract = {Tyrosine hydroxylase, the rate-limiting enzyme of catecholamine biosysthesis, is predominantly expressed in several cell groups within the brain, including the dopaminergic neurons of the substantia nigra and ventral tegmental area. We evaluated the efficacy of this protein-detection method in detecting tyrosine hydroxylase in normal and oxidative stress damaged dopaminergic cells. In this study, a coupling of DNA barcode and bead-based immnunoassay for detecting tyrosine hydroxylaser with PCR-like sensitivity is reported. The method relies on magnetic nanoparticles with antibodies and nanoparticles that are encoded with DNA and antibodies that can sandwich the target protein captured by the nanoparticle-bound antibodies. The aggregate sandwich structures are magnetically separated from solution, and treated to remove the conjugated barcode DNA. The DNA barcodes were identified by PCR analysis. The concentration of tyrosine hydroxylase in dopaminergic cell can be easily and rapidly detected using bio-barcode assay. The bio-barcode assay is a rapid and high-throughput screening tool to detect of neurotransmitter such as dopamine.},
}
@article {pmid23618625,
year = {2013},
author = {Li, Y and Jiao, L and Yao, YJ},
title = {Non-concerted ITS evolution in fungi, as revealed from the important medicinal fungus Ophiocordyceps sinensis.},
journal = {Molecular phylogenetics and evolution},
volume = {68},
number = {2},
pages = {373-379},
doi = {10.1016/j.ympev.2013.04.010},
pmid = {23618625},
issn = {1095-9513},
mesh = {Base Composition ; Base Sequence ; Bayes Theorem ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/*genetics ; *Evolution, Molecular ; Hypocreales/classification/*genetics ; Medicine, Chinese Traditional ; Models, Molecular ; Molecular Sequence Data ; Multilocus Sequence Typing ; Mycological Typing Techniques ; Nucleic Acid Conformation ; Phylogeny ; Sequence Analysis, DNA ; Thermodynamics ; },
abstract = {The internal transcribed spacer (ITS) of nuclear ribosomal DNA (nrDNA) has been widely used as a molecular marker in phylogenetic studies and has been selected as a DNA barcode for fungi. It is generally believed that nrDNA conforms to concerted evolution in most eukaryotes; however, intraindividual-intraspecific polymorphisms of this region were reported in various organisms, suggesting a non-concerted evolutionary process. In Ophiocordyceps sinensis, one of the most valuable medicinal fungi, a remarkable variation of the ITS region has been revealed. Some highly divergent sequences were thought to represent cryptic species, different species or genotypes in previous studies. To clarify the unusual ITS polymorphisms observed in O. sinensis, specific primers were designed to amplify ITS paralogs from pure cultures of both single-ascospore and tissue isolates in this study. All of the available ITS sequences, including those generated by this group and those in GenBank, were analyzed. Several AT-biased ITS paralogs were classified as pseudogenes based on their nucleotide compositions, secondary structures and minimum free energies of their 5.8S rRNAs, substitution rates, phylogenetic positions and gene expression analyses. Furthermore, ITS pseudogenes were amplified with specific primers from 10 of the 28 strains tested, including eight single-ascospore and two tissue isolates. Divergent ITS paralogs were proved to coexist in individual genomes, suggesting a non-concerted mechanism of evolution in the ITS region of O. sinensis. The hypotheses that divergent ITS paralogs represent cryptic or other species or different genotypes were thus rejected.},
}
@article {pmid23613175,
year = {2013},
author = {Novo, S and Ibáñez, E and Barrios, L and Castell, O and Nogués, C},
title = {Biomolecule screening for efficient attachment of biofunctionalized microparticles to the zona pellucida of mammalian oocytes and embryos.},
journal = {Biomedical microdevices},
volume = {15},
number = {5},
pages = {801-809},
doi = {10.1007/s10544-013-9766-8},
pmid = {23613175},
issn = {1572-8781},
mesh = {Animals ; Antibodies, Monoclonal/chemistry ; Binding Sites ; Embryo, Mammalian/cytology/drug effects/metabolism ; Female ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Inbred CBA ; Microscopy, Electron, Scanning ; Microspheres ; Oocytes/drug effects/*metabolism ; Phytohemagglutinins/chemistry/toxicity ; Staining and Labeling/*methods ; Wheat Germ Agglutinins/chemistry/toxicity ; Zona Pellucida/*metabolism ; },
abstract = {Individual tagging of oocytes and embryos through the attachment of micrometer-sized polysilicon barcodes to their zona pellucida (ZP) is a promising approach to ensure their correct identification and traceability in human assisted reproduction and in animal production programs. To provide barcodes with the capacity of binding to the ZP, they must be first biofunctionalized with a biomolecule capable of binding to the ZP of both oocytes and embryos. The aim of this work was to select, among an anti-ZP2 antibody and the two lectins wheat germ agglutinin (WGA) and phytohemagglutinin-L, the most optimal biomolecule for the eventual biofunctionalization of barcodes, using mouse oocytes and embryos and commercially available microspheres as a model. Despite the anti-ZP2 antibody showed the highest number of binding sites onto the ZP surface, as determined by field emission scanning electron microscopy, the binding of anti-ZP2-biofunctionalized microspheres to the ZP of cultured oocytes and embryos was less robust and less stable than the binding of lectin-biofunctionalized ones. WGA proved to be, among the three candidates tested, the most appropriate biomolecule to biofunctionalize microparticles with the aim to attach them to the ZP of both oocytes and embryos and to maintain them attached through oocyte activation (zona reaction) and in vitro culture up to the blastocyst stage. As saccharides recognized by WGA are highly abundant in the ZP of most mammalian species, WGA-biofuncionalized microparticles would be able to attach to the ZP of oocytes/embryos of species other than the mouse, such as humans and farm animals.},
}
@article {pmid23612293,
year = {2013},
author = {Liong, M and Hoang, AN and Chung, J and Gural, N and Ford, CB and Min, C and Shah, RR and Ahmad, R and Fernandez-Suarez, M and Fortune, SM and Toner, M and Lee, H and Weissleder, R},
title = {Magnetic barcode assay for genetic detection of pathogens.},
journal = {Nature communications},
volume = {4},
number = {},
pages = {1752},
pmid = {23612293},
issn = {2041-1723},
support = {T32 CA079443/CA/NCI NIH HHS/United States ; R01 EB010011/EB/NIBIB NIH HHS/United States ; R01-EB010011/EB/NIBIB NIH HHS/United States ; T32 AI007638/AI/NIAID NIH HHS/United States ; DP2 OD001378/OD/NIH HHS/United States ; T32CA79443/CA/NCI NIH HHS/United States ; R01-EB00462605A1/EB/NIBIB NIH HHS/United States ; P41 EB002503/EB/NIBIB NIH HHS/United States ; R01-HL113156/HL/NHLBI NIH HHS/United States ; DP2 0D001378/DP/NCCDPHP CDC HHS/United States ; U19 AI076217/AI/NIAID NIH HHS/United States ; HHSN268201000044C/HL/NHLBI NIH HHS/United States ; R01 EB004626/EB/NIBIB NIH HHS/United States ; R01 HL113156/HL/NHLBI NIH HHS/United States ; },
mesh = {Base Sequence ; DNA Barcoding, Taxonomic/*methods ; DNA, Bacterial/genetics ; Genome, Bacterial/genetics ; Humans ; Magnetics/*methods ; Molecular Sequence Data ; Mutation/genetics ; Mycobacterium tuberculosis/*genetics/*isolation &amp; purification ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide/genetics ; Sensitivity and Specificity ; },
abstract = {The task of rapidly identifying patients infected with Mycobacterium tuberculosis in resource-constrained environments remains a challenge. A sensitive and robust platform that does not require bacterial isolation or culture is critical in making informed diagnostic and therapeutic decisions. Here we introduce a platform for the detection of nucleic acids based on a magnetic barcoding strategy. PCR-amplified mycobacterial genes are sequence-specifically captured on microspheres, labelled by magnetic nanoprobes and detected by nuclear magnetic resonance. All components are integrated into a single, small fluidic cartridge for streamlined on-chip operation. We use this platform to detect M. tuberculosis and identify drug-resistance strains from mechanically processed sputum samples within 2.5 h. The specificity of the assay is confirmed by detecting a panel of clinically relevant non-M. tuberculosis bacteria, and the clinical utility is demonstrated by the measurements in M. tuberculosis-positive patient specimens. Combined with portable systems, the magnetic barcode assay holds promise to become a sensitive, high-throughput and low-cost platform for point-of-care diagnostics.},
}
@article {pmid23606771,
year = {2012},
author = {Crous, PW and Shivas, RG and Wingfield, MJ and Summerell, BA and Rossman, AY and Alves, JL and Adams, GC and Barreto, RW and Bell, A and Coutinho, ML and Flory, SL and Gates, G and Grice, KR and Hardy, GE and Kleczewski, NM and Lombard, L and Longa, CM and Louis-Seize, G and Macedo, F and Mahoney, DP and Maresi, G and Martin-Sanchez, PM and Marvanová, L and Minnis, AM and Morgado, LN and Noordeloos, ME and Phillips, AJ and Quaedvlieg, W and Ryan, PG and Saiz-Jimenez, C and Seifert, KA and Swart, WJ and Tan, YP and Tanney, JB and Thu, PQ and Videira, SI and Walker, DM and Groenewald, JZ},
title = {Fungal Planet description sheets: 128-153.},
journal = {Persoonia},
volume = {29},
number = {},
pages = {146-201},
pmid = {23606771},
issn = {0031-5850},
abstract = {Novel species of microfungi described in the present study include the following from Australia: Catenulostroma corymbiae from Corymbia, Devriesia stirlingiae from Stirlingia, Penidiella carpentariae from Carpentaria, Phaeococcomyces eucalypti from Eucalyptus, Phialophora livistonae from Livistona, Phyllosticta aristolochiicola from Aristolochia, Clitopilus austroprunulus on sclerophyll forest litter of Eucalyptus regnans and Toxicocladosporium posoqueriae from Posoqueria. Several species are also described from South Africa, namely: Ceramothyrium podocarpi from Podocarpus, Cercospora chrysanthemoides from Chrysanthemoides, Devriesia shakazului from Aloe, Penidiella drakensbergensis from Protea, Strelitziana cliviae from Clivia and Zasmidium syzygii from Syzygium. Other species include Bipolaris microstegii from Microstegium and Synchaetomella acerina from Acer (USA), Brunneiapiospora austropalmicola from Rhopalostylis (New Zealand), Calonectria pentaseptata from Eucalyptus and Macadamia (Vietnam), Ceramothyrium melastoma from Melastoma (Indonesia), Collembolispora aristata from stream foam (Czech Republic), Devriesia imbrexigena from glazed decorative tiles (Portugal), Microcyclospora rhoicola from Rhus (Canada), Seiridium phylicae from Phylica (Tristan de Cunha, Inaccessible Island), Passalora lobeliae-fistulosis from Lobelia (Brazil) and Zymoseptoria verkleyi from Poa (The Netherlands). Valsalnicola represents a new ascomycete genus from Alnus (Austria) and Parapenidiella a new hyphomycete genus from Eucalyptus (Australia). Morphological and culture characteristics along with ITS DNA barcodes are also provided.},
}
@article {pmid23606768,
year = {2012},
author = {Quaedvlieg, W and Groenewald, JZ and de Jesús Yáñez-Morales, M and Crous, PW},
title = {DNA barcoding of Mycosphaerella species of quarantine importance to Europe.},
journal = {Persoonia},
volume = {29},
number = {},
pages = {101-115},
pmid = {23606768},
issn = {0031-5850},
abstract = {The EU 7th Framework Program provided funds for Quarantine Barcoding of Life (QBOL) to develop a quick, reliable and accurate DNA barcode-based diagnostic tool for selected species on the European and Mediterranean Plant Protection Organization (EPPO) A1/A2 quarantine lists. Seven nuclear genomic loci were evaluated to determine those best suited for identifying species of Mycosphaerella and/or its associated anamorphs. These genes included β-tubulin (Btub), internal transcribed spacer regions of the nrDNA operon (ITS), 28S nrDNA (LSU), Actin (Act), Calmodulin (Cal), Translation elongation factor 1-alpha (EF-1α) and RNA polymerase II second largest subunit (RPB2). Loci were tested on their Kimura-2-parameter-based inter- and intraspecific variation, PCR amplification success rate and ability to distinguish between quarantine species and closely related taxa. Results showed that none of these loci was solely suited as a reliable barcoding locus for the tested fungi. A combination of a primary and secondary barcoding locus was found to compensate for individual weaknesses and provide reliable identification. A combination of ITS with either EF-1α or Btub was reliable as barcoding loci for EPPO A1/A2-listed Mycosphaerella species. Furthermore, Lecanosticta acicola was shown to represent a species complex, revealing two novel species described here, namely L. brevispora sp. nov. on Pinus sp. from Mexico and L. guatemalensis sp. nov. on Pinus oocarpa from Guatemala. Epitypes were also designated for L. acicola and L. longispora to resolve the genetic application of these names.},
}
@article {pmid23606764,
year = {2012},
author = {Yilmaz, N and Houbraken, J and Hoekstra, ES and Frisvad, JC and Visagie, CM and Samson, RA},
title = {Delimitation and characterisation of Talaromyces purpurogenus and related species.},
journal = {Persoonia},
volume = {29},
number = {},
pages = {39-54},
pmid = {23606764},
issn = {0031-5850},
abstract = {Taxa of the Talaromyces purpurogenus complex were studied using a polyphasic approach. ITS barcodes were used to show relationships between species of the T. purpurogenus complex and other Talaromyces species. RPB1, RPB2, β-tubulin and calmodulin sequences were used to delimit phylogenetic species in the complex. These data, combined with phenotypic characters, showed that the complex contains four species: T. purpurogenus, T. ruber comb. nov. and two new species T. amestolkiae sp. nov. and T. stollii sp. nov. The latter three species belong to the same clade and T. purpurogenus is located in a phylogenetic distant clade. The four species all share similar conidiophore morphologies, but can be distinguished by macromorphological characters. Talaromyces ruber has a very distinct colony texture on malt extract agar (MEA), produces bright yellow and red mycelium on yeast extract sucrose agar (YES) and does not produce acid on creatine sucrose agar (CREA). In contrast, T. amestolkiae and T. stollii produce acid on CREA. These two species can be differentiated by the slower growth rate of T. amestolkiae on CYA incubated at 36 °C. Furthermore, T. stollii produces soft synnemata-like structures in the centre of colonies on most media. Extrolite analysis confirms the distinction of four species in the T. purpurogenus complex. The red diffusing pigment in T. purpurogenus is a mixture of the azaphilone extrolites also found in Monascus species, including N-glutarylrubropunctamine and rubropunctatin. Talaromyces purpurogenus produced four different kinds of mycotoxins: rubratoxins, luteoskyrin, spiculisporic acid and rugulovasins and these mycotoxins were not detected in the other three species.},
}
@article {pmid23599672,
year = {2013},
author = {Barlas, S},
title = {Hospitals worry about new FDA proposal for medical devices: technical complexities of labels could compromise utility.},
journal = {P &amp; T : a peer-reviewed journal for formulary management},
volume = {38},
number = {2},
pages = {69-108},
pmid = {23599672},
issn = {1052-1372},
abstract = {A proposed FDA rule on unique device identification could complicate billing and bar-coding procedures for hospitals.},
}
@article {pmid23597753,
year = {2013},
author = {Rolo, EA and Oliveira, AR and Dourado, CG and Farinha, A and Rebelo, MT and Dias, D},
title = {Identification of sarcosaprophagous Diptera species through DNA barcoding in wildlife forensics.},
journal = {Forensic science international},
volume = {228},
number = {1-3},
pages = {160-164},
doi = {10.1016/j.forsciint.2013.02.038},
pmid = {23597753},
issn = {1872-6283},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Diptera/*genetics ; Electron Transport Complex IV/genetics ; Feeding Behavior ; Forensic Pathology ; Phylogeny ; Sequence Analysis ; Species Specificity ; },
abstract = {In recent years, forensic entomology has been applied in wildlife crimes, such as neglect cases, animal cruelty and illegal poaching. Likewise in human death investigations, in which insects can help to provide information about postmortem interval (PMI) and corpse transfer, entomology may be an important source of information in animal murder suspicion. The use of insects in forensic context relies primarily on its identification at the species level. To overcome some problems of morphological determination, molecular identification has gained relevance and has been applied frequently in forensic areas. Cytochrome c oxidase I (COI) gene was adopted in DNA barcoding approach. This methodology intends to unify the DNA-based identification using a specific region of mitochondrial DNA. COI sequences have been collected into the BOLD online database, allowing the molecular identification of sequences from unknown specimens. Nonetheless, to achieve a correct identification of an unknown sample, it is necessary that sequences from species under study exist, for comparison, in online databases. Due to the geographic differences, it is of huge importance to have samples from a certain species from its distribution range. In that sense, the aim of this research is to contribute to the potential and accuracy improvement of such databases in identification of species commonly found in wildlife carcasses. A portion of COI was sequenced from 95 specimens of seven species belonging to two families of Diptera (Calliphoridae and Muscidae) found in wildlife carcasses-baited traps in Serra da Estrela (Portugal). All specimens were identified at species level with a high specimen similarity and maximum identity percentage (through BOLD Systems and GenBank online databases, respectively). We also demonstrate the correct discrimination of all species through phylogenic and sequence divergence analyses proposed in DNA barcoding studies, reinforcing the suitability of this marker.},
}
@article {pmid23597081,
year = {2013},
author = {Bourke, BP and Oliveira, TP and Suesdek, L and Bergo, ES and Sallum, MA},
title = {A multi-locus approach to barcoding in the Anopheles strodei subgroup (Diptera: Culicidae).},
journal = {Parasites &amp; vectors},
volume = {6},
number = {},
pages = {111},
pmid = {23597081},
issn = {1756-3305},
mesh = {Animals ; Anopheles/*classification/*genetics ; Brazil ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; Entomology/*methods ; Female ; Humans ; Male ; Molecular Sequence Data ; *Multilocus Sequence Typing ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The ability to successfully identify and incriminate pathogen vectors is fundamental to effective pathogen control and management. This task is confounded by the existence of cryptic species complexes. Molecular markers can offer a highly effective means of species identification in such complexes and are routinely employed in the study of medical entomology. Here we evaluate a multi-locus system for the identification of potential malaria vectors in the Anopheles strodei subgroup.<br><br>METHODS: Larvae, pupae and adult mosquitoes (n = 61) from the An. strodei subgroup were collected from 21 localities in nine Brazilian states and sequenced for the COI, ITS2 and white gene. A Bayesian phylogenetic approach was used to describe the relationships in the Strodei Subgroup and the utility of COI and ITS2 barcodes was assessed using the neighbor joining tree and "best close match" approaches.<br><br>RESULTS: Bayesian phylogenetic analysis of the COI, ITS2 and white gene found support for seven clades in the An. strodei subgroup. The COI and ITS2 barcodes were individually unsuccessful at resolving and identifying some species in the Subgroup. The COI barcode failed to resolve An. albertoi and An. strodei but successfully identified approximately 92% of all species queries, while the ITS2 barcode failed to resolve An. arthuri and successfully identified approximately 60% of all species queries. A multi-locus COI-ITS2 barcode, however, resolved all species in a neighbor joining tree and successfully identified all species queries using the "best close match" approach.<br><br>CONCLUSIONS: Our study corroborates the existence of An. albertoi, An. CP Form and An. strodei in the An. strodei subgroup and identifies four species under An. arthuri informally named A-D herein. The use of a multi-locus barcode is proposed for species identification, which has potentially important utility for vector incrimination. Individuals previously found naturally infected with Plasmodium vivax in the southern Amazon basin and reported as An. strodei are likely to have been from An. arthuri C identified in this study.},
}
@article {pmid23597078,
year = {2013},
author = {Yang, JB and Tang, M and Li, HT and Zhang, ZR and Li, DZ},
title = {Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses.},
journal = {BMC evolutionary biology},
volume = {13},
number = {},
pages = {84},
pmid = {23597078},
issn = {1471-2148},
mesh = {Chromosome Mapping ; DNA, Chloroplast/genetics ; *Genome, Chloroplast ; Orchidaceae/*classification/cytology/*genetics ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {BACKGROUND: Cymbidium orchids, including some 50 species, are the famous flowers, and they possess high commercial value in the floricultural industry. Furthermore, the values of different orchids are great differences. However, species identification is very difficult. To a certain degree, chloroplast DNA sequence data are a versatile tool for species identification and phylogenetic implications in plants. Different chloroplast loci have been utilized for evaluating phylogenetic relationships at each classification level among plant species, including at the interspecies and intraspecies levels. However, there is no evidence that a short sequence can distinguish all plant species from each other in order to infer phylogenetic relationships. Molecular markers derived from the complete chloroplast genome can provide effective tools for species identification and phylogenetic resolution.<br><br>RESULTS: The complete nucleotide sequences of eight individuals from a total of five Cymbidium species' chloroplast (cp) genomes were determined using Illumina sequencing technology of the total DNA via a combination of de novo and reference-guided assembly. The length of the Cymbidium cp genome is about 155&#xa0;kb. The cp genomes contain 123 unique genes, and the IR regions contain 24 duplicates. Although the genomes, including genome structure, gene order and orientation, are similar to those of other orchids, they are not evolutionarily conservative. The cp genome of Cymbidium evolved moderately with more than 3% sequence divergence, which could provide enough information for phylogeny. Rapidly evolving chloroplast genome regions were identified and 11 new divergence hotspot regions were disclosed for further phylogenetic study and species identification in Orchidaceae.<br><br>CONCLUSIONS: Phylogenomic analyses were conducted using 10 complete chloroplast genomes from seven orchid species. These data accurately identified the individuals and established the phylogenetic relationships between the species. The results reveal that phylogenomics based on organelle genome sequencing lights the species identification-organelle-scale "barcodes", and is also an effective approach for studying whole populations and phylogenetic characteristics of Cymbidium.},
}
@article {pmid23592960,
year = {2013},
author = {Lonardi, S and Duma, D and Alpert, M and Cordero, F and Beccuti, M and Bhat, PR and Wu, Y and Ciardo, G and Alsaihati, B and Ma, Y and Wanamaker, S and Resnik, J and Bozdag, S and Luo, MC and Close, TJ},
title = {Combinatorial pooling enables selective sequencing of the barley gene space.},
journal = {PLoS computational biology},
volume = {9},
number = {4},
pages = {e1003010},
pmid = {23592960},
issn = {1553-7358},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Chromosomes, Artificial, Bacterial ; Cloning, Molecular ; Computational Biology/methods ; Computer Simulation ; Contig Mapping/*methods ; Genes, Plant ; Genetic Markers/genetics ; Genomic Library ; Genomics ; Hordeum/*genetics ; Models, Genetic ; Oryza/genetics ; Physical Chromosome Mapping ; *Sequence Analysis, DNA ; Species Specificity ; },
abstract = {For the vast majority of species - including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution) so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding.},
}
@article {pmid23590277,
year = {2013},
author = {Kermarrec, L and Franc, A and Rimet, F and Chaumeil, P and Humbert, JF and Bouchez, A},
title = {Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms.},
journal = {Molecular ecology resources},
volume = {13},
number = {4},
pages = {607-619},
doi = {10.1111/1755-0998.12105},
pmid = {23590277},
issn = {1755-0998},
mesh = {DNA, Mitochondrial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Diatoms/*classification/*genetics ; Electron Transport Complex IV/genetics ; Fresh Water/*microbiology ; *Genetic Variation ; High-Throughput Nucleotide Sequencing/*methods ; *Metagenome ; Molecular Sequence Data ; RNA, Ribosomal, 18S/genetics ; Ribulose-Bisphosphate Carboxylase/genetics ; },
abstract = {The recent emergence of barcoding approaches coupled to those of next-generation sequencing (NGS) has raised new perspectives for studying environmental communities. In this framework, we tested the possibility to derive accurate inventories of diatom communities from pyrosequencing outputs with an available DNA reference library. We used three molecular markers targeting the nuclear, chloroplast and mitochondrial genomes (SSU rDNA, rbcL and cox1) and three samples of a mock community composed of 30 known diatom strains belonging to 21 species. In the goal to detect methodological biases, one sample was constituted directly from pooled cultures, whereas the others consisted of pooled PCR products. The NGS reads obtained by pyrosequencing (Roche 454) were compared first to a DNA reference library including the sequences of all the species used to constitute the mock community, and second to a complete DNA reference library with a larger taxonomic coverage. A stringent taxonomic assignation gave inventories that were compared to the real one. We detected biases due to DNA extraction and PCR amplification that resulted in false-negative detection. Conversely, pyrosequencing errors appeared to generate false positives, especially in case of closely allied species. The taxonomic coverage of DNA reference libraries appears to be the most crucial factor, together with marker polymorphism which is essential to identify taxa at the species level. RbcL offers a high resolving power together with a large DNA reference library. Although needing further optimization, pyrosequencing is suitable for identifying diatom assemblages and may find applications in the field of freshwater biomonitoring.},
}
@article {pmid23590207,
year = {2013},
author = {Deagle, BE and Thomas, AC and Shaffer, AK and Trites, AW and Jarman, SN},
title = {Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?.},
journal = {Molecular ecology resources},
volume = {13},
number = {4},
pages = {620-633},
doi = {10.1111/1755-0998.12103},
pmid = {23590207},
issn = {1755-0998},
mesh = {Animals ; Bias ; *Biodiversity ; Diet ; Feces/*microbiology ; High-Throughput Nucleotide Sequencing/*methods/*standards ; Phoca/*microbiology ; Specimen Handling/*methods/*standards ; },
abstract = {A goal of many environmental DNA barcoding studies is to infer quantitative information about relative abundances of different taxa based on sequence read proportions generated by high-throughput sequencing. However, potential biases associated with this approach are only beginning to be examined. We sequenced DNA amplified from faeces (scats) of captive harbour seals (Phoca vitulina) to investigate whether sequence counts could be used to quantify the seals' diet. Seals were fed fish in fixed proportions, a chordate-specific mitochondrial 16S marker was amplified from scat DNA and amplicons sequenced using an Ion Torrent PGM™. For a given set of bioinformatic parameters, there was generally low variability between scat samples in proportions of prey species sequences recovered. However, proportions varied substantially depending on sequencing direction, level of quality filtering (due to differences in sequence quality between species) and minimum read length considered. Short primer tags used to identify individual samples also influenced species proportions. In addition, there were complex interactions between factors; for example, the effect of quality filtering was influenced by the primer tag and sequencing direction. Resequencing of a subset of samples revealed some, but not all, biases were consistent between runs. Less stringent data filtering (based on quality scores or read length) generally produced more consistent proportional data, but overall proportions of sequences were very different than dietary mass proportions, indicating additional technical or biological biases are present. Our findings highlight that quantitative interpretations of sequence proportions generated via high-throughput sequencing will require careful experimental design and thoughtful data analysis.},
}
@article {pmid23590182,
year = {2013},
author = {Fernández-Flores, S and Fernández-Triana, JL and Martínez, JJ and Zaldívar-Riverón, A},
title = {DNA barcoding species inventory of Microgastrinae wasps (Hymenoptera, Braconidae) from a Mexican tropical dry forest.},
journal = {Molecular ecology resources},
volume = {13},
number = {6},
pages = {1146-1150},
doi = {10.1111/1755-0998.12102},
pmid = {23590182},
issn = {1755-0998},
mesh = {Animals ; Biodiversity ; *DNA Barcoding, Taxonomic ; Female ; Male ; Mexico ; Molecular Sequence Data ; Trees ; Wasps/classification/*genetics ; },
abstract = {The cosmopolitan Microgastrinae is probably the most diverse braconid subfamily of parasitoid wasps, yet its species diversity is far from being known. As part of a global initiative for DNA barcoding Microgastrinae species, here we show the results of a study that assessed the species richness of this subfamily in a Mexican tropical dry forest located in the Chamela region, near the Pacific coast of Jalisco. Barcoding sequences of a total of 551 microgastrine specimens were generated, corresponding to 238 haplotypes. Performance of two species delineation approaches, a 2% corrected pairwise distance criterion and the general mixed Yule-coalescent (GMYC) method, yielded 100 and 112 putative species, respectively, which belong to 13 genera. The species delimited by the above two approaches were mostly congruent with our morphospecies identification. Ten molecular operational taxonomic units (MOTUs) were split into twenty-two species by the GMYC approach. We found morphological differences between the GMYC species corresponding to three of these MOTUs. Thus, a total of 103 microgastrine species were confirmed for the region of study. Thirty-three species were only represented by males, and therefore, their generic assignment is only tentatively proposed. Fornicia, Dolichogenoidea, Distatrix, Glyptapanteles and Pholetesor represent new generic records for the Mexican territory. A new record for the country is also provided for the Diolcogaster-basimacula species group. Based on a comparison of nearly 20 000 barcoding sequences released for Microgastrinae from 75 countries, only five microgastrine species from Chamela were found to occur in other countries, four in Costa Rica and one in Canada and the United States.},
}
@article {pmid23587339,
year = {2013},
author = {Zhou, X and Li, Y and Liu, S and Yang, Q and Su, X and Zhou, L and Tang, M and Fu, R and Li, J and Huang, Q},
title = {Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification.},
journal = {GigaScience},
volume = {2},
number = {1},
pages = {4},
pmid = {23587339},
issn = {2047-217X},
abstract = {BACKGROUND: Next-generation-sequencing (NGS) technologies combined with a classic DNA barcoding approach have enabled fast and credible measurement for biodiversity of mixed environmental samples. However, the PCR amplification involved in nearly all existing NGS protocols inevitably introduces taxonomic biases. In the present study, we developed new Illumina pipelines without PCR amplifications to analyze terrestrial arthropod communities.<br><br>RESULTS: Mitochondrial enrichment directly followed by Illumina shotgun sequencing, at an ultra-high sequence volume, enabled the recovery of Cytochrome c Oxidase subunit 1 (COI) barcode sequences, which allowed for the estimation of species composition at high fidelity for a terrestrial insect community. With 15.5 Gbp Illumina data, approximately 97% and 92% were detected out of the 37 input Operational Taxonomic Units (OTUs), whether the reference barcode library was used or not, respectively, while only 1 novel OTU was found for the latter. Additionally, relatively strong correlation between the sequencing volume and the total biomass was observed for species from the bulk sample, suggesting a potential solution to reveal relative abundance.<br><br>CONCLUSIONS: The ability of the new Illumina PCR-free pipeline for DNA metabarcoding to detect small arthropod specimens and its tendency to avoid most, if not all, false positives suggests its great potential in biodiversity-related surveillance, such as in biomonitoring programs. However, further improvement for mitochondrial enrichment is likely needed for the application of the new pipeline in analyzing arthropod communities at higher diversity.},
}
@article {pmid23587049,
year = {2013},
author = {Parducci, L and Matetovici, I and Fontana, SL and Bennett, KD and Suyama, Y and Haile, J and Kjaer, KH and Larsen, NK and Drouzas, AD and Willerslev, E},
title = {Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia.},
journal = {Molecular ecology},
volume = {22},
number = {13},
pages = {3511-3524},
doi = {10.1111/mec.12298},
pmid = {23587049},
issn = {1365-294X},
mesh = {Biodiversity ; Cloning, Molecular ; DNA Barcoding, Taxonomic ; DNA Primers ; DNA, Plant/analysis/genetics ; Fossils ; Geologic Sediments/*analysis ; Lakes/*analysis ; Plants/classification/*genetics ; Pollen/*chemistry ; Scandinavian and Nordic Countries ; Sequence Alignment ; Species Specificity ; },
abstract = {Plant and animal biodiversity can be studied by obtaining DNA directly from the environment. This new approach in combination with the use of generic barcoding primers (metabarcoding) has been suggested as complementary or alternative to traditional biodiversity monitoring in ancient soil sediments. However, the extent to which metabarcoding truly reflects plant composition remains unclear, as does its power to identify species with no pollen or macrofossil evidence. Here, we compared pollen-based and metabarcoding approaches to explore the Holocene plant composition around two lakes in central Scandinavia. At one site, we also compared barcoding results with those obtained in earlier studies with species-specific primers. The pollen analyses revealed a larger number of taxa (46), of which the majority (78%) was not identified by metabarcoding. The metabarcoding identified 14 taxa (MTUs), but allowed identification to a lower taxonomical level. The combined analyses identified 52 taxa. The barcoding primers may favour amplification of certain taxa, as they did not detect taxa previously identified with species-specific primers. Taphonomy and selectiveness of the primers are likely the major factors influencing these results. We conclude that metabarcoding from lake sediments provides a complementary, but not an alternative, tool to pollen analysis for investigating past flora. In the absence of other fossil evidence, metabarcoding gives a local and important signal from the vegetation, but the resulting assemblages show limited capacity to detect all taxa, regardless of their abundance around the lake. We suggest that metabarcoding is followed by pollen analysis and the use of species-specific primers to provide the most comprehensive signal from the environment.},
}
@article {pmid23582202,
year = {2013},
author = {Feinauer, CJ and Hofmann, A and Goldt, S and Liu, L and Máté, G and Heermann, DW},
title = {Zinc finger proteins and the 3D organization of chromosomes.},
journal = {Advances in protein chemistry and structural biology},
volume = {90},
number = {},
pages = {67-117},
doi = {10.1016/B978-0-12-410523-2.00003-1},
pmid = {23582202},
issn = {1876-1631},
mesh = {Amino Acid Sequence ; Animals ; CCCTC-Binding Factor ; Cell Nucleus/chemistry ; Chromatin/chemistry/metabolism ; Chromosomes/chemistry/*metabolism ; DNA-Binding Proteins/chemistry/*metabolism ; Humans ; *Models, Biological ; Molecular Sequence Data ; Protein Binding ; Repressor Proteins/chemistry/metabolism ; Xenopus laevis/metabolism ; Zinc Fingers ; },
abstract = {Zinc finger domains are one of the most common structural motifs in eukaryotic cells, which employ the motif in some of their most important proteins (including TFIIIA, CTCF, and ZiF268). These DNA binding proteins contain up to 37 zinc finger domains connected by flexible linker regions. They have been shown to be important organizers of the 3D structure of chromosomes and as such are called the master weaver of the genome. Using NMR and numerical simulations, much progress has been made during the past few decades in understanding their various functions and their ways of binding to the DNA, but a large knowledge gap remains to be filled. One problem of the hitherto existing theoretical models of zinc finger protein DNA binding in this context is that they are aimed at describing specific binding. Furthermore, they exclusively focus on the microscopic details or approach the problem without considering such details at all. We present the Flexible Linker Model, which aims explicitly at describing nonspecific binding. It takes into account the most important effects of flexible linkers and allows a qualitative investigation of the effects of these linkers on the nonspecific binding affinity of zinc finger proteins to DNA. Our results indicate that the binding affinity is increased by the flexible linkers by several orders of magnitude. Moreover, they show that the binding map for proteins with more than one domain presents interesting structures, which have been neither observed nor described before, and can be interpreted to fit very well with existing theories of facilitated target location. The effect of the increased binding affinity is also in agreement with recent experiments that until now have lacked an explanation. We further explore the class of proteins with flexible linkers, which are unstructured until they bind. We have developed a methodology to characterize these flexible proteins. Employing the concept of barcodes, we propose a measure to compare such flexible proteins in terms of a similarity measure. This measure is validated by a comparison between a geometric similarity measure and the topological similarity measure that takes geometry as well as topology into account.},
}
@article {pmid23580546,
year = {2013},
author = {Casbon, JA and Slatter, AF and Musgrave-Brown, E and Osborne, RJ and Lichtenstein, CP and Brenner, S},
title = {Reflex: intramolecular barcoding of long-range PCR products for sequencing multiple pooled DNAs.},
journal = {Nucleic acids research},
volume = {41},
number = {10},
pages = {e112},
pmid = {23580546},
issn = {1362-4962},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Cytochrome P-450 CYP2D6/genetics ; DNA Primers/chemistry ; Humans ; *Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; },
abstract = {We present an intramolecular reaction, Reflex™, to derive shorter, sequencer-ready, daughter polymerase chain reaction products from a pooled population of barcoded long-range polymerase chain reaction products, whilst still preserving the cognate DNA barcodes. Our Reflex workflow needs only a small number of primer extension steps to rapidly enable uniform sequence coverage of long contiguous sequence targets in large numbers of samples at low cost on desktop next-generation sequencers.},
}
@article {pmid23579925,
year = {2013},
author = {Leray, M and Agudelo, N and Mills, SC and Meyer, CP},
title = {Effectiveness of annealing blocking primers versus restriction enzymes for characterization of generalist diets: unexpected prey revealed in the gut contents of two coral reef fish species.},
journal = {PloS one},
volume = {8},
number = {4},
pages = {e58076},
pmid = {23579925},
issn = {1932-6203},
mesh = {Animals ; Coral Reefs ; DNA Barcoding, Taxonomic/methods ; DNA Primers ; DNA Restriction Enzymes ; *Diet ; Fishes/*classification ; *Food Chain ; *Gastrointestinal Contents/chemistry ; Phylogeny ; Polymerase Chain Reaction/methods ; *Predatory Behavior ; },
abstract = {Characterization of predator-prey interactions is challenging as researchers have to rely on indirect methods that can be costly, biased and too imprecise to elucidate the complexity of food webs. DNA amplification and sequencing techniques of gut and fecal contents are promising approaches, but their success largely depends on the ability to amplify the taxonomic array of prey consumed and then match prey amplicons with reference sequences. When little a priori information on diet is available or a generalist predator is targeted, versatile primer sets (also referred to as universal or general primers) as opposed to group- or species-specific primer sets are the most powerful to unveil the full range of prey consumed. However, versatile primers are likely to preferentially amplify the predominant, less degraded predator DNA if no manipulation is performed to exclude this confounding DNA template. In this study we compare two approaches that eliminate the confounding predator template: restriction digestion and the use of annealing blocking primers. First, we use a preliminary DNA barcode library provided by the Moorea BIOCODE project to 1) evaluate the cutting frequency of commercially available restriction enzymes and 2) design predator specific annealing blocking primers. We then compare the performance of the two predator removal strategies for the detection of prey templates using two versatile primer sets from the gut contents of two generalist coral reef fish species sampled in Moorea. Our study demonstrates that blocking primers should be preferentially used over restriction digestion for predator DNA removal as they recover greater prey diversity. We also emphasize that a combination of versatile primers may be required to best represent the breadth of a generalist's diet.},
}
@article {pmid23577154,
year = {2013},
author = {Prévot, V and Jordaens, K and Sonet, G and Backeljau, T},
title = {Exploring species level taxonomy and species delimitation methods in the facultatively self-fertilizing land snail genus Rumina (gastropoda: pulmonata).},
journal = {PloS one},
volume = {8},
number = {4},
pages = {e60736},
pmid = {23577154},
issn = {1932-6203},
mesh = {Animals ; Classification/*methods ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics ; *Fertilization ; Genetic Markers/genetics ; Models, Statistical ; Phylogeny ; Snails/*classification/genetics/*physiology ; },
abstract = {Delimiting species in facultatively selfing taxa is a challenging problem of which the terrestrial pulmonate snail genus Rumina is a good example. These snails have a mixed breeding system and show a high degree of shell and color variation. Three nominal species (R. decollata, R. saharica and R. paivae) and two color morphs within R. decollata (dark and light) are currently recognized. The present study aims at evaluating to what extent these entities reflect evolutionary diverging taxonomic units, rather than fixed polymorphisms due to sustained selfing. Therefore, a phylogenetic analysis of nuclear (ITS1, ITS2) and mitochondrial DNA (COI, CytB, 12S rDNA, 16S rDNA) sequences was performed. Putative species in Rumina, inferred from the mitochondrial DNA phylogeny, were compared with those proposed on the basis of the COI gene by (1) DNA barcoding gap analysis, (2) Automatic Barcode Gap Discovery, (3) the species delimitation plug-in of the Geneious software, (4) the Genealogical Sorting Index, and (5) the General Mixed Yule Coalescent model. It is shown that these methods produce a variety of different species hypotheses and as such one may wonder to what extent species delimitation methods are really useful. With respect to Rumina, the data suggest at least seven species, one corresponding to R. saharica and six that are currently grouped under the name R. decollata. The species-level status of R. paivae is rejected.},
}
@article {pmid23576076,
year = {2013},
author = {He, P and Zhang, Y and Liu, L and Qiao, W and Zhang, S},
title = {Ultrasensitive SERS detection of lysozyme by a target-triggering multiple cycle amplification strategy based on a gold substrate.},
journal = {Chemistry (Weinheim an der Bergstrasse, Germany)},
volume = {19},
number = {23},
pages = {7452-7460},
doi = {10.1002/chem.201203224},
pmid = {23576076},
issn = {1521-3765},
mesh = {DNA/*chemistry ; Gold/*chemistry ; Humans ; Limit of Detection ; Muramidase/*analysis/*chemistry ; Nanoparticles/*chemistry ; Spectrum Analysis, Raman/*methods ; },
abstract = {An ultrasensitive surface enhanced Raman scattering (SERS) method has been designed to selectively and sensitively detect lysozyme. The gold chip as the detection substrate, the aptamer-based target-triggering cascade multiple cycle amplification, and gold nanoparticles (AuNPs) bio-barcode Raman probe enhancement on the gold substrate are employed to enhance the SERS signals. The cascade amplification process consists of the nicking enzyme signaling amplification (NESA), the strand displacement amplification (SDA), and the circular-hairpin-assisted exponential amplification reaction (HA-EXPAR). With the involvement of an aptamer-based probe, two amplification reaction templates, and a Raman probe, the whole circle amplification process is triggered by the target recognition of lysozyme. The products of the upstream cycle (NESA) could act as the "DNA trigger" of the downstream cycle (SDA and circular HA-EXPAR) to generate further signal amplification, resulting in the immobility of abundant AuNPs Raman probes on the gold substrate. "Hot spots" are produced between the Raman probe and the gold film, leading to significant SERS enhancement. This detection method exhibits excellent specificity and sensitivity towards lysozyme with a detection limit of 1.0×10(-15) M. Moreover, the practical determination of lysozyme in human serum demonstrates the feasibility of this SERS approach in the analysis of a variety of biological specimens.},
}
@article {pmid23568538,
year = {2013},
author = {Yoo, HS and Eah, JY and Kim, JS and Kim, YJ and Min, MS and Paek, WK and Lee, H and Kim, CB},
title = {Retraction note: DNA barcoding Korean birds. Mol. Cells 22 (2006) 323-7.},
journal = {Molecules and cells},
volume = {35},
number = {4},
pages = {357},
doi = {10.1007/s10059-013-3151-6},
pmid = {23568538},
issn = {0219-1032},
}
@article {pmid23566251,
year = {2013},
author = {Hsu, TH and Ning, Y and Gwo, JC and Zeng, ZN},
title = {DNA barcoding reveals cryptic diversity in the peanut worm Sipunculus nudus.},
journal = {Molecular ecology resources},
volume = {13},
number = {4},
pages = {596-606},
doi = {10.1111/1755-0998.12097},
pmid = {23566251},
issn = {1755-0998},
mesh = {Animals ; Arachis/*parasitology ; China ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Helminths/classification/genetics ; Molecular Sequence Data ; Phylogeography ; Polychaeta/*classification/*genetics ; Sequence Analysis, DNA ; Taiwan ; },
abstract = {Peanut worm (Sipunculus nudus) is a cosmopolitan species mainly distributed in tropical and subtropical coastal waters. Analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene sequences among S. nudus from GenBank revealed high genetic variation (p-distance, 0.115-0.235; k2p, 0.128-0.297) and paraphyletic relationships. These indicated misidentification and/or cryptic diversity may be present in the genus Sipunculus. To understand the genetic diversity and to manage the recourse of S. nudus, we collected specimens from coastal waters of southern China and Taiwan. In the phylogenetic topology, specimens can be separated into four distinct clades; three of these clades (clade A, B and C) were only represented from this region (southern China and Taiwan), but the clade D grouped with individuals from Central America (Atlantic coast). Furthermore, individuals of clades A and D were collected at the same location, which does not support the hypothesis that this genetic break reflects contemporary geographical isolation. The four distinct clades observed among coastal waters of southern China and Taiwan indicated underestimated diversity. It is noteworthy that the cryptic diversity is vulnerable under high pressure of human activity.},
}
@article {pmid23565134,
year = {2013},
author = {Parmentier, I and Duminil, J and Kuzmina, M and Philippe, M and Thomas, DW and Kenfack, D and Chuyong, GB and Cruaud, C and Hardy, OJ},
title = {How effective are DNA barcodes in the identification of African rainforest trees?.},
journal = {PloS one},
volume = {8},
number = {4},
pages = {e54921},
pmid = {23565134},
issn = {1932-6203},
mesh = {Cameroon ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Genes, Plant ; Plastids/genetics ; Polymorphism, Genetic ; Species Specificity ; Trees/*classification/*genetics ; Tropical Climate ; },
abstract = {BACKGROUND: DNA barcoding of rain forest trees could potentially help biologists identify species and discover new ones. However, DNA barcodes cannot always distinguish between closely related species, and the size and completeness of barcode databases are key parameters for their successful application. We test the ability of rbcL, matK and trnH-psbA plastid DNA markers to identify rain forest trees at two sites in Atlantic central Africa under the assumption that a database is exhaustive in terms of species content, but not necessarily in terms of haplotype diversity within species.<br><br>We assess the accuracy of identification to species or genus using a genetic distance matrix between samples either based on a global multiple sequence alignment (GD) or on a basic local alignment search tool (BLAST). Where a local database is available (within a 50 ha plot), barcoding was generally reliable for genus identification (95-100% success), but less for species identification (71-88%). Using a single marker, best results for species identification were obtained with trnH-psbA. There was a significant decrease of barcoding success in species-rich clades. When the local database was used to identify the genus of trees from another region and did include all genera from the query individuals but not all species, genus identification success decreased to 84-90%. The GD method performed best but a global multiple sequence alignment is not applicable on trnH-psbA.<br><br>CONCLUSIONS/SIGNIFICANCE: Barcoding is a useful tool to assign unidentified African rain forest trees to a genus, but identification to a species is less reliable, especially in species-rich clades, even using an exhaustive local database. Combining two markers improves the accuracy of species identification but it would only marginally improve genus identification. Finally, we highlight some limitations of the BLAST algorithm as currently implemented and suggest possible improvements for barcoding applications.},
}
@article {pmid23563901,
year = {2013},
author = {Dabert, J and Dabert, M and Gal, AF and Miclăuş, V and Mihalca, AD and Sándor, AD},
title = {Multidisciplinary analysis of Knemidocoptes jamaicensis parasitising the Common Chaffinch, Fringilla coelebs: proofs for a multispecies complex?.},
journal = {Parasitology research},
volume = {112},
number = {6},
pages = {2373-2380},
pmid = {23563901},
issn = {1432-1955},
mesh = {Acari/anatomy &amp; histology/*classification/genetics/*physiology ; Animals ; Biometry ; Bird Diseases/*parasitology/*pathology ; DNA Barcoding, Taxonomic ; Ectoparasitic Infestations/parasitology/*veterinary ; Electron Transport Complex IV/genetics ; Entomology ; Host Specificity ; Molecular Sequence Data ; Passeriformes/*parasitology ; Phylogeography ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Romania ; Sequence Analysis, DNA ; },
abstract = {The number of studies discussing the pathology and host specificity in Knemidocoptinae is very limited. In Knemidocoptes jamaicensis, the host specificity seems to be very broad, and there is a clear morphological variability in individuals originating from various bird species; hence, serious doubts appear about the species status of this mite. We report a multidisciplinary approach to the taxonomy, morphology, ecology, and pathology of K. jamaicensis. The source of the mites in our study was a second year aged female of the Common Chaffinch, Fringilla coelebs, which accidentally died in the mist net during a field study in Dumbrava, Cluj County, Romania in March 2011. Comparisons of the biometrical data regarding the body dimensions, length of certain setae, and distances between bases of dorsal setae with other published data showed a great variability of certain measurements between populations infecting various hosts and localities and sometimes even within single populations. Gross and histologic lesions consisted in severe bilateral orthokeratotic hyperkeratosis and epidermal spongiosis. Lesions also involved the skin of the joints. Skin inflammation was absent, and no lesions were noticed in the metatarsus bone. Following molecular analysis, the 518-base-long sequence differed from the published 18S rDNA in nine positions. Additionally, our paper reports for the first time the DNA barcode sequences of K. jamaicensis and, together with the synoptic analysis of host spectrum, geographical distribution and morphological variability it brings important evidences to sustain the hypothesis of multispecies complex for K. jamaicensis.},
}
@article {pmid23560107,
year = {2013},
author = {Hibert, F and Taberlet, P and Chave, J and Scotti-Saintagne, C and Sabatier, D and Richard-Hansen, C},
title = {Unveiling the diet of elusive rainforest herbivores in next generation sequencing era? The tapir as a case study.},
journal = {PloS one},
volume = {8},
number = {4},
pages = {e60799},
pmid = {23560107},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/classification/*genetics ; Diet ; Ecosystem ; Feces/chemistry ; French Guiana ; Herbivory/physiology ; High-Throughput Nucleotide Sequencing ; Perissodactyla/physiology ; *Phylogeny ; Plants/classification/*genetics ; Plastids/classification/*genetics ; Ribosomes/chemistry ; },
abstract = {Characterizing the trophic relationships between large herbivores and the outstanding plant diversity in rainforest is a major challenge because of their elusiveness. This is crucial to understand the role of these herbivores in the functioning of the rainforest ecosystems. We tested a non-invasive approach based on the high-throughput sequencing of environmental samples using small plant plastid sequences (the trnL P6 loop) and ribosomal ITS1 primers, referred to as DNA metabarcoding, to investigate the diet of the largest neotropical herbivore, the lowland tapir. Sequencing was performed on plant DNA extracted from tapir faeces collected at the Nouragues station, a protected area of French Guiana. In spite of a limited sampling, our approach reliably provided information about the lowland tapir's diet at this site. Indeed, 95.1% and 74.4% of the plant families and genera identified thanks to the trnL P6 loop, respectively, matched with taxa already known to be consumed by tapirs. With this approach we were able to show that two families and eight new genera are also consumed by the lowland tapir. The taxonomic resolution of this method is limited to the plant family and genera. Complementary barcodes, such as a small portion of ITS1, can be used to efficiently narrow identifications down to the species in some problematic families. We will discuss the remaining limitations of this approach and how useful it is at this stage to unravel the diet of elusive rainforest herbivores and better understand their role as engineers of the ecosystem.},
}
@article {pmid23559409,
year = {2013},
author = {Halbritter, J and Porath, JD and Diaz, KA and Braun, DA and Kohl, S and Chaki, M and Allen, SJ and Soliman, NA and Hildebrandt, F and Otto, EA and , },
title = {Identification of 99 novel mutations in a worldwide cohort of 1,056 patients with a nephronophthisis-related ciliopathy.},
journal = {Human genetics},
volume = {132},
number = {8},
pages = {865-884},
pmid = {23559409},
issn = {1432-1203},
support = {R01 DK068306/DK/NIDDK NIH HHS/United States ; RC4 DK090917/DK/NIDDK NIH HHS/United States ; RC4-DK090917/DK/NIDDK NIH HHS/United States ; },
mesh = {Adaptor Proteins, Signal Transducing/genetics ; Caroli Disease/*genetics/pathology ; Cilia/*genetics/*pathology ; Cohort Studies ; Cytoskeletal Proteins ; DNA Mutational Analysis ; Female ; Genes, Recessive/*genetics ; Global Health ; High-Throughput Nucleotide Sequencing ; Humans ; Kidney Diseases, Cystic/*genetics/pathology ; Male ; Membrane Proteins/*genetics ; Multiplex Polymerase Chain Reaction ; Mutation/*genetics ; Pedigree ; Pilot Projects ; },
abstract = {Nephronophthisis-related ciliopathies (NPHP-RC) are autosomal-recessive cystic kidney diseases. More than 13 genes are implicated in its pathogenesis to date, accounting for only 40 % of all cases. High-throughput mutation screenings of large patient cohorts represent a powerful tool for diagnostics and identification of novel NPHP genes. We here performed a new high-throughput mutation analysis method to study 13 established NPHP genes (NPHP1-NPHP13) in a worldwide cohort of 1,056 patients diagnosed with NPHP-RC. We first applied multiplexed PCR-based amplification using Fluidigm Access-Array™ technology followed by barcoding and next-generation resequencing on an Illumina platform. As a result, we established the molecular diagnosis in 127/1,056 independent individuals (12.0 %) and identified a single heterozygous truncating mutation in an additional 31 individuals (2.9 %). Altogether, we detected 159 different mutations in 11 out of 13 different NPHP genes, 99 of which were novel. Phenotypically most remarkable were two patients with truncating mutations in INVS/NPHP2 who did not present as infants and did not exhibit extrarenal manifestations. In addition, we present the first case of Caroli disease due to mutations in WDR19/NPHP13 and the second case ever with a recessive mutation in GLIS2/NPHP7. This study represents the most comprehensive mutation analysis in NPHP-RC patients, identifying the largest number of novel mutations in a single study worldwide.},
}
@article {pmid23557683,
year = {2013},
author = {Palinauskas, V and Iezhova, TA and Križanauskienė, A and Markovets, MY and Bensch, S and Valkiūnas, G},
title = {Molecular characterization and distribution of Haemoproteus minutus (Haemosporida, Haemoproteidae): a pathogenic avian parasite.},
journal = {Parasitology international},
volume = {62},
number = {4},
pages = {358-363},
doi = {10.1016/j.parint.2013.03.006},
pmid = {23557683},
issn = {1873-0329},
mesh = {Animals ; Bird Diseases/epidemiology/*parasitology ; Birds/blood/*parasitology ; Cytochromes b/genetics ; DNA, Protozoan/genetics ; Haemosporida/classification/*genetics ; Mitochondria/genetics ; Phylogeny ; *Protozoan Infections, Animal ; },
abstract = {Recently, the lineage hTURDUS2 of Haemoproteus minutus (Haemosporida, Haemoproteidae) was reported to cause mortality in captive parrots. This parasite lineage is widespread and prevalent in the blackbird Turdus merula throughout its entire distribution range. Species identity of other closely related lineages recently reported in dead parrots remains unclear, but will be important to determine for a better understanding of the epidemiology of haemoproteosis. Using polymerase chain reaction (PCR)-based and microscopic methods, we analyzed 265 blood samples collected from 52 species of wild birds in Eurasia (23 samples from Kamchatka Peninsula, 73 from Sakhalin Island, 150 from Ekaterinburg and 19 from Irkutsk regions of Russia). Single infections of the lineages hTURDUS2 (hosts are redwing Turdus iliacus and fieldfare Turdus pilaris), hTUPHI1 (song thrush Turdus philomelos) and hTUCHR01 (fieldfare, redwing, song thrush and brown-headed thrush Turdus chysolaus) were detected. We identified species of these haemoproteids based on morphology of their blood stages and conclude that these lineages belong to H. minutus, a widespread parasite of different species of thrushes (genus Turdus), which serve as reservoir hosts of this haemoproteid infection. Phylogenetic analysis shows that the lineages hTURDUS2, hTUCHR01 and hTUPHI1 of H. minutus are closely related to Haemoproteus pallidus (lineages hPFC1 and hCOLL2), Haemoproteus pallidulus (hSYAT03), and Haemoproteus sp. (hMEUND3); genetic distance among their mitochondrial cytochrome b (cyt b) lineages is small (<1% or<4 nucleotides). All these blood parasites are different in many morphological characters, but are similar due to one feature, which is the pale staining of their macrogametocytes' cytoplasm with Giemsa. Because of the recent publications about mortality caused by the lineages hTUPHI1 and hTURDUS2 of H. minutus in captive parrots in Europe, H. minutus and the closely related H. pallidus and H. pallidulus are worth more attention as these are possible agents of haemoproteosis in exotic birds. The present study provides barcodes for molecular detection of different lineages of H. minutus, and extends information about the distribution of this blood parasite.},
}
@article {pmid23557319,
year = {2013},
author = {Ball, RE and Jones, CS and Lynghammar, A and Noble, LR and Griffiths, AM},
title = {The first confirmed cases of full albinism in rajid species.},
journal = {Journal of fish biology},
volume = {82},
number = {4},
pages = {1433-1440},
doi = {10.1111/jfb.12072},
pmid = {23557319},
issn = {1095-8649},
mesh = {*Albinism ; Animals ; DNA Barcoding, Taxonomic ; Male ; North Sea ; Pigmentation/genetics/physiology ; Skates, Fish/genetics/*physiology ; },
abstract = {Three albino skate specimens (Rajidae) were captured from the North Sea and English Channel between 2008 and 2011. Using DNA barcoding (COI gene) and morphometric analyses, species were identified as a spotted ray Raja montagui, a blonde ray Raja brachyura and a thornback ray Raja clavata. This finding represents the first record of full albinism (a lack of skin and retinal pigmentation) in rajid species.},
}
@article {pmid23557180,
year = {2013},
author = {Laforest, BJ and Winegardner, AK and Zaheer, OA and Jeffery, NW and Boyle, EE and Adamowicz, SJ},
title = {Insights into biodiversity sampling strategies for freshwater microinvertebrate faunas through bioblitz campaigns and DNA barcoding.},
journal = {BMC ecology},
volume = {13},
number = {},
pages = {13},
pmid = {23557180},
issn = {1472-6785},
mesh = {Animals ; *Biodiversity ; Crustacea/*classification/*genetics ; DNA/genetics ; DNA Barcoding, Taxonomic/methods ; Fresh Water/*parasitology ; Manitoba ; Phylogeny ; },
abstract = {BACKGROUND: Biodiversity surveys have long depended on traditional methods of taxonomy to inform sampling protocols and to determine when a representative sample of a given species pool of interest has been obtained. Questions remain as to how to design appropriate sampling efforts to accurately estimate total biodiversity. Here we consider the biodiversity of freshwater ostracods (crustacean class Ostracoda) from the region of Churchill, Manitoba, Canada. Through an analysis of observed species richness and complementarity, accumulation curves, and richness estimators, we conduct an a posteriori analysis of five bioblitz-style collection strategies that differed in terms of total duration, number of sites, protocol flexibility to heterogeneous habitats, sorting of specimens for analysis, and primary purpose of collection. We used DNA barcoding to group specimens into molecular operational taxonomic units for comparison.<br><br>RESULTS: Forty-eight provisional species were identified through genetic divergences, up from the 30 species previously known and documented in literature from the Churchill region. We found differential sampling efficiency among the five strategies, with liberal sorting of specimens for molecular analysis, protocol flexibility (and particularly a focus on covering diverse microhabitats), and a taxon-specific focus to collection having strong influences on garnering more accurate species richness estimates.<br><br>CONCLUSIONS: Our findings have implications for the successful design of future biodiversity surveys and citizen-science collection projects, which are becoming increasingly popular and have been shown to produce reliable results for a variety of taxa despite relying on largely untrained collectors. We propose that efficiency of biodiversity surveys can be increased by non-experts deliberately selecting diverse microhabitats; by conducting two rounds of molecular analysis, with the numbers of samples processed during round two informed by the singleton prevalence during round one; and by having sub-teams (even if all non-experts) focus on select taxa. Our study also provides new insights into subarctic diversity of freshwater Ostracoda and contributes to the broader "Barcoding Biotas" campaign at Churchill. Finally, we comment on the associated implications and future research directions for community ecology analyses and biodiversity surveys through DNA barcoding, which we show here to be an efficient technique enabling rapid biodiversity quantification in understudied taxa.},
}
@article {pmid23557118,
year = {2013},
author = {Elmas, A and Jajamovich, GH and Wang, X and Samoilov, MS},
title = {Designing DNA barcodes orthogonal in melting temperature by simulated annealing optimization.},
journal = {Nucleic acid therapeutics},
volume = {23},
number = {2},
pages = {140-151},
doi = {10.1089/nat.2012.0394},
pmid = {23557118},
issn = {2159-3345},
mesh = {Algorithms ; DNA/chemistry/*genetics ; *DNA Barcoding, Taxonomic ; *DNA Probes ; *Nucleic Acid Denaturation ; Nucleic Acid Hybridization/genetics ; Oligonucleotides/chemistry/genetics ; },
abstract = {Molecular barcode arrays are widely employed in the analysis of large strain libraries, whereby probes linked to unique oligonucleotides ("antitags") are used to detect selected DNA targets ("tags") by highly specific hybridization. One of the major problems for such screen designs is thus insuring a high degree of probe-target specificity and a low level of nonspecific binding (in sum, "orthogonality") across the entire tag population ("collection"). Several approaches have been previously proposed for designing orthogonal DNA tags by-among others-focusing on their individual or pair-wise structures, such as Smith Waterman sequence similarity, the widely used nearest neighbor method, and full thermodynamic estimates of sequences. However, these methods generally involve imposing various heuristic constraints ("design rules") on possible tag/antitag (TaT) sequences in order to achieve probe-target specificity across the collection. The resulting lack of freedom in considering all putative sequences can lead to potentially suboptimal designs and to the ensuing reduction in the degree of orthogonality within the constructed TaT collections. Here, we demonstrate that a randomized-search algorithm based on simulated annealing optimization can be used in order to substantially free the design process from the limitations of sequence constraints-allowing for the elucidation of potentially more optimal DNA tag collections. The designed sets of DNA oligonucleotides are optimized for the highest degree of orthogonality as quantified by melting temperature Tm-an experimentally relevant system property, which could also be used as a theoretically meaningful thermodynamic metric for optimizing TaT binding specificity. That is, this work describes an approach to constructing tag/antitag libraries, which offer the greatest melting temperature separation between specific probe-target duplexes and other nonspecific structures. The proposed method finds, with high probability, the global solution that maximizes the difference in Tm between the specific and nonspecific tag-antitag hybridizations across a collection of given size for TaTs of specified length. An application of this approach is demonstrated using 2 different DNA probe sets.},
}
@article {pmid23554255,
year = {2013},
author = {Grosselin, J and Sii-Felice, K and Payen, E and Chretien, S and Tronik-Le Roux, D and Leboulch, P},
title = {Arrayed lentiviral barcoding for quantification analysis of hematopoietic dynamics.},
journal = {Stem cells (Dayton, Ohio)},
volume = {31},
number = {10},
pages = {2162-2171},
doi = {10.1002/stem.1383},
pmid = {23554255},
issn = {1549-4918},
mesh = {Animals ; Cell Tracking/methods ; DNA Barcoding, Taxonomic ; Genetic Vectors ; HEK293 Cells ; Hematopoietic Stem Cell Transplantation ; Hematopoietic Stem Cells/*physiology ; Humans ; Lentivirus/*genetics ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Phenotype ; },
abstract = {Our understanding of system dynamics of mixed cell populations in whole organisms has benefited from the advent of individual cell marking by nonarrayed DNA barcodes subsequently analyzed by high-throughput DNA sequencing. However, key limitations include statistical biases compromising quantification and the lack of applicability to deconvolute individual cell fate in vivo after pooling single cells differentially exposed to different conditions ex vivo. Here, we have derived an arrayed lentiviral library of DNA barcodes and obtained a proof-of-concept of its resolving capacity by quantifying hematopoietic regeneration after engraftment of mice with genetically modified autologous cells. This method has helped clarify and bridge the seemingly opposed clonal-succession and continuous-recruitment models of hematopoietic stem cell behavior and revealed that myeloid-lymphoid biases are common occurrences in steady-state hematopoiesis. Arrayed lentiviral barcoding should prove a versatile and powerful approach to deconvolute cell dynamics in vivo with applications in hematology, embryology, and cancer biology.},
}
@article {pmid23552896,
year = {2013},
author = {Naik, SH and Perié, L and Swart, E and Gerlach, C and van Rooij, N and de Boer, RJ and Schumacher, TN},
title = {Diverse and heritable lineage imprinting of early haematopoietic progenitors.},
journal = {Nature},
volume = {496},
number = {7444},
pages = {229-232},
pmid = {23552896},
issn = {1476-4687},
mesh = {Animals ; Cell Differentiation/*genetics ; *Cell Lineage ; DNA Barcoding, Taxonomic ; Dendritic Cells/cytology/metabolism ; *Genomic Imprinting ; Hematopoietic Stem Cells/*cytology/*metabolism ; Lymphocytes/cytology/metabolism ; Mice ; Mice, Inbred C57BL ; Multipotent Stem Cells/cytology/metabolism ; Myeloid Cells/cytology/metabolism ; Single-Cell Analysis ; },
abstract = {Haematopoietic stem cells (HSCs) and their subsequent progenitors produce blood cells, but the precise nature and kinetics of this production is a contentious issue. In one model, lymphoid and myeloid production branch after the lymphoid-primed multipotent progenitor (LMPP), with both branches subsequently producing dendritic cells. However, this model is based mainly on in vitro clonal assays and population-based tracking in vivo, which could miss in vivo single-cell complexity. Here we avoid these issues by using a new quantitative version of 'cellular barcoding' to trace the in vivo fate of hundreds of LMPPs and HSCs at the single-cell level. These data demonstrate that LMPPs are highly heterogeneous in the cell types that they produce, separating into combinations of lymphoid-, myeloid- and dendritic-cell-biased producers. Conversely, although we observe a known lineage bias of some HSCs, most cellular output is derived from a small number of HSCs that each generates all cell types. Crucially, in vivo analysis of the output of sibling cells derived from single LMPPs shows that they often share a similar fate, suggesting that the fate of these progenitors was imprinted. Furthermore, as this imprinting is also observed for dendritic-cell-biased LMPPs, dendritic cells may be considered a distinct lineage on the basis of separate ancestry. These data suggest a 'graded commitment' model of haematopoiesis, in which heritable and diverse lineage imprinting occurs earlier than previously thought.},
}
@article {pmid23551841,
year = {2013},
author = {Bribiesca-Contreras, G and Solís-Marín, FA and Laguarda-Figueras, A and Zaldívar-Riverón, A},
title = {Identification of echinoderms (Echinodermata) from an anchialine cave in Cozumel Island, Mexico, using DNA barcodes.},
journal = {Molecular ecology resources},
volume = {13},
number = {6},
pages = {1137-1145},
doi = {10.1111/1755-0998.12098},
pmid = {23551841},
issn = {1755-0998},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry/classification ; Echinodermata/classification/*genetics ; Mexico ; Molecular Sequence Data ; },
abstract = {The echinoderm species richness of the Aerolito de Paraiso anchialine cave, on Cozumel Island, in the Mexican Caribbean, is assessed on the basis of morphological and DNA barcoding data. We included specimens from this cave system and from different open sea areas, and employed two different approaches for species delineation based on DNA barcoding data: a 2% cox1 divergence and the general mixed Yule-coalescent (GMYC) approaches. We subsequently compared the results derived from these approaches with our morphospecies discrimination. A total of 188 cox1 sequences belonging to specimens of four echinoderm classes were examined. The 2% cox1 divergence and GMYC approaches recovered 78 and 70 putative species, respectively, 24 and 22 of which corresponded to specimens from the anchialine system. Of 26 echinoderm species identified in the cave system, seven appear to be endemic to it. Among these are Copidaster carvenicola Solís-Marín &amp; Laguarda-Figueras, 2010, two morphologically distinctive, undescribed species belonging to Asterinides and Ophionereis and four probably cryptic undescribed species originally assigned to Amphipholis squamata (Delle Chiaje, 1839), Astropecten duplicatus Gray, 1840, Copidaster lymani (AH Clark, 1948) and Ophiothrix angulata (Say, 1825). Further research and protection of this particularly fragile ecosystem becomes urgent because construction of tourism developments is planned nearby.},
}
@article {pmid23544616,
year = {2013},
author = {Khan, HA and Arif, IA},
title = {COI barcodes and phylogeny of doves (Columbidae family).},
journal = {Mitochondrial DNA},
volume = {24},
number = {6},
pages = {689-696},
doi = {10.3109/19401736.2013.773319},
pmid = {23544616},
issn = {1940-1744},
mesh = {Animals ; Columbidae/classification/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; *Phylogeny ; Polymerase Chain Reaction ; },
abstract = {Cytochrome oxidase subunit I (COI) gene has been recognized as an authentic tool for species identification. Besides its potential barcoding capacity, COI sequences have also been used for inferring the phylogeny. Phylogenetic relationships among genera of Columbidae (pigeons and doves family) have not been fully resolved because of scarce sampling of taxa and limited availability of sequence data. In this study, we have evaluated the efficiency of COI barcodes for species identification and phylogenetic analysis of various doves. We sequenced the 693 bp region of COI gene of three species of doves including Oena capensis, Streptopelia decaocto, and Streptopelia senegalensis. After retrieving the relevant sequences from the GenBank, the entire data-set of 85 sequences represented 25 dove species from 11 different genera of the family Columbidae. The COI sequences of four species including Chalcophaps indica (two specimens), Columbina inca (five specimens), Geopelia striata (three specimens), and Macropygia phasianella (three specimens) were identical. The mean intraspecific base differences ranged from 0 to 37 while the P-distances ranged between 0 and 0.058. For most of the species, the P-distances were ≤ 0.008. Phylogenetic analysis differentiated the taxa into three major clusters. One of the clusters grouped five genera including Claravis, Columbina, Gallicolumba, Geopelia, and Geotrygon. The remaining two clusters grouped three genera each including Chalcophaps, Oena, and Turtur in one cluster and Macropygia, Streptopelia, and Zenaida in another cluster. Further sub-clustering clearly separated all the genera into individual clusters except two discrepancies for the genera Streptopelia and Turtur. Species-level cladistics clearly separated all the species into distinctive clades. In conclusion, COI barcoding is a powerful tool for species identification with added information on phylogenetic inference. The finding of this study will help to understand the complex phylogeny of the family Columbidae.},
}
@article {pmid23542455,
year = {2013},
author = {Chibwana, FD and Blasco-Costa, I and Georgieva, S and Hosea, KM and Nkwengulila, G and Scholz, T and Kostadinova, A},
title = {A first insight into the barcodes for African diplostomids (Digenea: Diplostomidae): brain parasites in Clarias gariepinus (Siluriformes: Clariidae).},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {17},
number = {},
pages = {62-70},
doi = {10.1016/j.meegid.2013.03.037},
pmid = {23542455},
issn = {1567-7257},
mesh = {Animals ; Brain/*parasitology ; Catfishes/*parasitology ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Phylogeny ; Tanzania ; Trematoda/anatomy &amp; histology/*classification/*genetics ; },
abstract = {Diplostomid trematodes comprise a large and diverse group of widespread digeneans whose larval stages are important parasitic pathogens that may exert serious impacts in wild and cultured freshwater fish. However, our understanding of their diversity remains incomplete especially in the tropics. Our study is the first application of a DNA-based approach to diplostomid diversity in the African continent by generating a database linking sequences for the mitochondrial cytochrome c oxidase subunit 1 (cox1) barcode region and ITS1-5.8S-ITS2 rRNA gene cluster for brain-infecting diplostomid metacercariae from the catfish Clarias gariepinus. Analyses of newly-generated partial cox1 sequences for 34 larval isolates of Tylodelphys spp. from Tanzania and Diplostomum spp. from Tanzania and Nigeria revealed three strongly supported reciprocally monophyletic lineages of Tylodelphys spp. and one of an unknown species of Diplostomum. The average intraspecific divergence for the cox1 sequences for each recognised novel lineage was distinctly lower compared with interspecific divergence (0.46-0.75% vs 11.7-14.8%). The phylogenetic hypotheses estimated from Bayesian inference and maximum likelihood analyses of ITS1-5.8S-ITS2 data exhibited congruent strong support for the cox1-derived lineages. Our study thus provides molecular-based evidence for the existence of three distinct brain-infecting species co-occurring in natural populations of C. gariepinus. Based on phylogenetic analyses, we re-allocated Diplostomum mashonenseBeverley-Burton (1963) to the genus Tylodelphys as a new combination. We also generated cox1 and ITS1-5.8S-ITS2 sequences for an unknown species of Diplostomum from another African fish host, Synodontis nigrita.},
}
@article {pmid23539952,
year = {2013},
author = {Glowska, E and Dragun-Damian, A and Dabert, J},
title = {DNA-barcoding contradicts morphology in quill mite species Torotrogla merulae and T. rubeculi (Prostigmata: Syringophilidae).},
journal = {Folia parasitologica},
volume = {60},
number = {1},
pages = {51-60},
doi = {10.14411/fp.2013.007},
pmid = {23539952},
issn = {0015-5683},
mesh = {Animals ; Birds ; *DNA Barcoding, Taxonomic ; Feathers/parasitology ; Female ; Haplotypes ; Mite Infestations/parasitology ; Mites/*anatomy &amp; histology/classification/*genetics ; Phylogeny ; },
abstract = {Torotrogla merulae Skoracki, Dabert et Ehrnsberger, 2000 and T. rubeculi Skoracki, 2004 have been considered as distinct steno- and monoxenous quill mite species (Acari: Prostigmata: Syringophilidae) parasitizing the thrushes of the genus Turdus Linnaeus and the European robin Erithacus rubecula (Linnaeus), respectively. Morphological and molecular studies on the taxonomical status of these two species provided contradictory results. Well defined differences in morphology were not supported by substantial genetic distance in nucleotide sequences of the DNA barcode (mitochondrial cytochrome c oxidase subunit I, COI, and D2 domain of the nuclear 28S rRNA gene), by the topology of the phylogenetic trees (neighbor-joining, maximum parsimony, maximum likelihood) and the network analyses of the COI haplotype genealogy (median-joining, statistical parsimony) that reveal rubeculi populations nested within merulae haplotypes. Since detected differences between T. merulae and T. rubeculi populations (1.6-2.4% for COI and 0.1% for D2) are comparable to the intraspecific level observed in majority of currently recognized European Torotrogla species and are much lower than the interspecific distances observed in the genus, we postulate their conspecificity. Because main morphological distinctions concern the structures used for feeding, we hypothesize that they are the result of phenotypic plasticity evoked by specific and different environmental conditions prevailing on the host bodies (thickness of the feather quill wall).},
}
@article {pmid23539604,
year = {2013},
author = {Clemmensen, KE and Bahr, A and Ovaskainen, O and Dahlberg, A and Ekblad, A and Wallander, H and Stenlid, J and Finlay, RD and Wardle, DA and Lindahl, BD},
title = {Roots and associated fungi drive long-term carbon sequestration in boreal forest.},
journal = {Science (New York, N.Y.)},
volume = {339},
number = {6127},
pages = {1615-1618},
doi = {10.1126/science.1231923},
pmid = {23539604},
issn = {1095-9203},
support = {205905/ERC_/European Research Council/International ; },
mesh = {Biomarkers/metabolism ; *Carbon Cycle ; Carbon Radioisotopes/metabolism ; Ergosterol/metabolism ; Fungi/*metabolism ; Glucosamine/metabolism ; Plant Roots/*metabolism/*microbiology ; Soil ; Trees/*metabolism/*microbiology ; },
abstract = {Boreal forest soils function as a terrestrial net sink in the global carbon cycle. The prevailing dogma has focused on aboveground plant litter as a principal source of soil organic matter. Using (14)C bomb-carbon modeling, we show that 50 to 70% of stored carbon in a chronosequence of boreal forested islands derives from roots and root-associated microorganisms. Fungal biomarkers indicate impaired degradation and preservation of fungal residues in late successional forests. Furthermore, 454 pyrosequencing of molecular barcodes, in conjunction with stable isotope analyses, highlights root-associated fungi as important regulators of ecosystem carbon dynamics. Our results suggest an alternative mechanism for the accumulation of organic matter in boreal forests during succession in the long-term absence of disturbance.},
}
@article {pmid23536846,
year = {2013},
author = {Janouškovec, J and Liu, SL and Martone, PT and Carré, W and Leblanc, C and Collén, J and Keeling, PJ},
title = {Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers.},
journal = {PloS one},
volume = {8},
number = {3},
pages = {e59001},
pmid = {23536846},
issn = {1932-6203},
support = {MOP-42517//Canadian Institutes of Health Research/Canada ; },
mesh = {Amino Acid Sequence ; DNA Barcoding, Taxonomic ; Endoribonucleases/metabolism ; *Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; Genes, Plant ; Genetic Markers ; *Genome, Plastid ; Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; Nucleotidyltransferases/metabolism ; Operon/genetics ; Phylogeny ; RNA, Transfer/chemistry/genetics ; Rhodophyta/*classification/*genetics ; Sequence Alignment ; Species Specificity ; },
abstract = {Red algae have the most gene-rich plastid genomes known, but despite their evolutionary importance these genomes remain poorly sampled. Here we characterize three complete and one partial plastid genome from a diverse range of florideophytes. By unifying annotations across all available red algal plastid genomes we show they all share a highly compact and slowly-evolving architecture and uniquely rich gene complements. Both chromosome structure and gene content have changed very little during red algal diversification, and suggest that plastid-to nucleus gene transfers have been rare. Despite their ancient character, however, the red algal plastids also contain several unprecedented features, including a group II intron in a tRNA-Met gene that encodes the first example of red algal plastid intron maturase - a feature uniquely shared among florideophytes. We also identify a rare case of a horizontally-acquired proteobacterial operon, and propose this operon may have been recruited for plastid function and potentially replaced a nucleus-encoded plastid-targeted paralogue. Plastid genome phylogenies yield a fully resolved tree and suggest that plastid DNA is a useful tool for resolving red algal relationships. Lastly, we estimate the evolutionary rates among more than 200 plastid genes, and assess their usefulness for species and subspecies taxonomy by comparison to well-established barcoding markers such as cox1 and rbcL. Overall, these data demonstrates that red algal plastid genomes are easily obtainable using high-throughput sequencing of total genomic DNA, interesting from evolutionary perspectives, and promising in resolving red algal relationships at evolutionarily-deep and species/subspecies levels.},
}
@article {pmid23536818,
year = {2013},
author = {Tai, V and James, ER and Perlman, SJ and Keeling, PJ},
title = {Single-Cell DNA barcoding using sequences from the small subunit rRNA and internal transcribed spacer region identifies new species of Trichonympha and Trichomitopsis from the hindgut of the termite Zootermopsis angusticollis.},
journal = {PloS one},
volume = {8},
number = {3},
pages = {e58728},
pmid = {23536818},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/*genetics ; Hypermastigia/*classification/*genetics ; Isoptera/*parasitology ; Molecular Sequence Data ; Phylogeny ; Protozoan Infections/parasitology ; RNA, Ribosomal/*genetics ; Single-Cell Analysis ; },
abstract = {To aid in their digestion of wood, lower termites are known to harbour a diverse community of prokaryotes as well as parabasalid and oxymonad protist symbionts. One of the best-studied lower termite gut communities is that of Zootermopsis angusticollis which has been known for almost 100 years to possess 3 species of Trichonympha (T. campanula, T. collaris, and T. sphaerica), 1 species of Trichomitopsis (T. termopsidis), as well as smaller flagellates. We have re-assessed this community by sequencing the small subunit (SSU) rRNA gene and the internal transcribed spacer (ITS) region from a large number of single Trichonympha and Trichomitopsis cells for which morphology was also documented. Based on phylogenetic clustering and sequence divergence, we identify 3 new species: Trichonympha postcylindrica, Trichomitopsis minor, and Trichomitopsis parvus spp. nov. Once identified by sequencing, the morphology of the isolated cells for all 3 new species was re-examined and found to be distinct from the previously described species: Trichonympha postcylindrica can be morphologically distinguished from the other Trichonympha species by an extension on its posterior end, whereas Trichomitopsis minor and T. parvus are smaller than T. termopsidis but similar in size to each other and cannot be distinguished based on morphology using light microscopy. Given that Z. angusticollis has one of the best characterized hindgut communities, the near doubling of the number of the largest and most easily identifiable symbiont species suggests that the diversity of hindgut symbionts is substantially underestimated in other termites as well. Accurate descriptions of the diversity of these microbial communities are essential for understanding hindgut ecology and disentangling the interactions among the symbionts, and molecular barcoding should be a priority for these systems.},
}
@article {pmid23532322,
year = {2013},
author = {Novo, S and Penon, O and Barrios, L and Nogués, C and Santaló, J and Durán, S and Gómez-Matínez, R and Samitier, J and Plaza, JA and Pérez-García, L and Ibáñez, E},
title = {Direct embryo tagging and identification system by attachment of biofunctionalized polysilicon barcodes to the zona pellucida of mouse embryos.},
journal = {Human reproduction (Oxford, England)},
volume = {28},
number = {6},
pages = {1519-1527},
doi = {10.1093/humrep/det083},
pmid = {23532322},
issn = {1460-2350},
mesh = {Animal Identification Systems ; Animals ; Cryopreservation ; Embryo Culture Techniques ; Embryo, Mammalian/*ultrastructure ; Embryonic Development ; Female ; Mice ; Reproductive Techniques, Assisted ; Silicon Compounds ; Zona Pellucida/*ultrastructure ; },
abstract = {STUDY QUESTION: Is the attachment of biofunctionalized polysilicon barcodes to the outer surface of the zona pellucida an effective approach for the direct tagging and identification of cultured embryos?<br><br>SUMMARY ANSWER: The results achieved provide a proof of concept for a direct embryo tagging system using biofunctionalized polysilicon barcodes, which could help to minimize the risk of mismatching errors (mix-ups) in human assisted reproduction technologies.<br><br>WHAT IS KNOWN ALREADY: Even though the occurrence of mix-ups is rare, several cases have been reported in fertility clinics around the world. Measures to prevent the risk of mix-ups in human assisted reproduction technologies are therefore required.<br><br>STUDY DESIGN, SIZE, DURATION: Mouse embryos were tagged with 10 barcodes and the effectiveness of the tagging system was tested during fresh in vitro culture (n=140) and after embryo cryopreservation (n = 84). Finally, the full-term development of tagged embryos was evaluated (n =105).<br><br>Mouse pronuclear embryos were individually rolled over wheat germ agglutinin-biofunctionalized polysilicon barcodes to distribute them uniformly around the ZONA PELLUCIDA surface. Embryo viability and retention of barcodes were determined during 96 h of culture. The identification of tagged embryos was performed every 24 h in an inverted microscope and without embryo manipulation to simulate an automatic reading procedure. Full-term development of the tagged embryos was assessed after their transfer to pseudo-pregnant females. To test the validity of the embryo tagging system after a cryopreservation process, tagged embryos were frozen at the 2-cell stage using a slow freezing protocol, and followed in culture for 72 h after thawing.<br><br>Neither the in vitro or in vivo development of tagged embryos was adversely affected. The tagging system also proved effective during an embryo cryopreservation process. Global identification rates higher than 96 and 92% in fresh and frozen-thawed tagged embryos, respectively, were obtained when simulating an automatic barcode reading system, although these rates could be increased to 100% by simply rotating the embryos during the reading process.<br><br>The direct embryo tagging developed here has exclusively been tested in mouse embryos. Its effectiveness in other species, such as the human, is currently being tested.<br><br>The direct embryo tagging system developed here, once tested in human embryos, could provide fertility clinics with a novel tool to reduce the risk of mix-ups in human assisted reproduction technologies.},
}
@article {pmid23530893,
year = {2013},
author = {López-Caballero, J and Oceguera-Figueroa, A and León-Règagnon, V},
title = {Detection of multiple species of human Paragonimus from Mexico using morphological data and molecular barcodes.},
journal = {Molecular ecology resources},
volume = {13},
number = {6},
pages = {1125-1136},
doi = {10.1111/1755-0998.12093},
pmid = {23530893},
issn = {1755-0998},
mesh = {Animals ; Biodiversity ; *DNA Barcoding, Taxonomic ; Humans ; Paragonimus/anatomy &amp; histology/classification/*genetics/isolation &amp; purification ; Sequence Alignment ; Species Specificity ; },
abstract = {Paragonimus mexicanus is the causal agent of human paragonimiasis in several countries of the Americas. It is considered to be the only species of the genus present in Mexico, where it is responsible for human infection. Through the investigation of P. mexicanus specimens from several places throughout Mexico, we provide morphological, molecular and geographical evidence that strongly suggests the presence of at least three species from this genus in Mexico. These results raise questions regarding the diagnosis, treatment, prophylaxis and control of human paragonimiasis in Mexico. We also provide a brief discussion regarding biodiversity inventories and the convenience of providing molecular and morphological information in biodiversity studies.},
}
@article {pmid23527060,
year = {2013},
author = {Quéméré, E and Hibert, F and Miquel, C and Lhuillier, E and Rasolondraibe, E and Champeau, J and Rabarivola, C and Nusbaumer, L and Chatelain, C and Gautier, L and Ranirison, P and Crouau-Roy, B and Taberlet, P and Chikhi, L},
title = {A DNA metabarcoding study of a primate dietary diversity and plasticity across its entire fragmented range.},
journal = {PloS one},
volume = {8},
number = {3},
pages = {e58971},
pmid = {23527060},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; Conservation of Natural Resources ; *DNA Barcoding, Taxonomic ; Diet/*classification ; Ecosystem ; *Endangered Species ; Environment ; *Feeding Behavior ; Geography ; *Lemur ; Plants ; },
abstract = {In tropical regions, most primary ecosystems have been replaced by mosaic landscapes in which species must cope with a large shift in the distribution of their habitat and associated food resources. Primates are particularly vulnerable to habitat modifications. Most species persist in small fragments surrounded by complex human-mediated matrices whose structure and connectivity may strongly influence their dispersal and feeding behavior. Behavioral plasticity appears to be a crucial parameter governing the ability of organisms to exploit the resources offered by new matrix habitats and thus to persist in fragmented habitats. In this study, we were interested in the dietary plasticity of the golden-crowned sifaka (Propithecus tattersalli), an endangered species of lemur, found only in the Daraina region in north-eastern Madagascar. We used a DNA-based approach combining the barcoding concept and Illumina next-generation sequencing to (i) describe the species diet across its entire range and (ii) evaluate the influence of landscape heterogeneity on diet diversity and composition. Faeces from 96 individuals were sampled across the entire species range and their contents were analyzed using the trnL metabarcoding approach. In parallel, we built a large DNA reference database based on a checklist of the plant species of the Daraina region. Our results suggest that golden-crowned sifakas exhibit remarkable dietary diversity with at least 130 plant species belonging to 80 genera and 49 different families. We highlighted an influence of both habitat type and openness on diet composition suggesting a high flexibility of foraging strategies. Moreover, we observed the presence of numerous cultivated and naturalized plants in the faeces of groups living in forest edge areas. Overall, our findings support our initial expectation that P. tattersalli is able to cope with the current level of alteration of the landscape and confirm our previous results on the distribution and the dispersal ability of this species.},
}
@article {pmid23526991,
year = {2013},
author = {James, ER and Okamoto, N and Burki, F and Scheffrahn, RH and Keeling, PJ},
title = {Cthulhu Macrofasciculumque n. g., n. sp. and Cthylla Microfasciculumque n. g., n. sp., a newly identified lineage of parabasalian termite symbionts.},
journal = {PloS one},
volume = {8},
number = {3},
pages = {e58509},
pmid = {23526991},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; DNA Barcoding, Taxonomic ; DNA, Protozoan/genetics ; Isoptera/genetics/*parasitology ; Molecular Sequence Data ; Parabasalidea/*classification/*genetics/physiology ; Phylogeny ; RNA, Ribosomal/genetics ; Symbiosis ; },
abstract = {The parabasalian symbionts of lower termite hindgut communities are well-known for their large size and structural complexity. The most complex forms evolved multiple times independently from smaller and simpler flagellates, but we know little of the diversity of these small flagellates or their phylogenetic relationships to more complex lineages. To understand the true diversity of Parabasalia and how their unique cellular complexity arose, more data from smaller and simpler flagellates are needed. Here, we describe two new genera of small-to-intermediate size and complexity, represented by the type species Cthulhu macrofasciculumque and Cthylla microfasciculumque from Prorhinotermes simplex and Reticulitermes virginicus, respectively (both hosts confirmed by DNA barcoding). Both genera have a single anterior nucleus embeded in a robust protruding axostyle, and an anterior bundle flagella (and likely a single posterior flagellum) that emerge slightly subanteriorly and have a distinctive beat pattern. Cthulhu is relatively large and has a distinctive bundle of over 20 flagella whereas Cthylla is smaller, has only 5 anterior flagella and closely resembles several other parababsalian genera. Molecular phylogenies based on small subunit ribosomal RNA (SSU rRNA) show both genera are related to previously unidentified environmental sequences from other termites (possibly from members of the Tricercomitidae), which all branch as sisters to the Hexamastigitae. Altogether, Cthulhu likely represents another independent origin of relatively high cellular complexity within parabasalia, and points to the need for molecular characterization of other key taxa, such as Tricercomitus.},
}
@article {pmid23523575,
year = {2013},
author = {Martin, BT and Bernstein, NP and Birkhead, RD and Koukl, JF and Mussmann, SM and Placyk, JS},
title = {Sequence-based molecular phylogenetics and phylogeography of the American box turtles (Terrapene spp.) with support from DNA barcoding.},
journal = {Molecular phylogenetics and evolution},
volume = {68},
number = {1},
pages = {119-134},
doi = {10.1016/j.ympev.2013.03.006},
pmid = {23523575},
issn = {1095-9513},
mesh = {Analysis of Variance ; Animals ; Bayes Theorem ; Cytochromes b/classification/genetics ; DNA Barcoding, Taxonomic/statistics &amp; numerical data ; DNA, Mitochondrial/*classification/genetics ; Electron Transport Complex IV/classification/genetics ; *Genetic Speciation ; Glyceraldehyde-3-Phosphate Dehydrogenases/classification/genetics ; Haplotypes ; *Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Turtles/*classification/genetics ; },
abstract = {The classification of the American box turtles (Terrapene spp.) has remained enigmatic to systematists. Previous comprehensive phylogenetic studies focused primarily on morphology. The goal of this study was to re-assess the classification of Terrapene spp. by obtaining DNA sequence data from a broad geographic range and from all four recognized species and 11 subspecies within the genus. Tissue samples were obtained for all taxa except for Terrapene nelsoni klauberi. DNA was extracted, and the mitochondrial DNA (mtDNA) cytochrome b (Cytb) and nuclear DNA (nucDNA) glyceraldehyde-3-phosphate-dehydrogenase (GAPD) genes were amplified via polymerase chain reaction and sequenced. In addition, the mtDNA gene commonly used for DNA barcoding (cytochrome oxidase c subunit I; COI) was amplified and sequenced to calculate pairwise percent DNA sequence divergence comparisons for each Terrapene taxon. The sequence data were analyzed using maximum likelihood and Bayesian phylogenetic inference, a molecular clock, AMOVAs, SAMOVAs, haplotype networks, and pairwise percent sequence divergence comparisons. Terrapene carolina mexicana and T. c. yucatana formed a monophyletic clade with T. c. triunguis, and this clade was paraphyletic to the rest of T. carolina. Terrapene ornata ornata and T. o. luteola lacked distinction phylogenetically, and Terrapene nelsoni was confirmed to be the sister taxon of T. ornata. Terrapene c. major, T. c. bauri, and Terrapene coahuila were not well resolved for some of the analyses. The DNA barcoding results indicated that all taxa were different species (>2% sequence divergence) except for T. c. triunguis - T. c. mexicana and T. o. ornata - T. o. luteola. The results suggest that T. c. triunguis should be elevated to species status (Terrapene mexicana), and mexicana and yucatana should be included in this group as subspecies. In addition, T. o. ornata and T. o. luteola should not be considered separate subspecies. The DNA barcoding data support these recommended taxonomic revisions. Because conservation efforts are typically species-based, these results will be important for facilitating successful conservation management strategies.},
}
@article {pmid23521634,
year = {2013},
author = {Lakra, WS and Goswami, M and Singh, A},
title = {Genetic relatedness and phylogenetics of five Indian pufferfishes.},
journal = {Mitochondrial DNA},
volume = {24},
number = {5},
pages = {602-609},
doi = {10.3109/19401736.2013.772149},
pmid = {23521634},
issn = {1940-1744},
mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial ; *Genetic Speciation ; India ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Tetraodontiformes/*classification/*genetics ; },
abstract = {The taxonomy and phylogeny of the pufferfishes belonging to the family Tetraodontidae found in India are poorly understood. We investigated five species of freshwater and marine pufferfishes using partial sequences of 16S rRNA and cytochrome c oxidase subunit I (COI) of mitochondrial genes. The sequence alignment of 16S rRNA yielded 573 bp, whereas COI gene sequence alignment yielded 614 bp. The sequence analysis of the genes revealed two distinct groups of freshwater and marine origin, which are genetically distinct from each other and exhibit identical phylogenetic resolution. The partial sequences of both the genes provided sufficient phylogenetic resolution to distinguish all the five species of pufferfishes. The COI sequences could be used as DNA barcodes for identification of the pufferfishes.},
}
@article {pmid23519209,
year = {2013},
author = {Keshavmurthy, S and Yang, SY and Alamaru, A and Chuang, YY and Pichon, M and Obura, D and Fontana, S and De Palmas, S and Stefani, F and Benzoni, F and MacDonald, A and Noreen, AM and Chen, C and Wallace, CC and Pillay, RM and Denis, V and Amri, AY and Reimer, JD and Mezaki, T and Sheppard, C and Loya, Y and Abelson, A and Mohammed, MS and Baker, AC and Mostafavi, PG and Suharsono, BA and Chen, CA},
title = {DNA barcoding reveals the coral "laboratory-rat", Stylophora pistillata encompasses multiple identities.},
journal = {Scientific reports},
volume = {3},
number = {},
pages = {1520},
pmid = {23519209},
issn = {2045-2322},
mesh = {Animals ; Anthozoa/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Phylogeny ; Reference Standards ; Species Specificity ; },
abstract = {Stylophora pistillata is a widely used coral "lab-rat" species with highly variable morphology and a broad biogeographic range (Red Sea to western central Pacific). Here we show, by analysing Cytochorme Oxidase I sequences, from 241 samples across this range, that this taxon in fact comprises four deeply divergent clades corresponding to the Pacific-Western Australia, Chagos-Madagascar-South Africa, Gulf of Aden-Zanzibar-Madagascar, and Red Sea-Persian/Arabian Gulf-Kenya. On the basis of the fossil record of Stylophora, these four clades diverged from one another 51.5-29.6 Mya, i.e., long before the closure of the Tethyan connection between the tropical Indo-West Pacific and Atlantic in the early Miocene (16-24 Mya) and should be recognised as four distinct species. These findings have implications for comparative ecological and/or physiological studies carried out using Stylophora pistillata as a model species, and highlight the fact that phenotypic plasticity, thought to be common in scleractinian corals, can mask significant genetic variation.},
}
@article {pmid23517322,
year = {2013},
author = {Newmaster, SG and Ragupathy, S and Dhivya, S and Jijo, CJ and Sathishkumar, R and Patel, K},
title = {Genomic valorization of the fine scale classification of small millet landraces in southern India.},
journal = {Genome},
volume = {56},
number = {2},
pages = {123-127},
doi = {10.1139/gen-2012-0183},
pmid = {23517322},
issn = {1480-3321},
mesh = {*DNA Barcoding, Taxonomic ; Genetic Variation ; *Genome, Plant ; Genome, Plastid ; India ; Panicum/classification/*genetics ; Phylogeny ; Quantitative Trait, Heritable ; },
abstract = {Our research seeks to investigate genomic diversity of landraces of millet, addressing a key uncertainty that will provide a framework for (i) a DNA barcode method that could be used for fast, sensitive, and accurate identification of millet landraces, and (ii) millet landrace conservation including biocultural diversity. We found considerable intraspecific variation among 15 landraces representing six species of small millets using nuclear regions (ITS, ITS1, and ITS2); there was no variation in plastid regions (rbcL, matK, and trnH-psbA). An efficacious ITS2 DNA barcode was used to make 100% accurate landrace assignments for 150 blind samples representing 15 landraces. Our research revealed that genomic variation is aligned with a fine-scale classification of landraces using traditional knowledge (TK) of local farmers. The landrace classification was highly correlated with traits (morphological, agricultural, and cultural utility) associated with considerable factors such as yield, drought tolerance, growing season, medicinal properties, and nutrition. This could provide a DNA-based model for conservation of genetic diversity and the associated bicultural diversity (TK) of millet landraces, which has sustained marginal farming communities in harsh environments for many generations.},
}
@article {pmid23515963,
year = {2013},
author = {Zeng, DN and Fan, ZY and Chi, L and Wang, X and Qu, WD and Quan, ZX},
title = {Analysis of the bacterial communities associated with different drinking water treatment processes.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {29},
number = {9},
pages = {1573-1584},
pmid = {23515963},
issn = {1573-0972},
mesh = {Actinobacteria/classification/genetics ; Bacteria/*classification/genetics ; Bacteroidetes/classification/genetics ; Biodiversity ; DNA Primers ; DNA, Bacterial/*analysis/*genetics ; Drinking Water/*microbiology ; Ecosystem ; Filtration ; Humans ; Mycobacterium/classification/genetics ; Phylogeny ; Proteobacteria/classification/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Water Microbiology ; Water Purification/*methods ; },
abstract = {A drinking water plant was surveyed to determine the bacterial composition of different drinking water treatment processes (DWTP). Water samples were collected from different processing steps in the plant (i.e., coagulation, sedimentation, sand filtration, and chloramine disinfection) and from distantly piped water. The samples were pyrosequensed using sample-specific oligonucleotide barcodes. The taxonomic composition of the microbial communities of different DWTP and piped water was dominated by the phylum Proteobacteria. Additionally, a large proportion of the sequences were assigned to the phyla Actinobacteria and Bacteroidetes. The piped water exhibited increasing taxonomic diversity, including human pathogens such as the Mycobacterium, which revealed a threat to the safety of drinking water. Surprisingly, we also found that a sister group of SAR11 (LD12) persisted throughout the DWTP, which was always detected in freshwater aquatic systems. Moreover, Polynucleobacter, Rhodoferax, and a group of Actinobacteria, hgcI clade, were relatively consistent throughout the processes. It is concluded that smaller-size microorganisms tended to survive against the present treatment procedure. More improvement should be made to ensure the long-distance transmission drinking water.},
}
@article {pmid23512712,
year = {2013},
author = {Kheradpour, P and Ernst, J and Melnikov, A and Rogov, P and Wang, L and Zhang, X and Alston, J and Mikkelsen, TS and Kellis, M},
title = {Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay.},
journal = {Genome research},
volume = {23},
number = {5},
pages = {800-811},
pmid = {23512712},
issn = {1549-5469},
support = {R01 HG004037/HG/NHGRI NIH HHS/United States ; R01 HG006785/HG/NHGRI NIH HHS/United States ; HG004037/HG/NHGRI NIH HHS/United States ; HG004037-S1/HG/NHGRI NIH HHS/United States ; },
mesh = {Base Sequence ; Binding Sites ; Cells/classification/metabolism ; Chromatin/*genetics ; Chromosome Mapping ; Conserved Sequence ; *Enhancer Elements, Genetic ; Gene Expression Regulation ; Genes, Reporter ; Genome, Human ; Hep G2 Cells ; Humans ; Nucleotide Motifs/*genetics ; Promoter Regions, Genetic ; *Transcription, Genetic ; },
abstract = {Genome-wide chromatin annotations have permitted the mapping of putative regulatory elements across multiple human cell types. However, their experimental dissection by directed regulatory motif disruption has remained unfeasible at the genome scale. Here, we use a massively parallel reporter assay (MPRA) to measure the transcriptional levels induced by 145-bp DNA segments centered on evolutionarily conserved regulatory motif instances within enhancer chromatin states. We select five predicted activators (HNF1, HNF4, FOXA, GATA, NFE2L2) and two predicted repressors (GFI1, ZFP161) and measure reporter expression in erythroleukemia (K562) and liver carcinoma (HepG2) cell lines. We test 2104 wild-type sequences and 3314 engineered enhancer variants containing targeted motif disruptions, each using 10 barcode tags and two replicates. The resulting data strongly confirm the enhancer activity and cell-type specificity of enhancer chromatin states, the ability of 145-bp segments to recapitulate both, the necessary role of regulatory motifs in enhancer function, and the complementary roles of activator and repressor motifs. We find statistically robust evidence that (1) disrupting the predicted activator motifs abolishes enhancer function, while silent or motif-improving changes maintain enhancer activity; (2) evolutionary conservation, nucleosome exclusion, binding of other factors, and strength of the motif match are predictive of enhancer activity; (3) scrambling repressor motifs leads to aberrant reporter expression in cell lines where the enhancers are usually inactive. Our results suggest a general strategy for deciphering cis-regulatory elements by systematic large-scale manipulation and provide quantitative enhancer activity measurements across thousands of constructs that can be mined to develop predictive models of gene expression.},
}
@article {pmid23510760,
year = {2013},
author = {Ebihara, A and Yamaoka, A and Mizukami, N and Sakoda, A and Nitta, JH and Imaichi, R},
title = {A survey of the fern gametophyte flora of Japan: Frequent independent occurrences of noncordiform gametophytes.},
journal = {American journal of botany},
volume = {100},
number = {4},
pages = {735-743},
doi = {10.3732/ajb.1200555},
pmid = {23510760},
issn = {1537-2197},
mesh = {Biodiversity ; Ferns/*anatomy &amp; histology ; Germ Cells, Plant ; Japan ; },
abstract = {PREMISE OF THE STUDY: Ferns and lycophytes are the only extant land plants with two free-living generations (sporophytes and gametophytes); hence, a single species may have two different distributions. The distribution of the gametophytes of most fern species, which are much smaller in size than sporophytes, are almost unknown due to the difficulty of identifying gametophytes using morphological characters.<br><br>METHODS: Twelve quadrats (1 m(2) or 0.25 m(2)), each subdivided into a grid of 100 (10 &#xd7; 10) or 25 (5 &#xd7; 5) squares, were used to survey gametophytes in the Japanese Archipelago, where distribution data of sporophytes and "DNA barcodes" for identification of gametophytes have fully been established in previous studies. Collected gametophytes were identified using the plastid rbcL-a region.<br><br>KEY RESULTS: In total, gametophytes of 38 species in two broad morphological categories (28 cordiform and 10 noncordiform species) were identified among 407 collections. The cordiform gametophytes discovered are without exception accompanied by their conspecific sporophytes at the periphery of the quadrats. On the other hand, the sporophytic counterparts of the noncordiform gametophytes are often not found or are rare around the sites.<br><br>CONCLUSIONS: This study demonstrates with a regional flora that fern gametophytes do not always co-occur with sporophytes of the same species. In particular, noncordiform gametophytes tended to occur independently of conspecific sporophytes. This pattern may be due to the capability for indeterminate growth and vegetative reproduction by gemmae in noncordiform gametophytes.},
}
@article {pmid23503053,
year = {2013},
author = {Mali, P and Aach, J and Lee, JH and Levner, D and Nip, L and Church, GM},
title = {Barcoding cells using cell-surface programmable DNA-binding domains.},
journal = {Nature methods},
volume = {10},
number = {5},
pages = {403-406},
pmid = {23503053},
issn = {1548-7105},
support = {P50 HG005550/HG/NHGRI NIH HHS/United States ; },
mesh = {Cell Membrane/metabolism ; *DNA Barcoding, Taxonomic ; Zinc Fingers ; },
abstract = {We report an approach to barcode cells through cell-surface expression of programmable zinc-finger DNA-binding domains (surface zinc fingers, sZFs). We show that sZFs enable sequence-specific labeling of living cells by dsDNA, and we develop a sequential labeling approach to image more than three cell types in mixed populations using three fluorophores. We demonstrate the versatility of sZFs through applications in which they serve as surrogate reporters, function as selective cell capture reagents and facilitate targeted cellular delivery of viruses.},
}
@article {pmid23500333,
year = {2013},
author = {Bhargava, M and Sharma, A},
title = {DNA barcoding in plants: evolution and applications of in silico approaches and resources.},
journal = {Molecular phylogenetics and evolution},
volume = {67},
number = {3},
pages = {631-641},
doi = {10.1016/j.ympev.2013.03.002},
pmid = {23500333},
issn = {1095-9513},
mesh = {Algorithms ; Computational Biology/methods ; *DNA Barcoding, Taxonomic/methods ; Evolution, Molecular ; Plants/*classification/*genetics ; Software ; },
abstract = {Bioinformatics has played an important role in the analysis of DNA barcoding data. The process of DNA barcoding initially involves the available data collection from the existing databases. Many databases have been developed in recent years, e.g. MMDBD [Medicinal Materials DNA Barcode Database], BioBarcode, etc. In case of non-availability of sequences, sequencing has to be done in vitro for which a recently developed software ecoPrimers can be helpful. This is followed by multiple sequence alignment. Further, basic sequence statistics computation and phylogenetic analysis can be performed by MEGA and PHYLIP/PAUP tools respectively. Some of the recent tools for in silico and statistical analysis specifically designed for barcoding viz. CAOS (Character Based DNA Barcoding), BRONX (DNA Barcode Sequence Identification Incorporating Taxonomic Hierarchy and within Taxon Variability), Spider (Analysis of species identity and evolution, particularly DNA barcoding), jMOTU and Taxonerator (Turning DNA Barcode Sequences into Annotated OTUs), OTUbase (Analysis of OTU data and taxonomic data), SAP (Statistical Assignment Package), etc. have been discussed and analysed in this review. The paper presents a comprehensive overview of the various in silico methods, tools, softwares and databases used for DNA barcoding of plants.},
}
@article {pmid23497346,
year = {2013},
author = {Pereira, LH and Hanner, R and Foresti, F and Oliveira, C},
title = {Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna?.},
journal = {BMC genetics},
volume = {14},
number = {},
pages = {20},
pmid = {23497346},
issn = {1471-2156},
mesh = {Animals ; Biodiversity ; Catfishes/classification/*genetics ; Characiformes/*classification/genetics ; *DNA Barcoding, Taxonomic ; Perciformes/*classification/genetics ; Phylogeny ; Rivers ; South America ; },
abstract = {BACKGROUND: The megadiverse Neotropical freshwater ichthyofauna is the richest in the world with approximately 6,000 recognized species. Interestingly, they are distributed among only 17 orders, and almost 80% of them belong to only three orders: Characiformes, Siluriformes and Perciformes. Moreover, evidence based on molecular data has shown that most of the diversification of the Neotropical ichthyofauna occurred recently. These characteristics make the taxonomy and identification of this fauna a great challenge, even when using molecular approaches. In this context, the present study aimed to test the effectiveness of the barcoding methodology (COI gene) to identify the mega diverse freshwater fish fauna from the Neotropical region. For this purpose, 254 species of fishes were analyzed from the Upper Parana River basin, an area representative of the larger Neotropical region.<br><br>RESULTS: Of the 254 species analyzed, 252 were correctly identified by their barcode sequences (99.2%). The main K2P intra- and inter-specific genetic divergence values (0.3% and 6.8%, respectively) were relatively low compared with similar values reported in the literature, reflecting the higher number of closely related species belonging to a few higher taxa and their recent radiation. Moreover, for 84 pairs of species that showed low levels of genetic divergence (<2%), application of a complementary character-based nucleotide diagnostic approach proved useful in discriminating them. Additionally, 14 species displayed high intra-specific genetic divergence (>2%), pointing to at least 23 strong candidates for new species.<br><br>CONCLUSIONS: Our study is the first to examine a large number of freshwater fish species from the Neotropical area, including a large number of closely related species. The results confirmed the efficacy of the barcoding methodology to identify a recently radiated, megadiverse fauna, discriminating 99.2% of the analyzed species. The power of the barcode sequences to identify species, even with low interspecific divergence, gives us an idea of the distribution of inter-specific genetic divergence in these megadiverse fauna. The results also revealed hidden genetic divergences suggestive of reproductive isolation and putative cryptic speciation in some species (23 candidates for new species). Finally, our study constituted an important contribution to the international Barcoding of Life (iBOL.org) project, providing barcode sequences for use in identification of these species by experts and non-experts, and allowing them to be available for use in other applications.},
}
@article {pmid23497234,
year = {2013},
author = {Saunders, GW and McDevit, DC},
title = {DNA barcoding unmasks overlooked diversity improving knowledge on the composition and origins of the Churchill algal flora.},
journal = {BMC ecology},
volume = {13},
number = {},
pages = {9},
pmid = {23497234},
issn = {1472-6785},
mesh = {*Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Algal/genetics ; Manitoba ; Seaweed/*classification/genetics ; },
abstract = {BACKGROUND: Sampling expeditions to Churchill in the Canadian subarctic were completed with the aim of compiling a molecular-assisted survey of the macroalgal flora (seaweeds) for comparison to published accounts for this area, which are based on morphological identifications. Further, because the Churchill region was covered by ice until recently (~10,000 before present), the current algal flora has had to migrate from adjacent waters into that region. We used our DNA barcode data to predict the relative contribution of the North Atlantic and North Pacific floras (Likely Source Region) in repopulating the Churchill region following the most recent glacial retreat.<br><br>RESULTS: We processed 422 collections representing ~50 morpho-species, which is the approximate number reported for this region, and generated DNA barcode data for 346 of these. In contrast to the morpho-species count, we recovered 57 genetic groups indicating overlooked species (this despite failing to generate barcode data for six of the ~50 morpho-species). However, we additionally uncovered numerous inconsistencies between the species that are currently listed in the Churchill flora (again as a result of overlooked species diversity, but combined with taxonomic confusion) and those identified following our molecular analyses including eight new records and another 17 genetic complexes in need of further study. Based on a comparison of DNA barcode data from the Churchill flora to collections from the contiguous Atlantic and Pacific floras we estimate that minimally 21% (possibly as much as 44%) of the Churchill flora was established by migration from the Pacific region with the balance of species arriving from the Atlantic (predominantly North American populations) following the last glacial retreat.<br><br>CONCLUSIONS: Owing to difficulties associated with the morphological identification of macroalgae, our results indicate that current comprehension of the Canadian Arctic flora is weak. We consider that morphology-based field-identifications are ill-advised in carrying out floristic and ecological surveys for macroalgae and that much of the current data, at least for the Canadian Arctic, should be used with caution. Our efforts to use DNA barcode data to identify the most Likely Source Regions for macroalgal species currently found in Churchill suggests that migration from both the Atlantic and the Pacific have played important roles in establishing the Canadian Arctic flora. This result has significance for understanding both the current and future biodiversity and biogeography of macroalgae in these waters.},
}
@article {pmid23496857,
year = {2013},
author = {Young, MK and McKelvey, KS and Pilgrim, KL and Schwartz, MK},
title = {DNA barcoding at riverscape scales: assessing biodiversity among fishes of the genus Cottus (Teleostei) in northern Rocky Mountain streams.},
journal = {Molecular ecology resources},
volume = {13},
number = {4},
pages = {583-595},
doi = {10.1111/1755-0998.12091},
pmid = {23496857},
issn = {1755-0998},
mesh = {Animals ; *Biodiversity ; Chordata/*classification/*genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/genetics ; Molecular Sequence Data ; *Rivers ; Sequence Analysis, DNA ; United States ; },
abstract = {There is growing interest in broad-scale biodiversity assessments that can serve as benchmarks for identifying ecological change. Genetic tools have been used for such assessments for decades, but spatial sampling considerations have largely been ignored. Here, we demonstrate how intensive sampling efforts across a large geographical scale can influence identification of taxonomic units. We used sequences of mtDNA cytochrome c oxidase subunit 1 and cytochrome b, analysed with maximum parsimony networks, maximum-likelihood trees and genetic distance thresholds, as indicators of biodiversity and species identity among the taxonomically challenging fishes of the genus Cottus in the northern Rocky Mountains, USA. Analyses of concatenated sequences from fish collected in all major watersheds of this area revealed eight groups with species-level differences that were also geographically circumscribed. Only two of these groups, however, were assigned to recognized species, and these two assignments resulted in intraspecific genetic variation (>2.0%) regarded as atypical for individual species. An incomplete inventory of individuals from throughout the geographical ranges of many species represented in public databases, as well as sample misidentification and a poorly developed taxonomy, may have hampered species assignment and discovery. We suspect that genetic assessments based on spatially robust sampling designs will reveal previously unrecognized biodiversity in many other taxa.},
}
@article {pmid23494457,
year = {2013},
author = {Chetverikov, PE and Cvrković, T and Vidović, B and Petanović, RU},
title = {Description of a new relict eriophyoid mite, Loboquintus subsquamatus n. gen. &amp; n. sp. (Eriophyoidea, Phytoptidae, Pentasetacini) based on confocal microscopy, SEM, COI barcoding and novel CLSM anatomy of internal genitalia.},
journal = {Experimental &amp; applied acarology},
volume = {61},
number = {1},
pages = {1-30},
pmid = {23494457},
issn = {1572-9702},
mesh = {Amino Acid Sequence ; Animals ; Base Composition ; Classification/methods ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry ; Electron Transport Complex IV/chemistry/genetics ; Female ; Genitalia/ultrastructure ; Male ; Microscopy, Electron, Scanning ; Mites/anatomy &amp; histology/*classification/genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, Protein ; },
abstract = {A new pentasetacine mite Loboquintus subsquamatus n. gen. &amp; n. sp. was found living under scale-like leaves of 2-3 years old twigs of Cupressus sempervirens in Montenegro. This mite species possesses a number of morphological features (uncommon teardrop-shaped body, traits of prosoma, atypical primitive anatomy of the genital apparatus and morphological traits of immatures) which clearly distinguish it from all other known eriophyoids. Adults of L. subsquamatus have seta vi situated on the anterior margin of a uniquely elongate lingua-like thin frontal lobe, three pits on the posterior prodorsal shield margin, a remarkable tube-like structure in the basal part of gnathosoma, a complicated three-layered epigynium, spermathecae directed antero-laterad, short spermathecal tubes and setae eu suppressed in males and possibly expressed in females. External genitalia of males and females of L. subsquamatus are fundamentally similar. Hypothesized remnants of coxisterna III or IV (forming a postgenital plate) are remarkably distinct in males. Two new morphometrical variables are proposed to supplement the CLSM protocol for description of internal genitalia of eriophyoids proposed by Chetverikov et al. (Zootaxa 3560:41-60, 2012b): (a) the length of ventral projection of the transvers genital apodeme and (b) the length of the posterior (=postspermathecal) part of the longitudinal bridge which in L. subsquamatus is remarkably long, whereas in many other eriophyoids it is reduced.},
}
@article {pmid23484986,
year = {2013},
author = {Hariharan, D and Lobo, DN},
title = {Retained surgical sponges, needles and instruments.},
journal = {Annals of the Royal College of Surgeons of England},
volume = {95},
number = {2},
pages = {87-92},
pmid = {23484986},
issn = {1478-7083},
mesh = {Early Diagnosis ; Foreign Bodies/etiology/*prevention &amp; control ; Humans ; Incidence ; Medical Errors/*prevention &amp; control ; *Needles ; Risk Factors ; *Surgical Instruments ; *Surgical Sponges ; },
abstract = {INTRODUCTION: Retained sponges and instruments (RSI) due to surgery are a recognised medical 'never event' and have catastrophic implications for patients, healthcare professionals and medical care providers. The aim of this review was to elucidate the extent of the problem of RSI and to identify preventative strategies.<br><br>METHODS: A comprehensive literature search was performed on MEDLINE(&#xae;), Embase&#x2122;, the Science Citation Index and Google&#x2122; Scholar for articles published in English between January 2000 and June 2012. Studies outlining the incidence, risk, management and attempts to prevent RSI following surgical intervention were retrieved.<br><br>RESULTS: The overall incidence of RSI is low although its incidence is substantially higher in operations performed on open cavities. Sponges are the most commonly retained item when compared with needles and instruments. Clinical presentation is varied, leading to avoidable morbidity, and the error is indefensible medicolegally. Risk factors include emergency operations, operations involving unexpected change in procedure, raised body mass index, and a failure to perform accurate sponge and instrument counts. The existing strategy for prevention is manual counting of sponges and instruments undertaken by surgical personnel. This, however, is fallible. Computer assisted counting of sponges using barcodes and gauze sponges tagged with a radiofrequency identification device aiding manual counting have been trialled recently, with success.<br><br>CONCLUSIONS: Vigilance among operating theatre personnel is paramount if RSI is to be prevented. Prospective multicentre trials to assess efficacy of new technologies aiding manual counting should be undertaken if this medical error is to be eliminated completely.},
}
@article {pmid23484151,
year = {2013},
author = {Han, J and Zhu, Y and Chen, X and Liao, B and Yao, H and Song, J and Chen, S and Meng, F},
title = {The short ITS2 sequence serves as an efficient taxonomic sequence tag in comparison with the full-length ITS.},
journal = {BioMed research international},
volume = {2013},
number = {},
pages = {741476},
pmid = {23484151},
issn = {2314-6141},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; *Expressed Sequence Tags ; Magnoliopsida/*classification/*genetics ; },
abstract = {An ideal DNA barcoding region should be short enough to be amplified from degraded DNA. In this paper, we discuss the possibility of using a short nuclear DNA sequence as a barcode to identify a wide range of medicinal plant species. First, the PCR and sequencing success rates of ITS and ITS2 were evaluated based entirely on materials from dry medicinal product and herbarium voucher specimens, including some samples collected back to 90 years ago. The results showed that ITS2 could recover 91% while ITS could recover only 23% efficiency of PCR and sequencing by using one pair of primer. Second, 12861 ITS and ITS2 plant sequences were used to compare the identification efficiency of the two regions. Four identification criteria (BLAST, inter- and intradivergence Wilcoxon signed rank tests, and TaxonDNA) were evaluated. Our results supported the hypothesis that ITS2 can be used as a minibarcode to effectively identify species in a wide variety of specimens and medicinal materials.},
}
@article {pmid23480472,
year = {2013},
author = {Alcántar-Escalera, FJ and García-Varela, M and Vázquez-Domínguez, E and Pérez-Ponce de León, G},
title = {Using DNA barcoding to link cystacanths and adults of the acanthocephalan Polymorphus brevis in central Mexico.},
journal = {Molecular ecology resources},
volume = {13},
number = {6},
pages = {1116-1124},
doi = {10.1111/1755-0998.12090},
pmid = {23480472},
issn = {1755-0998},
mesh = {Acanthocephala/anatomy &amp; histology/classification/*genetics/growth &amp; development ; Animals ; *DNA Barcoding, Taxonomic ; Larva/anatomy &amp; histology/classification/genetics ; Mexico ; Molecular Sequence Data ; Sequence Alignment ; },
abstract = {In parasitic organisms, particularly helminths, the usage of the mitochondrial cytochrome c oxidase subunit I gene as the standard DNA barcoding region for species identification and discovery has been very limited. Here, we present an integrated study, based on both DNA barcoding and morphological analyses, for acanthocephalans belonging to the genus Polymorphus, whose larvae (cystacanths) are commonly found in the mesentery of freshwater fishes, while adults are found in the intestine of fish-eating birds. The alpha taxonomy of parasitic helminths is based on adult morphological traits, and because of that larval forms cannot be identified to species level based on morphology alone. DNA barcoding offers an alternative tool for linking larval stages of parasitic organisms to known adults. We sequenced cystacanths collected from freshwater fishes in localities across central Mexico and adults obtained from fish-eating birds, to determine whether they were conspecific. To corroborate the molecular results, we conducted a morphometric analysis with 'Proboscis profiler', which is a software tool developed to detect heterogeneity in morphologically similar acanthocephalans based on the multivariate statistical analysis of proboscis hook dimensions. Both sources of information indicate that cystacanths infecting freshwater fishes in central Mexico belong to a single species, Polymorphus brevis.},
}
@article {pmid23480447,
year = {2013},
author = {Ashfaq, M and Asif, M and Anjum, ZI and Zafar, Y},
title = {Evaluating the capacity of plant DNA barcodes to discriminate species of cotton (Gossypium: Malvaceae).},
journal = {Molecular ecology resources},
volume = {13},
number = {4},
pages = {573-582},
doi = {10.1111/1755-0998.12089},
pmid = {23480447},
issn = {1755-0998},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Endoribonucleases/genetics ; Genetic Loci ; Gossypium/*classification/*genetics ; Molecular Sequence Data ; Nucleotidyltransferases/genetics ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Analysis, DNA ; },
abstract = {Although two plastid regions have been adopted as the standard markers for plant DNA barcoding, their limited resolution has provoked the consideration of other gene regions, especially in taxonomically diverse genera. The genus Gossypium (cotton) includes eight diploid genome groups (A-G, and K) and five allotetraploid species which are difficult to discriminate morphologically. In this study, we tested the effectiveness of three widely used markers (matK, rbcL, and ITS2) in the discrimination of 20 diploid and five tetraploid species of cotton. Sequences were analysed locus-wise and in combinations to determine the most effective strategy for species identification. Sequence recovery was high, ranging from 92% to 100% with mean pairwise interspecific distance highest for ITS2 (3.68%) and lowest for rbcL (0.43%). At a 0.5% threshold, the combination of matK+ITS2 produced the greatest number of species clusters. Based on 'best match' analysis, the combination of matK+ITS2 was best, while based on 'all species barcodes' analysis, ITS2 gave the highest percentage of correct species identifications (98.93%). The combination of sequences for all three markers produced the best resolved tree. The disparity index test based on matK+rbcL+ITS2 was significant (P < 0.05) for a higher number of species pairs than the individual gene sequences. Although all three barcodes separated the species with respect to their genome type, no single combination of barcodes could differentiate all the Gossypium species, and tetraploid species were particularly difficult.},
}
@article {pmid23479155,
year = {2013},
author = {Kaewdoungdee, N and Tanee, T},
title = {A molecular marker for in situ genetic resource conservation of Capsicum annuum var. acuminatum (Solanaceae).},
journal = {Genetics and molecular research : GMR},
volume = {12},
number = {3},
pages = {3529-3539},
doi = {10.4238/2013.February.28.10},
pmid = {23479155},
issn = {1676-5680},
mesh = {Capsicum/*genetics ; *Conservation of Natural Resources ; DNA Barcoding, Taxonomic ; *DNA Fingerprinting ; Humans ; Species Specificity ; Thailand ; },
abstract = {The Thailand cultivar pepper 'phrik man bangchang' (Capsicum annuum var. acuminatum, Solanaceae) was originally cultivated in the Bangchang Subdistrict, Amphawa District in Samut Songkhram Province. The cultivated areas are limited; we verified its distribution in Thailand for in situ 'phrik man bangchang' genetic resource conservation. Samples were collected from the original cultivation area of Bangchang Subdistrict (Or) and were randomly explored in Ratchaburi Province (RB), Khon Kaen Province (KK), and Sakon Nakhon Province (SN). A pure line from The Tropical Vegetable Research Center at Kasetsart University was used as the standard indicator. Two more Capsicum species, C. chinensis and C. frutescens, and a species from another genus in the family, Solanum melongena, were included. A dendrogram constructed from random amplified polymorphic DNA fingerprints indicated that the Or, RB, KK, and SN samples were C. annuum var. acuminatum with supportive similarity coefficients of 0.79 to 0.98. Finally, DNA barcodes, from psbA-trnH spacer region, were provided for the 3 wild species, C. annuum var. acuminatum, C. chinensis, and C. frutescens under GenBank accession Nos. JQ087869-JQ087871. The nucleotide variations between species were 0.23 to 0.26. In summary, 'phrik man bangchang' is still being planted in Bangchang Subdistrict, but only in small areas. The distribution of planting areas is expected to be throughout Thailand.},
}
@article {pmid23472476,
year = {2013},
author = {Phoolcharoen, W and Sukrong, S},
title = {Molecular analysis of Vitex species using candidate DNA barcoding and PCR-RFLP of the matK gene for authentication of Vitex glabrata.},
journal = {Natural product communications},
volume = {8},
number = {1},
pages = {125-128},
pmid = {23472476},
issn = {1934-578X},
mesh = {DNA Barcoding, Taxonomic ; Genes, Plant ; Plants, Medicinal/classification/genetics ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Species Specificity ; Vitex/*classification/genetics ; },
abstract = {Several species of the Vitex genus, family Lamiaceae, are used in folk medicine for a variety of remedies. V. glabrata is unique among Vitex species because its main effect is sexual enhancement. However, crude drugs derived from different Vitex species might not be easily distinguishable, which could lead to their misidentification and misuse. Therefore, the accurate authentication of V. glabrata is critical for its effective medicinal use. In this study, the matK gene and the psbA-trnH intergenic spacer candidate DNA barcodes were sequenced and analyzed to identify five different Vitex species that are medicinally used in Thailand: V. negundo, V. trifolia, V. rotundifolia, V. limonifolia, and V. glabrata. Each region was successfully amplified from the leaves of the five species using a single set of primers, and the sequences determined. The size difference in PCR products of psbA-trnH and PCR restriction fragment length polymorphism (PCR-RFLP) of the matK gene sequences were used to differentiate V. glabrata from other Vitex species. These results indicate both the matK gene and the psbA-trnH intergenic spacer as candidate DNA barcodes of Vitex species and suggest that the difference of psbA-trnH PCR products and PCR-RFLP analysis based on the matK gene are effective for the authentication of V. glabrata.},
}
@article {pmid23469803,
year = {2013},
author = {Yoon, B and Shin, H and Kang, EM and Cho, DW and Shin, K and Chung, H and Lee, CW and Kim, JM},
title = {Inkjet-compatible single-component polydiacetylene precursors for thermochromic paper sensors.},
journal = {ACS applied materials &amp; interfaces},
volume = {5},
number = {11},
pages = {4527-4535},
doi = {10.1021/am303300g},
pmid = {23469803},
issn = {1944-8252},
mesh = {Biosensing Techniques/*methods ; Hydrogen Bonding ; *Ink ; Paper ; Polyacetylene Polymer ; Polymers/*chemistry ; Polyynes/*chemistry ; Printing/*methods ; Temperature ; Ultraviolet Rays ; Water/chemistry ; },
abstract = {Inkjet-printable diacetylene (DA) supramolecules, which can be dispersed in water without using additional surfactants, have been developed. The supramolecules are generated from DA monomers that contain bisurea groups, which are capable of forming hydrogen-bonding networks, and hydrophilic oligoethylene oxide moieties. Because of suitable size distribution and stability characteristics, the single DA component ink can be readily transferred to paper substrates by utilizing a common office inkjet printer. UV irradiation of the DA-printed paper results in generation of blue-colored polydiacetylene (PDA) images, which show reversible thermochromic transitions in specific temperature ranges. Inkjet-printed PDAs, in the format of a two-dimensional (2D) quick response (QR) code on a real parking ticket, serve as a dual anticounterfeiting system that combines easy decoding of the QR code and colorimetric PDA reversibility for validating the authenticity of the tickets. This single-component ink system has great potential for use in paper-based devices, temperature sensors, and anticounterfeiting barcodes.},
}
@article {pmid23469211,
year = {2013},
author = {Ramirez-Gonzalez, R and Yu, DW and Bruce, C and Heavens, D and Caccamo, M and Emerson, BC},
title = {PyroClean: denoising pyrosequences from protein-coding amplicons for the recovery of interspecific and intraspecific genetic variation.},
journal = {PloS one},
volume = {8},
number = {3},
pages = {e57615},
pmid = {23469211},
issn = {1932-6203},
mesh = {*Algorithms ; Animals ; Arthropods/classification/*genetics ; Base Sequence ; DNA, Mitochondrial/classification/*genetics/isolation &amp; purification ; Electron Transport Complex IV/classification/*genetics/isolation &amp; purification ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Data ; *Open Reading Frames ; Phylogeny ; Polymerase Chain Reaction ; Ribosomes/genetics ; Sequence Analysis, DNA ; Signal-To-Noise Ratio ; *Software ; },
abstract = {High-throughput parallel sequencing is a powerful tool for the quantification of microbial diversity through the amplification of nuclear ribosomal gene regions. Recent work has extended this approach to the quantification of diversity within otherwise difficult-to-study metazoan groups. However, nuclear ribosomal genes present both analytical challenges and practical limitations that are a consequence of the mutational properties of nuclear ribosomal genes. Here we exploit useful properties of protein-coding genes for cross-species amplification and denoising of 454 flowgrams. We first use experimental mixtures of species from the class Collembola to amplify and pyrosequence the 5' region of the COI barcode, and we implement a new algorithm called PyroClean for the denoising of Roche GS FLX pyrosequences. Using parameter values from the analysis of experimental mixtures, we then analyse two communities sampled from field sites on the island of Tenerife. Cross-species amplification success of target mitochondrial sequences in experimental species mixtures is high; however, there is little relationship between template DNA concentrations and pyrosequencing read abundance. Homopolymer error correction and filtering against a consensus reference sequence reduced the volume of unique sequences to approximately 5% of the original unique raw reads. Filtering of remaining non-target sequences attributed to PCR error, sequencing error, or numts further reduced unique sequence volume to 0.8% of the original raw reads. PyroClean reduces or eliminates the need for an additional, time-consuming step to cluster reads into Operational Taxonomic Units, which facilitates the detection of intraspecific DNA sequence variation. PyroCleaned sequence data from field sites in Tenerife demonstrate the utility of our approach for quantifying evolutionary diversity and its spatial structure. Comparison of our sequence data to public databases reveals that we are able to successfully recover both interspecific and intraspecific sequence diversity.},
}
@article {pmid23469199,
year = {2013},
author = {Costea, PI and Lundeberg, J and Akan, P},
title = {TagGD: fast and accurate software for DNA Tag generation and demultiplexing.},
journal = {PloS one},
volume = {8},
number = {3},
pages = {e57521},
pmid = {23469199},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic/instrumentation/*methods/standards ; High-Throughput Nucleotide Sequencing ; Humans ; Sequence Analysis, DNA ; *Software ; },
abstract = {Multiplexing is of vital importance for utilizing the full potential of next generation sequencing technologies. We here report TagGD (DNA-based Tag Generator and Demultiplexor), a fully-customisable, fast and accurate software package that can generate thousands of barcodes satisfying user-defined constraints and can guarantee full demultiplexing accuracy. The barcodes are designed to minimise their interference with the experiment. Insertion, deletion and substitution events are considered when designing and demultiplexing barcodes. 20,000 barcodes of length 18 were designed in 5 minutes and 2 million barcoded Illumina HiSeq-like reads generated with an error rate of 2% were demultiplexed with full accuracy in 5 minutes. We believe that our software meets a central demand in the current high-throughput biology and can be utilised in any field with ample sample abundance. The software is available on GitHub (https://github.com/pelinakan/UBD.git).},
}
@article {pmid23469083,
year = {2013},
author = {Sasakawa, K},
title = {A novel technique for identifying the instar of field-collected insect larvae.},
journal = {PloS one},
volume = {8},
number = {2},
pages = {e57836},
pmid = {23469083},
issn = {1932-6203},
mesh = {Animals ; Body Size ; Discriminant Analysis ; Insecta/*classification/growth &amp; development ; Larva/classification/growth &amp; development ; Linear Models ; Statistics as Topic/*methods ; },
abstract = {Many field studies of insects have focused on the adult stage alone, likely because immature stages are unknown in most insect species. Molecular species identification (e.g., DNA barcoding) has helped ascertain the immature stages of many insects, but larval developmental stages (instars) cannot be identified. The identification of the growth stages of collected individuals is indispensable from both ecological and taxonomic perspectives. Using a larval-adult body size relationship across species, I present a novel technique for identifying the instar of field-collected insect larvae that are identified by molecular species identification technique. This method is based on the assumption that classification functions derived from discriminant analyses, performed with larval instar as a response variable and adult and larval body sizes as explanatory variables, can be used to determine the instar of a given larval specimen that was not included in the original data set, even at the species level. This size relationship has been demonstrated in larval instars for many insects (Dyar's rule), but no attempt has been made to include the adult stage. Analysis of a test data set derived from the beetle family Carabidae (Coleoptera) showed that classification functions obtained from data sets derived from related species had a correct classification rate of 81-100%. Given that no reliable method has been established to identify the instar of field-collected insect larvae, these values may have sufficient accuracy as an analytical method for field-collected samples. The chief advantage of this technique is that the instar can be identified even when only one specimen is available per species if classification functions are determined for groups to which the focal species belongs. Similar classification functions should be created for other insect groups. By using those functions together with molecular species identification, future studies could include larval stages as well as adults.},
}
@article {pmid23468874,
year = {2013},
author = {Roos, S and Dicksved, J and Tarasco, V and Locatelli, E and Ricceri, F and Grandin, U and Savino, F},
title = {454 pyrosequencing analysis on faecal samples from a randomized DBPC trial of colicky infants treated with Lactobacillus reuteri DSM 17938.},
journal = {PloS one},
volume = {8},
number = {2},
pages = {e56710},
pmid = {23468874},
issn = {1932-6203},
mesh = {Bacteria/classification/genetics ; Colic/*therapy ; Feces/*microbiology ; Female ; Humans ; Infant ; Infant, Newborn ; Limosilactobacillus reuteri/*physiology ; Male ; *Metagenome ; },
abstract = {OBJECTIVE: To analyze the global microbial composition, using large-scale DNA sequencing of 16 S rRNA genes, in faecal samples from colicky infants given L. reuteri DSM 17938 or placebo.<br><br>METHODS: Twenty-nine colicky infants (age 10-60 days) were enrolled and randomly assigned to receive either Lactobacillus reuteri (10(8) cfu) or a placebo once daily for 21 days. Responders were defined as subjects with a decrease of 50% in daily crying time at day 21 compared with the starting point. The microbiota of faecal samples from day 1 and 21 were analyzed using 454 pyrosequencing. The primers: Bakt_341F and Bakt_805R, complemented with 454 adapters and sample specific barcodes were used for PCR amplification of the 16 S rRNA genes. The structure of the data was explored by using permutational multivariate analysis of variance and effects of different variables were visualized with ordination analysis.<br><br>RESULTS: The infants' faecal microbiota were composed of Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes as the four main phyla. The composition of the microbiota in infants with colic had very high inter-individual variability with Firmicutes/Bacteroidetes ratios varying from 4000 to 0.025. On an individual basis, the microbiota was, however, relatively stable over time. Treatment with L. reuteri DSM 17938 did not change the global composition of the microbiota, but when comparing responders with non-responders the group responders had an increased relative abundance of the phyla Bacteroidetes and genus Bacteroides at day 21 compared with day 0. Furthermore, the phyla composition of the infants at day 21 could be divided into three enterotype groups, dominated by Firmicutes, Bacteroidetes, and Actinobacteria, respectively.<br><br>CONCLUSION: L. reuteri DSM 17938 did not affect the global composition of the microbiota. However, the increase of Bacteroidetes in the responder infants indicated that a decrease in colicky symptoms was linked to changes of the microbiota.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov NCT00893711.},
}
@article {pmid23468228,
year = {2013},
author = {Paunescu, D and Fuhrer, R and Grass, RN},
title = {Protection and deprotection of DNA--high-temperature stability of nucleic acid barcodes for polymer labeling.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {52},
number = {15},
pages = {4269-4272},
doi = {10.1002/anie.201208135},
pmid = {23468228},
issn = {1521-3773},
mesh = {DNA/*chemistry/genetics ; Molecular Structure ; Nucleic Acid Denaturation ; Nucleic Acids/*chemistry ; Polymers/*chemistry ; Silicon Dioxide/*chemistry ; *Staining and Labeling ; *Temperature ; },
}
@article {pmid23464748,
year = {2013},
author = {Yacoub, HA and Fathi, MM and Mahmoud, WM},
title = {DNA barcode through cytochrome b gene information of mtDNA in native chicken strains.},
journal = {Mitochondrial DNA},
volume = {24},
number = {5},
pages = {528-537},
doi = {10.3109/19401736.2013.770489},
pmid = {23464748},
issn = {1940-1744},
mesh = {Animals ; Base Sequence ; Chickens/classification/*genetics ; Cytochromes b/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Single Nucleotide ; Saudi Arabia ; Sequence Alignment ; Species Specificity ; },
abstract = {This study was carried out to figure out the potentiality of a cytochrome b gene as a barcoding tool in discriminating native chicken strains and other Gallus gallus species. We performed PCR amplification using universal primer to amplify around 415 bp fragment of cytochrome b gene of mtDNA. The results revealed that all Saudi chicken strains were identical to each other but when compared with other species of Gallus the differences were exciting. The phylogenetic tree revealed that there were seven clusters represented for native strains and were clustered together especially in black strain and dark brown ones. The results have confirmed that using cytochrome b gene to discriminate between Saudi chicken strains and other species of G. gallus fowl was a very sufficient tool. Moreover, we can consider short fragment of cytochrome b gene of mtDNA as a universal DNA barcode region. It was a much more accurate and efficient tool to discriminate interspecies than intraspecies. We think it needs more studies to confirm this concept, and we have to apply that tool for many species of vertebrate and invertebrate as well.},
}
@article {pmid23460980,
year = {2012},
author = {Luo, K and Ma, P and Yao, H and Xin, TY and Hu, Y and Zheng, SH and Huang, LF and Liu, J and Song, JY},
title = {[Identification of gentianae macrophyllae radix using the ITS2 barcodes].},
journal = {Yao xue xue bao = Acta pharmaceutica Sinica},
volume = {47},
number = {12},
pages = {1710-1717},
pmid = {23460980},
issn = {0513-4870},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/analysis/genetics ; Drug Contamination ; Genetic Variation ; *Genome, Plant ; Gentiana/classification/*genetics ; Plant Roots/genetics ; Plants, Medicinal/*genetics ; Polymerase Chain Reaction/methods ; Quality Control ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {DNA barcoding is a rapidly developing frontier technology in the world and will be useful in promoting the quality control and standardization of traditional Chinese medicine. Until now, many studies concerning DNA barcoding have focused on leaf samples but rarely on Chinese herbal medicine. There are three issues involved in DNA barcoding for traditional Chinese medicinal materials: (1) the extraction methods for total DNA of the rhizomes of the medicinal materials; (2) intra-specific variation among samples from different places of origin; (3) accuracy and stability of this method. In this study, Gentianae Macrophyllae Radix was used to verify the stability and accuracy of DNA barcoding technology. Five regions (ITS2, psbA-trnH, matK, rbcL, and ITS) were tested for their ability to identify 86 samples of Gentianae Macrophyllae Radix and their adulterants. After improving the DNA extraction method, genomic DNA from all samples was successfully obtained. To evaluate each barcode's utility for species authentication, PCR amplification efficiency, genetic divergence, and species authentication were assessed. Among all tested regions only ITS2 locus showed 100% of PCR amplification and identification efficiencies. Based on the established method, we successfully identified two samples of Gentianae Macrophyllae Radix bought in pharmacy to the original species.},
}
@article {pmid23460915,
year = {2013},
author = {Tripathi, AM and Tyagi, A and Kumar, A and Singh, A and Singh, S and Chaudhary, LB and Roy, S},
title = {The internal transcribed spacer (ITS) region and trnH-psbA [corrected] are suitable candidate loci for DNA barcoding of tropical tree species of India.},
journal = {PloS one},
volume = {8},
number = {2},
pages = {e57934},
pmid = {23460915},
issn = {1932-6203},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/*genetics ; Genes, Plant/*genetics ; Genetic Loci/*genetics ; Genetic Variation ; Geography ; India ; Molecular Sequence Data ; Phylogeny ; Reference Standards ; Satellite Communications ; Species Specificity ; Trees/*classification/*genetics ; *Tropical Climate ; },
abstract = {BACKGROUND: DNA barcoding as a tool for species identification has been successful in animals and other organisms, including certain groups of plants. The exploration of this new tool for species identification, particularly in tree species, is very scanty from biodiversity-rich countries like India. rbcL and matK are standard barcode loci while ITS, and trnH-psbA are considered as supplementary loci for plants.<br><br>Plant barcode loci, namely, rbcL, matK, ITS, trnH-psbA, and the recently proposed ITS2, were tested for their efficacy as barcode loci using 300 accessions of tropical tree species. We tested these loci for PCR, sequencing success, and species discrimination ability using three methods. rbcL was the best locus as far as PCR and sequencing success rate were concerned, but not for the species discrimination ability of tropical tree species. ITS and trnH-psbA were the second best loci in PCR and sequencing success, respectively. The species discrimination ability of ITS ranged from 24.4 percent to 74.3 percent and that of trnH-psbA was 25.6 percent to 67.7 percent, depending upon the data set and the method used. matK provided the least PCR success, followed by ITS2 (59. 0%). Species resolution by ITS2 and rbcL ranged from 9.0 percent to 48.7 percent and 13.2 percent to 43.6 percent, respectively. Further, we observed that the NCBI nucleotide database is poorly represented by the sequences of barcode loci studied here for tree species.<br><br>CONCLUSION: Although a conservative approach of a success rate of 60-70 percent by both ITS and trnH-psbA may not be considered as highly successful but would certainly help in large-scale biodiversity inventorization, particularly for tropical tree species, considering the standard success rate of plant DNA barcode program reported so far. The recommended matK and rbcL primers combination may not work in tropical tree species as barcode markers.},
}
@article {pmid23459119,
year = {2013},
author = {Robe, LJ and De Ré, FC and Ludwig, A and Loreto, EL},
title = {The Drosophila flavopilosa species group (Diptera, Drosophilidae): an array of exciting questions.},
journal = {Fly},
volume = {7},
number = {2},
pages = {59-69},
pmid = {23459119},
issn = {1933-6942},
mesh = {Animals ; Biological Evolution ; Cestrum ; DNA Barcoding, Taxonomic ; Drosophila/*classification/genetics ; Female ; Geography ; Male ; *Phylogeny ; Species Specificity ; },
abstract = {The D. flavopilosa group encompasses an ecologically restricted set of species strictly adapted to hosting flowers of Cestrum (Solanaceae). This group presents potential to be used as a model to the study of different questions regarding ecologically restricted species macro and microevolutionary responses, geographical vs. ecological speciation and intra and interspecific competition. This review aims to revisit and reanalyze the patterns and processes that are subjacent to the interesting ecological and evolutionary properties of these species. Biotic and abiotic niche properties of some species were reanalyzed in face of ecological niche modeling approaches in order to get some insights into their ecological evolution. A test of the potential of DNA-Barcoding provided evidences that this technology may be a way of overcoming difficulties related to cryptic species differentiation. The new focus replenishes the scenario with new questions, presenting a case where neither geographical nor ecological speciation may be as yet suggested.},
}
@article {pmid25202518,
year = {2013},
author = {Stull, GW and Moore, MJ and Mandala, VS and Douglas, NA and Kates, HR and Qi, X and Brockington, SF and Soltis, PS and Soltis, DE and Gitzendanner, MA},
title = {A targeted enrichment strategy for massively parallel sequencing of angiosperm plastid genomes.},
journal = {Applications in plant sciences},
volume = {1},
number = {2},
pages = {},
pmid = {25202518},
issn = {2168-0450},
abstract = {PREMISE OF THE STUDY: We explored a targeted enrichment strategy to facilitate rapid and low-cost next-generation sequencing (NGS) of numerous complete plastid genomes from across the phylogenetic breadth of angiosperms. •<br><br>METHODS AND RESULTS: A custom RNA probe set including the complete sequences of 22 previously sequenced eudicot plastomes was designed to facilitate hybridization-based targeted enrichment of eudicot plastid genomes. Using this probe set and an Agilent SureSelect targeted enrichment kit, we conducted an enrichment experiment including 24 angiosperms (22 eudicots, two monocots), which were subsequently sequenced on a single lane of the Illumina GAIIx with single-end, 100-bp reads. This approach yielded nearly complete to complete plastid genomes with exceptionally high coverage (mean coverage: 717&#xd7;), even for the two monocots. &#x2022;<br><br>CONCLUSIONS: Our enrichment experiment was highly successful even though many aspects of the capture process employed were suboptimal. Hence, significant improvements to this methodology are feasible. With this general approach and probe set, it should be possible to sequence more than 300 essentially complete plastid genomes in a single Illumina GAIIx lane (achieving &#x223c;50&#xd7; mean coverage). However, given the complications of pooling numerous samples for multiplex sequencing and the limited number of barcodes (e.g., 96) available in commercial kits, we recommend 96 samples as a current practical maximum for multiplex plastome sequencing. This high-throughput approach should facilitate large-scale plastid genome sequencing at any level of phylogenetic diversity in angiosperms.},
}
@article {pmid25602592,
year = {2013},
author = {Tekin, E and Vásquez, D and Coughlan, JM},
title = {S-K Smartphone Barcode Reader for the Blind.},
journal = {Journal on technology and persons with disabilities : ... Annual International Technology and Persons with Disabilities Conference},
volume = {28},
number = {},
pages = {230-239},
pmid = {25602592},
issn = {2330-4219},
support = {R01 EY018890/EY/NEI NIH HHS/United States ; },
abstract = {We describe a new smartphone app called BLaDE (Barcode Localization and Decoding Engine), designed to enable a blind or visually impaired user find and read product barcodes. Developed at The Smith-Kettlewell Eye Research Institute, the BLaDE Android app has been released as open source software, which can be used for free or modified for commercial or non-commercial use. Unlike popular commercial smartphone apps, BLaDE provides real-time audio feedback to help visually impaired users locate a barcode, which is a prerequisite to being able to read it. We describe experiments performed with five blind/visually impaired volunteer participants demonstrating that BLaDE is usable and that the audio feedback is key to its usability.},
}
@article {pmid25325088,
year = {2013},
author = {Blank, SM and Shinohara, A and Altenhofer, E},
title = {The Eurasian species of Xyela (Hymenoptera, Xyelidae): taxonomy, host plants and distribution.},
journal = {Zootaxa},
volume = {3629},
number = {},
pages = {1-106},
doi = {10.11646/zootaxa.3629.1.1},
pmid = {25325088},
issn = {1175-5326},
mesh = {Animal Distribution ; Animals ; Asia ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Europe ; Feeding Behavior ; Female ; Food Chain ; Hymenoptera/anatomy &amp; histology/*classification/genetics/*physiology ; Insect Proteins/genetics ; Larva/anatomy &amp; histology/classification/genetics/physiology ; Male ; Molecular Sequence Data ; Phylogeny ; Plants ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The 28 Eurasian species of Xyela Dalman, 1819 are revised based on material of ca 7,500 imagines including about 10 % reared specimens. Larvae of Eurasian Xyela usually are monophagous and feed inside the staminate cones of pines (Pinus spp., Pinaceae). Based on the reared material, on identification by barcoding and on additional collection observations, the larval host associations for the Xyela species are summarized and additional biological observations are noted. An illustrated key to the species and distribution maps are presented. Eight species are described as new: X. altenhoferi Blank, sp. nov. (Croatia), X. heldreichii Blank, sp. nov. (Albania, Greece), X. koraiensis Blank &amp; Shinohara, sp. nov. (Russia, South Korea), X. peuce Blank, sp. nov. (Bulgaria), X. pumilae Blank &amp; Shinohara, sp. nov. (Japan), X. rasnitsyni Blank &amp; Shinohara, sp. nov. (China, Russia, South Korea), X. sibiricae Blank, sp. nov. (Mongolia, Russia), and X. uncinatae Blank, sp. nov. (Andorra, France, Spain, Switzerland). For the other species redescriptions are given. A lectotype is designated for X. longula Dalman, 1819, and neotypes are designated for X. graeca J.P.E.F. Stein, 1876 and Pinicola julii Brébisson, 1818. The following new synonymies are proposed: X. lii Xiao, 1988, syn. nov. of X. sinicola Maa, 1947; X. nigroabscondita Haris &amp; Gyurkovics, 2011, syn. nov. of X. lugdunensis (Berland, 1943); and X. suwonae Ryu &amp; Lee, 1992, syn. nov. of X. ussuriensis Rasnitsyn, 1965.},
}
@article {pmid25277910,
year = {2013},
author = {Cline, AR and Skelley, PE and Audisio, P},
title = {Morphology and life history of Brachypeplus glaber LeConte(Coleoptera: Nitidulidae), with a discussion of multiple life stage data for phylogenetic analyses.},
journal = {Zootaxa},
volume = {3734},
number = {},
pages = {259-272},
doi = {10.11646/zootaxa.3734.2.9},
pmid = {25277910},
issn = {1175-5326},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology ; Animals ; Coleoptera/anatomy &amp; histology/classification/*genetics/*growth &amp; development ; Ecosystem ; Female ; Life Cycle Stages ; Male ; Phylogeny ; },
abstract = {A detailed description of the sap beetle Brachypeplus glaber LeConte (Nitidulidae) is provided, including egg, larval, pupal and adult stages. Rearing and DNA barcoding were used to confirm life stage identifications. This is the first New World Brachypeplus species for which larval and pupal descriptions are available. Characters and character states for larvae, pupae, and adults are discussed at the species and generic levels within the context of phylogenetic revisions at different hierarchical levels.},
}
@article {pmid25250444,
year = {2013},
author = {Harbach, RE and Kitching, IJ and Culverwell, CL and Howard, TM and Linton, YM},
title = {Nyx pholeocola, a new genus and cavernicolous species of tribe Aedini (Diptera: Culicidae) from southern Thailand based on morphological and molecular data.},
journal = {Zootaxa},
volume = {3683},
number = {},
pages = {159-177},
doi = {10.11646/zootaxa.3683.2.5},
pmid = {25250444},
issn = {1175-5326},
mesh = {Animals ; *Culicidae/anatomy &amp; histology/classification/genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics/metabolism ; Electron Transport Complex IV/genetics/metabolism ; Female ; Insect Proteins/genetics/metabolism ; Larva/anatomy &amp; histology ; Male ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Pupa/anatomy &amp; histology ; Sequence Analysis, DNA ; Species Specificity ; Thailand ; },
abstract = {Nyx Harbach &amp; Linton, gen. nov., is introduced as a new mosquito genus of tribe Aedini for a previously unknown cave-dwelling species, Nyx pholeocola Linton &amp; Harbach, sp. nov., from southern Thailand. A diagnosis of the genus is provided that features unique anatomical characters of the adult, pupal and larval stages of the type species. The affinities of Nyx are discussed in terms of its position in the phylogeny of Aedini. Nyx is more closely related to Borichinda and Isoaedes than to other genera of tribe Aedini. Salient differences that distinguish these three genera are contrasted. The male and female genitalia, pupa and fourth-instar larva of the new species are illustrated. DNA sequence for the second nuclear internal spacer region (ITS2) and the 658-bp barcode fragment of the mitochondrial cytochrome c oxidase I (COI) gene reveal very low similarity with published sequences, supporting the unique status of the new species.},
}
@article {pmid25113597,
year = {2013},
author = {Landry, JF and Nazari, V and Dewaard, JR and Mutanen, M and Lopez-Vaamonde, C and Huemer, P and Hebert, PD},
title = {Shared but overlooked: 30 species of Holarctic Microlepidoptera revealed by DNA barcodes and morphology.},
journal = {Zootaxa},
volume = {3749},
number = {},
pages = {1-93},
doi = {10.11646/zootaxa.3749.1.1},
pmid = {25113597},
issn = {1175-5326},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Female ; Lepidoptera/anatomy &amp; histology/*classification/*genetics ; Male ; Species Specificity ; },
abstract = {This study reports 30 species of Lepidoptera previously known from either the Palearctic or the Nearctic that are newly recorded as Holarctic. For 28 of these species, their intercontinental distributions were initially detected through DNA barcode analysis and subsequently confirmed by morphological examination; two Palearctic species were first detected in North America through morphology and then barcoded. When possible, the origin and status of each species (introduced, overlooked Holarctic species, or unknowingly re-described) is discussed, and its morphology is diagnosed and illustrated. The species involved include Tineidae: Scardia amurensis Zagulajev, Triaxomera parasitella (Hübner), Nemapogon cloacella (Haworth), Elatobia montelliella (Schantz), Tinea svenssoni Opheim; Gracillariidae: Caloptilia suberinella (Tengström), Parornix betulae (Stainton); Phyllonorycter maestingella (Müller); Yponomeutidae: Paraswammerdamia albicapitella (Scharfenberg), P. conspersella (Tengström); Plutellidae: Plutella hyperboreella Strand; Lyonetiidae: Lyonetia pulverulentella Zeller; Autostichidae: Oegoconia deauratella (Herrich-Schäffer), O. novimundi (Busck); Blastobasidae: Blastobasis glandulella (Riley), B. maroccanella (Amsel), B. tarda Meyrick; Depressariidae: Agonopterix conterminella (Zeller), Depressaria depressana (F.); Coleophoridae: Coleophora atriplicis Meyrick, C. glitzella Hofmann, C. granulatella Zeller, C. texanella Chambers, C. vitisella Gregson; Scythrididae: Scythris sinensis (Felder &amp; Rogenhofer); Gelechiidae: Altenia perspersella (Wocke), Gnorimoschema jalavai Povolný, Scrobipalpa acuminatella (Sircom), Sophronia gelidella Nordman; Choreutidae: Anthophila fabriciana (L.); and Tortricidae: Phiaris bipunctana (F.). These cases of previously unrecognized faunal overlap have led to their redescription in several instances. Five new synonyms are proposed: Blastobasis glandulella (Riley, 1871) = B. huemeri Sinev, 1993, syn. nov.; B. tarda Meyrick, 1902 = Neoblastobasis ligurica Nel &amp; Varenne, 2004, syn. nov.; Coleophora atriplicis Meyrick, 1928 = C. cervinella McDunnough, 1946, syn. nov.; C. texanella Chambers, 1878 = C. coxi Baldizzone &amp; van der Wolf, 2007, syn. nov., and = C. vagans Walsingham, 1907, syn. nov. Lectotypes are designated for Blastobasis tarda Meyrick and Coleophora texanella Chambers. Type specimens were examined where pertinent to establish new synonymies. We identify 12 previously overlooked cases of species introductions, highlighting the power of DNA barcoding as a tool for biosurveillance.},
}
@article {pmid25113496,
year = {2013},
author = {Bañón, R and Arronte, JC and Barros-García, D and Vázquez-Dorado, S and De Carlos, A},
title = {Taxonomic study of Bathygadidae fishes (Gadiformes) from Atlantic Spanish waters combining morphological and molecular approaches.},
journal = {Zootaxa},
volume = {3746},
number = {},
pages = {552-566},
doi = {10.11646/zootaxa.3746.4.3},
pmid = {25113496},
issn = {1175-5326},
mesh = {Animals ; Atlantic Ocean ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Gadiformes/anatomy &amp; histology/*classification/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Spain ; },
abstract = {From 2009 to 2011 eleven specimens belonging to four bathygadid species of the family Bathygadidae were captured in two different locations in the northern waters of Spain. The morphometric measurements and meristic characters of these specimens are given. The specimens were identified as belonging to the genera Gadomus Regan, 1903, and Bathygadus Günther, 1878, including the following species: Gadomus dispar (Vaillant, 1888), Gadomus longifilis (Goode &amp; Bean, 1885), Gadomus arcuatus (Goode &amp; Bean, 1886) and Bathygadus melanobranchus Vaillant, 1888. As a result, a new northern limit of distribution of G. arcuatus from the northeastern Atlantic is reported. The first molecular identification and genetic interrelationships of Bathygadidae species, based on the mitochondrial COI nucleotide sequences -DNA barcodes- is reported. Sequences corresponding to specimens from the same species were identical and the overall mean genetic diversity (uncorrected p-distance) was 0.096 ± 0.008. Based on a morphological and meristic examination of the specimens, as well as on the available literature, an updated key of the members of the family Bathygadidae from the north-eastern Atlantic Ocean is provided.},
}
@article {pmid25113469,
year = {2013},
author = {Huemer, P and Elsner, G and Karsholt, O},
title = {Review of the Eulamprotes wilkella species-group based on morphology and DNA barcodes, with descriptions of new taxa (Lepidoptera, Gelechiidae).},
journal = {Zootaxa},
volume = {3746},
number = {},
pages = {69-100},
doi = {10.11646/zootaxa.3746.1.3},
pmid = {25113469},
issn = {1175-5326},
mesh = {Animals ; Asia ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Europe ; Female ; Insect Proteins/genetics ; Male ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; Moths/anatomy &amp; histology/*classification/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The Eulamprotes wilkella species-group is revised based on morphological characters and on DNA barcodes of the mtCOI (Cytochrome c Oxidase 1) gene. Adult morphology combined with sequence information for 9 species supports the existence of 12 species, 7 of which are described as new to science: E. mirusella Huemer &amp; Karsholt sp. nov. (France), E. baldizzonei Karsholt &amp; Huemer sp. nov. (Italy, Slovenia, Croatia), E. atrifrontella Karsholt &amp; Huemer sp. nov. (Turkey), E. wieseri Huemer &amp; Karsholt sp. nov. (Kyrgizia), E. altaicella Huemer &amp; Karsholt sp. nov. (Russia: Altai, Buryatia, Tuva Republic), E. kailai Karsholt &amp; Huemer sp. nov. (Kazakhstan, Kyrgizia, Russia: Buryatia, Tuva Republic) and E. gemerensis Elsner sp. nov. (Slovakia). E. buvati Leraut, 1991 syn. nov. is synonymized with E. ochricapilla (Rebel, 1903).},
}
@article {pmid25113355,
year = {2013},
author = {Han, T and Lee, Y and Kim, N and Park, S and Suzuki, W and Lee, S and Park, H},
title = {A new species, Hemicrepidius (Miwacrepidius) rubriventris sp. nov. (Coleoptera, Elateridae, Denticollinae) from Republic of Korea.},
journal = {Zootaxa},
volume = {3745},
number = {},
pages = {379-387},
doi = {10.11646/zootaxa.3745.3.5},
pmid = {25113355},
issn = {1175-5326},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology ; Animals ; Coleoptera/anatomy &amp; histology/*classification/genetics ; Ecosystem ; Female ; Molecular Sequence Data ; Phylogeny ; Republic of Korea ; },
abstract = {The subgenus Miwacrepidius of the genus Hemicrepidius is represented by a monotypic species, H. (M.) subcyaneus (Motschulsky 1866) from Japan, and no other congener of the subgenus has been known until now. However, three female specimens of a novel species belonging to this subgenus were recently collected from the Republic of Korea. To delimitate the species boundary of the new species compared with the monotypic species, H. (M.) subcyaneus, we attempted an integrative taxonomy based on both morphological and DNA barcoding approaches. An examination of the results revealed ten diagnostic characteristics and large genetic distances, ranging from 8.40%, between these two species; therefore, we herein describe and illustrate the new species, Hemicrepidius (Miwacrepidius) rubriventris sp. nov., based on female types.},
}
@article {pmid25113001,
year = {2013},
author = {Proulx, I and Martin, J and Carew, M and Hare, L},
title = {Using various lines of evidence to identify Chironomus species (Diptera: Chironomidae) in eastern Canadian lakes.},
journal = {Zootaxa},
volume = {3741},
number = {},
pages = {401-458},
doi = {10.11646/zootaxa.3741.4.1},
pmid = {25113001},
issn = {1175-5326},
mesh = {Animals ; Base Sequence ; Canada ; Chironomidae/anatomy &amp; histology/*classification/genetics ; Cyclooxygenase 1/genetics ; DNA Barcoding, Taxonomic ; DNA Primers/genetics ; Globins/genetics ; Insect Proteins/genetics ; Lakes ; Larva ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; },
abstract = {Chironomus Meigen (Diptera, Chironomidae) larvae are usually the largest sediment-burrowing chironomids, and as such often constitute a major part of the freshwater infaunal biomass. However, use of this genus in ecological, environmental and paleoecological studies is hampered by the fact that Chironomus larvae are difficult to identify to species because the larvae of many species are morphologically similar. We used a combination of morphological, cytological and genetic techniques to distinguish Chironomus larvae collected from 31 water bodies located in eastern Canada, producing 17 distinguishable groupings. These groups of larvae were ultimately identified as belonging to 14 known species (C. anthracinus, C. bifurcatus, C. cucini, C. decorus-group sp. 2, C. dilutus, C. entis, C. frommeri, C. harpi, C. maturus, C. nr. atroviridis (sp. 2i), C. ochreatus, C. plumosus, C. staegeri and C. 'tigris') and three other species that remain unidentified (C. sp. NAI-III). No single approach served to delimit and identify larvae of all 17 Chironomus species that we collected. Although we expected that morphological criteria alone would be insufficient, our results suggest that DNA barcoding, using either the mitochondrial cox1 or the nuclear gb2β gene, was also inadequate for separating some Chironomus species. Thus we suggest that multiple approaches will often be needed to correctly identify Chironomus larvae to species.},
}
@article {pmid25112740,
year = {2013},
author = {Lin, CW and Tsuchida, S and Lin, S and Berndt, C and Chan, TY},
title = {Munidopsis lauensis Baba &amp; de Saint Laurent, 1992 (Decapoda, Anomura, Munidopsidae), a newly recorded squat lobster from a cold seep in Taiwan.},
journal = {Zootaxa},
volume = {3737},
number = {},
pages = {92-96},
doi = {10.11646/zootaxa.3737.1.8},
pmid = {25112740},
issn = {1175-5326},
mesh = {Animal Distribution ; Animal Shells ; Animals ; *Decapoda ; Eye ; Taiwan ; },
abstract = {The squat lobster, Munidopsis lauensis Baba &amp; de Saint Laurent, 1992, is recorded from Taiwan for the first time. This species was previously known only from deep-sea hydrothermal vents in the South-West Pacific but it was now found at a deep-sea cold seep site off southwestern Taiwan. The identity of the Taiwanese material is confirmed by comparison of sequences from the barcoding gene COI. Munidopsis lauensis can be easily separated from other congeners in Taiwanese waters by the eyes bearing a strong mesiodorsal spine and a small mesioventral spine, smooth carapace, fingers of the cheliped distally spooned and fixed finger without a denticulate carina on the distolateral margin. The discovery of this species in Taiwan increases the Munidopsis fauna of the island to 38 species. A color photograph and line drawings illustrating distinctive characters are provided for the Taiwanese material.},
}
@article {pmid24758794,
year = {2013},
author = {Križanauskienė, A and Iezhova, TA and Sehgal, RN and Carlson, JS and Palinauskas, V and Bensch, S and Valkiūnas, G},
title = {Molecular characterization of Haemoproteus sacharovi (Haemosporida, Haemoproteidae), a common parasite of columbiform birds, with remarks on classification of haemoproteids of doves and pigeons.},
journal = {Zootaxa},
volume = {3616},
number = {},
pages = {85-94},
doi = {10.11646/zootaxa.3616.1.7},
pmid = {24758794},
issn = {1175-5326},
mesh = {Animals ; Bird Diseases/*parasitology ; Columbidae ; DNA, Protozoan/genetics ; Haemosporida/*classification/genetics/growth &amp; development/*isolation &amp; purification ; Molecular Sequence Data ; Protozoan Infections, Animal/*parasitology ; },
abstract = {Haemoproteus (Haemosporida, Haemoproteidae) is the largest genus of avian haemosporidian parasites, some species of which cause lethal diseases in birds. Subgenera Parahaemoproteus and Haemoproteus are usually accepted in this genus; these parasites are transmitted by biting midges (Ceratopogonidae) and hippoboscid flies (Hippoboscidae), respectively. As of yet, species of Parahaemoproteus have not been reported to infect doves and pigeons (Columbiformes), parasites of these birds have not been reported to be transmitted by biting midges (Ceratopogonidae). Applying microscopy and PCR based methods, we identified mitochondrial cytochrome b (cyt b) sequences of Haemoproteus sacharovi, a wide-spread parasite of doves and pigeons. Phylogenetic relationships of dove haemoproteids, which traditionally have been classified in the subgenus Haemoproteus, showed that H. sacharovi and H. turtur, common parasites of doves, branch in the clade with Parahaemoproteus species, indicating that these haemoproteids may belong to this subgenus and are likely transmitted by biting midges. This study provides barcodes for H. sacharovi, clarifies the taxonomic positions of H. sacharovi and H. turtur, and indicates directions for development of classification of avian haemoproteid species. Our analysis shows that the current subgeneric classification of avian haemoproteids is generally effective, but the position of some species may need to be revised.},
}
@article {pmid24723780,
year = {2013},
author = {Miller, JA and Belgers, JD and Beentjes, KK and Zwakhals, K and van Helsdingen, P},
title = {Spider hosts (Arachnida, Araneae) and wasp parasitoids (Insecta, Hymenoptera, Ichneumonidae, Ephialtini) matched using DNA barcodes.},
journal = {Biodiversity data journal},
volume = {},
number = {1},
pages = {e992},
pmid = {24723780},
issn = {1314-2828},
abstract = {The study of parasitoids and their hosts suffers from a lack of reliable taxonomic data. We use a combination of morphological characters and DNA sequences to produce taxonomic determinations that can be verified with reference to specimens in an accessible collection and DNA barcode sequences posted to the Barcode of Life database (BOLD). We demonstrate that DNA can be successfully extracted from consumed host spiders and the shed pupal case of a wasp using non-destructive methods. We found Acrodactylaquadrisculpta to be a parasitoid of Tetragnathamontana; Zatypotapercontatoria and Zatypotabohemani both are parasitoids of Neottiurabimaculata. Zatypotaanomala is a parasitoid of an as yet unidentified host in the family Dictynidae, but the host species may be possible to identify in the future as the library of reference sequences on BOLD continues to grow. The study of parasitoids and their hosts traditionally requires specialized knowledge and techniques, and accumulating data is a slow process. DNA barcoding could allow more professional and amateur naturalists to contribute data to this field of study. A publication venue dedicated to aggregating datasets of all sizes online is well suited to this model of distributed science.},
}
@article {pmid24723774,
year = {2013},
author = {Candek, K and Gregorič, M and Kostanjšek, R and Frick, H and Kropf, C and Kuntner, M},
title = {Targeting a portion of central European spider diversity for permanent preservation.},
journal = {Biodiversity data journal},
volume = {},
number = {1},
pages = {e980},
pmid = {24723774},
issn = {1314-2828},
abstract = {Given the limited success of past and current conservation efforts, an alternative approach is to preserve tissues and genomes of targeted organisms in cryobanks to make them accessible for future generations. Our pilot preservation project aimed to obtain, expertly identify, and permanently preserve a quarter of the known spider species diversity shared between Slovenia and Switzerland, estimated at 275 species. We here report on the faunistic part of this project, which resulted in 324 species (227 in Slovenia, 143 in Switzerland) for which identification was reasonably established. This material is now preserved in cryobanks, is being processed for DNA barcoding, and is available for genomic studies.},
}
@article {pmid24723752,
year = {2013},
author = {Stoev, P and Komerički, A and Akkari, N and Liu, S and Zhou, X and Weigand, AM and Hostens, J and Hunter, CI and Edmunds, SC and Porco, D and Zapparoli, M and Georgiev, T and Mietchen, D and Roberts, D and Faulwetter, S and Smith, V and Penev, L},
title = {Eupolybothrus cavernicolus Komerički &amp; Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data.},
journal = {Biodiversity data journal},
volume = {},
number = {1},
pages = {e1013},
pmid = {24723752},
issn = {1314-2828},
abstract = {We demonstrate how a classical taxonomic description of a new species can be enhanced by applying new generation molecular methods, and novel computing and imaging technologies. A cave-dwelling centipede, Eupolybothrus cavernicolus Komerički &amp; Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae), found in a remote karst region in Knin, Croatia, is the first eukaryotic species for which, in addition to the traditional morphological description, we provide a fully sequenced transcriptome, a DNA barcode, detailed anatomical X-ray microtomography (micro-CT) scans, and a movie of the living specimen to document important traits of its ex-situ behaviour. By employing micro-CT scanning in a new species for the first time, we create a high-resolution morphological and anatomical dataset that allows virtual reconstructions of the specimen and subsequent interactive manipulation to test the recently introduced 'cybertype' notion. In addition, the transcriptome was recorded with a total of 67,785 scaffolds, having an average length of 812 bp and N50 of 1,448 bp (see GigaDB). Subsequent annotation of 22,866 scaffolds was conducted by tracing homologs against current available databases, including Nr, SwissProt and COG. This pilot project illustrates a workflow of producing, storing, publishing and disseminating large data sets associated with a description of a new taxon. All data have been deposited in publicly accessible repositories, such as GigaScience GigaDB, NCBI, BOLD, Morphbank and Morphosource, and the respective open licenses used ensure their accessibility and re-usability.},
}
@article {pmid24699621,
year = {2013},
author = {Aguiar, AP},
title = {Publishing large DNA sequence data in reduced spaces and lasting formats, in paper or PDF.},
journal = {Zootaxa},
volume = {3609},
number = {},
pages = {593-600},
doi = {10.11646/zootaxa.3609.6.5},
pmid = {24699621},
issn = {1175-5326},
mesh = {Animals ; *Base Sequence ; Data Compression/*methods ; *Databases, Genetic ; Internet ; *Molecular Sequence Data ; *Publishing ; Software ; },
abstract = {Scientific publications carry a practical moral duty: they must last. Along that line of thinking, some methods are proposed to allow economically and structurally viable publication of DNA sequence data of any size in printed matter and PDFs. The proposal is primarily aimed at contributing for preserving information for the future, while allowing authors to avoid information splitting and complement storage ex situ, that is, in server machines, outside the publication proper. The technique may also help to solve the impasse between the ICZN Code requirement that a new nomen be associated to diagnostic characters for the taxon vs. the phylogenetic definition of taxa, based on cladograms only: sequence data are characters, and can now be easily and comfortably included in taxonomic publications, with direct textual mention to their diagnostic sections. The compression level achieved allows the inclusion of all wanted DNA or RNA sequences in the same printed matter or PDF publications where the sequences are cited and discussed. Reduced font sizes, invisible fonts, and original 2D black &amp; white and color barcodes are illustrated and briefly discussed. The level of data compression achieved can allow each full page of sequence data, or about 5000 characters, to be precisely coded into a color barcode as small as a square of 1.5 mm. A practical example is provided with Taeniogonalos woodorum Smith (Hymenoptera, Trigonalidae). Free software to generate publishable barcodes from txt or FASTA files is provided at www.systaxon.ufes.br/dna.},
}
@article {pmid24614457,
year = {2013},
author = {Lis, B and Lis, JA and Ziaja, DJ},
title = {Identification of the nymphal stages of two European seed bugs, L. equestris and L. simulans (Hemiptera: Heteroptera: Lygaeidae), using DNA barcodes.},
journal = {Zootaxa},
volume = {3608},
number = {},
pages = {147-150},
doi = {10.11646/zootaxa.3608.2.5},
pmid = {24614457},
issn = {1175-5326},
mesh = {Animals ; Czech Republic ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Heteroptera/*classification/genetics/*growth &amp; development ; Molecular Sequence Data ; Nymph/classification/genetics/growth &amp; development ; Phylogeny ; Poland ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
}
@article {pmid24614000,
year = {2013},
author = {Shen, HP and Chang, CH and Li, CL and Chih, WJ and Chen, JH},
title = {Four new earthworm species of the genus Amynthas (Oligochaeta: Megascolecidae) from Kinmen, Taiwan.},
journal = {Zootaxa},
volume = {3599},
number = {},
pages = {471-482},
doi = {10.11646/zootaxa.3599.5.4},
pmid = {24614000},
issn = {1175-5326},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Hermaphroditic Organisms/*classification ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; Oligochaeta/anatomy &amp; histology/*classification/genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Taiwan ; },
abstract = {Four new species of terrestrial earthworms belonging to the genus Amynthas were collected on the islands of Kinmen and Lieyu, Taiwan from March to November, 2008. They are Amynthas kinmenensis sp. nov., Amynthas wuhumontis sp. nov., Amynthas wujhouensis sp. nov., and Amynthas taiwumontis sp. nov. Amynthas kinmenensis sp. nov. is quadrithecal and is the most abundant earthworm widely distributed on the main island of Kinmen. It has numerous small genital papillae and is closely related to Amynthas polyglandularis (Tsai, 1964) from northern Taiwan. Amynthas wuhumontis sp. nov. is sexthecal and is distributed only in areas around Mt. Wuhu and Mt. Taiwu in east Kinmen. It has male pores each surrounded by three genital papillae: one anterior, one posterior and one medial. Amynthas wujhouensis sp. nov. and Amynthas taiwumontis sp. nov. are octothecal. The former has a sporadic distribution in Kinmen while the latter was only found in areas around Mt. Taiwu. Amynthas wujhouensis sp. nov. has a pair of large genital papillae closely adjacent to the crescent or semicircular shaped male porophores in XVIII. Amynthas taiwumontis sp. nov. has simple male pore structure and no genital papillae or genital markings. DNA barcodes (the 5' end sequences of the mitochondrial cytochrome c oxidase subunit 1 gene) from type specimens and other materials of the first three species are also reported.},
}
@article {pmid25587492,
year = {2012},
author = {Valdivia-Granda, WA},
title = {Biodefense Oriented Genomic-Based Pathogen Classification Systems: Challenges and Opportunities.},
journal = {Journal of bioterrorism &amp; biodefense},
volume = {3},
number = {1},
pages = {1000113},
pmid = {25587492},
issn = {2157-2526},
support = {P01 AG000001/AG/NIA NIH HHS/United States ; R13 ES013910/ES/NIEHS NIH HHS/United States ; U54 AI057158/AI/NIAID NIH HHS/United States ; },
abstract = {Countermeasures that will effectively prevent or diminish the impact of a biological attack will depend on the rapid and accurate generation and analysis of genomic information. Because of their increasing level of sensitivity, rapidly decreasing cost, and their ability to effectively interrogate the genomes of previously unknown organisms, Next Generation Sequencing (NGS) technologies are revolutionizing the biological sciences. However, the exponential accumulation microbial data is equally outpacing the computational performance of existing analytical tools in their ability to translate DNA information into reliable detection, prophylactic and therapeutic countermeasures. It is now evident that the bottleneck for next-generation sequence data analysis will not be solved simply by scaling up our computational resources, but rather accomplished by implementing novel biodefense-oriented algorithms that overcome exiting vulnerabilities of speed, sensitivity and accuracy. Considering these circumstances, this document highlights the challenges and opportunities that biodefense stakeholders must consider in order to exploit more efficiently genomic information and translate this data into integrated countermeasures. The document overviews different genome analysis methods and explains concepts of DNA fingerprints, motif fingerprints, genomic barcodes and genomic signatures. A series of recommendations to promote genomics and bioinformatics as an effective form of deterrence and a valuable scientific platform for rapid technological insertion of detection, prophylactic, therapeutic countermeasures are discussed.},
}
@article {pmid24849750,
year = {2012},
author = {Maya-Soriano, MJ and Holt, WV and Lloyd, RE},
title = {Biobanked Amphibian Samples Confirmed To Species Level Using 16S rRNA DNA Barcodes.},
journal = {Biopreservation and biobanking},
volume = {10},
number = {1},
pages = {22-28},
doi = {10.1089/bio.2011.0036},
pmid = {24849750},
issn = {1947-5535},
abstract = {The DNA barcoding technique is often used as a tool for validating species identity in biobanks. In the case of amphibians, the mitochondrial DNA (mtDNA) 16S ribosomal RNA (rRNA) gene is reported to fulfill the requirements of a universal DNA barcoding marker. The 16S primers are designed to specifically bind to the 16S rRNA gene, which is a very well-conserved mtDNA gene sequence in amphibians. DNA was extracted from thirteen known but different species of amphibians within the Zoological Society of London/Amphibian Ark's cryobank. After this, the DNA was amplified and analyzed by (1) the traditional DNA barcoding procedure that involves conventional polymerase chain reaction (PCR) and DNA sequencing and (2) a novel procedure, involving real-time PCR and melting temperatures. Both procedures used the same 16S primers. Successful DNA amplification and validation to the species or genus level was achieved in 10 out the 13 cases using the traditional approach. Nevertheless, after real-time PCR and melting temperature analysis, some variability was found between Common Frog samples but more concerning, the same melting temperature was recorded in unrelated species (Common Toad, Common Frog and Amazon Milk Frog), despite their 16S sequences exhibiting a high degree of variability. We conclude that traditional DNA barcoding using 16S rRNA sequences is suitable for validating the specific identity of amphibian samples within biobanks and that modification of the current 16S real-time PCR and melting temperature analysis is required before it can be employed as a cheaper and faster alternative.},
}
@article {pmid24832523,
year = {2012},
author = {Dodt, M and Roehr, JT and Ahmed, R and Dieterich, C},
title = {FLEXBAR-Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms.},
journal = {Biology},
volume = {1},
number = {3},
pages = {895-905},
pmid = {24832523},
issn = {2079-7737},
abstract = {Quantitative and systems biology approaches benefit from the unprecedented depth of next-generation sequencing. A typical experiment yields millions of short reads, which oftentimes carry particular sequence tags. These tags may be: (a) specific to the sequencing platform and library construction method (e.g., adapter sequences); (b) have been introduced by experimental design (e.g., sample barcodes); or (c) constitute some biological signal (e.g., splice leader sequences in nematodes). Our software FLEXBAR enables accurate recognition, sorting and trimming of sequence tags with maximal flexibility, based on exact overlap sequence alignment. The software supports data formats from all current sequencing platforms, including color-space reads. FLEXBAR maintains read pairings and processes separate barcode reads on demand. Our software facilitates the fine-grained adjustment of sequence tag detection parameters and search regions. FLEXBAR is a multi-threaded software and combines speed with precision. Even complex read processing scenarios might be executed with a single command line call. We demonstrate the utility of the software in terms of read mapping applications, library demultiplexing and splice leader detection. FLEXBAR and additional information is available for academic use from the website: http://sourceforge.net/projects/flexbar/.},
}
@article {pmid23459182,
year = {2012},
author = {Yáñez-Rivera, B and Carrera-Parra, LF},
title = {Reestablishment of Notopygos megalops McIntosh, description of N. caribea sp. n. from the Greater Caribbean and barcoding of "amphiamerican" Notopygos species (Annelida, Amphinomidae).},
journal = {ZooKeys},
volume = {},
number = {223},
pages = {69-84},
pmid = {23459182},
issn = {1313-2970},
abstract = {The species of the genus Notopygos Grube, 1855 are characterized by an ovate body, a prominent caruncle with three lobes, dendritic branchiae, and double dorsal cirri. Twenty-two species belonging to Notopygos have been described, mostly from the Indo-Pacific region. In America, few species are frequently recorded: Notopygos crinita Grube, 1855 from St. Helena Island (Atlantic) and Notopygos ornata Grube and Ørsted in Grube 1857 from Costa Rica (Pacific). Notopygos crinita is a widely distributed species in the Western Atlantic with additional reports in the Mediterranean Sea (as a questionable alien species) and in the Pacific Ocean. However, only the genus features have been considered, consequently some records could be misidentifications. During a revision of materials from collections and the barcode project, 'Mexican Barcode of Life, MEXBOL', we found specimens of Notopygos megalops and an undescribed species from reef zones in the Caribbean; the former had been considered a junior synonym of Notopygos crinita. Herein, Notopygos megalops is reestablished and Notopygos caribeasp. n. is described. A morphological and DNA barcode approach was used to explain the records of Notopygos ornata in the Atlantic and to show the differences with the new species, since both species share features such as complex pigmentation patterns, and circular projections in the median lobe of the caruncle.},
}
@article {pmid25214135,
year = {2011},
author = {Kumar, S and Kahlon, T and Chaudhary, S},
title = {A rapid screening for adulterants in olive oil using DNA barcodes.},
journal = {Food chemistry},
volume = {127},
number = {3},
pages = {1335-1341},
doi = {10.1016/j.foodchem.2011.01.094},
pmid = {25214135},
issn = {0308-8146},
abstract = {A distinctive methodology is developed to trace out the mixing into olive oil, which is marketed every year with 20% or more fraudulent oils. Such adulteration has been difficult to differentiate using fatty acid analysis and other available current techniques, as chemically fatty acids are same regardless of their source. The total genomic DNA isolated from olive oil, contaminated with canola and sunflower was analysed for single nucleotide polymorphism (SNP) variation in noncoding spacer region between psbA-trnH and partial coding region of matK of plastid genome. These DNA regions were amplified by PCR using specific primers and resulting DNA sequences were matched to the predetermined consensus DNA barcode sequences of canola and sunflower for discerning the contaminations in olive oil samples. The matching of an adulterant DNA sequence with their respective DNA barcode revealed the mixing of canola and sunflower oil into olive is simpler way and the combined approach of molecular biology and bioinformatics technology can be used as an inexpensive method for ensuring the purity of olive. This plastid based molecular DNA technology can be used for rapid detection of adulteration easily up to 5% in olive oil.},
}
@article {pmid23479788,
year = {2011},
author = {Nolan, MJ and Jex, AR and Upcroft, JA and Upcroft, P and Gasser, RB},
title = {Barcoding of Giardia duodenalis isolates and derived lines from an established cryobank by a mutation scanning-based approach.},
journal = {Electrophoresis},
volume = {32},
number = {16},
pages = {2075-2090},
pmid = {23479788},
issn = {1522-2683},
support = {U01 AI075527/AI/NIAID NIH HHS/United States ; AI75527/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Cats ; Cattle ; DNA Fingerprinting ; Electronic Data Processing ; Giardia lamblia/classification/*genetics/isolation &amp; purification ; Giardiasis/*parasitology/*veterinary ; Humans ; Molecular Sequence Data ; Molecular Typing/methods ; Mutation ; Phylogeny ; Polymorphism, Single-Stranded Conformational ; Sequence Analysis, DNA/methods ; },
abstract = {We barcoded 25 in vitro isolates (representing 92 samples) of Giardia duodenalis from humans and other animals, which have been assembled by the Upcroft team at the Queensland Institute of Medical Research over a period of almost three decades. We used mutation scanning-coupled sequencing of loci in the triosephosphate isomerase, glutamate dehydrogenase and β-giardin genes, combined with phylogenetic analysis, to genetically characterise them. Specifically, the isolates (n514) of G. duodenalis from humans from Australia (AD113; BRIS/83/HEPU/106; BRIS/87/HEPU/713; BRIS/89/HEPU/1003; BRIS/92/HEPU/1541; BRIS/92/HEPU/1590; BRIS/92/HEPU/2443; BRIS/93/HEPU/1706), Malaysia (KL/92/IMR/1106) and Afghanistan (WB), a cat from Australia (BAC2), a sheep from Canada (OAS1) and a sulphur-crested cockatoo from Australia (BRIS/95/HEPU/2041) represented assemblage A (sub-assemblage AI-1, AI-2 or AII-2); isolates (n510) from humans from Australia (BRIS/91/HEPU/1279; BRIS/92/HEPU/2342; BRIS/92/HEPU/2348; BRIS/93/HEPU/1638; BRIS/93/HEPU/1653; BRIS/93/HEPU/1705; BRIS/93/HEPU/1718; BRIS/93/HEPU/1727), Papua New Guinea (BRIS/92/HEPU/1487) and Canada (H7) represented assemblage B (sub-assemblage BIV) and an isolate from cattle from Australia (BRIS/92/HEPU/1709) had a match to assemblage E. Isolate BRIS/90/HEPU/1229 from a human from Australia was shown to represent a mixed population of assemblages A and B. These barcoded isolates (including stocks and derived lines) now allow direct comparisons of experimental data among laboratories and represent a massive resource for transcriptomic, proteomic, metabolic and functional genomic studies using advanced molecular technologies.},
}
@article {pmid24260629,
year = {2011},
author = {Sourakov, A and Zakharov, EV},
title = {"Darwin's butterflies"? DNA barcoding and the radiation of the endemic Caribbean butterfly genus Calisto (Lepidoptera, Nymphalidae, Satyrinae).},
journal = {Comparative cytogenetics},
volume = {5},
number = {3},
pages = {191-210},
pmid = {24260629},
issn = {1993-0771},
abstract = {The genus Calisto Hübner, 1823 is the only member of the diverse, global subfamily Satyrinae found in the West Indies, and by far the richest endemic Caribbean butterfly radiation. Calisto species occupy an extremely diverse array of habitats, suggestive of adaptive radiation on the scale of other classic examples such as the Galápagos or Darwin's finches. However, a reliable species classification is a key requisite before further evolutionary or ecological research. An analysis of 111 DNA 'barcodes' (655 bp of the mitochondrial gene COI) from 29 putative Calisto species represented by 31 putative taxa was therefore conducted to elucidate taxonomic relationships among these often highly cryptic and confusing taxa. The sympatric, morphologically and ecologically similar taxa Calisto confusa Lathy, 1899 and Calisto confusa debarriera Clench, 1943 proved to be extremely divergent, and we therefore recognize Calisto debarriera stat. n. as a distinct species, with Calisto neiba Schwartz &amp; Gali, 1984 as a junior synonym syn. n. Species status of certain allopatric, morphologically similar sister species has been confirmed: Calisto hysius (Godart, 1824) (including its subspecies Calisto hysius aleucosticha Correa et Schwartz, 1986, stat. n.), and its former subspecies Calisto batesi Michener, 1943 showed a high degree of divergence (above 6%) and should be considered separate species. Calisto lyceius Bates, 1935/Calisto crypta Gali, 1985/Calisto franciscoi Gali, 1985 complex, also showed a high degree of divergence (above 6%), confirming the species status of these taxa. In contrast, our data suggest that the Calisto grannus Bates, 1939 species complex (including Calisto grannus dilemma González, 1987, Calisto grannus amazona González, 1987, stat. n., Calisto grannus micrommata Schwartz &amp; Gali, 1984, stat. n., Calisto grannus dystacta González, 1987, stat. n., Calisto grannus phoinix González, 1987, stat. n., Calisto grannus sommeri Schwartz &amp; Gali, 1984, stat. n., and Calisto grannus micheneri Clench, 1944, stat. n.) should be treated as a single polytypic species, as genetic divergence among sampled populations representing these taxa is low (and stable morphological apomorphies are absent). A widely-distributed pest of sugar cane, Calisto pulchella Lathy, 1899 showed higher diversification among isolated populations (3.5%) than expected, hence supporting former separation of this species into two taxa (pulchella and darlingtoni Clench, 1943), of which the latter might prove to be a separate species rather than subspecies. The taxonomic revisions presented here result in Calisto now containing 34 species and 17 subspecies. Three species endemic to islands other than Hispaniola appear to be derived lineages of various Hispaniolan clades, indicating ancient dispersal events from Hispaniola to Puerto Rico, Cuba, and Jamaica. Overall, the degree of intrageneric and intraspecific divergence within Calisto suggests a long and continuous diversification period of 4-8 Myr. The maximum divergence within the genus (ca. 13.3%) is almost equivalent to the maximum divergence of Calisto from the distant pronophiline relative Auca Hayward, 1953 from the southern Andes (14.1%) and from the presumed closest relative Eretris Thieme, 1905 (14.4%), suggesting that the genus began to diversify soon after its split from its continental sister taxon. In general, this 'barcode' divergence corresponds to the high degree of morphological and ecological variation found among major lineages within the genus.},
}
@article {pmid24391248,
year = {2010},
author = {Pereira, TJ and Fonseca, G and Mundo-Ocampo, M and Guilherme, BC and Rocha-Olivares, A},
title = {Diversity of free-living marine nematodes (Enoplida) from Baja California assessed by integrative taxonomy.},
journal = {Marine biology},
volume = {157},
number = {8},
pages = {1665-1678},
pmid = {24391248},
issn = {0025-3162},
abstract = {We used morphological and molecular approaches to evaluate the diversity of free-living marine nematodes (order Enoplida) at four coastal sites in the Gulf of California and three on the Pacific coast of Baja California, Mexico. We identified 22 morphological species belonging to six families, of which Thoracostomopsidae and Oncholaimidae were the most diverse. The genus Mesacanthion (Thoracostomopsidae) was the most widespread and diverse. Five allopatric species, genetically and morphologically differentiated, were found in two localities in the Gulf of California (M. sp1 and M. sp2) and three in the Pacific coast (M. sp3, M. sp4 and M. sp5). Overall, we produced 19 and 20 sequences for the 18S and 28S genes, respectively. Neither gene displayed intraspecific polymorphisms, which allowed us to establish that some morphological variation was likely either ontogenetic or due to phenotypic plasticity. Although 18S and 28S phylogenies were topologically congruent (incongruence length difference test, P > 0.05), divergences between species were much higher in the 28S gene. Moreover, this gene possessed a stronger phylogenetic signal to resolve relationships involving Rhabdodemania and Bathylaimus. On the other hand, the close relationship of Pareurystomina (Enchilidiidae) with oncholaimids warrants further study. The 28S sequences (D2D3 domain) may be better suited for DNA barcoding of marine nematodes than those from the 18S rDNA, particularly for differentiating closely related or cryptic species. Finally, our results underline the relevance of adopting an integrative approach encompassing morphological and molecular analyses to improve the assessment of marine nematode diversity and advance their taxonomy.},
}
@article {pmid23965368,
year = {2010},
author = {McElhiney, LF},
title = {Unit-dose packaging and repackaging of solid and liquid dosage forms in an institutional setting.},
journal = {International journal of pharmaceutical compounding},
volume = {14},
number = {1},
pages = {32-38},
pmid = {23965368},
issn = {1092-4221},
abstract = {Although repackaging drugs into unit-dose packages can be time consuming and labor intensive, it can significantly reduce medication errors and improve patient safety in health systems. Pharmacists can play a vital role in choosing appropriate repackaging equipment and labeling programs that are compatible with the health system's Bar-Code-Enabled Medication Administration system. They can develop policies and procedures for repackaging drugs and ensuring that all medications have scan-able barcodes or identifiers. Pharmacists can also develop a quality-assurance program to ensure that the Bar-Code-Enabled Medication Administration system is effective and that the unit-dose packaging operations meet United States Pharmacopeial Convention standards and other professional guidelines.},
}
@article {pmid23653719,
year = {2010},
author = {Dunbar, D and Nielsen, C},
title = {Development of a DNA Bar-coding Project as a Biology Laboratory Module.},
journal = {Journal of microbiology &amp; biology education},
volume = {11},
number = {2},
pages = {160-161},
pmid = {23653719},
issn = {1935-7877},
}
@article {pmid23616837,
year = {2010},
author = {T, H and Heelon, M and Siano, B and Douglass, L and Liebro, P and Spath, B and Kudler, N and Kerr, G},
title = {Medication safety improves after implementation of positive patient identification.},
journal = {Applied clinical informatics},
volume = {1},
number = {3},
pages = {213-220},
pmid = {23616837},
issn = {1869-0327},
abstract = {OBJECTIVE: To report the incidence and severity of medication safety events before and after initiation of barcode scanning for positive patient identification (PPID) in a large teaching hospital.<br><br>METHODS: Retrospective analysis of data from an existing safety reporting system with anonymous and non-punitive self-reporting. Medication safety events were categorized as "near-miss" (unsafe conditions or caught before reaching the patient) or reaching the patient, with requisite additional monitoring or treatment. Baseline and post-PPID implementation data on events per 1,000,000 drug administrations were compared by chi-square with p<0.05 considered significant.<br><br>RESULTS: An average of 510,541 doses were dispensed each month in 2008. Total self-reported medication errors initially increased from 20 per million doses dispensed pre-barcoding (first quarter 2008) to 38 per million doses dispensed immediately post-intervention (last quarter 2008), but errors reaching the patient decreased from 3.26 per million to 0.8 per million despite the increase in "near-misses". A number of process issues were identified and improved, including additional training and equipment, instituting ParX scanning when filling Pyxis machines, and lobbying for a manufacturing change in how bar codes were printed on bags of intravenous solutions to reduce scanning failures.<br><br>CONCLUSION: Introduction of barcoding of medications and patient wristbands reduced serious medication dispensing errors reaching the patient, but temporarily increased the number of "near-miss" situations reported. Overall patient safety improved with the barcoding and positive patient identification initiative. These results have been sustained during the 18 months following full implementation.},
}
@article {pmid23969927,
year = {2008},
author = {Bailey, E},
title = {Symbols: historic and current uses.},
journal = {International journal of pharmaceutical compounding},
volume = {12},
number = {6},
pages = {505-507},
pmid = {23969927},
issn = {1092-4221},
abstract = {From hieroglyphs to barcodes, symbols have been used throughout history. Symbols can be observed on traffic signs, warning signs that are affixed to building fronts, doors of public restrooms to show gender-specific usage, and caution signs on caustic or poisonous chemicals; even Braille, a system of writing and printing for the blind, is a symbol form. This article includes a brief discussion on the psychology of symbols, history of symbols, symbols used by alchemists and pharmacists, and the current use of symbols.},
}
@article {pmid23458744,
year = {2013},
author = {Jiang, F and Li, ZH and Deng, YL and Wu, JJ and Liu, RS and Buahom, N},
title = {Rapid diagnosis of the economically important fruit fly, Bactrocera correcta (Diptera: Tephritidae) based on a species-specific barcoding cytochrome oxidase I marker.},
journal = {Bulletin of entomological research},
volume = {103},
number = {3},
pages = {363-371},
doi = {10.1017/S0007485312000806},
pmid = {23458744},
issn = {1475-2670},
mesh = {Animal Distribution ; Animals ; Asia, Southeastern ; Base Sequence ; China ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Electron Transport Complex IV/*genetics ; Genetic Markers/*genetics ; Geographic Information Systems ; *Introduced Species ; Life Cycle Stages/genetics ; Molecular Sequence Data ; Polymerase Chain Reaction/methods ; Sensitivity and Specificity ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; Tephritidae/*genetics/growth &amp; development ; },
abstract = {The guava fruit fly, Bactrocera correcta (Bezzi) (Diptera: Tephritidae), is an invasive pest of fruit and vegetable crops that primarily inhabits Southeast Asia and which has the potential to become a major threat within both the Oriental and Australian oceanic regions as well as California and Florida. In light of the threat posed, it is important to develop a rapid, accurate and reliable method to identify B. correcta in quarantine work in order to provide an early warning to prevent its widespread invasion. In the present study, we describe a species-specific polymerase chain reaction assay for the diagnosis of B. correcta using mitochondrial DNA cytochrome oxidase I (mtDNA COI) barcoding genes. A B. correcta-specific primer pair was designed according to variations in the mtDNA COI barcode sequences among 14 fruit fly species. The specificity and sensitivity of the B. correcta-specific primer pair was tested based on the presence or absence of a band in the gel profile. A pair of species-specific B. correcta primers was successfully designed and named BCOR-F/BCOR-R. An ∼280 bp fragment was amplified from specimens belonging to 17 geographical populations and four life stages of B. correcta, while no such diagnostic bands were present in any of the 14 other related fruit fly species examined. Sensitivity test results demonstrated that successful amplification can be obtained with as little as 1 ng μl[-1] of template DNA. The species-specific PCR analysis was able to successfully diagnose B. correcta, even in immature life stages, and from adult body parts. This method proved to be a robust single-step molecular technique for the diagnosis of B. correcta with respect to potential plant quarantine.},
}
@article {pmid23458029,
year = {2013},
author = {Eurlings, MC and Lens, F and Pakusza, C and Peelen, T and Wieringa, JJ and Gravendeel, B},
title = {Forensic identification of Indian snakeroot (Rauvolfia serpentina Benth. ex Kurz) using DNA barcoding.},
journal = {Journal of forensic sciences},
volume = {58},
number = {3},
pages = {822-830},
doi = {10.1111/1556-4029.12072},
pmid = {23458029},
issn = {1556-4029},
mesh = {Commerce/legislation &amp; jurisprudence ; Crime/legislation &amp; jurisprudence ; *DNA Barcoding, Taxonomic ; DNA Degradation, Necrotic ; DNA, Chloroplast/*genetics ; Electrophoresis, Agar Gel ; Endangered Species ; Humans ; Introns ; Polymerase Chain Reaction ; Rauwolfia/*genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; },
abstract = {Indian snakeroot (Rauvolfia serpentina) is a valuable forest product, root extracts of which are used as an antihypertensive drug. Increasing demand led to overharvesting in the wild. Control of international trade is hampered by the inability to identify root samples to the species level. We therefore evaluated the potential of molecular identification by searching for species-specific DNA polymorphisms. We found two species-specific indels in the rps16 intron region for R. serpentina. Our DNA barcoding method was tested for its specificity, reproducibility, sensitivity and stability. We included samples of various tissues and ages, which had been treated differently for preservation. DNA extractions were tested in a range of amplification settings and dilutions. Species-specific rps16 intron sequences were obtained from 79 herbarium accessions and one confiscated root, encompassing 39 different species. Our results demonstrate that molecular analysis provides new perspectives for forensic identification of Indian snakeroot.},
}
@article {pmid23457606,
year = {2013},
author = {Mao, F and Olman, V and Wang, Y and Xu, Y},
title = {Barcode server: a visualization-based genome analysis system.},
journal = {PloS one},
volume = {8},
number = {2},
pages = {e56726},
pmid = {23457606},
issn = {1932-6203},
mesh = {Algorithms ; Cluster Analysis ; *Computer Graphics ; Data Mining ; Escherichia coli K12/genetics ; Escherichia coli O157/genetics ; Genomic Islands/genetics ; Genomics/*methods ; Metagenomics ; Sequence Analysis ; *Software ; },
abstract = {We have previously developed a computational method for representing a genome as a barcode image, which makes various genomic features visually apparent. We have demonstrated that this visual capability has made some challenging genome analysis problems relatively easy to solve. We have applied this capability to a number of challenging problems, including (a) identification of horizontally transferred genes, (b) identification of genomic islands with special properties and (c) binning of metagenomic sequences, and achieved highly encouraging results. These application results inspired us to develop this barcode-based genome analysis server for public service, which supports the following capabilities: (a) calculation of the k-mer based barcode image for a provided DNA sequence; (b) detection of sequence fragments in a given genome with distinct barcodes from those of the majority of the genome, (c) clustering of provided DNA sequences into groups having similar barcodes; and (d) homology-based search using Blast against a genome database for any selected genomic regions deemed to have interesting barcodes. The barcode server provides a job management capability, allowing processing of a large number of analysis jobs for barcode-based comparative genome analyses. The barcode server is accessible at http://csbl1.bmb.uga.edu/Barcode.},
}
@article {pmid23452350,
year = {2013},
author = {D'Amato, ME and Alechine, E and Cloete, KW and Davison, S and Corach, D},
title = {Where is the game? Wild meat products authentication in South Africa: a case study.},
journal = {Investigative genetics},
volume = {4},
number = {1},
pages = {6},
pmid = {23452350},
issn = {2041-2223},
abstract = {BACKGROUND: Wild animals' meat is extensively consumed in South Africa, being obtained either from ranching, farming or hunting. To test the authenticity of the commercial labels of meat products in the local market, we obtained DNA sequence information from 146 samples (14 beef and 132 game labels) for barcoding cytochrome c oxidase subunit I and partial cytochrome b and mitochondrial fragments. The reliability of species assignments were evaluated using BLAST searches in GenBank, maximum likelihood phylogenetic analysis and the character-based method implemented in BLOG. The Kimura-2-parameter intra- and interspecific variation was evaluated for all matched species.<br><br>RESULTS: The combined application of similarity, phylogenetic and character-based methods proved successful in species identification. Game meat samples showed 76.5% substitution, no beef samples were substituted. The substitutions showed a variety of domestic species (cattle, horse, pig, lamb), common game species in the market (kudu, gemsbok, ostrich, impala, springbok), uncommon species in the market (giraffe, waterbuck, bushbuck, duiker, mountain zebra) and extra-continental species (kangaroo). The mountain zebra Equus zebra is an International Union for Conservation of Nature (IUCN) red listed species. We also detected Damaliscus pygargus, which is composed of two subspecies with one listed by IUCN as 'near threatened'; however, these mitochondrial fragments were insufficient to distinguish between the subspecies. The genetic distance between African ungulate species often overlaps with within-species distance in cases of recent speciation events, and strong phylogeographic structure determines within-species distances that are similar to the commonly accepted distances between species.<br><br>CONCLUSIONS: The reliability of commercial labeling of game meat in South Africa is very poor. The extensive substitution of wild game has important implications for conservation and commerce, and for the consumers making decisions on the basis of health, religious beliefs or personal choices.Distance would be a poor indicator for identification of African ungulates species. The efficiency of the character-based method is reliant upon availability of large reference data. The current higher availability of cytochrome b data would make this the marker of choice for African ungulates. The encountered problems of incomplete or erroneous information in databases are discussed.},
}
@article {pmid23448201,
year = {2013},
author = {Germain, JF and Chatot, C and Meusnier, I and Artige, E and Rasplus, JY and Cruaud, A},
title = {Molecular identification of Epitrix potato flea beetles (Coleoptera: Chrysomelidae) in Europe and North America.},
journal = {Bulletin of entomological research},
volume = {103},
number = {3},
pages = {354-362},
doi = {10.1017/S000748531200079X},
pmid = {23448201},
issn = {1475-2670},
mesh = {Animals ; Base Sequence ; Coleoptera/*genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Intergenic/genetics ; Electron Transport Complex IV/genetics ; Europe ; Genetic Markers/*genetics ; Insect Control/methods ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; North America ; Phylogeny ; Polymorphism, Restriction Fragment Length/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Solanum tuberosum/*parasitology ; Species Specificity ; },
abstract = {Epitrix species (Coleoptera: Chrysomelidae) feed mostly on plants from the family Solanaceae and some of them are major pests of potato crops. All Epitrix species are morphologically highly similar, which makes them difficult to identify and limits their study and management. Identification of species is mostly based on the observation of the genitalia and requires a high level of expertise. Here, we propose a tool to reliably identify all developmental stages of the most economically important Epitrix species feeding on potato in Europe and North America (Epitrix cucumeris, Epitrix similaris, Epitrix tuberis, Epitrix subcrinita and Epitrix hirtipennis). We first sequenced two DNA markers (mitochondrial cytochrome c oxidase I (COI) and nuclear internal transcribed spacer 2 (ITS2)) to test their effectiveness in differentiating among six Epitrix species (126 specimens). Morphospecies of Epitrix were well-differentiated by both DNA barcodes and no mitochondrial introgression was detected. Then, we developed an RFLP-based diagnostic method and showed that unambiguous species discrimination can be achieved by using the sole restriction enzyme TaqI on COI polymerase chain reaction products. The tool proposed here should improve our knowledge about Epitrix species biology, distribution and host range, three capacities that are particularly important in the detection and management of these pest species. Specifically, this tool should help prevent the introduction of E. tuberis and E. subcrinita in Europe and limit the spread of the recently introduced E. cucumeris and E. similaris, with minimal disruption to Solanaceae trade.},
}
@article {pmid23448061,
year = {2013},
author = {Barr, N and Ruiz-Arce, R and Obregón, O and De Leon, R and Foster, N and Reuter, C and Boratynski, T and Vacek, D},
title = {Molecular diagnosis of populational variants of Anthonomus grandis (Coleoptera: Curculionidae) in North America.},
journal = {Journal of economic entomology},
volume = {106},
number = {1},
pages = {437-449},
doi = {10.1603/ec12340},
pmid = {23448061},
issn = {0022-0493},
mesh = {Animals ; Base Sequence ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial ; *Gossypium ; Haplotypes ; Mexico ; Mississippi ; Molecular Sequence Data ; Nucleic Acid Amplification Techniques ; Phylogeny ; Southwestern United States ; Weevils/*classification/genetics ; },
abstract = {The utility of the cytochrome oxidase I (COI) DNA sequence used for DNA barcoding and a Sequence Characterized Amplified Region for diagnosing boll weevil, Anthonomus grandis Boheman, variants was evaluated. Maximum likelihood analysis of COI DNA sequences from 154 weevils collected from the United States and Mexico supports previous evidence for limited gene flow between weevil populations on wild cotton and commercial cotton in northern Mexico and southern United States. The wild cotton populations represent a variant of the species called the thurberia weevil, which is not regarded as a significant pest. The 31 boll weevil COI haplotypes observed in the study form two distinct haplogroups (A and B) that are supported by five fixed nucleotide differences and a phylogenetic analysis. Although wild and commercial cotton populations are closely associated with specific haplogroups, there is not a fixed difference between the thurberia weevil variant and other populations. The Sequence Characterized Amplified Region marker generated a larger number of inconclusive results than the COI gene but also supported evidence of shared genotypes between wild and commercial cotton weevil populations. These methods provide additional markers that can assist in the identification of pest weevil populations but not definitively diagnose samples.},
}
@article {pmid23448059,
year = {2013},
author = {Yang, Q and Zhao, S and Kucerová, Z and Stejskal, V and Opit, G and Qin, M and Cao, Y and Li, F and Li, Z},
title = {Validation of the 16S rDNA and COI DNA barcoding technique for rapid molecular identification of stored product psocids (Insecta: Psocodea: Liposcelididae).},
journal = {Journal of economic entomology},
volume = {106},
number = {1},
pages = {419-425},
doi = {10.1603/ec12163},
pmid = {23448059},
issn = {0022-0493},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Female ; Food Contamination ; Insecta/*classification/*genetics/ultrastructure ; Nymph ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {Psocids are serious storage pests, and their control is hampered by the fact that different species respond differently to insecticides used for the control of stored-product insect pests. Additionally, psocids of genus Liposcelis that are commonly associated with stored-products are difficult to identify using morphological characteristics. The goal of this study was to validate molecular identification of stored-product psocids of genus Liposcelis based on 16S rDNA and cytochrome oxidase I (COI) DNA barcoding. Unidentified liposcelids (Liposcelis DK) imported from Denmark to China were compared with 14 population samples of seven common species (L. bostrychophila, L. brunnea, L. corrodens, L. decolor, L. entomophila, L. mendax, and L. paeta). The explored species (DK) liposcelids shared >98% sequence similarity for both the 16S rDNA and COI genes with the reference L. corrodens samples (98.32 and 98.94% for 16S rDNA and COI, respectively). A neighbor-joining tree revealed that the explored DK sample and the reference L. corrodens samples belong to the same clade. These molecular results were verified by morphological identification of DK specimens, facilitated by SEM microphotography. The DNA barcoding method and the neighbor-joining phylogenetic analyses indicated that both the 16S rDNA and COI genes were suitable for Liposcelis species identification. DNA barcoding has great potential for use in fast and accurate liposcelid identification.},
}
@article {pmid23444796,
year = {2012},
author = {Błaszkowska, J and Wójcik, A},
title = {Current problems concerning parasitology and mycology with regard to diseases of the skin and its appendages.},
journal = {Annals of parasitology},
volume = {58},
number = {3},
pages = {111-123},
pmid = {23444796},
issn = {2299-0631},
mesh = {Animals ; Dermatomycoses/diagnosis/epidemiology/therapy/transmission ; Humans ; Mycoses/*diagnosis/epidemiology/*therapy/transmission ; Parasitic Diseases/*diagnosis/epidemiology/*therapy/transmission ; Zoonoses/microbiology/parasitology/transmission ; },
abstract = {Current issues concerning Parasitology and Mycology with regard to diseases of the skin and its appendages are presented. Aspects of diagnostics, clinical picture and therapy of skin and nail mycoses, as well as difficulties in the diagnosis and treatment of both native parasitoses (toxoplasmosis) and imported human tropical parasitoses (malaria, filariosis) have been emphasised. The clinical importance of environmental mould fungi in nosocomial infections and fungal meningitis, as well as selected properties of fungi isolated from patients with head and neck neoplasms treated by radiotherapy are discussed. Other mycological topics include the characteristics of newly-synthesized thiosemicarbazides and thiadiazoles as potential drugs against toxoplasmosis and their biological activity against Toxoplasma gondii tachyzoites, selected molecular mechanisms of resistance to azoles, Candida albicans strains and a new tool (barcoding DNA) for describing the biodiversity of potential allergenic molds. The importance of environmental factors in pathogenesis of mycoses and parasitoses is noted. The characteristics of pathogenic fungi isolated from natural ponds in Bialystok and potentially pathogenic yeast-like fungi isolated from children's recreation areas in Lodz are presented. The ongoing problem of anthropozoonoses is considered, as are the roles of stray cats and dogs in contaminating soil with the developing forms of intestinal parasites. The characteristics of the human microbiome, including population composition, activity and their importance in normal human physiology, are presented, as are the major goals of the Human Microbiome Project initiated by National Institutes of Health (NIH).},
}
@article {pmid23442684,
year = {2012},
author = {Cunha, SC and Faria, MA and Sousa, T and Nunes, E},
title = {Isoflavone determination in spontaneous legumes identified by DNA barcodes.},
journal = {Food chemistry},
volume = {134},
number = {4},
pages = {2262-2267},
doi = {10.1016/j.foodchem.2012.03.028},
pmid = {23442684},
issn = {1873-7072},
mesh = {DNA Barcoding, Taxonomic/methods ; DNA, Plant/genetics ; Fabaceae/*chemistry/*classification/genetics ; Isoflavones/*analysis ; Molecular Sequence Data ; Phylogeny ; Vegetables/*chemistry/*classification/genetics ; },
abstract = {Isoflavones have been associated with several health protective effects. In this work spontaneous legume plants were screened as putative sources of dietary isoflavones. A molecular identification of the collected species was performed throughout DNA barcoding using ITS, rbcL, rpoC1 and matK sequences. The use of a multi-locus barcoding system complemented with basic morphological information allowed the unequivocal identification at the species level of 90% of the samples. The determination of isoflavone content was performed by high-performance liquid chromatography with diode-array detection. Total average contents in the studied species were significantly different, Ononis natrix and Cytisus scoparius possessing the highest total isoflavones content (396 and 273 mg kg(-1), respectively) and Lotus creticus, the lowest (20 mg kg(-1)). The correlation of total isoflavone content with the phylogeny of this set of plants as determined by the rpoC1 sequences was evaluated for the first time.},
}
@article {pmid23438061,
year = {2013},
author = {Gao, Y and Lam, AW and Chan, WC},
title = {Automating quantum dot barcode assays using microfluidics and magnetism for the development of a point-of-care device.},
journal = {ACS applied materials &amp; interfaces},
volume = {5},
number = {8},
pages = {2853-2860},
doi = {10.1021/am302633h},
pmid = {23438061},
issn = {1944-8252},
support = {//Canadian Institutes of Health Research/Canada ; },
mesh = {HIV Infections/*diagnosis/virology ; HIV-1/genetics/isolation &amp; purification ; Hepatitis B/*diagnosis/virology ; Hepatitis B virus/genetics/isolation &amp; purification ; Humans ; Magnetics/instrumentation/*methods ; Microfluidics/instrumentation/*methods ; *Point-of-Care Systems ; *Quantum Dots ; Syphilis/*diagnosis/microbiology ; Treponema denticola/genetics/isolation &amp; purification ; },
abstract = {The impact of detecting multiple infectious diseases simultaneously at point-of-care with good sensitivity, specificity, and reproducibility would be enormous for containing the spread of diseases in both resource-limited and rich countries. Many barcoding technologies have been introduced for addressing this need as barcodes can be applied to detecting thousands of genetic and protein biomarkers simultaneously. However, the assay process is not automated and is tedious and requires skilled technicians. Barcoding technology is currently limited to use in resource-rich settings. Here we used magnetism and microfluidics technology to automate the multiple steps in a quantum dot barcode assay. The quantum dot-barcoded microbeads are sequentially (a) introduced into the chip, (b) magnetically moved to a stream containing target molecules, (c) moved back to the original stream containing secondary probes, (d) washed, and (e) finally aligned for detection. The assay requires 20 min, has a limit of detection of 1.2 nM, and can detect genetic targets for HIV, hepatitis B, and syphilis. This study provides a simple strategy to automate the entire barcode assay process and moves barcoding technologies one step closer to point-of-care applications.},
}
@article {pmid23437908,
year = {2013},
author = {Pino-Bodas, R and Martín, MP and Burgaz, AR and Lumbsch, HT},
title = {Species delimitation in Cladonia (Ascomycota): a challenge to the DNA barcoding philosophy.},
journal = {Molecular ecology resources},
volume = {13},
number = {6},
pages = {1058-1068},
doi = {10.1111/1755-0998.12086},
pmid = {23437908},
issn = {1755-0998},
mesh = {Ascomycota/classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Fungal/chemistry/classification ; Genetic Variation ; Species Specificity ; },
abstract = {The lichen-forming fungal genus Cladonia is species-rich with approximately 500 described species. The accepted barcode for fungi (ITS rDNA) often fails in identifying Cladonia spp. In order to find other markers that, in combination with the ITS rDNA region can be used for species identification in Cladonia, we studied the loci IGS rDNA, ef1α, rpb2 and cox1. A total of 782 sequences from 36 species have been analyzed. PCR amplification success rate, intraspecific and interspecific genetic distance variation, calculated using the K2P model, and the correct identification percentage (PCI) were taken into account to assess possible barcode regions. The marker showing the least intraspecific genetic distance range was cox1, followed by ITS rDNA and ef1α. Of the five studied markers only cox1 showed a barcoding gap. The rpb2 locus showed the highest PCI values, but it was the most difficult to amplify. The highest correct identification rates using blast method were obtained with rpb2.},
}
@article {pmid23433986,
year = {2013},
author = {Marucci, G and Interisano, M and La Rosa, G and Pozio, E},
title = {Molecular identification of nematode larvae different from those of the Trichinella genus detected by muscle digestion.},
journal = {Veterinary parasitology},
volume = {194},
number = {2-4},
pages = {117-120},
doi = {10.1016/j.vetpar.2013.01.034},
pmid = {23433986},
issn = {1873-2550},
mesh = {Animals ; Bird Diseases/diagnosis/*parasitology ; Birds ; DNA, Helminth/chemistry/genetics ; DNA, Mitochondrial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Diagnosis, Differential ; Electron Transport Complex IV/genetics ; False Positive Reactions ; Larva ; Muscles/*parasitology ; Mustelidae/*parasitology ; Nematoda/classification/genetics/*isolation &amp; purification ; Polymerase Chain Reaction/veterinary ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA/veterinary ; Sus scrofa ; Swine ; Swine Diseases/diagnosis/*parasitology ; Trichinella/classification/genetics/isolation &amp; purification ; Trichinellosis/diagnosis/parasitology/*veterinary ; },
abstract = {Although larvae of the genus Trichinella are the most common parasite species detected in vertebrate muscles using artificial digestion, nematode larvae belonging to other genera are sometimes detected and incorrectly identified as Trichinella. However, it is often very difficult to identify these larvae at the species, genus or family level using microscopy because of the absence of specific morphological characters or cuticle damage, and the only means of identification is PCR and sequencing of specific molecular markers (12S mtDNA; COI; 18S rDNA; and ITS1). From 2008 to 2011, 18 nematode isolates not belonging to the genus Trichinella were collected from different host species. Eleven of these isolates were successfully identified at the species, genus or superfamily level: larvae from two common kestrels, three hooded crows, a hen harrier and a domestic pig were identified as Toxocara cati; larvae from a badger were identified as Toxocara canis; larvae from a domestic pig were identified as a free-living nematode of the genus Panagrolaimus; larvae from a wild boar were identified as belonging to the Metastrongylus genus; and larvae from a rough-legged buzzard were identified as belonging to the superfamily Filarioidea. The recovery of nematodes belonging to genera other than Trichinella during routine meat inspection suggests that the persons performing the analyses need to be informed of the possibility of false positives and that a molecular-based identification system that allows for a rapid and reliable response must be adopted (i.e., a DNA barcoding-like system).},
}
@article {pmid23433320,
year = {2013},
author = {Prosser, SW and Velarde-Aguilar, MG and León-Règagnon, V and Hebert, PD},
title = {Advancing nematode barcoding: a primer cocktail for the cytochrome c oxidase subunit I gene from vertebrate parasitic nematodes.},
journal = {Molecular ecology resources},
volume = {13},
number = {6},
pages = {1108-1115},
doi = {10.1111/1755-0998.12082},
pmid = {23433320},
issn = {1755-0998},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/chemistry/classification/genetics ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Data ; Nematoda/chemistry/*genetics ; Phylogeny ; Vertebrates/parasitology ; },
abstract = {Although nematodes are one of the most diverse metazoan phyla, species identification through morphology is difficult. Several genetic markers have been used for their identification, but most do not provide species-level resolution in all groups, and those that do lack primer sets effective across the phylum, precluding high-throughput processing. This study describes a cocktail of three novel primer pairs that overcome this limitation by recovering cytochrome c oxidase I (COI) barcodes from diverse nematode lineages parasitic on vertebrates, including members of three orders and eight families. Its effectiveness across a broad range of nematodes enables high-throughput processing.},
}
@article {pmid23433240,
year = {2013},
author = {García-Morales, AE and Elías-Gutiérrez, M},
title = {DNA barcoding of freshwater rotifera in Mexico: evidence of cryptic speciation in common rotifers.},
journal = {Molecular ecology resources},
volume = {13},
number = {6},
pages = {1097-1107},
doi = {10.1111/1755-0998.12080},
pmid = {23433240},
issn = {1755-0998},
mesh = {Animals ; Classification/methods ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/chemistry/classification/genetics ; *Fresh Water ; *Genetic Speciation ; Genetic Variation ; Mexico ; Molecular Sequence Data ; Phylogeny ; Rotifera/classification/*genetics ; Species Specificity ; },
abstract = {DNA barcodes are useful tools to identify and discover new species in a wide range of taxa. Here, we report the first barcode study of monogonont rotifers from fresh and brackish waters in Mexico, and discuss the taxonomic implications of this work. We used DNA barcodes based on the sequence of cytochrome oxidase I to examine patterns of divergence among 417 specimens that represented 63 morphological taxa of rotifers. The mean sequence divergence among conspecific rotifer individuals was 0.75%, whereas the mean sequence divergence among congeneric taxa was 20.8%. The barcodes could discriminate between all the morphospecies identified. Moreover, the barcoding data revealed the presence of possible cryptic species in Ascomorpha ovalis, Lecane bulla, L. cornuta, L. curvicornis, L. crepida, L. lunaris, L. hastata, Platyias quadricornis, Keratella cochlearis, Brachionus calyciflorus and Testudinella patina, as well as in some forms and varieties such as B. quadridentatus f. brevispinus, B. quadridentatus f. cluniorbicularis and Mytilina ventralis var. macracantha. Barcode analysis also enabled some forms and varieties of common species to be identified as separate species. The results obtained support recent taxonomic revisions, such as the recognition of the genus Plationus, and the presence of cryptic speciation in L. bulla. This work shows that DNA barcoding identifies species effectively, can aid taxonomists by identifying cryptic species, and is an important tool for resolving taxonomic controversies.},
}
@article {pmid23433106,
year = {2013},
author = {Nevill, PG and Wallace, MJ and Miller, JT and Krauss, SL},
title = {DNA barcoding for conservation, seed banking and ecological restoration of Acacia in the Midwest of Western Australia.},
journal = {Molecular ecology resources},
volume = {13},
number = {6},
pages = {1033-1042},
doi = {10.1111/1755-0998.12060},
pmid = {23433106},
issn = {1755-0998},
mesh = {Acacia/classification/*genetics ; Australia ; Conservation of Natural Resources/*methods ; *DNA Barcoding, Taxonomic ; DNA, Plant/classification/genetics ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; },
abstract = {We used DNA barcoding to address an important conservation issue in the Midwest of Western Australia, working on Australia's largest genus of flowering plant. We tested whether or not currently recommended plant DNA barcoding regions (matK and rbcL) were able to discriminate Acacia taxa of varying phylogenetic distances, and ultimately identify an ambiguously labelled seed collection from a mine-site restoration project. Although matK successfully identified the unknown seed as the rare and conservation priority listed A. karina, and was able to resolve six of the eleven study species, this region was difficult to amplify and sequence. In contrast, rbcL was straightforward to recover and align, but could not determine the origin of the seed and only resolved 3 of the 11 species. Other chloroplast regions (rpl32-trnL, psbA-trnH, trnL-F and trnK) had mixed success resolving the studied taxa. In general, species were better resolved in multilocus data sets compared to single-locus data sets. We recommend using the formal barcoding regions supplemented with data from other plastid regions, particularly rpl32-trnL, for barcoding in Acacia. Our study demonstrates the novel use of DNA barcoding for seed identification and illustrates the practical potential of DNA barcoding for the growing discipline of restoration ecology.},
}
@article {pmid23431400,
year = {2013},
author = {Shen, YY and Chen, X and Murphy, RW},
title = {Assessing DNA barcoding as a tool for species identification and data quality control.},
journal = {PloS one},
volume = {8},
number = {2},
pages = {e57125},
pmid = {23431400},
issn = {1932-6203},
mesh = {Animals ; Cytochromes b/genetics ; DNA Barcoding, Taxonomic/*standards ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Genetic Variation ; Humans ; Models, Genetic ; Quality Control ; Reference Standards ; Species Specificity ; },
abstract = {In recent years, the number of sequences of diverse species submitted to GenBank has grown explosively and not infrequently the data contain errors. This problem is extensively recognized but not for invalid or incorrectly identified species, sample mixed-up, and contamination. DNA barcoding is a powerful tool for identifying and confirming species and one very important application involves forensics. In this study, we use DNA barcoding to detect erroneous sequences in GenBank by evaluating deep intraspecific and shallow interspecific divergences to discover possible taxonomic problems and other sources of error. We use the mitochondrial DNA gene encoding cytochrome b (Cytb) from turtles to test the utility of barcoding for pinpointing potential errors. This gene is widely used in phylogenetic studies of the speciose group. Intraspecific variation is usually less than 2.0% and in most cases it is less than 1.0%. In comparison, most species differ by more than 10.0% in our dataset. Overlapping intra- and interspecific percentages of variation mainly involve problematic identifications of species and outdated taxonomies. Further, we detect identical problems in Cytb from Insectivora and Chiroptera. Upon applying this strategy to 47,524 mammalian CoxI sequences, we resolve a suite of potentially problematic sequences. Our study reveals that erroneous sequences are not rare in GenBank and that the DNA barcoding can serve to confirm sequencing accuracy and discover problems such as misidentified species, inaccurate taxonomies, contamination, and potential errors in sequencing.},
}
@article {pmid23428595,
year = {2013},
author = {Levy-Sakin, M and Ebenstein, Y},
title = {Beyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopy.},
journal = {Current opinion in biotechnology},
volume = {24},
number = {4},
pages = {690-698},
doi = {10.1016/j.copbio.2013.01.009},
pmid = {23428595},
issn = {1879-0429},
mesh = {Chromosomes/*chemistry ; DNA/*chemistry ; *Genome, Human ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; Microscopy/*methods ; Microscopy, Fluorescence/methods ; Nanotechnology/*methods ; Sequence Analysis, DNA ; },
abstract = {Next generation sequencing (NGS) is revolutionizing all fields of biological research but it fails to extract the full range of information associated with genetic material. Optical mapping of DNA grants access to genetic and epigenetic information on individual DNA molecules up to ∼1 Mbp in length. Fluorescent labeling of specific sequence motifs, epigenetic marks and other genomic information on individual DNA molecules generates a high content optical barcode along the DNA. By stretching the DNA to a linear configuration this barcode may be directly visualized by fluorescence microscopy. We discuss the advances of these methods in light of recent developments in nano-fabrication and super-resolution optical imaging (nanoscopy) and review the latest achievements of optical mapping in the context of genomic analysis.},
}
@article {pmid23425021,
year = {2013},
author = {Ruiter, DE and Boyle, EE and Zhou, X},
title = {DNA barcoding facilitates associations and diagnoses for Trichoptera larvae of the Churchill (Manitoba, Canada) area.},
journal = {BMC ecology},
volume = {13},
number = {},
pages = {5},
pmid = {23425021},
issn = {1472-6785},
mesh = {Animals ; Biodiversity ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; Insecta/*classification/genetics/growth &amp; development ; Larva/classification/genetics/growth &amp; development ; Manitoba ; },
abstract = {BACKGROUND: The North American Trichoptera larvae are poorly known at the species level, despite their importance in the understanding of freshwater fauna and critical use in biomonitoring. This study focused on morphological diagnoses for larvae occurring in the Churchill, Manitoba area, representing the largest larval association effort for the caddisflies at any given locality thus far. The current DNA barcode reference library of Trichoptera (available on the Barcode of Life Data Systems) was utilized to provide larval-adult associations.<br><br>RESULTS: The present study collected an additional 23 new species records for the Churchill area, increasing the total Trichoptera richness to 91 species. We were able to associate 62 larval taxa, comprising 68.1% of the Churchill area Trichoptera taxa. This endeavor to identify immature life stage for the caddisflies enabled the development of morphological diagnoses, production of photographs and an appropriate taxonomic key to facilitate larval species analyses in the area.<br><br>CONCLUSIONS: The use of DNA for associations of unknown larvae with known adults proved rapid and successful. This method should accelerate the state-of-knowledge for North American Trichoptera larvae as well as other taxonomic lineages. The morphological analysis should be useful for determination of material from the Churchill area.},
}
@article {pmid23417807,
year = {2013},
author = {Mansell, TJ and Warner, JR and Gill, RT},
title = {Trackable multiplex recombineering for gene-trait mapping in E. coli.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {985},
number = {},
pages = {223-246},
doi = {10.1007/978-1-62703-299-5_12},
pmid = {23417807},
issn = {1940-6029},
mesh = {Base Sequence ; Cloning, Molecular/methods ; DNA Barcoding, Taxonomic ; Escherichia coli/*genetics ; Escherichia coli Proteins/genetics ; Gene Knockdown Techniques ; Genetic Engineering/*methods ; Genome, Bacterial ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Phenotype ; Recombinant Proteins/genetics ; Transcriptome ; },
abstract = {Recent advances in homologous recombination in Escherichia coli have enabled improved genome engineering by multiplex recombineering. In this chapter, we present trackable multiplex recombineering (TRMR), a method for gene-trait mapping which creates simulated knockdown and overexpression mutants for virtually all genes in the E. coli genome. The method combines oligonucleotide synthesis with multiplex recombineering to create two libraries comprising of over 8,000 E. coli strains in total that can be selected for traits of interest via high-throughput screening or selection. DNA barcodes included in the recombineering cassette allow for rapid characterization of a naïve or selected population via DNA microarray analysis. Important considerations for oligonucleotide design, DNA library construction, recombineering, strain characterization, and selection are discussed.},
}
@article {pmid23416325,
year = {2013},
author = {Chen, JB and Chuang, LY and Lin, YD and Liou, CW and Lin, TK and Lee, WC and Cheng, BC and Chang, HW and Yang, CH},
title = {Preventive SNP-SNP interactions in the mitochondrial displacement loop (D-loop) from chronic dialysis patients.},
journal = {Mitochondrion},
volume = {13},
number = {6},
pages = {698-704},
doi = {10.1016/j.mito.2013.01.013},
pmid = {23416325},
issn = {1872-8278},
mesh = {Algorithms ; DNA Barcoding, Taxonomic ; Humans ; Mitochondria/*genetics ; *Polymorphism, Single Nucleotide ; *Renal Dialysis ; },
abstract = {Chronic dialysis association study involving individual single nucleotide polymorphisms (SNPs) in the mitochondrial displacement loop (D-loop) has previously been reported. However, possible SNP-SNP interactions for SNPs in the D-loop which could be associated with a reduced risk for chronic dialysis were not investigated. The purpose of this study was to propose an effective algorithm to identify protective SNP-SNP interactions in the D-loop from chronic dialysis patients. We introduce ISGA that uses an initialization strategy for genetic algorithms (GA) to improve the computational analysis for protective SNP-SNP interactions. ISGA generates genotype patterns with combined SNPs (SNP barcodes) for chronic dialysis. Using our previously reported 77 SNPs in the D-loop, the algorithm-generated protective SNP barcodes for chronic dialysis were evaluated. ISGA provides the SNP barcodes with the maximum frequency differences of occurrence between the cases and controls. The identified SNP barcodes with the lowest odds ratio (OR) values were regarded as the best preventive SNP barcodes against chronic dialysis. The best ISGA-generated SNP barcodes (two to nine SNPs) are more closely associated with the prevention of chronic dialysis when more SNPs are chosen (OR=0.64 to 0.32; 95% confidence interval=0.882 to 0.198). The cumulative effects of SNP-SNP interactions were more dominant in ISGA rather than in GA without the initialization strategy. We provide a fast identification of chronic dialysis-associated protective SNP barcodes and demonstrate that the SNP-SNP interactions may have a cumulative effect on prediction for chronic dialysis.},
}
@article {pmid23409092,
year = {2013},
author = {Zhang, W and Fan, X and Zhu, S and Zhao, H and Fu, L},
title = {Species-specific identification from incomplete sampling: applying DNA barcodes to monitoring invasive solanum plants.},
journal = {PloS one},
volume = {8},
number = {2},
pages = {e55927},
pmid = {23409092},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic ; Evolution, Molecular ; Genes, Plant ; Introduced Species ; Phylogeny ; Plants/*classification/*genetics ; Solanum/classification/genetics ; *Species Specificity ; },
abstract = {Comprehensive sampling is crucial to DNA barcoding, but it is rarely performed because materials are usually unavailable. In practice, only a few rather than all species of a genus are required to be identified. Thus identification of a given species using a limited sample is of great importance in current application of DNA barcodes. Here, we selected 70 individuals representing 48 species from each major lineage of Solanum, one of the most species-rich genera of seed plants, to explore whether DNA barcodes can provide reliable specific-species discrimination in the context of incomplete sampling. Chloroplast genes ndhF and trnS-trnG and the nuclear gene waxy, the commonly used markers in Solanum phylogeny, were selected as the supplementary barcodes. The tree-building and modified barcode gap methods were employed to assess species resolution. The results showed that four Solanum species of quarantine concern could be successfully identified through the two-step barcoding sampling strategy. In addition, discrepancies between nuclear and cpDNA barcodes in some samples demonstrated the ability to discriminate hybrid species, and highlights the necessity of using barcode regions with different modes of inheritance. We conclude that efficient phylogenetic markers are good candidates as the supplementary barcodes in a given taxonomic group. Critically, we hypothesized that a specific-species could be identified from a phylogenetic framework using incomplete sampling-through this, DNA barcoding will greatly benefit the current fields of its application.},
}
@article {pmid23409064,
year = {2013},
author = {Yan, D and Luo, JY and Han, YM and Peng, C and Dong, XP and Chen, SL and Sun, LG and Xiao, XH},
title = {Forensic DNA barcoding and bio-response studies of animal horn products used in traditional medicine.},
journal = {PloS one},
volume = {8},
number = {2},
pages = {e55854},
pmid = {23409064},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Horns/*chemistry ; Medicine, Traditional ; Phylogeny ; Ruminants ; },
abstract = {BACKGROUND: Animal horns (AHs) have been applied to traditional medicine for more than thousands of years, of which clinical effects have been confirmed by the history. But now parts of AHs have been listed in the items of wildlife conservation, which limits the use for traditional medicine. The contradiction between the development of traditional medicine and the protection of wild resources has already become the common concern of zoophilists, traditional medical professionals, economists, sociologists. We believe that to strengthen the identification for threatened animals, to prevent the circulation of them, and to seek fertile animals of corresponding bioactivities as substitutes are effective strategies to solve this problem.<br><br>A powerful technique of DNA barcoding based on the mitochondrial gene cytochrome c oxidase I (COI) was used to identify threatened animals of Bovidae and Cervidae, as well as their illegal adulterants (including 10 species and 47 specimens). Meanwhile, the microcalorimetric technique was used to characterize the differences of bio-responses when those animal specimens acted on model organism (Escherichia coli). We found that the COI gene could be used as a universal primer to identify threatened animals and illegal adulterants mentioned above. By analyzing 223 mitochondrial COI sequences, a 100% identification success rate was achieved. We further found that the horns of Mongolian Gazelle and Red Deer could be exploited as a substitute for some functions of endangered Saiga Antelope and Sika Deer in traditional medicine, respectively.<br><br>CONCLUSION/SIGNIFICANCE: Although it needs a more comprehensive evaluation of bioequivalence in order to completely solve the problem of substitutes for threatened animals, we believe that the identification (DNA barcoding) of threatened animals combined with seeking substitutions (bio-response) can yet be regarded as a valid strategy for establishing a balance between the protection of threatened animals and the development of traditional medicine.},
}
@article {pmid23408859,
year = {2013},
author = {Tan, L and Xiong, L and Xu, W and Wu, F and Huang, N and Xu, Y and Kong, L and Zheng, L and Schwartz, L and Shi, Y and Shi, YG},
title = {Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by a new comparative hMeDIP-seq method.},
journal = {Nucleic acids research},
volume = {41},
number = {7},
pages = {e84},
pmid = {23408859},
issn = {1362-4962},
support = {P30 HD018655/HD/NICHD NIH HHS/United States ; U54 HD090255/HD/NICHD NIH HHS/United States ; GM078458/GM/NIGMS NIH HHS/United States ; DK077036/DK/NIDDK NIH HHS/United States ; },
mesh = {5-Methylcytosine/analogs &amp; derivatives ; Animals ; Cell Lineage ; Cells, Cultured ; Cytosine/*analogs &amp; derivatives/analysis/metabolism ; DNA Methylation ; Embryonic Stem Cells/cytology/*metabolism ; Gene Expression ; Genome ; High-Throughput Nucleotide Sequencing/*methods ; *Immunoprecipitation ; Mice ; Neural Stem Cells/*metabolism ; Sequence Analysis, DNA/*methods ; },
abstract = {The genome-wide distribution patterns of the '6th base' 5-hydroxymethylcytosine (5hmC) in many tissues and cells have recently been revealed by hydroxymethylated DNA immunoprecipitation (hMeDIP) followed by high throughput sequencing or tiling arrays. However, it has been challenging to directly compare different data sets and samples using data generated by this method. Here, we report a new comparative hMeDIP-seq method, which involves barcoding different input DNA samples at the start and then performing hMeDIP-seq for multiple samples in one hMeDIP reaction. This approach extends the barcode technology from simply multiplexing the DNA deep sequencing outcome and provides significant advantages for quantitative control of all experimental steps, from unbiased hMeDIP to deep sequencing data analysis. Using this improved method, we profiled and compared the DNA hydroxymethylomes of mouse ES cells (ESCs) and mouse ESC-derived neural progenitor cells (NPCs). We identified differentially hydroxymethylated regions (DHMRs) between ESCs and NPCs and uncovered an intricate relationship between the alteration of DNA hydroxymethylation and changes in gene expression during neural lineage commitment of ESCs. Presumably, the DHMRs between ESCs and NPCs uncovered by this approach may provide new insight into the function of 5hmC in gene regulation and neural differentiation. Thus, this newly developed comparative hMeDIP-seq method provides a cost-effective and user-friendly strategy for direct genome-wide comparison of DNA hydroxymethylation across multiple samples, lending significant biological, physiological and clinical implications.},
}
@article {pmid23405227,
year = {2013},
author = {Ironside, JE},
title = {Diversity and recombination of dispersed ribosomal DNA and protein coding genes in microsporidia.},
journal = {PloS one},
volume = {8},
number = {2},
pages = {e55878},
pmid = {23405227},
issn = {1932-6203},
mesh = {Biological Evolution ; DNA, Fungal/*genetics ; DNA, Ribosomal/*genetics ; Fungal Proteins/*genetics ; Genetic Variation/*genetics ; Haplotypes/genetics ; Nosema/classification/*genetics/metabolism ; Polymerase Chain Reaction ; Recombination, Genetic/*genetics ; Species Specificity ; },
abstract = {Microsporidian strains are usually classified on the basis of their ribosomal DNA (rDNA) sequences. Although rDNA occurs as multiple copies, in most non-microsporidian species copies within a genome occur as tandem arrays and are homogenised by concerted evolution. In contrast, microsporidian rDNA units are dispersed throughout the genome in some species, and on this basis are predicted to undergo reduced concerted evolution. Furthermore many microsporidian species appear to be asexual and should therefore exhibit reduced genetic diversity due to a lack of recombination. Here, DNA sequences are compared between microsporidia with different life cycles in order to determine the effects of concerted evolution and sexual reproduction upon the diversity of rDNA and protein coding genes. Comparisons of cloned rDNA sequences between microsporidia of the genus Nosema with different life cycles provide evidence of intragenomic variability coupled with strong purifying selection. This suggests a birth and death process of evolution. However, some concerted evolution is suggested by clustering of rDNA sequences within species. Variability of protein-coding sequences indicates that considerable intergenomic variation also occurs between microsporidian cells within a single host. Patterns of variation in microsporidian DNA sequences indicate that additional diversity is generated by intragenomic and/or intergenomic recombination between sequence variants. The discovery of intragenomic variability coupled with strong purifying selection in microsporidian rRNA sequences supports the hypothesis that concerted evolution is reduced when copies of a gene are dispersed rather than repeated tandemly. The presence of intragenomic variability also renders the use of rDNA sequences for barcoding microsporidia questionable. Evidence of recombination in the single-copy genes of putatively asexual microsporidia suggests that these species may undergo cryptic sexual reproduction, a possibility with profound implications for the evolution of virulence, host range and drug resistance in these species.},
}
@article {pmid23404314,
year = {2012},
author = {Kvie, KS and Hogner, S and Aarvik, L and Lifjeld, JT and Johnsen, A},
title = {Deep sympatric mtDNA divergence in the autumnal moth (Epirrita autumnata).},
journal = {Ecology and evolution},
volume = {3},
number = {1},
pages = {126-144},
pmid = {23404314},
issn = {2045-7758},
abstract = {Deep sympatric intraspecific divergence in mtDNA may reflect cryptic species or formerly distinct lineages in the process of remerging. Preliminary results from DNA barcoding of Scandinavian butterflies and moths showed high intraspecific sequence variation in the autumnal moth, Epirrita autumnata. In this study, specimens from different localities in Norway and some samples from Finland and Scotland, with two congeneric species as outgroups, were sequenced with mitochondrial and nuclear markers to resolve the discrepancy found between mtDNA divergence and present species-level taxonomy. We found five COI sub-clades within the E. autumnata complex, most of which were sympatric and with little geographic structure. Nuclear markers (ITS2 and Wingless) showed little variation and gave no indications that E. autumnata comprises more than one species. The samples were screened with primers for Wolbachia outer surface gene (wsp) and 12% of the samples tested positive. Two Wolbachia strains were associated with different mtDNA sub-clades within E. autumnata, which may indicate indirect selection/selective sweeps on haplotypes. Our results demonstrate that deep mtDNA divergences are not synonymous with cryptic speciation and this has important implications for the use of mtDNA in species delimitation, like in DNA barcoding.},
}
@article {pmid23401945,
year = {2012},
author = {Danabalan, R and Ponsonby, DJ and Lintoni, YM},
title = {A critical assessment of available molecular identification tools for determining the status of Culex pipiens s.l. in the United Kingdom.},
journal = {Journal of the American Mosquito Control Association},
volume = {28},
number = {4 Suppl},
pages = {68-74},
doi = {10.2987/8756-971X-28.0.68},
pmid = {23401945},
issn = {8756-971X},
mesh = {*Animal Distribution ; Animals ; Culex/anatomy &amp; histology/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Female ; Insect Proteins/genetics ; Male ; Microsatellite Repeats/genetics ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/*methods ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; United Kingdom ; },
abstract = {Until the relatively recent application of molecular identification tools, identification of Culex pipiens f. pipiens and Cx. pipiens f. molestus relied on expressed ecological characteristics, including autogeny, host preference and stenogamy. Herein we test two DNA assays, one based on the microsatellite locus CQ11 and the other on species-diagnostic nucleotide bases in the mtDNA cytochrome oxidase I, on 322 wild-caught Cx. pipiens s.l. collected in above ground habitats from 6 counties across southern England and Wales. Of the 322 Culex pipiens s.l. screened using the CQ11 assay, 205 were identified as Cx. pipiens f. pipiens, 95 as Cx. pipiens f. molestus and 22 were determined as hybrids. Neither above ground Cx. pipiens f. molestus, nor hybrids have previously been reported in UK. However, comparison of COI barcodes (658bp) from 30 individuals from the above defined grouping indicated that inadvertent inclusion of specimens of Cx. torrentium resulted in the expected product sizes purportedly diagnostic for Cx. pipiens f. molestus, Cx. pipiens f. pipiens and hybrids in the CQ11 assay. COI sequences showed Cx. torrentium was misidentified as Cx. pipiens s.l. in more than 50% of cases and that all above ground Cx. pipiens s.l. collected in this study were in fact Cx. pipiens f. pipiens. Thus in regions of the Palearctic where Cx. torrentium and Cx. pipiens s.l. are sympatric, we showed that the CQ11 assay produces misleading results and should not be used.},
}
@article {pmid23400707,
year = {2013},
author = {Ganopoulos, I and Bazakos, C and Madesis, P and Kalaitzis, P and Tsaftaris, A},
title = {Barcode DNA high-resolution melting (Bar-HRM) analysis as a novel close-tubed and accurate tool for olive oil forensic use.},
journal = {Journal of the science of food and agriculture},
volume = {93},
number = {9},
pages = {2281-2286},
doi = {10.1002/jsfa.6040},
pmid = {23400707},
issn = {1097-0010},
mesh = {Brassica napus/chemistry/metabolism ; *DNA Barcoding, Taxonomic ; DNA, Plant/*analysis/metabolism ; Fatty Acids, Monounsaturated/analysis/chemistry ; Food Contamination ; Food Inspection/*methods ; *Food Labeling ; Forensic Toxicology/methods ; Fruit/*chemistry/metabolism ; Greece ; Limit of Detection ; Nucleic Acid Denaturation ; Olea/*chemistry/metabolism ; Olive Oil ; Plant Oils/*chemistry ; Plant Proteins/genetics/metabolism ; Rapeseed Oil ; Real-Time Polymerase Chain Reaction ; Ribulose-Bisphosphate Carboxylase/genetics/metabolism ; },
abstract = {BACKGROUND: The adulteration of high-priced olive oil with low-cost oils and the fraudulent labelling of oil products make the identification and traceability of vegetable oil species in the food chain very important. This paper describes a high-resolution melting analysis-based method using chloroplast barcoding regions as target (Bar-HRM) to obtain barcoding information for the major vegetable oil species and to quantitatively identify the botanical origin of plant oils. The detection of adulteration of olive oil with canola oil was used as a case study.<br><br>RESULTS: The proposed method was capable of distinguishing among different vegetable oil species and detecting a level of 1% (w/w) of canola oil in olive oil.<br><br>CONCLUSION: Bar-HRM analysis is a more accurate, faster and less costly alternative method to authenticate vegetable oils, including olive oil, and to detect mixtures of oils.},
}
@article {pmid23399014,
year = {2013},
author = {Broussard, BS and Broussard, AB},
title = {Using electronic communication safely in health care settings.},
journal = {Nursing for women's health},
volume = {17},
number = {1},
pages = {59-62},
doi = {10.1111/1751-486X.12007},
pmid = {23399014},
issn = {1751-486X},
mesh = {Cell Phone ; Confidentiality ; Delivery of Health Care/*organization &amp; administration ; Humans ; Infection Control ; Nurse-Patient Relations ; *Nursing Informatics ; Organizational Policy ; *Patient Safety ; *Telecommunications ; },
abstract = {Nurses are increasingly using mobile and other devices, such as cell phones, smartphones, tablets, bar-coding scanners, monitoring equipment and bedside computers, to communicate with members of the health care team and with patients. Communication accomplished with such devices includes direct verbal communication, text-messaging, emailing, obtaining patient care information and accessing medical records for order entry and for documenting nursing care. Problems that could occur with such communication methods include distraction, errors, de-personalized care, violation of confidentiality and transmission of nosocomial pathogens. Policies are needed to prevent inappropriate use of technological devices in patient care and to promote patient safety and quality care with their use.},
}
@article {pmid23398631,
year = {2013},
author = {Pradeep Kumar, N and Krishnamoorthy, N and Sahu, SS and Rajavel, AR and Sabesan, S and Jambulingam, P},
title = {DNA Barcodes indicate members of the Anopheles fluviatilis (Diptera: Culicidae) species complex to be conspecific in India.},
journal = {Molecular ecology resources},
volume = {13},
number = {3},
pages = {354-361},
doi = {10.1111/1755-0998.12076},
pmid = {23398631},
issn = {1755-0998},
mesh = {Animals ; Anopheles/*genetics ; Base Sequence ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Electron Transport Complex IV/genetics ; Genetic Markers/*genetics ; India ; Insect Vectors/*genetics ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Anopheles fluviatilis, a major vector of malaria in India has been described as a complex of three sibling species members, named as S, T and U, based on variations in chromosomal inversions. Also, ribosomal DNA markers (repetitive Internal Transcribed Spacer 2 (ITS2) and 28S D3 region) were described to differentiate these three sibling species members. However, controversies prevail on the genetic isolation status of these cryptic species. Hence, we evaluated this taxonomic incongruence employing DNA barcoding, the well established methodology for species identification, using 60 An. fluviatilis sensu lato specimens, collected from two malaria endemic eastern states of India. These specimens were also subjected to sibling species characterization by ITS2 and D3 DNA markers. The former marker identified 31 specimens among these as An. fluviatilis S and 21 as An. fluviatilis T. Eight specimens amplified DNA fragments specific for both S and T. The D3 marker characterized 39 specimens belonging to species S and 21 to species T. Neither marker identified species U. Neighbor Joining analysis of mitochondrial cytochrome c oxidase gene 1 sequences (the DNA barcode) categorized all the 60 specimens into a single operational taxonomic unit, their Kimura 2 parameter (K2P) genetic variability being only 0.8%. The genetic differentiation (FST) and gene flow (Nm) estimates were 0.00799 and 62.07, respectively, indicating these two 'species' (S &amp; T) as genetically con-specific intermixing populations with negligible genetic differentiation. Earlier investigations have refuted the existence of species U. Also, this study demonstrated that An. fluviatilis and the closely related An. minimus could be taxonomically differentiated by the DNA Barcode approach (K2P = 5.0%).},
}
@article {pmid23394592,
year = {2013},
author = {Pillon, Y and Johansen, J and Sakishima, T and Chamala, S and Barbazuk, WB and Roalson, EH and Price, DK and Stacy, EA},
title = {Potential use of low-copy nuclear genes in DNA barcoding: a comparison with plastid genes in two Hawaiian plant radiations.},
journal = {BMC evolutionary biology},
volume = {13},
number = {},
pages = {35},
pmid = {23394592},
issn = {1471-2148},
mesh = {Campanulaceae/*classification/genetics ; Cell Nucleus/genetics ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Haplotypes ; Hawaii ; Magnoliopsida/*classification/genetics ; Phylogeography ; Plastids/*genetics ; },
abstract = {BACKGROUND: DNA barcoding of land plants has relied traditionally on a small number of markers from the plastid genome. In contrast, low-copy nuclear genes have received little attention as DNA barcodes because of the absence of universal primers for PCR amplification.<br><br>RESULTS: From pooled-species 454 transcriptome data we identified two variable intron-less nuclear loci for each of two species-rich genera of the Hawaiian flora: Clermontia (Campanulaceae) and Cyrtandra (Gesneriaceae) and compared their utility as DNA barcodes with that of plastid genes. We found that nuclear genes showed an overall greater variability, but also displayed a high level of heterozygosity, intraspecific variation, and retention of ancient alleles. Thus, nuclear genes displayed fewer species-diagnostic haplotypes compared to plastid genes and no interspecies gaps.<br><br>CONCLUSIONS: The apparently greater coalescence times of nuclear genes are likely to limit their utility as barcodes, as only a small proportion of their alleles were fixed and unique to individual species. In both groups, species-diagnostic markers from either genome were scarce on the youngest island; a minimum age of ca. two million years may be needed for a species flock to be barcoded. For young plant groups, nuclear genes may not be a superior alternative to slowly evolving plastid genes.},
}
@article {pmid23394155,
year = {2013},
author = {Su, M},
title = {Multiplexed detection of molecular biomarkers with phase-change nanoparticles.},
journal = {Nanomedicine (London, England)},
volume = {8},
number = {2},
pages = {253-263},
pmid = {23394155},
issn = {1748-6963},
support = {DP2 EB016572/EB/NIBIB NIH HHS/United States ; },
mesh = {Animals ; Biomarkers/*analysis ; Humans ; Nanoparticles/*chemistry ; Temperature ; },
abstract = {This review describes a new biosensing method based on nanoparticles of solid-to-liquid phase-change materials, in which a panel of metallic nanoparticles (metals and eutectic alloys) that have different compositions and melting temperatures are used as thermal reporters. Each type of nanoparticle will be conjugated to a ligand that can specifically bind to one type of molecular biomarker (protein or DNA) and then immobilized onto a substrate that is comodified with multiple ligands by forming sandwiched antibody-antigen complexes or DNA double helices. After removing unbound nanoparticles by washing, the nature and concentration of the biomarkers are determined by detecting the melting temperature and fusion enthalpy of the nanoparticles using differential scanning calorimetry. Furthermore, an even larger panel of thermal barcodes can be formed by encapsulating selected phase-change nanoparticles inside non-melting shells, such as silica, where each microparticle will have a characteristic signature that can be determined from its thermal signatures.},
}
@article {pmid23393754,
year = {2012},
author = {Dusfour, I and Jarjaval, F and Gaborit, P and Mura, M and Girod, R and Pagès, F},
title = {Confirmation of the occurrence of Anopheles (Nyssorhynchus) marajoara in French Guiana.},
journal = {Journal of the American Mosquito Control Association},
volume = {28},
number = {4},
pages = {309-311},
doi = {10.2987/12-6248R.1},
pmid = {23393754},
issn = {8756-971X},
mesh = {Animals ; Anopheles/*classification/genetics/*physiology ; Demography ; Electron Transport Complex IV/genetics/metabolism ; French Guiana ; Gene Expression Regulation, Enzymologic ; Protein Subunits/genetics/metabolism ; },
abstract = {Throughout the early entomological campaigns in French Guiana (1900-1945), the presence of members of the Anopheles albitarsis Complex was reported in many places across the territory. However, since then no specimen has been caught despite many entomological studies conducted on the littoral and along the main rivers in places where malaria was endemic. We report here the 1st catches in the modern period of specimens of the An. albitarsis Complex in the deep rainforest. During a military intervention, Mosquito-Magnet traps and the Centers for Disease Control and Prevention light traps were used to sample malaria vectors in an illegal gold mining area and a permanent checkpoint. Members of the An. albitarsis caught were molecularly identified using DNA barcoding. In the 2 sites where An. albitarsis s.l. were caught, all specimens were An. marajoara. As An. marajoara is considered as an important malaria vector in Amazonia, the highest interest must be shown to this species in French Guiana.},
}
@article {pmid23390499,
year = {2013},
author = {Suwannasai, N and Martín, MP and Phosri, C and Sihanonth, P and Whalley, AJ and Spouge, JL},
title = {Fungi in Thailand: a case study of the efficacy of an ITS barcode for automatically identifying species within the Annulohypoxylon and Hypoxylon genera.},
journal = {PloS one},
volume = {8},
number = {2},
pages = {e54529},
pmid = {23390499},
issn = {1932-6203},
mesh = {Base Sequence ; Biodiversity ; Computational Biology/*methods/statistics &amp; numerical data ; *DNA Barcoding, Taxonomic ; DNA, Intergenic/*classification ; Internet ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; Thailand ; Xylariales/*classification/*genetics ; },
abstract = {Thailand, a part of the Indo-Burma biodiversity hotspot, has many endemic animals and plants. Some of its fungal species are difficult to recognize and separate, complicating assessments of biodiversity. We assessed species diversity within the fungal genera Annulohypoxylon and Hypoxylon, which produce biologically active and potentially therapeutic compounds, by applying classical taxonomic methods to 552 teleomorphs collected from across Thailand. Using probability of correct identification (PCI), we also assessed the efficacy of automated species identification with a fungal barcode marker, ITS, in the model system of Annulohypoxylon and Hypoxylon. The 552 teleomorphs yielded 137 ITS sequences; in addition, we examined 128 GenBank ITS sequences, to assess biases in evaluating a DNA barcode with GenBank data. The use of multiple sequence alignment in a barcode database like BOLD raises some concerns about non-protein barcode markers like ITS, so we also compared species identification using different alignment methods. Our results suggest the following. (1) Multiple sequence alignment of ITS sequences is competitive with pairwise alignment when identifying species, so BOLD should be able to preserve its present bioinformatics workflow for species identification for ITS, and possibly therefore with at least some other non-protein barcode markers. (2) Automated species identification is insensitive to a specific choice of evolutionary distance, contributing to resolution of a current debate in DNA barcoding. (3) Statistical methods are available to address, at least partially, the possibility of expert misidentification of species. Phylogenetic trees discovered a cryptic species and strongly supported monophyletic clades for many Annulohypoxylon and Hypoxylon species, suggesting that ITS can contribute usefully to a barcode for these fungi. The PCIs here, derived solely from ITS, suggest that a fungal barcode will require secondary markers in Annulohypoxylon and Hypoxylon, however. The URL http://tinyurl.com/spouge-barcode contains computer programs and other supplementary material relevant to this article.},
}
@article {pmid23390494,
year = {2013},
author = {Foster, PG and Bergo, ES and Bourke, BP and Oliveira, TM and Nagaki, SS and Sant'Ana, DC and Sallum, MA},
title = {Phylogenetic analysis and DNA-based species confirmation in Anopheles (Nyssorhynchus).},
journal = {PloS one},
volume = {8},
number = {2},
pages = {e54063},
pmid = {23390494},
issn = {1932-6203},
mesh = {ATP-Binding Cassette Transporters/classification/*genetics ; Animals ; Anopheles/classification/*genetics ; Bayes Theorem ; DNA/classification/*genetics ; Electron Transport Complex IV/classification/*genetics ; Female ; Insect Proteins/classification/*genetics ; Male ; *Phylogeny ; Phylogeography ; South America ; Species Specificity ; Transcription Factors/classification/*genetics ; },
abstract = {Specimens of neotropical Anopheles (Nyssorhynchus) were collected and identified morphologically. We amplified three genes for phylogenetic analysis-the single copy nuclear white and CAD genes, and the COI barcode region. Since we had multiple specimens for most species we were able to test how well the single or combined genes were able to corroborate morphologically defined species by placing the species into exclusive groups. We found that single genes, including the COI barcode region, were poor at confirming species, but that the three genes combined were able to do so much better. This has implications for species identification, species delimitation, and species discovery, and we caution that single genes are not enough. Higher level groupings were partially resolved with some well-supported groupings, whereas others were found to be either polyphyletic or paraphyletic. There were examples of known groups, such as the Myzorhynchella Section, which were poorly supported with single genes but were well supported with combined genes. From this we can infer that more sequence data will be needed in order to show more higher-level groupings with good support. We got unambiguously good support (0.94-1.0 Bayesian posterior probability) from all DNA-based analyses for a grouping of An. dunhami with An. nuneztovari and An. goeldii, and because of this and because of morphological similarities we propose that An. dunhami be included in the Nuneztovari Complex. We obtained phylogenetic corroboration for new species which had been recognised by morphological differences; these will need to be formally described and named.},
}
@article {pmid23387292,
year = {2013},
author = {Keskin, E and Atar, HH},
title = {DNA barcoding commercially important aquatic invertebrates of Turkey.},
journal = {Mitochondrial DNA},
volume = {24},
number = {4},
pages = {440-450},
doi = {10.3109/19401736.2012.762576},
pmid = {23387292},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; Base Sequence ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Fisheries/methods ; Invertebrates/*genetics ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Turkey ; },
abstract = {DNA barcoding was used in order to identify aquatic invertebrates sampled from fisheries bycatch and discards. A total of 440 unique cytochrome c oxidase sub unit I (COI) barcodes were generated for 22 species from three important phyla (Arthropoda, Cnidaria, and Mollusca). All the species were sequenced and submitted to GenBank and Barcode of Life Database (BOLD) databases using 654 bp-long fragment of mitochondrial COI gene. Two of them (Pontastacus leptodactylus and Rapana bezoar) were first records of the species for the BOLD database and six of them (Carcinus aestuarii, Loligo vulgaris, Melicertus kerathurus, Nephrops norvegicus, Scyllarides latus, and Scyllarus arctus) were first standard (>648 bp) COI barcode records for the GenBank database. COI barcodes were analyzed for nucleotide composition, nucleotide pair frequencies, and Kimura's two-parameter genetic distance. Mean genetic distance among species was found increasing at higher taxonomic levels. Neighbor-joining trees generated were congruent with morphometric-based taxonomic classification. Findings of this study clearly demonstrate that DNA barcodes could be used as an efficient molecular tool in identification of not only target species from fisheries but also bycatch and discard species, and so it could provide us leverage for a better understanding in monitoring and management of fisheries and biodiversity.},
}
@article {pmid23385930,
year = {2013},
author = {Wu, B and Gong, HQ},
title = {Predefinable colorimetric quantum-dot barcodes with simple and express identification algorithm.},
journal = {Applied optics},
volume = {52},
number = {4},
pages = {866-870},
doi = {10.1364/AO.52.000866},
pmid = {23385930},
issn = {1539-4522},
abstract = {Specific fluorescent profiles were created by loading quantum-dot (Qdot) mixtures in liquid cores of monodispersed polymer microcapsules, which were used as colorimetric barcodes for small object identification. Since the emission intensities of Qdot-loaded liquid cores maintain a linear relation to the Qdot concentrations and the Qdots in the liquid cores with different emission peaks have no obvious interference, the colorimetric barcodes can be predefined by the compositions of Qdot mixtures. The colorimetric barcodes can be identified easily by recording the emission intensities of the encoded microcapsules at respective Qdot emission peaks with a simple and express algorithm, which are suitable to conduct high-throughput multiplexed assays by flow cytometer for biological screening applications.},
}
@article {pmid23384430,
year = {2013},
author = {James, ER and Burki, F and Todd Harper, J and Scheffrahn, RH and Keeling, PJ},
title = {Molecular characterization of parabasalian symbionts Coronympha clevelandii and Trichonympha subquasilla from the Hawaiian lowland tree termite Incisitermes immigrans.},
journal = {The Journal of eukaryotic microbiology},
volume = {60},
number = {3},
pages = {313-316},
doi = {10.1111/jeu.12027},
pmid = {23384430},
issn = {1550-7408},
mesh = {Animals ; Hypermastigia/classification/genetics/*physiology ; Isoptera/*parasitology ; Parabasalidea/classification/genetics/*physiology ; Phylogeny ; RNA, Ribosomal/genetics ; Symbiosis ; },
abstract = {An important and undervalued challenge in characterizing symbiotic protists is the accurate identification of their host species. Here, we use DNA barcoding to resolve one confusing case involving parabasalian symbionts in the hindgut of the Hawaiian lowland tree termite, Incisitermes immigrans, which is host to several parabasalians, including the type species for the genus Coronympha, C. clevelandii. We collected I. immigrans from its type locality (Hawaii), confirmed its identity by DNA barcoding, and characterized the phylogenetic position of two symbionts, C. clevelandii and Trichonympha subquasilla. These data show that previous molecular surveys of "I. immigrans" are, in fact, mainly derived from the Caribbean termite I. schwarzi, and perhaps also another related species. These results emphasize the need for host barcoding, clarify the relationship between morphologically distinct Coronympha species, and also suggest some interesting distribution patterns of nonendemic termite species and their symbionts.},
}
@article {pmid23382845,
year = {2013},
author = {Ko, HL and Wang, YT and Chiu, TS and Lee, MA and Leu, MY and Chang, KZ and Chen, WY and Shao, KT},
title = {Evaluating the accuracy of morphological identification of larval fishes by applying DNA barcoding.},
journal = {PloS one},
volume = {8},
number = {1},
pages = {e53451},
pmid = {23382845},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Fishes/*genetics ; Larva/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Taiwan ; },
abstract = {Due to insufficient morphological diagnostic characters in larval fishes, it is easy to misidentify them and difficult to key to the genus or species level. The identification results from different laboratories are often inconsistent. This experiment aims to find out, by applying DNA barcoding, how inconsistent the identifications can be among larval fish taxonomists. One hundred morphotypes of larval fishes were chosen as test specimens. The fishes were collected with either larval fish nets or light traps in the northern, southern and northwestern waters of Taiwan. After their body lengths (SL) were measured and specimen photos were taken, all specimens were delivered, in turn, to five laboratories (A-E) in Taiwan to be identified independently. When all the results were collected, these specimens were then identified using COI barcoding. Out of a total of 100 specimens, 87 were identified to the family level, 79 to the genus level and 69 to the species level, based on the COI database currently available. The average accuracy rates of the five laboratories were quite low: 80.1% for the family level, 41.1% for the genus level, and 13.5% for the species level. If the results marked as "unidentified" were excluded from calculations, the rates went up to 75.4% and 43.7% for the genus and species levels, respectively. Thus, we suggest that larval fish identification should be more conservative; i.e., when in doubt, it is better to key only to the family and not to the genus or species level. As to the most misidentified families in our experiment, they were Sparidae, Scorpaenidae, Scombridae, Serranidae and Malacanthidae. On the other hand, Mene maculata and Microcanthus strigatus were all correctly identified to the species level because their larvae have distinct morphology. Nevertheless, barcoding remains one of the best methods to confirm species identification.},
}
@article {pmid23382648,
year = {2013},
author = {Santschi, L and Hanner, RH and Ratnasingham, S and Riconscente, M and Imondi, R},
title = {Barcoding life's matrix: translating biodiversity genomics into high school settings to enhance life science education.},
journal = {PLoS biology},
volume = {11},
number = {1},
pages = {e1001471},
pmid = {23382648},
issn = {1545-7885},
mesh = {Biodiversity ; Biological Science Disciplines/*education ; Computer-Assisted Instruction ; *DNA Barcoding, Taxonomic ; Education/*standards ; Genetic Variation ; Genomics/*education ; Guidelines as Topic ; Humans ; Schools/*standards ; },
abstract = {From biomes to genomes: Innovating life science education by engaging students as citizen scientists in the International Barcode of Life project.},
}
@article {pmid23380240,
year = {2013},
author = {Chen, CW and Huang, YM and Kuo, LY and Nguyen, QD and Luu, HT and Callado, JR and Farrar, DR and Chiou, WL},
title = {trnL-F is a powerful marker for DNA identification of field vittarioid gametophytes (Pteridaceae).},
journal = {Annals of botany},
volume = {111},
number = {4},
pages = {663-673},
pmid = {23380240},
issn = {1095-8290},
mesh = {Amino Acid Sequence ; DNA Barcoding, Taxonomic/*methods ; Ecosystem ; *Genetic Markers ; Germ Cells, Plant/physiology ; Molecular Sequence Data ; Phylogeny ; Pteridaceae/*genetics ; Taiwan ; },
abstract = {BACKGROUND AND AIMS: The gametophyte phase of ferns plays an important role in habitat selection, dispersal, adaptation and evolution. However, ecological studies on fern gametophytes have been impeded due to the difficulty of species identification of free-living gametophytes. DNA barcoding provides an alternative approach to identifying fern gametophytes but is rarely applied to field studies. In this study, an example of field vittarioid gametophyte identification using DNA barcoding, which has not been done before, is given.<br><br>METHODS: A combination of distance-based and tree-based approaches was performed to evaluate the discriminating power of three candidate barcodes (matK, rbcL and trnL-F) on 16 vittarioid sporophytes. Sequences of the trnL-F region were generated from 15 fern gametophyte populations by tissue-direct PCR and were compared against the sporophyte dataset, using BLAST.<br><br>KEY RESULTS: trnL-F earns highest primer universality and discriminatory ability scores, whereas PCR success rates were very low for matK and rbcL regions (10&#xb7;8 % and 41&#xb7;3 %, respectively). BLAST analyses showed that all the sampled field gametophytes could be successfully identified to species level. Three gametophyte populations were also discovered to be living beyond the known occurrence of their sporophyte counterparts.<br><br>CONCLUSIONS: This study demonstrates that DNA barcoding (i.e. reference databasing, tissue-direct PCR and molecular analysis), especially the trnL-F region, is an efficient tool to identify field gametophytes, and has considerable potential in exploring the ecology of fern gametophytes.},
}
@article {pmid23378811,
year = {2012},
author = {Bond, JE},
title = {Phylogenetic treatment and taxonomic revision of the trapdoor spider genus Aptostichus Simon (Araneae, Mygalomorphae, Euctenizidae).},
journal = {ZooKeys},
volume = {},
number = {252},
pages = {1-209},
pmid = {23378811},
issn = {1313-2989},
abstract = {This systematic study documents the taxonomy, diversity, and distribution of 40 species of the predominately Californian trapdoor spider genus Aptostichus Simon, 1891. Thirty-three of these species are newly described: Aptostichus dantrippi, Aptostichus cabrillo, Aptostichus pennjillettei, Aptostichus asmodaeus, Aptostichus nateevansi, Aptostichus chiricahua, Aptostichus icenoglei, Aptostichus isabella, Aptostichus muiri, Aptostichus barackobamai, Aptostichus sinnombre, Aptostichus hedinorum, Aptostichus aguacaliente, Aptostichus chemehuevi, Aptostichus sarlacc, Aptostichus derhamgiulianii, Aptostichus anzaborrego, Aptostichus serrano, Aptostichus mikeradtkei, Aptostichus edwardabbeyi, Aptostichus killerdana, Aptostichus cahuilla, Aptostichus satleri, Aptostichus elisabethae, Aptostichus fornax, Aptostichus lucerne, Aptostichus fisheri, Aptostichus bonoi, Aptostichus cajalco, Aptostichus sierra, Aptostichus huntington, Aptostichus dorothealangeae, and Aptostichus chavezi. Most of these species are restricted to the California Floristic Province, a known biodiversity hotspot. Of the 40 recognized species, over half are considered to be imperiled or vulnerable and two have likely gone extinct over the past half-century; the conservation status of only 11 species is considered to be secure. Using 73 quantitative and qualitative morphological characters I propose a preliminary phylogeny for the genus that recognizes four major lineages: the Atomarius, Simus, Hesperus, and Sierra species groups. Additionally, the phylogenetic analysis indicates that adaptations favoring the invasion of the arid desert habitats of southern California have evolved multiple times across the group. The existence of both desert and non - desert species in three of the four species groups makes this genus an ideal candidate for the study of the evolutionary ecology of desert arthropods. A set of molecular characters based on the contiguous mitochondrial DNA genes 16S-tRNA valine-12S is used in an independent analysis to assist in placement of specimens into species. The taxonomy section explicitly identifies the concept employed in species delimitation. Niche based distribution models are constructed to predict the ranges of species for which an adequate number of sampling sites were known.},
}
@article {pmid23372415,
year = {2012},
author = {Marek, PE and Shear, WA and Bond, JE},
title = {A redescription of the leggiest animal, the millipede Illacme plenipes, with notes on its natural history and biogeography (Diplopoda, Siphonophorida, Siphonorhinidae).},
journal = {ZooKeys},
volume = {},
number = {241},
pages = {77-112},
pmid = {23372415},
issn = {1313-2989},
support = {K12 GM000708/GM/NIGMS NIH HHS/United States ; },
abstract = {With up to 750 legs, the millipede Illacme plenipes Cook and Loomis, 1928 is the leggiest animal known on Earth. It is endemic to the northwestern foothills of the Gabilan Range in San Benito County, California, where it is the only known species of the family Siphonorhinidae in the Western Hemisphere. Illacme plenipes is only known from 3 localities in a 4.5 km(2) area; the 1926 holotype locality is uncertain. Individuals of the species are strictly associated with large arkose sandstone boulders, and are extremely rare, with only 17 specimens known to exist in natural history collections. In contrast with its small size and unassuming outward appearance, the microanatomy of the species is strikingly complex. Here we provide a detailed redescription of the species, natural history notes, DNA barcodes for Illacme plenipes and similar-looking species, and a predictive occurrence map of the species inferred using niche based distribution modeling. Based on functional morphology of related species, the extreme number of legs is hypothesized to be associated with a life spent burrowing deep underground, and clinging to the surface of sandstone boulders.},
}
@article {pmid23368628,
year = {2013},
author = {Hassel, K and Segreto, R and Ekrem, T},
title = {Restricted variation in plant barcoding markers limits identification in closely related bryophyte species.},
journal = {Molecular ecology resources},
volume = {13},
number = {6},
pages = {1047-1057},
doi = {10.1111/1755-0998.12074},
pmid = {23368628},
issn = {1755-0998},
mesh = {Bryophyta/classification/*genetics ; *DNA Barcoding, Taxonomic ; Databases, Nucleic Acid ; Genetic Variation ; Phylogeny ; Species Specificity ; },
abstract = {Species-level identification and delimitation of bryophytes using the proposed general barcode markers for land plants has been challenging. Bryophyta (mosses) is the second most species-rich group of land plants after angiosperms, and it is thus of great importance to find useful barcoding regions also for this group of plants. We investigated how the plastid regions atpF-atpH, rbcL and trnH-psbA and the nuclear ITS2 region performed as barcode markers on closely related bryophyte taxa of selected moss (Bartramia, Distichium, Fissidens, Meesia and Syntrichia) and liverwort (Blepharostoma) genera from boreal and arctic regions. We also evaluated how sequencing success of herbarium specimens is related to length of the sequenced fragment, specimen age and taxonomic group. Sequencing success was higher for shorter fragments and younger herbarium specimens, but was lower than expected in the genera Distichium and Fissidens, indicating imperfect universality of the primers used. None of the studied DNA barcode regions showed a consistent barcode gap across the studied genera. As a single locus, the region atpF-atpH performed slightly better than rbcL and ITS2 and much better than trnH-psbA in terms of grouping conspecific sequences in monophyletic groups. This marker also gave a higher percentage of correct hits when conducting blast searches on a local database of identified sequences. Concatenated data sets of two and three markers grouped more conspecific sequences in monophyletic groups, but the improvement was not great compared with atpF-atpH alone. A discussion of recent studies testing barcode regions for bryophytes is given. We conclude that atpF-atpH, rbcL and ITS2 are to be the most promising barcode markers for mosses.},
}
@article {pmid23361043,
year = {2013},
author = {Zhou, J and Zhuang, J and Tang, J and Li, Q and Tang, D and Chen, G},
title = {Dual-nanogold-linked bio-barcodes with superstructures for in situ amplified electronic detection of low-abundance proteins.},
journal = {Molecular bioSystems},
volume = {9},
number = {4},
pages = {622-625},
doi = {10.1039/c3mb25536k},
pmid = {23361043},
issn = {1742-2051},
mesh = {*Biosensing Techniques/methods ; Carcinoembryonic Antigen/chemistry ; DNA/chemistry ; *Gold/chemistry ; Immunoassay/methods ; *Metal Nanoparticles/chemistry/ultrastructure ; Nucleic Acid Hybridization/methods ; Proteins/*chemistry ; },
abstract = {A novel and nonenzyme immunosensing protocol is proposed for ultrahighly sensitive detection of low-abundance-proteins (carcinoembryonic antigen as a model) using dual nanogold-linked complementary bio-barcodes with superstructures for in situ amplified electronic signals.},
}
@article {pmid23356387,
year = {2013},
author = {Xu, J and Turner, JW and Idso, M and Biryukov, SV and Rognstad, L and Gong, H and Trainer, VL and Wells, ML and Strom, MS and Yu, Q},
title = {In situ strain-level detection and identification of Vibrio parahaemolyticus using surface-enhanced Raman spectroscopy.},
journal = {Analytical chemistry},
volume = {85},
number = {5},
pages = {2630-2637},
doi = {10.1021/ac3021888},
pmid = {23356387},
issn = {1520-6882},
mesh = {Electricity ; Glass/chemistry ; Gold/chemistry ; Limit of Detection ; Nanostructures/chemistry ; Spectrum Analysis, Raman/instrumentation/*methods ; Surface Properties ; Time Factors ; Tin Compounds/chemistry ; Vibrio parahaemolyticus/*isolation &amp; purification ; },
abstract = {The outer membrane of a bacterium is composed of chemical and biological components that carry specific molecular information related to strains, growth stages, expressions to stimulation, and maybe even geographic differences. In this work, we demonstrate that the biochemical information embedded in the outer membrane can be used for rapid detection and identification of pathogenic bacteria using surface-enhanced Raman spectroscopy (SERS). We used seven different strains of the marine pathogen Vibrio parahaemolyticus as a model system. The strains represent four genetically distinct clades isolated from clinical and environmental sources in Washington, U.S.A. The unique quasi-3D (Q3D) plasmonic nanostructure arrays, optimized using finite-difference time-domain (FDTD) calculations, were used as SERS-active substrates for sensitive and reproducible detection of these bacteria. SERS barcodes were generated on the basis of SERS spectra and were used to successfully detect individual strains in both blind samples and mixtures. The sensing and detection methods developed in this work could have broad applications in the areas of environmental monitoring, biomedical diagnostics, and homeland security.},
}
@article {pmid23356053,
year = {2012},
author = {Pelletier, Y and Nie, X and Giguère, MA and Nanayakkara, U and Maw, E and Foottit, R},
title = {A new approach for the identification of aphid vectors (Hemiptera: Aphididae) of potato virus Y.},
journal = {Journal of economic entomology},
volume = {105},
number = {6},
pages = {1909-1914},
doi = {10.1603/ec12085},
pmid = {23356053},
issn = {0022-0493},
mesh = {Animals ; Aphids/*classification/virology ; Herbivory ; Insect Vectors/*classification/virology ; Plant Diseases/*virology ; Potyvirus/*isolation &amp; purification ; Solanum tuberosum/*virology ; },
abstract = {Potato virus Y (PVY) is one of the most economically important viruses affecting potato crops worldwide. PVY can be transmitted from potato to potato by several aphid species, most of which do not colonize the potato crop. New methods including preservation of viral RNA on stylets of aphids collected from yellow pan trap samples, polymerase chain reaction detection of PVY from the stylets of one aphid, and aphid identification using DNA barcoding were used to identify possible PVY vectors from field samples. In total, 65 aphid taxa were identified from the samples that tested positive for PVY. Among those, 45 taxa had never been evaluated for their ability to transmit PVY, and 7 were previously labeled as nonvectors. These results demonstrated that the list of PVY vectors is likely longer than previously reported and that most (if not all) species of aphids could be considered as potential vectors. This premise has important implications in the management of PVY in seed potato production.},
}
@article {pmid23351160,
year = {2013},
author = {Stahlhut, JK and Fernández-Triana, J and Adamowicz, SJ and Buck, M and Goulet, H and Hebert, PD and Huber, JT and Merilo, MT and Sheffield, CS and Woodcock, T and Smith, MA},
title = {DNA barcoding reveals diversity of Hymenoptera and the dominance of parasitoids in a sub-arctic environment.},
journal = {BMC ecology},
volume = {13},
number = {},
pages = {2},
pmid = {23351160},
issn = {1472-6785},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Hymenoptera/classification/*genetics ; Manitoba ; },
abstract = {BACKGROUND: Insect diversity typically declines with increasing latitude, but previous studies have shown conflicting latitude-richness gradients for some hymenopteran parasitoids. However, historical estimates of insect diversity and species richness can be difficult to confirm or compare, because they may be based upon dissimilar methods. As a proxy for species identification, we used DNA barcoding to identify molecular operational taxonomic units (MOTUs) for 7870 Hymenoptera specimens collected near Churchill, Manitoba, from 2004 through 2010.<br><br>RESULTS: We resolved 1630 MOTUs for this collection, of which 75% (1228) were ichneumonoids (Ichneumonidae + Braconidae) and 91% (1484) were parasitoids. We estimate the total number of Hymenoptera MOTUs in this region at 2624-2840.<br><br>CONCLUSIONS: The diversity of parasitoids in this sub-Arctic environment implies a high diversity of potential host species throughout the same range. We discuss these results in the contexts of resolving interspecific interactions that may include cryptic species, and developing reproducible methods to estimate and compare species richness across sites and between surveys, especially when morphological specialists are not available to identify every specimen.},
}
@article {pmid23350601,
year = {2013},
author = {Weitschek, E and Van Velzen, R and Felici, G and Bertolazzi, P},
title = {BLOG 2.0: a software system for character-based species classification with DNA Barcode sequences. What it does, how to use it.},
journal = {Molecular ecology resources},
volume = {13},
number = {6},
pages = {1043-1046},
doi = {10.1111/1755-0998.12073},
pmid = {23350601},
issn = {1755-0998},
mesh = {Classification/methods ; *DNA Barcoding, Taxonomic ; *Software ; Species Specificity ; User-Computer Interface ; },
abstract = {BLOG (Barcoding with LOGic) is a diagnostic and character-based DNA Barcode analysis method. Its aim is to classify specimens to species based on DNA Barcode sequences and on a supervised machine learning approach, using classification rules that compactly characterize species in terms of DNA Barcode locations of key diagnostic nucleotides. The BLOG 2.0 software, its fundamental modules, online/offline user interfaces and recent improvements are described. These improvements affect both methodology and software design, and lead to the availability of different releases on the website http://dmb.iasi.cnr.it/blog-downloads.php. Previous and new experimental tests show that BLOG 2.0 outperforms previous versions as well as other DNA Barcode analysis methods.},
}
@article {pmid23344697,
year = {2013},
author = {, },
title = {Progress in immunization information systems--United States, 2011.},
journal = {MMWR. Morbidity and mortality weekly report},
volume = {62},
number = {3},
pages = {48-51},
pmid = {23344697},
issn = {1545-861X},
mesh = {Child ; Child, Preschool ; Data Collection ; Healthy People Programs ; Humans ; Immunization/*statistics &amp; numerical data ; Immunization Programs/statistics &amp; numerical data ; Infant ; Information Systems/*trends ; Medical Records/statistics &amp; numerical data ; Product Labeling ; United States ; Vaccines/*administration &amp; dosage/classification/supply &amp; distribution ; },
abstract = {Immunization information systems (IIS) are confidential, computerized, population-based systems that collect and consolidate vaccination data from vaccination providers and provide important tools for designing and sustaining effective immunization strategies. A Healthy People 2020 objective (IID-18) is to increase to 95% the proportion of children aged <6 years whose immunization records are in fully operational, population-based IIS. The National Vaccine Advisory Committee (NVAC) has published goals for IIS, including required and optional core data elements for which IIS should collect information. Two of the required core data elements are vaccine manufacturer and vaccine lot number. To monitor progress toward achieving these and other program goals, CDC annually surveys 56 immunization program grantees using the IIS Annual Report (IISAR). Results from the 2011 IISAR (completed by 54 grantees) indicate that 84% (19.2 million) of U.S. children aged <6 years participated in IIS, as defined by having at least two recorded vaccinations, an increase from 82% (18.8 million) in 2010. Grantees reported that an average of 63% of vaccination records for these children contained data in the field for vaccine manufacturer and 60% contained data in the field for lot number. A new project under way to capture vaccine product information, expiration date, and lot number on two-dimensional (2D) barcodes on vaccine vials might increase completeness, accuracy, and availability of these data elements in patient medical records and IIS, which in turn might enhance vaccine safety and support vaccine inventory management.},
}
@article {pmid23341979,
year = {2013},
author = {Laskar, BA and Bhattacharjee, MJ and Dhar, B and Mahadani, P and Kundu, S and Ghosh, SK},
title = {The species dilemma of Northeast Indian Mahseer (Actinopterygii: Cyprinidae): DNA barcoding in clarifying the riddle.},
journal = {PloS one},
volume = {8},
number = {1},
pages = {e53704},
pmid = {23341979},
issn = {1932-6203},
mesh = {Animals ; Conservation of Natural Resources ; Cyprinidae/anatomy &amp; histology/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; Polymerase Chain Reaction ; },
abstract = {BACKGROUND: The taxonomic validity of Northeast Indian endemic Mahseer species, Tor progeneius and Neolissochilus hexastichus, has been argued repeatedly. This is mainly due to disagreements in recognizing the species based on morphological characters. Consequently, both the species have been concealed for many decades. DNA barcoding has become a promising and an independent technique for accurate species level identification. Therefore, utilization of such technique in association with the traditional morphotaxonomic description can resolve the species dilemma of this important group of sport fishes.<br><br>Altogether, 28 mahseer specimens including paratypes were studied from different locations in Northeast India, and 24 morphometric characters were measured invariably. The Principal Component Analysis with morphometric data revealed five distinct groups of sample that were taxonomically categorized into 4 species, viz., Tor putitora, T. progeneius, Neolissochilus hexagonolepis and N. hexastichus. Analysis with a dataset of 76 DNA barcode sequences of different mahseer species exhibited that the queries of T. putitora and N. hexagonolepis clustered cohesively with the respective conspecific database sequences maintaining 0.8% maximum K2P divergence. The closest congeneric divergence was 3 times higher than the mean conspecific divergence and was considered as barcode gap. The maximum divergence among the samples of T. progeneius and T. putitora was 0.8% that was much below the barcode gap, indicating them being synonymous. The query sequences of N. hexastichus invariably formed a discrete and a congeneric clade with the database sequences and maintained the interspecific divergence that supported its distinct species status. Notably, N. hexastichus was encountered in a single site and seemed to be under threat.<br><br>CONCLUSION: This study substantiated the identification of N. hexastichus to be a true species, and tentatively regarded T. progeneius to be a synonym of T. putitora. It would guide the conservationists to initiate priority conservation of N. hexastichus and T. putitora.},
}
@article {pmid23341927,
year = {2013},
author = {Stech, M and Veldman, S and Larraín, J and Muñoz, J and Quandt, D and Hassel, K and Kruijer, H},
title = {Molecular species delimitation in the Racomitrium canescens complex (Grimmiaceae) and implications for DNA barcoding of species complexes in mosses.},
journal = {PloS one},
volume = {8},
number = {1},
pages = {e53134},
pmid = {23341927},
issn = {1932-6203},
mesh = {Base Sequence ; Bryophyta/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; Genetic Variation ; Species Specificity ; },
abstract = {In bryophytes a morphological species concept is still most commonly employed, but delimitation of closely related species based on morphological characters is often difficult. Here we test morphological species circumscriptions in a species complex of the moss genus Racomitrium, the R. canescens complex, based on variable DNA sequence markers from the plastid (rps4-trnT-trnL region) and nuclear (nrITS) genomes. The extensive morphological variability within the complex has led to different opinions about the number of species and intraspecific taxa to be distinguished. Molecular phylogenetic reconstructions allowed to clearly distinguish all eight currently recognised species of the complex plus a ninth species that was inferred to belong to the complex in earlier molecular analyses. The taxonomic significance of intraspecific sequence variation is discussed. The present molecular data do not support the division of the R. canescens complex into two groups of species (subsections or sections). Most morphological characters, albeit being in part difficult to apply, are reliable for species identification in the R. canescens complex. However, misidentification of collections that were morphologically intermediate between species questioned the suitability of leaf shape as diagnostic character. Four partitions of the molecular markers (rps4-trnT, trnT-trnL, ITS1, ITS2) that could potentially be used for molecular species identification (DNA barcoding) performed almost equally well concerning amplification and sequencing success. Of these, ITS1 provided the highest species discrimination capacity and should be considered as a DNA barcoding marker for mosses, especially in complexes of closely related species. Molecular species identification should be complemented by redefining morphological characters, to develop a set of easy-to-use molecular and non-molecular identification tools for improving biodiversity assessments and ecological research including mosses.},
}
@article {pmid23335979,
year = {2013},
author = {Maas, AE and Blanco-Bercial, L and Lawson, GL},
title = {Reexamination of the species assignment of Diacavolinia pteropods using DNA barcoding.},
journal = {PloS one},
volume = {8},
number = {1},
pages = {e53889},
pmid = {23335979},
issn = {1932-6203},
mesh = {Animals ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Gastropoda/anatomy &amp; histology/*classification/*genetics ; Haplotypes ; Molecular Sequence Data ; Phylogeny ; },
abstract = {Thecosome pteropods (Mollusca, Gastropoda) are an ecologically important, diverse, and ubiquitous group of holoplanktonic animals that are the focus of intense research interest due to their external aragonite shell and vulnerability to ocean acidification. Characterizing the response of these animals to low pH and other environmental stressors has been hampered by continued uncertainty in their taxonomic identification. An example of this confusion in species assignment is found in the genus Diacavolinia. All members of this genus were originally indentified as a single species, Cavolinia longirostris, but over the past fifty years the taxonomy has been revisited multiple times; currently the genus comprises 22 different species. This study examines five species of Diacavolinia, including four sampled in the Northeast Atlantic (78 individuals) and one from the Eastern tropical North Pacific (15 individuals). Diacavolina were identified to species based on morphological characteristics according to the current taxonomy, photographed, and then used to determine the sequence of the "DNA barcoding" region of the cytochrome c oxidase subunit I (COI). Specimens from the Atlantic, despite distinct differences in shell morphology, showed polyphyly and a genetic divergence of <3% (K2P distance) whereas the Pacific and Atlantic samples were more distant (≈ 19%). Comparisons of Diacavolinia spp. with other Cavolinia spp. reveal larger distances (≈ 24%). These results indicate that specimens from the Atlantic comprise a single monophyletic species and suggest possible species-level divergence between Atlantic and Pacific populations. The findings support the maintenance of Diacavolinia as a separate genus, yet emphasize the inadequacy of our current taxonomic understanding of pteropods. They highlight the need for accurate species identifications to support estimates of biodiversity, range extent and natural exposure of these planktonic calcifiers to environmental variability; furthermore, the apparent variation of the pteropods shell may have implications for our understanding of the species' sensitivity to ocean acidification.},
}
@article {pmid23331872,
year = {2013},
author = {Patricelli, D and Sielezniew, M and Ponikwicka-Tyszko, D and Ratkiewicz, M and Bonelli, S and Barbero, F and Witek, M and Buś, MM and Rutkowski, R and Balletto, E},
title = {Contrasting genetic structure of rear edge and continuous range populations of a parasitic butterfly infected by Wolbachia.},
journal = {BMC evolutionary biology},
volume = {13},
number = {},
pages = {14},
pmid = {23331872},
issn = {1471-2148},
mesh = {Animals ; Butterflies/*genetics/microbiology ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Genetic Variation ; *Genetics, Population ; Geography ; Haplotypes ; Italy ; Poland ; Polymorphism, Genetic ; Sequence Analysis, DNA ; *Wolbachia ; },
abstract = {BACKGROUND: Climatic oscillations are among the long-term factors shaping the molecular features of animals and plants and it is generally supposed that the rear edges (i.e., the low-latitude limits of distribution of any given specialised species) situated closer to glacial refugia are vital long-term stores of genetic diversity. In the present study, we compared the genetic structure of several populations of an endangered and obligate myrmecophilous butterfly (Maculinea arion) from two distinct and geographically distant parts of its European distribution (i.e., Italy and Poland), which fully represent the ecological and morphological variation occurring across the continent.<br><br>RESULTS: We sequenced the COI mitochondrial DNA gene (the 'barcoding gene') and the EF-1&#x3b1; nuclear gene and found substantial genetic differentiation among M. arion Italian populations in both markers. Eleven mtDNA haplotypes were present in Italy. In contrast, almost no mtDNA polymorphisms was found in the Polish M. arion populations, where genetic differentiation at the nuclear gene was low to moderate. Interestingly, the within-population diversity levels in the EF-1&#x3b1; gene observed in Italy and in Poland were comparable. The genetic data did not support any subspecies divisions or any ecological specialisations. All of the populations studied were infected with a single strain of Wolbachia and our screening suggested 100% prevalence of the bacterium.<br><br>CONCLUSIONS: Differences in the genetic structure of M. arion observed in Italy and in Poland may be explained by the rear edge theory. Although we were not able to pinpoint any specific evolutionarily significant units, we suggest that the Italian peninsula should be considered as a region of special conservation concern and one that is important for maintaining the genetic diversity of M. arion in Europe. The observed pattern of mtDNA differentiation among the populations could not be explained by an endosymbiotic infection.},
}
@article {pmid23327366,
year = {2013},
author = {Chen, HN and Høeg, JT and Chan, BK},
title = {Morphometric and molecular identification of individual barnacle cyprids from wild plankton: an approach to detecting fouling and invasive barnacle species.},
journal = {Biofouling},
volume = {29},
number = {2},
pages = {133-145},
doi = {10.1080/08927014.2012.753061},
pmid = {23327366},
issn = {1029-2454},
mesh = {Animals ; *Biofouling ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/analysis/genetics ; Ecosystem ; Electron Transport Complex IV/genetics ; Genetic Variation ; Introduced Species ; Larva/classification/genetics/ultrastructure ; Microscopy, Electron, Scanning ; Mitochondria/genetics ; Multivariate Analysis ; Phylogeny ; Species Specificity ; Taiwan ; Thoracica/anatomy &amp; histology/*classification/genetics ; },
abstract = {The present study used DNA barcodes to identify individual cyprids to species. This enables accurate quantification of larvae of potential fouling species in the plankton. In addition, it explains the settlement patterns of barnacles and serves as an early warning system of unwanted immigrant species. Sequences from a total of 540 individual cypris larvae from Taiwanese waters formed 36 monophyletic clades (species) in a phylogenetic tree. Of these clades, 26 were identified to species, but 10 unknown monophyletic clades represented non-native species. Cyprids of the invasive barnacle, Megabalanus cocopoma, were identified. Multivariate analysis of antennular morphometric characters revealed three significant clusters in a nMDS plot, viz. a bell-shaped attachment organ (most species), a shoe-shaped attachment organ (some species), and a spear-shaped attachment organ (coral barnacles only). These differences in attachment organ structure indicate that antennular structures interact directly with the diverse substrata involved in cirripede settlement.},
}
@article {pmid23317871,
year = {2013},
author = {Jones, YL and Peters, SM and Weland, C and Ivanova, NV and Yancy, HF},
title = {Potential use of DNA barcodes in regulatory science: identification of the U.S. Food and Drug Administration's "Dirty 22," contributors to the spread of foodborne pathogens.},
journal = {Journal of food protection},
volume = {76},
number = {1},
pages = {144-149},
doi = {10.4315/0362-028X.JFP-12-168},
pmid = {23317871},
issn = {1944-9097},
mesh = {Animals ; Consumer Product Safety ; DNA/*analysis ; Food Contamination/*analysis/*legislation &amp; jurisprudence/prevention &amp; control ; Food Microbiology ; Food-Processing Industry/*standards ; Humans ; *Public Health ; Species Specificity ; United States ; United States Food and Drug Administration ; },
abstract = {The U.S. Food, Drug, and Cosmetic Act prohibits the distribution of food that is adulterated, and the regulatory mission of the U.S. Food and Drug Administration (FDA) is to enforce this Act. FDA field laboratories have identified the 22 most common pests that contribute to the spread of foodborne disease (the "Dirty 22"). The current method of detecting filth and extraneous material (tails, legs, carcasses, etc.) is visual inspection using microscopy. Because microscopy can be time-consuming and may yield inaccurate and/or nonspecific results due to lack of expertise, an alternative method of detecting these adulterants is needed. In this study, we sequenced DNA from the 5' region of the cytochrome oxidase I gene of these 22 common pests that contribute to the spread of foodborne pathogens. Here, we describe the generation of DNA barcodes for all 22 species. To date, this is the first attempt to develop a sequence-based regulatory database and systematic primer strategy to identify these FDA-targeted species. DNA barcoding can be a powerful tool that can aid the FDA in promoting the protection and safety of the U.S. food supply.},
}
@article {pmid23317705,
year = {2012},
author = {Selvaraj, D and Shanmughanandhan, D and Sarma, RK and Joseph, JC and Srinivasan, RV and Ramalingam, S},
title = {DNA barcode ITS effectively distinguishes the medicinal plant Boerhavia diffusa from its adulterants.},
journal = {Genomics, proteomics &amp; bioinformatics},
volume = {10},
number = {6},
pages = {364-367},
pmid = {23317705},
issn = {2210-3244},
mesh = {Base Sequence ; Chloroplasts/genetics ; *DNA Barcoding, Taxonomic ; DNA, Plant/chemistry/*genetics ; DNA, Ribosomal Spacer/chemistry/*genetics ; India ; Nyctaginaceae/*classification/genetics ; Phylogeny ; Plants, Medicinal/*classification/genetics ; Sequence Alignment ; Species Specificity ; },
abstract = {Boerhavia diffusa (B. diffusa), also known as Punarnava, is an indigenous plant in India and an important component in traditional Indian medicine. The accurate identification and collection of this medicinal herb is vital to enhance the drug's efficacy and biosafety. In this study, a DNA barcoding technique has been applied to identify and distinguish B. diffusa from its closely-related species. The phylogenetic analysis was carried out for the four species of Boerhavia using barcode candidates including nuclear ribosomal DNA regions ITS, ITS1, ITS2 and the chloroplast plastid gene psbA-trnH. Sequence alignment revealed 26% polymorphic sites in ITS, 30% in ITS1, 16% in ITS2 and 6% in psbA-trnH, respectively. Additionally, a phylogenetic tree was constructed for 15 species using ITS sequences which clearly distinguished B. diffusa from the other species. The ITS1 demonstrates a higher transition/transversion ratio, percentage of variation and pairwise distance which differentiate B. diffusa from other species of Boerhavia. Our study revealed that ITS and ITS1 could be used as potential candidate regions for identifying B. diffusa and for authenticating its herbal products.},
}
@article {pmid23314250,
year = {2013},
author = {Østergaard, PF and Matteucci, M and Reisner, W and Taboryski, R},
title = {DNA barcoding via counterstaining with AT/GC sensitive ligands in injection-molded all-polymer nanochannel devices.},
journal = {The Analyst},
volume = {138},
number = {4},
pages = {1249-1255},
doi = {10.1039/c2an36522g},
pmid = {23314250},
issn = {1364-5528},
mesh = {DNA/analysis ; DNA Barcoding, Taxonomic/*methods ; Ligands ; Nanotechnology/*methods ; Polymers/*chemistry ; Purines/*analysis ; Pyrimidines/*analysis ; },
abstract = {Nanochannel technology, coupled with a suitable DNA labeling chemistry, is a powerful approach for performing high-throughput single-molecule mapping of genomes. Yet so far nanochannel technology has remained inaccessible to the broader research community due to high fabrication cost and/or requirement of specialized facilities/skill-sets. In this article we show that nanochannel-based mapping can be performed in all polymer chips fabricated via injection molding: a fabrication process so inexpensive that the devices can be considered disposable. Fluorescent intensity variations can be obtained from molecules extended in the polymer nanochannels via chemical counterstaining against YOYO-1. In particular, we demonstrate that the counterstaining induced fluorescent intensity variations to a large degree appear to be proportional to the theoretically computed sequence-maps of both local AT and GC variation along DNA sequences.},
}
@article {pmid23311518,
year = {2013},
author = {Meiklejohn, KA and Wallman, JF and Dowton, M},
title = {DNA barcoding identifies all immature life stages of a forensically important flesh fly (Diptera: Sarcophagidae).},
journal = {Journal of forensic sciences},
volume = {58},
number = {1},
pages = {184-187},
doi = {10.1111/j.1556-4029.2012.02220.x},
pmid = {23311518},
issn = {1556-4029},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Larva/genetics ; Pupa/genetics ; Sarcophagidae/*genetics ; Sequence Analysis, DNA ; },
abstract = {Carrion-breeding insects, such as flesh flies (Diptera: Sarcophagidae), can be used as evidence in forensic investigations. Despite their considerable forensic potential, their use has been limited because morphological species identification, at any life stage, is very challenging. This study investigated whether DNA could be extracted and cytochrome oxidase subunit I (COI) barcode sequences obtained for molecular identification of each immature life stage of the forensically important Australian flesh fly, Sarcophaga (Sarcorohdendorfia) impatiens (Walker). Genomic DNA extracts were prepared from all larval instars and puparia. Amplification of the barcoding region was successful from all extracts, but puparia amplicons were weak. All sequences were identified as S. impatiens with 99.95% confidence using the Barcoding of Life Database (BOLD). Importantly, crop removal was necessary to eliminate PCR inhibition for specimens from late second and early third instars. Similar results are expected for immatures of other carrion-breeding species, enhancing the use of evidence from immature flies in forensic investigations.},
}
@article {pmid23311467,
year = {2013},
author = {Jeong, TJ and Jun, J and Han, S and Kim, HT and Oh, K and Kwak, M},
title = {DNA barcode reference data for the Korean herpetofauna and their applications.},
journal = {Molecular ecology resources},
volume = {13},
number = {6},
pages = {1019-1032},
doi = {10.1111/1755-0998.12055},
pmid = {23311467},
issn = {1755-0998},
mesh = {Amphibians/classification/*genetics ; Animals ; Cytochromes b/chemistry/genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry/classification ; *Databases, Nucleic Acid ; Electron Transport Complex IV/chemistry/genetics ; Endangered Species ; Genetic Markers ; Genetic Variation ; Phylogeny ; Reptiles/classification/*genetics ; Republic of Korea ; Species Specificity ; },
abstract = {Recently, amphibians and reptiles have drawn attention because of declines in species and populations caused mainly by habitat loss, overexploitation and climate change. This study constructed a DNA barcode database for the Korean herpetofauna, including all the recorded amphibians and 68% of the recorded reptiles, to provide a useful, standardized tool for species identification in monitoring and management. A total of 103 individuals from 18 amphibian and 17 reptile species were used to generate barcode sequences using partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene and to compare it with other suggested barcode loci. Comparing 16S rRNA, cytochrome b (Cytb) and COI for amphibians and 12S rRNA, Cytb and COI for reptiles, our results revealed that COI is better than the other markers in terms of a high level of sequence variation without length variation and moderate amplification success. Although the COI marker had no clear barcoding gap because of the high level of intraspecific variation, all of the analysed individuals from the same species clustered together in a neighbour-joining tree. High intraspecific variation suggests the possibility of cryptic species. Finally, using this database, confiscated snakes were identified as Elaphe schrenckii, designated as endangered in Korea and a food contaminant was identified as the lizard Takydromus amurensis.},
}
@article {pmid23308131,
year = {2013},
author = {Sukhdeo, K and Paramban, RI and Vidal, JG and Elia, J and Martin, J and Rivera, M and Carrasco, DR and Jarrar, A and Kalady, MF and Carson, CT and Balderas, R and Hjelmeland, AB and Lathia, JD and Rich, JN},
title = {Multiplex flow cytometry barcoding and antibody arrays identify surface antigen profiles of primary and metastatic colon cancer cell lines.},
journal = {PloS one},
volume = {8},
number = {1},
pages = {e53015},
pmid = {23308131},
issn = {1932-6203},
support = {CA157948/CA/NCI NIH HHS/United States ; F30 CA165857/CA/NCI NIH HHS/United States ; R01 CA116659/CA/NCI NIH HHS/United States ; K99 CA157948/CA/NCI NIH HHS/United States ; CA112958/CA/NCI NIH HHS/United States ; UL1 TR000439/TR/NCATS NIH HHS/United States ; T32 GM088088/GM/NIGMS NIH HHS/United States ; R00 CA157948/CA/NCI NIH HHS/United States ; CA154130/CA/NCI NIH HHS/United States ; CA116659/CA/NCI NIH HHS/United States ; T32 GM007250/GM/NIGMS NIH HHS/United States ; R01 CA154130/CA/NCI NIH HHS/United States ; },
mesh = {Antigens/*analysis ; Biomarkers, Tumor/*analysis ; Cell Line, Tumor ; Colon/*pathology ; Colonic Neoplasms/*pathology ; Computational Biology/methods/organization &amp; administration ; Flow Cytometry/*methods ; Fluorescent Antibody Technique/methods ; High-Throughput Screening Assays/methods ; Humans ; Immunohistochemistry/methods ; Neoplasm Metastasis/*pathology ; Protein Array Analysis/*methods ; Tumor Cells, Cultured ; },
abstract = {Colon cancer is a deadly disease affecting millions of people worldwide. Current treatment challenges include management of disease burden as well as improvements in detection and targeting of tumor cells. To identify disease state-specific surface antigen signatures, we combined fluorescent cell barcoding with high-throughput flow cytometric profiling of primary and metastatic colon cancer lines (SW480, SW620, and HCT116). Our multiplexed technique offers improvements over conventional methods by permitting the simultaneous and rapid screening of cancer cells with reduced effort and cost. The method uses a protein-level analysis with commercially available antibodies on live cells with intact epitopes to detect potential tumor-specific targets that can be further investigated for their clinical utility. Multiplexed antibody arrays can easily be applied to other tumor types or pathologies for discovery-based approaches to target identification.},
}
@article {pmid23308128,
year = {2013},
author = {García-Robledo, C and Erickson, DL and Staines, CL and Erwin, TL and Kress, WJ},
title = {Tropical plant-herbivore networks: reconstructing species interactions using DNA barcodes.},
journal = {PloS one},
volume = {8},
number = {1},
pages = {e52967},
pmid = {23308128},
issn = {1932-6203},
mesh = {Animals ; Coleoptera/*physiology ; *DNA Barcoding, Taxonomic ; DNA, Plant/*genetics/*isolation &amp; purification ; *Herbivory ; Plant Leaves/genetics ; Plants/*genetics ; },
abstract = {Plants and their associated insect herbivores, represent more than 50% of all known species on earth. The first step in understanding the mechanisms generating and maintaining this important component of biodiversity is to identify plant-herbivore associations. In this study we determined insect-host plant associations for an entire guild of insect herbivores using plant DNA extracted from insect gut contents. Over two years, in a tropical rain forest in Costa Rica (La Selva Biological Station), we recorded the full diet breadth of rolled-leaf beetles, a group of herbivores that feed on plants in the order Zingiberales. Field observations were used to determine the accuracy of diet identifications using a three-locus DNA barcode (rbcL, trnH-psbA and ITS2). Using extraction techniques for ancient DNA, we obtained high-quality sequences for two of these loci from gut contents (rbcL and ITS2). Sequences were then compared to a comprehensive DNA barcode library of the Zingiberales. The rbcL locus identified host plants to family (success/sequence = 58.8%) and genus (success/sequence = 47%). For all Zingiberales except Heliconiaceae, ITS2 successfully identified host plants to genus (success/sequence = 67.1%) and species (success/sequence = 61.6%). Kindt's sampling estimates suggest that by collecting ca. four individuals representing each plant-herbivore interaction, 99% of all host associations included in this study can be identified to genus. For plants that amplified ITS2, 99% of the hosts can be identified to species after collecting at least four individuals representing each interaction. Our study demonstrates that host plant identifications at the species-level using DNA barcodes are feasible, cost-effective, and reliable, and that reconstructing plant-herbivore networks with these methods will become the standard for a detailed understanding of these interactions.},
}
@article {pmid23308097,
year = {2013},
author = {Stein, ED and White, BP and Mazor, RD and Miller, PE and Pilgrim, EM},
title = {Evaluating ethanol-based sample preservation to facilitate use of DNA barcoding in routine freshwater biomonitoring programs using benthic macroinvertebrates.},
journal = {PloS one},
volume = {8},
number = {1},
pages = {e51273},
pmid = {23308097},
issn = {1932-6203},
mesh = {Animals ; Aquatic Organisms/genetics ; Base Sequence ; Biodiversity ; DNA/*genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Electron Transport Complex IV/genetics ; Ethanol/*chemistry ; Gastropoda/*genetics ; Insect Proteins/genetics ; Insecta/*genetics ; Preservation, Biological/*methods ; },
abstract = {Molecular methods, such as DNA barcoding, have the potential to enhance biomonitoring programs worldwide. Altering routinely used sample preservation methods to protect DNA from degradation may pose a potential impediment to application of DNA barcoding and metagenomics for biomonitoring using benthic macroinvertebrates. Using higher volumes or concentrations of ethanol, requirements for shorter holding times, or the need to include additional filtering may increase cost and logistical constraints to existing biomonitoring programs. To address this issue we evaluated the efficacy of various ethanol-based sample preservation methods at maintaining DNA integrity. We evaluated a series of methods that were minimally modified from typical field protocols in order to identify an approach that can be readily incorporated into existing monitoring programs. Benthic macroinvertebrates were collected from a minimally disturbed stream in southern California, USA and subjected to one of six preservation treatments. Ten individuals from five taxa were selected from each treatment and processed to produce DNA barcodes from the mitochondrial gene cytochrome c oxidase I (COI). On average, we obtained successful COI sequences (i.e. either full or partial barcodes) for between 93-99% of all specimens across all six treatments. As long as samples were initially preserved in 95% ethanol, successful sequencing of COI barcodes was not affected by a low dilution ratio of 2∶1, transfer to 70% ethanol, presence of abundant organic matter, or holding times of up to six months. Barcoding success varied by taxa, with Leptohyphidae (Ephemeroptera) producing the lowest barcode success rate, most likely due to poor PCR primer efficiency. Differential barcoding success rates have the potential to introduce spurious results. However, routine preservation methods can largely be used without adverse effects on DNA integrity.},
}
@article {pmid23304237,
year = {2012},
author = {Li, H and Liu, C},
title = {A dynamic data-driven framework for biological data using 2D barcodes.},
journal = {Computational and mathematical methods in medicine},
volume = {2012},
number = {},
pages = {892098},
pmid = {23304237},
issn = {1748-6718},
mesh = {Algorithms ; Animals ; Computational Biology/instrumentation/*methods ; Computer Simulation ; Electronic Data Processing/*instrumentation ; Humans ; Models, Statistical ; Reproducibility of Results ; *Signal Processing, Computer-Assisted ; },
abstract = {Biology data is increasing exponentially from biological laboratories. It is a complicated problem for further processing the data. Processing computational data and data from biological laboratories manually may lead to potential errors in further analysis. In this paper, we proposed an efficient data-driven framework to inspect laboratory equipment and reduce impending failures. Our method takes advantage of the 2D barcode technology which can be installed on the specimen as a trigger for the data-driven system. For this end, we proposed a series of algorithms to speed up the data processing. The results show that the proposed system increases the system's scalability and flexibility. Also, it demonstrates the ability of linking a physical object with digital information to reduce the manual work related to experimental specimen. The characteristics such as high capacity of storage and data management of the 2D barcode technology provide a solution to collect experimental laboratory data in a quick and accurate fashion.},
}
@article {pmid23303722,
year = {2013},
author = {Nallala, J and Piot, O and Diebold, MD and Gobinet, C and Bouché, O and Manfait, M and Sockalingum, GD},
title = {Infrared imaging as a cancer diagnostic tool: introducing a new concept of spectral barcodes for identifying molecular changes in colon tumors.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {83},
number = {3},
pages = {294-300},
doi = {10.1002/cyto.a.22249},
pmid = {23303722},
issn = {1552-4930},
mesh = {Colonic Neoplasms/*diagnosis ; Diagnostic Imaging/*methods ; Humans ; Infrared Rays ; Molecular Diagnostic Techniques/*methods ; Multivariate Analysis ; *Spectrophotometry, Infrared ; },
abstract = {Complementary diagnostic methods to conventional histopathology are under scrutiny for various types of cancers for rapid and molecular level diagnostics. In this perspective, a biophotonic approach based on infrared spectral micro-imaging combined with multivariate statistical analysis has been implemented on colon tissues. The ability of infrared imaging to investigate the intrinsic biochemical features of cells and tissues has been exploited to develop a new concept of spectral bar coding. To implement this concept, 10 frozen colon tissue samples (five nontumoral and tumoral pairs from five patients) were imaged using infrared spectral micro-imaging in a nondestructive manner. The spectral images were processed by a multivariate clustering method to identify the histological organization in a label-free manner. Spectral information from the epithelial components was then automatically recovered on the basis of their intrinsic biochemical composition, and compared using a statistical method (Mann-Whitney U-test) to construct spectral barcodes specific to each patient. The spectral barcodes representing the discriminant infrared spectral wavenumbers (900-1,800 cm(-1)) enabled characterization of some of the malignancy-associated biochemical alterations associated with mucin, nucleotides, carbohydrates, and protein regions. This approach not only allowed the identification of common biochemical alterations among all the colon cancer patients, but also revealed a difference of gradient within individual patients. This new concept of spectral bar coding gives insight into the potential of infrared spectral micro-imaging as a complementary diagnostic tool to conventional histopathology, for biochemical level understanding of malignancy in colon cancers in an objective and label-free manner.},
}
@article {pmid23282079,
year = {2012},
author = {Biswal, DK and Debnath, M and Kumar, S and Tandon, P},
title = {Phylogenetic reconstruction in the order Nymphaeales: ITS2 secondary structure analysis and in silico testing of maturase k (matK) as a potential marker for DNA bar coding.},
journal = {BMC bioinformatics},
volume = {13 Suppl 17},
number = {Suppl 17},
pages = {S26},
pmid = {23282079},
issn = {1471-2105},
mesh = {Bayes Theorem ; Chloroplasts/genetics ; Computer Simulation ; DNA Barcoding, Taxonomic/*methods/statistics &amp; numerical data ; DNA, Chloroplast/genetics ; DNA, Intergenic/genetics ; DNA, Plant/genetics ; Endoribonucleases/chemistry/*genetics ; Fossils ; Genetic Markers ; Likelihood Functions ; Nucleic Acid Conformation ; Nucleotidyltransferases/chemistry/*genetics ; Nymphaeaceae/*classification/genetics ; Phylogeny ; Protein Structure, Secondary ; Sequence Alignment ; },
abstract = {BACKGROUND: The Nymphaeales (waterlilly and relatives) lineage has diverged as the second branch of basal angiosperms and comprises of two families: Cabombaceae and Nymphaceae. The classification of Nymphaeales and phylogeny within the flowering plants are quite intriguing as several systems (Thorne system, Dahlgren system, Cronquist system, Takhtajan system and APG III system (Angiosperm Phylogeny Group III system) have attempted to redefine the Nymphaeales taxonomy. There have been also fossil records consisting especially of seeds, pollen, stems, leaves and flowers as early as the lower Cretaceous. Here we present an in silico study of the order Nymphaeales taking maturaseK (matK) and internal transcribed spacer (ITS2) as biomarkers for phylogeny reconstruction (using character-based methods and Bayesian approach) and identification of motifs for DNA barcoding.<br><br>RESULTS: The Maximum Likelihood (ML) and Bayesian approach yielded congruent fully resolved and well-supported trees using a concatenated (ITS2+ matK) supermatrix aligned dataset. The taxon sampling corroborates the monophyly of Cabombaceae. Nuphar emerges as a monophyletic clade in the family Nymphaeaceae while there are slight discrepancies in the monophyletic nature of the genera Nymphaea owing to Victoria-Euryale and Ondinea grouping in the same node of Nymphaeaceae. ITS2 secondary structures alignment corroborate the primary sequence analysis. Hydatellaceae emerged as a sister clade to Nymphaeaceae and had a basal lineage amongst the water lilly clades. Species from Cycas and Ginkgo were taken as outgroups and were rooted in the overall tree topology from various methods.<br><br>CONCLUSIONS: MatK genes are fast evolving highly variant regions of plant chloroplast DNA that can serve as potential biomarkers for DNA barcoding and also in generating primers for angiosperms with identification of unique motif regions. We have reported unique genus specific motif regions in the Order Nymphaeles from matK dataset which can be further validated for barcoding and designing of PCR primers. Our analysis using a novel approach of sequence-structure alignment and phylogenetic reconstruction using molecular morphometrics congrue with the current placement of Hydatellaceae within the early-divergent angiosperm order Nymphaeales. The results underscore the fact that more diverse genera, if not fully resolved to be monophyletic, should be represented by all major lineages.},
}
@article {pmid23301165,
year = {2012},
author = {Hogner, S and Laskemoen, T and Lifjeld, JT and Porkert, J and Kleven, O and Albayrak, T and Kabasakal, B and Johnsen, A},
title = {Deep sympatric mitochondrial divergence without reproductive isolation in the common redstart Phoenicurus phoenicurus.},
journal = {Ecology and evolution},
volume = {2},
number = {12},
pages = {2974-2988},
pmid = {23301165},
issn = {2045-7758},
abstract = {Mitochondrial DNA usually shows low sequence variation within and high sequence divergence among species, which makes it a useful marker for phylogenetic inference and DNA barcoding. A previous study on the common redstart (Phoenicurus phoenicurus) revealed two very different mtDNA haplogroups (5% K2P distance). This divergence is comparable to that among many sister species; however, both haplogroups coexist and interbreed in Europe today. Herein, we describe the phylogeographic pattern of these lineages and test hypotheses for how such high diversity in mtDNA has evolved. We found no evidence for mitochondrial pseudogenes confirming that both haplotypes are of mitochondrial origin. When testing for possible reproductive barriers, we found no evidence for lineage-specific assortative mating and no difference in sperm morphology, indicating that they are not examples of cryptic species, nor likely to reflect the early stages of speciation. A gene tree based on a short fragment of cytochrome c oxidase subunit 1 from the common redstart and 10 other Phoenicurus species, showed no introgression from any of the extant congenerics. However, introgression from an extinct congeneric cannot be excluded. Sequences from two nuclear introns did not show a similar differentiation into two distinct groups. Mismatch distributions indicated that the lineages have undergone similar demographic changes. Taken together, these results confirm that deeply divergent mitochondrial lineages can coexist in biological species. Sympatric mtDNA divergences are relatively rare in birds, but the fact that they occur argues against the use of threshold mtDNA divergences in species delineation.},
}
@article {pmid23298166,
year = {2013},
author = {Keskin, E and Ağdamar, S and Tarkan, AS},
title = {DNA barcoding common non-native freshwater fish species in Turkey: low genetic diversity but high population structuring.},
journal = {Mitochondrial DNA},
volume = {24},
number = {3},
pages = {276-287},
doi = {10.3109/19401736.2012.748041},
pmid = {23298166},
issn = {1940-1744},
mesh = {Animals ; Base Sequence ; *DNA Barcoding, Taxonomic ; DNA Primers ; Fishes/*genetics ; Fresh Water ; *Genetic Variation ; Polymerase Chain Reaction ; Turkey ; },
abstract = {Negative impacts of introduced non-native freshwater species on native species have been increasingly recognized in the world as well as in Turkey. However, there has been relatively little attention on genetic characterization of alien freshwater fishes in their non-native distribution range and virtually no study has been conducted in Turkey despite its crucial importance in invasion biology. The purpose of this study was to elucidate genetic diversity of common non-native freshwater fish species (Carassius auratus, Carassius gibelio, Gambusia holbrooki, Lepomis gibbosus, and Pseudorasbora parva) using mitochondrial Cytochrome c oxidase subunit I (COI) sequences; known as DNA barcodes. Through the whole dataset, seventeen haplotypes (haplotype diversity = 0.8908) were found containing 145 COI sequences. Mean Kimura two-parameter genetic distances were calculated as 0.209 for interspecific distance and 0.009 for intraspecific variation. COI barcode diversity among populations of the same species was found to be low, especially for C. gibelio, G. holbrooki, and L. gibbosus populations which were 0.5%, 0.6%, and 0.3%, respectively. Our results clearly demonstrate the effectiveness of the DNA barcoding approach both for identifications at species level and revealing intraspecific variation among populations, which could be used for effective management measures for invasive species and conservation strategies for indigenous and endemic species.},
}
@article {pmid23288465,
year = {2013},
author = {Wong, KH and Jin, Y and Moqtaderi, Z},
title = {Multiplex Illumina sequencing using DNA barcoding.},
journal = {Current protocols in molecular biology},
volume = {Chapter 7},
number = {},
pages = {Unit 7.11.},
doi = {10.1002/0471142727.mb0711s101},
pmid = {23288465},
issn = {1934-3647},
mesh = {Chromatin Immunoprecipitation ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Staining and Labeling/*methods ; },
abstract = {The amount of sequence obtained by modern sequencing machines greatly exceeds the sequencing depth requirements of many experiments, especially those involving organisms with small genomes. In the interest of economy and efficiency, various strategies have been developed for multiplexing, in which samples are uniquely tagged with short identifying sequences known as barcodes, pooled, and then sequenced together in a single lane. The resulting combined sequence data are subsequently sorted by barcode before bioinformatic analysis. This unit contains a barcoding protocol for the preparation of up to 96 ChIP samples for multiplex sequencing in a single flow cell lane on the Illumina platform. This strategy may be extended to even larger numbers of samples and may also be generalized to other sequencing applications or sequencing platforms.},
}
@article {pmid23286377,
year = {2013},
author = {Olteanu, M and Nicolas, V and Schaeffer, B and Denys, C and Missoup, AD and Kennis, J and Larédo, C},
title = {Nonlinear projection methods for visualizing Barcode data and application on two data sets.},
journal = {Molecular ecology resources},
volume = {13},
number = {6},
pages = {976-990},
doi = {10.1111/1755-0998.12047},
pmid = {23286377},
issn = {1755-0998},
mesh = {Animals ; Cluster Analysis ; Computer Graphics ; *DNA Barcoding, Taxonomic ; Molecular Sequence Data ; Moths/*genetics ; Murinae/*genetics ; Nonlinear Dynamics ; Phylogeny ; Species Specificity ; },
abstract = {Developing tools for visualizing DNA sequences is an important issue in the Barcoding context. Visualizing Barcode data can be put in a purely statistical context, unsupervised learning. Clustering methods combined with projection methods have two closely linked objectives, visualizing and finding structure in the data. Multidimensional scaling (MDS) and Self-organizing maps (SOM) are unsupervised statistical tools for data visualization. Both algorithms map data onto a lower dimensional manifold: MDS looks for a projection that best preserves pairwise distances while SOM preserves the topology of the data. Both algorithms were initially developed for Euclidean data and the conditions necessary to their good implementation were not satisfied for Barcode data. We developed a workflow consisting in four steps: collapse data into distinct sequences; compute a dissimilarity matrix; run a modified version of SOM for dissimilarity matrices to structure the data and reduce dimensionality; project the results using MDS. This methodology was applied to Astraptes fulgerator and Hylomyscus, an African rodent with debated taxonomy. We obtained very good results for both data sets. The results were robust against unbalanced species. All the species in Astraptes were well displayed in very distinct groups in the various visualizations, except for LOHAMP and FABOV that were mixed up. For Hylomyscus, our findings were consistent with known species, confirmed the existence of four unnamed taxa and suggested the existence of potentially new species.},
}
@article {pmid23285223,
year = {2012},
author = {Tan, J and Lim, PE and Phang, SM and Hong, DD and Sunarpi, H and Hurtado, AQ},
title = {Assessment of four molecular markers as potential DNA barcodes for red algae Kappaphycus Doty and Eucheuma J. Agardh (Solieriaceae, Rhodophyta).},
journal = {PloS one},
volume = {7},
number = {12},
pages = {e52905},
pmid = {23285223},
issn = {1932-6203},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Intergenic/genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/analysis/genetics ; Genes, Plant ; Genetic Markers/*physiology ; Molecular Sequence Data ; Phylogeny ; Rhodophyta/*classification/*genetics ; },
abstract = {DNA barcoding has been a major advancement in the field of taxonomy, seeing much effort put into the barcoding of wide taxa of organisms, macro and microalgae included. The mitochondrial-encoded cox1 and plastid-encoded rbcL has been proposed as potential DNA barcodes for rhodophytes, but are yet to be tested on the commercially important carrageenophytes Kappaphycus and Eucheuma. This study gauges the effectiveness of four markers, namely the mitochondrial cox1, cox2, cox2-3 spacer and the plastid rbcL in DNA barcoding on selected Kappaphycus and Eucheuma from Southeast Asia. Marker assessments were performed using established distance and tree-based identification criteria from earlier studies. Barcoding patterns on a larger scale were simulated by empirically testing on the commonly used cox2-3 spacer. The phylogeny of these rhodophytes was also briefly described. In this study, the cox2 marker which satisfies the prerequisites of DNA barcodes was found to exhibit moderately high interspecific divergences with no intraspecific variations, thus a promising marker for the DNA barcoding of Kappaphycus and Eucheuma. However, the already extensively used cox2-3 spacer was deemed to be in overall more appropriate as a DNA barcode for these two genera. On a wider scale, cox1 and rbcL were still better DNA barcodes across the rhodophyte taxa when practicality and cost-efficiency were taken into account. The phylogeny of Kappaphycus and Eucheuma were generally similar to those earlier reported. Still, the application of DNA barcoding has demonstrated our relatively poor taxonomic comprehension of these seaweeds, thus suggesting more in-depth efforts in taxonomic restructuring as well as establishment.},
}
@article {pmid23284767,
year = {2012},
author = {Morise, H and Miyazaki, E and Yoshimitsu, S and Eki, T},
title = {Profiling nematode communities in unmanaged flowerbed and agricultural field soils in Japan by DNA barcode sequencing.},
journal = {PloS one},
volume = {7},
number = {12},
pages = {e51785},
pmid = {23284767},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Helminth/*genetics ; DNA, Plant/*genetics ; DNA, Ribosomal/*genetics ; Electron Transport Complex IV/genetics ; Flowers/*genetics/parasitology ; Japan ; Nematoda/*classification/genetics/growth &amp; development ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Soil/*parasitology ; },
abstract = {Soil nematodes play crucial roles in the soil food web and are a suitable indicator for assessing soil environments and ecosystems. Previous nematode community analyses based on nematode morphology classification have been shown to be useful for assessing various soil environments. Here we have conducted DNA barcode analysis for soil nematode community analyses in Japanese soils. We isolated nematodes from two different environmental soils of an unmanaged flowerbed and an agricultural field using the improved flotation-sieving method. Small subunit (SSU) rDNA fragments were directly amplified from each of 68 (flowerbed samples) and 48 (field samples) isolated nematodes to determine the nucleotide sequence. Sixteen and thirteen operational taxonomic units (OTUs) were obtained by multiple sequence alignment from the flowerbed and agricultural field nematodes, respectively. All 29 SSU rDNA-derived OTUs (rOTUs) were further mapped onto a phylogenetic tree with 107 known nematode species. Interestingly, the two nematode communities examined were clearly distinct from each other in terms of trophic groups: Animal predators and plant feeders were markedly abundant in the flowerbed soils, in contrast, bacterial feeders were dominantly observed in the agricultural field soils. The data from the flowerbed nematodes suggests a possible food web among two different trophic nematode groups and plants (weeds) in the closed soil environment. Finally, DNA sequences derived from the mitochondrial cytochrome oxidase c subunit 1 (COI) gene were determined as a DNA barcode from 43 agricultural field soil nematodes. These nematodes were assigned to 13 rDNA-derived OTUs, but in the COI gene analysis were assigned to 23 COI gene-derived OTUs (cOTUs), indicating that COI gene-based barcoding may provide higher taxonomic resolution than conventional SSU rDNA-barcoding in soil nematode community analysis.},
}
@article {pmid23280343,
year = {2013},
author = {Crawford, AJ and Cruz, C and Griffith, E and Ross, H and Ibáñez, R and Lips, KR and Driskell, AC and Bermingham, E and Crump, P},
title = {DNA barcoding applied to ex situ tropical amphibian conservation programme reveals cryptic diversity in captive populations.},
journal = {Molecular ecology resources},
volume = {13},
number = {6},
pages = {1005-1018},
doi = {10.1111/1755-0998.12054},
pmid = {23280343},
issn = {1755-0998},
mesh = {Amphibians/*classification/genetics ; Animals ; *Conservation of Natural Resources ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry/classification ; Endangered Species ; Genetic Variation ; Likelihood Functions ; Panama ; Phylogeny ; Species Specificity ; },
abstract = {Amphibians constitute a diverse yet still incompletely characterized clade of vertebrates, in which new species are still being discovered and described at a high rate. Amphibians are also increasingly endangered, due in part to disease-driven threats of extinctions. As an emergency response, conservationists have begun ex situ assurance colonies for priority species. The abundance of cryptic amphibian diversity, however, may cause problems for ex situ conservation. In this study we used a DNA barcoding approach to survey mitochondrial DNA (mtDNA) variation in captive populations of 10 species of Neotropical amphibians maintained in an ex situ assurance programme at El Valle Amphibian Conservation Center (EVACC) in the Republic of Panama. We combined these mtDNA sequences with genetic data from presumably conspecific wild populations sampled from across Panama, and applied genetic distance-based and character-based analyses to identify cryptic lineages. We found that three of ten species harboured substantial cryptic genetic diversity within EVACC, and an additional three species harboured cryptic diversity among wild populations, but not in captivity. Ex situ conservation efforts focused on amphibians are therefore vulnerable to an incomplete taxonomy leading to misidentification among cryptic species. DNA barcoding may therefore provide a simple, standardized protocol to identify cryptic diversity readily applicable to any amphibian community.},
}
@article {pmid23280321,
year = {2013},
author = {Brodin, Y and Ejdung, G and Strandberg, J and Lyrholm, T},
title = {Improving environmental and biodiversity monitoring in the Baltic Sea using DNA barcoding of Chironomidae (Diptera).},
journal = {Molecular ecology resources},
volume = {13},
number = {6},
pages = {996-1004},
doi = {10.1111/1755-0998.12053},
pmid = {23280321},
issn = {1755-0998},
mesh = {Animals ; Baltic States ; Bayes Theorem ; *Biodiversity ; Chironomidae/*classification ; *DNA Barcoding, Taxonomic ; Databases, Nucleic Acid ; Electron Transport Complex IV/chemistry/genetics ; Molecular Sequence Data ; Oceans and Seas ; Phylogeny ; },
abstract = {As for many other regions, environmental and biodiversity monitoring of the brackish Baltic Sea suffers from low species resolution for several taxa. One such case is the benthic larvae of midges Chironomidae (Diptera), which are estimated to constitute about 30% of the macrozoobenthos species of the Baltic Sea and are important indicators of environmental quality. We assessed the usefulness of COI (cytochrome oxidase I) gene barcoding to improve species resolution and its potential for implementation in monitoring programmes. Neighbour-Joining, Maximum parsimony and Bayesian-inference analyses all provided high congruency with morphological analyses of adult males for almost all 42 species studied. Barcoding was helpful to elucidate some cases of taxonomical difficulties, such as synonyms. In contrast to the high identification accuracy when using our local database, there were a number of cases where matching with GenBank and BOLD provided puzzling results. For reliable species identification at least 15-30 specimens from 5-10 well-distributed sites within the geographical range of the species might be needed in a database to adequately cover the intraspecific variability of chironomids. Implementation of DNA barcoding, as applied here, in monitoring would result in an increase from at present less than 10% to more than 90% successful chironomid species identification of Baltic Sea benthic samples, as it also would for many nearby lakes. Routine monitoring of benthic environmental samples based on Next-Generation sequencing techniques would provide a cost effective way to obtain a taxonomically much more complete assessment of environmental quality and biodiversity, as required by EU directives and national legislation.},
}
@article {pmid23280134,
year = {2013},
author = {Liu, D and Liu, L and Guo, G and Wang, W and Sun, Q and Parani, M and Ma, J},
title = {BOLDMirror: a global mirror system of DNA barcode data.},
journal = {Molecular ecology resources},
volume = {13},
number = {6},
pages = {991-995},
doi = {10.1111/1755-0998.12048},
pmid = {23280134},
issn = {1755-0998},
mesh = {Classification/methods ; *DNA Barcoding, Taxonomic ; *Databases, Nucleic Acid ; Software ; Species Specificity ; },
abstract = {DNA barcoding is a novel concept for taxonomic identification using short, specific genetic markers and has been applied to study a large number of eukaryotes. The huge amount of data output generated by DNA barcoding requires well-organized information systems. Besides the Barcode of Life Data system (BOLD) established in Canada, the mirror system is also important for the international barcode of life project (iBOL). For this purpose, we developed the BOLDMirror, a global mirror system of DNA barcode data. It is open-sourced and can run on the LAMP (Linux + Apache + MySQL + PHP) environment. BOLDMirror has data synchronization, data representation and statistics modules, and also provides spaces to store user operation history. BOLDMirror can be accessed at http://www.boldmirror.net and several countries have used it to setup their site of DNA barcoding.},
}
@article {pmid23280099,
year = {2013},
author = {Collins, RA and Cruickshank, RH},
title = {The seven deadly sins of DNA barcoding.},
journal = {Molecular ecology resources},
volume = {13},
number = {6},
pages = {969-975},
doi = {10.1111/1755-0998.12046},
pmid = {23280099},
issn = {1755-0998},
mesh = {Biodiversity ; DNA Barcoding, Taxonomic/*methods/standards ; Databases, Genetic ; *Phylogeny ; Research Design ; Species Specificity ; },
abstract = {Despite the broad benefits that DNA barcoding can bring to a diverse range of biological disciplines, a number of shortcomings still exist in terms of the experimental design of studies incorporating this approach. One underlying reason for this lies in the confusion that often exists between species discovery and specimen identification, and this is reflected in the way that hypotheses are generated and tested. Although these aims can be associated, they are quite distinct and require different methodological approaches, but their conflation has led to the frequently inappropriate use of commonly used analytical methods such as neighbour-joining trees, bootstrap resampling and fixed distance thresholds. Furthermore, the misidentification of voucher specimens can also have serious implications for end users of reference libraries such as the Barcode of Life Data Systems, and in this regard we advocate increased diligence in the a priori identification of specimens to be used for this purpose. This commentary provides an assessment of seven deficiencies that we identify as common in the DNA barcoding literature, and outline some potential improvements for its adaptation and adoption towards more reliable and accurate outcomes.},
}
@article {pmid23275754,
year = {2012},
author = {Skale, A and Tänzler, R and Hendrich, L and Balke, M},
title = {High mitochondrial DNA sequence divergence in New Guinea Carabdytes stream beetles and the taxonomist's dilemma when other evidence is kind of subtle… (and collecting localities are far far away).},
journal = {ZooKeys},
volume = {},
number = {247},
pages = {31-43},
pmid = {23275754},
issn = {1313-2989},
abstract = {Carabdytes upin tindigessp. n. is described from the Arfak Mountains Bird's Head Indonesian Papua. It is morphologically very similar to Carabdytes upin upin Balke et al. 1992 known from eastern Indonesian Papua eastward to the western limits of the Papuan Peninsula of Papua New Guinea. For 726 bp at the 3' end of the mitochondrial cox1 gene the subspecies differ by 8.1-9.2% uncorrected p-distance. However we also document considerable cox1 divergence within Carabdytes upin upin. We find few diagnostic positions in the nuclear genes argenine kinase as well as elongation factor 1 alpha that suggest there are indeed two isolated groups of Carabdytes but evidence in elongation factor 1 alpha is not unambiguous. We decided to highlight this phenomenon of ambiguous evidence for ongoing/just attained speciation by describing a subspecies. We argue that such cases are actually common once mitochondrial sequence data are routinely added to the taxonomist's toolkit and sometimes simply adding data from few nuclear genes will not suffice the solve taxonomic riddles. Here detailed population genetic investigations would be required - for which sufficient numbers of specimens from a sufficiently wide geographical sampling might be nearly impossible to acquire.},
}
@article {pmid23273270,
year = {2012},
author = {Zhang, Z and Theurkauf, WE and Weng, Z and Zamore, PD},
title = {Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection.},
journal = {Silence},
volume = {3},
number = {1},
pages = {9},
pmid = {23273270},
issn = {1758-907X},
support = {R01 GM062862/GM/NIGMS NIH HHS/United States ; R01 GM065236/GM/NIGMS NIH HHS/United States ; R01 HD049116/HD/NICHD NIH HHS/United States ; R37 GM062862/GM/NIGMS NIH HHS/United States ; },
abstract = {BACKGROUND: High throughput DNA sequencing technology has enabled quantification of all the RNAs in a cell or tissue, a method widely known as RNA sequencing (RNA-Seq). However, non-coding RNAs such as rRNA are highly abundant and can consume >70% of sequencing reads. A common approach is to extract only polyadenylated mRNA; however, such approaches are blind to RNAs with short or no poly(A) tails, leading to an incomplete view of the transcriptome. Another challenge of preparing RNA-Seq libraries is to preserve the strand information of the RNAs.<br><br>DESIGN: Here, we describe a procedure for preparing RNA-Seq libraries from 1 to 4 &#x3bc;g total RNA without poly(A) selection. Our method combines the deoxyuridine triphosphate (dUTP)/uracil-DNA glycosylase (UDG) strategy to achieve strand specificity with AMPure XP magnetic beads to perform size selection. Together, these steps eliminate gel purification, allowing a library to be made in less than two days. We barcode each library during the final PCR amplification step, allowing several samples to be sequenced in a single lane without sacrificing read length. Libraries prepared using this protocol are compatible with Illumina GAII, GAIIx and HiSeq 2000 platforms.<br><br>DISCUSSION: The RNA-Seq protocol described here yields strand-specific transcriptome libraries without poly(A) selection, which provide approximately 90% mappable sequences. Typically, more than 85% of mapped reads correspond to protein-coding genes and only 6% derive from non-coding RNAs. The protocol has been used to measure RNA transcript identity and abundance in tissues from flies, mice, rats, chickens, and frogs, demonstrating its general applicability.},
}
@article {pmid23272216,
year = {2012},
author = {Makarova, O and Contaldo, N and Paltrinieri, S and Kawube, G and Bertaccini, A and Nicolaisen, M},
title = {DNA barcoding for identification of 'Candidatus Phytoplasmas' using a fragment of the elongation factor Tu gene.},
journal = {PloS one},
volume = {7},
number = {12},
pages = {e52092},
pmid = {23272216},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic ; Databases, Nucleic Acid ; Internet ; Peptide Elongation Factor Tu/*genetics ; Phylogeny ; Phytoplasma/*classification/*genetics ; Plants/microbiology ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Phytoplasmas are bacterial phytopathogens responsible for significant losses in agricultural production worldwide. Several molecular markers are available for identification of groups or strains of phytoplasmas. However, they often cannot be used for identification of phytoplasmas from different groups simultaneously or are too long for routine diagnostics. DNA barcoding recently emerged as a convenient tool for species identification. Here, the development of a universal DNA barcode based on the elongation factor Tu (tuf) gene for phytoplasma identification is reported.<br><br>We designed a new set of primers and amplified a 420-444 bp fragment of tuf from all 91 phytoplasmas strains tested (16S rRNA groups -I through -VII, -IX through -XII, -XV, and -XX). Comparison of NJ trees constructed from the tuf barcode and a 1.2 kbp fragment of the 16S ribosomal gene revealed that the tuf tree is highly congruent with the 16S rRNA tree and had higher inter- and intra- group sequence divergence. Mean K2P inter-/intra- group divergences of the tuf barcode did not overlap and had approximately one order of magnitude difference for most groups, suggesting the presence of a DNA barcoding gap. The use of the tuf barcode allowed separation of main ribosomal groups and most of their subgroups. Phytoplasma tuf barcodes were deposited in the NCBI GenBank and Q-bank databases.<br><br>CONCLUSIONS/SIGNIFICANCE: This study demonstrates that DNA barcoding principles can be applied for identification of phytoplasmas. Our findings suggest that the tuf barcode performs as well or better than a 1.2 kbp fragment of the 16S rRNA gene and thus provides an easy procedure for phytoplasma identification. The obtained sequences were used to create a publicly available reference database that can be used by plant health services and researchers for online phytoplasma identification.},
}
@article {pmid23269555,
year = {2013},
author = {Zheng, H and Zhuang, W},
title = {Four new species of the genus Hymenoscyphus (fungi) based on morphology and molecular data.},
journal = {Science China. Life sciences},
volume = {56},
number = {1},
pages = {90-100},
doi = {10.1007/s11427-012-4429-1},
pmid = {23269555},
issn = {1869-1889},
mesh = {Ascomycota/classification/*genetics/growth &amp; development ; DNA Barcoding, Taxonomic/methods ; DNA, Fungal/chemistry/*genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Host Specificity ; Molecular Sequence Data ; Phylogeny ; Plant Leaves/microbiology ; Plant Stems/microbiology ; RNA, Ribosomal/chemistry/*genetics ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; RNA, Ribosomal, 5.8S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Spores, Fungal/*genetics/growth &amp; development/physiology ; },
abstract = {Four new species of Hymenoscyphus (H. brevicellulus, H. hyaloexcipulus, H. microcaudatus, and H. subsymmetricus) and a new Chinese record (H. subpallescens) are described. These five species share common characteristics: small apothecia (<3 mm in diameter); hymenium whitish, pale yellow, to yellow in color; ectal excipulum of textura prismatica; asci arising from simple septa; ascospores scutuloid and guttulate; saprophytic nutrition; and leaf habitats, except for H. subsymmetricus, which grows on herbaceous stems. Phylogenetic analyses of internal transcribed spacer nuclear ribosomal DNA sequences, the universal DNA barcode for fungi, for 16 species in the genus indicated that these taxa were closely related to H. microserotinus, in accordance with their morphological features, but represented independent species. The distinguishing features of each new species from its relatives are discussed, and their phylogenetic relationships explored.},
}
@article {pmid23269202,
year = {2013},
author = {Silveira, P and Belo, NO and Lacorte, GA and Kolesnikovas, CK and Vanstreels, RE and Steindel, M and Catão-Dias, JL and Valkiūnas, G and Braga, EM},
title = {Parasitological and new molecular-phylogenetic characterization of the malaria parasite Plasmodium tejerai in South American penguins.},
journal = {Parasitology international},
volume = {62},
number = {2},
pages = {165-171},
doi = {10.1016/j.parint.2012.12.004},
pmid = {23269202},
issn = {1873-0329},
mesh = {Animals ; Base Sequence ; Brazil ; Cytochromes b/genetics ; DNA, Protozoan/chemistry/genetics ; Endothelial Cells/parasitology ; Fatal Outcome ; Macrophages/parasitology ; Malaria, Avian/blood/*parasitology/pathology ; Mitochondria/metabolism ; Molecular Sequence Data ; Myocardium/pathology ; Parasitemia ; Phylogeny ; Plasmodium/classification/cytology/genetics/*isolation &amp; purification ; Protozoan Proteins/genetics ; Sequence Analysis, DNA ; Species Specificity ; Spheniscidae/*parasitology ; },
abstract = {This study is the first report on mortality of Spheniscus magellanicus, penguin of South America, caused by Plasmodium tejerai, which was identified using morphological and molecular analyses. Blood stages (trophozoites, meronts and gametocytes) were reported and illustrated. The necropsy revealed marked splenomegaly and pulmonary edema, as well as moderate hepatomegaly and hydropericardium. The histopathology revealed the presence of tissue meronts in the macrophages and endothelial cells of multiple organs. The molecular analyses showed 5.6% of genetic divergence in cytochrome b gene between P. tejerai and Plasmodium relictum. Morphology of blood and tissue stages of P. tejerai is similar to P. relictum; the distinction between these two species requires experience in the identification of avian Plasmodium species. Molecular studies associated with reliably identified morphological species are useful for barcoding and comparisons with previous studies of wildlife malaria infections as well as for posterior phylogenetic and phylogeographic studies. S. magellanicus is a new host record of P. tejerai, which is the virulent parasite and worth more attention in avian conservation and veterinary medicine projects in South America.},
}
@article {pmid23266979,
year = {2012},
author = {Wang, CY and Feng, Y and Chen, XM},
title = {[DNA barcoding analysis of processed medicinal insect Catharsius molossus].},
journal = {Dong wu xue yan jiu = Zoological research},
volume = {33},
number = {6},
pages = {597-602},
doi = {10.3724/SP.J.1141.2012.06597},
pmid = {23266979},
issn = {0254-5853},
mesh = {Animals ; Base Sequence ; Coleoptera/*classification/*genetics ; DNA Barcoding, Taxonomic ; Medicine, Chinese Traditional ; Molecular Sequence Data ; Phylogeny ; },
abstract = {The identification of medicinal insects is a complex task, especially when they are processed into pieces or powders. This difficulty has potential to create severe complications. For example, inaccurate identification can affect the safety of clinical application for corresponding medicinal insects. A quick and accurate method to identify these kinds of organisms is needed. Here, we amplified and sequenced the mtCOI gene in processed product of Catharsius molossus, including intact individuals and broken individuals, to test the feasibility of DNA barcoding this kind of sample. After comparing results of different DNA extraction methods, we finally succeed in amplifying and sequencing the barcoding segments in these samples. Our method's barcoding sequences could clearly distinguish between C. molossus and its allied species. The data also indicated that a degree of interfusion of other insects was present in the broken medicinal C. molossus product. These results are quite promising to the establishment of performance criteria for future identification of medicinal C.molossus that will help ensure the safety application of these medicinal insects.},
}
@article {pmid23264020,
year = {2013},
author = {Andru, J and Cosson, JF and Caliman, JP and Benoit, E},
title = {Coumatetralyl resistance of Rattus tanezumi infesting oil palm plantations in Indonesia.},
journal = {Ecotoxicology (London, England)},
volume = {22},
number = {2},
pages = {377-386},
pmid = {23264020},
issn = {1573-3017},
mesh = {4-Hydroxycoumarins/*pharmacology ; *Agriculture ; Animals ; *Arecaceae/chemistry ; DNA Barcoding, Taxonomic ; DNA Mutational Analysis ; *Drug Resistance/genetics ; Genotype ; Indonesia ; Mixed Function Oxygenases/genetics ; Mutation ; Palm Oil ; Phenotype ; *Plant Oils/isolation &amp; purification ; Polymorphism, Genetic ; Rats ; Rodent Control/*methods ; Rodenticides/*pharmacology ; *Trees/chemistry ; Vitamin K Epoxide Reductases ; },
abstract = {Rodent control is an important issue in human health and agriculture. Oil palm plantations are rapidly expanding in Indonesia and this is having a major economic and ecological impact. Rodent control in oil palm plantations is based principally on the use of anti-vitamin K (AVK), the main anticoagulant used being coumatetralyl, a first-generation AVK. We conducted a comparative study in two well established oil palm plantations in Indonesia: (1) one without chemical control in Riau and (2) another with intensive coumatetralyl use on Bangka Island. Rat species were identified by the molecular barcoding method. Susceptibility to coumatetralyl was then assessed within the two populations and we screened for mutations in vkorc1, which encodes the molecular target of AVK. Different species were found in the two areas: Rattus tiomanicus in Riau, and a mix of R. tanezumi and a close relative one in Bangka. The rats in Riau were much more susceptible to coumatetralyl than those in Bangka. This study is the first to demonstrate physiological tolerance to AVK in these species. vkorc1 displayed low levels of polymorphism, and no SNP was associated with the high-tolerance phenotypes of R. tanezumi clade, even those exposed to very high concentrations (32 × the effective dose of 0.36 mg kg(-1)). The biochemical basis of this tolerance remains unknown, but may involve the vkorc1 promoter and/or cytochrome P450 metabolism. We discuss our results and the selective role of anticoagulant use in the occurrence of phenotypic tolerance.},
}
@article {pmid23263454,
year = {2013},
author = {Zimmermann, T and Bocksberger, G and Brüggemann, W and Berberich, T},
title = {Phylogenetic relationship and molecular taxonomy of African grasses of the genus Panicum inferred from four chloroplast DNA-barcodes and nuclear gene sequences.},
journal = {Journal of plant research},
volume = {126},
number = {3},
pages = {363-371},
pmid = {23263454},
issn = {1618-0860},
mesh = {Africa ; Cell Nucleus/genetics/metabolism ; *DNA Barcoding, Taxonomic ; DNA, Chloroplast/*genetics/metabolism ; Evolution, Molecular ; Molecular Sequence Data ; Panicum/*classification/*genetics ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sequence Homology ; },
abstract = {The genus Panicum s.l. comprises about 450 grass species in which the C4 and the C3 metabolic pathways of photosynthesis are realized. In the West African savannah, Panicum spp. and closely related taxa dominate the landscape, with species differentially adapted to drought conditions. We obtained four chloroplast DNA barcode sequences, rbcL, matK, ndhF and trnH-psbA intergenic region, for nine Panicum spp. with a focus on West African species, and we performed maximum likelihood analysis to infer their phylogenetic relationship. Furthermore the phylogenetic placement of five newly sequenced taxa was achieved using a published phylogeny of more than 300 Panicoids based on ndhF sequences. The comparison of the resulting phylogenetic tree constructed from a combination of all four barcode sequences with the one based on rbcL and matK showed that the latter combination of the two, is sufficient for the analysis. A tree constructed from amino acid sequences derived from isolated cDNAs of the nucleus-encoded phosphoenolpyruvate carboxylase displayed a similar topology. All ppc-sequences could be annotated to either ppc-B2 or ppc-aR. Moreover the inclusion of the West African Panicum species in an extensive dataset of Panicoids supports the proposition that within the subtribe Panicinae only the NAD-malic enzyme type of C4 photosynthesis is present.},
}
@article {pmid23261711,
year = {2013},
author = {Vuataz, L and Sartori, M and Gattolliat, JL and Monaghan, MT},
title = {Endemism and diversification in freshwater insects of Madagascar revealed by coalescent and phylogenetic analysis of museum and field collections.},
journal = {Molecular phylogenetics and evolution},
volume = {66},
number = {3},
pages = {979-991},
doi = {10.1016/j.ympev.2012.12.003},
pmid = {23261711},
issn = {1095-9513},
mesh = {*Animal Distribution ; Animals ; Base Sequence ; *Biodiversity ; DNA Barcoding, Taxonomic ; DNA Primers/genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Insecta/*classification/*genetics ; Likelihood Functions ; Madagascar ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The biodiversity and endemism of Madagascar are among the most extraordinary and endangered in the world. This includes the island's freshwater biodiversity, although detailed knowledge of the diversity, endemism, and biogeographic origin of freshwater invertebrates is lacking. The aquatic immature stages of mayflies (Ephemeroptera) are widely used as bio-indicators and form an important component of Malagasy freshwater biodiversity. Many species are thought to be microendemics, restricted to single river basins in forested areas, making them particularly sensitive to habitat reduction and degradation. The Heptageniidae are a globally diverse family of mayflies (>500 species) but remain practically unknown in Madagascar except for two species described in 1996. The standard approach to understanding their diversity, endemism, and origin would require extensive field sampling on several continents and years of taxonomic work followed by phylogenetic analysis. Here we circumvent this using museum collections and freshly collected individuals in a combined approach of DNA taxonomy and phylogeny. The coalescent-based GMYC analysis of DNA barcode data (mitochondrial COI) revealed 14 putative species on Madagascar, 70% of which were microendemics. A phylogenetic analysis that included African and Asian species and data from two mitochondrial and four nuclear loci indicated the Malagasy Heptageniidae are monophyletic and sister to African species. The genus Compsoneuria is shown to be paraphyletic and the genus Notonurus is reinstalled for African and Malagasy species previously placed in Compsoneuria. A molecular clock excluded a Gondwanan vicariance origin and instead favoured a more recent overseas colonization of Madagascar. The observed monophyly and high microendemism highlight their conservation importance and suggest the DNA-based approach can rapidly provide information on the diversity, endemism, and origin of freshwater biodiversity. Our results underline the important role that museum collections can play in molecular studies, especially in critically endangered biodiversity hotspots like Madagascar where entire species or populations may go extinct very quickly.},
}
@article {pmid23259585,
year = {2012},
author = {Hajibabaei, M and Spall, JL and Shokralla, S and van Konynenburg, S},
title = {Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol.},
journal = {BMC ecology},
volume = {12},
number = {},
pages = {28},
pmid = {23259585},
issn = {1472-6785},
mesh = {Animals ; *Biodiversity ; DNA/*isolation &amp; purification ; *DNA Barcoding, Taxonomic ; *Ethanol ; Fresh Water ; Gene Library ; Invertebrates/*classification/genetics ; Multiplex Polymerase Chain Reaction ; },
abstract = {BACKGROUND: Characterizing biodiversity in a habitat or in targeted taxonomically or socioeconomically important groups remains a challenge. Standard DNA-based biodiversity identification tools such as DNA barcoding coupled with high-throughput Next-Generation Sequencing (NGS) technologies are rapidly changing the landscape of biodiversity analysis by targeting various habitats and a wide array of organisms. However, effective use of these technological advances requires optimized protocols and benchmarking against traditional tools. Here we investigate the use of commonly used preservative ethanol as a non-destructive and inexpensive source of DNA for NGS biodiversity analysis of benthic macroinvertebrates. We used the preservative ethanol added to field collected organisms (live sorted bulk benthic samples) as a source of community DNA for NGS environmental barcoding. We directly compare this approach with a DNA barcode library generated using Sanger sequencing of all individuals separated from abenthic sample as well as with NGS environmental barcoding of DNA extracted from mixed/homogenized tissue specimens of the same benthic sample. We also evaluate a multiplex PCR strategy, as compared to commonly used single amplicon workflow, using three newly designed primer sets targeting a wide array of benthic macroinvertebrate taxa.<br><br>RESULTS: Our results indicate the effectiveness of ethanol-based DNA in providing sequence information from 87% of taxa identified individually from mixture as compared to 89% in conventional tissue extracted DNA. Missing taxa in both DNA sources were from species with the lowest abundance (e.g. 1 individual) in the benthic mixture. Interestingly, we achieved 100% detection for taxa represented with more than 1% individuals in the mixture in both sources of DNA. Our multiplex amplification regime increased the detection as compared to any single primer set indicating the usefulness of using multiple primer sets in initial amplification of target genes.<br><br>CONCLUSIONS: Although NGS approaches have significantly increased the potential of using DNA information in biodiversity analysis, robust methods are needed to provide reliable data and alleviate sample-processing bottlenecks. Here we coupled non-destructive DNA access and a multiplex PCR approach in NGS environmental barcoding for effective data generation from benthic live-sorted samples collected in bulk and preserved in ethanol. Our study provides a possible solution to sampling and vouchering challenges in using benthic samples through next-generation environmental barcoding and facilitates wider utility of DNA information, especially species-specific DNA barcodes, in ecological and environmental studies and real-world applications such as biomonitoring programs.},
}
@article {pmid23259499,
year = {2012},
author = {Houston, DD and Elzinga, DB and Maughan, PJ and Smith, SM and Kauwe, JS and Evans, RP and Stinger, RB and Shiozawa, DK},
title = {Single nucleotide polymorphism discovery in cutthroat trout subspecies using genome reduction, barcoding, and 454 pyro-sequencing.},
journal = {BMC genomics},
volume = {13},
number = {},
pages = {724},
pmid = {23259499},
issn = {1471-2164},
mesh = {Animals ; Base Sequence ; Computational Biology ; DNA Barcoding, Taxonomic/*methods ; Fisheries/methods ; Genome/*genetics ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; *Hybridization, Genetic ; Molecular Sequence Data ; Oncorhynchus/*genetics ; Polymorphism, Single Nucleotide/*genetics ; },
abstract = {BACKGROUND: Salmonids are popular sport fishes, and as such have been subjected to widespread stocking throughout western North America. Historically, stocking was done with little regard for genetic variation among populations and has resulted in genetic mixing among species and subspecies in many areas, thus putting the genetic integrity of native salmonid populations at risk and creating a need to assess the genetic constitution of native salmonid populations. Cutthroat trout is a salmonid species with pronounced geographic structure (there are 10 extant subspecies) and a recent history of hybridization with introduced rainbow trout in many populations. Genetic admixture has also occurred among cutthroat trout subspecies in areas where introductions have brought two or more subspecies into contact. Consequently, management agencies have increased their efforts to evaluate the genetic composition of cutthroat trout populations to identify populations that remain uncompromised and manage them accordingly, but additional genetic markers are needed to do so effectively. Here we used genome reduction, MID-barcoding, and 454-pyrosequencing to discover single nucleotide polymorphisms that differentiate cutthroat trout subspecies and can be used as a rapid, cost-effective method to characterize the genetic composition of cutthroat trout populations.<br><br>RESULTS: Thirty cutthroat and six rainbow trout individuals were subjected to genome reduction and next-generation sequencing. A total of 1,499,670 reads averaging 379 base pairs in length were generated by 454-pyrosequencing, resulting in 569,060,077 total base pairs sequenced. A total of 43,558 putative SNPs were identified, and of those, 125 SNP primers were developed that successfully amplified 96 cutthroat trout and rainbow trout individuals. These SNP loci were able to differentiate most cutthroat trout subspecies using distance methods and Structure analyses.<br><br>CONCLUSIONS: Genomic and bioinformatic protocols were successfully implemented to identify 125 nuclear SNPs that are capable of differentiating most subspecies of cutthroat trout from one another. The ability to use this suite of SNPs to identify individuals of unknown genetic background to subspecies can be a valuable tool for management agencies in their efforts to evaluate the genetic structure of cutthroat trout populations prior to constructing and implementing conservation plans.},
}
@article {pmid23253798,
year = {2013},
author = {McCusker, MR and Denti, D and Van Guelpen, L and Kenchington, E and Bentzen, P},
title = {Barcoding Atlantic Canada's commonly encountered marine fishes.},
journal = {Molecular ecology resources},
volume = {13},
number = {2},
pages = {177-188},
doi = {10.1111/1755-0998.12043},
pmid = {23253798},
issn = {1755-0998},
mesh = {Animals ; Atlantic Ocean ; Canada ; DNA Barcoding, Taxonomic ; Fishes/*classification/*genetics ; Phylogeny ; },
abstract = {Marine fishes from the northwest Atlantic Ocean were analysed to determine whether barcoding was effective at identifying species. Our data included 177 species, 136 genera, 81 families and 28 orders. Overall, 88% of nominal species formed monophyletic clusters based on >500 bp of the CO1 region, and the average bootstrap value for these species was 98%. Although clearly effective, the percentage of species that were distinguishable with barcoding based on the criterion of reciprocal monophyletic clusters was slightly lower than has been documented in other studies of marine fishes. Eelpouts, sculpins and rocklings proved to be among the most challenging groups for barcoding, although we suspect that difficult identifications based on traditional (morphology based) taxonomy played a role. Within several taxa, speciation may have occurred too recently for barcoding to be effective (e.g. within Sebastes, Thunnus and Ammodytes) or the designation of distinct species may have been erroneous (e.g. within Antimora and Macrourus). Results were consistent with previous work recognizing particularly high levels of divergence within certain taxa, some of which have been recognized as distinct species (e.g. Osmerus mordax and Osmerus dentex; and Liparis gibbus and Liparis bathyarcticus), and some of which have not (e.g. within Halargyreus johnsonii and within Mallotus villosus). The results from this study suggest that morphology-based identification and taxonomy can be challenging in marine fishes, even within a region as well characterized as Atlantic Canada. Barcoding proved to be a very useful tool for species identification that will likely find a wide range of applications, including the fisheries trade, studies of range expansion, ecological analyses and population assessments.},
}
@article {pmid23249185,
year = {2013},
author = {Zhao, Y and Gu, H and Xie, Z and Shum, HC and Wang, B and Gu, Z},
title = {Bioinspired multifunctional Janus particles for droplet manipulation.},
journal = {Journal of the American Chemical Society},
volume = {135},
number = {1},
pages = {54-57},
doi = {10.1021/ja310389w},
pmid = {23249185},
issn = {1520-5126},
mesh = {Air ; Magnetite Nanoparticles/chemistry ; Particle Size ; Surface Properties ; Water/*chemistry ; Wettability ; },
abstract = {Inspired by the nipple arrays covering mosquitoes' eyes and the heterogeneous textured bumps on beetles' backs, we have developed a new kind of Janus particle with multiplexed features, such as different boss arrays and wettability compartmentalized on the same surface, and an anisotropic color and magnetic properties. The prepared Janus particles can be anchored at the air-water interface and act as a highly flexible barrier for preventing coalescence of water droplets. The incorporation of magnetic nanoparticles can give the Janus particles magnetic responsiveness for controlled transportation and coalescence of liquid marbles, while the structural colors in the Janus particles can be employed for barcoding of the encapsulated liquid marbles. We believe that these small Janus particles have great potential as components for constructing intelligent interfacial objects.},
}
@article {pmid23247852,
year = {2013},
author = {Blasinski, H and Bulan, O and Sharma, G},
title = {Per-colorant-channel color barcodes for mobile applications: an interference cancellation framework.},
journal = {IEEE transactions on image processing : a publication of the IEEE Signal Processing Society},
volume = {22},
number = {4},
pages = {1498-1511},
doi = {10.1109/TIP.2012.2233483},
pmid = {23247852},
issn = {1941-0042},
abstract = {We propose a color barcode framework for mobile phone applications by exploiting the spectral diversity afforded by the cyan (C), magenta (M), and yellow (Y) print colorant channels commonly used for color printing and the complementary red (R), green (G), and blue (B) channels, respectively, used for capturing color images. Specifically, we exploit this spectral diversity to realize a three-fold increase in the data rate by encoding independent data in the C, M, and Y print colorant channels and decoding the data from the complementary R, G, and B channels captured via a mobile phone camera. To mitigate the effect of cross-channel interference among the print-colorant and capture color channels, we develop an algorithm for interference cancellation based on a physically-motivated mathematical model for the print and capture processes. To estimate the model parameters required for cross-channel interference cancellation, we propose two alternative methodologies: a pilot block approach that uses suitable selections of colors for the synchronization blocks and an expectation maximization approach that estimates the parameters from regions encoding the data itself. We evaluate the performance of the proposed framework using specific implementations of the framework for two of the most commonly used barcodes in mobile applications, QR and Aztec codes. Experimental results show that the proposed framework successfully overcomes the impact of the color interference, providing a low bit error rate and a high decoding rate for each of the colorant channels when used with a corresponding error correction scheme.},
}
@article {pmid23244441,
year = {2012},
author = {Jörger, KM and Norenburg, JL and Wilson, NG and Schrödl, M},
title = {Barcoding against a paradox? Combined molecular species delineations reveal multiple cryptic lineages in elusive meiofaunal sea slugs.},
journal = {BMC evolutionary biology},
volume = {12},
number = {},
pages = {245},
pmid = {23244441},
issn = {1471-2148},
mesh = {Animals ; Bayes Theorem ; Biological Evolution ; DNA Barcoding, Taxonomic/*methods ; Gastropoda/anatomy &amp; histology/*classification/*genetics ; Likelihood Functions ; Phylogeography ; },
abstract = {BACKGROUND: Many marine meiofaunal species are reported to have wide distributions, which creates a paradox considering their hypothesized low dispersal abilities. Correlated with this paradox is an especially high taxonomic deficit for meiofauna, partly related to a lower taxonomic effort and partly to a high number of putative cryptic species. Molecular-based species delineation and barcoding approaches have been advocated for meiofaunal biodiversity assessments to speed up description processes and uncover cryptic lineages. However, these approaches show sensitivity to sampling coverage (taxonomic and geographic) and the success rate has never been explored on mesopsammic Mollusca.<br><br>RESULTS: We collected the meiofaunal sea-slug Pontohedyle (Acochlidia, Heterobranchia) from 28 localities worldwide. With a traditional morphological approach, all specimens fall into two morphospecies. However, with a multi-marker genetic approach, we reveal multiple lineages that are reciprocally monophyletic on single and concatenated gene trees in phylogenetic analyses. These lineages are largely concordant with geographical and oceanographic parameters, leading to our primary species hypothesis (PSH). In parallel, we apply four independent methods of molecular based species delineation: General Mixed Yule Coalescent model (GMYC), statistical parsimony, Bayesian Species Delineation (BPP) and Automatic Barcode Gap Discovery (ABGD). The secondary species hypothesis (SSH) is gained by relying only on uncontradicted results of the different approaches ('minimum consensus approach'), resulting in the discovery of a radiation of (at least) 12 mainly cryptic species, 9 of them new to science, some sympatric and some allopatric with respect to ocean boundaries. However, the meiofaunal paradox still persists in some Pontohedyle species identified here with wide coastal and trans-archipelago distributions.<br><br>CONCLUSIONS: Our study confirms extensive, morphologically cryptic diversity among meiofauna and accentuates the taxonomic deficit that characterizes meiofauna research. We observe for Pontohedyle slugs a high degree of morphological simplicity and uniformity, which we expect might be a general rule for meiofauna. To tackle cryptic diversity in little explored and hard-to-sample invertebrate taxa, at present, a combined approach seems most promising, such as multi-marker-barcoding (i.e., molecular systematics using mitochondrial and nuclear markers and the criterion of reciprocal monophyly) combined with a minimum consensus approach across independent methods of molecular species delineation to define candidate species.},
}
@article {pmid23241208,
year = {2013},
author = {Bañón, R and Arronte, JC and Vázquez-Dorado, S and Del Río, JL and de Carlos, A},
title = {DNA barcoding of the genus Lepidion (Gadiformes: Moridae) with recognition of Lepidion eques as a junior synonym of Lepidion lepidion.},
journal = {Molecular ecology resources},
volume = {13},
number = {2},
pages = {189-199},
doi = {10.1111/1755-0998.12045},
pmid = {23241208},
issn = {1755-0998},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Gadiformes/*classification/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {DNA sequences of cytochrome c oxidase I gene (COI) from Lepidion spp. were employed to test the efficiency of species identification. A sample of 32 individuals from five Lepidion species was sequenced and combined with 26 sequences from other BOLD projects. As a result, 58 Lepidion DNA sequences of the COI gene belonging to eight of the nine recognized Lepidion species were analysed. Sequences were aligned and formed seven clades in a Bayesian phylogenetic tree, where Lepidion lepidion and Lepidion eques grouped jointly. The Kimura 2-parameter genetic distances, among congeners were, on average, 4.28%, 16 times greater than among conspecifics (0.27%). The main diagnostic meristic data of Lepidion spp. were compiled and a detailed morphological revision of the congeneric species L. eques and L. lepidion was made. The eye diameter was significantly different between L. eques and L. lepidion (P < 0.001). The number of anal fin rays ranged from 45 to 51 in L. lepidion and from 47 to 54 in L. eques, but no significant differences were obtained in the mean values of this variable (P = 0.07). According to the morphological and genetic analyses, the results strongly suggest that the Mediterranean codling L. lepidion and the North Atlantic codling L. eques are conspecific, making L. eques a junior synonym of L. lepidion.},
}
@article {pmid23240000,
year = {2012},
author = {López-Alvarez, D and López-Herranz, ML and Betekhtin, A and Catalán, P},
title = {A DNA barcoding method to discriminate between the model plant Brachypodium distachyon and its close relatives B. stacei and B. hybridum (Poaceae).},
journal = {PloS one},
volume = {7},
number = {12},
pages = {e51058},
pmid = {23240000},
issn = {1932-6203},
mesh = {Brachypodium/*genetics ; DNA Barcoding, Taxonomic/*methods ; Genome, Plant ; *Phylogeny ; Plastids/genetics ; Poaceae/*genetics ; Species Specificity ; },
abstract = {BACKGROUND: Brachypodium distachyon s. l. has been widely investigated across the world as a model plant for temperate cereals and biofuel grasses. However, this annual plant shows three cytotypes that have been recently recognized as three independent species, the diploids B. distachyon (2n = 10) and B. stacei (2n = 20) and their derived allotetraploid B. hybridum (2n = 30).<br><br>We propose a DNA barcoding approach that consists of a rapid, accurate and automatable species identification method using the standard DNA sequences of complementary plastid (trnLF) and nuclear (ITS, GI) loci. The highly homogenous but largely divergent B. distachyon and B. stacei diploids could be easily distinguished (100% identification success) using direct trnLF (2.4%), ITS (5.5%) or GI (3.8%) sequence divergence. By contrast, B. hybridum could only be unambiguously identified through the use of combined trnLF+ITS sequences (90% of identification success) or by cloned GI sequences (96.7%) that showed 5.4% (ITS) and 4% (GI) rate divergence between the two parental sequences found in the allopolyploid.<br><br>CONCLUSION/SIGNIFICANCE: Our data provide an unbiased and effective barcode to differentiate these three closely-related species from one another. This procedure overcomes the taxonomic uncertainty generated from methods based on morphology or flow cytometry identifications that have resulted in some misclassifications of the model plant and its allies. Our study also demonstrates that the allotetraploid B. hybridum has resulted from bi-directional crosses of B. distachyon and B. stacei plants acting either as maternal or paternal parents.},
}
@article {pmid23239988,
year = {2012},
author = {Jin, Q and He, LJ and Zhang, AB},
title = {A simple 2D non-parametric resampling statistical approach to assess confidence in species identification in DNA barcoding--an alternative to likelihood and bayesian approaches.},
journal = {PloS one},
volume = {7},
number = {12},
pages = {e50831},
pmid = {23239988},
issn = {1932-6203},
mesh = {Algorithms ; Animals ; Bayes Theorem ; Butterflies/genetics ; Computer Simulation ; *DNA Barcoding, Taxonomic ; Genetics, Population ; Likelihood Functions ; Models, Genetic ; Models, Theoretical ; *Software ; Species Specificity ; *Statistics, Nonparametric ; },
abstract = {In the recent worldwide campaign for the global biodiversity inventory via DNA barcoding, a simple and easily used measure of confidence for assigning sequences to species in DNA barcoding has not been established so far, although the likelihood ratio test and the bayesian approach had been proposed to address this issue from a statistical point of view. The TDR (Two Dimensional non-parametric Resampling) measure newly proposed in this study offers users a simple and easy approach to evaluate the confidence of species membership in DNA barcoding projects. We assessed the validity and robustness of the TDR approach using datasets simulated under coalescent models, and an empirical dataset, and found that TDR measure is very robust in assessing species membership of DNA barcoding. In contrast to the likelihood ratio test and bayesian approach, the TDR method stands out due to simplicity in both concepts and calculations, with little in the way of restrictive population genetic assumptions. To implement this approach we have developed a computer program package (TDR1.0beta) freely available from ftp://202.204.209.200/education/video/TDR1.0beta.rar.},
}
@article {pmid23228011,
year = {2013},
author = {Alex Smith, M and Fernández-Triana, JL and Eveleigh, E and Gómez, J and Guclu, C and Hallwachs, W and Hebert, PD and Hrcek, J and Huber, JT and Janzen, D and Mason, PG and Miller, S and Quicke, DL and Rodriguez, JJ and Rougerie, R and Shaw, MR and Várkonyi, G and Ward, DF and Whitfield, JB and Zaldívar-Riverón, A},
title = {DNA barcoding and the taxonomy of Microgastrinae wasps (Hymenoptera, Braconidae): impacts after 8 years and nearly 20 000 sequences.},
journal = {Molecular ecology resources},
volume = {13},
number = {2},
pages = {168-176},
doi = {10.1111/1755-0998.12038},
pmid = {23228011},
issn = {1755-0998},
mesh = {Animals ; Base Sequence ; *DNA Barcoding, Taxonomic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Wasps/*classification/*genetics ; },
abstract = {Microgastrine wasps are among the most species-rich and numerous parasitoids of caterpillars (Lepidoptera). They are often host-specific and thus are extensively used in biological control efforts and figure prominently in trophic webs. However, their extraordinary diversity coupled with the occurrence of many cryptic species produces a significant taxonomic impediment. We present and release the results of 8 years (2004-2011) of DNA barcoding microgastrine wasps. Currently they are the best represented group of parasitoid Hymenoptera in the Barcode of Life Data System (BOLD), a massive barcode storage and analysis data management site for the International Barcoding of Life (iBOL) program. There are records from more than 20 000 specimens from 75 countries, including 50 genera (90% of the known total) and more than 1700 species (as indicated by Barcode Index Numbers and 2% MOTU). We briefly discuss the importance of this DNA data set and its collateral information for future research in: (1) discovery of cryptic species and description of new taxa; (2) estimating species numbers in biodiversity inventories; (3) clarification of generic boundaries; (4) biological control programmes; (5) molecular studies of host-parasitoid biology and ecology; (6) evaluation of shifts in species distribution and phenology; and (7) fostering collaboration at national, regional and world levels. The integration of DNA barcoding with traditional morphology-based taxonomy, host records, and other data has substantially improved the accuracy of microgastrine wasp identifications and will significantly accelerate further studies on this group of parasitoids.},
}
@article {pmid23227308,
year = {2012},
author = {Nahum, LA and Mourão, MM and Oliveira, G},
title = {New frontiers in schistosoma genomics and transcriptomics.},
journal = {Journal of parasitology research},
volume = {2012},
number = {},
pages = {849132},
pmid = {23227308},
issn = {2090-0031},
support = {D43 TW007012/TW/FIC NIH HHS/United States ; },
abstract = {Schistosomes are digenean blood flukes of aves and mammals comprising 23 species. Some species are causative agents of human schistosomiasis, the second major neglected disease affecting over 230 million people worldwide. Modern technologies including the sequencing and characterization of nucleic acids and proteins have allowed large-scale analyses of parasites and hosts, opening new frontiers in biological research with potential biomedical and biotechnological applications. Nuclear genomes of the three most socioeconomically important species (S. haematobium, S. japonicum, and S. mansoni) have been sequenced and are under intense investigation. Mitochondrial genomes of six Schistosoma species have also been completely sequenced and analysed from an evolutionary perspective. Furthermore, DNA barcoding of mitochondrial sequences is used for biodiversity assessment of schistosomes. Despite the efforts in the characterization of Schistosoma genomes and transcriptomes, many questions regarding the biology and evolution of this important taxon remain unanswered. This paper aims to discuss some advances in the schistosome research with emphasis on genomics and transcriptomics. It also aims to discuss the main challenges of the current research and to point out some future directions in schistosome studies.},
}
@article {pmid23223015,
year = {2013},
author = {Pacheu-Grau, D and Gómez-Durán, A and Iglesias, E and López-Gallardo, E and Montoya, J and Ruiz-Pesini, E},
title = {Mitochondrial antibiograms in personalized medicine.},
journal = {Human molecular genetics},
volume = {22},
number = {6},
pages = {1132-1139},
doi = {10.1093/hmg/dds517},
pmid = {23223015},
issn = {1460-2083},
mesh = {Anti-Bacterial Agents/*therapeutic use ; Bacterial Infections/*drug therapy/genetics/metabolism ; Cell Line ; Humans ; *Microbial Sensitivity Tests ; Mitochondria/*drug effects/genetics/metabolism ; Molecular Sequence Data ; *Precision Medicine ; Protein Biosynthesis/drug effects ; },
abstract = {Some ribosomal antibiotics used in clinical practice to fight pathogenic bacteria can provoke serious adverse drug reactions in patients. Sensitivity to the antibiotics is a multifactorial trait but the genetic variation of sensitive individuals to off-target effects of the drugs might be one of the factors contributing to this condition. Thus, the protein synthesis apparatus of mitochondria is similar to that of bacteria because of its endosymbiotic origin and, therefore, mitochondrial ribosomes are frequently unintended off-targets of these antibiotics. Because of the limitations of epidemiologic studies of pharmacogenomics, we constructed 25 transmitochondrial cell lines using platelets from individuals belonging to high-frequency European mitochondrial DNA (mtDNA) haplogroups and grew them in the absence or presence of commonly used ribosomal antibiotics. Next, we analyzed the mitochondrial synthesis of proteins and the mitochondrial oxygen consumption to ascertain whether some side effects of ribosomal drugs are due to their interaction with particular mtDNA haplogroup-defining polymorphisms. The amount of mitochondrial translation products, the p.MT-CO1/succinate dehydrogenase subunit A ratio and the ratio of respiratory complex IV quantity to citrate synthase (CS)-specific activity were significantly lower, after the treatment with linezolid, in cybrids harboring the highly frequent m.3010A allele. These results suggest that mitochondrial antibiograms should be implemented for at least the most frequent mitochondrial ribosomal RNA (rRNA) polymorphisms and combinations of polymorphisms and the most frequently used ribosomal antibiotics. In this way, we would obtain individualized barcodes for antibiotic therapy, avoid the side effects of the antibiotics and enable appropriate personalized medicine.},
}
@article {pmid23210271,
year = {2012},
author = {Colpas, P},
title = {Unlocking the power of barcoding.},
journal = {Health management technology},
volume = {33},
number = {11},
pages = {6-7},
pmid = {23210271},
issn = {1074-4770},
mesh = {*Efficiency, Organizational ; Electronic Data Processing/*instrumentation ; *Equipment and Supplies, Hospital ; Patient Identification Systems/methods ; Patient Safety ; Prostheses and Implants ; United States ; },
}
@article {pmid23209586,
year = {2012},
author = {Mat Jaafar, TN and Taylor, MI and Mohd Nor, SA and de Bruyn, M and Carvalho, GR},
title = {DNA barcoding reveals cryptic diversity within commercially exploited Indo-Malay Carangidae (Teleosteii: Perciformes).},
journal = {PloS one},
volume = {7},
number = {11},
pages = {e49623},
pmid = {23209586},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Malaysia ; Oceans and Seas ; Perciformes/*classification/*genetics ; Phylogeny ; },
abstract = {BACKGROUND: DNA barcodes, typically focusing on the cytochrome oxidase I gene (COI) in many animals, have been used widely as a species-identification tool. The ability of DNA barcoding to distinguish species from a range of taxa and to reveal cryptic species has been well documented. Despite the wealth of DNA barcode data for fish from many temperate regions, there are relatively few available from the Southeast Asian region. Here, we target the marine fish Family Carangidae, one of the most commercially-important families from the Indo-Malay Archipelago (IMA), to produce an initial reference DNA barcode library.<br><br>Here, a 652 bp region of COI was sequenced for 723 individuals from 36 putative species of Family Carangidae distributed within IMA waters. Within the newly-generated dataset, three described species exhibited conspecific divergences up to ten times greater (4.32-4.82%) than mean estimates (0.24-0.39%), indicating a discrepancy with assigned morphological taxonomic identification, and the existence of cryptic species. Variability of the mitochondrial DNA COI region was compared within and among species to evaluate the COI region's suitability for species identification. The trend in range of mean K2P distances observed was generally in accordance with expectations based on taxonomic hierarchy: 0% to 4.82% between individuals within species, 0% to 16.4% between species within genera, and 8.64% to 25.39% between genera within families. The average Kimura 2-parameter (K2P) distance between individuals, between species within genera, and between genera within family were 0.37%, 10.53% and 16.56%, respectively. All described species formed monophyletic clusters in the Neighbour-joining phylogenetic tree, although three species representing complexes of six potential cryptic species were detected in Indo-Malay Carangidae; Atule mate, Selar crumenophthalmus and Seriolina nigrofasciata.<br><br>CONCLUSION/SIGNIFICANCE: This study confirms that COI is an effective tool for species identification of Carangidae from the IMA. There were moderate levels of cryptic diversity among putative species within the central IMA. However, to explain the hypothesis of species richness in the IMA, it is necessary to sample the whole family across their broad geographic range. Such insights are helpful not only to document mechanisms driving diversification and recruitment in Carangidae, but also to provide a scientific framework for management strategies and conservation of commercially-important fisheries resources.},
}
@article {pmid23205933,
year = {2012},
author = {Yamanaka, YJ and Szeto, GL and Gierahn, TM and Forcier, TL and Benedict, KF and Brefo, MS and Lauffenburger, DA and Irvine, DJ and Love, JC},
title = {Cellular barcodes for efficiently profiling single-cell secretory responses by microengraving.},
journal = {Analytical chemistry},
volume = {84},
number = {24},
pages = {10531-10536},
pmid = {23205933},
issn = {1520-6882},
support = {1R56AI104274/AI/NIAID NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; U19 AI089992/AI/NIAID NIH HHS/United States ; U01 AI068618/AI/NIAID NIH HHS/United States ; 5U01AI068618/AI/NIAID NIH HHS/United States ; 1U19AI089992/AI/NIAID NIH HHS/United States ; R56 AI104274/AI/NIAID NIH HHS/United States ; },
mesh = {Fluorescent Dyes/analysis/chemistry ; Humans ; Leukocytes, Mononuclear/*chemistry/*metabolism ; Single-Cell Analysis/*methods ; T-Lymphocytes/*chemistry/*metabolism ; },
abstract = {We present a method that uses fluorescent cellular barcodes to increase the number of unique samples that can be analyzed simultaneously by microengraving, a nanowell array-based technique for quantifying the secretory responses of thousands of single cells in parallel. Using n different fluorescent dyes to generate 2(n) unique cellular barcodes, we achieved a 2(n)-fold reduction in the number of arrays and quantity of reagents required per sample. The utility of this approach was demonstrated in three applications of interest in clinical and experimental immunology. Using barcoded human peripheral blood mononuclear cells and T cells, we constructed dose-response curves, profiled the secretory behavior of cells treated with mechanistically distinct stimuli, and tracked the secretory behaviors of different lineages of CD4(+) T helper cells. In addition to increasing the number of samples analyzed by generating secretory profiles of single cells from multiple populations in a time- and reagent-efficient manner, we expect that cellular barcoding in combination with microengraving will facilitate unique experimental opportunities for quantitatively analyzing interactions among heterogeneous cells isolated in small groups (~2-5 cells).},
}
@article {pmid23205725,
year = {2013},
author = {Wang, G and Leng, Y and Dou, H and Wang, L and Li, W and Wang, X and Sun, K and Shen, L and Yuan, X and Li, J and Sun, K and Han, J and Xiao, H and Li, Y},
title = {Highly efficient preparation of multiscaled quantum dot barcodes for multiplexed hepatitis B detection.},
journal = {ACS nano},
volume = {7},
number = {1},
pages = {471-481},
doi = {10.1021/nn3045215},
pmid = {23205725},
issn = {1936-086X},
mesh = {Hepatitis B virus/*isolation &amp; purification/*ultrastructure ; *Quantum Dots ; Staining and Labeling/methods ; },
abstract = {Both disease diagnosis and therapeutic treatments require real-time information from assays capable of identifying multiple targets. Among various multiplexed biochips, multiplexed suspension assays of quantum dot (QD)-encoded microspheres are highly advantageous. This arises from the excellent fluorescent properties of the QDs incorporated into these microspheres, thus allowing them to serve as "QD barcodes". QD barcodes can be prepared through various approaches. However, the formulation of improved synthetic techniques that may allow more efficient preparation of QD barcodes with better encoding accuracy still remains a challenge. In this report, we describe a combined membrane emulsification-solvent evaporation (MESE) approach for the efficient preparation of QD barcodes. By combining the advantages of the MESE approach in controlling the barcode sizes with accurate encoding, a three-dimensional barcode library that integrates the signals of the forward scattering, fluorescence 1, and fluorescence 4 channels was established via flow cytometry. The five indexes of hepatitis B viruses were chosen as diagnostic targets to examine the feasibility of the QD barcodes in high-throughput diagnosis. On the basis of showing that singleplex detection is feasible, we demonstrate the ability of these QD barcodes to simultaneously and selectively detect a multitude of diverse biomolecular targets.},
}
@article {pmid23201627,
year = {2013},
author = {Singh, P and Foley, SL and Nayak, R and Kwon, YM},
title = {Massively parallel sequencing of enriched target amplicons for high-resolution genotyping of Salmonella serovars.},
journal = {Molecular and cellular probes},
volume = {27},
number = {2},
pages = {80-85},
doi = {10.1016/j.mcp.2012.11.004},
pmid = {23201627},
issn = {1096-1194},
mesh = {Bacterial Typing Techniques/*methods ; Molecular Typing ; Multilocus Sequence Typing/*methods ; Nucleic Acid Amplification Techniques ; Phylogeny ; Salmonella/*classification/*genetics ; },
abstract = {With next generation sequencing (NGS) technology, it is now possible to carry out in-depth, large-scale sequencing projects, such as whole genome sequencing, in a fast and inexpensive manner. However, often it is more practical and convenient to sequence and analyze multiple, smaller regions of the bacterial genome to gain valuable information about an organism. One such application is genotyping of bacterial strains by multilocus sequence typing (MLST) that involves PCR and sequencing analysis of typically 7 housekeeping genes. Recently, we described a novel MLST method, called MLST-seq that combines a PCR-based target enrichment method and NGS technology to simultaneously analyze numerous target gene sequences, thereby improving the resolution and high-throughput capacity of current MLST approaches. However, the performance of the MLST-seq method was hampered from a substantial bias in target enrichment step. In this study, we used an improved target enrichment method using hairpin selectors to amplify 21 target genes simultaneously from each of 41 Salmonella strains. The resulting amplicons tagged with strain-specific barcodes were pooled and sequenced en masse by 454 pyrosequencing. Analysis of sequence data from 38 Salmonella strains using combinations of 3, 7 and 14 target genes resulted in 23, 32 and 37 distinct allelic profiles, respectively. These results demonstrated that MLST-seq with an increased number of target genes is an efficient way to improve discrimination among closely-related strains of Salmonella. With the rapidly increasing sequencing capacity of NGS technologies combined with further improvements in target capturing methods, MLST-seq could become a promising approach to perform high-resolution strain typing of a large collection of Salmonella, and likely other genera in a labor- and cost-efficient manner in the future.},
}
@article {pmid23193267,
year = {2013},
author = {Guillou, L and Bachar, D and Audic, S and Bass, D and Berney, C and Bittner, L and Boutte, C and Burgaud, G and de Vargas, C and Decelle, J and Del Campo, J and Dolan, JR and Dunthorn, M and Edvardsen, B and Holzmann, M and Kooistra, WH and Lara, E and Le Bescot, N and Logares, R and Mahé, F and Massana, R and Montresor, M and Morard, R and Not, F and Pawlowski, J and Probert, I and Sauvadet, AL and Siano, R and Stoeck, T and Vaulot, D and Zimmermann, P and Christen, R},
title = {The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy.},
journal = {Nucleic acids research},
volume = {41},
number = {Database issue},
pages = {D597-604},
pmid = {23193267},
issn = {1362-4962},
mesh = {DNA Barcoding, Taxonomic ; DNA, Ribosomal/*chemistry ; *Databases, Nucleic Acid ; Eukaryota/classification/genetics ; *Genes, rRNA ; High-Throughput Nucleotide Sequencing ; Internet ; RNA, Ribosomal/*chemistry ; Ribosome Subunits, Small, Eukaryotic/*chemistry ; },
abstract = {The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR(2), http://ssu-rrna.org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total, 136 866 sequences are nuclear encoded, 45 708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists.},
}
@article {pmid23190419,
year = {2012},
author = {Kuzmina, ML and Johnson, KL and Barron, HR and Hebert, PD},
title = {Identification of the vascular plants of Churchill, Manitoba, using a DNA barcode library.},
journal = {BMC ecology},
volume = {12},
number = {},
pages = {25},
pmid = {23190419},
issn = {1472-6785},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; *Gene Library ; Genes, Plant ; High-Throughput Nucleotide Sequencing ; Manitoba ; Plants/*classification/genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Because arctic plant communities are highly vulnerable to climate change, shifts in their composition require rapid, accurate identifications, often for specimens that lack diagnostic floral characters. The present study examines the role that DNA barcoding can play in aiding floristic evaluations in the arctic by testing the effectiveness of the core plant barcode regions (rbcL, matK) and a supplemental ribosomal DNA (ITS2) marker for a well-studied flora near Churchill, Manitoba.<br><br>RESULTS: This investigation examined 900 specimens representing 312 of the 354 species of vascular plants known from Churchill. Sequencing success was high for rbcL: 95% for fresh specimens and 85% for herbarium samples (mean age 20 years). ITS2 worked equally well for the fresh and herbarium material (89% and 88%). However, sequencing success was lower for matK, despite two rounds of PCR amplification, which reflected less effective primer binding and sensitivity to the DNA degradation (76% of fresh, 45% of herbaria samples). A species was considered as taxonomically resolved if its members showed at least one diagnostic difference from any other taxon in the study and formed a monophyletic clade. The highest species resolution (69%) was obtained by combining information from all three genes. The joint sequence information for rbcL and matK distinguished 54% of 286 species, while rbcL and ITS2 distinguished 63% of 285 species. Discrimination of species within Salix, which constituted 8% of the flora, was particularly problematic. Despite incomplete resolution, the barcode results revealed 22 misidentified herbarium specimens, and enabled the identification of field specimens which were otherwise too immature to identify. Although seven cases of ITS2 paralogy were noted in the families Cyperaceae, Juncaceae and Juncaginaceae, this intergenic spacer played an important role in resolving congeneric plant species at Churchill.<br><br>CONCLUSIONS: Our results provided fast and cost-effective solution to create a comprehensive, effective DNA barcode reference library for a local flora.},
}
@article {pmid23189159,
year = {2012},
author = {Links, MG and Dumonceaux, TJ and Hemmingsen, SM and Hill, JE},
title = {The chaperonin-60 universal target is a barcode for bacteria that enables de novo assembly of metagenomic sequence data.},
journal = {PloS one},
volume = {7},
number = {11},
pages = {e49755},
pmid = {23189159},
issn = {1932-6203},
support = {//Canadian Institutes of Health Research/Canada ; },
mesh = {Bacteria/classification/*genetics/*metabolism ; Chaperonin 60/genetics/*metabolism ; DNA Barcoding, Taxonomic ; Genes, Bacterial ; Genome, Bacterial ; *Metagenomics ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; },
abstract = {Barcoding with molecular sequences is widely used to catalogue eukaryotic biodiversity. Studies investigating the community dynamics of microbes have relied heavily on gene-centric metagenomic profiling using two genes (16S rRNA and cpn60) to identify and track Bacteria. While there have been criteria formalized for barcoding of eukaryotes, these criteria have not been used to evaluate gene targets for other domains of life. Using the framework of the International Barcode of Life we evaluated DNA barcodes for Bacteria. Candidates from the 16S rRNA gene and the protein coding cpn60 gene were evaluated. Within complete bacterial genomes in the public domain representing 983 species from 21 phyla, the largest difference between median pairwise inter- and intra-specific distances ("barcode gap") was found from cpn60. Distribution of sequence diversity along the ∼555 bp cpn60 target region was remarkably uniform. The barcode gap of the cpn60 universal target facilitated the faithful de novo assembly of full-length operational taxonomic units from pyrosequencing data from a synthetic microbial community. Analysis supported the recognition of both 16S rRNA and cpn60 as DNA barcodes for Bacteria. The cpn60 universal target was found to have a much larger barcode gap than 16S rRNA suggesting cpn60 as a preferred barcode for Bacteria. A large barcode gap for cpn60 provided a robust target for species-level characterization of data. The assembly of consensus sequences for barcodes was shown to be a reliable method for the identification and tracking of novel microbes in metagenomic studies.},
}
@article {pmid23188109,
year = {2012},
author = {Halbritter, J and Diaz, K and Chaki, M and Porath, JD and Tarrier, B and Fu, C and Innis, JL and Allen, SJ and Lyons, RH and Stefanidis, CJ and Omran, H and Soliman, NA and Otto, EA},
title = {High-throughput mutation analysis in patients with a nephronophthisis-associated ciliopathy applying multiplexed barcoded array-based PCR amplification and next-generation sequencing.},
journal = {Journal of medical genetics},
volume = {49},
number = {12},
pages = {756-767},
doi = {10.1136/jmedgenet-2012-100973},
pmid = {23188109},
issn = {1468-6244},
support = {RC4-DK090917/DK/NIDDK NIH HHS/United States ; },
mesh = {Base Sequence ; Cilia/pathology ; Computational Biology/methods ; *DNA Mutational Analysis ; Exons ; Genotype ; *High-Throughput Nucleotide Sequencing ; Humans ; Kidney Diseases, Cystic/*congenital/genetics/pathology ; *Multiplex Polymerase Chain Reaction ; Mutation ; Reproducibility of Results ; },
abstract = {OBJECTIVE: To identify disease-causing mutations within coding regions of 11 known NPHP genes (NPHP1-NPHP11) in a cohort of 192 patients diagnosed with a nephronophthisis-associated ciliopathy, at low cost.<br><br>METHODS: Mutation analysis was carried out using PCR-based 48.48 Access Array microfluidic technology (Fluidigm) with consecutive next-generation sequencing. We applied a 10-fold primer multiplexing approach allowing PCR-based amplification of 475 amplicons (251 exons) for 48 DNA samples simultaneously. After four rounds of amplification followed by indexing all of 192 patient-derived products with different barcodes in a subsequent PCR, 2 &#xd7; 100 paired-end sequencing was performed on one lane of a HiSeq2000 instrument (Illumina). Bioinformatics analysis was performed using 'CLC Genomics Workbench' software. Potential mutations were confirmed by Sanger sequencing and shown to segregate.<br><br>RESULTS: Bioinformatics analysis revealed sufficient coverage of 30 &#xd7; for 168/192 (87.5%) DNA samples (median 449 &#xd7;) and of 234 out of 251 targeted coding exons (sensitivity: 93.2%). For proof-of-principle, we analysed 20 known mutations and identified 18 of them in the correct zygosity state (90%). Likewise, we identified pathogenic mutations in 34/192 patients (18%) and discovered 23 novel mutations in the genes NPHP3 (7), NPHP4 (3), IQCB1 (4), CEP290 (7), RPGRIP1L (1), and TMEM67 (1). Additionally, we found 40 different single heterozygous missense variants of unknown significance.<br><br>CONCLUSIONS: We conclude that the combined approach of array-based multiplexed PCR-amplification on a Fluidigm Access Array platform followed by next-generation sequencing is highly cost-efficient and strongly facilitates diagnostic mutation analysis in broadly heterogeneous Mendelian disorders.},
}
@article {pmid23185984,
year = {2012},
author = {Penon, O and Novo, S and Durán, S and Ibañez, E and Nogués, C and Samitier, J and Duch, M and Plaza, JA and Pérez-García, L},
title = {Efficient biofunctionalization of polysilicon barcodes for adhesion to the zona pellucida of mouse embryos.},
journal = {Bioconjugate chemistry},
volume = {23},
number = {12},
pages = {2392-2402},
doi = {10.1021/bc3004205},
pmid = {23185984},
issn = {1520-4812},
mesh = {Animals ; Cell Tracking/*methods ; Cells, Cultured ; Crosses, Genetic ; Embryo, Mammalian ; Female ; Mice ; Mice, Inbred C57BL ; Mice, Inbred CBA ; Microscopy, Atomic Force ; Microscopy, Fluorescence ; Polymerization ; Silicon/*chemistry ; Spectrometry, Mass, Secondary Ion ; Staining and Labeling/*methods ; Surface Properties ; Wheat Germ Agglutinins/*chemistry ; Zona Pellucida/*chemistry/metabolism/ultrastructure ; },
abstract = {Cell tracking is an emergent area in nanobiotechnology, promising the study of individual cells or the identification of populations of cultured cells. In our approach, microtools designed for extracellular tagging are prepared, because using biofunctionalized polysilicon barcodes to tag cell membranes externally avoids the inconveniences of cell internalization. The crucial covalent biofunctionalization process determining the ultimate functionality was studied in order to find the optimum conditions to link a biomolecule to a polysilicon barcode surface using a self-assembled monolayer (SAM) as the connector. Specifically, a lectin (wheat germ agglutinin, WGA) was used because of its capacity to recognize some specific carbohydrates present on the surface of most mammalian cells. Self-assembled monolayers were prepared on polysilicon surfaces including aldehyde groups as terminal functions to study the suitability of their covalent chemical bonding to WGA. Some parameters, such as the polysilicon surface roughness or the concentration of WGA, proved to be crucial for successful biofunctionalization and bioactivity. The SAMs were characterized by contact angle measurements, time-of-flight secondary ion mass spectrometry (TOF-SIMS), laser desorption/ionization time-of-flight mass spectrometry (LDI-TOF MS), and atomic force microscopy (AFM). The biofunctionalization step was also characterized by fluorescence microscopy and, in the case of barcodes, by adhesion experiments to the zona pellucida of mouse embryos. These experiments showed high barcode retention rates after 96 h of culture as well as high embryo viability to the blastocyst stage, indicating the robustness of the biofunctionalization and, therefore, the potential of these new microtools to be used for cell tagging.},
}
@article {pmid23185414,
year = {2012},
author = {Strutzenberger, P and Brehm, G and Fiedler, K},
title = {DNA barcode sequencing from old type specimens as a tool in taxonomy: a case study in the diverse genus Eois (Lepidoptera: Geometridae).},
journal = {PloS one},
volume = {7},
number = {11},
pages = {e49710},
pmid = {23185414},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; Biological Evolution ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Genetic Variation ; Moths/*genetics/physiology ; Phylogeny ; Plants ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; Species Specificity ; Time Factors ; },
abstract = {In this study we report on the sequencing of the COI barcode region from 96 historical specimens (92 type specimens +4 non-types) of Eois. Eois is a diverse clade of tropical geometrid moths and is the target of a number of ongoing studies on life-histories, phylogeny, co-evolution with host plants or parasitoids, and diversity patterns across temporal and spatial dimensions. The unequivocal application of valid names is crucial for all aspects of biodiversity research as well as monitoring and conservation efforts. The availability of barcodes from historical type specimens has the potential to facilitate the much-needed acceleration of species description. We performed non-destructive DNA extraction on the abdomens of Eois specimens between 79 and 157 years of age. We used six primer combinations (recovering between 109 and 130 bp each) to target the full-length barcode sequence of each specimen. We were able to obtain sequences for 91 of 96 specimens (success rate 94.8%). Sequence length ranged from 121 bp to full barcode sequences (658 bp), the average sequence length was ~500 bp. We detected a moderately strong and statistically significant negative correlation between specimen age and total sequence length, which is in agreement with expectations. The abdomen proved to be an exceedingly valuable source of DNA in old specimens of Lepidoptera. Barcode sequences obtained in this study are currently being used in an effort towards a step-wise taxonomic revision of Eois. We encourage that DNA barcodes obtained from types specimens should be included in all species descriptions and revisions whenever feasible.},
}
@article {pmid23180801,
year = {2013},
author = {Tang, DT and Plessy, C and Salimullah, M and Suzuki, AM and Calligaris, R and Gustincich, S and Carninci, P},
title = {Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching.},
journal = {Nucleic acids research},
volume = {41},
number = {3},
pages = {e44},
pmid = {23180801},
issn = {1362-4962},
mesh = {Animals ; *Artifacts ; Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Mice ; RNA/blood/chemistry ; Rats ; Sensitivity and Specificity ; Sequence Analysis, RNA/*methods ; Templates, Genetic ; },
abstract = {Template switching (TS) has been an inherent mechanism of reverse transcriptase, which has been exploited in several transcriptome analysis methods, such as CAGE, RNA-Seq and short RNA sequencing. TS is an attractive option, given the simplicity of the protocol, which does not require an adaptor mediated step and thus minimizes sample loss. As such, it has been used in several studies that deal with limited amounts of RNA, such as in single cell studies. Additionally, TS has also been used to introduce DNA barcodes or indexes into different samples, cells or molecules. This labeling allows one to pool several samples into one sequencing flow cell, increasing the data throughput of sequencing and takes advantage of the increasing throughput of current sequences. Here, we report TS artifacts that form owing to a process called strand invasion. Due to the way in which barcodes/indexes are introduced by TS, strand invasion becomes more problematic by introducing unsystematic biases. We describe a strategy that eliminates these artifacts in silico and propose an experimental solution that suppresses biases from TS.},
}
@article {pmid23179313,
year = {2013},
author = {Pang, X and Shi, L and Song, J and Chen, X and Chen, S},
title = {Use of the potential DNA barcode ITS2 to identify herbal materials.},
journal = {Journal of natural medicines},
volume = {67},
number = {3},
pages = {571-575},
pmid = {23179313},
issn = {1861-0293},
mesh = {Counterfeit Drugs ; *DNA Barcoding, Taxonomic/methods ; DNA, Plant/*analysis ; Drug Contamination/prevention &amp; control ; Drugs, Chinese Herbal/*standards ; Genetic Variation ; Phytotherapy ; Plants, Medicinal/classification/*genetics ; Quality Control ; Species Specificity ; },
abstract = {A potential DNA barcode, ITS2, was studied to discriminate herbal materials to confirm their identities and ensure their safe application in pharmaceuticals. Here, a total of 4385 samples of 2431 species were collected, and these samples are from 61 commonly used herbs and their closely related species or adulterants. Based on assessments of the extent of genetic divergence, the DNA barcoding gap and the ability for species discrimination, our results suggest that ITS2 is a powerful tool for distinguishing herbs. For the first dataset including 61 herbs, ITS2 correctly identified 100% of them. For the second dataset containing 51 herbs and their 2382 closely related species, ITS2 could discriminate correctly 48 herbs from their closely related species. For the third dataset comprising 34 herbs and their 111 adulterants, ITS2 could distinguish successfully all the herbs from their adulterants. In conclusion, the ITS2 region is an efficient marker for the authentication of herbal materials, and our study will accelerate the process of the application of the DNA barcoding technique in differentiating herbs.},
}
@article {pmid23178478,
year = {2013},
author = {Cai, L},
title = {Turning single cells into microarrays by super-resolution barcoding.},
journal = {Briefings in functional genomics},
volume = {12},
number = {2},
pages = {75-80},
pmid = {23178478},
issn = {2041-2657},
support = {1DP2OD008530/OD/NIH HHS/United States ; },
mesh = {Animals ; Fluorescent Dyes/*metabolism ; Humans ; Oligonucleotide Array Sequence Analysis/*methods ; RNA, Messenger/genetics/metabolism ; Single-Cell Analysis/*methods ; *Staining and Labeling ; },
abstract = {In this review, we discuss a strategy to bring genomics and proteomics into single cells by super-resolution microscopy. The basis for this new approach are the following: given the 10 nm resolution of a super-resolution microscope and a typical cell with a size of (10 µm)(3), individual cells contain effectively 10(9) super-resolution pixels or bits of information. Most eukaryotic cells have 10(4) genes and cellular abundances of 10-100 copies per transcript. Thus, under a super-resolution microscope, an individual cell has 1000 times more pixel volume or information capacities than is needed to encode all transcripts within that cell. Individual species of mRNA can be uniquely identified by labeling them each with a distinct combination of fluorophores by fluorescence in situ hybridization. With at least 15 fluorophores available in super-resolution, hundreds of genes in can be barcoded with a three-color barcode (3C15 = 455). These calculations suggest that by combining super-resolution microscopy and barcode labeling, single cells can be turned into informatics platforms denser than microarrays and that molecular species in individual cells can be profiled in a massively parallel fashion.},
}
@article {pmid23173946,
year = {2012},
author = {Renaud, AK and Savage, J and Adamowicz, SJ},
title = {DNA barcoding of Northern Nearctic Muscidae (Diptera) reveals high correspondence between morphological and molecular species limits.},
journal = {BMC ecology},
volume = {12},
number = {},
pages = {24},
pmid = {23173946},
issn = {1472-6785},
mesh = {Animals ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; *Databases, Genetic ; Female ; Genes, Insect ; Male ; Muscidae/*classification/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND: Various methods have been proposed to assign unknown specimens to known species using their DNA barcodes, while others have focused on using genetic divergence thresholds to estimate "species" diversity for a taxon, without a well-developed taxonomy and/or an extensive reference library of DNA barcodes. The major goals of the present work were to: a) conduct the largest species-level barcoding study of the Muscidae to date and characterize the range of genetic divergence values in the northern Nearctic fauna; b) evaluate the correspondence between morphospecies and barcode groupings defined using both clustering-based and threshold-based approaches; and c) use the reference library produced to address taxonomic issues.<br><br>RESULTS: Our data set included 1114 individuals and their COI sequences (951 from Churchill, Manitoba), representing 160 morphologically-determined species from 25 genera, covering 89% of the known fauna of Churchill and 23% of the Nearctic fauna. Following an iterative process through which all specimens belonging to taxa with anomalous divergence values and/or monophyly issues were re-examined, identity was modified for 9 taxa, including the reinstatement of Phaonia luteva (Walker) stat. nov. as a species distinct from Phaonia errans (Meigen). In the post-reassessment data set, no distinct gap was found between maximum pairwise intraspecific distances (range 0.00-3.01%) and minimum interspecific distances (range: 0.77-11.33%). Nevertheless, using a clustering-based approach, all individuals within 98% of species grouped with their conspecifics with high (>95%) bootstrap support; in contrast, a maximum species discrimination rate of 90% was obtained at the optimal threshold of 1.2%. DNA barcoding enabled the determination of females from 5 ambiguous species pairs and confirmed that 16 morphospecies were genetically distinct from named taxa. There were morphological differences among all distinct genetic clusters; thus, no cases of cryptic species were detected.<br><br>CONCLUSIONS: Our findings reveal the great utility of building a well-populated, species-level reference barcode database against which to compare unknowns. When such a library is unavailable, it is still possible to obtain a fairly accurate (within ~10%) rapid assessment of species richness based upon a barcode divergence threshold alone, but this approach is most accurate when the threshold is tuned to a particular taxon.},
}
@article {pmid23173521,
year = {2012},
author = {Wray, BR},
title = {Barcodes: a useful tool for the lab.},
journal = {MLO: medical laboratory observer},
volume = {44},
number = {11},
pages = {28, 31},
pmid = {23173521},
issn = {0580-7247},
mesh = {*Electronic Data Processing/instrumentation/methods ; *Laboratories ; United States ; },
}
@article {pmid23172674,
year = {2012},
author = {Huang, CH and Chang, MT and Huang, L},
title = {Species identification of Wickerhamomyces anomalus and related taxa using β-tubulin (β-tub) DNA barcode marker.},
journal = {Yeast (Chichester, England)},
volume = {29},
number = {12},
pages = {531-535},
doi = {10.1002/yea.2933},
pmid = {23172674},
issn = {1097-0061},
mesh = {Base Sequence ; *DNA Barcoding, Taxonomic ; DNA Primers/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Fungal Proteins/genetics ; Genetic Markers/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Saccharomycetales/classification/genetics/*isolation &amp; purification ; Sequence Analysis, DNA ; Species Specificity ; Tubulin/*genetics ; },
abstract = {Wickerhamomyces anomalus is used in food and feed processing, although the species has been reported as an opportunistic human pathogen, predominantly in neonates. Neither phenotypic nor the most frequently applied genotypic marker (D1/D2 LSU ribosomal DNA) provide sufficient resolution for accurate identification of this yeast. In this study, the β-tubulin gene was used for species identification by direct DNA sequencing and as marker in a species-specific PCR assay. The results showed that all examined W. anomalus strains were clearly distinguished from the closely related species by comparative sequence analysis of the β-tubulin gene. In addition, the species-specific primers were also developed based on the β-tubulin gene, which was employed for polymerase chain reaction with the template DNA of Wickerhamomyces strains. A single 218 bp species-specific band was found only in W. anomalus. Our data indicate that the phylogenetic relationships between these strains are easily resolved by sequencing of the β-tubulin gene and combined with species-specific PCR assay.},
}
@article {pmid23172022,
year = {2012},
author = {Bejdák, P and Lengerová, M and Paloušová, D and Volfová, P and Kocmanová, I and Mayer, J and Ráčil, Z},
title = {[Detection and identification of filamentous fungi causing mycoses using molecular genetic methods].},
journal = {Klinicka mikrobiologie a infekcni lekarstvi},
volume = {18},
number = {4},
pages = {109-114},
pmid = {23172022},
issn = {1211-264X},
mesh = {DNA, Fungal/genetics ; Fungi/classification/*genetics ; Humans ; Molecular Biology ; *Molecular Diagnostic Techniques ; Mycoses/*diagnosis/microbiology ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {Methods of molecular genetics offer rapid and sensitive detection and identification of fungal pathogens. The currently used methods are based mainly on PCR. With regard to the ubiquitous presence of fungi, it is important to prevent contamination during the whole process, from sampling to laboratory analyses. Molecular genetic methods are not included among the EORTC/MSG criteria used for the diagnosis of invasive fungal diseases since interlaboratory standardization is still missing. Another reason is the use of different target genes for PCR. ITS sequences from rDNA clusters are recommended for DNA barcoding of fungi. The use of DNA sequencing for identification of fungi in clinical samples has certain limitations and interpretation of results could be problematic in some cases. DNA sequences are searched and compared in public databases on the Internet, the best known of them being the GenBank. However, more reliable data for identification of fungi are offered by specialized mycological databases.},
}
@article {pmid23166801,
year = {2012},
author = {Bhattacharjee, MJ and Laskar, BA and Dhar, B and Ghosh, SK},
title = {Identification and re-evaluation of freshwater catfishes through DNA barcoding.},
journal = {PloS one},
volume = {7},
number = {11},
pages = {e49950},
pmid = {23166801},
issn = {1932-6203},
mesh = {Animals ; Aquaculture/*methods ; Catfishes/anatomy &amp; histology/*classification/*genetics ; Conservation of Natural Resources/*methods ; DNA Barcoding, Taxonomic/methods/*veterinary ; Fresh Water ; India ; Species Specificity ; },
abstract = {BACKGROUND: Catfishes are globally demanded as human food, angling sport and aquariums keeping thus are highly exploited all over the world. North-East India possess high abundance of catfishes and are equally exploited through decades. The strategies for conservation necessitate understanding the actual species composition, which is hampered due to sporadic descriptions of the species through traditional taxonomy. Therefore, actual catfish diversity in this region is important to be studied through the combined approach of morphological and molecular technique of DNA barcoding.<br><br>Altogether 75 native catfish specimens were collected from across the North-East India and their morphological features were compared with the taxonomic keys. The detailed taxonomic study identified 25 species belonging to 17 genera and 9 families. The cytochrome oxidase c subunit-I gene fragment were then sequenced from the samples in accordance with the standard DNA barcoding protocols. The sequences were compared with public databases, viz., GenBank and BOLD. Sequences developed in the current study and from databases of the same and related taxa were analyzed to calculate the congeneric and conspecific genetic divergences using Kimura 2-parameter distance model, and a Neighbor Joining tree was created using software MEGA5.1. The DNA barcoding approach delineated 21 distinct species showing 4.33 folds of difference between the nearest congeners. Four species, viz., Amblyceps apangi, Glyptothorax telchitta, G. trilineatus and Erethistes pusillus, showed high conspecific divergence; hence their identification through molecular approach remained inconclusive. On the other hand, the database sequences for three species, viz., Mystus horai, Bagarius yarrelli and Clarias batrachus, appeared mislabeled.<br><br>CONCLUSION: The efficiency of DNA barcoding was reaffirmed from its success by easily identifying the major share (84%) of the studied catfish into 21 distinct species. The study contributed 27 new barcodes for 7 species and confirmed the range expansion of 2 important species in NE India.},
}
@article {pmid23166532,
year = {2012},
author = {Kim, DW and Yoo, WG and Park, HC and Yoo, HS and Kang, DW and Jin, SD and Min, HK and Paek, WK and Lim, J},
title = {DNA barcoding of fish, insects, and shellfish in Korea.},
journal = {Genomics &amp; informatics},
volume = {10},
number = {3},
pages = {206-211},
pmid = {23166532},
issn = {2234-0742},
abstract = {DNA barcoding has been widely used in species identification and biodiversity research. A short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) sequence serves as a DNA bio-barcode. We collected DNA barcodes, based on COI sequences from 156 species (529 sequences) of fish, insects, and shellfish. We present results on phylogenetic relationships to assess biodiversity the in the Korean peninsula. Average GC% contents of the 68 fish species (46.9%), the 59 shellfish species (38.0%), and the 29 insect species (33.2%) are reported. Using the Kimura 2 parameter in all possible pairwise comparisons, the average interspecific distances were compared with the average intraspecific distances in fish (3.22 vs. 0.41), insects (2.06 vs. 0.25), and shellfish (3.58 vs. 0.14). Our results confirm that distance-based DNA barcoding provides sufficient information to identify and delineate fish, insect, and shellfish species by means of all possible pairwise comparisons. These results also confirm that the development of an effective molecular barcode identification system is possible. All DNA barcode sequences collected from our study will be useful for the interpretation of species-level identification and community-level patterns in fish, insects, and shellfish in Korea, although at the species level, the rate of correct identification in a diversified environment might be low.},
}
@article {pmid23166460,
year = {2012},
author = {Nunes, JF and Zaldívar-Riverón, A and de Castro, CS and Marsh, PM and Penteado-Dias, AM and Briceño, R and Martínez, JJ},
title = {Doryctopambolus Nunes &amp; Zaldívar-Riverón (Braconidae), a new neotropical doryctine wasp genus with propodeal spines.},
journal = {ZooKeys},
volume = {},
number = {223},
pages = {53-67},
pmid = {23166460},
issn = {1313-2970},
abstract = {The new Neotropical doryctine genus Doryctopambolusgen. n. is erected to contain Doryctopambolus pilcomayensis (van Achterberg &amp; Braet, 2004), comb. n., which was previously placed within Pambolus (Pambolinae), as well as three new species, Doryctopambolus clebschisp. n., Doryctopambolus dominicanussp. n. and Doryctopambolus sarochensissp. n. Members of this new genus are mainly characterised by the presence of at least one pair of conspicuous propodeal apico-lateral projections, which are similar to those present in all members of Pambolinae and in species of three Australasian doryctine genera. We generated DNA barcoding sequences for the three newly described species. We discuss the morphological similarity between species of the Australasian Echinodoryctes Belokobylskij, Iqbal &amp; Austin and Doryctopambolus. A key for the described species of Doryctopambolus is provided.},
}
@article {pmid23162910,
year = {2012},
author = {Xin, TY and Yao, H and Luo, K and Xiang, L and Ma, XC and Han, JP and Lin, YL and Song, JY and Chen, SL},
title = {[Stability and accuracy of the identification of Notopterygii Rhizoma et Radix using the ITS/ITS2 barcodes].},
journal = {Yao xue xue bao = Acta pharmaceutica Sinica},
volume = {47},
number = {8},
pages = {1098-1105},
pmid = {23162910},
issn = {0513-4870},
mesh = {Apiaceae/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/*genetics ; Phylogeny ; Plant Roots/genetics ; Plants, Medicinal/genetics ; Rhizome/genetics ; },
abstract = {In this study, Notopterygii Rhizoma et Radix was used to verify the stability and accuracy of DNA barcodes in identification of Chinese materia medica for the first time. All genomic DNAs from thirty one samples were extracted. The ITS (internal transcribed spacer) regions were amplified and sequenced bi-directionally. Obtained sequences were assembled using the CodonCode Aligner. And the sequences of the ITS regions were aligned through Clustal-W and the genetic distances were computed using MEGA 5.0 in accordance with the kimura 2-parameter (K2P) model. The neighbor-joining (NJ) phylogenetic trees were constructed. The ITS2 regions were obtained by using the hidden Markov model (HMM)-based annotation methods from the ITS sequences. Results indicated that the lengths of ITS regions of Notopterygii Rhizoma et Radix were 603-604 bp, while the lengths of ITS2 regions were 228 bp. The haplotypes of ITS/ITS2 regions of Notopterygii Rhizoma et Radix were the same as those of the original plant leaves. The intra-specific genetic distances were smaller than inter-specific ones in ITS/ITS2 regions of Notopterygium incisum and N. franchetii. The NJ trees showed that N. incisum, N. franchetii and its adulterants can be easily differentiated according to their monophyly. Therefore, ITS/ITS2 regions as DNA barcodes can stably and accurately distinguish Notopterygii Rhizoma et Radix from its adulterants and could provide a new technique to ensure clinical safety in utilization of traditional Chinese medicines.},
}
@article {pmid23157266,
year = {2012},
author = {Degtjareva, GV and Logacheva, MD and Samigullin, TH and Terentieva, EI and Valiejo-Roman, CM},
title = {Organization of chloroplast psbA-trnH intergenic spacer in dicotyledonous angiosperms of the family Umbelliferae.},
journal = {Biochemistry. Biokhimiia},
volume = {77},
number = {9},
pages = {1056-1064},
doi = {10.1134/S0006297912090131},
pmid = {23157266},
issn = {1608-3040},
mesh = {Apiaceae/*genetics ; Chloroplasts/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Chloroplast/*genetics ; DNA, Intergenic/*genetics ; Phylogeny ; },
abstract = {Chloroplast intergenic psbA-trnH spacer has recently become a popular tool in plant molecular phylogenetic studies at low taxonomic level and as suitable for DNA barcoding studies. In present work, we studied the organization of psbA-trnH in the large family Umbelliferae and its potential as a DNA barcode and phylogenetic marker in this family. Organization of the spacer in Umbelliferae is consistent with a general pattern evident for angiosperms. The 5'-region of the spacer situated directly after the psbA gene is more conserved in length compared to the 3'-region, which has greater sequence variation. This pattern can be attributed to the maintenance of the secondary structural elements in the 5'-region of the spacer needed for posttranscriptional regulation of psbA gene expression. In Umbelliferae only, the conserved region contains a duplication of the fragment corresponding to the loop of the stem-loop structure and an independent appearance of identical sequence complementarities (traits) necessary to stabilize the stem-loop structure in different lineages. The 3'-region of the spacer nearest to trnH ranges greatly in size, mainly due to deletions, and the decrease in spacer length is a general trend in the evolution psbA-trnH in Umbelliferae. The features revealed in spacer organization allow us to use it as phylogenetic marker, and indels seem to be more informative for analyses than nucleotide substitutions. However, high conservation among closely related taxa and occurrence of homoplastic inversions in the stem-loop structure limit its application as DNA barcode.},
}
@article {pmid23156182,
year = {2012},
author = {Mirnezhad, M and Schidlo, N and Klinkhamer, PG and Leiss, KA},
title = {Variation in genetics and performance of Dutch western flower thrips populations.},
journal = {Journal of economic entomology},
volume = {105},
number = {5},
pages = {1816-1824},
doi = {10.1603/ec11357},
pmid = {23156182},
issn = {0022-0493},
mesh = {Amplified Fragment Length Polymorphism Analysis ; Animals ; *Chrysanthemum ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Feeding Behavior ; Female ; Genotype ; Insect Proteins/genetics ; *Lactuca ; Molecular Sequence Data ; Netherlands ; *Onions ; Polymorphism, Genetic ; Reproduction ; Thysanoptera/classification/genetics/*physiology ; },
abstract = {Invasion of pests may result in local adaptation and the development of biotypes specialized in different hosts. In this study, we investigated western flower thrips, Frankliniella occidentalis (Pergande), an invasive pest in Europe. Thrips from different commercial glasshouse crops within the Dutch Westland and a lab culture kept on chrysanthemum were compared. Genetic barcoding was applied for the identification of potential western flower thrips cryptic species in the Netherlands revealing that all western flower thrips populations studied belonged to the "glasshouse" strain reported in California as the only existing species in the Netherlands. Feeding and reproduction parameters in leaf disc and whole plant bioassays were scored. We detected significant differences in thrips feeding among host plants and thrips origin. Host plants differed in average thrips damage while thrips from different origins caused similar amounts of damage across host plants. In contrast, reproductive success of thrips on all plant species depended strongly on thrips origin. The thrips lab culture maintained on chrysanthemum obtained the highest levels of reproduction on chrysanthemum. Differences among the other thrips populations were relatively small. Amplified fragment length polymorphisms analyses were used to study genetic differences between western flower thrips populations and confirmed that the lab culture population was also genetically the most different of all studied populations. The results of the amplified fragment length polymorphisms analyses together with the better reproductive performance of thrips on the host plant on which they were maintained demonstrate the evolution of a lab biotype specialized in a particular host. This finding has potential relevance for future crop control and breeding programs.},
}
@article {pmid23155412,
year = {2012},
author = {Pang, X and Liu, C and Shi, L and Liu, R and Liang, D and Li, H and Cherny, SS and Chen, S},
title = {Utility of the trnH-psbA intergenic spacer region and its combinations as plant DNA barcodes: a meta-analysis.},
journal = {PloS one},
volume = {7},
number = {11},
pages = {e48833},
pmid = {23155412},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic ; *DNA, Intergenic ; DNA, Plant/*genetics ; Databases, Genetic ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND: The trnH-psbA intergenic spacer region has been used in many DNA barcoding studies. However, a comprehensive evaluation with rigorous sequence preprocessing and statistical testing on the utility of trnH-psbA and its combinations as DNA barcodes is lacking.<br><br>Sequences were searched from GenBank for a meta-analysis on the usefulness of trnH-psbA and its combinations as DNA barcodes. After preprocessing, we constructed full and matching data sets that contained 17 983 trnH-psbA sequences and 2190 sets of trnH-psbA, matK, rbcL, and ITS2 sequences from the same sample, repectively. These datasets were used to analyze the ability of trnH-psbA and its combinations to discriminate species by the BLAST and BLAST+P methods. The Fisher's exact test was used to evaluate the significance of performance differences. For the full data set, the identification success rates of trnH-psbA exceeded 70% in 18 families and 12 genera, respectively. For the matching data set, the identification rates of trnH-psbA were significantly higher than those of the other loci in two families and four genera. Similarly, the identification rates of trnH-psbA+ITS2 were significantly higher than those of matK+rbcL in 18 families and 21 genera. CONCLUSION/SIGNIFICANE: This study provides valuable information on the higher utility of trnH-psbA and its combinations. We found that trnH-psbA+ITS2 combination performs better or equally well compared with other combinations in most taxonomic groups investigated. This information will guide the optimal usage of trnH-psbA and its combinations for species identification.},
}
@article {pmid23148716,
year = {2012},
author = {Shearer, AE and Hildebrand, MS and Ravi, H and Joshi, S and Guiffre, AC and Novak, B and Happe, S and LeProust, EM and Smith, RJ},
title = {Pre-capture multiplexing improves efficiency and cost-effectiveness of targeted genomic enrichment.},
journal = {BMC genomics},
volume = {13},
number = {},
pages = {618},
pmid = {23148716},
issn = {1471-2164},
support = {R01S DC012049/DC/NIDCD NIH HHS/United States ; R01S DC002842/DC/NIDCD NIH HHS/United States ; 1F30DC011674/DC/NIDCD NIH HHS/United States ; R01S DC003544/DC/NIDCD NIH HHS/United States ; T32 GM007337/GM/NIGMS NIH HHS/United States ; R01 DC003544/DC/NIDCD NIH HHS/United States ; F30 DC011674/DC/NIDCD NIH HHS/United States ; R01 DC012049/DC/NIDCD NIH HHS/United States ; R01 DC002842/DC/NIDCD NIH HHS/United States ; },
mesh = {Case-Control Studies ; Cost-Benefit Analysis ; DNA Barcoding, Taxonomic ; *Genome, Human ; *Genomics ; Hearing Loss/*genetics ; High-Throughput Nucleotide Sequencing/economics/*methods ; Humans ; Mutation ; Oligonucleotide Array Sequence Analysis ; Oligonucleotides/genetics ; Sequence Analysis, DNA/economics/*methods ; },
abstract = {BACKGROUND: Targeted genomic enrichment (TGE) is a widely used method for isolating and enriching specific genomic regions prior to massively parallel sequencing. To make effective use of sequencer output, barcoding and sample pooling (multiplexing) after TGE and prior to sequencing (post-capture multiplexing) has become routine. While previous reports have indicated that multiplexing prior to capture (pre-capture multiplexing) is feasible, no thorough examination of the effect of this method has been completed on a large number of samples. Here we compare standard post-capture TGE to two levels of pre-capture multiplexing: 12 or 16 samples per pool. We evaluated these methods using standard TGE metrics and determined the ability to identify several classes of genetic mutations in three sets of 96 samples, including 48 controls. Our overall goal was to maximize cost reduction and minimize experimental time while maintaining a high percentage of reads on target and a high depth of coverage at thresholds required for variant detection.<br><br>RESULTS: We adapted the standard post-capture TGE method for pre-capture TGE with several protocol modifications, including redesign of blocking oligonucleotides and optimization of enzymatic and amplification steps. Pre-capture multiplexing reduced costs for TGE by at least 38% and significantly reduced hands-on time during the TGE protocol. We found that pre-capture multiplexing reduced capture efficiency by 23 or 31% for pre-capture pools of 12 and 16, respectively. However efficiency losses at this step can be compensated by reducing the number of simultaneously sequenced samples. Pre-capture multiplexing and post-capture TGE performed similarly with respect to variant detection of positive control mutations. In addition, we detected no instances of sample switching due to aberrant barcode identification.<br><br>CONCLUSIONS: Pre-capture multiplexing improves efficiency of TGE experiments with respect to hands-on time and reagent use compared to standard post-capture TGE. A decrease in capture efficiency is observed when using pre-capture multiplexing; however, it does not negatively impact variant detection and can be accommodated by the experimental design.},
}
@article {pmid23145324,
year = {2012},
author = {Bracken-Grissom, HD and Felder, DL and Vollmer, NL and Martin, JW and Crandall, KA},
title = {Phylogenetics links monster larva to deep-sea shrimp.},
journal = {Ecology and evolution},
volume = {2},
number = {10},
pages = {2367-2373},
pmid = {23145324},
issn = {2045-7758},
abstract = {Mid-water plankton collections commonly include bizarre and mysterious developmental stages that differ conspicuously from their adult counterparts in morphology and habitat. Unaware of the existence of planktonic larval stages, early zoologists often misidentified these unique morphologies as independent adult lineages. Many such mistakes have since been corrected by collecting larvae, raising them in the lab, and identifying the adult forms. However, challenges arise when the larva is remarkably rare in nature and relatively inaccessible due to its changing habitats over the course of ontogeny. The mid-water marine species Cerataspis monstrosa (Gray 1828) is an armored crustacean larva whose adult identity has remained a mystery for over 180 years. Our phylogenetic analyses, based in part on recent collections from the Gulf of Mexico, provide definitive evidence that the rare, yet broadly distributed larva, C. monstrosa, is an early developmental stage of the globally distributed deepwater aristeid shrimp, Plesiopenaeus armatus. Divergence estimates and phylogenetic relationships across five genes confirm the larva and adult are the same species. Our work demonstrates the diagnostic power of molecular systematics in instances where larval rearing seldom succeeds and morphology and habitat are not indicative of identity. Larval-adult linkages not only aid in our understanding of biodiversity, they provide insights into the life history, distribution, and ecology of an organism.},
}
@article {pmid23145200,
year = {2012},
author = {Webster, BL and Emery, AM and Webster, JP and Gouvras, A and Garba, A and Diaw, O and Seye, MM and Tchuente, LA and Simoonga, C and Mwanga, J and Lange, C and Kariuki, C and Mohammed, KA and Stothard, JR and Rollinson, D},
title = {Genetic diversity within Schistosoma haematobium: DNA barcoding reveals two distinct groups.},
journal = {PLoS neglected tropical diseases},
volume = {6},
number = {10},
pages = {e1882},
pmid = {23145200},
issn = {1935-2735},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Africa ; Animals ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; DNA, Helminth/chemistry/genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Haplotypes ; Humans ; Indian Ocean Islands ; Male ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; NADH Dehydrogenase/genetics ; Schistosoma haematobium/*classification/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Schistosomiasis in one of the most prevalent parasitic diseases, affecting millions of people and animals in developing countries. Amongst the human-infective species S. haematobium is one of the most widespread causing urogenital schistosomiasis, a major human health problem across Africa, however in terms of research this human pathogen has been severely neglected.<br><br>To elucidate the genetic diversity of Schistosoma haematobium, a DNA 'barcoding' study was performed on parasite material collected from 41 localities representing 18 countries across Africa and the Indian Ocean Islands. Surprisingly low sequence variation was found within the mitochondrial cytochrome oxidase subunit I (cox1) and the NADH-dehydrogenase subunit 1 snad1). The 61 haplotypes found within 1978 individual samples split into two distinct groups; one (Group 1) that is predominately made up of parasites from the African mainland and the other (Group 2) that is made up of samples exclusively from the Indian Ocean Islands and the neighbouring African coastal regions. Within Group 1 there was a dominance of one particular haplotype (H1) representing 1574 (80%) of the samples analyzed. Population genetic diversity increased in samples collected from the East African coastal regions and the data suggest that there has been movement of parasites between these areas and the Indian Ocean Islands.<br><br>CONCLUSIONS/SIGNIFICANCE: The high occurrence of the haplotype (H1) suggests that at some point in the recent evolutionary history of S. haematobium in Africa the population may have passed through a genetic 'bottleneck' followed by a population expansion. This study provides novel and extremely interesting insights into the population genetics of S. haematobium on a large geographic scale, which may have consequence for control and monitoring of urogenital schistosomiasis.},
}
@article {pmid23145160,
year = {2012},
author = {Riehl, T and Kaiser, S},
title = {Conquered from the deep sea? A new deep-sea isopod species from the Antarctic shelf shows pattern of recent colonization.},
journal = {PloS one},
volume = {7},
number = {11},
pages = {e49354},
pmid = {23145160},
issn = {1932-6203},
mesh = {Animal Migration ; Animals ; Climate Change ; DNA Barcoding, Taxonomic ; Female ; Genetic Markers ; Geography ; Isopoda/anatomy &amp; histology/*genetics/physiology ; Male ; *Phylogeny ; },
abstract = {The Amundsen Sea, Antarctica, is amongst the most rapidly changing environments of the world. Its benthic inhabitants are barely known and the BIOPEARL 2 project was one of the first to biologically explore this region. Collected during this expedition, Macrostylis roaldi sp. nov. is described as the first isopod discovered on the Amundsen-Sea shelf. Amongst many characteristic features, the most obvious characters unique for M. roaldi are the rather short pleotelson and short operculum as well as the trapezoid shape of the pleotelson in adult males. We used DNA barcodes (COI) and additional mitochondrial markers (12S, 16S) to reciprocally illuminate morphological results and nucleotide variability. In contrast to many other deep-sea isopods, this species is common and shows a wide distribution. Its range spreads from Pine Island Bay at inner shelf right to the shelf break and across 1,000 m bathymetrically. Its gene pool is homogenized across space and depth. This is indicative for a genetic bottleneck or a recent colonization history. Our results suggest further that migratory or dispersal capabilities of some species of brooding macrobenthos have been underestimated. This might be relevant for the species' potential to cope with effects of climate change. To determine where this species could have survived the last glacial period, alternative refuge possibilities are discussed.},
}
@article {pmid23144869,
year = {2012},
author = {Galan, M and Pagès, M and Cosson, JF},
title = {Next-generation sequencing for rodent barcoding: species identification from fresh, degraded and environmental samples.},
journal = {PloS one},
volume = {7},
number = {11},
pages = {e48374},
pmid = {23144869},
issn = {1932-6203},
mesh = {Animals ; Cats ; Cytochromes b/genetics ; DNA Barcoding, Taxonomic/*methods/standards ; Electron Transport Complex IV/genetics ; Feces/chemistry ; Foxes ; Haplotypes ; *High-Throughput Nucleotide Sequencing ; Likelihood Functions ; Phylogeny ; Reference Standards ; Rodentia/*classification/genetics ; Skin/chemistry ; Specimen Handling ; Strigiformes ; },
abstract = {Rodentia is the most diverse order among mammals, with more than 2,000 species currently described. Most of the time, species assignation is so difficult based on morphological data solely that identifying rodents at the specific level corresponds to a real challenge. In this study, we compared the applicability of 100 bp mini-barcodes from cytochrome b and cytochrome c oxidase 1 genes to enable rodent species identification. Based on GenBank sequence datasets of 115 rodent species, a 136 bp fragment of cytochrome b was selected as the most discriminatory mini-barcode, and rodent universal primers surrounding this fragment were designed. The efficacy of this new molecular tool was assessed on 946 samples including rodent tissues, feces, museum samples and feces/pellets from predators known to ingest rodents. Utilizing next-generation sequencing technologies able to sequence mixes of DNA, 1,140 amplicons were tagged, multiplexed and sequenced together in one single 454 GS-FLX run. Our method was initially validated on a reference sample set including 265 clearly identified rodent tissues, corresponding to 103 different species. Following validation, 85.6% of 555 rodent samples from Europe, Asia and Africa whose species identity was unknown were able to be identified using the BLASTN program and GenBank reference sequences. In addition, our method proved effective even on degraded rodent DNA samples: 91.8% and 75.9% of samples from feces and museum specimens respectively were correctly identified. Finally, we succeeded in determining the diet of 66.7% of the investigated carnivores from their feces and 81.8% of owls from their pellets. Non-rodent species were also identified, suggesting that our method is sensitive enough to investigate complete predator diets. This study demonstrates how this molecular identification method combined with high-throughput sequencing can open new realms of possibilities in achieving fast, accurate and inexpensive species identification.},
}
@article {pmid23139639,
year = {2012},
author = {Pawlowski, J and Audic, S and Adl, S and Bass, D and Belbahri, L and Berney, C and Bowser, SS and Cepicka, I and Decelle, J and Dunthorn, M and Fiore-Donno, AM and Gile, GH and Holzmann, M and Jahn, R and Jirků, M and Keeling, PJ and Kostka, M and Kudryavtsev, A and Lara, E and Lukeš, J and Mann, DG and Mitchell, EA and Nitsche, F and Romeralo, M and Saunders, GW and Simpson, AG and Smirnov, AV and Spouge, JL and Stern, RF and Stoeck, T and Zimmermann, J and Schindel, D and de Vargas, C},
title = {CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms.},
journal = {PLoS biology},
volume = {10},
number = {11},
pages = {e1001419},
pmid = {23139639},
issn = {1545-7885},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Ecosystem ; Eukaryota/classification/*genetics ; Eukaryotic Cells/cytology ; Genetic Markers ; *Genetic Variation ; Internet ; Phylogeny ; Plants/genetics ; RNA, Ribosomal, 18S/analysis/genetics ; Ribosomes/genetics ; *Software ; Species Specificity ; },
abstract = {A group of protist experts proposes a two-step DNA barcoding approach, comprising a universal eukaryotic pre-barcode followed by group-specific barcodes, to unveil the hidden biodiversity of microbial eukaryotes.},
}
@article {pmid23136460,
year = {2012},
author = {Cannon, PF and Damm, U and Johnston, PR and Weir, BS},
title = {Colletotrichum - current status and future directions.},
journal = {Studies in mycology},
volume = {73},
number = {1},
pages = {181-213},
pmid = {23136460},
issn = {1872-9797},
abstract = {A review is provided of the current state of understanding of Colletotrichum systematics, focusing on species-level data and the major clades. The taxonomic placement of the genus is discussed, and the evolution of our approach to species concepts and anamorph-teleomorph relationships is described. The application of multilocus technologies to phylogenetic analysis of Colletotrichum is reviewed, and selection of potential genes/loci for barcoding purposes is discussed. Host specificity and its relation to speciation and taxonomy is briefly addressed. A short review is presented of the current status of classification of the species clusters that are currently without comprehensive multilocus analyses, emphasising the orbiculare and destructivum aggregates. The future for Colletotrichum biology will be reliant on consensus classification and robust identification tools. In support of these goals, a Subcommission on Colletotrichum has been formed under the auspices of the International Commission on Taxonomy of Fungi, which will administer a carefully curated barcode database for sequence-based identification of species within the BioloMICS web environment.},
}
@article {pmid23136459,
year = {2012},
author = {Weir, BS and Johnston, PR and Damm, U},
title = {The Colletotrichum gloeosporioides species complex.},
journal = {Studies in mycology},
volume = {73},
number = {1},
pages = {115-180},
pmid = {23136459},
issn = {1872-9797},
abstract = {UNLABELLED: The limit of the Colletotrichum gloeosporioides species complex is defined genetically, based on a strongly supported clade within the Colletotrichum ITS gene tree. All taxa accepted within this clade are morphologically more or less typical of the broadly defined C. gloeosporioides, as it has been applied in the literature for the past 50 years. We accept 22 species plus one subspecies within the C. gloeosporioides complex. These include C. asianum, C. cordylinicola, C. fructicola, C. gloeosporioides, C. horii, C. kahawae subsp. kahawae, C. musae, C. nupharicola, C. psidii, C. siamense, C. theobromicola, C. tropicale, and C. xanthorrhoeae, along with the taxa described here as new, C. aenigma, C. aeschynomenes, C. alatae, C. alienum, C. aotearoa, C. clidemiae, C. kahawae subsp. ciggaro, C. salsolae, and C. ti, plus the nom. nov. C. queenslandicum (for C. gloeosporioides var. minus). All of the taxa are defined genetically on the basis of multi-gene phylogenies. Brief morphological descriptions are provided for species where no modern description is available. Many of the species are unable to be reliably distinguished using ITS, the official barcoding gene for fungi. Particularly problematic are a set of species genetically close to C. musae and another set of species genetically close to C. kahawae, referred to here as the Musae clade and the Kahawae clade, respectively. Each clade contains several species that are phylogenetically well supported in multi-gene analyses, but within the clades branch lengths are short because of the small number of phylogenetically informative characters, and in a few cases individual gene trees are incongruent. Some single genes or combinations of genes, such as glyceraldehyde-3-phosphate dehydrogenase and glutamine synthetase, can be used to reliably distinguish most taxa and will need to be developed as secondary barcodes for species level identification, which is important because many of these fungi are of biosecurity significance. In addition to the accepted species, notes are provided for names where a possible close relationship with C. gloeosporioides sensu lato has been suggested in the recent literature, along with all subspecific taxa and formae speciales within C. gloeosporioides and its putative teleomorph Glomerella cingulata.<br><br>TAXONOMIC NOVELTIES: Name replacement - C. queenslandicum B. Weir &amp; P.R. Johnst. New species - C. aenigma B. Weir &amp; P.R. Johnst., C. aeschynomenes B. Weir &amp; P.R. Johnst., C. alatae B. Weir &amp; P.R. Johnst., C. alienum B. Weir &amp; P.R. Johnst, C. aotearoa B. Weir &amp; P.R. Johnst., C. clidemiae B. Weir &amp; P.R. Johnst., C. salsolae B. Weir &amp; P.R. Johnst., C. ti B. Weir &amp; P.R. Johnst. New subspecies - C. kahawae subsp. ciggaro B. Weir &amp; P.R. Johnst. Typification: Epitypification - C. queenslandicum B. Weir &amp; P.R. Johnst.},
}
@article {pmid23133656,
year = {2012},
author = {Young, MR and Behan-Pelletier, VM and Hebert, PD},
title = {Revealing the hyperdiverse mite fauna of subarctic Canada through DNA barcoding.},
journal = {PloS one},
volume = {7},
number = {11},
pages = {e48755},
pmid = {23133656},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; Biological Evolution ; Canada ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; Genetic Variation ; Geography ; Manitoba ; Models, Statistical ; Plants/metabolism ; Sequence Analysis, DNA ; Species Specificity ; Statistics as Topic ; },
abstract = {Although mites are one of the most abundant and diverse groups of arthropods, they are rarely targeted for detailed biodiversity surveys due to taxonomic constraints. We address this gap through DNA barcoding, evaluating acarine diversity at Churchill, Manitoba, a site on the tundra-taiga transition. Barcode analysis of 6279 specimens revealed nearly 900 presumptive species of mites with high species turnover between substrates and between forested and non-forested sites. Accumulation curves have not reached an asymptote for any of the three mite orders investigated, and estimates suggest that more than 1200 species of Acari occur at this locality. The coupling of DNA barcode results with taxonomic assignments revealed that Trombidiformes compose 49% of the fauna, a larger fraction than expected based on prior studies. This investigation demonstrates the efficacy of DNA barcoding in facilitating biodiversity assessments of hyperdiverse taxa.},
}
@article {pmid23129985,
year = {2012},
author = {Faynel, C and Busby, RC and Robbins, RK},
title = {Review of the species level taxonomy of the neotropical butterfly genus Oenomaus (Lycaenidae, Theclinae, Eumaeini).},
journal = {ZooKeys},
volume = {},
number = {222},
pages = {11-45},
pmid = {23129985},
issn = {1313-2970},
abstract = {Seven new species of the Neotropical hairstreak genus Oenomaus are described: Oenomaus mancha Busby &amp; Faynel, sp. n. (type locality Ecuador); Oenomaus gwenish Robbins &amp; Faynel, sp. n. (type locality Panama); Oenomaus lea Faynel &amp; Robbins, sp. n. (type locality Ecuador); Oenomaus myrteana Busby, Robbins &amp; Faynel, sp. n. (type locality Ecuador); Oenomaus mentirosa Faynel &amp; Robbins, sp. n. (type locality Peru); Oenomaus andi Busby &amp; Faynel, sp. n. (type locality Ecuador) and Oenomaus moseri Robbins &amp; Faynel, sp. n. (type locality Brazil, Santa Catarina). For each new Oenomaus species, we present diagnostic characters and notes on its habitat and biology. We illustrate adults, genitalia, and distribution. New distributional and biological data are presented for 21 previously described Oenomaus species. Oenomaus melleus guyanensis Faynel, 2008 is treated as a new synonym of Oenomaus melleus melleus (Druce, 1907). Females are described and associated with males for ten species using a variety of factors, including mitochondrial COI DNA "barcode" sequences. We summarize the reasons why the number of recognized Oenomaus species has grown in the past decade from one species to 28 species. Finally, we overview the habitats that Oenomaus species occupy and note that the agricultural pest on Annonaceae, Oenomaus ortygnus, is the only Oenomaus species that regularly occurs in greatly disturbed habitats.},
}
@article {pmid23129979,
year = {2012},
author = {Bu, Y and Gao, Y and Potapov, MB and Luan, YX},
title = {Redescription of arenicolous dipluran Parajapyx pauliani (Diplura, Parajapygidae) and DNA barcoding analyses of Parajapyx from China.},
journal = {ZooKeys},
volume = {},
number = {221},
pages = {19-29},
pmid = {23129979},
issn = {1313-2970},
abstract = {Littoral dipluran Parajapyx pauliani Pagés, 1959 was redescribed based on the specimens collected in Hainan Island, South China. The littoral habitat was confirmed for the species, as the first report of arenicolous dipluran in China. DNA barcoding fragment was sequenced for five Parajapyx species (18 individuals) from China, and this is the first report on DNA barcodes used for dipluran identification. The mean intra- and interspecific divergencesare 1.9% and 19.1% respectively. Synonymy of Parajapyx paucidentis and Parajapyx isabellae was confirmed.},
}
@article {pmid23125510,
year = {2012},
author = {Rai, PS and Bellampalli, R and Dobriyal, RM and Agarwal, A and Satyamoorthy, K and Narayana, DA},
title = {DNA barcoding of authentic and substitute samples of herb of the family Asparagaceae and Asclepiadaceae based on the ITS2 region.},
journal = {Journal of Ayurveda and integrative medicine},
volume = {3},
number = {3},
pages = {136-140},
pmid = {23125510},
issn = {0976-2809},
abstract = {BACKGROUND: Herbal drugs used to treat illness according to Ayurveda are often misidentified or adulterated with similar plant materials.<br><br>OBJECTIVE: To aid taxonomical identification, we used DNA barcoding to evaluate authentic and substitute samples of herb and phylogenetic relationship of four medicinal plants of family Asparagaceace and Asclepiadaceae.<br><br>MATERIALS AND METHODS: DNA extracted from dry root samples of two authentic and two substitutes of four specimens belonging to four species were subjected to polymerase chain reaction (PCR) and DNA sequencing. Primers for nuclear DNA (nu ITS2) and plastid DNA (matK and rpoC1) were used for PCR and sequence analysis was performed by Clustal W. The intraspecific variation and interspecific divergence were calculated using MEGA V 4.0.<br><br>STATISTICAL ANALYSIS: Kimura's two parameter model, neighbor joining and bootstrapping methods were used in this work.<br><br>RESULTS: The result indicates the efficiency of amplification for ITS2 candidate DNA barcodes was 100% for four species tested. The average interspecific divergence is 0.12 and intraspecific variation was 0.232 in the case of two Asparagaceae species. In two Asclepiadaceae species, average interspecific divergence and intraspecific variation were 0.178 and 0.004 respectively.<br><br>CONCLUSIONS: Our findings show that the ITS2 region can effectively discriminate Asparagus racemosus and Hemidesmus indicus from its substitute samples and hence can resolve species admixtures in raw samples. The ITS2 region may be used as one of the standard DNA barcodes to identify closely related species of family Asclepiadaceae but was noninformative for Asparagaceae species suggesting a need for the development of new markers for each family. More detailed studies involving more species and substitutes are warranted.},
}
@article {pmid23124743,
year = {2012},
author = {Oh, J and Kim, BK and Cho, WS and Hong, SG and Kim, KM},
title = {PyroTrimmer: a software with GUI for pre-processing 454 amplicon sequences.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {50},
number = {5},
pages = {766-769},
pmid = {23124743},
issn = {1976-3794},
mesh = {Bacteria/genetics ; DNA Primers/analysis ; Databases, Nucleic Acid ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA/*instrumentation ; *Software ; },
abstract = {The ultimate goal of metagenome research projects is to understand the ecological roles and physiological functions of the microbial communities in a given natural environment. The 454 pyrosequencing platform produces the longest reads among the most widely used next generation sequencing platforms. Since the relatively longer reads of the 454 platform provide more information for identification of microbial sequences, this platform is dedicated to microbial community and population studies. In order to accurately perform the downstream analysis of the 454 multiplex datasets, it is necessary to remove artificially designed sequences located at either ends of individual reads and to correct low-quality sequences. We have developed a program called PyroTrimmer that removes the barcodes, linkers, and primers, trims sequence regions with low quality scores, and filters out low-quality sequence reads. Although these functions have previously been implemented in other programs as well, PyroTrimmer has novelty in terms of the following features: i) more sensitive primer detection using Levenstein distance and global pairwise alignment, ii) the first stand-alone software with a graphic user interface, and iii) various options for trimming and filtering out the low-quality sequence reads. PyroTrimmer, written in JAVA, is compatible with multiple operating systems and can be downloaded free at http://pyrotrimmer.kobic.re.kr.},
}
@article {pmid23121735,
year = {2013},
author = {Osmundson, TW and Eyre, CA and Hayden, KM and Dhillon, J and Garbelotto, MM},
title = {Back to basics: an evaluation of NaOH and alternative rapid DNA extraction protocols for DNA barcoding, genotyping, and disease diagnostics from fungal and oomycete samples.},
journal = {Molecular ecology resources},
volume = {13},
number = {1},
pages = {66-74},
doi = {10.1111/1755-0998.12031},
pmid = {23121735},
issn = {1755-0998},
mesh = {Cetrimonium ; Cetrimonium Compounds ; Chloroform ; DNA/*isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Endopeptidase K/chemistry ; Fagaceae/*microbiology ; Fungi/*genetics ; Genotype ; Nucleic Acid Amplification Techniques/*methods ; Phenol ; Phytophthora/*genetics ; Plant Leaves/chemistry/microbiology ; Polynesia ; Resins, Synthetic/chemistry ; Sodium Hydroxide/*chemistry ; Specimen Handling/methods ; },
abstract = {The ubiquity, high diversity and often-cryptic manifestations of fungi and oomycetes frequently necessitate molecular tools for detecting and identifying them in the environment. In applications including DNA barcoding, pathogen detection from plant samples, and genotyping for population genetics and epidemiology, rapid and dependable DNA extraction methods scalable from one to hundreds of samples are desirable. We evaluated several rapid extraction methods (NaOH, Rapid one-step extraction (ROSE), Chelex 100, proteinase K) for their ability to obtain DNA of quantity and quality suitable for the following applications: PCR amplification of the multicopy barcoding locus ITS1/5.8S/ITS2 from various fungal cultures and sporocarps; single-copy microsatellite amplification from cultures of the phytopathogenic oomycete Phytophthora ramorum; probe-based P. ramorum detection from leaves. Several methods were effective for most of the applications, with NaOH extraction favored in terms of success rate, cost, speed and simplicity. Frozen dilutions of ROSE and NaOH extracts maintained PCR viability for over 32 months. DNA from rapid extractions performed poorly compared to CTAB/phenol-chloroform extracts for TaqMan diagnostics from tanoak leaves, suggesting that incomplete removal of PCR inhibitors is an issue for sensitive diagnostic procedures, especially from plants with recalcitrant leaf chemistry. NaOH extracts exhibited lower yield and size than CTAB/phenol-chloroform extracts; however, NaOH extraction facilitated obtaining clean sequence data from sporocarps contaminated by other fungi, perhaps due to dilution resulting from low DNA yield. We conclude that conventional extractions are often unnecessary for routine DNA sequencing or genotyping of fungi and oomycetes, and recommend simpler strategies where source materials and intended applications warrant such use.},
}
@article {pmid23115257,
year = {2013},
author = {Stensvold, CR},
title = {Comparison of sequencing (barcode region) and sequence-tagged-site PCR for Blastocystis subtyping.},
journal = {Journal of clinical microbiology},
volume = {51},
number = {1},
pages = {190-194},
pmid = {23115257},
issn = {1098-660X},
mesh = {Blastocystis/*classification/*genetics ; Blastocystis Infections/*parasitology ; DNA Barcoding, Taxonomic/methods ; DNA Primers/genetics ; DNA, Protozoan/chemistry/*genetics ; Genotype ; Humans ; Molecular Epidemiology/methods ; Parasitology/*methods ; Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; Sequence Analysis, DNA/*methods ; Sequence Tagged Sites ; },
abstract = {Blastocystis is the most common nonfungal microeukaryote of the human intestinal tract and comprises numerous subtypes (STs), nine of which have been found in humans (ST1 to ST9). While efforts continue to explore the relationship between human health status and subtypes, no consensus regarding subtyping methodology exists. It has been speculated that differences detected in subtype distribution in various cohorts may to some extent reflect different approaches. Blastocystis subtypes have been determined primarily in one of two ways: (i) sequencing of small subunit rRNA gene (SSU-rDNA) PCR products and (ii) PCR with subtype-specific sequence-tagged-site (STS) diagnostic primers. Here, STS primers were evaluated against a panel of samples (n = 58) already subtyped by SSU-rDNA sequencing (barcode region), including subtypes for which STS primers are not available, and a small panel of DNAs from four other eukaryotes often present in feces (n = 18). Although the STS primers appeared to be highly specific, their sensitivity was only moderate, and the results indicated that some infections may go undetected when this method is used. False-negative STS results were not linked exclusively to certain subtypes or alleles, and evidence of substantial genetic variation in STS loci was obtained. Since the majority of DNAs included here were extracted from feces, it is possible that STS primers may generally work better with DNAs extracted from Blastocystis cultures. In conclusion, due to its higher applicability and sensitivity, and since sequence information is useful for other forms of research, SSU-rDNA barcoding is recommended as the method of choice for Blastocystis subtyping.},
}
@article {pmid23113152,
year = {2012},
author = {Rezaei-Matehkolaei, A and Makimura, K and Shidfar, M and Zaini, F and Eshraghian, M and Jalalizand, N and Nouripour-Sisakht, S and Hosseinpour, L and Mirhendi, H},
title = {Use of Single-enzyme PCR-restriction Digestion Barcode Targeting the Internal Transcribed Spacers (ITS rDNA) to Identify Dermatophyte Species.},
journal = {Iranian journal of public health},
volume = {41},
number = {3},
pages = {82-94},
pmid = {23113152},
issn = {2251-6085},
abstract = {BACKGROUND: Dermatophytes are the most common causative agents of superficial mycoses. Species identification of these fungi is important from therapeutic and epidemiological point of wive. Traditional approaches for identification of dermatophytes at the species level, relying on macroscopic and microscopic features of the colonies, usually are time-consuming and unreliable in many circumstances. Recently a broad varieties of rapid and accurate DNA-based techniques were successfuly utilized for species delineation of dermatophytes.<br><br>METHODS: The ITS1-5.8S-ITS2 region of rDNA from various reference strains of dermatophyte species were amplified using the universal fungal primers ITS1 and ITS4.The PCR products were digested by a single restriction enzyme, MvaI. The enzyme was evaluated in both in silico and practical PCR-RFLP assay to find the exact differentiating restriction profiles for each species. To validate the standardized PCR-RFLP system, all tested strains were subjected to sequencing and sequence analysis.<br><br>RESULTS: The obtained RFLP patterns were specific for many species including T. interdigitale, T. rubrum, T. violaceum, M. persicolor, M. audouinii, M. nanum (A. obtusum) and E. floccosum but were similar for some closely related species such as M. canis / M. ferrugineum. Sequencing of the ITS1-5.8S-ITS2 fragment from all type strains affirmed the RFLP findings.<br><br>CONCLUSION: It was practically revealed that the ITS-PCR followed by MvaI-RFLP is a useful and reliable schema for identification and differentiation of several pathogenic species and can be used for rapid screening of even closely related species of dermatophytes in clinical and epidemiological settings.},
}
@article {pmid23111094,
year = {2013},
author = {Silva-Iturriza, A and Nassar, JM and García-Rawlins, AM and Rosales, R and Mijares, A},
title = {Trypanosoma evansi kDNA minicircle found in the Venezuelan nectar-feeding bat Leptonycteris curasoae (Glossophaginae), supports the hypothesis of multiple origins of that parasite in South America.},
journal = {Parasitology international},
volume = {62},
number = {2},
pages = {95-99},
doi = {10.1016/j.parint.2012.10.003},
pmid = {23111094},
issn = {1873-0329},
mesh = {Animals ; Base Sequence ; Cattle ; Cattle Diseases/parasitology ; Chiroptera/*parasitology ; DNA Barcoding, Taxonomic ; DNA, Kinetoplast/*isolation &amp; purification ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Glyceraldehyde-3-Phosphate Dehydrogenases/genetics ; Horse Diseases/parasitology ; Horses ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Protozoan Proteins/genetics ; Sequence Analysis, DNA/veterinary ; Trypanosoma/classification/genetics/*isolation &amp; purification ; Trypanosomiasis/parasitology/*veterinary ; Venezuela ; },
abstract = {Trypanosoma evansi is a mammal generalist protozoon which causes negative effects on health and productivity in bovine and equine herds in South America, Europe, Asia and Africa. By molecular methods, we screened the presence of that parasite together with other trypanosome species in 105 bats of 10 species collected in arid zones of northern Venezuela. The first molecular approach was fluorescent fragment length barcoding (FFLB), which relies on amplification of relative small regions of rRNA genes (four loci) and fluorescence detection. By FFLB, 17 samples showed patterns of possible trypanosomatid infections. These samples were used to test presence of trypanosomes by PCR using the following DNA markers: V7-V8 SSU rRNA, gGAPDH and kDNA minicircle regions. Only in one individual of the nectar-feeding bat, Leptonycteris curasoae, we were able to amplify 1000bp of the trypanosome kDNA minicircle. That PCR product was sequenced and the parasite species was determined by NCBI-BLAST and phylogenetic analysis. Both analyses showed that the minicircle sequence corresponds to Trypanosoma evansi. The phylogenetic analysis of the sequence obtained in this study clustered with a T. evansi sequence obtained in a Venezuelan capybara, Hydrochoerus hydrochaeris, and distant of others two T. evansi sequences obtained in a Colombian capybara and horse. This result supports the hypothesis of multiple origins of T. evansi in South America.},
}
@article {pmid23110936,
year = {2012},
author = {Gasser, RB and Jabbar, A and Mohandas, N and Höglund, J and Hall, RS and Littlewood, DT and Jex, AR},
title = {Assessment of the genetic relationship between Dictyocaulus species from Bos taurus and Cervus elaphus using complete mitochondrial genomic datasets.},
journal = {Parasites &amp; vectors},
volume = {5},
number = {},
pages = {241},
pmid = {23110936},
issn = {1756-3305},
support = {BB/H023534/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Computational Biology ; DNA, Helminth/chemistry/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Dictyocaulus/*classification/*genetics/isolation &amp; purification ; Dictyocaulus Infections/*parasitology ; *Genetic Variation ; Male ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Ruminants/*parasitology ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; },
abstract = {BACKGROUND: Dictyocaulus species are strongylid nematodes of major veterinary significance in ruminants, such as cattle and cervids, and cause serious bronchitis or pneumonia (dictyocaulosis or "husk"). There has been ongoing controversy surrounding the validity of some Dictyocaulus species and their host specificity. Here, we sequenced and characterized the mitochondrial (mt) genomes of Dictyocaulus viviparus (from Bos taurus) with Dictyocaulus sp. cf. eckerti from red deer (Cervus elaphus), used mt datasets to assess the genetic relationship between these and related parasites, and predicted markers for future population genetic or molecular epidemiological studies.<br><br>METHODS: The mt genomes were amplified from single adult males of D. viviparus and Dictyocaulus sp. cf. eckerti (from red deer) by long-PCR, sequenced using 454-technology and annotated using bioinformatic tools. Amino acid sequences inferred from individual genes of each of the two mt genomes were compared, concatenated and subjected to phylogenetic analysis using Bayesian inference (BI), also employing data for other strongylids for comparative purposes.<br><br>RESULTS: The circular mt genomes were 13,310 bp (D. viviparus) and 13,296 bp (Dictyocaulus sp. cf. eckerti) in size, and each contained 12 protein-encoding, 22 transfer RNA and 2 ribosomal RNA genes, consistent with other strongylid nematodes sequenced to date. Sliding window analysis identified genes with high or low levels of nucleotide diversity between the mt genomes. At the predicted mt proteomic level, there was an overall sequence difference of 34.5% between D. viviparus and Dictyocaulus sp. cf. eckerti, and amino acid sequence variation within each species was usually much lower than differences between species. Phylogenetic analysis of the concatenated amino acid sequence data for all 12 mt proteins showed that both D. viviparus and Dictyocaulus sp. cf. eckerti were closely related, and grouped to the exclusion of selected members of the superfamilies Metastrongyloidea, Trichostrongyloidea, Ancylostomatoidea and Strongyloidea.<br><br>CONCLUSIONS: Consistent with previous findings for nuclear ribosomal DNA sequence data, the present analyses indicate that Dictyocaulus sp. cf. eckerti (red deer) and D. viviparus are separate species. Barcodes in the two mt genomes and proteomes should serve as markers for future studies of the population genetics and/or epidemiology of these and related species of Dictyocaulus.},
}
@article {pmid23109909,
year = {2012},
author = {Zador, AM and Dubnau, J and Oyibo, HK and Zhan, H and Cao, G and Peikon, ID},
title = {Sequencing the connectome.},
journal = {PLoS biology},
volume = {10},
number = {10},
pages = {e1001411},
pmid = {23109909},
issn = {1545-7885},
support = {R01 NS073129/NS/NINDS NIH HHS/United States ; 5R01NS073129/NS/NINDS NIH HHS/United States ; },
mesh = {Animals ; Brain Mapping/methods ; *Connectome ; Humans ; Neural Pathways/physiology ; Neurons/physiology ; Sequence Analysis, DNA/methods ; },
abstract = {Connectivity determines the function of neural circuits. Historically, circuit mapping has usually been viewed as a problem of microscopy, but no current method can achieve high-throughput mapping of entire circuits with single neuron precision. Here we describe a novel approach to determining connectivity. We propose BOINC ("barcoding of individual neuronal connections"), a method for converting the problem of connectivity into a form that can be read out by high-throughput DNA sequencing. The appeal of using sequencing is that its scale--sequencing billions of nucleotides per day is now routine--is a natural match to the complexity of neural circuits. An inexpensive high-throughput technique for establishing circuit connectivity at single neuron resolution could transform neuroscience research.},
}
@article {pmid23109189,
year = {2012},
author = {Atas, E and Singer, A and Meller, A},
title = {DNA sequencing and bar-coding using solid-state nanopores.},
journal = {Electrophoresis},
volume = {33},
number = {23},
pages = {3437-3447},
pmid = {23109189},
issn = {1522-2683},
support = {R01 HG005871/HG/NHGRI NIH HHS/United States ; R01 HG-005871/HG/NHGRI NIH HHS/United States ; },
mesh = {Electronic Data Processing/*methods ; Genes, pol ; Genotyping Techniques/*methods ; HIV/chemistry/genetics ; Humans ; Molecular Diagnostic Techniques/*methods ; *Nanopores ; Nanotechnology/*legislation &amp; jurisprudence ; Peptide Nucleic Acids/analysis/chemistry ; Sequence Analysis, DNA/*methods ; Spectrometry, Fluorescence/methods ; },
abstract = {Nanopores have emerged as a prominent single-molecule analytic tool with particular promise for genomic applications. In this review, we discuss two potential applications of the nanopore sensors: First, we present a nanopore-based single-molecule DNA sequencing method that utilizes optical detection for massively parallel throughput. Second, we describe a method by which nanopores can be used as single-molecule genotyping tools. For DNA sequencing, the distinction among the four types of DNA nucleobases is achieved by employing a biochemical procedure for DNA expansion. In this approach, each nucleobase in each DNA strand is converted into one of four predefined unique 16-mers in a process that preserves the nucleobase sequence. The resulting converted strands are then hybridized to a library of four molecular beacons, each carrying a unique fluorophore tag, that are perfect complements to the 16-mers used for conversion. Solid-state nanopores are then used to sequentially remove these beacons, one after the other, leading to a series of photon bursts in four colors that can be optically detected. Single-molecule genotyping is achieved by tagging the DNA fragments with γ-modified synthetic peptide nucleic acid probes coupled to an electronic characterization of the complexes using solid-state nanopores. This method can be used to identify and differentiate genes with a high level of sequence similarity at the single-molecule level, but different pathology or response to treatment. We will illustrate this method by differentiating the pol gene for two highly similar human immunodeficiency virus subtypes, paving the way for a novel diagnostics platform for viral classification.},
}
@article {pmid23108662,
year = {2013},
author = {Christa, G and Wescott, L and Schäberle, TF and König, GM and Wägele, H},
title = {What remains after 2 months of starvation? Analysis of sequestered algae in a photosynthetic slug, Plakobranchus ocellatus (Sacoglossa, Opisthobranchia), by barcoding.},
journal = {Planta},
volume = {237},
number = {2},
pages = {559-572},
pmid = {23108662},
issn = {1432-2048},
mesh = {Animals ; Chlorophyta/genetics/*physiology ; Chloroplast Proteins/genetics/metabolism ; Chloroplasts/genetics/metabolism ; DNA Barcoding, Taxonomic/*methods ; Darkness ; Feeding Behavior/physiology ; Gastropoda/classification/genetics/metabolism/*physiology ; *Genes, Plant ; Genetic Markers ; Light ; Philippines ; Photosynthesis ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Ribulose-Bisphosphate Carboxylase/genetics/metabolism ; Species Specificity ; Time Factors ; },
abstract = {The sacoglossan sea slug, Plakobranchus ocellatus, is a so-called long-term retention form that incorporates chloroplasts for several months and thus is able to starve while maintaining photosynthetic activity. Little is known regarding the taxonomy and food sources of this sacoglossan, but it is suggested that P. ocellatus is a species complex and feeds on a broad variety of Ulvophyceae. In particular, we analysed specimens from the Philippines and starved them under various light conditions (high light, low light and darkness) and identified the species of algal food sources depending on starvation time and light treatment by means of DNA-barcoding using for the first time the combination of two algal chloroplast markers, rbcL and tufA. Comparison of available CO1 and 16S sequences of specimens from various localities indicate a species complex with likely four distinct clades, but food analyses do not indicate an ecological separation of the investigated clades into differing foraging strategies. The combined results from both algal markers suggest that, in general, P. ocellatus has a broad food spectrum, including members of the genera Halimeda, Caulerpa, Udotea, Acetabularia and further unidentified algae, with an emphasis on H. macroloba. Independent of the duration of starvation and light exposure, this algal species and a further unidentified Halimeda species seem to be the main food source of P. ocellatus from the Philippines. It is shown here that at least two (or possibly three) barcode markers are required to cover the entire food spectrum in future analyses of Sacoglossa.},
}
@article {pmid23107924,
year = {2012},
author = {Paz, A and Crawford, AJ},
title = {Molecular-based rapid inventories of sympatric diversity: a comparison of DNA barcode clustering methods applied to geography-based vs clade-based sampling of amphibians.},
journal = {Journal of biosciences},
volume = {37},
number = {5},
pages = {887-896},
pmid = {23107924},
issn = {0973-7138},
mesh = {Algorithms ; Amphibians/*genetics ; Animals ; Biodiversity ; *DNA Barcoding, Taxonomic ; *Genetic Speciation ; Madagascar ; *Multigene Family ; Panama ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; *Software ; Species Specificity ; Sympatry ; },
abstract = {Molecular markers offer a universal source of data for quantifying biodiversity. DNA barcoding uses a standardized genetic marker and a curated reference database to identify known species and to reveal cryptic diversity within wellsampled clades. Rapid biological inventories, e.g. rapid assessment programs (RAPs), unlike most barcoding campaigns, are focused on particular geographic localities rather than on clades. Because of the potentially sparse phylogenetic sampling, the addition of DNA barcoding to RAPs may present a greater challenge for the identification of named species or for revealing cryptic diversity. In this article we evaluate the use of DNA barcoding for quantifying lineage diversity within a single sampling site as compared to clade-based sampling, and present examples from amphibians. We compared algorithms for identifying DNA barcode clusters (e.g. species, cryptic species or Evolutionary Significant Units) using previously published DNA barcode data obtained from geography-based sampling at a site in Central Panama, and from clade-based sampling in Madagascar. We found that clustering algorithms based on genetic distance performed similarly on sympatric as well as clade-based barcode data, while a promising coalescent-based method performed poorly on sympatric data. The various clustering algorithms were also compared in terms of speed and software implementation. Although each method has its shortcomings in certain contexts, we recommend the use of the ABGD method, which not only performs fairly well under either sampling method, but does so in a few seconds and with a user-friendly Web interface.},
}
@article {pmid23106981,
year = {2012},
author = {Elzinga, JA and Chevasco, V and Mappes, J and Grapputo, A},
title = {Low parasitism rates in parthenogenetic bagworm moths do not support the parasitoid hypothesis for sex.},
journal = {Journal of evolutionary biology},
volume = {25},
number = {12},
pages = {2547-2558},
doi = {10.1111/jeb.12000},
pmid = {23106981},
issn = {1420-9101},
mesh = {Animals ; Biological Evolution ; Female ; *Host-Parasite Interactions ; Larva ; Male ; Moths/*parasitology ; *Parthenogenesis ; Sympatry ; Wasps/*physiology ; },
abstract = {The parasite hypothesis for sex is one of the many theories that have been suggested to solve the mystery of the widespread occurrence of sex despite its high short-term costs. It suggests that sexual lineages have an evolutionary advantage over parthenogens because they can frequently generate new genotypes that are temporarily less prone to coevolving parasites. In this study, we looked for further supporting evidence for the parasite hypothesis of sex in an attempt to understand the coexistence of sexual and parthenogenetic bagworm moths (Naryciinae). The bagworm moths and their parasitoids form one of the few natural host-parasite systems where sexual and parthenogenetic hosts are apparently not separated by ecological or geographical barriers. Furthermore, in support of the parasite hypothesis for sex, parthenogenetic presence is negatively correlated with parasitism rate. We specifically tested, by identifying the reproductive mode of the parasitized individuals, whether parasitoids preferentially attack the parthenogens in sites with both sexual and parthenogenetic forms, as predicted by the parasite hypothesis. We collected hosts from sites with different frequencies of parthenogenetic and sexual moths. A DNA barcoding approach was used to determine the reproductive mode of the parasitized hosts. Furthermore, we investigated whether differences in host and parasitoid phenology could provide an alternative explanation for the variation in parasitism rates between parthenogens and sexuals. Our results contradict the prediction of the parasite hypothesis because parthenogenetic bagworm moths were less parasitized than sexuals in sympatric sites. Our findings can be explained by differences in phenology between the parthenogenetic and sexual moths rather than genetic incompatibility between parthenogenetic hosts and parasitoids. The stable coexistence of sexual and parthenogenetic Naryciinae despite the many apparent costs of sex in this system remains a mystery. Our work adds to the list of studies were the assumptions of the parasite hypothesis for sex are not all met.},
}
@article {pmid23106166,
year = {2013},
author = {Ander, M and Troell, K and Chirico, J},
title = {Barcoding of biting midges in the genus Culicoides: a tool for species determination.},
journal = {Medical and veterinary entomology},
volume = {27},
number = {3},
pages = {323-331},
doi = {10.1111/j.1365-2915.2012.01050.x},
pmid = {23106166},
issn = {1365-2915},
mesh = {Animals ; Ceratopogonidae/*classification/*genetics ; DNA/analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Complementary/analysis ; Electron Transport Complex IV/genetics ; Female ; Insect Proteins/genetics ; Insect Vectors/*classification/*genetics ; Male ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sweden ; },
abstract = {Biting midges of the genus Culicoides (Diptera: Ceratopogonidae) are insect vectors of economically important veterinary diseases such as African horse sickness virus and bluetongue virus. However, the identification of Culicoides based on morphological features is difficult. The sequencing of mitochondrial cytochrome oxidase subunit I (COI), referred to as DNA barcoding, has been proposed as a tool for rapid identification to species. Hence, a study was undertaken to establish DNA barcodes for all morphologically determined Culicoides species in Swedish collections. In total, 237 specimens of Culicoides representing 37 morphologically distinct species were used. The barcoding generated 37 supported clusters, 31 of which were in agreement with the morphological determination. However, two pairs of closely related species could not be separated using the DNA barcode approach. Moreover, Culicoides obsoletus Meigen and Culicoides newsteadi Austen showed relatively deep intraspecific divergence (more than 10 times the average), which led to the creation of two cryptic species within each of C. obsoletus and C. newsteadi. The use of COI barcodes as a tool for the species identification of biting midges can differentiate 95% of species studied. Identification of some closely related species should employ a less conserved region, such as a ribosomal internal transcribed spacer.},
}
@article {pmid23105159,
year = {2012},
author = {Crous, PW and Summerell, BA and Shivas, RG and Burgess, TI and Decock, CA and Dreyer, LL and Granke, LL and Guest, DI and Hardy, GE and Hausbeck, MK and Hüberli, D and Jung, T and Koukol, O and Lennox, CL and Liew, EC and Lombard, L and McTaggart, AR and Pryke, JS and Roets, F and Saude, C and Shuttleworth, LA and Stukely, MJ and Vánky, K and Webster, BJ and Windstam, ST and Groenewald, JZ},
title = {Fungal Planet description sheets: 107-127.},
journal = {Persoonia},
volume = {28},
number = {},
pages = {138-182},
pmid = {23105159},
issn = {1878-9080},
abstract = {Novel species of microfungi described in the present study include the following from Australia: Phytophthora amnicola from still water, Gnomoniopsis smithogilvyi from Castanea sp., Pseudoplagiostoma corymbiae from Corymbia sp., Diaporthe eucalyptorum from Eucalyptus sp., Sporisorium andrewmitchellii from Enneapogon aff. lindleyanus, Myrmecridium banksiae from Banksia, and Pilidiella wangiensis from Eucalyptus sp. Several species are also described from South Africa, namely: Gondwanamyces wingfieldii from Protea caffra, Montagnula aloes from Aloe sp., Diaporthe canthii from Canthium inerne, Phyllosticta ericarum from Erica gracilis, Coleophoma proteae from Protea caffra, Toxicocladosporium strelitziae from Strelitzia reginae, and Devriesia agapanthi from Agapanthus africanus. Other species include Phytophthora asparagi from Asparagus officinalis (USA), and Diaporthe passiflorae from Passiflora edulis (South America). Furthermore, novel genera of coelomycetes include Chrysocrypta corymbiae from Corymbia sp. (Australia), Trinosporium guianense, isolated as a contaminant (French Guiana), and Xenosonderhenia syzygii, from Syzygium cordatum (South Africa). Pseudopenidiella piceae from Picea abies (Czech Republic), and Phaeocercospora colophospermi from Colophospermum mopane (South Africa) represent novel genera of hyphomycetes. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.},
}
@article {pmid23095939,
year = {2013},
author = {Aubriot, X and Lowry, PP and Cruaud, C and Couloux, A and Haevermans, T},
title = {DNA barcoding in a biodiversity hot spot: potential value for the identification of Malagasy Euphorbia L. listed in CITES Appendices I and II.},
journal = {Molecular ecology resources},
volume = {13},
number = {1},
pages = {57-65},
doi = {10.1111/1755-0998.12028},
pmid = {23095939},
issn = {1755-0998},
mesh = {Base Sequence ; *Biodiversity ; Conservation of Natural Resources/legislation &amp; jurisprudence/*methods ; DNA Barcoding, Taxonomic/*methods ; DNA, Intergenic/genetics ; Euphorbia/*genetics ; Madagascar ; Molecular Sequence Data ; Sequence Analysis, DNA ; },
abstract = {The island of Madagascar is a key hot spot for the genus Euphorbia, with at least 170 native species, almost all endemic. Threatened by habitat loss and illegal collection of wild plants, nearly all Malagasy Euphorbia are listed in CITES Appendices I and II. The absence of a reliable taxonomic revision makes it particularly difficult to identify these plants, even when fertile, and thereby compromises the application of CITES regulations. DNA barcoding, which can facilitate species-level identification irrespective of developmental stage and the presence of flowers or fruits, may be a promising tool for monitoring and controlling trade involving threatened species. In this study, we test the potential value of barcoding on 41 Euphorbia species representative of the genus in Madagascar, using the two widely adopted core barcode markers (matK and rbcL), along with two additional DNA regions, nuclear internal transcribed spacer (ITS) and the chloroplastic intergenic spacer psbA-trnH. For each marker and for selected marker combinations, inter- and intraspecific distance estimates and species discrimination rates are calculated. Results using just the 'official' barcoding markers yield overlapping inter- and intraspecific ranges and species discrimination rates below 60%. When ITS is used, whether alone or in combination with the core markers, species discrimination increases to nearly 100%, whereas the addition of psbA-trnH produces less satisfactory results. This study, the first ever to test barcoding on the large, commercially important genus Euphorbia shows that this method could be developed into a powerful identification tool and thereby contribute to more effective application of CITES regulations.},
}
@article {pmid23095787,
year = {2013},
author = {Barbosa, S and Pauperio, J and Searle, JB and Alves, PC},
title = {Genetic identification of Iberian rodent species using both mitochondrial and nuclear loci: application to noninvasive sampling.},
journal = {Molecular ecology resources},
volume = {13},
number = {1},
pages = {43-56},
doi = {10.1111/1755-0998.12024},
pmid = {23095787},
issn = {1755-0998},
mesh = {Animals ; Base Sequence ; Bone and Bones/chemistry ; Conservation of Natural Resources/*methods ; Cytochromes b/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Eye Proteins/genetics ; Feces/chemistry ; Molecular Sequence Data ; *Phylogeny ; Portugal ; Retinol-Binding Proteins/genetics ; Rodentia/*genetics ; Sequence Analysis, DNA ; Spain ; Species Specificity ; },
abstract = {Species identification through noninvasive sampling is increasingly used in animal conservation genetics, given that it obviates the need to handle free-living individuals. Noninvasive sampling is particularly valuable for elusive and small species such as rodents. Although rodents are not usually assumed to be the most obvious target for conservation, of the 21 species or near-species present in Iberia, three are considered endangered and declining, while several others are poorly studied. Here, we develop a genetic tool for identifying all rodent species in Iberia by noninvasive genetic sampling. To achieve this purpose, we selected one mitochondrial gene [cytochrome b (cyt-b)] and one nuclear gene [interphotoreceptor retinoid-binding protein (IRBP)], which we first sequenced using tissue samples. Both genes allow for the phylogenetic distinction of all species except the sibling species Microtus lusitanicus and Microtus duodecimcostatus. Overall, cyt-b showed higher resolution than IRBP, revealing a clear barcoding gap. To allow these markers to be applied to noninvasive samples, we selected a short highly diagnostic fragment from each gene, which we used to obtain sequences from faeces and bones from owl pellets. Amplification success for the cyt-b and IRBP fragment was 85% and 43% in faecal and 88% and 64% in owl-pellet DNA extractions, respectively. The method allows the unambiguous identification of the great majority of Iberian rodent species from noninvasive samples, with application in studies of distribution, spatial ecology and population dynamics, and for conservation.},
}
@article {pmid23095137,
year = {2013},
author = {Standley, CJ and Mugisha, L and Adriko, M and Arinaitwe, M and Rukundo, J and Ajarova, L and Mopya, S and Betson, M and Kabatereine, NB and Stothard, JR},
title = {Intestinal schistosomiasis in chimpanzees on Ngamba Island, Uganda: observations on liver fibrosis, schistosome genetic diversity and praziquantel treatment.},
journal = {Parasitology},
volume = {140},
number = {3},
pages = {285-295},
doi = {10.1017/S0031182012001576},
pmid = {23095137},
issn = {1469-8161},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Anthelmintics/administration &amp; dosage/therapeutic use ; Ape Diseases/diagnostic imaging/drug therapy/*parasitology ; DNA Barcoding, Taxonomic ; Feces/parasitology ; Female ; *Genetic Variation ; Humans ; Liver Cirrhosis/diagnosis/drug therapy/parasitology/*veterinary ; Male ; Pan troglodytes ; Parasite Egg Count ; Praziquantel/administration &amp; dosage/therapeutic use ; Schistosoma mansoni/*drug effects/*genetics/isolation &amp; purification ; Schistosomiasis mansoni/diagnostic imaging/drug therapy/parasitology/*veterinary ; Treatment Outcome ; Uganda ; Ultrasonography ; Urine/parasitology ; },
abstract = {Despite treatment with praziquantel (PZQ) at 40 mg/kg in food, several chimpanzees on Ngamba Island Chimpanzee Sanctuary (NICS) continue to excrete eggs of Schistosoma mansoni. To monitor disease, 8 animals were closely examined under anaesthesia in March 2011 with portable ultrasonography and by rectal snip biopsy. Schistosome genetic diversity had been previously assayed within 4 of these chimpanzees, finding extensive diversity with 27 DNA barcodes encountered, although none was common to all animals. Calcified schistosome eggs were found in the rectal snips from 5 chimpanzees and liver fibrosis was clearly documented, indicative of progressive disease in 6 animals, the latter being surprisingly advanced in a younger chimpanzee. All 8 animals were treated under anaesthesia by oral gavage with PZQ at 60 mg/kg dosing that was well tolerated. These animals were again re-examined in June 2012 using stool and urine sampling. Only 1 chimpanzee appeared to be free from infection and active egg excretion was confirmed in 6 animals. If intestinal schistosomiasis is to be controlled within this setting, a long-term disease management plan is required which should combine active case-detection with an insistent treatment regime with praziquantel for these chimpanzees, exploring perhaps the performance of even higher dosing.},
}
@article {pmid23092751,
year = {2013},
author = {Hendrixson, BE and DeRussy, BM and Hamilton, CA and Bond, JE},
title = {An exploration of species boundaries in turret-building tarantulas of the Mojave Desert (Araneae, Mygalomorphae, Theraphosidae, Aphonopelma).},
journal = {Molecular phylogenetics and evolution},
volume = {66},
number = {1},
pages = {327-340},
doi = {10.1016/j.ympev.2012.10.004},
pmid = {23092751},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; Sequence Alignment ; Southwestern United States ; Species Specificity ; Spiders/anatomy &amp; histology/*classification/genetics ; },
abstract = {Tarantulas in the North American genus Aphonopelma are poorly known due to their challenging patterns of morphological variation and questionable taxonomy; few specimens can be confidently identified using existing keys or comparisons to original descriptions. In an effort to identify new strategies for resolving what has been characterized as a "taxonomic and nomenclatural nightmare", we employed five different approaches for delimiting species in a group of closely related tarantulas from the Mojave Desert in the southwestern United States. These methods included the application of single techniques (morphology, DNA barcoding, shared genealogical exclusivity among independent loci, and generalized mixed Yule coalescent) and an integrative approach that incorporates genealogical and ecological information. Results demonstrate that the taxonomy of these spiders as presently defined underestimates actual species-level diversity and the group is in need of revision. The number of species delimited by each approach, however, was variable and we argue that it is this discordance that emphasizes the importance of incorporating multiple lines of evidence into an integrative taxonomic framework that can be used for constructing robust taxonomic hypotheses for Aphonopelma species.},
}
@article {pmid23092639,
year = {2013},
author = {Kosakyan, A and Gomaa, F and Mitchell, EA and Heger, TJ and Lara, E},
title = {Using DNA-barcoding for sorting out protist species complexes: a case study of the Nebela tincta-collaris-bohemica group (Amoebozoa; Arcellinida, Hyalospheniidae).},
journal = {European journal of protistology},
volume = {49},
number = {2},
pages = {222-237},
doi = {10.1016/j.ejop.2012.08.006},
pmid = {23092639},
issn = {1618-0429},
mesh = {Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Lobosea/*classification/cytology/*genetics ; Microscopy ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Species identification by means of morphology is often problematic in protists. Nebela tincta-collaris-bohemica (Arcellinida) is a species complex of small to medium-sized (ca.100 μm) testate amoebae common in peat bogs and forest soils. The taxonomic validity of characters used to define species within this group is debated and causes confusion in studies of biogeography, and applications in palaeoecology. We examined the relationship between morphological and genetic diversity within this species complex by combined analyses of light microscopy imaging and Cytochrome Oxidase Subunit 1(COI) sequences obtained from the same individual amoeba cells. Our goals were (1) to clarify the taxonomy and the phylogenetic relationships within this group, and (2) to evaluate if individual genotypes corresponded to specific morphotypes and the extent of phenotypic plasticity. We show here that small variations in test morphology that have been often overlooked by traditional taxonomy correspond to distinct haplotypes. We therefore revise the taxonomy of the group. We redefine Nebela tincta (Leidy) Kosakyan et Lara and N. collaris (Ehrenberg 1848) Kosakyan et Gomaa, change N. tincta var. rotunda Penard to N. rotunda (Penard 1890), describe three new species: N. guttata n. sp. Kosakyan et Lara, N. pechorensis n. sp. Kosakyan et Mitchell, and N. aliciae n. sp. Mitchell et Lara.},
}
@article {pmid23092113,
year = {2012},
author = {Agasti, SS and Liong, M and Peterson, VM and Lee, H and Weissleder, R},
title = {Photocleavable DNA barcode-antibody conjugates allow sensitive and multiplexed protein analysis in single cells.},
journal = {Journal of the American Chemical Society},
volume = {134},
number = {45},
pages = {18499-18502},
pmid = {23092113},
issn = {1520-5126},
support = {P50 CA086355/CA/NCI NIH HHS/United States ; HHSN268201000044C/HL/NHLBI NIH HHS/United States ; 2P50CA086355-12/CA/NCI NIH HHS/United States ; R01 EB010011/EB/NIBIB NIH HHS/United States ; R01EB010011/EB/NIBIB NIH HHS/United States ; },
mesh = {3T3 Cells ; Animals ; Antibodies/*chemistry ; Cell Line, Tumor ; *DNA Barcoding, Taxonomic ; Fluorescent Dyes/chemistry ; Humans ; Mice ; Photochemical Processes ; Proteins/*analysis ; },
abstract = {DNA barcoding is an attractive technology, as it allows sensitive and multiplexed target analysis. However, DNA barcoding of cellular proteins remains challenging, primarily because barcode amplification and readout techniques are often incompatible with the cellular microenvironment. Here we describe the development and validation of a photocleavable DNA barcode-antibody conjugate method for rapid, quantitative, and multiplexed detection of proteins in single live cells. Following target binding, this method allows DNA barcodes to be photoreleased in solution, enabling easy isolation, amplification, and readout. As a proof of principle, we demonstrate sensitive and multiplexed detection of protein biomarkers in a variety of cancer cells.},
}
@article {pmid23087912,
year = {2012},
author = {Toapanta, FR and Bernal, PJ and Sztein, MB},
title = {Diverse phosphorylation patterns of B cell receptor-associated signaling in naïve and memory human B cells revealed by phosphoflow, a powerful technique to study signaling at the single cell level.},
journal = {Frontiers in cellular and infection microbiology},
volume = {2},
number = {},
pages = {128},
pmid = {23087912},
issn = {2235-2988},
support = {R01 AI036525/AI/NIAID NIH HHS/United States ; U19 AI082655/AI/NIAID NIH HHS/United States ; R01-AI036525/AI/NIAID NIH HHS/United States ; },
mesh = {Adult ; B-Lymphocytes/*chemistry/*immunology ; Cells, Cultured ; Cytological Techniques/*methods ; Healthy Volunteers ; Humans ; Phosphoproteins/*analysis ; Phosphorylation ; *Protein Processing, Post-Translational ; Salmonella typhi/immunology ; *Signal Transduction ; Streptococcus pneumoniae/immunology ; },
abstract = {Following interaction with cognate antigens, B cells undergo cell activation, proliferation, and differentiation. Ligation of the B cell receptor (BCR) leads to the phosphorylation of BCR-associated signaling proteins within minutes of antigen binding, a process with profound consequences for the fate of the cells and development of effector immunity. Phosphoflow allows a rapid evaluation of various signaling pathways in complex heterogenous cell subsets. This novel technique was used in combination with multi-chromatic flow cytometry (FC) and fluorescent-cell barcoding (FCB) to study phosphorylation of BCR-associated signaling pathways in naïve and memory human B cell subsets. Proteins of the initiation (Syk), propagation (Btk, Akt), and integration (p38MAPK and Erk1/2) signaling units were studied. Switched memory (Sm) CD27+ and Sm CD27- phosphorylation patterns were similar when stimulated with anti-IgA or -IgG. In contrast, naïve and unswitched memory (Um) cells showed significant differences following IgM stimulation. Enhanced phosphorylation of Syk was observed in Um cells, suggesting a lower activation threshold. This is likely the result of higher amounts of IgM on the cell surface, higher pan-Syk levels, and enhanced susceptibility to phosphatase inhibition. All other signaling proteins evaluated also showed some degree of enhanced phosphorylation in Um cells. Furthermore, both the phospholipase C-γ2 (PLC-γ2) and phosphatidylinositol 3-kinase (PI3K) pathways were activated in Um cells, while only the PI3K pathway was activated on naïve cells. Um cells were the only ones that activated signaling pathways when stimulated with fluorescently labeled S. Typhi and S. pneumoniae. Finally, simultaneous evaluation of signaling proteins at the single cell level (multiphosphorylated cells) revealed that interaction with gram positive and negative bacteria resulted in complex and diverse signaling patterns. Phosphoflow holds great potential to accelerate vaccine development by identifying signaling profiles in good/poor responders.},
}
@article {pmid23085639,
year = {2013},
author = {Steyrer, J and Schiffinger, M and Huber, C and Valentin, A and Strunk, G},
title = {Attitude is everything? The impact of workload, safety climate, and safety tools on medical errors: a study of intensive care units.},
journal = {Health care management review},
volume = {38},
number = {4},
pages = {306-316},
doi = {10.1097/HMR.0b013e318272935a},
pmid = {23085639},
issn = {1550-5030},
mesh = {Attitude of Health Personnel ; Cross-Sectional Studies ; Female ; Humans ; Intensive Care Units/*organization &amp; administration/standards/statistics &amp; numerical data ; Male ; Medical Errors/*prevention &amp; control ; Middle Aged ; Organizational Culture ; *Patient Safety ; Prospective Studies ; Safety Management/*organization &amp; administration ; Workforce ; *Workload ; },
abstract = {BACKGROUND: Hospitals face an increasing pressure toward efficiency and cost reduction while ensuring patient safety. This warrants a closer examination of the trade-off between production and protection posited in the literature for a high-risk hospital setting (intensive care).<br><br>PURPOSES: On the basis of extant literature and concepts on both safety management and organizational/safety culture, this study investigates to which extent production pressure (i.e., increased staff workload and capacity utilization) and safety culture (consisting of safety climate among staff and safety tools implemented by management) influence the occurrence of medical errors and if/how safety climate and safety tools interact.<br><br>METHODOLOGY/APPROACH: A prospective, observational, 48-hour cross-sectional study was conducted in 57 intensive care units. The dependent variable is the incidence of errors affecting those 378 patients treated throughout the entire observation period. Capacity utilization and workload were measured by indicators such as unit occupancy, nurse-to-patient/physician-to-patient ratios, levels of care, or NEMS scores. The safety tools considered include Critical Incidence Reporting Systems, audits, training, mission statements, SOPs/checklists, and the use of barcodes. Safety climate was assessed using a psychometrically validated four-dimensional questionnaire.Linear regression was employed to identify the effects of the predictor variables on error rate as well as interaction effects between safety tools and safety climate.<br><br>FINDINGS: Higher workload has a detrimental effect on safety, whereas safety climate-unlike the examined safety tools-has a virtually equal opposite effect. Correlations between safety tools and safety climate as well as their interaction effects on error rate are mostly nonsignificant.<br><br>PRACTICE IMPLICATIONS: Increased workload and capacity utilization increase the occurrence of medical error, an effect that can be offset by a positive safety climate but not by formally implemented safety procedures and policies.},
}
@article {pmid23085327,
year = {2013},
author = {Levitz, S and Standley, CJ and Adriko, M and Kabatereine, NB and Stothard, JR},
title = {Environmental epidemiology of intestinal schistosomiasis and genetic diversity of Schistosoma mansoni infections in snails at Bugoigo village, Lake Albert.},
journal = {Acta tropica},
volume = {128},
number = {2},
pages = {284-291},
doi = {10.1016/j.actatropica.2012.10.003},
pmid = {23085327},
issn = {1873-6254},
mesh = {Animals ; Biomphalaria/*parasitology ; DNA Barcoding, Taxonomic ; *Genetic Variation ; Genotype ; Humans ; Molecular Epidemiology ; Schistosoma mansoni/*classification/genetics/*isolation &amp; purification ; Schistosomiasis mansoni/*epidemiology ; Uganda/epidemiology ; },
abstract = {Intestinal schistosomiasis continues to be hyper-endemic in the fishing community of Bugoigo located on the eastern shore of Lake Albert, Uganda. Our study aimed to identify the factors that determine the local distribution and abundance of Biomphalaria, as well as infection(s) with Schistosoma mansoni inclusive of their genetic diversity. In addition, a DNA barcoding approach was taken to genotype schistosome cercariae, exploring the micro-epidemiology of infections. Over a 3-week period in June-July 2010, several hundred Biomphalaria spp. were collected, together with environmental information, from 10 selected sites, representative of both putative wave-exposed (n=5) and wave-sheltered shorelines (n=5). A Mann-Whitney U-test and a generalized linear model were used to assess associations with snail abundance and parasite infections across the shoreline. Levels of local wave action were recorded over the 19-day period using digital accelerometers. The general absence of wave action on the sheltered shoreline likely helped to raise and focalize other environmental parameters, such as water conductivity by lack of mixing, that foster transmission of intestinal schistosomiasis. Over the study period, a total of 10 infected snails were encountered and a selection of schistosome cercariae from each infected snail was harvested for analysis by DNA barcoding. In total, 91 DNA barcodes were generated with 15 unique barcode types identified. Of these, 4 barcodes had been found previously in Lake Albert and (or) Victoria, the remaining 11 were newly encountered here and described. The distribution of DNA barcodes across infected snails and sampled locations revealed a complicated spatial sub-structuring. By shedding new light on the fine-scale patterning of infections, DNA barcoding has revealed a rather heterogeneous landscape of cercariae, likely inclusive of multi-miracidial infections within the snail, which will in turn interplay with human water contact activities to shape the genetic diversity of worm populations within infected people.},
}
@article {pmid23071774,
year = {2012},
author = {Zou, S and Li, Q and Kong, L},
title = {Monophyly, distance and character-based multigene barcoding reveal extraordinary cryptic diversity in Nassarius: a complex and dangerous community.},
journal = {PloS one},
volume = {7},
number = {10},
pages = {e47276},
pmid = {23071774},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry ; DNA, Ribosomal/chemistry ; Electron Transport Complex IV/chemistry ; Food Safety ; Phylogeny ; RNA, Ribosomal, 16S/chemistry ; Sequence Analysis, DNA ; Snails/anatomy &amp; histology/classification/*genetics ; Species Specificity ; },
abstract = {BACKGROUND: Correct identification and cryptic biodiversity revelation for marine organisms are pressing since the marine life is important in maintaining the balance of ecological system and is facing the problem of biodiversity crisis or food safety. DNA barcoding has been proved successful to provide resolution beyond the boundaries of morphological information. Nassarius, the common mudsnail, plays an important role in marine environment and has problem in food safety, but the classification of it is quite confused because of the complex morphological diversity.<br><br>Here we report a comprehensive barcoding analysis of 22 Nassarius species. We integrated the mitochondrial and nuclear sequences and the morphological characters to determine 13 Nassarius species studied and reveal four cryptic species and one pair synonyms. Distance, monophyly, and character-based barcoding methods were employed.<br><br>CONCLUSIONS/SIGNIFICANCE: Such successful identification and unexpected cryptic discovery is significant for Nassarius in food safety and species conversation and remind us to pay more attention to the hidden cryptic biodiversity ignored in marine life. Distance, monophyly, and character-based barcoding methods are all very helpful in identification but the character-based method shows some advantages.},
}
@article {pmid23071761,
year = {2012},
author = {Mutanen, M and Hausmann, A and Hebert, PD and Landry, JF and de Waard, JR and Huemer, P},
title = {Allopatry as a gordian knot for taxonomists: patterns of DNA barcode divergence in arctic-alpine lepidoptera.},
journal = {PloS one},
volume = {7},
number = {10},
pages = {e47214},
pmid = {23071761},
issn = {1932-6203},
mesh = {Animals ; Arctic Regions ; *DNA Barcoding, Taxonomic ; Genetic Variation ; Geography ; Lepidoptera/classification/*genetics ; North America ; Phylogeny ; Species Specificity ; },
abstract = {Many cold adapted species occur in both montane settings and in the subarctic. Their disjunct distributions create taxonomic complexity because there is no standardized method to establish whether their allopatric populations represent single or different species. This study employs DNA barcoding to gain new perspectives on the levels and patterns of sequence divergence among populations of 122 arctic-alpine species of Lepidoptera from the Alps, Fennoscandia and North America. It reveals intraspecific variability in the barcode region ranging from 0.00-10.08%. Eleven supposedly different species pairs or groups show close genetic similarity, suggesting possible synonymy in many cases. However, a total of 33 species show evidence of cryptic diversity as evidenced by the presence of lineages with over 2% maximum barcode divergence in Europe, in North America or between the two continents. Our study also reveals cases where taxonomic names have been used inconsistently between regions and exposes misidentifications. Overall, DNA barcodes have great potential to both increase taxonomic resolution and to make decisions concerning the taxonomic status of allopatric populations more objective.},
}
@article {pmid23071708,
year = {2012},
author = {Wang, G and Li, C and Guo, X and Xing, D and Dong, Y and Wang, Z and Zhang, Y and Liu, M and Zheng, Z and Zhang, H and Zhu, X and Wu, Z and Zhao, T},
title = {Identifying the main mosquito species in China based on DNA barcoding.},
journal = {PloS one},
volume = {7},
number = {10},
pages = {e47051},
pmid = {23071708},
issn = {1932-6203},
mesh = {Animals ; China ; Culicidae/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Phylogeny ; },
abstract = {Mosquitoes are insects of the Diptera, Nematocera, and Culicidae families, some species of which are important disease vectors. Identifying mosquito species based on morphological characteristics is difficult, particularly the identification of specimens collected in the field as part of disease surveillance programs. Because of this difficulty, we constructed DNA barcodes of the cytochrome c oxidase subunit 1, the COI gene, for the more common mosquito species in China, including the major disease vectors. A total of 404 mosquito specimens were collected and assigned to 15 genera and 122 species and subspecies on the basis of morphological characteristics. Individuals of the same species grouped closely together in a Neighborhood-Joining tree based on COI sequence similarity, regardless of collection site. COI gene sequence divergence was approximately 30 times higher for species in the same genus than for members of the same species. Divergence in over 98% of congeneric species ranged from 2.3% to 21.8%, whereas divergence in conspecific individuals ranged from 0% to 1.67%. Cryptic species may be common and a few pseudogenes were detected.},
}
@article {pmid23071400,
year = {2012},
author = {Christensen, H and Nielsen, JS and Sørensen, KM and Melbye, M and Brandslund, I},
title = {New national Biobank of The Danish Center for Strategic Research on Type 2 Diabetes (DD2).},
journal = {Clinical epidemiology},
volume = {4},
number = {},
pages = {37-42},
pmid = {23071400},
issn = {1179-1349},
abstract = {Long-term storage of biological samples from patients has become increasingly important in studies of disease control and treatment. The first nationwide Danish diabetes project, ie, The Danish Center for Strategic Research in Type II Diabetes (DD2), aims to improve treatment and the long-term outcome of patients with newly diagnosed type 2 diabetes (T2D). The DD2 project includes establishment of a biobank with samples from 50,000 patients with newly diagnosed T2D. This paper describes how blood and urine samples from 10,000 patients per year are collected, handled, and stored. The biobank includes whole blood, DNA, and plasma and urine samples, all frozen at -80°C. Sampling tubes have been standardized and are sent to hospital outpatient clinics and general practitioners where samples are taken, handled, aliquoted, and returned by mail overnight in standardized cryostorage tubes. When received at the biobank, samples are frozen without further treatment. From each patient, 24 cryostorage tubes are stored. Each tube is labeled with a barcode that links the data to other information available in a clinical databank registry. When patients are enrolled in DD2, a questionnaire is filled out and a quality monitoring system ensures that patients, samples, and questionnaires can be linked together at all times. The biobank is located at Vejle Hospital and the Danish National Biobank at Statens Serum Institut. As of the end of March 2012, samples from 1186 patients have been stored, and currently samples from 8-10 patients arrive per day. We have established the first national biobank in Denmark where blood, DNA, and plasma and urine samples from patients with newly diagnosed T2D are systematically collected and stored. This biobank enables sophisticated analysis of genetic variation and response to treatment, as well as disease marker studies that better classify disease status, progression, and complications.},
}
@article {pmid23068182,
year = {2012},
author = {Rebijith, KB and Asokan, R and Kumar, NK and Srikumar, KK and Ramamurthy, VV and Bhat, PS},
title = {DNA barcoding and development of species-specific markers for the identification of tea mosquito bugs (Miridae: Heteroptera) in India.},
journal = {Environmental entomology},
volume = {41},
number = {5},
pages = {1239-1245},
doi = {10.1603/EN12096},
pmid = {23068182},
issn = {1938-2936},
mesh = {Animals ; Base Sequence ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Genetic Variation ; Heteroptera/*classification/genetics/growth &amp; development ; India ; Molecular Sequence Data ; Nymph/classification ; Ovum/classification ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Rapid, accurate, and timely identification of insects as a group is important and challenging worldwide, as they outnumber all other animals in number and diversity. DNA barcoding is a method for the identification of species in a wide range of animal taxa, which uses the 5' region of the mitochondrial cytochrome c oxidase-I (CO-I). Yet another easy, accurate, and economical method of species discrimination is by developing species-specific markers, which produce specific amplicon for the species in question. The method is handy because it is not limited by life stages, sex, polymorphism, and other factors. Herein, we measured the usefulness of CO-I for the species discrimination of mirids in India viz. Helopeltis antonii Signoret, H. thievora Waterhouse, H. bradyi Waterhouse, and Pachypeltis maesarum Kirkaldy in their various life stages. Furthermore, our study showed the utility of species-specific markers in differentiating H. antonii (295) and H. bradyi (514) regardless of their life stages. Analysis of CO-I gene revealed <1% intraspecific divergence for all four species examined, whereas the interspecific distances ranged from 7 to 13%. This study showed that the DNA barcode and species-specific markers will aid the identification of mirids in India and will stand as a decisive tool in formulating integrated pest management (IPM) strategy, quick identification of invasive and cryptic species, haplotypes, biotypes, and other factors, if any.},
}
@article {pmid23056258,
year = {2012},
author = {Chen, R and Jiang, LY and Qiao, GX},
title = {The effectiveness of three regions in mitochondrial genome for aphid DNA barcoding: a case in Lachininae.},
journal = {PloS one},
volume = {7},
number = {10},
pages = {e46190},
pmid = {23056258},
issn = {1932-6203},
mesh = {Animals ; Aphids/anatomy &amp; histology/classification/*genetics ; Cytochromes b/classification/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/chemistry/*genetics ; Electron Transport Complex IV/classification/genetics ; Genetic Variation ; Genome, Mitochondrial/*genetics ; Insect Proteins/classification/genetics ; Phylogeny ; Protein Subunits/classification/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND: The mitochondrial gene COI has been widely used by taxonomists as a standard DNA barcode sequence for the identification of many animal species. However, the COI region is of limited use for identifying certain species and is not efficiently amplified by PCR in all animal taxa. To evaluate the utility of COI as a DNA barcode and to identify other barcode genes, we chose the aphid subfamily Lachninae (Hemiptera: Aphididae) as the focus of our study. We compared the results obtained using COI with two other mitochondrial genes, COII and Cytb. In addition, we propose a new method to improve the efficiency of species identification using DNA barcoding.<br><br>Three mitochondrial genes (COI, COII and Cytb) were sequenced and were used in the identification of over 80 species of Lachninae. The COI and COII genes demonstrated a greater PCR amplification efficiency than Cytb. Species identification using COII sequences had a higher frequency of success (96.9% in "best match" and 90.8% in "best close match") and yielded lower intra- and higher interspecific genetic divergence values than the other two markers. The use of "tag barcodes" is a new approach that involves attaching a species-specific tag to the standard DNA barcode. With this method, the "barcoding overlap" can be nearly eliminated. As a result, we were able to increase the identification success rate from 83.9% to 95.2% by using COI and the "best close match" technique.<br><br>CONCLUSIONS/SIGNIFICANCE: A COII-based identification system should be more effective in identifying lachnine species than COI or Cytb. However, the Cytb gene is an effective marker for the study of aphid population genetics due to its high sequence diversity. Furthermore, the use of "tag barcodes" can improve the accuracy of DNA barcoding identification by reducing or removing the overlap between intra- and inter-specific genetic divergence values.},
}
@article {pmid23053544,
year = {2013},
author = {Bog, M and Schneider, P and Hellwig, F and Sachse, S and Kochieva, EZ and Martyrosian, E and Landolt, E and Appenroth, KJ},
title = {Genetic characterization and barcoding of taxa in the genus Wolffia Horkel ex Schleid. (Lemnaceae) as revealed by two plastidic markers and amplified fragment length polymorphism (AFLP).},
journal = {Planta},
volume = {237},
number = {1},
pages = {1-13},
pmid = {23053544},
issn = {1432-2048},
mesh = {Amplified Fragment Length Polymorphism Analysis/*methods ; Araceae/classification/*genetics ; Cluster Analysis ; DNA Barcoding, Taxonomic ; DNA, Plant/chemistry/genetics ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/classification/*genetics ; Plastids/*genetics ; Ribosomal Proteins/classification/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The genus Wolffia of the duckweed family (Lemnaceae) contains the smallest flowering plants. Presently, 11 species are recognized and categorized mainly on the basis of morphology. Because of extreme reduction of structure of all species, molecular methods are especially required for barcoding and identification of species and clones of this genus. We applied AFLP combined with Bayesian analysis of population structure to 66 clones covering all 11 species. Nine clusters were identified: (1) W. angusta and W. microscopica (only one clone), (2) W. arrhiza, (3) W. cylindracea (except one clone that might be a transition form), (4) W. australiana, (5) W. globosa, (6) W. globosa, W. neglecta, and W. borealis, (7) W. brasiliensis, and W. columbiana, (8) W. columbiana, (9) W. elongata. Furthermore, we investigated the sequences of plastidic regions rps16 (54 clones) and rpl16 (55 clones), and identified the following species: W. angusta, W. australiana, W. brasiliensis, W. cylindracea, W. elongata, W. microscopica, and W. neglecta. Wolffia globosa has been separated into two groups by both methods. One group which consists only of clones from North America and East Asia was labelled here "typical W. globosa". The other group of W. globosa, termed operationally "W. neglecta", contains also clones of W. neglecta and shows high similarity to W. borealis. None of the methods recognized W. borealis as a distinct species. Although each clone could be characterized individually by AFLP and plastidic sequences, and most species could be bar-coded, the presently available data are not sufficient to identify all taxa of Wolffia.},
}
@article {pmid23050303,
year = {2012},
author = {Galbraith, W and Shadid, J},
title = {Compounding &amp; dispensing errors before and after implementing barcode technology in a nuclear pharmacy.},
journal = {International journal of pharmaceutical compounding},
volume = {16},
number = {3},
pages = {253-256},
pmid = {23050303},
issn = {1092-4221},
mesh = {*Drug Compounding ; *Electronic Data Processing ; Medication Errors/*prevention &amp; control ; Nuclear Medicine ; Pharmacy ; Retrospective Studies ; },
abstract = {The objective of this study was to determine whether the incidence of compounding and dispensing errors changed significantly in a nuclear pharmacy after the pharmacy adopted a barcode assistance system. Nuclear pharmacy dispensing errors are extremely low compared to that of busy traditional pharmacies, but there is no data available describing the use of bar-coding assistance on the rate of dispensing errors in nuclear pharmacy. A retrospective review of dispensing errors pre-barcode assistance system implementation (2001 through 2004) and post-barcode assistance system implementation (February 2005 through 2009) was conducted using data from a nuclear pharmacy that dispenses approximately 500 prescriptions per day to nuclear medicine clinics and hospitals. Data was obtained from pharmacy error logs filed by the pharmacy as reported by an end user receiving the compounded preparation or the pharmacist having recognized the error before it reached the end user. Dispensing errors were defined as any deviation in the dispensed preparation from the prescribed order. Categories identified as incorrect were: dosage, drug, volume, procedure, patient, and delivery destination. Implementation of the barcode assistance system included installation of computers, software, barcoding devices, and training of personnel. The barcode assistance system provided barcodes for each compounding component, final preparation, syringe label, prescription, and shipping material. The barcode assistant system communicated directly with the dose calibrator, enabling the dose calibrator settings to automatically change according to time of administration and isotope required. The average error rate pre- and post-barcode assistance system was 0.012% and 0.002%, respectively (P<0.0001). Pre-barcode assistance system, two major categories represented 88% of all dispensing errors: wrong dosage (60%) and wrong drug (28%). Post-barcode assistance system, the major category was delivery destination (90%). The results suggest that the barcode assistance system has been instrumental in significantly decreasing compounding errors. The implementation of barcoding during compounding and dispensing has allowed improvement of the processes so much so that it enabled the identification of other sources of routine error.},
}
@article {pmid23049931,
year = {2012},
author = {Porco, D and Potapov, M and Bedos, A and Busmachiu, G and Weiner, WM and Hamra-Kroua, S and Deharveng, L},
title = {Cryptic diversity in the ubiquist species Parisotoma notabilis (Collembola, Isotomidae): a long-used chimeric species?.},
journal = {PloS one},
volume = {7},
number = {9},
pages = {e46056},
pmid = {23049931},
issn = {1932-6203},
mesh = {Animals ; Arthropods/*classification/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Parisotoma notabilis is the most common species of Collembola in Europe and is currently designated as ubiquist. This species has been extensively used in numerous studies and is considered as well characterized on a morphological ground. Despite the homogeneity of its morphology, the sequencing of the barcoding fragment (5' end of COI) for several populations throughout Europe and North America revealed four distinct genetic lineages. The divergence found between these lineages was similar to the genetic distance among other species of the genus Parisotoma included in the analysis. All four lineages have been confirmed by the nuclear gene 28S. This congruence between mitochondrial and nuclear signals, as well as the geographical distribution pattern of lineages observed in Europe, supports the potential specific status of these lineages. Based on specimens from the type locality (Hamburg), the species name was successfully assigned to one of these lineages. This finding raises several problems as Parisotoma notabilis has been widely used in many ecological studies. Accumulation of new data for the different lineages detected, especially ecological information and life history traits, is needed to help resolve this situation.},
}
@article {pmid23043935,
year = {2012},
author = {Nelson, LA and Lambkin, CL and Batterham, P and Wallman, JF and Dowton, M and Whiting, MF and Yeates, DK and Cameron, SL},
title = {Beyond barcoding: a mitochondrial genomics approach to molecular phylogenetics and diagnostics of blowflies (Diptera: Calliphoridae).},
journal = {Gene},
volume = {511},
number = {2},
pages = {131-142},
doi = {10.1016/j.gene.2012.09.103},
pmid = {23043935},
issn = {1879-0038},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Diptera/*genetics ; Polymerase Chain Reaction ; },
abstract = {Members of the Calliphoridae (blowflies) are significant for medical and veterinary management, due to the ability of some species to consume living flesh as larvae, and for forensic investigations due to the ability of others to develop in corpses. Due to the difficulty of accurately identifying larval blowflies to species there is a need for DNA-based diagnostics for this family, however the widely used DNA-barcoding marker, cox1, has been shown to fail for several groups within this family. Additionally, many phylogenetic relationships within the Calliphoridae are still unresolved, particularly deeper level relationships. Sequencing whole mt genomes has been demonstrated both as an effective method for identifying the most informative diagnostic markers and for resolving phylogenetic relationships. Twenty-seven complete, or nearly so, mt genomes were sequenced representing 13 species, seven genera and four calliphorid subfamilies and a member of the related family Tachinidae. PCR and sequencing primers developed for sequencing one calliphorid species could be reused to sequence related species within the same superfamily with success rates ranging from 61% to 100%, demonstrating the speed and efficiency with which an mt genome dataset can be assembled. Comparison of molecular divergences for each of the 13 protein-coding genes and 2 ribosomal RNA genes, at a range of taxonomic scales identified novel targets for developing as diagnostic markers which were 117-200% more variable than the markers which have been used previously in calliphorids. Phylogenetic analysis of whole mt genome sequences resulted in much stronger support for family and subfamily-level relationships. The Calliphoridae are polyphyletic, with the Polleninae more closely related to the Tachinidae, and the Sarcophagidae are the sister group of the remaining calliphorids. Within the Calliphoridae, there was strong support for the monophyly of the Chrysomyinae and Luciliinae and for the sister-grouping of Luciliinae with Calliphorinae. Relationships within Chrysomya were not well resolved. Whole mt genome data, supported the previously demonstrated paraphyly of Lucilia cuprina with respect to L. sericata and allowed us to conclude that it is due to hybrid introgression prior to the last common ancestor of modern sericata populations, rather than due to recent hybridisation, nuclear pseudogenes or incomplete lineage sorting.},
}
@article {pmid23041355,
year = {2012},
author = {Lefoulon, E and Gavotte, L and Junker, K and Barbuto, M and Uni, S and Landmann, F and Laaksonen, S and Saari, S and Nikander, S and de Souza Lima, S and Casiraghi, M and Bain, O and Martin, C},
title = {A new type F Wolbachia from Splendidofilariinae (Onchocercidae) supports the recent emergence of this supergroup.},
journal = {International journal for parasitology},
volume = {42},
number = {11},
pages = {1025-1036},
doi = {10.1016/j.ijpara.2012.09.004},
pmid = {23041355},
issn = {1879-0135},
mesh = {Animals ; DNA, Bacterial/genetics ; Gene Expression Regulation, Bacterial ; Genetic Variation ; Molecular Sequence Data ; Nematoda/*microbiology ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal/genetics/metabolism ; Wolbachia/*classification/*genetics ; },
abstract = {Wolbachia are vertically transmitted endosymbiotic bacteria of arthropods and onchocercid nematodes. It is commonly accepted that they co-evolved with their filarial hosts, and have secondarily been lost in some species. However, most of the data on the Wolbachia/Onchocercidae relationship have been derived from studies on two subfamilies, the Dirofilariinae and the Onchocercinae, which harbour parasites of humans and domestic animals. Within the last few years, analyses of more diverse material have suggested that some groups of Onchocercidae do not have Wolbachia, such as recently studied Splendidofilariinae from birds. This study takes advantage of the analysis of additional Splendidofilariinae, Rumenfilaria andersoni from a Finnish reindeer and Madathamugadia hiepei from a South African gecko, using PCR, immunohistochemical staining and whole-mount fluorescent analysis to detect Wolbachia and describe its strains. A DNA barcoding approach and phylogenetic analyses were used to investigate the symbiosis between Wolbachia and the Onchocercidae. A new supergroup F Wolbachia was demonstrated in M. hiepei, representing the first filarial nematode harbouring Wolbachia described in a non-mammalian host. In the adult, Wolbachia infects the female germline but not the hypodermis, and intestinal cells are also infected. The phylogenetic analyses confirmed a recent emergence of supergroup F. They also suggested several events of horizontal transmission between nematodes and arthropods in this supergroup, and the existence of different metabolic interactions between the filarial nematodes and their symbionts.},
}
@article {pmid23039943,
year = {2013},
author = {Ghahramanzadeh, R and Esselink, G and Kodde, LP and Duistermaat, H and van Valkenburg, JL and Marashi, SH and Smulders, MJ and van de Wiel, CC},
title = {Efficient distinction of invasive aquatic plant species from non-invasive related species using DNA barcoding.},
journal = {Molecular ecology resources},
volume = {13},
number = {1},
pages = {21-31},
doi = {10.1111/1755-0998.12020},
pmid = {23039943},
issn = {1755-0998},
mesh = {Aquatic Organisms/*genetics ; Base Sequence ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Chloroplast/genetics ; DNA, Intergenic/genetics ; *Introduced Species ; Magnoliopsida/*genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Biological invasions are regarded as threats to global biodiversity. Among invasive aliens, a number of plant species belonging to the genera Myriophyllum, Ludwigia and Cabomba, and to the Hydrocharitaceae family pose a particular ecological threat to water bodies. Therefore, one would try to prevent them from entering a country. However, many related species are commercially traded, and distinguishing invasive from non-invasive species based on morphology alone is often difficult for plants in a vegetative stage. In this regard, DNA barcoding could become a good alternative. In this study, 242 samples belonging to 26 species from 10 genera of aquatic plants were assessed using the chloroplast loci trnH-psbA, matK and rbcL. Despite testing a large number of primer sets and several PCR protocols, the matK locus could not be amplified or sequenced reliably and therefore was left out of the analysis. Using the other two loci, eight invasive species could be distinguished from their respective related species, a ninth one failed to produce sequences of sufficient quality. Based on the criteria of universal application, high sequence divergence and level of species discrimination, the trnH-psbA noncoding spacer was the best performing barcode in the aquatic plant species studied. Thus, DNA barcoding may be helpful with enforcing a ban on trade of such invasive species, such as is already in place in the Netherlands. This will become even more so once DNA barcoding would be turned into machinery routinely operable by a nonspecialist in botany and molecular genetics.},
}
@article {pmid23038992,
year = {2013},
author = {Rakauskas, R and Bašilova, J},
title = {Barcoding of aphids (Hemiptera, Aphididae and Adelgidae): proper usage of the global data set.},
journal = {Molecular ecology resources},
volume = {13},
number = {1},
pages = {6-9},
doi = {10.1111/1755-0998.12026},
pmid = {23038992},
issn = {1755-0998},
mesh = {Animals ; Aphids/*classification/*genetics ; *Phylogeny ; },
abstract = {Basics of DNA barcoding suppose the creation and operation of an extensive library based on reliably (including possibility for validation) identified specimens. Therefore, information concerning morphological identification of the individual samples used for DNA barcoding, for example, identification keys and descriptions used, must be clearly explained. In addition, the maximum available data set of sequences must be used. Access to currently private data appears to be of special interest, especially when such possibility is provided by the database regulations, because it encourages the cooperation of research and saves both time and resources. The cryptic aphid species complexes Aphis oenotherae-holoenotherae and A. pomi-spiraecola are used to illustrate the above statements.},
}
@article {pmid23030345,
year = {2012},
author = {Robe, LJ and Machado, S and Bartholomei-Santos, ML},
title = {The DNA barcoding and the caveats with respect to its application to some species of Palaemonidae (Crustacea, Decapoda).},
journal = {Zoological science},
volume = {29},
number = {10},
pages = {714-724},
doi = {10.2108/zsj.29.714},
pmid = {23030345},
issn = {0289-0003},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Palaemonidae/*genetics ; Phylogeny ; Species Specificity ; },
abstract = {DNA-barcoding has recently attracted considerable attention due to its potential utility in aiding in species identification and discovery through the use of a short standardized sequence of mitochondrial DNA. Nevertheless, despite the fact that this technology has been proven a useful tool in several animal taxa, it also demonstrated limitations that may hinder correct application. Thus, its validity needs to be empirically evaluated in each taxonomic category before forward implementation. As the use of DNA barcoding within Palaemonidae may be of special interest, given its great interspecific morphological conservatism associated with considerable intraspecific morphological variation, we analyze here the potential of this technology in distinguishing and recovering some taxonomic boundaries within this family. We asked whether two GenBank-retrieved sets of COI sequences encompassing the conventional Barcode and Jerry-Pat regions possess the desired properties of reciprocal monophyly among species, and existence of a barcoding gap between intra- and interspecific variations, after performing a careful analysis of numt (nuclear mitochondrial DNA) contamination. These analyses revealed nine non-monophyletic species, with some cases of divergent intraspecific sequences, contrasted with interspecific similarity attained in others. Moreover, we were unable to identify any barcoding gap between intraspecific and interspecific divergences within Palaemonidae, although a threshold of 0.18 substitutions per site would differentiate intraspecific and congeneric divergences in 95% of the cases for the barcoding region. A fraction of the overlap could be certainly attributed to artifacts related to poor taxonomy, but even from this perspective DNA barcoding studies may help to uncover previously disregarded taxonomic and evolutionary issues.},
}
@article {pmid23029169,
year = {2012},
author = {Luddington, IA and Kaczmarska, I and Lovejoy, C},
title = {Distance and character-based evaluation of the V4 region of the 18S rRNA gene for the identification of diatoms (Bacillariophyceae).},
journal = {PloS one},
volume = {7},
number = {9},
pages = {e45664},
pmid = {23029169},
issn = {1932-6203},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic ; DNA Primers ; Diatoms/classification/*genetics/ultrastructure ; Likelihood Functions ; Microscopy, Electron, Scanning ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/*genetics ; Sequence Homology, Nucleic Acid ; },
abstract = {DNA barcoding is a molecular tool that exploits a unique DNA sequence of a standardized gene or non-coding region for the species identification of unknown individuals. The investigation into a suitable barcode for diatoms is ongoing and there are several promising candidates including mitochondrial, plastidial and nuclear markers. We analyzed 272 sequences from 76 diatoms species in the orders Thalassiosirales, Lithodesmiales and Cymatosirales, using distance and character based approaches, to assess the applicability of a DNA barcode based on the hypervariable V4 region of the nuclear 18S rRNA gene. We show that the proposed V4 barcode separated ca. 97% of all centric diatom taxa tested using a threshold p-distance of 0.02 and that many problem pairs were further separated using a character based approach. The reliability of amplification, extensive reference library and variability seen in the V4 region make it the most promising candidate to date for a barcode marker for diatoms particularly when combined with DNA character analysis.},
}
@article {pmid23029093,
year = {2012},
author = {Baco, AR and Cairns, SD},
title = {Comparing molecular variation to morphological species designations in the deep-sea coral Narella reveals new insights into seamount coral ranges.},
journal = {PloS one},
volume = {7},
number = {9},
pages = {e45555},
pmid = {23029093},
issn = {1932-6203},
mesh = {Animals ; Anthozoa/anatomy &amp; histology/classification/*genetics ; DNA, Mitochondrial ; Evolution, Molecular ; *Genetic Variation ; Haplotypes ; Hawaii ; NADH Dehydrogenase/genetics ; Natural Cytotoxicity Triggering Receptor 1/genetics ; *Oceans and Seas ; Phylogeny ; Phylogeography ; },
abstract = {Recent studies have countered the paradigm of seamount isolation, confounding conservation efforts at a critical time. Efforts to study deep-sea corals, one of the dominant taxa on seamounts, to understand seamount connectivity, are hampered by a lack of taxonomic keys. A prerequisite for connectivity is species overlap. Attempts to better understand species overlap using DNA barcoding methods suggest coral species are widely distributed on seamounts and nearby features. However, no baseline has been established for variation in these genetic markers relative to morphological species designations for deep-sea octocoral families. Here we assess levels of genetic variation in potential octocoral mitochondrial barcode markers relative to thoroughly examined morphological species in the genus Narella. The combination of six markers used here, approximately 3350 bp of the mitochondrial genome, resolved 83% of the morphological species. Our results show that two of the markers, ND2 and NCR1, are not sufficient to resolve genera within Primnoidae, let alone species. Re-evaluation of previous studies of seamount octocorals based on these results suggest that those studies were looking at distributions at a level higher than species, possibly even genus or subfamily. Results for Narella show that using more markers provides haplotypes with relatively narrow depth ranges on the seamounts studied. Given the lack of 100% resolution of species with such a large portion of the mitochondrial genome, we argue that previous genetic studies have not resolved the degree of species overlap on seamounts and that we may not have the power to even test the hypothesis of seamount isolation using mitochondrial markers, let alone refute it. Thus a precautionary approach is advocated in seamount conservation and management, and the potential for depth structuring should be considered.},
}
@article {pmid23028909,
year = {2012},
author = {Duarte, S and Seena, S and Bärlocher, F and Cássio, F and Pascoal, C},
title = {Preliminary insights into the phylogeography of six aquatic hyphomycete species.},
journal = {PloS one},
volume = {7},
number = {9},
pages = {e45289},
pmid = {23028909},
issn = {1932-6203},
mesh = {Australia ; DNA Barcoding, Taxonomic ; DNA, Fungal/classification/*genetics ; DNA, Ribosomal Spacer/classification/*genetics ; Ecosystem ; Europe ; Fresh Water/microbiology ; Genetic Variation ; Haplotypes ; Mitosporic Fungi/classification/*genetics ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; },
abstract = {Aquatic hyphomycetes occur worldwide on a wide range of plant substrates decomposing in freshwaters, and are known to play a key role in organic matter turnover. The presumed worldwide distribution of many aquatic hyphomycete species has been based on morphology-based taxonomy and identification, which may overlook cryptic species, and mask global-scale biogeographical patterns. This might be circumvented by using DNA sequence data. The internal transcribed spacer (ITS) region from rDNA was recently designated as the most suitable barcode for fungal identification. In this study, we generated ITS barcodes of 130 isolates belonging to 6 aquatic hyphomycete species (Anguillospora filiformis, Flagellospora penicillioides, Geniculospora grandis, Lunulospora curvula, Tetrachaetum elegans and Tricladium chaetocladium), and collected from streams of Southwest Europe (86 isolates) and East Australia (44 isolates). European and Australian populations of 4 species (A. filiformis, F. penicillioides, G. grandis and T. elegans) grouped into different clades, and molecular diversity indices supported significant differentiation. Continents did not share haplotypes, except for T. chaetocladium. Overall results show substantial population diversity for all tested species and suggests that the biogeography of aquatic hyphomycetes may be species-specific.},
}
@article {pmid23028649,
year = {2012},
author = {Khamis, FM and Masiga, DK and Mohamed, SA and Salifu, D and de Meyer, M and Ekesi, S},
title = {Taxonomic identity of the invasive fruit fly pest, Bactrocera invadens: concordance in morphometry and DNA barcoding.},
journal = {PloS one},
volume = {7},
number = {9},
pages = {e44862},
pmid = {23028649},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Evolution, Molecular ; *Introduced Species ; Male ; Multivariate Analysis ; Phylogeny ; Principal Component Analysis ; Tephritidae/*anatomy &amp; histology/*classification ; },
abstract = {In 2003, a new fruit fly pest species was recorded for the first time in Kenya and has subsequently been found in 28 countries across tropical Africa. The insect was described as Bactrocera invadens, due to its rapid invasion of the African continent. In this study, the morphometry and DNA Barcoding of different populations of B. invadens distributed across the species range of tropical Africa and a sample from the pest's putative aboriginal home of Sri Lanka was investigated. Morphometry using wing veins and tibia length was used to separate B. invadens populations from other closely related Bactrocera species. The Principal component analysis yielded 15 components which correspond to the 15 morphometric measurements. The first two principal axes contributed to 90.7% of the total variance and showed partial separation of these populations. Canonical discriminant analysis indicated that only the first five canonical variates were statistically significant. The first two canonical variates contributed a total of 80.9% of the total variance clustering B. invadens with other members of the B. dorsalis complex while distinctly separating B. correcta, B. cucurbitae, B. oleae and B. zonata. The largest Mahalanobis squared distance (D(2) = 122.9) was found to be between B. cucurbitae and B. zonata, while the lowest was observed between B. invadens populations against B. kandiensis (8.1) and against B. dorsalis s.s (11.4). Evolutionary history inferred by the Neighbor-Joining method clustered the Bactrocera species populations into four clusters. First cluster consisted of the B. dorsalis complex (B. invadens, B. kandiensis and B. dorsalis s. s.), branching from the same node while the second group was paraphyletic clades of B. correcta and B. zonata. The last two are monophyletic clades, consisting of B. cucurbitae and B. oleae, respectively. Principal component analysis using the genetic distances confirmed the clustering inferred by the NJ tree.},
}
@article {pmid23028478,
year = {2012},
author = {Rougerie, R and Naumann, S and Nässig, WA},
title = {Morphology and molecules reveal unexpected cryptic diversity in the enigmatic genus Sinobirma Bryk, 1944 (Lepidoptera: Saturniidae).},
journal = {PloS one},
volume = {7},
number = {9},
pages = {e43920},
pmid = {23028478},
issn = {1932-6203},
mesh = {Animals ; China ; DNA Barcoding, Taxonomic ; Female ; *Genetic Variation ; Male ; Moths/*anatomy &amp; histology/classification/*genetics ; Phylogeny ; RNA, Ribosomal, 28S ; },
abstract = {The wild silkmoth genus Sinobirma Bryk, 1944 is a poorly known monotypic taxon from the eastern end of the Himalaya Range. It was convincingly proposed to be closely related to some members of an exclusively Afro-tropical group of Saturniidae, but its biogeographical and evolutionary history remains enigmatic. After examining recently collected material from Tibet, northern India, and northeastern Myanmar, we realized that this unique species, S. malaisei Bryk, 1944 only known so far from a few specimens and from a very restricted area near the border between north-eastern Myanmar and the Yunnan province of China, may in fact belong to a group of closely related cryptic species. In this work, we combined morphological comparative study, DNA barcoding, and the sequences of a nuclear marker (D2 expansion segment of the 28S rRNA gene) to unequivocally delimit three distinct species in the genus Sinobirma, of which two are described as new to science: S. myanmarensis sp. n. and S. bouyeri sp. n. An informative DNA barcode sequence was obtained from the female holotype of S. malaisei--collected in 1934--ensuring the proper assignation of this name to the newly collected and studied specimens. Our findings represent another example of the potential of coupling traditional taxonomy and DNA barcoding for revealing and solving difficult cases of cryptic diversity. This approach is now being generalized to the world fauna of Saturniidae, with the participation of most of the taxonomists studying these moths.},
}
@article {pmid23028445,
year = {2012},
author = {Mahé, S and Duhamel, M and Le Calvez, T and Guillot, L and Sarbu, L and Bretaudeau, A and Collin, O and Dufresne, A and Kiers, ET and Vandenkoornhuyse, P},
title = {PHYMYCO-DB: a curated database for analyses of fungal diversity and evolution.},
journal = {PloS one},
volume = {7},
number = {9},
pages = {e43117},
pmid = {23028445},
issn = {1932-6203},
mesh = {Base Sequence ; *Databases, Nucleic Acid ; *Evolution, Molecular ; Fungi/classification/*genetics ; *Genetic Variation ; Internet ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/genetics ; Sequence Alignment ; },
abstract = {BACKGROUND: In environmental sequencing studies, fungi can be identified based on nucleic acid sequences, using either highly variable sequences as species barcodes or conserved sequences containing a high-quality phylogenetic signal. For the latter, identification relies on phylogenetic analyses and the adoption of the phylogenetic species concept. Such analysis requires that the reference sequences are well identified and deposited in public-access databases. However, many entries in the public sequence databases are problematic in terms of quality and reliability and these data require screening to ensure correct phylogenetic interpretation.<br><br>To facilitate phylogenetic inferences and phylogenetic assignment, we introduce a fungal sequence database. The database PHYMYCO-DB comprises fungal sequences from GenBank that have been filtered to satisfy stringent sequence quality criteria. For the first release, two widely used molecular taxonomic markers were chosen: the nuclear SSU rRNA and EF1-&#x3b1; gene sequences. Following the automatic extraction and filtration, a manual curation is performed to remove problematic sequences while preserving relevant sequences useful for phylogenetic studies. As a result of curation, ~20% of the automatically filtered sequences have been removed from the database. To demonstrate how PHYMYCO-DB can be employed, we test a set of environmental Chytridiomycota sequences obtained from deep sea samples.<br><br>CONCLUSION: PHYMYCO-DB offers the tools necessary to: (i) extract high quality fungal sequences for each of the 5 fungal phyla, at all taxonomic levels, (ii) extract already performed alignments, to act as 'reference alignments', (iii) launch alignments of personal sequences along with stored data. A total of 9120 SSU rRNA and 672 EF1-&#x3b1; high-quality fungal sequences are now available. The PHYMYCO-DB is accessible through the URL http://phymycodb.genouest.org/.},
}
@article {pmid23023839,
year = {2012},
author = {Cohen, MR and Smetzer, JL and Westphal, JE and Comden, SC and Horn, DM},
title = {Risk models to improve safety of dispensing high-alert medications in community pharmacies.},
journal = {Journal of the American Pharmacists Association : JAPhA},
volume = {52},
number = {5},
pages = {584-602},
doi = {10.1331/JAPhA.2012.10145},
pmid = {23023839},
issn = {1544-3450},
support = {1P20HS017107/HS/AHRQ HHS/United States ; },
mesh = {*Algorithms ; Community Pharmacy Services/*organization &amp; administration ; Humans ; Incidence ; Medication Errors/*prevention &amp; control ; *Models, Theoretical ; Reproducibility of Results ; Risk Assessment ; Safety Management/*organization &amp; administration ; United States ; },
abstract = {OBJECTIVES: To determine whether sociotechnical probabilistic risk assessment can create accurate approximations of detailed risk models that describe error pathways, estimate the incidence of preventable adverse drug events (PADEs) with high-alert medications, rank the effectiveness of interventions, and provide a more informative picture of risk in the community pharmacy setting than is available currently.<br><br>DESIGN: Developmental study.<br><br>SETTING: 22 community pharmacies representing three U.S. regions.<br><br>PARTICIPANTS: Model-building group: six pharmacists and three technicians. Model validation group: 11 pharmacists; staff at two pharmacies observed.<br><br>INTERVENTION: A model-building team built 10 event trees that estimated the incidence of PADEs for four high-alert medications: warfarin, fentanyl transdermal systems, oral methotrexate, and insulin analogs.<br><br>MAIN OUTCOME MEASURES: Validation of event tree structure and incidence of defined PADEs with targeted medications.<br><br>RESULTS: PADEs with the highest incidence included dispensing the wrong dose/strength of warfarin as a result of data entry error (1.83/1,000 prescriptions), dispensing warfarin to the wrong patient (1.22/1,000 prescriptions), and dispensing an inappropriate fentanyl system dose due to a prescribing error (7.30/10,000 prescriptions). PADEs with the lowest incidence included dispensing the wrong drug when filling a warfarin prescription (9.43/1 billion prescriptions). The largest quantifiable reductions in risk were provided by increasing patient counseling (27-68% reduction), conducting a second data entry verification process during product verification (50-87% reduction), computer alerts that can't be bypassed easily (up to 100% reduction), opening the bag at the point of sale (56% reduction), and use of barcoding technology (almost a 100,000% increase in risk if technology not used). Combining two or more interventions resulted in further overall reduction in risk.<br><br>CONCLUSION: The risk models define thousands of ways process failures and behavioral elements combine to lead to PADEs. This level of detail is unavailable from any other source.},
}
@article {pmid23019027,
year = {2012},
author = {Cheng, L and Chang, YM and Lu, CY and Cao, DC and Sun, XW},
title = {[DNA barcoding and species and subspecies classification within genus Carassius].},
journal = {Dong wu xue yan jiu = Zoological research},
volume = {33},
number = {5},
pages = {463-472},
doi = {10.3724/SP.J.1141.2012.05463},
pmid = {23019027},
issn = {0254-5853},
mesh = {Animals ; China ; Cyprinidae/*classification/genetics ; DNA Barcoding, Taxonomic ; Fish Proteins/genetics ; Genetic Variation ; Molecular Sequence Data ; Phylogeny ; },
abstract = {The classification of Carassius has not been well established due to its great variability and wide distribution. Usually, Carassius is identified as three species: C. carassius, C. cuvieri and C. auratus, the latter including several subspecies, such as goldfish. Out of these subspecies, C. auratus gibelio have recently been thought of as a valid species of Carassius. In this study we collected the 5'end 651 bp segments of the mitochondrial cytochrome c oxidase I (COI) gene from 128 specimens, including C. carassius, C. cuvieri, C. auratus auratus, C. auratus gibelio and C. auratus langsdorfii. All three species of Carassius (C. carassius, C. cuvieri, C. auratus) were found to be valid, meanwhile genetic differentiation between the Eurasian C. auratus and Japanese C. auratus has reached a high level. However, several haplotypes were shared between C. auratus auratus and C. auratus gibelio. Consequently, C. auratus gibelio should be regarded as a subspecies of C. auratus rather than a valid species. Moreover, because both diploids and triploids exist in C. auratus auratus and C. auratus gibelio, ploidy level should not be used as criteria for the classification of species or subspecies in Carassius.},
}
@article {pmid23010364,
year = {2012},
author = {Sharma, A and Folch, JL and Cardoso-Taketa, A and Lorence, A and Villarreal, ML},
title = {DNA barcoding of the Mexican sedative and anxiolytic plant Galphimia glauca.},
journal = {Journal of ethnopharmacology},
volume = {144},
number = {2},
pages = {371-378},
pmid = {23010364},
issn = {1872-7573},
support = {P20 GM103429/GM/NIGMS NIH HHS/United States ; P20 RR016460/RR/NCRR NIH HHS/United States ; 8P20GM103429-11/GM/NIGMS NIH HHS/United States ; 5P20RR016460-11/RR/NCRR NIH HHS/United States ; },
mesh = {Anti-Anxiety Agents ; DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; Galphimia/*genetics ; Hypnotics and Sedatives ; Least-Squares Analysis ; Mexico ; *Phylogeny ; Plant Leaves ; Plant Proteins/genetics ; },
abstract = {ETHNOPHARMACOLOGY RELEVANCE: Galphimia glauca (Malpighiaceae) is a Mexican plant popularly used as a tranquilizer in the treatment of nervous system disorders, although it is also used to treat other common illnesses.<br><br>AIM OF THE STUDY: The aim of this investigation is to find out if populations of Galphimia glauca collected in different regions and ecosystems in Mexico actually belong to the same species by using the contemporary technique of DNA barcodes. Our previous metabolic profiling study demonstrates that different collections of this plant obtained from various geographical areas exhibited diverse chemical profiles in terms of the active compounds named Galphimines. We expected the DNA barcodes apart from indicating the different species of Galphimia would indicate the active populations.<br><br>MATERIALS AND METHODS: We employed matK, rpoC1 and rbcL DNA barcodes to indicate the different species. Furthermore to investigate the possible impact of the several different ecosystems where the seven populations were collected, thin layer chromatography was employed to create a partial chemical profile, which was then compared with the metabolic profiles obtained by (1)H-NMR and multivariate data analysis.<br><br>RESULTS AND CONCLUSIONS: This study showed that the seven populations here analyzed contain at least three different species of the genus Galphimia, although each individual population is homogeneous. Interestingly our TLC analysis clearly showed that the active populations displayed a distinctively unique chemical profile. This work also showed that the use of DNA barcodes combined with chemical profile analysis is an excellent approach to solve the problems of quality control in the development of Galphimia-based medicines as well as for any breeding programs for this species.},
}
@article {pmid23010161,
year = {2013},
author = {Stothard, JR and Ameri, H and Khamis, IS and Blair, L and Nyandindi, US and Kane, RA and Johnston, DA and Webster, BL and Rollinson, D},
title = {Parasitological and malacological surveys reveal urogenital schistosomiasis on Mafia Island, Tanzania to be an imported infection.},
journal = {Acta tropica},
volume = {128},
number = {2},
pages = {326-333},
doi = {10.1016/j.actatropica.2012.09.006},
pmid = {23010161},
issn = {1873-6254},
mesh = {Adolescent ; Animals ; Bulinus/classification/genetics/*parasitology ; Child ; DNA Barcoding, Taxonomic ; Data Collection ; *Endemic Diseases ; Female ; Humans ; Male ; Molecular Epidemiology ; Prevalence ; Schistosoma haematobium/classification/genetics/*isolation &amp; purification ; Schistosomiasis haematobia/*epidemiology/parasitology/*transmission ; Schools ; Tanzania/epidemiology ; Young Adult ; },
abstract = {To confirm the local endemicity of Schistosoma haematobium on Mafia Island, Tanzania, conjoint parasitological and malacological surveys were undertaken in July 2006 with parasitological investigations supplemented with case-history questionnaires. A total of 238 children (125 girls and 113 boys, mean age of 13.9 years) across 9 primary schools were examined. The prevalence of micro-haematuria and egg-patent infection was 18.1% (CI95=9.6-33.6) and 4.2% (CI95=1.9-7.6), respectively but a strong female bias was observed for micro-haematuria (5.6F:1M) contrasting with a strong male bias for the presence of eggs (1F:4M). All egg-patent infections were of light-intensity (<10eggs/10ml). No clear associations between infection prevalence and local water-contact, by school, were found and all 10 of the egg-positive children had a travel history to the nearby mainland or Zanzibar. Inspection of community diagnostic registers at Kilindoni Hospital revealed a low proportion (<2%) of egg-patent infection for 20,306 samples tested in the 2000-2005 period. A total of 43 freshwater sites, a third of which were previously sampled in 1999 and 2002, were surveyed and 11 species of freshwater mollusc were found. Four species of Bulinus (B. nasutus, B. forskalii, B. barthi and B. sp.) were encountered across 13 sites with B. nasutus restricted to 3 of these towards the north of the island. No collected snail was observed to shed schistosome cercariae. Further characterisation of B. nasutus and S. haematobium included infection challenge on two occasions, with miracidia obtained from egg-patent children from Mafia and Unguja islands as well as DNA barcoding of snails and schistosomes. B. nasutus was shown refractory to infection. With the substantial travel to and from Mafia, the refractory nature of local snails and evidence from DNA barcoding in schistosomes and snails, we conclude that urogenital schistosomiasis is an imported infection.},
}
@article {pmid23009593,
year = {2012},
author = {Tae, H and Ryu, D and Sureshchandra, S and Choi, JH},
title = {ESTclean: a cleaning tool for next-gen transcriptome shotgun sequencing.},
journal = {BMC bioinformatics},
volume = {13},
number = {},
pages = {247},
pmid = {23009593},
issn = {1471-2105},
support = {CA134304/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; DNA Primers/genetics ; DNA, Complementary/genetics ; Drosophila melanogaster/genetics ; *Expressed Sequence Tags ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA/*methods ; *Software ; *Transcriptome ; },
abstract = {BACKGROUND: With the advent of next-generation sequencing (NGS) technologies, full cDNA shotgun sequencing has become a major approach in the study of transcriptomes, and several different protocols in 454 sequencing have been invented. As each protocol uses its own short DNA tags or adapters attached to the ends of cDNA fragments for labeling or sequencing, different contaminants may lead to mis-assembly and inaccurate sequence products.<br><br>RESULTS: We have designed and implemented a new program for raw sequence cleaning in a graphical user interface and a batch script. The cleaning process consists of several modules including barcode trimming, sequencing adapter trimming, amplification primer trimming, poly-A tail trimming, vector screening and low quality region trimming. These modules can be combined based on various sequencing applications.<br><br>CONCLUSIONS: ESTclean is a software package not only for cleaning cDNA sequences, but also for helping to develop sequencing protocols by providing summary tables and figures for sequencing quality control in a graphical user interface. It outperforms in cleaning read sequences from complicated sequencing protocols which use barcodes and multiple amplification primers.},
}
@article {pmid23008247,
year = {2012},
author = {Lee, H and Kang, H and Chung, MK and Kim, BN and Lee, DS},
title = {Persistent brain network homology from the perspective of dendrogram.},
journal = {IEEE transactions on medical imaging},
volume = {31},
number = {12},
pages = {2267-2277},
doi = {10.1109/TMI.2012.2219590},
pmid = {23008247},
issn = {1558-254X},
mesh = {Attention Deficit Disorder with Hyperactivity/diagnostic imaging/physiopathology ; Brain Mapping/*methods ; Case-Control Studies ; Child ; Child Development Disorders, Pervasive/diagnostic imaging/physiopathology ; Child, Preschool ; Cluster Analysis ; Female ; Fluorodeoxyglucose F18 ; Humans ; Image Processing, Computer-Assisted/*methods ; Male ; Neural Pathways/diagnostic imaging/physiology/physiopathology ; Positron-Emission Tomography/*methods ; Radiopharmaceuticals ; },
abstract = {The brain network is usually constructed by estimating the connectivity matrix and thresholding it at an arbitrary level. The problem with this standard method is that we do not have any generally accepted criteria for determining a proper threshold. Thus, we propose a novel multiscale framework that models all brain networks generated over every possible threshold. Our approach is based on persistent homology and its various representations such as the Rips filtration, barcodes, and dendrograms. This new persistent homological framework enables us to quantify various persistent topological features at different scales in a coherent manner. The barcode is used to quantify and visualize the evolutionary changes of topological features such as the Betti numbers over different scales. By incorporating additional geometric information to the barcode, we obtain a single linkage dendrogram that shows the overall evolution of the network. The difference between the two networks is then measured by the Gromov-Hausdorff distance over the dendrograms. As an illustration, we modeled and differentiated the FDG-PET based functional brain networks of 24 attention-deficit hyperactivity disorder children, 26 autism spectrum disorder children, and 11 pediatric control subjects.},
}
@article {pmid23006488,
year = {2013},
author = {Puckridge, M and Andreakis, N and Appleyard, SA and Ward, RD},
title = {Cryptic diversity in flathead fishes (Scorpaeniformes: Platycephalidae) across the Indo-West Pacific uncovered by DNA barcoding.},
journal = {Molecular ecology resources},
volume = {13},
number = {1},
pages = {32-42},
doi = {10.1111/1755-0998.12022},
pmid = {23006488},
issn = {1755-0998},
mesh = {Animals ; Base Sequence ; Cluster Analysis ; Computational Biology ; Conservation of Natural Resources/methods ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Fishes/*genetics ; Genetic Variation/*genetics ; Indian Ocean ; Molecular Sequence Data ; Pacific Ocean ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Identification of taxonomical units underpins most biological endeavours ranging from accurate biodiversity estimates to the effective management of sustainably harvested, protected or endangered species. Successful species identification is now frequently based on a combination of approaches including morphometrics and DNA markers. Sequencing of the mitochondrial COI gene is an established methodology with an international campaign directed at barcoding all fishes. We employed COI sequencing alongside traditional taxonomic identification methods and uncovered instances of deep intraspecific genetic divergences among flathead species. Sixty-five operational taxonomic units (OTUs) were observed across the Indo-West Pacific from just 48 currently recognized species. The most comprehensively sampled taxon, Platycephalus indicus, exhibited the highest levels of genetic diversity with eight lineages separated by up to 16.37% genetic distance. Our results clearly indicate a thorough reappraisal of the current taxonomy of P. indicus (and its three junior synonyms) is warranted in conjunction with detailed taxonomic work on the other additional Platycephalidae OTUs detected by DNA barcoding.},
}
@article {pmid23006448,
year = {2012},
author = {León-Romero, Y and Mejía, O and Soto-Galera, E},
title = {DNA barcoding reveals taxonomic conflicts in the Herichthys bartoni species group (Pisces: Cichlidae).},
journal = {Molecular ecology resources},
volume = {12},
number = {6},
pages = {1021-1026},
doi = {10.1111/1755-0998.12018},
pmid = {23006448},
issn = {1755-0998},
mesh = {Animals ; Cichlids/*classification/*genetics ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; *Genetic Variation ; Phylogeny ; },
abstract = {Fishes of the genus Herichthys are the only representatives of the family Cichlidae to have colonized the Neartic region. In this study, we used DNA barcode of 64 individuals of the Herichthys bartoni species group to test the monophyly of the species and the efficiency of this tool to discriminate among species. The Bayesian phylogenetic tree and the neighbour joining (NJ) tree obtained from the Kimura two-parameter model (K2P) give similar topologies. DNA barcoding resolution was very poor (25%). Additionally, the low levels of genetic divergence among taxa preclude the use of threshold values as has been suggested in earlier studies.},
}
@article {pmid23001670,
year = {2012},
author = {Emanuel, PA and Buckley, PE and Sutton, TA and Edmonds, JM and Bailey, AM and Rivers, BA and Kim, MH and Ginley, WJ and Keiser, CC and Doherty, RW and Kragl, FJ and Narayanan, FE and Katoski, SE and Paikoff, S and Leppert, SP and Strawbridge, JB and VanReenen, DR and Biberos, SS and Moore, D and Phillips, DW and Mingioni, LR and Melles, O and Ondercin, DG and Hirsh, B and Bieschke, KM and Harris, CL and Omberg, KM and Rastogi, VK and Van Cuyk, S and Gibbons, HS},
title = {Detection and tracking of a novel genetically tagged biological simulant in the environment.},
journal = {Applied and environmental microbiology},
volume = {78},
number = {23},
pages = {8281-8288},
pmid = {23001670},
issn = {1098-5336},
mesh = {*Air Microbiology ; Bacillus anthracis/isolation &amp; purification ; Bacillus thuringiensis/classification/*genetics/*isolation &amp; purification ; Bacteriological Techniques/*methods ; DNA Barcoding, Taxonomic/*methods ; Models, Biological ; Real-Time Polymerase Chain Reaction/methods ; Spores, Bacterial/classification/genetics/isolation &amp; purification ; Staining and Labeling/methods ; Time Factors ; },
abstract = {A variant of Bacillus thuringiensis subsp. kurstaki containing a single, stable copy of a uniquely amplifiable DNA oligomer integrated into the genome for tracking the fate of biological agents in the environment was developed. The use of genetically tagged spores overcomes the ambiguity of discerning the test material from pre-existing environmental microflora or from previously released background material. In this study, we demonstrate the utility of the genetically "barcoded" simulant in a controlled indoor setting and in an outdoor release. In an ambient breeze tunnel test, spores deposited on tiles were reaerosolized and detected by real-time PCR at distances of 30 m from the point of deposition. Real-time PCR signals were inversely correlated with distance from the seeded tiles. An outdoor release of powdered spore simulant at Aberdeen Proving Ground, Edgewood, MD, was monitored from a distance by a light detection and ranging (LIDAR) laser. Over a 2-week period, an array of air sampling units collected samples were analyzed for the presence of viable spores and using barcode-specific real-time PCR assays. Barcoded B. thuringiensis subsp. kurstaki spores were unambiguously identified on the day of the release, and viable material was recovered in a pattern consistent with the cloud track predicted by prevailing winds and by data tracks provided by the LIDAR system. Finally, the real-time PCR assays successfully differentiated barcoded B. thuringiensis subsp. kurstaki spores from wild-type spores under field conditions.},
}
@article {pmid23001658,
year = {2012},
author = {Buckley, P and Rivers, B and Katoski, S and Kim, MH and Kragl, FJ and Broomall, S and Krepps, M and Skowronski, EW and Rosenzweig, CN and Paikoff, S and Emanuel, P and Gibbons, HS},
title = {Genetic barcodes for improved environmental tracking of an anthrax simulant.},
journal = {Applied and environmental microbiology},
volume = {78},
number = {23},
pages = {8272-8280},
pmid = {23001658},
issn = {1098-5336},
mesh = {Bacillus anthracis/isolation &amp; purification ; Bacillus thuringiensis/classification/*genetics/*isolation &amp; purification ; Bacteriological Techniques/*methods ; DNA Barcoding, Taxonomic/*methods ; *Environmental Microbiology ; Genomic Instability ; Models, Biological ; Molecular Biology/*methods ; Staining and Labeling/methods ; },
abstract = {The development of realistic risk models that predict the dissemination, dispersion and persistence of potential biothreat agents have utilized nonpathogenic surrogate organisms such as Bacillus atrophaeus subsp. globigii or commercial products such as Bacillus thuringiensis subsp. kurstaki. Comparison of results from outdoor tests under different conditions requires the use of genetically identical strains; however, the requirement for isogenic strains limits the ability to compare other desirable properties, such as the behavior in the environment of the same strain prepared using different methods. Finally, current methods do not allow long-term studies of persistence or reaerosolization in test sites where simulants are heavily used or in areas where B. thuringiensis subsp. kurstaki is applied as a biopesticide. To create a set of genetically heterogeneous yet phenotypically indistinguishable strains so that variables intrinsic to simulations (e.g., sample preparation) can be varied and the strains can be tested under otherwise identical conditions, we have developed a strategy of introducing small genetic signatures ("barcodes") into neutral regions of the genome. The barcodes are stable over 300 generations and do not impact in vitro growth or sporulation. Each barcode contains common and specific tags that allow differentiation of marked strains from wild-type strains and from each other. Each tag is paired with specific real-time PCR assays that facilitate discrimination of barcoded strains from wild-type strains and from each other. These uniquely barcoded strains will be valuable tools for research into the environmental fate of released organisms by providing specific artificial detection signatures.},
}
@article {pmid23000997,
year = {2012},
author = {Lin, C and Jungmann, R and Leifer, AM and Li, C and Levner, D and Church, GM and Shih, WM and Yin, P},
title = {Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA.},
journal = {Nature chemistry},
volume = {4},
number = {10},
pages = {832-839},
pmid = {23000997},
issn = {1755-4349},
support = {DP2 OD004641/OD/NIH HHS/United States ; P50 HG005550/HG/NHGRI NIH HHS/United States ; 1DP2OD007292/OD/NIH HHS/United States ; DP2 OD007292/OD/NIH HHS/United States ; 1DP2OD004641/OD/NIH HHS/United States ; },
mesh = {DNA/*chemistry ; Fluorescent Dyes/*chemistry ; Microscopy, Fluorescence ; Nanotubes/chemistry ; },
abstract = {The identification and differentiation of a large number of distinct molecular species with high temporal and spatial resolution is a major challenge in biomedical science. Fluorescence microscopy is a powerful tool, but its multiplexing ability is limited by the number of spectrally distinguishable fluorophores. Here, we used (deoxy)ribonucleic acid (DNA)-origami technology to construct submicrometre nanorods that act as fluorescent barcodes. We demonstrate that spatial control over the positioning of fluorophores on the surface of a stiff DNA nanorod can produce 216 distinct barcodes that can be decoded unambiguously using epifluorescence or total internal reflection fluorescence microscopy. Barcodes with higher spatial information density were demonstrated via the construction of super-resolution barcodes with features spaced by ∼40 nm. One species of the barcodes was used to tag yeast surface receptors, which suggests their potential applications as in situ imaging probes for diverse biomolecular and cellular entities in their native environments.},
}
@article {pmid22997026,
year = {2012},
author = {Frischbutter, S and Schultheis, K and Pätzel, M and Radbruch, A and Baumgrass, R},
title = {Evaluation of calcineurin/NFAT inhibitor selectivity in primary human Th cells using bar-coding and phospho-flow cytometry.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {81},
number = {11},
pages = {1005-1011},
doi = {10.1002/cyto.a.22204},
pmid = {22997026},
issn = {1552-4930},
mesh = {Arachidonic Acids/pharmacology ; *Calcineurin Inhibitors ; Drug Evaluation, Preclinical ; Electronic Data Processing/*methods ; Flow Cytometry/*methods ; Fluorescence ; Genes, Reporter ; Humans ; Imidazoles/pharmacology ; Inhibitory Concentration 50 ; MAP Kinase Signaling System ; NFATC Transcription Factors/*antagonists &amp; inhibitors/metabolism ; Nitriles/pharmacology ; Phosphorylation ; Pyridines/pharmacology ; Sulfones/pharmacology ; T-Lymphocytes, Helper-Inducer/*drug effects/metabolism ; Transcription Factor RelA/*antagonists &amp; inhibitors/metabolism ; p38 Mitogen-Activated Protein Kinases/antagonists &amp; inhibitors/metabolism ; },
abstract = {Small molecular inhibitors are excellent tools for manipulating cell reactions. They are widely used in scientific research to study molecular mechanisms of cells under physiological and pathophysiological conditions as well as in clinical applications to treat patients. However, their selectivity is often not well known. Moreover, it can vary according to cell types and the analysis methods used. Therefore, it is usually not possible to make comparisons between the data presented in the literature. Here we analyzed the selectivity of five chosen inhibitors of calcineurin/NFAT activation under the same conditions. Using a combination of fluorescent cell barcoding and phospho-specific flow cytometry we studied the inhibition of activation of NF-κBp65 and MAPK pathways in stimulated primary human Th cells. This semi-high throughput approach enabled us to demonstrate that (i) CsA and NCI3 are around 5 to 10- and 20-fold less potent, respectively, at inhibiting phosphorylation of NF-κBp65 and p38 than activation of NFAT, (ii) AM404 is at least 15-fold selective for NFAT but already toxic at concentrations above 40 μM, (iii) INCA6 is not selective at all, and (iv) BTP1 is at least 100-fold selective for inhibition of NFAT activation relative to NF-κBp65, p38 and ERK1/2 phosphorylation. Altogether, our results not only show the applicability of a semi-high throughput inhibitor test system but also that BTP1 is the most selective inhibitor of calcineurin/NFAT activation among the studied inhibitors under the used conditions.},
}
@article {pmid22989063,
year = {2012},
author = {Wang, ZD and Guo, YS and Liu, XM and Fan, YB and Liu, CW},
title = {DNA barcoding South China Sea fishes.},
journal = {Mitochondrial DNA},
volume = {23},
number = {5},
pages = {405-410},
doi = {10.3109/19401736.2012.710204},
pmid = {22989063},
issn = {1940-1744},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Fishes/classification/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {We have determined 222 DNA barcode sequences of 95 fish species in 86 genera of 69 families from 15 orders. Fish were captured by trawl from two important fisheries regions in South China Sea: Spratly Islands (Nansha Islands) and Beibu Gulf. The average genetic distances between intraspecies were about 60-fold less than those of interspecies within different taxonomic levels, as Kimura two-parameter genetic distances averaged 17.260% among congeners, 20.097% among genus, and only 0.317% for intraspecific individuals. There were a few examples of deep divergence within species, suggesting the need for further taxonomic work, and a few examples of closely allied species, perhaps reflecting introgressive hybridization. The results provide further evidence for the reliability and accessibility of DNA barcodes for marine fish identification, and also highlight their effectiveness for flagging cases needing taxonomical reexamination.},
}
@article {pmid22987426,
year = {2013},
author = {Makarova, O and Contaldo, N and Paltrinieri, S and Bertaccini, A and Nyskjold, H and Nicolaisen, M},
title = {DNA bar-coding for phytoplasma identification.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {938},
number = {},
pages = {301-317},
doi = {10.1007/978-1-62703-089-2_26},
pmid = {22987426},
issn = {1940-6029},
mesh = {Base Sequence ; Computational Biology/methods ; DNA/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; DNA, Bacterial/*chemistry ; Databases, Nucleic Acid ; Genes, Bacterial ; Internet ; Molecular Sequence Data ; Phytoplasma/*classification/genetics/isolation &amp; purification ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/chemistry/genetics ; Sequence Analysis, DNA ; },
abstract = {Phytoplasma identification has proved difficult due to their inability to be maintained in vitro. DNA barcoding is an identification method based on comparison of a short DNA sequence with known sequences from a database. A DNA barcoding tool has been developed for phytoplasma identification. While other sequence-based methods may be well adapted to identification of particular strains of phytoplasmas, often they cannot be used for the simultaneous identification of phytoplasmas from different groups. The phytoplasma DNA barcoding protocol in this chapter, based on the tuf and 16SrRNA genes, can be used to identify the following phytoplasma groups: 16SrI, 16SrII, 16SrIII, 16SrIV, 16SrV, 16SrVI, 16SrVII, 16SrIX, 16SrX, 16SrXI, 16SrXII, 16SrXV, 16SrXX, 16SrXXI.},
}
@article {pmid22984883,
year = {2012},
author = {Rosso, JJ and Mabragaña, E and Castro, MG and de Astarloa, JM},
title = {DNA barcoding Neotropical fishes: recent advances from the Pampa Plain, Argentina.},
journal = {Molecular ecology resources},
volume = {12},
number = {6},
pages = {999-1011},
doi = {10.1111/1755-0998.12010},
pmid = {22984883},
issn = {1755-0998},
mesh = {Animals ; Argentina ; *Biodiversity ; Cluster Analysis ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Fishes/*classification/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The fish fauna of the Pampa Plain, the southernmost distribution range of many Neotropical species, was barcoded in this study. COI sequences were analysed by means of distance (K2P/NJ) and character-based (ML) models, as well as the Barcode Index Number (BIN). K2P/NJ analysis was able to discriminate among all previously identified species while also revealing the likely occurrence of two cryptic species that were further supported by BIN and ML analyses. On the other hand, both BIN and ML were not able to discriminate between two species of Rineloricaria. Despite the small genetic divergence between A. cf. pampa and A. eigenmanniorum, a tight array of haplotypes was observed for each species in both the distance and character-based methods. Deep intraspecific divergences were detected in Cnesterodon decemmaculatus (5%) and Salminus brasiliensis (6%). For Salminus brasiliensis, these findings were further supported by character-based (ML) evidence and meristic and morphological data. Our results also showed that Pampa Plain representatives of Salminus brasiliensis, Rhamdia quelen, Hoplias malabaricus, Synbranchus marmoratus, Australoheros facetus, Oligosarcus jenynsii and Corydoras paleatus differed by more than 3% from their conspecifics from other parts of South America. Overall, this study was able to highlight the likely occurrence of a cryptic species in Salminus brasiliensis and also illustrate the strong geographical structure in the COI sequence composition of seven fish species from South America.},
}
@article {pmid22984477,
year = {2012},
author = {Halvorsen, K and Wong, WP},
title = {Binary DNA nanostructures for data encryption.},
journal = {PloS one},
volume = {7},
number = {9},
pages = {e44212},
pmid = {22984477},
issn = {1932-6203},
mesh = {*Computer Security ; DNA/*chemistry ; Electrophoresis, Agar Gel ; Nanostructures/*chemistry ; },
abstract = {We present a simple and secure system for encrypting and decrypting information using DNA self-assembly. Binary data is encoded in the geometry of DNA nanostructures with two distinct conformations. Removing or leaving out a single component reduces these structures to an encrypted solution of ssDNA, whereas adding back this missing "decryption key" causes the spontaneous formation of the message through self-assembly, enabling rapid read out via gel electrophoresis. Applications include authentication, secure messaging, and barcoding.},
}
@article {pmid22978681,
year = {2012},
author = {Carneiro, J and Pereira, F and Amorim, A},
title = {SPInDel: a multifunctional workbench for species identification using insertion/deletion variants.},
journal = {Molecular ecology resources},
volume = {12},
number = {6},
pages = {1190-1195},
doi = {10.1111/1755-0998.12011},
pmid = {22978681},
issn = {1755-0998},
mesh = {Animals ; Anura/classification/genetics ; Asia, Southeastern ; Classification/*methods ; Computational Biology/*methods ; Genomics/*methods ; *INDEL Mutation ; Perciformes/classification/genetics ; Software ; },
abstract = {The majority of the available methods for the molecular identification of species use pairwise sequence divergences between the query and reference sequences (DNA barcoding). The presence of multiple insertions and deletions (indels) in the target genomic regions is generally regarded as a problem, as it introduces ambiguities in sequence alignments. However, we have recently shown that a high level of species discrimination is attainable in all taxa of life simply by considering the length of hypervariable regions defined by indel variants. Each species is tagged with a numeric profile of fragment lengths-a true numeric barcode. In this study, we describe a multifunctional computational workbench (named SPInDel for SPecies Identification by Insertions/Deletions) to assist researchers using variable-length DNA sequences, and we demonstrate its applicability in molecular ecology. The SPInDel workbench provides a step-by-step environment for the alignment of target sequences, selection of informative hypervariable regions, design of PCR primers and the statistical validation of the species-identification process. In our test data sets, we were able to discriminate all species from two genera of frogs (Ansonia and Leptobrachium) inhabiting lowland rainforests and mountain regions of South-East Asia and species from the most common genus of coral reef fishes (Apogon). Our method can complement conventional DNA barcoding systems when indels are common (e.g. in rRNA genes) without the required step of DNA sequencing. The executable files, source code, documentation and test data sets are freely available at http://www.portugene.com/SPInDel/SPInDel_webworkbench.html.},
}
@article {pmid22973283,
year = {2012},
author = {Kumar, R and Ichihashi, Y and Kimura, S and Chitwood, DH and Headland, LR and Peng, J and Maloof, JN and Sinha, NR},
title = {A High-Throughput Method for Illumina RNA-Seq Library Preparation.},
journal = {Frontiers in plant science},
volume = {3},
number = {},
pages = {202},
pmid = {22973283},
issn = {1664-462X},
abstract = {With the introduction of cost effective, rapid, and superior quality next generation sequencing techniques, gene expression analysis has become viable for labs conducting small projects as well as large-scale gene expression analysis experiments. However, the available protocols for construction of RNA-sequencing (RNA-Seq) libraries are expensive and/or difficult to scale for high-throughput applications. Also, most protocols require isolated total RNA as a starting point. We provide a cost-effective RNA-Seq library synthesis protocol that is fast, starts with tissue, and is high-throughput from tissue to synthesized library. We have also designed and report a set of 96 unique barcodes for library adapters that are amenable to high-throughput sequencing by a large combination of multiplexing strategies. Our developed protocol has more power to detect differentially expressed genes when compared to the standard Illumina protocol, probably owing to less technical variation amongst replicates. We also address the problem of gene-length biases affecting differential gene expression calls and demonstrate that such biases can be efficiently minimized during mRNA isolation for library preparation.},
}
@article {pmid22972696,
year = {2012},
author = {Liang, WE and Thomas, DC and Conti, DV},
title = {Analysis and optimal design for association studies using next-generation sequencing with case-control pools.},
journal = {Genetic epidemiology},
volume = {36},
number = {8},
pages = {870-881},
pmid = {22972696},
issn = {1098-2272},
support = {P30 ES007048/ES/NIEHS NIH HHS/United States ; P01 ES009581/ES/NIEHS NIH HHS/United States ; P50HG002790/HG/NHGRI NIH HHS/United States ; R01 MH084678/MH/NIMH NIH HHS/United States ; R01 CA140561/CA/NCI NIH HHS/United States ; R01 ES019876/ES/NIEHS NIH HHS/United States ; R01 CA143237/CA/NCI NIH HHS/United States ; R01ES019876/ES/NIEHS NIH HHS/United States ; R01CA140561/CA/NCI NIH HHS/United States ; R01CA143237/CA/NCI NIH HHS/United States ; P50 HG002790/HG/NHGRI NIH HHS/United States ; R01HL087680/HL/NHLBI NIH HHS/United States ; U19 CA148107/CA/NCI NIH HHS/United States ; R01MH084678/MH/NIMH NIH HHS/United States ; R01 ES016813/ES/NIEHS NIH HHS/United States ; R01 HL087680/HL/NHLBI NIH HHS/United States ; P30ES007048/ES/NIEHS NIH HHS/United States ; },
mesh = {Bayes Theorem ; Case-Control Studies ; Gene Frequency ; Genome, Human/genetics ; Genome-Wide Association Study/*methods ; Genotype ; *High-Throughput Nucleotide Sequencing ; Humans ; Models, Genetic ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results ; Research Design ; Sample Size ; *Sequence Analysis, DNA ; },
abstract = {With its potential to discover a much greater amount of genetic variation, next-generation sequencing is fast becoming an emergent tool for genetic association studies. However, the cost of sequencing all individuals in a large-scale population study is still high in comparison to most alternative genotyping options. While the ability to identify individual-level data is lost (without bar-coding), sequencing pooled samples can substantially lower costs without compromising the power to detect significant associations. We propose a hierarchical Bayesian model that estimates the association of each variant using pools of cases and controls, accounting for the variation in read depth across pools and sequencing error. To investigate the performance of our method across a range of number of pools, number of individuals within each pool, and average coverage, we undertook extensive simulations varying effect sizes, minor allele frequencies, and sequencing error rates. In general, the number of pools and pool size have dramatic effects on power while the total depth of coverage per pool has only a moderate impact. This information can guide the selection of a study design that maximizes power subject to cost, sample size, or other laboratory constraints. We provide an R package (hiPOD: hierarchical Pooled Optimal Design) to find the optimal design, allowing the user to specify a cost function, cost, and sample size limitations, and distributions of effect size, minor allele frequency, and sequencing error rate.},
}
@article {pmid22971078,
year = {2013},
author = {Sudheendra, US and Sowmya, K and Vidhi, M and Shreenivas, K and Prathamesh, J},
title = {2D barcodes: a novel and simple method for denture identification.},
journal = {Journal of forensic sciences},
volume = {58},
number = {1},
pages = {170-172},
doi = {10.1111/j.1556-4029.2012.02275.x},
pmid = {22971078},
issn = {1556-4029},
mesh = {Denture Identification Marking/*instrumentation/*methods ; Denture, Complete ; Denture, Partial ; *Electronic Data Processing ; Forensic Dentistry ; Humans ; Software ; },
abstract = {Several methods of denture marking have been described in the literature. However, most of them are expensive, time-consuming, and do not permit the incorporation of large amounts of information. We propose a novel and simple method incorporating 2D codes which has several advantages over the existing methods. A 2D code was generated in the dental office and inserted into a maxillary denture. The code was then read using software downloaded into a mobile phone giving access to the website containing details about the patient. The denture was also subjected to durability tests, which did not hamper the efficacy of the 2D code. 2D coding for dentures is a simple, less expensive method with the potential of storing a large amount of information that can be accessed on-site by the forensic investigator, thus allowing quick identification of the denture wearer.},
}
@article {pmid22970567,
year = {2012},
author = {Baker, DA and Stevenson, DW and Little, DP},
title = {DNA barcode identification of black cohosh herbal dietary supplements.},
journal = {Journal of AOAC International},
volume = {95},
number = {4},
pages = {1023-1034},
doi = {10.5740/jaoacint.11-261},
pmid = {22970567},
issn = {1060-3271},
mesh = {Base Sequence ; Cimicifuga/*metabolism ; Dietary Supplements/*analysis ; Drug Contamination/*prevention &amp; control ; *Electronic Data Processing ; Genetic Variation ; Humans ; Molecular Sequence Data ; Nonprescription Drugs/*analysis/standards ; Nucleotides/chemistry ; Phytotherapy/adverse effects ; Plant Extracts/*analysis ; Polymerase Chain Reaction/methods ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; Species Specificity ; },
abstract = {Black cohosh (Actaea racemosa) herbal dietary supplements are commonly consumed to treat menopausal symptoms, but there are reports of adverse events and toxicities associated with their use. Accidental misidentification and/or deliberate adulteration results in harvesting other related species that are then marketed as black cohosh. Some of these species are known to be toxic to humans. We have identified two matK nucleotides that consistently distinguish black cohosh from related species. Using these nucleotides, an assay was able to correctly identify all of the black cohosh samples in the validation set. None of the other Actaea species in the validation set were falsely identified as black cohosh. Of 36 dietary supplements sequenced, 27 (75%) had a sequence that exactly matched black cohosh. The remaining nine samples (25%) had a sequence identical to that of three Asian Actaea species (A. cimicifuga, A. dahurica, and A. simplex). Manufacturers should routinely test plant material using a reliable assay to ensure accurate labeling.},
}
@article {pmid22970123,
year = {2012},
author = {Bruni, I and De Mattia, F and Martellos, S and Galimberti, A and Savadori, P and Casiraghi, M and Nimis, PL and Labra, M},
title = {DNA barcoding as an effective tool in improving a digital plant identification system: a case study for the area of Mt. Valerio, Trieste (NE Italy).},
journal = {PloS one},
volume = {7},
number = {9},
pages = {e43256},
pmid = {22970123},
issn = {1932-6203},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; Genetic Markers ; Italy ; Plants/*classification/*genetics ; Polymerase Chain Reaction ; },
abstract = {BACKGROUND: Identification keys are decision trees which require the observation of one or more morphological characters of an organism at each step of the process. While modern digital keys can overcome several constraints of classical paper-printed keys, their performance is not error-free. Moreover, identification cannot be always achieved when a specimen lacks some morphological features (i.e. because of season, incomplete development or miss-collecting). DNA barcoding was proven to have great potential in plant identification, while it can be ineffective with some closely related taxa, in which the relatively brief evolutionary distance did not produce differences in the core-barcode sequences.<br><br>In this paper, we investigated how the DNA barcoding can support the modern digital approaches to the identification of organisms, using as a case study a local flora, that of Mt. Valerio, a small hill near the centre of Trieste (NE Italy). The core barcode markers (plastidial rbcL and matK), plus the additional trnH-psbA region, were used to identify vascular plants specimens. The usefulness of DNA barcoding data in enhancing the performance of a digital identification key was tested on three independent simulated scenarios.<br><br>CONCLUSIONS/SIGNIFICANCE: Our results show that the core barcode markers univocally identify most species of our local flora (96%). The trnH-psbA data improve the discriminating power of DNA barcoding among closely related plant taxa. In the multiparametric digital key, DNA barcoding data improves the identification success rate; in our simulation, DNA data overcame the absence of some morphological features, reaching a correct identification for 100% of the species. FRIDA, the software used to generate the digital key, has the potential to combine different data sources: we propose to use this feature to include molecular data as well, creating an integrated identification system for plant biodiversity surveys.},
}
@article {pmid22970104,
year = {2012},
author = {Hoef-Emden, K},
title = {Pitfalls of establishing DNA barcoding systems in protists: the cryptophyceae as a test case.},
journal = {PloS one},
volume = {7},
number = {8},
pages = {e43652},
pmid = {22970104},
issn = {1932-6203},
mesh = {Algorithms ; Base Sequence ; Bayes Theorem ; Cryptophyta/classification/*genetics ; Cyclooxygenase 1/genetics ; *DNA Barcoding, Taxonomic ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Monte Carlo Method ; Phylogeny ; Ribosome Subunits, Large, Eukaryotic/genetics ; },
abstract = {A DNA barcode is a preferrably short and highly variable region of DNA supposed to facilitate a rapid identification of species. In many protistan lineages, a lack of species-specific morphological characters hampers an identification of species by light or electron microscopy, and difficulties to perform mating experiments in laboratory cultures also do not allow for an identification of biological species. Thus, testing candidate barcode markers as well as establishment of accurately working species identification systems are more challenging than in multicellular organisms. In cryptic species complexes the performance of a potential barcode marker can not be monitored using morphological characters as a feedback, but an inappropriate choice of DNA region may result in artifactual species trees for several reasons. Therefore a priori knowledge of the systematics of a group is required. In addition to identification of known species, methods for an automatic delimitation of species with DNA barcodes have been proposed. The Cryptophyceae provide a mixture of systematically well characterized as well as badly characterized groups and are used in this study to test the suitability of some of the methods for protists. As species identification method the performance of blast in searches against badly to well-sampled reference databases has been tested with COI-5P and 5'-partial LSU rDNA (domains A to D of the nuclear LSU rRNA gene). In addition the performance of two different methods for automatic species delimitation, fixed thresholds of genetic divergence and the general mixed Yule-coalescent model (GMYC), have been examined. The study demonstrates some pitfalls of barcoding methods that have to be taken care of. Also a best-practice approach towards establishing a DNA barcode system in protists is proposed.},
}
@article {pmid22960880,
year = {2013},
author = {Jordaens, K and Sonet, G and Richet, R and Dupont, E and Braet, Y and Desmyter, S},
title = {Identification of forensically important Sarcophaga species (Diptera: Sarcophagidae) using the mitochondrial COI gene.},
journal = {International journal of legal medicine},
volume = {127},
number = {2},
pages = {491-504},
pmid = {22960880},
issn = {1437-1596},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Entomology ; Female ; Male ; Polymerase Chain Reaction ; Sarcophagidae/classification/*genetics ; Sequence Analysis ; },
abstract = {The identification of species of the forensically important genus Sarcophaga is very difficult and requires strong taxonomic expertise. In this study, we sequenced the mitochondrial cytochrome c oxidase subunit I (COI) gene of 126 specimens of 56 W European Sarcophaga species and added GenBank data to our database to yield a total dataset of 270 COI sequences from 99 Sarcophaga species to evaluate the COI gene as a molecular diagnostic tool for species identification in this genus. Using two simple criteria (Best Match, BM and Best Close Match, BCM), we showed that the identification success using a mini-barcode region of 127 bp was very low (80.7-82.5 %) and the use of this region is not recommended as a species identifier. In contrast, identification success was very high using the standard barcode region (658 bp) or using the entire COI region (1,535 bp) (98.2-99.3 %). Yet, there was a low interspecific sequence divergence (<2 %) in six species groups so that for 16 out of the 99 species (nine of which are of forensic importance), the use of COI barcodes as species identifier should be done with care. For these species, additional markers will be necessary to achieve a 100 % identification success. We further illustrate how such reference databases can improve local reference databases for forensic entomologists.},
}
@article {pmid22958713,
year = {2012},
author = {Ribeiro, AO and Caires, RA and Mariguela, TC and Pereira, LH and Hanner, R and Oliveira, C},
title = {DNA barcodes identify marine fishes of São Paulo State, Brazil.},
journal = {Molecular ecology resources},
volume = {12},
number = {6},
pages = {1012-1020},
doi = {10.1111/1755-0998.12007},
pmid = {22958713},
issn = {1755-0998},
mesh = {Animals ; Aquatic Organisms/*classification/*genetics ; *Biodiversity ; Brazil ; Cluster Analysis ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Fishes/*classification/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {Anthropogenic impacts are an increasing threat to the diversity of fishes, especially in areas around large urban centres, and many effective conservation actions depend on accurate species identification. Considering the utility of DNA barcoding as a global system for species identification and discovery, this study aims to assemble a DNA barcode reference sequence library for marine fishes from the coastal region of São Paulo State, Brazil. The standard 652 bp 'barcode' fragment of the cytochrome c oxidase subunit I (COI) gene was PCR amplified and bidirectionally sequenced from 678 individuals belonging to 135 species. A neighbour-joining analysis revealed that this approach can unambiguously discriminate 97% of the species surveyed. Most species exhibited low intraspecific genetic distances (0.31%), about 43-fold less than the distance among species within a genus. Four species showed higher intraspecific divergences ranging from 2.2% to 7.6%, suggesting overlooked diversity. Notably, just one species-pair exhibited barcode divergences of <1%. This library is a first step to better know the molecular diversity of marine fish species from São Paulo, providing a basis for further studies of this fauna - extending the ability to identify these species from all life stages and even fragmentary remains, setting the stage for a better understanding of interactions among species, calibrating the estimations about species composition and richness in an ecosystem, and providing tools for authenticating bioproducts and monitoring illegal species exploitation.},
}
@article {pmid22954235,
year = {2013},
author = {Li, Y and Wang, J and Peng, Z},
title = {The complete mitochondrial genome of Percocypris pingi (Teleostei, Cypriniformes).},
journal = {Mitochondrial DNA},
volume = {24},
number = {1},
pages = {40-42},
doi = {10.3109/19401736.2012.716055},
pmid = {22954235},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; China ; Cypriniformes/*genetics ; DNA, Intergenic ; DNA, Mitochondrial/genetics ; Gene Order ; Genes, Mitochondrial ; Genes, rRNA ; *Genome, Mitochondrial ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; },
abstract = {Percocypris pingi is an endemic and economic fish species only found in the upper Yangtze River basin in China. It has become endangered in recent years due to overfishing and/or dam construction. However, the available genetic data are still scarce for this species. Here, we sequenced the complete mitochondrial genome sequence of P. pingi using long polymerase chain reactions. The complete mitogenome sequence has 16,586 bp and contains the usual 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA (tRNA) genes, and 1 control region, the gene composition and order of which are similar to most of other vertebrates. Most mitochondrial genes except ND6 and eight tRNAs are encoded on the heavy strand. The overall base composition of the heavy strand is 30.9% A, 25.7% T, 26.6% C, and 16.8% G with a slight AT bias of 56.6%. There are seven regions of gene overlaps totaling 23 bp and 11 intergenic spacer regions totaling 35 bp. Combined with the COI barcoding region sequences of other 25 cyprinids, the phylogenetic position of P. pingi was estimated using neighbor-joining method. The results showed that P. pingi had a close phylogenetic relationship with the species from genus Schizothorax. This mitogenome sequence data of P. pingi would provide the fundamental genetic data for further conservation genetic studies for this endangered fish species.},
}
@article {pmid22953906,
year = {2012},
author = {Li, M and Au, KY and Lam, H and Cheng, L and Jiang, RW and But, PP and Shaw, PC},
title = {Identification of Baiying (Herba Solani Lyrati) commodity and its toxic substitute Xungufeng (Herba Aristolochiae Mollissimae) using DNA barcoding and chemical profiling techniques.},
journal = {Food chemistry},
volume = {135},
number = {3},
pages = {1653-1658},
doi = {10.1016/j.foodchem.2012.06.049},
pmid = {22953906},
issn = {1873-7072},
mesh = {Animals ; Aristolochia/*chemistry/classification/*genetics ; Chlorocebus aethiops ; DNA Barcoding, Taxonomic ; *Drug Contamination ; Drugs, Chinese Herbal/*analysis/standards/toxicity ; HEK293 Cells ; Humans ; Molecular Sequence Data ; Plant Proteins/genetics ; Quality Control ; Solanum/*chemistry/classification/*genetics ; Vero Cells ; },
abstract = {Baiying derived from Solanum lyratum Hance is a commonly consumed natural product for ethnomedical treatment of cancer. One of the substitutes present in the market is a carcinogenic aristolochic acids-containing herb Xungufeng derived from Aristolochia mollissima Thunb. The purpose of this study is to establish DNA barcodes, thin layer chromatography (TLC), high performance liquid chromatography (HPLC) and cytotoxicity assay to differentiate Baiying from Xungufeng. A total of 30 DNA sequences from five DNA barcodes (ITS, matK, rbcL, trnH-psbA and trnL-trnF) were generated to differentiate S. lyratum from A. mollissima and authenticate ten samples of Baiying and Xungufeng commodities. Using aristolochic acids as standard markers, TLC and HPLC analyses also successfully authenticated these commodities. In vitro cytotoxicity assay using HEK-293 and Vero cells demonstrated that Xungufeng was significantly more toxic than Baiying. This is the first study applying an integrated molecular, chemical and biological approach to differentiate traditional Chinese medicine from Aristolochia adulterant.},
}
@article {pmid22952842,
year = {2012},
author = {Stoeckle, MY and Kerr, KC},
title = {Frequency matrix approach demonstrates high sequence quality in avian BARCODEs and highlights cryptic pseudogenes.},
journal = {PloS one},
volume = {7},
number = {8},
pages = {e43992},
pmid = {22952842},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Birds/classification/*genetics ; DNA Barcoding, Taxonomic/*standards ; Databases, Genetic ; Polymorphism, Single Nucleotide/genetics ; Pseudogenes/*genetics ; Quality Control ; Sequence Analysis, DNA/*standards ; },
abstract = {The accuracy of DNA barcode databases is critical for research and practical applications. Here we apply a frequency matrix to assess sequencing errors in a very large set of avian BARCODEs. Using 11,000 sequences from 2,700 bird species, we show most avian cytochrome c oxidase I (COI) nucleotide and amino acid sequences vary within a narrow range. Except for third codon positions, nearly all (96%) sites were highly conserved or limited to two nucleotides or two amino acids. A large number of positions had very low frequency variants present in single individuals of a species; these were strongly concentrated at the ends of the barcode segment, consistent with sequencing error. In addition, a small fraction (0.1%) of BARCODEs had multiple very low frequency variants shared among individuals of a species; these were found to represent overlooked cryptic pseudogenes lacking stop codons. The calculated upper limit of sequencing error was 8 × 10(-5) errors/nucleotide, which was relatively high for direct Sanger sequencing of amplified DNA, but unlikely to compromise species identification. Our results confirm the high quality of the avian BARCODE database and demonstrate significant quality improvement in avian COI records deposited in GenBank over the past decade. This approach has potential application for genetic database quality control, discovery of cryptic pseudogenes, and studies of low-level genetic variation.},
}
@article {pmid22952830,
year = {2012},
author = {Song, J and Shi, L and Li, D and Sun, Y and Niu, Y and Chen, Z and Luo, H and Pang, X and Sun, Z and Liu, C and Lv, A and Deng, Y and Larson-Rabin, Z and Wilkinson, M and Chen, S},
title = {Extensive pyrosequencing reveals frequent intra-genomic variations of internal transcribed spacer regions of nuclear ribosomal DNA.},
journal = {PloS one},
volume = {7},
number = {8},
pages = {e43971},
pmid = {22952830},
issn = {1932-6203},
mesh = {Cell Nucleus/*genetics ; DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/*genetics ; Evolution, Molecular ; Genetic Variation/*genetics ; Genome, Plant/*genetics ; Plants/classification/genetics ; Reproducibility of Results ; *Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Internal transcribed spacer of nuclear ribosomal DNA (nrDNA) is already one of the most popular phylogenetic and DNA barcoding markers. However, the existence of its multiple copies has complicated such usage and a detailed characterization of intra-genomic variations is critical to address such concerns.<br><br>In this study, we used sequence-tagged pyrosequencing and genome-wide analyses to characterize intra-genomic variations of internal transcribed spacer 2 (ITS2) regions from 178 plant species. We discovered that mutation of ITS2 is frequent, with a mean of 35 variants per species. And on average, three of the most abundant variants make up 91% of all ITS2 copies. Moreover, we found different congeneric species share identical variants in 13 genera. Interestingly, different species across different genera also share identical variants. In particular, one minor variant of ITS2 in Eleutherococcus giraldii was found identical to the ITS2 major variant of Panax ginseng, both from Araliaceae family. In addition, DNA barcoding gap analysis showed that the intra-genomic distances were markedly smaller than those of the intra-specific or inter-specific variants. When each of 5543 variants were examined for its species discrimination efficiency, a 97% success rate was obtained at the species level.<br><br>CONCLUSIONS: Identification of identical ITS2 variants across intra-generic or inter-generic species revealed complex species evolutionary history, possibly, horizontal gene transfer and ancestral hybridization. Although intra-genomic multiple variants are frequently found within each genome, the usage of the major variants alone is sufficient for phylogeny construction and species determination in most cases. Furthermore, the inclusion of minor variants further improves the resolution of species identification.},
}
@article {pmid22952792,
year = {2012},
author = {Kanzaki, N and Giblin-Davis, RM and Scheffrahn, RH and Taki, H and Esquivel, A and Davies, KA and Herre, EA},
title = {Reverse taxonomy for elucidating diversity of insect-associated nematodes: a case study with termites.},
journal = {PloS one},
volume = {7},
number = {8},
pages = {e43865},
pmid = {22952792},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; Classification/*methods ; Isoptera/*classification ; Nematoda/*parasitology ; Phylogeny ; },
abstract = {BACKGROUND: The molecular operational taxonomic unit (MOTU) has recently been applied to microbial and microscopic animal biodiversity surveys. However, in many cases, some of the MOTUs cannot be definitively tied to any of the taxonomic groups in current databases. To surmount these limitations, the concept of "reverse taxonomy" has been proposed, i.e. to primarily list the MOTUs with morphological information, and then identify and/or describe them at genus/species level using subsamples or by re-isolating the target organisms. Nevertheless, the application of "reverse taxonomy" has not been sufficiently evaluated. Therefore, the practical applicability of "reverse taxonomy" is tested using termite-associated nematodes as a model system for phoretic/parasitic organisms which have high habitat specificity and a potential handle (their termite host species) for re-isolation attempts.<br><br>METHODOLOGY: Forty-eight species (from 298 colonies) of termites collected from the American tropics and subtropics were examined for their nematode associates using the reverse taxonomy method and culturing attempts (morphological identification and further sequencing efforts). The survey yielded 51 sequence types (&#x200a;=&#x200a; MOTUs) belonging to 19 tentatively identified genera. Within these, four were identified based on molecular data with preliminary morphological observation, and an additional seven were identified or characterized from successful culturing, leaving eight genera unidentified.<br><br>CONCLUSIONS: That 1/3 of the genera were not successfully identified suggests deficiencies in the depth of available sequences in the database and biological characters, i.e. usually isolated as phoretic/parasitic stages which are not available for morphological identification, and too many undiscovered lineages of nematodes. Although there still is the issue of culturability of nematodes, culturing attempts could help to make reverse taxonomy methods more effective. However, expansion of the database, i.e., production of more DNA barcodes tied to biological information by finding and characterizing additional new and known lineages, is necessary for analyzing functional diversity.},
}
@article {pmid22952770,
year = {2012},
author = {Särkinen, T and Staats, M and Richardson, JE and Cowan, RS and Bakker, FT},
title = {How to open the treasure chest? Optimising DNA extraction from herbarium specimens.},
journal = {PloS one},
volume = {7},
number = {8},
pages = {e43808},
pmid = {22952770},
issn = {1932-6203},
mesh = {Biodiversity ; Chemical Fractionation/*methods ; DNA, Plant/genetics/*isolation &amp; purification ; DNA-Directed DNA Polymerase/metabolism ; Desiccation ; Phylogeny ; *Plants/classification ; Polymerase Chain Reaction ; *Preservation, Biological ; Silicon Dioxide/chemistry ; },
abstract = {Herbarium collections are potentially an enormous resource for DNA studies, but the use of herbarium specimens in molecular studies has thus far been slowed down by difficulty in obtaining amplifiable DNA. Here we compare a set of commercially available DNA extraction protocols and their performance in terms of DNA purity and yield, and PCR amplification success as measured by using three differentially sized markers, the rbcL barcoding marker (cpDNA), the LEAFY exon 3 (nrDNA), and the trnL((UAA)) P6 loop (cpDNA). Results reveal large differences between extraction methods, where DNA purity rather than yield is shown to be strongly correlated with PCR success. Amplicon size shows similarly strong correlation with PCR success, with the shortest fragment showing the highest success rate (78%, P6 loop, 10-143 base pairs (bp)) and the largest fragment the lowest success (10%, rbcL, 670 bp). The effect of specimen preparation method on PCR success was also tested. Results show that drying method strongly affects PCR success, especially the availability of fragments longer than 250 bp, where longer fragments are more available for PCR amplification in air dried material compared to alcohol dried specimens. Results from our study indicate that projects relying on poor-quality starting material such as herbarium or scat samples should focus on extracting pure DNA and aim to amplify short target regions (<200-300 bp) in order to maximise outcomes. Development of shorter barcoding regions, or mini-barcodes within existing ones should be of high importance as only a few options are currently available; this is particularly important if we hope to incorporate the millions of herbarium samples available into barcoding initiatives and other molecular studies.},
}
@article {pmid22952689,
year = {2012},
author = {Lu, L and Chesters, D and Zhang, W and Li, G and Ma, Y and Ma, H and Song, X and Wu, H and Meng, F and Zhu, C and Liu, Q},
title = {Small mammal investigation in spotted fever focus with DNA-barcoding and taxonomic implications on rodents species from Hainan of China.},
journal = {PloS one},
volume = {7},
number = {8},
pages = {e43479},
pmid = {22952689},
issn = {1932-6203},
mesh = {Animals ; China ; Cluster Analysis ; Cytochromes b/metabolism ; DNA Barcoding, Taxonomic/*methods ; Ecology ; Electron Transport Complex IV/metabolism ; Geography ; Models, Genetic ; Phylogeny ; Phylogeography ; Rats ; Rickettsia Infections/*genetics ; Rodentia/*genetics ; Species Specificity ; },
abstract = {Although mammals are a well-studied group of animals, making accurate field identification of small mammals is still complex because of morphological variation across developmental stages, color variation of pelages, and often damaged osteological and dental characteristics. In 2008, small mammals were collected for an epidemiological study of a spotted fever outbreak in Hainan, China. Ten species of small mammals were identified by morphological characters in the field, most using pelage color characters only. The study is extended here, in order to assess whether DNA barcoding would be suitable as an identification tool in these small mammals. Barcode clusters showed some incongruence with morphospecies, especially for some species of Rattus and Niviventer, so molecular delineation was carried out with an expanded dataset of combined cytochrome b (Cyt-b) and cytochrome c oxidase subunit I (COI) sequences. COI sequences were successfully amplified from 83% of collected mammals, but failed in all specimens of Suncus murinus, which were thus excluded in DNA barcoding analysis. Of note, ten molecular taxonomic units were found from samples of nine morphologically identified species. Accordingly, 11 species of small mammals were present in the investigated areas, including four Rattus species, three Niviventer species, Callosciurus erythraeus, Neohylomys hainanensis, Tupaia belangeri, and Suncus murinus. Based on the results of the phylogenetic and molecular delineation analyses, the systematic status of some rodent species should be redefined. R. rattus hainanicus and R. rattus sladeni are synonyms of R. andamanensis. R. losea from China and Southeast Asia comprises two independent species: R. losea and R. sakeratensis. Finally, the taxonomic status of three putative species of Niviventer should be further confirmed according to morphological, molecular and ecological characters.},
}
@article {pmid22951379,
year = {2013},
author = {Whang, I and Kang, HS and Lee, J},
title = {Identification of scuticociliates (Pseudocohnilembus persalinus, P. longisetus, Uronema marinum and Miamiensis avidus) based on the cox1 sequence.},
journal = {Parasitology international},
volume = {62},
number = {1},
pages = {7-13},
doi = {10.1016/j.parint.2012.08.002},
pmid = {22951379},
issn = {1873-0329},
mesh = {Animals ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/*genetics ; Molecular Sequence Data ; Oligohymenophorea/*classification/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Homology, Nucleic Acid ; Species Specificity ; },
abstract = {Scuticociliatosis is characterized as highly histophagous, causing systemic tissue destruction and high mortality in cultured marine fish. Some of the scuticociliates have been implicated as the causative agents of scuticociliatosis. Here, we describe our study to differentially identify various species in complex animal-sourced samples, namely olive flounder Paralichthys olivaceus and black rockfish Sebastes schlegelii suffering from scuticociliatosis. The mitochondrial cytochrome c oxidase 1 (cox1) gene from the scuticociliates was amplified and sequenced. The divergence percentage of small subunit ribosomal DNA sequence between average scuticociliate species was found to be low (8.3%) but the genetic divergence of cox1 sequence reached 23.5%, suggesting that a hyper-variable region of the cox1 gene could be used as a diagnostic DNA barcoding region. Thus, we developed species-specific primers for use in multiplex PCR of complex (pooled) samples. The primers yielded species-specific fragments (of distinct size) that allowed for simple, rapid, and effective identification and differentiation of multiple species present in a single sample.},
}
@article {pmid22951138,
year = {2012},
author = {Hajibabaei, M},
title = {The golden age of DNA metasystematics.},
journal = {Trends in genetics : TIG},
volume = {28},
number = {11},
pages = {535-537},
doi = {10.1016/j.tig.2012.08.001},
pmid = {22951138},
issn = {0168-9525},
mesh = {Animals ; DNA/*genetics ; Genetic Techniques ; Genetic Variation ; Humans ; },
abstract = {The convergence of next-generation sequencing and DNA barcoding has sparked a golden age of 'DNA metasystematics', allowing researchers to understand the biodiversity of an entire ecosystem solely through DNA information, and transforming the way we view the living world around us.},
}
@article {pmid22942731,
year = {2012},
author = {Liu, J and Provan, J and Gao, LM and Li, DZ},
title = {Sampling strategy and potential utility of indels for DNA barcoding of closely related plant species: a case study in taxus.},
journal = {International journal of molecular sciences},
volume = {13},
number = {7},
pages = {8740-8751},
pmid = {22942731},
issn = {1422-0067},
mesh = {Chloroplasts/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Chloroplast/*genetics ; Taxus/*genetics ; },
abstract = {Although DNA barcoding has become a useful tool for species identification and biodiversity surveys in plant sciences, there remains little consensus concerning appropriate sampling strategies and the treatment of indels. To address these two issues, we sampled 39 populations for nine Taxus species across their entire ranges, with two to three individuals per population randomly sampled. We sequenced one core DNA barcode (matK) and three supplementary regions (trnH-psbA, trnL-trnF and ITS) for all samples to test the effects of sampling design and the utility of indels. Our results suggested that increasing sampling within-population did not change the clustering of individuals, and that meant within-population P-distances were zero for most populations in all regions. Based on the markers tested here, comparison of methods either including or excluding indels indicated that discrimination and nodal support of monophyletic groups were significantly increased when indels were included. Thus we concluded that one individual per population was adequate to represent the within-population variation in these species for DNA barcoding, and that intra-specific sampling was best focused on representing the entire ranges of certain taxa. We also found that indels occurring in the chloroplast trnL-trnF and trnH-psbA regions were informative to differentiate among for closely related taxa barcoding, and we proposed that indel-coding methods should be considered for use in future for closed related plant species DNA barcoding projects on or below generic level.},
}
@article {pmid22939981,
year = {2012},
author = {Hashimshony, T and Wagner, F and Sher, N and Yanai, I},
title = {CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification.},
journal = {Cell reports},
volume = {2},
number = {3},
pages = {666-673},
doi = {10.1016/j.celrep.2012.08.003},
pmid = {22939981},
issn = {2211-1247},
mesh = {Animals ; Caenorhabditis elegans ; Gene Expression Regulation/physiology ; Multiplex Polymerase Chain Reaction/*methods ; RNA, Helminth/biosynthesis/genetics ; RNA, Messenger/biosynthesis/genetics ; Reverse Transcriptase Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA/*methods ; },
abstract = {High-throughput sequencing has allowed for unprecedented detail in gene expression analyses, yet its efficient application to single cells is challenged by the small starting amounts of RNA. We have developed CEL-Seq, a method for overcoming this limitation by barcoding and pooling samples before linearly amplifying mRNA with the use of one round of in vitro transcription. We show that CEL-Seq gives more reproducible, linear, and sensitive results than a PCR-based amplification method. We demonstrate the power of this method by studying early C. elegans embryonic development at single-cell resolution. Differential distribution of transcripts between sister cells is seen as early as the two-cell stage embryo, and zygotic expression in the somatic cell lineages is enriched for transcription factors. The robust transcriptome quantifications enabled by CEL-Seq will be useful for transcriptomic analyses of complex tissues containing populations of diverse cell types.},
}
@article {pmid22935316,
year = {2013},
author = {Webster, BL and Webster, JP and Gouvras, AN and Garba, A and Lamine, MS and Diaw, OT and Seye, MM and Tchuem Tchuenté, LA and Simoonga, C and Mubila, L and Mwanga, JR and Lwambo, NJ and Kabatereine, NB and Lange, CN and Kariuki, C and Mkoji, GM and Rollinson, D and Stothard, JR},
title = {DNA 'barcoding' of Schistosoma mansoni across sub-Saharan Africa supports substantial within locality diversity and geographical separation of genotypes.},
journal = {Acta tropica},
volume = {128},
number = {2},
pages = {250-260},
doi = {10.1016/j.actatropica.2012.08.009},
pmid = {22935316},
issn = {1873-6254},
mesh = {Africa South of the Sahara ; Animals ; Child ; Child, Preschool ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; DNA, Helminth/chemistry/genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Genotype ; Humans ; Molecular Sequence Data ; *Phylogeography ; Schistosoma mansoni/*classification/*genetics/isolation &amp; purification ; Schistosomiasis mansoni/*parasitology ; Sequence Analysis, DNA ; },
abstract = {Schistosoma mansoni is a widespread human helminth and causes intestinal schistosomiasis in 54 countries, mainly across Africa but also in Madagascar, the Arabian Peninsula and the neotropics. The geographical range of this parasite relies on the distribution of certain species of freshwater pulmonate snails of the genus Biomphalaria. Whilst S. mansoni is known to exhibit high population diversity the true extent of this diversity is still to be fully elucidated as sampling of this taxon progressively accrues. Here a DNA 'barcoding' approach is taken using sequence analysis of a 450bp region within the mitochondrial cox1 gene to assess the genetic diversity within a large number of S. mansoni larval stages collected from their natural human hosts across sub-Saharan Africa. Five hundred and sixty one individual parasite samples were examined from 22 localities and 14 countries. Considerable within-species diversity was found with 120 unique haplotypes splitting geographically into five discrete lineages. The highest diversity was found in East Africa with samples forming three of the five lineages. Less diversity was found in the Far and Central Western regions of Africa with haplotypes from the New World showing a close affinity to the Far Western African S. mansoni populations supporting the hypothesis of a colonisation of South America via the West African slave trade. The data are discussed in relation to parasite diversity and disease epidemiology.},
}
@article {pmid22935171,
year = {2012},
author = {Dong, H and Liu, J and Zhu, H and Ou, CY and Xing, W and Qiu, M and Zhang, G and Xiao, Y and Yao, J and Pan, P and Jiang, Y},
title = {Two types of nanoparticle-based bio-barcode amplification assays to detect HIV-1 p24 antigen.},
journal = {Virology journal},
volume = {9},
number = {},
pages = {180},
pmid = {22935171},
issn = {1743-422X},
mesh = {Antibodies, Monoclonal ; Electrophoresis, Agar Gel/methods ; HIV Antibodies ; HIV Core Protein p24/*analysis ; HIV Infections/*diagnosis/virology ; HIV-1/immunology/*isolation &amp; purification ; Humans ; Molecular Diagnostic Techniques/*methods ; *Nanoparticles ; Nucleic Acid Amplification Techniques/*methods ; Sensitivity and Specificity ; Virology/*methods ; },
abstract = {BACKGROUND: HIV-1 p24 antigen is a major viral component of human immunodeficiency virus type 1 (HIV-1) which can be used to identify persons in the early stage of infection and transmission of HIV-1 from infected mothers to infants. The detection of p24 is usually accomplished by using an enzyme-linked immunosorbent assay (ELISA) with low detection sensitivity. Here we report the use of two bio-barcode amplification (BCA) assays combined with polymerase chain reaction (PCR) and gel electrophoresis to quantify HIV-1 p24 antigen.<br><br>METHOD: A pair of anti-p24 monoclonal antibodies (mAbs) were used in BCA assays to capture HIV-1 p24 antigen in a sandwich format and allowed for the quantitative measurement of captured p24 using PCR and gel electrophoresis. The first 1&#x2009;G12 mAb was coated on microplate wells or magnetic microparticles (MMPs) to capture free p24 antigens. Captured p24 in turn captured 1D4 mAb coated gold nanoparticle probes (GNPs) containing double-stranded DNA oligonucleotides. One strand of the oligonucleotides was covalently immobilized whereas the unbound complimentary bio-barcode DNA strand could be released upon heating. The released bio-barcode DNA was amplified by PCR, electrophoresed in agarose gel and quantified.<br><br>RESULTS: The in-house ELISA assay was found to quantify p24 antigen with a limit of detection (LOD) of 1,000&#x2009;pg/ml and a linear range between 3,000 and 100,000&#x2009;pg/ml. In contrast, the BCA-based microplate method yielded an LOD of 1&#x2009;pg/ml and a linear detection range from 1 to 10,000&#x2009;pg/ml. The BCA-based MMP method yielded an LOD of 0.1&#x2009;pg/ml and a linear detection range from 0.1 to 1,000&#x2009;pg/ml.<br><br>CONCLUSIONS: When combined with PCR and simple gel electrophoresis, BCA-based microplate and MMPs assays can be used to quantify HIV-1 p24 antigen. These methods are 3-4 orders of magnitude more sensitive than our in-house ELISA-based assay and may provide a useful approach to detect p24 in patients newly infected with HIV.},
}
@article {pmid22931682,
year = {2012},
author = {Magnacca, KN and Brown, MJ},
title = {DNA barcoding a regional fauna: Irish solitary bees.},
journal = {Molecular ecology resources},
volume = {12},
number = {6},
pages = {990-998},
doi = {10.1111/1755-0998.12001},
pmid = {22931682},
issn = {1755-0998},
mesh = {Animals ; Bees/*classification/*genetics ; *Biota ; *DNA Barcoding, Taxonomic ; Entomology/*methods ; Ireland ; Molecular Sequence Data ; Sensitivity and Specificity ; Sequence Analysis, DNA ; },
abstract = {As the globally dominant group of pollinators, bees provide a key ecosystem service for natural and agricultural landscapes. Their corresponding global decline thus poses an important threat to plant populations and the ecosystems they support. Bee conservation requires rapid and effective tools to identify and delineate species. Here, we apply DNA barcoding to Irish solitary bees as the first step towards a DNA barcode library for European solitary bees. Using the standard barcoding sequence, we were able to identify 51 of 55 species. Potential problems included a suite of species in the genus Andrena, which were recalcitrant to sequencing, mitochondrial heteroplasmy and parasitic flies, which led to the production of erroneous sequences from DNA extracts. DNA barcoding enabled the assignment of morphologically unidentifiable females of the parasitic genus Sphecodes to their nominal taxa. It also enabled correction of the Irish bee list for morphologically inaccurately identified specimens. However, the standard COI barcode was unable to differentiate the recently diverged taxa Sphecodes ferruginatus and S. hyalinatus. Overall, our results show that DNA barcoding provides an excellent identification tool for Irish solitary bees and should be rolled out to provide a database for solitary bees globally.},
}
@article {pmid22919833,
year = {2012},
author = {Pei, NC},
title = {[Identification of plant species based on DNA barcode technology].},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {23},
number = {5},
pages = {1240-1246},
pmid = {22919833},
issn = {1001-9332},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*analysis/genetics/isolation &amp; purification ; Ecosystem ; Plants/*classification/*genetics ; Species Specificity ; },
abstract = {It is crucial for the studies of taxonomy and biodiversity by using DNA barcode technology to fast and accurately make species identification in the forests across tropics and temperate zones. In this study, the 183 plant species in a 20 hm2 subtropical forest plot in Dinghushan (DHS) National Nature Reserve of South China were sampled and sequenced, and the matK, rbcL, and psbA-trnH were employed to generate multi-locus barcodes. For the plot, the psbA-trnH possessed the highest integral success rate, i. e., the product of sequencing recovery and correct species identification (75%), followed by matK (70%), and rbcL (56%). A combination of three-locus barcode (matK, rbcL and psbA-trnH) could identify greater than 87% of the total species, followed by two-locus barcode (85% for matK+psbA-trnH, 83% for rbcL+psbA-trnH, and 81% for matK+rbcL). A comparison was made with the previously published results from one subtropical forest plot (LFDP in Puerto Rico, 143 species) and two tropical forest plots (BCI in Panama, 296 species; and NRS in French Guiana, 254 species) to evaluate the universality and species identification correctness of the proposed DNA barcodes for these four forest plots. For the plots in tropics and subtropics, the sequencing success rate of rbcL, psbA-trnH and matK were 93% and 95.1%, 91.5% and 94.6%, and 68.5% and 79.7%, respectively. The combination of matK + rbcL showed a high identification capacity in geographically restricted regions in taxonomic groups, whereas the three-locus barcode had a high rate of correct species identification both in tropics (84%) and in subtropics (90%).},
}
@article {pmid22917848,
year = {2013},
author = {Forsdyke, DR},
title = {Base composition, speciation, and barcoding.},
journal = {Trends in ecology &amp; evolution},
volume = {28},
number = {2},
pages = {73-74},
doi = {10.1016/j.tree.2012.08.010},
pmid = {22917848},
issn = {1872-8383},
mesh = {Base Composition ; DNA/*analysis ; *DNA Barcoding, Taxonomic ; *Genetic Speciation ; },
abstract = {Cryptic mutations producing no observable effect on phenotype can both spark divergence into species and assist species identification. Unlike most protein-encoding sequences, a barcode sequence of great utility in phylogenetic analysis displays few interspecies differences at amino acid-determining codon positions (static conventional phenotype), but many at third codon positions (mobile genome phenotype).},
}
@article {pmid22917217,
year = {2012},
author = {Mejía, O and León-Romero, Y and Soto-Galera, E},
title = {DNA barcoding of the ichthyofauna of Pánuco-Tamesí complex: evidence for taxonomic conflicts in some groups.},
journal = {Mitochondrial DNA},
volume = {23},
number = {6},
pages = {471-476},
doi = {10.3109/19401736.2012.710207},
pmid = {22917217},
issn = {1940-1744},
mesh = {Animals ; Cichlids/*classification/*genetics ; Conflict, Psychological ; DNA Barcoding, Taxonomic/*methods/standards ; Fresh Water ; Geography ; Mexico ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The Pánuco-Tamesí complex in eastern Mexico is globally recognized as an important ecoregion due to its high level of endemism. In this study, DNA barcodes were generated for 152 individuals of 31 species. Additionally, 170 DNA barcodes for the related species available in the Barcode of Life Database (BOLD) system were included to test the ability of barcoding technique to discriminate between the closely related species. DNA barcoding allowed the discrimination of 79.2% of the analyzed species; poor resolution was observed in four genera in which the levels of resolution ranged from 16.6% in the genus Herichthys to 77.7% in the genus Xiphophorus. The results of this study demonstrate that DNA barcoding is a useful exploratory tool but fails to discriminate between closely related species.},
}
@article {pmid22916158,
year = {2012},
author = {Stern, RF and Andersen, RA and Jameson, I and Küpper, FC and Coffroth, MA and Vaulot, D and Le Gall, F and Véron, B and Brand, JJ and Skelton, H and Kasai, F and Lilly, EL and Keeling, PJ},
title = {Evaluating the ribosomal internal transcribed spacer (ITS) as a candidate dinoflagellate barcode marker.},
journal = {PloS one},
volume = {7},
number = {8},
pages = {e42780},
pmid = {22916158},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Dinoflagellida/classification/enzymology/*genetics ; Electron Transport Complex IV/genetics ; *Genetic Markers ; Phylogeny ; Ribosomes/*metabolism ; },
abstract = {BACKGROUND: DNA barcoding offers an efficient way to determine species identification and to measure biodiversity. For dinoflagellates, an ancient alveolate group of about 2000 described extant species, DNA barcoding studies have revealed large amounts of unrecognized species diversity, most of which is not represented in culture collections. To date, two mitochondrial gene markers, Cytochrome Oxidase I (COI) and Cytochrome b oxidase (COB), have been used to assess DNA barcoding in dinoflagellates, and both failed to amplify all taxa and suffered from low resolution. Nevertheless, both genes yielded many examples of morphospecies showing cryptic speciation and morphologically distinct named species being genetically similar, highlighting the need for a common marker. For example, a large number of cultured Symbiodinium strains have neither taxonomic identification, nor a common measure of diversity that can be used to compare this genus to other dinoflagellates.<br><br>The purpose of this study was to evaluate the Internal Transcribed Spacer units 1 and 2 (ITS) of the rDNA operon, as a high resolution marker for distinguishing species dinoflagellates in culture. In our study, from 78 different species, the ITS barcode clearly differentiated species from genera and could identify 96% of strains to a known species or sub-genus grouping. 8.3% showed evidence of being cryptic species. A quarter of strains identified had no previous species identification. The greatest levels of hidden biodiversity came from Scrippsiella and the Pfiesteriaceae family, whilst Heterocapsa strains showed a high level of mismatch to their given species name.<br><br>CONCLUSIONS/SIGNIFICANCE: The ITS marker was successful in confirming species, revealing hidden diversity in culture collections. This marker, however, may have limited use for environmental barcoding due to paralogues, the potential for unidentifiable chimaeras and priming across taxa. In these cases ITS would serve well in combination with other markers or for specific taxon studies.},
}
@article {pmid22916072,
year = {2012},
author = {Zhang, Y and Wang, TH},
title = {Quantum dot enabled molecular sensing and diagnostics.},
journal = {Theranostics},
volume = {2},
number = {7},
pages = {631-654},
pmid = {22916072},
issn = {1838-7640},
support = {R01 CA155305/CA/NCI NIH HHS/United States ; U54 CA151838/CA/NCI NIH HHS/United States ; },
abstract = {Since its emergence, semiconductor nanoparticles known as quantum dots (QDs) have drawn considerable attention and have quickly extended their applicability to numerous fields within the life sciences. This is largely due to their unique optical properties such as high brightness and narrow emission band as well as other advantages over traditional organic fluorophores. New molecular sensing strategies based on QDs have been developed in pursuit of high sensitivity, high throughput, and multiplexing capabilities. For traditional biological applications, QDs have already begun to replace traditional organic fluorophores to serve as simple fluorescent reporters in immunoassays, microarrays, fluorescent imaging applications, and other assay platforms. In addition, smarter, more advanced QD probes such as quantum dot fluorescence resonance energy transfer (QD-FRET) sensors, quenching sensors, and barcoding systems are paving the way for highly-sensitive genetic and epigenetic detection of diseases, multiplexed identification of infectious pathogens, and tracking of intracellular drug and gene delivery. When combined with microfluidics and confocal fluorescence spectroscopy, the detection limit is further enhanced to single molecule level. Recently, investigations have revealed that QDs participate in series of new phenomena and exhibit interesting non-photoluminescent properties. Some of these new findings are now being incorporated into novel assays for gene copy number variation (CNV) studies and DNA methylation analysis with improved quantification resolution. Herein, we provide a comprehensive review on the latest developments of QD based molecular diagnostic platforms in which QD plays a versatile and essential role.},
}
@article {pmid22912682,
year = {2012},
author = {Cruz-Barraza, JA and Carballo, JL and Rocha-Olivares, A and Ehrlich, H and Hog, M},
title = {Integrative taxonomy and molecular phylogeny of genus Aplysina (Demospongiae: Verongida) from Mexican Pacific.},
journal = {PloS one},
volume = {7},
number = {8},
pages = {e42049},
pmid = {22912682},
issn = {1932-6203},
mesh = {Animals ; Caribbean Region ; Classification/*methods ; DNA, Mitochondrial/genetics ; Ecosystem ; Evolution, Molecular ; Mexico ; Pacific Ocean ; *Phylogeny ; Porifera/anatomy &amp; histology/*classification/genetics ; Sequence Analysis, DNA ; },
abstract = {Integrative taxonomy provides a major approximation to species delimitation based on integration of different perspectives (e.g. morphology, biochemistry and DNA sequences). The aim of this study was to assess the relationships and boundaries among Eastern Pacific Aplysina species using morphological, biochemical and molecular data. For this, a collection of sponges of the genus Aplysina from the Mexican Pacific was studied on the basis of their morphological, chemical (chitin composition), and molecular markers (mitochondrial COI and nuclear ribosomal rDNA: ITS1-5.8-ITS2). Three morphological species were identified, two of which are new to science. A. clathrata sp. nov. is a yellow to yellow-reddish or -brownish sponge, characterized by external clathrate-like morphology; A. revillagigedi sp. nov. is a lemon yellow to green, cushion-shaped sometimes lobate sponge, characterized by conspicuous oscules, which are slightly elevated and usually linearly distributed on rims; and A. gerardogreeni a known species distributed along the Mexican Pacific coast. Chitin was identified as the main structural component within skeletons of the three species using FTIR, confirming that it is shared among Verongida sponges. Morphological differences were confirmed by DNA sequences from nuclear ITS1-5.8-ITS2. Mitochondrial COI sequences showed extremely low but diagnostic variability for Aplysina revillagigedi sp. nov., thus our results corroborate that COI has limited power for DNA-barcoding of sponges and should be complemented with other markers (e.g. rDNA). Phylogenetic analyses of Aplysina sequences from the Eastern Pacific and Caribbean, resolved two allopatric and reciprocally monophyletic groups for each region. Eastern Pacific species were grouped in general accordance with the taxonomic hypothesis based on morphological characters. An identification key of Eastern Pacific Aplysina species is presented. Our results constitute one of the first approximations to integrative taxonomy, phylogeny and evolutionary biogeography of Eastern Pacific marine sponges; an approach that will significantly contribute to our better understanding of their diversity and evolutionary history.},
}
@article {pmid22906810,
year = {2012},
author = {Lou, M and Golding, GB},
title = {The effect of sampling from subdivided populations on species identification with DNA barcodes using a Bayesian statistical approach.},
journal = {Molecular phylogenetics and evolution},
volume = {65},
number = {2},
pages = {765-773},
doi = {10.1016/j.ympev.2012.07.033},
pmid = {22906810},
issn = {1095-9513},
mesh = {Algorithms ; Animals ; *Bayes Theorem ; Computational Biology/*methods ; Computer Simulation ; *DNA Barcoding, Taxonomic ; *Models, Genetic ; Moths/classification/genetics ; },
abstract = {Barcoding is an initiative to define a standard fragment of DNA to be used to assign sequences of unknown origin to existing known species whose sequences are recorded in databases. This is a difficult task when species are closely related and individuals of these species might have more than one origin. Using a previously introduced Bayesian statistical tree-less assignment algorithm based on segregating sites, we examine how it functions in the presence of hidden population subdivision with closely related species using simulations. Not surprisingly, adding samples to the database from a greater proportion of the species range leads to a consistently higher number of accurate results. Without such samples, query sequences that originate from outside of the sampled range are easily misinterpreted as coming from other species. However, we show that even the addition of a single sample from a different subpopulation is sufficient to greatly increase the probability of placement of unknown queries into the correct species group. This study highlights the importance of broad sampling, even with five reference samples per species, in the creation of a reference database.},
}
@article {pmid22905208,
year = {2012},
author = {Pinto, AJ and Raskin, L},
title = {PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets.},
journal = {PloS one},
volume = {7},
number = {8},
pages = {e43093},
pmid = {22905208},
issn = {1932-6203},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Computational Biology/methods ; DNA Primers/genetics ; Databases, Genetic ; Genes, Archaeal ; Genes, Bacterial ; Genetic Techniques ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; },
abstract = {As 16S rRNA gene targeted massively parallel sequencing has become a common tool for microbial diversity investigations, numerous advances have been made to minimize the influence of sequencing and chimeric PCR artifacts through rigorous quality control measures. However, there has been little effort towards understanding the effect of multi-template PCR biases on microbial community structure. In this study, we used three bacterial and three archaeal mock communities consisting of, respectively, 33 bacterial and 24 archaeal 16S rRNA gene sequences combined in different proportions to compare the influences of (1) sequencing depth, (2) sequencing artifacts (sequencing errors and chimeric PCR artifacts), and (3) biases in multi-template PCR, towards the interpretation of community structure in pyrosequencing datasets. We also assessed the influence of each of these three variables on α- and β-diversity metrics that rely on the number of OTUs alone (richness) and those that include both membership and the relative abundance of detected OTUs (diversity). As part of this study, we redesigned bacterial and archaeal primer sets that target the V3-V5 region of the 16S rRNA gene, along with multiplexing barcodes, to permit simultaneous sequencing of PCR products from the two domains. We conclude that the benefits of deeper sequencing efforts extend beyond greater OTU detection and result in higher precision in β-diversity analyses by reducing the variability between replicate libraries, despite the presence of more sequencing artifacts. Additionally, spurious OTUs resulting from sequencing errors have a significant impact on richness or shared-richness based α- and β-diversity metrics, whereas metrics that utilize community structure (including both richness and relative abundance of OTUs) are minimally affected by spurious OTUs. However, the greatest obstacle towards accurately evaluating community structure are the errors in estimated mean relative abundance of each detected OTU due to biases associated with multi-template PCR reactions.},
}
@article {pmid22902532,
year = {2012},
author = {Bodenmiller, B and Zunder, ER and Finck, R and Chen, TJ and Savig, ES and Bruggner, RV and Simonds, EF and Bendall, SC and Sachs, K and Krutzik, PO and Nolan, GP},
title = {Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators.},
journal = {Nature biotechnology},
volume = {30},
number = {9},
pages = {858-867},
pmid = {22902532},
issn = {1546-1696},
support = {T32 CA009302/CA/NCI NIH HHS/United States ; R01 CA130826/CA/NCI NIH HHS/United States ; P01 CA034233/CA/NCI NIH HHS/United States ; U19 AI100627/AI/NIAID NIH HHS/United States ; F32 GM093508/GM/NIGMS NIH HHS/United States ; T32 AI007328/AI/NIAID NIH HHS/United States ; F32GM093508/GM/NIGMS NIH HHS/United States ; U54 CA149145/CA/NCI NIH HHS/United States ; HHSN272200700038C/AI/NIAID NIH HHS/United States ; HHSN268201000034C/HL/NHLBI NIH HHS/United States ; U19 AI057229/AI/NIAID NIH HHS/United States ; T15 LM007033/LM/NLM NIH HHS/United States ; 1R01CA130826/CA/NCI NIH HHS/United States ; },
mesh = {Chelating Agents ; Flow Cytometry/*methods ; Heterocyclic Compounds, 1-Ring ; High-Throughput Screening Assays/*methods ; Humans ; K562 Cells ; Leukocytes, Mononuclear/*cytology/drug effects/metabolism ; Phosphorylation ; Principal Component Analysis ; Protein Kinase Inhibitors/pharmacology ; Signal Transduction ; Systems Biology/*methods ; },
abstract = {Mass cytometry facilitates high-dimensional, quantitative analysis of the effects of bioactive molecules on human samples at single-cell resolution, but instruments process only one sample at a time. Here we describe mass-tag cellular barcoding (MCB), which increases mass cytometry throughput by using n metal ion tags to multiplex up to 2n samples. We used seven tags to multiplex an entire 96-well plate, and applied MCB to characterize human peripheral blood mononuclear cell (PBMC) signaling dynamics and cell-to-cell communication, signaling variability between PBMCs from eight human donors, and the effects of 27 inhibitors on this system. For each inhibitor, we measured 14 phosphorylation sites in 14 PBMC types at 96 conditions, resulting in 18,816 quantified phosphorylation levels from each multiplexed sample. This high-dimensional, systems-level inquiry allowed analysis across cell-type and signaling space, reclassified inhibitors and revealed off-target effects. High-content, high-throughput screening with MCB should be useful for drug discovery, preclinical testing and mechanistic investigation of human disease.},
}
@article {pmid22891635,
year = {2012},
author = {Dupuis, JR and Roe, AD and Sperling, FA},
title = {Multi-locus species delimitation in closely related animals and fungi: one marker is not enough.},
journal = {Molecular ecology},
volume = {21},
number = {18},
pages = {4422-4436},
doi = {10.1111/j.1365-294X.2012.05642.x},
pmid = {22891635},
issn = {1365-294X},
mesh = {Amplified Fragment Length Polymorphism Analysis ; Animals ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Fungi/*classification/genetics ; *Genetic Markers ; Genetic Variation ; Microsatellite Repeats ; Multilocus Sequence Typing/*methods ; *Phylogeny ; Species Specificity ; },
abstract = {Despite taxonomy's 250-year history, the past 20 years have borne witness to remarkable advances in technology and techniques, as well as debate. DNA barcoding has generated a substantial proportion of this debate, with its proposition that a single mitochondrial sequence will consistently identify and delimit species, replacing more evidence-rich and time-intensive methods. Although mitochondrial DNA (mtDNA) has since been the focus of voluminous discussion and case studies, little effort has been made to comprehensively evaluate its success in delimiting closely related species. We have conducted the first broadly comparative literature review addressing the efficacy of molecular markers for delimiting such species over a broad taxonomic range. By considering only closely related species, we sought to avoid confusion of success rates with those due to deeply divergent taxa. We also address whether increased population-level or geographic sampling affects delimitation success. Based on the results from 101 studies, we found that all marker groups had approximately equal success rates (~70%) in delimiting closely related species and that the use of additional loci increased average delimitation success. We also found no relationship between increased sampling of intraspecific variability and delimitation success. Ultimately, our results support a multi-locus integrative approach to species delimitation and taxonomy.},
}
@article {pmid22879881,
year = {2012},
author = {Ranasinghe, JA and Stein, ED and Miller, PE and Weisberg, SB},
title = {Performance of two Southern California benthic community condition indices using species abundance and presence-only data: relevance to DNA barcoding.},
journal = {PloS one},
volume = {7},
number = {8},
pages = {e40875},
pmid = {22879881},
issn = {1932-6203},
mesh = {Aquatic Organisms/*classification/*genetics ; Base Sequence ; *Biodiversity ; Calibration ; California ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Geologic Sediments/chemistry ; Metals/analysis ; Nitrogen/analysis ; Seasons ; Species Specificity ; Water Pollutants, Chemical/analysis ; Water Pollution/analysis ; },
abstract = {DNA barcoding, as it is currently employed, enhances use of marine benthic macrofauna as environmental condition indicators by improving the speed and accuracy of the underlying taxonomic identifications. The next generation of barcoding applications, processing bulk environmental samples, will likely only provide presence information. However, macrofauna indices presently used to interpret these data are based on species abundances. To assess the importance of this difference, we evaluated the performance of the Southern California Benthic Response Index (BRI) and the AZTI Marine Biotic Index (AMBI) when species abundance data were removed from their calculation. Presence only versions of these two indices were created by eliminating abundance weighting while preserving species identity. Associations between the presence and abundance BRI, and the presence and abundance AMBI were highly significant, with correlation coefficients of 0.99 and 0.81, respectively. The presence versions validated almost equally to the abundance-based indices when applied to the spatial and the temporal monitoring data used to validate the original indices. Simulations in which taxa were systematically removed from calculation of the indices were also conducted to assess how large the barcode library must be for the indices to be effective. Correlation between the BRI-P and BRI remained above 0.9 with only 370 species in the library and reducing the number of species to 450 had almost no effect on correlation between the presence and abundance versions of the AMBI.},
}
@article {pmid22869548,
year = {2012},
author = {Bafeel, SO and Arif, IA and Bakir, MA and Al Homaidan, AA and Al Farhan, AH and Khan, HA},
title = {DNA barcoding of arid wild plants using rbcL gene sequences.},
journal = {Genetics and molecular research : GMR},
volume = {11},
number = {3},
pages = {1934-1941},
doi = {10.4238/2012.July.19.12},
pmid = {22869548},
issn = {1676-5680},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; Databases, Genetic ; *Desert Climate ; Genes, Plant/*genetics ; Molecular Sequence Data ; Phylogeny ; Plants/*genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; },
abstract = {DNA barcoding is currently gaining popularity due to its simplicity and high accuracy as compared to the complexity and subjective biases associated with morphology-based identification of taxa. The standard chloroplast DNA barcode for land plants recommended by the Consortium for the Barcode of Life (CBOL) plant working group needs to be evaluated for a wide range of plant species. We therefore tested the potential of the rbcL marker for the identification of wild plants belonging to diverse families of arid regions. Maximum likelihood tree analysis was performed to evaluate the discriminatory power of the rbcL gene. Our findings showed that using rbcL gene sequences enabled identification of the majority of the samples (92%) to genus level and only 17% to species level.},
}
@article {pmid22869075,
year = {2012},
author = {Madesis, P and Ganopoulos, I and Ralli, P and Tsaftaris, A},
title = {Barcoding the major Mediterranean leguminous crops by combining universal chloroplast and nuclear DNA sequence targets.},
journal = {Genetics and molecular research : GMR},
volume = {11},
number = {3},
pages = {2548-2558},
doi = {10.4238/2012.July.10.10},
pmid = {22869075},
issn = {1676-5680},
mesh = {Base Sequence ; Cell Nucleus/*genetics ; Crops, Agricultural/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Chloroplast/*genetics ; DNA, Plant/*genetics ; Fabaceae/*classification/*genetics ; Mediterranean Region ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; },
abstract = {The ability to discriminate all species is the ultimate target in barcoding. The Mediterranean basin is a center of origin for legumes and thus they have played a key role in feeding the Mediterranean population. It is also a region with important protected designation of origin and protected geographical indication legumes that provide income in rural areas. We evaluated the use of two chloroplast regions, trnL and rpoC1, and a nuclear internal transcriber region, ITS2, for their efficiency to barcode the main Mediterranean leguminous crops. Twenty-five legume species were studied. Plant material of pasture and legumes was obtained from the Greek GenBank and the Fodder Crops and Pastures Institute (National Agricultural Research Foundation). DNA was extracted with the Qiagen DNeasy plant mini-kit and PCR amplification was performed using the Kapa Taq DNA polymerase using primers amplifying the chloroplast trnL and rpoC1 regions or the nuclear region ITS2. PCR products were sequenced and the sequences were aligned using CLUSTAL W. Species identification based on the sequence similarity approach was performed using the GenBank database. In order to evaluate intraspecific and interspecific divergence in legumes we used Molecular Evolutionary Genetics Analysis 5 and for pairwise Kimura 2-parameter distance calculations for all 3 DNA regions (2 chloroplast regions, trnL and rpoC1, and the nuclear region ITS2). Four tree-based methods (neighbor joining and maximum parsimony, maximum likelihood, and Bayesian inference analyses) were used to exhibit the molecular identification results to represent differences as an uprooted dendrogram. Additionally, the sequence character-based method was used with DnaSP and the information from each site was treated as a character to distinguish the species from one another. The DNA regions trnL and ITS2 successfully (100%) discriminated the Mediterranean crop legume species used, while rpoC1 identified only 72% of them. Furthermore, the use of the trnL region enabled the discrimination of even very closely related species, like Phaseolus lunatus and P. coccineus or Vicia faba subsp major with V. faba subsp minor, which are so closely related that even in NCBI they were both referred as Phaseolus vulgaris and V. faba, respectively. We conclude that trnL and ITS2 are efficient DNA barcoding target regions in order to discriminate Mediterranean leguminous crops and provide a reliable and efficient tool for the scientific, agricultural and industrial community.},
}
@article {pmid22864809,
year = {2013},
author = {Kwanda, N and Noikotr, K and Sudmoon, R and Tanee, T and Chaveerach, A},
title = {Medicinal parasitic plants on diverse hosts with their usages and barcodes.},
journal = {Journal of natural medicines},
volume = {67},
number = {3},
pages = {438-445},
pmid = {22864809},
issn = {1861-0293},
mesh = {Base Sequence ; *DNA Barcoding, Taxonomic ; DNA, Intergenic ; DNA, Plant/*analysis/classification ; Databases, Genetic ; Ethnobotany ; Expressed Sequence Tags ; Gene Expression Regulation, Plant ; Genetic Markers ; Genotype ; *Host-Parasite Interactions ; Loranthaceae/classification/*genetics ; Molecular Sequence Data ; Phenotype ; Photosynthetic Reaction Center Complex Proteins/genetics ; Phytotherapy ; Plants, Medicinal ; Ribulose-Bisphosphate Carboxylase/genetics ; Species Specificity ; Thailand ; Viscaceae/classification/*genetics ; },
abstract = {Medicinal properties of parasitic plants were investigated by means of ethnobotanical study in some areas of northeastern Thailand. Important traditional usages are: Scurrula atropurpurea nourishes blood, Dendrophthoe pentandra decreases high blood pressure, and Helixanthera parasitica treats liver disease. Their systematics were also determined. The research is based on findings obtained from 100 parasite-host pairs. Of these, eight parasitic species were recorded; they are members of two families, viz. family Loranthaceae, namely D. lanosa, D. pentandra, H. parasitica, Macrosolen brandisianus, M. cochinchinensis and S. atropurpurea, and family Viscaceae, namely Viscum articulatum and V. ovalifolium. In addition, each parasitic species is found on diverse hosts, indicating non-host-parasitic specificity. Species-specific tagging of all species studied was carried out using the rbcL and psbA-trnH chloroplast regions. These tag sequences are submitted to GenBank databases under accession numbers JN687563-JN687578. Genetic distances calculated from nucleotide variations in a couple of species of each genus, Dendrophthoe, Macrosolen, and Viscum, were 0.032, 0.067 and 0.036 in the rbcL region, and 0.269, 0.073 and 0.264 in the psbA-trnH spacer region, respectively. These variations will be used for further identification of incomplete plant parts or other forms such as capsule, powder, dried or chopped pieces.},
}
@article {pmid22859892,
year = {2012},
author = {Schuh, RT},
title = {Integrating specimen databases and revisionary systematics.},
journal = {ZooKeys},
volume = {},
number = {209},
pages = {255-267},
pmid = {22859892},
issn = {1313-2970},
abstract = {Arguments are presented for the merit of integrating specimen databases into the practice of revisionary systematics. Work flows, data connections, data outputs, and data standardization are enumerated as critical aspects of such integration. Background information is provided on the use of "barcodes" as unique specimen identifiers and on methods for efficient data capture. Examples are provided on how to achieve efficient workflows and data standardization, as well as data outputs and data integration.},
}
@article {pmid22859880,
year = {2012},
author = {van Oever, JP and Gofferjé, M},
title = {'From Pilot to production': Large Scale Digitisation project at Naturalis Biodiversity Center.},
journal = {ZooKeys},
volume = {},
number = {209},
pages = {87-92},
doi = {10.3897/zookeys.209.3609},
pmid = {22859880},
issn = {1313-2970},
abstract = {By the end of 2009 the Dutch Government awarded the establishment of NCB Naturalis with €30M funding. The amount is invested in three programs: Scientific Infrastructure for DNA Barcoding, Integration and Relocation of collections and Collection Digitisation. In this article we describe the highlights of the Digitisation Programme.},
}
@article {pmid22848736,
year = {2012},
author = {Li, CP and Yu, ZG and Han, GS and Chu, KH},
title = {Analyzing multi-locus plant barcoding datasets with a composition vector method based on adjustable weighted distance.},
journal = {PloS one},
volume = {7},
number = {7},
pages = {e42154},
pmid = {22848736},
issn = {1932-6203},
mesh = {DNA Barcoding, Taxonomic/*methods ; *Data Interpretation, Statistical ; Genetic Loci/*genetics ; Plants/*classification/*genetics ; },
abstract = {BACKGROUND: The composition vector (CV) method has been proved to be a reliable and fast alignment-free method to analyze large COI barcoding data. In this study, we modify this method for analyzing multi-gene datasets for plant DNA barcoding. The modified method includes an adjustable-weighted algorithm for the vector distance according to the ratio in sequence length of the candidate genes for each pair of taxa.<br><br>Three datasets, matK+rbcL dataset with 2,083 sequences, matK+rbcL dataset with 397 sequences and matK+rbcL+trnH-psbA dataset with 397 sequences, were tested. We showed that the success rates of grouping sequences at the genus/species level based on this modified CV approach are always higher than those based on the traditional K2P/NJ method. For the matK+rbcL datasets, the modified CV approach outperformed the K2P-NJ approach by 7.9% in both the 2,083-sequence and 397-sequence datasets, and for the matK+rbcL+trnH-psbA dataset, the CV approach outperformed the traditional approach by 16.7%.<br><br>CONCLUSIONS: We conclude that the modified CV approach is an efficient method for analyzing large multi-gene datasets for plant DNA barcoding. Source code, implemented in C++ and supported on MS Windows, is freely available for download at http://math.xtu.edu.cn/myphp/math/research/source/Barcode_source_codes.zip.},
}
@article {pmid22847014,
year = {2012},
author = {Gismondi, A and Rolfo, MF and Leonardi, D and Rickards, O and Canini, A},
title = {Identification of ancient Olea europaea L. and Cornus mas L. seeds by DNA barcoding.},
journal = {Comptes rendus biologies},
volume = {335},
number = {7},
pages = {472-479},
doi = {10.1016/j.crvi.2012.05.004},
pmid = {22847014},
issn = {1768-3238},
mesh = {Agriculture/*history ; Archaeology/*methods ; Caves ; Cornus/classification/*genetics ; DNA Barcoding, Taxonomic ; DNA, Plant/*analysis/isolation &amp; purification ; Databases, Genetic ; *Fossils ; *Genes, Plant ; History, Ancient ; Italy ; Microscopy, Electron, Scanning ; Olea/classification/*genetics ; Polymerase Chain Reaction/methods ; Seeds/*chemistry/ultrastructure ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Species Specificity ; },
abstract = {The analysis of ancient DNA (aDNA) provides archaeologists and anthropologists with innovative, scientific and accurate data to study and understand the past. In this work, ancient seeds, found in the "Mora Cavorso" archaeological site (Latium, Central Italy), were analyzed to increase information about Italian Neolithic populations (plant use, agriculture, diet, trades, customs and ecology). We performed morphological and genetic techniques to identify fossil botanical species. In particular, this study also suggests and emphasizes the use of DNA barcode method for ancient plant sample analysis. Scanning electron microscope (SEM) observations showed seed compact structure and irregular surface but they did not permit a precise nor empirical classification: so, a molecular approach was necessary. DNA was extracted from ancient seeds and then it was used, as template, for PCR amplifications of standardized barcode genes. Although aDNA could be highly degraded by the time, successful PCR products were obtained, sequenced and compared to nucleotide sequence databases. Positive outcomes (supported by morphological comparison with modern seeds, geographical distribution and historical data) indicated that seeds could be identified as belonging to two plant species: Olea europaea L. and Cornus mas L.},
}
@article {pmid22829879,
year = {2012},
author = {Kadarusman, and Hubert, N and Hadiaty, RK and Sudarto, and Paradis, E and Pouyaud, L},
title = {Cryptic diversity in Indo-Australian rainbowfishes revealed by DNA barcoding: implications for conservation in a biodiversity hotspot candidate.},
journal = {PloS one},
volume = {7},
number = {7},
pages = {e40627},
pmid = {22829879},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Fishes/classification/*genetics ; Phylogeny ; },
abstract = {The rainbowfishes of the family Melanotaeniidae represent one of the largest radiations of freshwater fishes from the Indo-Australian archipelago. A total of 75 nominal species have been described, among which several have become very popular among tropical fish hobbyists because of their tendency to form large schools of colourful individuals. Facing habitat loss and competition or predation by introduced species, this group has become a priority in the conservation of ornamental fishes in Indonesia. In this context, several expeditions have been conducted between 2007 and 2010 in Indonesian Papua with the aim to initiate a large-scale survey of the genetic resources in this group. We assessed the diversity of the Papua rainbowfishes with DNA barcoding. We sequenced the mitochondrial COI gene for 350 specimens belonging to 53 nominal species throughout the Indo-Australian archipelago. Unexpected levels of cryptic diversity and endemism were detected since additional cryptic lineages were detected in several watersheds from the Vogelkop and the Lengguru massif. DNA barcoding supports the presence of nearly 30 evolutionary lineages among the 15 nominal species sampled in the Vogelkop and all these lineages are endemic to a single lake or watershed. This result highlights that the diversity of the family has been largely underestimated and urges for the identification of conservation priorities in Papua.},
}
@article {pmid22827913,
year = {2012},
author = {Martínez-de la Puente, J and Martínez, J and Ferraguti, M and Morales-de la Nuez, A and Castro, N and Figuerola, J},
title = {Genetic characterization and molecular identification of the bloodmeal sources of the potential bluetongue vector Culicoides obsoletus in the Canary Islands, Spain.},
journal = {Parasites &amp; vectors},
volume = {5},
number = {},
pages = {147},
pmid = {22827913},
issn = {1756-3305},
mesh = {Animals ; Bluetongue/*transmission ; Ceratopogonidae/*genetics/*physiology ; Female ; Goats/*blood ; Insect Vectors/physiology ; Male ; Sheep/*blood ; Spain/epidemiology ; },
abstract = {BACKGROUND: Culicoides (Diptera: Ceratopogonidae) biting midges are vectors for a diversity of pathogens including bluetongue virus (BTV) that generate important economic losses. BTV has expanded its range in recent decades, probably due to the expansion of its main vector and the presence of other autochthonous competent vectors. Although the Canary Islands are still free of bluetongue disease (BTD), Spain and Europe have had to face up to a spread of bluetongue with disastrous consequences. Therefore, it is essential to identify the distribution of biting midges and understand their feeding patterns in areas susceptible to BTD. To that end, we captured biting midges on two farms in the Canary Islands (i) to identify the midge species in question and characterize their COI barcoding region and (ii) to ascertain the source of their bloodmeals using molecular tools.<br><br>METHODS: Biting midges were captured using CDC traps baited with a 4-W blacklight (UV) bulb on Gran Canaria and on Tenerife. Biting midges were quantified and identified according to their wing patterns. A 688 bp segment of the mitochondrial COI gene of 20 biting midges (11 from Gran Canaria and 9 from Tenerife) were PCR amplified using the primers LCO1490 and HCO2198. Moreover, after selected all available females showing any rest of blood in their abdomen, a nested-PCR approach was used to amplify a fragment of the COI gene from vertebrate DNA contained in bloodmeals. The origin of bloodmeals was identified by comparison with the nucleotide-nucleotide basic alignment search tool (BLAST).<br><br>RESULTS: The morphological identification of 491 female biting midges revealed the presence of a single morphospecies belonging to the Obsoletus group. When sequencing the barcoding region of the 20 females used to check genetic variability, we identified two haplotypes differing in a single base. Comparison analysis using the nucleotide-nucleotide basic alignment search tool (BLAST) showed that both haplotypes belong to Culicoides obsoletus, a potential BTV vector. As well, using molecular tools we identified the feeding sources of 136 biting midges and were able to confirm that C. obsoletus females feed on goats and sheep on both islands.<br><br>CONCLUSIONS: These results confirm that the feeding pattern of C. obsoletus is a potentially important factor in BTV transmission to susceptible hosts in case of introduction into the archipelago. Consequently, in the Canary Islands it is essential to maintain vigilance of Culicoides-transmitted viruses such as BTV and the novel Schmallenberg virus.},
}
@article {pmid22824422,
year = {2012},
author = {Lassen, SB and Nielsen, SA and Kristensen, M},
title = {Identity and diversity of blood meal hosts of biting midges (Diptera: Ceratopogonidae: Culicoides Latreille) in Denmark.},
journal = {Parasites &amp; vectors},
volume = {5},
number = {},
pages = {143},
pmid = {22824422},
issn = {1756-3305},
mesh = {Animals ; Birds/*blood ; Ceratopogonidae/*physiology ; Denmark ; Feeding Behavior ; Female ; Mammals/*blood ; Species Specificity ; },
abstract = {BACKGROUND: Host preference studies in haematophagous insects e.g. Culicoides biting midges are pivotal to assess transmission routes of vector-borne diseases and critical for the development of veterinary contingency plans to identify which species should be included due to their risk potential. Species of Culicoides have been found in almost all parts of the world and known to live in a variety of habitats. Several parasites and viruses are transmitted by Culicoides biting midges including Bluetongue virus and Schmallenberg virus. The aim of the present study was to determine the identity and diversity of blood meals taken from vertebrate hosts in wild-caught Culicoides biting midges near livestock farms.<br><br>METHODS: Biting midges were collected at weekly intervals for 20 weeks from May to October 2009 using light traps at four collection sites on the island Sealand, Denmark. Blood-fed female biting midges were sorted and head and wings were removed for morphological species identification. The thoraxes and abdomens including the blood meals of the individual females were subsequently subjected to DNA isolation. The molecular marker cytochrome oxidase I (COI barcode) was applied to identify the species of the collected biting midges (GenBank accessions JQ683259-JQ683374). The blood meals were first screened with a species-specific cytochrome b primer pair for cow and if negative with a universal cytochrome b primer pair followed by sequencing to identify mammal or avian blood meal hosts.<br><br>RESULTS: Twenty-four species of biting midges were identified from the four study sites. A total of 111,356 Culicoides biting midges were collected, of which 2,164 were blood-fed. Specimens of twenty species were identified with blood in their abdomens. Blood meal sources were successfully identified by DNA sequencing from 242 (76%) out of 320 Culicoides specimens. Eight species of mammals and seven species of birds were identified as blood meal hosts. The most common host species was the cow, which constituted 77% of the identified blood meals. The second most numerous host species was the common wood pigeon, which constituted 6% of the identified blood meals.<br><br>CONCLUSIONS: Our results suggest that some Culicoides species are opportunistic and readily feed on a variety of mammals and birds, while others seems to be strictly mammalophilic or ornithophilic. Based on their number, dispersal potential and blood feeding behaviour, we conclude that Culicoides biting midges are potential vectors for many pathogens not yet introduced to Denmark.},
}
@article {pmid22823139,
year = {2012},
author = {Piry, S and Guivier, E and Realini, A and Martin, JF},
title = {|SE|S|AM|E| Barcode: NGS-oriented software for amplicon characterization--application to species and environmental barcoding.},
journal = {Molecular ecology resources},
volume = {12},
number = {6},
pages = {1151-1157},
doi = {10.1111/j.1755-0998.2012.03171.x},
pmid = {22823139},
issn = {1755-0998},
mesh = {Biostatistics/*methods ; Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; Genomics/*methods ; *Software ; },
abstract = {Progress in NGS technologies has opened up new opportunities for characterizing biodiversity, both for individual specimen identification and for environmental barcoding. Although the amount of data available to biologist is increasing, user-friendly tools to facilitate data analysis have yet to be developed. Our aim, with |SE|S|AM|E| Barcode, is to provide such support through a unified platform. The sequences are analysed through a pipeline that (i) processes NGS amplicon runs, filtering markers and samples, (ii) builds reference libraries and finally (iii) identifies (barcodes) the sequences in each amplicon from the reference library. We use a simulated data set for specimen identification and a recently published data set for environmental barcoding to validate the method. The results obtained are consistent with the expected characterizations (in silico and previously published, respectively). |SE|S|AM|E| Barcode and its documentation are freely available under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported Licence for Windows and Linux from http://www1.montpellier.inra.fr/CBGP/NGS/.},
}
@article {pmid22819855,
year = {2012},
author = {Matochko, WL and Chu, K and Jin, B and Lee, SW and Whitesides, GM and Derda, R},
title = {Deep sequencing analysis of phage libraries using Illumina platform.},
journal = {Methods (San Diego, Calif.)},
volume = {58},
number = {1},
pages = {47-55},
doi = {10.1016/j.ymeth.2012.07.006},
pmid = {22819855},
issn = {1095-9130},
mesh = {Amino Acid Sequence ; Bacteriophage M13/*genetics ; Base Sequence ; Cluster Analysis ; Consensus Sequence ; DNA, Viral/*genetics/isolation &amp; purification ; Genetic Vectors ; *High-Throughput Nucleotide Sequencing ; Molecular Sequence Data ; Oligonucleotides/genetics/isolation &amp; purification ; Peptide Fragments/chemistry/genetics ; Peptide Library ; *Sequence Analysis, DNA ; Software ; },
abstract = {This paper presents an analysis of phage-displayed libraries of peptides using Illumina. We describe steps for the preparation of short DNA fragments for deep sequencing and MatLab software for the analysis of the results. Screening of peptide libraries displayed on the surface of bacteriophage (phage display) can be used to discover peptides that bind to any target. The key step in this discovery is the analysis of peptide sequences present in the library. This analysis is usually performed by Sanger sequencing, which is labor intensive and limited to examination of a few hundred phage clones. On the other hand, Illumina deep-sequencing technology can characterize over 10(7) reads in a single run. We applied Illumina sequencing to analyze phage libraries. Using PCR, we isolated the variable regions from M13KE phage vectors from a phage display library. The PCR primers contained (i) sequences flanking the variable region, (ii) barcodes, and (iii) variable 5'-terminal region. We used this approach to examine how diversity of peptides in phage display libraries changes as a result of amplification of libraries in bacteria. Using HiSeq single-end Illumina sequencing of these fragments, we acquired over 2×10(7) reads, 57 base pairs (bp) in length. Each read contained information about the barcode (6bp), one complimentary region (12bp) and a variable region (36bp). We applied this sequencing to a model library of 10(6) unique clones and observed that amplification enriches ∼150 clones, which dominate ∼20% of the library. Deep sequencing, for the first time, characterized the collapse of diversity in phage libraries. The results suggest that screens based on repeated amplification and small-scale sequencing identify a few binding clones and miss thousands of useful clones. The deep sequencing approach described here could identify under-represented clones in phage screens. It could also be instrumental in developing new screening strategies, which can preserve diversity of phage clones and identify ligands previously lost in phage display screens.},
}
@article {pmid22815928,
year = {2012},
author = {Stampar, SN and Maronna, MM and Vermeij, MJ and Silveira, FL and Morandini, AC},
title = {Evolutionary diversification of banded tube-dwelling anemones (Cnidaria; Ceriantharia; Isarachnanthus) in the Atlantic Ocean.},
journal = {PloS one},
volume = {7},
number = {7},
pages = {e41091},
pmid = {22815928},
issn = {1932-6203},
mesh = {Algorithms ; Anemone/*genetics/physiology ; Animals ; Bayes Theorem ; Biodiversity ; Cnidaria/*genetics/physiology ; DNA Barcoding, Taxonomic ; Evolution, Molecular ; Genetic Variation ; Geography ; Likelihood Functions ; Models, Genetic ; Models, Statistical ; Oceans and Seas ; Phylogeny ; },
abstract = {The use of molecular data for species delimitation in Anthozoa is still a very delicate issue. This is probably due to the low genetic variation found among the molecular markers (primarily mitochondrial) commonly used for Anthozoa. Ceriantharia is an anthozoan group that has not been tested for genetic divergence at the species level. Recently, all three Atlantic species described for the genus Isarachnanthus of Atlantic Ocean, were deemed synonyms based on morphological simmilarities of only one species: Isarachnanthus maderensis. Here, we aimed to verify whether genetic relationships (using COI, 16S, ITS1 and ITS2 molecular markers) confirmed morphological affinities among members of Isarachnanthus from different regions across the Atlantic Ocean. Results from four DNA markers were completely congruent and revealed that two different species exist in the Atlantic Ocean. The low identification success and substantial overlap between intra and interspecific COI distances render the Anthozoa unsuitable for DNA barcoding, which is not true for Ceriantharia. In addition, genetic divergence within and between Ceriantharia species is more similar to that found in Medusozoa (Hydrozoa and Scyphozoa) than Anthozoa and Porifera that have divergence rates similar to typical metazoans. The two genetic species could also be separated based on micromorphological characteristics of their cnidomes. Using a specimen of Isarachnanthus bandanensis from Pacific Ocean as an outgroup, it was possible to estimate the minimum date of divergence between the clades. The cladogenesis event that formed the species of the Atlantic Ocean is estimated to have occured around 8.5 million years ago (Miocene) and several possible speciation scenarios are discussed.},
}
@article {pmid22815912,
year = {2012},
author = {Weigt, LA and Baldwin, CC and Driskell, A and Smith, DG and Ormos, A and Reyier, EA},
title = {Using DNA barcoding to assess Caribbean reef fish biodiversity: expanding taxonomic and geographic coverage.},
journal = {PloS one},
volume = {7},
number = {7},
pages = {e41059},
pmid = {22815912},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; Caribbean Region ; Coral Reefs ; DNA/genetics/metabolism ; *DNA Barcoding, Taxonomic ; Fishes ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {This paper represents a DNA barcode data release for 3,400 specimens representing 521 species of fishes from 6 areas across the Caribbean and western central Atlantic regions (FAO Region 31). Merged with our prior published data, the combined efforts result in 3,964 specimens representing 572 species of marine fishes and constitute one of the most comprehensive DNA barcoding "coverages" for a region reported to date. The barcode data are providing new insights into Caribbean shorefish diversity, allowing for more and more accurate DNA-based identifications of larvae, juveniles, and unknown specimens. Examples are given correcting previous work that was erroneous due to database incompleteness.},
}
@article {pmid22815712,
year = {2012},
author = {Boers, SA and van der Reijden, WA and Jansen, R},
title = {High-throughput multilocus sequence typing: bringing molecular typing to the next level.},
journal = {PloS one},
volume = {7},
number = {7},
pages = {e39630},
pmid = {22815712},
issn = {1932-6203},
mesh = {Alleles ; Bacteria/classification/genetics ; Genes, Bacterial/genetics ; Genetic Loci/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Molecular Typing/*methods ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; },
abstract = {Multilocus sequence typing (MLST) is a widely used system for typing microorganisms by sequence analysis of housekeeping genes. The main advantage of MLST in comparison to other typing techniques is the unambiguity and transferability of sequence data. However, a main disadvantage is the high cost of DNA sequencing. Here we introduce a high-throughput MLST (HiMLST) method that employs next-generation sequencing (NGS) technology (Roche 454), to generate large quantities of high-quality MLST data at low costs. The HiMLST protocol consists of two steps. In the first step MLST target genes are amplified by PCR in multi-well plates. During this PCR the amplicons of each bacterial isolate are provided with a unique DNA barcode, the multiplex identifier (MID). In the second step all amplicons are pooled and sequenced in a single NGS-run. The MLST profile of each individual isolate can be retrieved easily using its unique MID. With HiMLST we have profiled 575 isolates of Legionella pneumophila, Staphylococcus aureus, Pseudomonas aeruginosa and Streptococcus pneumoniae in mixed species HiMLST experiments. In conclusion, the introduction of HiMLST paves the way for a broad employment of the MLST as a high-quality and cost-effective method for typing microbial species.},
}
@article {pmid22815589,
year = {2012},
author = {Bensch, K and Braun, U and Groenewald, JZ and Crous, PW},
title = {The genus Cladosporium.},
journal = {Studies in mycology},
volume = {72},
number = {1},
pages = {1-401},
pmid = {22815589},
issn = {1872-9797},
abstract = {UNLABELLED: A monographic revision of the hyphomycete genus Cladosporium s. lat. (Cladosporiaceae, Capnodiales) is presented. It includes a detailed historic overview of Cladosporium and allied genera, with notes on their phylogeny, systematics and ecology. True species of Cladosporium s. str. (anamorphs of Davidiella), are characterised by having coronate conidiogenous loci and conidial hila, i.e., with a convex central dome surrounded by a raised periclinal rim. Recognised species are treated and illustrated with line drawings and photomicrographs (light as well as scanning electron microscopy). Species known from culture are described in vivo as well as in vitro on standardised media and under controlled conditions. Details on host range/substrates and the geographic distribution are given based on published accounts, and a re-examination of numerous herbarium specimens. Various keys are provided to support the identification of Cladosporium species in vivo and in vitro. Morphological datasets are supplemented by DNA barcodes (nuclear ribosomal RNA gene operon, including the internal transcribed spacer regions ITS1 and ITS2, the 5.8S nrDNA, as well as partial actin and translation elongation factor 1-α gene sequences) diagnostic for individual species. In total 993 names assigned to Cladosporium s. lat., including Heterosporium (854 in Cladosporium and 139 in Heterosporium), are treated, of which 169 are recognized in Cladosporium s. str. The other taxa are doubtful, insufficiently known or have been excluded from Cladosporium in its current circumscription and re-allocated to other genera by the authors of this monograph or previous authors.<br><br>TAXONOMIC NOVELTIES: Cladosporium allicinum (Fr.: Fr.) Bensch, U. Braun &amp; Crous, comb. nov., C. astroideum var. catalinense U. Braun, var. nov., Fusicladium tectonicola (Yong H. He &amp; Z.Y. Zhang) U. Braun &amp; Bensch, comb. nov., Septoidium uleanum (Henn.) U. Braun, comb. nov., Zasmidium adeniae (Hansf.) U. Braun, comb. nov., Zasmidium dianellae (Sawada &amp; Katsuki) U. Braun, comb. nov., Zasmidium lythri (Westend.) U. Braun &amp; H.D. Shin, comb. nov., Zasmidium wikstroemiae (Petch) U. Braun, comb. nov.},
}
@article {pmid22808280,
year = {2012},
author = {Toju, H and Tanabe, AS and Yamamoto, S and Sato, H},
title = {High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples.},
journal = {PloS one},
volume = {7},
number = {7},
pages = {e40863},
pmid = {22808280},
issn = {1932-6203},
mesh = {Ascomycota/*classification/*genetics ; Base Pair Mismatch ; Base Sequence ; Basidiomycota/*classification/*genetics ; Cell Nucleus/genetics ; Computational Biology ; DNA Primers/*metabolism ; DNA, Fungal/*genetics ; DNA, Intergenic/*genetics ; Environmental Microbiology ; Mycological Typing Techniques ; Nucleic Acid Renaturation/genetics ; Plants/genetics ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; Temperature ; },
abstract = {The kingdom Fungi is estimated to include 1.5 million or more species, playing key roles as decomposers, mutualists, and parasites in every biome on the earth. To comprehensively understand the diversity and ecology of this huge kingdom, DNA barcoding targeting the internal transcribed spacer (ITS) region of the nuclear ribosomal repeat has been regarded as a prerequisite procedure. By extensively surveying ITS sequences in public databases, we designed new ITS primers with improved coverage across diverse taxonomic groups of fungi compared to existing primers. An in silico analysis based on public sequence databases indicated that the newly designed primers matched 99% of ascomycete and basidiomycete ITS taxa (species, subspecies or varieties), causing little taxonomic bias toward either fungal group. Two of the newly designed primers could inhibit the amplification of plant sequences and would enable the selective investigation of fungal communities in mycorrhizal associations, soil, and other types of environmental samples. Optimal PCR conditions for the primers were explored in an in vitro investigation. The new primers developed in this study will provide a basis for ecological studies on the diversity and community structures of fungi in the era of massive DNA sequencing.},
}
@article {pmid22808168,
year = {2012},
author = {Pilloni, G and Granitsiotis, MS and Engel, M and Lueders, T},
title = {Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes.},
journal = {PloS one},
volume = {7},
number = {7},
pages = {e40467},
pmid = {22808168},
issn = {1932-6203},
mesh = {Bacteria/*genetics ; DNA Fingerprinting/*methods ; DNA, Bacterial/genetics ; Gene Library ; Genes, Bacterial/genetics ; Genetic Variation ; Groundwater/*microbiology ; Polymorphism, Restriction Fragment Length/*genetics ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; },
abstract = {The characterization of microbial community structure via 16S rRNA gene profiling has been greatly advanced in recent years by the introduction of amplicon pyrosequencing. The possibility of barcoding gives the opportunity to massively screen multiple samples from environmental or clinical sources for community details. However, an on-going debate questions the reproducibility and semi-quantitative rigour of pyrotag sequencing, similar to the early days of community fingerprinting. In this study we demonstrate the reproducibility of bacterial 454 pyrotag sequencing over biological and technical replicates of aquifer sediment bacterial communities. Moreover, we explore the potential of recovering specific template ratios via quantitatively defined template spiking to environmental DNA. We sequenced pyrotag libraries of triplicate sediment samples taken in annual sampling campaigns at a tar oil contaminated aquifer in Düsseldorf, Germany. The abundance of dominating lineages was highly reproducible with a maximal standard deviation of ~4% read abundance across biological, and ~2% across technical replicates. Our workflow also allows for the linking of read abundances within defined assembled pyrotag contigs to that of specific 'in vivo' fingerprinting signatures. Thus we demonstrate that both terminal restriction fragment length polymorphism (T-RFLP) analysis and pyrotag sequencing are capable of recovering highly comparable community structure. Overall diversity was roughly double in amplicon sequencing. Pyrotag libraries were also capable of linearly recovering increasing ratios (up to 20%) of 16S rRNA gene amendments from a pure culture of Aliivibrio fisheri spiked to sediment DNA. Our study demonstrates that 454 pyrotag sequencing is a robust and reproducible method, capable of reliably recovering template abundances and overall community structure within natural microbial communities.},
}
@article {pmid22808155,
year = {2012},
author = {Hammond, M and Nong, RY and Ericsson, O and Pardali, K and Landegren, U},
title = {Profiling cellular protein complexes by proximity ligation with dual tag microarray readout.},
journal = {PloS one},
volume = {7},
number = {7},
pages = {e40405},
pmid = {22808155},
issn = {1932-6203},
support = {R21 CA126727/CA/NCI NIH HHS/United States ; 1R21CA126727-01A1/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Cell Extracts ; Cell Line ; Humans ; Protein Array Analysis/*instrumentation/*methods ; Protein Binding ; Protein Interaction Mapping/*methods ; Proteins/*metabolism ; },
abstract = {Patterns of protein interactions provide important insights in basic biology, and their analysis plays an increasing role in drug development and diagnostics of disease. We have established a scalable technique to compare two biological samples for the levels of all pairwise interactions among a set of targeted protein molecules. The technique is a combination of the proximity ligation assay with readout via dual tag microarrays. In the proximity ligation assay protein identities are encoded as DNA sequences by attaching DNA oligonucleotides to antibodies directed against the proteins of interest. Upon binding by pairs of antibodies to proteins present in the same molecular complexes, ligation reactions give rise to reporter DNA molecules that contain the combined sequence information from the two DNA strands. The ligation reactions also serve to incorporate a sample barcode in the reporter molecules to allow for direct comparison between pairs of samples. The samples are evaluated using a dual tag microarray where information is decoded, revealing which pairs of tags that have become joined. As a proof-of-concept we demonstrate that this approach can be used to detect a set of five proteins and their pairwise interactions both in cellular lysates and in fixed tissue culture cells. This paper provides a general strategy to analyze the extent of any pairwise interactions in large sets of molecules by decoding reporter DNA strands that identify the interacting molecules.},
}
@article {pmid22805582,
year = {2012},
author = {Chariton, A},
title = {Short and informative DNA products to indirectly measure vascular plant biodiversity.},
journal = {Molecular ecology},
volume = {21},
number = {15},
pages = {3637-3639},
doi = {10.1111/j.1365-294X.2012.05633.x},
pmid = {22805582},
issn = {1365-294X},
mesh = {*Biodiversity ; DNA, Plant/*analysis ; Plants/*classification ; Soil/*analysis ; },
abstract = {Anthropogenic activities are having a deleterious effect on biodiversity. To understand the magnitude of this issue, and ultimately temper its pace, requires reproducible biodiversity measurements at suitable spatio-temporal scales. Procuring such data solely by existing approaches is unachievable because of the costs, time and the taxonomic expertise required. High-throughput molecular biodiversity analysis shows great promise, increasing the breadth of biota sampled and accelerating the rate of data collection. In this issue of Molecular Ecology, Yoccoz et al. (2012) use short informative DNA product 'meta-barcodes' to provide an insight into above-ground vascular plant diversity from boreal, temperate and tropical environments. Interestingly, their molecular analysis was derived from the soils and not the plants themselves, with the molecular signatures of the soils not only strongly reflecting current diversity, but also traces of crops not sown for up to one hundred years. Importantly, the research examines the complexities associated with deriving biomass estimates from molecular data and the need to consider biomass turnover. The use of soil-derived meta-barcodes extends beyond estimating vascular plant diversity, with the approach being suited to the range of ecological applications, especially scenarios where DNA may be degraded.},
}
@article {pmid22805530,
year = {2012},
author = {Silvertown, J and Araya, YN and Linder, HP and Gowing, DJ},
title = {Experimental investigation of the origin of fynbos plant community structure after fire.},
journal = {Annals of botany},
volume = {110},
number = {7},
pages = {1377-1383},
pmid = {22805530},
issn = {1095-8290},
mesh = {Biodiversity ; Biomass ; DNA Barcoding, Taxonomic ; Ecosystem ; Fires ; Hydrology ; Magnoliopsida/growth &amp; development/*physiology ; Plant Roots/growth &amp; development/physiology ; Seedlings/growth &amp; development/*physiology ; Seeds/growth &amp; development/physiology ; Soil ; South Africa ; Species Specificity ; Water/*physiology ; },
abstract = {BACKGROUND AND AIMS: Species in plant communities segregate along fine-scale hydrological gradients. Although this phenomenon is not unique to fynbos, this community regenerates after fire and therefore provides an opportunity to study the ecological genesis of hydrological niche segregation.<br><br>METHODS: Following wildfires at two field sites where we had previously mapped the vegetation and monitored the hydrology, seeds were moved experimentally in >2500 intact soil cores up and down soil-moisture gradients to test the hypothesis that hydrological niche segregation is established during the seedling phase of the life cycle. Seedling numbers and growth were then monitored and they were identified using DNA bar-coding, the first use of this technology for an experiment of this kind.<br><br>KEY RESULTS: At the site where niche segregation among Restionaceae had previously been found, the size of seedlings was significantly greater, the wetter the location into which they were moved, regardless of the soil moisture status of their location of origin, or of the species. Seedling weight was also significantly greater in a competition treatment where the roots of other species were excluded. No such effects were detected at the control site where niche segregation among Restionaceae was previously found to be absent.<br><br>CONCLUSIONS: The finding that seedling growth on hydrological gradients in the field is affected by soil moisture status and by root competition shows that hydrological niche segregation could potentially originate in the seedling stage. The methodology, applied at a larger scale and followed-through for a longer period, could be used to determine whether species are differently affected by soil moisture.},
}
@article {pmid22802937,
year = {2012},
author = {Vargas, S and Schuster, A and Sacher, K and Büttner, G and Schätzle, S and Läuchli, B and Hall, K and Hooper, JN and Erpenbeck, D and Wörheide, G},
title = {Barcoding sponges: an overview based on comprehensive sampling.},
journal = {PloS one},
volume = {7},
number = {7},
pages = {e39345},
pmid = {22802937},
issn = {1932-6203},
mesh = {Animals ; Biological Evolution ; *DNA Barcoding, Taxonomic ; Phylogeny ; Porifera/*classification ; },
abstract = {BACKGROUND: Phylum Porifera includes ∼8,500 valid species distributed world-wide in aquatic ecosystems ranging from ephemeral fresh-water bodies to coastal environments and the deep-sea. The taxonomy and systematics of sponges is complicated, and morphological identification can be both time consuming and erroneous due to phenotypic convergence and secondary losses, etc. DNA barcoding can provide sponge biologists with a simple and rapid method for the identification of samples of unknown taxonomic membership. The Sponge Barcoding Project (www.spongebarcoding.org), the first initiative to barcode a non-bilaterian metazoan phylum, aims to provide a comprehensive DNA barcode database for Phylum Porifera.<br><br>&#x223c;7,400 sponge specimens have been extracted, and amplification of the standard COI barcoding fragment has been attempted for approximately 3,300 museum samples with &#x223c;25% mean amplification success. Based on this comprehensive sampling, we present the first report on the workflow and progress of the sponge barcoding project, and discuss some common pitfalls inherent to the barcoding of sponges.<br><br>CONCLUSION: A DNA-barcoding workflow capable of processing potentially large sponge collections has been developed and is routinely used for the Sponge Barcoding Project with success. Sponge specific problems such as the frequent co-amplification of non-target organisms have been detected and potential solutions are currently under development. The initial success of this innovative project have already demonstrated considerable refinement of sponge systematics, evaluating morphometric character importance, geographic phenotypic variability, and the utility of the standard barcoding fragment for Porifera (despite its conserved evolution within this basal metazoan phylum).},
}
@article {pmid22802133,
year = {2013},
author = {Sun, Z and Chen, S},
title = {Identification of cortex herbs using the DNA barcode nrITS2.},
journal = {Journal of natural medicines},
volume = {67},
number = {2},
pages = {296-302},
pmid = {22802133},
issn = {1861-0293},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/*genetics ; Medicine, Chinese Traditional/*methods ; Phylogeny ; },
abstract = {To discriminate the cortex herbs of Chinese Pharmacopoeia, the second internal transcribed spacer (ITS2) of ribosomal DNA of 51 samples belonging to 19 kinds of cortex herbs were analyzed in this paper. Sequence assembly was performed using the CodonCode Aligner. Phylogenetic study was performed using the molecular evolutionary genetics analysis (MEGA) 4.0 software in accordance with the Kimura 2-Parameter (K2P) model. Phylogenetic tree was constructed using the neighbor-joining (NJ) method. We found that the ITS2 sequences of the studied samples ranged from 207 to 256 bp in length and easy to be amplified. The intraspecific genetic distance of the cortex herbs was between 0 and 0.073, which was lower than their interspecific genetic distance (mean, 0.868; minimum, 0.101). In the cluster dendrogram, all the studied medicinal materials with several samples, were monophyletic. It is concluded that ITS2 barcode is suitable for the identification of cortex herbs of Chinese Pharmacopoeia, and it will play an important role in the field of identification of traditional Chinese medicine (TCM).},
}
@article {pmid22797043,
year = {2012},
author = {Stell, A and Sinnott, R},
title = {The ENSAT registry: a digital repository supporting adrenal cancer research.},
journal = {Studies in health technology and informatics},
volume = {178},
number = {},
pages = {207-212},
pmid = {22797043},
issn = {0926-9630},
mesh = {*Adrenal Gland Neoplasms ; *Biomedical Research/organization &amp; administration ; Data Collection ; Humans ; Medical Record Linkage ; *Registries ; User-Computer Interface ; },
abstract = {The very nature of rare diseases means that information is often sparse and highly distributed, and as a result progress in the field is more challenging to conduct. ENSAT-CANCER is an EU-FP7 funded initiative to develop a virtual research environment (VRE) offering a digitally interconnected infrastructure for distributed clinicians specialising in rare adrenal tumours to communicate and collaborate with distributed biomedical research communities. The core of the VRE is a registry that holds vital patient information from specialist centres around Europe, covering different types of adrenal tumours. The VRE also hosts a range of other enabling services including sample barcoding, bio-sample exchange mechanisms, an integrated linkage scheme to other trials and studies, summary statistics and report generation, image hosting - all of which are available in a seamless, security-driven environment. This paper presents the key challenges of this endeavour, the technical solutions that have been developed to address them and reporting the uptake and adoption of the work (currently at 2472 patient records and rising).},
}
@article {pmid22796448,
year = {2012},
author = {Gou, H and Guan, G and Liu, A and Ma, M and Xu, Z and Liu, Z and Ren, Q and Li, Y and Yang, J and Chen, Z and Yin, H and Luo, J},
title = {A DNA barcode for Piroplasmea.},
journal = {Acta tropica},
volume = {124},
number = {1},
pages = {92-97},
doi = {10.1016/j.actatropica.2012.07.001},
pmid = {22796448},
issn = {1873-6254},
mesh = {Babesia/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Protozoan/genetics ; Parasitology/*methods ; Polymerase Chain Reaction/*methods ; Polymorphism, Genetic ; },
abstract = {Due to the difficulty in morphological identification the development of reliable molecular tools for species distinction is a priority for piroplasma. Previous studies based on 18S rRNA and other gene sequences provided a backbone for the phylogeny of piroplasma. However, it is difficult to discriminate species in a comprehensive sample. Here, the abilities of eight DNA regions including 18S rRNA, 28S rRNA, internal transcribed spacer (ITS) regions and COI genes, have been compared as candidates of DNA barcodes for piroplasma. In total, 484 sequences of piroplasma were collected from this study and GenBank. The eight proposed DNA regions were evaluated according to the criterion of Consortium for the Barcode of Life (CBOL). From this evaluation, ITS2 had 100% PCR amplification efficiency, an ideal sequence length, the largest gap between the intra- and inter-specific divergence, 98% identification efficiency at the genus level, and 92% at the species level. Thus, we propose that ITS2 is the most ideal DNA barcode based on the current database for piroplasma.},
}
@article {pmid22787423,
year = {2012},
author = {Gowda, V and Kress, WJ and Htun, T},
title = {Two new species of Gingers (Zingiberaceae) from Myanmar.},
journal = {PhytoKeys},
volume = {},
number = {13},
pages = {5-14},
pmid = {22787423},
issn = {1314-2003},
abstract = {Two new species of gingers (Zingiberaceae), Globba sherwoodiana W.J. Kress &amp; V. Gowda sp. nov., and Curcuma arracanensis W.J. Kress &amp; V. Gowda sp. nov., from Myanmar are described. The new species of Globba is currently only known in cultivation and is commonly grown and sold in markets in Myanmar. In contrast Curcuma arracanensis has been collected from a single restricted region in the cloud forests of the Rakhine Yoma above the Bay of Bengal in western Myanmar. Three-locus DNA barcodes were generated as aids for the identification of the two new species.},
}
@article {pmid22785187,
year = {2012},
author = {Heinrichs, G and de Hoog, GS and Haase, G},
title = {Barcode identifiers as a practical tool for reliable species assignment of medically important black yeast species.},
journal = {Journal of clinical microbiology},
volume = {50},
number = {9},
pages = {3023-3030},
pmid = {22785187},
issn = {1098-660X},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Databases, Genetic ; Humans ; Mycoses/diagnosis/microbiology ; Yeasts/*classification/*genetics/isolation &amp; purification ; },
abstract = {Herpotrichiellaceous black yeasts and relatives comprise severe pathogens flanked by nonpathogenic environmental siblings. Reliable identification by conventional methods is notoriously difficult. Molecular identification is hampered by the sequence variability in the internal transcribed spacer (ITS) domain caused by difficult-to-sequence homopolymeric regions and by poor taxonomic attribution of sequences deposited in GenBank. Here, we present a potential solution using short barcode identifiers (27 to 50 bp) based on ITS2 ribosomal DNA (rDNA), which allows unambiguous definition of species-specific fragments. Starting from proven sequences of ex-type and authentic strains, we were able to describe 103 identifiers. Multiple BLAST searches of these proposed barcode identifiers in GenBank revealed uniqueness for 100 taxonomic entities, whereas the three remaining identifiers each matched with two entities, but the species of these identifiers could easily be discriminated by differences in the remaining ITS regions. Using the proposed barcode identifiers, a 4.1-fold increase of 100% matches in GenBank was achieved in comparison to the classical approach using the complete ITS sequences. The proposed barcode identifiers will be made accessible for the diagnostic laboratory in a permanently updated online database, thereby providing a highly practical, reliable, and cost-effective tool for identification of clinically important black yeasts and relatives.},
}
@article {pmid22784409,
year = {2012},
author = {Scheffers, BR and Joppa, LN and Pimm, SL and Laurance, WF},
title = {What we know and don't know about Earth's missing biodiversity.},
journal = {Trends in ecology &amp; evolution},
volume = {27},
number = {9},
pages = {501-510},
doi = {10.1016/j.tree.2012.05.008},
pmid = {22784409},
issn = {1872-8383},
mesh = {*Biodiversity ; Classification/*methods ; Ecosystem ; Extinction, Biological ; Phylogeny ; Species Specificity ; },
abstract = {Estimates of non-microbial diversity on Earth range from 2 million to over 50 million species, with great uncertainties in numbers of insects, fungi, nematodes, and deep-sea organisms. We summarize estimates for major taxa, the methods used to obtain them, and prospects for further discoveries. Major challenges include frequent synonymy, the difficulty of discriminating certain species by morphology alone, and the fact that many undiscovered species are small, difficult to find, or have small geographic ranges. Cryptic species could be numerous in some taxa. Novel techniques, such as DNA barcoding, new databases, and crowd-sourcing, could greatly accelerate the rate of species discovery. Such advances are timely. Most missing species probably live in biodiversity hotspots, where habitat destruction is rife, and so current estimates of extinction rates from known species are too low.},
}
@article {pmid22784095,
year = {2012},
author = {Balakirev, ES and Krupnova, TN and Ayala, FJ},
title = {DNA variation in the phenotypically-diverse brown alga Saccharina japonica.},
journal = {BMC plant biology},
volume = {12},
number = {},
pages = {108},
pmid = {22784095},
issn = {1471-2229},
mesh = {Base Sequence ; Cell Nucleus/genetics ; DNA, Algal/*genetics ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Electron Transport Complex IV/genetics ; Genetic Markers ; Mitochondria/genetics ; Molecular Sequence Data ; Phaeophyceae/*genetics ; *Phenotype ; Phylogeny ; Plastids/genetics ; *Polymorphism, Genetic ; Recombination, Genetic ; Ribulose-Bisphosphate Carboxylase/genetics ; },
abstract = {BACKGROUND: Saccharina japonica (Areschoug) Lane, Mayes, Druehl et Saunders is an economically important and highly morphologically variable brown alga inhabiting the northwest Pacific marine waters. On the basis of nuclear (ITS), plastid (rbcLS) and mitochondrial (COI) DNA sequence data, we have analyzed the genetic composition of typical Saccharina japonica (TYP) and its two common morphological varieties, known as the "longipes" (LON) and "shallow-water" (SHA) forms seeking to clarify their taxonomical status and to evaluate the possibility of cryptic species within S. japonica.<br><br>RESULTS: The data show that the TYP and LON forms are very similar genetically in spite of drastic differences in morphology, life history traits, and ecological preferences. Both, however, are genetically quite different from the SHA form. The two Saccharina lineages are distinguished by 109 fixed single nucleotide differences as well as by seven fixed length polymorphisms (based on a 4,286 bp concatenated dataset that includes three gene regions). The GenBank database reveals a close affinity of the TYP and LON forms to S. japonica and the SHA form to S. cichorioides. The three gene markers used in the present work have different sensitivity for the algal species identification. COI gene was the most discriminant gene marker. However, we have detected instances of interspecific COI recombination reflecting putative historical hybridization events between distantly related algal lineages. The recombinant sequences show highly contrasted level of divergence in the 5'- and 3'- regions of the gene, leading to significantly different tree topologies depending on the gene segment (5'- or 3'-) used for tree reconstruction. Consequently, the 5'-COI "barcoding" region (~ 650 bp) can be misleading for identification purposes, at least in the case of algal species that might have experienced historical hybridization events.<br><br>CONCLUSION: Taking into account the potential roles of phenotypic plasticity in evolution, we conclude that the TYP and LON forms represent examples of algae phenotypic diversification that enables successful adaptation to contrasting shallow- and deep-water marine environments, while the SHA form is very similar to S. cichorioides and should be considered a different species. Practical applications for algal management and conservation are briefly considered.},
}
@article {pmid22782626,
year = {2012},
author = {Sousa, LC and Gontijo, CM and Lacorte, GA and Meireles, SN and Silva, AP and Fonseca, CG},
title = {Molecular characterization of an opossum Didelphis albiventris (Marsupialia: Didelphidae) population in an urban fragment of the Brazilian Atlantic rainforest and support to species barcode identification.},
journal = {Genetics and molecular research : GMR},
volume = {11},
number = {3},
pages = {2487-2496},
doi = {10.4238/2012.June.15.4},
pmid = {22782626},
issn = {1676-5680},
mesh = {Animals ; Atlantic Ocean ; Brazil ; *Cities ; DNA Barcoding, Taxonomic/*methods ; Didelphis/*classification/*genetics ; Genetics, Population ; Geography ; Haplotypes/genetics ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; *Trees ; },
abstract = {We made a molecular study of 40 opossums, Didelphis albiventris, from an urban fragment of the Atlantic Rainforest in southeastern Brazil, analyzing a 653-bp sequence of cytochrome c oxidase, subunit I. We found three close connected haplotypes, with low nucleotide diversity and a haplotype diversity of 59.1% and confirmed sympatry between D. albiventris and D. aurita in this region. The clear phylogenetic separation shows the appropriateness of DNA barcode identification methodology for effectively discriminating between these opossum species.},
}
@article {pmid22779361,
year = {2012},
author = {Pang, X and Song, J and Xu, H and Yao, H},
title = {[Using ITS2 barcode to identify ephedrae herba].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {37},
number = {8},
pages = {1118-1121},
pmid = {22779361},
issn = {1001-5302},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/*genetics ; Ephedra sinica/classification/*genetics ; },
abstract = {OBJECTIVE: To identify Ephedrae Herba using the ITS2 barcode and to secure its quality and safety in medication.<br><br>METHOD: Total genomic DNA was isolated from Ephedrae Herba and its closely related species. Nuclear DNA ITS2 sequences were amplified, and purified PCR products were sequenced. Sequence assembly and consensus sequence generation were performed using the CodonCode Aligner. The Kimura 2-Parameter (K2P) distances were calculated using software MEGA 5.0. Identification analyses were performed using BLAST1, Nearest Distance and neighbor-joining (NJ) methods.<br><br>RESULT: The intra-specific genetic distances of Ephedrae Herba were ranged from 0 to 0.002. The inter-specific genetic distances between Ephedrae Herba and its closely related species were ranged from 0.004 to 0.034. All the three methods showed that ITS2 could discriminate Ephedrae Herba from its closely related species correctly.<br><br>CONCLUSION: The ITS2 region is suitable to be used for authentication of Ephedrae Herba, and our study further confirmed the effectiveness of ITS2 to identify traditional Chinese medicinal materials.},
}
@article {pmid22779360,
year = {2012},
author = {Pang, X and Xu, H and Han, J and Song, J},
title = {[Applying DNA barcoding technique to identify menthae haplocalycis herba].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {37},
number = {8},
pages = {1114-1117},
pmid = {22779360},
issn = {1001-5302},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/*genetics ; Plants, Medicinal/classification/*genetics ; Sequence Analysis, DNA/methods ; },
abstract = {OBJECTIVE: To identify Menthae Haplocalycis Herba and its closely related species using DNA barcoding technique.<br><br>METHOD: Total genomic DNA was isolated from Mentha canadensis and its closely related species. Nuclear DNA ITS2 sequences were amplified, and purified PCR products were sequenced. Sequence assembly and consensus sequence generation were performed using the CodonCode Aligner V3.0. The Kimura 2-Parameter (K2P) distances were calculated using software MEGA 5.0. Identification analyses were performed using BLAST1, Nearest Distance and neighbor-joining (NJ) methods.<br><br>RESULT: The intra-specific genetic distances of M. canadensis were ranged from 0 to 0.006, which were lower than inter-specific genetic distances between M. canadensis and its closely related species (0.071-0.231). All the three methods showed that ITS2 could discriminate M. canadensis from its closely related species correctly.<br><br>CONCLUSION: The ITS2 region is an efficient barcode for identification of Menthae Haplocalycis Herba, which provides a scientific basis for fast and accurate identification of the herb.},
}
@article {pmid22779359,
year = {2012},
author = {Chen, Q and Liu, Y and Liu, Z and Chen, S and Chen, K},
title = {[DNA bacording of Verbenaceae medicinal plant by using ITS2 and psbA-trnH region].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {37},
number = {8},
pages = {1107-1113},
pmid = {22779359},
issn = {1001-5302},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; DNA, Ribosomal Spacer/*genetics ; Plants, Medicinal/classification/*genetics ; Verbenaceae/classification/*genetics ; },
abstract = {OBJECTIVE: To evaluate the ability of several hotspot candidate sequence of DNA barcodes for identifying medicinal plant species in Verbenaceae.<br><br>METHOD: Using universal primers, three chloroplast sequences, psbA-trnH, rbcL, matK, two nuclear ribosomal DNA ITS2 and ITS were amplified and sequenced. PCR amplification and sequencing efficiency, intra- and inter-specific variation, barcoding gap and identification efficiency (with BLAST 1 and Nearest Distance methods) were used to evaluate these loci.<br><br>RESULT: The rate of successful amplification using matK was too low to further analyze, and the rate of successful amplification and sequencing using psbA-trnH, ITS, and ITS2 and rbcL sequence was 83.6%, 83.6%, 96.4%, 98.2%, respectively. The rate of successful identification using psbA-trnH, ITS, and ITS2 was 100% at the species level except that rbcL was 77.8%, 75.9% for 55 samples belonging to 32 species, but ITS2 did better in intra- and inter-specific variation, barcoding gap than the other loci. The rate of successful identification of ITS2 was 89.5%, 87.6% even when joining the date of 165 samples from GenBank.<br><br>CONCLUSION: It proposes that the combination of ITS2 and psbA-trnH senquence is promising for the identification of the species in Verbenaceae.},
}
@article {pmid22779358,
year = {2012},
author = {Zhang, B and Yuan, Q and Huang, L and Liu, X and Li, X and Lin, S and Chen, M and Ge, X},
title = {[Locality identification of Chinese medicinal plant Scutellaria baicalensis (Lamiaceae) population-level DNA barcoding].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {37},
number = {8},
pages = {1100-1106},
pmid = {22779358},
issn = {1001-5302},
mesh = {DNA Barcoding, Taxonomic/*methods ; Haplotypes ; Medicine, Chinese Traditional/*methods ; Phylogeny ; Scutellaria baicalensis/classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {Scutellaria baicalensis is an important traditional Chinese medicine and Scutellaria flavonoids have received worldwide attention in recent years. It is the basis of controlling quality of S. baicalensis to develop a reliable genetic marker system used to identify locality of origin. Because of the characteristics of maternal inherited and high-rate of evolution, the cpDNA intergenic spacer can effectively elucidate the degree of genetic variation in different areas of the same species (populations), which can be used as the population-level DNA barcoding to locality identify. In this study, we have used the molecular phylogeography analysis for the three cpDNA intergenic spacers atpB-rbcL, trnL-trnF and psbA-trnH of 17 wild populations from different localities, which reveals the 20 haplotypes, including 13 polymorphic sites and constitutes a shallow gene tree. The authers have divided the haplotypes of S. baicalensis into three grades of population-level DNA barcoding according to the frequence and geographic distribution: 3 highest-frequency haplotypes as area-population-level DNA barcoding, 3 haplotypes were mainly shared by 2-3 adjacent populations as region-population-level DNA barcoding, and there are also 8 unique-population haplotypes as unique-population-level DNA barcoding. The result of this study reveals that population-level DNA barcoding is a reliable genetic marker used to locality identify of S. baicalensis.},
}
@article {pmid22779357,
year = {2012},
author = {Pang, X and Song, J and Chen, S},
title = {[Identification of Junci Medulla using DNA barcoding technique].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {37},
number = {8},
pages = {1097-1099},
pmid = {22779357},
issn = {1001-5302},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant ; DNA, Ribosomal Spacer ; Plants, Medicinal/classification/*genetics ; },
abstract = {OBJECTIVE: To identify Junci Medulla using the ITS2 barcode.<br><br>METHOD: The ITS2 regions of Juncus effuses and its closely related species were PCR amplified and sequenced. Sequence assembly and consensus sequence generation were performed using the CodonCode Aligner. The Kimura 2-Parameter (K2P) distances were calculated using software MEGA 5.0. Identification analyses were performed using BLAST1, Nearest Distance, PWG Distance and neighbor-joining (NJ) methods.<br><br>RESULT: The intra-specific genetic distances of J. effuses were ranged from 0 to 0.005, which were far lower than inter-specific genetic distances between J. effuses and its closely related species (0.215-0.614). All the four methods showed that ITS2 could discriminate J. effuses from its closely related species correctly.<br><br>CONCLUSION: The ITS2 region is an efficient barcode for authentication of Junci Medulla, and our study further confirmed the ability of ITS2 to identify traditional Chinese medicinal materials.},
}
@article {pmid22779349,
year = {2012},
author = {Han, J and Song, J and Yao, H and Chen, X and Chen, S},
title = {[Comparison of DNA barcoders in identifying medicinal materials].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {37},
number = {8},
pages = {1056-1061},
pmid = {22779349},
issn = {1001-5302},
mesh = {DNA Barcoding, Taxonomic/*methods ; Genes, Chloroplast ; Medicine, Chinese Traditional ; Plants, Medicinal/classification/genetics ; },
abstract = {The DNA barcoding of traditional Chinese medicine was summarized in this article. Based on analyzing a number of research findings, the authors discussed the possibility of nuclear DNA sequence and chloroplast genes in identifying medicinal materials. ITS was considered to evolve faster, which was used for plant molecular systematics analysis and species identification,while ITS2 was more suitable to identify medicinal materials. So, it is important that we should select suitable DNA sequences as barcodes based on the objective of a study. With the cost reduction of sequencing, identifying medicinal materials by cp-genome barcoding would be applied broadly and effectively in the future.},
}
@article {pmid22779348,
year = {2012},
author = {Chen, S and Guo, B and Zhang, G and Yan, Z and Luo, G and Sun, S and Wu, H and Huang, L and Pang, X and Chen, J},
title = {[Advances of studies on new technology and method for identifying traditional Chinese medicinal materials].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {37},
number = {8},
pages = {1043-1055},
pmid = {22779348},
issn = {1001-5302},
mesh = {DNA Barcoding, Taxonomic ; Drugs, Chinese Herbal/*chemistry ; Medicine, Chinese Traditional ; Oligonucleotide Array Sequence Analysis ; Polymerase Chain Reaction ; },
abstract = {In this review, the authors summarized the new technologies and methods for identifying traditional Chinese medicinal materials, including molecular identification, chemical identification, morphological identification, microscopic identification and identification based on biological effects. The authors introduced the principle, characteristics, application and prospect on each new technology or method and compared their advantages and disadvantages. In general, new methods make the result more objective and accurate. DNA barcoding technique and spectroscopy identification have their owner obvious strongpoint in universality and digitalization. In the near future, the two techniques are promising to be the main trend for identifying traditional Chinese medicinal materials. The identification techniques based on microscopy, liquid chromatography, PCR, biological effects and DNA chip will be indispensable supplements. However, the bionic identification technology is just placed in the developing stage at present.},
}
@article {pmid22768134,
year = {2012},
author = {Hartig, G and Peters, RS and Borner, J and Etzbauer, C and Misof, B and Niehuis, O},
title = {Oligonucleotide primers for targeted amplification of single-copy nuclear genes in apocritan Hymenoptera.},
journal = {PloS one},
volume = {7},
number = {6},
pages = {e39826},
pmid = {22768134},
issn = {1932-6203},
mesh = {Animals ; Cell Nucleus/*genetics ; DNA Primers/*metabolism ; Electrophoresis, Agar Gel ; Gene Dosage/*genetics ; Genes, Insect/*genetics ; Hymenoptera/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/*methods ; Sequence Homology, Nucleic Acid ; },
abstract = {BACKGROUND: Published nucleotide sequence data from the mega-diverse insect order Hymenoptera (sawflies, bees, wasps, and ants) are taxonomically scattered and still inadequate for reconstructing a well-supported phylogenetic tree for the order. The analysis of comprehensive multiple gene data sets obtained via targeted PCR could provide a cost-effective solution to this problem. However, oligonucleotide primers for PCR amplification of nuclear genes across a wide range of hymenopteran species are still scarce.<br><br>FINDINGS: Here we present a suite of degenerate oligonucleotide primer pairs for PCR amplification of 154 single-copy nuclear protein-coding genes from Hymenoptera. These primers were inferred from genome sequence data from nine Hymenoptera (seven species of ants, the honeybee, and the parasitoid wasp Nasonia vitripennis). We empirically tested a randomly chosen subset of these primer pairs for amplifying target genes from six Hymenoptera, representing the families Chrysididae, Crabronidae, Gasteruptiidae, Leucospidae, Pompilidae, and Stephanidae. Based on our results, we estimate that these primers are suitable for studying a large number of nuclear genes across a wide range of apocritan Hymenoptera (i.e., all hymenopterans with a wasp-waist) and of aculeate Hymenoptera in particular (i.e., apocritan wasps with stingers).<br><br>CONCLUSIONS: The amplified nucleotide sequences are (a) with high probability from single-copy genes, (b) easily generated at low financial costs, especially when compared to phylogenomic approaches, (c) easily sequenced by means of an additionally provided set of sequencing primers, and (d) suitable to address a wide range of phylogenetic questions and to aid rapid species identification via barcoding, as many amplicons contain both exonic and fast-evolving intronic nucleotides.},
}
@article {pmid22767882,
year = {2012},
author = {Uysal, I and Hohberger, C and Rasmussen, RS and Ulrich, DA and Emond, JP and Gutierrez, A},
title = {Effects of radio frequency identification-related radiation on in vitro biologics.},
journal = {PDA journal of pharmaceutical science and technology},
volume = {66},
number = {4},
pages = {333-345},
doi = {10.5731/pdajpst.2012.00875},
pmid = {22767882},
issn = {1948-2124},
mesh = {*Biological Products ; Consumer Product Safety ; Electromagnetic Fields ; Erythrocytes/radiation effects ; In Vitro Techniques ; Pharmaceutical Preparations ; *Radio Frequency Identification Device ; Radio Waves ; },
abstract = {UNLABELLED: The recent developments on the use of e-pedigree to identify the chain of custody of drugs suggests the use of advanced track and trace technologies such as two-dimensional barcodes and radio frequency identification (RFID) tags. RFID technology is used mainly for valuable commodities such as pharmaceutical products while incorporating additional functionalities like monitoring environmental variables to ensure product safety and quality. In its guidance for the use of RFID technologies for drugs (Compliance Policy Guide Section 400.210), the Food and Drug Administration outlined multiple parameters that would apply to any study or application using RFID. However, drugs approved under a Biologics License Application or protein drugs covered by a New Drug Application were excluded mainly due to concerns about the effects of radio frequency radiation (thermal and/or non-thermal) on biologics. Even though the thermal effects of radio frequency on biologics are relatively well understood, there are few studies in the literature about the non-thermal effects of radio frequency with regards to the protein structure integrity. In this paper, we analyze the non-thermal effects of radio frequency radiation by exposing a wide variety of biologics including biopharmaceuticals with vaccines, hormones, and immunoglobulins, as well as cellular blood products such as red blood cells and whole blood-derived platelets as well as fresh frozen plasma. In order to represent the majority of the frequency spectrum used in RFID applications, five different frequencies (13.56 MHz, 433 MHz, 868 MHz, 915 MHz, and 2.4 GHz) are used to account for the most commonly used international frequency bands for RFID. With the help of specialized radio frequency signal-generating hardware, magnetic and electromagnetic fields are created around the exposed products with power levels greater than Federal Communications Commission-regulated limits. The in vitro test results on more than 100 biopharmaceutical products from eight major pharmaceutical companies as well, as different blood products, show no non-thermal effect by radio frequency radiation.<br><br>LAY ABSTRACT: Forthcoming requirements, such as the California Board of Pharmacy Track and Trace initiative regarding the use of e-pedigree to identify the chain of custody of drugs, suggest the use of advanced track and trace technologies such as two-dimensional barcodes and radio frequency identification (RFID) tags. When used for pharmaceuticals, RFID technology can support additional functionalities like monitoring temperature to ensure product safety. In its guidance for the use of RFID technologies for drugs, the Food and Drug Administration outlined multiple parameters that would apply to pilot studies using RFID while excluding drugs approved under a Biologics License Application or protein drugs covered by a New Drug Application due to concerns about the effects of radio frequency radiation on biologics. Even though the effects of radio frequency on biologics due to temperature changes are relatively well understood, there are few studies in the literature about other effects of radio frequency that can occur without a noticeable change in temperature. In this paper, we expose a wide variety of biologics including biopharmaceuticals to radio frequency radiation at different frequencies, as well as cellular blood products and plasma to high frequency radiation. The in vitro test results show no detectable effect due to radio frequency radiation.},
}
@article {pmid22761951,
year = {2012},
author = {Galimberti, A and Spada, M and Russo, D and Mucedda, M and Agnelli, P and Crottini, A and Ferri, E and Martinoli, A and Casiraghi, M},
title = {Integrated operational taxonomic units (IOTUs) in echolocating bats: a bridge between molecular and traditional taxonomy.},
journal = {PloS one},
volume = {7},
number = {6},
pages = {e40122},
pmid = {22761951},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Chiroptera/classification/*physiology ; DNA Barcoding, Taxonomic ; DNA Primers ; *Echolocation ; Polymerase Chain Reaction ; },
abstract = {BACKGROUND: Nowadays, molecular techniques are widespread tools for the identification of biological entities. However, until very few years ago, their application to taxonomy provoked intense debates between traditional and molecular taxonomists. To prevent every kind of disagreement, it is essential to standardize taxonomic definitions. Along these lines, we introduced the concept of Integrated Operational Taxonomic Unit (IOTU). IOTUs come from the concept of Operational Taxonomic Unit (OTU) and paralleled the Molecular Operational Taxonomic Unit (MOTU). The latter is largely used as a standard in many molecular-based works (even if not always explicitly formalized). However, while MOTUs are assigned solely on molecular variation criteria, IOTUs are identified from patterns of molecular variation that are supported by at least one more taxonomic characteristic.<br><br>We tested the use of IOTUs on the widest DNA barcoding dataset of Italian echolocating bats species ever assembled (i.e. 31 species, 209 samples). We identified 31 molecular entities, 26 of which corresponded to the morphologically assigned species, two MOTUs and three IOTUs. Interestingly, we found three IOTUs in Myotis nattereri, one of which is a newly described lineage found only in central and southern Italy. In addition, we found a level of molecular variability within four vespertilionid species deserving further analyses. According to our scheme two of them (i.e. M.bechsteinii and Plecotus auritus) should be ranked as unconfirmed candidate species (UCS).<br><br>CONCLUSIONS/SIGNIFICANCE: From a systematic point of view, IOTUs are more informative than the general concept of OTUs and the more recent MOTUs. According to information content, IOTUs are closer to species, although it is important to underline that IOTUs are not species. Overall, the use of a more precise panel of taxonomic entities increases the clarity in the systematic field and has the potential to fill the gaps between modern and traditional taxonomy.},
}
@article {pmid22761800,
year = {2012},
author = {Kool, A and de Boer, HJ and Krüger, A and Rydberg, A and Abbad, A and Björk, L and Martin, G},
title = {Molecular identification of commercialized medicinal plants in southern Morocco.},
journal = {PloS one},
volume = {7},
number = {6},
pages = {e39459},
pmid = {22761800},
issn = {1932-6203},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; Molecular Sequence Data ; Morocco ; Plant Roots/*genetics ; Plants, Medicinal/*genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Medicinal plant trade is important for local livelihoods. However, many medicinal plants are difficult to identify when they are sold as roots, powders or bark. DNA barcoding involves using a short, agreed-upon region of a genome as a unique identifier for species- ideally, as a global standard.<br><br>RESEARCH QUESTION: What is the functionality, efficacy and accuracy of the use of barcoding for identifying root material, using medicinal plant roots sold by herbalists in Marrakech, Morocco, as a test dataset.<br><br>METHODOLOGY: In total, 111 root samples were sequenced for four proposed barcode regions rpoC1, psbA-trnH, matK and ITS. Sequences were searched against a tailored reference database of Moroccan medicinal plants and their closest relatives using BLAST and Blastclust, and through inference of RAxML phylograms of the aligned market and reference samples.<br><br>PRINCIPAL FINDINGS: Sequencing success was high for rpoC1, psbA-trnH, and ITS, but low for matK. Searches using rpoC1 alone resulted in a number of ambiguous identifications, indicating insufficient DNA variation for accurate species-level identification. Combining rpoC1, psbA-trnH and ITS allowed the majority of the market samples to be identified to genus level. For a minority of the market samples, the barcoding identification differed significantly from previous hypotheses based on the vernacular names.<br><br>CONCLUSIONS/SIGNIFICANCE: Endemic plant species are commercialized in Marrakech. Adulteration is common and this may indicate that the products are becoming locally endangered. Nevertheless the majority of the traded roots belong to species that are common and not known to be endangered. A significant conclusion from our results is that unknown samples are more difficult to identify than earlier suggested, especially if the reference sequences were obtained from different populations. A global barcoding database should therefore contain sequences from different populations of the same species to assure the reference sequences characterize the species throughout its distributional range.},
}
@article {pmid22760212,
year = {2012},
author = {Vallania, F and Ramos, E and Cresci, S and Mitra, RD and Druley, TE},
title = {Detection of rare genomic variants from pooled sequencing using SPLINTER.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {64},
pages = {},
pmid = {22760212},
issn = {1940-087X},
support = {U01AG023746/AG/NIA NIH HHS/United States ; 3R01DA025744-02S1/DA/NIDA NIH HHS/United States ; P30 CA091842/CA/NCI NIH HHS/United States ; UL1 TR000448/TR/NCATS NIH HHS/United States ; U01 AG023746/AG/NIA NIH HHS/United States ; K08 CA140720/CA/NCI NIH HHS/United States ; 1R01DA025744-01/DA/NIDA NIH HHS/United States ; UL1RR024992/RR/NCRR NIH HHS/United States ; UL1 RR024992/RR/NCRR NIH HHS/United States ; P30 CA91842/CA/NCI NIH HHS/United States ; R01 DA025744/DA/NIDA NIH HHS/United States ; 1K08CA140720-01A1/CA/NCI NIH HHS/United States ; },
mesh = {*Algorithms ; Alleles ; Base Sequence ; DNA/*chemistry/*genetics ; DNA, Neoplasm/chemistry/genetics ; Genetic Loci ; Genomics/*methods ; Molecular Sequence Data ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/*methods ; Software ; },
abstract = {As DNA sequencing technology has markedly advanced in recent years(2), it has become increasingly evident that the amount of genetic variation between any two individuals is greater than previously thought(3). In contrast, array-based genotyping has failed to identify a significant contribution of common sequence variants to the phenotypic variability of common disease(4,5). Taken together, these observations have led to the evolution of the Common Disease / Rare Variant hypothesis suggesting that the majority of the "missing heritability" in common and complex phenotypes is instead due to an individual's personal profile of rare or private DNA variants(6-8). However, characterizing how rare variation impacts complex phenotypes requires the analysis of many affected individuals at many genomic loci, and is ideally compared to a similar survey in an unaffected cohort. Despite the sequencing power offered by today's platforms, a population-based survey of many genomic loci and the subsequent computational analysis required remains prohibitive for many investigators. To address this need, we have developed a pooled sequencing approach(1,9) and a novel software package(1) for highly accurate rare variant detection from the resulting data. The ability to pool genomes from entire populations of affected individuals and survey the degree of genetic variation at multiple targeted regions in a single sequencing library provides excellent cost and time savings to traditional single-sample sequencing methodology. With a mean sequencing coverage per allele of 25-fold, our custom algorithm, SPLINTER, uses an internal variant calling control strategy to call insertions, deletions and substitutions up to four base pairs in length with high sensitivity and specificity from pools of up to 1 mutant allele in 500 individuals. Here we describe the method for preparing the pooled sequencing library followed by step-by-step instructions on how to use the SPLINTER package for pooled sequencing analysis (http://www.ibridgenetwork.org/wustl/splinter). We show a comparison between pooled sequencing of 947 individuals, all of whom also underwent genome-wide array, at over 20kb of sequencing per person. Concordance between genotyping of tagged and novel variants called in the pooled sample were excellent. This method can be easily scaled up to any number of genomic loci and any number of individuals. By incorporating the internal positive and negative amplicon controls at ratios that mimic the population under study, the algorithm can be calibrated for optimal performance. This strategy can also be modified for use with hybridization capture or individual-specific barcodes and can be applied to the sequencing of naturally heterogeneous samples, such as tumor DNA.},
}
@article {pmid22750145,
year = {2012},
author = {Snyder, SR and Favoretto, AM and Derzon, JH and Christenson, RH and Kahn, SE and Shaw, CS and Baetz, RA and Mass, D and Fantz, CR and Raab, SS and Tanasijevic, MJ and Liebow, EB},
title = {Effectiveness of barcoding for reducing patient specimen and laboratory testing identification errors: a Laboratory Medicine Best Practices systematic review and meta-analysis.},
journal = {Clinical biochemistry},
volume = {45},
number = {13-14},
pages = {988-998},
pmid = {22750145},
issn = {1873-2933},
support = {CC999999/ImCDC/Intramural CDC HHS/United States ; W911NF-07-D-0001/DO 0191/TCN 07235//PHS HHS/United States ; },
mesh = {Centers for Disease Control and Prevention, U.S. ; Clinical Laboratory Techniques/methods/*standards ; Databases, Factual ; Diagnostic Errors/*prevention &amp; control ; Electronic Data Processing/methods ; Evidence-Based Practice/methods/*standards ; Humans ; Odds Ratio ; Practice Guidelines as Topic/standards ; Program Evaluation/*methods ; Quality Assurance, Health Care/standards ; United States ; },
abstract = {OBJECTIVES: This is the first systematic review of the effectiveness of barcoding practices for reducing patient specimen and laboratory testing identification errors.<br><br>DESIGN AND METHODS: The CDC-funded Laboratory Medicine Best Practices Initiative systematic review methods for quality improvement practices were used.<br><br>RESULTS: A total of 17 observational studies reporting on barcoding systems are included in the body of evidence; 10 for patient specimens and 7 for point-of-care testing. All 17 studies favored barcoding, with meta-analysis mean odds ratios for barcoding systems of 4.39 (95% CI: 3.05-6.32) and for point-of-care testing of 5.93 (95% CI: 5.28-6.67).<br><br>CONCLUSIONS: Barcoding is effective for reducing patient specimen and laboratory testing identification errors in diverse hospital settings and is recommended as an evidence-based "best practice." The overall strength of evidence rating is high and the effect size rating is substantial. Unpublished studies made an important contribution comprising almost half of the body of evidence.},
}
@article {pmid22742754,
year = {2012},
author = {Brusco, JM},
title = {Incorporating barcoding into the perioperative setting.},
journal = {AORN journal},
volume = {96},
number = {1},
pages = {86-89},
doi = {10.1016/j.aorn.2012.04.026},
pmid = {22742754},
issn = {1878-0369},
mesh = {*Electronic Data Processing/standards ; Inventories, Hospital ; Medication Systems, Hospital ; Patient Identification Systems ; *Perioperative Nursing ; United States ; },
}
@article {pmid22726897,
year = {2012},
author = {Yang, CH and Chuang, LY and Cheng, YH and Lin, YD and Wang, CL and Wen, CH and Chang, HW},
title = {Single nucleotide polymorphism barcoding to evaluate oral cancer risk using odds ratio-based genetic algorithms.},
journal = {The Kaohsiung journal of medical sciences},
volume = {28},
number = {7},
pages = {362-368},
doi = {10.1016/j.kjms.2012.02.002},
pmid = {22726897},
issn = {2410-8650},
mesh = {*Algorithms ; Confidence Intervals ; Humans ; *Models, Genetic ; Mouth Neoplasms/*genetics ; Odds Ratio ; *Polymorphism, Single Nucleotide ; Risk Factors ; },
abstract = {Cancers often involve the synergistic effects of gene-gene interactions, but identifying these interactions remains challenging. Here, we present an odds ratio-based genetic algorithm (OR-GA) that is able to solve the problems associated with the simultaneous analysis of multiple independent single nucleotide polymorphisms (SNPs) that are associated with oral cancer. The SNP interactions between four SNPs-namely rs1799782, rs2040639, rs861539, rs2075685, and belonging to four genes (XRCC1, XRCC2, XRCC3, and XRCC4)-were tested in this study, respectively. The GA decomposes the SNPs sets into different SNP combinations with their corresponding genotypes (called SNP barcodes). The GA can effectively identify a specific SNP barcode that has an optimized fitness value and uses this to calculate the difference between the case and control groups. The SNP barcodes with a low fitness value are naturally removed from the population. Using two to four SNPs, the best SNP barcodes with maximum differences in occurrence between the case and control groups were generated by GA algorithm. Subsequently, the OR provides a quantitative measure of the multiple SNP synergies between the oral cancer and control groups by calculating the risk related to the best SNP barcodes and others. When these were compared to their corresponding non-SNP barcodes, the estimated ORs for oral cancer were found to be great than 1 [approx. 1.72-2.23; confidence intervals (CIs): 0.94-5.30, p < 0.03-0.07] for various specific SNP barcodes with two to four SNPs. In conclusion, the proposed OR-GA method successfully generates SNP barcodes, which allow oral cancer risk to be evaluated and in the process the OR-GA method identifies possible SNP-SNP interactions.},
}
@article {pmid22724511,
year = {2012},
author = {Nicholls, JA and Challis, RJ and Mutun, S and Stone, GN},
title = {Mitochondrial barcodes are diagnostic of shared refugia but not species in hybridizing oak gallwasps.},
journal = {Molecular ecology},
volume = {21},
number = {16},
pages = {4051-4062},
doi = {10.1111/j.1365-294X.2012.05683.x},
pmid = {22724511},
issn = {1365-294X},
support = {G0900740/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; Genetic Variation ; *Genetics, Population ; *Hybridization, Genetic ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeography ; Wasps/classification/*genetics ; },
abstract = {Mitochondrial DNA barcodes provide a simple taxonomic tool for systematic and ecological research, with particular benefit for poorly studied or species-rich taxa. Barcoding assumes genetic diversity follows species boundaries; however, many processes disrupt species-level monophyly of barcodes leading to incorrect classifications. Spatial population structure, particularly when shared across closely related and potentially hybridizing taxa, can invalidate barcoding approaches yet few data exist to examine its impacts. We test how shared population structure across hybridizing species impacts upon mitochondrial barcodes by sequencing the cytochrome b gene for 518 individuals of four well-delimited Western Palaearctic gallwasp species within the Andricus quercuscalicis species group. Mitochondrial barcodes clustered individuals into mixed-species clades corresponding to refugia, with no difference in within- and between-species divergence. Four nuclear genes were also sequenced from 4 to 11 individuals per refugial population of each species. Multi-locus analyses of these data supported established species, with no support for the refugial clustering across species seen in mitochondrial barcodes. This pattern is consistent with mitochondrial introgression among populations of species sharing the same glacial refugium, such that mitochondrial barcodes identify a shared history of population structure rather than species. Many taxa show phylogeographic structure across glacial refugia, suggesting that mitochondrial barcoding may fail when applied to other sets of co-distributed, closely related species. Robust barcoding approaches must sample extensively across population structure to disentangle spatial from species-level variation. Methods incorporating multiple unlinked loci are also essential to accommodate coalescent variation among genes and provide power to resolve recently diverged species.},
}
@article {pmid22721826,
year = {2013},
author = {Webster, BL and Culverwell, CL and Khamis, IS and Mohammed, KA and Rollinson, D and Stothard, JR},
title = {DNA barcoding of Schistosoma haematobium on Zanzibar reveals substantial genetic diversity and two major phylogenetic groups.},
journal = {Acta tropica},
volume = {128},
number = {2},
pages = {206-217},
doi = {10.1016/j.actatropica.2012.06.002},
pmid = {22721826},
issn = {1873-6254},
mesh = {Adolescent ; Animals ; Child ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; *Genetic Variation ; Genotype ; Haplotypes ; Humans ; Male ; Molecular Epidemiology ; Molecular Sequence Data ; Molecular Typing/methods ; NADH Dehydrogenase/genetics ; Parasitology/methods ; *Phylogeny ; Schistosoma haematobium/*classification/*genetics/isolation &amp; purification ; Schistosomiasis haematobia/epidemiology/*parasitology ; Sequence Analysis, DNA ; Tanzania/epidemiology ; },
abstract = {To shed light on the genetic diversity of Schistosoma haematobium on Zanzibar a DNA barcoding study was performed on parasite material isolated from different time-points 4 years apart. Substantive sequence variation was found within the mitochondrial cytochrome oxidase subunit I (cox1) and the NADH-dehydrogenase subunit 1 (nad1) with 27 and 22 unique haplotypes identified respectively and 38 when both gene regions were considered. Upon phylogenetic analysis and comparison with other S. haematobium isolates, haplotypes or barcode types partitioned into two discrete major groups, designated Group 1 and Group 2. Whilst Group 1 isolates were recovered from both Zanzibar and the African mainland, Group 2 isolates were exclusive to Zanzibar. A mixture of Group 1 and 2 parasites were recovered from individual children with no child shedding parasites of a single group haplotype alone. Whilst changes in general levels of genetic diversity between the two parasite isolation time-points were observed, no obvious change in genetic diversity was detected, despite large-scale drug distribution of praziquantel during the intervening period and there was no biased of Group 1 or 2 parasites persisting at the different time-points. To assist in future genetic screening of schistosome larval stages e.g. eggs, miracidia or cercariae, two new DNA-typing assays based on group-specific PCR primers and SNaPshot™ probes have been developed to distinguish Group 1 and 2 haplotypes.},
}
@article {pmid22715304,
year = {2012},
author = {Nagpure, NS and Rashid, I and Pathak, AK and Singh, M and Singh, SP and Sarkar, UK},
title = {FBIS: A regional DNA barcode archival &amp; analysis system for Indian fishes.},
journal = {Bioinformation},
volume = {8},
number = {10},
pages = {483-488},
pmid = {22715304},
issn = {0973-2063},
abstract = {UNLABELLED: DNA barcode is a new tool for taxon recognition and classification of biological organisms based on sequence of a fragment of mitochondrial gene, cytochrome c oxidase I (COI). In view of the growing importance of the fish DNA barcoding for species identification, molecular taxonomy and fish diversity conservation, we developed a Fish Barcode Information System (FBIS) for Indian fishes, which will serve as a regional DNA barcode archival and analysis system. The database presently contains 2334 sequence records of COI gene for 472 aquatic species belonging to 39 orders and 136 families, collected from available published data sources. Additionally, it contains information on phenotype, distribution and IUCN Red List status of fishes. The web version of FBIS was designed using MySQL, Perl and PHP under Linux operating platform to (a) store and manage the acquisition (b) analyze and explore DNA barcode records (c) identify species and estimate genetic divergence. FBIS has also been integrated with appropriate tools for retrieving and viewing information about the database statistics and taxonomy. It is expected that FBIS would be useful as a potent information system in fish molecular taxonomy, phylogeny and genomics.<br><br>AVAILABILITY: The database is available for free at http://mail.nbfgr.res.in/fbis/},
}
@article {pmid22715287,
year = {2012},
author = {Kiss, L},
title = {Limits of nuclear ribosomal DNA internal transcribed spacer (ITS) sequences as species barcodes for Fungi.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {109},
number = {27},
pages = {E1811; author reply E1812},
pmid = {22715287},
issn = {1091-6490},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/*genetics ; DNA, Ribosomal Spacer/*genetics ; Fungi/*genetics ; },
}
@article {pmid22705793,
year = {2012},
author = {Kim, H and Han, H and Ahn, J and Lee, J and Cho, N and Jang, H and Kim, H and Kwon, S and Bang, D},
title = {'Shotgun DNA synthesis' for the high-throughput construction of large DNA molecules.},
journal = {Nucleic acids research},
volume = {40},
number = {18},
pages = {e140},
pmid = {22705793},
issn = {1362-4962},
mesh = {DNA/*biosynthesis ; *High-Throughput Nucleotide Sequencing ; Oligonucleotide Array Sequence Analysis ; Penicillins/biosynthesis ; Polymerase Chain Reaction ; Synthetic Biology ; },
abstract = {We developed a highly scalable 'shotgun' DNA synthesis technology by utilizing microchip oligonucleotides, shotgun assembly and next-generation sequencing technology. A pool of microchip oligonucleotides targeting a penicillin biosynthetic gene cluster were assembled into numerous random fragments, and tagged with 20 bp degenerate barcode primer pairs. An optimal set of error-free fragments were identified by high-throughput DNA sequencing, selectively amplified using the barcode sequences, and successfully assembled into the target gene cluster.},
}
@article {pmid22701588,
year = {2012},
author = {de Vere, N and Rich, TC and Ford, CR and Trinder, SA and Long, C and Moore, CW and Satterthwaite, D and Davies, H and Allainguillaume, J and Ronca, S and Tatarinova, T and Garbett, H and Walker, K and Wilkinson, MJ},
title = {DNA barcoding the native flowering plants and conifers of Wales.},
journal = {PloS one},
volume = {7},
number = {6},
pages = {e37945},
pmid = {22701588},
issn = {1932-6203},
mesh = {Base Sequence ; Cluster Analysis ; Computational Biology/*methods ; *DNA Barcoding, Taxonomic ; *Databases, Genetic ; Demography ; Magnoliopsida/classification/*genetics ; Molecular Sequence Data ; Phylogeny ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; Tracheophyta/classification/*genetics ; Wales ; },
abstract = {We present the first national DNA barcode resource that covers the native flowering plants and conifers for the nation of Wales (1143 species). Using the plant DNA barcode markers rbcL and matK, we have assembled 97.7% coverage for rbcL, 90.2% for matK, and a dual-locus barcode for 89.7% of the native Welsh flora. We have sampled multiple individuals for each species, resulting in 3304 rbcL and 2419 matK sequences. The majority of our samples (85%) are from DNA extracted from herbarium specimens. Recoverability of DNA barcodes is lower using herbarium specimens, compared to freshly collected material, mostly due to lower amplification success, but this is balanced by the increased efficiency of sampling species that have already been collected, identified, and verified by taxonomic experts. The effectiveness of the DNA barcodes for identification (level of discrimination) is assessed using four approaches: the presence of a barcode gap (using pairwise and multiple alignments), formation of monophyletic groups using Neighbour-Joining trees, and sequence similarity in BLASTn searches. These approaches yield similar results, providing relative discrimination levels of 69.4 to 74.9% of all species and 98.6 to 99.8% of genera using both markers. Species discrimination can be further improved using spatially explicit sampling. Mean species discrimination using barcode gap analysis (with a multiple alignment) is 81.6% within 10×10 km squares and 93.3% for 2×2 km squares. Our database of DNA barcodes for Welsh native flowering plants and conifers represents the most complete coverage of any national flora, and offers a valuable platform for a wide range of applications that require accurate species identification.},
}
@article {pmid22701556,
year = {2012},
author = {Cerutti-Pereyra, F and Meekan, MG and Wei, NW and O'Shea, O and Bradshaw, CJ and Austin, CM},
title = {Identification of rays through DNA barcoding: an application for ecologists.},
journal = {PloS one},
volume = {7},
number = {6},
pages = {e36479},
pmid = {22701556},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Evolution, Molecular ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Skates, Fish/*classification/*genetics ; Species Specificity ; Western Australia ; },
abstract = {DNA barcoding potentially offers scientists who are not expert taxonomists a powerful tool to support the accuracy of field studies involving taxa that are diverse and difficult to identify. The taxonomy of rays has received reasonable attention in Australia, although the fauna in remote locations such as Ningaloo Reef, Western Australia is poorly studied and the identification of some species in the field is problematic. Here, we report an application of DNA-barcoding to the identification of 16 species (from 10 genera) of tropical rays as part of an ecological study. Analysis of the dataset combined across all samples grouped sequences into clearly defined operational taxonomic units, with two conspicuous exceptions: the Neotrygon kuhlii species complex and the Aetobatus species complex. In the field, the group that presented the most difficulties for identification was the spotted whiptail rays, referred to as the 'uarnak' complex. Two sets of problems limited the successful application of DNA barcoding: (1) the presence of cryptic species, species complexes with unresolved taxonomic status and intra-specific geographical variation, and (2) insufficient numbers of entries in online databases that have been verified taxonomically, and the presence of lodged sequences in databases with inconsistent names. Nevertheless, we demonstrate the potential of the DNA barcoding approach to confirm field identifications and to highlight species complexes where taxonomic uncertainty might confound ecological data.},
}
@article {pmid22690927,
year = {2012},
author = {Condamine, FL and Silva-Brandão, KL and Kergoat, GJ and Sperling, FA},
title = {Biogeographic and diversification patterns of Neotropical Troidini butterflies (Papilionidae) support a museum model of diversity dynamics for Amazonia.},
journal = {BMC evolutionary biology},
volume = {12},
number = {},
pages = {82},
pmid = {22690927},
issn = {1471-2148},
mesh = {Animals ; Aristolochia ; Bayes Theorem ; Biodiversity ; Butterflies/*classification/*genetics ; Genetic Speciation ; *Phylogeography ; South America ; },
abstract = {BACKGROUND: The temporal and geographical diversification of Neotropical insects remains poorly understood because of the complex changes in geological and climatic conditions that occurred during the Cenozoic. To better understand extant patterns in Neotropical biodiversity, we investigated the evolutionary history of three Neotropical swallowtail Troidini genera (Papilionidae). First, DNA-based species delimitation analyses were conducted to assess species boundaries within Neotropical Troidini using an enlarged fragment of the standard barcode gene. Molecularly delineated species were then used to infer a time-calibrated species-level phylogeny based on a three-gene dataset and Bayesian dating analyses. The corresponding chronogram was used to explore their temporal and geographical diversification through distinct likelihood-based methods.<br><br>RESULTS: The phylogeny for Neotropical Troidini was well resolved and strongly supported. Molecular dating and biogeographic analyses indicate that the extant lineages of Neotropical Troidini have a late Eocene (33-42&#x2009;Ma) origin in North America. Two independent lineages (Battus and Euryades+Parides) reached South America via the GAARlandia temporary connection, and later became extinct in North America. They only began substantive diversification during the early Miocene in Amazonia. Macroevolutionary analysis supports the "museum model" of diversification, rather than Pleistocene refugia, as the best explanation for the diversification of these lineages.<br><br>CONCLUSIONS: This study demonstrates that: (i) current Neotropical biodiversity may have originated ex situ; (ii) the GAARlandia bridge was important in facilitating invasions of South America; (iii) colonization of Amazonia initiated the crown diversification of these swallowtails; and (iv) Amazonia is not only a species-rich region but also acted as a sanctuary for the dynamics of this diversity. In particular, Amazonia probably allowed the persistence of old lineages and contributed to the steady accumulation of diversity over time with constant net diversification rates, a result that contrasts with previous studies on other South American butterflies.},
}
@article {pmid22684971,
year = {2012},
author = {Erickson, DL and Kress, WJ},
title = {Future directions.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {459-465},
doi = {10.1007/978-1-61779-591-6_23},
pmid = {22684971},
issn = {1940-6029},
mesh = {Biodiversity ; Classification/methods ; DNA Barcoding, Taxonomic/*trends ; Phylogeny ; },
abstract = {It is a risky task to attempt to predict the direction that DNA barcoding and its applications may take in the future. In a very short time, the endeavor of DNA barcoding has gone from being a tool to facilitate taxonomy in difficult to identify species, to an ambitious, global initiative that seeks to tackle such pertinent and challenging issues as quantifying global biodiversity, revolutionizing the forensic identifications of species, advancing the study of interactions among species, and promoting the reconstruction of evolutionary relationships within communities. The core element of DNA barcoding will always remain the same: the generation of a set of well-identified samples collected and genotyped at one or more genetic barcode markers and assembled into a properly curated database. But the application of this body of data will depend on the creativity and need of the research community in using a "gold standard" of annotated DNA sequence data at the species level. We foresee several areas where the application of DNA barcode data is likely to yield important evolutionary, ecological, and societal insights, and while far from exclusive, provide examples of how DNA barcode data will continue to empower scientists to address hypothesis-driven research. Three areas of immediate and obvious concern are (1) biodiversity inventories, (2) phylogenetic applications, and (3) species interactions.},
}
@article {pmid22684970,
year = {2012},
author = {Kress, WJ and Lopez, IC and Erickson, DL},
title = {Generating plant DNA barcodes for trees in long-term forest dynamics plots.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {441-458},
doi = {10.1007/978-1-61779-591-6_22},
pmid = {22684970},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; Phylogeny ; Trees/classification/*genetics/*growth &amp; development ; },
abstract = {Long-term forest dynamics plots, such as those maintained and coordinated by the Center for Tropical Forest Science and Smithsonian Institution Global Earth Observatories (CTFS/SIGEO), are a rich source of biological data that describe the demographics, ecology, and evolution of pristine and disturbed forest habitats across ecosystems. As molecular techniques for plant systematic and ecological studies, including DNA barcodes, have improved so have the methods for collecting tissue samples, generating DNA sequences, and managing genetic data. Tissue samples can be processed at the point of collection and stored in silica gel for extended periods of time or samples can be taken from historical museum collections with sufficient DNA yields for study. In this chapter, we provide a workflow that includes the tracking of data from field collection of tissue samples to the DNA barcode sequence laboratory to final analyses for forensic and phylogenetic investigations.},
}
@article {pmid22684969,
year = {2012},
author = {Ward, RD},
title = {FISH-BOL, a case study for DNA barcodes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {423-439},
doi = {10.1007/978-1-61779-591-6_21},
pmid = {22684969},
issn = {1940-6029},
mesh = {Animals ; DNA/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Fishes/*classification/*genetics ; },
abstract = {The FISH-BOL campaign was initiated in 2005, and currently has barcoded for the cytochrome c oxidase subunit I (COI) gene about 8,000 of the 31,000 fish species currently recognised. This includes the great majority of the world's most important commercial species. Results thus far show that about 98% and 93% of marine and freshwater species, respectively, are barcode distinguishable. One important issue that needs to be more fully addressed in FISH-BOL concerns the initial misidentification of a small number of barcode reference specimens. This is unsurprising considering the large number of fish species, some of which are morphologically very similar and others as yet unrecognised, but constant vigilance and ongoing attention by the FISH-BOL community is required to eliminate such errors. Once the reference library has been established, barcoding enables the identification of unknown fishes at any life history stage or from their fragmentary remains. The many uses of the FISH-BOL barcode library include detecting consumer fraud, aiding fisheries management, improving ecological analyses including food web syntheses, and assisting with taxonomic revisions.},
}
@article {pmid22684968,
year = {2012},
author = {Swenson, NG},
title = {Phylogenetic analyses of ecological communities using DNA barcode data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {409-419},
doi = {10.1007/978-1-61779-591-6_20},
pmid = {22684968},
issn = {1940-6029},
mesh = {DNA/*genetics ; *DNA Barcoding, Taxonomic ; Ecology ; *Phylogeny ; },
abstract = {Ecologists and conservation biologists are increasingly focusing on quantifying the phylogenetic component of biodiversity in order to inform basic and applied research. A major obstacle of this approach in tropical ecosystems has been the difficulty of generating high-quality phylogenetic trees for the vast numbers of species in these systems. Phylogenetic trees inferred from DNA barcodes hold the potential to overcome this obstacle. Here, I present a methodological framework for analyzing the phylogenetic alpha and beta diversity of ecological communities using a phylogenetic tree. The analytical approach is presented using the freely available and widely used software platform "R".},
}
@article {pmid22684967,
year = {2012},
author = {Erickson, DL and Driskell, AC},
title = {Construction and analysis of phylogenetic trees using DNA barcode data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {395-408},
doi = {10.1007/978-1-61779-591-6_19},
pmid = {22684967},
issn = {1940-6029},
mesh = {DNA/*genetics ; *DNA Barcoding, Taxonomic ; *Phylogeny ; },
abstract = {The assembly of sequence data obtained from DNA barcodes into phylogenies or NJ trees has proven highly useful in estimating relatedness among species as well as providing a framework in which hypotheses regarding the evolution of traits or species distributions may be investigated. In this chapter, we outline the process by which DNA sequence data is assembled into a phylogenetically informative matrix, and then provide details on the methods to reconstruct NJ or phylogenetic trees that employ DNA barcode data, using only barcode data or combining barcodes with other data.},
}
@article {pmid22684966,
year = {2012},
author = {Dick, CW and Webb, CO},
title = {Plant DNA barcodes, taxonomic management, and species discovery in tropical forests.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {379-393},
doi = {10.1007/978-1-61779-591-6_18},
pmid = {22684966},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; Gene Library ; Plants/*classification/*genetics ; Trees/*physiology ; },
abstract = {DNA barcodes have great potential for species identification and taxonomic discovery in tropical forests. This use of DNA barcodes requires a reference DNA library of known taxa with which to match DNA from unidentified specimens. At an even more basic level, it presupposes that the species in the regional species pool have Latin binomials. This is not the case in species-rich tropical forests in which many species are new to science or members of poorly circumscribed species complexes. This chapter describes a workflow geared toward taxonomic discovery, which includes the discovery of new species, distribution records, and hybrid forms, and to management of taxonomic entities in forest inventory plots. It outlines the roles of laboratory technicians, field workers and herbarium-based taxonomists, and concludes with a discussion of potential multilocus nuclear DNA approaches for identifying species in recently evolved clades.},
}
@article {pmid22684965,
year = {2012},
author = {Spouge, JL and Mariño-Ramírez, L},
title = {The practical evaluation of DNA barcode efficacy.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {365-377},
pmid = {22684965},
issn = {1940-6029},
support = {Z99 MH999999/ImNIH/Intramural NIH HHS/United States ; Z99 LM999999/ImNIH/Intramural NIH HHS/United States ; ZIA LM200883-04/ImNIH/Intramural NIH HHS/United States ; Z99 CL999999/ImNIH/Intramural NIH HHS/United States ; Z99 HL999999/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Base Sequence ; DNA/*genetics ; *DNA Barcoding, Taxonomic ; Databases, Nucleic Acid ; Sequence Alignment ; },
abstract = {This chapter describes a workflow for measuring the efficacy of a barcode in identifying species. First, assemble individual sequence databases corresponding to each barcode marker. A controlled collection of taxonomic data is preferable to GenBank data, because GenBank data can be problematic, particularly when comparing barcodes based on more than one marker. To ensure proper controls when evaluating species identification, specimens not having a sequence in every marker database should be discarded. Second, select a computer algorithm for assigning species to barcode sequences. No algorithm has yet improved notably on assigning a specimen to the species of its nearest neighbor within a barcode database. Because global sequence alignments (e.g., with the Needleman-Wunsch algorithm, or some related algorithm) examine entire barcode sequences, they generally produce better species assignments than local sequence alignments (e.g., with BLAST). No neighboring method (e.g., global sequence similarity, global sequence distance, or evolutionary distance based on a global alignment) has yet shown a notable superiority in identifying species. Finally, "the probability of correct identification" (PCI) provides an appropriate measurement of barcode efficacy. The overall PCI for a data set is the average of the species PCIs, taken over all species in the data set. This chapter states explicitly how to calculate PCI, how to estimate its statistical sampling error, and how to use data on PCR failure to set limits on how much improvements in PCR technology can improve species identification.},
}
@article {pmid22684964,
year = {2012},
author = {Machida, RJ and Knowlton, N},
title = {Ways to mix multiple PCR amplicons into single 454 run for DNA barcoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {355-361},
doi = {10.1007/978-1-61779-591-6_16},
pmid = {22684964},
issn = {1940-6029},
mesh = {DNA/*genetics ; DNA Barcoding, Taxonomic/*methods ; *Polymerase Chain Reaction ; },
abstract = {Metagenetic analysis using second-generation sequencing offers a novel methodology for measuring the diversity of metazoan communities. Among commercially available second-generation sequencers, the 454 GS FLX Titanium (Roche Diagnostics) offers by far the longest read length and can produce one million sequences from a single run. Compared to the large number of sequences produced from single run, however, number of samples these machines can process is rather low. In this chapter, we describe the use of MID adapters to mix multiple PCR amplicons into a single 454 run. This strategy is rather easy to use and up to 132 samples can be multiplexed into a single 454 run. If a large number of samples are going to be mixed into a single 454 run, however, high cost might be next bottleneck. In this context, we also discuss other ways of multiplexing, including the use of fusion primers and Parallel Tagged Sequencing and weigh their advantages and disadvantages.},
}
@article {pmid22684963,
year = {2012},
author = {Hajibabaei, M and McKenna, C},
title = {DNA mini-barcodes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {339-353},
doi = {10.1007/978-1-61779-591-6_15},
pmid = {22684963},
issn = {1940-6029},
mesh = {Animals ; DNA/*genetics/isolation &amp; purification ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics/isolation &amp; purification ; Mitochondria/enzymology ; Polymerase Chain Reaction ; },
abstract = {Conventional DNA barcoding uses an approximately 650 bp DNA barcode of the mitochondrial gene COI for species identification in animal groups. Similar size fragments from chloroplast genes have been proposed as barcode markers for plants. While PCR amplification and sequencing of a 650 bp fragment is consistent in freshly collected and well-preserved specimens, it is difficult to obtain a full-length barcode in older museum specimens and samples which have been preserved in formalin or similar DNA-unfriendly preservatives. A comparable issue may prevent effective DNA-based authentication and testing in processed biological materials, such as food products, pharmaceuticals, and nutraceuticals. In these cases, shorter DNA sequences-mini-barcodes-have been robustly recovered and shown to be effective in identifying majority of specimens to a species level. Furthermore, short DNA regions can be utilized via high-throughput sequencing platforms providing an inexpensive and comprehensive means of large-scale species identification. These properties of mini-barcodes, coupled with the availability of standardized and universal primers make mini-barcodes a feasible option for DNA barcode analysis in museum samples and applied diagnostic and environmental biodiversity analysis.},
}
@article {pmid22684962,
year = {2012},
author = {Knebelsberger, T and Stöger, I},
title = {DNA extraction, preservation, and amplification.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {311-338},
doi = {10.1007/978-1-61779-591-6_14},
pmid = {22684962},
issn = {1940-6029},
mesh = {DNA/*genetics/*isolation &amp; purification ; *DNA Barcoding, Taxonomic ; *Polymerase Chain Reaction ; },
abstract = {The effectiveness of DNA barcoding as a routine practice in biodiversity research is strongly dependent on the quality of the source material, DNA extraction method, and selection of adequate primers in combination with optimized polymerase chain reaction (PCR) conditions. For the isolation of nucleic acids, silica-gel membrane methods are to be favored because they are easy to handle, applicable for high sample throughput, relatively inexpensive, and provide high DNA quality, quantity, and purity which are pre-requisites for successful PCR amplification and long-term storage of nucleic acids in biorepositories, such as DNA banks. In this section, standard protocols and workflow schemes for sample preparation, DNA isolation, DNA storage, PCR amplification, PCR product quality control, and PCR product cleanup are proposed and described in detail. A PCR troubleshooting and primer design section may help to solve problems that hinder successful amplification of the desired barcoding gene region.},
}
@article {pmid22684961,
year = {2012},
author = {Parker, M and Stones-Havas, S and Starger, C and Meyer, C},
title = {Laboratory information management systems for DNA barcoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {269-310},
doi = {10.1007/978-1-61779-591-6_13},
pmid = {22684961},
issn = {1940-6029},
mesh = {*Clinical Laboratory Information Systems/standards ; Computational Biology ; DNA Barcoding, Taxonomic/*methods ; Polymerase Chain Reaction ; Software ; },
abstract = {In the field of molecular biology, laboratory information management systems (LIMSs) have been created to track workflows through a process pipeline. For the purposes of DNA barcoding, this workflow involves tracking tissues through extraction, PCR, cycle sequencing, and consensus assembly. Importantly, a LIMS that serves the DNA barcoding community must link required elements for public submissions (e.g., primers, trace files) that are generated in the molecular lab with specimen metadata. Here, we demonstrate an example workflow of a specimen's entry into the LIMS database to the publishing of the specimen's genetic data to a public database using Geneious bioinformatics software. Throughout the process, the connections between steps in the workflow are maintained to facilitate post-processing annotation, structured reporting, and fully transparent edits to reduce subjectivity and increase repeatability.},
}
@article {pmid22684960,
year = {2012},
author = {Deck, J and Gross, J and Stones-Havas, S and Davies, N and Shapley, R and Meyer, C},
title = {Field information management systems for DNA barcoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {255-267},
doi = {10.1007/978-1-61779-591-6_12},
pmid = {22684960},
issn = {1940-6029},
mesh = {DNA Barcoding, Taxonomic/*methods/standards ; *Database Management Systems ; *Information Management/standards ; *Information Systems/standards ; },
abstract = {Information capture pertaining to the "what?", "where?", and "when?" of biodiversity data is critical to maintain data integrity, interoperability, and utility. Moreover, DNA barcoding and other biodiversity studies must adhere to agreed upon data standards in order to effectively contextualize the biota encountered. A field information management system (FIMS) is presented that locks down metadata associated with collecting events, specimens, and tissues. Emphasis is placed on ease of use and flexibility of operation. Standardized templates for data entry are validated through a flexible, project-oriented validation process that assures adherence to data standards and thus data quality. Furthermore, we provide export functionality to existing cloud-based solutions, including Google Fusion Tables and Flickr to allow sharing of these data elements across research collaboration teams and other potential data harvesters via API services.},
}
@article {pmid22684959,
year = {2012},
author = {Fazekas, AJ and Kuzmina, ML and Newmaster, SG and Hollingsworth, PM},
title = {DNA barcoding methods for land plants.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {223-252},
doi = {10.1007/978-1-61779-591-6_11},
pmid = {22684959},
issn = {1940-6029},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics/isolation &amp; purification ; Plants/*genetics ; Polymerase Chain Reaction ; },
abstract = {DNA barcoding in the land plants presents a number of challenges compared to DNA barcoding in many animal clades. The CO1 animal DNA barcode is not effective for plants. Plant species hybridize frequently, and there are many cases of recent speciation via mechanisms, such as polyploidy and breeding system transitions. Additionally, there are many life-history trait combinations, which combine to reduce the likelihood of a small number of markers effectively tracking plant species boundaries. Recent results, however, from the two chosen core plant DNA barcode regions rbcL and matK plus two supplementary regions trnH-psbA and internal transcribed spacer (ITS) (or ITS2) have demonstrated reasonable levels of species discrimination in both floristic and taxonomically focused studies. We describe sampling techniques, extraction protocols, and PCR methods for each of these two core and two supplementary plant DNA barcode regions, with extensive notes supporting their implementation for both low- and high-throughput facilities.},
}
@article {pmid22684958,
year = {2012},
author = {Saunders, GW and McDevit, DC},
title = {Methods for DNA barcoding photosynthetic protists emphasizing the macroalgae and diatoms.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {207-222},
doi = {10.1007/978-1-61779-591-6_10},
pmid = {22684958},
issn = {1940-6029},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Algal/*genetics/isolation &amp; purification ; Diatoms/*genetics ; Photosynthesis ; Phylogeny ; Polymerase Chain Reaction ; Seaweed/*genetics ; },
abstract = {This chapter outlines the current practices used in our laboratory for routine DNA barcode analyses of the three major marine macroalgal groups, viz., brown (Phaeophyceae), red (Rhodophyta), and green (Chlorophyta) algae, as well as for the microscopic diatoms (Bacillariophyta). We start with an outline of current streamlined field protocols, which facilitate the collection of substantial (hundreds to thousands) specimens during short (days to weeks) field excursions. We present the current high-throughput DNA extraction protocols, which can, nonetheless, be easily modified for manual molecular laboratory use. We are advocating a two-marker approach for the DNA barcoding of protists with each major lineage having a designated primary and secondary barcode marker of which one is always the LSU D2/D3 (divergent domains D2/D3 of the nuclear ribosomal large subunit DNA). We provide a listing of the primers that we currently use in our laboratory for amplification of DNA barcode markers from the groups that we study: LSU D2/D3, which we advocate as a eukaryote-wide barcode marker to facilitate broad ecological and environmental surveys (secondary barcode marker in this capacity); COI-5P (the standard DNA barcode region of the mitochondrial cytochrome c oxidase 1 gene) as the primary barcode marker for brown and red algae; rbcL-3P (the 3' region of the plastid large subunit of ribulose-l-5-bisphosphate carboxylase/oxygenase) as the primary barcode marker for diatoms; and tufA (plastid elongation factor Tu gene) as the primary barcode marker for chlorophytan green algae. We outline our polymerase chain reaction and DNA sequencing methodologies, which have been streamlined for efficiency and to reduce unnecessary cleaning steps. The combined information should provide a helpful guide to those seeking to complete barcode research on these and related "protistan" groups (the term protist is not used in a phylogenetic context; it is simply a catch-all term for the bulk of eukaryotic diversity, i.e., all lineages excluding animals, true fungi, and plants).},
}
@article {pmid22684957,
year = {2012},
author = {Eberhardt, U},
title = {Methods for DNA barcoding of fungi.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {183-205},
doi = {10.1007/978-1-61779-591-6_9},
pmid = {22684957},
issn = {1940-6029},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/*genetics/isolation &amp; purification ; Gene Library ; Polymerase Chain Reaction ; },
abstract = {This chapter describes methods currently used for DNA barcoding of fungi, including some comments on the barcoding of aged herbarium material. The collecting procedures are focussed on macro-fungi. The laboratory methods are for medium-throughput DNA barcoding, targeted at the 96-well format, but without the assistance of robotics. In the absence of an approved and standardized DNA barcoding locus for fungi, the chapter outlines the amplification and sequencing of nuclear ribosomal genes, ITS, and LSU D1/D2 which are most widely used for the identification of fungi from diverse environments.},
}
@article {pmid22684956,
year = {2012},
author = {Ivanova, NV and Clare, EL and Borisenko, AV},
title = {DNA barcoding in mammals.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {153-182},
doi = {10.1007/978-1-61779-591-6_8},
pmid = {22684956},
issn = {1940-6029},
mesh = {Animals ; DNA/*genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics/isolation &amp; purification ; Gene Library ; Humans ; Mammals/*genetics ; Polymerase Chain Reaction ; },
abstract = {DNA barcoding provides an operational framework for mammalian taxonomic identification and cryptic species discovery. Focused effort to build a reference library of genetic data has resulted in the assembly of over 35 K mammalian cytochrome c oxidase subunit I sequences and outlined the scope of mammal-related barcoding projects. Based on the above experience, this chapter recounts three typical methodological pathways involved in mammalian barcoding: routine methods aimed at assembling the reference sequence library from high quality samples, express approaches used to attain cheap and fast taxonomic identifications for applied purposes, and forensic techniques employed when dealing with degraded material. Most of the methods described are applicable to a range of vertebrate taxa outside Mammalia.},
}
@article {pmid22684955,
year = {2012},
author = {Lijtmaer, DA and Kerr, KC and Stoeckle, MY and Tubaro, PL},
title = {DNA barcoding birds: from field collection to data analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {127-152},
doi = {10.1007/978-1-61779-591-6_7},
pmid = {22684955},
issn = {1940-6029},
mesh = {Animals ; Birds/*genetics ; DNA/*genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics/isolation &amp; purification ; Mitochondria/enzymology ; Polymerase Chain Reaction ; },
abstract = {As of February 2011, COI DNA barcode sequences (a 648-bp segment of the 5' end of the mitochondrial gene cytochrome c oxidase I, the standard DNA barcode for animals) have been collected from over 23,000 avian specimens representing 3,800 species, more than one-third of the world's avifauna. Here, we detail the methodology for obtaining DNA barcodes from birds, covering the entire process from field collection to data analysis. We emphasize key aspects of the process and describe in more detail those that are particularly relevant in the case of birds. We provide elemental information about collection of specimens, detailed protocols for DNA extraction and PCR, and basic aspects of sequencing methodology. In particular, we highlight the primer pairs and thermal cycling profiles associated with successful amplification and sequencing from a broad range of avian species. Finally, we succinctly review the methodology for data analysis, including the detection of errors (such as contamination, misidentifications, or amplification of pseudogenes), assessment of species resolution, detection of divergent intraspecific lineages, and identification of unknown specimens.},
}
@article {pmid22684954,
year = {2012},
author = {Weigt, LA and Driskell, AC and Baldwin, CC and Ormos, A},
title = {DNA barcoding fishes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {109-126},
doi = {10.1007/978-1-61779-591-6_6},
pmid = {22684954},
issn = {1940-6029},
mesh = {Animals ; DNA/*genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Fishes/*genetics ; Polymerase Chain Reaction ; },
abstract = {This chapter is an overview of the techniques for DNA barcoding of fishes from field collection to DNA sequence analysis. Recommendations for modifications of field protocols and best tissue sampling practices are made. A variety of DNA extraction protocols is provided, including high-throughput robot-assisted methods. A pair of well-tested forward and reverse primers for PCR amplification and sequencing are presented. These primers have been successfully used for DNA barcode on a wide array of marine fish taxa and also work well in most freshwater and cartilaginous fishes. Recipes and cycling protocols for both PCR amplification and sequencing and cleanup methods for the reaction products are provided. A method for the consistent production of high-quality DNA barcodes from DNA sequence data is given and stringent guidelines for judging the quality of raw sequence data are laid out.},
}
@article {pmid22684953,
year = {2012},
author = {Vences, M and Nagy, ZT and Sonet, G and Verheyen, E},
title = {DNA barcoding amphibians and reptiles.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {79-107},
doi = {10.1007/978-1-61779-591-6_5},
pmid = {22684953},
issn = {1940-6029},
mesh = {Amphibians/*genetics ; Animals ; DNA/*genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Polymerase Chain Reaction ; Reptiles/*genetics ; },
abstract = {Only a few major research programs are currently targeting COI barcoding of amphibians and reptiles (including chelonians and crocodiles), two major groups of tetrapods. Amphibian and reptile species are typically old, strongly divergent, and contain deep conspecific lineages which might lead to problems in species assignment with incomplete reference databases. As far as known, there is no single pair of COI primers that will guarantee a sufficient rate of success across all amphibian and reptile taxa, or within major subclades of amphibians and reptiles, which means that the PCR amplification strategy needs to be adjusted depending on the specific research question. In general, many more amphibian and reptile taxa have been sequenced for 16S rDNA, which for some purposes may be a suitable complementary marker, at least until a more comprehensive COI reference database becomes available. DNA barcoding has successfully been used to identify amphibian larval stages (tadpoles) in species-rich tropical assemblages. Tissue sampling, DNA extraction, and amplification of COI is straightforward in amphibians and reptiles. Single primer pairs are likely to have a failure rate between 5 and 50% if taxa of a wide taxonomic range are targeted; in such cases the use of primer cocktails or subsequent hierarchical usage of different primer pairs is necessary. If the target group is taxonomically limited, many studies have followed a strategy of designing specific primers which then allow an easy and reliable amplification of all samples.},
}
@article {pmid22684952,
year = {2012},
author = {Evans, N and Paulay, G},
title = {DNA barcoding methods for invertebrates.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {47-77},
doi = {10.1007/978-1-61779-591-6_4},
pmid = {22684952},
issn = {1940-6029},
mesh = {Animals ; DNA/*genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Insecta/genetics ; Invertebrates/*genetics ; Polymerase Chain Reaction ; },
abstract = {Invertebrates comprise approximately 34 phyla, while vertebrates represent one subphylum and insects a (very large) class. Thus, the clades excepting vertebrates and insects encompass almost all of animal diversity. Consequently, the barcoding challenge in invertebrates is that of barcoding animals in general. While standard extraction, cleaning, PCR methods, and universal primers work for many taxa, taxon-specific challenges arise because of the shear genetic and biochemical diversity present across the kingdom, and because problems arising as a result of this diversity, and solutions to them, are still poorly characterized for many metazoan clades. The objective of this chapter is to emphasize general approaches, and give practical advice for overcoming the diverse challenges that may be encountered across animal taxa, but we stop short of providing an exhaustive inventory. Rather, we encourage researchers, especially those working on poorly studied taxa, to carefully consider methodological issues presented below, when standard approaches perform poorly.},
}
@article {pmid22684951,
year = {2012},
author = {Wilson, JJ},
title = {DNA barcodes for insects.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {17-46},
doi = {10.1007/978-1-61779-591-6_3},
pmid = {22684951},
issn = {1940-6029},
mesh = {Animals ; DNA/*genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Insecta/*genetics ; Polymerase Chain Reaction ; },
abstract = {DNA barcoding refers to the technique of sequencing a short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene, the "DNA barcode," from a taxonomically unknown specimen and performing comparisons with a reference library of barcodes of known species origin to establish a species-level identification. The library barcodes gain their value due to an intimate association-through the vouchered specimens from where they came-with other data; particularly Linnaean names, collection localities, and morphology in the form of digital images. Consequently, this chapter details means of efficiently obtaining barcodes along two general streams: rapid barcode assembly to populate the library and retrieval of barcodes from highly prized specimens, but also emphasizes organization and collection of the barcode collaterals.},
}
@article {pmid22684950,
year = {2012},
author = {Weigt, LA and Driskell, AC and Ormos, A and Meyer, C and Collins, A},
title = {Introduction to animal DNA barcoding protocols.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {11-16},
doi = {10.1007/978-1-61779-591-6_2},
pmid = {22684950},
issn = {1940-6029},
mesh = {Animals ; DNA/*genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Polymerase Chain Reaction ; },
abstract = {Procedures and protocols common to many DNA barcoding projects are summarized. Planning for any project should emphasize front-end procedures, especially the "genetic lockdown" of collected materials for downstream genetic procedures. Steps further into the DNA barcoding process chain, such as sequencing, data processing, and other back-end functions vary slightly, if at all, among projects and are presented elsewhere in the volume. Point-of-collection sample and tissue handling and data/metadata handling are stressed. Specific predictions of the future workflows and mechanics of DNA barcoding are difficult, so focus is on that which most or all future methods and technologies will surely share.},
}
@article {pmid22684949,
year = {2012},
author = {Kress, WJ and Erickson, DL},
title = {DNA barcodes: methods and protocols.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {858},
number = {},
pages = {3-8},
doi = {10.1007/978-1-61779-591-6_1},
pmid = {22684949},
issn = {1940-6029},
mesh = {Animals ; DNA/*genetics ; DNA Barcoding, Taxonomic/*methods ; Gene Library ; },
abstract = {DNA barcoding, a new method for the quick identification of any species based on extracting a DNA sequence from a tiny tissue sample of any organism, is now being applied to taxa across the tree of life. As a research tool for taxonomists, DNA barcoding assists in identification by expanding the ability to diagnose species by including all life history stages of an organism. As a biodiversity discovery tool, DNA barcoding helps to flag species that are potentially new to science. As a biological tool, DNA barcoding is being used to address fundamental ecological and evolutionary questions, such as how species in plant communities are assembled. The process of DNA barcoding entails two basic steps: (1) building the DNA barcode library of known species and (2) matching the barcode sequence of the unknown sample against the barcode library for identification. Although DNA barcoding as a methodology has been in use for less than a decade, it has grown exponentially in terms of the number of sequences generated as barcodes as well as its applications. This volume provides the latest information on generating, applying, and analyzing DNA barcodes across the Tree of Life from animals and fungi to protists, algae, and plants.},
}
@article {pmid22679848,
year = {2012},
author = {Srinivasan, R and Jambulingam, P},
title = {Morphological and anatomical variations among Phlebotomus (Phlebotomus) papatasi sensu lato (Diptera: Psychodidae).},
journal = {Journal of medical entomology},
volume = {49},
number = {3},
pages = {441-444},
doi = {10.1603/me11105},
pmid = {22679848},
issn = {0022-2585},
mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Female ; Genetic Variation ; India ; Male ; Phlebotomus/*anatomy &amp; histology/genetics ; Sex Characteristics ; },
abstract = {Phlebotomus (Phlebotomus) papatasi (Scopoli) collected in human dwellings from an agricultural villages Chaura, located in Gaya district, Bihar, India, showed morphological and anatomical variations. Male sand flies of this species exhibited variations in the genital structures, while females showed differences in the spermathecae and antenna segment three (A3). When the mitochondrial DNA of both male and female P. (P.) papatasi sensu lato population subjected to DNA barcoding, both the sexes of P. (P.) papatasi variants were found to be associated. The differences in the morphometric characteristics clearly constitutes preliminary evidence for infraspecific variation in P. (P.) papatasi s.1. population in India.},
}
@article {pmid22679589,
year = {2011},
author = {Braun, U and Crous, PW and Groenewald, JZ and Scheuer, C},
title = {Pseudovirgaria, a fungicolous hyphomycete genus.},
journal = {IMA fungus},
volume = {2},
number = {1},
pages = {65-69},
pmid = {22679589},
issn = {2210-6359},
abstract = {The genus Pseudovirgaria, based on P. hyperparasitica, was recently introduced for a mycoparasite of rust sori of various species of Frommeëlla, Pucciniastrum and Phragmidium in Korea. In the present study, an older name introduced by Saccardo based on European material, Rhinotrichum griseum, is shown to resemble P. hyperparasitica. Morphological study and ITS barcodes from fresh collections of R. griseum from Austria on uredinia and telia of Phragmidium bulbosum on Rubus spp. reveal that it is distinct from P. hyperparasitica. The status of the genus Rhinotrichum, introduced for a fungus occurring on dry wood, remains unclear. Pseudovirgaria grisea comb. nov. is therefore proposed for the mycoparasite occurring on rust fungi in Europe, and an epitype is designated from the recent collections.},
}
@article {pmid22675470,
year = {2012},
author = {Valdez-Moreno, M and Quintal-Lizama, C and Gómez-Lozano, R and García-Rivas, Mdel C},
title = {Monitoring an alien invasion: DNA barcoding and the identification of lionfish and their prey on coral reefs of the Mexican Caribbean.},
journal = {PloS one},
volume = {7},
number = {6},
pages = {e36636},
pmid = {22675470},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Caribbean Region ; *Coral Reefs ; Crustacea/classification/genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Fishes/*classification/*genetics ; Gastric Mucosa/metabolism ; *Introduced Species ; Mexico ; Phylogeny ; *Predatory Behavior ; Specimen Handling ; },
abstract = {BACKGROUND: In the Mexican Caribbean, the exotic lionfish Pterois volitans has become a species of great concern because of their predatory habits and rapid expansion onto the Mesoamerican coral reef, the second largest continuous reef system in the world. This is the first report of DNA identification of stomach contents of lionfish using the barcode of life reference database (BOLD).<br><br>We confirm with barcoding that only Pterois volitans is apparently present in the Mexican Caribbean. We analyzed the stomach contents of 157 specimens of P. volitans from various locations in the region. Based on DNA matches in the Barcode of Life Database (BOLD) and GenBank, we identified fishes from five orders, 14 families, 22 genera and 34 species in the stomach contents. The families with the most species represented were Gobiidae and Apogonidae. Some prey taxa are commercially important species. Seven species were new records for the Mexican Caribbean: Apogon mosavi, Coryphopterus venezuelae, C. thrix, C. tortugae, Lythrypnus minimus, Starksia langi and S. ocellata. DNA matches, as well as the presence of intact lionfish in the stomach contents, indicate some degree of cannibalism, a behavior confirmed in this species by the first time. We obtained 45 distinct crustacean prey sequences, from which only 20 taxa could be identified from the BOLD and GenBank databases. The matches were primarily to Decapoda but only a single taxon could be identified to the species level, Euphausia americana.<br><br>CONCLUSIONS/SIGNIFICANCE: This technique proved to be an efficient and useful method, especially since prey species could be identified from partially-digested remains. The primary limitation is the lack of comprehensive coverage of potential prey species in the region in the BOLD and GenBank databases, especially among invertebrates.},
}
@article {pmid22666489,
year = {2012},
author = {Boyer, S and Brown, SD and Collins, RA and Cruickshank, RH and Lefort, MC and Malumbres-Olarte, J and Wratten, SD},
title = {Sliding window analyses for optimal selection of mini-barcodes, and application to 454-pyrosequencing for specimen identification from degraded DNA.},
journal = {PloS one},
volume = {7},
number = {5},
pages = {e38215},
pmid = {22666489},
issn = {1932-6203},
mesh = {Animals ; Computational Biology ; DNA/*chemistry/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal/chemistry/genetics ; Digestion ; Genetic Markers/genetics ; Mollusca/physiology ; Oligochaeta/classification/genetics ; },
abstract = {DNA barcoding remains a challenge when applied to diet analyses, ancient DNA studies, environmental DNA samples and, more generally, in any cases where DNA samples have not been adequately preserved. Because the size of the commonly used barcoding marker (COI) is over 600 base pairs (bp), amplification fails when the DNA molecule is degraded into smaller fragments. However, relevant information for specimen identification may not be evenly distributed along the barcoding region, and a shorter target can be sufficient for identification purposes. This study proposes a new, widely applicable, method to compare the performance of all potential 'mini-barcodes' for a given molecular marker and to objectively select the shortest and most informative one. Our method is based on a sliding window analysis implemented in the new R package SPIDER (Species IDentity and Evolution in R). This method is applicable to any taxon and any molecular marker. Here, it was tested on earthworm DNA that had been degraded through digestion by carnivorous landsnails. A 100 bp region of 16 S rDNA was selected as the shortest informative fragment (mini-barcode) required for accurate specimen identification. Corresponding primers were designed and used to amplify degraded earthworm (prey) DNA from 46 landsnail (predator) faeces using 454-pyrosequencing. This led to the detection of 18 earthworm species in the diet of the snail. We encourage molecular ecologists to use this method to objectively select the most informative region of the gene they aim to amplify from degraded DNA. The method and tools provided here, can be particularly useful (1) when dealing with degraded DNA for which only small fragments can be amplified, (2) for cases where no consensus has yet been reached on the appropriate barcode gene, or (3) to allow direct analysis of short reads derived from massively parallel sequencing without the need for bioinformatic consolidation.},
}
@article {pmid22666447,
year = {2012},
author = {Webb, JM and Jacobus, LM and Funk, DH and Zhou, X and Kondratieff, B and Geraci, CJ and DeWalt, RE and Baird, DJ and Richard, B and Phillips, I and Hebert, PD},
title = {A DNA barcode library for North American Ephemeroptera: progress and prospects.},
journal = {PloS one},
volume = {7},
number = {5},
pages = {e38063},
pmid = {22666447},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Female ; Insecta/*classification/growth &amp; development ; Life Cycle Stages ; Male ; North America ; Species Specificity ; },
abstract = {DNA barcoding of aquatic macroinvertebrates holds much promise as a tool for taxonomic research and for providing the reliable identifications needed for water quality assessment programs. A prerequisite for identification using barcodes is a reliable reference library. We gathered 4165 sequences from the barcode region of the mitochondrial cytochrome c oxidase subunit I gene representing 264 nominal and 90 provisional species of mayflies (Insecta: Ephemeroptera) from Canada, Mexico, and the United States. No species shared barcode sequences and all can be identified with barcodes with the possible exception of some Caenis. Minimum interspecific distances ranged from 0.3-24.7% (mean: 12.5%), while the average intraspecific divergence was 1.97%. The latter value was inflated by the presence of very high divergences in some taxa. In fact, nearly 20% of the species included two or three haplotype clusters showing greater than 5.0% sequence divergence and some values are as high as 26.7%. Many of the species with high divergences are polyphyletic and likely represent species complexes. Indeed, many of these polyphyletic species have numerous synonyms and individuals in some barcode clusters show morphological attributes characteristic of the synonymized species. In light of our findings, it is imperative that type or topotype specimens be sequenced to correctly associate barcode clusters with morphological species concepts and to determine the status of currently synonymized species.},
}
@article {pmid22666375,
year = {2012},
author = {Chesters, D and Wang, Y and Yu, F and Bai, M and Zhang, TX and Hu, HY and Zhu, CD and Li, CD and Zhang, YZ},
title = {The integrative taxonomic approach reveals host specific species in an encyrtid parasitoid species complex.},
journal = {PloS one},
volume = {7},
number = {5},
pages = {e37655},
pmid = {22666375},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Classification/*methods ; DNA Barcoding, Taxonomic ; Female ; Genetic Loci/genetics ; Haplotypes ; *Host Specificity ; Male ; Molecular Sequence Data ; Parasites/*classification/genetics ; Phylogeny ; Sexual Behavior, Animal ; Wasps/*classification/genetics ; },
abstract = {Integrated taxonomy uses evidence from a number of different character types to delimit species and other natural groupings. While this approach has been advocated recently, and should be of particular utility in the case of diminutive insect parasitoids, there are relatively few examples of its application in these taxa. Here, we use an integrated framework to delimit independent lineages in Encyrtus sasakii (Hymenoptera: Chalcidoidea: Encyrtidae), a parasitoid morphospecies previously considered a host generalist. Sequence variation at the DNA barcode (cytochrome c oxidase I, COI) and nuclear 28S rDNA loci were compared to morphometric recordings and mating compatibility tests, among samples of this species complex collected from its four scale insect hosts, covering a broad geographic range of northern and central China. Our results reveal that Encyrtus sasakii comprises three lineages that, while sharing a similar morphology, are highly divergent at the molecular level. At the barcode locus, the median K2P molecular distance between individuals from three primary populations was found to be 11.3%, well outside the divergence usually observed between Chalcidoidea conspecifics (0.5%). Corroborative evidence that the genetic lineages represent independent species was found from mating tests, where compatibility was observed only within populations, and morphometric analysis, which found that despite apparent morphological homogeneity, populations clustered according to forewing shape. The independent lineages defined by the integrated analysis correspond to the three scale insect hosts, suggesting the presence of host specific cryptic species. The finding of hidden host specificity in this species complex demonstrates the critical role that DNA barcoding will increasingly play in revealing hidden biodiversity in taxa that present difficulties for traditional taxonomic approaches.},
}
@article {pmid22665274,
year = {2012},
author = {Wheat, CW},
title = {SNP discovery in non-model organisms using 454 next generation sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {888},
number = {},
pages = {33-53},
doi = {10.1007/978-1-61779-870-2_3},
pmid = {22665274},
issn = {1940-6029},
mesh = {Animals ; Base Sequence ; Contig Mapping ; DNA Barcoding, Taxonomic ; *Genome ; Genome Size ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Data ; Polymorphism, Single Nucleotide/*genetics ; Transcriptome/*genetics ; },
abstract = {Roche 454 sequencing of the transcriptome has become a standard approach for efficiently obtaining single nucleotide polymorphisms (SNPs) in non-model species. In this chapter, the primary issues facing the development of SNPs from the transcriptome in non-model species are presented: tissue and sampling choices, mRNA preparation, considerations of normalization, pooling and barcoding, how much to sequence, how to assemble the data and assess the assembly, calling transcriptome SNPs, developing these into genomic SNPs, and publishing the work. Discussion also covers the comparison of this approach to RAD-tag sequencing and the potential of using other sequencing platforms for SNP development.},
}
@article {pmid22663346,
year = {2012},
author = {Pramual, P and Kuvangkadilok, C},
title = {Integrated cytogenetic, ecological, and DNA barcode study reveals cryptic diversity in Simulium (Gomphostilbia) angulistylum (Diptera: Simuliidae).},
journal = {Genome},
volume = {55},
number = {6},
pages = {447-458},
doi = {10.1139/g2012-031},
pmid = {22663346},
issn = {1480-3321},
mesh = {Animals ; Chromosome Inversion/*genetics ; Chromosomes, Insect ; Cytogenetic Analysis ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/classification/*genetics ; Electron Transport Complex IV/classification/*genetics ; Environment ; Genetic Variation ; Genetics, Population ; Haplotypes ; Karyotyping ; Phylogeny ; Simuliidae/classification/*genetics ; Thailand ; },
abstract = {An integrated approach based on cytogenetics, molecular genetics, and ecology was used to examine diversity in the black fly Simulium angulistylum Takaoka &amp; Davies in Thailand. Cytological analysis revealed three cytoforms (A, B, and C) of S. angulistylum differentiated by fixed chromosome inversions. Distributions of these cytoforms were associated with ecology. Cytoforms A and B were found in low-altitude habitats (<600 m above sea level), whereas cytoform C occurred at high altitudes (>1000 m above sea level). Mitochondrial DNA sequences of the cytochrome oxidase subunit I barcoding region revealed significant genetic differentiation among the cytoforms. The mitochondrial DNA haplotype network revealed divergent lineages within cytoforms, indicating additional hidden diversity. Therefore, integrated approaches are necessary for fully understanding black fly biodiversity. Population genetic analysis revealed high genetic structuring that could be due to the habitat preferences of S. angulistylum. Phylogeographic analyses indicated population demographic expansion at the mid-Pleistocene (900 000 years ago), which is older than for other black flies and insects in the Southeast Asian mainland. The high level of genetic structure and diversity, therefore, could also be due to the long demographic history of S. angulistylum.},
}
@article {pmid22658618,
year = {2012},
author = {Pritchard, CC and Smith, C and Salipante, SJ and Lee, MK and Thornton, AM and Nord, AS and Gulden, C and Kupfer, SS and Swisher, EM and Bennett, RL and Novetsky, AP and Jarvik, GP and Olopade, OI and Goodfellow, PJ and King, MC and Tait, JF and Walsh, T},
title = {ColoSeq provides comprehensive lynch and polyposis syndrome mutational analysis using massively parallel sequencing.},
journal = {The Journal of molecular diagnostics : JMD},
volume = {14},
number = {4},
pages = {357-366},
pmid = {22658618},
issn = {1943-7811},
support = {K08 CA142892/CA/NCI NIH HHS/United States ; R01 CA157744/CA/NCI NIH HHS/United States ; R01 CA175716/CA/NCI NIH HHS/United States ; R01CA157744/CA/NCI NIH HHS/United States ; },
mesh = {Adaptor Proteins, Signal Transducing/genetics ; Adenomatous Polyposis Coli/*genetics ; Colorectal Neoplasms, Hereditary Nonpolyposis/*genetics ; DNA Glycosylases/genetics ; DNA Mutational Analysis/*methods ; DNA-Binding Proteins/genetics ; Humans ; MutL Protein Homolog 1 ; MutS Homolog 2 Protein/genetics ; Nuclear Proteins/genetics ; },
abstract = {Lynch syndrome (hereditary nonpolyposis colon cancer) and adenomatous polyposis syndromes frequently have overlapping clinical features. Current approaches for molecular genetic testing are often stepwise, taking a best-candidate gene approach with testing of additional genes if initial results are negative. We report a comprehensive assay called ColoSeq that detects all classes of mutations in Lynch and polyposis syndrome genes using targeted capture and massively parallel next-generation sequencing on the Illumina HiSeq2000 instrument. In blinded specimens and colon cancer cell lines with defined mutations, ColoSeq correctly identified 28/28 (100%) pathogenic mutations in MLH1, MSH2, MSH6, PMS2, EPCAM, APC, and MUTYH, including single nucleotide variants (SNVs), small insertions and deletions, and large copy number variants. There was 100% reproducibility of detection mutation between independent runs. The assay correctly identified 222 of 224 heterozygous SNVs (99.4%) in HapMap samples, demonstrating high sensitivity of calling all variants across each captured gene. Average coverage was greater than 320 reads per base pair when the maximum of 96 index samples with barcodes were pooled. In a specificity study of 19 control patients without cancer from different ethnic backgrounds, we did not find any pathogenic mutations but detected two variants of uncertain significance. ColoSeq offers a powerful, cost-effective means of genetic testing for Lynch and polyposis syndromes that eliminates the need for stepwise testing and multiple follow-up clinical visits.},
}
@article {pmid22653718,
year = {2012},
author = {Meyer-Massetti, C and Conen, D},
title = {[Assessment, frequency, causes, and prevention of medication errors - a critical analysis].},
journal = {Therapeutische Umschau. Revue therapeutique},
volume = {69},
number = {6},
pages = {347-352},
doi = {10.1024/0040-5930/a000296},
pmid = {22653718},
issn = {0040-5930},
mesh = {Causality ; Cross-Sectional Studies ; Drug-Related Side Effects and Adverse Reactions/epidemiology/prevention &amp; control ; Evidence-Based Medicine ; Humans ; Medication Errors/*prevention &amp; control/*statistics &amp; numerical data ; *Patient Safety/standards ; Prescription Drugs/adverse effects ; Risk Factors ; Switzerland ; *Task Performance and Analysis ; },
abstract = {Medication errors are responsible for up to 50% of errors in healthcare. Therefore, they are an important target for the improvement of patient safety. The application of evidence-based methods for the analysis of institution-specific medication safety hotspots is crucial. Recommended methods for the identification of medication safety problems have individual strengths and weaknesses, but there is little overlap. Consequently, a combination of methods is recommended. While the analysis of critical incident reporting systems preferentially identifies serious medication errors, trigger tool represents an effective and cost-efficient approach. Evidence-based data for improvement methods is limited. However, the implementation of clinical pharmacy services, IT tools (electronic prescribing, barcoding) and standardized double-check showed a significant impact on error reduction. In addition, the support of institutional leadership is an important prerequisite.},
}
@article {pmid22652049,
year = {2012},
author = {Kokel, D and Rennekamp, AJ and Shah, AH and Liebel, U and Peterson, RT},
title = {Behavioral barcoding in the cloud: embracing data-intensive digital phenotyping in neuropharmacology.},
journal = {Trends in biotechnology},
volume = {30},
number = {8},
pages = {421-425},
pmid = {22652049},
issn = {1879-3096},
support = {R21 MH085205/MH/NIMH NIH HHS/United States ; K01MH091449/MH/NIMH NIH HHS/United States ; MH085205/MH/NIMH NIH HHS/United States ; K01 MH091449/MH/NIMH NIH HHS/United States ; R01 MH086867/MH/NIMH NIH HHS/United States ; MH086867/MH/NIMH NIH HHS/United States ; T32 HL007208/HL/NHLBI NIH HHS/United States ; T32HL07208/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Behavior, Animal/*drug effects ; *Computational Biology ; *Data Mining ; *Databases, Factual ; Drug Discovery/*methods ; Neuropharmacology/*methods ; Zebrafish ; },
abstract = {For decades, studying the behavioral effects of individual drugs and genetic mutations has been at the heart of efforts to understand and treat nervous system disorders. High-throughput technologies adapted from other disciplines (e.g., high-throughput chemical screening, genomics) are changing the scale of data acquisition in behavioral neuroscience. Massive behavioral datasets are beginning to emerge, particularly from zebrafish labs, where behavioral assays can be performed rapidly and reproducibly in 96-well, high-throughput format. Mining these datasets and making comparisons across different assays are major challenges for the field. Here, we review behavioral barcoding, a process by which complex behavioral assays are reduced to a string of numeric features, facilitating analysis and comparison within and across datasets.},
}
@article {pmid22651385,
year = {2012},
author = {Ergunay, K and Erisoz Kasap, O and Kocak Tufan, Z and Turan, MH and Ozkul, A and Alten, B},
title = {Molecular evidence indicates that Phlebotomus major sensu lato (Diptera: Psychodidae) is the vector species of the recently-identified sandfly fever Sicilian virus variant: sandfly fever turkey virus.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {12},
number = {8},
pages = {690-698},
doi = {10.1089/vbz.2011.0927},
pmid = {22651385},
issn = {1557-7759},
mesh = {Animals ; Base Sequence ; Cattle ; DNA, Complementary/chemistry/genetics ; Dogs ; Female ; Humans ; Insect Vectors/*virology ; Male ; Molecular Sequence Data ; Phlebotomus/*virology ; Phlebotomus Fever/*epidemiology/transmission/virology ; Phlebovirus/genetics/*isolation &amp; purification ; Phylogeny ; RNA, Viral/chemistry/genetics ; Sequence Analysis, DNA ; Turkey/epidemiology ; },
abstract = {Sandfly fever turkey virus (SFTV) is a recently-discovered sandfly fever Sicilian virus (SFSV) variant (family Bunyaviridae, genus Phlebovirus), characterized during retrospective evaluation of febrile disease outbreaks in Turkey. In addition to causing sandfly fever, SFTV was observed to induce elevation of liver enzymes, and to cause thrombocytopenia in affected individuals. This study was conducted to identify vectors for phleboviruses including SFTV in Ankara province, Turkey, where evidence indicates ongoing circulation of SFTV, as well as Toscana virus. Sandfly sampling was performed in Ankara province in the vicinity or in animal housing facilities in 15 peri-domestic sites. Male sandflies were identified morphologically, whereas females were evaluated individually for Phlebovirus RNA via a nested-PCR assay with consensus primers. Selected individuals and PCR-positive sandflies were subjected to barcoding via cytochrome c oxidase sequence analyses. The source of blood meals in virus-infected sandflies was investigated using a multiplexed PCR targeting the mitochondrial cytochrome b gene of various vertebrates. A total of 667 sandflies were captured in 11 locations. Morphological identification of males (n=226) revealed Phlebotomus major sensu lato as the most abundant species (38.9%), followed by Phlebotomus sergenti (20.4%), Phlebotomus halepensis (17.7%), Phlebotomus papatasi (10.2%), Phlebotomus simici (3.98%), Larrousius spp. (3.53%), Phlebotomus tobbi (1.32%), Phlebotomus perfiliewi perfiliewi (1.32%), and others. Virus sequences were detected in 3 (3/441) sandflies, two of which were characterized as P. major s.l. via barcoding. The detected sequences in sandflies were identified as SFTV, and were identical or similar to sequences from patients from the same area and the prototype SFTV strain. Bovine and human blood meals were demonstrated in SFTV-infected sandflies. P. major s.l. has been identified as the vector species for SFTV. Bovidae need to be evaluated as probable amplifying hosts for SFTV.},
}
@article {pmid22649793,
year = {2012},
author = {Spinks, PQ and Thomson, RC and Zhang, Y and Che, J and Wu, Y and Shaffer, HB},
title = {Species boundaries and phylogenetic relationships in the critically endangered Asian box turtle genus Cuora.},
journal = {Molecular phylogenetics and evolution},
volume = {63},
number = {3},
pages = {656-667},
doi = {10.1016/j.ympev.2012.02.014},
pmid = {22649793},
issn = {1095-9513},
mesh = {Animals ; Asia, Southeastern ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; *Endangered Species ; Models, Genetic ; Multilocus Sequence Typing ; *Phylogeny ; Species Specificity ; Turtles/classification/*genetics ; },
abstract = {Turtles are currently the most endangered major clade of vertebrates on earth, and Asian box turtles (Cuora) are in catastrophic decline. Effective management of this diverse turtle clade has been hampered by human-mediated, and perhaps natural hybridization, resulting in discordance between mitochondrial and nuclear markers and confusion regarding species boundaries and phylogenetic relationships among hypothesized species of Cuora. Here, we present analyses of mitochondrial and nuclear DNA data for all 12 currently hypothesized species to resolve both species boundaries and phylogenetic relationships. Our 15-gene, 40-individual nuclear data set was frequently in conflict with our mitochondrial data set; based on its general concordance with published morphological analyses and the strength of 15 independent estimates of evolutionary history, we interpret the nuclear data as representing the most reliable estimate of species boundaries and phylogeny of Cuora. Our results strongly reiterate the necessity of using multiple nuclear markers for phylogeny and species delimitation in these animals, including any form of DNA "barcoding", and point to Cuora as an important case study where reliance on mitochondrial DNA can lead to incorrect species identification.},
}
@article {pmid22648811,
year = {2012},
author = {Hlavacek, A and Skládal, P},
title = {Isotachophoretic purification of nanoparticles: tuning optical properties of quantum dots.},
journal = {Electrophoresis},
volume = {33},
number = {9-10},
pages = {1427-1430},
doi = {10.1002/elps.201100696},
pmid = {22648811},
issn = {1522-2683},
mesh = {Cadmium Compounds/chemistry ; Isotachophoresis/*methods ; Nanoparticles/*chemistry ; Particle Size ; *Quantum Dots ; Tellurium/chemistry ; },
abstract = {Synthesized nanoparticles often require fine fractionation according to shape, dimension, mass, chemical composition, charge, and other properties in order to become suitable for practical use. Quantum dots (QDs) are luminescent nanocrystals with narrow emission peaks. This property has been widely utilized for the multiplexed sensing and barcoding of microparticles. QDs with narrower emission peaks are preferred for such applications. The width of the emission peaks can be significantly reduced after purification. A newly developed preparative isotachophoretic method employs the dependence of spectral properties and electrophoretic mobility on the diameter of QDs. Separated fractions of QDs revealed narrower emission peaks (72% of the original width) and improved quantum yield (two-fold). The usefulness of the developed isotachophoresis for purification and analysis of other nanostructures, for example, plasmonic nanoparticles and nanobioconjugates, is expected, too.},
}
@article {pmid22646220,
year = {2012},
author = {Clement, WL and Donoghue, MJ},
title = {Barcoding success as a function of phylogenetic relatedness in Viburnum, a clade of woody angiosperms.},
journal = {BMC evolutionary biology},
volume = {12},
number = {},
pages = {73},
pmid = {22646220},
issn = {1471-2148},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Chloroplast/genetics ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Genetic Variation ; *Phylogeny ; Species Specificity ; Viburnum/classification/*genetics ; },
abstract = {BACKGROUND: The chloroplast genes matK and rbcL have been proposed as a "core" DNA barcode for identifying plant species. Published estimates of successful species identification using these loci (70-80%) may be inflated because they may have involved comparisons among distantly related species within target genera. To assess the ability of the proposed two-locus barcode to discriminate closely related species, we carried out a hierarchically structured set of comparisons within Viburnum, a clade of woody angiosperms containing ca. 170 species (some 70 of which are currently used in horticulture). For 112 Viburnum species, we evaluated rbcL + matK, as well as the chloroplast regions rpl32-trnL, trnH-psbA, trnK, and the nuclear ribosomal internal transcribed spacer region (nrITS).<br><br>RESULTS: At most, rbcL + matK could discriminate 53% of all Viburnum species, with only 18% of the comparisons having genetic distances >1%. When comparisons were progressively restricted to species within major Viburnum subclades, there was a significant decrease in both the discriminatory power and the genetic distances. trnH-psbA and nrITS show much higher levels of variation and potential discriminatory power, and their use in plant barcoding should be reconsidered. As barcoding has often been used to discriminate species within local areas, we also compared Viburnum species within two regions, Japan and Mexico and Central America. Greater success in discriminating among the Japanese species reflects the deeper evolutionary history of Viburnum in that area, as compared to the recent radiation of a single clade into the mountains of Latin America.<br><br>CONCLUSIONS: We found very low levels of discrimination among closely related species of Viburnum, and low levels of variation in the proposed barcoding loci may limit success within other clades of long-lived woody plants. Inclusion of the supplementary barcodes trnH-psbA and nrITS increased discrimination rates but were often more effective alone rather than in combination with rbcL + matK. We surmise that the efficacy of barcoding in plants has often been overestimated because of the lack of comparisons among closely related species. Phylogenetic information must be incorporated to properly evaluate relatedness in assessing the utility of barcoding loci.},
}
@article {pmid22639539,
year = {2012},
author = {Pilipenko, VE and Salmela, J and Vesterinen, EJ},
title = {Description and DNA barcoding of Tipula (Pterelachisus) recondita sp. n. from the Palaearctic region (Diptera, Tipulidae).},
journal = {ZooKeys},
volume = {},
number = {192},
pages = {51-65},
pmid = {22639539},
issn = {1313-2970},
abstract = {Tipula (Pterelachisus) recondita Pilipenko &amp; Salmela, sp. n. is described. The new species is collected from two localities: Finland, Kittilä (North boreal ecoregion) and Russia, Primorski kray (Zone of temperate broadleaf and mixed forests). Although variation in the structure of male hypopygium between the Finnish and Russian populations is observed, DNA barcode sequences differ only by three nucleotides (0.2 % K2P distance), supporting presence of one widespread species. K2P minimum distances between the new species and 17 other species of the subgenus range from 5.3 to 15.8 % (mean 8.8 %). The new species is forest-dwelling, known from an old-growth herb-rich forest (Finland) and Quercus mongolica forest (Russia). The new species is perhaps closest to Tipula (Pterelachisus) imitator Alexander and in lesser extent to Tipula (Pterelachisus) pauli Mannheims; the inner gonostylus of both species are illustrated.},
}
@article {pmid22639145,
year = {2012},
author = {Peterson, SW},
title = {Aspergillus and Penicillium identification using DNA sequences: barcode or MLST?.},
journal = {Applied microbiology and biotechnology},
volume = {95},
number = {2},
pages = {339-344},
doi = {10.1007/s00253-012-4165-2},
pmid = {22639145},
issn = {1432-0614},
mesh = {Aspergillus/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/*chemistry/genetics ; Multilocus Sequence Typing/*methods ; Penicillium/*classification/*genetics ; },
abstract = {Current methods in DNA technology can detect single nucleotide polymorphisms with measurable accuracy using several different approaches appropriate for different uses. If there are even single nucleotide differences that are invariant markers of the species, we can accomplish identification through rapid DNA-based tests. The question of whether we can reliably detect and identify species of Aspergillus and Penicillium turns mainly upon the completeness of our alpha taxonomy, our species concepts, and how well the available DNA data coincide with the taxonomic diversity in the family Trichocomaceae. No single gene is yet known that is invariant within species and variable between species as would be optimal for the barcode approach. Data are published that would make an MLST approach to isolate identification possible in the most well-studied clades of Aspergillus and Penicillium.},
}
@article {pmid22623973,
year = {2012},
author = {Chuang, LY and Lin, YD and Chang, HW and Yang, CH},
title = {An improved PSO algorithm for generating protective SNP barcodes in breast cancer.},
journal = {PloS one},
volume = {7},
number = {5},
pages = {e37018},
pmid = {22623973},
issn = {1932-6203},
mesh = {*Algorithms ; Breast Neoplasms/*diagnosis/*genetics ; Computer Simulation ; Female ; Genotype ; Gonadal Steroid Hormones/metabolism ; Humans ; Metabolic Networks and Pathways/genetics ; Multilocus Sequence Typing/*methods ; Odds Ratio ; Polymorphism, Single Nucleotide/*genetics ; },
abstract = {BACKGROUND: Possible single nucleotide polymorphism (SNP) interactions in breast cancer are usually not investigated in genome-wide association studies. Previously, we proposed a particle swarm optimization (PSO) method to compute these kinds of SNP interactions. However, this PSO does not guarantee to find the best result in every implement, especially when high-dimensional data is investigated for SNP-SNP interactions.<br><br>In this study, we propose IPSO algorithm to improve the reliability of PSO for the identification of the best protective SNP barcodes (SNP combinations and genotypes with maximum difference between cases and controls) associated with breast cancer. SNP barcodes containing different numbers of SNPs were computed. The top five SNP barcode results are retained for computing the next SNP barcode with a one-SNP-increase for each processing step. Based on the simulated data for 23 SNPs of six steroid hormone metabolisms and signalling-related genes, the performance of our proposed IPSO algorithm is evaluated. Among 23 SNPs, 13 SNPs displayed significant odds ratio (OR) values (1.268 to 0.848; p<0.05) for breast cancer. Based on IPSO algorithm, the jointed effect in terms of SNP barcodes with two to seven SNPs show significantly decreasing OR values (0.84 to 0.57; p<0.05 to 0.001). Using PSO algorithm, two to four SNPs show significantly decreasing OR values (0.84 to 0.77; p<0.05 to 0.001). Based on the results of 20 simulations, medians of the maximum differences for each SNP barcode generated by IPSO are higher than by PSO. The interquartile ranges of the boxplot, as well as the upper and lower hinges for each n-SNP barcode (n&#x200a;=&#x200a;3&#x223c;10) are more narrow in IPSO than in PSO, suggesting that IPSO is highly reliable for SNP barcode identification.<br><br>CONCLUSIONS/SIGNIFICANCE: Overall, the proposed IPSO algorithm is robust to provide exact identification of the best protective SNP barcodes for breast cancer.},
}
@article {pmid22615825,
year = {2012},
author = {Bystrykh, LV},
title = {Generalized DNA barcode design based on Hamming codes.},
journal = {PloS one},
volume = {7},
number = {5},
pages = {e36852},
pmid = {22615825},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic ; },
abstract = {The diversity and scope of multiplex parallel sequencing applications is steadily increasing. Critically, multiplex parallel sequencing applications methods rely on the use of barcoded primers for sample identification, and the quality of the barcodes directly impacts the quality of the resulting sequence data. Inspection of the recent publications reveals a surprisingly variable quality of the barcodes employed. Some barcodes are made in a semi empirical fashion, without quantitative consideration of error correction or minimal distance properties. After systematic comparison of published barcode sets, including commercially distributed barcoded primers from Illumina and Epicentre, methods for improved, Hamming code-based sequences are suggested and illustrated. Hamming barcodes can be employed for DNA tag designs in many different ways while preserving minimal distance and error-correcting properties. In addition, Hamming barcodes remain flexible with regard to essential biological parameters such as sequence redundancy and GC content. Wider adoption of improved Hamming barcodes is encouraged in multiplex parallel sequencing applications.},
}
@article {pmid22615397,
year = {2012},
author = {Schlecht, U and Miranda, M and Suresh, S and Davis, RW and St Onge, RP},
title = {Multiplex assay for condition-dependent changes in protein-protein interactions.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {109},
number = {23},
pages = {9213-9218},
pmid = {22615397},
issn = {1091-6490},
support = {R21 HG005785/HG/NHGRI NIH HHS/United States ; R21HG005785-01/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; Computational Biology ; DNA-Binding Proteins ; Mice ; Microarray Analysis ; Protein Interaction Mapping/*methods ; Protein Interaction Maps/*genetics ; Real-Time Polymerase Chain Reaction ; Receptors, Formyl Peptide/metabolism ; Saccharomyces cerevisiae Proteins ; Small Molecule Libraries/*metabolism ; Tacrolimus ; Tetrahydrofolate Dehydrogenase/*metabolism ; Yeasts ; },
abstract = {Changes in protein-protein interactions that occur in response to environmental cues are difficult to uncover and have been poorly characterized to date. Here we describe a yeast-based assay that allows many binary protein interactions to be assessed in parallel and under various conditions. This method combines molecular bar-coding and tag array technology with the murine dihydrofolate reductase-based protein-fragment complementation assay. A total of 238 protein-fragment complementation assay strains, each representing a unique binary protein complex, were tagged with molecular barcodes, pooled, and then interrogated against a panel of 80 diverse small molecules. Our method successfully identified specific disruption of the Hom3:Fpr1 interaction by the immunosuppressant FK506, illustrating the assay's capacity to identify chemical inhibitors of protein-protein interactions. Among the additional findings was specific cellular depletion of the Dst1:Rbp9 complex by the anthracycline drug doxorubicin, but not by the related drug idarubicin. The assay also revealed chemical-induced accumulation of several binary multidrug transporter complexes that largely paralleled increases in transcript levels. Further assessment of two such interactions (Tpo1:Pdr5 and Snq2:Pdr5) in the presence of 1,246 unique chemical compounds revealed a positive correlation between drug lipophilicity and the drug response in yeast.},
}
@article {pmid22606302,
year = {2012},
author = {Nie, X and Lv, S and Zhang, Y and Du, X and Wang, L and Biradar, SS and Tan, X and Wan, F and Weining, S},
title = {Complete chloroplast genome sequence of a major invasive species, crofton weed (Ageratina adenophora).},
journal = {PloS one},
volume = {7},
number = {5},
pages = {e36869},
pmid = {22606302},
issn = {1932-6203},
mesh = {Ageratina/classification/*genetics ; Chromosome Mapping ; Codon/genetics ; DNA, Chloroplast/genetics ; Evolution, Molecular ; Exons ; *Genome, Chloroplast ; Introduced Species ; Introns ; Inverted Repeat Sequences ; Phylogeny ; Sequence Homology, Nucleic Acid ; Species Specificity ; },
abstract = {BACKGROUND: Crofton weed (Ageratina adenophora) is one of the most hazardous invasive plant species, which causes serious economic losses and environmental damages worldwide. However, the sequence resource and genome information of A. adenophora are rather limited, making phylogenetic identification and evolutionary studies very difficult. Here, we report the complete sequence of the A. adenophora chloroplast (cp) genome based on Illumina sequencing.<br><br>The A. adenophora cp genome is 150, 689 bp in length including a small single-copy (SSC) region of 18, 358 bp and a large single-copy (LSC) region of 84, 815 bp separated by a pair of inverted repeats (IRs) of 23, 755 bp. The genome contains 130 unique genes and 18 duplicated in the IR regions, with the gene content and organization similar to other Asteraceae cp genomes. Comparative analysis identified five DNA regions (ndhD-ccsA, psbI-trnS, ndhF-ycf1, ndhI-ndhG and atpA-trnR) containing parsimony-informative characters higher than 2%, which may be potential informative markers for barcoding and phylogenetic analysis. Repeat structure, codon usage and contraction of the IR were also investigated to reveal the pattern of evolution. Phylogenetic analysis demonstrated a sister relationship between A. adenophora and Guizotia abyssinica and supported a monophyly of the Asterales.<br><br>CONCLUSION: We have assembled and analyzed the chloroplast genome of A. adenophora in this study, which was the first sequenced plastome in the Eupatorieae tribe. The complete chloroplast genome information is useful for plant phylogenetic and evolutionary studies within this invasive species and also within the Asteraceae family.},
}
@article {pmid22595653,
year = {2012},
author = {Gentekaki, E and Lynn, D},
title = {Spatial genetic variation, phylogeography and barcoding of the peritrichous ciliate Carchesium polypinum.},
journal = {European journal of protistology},
volume = {48},
number = {4},
pages = {305-313},
doi = {10.1016/j.ejop.2012.04.001},
pmid = {22595653},
issn = {1618-0429},
mesh = {DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Oligohymenophorea/*classification/*genetics/isolation &amp; purification ; *Phylogeny ; Phylogeography ; Sequence Homology, Nucleic Acid ; },
abstract = {Most recent studies of geographic distribution of microbial eukaryotes have focused on marine rather than freshwater protists. Here, we used the freshwater peritrich ciliate Carchesium polypinum to quantify the degree of genetic diversity of four closely related and previously described lineages and to determine whether patterns of genetic differentiation showed geographic partitioning. Using an expanded dataset of 100 isolates and employing the mitochondrial marker cytochrome oxidase c subunit I (cox-1), we enriched the 6 previously identified clades of Carchesium polypinum. We found a large degree of geographic overlap among the different clades (e.g. to the level of range of sampling), but also a spatially restricted clade (e.g. to the level of one river basin). Furthermore, we present evidence of a clear geographic separation in one of the lineages with Canadian and North Carolinian isolates grouping in two distinct clusters.},
}
@article {pmid22591275,
year = {2012},
author = {Lu, D and Lei, J and Wang, L and Zhang, J},
title = {Multifluorescently traceable nanoparticle by a single-wavelength excitation with color-related drug release performance.},
journal = {Journal of the American Chemical Society},
volume = {134},
number = {21},
pages = {8746-8749},
doi = {10.1021/ja301691j},
pmid = {22591275},
issn = {1520-5126},
mesh = {Color ; Drug Carriers/*chemistry ; Fluorescent Dyes/*chemistry ; HeLa Cells ; Humans ; Nanoparticles/*chemistry ; Organosilicon Compounds/chemistry ; Porosity ; },
abstract = {Monodisperse and nanometer-sized periodic mesoporous organosilicas co-doped with fluorescence resonance energy transfer cascades composed of triple fluorophores at various ratios were prepared. These nanoparticles exhibit multifluorescent emissions by a single-wavelength excitation and were designed for the application as multichannelly traceable drug carriers. Different from the hydrophilic framework of inorganic mesoporous silica and hydrophobic framework of mesoporous carbon, these multifluorescent nanoparticles have intrinsically different and finely tunable pore surface polarities governed by the type and amount of fluorophore inside the framework. When applied as drug carriers, they can achieve synchronous or asynchronous release of different drugs by simply choosing different colored nanoparticles. These colorful mesoporous composites with finely tunable color-related drug release performance provide a strong barcoding system for the potential applications of fluorescent nanoparticles in effective screening of drugs and therapeutic protocols for diseases.},
}
@article {pmid22586856,
year = {2012},
author = {Stone, S and Munoz, J},
title = {Barcoding: the way to patient safety.},
journal = {MLO: medical laboratory observer},
volume = {44},
number = {4},
pages = {46},
pmid = {22586856},
issn = {0580-7247},
mesh = {*Electronic Data Processing ; Humans ; Medical Errors/prevention &amp; control ; *Safety Management ; Specimen Handling/methods ; United States ; },
}
@article {pmid22581825,
year = {2012},
author = {Narayan, A and Carriero, NJ and Gettinger, SN and Kluytenaar, J and Kozak, KR and Yock, TI and Muscato, NE and Ugarelli, P and Decker, RH and Patel, AA},
title = {Ultrasensitive measurement of hotspot mutations in tumor DNA in blood using error-suppressed multiplexed deep sequencing.},
journal = {Cancer research},
volume = {72},
number = {14},
pages = {3492-3498},
pmid = {22581825},
issn = {1538-7445},
support = {UL1 RR024139/RR/NCRR NIH HHS/United States ; UL1 TR000427/TR/NCATS NIH HHS/United States ; KL2 RR024138/RR/NCRR NIH HHS/United States ; UL1 RR025011/RR/NCRR NIH HHS/United States ; 5KL2RR024138/RR/NCRR NIH HHS/United States ; UL1RR024139/RR/NCRR NIH HHS/United States ; },
mesh = {Carcinoma, Non-Small-Cell Lung/blood/genetics ; Cell Line, Tumor ; DNA, Neoplasm/*blood ; Female ; *High-Throughput Nucleotide Sequencing ; Humans ; Lung Neoplasms/blood/genetics ; Male ; Mutation ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; },
abstract = {Detection of cell-free tumor DNA in the blood has offered promise as a cancer biomarker, but practical clinical implementations have been impeded by the lack of a sensitive and accurate method for quantitation that is also simple, inexpensive, and readily scalable. Here we present an approach that uses next-generation sequencing to quantify the small fraction of DNA molecules that contain tumor-specific mutations within a background of normal DNA in plasma. Using layers of sequence redundancy designed to distinguish true mutations from sequencer misreads and PCR misincorporations, we achieved a detection sensitivity of approximately 1 variant in 5,000 molecules. In addition, the attachment of modular barcode tags to the DNA fragments to be sequenced facilitated the simultaneous analysis of more than 100 patient samples. As proof-of-principle, we showed the successful use of this method to follow treatment-associated changes in circulating tumor DNA levels in patients with non-small cell lung cancer. Our findings suggest that the deep sequencing approach described here may be applied to the development of a practical diagnostic test that measures tumor-derived DNA levels in blood.},
}
@article {pmid22578874,
year = {2013},
author = {Carrier, C and Cholette, F and Quintero, C and Fulcher, C},
title = {Potential use of DNA barcoding for the identification of tobacco seized from waterpipes.},
journal = {Forensic science international. Genetics},
volume = {7},
number = {1},
pages = {194-197},
doi = {10.1016/j.fsigen.2012.04.005},
pmid = {22578874},
issn = {1878-0326},
mesh = {Base Sequence ; *DNA Barcoding, Taxonomic ; DNA Primers ; DNA, Plant/*genetics ; Polymerase Chain Reaction ; Nicotiana/*genetics ; },
abstract = {DNA barcoding was adopted in our laboratory for the identification of tobacco (Nicotiana spp.) in moassel samples seized from "hookah bars". As recommended by the CBOL Plant Working Group, we used a 2-locus combination of rbcL and matK as the plant barcode. As previously reported rbcL routinely produced high quality bi-directional reads but had a lower discriminating power than matK. It was much more difficult obtaining high quality bi-directional reads with matK possibly because of poor sample quality. DNA barcoding successfully identified tobacco in over 60 commercial tobacco moassel products. On the other hand, negative results (no amplification) or the identification of non-tobacco species were obtained from herbal moassel products. Our study clearly demonstrates the practical utility of DNA barcoding beyond taxonomy.},
}
@article {pmid22574964,
year = {2012},
author = {Bazinet, AL and Cummings, MP},
title = {A comparative evaluation of sequence classification programs.},
journal = {BMC bioinformatics},
volume = {13},
number = {},
pages = {92},
pmid = {22574964},
issn = {1471-2105},
mesh = {*Algorithms ; Computational Biology/*methods ; Genomics/*methods ; Metagenomics ; Phylogeny ; Sequence Alignment ; *Software ; },
abstract = {BACKGROUND: A fundamental problem in modern genomics is to taxonomically or functionally classify DNA sequence fragments derived from environmental sampling (i.e., metagenomics). Several different methods have been proposed for doing this effectively and efficiently, and many have been implemented in software. In addition to varying their basic algorithmic approach to classification, some methods screen sequence reads for 'barcoding genes' like 16S rRNA, or various types of protein-coding genes. Due to the sheer number and complexity of methods, it can be difficult for a researcher to choose one that is well-suited for a particular analysis.<br><br>RESULTS: We divided the very large number of programs that have been released in recent years for solving the sequence classification problem into three main categories based on the general algorithm they use to compare a query sequence against a database of sequences. We also evaluated the performance of the leading programs in each category on data sets whose taxonomic and functional composition is known.<br><br>CONCLUSIONS: We found significant variability in classification accuracy, precision, and resource consumption of sequence classification programs when used to analyze various metagenomics data sets. However, we observe some general trends and patterns that will be useful to researchers who use sequence classification programs.},
}
@article {pmid22574186,
year = {2012},
author = {Nicolas, V and Schaeffer, B and Missoup, AD and Kennis, J and Colyn, M and Denys, C and Tatard, C and Cruaud, C and Laredo, C},
title = {Assessment of three mitochondrial genes (16S, Cytb, CO1) for identifying species in the Praomyini tribe (Rodentia: Muridae).},
journal = {PloS one},
volume = {7},
number = {5},
pages = {e36586},
pmid = {22574186},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; Cytochromes b/genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial/*genetics ; Muridae/*classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {The Praomyini tribe is one of the most diverse and abundant groups of Old World rodents. Several species are known to be involved in crop damage and in the epidemiology of several human and cattle diseases. Due to the existence of sibling species their identification is often problematic. Thus an easy, fast and accurate species identification tool is needed for non-systematicians to correctly identify Praomyini species. In this study we compare the usefulness of three genes (16S, Cytb, CO1) for identifying species of this tribe. A total of 426 specimens representing 40 species (sampled across their geographical range) were sequenced for the three genes. Nearly all of the species included in our study are monophyletic in the neighbour joining trees. The degree of intra-specific variability tends to be lower than the divergence between species, but no barcoding gap is detected. The success rate of the statistical methods of species identification is excellent (up to 99% or 100% for statistical supervised classification methods as the k-Nearest Neighbour or Random Forest). The 16S gene is 2.5 less variable than the Cytb and CO1 genes. As a result its discriminatory power is smaller. To sum up, our results suggest that using DNA markers for identifying species in the Praomyini tribe is a largely valid approach, and that the CO1 and Cytb genes are better DNA markers than the 16S gene. Our results confirm the usefulness of statistical methods such as the Random Forest and the 1-NN methods to assign a sequence to a species, even when the number of species is relatively large. Based on our NJ trees and the distribution of all intraspecific and interspecific pairwise nucleotide distances, we highlight the presence of several potentially new species within the Praomyini tribe that should be subject to corroboration assessments.},
}
@article {pmid22574113,
year = {2012},
author = {Liu, C and Shi, L and Xu, X and Li, H and Xing, H and Liang, D and Jiang, K and Pang, X and Song, J and Chen, S},
title = {DNA barcode goes two-dimensions: DNA QR code web server.},
journal = {PloS one},
volume = {7},
number = {5},
pages = {e35146},
pmid = {22574113},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; Data Compression ; *Internet ; Plants/classification/genetics ; },
abstract = {The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, "DNA barcode" actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three different types of one-dimensional and ten two-dimensional barcode symbologies were compared based on different criteria, such as coding capacity, compression efficiency, and error detection ability. The quick response (QR) code was found to have the largest coding capacity and relatively high compression ratio. To facilitate the further usage of QR code-based DNA barcodes, a web server was developed and is accessible at http://qrfordna.dnsalias.org. The web server allows users to retrieve the QR code for a species of interests, convert a DNA sequence to and from a QR code, and perform species identification based on local and global sequence similarities. In summary, the first comprehensive evaluation of various barcode symbologies has been carried out. The QR code has been found to be the most appropriate symbology for DNA barcode sequences. A web server has also been constructed to allow biologists to utilize QR codes in practical DNA barcoding applications.},
}
@article {pmid22573948,
year = {2012},
author = {Davis, DR and Landry, JF},
title = {A review of the North American genus Epimartyria (Lepidoptera, Micropterigidae) with a discussion of the larval plastron.},
journal = {ZooKeys},
volume = {},
number = {183},
pages = {37-83},
pmid = {22573948},
issn = {1313-2970},
abstract = {The indigenous North American micropterigid genus Epimartyria Walsingham,1898 is revised. Three species are recognized, including Epimartyria auricrinella Walsingham, 1898 which occurs widely over much of the northeastern United States and Canada, a new species, Epimartyria bimaculella Davis &amp; Landry from northwestern United States and Canada, and Epimartyria pardella (Walsingham, 1880) from northern California to northern Oregon. The larva of Epimartyria auricrinella is described in detail, supplemented with illustrations of the external structure of the larval integument. The larval plastron is described and illustrated for Epimartyria, and this is compared with the plastrons of Neomicropteryx Issiki, 1931 and Micropterix Hübner, 1825. COI barcode sequences show that the three species are genetically distinct, congruent with morphological differences. Marked haplotype divergence within some Epimartyria auricrinella populations appears to be unrelated to morphology, geography or phenology.},
}
@article {pmid22567162,
year = {2012},
author = {Smith, MA and Bertrand, C and Crosby, K and Eveleigh, ES and Fernandez-Triana, J and Fisher, BL and Gibbs, J and Hajibabaei, M and Hallwachs, W and Hind, K and Hrcek, J and Huang, DW and Janda, M and Janzen, DH and Li, Y and Miller, SE and Packer, L and Quicke, D and Ratnasingham, S and Rodriguez, J and Rougerie, R and Shaw, MR and Sheffield, C and Stahlhut, JK and Steinke, D and Whitfield, J and Wood, M and Zhou, X},
title = {Wolbachia and DNA barcoding insects: patterns, potential, and problems.},
journal = {PloS one},
volume = {7},
number = {5},
pages = {e36514},
pmid = {22567162},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Insecta/classification/*genetics/*microbiology ; Phylogeny ; Wolbachia/*genetics ; },
abstract = {Wolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Using both standard PCR assays (Wolbachia surface coding protein--wsp), and bacterial COI fragments we found evidence of Wolbachia in insect total genomic extracts created for DNA barcoding library construction. When >2 million insect COI trace files were examined on the Barcode of Life Datasystem (BOLD) Wolbachia COI was present in 0.16% of the cases. It is possible to generate Wolbachia COI using standard insect primers; however, that amplicon was never confused with the COI of the host. Wolbachia alleles recovered were predominantly Supergroup A and were broadly distributed geographically and phylogenetically. We conclude that the presence of the Wolbachia DNA in total genomic extracts made from insects is unlikely to compromise the accuracy of the DNA barcode library; in fact, the ability to query this DNA library (the database and the extracts) for endosymbionts is one of the ancillary benefits of such a large scale endeavor--which we provide several examples. It is our conclusion that regular assays for Wolbachia presence and type can, and should, be adopted by large scale insect barcoding initiatives. While COI is one of the five multi-locus sequence typing (MLST) genes used for categorizing Wolbachia, there is limited overlap with the eukaryotic DNA barcode region.},
}
@article {pmid22567120,
year = {2012},
author = {Nzeduru, CV and Ronca, S and Wilkinson, MJ},
title = {DNA barcoding simplifies environmental risk assessment of genetically modified crops in biodiverse regions.},
journal = {PloS one},
volume = {7},
number = {5},
pages = {e35929},
pmid = {22567120},
issn = {1932-6203},
mesh = {Animals ; Bacillus thuringiensis/genetics ; Crops, Agricultural/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; Insecta/parasitology ; Lepidoptera/parasitology ; Plants, Genetically Modified/classification/*genetics ; Risk Assessment/*methods ; Transgenes/genetics/physiology ; },
abstract = {Transgenes encoding for insecticidal crystal (Cry) proteins from the soil-dwelling bacterium Bacillus Thuringiensis have been widely introduced into Genetically Modified (GM) crops to confer protection against insect pests. Concern that these transgenes may also harm beneficial or otherwise valued insects (so-called Non Target Organisms, NTOs) represents a major element of the Environmental Risk Assessments (ERAs) used by all countries prior to commercial release. Compiling a comprehensive list of potentially susceptible NTOs is therefore a necessary part of an ERA for any Cry toxin-containing GM crop. In partly-characterised and biodiverse countries, NTO identification is slowed by the need for taxonomic expertise and time to enable morphological identifications. This limitation represents a potentially serious barrier to timely adoption of GM technology in some developing countries. We consider Bt Cry1A cowpea (Vigna unguiculata) in Nigeria as an exemplar to demonstrate how COI barcoding can provide a simple and cost-effective means of addressing this problem. Over a period of eight weeks, we collected 163 insects from cowpea flowers across the agroecological and geographic range of the crop in Nigeria. These individuals included 32 Operational Taxonomic Units (OTUs) spanning four Orders and that could mostly be assigned to genus or species level. They included 12 Lepidopterans and two Coleopterans (both potentially sensitive to different groups of Cry proteins). Thus, barcode-assisted diagnoses were highly harmonised across groups (typically to genus or species level) and so were insensitive to expertise or knowledge gaps. Decisively, the entire study was completed within four months at a cost of less than 10,000 US$. The broader implications of the findings for food security and the capacity for safe adoption of GM technology are briefly explored.},
}
@article {pmid22564785,
year = {2012},
author = {Johnson, AJ and Weintraub, PG and Katoch, R and Schemerhorn, BJ and Shukle, RH},
title = {Biological and molecular characterization of Hessian fly (Diptera: Cecidomyiidae) from Israel.},
journal = {Bulletin of entomological research},
volume = {102},
number = {6},
pages = {632-643},
doi = {10.1017/S0007485312000235},
pmid = {22564785},
issn = {1475-2670},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Diptera/anatomy &amp; histology/pathogenicity/*physiology ; Female ; Genetic Complementation Test ; Genotyping Techniques ; Herbivory ; Male ; Microsatellite Repeats ; Oviposition ; Population Density ; Triticum/*genetics ; Virulence ; },
abstract = {Samples of a dipteran pest of wheat were tested to confirm identity, describe local populations and suggest the use of deploying resistance (R) genes in wheat cultivars for control of Mayetiola destructor, Hessian fly (HF). Morphological evaluation of adults and a free-choice oviposition preference test documenting that females overwhelmingly preferred to oviposit on wheat instead of barley supported they were HF. Using the cytochrome c oxidase subunit I (coxI), the Barcoding Region, nine haplotypes were revealed. Two were found only in the Israeli collections and averaged 3% sequence divergence compared to the other seven haplotypes found in the United States, Israel and Syria. In evaluations of virulence, the Israeli HF in culture was virulent to 11 of the 19 (R) genes tested, and complementation analysis documented that, for four of the R genes tested, the Israeli HF shared loci for virulence with HF from the United States. Levels of HF infestation at seven Israeli fields were at least at the 5-8% level, which historically has indicated a significant yield loss. Microsatellite genotyping of the five HF collections from Israel revealed mixed populations in Israel that are distinctly separate from the single population in Syria.},
}
@article {pmid22560779,
year = {2012},
author = {Rützler, K},
title = {The role of sponges in the Mesoamerican Barrier-Reef Ecosystem, Belize.},
journal = {Advances in marine biology},
volume = {61},
number = {},
pages = {211-271},
doi = {10.1016/B978-0-12-387787-1.00002-7},
pmid = {22560779},
issn = {0065-2881},
mesh = {Animals ; Atlantic Ocean ; Belize ; *Coral Reefs ; Demography ; Porifera/classification/*physiology ; },
abstract = {Over the past four decades, sponge research has advanced by leaps and bounds through endeavours such as the Caribbean Coral Reef Ecosystems (CCRE) programme at the U.S. National Museum of Natural History in Washington, D.C. Since its founding in the early 1970s, the programme has been dedicated to a detailed multidisciplinary study of a section of the Mesoamerican Barrier Reef, the Atlantic's largest reef complex, and has generated data far beyond the capability of lone investigators and brief expeditions. This reef complex extends 250 km southward from Yucatan, Mexico, into the Gulf of Honduras, most of it lying 20-40 km off the coast of Belize. A relatively unspoiled ecosystem, it features a great variety of habitats in close proximity, ranging from mangrove islands, seagrass meadows, and patch reefs in its lagoon to the barrier reef along the margin of the continental shelf. Among its varied macrobenthos, sponges stand out for their ubiquity, range of colours, rich species and biomass, and ecological importance; they populate rocky substrates, some sandy bottoms, and the subtidal stilt roots and peat banks of mangroves. Working from a field station established in 1972 on Carrie Bow Cay, a sand islet atop the reef off southern Belize, experts in numerous disciplines from both the Museum and academic institutions throughout the world have explored the area's biodiversity in the broadest sense and community development over time. At last count, 113 researchers (88 working on site) have focused on the biological and geological role of Porifera in Carrie Bow's reef communities, with the results reported in 125 scientific papers to date. The majority of these sponge studies have centred on systematics and faunistics, including quantitative distribution among the various habitats. Taxonomic approaches have ranged from basic morphology to fine structure, DNA barcoding, and ecological manipulations and culminated in a mini-workshop involving several experts on Caribbean Porifera. Ecological work has covered a broad spectrum as well: bioerosion, silica and nutrient cycling, symbiosis, mutualism, space competition, predation, disease, and the effects on sponge individuals and populations of environmental factors such as light, temperature, salinity, desiccation, substrate, and sedimentation. Many projects were enhanced by scientific illustration, laboratory studies of larvae settlement preferences and development, and investigations of microbial and invertebrate sponge associates, notably symbiotic cyanobacteria, parazoanthid epizoans, and crustacean and ophiuroid endobionts. Of the striking discoveries, the work on alpheid shrimps colonizing sponges off Carrie Bow Cay has yielded the first report of eusociality in marine organisms.},
}
@article {pmid22559142,
year = {2012},
author = {Laetsch, DR and Heitlinger, EG and Taraschewski, H and Nadler, SA and Blaxter, ML},
title = {The phylogenetics of Anguillicolidae (Nematoda: Anguillicoloidea), swimbladder parasites of eels.},
journal = {BMC evolutionary biology},
volume = {12},
number = {},
pages = {60},
pmid = {22559142},
issn = {1471-2148},
mesh = {Air Sacs/parasitology ; Anguilla/*parasitology ; Animals ; DNA, Mitochondrial/genetics ; Dracunculoidea/*classification ; Genetic Variation ; *Phylogeny ; Ribosome Subunits, Large, Eukaryotic/genetics ; Ribosome Subunits, Small, Eukaryotic/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND: Anguillicolidae Yamaguti, 1935 is a family of parasitic nematode infecting fresh-water eels of the genus Anguilla, comprising five species in the genera Anguillicola and Anguillicoloides. Anguillicoloides crassus is of particular importance, as it has recently spread from its endemic range in the Eastern Pacific to Europe and North America, where it poses a significant threat to new, naïve hosts such as the economic important eel species Anguilla anguilla and Anguilla rostrata. The Anguillicolidae are therefore all potentially invasive taxa, but the relationships of the described species remain unclear. Anguillicolidae is part of Spirurina, a diverse clade made up of only animal parasites, but placement of the family within Spirurina is based on limited data.<br><br>RESULTS: We generated an extensive DNA sequence dataset from three loci (the 5' one-third of the nuclear small subunit ribosomal RNA, the D2-D3 region of the nuclear large subunit ribosomal RNA and the 5' half of the mitochondrial cytochrome c oxidase I gene) for the five species of Anguillicolidae and used this to investigate specific and generic boundaries within the family, and the relationship of Anguillicolidae to other spirurine nematodes. Neither nuclear nor mitochondrial sequences supported monophyly of Anguillicoloides. Genetic diversity within the African species Anguillicoloides papernai was suggestive of cryptic taxa, as was the finding of distinct lineages of Anguillicoloides novaezelandiae in New Zealand and Tasmania. Phylogenetic analysis of the Spirurina grouped the Anguillicolidae together with members of the Gnathostomatidae and Seuratidae.<br><br>CONCLUSIONS: The Anguillicolidae is part of a complex radiation of parasitic nematodes of vertebrates with wide host diversity (chondrichthyes, teleosts, squamates and mammals), most closely related to other marine vertebrate parasites that also have complex life cycles. Molecular analyses do not support the recent division of Anguillicolidae into two genera. The described species may hide cryptic taxa, identified here by DNA taxonomy, and this DNA barcoding approach may assist in tracking species invasions. The propensity for host switching, and thus the potential for invasive behaviour, is found in A. crassus, A. novaezelandiae and A. papernai, and thus may be common to the group.},
}
@article {pmid22559009,
year = {2012},
author = {Shearer, AE and Hildebrand, MS and Smith, RJ},
title = {Solution-based targeted genomic enrichment for precious DNA samples.},
journal = {BMC biotechnology},
volume = {12},
number = {},
pages = {20},
pmid = {22559009},
issn = {1472-6750},
support = {DC012049/DC/NIDCD NIH HHS/United States ; T32 GM007337/GM/NIGMS NIH HHS/United States ; R01 DC003544/DC/NIDCD NIH HHS/United States ; F30 DC011674/DC/NIDCD NIH HHS/United States ; 1F30DC011674/DC/NIDCD NIH HHS/United States ; DC002842/DC/NIDCD NIH HHS/United States ; R01 DC012049/DC/NIDCD NIH HHS/United States ; R01 DC002842/DC/NIDCD NIH HHS/United States ; },
mesh = {DNA/*genetics ; Genomics/*methods ; Polymerase Chain Reaction ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: Solution-based targeted genomic enrichment (TGE) protocols permit selective sequencing of genomic regions of interest on a massively parallel scale. These protocols could be improved by: 1) modifying or eliminating time consuming steps; 2) increasing yield to reduce input DNA and excessive PCR cycling; and 3) enhancing reproducible.<br><br>RESULTS: We developed a solution-based TGE method for downstream Illumina sequencing in a non-automated workflow, adding standard Illumina barcode indexes during the post-hybridization amplification to allow for sample pooling prior to sequencing. The method utilizes Agilent SureSelect baits, primers and hybridization reagents for the capture, off-the-shelf reagents for the library preparation steps, and adaptor oligonucleotides for Illumina paired-end sequencing purchased directly from an oligonucleotide manufacturing company.<br><br>CONCLUSIONS: This solution-based TGE method for Illumina sequencing is optimized for small- or medium-sized laboratories and addresses the weaknesses of standard protocols by reducing the amount of input DNA required, increasing capture yield, optimizing efficiency, and improving reproducibility.},
}
@article {pmid22558256,
year = {2012},
author = {Seena, S and Duarte, S and Pascoal, C and Cássio, F},
title = {Intraspecific variation of the aquatic fungus Articulospora tetracladia: an ubiquitous perspective.},
journal = {PloS one},
volume = {7},
number = {4},
pages = {e35884},
pmid = {22558256},
issn = {1932-6203},
mesh = {Aquatic Organisms/classification/*genetics/isolation &amp; purification ; Canada ; DNA Barcoding, Taxonomic ; DNA Fingerprinting ; DNA, Intergenic/*genetics ; Denaturing Gradient Gel Electrophoresis ; Europe ; Genetic Variation ; Japan ; Malaysia ; Mitosporic Fungi/classification/*genetics/isolation &amp; purification ; Phylogeny ; Phylogeography ; Polymerase Chain Reaction ; Rivers/microbiology ; },
abstract = {The worldwide-distributed aquatic fungus Articulospora tetracladia Ingold is a dominant sporulating species in streams of the Northwest Iberian Peninsula. To elucidate the genetic diversity of A. tetracladia, we analyzed isolates collected from various types of plant litter or foam in streams from North and Central Portugal and North Spain, between 2000 and 2010. Genetic diversity of these fungal populations was assessed by denaturing gradient gel electrophoresis (DGGE) fingerprints and by using ITS1-5.8S-ITS2 barcodes. Moreover, ITS1-5.8S-ITS2 barcodes of A. tetracladia reported in other parts of the world (Central Europe, United Kingdom, Canada, Japan and Malaysia) were retrieved from the National Center for Biotechnology (NCBI) and the National Institute of Technology and Evaluation Biological Resource Center (NBRC) to probe into genetic diversity of A. tetracladia. PCR-DGGE of ITS2 region of 50 Iberian fungal isolates distinguished eight operational taxonomic units (OTUs), which were similar to those obtained from neighboring trees based on ITS2 gene sequences. On the other hand, ITS1-5.8S-ITS2 barcodes of 68 fungal isolates yielded nine OTUs, but five fungal isolates were not assigned to any of these OTUs. Molecular diversity was highest for OTU-8, which included only European isolates. Two haplotypes were observed within OTU-8 and OTU-9, while only one haplotype was found within each of the remaining OTUs. Malaysia did not share haplotypes with other countries. Overall results indicate that, apart from the Malaysian genotypes, A. tetracladia genotypes were geographically widespread irrespective of sampling time, sites or substrates. Furthermore, PCR-DGGE appeared to be a rapid tool for assessing intraspecific diversity of aquatic hyphomycetes.},
}
@article {pmid22558244,
year = {2012},
author = {Costa, FO and Landi, M and Martins, R and Costa, MH and Costa, ME and Carneiro, M and Alves, MJ and Steinke, D and Carvalho, GR},
title = {A ranking system for reference libraries of DNA barcodes: application to marine fish species from Portugal.},
journal = {PloS one},
volume = {7},
number = {4},
pages = {e35858},
pmid = {22558244},
issn = {1932-6203},
mesh = {Animals ; Aquatic Organisms/classification/*genetics ; DNA Barcoding, Taxonomic/methods/*standards ; DNA, Mitochondrial/classification/*genetics ; Electron Transport Complex IV/classification/*genetics ; Fishes/classification/*genetics ; Gene Library ; Phylogeny ; Phylogeography ; Portugal ; },
abstract = {BACKGROUND: The increasing availability of reference libraries of DNA barcodes (RLDB) offers the opportunity to the screen the level of consistency in DNA barcode data among libraries, in order to detect possible disagreements generated from taxonomic uncertainty or operational shortcomings. We propose a ranking system to attribute a confidence level to species identifications associated with DNA barcode records from a RLDB. Here we apply the proposed ranking system to a newly generated RLDB for marine fish of Portugal.<br><br>Specimens (n&#x200a;=&#x200a;659) representing 102 marine fish species were collected along the continental shelf of Portugal, morphologically identified and archived in a museum collection. Samples were sequenced at the barcode region of the cytochrome oxidase subunit I gene (COI-5P). Resultant DNA barcodes had average intra-specific and inter-specific Kimura-2-parameter distances (0.32% and 8.84%, respectively) within the range usually observed for marine fishes. All specimens were ranked in five different levels (A-E), according to the reliability of the match between their species identification and the respective diagnostic DNA barcodes. Grades A to E were attributed upon submission of individual specimen sequences to BOLD-IDS and inspection of the clustering pattern in the NJ tree generated. Overall, our study resulted in 73.5% of unambiguous species IDs (grade A), 7.8% taxonomically congruent barcode clusters within our dataset, but awaiting external confirmation (grade B), and 18.7% of species identifications with lower levels of reliability (grades C/E).<br><br>CONCLUSION/SIGNIFICANCE: We highlight the importance of implementing a system to rank barcode records in RLDB, in order to flag taxa in need of taxonomic revision, or reduce ambiguities of discordant data. With increasing DNA barcode records publicly available, this cross-validation system would provide a metric of relative accuracy of barcodes, while enabling the continuous revision and annotation required in taxonomic work.},
}
@article {pmid22554201,
year = {2012},
author = {Chen, BR and Hale, DC and Ciolek, PJ and Runge, KW},
title = {Generation and analysis of a barcode-tagged insertion mutant library in the fission yeast Schizosaccharomyces pombe.},
journal = {BMC genomics},
volume = {13},
number = {},
pages = {161},
pmid = {22554201},
issn = {1471-2164},
support = {R01 AG019960/AG/NIA NIH HHS/United States ; R01 GM050752/GM/NIGMS NIH HHS/United States ; R01AG019960/AG/NIA NIH HHS/United States ; },
mesh = {DNA/chemistry/metabolism ; Deoxyribonucleases, Type II Site-Specific/metabolism ; Gene Library ; Genes, Fungal ; *Mutagenesis, Insertional ; Schizosaccharomyces/*genetics ; Schizosaccharomyces pombe Proteins/genetics/metabolism ; },
abstract = {BACKGROUND: Barcodes are unique DNA sequence tags that can be used to specifically label individual mutants. The barcode-tagged open reading frame (ORF) haploid deletion mutant collections in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe allow for high-throughput mutant phenotyping because the relative growth of mutants in a population can be determined by monitoring the proportions of their associated barcodes. While these mutant collections have greatly facilitated genome-wide studies, mutations in essential genes are not present, and the roles of these genes are not as easily studied. To further support genome-scale research in S. pombe, we generated a barcode-tagged fission yeast insertion mutant library that has the potential of generating viable mutations in both essential and non-essential genes and can be easily analyzed using standard molecular biological techniques.<br><br>RESULTS: An insertion vector containing a selectable ura4+ marker and a random barcode was used to generate a collection of 10,000 fission yeast insertion mutants stored individually in 384-well plates and as six pools of mixed mutants. Individual barcodes are flanked by Sfi I recognition sites and can be oligomerized in a unique orientation to facilitate barcode sequencing. Independent genetic screens on a subset of mutants suggest that this library contains a diverse collection of single insertion mutations. We present several approaches to determine insertion sites.<br><br>CONCLUSIONS: This collection of S. pombe barcode-tagged insertion mutants is well-suited for genome-wide studies. Because insertion mutations may eliminate, reduce or alter the function of essential and non-essential genes, this library will contain strains with a wide range of phenotypes that can be assayed by their associated barcodes. The design of the barcodes in this library allows for barcode sequencing using next generation or standard benchtop cloning approaches.},
}
@article {pmid22551496,
year = {2012},
author = {Laroche, JA and Diniz, AJ},
title = {Immunisation registers in Canada: progress made, current situation, and challenges for the future.},
journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin},
volume = {17},
number = {17},
pages = {},
doi = {10.2807/ese.17.17.20158-en},
pmid = {22551496},
issn = {1560-7917},
mesh = {Canada ; Humans ; Immunization Programs/*trends ; *Registries ; },
abstract = {Immunisation registers have the capacity to capture data on the administration of vaccine doses at the individual level within the population and represent an important tool in assessing immunisation coverage and vaccine uptake. In 1999, the National Advisory Committee on Immunization recommended that a network of immunisation registers be established in Canada. The Canadian Immunization Registry Network (CIRN) was established to coordinate the development of standards and facilitate the sharing of knowledge and experience to develop a national network of such registers. In 2003, the National Immunization Strategy identified immunisation registers as an important component in improving national immunisation surveillance. In addition, there has been consistent public and professional interest in a national immunisation register being available and considerable progress has been made in developing technologies to facilitate the capture of immunisation-related data. More specifically, the automated identification of vaccines, through the use of barcodes on vaccines, will facilitate collection of data related to administered vaccine doses. Nevertheless, challenges remain in the implementation of immunisation registers in all Canadian provinces and territories such that Canada still does not currently have a fully functional network of immunisation registers with the capacity to be interoperable between jurisdictions and to allow for data to be captured at the national level.},
}
@article {pmid22551463,
year = {2012},
author = {Bernal-González, PJ and Navarro-Alonso, JA and Pérez-Martin, JJ},
title = {Computerised vaccination register for the Murcia region, Spain, 1991 to 2011.},
journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin},
volume = {17},
number = {16},
pages = {},
pmid = {22551463},
issn = {1560-7917},
mesh = {Adolescent ; Child ; Child, Preschool ; Communicable Disease Control/*organization &amp; administration/*statistics &amp; numerical data/trends ; Female ; Humans ; Immunization Programs/organization &amp; administration/*statistics &amp; numerical data ; Immunization Schedule ; Infant ; Infant, Newborn ; Male ; Measles-Mumps-Rubella Vaccine/*administration &amp; dosage ; *Medical Records Systems, Computerized ; Population Surveillance ; *Registries ; Spain ; Vaccination/*statistics &amp; numerical data ; },
abstract = {We describe the Murcia regional vaccination register in Spain, which was set up in 1991, detailing its main features, advantages and limitations. We also report on some recent special actions carried out that led to an improvement in vaccination coverage against measles, rubella and mumps (MMR): by using the vaccination register, we were able to identify and vaccinate persons aged under 20 years in a measles outbreak in 2010 in the town of Jumilla who were not adequately vaccinated for their age with MMR vaccine. From spring 2012, use of our register will enable us to identify susceptible individuals in our region under 40 years of age who have received fewer than two doses of MMR vaccine and call them for the appropriate vaccination. We also set out our experience in the use of barcodes to identify individuals and collect vaccine data: our data show that the barcodes help to improve data quality and completeness. Finally, we identify certain challenges in search of greater standardisation for systems and encoding that is necessary to enable an easy exchange of data between different registers.},
}
@article {pmid22548741,
year = {2012},
author = {Deng, J and Yu, F and Zhang, TX and Hu, HY and Zhu, CD and Wu, SA and Zhang, YZ},
title = {DNA barcoding of six Ceroplastes species (Hemiptera: Coccoidea: Coccidae) from China.},
journal = {Molecular ecology resources},
volume = {12},
number = {5},
pages = {791-796},
doi = {10.1111/j.1755-0998.2012.03152.x},
pmid = {22548741},
issn = {1755-0998},
mesh = {Animals ; Base Composition ; China ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Hemiptera/*classification/*genetics ; Molecular Sequence Data ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; },
abstract = {Ceroplastes Gray (wax scales) is one of the genera of Coccidae, most species of which are considered to be serious economic pests. However, identification of Ceroplastes species is always difficult owing to the shortage of easily distinguishable morphological characters. Mitochondrial cytochrome c oxidase I (COI) sequences (or DNA barcodes) and the D2 expansion segments of the large subunit ribosomal RNA gene 28S were used for accurate identification of six Ceroplastes species (C. floridensis Comstock, C. japonicus Green, C. ceriferus (Fabricius), C. pseudoceriferus Green, C. rubens Maskell and C. kunmingensis Tang et Xie) from 20 different locations in China. For COI data, low G·C content was found in all species, averaging about 20.4%. Sequence divergences (K2P) between congeneric species averaged 12.19%, while intra-specific divergences averaged 0.42%. All 112 samples fell into six reciprocally monophyletic clades in the COI neighbour-joining (NJ) tree. The NJ tree inferred from 28S showed almost same results, but samples of two closely related species, C. ceriferus and C. pseudoceriferus, were clustered together. This research indicates that the standard barcode region of COI can efficiently identify similar Ceroplastes species. This study provides an example of the usefulness of barcoding for Ceroplastes identification.},
}
@article {pmid22545129,
year = {2012},
author = {Alberdi, A and Garin, I and Aizpurua, O and Aihartza, J},
title = {The foraging ecology of the mountain long-eared bat Plecotus macrobullaris revealed with DNA mini-barcodes.},
journal = {PloS one},
volume = {7},
number = {4},
pages = {e35692},
pmid = {22545129},
issn = {1932-6203},
mesh = {Animal Nutritional Physiological Phenomena ; Animals ; Chiroptera/*physiology ; DNA/analysis/isolation &amp; purification ; Diet ; Diptera/genetics ; Electronic Data Processing ; Feeding Behavior ; Lepidoptera/genetics ; *Predatory Behavior ; Sequence Analysis, DNA/methods ; },
abstract = {Molecular analysis of diet overcomes the considerable limitations of traditional techniques for identifying prey remains in bat faeces. We collected faeces from individual Mountain Long-eared Bats Plecotus macrobullaris trapped using mist nets during the summers of 2009 and 2010 in the Pyrenees. We analysed their diet using DNA mini-barcodes to identify prey species. In addition, we inferred some basic features of the bat's foraging ecology that had not yet been addressed. P. macrobullaris fed almost exclusively on moths (97.8%). As prey we detected one dipteran genus (Tipulidae) and 29 moth taxa: 28 were identified at species level (23 Noctuidae, 1 Crambidae, 1 Geometridae, 1 Pyralidae, 1 Sphingidae, 1 Tortricidae), and one at genus level (Rhyacia sp., Noctuidae). Known ecological information about the prey species allowed us to determine that bats had foraged at elevations between 1,500 and 2,500 m amsl (above mean sea level), mostly in subalpine meadows, followed by other open habitats such as orophilous grasslands and alpine meadows. No forest prey species were identified in the diet. As 96.4% of identified prey species were tympanate moths and no evidence of gleaning behaviour was revealed, we suggest P. macrobullaris probably forages by aerial hawking using faint echolocation pulses to avoid detection by hearing moths. As we could identify 87.8% of the analysed sequences (64.1% of the MOTUs, Molecular Operational Taxonomic Units) at species level, we conclude that DNA mini-barcodes are a very useful tool to analyse the diet of moth-specialist bats.},
}
@article {pmid22539880,
year = {2012},
author = {Randrianiaina, RD and Strauß, A and Glos, J and Vences, M},
title = {Diversity of the strongly rheophilous tadpoles of Malagasy tree frogs, genus Boophis (Anura, Mantellidae), and identification of new candidate species via larval DNA sequence and morphology.},
journal = {ZooKeys},
volume = {},
number = {178},
pages = {59-124},
pmid = {22539880},
issn = {1313-2970},
abstract = {This study provides detailed morphological descriptions of previously unknown tadpoles of the treefrog genus Boophis Tschudi and analyses of habitat preferences of several of these tadpoles in Ranomafana National Park. A total of twenty-two tadpoles determined via DNA barcoding are characterized morphologically herein, fourteen of them for the first time. Twelve of these tadpoles belong to taxonomically undescribed candidate species which in several cases are so far only known from their larval stages. Our data show that the larvae of some of these candidate species occur syntopically yet maintaining a clearly correlated genetic and morphological identity, suggesting that they indeed are true biological and evolutionary species. Tadpoles considered to belong to the "adherent" ecomorphological guild inhabit fast-running waters and their oral disc is commonly to continuously attached to the rocky substrate, supposedly to keep their position in the water current. Some of these species are characterized by the presence of a dorsal gap of papillae and the absence of an upper jaw sheath. This guild includes the tadpoles of the Boophis albipuncatus group (Boophis ankaratra, Boophis schuboeae, Boophis albipunctatus, Boophis sibilans, Boophis luciae), and of the Boophis mandraka group (Boophis sambirano and six candidate species related to this species and to Boophis mandraka). Tadpoles considered belonging to the "suctorial" guild inhabit fast-running waters where they use frequently their oral disc to attach to the substrate. They have an enlarged oral disc without any dorsal gap, including two nominal species (Boophis marojezensis, Boophis vittatus), and five candidate species related to Boophis marojezensis. An ecological analysis of the tadpoles of Boophis luciae, Boophis schuboeae and Boophis marojezensis [Ca51 JQ518198] from Ranomafana National Park did not provide evidence for a clear preference of these tadpoles to the fast flowing microhabitat sections of the stream, although the tadpoles discussed in this study are typically caught in this habitat.},
}
@article {pmid22537273,
year = {2012},
author = {Li, HQ and Chen, JY and Wang, S and Xiong, SZ},
title = {Evaluation of six candidate DNA barcoding loci in Ficus (Moraceae) of China.},
journal = {Molecular ecology resources},
volume = {12},
number = {5},
pages = {783-790},
doi = {10.1111/j.1755-0998.2012.03147.x},
pmid = {22537273},
issn = {1755-0998},
mesh = {Cell Nucleus ; China ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/chemistry/*genetics ; Ficus/*classification/*genetics ; Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Plastids/genetics ; Sequence Analysis, DNA ; },
abstract = {Ficus, with about 755 species, diverse habits and complicated co-evolutionary history with fig wasps, is a notoriously difficult group in taxonomy. DNA barcoding is expected to bring light to the identification of Ficus but needs evaluation of candidate loci. Based on five plastid loci (rbcL, matK, trnH-psbA, psbK-psbI, atpF-atpH) and a nuclear locus [internal transcribed spacer (ITS)], we calculated genetic distances and DNA barcoding gaps individually and in combination and constructed phylogenetic trees to test their ability to distinguish the species of the genus. A total of 228 samples representing 63 putative species in Ficus (Moraceae) of China were included in this study. The results demonstrated that ITS has the most variable sites, greater intra- and inter-specific divergences, the highest species discrimination rate (72%) and higher primer universality among the single loci. It is followed by psbK-psbI and trnH-psbA with moderate variation and considerably lower species discrimination rates (about 19%), whereas matK, rbcL and atpF-atpH could not effectively separate the species. Among the possible combinations of loci, ITS + trnH-psbA performed best but only marginally improved species resolution over ITS alone (75% vs. 72%). Therefore, we recommend using ITS as a single DNA barcoding locus in Ficus.},
}
@article {pmid22535389,
year = {2012},
author = {Elmeer, K and Almalki, A and Mohran, KA and Al-Qahtani, KN and Almarri, M},
title = {DNA barcoding of Oryx leucoryx using the mitochondrial cytochrome C oxidase gene.},
journal = {Genetics and molecular research : GMR},
volume = {11},
number = {1},
pages = {539-547},
doi = {10.4238/2012.March.8.2},
pmid = {22535389},
issn = {1676-5680},
mesh = {Animals ; Antelopes/*classification/*genetics ; Base Sequence ; *DNA Barcoding, Taxonomic ; *DNA, Mitochondrial ; Electron Transport Complex IV/*genetics ; Female ; Male ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/chemistry ; Sequence Analysis, DNA ; },
abstract = {The massive destruction and deterioration of the habitat of Oryx leucoryx and illegal hunting have decimated Oryx populations significantly, and now these animals are almost extinct in the wild. Molecular analyses can significantly contribute to captive breeding and reintroduction strategies for the conservation of this endangered animal. A representative 32 identical sequences used for species identification through BOLD and GenBank/NCBI showed maximum homology 96.06% with O. dammah, which is a species of Oryx from Northern Africa, the next closest species 94.33% was O. gazella, the African antelope. DNA barcode sequences of the mitochondrial cytochrome C oxidase (COI) gene were determined for O. leucoryx; identification through BOLD could only recognize the genus correctly, whereas the species could not be identified. This was due to a lack of sequence data for O. leucoryx on BOLD. Similarly, BLAST analysis of the NCBI data base also revealed no COI sequence data for the genus Oryx.},
}
@article {pmid22532782,
year = {2012},
author = {Webber, MM and Graham, MR and Jaeger, JR},
title = {Wernerius inyoensis, an elusive new scorpion from the Inyo Mountains of California (Scorpiones, Vaejovidae).},
journal = {ZooKeys},
volume = {},
number = {177},
pages = {1-13},
pmid = {22532782},
issn = {1313-2970},
abstract = {A new scorpion species is described from the Inyo Mountains of California (USA). The presence of a strong subaculear spine, along with other characters, places the new species within Wernerius, an incredibly rare genus that until now consisted of only two species. Wernerius inyoensissp. n. can be most easily distinguished from the other members of the genus by smaller adult size, femur and pedipalp dimensions, and differences in hemispermatophore morphology. Previous studies have suggested that the elusive nature of this genus may be attributed to low densities and sporadic surface activity. Herein, we provide another hypothesis, that Wernerius are primarily subterranean. Mitochondrial sequence data are provided for the holotype.},
}
@article {pmid22524054,
year = {2012},
author = {An, JH and Kim, TH and Oh, BK and Choi, JW},
title = {Detection of dopamine in dopaminergic cell using nanoparticles-based barcode DNA analysis.},
journal = {Journal of nanoscience and nanotechnology},
volume = {12},
number = {1},
pages = {764-768},
doi = {10.1166/jnn.2012.5403},
pmid = {22524054},
issn = {1533-4880},
mesh = {Cell Line ; DNA/*chemistry/*metabolism ; DNA Barcoding, Taxonomic/*methods ; Dopamine/*metabolism ; Dopaminergic Neurons/*metabolism ; Humans ; Nanostructures/*chemistry/*ultrastructure ; Particle Size ; },
abstract = {Nanotechnology-based bio-barcode-amplification analysis may be an innovative approach to dopamine detection. In this study, we evaluated the efficacy of this bio-barcode DNA method in detecting dopamine from dopaminergic cells. Herein, a combination DNA barcode and bead-based immunoassay for neurotransmitter detection with PCR-like sensitivity is described. This method relies on magnetic nanoparticles with antibodies and nanoparticles that are encoded with DNA, and antibodies that can sandwich the target protein captured by the nanoparticle-bound antibodies. The aggregate sandwich structures are magnetically separated from solution, and treated in order to remove the conjugated barcode DNA. The DNA barcodes were then identified via PCR analysis. The dopamine concentration in dopaminergic cells can be readily and rapidly detected via the bio-barcode assay method. The bio-barcode assay method is, therefore, a rapid and high-throughput screening tool for the detection of neurotransmitters such as dopamine.},
}
@article {pmid22521574,
year = {2012},
author = {Shivali, K and Sasikala, Ch and Ramana, ChV},
title = {MLSA barcoding of Marichromatium spp. and reclassification of Marichromatium fluminis (Sucharita et al., 2010) as Phaeochromatium fluminis gen. nov. comb. nov.},
journal = {Systematic and applied microbiology},
volume = {35},
number = {4},
pages = {221-225},
doi = {10.1016/j.syapm.2012.03.002},
pmid = {22521574},
issn = {1618-0984},
mesh = {Bacterial Proteins/genetics ; Chromatiaceae/*classification/*genetics ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/chemistry/genetics ; Multilocus Sequence Typing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Restriction Mapping/methods ; },
abstract = {Thirty-one members of the genus Marichromatium were analysed based on multilocus sequence analysis (MLSA) of four concatenated protein-coding genes (fusA, pufM, dnaK, recA) along with the internal transcribed spacer (ITS; 16S-23S rRNA) region and 16S rRNA gene. The restriction patterns obtained from the in silico analysis of the concatenated sequences were good barcodes for the identification of Marichromatium spp. Distinct phenotypic, chemotaxonomic and molecular differences allowed the separation of Marichromatium fluminis JA418(T) into a new genus in the family Chromatiaceae, for which we propose the name Phaeochromatium fluminis gen. nov. comb. nov.},
}
@article {pmid22518333,
year = {2012},
author = {Li, YF and Wen, SY and Kawai, K and Gao, JJ and Hu, YG and Segawa, R and Toda, MJ},
title = {DNA Barcoding and Molecular Phylogeny of Drosophila lini and Its Sibling Species.},
journal = {International journal of evolutionary biology},
volume = {2012},
number = {},
pages = {329434},
pmid = {22518333},
issn = {2090-052X},
abstract = {Drosophila lini and its two sibling species, D. ohnishii and D. ogumai, are hardly distinguishable from one another in morphology. These species are more or less reproductively isolated. The mitochondrial ND2 and COI-COII and the nuclear ITS1-ITS2 regions were sequenced to seek for the possibility of DNA barcoding and to reconstruct the phylogeny of them. The character-based approach for DNA barcoding detected some diagnostic nucleotides only for monophyletic D. ogumai, but no informative sites for the other two very closely species, D. lini and D. ohnishii, of which strains intermingled in the molecular phylogenetic trees. Thus, this study provides another case of limited applicability of DNA barcoding in species delineation, as in other cases of related Drosophila species. The molecular phylogenetic tree inferred from the concatenated sequences strongly supported the monophyly of the cluster of the three species, that is, the lini clade. We propose some hypotheses of evolutionary events in this clade.},
}
@article {pmid22511980,
year = {2012},
author = {Dong, W and Liu, J and Yu, J and Wang, L and Zhou, S},
title = {Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding.},
journal = {PloS one},
volume = {7},
number = {4},
pages = {e35071},
pmid = {22511980},
issn = {1932-6203},
mesh = {Chloroplasts/*genetics ; *DNA Barcoding, Taxonomic ; Genetic Markers ; *Genetic Variation ; Genome, Plant ; *Phylogeny ; Plants/*classification ; },
abstract = {BACKGROUND: At present, plant molecular systematics and DNA barcoding techniques rely heavily on the use of chloroplast gene sequences. Because of the relatively low evolutionary rates of chloroplast genes, there are very few choices suitable for molecular studies on angiosperms at low taxonomic levels, and for DNA barcoding of species.<br><br>We scanned the entire chloroplast genomes of 12 genera to search for highly variable regions. The sequence data of 9 genera were from GenBank and 3 genera were of our own. We identified nearly 5% of the most variable loci from all variable loci in the chloroplast genomes of each genus, and then selected 23 loci that were present in at least three genera. The 23 loci included 4 coding regions, 2 introns, and 17 intergenic spacers. Of the 23 loci, the most variable (in order from highest variability to lowest) were intergenic regions ycf1-a, trnK, rpl32-trnL, and trnH-psbA, followed by trnS(UGA)-trnG(UCC), petA-psbJ, rps16-trnQ, ndhC-trnV, ycf1-b, ndhF, rpoB-trnC, psbE-petL, and rbcL-accD. Three loci, trnS(UGA)-trnG(UCC), trnT-psbD, and trnW-psaJ, showed very high nucleotide diversity per site (&#x3c0; values) across three genera. Other loci may have strong potential for resolving phylogenetic and species identification problems at the species level. The loci accD-psaI, rbcL-accD, rpl32-trnL, rps16-trnQ, and ycf1 are absent from some genera. To amplify and sequence the highly variable loci identified in this study, we designed primers from their conserved flanking regions. We tested the applicability of the primers to amplify target sequences in eight species representing basal angiosperms, monocots, eudicots, rosids, and asterids, and confirmed that the primers amplified the desired sequences of these species.<br><br>SIGNIFICANCE/CONCLUSIONS: Chloroplast genome sequences contain regions that are highly variable. Such regions are the first consideration when screening the suitable loci to resolve closely related species or genera in phylogenetic analyses, and for DNA barcoding.},
}
@article {pmid22509245,
year = {2012},
author = {Dai, QY and Gao, Q and Wu, CS and Chesters, D and Zhu, CD and Zhang, AB},
title = {Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus) in China with multiple gene markers.},
journal = {PloS one},
volume = {7},
number = {4},
pages = {e32544},
pmid = {22509245},
issn = {1932-6203},
mesh = {Algorithms ; Animals ; China ; DNA Barcoding, Taxonomic/*methods ; DNA, Intergenic/genetics ; Evolution, Molecular ; Genetic Markers/*genetics ; Haplotypes/genetics ; Moths/*genetics ; Neural Networks, Computer ; *Phylogeny ; Species Specificity ; },
abstract = {Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI) gene and two alternative internal transcribed spacer (ITS) genes (ITS1 and ITS2). Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML)/Neighbor-joining (NJ), "best close match" (BCM), Minimum distance (MD), and BP-based method (BP)), representing commonly used methodology (tree-based and non-tree based) in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10-97.40%, while ITS1 and ITS2 obtained a success rate of 64.70-81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In addition, our results indicate that the most closely related species D. punctatus, D. tabulaeformis, and D. spectabilis, may be still in the process of incomplete lineage sorting, with occasional hybridizations occurring among them.},
}
@article {pmid22508485,
year = {2012},
author = {Bodmer, T and Ströhle, A},
title = {Diagnosing pulmonary tuberculosis with the Xpert MTB/RIF test.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {62},
pages = {e3547},
pmid = {22508485},
issn = {1940-087X},
mesh = {Antibiotics, Antitubercular/pharmacology ; Humans ; Molecular Diagnostic Techniques/*methods ; Mycobacterium tuberculosis/isolation &amp; purification ; Rifampin/pharmacology ; Tuberculosis, Multidrug-Resistant/diagnosis ; Tuberculosis, Pulmonary/*diagnosis ; },
abstract = {Tuberculosis (TB) due to Mycobacterium tuberculosis (MTB) remains a major public health issue: the infection affects up to one third of the world population(1), and almost two million people are killed by TB each year. Universal access to high-quality, patient-centered treatment for all TB patients is emphasized by WHO's Stop TB Strategy. The rapid detection of MTB in respiratory specimens and drug therapy based on reliable drug resistance testing results are a prerequisite for the successful implementation of this strategy. However, in many areas of the world, TB diagnosis still relies on insensitive, poorly standardized sputum microscopy methods. Ineffective TB detection and the emergence and transmission of drug-resistant MTB strains increasingly jeopardize global TB control activities. Effective diagnosis of pulmonary TB requires the availability - on a global scale - of standardized, easy-to-use, and robust diagnostic tools that would allow the direct detection of both the MTB complex and resistance to key antibiotics, such as rifampicin (RIF). The latter result can serve as marker for multidrug-resistant MTB (MDR TB) and has been reported in > 95% of the MDR-TB isolates. The rapid availability of reliable test results is likely to directly translate into sound patient management decisions that, ultimately, will cure the individual patient and break the chain of TB transmission in the community. Cepheid's (Sunnyvale, CA, U.S.A.) Xpert MTB/RIF assay meets the demands outlined above in a remarkable manner. It is a nucleic-acids amplification test for 1) the detection of MTB complex DNA in sputum or concentrated sputum sediments; and 2) the detection of RIF resistance-associated mutations of the rpoB gene. It is designed for use with Cepheid's GeneXpert Dx System that integrates and automates sample processing, nucleic acid amplification, and detection of the target sequences using real-time PCR and reverse transcriptase PCR. The system consists of an instrument, personal computer, barcode scanner, and preloaded software for running tests and viewing the results. It employs single-use disposable Xpert MTB/RIF cartridges that hold PCR reagents and host the PCR process. Because the cartridges are self-contained, cross-contamination between samples is eliminated. Current nucleic acid amplification methods used to detect MTB are complex, labor-intensive, and technically demanding. The Xpert MTB/RIF assay has the potential to bring standardized, sensitive and very specific diagnostic testing for both TB and drug resistance to universal-access point-of-care settings, provided that they will be able to afford it. In order to facilitate access, the Foundation for Innovative New Diagnostics (FIND) has negotiated significant price reductions. Current FIND-negotiated prices, along with the list of countries eligible for the discounts, are available on the web.},
}
@article {pmid22503670,
year = {2012},
author = {Kashiwagi, T and Marshall, AD and Bennett, MB and Ovenden, JR},
title = {The genetic signature of recent speciation in manta rays (Manta alfredi and M. birostris).},
journal = {Molecular phylogenetics and evolution},
volume = {64},
number = {1},
pages = {212-218},
doi = {10.1016/j.ympev.2012.03.020},
pmid = {22503670},
issn = {1095-9513},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; DNA Primers/genetics ; DNA, Mitochondrial/genetics ; *Ecosystem ; Elasmobranchii/classification/*genetics ; Gene Flow/genetics ; Genes, RAG-1/genetics ; *Genetic Speciation ; *Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; Indonesia ; Japan ; Likelihood Functions ; Mexico ; *Models, Genetic ; Molecular Sequence Data ; Mozambique ; Sequence Analysis, DNA ; South Africa ; Species Specificity ; Western Australia ; },
abstract = {Manta rays have been taxonomically revised as two species, Manta alfredi and M. birostris, on the basis of morphological and meristic data, yet the two species occur in extensive mosaic sympatry. We analysed the genetic signatures of the species boundary using a portion of the nuclear RAG1 (681 base pairs), mitochondrial CO1 (574 bp) and ND5 genes (1188 bp). The assay with CO1 sequences, widely used in DNA barcoding, failed to distinguish the two species. The two species were clearly distinguishable, however, with no shared RAG1 or ND5 haplotypes. The species were reciprocally monophyletic for RAG1, but paraphyletic for ND5 sequences. Qualitative evidence and statistical inferences using the 'Isolation-with-Migration models' indicated that these results were better explained with post-divergence gene flow in the recent past rather than incomplete lineage sorting with zero gene flow since speciation. An estimate of divergence time was less than 0.5 Ma with an upper confidence limit of within 1 Ma. Recent speciation of highly mobile species in the marine environment is of great interest, as it suggests that speciation may have occurred in the absence of long-term physical barriers to gene flow. We propose that the ecologically driven forces such as habitat choice played a significant role in speciation in manta rays.},
}
@article {pmid22496874,
year = {2012},
author = {Mantri, N and Olarte, A and Li, CG and Xue, C and Pang, EC},
title = {Fingerprinting the Asterid species using subtracted diversity array reveals novel species-specific sequences.},
journal = {PloS one},
volume = {7},
number = {4},
pages = {e34873},
pmid = {22496874},
issn = {1932-6203},
mesh = {Apiaceae/classification/*genetics ; Asteraceae/classification/*genetics ; Base Sequence ; DNA Fingerprinting/*methods ; Genetic Variation/genetics ; Lamiaceae/classification/*genetics ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis/*methods ; Plants, Medicinal/genetics ; Species Specificity ; },
abstract = {BACKGROUND: Asterids is one of the major plant clades comprising of many commercially important medicinal species. One of the major concerns in medicinal plant industry is adulteration/contamination resulting from misidentification of herbal plants. This study reports the construction and validation of a microarray capable of fingerprinting medicinally important species from the Asterids clade.<br><br>Pooled genomic DNA of 104 non-asterid angiosperm and non-angiosperm species was subtracted from pooled genomic DNA of 67 asterid species. Subsequently, 283 subtracted DNA fragments were used to construct an Asterid-specific array. The validation of Asterid-specific array revealed a high (99.5%) subtraction efficiency. Twenty-five Asterid species (mostly medicinal) representing 20 families and 9 orders within the clade were hybridized onto the array to reveal its level of species discrimination. All these species could be successfully differentiated using their hybridization patterns. A number of species-specific probes were identified for commercially important species like tea, coffee, dandelion, yarrow, motherwort, Japanese honeysuckle, valerian, wild celery, and yerba mate. Thirty-seven polymorphic probes were characterized by sequencing. A large number of probes were novel species-specific probes whilst some of them were from chloroplast region including genes like atpB, rpoB, and ndh that have extensively been used for fingerprinting and phylogenetic analysis of plants.<br><br>CONCLUSIONS/SIGNIFICANCE: Subtracted Diversity Array technique is highly efficient in fingerprinting species with little or no genomic information. The Asterid-specific array could fingerprint all 25 species assessed including three species that were not used in constructing the array. This study validates the use of chloroplast genes for bar-coding (fingerprinting) plant species. In addition, this method allowed detection of several new loci that can be explored to solve existing discrepancies in phylogenetics and fingerprinting of plants.},
}
@article {pmid22494453,
year = {2012},
author = {Puillandre, N and Modica, MV and Zhang, Y and Sirovich, L and Boisselier, MC and Cruaud, C and Holford, M and Samadi, S},
title = {Large-scale species delimitation method for hyperdiverse groups.},
journal = {Molecular ecology},
volume = {21},
number = {11},
pages = {2671-2691},
doi = {10.1111/j.1365-294X.2012.05559.x},
pmid = {22494453},
issn = {1365-294X},
support = {GM088096/GM/NIGMS NIH HHS/United States ; },
mesh = {Animal Shells/anatomy &amp; histology/physiology ; Animals ; Biodiversity ; Electron Transport Complex IV/genetics ; Genetic Variation ; *Models, Genetic ; Molecular Sequence Data ; Mollusca/*classification/*genetics ; Phylogeny ; Phylogeography ; RNA, Ribosomal, 28S ; Reproducibility of Results ; },
abstract = {Accelerating the description of biodiversity is a major challenge as extinction rates increase. Integrative taxonomy combining molecular, morphological, ecological and geographical data is seen as the best route to reliably identify species. Classic molluscan taxonomic methodology proposes primary species hypotheses (PSHs) based on shell morphology. However, in hyperdiverse groups, such as the molluscan family Turridae, where most of the species remain unknown and for which homoplasy and plasticity of morphological characters is common, shell-based PSHs can be arduous. A four-pronged approach was employed to generate robust species hypotheses of a 1000 specimen South-West Pacific Turridae data set in which: (i) analysis of COI DNA Barcode gene is coupled with (ii) species delimitation tools GMYC (General Mixed Yule Coalescence Method) and ABGD (Automatic Barcode Gap Discovery) to propose PSHs that are then (iii) visualized using Klee diagrams and (iv) evaluated with additional evidence, such as nuclear gene rRNA 28S, morphological characters, geographical and bathymetrical distribution to determine conclusive secondary species hypotheses (SSHs). The integrative taxonomy approach applied identified 87 Turridae species, more than doubling the amount previously known in the Gemmula genus. In contrast to a predominantly shell-based morphological approach, which over the last 30 years proposed only 13 new species names for the Turridae genus Gemmula, the integrative approach described here identified 27 novel species hypotheses not linked to available species names in the literature. The formalized strategy applied here outlines an effective and reproducible protocol for large-scale species delimitation of hyperdiverse groups.},
}
@article {pmid22493817,
year = {2012},
author = {Li, XW and Hu, ZG and Lin, XH and Li, Q and Gao, HH and Luo, GA and Chen, SL},
title = {[High-throughput pyrosequencing of the complete chloroplast genome of Magnolia officinalis and its application in species identification].},
journal = {Yao xue xue bao = Acta pharmaceutica Sinica},
volume = {47},
number = {1},
pages = {124-130},
pmid = {22493817},
issn = {0513-4870},
mesh = {Base Sequence ; Chloroplasts/*genetics ; DNA, Chloroplast/genetics ; Genes, Chloroplast ; *Genes, Plant ; *Genome, Chloroplast ; Genome, Plant ; High-Throughput Nucleotide Sequencing ; Magnolia/classification/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Chloroplast genome sequences have comprehensive application prospects in DNA barcoding and chloroplast engineering in traditional Chinese medicine. The complete chloroplast genome of Magnolia officinalis sequenced by high-throughput pyrosequencing and a sequencing procedure was established. Fourteen contigs were obtained after de nove assembly. The sequencing percent of coverage was 99.99%. The chloroplast genome is 160 183 bp in size, and has a typical quadripartite structure with the large (LSC, 88 210 bp) and small copy (SSC, 18 843 bp) regions separated by two copies of an inverted repeat (IRs, 26 565 bp each). chloroplast genes were successfully annotated, of which 17 genes located in each IR region. The chloroplast genome features in Magnolia officinalis are nearly identical to those from other Magnoliid chloroplast genomes. Phylogenetic analyses were performed based on 81 shared coding-genes for a total of 9 Magnolia samples of 5 closely related species. Results showed that distinguishing among species was generally straightforward at the species and population level. This study confirmed the effectiveness of our chloroplast genome sequencing procedure. The chloroplast genome can provide distinguishing differences to help identify Magnolia officinalis and its closely related plants.},
}
@article {pmid22487608,
year = {2012},
author = {Quicke, DL and Smith, MA and Janzen, DH and Hallwachs, W and Fernandez-Triana, J and Laurenne, NM and Zaldívar-Riverón, A and Shaw, MR and Broad, GR and Klopfstein, S and Shaw, SR and Hrcek, J and Hebert, PD and Miller, SE and Rodriguez, JJ and Whitfield, JB and Sharkey, MJ and Sharanowski, BJ and Jussila, R and Gauld, ID and Chesters, D and Vogler, AP},
title = {Utility of the DNA barcoding gene fragment for parasitic wasp phylogeny (Hymenoptera: Ichneumonoidea): data release and new measure of taxonomic congruence.},
journal = {Molecular ecology resources},
volume = {12},
number = {4},
pages = {676-685},
doi = {10.1111/j.1755-0998.2012.03143.x},
pmid = {22487608},
issn = {1755-0998},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA Primers ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Mitochondria ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Wasps/*classification/*genetics ; },
abstract = {The enormous cytochrome oxidase subunit I (COI) sequence database being assembled from the various DNA barcoding projects as well as from independent phylogenetic studies constitutes an almost unprecedented amount of data for molecular systematics, in addition to its role in species identification and discovery. As part of a study of the potential of this gene fragment to improve the accuracy of phylogenetic reconstructions, and in particular, exploring the effects of dense taxon sampling, we have assembled a data set for the hyperdiverse, cosmopolitan parasitic wasp superfamily Ichneumonoidea, including the release of 1793 unpublished sequences. Of approximately 84 currently recognized Ichneumonoidea subfamilies, 2500 genera and 41,000 described species, barcoding 5'-COI data were assembled for 4168 putative species-level terminals (many undescribed), representing 671 genera and all but ten of the currently recognized subfamilies. After the removal of identical and near-identical sequences, the 4174 initial sequences were reduced to 3278. We show that when subjected to phylogenetic analysis using both maximum likelihood and parsimony, there is a broad correlation between taxonomic congruence and number of included sequences. We additionally present a new measure of taxonomic congruence based upon the Simpson diversity index, the Simpson dominance index, which gives greater weight to morphologically recognized taxonomic groups (subfamilies) recovered with most representatives in one or a few contiguous groups or subclusters.},
}
@article {pmid22486824,
year = {2012},
author = {Taberlet, P and Coissac, E and Pompanon, F and Brochmann, C and Willerslev, E},
title = {Towards next-generation biodiversity assessment using DNA metabarcoding.},
journal = {Molecular ecology},
volume = {21},
number = {8},
pages = {2045-2050},
doi = {10.1111/j.1365-294X.2012.05470.x},
pmid = {22486824},
issn = {1365-294X},
mesh = {*Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Ecology/methods ; *Ecosystem ; Environmental Monitoring/methods ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
abstract = {Virtually all empirical ecological studies require species identification during data collection. DNA metabarcoding refers to the automated identification of multiple species from a single bulk sample containing entire organisms or from a single environmental sample containing degraded DNA (soil, water, faeces, etc.). It can be implemented for both modern and ancient environmental samples. The availability of next-generation sequencing platforms and the ecologists' need for high-throughput taxon identification have facilitated the emergence of DNA metabarcoding. The potential power of DNA metabarcoding as it is implemented today is limited mainly by its dependency on PCR and by the considerable investment needed to build comprehensive taxonomic reference libraries. Further developments associated with the impressive progress in DNA sequencing will eliminate the currently required DNA amplification step, and comprehensive taxonomic reference libraries composed of whole organellar genomes and repetitive ribosomal nuclear DNA can be built based on the well-curated DNA extract collections maintained by standardized barcoding initiatives. The near-term future of DNA metabarcoding has an enormous potential to boost data acquisition in biodiversity research.},
}
@article {pmid22486822,
year = {2012},
author = {Coissac, E and Riaz, T and Puillandre, N},
title = {Bioinformatic challenges for DNA metabarcoding of plants and animals.},
journal = {Molecular ecology},
volume = {21},
number = {8},
pages = {1834-1847},
doi = {10.1111/j.1365-294X.2012.05550.x},
pmid = {22486822},
issn = {1365-294X},
mesh = {Animals ; Base Sequence ; Biodiversity ; Computational Biology/*methods ; DNA/analysis/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA Primers ; DNA, Plant/analysis/genetics ; Plants/genetics ; Species Specificity ; },
abstract = {Almost all empirical studies in ecology have to identify the species involved in the ecological process under examination. DNA metabarcoding, which couples the principles of DNA barcoding with next generation sequencing technology, provides an opportunity to easily produce large amounts of data on biodiversity. Microbiologists have long used metabarcoding approaches, but use of this technique in the assessment of biodiversity in plant and animal communities is under-explored. Despite its relationship with DNA barcoding, several unique features of DNA metabarcoding justify the development of specific data analysis methodologies. In this review, we describe the bioinformatics tools available for DNA metabarcoding of plants and animals, and we revisit others developed for DNA barcoding or microbial metabarcoding. We also discuss the principles and associated tools for evaluating and comparing DNA barcodes in the context of DNA metabarcoding, for designing new custom-made barcodes adapted to specific ecological question, for dealing with PCR and sequencing errors, and for inferring taxonomical data from sequences.},
}
@article {pmid22486820,
year = {2012},
author = {Shokralla, S and Spall, JL and Gibson, JF and Hajibabaei, M},
title = {Next-generation sequencing technologies for environmental DNA research.},
journal = {Molecular ecology},
volume = {21},
number = {8},
pages = {1794-1805},
doi = {10.1111/j.1365-294X.2012.05538.x},
pmid = {22486820},
issn = {1365-294X},
mesh = {DNA/*analysis/genetics ; Environmental Monitoring/*methods ; *High-Throughput Nucleotide Sequencing/instrumentation/methods ; *Metagenomics ; },
abstract = {Since 2005, advances in next-generation sequencing technologies have revolutionized biological science. The analysis of environmental DNA through the use of specific gene markers such as species-specific DNA barcodes has been a key application of next-generation sequencing technologies in ecological and environmental research. Access to parallel, massive amounts of sequencing data, as well as subsequent improvements in read length and throughput of different sequencing platforms, is leading to a better representation of sample diversity at a reasonable cost. New technologies are being developed rapidly and have the potential to dramatically accelerate ecological and environmental research. The fast pace of development and improvements in next-generation sequencing technologies can reflect on broader and more robust applications in environmental DNA research. Here, we review the advantages and limitations of current next-generation sequencing technologies in regard to their application for environmental DNA analysis.},
}
@article {pmid22483982,
year = {2012},
author = {Yin, HQ and Jia, MX and Yang, S and Jing, PP and Wang, R and Zhang, JG},
title = {Development of a highly sensitive gold nanoparticle probe-based assay for bluetongue virus detection.},
journal = {Journal of virological methods},
volume = {183},
number = {1},
pages = {45-48},
doi = {10.1016/j.jviromet.2012.03.027},
pmid = {22483982},
issn = {1879-0984},
mesh = {Animals ; Antibodies, Viral ; Antigens, Viral/analysis ; Bluetongue/*diagnosis/virology ; Bluetongue virus/*isolation &amp; purification ; Clinical Laboratory Techniques/*methods ; Immunoassay/methods ; *Nanoparticles ; Polymerase Chain Reaction/methods ; Sensitivity and Specificity ; Sheep ; Veterinary Medicine/*methods ; Viral Core Proteins/*analysis ; Virology/*methods ; },
abstract = {A simple gold nanoparticle (GNP) probe based assay (GNPA) that was modified from a bio-barcode assay (BCA) technique, was developed for ultra-sensitive, rapid detection of the bluetongue virus (BTV) VP7 outer-core protein. This assay captures the VP7 target antigen using the GNP probe coated with anti-VP7 polyclonal antibodies and single-stranded signal DNA. Magnetic microparticle (MMP) probes coated with anti-VP7 monoclonal antibodies were then added to form a sandwich immuno-complex. The single-stranded signal DNA coated onto the GNP probe present in the immuno-complex could then be detected by PCR and real-time fluorescence PCR using a TaqMan probe. The assay has a purified VP7 detection limit of 10(-2)fg/ml which is 8 orders of magnitude greater than that of conventional antigen capture ELISAs and 1 order of magnitude more sensitive than that of a conventional BCA. These results indicate that the GNPA is a highly sensitive method for easy detection of BTV proteins and that it can be modified as needed to measure the presence of other proteins.},
}
@article {pmid22481528,
year = {2012},
author = {Islam, S and Kjällquist, U and Moliner, A and Zajac, P and Fan, JB and Lönnerberg, P and Linnarsson, S},
title = {Highly multiplexed and strand-specific single-cell RNA 5' end sequencing.},
journal = {Nature protocols},
volume = {7},
number = {5},
pages = {813-828},
pmid = {22481528},
issn = {1750-2799},
support = {261063/ERC_/European Research Council/International ; },
mesh = {*5' Untranslated Regions ; DNA, Complementary/chemistry ; Flow Cytometry ; Nucleic Acid Amplification Techniques ; Polymerase Chain Reaction ; RNA, Messenger/*chemistry ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis/*methods ; },
abstract = {Single-cell analysis of gene expression is increasingly important for the analysis of complex tissues, including cancer, developing organs and adult stem cell niches. Here we present a detailed protocol for quantitative gene expression analysis in single cells, by the sequencing of mRNA 5' ends. In all, 96 cells are lysed, and their mRNA is converted to cDNA. By using a template-switching mechanism, a bar code and an upstream primer-binding sequence are introduced simultaneously with reverse transcription. All cDNA is pooled and then prepared for 5' end sequencing, including fragmentation, adapter ligation and PCR amplification. The chief advantage of this approach is the great reduction in cost and time, afforded by the early bar-coding strategy. Compared with previous methods, it is more suitable for large-scale quantitative analysis, as well as for the characterization of transcription start sites, but it is unsuitable for the detection of alternatively spliced transcripts. Sample preparation takes 3 d, and two sets of 96 cells can be prepared in parallel. Finally, the sequencing and data analysis can take an additional 4 d altogether.},
}
@article {pmid22479640,
year = {2012},
author = {Zhou, C and Kandemir, I and Walsh, DB and Zalom, FG and Lavine, LC},
title = {Identification of Lygus hesperus by DNA barcoding reveals insignificant levels of genetic structure among distant and habitat diverse populations.},
journal = {PloS one},
volume = {7},
number = {3},
pages = {e34528},
pmid = {22479640},
issn = {1932-6203},
mesh = {Animals ; DNA/genetics/isolation &amp; purification ; *DNA Barcoding, Taxonomic ; Ecosystem ; Fragaria/*parasitology ; Genetic Structures ; Heteroptera/*genetics ; Medicago sativa/*parasitology ; Phylogeny ; United States ; },
abstract = {BACKGROUND: The western tarnished plant bug Lygus hesperus is an economically important pest that belongs to a complex of morphologically similar species that makes identification problematic. The present study provides evidence for the use of DNA barcodes from populations of L. hesperus from the western United States of America for accurate identification.<br><br>This study reports DNA barcodes for 134 individuals of the western tarnished plant bug from alfalfa and strawberry agricultural fields in the western United States of America. Sequence divergence estimates of <3% reveal that morphologically variable individuals presumed to be L. hesperus were accurately identified. Paired estimates of F(st) and subsequent estimates of gene flow show that geographically distinct populations of L. hesperus are genetically similar. Therefore, our results support and reinforce the relatively recent (<100 years) migration of the western tarnished plant bug into agricultural habitats across the western United States.<br><br>CONCLUSIONS/SIGNIFICANCE: This study reveals that despite wide host plant usage and phenotypically plastic morphological traits, the commonly recognized western tarnished plant bug belongs to a single species, Lygus hesperus. In addition, no significant genetic structure was found for the geographically diverse populations of western tarnished plant bug used in this study.},
}
@article {pmid22479636,
year = {2012},
author = {Nagy, ZT and Sonet, G and Glaw, F and Vences, M},
title = {First large-scale DNA barcoding assessment of reptiles in the biodiversity hotspot of Madagascar, based on newly designed COI primers.},
journal = {PloS one},
volume = {7},
number = {3},
pages = {e34506},
pmid = {22479636},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Electron Transport Complex IV/*genetics ; Madagascar ; Protein Subunits/genetics ; Reptiles/*genetics ; Reptilian Proteins/*genetics ; },
abstract = {BACKGROUND: DNA barcoding of non-avian reptiles based on the cytochrome oxidase subunit I (COI) gene is still in a very early stage, mainly due to technical problems. Using a newly developed set of reptile-specific primers for COI we present the first comprehensive study targeting the entire reptile fauna of the fourth-largest island in the world, the biodiversity hotspot of Madagascar.<br><br>Representatives of the majority of Madagascan non-avian reptile species (including Squamata and Testudines) were sampled and successfully DNA barcoded. The new primer pair achieved a constantly high success rate (72.7-100%) for most squamates. More than 250 species of reptiles (out of the 393 described ones; representing around 64% of the known diversity of species) were barcoded. The average interspecific genetic distance within families ranged from a low of 13.4% in the Boidae to a high of 29.8% in the Gekkonidae. Using the average genetic divergence between sister species as a threshold, 41-48 new candidate (undescribed) species were identified. Simulations were used to evaluate the performance of DNA barcoding as a function of completeness of taxon sampling and fragment length. Compared with available multi-gene phylogenies, DNA barcoding correctly assigned most samples to species, genus and family with high confidence and the analysis of fewer taxa resulted in an increased number of well supported lineages. Shorter marker-lengths generally decreased the number of well supported nodes, but even mini-barcodes of 100 bp correctly assigned many samples to genus and family.<br><br>CONCLUSIONS/SIGNIFICANCE: The new protocols might help to promote DNA barcoding of reptiles and the established library of reference DNA barcodes will facilitate the molecular identification of Madagascan reptiles. Our results might be useful to easily recognize undescribed diversity (i.e. novel taxa), to resolve taxonomic problems, and to monitor the international pet trade without specialized expert knowledge.},
}
@article {pmid22479532,
year = {2012},
author = {Arca, M and Hinsinger, DD and Cruaud, C and Tillier, A and Bousquet, J and Frascaria-Lacoste, N},
title = {Deciduous trees and the application of universal DNA barcodes: a case study on the circumpolar Fraxinus.},
journal = {PloS one},
volume = {7},
number = {3},
pages = {e34089},
pmid = {22479532},
issn = {1932-6203},
mesh = {Algorithms ; Chloroplasts/genetics ; *DNA Barcoding, Taxonomic ; DNA, Chloroplast/genetics ; DNA, Intergenic/genetics ; DNA, Plant/genetics ; Fraxinus/*genetics ; Genes, Plant ; Genetic Variation ; Genome, Chloroplast ; Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Software ; Species Specificity ; Temperature ; },
abstract = {The utility of DNA barcoding for identifying representative specimens of the circumpolar tree genus Fraxinus (56 species) was investigated. We examined the genetic variability of several loci suggested in chloroplast DNA barcode protocols such as matK, rpoB, rpoC1 and trnH-psbA in a large worldwide sample of Fraxinus species. The chloroplast intergenic spacer rpl32-trnL was further assessed in search for a potentially variable and useful locus. The results of the study suggest that the proposed cpDNA loci, alone or in combination, cannot fully discriminate among species because of the generally low rates of substitution in the chloroplast genome of Fraxinus. The intergenic spacer trnH-psbA was the best performing locus, but genetic distance-based discrimination was moderately successful and only resulted in the separation of the samples at the subgenus level. Use of the BLAST approach was better than the neighbor-joining tree reconstruction method with pairwise Kimura's two-parameter rates of substitution, but allowed for the correct identification of only less than half of the species sampled. Such rates are substantially lower than the success rate required for a standardised barcoding approach. Consequently, the current cpDNA barcodes are inadequate to fully discriminate Fraxinus species. Given that a low rate of substitution is common among the plastid genomes of trees, the use of the plant cpDNA "universal" barcode may not be suitable for the safe identification of tree species below a generic or sectional level. Supplementary barcoding loci of the nuclear genome and alternative solutions are proposed and discussed.},
}
@article {pmid22479068,
year = {2011},
author = {Brisseau, L and Chiveri, A and Lebel, D and Bussières, JF},
title = {A pilot study of bar codes in a canadian hospital.},
journal = {The Canadian journal of hospital pharmacy},
volume = {64},
number = {4},
pages = {257-261},
pmid = {22479068},
issn = {1920-2903},
abstract = {BACKGROUND: In 2004, the US Food and Drug Administration issued a new rule requiring most prescription and some over-the-counter pharmaceutical products to carry bar codes down to the level of individual doses, with the intent of reducing the number of medication errors. Despite these regulatory changes in the United States, Health Canada has not yet adopted any mandatory bar-coding of drugs.<br><br>OBJECTIVE: To evaluate the feasibility of using commercial bar codes for receipt and preparation of drug products and to evaluate the readability of the bar codes printed on various levels of drug packaging.<br><br>METHODS: This cross-sectional observational pilot study was conducted in the Pharmacy Department of a Canadian mother-child university hospital centre in July 2010. For the purposes of the study, research drugs and cytotoxic drugs in various storage areas, as well as locally compounded medications with bar codes generated in house, were excluded. For all other drug products, the presence or absence of bar codes was documented for each level of packaging, along with the trade and generic names, content (i.e., drug product), quantity of doses or level of packaging, therapeutic class (if applicable), type of bar code (1- or 2-dimensional symbology), alphanumeric value contained in the bar code, standard of reference used to generate the alphanumeric value (Universal Product Code [UPC], Global Trade Item Number [GTIN], or unknown), and readability of the bar codes by 2 scanners.<br><br>RESULTS: Only 33 (1.9%) of the 1734 products evaluated had no bar codes on any level of packaging. Of the 2875 levels of packaging evaluated, 2021 (70.3%) had at least one bar code. Of the 2384 bar codes evaluated, 2353 (98.7%) were linear (1-dimensional) and 31 (1.3%) were 2-dimensional. Well over three-quarters (2112 or 88.6%) of the evaluated bar codes were readable by at least 1 of the 2 scanners used in the study.<br><br>CONCLUSIONS: On the basis of these results, bar-coding could be used for receipt of 80.9% of the drug products at this Canadian hospital and for the preparation and dispensing of 70.1% of the products.},
}
@article {pmid22471892,
year = {2012},
author = {Gariepy, TD and Lindsay, R and Ogden, N and Gregory, TR},
title = {Identifying the last supper: utility of the DNA barcode library for bloodmeal identification in ticks.},
journal = {Molecular ecology resources},
volume = {12},
number = {4},
pages = {646-652},
doi = {10.1111/j.1755-0998.2012.03140.x},
pmid = {22471892},
issn = {1755-0998},
mesh = {Animals ; Arthropod Vectors ; Blood ; *DNA Barcoding, Taxonomic ; Disease Vectors ; Feeding Behavior ; Host-Parasite Interactions ; Sequence Analysis, DNA ; *Ticks ; Vertebrates/classification/*genetics ; },
abstract = {Ticks are among the most important vectors of disease in the Northern Hemisphere, and a better understanding of their feeding behaviour and life cycle is critical to the management and control of tick-borne zoonoses. DNA-based tools for the identification of residual bloodmeals in hematophagous arthropods have proven useful in the investigation of patterns of host use in nature. Using a blind test approach, we challenged the utility of the DNA barcode library for the identification of vertebrate bloodmeals in engorged, field-collected Ixodes scapularis. Universal vertebrate primers for the COI barcode region successfully amplified DNA from the host bloodmeal and only rarely amplified tick DNA. Of the 61 field-collected ticks, conclusive genus- and species-level identification was possible for 72% of the specimens. In all but two cases, barcode-based identification of the bloodmeal was consistent with the morphological identification of the vertebrate host the ticks were collected from. Possible explanations for mismatches or ambiguities are presented. This study validates the utility of the DNA barcode library as a valuable and reliable resource for the identification of unknown bloodmeals in arthropod vectors of disease. Future directions aimed at the refinement of these techniques to gain additional information and to improve the amplification success of digested vertebrate DNA in tick bloodmeals are discussed.},
}
@article {pmid22470142,
year = {2012},
author = {Vigneault, F and Ter-Ovanesyan, D and Alon, S and Eminaga, S and C Christodoulou, D and Seidman, JG and Eisenberg, E and M Church, G},
title = {High-throughput multiplex sequencing of miRNA.},
journal = {Current protocols in human genetics},
volume = {Chapter 11},
number = {},
pages = {11.12.1-11.12.10},
pmid = {22470142},
issn = {1934-8258},
support = {U01 HL066582/HL/NHLBI NIH HHS/United States ; /CAPMC/CIHR/Canada ; T32 GM007598/GM/NIGMS NIH HHS/United States ; R01 HL080494/HL/NHLBI NIH HHS/United States ; R01 HL084553/HL/NHLBI NIH HHS/United States ; U01 HL098166/HL/NHLBI NIH HHS/United States ; },
mesh = {Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; MicroRNAs/*chemistry ; Sequence Analysis, RNA/*methods ; },
abstract = {Next-generation sequencing offers many advantages over other methods of microRNA (miRNA) expression profiling, such as sample throughput and the capability to discover novel miRNAs. As the sequencing depth of current sequencing platforms exceeds what is necessary to quantify miRNAs, multiplexing several samples in one sequencing run offers a significant cost advantage. Although previous studies have achieved this goal by adding bar codes to miRNA libraries at the ligation step, this was recently shown to introduce significant bias into the miRNA expression data. This bias can be avoided, however, by bar coding the miRNA libraries at the PCR step instead. Here, we describe a user-friendly PCR bar-coding method of preparing multiplexed microRNA libraries for Illumina-based sequencing. The method also prevents the production of adapter dimers and can be completed in one day.},
}
@article {pmid22454494,
year = {2012},
author = {Schoch, CL and Seifert, KA and Huhndorf, S and Robert, V and Spouge, JL and Levesque, CA and Chen, W and , and , },
title = {Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {109},
number = {16},
pages = {6241-6246},
pmid = {22454494},
issn = {1091-6490},
mesh = {Cell Nucleus/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/*genetics ; DNA, Ribosomal Spacer/*genetics ; Fungi/classification/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Reproducibility of Results ; Species Specificity ; },
abstract = {Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.},
}
@article {pmid22451517,
year = {2012},
author = {Melton-Witt, JA and McKay, SL and Portnoy, DA},
title = {Development of a single-gene, signature-tag-based approach in combination with alanine mutagenesis to identify listeriolysin O residues critical for the in vivo survival of Listeria monocytogenes.},
journal = {Infection and immunity},
volume = {80},
number = {6},
pages = {2221-2230},
pmid = {22451517},
issn = {1098-5522},
support = {5T32CA009179-34/CA/NCI NIH HHS/United States ; F32 AI072988/AI/NIAID NIH HHS/United States ; T32 CA009179/CA/NCI NIH HHS/United States ; P01 A1063302//PHS HHS/United States ; R01 AI027655/AI/NIAID NIH HHS/United States ; P01 AI063302/AI/NIAID NIH HHS/United States ; R01 AI27655/AI/NIAID NIH HHS/United States ; },
mesh = {Alanine ; Amino Acid Sequence ; Animals ; Bacterial Toxins/genetics/*metabolism ; DNA, Bacterial ; Female ; Gene Expression Regulation, Bacterial/physiology ; Heat-Shock Proteins/genetics/*metabolism ; Hemolysin Proteins/genetics/*metabolism ; Listeria monocytogenes/genetics/*pathogenicity ; Mice ; Models, Molecular ; Mutagenesis, Site-Directed ; Mutation ; Phenotype ; Polymerase Chain Reaction ; Protein Conformation ; Protein Structure, Tertiary ; },
abstract = {Listeriolysin O (LLO) is a pore-forming toxin of the cholesterol-dependent cytolysin (CDC) family and a primary virulence factor of the intracellular pathogen Listeria monocytogenes. LLO mediates rupture of phagosomal membranes, thereby releasing bacteria into the growth-permissive host cell cytosol. Several unique features of LLO allow its activity to be precisely regulated in order to facilitate phagosomal escape, intracellular growth, and cell-to-cell spread. To improve our understanding of the multifaceted contribution of LLO to the pathogenesis of L. monocytogenes, we developed a screen that combined saturation mutagenesis and signature tags, termed in vivo analysis by saturation mutagenesis and signature tags (IVASS). We generated a library of LLO mutant strains, each harboring a single amino acid substitution and a signature tag, by using the previously described pPL2 integration vector. The signature tags acted as molecular barcodes, enabling high-throughput, parallel analysis of 40 mutants in a single animal and identification of attenuated mutants by negative selection. Using the IVASS technique we were able to screen over 90% of the 505 amino acids present in LLO and identified 60 attenuated mutants. Of these, 39 LLO residues were previously uncharacterized and potentially revealed novel functions of the toxin during infection. The mutants that were subsequently analyzed in vivo each conferred a 2- to 4-orders of magnitude loss in virulence compared to wild type, thereby validating the screening methods. Phenotypic analysis of the LLO mutant library using common in vitro techniques suggested that the functional contributions of some residues could only have been revealed through in vivo analysis.},
}
@article {pmid22450992,
year = {2012},
author = {Riutort, M and Álvarez-Presas, M and Lázaro, E and Solà, E and Paps, J},
title = {Evolutionary history of the Tricladida and the Platyhelminthes: an up-to-date phylogenetic and systematic account.},
journal = {The International journal of developmental biology},
volume = {56},
number = {1-3},
pages = {5-17},
doi = {10.1387/ijdb.113441mr},
pmid = {22450992},
issn = {1696-3547},
mesh = {Animals ; *Biological Evolution ; *Phylogeny ; Platyhelminths/*classification/*genetics ; },
abstract = {Within the free-living platyhelminths, the triclads, or planarians, are the best-known group, largely as a result of long-standing and intensive research on regeneration, pattern formation and Hox gene expression. However, the group's evolutionary history has been long debated, with controversies ranging from their phyletic structure and position within the Metazoa to the relationships among species within the Tricladida. Over the the last decade, with the advent of molecular phylogenies, some of these issues have begun to be resolved. Here, we present an up-to-date summary of the main phylogenetic changes and novelties with some comments on their evolutionary implications. The phylum has been split into two groups, and the position of the main group (the Rhabdithophora and the Catenulida), close to the Annelida and the Mollusca within the Lophotrochozoa, is now clear. Their internal relationships, although not totally resolved, have been clarified. Tricladida systematics has also experienced a revolution since the implementation of molecular data. The terrestrial planarians have been demonstrated to have emerged from one of the freshwater families, giving a different view of their evolution and greatly altering their classification. The use of molecular data is also facilitating the identification of Tricladida species by DNA barcoding, allowing better knowledge of their distribution and genetic diversity. Finally, molecular phylogenetic and phylogeographical analyses, taking advantage of recent data, are beginning to give a clear picture of the recent history of the Dugesia and Schmidtea species in the Mediterranean.},
}
@article {pmid22449174,
year = {2012},
author = {Liang, C and Chu, Y and Cheng, S and Wu, H and Kajiyama, T and Kambara, H and Zhou, G},
title = {Multiplex loop-mediated isothermal amplification detection by sequence-based barcodes coupled with nicking endonuclease-mediated pyrosequencing.},
journal = {Analytical chemistry},
volume = {84},
number = {8},
pages = {3758-3763},
doi = {10.1021/ac3003825},
pmid = {22449174},
issn = {1520-6882},
mesh = {Base Sequence ; *Electronic Data Processing ; Endonucleases/*chemistry ; HIV/genetics ; HIV Infections/blood/*diagnosis ; Hepacivirus/genetics ; Hepatitis/blood/*diagnosis ; Hepatitis B virus/genetics ; Humans ; Molecular Sequence Data ; Nucleic Acid Amplification Techniques ; *Sequence Analysis, DNA ; Time Factors ; Treponema ; Treponemal Infections/blood/*diagnosis ; },
abstract = {The loop-mediated isothermal amplification (LAMP) is a well-developed method for replicating a targeted DNA sequence with a high specificity, but multiplex LAMP detection is difficult because LAMP amplicons are very complicated in structure. To allow simultaneous detection of multiple LAMP products, a series of target-specific barcodes were designed and tagged in LAMP amplicons by FIP primers. The targeted barcodes were decoded by pyrosequencing on nicked LAMP amplicons. To enable the nicking reaction to occur just near the barcode regions, the recognition sequence of the nicking endonuclease (NEase) was also introduced into the FIP primer. After the nicking reaction, pyrosequencing started at the nicked 3' end when the added deoxyribonucleoside triphosphate (dNTP) was complementary to the non-nicked strand. To efficiently encode multiple targets, the barcodes were designed with a reporter base and two stuffer bases, so that the decoding of a target-specific barcode only required a single peak in a pyrogram. We have successfully detected the four kinds of pathogens including hepatitis B virus (HBV), hepatitis C virus (HCV), human immunodeficiency virus (HIV), and Treponema pallidum (TP), which are easily infected in blood, by a 4-plex LAMP in a single tube, indicating that barcoded LAMP coupled with NEase-mediated pyrosequencing is a simple, rapid, and reliable way in multiple target identification.},
}
@article {pmid22448675,
year = {2012},
author = {Standley, CJ and Stothard, JR},
title = {DNA barcoding of schistosome cercariae reveals a novel sub-lineage within Schistosoma rodhaini from Ngamba Island Chimpanzee Sanctuary, Lake Victoria.},
journal = {The Journal of parasitology},
volume = {98},
number = {5},
pages = {1049-1051},
doi = {10.1645/GE-3091.1},
pmid = {22448675},
issn = {1937-2345},
mesh = {Animals ; Ape Diseases/*parasitology ; Biomphalaria/parasitology ; Cercaria/classification/genetics ; Cyclooxygenase 1/genetics ; *DNA Barcoding, Taxonomic ; DNA, Helminth/*chemistry/genetics ; Haplotypes ; Humans ; Molecular Sequence Data ; Otters ; Pan troglodytes/*parasitology ; Phylogeny ; Rodentia ; Schistosoma/*classification/genetics ; Schistosomiasis/*parasitology ; Uganda ; },
abstract = {While Schistosoma rodhaini is typically considered a parasite of small mammals and is very scantly distributed in the Lake Victoria basin, it is known to hybridize with the more widespread Schistosoma mansoni, the causative agent of intestinal schistosomiasis. As part of broader parasitological and malacological surveys for S. mansoni across Lake Victoria, schistosome cercariae were harvested from a field-caught Biomphalaria choanomphala taken on Ngamba Island Chimpanzee Sanctuary, Uganda. Upon DNA barcoding, these cercariae were found to be a mixture of both S. rodhaini and S. mansoni, with further phylogenetic analysis revealing a hitherto unknown sub-lineage within S. rodhaini. Despite repeated sampling for eggs and miracidia from both chimpanzees and staff on Ngamba Island Sanctuary, detection of S. rodhaini within local definitive hosts awaits additional efforts, which should be mindful of a potential host role of spotted-necked otters.},
}
@article {pmid22440462,
year = {2011},
author = {Li, Y and Zhao, X and Pan, Z and Xie, Z and Liu, H and Xu, Y and Li, Q},
title = {The origin of the Tibetan Mastiff and species identification of Canis based on mitochondrial cytochrome c oxidase subunit I (COI) gene and COI barcoding.},
journal = {Animal : an international journal of animal bioscience},
volume = {5},
number = {12},
pages = {1868-1873},
doi = {10.1017/S1751731111001042},
pmid = {22440462},
issn = {1751-732X},
abstract = {DNA barcoding is an effective technique to identify species and analyze phylogenesis and evolution. However, research on and application of DNA barcoding in Canis have not been carried out. In this study, we analyzed two species of Canis, Canis lupus (n = 115) and Canis latrans (n = 4), using the cytochrome c oxidase subunit I (COI) gene (1545 bp) and COI barcoding (648 bp DNA sequence of the COI gene). The results showed that the COI gene, as the moderate variant sequence, applied to the analysis of the phylogenesis of Canis members, and COI barcoding applied to species identification of Canis members. Phylogenetic trees and networks showed that domestic dogs had four maternal origins (A to D) and that the Tibetan Mastiff originated from Clade A; this result supports the theory of an East Asian origin of domestic dogs. Clustering analysis and networking revealed the presence of a closer relative between the Tibetan Mastiff and the Old English sheepdog, Newfoundland, Rottweiler and Saint Bernard, which confirms that many well-known large breed dogs in the world, such as the Old English sheepdog, may have the same blood lineage as that of the Tibetan Mastiff.},
}
@article {pmid22438862,
year = {2012},
author = {Hubert, N and Meyer, CP and Bruggemann, HJ and Guérin, F and Komeno, RJ and Espiau, B and Causse, R and Williams, JT and Planes, S},
title = {Cryptic diversity in Indo-Pacific coral-reef fishes revealed by DNA-barcoding provides new support to the centre-of-overlap hypothesis.},
journal = {PloS one},
volume = {7},
number = {3},
pages = {e28987},
pmid = {22438862},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; *Coral Reefs ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Fish Proteins/genetics ; Fishes/*classification/*genetics ; Genetic Variation ; Indian Ocean ; *Models, Genetic ; Pacific Ocean ; },
abstract = {Diversity in coral reef fishes is not evenly distributed and tends to accumulate in the Indo-Malay-Philippines Archipelago (IMPA). The comprehension of the mechanisms that initiated this pattern is in its infancy despite its importance for the conservation of coral reefs. Considering the IMPA either as an area of overlap or a cradle of marine biodiversity, the hypotheses proposed to account for this pattern rely on extant knowledge about taxonomy and species range distribution. The recent large-scale use of standard molecular data (DNA barcoding), however, has revealed the importance of taking into account cryptic diversity when assessing tropical biodiversity. We DNA barcoded 2276 specimens belonging to 668 coral reef fish species through a collaborative effort conducted concomitantly in both Indian and Pacific oceans to appraise the importance of cryptic diversity in species with an Indo-Pacific distribution range. Of the 141 species sampled on each side of the IMPA, 62 presented no spatial structure whereas 67 exhibited divergent lineages on each side of the IMPA with K2P distances ranging between 1% and 12%, and 12 presented several lineages with K2P distances ranging between 3% and 22%. Thus, from this initial pool of 141 nominal species with Indo-Pacific distribution, 79 dissolved into 165 biological units among which 162 were found in a single ocean. This result is consistent with the view that the IMPA accumulates diversity as a consequence of its geological history, its location on the junction between the two main tropical oceans and the presence of a land bridge during glacial times in the IMPA that fostered allopatric divergence and secondary contacts between the Indian and Pacific oceans.},
}
@article {pmid22438660,
year = {2012},
author = {Liu, Y and Zhang, L and Liu, Z and Luo, K and Chen, S and Chen, K},
title = {Species identification of Rhododendron (Ericaceae) using the chloroplast deoxyribonucleic acid PsbA-trnH genetic marker.},
journal = {Pharmacognosy magazine},
volume = {8},
number = {29},
pages = {29-36},
pmid = {22438660},
issn = {0976-4062},
abstract = {BACKGROUND: Rhododendron is a group of famous landscape plants with high medicinal value. However, there is no simple or universal manner to discriminate the various species of this group. Deoxyribonucleic acid (DNA) barcoding technique is a new biological tool that can accurately and objectively identify species by using short and standard DNA regions.<br><br>OBJECTIVE: To choose a suitable DNA marker to authenticate the Rhododendron species.<br><br>MATERIALS AND METHODS: Four candidate DNA barcodes (rbcL, matK, psbAtrnH, and ITS2 intergenic spacer) were tested on 68 samples of 38 species.<br><br>RESULTS: The psbAtrnH candidate barcode yielded 86.8% sequencing efficiency. The highest interspecific divergence was provided by the psbA-trnH intergenic spacer, based on six parameters, and the Wilcoxon signed rank tests. Although there was not a clear barcoding gap, the Wilcoxon Two sample tests indicated that the interspecific divergence of the psbA-trnH intergenic spacer was significantly higher than the relevant intraspecific variation. The psbA-trnH DNA barcode possessed the highest species identification efficiency at 100% by the BLAST1 method. The present results showed that the psbA-trnH intergenic spacer was the most promising one of the four markers for barcoding the Rhododendron species. To further evaluate the ability of the psbA-trnH marker, to discriminate the closely related species, the samples were expanded to 94 samples of 53 species in the genus, and the rate of successful identification was 93.6%. The psbA-trnH region would be useful even for unidentified samples, as it could significantly narrow their possible taxa to a small area.<br><br>CONCLUSION: The psbA-trnH intergenic region is a valuable DNA marker for identifying the Rhododendron species.},
}
@article {pmid22438656,
year = {2012},
author = {Liu, Z and Chen, SL and Song, JY and Zhang, SJ and Chen, KL},
title = {Application of deoxyribonucleic acid barcoding in Lauraceae plants.},
journal = {Pharmacognosy magazine},
volume = {8},
number = {29},
pages = {4-11},
pmid = {22438656},
issn = {0976-4062},
abstract = {BACKGROUND: This study aims to determine the candidate markers that can be used as DNA barcode in the Lauraceae family.<br><br>MATERIAL AND METHODS: Polymerase chain reaction amplification, sequencing efficiency, differential intra- and interspecific divergences, DNA barcoding gap, and identification efficiency were used to evaluate the four different DNA sequences of psbA-trnH, matK, rbcL, and ITS2. We tested the discrimination ability of psbA-trnH in 68 plant samples belonging to 42 species from 11 distinct genera and found that the rate of successful identification with the psbA-trnH was 82.4% at the species level. However, the correct identification of matK and rbcL were only 30.9% and 25.0%, respectively, using BLAST1. The PCR amplification efficiency of the ITS2 region was poor; thus, ITS2 was not included in subsequent experiments. To verify the capacity of the identification of psbA-trnH in more samples, 175 samples belonging to 117 species from the experimental data and from the GenBank database of the Lauraceae family were tested.<br><br>RESULTS: Using the BLAST1 method, the identification efficiency were 84.0% and 92.3% at the species and genus level, respectively.<br><br>CONCLUSION: Therefore, psbA-trnH is confirmed as a useful marker for differentiating closely related species within Lauraceae.},
}
@article {pmid22438314,
year = {2012},
author = {Edwards, BS and Zhu, J and Chen, J and Carter, MB and Thal, DM and Tesmer, JJ and Graves, SW and Sklar, LA},
title = {Cluster cytometry for high-capacity bioanalysis.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {81},
number = {5},
pages = {419-429},
pmid = {22438314},
issn = {1552-4930},
support = {R03 DA030557-01A1/DA/NIDA NIH HHS/United States ; U54 MH084690-04/MH/NIMH NIH HHS/United States ; R01 HG005066-02/HG/NHGRI NIH HHS/United States ; U54 MH084690/MH/NIMH NIH HHS/United States ; UL1 TR001449/TR/NCATS NIH HHS/United States ; R03MH093184-01A1/MH/NIMH NIH HHS/United States ; R03 MH093184/MH/NIMH NIH HHS/United States ; R01 HL071818/HL/NHLBI NIH HHS/United States ; R03 MH093184-01A1/MH/NIMH NIH HHS/United States ; R03 DA030557-02/DA/NIDA NIH HHS/United States ; R01 HG005066-01/HG/NHGRI NIH HHS/United States ; R01 HL071818-10/HL/NHLBI NIH HHS/United States ; R03 MH093184-02/MH/NIMH NIH HHS/United States ; R01 HG005066/HG/NHGRI NIH HHS/United States ; UL1 TR000041/TR/NCATS NIH HHS/United States ; U54MH084690/MH/NIMH NIH HHS/United States ; R03 DA030557/DA/NIDA NIH HHS/United States ; R01HG005066/HG/NHGRI NIH HHS/United States ; },
mesh = {Equipment Design ; Flow Cytometry/*instrumentation/methods ; High-Throughput Screening Assays/*methods ; Software ; },
abstract = {Flow cytometry specializes in high-content measurements of cells and particles in suspension. Having long excelled in analytical throughput of single cells and particles, only recently with the advent of HyperCyt sampling technology, flow cytometry's multiexperiment throughput has begun to approach the point of practicality for efficiently analyzing hundreds-of-thousands of samples, the realm of high-throughput screening (HTS). To extend performance and automation compatibility, we built a HyperCyt-linked Cluster Cytometer platform, a network of flow cytometers for analyzing samples displayed in high-density, 1,536-well plate format. To assess the performance, we used cell- and microsphere-based HTS assays that had been well characterized in the previous studies. Experiments addressed important technical issues: challenges of small wells (assay volumes 10 μL or less, reagent mixing, cell and particle suspension), detecting and correcting for differences in performance of individual flow cytometers, and the ability to reanalyze a plate in the event of problems encountered during the primary analysis. Boosting sample throughput an additional fourfold, this platform is uniquely positioned to synergize with expanding suspension array and cell barcoding technologies in which as many as 100 experiments are performed in a single well or sample. As high-performance flow cytometers shrink in cost and size, cluster cytometry promises to become a practical, productive approach for HTS, and other large-scale investigations of biological complexity.},
}
@article {pmid22427924,
year = {2012},
author = {Williams, PH and An, J and Brown, MJ and Carolan, JC and Goulson, D and Huang, J and Ito, M},
title = {Cryptic bumblebee species: consequences for conservation and the trade in greenhouse pollinators.},
journal = {PloS one},
volume = {7},
number = {3},
pages = {e32992},
pmid = {22427924},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; Bees/*classification/*genetics/physiology ; China ; Conservation of Natural Resources/*methods ; DNA Barcoding, Taxonomic/methods ; Genetics, Population ; Japan ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; *Pollination ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Commercial greenhouse growers in both Japan and China are increasingly using reared orange-tailed bumblebees known previously as Bombus hypocrita Pérez as pollinators. Phylogenetic analysis of the DNA (COI) barcodes with Bayesian methods shows that this "species" is a long-standing confusion of two cryptic species. We find that the orange-tailed bumblebees in North China are actually part of the widespread Russian (otherwise white-tailed) B. patagiatus Nylander (as B. patagiatus ganjsuensis Skorikov, n. comb.), whereas the orange-tailed bees in Japan are true B. hypocrita. This situation has been further complicated because two other cryptic species from North China that were previously confused with the Russian B. patagiatus are now recognised as separate: B. lantschouensis Vogt n. stat. and B. minshanensis Bischoff n. stat.. As demand for pollination services by greenhouse growers inevitably increases, these bees are more likely to be transported between countries. In order to conserve genetic resources of pollinator species for their option value for future food security, we advocate preventing trade and movement of B. patagiatus from China into Japan and of B. hypocrita from Japan into China.},
}
@article {pmid22422764,
year = {2012},
author = {Simon, UK and Trajanoski, S and Kroneis, T and Sedlmayr, P and Guelly, C and Guttenberger, H},
title = {Accession-specific haplotypes of the internal transcribed spacer region in Arabidopsis thaliana--a means for barcoding populations.},
journal = {Molecular biology and evolution},
volume = {29},
number = {9},
pages = {2231-2239},
doi = {10.1093/molbev/mss093},
pmid = {22422764},
issn = {1537-1719},
mesh = {Arabidopsis/classification/*genetics ; Base Sequence ; *DNA Barcoding, Taxonomic ; *DNA, Ribosomal Spacer ; *Haplotypes ; INDEL Mutation ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Genetic ; },
abstract = {Eukaryote genomes contain multiple copies of nuclear ribosomal DNA (nrDNA) harboring both highly conserved and variable regions. This has made nrDNA the most popular genetic marker for phylogenetic studies and the region of choice for barcoding projects. Furthermore, many scientists believe that all copies of nrDNA within one nucleus are practically identical due to concerted evolution. Here, we investigate the model plant species Arabidopsis thaliana for intragenomic variation of the internal transcribed spacer (ITS) region of nrDNA. Based on a modified deep sequencing approach, we provide a comprehensive list of ITS polymorphisms present in the two most widely used accessions of A. thaliana-Col-0 and Ler. Interestingly, we found that some polymorphisms are shared between these genetically very distinct accessions. On the other hand, the high number of accession-specific polymorphisms shows that each accession can be clearly and easily characterized by its specific ITS polymorphism patterns and haplotypes. Network analysis based on the detected haplotypes demonstrates that the study of ITS polymorphism patterns and haplotypes is an extremely powerful tool for population genetics. Using the methods proposed here, it will now be possible to extend the traditionally species-bound barcoding concept to populations.},
}
@article {pmid22420049,
year = {2012},
author = {Gross, M},
title = {Barcoding biodiversity.},
journal = {Current biology : CB},
volume = {22},
number = {3},
pages = {R73-6},
doi = {10.1016/j.cub.2012.01.036},
pmid = {22420049},
issn = {1879-0445},
mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry ; Databases, Genetic ; Fishes/genetics ; },
abstract = {Analysis of short, species-specific sequences known as DNA barcodes has become a widespread practice in biodiversity and ecological research, and also finds practical applications from trade control to biomedicine. One of the challenges is to ensure that the molecular information is reliably linked to physical specimens in collections.},
}
@article {pmid22419497,
year = {2012},
author = {Diaz, PL and Hennell, JR and Sucher, NJ},
title = {Genomic DNA extraction and barcoding of endophytic fungi.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {862},
number = {},
pages = {171-179},
doi = {10.1007/978-1-61779-609-8_14},
pmid = {22419497},
issn = {1940-6029},
mesh = {DNA, Fungal/genetics/*isolation &amp; purification ; DNA, Ribosomal/chemistry ; Endophytes/*genetics ; Fungi ; Genome, Fungal ; Plants/microbiology ; RNA, Ribosomal/chemistry ; Symbiosis ; },
abstract = {Endophytes live inter- and/or intracellularly inside healthy aboveground tissues of plants without causing disease. Endophytic fungi are found in virtually every vascular plant species examined. The origins of this symbiotic relationship between endophytes go back to the emergence of vascular plants. Endophytic fungi receive nutrition and protection from their hosts while the plants benefit from the production of fungal secondary metabolites, which enhance the host plants' resistance to herbivores, pathogens, and various abiotic stresses. Endophytic fungi have attracted increased interest as potential sources of secondary metabolites with agricultural, industrial, and medicinal use. This chapter provides detailed protocols for isolation of genomic DNA from fungal endophytes and its use in polymerase chain reaction-based amplification of the internal transcribed spacer region between the conserved flanking regions of the small and large subunit of ribosomal RNA for barcoding purposes.},
}
@article {pmid22419487,
year = {2012},
author = {Zaya, DN and Ashley, MV},
title = {Plant genetics for forensic applications.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {862},
number = {},
pages = {35-52},
doi = {10.1007/978-1-61779-609-8_4},
pmid = {22419487},
issn = {1940-6029},
mesh = {DNA Fingerprinting/*methods ; DNA, Plant/*chemistry ; Forensic Medicine/methods ; Genotype ; Microsatellite Repeats ; },
abstract = {An emerging application for plant DNA fingerprinting and barcoding involves forensic investigations. Examples of DNA analysis of botanical evidence include crime scene analysis, identifying the source of commercial plant products, and investigation of trade in illicit drugs. Here, we review real and potential applications of DNA-based forensic botany and provide a protocol for microsatellite genotyping of leaf material, a protocol that could be used to link a suspect to a victim or to a crime scene.},
}
@article {pmid22419486,
year = {2012},
author = {Cowan, RS and Fay, MF},
title = {Challenges in the DNA barcoding of plant material.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {862},
number = {},
pages = {23-33},
doi = {10.1007/978-1-61779-609-8_3},
pmid = {22419486},
issn = {1940-6029},
mesh = {DNA, Plant/*chemistry ; Genes, Plant ; Plants/genetics ; Plastids/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {DNA barcoding, using a short gene sequence from a standardized region of the genome, is a species identification tool which would not only aid species discovery but would also have applications ranging from large-scale biodiversity surveys through to identification of a single fragment of material in forensic contexts. To fulfill this vision a universal, relatively cheap, scalable system needs to be in place. The mitochondrial locus being used for many animal groups and algae is not suitable for use in land plants, and an appropriate alternative is needed.Progress has been made in the selection of two alternative regions for plant DNA barcoding. There are however many challenges in finding a solution that fulfills all the requirements of a successful, universally applicable barcode, and in the short term a pragmatic solution that achieves as much as possible and has payoffs in most areas has been chosen. Research continues in areas ranging from the technicalities of sequencing the regions to data analysis and the potential improvements that may result from the developing technology and data analysis systems.The ultimate success of DNA barcoding as a plant identification tool for all occasions depends on the building of a reference database and it fulfilling the requirements of potential users such that they are able to achieve valid results through its use, that would be more time consuming and costly, and less reliable using other techniques.},
}
@article {pmid22419485,
year = {2012},
author = {Sucher, NJ and Hennell, JR and Carles, MC},
title = {DNA fingerprinting, DNA barcoding, and next generation sequencing technology in plants.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {862},
number = {},
pages = {13-22},
doi = {10.1007/978-1-61779-609-8_2},
pmid = {22419485},
issn = {1940-6029},
mesh = {DNA Fingerprinting/*methods ; DNA, Plant/*chemistry ; Genome, Plant ; Genomics ; Plants/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {DNA fingerprinting of plants has become an invaluable tool in forensic, scientific, and industrial laboratories all over the world. PCR has become part of virtually every variation of the plethora of approaches used for DNA fingerprinting today. DNA sequencing is increasingly used either in combination with or as a replacement for traditional DNA fingerprinting techniques. A prime example is the use of short, standardized regions of the genome as taxon barcodes for biological identification of plants. Rapid advances in "next generation sequencing" (NGS) technology are driving down the cost of sequencing and bringing large-scale sequencing projects into the reach of individual investigators. We present an overview of recent publications that demonstrate the use of "NGS" technology for DNA fingerprinting and DNA barcoding applications.},
}
@article {pmid22418382,
year = {2012},
author = {Goss, KC and Messier, GG and Potter, ME},
title = {Data detection algorithms for multiplexed quantum dot encoding.},
journal = {Optics express},
volume = {20},
number = {5},
pages = {5762-5774},
doi = {10.1364/OE.20.005762},
pmid = {22418382},
issn = {1094-4087},
mesh = {*Algorithms ; Electronic Data Processing/*methods ; Information Storage and Retrieval/*methods ; *Quantum Dots ; Signal Processing, Computer-Assisted/*instrumentation ; },
abstract = {A group of quantum dots can be designed to have a unique spectral emission by varying the size of the quantum dots (wavelength) and number of quantum dots (intensity). This technique has been previously proposed for biological tags and object identification. The potential of this system lies in the ability to have a large number of distinguishable wavelengths and intensity levels. This paper presents a communications system model for MxQDs including the interference between neighbouring QD colours and detector noise. An analytical model of the signal-to-noise ratio of a Charge-Coupled Device (CCD) spectrometer is presented and confirmed with experimental results. We then apply a communications system perspective and propose data detection algorithms that increase the readability of the quantum dots tags. It is demonstrated that multiplexed quantum dot barcodes can be read with 99.7% accuracy using the proposed data detection algorithms in a system with 6 colours and 6 intensity values resulting in 46,655 unique spectral codes.},
}
@article {pmid22414242,
year = {2012},
author = {Derocles, SA and Plantegenest, M and Simon, JC and Taberlet, P and Le Ralec, A},
title = {A universal method for the detection and identification of Aphidiinae parasitoids within their aphid hosts.},
journal = {Molecular ecology resources},
volume = {12},
number = {4},
pages = {634-645},
doi = {10.1111/j.1755-0998.2012.03131.x},
pmid = {22414242},
issn = {1755-0998},
mesh = {Animals ; Aphids/*genetics/*parasitology ; Base Sequence ; *DNA Barcoding, Taxonomic ; DNA Primers ; DNA, Intergenic ; Host Specificity/genetics ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Wasps/classification/*genetics ; },
abstract = {Molecular methods are increasingly used to detect and identify parasites in their hosts. However, existing methods are generally not appropriate for studying complex host-parasite interactions because they require prior knowledge of species composition. DNA barcoding is a molecular method that allows identifying species using DNA sequences as an identification key. We used DNA amplification with primers common to aphid parasitoids and sequencing of the amplified fragment to detect and identify parasitoids in their hosts, without prior knowledge on the species potentially present. To implement this approach, we developed a method based on 16S rRNA mitochondrial gene and LWRh nuclear gene. First, we designed two primer pairs specific to Aphidiinae (Hymenoptera), the main group of aphid parasitoids. Second, we tested whether the amplified regions could correctly identify Aphidiinae species and found that 61 species were accurately identified of 75 tested. We then determined the ability of each primer pair to detect immature parasitoids inside their aphid host. Detection was earlier for 16S than for LWRh, with parasitoids detected, respectively, 24 and 48 h after egg injection. Finally, we applied this method to assess parasitism rate in field populations of several aphid species. The interest of this tool for analysing aphid-parasitoid food webs is discussed.},
}
@article {pmid22412956,
year = {2012},
author = {Vanhaecke, D and Garcia de Leaniz, C and Gajardo, G and Young, K and Sanzana, J and Orellana, G and Fowler, D and Howes, P and Monzon-Arguello, C and Consuegra, S},
title = {DNA barcoding and microsatellites help species delimitation and hybrid identification in endangered galaxiid fishes.},
journal = {PloS one},
volume = {7},
number = {3},
pages = {e32939},
pmid = {22412956},
issn = {1932-6203},
mesh = {Alleles ; Animals ; Chile ; Chimera/classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; Endangered Species ; Falkland Islands ; Female ; Fishes/*classification/*genetics ; Genetic Variation ; Genotype ; Male ; *Microsatellite Repeats ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The conservation of data deficient species is often hampered by inaccurate species delimitation. The galaxiid fishes Aplochiton zebra and Aplochiton taeniatus are endemic to Patagonia (and for A. zebra the Falkland Islands), where they are threatened by invasive salmonids. Conservation of Aplochiton is complicated because species identification is hampered by the presence of resident as well as migratory ecotypes that may confound morphological discrimination. We used DNA barcoding (COI, cytochrome b) and a new developed set of microsatellite markers to investigate the relationships between A. zebra and A. taeniatus and to assess their distributions and relative abundances in Chilean Patagonia and the Falkland Islands. Results from both DNA markers were 100% congruent and revealed that phenotypic misidentification was widespread, size-dependent, and highly asymmetric. While all the genetically classified A. zebra were correctly identified as such, 74% of A. taeniatus were incorrectly identified as A. zebra, the former species being more widespread than previously thought. Our results reveal, for the first time, the presence in sympatry of both species, not only in Chilean Patagonia, but also in the Falkland Islands, where A. taeniatus had not been previously described. We also found evidence of asymmetric hybridisation between female A. taeniatus and male A. zebra in areas where invasive salmonids have become widespread. Given the potential consequences that species misidentification and hybridisation can have for the conservation of these endangered species, we advocate the use of molecular markers in order to reduce epistemic uncertainty.},
}
@article {pmid22409763,
year = {2012},
author = {Kwon, YS and Kim, JH and Choe, JC and Park, YC},
title = {Low resolution of mitochondrial COI barcodes for identifying species of the genus Larus (Charadriiformes: Laridae).},
journal = {Mitochondrial DNA},
volume = {23},
number = {2},
pages = {157-166},
doi = {10.3109/19401736.2012.660921},
pmid = {22409763},
issn = {1940-1744},
mesh = {Animals ; Charadriiformes/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Haplotypes ; Mitochondria/*enzymology/genetics ; Republic of Korea ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {We evaluated whether cytochrome c oxidase subunit I (COI) barcodes that have been previously suggested for birds are useful for identifying species of the genus Larus, which are resident or migratory birds in Korea. We found 31 intra- or interspecific COI haplotypes from 12 of 13 Larus species in Korea. Haplotype analyses showed that the COI barcodes could not distinguish some interspecific haplotypes from 6 of 12 Larus species because there were no nucleotide substitutions among their COI haplotypes. The neighbor-joining tree formed shallow branches in the clades expected for L. saundersi, L. crassirostris, L. canus, L relictus, and L. ridbundus. In the nine Larus species, COI haplotypes were not grouped as distinct entities that were correctly assigned to their corresponding species, resulting in polytypic clades. These results indicate that the COI sequences need to be cautiously selected as a DNA barcode for identifying species of Korean Larus birds.},
}
@article {pmid22408462,
year = {2012},
author = {Arif, IA and Khan, HA and Williams, JB and Shobrak, M and Arif, WI},
title = {DNA barcodes of Asian Houbara Bustard (Chlamydotis undulata macqueenii).},
journal = {International journal of molecular sciences},
volume = {13},
number = {2},
pages = {2425-2438},
pmid = {22408462},
issn = {1422-0067},
mesh = {Animals ; Base Sequence ; Birds/*classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; },
abstract = {Populations of Houbara Bustards have dramatically declined in recent years. Captive breeding and reintroduction programs have had limited success in reviving population numbers and thus new technological solutions involving molecular methods are essential for the long term survival of this species. In this study, we sequenced the 694 bp segment of COI gene of the four specimens of Asian Houbara Bustard (Chlamydotis undulata macqueenii). We also compared these sequences with earlier published barcodes of 11 individuals comprising different families of the orders Gruiformes, Ciconiiformes, Podicipediformes and Crocodylia (out group). The pair-wise sequence comparison showed a total of 254 variable sites across all the 15 sequences from different taxa. Three of the four specimens of Houbara Bustard had an identical sequence of COI gene and one individual showed a single nucleotide difference (G > A transition at position 83). Within the bustard family (Otididae), comparison among the three species (Asian Houbara Bustard, Great Bustard (Otis tarda) and the Little Bustard (Tetrax tetrax)), representing three different genera, showed 116 variable sites. For another family (Rallidae), the intra-family variable sites among the individuals of four different genera were found to be 146. The COI genetic distances among the 15 individuals varied from 0.000 to 0.431. Phylogenetic analysis using 619 bp nucleotide segment of COI clearly discriminated all the species representing different genera, families and orders. All the four specimens of Houbara Bustard formed a single clade and are clearly separated from other two individuals of the same family (Otis tarda and Tetrax tetrax). The nucleotide sequence of partial segment of COI gene effectively discriminated the closely related species. This is the first study reporting the barcodes of Houbara Bustard and would be helpful in future molecular studies, particularly for the conservation of this threatened bird in Saudi Arabia.},
}
@article {pmid22408380,
year = {2012},
author = {van Nieukerken, EJ and Wagner, DL and Baldessari, M and Mazzon, L and Angeli, G and Girolami, V and Duso, C and Doorenweerd, C},
title = {Antispila oinophylla new species (Lepidoptera, Heliozelidae), a new North American grapevine leafminer invading Italian vineyards: taxonomy, DNA barcodes and life cycle.},
journal = {ZooKeys},
volume = {},
number = {170},
pages = {29-77},
pmid = {22408380},
issn = {1313-2970},
abstract = {A grapevine leafminer Antispila oinophylla van Nieukerken &amp; Wagner, sp. n., is described both from eastern North America (type locality: Georgia) and as a new important invader in North Italian vineyards (Trentino and Veneto Region) since 2006. The species is closely related to, and previously confused with Antispila ampelopsifoliella Chambers, 1874, a species feeding on Virginia creeper Parthenocissus quinquefolia (L.) Planchon., and both are placed in an informal Antispila ampelopsifoliella group. Wing pattern, genitalia, and DNA barcode data all confirm the conspecificity of native North American populations and Italian populations. COI barcodes differ by only 0-1.23%, indicating that the Italian populations are recently established from eastern North America. The new species feeds on various wild Vitis species in North America, on cultivated Vitis vinifera L. in Italy, and also on Parthenocissus quinquefolia in Italy. North American Antispila feeding on Parthenocissus include at least two other species, one of which is Antispila ampelopsifoliella. Morphology and biology of the new species are contrasted with those of North American Antispila Hübner, 1825 species and European Holocacista rivillei (Stainton, 1855). The source population of the introduction is unknown, but cases with larvae or pupae, attached to imported plants, are a likely possibility. DNA barcodes of the three European grapevine leafminers and those of all examined Heliozelidae are highly diagnostic. North American Vitaceae-feeding Antispila form two species complexes and include several as yet unnamed taxa. The identity of three out of the four previously described North American Vitaceae-feeding species cannot be unequivocally determined without further revision, but these are held to be different from Antispila oinophylla. In Italy the biology of Antispila oinophylla was studied in a vineyard in the Trento Province (Trentino-Alto Adige Region) in 2008 and 2009. Mature larvae overwinter inside their cases, fixed to vine trunks or training stakes. The first generation flies in June. An additional generation occurs from mid-August onwards. The impact of the pest in this vineyard was significant with more than 90% of leaves infested in mid-summer. Since the initial discovery in 2006, the pest spread to several additional Italian provinces, in 2010 the incidence of infestation was locally high in commercial vineyards. Preliminary phylogenetic analyses suggest that Antispila is paraphyletic, and that the Antispila ampelopsifoliella group is related to Coptodisca Walsingham, 1895, Holocacista Walsingham &amp; Durrant, 1909 and Antispilina Hering, 1941, all of which possess reduced wing venation. Vitaceae may be the ancestral hostplant family for modern Heliozelidae.},
}
@article {pmid22408329,
year = {2011},
author = {Nalawade, SN and Lagdive, SB and Gangadhar, S and Bhandari, AJ},
title = {A simple and inexpensive bar-coding technique for denture identification.},
journal = {Journal of forensic dental sciences},
volume = {3},
number = {2},
pages = {92-94},
pmid = {22408329},
issn = {0975-2137},
abstract = {A number of commercial methods for identifying dentures are available. They can be either invasive or noninvasive techniques. The less sophisticated procedures include simple engraving with bur, and more sophisticated procedures use labels or chips. Bar coding system is a way of transferring data to the computer and huge data can be stored as a record. Bar coding can be easily incorporated during acrylization of the denture and thus could be used in individual identification.},
}
@article {pmid22406497,
year = {2012},
author = {Liu, Z and Zeng, X and Yang, D and Chu, G and Yuan, Z and Chen, S},
title = {Applying DNA barcodes for identification of plant species in the family Araliaceae.},
journal = {Gene},
volume = {499},
number = {1},
pages = {76-80},
doi = {10.1016/j.gene.2012.02.016},
pmid = {22406497},
issn = {1879-0038},
mesh = {Araliaceae/*classification/*genetics/metabolism ; China ; *DNA Barcoding, Taxonomic ; DNA, Plant/analysis/genetics ; Efficiency ; Genetic Speciation ; Japan ; Phylogeny ; Polymerase Chain Reaction ; Species Specificity ; },
abstract = {An effective DNA marker in authentication of the family Araliaceae was screened out of the five DNA regions (matK, rbcL, ITS2, psbA-trnH and ycf5). In the present study, 1113 sequences of 276 species from 23 genera (Araliaceae) were collected from DNA sequencing and GenBank, in which 16 specimens were from 5 provinces in China and Japan. All of the sequences were assessed in the success rates of PCR amplifications, intra- and inter-specific divergence, DNA barcoding gaps and efficiency of identification. Compared with other markers, ITS2 showed superiority in species discrimination with an accurate identification of 85.23% and 97.29% at the species and genus levels, respectively, in plant samples from the 589 sequences derived from Araliaceae. Consequently, as one of the most popular phylogenetic markers, our study indicated that ITS2 was a powerful barcode for Araliaceae identification.},
}
@article {pmid22406111,
year = {2012},
author = {Fehér, T and Burland, V and Pósfai, G},
title = {In the fast lane: large-scale bacterial genome engineering.},
journal = {Journal of biotechnology},
volume = {160},
number = {1-2},
pages = {72-79},
doi = {10.1016/j.jbiotec.2012.02.012},
pmid = {22406111},
issn = {1873-4863},
mesh = {Bacteria/genetics/metabolism ; Biotechnology/methods ; Genetic Engineering/*methods ; *Genome, Bacterial ; High-Throughput Screening Assays/*methods ; Synthetic Biology/methods ; },
abstract = {The last few years have witnessed rapid progress in bacterial genome engineering. The long-established, standard ways of DNA synthesis, modification, transfer into living cells, and incorporation into genomes have given way to more effective, large-scale, robust genome modification protocols. Expansion of these engineering capabilities is due to several factors. Key advances include: (i) progress in oligonucleotide synthesis and in vitro and in vivo assembly methods, (ii) optimization of recombineering techniques, (iii) introduction of parallel, large-scale, combinatorial, and automated genome modification procedures, and (iv) rapid identification of the modifications by barcode-based analysis and sequencing. Combination of the brute force of these techniques with sophisticated bioinformatic design and modeling opens up new avenues for the analysis of gene functions and cellular network interactions, but also in engineering more effective producer strains. This review presents a summary of recent technological advances in bacterial genome engineering.},
}
@article {pmid22403481,
year = {2011},
author = {Crous, PW and Summerell, BA and Shivas, RG and Romberg, M and Mel'nik, VA and Verkley, GJ and Groenewald, JZ},
title = {Fungal Planet description sheets: 92-106.},
journal = {Persoonia},
volume = {27},
number = {},
pages = {130-162},
pmid = {22403481},
issn = {1878-9080},
abstract = {Novel species of microfungi described in the present study include the following from Australia: Diaporthe ceratozamiae on Ceratozamia robusta, Seiridium banksiae on Banksia marginata, Phyllosticta hymenocallidicola on Hymenocallis littoralis, Phlogicylindrium uniforme on Eucalyptus cypellocarpa, Exosporium livistonae on Livistona benthamii and Coleophoma eucalyptorum on Eucalyptus piperita. Several species are also described from South Africa, namely: Phoma proteae, Pyrenochaeta protearum and Leptosphaeria proteicola on Protea spp., Phaeomoniella niveniae on Nivenia stokoei, Toxicocladosporium leucadendri on Leucadendron sp. and Scorias leucadendri on Leucadendron muirii. Other species include Myrmecridium phragmitis on Phragmites australis (Netherlands) and Camarographium carpini on Carpinus betulus (Russia). Furthermore, Pseudoidriella syzygii on Syzygium sp. represents a novel genus of hyphomycetes collected in Australia. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.},
}
@article {pmid22403480,
year = {2011},
author = {Seifert, KA and Gams, W},
title = {The genera of Hyphomycetes - 2011 update.},
journal = {Persoonia},
volume = {27},
number = {},
pages = {119-129},
pmid = {22403480},
issn = {1878-9080},
abstract = {This supplement to the taxonomic monograph The Genera of Hyphomycetes summarises information on 23 accepted new genera and c. 160 species described in 2011. These include three dematiaceous genera (Funbolia, Noosia, Pyrigemmula, all related to Dothideomycetes), a bulbil-producing genus, Spiroplana (Pleosporales), and two endophytic genera, the sterile Periglandula (Clavicipitaceae), and the hyaline, sympodial Micronematobotrys (Pyronemataceae). Slow-growing, morphologically-reduced, darkly pigmented fungi continue to be the source of new taxa, including the new genus Atramixtia (Dothioraceae). Eight new genera of darkly pigmented chlamydospore-like anamorphs were described from marine or subtidal environments (Glomerulispora, Halozoön, Hiogispora, Matsusporium, Moheitospora, Moleospora, Moromyces), mostly associated with subclades of the Lulworthiales. Several genera that are morphologically similar to but phylogenetically distinct from genera of the Capnodiales (Pseudopassalora, Scleroramularia) were introduced, as well as segregates from the classical concepts of Alternaria (Sinomyces), Chalara and Phialophora (Brachyalara, Infundichalara, Lasiadelphia), and Paecilomyces (Purpureocillium for the former Paecilomyces lilacinus complex). In addition, in anticipation of the new nomenclatural rules, newly configured formerly-teleomorph genera were proposed as segregates from classical hyphomycete genera in the Hypocreales, namely Acremonium (Cosmospora), Fusarium (Cyanonectria, Dialonectria, Geejayessia, Macroconia, Stylonectria), and Volutella (Pseudonectria) and the Trichocomaceae, Eurotiales, Penicillium (Talaromyces for the former Penicillium subg. Biverticillium). Standardized generic mini-diagnoses are provided for the accepted new genera, along with details of distribution, substrates, numbers of new species and phylogenetic affinities within the Dikarya. GenBank accession numbers for ITS DNA-barcodes are provided where available. New information on generic concepts of previously recognised genera, phylogenetic relationships, and corrections of factual errors are also included. Only two newly described genera, Fecundostilbum and Utrechtiana, seem to be synonyms of previously described genera.},
}
@article {pmid22401591,
year = {2012},
author = {David, O and Larédo, C and Leblois, R and Schaeffer, B and Vergne, N},
title = {Coalescent-based DNA barcoding: multilocus analysis and robustness.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {19},
number = {3},
pages = {271-278},
doi = {10.1089/cmb.2011.0122},
pmid = {22401591},
issn = {1557-8666},
mesh = {Algorithms ; Animals ; Bayes Theorem ; Computer Simulation ; DNA Barcoding, Taxonomic/*methods ; Genes, Mitochondrial ; Lepidoptera/classification/genetics ; *Models, Genetic ; Multilocus Sequence Typing/*methods ; Mutation ; Phylogeny ; Poisson Distribution ; },
abstract = {DNA barcoding is the assignment of individuals to species using standardized mitochondrial sequences. Nuclear data are sometimes added to the mitochondrial data to increase power. A barcoding method for analysing mitochondrial and nuclear data is developed. It is a Bayesian method based on the coalescent model. Then this method is assessed using simulated and real data. It is found that adding nuclear data can reduce the number of ambiguous assignments. Finally, the robustness of coalescent-based barcoding to departures from model assumptions is studied using simulations. This method is found to be robust to past population size variations, to within-species population structures, and to designs that poorly sample populations within species. Supplementary Material is available online at www.liebertonline.com/cmb.},
}
@article {pmid22400127,
year = {2012},
author = {Zhou, X and Duan, R and Xing, D},
title = {Highly sensitive detection of protein and small molecules based on aptamer-modified electrochemiluminescence nanoprobe.},
journal = {The Analyst},
volume = {137},
number = {8},
pages = {1963-1969},
doi = {10.1039/c2an00020b},
pmid = {22400127},
issn = {1364-5528},
mesh = {Aptamers, Nucleotide/*chemistry ; *Electrochemical Techniques ; Limit of Detection ; *Luminescence ; Proteins/*analysis ; },
abstract = {Amplified optical detection of biomolecules using nanoparticle as the carrier has attracted considerable interest in the scientific community. In this study, a promising aptasensor was developed for highly sensitive detection of protein and small molecules based on the construction of aptamer-modified electrochemiluminescence (ECL) nanoprobe. Specifically, thrombin and ATP serve as the examples for detection. By taking advantage of sandwich binding of two affinity aptamers for high specificity, tris-(2,2'-bipyridyl)ruthenium (TBR)-cysteamine loaded in gold nanoparticle (GNP) as barcodes for signal amplification, and micromagnetic particles (MMPs) based ECL technology for rapid detection, a novel assay for biomolecules quantification was developed. The sandwich complex containing targets could be selectively captured by MMPs and then quantified by ECL intensity. We have demonstrated that the detection limits of human thrombin and ATP are 1 pM and 10 pM, respectively, with high specificity. The proposed technology is expected to become a powerful tool for biomolecule analysis.},
}
@article {pmid22398121,
year = {2012},
author = {Bergsten, J and Bilton, DT and Fujisawa, T and Elliott, M and Monaghan, MT and Balke, M and Hendrich, L and Geijer, J and Herrmann, J and Foster, GN and Ribera, I and Nilsson, AN and Barraclough, TG and Vogler, AP},
title = {The effect of geographical scale of sampling on DNA barcoding.},
journal = {Systematic biology},
volume = {61},
number = {5},
pages = {851-869},
pmid = {22398121},
issn = {1076-836X},
mesh = {Animals ; Coleoptera/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Europe ; Evolution, Molecular ; *Genetic Variation ; Geography ; Insect Proteins/genetics ; Iran ; Molecular Sequence Data ; Morocco ; Phylogeny ; Phylogeography/*methods ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Eight years after DNA barcoding was formally proposed on a large scale, CO1 sequences are rapidly accumulating from around the world. While studies to date have mostly targeted local or regional species assemblages, the recent launch of the global iBOL project (International Barcode of Life), highlights the need to understand the effects of geographical scale on Barcoding's goals. Sampling has been central in the debate on DNA Barcoding, but the effect of the geographical scale of sampling has not yet been thoroughly and explicitly tested with empirical data. Here, we present a CO1 data set of aquatic predaceous diving beetles of the tribe Agabini, sampled throughout Europe, and use it to investigate how the geographic scale of sampling affects 1) the estimated intraspecific variation of species, 2) the genetic distance to the most closely related heterospecific, 3) the ratio of intraspecific and interspecific variation, 4) the frequency of taxonomically recognized species found to be monophyletic, and 5) query identification performance based on 6 different species assignment methods. Intraspecific variation was significantly correlated with the geographical scale of sampling (R-square = 0.7), and more than half of the species with 10 or more sampled individuals (N = 29) showed higher intraspecific variation than 1% sequence divergence. In contrast, the distance to the closest heterospecific showed a significant decrease with increasing geographical scale of sampling. The average genetic distance dropped from > 7% for samples within 1 km, to < 3.5% for samples up to > 6000 km apart. Over a third of the species were not monophyletic, and the proportion increased through locally, nationally, regionally, and continentally restricted subsets of the data. The success of identifying queries decreased with increasing spatial scale of sampling; liberal methods declined from 100% to around 90%, whereas strict methods dropped to below 50% at continental scales. The proportion of query identifications considered uncertain (more than one species < 1% distance from query) escalated from zero at local, to 50% at continental scale. Finally, by resampling the most widely sampled species we show that even if samples are collected to maximize the geographical coverage, up to 70 individuals are required to sample 95% of intraspecific variation. The results show that the geographical scale of sampling has a critical impact on the global application of DNA barcoding. Scale-effects result from the relative importance of different processes determining the composition of regional species assemblages (dispersal and ecological assembly) and global clades (demography, speciation, and extinction). The incorporation of geographical information, where available, will be required to obtain identification rates at global scales equivalent to those in regional barcoding studies. Our result hence provides an impetus for both smarter barcoding tools and sprouting national barcoding initiatives-smaller geographical scales deliver higher accuracy.},
}
@article {pmid22397381,
year = {2012},
author = {He, Y and Hou, P and Fan, G and Song, Z and Arain, S and Shu, H and Tang, C and Yue, Q and Zhang, Y},
title = {Authentication of Angelica anomala Avé-Lall cultivars through DNA barcodes.},
journal = {Mitochondrial DNA},
volume = {23},
number = {2},
pages = {100-105},
doi = {10.3109/19401736.2012.660924},
pmid = {22397381},
issn = {1940-1744},
mesh = {Angelica/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA Primers ; DNA, Plant/*analysis/genetics ; DNA, Ribosomal Spacer/analysis ; *Medicine, Chinese Traditional ; Plants, Medicinal/classification/genetics ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Angelica anomala Avé-Lall (Chuanbaizhi in Chinese) is an important medicinal plant which can be used in traditional Chinese medicines; however, there are no authentic and universal methods to differentiate this Sichuan famous-region drug of A. anomala from a large number of non-famous-region and false drugs. It has been demonstrated that DNA barcoding is a molecular diagnostic method for species identification, which uses a single standardized DNA fragment. In this study, we tested five DNA barcoding candidates (matK, ITS, ITS2, rbcL, and psbA-trnH), and we found that ITS was the best candidate to authenticate the famous-region drug of A. anomala. Moreover, through comparative analysis of these five DNA barcodes between A. anomala and Angelica dahurica, we found that ITS had the most and ITS2 had more variable regions, but the psbA-trnH, rbcL, and matK regions were identical. Hence, we suggest ITS as the DNA barcoding to identify A. anomala and A. dahurica. Moreover, we are determined to adopt the A. anomala as the accurate Latin name of Chuanbaizhi.},
}
@article {pmid22397375,
year = {2012},
author = {Keskin, E and Atar, HH},
title = {Genetic structuring of European anchovy (Engraulis encrasicolus) populations through mitochondrial DNA sequences.},
journal = {Mitochondrial DNA},
volume = {23},
number = {2},
pages = {62-69},
doi = {10.3109/19401736.2011.653798},
pmid = {22397375},
issn = {1940-1744},
mesh = {Animals ; Black Sea ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Europe ; Evolution, Molecular ; Fishes/classification/*genetics ; Genetics, Population ; Haplotypes ; Mediterranean Sea ; Molecular Sequence Data ; Oceans and Seas ; *Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {Mitochondrial DNA sequence variation in 655 bpfragments of the cytochrome oxidase c subunit I gene, known as the DNA barcode, of European anchovy (Engraulis encrasicolus) was evaluated by analyzing 1529 individuals representing 16 populations from the Black Sea, through the Marmara Sea and the Aegean Sea to the Mediterranean Sea. A total of 19 (2.9%) variable sites were found among individuals, and these defined 10 genetically diverged populations with an overall mean distance of 1.2%. The highest nucleotide divergence was found between samples of eastern Mediterranean and northern Aegean (2.2%). Evolutionary history analysis among 16 populations clustered the Mediterranean Sea clades in one main branch and the other clades in another branch. Diverging pattern of the European anchovy populations correlated with geographic dispersion supports the genetic structuring through the Black Sea-Marmara Sea-Aegean Sea-Mediterranean Sea quad.},
}
@article {pmid22396761,
year = {2012},
author = {Lörz, AN and Linse, K and Smith, PJ and Steinke, D},
title = {First molecular evidence for underestimated biodiversity of Rhachotropis (Crustacea, Amphipoda), with description of a new species.},
journal = {PloS one},
volume = {7},
number = {3},
pages = {e32365},
pmid = {22396761},
issn = {1932-6203},
mesh = {Amphipoda/classification/*genetics ; Animals ; Biodiversity ; Crustacea/classification/*genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Female ; Geography ; Microscopy, Electron, Scanning/methods ; Models, Anatomic ; Models, Genetic ; New Zealand ; Oceans and Seas ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The crustacean genus Rhachotropis has a worldwide distribution and amongst the largest bathymetric range known from any amphipod genus. DNA barcoding of new material from around New Zealand and the Ross Sea indicated depth-related biogeographic patterns. New Zealand Rhachotropis do not form a monophyletic clade. Species from bathyal depths on the Chatham Rise, east of New Zealand, show lower sequence divergence to bathyal species from California and the Arctic than to abyssal New Zealand species. Species sampled in the Kermadec Trench, north of New Zealand below 5000 m, seem to be more closely related to Ross Sea abyssal species than to the New Zealand shelf species. The worldwide geographic and bathymetric distribution for all Rhachotropis species is presented here. Depth may have a greater influence on phylogeny than geographic distance.Molecular and morphological investigations of Rhachotropis specimens from the Chatham Rise, New Zealand revealed a species new to science which is described in detail, including scanning electron microscopy. This increases the number of described species of Rhachotropis to 60 worldwide.},
}
@article {pmid22394710,
year = {2012},
author = {Theodoridis, S and Stefanaki, A and Tezcan, M and Aki, C and Kokkini, S and Vlachonasios, KE},
title = {DNA barcoding in native plants of the Labiatae (Lamiaceae) family from Chios Island (Greece) and the adjacent Çeşme-Karaburun Peninsula (Turkey).},
journal = {Molecular ecology resources},
volume = {12},
number = {4},
pages = {620-633},
doi = {10.1111/j.1755-0998.2012.03129.x},
pmid = {22394710},
issn = {1755-0998},
mesh = {Base Sequence ; Chloroplasts/genetics ; *DNA Barcoding, Taxonomic ; DNA, Chloroplast/analysis/*genetics ; DNA, Plant/analysis/genetics ; Greece ; Lamiaceae/*classification/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Turkey ; },
abstract = {The plant family Labiatae (Lamiaceae) is known for its fine medicinal and aromatic herbs like lavender, mint, oregano, sage and thyme and is a rich source of essential oils for the food, pharmaceutical and cosmetic industry. Besides its great economic importance, the Labiatae family contributes significantly to the endemic flora of Greece and Turkey. Owing to its economic and biological significance and to the difficult identification based on morphological characters of several of its taxa, the Labiatae family is an ideal case for developing DNA barcodes. The purpose of this study is to evaluate the utility of DNA barcoding on a local scale in discriminating Labiatae species in Chios Island (Greece) and the adjacent Çeşme-Karaburun Peninsula (Turkey). We chose three cpDNA regions (matK, rbcL, trnH-psbA) that were proposed by previous studies and tested them either as single region or as multiregion barcodes based on the criteria determined by Consortium for the Barcode of Life (CBOL). Our results show that matK and trnH-psbA taken as useful in discriminating species of the Labiatae, for the species we examined, as any multiregion combination. matK and trnH-psbA could serve as single-region barcodes for Labiatae species contributing to the conservation and the trade control of valuable plant resources.},
}
@article {pmid22394382,
year = {2012},
author = {Naciri, Y and Caetano, S and Salamin, N},
title = {Plant DNA barcodes and the influence of gene flow.},
journal = {Molecular ecology resources},
volume = {12},
number = {4},
pages = {575-580},
doi = {10.1111/j.1755-0998.2012.03130.x},
pmid = {22394382},
issn = {1755-0998},
mesh = {Bryophyta/classification/*genetics ; Cell Nucleus/genetics ; Cycadopsida/classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; *Gene Flow ; Genetic Markers ; Magnoliopsida/classification/*genetics ; Phylogeny ; Plastids/genetics ; },
abstract = {Success of species assignment using DNA barcodes has been shown to vary among plant lineages because of a wide range of different factors. In this study, we confirm the theoretical prediction that gene flow influences species assignment with simulations and a literature survey. We show that the genome experiencing the highest gene flow is, in the majority of the cases, the best suited for species delimitation. Our results clearly suggest that, for most angiosperm groups, plastid markers will not be the most appropriate for use as DNA barcodes. We therefore advocate shifting the focus from plastid to nuclear markers to achieve an overall higher success using DNA barcodes.},
}
@article {pmid22373238,
year = {2011},
author = {Liu, C and Liang, D and Gao, T and Pang, X and Song, J and Yao, H and Han, J and Liu, Z and Guan, X and Jiang, K and Li, H and Chen, S},
title = {PTIGS-IdIt, a system for species identification by DNA sequences of the psbA-trnH intergenic spacer region.},
journal = {BMC bioinformatics},
volume = {12 Suppl 13},
number = {Suppl 13},
pages = {S4},
pmid = {22373238},
issn = {1471-2105},
mesh = {*Algorithms ; *DNA Barcoding, Taxonomic ; DNA, Intergenic ; DNA, Plant/analysis ; Markov Chains ; Plants/*classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: DNA barcoding technology, which uses a short piece of DNA sequence to identify species, has wide ranges of applications. Until today, a universal DNA barcode marker for plants remains elusive. The rbcL and matK regions have been proposed as the "core barcode" for plants and the ITS2 and psbA-trnH intergenic spacer (PTIGS) regions were later added as supplemental barcodes. The use of PTIGS region as a supplemental barcode has been limited by the lack of computational tools that can handle significant insertions and deletions in the PTIGS sequences. Here, we compared the most commonly used alignment-based and alignment-free methods and developed a web server to allow the biologists to carry out PTIGS-based DNA barcoding analyses.<br><br>RESULTS: First, we compared several alignment-based methods such as BLAST and those calculating P distance and Edit distance, alignment-free methods Di-Nucleotide Frequency Profile (DNFP) and their combinations. We found that the DNFP and Edit-distance methods increased the identification success rate to ~80%, 20% higher than the most commonly used BLAST method. Second, the combined methods showed overall better success rate and performance. Last, we have developed a web server that allows (1) retrieving various sub-regions and the consensus sequences of PTIGS, (2) annotating novel PTIGS sequences, (3) determining species identity by PTIGS sequences using eight methods, and (4) examining identification efficiency and performance of the eight methods for various taxonomy groups.<br><br>CONCLUSIONS: The Edit distance and the DNFP methods have the highest discrimination powers. Hybrid methods can be used to achieve significant improvement in performance. These methods can be extended to applications using the core barcodes and the other supplemental DNA barcode ITS2. To our knowledge, the web server developed here is the only one that allows species determination based on PTIGS sequences. The web server can be accessed at http://psba-trnh-plantidit.dnsalias.org.},
}
@article {pmid22384191,
year = {2012},
author = {Paraschiv-Ionescu, A and Perruchoud, C and Buchser, E and Aminian, K},
title = {Barcoding human physical activity to assess chronic pain conditions.},
journal = {PloS one},
volume = {7},
number = {2},
pages = {e32239},
pmid = {22384191},
issn = {1932-6203},
mesh = {Activities of Daily Living ; Aged ; Area Under Curve ; Behavior ; Chronic Pain/*diagnosis ; *Electronic Data Processing ; Emotions ; Entropy ; Female ; Humans ; Longitudinal Studies ; Male ; Medical Informatics/*instrumentation/methods ; Middle Aged ; Models, Statistical ; Motor Activity ; Pain Measurement/*instrumentation/*methods ; Prospective Studies ; ROC Curve ; Retrospective Studies ; },
abstract = {BACKGROUND: Modern theories define chronic pain as a multidimensional experience - the result of complex interplay between physiological and psychological factors with significant impact on patients' physical, emotional and social functioning. The development of reliable assessment tools capable of capturing the multidimensional impact of chronic pain has challenged the medical community for decades. A number of validated tools are currently used in clinical practice however they all rely on self-reporting and are therefore inherently subjective. In this study we show that a comprehensive analysis of physical activity (PA) under real life conditions may capture behavioral aspects that may reflect physical and emotional functioning.<br><br>METHODOLOGY: PA was monitored during five consecutive days in 60 chronic pain patients and 15 pain-free healthy subjects. To analyze the various aspects of pain-related activity behaviors we defined the concept of PA 'barcoding'. The main idea was to combine different features of PA (type, intensity, duration) to define various PA states. The temporal sequence of different states was visualized as a 'barcode' which indicated that significant information about daily activity can be contained in the amount and variety of PA states, and in the temporal structure of sequence. This information was quantified using complementary measures such as structural complexity metrics (information and sample entropy, Lempel-Ziv complexity), time spent in PA states, and two composite scores, which integrate all measures. The reliability of these measures to characterize chronic pain conditions was assessed by comparing groups of subjects with clinically different pain intensity.<br><br>CONCLUSION: The defined measures of PA showed good discriminative features. The results suggest that significant information about pain-related functional limitations is captured by the structural complexity of PA barcodes, which decreases when the intensity of pain increases. We conclude that a comprehensive analysis of daily-life PA can provide an objective appraisal of the intensity of pain.},
}
@article {pmid22372841,
year = {2012},
author = {Hernández-Dávila, A and Vargas, JA and Martínez-Méndez, N and Lim, BK and Engstrom, MD and Ortega, J},
title = {DNA barcoding and genetic diversity of phyllostomid bats from the Yucatan Peninsula with comparisons to Central America.},
journal = {Molecular ecology resources},
volume = {12},
number = {4},
pages = {590-597},
doi = {10.1111/j.1755-0998.2012.03125.x},
pmid = {22372841},
issn = {1755-0998},
mesh = {Animals ; Central America ; Chiroptera/*classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Geography ; Mexico ; Mitochondria/genetics ; Phylogeography ; },
abstract = {The mitochondrial cytochrome c oxidase subunit I gene is the standard DNA barcoding region used for species identification and discovery. We examined the variation of COI (454 bp) to discriminate 20 species of bats in the family Phyllostomidae that are found in the Yucatan Peninsula of southeastern Mexico and northern Guatemala and compared them genetically to other samples from Central America. The majority of these species had low intraspecific variation (mean = 0.75%), but some taxa had intraspecific variation ranging to 8.8%, suggesting the possibility of cryptic species (i.e. Desmodus rotundus and Artibeus jamaicensis). There was a recurring biogeographic pattern in eight species with a separation of northern and southern Middle American localities. The Yucatan Peninsula was a discrete area identified in four species, whereas Panama was recovered in five species of phyllostomid bats. Our study establishes a foundation for further molecular work incorporating broader taxonomic and geographic coverage to better understand the phylogeography and genetic diversity that have resulted from the ecological constraints in this region and the remarkable differentiation of bats in the Neotropics.},
}
@article {pmid22369549,
year = {2012},
author = {Blacket, MJ and Semeraro, L and Malipatil, MB},
title = {Barcoding Queensland Fruit Flies (Bactrocera tryoni): impediments and improvements.},
journal = {Molecular ecology resources},
volume = {12},
number = {3},
pages = {428-436},
doi = {10.1111/j.1755-0998.2012.03124.x},
pmid = {22369549},
issn = {1755-0998},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Electron Transport Complex IV/genetics ; Molecular Sequence Data ; Queensland ; Sequence Analysis, DNA ; Tephritidae/*classification/*genetics ; },
abstract = {Identification of adult fruit flies primarily involves microscopic examination of diagnostic morphological characters, while immature stages, such as larvae, can be more problematic. One of the Australia's most serious horticultural pests, the Queensland Fruit Fly (Bactrocera tryoni: Tephritidae), is of particular biosecurity/quarantine concern as the immature life stages occur within food produce and can be difficult to identify using morphological characteristics. DNA barcoding of the mitochondrial Cytochrome Oxidase I (COI) gene could be employed to increase the accuracy of fruit fly species identifications. In our study, we tested the utility of standard DNA barcoding techniques and found them to be problematic for Queensland Fruit Flies, which (i) possess a nuclear copy (a numt pseudogene) of the barcoding region of COI that can be co-amplified; and (ii) as in previous COI phylogenetic analyses closely related B. tryoni complex species appear polyphyletic. We found that the presence of a large deletion in the numt copy of COI allowed an alternative primer to be designed to only amplify the mitochondrial COI locus in tephritid fruit flies. Comparisons of alternative commonly utilized mitochondrial genes, Cytochrome Oxidase II and Cytochrome b, revealed a similar level of variation to COI; however, COI is the most informative for DNA barcoding, given the large number of sequences from other tephritid fruit fly species available for comparison. Adopting DNA barcoding for the identification of problematic fly specimens provides a powerful tool to distinguish serious quarantine fruit fly pests (Tephritidae) from endemic fly species of lesser concern.},
}
@article {pmid22363795,
year = {2012},
author = {Sun, XQ and Zhu, YJ and Guo, JL and Peng, B and Bai, MM and Hang, YY},
title = {DNA barcoding the Dioscorea in China, a vital group in the evolution of monocotyledon: use of matK gene for species discrimination.},
journal = {PloS one},
volume = {7},
number = {2},
pages = {e32057},
pmid = {22363795},
issn = {1932-6203},
mesh = {China ; DNA Barcoding, Taxonomic/*methods ; Dioscorea/*classification/*genetics ; *Evolution, Molecular ; Genes, Plant/*genetics ; Genetic Loci/genetics ; Genetic Variation ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; Statistics, Nonparametric ; },
abstract = {BACKGROUND: Dioscorea is an important plant genus in terms of food supply and pharmaceutical applications. However, its classification and identification are controversial. DNA barcoding is a recent aid to taxonomic identification and uses a short standardized DNA region to discriminate plant species. In this study, the applicability of three candidate DNA barcodes (rbcL, matK, and psbA-trnH) to identify species within Dioscorea was tested.<br><br>One-hundred and forty-eight individual plant samples of Dioscorea, encompassing 38 species, seven varieties and one subspecies, representing majority species distributed in China of this genus, were collected from its main distributing areas. Samples were assessed by PCR amplification, sequence quality, extent of specific genetic divergence, DNA barcoding gap, and the ability to discriminate between species. matK successfully identified 23.26% of all species, compared with 9.30% for rbcL and 11.63% for psbA-trnH. Therefore, matK is recommended as the best DNA barcoding candidate. We found that the combination of two or three loci achieved a higher success rate of species discrimination than one locus alone. However, experimental cost would be much higher if two or three loci, rather than a single locus, were assessed.<br><br>CONCLUSIONS: We conclude that matK is a strong, although not perfect, candidate as a DNA barcode for Dioscorea identification. This assessment takes into account both its ability for species discrimination and the cost of experiments.},
}
@article {pmid22363527,
year = {2012},
author = {Zhang, AB and Feng, J and Ward, RD and Wan, P and Gao, Q and Wu, J and Zhao, WZ},
title = {A new method for species identification via protein-coding and non-coding DNA barcodes by combining machine learning with bioinformatic methods.},
journal = {PloS one},
volume = {7},
number = {2},
pages = {e30986},
pmid = {22363527},
issn = {1932-6203},
mesh = {Animals ; Aquatic Organisms ; *Artificial Intelligence ; Base Sequence ; Canada ; Chiroptera/genetics ; Computational Biology/*methods ; DNA/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/genetics ; Databases, Genetic ; Electron Transport Complex IV/genetics ; Fishes/genetics ; Fungi/genetics ; Molecular Sequence Data ; Open Reading Frames/*genetics ; Pacific Ocean ; Phaeophyceae/genetics ; Species Specificity ; Time Factors ; Tropical Climate ; },
abstract = {Species identification via DNA barcodes is contributing greatly to current bioinventory efforts. The initial, and widely accepted, proposal was to use the protein-coding cytochrome c oxidase subunit I (COI) region as the standard barcode for animals, but recently non-coding internal transcribed spacer (ITS) genes have been proposed as candidate barcodes for both animals and plants. However, achieving a robust alignment for non-coding regions can be problematic. Here we propose two new methods (DV-RBF and FJ-RBF) to address this issue for species assignment by both coding and non-coding sequences that take advantage of the power of machine learning and bioinformatics. We demonstrate the value of the new methods with four empirical datasets, two representing typical protein-coding COI barcode datasets (neotropical bats and marine fish) and two representing non-coding ITS barcodes (rust fungi and brown algae). Using two random sub-sampling approaches, we demonstrate that the new methods significantly outperformed existing Neighbor-joining (NJ) and Maximum likelihood (ML) methods for both coding and non-coding barcodes when there was complete species coverage in the reference dataset. The new methods also out-performed NJ and ML methods for non-coding sequences in circumstances of potentially incomplete species coverage, although then the NJ and ML methods performed slightly better than the new methods for protein-coding barcodes. A 100% success rate of species identification was achieved with the two new methods for 4,122 bat queries and 5,134 fish queries using COI barcodes, with 95% confidence intervals (CI) of 99.75-100%. The new methods also obtained a 96.29% success rate (95%CI: 91.62-98.40%) for 484 rust fungi queries and a 98.50% success rate (95%CI: 96.60-99.37%) for 1094 brown algae queries, both using ITS barcodes.},
}
@article {pmid22363454,
year = {2012},
author = {Zhang, J and Hanner, R},
title = {Molecular approach to the identification of fish in the South China Sea.},
journal = {PloS one},
volume = {7},
number = {2},
pages = {e30621},
pmid = {22363454},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; China ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Fishes/*genetics ; Genetic Markers ; Genetic Variation ; Geography ; Molecular Sequence Data ; Oceans and Seas ; Phylogeny ; Species Specificity ; },
abstract = {BACKGROUND: DNA barcoding is one means of establishing a rapid, accurate, and cost-effective system for the identification of species. It involves the use of short, standard gene targets to create sequence profiles of known species against sequences of unknowns that can be matched and subsequently identified. The Fish Barcode of Life (FISH-BOL) campaign has the primary goal of gathering DNA barcode records for all the world's fish species. As a contribution to FISH-BOL, we examined the degree to which DNA barcoding can discriminate marine fishes from the South China Sea.<br><br>DNA barcodes of cytochrome oxidase subunit I (COI) were characterized using 1336 specimens that belong to 242 species fishes from the South China Sea. All specimen provenance data (including digital specimen images and geospatial coordinates of collection localities) and collateral sequence information were assembled using Barcode of Life Data System (BOLD; www.barcodinglife.org). Small intraspecific and large interspecific differences create distinct genetic boundaries among most species. In addition, the efficiency of two mitochondrial genes, 16S rRNA (16S) and cytochrome b (cytb), and one nuclear ribosomal gene, 18S rRNA (18S), was also evaluated for a few select groups of species.<br><br>CONCLUSIONS/SIGNIFICANCE: The present study provides evidence for the effectiveness of DNA barcoding as a tool for monitoring marine biodiversity. Open access data of fishes from the South China Sea can benefit relative applications in ecology and taxonomy.},
}
@article {pmid22360997,
year = {2012},
author = {Abd-Rabou, S and Shalaby, H and Germain, JF and Ris, N and Kreiter, P and Malausa, T},
title = {Identification of mealybug pest species (Hemiptera: Pseudococcidae) in Egypt and France, using a DNA barcoding approach.},
journal = {Bulletin of entomological research},
volume = {102},
number = {5},
pages = {515-523},
doi = {10.1017/S0007485312000041},
pmid = {22360997},
issn = {1475-2670},
mesh = {Animals ; Base Sequence ; *DNA Barcoding, Taxonomic ; DNA, Intergenic/genetics ; Egypt ; Electron Transport Complex IV/genetics ; Female ; France ; Haplotypes ; Hemiptera/*classification/*genetics ; Insect Control ; Insect Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 28S/genetics ; Sequence Alignment ; },
abstract = {Pseudococcidae (mealybugs) is a large taxonomic group, including a number of agronomic pests. Taxonomic identification of mealybug species is a recurrent problem and represents a major barrier to the establishment of adequate pest management strategies. We combined molecular analysis of three DNA markers (28S-D2, cytochrome oxidase I and internal transcribed spacer 2) with morphological examination, for the identification of 176 specimens collected from 40 mealybug populations infesting various crops and ornamental plants in Egypt and France. This combination of DNA and morphological analyses led to the identification of 17 species: seven in Egypt (Planococcus citri (Risso), Planococcus ficus (Signoret), Maconellicoccus hirsutus (Green), Ferrisia virgata (Cockerell), Phenacoccus solenopsis Tinsley, Phenacoccus parvus Morrison and Saccharicoccus sacchari (Cockerell)) and 11 in France (Planococcus citri, Pseudococcus viburni Signoret, Pseudococcus longispinus (Targioni-Tozzetti), Pseudococcus comstocki (Kuwana), Rhizoecus amorphophalli Betrem, Trionymus bambusae (Green), Balanococcus diminutus (Leonardi), Phenacoccus madeirensis Green, Planococcus vovae (Nasonov), Dysmicoccus brevipes (Cockerell) and Phenacoccus aceris Signoret), Pl. citri being found in both countries. We also found genetic variation between populations considered to belong to the same species, justifying further investigation of the possible occurrence of complexes of cryptic taxa.},
}
@article {pmid22359600,
year = {2012},
author = {Virgilio, M and Jordaens, K and Breman, FC and Backeljau, T and De Meyer, M},
title = {Identifying insects with incomplete DNA barcode libraries, African fruit flies (Diptera: Tephritidae) as a test case.},
journal = {PloS one},
volume = {7},
number = {2},
pages = {e31581},
pmid = {22359600},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods/standards ; Diptera/genetics ; Electronic Data Processing ; Gene Library ; Insecta/genetics ; Tephritidae/*genetics ; },
abstract = {We propose a general working strategy to deal with incomplete reference libraries in the DNA barcoding identification of species. Considering that (1) queries with a large genetic distance with their best DNA barcode match are more likely to be misidentified and (2) imposing a distance threshold profitably reduces identification errors, we modelled relationships between identification performances and distance thresholds in four DNA barcode libraries of Diptera (n = 4270), Lepidoptera (n = 7577), Hymenoptera (n = 2067) and Tephritidae (n = 602 DNA barcodes). In all cases, more restrictive distance thresholds produced a gradual increase in the proportion of true negatives, a gradual decrease of false positives and more abrupt variations in the proportions of true positives and false negatives. More restrictive distance thresholds improved precision, yet negatively affected accuracy due to the higher proportions of queries discarded (viz. having a distance query-best match above the threshold). Using a simple linear regression we calculated an ad hoc distance threshold for the tephritid library producing an estimated relative identification error <0.05. According to the expectations, when we used this threshold for the identification of 188 independently collected tephritids, less than 5% of queries with a distance query-best match below the threshold were misidentified. Ad hoc thresholds can be calculated for each particular reference library of DNA barcodes and should be used as cut-off mark defining whether we can proceed identifying the query with a known estimated error probability (e.g. 5%) or whether we should discard the query and consider alternative/complementary identification methods.},
}
@article {pmid22359559,
year = {2012},
author = {Green, J and Wang, D and Lilley, CJ and Urwin, PE and Atkinson, HJ},
title = {Transgenic potatoes for potato cyst nematode control can replace pesticide use without impact on soil quality.},
journal = {PloS one},
volume = {7},
number = {2},
pages = {e30973},
pmid = {22359559},
issn = {1932-6203},
support = {BB/D001749/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Cysteine Proteinase Inhibitors/pharmacology ; Nematoda ; Peptides/pharmacology ; Pesticides ; Plant Diseases/parasitology/*prevention &amp; control ; *Plants, Genetically Modified ; Soil/standards ; Solanum tuberosum/*parasitology ; Tylenchoidea ; },
abstract = {Current and future global crop yields depend upon soil quality to which soil organisms make an important contribution. The European Union seeks to protect European soils and their biodiversity for instance by amending its Directive on pesticide usage. This poses a challenge for control of Globodera pallida (a potato cyst nematode) for which both natural resistance and rotational control are inadequate. One approach of high potential is transgenically based resistance. This work demonstrates the potential in the field of a new transgenic trait for control of G. pallida that suppresses root invasion. It also investigates its impact and that of a second transgenic trait on the non-target soil nematode community. We establish that a peptide that disrupts chemoreception of nematodes without a lethal effect provides resistance to G. pallida in both a containment and a field trial when precisely targeted under control of a root tip-specific promoter. In addition we combine DNA barcoding and quantitative PCR to recognise nematode genera from soil samples without microscope-based observation and use the method for nematode faunal analysis. This approach establishes that the peptide and a cysteine proteinase inhibitor that offer distinct bases for transgenic plant resistance to G. pallida do so without impact on the non-target nematode soil community.},
}
@article {pmid22356472,
year = {2012},
author = {Taylor, HR and Harris, WE},
title = {An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding.},
journal = {Molecular ecology resources},
volume = {12},
number = {3},
pages = {377-388},
doi = {10.1111/j.1755-0998.2012.03119.x},
pmid = {22356472},
issn = {1755-0998},
mesh = {Classification/*methods ; DNA Barcoding, Taxonomic/*methods/*trends ; High-Throughput Nucleotide Sequencing ; Museums ; },
abstract = {DNA barcoding has become a well-funded, global enterprise since its proposition as a technique for species identification, delimitation and discovery in 2003. However, the rapid development of next generation sequencing (NGS) has the potential to render DNA barcoding irrelevant because of the speed with which it generates large volumes of genomic data. To avoid obsolescence, the DNA barcoding movement must adapt to use this new technology. This review examines the DNA barcoding enterprise, its continued resistance to improvement and the implications of this on the future of the discipline. We present the consistent failure of DNA barcoding to recognize its limitations and evolve its methodologies, reducing the usefulness of the data produced by the movement and throwing into doubt its ability to embrace NGS.},
}
@article {pmid22355625,
year = {2011},
author = {Sandberg, J and Werne, B and Dessing, M and Lundeberg, J},
title = {Rapid flow-sorting to simultaneously resolve multiplex massively parallel sequencing products.},
journal = {Scientific reports},
volume = {1},
number = {},
pages = {108},
pmid = {22355625},
issn = {2045-2322},
mesh = {Emulsions ; Flow Cytometry ; Fluorescent Dyes ; Polymerase Chain Reaction/*methods ; },
abstract = {Sample preparation for Roche/454, ABI/SOLiD and Life Technologies/Ion Torrent sequencing are based on amplification of library fragments on the surface of beads prior to sequencing. Commonly, libraries are barcoded and pooled, to maximise the sequence output of each sequence run. Here, we describe a novel approach for normalization of multiplex next generation sequencing libraries after emulsion PCR. Briefly, amplified libraries carrying unique barcodes are prepared by fluorescent tagging of complementary sequences and then resolved by high-speed flow cytometric sorting of labeled emulsion PCR beads. The protocol is simple and provides an even sequence distribution of multiplex libraries when sequencing the flow-sorted beads. Moreover, since many empty and mixed emulsion PCR beads are removed, the approach gives rise to a substantial increase in sequence quality and mean read length, as compared to that obtained by standard enrichment protocols.},
}
@article {pmid22355561,
year = {2011},
author = {Stoeckle, MY and Gamble, CC and Kirpekar, R and Young, G and Ahmed, S and Little, DP},
title = {Commercial teas highlight plant DNA barcode identification successes and obstacles.},
journal = {Scientific reports},
volume = {1},
number = {},
pages = {42},
pmid = {22355561},
issn = {2045-2322},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*analysis/*genetics ; Food Labeling/*methods ; Reproducibility of Results ; Sensitivity and Specificity ; Tea/*classification/*genetics ; },
abstract = {Appearance does not easily identify the dried plant fragments used to prepare teas to species. Here we test recovery of standard DNA barcodes for land plants from a large array of commercial tea products and analyze their performance in identifying tea constituents using existing databases. Most (90%) of 146 tea products yielded rbcL or matK barcodes using a standard protocol. Matching DNA identifications to listed ingredients was limited by incomplete databases for the two markers, shared or nearly identical barcodes among some species, and lack of standard common names for plant species. About 1/3 of herbal teas generated DNA identifications not found on labels. Broad scale adoption of plant DNA barcoding may require algorithms that place search results in context of standard plant names and character-based keys for distinguishing closely-related species. Demonstrating the importance of accessible plant barcoding, our findings indicate unlisted ingredients are common in herbal teas.},
}
@article {pmid22353709,
year = {2012},
author = {Liu, Z and Zeng, X and Yang, D and Ren, G and Chu, G and Yuan, Z and Luo, K and Xiao, P and Chen, S},
title = {Identification of medicinal vines by ITS2 using complementary discrimination methods.},
journal = {Journal of ethnopharmacology},
volume = {141},
number = {1},
pages = {242-249},
doi = {10.1016/j.jep.2012.01.057},
pmid = {22353709},
issn = {1872-7573},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/*analysis ; Databases, Nucleic Acid ; *Discriminant Analysis ; Ethnopharmacology ; *Genetic Markers ; *Medicine, Chinese Traditional ; Models, Molecular ; Nucleic Acid Conformation ; Phylogeny ; *Phytotherapy ; Plant Preparations/isolation &amp; purification/*therapeutic use ; Plant Stems ; Plants, Medicinal/chemistry/classification/*genetics ; Polymerase Chain Reaction ; },
abstract = {Medicinal vines listed in Chinese pharmacopoeia possess important medicinal efficacy in traditional Chinese medicines.<br><br>AIM OF THE STUDY: The ITS2 region, which has several characteristics that make it a valuable DNA barcode, was studied to discriminate the stems of medicinal vines to confirm their identities and ensure their safe application in pharmaceuticals by using complementary discrimination methods.<br><br>MATERIALS AND METHODS: Complementary discrimination methods were performed on two datasets, including 393 samples of 170 species from 22 genera 13 families, which belonged to medicinal vines and their adulterants. Based on the primary ITS2 sequences, three main discrimination methods (phylogenetic tree, the nearest distance, and BLAST 1) were adopted to identify species. Moreover, we applied both two-dimensional (2-D) and three-dimensional (3-D) structures of ITS2 to differentiate species.<br><br>RESULTS: ITS2 performed well, with over 95.0% of species and 100% of genera being correctly differentiated for the two datasets. All results showed that the ITS2 region unveiled a remarkable ability to identify closely related species within different families and genera.<br><br>CONCLUSION: Our findings supported that the ITS2 region was an efficient marker for authentication of medicinal vines.},
}
@article {pmid22353437,
year = {2012},
author = {Ruiz-Lopez, F and Wilkerson, RC and Conn, JE and McKeon, SN and Levin, DM and Quiñones, ML and Póvoa, MM and Linton, YM},
title = {DNA barcoding reveals both known and novel taxa in the Albitarsis Group (Anopheles: Nyssorhynchus) of Neotropical malaria vectors.},
journal = {Parasites &amp; vectors},
volume = {5},
number = {},
pages = {44},
pmid = {22353437},
issn = {1756-3305},
support = {R01 AI054139/AI/NIAID NIH HHS/United States ; 2R01AI054139/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Anopheles/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/chemistry/genetics ; *Disease Vectors ; Electron Transport Complex IV/genetics ; Entomology/*methods ; *Genetic Variation ; Molecular Sequence Data ; Sequence Analysis, DNA ; South America ; },
abstract = {BACKGROUND: Mosquitoes belonging to the Albitarsis Group (Anopheles: Nyssorhynchus) are of importance as malaria vectors across the Neotropics. The Group currently comprises six known species, and recent studies have indicated further hidden biodiversity within the Group. DNA barcoding has been proposed as a highly useful tool for species recognition, although its discriminatory utility has not been verified in closely related taxa across a wide geographic distribution.<br><br>METHODS: DNA barcodes (658 bp of the mtDNA Cytochrome c Oxidase--COI) were generated for 565 An. albitarsis s.l. collected in Argentina, Brazil, Colombia, Paraguay, Trinidad and Venezuela over the past twenty years, including specimens from type series and type localities. Here we test the utility of currently advocated barcoding methodologies, including the Kimura-two-parameter distance model (K2P) and Neighbor-joining analysis (NJ), for determining species delineation within mosquitoes of the Neotropical Albitarsis Group of malaria vectors (Anopheles: Nyssorhynchus), and compare results with Bayesian analysis.<br><br>RESULTS: Species delineation through barcoding analysis and Bayesian phylogenetic analysis, fully concur. Analysis of 565 sequences (302 unique haplotypes) resolved nine NJ tree clusters, with less than 2% intra-node variation. Mean intra-specific variation (K2P) was 0.009 (range 0.002-0.014), whereas mean inter-specific divergence were several-fold higher at 0.041 (0.020-0.056), supporting the reported "barcoding gap". These results show full support for separate species status of the six known species in the Albitarsis Group (An. albitarsis s.s., An. albitarsis F, An. deaneorum, An. janconnae, An. marajoara and An. oryzalimnetes), and also support species level status for two previously detected lineages--An. albitarsis G &amp;An. albitarsis I (designated herein). In addition, we highlight the presence of a unique mitochondrial lineage close to An. deaneorum and An. marajoara (An. albitarsis H) from Rond&#xf4;nia and Mato Grosso in southwestern Brazil. Further integrated studies are required to confirm the status of this lineage.<br><br>CONCLUSIONS: DNA barcoding provides a reliable means of identifying both known and undiscovered biodiversity within the closely related taxa of the Albitarsis Group. We advocate its usage in future studies to elucidate the vector competence and respective distributions of all eight species in the Albitarsis Group and the novel mitochondrial lineage (An. albitarsis H) recovered in this study.},
}
@article {pmid22353194,
year = {2012},
author = {Lotta, LA and Wang, M and Yu, J and Martinelli, I and Yu, F and Passamonti, SM and Consonni, D and Pappalardo, E and Menegatti, M and Scherer, SE and Lewis, LL and Akbar, H and Wu, Y and Bainbridge, MN and Muzny, DM and Mannucci, PM and Gibbs, RA and Peyvandi, F},
title = {Identification of genetic risk variants for deep vein thrombosis by multiplexed next-generation sequencing of 186 hemostatic/pro-inflammatory genes.},
journal = {BMC medical genomics},
volume = {5},
number = {},
pages = {7},
pmid = {22353194},
issn = {1755-8794},
support = {U54 HG003273/HG/NHGRI NIH HHS/United States ; },
mesh = {Adult ; Case-Control Studies ; Female ; Genetic Predisposition to Disease/*genetics ; Genetic Variation/*genetics ; Genomics ; Hemostasis/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Inflammation/genetics ; Male ; Pilot Projects ; Sequence Analysis, DNA/*methods ; Venous Thrombosis/*genetics/*physiopathology ; },
abstract = {BACKGROUND: Next-generation DNA sequencing is opening new avenues for genetic association studies in common diseases that, like deep vein thrombosis (DVT), have a strong genetic predisposition still largely unexplained by currently identified risk variants. In order to develop sequencing and analytical pipelines for the application of next-generation sequencing to complex diseases, we conducted a pilot study sequencing the coding area of 186 hemostatic/proinflammatory genes in 10 Italian cases of idiopathic DVT and 12 healthy controls.<br><br>RESULTS: A molecular-barcoding strategy was used to multiplex DNA target capture and sequencing, while retaining individual sequence information. Genomic libraries with barcode sequence-tags were pooled (in pools of 8 or 16 samples) and enriched for target DNA sequences. Sequencing was performed on ABI SOLiD-4 platforms. We produced > 12 gigabases of raw sequence data to sequence at high coverage (average: 42X) the 700-kilobase target area in 22 individuals. A total of 1876 high-quality genetic variants were identified (1778 single nucleotide substitutions and 98 insertions/deletions). Annotation on databases of genetic variation and human disease mutations revealed several novel, potentially deleterious mutations. We tested 576 common variants in a case-control association analysis, carrying the top-5 associations over to replication in up to 719 DVT cases and 719 controls. We also conducted an analysis of the burden of nonsynonymous variants in coagulation factor and anticoagulant genes. We found an excess of rare missense mutations in anticoagulant genes in DVT cases compared to controls and an association for a missense polymorphism of FGA (rs6050; p = 1.9 &#xd7; 10(-5), OR 1.45; 95% CI, 1.22-1.72; after replication in > 1400 individuals).<br><br>CONCLUSIONS: We implemented a barcode-based strategy to efficiently multiplex sequencing of hundreds of candidate genes in several individuals. In the relatively small dataset of our pilot study we were able to identify bona fide associations with DVT. Our study illustrates the potential of next-generation sequencing for the discovery of genetic variation predisposing to complex diseases.},
}
@article {pmid22352964,
year = {2012},
author = {Singer, A and Rapireddy, S and Ly, DH and Meller, A},
title = {Electronic barcoding of a viral gene at the single-molecule level.},
journal = {Nano letters},
volume = {12},
number = {3},
pages = {1722-1728},
pmid = {22352964},
issn = {1530-6992},
support = {R01 HG005871/HG/NHGRI NIH HHS/United States ; R01 HG-005871/HG/NHGRI NIH HHS/United States ; },
mesh = {DNA Barcoding, Taxonomic/*methods ; Nanotechnology/*methods ; Viral Proteins/*analysis/*genetics ; },
abstract = {A new single-molecule approach for rapid and purely electronic discrimination among similar genes is presented. Combining solid-state nanopores and γ-modified synthetic peptide nucleic acid probes, we accurately barcode genes by counting the number of probes attached to each gene and measuring their relative spacing. We illustrate our method by sensing individual genes from two highly similar human immunodeficiency virus subtypes, demonstrating feasibility of a novel, single-molecule diagnostic platform for rapid pathogen classification.},
}
@article {pmid22348331,
year = {2012},
author = {Dai, L and Zheng, X and Kong, L and Li, Q},
title = {DNA barcoding analysis of Coleoidea (Mollusca: Cephalopoda) from Chinese waters.},
journal = {Molecular ecology resources},
volume = {12},
number = {3},
pages = {437-447},
doi = {10.1111/j.1755-0998.2012.03118.x},
pmid = {22348331},
issn = {1755-0998},
mesh = {Animals ; Cephalopoda/*classification/*genetics ; China ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; DNA, Mitochondrial/chemistry/*genetics ; DNA, Ribosomal/chemistry/*genetics ; Electron Transport Complex IV/genetics ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Water/parasitology ; },
abstract = {Coleoids are part of the Cephalopoda class, which occupy an important position in most oceans both at an ecological level and at a commercial level. Nevertheless, some coleoid species are difficult to distinguish with traditional morphological identification in cases when specimens are heavily damaged during collection or when closely related taxa are existent. As a useful tool for rapid species assignment, DNA barcoding may offer significant potential for coleoid identification. Here, we used two mitochondrial fragments, cytochrome c oxidase I and the large ribosomal subunit (16S rRNA), to assess whether 34 coleoids accounting for about one-third of the Chinese coleoid fauna could be identified by DNA barcoding technique. The pairwise intra- and interspecific distances were assessed, and relationships among species were estimated by NJ and bayesian analyses. High levels of genetic differentiation within Loliolus beka led to an overlap between intra- and interspecific distances. All remaining species forming well-differentiated clades in the NJ and bayesian trees were identical for both fragments. Loliolus beka possessed two mitochondrial lineages with high levels of intraspecific distances, suggesting the occurrence of cryptic species. This study confirms the efficacy of DNA barcoding for identifying species as well as discovering cryptic diversity of Chinese coleoids. It also lays a foundation for other ecological and biological studies of Coleoidea.},
}
@article {pmid22347512,
year = {2012},
author = {Yozwiak, NL and Skewes-Cox, P and Stenglein, MD and Balmaseda, A and Harris, E and DeRisi, JL},
title = {Virus identification in unknown tropical febrile illness cases using deep sequencing.},
journal = {PLoS neglected tropical diseases},
volume = {6},
number = {2},
pages = {e1485},
pmid = {22347512},
issn = {1935-2735},
support = {T32 HL007185/HL/NHLBI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; U54-AI65359/AI/NIAID NIH HHS/United States ; 5T32HL007185-34/HL/NHLBI NIH HHS/United States ; U54 AI065359/AI/NIAID NIH HHS/United States ; },
mesh = {Adolescent ; Child ; Child, Preschool ; Computational Biology/methods ; Female ; Fever of Unknown Origin/*diagnosis ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Infant ; Male ; Microarray Analysis/methods ; Molecular Sequence Data ; Nicaragua ; Sequence Analysis, DNA ; Serum/virology ; Tropical Climate ; Virology/*methods ; Virus Diseases/*diagnosis/*virology ; Viruses/*classification/*isolation &amp; purification ; },
abstract = {Dengue virus is an emerging infectious agent that infects an estimated 50-100 million people annually worldwide, yet current diagnostic practices cannot detect an etiologic pathogen in ∼40% of dengue-like illnesses. Metagenomic approaches to pathogen detection, such as viral microarrays and deep sequencing, are promising tools to address emerging and non-diagnosable disease challenges. In this study, we used the Virochip microarray and deep sequencing to characterize the spectrum of viruses present in human sera from 123 Nicaraguan patients presenting with dengue-like symptoms but testing negative for dengue virus. We utilized a barcoding strategy to simultaneously deep sequence multiple serum specimens, generating on average over 1 million reads per sample. We then implemented a stepwise bioinformatic filtering pipeline to remove the majority of human and low-quality sequences to improve the speed and accuracy of subsequent unbiased database searches. By deep sequencing, we were able to detect virus sequence in 37% (45/123) of previously negative cases. These included 13 cases with Human Herpesvirus 6 sequences. Other samples contained sequences with similarity to sequences from viruses in the Herpesviridae, Flaviviridae, Circoviridae, Anelloviridae, Asfarviridae, and Parvoviridae families. In some cases, the putative viral sequences were virtually identical to known viruses, and in others they diverged, suggesting that they may derive from novel viruses. These results demonstrate the utility of unbiased metagenomic approaches in the detection of known and divergent viruses in the study of tropical febrile illness.},
}
@article {pmid22344310,
year = {2012},
author = {Vu, TD and Eberhardt, U and Szöke, S and Groenewald, M and Robert, V},
title = {A laboratory information management system for DNA barcoding workflows.},
journal = {Integrative biology : quantitative biosciences from nano to macro},
volume = {4},
number = {7},
pages = {744-755},
doi = {10.1039/c2ib00146b},
pmid = {22344310},
issn = {1757-9708},
mesh = {Algorithms ; Automation ; *Clinical Laboratory Information Systems ; Cluster Analysis ; Computational Biology/*methods ; Computer Graphics ; Computer Systems ; DNA/*genetics ; DNA Barcoding, Taxonomic/*methods ; Fungal Proteins ; *Genes, Fungal ; Models, Statistical ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; Software ; },
abstract = {This paper presents a laboratory information management system for DNA sequences (LIMS) created and based on the needs of a DNA barcoding project at the CBS-KNAW Fungal Biodiversity Centre (Utrecht, the Netherlands). DNA barcoding is a global initiative for species identification through simple DNA sequence markers. We aim at generating barcode data for all strains (or specimens) included in the collection (currently ca. 80 k). The LIMS has been developed to better manage large amounts of sequence data and to keep track of the whole experimental procedure. The system has allowed us to classify strains more efficiently as the quality of sequence data has improved, and as a result, up-to-date taxonomic names have been given to strains and more accurate correlation analyses have been carried out.},
}
@article {pmid22341828,
year = {2012},
author = {Wang, Q and Lonergan, SM and Yu, C},
title = {Rapid determination of pork sensory quality using Raman spectroscopy.},
journal = {Meat science},
volume = {91},
number = {3},
pages = {232-239},
doi = {10.1016/j.meatsci.2012.01.017},
pmid = {22341828},
issn = {1873-4138},
mesh = {Animals ; Food Technology/*methods ; Humans ; Least-Squares Analysis ; Meat/*analysis/standards ; Multivariate Analysis ; Reproducibility of Results ; Spectrum Analysis, Raman/*methods ; Support Vector Machine ; Sus scrofa ; },
abstract = {Existing objective methods to predict sensory attributes of pork in general do not yield satisfactory correlation to panel evaluations, and their applications in meat industry are limited. In this study, a Raman spectroscopic method was developed to evaluate and predict tenderness, juiciness and chewiness of fresh, uncooked pork loins from 169 pigs. Partial Least Square Regression models were developed based on Raman spectroscopic characteristics of the pork loins to predict the values of the sensory attributes. Furthermore, binary barcodes were created based on spectroscopic characteristics of the pork loins, and subjected to multivariate statistical discriminant analysis (i.e., Support Vector Machine) to differentiate and classify pork loins into quality grades ("good" and "bad" in terms of tenderness and chewiness). Good agreement (>83% correct predictions) with sensory panel results was obtained. The method developed in this report has the potential to become a rapid objective assay for tenderness and chewiness of pork products that may find practical applications in pork industry.},
}
@article {pmid22333298,
year = {2012},
author = {Monson-Miller, J and Sanchez-Mendez, DC and Fass, J and Henry, IM and Tai, TH and Comai, L},
title = {Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing.},
journal = {BMC genomics},
volume = {13},
number = {},
pages = {72},
pmid = {22333298},
issn = {1471-2164},
mesh = {Arabidopsis/genetics ; Deoxyribonucleases, Type II Site-Specific/*metabolism ; *Genome, Plant ; Genotype ; *Mutation ; Oryza/genetics ; Polymorphism, Single Nucleotide ; Reference Values ; Sequence Analysis, DNA/*methods/standards ; },
abstract = {BACKGROUND: The availability of low cost sequencing has spurred its application to discovery and typing of variation, including variation induced by mutagenesis. Mutation discovery is challenging as it requires a substantial amount of sequencing and analysis to detect very rare changes and distinguish them from noise. Also challenging are the cases when the organism of interest has not been sequenced or is highly divergent from the reference.<br><br>RESULTS: We describe the development of a simple method for reduced representation sequencing. Input DNA was digested with a single restriction enzyme and ligated to Y adapters modified to contain a sequence barcode and to provide a compatible overhang for ligation. We demonstrated the efficiency of this method at SNP discovery using rice and arabidopsis. To test its suitability for the discovery of very rare SNP, one control and three mutagenized rice individuals (1, 5 and 10 mM sodium azide) were used to prepare genomic libraries for Illumina sequencers by ligating barcoded adapters to NlaIII restriction sites. For genome-dependent discovery 15-30 million of 80 base reads per individual were aligned to the reference sequence achieving individual sequencing coverage from 7 to 15&#xd7;. We identified high-confidence base changes by comparing sequences across individuals and identified instances consistent with mutations, i.e. changes that were found in a single treated individual and were solely GC to AT transitions. For genome-independent discovery 70-mers were extracted from the sequence of the control individual and single-copy sequence was identified by comparing the 70-mers across samples to evaluate copy number and variation. This de novo "genome" was used to align the reads and identify mutations as above. Covering approximately 1/5 of the 380 Mb genome of rice we detected mutation densities ranging from 0.6 to 4 per Mb of diploid DNA depending on the mutagenic treatment.<br><br>CONCLUSIONS: The combination of a simple and cost-effective library construction method, with Illumina sequencing, and the use of a bioinformatic pipeline allows practical SNP discovery regardless of whether a genomic reference is available.},
}
@article {pmid22331820,
year = {2012},
author = {Desmarais, SM and Leitner, T and Barron, AE},
title = {Quantitative experimental determination of primer-dimer formation risk by free-solution conjugate electrophoresis.},
journal = {Electrophoresis},
volume = {33},
number = {3},
pages = {483-491},
pmid = {22331820},
issn = {1522-2683},
support = {RC2 HG005596/HG/NHGRI NIH HHS/United States ; 1 RC2 HG005596-01/HG/NHGRI NIH HHS/United States ; },
mesh = {Base Sequence ; DNA Primers/*chemistry/metabolism ; Dimerization ; Electrophoresis, Capillary/*methods/standards ; Electrophoretic Mobility Shift Assay ; Fluorescent Dyes/chemistry ; Molecular Sequence Data ; Peptoids/chemistry ; Thermodynamics ; },
abstract = {DNA barcodes are short, unique ssDNA primers that "mark" individual biomolecules. To gain better understanding of biophysical parameters constraining primer-dimer formation between primers that incorporate barcode sequences, we have developed a capillary electrophoresis method that utilizes drag-tag-DNA conjugates to quantify dimerization risk between primer-barcode pairs. Results obtained with this unique free-solution conjugate electrophoresis approach are useful as quantitatively precise input data to parameterize computation models of dimerization risk. A set of fluorescently labeled, model primer-barcode conjugates were designed with complementary regions of differing lengths to quantify heterodimerization as a function of temperature. Primer-dimer cases comprised two 30-mer primers, one of which was covalently conjugated to a lab-made, chemically synthesized poly-N-methoxyethylglycine drag-tag, which reduced electrophoretic mobility of ssDNA to distinguish it from ds primer-dimers. The drag-tags also provided a shift in mobility for the dsDNA species, which allowed us to quantitate primer-dimer formation. In the experimental studies, pairs of oligonucleotide primer barcodes with fully or partially complementary sequences were annealed, and then separated by free-solution conjugate CE at different temperatures, to assess effects on primer-dimer formation. When less than 30 out of 30 base-pairs were bonded, dimerization was inversely correlated to temperature. Dimerization occurred when more than 15 consecutive base-pairs formed, yet non-consecutive base-pairs did not create stable dimers even when 20 out of 30 possible base-pairs bonded. The use of free-solution electrophoresis in combination with a peptoid drag-tag and different fluorophores enabled precise separation of short DNA fragments to establish a new mobility shift assay for detection of primer-dimer formation.},
}
@article {pmid22327649,
year = {2012},
author = {Avin, FA and Bhassu, S and Shin, TY and Sabaratnam, V},
title = {Molecular classification and phylogenetic relationships of selected edible Basidiomycetes species.},
journal = {Molecular biology reports},
volume = {39},
number = {7},
pages = {7355-7364},
pmid = {22327649},
issn = {1573-4978},
mesh = {Base Sequence ; Basidiomycota/*classification/*genetics ; DNA Barcoding, Taxonomic ; DNA, Fungal/*genetics ; DNA, Ribosomal Spacer/*genetics ; Food ; Genetic Variation ; Haplotypes ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; },
abstract = {Morphological identification of edible mushrooms can sometimes prove troublesome, because phenotypic variation in fungi can be affected by substrate and environmental factors. One of the most important problems for mushroom breeders is the lack of a systematic consensus tool to distinguish different species, which are sometimes morphologically identical. Basidiomycetes as one of the largest groups of edible mushrooms have become more important in recent times for their medicinal and nutritional properties. Partial rDNA sequences, including the Internal Transcribed Spacer I-5.8SrDNA-Internal Transcribed Spacer II, were used in this study for molecular identification and assessment of phylogenetic relationships between selected edible species of the Basidiomycetes. Phylogenetic trees showed five distinct clades; each clade belonging to a separate family group. The first clade included all the species belonging to the Pleurotaceae (Pleurotus spp.) family; similarly, the second, third, fourth, and fifth clades consist of species from the Agaricaceae (Agaricus sp.), Lyophllaceae (Hypsigygus sp.), Marasmiaceae (Lentinula edodes sp.) and Physalacriaceae (Flammulina velutipes sp.) families, respectively. Moreover, different species of each family were clearly placed in a distinct sub-cluster and a total of 13 species were taken for analysis. Species differentiation was re-confirmed by AMOVA analysis (among the populations: 99.67%; within: 0.33%), nucleotide divergence, haplotyping and P value. Polymorphism occurred throughout the ITS regions due to insertion-deletion and point mutations, and can be clearly differentiated within the families as well as genera. Moreover, this study proves that the sequence of the ITS region is a superior molecular DNA barcode for taxonomic identification of Basidiomycetes.},
}
@article {pmid22316288,
year = {2012},
author = {Golding, N and Nunn, MA and Medlock, JM and Purse, BV and Vaux, AG and Schäfer, SM},
title = {West Nile virus vector Culex modestus established in southern England.},
journal = {Parasites &amp; vectors},
volume = {5},
number = {},
pages = {32},
pmid = {22316288},
issn = {1756-3305},
mesh = {Animals ; Culex/*virology ; DNA Barcoding, Taxonomic ; England/epidemiology ; Female ; France/epidemiology ; Humans ; Insect Vectors/*virology ; Introduced Species ; Male ; Phylogeny ; Seasons ; Sequence Analysis, DNA ; West Nile Fever/epidemiology/*transmission/virology ; West Nile virus/genetics/*isolation &amp; purification ; Wetlands ; },
abstract = {BACKGROUND: The risk posed to the United Kingdom by West Nile virus (WNV) has previously been considered low, due to the absence or scarcity of the main Culex sp. bridge vectors. The mosquito Culex modestus is widespread in southern Europe, where it acts as the principle bridge vector of WNV. This species was not previously thought to be present in the United Kingdom.<br><br>FINDINGS: Mosquito larval surveys carried out in 2010 identified substantial populations of Cx. modestus at two sites in marshland in southeast England. Host-seeking-adult traps placed at a third site indicate that the relative seasonal abundance of Cx. modestus peaks in early August. DNA barcoding of these specimens from the United Kingdom and material from southern France confirmed the morphological identification.<br><br>CONCLUSIONS: Cx. modestus appears to be established in the North Kent Marshes, possibly as the result of a recent introduction. The addition of this species to the United Kingdom's mosquito fauna may increase the risk posed to the United Kingdom by WNV.},
}
@article {pmid22315491,
year = {2012},
author = {Corrales, I and Catarino, S and Ayats, J and Arteta, D and Altisent, C and Parra, R and Vidal, F},
title = {High-throughput molecular diagnosis of von Willebrand disease by next generation sequencing methods.},
journal = {Haematologica},
volume = {97},
number = {7},
pages = {1003-1007},
pmid = {22315491},
issn = {1592-8721},
mesh = {Genetic Testing ; High-Throughput Nucleotide Sequencing ; Humans ; Molecular Diagnostic Techniques/*methods ; Multiplex Polymerase Chain Reaction ; *Mutation ; Sequence Analysis, DNA/*methods ; *von Willebrand Diseases/diagnosis/genetics ; von Willebrand Factor/*genetics ; },
abstract = {Genetic analysis of von Willebrand disease by von Willebrand factor gene sequencing has not yet become routine practice. Nevertheless, the prospects for molecular diagnosis have changed dramatically in recent years with the unveiling of next-generation sequencing platforms. With the goal of applying this technology to von Willebrand disease, we designed a strategy for von Willebrand factor gene enrichment and multiplexing based on short polymerase chain reactions. Forty patients were simultaneously analyzed enabling the identification of 43 mutations, including 36 substitutions, 2 intronic splice site mutations, 2 indels, and 3 deletions. By pooling patient genomic DNA before polymerase chain reaction enrichment, indexing samples with barcode tags, and re-sequencing on the next-generation sequencing instrument, at least 350 patients and relatives per run can be simultaneously analyzed in a fast, inexpensive manner. This is one of the first reports in which this technology has been shown to be feasible for large-scale mutation screening by single gene re-sequencing.},
}
@article {pmid22314494,
year = {2012},
author = {Zeng, Z and Zhao, P and Luo, J and Zhuang, W and Yu, Z},
title = {Selection of a DNA barcode for Nectriaceae from fungal whole-genomes.},
journal = {Science China. Life sciences},
volume = {55},
number = {1},
pages = {80-88},
doi = {10.1007/s11427-012-4266-2},
pmid = {22314494},
issn = {1869-1889},
mesh = {DNA/*genetics ; *Electronic Data Processing ; Genetic Markers ; Genetic Variation ; *Genome, Fungal ; Hypocreales/classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {A DNA barcode is a short segment of sequence that is able to distinguish species. A barcode must ideally contain enough variation to distinguish every individual species and be easily obtained. Fungi of Nectriaceae are economically important and show high species diversity. To establish a standard DNA barcode for this group of fungi, the genomes of Neurospora crassa and 30 other filamentous fungi were compared. The expect value was treated as a criterion to recognize homologous sequences. Four candidate markers, Hsp90, AAC, CDC48, and EF3, were tested for their feasibility as barcodes in the identification of 34 well-established species belonging to 13 genera of Nectriaceae. Two hundred and fifteen sequences were analyzed. Intra- and inter-specific variations and the success rate of PCR amplification and sequencing were considered as important criteria for estimation of the candidate markers. Ultimately, the partial EF3 gene met the requirements for a good DNA barcode: No overlap was found between the intra- and inter-specific pairwise distances. The smallest inter-specific distance of EF3 gene was 3.19%, while the largest intra-specific distance was 1.79%. In addition, there was a high success rate in PCR and sequencing for this gene (96.3%). CDC48 showed sufficiently high sequence variation among species, but the PCR and sequencing success rate was 84% using a single pair of primers. Although the Hsp90 and AAC genes had higher PCR and sequencing success rates (96.3% and 97.5%, respectively), overlapping occurred between the intra- and inter-specific variations, which could lead to misidentification. Therefore, we propose the EF3 gene as a possible DNA barcode for the nectriaceous fungi.},
}
@article {pmid22311172,
year = {2012},
author = {Yin, H and Zhou, Y and Chen, C and Zhu, L and Ai, S},
title = {An electrochemical signal 'off-on' sensing platform for microRNA detection.},
journal = {The Analyst},
volume = {137},
number = {6},
pages = {1389-1395},
doi = {10.1039/c2an16098f},
pmid = {22311172},
issn = {1364-5528},
mesh = {Biomarkers, Tumor/analysis ; Biosensing Techniques/*methods ; Cell Line, Tumor ; Electrochemistry/*methods ; Gold/chemistry ; Graphite/chemistry ; Humans ; Limit of Detection ; MicroRNAs/*analysis/genetics ; Models, Molecular ; *Neoplasms/chemistry/diagnosis/genetics ; },
abstract = {The abnormal expression of microRNAs (miRNAs) in many solid tumors makes miRNAs potential biomarkers for disease diagnosis and highlights the need for the sensitive and selective detection of miRNAs. In the present work, an 'off-on' signaling genosensor platform for miRNA-21 detection was well developed. This tactic was based on a locked nucleic acid-integrated nucleic acid hairpin probe, a biotin-labeled bridge DNA-AuNPs-bio-barcode signal amplification unit and enzymatic signal amplification. The test is simple, fast and ultrasensitive with a linear range of 0.01-700 pM. The detection limit was estimated to be 6 fM. The overexpression of miRNA-21 was confirmed in total RNA extracted from human hepatocarcinoma cells BEL-7402 and human HeLa cells compared with the control sample extracted from normal human hepatic L02 cells. This method does not need miRNA-21 labeling, isolation, enrichment or PCR amplification. The performance of the assay developed here could satisfy the need for rapid, easy, sensitive and specific early cancer diagnosis in clinical diagnostics.},
}
@article {pmid22309105,
year = {2012},
author = {Pang, X and Luo, H and Sun, C},
title = {Assessing the potential of candidate DNA barcodes for identifying non-flowering seed plants.},
journal = {Plant biology (Stuttgart, Germany)},
volume = {14},
number = {5},
pages = {839-844},
doi = {10.1111/j.1438-8677.2011.00554.x},
pmid = {22309105},
issn = {1438-8677},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; Genetic Loci ; Genetic Variation ; Magnoliopsida/*genetics ; Polymerase Chain Reaction ; Seeds/*genetics ; Species Specificity ; },
abstract = {In plants, matK and rbcL have been selected as core barcodes by the Consortium for the Barcode of Life (CBOL) Plant Working Group (PWG), and ITS/ITS2 and psbA-trnH were suggested as supplementary loci. Yet, research on DNA barcoding of non-flowering seed plants has been less extensive, and the evaluation of DNA barcodes in this division has been limited thus far. Here, we evaluated seven markers (psbA-trnH, matK, rbcL, rpoB, rpoC1, ITS and ITS2) from non-flowering seed plants. The usefulness of each region was assessed using four criteria: the success rate of PCR amplification, the differential intra- and inter-specific divergences, the DNA barcoding gap and the ability to discriminate species. Among the seven loci tested, ITS2 produced the best results in the barcoding of non-flowering seed plants. In addition, we compared the abilities of the five most-recommended markers (psbA-trnH, matK, rbcL, ITS and ITS2) to identify additional species using a large database of gymnosperms from GenBank. ITS2 remained effective for species identification in a wide range of non-flowering seed plants: for the 1531 samples from 608 species of 80 diverse genera, ITS2 correctly authenticated 66% of them at the species level. In conclusion, the ITS2 region can serve as a useful barcode to discriminate non-flowering seed plants, and this study will contribute valuable information for the barcoding of plant species.},
}
@article {pmid22308047,
year = {2011},
author = {Rivera, KG and Seifert, KA},
title = {A taxonomic and phylogenetic revision of the Penicillium sclerotiorum complex.},
journal = {Studies in mycology},
volume = {70},
number = {1},
pages = {139-158},
pmid = {22308047},
issn = {1872-9797},
abstract = {UNLABELLED: The morphological concept of Penicillium sclerotiorum (subgenus Aspergilloides) includes strains with monoverticillate, vesiculate conidiophores, and vivid orange to red colony colours, with colourful sclerotia sometimes produced. Multigene phylogenetic analyses with the nuclear ribosomal internal transcribed spacer (ITS) region, cytochrome c oxidase subunit 1 (cox1), β-tubulin (benA), translation elongation factor 1-α (tef1-α), and calmodulin (cmd), reveal that the P. sclerotiorum morphospecies is a complex of seven phylogenetically distinct species, three of which were recently described, namely P. guanacastense, P. mallochii, and P. viticola. Three previously unidentified species are described here as P. cainii, P. jacksonii, and P. johnkrugii. The phylogenetic species are morphologically similar, but differ in combinations of colony characters, sclerotium production, conidiophore stipe roughening and branching, and conidial shape. Ecological characters and differences in geographical distribution further characterise some of the species, but increased sampling is necessary to confirm these differences. The fungal DNA barcode, the ITS, and the animal DNA barcode, cox1, have lower species resolving ability in our phylogenetic analyses, but still allow identification of all the species. Tef1-α and cmd were superior in providing fully resolved, statistically well-supported phylogenetic trees for this species complex, whereas benA resolved all species but had some issues with paraphyly. Penicilliumadametzioides and P. multicolor, considered synonyms of P. sclerotiorum by some previous authors, do not belong to the P. sclerotiorum complex.<br><br>TAXONOMIC NOVELTIES: New species:Penicillium cainii K.G. Rivera, Malloch &amp; Seifert, P. jacksonii K.G. Rivera, Houbraken &amp; Seifert, P. johnkrugii K.G. Rivera, Houbraken &amp; Seifert.},
}
@article {pmid22303829,
year = {2012},
author = {Tweed, JA and Walton, J and Gu, Z},
title = {Automated supported liquid extraction using 2D barcode processing for routine toxicokinetic portfolio support.},
journal = {Bioanalysis},
volume = {4},
number = {3},
pages = {249-262},
doi = {10.4155/bio.11.314},
pmid = {22303829},
issn = {1757-6199},
mesh = {Chromatography, High Pressure Liquid ; *Electronic Data Processing ; Liquid-Liquid Extraction/*standards ; Mass Spectrometry ; Pharmaceutical Preparations/chemistry ; Pharmacokinetics ; Quality Control ; Software ; },
abstract = {BACKGROUND: A new bioanalytical sample preparation approach has been developed to enhance the efficiency, reduce errors and improve the data quality supporting routine toxicokinetic (TK) study samples analysis, via the implementation of 2D barcode processing coupled with fully automated supported liquid extraction (SLE).<br><br>RESULTS: A fully automated SLE was validated and used to determine TK drug concentrations of over 500 unknown samples via 2D barcode processing. Assay performance calculated from a total of 291 quality control samples over the period of validation through sample analysis demonstrated inter-day precision and accuracy within 10 and 7.3%, respectively.<br><br>CONCLUSION: A new logistical approach implementing the use of 2D barcodes and automated SLE demonstrates the potential of a new methodology for the routine bioanalytical support of TK study sample analysis.},
}
@article {pmid22303347,
year = {2011},
author = {Wang, T and Pradhan, K and Ye, K and Wong, LJ and Rohan, TE},
title = {Estimating allele frequency from next-generation sequencing of pooled mitochondrial DNA samples.},
journal = {Frontiers in genetics},
volume = {2},
number = {},
pages = {51},
pmid = {22303347},
issn = {1664-8021},
support = {KL2 RR025749/RR/NCRR NIH HHS/United States ; P60 DK020541/DK/NIDDK NIH HHS/United States ; TL1 RR025748/RR/NCRR NIH HHS/United States ; UL1 RR025750/RR/NCRR NIH HHS/United States ; },
abstract = {BACKGROUND: Both common and rare mitochondrial DNA (mtDNA) variants may contribute to genetic susceptibility to some complex human diseases. Understanding of the role of mtDNA variants will provide valuable insights into the etiology of these diseases. However, to date, there have not been any large-scale, genome-wide association studies of complete mtDNA variants and disease risk. One reason for this might be the substantial cost of sequencing the large number of samples required for genetic epidemiology studies. Next-generation sequencing of pooled mtDNA samples will dramatically reduce the cost of such studies and may represent an appealing approach for large-scale genetic epidemiology studies. However, the performance of the different designs of sequencing pooled mtDNA has not been evaluated.<br><br>METHODS: We examined the approach of sequencing pooled mtDNA of multiple individuals for estimating allele frequency using the Illumina genome analyzer (GA) II sequencing system. In this study the pool included mtDNA samples of 20 subjects that had been sequenced previously using Sanger sequencing. Each pool was replicated once to assess variation of the sequencing error between pools. To reduce such variation, barcoding was used for sequencing different pools in the same lane of the flow cell. To evaluate the effect of different pooling strategies pooling was done at both the pre- and post-PCR amplification step.<br><br>RESULTS: The sequencing error rate was close to that expected based on the Phred score. When only reads with Phred&#x2009;&#x2265;&#x2009;20 were considered, the average error rate was about 0.3%. However, there was significant variation of the base-calling errors for different types of bases or at different loci. Using the results of the Sanger sequencing as the standard, the sensitivity of single nucleotide polymorphism detection with post-PCR pooling (about 99%) was higher than that of the pre-PCR pooling (about 82%), while the two approaches had similar specificity (about 99%). Among a total of 298 variants in the sample, the allele frequencies of 293 variants (98%) were correctly estimated with post-PCR pooling, the correlation between the estimated and the true allele frequencies being >0.99, while only 206 allele frequencies (69%) were correctly estimated in the pre-PCR pooling, the correlation being 0.89.<br><br>CONCLUSION: Sequencing of mtDNA pooled after PCR amplification is a viable tool for screening mitochondrial variants potentially related to human diseases.},
}
@article {pmid22303130,
year = {2012},
author = {Bousquet, Y},
title = {Description of a new species of Platynus Bonelli from the Appalachian Mountains of eastern North America (Coleoptera, Carabidae).},
journal = {ZooKeys},
volume = {},
number = {163},
pages = {69-81},
doi = {10.3897/zookeys.163.2295},
pmid = {22303130},
issn = {1313-2970},
abstract = {A new species of the genus Platynus Bonelli, Platynus daviesi, is described from specimens collected in the Appalachian Mountains. The species is structurally most similar to Platynus parmarginatus Hamilton but differs in having the coloration of the body dorsally darker on average, the elytra proportionally longer and wider, the vertex and disc of pronotum with well impressed microsculpture, the elytral interval 3 with four or five discal setae in most specimens, and the median lobe of aedeagus less curved overall. DNA barcoding was performed on several species of eastern North American Platynus species and Platynus daviesi was found to be genetically distinct from Platynus parmarginatus. A key to the 12 species of Platynus found east of the Mississippi River is provided.},
}
@article {pmid22303127,
year = {2012},
author = {Miller, J and Rahmadi, C},
title = {A troglomorphic spider from Java (Araneae, Ctenidae, Amauropelma).},
journal = {ZooKeys},
volume = {},
number = {163},
pages = {1-11},
pmid = {22303127},
issn = {1313-2970},
abstract = {A new troglomorphic spider from caves in Central Java, Indonesia, is described and placed in the ctenid genus Amauropelma Raven, Stumkat &amp; Gray, until now containing only species from Queensland, Australia. Only juveniles and mature females of the new species are known. We give our reasons for placing the new species in Amauropelma, discuss conflicting characters, and make predictions about the morphology of the as yet undiscovered male that will test our taxonomic hypothesis. The description includes DNA barcode sequence data.},
}
@article {pmid22303099,
year = {2011},
author = {Spelda, J and Reip, HS and Oliveira-Biener, U and Melzer, RR},
title = {Barcoding Fauna Bavarica: Myriapoda - a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda).},
journal = {ZooKeys},
volume = {},
number = {156},
pages = {123-139},
pmid = {22303099},
issn = {1313-2970},
abstract = {We give a first account of our ongoing barcoding activities on Bavarian myriapods in the framework of the Barcoding Fauna Bavarica project and IBOL, the International Barcode of Life. Having analyzed 126 taxa (including 122 species) belonging to all major German chilopod and diplopod lineages, often using four or more specimens each, at the moment our species stock includes 82% of the diplopods and 65% of the chilopods found in Bavaria, southern Germany. The partial COI sequences allow correct identification of more than 95% of the current set of Bavarian species. Moreover, most of the myriapod orders and families appear as distinct clades in neighbour-joining trees, although the phylogenetic relationships between them are not always depicted correctly. We give examples of (1) high interspecific sequence variability among closely related species; (2) low interspecific variability in some chordeumatidan genera, indicating that recent speciations cannot be resolved with certainty using COI DNA barcodes; (3) high intraspecific variation in some genera, suggesting the existence of cryptic lineages; and (4) the possible polyphyly of some taxa, i.e. the chordeumatidan genus Ochogona. This shows that, in addition to species identification, our data may be useful in various ways in the context of species delimitations, taxonomic revisions and analyses of ongoing speciation processes.},
}
@article {pmid22301895,
year = {2012},
author = {Kane, N and Sveinsson, S and Dempewolf, H and Yang, JY and Zhang, D and Engels, JM and Cronk, Q},
title = {Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA.},
journal = {American journal of botany},
volume = {99},
number = {2},
pages = {320-329},
doi = {10.3732/ajb.1100570},
pmid = {22301895},
issn = {1537-2197},
mesh = {Cacao/classification/*genetics ; Cell Nucleus/*genetics ; Chloroplasts/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; DNA, Ribosomal/*genetics ; *Genome, Chloroplast ; Genotype ; High-Throughput Nucleotide Sequencing ; Polymorphism, Single Nucleotide ; Ribosomes/*genetics ; Sequence Analysis, DNA/methods ; },
abstract = {PREMISE OF STUDY: To reliably identify lineages below the species level such as subspecies or varieties, we propose an extension to DNA-barcoding using next-generation sequencing to produce whole organellar genomes and substantial nuclear ribosomal sequence. Because this method uses much longer versions of the traditional DNA-barcoding loci in the plastid and ribosomal DNA, we call our approach ultra-barcoding (UBC).<br><br>METHODS: We used high-throughput next-generation sequencing to scan the genome and generate reliable sequence of high copy number regions. Using this method, we examined whole plastid genomes as well as nearly 6000 bases of nuclear ribosomal DNA sequences for nine genotypes of Theobroma cacao and an individual of the related species T. grandiflorum, as well as an additional publicly available whole plastid genome of T. cacao.<br><br>KEY RESULTS: All individuals of T. cacao examined were uniquely distinguished, and evidence of reticulation and gene flow was observed. Sequence variation was observed in some of the canonical barcoding regions between species, but other regions of the chloroplast were more variable both within species and between species, as were ribosomal spacers. Furthermore, no single region provides the level of data available using the complete plastid genome and rDNA.<br><br>CONCLUSIONS: Our data demonstrate that UBC is a viable, increasingly cost-effective approach for reliably distinguishing varieties and even individual genotypes of T. cacao. This approach shows great promise for applications where very closely related or interbreeding taxa must be distinguished.},
}
@article {pmid22300283,
year = {2012},
author = {Siddall, ME and Kvist, S and Phillips, A and Oceguera-Figuero, A},
title = {DNA barcoding of parasitic nematodes: is it kosher?.},
journal = {The Journal of parasitology},
volume = {98},
number = {3},
pages = {692-694},
doi = {10.1645/GE-2994.1},
pmid = {22300283},
issn = {1937-2345},
mesh = {Animals ; DNA, Helminth/analysis ; Electron Transport Complex IV/genetics ; Electronic Data Processing/*standards ; Fish Products/*standards ; Fishes ; Food Handling/methods/*standards ; *Judaism ; Meat/parasitology/*standards ; Nematoda/classification/genetics/*isolation &amp; purification ; Phylogeny ; },
abstract = {Nematode parasites were encountered in kosher-certified fish meat and roe, and the question was raised as to whether or not these food products were kosher as concerns food preparation standards-a matter that pertains to the identity and, by extension, the life cycle of the parasites. To ascertain the identities of parasitic nematodes, given the distorted or damaged nature of the specimens, molecular techniques were applied in the form of DNA barcoding. To our knowledge, this is the first application of this technique to an obviously cultural concern as opposed to one of health or economic significance. Results, based both on cytochrome c oxidase subunits I and II, suggested that the parasite species found in the fish products are anisakine species that do not inhabit the intestinal lumen of the fish hosts examined. Thus, there was no evidence of failure to adhere to food preparation practices consistent with the proscriptions of Orthodox Judaism. Notwithstanding the success of DNA barcoding in determining at least the higher taxonomic identities of the parasites, some shortcomings of the DNA barcoding pipeline as it pertains to nematode parasites were encountered; specifically, the paucity of data available for the DNA barcoding locus, even for very common nematode taxa.},
}
@article {pmid22299023,
year = {2012},
author = {Wang, Y and Reinhart, WF and Tree, DR and Dorfman, KD},
title = {Resolution limit for DNA barcodes in the Odijk regime.},
journal = {Biomicrofluidics},
volume = {6},
number = {1},
pages = {14101-141019},
pmid = {22299023},
issn = {1932-1058},
support = {R21 GM103409/GM/NIGMS NIH HHS/United States ; R21 RR031230/RR/NCRR NIH HHS/United States ; R21 RR031230-02/RR/NCRR NIH HHS/United States ; R01 HG005216/HG/NHGRI NIH HHS/United States ; R01 HG005216-02/HG/NHGRI NIH HHS/United States ; },
abstract = {We develop an approximation for the probability of optically resolving two fluorescent labels on the backbone of a DNA molecule confined in a nanochannel in the Odijk regime as a function of the fluorescence wavelength, channel size, and the properties of the DNA (persistence length and effective width). The theoretical predictions agree well with equivalent data produced by Monte Carlo simulations of a touching wormlike bead model of DNA in a high ionic strength buffer. Although the theory is only strictly valid in the limit where the effective width of the nanochannel is small compared with the persistence length of the DNA, simulations indicate that the theoretical predictions are reasonably accurate for channel widths up to two-thirds of the persistence length. Our results quantify the conjecture that DNA barcoding has kilobase pair resolution-provided the nanochannel lies in the Odijk regime.},
}
@article {pmid22295861,
year = {2012},
author = {Malakar, AK and Lakra, WS and Goswami, M and Singh, M and Mishra, RM},
title = {Molecular identification of three Ompok species using mitochondrial COI gene.},
journal = {Mitochondrial DNA},
volume = {23},
number = {1},
pages = {20-24},
doi = {10.3109/19401736.2011.643876},
pmid = {22295861},
issn = {1940-1744},
mesh = {Animals ; Base Sequence ; Catfishes/classification/*genetics ; DNA Primers ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; India ; },
abstract = {A DNA-based barcode identification system that is applicable to all animal species will provide a simple, universal tool for the identification of fish species. The barcode system is based on sequence diversity in subunit 1 cytochrome c oxidase (COI) gene. Identification and characterization of fish species based on morphological characters are sometimes found to be erroneous and environmentally affected. There are no studies on the genus Ompok in India at molecular level and species identification of the Ompok is usually carried out through morphological features. A total of 106 samples from three species Ompok pabda, O. pabo and O. bimaculatus were collected from eight sampling sites of seven Indian rivers. One hundred and six sequences were generated from COI region of three Ompok species and 21 haplotypes were observed. The sequence analysis of COI gene revealed three genetically distinct Ompok species and exhibited identical phylogenetic resolution among them. The partial COI gene sequence can be used as a diagnostic molecular marker for identification and resolution of taxonomic ambiguity of Ompok species.},
}
@article {pmid22291168,
year = {2012},
author = {Steele, PR and Hertweck, KL and Mayfield, D and McKain, MR and Leebens-Mack, J and Pires, JC},
title = {Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae.},
journal = {American journal of botany},
volume = {99},
number = {2},
pages = {330-348},
doi = {10.3732/ajb.1100491},
pmid = {22291168},
issn = {1537-2197},
mesh = {Cell Nucleus/genetics ; Computational Biology/methods ; DNA, Plant/genetics ; DNA, Ribosomal/genetics ; Databases, Genetic ; Evolution, Molecular ; Genome Size ; *Genome, Chloroplast ; Genome, Mitochondrial ; Liliaceae/classification/*genetics ; Mitochondria/genetics ; Molecular Sequence Annotation ; Phylogeny ; Plastids/genetics ; Poaceae/classification/*genetics ; Reference Standards ; Sensitivity and Specificity ; Sequence Analysis, DNA/methods ; },
abstract = {PREMISE OF THE STUDY: Genome survey sequences (GSS) from massively parallel sequencing have potential to provide large, cost-effective data sets for phylogenetic inference, replace single gene or spacer regions as DNA barcodes, and provide a plethora of data for other comparative molecular evolution studies. Here we report on the application of this method to estimating the molecular phylogeny of core Asparagales, investigating plastid gene losses, assembling complete plastid genomes, and determining the type and quality of assembled genomic data attainable from Illumina 80-120-bp reads.<br><br>METHODS: We sequenced total genomic DNA from samples in two lineages of monocotyledonous plants, Poaceae and Asparagales, on the Illumina platform in a multiplex arrangement. We compared reference-based assemblies to de novo contigs, evaluated consistency of assemblies resulting from use of various references sequences, and assessed our methods to obtain sequence assemblies in nonmodel taxa.<br><br>KEY RESULTS: Our method returned reliable, robust organellar and nrDNA sequences in a variety of plant lineages. High quality assemblies are not dependent on genome size, amount of plastid present in the total genomic DNA template, or relatedness of available reference sequences for assembly. Phylogenetic results revealed familial and subfamilial relationships within Asparagales with high bootstrap support, although placement of the monotypic genus Aphyllanthes was placed with moderate confidence.<br><br>CONCLUSIONS: The well-supported molecular phylogeny provides evidence for delineation of subfamilies within core Asparagales. With advances in technology and bioinformatics tools, the use of massively parallel sequencing will continue to become easier and more affordable for phylogenomic and molecular evolutionary biology investigations.},
}
@article {pmid22289766,
year = {2012},
author = {Basiewicz, M and Weiss, M and Kogel, KH and Langen, G and Zorn, H and Zuccaro, A},
title = {Molecular and phenotypic characterization of Sebacina vermifera strains associated with orchids, and the description of Piriformospora williamsii sp. nov.},
journal = {Fungal biology},
volume = {116},
number = {2},
pages = {204-213},
doi = {10.1016/j.funbio.2011.11.003},
pmid = {22289766},
issn = {1878-6146},
mesh = {Basidiomycota/*classification/genetics/*isolation &amp; purification ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Enzymes/analysis ; Genes, rRNA ; Glomeromycota/classification/genetics/isolation &amp; purification ; Introns ; Karyotype ; Molecular Sequence Data ; Orchidaceae/*microbiology ; Peptide Elongation Factor 1/genetics ; Phylogeny ; RNA, Fungal/genetics ; RNA, Ribosomal, 28S/genetics ; RNA, Ribosomal, 5.8S/genetics ; Sequence Analysis, DNA ; },
abstract = {Sebacinales was described in 2004 and is currently recognized as the earliest diverging lineage of mycorrhizal Basidiomycota. In addition, recent research has demonstrated that no other known fungal order harbours a broader spectrum of mycorrhizal types. Yet because of the character poor morphology of these inconspicuous fungi, a reliable systematic framework for Sebacinales is still out of reach. In order to increase the body of comparative data on Sebacinales, we followed a polyphasic approach using a sampling of seven diverse Sebacinales strains, including several isolates of Australian orchid mycorrhizae, Piriformospora indica, and a multinucleate rhizoctonia isolated from a pot culture of Glomus fasciculatum (Williams 1985) with clover. We performed molecular phylogenetic analyses from candidate barcoding regions [rDNA: internal transcribed spacer (ITS)1-5.8-ITS2, 28S; translation elongation factor 1-α (TEF)], enzymatic profiling, genome size estimation by quantitative polymerase chain reaction (PCR), and karyotype analysis using pulsed field gel electrophoresis. Here, we report significant differences in the physiological and molecular parameters inferred from these morphologically very similar strains. Particularly, our results indicate that intron sequences of the TEF gene are useful markers for Sebacinales at the species level. As a first taxonomic consequence, we describe Piriformospora williamsii as a new member of the so far monotypic genus Piriformospora and show that this genus contains still undescribed species that were recently discovered as endophytes of field-collected specimens of Anthyllis, Medicago, and Lolium in Germany.},
}
@article {pmid22289489,
year = {2012},
author = {Kohlmann, A and Grossmann, V and Haferlach, T},
title = {Integration of next-generation sequencing into clinical practice: are we there yet?.},
journal = {Seminars in oncology},
volume = {39},
number = {1},
pages = {26-36},
doi = {10.1053/j.seminoncol.2011.11.008},
pmid = {22289489},
issn = {1532-8708},
mesh = {*High-Throughput Nucleotide Sequencing ; Humans ; Leukemia, Myelomonocytic, Chronic/*genetics ; Proto-Oncogene Proteins/*genetics ; Sequence Analysis, DNA ; },
abstract = {Next-generation sequencing (NGS) platforms have evolved to provide an accurate and comprehensive means for the detection of molecular mutations in heterogeneous tumor specimens. Here, we review potential applications of this novel laboratory technology. In particular, we focus on the utility of amplicon deep-sequencing assays in characterizing myeloid neoplasms where the number of molecular markers applied for disease classification, patient stratification, and individualized monitoring of minimal residual disease is constantly increasing. We highlight the potential of this technology by discussing data from a recent study on chronic myelomonocytic leukemia (CMML). Although many facets of this assay need to be taken into account, eg, the preparation of sequencing libraries with molecular barcodes, specific experimental design options when considering sequencing coverage to calculate diagnostic sensitivity, or the use of suitable software and data processing solutions to obtain accurate results, amplicon deep-sequencing has already demonstrated a promising technical performance that warrants the further development towards a routine application of this technology in diagnostic laboratories so that an impact on clinical practice can be achieved.},
}
@article {pmid22287908,
year = {2011},
author = {Schindel, DE and Stoeckle, MY and Milensky, C and Trizna, M and Schmidt, B and Gebhard, C and Graves, G},
title = {Project description: DNA barcodes of bird species in the national museum of natural history, smithsonian institution, USA.},
journal = {ZooKeys},
volume = {},
number = {152},
pages = {87-92},
doi = {10.3897/zookeys.152.2473},
pmid = {22287908},
issn = {1313-2970},
abstract = {The Division of Birds, National Museum of Natural History, Smithsonian Institution in Washington, DC, has obtained and released DNA barcodes for 2808 frozen tissue samples. Of the 1,403 species represented by these samples, 1,147 species have not been barcoded previously. This data release increases the number of bird species with standard barcodes by 91%. These records meet the data standard of the Consortium for the Barcode of Life and they have the reserved keyword BARCODE in GenBank. The data are now available on GenBank and the Barcode of Life Data Systems.},
}
@article {pmid22287894,
year = {2011},
author = {Syaukani, and Thompson, GJ},
title = {Taxonomic Notes on Nasutitermes and Bulbitermes (Termitidae, Nasutitermitinae) from the Sunda region of Southeast Asia based on morphological and molecular characters.},
journal = {ZooKeys},
volume = {},
number = {148},
pages = {135-160},
pmid = {22287894},
issn = {1313-2970},
abstract = {The Sunda region of Southeastern Asia is rich in termite fauna, but termites from this region have been poorly described. In this study, we described eight species from two diverse genera from this region, and from the family Termitidae. We describe Bulbitermes 4 spp. and Nasutitermes 4 spp. from new field collections. Where possible we examine original holotype specimens, and describe the essential morphological characters for soldier and worker castes. We devise two new bifurcating keys to guide the field identification of each species. In addition, we develop a nucleotide sequence profile for the COI gene. From this molecular character matrix, we use Neighbour-Joining analysis to test the monophyly of each morphospecies and genus. We find that the morphological and molecular characters are highly concordant, whereby all taxa appear to represent distinct molecular clades. For termites, there is therefore agreement between the morphological taxonomic characters used to sort species from a bifurcating key and the molecular taxonomic characters used to sort species on a bifurcating tree. This joint analysis suggests that DNA barcoding holds considerable promise for termite taxonomy, especially for diverse clades like Bulbitermes and Nasutitermes for which a global morphological key would be intractable.},
}
@article {pmid22284888,
year = {2012},
author = {Wang, J and Chen, WF and Li, QX},
title = {Rapid identification and classification of Mycobacterium spp. using whole-cell protein barcodes with matrix assisted laser desorption ionization time of flight mass spectrometry in comparison with multigene phylogenetic analysis.},
journal = {Analytica chimica acta},
volume = {716},
number = {},
pages = {133-137},
doi = {10.1016/j.aca.2011.12.016},
pmid = {22284888},
issn = {1873-4324},
mesh = {Bacterial Proteins/analysis ; Bacterial Typing Techniques/*methods ; Chaperonin 60/analysis ; DNA-Directed RNA Polymerases ; Mycobacterium/*classification/metabolism ; Phenotype ; *Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/analysis ; Software ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {The need of quick diagnostics and increasing number of bacterial species isolated necessitate development of a rapid and effective phenotypic identification method. Mass spectrometry (MS) profiling of whole cell proteins has potential to satisfy the requirements. The genus Mycobacterium contains more than 154 species that are taxonomically very close and require use of multiple genes including 16S rDNA for phylogenetic identification and classification. Six strains of five Mycobacterium species were selected as model bacteria in the present study because of their 16S rDNA similarity (98.4-99.8%) and the high similarity of the concatenated 16S rDNA, rpoB and hsp65 gene sequences (95.9-99.9%), requiring high identification resolution. The classification of the six strains by MALDI TOF MS protein barcodes was consistent with, but at much higher resolution than, that of the multi-locus sequence analysis of using 16S rDNA, rpoB and hsp65. The species were well differentiated using MALDI TOF MS and MALDI BioTyper™ software after quick preparation of whole-cell proteins. Several proteins were selected as diagnostic markers for species confirmation. An integration of MALDI TOF MS, MALDI BioTyper™ software and diagnostic protein fragments provides a robust phenotypic approach for bacterial identification and classification.},
}
@article {pmid22280360,
year = {2012},
author = {Triplet, T and Butler, G},
title = {The EnzymeTracker: an open-source laboratory information management system for sample tracking.},
journal = {BMC bioinformatics},
volume = {13},
number = {},
pages = {15},
pmid = {22280360},
issn = {1471-2105},
mesh = {Algorithms ; *Clinical Laboratory Information Systems ; *Database Management Systems ; Databases, Genetic ; Fungi/enzymology/genetics ; Information Dissemination ; Internet ; Management Information Systems ; Quality Control ; Software ; User-Computer Interface ; },
abstract = {BACKGROUND: In many laboratories, researchers store experimental data on their own workstation using spreadsheets. However, this approach poses a number of problems, ranging from sharing issues to inefficient data-mining. Standard spreadsheets are also error-prone, as data do not undergo any validation process. To overcome spreadsheets inherent limitations, a number of proprietary systems have been developed, which laboratories need to pay expensive license fees for. Those costs are usually prohibitive for most laboratories and prevent scientists from benefiting from more sophisticated data management systems.<br><br>RESULTS: In this paper, we propose the EnzymeTracker, a web-based laboratory information management system for sample tracking, as an open-source and flexible alternative that aims at facilitating entry, mining and sharing of experimental biological data. The EnzymeTracker features online spreadsheets and tools for monitoring numerous experiments conducted by several collaborators to identify and characterize samples. It also provides libraries of shared data such as protocols, and administration tools for data access control using OpenID and user/team management. Our system relies on a database management system for efficient data indexing and management and a user-friendly AJAX interface that can be accessed over the Internet. The EnzymeTracker facilitates data entry by dynamically suggesting entries and providing smart data-mining tools to effectively retrieve data. Our system features a number of tools to visualize and annotate experimental data, and export highly customizable reports. It also supports QR matrix barcoding to facilitate sample tracking.<br><br>CONCLUSIONS: The EnzymeTracker was designed to be easy to use and offers many benefits over spreadsheets, thus presenting the characteristics required to facilitate acceptance by the scientific community. It has been successfully used for 20 months on a daily basis by over 50 scientists. The EnzymeTracker is freely available online at http://cubique.fungalgenomics.ca/enzymedb/index.html under the GNU GPLv3 license.},
}
@article {pmid22277023,
year = {2012},
author = {Kumar, NP and Srinivasan, R and Jambulingam, P},
title = {DNA barcoding for identification of sand flies (Diptera: Psychodidae) in India.},
journal = {Molecular ecology resources},
volume = {12},
number = {3},
pages = {414-420},
doi = {10.1111/j.1755-0998.2012.03117.x},
pmid = {22277023},
issn = {1755-0998},
mesh = {Animals ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/genetics ; Genotype ; India ; Molecular Sequence Data ; Phlebotomus/*classification/*genetics ; Psychodidae/*classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {About 50 species of sand flies have been reported to be prevalent in India. We explored the utility of the DNA barcode approach towards species identification of these medically important insects. A total of 62 specimens belonging to seven morphologically identified species of two genera, Phlebotomus and Sergentomyia, collected from Puducherry Union Territory, Maharashtra and Rajasthan states of India were subjected to the analysis. Neighbor-joining (NJ) analysis of DNA barcode sequences identified the individuals of seven morphological species into eight distinct species, as presented in the designed NJ tree. This methodology delineated morphologically identified species, S. bailyi, into two genetically isolated groups. Also, this study characterizes DNA barcodes of P. argentipes and P. papatasi, the vector species of leishmaniasis in India, for the first time.},
}
@article {pmid22276739,
year = {2012},
author = {Tu, J and Ge, Q and Wang, S and Wang, L and Sun, B and Yang, Q and Bai, Y and Lu, Z},
title = {Pair-barcode high-throughput sequencing for large-scale multiplexed sample analysis.},
journal = {BMC genomics},
volume = {13},
number = {},
pages = {43},
pmid = {22276739},
issn = {1471-2164},
mesh = {Breast Neoplasms/genetics/metabolism ; Databases, Factual ; Electronic Data Processing ; Female ; Humans ; MicroRNAs/genetics ; Sequence Analysis, DNA/*methods ; Transcriptome ; },
abstract = {BACKGROUND: The multiplexing becomes the major limitation of the next-generation sequencing (NGS) in application to low complexity samples. Physical space segregation allows limited multiplexing, while the existing barcode approach only permits simultaneously analysis of up to several dozen samples.<br><br>RESULTS: Here we introduce pair-barcode sequencing (PBS), an economic and flexible barcoding technique that permits parallel analysis of large-scale multiplexed samples. In two pilot runs using SOLiD sequencer (Applied Biosystems Inc.), 32 independent pair-barcoded miRNA libraries were simultaneously discovered by the combination of 4 unique forward barcodes and 8 unique reverse barcodes. Over 174,000,000 reads were generated and about 64% of them are assigned to both of the barcodes. After mapping all reads to pre-miRNAs in miRBase, different miRNA expression patterns are captured from the two clinical groups. The strong correlation using different barcode pairs and the high consistency of miRNA expression in two independent runs demonstrates that PBS approach is valid.<br><br>CONCLUSIONS: By employing PBS approach in NGS, large-scale multiplexed pooled samples could be practically analyzed in parallel so that high-throughput sequencing economically meets the requirements of samples which are low sequencing throughput demand.},
}
@article {pmid22276096,
year = {2012},
author = {Collins, RA and Armstrong, KF and Meier, R and Yi, Y and Brown, SD and Cruickshank, RH and Keeling, S and Johnston, C},
title = {Barcoding and border biosecurity: identifying cyprinid fishes in the aquarium trade.},
journal = {PloS one},
volume = {7},
number = {1},
pages = {e28381},
pmid = {22276096},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Fishes/*classification/*genetics ; },
abstract = {BACKGROUND: Poorly regulated international trade in ornamental fishes poses risks to both biodiversity and economic activity via invasive alien species and exotic pathogens. Border security officials need robust tools to confirm identifications, often requiring hard-to-obtain taxonomic literature and expertise. DNA barcoding offers a potentially attractive tool for quarantine inspection, but has yet to be scrutinised for aquarium fishes. Here, we present a barcoding approach for ornamental cyprinid fishes by: (1) expanding current barcode reference libraries; (2) assessing barcode congruence with morphological identifications under numerous scenarios (e.g. inclusion of GenBank data, presence of singleton species, choice of analytical method); and (3) providing supplementary information to identify difficult species.<br><br>We sampled 172 ornamental cyprinid fish species from the international trade, and provide data for 91 species currently unrepresented in reference libraries (GenBank/Bold). DNA barcodes were found to be highly congruent with our morphological assignments, achieving success rates of 90-99%, depending on the method used (neighbour-joining monophyly, bootstrap, nearest neighbour, GMYC, percent threshold). Inclusion of data from GenBank (additional 157 spp.) resulted in a more comprehensive library, but at a cost to success rate due to the increased number of singleton species. In addition to DNA barcodes, our study also provides supporting data in the form of specimen images, morphological characters, taxonomic bibliography, preserved vouchers, and nuclear rhodopsin sequences. Using this nuclear rhodopsin data we also uncovered evidence of interspecific hybridisation, and highlighted unrecognised diversity within popular aquarium species, including the endangered Indian barb Puntius denisonii.<br><br>CONCLUSIONS/SIGNIFICANCE: We demonstrate that DNA barcoding provides a highly effective biosecurity tool for rapidly identifying ornamental fishes. In cases where DNA barcodes are unable to offer an identification, we improve on previous studies by consolidating supplementary information from multiple data sources, and empower biosecurity agencies to confidently identify high-risk fishes in the aquarium trade.},
}
@article {pmid22272356,
year = {2012},
author = {van Velzen, R and Weitschek, E and Felici, G and Bakker, FT},
title = {DNA barcoding of recently diverged species: relative performance of matching methods.},
journal = {PloS one},
volume = {7},
number = {1},
pages = {e30490},
pmid = {22272356},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Computational Biology/*methods ; Computer Simulation ; DNA Barcoding, Taxonomic/*methods ; Drosophila/classification/genetics ; Fabaceae/classification/genetics ; *Genetic Variation ; Mollusca/classification/genetics ; *Phylogeny ; Reproducibility of Results ; Sequence Homology, Nucleic Acid ; Species Specificity ; },
abstract = {Recently diverged species are challenging for identification, yet they are frequently of special interest scientifically as well as from a regulatory perspective. DNA barcoding has proven instrumental in species identification, especially in insects and vertebrates, but for the identification of recently diverged species it has been reported to be problematic in some cases. Problems are mostly due to incomplete lineage sorting or simply lack of a 'barcode gap' and probably related to large effective population size and/or low mutation rate. Our objective was to compare six methods in their ability to correctly identify recently diverged species with DNA barcodes: neighbor joining and parsimony (both tree-based), nearest neighbor and BLAST (similarity-based), and the diagnostic methods DNA-BAR, and BLOG. We analyzed simulated data assuming three different effective population sizes as well as three selected empirical data sets from published studies. Results show, as expected, that success rates are significantly lower for recently diverged species (∼75%) than for older species (∼97%) (P<0.00001). Similarity-based and diagnostic methods significantly outperform tree-based methods, when applied to simulated DNA barcode data (P<0.00001). The diagnostic method BLOG had highest correct query identification rate based on simulated (86.2%) as well as empirical data (93.1%), indicating that it is a consistently better method overall. Another advantage of BLOG is that it offers species-level information that can be used outside the realm of DNA barcoding, for instance in species description or molecular detection assays. Even though we can confirm that identification success based on DNA barcoding is generally high in our data, recently diverged species remain difficult to identify. Nevertheless, our results contribute to improved solutions for their accurate identification.},
}
@article {pmid22268756,
year = {2012},
author = {Huxley-Jones, E and Shaw, JL and Fletcher, C and Parnell, J and Watts, PC},
title = {Use of DNA barcoding to reveal species composition of convenience seafood.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {26},
number = {2},
pages = {367-371},
doi = {10.1111/j.1523-1739.2011.01813.x},
pmid = {22268756},
issn = {1523-1739},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Fishes/classification/*genetics ; *Seafood ; Species Specificity ; },
abstract = {Increased education of consumers can be an effective tool for conservation of commercially harvested marine species when product labeling is accurate and allows an informed choice. However, generic labeling (e.g., as white fish or surimi) and mislabeling of seafood prevents this and may erode consumer confidence in seafood product labels in general. We used DNA barcoding to identify the species composition of two types of convenience seafood (i.e., products processed for ease of consumption): fish fingers (long pieces of fish covered with bread crumbs or batter, n = 241) and seafood sticks (long pieces of cooked fish, n = 30). In products labeled as either white fish or surimi, four teleost species were present. Less than 1.5% of fish fingers with species-specific information were mislabeled. Results of other studies show substantially more mislabeling (e.g., >25%) of teleost products, which likely reflects the lower economic gains associated with mislabeling of convenience seafood compared with whole fillets. In addition to species identification, seafood product labels should be required to contain information about, for example, harvesting practices, and our data indicate that consumers can have reasonable confidence in the accuracy of the labels of convenience seafood and thus select brands on the basis of information about current fisheries practice.},
}
@article {pmid22267905,
year = {2012},
author = {Linard, B and Nguyen, NH and Prosdocimi, F and Poch, O and Thompson, JD},
title = {EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data.},
journal = {Evolutionary bioinformatics online},
volume = {8},
number = {},
pages = {61-77},
pmid = {22267905},
issn = {1176-9343},
abstract = {Evolutionary systems biology aims to uncover the general trends and principles governing the evolution of biological networks. An essential part of this process is the reconstruction and analysis of the evolutionary histories of these complex, dynamic networks. Unfortunately, the methodologies for representing and exploiting such complex evolutionary histories in large scale studies are currently limited. Here, we propose a new formalism, called EvoluCode (Evolutionary barCode), which allows the integration of different evolutionary parameters (eg, sequence conservation, orthology, synteny …) in a unifying format and facilitates the multilevel analysis and visualization of complex evolutionary histories at the genome scale. The advantages of the approach are demonstrated by constructing barcodes representing the evolution of the complete human proteome. Two large-scale studies are then described: (i) the mapping and visualization of the barcodes on the human chromosomes and (ii) automatic clustering of the barcodes to highlight protein subsets sharing similar evolutionary histories and their functional analysis. The methodologies developed here open the way to the efficient application of other data mining and knowledge extraction techniques in evolutionary systems biology studies. A database containing all EvoluCode data is available at: http://lbgi.igbmc.fr/barcodes.},
}
@article {pmid22267902,
year = {2012},
author = {Boykin, LM and Armstrong, KF and Kubatko, L and De Barro, P},
title = {Species delimitation and global biosecurity.},
journal = {Evolutionary bioinformatics online},
volume = {8},
number = {},
pages = {1-37},
pmid = {22267902},
issn = {1176-9343},
abstract = {Species delimitation directly impacts on global biosecurity. It is a critical element in the decisions made by national governments in regard to the flow of trade and to the biosecurity measures imposed to protect countries from the threat of invasive species. Here we outline a novel approach to species delimitation, "tip to root", for two highly invasive insect pests, Bemisia tabaci (sweetpotato whitefly) and Lymantria dispar (Asian gypsy moth). Both species are of concern to biosecurity, but illustrate the extremes of phylogenetic resolution that present the most complex delimitation issues for biosecurity; B. tabaci having extremely high intra-specific genetic variability and L. dispar composed of relatively indistinct subspecies. This study tests a series of analytical options to determine their applicability as tools to provide more rigorous species delimitation measures and consequently more defensible species assignments and identification of unknowns for biosecurity. Data from established DNA barcode datasets (COI), which are becoming increasingly considered for adoption in biosecurity, were used here as an example. The analytical approaches included the commonly used Kimura two-parameter (K2P) inter-species distance plus four more stringent measures of taxon distinctiveness, (1) Rosenberg's reciprocal monophyly, (P(AB)),1 (2) Rodrigo's (P(randomly distinct)),2 (3) genealogical sorting index, (gsi),3 and (4) General mixed Yule-coalescent (GMYC).4,5 For both insect datasets, a comparative analysis of the methods revealed that the K2P distance method does not capture the same level of species distinctiveness revealed by the other three measures; in B. tabaci there are more distinct groups than previously identified using the K2P distances and for L. dipsar far less variation is apparent within the predefined subspecies. A consensus for the results from P(AB), P(randomly distinct) and gsi offers greater statistical confidence as to where genetic limits might be drawn. In the species cases here, the results clearly indicate that there is a need for more gene sampling to substantiate either the new cohort of species indicated for B. tabaci or to detect the established subspecies taxonomy of L. dispar. Given the ease of use through the Geneious species delimitation plugins, similar analysis of such multi-gene datasets would be easily accommodated. Overall, the tip to root approach described here is recommended where careful consideration of species delimitation is required to support crucial biosecurity decisions based on accurate species identification.},
}
@article {pmid22267084,
year = {2012},
author = {Chen, Z and Fu, X and Zhang, X and Liu, X and Zou, B and Wu, H and Song, Q and Li, J and Kajiyama, T and Kambara, H and Zhou, G},
title = {Pyrosequencing-based barcodes for a dye-free multiplex bioassay.},
journal = {Chemical communications (Cambridge, England)},
volume = {48},
number = {18},
pages = {2445-2447},
doi = {10.1039/c2cc17618a},
pmid = {22267084},
issn = {1364-548X},
mesh = {Actins/genetics ; Animals ; Base Sequence ; Biological Assay/*methods ; Cyclin-Dependent Kinase 4/genetics ; Mice ; Sequence Analysis/*methods ; Staining and Labeling ; },
abstract = {A novel dye-free labeling method for a multiplex bioassay was proposed by using short sequence-based barcodes consisting of a reporter base and repeats of two stuffer bases; then, the barcodes were quantitatively decoded by a single pyrosequencing assay without any pre-separation.},
}
@article {pmid22266815,
year = {2012},
author = {Santos, A and Balderrama, VS and Alba, M and Formentín, P and Ferré-Borrull, J and Pallarès, J and Marsal, LF},
title = {Nanoporous anodic alumina barcodes: toward smart optical biosensors.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {24},
number = {8},
pages = {1050-1054},
doi = {10.1002/adma.201104490},
pmid = {22266815},
issn = {1521-4095},
mesh = {Aluminum Oxide/*chemistry ; Biosensing Techniques/*methods ; Electrodes ; Luminescent Measurements ; *Nanopores ; *Optical Phenomena ; },
abstract = {Toward a smart optical biosensor based on nanoporous anodic alumina (NAA): by modifying the pore geometry in nanoporous anodic alumina we are able to change the effective medium at will and tune the photoluminescence of NAA. The oscillations in the PL spectrum are converted into exclusive barcodes, which are useful for developing optical biomedical sensors in the UV-Visible region.},
}
@article {pmid22265301,
year = {2012},
author = {Park, EJ and Chun, J and Cha, CJ and Park, WS and Jeon, CO and Bae, JW},
title = {Bacterial community analysis during fermentation of ten representative kinds of kimchi with barcoded pyrosequencing.},
journal = {Food microbiology},
volume = {30},
number = {1},
pages = {197-204},
doi = {10.1016/j.fm.2011.10.011},
pmid = {22265301},
issn = {1095-9998},
mesh = {Bacteria/classification/*isolation &amp; purification ; Brassica/*microbiology ; DNA, Bacterial/genetics/isolation &amp; purification ; *Fermentation ; Food Contamination/analysis ; Food Microbiology/*methods ; Metagenomics/methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Vegetables/microbiology ; },
abstract = {Kimchi, a food made of fermented vegetables, is densely populated by indigenous microorganisms that originate from the raw ingredients under normal conditions. Most microbiological studies on kimchi have been on the most popular dish, baechu-kimchi (Chinese cabbage kimchi). Therefore, relatively little is known about the various other kinds of kimchi (depending on the region, season, main ingredient, starter culture inoculation and recipe). In this study, we collected 100 samples periodically during the fermentation of ten representative kinds of kimchi (including starter-inoculated kimchi) that were stored in the refrigerator (4 °C) during the 30-35 days fermentation period. The multiplex barcoded pyrosequencing of a hypervariable V1-V3 region of the 16S ribosomal RNA (rRNA) gene tagged with sample-specific barcodes for multiplex identifiers was employed for bacterial community profiling. We found that bacterial communities differed between starter-inoculated and non-inoculated kimchi at the early stages of fermentation, but overall there were no significant differences in the late phases. Also, the diversity and richness of bacterial communities varied depending on the various types of kimchi, and these differences could largely be explained by the major ingredients and the manufacture processes of each types of kimchi. This study provides the comprehensive understanding of the factors influencing the biodiversity of the kimchi ecosystem.},
}
@article {pmid22264493,
year = {2013},
author = {Santoferrara, LF and McManus, GB and Alder, VA},
title = {Utility of genetic markers and morphology for species discrimination within the order Tintinnida (Ciliophora, Spirotrichea).},
journal = {Protist},
volume = {164},
number = {1},
pages = {24-36},
doi = {10.1016/j.protis.2011.12.002},
pmid = {22264493},
issn = {1618-0941},
mesh = {Ciliophora/classification/*cytology/*genetics ; Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Microscopy ; Molecular Sequence Data ; Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; },
abstract = {We evaluated the small- and large-subunit rDNA (SSU and LSU, respectively) for their ability to discriminate morphospecies of tintinnid ciliates. Multiple individuals from 29 morphospecies were identified according to microscopically-observed characteristics of the lorica, and then sequenced for both loci (21 new species for SSU and all of them new for LSU). Sequences from public databases were included in our analyses, and two hypervariable SSU regions (V4 and V9) were separately examined. Of the four regions, LSU is the most useful as a potential barcoding tool. It showed a gap in distances within and between species, and discriminated the maximum number of phylotypes (86% at 1% cut-off). SSU and V4 were less consistent, sometimes lumping together very distinctive morphospecies, even at the 1% level of sequence divergence. V9 was the least reliable marker in delimitating morphospecies. The agreement in sequences and morphology suggests that the lorica is useful for species discrimination, even in agglomerated forms. However, the observation of both genetically constant yet polymorphic groups of species, as well as similar morphospecies with divergent sequences, indicates that previous taxonomic schemes are complementary to the emerging molecular database.},
}
@article {pmid22263854,
year = {2012},
author = {Vergilino, R and Dionne, K and Nozais, C and Dufresne, F and Belzile, C},
title = {Genome size differences in Hyalella cryptic species.},
journal = {Genome},
volume = {55},
number = {2},
pages = {134-139},
doi = {10.1139/g11-085},
pmid = {22263854},
issn = {1480-3321},
mesh = {Amphipoda/*genetics ; Animals ; Base Sequence ; Bayes Theorem ; Denaturing Gradient Gel Electrophoresis ; Electron Transport Complex IV/genetics ; Flow Cytometry ; Genome Size/*genetics ; Haplotypes/genetics ; Lakes ; Models, Genetic ; Molecular Sequence Data ; Quebec ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The Hyalella azteca (Saussure) complex includes numerous amphipod cryptic species in freshwater habitats in America as revealed by DNA barcoding surveys. Two ecomorphs (small and large) have evolved numerous times in this complex. Few phenotypic criteria have been found to differentiate between the numerous species of this complex. The present study aims to explore genome size differences between some species of the H. azteca complex co-occurring in a Canadian boreal lake using flow cytometry. Nuclear DNA content was estimated for 50 individuals belonging to six COI haplotypes corresponding to four provisional species of the H. azteca complex. Species from the large ecomorph had C-values significantly larger than species from the small ecomorph, whereas slight differences were found among species of the small ecomorph. These differences in genome sizes might be linked to ecological and physiological differences among species of the H. azteca complex.},
}
@article {pmid22260646,
year = {2012},
author = {Singh, HK and Parveen, I and Raghuvanshi, S and Babbar, SB},
title = {The loci recommended as universal barcodes for plants on the basis of floristic studies may not work with congeneric species as exemplified by DNA barcoding of Dendrobium species.},
journal = {BMC research notes},
volume = {5},
number = {},
pages = {42},
pmid = {22260646},
issn = {1756-0500},
abstract = {BACKGROUND: Based on the testing of several loci, predominantly against floristic backgrounds, individual or different combinations of loci have been suggested as possible universal DNA barcodes for plants. The present investigation was undertaken to check the applicability of the recommended locus/loci for congeneric species with Dendrobium species as an illustrative example.<br><br>RESULTS: Six loci, matK, rbcL, rpoB, rpoC1, trnH-psbA spacer from the chloroplast genome and ITS, from the nuclear genome, were compared for their amplification, sequencing and species discrimination success rates among multiple accessions of 36 Dendrobium species. The trnH-psbA spacer could not be considered for analysis as good quality sequences were not obtained with its forward primer. Among the tested loci, ITS, recommended by some as a possible barcode for plants, provided 100% species identification. Another locus, matK, also recommended as a universal barcode for plants, resolved 80.56% species. ITS remained the best even when sequences of investigated loci of additional Dendrobium species available on the NCBI GenBank (93, 33, 20, 18 and 17 of ITS, matK, rbcL, rpoB and rpoC1, respectively) were also considered for calculating the percent species resolution capabilities. The species discrimination of various combinations of the loci was also compared based on the 36 investigated species and additional 16 for which sequences of all the five loci were available on GenBank. Two-locus combination of matK+rbcL recommended by the Plant Working Group of Consortium for Barcoding of Life (CBOL) could discriminate 86.11% of 36 species. The species discriminating ability of this barcode was reduced to 80.77% when additional sequences available on NCBI were included in the analysis. Among the recommended combinations, the barcode based on three loci - matK, rpoB and rpoC1- resolved maximum number of species.<br><br>CONCLUSIONS: Any recommended barcode based on the loci tested so far, is not likely to provide 100% species identification across the plant kingdom and thus is not likely to act as a universal barcode. It appears that barcodes, if based on single or limited locus(i), would be taxa specific as is exemplified by the success of ITS among Dendrobium species, though it may not be suitable for other plants because of the problems that are discussed.},
}
@article {pmid22260038,
year = {2011},
author = {Han, JP and Li, MN and Luo, K and Liu, MZ and Chen, XC and Chen, SL},
title = {[Identification of Daturae flos and its adulterants based on DNA barcoding technique].},
journal = {Yao xue xue bao = Acta pharmaceutica Sinica},
volume = {46},
number = {11},
pages = {1408-1412},
pmid = {22260038},
issn = {0513-4870},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic/*methods ; DNA, Intergenic/genetics ; DNA, Plant/genetics ; Datura/classification/*genetics ; Datura metel/*genetics ; Datura stramonium/genetics ; *Drug Contamination ; Flowers/genetics ; Phylogeny ; Plants, Medicinal/*genetics ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Solanaceae/genetics ; Species Specificity ; },
abstract = {To identify the original plant of Daturae Flos from its adulterants by DNA barcoding, the sequences of ITS2, psbA-trnH, matK, rbcL of four species including Datura metel, Darura innoxia, Darura stramonium and Brugmansia arborea were compared and analyzed. The PCR and sequencing success rate of the four regions (ITS2, psbA-trnH, matK, rbcL) was 100%, 90%, 100% and 85%, respectively. Sequences were assembled with CodonCode Aligner. K2P distances were calculated and NJ tree was performed by MEGA 4.1. Thirty SNPs were found among ITS2 sequences, and 33 insert/deletes were found among psbA-trnH intergenic regions. The interspecific K2P distance of ITS2 and psbA-trnH was obviously higher than that of the intraspecific one. As to matK and rbcL, there was no "Barcoding Gap" existing between inter- and intra-specific distances. The NJ trees of the four regions/combinations were built separately. Samples of Brugmansia arborea were clustered into one clade, and the other species of Datura L. formed another clade. The results showed that either ITS2 or psbA-trnH was useful to identify Daturae Flos from its adulterants.},
}
@article {pmid22259307,
year = {2011},
author = {Lai, YT and Nakano, T and Chen, JH},
title = {Three species of land leeches from Taiwan, Haemadipsa rjukjuana comb. n., a new record for Haemadipsa picta Moore, and an updated description of Tritetrabdella taiwana (Oka).},
journal = {ZooKeys},
volume = {},
number = {139},
pages = {1-22},
pmid = {22259307},
issn = {1313-2970},
abstract = {Three species of land leeches, including a new combination Haemadipsa rjukjuanacomb. n., a new record for Haemadipsa picta Moore, as well as an updated description for Tritetrabdella taiwana (Oka), are reported in this study. Morphological characters and DNA barcode analysis were used to identify these species. In addition, since Haemadipsa rjukjuana had been regarded as a variety of the Japanese land leech Haemadipsa japonica for a century, morphological differences between these two species were also compared.},
}
@article {pmid22253849,
year = {2012},
author = {Lucas, C and Thangaradjou, T and Papenbrock, J},
title = {Development of a DNA barcoding system for seagrasses: successful but not simple.},
journal = {PloS one},
volume = {7},
number = {1},
pages = {e29987},
pmid = {22253849},
issn = {1932-6203},
mesh = {Aquatic Organisms/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; Genetic Loci/genetics ; Magnoliopsida/*classification/*genetics ; Phylogeny ; Species Specificity ; },
abstract = {Seagrasses, a unique group of submerged flowering plants, profoundly influence the physical, chemical and biological environments of coastal waters through their high primary productivity and nutrient recycling ability. They provide habitat for aquatic life, alter water flow, stabilize the ground and mitigate the impact of nutrient pollution. at the coast region. Although on a global scale seagrasses represent less than 0.1% of the angiosperm taxa, the taxonomical ambiguity in delineating seagrass species is high. Thus, the taxonomy of several genera is unsolved. While seagrasses are capable of performing both, sexual and asexual reproduction, vegetative reproduction is common and sexual progenies are always short lived and epimeral in nature. This makes species differentiation often difficult, especially for non-taxonomists since the flower as a distinct morphological trait is missing. Our goal is to develop a DNA barcoding system assisting also non-taxonomists to identify regional seagrass species. The results will be corroborated by publicly available sequence data. The main focus is on the 14 described seagrass species of India, supplemented with seagrasses from temperate regions. According to the recommendations of the Consortium for the Barcoding of Life (CBOL) rbcL and matK were used in this study. After optimization of the DNA extraction method from preserved seagrass material, the respective sequences were amplified from all species analyzed. Tree- and character-based approaches demonstrate that the rbcL sequence fragment is capable of resolving up to family and genus level. Only matK sequences were reliable in resolving species and partially the ecotype level. Additionally, a plastidic gene spacer was included in the analysis to confirm the identification level. Although the analysis of these three loci solved several nodes, a few complexes remained unsolved, even when constructing a combined tree for all three loci. Our approaches contribute to the understanding of the morphological plasticity of seagrasses versus genetic differentiation.},
}
@article {pmid22253812,
year = {2012},
author = {Maia, VH and Mata, CS and Franco, LO and Cardoso, MA and Cardoso, SR and Hemerly, AS and Ferreira, PC},
title = {DNA barcoding Bromeliaceae: achievements and pitfalls.},
journal = {PloS one},
volume = {7},
number = {1},
pages = {e29877},
pmid = {22253812},
issn = {1932-6203},
mesh = {Base Sequence ; Bromeliaceae/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; Databases, Genetic ; Phylogeny ; Plastids/genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: DNA barcoding has been successfully established in animals as a tool for organismal identification and taxonomic clarification. Slower nucleotide substitution rates in plant genomes have made the selection of a DNA barcode for land plants a much more difficult task. The Plant Working Group of the Consortium for the Barcode of Life (CBOL) recommended the two-marker combination rbcL/matK as a pragmatic solution to a complex trade-off between universality, sequence quality, discrimination, and cost.<br><br>It is expected that a system based on any one, or a small number of plastid genes will fail within certain taxonomic groups with low amounts of plastid variation, while performing well in others. We tested the effectiveness of the proposed CBOL Plant Working Group barcoding markers for land plants in identifying 46 bromeliad species, a group rich in endemic species from the endangered Brazilian Atlantic Rainforest. Although we obtained high quality sequences with the suggested primers, species discrimination in our data set was only 43.48%. Addition of a third marker, trnH-psbA, did not show significant improvement. This species identification failure in Bromeliaceaecould also be seen in the analysis of the GenBank's matK data set. Bromeliaceae's sequence divergence was almost three times lower than the observed for Asteraceae and Orchidaceae. This low variation rate also resulted in poorly resolved tree topologies. Among the three Bromeliaceae subfamilies sampled, Tillandsioideae was the only one recovered as a monophyletic group with high bootstrap value (98.6%). Species paraphyly was a common feature in our sampling.<br><br>CONCLUSIONS/SIGNIFICANCE: Our results show that although DNA barcoding is an important tool for biodiversity assessment, it tends to fail in taxonomy complicated and recently diverged plant groups, such as Bromeliaceae. Additional research might be needed to develop markers capable to discriminate species in these complex botanical groups.},
}
@article {pmid22253699,
year = {2012},
author = {Tänzler, R and Sagata, K and Surbakti, S and Balke, M and Riedel, A},
title = {DNA barcoding for community ecology--how to tackle a hyperdiverse, mostly undescribed Melanesian fauna.},
journal = {PloS one},
volume = {7},
number = {1},
pages = {e28832},
pmid = {22253699},
issn = {1932-6203},
mesh = {Animals ; *Biota ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; Databases as Topic ; Electron Transport Complex IV/genetics ; Genetic Markers ; Geography ; Likelihood Functions ; Melanesia ; Models, Biological ; Molecular Sequence Data ; New Guinea ; Sequence Analysis, DNA ; Species Specificity ; Weevils/*genetics ; },
abstract = {BACKGROUND: Trigonopterus weevils are widely distributed throughout Melanesia and hyperdiverse in New Guinea. They are a dominant feature in natural forests, with narrow altitudinal zonation. Their use in community ecology has been precluded by the "taxonomic impediment".<br><br>We sampled >6,500 specimens from seven areas across New Guinea; 1,002 specimens assigned to 270 morphospecies were DNA sequenced. Objective clustering of a refined dataset (excluding nine cryptic species) at 3% threshold revealed 324 genetic clusters (DNA group count relative to number of morphospecies&#x200a;=&#x200a;20.0% overestimation of species diversity, or 120.0% agreement) and 85.6% taxonomic accuracy (the proportion of DNA groups that "perfectly" agree with morphology-based species hypotheses). Agreement and accuracy were best at an 8% threshold. GMYC analysis revealed 328 entities (21.5% overestimation) with 227 perfect GMYC entities (84.1% taxonomic accuracy). Both methods outperform the parataxonomist (19% underestimation; 31.6% taxonomic accuracy). The number of species found in more than one sampling area was highest in the Eastern Highlands and Huon (S&#xf8;rensen similarity index 0.07, 4 shared species); &#x2153; of all areas had no species overlap. Success rates of DNA barcoding methods were lowest when species showed a pronounced geographical structure. In general, Trigonopterus show high &#x3b1; and &#x3b2;-diversity across New Guinea.<br><br>CONCLUSIONS/SIGNIFICANCE: DNA barcoding is an excellent tool for biodiversity surveys but success rates might drop when closer localities are included. Hyperdiverse Trigonopterus are a useful taxon for evaluating forest remnants in Melanesia, allowing finer-grained analyses than would be possible with vertebrate taxa commonly used to date. Our protocol should help establish other groups of hyperdiverse fauna as target taxa for community ecology. Sequencing delivers objective data on taxa of incredible diversity but mostly without a solid taxonomic foundation and should help pave the road for the eventual formal naming of new species.},
}
@article {pmid22245612,
year = {2012},
author = {Sharma, SK and Dkhar, J and Kumaria, S and Tandon, P and Rao, SR},
title = {Assessment of phylogenetic inter-relationships in the genus Cymbidium (Orchidaceae) based on internal transcribed spacer region of rDNA.},
journal = {Gene},
volume = {495},
number = {1},
pages = {10-15},
doi = {10.1016/j.gene.2011.12.052},
pmid = {22245612},
issn = {1879-0038},
mesh = {Base Sequence ; DNA, Ribosomal Spacer/*genetics ; Molecular Sequence Data ; Orchidaceae/*classification/genetics ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Sequence data obtained from nrITS region were used to assess phylogenetic inter-relationships and infrageneric classification of ten Cymbidium species collected from north-east India. The final aligned data matrix of combined ITS 1, 5.8S and ITS 2 yielded 684 characters. The ITS 1 and ITS 2 regions showed variable sequence lengths and G+C content (%). The 5.8S region was found to be more conserved (98.71%) followed by ITS 1 (86.12%) and ITS 2 (69.40%). ITS 2 recorded highest percentage of parsimony informative sites (7.46%), high sequence divergence with indels (24.63%), high number of transitions and transversions. ITS sequence data determined the phylogeny of Asiatic Cymbidiums with high bootstrap values. All three proposed subgenera could be distinguished clearly by all four (MP, ML, NJ, and BI) phylogenetic methods. This study validates the utility of ITS rDNA region as a reliable indicator of phylogenetic relationships, especially ITS 2 as probable DNA barcode at higher levels and can serve as an additional approach for identification of broader range of plant taxa especially orchids.},
}
@article {pmid22243808,
year = {2012},
author = {Brown, SD and Collins, RA and Boyer, S and Lefort, MC and Malumbres-Olarte, J and Vink, CJ and Cruickshank, RH},
title = {Spider: an R package for the analysis of species identity and evolution, with particular reference to DNA barcoding.},
journal = {Molecular ecology resources},
volume = {12},
number = {3},
pages = {562-565},
doi = {10.1111/j.1755-0998.2011.03108.x},
pmid = {22243808},
issn = {1755-0998},
mesh = {Classification/*methods ; Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; Molecular Diagnostic Techniques/*methods ; *Software ; },
abstract = {Spider: SPecies IDentity and Evolution in R is a new R package implementing a number of useful analyses for DNA barcoding studies and associated research into species delimitation and speciation. Included are functions essential for generating important summary statistics from DNA barcode data, assessing specimen identification efficacy, and for testing and optimizing divergence threshold limits. In terms of investigating evolutionary and taxonomic questions, techniques for assessing diagnostic nucleotides and probability of reciprocal monophyly are also provided. Additionally, a sliding window function offers opportunities to analyse information across a gene, essential for marker design in degraded DNA studies. Spider capitalizes on R's extensible ethos and offers an integrated platform ideal for the analysis of both nucleotide and morphological data. The program can be obtained from the comprehensive R archive network (CRAN, http://cran.r-project.org) and from the R-Forge package development site (http://spider.r-forge.r-project.org/).},
}
@article {pmid22239735,
year = {2011},
author = {Nagoshi, RN and Brambila, J and Meagher, RL},
title = {Use of DNA barcodes to identify invasive armyworm Spodoptera species in Florida.},
journal = {Journal of insect science (Online)},
volume = {11},
number = {},
pages = {154},
pmid = {22239735},
issn = {1536-2442},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Environmental Monitoring ; Florida ; Introduced Species ; Male ; Spodoptera/*classification/genetics ; },
abstract = {A critical component for sustaining adequate food production is the protection of local agriculture from invasive pest insects. Essential to this goal is the ability to accurately distinguish foreign from closely related domestic species, a process that has traditionally required identification using diagnostic morphological "keys" that can be both subtle and labor-intensive. This is the case for the Lepidopteran group of insects represented by Spodoptera, a genus of Noctuidae "armyworm" moths that includes several important agricultural pests. Two of the most destructive species, Spodoptera littoralis (Boisduval) (Lepidoptera: Noctuidae) and S. litura (F.) are not yet established in North America. To facilitate the monitoring for these pests, the feasibility of using DNA barcoding methodology for distinguishing between domestic and foreign Spodoptera species was tested. A DNA barcoding database was derived for a subset of Spodoptera species native to Florida, with an emphasis on those attracted to pheromone blends developed for S. litura or S. littoralis. These were then compared to the barcode sequences of S. litura collected from Taiwan and S. littoralis from Portugal. Consistent discrimination of the different species was obtained with phenetic relationships produced that were generally in agreement with phylogenetic studies using morphological characteristics. The data presented here indicate that DNA barcoding has the potential to be an efficient and accurate supplement to morphological methods for the identification of invasive Spodoptera pests in North America.},
}
@article {pmid22238595,
year = {2012},
author = {Carolan, JC and Murray, TE and Fitzpatrick, &#xda; and Crossley, J and Schmidt, H and Cederberg, B and McNally, L and Paxton, RJ and Williams, PH and Brown, MJ},
title = {Colour patterns do not diagnose species: quantitative evaluation of a DNA barcoded cryptic bumblebee complex.},
journal = {PloS one},
volume = {7},
number = {1},
pages = {e29251},
pmid = {22238595},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Bees/anatomy &amp; histology/*classification/*genetics/*physiology ; Body Size/genetics ; Color ; DNA Barcoding, Taxonomic/*methods/standards ; Genome, Insect/physiology ; Phylogeny ; Pigmentation/*physiology ; Sequence Analysis, DNA ; Species Specificity ; Thorax/anatomy &amp; histology ; },
abstract = {Cryptic diversity within bumblebees (Bombus) has the potential to undermine crucial conservation efforts designed to reverse the observed decline in many bumblebee species worldwide. Central to such efforts is the ability to correctly recognise and diagnose species. The B. lucorum complex (Bombus lucorum, B. cryptarum and B. magnus) comprises one of the most abundant and important group of wild plant and crop pollinators in northern Europe. Although the workers of these species are notoriously difficult to diagnose morphologically, it has been claimed that queens are readily diagnosable from morphological characters. Here we assess the value of colour-pattern characters in species identification of DNA-barcoded queens from the B. lucorum complex. Three distinct molecular operational taxonomic units were identified each representing one species. However, no uniquely diagnostic colour-pattern character state was found for any of these three molecular units and most colour-pattern characters showed continuous variation among the units. All characters previously deemed to be unique and diagnostic for one species were displayed by specimens molecularly identified as a different species. These results presented here raise questions on the reliability of species determinations in previous studies and highlights the benefits of implementing DNA barcoding prior to ecological, taxonomic and conservation studies of these important key pollinators.},
}
@article {pmid22237533,
year = {2012},
author = {Knapp, M and Stiller, M and Meyer, M},
title = {Generating barcoded libraries for multiplex high-throughput sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {840},
number = {},
pages = {155-170},
doi = {10.1007/978-1-61779-516-9_19},
pmid = {22237533},
issn = {1940-6029},
mesh = {Base Sequence ; DNA/chemistry/*genetics ; DNA Barcoding, Taxonomic ; Fossils ; *Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Multiplex Polymerase Chain Reaction/methods ; },
abstract = {Molecular barcoding is an essential tool to use the high throughput of next generation sequencing platforms optimally in studies involving more than one sample. Various barcoding strategies allow for the incorporation of short recognition sequences (barcodes) into sequencing libraries, either by ligation or polymerase chain reaction (PCR). Here, we present two approaches optimized for generating barcoded sequencing libraries from low copy number extracts and amplification products typical of ancient DNA studies.},
}
@article {pmid22235317,
year = {2012},
author = {Core, A and Runckel, C and Ivers, J and Quock, C and Siapno, T and Denault, S and Brown, B and Derisi, J and Smith, CD and Hafernik, J},
title = {A new threat to honey bees, the parasitic phorid fly Apocephalus borealis.},
journal = {PloS one},
volume = {7},
number = {1},
pages = {e29639},
pmid = {22235317},
issn = {1932-6203},
support = {//Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; Bees/*parasitology ; DNA Barcoding, Taxonomic ; Diptera/classification/genetics/*physiology ; Female ; Homing Behavior ; Larva/physiology ; Oligonucleotide Array Sequence Analysis ; Species Specificity ; Time Factors ; },
abstract = {Honey bee colonies are subject to numerous pathogens and parasites. Interaction among multiple pathogens and parasites is the proposed cause for Colony Collapse Disorder (CCD), a syndrome characterized by worker bees abandoning their hive. Here we provide the first documentation that the phorid fly Apocephalus borealis, previously known to parasitize bumble bees, also infects and eventually kills honey bees and may pose an emerging threat to North American apiculture. Parasitized honey bees show hive abandonment behavior, leaving their hives at night and dying shortly thereafter. On average, seven days later up to 13 phorid larvae emerge from each dead bee and pupate away from the bee. Using DNA barcoding, we confirmed that phorids that emerged from honey bees and bumble bees were the same species. Microarray analyses of honey bees from infected hives revealed that these bees are often infected with deformed wing virus and Nosema ceranae. Larvae and adult phorids also tested positive for these pathogens, implicating the fly as a potential vector or reservoir of these honey bee pathogens. Phorid parasitism may affect hive viability since 77% of sites sampled in the San Francisco Bay Area were infected by the fly and microarray analyses detected phorids in commercial hives in South Dakota and California's Central Valley. Understanding details of phorid infection may shed light on similar hive abandonment behaviors seen in CCD.},
}
@article {pmid22233209,
year = {2012},
author = {Galimberti, A and Romano, DF and Genchi, M and Paoloni, D and Vercillo, F and Bizzarri, L and Sassera, D and Bandi, C and Genchi, C and Ragni, B and Casiraghi, M},
title = {Integrative taxonomy at work: DNA barcoding of taeniids harboured by wild and domestic cats.},
journal = {Molecular ecology resources},
volume = {12},
number = {3},
pages = {403-413},
doi = {10.1111/j.1755-0998.2011.03110.x},
pmid = {22233209},
issn = {1755-0998},
mesh = {Animals ; Cat Diseases/parasitology ; Cats ; Cyclooxygenase 1/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/chemistry/genetics ; Italy ; Molecular Sequence Data ; Sequence Analysis, DNA ; Taenia/*classification/*genetics/isolation &amp; purification ; Taeniasis/parasitology/veterinary ; },
abstract = {In modern taxonomy, DNA barcoding is particularly useful where biometric parameters are difficult to determine or useless owing to the poor quality of samples. These situations are frequent in parasitology. Here, we present an integrated study, based on both DNA barcoding and morphological analysis, on cestodes belonging to the genus Taenia, for which biodiversity is still largely underestimated. In particular, we characterized cestodes from Italian wildcats (Felis silvestris silvestris), free-ranging domestic cats (Felis silvestris catus) and hybrids populations. Adult taeniids were collected by post-mortem examinations of the hosts and morphologically identified as Taenia taeniaeformis. We produced cox1 barcode sequences for all the analysed specimens, and we compared them with reference sequences of individuals belonging to the genus Taenia retrieved from GenBank. In order to evaluate the performance of a DNA barcoding approach to discriminate these parasites, the strength of correlation between species identification based on classical morphology and the molecular divergence of cox1 sequences was measured. Our study provides clear evidence that DNA barcoding is highly efficient to reveal the presence of cryptic lineages within already-described taeniid species. Indeed, we detected three well-defined molecular lineages within the whole panel of specimens morphologically identified as T. taeniaeformis. Two of these molecular groups were already identified by other authors and should be ranked at species level. The third molecular group encompasses only samples collected in Italy during this study, and it represents a third candidate species, still morphologically undescribed.},
}
@article {pmid22232921,
year = {2011},
author = {Batishcheva, NM and Kartavtsev, IuF and Bogutskaia, NG},
title = {[Phylogenetic analysis of Altai osmans of the genus Oreoleuciscus (Pisces, Cyprinidae, Leuciscinae), based on the analysis of the cytochrome oxidase 1 gene (Co-1) sequence].},
journal = {Genetika},
volume = {47},
number = {10},
pages = {1335-1345},
pmid = {22232921},
issn = {0016-6758},
mesh = {Animals ; Bayes Theorem ; Cyprinidae/*classification/*genetics ; Electron Transport Complex IV/classification/*genetics ; Evolution, Molecular ; Genes, Mitochondrial/genetics ; Lakes ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; },
abstract = {Molecular genetic analysis of Altai osmans of the genus Oreoleuciscus from two different parts of the range was carried out. In this study, based on the mitochondrial Co-1 gene sequence, a total of 25 fish specimens belonging to four genera were examined: (1) O. humilis, 2 specimens; O. potanini, 13 specimens; (2) Pseudaspius leptocephalus, 1 specimen; (3) Tribolodon brandtii, T. hakonensis, and T. sachalinensis from the GenBank database, 8 speciens; and (4) Leuciscus waleckii, 1 specimen (used as an outgroup). The p-distances were very low both within and between the species: (1) 0.20 +/- 0.03%; (2) 0.40 +/- 0.12%; and (1-2) 0.80 +/- 0.04%. To visualize the relationships among all of the species examined, the neighbor joining (NJ), maximum parsimony (MP), Bayesian (BA), and maximum likelihood (ML) trees were constructed. The results obtained using these methods were very similar. It was demonstrated that species assignment of the individuals (barcoding) with the help Co-1 gene was effective, despite of very low divergence of the two osman taxa, which was comparable with typical intraspecific values in other animal groups. Taxonomic status of O. potanini and O. humilis requires further investigation with paying attention to low genetic distances between these species along with the lack of material from sympatric parts of the ranges.},
}
@article {pmid22232676,
year = {2012},
author = {Shiroguchi, K and Jia, TZ and Sims, PA and Xie, XS},
title = {Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {109},
number = {4},
pages = {1347-1352},
pmid = {22232676},
issn = {1091-6490},
support = {R01 HG005097/HG/NHGRI NIH HHS/United States ; RC2 HG005613/HG/NHGRI NIH HHS/United States ; HG005097-01/HG/NHGRI NIH HHS/United States ; 1RC2HG005613-01/HG/NHGRI NIH HHS/United States ; },
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Complementary/genetics ; Escherichia coli/genetics ; Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing/methods ; Polymerase Chain Reaction/methods ; Sequence Analysis, RNA/*methods ; Systems Biology/*methods ; },
abstract = {RNA sequencing (RNA-Seq) is a powerful tool for transcriptome profiling, but is hampered by sequence-dependent bias and inaccuracy at low copy numbers intrinsic to exponential PCR amplification. We developed a simple strategy for mitigating these complications, allowing truly digital RNA-Seq. Following reverse transcription, a large set of barcode sequences is added in excess, and nearly every cDNA molecule is uniquely labeled by random attachment of barcode sequences to both ends. After PCR, we applied paired-end deep sequencing to read the two barcodes and cDNA sequences. Rather than counting the number of reads, RNA abundance is measured based on the number of unique barcode sequences observed for a given cDNA sequence. We optimized the barcodes to be unambiguously identifiable, even in the presence of multiple sequencing errors. This method allows counting with single-copy resolution despite sequence-dependent bias and PCR-amplification noise, and is analogous to digital PCR but amendable to quantifying a whole transcriptome. We demonstrated transcriptome profiling of Escherichia coli with more accurate and reproducible quantification than conventional RNA-Seq.},
}
@article {pmid22221866,
year = {2012},
author = {Puillandre, N and Bouchet, P and Boisselier-Dubayle, MC and Brisset, J and Buge, B and Castelin, M and Chagnoux, S and Christophe, T and Corbari, L and Lambourdière, J and Lozouet, P and Marani, G and Rivasseau, A and Silva, N and Terryn, Y and Tillier, S and Utge, J and Samadi, S},
title = {New taxonomy and old collections: integrating DNA barcoding into the collection curation process.},
journal = {Molecular ecology resources},
volume = {12},
number = {3},
pages = {396-402},
doi = {10.1111/j.1755-0998.2011.03105.x},
pmid = {22221866},
issn = {1755-0998},
mesh = {Animals ; Computational Biology/methods ; Crustacea/*classification/*genetics ; DNA/genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Mollusca/*classification/*genetics ; *Museums ; Paris ; },
abstract = {Because they house large biodiversity collections and are also research centres with sequencing facilities, natural history museums are well placed to develop DNA barcoding best practices. The main difficulty is generally the vouchering system: it must ensure that all data produced remain attached to the corresponding specimen, from the field to publication in articles and online databases. The Museum National d'Histoire Naturelle in Paris is one of the leading laboratories in the Marine Barcode of Life (MarBOL) project, which was used as a pilot programme to include barcode collections for marine molluscs and crustaceans. The system is based on two relational databases. The first one classically records the data (locality and identification) attached to the specimens. In the second one, tissue-clippings, DNA extractions (both preserved in 2D barcode tubes) and PCR data (including primers) are linked to the corresponding specimen. All the steps of the process [sampling event, specimen identification, molecular processing, data submission to Barcode Of Life Database (BOLD) and GenBank] are thus linked together. Furthermore, we have developed several web-based tools to automatically upload data into the system, control the quality of the sequences produced and facilitate the submission to online databases. This work is the result of a joint effort from several teams in the Museum National d'Histoire Naturelle (MNHN), but also from a collaborative network of taxonomists and molecular systematists outside the museum, resulting in the vouchering so far of ∼41,000 sequences and the production of ∼11,000 COI sequences.},
}
@article {pmid22221342,
year = {2012},
author = {Stoof-Leichsenring, KR and Epp, LS and Trauth, MH and Tiedemann, R},
title = {Hidden diversity in diatoms of Kenyan Lake Naivasha: a genetic approach detects temporal variation.},
journal = {Molecular ecology},
volume = {21},
number = {8},
pages = {1918-1930},
doi = {10.1111/j.1365-294X.2011.05412.x},
pmid = {22221342},
issn = {1365-294X},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA Primers ; Diatoms/classification/*genetics/isolation &amp; purification/physiology ; *Genetic Variation ; Geologic Sediments/*microbiology ; Haplotypes ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Kenya ; Lakes/*microbiology ; Lead Radioisotopes/analysis ; Phylogeny ; Polymerase Chain Reaction/methods ; Ribulose-Bisphosphate Carboxylase/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {This study provides insights into the morphological and genetic diversity in diatoms occurring in core sediments from tropical lakes in Kenya. We developed a genetic survey technique specific for diatoms utilizing a short region (76-67 bp) of the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene as genetic barcode. Our analyses (i) validated the use of rbcL as a barcoding marker for diatoms, applied to sediment samples, (ii) showed a significant correlation between the results obtained by morphological and molecular data and (iii) indicated temporal variation in diatom assemblages on the inter- and intra-specific level. Diatom assemblages from a short core from Lake Naivasha show a drastic shift over the last 200 years, as littoral species (e.g. Navicula) are replaced by more planktonic ones (e.g. Aulacoseira). Within that same period, we detected periodic changes in the respective frequencies of distinct haplotype groups of Navicula, which coincide with wet and dry periods of Lake Naivasha between 1820 and 1938 AD. Our genetic analyses on historical lake sediments revealed inter- and intra-specific variation in diatoms, which is partially hidden behind single morphotypes. The occurrence of particular genetic lineages is probably correlated with environmental factors.},
}
@article {pmid22209540,
year = {2012},
author = {Boenigk, J and Ereshefsky, M and Hoef-Emden, K and Mallet, J and Bass, D},
title = {Concepts in protistology: species definitions and boundaries.},
journal = {European journal of protistology},
volume = {48},
number = {2},
pages = {96-102},
doi = {10.1016/j.ejop.2011.11.004},
pmid = {22209540},
issn = {1618-0429},
mesh = {Eukaryota/*physiology ; Species Specificity ; *Terminology as Topic ; },
abstract = {This paper summarises the Symposium 'Concepts in Protistology', during the VI European Congress of Protistology, Berlin, 25-29 July 2011. There is an increasing focus on cataloguing the number of species on earth, species barcoding initiatives, and the increasing need to reconcile molecular with morphological data in protists within a taxonomic framework. We identify several obstructions to defining species in protists, including the high incidence of asexuality, high levels of both morphological conservation and evolutionary convergence, high levels of genetic diversity that cannot so far be correlated with phenotypic characters, conflicting signals between both genetic and phenotypic taxonomic markers, and different requirements and challenges of species definition in different protist groups. We assert that there is no species 'category' for protists, and recommend that a working definition of species is clarified on a case-by-case basis. Thus, a consensus approach may emerge within protist groups, but any one approach is unlikely to encompass a wide phylogenetic range. However, as long as clarity of intent and method is maintained, the utility of the term 'species' in protists will also be maintained as a reproducible and convenient (if artificial) way of referring to particular lineages within a tightly defined context.},
}
@article {pmid22205827,
year = {2011},
author = {Riegert-Johnson, D and Roberts, M},
title = {Barcoding allows immediate downloading of PowerPoint presentations by smart phones.},
journal = {Medical education online},
volume = {16},
number = {},
pages = {},
doi = {10.3402/meo.v16i0.11743},
pmid = {22205827},
issn = {1087-2981},
mesh = {*Cell Phone ; Education, Medical ; *Electronic Data Processing ; Information Storage and Retrieval/*methods ; *Software ; },
}
@article {pmid22194213,
year = {2011},
author = {Yu, DB and Chen, R and Kaleri, HA and Jiang, BC and Xu, HX and Du, WX},
title = {Testing the utility of mitochondrial cytochrome oxidase subunit 1 sequences for phylogenetic estimates of relationships between crane (Grus) species.},
journal = {Genetics and molecular research : GMR},
volume = {10},
number = {4},
pages = {4048-4062},
doi = {10.4238/2011.December.21.7},
pmid = {22194213},
issn = {1676-5680},
mesh = {Animals ; Birds/*genetics/metabolism ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry ; Electron Transport Complex IV/*genetics/metabolism ; Evolution, Molecular ; Genes, Mitochondrial ; Genetic Variation ; Mitochondria/*enzymology/metabolism ; *Phylogeny ; Protein Subunits/genetics ; },
abstract = {Morphology and biogeography are widely used in animal taxonomy. Recent study has suggested that a DNA-based identification system, using a 648-bp portion of the mitochondrial gene cytochrome oxidase subunit 1 (CO1), also known as the barcoding gene, can aid in the resolution of inferences concerning phylogenetic relationships and for identification of species. However, the effectiveness of DNA barcoding for identifying crane species is unknown. We amplified and sequenced 894-bp DNA fragments of CO1 from Grus japonensis (Japanese crane), G. grus (Eurasian crane), G. monacha (hooded crane), G. canadensis (sandhill crane), G. leucogeranus (Siberian crane), and Balearica pavonina (crowned crane), along with those of 15 species obtained from GenBank and DNA barcoding, to construct four algorithms using Tringa stagnatilis, Scolopax rusticola, and T. erythropus as outgroups. The four phylum profiles showed good resolution of the major taxonomic groups. We concluded that reconstruction of the molecular phylogenetic tree can be helpful for classification and that CO1 sequences are suitable for studying the molecular evolution of cranes. Although support for several deeper branches was limited, CO1 data gave remarkably good separations, especially considering that our analysis was based on just a fragment of the gene and that CO1 has generally been viewed as useful only for resolving shallow divergences.},
}
@article {pmid22189587,
year = {2012},
author = {Bennett, DH and Wu, XM and Teague, CH and Lee, K and Cassady, DL and Ritz, B and Hertz-Picciotto, I},
title = {Passive sampling methods to determine household and personal care product use.},
journal = {Journal of exposure science &amp; environmental epidemiology},
volume = {22},
number = {2},
pages = {148-160},
doi = {10.1038/jes.2011.40},
pmid = {22189587},
issn = {1559-064X},
mesh = {Air Pollutants/analysis ; California ; Child ; Child, Preschool ; Databases, Factual ; Electronic Data Processing/methods ; Environmental Exposure/*analysis ; Environmental Monitoring/*methods ; Family Characteristics ; Household Products/*analysis/*statistics &amp; numerical data ; Humans ; Longitudinal Studies ; Middle Aged ; },
abstract = {Traditionally, use of household and personal care products has been collected through questionnaires, which is very time consuming, a burden on participants, and prone to recall bias. As part of the SUPERB Project (Study of Use of Products and Exposure-Related Behaviors), a novel platform was developed using bar codes to quickly and reliably determine what household and personal care products people have in their homes and determine the amount used over a 1-week period. We evaluated the acceptability and feasibility of our methodology in a longitudinal field study that included 47 California households, 30 with young children and 17 with an older adult. Acceptability was defined by refusal rates; feasibility was evaluated in terms of readable bar codes, useful product information in our database for all readable barcodes, and ability to find containers at both the start and end of the week. We found 63% of personal care products and 87% of the household care products had readable barcodes with 47% and 41% having sufficient data for product identification, respectively and secondly, the amount used could be determined most of the time. We present distributions for amount used by product category and compare inter- and intra-person variability. In summary, our method appears to be appropriate, acceptable, and useful for gathering information related to potential exposures stemming from the use of personal and household care products. A very low drop-out rate suggests that this methodology can be useful in longitudinal studies of exposure to household and personal care products.},
}
@article {pmid22186975,
year = {2012},
author = {Boehme, P and Amendt, J and Zehner, R},
title = {The use of COI barcodes for molecular identification of forensically important fly species in Germany.},
journal = {Parasitology research},
volume = {110},
number = {6},
pages = {2325-2332},
pmid = {22186975},
issn = {1432-1955},
mesh = {Animals ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Diptera/*classification/*genetics ; Electron Transport Complex IV/genetics ; Entomology/*methods ; Forensic Sciences/*methods ; Genotype ; Germany ; Humans ; Molecular Sequence Data ; Polymorphism, Genetic ; Sequence Analysis, DNA ; },
abstract = {Deoxyribonucleic acid (DNA)-based insect identification has become a routine and accurate tool in forensic entomology. In the present study, we demonstrate the utility of the mitochondrial DNA cytochrome oxidase I gene "barcoding region" as a universal marker for molecular identification of forensically important Diptera. We analyzed 111 specimens belonging to 13 species originating from Frankfurt am Main, Germany (Calliphoridae: Calliphora vicina, Calliphora vomitoria, Lucilia ampullacea, Lucilia caesar, Lucilia illustris, Lucilia sericata, Lucilia silvarum, Phormia regina, Protophormia terraenovae; Piophilidae: Parapiophila vulgaris; Muscidae: Hydrotaea dentipes, Hydrotaea ignava, Hydrotaea similis). Intraspecific variation ranged from 0 to 1.17% and interspecific variation occurred between 1.17% and 15.21%. Although differences within species were generally less than among species, divergence percentages overlapped due to low interspecific nucleotide divergence of the recently separated sister species L. caesar and L. illustris. However, all species formed distinct monophyletic clades and thus the cytochrome oxidase 1 (COI) barcode has been shown suitable for clear differentiation and identification of forensically relevant Diptera in Germany.},
}
@article {pmid22183677,
year = {2012},
author = {Rintoul, TL and Eggertson, QA and Lévesque, CA},
title = {Multigene phylogenetic analyses to delimit new species in fungal plant pathogens.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {835},
number = {},
pages = {549-569},
doi = {10.1007/978-1-61779-501-5_34},
pmid = {22183677},
issn = {1940-6029},
mesh = {DNA, Fungal/genetics/isolation &amp; purification ; Fungi/*genetics ; Multigene Family ; *Phylogeny ; Plants/*microbiology ; Sequence Analysis, DNA/methods ; Species Specificity ; },
abstract = {Supporting the identification of unknown strains or specimens by sequencing a genetic marker commonly used for phylogenetics or DNA barcoding is now standard practice for mycologists and plant pathologists. Does one have a new species when a strain differs by a few base pairs when compared to reference sequences from taxonomically well-characterized species that do not differ morphologically from this new strain? If variation at the intra- and interspecific levels for the locus used for identification is already understood for all the closely related species, it is possible to make a reliable prediction of a new species status, but ultimately this question can only be properly addressed by determining the presence or absence of gene flow among a group of strains of the putative new species and strains of previously delimited species. The Phylogenetic Species Concept (PSC) and its assessment using multigene phylogeny and Genealogical Concordance Phylogenetic Species Recognition (GCPSR) are the basis for this chapter. The theoretical framework and a variety of tools to apply these concepts are explained, to assist in the assessment of whether a species is distinct or new when confronted with some sequence divergence from reference data.},
}
@article {pmid22182989,
year = {2012},
author = {Kwong, S and Srivathsan, A and Vaidya, G and Meier, R},
title = {Is the COI barcoding gene involved in speciation through intergenomic conflict?.},
journal = {Molecular phylogenetics and evolution},
volume = {62},
number = {3},
pages = {1009-1012},
doi = {10.1016/j.ympev.2011.11.034},
pmid = {22182989},
issn = {1095-9513},
mesh = {Amino Acid Substitution ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Species Specificity ; },
abstract = {We here test the proposition that changes in the barcoding region of COI are commonly involved in speciation through intergenomic conflict. We demonstrate that this is unlikely given that even with incomplete taxon sampling, 78-90% of closely-related animal species have identical COI amino acid sequences. In addition, in those cases where amino acid substitutions between closely related species are observed, the inter- and intra-specific substitution patterns are very similar and/or lack consistent differences in the number, position and type of amino acid change. Overall, we conclude that there is little evidence for a widespread involvement of the barcoding gene in speciation.},
}
@article {pmid22177214,
year = {2011},
author = {Brumbaugh, CD and Kim, HJ and Giovacchini, M and Pourmand, N},
title = {NanoStriDE: normalization and differential expression analysis of NanoString nCounter data.},
journal = {BMC bioinformatics},
volume = {12},
number = {},
pages = {479},
pmid = {22177214},
issn = {1471-2105},
support = {P01-35HG000205/HG/NHGRI NIH HHS/United States ; },
mesh = {Gene Expression Profiling/*methods ; Humans ; Internet ; Nanotechnology/methods ; Oligonucleotide Array Sequence Analysis ; },
abstract = {BACKGROUND: The nCounter analysis system (NanoString Technologies, Seattle, WA) is a technology that enables the digital quantification of multiplexed target RNA molecules using color-coded molecular barcodes and single-molecule imaging. This system gives discrete counts of RNA transcripts and is capable of providing a high level of precision and sensitivity at less than one transcript copy per cell.<br><br>RESULTS: We have designed a web application compatible with any modern web browser that accepts the raw count data produced by the NanoString nCounter analysis system, normalizes it according to guidelines provided by NanoString Technologies, performs differential expression analysis on the normalized data, and provides a heatmap of the results from the differential expression analysis.<br><br>CONCLUSION: NanoStriDE allows biologists to take raw data produced by a NanoString nCounter analysis system and easily interpret differential expression analysis of this data represented through a heatmap. NanoStriDE is freely accessible to use on the NanoStriDE website and is available to use under the GPL v2 license.},
}
@article {pmid22174860,
year = {2011},
author = {Mabragaña, E and Díaz de Astarloa, JM and Hanner, R and Zhang, J and González Castro, M},
title = {DNA barcoding identifies Argentine fishes from marine and brackish waters.},
journal = {PloS one},
volume = {6},
number = {12},
pages = {e28655},
pmid = {22174860},
issn = {1932-6203},
mesh = {Animals ; Argentina ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Fishes/*classification/*genetics ; Geography ; Haplotypes/genetics ; Phylogeny ; *Salts ; *Seawater ; },
abstract = {BACKGROUND: DNA barcoding has been advanced as a promising tool to aid species identification and discovery through the use of short, standardized gene targets. Despite extensive taxonomic studies, for a variety of reasons the identification of fishes can be problematic, even for experts. DNA barcoding is proving to be a useful tool in this context. However, its broad application is impeded by the need to construct a comprehensive reference sequence library for all fish species. Here, we make a regional contribution to this grand challenge by calibrating the species discrimination efficiency of barcoding among 125 Argentine fish species, representing nearly one third of the known fauna, and examine the utility of these data to address several key taxonomic uncertainties pertaining to species in this region.<br><br>Specimens were collected and morphologically identified during crusies conducted between 2005 and 2008. The standard BARCODE fragment of COI was amplified and bi-directionally sequenced from 577 specimens (mean of 5 specimens/species), and all specimens and sequence data were archived and interrogated using analytical tools available on the Barcode of Life Data System (BOLD; www.barcodinglife.org). Nearly all species exhibited discrete clusters of closely related haplogroups which permitted the discrimination of 95% of the species (i.e. 119/125) examined while cases of shared haplotypes were detected among just three species-pairs. Notably, barcoding aided the identification of a new species of skate, Dipturus argentinensis, permitted the recognition of Genypterus brasiliensis as a valid species and questions the generic assignment of Paralichthys isosceles.<br><br>CONCLUSIONS/SIGNIFICANCE: This study constitutes a significant contribution to the global barcode reference sequence library for fishes and demonstrates the utility of barcoding for regional species identification. As an independent assessment of alpha taxonomy, barcodes provide robust support for most morphologically based taxon concepts and also highlight key areas of taxonomic uncertainty worthy of reappraisal.},
}
@article {pmid22171763,
year = {2012},
author = {Pompanon, F and Deagle, BE and Symondson, WO and Brown, DS and Jarman, SN and Taberlet, P},
title = {Who is eating what: diet assessment using next generation sequencing.},
journal = {Molecular ecology},
volume = {21},
number = {8},
pages = {1931-1950},
doi = {10.1111/j.1365-294X.2011.05403.x},
pmid = {22171763},
issn = {1365-294X},
mesh = {Animals ; DNA/*genetics ; DNA Barcoding, Taxonomic/*methods ; *Diet ; Feces ; *Food Chain ; Sequence Analysis, DNA/*methods ; },
abstract = {The analysis of food webs and their dynamics facilitates understanding of the mechanistic processes behind community ecology and ecosystem functions. Having accurate techniques for determining dietary ranges and components is critical for this endeavour. While visual analyses and early molecular approaches are highly labour intensive and often lack resolution, recent DNA-based approaches potentially provide more accurate methods for dietary studies. A suite of approaches have been used based on the identification of consumed species by characterization of DNA present in gut or faecal samples. In one approach, a standardized DNA region (DNA barcode) is PCR amplified, amplicons are sequenced and then compared to a reference database for identification. Initially, this involved sequencing clones from PCR products, and studies were limited in scale because of the costs and effort required. The recent development of next generation sequencing (NGS) has made this approach much more powerful, by allowing the direct characterization of dozens of samples with several thousand sequences per PCR product, and has the potential to reveal many consumed species simultaneously (DNA metabarcoding). Continual improvement of NGS technologies, on-going decreases in costs and current massive expansion of reference databases make this approach promising. Here we review the power and pitfalls of NGS diet methods. We present the critical factors to take into account when choosing or designing a suitable barcode. Then, we consider both technical and analytical aspects of NGS diet studies. Finally, we discuss the validation of data accuracy including the viability of producing quantitative data.},
}
@article {pmid22166208,
year = {2012},
author = {Nyberg, LK and Persson, F and Berg, J and Bergström, J and Fransson, E and Olsson, L and Persson, M and Stålnacke, A and Wigenius, J and Tegenfeldt, JO and Westerlund, F},
title = {A single-step competitive binding assay for mapping of single DNA molecules.},
journal = {Biochemical and biophysical research communications},
volume = {417},
number = {1},
pages = {404-408},
doi = {10.1016/j.bbrc.2011.11.128},
pmid = {22166208},
issn = {1090-2104},
mesh = {Base Composition ; Benzoxazoles/chemistry ; Binding, Competitive ; DNA/*chemistry ; Fluorescence ; Fluorescent Dyes/chemistry ; *Microfluidic Analytical Techniques ; Netropsin/chemistry ; Quinolinium Compounds/chemistry ; },
abstract = {Optical mapping of genomic DNA is of relevance for a plethora of applications such as scaffolding for sequencing and detection of structural variations as well as identification of pathogens like bacteria and viruses. For future clinical applications it is desirable to have a fast and robust mapping method based on as few steps as possible. We here demonstrate a single-step method to obtain a DNA barcode that is directly visualized using nanofluidic devices and fluorescence microscopy. Using a mixture of YOYO-1, a bright DNA dye, and netropsin, a natural antibiotic with very high AT specificity, we obtain a DNA map with a fluorescence intensity profile along the DNA that reflects the underlying sequence. The netropsin binds to AT-tetrads and blocks these binding sites from YOYO-1 binding which results in lower fluorescence intensity from AT-rich regions of the DNA. We thus obtain a DNA barcode that is dark in AT-rich regions and bright in GC-rich regions with kilobasepair resolution. We demonstrate the versatility of the method by obtaining a barcode on DNA from the phage T4 that captures its circular permutation and agrees well with its known sequence.},
}
@article {pmid22163311,
year = {2011},
author = {Tavares, ES and Gonçalves, P and Miyaki, CY and Baker, AJ},
title = {DNA barcode detects high genetic structure within neotropical bird species.},
journal = {PloS one},
volume = {6},
number = {12},
pages = {e28543},
pmid = {22163311},
issn = {1932-6203},
mesh = {Algorithms ; Animals ; Birds/*genetics/physiology ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Geography ; Likelihood Functions ; Models, Genetic ; Phylogeny ; Phylogeography/methods ; South America ; Species Specificity ; Tropical Climate ; },
abstract = {BACKGROUND: Towards lower latitudes the number of recognized species is not only higher, but also phylogeographic subdivision within species is more pronounced. Moreover, new genetically isolated populations are often described in recent phylogenies of Neotropical birds suggesting that the number of species in the region is underestimated. Previous COI barcoding of Argentinean bird species showed more complex patterns of regional divergence in the Neotropical than in the North American avifauna.<br><br>METHODS AND FINDINGS: Here we analyzed 1,431 samples from 561 different species to extend the Neotropical bird barcode survey to lower latitudes, and detected even higher geographic structure within species than reported previously. About 93% (520) of the species were identified correctly from their DNA barcodes. The remaining 41 species were not monophyletic in their COI sequences because they shared barcode sequences with closely related species (N&#x200a;=&#x200a;21) or contained very divergent clusters suggestive of putative new species embedded within the gene tree (N&#x200a;=&#x200a;20). Deep intraspecific divergences overlapping with among-species differences were detected in 48 species, often with samples from large geographic areas and several including multiple subspecies. This strong population genetic structure often coincided with breaks between different ecoregions or areas of endemism.<br><br>CONCLUSIONS: The taxonomic uncertainty associated with the high incidence of non-monophyletic species and discovery of putative species obscures studies of historical patterns of species diversification in the Neotropical region. We showed that COI barcodes are a valuable tool to indicate which taxa would benefit from more extensive taxonomic revisions with multilocus approaches. Moreover, our results support hypotheses that the megadiversity of birds in the region is associated with multiple geographic processes starting well before the Quaternary and extending to more recent geological periods.},
}
@article {pmid22155423,
year = {2012},
author = {Astrin, JJ and Stüben, PE and Misof, B and Wägele, JW and Gimnich, F and Raupach, MJ and Ahrens, D},
title = {Exploring diversity in cryptorhynchine weevils (Coleoptera) using distance-, character- and tree-based species delineation.},
journal = {Molecular phylogenetics and evolution},
volume = {63},
number = {1},
pages = {1-14},
doi = {10.1016/j.ympev.2011.11.018},
pmid = {22155423},
issn = {1095-9513},
mesh = {Animals ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; *Genetic Speciation ; *Genetic Variation ; Weevils/*classification/genetics ; },
abstract = {Species boundaries are studied in a group of beetles, the western Palaearctic Cryptorhynchinae. We test for congruence of 'traditionally' identified morphospecies with species inferred through parsimony networks, distance-based clustering and the ultrametric tree-based generalized mixed yule-coalescent (GMYC) approach. For that purpose, we sequenced two variable fragments of mitochondrial DNA (CO1 and 16S) for a total of 791 specimens in 217 species of Cryptorhynchinae. Parsimony networks, morphology-calibrated distance clusters and the different tree-based species inferences all achieved low congruence with morphospecies, at best 60%. Although the degree of match with morphospecies was often similar for the different approaches, the composition of clusters partially varied. A barcoding gap was absent in morphospecies-oriented distances as well as for GMYC species clusters. This demonstrates that not only erroneous taxonomic assignments, incomplete lineage sorting, hybridization, or insufficient sampling can compromise distance-based identification, but also differences in speciation rates and uneven tree structure. The initially low match between morphospecies and the different molecular species delineation methods in this case study shows the necessity of combining the output of various methods in an integrative approach. Thereby we obtain an idea about the reliability of the different results and signals, which enables us to fine-tune sampling, delineation technique and data collection, and to identify species that require taxonomic revision.},
}
@article {pmid22150605,
year = {2012},
author = {Guo, YD and Cai, JF and Meng, FM and Chang, YF and Gu, Y and Lan, LM and Liang, L and Wen, JF},
title = {Identification of forensically important flesh flies based on a shorter fragment of the cytochrome oxidase subunit I gene in China.},
journal = {Medical and veterinary entomology},
volume = {26},
number = {3},
pages = {307-313},
doi = {10.1111/j.1365-2915.2011.01003.x},
pmid = {22150605},
issn = {1365-2915},
mesh = {Animals ; China ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Entomology/*methods ; Forensic Sciences/*methods ; Insect Proteins/genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sarcophagidae/*classification/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {With the development of molecular identification, there has been a great deal of discussion about the feature of the mitochondrial DNA (mtDNA) fragments. Although longer fragments may minimize stochastic variation across taxa and be more likely to reflect broader patterns of nucleotide divergence, shorter fragments have many advantages, such as quick, easy and economical. Extensive application of long mtDNA segments for species identification cannot always be achieved as a result of constraints in time and money. In the present study, a molecular identification method involving the sequencing of a 272-bp 'barcode' fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene from 55 specimens, representing 7 Chinese sarcophagid species from varying populations, was evaluated. Phylogenetic analysis of the sequenced segments showed that all sarcophagid specimens were properly assigned into seven species, which indicated the possibility of separation congeneric species with the short fragments. The results of this research will be instrumental for the implementation of the Chinese Sarcophagidae database.},
}
@article {pmid22145866,
year = {2012},
author = {Che, J and Chen, HM and Yang, JX and Jin, JQ and Jiang, K and Yuan, ZY and Murphy, RW and Zhang, YP},
title = {Universal COI primers for DNA barcoding amphibians.},
journal = {Molecular ecology resources},
volume = {12},
number = {2},
pages = {247-258},
doi = {10.1111/j.1755-0998.2011.03090.x},
pmid = {22145866},
issn = {1755-0998},
mesh = {Amphibian Proteins/*genetics ; Amphibians/*classification/genetics ; Animals ; DNA Barcoding, Taxonomic/instrumentation/*methods ; DNA Primers/*genetics ; Electron Transport Complex IV/*genetics ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; },
abstract = {DNA barcoding is a proven tool for the rapid and unambiguous identification of species, which is essential for many activities including the vouchering tissue samples in the genome 10K initiative, genealogical reconstructions, forensics and biodiversity surveys, among many other applications. A large-scale effort is underway to barcode all amphibian species using the universally sequenced DNA region, a partial fragment of mitochondrial cytochrome oxidase subunit I COI. This fragment is desirable because it appears to be superior to 16S for barcoding, at least for some groups of salamanders. The barcoding of amphibians is essential in part because many species are now endangered. Unfortunately, existing primers for COI often fail to achieve this goal. Herein, we report two new pairs of primers (➀, ➁) that in combination serve to universally amplify and sequence all three orders of Chinese amphibians as represented by 36 genera. This taxonomic diversity, which includes caecilians, salamanders and frogs, suggests that the new primer pairs will universally amplify COI for the vast majority species of amphibians.},
}
@article {pmid22144201,
year = {2012},
author = {Linsen, SE and Cuppen, E},
title = {Methods for small RNA preparation for digital gene expression profiling by next-generation sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {822},
number = {},
pages = {205-217},
doi = {10.1007/978-1-61779-427-8_14},
pmid = {22144201},
issn = {1940-6029},
mesh = {Base Sequence ; DNA/isolation &amp; purification ; DNA, Complementary ; Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Polymerase Chain Reaction/methods ; Polynucleotides/chemistry ; RNA, Small Untranslated/*analysis/*isolation &amp; purification ; Sequence Analysis, RNA/*methods ; },
abstract = {Digital gene expression (DGE) profiling techniques are playing an eminent role in the detection, localization, and differential expression quantification of many small RNA species, including microRNAs (1-3). Procedures in small RNA library preparation techniques typically include adapter ligation by RNA ligase, followed by reverse transcription and amplification by PCR. This chapter describes three protocols that were successfully applied to generate small RNA sequencing SOLiD(TM) libraries. The Ambion SREK(TM)-adopted protocol can be readily used for multiplexing samples; the modban-based protocol is cost-efficient, but biased toward certain microRNAs; the poly(A)-based protocol is less biased, but less precise because of the A-tail that is introduced. In summary, each of these protocols has its advantages and disadvantages with respect to the ease of including barcodes, costs, and outcome.},
}
@article {pmid22139666,
year = {2012},
author = {Ferri, G and Corradini, B and Alù, M},
title = {Capillary electrophoresis of multigene barcoding chloroplast markers for species identification of botanical trace evidence.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {830},
number = {},
pages = {253-263},
doi = {10.1007/978-1-61779-461-2_18},
pmid = {22139666},
issn = {1940-6029},
mesh = {Botany/*methods ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/isolation &amp; purification ; Databases, Genetic ; Electrophoresis, Agar Gel ; Electrophoresis, Capillary/*methods ; Genes, Chloroplast/*genetics ; Genes, Plant/*genetics ; Genetic Markers ; Polymerase Chain Reaction ; Species Specificity ; },
abstract = {The analysis of nonhuman biological evidence both animal and botanical to find out the correct species of a sample comes as a great help to crime investigators. Particularly, forensic botany may be useful in many criminal and civil cases, e.g., for linking an individual to a crime scene or physical evidence to a geographic location, or tracking marijuana distribution patterns.Despite many molecular techniques for species identification so far applied, botanical evidences are still overlooked by forensic scientists due to the lack of reproducible and efficient protocols standardized across a wide range of different organisms and among different laboratories.Recently, the term "DNA barcoding" has been coined to describe the use of a short gene sequence from a standardized region of the genome as a molecular tool for species identification. DNA barcodes have been successfully applied to a number of animal groups and introduced in forensic science with the application of the mitochondrial gene COI. Building on this success, ongoing investigations have searched for the best barcode to apply to all land plants. Here we describe the basic protocol based on amplification and sequence analysis of barcoding markers for land plants considering the latest developments of Plant DNA barcoding Project. The aim of this chapter is to provide forensic scientists an accurate and reliable tool for assigning unidentified botanical specimens to the correct species as powerful mainstay in investigations, increasing the contributions from nonhuman DNA to forensics.},
}
@article {pmid22138764,
year = {2012},
author = {Kim, S and Song, KH and Ree, HI and Kim, W},
title = {A DNA barcode library for Korean Chironomidae (Insecta: Diptera) and indexes for defining barcode gap.},
journal = {Molecules and cells},
volume = {33},
number = {1},
pages = {9-17},
pmid = {22138764},
issn = {0219-1032},
mesh = {Animals ; Chironomidae/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; Gene Library ; Nucleic Acid Amplification Techniques ; Republic of Korea ; },
abstract = {Non-biting midges (Diptera: Chironomidae) are a diverse population that commonly causes respiratory allergies in humans. Chironomid larvae can be used to indicate freshwater pollution, but accurate identification on the basis of morphological characteristics is difficult. In this study, we constructed a mitochondrial cytochrome c oxidase subunit I (COI)-based DNA barcode library for Korean chironomids. This library consists of 211 specimens from 49 species, including adults and unidentified larvae. The interspecies and intraspecies COI sequence variations were analyzed. Sophisticated indexes were developed in order to properly evaluate indistinct barcode gaps that are created by insufficient sampling on both the interspecies and intraspecies levels and by variable mutation rates across taxa. In a variety of insect datasets, these indexes were useful for re-evaluating large barcode datasets and for defining COI barcode gaps. The COI-based DNA barcode library will provide a rapid and reliable tool for the molecular identification of Korean chironomid species. Furthermore, this reverse-taxonomic approach will be improved by the continuous addition of other speceis' sequences to the library.},
}
@article {pmid22136257,
year = {2012},
author = {Yang, JB and Wang, YP and Möller, M and Gao, LM and Wu, D},
title = {Applying plant DNA barcodes to identify species of Parnassia (Parnassiaceae).},
journal = {Molecular ecology resources},
volume = {12},
number = {2},
pages = {267-275},
doi = {10.1111/j.1755-0998.2011.03095.x},
pmid = {22136257},
issn = {1755-0998},
mesh = {Celastraceae/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; Phylogeny ; },
abstract = {DNA barcoding is a technique to identify species by using standardized DNA sequences. In this study, a total of 105 samples, representing 30 Parnassia species, were collected to test the effectiveness of four proposed DNA barcodes (rbcL, matK, trnH-psbA and ITS) for species identification. Our results demonstrated that all four candidate DNA markers have a maximum level of primer universality and sequencing success. As a single DNA marker, the ITS region provided the highest species resolution with 86.7%, followed by trnH-psbA with 73.3%. The combination of the core barcode regions, matK+rbcL, gave the lowest species identification success (63.3%) among any combination of multiple markers and was found unsuitable as DNA barcode for Parnassia. The combination of ITS+trnH-psbA achieved the highest species discrimination with 90.0% resolution (27 of 30 sampled species), equal to the four-marker combination and higher than any two or three marker combination including rbcL or matK. Therefore, matK and rbcL should not be used as DNA barcodes for the species identification of Parnassia. Based on the overall performance, the combination of ITS+trnH-psbA is proposed as the most suitable DNA barcode for identifying Parnassia species. DNA barcoding is a useful technique and provides a reliable and effective mean for the discrimination of Parnassia species, and in combination with morphology-based taxonomy, will be a robust approach for tackling taxonomically complex groups. In the light of our findings, we found among the three species not identified a possible cryptic speciation event in Parnassia.},
}
@article {pmid22136234,
year = {2011},
author = {Skelton, PH and Swartz, ER},
title = {Walking the tightrope: trends in African freshwater systematic ichthyology.},
journal = {Journal of fish biology},
volume = {79},
number = {6},
pages = {1413-1435},
doi = {10.1111/j.1095-8649.2011.03085.x},
pmid = {22136234},
issn = {1095-8649},
mesh = {Africa ; Animals ; *Classification ; *Fishes ; *Fresh Water ; Zoology/*trends ; },
abstract = {Africa is blessed with an abundance and rich diversity of freshwater fishes, reflecting its Gondwanan history and geographical position astride the equator. Africa is, however, relatively poorly serviced scientifically, in this respect presenting a challenge to the tension between conserving biodiversity and sustainable development. Biosystematics has experienced several paradigm shifts in the past half century, including the rise of cladistics and more recently the adoption of molecular DNA applications to taxonomy and phylogeny and the assembly and manipulation of large data sets in an era of major development of bioinformatics. The richness of African biodiversity is a magnet to the global systematic community that, to a degree, offsets the disadvantage of an impoverished indigenous scientific capacity. Conservation biology, however, is rooted more closely to the local situation and therefore requires indigenous taxonomic services that are inevitably scarce. Balancing this network of tensions between scientific knowledge generation and application is like walking a tightrope for existing African scientific resources, and to cope it is essential to embrace modern innovative approaches such as barcoding to identify organisms. This paper considers the historical development of African freshwater ichthyology, presents a suite of recent examples illustrating trends in systematic ichthyology in Africa and draws conclusions to suggest that both traditional and new-age approaches to taxonomy are necessary for a complete understanding and appreciation of African freshwater fish diversity and its conservation. The chosen examples also suggest that the tensions between the approaches can be effectively managed provided exponents work collaboratively. The emerging evidence indicates that the combined skills and insight of complex scientific teams including systematists, ecologists, molecular biologists and earth scientists are needed to resolve the deep complexity of evolution in terms of space, time and form.},
}
@article {pmid22132140,
year = {2011},
author = {Prado, BR and Pozo, C and Valdez-Moreno, M and Hebert, PD},
title = {Beyond the colours: discovering hidden diversity in the Nymphalidae of the Yucatan Peninsula in Mexico through DNA barcoding.},
journal = {PloS one},
volume = {6},
number = {11},
pages = {e27776},
pmid = {22132140},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Butterflies/*classification/*genetics ; Cluster Analysis ; Costa Rica ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Larva/genetics ; Mexico ; Phylogeny ; Pigmentation/*genetics ; Species Specificity ; },
abstract = {BACKGROUND: Recent studies have demonstrated the utility of DNA barcoding in the discovery of overlooked species and in the connection of immature and adult stages. In this study, we use DNA barcoding to examine diversity patterns in 121 species of Nymphalidae from the Yucatan Peninsula in Mexico. Our results suggest the presence of cryptic species in 8 of these 121 taxa. As well, the reference database derived from the analysis of adult specimens allowed the identification of nymphalid caterpillars providing new details on host plant use.<br><br>We gathered DNA barcode sequences from 857 adult Nymphalidae representing 121 different species. This total includes four species (Adelpha iphiclus, Adelpha malea, Hamadryas iphtime and Taygetis laches) that were initially overlooked because of their close morphological similarity to other species. The barcode results showed that each of the 121 species possessed a diagnostic array of barcode sequences. In addition, there was evidence of cryptic taxa; seven species included two barcode clusters showing more than 2% sequence divergence while one species included three clusters. All 71 nymphalid caterpillars were identified to a species level by their sequence congruence to adult sequences. These caterpillars represented 16 species, and included Hamadryas julitta, an endemic species from the Yucatan Peninsula whose larval stages and host plant (Dalechampia schottii, also endemic to the Yucatan Peninsula) were previously unknown.<br><br>CONCLUSIONS/SIGNIFICANCE: This investigation has revealed overlooked species in a well-studied museum collection of nymphalid butterflies and suggests that there is a substantial incidence of cryptic species that await full characterization. The utility of barcoding in the rapid identification of caterpillars also promises to accelerate the assembly of information on life histories, a particularly important advance for hyperdiverse tropical insect assemblages.},
}
@article {pmid22130886,
year = {2012},
author = {Ramsköld, D and Kavak, E and Sandberg, R},
title = {How to analyze gene expression using RNA-sequencing data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {802},
number = {},
pages = {259-274},
doi = {10.1007/978-1-61779-400-1_17},
pmid = {22130886},
issn = {1940-6029},
mesh = {Animals ; Computational Biology/methods ; Gene Expression Profiling/*methods ; Genome ; Humans ; Internet ; Mice ; Sequence Analysis, RNA/*methods ; Transcriptome ; User-Computer Interface ; },
abstract = {RNA-Seq is arising as a powerful method for transcriptome analyses that will eventually make microarrays obsolete for gene expression analyses. Improvements in high-throughput sequencing and efficient sample barcoding are now enabling tens of samples to be run in a cost-effective manner, competing with microarrays in price, excelling in performance. Still, most studies use microarrays, partly due to the ease of data analyses using programs and modules that quickly turn raw microarray data into spreadsheets of gene expression values and significant differentially expressed genes. Instead RNA-Seq data analyses are still in its infancy and the researchers are facing new challenges and have to combine different tools to carry out an analysis. In this chapter, we provide a tutorial on RNA-Seq data analysis to enable researchers to quantify gene expression, identify splice junctions, and find novel transcripts using publicly available software. We focus on the analyses performed in organisms where a reference genome is available and discuss issues with current methodology that have to be solved before RNA-Seq data can utilize its full potential.},
}
@article {pmid22130576,
year = {2012},
author = {Kosakyan, A and Heger, TJ and Leander, BS and Todorov, M and Mitchell, EA and Lara, E},
title = {COI barcoding of Nebelid testate amoebae (Amoebozoa: Arcellinida): extensive cryptic diversity and redefinition of the Hyalospheniidae Schultze.},
journal = {Protist},
volume = {163},
number = {3},
pages = {415-434},
doi = {10.1016/j.protis.2011.10.003},
pmid = {22130576},
issn = {1618-0941},
mesh = {Amoebozoa/*classification/enzymology/genetics/*isolation &amp; purification ; *Biodiversity ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Molecular Sequence Data ; Phylogeny ; Protozoan Proteins/*genetics ; Sphagnopsida/*parasitology ; },
abstract = {We used Cytochrome Oxidase Subunit 1 (COI) to assess the phylogenetic relationships and taxonomy of Nebela sensu stricto and similar taxa (Nebela group, Arcellinida) in order to clarify the taxonomic validity of morphological characters. The COI data not only successfully separated all studied morphospecies but also revealed the existence of several potential cryptic species. The taxonomic implications of the results are: (1) Genus Nebela is paraphyletic and will need to be split into at least two monophyletic assemblages when taxon sampling is further expanded. (2) Genus Quadrulella, one of the few arcellinid genera building its shell from self-secreted siliceous elements, and the mixotrophic Hyalosphenia papilio branch within the Nebela group in agreement with the general morphology of their shell and the presence of an organic rim around the aperture (synapomorphy for Hyalospheniidae). We thus synonymise Hyalospheniidae and Nebelidae. Hyalospheniidae takes precedence and now includes Hyalosphenia, Quadrulella (previously in the Lesquereusiidae) and all Nebelidae with the exception of Argynnia and Physochila. Leptochlamys is Arcellinida incertae sedis. We describe a new genus Padaungiella Lara et Todorov and a new species Nebela meisterfeldi n. sp. Heger et Mitchell and revise the taxonomic position (and rank) of several taxa. These results show that the traditional morphology-based taxonomy underestimates the diversity within the Nebela group, and that phylogenetic relationships are best inferred from shell shape rather than from the material used to build the shell.},
}
@article {pmid22119585,
year = {2012},
author = {Pereira, JA and Quach, S and Hamid, JS and Heidebrecht, CL and Quan, SD and Nassif, J and Diniz, AJ and Van Exan, R and Malawski, J and Gentry, A and Finkelstein, M and Guay, M and Buckeridge, DL and Bettinger, JA and Kalailieff, D and Kwong, JC and , },
title = {Exploring the feasibility of integrating barcode scanning technology into vaccine inventory recording in seasonal influenza vaccination clinics.},
journal = {Vaccine},
volume = {30},
number = {4},
pages = {794-802},
doi = {10.1016/j.vaccine.2011.11.043},
pmid = {22119585},
issn = {1873-2518},
support = {IRR - 96974//Canadian Institutes of Health Research/Canada ; },
mesh = {Drug Storage/*methods/*standards ; *Equipment and Supplies ; Health Personnel ; Humans ; Influenza Vaccines/*administration &amp; dosage ; Ontario ; Personal Satisfaction ; Vaccination/*standards ; },
abstract = {BACKGROUND: In response to the need for improved quality of vaccine inventory and client immunization records, barcodes containing a unique identifier and lot number will be placed on all vaccine vials in Canada. We conducted feasibility studies to examine integration of barcode scanning into inventory recording workflow for mass immunization clinics.<br><br>METHODS: During the 2010-2011 seasonal influenza vaccination campaign, Ontario public health units (PHUs) using an electronic immunization system were randomized to record clinic inventory data (including vaccine lot number and expiry date) through: (i) barcode scanning of vials; or (ii) drop-down menus. A third group of PHUs recording vaccine inventory on paper served as an observation arm. We visited a sample of clinics within each PHU to assess barcode readability, method efficiency and data quality. Clinic staff completed a survey examining method perceptions.<br><br>RESULTS: We observed 20 clinics using barcode scanning to record inventory data (eight PHUs), 20 using drop-down menus (eight PHUs), and 21 using paper forms (five PHUs). Mean time spent recording data per vial was 4.3s using barcode scanners with 1.3 scan attempts per vial, 0.5s using drop-down menus, and 1.7s using paper. Few errors were observed. Sixty-four perception surveys were completed by inventory staff; barcode scanning users indicated fairly strong overall satisfaction with the method (74%), and the majority agreed that barcode scanning improved client safety (84%) and inventory record accuracy (77%). However, 38% of barcode scanning users felt that individually scanning vials took longer than the other approaches and 26% indicated that this increased time would discourage them from adopting the method.<br><br>CONCLUSIONS: Our study demonstrated good readability of barcodes but scanning individual vials for high-volume clinics was time-consuming; modifying the process will improve feasibility to facilitate adoption in Canada, while serving as an example for other countries considering this technology.},
}
@article {pmid22117405,
year = {2011},
author = {Haider, N and Wilkinson, MJ},
title = {A set of plastid DNA-specific universal primers for flowering plants.},
journal = {Genetika},
volume = {47},
number = {9},
pages = {1204-1215},
pmid = {22117405},
issn = {0016-6758},
mesh = {DNA Primers/*genetics ; DNA, Plant/*genetics ; Genetic Loci/*physiology ; Genetic Markers ; Magnoliopsida/*genetics ; Plastids/*genetics ; Polymerase Chain Reaction/methods ; },
abstract = {MatKand rbcL are recommended as the official barcode loci for higher plants but there remains a need for additional universal markers. We generated a series of 84 new universal primers targeting 42 plastid loci that all yielded single amplicons when applied to DNA templates from 19 diverse higher plant families. Marker utility ultimately depends on sequence variability, with rapidly evolving loci being useful for barcoding or biogeographic applications and more conserved loci being better suited to deep phylogeny reconstruction. Whereas excessive size variation is undesirable for many applications, modest size variability caused by indels and the sequence variation frequently associated with indels are highly desirable. We therefore performed a quick screen of the markers for size and sequence variation using pooled DNA templates from 96 taxonomically diverse species. All markers produced little or no size variation (consistent with the presence of minor indels). The seven regions exhibiting most size variation in pooled (rpl23&amp;rpl2.1, 16S, 23S, 4.5S&amp;5S, petB&amp;D, and rpl2, rpoCl and trnK introns) were then amplified for all species individually, confirming the pooled template results. When the most variable loci (introns of trnK and rpoC1) were sequenced for all 96 species, a high level of sequence variation (nucleotide substitutions and indels) was observed among congeneric species groups for both loci. Both markers therefore have potential as supplementary barcode markers.},
}
@article {pmid22115445,
year = {2011},
author = {Alper, I and Frenette, M and Labrie, S},
title = {Ribosomal DNA polymorphisms in the yeast Geotrichum candidum.},
journal = {Fungal biology},
volume = {115},
number = {12},
pages = {1259-1269},
doi = {10.1016/j.funbio.2011.09.002},
pmid = {22115445},
issn = {1878-6146},
mesh = {Animals ; Base Sequence ; Cattle ; Cheese/microbiology ; DNA, Fungal/*genetics ; DNA, Ribosomal/*genetics ; Evolution, Molecular ; Geotrichum/classification/*genetics/isolation &amp; purification ; Milk/microbiology ; Molecular Sequence Data ; Phylogeny ; *Polymorphism, Genetic ; Zea mays/microbiology ; },
abstract = {The dimorphic yeast Geotrichum candidum (teleomorph: Galactomyces candidus) is commonly used to inoculate washed-rind and bloomy-rind cheeses. However, little is known about the phylogenetic lineage of this microorganism. We have sequenced the complete 18S, 5.8S, 26S ribosomal RNA genes and their internal transcribed spacers (ITS1) and ITS2 regions (5126 nucleotides) from 18 G. candidum strains from various environmental niches, with a focus on dairy strains. Multiple sequence alignments revealed the presence of 60 polymorphic sites, which is generally unusual for ribosomal DNA (rDNA) within a given species because of the concerted evolution mechanism. This mechanism drives genetic homogenization to prevent the divergent evolution of rDNA copies within individuals. While the polymorphisms observed were mainly substitutions, one insertion/deletion (indel) polymorphism was detected in ITS1. No polymorphic sites were detected downstream from this indel site, that is, in 5.8S and ITS2. More surprisingly, many sequence electrophoregrams generated during the sequencing of the rDNA had dual peaks, suggesting that many individuals exhibited intragenomic rDNA variability. The ITS1-5.8S-ITS2 regions of four strains were cloned. The sequence analysis of 68 clones revealed 32 different ITS1-5.8S-ITS2 variants within these four strains. Depending on the strain, from four to twelve variants were detected, indicating that multiple rDNA copies were present in the genomes of these G. candidum strains. These results contribute to the debate concerning the use of the ITS region for barcoding fungi and suggest that community profiling techniques based on rDNA should be used with caution.},
}
@article {pmid22114141,
year = {2011},
author = {Kornberg, TB},
title = {Barcoding Hedgehog for intracellular transport.},
journal = {Science signaling},
volume = {4},
number = {200},
pages = {pe44},
pmid = {22114141},
issn = {1937-9145},
support = {R01 GM030637/GM/NIGMS NIH HHS/United States ; R01 GM077407/GM/NIGMS NIH HHS/United States ; R01 GM105987/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Cholesterol/metabolism ; Hedgehog Proteins/*metabolism ; Humans ; Lipoylation/*physiology ; *Models, Biological ; Palmitic Acid/metabolism ; Protein Processing, Post-Translational/*physiology ; Protein Structure, Tertiary ; Protein Transport/physiology ; Signal Transduction/*physiology ; },
abstract = {Hedgehog, an essential protein for the development of many vertebrate and invertebrate organs, signals at both short and long distances to control growth and patterning. The mechanism by which it moves between source and target cells is not known, but characterization of the covalent modification of its N terminus with palmitate and of its C terminus with cholesterol has led to the suggestion that the lipophilic properties of the modified protein serve to regulate movement after its secretion into the extracellular space. Another interpretation and model is that the C-terminal cholesterol acts to target Hedgehog to an intracellular trafficking pathway that prepares Hedgehog for release in an encapsulated form.},
}
@article {pmid22109553,
year = {2011},
author = {Hollingsworth, PM},
title = {Refining the DNA barcode for land plants.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {108},
number = {49},
pages = {19451-19452},
pmid = {22109553},
issn = {1091-6490},
mesh = {Cycadopsida/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/*genetics ; Magnoliopsida/*genetics ; },
}
@article {pmid22103856,
year = {2011},
author = {Kiontke, KC and Félix, MA and Ailion, M and Rockman, MV and Braendle, C and Pénigault, JB and Fitch, DH},
title = {A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits.},
journal = {BMC evolutionary biology},
volume = {11},
number = {},
pages = {339},
pmid = {22103856},
issn = {1471-2148},
support = {K99 MH082109/MH/NIMH NIH HHS/United States ; R01 GM089972/GM/NIGMS NIH HHS/United States ; 5U01HG004276-04/HG/NHGRI NIH HHS/United States ; K99MH082109/MH/NIMH NIH HHS/United States ; },
mesh = {Animals ; Caenorhabditis/anatomy &amp; histology/*classification/*genetics/physiology ; DNA Barcoding, Taxonomic ; DNA, Helminth/analysis ; DNA, Ribosomal Spacer/analysis ; Flowers ; Fruit ; Genetic Variation ; Herbivory ; Phylogeny ; Plants ; },
abstract = {BACKGROUND: The nematode Caenorhabditis elegans is a major laboratory model in biology. Only ten Caenorhabditis species were available in culture at the onset of this study. Many of them, like C. elegans, were mostly isolated from artificial compost heaps, and their more natural habitat was unknown.<br><br>RESULTS: Caenorhabditis nematodes were found to be proliferating in rotten fruits, flowers and stems. By collecting a large worldwide set of such samples, 16 new Caenorhabditis species were discovered. We performed mating tests to establish biological species status and found some instances of semi-fertile or sterile hybrid progeny. We established barcodes for all species using ITS2 rDNA sequences. By obtaining sequence data for two rRNA and nine protein-coding genes, we determined the likely phylogenetic relationships among the 26 species in culture. The new species are part of two well-resolved sister clades that we call the Elegans super-group and the Drosophilae super-group. We further scored phenotypic characters such as reproductive mode, mating behavior and male tail morphology, and discuss their congruence with the phylogeny. A small space between rays 2 and 3 evolved once in the stem species of the Elegans super-group; a narrow fan and spiral copulation evolved once in the stem species of C. angaria, C. sp. 8 and C. sp. 12. Several other character changes occurred convergently. For example, hermaphroditism evolved three times independently in C. elegans, C. briggsae and C. sp. 11. Several species can co-occur in the same location or even the same fruit. At the global level, some species have a cosmopolitan distribution: C. briggsae is particularly widespread, while C. elegans and C. remanei are found mostly or exclusively in temperate regions, and C. brenneri and C. sp. 11 exclusively in tropical zones. Other species have limited distributions, for example C. sp. 5 appears to be restricted to China, C. sp. 7 to West Africa and C. sp. 8 to the Eastern United States.<br><br>CONCLUSIONS: Caenorhabditis are "fruit worms", not soil nematodes. The 16 new species provide a resource and their phylogeny offers a framework for further studies into the evolution of genomic and phenotypic characters.},
}
@article {pmid22102673,
year = {2011},
author = {Lee, DH and Park, JK and Youn, HN and Lee, YN and Lim, TH and Kim, MS and Lee, JB and Park, SY and Choi, IS and Song, CS},
title = {Surveillance and isolation of HPAI H5N1 from wild Mandarin Ducks (Aix galericulata).},
journal = {Journal of wildlife diseases},
volume = {47},
number = {4},
pages = {994-998},
doi = {10.7589/0090-3558-47.4.994},
pmid = {22102673},
issn = {1943-3700},
mesh = {Animals ; Animals, Wild ; China/epidemiology ; Disease Reservoirs/veterinary/virology ; *Ducks ; Feces/virology ; Female ; Influenza A Virus, H5N1 Subtype/*isolation &amp; purification ; Influenza in Birds/*epidemiology ; Male ; },
abstract = {Highly pathogenic avian influenza (HPAI) H5N1 virus circulates among a variety of free-ranging wild birds and continually poses a threat to animal and human health. During the winter of 2010-2011, we surveyed Korean wild bird habitats. From 728 fresh fecal samples, 14 HPAI H5N1 viruses were identified. The isolates phylogenetically clustered with other recently isolated clade 2.3.2 HPAI H5N1 viruses isolated from wild birds in Mongolia. All HPAI-positive fecal samples were analyzed by DNA barcoding for host-species identification. Twelve of the 14 HPAI-positive samples were typed as Mandarin Duck (Aix galericulata). The high incidence of HPAI subtype H5N1 viruses in wild Mandarin Duck droppings is a novel finding and underscores the need for enhanced avian influenza virus surveillance in wild Mandarin Ducks. Further investigation of the susceptibility of Mandarin Ducks to HPAI H5N1 clade 2.3.2 virus would aid the understanding of HPAI ecology and epidemiology in wild birds.},
}
@article {pmid22100737,
year = {2011},
author = {, and Li, DZ and Gao, LM and Li, HT and Wang, H and Ge, XJ and Liu, JQ and Chen, ZD and Zhou, SL and Chen, SL and Yang, JB and Fu, CX and Zeng, CX and Yan, HF and Zhu, YJ and Sun, YS and Chen, SY and Zhao, L and Wang, K and Yang, T and Duan, GW},
title = {Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {108},
number = {49},
pages = {19641-19646},
pmid = {22100737},
issn = {1091-6490},
mesh = {Cell Nucleus/genetics ; Cycadopsida/classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Chloroplast/classification/genetics ; DNA, Intergenic/classification/genetics ; DNA, Ribosomal Spacer/*genetics ; Databases, Genetic/statistics &amp; numerical data ; Endoribonucleases/classification/genetics ; Magnoliopsida/classification/*genetics ; Nucleotidyltransferases/classification/genetics ; Phylogeny ; Plant Proteins/classification/genetics ; Reproducibility of Results ; Ribulose-Bisphosphate Carboxylase/classification/genetics ; Species Specificity ; },
abstract = {A two-marker combination of plastid rbcL and matK has previously been recommended as the core plant barcode, to be supplemented with additional markers such as plastid trnH-psbA and nuclear ribosomal internal transcribed spacer (ITS). To assess the effectiveness and universality of these barcode markers in seed plants, we sampled 6,286 individuals representing 1,757 species in 141 genera of 75 families (42 orders) by using four different methods of data analysis. These analyses indicate that (i) the three plastid markers showed high levels of universality (87.1-92.7%), whereas ITS performed relatively well (79%) in angiosperms but not so well in gymnosperms; (ii) in taxonomic groups for which direct sequencing of the marker is possible, ITS showed the highest discriminatory power of the four markers, and a combination of ITS and any plastid DNA marker was able to discriminate 69.9-79.1% of species, compared with only 49.7% with rbcL + matK; and (iii) where multiple individuals of a single species were tested, ascriptions based on ITS and plastid DNA barcodes were incongruent in some samples for 45.2% of the sampled genera (for genera with more than one species sampled). This finding highlights the importance of both sampling multiple individuals and using markers with different modes of inheritance. In cases where it is difficult to amplify and directly sequence ITS in its entirety, just using ITS2 is a useful backup because it is easier to amplify and sequence this subset of the marker. We therefore propose that ITS/ITS2 should be incorporated into the core barcode for seed plants.},
}
@article {pmid22096501,
year = {2011},
author = {Costion, C and Ford, A and Cross, H and Crayn, D and Harrington, M and Lowe, A},
title = {Plant DNA barcodes can accurately estimate species richness in poorly known floras.},
journal = {PloS one},
volume = {6},
number = {11},
pages = {e26841},
pmid = {22096501},
issn = {1932-6203},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; Phylogeny ; Plant Proteins/genetics ; Plants/classification/*genetics ; Trees/classification/*genetics ; },
abstract = {BACKGROUND: Widespread uptake of DNA barcoding technology for vascular plants has been slow due to the relatively poor resolution of species discrimination (∼70%) and low sequencing and amplification success of one of the two official barcoding loci, matK. Studies to date have mostly focused on finding a solution to these intrinsic limitations of the markers, rather than posing questions that can maximize the utility of DNA barcodes for plants with the current technology.<br><br>Here we test the ability of plant DNA barcodes using the two official barcoding loci, rbcLa and matK, plus an alternative barcoding locus, trnH-psbA, to estimate the species diversity of trees in a tropical rainforest plot. Species discrimination accuracy was similar to findings from previous studies but species richness estimation accuracy proved higher, up to 89%. All combinations which included the trnH-psbA locus performed better at both species discrimination and richness estimation than matK, which showed little enhanced species discriminatory power when concatenated with rbcLa. The utility of the trnH-psbA locus is limited however, by the occurrence of intraspecific variation observed in some angiosperm families to occur as an inversion that obscures the monophyly of species.<br><br>CONCLUSIONS/SIGNIFICANCE: We demonstrate for the first time, using a case study, the potential of plant DNA barcodes for the rapid estimation of species richness in taxonomically poorly known areas or cryptic populations revealing a powerful new tool for rapid biodiversity assessment. The combination of the rbcLa and trnH-psbA loci performed better for this purpose than any two-locus combination that included matK. We show that although DNA barcodes fail to discriminate all species of plants, new perspectives and methods on biodiversity value and quantification may overshadow some of these shortcomings by applying barcode data in new ways.},
}
@article {pmid22095605,
year = {2011},
author = {Al-Qurainy, F and Khan, S and Tarroum, M and Al-Hemaid, FM and Ali, MA},
title = {Molecular authentication of the medicinal herb Ruta graveolens (Rutaceae) and an adulterant using nuclear and chloroplast DNA markers.},
journal = {Genetics and molecular research : GMR},
volume = {10},
number = {4},
pages = {2806-2816},
doi = {10.4238/2011.November.10.3},
pmid = {22095605},
issn = {1676-5680},
mesh = {DNA, Chloroplast/*genetics/isolation &amp; purification ; DNA, Ribosomal/*genetics/isolation &amp; purification ; Euphorbia/genetics ; Genetic Markers ; *Polymerase Chain Reaction ; Ruta/*genetics ; Sequence Alignment/methods ; *Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Dried parts of different plant species often look alike, especially in powdered form, making them very difficult to identify. Ruta graveolens, sold as a dried medicinal herb, can be adulterated with Euphorbia dracunculoides. The genomic DNA was isolated from the leaf powder (100 mg each) using the modified CTAB method. Internal transcribed spacer sequences of nuclear ribosomal DNA (nrDNA-ITS), and chloroplast spacer sequences (rpoB and rpoC1) are regarded as potential genes for plant DNA barcoding. We amplified and sequenced these spacer sequences and confirmed the sequences with a BLAST search. Sequence alignment was performed using ClustalX to look for differences in the sequences. A DNA marker was developed based on rpoB and rpoC1 of the nrDNA-ITS for the identification of the adulterant E. dracunculoides in samples of R. graveolens that are sold in local herbal markets. Sequence-characterized amplified region markers of 289 and 264 bp for R. graveolens and 424 bp for E. dracunculoides were developed from dissimilar sequences of this nrDNA-ITS to speed up the authentication process. This marker successfully distinguished these species in extracted samples with as little as 5 ng DNA/μL extract.},
}
@article {pmid22092527,
year = {2011},
author = {MacGillivary, ML and Kaczmarska, I},
title = {Survey of the efficacy of a short fragment of the rbcL gene as a supplemental DNA barcode for diatoms.},
journal = {The Journal of eukaryotic microbiology},
volume = {58},
number = {6},
pages = {529-536},
doi = {10.1111/j.1550-7408.2011.00585.x},
pmid = {22092527},
issn = {1550-7408},
mesh = {DNA Barcoding, Taxonomic/*methods ; Diatoms/*classification/*genetics ; Molecular Sequence Data ; RNA, Ribosomal, 18S/*genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; Sensitivity and Specificity ; Sequence Analysis, DNA ; },
abstract = {DNA barcoding is a tool that uses a short, standard segment of DNA to identify organisms. In diatoms, a consensus on an appropriate DNA barcode has not been reached, but several markers show promise. These include the 5.8S gene plus a fragment of the internal transcribed spacer 2 (ITS-2) of nuclear-encoded ribosomal RNA, a 420-bp segment of the 18S rRNA gene, and a 748-bp fragment at the 3'-end of the ribulose bisophosphate carboxylase large subunit (rbcL) gene. Here, we tested a 540-bp fragment 417-bp downstream of the start codon of the rbcL gene for its efficacy in distinguishing diatom species in a wide range of taxa. Overall, 381 sequences representing 66 genera and 245 species from the classes Mediophyceae and Bacillariophyceae were examined. Intra/interspecific thresholds were set at p = 0.01 differences per site (diff./site) for Mediophyceae and p = 0.02 diff./site for Bacillariophyceae and correctly segregated 96% and 93% of morphological congeners, respectively. When testing reproductively isolated or biological species, which are only available from Bacillariophyceae, 80% of species were discriminated. Therefore, we concluded that, alone, the rbcL region tested herein as potential a DNA barcode was not a sufficient discriminator of all diatoms. We suggest that this fragment could be used in a dual-locus barcode with the more variable 5.8S+ITS-2 to discriminate species without sufficient interspecific divergences in the tested rbcL region and to provide insight into species identity from a separately evolved genome.},
}
@article {pmid22090378,
year = {2012},
author = {Parkinson, NJ and Maslau, S and Ferneyhough, B and Zhang, G and Gregory, L and Buck, D and Ragoussis, J and Ponting, CP and Fischer, MD},
title = {Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA.},
journal = {Genome research},
volume = {22},
number = {1},
pages = {125-133},
pmid = {22090378},
issn = {1549-5469},
support = {090532//Wellcome Trust/United Kingdom ; G0900747/MRC_/Medical Research Council/United Kingdom ; MC_U137761446/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; DNA, Bacterial/*chemistry/genetics/isolation &amp; purification ; Escherichia coli K12/*chemistry/genetics ; *Gene Library ; Mice ; Sequence Analysis, DNA/*methods ; },
abstract = {New sequencing technologies can address diverse biomedical questions but are limited by a minimum required DNA input of typically 1 μg. We describe how sequencing libraries can be reproducibly created from 20 pg of input DNA using a modified transpososome-mediated fragmentation technique. Resulting libraries incorporate in-line bar-coding, which facilitates sample multiplexes that can be sequenced using Illumina platforms with the manufacturer's sequencing primer. We demonstrate this technique by providing deep coverage sequence of the Escherichia coli K-12 genome that shows equivalent target coverage to a 1-μg input library prepared using standard Illumina methods. Reducing template quantity does, however, increase the proportion of duplicate reads and enriches coverage in low-GC regions. This finding was confirmed with exhaustive resequencing of a mouse library constructed from 20 pg of gDNA input (about seven haploid genomes) resulting in ∼0.4-fold statistical coverage of uniquely mapped fragments. This implies that a near-complete coverage of the mouse genome is obtainable with this approach using 20 genomes as input. Application of this new method now allows genomic studies from low mass samples and routine preparation of sequencing libraries from enrichment procedures.},
}
@article {pmid22087242,
year = {2011},
author = {Moftah, M and Abdel Aziz, SH and Elramah, S and Favereaux, A},
title = {Classification of sharks in the Egyptian Mediterranean waters using morphological and DNA barcoding approaches.},
journal = {PloS one},
volume = {6},
number = {11},
pages = {e27001},
pmid = {22087242},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Databases, Genetic ; Egypt ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial ; Internet ; Mediterranean Sea ; Sharks/*classification/genetics ; },
abstract = {The identification of species constitutes the first basic step in phylogenetic studies, biodiversity monitoring and conservation. DNA barcoding, i.e. the sequencing of a short standardized region of DNA, has been proposed as a new tool for animal species identification. The present study provides an update on the composition of shark in the Egyptian Mediterranean waters off Alexandria, since the latest study to date was performed 30 years ago, DNA barcoding was used in addition to classical taxonomical methodologies. Thus, 51 specimen were DNA barcoded for a 667 bp region of the mitochondrial COI gene. Although DNA barcoding aims at developing species identification systems, some phylogenetic signals were apparent in the data. In the neighbor-joining tree, 8 major clusters were apparent, each of them containing individuals belonging to the same species, and most with 100% bootstrap value. This study is the first to our knowledge to use DNA barcoding of the mitochondrial COI gene in order to confirm the presence of species Squalus acanthias, Oxynotus centrina, Squatina squatina, Scyliorhinus canicula, Scyliorhinus stellaris, Mustelus mustelus, Mustelus punctulatus and Carcharhinus altimus in the Egyptian Mediterranean waters. Finally, our study is the starting point of a new barcoding database concerning shark composition in the Egyptian Mediterranean waters (Barcoding of Egyptian Mediterranean Sharks [BEMS], http://www.boldsystems.org/views/projectlist.php?&amp;#Barcoding%20Fish%20%28FishBOL%29).},
}
@article {pmid22087233,
year = {2011},
author = {Rosani, U and Varotto, L and Rossi, A and Roch, P and Novoa, B and Figueras, A and Pallavicini, A and Venier, P},
title = {Massively parallel amplicon sequencing reveals isotype-specific variability of antimicrobial peptide transcripts in Mytilus galloprovincialis.},
journal = {PloS one},
volume = {6},
number = {11},
pages = {e26680},
pmid = {22087233},
issn = {1932-6203},
mesh = {*Alternative Splicing ; Animals ; Antimicrobial Cationic Peptides/*genetics ; Europe ; Genetic Variation ; Hemocytes ; Hemolymph ; Mytilus/*genetics ; Nucleic Acid Amplification Techniques ; Polymorphism, Single Nucleotide ; RNA, Messenger/*genetics ; Sequence Analysis, DNA/*methods ; Transcriptome ; },
abstract = {BACKGROUND: Effective innate responses against potential pathogens are essential in the living world and possibly contributed to the evolutionary success of invertebrates. Taken together, antimicrobial peptide (AMP) precursors of defensin, mytilin, myticin and mytimycin can represent about 40% of the hemocyte transcriptome in mussels injected with viral-like and bacterial preparations, and unique profiles of myticin C variants are expressed in single mussels. Based on amplicon pyrosequencing, we have ascertained and compared the natural and Vibrio-induced diversity of AMP transcripts in mussel hemocytes from three European regions.<br><br>Hemolymph was collected from mussels farmed in the coastal regions of Palavas (France), Vigo (Spain) and Venice (Italy). To represent the AMP families known in M. galloprovincialis, nine transcript sequences have been selected, amplified from hemocyte RNA and subjected to pyrosequencing. Hemolymph from farmed (offshore) and wild (lagoon) Venice mussels, both injected with 10(7) Vibrio cells, were similarly processed. Amplicon pyrosequencing emphasized the AMP transcript diversity, with Single Nucleotide Changes (SNC) minimal for mytilin B/C and maximal for arthropod-like defensin and myticin C. Ratio of non-synonymous vs. synonymous changes also greatly differed between AMP isotypes. Overall, each amplicon revealed similar levels of nucleotidic variation across geographical regions, with two main sequence patterns confirmed for mytimycin and no substantial changes after immunostimulation.<br><br>CONCLUSIONS/SIGNIFICANCE: Barcoding and bidirectional pyrosequencing allowed us to map and compare the transcript diversity of known mussel AMPs. Though most of the genuine cds variation was common to the analyzed samples we could estimate from 9 to 106 peptide variants in hemolymph pools representing 100 mussels, depending on the AMP isoform and sampling site. In this study, no prevailing SNC patterns related to geographical origin or Vibrio injection emerged. Whether or not the contact with potential pathogens can increase the amount of AMP transcript variants in mussels requires additional study.},
}
@article {pmid22079550,
year = {2012},
author = {Ceccarelli, FS and Sharkey, MJ and Zaldívar-Riverón, A},
title = {Species identification in the taxonomically neglected, highly diverse, neotropical parasitoid wasp genus Notiospathius (Braconidae: Doryctinae) based on an integrative molecular and morphological approach.},
journal = {Molecular phylogenetics and evolution},
volume = {62},
number = {1},
pages = {485-495},
doi = {10.1016/j.ympev.2011.10.018},
pmid = {22079550},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Cytochromes b/genetics ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial ; Genetic Variation ; Insect Proteins/genetics ; Markov Chains ; Models, Genetic ; Monte Carlo Method ; Multilocus Sequence Typing ; Phylogeny ; Tropical Climate ; Wasps/anatomy &amp; histology/*classification/*genetics ; },
abstract = {Various DNA sequence-based methods for species delineation have recently been developed to assess the species-richness of highly diverse, neglected invertebrate taxa. These methods, however, need to be tested under a variety of conditions, including the use of different markers and parameters. Here, we explored the species diversity of a species-rich group of braconid parasitoid wasps, the Neotropical genus Notiospathius, including 233 specimens from 10 different countries. We examined sequences of two mitochondrial (mt) (COI, cyt b) and one nuclear (wg) gene fragments. We analysed them separately as well as concatenating the mt data with the general mixed Yule-coalescent (GMYC) model for species delineation using different tree-building methods and parameters for reconstructing ultrametric trees. We evaluated the performance of GMYC analyses by comparing their species delineations with our morphospecies identifications. Reconstructing ultrametric trees with a relaxed lognormal clock rate using the program BEAST gave the most congruent results with morphology for the two mt markers. A tree obtained with wg using the programs MrBayes+Pathd8 had the fewest cases of incongruence with morphology, though the performance of this nuclear marker was considerably lower than that of COI and cyt b. Species delimitation using the coalescent prior to obtain ultrametric trees was morphologically more congruent with COI, whereas the Yule prior was more congruent with cyt b. The analyses concatenating the mt datasets failed to recover some species supported both by morphology and the separate analyses of the mt markers. The highest morphological congruence was obtained with the GMYC analysis on an ultrametric tree reconstructed with cyt b using the relaxed lognormal clock rate and the Yule prior, thus supporting the importance of using alternative markers when the information of the barcoding locus (COI) is not concordant with morphological evidence. Seventy-one species were delimited based on the congruence found among COI, cyt b and morphology. Both mt markers also revealed the existence of seven potential cryptic species. This high species richness from a scattered geographical sampling indicates that there is a remarkable number of Notiospathius species that remains undiscovered.},
}
@article {pmid22079476,
year = {2012},
author = {Hohberger, C and Davis, R and Briggs, L and Gutierrez, A and Veeramani, D},
title = {Applying radio-frequency identification (RFID) technology in transfusion medicine.},
journal = {Biologicals : journal of the International Association of Biological Standardization},
volume = {40},
number = {3},
pages = {209-213},
doi = {10.1016/j.biologicals.2011.10.008},
pmid = {22079476},
issn = {1095-8320},
mesh = {Blood Banks/*standards ; Blood Donors ; Blood Preservation/methods/standards ; Blood Transfusion/methods/*standards ; Electronic Data Processing/methods/standards ; Humans ; Medical Errors/prevention &amp; control ; Patient Identification Systems/methods/standards ; Product Labeling/methods/*standards ; Radio Frequency Identification Device/methods/*standards ; Reproducibility of Results ; Blood Banking/methods ; },
abstract = {ISO/IEC 18000-3 mode 1 standard 13.56 MHz RFID tags have been accepted by the International Society for Blood Transfusion (ISBT) and the United States Food and Drug Administration (FDA) as data carriers to integrate with and augment ISBT 128 barcode data carried on blood products. The use of 13.56 MHz RFID carrying ISBT 128 data structures allows the global deployment and use of RFID, supporting both international transfer of blood and international disaster relief. The deployment in process at the BloodCenter of Wisconsin and testing at the University of Iowa Health Center is the first FDA-permitted implementation of RFID throughout in all phases of blood banking, donation through transfusion. RFID technology and equipment selection will be discussed along with FDA-required RF safety testing; integration with the blood enterprise computing system and required RFID tag performance. Tag design and survivability is an issue due to blood bag centrifugation and irradiation. Deployment issues will be discussed. Use of RFID results in significant return on investment over the use of barcodes in the blood center operations through labor savings and error reduction.},
}
@article {pmid22078886,
year = {2011},
author = {Khan, M and Vaes, E and Mombaerts, P},
title = {Regulation of the probability of mouse odorant receptor gene choice.},
journal = {Cell},
volume = {147},
number = {4},
pages = {907-921},
doi = {10.1016/j.cell.2011.09.049},
pmid = {22078886},
issn = {1097-4172},
mesh = {Animals ; Enhancer Elements, Genetic ; Gene Expression Profiling/*methods ; Gene Expression Regulation ; In Situ Hybridization/methods ; Mice ; Mice, Inbred C57BL ; Mutagenesis, Site-Directed ; Olfactory Mucosa/metabolism ; Olfactory Receptor Neurons/metabolism ; Receptors, Odorant/*genetics/metabolism ; *Regulatory Sequences, Nucleic Acid ; },
abstract = {Each olfactory sensory neuron (OSN) in mouse chooses one of 1,200 odorant receptor (OR) genes for expression. OR genes are chosen for expression by greatly varying numbers of OSNs. The mechanisms that regulate the probability of OR gene choice remain unclear. Here, we have applied the NanoString platform of fluorescent barcodes and digital readout to measure RNA levels of 577 OR genes in a single reaction, with probes designed against coding sequences. In an inbred mouse strain with a targeted deletion in the P element, we find that this element regulates OR gene choice differentially across its cluster of 24 OR genes. Importantly, the fold changes of NanoString counts in ΔP or ΔH mice are in very close agreement with the fold changes of cell counts, determined by in situ hybridization. Thus, the P and H elements regulate the probability of OR gene choice, not OR transcript level per OSN.},
}
@article {pmid22078751,
year = {2012},
author = {Genovese, G and Faggio, C and Gugliandolo, C and Torre, A and Spanò, A and Morabito, M and Maugeri, TL},
title = {In vitro evaluation of antibacterial activity of Asparagopsis taxiformis from the Straits of Messina against pathogens relevant in aquaculture.},
journal = {Marine environmental research},
volume = {73},
number = {},
pages = {1-6},
doi = {10.1016/j.marenvres.2011.10.002},
pmid = {22078751},
issn = {1879-0291},
mesh = {Animals ; Anti-Bacterial Agents/isolation &amp; purification/*pharmacology/toxicity ; *Aquaculture ; DNA Barcoding, Taxonomic ; Gram-Negative Bacteria/*drug effects ; Mediterranean Sea ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Mytilus/drug effects ; Phylogeny ; Rhodophyta/*chemistry/classification/genetics ; },
abstract = {Ethanol extracts of Asparagopsis taxiformis collected from the Straits of Messina (Italy) were screened for antibacterial activity against pathogenic shellfish and fish bacteria previously isolated from local marine and brackish environments. Genetic labelling by DNA barcoding allowed us to identify the algal population as a biogeographical strain conspecific to A. taxiformis. The extract obtained in May showed the broadest antibacterial activity against all tested pathogenic bacteria, especially against Vibrio alginolyticus, Vibrio vulnificus and Aeromonas salmonicida subsp. salmonicida. Moderate activity was observed against Photobacterium damselae subsp. damselae and Photobacterium damselae subsp. piscicida, Salmonella sp., Vibrio cholerae, Vibrio harveyi and Vibrio parahaemolyticus. The absence of cytotoxic effects of active algal extracts was verified using trypan blue exclusion test on cells of digestive glands of Mytilus galloprovincialis. The results indicated that ethanol extracts of A. taxiformis could represent a source of antibacterial substances with potential use in aquaculture.},
}
@article {pmid22075920,
year = {2012},
author = {Wylie, SJ and Luo, H and Li, H and Jones, MG},
title = {Multiple polyadenylated RNA viruses detected in pooled cultivated and wild plant samples.},
journal = {Archives of virology},
volume = {157},
number = {2},
pages = {271-284},
doi = {10.1007/s00705-011-1166-x},
pmid = {22075920},
issn = {1432-8798},
mesh = {Genome, Viral ; Molecular Sequence Data ; Phylogeny ; Plants/*virology ; RNA Viruses/*classification/genetics/*isolation &amp; purification ; RNA, Messenger/*genetics/isolation &amp; purification ; RNA, Viral/*genetics/isolation &amp; purification ; },
abstract = {RNA extracted from 120 leaf specimens from 17 plant species was pooled, and polyadenylated RNA species were sequenced together without barcoding in one lane using massively parallel sequencing technology. After analysis, complete or partial genome sequences representing 20 virus isolates of 16 polyadenylated RNA species were identified. In three cases, 2-3 distinct isolates of a virus species co-infected the same plant. Twelve of the viruses identified were described previously and belonged to the genera Potyvirus, Nepovirus, Allexivirus, and Carlavirus. Four were unknown and are proposed as members of the genera Potyvirus, Sadwavirus, and Trichovirus. Virus sequences were subsequently matched to original host plants using RT-PCR assays.},
}
@article {pmid22073120,
year = {2011},
author = {Vandeputte, P and Ischer, F and Sanglard, D and Coste, AT},
title = {In vivo systematic analysis of Candida albicans Zn2-Cys6 transcription factors mutants for mice organ colonization.},
journal = {PloS one},
volume = {6},
number = {10},
pages = {e26962},
pmid = {22073120},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Candida albicans/*growth &amp; development/*pathogenicity ; Candidiasis/*microbiology ; Cysteine ; DNA, Fungal/genetics ; Female ; Fungal Proteins/*genetics/metabolism ; Gene Expression Regulation, Fungal ; Host-Pathogen Interactions ; Kidney/*microbiology ; Mice ; Mice, Inbred BALB C ; Models, Animal ; Molecular Sequence Data ; Mutation/*genetics ; Phenotype ; Real-Time Polymerase Chain Reaction ; Sequence Homology, Nucleic Acid ; Transcription Factors/chemistry/*genetics/metabolism ; Virulence ; Zinc ; },
abstract = {The incidence of fungal infections in immuno-compromised patients increased considerably over the last 30 years. New treatments are therefore needed against pathogenic fungi. With Candida albicans as a model, study of host-fungal pathogen interactions might reveal new sources of therapies. Transcription factors (TF) are of interest since they integrate signals from the host environment and participate in an adapted microbial response. TFs of the Zn2-Cys6 class are specific to fungi and are important regulators of fungal metabolism. This work analyzed the importance of the C. albicans Zn2-Cys6 TF for mice kidney colonization. For this purpose, 77 Zn2-Cys6 TF mutants were screened in a systemic mice model of infection by pools of 10 mutants. We developed a simple barcoding strategy to specifically detect each mutant DNA from mice kidney by quantitative PCR. Among the 77 TF mutant strains tested, eight showed a decreased colonization including mutants for orf19.3405, orf19.255, orf19.5133, RGT1, UGA3, orf19.6182, SEF1 and orf19.2646, and four an increased colonization including mutants for orf19.4166, ZFU2, orf19.1685 and UPC2 as compared to the isogenic wild type strain. Our approach was validated by comparable results obtained with the same animal model using a single mutant and the revertant for an ORF (orf19.2646) with still unknown functions. In an attempt to identify putative involvement of such TFs in already known C. albicans virulence mechanisms, we determined their in vitro susceptibility to pH, heat and oxidative stresses, as well as ability to produce hyphae and invade agar. A poor correlation was found between in vitro and in vivo assays, thus suggesting that TFs needed for mice kidney colonization may involve still unknown mechanisms. This large-scale analysis of mice organ colonization by C. albicans can now be extended to other mutant libraries since our in vivo screening strategy can be adapted to any preexisting mutants.},
}
@article {pmid22066202,
year = {2011},
author = {Barr, NB and Ledezma, LA and Farris, RE and Epstein, ME and Gilligan, TM},
title = {A multiplex real-time polymerase chain reaction assay to diagnose Epiphyas postvittana (Lepidoptera: Tortricidae).},
journal = {Journal of economic entomology},
volume = {104},
number = {5},
pages = {1706-1719},
doi = {10.1603/ec11093},
pmid = {22066202},
issn = {0022-0493},
mesh = {Animals ; California ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Genetic Markers ; Molecular Sequence Data ; Moths/classification/*genetics ; North America ; RNA, Ribosomal, 18S/genetics ; Real-Time Polymerase Chain Reaction/*methods ; Sequence Alignment ; },
abstract = {A molecular assay for diagnosis of light brown apple moth, Epiphyas postvittana (Walker) (Lepidoptera: Tortricidae), in North America is reported. The assay multiplexes two TaqMan real-time polymerase chain reaction (RT-PCR) probe systems that are designed to target DNA segments of the internal transcribed spacer region 2 (ITS2) and 18S rRNA gene. The RT-PCR probe designed for the 18S target recognizes a DNA sequence conserved in all of the moths included in the study and functions as a control in the assay. The second probe recognizes a segment of the ITS2 specifically found in E. postvittana and not found in the other moths included in the study, i.e., this segment is not conserved. Inclusion of the two markers in a single multiplex reaction did not affect assay performance. The assay was tested against 637 moths representing > 90 taxa in 15 tribes in all three subfamilies in the Tortricidae. The assay generated no false negatives based on analysis of 355 E. postvittana collected from California, Hawaii, England, New Zealand, and Australia. Analysis of a data set including 282 moths representing 41 genera generated no false positives. Only three inconclusive results were generated from the 637 samples. Spike experiments demonstrated that DNA contamination in the assay can affect samples differently. Contaminated samples analyzed with the ITS2 RT-PCR assay and DNA barcode methodology by using the cytochrome oxidase I gene can generate contradictory diagnoses.},
}
@article {pmid22057991,
year = {2011},
author = {Arif, IA and Khan, HA and Al Sadoon, M and Shobrak, M},
title = {Limited efficiency of universal mini-barcode primers for DNA amplification from desert reptiles, birds and mammals.},
journal = {Genetics and molecular research : GMR},
volume = {10},
number = {4},
pages = {3559-3564},
doi = {10.4238/2011.October.31.3},
pmid = {22057991},
issn = {1676-5680},
mesh = {Animals ; Birds/*genetics ; DNA/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/*metabolism ; Desert Climate ; Electrophoresis, Agar Gel ; Mammals/*genetics ; Polymerase Chain Reaction/*methods ; Reptiles/*genetics ; Species Specificity ; },
abstract = {In recent years, DNA barcoding has emerged as a powerful tool for species identification. We report an extended validation of a universal DNA mini-barcode for amplification of 130-bp COI segments from 23 specimens collected from a desert environment, including 11 reptiles, five mammals and seven birds. Besides the standard double-annealing protocol, we also tested a more stringent single-annealing protocol. The PCR success rate for the amplification of the mini-barcode region was: mammals (4/5), reptiles (5/11) and birds (4/7). These findings demonstrate the limited utility of universal primers for mini-barcoding, at least for these vertebrate taxa that we collected from the Saudi Arabian desert.},
}
@article {pmid22056135,
year = {2011},
author = {Glimm, H and Ball, CR and von Kalle, C},
title = {You can count on this: barcoded hematopoietic stem cells.},
journal = {Cell stem cell},
volume = {9},
number = {5},
pages = {390-392},
doi = {10.1016/j.stem.2011.10.013},
pmid = {22056135},
issn = {1875-9777},
abstract = {Understanding how individual hematopoietic stem cells contribute to blood formation requires analysis at the single-cell level. Recently in Nature Biotechnology, Lu et al. (2011) tagged HSCs with unique molecular barcodes and used high-throughput sequencing to track their progeny after transplantation.},
}
@article {pmid22053744,
year = {2011},
author = {del Mercato, LL and Abbasi, AZ and Ochs, M and Parak, WJ},
title = {Multiplexed sensing of ions with barcoded polyelectrolyte capsules.},
journal = {ACS nano},
volume = {5},
number = {12},
pages = {9668-9674},
doi = {10.1021/nn203344w},
pmid = {22053744},
issn = {1936-086X},
mesh = {Electrolytes/*chemistry ; *Electronic Data Processing ; Ions/*analysis ; *Molecular Probe Techniques ; Nanocapsules/*chemistry ; Staining and Labeling/methods ; },
abstract = {Multiplexed detection of analytes is a challenge for numerous medical and biochemical applications. Many fluorescent particulate devices are being developed as ratiometric optical sensors to measure the concentration of intracellular analytes. The response of these sensors is based on changes of the emission intensity of analyte-sensitive probes, entrapped into the carrier system, which depends on the concentration of a specific analyte. However, there are a series of technical limits that prevent their use for quantitative detection of several analytes in parallel (e.g., emission crosstalk between different sensor molecules). Here we demonstrate that double-wall barcoded sensor capsules can be used for multiplexed analysis of proton, sodium, and potassium ions. The sensor detection methodology is based on porous microcapsules which carry ion-sensitive probes in their inner cavity for ion detection and a unique QD barcode in their outermost wall as tag for identification of individual sensors. The engineering of QD barcodes to capsules walls represents a promising strategy for optical multianalyte determination.},
}
@article {pmid22053360,
year = {2011},
author = {Baillie, J},
title = {Calls for concerted barcoding drive.},
journal = {Health estate},
volume = {65},
number = {9},
pages = {57-61},
pmid = {22053360},
mesh = {*Diffusion of Innovation ; Electronic Data Processing/*statistics &amp; numerical data ; Equipment and Supplies, Hospital ; Hospitals, Public ; Product Labeling/*methods ; State Medicine ; United Kingdom ; },
abstract = {With the NHS in England spending some pound 6 billion annually on hospital supplies, but (says the Department of Health) some English hospitals paying nearly three times as much for the same items as their counterparts, Health Minister, Simon Burns, has called on suppliers to significantly extend use of standardised GS1 barcodes in an attempt to improve "transparency" for procurement staff. The Minister argues that individually barcoding many more hospital-bound items would give procurement teams a clearer, more accurate picture of what they were buying, enable fairer price comparison, and radically improve stock control in many NHS hospitals, potentially reducing NHS procurement costs by millions of pounds. Other anticipated benefits include fewer medication errors, lower risk of wrong-site surgery, and the ability to track and trace everything from surgical instruments to patient beds. HEJ editor Jonathan Baillie reports.},
}
@article {pmid22046424,
year = {2011},
author = {Van Nieuwerburgh, F and Soetaert, S and Podshivalova, K and Ay-Lin Wang, E and Schaffer, L and Deforce, D and Salomon, DR and Head, SR and Ordoukhanian, P},
title = {Quantitative bias in Illumina TruSeq and a novel post amplification barcoding strategy for multiplexed DNA and small RNA deep sequencing.},
journal = {PloS one},
volume = {6},
number = {10},
pages = {e26969},
pmid = {22046424},
issn = {1932-6203},
support = {R01 AI081757/AI/NIAID NIH HHS/United States ; TL1 RR025772/RR/NCRR NIH HHS/United States ; U19 302 A1063603-06//PHS HHS/United States ; TL1 RR025772-03/RR/NCRR NIH HHS/United States ; },
mesh = {High-Throughput Nucleotide Sequencing ; Methods ; MicroRNAs ; Multiplex Polymerase Chain Reaction ; Reference Standards ; Sequence Analysis, DNA/*methods ; Sequence Analysis, RNA/*methods ; },
abstract = {Here we demonstrate a method for unbiased multiplexed deep sequencing of RNA and DNA libraries using a novel, efficient and adaptable barcoding strategy called Post Amplification Ligation-Mediated (PALM). PALM barcoding is performed as the very last step of library preparation, eliminating a potential barcode-induced bias and allowing the flexibility to synthesize as many barcodes as needed. We sequenced PALM barcoded micro RNA (miRNA) and DNA reference samples and evaluated the quantitative barcode-induced bias in comparison to the same reference samples prepared using the Illumina TruSeq barcoding strategy. The Illumina TruSeq small RNA strategy introduces the barcode during the PCR step using differentially barcoded primers, while the TruSeq DNA strategy introduces the barcode before the PCR step by ligation of differentially barcoded adaptors. Results show virtually no bias between the differentially barcoded miRNA and DNA samples, both for the PALM and the TruSeq sample preparation methods. We also multiplexed miRNA reference samples using a pre-PCR barcode ligation. This barcoding strategy results in significant bias.},
}
@article {pmid22043291,
year = {2011},
author = {Stam, J and Abdulahad, W and Huitema, MG and Roozendaal, C and Limburg, PC and van Stuijvenberg, M and Schölvinck, EH},
title = {Fluorescent cell barcoding as a tool to assess the age-related development of intracellular cytokine production in small amounts of blood from infants.},
journal = {PloS one},
volume = {6},
number = {10},
pages = {e25690},
pmid = {22043291},
issn = {1932-6203},
mesh = {Age Factors ; Antigens/pharmacology ; Blood/immunology ; Cytokines/*biosynthesis/blood ; Flow Cytometry/*methods ; Humans ; Infant ; Intracellular Space/metabolism ; T-Lymphocytes/*immunology/metabolism ; },
abstract = {Fluorescent Cell Barcoding (FCB) is a flow cytometric technique which has been used for assessing signaling proteins. This FCB technique has the potential to be applied in other multiparameter analyses. Since data on antigen (Ag)-specific T-cell immune responses, like intracellular cytokine production, are still lacking in infants because limited blood volumes can be obtained for analysis, the FCB technique could be very useful for this purpose. The objectives of this study were to modify the FCB method to be able to measure multiple Ag-specific cytokine reponses in T-cells upon simultaneous stimulation by various antigens and mitogens in small amounts of blood and to investigate the cytokine pattern of T-cell subsets in healthy infants aged six and twelve months. Blood samples, collected from 20 healthy infants aged six and twelve months, were stimulated in vitro with the antigens: phorbol-myristate-acetate (PMA), purified-protein-derivative (PPD), Tetanus-toxoid (TT), Staphylococcal-enterotoxin-B (SEB), and phytohemagglutinin (PHA). Each stimulus was barcoded by labelling with different intensities of fluorescent cell barcoding (FCB) markers. Intracellular production of interleukin-2, interferon-gamma, and tumor necrosis factor-alpha was measured simultaneously in just one blood sample of 600 µl whole blood. Significant age-related differences in cytokine production were shown for PMA, PHA, and TT in CD4(+) T-cells, and for PMA, PHA, SEB, and TT in CD8(+) T-cells. The intracellular cytokine production by CD4(+) and CD8(+) T-cells was higher at twelve months compared to six months of age for all antigens, except for PMA, which was lower at the age of twelve months. Based on the consistency in both T-cell subsets, we conclude that the new FCB method is a promising tool to investigate the age-related development of intracellular cytokine production in infants.},
}
@article {pmid22040164,
year = {2011},
author = {Chan, HM and Li, HW},
title = {Multifunctional encoded self-assembling protein nanofibrils as platform for high-throughput and multiplexed detection of biomolecules.},
journal = {Analytical chemistry},
volume = {83},
number = {24},
pages = {9370-9377},
doi = {10.1021/ac2019602},
pmid = {22040164},
issn = {1520-6882},
mesh = {Amyloid beta-Peptides/chemistry ; *Biosensing Techniques ; Biotin/chemistry ; DNA/*analysis ; DNA Probes/chemistry ; Fluorescent Dyes/chemistry ; Immobilized Proteins/chemistry ; Nanofibers/*chemistry ; Peptide Fragments/chemistry ; Spectrometry, Fluorescence ; },
abstract = {A one-dimensional nanofibrillar array formed by the co-assembly of native and biotin-functionalized beta-amyloid (Aβ) peptide was developed for biomolecule sensing. With the presence of biotin moiety, a variety of biomolecular probes can be conjugated onto the nanofibrils, thus converting the protein assembly into a miniature biosensor. In this work, DNA probes were immobilized onto the fibril for the detection of cDNA sequences. The as-developed "DNA-nanoarray" achieved a detection limit at subattomole level (183 fM in 10 μL). This highly sensitive, yet simple, assay requires a trace amount of sample consumption (<10 μL) and is pretreatment-free. In addition, we reported the preparation of alternate-segmented amyloid nanofibrils with multifunctionality. The fibrils hereby serve as an encoded template that can be visualized with various fluorescence labeling dyes for barcode recognition purpose, and, hence, multiplex detection of biomolecules was achieved. Regarding that each protein nanofibril represents a single detection platform, a large number of single fibrils simultaneously are monitored with the dual-color TIRFM in a high-throughput manner.},
}
@article {pmid22040082,
year = {2011},
author = {Aquino, LM and Tango, JM and Canoy, RJ and Fontanilla, IK and Basiao, ZU and Ong, PS and Quilang, JP},
title = {DNA barcoding of fishes of Laguna de Bay, Philippines.},
journal = {Mitochondrial DNA},
volume = {22},
number = {4},
pages = {143-153},
doi = {10.3109/19401736.2011.624613},
pmid = {22040082},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial ; Electron Transport Complex IV/*genetics ; Fishes/*classification/genetics ; Genes, Mitochondrial/*genetics ; Lakes ; Philippines ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Laguna de Bay, the largest lake in the Philippines, is an important part of the country's fisheries industry. It is also home to a number of endemic fishes including Gobiopterus lacustris (Herre 1927) of family Gobiidae, Leiopotherapon plumbeus (Kner 1864) of family Terapontidae, Zenarchopterus philippinus (Peters 1868) of family Hemiramphidae and Arius manillensis Valenciennes 1840 of family Ariidae. Over the years, a steady decline has been observed in the abundance and diversity of native fishes in the lake due to anthropogenic disturbances. In this study, a total of 71 specimens of 18 different species belonging to 18 genera, 16 families, and seven orders were DNA barcoded using the mitochondrial cytochrome c oxidase subunit I (COI) gene. All of the fish species were discriminated by their COI sequences and one endemic species G. lacustris, showing deep genetic divergence, was highlighted for further taxonomic investigation. Average Kimura 2-parameter genetic distances within species, family, and order were 1.33%, 18.91%, and 24.22%, respectively. These values show that COI divergence increases as taxa become less exclusive. All of the COI sequences obtained were grouped together according to their species designation in the Neighbor-joining tree that was constructed. This study demonstrated that DNA barcoding has great potential as a tool for fast and accurate species identification and also for highlighting species that warrant further taxonomic investigation.},
}
@article {pmid22039517,
year = {2011},
author = {Zou, S and Li, Q and Kong, L and Yu, H and Zheng, X},
title = {Comparing the usefulness of distance, monophyly and character-based DNA barcoding methods in species identification: a case study of neogastropoda.},
journal = {PloS one},
volume = {6},
number = {10},
pages = {e26619},
pmid = {22039517},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; *DNA Barcoding, Taxonomic ; DNA Primers ; DNA, Ribosomal/genetics ; Gastropoda/*classification/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: DNA barcoding has recently been proposed as a promising tool for the rapid species identification in a wide range of animal taxa. Two broad methods (distance and monophyly-based methods) have been used. One method is based on degree of DNA sequence variation within and between species while another method requires the recovery of species as discrete clades (monophyly) on a phylogenetic tree. Nevertheless, some issues complicate the use of both methods. A recently applied new technique, the character-based DNA barcode method, however, characterizes species through a unique combination of diagnostic characters.<br><br>Here we analyzed 108 COI and 102 16S rDNA sequences of 40 species of Neogastropoda from a wide phylogenetic range to assess the performance of distance, monophyly and character-based methods of DNA barcoding. The distance-based method for both COI and 16S rDNA genes performed poorly in terms of species identification. Obvious overlap between intraspecific and interspecific divergences for both genes was found. The "10&#xd7; rule" threshold resulted in lumping about half of distinct species for both genes. The neighbour-joining phylogenetic tree of COI could distinguish all species studied. However, the 16S rDNA tree could not distinguish some closely related species. In contrast, the character-based barcode method for both genes successfully identified 100% of the neogastropod species included, and performed well in discriminating neogastropod genera.<br><br>CONCLUSIONS/SIGNIFICANCE: This present study demonstrates the effectiveness of the character-based barcoding method for species identification in different taxonomic levels, especially for discriminating the closely related species. While distance and monophyly-based methods commonly use COI as the ideal gene for barcoding, the character-based approach can perform well for species identification using relatively conserved gene markers (e.g., 16S rDNA in this study). Nevertheless, distance and monophyly-based methods, especially the monophyly-based method, can still be used to flag species.},
}
@article {pmid22039414,
year = {2011},
author = {Pappalardo, AM and Guarino, F and Reina, S and Messina, A and De Pinto, V},
title = {Geographically widespread swordfish barcode stock identification: a case study of its application.},
journal = {PloS one},
volume = {6},
number = {10},
pages = {e25516},
pmid = {22039414},
issn = {1932-6203},
mesh = {Animals ; Cluster Analysis ; *Electronic Data Processing ; *Geography ; Perciformes/*classification ; Phylogeny ; *Seafood ; },
abstract = {BACKGROUND: The swordfish (Xiphias gladius) is a cosmopolitan large pelagic fish inhabiting tempered and tropical waters and it is a target species for fisheries all around the world. The present study investigated the ability of COI barcoding to reliably identify swordfish and particularly specific stocks of this commercially important species.<br><br>METHODOLOGY: We applied the classical DNA barcoding technology, upon a 682 bp segment of COI, and compared swordfish sequences from different geographical sources (Atlantic, Indian Oceans and Mediterranean Sea). The sequences of the 5' hyper-variable fragment of the control region (5'dloop), were also used to validate the efficacy of COI as a stock-specific marker.<br><br>CASE REPORT: This information was successfully applied to the discrimination of unknown samples from the market, detecting in some cases mislabeled seafood products.<br><br>CONCLUSIONS: The NJ distance-based phenogram (K2P model) obtained with COI sequences allowed us to correlate the swordfish haplotypes to the different geographical stocks. Similar results were obtained with 5'dloop. Our preliminary data in swordfish Xiphias gladius confirm that Cytochrome Oxidase I can be proposed as an efficient species-specific marker that has also the potential to assign geographical provenance. This information might speed the samples analysis in commercial application of barcoding.},
}
@article {pmid22037825,
year = {2012},
author = {Lassen, SB and Nielsen, SA and Skovgård, H and Kristensen, M},
title = {Molecular differentiation of Culicoides biting midges (Diptera: Ceratopogonidae) from the subgenus Culicoides Latreille in Denmark.},
journal = {Parasitology research},
volume = {110},
number = {5},
pages = {1765-1771},
pmid = {22037825},
issn = {1432-1955},
support = {BBS/E/I/00001701/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Ceratopogonidae/*classification/*genetics ; Cluster Analysis ; DNA, Mitochondrial/chemistry/*genetics ; Denmark ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Identification of Culicoides biting midges to species has attracted attention due to the recent outbreak of bluetongue disease in Northern Europe. Identification of Culicoides to species level has been based on morphological characters and is difficult as several species belonging to species complexes are hard to distinguish. We evaluated the use of the mitochondrial DNA cytochrome oxidase I gene (COI) barcode region in the identification of species within the subgenus Culicoides. COI barcode sequence divergence within species was <1%, whereas it ranged from 12.5% to 19.8% between subgenus Culicoides species. The divergence of subgenus Culicoides species to C. nubeculosus from the subgenus Monoculicoides ranged from 24.4% to 26.1%. Specimens were differentiated into eight unique clusters, including the four common Palaearctic species Culicoides punctatus, Culicoides pulicaris, Culicoides impunctatus, and Culicoides grisescens. Additionally, this study confirms the existence of Culicoides halophilus as a valid taxon and presents the first Culicoides deltus barcode sequences. Three additional groups of specimens were identified: Culicoides dk1 with a COI barcode diverging by 14.3% to 17.2% from other subgenus Culicoides species and Culicoides Kalix and Culicoides dk3, which diverged by 5.9% from each other and showed 12.5% to 17.6% divergence in COI barcode to subgenus Culicoides specimens.},
}
@article {pmid22035309,
year = {2011},
author = {Yoshida, R and Osawa, M and Hirose, M and Hirose, E},
title = {A new genus and two new species of Peltogastridae (Crustacea: Cirripedia: Rhizocephala) parasitizing hermit crabs from Okinawa Island (Ryukyu Archipelago, Japan), and their DNA-barcodes.},
journal = {Zoological science},
volume = {28},
number = {11},
pages = {853-862},
doi = {10.2108/zsj.28.853},
pmid = {22035309},
issn = {0289-0003},
mesh = {Animals ; Crustacea/*classification/*parasitology/physiology ; DNA/*genetics ; *DNA Barcoding, Taxonomic ; Host-Parasite Interactions ; Japan ; },
abstract = {A new genus and two new species of Peltogastridae, Peltogaster postica sp. nov. and Ommatogaster nana gen. et sp. nov., are described from Okinawa Island, Ryukyu Islands, southwestern Japan. The two new rhizocephalans were found to be parasitic on the estuarine hermit crabs, Pagurus minutus Hess, 1865 and Diogenes leptocerus Forest, 1956, respectively. Peltogaster postica sp. nov. is allied to P. curvata Kossmann, 1874, P. paguri Rathke, 1842 , and P. reticulata Shiino, 1943 , but is distinguished by its relative length and internal and external structures of the mature externa. Ommatogaster gen. nov. is established for the present new species O. nana based on the morphologies of the visceral mass of the externa and the presence of a nauplius eye in the larvae. Partial COI sequences were obtained from the two new species and one known species, Dipterosaccus indicus Van Kampen and Boschma, 1925, to test the possible usefulness of the sequences as tags for species identification.},
}
@article {pmid22035300,
year = {2011},
author = {Oba, Y and Branham, MA and Fukatsu, T},
title = {The terrestrial bioluminescent animals of Japan.},
journal = {Zoological science},
volume = {28},
number = {11},
pages = {771-789},
doi = {10.2108/zsj.28.771},
pmid = {22035300},
issn = {0289-0003},
mesh = {Animals ; Arthropods/*physiology ; Japan ; *Luminescence ; Oligochaeta/*physiology ; },
abstract = {Light production by organisms, or bioluminescence, has fascinated not only scientists but also ordinary people all over the world, and it has been especially so in Japan. Here we review the biological information available to date for all luminous terrestrial animals known from Japan, particularly focusing on their diversity and systematics, their biology and ecology in Japan, and putative function and biochemistry of their luminescence. In total 58 luminous terrestrial animals have been described from Japan, which consist of 50 fireflies (Coleoptera: Lampyridae), one glowworm beetle (Coleoptera: Phengodidae), two fungus gnats (Diptera: Keroplatidae), one springtail (Collembola), one millipede (Diplopoda), one centipede (Chilopoda) and two earthworms (Oligochaeta). For all except some firefly species, the DNA "barcode" sequences of a cytochrome oxidase subunit I region are provided. We also introduce how intricately the seasonal appearance and glimmering of luminous insects, in particular those of fireflies, have been interwoven into the culture, art, literature and mentality of Japanese people.},
}
@article {pmid22035191,
year = {2012},
author = {Sun, Y and Li, Q and Kong, L and Zheng, X},
title = {DNA barcoding of Caenogastropoda along coast of China based on the COI gene.},
journal = {Molecular ecology resources},
volume = {12},
number = {2},
pages = {209-218},
doi = {10.1111/j.1755-0998.2011.03085.x},
pmid = {22035191},
issn = {1755-0998},
mesh = {Animals ; China ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Gastropoda/*classification/*genetics ; Molecular Sequence Data ; Phylogeny ; },
abstract = {DNA barcoding provides an efficient method for species-level identifications. In this study, we have amplified partial sequences of mitochondrial cytochrome c oxidase I (COI) gene from 110 specimens of 45 species of Caenogastropoda collected from the coast along China to evaluate whether DNA barcodes can distinguish these species accurately. The average Kimura 2-parameter (K2P) distances within species, genera and families were 0.44%, 13.96% and 22.27%, respectively. Both the neighbour-joining tree and the Bayesian tree showed a clear discrimination of all the species in our study with highly supported clades. These results proved that the species of Caenogastropoda can be efficiently and accurately identified by DNA barcoding based on the COI gene.},
}
@article {pmid22033901,
year = {2011},
author = {Arif, IA and Khan, HA and Shobrak, M and Williams, J},
title = {Cytochrome c oxidase subunit I barcoding of the green bee-eater (Merops orientalis).},
journal = {Genetics and molecular research : GMR},
volume = {10},
number = {4},
pages = {3992-3998},
doi = {10.4238/2011.October.21.2},
pmid = {22033901},
issn = {1676-5680},
mesh = {Animals ; Base Sequence ; Birds/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry ; Electron Transport Complex IV/*genetics/metabolism ; Evolution, Molecular ; Genetic Variation ; Mitochondria/enzymology/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Subunits/genetics/metabolism ; Saudi Arabia ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {DNA barcoding using mitochondrial cytochrome c oxidase subunit I (COI) is regarded as a standard method for species identification. Recent reports have also shown extended applications of COI gene analysis in phylogeny and molecular diversity studies. The bee-eaters are a group of near passerine birds in the family Meropidae. There are 26 species worldwide; five of them are found in Saudi Arabia. Until now, GenBank included a COI barcode for only one species of bee-eater, the European bee-eater (Merops apiaster). We sequenced the 694-bp segment of the COI gene of the green bee-eater M. orientalis and compared the sequences with those of M. apiaster. Pairwise sequence comparison showed 66 variable sites across all the eight sequences from both species, with an interspecific genetic distance of 0.0362. Two and one within-species variable sites were found, with genetic distances of 0.0005 and 0.0003 for M. apiaster and M. orientalis, respectively. This is the first study reporting barcodes for M. orientalis.},
}
@article {pmid22028918,
year = {2011},
author = {Li, FW and Kuo, LY and Rothfels, CJ and Ebihara, A and Chiou, WL and Windham, MD and Pryer, KM},
title = {rbcL and matK earn two thumbs up as the core DNA barcode for ferns.},
journal = {PloS one},
volume = {6},
number = {10},
pages = {e26597},
pmid = {22028918},
issn = {1932-6203},
mesh = {DNA Barcoding, Taxonomic/*methods ; Ferns/*classification/*genetics ; Genetic Loci/genetics ; Genetic Variation ; Plant Proteins/*genetics ; Pteridaceae/classification/genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; },
abstract = {BACKGROUND: DNA barcoding will revolutionize our understanding of fern ecology, most especially because the accurate identification of the independent but cryptic gametophyte phase of the fern's life history--an endeavor previously impossible--will finally be feasible. In this study, we assess the discriminatory power of the core plant DNA barcode (rbcL and matK), as well as alternatively proposed fern barcodes (trnH-psbA and trnL-F), across all major fern lineages. We also present plastid barcode data for two genera in the hyperdiverse polypod clade--Deparia (Woodsiaceae) and the Cheilanthes marginata group (currently being segregated as a new genus of Pteridaceae)--to further evaluate the resolving power of these loci.<br><br>PRINCIPAL FINDINGS: Our results clearly demonstrate the value of matK data, previously unavailable in ferns because of difficulties in amplification due to a major rearrangement of the plastid genome. With its high sequence variation, matK complements rbcL to provide a two-locus barcode with strong resolving power. With sequence variation comparable to matK, trnL-F appears to be a suitable alternative barcode region in ferns, and perhaps should be added to the core barcode region if universal primer development for matK fails. In contrast, trnH-psbA shows dramatically reduced sequence variation for the majority of ferns. This is likely due to the translocation of this segment of the plastid genome into the inverted repeat regions, which are known to have a highly constrained substitution rate.<br><br>CONCLUSIONS: Our study provides the first endorsement of the two-locus barcode (rbcL+matK) in ferns, and favors trnL-F over trnH-psbA as a potential back-up locus. Future work should focus on gathering more fern matK sequence data to facilitate universal primer development.},
}
@article {pmid22028897,
year = {2011},
author = {Wang, J and Wu, Y and Ren, G and Guo, Q and Liu, J and Lascoux, M},
title = {Genetic differentiation and delimitation between ecologically diverged Populus euphratica and P. pruinosa.},
journal = {PloS one},
volume = {6},
number = {10},
pages = {e26530},
pmid = {22028897},
issn = {1932-6203},
mesh = {DNA, Chloroplast/genetics ; DNA, Ribosomal Spacer/genetics ; Desert Climate ; *Ecological and Environmental Phenomena ; Evolution, Molecular ; Genetic Loci/genetics ; Genetic Markers/genetics ; Microsatellite Repeats/genetics ; Phylogeny ; Polymorphism, Genetic/*genetics ; Populus/*genetics ; },
abstract = {BACKGROUND: The fixed genetic differences between ecologically divergent species were found to change greatly depending on the markers examined. With such species it is difficult to differentiate between shared ancestral polymorphisms and past introgressions between the diverging species. In order to disentangle these possibilities and provide a further case for DNA barcoding of plants, we examine genetic differentiation between two ecologically divergent poplar species, Populus euphratica Oliver and P. pruinosa Schrenk using three different types of genetic marker.<br><br>We genotyped 290 individuals from 29 allopatric and sympatric populations, using chloroplast (cp) DNA, nuclear (nr) ITS sequences and eight simple sequence repeat (SSR) loci. Three major cpDNA haplotypes were widely shared between the two species and between-species cpDNA differentiation (F(CT)) was very low, even lower than among single species populations. The average SSR F(CT) values were higher. Bayesian clustering analysis of all loci allowed a clear delineation of the two species. Gene flow, determined by examining all SSR loci, was obvious but only slightly asymmetrical. However, the two species were almost fixed for two different nrITS genotypes that had the highest F(CT), although a few introgressed individuals were detected both in allopatric and sympatric populations.<br><br>CONCLUSIONS: The two species shared numerous ancestral polymorphisms at cpDNA and a few SSR loci. Both ITS and a combination of nuclear SSR data could be used to differentiate between the two species. Introgressions and gene flow were obvious between the two species either during or after their divergence. Our findings underscore the complex genetic differentiations between ecologically diverged species and highlight the importance of nuclear DNA (especially ITS) differentiation for delimiting closely related plant species.},
}
@article {pmid22025808,
year = {2011},
author = {Crous, PW and Groenewald, JZ and Shivas, RG and Edwards, J and Seifert, KA and Alfenas, AC and Alfenas, RF and Burgess, TI and Carnegie, AJ and Hardy, GE and Hiscock, N and Hüberli, D and Jung, T and Louis-Seize, G and Okada, G and Pereira, OL and Stukely, MJ and Wang, W and White, GP and Young, AJ and McTaggart, AR and Pascoe, IG and Porter, IJ and Quaedvlieg, W},
title = {Fungal Planet description sheets: 69-91.},
journal = {Persoonia},
volume = {26},
number = {},
pages = {108-156},
pmid = {22025808},
issn = {1878-9080},
abstract = {Novel species of microfungi described in the present study include the following from Australia: Bagadiella victoriae and Bagadiella koalae on Eucalyptus spp., Catenulostroma eucalyptorum on Eucalyptus laevopinea, Cercospora eremochloae on Eremochloa bimaculata, Devriesia queenslandica on Scaevola taccada, Diaporthe musigena on Musa sp., Diaporthe acaciigena on Acacia retinodes, Leptoxyphium kurandae on Eucalyptus sp., Neofusicoccum grevilleae on Grevillea aurea, Phytophthora fluvialis from water in native bushland, Pseudocercospora cyathicola on Cyathea australis, and Teratosphaeria mareebensis on Eucalyptus sp. Other species include Passalora leptophlebiae on Eucalyptus leptophlebia (Brazil), Exophiala tremulae on Populus tremuloides and Dictyosporium stellatum from submerged wood (Canada), Mycosphaerella valgourgensis on Yucca sp. (France), Sclerostagonospora cycadis on Cycas revoluta (Japan), Rachicladosporium pini on Pinus monophylla (Netherlands), Mycosphaerella wachendorfiae on Wachendorfia thyrsifolia and Diaporthe rhusicola on Rhus pendulina (South Africa). Novel genera of hyphomycetes include Noosia banksiae on Banksia aemula (Australia), Utrechtiana cibiessia on Phragmites australis (Netherlands), and Funbolia dimorpha on blackened stem bark of an unidentified tree (USA). Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.},
}
@article {pmid22023826,
year = {2012},
author = {Fregin, S and Haase, M and Olsson, U and Alström, P},
title = {Pitfalls in comparisons of genetic distances: a case study of the avian family Acrocephalidae.},
journal = {Molecular phylogenetics and evolution},
volume = {62},
number = {1},
pages = {319-328},
doi = {10.1016/j.ympev.2011.10.003},
pmid = {22023826},
issn = {1095-9513},
mesh = {Animals ; Avian Proteins/genetics ; Base Sequence ; Cytochromes b/genetics ; DNA Barcoding, Taxonomic/methods ; Haplotypes ; Phylogeny ; Sequence Alignment ; Songbirds/classification/*genetics ; },
abstract = {Genetic distances are increasingly being used for identification and species delimitation, especially since the introduction of "barcoding". While for phylogenetic inferences great care is generally taken to choose the best-fit evolutionary model, this is usually neglected in calculating genetic distances. Moreover, distances obtained from others than best-fit models, different lengths of sequences, and even different loci are often freely compared. We examined the influence of different methods on calculating genetic distances using mitochondrial cytochrome b sequences for the passerine family Acrocephalidae. We found substantial differences between: (1) corrected distances based on the best-fit model (TrN+Γ) vs. uncorrected p-distances; (2) distances calculated based on different parts of the same gene; and (3) distances calculated using the methods of "complete deletion" vs. "pairwise deletion" for sequences that included uncertain nucleotides. All these methodological differences affected comparisons between species and potential taxonomical conclusions. We suggest that (1) different loci are incomparable. (2) Only perfectly homologous regions (same length, same part of locus) should be compared. (3) In the case of sequences with some uncertain nucleotides, only distances calculated by the method of "complete deletion" are fully comparable. (4) Only distances based on the optimal substitution model should be used. (5) Even within the same locus, corrected genetic distances are unique to the study in which they are calculated, as they are conditional on the particular dataset and model selected for that dataset.},
}
@article {pmid22022570,
year = {2011},
author = {Hamilton, CA and Formanowicz, DR and Bond, JE},
title = {Species delimitation and phylogeography of Aphonopelma hentzi (Araneae, Mygalomorphae, Theraphosidae): cryptic diversity in North American tarantulas.},
journal = {PloS one},
volume = {6},
number = {10},
pages = {e26207},
pmid = {22022570},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; *Genetic Variation ; Haplotypes/genetics ; Molecular Sequence Data ; North America ; Phylogeny ; *Phylogeography ; Species Specificity ; Spiders/classification/*genetics ; Time Factors ; },
abstract = {BACKGROUND: The primary objective of this study is to reconstruct the phylogeny of the hentzi species group and sister species in the North American tarantula genus, Aphonopelma, using a set of mitochondrial DNA markers that include the animal "barcoding gene". An mtDNA genealogy is used to consider questions regarding species boundary delimitation and to evaluate timing of divergence to infer historical biogeographic events that played a role in shaping the present-day diversity and distribution. We aimed to identify potential refugial locations, directionality of range expansion, and test whether A. hentzi post-glacial expansion fit a predicted time frame.<br><br>METHODS AND FINDINGS: A Bayesian phylogenetic approach was used to analyze a 2051 base pair (bp) mtDNA data matrix comprising aligned fragments of the gene regions CO1 (1165 bp) and ND1-16S (886 bp). Multiple species delimitation techniques (DNA tree-based methods, a "barcode gap" using percent of pairwise sequence divergence (uncorrected p-distances), and the GMYC method) consistently recognized a number of divergent and genealogically exclusive groups.<br><br>CONCLUSIONS: The use of numerous species delimitation methods, in concert, provide an effective approach to dissecting species boundaries in this spider group; as well they seem to provide strong evidence for a number of nominal, previously undiscovered, and cryptic species. Our data also indicate that Pleistocene habitat fragmentation and subsequent range expansion events may have shaped contemporary phylogeographic patterns of Aphonopelma diversity in the southwestern United States, particularly for the A. hentzi species group. These findings indicate that future species delimitation approaches need to be analyzed in context of a number of factors, such as the sampling distribution, loci used, biogeographic history, breadth of morphological variation, ecological factors, and behavioral data, to make truly integrative decisions about what constitutes an evolutionary lineage recognized as a "species".},
}
@article {pmid22022371,
year = {2011},
author = {Plaisance, L and Caley, MJ and Brainard, RE and Knowlton, N},
title = {The diversity of coral reefs: what are we missing?.},
journal = {PloS one},
volume = {6},
number = {10},
pages = {e25026},
pmid = {22022371},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; Caribbean Region ; *Coral Reefs ; Geography ; Hawaii ; Molecular Sequence Data ; Oceans and Seas ; Species Specificity ; },
abstract = {Tropical reefs shelter one quarter to one third of all marine species but one third of the coral species that construct reefs are now at risk of extinction. Because traditional methods for assessing reef diversity are extremely time consuming, taxonomic expertise for many groups is lacking, and marine organisms are thought to be less vulnerable to extinction, most discussions of reef conservation focus on maintenance of ecosystem services rather than biodiversity loss. In this study involving the three major oceans with reef growth, we provide new biodiversity estimates based on quantitative sampling and DNA barcoding. We focus on crustaceans, which are the second most diverse group of marine metazoans. We show exceptionally high numbers of crustacean species associated with coral reefs relative to sampling effort (525 species from a combined, globally distributed sample area of 6.3 m(2)). The high prevalence of rare species (38% encountered only once), the low level of spatial overlap (81% found in only one locality) and the biogeographic patterns of diversity detected (Indo-West Pacific>Central Pacific>Caribbean) are consistent with results from traditional survey methods, making this approach a reliable and efficient method for assessing and monitoring biodiversity. The finding of such large numbers of species in a small total area suggests that coral reef diversity is seriously under-detected using traditional survey methods, and by implication, underestimated.},
}
@article {pmid22020254,
year = {2011},
author = {Ruangsittichai, J and Apiwathnasorn, C and Dujardin, JP},
title = {Interspecific and sexual shape variation in the filariasis vectors Mansonia dives and Ma. bonneae.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {11},
number = {8},
pages = {2089-2094},
doi = {10.1016/j.meegid.2011.10.002},
pmid = {22020254},
issn = {1567-7257},
mesh = {Animals ; Biological Evolution ; DNA Barcoding, Taxonomic/methods ; Ecosystem ; Female ; Filariasis/*transmission ; Insect Vectors/*anatomy &amp; histology/*classification/genetics ; Male ; Malvaceae/*anatomy &amp; histology/*classification/genetics ; Myanmar ; *Sex Characteristics ; Thailand ; Wetlands ; Wings, Animal/anatomy &amp; histology ; },
abstract = {In the South of Thailand, six Mansonia species are recorded as filariasis vectors, among which Ma. bonneae and Ma. dives. These two species are distributed in the same breeding place, mainly the swamp forest, but appear to be of problematic identification using traditional morphological characters. Because of the risk of wrong identification during epidemiological or biological studies, complementary techniques are needed to distinguish the two species. We used on the same field collected specimens both genetic (DNA barcoding) and phenetic (geometric morphometrics) techniques. Both methods converged to identify two separate entities in accordance with morphological differences and geographic origins. Shape divergence between species was more pronounced in males than in females. Notably, the amount of within species sexual shape dimorphism was much larger than shape divergence as recorded between species. In spite of these two species of Mansonia being evolutionary very close, simple DNA barcoding was resolutive. Geometric morphometrics, because it is a fast and low-cost procedure, appeared as an interesting complement to modern diagnostic techniques applied in medical entomology. It also was able to provide information relevant to the ecology of the two species.},
}
@article {pmid22019936,
year = {2012},
author = {Duminil, J and Kenfack, D and Viscosi, V and Grumiau, L and Hardy, OJ},
title = {Testing species delimitation in sympatric species complexes: the case of an African tropical tree, Carapa spp. (Meliaceae).},
journal = {Molecular phylogenetics and evolution},
volume = {62},
number = {1},
pages = {275-285},
doi = {10.1016/j.ympev.2011.09.020},
pmid = {22019936},
issn = {1095-9513},
mesh = {Analysis of Variance ; Bayes Theorem ; Cameroon ; DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/genetics ; Gene Flow ; Genes, Chloroplast ; Genetic Markers ; Genetic Speciation ; Haplotypes ; Meliaceae/anatomy &amp; histology/classification/*genetics ; Microsatellite Repeats ; Models, Genetic ; Molecular Sequence Data ; Multilocus Sequence Typing ; Phylogeny ; Plant Leaves/anatomy &amp; histology ; Polymorphism, Genetic ; Sympatry ; },
abstract = {Plant species delimitation within tropical ecosystems is often difficult because of the lack of diagnostic morphological characters that are clearly visible. The development of an integrated approach, which utilizes several different types of markers (both morphological and molecular), would be extremely useful in this context. Here we have addressed species delimitation of sympatric tropical tree species that belong to Carapa spp. (Meliaceae) in Central Africa. We adopted a population genetics approach, sampling numerous individuals from three locations where sympatric Carapa species are known to exist. Comparisons between morphological markers (the presence or absence of characters, leaf-shape traits) and molecular markers (chloroplast sequences, ribosomal internal transcribed spacer region (ITS) sequences, and nuclear microsatellites) demonstrated the following: (i) a strong correlation between morphological and nuclear markers; (ii) despite substantial polymorphism, the inability of chloroplast DNA to discriminate between species, suggesting that cytoplasmic markers represent ineffective DNA barcodes; (iii) lineage sorting effects when using ITS sequences; and (iv) a complex evolutionary history within the genus Carapa, which includes frequent inter-specific gene flow. Our results support the use of a population genetics approach, based on ultra-polymorphic markers, to address species delimitation within complex taxonomic groups.},
}
@article {pmid22008190,
year = {2012},
author = {Beltrà, A and Soto, A and Malausa, T},
title = {Molecular and morphological characterisation of Pseudococcidae surveyed on crops and ornamental plants in Spain.},
journal = {Bulletin of entomological research},
volume = {102},
number = {2},
pages = {165-172},
doi = {10.1017/S0007485311000514},
pmid = {22008190},
issn = {1475-2670},
mesh = {Animals ; Bayes Theorem ; Electron Transport Complex IV/genetics ; Female ; France ; *Genetic Variation ; Haplotypes ; Hemiptera/*anatomy &amp; histology/classification/*genetics ; Insect Proteins/genetics ; Molecular Sequence Data ; Multilocus Sequence Typing ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Spain ; Species Specificity ; },
abstract = {Mealybugs (Hemiptera: Pseudococcidae) are common invasive pests in Europe, causing major problems on crops and ornamental plants. However, very few data are available concerning the mealybug fauna of southern Europe. This lack of data and the difficulty of identifying mealybugs morphologically by traditional techniques currently limit the perspectives for efficient specific pest management. The aim of this study was to provide multi-criterion characterization of mealybugs surveyed in eastern Spain in order to facilitate their routine identification through DNA sequencing or the use of derived species-specific molecular tools. We characterised 33 mealybug populations infesting crops and ornamental plants in eastern Spain, using a combination of molecular and morphological techniques, including the sequencing of the universal barcode DNA region cytochrome c oxidase subunit I (COI). This characterisation has led to the identification of ten species and provides sequence data for three previously unsequenced species, contributing to the phylogenetic knowledge of the family Pseudococcidae. In addition, the intraspecific variations found in the populations of five mealybug species provide insight into their invasion history.},
}
@article {pmid22005297,
year = {2012},
author = {Yin, HQ and Jia, MX and Yang, S and Wang, SQ and Zhang, JG},
title = {A nanoparticle-based bio-barcode assay for ultrasensitive detection of ricin toxin.},
journal = {Toxicon : official journal of the International Society on Toxinology},
volume = {59},
number = {1},
pages = {12-16},
doi = {10.1016/j.toxicon.2011.10.003},
pmid = {22005297},
issn = {1879-3150},
mesh = {Antigens/analysis/chemistry ; DNA Barcoding, Taxonomic ; Gold ; Immunoassay/*methods ; Limit of Detection ; Magnetics ; Metal Nanoparticles ; Plant Proteins/analysis/chemistry ; Reproducibility of Results ; Ricin/*analysis/chemistry ; },
abstract = {The ultrasensitive bio-barcode amplification assay (BCA) technique was developed for the specific detection of the A chain of ricin toxin. The target antigen A chain was first captured by gold nanoparticles (GNPs) coated with polyclonal antibodies. Magnetic microparticles (MMPs) coated with A chain monoclonal antibody were then added to form a sandwich immuno-complex. After the immuno-complex was formed, signal DNA annealed to DNA strands covalently bound to the GNPs were released by heating and characterized by PCR and real-time fluorescence PCR. A detection limit of 1fg/ml was measured for A chain, six orders of magnitude more sensitive than that of conventional antigen-capture ELISA. The coefficient of variation (CV) of intra-assay and inter-assay ranged from 3.39% to 6.84%. The BCA can detect the A chain in milk and water mimic samples. In the following work it is demonstrated that this assay is a highly sensitive method for the detection of ricin proteins that could be adapted to measure other proteins.},
}
@article {pmid22004100,
year = {2012},
author = {Derocles, SA and LE Ralec, A and Plantegenest, M and Chaubet, B and Cruaud, C and Cruaud, A and Rasplus, JY},
title = {Identification of molecular markers for DNA barcoding in the Aphidiinae (Hym. Braconidae).},
journal = {Molecular ecology resources},
volume = {12},
number = {2},
pages = {197-208},
doi = {10.1111/j.1755-0998.2011.03083.x},
pmid = {22004100},
issn = {1755-0998},
mesh = {Animals ; Aphids/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Genetic Markers ; Insect Proteins/genetics ; Molecular Sequence Data ; Phylogeny ; },
abstract = {Reliable identification of Aphidiinae species (Braconidae) is a prerequisite for conducting studies on aphid-parasitoid interactions at the community level. However, morphological identification of Aphidiinae species remains problematic even for specialists and is almost impossible with larval stages. Here, we compared the efficiency of two molecular markers [mitochondrial cytochrome c oxydase I (COI) and nuclear long wavelength rhodopsin (LWRh)] that could be used to accurately identify about 50 species of Aphidiinae that commonly occur in aphid-parasitoid networks in northwestern Europe. We first identified species on a morphological basis and then assessed the consistency of genetic and morphological data. Probably because of mitochondrial introgression, Aphidius ervi and A. microlophii were indistinguishable on the basis of their COI sequences, whereas LWRh sequences discriminated these species. Conversely, because of its lower variability, LWRh failed to discriminate two pairs of species (Aphidius aquilus, Aphidius salicis, Lysiphlebus confusus and Lysiphlebus fabarum). Our study showed that no unique locus but a combination of two genes should be used to accurately identify members of Aphidiinae.},
}
@article {pmid22001855,
year = {2012},
author = {Morrow, CC and Picton, BE and Erpenbeck, D and Boury-Esnault, N and Maggs, CA and Allcock, AL},
title = {Congruence between nuclear and mitochondrial genes in Demospongiae: a new hypothesis for relationships within the G4 clade (Porifera: Demospongiae).},
journal = {Molecular phylogenetics and evolution},
volume = {62},
number = {1},
pages = {174-190},
doi = {10.1016/j.ympev.2011.09.016},
pmid = {22001855},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; *Genes, Mitochondrial ; Likelihood Functions ; Models, Genetic ; Phylogeny ; Porifera/anatomy &amp; histology/classification/*genetics ; RNA, Ribosomal, 28S/genetics ; },
abstract = {The current morphological classification of the Demospongiae G4 clade was tested using large subunit ribosomal RNA (LSU rRNA) sequences from 119 taxa. Fifty-three mitochondrial cytochrome oxidase 1 (CO1) barcoding sequences were also analysed to test whether the 28S phylogeny could be recovered using an independent gene. This is the largest and most comprehensive study of the Demospongiae G4 clade. The 28S and CO1 genetrees result in congruent clades but conflict with the current morphological classification. The results confirm the polyphyly of Halichondrida, Hadromerida, Dictyonellidae, Axinellidae and Poecilosclerida and show that several of the characters used in morphological classifications are homoplasious. Robust clades are clearly shown and a new hypothesis for relationships of taxa allocated to G4 is proposed.},
}
@article {pmid21999860,
year = {2011},
author = {Taudien, S and Steuernagel, B and Ariyadasa, R and Schulte, D and Schmutzer, T and Groth, M and Felder, M and Petzold, A and Scholz, U and Mayer, KF and Stein, N and Platzer, M},
title = {Sequencing of BAC pools by different next generation sequencing platforms and strategies.},
journal = {BMC research notes},
volume = {4},
number = {},
pages = {411},
pmid = {21999860},
issn = {1756-0500},
abstract = {BACKGROUND: Next generation sequencing of BACs is a viable option for deciphering the sequence of even large and highly repetitive genomes. In order to optimize this strategy, we examined the influence of read length on the quality of Roche/454 sequence assemblies, to what extent Illumina/Solexa mate pairs (MPs) improve the assemblies by scaffolding and whether barcoding of BACs is dispensable.<br><br>RESULTS: Sequencing four BACs with both FLX and Titanium technologies revealed similar sequencing accuracy, but showed that the longer Titanium reads produce considerably less misassemblies and gaps. The 454 assemblies of 96 barcoded BACs were improved by scaffolding 79% of the total contig length with MPs from a non-barcoded library.Assembly of the unmasked 454 sequences without separation by barcodes revealed chimeric contig formation to be a major problem, encompassing 47% of the total contig length. Masking the sequences reduced this fraction to 24%.<br><br>CONCLUSION: Optimal BAC pool sequencing should be based on the longest available reads, with barcoding essential for a comprehensive assessment of both repetitive and non-repetitive sequence information. When interest is restricted to non-repetitive regions and repeats are masked prior to assembly, barcoding is non-essential. In any case, the assemblies can be improved considerably by scaffolding with non-barcoded BAC pool MPs.},
}
@article {pmid21998594,
year = {2011},
author = {Verzijlbergen, KF and van Welsem, T and Sie, D and Lenstra, TL and Turner, DJ and Holstege, FC and Kerkhoven, RM and van Leeuwen, F},
title = {A barcode screen for epigenetic regulators reveals a role for the NuB4/HAT-B histone acetyltransferase complex in histone turnover.},
journal = {PLoS genetics},
volume = {7},
number = {10},
pages = {e1002284},
pmid = {21998594},
issn = {1553-7404},
mesh = {Cell Cycle Proteins/genetics/metabolism ; Chromatin/genetics/metabolism ; Chromatin Assembly and Disassembly/genetics ; Chromatin Immunoprecipitation ; DNA Barcoding, Taxonomic ; Epigenesis, Genetic/*genetics ; *Gene Expression Regulation, Fungal ; Histone Acetyltransferases/genetics/*metabolism ; Histones/genetics/*metabolism ; Molecular Chaperones/genetics/metabolism ; Nuclear Export Signals/genetics ; Saccharomyces cerevisiae/cytology/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; },
abstract = {Dynamic modification of histone proteins plays a key role in regulating gene expression. However, histones themselves can also be dynamic, which potentially affects the stability of histone modifications. To determine the molecular mechanisms of histone turnover, we developed a parallel screening method for epigenetic regulators by analyzing chromatin states on DNA barcodes. Histone turnover was quantified by employing a genetic pulse-chase technique called RITE, which was combined with chromatin immunoprecipitation and high-throughput sequencing. In this screen, the NuB4/HAT-B complex, containing the conserved type B histone acetyltransferase Hat1, was found to promote histone turnover. Unexpectedly, the three members of this complex could be functionally separated from each other as well as from the known interacting factor and histone chaperone Asf1. Thus, systematic and direct interrogation of chromatin structure on DNA barcodes can lead to the discovery of genes and pathways involved in chromatin modification and dynamics.},
}
@article {pmid21998534,
year = {2011},
author = {Veijalainen, A and Broad, GR and Wahlberg, N and Longino, JT and Sääksjärvi, IE},
title = {DNA barcoding and morphology reveal two common species in one: Pimpla molesta stat. rev. separated from P. croceipes (Hymenoptera, Ichneumonidae).},
journal = {ZooKeys},
volume = {},
number = {124},
pages = {59-70},
pmid = {21998534},
issn = {1313-2970},
abstract = {Correct species identification is the basis of ecological studies. Nevertheless, morphological examination alone may not be enough to tell species apart. Here, our integrated molecular and morphological studies demonstrate that the relatively widespread and common neotropical parasitoid wasp Pimpla croceipes Cresson, 1874 (Hymenoptera: Ichneumonidae: Pimplinae) actually consists of two distinct species. The name Pimpla molesta (Smith, 1879), stat. rev. is available for the second species. The two species were identified by DNA barcoding and minor differences in morphology and colouration. Our results support the previous notions that DNA barcoding can complement morphological identification and aid the discovery of cryptic species complexes.},
}
@article {pmid21998527,
year = {2011},
author = {Borth, R and Ivinskis, P and Saldaitis, A and Yakovlev, R},
title = {Cossidae of the socotra archipelago (yemen).},
journal = {ZooKeys},
volume = {},
number = {122},
pages = {45-69},
pmid = {21998527},
issn = {1313-2970},
abstract = {The faunistic composition of the family Cossidae (Lepidoptera) of the Socotra Archipelago is revised. Five species are recognized, including two new species (Mormogystia brandstetteri and Meharia hackeri), and dubious identifications and records are discussed. Adults and genitalia are illustrated and bionomic details, DNA barcodes and a synonymic checklist for Socotran cossids are provided. A review of their distribution reveals that at least 80 percent of Socotra's cossids are unique to the archipelago, which is renowned for its endemism. A checklist listing all the species from generas Meharia, Mormogystia, Aethalopteryx, Azygophleps, as well as the synonymy and distribution is provided.},
}
@article {pmid21993779,
year = {2011},
author = {Thomas, MA and Schötz, EM},
title = {SAPling: a Scan-Add-Print barcoding database system to label and track asexual organisms.},
journal = {The Journal of experimental biology},
volume = {214},
number = {Pt 21},
pages = {3518-3523},
pmid = {21993779},
issn = {1477-9145},
support = {P50 GM071508/GM/NIGMS NIH HHS/United States ; },
mesh = {Animal Identification Systems/*methods ; Animals ; *Databases, Factual ; Electronic Data Processing/*methods ; Planarians/*physiology ; Population Dynamics ; *Reproduction, Asexual ; *Software ; Species Specificity ; },
abstract = {We have developed a 'Scan-Add-Print' database system, SAPling, to track and monitor asexually reproducing organisms. Using barcodes to uniquely identify each animal, we can record information on the life of the individual in a computerized database containing its entire family tree. SAPling has enabled us to carry out large-scale population dynamics experiments with thousands of planarians and keep track of each individual. The database stores information such as family connections, birth date, division date and generation. We show that SAPling can be easily adapted to other asexually reproducing organisms and has a strong potential for use in large-scale and/or long-term population and senescence studies as well as studies of clonal diversity. The software is platform-independent, designed for reliability and ease of use, and provided open source from our webpage to allow project-specific customization.},
}
@article {pmid21991372,
year = {2011},
author = {Hibert, F and Sabatier, D and Andrivot, J and Scotti-Saintagne, C and Gonzalez, S and Prévost, MF and Grenand, P and Chave, J and Caron, H and Richard-Hansen, C},
title = {Botany, genetics and ethnobotany: a crossed investigation on the elusive tapir's diet in French Guiana.},
journal = {PloS one},
volume = {6},
number = {10},
pages = {e25850},
pmid = {21991372},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; *Diet ; Ethnobotany ; Feces ; French Guiana ; Fruit ; Geography ; Herbivory/physiology ; Perissodactyla/*physiology ; Plants/*genetics ; Seasons ; Species Specificity ; },
abstract = {While the populations of large herbivores are being depleted in many tropical rainforests, the importance of their trophic role in the ecological functioning and biodiversity of these ecosystems is still not well evaluated. This is due to the outstanding plant diversity that they feed upon and the inherent difficulties involved in observing their elusive behaviour. Classically, the diet of elusive tropical herbivores is studied through the observation of browsing signs and macroscopic analysis of faeces or stomach contents. In this study, we illustrate that the original coupling of classic methods with genetic and ethnobotanical approaches yields information both about the diet diversity, the foraging modalities and the potential impact on vegetation of the largest terrestrial mammal of Amazonia, the lowland tapir. The study was conducted in the Guianan shield, where the ecology of tapirs has been less investigated. We identified 92 new species, 51 new genera and 13 new families of plants eaten by tapirs. We discuss the relative contribution of our different approaches, notably the contribution of genetic barcoding, used for the first time to investigate the diet of a large tropical mammal, and how local traditional ecological knowledge is accredited and valuable for research on the ecology of elusive animals.},
}
@article {pmid21980986,
year = {2011},
author = {Hanner, R and Becker, S and Ivanova, NV and Steinke, D},
title = {FISH-BOL and seafood identification: geographically dispersed case studies reveal systemic market substitution across Canada.},
journal = {Mitochondrial DNA},
volume = {22 Suppl 1},
number = {},
pages = {106-122},
doi = {10.3109/19401736.2011.588217},
pmid = {21980986},
issn = {1940-1744},
mesh = {Animals ; Canada ; *Commerce ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Fishes/*classification/*genetics ; *Food Labeling/statistics &amp; numerical data ; Food Supply ; Gene Library ; Genes, Mitochondrial ; Polymerase Chain Reaction/methods ; Seafood/*classification/standards ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND AND AIMS: The Fish Barcode of Life campaign involves a broad international collaboration among scientists working to advance the identification of fishes using DNA barcodes. With over 25% of the world's known ichthyofauna currently profiled, forensic identification of seafood products is now feasible and is becoming routine.<br><br>MATERIALS AND METHODS: Driven by growing consumer interest in the food supply, investigative reporters from five different media establishments procured seafood samples (n = 254) from numerous retail establishments located among five Canadian metropolitan areas between 2008 and 2010. The specimens were sent to the Canadian Centre for DNA Barcoding for analysis. By integrating the results from these individual case studies in a summary analysis, we provide a broad perspective on seafood substitution across Canada.<br><br>RESULTS: Barcodes were recovered from 93% of the samples (n = 236), and identified using the Barcode of Life Data Systems "species identification" engine (www.barcodinglife.org). A 99% sequence similarity threshold was employed as a conservative matching criterion for specimen identification to the species level. Comparing these results against the Canadian Food Inspection Agency's "Fish List" a guideline to interpreting "false, misleading or deceptive" names (as per s 27 of the Fish Inspection regulations) demonstrated that 41% of the samples were mislabeled. Most samples were readily identified; however, this was not true in all cases because some samples had no close match. Others were ambiguous due to limited barcode resolution (or imperfect taxonomy) observed within a few closely related species complexes. The latter cases did not significantly impact the results because even the partial resolution achieved was sufficient to demonstrate mislabeling.<br><br>CONCLUSION: This work highlights the functional utility of barcoding for the identification of diverse market samples. It also demonstrates how barcoding serves as a bridge linking scientific nomenclature with approved market names, potentially empowering regulatory bodies to enforce labeling standards. By synchronizing taxonomic effort with sequencing effort and database curation, barcoding provides a molecular identification resource of service to applied forensics.},
}
@article {pmid21980985,
year = {2011},
author = {Hanner, R and Floyd, R and Bernard, A and Collette, BB and Shivji, M},
title = {DNA barcoding of billfishes.},
journal = {Mitochondrial DNA},
volume = {22 Suppl 1},
number = {},
pages = {27-36},
doi = {10.3109/19401736.2011.596833},
pmid = {21980985},
issn = {1940-1744},
mesh = {Animals ; DNA/analysis/genetics ; DNA Barcoding, Taxonomic/*methods/standards ; DNA, Mitochondrial/analysis/genetics ; Electron Transport Complex IV/genetics ; Genetic Variation ; Perciformes/*classification/*genetics ; Phylogeny ; Polymerase Chain Reaction/methods ; Rhodopsin/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {DNA barcoding is a method promising fast and accurate identification of animal species based on the sequencing of the mitochondrial c oxidase subunit (COI) gene. In this study, we explore the prospects for DNA barcoding in one particular fish group, the billfishes (suborder Xiphioidei--swordfish, marlins, spearfishes, and sailfish). We sequenced the mitochondrial COI gene from 296 individuals from the 10 currently recognized species of billfishes, and combined these data with a further 57 sequences from previously published projects. We also sequenced the rhodopsin gene from a subset of 72 individuals to allow comparison of mitochondrial results against a nuclear marker. Five of the 10 species are readily distinguishable by COI barcodes. Of the rest, the striped marlin (Kajikia audax) and white marlin (K. albida) show highly similar sequences and are not unambiguously distinguishable by barcodes alone, likewise are the three spearfishes Tetrapturus angustirostris, T. belone, and T. pfluegeri. We discuss the taxonomic status of these species groups in light of our and other data, molecular and morphological.},
}
@article {pmid21974603,
year = {2011},
author = {Ahmad, H and Sutherland, A and Shin, YS and Hwang, K and Qin, L and Krom, RJ and Heath, JR},
title = {A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins.},
journal = {The Review of scientific instruments},
volume = {82},
number = {9},
pages = {094301},
pmid = {21974603},
issn = {1089-7623},
support = {U54 CA151819/CA/NCI NIH HHS/United States ; 1U54CA151819-01/CA/NCI NIH HHS/United States ; },
mesh = {Automation ; Cell Line ; Humans ; Macrophages/metabolism ; Microfluidic Analytical Techniques/*instrumentation ; Oligonucleotide Array Sequence Analysis/*instrumentation ; Proteins/*genetics/*metabolism ; Robotics/*instrumentation ; Single-Cell Analysis/*instrumentation ; Software ; },
abstract = {Microfluidics flow-patterning has been utilized for the construction of chip-scale miniaturized DNA and protein barcode arrays. Such arrays have been used for specific clinical and fundamental investigations in which many proteins are assayed from single cells or other small sample sizes. However, flow-patterned arrays are hand-prepared, and so are impractical for broad applications. We describe an integrated robotics/microfluidics platform for the automated preparation of such arrays, and we apply it to the batch fabrication of up to eighteen chips of flow-patterned DNA barcodes. The resulting substrates are comparable in quality with hand-made arrays and exhibit excellent substrate-to-substrate consistency. We demonstrate the utility and reproducibility of robotics-patterned barcodes by utilizing two flow-patterned chips for highly parallel assays of a panel of secreted proteins from single macrophage cells.},
}
@article {pmid21973311,
year = {2012},
author = {Schroeder, H and Hoeltken, AM and Fladung, M},
title = {Differentiation of Populus species using chloroplast single nucleotide polymorphism (SNP) markers--essential for comprehensible and reliable poplar breeding.},
journal = {Plant biology (Stuttgart, Germany)},
volume = {14},
number = {2},
pages = {374-381},
doi = {10.1111/j.1438-8677.2011.00502.x},
pmid = {21973311},
issn = {1438-8677},
mesh = {Base Sequence ; Breeding ; Chloroplasts/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; DNA, Chloroplast/genetics ; DNA, Intergenic/*genetics ; Genes, Chloroplast/*genetics ; Genetic Markers/genetics ; Genome, Chloroplast/genetics ; INDEL Mutation ; Molecular Sequence Data ; Polymorphism, Restriction Fragment Length/genetics ; Polymorphism, Single Nucleotide/*genetics ; Populus/classification/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Within the genus Populus several species belonging to different sections are cross-compatible. Hence, high numbers of interspecies hybrids occur naturally and, additionally, have been artificially produced in huge breeding programmes during the last 100 years. Therefore, determination of a single poplar species, used for the production of 'multi-species hybrids' is often difficult, and represents a great challenge for the use of molecular markers in species identification. Within this study, over 20 chloroplast regions, both intergenic spacers and coding regions, have been tested for their ability to differentiate different poplar species using 23 already published barcoding primer combinations and 17 newly designed primer combinations. About half of the published barcoding primers yielded amplification products, whereas the new primers designed on the basis of the total sequenced cpDNA genome of Populus trichocarpa Torr. &amp; Gray yielded much higher amplification success. Intergenic spacers were found to be more variable than coding regions within the genus Populus. The highest discrimination power of Populus species was found in the combination of two intergenic spacers (trnG-psbK, psbK-psbl) and the coding region rpoC. In barcoding projects, the coding regions matK and rbcL are often recommended, but within the genus Populus they only show moderate variability and are not efficient in species discrimination.},
}
@article {pmid21968212,
year = {2011},
author = {Correa, AC and Escobar, JS and Noya, O and Velásquez, LE and González-Ramírez, C and Hurtrez-Boussès, S and Pointier, JP},
title = {Morphological and molecular characterization of Neotropic Lymnaeidae (Gastropoda: Lymnaeoidea), vectors of fasciolosis.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {11},
number = {8},
pages = {1978-1988},
doi = {10.1016/j.meegid.2011.09.003},
pmid = {21968212},
issn = {1567-7257},
mesh = {Animals ; Base Sequence ; DNA Barcoding, Taxonomic ; Disease Vectors/*classification ; Fasciola/genetics/pathogenicity ; Fascioliasis/*transmission ; Humans ; Lymnaea/anatomy &amp; histology/*classification/*genetics ; Molecular Sequence Data ; Phylogeny ; Principal Component Analysis ; Sequence Alignment ; },
abstract = {Lymnaeidae play a crucial role in the transmission of fasciolosis, a disease of medical and veterinary importance. In the Neotropic, a region where fasciolosis is emergent, eight Lymnaeidae species are currently considered valid. However, our knowledge of the diversity of this taxon is hindered by the fact that lymnaeids exhibit extremely homogeneous anatomical traits. Because most species are difficult to identify using classic taxonomy, it is difficult to establish an epidemiological risk map of fasciolosis in the Neotropic. In this paper, we contribute to our understanding of the diversity of lymnaeids in this region of the world. We perform conchological, anatomical and DNA-based analyses (phylogeny and barcoding) of almost all species of Lymnaeidae inhabiting the Neotropic to compare the reliability of classic taxonomy and DNA-based approaches, and to delimitate species boundaries. Our results demonstrate that while morphological traits are unable to separate phenotypically similar species, DNA-based approaches unambiguously ascribe individuals to one species or another. We demonstrate that a taxon found in Colombia and Venezuela (Galba sp.) is closely related yet sufficiently divergent from Galba truncatula, G. humilis, G. cousini, G. cubensis, G. neotropica and G. viatrix to be considered as a different species. In addition, barcode results suggest that G. cubensis, G. neotropica and G. viatrix might be conspecifics. We conclude that conchological and anatomical characters are uninformative to identify closely related species of Lymnaeidae and that DNA-based approaches should be preferred.},
}
@article {pmid21967641,
year = {2012},
author = {Zhang, CY and Wang, FY and Yan, HF and Hao, G and Hu, CM and Ge, XJ},
title = {Testing DNA barcoding in closely related groups of Lysimachia L. (Myrsinaceae).},
journal = {Molecular ecology resources},
volume = {12},
number = {1},
pages = {98-108},
doi = {10.1111/j.1755-0998.2011.03076.x},
pmid = {21967641},
issn = {1755-0998},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; Molecular Sequence Data ; Phylogeny ; Primulaceae/*classification/*genetics ; RNA, Ribosomal/genetics ; },
abstract = {It has been suggested that rbcL and matK are the core barcodes in plants, but they are not powerful enough to distinguish between closely related plant groups. Additional barcodes need to be evaluated to improve the level of discrimination between plant species. Because of their well-studied taxonomy and extreme diversity, we used Chinese Lysimachia (Myrsinaceae) species to test the performance of core barcodes (rbcL and matK) and two additional candidate barcodes (trnH-psbA and the nuclear ribosomal ITS); 97 accessions from four subgenus representing 34 putative Lysimachia species were included in this study. And many closely related species pairs in subgen. Lysimachia were covered to detect their discriminatory power. The inefficiency of rbcL and matK alone or combined in closely related plant groups was validated in this study. TrnH-psbA combined with rbcL + matK did not yet perform well in Lysimachia groups. In contrast, ITS, alone or combined with rbcL and/or matK, revealed high resolving ability in Lysimachia. We support ITS as a supplementary barcode on the basis of core barcode rbcL and matK. Besides, this study also illustrates several mistakes or underlying evolutionary events in Lysimachia detected by DNA barcoding.},
}
@article {pmid21966560,
year = {2011},
author = {Gomes, NC and Cleary, DF and Calado, R and Costa, R},
title = {Mangrove bacterial richness.},
journal = {Communicative &amp; integrative biology},
volume = {4},
number = {4},
pages = {419-423},
pmid = {21966560},
issn = {1942-0889},
abstract = {Mangroves are complex and dynamic ecosystems varying in salinity, water level and nutrient availability; they also contain diverse and distinct microbial communities. Studies of microbes and their interactions with other ecosystem components (e.g., tree roots) are critical for our understanding of mangrove ecosystem functioning and remediation. Using a barcoding pyrosequencing approach, we previously noted the persistence of terrestrial bacterial populations on mangrove roots when nursery raised saplings were transplanted back to their natural environment. Here we go into further detail about the potential functional associations of bacterial guilds with distinct mangrove microhabitats including the rhizosphere. We also use a nonparametric richness estimator to show that estimated operational taxonomic unit (OTU) richness is more than twice that observed. In the transplant microhabitat, our estimate suggests that there are almost 7,000 OTU's for a sample size of 10,400 individual sequences with no sign of an asymptote, indicating that "true" richness for this microhabitat is substantially larger. Results on the number of bacterial OTU's should, however, be viewed with caution given that the barcoding pyrosequencing technique used can yield sequencing artifacts that may inflate richness estimates if not properly removed.},
}
@article {pmid21966418,
year = {2011},
author = {Dentinger, BT and Didukh, MY and Moncalvo, JM},
title = {Comparing COI and ITS as DNA barcode markers for mushrooms and allies (Agaricomycotina).},
journal = {PloS one},
volume = {6},
number = {9},
pages = {e25081},
pmid = {21966418},
issn = {1932-6203},
mesh = {Agaricales/*genetics ; DNA Barcoding, Taxonomic/*methods ; *DNA, Intergenic ; DNA, Ribosomal/metabolism ; Electron Transport Complex IV/*genetics ; Electronic Data Processing/*methods ; Genetic Markers ; Genetic Techniques ; Introns ; Maryland ; Models, Genetic ; Ontario ; Phylogeny ; Polymerase Chain Reaction/methods ; Quebec ; Sequence Analysis, DNA/*methods ; },
abstract = {DNA barcoding is an approach to rapidly identify species using short, standard genetic markers. The mitochondrial cytochrome oxidase I gene (COI) has been proposed as the universal barcode locus, but its utility for barcoding in mushrooms (ca. 20,000 species) has not been established. We succeeded in generating 167 partial COI sequences (~450 bp) representing ~100 morphospecies from ~650 collections of Agaricomycotina using several sets of new primers. Large introns (~1500 bp) at variable locations were detected in ~5% of the sequences we obtained. We suspect that widespread presence of large introns is responsible for our low PCR success (~30%) with this locus. We also sequenced the nuclear internal transcribed spacer rDNA regions (ITS) to compare with COI. Among the small proportion of taxa for which COI could be sequenced, COI and ITS perform similarly as a barcode. However, in a densely sampled set of closely related taxa, COI was less divergent than ITS and failed to distinguish all terminal clades. Given our results and the wealth of ITS data already available in public databases, we recommend that COI be abandoned in favor of ITS as the primary DNA barcode locus in mushrooms.},
}
@article {pmid21964413,
year = {2011},
author = {Lu, R and Neff, NF and Quake, SR and Weissman, IL},
title = {Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding.},
journal = {Nature biotechnology},
volume = {29},
number = {10},
pages = {928-933},
pmid = {21964413},
issn = {1546-1696},
support = {U01 HL099999-04/HL/NHLBI NIH HHS/United States ; U01 HL099999/HL/NHLBI NIH HHS/United States ; R01 CA086065-13/CA/NCI NIH HHS/United States ; U01 HL099999-03/HL/NHLBI NIH HHS/United States ; R01-CA86065/CA/NCI NIH HHS/United States ; U01-HL099999/HL/NHLBI NIH HHS/United States ; R01 CA086065-11/CA/NCI NIH HHS/United States ; U01 HL099999-02/HL/NHLBI NIH HHS/United States ; R01 CA086065/CA/NCI NIH HHS/United States ; R01 HL058770/HL/NHLBI NIH HHS/United States ; R01 CA086065-12/CA/NCI NIH HHS/United States ; R01 CA086065-10/CA/NCI NIH HHS/United States ; U01 HL099999-01/HL/NHLBI NIH HHS/United States ; U01 HL099995/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Cell Differentiation/genetics/radiation effects ; Cell Lineage/genetics/radiation effects ; Clone Cells ; DNA Barcoding, Taxonomic/*methods ; Gene Library ; Hematopoietic Stem Cells/*cytology/radiation effects/*virology ; High-Throughput Nucleotide Sequencing/*methods ; Lentivirus/*genetics/radiation effects ; Mice ; Mice, Inbred C57BL ; Radiation ; Sequence Analysis, DNA ; Single-Cell Analysis/*methods ; },
abstract = {Disentangling cellular heterogeneity is a challenge in many fields, particularly in the stem cell and cancer biology fields. Here we demonstrate how to combine viral genetic barcoding with high-throughput sequencing to track single cells in a heterogeneous population. We use this technique to track the in vivo differentiation of unitary hematopoietic stem cells (HSCs). The results are consistent with single-cell transplantation studies but require two orders of magnitude fewer mice. In addition to its high throughput, the high sensitivity of the technique allows for a direct examination of the clonality of sparse cell populations such as HSCs. We show how these capabilities offer a clonal perspective of the HSC differentiation process. In particular, our data suggest that HSCs do not equally contribute to blood cells after irradiation-mediated transplantation, and that two distinct HSC differentiation patterns co-exist in the same recipient mouse after irradiation. This technique can be applied to any virus-accessible cell type for both in vitro and in vivo processes.},
}
@article {pmid21951690,
year = {2012},
author = {Dittrich-Schröder, G and Wingfield, MJ and Klein, H and Slippers, B},
title = {DNA extraction techniques for DNA barcoding of minute gall-inhabiting wasps.},
journal = {Molecular ecology resources},
volume = {12},
number = {1},
pages = {109-115},
doi = {10.1111/j.1755-0998.2011.03074.x},
pmid = {21951690},
issn = {1755-0998},
mesh = {Animals ; DNA/genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic ; Eucalyptus/*parasitology ; *Genetic Techniques ; Insect Proteins/genetics ; Larva/classification/genetics/growth &amp; development/physiology ; Phylogeny ; Plant Tumors/*parasitology ; Wasps/*classification/*genetics/growth &amp; development/physiology ; },
abstract = {DNA extraction from minute hymenopterans and their larvae is difficult and challenging because of their small size indicating a low amount of starting material. Hence, 11 DNA extraction methods were compared to determine their efficacy in isolating DNA. Success of each method was scored on a 2% agarose gel after PCR of the cox 1 mitochondrial locus. A silica-membrane-based approach was the most successful, followed by a method using a combination of incubation buffers and a method using magnetic beads. The method using buffers was the most cost- and time effective. Using this method, larvae from Eucalyptus seed capsule galls could be assigned a role (parasitoid, gall former or inquiline) in the gall-inhabiting complex.},
}
@article {pmid21951639,
year = {2012},
author = {Parveen, I and Singh, HK and Raghuvanshi, S and Pradhan, UC and Babbar, SB},
title = {DNA barcoding of endangered Indian Paphiopedilum species.},
journal = {Molecular ecology resources},
volume = {12},
number = {1},
pages = {82-90},
doi = {10.1111/j.1755-0998.2011.03071.x},
pmid = {21951639},
issn = {1755-0998},
mesh = {DNA Barcoding, Taxonomic ; *Endangered Species ; Genetic Variation ; India ; Molecular Sequence Data ; Orchidaceae/*classification/genetics ; Phylogeny ; Plant Proteins/genetics ; },
abstract = {The indiscriminate collections of Paphiopedilum species from the wild for their exotic ornamental flowers have rendered these plants endangered. Although the trade of these endangered species from the wild is strictly forbidden, it continues unabated in one or other forms that elude the current identification methods. DNA barcoding that offers identification of a species even if only a small fragment of the organism at any stage of development is available could be of great utility in scrutinizing the illegal trade of both endangered plant and animal species. Therefore, this study was undertaken to develop DNA barcodes of Indian species of Paphiopedilum along with their three natural hybrids using loci from both the chloroplast and nuclear genomes. The five loci tested for their potential as effective barcodes were RNA polymerase-β subunit (rpoB), RNA polymerase-β' subunit (rpoC1), Rubisco large subunit (rbcL) and maturase K (matK) from the chloroplast genome and nuclear ribosomal internal transcribed spacer (nrITS) from the nuclear genome. The intra- and inter-specific divergence values and species discrimination rates were calculated by Kimura 2 parameter (K2P) method using mega 4.0. The matK with 0.9% average inter-specific divergence value yielded 100% species resolution, thus could distinguish all the eight species of Paphiopedilum unequivocally. The species identification capability of these sequences was further confirmed as each of the matK sequences was found to be unique for the species when a blast analysis of these sequences was carried out on NCBI. nrITS, although had 4.4% average inter-specific divergence value, afforded only 50% species resolution. DNA barcodes of the three hybrids also reflected their parentage.},
}
@article {pmid21951625,
year = {2012},
author = {Jørgensen, T and Kjaer, KH and Haile, J and Rasmussen, M and Boessenkool, S and Andersen, K and Coissac, E and Taberlet, P and Brochmann, C and Orlando, L and Gilbert, MT and Willerslev, E},
title = {Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA meta-barcoding.},
journal = {Molecular ecology},
volume = {21},
number = {8},
pages = {1980-1988},
doi = {10.1111/j.1365-294X.2011.05278.x},
pmid = {21951625},
issn = {1365-294X},
mesh = {Arctic Regions ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/analysis ; DNA, Plant ; *Fossils ; Geologic Sediments/*chemistry ; Greenland ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; Ice ; *Ice Cover ; Plants/*genetics ; Species Specificity ; },
abstract = {Nunataks are isolated bedrocks protruding through ice sheets. They vary in age, but represent island environments in 'oceans' of ice through which organism dispersals and replacements can be studied over time. The J.A.D. Jensen's Nunataks at the southern Greenland ice sheet are the most isolated nunataks on the northern hemisphere - some 30 km from the nearest biological source. They constitute around 2 km(2) of ice-free land that was established in the early Holocene. We have investigated the changes in plant composition at these nunataks using both the results of surveys of the flora over the last 130 years and through reconstruction of the vegetation from the end of the Holocene Thermal Maximum (5528 ± 75 cal year BP) using meta-barcoding of plant DNA recovered from the nunatak sediments (sedaDNA). Our results show that several of the plant species detected with sedaDNA are described from earlier vegetation surveys on the nunataks (in 1878, 1967 and 2009). In 1967, a much higher biodiversity was detected than from any other of the studied periods. While this may be related to differences in sampling efforts for the oldest period, it is not the case when comparing the 1967 and 2009 levels where the botanical survey was exhaustive. As no animals and humans are found on the nunataks, this change in diversity over a period of just 42 years must relate to environmental changes probably being climate-driven. This suggests that even the flora of fairly small and isolated ice-free areas reacts quickly to a changing climate.},
}
@article {pmid21951545,
year = {2011},
author = {Kokel, D and Peterson, RT},
title = {Using the zebrafish photomotor response for psychotropic drug screening.},
journal = {Methods in cell biology},
volume = {105},
number = {},
pages = {517-524},
pmid = {21951545},
issn = {0091-679X},
support = {R21 MH085205/MH/NIMH NIH HHS/United States ; K01 MH091449/MH/NIMH NIH HHS/United States ; R01 MH086867/MH/NIMH NIH HHS/United States ; MH086867/MH/NIMH NIH HHS/United States ; MH085206/MH/NIMH NIH HHS/United States ; },
mesh = {Algorithms ; Animals ; Antipsychotic Agents/*pharmacology ; Automation, Laboratory ; Behavior, Animal/drug effects/physiology/radiation effects ; Dark Adaptation ; Drug Discovery/*methods ; Drug Evaluation, Preclinical/*methods ; Embryo, Nonmammalian/drug effects/*physiology/radiation effects ; *High-Throughput Screening Assays ; Humans ; Infrared Rays ; Motor Activity/drug effects/physiology/radiation effects ; Phenotype ; Psychotic Disorders/drug therapy ; Research Design ; Small Molecule Libraries/*pharmacology ; Video Recording/instrumentation/methods ; Zebrafish/embryology/*physiology ; },
abstract = {Because psychotropic drugs affect behavior, we can use changes in behavior to discover psychotropic drugs. The original prototypes of most neuroactive medicines were discovered in humans, rodents and other model organisms. Most of these discoveries were made by chance, but the process of behavior based drug discovery can be made more systematic and efficient. Fully automated platforms for analyzing the behavior of embryonic zebrafish capture digital video recordings of animals in each individual well of a 96-well plate before, during, and after a series of stimuli. To analyze systematically the thousands of behavioral recordings obtained from a large-scale chemical screen, we transform these behavioral recordings into numerical barcodes, providing a concise and interpretable summary of the observed phenotypes in each well. Systems-level analysis of these behavioral phenotypes generate testable hypotheses about the molecular mechanisms of poorly understood drugs and behaviors. By combining the in vivo relevance of behavior-based phenotyping with the scale and automation of modern drug screening technologies, systematic behavioral barcoding represents a means of discovering psychotropic drugs and provides a powerful, systematic approach for unraveling the complexities of vertebrate behavior.},
}
@article {pmid21949723,
year = {2011},
author = {Jones, FA and Erickson, DL and Bernal, MA and Bermingham, E and Kress, WJ and Herre, EA and Muller-Landau, HC and Turner, BL},
title = {The roots of diversity: below ground species richness and rooting distributions in a tropical forest revealed by DNA barcodes and inverse modeling.},
journal = {PloS one},
volume = {6},
number = {9},
pages = {e24506},
pmid = {21949723},
issn = {1932-6203},
mesh = {*Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; *Models, Theoretical ; Plant Roots/*growth &amp; development ; Soil ; Trees/*classification/*genetics ; *Tropical Climate ; },
abstract = {BACKGROUND: Plants interact with each other, nutrients, and microbial communities in soils through extensive root networks. Understanding these below ground interactions has been difficult in natural systems, particularly those with high plant species diversity where morphological identification of fine roots is difficult. We combine DNA-based root identification with a DNA barcode database and above ground stem locations in a floristically diverse lowland tropical wet forest on Barro Colorado Island, Panama, where all trees and lianas >1 cm diameter have been mapped to investigate richness patterns below ground and model rooting distributions.<br><br>DNA barcode loci, particularly the cpDNA locus trnH-psba, can be used to identify fine and small coarse roots to species. We recovered 33 species of roots from 117 fragments sequenced from 12 soil cores. Despite limited sampling, we recovered a high proportion of the known species in the focal hectare, representing approximately 14% of the measured woody plant richness. This high value is emphasized by the fact that we would need to sample on average 13 m(2) at the seedling layer and 45 m(2) for woody plants >1 cm diameter to obtain the same number of species above ground. Results from inverse models parameterized with the locations and sizes of adults and the species identifications of roots and sampling locations indicates a high potential for distal underground interactions among plants.<br><br>CONCLUSIONS: DNA barcoding techniques coupled with modeling approaches should be broadly applicable to studying root distributions in any mapped vegetation plot. We discuss the implications of our results and outline how second-generation sequencing technology and environmental sampling can be combined to increase our understanding of how root distributions influence the potential for plant interactions in natural ecosystems.},
}
@article {pmid21949364,
year = {2011},
author = {Palacios, MA and Benito-Peña, E and Manesse, M and Mazzeo, AD and Lafratta, CN and Whitesides, GM and Walt, DR},
title = {InfoBiology by printed arrays of microorganism colonies for timed and on-demand release of messages.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {108},
number = {40},
pages = {16510-16514},
pmid = {21949364},
issn = {1091-6490},
support = {K12 GM074869/GM/NIGMS NIH HHS/United States ; },
mesh = {Escherichia coli/*genetics/physiology ; Gene Expression Regulation, Bacterial/genetics/*physiology ; Genetic Engineering/*methods ; Green Fluorescent Proteins/metabolism ; Informatics/*methods ; Information Storage and Retrieval/*methods ; Species Specificity ; },
abstract = {This paper presents a proof-of-principle method, called InfoBiology, to write and encode data using arrays of genetically engineered strains of Escherichia coli with fluorescent proteins (FPs) as phenotypic markers. In InfoBiology, we encode, send, and release information using living organisms as carriers of data. Genetically engineered systems offer exquisite control of both genotype and phenotype. Living systems also offer the possibility for timed release of information as phenotypic features can take hours or days to develop. We use growth media and chemically induced gene expression as cipher keys or "biociphers" to develop encoded messages. The messages, called Steganography by Printed Arrays of Microbes (SPAM), consist of a matrix of spots generated by seven strains of E. coli, with each strain expressing a different FP. The coding scheme for these arrays relies on strings of paired, septenary digits, where each pair represents an alphanumeric character. In addition, the photophysical properties of the FPs offer another method for ciphering messages. Unique combinations of excited and emitted wavelengths generate distinct fluorescent patterns from the Steganography by Printed Arrays of Microbes (SPAM). This paper shows a new form of steganography based on information from engineered living systems. The combination of bio- and "photociphers" along with controlled timed-release exemplify the capabilities of InfoBiology, which could enable biometrics, communication through compromised channels, easy-to-read barcoding of biological products, or provide a deterrent to counterfeiting.},
}
@article {pmid21945689,
year = {2011},
author = {Mohd-Shamsudin, MI and Fard, MZ and Mather, PB and Suleiman, Z and Hassan, R and Othman, RY and Bhassu, S},
title = {Molecular characterization of relatedness among colour variants of Asian Arowana (Scleropages formosus).},
journal = {Gene},
volume = {490},
number = {1-2},
pages = {47-53},
doi = {10.1016/j.gene.2011.08.025},
pmid = {21945689},
issn = {1879-0038},
mesh = {Animals ; Asia, Southeastern ; Cytochromes b/genetics ; Electron Transport Complex IV/genetics ; Fishes/*genetics/*physiology ; Genes, Mitochondrial ; *Genetic Variation ; Phylogeny ; Skin Pigmentation/*genetics ; },
abstract = {Morphological identification of fish taxa can sometimes prove difficult because phenotypic variation is either being affected by environmental factors, phenotypic characters are highly conserved or marker selection has been inappropriate. DNA based markers especially neutral mitochondrial DNA (mtDNA) have been used widely in recent times to provide better resolution of systematic relationships among vertebrate taxa. The Asian Arowana (Scleropages formosus) is a high value ornamental fish belonging to the family Osteoglossidae with a number of different colour variants distributed geographically across different locations around Southeast Asia. Systematic relationships among colour variants still remain unresolved. Partial sequences of the Cytochrome B (Cyt B) and DNA barcoding gene, Cytochrome C Oxidase I (COI) were used here to assess genetic relationships among colour variants and as a tool for molecular identification for differentiating among colour variants in this species. Results of the study show that in general, colour pattern shows no relationship with extent of COI or Cyt B mtDNA differentiation and so cannot be used to identify taxa. Partial sequences of the mtDNA genes were sufficient however, to identify S. formosus from a closely related species within the order Osteoglossidae.},
}
@article {pmid21943065,
year = {2012},
author = {Casquet, J and Thebaud, C and Gillespie, RG},
title = {Chelex without boiling, a rapid and easy technique to obtain stable amplifiable DNA from small amounts of ethanol-stored spiders.},
journal = {Molecular ecology resources},
volume = {12},
number = {1},
pages = {136-141},
doi = {10.1111/j.1755-0998.2011.03073.x},
pmid = {21943065},
issn = {1755-0998},
mesh = {Animals ; DNA/genetics/*isolation &amp; purification ; *Genetic Techniques ; Hot Temperature ; Polymerase Chain Reaction ; Spiders/chemistry/*genetics ; },
abstract = {DNA barcoding projects require high-throughput generation of sequence data to assemble the comprehensive reference databases that are required to perform large-scale biodiversity inventories and molecular ecology studies. With the advent of new sequencing technologies, the extraction step, which often requires a considerable amount of time and money, represents a significant bottleneck in many studies. Here, we present a one-step Chelex double-stranded DNA extraction protocol that is quick, cheap, easy and works with a small quantity of ethanol-stored tissue. We developed this protocol by removing the denaturation step appearing in classic methods. This modification reduces the number of handling steps to one, thus simplifying the extraction procedure and reducing the risk of sample contamination, and yields double-stranded DNA instead of the single-stranded form that classical Chelex extraction protocols usually release. DNA obtained through our method is then suitable for long-term conservation (over 1.5 years). We tested our protocol on a highly diverse genus of spiders comprised of mainly very small species. We also apply the method to two other genera of spiders, one with average size species, the other one with giant species, to test the efficacy of the method with varying amounts of input tissue. We also discuss the advantages and limitations of this DNA extraction technique when working with arthropods.},
}
@article {pmid21938631,
year = {2012},
author = {Raghav, SK and Deplancke, B},
title = {Genome-wide profiling of DNA-binding proteins using barcode-based multiplex Solexa sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {786},
number = {},
pages = {247-262},
doi = {10.1007/978-1-61779-292-2_15},
pmid = {21938631},
issn = {1940-6029},
mesh = {3T3-L1 Cells ; Animals ; Chromatin Immunoprecipitation/*methods ; DNA-Binding Proteins/*genetics ; Electronic Data Processing/*methods ; Genome/*genetics ; Mice ; Oligonucleotide Array Sequence Analysis/*methods ; },
abstract = {Chromatin immunoprecipitation (ChIP) is a commonly used technique to detect the in vivo binding of proteins to DNA. ChIP is now routinely paired to microarray analysis (ChIP-chip) or next-generation sequencing (ChIP-Seq) to profile the DNA occupancy of proteins of interest on a genome-wide level. Because ChIP-chip introduces several biases, most notably due to the use of a fixed number of probes, ChIP-Seq has quickly become the method of choice as, depending on the sequencing depth, it is more sensitive, quantitative, and provides a greater binding site location resolution. With the ever increasing number of reads that can be generated per sequencing run, it has now become possible to analyze several samples simultaneously while maintaining sufficient sequence coverage, thus significantly reducing the cost per ChIP-Seq experiment. In this chapter, we provide a step-by-step guide on how to perform multiplexed ChIP-Seq analyses. As a proof-of-concept, we focus on the genome-wide profiling of RNA Polymerase II as measuring its DNA occupancy at different stages of any biological process can provide insights into the gene regulatory mechanisms involved. However, the protocol can also be used to perform multiplexed ChIP-Seq analyses of other DNA-binding proteins such as chromatin modifiers and transcription factors.},
}
@article {pmid21932281,
year = {2012},
author = {Feng, X and Yang, G and Liu, L and Lv, F and Yang, Q and Wang, S and Zhu, D},
title = {A convenient preparation of multi-spectral microparticles by bacteria-mediated assemblies of conjugated polymer nanoparticles for cell imaging and barcoding.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {24},
number = {5},
pages = {637-641},
doi = {10.1002/adma.201102026},
pmid = {21932281},
issn = {1521-4095},
mesh = {Cell Line ; Escherichia coli/cytology ; Flow Cytometry ; Fluorescent Dyes/*chemistry ; Humans ; Microscopy, Fluorescence/*methods ; Nanoparticles/*chemistry ; Polymers/*chemistry ; },
abstract = {A novel technique was developed for preparing encoded multicolour microparticles based on the self-assembly of bacteria and conjugated polymer nanoparticles (CPNs) by a very simple and time-saving manner. These bacteria-CPNs microparticles show multicolor emissions by tuning FRET efficiencies among CPNs under single excitation wavelength and can be successfully applied for cell imaging and optical barcoding.},
}
@article {pmid21931848,
year = {2011},
author = {Wilson, JJ},
title = {Assessing the value of DNA barcodes for molecular phylogenetics: effect of increased taxon sampling in lepidoptera.},
journal = {PloS one},
volume = {6},
number = {9},
pages = {e24769},
pmid = {21931848},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Lepidoptera/*classification/*genetics ; *Phylogeny ; },
abstract = {BACKGROUND: A common perception is that DNA barcode datamatrices have limited phylogenetic signal due to the small number of characters available per taxon. However, another school of thought suggests that the massively increased taxon sampling afforded through the use of DNA barcodes may considerably increase the phylogenetic signal present in a datamatrix. Here I test this hypothesis using a large dataset of macrolepidopteran DNA barcodes.<br><br>Taxon sampling was systematically increased in datamatrices containing macrolepidopteran DNA barcodes. Sixteen family groups were designated as concordance groups and two quantitative measures; the taxon consistency index and the taxon retention index, were used to assess any changes in phylogenetic signal as a result of the increase in taxon sampling. DNA barcodes alone, even with maximal taxon sampling (500 species per family), were not sufficient to reconstruct monophyly of families and increased taxon sampling generally increased the number of clades formed per family. However, the scores indicated a similar level of taxon retention (species from a family clustering together) in the cladograms as the number of species included in the datamatrix was increased, suggesting substantial phylogenetic signal below the 'family' branch.<br><br>CONCLUSIONS/SIGNIFICANCE: The development of supermatrix, supertree or constrained tree approaches could enable the exploitation of the massive taxon sampling afforded through DNA barcodes for phylogenetics, connecting the twigs resolved by barcodes to the deep branches resolved through phylogenomics.},
}
@article {pmid21930509,
year = {2011},
author = {Riaz, T and Shehzad, W and Viari, A and Pompanon, F and Taberlet, P and Coissac, E},
title = {ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis.},
journal = {Nucleic acids research},
volume = {39},
number = {21},
pages = {e145},
pmid = {21930509},
issn = {1362-4962},
mesh = {Algorithms ; Animals ; DNA Barcoding, Taxonomic/*methods ; *DNA Primers ; Data Mining ; Genetic Markers ; Genome, Bacterial ; Genome, Chloroplast ; Genome, Mitochondrial ; Genomics/*methods ; Polymerase Chain Reaction ; *Software ; Vertebrates/genetics ; },
abstract = {Using non-conventional markers, DNA metabarcoding allows biodiversity assessment from complex substrates. In this article, we present ecoPrimers, a software for identifying new barcode markers and their associated PCR primers. ecoPrimers scans whole genomes to find such markers without a priori knowledge. ecoPrimers optimizes two quality indices measuring taxonomical range and discrimination to select the most efficient markers from a set of reference sequences, according to specific experimental constraints such as marker length or specifically targeted taxa. The key step of the algorithm is the identification of conserved regions among reference sequences for anchoring primers. We propose an efficient algorithm based on data mining, that allows the analysis of huge sets of sequences. We evaluate the efficiency of ecoPrimers by running it on three different sequence sets: mitochondrial, chloroplast and bacterial genomes. Identified barcode markers correspond either to barcode regions already in use for plants or animals, or to new potential barcodes. Results from empirical experiments carried out on a promising new barcode for analyzing vertebrate diversity fully agree with expectations based on bioinformatics analysis. These tests demonstrate the efficiency of ecoPrimers for inferring new barcodes fitting with diverse experimental contexts. ecoPrimers is available as an open source project at: http://www.grenoble.prabi.fr/trac/ecoPrimers.},
}
@article {pmid21923775,
year = {2011},
author = {Liu, J and Li, Q and Kong, L and Zheng, X},
title = {Cryptic diversity in the pen shell Atrina pectinata (Bivalvia: Pinnidae): high divergence and hybridization revealed by molecular and morphological data.},
journal = {Molecular ecology},
volume = {20},
number = {20},
pages = {4332-4345},
doi = {10.1111/j.1365-294X.2011.05275.x},
pmid = {21923775},
issn = {1365-294X},
mesh = {Animals ; Bivalvia/*genetics ; China ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genetic Speciation ; Hybridization, Genetic ; Japan ; Molecular Sequence Data ; *Phylogeny ; },
abstract = {Cryptic species have been increasingly revealed in the marine realm through an analytical approach incorporating multiple lines of evidence (e.g., mtDNA, nuclear genes and morphology). Illustrations of cryptic taxa improve our understanding of species diversity and evolutionary histories within marine animals. The pen shell Atrina pectinata is known to exhibit extensive morphological variations that may harbour cryptic diversity. In this study, we investigated A. pectinata populations along the coast of China and one from Japan to explore possible cryptic diversity and hybridization using a combination of mitochondrial (cytochrome c oxidase subunit I, mtCOI) and nuclear (ribosomal internal transcribed spacer, nrITS) genes as well as morphology. Phylogenetic analyses of mtCOI 'DNA barcoding gene' sequences resolved six divergent lineages with intralineage divergences between 0.4% and 0.8%. Interlineage sequence differences ranged from 4.3% to 22.0%, suggesting that six candidate cryptic species are present. The nrITS gene revealed five deep lineages with Kimura 2-parameter distances of 3.7-30.3%. The five nuclear lineages generally corresponded to mtCOI lineages 1-4 and (5+6), suggestive of five distinct evolutionary lineages. Multiple nrITS sequences of significant variance were found within an individual, clearly implying recent hybridization events between/among the evolutionary lineages, which contributed to cytonuclear discordance. Morphologically, five morphotypes matched the five genetic lineages, although the intermediates may well blur the boundaries of different morphotypes. This study demonstrates the importance of combining multiple lines of evidence to explore species cryptic diversity and past evolutionary histories.},
}
@article {pmid21917035,
year = {2012},
author = {Andersen, K and Bird, KL and Rasmussen, M and Haile, J and Breuning-Madsen, H and Kjaer, KH and Orlando, L and Gilbert, MT and Willerslev, E},
title = {Meta-barcoding of 'dirt' DNA from soil reflects vertebrate biodiversity.},
journal = {Molecular ecology},
volume = {21},
number = {8},
pages = {1966-1979},
doi = {10.1111/j.1365-294X.2011.05261.x},
pmid = {21917035},
issn = {1365-294X},
mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*analysis ; High-Throughput Nucleotide Sequencing ; Plants/classification/genetics ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; Soil/*analysis ; Vertebrates/classification/*genetics ; },
abstract = {DNA molecules originating from animals and plants can be retrieved directly from sediments and have been used for reconstructing both contemporary and past ecosystems. However, the extent to which such 'dirt' DNA reflects taxonomic richness and structural diversity remains contentious. Here, we couple second generation high-throughput sequencing with 16S mitochondrial DNA (mtDNA) meta-barcoding, to explore the accuracy and sensitivity of 'dirt' DNA as an indicator of vertebrate diversity, from soil sampled at safari parks, zoological gardens and farms with known species compositions. PCR amplification was successful in the full pH range of the investigated soils (6.2 ± 0.2 to 8.3 ± 0.2), but inhibition was detected in extracts from soil of high organic content. DNA movement (leaching) through strata was evident in some sporadic cases and is influenced by soil texture and structure. We find that DNA from the soil surface reflects overall taxonomic richness and relative biomass of individual species. However, one species that was recently introduced was not detected. Furthermore, animal behaviour was shown to influence DNA deposition rates. The approach potentially provides a quick methodological alternative to classical ecological surveys of biodiversity, and most reliable results are obtained with spatial sample replicates, while relative amounts of soil processed per site is of less importance.},
}
@article {pmid21909353,
year = {2011},
author = {Stöger, R and Genereux, DP and Hagerman, RJ and Hagerman, PJ and Tassone, F and Laird, CD},
title = {Testing the FMR1 promoter for mosaicism in DNA methylation among CpG sites, strands, and cells in FMR1-expressing males with fragile X syndrome.},
journal = {PloS one},
volume = {6},
number = {8},
pages = {e23648},
pmid = {21909353},
issn = {1932-6203},
support = {T32 HG 00035/HG/NHGRI NIH HHS/United States ; R01 GM077464/GM/NIGMS NIH HHS/United States ; P30 HD002274/HD/NICHD NIH HHS/United States ; T32 HG000035/HG/NHGRI NIH HHS/United States ; HD002274/HD/NICHD NIH HHS/United States ; GM077464/GM/NIGMS NIH HHS/United States ; },
mesh = {Alleles ; Base Sequence ; Case-Control Studies ; CpG Islands/*genetics ; Cytosine/metabolism ; DNA/genetics ; DNA Methylation/*genetics ; Female ; Fragile X Mental Retardation Protein/*genetics ; Fragile X Syndrome/*genetics/*pathology ; Humans ; Male ; Molecular Sequence Data ; *Mosaicism ; Mutation/genetics ; Nucleic Acid Conformation ; Polymerase Chain Reaction ; *Promoter Regions, Genetic ; },
abstract = {Variability among individuals in the severity of fragile X syndrome (FXS) is influenced by epigenetic methylation mosaicism, which may also be common in other complex disorders. The epigenetic signal of dense promoter DNA methylation is usually associated with gene silencing, as was initially reported for FMR1 alleles in individuals with FXS. A paradox arose when significant levels of FMR1 mRNA were reported for some males with FXS who had been reported to have predominately methylated alleles. We have used hairpin-bisufite PCR, validated with molecular batch-stamps and barcodes, to collect and assess double-stranded DNA methylation patterns from these previously studied males. These patterns enable us to distinguish among three possible forms of methylation mosaicism, any one of which could explain FMR1 expression in these males. Our data indicate that cryptic inter-cell mosaicism in DNA methylation can account for the presence of FMR1 mRNA in some individuals with FXS.},
}
@article {pmid21899722,
year = {2011},
author = {Federhen, S},
title = {Comment on 'Birdstrikes and barcoding: can DNA methods help make the airways safer?'.},
journal = {Molecular ecology resources},
volume = {11},
number = {6},
pages = {937-8; discussion 939-42},
pmid = {21899722},
issn = {1755-0998},
support = {Z99 CL999999/ImNIH/Intramural NIH HHS/United States ; Z99 HL999999/ImNIH/Intramural NIH HHS/United States ; Z99 LM999999/ImNIH/Intramural NIH HHS/United States ; Z99 MH999999/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Animals ; Aphids/*classification/*genetics ; Birds/*classification ; DNA Barcoding, Taxonomic/*methods ; },
abstract = {GenBank is the database of record for public sequence data. Results reported in the scientific literature that are based on sequence data cannot be evaluated if the underlying data is not in the public record.},
}
@article {pmid21897854,
year = {2011},
author = {Fernandez-Triana, J and Smith, MA and Boudreault, C and Goulet, H and Hebert, PD and Smith, AC and Roughley, R},
title = {A poorly known high-latitude parasitoid wasp community: unexpected diversity and dramatic changes through time.},
journal = {PloS one},
volume = {6},
number = {8},
pages = {e23719},
pmid = {21897854},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; Canada ; Climate Change ; DNA Barcoding, Taxonomic ; Parasites/*classification/genetics ; Temperature ; Time Factors ; Wasps/*classification/genetics ; },
abstract = {Climate change will have profound and unanticipated effects on species distributions. The pace and nature of this change is largely unstudied, especially for the most diverse elements of terrestrial communities--the arthropods--here we have only limited knowledge concerning the taxonomy and the ecology of these groups. Because Arctic ecosystems have already experienced significant increases in temperature over the past half century, shifts in community structure may already be in progress. Here we utilise collections of a particularly hyperdiverse insect group--parasitoid wasps (Hymenoptera; Braconidae; Microgastrinae)--at Churchill, Manitoba, Canada in the early and mid-twentieth century to compare the composition of the contemporary community to that present 50-70 years ago. Morphological and DNA barcoding results revealed the presence of 79 species of microgastrine wasps in collections from Churchill, but we estimate that 20% of the local fauna awaits detection. Species composition and diversity between the two time periods differ significantly; species that were most common in historic collections were not found in contemporary collections and vice versa. Using barcodes we compared these collections to others from across North America; contemporary Churchill species are most affiliated with more south-western collections, while historic collections were more affiliated with eastern collections. The past five decades has clearly seen a dramatic change of species composition within the area studied coincident with rising temperature.},
}
@article {pmid21893776,
year = {2011},
author = {Harvey, J and Avery, A and Waring, J and Hibberd, R and Barber, N},
title = {A constructivist approach? using formative evaluation to inform the electronic prescription service implementation in primary care, England.},
journal = {Studies in health technology and informatics},
volume = {169},
number = {},
pages = {374-378},
pmid = {21893776},
issn = {0926-9630},
mesh = {Automation ; Community Pharmacy Services/*organization &amp; administration ; Diffusion of Innovation ; Electronic Data Processing ; England ; Humans ; Medical Order Entry Systems ; Outcome and Process Assessment, Health Care ; Pharmacists ; Primary Health Care/*organization &amp; administration ; Program Development ; Program Evaluation ; Quality of Health Care ; Workflow ; },
abstract = {As part of the National Programme for IT (NPfIT) in England, the Electronic Prescription Service (EPS) is being implemented in two releases. The first release placed barcodes on prescriptions and is widely implemented. Release two (EPS2), the electronic transmission of prescriptions between GP, pharmacy and the reimbursement body, has just started implementation. On the NPfIT agenda, community pharmacies have been predicted to benefit from changes in work practice following the full EPS implementation. The study focused on how the advanced EPS (EPS2) might alter dispensing work practice in community pharmacies on issues such as workflow and workload; and the bearing of these issues on improvement in quality of service and safety. This paper demonstrates how findings of the pre-implementation study were used to provide formative feedback to the implementers. A mixed ethnographical method that combined non- participant observations, shadowing and interviews, before and after implementation, was used to qualitatively study eight community pharmacies across three early adopter Primary Care Trusts (PCTs) in England. Key implementation issues were fed-back to the PCTs as part of the EPS2 rolling-out process. Staff access to dispensing terminals needs to be improved if electronic dispensing is to be encouraged. Also, as a safety issue, pharmacists are planning to print off electronic prescriptions (tokens) and dispense from them. Although safer, this could increase workload. The EPS2 could positively alter work practice by improving certain demanding aspects of dispensing whilst reducing human errors. For example, the high demand of customers handing in prescriptions and waiting for them to be dispensed could be reduced through automation. Also, the extreme variation in workload during various times of the day could be evened out to improve workflow and provide a better service; however, in order for this to be fully realized, technical issues such as number of staff per dispensing station and dispensing from tokens would need to be addressed.},
}
@article {pmid21893764,
year = {2011},
author = {Sedlmayr, M and Prokosch, HU and Münch, U},
title = {Towards smart environments using smart objects.},
journal = {Studies in health technology and informatics},
volume = {169},
number = {},
pages = {315-319},
pmid = {21893764},
issn = {0926-9630},
mesh = {Biomedical Technology/*trends ; Computer Communication Networks ; Electronic Data Processing ; Hospitals ; Humans ; Internet ; Medical Informatics/*trends ; Monitoring, Physiologic/*methods ; Radio Frequency Identification Device ; },
abstract = {Barcodes, RFID, WLAN, Bluetooth and many more technologies are used in hospitals. They are the technological bases for different applications such as patient monitoring, asset management and facility management. However, most of these applications exist side by side with hardly any integration and even interoperability is not guaranteed. Introducing the concept of smart objects inspired by the Internet of Things can improve the situation by separating the capabilities and functions of an object from the implementing technology such as RFID or WLAN. By aligning technological and business developments smart objects have the power to transform a hospital from an agglomeration of technologies into a smart environment.},
}
@article {pmid21890899,
year = {2011},
author = {Jayaprakash, AD and Jabado, O and Brown, BD and Sachidanandam, R},
title = {Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing.},
journal = {Nucleic acids research},
volume = {39},
number = {21},
pages = {e141},
pmid = {21890899},
issn = {1362-4962},
support = {DP2DK083052-01/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Bias ; Gene Expression Profiling ; HEK293 Cells ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Mice ; *RNA Ligase (ATP) ; RNA, Small Untranslated/*chemistry/metabolism ; Sequence Analysis, RNA/*methods ; },
abstract = {Deep sequencing of small RNAs (sRNA-seq) is now the gold standard for small RNA profiling and discovery. Biases in sRNA-seq have been reported, but their etiology remains unidentified. Through a comprehensive series of sRNA-seq experiments, we establish that the predominant cause of the bias is the RNA ligases. We further demonstrate that RNA ligases have strong sequence-specific biases which distort the small RNA profiles considerably. We have devised a pooled adapter strategy to overcome this bias, and validated the method through data derived from microarray and qPCR. In light of our findings, published small RNA profiles, as well as barcoding strategies using adapter-end modifications, may need to be revisited. Importantly, by providing a wide spectrum of substrate for the ligase, the pooled-adapter strategy developed here provides a means to overcome issues of bias, and generate more accurate small RNA profiles.},
}
@article {pmid21890669,
year = {2011},
author = {Berry, D and Ben Mahfoudh, K and Wagner, M and Loy, A},
title = {Barcoded primers used in multiplex amplicon pyrosequencing bias amplification.},
journal = {Applied and environmental microbiology},
volume = {77},
number = {21},
pages = {7846-7849},
pmid = {21890669},
issn = {1098-5336},
support = {P 20185/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {DNA Primers/*genetics ; *Diagnostic Errors ; Polymerase Chain Reaction/*methods ; Polymorphism, Restriction Fragment Length ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; },
abstract = {"Barcode-tagged" PCR primers used for multiplex amplicon sequencing generate a thus-far-overlooked amplification bias that produces variable terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing data from the same environmental DNA template. We propose a simple two-step PCR approach that increases reproducibility and consistently recovers higher genetic diversity in pyrosequencing libraries.},
}
@article {pmid21883979,
year = {2012},
author = {Chaves, PB and Graeff, VG and Lion, MB and Oliveira, LR and Eizirik, E},
title = {DNA barcoding meets molecular scatology: short mtDNA sequences for standardized species assignment of carnivore noninvasive samples.},
journal = {Molecular ecology resources},
volume = {12},
number = {1},
pages = {18-35},
doi = {10.1111/j.1755-0998.2011.03056.x},
pmid = {21883979},
issn = {1755-0998},
mesh = {Animals ; Carnivora/*classification/*genetics ; Classification/*methods ; Cytochromes b/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Feces/chemistry ; Molecular Sequence Data ; *Phylogeny ; },
abstract = {Although species assignment of scats is important to study carnivore biology, there is still no standardized assay for the identification of carnivores worldwide, which would allow large-scale routine assessments and reliable cross-comparison of results. Here, we evaluate the potential of two short mtDNA fragments [ATP6 (126 bp) and cytochrome oxidase I gene (COI) (187 bp)] to serve as standard markers for the Carnivora. Samples of 66 species were sequenced for one or both of these segments. Alignments were complemented with archival sequences and analysed with three approaches (tree-based, distance-based and character-based). Intraspecific genetic distances were generally lower than between-species distances, resulting in diagnosable clusters for 86% (ATP6) and 85% (COI) of the species. Notable exceptions were recently diverged species, most of which could still be identified using diagnostic characters and uniqueness of haplotypes or by reducing the geographic scope of the comparison. In silico analyses were also performed for a 110-bp cytochrome b (cytb) segment, whose identification success was lower (70%), possibly due to the smaller number of informative sites and/or the influence of misidentified sequences obtained from GenBank. Finally, we performed case studies with faecal samples, which supported the suitability of our two focal markers for poor-quality DNA and allowed an assessment of prey DNA co-amplification. No evidence of prey DNA contamination was found for ATP6, while some cases were observed for COI and subsequently eliminated by the design of more specific primers. Overall, our results indicate that these segments hold good potential as standard markers for accurate species-level identification in the Carnivora.},
}
@article {pmid21883587,
year = {2012},
author = {Puillandre, N and Lambert, A and Brouillet, S and Achaz, G},
title = {ABGD, Automatic Barcode Gap Discovery for primary species delimitation.},
journal = {Molecular ecology},
volume = {21},
number = {8},
pages = {1864-1877},
doi = {10.1111/j.1365-294X.2011.05239.x},
pmid = {21883587},
issn = {1365-294X},
mesh = {Automation ; Base Sequence ; Computational Biology/*methods ; DNA/analysis/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Phylogeny ; Sensitivity and Specificity ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Within uncharacterized groups, DNA barcodes, short DNA sequences that are present in a wide range of species, can be used to assign organisms into species. We propose an automatic procedure that sorts the sequences into hypothetical species based on the barcode gap, which can be observed whenever the divergence among organisms belonging to the same species is smaller than divergence among organisms from different species. We use a range of prior intraspecific divergence to infer from the data a model-based one-sided confidence limit for intraspecific divergence. The method, called Automatic Barcode Gap Discovery (ABGD), then detects the barcode gap as the first significant gap beyond this limit and uses it to partition the data. Inference of the limit and gap detection are then recursively applied to previously obtained groups to get finer partitions until there is no further partitioning. Using six published data sets of metazoans, we show that ABGD is computationally efficient and performs well for standard prior maximum intraspecific divergences (a few per cent of divergence for the five data sets), except for one data set where less than three sequences per species were sampled. We further explore the theoretical limitations of ABGD through simulation of explicit speciation and population genetics scenarios. Our results emphasize in particular the sensitivity of the method to the presence of recent speciation events, via (unrealistically) high rates of speciation or large numbers of species. In conclusion, ABGD is fast, simple method to split a sequence alignment data set into candidate species that should be complemented with other evidence in an integrative taxonomic approach.},
}
@article {pmid21883585,
year = {2012},
author = {Zhang, AB and Muster, C and Liang, HB and Zhu, CD and Crozier, R and Wan, P and Feng, J and Ward, RD},
title = {A fuzzy-set-theory-based approach to analyse species membership in DNA barcoding.},
journal = {Molecular ecology},
volume = {21},
number = {8},
pages = {1848-1863},
doi = {10.1111/j.1365-294X.2011.05235.x},
pmid = {21883585},
issn = {1365-294X},
mesh = {Algorithms ; Animals ; Bayes Theorem ; *Biodiversity ; Butterflies/classification/genetics ; Chiroptera/classification/genetics ; Computational Biology/*methods ; DNA/*genetics ; DNA Barcoding, Taxonomic/*methods ; Diptera/classification/genetics ; Fishes/classification/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Reliable assignment of an unknown query sequence to its correct species remains a methodological problem for the growing field of DNA barcoding. While great advances have been achieved recently, species identification from barcodes can still be unreliable if the relevant biodiversity has been insufficiently sampled. We here propose a new notion of species membership for DNA barcoding-fuzzy membership, based on fuzzy set theory-and illustrate its successful application to four real data sets (bats, fishes, butterflies and flies) with more than 5000 random simulations. Two of the data sets comprise especially dense species/population-level samples. In comparison with current DNA barcoding methods, the newly proposed minimum distance (MD) plus fuzzy set approach, and another computationally simple method, 'best close match', outperform two computationally sophisticated Bayesian and BootstrapNJ methods. The new method proposed here has great power in reducing false-positive species identification compared with other methods when conspecifics of the query are absent from the reference database.},
}
@article {pmid21877684,
year = {2011},
author = {Musumeci, D and Hu, C and Ward, MD},
title = {Anticounterfeit protection of pharmaceutical products with spatial mapping of X-ray-detectable barcodes and logos.},
journal = {Analytical chemistry},
volume = {83},
number = {19},
pages = {7444-7450},
doi = {10.1021/ac201570r},
pmid = {21877684},
issn = {1520-6882},
mesh = {*Counterfeit Drugs ; Drug Labeling/*methods/*standards ; Drug Packaging/standards ; *Electronic Data Processing ; Fraud/*prevention &amp; control ; Pharmaceutical Preparations/analysis/*standards ; Tablets/analysis/standards ; X-Ray Diffraction/*methods ; },
abstract = {Counterfeit pharmaceutical products are a global threat to public health, and they undermine the credibility and the financial success of the producers of genuine products. The escalating circulation of counterfeit drugs demands new anticounterfeit measures that permit rapid screening, are nondestructive, and cannot be circumvented easily. Herein we describe a micro-X-ray diffraction (μ-XRD) protocol for this purpose capable of reading barcodes and logos fabricated on various substrates using soft-lithography stamping of compounds that can be read by X-ray diffraction but are invisible to the naked eye or optical microscopy. This method is demonstrated with barcodes and logos of compounds, approved by the Food and Drug Administration, printed on flat substrates as well as commercial aspirin and ibuprofen tablets. The μ-XRD protocol is nondestructive, automated, and user-friendly and can be used to certify the authenticity of drug tablets by mapping hidden patterns printed under the tablet coating and on packages.},
}
@article {pmid21870015,
year = {2011},
author = {Jung, JH and Kim, GY and Seo, TS},
title = {An integrated passive micromixer-magnetic separation-capillary electrophoresis microdevice for rapid and multiplex pathogen detection at the single-cell level.},
journal = {Lab on a chip},
volume = {11},
number = {20},
pages = {3465-3470},
doi = {10.1039/c1lc20350a},
pmid = {21870015},
issn = {1473-0189},
mesh = {Bacteria/*cytology/genetics ; Base Sequence ; Cell Separation/*instrumentation ; DNA, Bacterial/analysis/genetics ; Electrophoresis, Capillary/*instrumentation ; *Lab-On-A-Chip Devices ; Limit of Detection ; *Magnets ; Point-of-Care Systems ; Single-Cell Analysis/*instrumentation ; *Systems Integration ; Time Factors ; },
abstract = {Here we report an integrated microdevice consisting of an efficient passive mixer, a magnetic separation chamber, and a capillary electrophoretic microchannel in which DNA barcode assay, target pathogen separation, and barcode DNA capillary electrophoretic analysis were performed sequentially within 30 min for multiplex pathogen detection at the single-cell level. The intestine-shaped serpentine 3D micromixer provides a high mixing rate to generate magnetic particle-pathogenic bacteria-DNA barcode labelled AuNP complexes quantitatively. After magnetic separation and purification of those complexes, the barcode DNA strands were released and analyzed by the microfluidic capillary electrophoresis within 5 min. The size of the barcode DNA strand was controlled depending on the target bacteria (Staphylococcus aureus, Escherichia coli O157:H7, and Salmonella typhimurium), and the different elution time of the barcode DNA peak in the electropherogram allows us to recognize the target pathogen with ease in the monoplex as well as in the multiplex analysis. In addition, the quantity of the DNA barcode strand (∼10(4)) per AuNP is enough to be observed in the laser-induced confocal fluorescence detector, thereby making single-cell analysis possible. This novel integrated microdevice enables us to perform rapid, sensitive, and multiplex pathogen detection with sample-in-answer-out capability to be applied for biosafety testing, environmental screening, and clinical trials.},
}
@article {pmid21869910,
year = {2011},
author = {Lim, SF and Karpusenko, A and Sakon, JJ and Hook, JA and Lamar, TA and Riehn, R},
title = {DNA methylation profiling in nanochannels.},
journal = {Biomicrofluidics},
volume = {5},
number = {3},
pages = {34106-341068},
pmid = {21869910},
issn = {1932-1058},
support = {R21 CA132075/CA/NCI NIH HHS/United States ; R21 HD065222/HD/NICHD NIH HHS/United States ; },
abstract = {We report the profiling of the 5-methyl cytosine distribution within single genomic-sized DNA molecules at a gene-relevant resolution. This method linearizes and stretches DNA molecules by confinement to channels with a dimension of about 250×200 nm(2). The methylation state is detected using fluorescently labeled methyl-CpG binding domain proteins (MBD), with high signal contrast and low background. DNA barcodes consisting of methylated and non-methylated segments are generated, with both short and long concatemers demonstrating spatially resolved MBD binding. The resolution of the technique is better than 10 kbp, and single-molecule read-lengths exceeding 140 kbp have been achieved.},
}
@article {pmid21868354,
year = {2011},
author = {Liggett, SB},
title = {Phosphorylation barcoding as a mechanism of directing GPCR signaling.},
journal = {Science signaling},
volume = {4},
number = {185},
pages = {pe36},
doi = {10.1126/scisignal.2002331},
pmid = {21868354},
issn = {1937-9145},
mesh = {Animals ; Arrestins/genetics/*metabolism ; G-Protein-Coupled Receptor Kinases/genetics/*metabolism ; Humans ; Phosphorylation/physiology ; Receptors, G-Protein-Coupled/genetics/*metabolism ; Signal Transduction/*physiology ; beta-Arrestins ; },
abstract = {A unifying mechanism by which G protein-coupled receptors (GPCRs) signal in cell type-dependent and G protein-independent ways has developed over the past decade. GPCR kinases (GRKs) are mediators of homologous desensitization: GRK phosphorylation of the receptors leads to the subsequent binding of β-arrestins, which partially quenches receptor coupling to G proteins. For some receptors, this GRK-mediated phosphorylation stimulates additional signaling through the scaffolding action of β-arrestin. These downstream signals are configured by β-arrestin conformation, which is dictated by the GRK phosphoacceptors on the receptors in a barcode-like fashion. Furthermore, each of the GRKs can potentially phosphorylate different serine and threonine residues on a given receptor, and the phosphorylation pattern can be biased by the receptor conformation established by bound ligand. Finally, the arrangement of potential GRK phosphorylation sites-and thus the conformation of β-arrestin and its effect on downstream signaling-can differ substantially between even closely related GPCRs stimulated by the same agonist. The diversity of the barcoding to flexible β-arrestin explains the multidimensional nature of signaling in the superfamily and represents new opportunities for drug discovery.},
}
@article {pmid21863493,
year = {2011},
author = {Delneri, D},
title = {Competition experiments coupled with high-throughput analyses for functional genomics studies in yeast.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {759},
number = {},
pages = {271-282},
doi = {10.1007/978-1-61779-173-4_16},
pmid = {21863493},
issn = {1940-6029},
mesh = {Batch Cell Culture Techniques ; Culture Media ; Culture Techniques/instrumentation/*methods ; Fermentation ; Genomics/*methods ; Mutation ; Nucleic Acid Amplification Techniques ; Nucleic Acid Hybridization ; Saccharomyces cerevisiae/*genetics/*growth &amp; development/isolation &amp; purification/metabolism ; },
abstract = {Competition experiments are an effective way to provide a measurement of the fitness of yeast strains. The availability of the Saccharomyces cerevisiae yeast knock-out (YKO) deletion collection allows scientists to retrieve fitness data for the ~6,000 S. cerevisiae genes at the same time in a given environment. The molecular barcodes, characterizing each yeast mutant, serve as strain identifiers, which can be detected in a single microarray analysis. Competition experiments in continuous culture using chemically defined media allow a more specific discrimination of the strains based on their fitness profile. With this high-throughput approach, a series of genes that, when one allele is missing, result in either defective (haplo-insufficient) or favored (haplo-proficient) growth phenotype have been discovered, for each nutrient-limiting condition tested. While haplo-insufficient genes seemed to overlap largely across all the media used, the haplo-proficient ones seem to be more environment specific. For example, genes involved in the protein secretion pathway were highly haplo-insufficient in all the contexts, whereas most of the genes encoding for proteasome components showed a haplo-proficient phenotype specific to nitrogen-limiting conditions. In this chapter, the method used for implementation of competition experiments for high-throughput studies in yeast is presented.},
}
@article {pmid21860376,
year = {2011},
author = {Smith, AM and Durbic, T and Oh, J and Urbanus, M and Proctor, M and Heisler, LE and Giaever, G and Nislow, C},
title = {Competitive genomic screens of barcoded yeast libraries.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {54},
pages = {},
pmid = {21860376},
issn = {1940-087X},
support = {MOP-84305/CAPMC/CIHR/Canada ; HG000205/HG/NHGRI NIH HHS/United States ; R01 HG003317/HG/NHGRI NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; P01 HG000205/HG/NHGRI NIH HHS/United States ; T32 HG00044/HG/NHGRI NIH HHS/United States ; P01 GH000205/GH/CGH CDC HHS/United States ; F32 HG000205/HG/NHGRI NIH HHS/United States ; },
mesh = {Candida albicans/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/analysis/*genetics ; Gene Knockout Techniques ; Genomics/*methods ; Mutation ; Oligonucleotide Array Sequence Analysis/methods ; },
abstract = {By virtue of advances in next generation sequencing technologies, we have access to new genome sequences almost daily. The tempo of these advances is accelerating, promising greater depth and breadth. In light of these extraordinary advances, the need for fast, parallel methods to define gene function becomes ever more important. Collections of genome-wide deletion mutants in yeasts and E. coli have served as workhorses for functional characterization of gene function, but this approach is not scalable, current gene-deletion approaches require each of the thousands of genes that comprise a genome to be deleted and verified. Only after this work is complete can we pursue high-throughput phenotyping. Over the past decade, our laboratory has refined a portfolio of competitive, miniaturized, high-throughput genome-wide assays that can be performed in parallel. This parallelization is possible because of the inclusion of DNA 'tags', or 'barcodes,' into each mutant, with the barcode serving as a proxy for the mutation and one can measure the barcode abundance to assess mutant fitness. In this study, we seek to fill the gap between DNA sequence and barcoded mutant collections. To accomplish this we introduce a combined transposon disruption-barcoding approach that opens up parallel barcode assays to newly sequenced, but poorly characterized microbes. To illustrate this approach we present a new Candida albicans barcoded disruption collection and describe how both microarray-based and next generation sequencing-based platforms can be used to collect 10,000-1,000,000 gene-gene and drug-gene interactions in a single experiment.},
}
@article {pmid21858028,
year = {2011},
author = {Hirakawa, Y and Howe, A and James, ER and Keeling, PJ},
title = {Morphological diversity between culture strains of a chlorarachniophyte, Lotharella globosa.},
journal = {PloS one},
volume = {6},
number = {8},
pages = {e23193},
pmid = {21858028},
issn = {1932-6203},
mesh = {Biodiversity ; Cell Nucleus/genetics/ultrastructure ; Cercozoa/*classification/*genetics/growth &amp; development ; DNA Barcoding, Taxonomic/methods ; DNA, Ribosomal/chemistry/*genetics ; Genetic Variation ; Microscopy, Electron, Transmission ; Mitochondria/ultrastructure ; Molecular Sequence Data ; Plastids/ultrastructure ; RNA, Ribosomal/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Chlorarachniophytes are marine unicellular algae that possess secondary plastids of green algal origin. Although chlorarachniophytes are a small group (the phylum of Chlorarachniophyta contains 14 species in 8 genera), they have variable and complex life cycles that include amoeboid, coccoid, and/or flagellate cells. The majority of chlorarachniophytes possess two or more cell types in their life cycles, and which cell types are found is one of the principle morphological criteria used for species descriptions. Here we describe an unidentified chlorarachniophyte that was isolated from an artificial coral reef that calls this criterion into question. The life cycle of the new strain includes all three major cell types, but DNA barcoding based on the established nucleomorph ITS sequences showed it to share 100% sequence identity with Lotharella globosa. The type strain of L. globosa was also isolated from a coral reef, but is defined as completely lacking an amoeboid stage throughout its life cycle. We conclude that L. globosa possesses morphological diversity between culture strains, and that the new strain is a variety of L. globosa, which we describe as Lotharella globosa var. fortis var. nov. to include the amoeboid stage in the formal description of L. globosa. This intraspecies variation suggest that gross morphological stages maybe lost rather rapidly, and specifically that the type strain of L. globosa has lost the ability to form the amoeboid stage, perhaps recently. This in turn suggests that even major morphological characters used for taxonomy of this group may be variable in natural populations, and therefore misleading.},
}
@article {pmid21857897,
year = {2011},
author = {Little, DP},
title = {DNA barcode sequence identification incorporating taxonomic hierarchy and within taxon variability.},
journal = {PloS one},
volume = {6},
number = {8},
pages = {e20552},
pmid = {21857897},
issn = {1932-6203},
mesh = {*Algorithms ; Animals ; Base Sequence ; Classification/*methods ; DNA Barcoding, Taxonomic/*methods ; Humans ; Molecular Sequence Data ; Phylogeny ; Plants/classification/genetics ; Protein-Tyrosine Kinases/genetics ; Reproducibility of Results ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Alignment/*methods ; Species Specificity ; },
abstract = {For DNA barcoding to succeed as a scientific endeavor an accurate and expeditious query sequence identification method is needed. Although a global multiple-sequence alignment can be generated for some barcoding markers (e.g. COI, rbcL), not all barcoding markers are as structurally conserved (e.g. matK). Thus, algorithms that depend on global multiple-sequence alignments are not universally applicable. Some sequence identification methods that use local pairwise alignments (e.g. BLAST) are unable to accurately differentiate between highly similar sequences and are not designed to cope with hierarchic phylogenetic relationships or within taxon variability. Here, I present a novel alignment-free sequence identification algorithm--BRONX--that accounts for observed within taxon variability and hierarchic relationships among taxa. BRONX identifies short variable segments and corresponding invariant flanking regions in reference sequences. These flanking regions are used to score variable regions in the query sequence without the production of a global multiple-sequence alignment. By incorporating observed within taxon variability into the scoring procedure, misidentifications arising from shared alleles/haplotypes are minimized. An explicit treatment of more inclusive terminals allows for separate identifications to be made for each taxonomic level and/or for user-defined terminals. BRONX performs better than all other methods when there is imperfect overlap between query and reference sequences (e.g. mini-barcode queries against a full-length barcode database). BRONX consistently produced better identifications at the genus-level for all query types.},
}
@article {pmid21857895,
year = {2011},
author = {Janzen, DH and Hallwachs, W and Burns, JM and Hajibabaei, M and Bertrand, C and Hebert, PD},
title = {Reading the complex skipper butterfly fauna of one tropical place.},
journal = {PloS one},
volume = {6},
number = {8},
pages = {e19874},
pmid = {21857895},
issn = {1932-6203},
mesh = {Animal Feed ; Animals ; Biodiversity ; Breeding ; Butterflies/*classification/*genetics/growth &amp; development ; Costa Rica ; DNA Barcoding, Taxonomic/*methods ; Ecology ; Electron Transport Complex IV/genetics ; Female ; Genetic Variation ; Geography ; Male ; *Phylogeny ; Plant Development ; Plants/parasitology ; Species Specificity ; Tropical Climate ; },
abstract = {BACKGROUND: An intense, 30-year, ongoing biodiversity inventory of Lepidoptera, together with their food plants and parasitoids, is centered on the rearing of wild-caught caterpillars in the 120,000 terrestrial hectares of dry, rain, and cloud forest of Area de Conservacion Guanacaste (ACG) in northwestern Costa Rica. Since 2003, DNA barcoding of all species has aided their identification and discovery. We summarize the process and results for a large set of the species of two speciose subfamilies of ACG skipper butterflies (Hesperiidae) and emphasize the effectiveness of barcoding these species (which are often difficult and time-consuming to identify).<br><br>Adults are DNA barcoded by the Biodiversity Institute of Ontario, Guelph, Canada; and they are identified by correlating the resulting COI barcode information with more traditional information such as food plant, facies, genitalia, microlocation within ACG, caterpillar traits, etc. This process has found about 303 morphologically defined species of eudamine and pyrgine Hesperiidae breeding in ACG (about 25% of the ACG butterfly fauna) and another 44 units indicated by distinct barcodes (n&#x200a;=&#x200a;9,094), which may be additional species and therefore may represent as much as a 13% increase. All but the members of one complex can be identified by their DNA barcodes.<br><br>CONCLUSIONS/SIGNIFICANCE: Addition of DNA barcoding to the methodology greatly improved the inventory, both through faster (hence cheaper) accurate identification of the species that are distinguishable without barcoding, as well as those that require it, and through the revelation of species "hidden" within what have long been viewed as single species. Barcoding increased the recognition of species-level specialization. It would be no more appropriate to ignore barcode data in a species inventory than it would be to ignore adult genitalia variation or caterpillar ecology.},
}
@article {pmid21857894,
year = {2011},
author = {Janzen, DH and Hallwachs, W},
title = {Joining inventory by parataxonomists with DNA barcoding of a large complex tropical conserved wildland in northwestern Costa Rica.},
journal = {PloS one},
volume = {6},
number = {8},
pages = {e18123},
pmid = {21857894},
issn = {1932-6203},
mesh = {Adult ; Animals ; Biodiversity ; Classification/methods ; Conservation of Natural Resources ; Costa Rica ; DNA Barcoding, Taxonomic/*methods ; Ecology ; Female ; Geography ; Humans ; Lepidoptera/*classification/*genetics/growth &amp; development ; Male ; Middle Aged ; Phylogeny ; Species Specificity ; *Tropical Climate ; Young Adult ; },
abstract = {BACKGROUND: The many components of conservation through biodiversity development of a large complex tropical wildland, Area de Conservacion Guanacaste (ACG), thrive on knowing what is its biodiversity and natural history. For 32 years a growing team of Costa Rican parataxonomists has conducted biodiversity inventory of ACG caterpillars, their food plants, and their parasitoids. In 2003, DNA barcoding was added to the inventory process.<br><br>We describe some of the salient consequences for the parataxonomists of barcoding becoming part of a field biodiversity inventory process that has centuries of tradition. From the barcoding results, the parataxonomists, as well as other downstream users, gain a more fine-scale and greater understanding of the specimens they find, rear, photograph, database and deliver. The parataxonomists also need to adjust to collecting more specimens of what appear to be the "same species"--cryptic species that cannot be distinguished by eye or even food plant alone--while having to work with the name changes and taxonomic uncertainty that comes with discovering that what looked like one species may be many.<br><br>CONCLUSIONS/SIGNIFICANCE: These career parataxonomists, despite their lack of formal higher education, have proven very capable of absorbing and working around the additional complexity and requirements for accuracy and detail that are generated by adding barcoding to the field base of the ACG inventory. In the process, they have also gained a greater understanding of the fine details of phylogeny, relatedness, evolution, and species-packing in their own tropical complex ecosytems. There is no reason to view DNA barcoding as incompatible in any way with tropical biodiversity inventory as conducted by parataxonomists. Their year-round on-site inventory effort lends itself well to the sampling patterns and sample sizes needed to build a thorough barcode library. Furthermore, the biological understanding that comes with barcoding increases the scientific penetrance of biodiversity information, DNA understanding, evolution, and ecology into the communities in which the parataxonomists and their families are resident.},
}
@article {pmid21840834,
year = {2011},
author = {Chaveerach, A and Tanee, T and Sudmoon, R},
title = {Molecular identification and barcodes for the genus Nymphaea.},
journal = {Acta biologica Hungarica},
volume = {62},
number = {3},
pages = {328-340},
doi = {10.1556/ABiol.62.2011.3.11},
pmid = {21840834},
issn = {0236-5383},
mesh = {Base Sequence ; DNA/analysis ; Electronic Data Processing ; Genes, Plant ; Genetic Markers ; Models, Biological ; Models, Genetic ; Molecular Sequence Data ; Nymphaea/*genetics/metabolism ; Phylogeny ; Plant Leaves/embryology ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; },
abstract = {Nymphaea species, the most popular decorative plants, were collected for specificity of inter-simple sequence repeat (ISSR) analyses in species identification and differentiation of cultivars and natural populations. Dendrogram constructed from ISSR analyses separated out wild species, namely Nymphaea cyanea, N. nouchali, N. capensis, N. lotus and an outgroup N. mexicana, and cultivars. The dendrogram indicates that the cultivars should be differentiated from N. capensis, as they are sister individuals of N. capensis. The ISSR banding data and the dendrogram are concordantly concluded that wild N. capensis would be an effective type species for producing different cultivars. After plant identification by ISSR markers, DNA barcodes of all sample materials were done to provide species specific markers which can be used for rapid and accurate further plant identification without morphological characters. DNA barcoding sequence analysis indicates genetic distance values. All sequences were recorded in GenBank database.},
}
@article {pmid21831139,
year = {2012},
author = {Gleason, LU and Burton, RS},
title = {High-throughput molecular identification of fish eggs using multiplex suspension bead arrays.},
journal = {Molecular ecology resources},
volume = {12},
number = {1},
pages = {57-66},
doi = {10.1111/j.1755-0998.2011.03059.x},
pmid = {21831139},
issn = {1755-0998},
mesh = {Animals ; DNA Primers/genetics ; Electron Transport Complex IV/genetics ; Fish Proteins/genetics ; Fishes/*classification/*genetics ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis/instrumentation/*methods ; Oligonucleotide Probes/genetics ; Ovum/*chemistry/classification ; },
abstract = {The location and abundance of fish eggs provide information concerning the timing and location of spawning activities and can provide fishery-independent estimates of spawning biomass. However, the full value of egg and larval surveys is severely restricted because many species' eggs and larvae are morphologically similar, making species-level identification difficult. Recent efforts have shown that nearly all species of fish may be identified by mitochondrial DNA (mtDNA) sequences (e.g. via 'DNA barcoding'). By taking advantage of a DNA barcode database, we have developed oligonucleotide probes for 23 marine fish species that produce pelagic eggs commonly found in California waters. Probes were coupled to fluorescent microspheres to create a suspension bead array. Biotin-labelled primers were used to amplify the mitochondrial cytochrome oxidase subunit I (COI) and 16S ribosomal rRNA genes from individual fish eggs. The amplicons were then hybridized to the bead array, and after the addition of a reporter fluorophore, samples were analysed by flow cytometry with Luminex 100 instrumentation. Probes specifically targeted eggs that are abundant and/or from morphologically indistinguishable species pairs. Results showed that the 33 different probes designed for this study accurately identified all samples when PCR was successful. Suspension bead arrays have a number of benefits over other methods of molecular identification; these arrays permit high multiplexing, simple addition of new probes, high throughput and lower cost than DNA sequencing. The increasing availability of DNA barcode data for numerous fish faunas worldwide suggests that bead arrays could be developed and widely used for fish egg, larval and tissue identifications.},
}
@article {pmid21829636,
year = {2011},
author = {Ardura, A and Planes, S and Garcia-Vazquez, E},
title = {Beyond biodiversity: fish metagenomes.},
journal = {PloS one},
volume = {6},
number = {8},
pages = {e22592},
pmid = {21829636},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; Fishes/classification/*genetics ; *Genome ; },
abstract = {Biodiversity and intra-specific genetic diversity are interrelated and determine the potential of a community to survive and evolve. Both are considered together in Prokaryote communities treated as metagenomes or ensembles of functional variants beyond species limits.Many factors alter biodiversity in higher Eukaryote communities, and human exploitation can be one of the most important for some groups of plants and animals. For example, fisheries can modify both biodiversity and genetic diversity (intra specific). Intra-specific diversity can be drastically altered by overfishing. Intense fishing pressure on one stock may imply extinction of some genetic variants and subsequent loss of intra-specific diversity. The objective of this study was to apply a metagenome approach to fish communities and explore its value for rapid evaluation of biodiversity and genetic diversity at community level. Here we have applied the metagenome approach employing the barcoding target gene coi as a model sequence in catch from four very different fish assemblages exploited by fisheries: freshwater communities from the Amazon River and northern Spanish rivers, and marine communities from the Cantabric and Mediterranean seas.Treating all sequences obtained from each regional catch as a biological unit (exploited community) we found that metagenomic diversity indices of the Amazonian catch sample here examined were lower than expected. Reduced diversity could be explained, at least partially, by overexploitation of the fish community that had been independently estimated by other methods.We propose using a metagenome approach for estimating diversity in Eukaryote communities and early evaluating genetic variation losses at multi-species level.},
}
@article {pmid21829451,
year = {2011},
author = {Carr, CM and Hardy, SM and Brown, TM and Macdonald, TA and Hebert, PD},
title = {A tri-oceanic perspective: DNA barcoding reveals geographic structure and cryptic diversity in Canadian polychaetes.},
journal = {PloS one},
volume = {6},
number = {7},
pages = {e22232},
pmid = {21829451},
issn = {1932-6203},
mesh = {Animals ; Canada ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; *Genetic Variation ; Genotype ; Geography ; Oceans and Seas ; Phylogeny ; Polychaeta/classification/*genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND: Although polychaetes are one of the dominant taxa in marine communities, their distributions and taxonomic diversity are poorly understood. Recent studies have shown that many species thought to have broad distributions are actually a complex of allied species. In Canada, 12% of polychaete species are thought to occur in Atlantic, Arctic, and Pacific Oceans, but the extent of gene flow among their populations has not been tested.<br><br>Sequence variation in a segment of the mitochondrial cytochrome c oxidase I (COI) gene was employed to compare morphological versus molecular diversity estimates, to examine gene flow among populations of widespread species, and to explore connectivity patterns among Canada's three oceans. Analysis of 1876 specimens, representing 333 provisional species, revealed 40 times more sequence divergence between than within species (16.5% versus 0.38%). Genetic data suggest that one quarter of previously recognized species actually include two or more divergent lineages, indicating that richness in this region is currently underestimated. Few species with a tri-oceanic distribution showed genetic cohesion. Instead, large genetic breaks occur between Pacific and Atlantic-Arctic lineages, suggesting their long-term separation. High connectivity among Arctic and Atlantic regions and low connectivity with the Pacific further supports the conclusion that Canadian polychaetes are partitioned into two distinct faunas.<br><br>CONCLUSIONS/SIGNIFICANCE: Results of this study confirm that COI sequences are an effective tool for species identification in polychaetes, and suggest that DNA barcoding will aid the recognition of species overlooked by the current taxonomic system. The consistent geographic structuring within presumed widespread species suggests that historical range fragmentation during the Pleistocene ultimately increased Canadian polychaete diversity and that the coastal British Columbia fauna played a minor role in Arctic recolonization following deglaciation. This study highlights the value of DNA barcoding for providing rapid insights into species distributions and biogeographic patterns in understudied groups.},
}
@article {pmid21827837,
year = {2011},
author = {Gupta, AK and Harish, and Rai, MK and Phulwaria, M and Shekhawat, NS},
title = {Isolation of genomic DNA suitable for community analysis from mature trees adapted to arid environment.},
journal = {Gene},
volume = {487},
number = {2},
pages = {156-159},
doi = {10.1016/j.gene.2011.06.029},
pmid = {21827837},
issn = {1879-0038},
mesh = {Adaptation, Biological/*genetics ; Algorithms ; Base Sequence ; Biota ; Cloning, Molecular/*methods ; DNA, Plant/*isolation &amp; purification ; Desert Climate ; Environment ; *Genome, Plant ; Molecular Sequence Data ; Nucleic Acid Amplification Techniques ; Trees/chemistry/*genetics/*physiology ; },
abstract = {Isolation of intact and pure genomic DNA (gDNA) is essential for many molecular biology applications. It is difficult to isolate pure DNA from mature trees of hot and dry desert regions because of the accumulation of high level of polysaccharides, phenolic compounds, tannins etc. We hereby report the standardized protocol for the isolation and purification of gDNA from seven ecologically and medically important tree species of Combretaceae viz. Anogeissus (Anogeissus sericea var. nummularia, Anogeissus pendula, and Anogeissus latifolia) and Terminalia (Terminalia arjuna, Terminalia bellirica, Terminalia catappa and Terminalia chebula). This method involves (i) washing the sample twice with Triton buffer (2%) then (ii) isolation of gDNA by modified-CTAB (cetyl trimethyl ammonium bromide) method employing a high concentration (4%) of PVP (Polyvinylpyrrolidone) and 50mM ascorbic acid, and (iii) purification of this CTAB-isolated gDNA by spin-column. gDNA isolated by modified CTAB or spin-column alone were not found suitable for PCR amplification. The Triton washing step is also critical. The quality of DNA was determined by the A(260)/A(280) absorbance ratio. gDNA was also observed for its intactness by running on 0.8% agarose gel. The suitability of extracted DNA for PCR was tested by amplification with RAPD primers, which was successful. Further, rbcLa (barcoding gene) was amplified and sequenced to check the quality of extracted gDNA for its downstream applications.},
}
@article {pmid21824335,
year = {2012},
author = {Xia, Y and Gu, HF and Peng, R and Chen, Q and Zheng, YC and Murphy, RW and Zeng, XM},
title = {COI is better than 16S rRNA for DNA barcoding Asiatic salamanders (Amphibia: Caudata: Hynobiidae).},
journal = {Molecular ecology resources},
volume = {12},
number = {1},
pages = {48-56},
doi = {10.1111/j.1755-0998.2011.03055.x},
pmid = {21824335},
issn = {1755-0998},
mesh = {Amphibian Proteins/*genetics ; Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Caudata/*classification/*genetics ; },
abstract = {The 5' region of the mitochondrial DNA (mtDNA) gene cytochrome c oxidase I (COI) is the standard marker for DNA barcoding. However, because COI tends to be highly variable in amphibians, sequencing is often challenging. Consequently, another mtDNA gene, 16S rRNA gene, is often advocated for amphibian barcoding. Herein, we directly compare the usefulness of COI and 16S in discriminating species of hynobiid salamanders using 130 individuals. Species identification and classification of these animals, which are endemic to Asia, are often based on morphology only. Analysis of Kimura 2-parameter genetic distances (K2P) documents the mean intraspecific variation for COI and 16S rRNA genes to be 1.4% and 0.3%, respectively. Whereas COI can always identify species, sometimes 16S cannot. Intra- and interspecific genetic divergences occasionally overlap in both markers, thus reducing the value of a barcoding gap to identify genera. Regardless, COI is the better DNA barcoding marker for hynobiids. In addition to the comparison of two potential markers, high levels of intraspecific divergence in COI (>5%) suggest that both Onychodactylus fischeri and Salamandrella keyserlingii might be composites of cryptic species.},
}
@article {pmid21824334,
year = {2012},
author = {Bell, D and Long, DG and Forrest, AD and Hollingsworth, ML and Blom, HH and Hollingsworth, PM},
title = {DNA barcoding of European Herbertus (Marchantiopsida, Herbertaceae) and the discovery and description of a new species.},
journal = {Molecular ecology resources},
volume = {12},
number = {1},
pages = {36-47},
doi = {10.1111/j.1755-0998.2011.03053.x},
pmid = {21824334},
issn = {1755-0998},
support = {MR/K001744/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Europe ; Hepatophyta/anatomy &amp; histology/*classification/genetics ; Molecular Sequence Data ; Phylogeny ; Plastids/genetics ; },
abstract = {DNA barcoding of a group of European liverwort species from the genus Herbertus was undertaken using three plastid (matK, rbcL and trnH-psbA) and one nuclear (ITS) marker. The DNA barcode data were effective in discriminating among the sampled species of Herbertus and contributed towards the detection of a previously overlooked European Herbertus species, described here as H. norenus sp. nov. This species shows clear-cut differences in DNA sequence for multiple barcode regions and is also morphologically distinct. The DNA barcode data were also useful in clarifying taxonomic relationships of the European species with some species from Asia and North America. In terms of the discriminatory power of the different barcode markers, ITS was the most informative region, followed closely by matK. All species were distinguishable by ITS alone, rbcL + matK and various other multimarker combinations.},
}
@article {pmid21821820,
year = {2012},
author = {Grant-Braham, B and Britton, J},
title = {Motor racing, tobacco company sponsorship, barcodes and alibi marketing.},
journal = {Tobacco control},
volume = {21},
number = {6},
pages = {529-535},
pmid = {21821820},
issn = {1468-3318},
support = {//British Heart Foundation/United Kingdom ; //Cancer Research UK/United Kingdom ; //Department of Health/United Kingdom ; //Medical Research Council/United Kingdom ; },
mesh = {Advertising/economics/*legislation &amp; jurisprudence ; Automobile Driving ; Electronic Data Processing ; European Union ; Financial Support ; Humans ; Marketing/economics/*legislation &amp; jurisprudence ; Sports/economics/*legislation &amp; jurisprudence ; Tobacco Industry/economics/*legislation &amp; jurisprudence ; },
abstract = {BACKGROUND: Sponsorship of Formula One (F1) motor racing, which has been used as an indirect medium of tobacco advertising for several decades, was prohibited by the 2005 European Union Tobacco Advertising Directive. Most F1 tobacco sponsorship of motor racing in the EU has since ceased, with the exception of the Scuderia Ferrari team, which continues to be funded by Philip Morris. In 2007, the Marlboro logo on Ferrari cars and other race regalia was replaced by an evolving 'barcode' design, which Ferrari later claimed was part of the livery of the car, and not a Marlboro advertisement.<br><br>OBJECTIVE: To determine whether the 'barcode' graphics used by Ferrari represent 'alibi' Marlboro advertising.<br><br>METHODS: Academic and grey literature, and online tobacco industry document archives, were searched using terms relevant to tobacco marketing and motorsport.<br><br>RESULTS: Tobacco sponsorship of F1 motor racing began in 1968, and Philip Morris has sponsored F1 teams since 1972. Phillip Morris first used a 'barcode' design, comprising red vertical parallel lines below the word Marlboro on the British Racing Motors F1 car in 1972. Vertical or horizontal 'barcode' designs have been used in this way, latterly without the word Marlboro, ever since. The modern 'barcode' logos occupied the same position on cars and drivers' clothing as conventional Marlboro logos in the past. The shared use of red colour by Marlboro and Ferrari is also recognised by Philip Morris as a means of promoting brand association between Marlboro and Ferrari.<br><br>CONCLUSION: The Ferrari 'barcode' designs are alibi Marlboro logos and hence constitute advertising prohibited by the 2005 EU Tobacco Advertising Directive.},
}
@article {pmid21818359,
year = {2011},
author = {Clare, EL and Lim, BK and Fenton, MB and Hebert, PD},
title = {Neotropical bats: estimating species diversity with DNA barcodes.},
journal = {PloS one},
volume = {6},
number = {7},
pages = {e22648},
pmid = {21818359},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; *Biodiversity ; Central America ; Chiroptera/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Geography ; Phylogeny ; South America ; Species Specificity ; Sympatry/genetics ; *Tropical Climate ; },
abstract = {DNA barcoding using the cytochrome c oxidase subunit 1 gene (COI) is frequently employed as an efficient method of species identification in animal life and may also be used to estimate species richness, particularly in understudied faunas. Despite numerous past demonstrations of the efficiency of this technique, few studies have attempted to employ DNA barcoding methodologies on a large geographic scale, particularly within tropical regions. In this study we survey current and potential species diversity using DNA barcodes with a collection of more than 9000 individuals from 163 species of Neotropical bats (order Chiroptera). This represents one of the largest surveys to employ this strategy on any animal group and is certainly the largest to date for land vertebrates. Our analysis documents the utility of this tool over great geographic distances and across extraordinarily diverse habitats. Among the 163 included species 98.8% possessed distinct sets of COI haplotypes making them easily recognizable at this locus. We detected only a single case of shared haplotypes. Intraspecific diversity in the region was high among currently recognized species (mean of 1.38%, range 0-11.79%) with respect to birds, though comparable to other bat assemblages. In 44 of 163 cases, well-supported, distinct intraspecific lineages were identified which may suggest the presence of cryptic species though mean and maximum intraspecific divergence were not good predictors of their presence. In all cases, intraspecific lineages require additional investigation using complementary molecular techniques and additional characters such as morphology and acoustic data. Our analysis provides strong support for the continued assembly of DNA barcoding libraries and ongoing taxonomic investigation of bats.},
}
@article {pmid21818256,
year = {2011},
author = {Shokralla, S and Zhou, X and Janzen, DH and Hallwachs, W and Landry, JF and Jacobus, LM and Hajibabaei, M},
title = {Pyrosequencing for mini-barcoding of fresh and old museum specimens.},
journal = {PloS one},
volume = {6},
number = {7},
pages = {e21252},
pmid = {21818256},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Lepidoptera/enzymology/*genetics ; *Museums ; Phylogeny ; *Temperature ; },
abstract = {DNA barcoding is an effective approach for species identification and for discovery of new and/or cryptic species. Sanger sequencing technology is the method of choice for obtaining standard 650 bp cytochrome c oxidase subunit I (COI) barcodes. However, DNA degradation/fragmentation makes it difficult to obtain a full-length barcode from old specimens. Mini-barcodes of 130 bp from the standard barcode region have been shown to be effective for accurate identification in many animal groups and may be readily obtained from museum samples. Here we demonstrate the application of an alternative sequencing technology, the four-enzymes single-specimen pyrosequencing, in rapid, cost-effective mini-barcode analysis. We were able to generate sequences of up to 100 bp from mini-barcode fragments of COI in 135 fresh and 50 old Lepidoptera specimens (ranging from 53-97 year-old). The sequences obtained using pyrosequencing were of high quality and we were able to robustly match all the tested pyro-sequenced samples to their respective Sanger-sequenced standard barcode sequences, where available. Simplicity of the protocol and instrumentation coupled with higher speed and lower cost per sequence than Sanger sequencing makes this approach potentially useful in efforts to link standard barcode sequences from unidentified specimens to known museum specimens with only short DNA fragments.},
}
@article {pmid21818252,
year = {2011},
author = {Lijtmaer, DA and Kerr, KC and Barreira, AS and Hebert, PD and Tubaro, PL},
title = {DNA barcode libraries provide insight into continental patterns of avian diversification.},
journal = {PloS one},
volume = {6},
number = {7},
pages = {e20744},
pmid = {21818252},
issn = {1932-6203},
mesh = {Animals ; Arctic Regions ; Argentina ; *Biodiversity ; Birds/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Gene Library ; Haplotypes/genetics ; Phylogeography ; Species Specificity ; },
abstract = {BACKGROUND: The causes for the higher biodiversity in the Neotropics as compared to the Nearctic and the factors promoting species diversification in each region have been much debated. The refuge hypothesis posits that high tropical diversity reflects high speciation rates during the Pleistocene, but this conclusion has been challenged. The present study investigates this matter by examining continental patterns of avian diversification through the analysis of large-scale DNA barcode libraries.<br><br>Standardized COI datasets from the avifaunas of Argentina, the Nearctic, and the Palearctic were analyzed. Average genetic distances between closest congeners and sister species were higher in Argentina than in North America reflecting a much higher percentage of recently diverged species in the latter region. In the Palearctic genetic distances between closely related species appeared to be more similar to those of the southern Neotropics. Average intraspecific variation was similar in Argentina and North America, while the Palearctic fauna had a higher value due to a higher percentage of variable species. Geographic patterning of intraspecific structure was more complex in the southern Neotropics than in the Nearctic, while the Palearctic showed an intermediate level of complexity.<br><br>CONCLUSIONS AND SIGNIFICANCE: DNA barcodes can reveal continental patterns of diversification. Our analysis suggests that avian species are older in Argentina than in the Nearctic, supporting the idea that the greater diversity of the Neotropical avifauna is not caused by higher recent speciation rates. Species in the Palearctic also appear to be older than those in the Nearctic. These results, combined with the patterns of geographic structuring found in each region, suggest a major impact of Pleistocene glaciations in the Nearctic, a lesser effect in the Palearctic and a mild effect in the southern Neotropics.},
}
@article {pmid21818249,
year = {2011},
author = {Sarkar, IN and Trizna, M},
title = {The Barcode of Life Data Portal: bridging the biodiversity informatics divide for DNA barcoding.},
journal = {PloS one},
volume = {6},
number = {7},
pages = {e14689},
pmid = {21818249},
issn = {1932-6203},
support = {R01 LM009725/LM/NLM NIH HHS/United States ; R01LM009725/LM/NLM NIH HHS/United States ; },
mesh = {Algorithms ; *Biodiversity ; Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; *Databases as Topic ; Publications ; Statistics as Topic ; },
abstract = {With the volume of molecular sequence data that is systematically being generated globally, there is a need for centralized resources for data exploration and analytics. DNA Barcode initiatives are on track to generate a compendium of molecular sequence-based signatures for identifying animals and plants. To date, the range of available data exploration and analytic tools to explore these data have only been available in a boutique form--often representing a frustrating hurdle for many researchers that may not necessarily have resources to install or implement algorithms described by the analytic community. The Barcode of Life Data Portal (BDP) is a first step towards integrating the latest biodiversity informatics innovations with molecular sequence data from DNA barcoding. Through establishment of community driven standards, based on discussion with the Data Analysis Working Group (DAWG) of the Consortium for the Barcode of Life (CBOL), the BDP provides an infrastructure for incorporation of existing and next-generation DNA barcode analytic applications in an open forum.},
}
@article {pmid21809386,
year = {2011},
author = {McMahon, KW and Manukyan, A and Dungrawala, H and Montgomery, M and Nordstrom, B and Wright, J and Abraham, L and Schneider, BL},
title = {FASTA barcodes: a simple method for the identification of yeast ORF deletions.},
journal = {Yeast (Chichester, England)},
volume = {28},
number = {9},
pages = {661-671},
doi = {10.1002/yea.1894},
pmid = {21809386},
issn = {1097-0061},
support = {R01GM077874/GM/NIGMS NIH HHS/United States ; R01GM077874-04S1/GM/NIGMS NIH HHS/United States ; },
mesh = {Base Sequence ; Computational Biology/instrumentation/*methods ; Databases, Nucleic Acid/instrumentation ; Electronic Data Processing/instrumentation/*methods ; Molecular Sequence Data ; *Open Reading Frames ; Saccharomyces cerevisiae/*genetics ; Sequence Analysis, DNA ; *Sequence Deletion ; *Software ; },
abstract = {A consortium of yeast geneticists have created -6000 individual ORF deletions, representing > 96% of the currently verified or predicted ORFs in S. cerevisiae. Importantly, molecular barcodes (each a unique 20 bp sequence termed either Uptag or Downtag) were used as identifiers for every ORF deletion. Microarray analyses of pooled yeast deletions has been used to identify thousands of genes involved in general fitness, haploinsufficiency, drug resistance and DNA damage repair. However, application of this powerful technology requires considerable expense, expertise and specialized equipment. While standard PCR techniques and specifically designed PCR primers can be used to confirm that a given ORF is in fact deleted, this procedure cannot be used to identify unknown deletions. In theory, every ORF deletion could be determined by barcode sequencing. However, neither a consolidated barcode database nor a reliable search engine is currently available for this purpose. To address this need, we have adapted a FASTA sequence program that utilizes the unique barcode database to allow users to identify individual ORF deletions, based upon simple sequencing reactions of PCR amplifications of either Uptag or Downtag barcodes. In silico and practical testing of this application reveals that it is an inexpensive, reliable and reproducible method for rapidly identifying unknown deletions. This approach allows laboratories to conduct small- or large-scale genetic screens with pooled yeast deletion strains and identify or verify any ORF deletion without the need for microarray technology.},
}
@article {pmid21806794,
year = {2011},
author = {Wilson, JJ and Rougerie, R and Schonfeld, J and Janzen, DH and Hallwachs, W and Hajibabaei, M and Kitching, IJ and Haxaire, J and Hebert, PD},
title = {When species matches are unavailable are DNA barcodes correctly assigned to higher taxa? An assessment using sphingid moths.},
journal = {BMC ecology},
volume = {11},
number = {},
pages = {18},
pmid = {21806794},
issn = {1472-6785},
mesh = {Animals ; Base Sequence ; DNA/genetics ; DNA Barcoding, Taxonomic/instrumentation/*methods ; Gene Library ; Molecular Sequence Data ; Moths/*classification/*genetics ; Phylogeny ; },
abstract = {BACKGROUND: When a specimen belongs to a species not yet represented in DNA barcode reference libraries there is disagreement over the effectiveness of using sequence comparisons to assign the query accurately to a higher taxon. Library completeness and the assignment criteria used have been proposed as critical factors affecting the accuracy of such assignments but have not been thoroughly investigated. We explored the accuracy of assignments to genus, tribe and subfamily in the Sphingidae, using the almost complete global DNA barcode reference library (1095 species) available for this family. Costa Rican sphingids (118 species), a well-documented, diverse subset of the family, with each of the tribes and subfamilies represented were used as queries. We simulated libraries with different levels of completeness (10-100% of the available species), and recorded assignments (positive or ambiguous) and their accuracy (true or false) under six criteria.<br><br>RESULTS: A liberal tree-based criterion assigned 83% of queries accurately to genus, 74% to tribe and 90% to subfamily, compared to a strict tree-based criterion, which assigned 75% of queries accurately to genus, 66% to tribe and 84% to subfamily, with a library containing 100% of available species (but excluding the species of the query). The greater number of true positives delivered by more relaxed criteria was negatively balanced by the occurrence of more false positives. This effect was most sharply observed with libraries of the lowest completeness where, for example at the genus level, 32% of assignments were false positives with the liberal criterion versus < 1% when using the strict. We observed little difference (< 8% using the liberal criterion) however, in the overall accuracy of the assignments between the lowest and highest levels of library completeness at the tribe and subfamily level.<br><br>CONCLUSIONS: Our results suggest that when using a strict tree-based criterion for higher taxon assignment with DNA barcodes, the likelihood of assigning a query a genus name incorrectly is very low, if a genus name is provided it has a high likelihood of being accurate, and if no genus match is available the query can nevertheless be assigned to a subfamily with high accuracy regardless of library completeness. DNA barcoding often correctly assigned sphingid moths to higher taxa when species matches were unavailable, suggesting that barcode reference libraries can be useful for higher taxon assignments long before they achieve complete species coverage.},
}
@article {pmid21804206,
year = {2011},
author = {Guo, X and Wang, X and Su, W and Zhang, G and Zhou, R},
title = {DNA barcodes for discriminating the medicinal plant Scutellaria baicalensis (Lamiaceae) and its adulterants.},
journal = {Biological &amp; pharmaceutical bulletin},
volume = {34},
number = {8},
pages = {1198-1203},
doi = {10.1248/bpb.34.1198},
pmid = {21804206},
issn = {1347-5215},
mesh = {DNA Barcoding, Taxonomic/*methods ; *DNA, Intergenic ; *DNA, Plant ; Drug Contamination/*prevention &amp; control ; Drugs, Chinese Herbal/*standards ; Electronic Data Processing ; Endoribonucleases/genetics ; *Genes, Plant ; Nucleotidyltransferases/genetics ; Plant Leaves ; Plant Roots/chemistry ; Ribulose-Bisphosphate Carboxylase/genetics ; Scutellaria baicalensis/*genetics ; Sequence Analysis, DNA/methods ; Sequence Homology, Nucleic Acid ; Species Specificity ; },
abstract = {Scutellaria baicalensis GEORGI (Lamiaceae) is the botanical origin of the well-known traditional Chinese medicine "Huang Qin" (Radix Scutellariae). Due to overexploitation that had induced a decline in natural sources, the dried roots of its congeners, S. amoena, S. rehderiana, and S. viscidula, have been used to adulterate it in recent years. This practice may cause a series of inconsistent therapeutic effects and quality control problems in the herbal medicine industry. Hence, we sequenced and analyzed three candidate DNA barcodes, the ribosomal RNA maturase gene (matK), the ribulose-1,4-bisphosphate carboxylase large subunit gene (rbcL), and the psbA-trnH intergenic spacer (psbA-trnH), to discriminate S. baicalensis and its adulterants. All candidate DNA barcodes had been successfully amplified from leaf samples. Comparatively, only psbA-trnH had been yielded from commercially prepared crude drug samples. Based on the sequence divergence, rbcL can assign S. baicalensis and its adulterants into the correct family and genus, whereas, either matK or psbA-trnH can accurately discriminate S. baicalensis and its adulterants. We proposed the multilocus barcodes rbcL+psbA-trnH for the species identification of S. baicalensis and its adulterants, and the unique barcode psbA-trnH for the authentication of commercial Radix Scutellariae. The DNA barcoding technique could be applied to the quality control of "Huang Qin"-based medicinal preparations and to the management of medicinal herb trade in the markets.},
}
@article {pmid21800986,
year = {2011},
author = {Hoy, MB},
title = {An introduction to QR Codes: linking libraries and mobile patrons.},
journal = {Medical reference services quarterly},
volume = {30},
number = {3},
pages = {295-300},
doi = {10.1080/02763869.2011.590423},
pmid = {21800986},
issn = {1540-9597},
mesh = {Cell Phone ; *Computers, Handheld ; *Electronic Data Processing ; Humans ; Information Storage and Retrieval/*methods ; Internet ; *Libraries ; Patients ; *Telecommunications ; },
abstract = {QR codes, or "Quick Response" codes, are two-dimensional barcodes that can be scanned by mobile smartphone cameras. These codes can be used to provide fast access to URLs, telephone numbers, and short passages of text. With the rapid adoption of smartphones, librarians are able to use QR codes to promote services and help library users find materials quickly and independently. This article will explain what QR codes are, discuss how they can be used in the library, and describe issues surrounding their use. A list of resources for generating and scanning QR codes is also provided.},
}
@article {pmid21798211,
year = {2010},
author = {Heimeier, D and Lavery, S and Sewell, MA},
title = {Using DNA barcoding and phylogenetics to identify Antarctic invertebrate larvae: Lessons from a large scale study.},
journal = {Marine genomics},
volume = {3},
number = {3-4},
pages = {165-177},
doi = {10.1016/j.margen.2010.09.004},
pmid = {21798211},
issn = {1876-7478},
abstract = {Ecological studies of the diversity and distribution of marine planktonic larvae are increasingly depending on molecular methods for accurate taxonomic identification. The greater coverage of reference marine species on genetic databases such as GenBank and BoLD (Barcoding of Life Data Systems; www.boldystems.org); together with the decreasing costs for DNA sequencing have made large scale larval identification studies using molecular methods more feasible. Here, we present the development and implementation of a practical molecular approach to identify over 2000 individual marine invertebrate larvae that were collected in the Ross Sea, Antarctica, during the austral summer over five years (2002-2007) as part of the LGP (Latitudinal Gradient Project). Larvae for molecular ID were morphologically identified to belong to the Phyla Mollusca, Echinodermata, Nemertea and Annelida (Class Polychaeta), but also included unidentified early developmental stages which could not be assigned a specific taxon (e.g., eggs, blastulae). The use of a 100μm mesh plankton net makes this one of the first larval identification studies to simultaneously consider both embryos and larvae. Molecular identification methods included amplification of up to three molecular loci for each specimen, a pre-identification step using BLAST with GenBank, phylogenetic reconstructions and cross-validation of assigned Molecular Operational Taxonomic Units (MOTUs). This combined approach of morphological and molecular methods assigned about 700 individuals to 53 MOTUs, which were identified to the lowest possible taxonomic level. During the course of this long-term study we identified several procedural difficulties, including issues with the collection of larvae, locus amplification, contamination, assignment and validation of MOTUs. The practical guidelines that we describe here should greatly assist other researchers to conduct reliable molecular identification studies of larvae in the future.},
}
@article {pmid21793699,
year = {2011},
author = {Kuang, DY and Wu, H and Wang, YL and Gao, LM and Zhang, SZ and Lu, L},
title = {Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): implication for DNA barcoding and population genetics.},
journal = {Genome},
volume = {54},
number = {8},
pages = {663-673},
doi = {10.1139/g11-026},
pmid = {21793699},
issn = {1480-3321},
mesh = {Base Composition ; Chloroplasts/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Chloroplast/*genetics ; Endangered Species ; Evolution, Molecular ; Gene Dosage ; *Genes, Plant ; Genetics, Population ; *Genome, Chloroplast ; *Genome, Plant ; High-Throughput Nucleotide Sequencing ; Magnolia/*genetics ; Open Reading Frames ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; },
abstract = {Here, we report a completely sequenced plastome using Illumina/Solexa sequencing-by-synthesis (SBS) technology. The plastome of Magnolia kwangsiensis Figlar &amp; Noot. is 159 667 bp in length with a typical quadripartite structure: 88 030 bp large single-copy (LSC) and 18 669 bp small single-copy (SSC) regions, separated by two 26 484 bp inverted repeat (IR) regions. The overall predicted gene number is 129, among which 17 genes are duplicated in IR regions. The plastome of M. kwangsiensis is identical in its gene order to previously published plastomes of magnoliids. Furthermore, the C-to-U type RNA editing frequency of 114 seed plants is positively correlated with plastome GC content and plastome length, whereas plastome length is not correlated with GC content. A total of 16 potential putative barcoding or low taxonomic level phylogenetic study markers in Magnoliaceae were detected by comparing the coding and noncoding regions of the plastome of M. kwangsiensis with that of Liriodendron tulipifera L. At least eight markers might be applied not only to Magnoliaceae but also to other taxa. The 86 mononucleotide cpSSRs that distributed in single-copy noncoding regions are highly valuable to study population genetics and conservation genetics of this endangered rare species.},
}
@article {pmid21786674,
year = {2011},
author = {Khrisanfova, GG and Lopatkin, AA and Shestak, AG and Mishchenkov, VA and Zhukova, TV and Akimova, LN and Semenova, SK},
title = {[Polymorphism of the coxl mtDNA gene from cercarian isolates of the avian schistosome Bilharziella polonica (Trematoda: Schistosomatidae) from Belarussian lakes].},
journal = {Genetika},
volume = {47},
number = {5},
pages = {684-690},
pmid = {21786674},
issn = {0016-6758},
mesh = {Animals ; Birds/*parasitology ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Fresh Water/parasitology ; Haplotypes/genetics ; Mollusca/genetics/*parasitology ; Phylogeny ; Population/genetics ; Republic of Belarus ; Schistosomatidae/*genetics/isolation &amp; purification ; },
abstract = {We have studied the phylogeographic structure of avian schistosomes Bilharziella polonica (class Trematoda, family Schistosomatidae), parasites of 18 molluscs Planorbius corneus (family Planorbidae) from three Belarussian lakes. Low nucleotide (pi<0.5%) and high haplotype (h=85.6%) diversity of the gene encoding the cytochrome C oxidase first subunit (coxl) was found on the part of the species range studied. The phylogeographic reconstructions showed that the sample examined consists of at least two lineages ofhaplotypes A and C. Haplotype diversity was somewhat higher in lineage C. The genetic divergence between these genealogical lines reached 0.55%, while the time of possible divergence was 180,000-270,000 years. Possible evolutionary scenarios for differentiation of the B. polonica lines and effectiveness of using coxl for barcoding trematode populations and finding coevolutionary parasite-host relationships are discussed.},
}
@article {pmid21784364,
year = {2011},
author = {Nesi, N and Nakouné, E and Cruaud, C and Hassanin, A},
title = {DNA barcoding of African fruit bats (Mammalia, Pteropodidae). The mitochondrial genome does not provide a reliable discrimination between Epomophorus gambianus and Micropteropus pusillus.},
journal = {Comptes rendus biologies},
volume = {334},
number = {7},
pages = {544-554},
doi = {10.1016/j.crvi.2011.05.003},
pmid = {21784364},
issn = {1768-3238},
mesh = {Animals ; Chiroptera/*classification/*genetics ; *DNA Barcoding, Taxonomic ; *Genome, Mitochondrial ; Reproducibility of Results ; },
abstract = {Sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene have been shown to be useful for species identification in various groups of animals. However, the DNA barcoding approach has never been tested on African fruit bats of the family Pteropodidae (Mammalia, Chiroptera). In this study, the COI gene was sequenced from 120 bats collected in the Central African Republic and belonging to either Epomophorus gambianus or Micropteropus pusillus, two species easily diagnosed on the basis of morphological characters, such as body size, skull shape and palatal ridges. Two additional molecular markers were used for comparisons: the complete mitochondrial cytochrome b gene and the intron 7 of the nuclear β-fibrinogen (FGB) gene. Our results reveal an unexpected discordance between mitochondrial and nuclear genes. The nuclear FGB signal agrees with our morphological identifications, as the three alleles detected for E. gambianus are divergent from the fourteen alleles found for M. pusillus. By contrast, this taxonomic distinction is not recovered with the analyses of mitochondrial genes, which support rather a polyphyletic pattern for both species. The conflict between molecular markers is explained by multiple mtDNA introgression events from M. pusillus into E. gambianus or, alternatively, by incomplete lineage sorting of mtDNA haplotypes associated with positive selection on FGB alleles of M. pusillus. Our work shows the failure of DNA barcoding to discriminate between two morphologically distinct fruit bat species and highlights the importance of using both mitochondrial and nuclear markers for taxonomic identification.},
}
@article {pmid21780468,
year = {2011},
author = {Chung, SH and Son, SJ and Min, J},
title = {Nano barcoding cell-based biosensor using fluorophor-embedded silica nanotubes.},
journal = {Journal of nanoscience and nanotechnology},
volume = {11},
number = {5},
pages = {4419-4423},
doi = {10.1166/jnn.2011.3667},
pmid = {21780468},
issn = {1533-4880},
mesh = {*Biosensing Techniques ; *Electronic Data Processing ; Fluorescent Dyes/*chemistry ; Magnetic Resonance Spectroscopy/methods ; *Nanotubes ; Silicon Dioxide/*chemistry ; Spectroscopy, Fourier Transform Infrared/methods ; },
abstract = {A simple and reliable drug screening method was developed using peptide hydrogel cell beads coded by quantum dot-embedded silica nanotubes. Very long silica nanotubes were fabricated upon a nanoporous alumina template using sol-gel techniques. The physical shapes of the nanotubes were measured by TEM (Transmission Electron Microscope). Green and red quantum dots embedded in silica nanotubes were applied to peptide hydrogel cell beads as coding materials. This was confirmed by confocal microscopy that examined fluorescence levels and quantum dot shapes. The peptide hydrogel cell beads coded with silica nanotubes were loaded into a PDMS single chamber in order to assess the effect of doxorubicin on HMEC and MCF-7 cells, which was measured in hydrogel cell beads by live and dead cell staining using coding materials. As a result, MCF-7 cancer cells were more affected by doxorubicin than HMEC; however, doxorubicin induced HMEC cell death at a relatively high concentration (> 5 microg/ml).},
}
@article {pmid21779811,
year = {2012},
author = {Kauserud, H and Kumar, S and Brysting, AK and Nordén, J and Carlsen, T},
title = {High consistency between replicate 454 pyrosequencing analyses of ectomycorrhizal plant root samples.},
journal = {Mycorrhiza},
volume = {22},
number = {4},
pages = {309-315},
pmid = {21779811},
issn = {1432-1890},
mesh = {Cluster Analysis ; DNA, Fungal/*chemistry/*genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Molecular Sequence Data ; Mycorrhizae/*classification/*genetics/isolation &amp; purification ; Phylogeny ; Plant Roots/*microbiology ; Polygonaceae/*microbiology ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; },
abstract = {In this methodological study, we compare 454 sequencing and a conventional cloning and Sanger sequencing approach in their ability to characterize fungal communities PCR amplified from four root systems of the ectomycorrhizal plant Bistorta vivipara. To examine variation introduced by stochastic processes during the laboratory work, we replicated all analyses using two independently obtained DNA extractions from the same root systems. The ITS1 region was used as DNA barcode and the sequences were clustered into OTUs as proxies for species using single linkage clustering (BLASTC: lust) and 97% sequence similarity cut-off. A relatively low overlap in fungal OTUs was observed between the 454 and the clone library datasets - even among the most abundant OTUs. In a non-metric multidimensional scaling analysis, the samples grouped more according to methodology compared to plant. Some OTUs frequently detected by 454, most notably those OTUs with taxonomic affinity to Glomales, were not detected in the Sanger dataset. Likewise, a few OTUs, including Cenococcum sp., only appeared in the clone libraries. Surprisingly, we observed a significant relationship between GC/AT content of the OTUs and their proportional abundances in the 454 versus the clone library datasets. Reassuringly, a very good consistency in OTU recovery was observed between replicate runs of both sequencing methods. This indicates that stochastic processes had little impact when applying the same sequencing technique on replicate samples.},
}
@article {pmid21777399,
year = {2011},
author = {Kerr, KC},
title = {Searching for evidence of selection in avian DNA barcodes.},
journal = {Molecular ecology resources},
volume = {11},
number = {6},
pages = {1045-1055},
doi = {10.1111/j.1755-0998.2011.03049.x},
pmid = {21777399},
issn = {1755-0998},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Birds/*genetics ; DNA Barcoding, Taxonomic/*methods ; Databases, Genetic ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; *Genetic Variation ; Molecular Sequence Data ; *Selection, Genetic ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The barcode of life project has assembled a tremendous number of mitochondrial cytochrome c oxidase I (COI) sequences. Although these sequences were gathered to develop a DNA-based system for species identification, it has been suggested that further biological inferences may also be derived from this wealth of data. Recurrent selective sweeps have been invoked as an evolutionary mechanism to explain limited intraspecific COI diversity, particularly in birds, but this hypothesis has not been formally tested. In this study, I collated COI sequences from previous barcoding studies on birds and tested them for evidence of selection. Using this expanded data set, I re-examined the relationships between intraspecific diversity and interspecific divergence and sampling effort, respectively. I employed the McDonald-Kreitman test to test for neutrality in sequence evolution between closely related pairs of species. Because amino acid sequences were generally constrained between closely related pairs, I also included broader intra-order comparisons to quantify patterns of protein variation in avian COI sequences. Lastly, using 22 published whole mitochondrial genomes, I compared the evolutionary rate of COI against the other 12 protein-coding mitochondrial genes to assess intragenomic variability. I found no conclusive evidence of selective sweeps. Most evidence pointed to an overall trend of strong purifying selection and functional constraint. The COI protein did vary across the class Aves, but to a very limited extent. COI was the least variable gene in the mitochondrial genome, suggesting that other genes might be more informative for probing factors constraining mitochondrial variation within species.},
}
@article {pmid21777058,
year = {2011},
author = {Nicolè, S and Erickson, DL and Ambrosi, D and Bellucci, E and Lucchin, M and Papa, R and Kress, WJ and Barcaccia, G},
title = {Biodiversity studies in Phaseolus species by DNA barcoding.},
journal = {Genome},
volume = {54},
number = {7},
pages = {529-545},
doi = {10.1139/g11-018},
pmid = {21777058},
issn = {1480-3321},
mesh = {*Biodiversity ; Cell Nucleus/genetics ; Consensus Sequence/genetics ; *DNA Barcoding, Taxonomic ; DNA, Chloroplast/genetics ; DNA, Plant/genetics ; Genetic Variation/genetics ; Phaseolus/classification/*genetics ; Phenotype ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Seeds/anatomy &amp; histology ; },
abstract = {The potential of DNA barcoding was tested as a system for studying genetic diversity and genetic traceability in bean germplasm. This technique was applied to several pure lines of Phaseolus vulgaris L. belonging to wild, domesticated, and cultivated common beans, along with some accessions of Phaseolus coccineus L., Phaseolus lunatus L., and Vigna unguiculata (L.) Walp. A multilocus approach was exploited using three chloroplast genic regions (rbcL, trnL, and matK), four intergenic spacers (rpoB-trnC, atpBrbcL, trnT-trnL, and psbA-trnH), and nuclear ITS1 and ITS2 rDNA sequences. Our main goals were to identify the markers and SNPs that show the best discriminant power at the variety level in common bean germplasm, to examine two methods (tree based versus character based) for biodiversity analysis and traceability assays, and to evaluate the overall utility of chloroplast DNA barcodes for reconstructing the origins of modern Italian varieties. Our results indicate that the neighbor-joining method is a powerful approach for comparing genetic diversity within plant species, but it is relatively uninformative for the genetic traceability of plant varieties. In contrast, the character-based method was able to identify several distinct haplotypes over all target regions corresponding to Mesoamerican or Andean accessions; Italian accessions originated from both gene pools. On the whole, our findings raise some concerns about the use of DNA barcoding for intraspecific genetic diversity studies in common beans and highlights its limitations for resolving genetic relationships between landraces and varieties.},
}
@article {pmid21768154,
year = {2011},
author = {Emerson, BC and Cicconardi, F and Fanciulli, PP and Shaw, PJ},
title = {Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {366},
number = {1576},
pages = {2391-2402},
pmid = {21768154},
issn = {1471-2970},
mesh = {Animals ; Arthropods/*genetics ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/chemistry/genetics ; *Evolution, Molecular ; Phylogeny ; Phylogeography/*methods ; *Soil Microbiology ; },
abstract = {There has been much recent interest and progress in the characterization of community structure and community assembly processes through the application of phylogenetic methods. To date most focus has been on groups of taxa for which some relevant detail of their ecology is known, for which community composition is reasonably easily quantified and where the temporal scale is such that speciation is not likely to feature. Here, we explore how we might apply a molecular genetic approach to investigate community structure and assembly at broad taxonomic and geographical scales, where we have little knowledge of species ecology, where community composition is not easily quantified, and where speciation is likely to be of some importance. We explore these ideas using the class Collembola as a focal group. Gathering molecular evidence for cryptic diversity suggests that the ubiquity of many species of Collembola across the landscape may belie greater community complexity than would otherwise be assumed. However, this morphologically cryptic species-level diversity poses a challenge for attempts to characterize diversity both within and among local species assemblages. Recent developments in high throughput parallel sequencing technology, combined with mtDNA barcoding, provide an advance that can bring together the fields of phylogenetic and phylogeographic analysis to bear on this problem. Such an approach could be standardized for analyses at any geographical scale for a range of taxonomic groups to quantify the formation and composition of species assemblages.},
}
@article {pmid21767431,
year = {2011},
author = {Verneau, O and Palacios, C and Platt, T and Alday, M and Billard, E and Allienne, JF and Basso, C and DU Preez, LH},
title = {Invasive species threat: parasite phylogenetics reveals patterns and processes of host-switching between non-native and native captive freshwater turtles.},
journal = {Parasitology},
volume = {138},
number = {13},
pages = {1778-1792},
doi = {10.1017/S0031182011000333},
pmid = {21767431},
issn = {1469-8161},
mesh = {Animals ; Animals, Wild/*parasitology ; Electron Transport Complex IV/genetics ; Fresh Water ; Helminthiasis, Animal/epidemiology/parasitology/*transmission ; *Host-Parasite Interactions ; *Introduced Species ; *Phylogeny ; Platyhelminths/classification/genetics/*pathogenicity/physiology ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; Turtles/*parasitology ; },
abstract = {One of the major threats to biodiversity involves biological invasions with direct consequences on the stability of ecosystems. In this context, the role of parasites is not negligible as it may enhance the success of invaders. The red-eared slider, Trachemys scripta elegans, has been globally considered among the worst invasive species. Since its introduction through the pet trade, T. s. elegans is now widespread and represents a threat for indigenous species. Because T. s. elegans coexists with Emys orbicularis and Mauremys leprosa in Europe, it has been suggested it may compete with the native turtle species and transmit pathogens. We examined parasite transfer from American captive to the two native species that co-exist in artificial pools of a Turtle Farm in France. As model parasite species we used platyhelminth worms of the family Polystomatidae (Monogenea) because polystomes have been described from American turtles in their native range. Phylogenetic relationships among polystomes parasitizing chelonian host species that are geographically widespread show patterns of diversification more complex than expected. Using DNA barcoding to identify species from adult and/or polystome eggs, several cases of host switching from exotic to indigenous individuals were illustrated, corroborating that parasite transmission is important when considering the pet trade and in reintroduction programmes to reinforce wild populations of indigenous species.},
}
@article {pmid21761562,
year = {2011},
author = {Friedrich, A and Hoheisel, JD and Knemeyer, JP and Marmé, N},
title = {A universally applicable process for preparing stoichiometrically 1:1 labelled functional proteins.},
journal = {Proteomics},
volume = {11},
number = {18},
pages = {3757-3760},
doi = {10.1002/pmic.201100168},
pmid = {21761562},
issn = {1615-9861},
mesh = {Base Sequence ; Carboxypeptidases A/chemistry ; DNA/*chemistry ; Enzyme Activation ; Escherichia coli/enzymology ; Fluorescent Dyes/chemistry ; Hydrophobic and Hydrophilic Interactions ; Proteins/chemistry/*isolation &amp; purification ; Sensitivity and Specificity ; Staining and Labeling/*methods ; beta-Galactosidase/chemistry ; },
abstract = {A universally applicable labelling and purification process was established to prepare biologically active proteins with a stoichiometric 1:1 ratio of attached dye-label. The dye-label is linked to a specific DNA sequence, which acts as a barcode-like tag for affinity purification. The DNA-dye tag is covalently bound to the target protein, which is present in excess to assure the binding of not more than one dye per molecule. Affinity purification occurs at magnetic beads that are functionalized with oligonucleotides that are complementary to the DNA-tag of the labelled proteins but for one or two mismatches. Washing removes all unbound, unlabelled molecules. The labelled protein is subsequently released by the addition of a fully complementary oligonucleotide. This process allows a gentle purification of a protein fraction that has exactly one label attached to each molecule under conditions that preserve protein structure.},
}
@article {pmid21757475,
year = {2011},
author = {Jeanson, ML and Labat, JN and Little, DP},
title = {DNA barcoding: a new tool for palm taxonomists?.},
journal = {Annals of botany},
volume = {108},
number = {8},
pages = {1445-1451},
pmid = {21757475},
issn = {1095-8290},
mesh = {Arecaceae/*classification/*genetics ; Asia, Southeastern ; Base Sequence ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Genetic Markers/genetics ; Molecular Sequence Data ; Phylogeny ; },
abstract = {BACKGROUND AND AIMS: In the last decade, a new tool - DNA barcoding - was proposed to identify species. The technique of DNA barcoding is still being developed. The Consortium for the Barcode of Life's Plant Working Group (CBOL-PWG) selected two core markers (matK and rbcL) that now must be tested in as many taxa as possible. Although the taxonomy of palms (Arecaceae/Palmae) has been greatly improved in the past decades, taxonomic problems remain. Species complexes, for example, could significantly benefit from DNA barcoding. Palms have never before been subjected to a DNA barcoding test.<br><br>METHODS: For this study, 40 out of the 48 species of the southeast Asian tribe Caryoteae (subfamily Coryphoideae) were included. In total, four DNA markers - three plastid encoded (matK, rbcL and psbA-trnH) and one nuclear encoded (nrITS2) - were analysed to determine if adequate variation exists to discriminate among species.<br><br>KEY RESULTS: The combination of three markers - matK, rbcL and nrITS2 - results in 92 % species discrimination. This rate is high for a barcoding experiment. The two core markers suggested by the CBOL-PWG, rbcL and matK, have a low species discrimination rate and need to be supplemented by another marker. In Caryoteae, nrITS2 should be chosen over psbA-trnH to supplement the two 'core' markers.<br><br>CONCLUSIONS: For the first time a test of DNA barcoding was conducted in Arecaceae. Considering that palms have highly variable mutation rates compared with other angiosperms, the results presented here are encouraging for developing DNA barcoding as a useful tool to identify species within this ecologically important tropical plant family.},
}
@article {pmid21754977,
year = {2011},
author = {Smith, MA and Eveleigh, ES and McCann, KS and Merilo, MT and McCarthy, PC and Van Rooyen, KI},
title = {Barcoding a quantified food web: crypsis, concepts, ecology and hypotheses.},
journal = {PloS one},
volume = {6},
number = {7},
pages = {e14424},
pmid = {21754977},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; *Food Chain ; Insecta/genetics/growth &amp; development ; *Models, Biological ; Parasites/genetics ; Phylogeny ; Population Dynamics ; },
abstract = {The efficient and effective monitoring of individuals and populations is critically dependent on correct species identification. While this point may seem obvious, identifying the majority of the more than 100 natural enemies involved in the spruce budworm (Choristoneura fumiferana--SBW) food web remains a non-trivial endeavor. Insect parasitoids play a major role in the processes governing the population dynamics of SBW throughout eastern North America. However, these species are at the leading edge of the taxonomic impediment and integrating standardized identification capacity into existing field programs would provide clear benefits. We asked to what extent DNA barcoding the SBW food web would alter our understanding of the diversity and connectence of the food web and the frequency of generalists vs. specialists in different forest habitats. We DNA barcoded over 10% of the insects collected from the SBW food web in three New Brunswick forest plots from 1983 to 1993. For 30% of these specimens, we amplified at least one additional nuclear region. When the nodes of the food web were estimated based on barcode divergences (using molecular operational taxonomic units (MOTU) or phylogenetic diversity (PD)--the food web became much more diverse and connectence was reduced. We tested one measure of food web structure (the "bird feeder effect") and found no difference compared to the morphologically based predictions. Many, but not all, of the presumably polyphagous parasitoids now appear to be morphologically-cryptic host-specialists. To our knowledge, this project is the first to barcode a food web in which interactions have already been well-documented and described in space, time and abundance. It is poised to be a system in which field-based methods permit the identification capacity required by forestry scientists. Food web barcoding provided an effective tool for the accurate identification of all species involved in the cascading effects of future budworm outbreaks. Integrating standardized barcodes within food webs may ultimately change the face of community ecology. This will be most poignantly felt in food webs that have not yet been quantified. Here, more accurate and precise connections will be within the grasp of any researcher for the first time.},
}
@article {pmid21750102,
year = {2011},
author = {Alon, S and Vigneault, F and Eminaga, S and Christodoulou, DC and Seidman, JG and Church, GM and Eisenberg, E},
title = {Barcoding bias in high-throughput multiplex sequencing of miRNA.},
journal = {Genome research},
volume = {21},
number = {9},
pages = {1506-1511},
pmid = {21750102},
issn = {1549-5469},
support = {//Canadian Institutes of Health Research/Canada ; },
mesh = {Animals ; Bias ; Cluster Analysis ; Gene Expression Profiling ; *High-Throughput Nucleotide Sequencing ; Humans ; Mice ; MicroRNAs/*metabolism ; *Sequence Analysis, RNA ; Sequence Tagged Sites ; },
abstract = {Second-generation sequencing is gradually becoming the method of choice for miRNA detection and expression profiling. Given the relatively small number of miRNAs and improvements in DNA sequencing technology, studying miRNA expression profiles of multiple samples in a single flow cell lane becomes feasible. Multiplexing strategies require marking each miRNA library with a DNA barcode. Here we report that barcodes introduced through adapter ligation confer significant bias on miRNA expression profiles. This bias is much higher than the expected Poisson noise and masks significant expression differences between miRNA libraries. This bias can be eliminated by adding barcodes during PCR amplification of libraries. The accuracy of miRNA expression measurement in multiplexed experiments becomes a function of sample number.},
}
@article {pmid21748589,
year = {2011},
author = {Zhao, P and Luo, J and Zhuang, W and Liu, X and Wu, B},
title = {DNA barcoding of the fungal genus Neonectria and the discovery of two new species.},
journal = {Science China. Life sciences},
volume = {54},
number = {7},
pages = {664-674},
doi = {10.1007/s11427-011-4184-8},
pmid = {21748589},
issn = {1869-1889},
mesh = {Base Sequence ; DNA, Fungal/*genetics ; Fungi/classification/*genetics ; Genetic Markers ; Molecular Sequence Data ; Sequence Analysis, DNA ; Spores, Fungal/genetics ; },
abstract = {To determine a suitable DNA barcode for the genus Neonectria, the internal transcribed spacer rDNA, β-tubulin, EF-1α, and RPB2 genes were selected as candidate markers. A total of 205 sequences from 19 species of the genus were analyzed. Intra- and inter-specific divergences and the ease of nucleotide sequence acquisition were treated as criteria to evaluate the feasibility of a DNA barcode. Our results indicated that any single gene among the candidate markers failed to serve as a successful barcode, while the combination of the partial EF-1α, and RPB2 genes recognized all species tested. We tentatively propose the combined partial EF-1α and RPB2 genes as a DNA barcode for the genus. During this study, two cryptic species were discovered, based on the combined data of morphology and DNA barcode information. We described and named these two new species N. ditissimopsis and N. microconidia.},
}
@article {pmid21738691,
year = {2011},
author = {Montero-Pau, J and Ramos-Rodríguez, E and Serra, M and Gómez, A},
title = {Long-term coexistence of rotifer cryptic species.},
journal = {PloS one},
volume = {6},
number = {6},
pages = {e21530},
pmid = {21738691},
issn = {1932-6203},
mesh = {Animals ; Ecosystem ; Lakes ; Population Dynamics ; Rotifera/*growth &amp; development ; },
abstract = {Despite their high morphological similarity, cryptic species often coexist in aquatic habitats presenting a challenge in the framework of niche differentiation theory and coexistence mechanisms. Here we use a rotifer species complex inhabiting highly unpredictable and fluctuating salt lakes to gain insights into the mechanisms involved in stable coexistence in cryptic species. We combined molecular barcoding surveys of planktonic populations and paleogenetic analysis of diapausing eggs to reconstruct the current and historical coexistence dynamics of two highly morphologically similar rotifer species, B. plicatilis and B. manjavacas. In addition, we carried out laboratory experiments using clones isolated from eight lakes where both species coexist to explore their clonal growth responses to salinity, a challenging, highly variable and unpredictable condition in Mediterranean salt lakes. We show that both species have co-occurred in a stable way in one lake, with population fluctuations in which no species was permanently excluded. The seasonal occurrence patterns of the plankton in two lakes agree with laboratory experiments showing that both species differ in their optimal salinity. These results suggest that stable species coexistence is mediated by differential responses to salinity and its fluctuating regime. We discuss the role of fluctuating salinity and a persistent diapausing egg banks as a mechanism for species coexistence in accordance with the 'storage effect'.},
}
@article {pmid21732719,
year = {2011},
author = {Bennett, CE and Wilson, BS and Desalle, R},
title = {DNA barcoding of an invasive mammal species, the small Indian mongoose (Herpestes javanicus; E. Geoffroy Saint-Hillaire 1818) in the Caribbean and Hawaiian Islands.},
journal = {Mitochondrial DNA},
volume = {22},
number = {1-2},
pages = {12-18},
doi = {10.3109/19401736.2010.542241},
pmid = {21732719},
issn = {1940-1744},
mesh = {Animals ; Base Sequence ; Caribbean Region ; DNA Barcoding, Taxonomic/*methods ; Hawaii ; Herpestidae/classification/*genetics ; *Introduced Species ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND AND AIM: The use of DNA barcodes has been proposed as a promising tool for identifying species. The efficacy of this tool for invasive species requires further exploration. The species status of the small Indian mongoose, an exotic invasive in several parts of the world, has been contentious due to morphological similarity with its congeners in its natural habitat. Although the small Indian mongoose is recognized as Herpestes javanicus, this nomenclature has been used interchangeably with Herpestes auropunctatus.<br><br>MATERIALS AND METHODS: Here, we demonstrate the utility of using DNA barcoding approaches with mtDNA cytochrome b to discriminate between the two species and other sympatric members of the genus Herpestes (Herpestes naso, Herpestes urva, and Herpestes edwardsii). Using the diagnostic DNA positions we obtain, we can identity specimens of nonnative populations of the small Indian mongoose from the Caribbean and Hawaiian Islands to their species of origin.<br><br>RESULTS: A singe diagnostic site accomplishes the identification of H. javanicus versus H. auropunctatus.<br><br>CONCLUSION: Our results indicate that the nonnative mongoose populations from the Caribbean and Hawaiian Islands are H. auropunctatus, and not H. javanicus.},
}
@article {pmid21732288,
year = {2011},
author = {Chee, SY and Devakie, MN and Siti Azizah, MN},
title = {Phylogenetic study and barcoding of the blood cockle, Tegillarca granosa, found on the west coast of peninsular Malaysia using the COI gene.},
journal = {Genetics and molecular research : GMR},
volume = {10},
number = {2},
pages = {1237-1244},
doi = {10.4238/vol10-2gmr1104},
pmid = {21732288},
issn = {1676-5680},
mesh = {Animals ; Cardiidae/classification/*genetics ; DNA/genetics ; Humans ; Malaysia ; *Phylogeny ; },
abstract = {Blood cockles are among the most economically important brackish water invertebrates found in Malaysia. However, our knowledge of blood cockle phylogeny and systematics is rudimentary, especially for the species Tegillarca granosa. It is unclear, for instance, whether the cockles occurring on the west coast of peninsular Malaysia constitute a single species, or multiple, phylogenetically distinct species. We performed the first DNA molecular phylogenetic analysis of T. granosa to distinguish it from other related species found in other parts of the world and to create a DNA database for the species. An approximately 585-nucleotide fragment of the mitochondrial DNA (cytochrome oxidase I, COI) was sequenced for 150 individual cockles, representing 10 populations: three from the north, four from the central part and three from the southern part of peninsular Malaysia. Phylogenetic analyses of the resulting dataset yielded tree topologies that not only showed the relationship between T. granosa and its closest relatives but its position in the evolutionary tree. Three mitochondrial clades were evident, each containing an individual genus. Using the mutation rate of the COI gene, the divergence time between T. granosa and its closest related species was estimated to be 460 thousand years ago. This study provides a phylogenetic framework for this ecologically prominent and commercially important cockle species.},
}
@article {pmid21722983,
year = {2011},
author = {Tkacz-Stachowska, K and Lund-Andersen, C and Velissarou, A and Myklebust, JH and Stokke, T and Syljuåsen, RG},
title = {The amount of DNA damage needed to activate the radiation-induced G2 checkpoint varies between single cells.},
journal = {Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology},
volume = {101},
number = {1},
pages = {24-27},
doi = {10.1016/j.radonc.2011.05.060},
pmid = {21722983},
issn = {1879-0887},
mesh = {Biomarkers, Tumor/metabolism ; Cell Survival ; *DNA Damage ; DNA Repair/genetics/physiology ; Fibroblasts/*radiation effects ; Flow Cytometry ; Fluorescent Antibody Technique ; G2 Phase Cell Cycle Checkpoints/*genetics ; Gamma Rays ; Genomic Instability/*genetics ; Histones/metabolism ; Humans ; Mitosis/genetics/radiation effects ; Osteosarcoma/*genetics/metabolism/*radiotherapy ; Radiation Dosage ; Reference Values ; Tumor Cells, Cultured/drug effects/radiation effects ; },
abstract = {BACKGROUND AND PURPOSE: The radiation-induced G2 checkpoint helps facilitate DNA repair before cell division. However, recent work has revealed that human cells often escape the G2 checkpoint with unrepaired DNA breaks. The purpose was to explore whether G2 checkpoint activation occurs according to a threshold level of DNA damage.<br><br>MATERIALS AND METHODS: G2 checkpoint activation was assayed at 75-90 min and 24-48 h after X-ray irradiation of BJ diploid fibroblasts and U2OS osteosarcoma cells. Multiparameter flow cytometry with pacific blue barcoding, and flow cytometry-based sorting of phospho-H3 positive cells to microscope slides, were used to examine the DNA damage marker &#x3b3;-H2AX in individual mitotic cells that had escaped the G2 checkpoint.<br><br>RESULTS: For all radiation doses and times tested, the number of &#x3b3;-H2AX foci varied between individual mitotic cells. At 75 min the median levels of &#x3b3;-H2AX in mitotic cells increased with higher radiation doses. At 24-48 h, following a prolonged G2 checkpoint, cells were more resistant to checkpoint re-activation by a second dose of radiation.<br><br>CONCLUSION: Our results suggest that different amounts of DNA damage are needed to activate the G2 checkpoint in individual cells. Such single cell variation in checkpoint activation may potentially contribute to radiation-induced genomic instability.},
}
@article {pmid21722327,
year = {2011},
author = {Xiang, XG and Hu, H and Wang, W and Jin, XH},
title = {DNA barcoding of the recently evolved genus Holcoglossum (Orchidaceae: Aeridinae): a test of DNA barcode candidates.},
journal = {Molecular ecology resources},
volume = {11},
number = {6},
pages = {1012-1021},
doi = {10.1111/j.1755-0998.2011.03044.x},
pmid = {21722327},
issn = {1755-0998},
mesh = {Base Sequence ; Bayes Theorem ; China ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/genetics ; Genetic Loci/genetics ; Models, Genetic ; Molecular Sequence Data ; Orchidaceae/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Orchidaceae is one of the largest families of flowering plants. Many species of orchid are endangered, and all species are included in Conventions on International Trade of Endangered Species of Fauna and Flora (CITES) I and II, but it is very difficult to identify orchid species, even those with fertile parts. The genus Holcoglossum (Orchidaceae: Aeridinae) has long been problematic in taxonomy. It consists of both long-evolved and radiated species and is an excellent case to use for testing DNA barcodes for Orchidaceae. We investigated the power of a subset of proposed plant barcoding loci [rbcL, matK, atpF-atpH, psbK-psbI, trnH-psbA and internal transcribed spacer (ITS)] to discriminate between species in this genus. Our results showed that all these DNA regions, except psbK-psbI and atpF-atpH, can be amplified easily from Holcoglossum and sequenced with established primers. The DNA regions matK and ITS had the highest variability. Among the six loci, matK resolved eight of the 12 Holcoglossum species and had the highest discriminatory ability. However, the combination of matK and ITS showed a greater ability to identify species than matK alone. Single or combined DNA markers discriminated between Holcoglossum species distributed in tropical areas effectively, but had less ability to identify radiated species from the temperate Hengduan Mountains of China. In the study, matK proved to be a useful DNA barcode for the genus Holcoglossum; however, complementary DNA regions are still required to accelerate the investigation and preservation of radiated species of orchid.},
}
@article {pmid21722114,
year = {2011},
author = {Chelsky Budarf, A and Burfeind, DD and Loh, WK and Tibbetts, IR},
title = {Identification of seagrasses in the gut of a marine herbivorous fish using DNA barcoding and visual inspection techniques.},
journal = {Journal of fish biology},
volume = {79},
number = {1},
pages = {112-121},
doi = {10.1111/j.1095-8649.2011.02999.x},
pmid = {21722114},
issn = {1095-8649},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Plant/*analysis ; DNA, Ribosomal Spacer/analysis ; Diet ; *Fishes ; Gastrointestinal Contents ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Single-Stranded Conformational ; Species Specificity ; Zosteraceae/*genetics ; },
abstract = {Traditional visual diet analysis techniques were compared with DNA barcoding in juvenile herbivorous rabbitfish Siganus fuscescens collected in Moreton Bay, Australia, where at least six species of seagrass occur. The intergenic spacer trnH-psbA, suggested as the optimal gene for barcoding angiosperms, was used for the first time to identify the seagrass in fish guts. Four seagrass species and one alga were identified visually from gut contents; however, there was considerable uncertainty in visual identification with 38 of 40 fish having unidentifiable plant fragments in their gut. PCR and single-strand conformational polymorphism (SSCP) were able to discriminate three seagrass families from visually cryptic gut contents. While effective in identifying cryptic gut content to family level, this novel method is likely to be most efficient when paired with visual identification techniques.},
}
@article {pmid21720128,
year = {2011},
author = {Arami, S and Sato, M and Futo, S},
title = {[Applicability of DNA barcode for identification of fish species].},
journal = {Shokuhin eiseigaku zasshi. Journal of the Food Hygienic Society of Japan},
volume = {52},
number = {3},
pages = {205-210},
doi = {10.3358/shokueishi.52.205},
pmid = {21720128},
issn = {1882-1006},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Fishes/*classification ; },
abstract = {DNA barcoding is a species identification technique, which uses a very short DNA sequence from a region of approximately 650 base-pairs in the 5'-end of the mitochondrial cytochrome c oxidase subunit I gene as a marker to identify species of mammals and fishes. The applicability of DNA barcoding for identification of fish species consumed in Japan was studied. Among thirty-one fresh or processed fishes were obtained from the market, two samples could not be identified due to lack of data in the Barcode of Life Data (BOLD) database. However, BLAST-search of 16S rRNA genes in the National Center for Biotechnology Information (NCBI) database and the PCR-RFLP method published by the Food and Agricultural Materials Inspection Center (FAMIC) were found to be applicable to identify these 2 fishes. The results show that the DNA barcoding technique is potentially useful as a tool for confirming the proper labeling of fish species in the Japanese market.},
}
@article {pmid21711388,
year = {2012},
author = {Acharya, AB and Anehosur, GV and Kanchi, PP and Naik, MG and Nadiger, RK},
title = {Perceptions and preferences on denture marking in an Indian sample.},
journal = {Gerodontology},
volume = {29},
number = {2},
pages = {117-124},
doi = {10.1111/j.1741-2358.2011.00499.x},
pmid = {21711388},
issn = {1741-2358},
mesh = {Adult ; Aged ; *Attitude to Health ; Denture Identification Marking/instrumentation/methods/*psychology ; Denture, Complete/psychology ; Electronic Data Processing ; Female ; Humans ; India ; Male ; Middle Aged ; Mouth, Edentulous/psychology ; Paper ; *Patient Preference/psychology ; Patient Satisfaction ; Photography ; Stainless Steel ; Surveys and Questionnaires ; },
abstract = {AIM: Denture marking is useful in institutional settings and post-mortem identification. Numerous markers have been developed, and their advantages and limitations assessed previously; however, patient perception to denture marking is paramount. We evaluated this in an Indian sample and also gauged their preference for different markers.<br><br>MATERIALS AND METHODS: One-hundred and one edentulous patients seeking prosthodontic treatment in our institution were shown four denture markers (stainless steel matrix band, paper strip with name inscribed on it, patient photograph and optically readable laminated bar code) and asked whether they wanted similar markers in their dentures; patients were also asked to rank the markers based on preference and indicate their satisfaction with it.<br><br>RESULTS: Approximately two-thirds of patients (65/101) were uninterested in getting their dentures marked; among the 36 who agreed, 10 preferred the stainless steel band followed by photographs (9), paper strip (6) and bar code (2); nine gave multiple responses and were excluded from analyses. Sixteen patients expressed dissatisfaction with the photographic marker and bar code, while this number reduced for the stainless steel band (13) and paper strip (10).<br><br>CONCLUSIONS: The results are in contrast to European studies wherein the majority of patients agreed to denture marking, indicating patient background (e.g. education level) may affect perception to denture marking; amongst those who agreed to marking, most preferred, or were satisfied with, the stainless steel and paper strip markers over photographic marker and a complex method such as bar-coding, implying that simple methods harbouring basic patient information may suffice in the Indian context.},
}
@article {pmid21707318,
year = {2011},
author = {Pereira, LH and Pazian, MF and Hanner, R and Foresti, F and Oliveira, C},
title = {DNA barcoding reveals hidden diversity in the Neotropical freshwater fish Piabina argentea (Characiformes: Characidae) from the Upper Paraná Basin of Brazil.},
journal = {Mitochondrial DNA},
volume = {22 Suppl 1},
number = {},
pages = {87-96},
doi = {10.3109/19401736.2011.588213},
pmid = {21707318},
issn = {1940-1744},
mesh = {Animals ; Biodiversity ; Brazil ; Characidae/*classification/*genetics ; Cytochromes b/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/analysis/genetics ; Electron Transport Complex IV/*genetics ; Fish Proteins/genetics ; Fresh Water ; Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; Tropical Climate ; },
abstract = {BACKGROUND AND AIMS: We analyzed a small and wide geographically distributed Neotropical freshwater fish, the Piabina argentea from the Upper Paraná Basin, to check the hypothesis that this species is composed of more than one biological unit, since it has a limited dispersion, through the DNA barcode technique.<br><br>MATERIALS AND METHODS: Partial mitochondrial COI and CytB gene sequences were obtained for 58 specimens drawn from 13 localities.<br><br>RESULTS: Phylogenetic analysis revealed six major clusters of P. argentea. Kimura-two-parameter (K2P) genetic divergences among these six P. argentea clusters ranged from 2 to 5.6% and from 2.3 to 5.4% for COI and CytB genes, respectively, and these values were on average approximately nine times greater than intra-cluster K2P divergences. The fixation index (F(ST)) among clusters showed very high values and the haplotype network analysis displayed seven unconnected units.<br><br>CONCLUSION: These results reinforce the hypothesis that the widely distributed P. argentea species concept as currently conceived actually represents more than one species (possibly six). These results demonstrate the efficacy of DNA barcoding for the discovery of hidden diversity in Neotropical freshwater fishes, and we conclude that barcoding is a useful tool for alpha taxonomy.},
}
@article {pmid21707317,
year = {2011},
author = {Carvalho, DC and Neto, DA and Brasil, BS and Oliveira, DA},
title = {DNA barcoding unveils a high rate of mislabeling in a commercial freshwater catfish from Brazil.},
journal = {Mitochondrial DNA},
volume = {22 Suppl 1},
number = {},
pages = {97-105},
doi = {10.3109/19401736.2011.588219},
pmid = {21707317},
issn = {1940-1744},
mesh = {Animals ; Brazil ; Catfishes/*classification/*genetics ; *Commerce ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Fish Products/classification ; *Food Labeling/standards ; Rivers ; Seafood/analysis/*standards ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND AND AIMS: Molecular markers have contributed to species authentication by flagging mislabeling and the misidentification of commercial landings. Such tools are of great value since the market substitution of fish of lower value for highly commercialized species is expected to become more pronounced due to a shortage of natural stocks.<br><br>MATERIALS AND METHODS: Here we report on the molecular identification 4results from processed fish products (i.e. fillets) and whole fishes sold in Brazilian markets under the common name surubim (Pseudoplatystoma spp.).<br><br>RESULTS: DNA barcoding revealed the incorrect labeling of around 80% of all samples analyzed, with mislabeling being more pronounced within fillets rather than whole fish.<br><br>CONCLUSION: To our knowledge, this is the first report correlating the rate of fraud with processed fish products. The establishment of an official list of acceptable common names for freshwater fish and seafood is urgently needed in Brazil for further trade regulations to take place.},
}
@article {pmid21705146,
year = {2011},
author = {Otranto, D and Brianti, E and Dantas-Torres, F and Weigl, S and Latrofa, MS and Gaglio, G and Cauquil, L and Giannetto, S and Bain, O},
title = {Morphological and molecular data on the dermal microfilariae of a species of Cercopithifilaria from a dog in Sicily.},
journal = {Veterinary parasitology},
volume = {182},
number = {2-4},
pages = {221-229},
doi = {10.1016/j.vetpar.2011.05.043},
pmid = {21705146},
issn = {1873-2550},
mesh = {Animals ; Dog Diseases/epidemiology/*parasitology ; Dogs ; Filariasis/epidemiology/parasitology/*veterinary ; Filarioidea/*anatomy &amp; histology/*genetics ; Phylogeny ; Sicily/epidemiology ; },
abstract = {Dermal microfilariae found in a dog from Sicily, Italy, were characterized morphologically and genetically and differentiated from those of all the other blood microfilariae commonly found in dogs. In particular, the microfilariae were short (mean length of 186.7 μm), presented a body flattened dorso-ventrally and a rounded head, bearing a tiny cephalic hook. The genetic identity of microfilariae herein studied was also assessed by molecular amplification, sequencing and analyzing of multiple ribosomal ITS-2 and mitochondrial (cox1 and 12S) target genes. Both morphologic and genetic characterization as well as the molecular phylogenetic history inferred using sequences of a barcoding dataset were concordant in supporting the identification of Cercopithifilaria at the genus level. Surprisingly, microfilariae here examined were well distinct from Cercopithifilaria grassii (Noè, 1907), from northern Italy, and resembled those of a species described in Brazil, Cercopithifilaria bainae Almeida &amp; Vicente, 1984. This paper provides evidence for the existence of a Cercopithifilaria species infesting a dog from Sicily and also presents a PCR protocol on skin samples as a tool for further epidemiological studies, which could provide evidence on the aetiology and the natural history of this filarial species.},
}
@article {pmid21701680,
year = {2011},
author = {Pei, N and Lian, JY and Erickson, DL and Swenson, NG and Kress, WJ and Ye, WH and Ge, XJ},
title = {Exploring tree-habitat associations in a Chinese subtropical forest plot using a molecular phylogeny generated from DNA barcode loci.},
journal = {PloS one},
volume = {6},
number = {6},
pages = {e21273},
pmid = {21701680},
issn = {1932-6203},
mesh = {China ; DNA Barcoding, Taxonomic ; *Ecosystem ; Humans ; *Phylogeny ; Trees/*classification/*genetics ; *Tropical Climate ; },
abstract = {Elucidating the ecological mechanisms underlying community assembly in subtropical forests remains a central challenge for ecologists. The assembly of species into communities can be due to interspecific differences in habitat associations, and there is increasing evidence that these associations may have an underlying phylogenetic structure in contemporary terrestrial communities. In other words, by examining the degree to which closely related species prefer similar habitats and the degree to which they co-occur, ecologists are able to infer the mechanisms underlying community assembly. Here we implement this approach in a diverse subtropical tree community in China using a long-term forest dynamics plot and a molecular phylogeny generated from three DNA barcode loci. We find that there is phylogenetic signal in plant-habitat associations (i.e. closely related species tend to prefer similar habitats) and that patterns of co-occurrence within habitats are typically non-random with respect to phylogeny. In particular, we found phylogenetic clustering in valley and low-slope habitats in this forest, indicating a filtering of lineages plays a dominant role in structuring communities in these habitats and we found evidence of phylogenetic overdispersion in high-slope, ridge-top and high-gully habitats, indicating that distantly related species tended to co-occur in these high elevation habitats and that lineage filtering is less important in structuring these communities. Thus we infer that non-neutral niche-based processes acting upon evolutionarily conserved habitat preferences explain the assembly of local scale communities in the forest studied.},
}
@article {pmid21699373,
year = {2011},
author = {de Carvalho, DC and Oliveira, DA and Pompeu, PS and Leal, CG and Oliveira, C and Hanner, R},
title = {Deep barcode divergence in Brazilian freshwater fishes: the case of the São Francisco River basin.},
journal = {Mitochondrial DNA},
volume = {22 Suppl 1},
number = {},
pages = {80-86},
doi = {10.3109/19401736.2011.588214},
pmid = {21699373},
issn = {1940-1744},
mesh = {Animals ; Biodiversity ; Brazil ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Fishes/*classification/*genetics ; Fresh Water ; Genetic Variation ; Phylogeography ; *Rivers ; Sequence Analysis, DNA ; Species Specificity ; Tropical Climate ; },
abstract = {BACKGROUND AND AIMS: The application of DNA barcoding as a global standard for fish identification is probing diverse worldwide realms (Nearctic, Australian and the Neotropics) and environments (e.g. marine and freshwater). Comparing the patterns of sequence divergence among conspecific and congeneric taxa between realms can provide valuable information on recent evolutionary histories of lineages as barcode data accumulates.<br><br>MATERIALS AND METHODS: Herein, we have analyzed over 100 species (around 50%) of the Neotropical fish fauna from the S&#xe3;o Francisco River, in southeast Brazil. Our aims were to test the performance of DNA barcoding in this biodiversity-rich region, and to compare patterns of genetic divergence with previous studies.<br><br>RESULTS: The mean Kimura two-parameter distances within species, genera, families, orders, and classes were 0.5, 10.6, 21.0, 22.7, and 24.4%, respectively, with 100% of the species examined successfully differentiated by barcoding. With the exception of Astyanax bimaculatus lacustris, Piabina argentea, and Bryconamericus stramineus, all other species yield a single, cohesive cluster of barcode sequences. The average 'nearest-neighbor distance' was 11.12%, 21-fold higher than the mean within species distance of around 0.54%. In a few instances, deep lineage divergences among conspecifics (up to 10%) and congenerics (up to 22.9%) taxa were revealed.<br><br>CONCLUSIONS: Reflecting possible cases of cryptic speciation and the deeper phylogeographic history of S&#xe3;o Francisco fish fauna, with some higher clades extending back into the late Cretaceous and Cenozoic (90 mya), when much of the diversification of the Neotropical region apparently took place. In addition, barcodes also highlighted misidentifications and helped to document range extensions for known species.},
}
@article {pmid21699372,
year = {2011},
author = {Kartavtsev, YP},
title = {Divergence at Cyt-b and Co-1 mtDNA genes on different taxonomic levels and genetics of speciation in animals.},
journal = {Mitochondrial DNA},
volume = {22},
number = {3},
pages = {55-65},
doi = {10.3109/19401736.2011.588215},
pmid = {21699372},
issn = {1940-1744},
mesh = {Algorithms ; Animals ; Base Sequence ; *Classification/methods ; Cytochromes b/*genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Genes, Mitochondrial/genetics ; *Genetic Speciation ; Genetic Variation/physiology ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; Vertebrates/genetics ; },
abstract = {Genetic divergence estimates using p-distances and similar measures were generated for 20,731 vertebrate and invertebrate animal species. The results of this analysis demonstrate that the data series are realistic and interpretable when the p-distance and its various derivates are used. The focus is on vertebrates and fish species in particular and the newest data set. Distance data reveal increasing levels of genetic divergence of the sequences of the two genes, cytochrome b (Cyt-b) and cytochrome c oxidase subunit 1 (Co-1), in the five groups compared: populations within species; subspecies, semi-species, or/and sibling species; species within a genus; species from different genera within a family; and species from separate families within an order. Mean unweighted scores of p-distances (%) for these five groups are Cyt-b-1.38 ± 0.30, 5.10 ± 0.91, 10.31 ± 0.93, 17.86 ± 1.36, and 26.36 ± 3.88, respectively; and Co-1-0.89 ± 0.16, 3.78 ± 1.18, 11.06 ± 0.53, 16.60 ± 0.69, and 20.57 ± 0.40, respectively. The estimates show good correspondence with other analyses. These results testify to the applicability of p-distance for most intra-species and inter-species comparisons of genetic divergence up to the order level in animals for the two genes compared. Data reviewed provide empirical and theoretical background on the geographic speciation mode prevalence in species origin and give a framework why per-individual species identification (DNA barcoding) is usually successful.},
}
@article {pmid21698181,
year = {2011},
author = {Chen, J and Li, Q and Kong, L and Yu, H},
title = {How DNA barcodes complement taxonomy and explore species diversity: the case study of a poorly understood marine fauna.},
journal = {PloS one},
volume = {6},
number = {6},
pages = {e21326},
pmid = {21698181},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; *Biodiversity ; *DNA Barcoding, Taxonomic ; DNA Primers ; *Marine Biology ; Mollusca/*classification/genetics ; },
abstract = {BACKGROUND: The species boundaries of some venerids are difficult to define based solely on morphological features due to their indistinct intra- and interspecific phenotypic variability. An unprecedented biodiversity crisis caused by human activities has emerged. Thus, to access the biological diversity and further the conservation of this taxonomically muddling bivalve group, a fast and simple approach that can efficiently examine species boundaries and highlight areas of unrecognized diversity is urgently needed. DNA barcoding has proved its effectiveness in high-volume species identification and discovery. In the present study, Chinese fauna was chosen to examine whether this molecular biomarker is sensitive enough for species delimitation, and how it complements taxonomy and explores species diversity.<br><br>A total of 315 specimens from around 60 venerid species were included, qualifying the present study as the first major analysis of DNA barcoding for marine bivalves. Nearly all individuals identified to species level based on morphological traits possessed distinct barcode clusters, except for the specimens of one species pair. Among the 26 individuals that were not assigned binomial names a priori, twelve respectively nested within a species genealogy. The remaining individuals formed five monophyletic clusters that potentially represent species new to science or at least unreported in China. Five putative hidden species were also uncovered in traditional morphospecies.<br><br>CONCLUSIONS/SIGNIFICANCE: The present study shows that DNA barcoding is effective in species delimitation and can aid taxonomists by indicating useful diagnostic morphological traits, informing needful revision, and flagging unseen species. Moreover, the BOLD system, which deposits barcodes, morphological, geographical and other data, has the potential as a convenient taxonomic platform.},
}
@article {pmid21693000,
year = {2011},
author = {Sutou, M and Kato, T and Ito, M},
title = {Recent discoveries of armyworms in Japan and their species identification using DNA barcoding.},
journal = {Molecular ecology resources},
volume = {11},
number = {6},
pages = {992-1001},
doi = {10.1111/j.1755-0998.2011.03040.x},
pmid = {21693000},
issn = {1755-0998},
mesh = {Animal Migration ; Animals ; Base Sequence ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Demography ; Diptera/classification/*genetics ; Japan ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Long columns of migrating larval sciarid armyworms were discovered in central and northern Japan, specifically Kanagawa, Gunma, Miyagi and Akita prefectures, as well as Hokkaido. This is the first examination of armyworms in East Asia. In Europe, armyworms have been identified as Sciara militaris, belonging to the family Sciaridae (sciarid flies or black fungus gnats), by rearing them to adulthood. In Japan, we were unable to obtain live samples for rearing; therefore, DNA barcodes were obtained from the samples of armyworms collected in the Gunma and Miyagi prefectures. The DNA barcodes were compared with those obtained from the following samples: pupae of S. militaris from UK, adults of Sciara kitakamiensis, Sciara humeralis, Sciara hemerobioides, Sciara thoracica, Sciara helvola and Sciara melanostyla from Japan, and adults of one undescribed Sciara species from Malaysia. Neighbour-joining, maximum parsimony, and maximum likelihood analyses revealed that the armyworms discovered in Japan are S. kitakamiensis. Although adults of this species have been recorded in several locations in Japan, this is the first report of migrating larval armyworms. DNA barcodes were effectively used to link different life stages of this species. The average intraspecific and interspecific pairwise genetic distances of the genus Sciara were 0.3% and 12.6%, respectively. The present study illustrates that DNA barcodes are an effective means of identifying sciarid flies in Japan.},
}
@article {pmid21689384,
year = {2011},
author = {Robideau, GP and De Cock, AW and Coffey, MD and Voglmayr, H and Brouwer, H and Bala, K and Chitty, DW and Désaulniers, N and Eggertson, QA and Gachon, CM and Hu, CH and Küpper, FC and Rintoul, TL and Sarhan, E and Verstappen, EC and Zhang, Y and Bonants, PJ and Ristaino, JB and Lévesque, CA},
title = {DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer.},
journal = {Molecular ecology resources},
volume = {11},
number = {6},
pages = {1002-1011},
pmid = {21689384},
issn = {1755-0998},
support = {P 22739/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Base Sequence ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; DNA, Ribosomal Spacer/*genetics ; Electron Transport Complex IV/*genetics ; Models, Genetic ; Molecular Sequence Data ; Oomycetes/*genetics ; Sequence Analysis, DNA ; },
abstract = {Oomycete species occupy many different environments and many ecological niches. The genera Phytophthora and Pythium for example, contain many plant pathogens which cause enormous damage to a wide range of plant species. Proper identification to the species level is a critical first step in any investigation of oomycetes, whether it is research driven or compelled by the need for rapid and accurate diagnostics during a pathogen outbreak. The use of DNA for oomycete species identification is well established, but DNA barcoding with cytochrome c oxidase subunit I (COI) is a relatively new approach that has yet to be assessed over a significant sample of oomycete genera. In this study we have sequenced COI, from 1205 isolates representing 23 genera. A comparison to internal transcribed spacer (ITS) sequences from the same isolates showed that COI identification is a practical option; complementary because it uses the mitochondrial genome instead of nuclear DNA. In some cases COI was more discriminative than ITS at the species level. This is in contrast to the large ribosomal subunit, which showed poor species resolution when sequenced from a subset of the isolates used in this study. The results described in this paper indicate that COI sequencing and the dataset generated are a valuable addition to the currently available oomycete taxonomy resources, and that both COI, the default DNA barcode supported by GenBank, and ITS, the de facto barcode accepted by the oomycete and mycology community, are acceptable and complementary DNA barcodes to be used for identification of oomycetes.},
}
@article {pmid21689383,
year = {2011},
author = {Cawthorn, DM and Steinman, HA and Witthuhn, RC},
title = {Establishment of a mitochondrial DNA sequence database for the identification of fish species commercially available in South Africa.},
journal = {Molecular ecology resources},
volume = {11},
number = {6},
pages = {979-991},
doi = {10.1111/j.1755-0998.2011.03039.x},
pmid = {21689383},
issn = {1755-0998},
mesh = {Animals ; Base Sequence ; Cluster Analysis ; *Commerce ; Conservation of Natural Resources/*methods ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics ; *Databases, Genetic ; Fishes/classification/*genetics ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; South Africa ; },
abstract = {The limitations intrinsic to morphology-based identification systems have created an urgent need for reliable genetic methods that enable the unequivocal recognition of fish species, particularly those that are prone to overexploitation and/or market substitution. The aim of this study was to develop a comprehensive reference library of DNA sequence data to allow the explicit identification of 53 commercially available fish species in South Africa, most of which were locally caught marine species. Sequences of approximately 655 base pairs were generated for all species from the cytochrome c oxidase I (COI) gene, the region widely adopted for DNA barcoding. Specimens of the genus Thunnus were examined in further detail, employing additional mitochondrial DNA control region sequencing. Cumulative analysis of the sequences from the COI region revealed mean conspecific, congeneric and confamilial Kimura 2-parameter distances of 0.10%, 4.58% and 15.43%, respectively. The results showed that the vast majority (98%) of fish species examined could be readily differentiated by their COI barcodes, but that supplementary control region sequencing was more useful for the discrimination of three Thunnus species. Additionally, the analysis of COI data raised the prospect that Thyrsites atun (snoek) could constitute a species pair. The present study has established the necessary genetic information to permit the unambiguous identification of 53 commonly marketed fish species in South Africa, the applications of which hold a plethora of benefits relating to ecology research, fisheries management and control of commercial practices.},
}
@article {pmid21687836,
year = {2011},
author = {Ji, XH and Cheng, W and Guo, F and Liu, W and Guo, SS and He, ZK and Zhao, XZ},
title = {On-demand preparation of quantum dot-encoded microparticles using a droplet microfluidic system.},
journal = {Lab on a chip},
volume = {11},
number = {15},
pages = {2561-2568},
doi = {10.1039/c1lc20150f},
pmid = {21687836},
issn = {1473-0189},
mesh = {Alginates/chemistry ; Glucuronic Acid/chemistry ; Hexuronic Acids/chemistry ; Hydrogels/chemistry ; Immunoassay/instrumentation/methods ; Microfluidic Analytical Techniques/*instrumentation/*methods ; Particle Size ; *Quantum Dots ; },
abstract = {Optical barcoding technology based on quantum dot (QD)-encoded microparticles has attracted increasing attention in high-throughput multiplexed biological assays, which is realized by embedding different-sized QDs into polymeric matrixes at precisely controlled ratios. Considering the advantage of droplet-based microfluidics, producing monodisperse particles with precise control over the size, shape and composition, we present a proof-of-concept approach for on-demand preparation of QD-encoded microparticles based on this versatile new strategy. Combining a flow-focusing microchannel with a double T-junction in a microfluidic chip, biocompatible QD-doped microparticles were constructed by shearing sodium alginate solution into microdroplets and on-chip gelating these droplets into a hydrogel matrix to encapsulate CdSe/ZnS QDs. Size-controllable QD-doped hydrogel microparticles were produced under the optimum flow conditions, and their fluorescent properties were investigated. A novel multiplex optical encoding strategy was realized by loading different sized QDs into a single droplet (and thus a hydrogel microparticle) with different concentrations, which was triggered by tuning the flow rates of the sodium alginate solutions entrapped with different-colored QDs. A series of QD-encoded microparticles were controllably, and continuously, produced in a single step with the present approach. Their application in a model immunoassay demonstrated the potential practicability of QD-encoded hydrogel microparticles in multiplexed biomolecular detection. This simple and robust strategy should be further improved and practically used in making barcode microparticles with various polymer matrixes.},
}
@article {pmid21687792,
year = {2011},
author = {Zhang, J},
title = {Species identification of marine fishes in china with DNA barcoding.},
journal = {Evidence-based complementary and alternative medicine : eCAM},
volume = {2011},
number = {},
pages = {978253},
pmid = {21687792},
issn = {1741-4288},
abstract = {DNA barcoding is a molecular method that uses a short standardized DNA sequence as a species identification tool. In this study, the standard 652 base-pair region of the mitochondrial cytochrome oxidase subunit I gene (COI) was sequenced in marine fish specimens captured in China. The average genetic distance was 50-fold higher between species than within species, as Kimura two parameter (K2P) genetic distances averaged 15.742% among congeners and only 0.319% for intraspecific individuals. There are no overlaps of pairwise genetic variations between conspecific and interspecific comparisons apart from the genera Pampus in which the introgressive hybridization was detected. High efficiency of species identification was demonstrated in the present study by DNA barcoding. Due to the incidence of cryptic species, an assumed threshold is suggested to expedite discovering of new species and biodiversity, especially involving biotas of few studies.},
}
@article {pmid21676192,
year = {2011},
author = {Aquilino, SV and Tango, JM and Fontanilla, IK and Pagulayan, RC and Basiao, ZU and Ong, PS and Quilang, JP},
title = {DNA barcoding of the ichthyofauna of Taal Lake, Philippines.},
journal = {Molecular ecology resources},
volume = {11},
number = {4},
pages = {612-619},
doi = {10.1111/j.1755-0998.2011.03000.x},
pmid = {21676192},
issn = {1755-0998},
mesh = {Animals ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/genetics ; Fishes/*classification/*genetics ; Fresh Water ; Genetic Variation ; Molecular Sequence Data ; Philippines ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {This study represents the first molecular survey of the ichthyofauna of Taal Lake and the first DNA barcoding attempt in Philippine fishes. Taal Lake, the third largest lake in the Philippines, is considered a very important fisheries resource and is home to the world's only freshwater sardine, Sardinella tawilis. However, overexploitation and introduction of exotic fishes have caused a massive decline in the diversity of native species as well as in overall productivity of the lake. In this study, 118 individuals of 23 native, endemic and introduced fishes of Taal Lake were barcoded using the partial DNA sequence of the mitochondrial cytochrome c oxidase subunit I (COI) gene. These species belong to 21 genera, 17 families and 9 orders. Divergence of sequences within and between species was determined using Kimura 2-parameter (K2P) distance model, and a neighbour-joining tree was generated with 1000 bootstrap replications using the K2P model. All COI sequences for each of the 23 species were clearly discriminated among genera. The average within species, within genus, within family and within order percent genetic divergence was 0.60%, 11.07%, 17.67% and 24.08%, respectively. Our results provide evidence that COI DNA barcodes are effective for the rapid and accurate identification of fishes and for identifying certain species that need further taxonomic investigation.},
}
@article {pmid21672623,
year = {2011},
author = {Boimel, PJ and Cruz, C and Segall, JE},
title = {A functional in vivo screen for regulators of tumor progression identifies HOXB2 as a regulator of tumor growth in breast cancer.},
journal = {Genomics},
volume = {98},
number = {3},
pages = {164-172},
pmid = {21672623},
issn = {1089-8646},
support = {R01 CA077522-08/CA/NCI NIH HHS/United States ; R21 CA125288-02/CA/NCI NIH HHS/United States ; R01 CA077522/CA/NCI NIH HHS/United States ; CA125288/CA/NCI NIH HHS/United States ; R21 CA125288/CA/NCI NIH HHS/United States ; T32 GM007288/GM/NIGMS NIH HHS/United States ; CA077522/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Breast Neoplasms/*genetics ; Cell Line, Tumor ; Cell Proliferation ; Disease Models, Animal ; Disease Progression ; Female ; *Gene Expression Regulation, Neoplastic ; Homeodomain Proteins/*genetics/metabolism ; Humans ; Mice ; Mice, SCID ; RNA, Small Interfering/genetics ; Real-Time Polymerase Chain Reaction ; Transcription Factors/*genetics/metabolism ; },
abstract = {Microarray profiling in breast cancer patients has identified genes correlated with prognosis whose functions are unknown. The purpose of this study was to develop an in vivo assay for functionally screening regulators of tumor progression using a mouse model. Transductant shRNA cell lines were made in the MDA-MB-231 breast cancer line. A pooled population of 25 transductants was injected into the mammary fat pads and tail veins of mice to evaluate tumor growth, and experimental metastasis. The proportions of transductants were evaluated in the tumor and metastases using barcodes specific to each shRNA transductant. We characterized the homeobox 2 transcription factor as a negative regulator, decreasing tumor growth in MDA-MB-231, T47D, and MTLn3 mammary adenocarcinoma cell lines. Homeobox genes have been correlated with cancer patient prognosis and tumorigenesis. Here we use a novel in vivo shRNA screen to identify a new role for a homeobox gene in human mammary adenocarcinoma.},
}
@article {pmid21671831,
year = {2012},
author = {Gabriel, F and Noel, T and Accoceberry, I},
title = {Lindnera (Pichia) fabianii blood infection after mesenteric ischemia.},
journal = {Medical mycology},
volume = {50},
number = {3},
pages = {310-314},
doi = {10.3109/13693786.2011.587455},
pmid = {21671831},
issn = {1460-2709},
mesh = {Acute Kidney Injury/complications ; Antifungal Agents/administration &amp; dosage ; Blood/microbiology ; Caspofungin ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Echinocandins/administration &amp; dosage ; Female ; Fungemia/*diagnosis/drug therapy/microbiology ; Genes, rRNA ; Humans ; Ischemia/*complications ; Lipopeptides ; Mesenteric Ischemia ; Middle Aged ; RNA, Fungal/genetics ; RNA, Ribosomal, 18S/genetics ; Saccharomycetales/*isolation &amp; purification ; Sequence Analysis, DNA ; Suicide ; Treatment Outcome ; Vascular Diseases/*complications ; },
abstract = {Lindnera (Pichia) fabianii (teleomorph of Candida fabianii) is a yeast species rarely involved in human infections. This report describes the first known human case of a Lindnera fabianii blood infection after mesenteric ischemia. The 53-year-old patient was hospitalized in the intensive care unit after a suicide attempt and was suffering from a mesenteric ischemia and acute renal failure. Lindnera fabianii was recovered from an oropharyngeal swab, then isolated from stool and urine samples before the diagnosis of the blood infection. Caspofungin intravenous treatment was associated with a successful outcome. Final unequivocal identification of the strain was done by sequencing the internal transcribed spacer (ITS) region, and regions of 18S rDNA gene and of the translation elongation factor-1α gene. Until our work, the genomic databases did not contain the complete ITS region of L. fabianii as a single nucleotide sequence (encompassing ITS1, the 5.8S rDNA and ITS2), and misidentification with other yeast species, e.g., Lindnera (Pichia) mississippiensis, could have occurred. Our work demonstrates that the usual DNA barcoding method based on sequencing of the ITS region may fail to provide the correct identification of some taxa, and that partial sequencing of the EF1α gene may be much more effective for the accurate delineation and molecular identification of new emerging opportunistic yeast pathogens.},
}
@article {pmid21670958,
year = {2012},
author = {Gaikwad, SS and Ghate, HV and Ghaskadbi, SS and Patole, MS and Shouche, YS},
title = {DNA barcoding of nymphalid butterflies (Nymphalidae: Lepidoptera) from Western Ghats of India.},
journal = {Molecular biology reports},
volume = {39},
number = {3},
pages = {2375-2383},
pmid = {21670958},
issn = {1573-4978},
mesh = {Animals ; Butterflies/*genetics ; Cluster Analysis ; Computational Biology/methods ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; *Genetic Variation ; India ; Species Specificity ; },
abstract = {We have checked the utility of DNA barcoding for species identification of nymphalid butterflies from Western Ghats of India by using 650 bp sequence of mitochondrial gene cytochrome c oxidase subunit I. Distinct DNA barcoding gap (i.e. difference between intraspecies and interspecies nucleotide divergence), exists between species studied here. When our sequences were compared with the sequences of the conspecifics submitted from different geographic regions, nine cases of deep intraspecies nucleotide divergences were observed. In spite of this, NJ (Neighbour Joining) clustering analysis successfully discriminated all species. Observed cases of deep intraspecies nucleotide divergences certainly warrant further study.},
}
@article {pmid21670289,
year = {2011},
author = {April, J and Mayden, RL and Hanner, RH and Bernatchez, L},
title = {Genetic calibration of species diversity among North America's freshwater fishes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {108},
number = {26},
pages = {10602-10607},
pmid = {21670289},
issn = {1091-6490},
mesh = {Animals ; *Biodiversity ; Calibration ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Fishes/*classification/genetics ; Fresh Water ; Molecular Sequence Data ; North America ; },
abstract = {Freshwater ecosystems are being heavily exploited and degraded by human activities all over the world, including in North America, where fishes and fisheries are strongly affected. Despite centuries of taxonomic inquiry, problems inherent to species identification continue to hamper the conservation of North American freshwater fishes. Indeed, nearly 10% of species diversity is thought to remain undescribed. To provide an independent calibration of taxonomic uncertainty and to establish a more accessible molecular identification key for its application, we generated a standard reference library of mtDNA sequences (DNA barcodes) derived from expert-identified museum specimens for 752 North American freshwater fish species. This study demonstrates that 90% of known species can be delineated using barcodes. Moreover, it reveals numerous genetic discontinuities indicative of independently evolving lineages within described species, which points to the presence of morphologically cryptic diversity. From the 752 species analyzed, our survey flagged 138 named species that represent as many as 347 candidate species, which suggests a 28% increase in species diversity. In contrast, several species of parasitic and nonparasitic lampreys lack such discontinuity and may represent alternative life history strategies within single species. Therefore, it appears that the current North American freshwater fish taxonomy at the species level significantly conceals diversity in some groups, although artificially creating diversity in others. In addition to providing an easily accessible digital identification system, this study identifies 151 fish species for which taxonomic revision is required.},
}
@article {pmid21669294,
year = {2011},
author = {Erpenbeck, D and Weier, T and de Voogd, NJ and Wörheide, G and Sutcliffe, P and Todd, JA and Michel, E},
title = {Insights into the evolution of freshwater sponges (Porifera: Demospongiae: Spongillina): Barcoding and phylogenetic data from Lake Tanganyika endemics indicate multiple invasions and unsettle existing taxonomy.},
journal = {Molecular phylogenetics and evolution},
volume = {61},
number = {1},
pages = {231-236},
doi = {10.1016/j.ympev.2011.05.021},
pmid = {21669294},
issn = {1095-9513},
mesh = {Animals ; Aquatic Organisms/classification/genetics ; *Biological Evolution ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/classification/genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Fresh Water ; Phylogeny ; Porifera/*classification/*genetics/physiology ; Ribonucleoproteins/genetics ; Tanzania ; },
abstract = {Sponges are a conspicuous element in many benthic habitats including in Africa's oldest, deepest lake, Lake Tanganyika. Despite their prevalence and pivotal ecological role as filter feeders, knowledge of the evolutionary history of sponges is in its infancy. Here, we provide the first molecular analysis targeting the evolution of sponges from Lake Tanganyika. Independent markers indicate the occurrence of several colonisation events which have shaped the current Tanganyikan lacustrine sponge biodiversity. This is in contrast to a range of previously studied organisms that have diversified within the lake from single lineages. Our tree reconstructions indicate the presence of two genera, Oncosclera and Eunapius, which are globally distributed. Therefore, we reject the hypothesis of monophyly for the sponges from Lake Tanganyika and challenge existing higher taxonomic structure for freshwater sponges.},
}
@article {pmid21659458,
year = {2011},
author = {Feau, N and Vialle, A and Allaire, M and Maier, W and Hamelin, RC},
title = {DNA barcoding in the rust genus Chrysomyxa and its implications for the phylogeny of the genus.},
journal = {Mycologia},
volume = {103},
number = {6},
pages = {1250-1266},
doi = {10.3852/10-426},
pmid = {21659458},
issn = {0027-5514},
mesh = {Basidiomycota/*classification/genetics ; DNA, Fungal/*genetics ; DNA, Ribosomal Spacer ; *Electronic Data Processing ; Phylogeny ; },
abstract = {Chrysomyxa rusts are fungal pathogens widely present in the boreal forest. Taxonomic delimitation and precise species identification are difficult within this genus because several species display similar morphological features. We applied a DNA barcode system based on the ribosomal internal transcribed spacer region (ITS), large subunit (28S) ribosomal RNA gene, mitochondrial cytochrome oxidase 1 (CO1) and mitochondrial NADH dehydrogenase subunit 6 (NAD6) in 86 strains from 16 different Chrysomyxa species, including members of the Chrysomyxa ledi species complex. The nuclear ITS and 28S loci revealed higher resolving power than the mitochondrial genes. Amplification of the full CO1 barcode region failed due to the presence of introns limiting the dataset obtained with this barcode. In most cases the ITS barcodes were in agreement with taxonomic species based on phenotypic characters. Nevertheless we observed genetically distinct (different DNA barcodes) lineages within Chrysomyxa pyrolae and Chrysomyxa rhododendri, providing some evidence for allopatric speciation within these morphologically defined species. This finding, together with the observed pattern of host specificities of the studied rust fungi, suggest that species diversification within the C. ledi species complex might be governed by a set of factors such as specialisation to certain Ericaceae species as telial hosts and to a lesser extent specialization to different spruce species as aecial hosts. Moreover allopatric speciation by geographic disruption of species also seems to take place. When our data were integrated into a broader phylogenetic framework the Chrysomyxa genus unexpectedly was not resolved as a monophyletic group. Indeed the spruce cone rusts C. pyrolae and C. monesis coalesced with the pine needle rusts belonging to the genus Coleosporium, whereas the microcyclic species Chrysomyxa weirii was embedded within a clade comprising the genus Melampsora.},
}
@article {pmid21658180,
year = {2011},
author = {Coulson, MW and Denti, D and Van Guelpen, L and Miri, C and Kenchington, E and Bentzen, P},
title = {DNA barcoding of Canada's skates.},
journal = {Molecular ecology resources},
volume = {11},
number = {6},
pages = {968-978},
doi = {10.1111/j.1755-0998.2011.03034.x},
pmid = {21658180},
issn = {1755-0998},
mesh = {Animals ; Atlantic Ocean ; Base Sequence ; Canada ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; *Genetic Variation ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Skates, Fish/*genetics ; Species Specificity ; },
abstract = {DNA-based identifications have been employed across broad taxonomic ranges and provide an especially useful tool in cases where external identification may be problematic. This study explored the utility of DNA barcoding in resolving skate species found in Atlantic Canadian waters. Most species were clearly resolved, expanding the utility for such identification on a taxonomically problematic group. Notably, one genus (Amblyraja) contained three of four species whose distributions do not overlap that could not be readily identified with this method. On the other hand, two common and partially sympatric species (Little and Winter skates) were readily identifiable. There were several instances of inconsistency between the voucher identification and the DNA sequence data. In some cases, these were at the intrageneric level among species acknowledged to be prone to misidentification. However, several instances of intergeneric discrepancies were also identified, suggesting either evidence of past introgressive hybridization or misidentification of vouchered specimens across broader taxonomic ranges. Such occurrences highlight the importance of retaining vouchered specimens for subsequent re-examination in the light of conflicting DNA evidence.},
}
@article {pmid21651976,
year = {2011},
author = {Kong, Y},
title = {Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies.},
journal = {Genomics},
volume = {98},
number = {2},
pages = {152-153},
doi = {10.1016/j.ygeno.2011.05.009},
pmid = {21651976},
issn = {1089-8646},
mesh = {Algorithms ; High-Throughput Nucleotide Sequencing/*methods ; Sequence Analysis, DNA/*methods ; *Software ; },
abstract = {Btrim is a fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines. It also can reliably identify barcodes and assign the reads to the original samples. Based on a modified Myers's bit-vector dynamic programming algorithm, Btrim can handle indels in adapters and barcodes. It removes low quality regions and trims off adapters at both or either end of the reads. A typical trimming of 30M reads with two sets of adapter pairs can be done in about a minute with a small memory footprint. Btrim is a versatile stand-alone tool that can be used as the first step in virtually all next-generation sequence analysis pipelines. The program is available at http://graphics.med.yale.edu/trim/.},
}
@article {pmid21637837,
year = {2011},
author = {Scarcelli, N and Barnaud, A and Eiserhardt, W and Treier, UA and Seveno, M and d'Anfray, A and Vigouroux, Y and Pintaud, JC},
title = {A set of 100 chloroplast DNA primer pairs to study population genetics and phylogeny in monocotyledons.},
journal = {PloS one},
volume = {6},
number = {5},
pages = {e19954},
pmid = {21637837},
issn = {1932-6203},
mesh = {Base Sequence ; DNA Primers/*metabolism ; DNA, Chloroplast/*genetics ; Genetics, Population/*methods ; Magnoliopsida/*genetics ; Minisatellite Repeats/genetics ; Molecular Sequence Data ; *Phylogeny ; Polymorphism, Genetic ; Polynucleotides/genetics ; Species Specificity ; },
abstract = {Chloroplast DNA sequences are of great interest for population genetics and phylogenetic studies. However, only a small set of markers are commonly used. Most of them have been designed for amplification in a large range of Angiosperms and are located in the Large Single Copy (LSC). Here we developed a new set of 100 primer pairs optimized for amplification in Monocotyledons. Primer pairs amplify coding (exon) and non-coding regions (intron and intergenic spacer). They span the different chloroplast regions: 72 are located in the LSC, 13 in the Small Single Copy (SSC) and 15 in the Inverted Repeat region (IR). Amplification and sequencing were tested in 13 species of Monocotyledons: Dioscorea abyssinica, D. praehensilis, D. rotundata, D. dumetorum, D. bulbifera, Trichopus sempervirens (Dioscoreaceae), Phoenix canariensis, P. dactylifera, Astrocaryum scopatum, A. murumuru, Ceroxylon echinulatum (Arecaceae), Digitaria excilis and Pennisetum glaucum (Poaceae). The diversity found in Dioscorea, Digitaria and Pennisetum mainly corresponded to Single Nucleotide Polymorphism (SNP) while the diversity found in Arecaceae also comprises Variable Number Tandem Repeat (VNTR). We observed that the most variable loci (rps15-ycf1, rpl32-ccsA, ndhF-rpl32, ndhG-ndhI and ccsA) are located in the SSC. Through the analysis of the genetic structure of a wild-cultivated species complex in Dioscorea, we demonstrated that this new set of primers is of great interest for population genetics and we anticipate that it will also be useful for phylogeny and bar-coding studies.},
}
@article {pmid21637336,
year = {2011},
author = {Hollingsworth, PM and Graham, SW and Little, DP},
title = {Choosing and using a plant DNA barcode.},
journal = {PloS one},
volume = {6},
number = {5},
pages = {e19254},
pmid = {21637336},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/*classification ; Gene Flow/genetics ; Genetic Markers ; Species Specificity ; },
abstract = {The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1 (CO1) mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. In this paper, we review the process of selecting and refining a plant barcode; evaluate the factors which influence the discriminatory power of the approach; describe some early applications of plant barcoding and summarise major emerging projects; and outline tool development that will be necessary for plant DNA barcoding to advance.},
}
@article {pmid21635698,
year = {2011},
author = {Reid, BN and LE, M and McCord, WP and Iverson, JB and Georges, A and Bergmann, T and Amato, G and Desalle, R and Naro-Maciel, E},
title = {Comparing and combining distance-based and character-based approaches for barcoding turtles.},
journal = {Molecular ecology resources},
volume = {11},
number = {6},
pages = {956-967},
doi = {10.1111/j.1755-0998.2011.03032.x},
pmid = {21635698},
issn = {1755-0998},
mesh = {Animals ; Base Sequence ; Cluster Analysis ; Conservation of Natural Resources/*methods ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; *Endangered Species ; *Genetic Variation ; Genotype ; *Models, Genetic ; Molecular Sequence Data ; *Phenotype ; Sequence Analysis, DNA ; Species Specificity ; Turtles/anatomy &amp; histology/*genetics ; },
abstract = {Molecular barcoding can serve as a powerful tool in wildlife forensics and may prove to be a vital aid in conserving organisms that are threatened by illegal wildlife trade, such as turtles (Order Testudines). We produced cytochrome oxidase subunit one (COI) sequences (650 bp) for 174 turtle species and combined these with publicly available sequences for 50 species to produce a data set representative of the breadth of the order. Variability within the barcode region was assessed, and the utility of both distance-based and character-based methods for species identification was evaluated. For species in which genetic material from more than one individual was available (n = 69), intraspecific divergences were 1.3% on average, although divergences greater than the customary 2% barcode threshold occurred within 15 species. High intraspecific divergences could indicate species with a high degree of internal genetic structure or possibly even cryptic species, although introgression is also probable in some of these taxa. Divergences between species of the same genus were 6.4% on average; however, 49 species were <2% divergent from congeners. Low levels of interspecific divergence could be caused by recent evolutionary radiations coupled with the low rates of mtDNA evolution previously observed in turtles. Complementing distance-based barcoding with character-based methods for identifying diagnostic sets of nucleotides provided better resolution in several cases where distance-based methods failed to distinguish species. An online identification engine was created to provide character-based identifications. This study constitutes the first comprehensive barcoding effort for this seriously threatened order.},
}
@article {pmid21633490,
year = {2011},
author = {Alreja, G and Setia, N and Nichols, J and Pantanowitz, L},
title = {Reducing patient identification errors related to glucose point-of-care testing.},
journal = {Journal of pathology informatics},
volume = {2},
number = {},
pages = {22},
pmid = {21633490},
issn = {2153-3539},
abstract = {BACKGROUND: Patient identification (ID) errors in point-of-care testing (POCT) can cause test results to be transferred to the wrong patient's chart or prevent results from being transmitted and reported. Despite the implementation of patient barcoding and ongoing operator training at our institution, patient ID errors still occur with glucose POCT. The aim of this study was to develop a solution to reduce identification errors with POCT.<br><br>MATERIALS AND METHODS: Glucose POCT was performed by approximately 2,400 clinical operators throughout our health system. Patients are identified by scanning in wristband barcodes or by manual data entry using portable glucose meters. Meters are docked to upload data to a database server which then transmits data to any medical record matching the financial number of the test result. With a new model, meters connect to an interface manager where the patient ID (a nine-digit account number) is checked against patient registration data from admission, discharge, and transfer (ADT) feeds and only matched results are transferred to the patient's electronic medical record. With the new process, the patient ID is checked prior to testing, and testing is prevented until ID errors are resolved.<br><br>RESULTS: When averaged over a period of a month, ID errors were reduced to 3 errors/month (0.015%) in comparison with 61.5 errors/month (0.319%) before implementing the new meters.<br><br>CONCLUSION: Patient ID errors may occur with glucose POCT despite patient barcoding. The verification of patient identification should ideally take place at the bedside before testing occurs so that the errors can be addressed in real time. The introduction of an ADT feed directly to glucose meters reduced patient ID errors in POCT.},
}
@article {pmid21631414,
year = {2011},
author = {Hull, C and Wray, B and Winslow, F and Vilicich, M},
title = {Tracking and controlling everything that affects quality is the key to a quality management system.},
journal = {Combinatorial chemistry &amp; high throughput screening},
volume = {14},
number = {9},
pages = {772-780},
doi = {10.2174/138620711796957125},
pmid = {21631414},
issn = {1875-5402},
mesh = {Humans ; Medical Errors/prevention &amp; control ; *Total Quality Management ; },
abstract = {Every laboratory has a need to track and control the variables that drive the quality of the results. However, each laboratory is unique and what one organization deems to be a critical process to track and control will likely differ from other organizations. Furthermore, there is more than just the end product or result that needs to be tracked and controlled. All of the intermediate products and resources play a significant role in producing the final product and each of these needs to be included in the LIMS. At a high level, this article will present ideas and opinions on the following topics in relation to implementing a LIMS process tracking and control system in a laboratory: The difference between tracking and controlling processes; What to track and control in the lab; The "product" of the laboratory; Preventing mistakes in a laboratory; Comprehensive software platform options; The value of seeing a system as opposed to imagining it; The use of barcodes in the laboratory; and an assessment on using the Risk Based Approach in deciding what to include in the tracking system.},
}
@article {pmid21625864,
year = {2012},
author = {Abe, H and Hayano, A and Inoue-Murayama, M},
title = {Forensic species identification of large macaws using DNA barcodes and microsatellite profiles.},
journal = {Molecular biology reports},
volume = {39},
number = {1},
pages = {693-699},
pmid = {21625864},
issn = {1573-4978},
mesh = {Animals ; Base Sequence ; Cluster Analysis ; Conservation of Natural Resources/methods ; *DNA Barcoding, Taxonomic ; DNA Primers/genetics ; Feathers/*chemistry ; Female ; Haplotypes/genetics ; Male ; Microsatellite Repeats/*genetics ; Models, Genetic ; Molecular Sequence Data ; Psittaciformes/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Using mitochondrial and nuclear markers species identification was conducted in the case of seized feathers. Earlier, we had sequenced cytochrome c oxidase subunit I (COI) both from 10 seized specimens and 43 validation specimens from captive macaws belonging to 4 Ara species (A. macao, A. chloropterus, A. ararauna, and A. ambiguus) and identified 19 haplotypes based on COI sequences. Species-level identification using Barcode of Life Data Systems showed that seized feathers shared the highest similarity with scarlet macaws (A. macao), and this result was supported by the tree-base identification with high bootstrap values. Moreover, microsatellite profiles in AgGT17 locus showed that patterns of allelic distribution in the seized feathers were apparently distinct from those of red-and-green macaw (A. chloropterus), but were overlapped with those of A. macao, suggesting that all of seized feathers were derived from several individuals of A. macao. We also determined the parentage of hybrid macaws by the combination of COI barcodes and microsatellite profiles. The technique presented here will contribute to forensic identification and future conservation of large macaws that have been lost due to deforestation.},
}
@article {pmid21621601,
year = {2011},
author = {Carr, IM and Morgan, JE and Diggle, CP and Sheridan, E and Markham, AF and Logan, CV and Inglehearn, CF and Taylor, GR and Bonthron, DT},
title = {Illuminator, a desktop program for mutation detection using short-read clonal sequencing.},
journal = {Genomics},
volume = {98},
number = {4},
pages = {302-309},
doi = {10.1016/j.ygeno.2011.05.004},
pmid = {21621601},
issn = {1089-8646},
support = {//Department of Health/United Kingdom ; },
mesh = {Base Sequence ; Cell Line, Tumor ; *Cloning, Molecular ; Electronic Data Processing ; Genes, BRCA1 ; Genes, BRCA2 ; Humans ; Molecular Sequence Data ; *Mutation ; Rhodopsin/genetics ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; *Software ; Tumor Suppressor Protein p53/genetics ; },
abstract = {Current methods for sequencing clonal populations of DNA molecules yield several gigabases of data per day, typically comprising reads of < 100 nt. Such datasets permit widespread genome resequencing and transcriptome analysis or other quantitative tasks. However, this huge capacity can also be harnessed for the resequencing of smaller (gene-sized) target regions, through the simultaneous parallel analysis of multiple subjects, using sample "tagging" or "indexing". These methods promise to have a huge impact on diagnostic mutation analysis and candidate gene testing. Here we describe a software package developed for such studies, offering the ability to resolve pooled samples carrying barcode tags and to align reads to a reference sequence using a mutation-tolerant process. The program, Illuminator, can identify rare sequence variants, including insertions and deletions, and permits interactive data analysis on standard desktop computers. It facilitates the effective analysis of targeted clonal sequencer data without dedicated computational infrastructure or specialized training.},
}
@article {pmid21619893,
year = {2011},
author = {Yin, HQ and Jia, MX and Shi, LJ and Yang, S and Zhang, LY and Zhang, QM and Wang, SQ and Li, G and Zhang, JG},
title = {Nanoparticle-based bio-barcode assay for the detection of bluetongue virus.},
journal = {Journal of virological methods},
volume = {178},
number = {1-2},
pages = {225-228},
doi = {10.1016/j.jviromet.2011.05.014},
pmid = {21619893},
issn = {1879-0984},
mesh = {Animals ; Antibodies, Monoclonal ; Antibodies, Viral ; Bluetongue/*diagnosis ; Bluetongue virus/genetics/immunology/*isolation &amp; purification ; Clinical Laboratory Techniques/*methods ; DNA Barcoding, Taxonomic/*methods ; Fluorescence ; Immunoassay/methods ; Immunomagnetic Separation/methods ; *Nanoparticles ; RNA, Viral/genetics ; Real-Time Polymerase Chain Reaction/methods ; Sensitivity and Specificity ; Serum/virology ; Sheep ; Veterinary Medicine/*methods ; Viral Core Proteins/analysis/immunology ; Virology/*methods ; },
abstract = {The ultrasensitive bio-barcode amplification assay (BCA) technique was developed for the specific detection of the outer-core protein VP7 of bluetongue virus (BTV). The target antigen VP7 was first captured by gold nanoparticles (GNPs) coated with polyclonal antibodies. Magnetic microparticles (MMP) coated with VP7 monoclonal antibody were then added to form a sandwich immuno-complex. After the immuno-complex was formed, signal DNA annealed to DNA strands covalently bound to the GNPs were released by heating and characterized by PCR and real-time fluorescence PCR. A detection limit of 0.1fg/ml was measured for purified VP7, seven orders of magnitude more sensitive than that of conventional antigen capture ELISA. The BCA demonstrated the same enhanced sensitivity for detecting BTV in serum samples from sheep. In the following work it is demonstrated that this assay is a highly sensitive method for the detection of BTV proteins that could be adapted to measure other proteins.},
}
@article {pmid21616891,
year = {2010},
author = {Pettengill, JB and Neel, MC},
title = {An evaluation of candidate plant DNA barcodes and assignment methods in diagnosing 29 species in the genus Agalinis (Orobanchaceae).},
journal = {American journal of botany},
volume = {97},
number = {8},
pages = {1391-1406},
doi = {10.3732/ajb.0900176},
pmid = {21616891},
issn = {0002-9122},
abstract = {PREMISE OF THE STUDY: DNA barcoding has been proposed as a useful technique within many disciplines (e.g., conservation biology and forensics) for determining the taxonomic identity of a sample based on nucleotide similarity to samples of known taxonomy. Application of DNA barcoding to plants has primarily focused on evaluating the success of candidate barcodes across a broad spectrum of evolutionary divergence. Less attention has been paid to evaluating performance when distinguishing congeners or to differential success of analytical techniques despite the fact that the practical application and utility of barcoding hinges on the ability to distinguish closely related species. •<br><br>METHODS: We tested the ability to distinguish among 92 samples representing 29 putative species in the genus Agalinis (Orobanchaceae) using 13 candidate barcodes and three analytical methods (i.e., threshold genetic distances, hierarchical tree-based, and diagnostic character differences). Due to questions regarding evolutionary distinctiveness of some taxa, we evaluated success under two taxonomic hypotheses. &#x2022;<br><br>KEY RESULTS: The psbA-trnH and trnT-trnL barcodes in conjunction with the "best close match" distance-based method best met the objectives of DNA barcoding. Success was also a function of the taxonomy used. &#x2022;<br><br>CONCLUSIONS: In addition to accurately identifying query sequences, our results showed that DNA barcoding is useful for detecting taxonomic uncertainty; determining whether erroneous taxonomy or incomplete lineage sorting is the cause requires additional information provided by traditional taxonomic approaches. The magnitude of differentiation within and among the Agalinis species sampled suggests that our results inform how DNA barcoding will perform among closely related species in other genera.},
}
@article {pmid21616856,
year = {2010},
author = {Bellstedt, DU and Pirie, MD and Visser, JC and de Villiers, MJ and Gehrke, B},
title = {A rapid and inexpensive method for the direct PCR amplification of DNA from plants.},
journal = {American journal of botany},
volume = {97},
number = {7},
pages = {e65-8},
doi = {10.3732/ajb.1000181},
pmid = {21616856},
issn = {0002-9122},
abstract = {PREMISE OF THE STUDY: We present a rapid and inexpensive alternative to DNA isolation for polymerase chain reaction (PCR) amplification from plants. •<br><br>METHODS AND RESULTS: The method involves direct PCR amplification from material macerated in one buffer, followed by dilution and incubation in a second buffer. We describe the procedure and demonstrate its application for nuclear and plastid DNA amplification across a broad range of vascular plants. &#x2022;<br><br>CONCLUSIONS: The method is fast, easy to perform, cost-effective, and consequently ideal for large sample numbers. It represents a considerable simplification of present approaches requiring DNA isolation prior to PCR amplification and will be useful in plant systematics and biotechnology, including applications such as DNA barcoding.},
}
@article {pmid21615927,
year = {2011},
author = {Shimizu, T and Yano, K},
title = {A post-labeling method for multiplexed and multicolored genotyping analysis of SSR, indel and SNP markers in single tube with bar-coded split tag (BStag).},
journal = {BMC research notes},
volume = {4},
number = {},
pages = {161},
pmid = {21615927},
issn = {1756-0500},
abstract = {BACKGROUND: Genotyping analysis using capillary DNA sequencing with fluorescently labeled primer pairs obtained by polymerase chain reaction (PCR) is widely used, but is expensive. The post-PCR labeling method using fluorescently labeled short oligonucleotides and nested PCR of the amplified product obtained from unlabeled primer pairs is a simple and inexpensive alternative. However, previously reported protocols often produced spurious peaks or inconsistent amplification under multiplexed analysis as a result of simultaneous progress of both the amplification and labeling reactions and local homology of the attached tag sequence.<br><br>RESULTS: A set of 16 bp-long oligonucleotide sequences termed bar-coded split tag (BStag), comprising a common basal region, a three-nucleotide 'bar-code' sequence, and a mismatched nucleotide at the middle position were designed for selective post-PCR labeling. The BStag was attached at the 5' end of the forward primer of interest. The melting temperature of the BStag was low enough to separate the labeling reaction from initial PCR amplification, and each sequence was minimally divergent but maintained maximum selectivity. Post-PCR labeling of the amplified product was achieved by extending for three cycles at a lower annealing temperature after the conventional amplification program with the appropriate fluorescently labeled BStag primer. No amplification was confirmed with BStag primers for 12 plant species. The electropherogram of the labeled product obtained using this method was consistent with that of prelabeled primer, except for their apparent size.<br><br>CONCLUSIONS: BStag enabled multiplexed post-PCR labeling of simple sequence repeat or insertion/deletion markers with different dyes in a single tube. BStag in conjunction with locus specific oligo and allele specific oligo was also useful for single nucleotide polymorphism analysis. The labeling protocol was simple and no additional operation was required. Single-tube multiplexed post-PCR labeling is useful for a wide variety of genotyping studies with maximal flexibility and minimal costs.},
}
@article {pmid21613172,
year = {2011},
author = {Shipunov, A and Shipunova, E},
title = {Haptanthus story: rediscovery of enigmatic flowering plant from Honduras.},
journal = {American journal of botany},
volume = {98},
number = {4},
pages = {761-763},
doi = {10.3732/ajb.1000307},
pmid = {21613172},
issn = {1537-2197},
mesh = {Base Sequence ; Buxaceae/*genetics ; DNA Barcoding, Taxonomic ; DNA, Plant/*analysis ; Expeditions ; *Extinction, Biological ; *Genes, Plant ; Honduras ; Nucleotides/analysis ; *Phylogeny ; Plant Proteins/*genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; },
abstract = {PREMISE OF THE STUDY: Finding a plant or animal that was previously considered extinct is a fortunate (but rare) event in biology. Haptanthus hazlettii was collected from Honduras (Central America) in 1980, but numerous attempts to re-collect it have failed. Reproductive organs of Haptanthus are unique among angiosperms and make the search for phylogenetic relations difficult. Unfortunately, all attempts to extract DNA from the existing sample were unsuccessful.<br><br>METHODS: In 2010, we organized a small expedition to Honduras and were able to re-collect this plant, extract DNA from dried samples, and sequence the barcoding region of rbcL.<br><br>KEY RESULTS AND CONCLUSIONS: We obtained phylogenetic trees with reliable support for the placement of Haptanthus as a new member of Buxaceae (boxwood family).},
}
@article {pmid21611176,
year = {2011},
author = {Hou, L and Phillips, C and Azaro, M and Brzustowicz, LM and Bartlett, CW},
title = {Validation of a cost-efficient multi-purpose SNP panel for disease based research.},
journal = {PloS one},
volume = {6},
number = {5},
pages = {e19699},
pmid = {21611176},
issn = {1932-6203},
support = {R01 DC009453/DC/NIDCD NIH HHS/United States ; },
mesh = {Brain-Derived Neurotrophic Factor/genetics ; Case-Control Studies ; Computer Simulation ; Cost-Benefit Analysis ; Disease/*genetics ; Genetic Research/*economics ; Genetics, Population ; Haplotypes/genetics ; Humans ; Odds Ratio ; Polymorphism, Single Nucleotide/*genetics ; Reproducibility of Results ; },
abstract = {BACKGROUND: Here we present convergent methodologies using theoretical calculations, empirical assessment on in-house and publicly available datasets as well as in silico simulations, that validate a panel of SNPs for a variety of necessary tasks in human genetics disease research before resources are committed to larger-scale genotyping studies on those samples. While large-scale well-funded human genetic studies routinely have up to a million SNP genotypes, samples in a human genetics laboratory that are not yet part of such studies may be productively utilized in pilot projects or as part of targeted follow-up work though such smaller scale applications require at least some genome-wide genotype data for quality control purposes such as DNA "barcoding" to detect swaps or contamination issues, determining familial relationships between samples and correcting biases due to population effects such as population stratification in pilot studies.<br><br>PRINCIPAL FINDINGS: Empirical performance in classification of relative types for any two given DNA samples (e.g., full siblings, parental, etc) indicated that for outbred populations the panel performs sufficiently to classify relationship in extended families and therefore also for smaller structures such as trios and for twin zygosity testing. Additionally, familial relationships do not significantly diminish the (mean match) probability of sharing SNP genotypes in pedigrees, further indicating the uniqueness of the "barcode." Simulation using these SNPs for an African American case-control disease association study demonstrated that population stratification, even in complex admixed samples, can be adequately corrected under a range of disease models using the SNP panel.<br><br>CONCLUSION: The panel has been validated for use in a variety of human disease genetics research tasks including sample barcoding, relationship verification, population substructure detection and statistical correction. Given the ease of genotyping our specific assay contained herein, this panel represents a useful and economical panel for human geneticists.},
}
@article {pmid21610864,
year = {2011},
author = {Jeffery, NW and Elías-Gutiérrez, M and Adamowicz, SJ},
title = {Species diversity and phylogeographical affinities of the Branchiopoda (Crustacea) of Churchill, Manitoba, Canada.},
journal = {PloS one},
volume = {6},
number = {5},
pages = {e18364},
pmid = {21610864},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; Crustacea/*genetics ; Electron Transport Complex IV/genetics ; Genetic Variation ; Manitoba ; Phylogeny ; *Phylogeography ; Species Specificity ; },
abstract = {The region of Churchill, Manitoba, contains a wide variety of habitats representative of both the boreal forest and arctic tundra and has been used as a model site for biodiversity studies for nearly seven decades within Canada. Much previous work has been done in Churchill to study the Daphnia pulex species complex in particular, but no study has completed a wide-scale survey on the crustacean species that inhabit Churchill's aquatic ecosystems using molecular markers. We have employed DNA barcoding to study the diversity of the Branchiopoda (Crustacea) in a wide variety of freshwater habitats and to determine the likely origins of the Churchill fauna following the last glaciation. The standard animal barcode marker (COI) was sequenced for 327 specimens, and a 3% divergence threshold was used to delineate potential species. We found 42 provisional and valid branchiopod species from this survey alone, including several cryptic lineages, in comparison with the 25 previously recorded from previous ecological works. Using published sequence data, we explored the phylogeographic affinities of Churchill's branchiopods, finding that the Churchill fauna apparently originated from all directions from multiple glacial refugia (including southern, Beringian, and high arctic regions). Overall, these microcrustaceans are very diverse in Churchill and contain multiple species complexes. The present study introduces among the first sequences for some understudied genera, for which further work is required to delineate species boundaries and develop a more complete understanding of branchiopod diversity over a larger spatial scale.},
}
@article {pmid21607545,
year = {2012},
author = {Zou, S and Li, Q and Kong, L},
title = {Multigene barcoding and phylogeny of geographically widespread muricids (Gastropoda: Neogastropoda) along the coast of China.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {14},
number = {1},
pages = {21-34},
pmid = {21607545},
issn = {1436-2236},
mesh = {Animal Shells ; Animals ; China ; *DNA Barcoding, Taxonomic ; DNA, Intergenic/genetics ; Demography ; Gastropoda/*genetics ; *Multigene Family ; *Phylogeny ; },
abstract = {The identification and phylogeny of muricids have been in a state of confusion for a long time due to the morphological convergence and plasticity. DNA-based identification and phylogeny methods often offer an analytically powerful addition or even an alternative. In this study, we employ a DNA barcoding method to identify 17 known and easily confused muricid species (120 individuals) from the whole China coast based on mitochondrial cytochrome c oxidase subunit I (COI) and 16S rRNA sequences, and nuclear ITS-1 and 28S rRNA sequences. The phylogeny of muricid subfamilies is also analysed based on all mitochondrial and nuclear sequences. The universal COI and 16S rRNA primers did not work broadly across the study group, necessitating the redesign of muricid specific COI and 16S rRNA primers in this paper. Our study demonstrates that COI gene is a suitable marker for barcoding muricids, which can distinguish all muricid species studied. Phylogenetic analysis of 16S rRNA, ITS-1 and 28S rRNA data also provide good support for the species resolution observed in COI data. The relationships of muricid subfamilies are resolved based on the separate and combined gene data that showed the monophyly of each the subfamilies Ergalataxinae, Rapaninae, Ocenebrinae and Muricinae, especially that Ergalataxinae did not fall within Rapaninae.},
}
@article {pmid21605883,
year = {2011},
author = {Betson, M and Halstead, FD and Nejsum, P and Imison, E and Khamis, IS and Sousa-Figueiredo, JC and Rollinson, D and Stothard, JR},
title = {A molecular epidemiological investigation of Ascaris on Unguja, Zanzibar using isoenyzme analysis, DNA barcoding and microsatellite DNA profiling.},
journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene},
volume = {105},
number = {7},
pages = {370-379},
doi = {10.1016/j.trstmh.2011.04.009},
pmid = {21605883},
issn = {1878-3503},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Ascariasis/*epidemiology ; Ascaris/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA Fingerprinting ; Genetic Variation ; Humans ; Microsatellite Repeats ; Molecular Epidemiology ; Molecular Sequence Data ; Phylogeography ; Rural Health ; Swine/parasitology ; Tanzania/epidemiology ; Uganda ; },
abstract = {Ascariasis is of public health importance on the islands of Zanzibar (Unguja and Pemba). To shed light on the molecular epidemiology of this parasite, 68 Ascaris worms, obtained from 14 individuals in four Ungujan villages, were examined by isoenzyme analysis (ISA), DNA barcoding and microsatellite DNA profiling. ISA revealed genetic variation, which was confirmed by DNA barcoding. Nineteen worms recovered from individuals in Uganda were included for comparison. Sixteen unique DNA barcodes were identified, 15 on Unguja and three in Uganda with two shared between. These two barcodes were found in all four Ungujan villages. Worms from Tumbatu-Jongowe, an isolated village on an islet off Unguja, seemed particularly diverse. Within our barcodes, three exact matches were found with Chinese Ascaris retrieved from pigs, which is perhaps surprising given the present rarity of these animals on Unguja. Microsatellite profiling and population genetic analysis revealed further genetic diversity within our samples although population sub-structuring within Unguja was minor in comparison to that between Unguja and Uganda. As African Ascaris has not been subjected to detailed molecular scrutiny, this new diversity represents an important piece in its evolutionary jigsaw and such population markers are informative in monitoring worm dynamics during ongoing control.},
}
@article {pmid21599519,
year = {2011},
author = {Yang, CH and Chuang, LY and Chen, YJ and Tseng, HF and Chang, HW},
title = {Computational analysis of simulated SNP interactions between 26 growth factor-related genes in a breast cancer association study.},
journal = {Omics : a journal of integrative biology},
volume = {15},
number = {6},
pages = {399-407},
doi = {10.1089/omi.2010.0028},
pmid = {21599519},
issn = {1557-8100},
mesh = {Algorithms ; Breast Neoplasms/*genetics ; Chromosomes, Human/genetics ; *Computer Simulation ; *Epistasis, Genetic ; Female ; *Genetic Association Studies ; Genetic Predisposition to Disease ; Humans ; Insulin-Like Growth Factor Binding Protein 3 ; Insulin-Like Growth Factor Binding Proteins/genetics ; Intercellular Signaling Peptides and Proteins/genetics ; Interleukin-10/genetics ; Models, Genetic ; Odds Ratio ; *Polymorphism, Single Nucleotide ; Receptor, IGF Type 1/genetics ; },
abstract = {Many association studies analyze the genotype frequencies of case and control data to predict susceptibility to diseases and cancers. Without providing the raw data for genotypes, many association studies cannot be interpreted fully. Often, the interactions of the single nucleotide polymorphisms (SNPs) are not addressed and this limits the potential of such studies. To solve these problems, we propose a novel computational method with source codes to generate a stimulated genotype dataset based on published SNP genotype frequencies. In this study we evaluate the combined effect of 26 SNP combinations related to eight published growth factor-related genes involved in carcinogenesis pathways of breast cancer. The genetic algorithm (GA) was chosen to provide simultaneous analysis of multiple independent SNPs. The GA can perform feature selection from different SNP combinations via their corresponding genotype (called the SNP barcode), and the approach is able to provide a specific SNP barcode with an optimized fitness value effectively. The best SNP barcode with the maximal occurrence difference between groups for the control and breast cancer, together with an odds ratio analysis, is used to evaluate breast cancer susceptibility. When they are compared to their corresponding non-SNP barcodes, the estimated odds ratios for breast cancer are less than 1 (about 0.85 and 0.87; confidence interval: 0.7473∼0.9585, p < 0.01) for specific SNP barcodes with two to five SNPs. Therefore, we were able to identify potential combined growth factor-related genes together with their SNP barcodes that were protective against breast cancer by in silico analysis.},
}
@article {pmid21599023,
year = {2011},
author = {Lin, D and Wu, J and Yan, F and Deng, S and Ju, H},
title = {Ultrasensitive immunoassay of protein biomarker based on electrochemiluminescent quenching of quantum dots by hemin bio-bar-coded nanoparticle tags.},
journal = {Analytical chemistry},
volume = {83},
number = {13},
pages = {5214-5221},
doi = {10.1021/ac200398x},
pmid = {21599023},
issn = {1520-6882},
mesh = {Base Sequence ; Biomarkers/*metabolism ; DNA Primers ; Electrochemistry ; Immunoassay/*methods ; Limit of Detection ; Luminescence ; Microscopy, Electron, Scanning ; *Nanoparticles ; Proteins/*metabolism ; *Quantum Dots ; Spectrophotometry, Ultraviolet ; },
abstract = {A hemin bio-bar-coded nanoparticle probe labeled antibody was designed by the assembly of antibody and alkylthiol-capped bar-code G-quadruplex DNA on gold nanoparticles and the interaction of hemin with the DNA to form a G-quadruplex/hemin bio-bar-code. An ultrasensitive immunoassay method was developed by combining the labeled antibody with an electrochemiluminescent (ECL) immunosensor for protein. The ECL immunosensor was constructed by a layer-by-layer modification of carbon nanotubes, CdS quantum dots (QDs), and capture antibody on a glassy carbon electrode. In air-saturated pH 8.0 PBS the immunosensor showed a carbon-nanotube-enhanced cathodic ECL emission of QDs. Upon the formation of immunocomplex, the ECL intensity decreased owing to the consumption of ECL coreactant in bio-bar-code electrocatalyzed reduction of dissolved oxygen. Using α-fetoprotein as model analyte, the quenched ECL could be used for immunoassay with a linear range of 0.01 pg mL(-1) to 1 ng mL(-1) and a detection limit of 1.0 fg mL(-1). The wide detection range and high sensitivity resulted from the enhanced ECL emission and highly efficient catalysis of the bio-bar-code. The immunosensor exhibited good stability and acceptable fabrication reproducibility and accuracy, showing great promise for clinical application.},
}
@article {pmid21594143,
year = {2011},
author = {Baldwin, CC and Castillo, CI and Weigt, LA and Victor, BC},
title = {Seven new species within western Atlantic Starksia atlantica, S. lepicoelia, and S. sluiteri (Teleostei, Labrisomidae), with comments on congruence of DNA barcodes and species.},
journal = {ZooKeys},
volume = {},
number = {79},
pages = {21-72},
pmid = {21594143},
issn = {1313-2970},
abstract = {Specimens of Starksia were collected throughout the western Atlantic, and a 650-bp portion of the mitochondrial gene cytochrome oxidase-c subunit I (COl) was sequenced as part of a re-analysis of species diversity of western Central Atlantic shorefishes. A neighbor-joining tree constructed from the sequence data suggests the existence of several cryptic species. Voucher specimens from each genetically distinct lineage and color photographs of vouchers taken prior to dissection and preservation were examined for diagnostic morphological characters. The results suggest that Starksia atlantica, Starksia lepicoelia, and Starksia sluiteri are species complexes, and each comprises three or more species. Seven new species are described. DNA data usually support morphological features, but some incongruence between genetic and morphological data exists. Genetic lineages are only recognized as species if supported by morphology. Genetic lineages within western Atlantic Starksia generally correspond to geography, such that members of each species complex have a very restricted geographical distribution. Increasing geographical coverage of sampling locations will almost certainly increase the number of Starksia species and species complexes recognized in the western Atlantic. Combining molecular and morphological investigations is bringing clarity to the taxonomy of many genera of morphologically similar fishes and increasing the number of currently recognized species. Future phylogenetic studies should help resolve species relationships and shed light on patterns of speciation in western Atlantic Starksia.},
}
@article {pmid21594142,
year = {2011},
author = {Hendrich, L and Balke, M},
title = {A simultaneous journal / wiki publication and dissemination of a new species description: Neobidessodes darwiniensis sp. n. from northern Australia (Coleoptera, Dytiscidae, Bidessini).},
journal = {ZooKeys},
volume = {},
number = {79},
pages = {11-20},
pmid = {21594142},
issn = {1313-2970},
abstract = {Here, we describe a new Australian species in journal format and simultaneously open the description in a wiki format on the www.species-id.net. The wiki format will always link to the fixed original journal description of the taxon, however it permits future edits and additions to species' taxonomy and biology. The diving beetle Neobidessodes darwiniensissp. n. (Coleoptera: Dytiscidae, Bidessini) is described based on a single female, collected in a rest pool of the Harriet Creek in the Darwin Area, Northern Territory. Within Neobidessodes the new species is well characterized by its elongate oval body with rounded sides, short and stout segments of antennae, length of body and dorsal surface coloration. In addition to external morphology, we used mitochondrial cox1 sequence data to support generic assignment and to delineate the new species from other Australian Bidessini including all other known Neobidessodes. Illustrations based on digital images are provided here and as online resources. A modified key is provided. Altogether ten species of the genus are now known worldwide, nine from Australia and one from New Guinea.},
}
@article {pmid21594070,
year = {2011},
author = {Davis, DR and De Prins, J},
title = {Systematics and biology of the new genus Macrosaccus with descriptions of two new species (Lepidoptera, Gracillariidae).},
journal = {ZooKeys},
volume = {},
number = {98},
pages = {29-82},
pmid = {21594070},
issn = {1313-2970},
abstract = {The new genus Macrosaccus Davis &amp; De Prins is proposed for three species formerly assigned to the genus Phyllonorycter: Macrosaccus robiniella (Clemens), Macrosaccus morrisella (Fitch), and Macrosaccus uhlerella (Fitch); two new, closely related species: Macrosaccus neomexicanus Davis and Macrosaccus gliricidius Davis, are also proposed. Descriptions of the adults, pupae, larvae, life histories, and distributions are supplemented with photographs, line drawings, and scanning electron micrographs. Larvae of all species are serpentine/blotch leaf miners on various genera of the plant family Fabaceae. The genus is endemic to the New World, with the invasive species Macrosaccus robiniella now widely established in Europe.},
}
@article {pmid21594066,
year = {2011},
author = {Davis, DR and Wagner, DL},
title = {Biology and systematics of the New World Phyllocnistis Zeller leafminers of the avocado genus Persea (Lepidoptera, Gracillariidae).},
journal = {ZooKeys},
volume = {},
number = {97},
pages = {39-73},
pmid = {21594066},
issn = {1313-2970},
abstract = {Four New World species of Phyllocnistis Zeller are described from serpentine mines in Persea (Family Lauraceae). Phyllocnistis hyperpersea,new species, mines the upper leaf surfaces of avocado, Persea americana Mill., and red bay, Persea borbonia (L.) Spreng. and ranges over much of the southeastern United States into Central America. Phyllocnistis subpersea,new species, mines the underside and occasionally upper sides of new leaves of Persea borbonia in southeastern United States. Phyllocnistis longipalpa, new species, known only from southern Florida also mines the undersides of new leaves of Persea borbonia. Phyllocnistis perseafolia,new species, mines both leaf surfaces and possibly fruits of Persea americana in Colombia, South America. As in all known species of Phyllocnistis, the early instars are subepidermal sapfeeders in young (not fully hardened) foliage, and the final instar is an extremely specialized, nonfeeding larval form, whose primary function is to spin the silken cocoon, at the mine terminus, prior to pupation. Early stages are illustrated and described for three of the species. The unusual morphology of the pupae, particularly the frontal process of the head, is shown to be one of the most useful morphological sources of diagnostic characters for species identification of Phyllocnistis. COI barcode sequence distances are provided for the four proposed species and a fifth, undescribed species from Costa Rica.},
}
@article {pmid21592313,
year = {2011},
author = {Liu, J and Li, Q and Kong, L and Yu, H and Zheng, X},
title = {Identifying the true oysters (Bivalvia: Ostreidae) with mitochondrial phylogeny and distance-based DNA barcoding.},
journal = {Molecular ecology resources},
volume = {11},
number = {5},
pages = {820-830},
doi = {10.1111/j.1755-0998.2011.03025.x},
pmid = {21592313},
issn = {1755-0998},
mesh = {Animals ; Base Sequence ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Ostrea/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; },
abstract = {Oysters (family Ostreidae), with high levels of phenotypic plasticity and wide geographic distribution, are a challenging group for taxonomists and phylogenetics. As a useful tool for molecular species identification, DNA barcoding might offer significant potential for oyster identification and taxonomy. This study used two mitochondrial fragments, cytochrome c oxidase I (COI) and the large ribosomal subunit (16S rDNA), to assess whether oyster species could be identified by phylogeny and distance-based DNA barcoding techniques. Relationships among species were estimated by the phylogenetic analyses of both genes, and then pairwise inter- and intraspecific genetic divergences were assessed. Species forming well-differentiated clades in the molecular phylogenies were identical for both genes even when the closely related species were included. Intraspecific variability of 16S rDNA overlapped with interspecific divergence. However, average intra- and interspecific genetic divergences for COI were 0-1.4% (maximum 2.2%) and 2.6-32.2% (minimum 2.2%), respectively, indicating the existence of a barcoding gap. These results confirm the efficacy of species identification in oysters via DNA barcodes and phylogenetic analysis.},
}
@article {pmid21590418,
year = {2011},
author = {Taylor, DL and Houston, S},
title = {A bioinformatics pipeline for sequence-based analyses of fungal biodiversity.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {722},
number = {},
pages = {141-155},
doi = {10.1007/978-1-61779-040-9_10},
pmid = {21590418},
issn = {1940-6029},
support = {2P20RR016466/RR/NCRR NIH HHS/United States ; },
mesh = {*Biodiversity ; Computational Biology/*methods ; DNA, Fungal/analysis/genetics ; DNA, Ribosomal Spacer/analysis ; Fungi/*classification/genetics ; High-Throughput Nucleotide Sequencing/*methods ; RNA, Ribosomal, 5.8S/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {The internal transcribed spacer (ITS) is the locus of choice with which to characterize fungal diversity in environmental samples. However, methods to analyze ITS datasets have lagged behind the capacity to generate large amounts of sequence information. Here, we describe our bioinformatics pipeline to process large fungal ITS sequence datasets, from raw chromatograms to a spreadsheet of operational taxonomic unit (OTU) abundances across samples. Steps include assembling of reads originating from one clone, identifying primer "barcodes" or "tags," trimming vectors and primers, marking low-quality base calls and removing low-quality sequences, orienting sequences, extracting the ITS region from longer amplicons, and grouping sequences into OTUs. We expect that the principles and tools presented here are relevant to datasets arising from ever-evolving new technologies.},
}
@article {pmid21589909,
year = {2011},
author = {Matzen da Silva, J and Creer, S and dos Santos, A and Costa, AC and Cunha, MR and Costa, FO and Carvalho, GR},
title = {Systematic and evolutionary insights derived from mtDNA COI barcode diversity in the Decapoda (Crustacea: Malacostraca).},
journal = {PloS one},
volume = {6},
number = {5},
pages = {e19449},
pmid = {21589909},
issn = {1932-6203},
mesh = {Animals ; Base Pairing ; Crustacea/classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; },
abstract = {BACKGROUND: Decapods are the most recognizable of all crustaceans and comprise a dominant group of benthic invertebrates of the continental shelf and slope, including many species of economic importance. Of the 17635 morphologically described Decapoda species, only 5.4% are represented by COI barcode region sequences. It therefore remains a challenge to compile regional databases that identify and analyse the extent and patterns of decapod diversity throughout the world.<br><br>We contributed 101 decapod species from the North East Atlantic, the Gulf of Cadiz and the Mediterranean Sea, of which 81 species represent novel COI records. Within the newly-generated dataset, 3.6% of the species barcodes conflicted with the assigned morphological taxonomic identification, highlighting both the apparent taxonomic ambiguity among certain groups, and the need for an accelerated and independent taxonomic approach. Using the combined COI barcode projects from the Barcode of Life Database, we provide the most comprehensive COI data set so far examined for the Order (1572 sequences of 528 species, 213 genera, and 67 families). Patterns within families show a general predicted molecular hierarchy, but the scale of divergence at each taxonomic level appears to vary extensively between families. The range values of mean K2P distance observed were: within species 0.285% to 1.375%, within genus 6.376% to 20.924% and within family 11.392% to 25.617%. Nucleotide composition varied greatly across decapods, ranging from 30.8 % to 49.4 % GC content.<br><br>CONCLUSIONS/SIGNIFICANCE: Decapod biological diversity was quantified by identifying putative cryptic species allowing a rapid assessment of taxon diversity in groups that have until now received limited morphological and systematic examination. We highlight taxonomic groups or species with unusual nucleotide composition or evolutionary rates. Such data are relevant to strategies for conservation of existing decapod biodiversity, as well as elucidating the mechanisms and constraints shaping the patterns observed.},
}
@article {pmid21585016,
year = {2011},
author = {Huang, L and Tang, S and Li, J and Zhao, J},
title = {[Research strategy on molecular identification of animal medical material].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {36},
number = {3},
pages = {234-236},
pmid = {21585016},
issn = {1001-5302},
mesh = {*Animal Structures ; Animals ; *DNA Barcoding, Taxonomic ; Databases, Genetic/standards ; *Materia Medica/analysis ; Mitochondria/genetics ; Research ; },
abstract = {This paper summarized and analyzed the status quo and problems about molecular identification of animal medical material, based on the facts, we proposed some research strategies, including uniting to tackle key problems, expanding the research species, accelerating manufacture and generalization of molecular identification kit, priming the research project of DNA barcoding, and establishing standard database on animal medical material.},
}
@article {pmid21567489,
year = {2011},
author = {Zhang, H and Fang, C and Zhang, S},
title = {Ultrasensitive electrochemical analysis of two analytes by using an autonomous DNA machine that works in a two-cycle mode.},
journal = {Chemistry (Weinheim an der Bergstrasse, Germany)},
volume = {17},
number = {27},
pages = {7531-7537},
doi = {10.1002/chem.201002767},
pmid = {21567489},
issn = {1521-3765},
mesh = {*Biosensing Techniques ; Cadmium Compounds/chemistry ; DNA/*analysis ; DNA Probes/*chemistry ; Electrochemistry ; Humans ; Nanoparticles/chemistry ; Sulfides/chemistry ; Tumor Cells, Cultured ; Zinc Compounds/chemistry ; },
abstract = {We report a novel autonomous DNA machine for amplified electrochemical analysis of two DNAs. The DNA machine operates in a two-cycle working mode to amplify DNA recognition events; the working mode is assisted by two different nicking endonucleases (NEases). Two bio-barcode probes, a ZnS nanoparticle (NP)-DNA probe and a CdS NP-DNA probe, were used to trace two target DNAs. The detection system was based on a sensitive differential pulse anodic stripping voltammetry (DPASV) method for the simultaneous detection of Zn(II) and Cd(II) tracers, which were obtained by dissolving the two probes. Under the optimised conditions, detection limits as low as 5.6×10(-17) (3σ) and 4.1×10(-17) M (3σ) for the two target DNAs were achieved. It has been proven that the DNA machine system can simultaneously amplify two target DNAs by more than four orders of magnitude within 30 min at room temperature. In addition, in combination with an aptamer recognition strategy, the DNA machine was further used in the aptamer-based amplification analysis of adenosine triphosphate (ATP) and lysozyme. With the amplification of the DNA machine, detection limits as low as 5.6×10(-9) M (3σ) for ATP and 5.2×10(-13) M (3σ) for lysozyme were simultaneously obtained. The satisfactory determination of ATP and lysozyme in Ramos cells reveals the good selectivity and feasibility of this protocol. The DNA machine is a promising tool for ultrasensitive and simultaneous multianalysis because of its remarkable signal amplification and simple machine-like operation.},
}
@article {pmid21565107,
year = {2010},
author = {Pryer, KM and Schuettpelz, E and Huiet, L and Grusz, AL and Rothfels, CJ and Avent, T and Schwartz, D and Windham, MD},
title = {DNA barcoding exposes a case of mistaken identity in the fern horticultural trade.},
journal = {Molecular ecology resources},
volume = {10},
number = {6},
pages = {979-985},
doi = {10.1111/j.1755-0998.2010.02858.x},
pmid = {21565107},
issn = {1755-0998},
abstract = {Using cheilanthoid ferns, we provide an example of how DNA barcoding approaches can be useful to the horticultural community for keeping plants in the trade accurately identified. We use plastid rbcL, atpA, and trnG-R sequence data to demonstrate that a fern marketed as Cheilanthes wrightii (endemic to the southwestern USA and northern Mexico) in the horticultural trade is, in fact, Cheilanthes distans (endemic to Australia and adjacent islands). Public and private (accessible with permission) databases contain a wealth of DNA sequence data that are linked to vouchered plant material. These data have uses beyond those for which they were originally generated, and they provide an important resource for fostering collaborations between the academic and horticultural communities. We strongly advocate the barcoding approach as a valuable new technology available to the horticulture industry to help correct plant identification errors in the international trade.},
}
@article {pmid21565106,
year = {2010},
author = {Händeler, K and Wägele, H and Wahrmund, U and Rüdinger, M and Knoop, V},
title = {Slugs' last meals: molecular identification of sequestered chloroplasts from different algal origins in Sacoglossa (Opisthobranchia, Gastropoda).},
journal = {Molecular ecology resources},
volume = {10},
number = {6},
pages = {968-978},
doi = {10.1111/j.1755-0998.2010.02853.x},
pmid = {21565106},
issn = {1755-0998},
abstract = {Some sacoglossan sea slugs have become famous for their unique capability to extract and incorporate functional chloroplasts from algal food organisms (mainly Ulvophyceae) into their gut cells. The functional incorporation of the so-called kleptoplasts allows the slugs to rely on photosynthetic products for weeks to months, enabling them to survive long periods of food shortage over most of their life-span. The algal food spectrum providing kleptoplasts as temporary, non-inherited endosymbionts appears to vary among sacoglossan slugs, but detailed knowledge is sketchy or unavailable. Accurate identification of algal donor species, which provide the chloroplasts for long-term retention is of primary importance to elucidate the biochemical mechanisms allowing long-term functionality of the captured chloroplast in the foreign animal cell environment. Whereas some sacoglossans forage on a variety of algal species, (e.g. Elysia crispata and E. viridis) others are more selective. Hence, characterizing the range of functional sacoglossan-chloroplast associations in nature is a prerequisite to understand the basis of this enigmatic endosymbiosis. Here, we present a suitable chloroplast gene (tufA) as a marker, which allows identification of the respective algal kleptoplast donor taxa by analysing DNA from whole animals. This novel approach allows identification of donor algae on genus or even species level, thus providing evidence for the taxonomic range of food organisms. We report molecular evidence that chloroplasts from different algal sources are simultaneously incorporated in some species of Elysia. NeigborNet analyses for species assignments are preferred over tree reconstruction methods because the former allow more reliable statements on species identification via barcoding, or rather visualize alternative allocations not to be seen in the latter.},
}
@article {pmid21565105,
year = {2010},
author = {Hoareau, TB and Boissin, E},
title = {Design of phylum-specific hybrid primers for DNA barcoding: addressing the need for efficient COI amplification in the Echinodermata.},
journal = {Molecular ecology resources},
volume = {10},
number = {6},
pages = {960-967},
doi = {10.1111/j.1755-0998.2010.02848.x},
pmid = {21565105},
issn = {1755-0998},
abstract = {Recent research has shown the usefulness of the Folmer region of the cytochrome oxidase I (COI) as a genetic barcode to assist in species delimitation of echinoderms. However, amplification of COI is often challenging in echinoderms (low success or pseudogenes). We present a method that allows the design of phylum-specific hybrid primers, and use this to develop COI primers for the Echinodermata. We aligned COI sequences from 310 echinoderm species and designed all possible primers along the consensus sequence with two methods (standard degenerate and hybrid). We found much lower degeneracy for hybrid primers (4-fold degeneracy) than for standard degenerate primers (≥48-fold degeneracy). We then designed the most conserved hybrid primers to amplify a >500-bp region within COI. These primers successfully amplified this gene region in all tested taxa (123 species across all echinoderm classes). Sequencing of 30 species among these confirmed both the quality of the sequences (>500 bp, no pseudogenes) and their utility as a DNA barcode. This method should be useful for developing primers for other mitochondrial genes and other phyla. The method will also be of interest for the development of future projects involving both community-based genetic assessments on macroorganisms and biodiversity assessment of environmental samples using high-throughput sequencing.},
}
@article {pmid21565104,
year = {2010},
author = {Roe, AD and Rice, AV and Bromilow, SE and Cooke, JE and Sperling, FA},
title = {Multilocus species identification and fungal DNA barcoding: insights from blue stain fungal symbionts of the mountain pine beetle.},
journal = {Molecular ecology resources},
volume = {10},
number = {6},
pages = {946-959},
doi = {10.1111/j.1755-0998.2010.02844.x},
pmid = {21565104},
issn = {1755-0998},
abstract = {There is strong community-wide interest in applying molecular techniques to fungal species delimitation and identification, but selection of a standardized region or regions of the genome has not been finalized. A single marker, the ribosomal DNA internal transcribed spacer region, has frequently been suggested as the standard for fungi. We used a group of closely related blue stain fungi associated with the mountain pine beetle (Dendroctonus ponderosae Hopkins) to examine the success of such single-locus species identification, comparing the internal transcribed spacer with four other nuclear markers. We demonstrate that single loci varied in their utility for identifying the six fungal species examined, while use of multiple loci was consistently successful. In a literature survey of 21 similar studies, individual loci were also highly variable in their ability to provide consistent species identifications and were less successful than multilocus diagnostics. Accurate species identification is the essence of any molecular diagnostic system, and this consideration should be central to locus selection. Moreover, our study and the literature survey demonstrate the value of using closely related species as the proving ground for developing a molecular identification system. We advocate use of a multilocus barcode approach that is similar to the practice employed by the plant barcode community, rather than reliance on a single locus.},
}
@article {pmid21565102,
year = {2010},
author = {Zhang, J},
title = {Exploiting formalin-preserved fish specimens for resources of DNA barcoding.},
journal = {Molecular ecology resources},
volume = {10},
number = {6},
pages = {935-941},
doi = {10.1111/j.1755-0998.2010.2838.x},
pmid = {21565102},
issn = {1755-0998},
abstract = {With the development of the DNA barcoding project, a large number of specimens are required to establish the library of reference barcode. Formalin-fixed samples from museums provide a potential resource for it. However, recovery of DNA and amplification of the target gene from formalin-fixed samples are challenging. In this study, a hot alkali pre-treatment accompanied by the use of cetyltrimethylammonium bromide (CTAB) method was employed for DNA recovery from formalin-preserved samples, with the purpose of pursuing the optimal condition for high quantity and quality of DNA and minimizing PCR inhibition. Meanwhile, a semi-nested PCR-based method was developed to enhance the efficacy of amplification. This advanced protocol was demonstrated to be reliable and effective. Even for 23-year-old samples, genomic DNA could be extracted, and COI gene was correctly sequenced.},
}
@article {pmid21565079,
year = {2010},
author = {Naciri, Y and Manen, JF},
title = {Potential DNA transfer from the chloroplast to the nucleus in Eryngium alpinum.},
journal = {Molecular ecology resources},
volume = {10},
number = {4},
pages = {728-731},
doi = {10.1111/j.1755-0998.2009.02816.x},
pmid = {21565079},
issn = {1755-0998},
abstract = {Very divergent psbA-trnH chloroplast sequences were, for some Eryngiun alpinum individuals, repeatedly obtained and could not be attributed to contaminations nor to casual intraspecific variation. The design of external primers allowed the amplification of two different sequences for the same individuals. The divergent sequences were found to be more variable than their counterparts, to have a low GC content and to display a nonsynonymous substitution in psbA C-terminal region, all reasons that led us to hypothesize that they are paraloguous fragments transferred into the nucleus (NuPt). Quantitative polymerase chain reactions confirmed this hypothesis. Such NuPt might have severe implications in plant phylogeography and barcoding.},
}
@article {pmid21565072,
year = {2010},
author = {Rohland, N and Siedel, H and Hofreiter, M},
title = {A rapid column-based ancient DNA extraction method for increased sample throughput.},
journal = {Molecular ecology resources},
volume = {10},
number = {4},
pages = {677-683},
doi = {10.1111/j.1755-0998.2009.02824.x},
pmid = {21565072},
issn = {1755-0998},
abstract = {Genetic analyses using museum specimens and ancient DNA from fossil samples are becoming increasingly important in phylogenetic and especially population genetic studies. Recent progress in ancient DNA sequencing technologies has substantially increased DNA sequence yields and, in combination with barcoding methods, has enabled large-scale studies using any type of DNA. Moreover, more and more studies now use nuclear DNA sequences in addition to mitochondrial ones. Unfortunately, nuclear DNA is, due to its much lower copy number in living cells compared to mitochondrial DNA, much more difficult to obtain from low-quality samples. Therefore, a DNA extraction method that optimizes DNA yields from low-quality samples and at the same time allows processing many samples within a short time frame is immediately required. In fact, the major bottleneck in the analysis process using samples containing low amounts of degraded DNA now lies in the extraction of samples, as column-based methods using commercial kits are fast but have proven to give very low yields, while more efficient methods are generally very time-consuming. Here, we present a method that combines the high DNA yield of batch-based silica extraction with the time-efficiency of column-based methods. Our results on Pleistocene cave bear samples show that DNA yields are quantitatively comparable, and in fact even slightly better than with silica batch extraction, while at the same time the number of samples that can conveniently be processed in parallel increases and both bench time and costs decrease using this method. Thus, this method is suited for harvesting the power of high-throughput sequencing using the DNA preserved in the millions of paleontological and museums specimens.},
}
@article {pmid21565068,
year = {2010},
author = {Uthicke, S and Byrne, M and Conand, C},
title = {Genetic barcoding of commercial Bêche-de-mer species (Echinodermata: Holothuroidea).},
journal = {Molecular ecology resources},
volume = {10},
number = {4},
pages = {634-646},
doi = {10.1111/j.1755-0998.2009.02826.x},
pmid = {21565068},
issn = {1755-0998},
abstract = {There are more than 47 species of holothurians used for bêche-de-mer production, many of which are locally overfished. With three exceptions, all bêche-de-mer species are Aspidochirotida and species identification of many of these is difficult. We analysed available genetic information and newly generated sequences to determine if genetic barcoding with the mitochondrial COI gene can be used to identify bêche-de-mer species. Although genetic data were available for ∼50% of bêche-de-mer species, sufficient information and within-species replication were only available for six species. We generated 96 new COI sequences extending the existing database to cover most common species. COI unambiguously identified most bêche-de-mer species providing a genetic barcode for the identification of known species. In addition, conspecific (1.3%) variation and congeneric (16.9%) divergence were well separated ('barcoding-gap') albeit with a small overlap, which may lead to some error if genetic sampling alone was applied for species discovery. In addition to identification of adults, COI sequences were useful to identify juveniles that are often morphologically different. Sequence data showed that large (deep) and small (shallow) morphotypes of Holothuria atra are the same species, but suggested potential cryptic species within this taxon. For bêche-de-mer, the COI barcode proved useful in species clarification and discovery, but further genetic and taxonomic work is essential for several species. Some bêche-de-mer clades were problematic with morphologically disparate specimens sharing the same barcode. Our study indicated the presence of undescribed species (Bohadschia sp.) and species that constitute separate species in the Indian and Pacific Ocean (e.g. Holothuria fuscogilva).},
}
@article {pmid21565067,
year = {2010},
author = {Dentinger, BT and Margaritescu, S and Moncalvo, JM},
title = {Rapid and reliable high-throughput methods of DNA extraction for use in barcoding and molecular systematics of mushrooms.},
journal = {Molecular ecology resources},
volume = {10},
number = {4},
pages = {628-633},
doi = {10.1111/j.1755-0998.2009.02825.x},
pmid = {21565067},
issn = {1755-0998},
abstract = {We present two methods for DNA extraction from fresh and dried mushrooms that are adaptable to high-throughput sequencing initiatives, such as DNA barcoding. Our results show that these protocols yield ∼85% sequencing success from recently collected materials. Tests with both recent (<2 year) and older (>100 years) specimens reveal that older collections have low success rates and may be an inefficient resource for populating a barcode database. However, our method of extracting DNA from herbarium samples using small amount of tissue is reliable and could be used for important historical specimens. The application of these protocols greatly reduces time, and therefore cost, of generating DNA sequences from mushrooms and other fungi vs. traditional extraction methods. The efficiency of these methods illustrates that standardization and streamlining of sample processing should be shifted from the laboratory to the field.},
}
@article {pmid21565066,
year = {2010},
author = {Moulton, MJ and Song, H and Whiting, MF},
title = {Assessing the effects of primer specificity on eliminating numt coamplification in DNA barcoding: a case study from Orthoptera (Arthropoda: Insecta).},
journal = {Molecular ecology resources},
volume = {10},
number = {4},
pages = {615-627},
doi = {10.1111/j.1755-0998.2009.02823.x},
pmid = {21565066},
issn = {1755-0998},
abstract = {DNA barcoding is a diagnostic method of species identification based on sequencing a short mitochondrial DNA fragment of cytochrome oxidase I (COI), but its ability to correctly diagnose species is limited by the presence of nuclear mitochondrial pseudogenes (numts). Numts can be coamplified with the mitochondrial orthologue when using universal primers, which can lead to incorrect species identification and an overestimation of the number of species. Some researchers have proposed that using more specific primers may help eliminate numt coamplification, but the efficacy of this method has not been thoroughly tested. In this study, we investigate the taxonomic distribution of numts in 11 lineages within the insect order Orthoptera, by analysing cloned COI sequences and further test the effects of primer specificity on eliminating numt coamplification in four lineages. We find that numts are coamplified in all 11 taxa using universal (barcoding) primers, which suggests that numts may be widespread in other taxonomic groups as well. Increased primer specificity is only effective at reducing numt coamplification in some species tested, and only eliminates it in one species tested. Furthermore, we find that a number of numts do not have stop codons or indels, making it difficult to distinguish them from mitochondrial orthologues, thus putting the efficacy of barcoding quality control measures under question. Our findings suggest that numt coamplification is a serious problem for DNA barcoding and more quality control measures should be implemented to identify and eliminate numts prior to using mitochondrial barcodes for species diagnoses.},
}
@article {pmid21565065,
year = {2010},
author = {Richard, B and Decaëns, T and Rougerie, R and James, SW and Porco, D and Hebert, PD},
title = {Re-integrating earthworm juveniles into soil biodiversity studies: species identification through DNA barcoding.},
journal = {Molecular ecology resources},
volume = {10},
number = {4},
pages = {606-614},
doi = {10.1111/j.1755-0998.2009.02822.x},
pmid = {21565065},
issn = {1755-0998},
abstract = {Species identification of earthworms is usually achieved by careful observation of morphological features, often sexual characters only present in adult specimens. Consequently, juveniles or cocoons are often impossible to identify, creating a possible bias in studies that aim to document species richness and abundance. DNA barcoding, the use of a short standardized DNA fragment for species identification, is a promising approach for species discrimination. When a reference library is available, DNA-based identification is possible for all life stages. In this study, we show that DNA barcoding is an unrivaled tool for high volume identification of juvenile earthworms. To illustrate this advance, we generated DNA barcodes for specimens of Lumbricus collected from three temperate grasslands in western France. The analysis of genetic distances between individuals shows that juvenile sequences unequivocally match DNA barcode clusters of previously identified adult specimens, demonstrating the potential of DNA barcoding to provide exhaustive specimen identification for soil ecological research.},
}
@article {pmid21565045,
year = {2010},
author = {VAN Houdt, JK and Breman, FC and Virgilio, M and DE Meyer, M},
title = {Recovering full DNA barcodes from natural history collections of Tephritid fruitflies (Tephritidae, Diptera) using mini barcodes.},
journal = {Molecular ecology resources},
volume = {10},
number = {3},
pages = {459-465},
doi = {10.1111/j.1755-0998.2009.02800.x},
pmid = {21565045},
issn = {1755-0998},
abstract = {The family of Tephritid fruit flies (Tephritidae, Diptera) is composed of more than 4000 species and more than 350 are of economic importance (EI). The Tephritid Barcoding Initiative (TBI) aims at obtaining DNA barcodes for all EI species and the majority of their congeners. Dry pinned specimens from natural history collections are an important resource for reference material, but were often collected decades ago. We observed a strong decrease in the success rate of obtaining a full COX1 DNA barcode (658 bp), with an increasing age of the specimens. Obtaining full barcodes is often not possible using standard protocols. We developed a universal Tephritid primer set for multiple overlapping mini-barcodes that allows reconstructing the full COX1 DNA barcode. These newly developed primers and the corresponding protocol will facilitate the utilization of the extensive natural history collection by the TBI consortium.},
}
@article {pmid21565044,
year = {2010},
author = {Campagna, L and Lijtmaer, DA and Kerr, KC and Barreira, AS and Hebert, PD and Lougheed, SC and Tubaro, PL},
title = {DNA barcodes provide new evidence of a recent radiation in the genus Sporophila (Aves: Passeriformes).},
journal = {Molecular ecology resources},
volume = {10},
number = {3},
pages = {449-458},
doi = {10.1111/j.1755-0998.2009.02799.x},
pmid = {21565044},
issn = {1755-0998},
abstract = {The capuchinos are a group of birds in the genus Sporophila that has apparently radiated recently, as evidenced by their lack of mitochondrial genetic diversity. We obtained cytochrome c oxidase I (COI) sequences (or DNA barcodes) for the 11 species of the group and various outgroups. We compared the patterns of COI variability of the capuchinos with those of the largest barcode data set from neotropical birds currently available (500 species representing 51% of avian richness in Argentina), and subjected COI sequences to neighbour-joining, maximum parsimony and Bayesian phylogenetic analyses as well as statistical parsimony network analysis. A clade within the capuchinos, the southern capuchinos, showed higher intraspecific and lower interspecific divergence than the remaining Argentine species. As most of the southern capuchinos shared COI haplotypes and pairwise distances within species were in many cases higher than distances between them, the phylogenetic affinities within the group remained unresolved. The observed genetic pattern is consistent with both incomplete lineage sorting and gene flow between species. The southern capuchinos constitute the only large group of species among the neotropical birds barcoded so far that are inseparable when using DNA barcodes, and one of few multispecies avian groups known to lack reciprocal monophyly. Extending the analysis to rapidly evolving nuclear and mitochondrial markers will be crucial to understanding this radiation. Apart from giving insights into the evolution of the capuchinos, this study shows how DNA barcoding can rapidly flag species or groups of species worthy of deeper study.},
}
@article {pmid21565043,
year = {2010},
author = {Tang, RW and Yau, C and Ng, WC},
title = {Identification of stomatopod larvae (Crustacea: Stomatopoda) from Hong Kong waters using DNA barcodes.},
journal = {Molecular ecology resources},
volume = {10},
number = {3},
pages = {439-448},
doi = {10.1111/j.1755-0998.2009.02794.x},
pmid = {21565043},
issn = {1755-0998},
abstract = {The Stomatopoda (Crustacea: Malacostraca) from the South China Sea region are of commercial importance and although limited studies have been conducted on the adults, no research has ever been attempted on the larval stages because of the lack of identification keys or taxonomic descriptions. In the first study of its kind in the region, DNA barcoding was used successfully to identify unknown stomatopod larvae from plankton samples. Sequences of two mitochondrial genes, namely the cytochrome c oxidase subunit-I (COI) and the large ribosomal subunit (16S) rRNA, were applied as the barcodes to match DNA sequences from unknown larval morphotypes against those of known, locally occurring adult species. Intraspecific variations for the COI and 16S rRNA genes were found to be <2.4% and <2.1% respectively in terms of Kimura 2-Parameter (K2P) divergence of the adults, whereas variations between genera ranged from 13% to 24% and 3% to 11% respectively. These results imply that both genes are suitable for use in species identification of stomatopods; thus 14 of the 16 larval morphotypes (87.5%) obtained in Hong Kong waters can be identified to seven species through DNA barcoding. The findings of this study would also facilitate future research on the larval ecology and phylogenetic relationship of these crustaceans.},
}
@article {pmid21565042,
year = {2010},
author = {Patel, S and Waugh, J and Millar, CD and Lambert, DM},
title = {Conserved primers for DNA barcoding historical and modern samples from New Zealand and Antarctic birds.},
journal = {Molecular ecology resources},
volume = {10},
number = {3},
pages = {431-438},
doi = {10.1111/j.1755-0998.2009.02793.x},
pmid = {21565042},
issn = {1755-0998},
abstract = {Our ability to DNA barcode the birds of the world is based on the effective amplification and sequencing of a 648 base pair (bp) region of the mitochondrial cytochrome c oxidase (COI or cox1) gene. For many geographic regions the large numbers of vouchered specimens necessary for the construction of a DNA barcoding database have already been collected and are available in museums and other institutions. However, many of these specimens are old (>20 years) and are stored as either fixed study skins or dried skeletons. DNA extracted from such historical samples is typically degraded and, generally, only short DNA fragments can be recovered from such specimens making the recovery of the barcoding region as a single fragment difficult. We report two sets of conserved primers that allow the amplification of the entire DNA barcoding region in either three or five overlapping fragments. These primer sets allow the recovery of DNA barcodes from valuable historical specimens that in many cases are unique in that they are unable or unlikely to be collected again. We also report three new primers that in combination allow the effective amplification from modern samples of the entire DNA barcoding region as a single DNA fragment for 17 orders of Southern Hemisphere birds.},
}
@article {pmid21565041,
year = {2010},
author = {Lara, A and Ponce de León, JL and Rodríguez, R and Casane, D and Côté, G and Bernatchez, L and García-Machado, E},
title = {DNA barcoding of Cuban freshwater fishes: evidence for cryptic species and taxonomic conflicts.},
journal = {Molecular ecology resources},
volume = {10},
number = {3},
pages = {421-430},
doi = {10.1111/j.1755-0998.2009.02785.x},
pmid = {21565041},
issn = {1755-0998},
abstract = {Despite ongoing efforts to protect species and ecosystems in Cuba, habitat degradation, overuse and introduction of alien species have posed serious challenges to native freshwater fish species. In spite of the accumulated knowledge on the systematics of this freshwater ichthyofauna, recent results suggested that we are far from having a complete picture of the Cuban freshwater fish diversity. It is estimated that 40% of freshwater Cuban fish are endemic; however, this number may be even higher. Partial sequences (652 bp) of the mitochondrial gene COI (cytochrome c oxidase subunit I) were used to barcode 126 individuals, representing 27 taxonomically recognized species in 17 genera and 10 families. Analysis was based on Kimura 2-parameter genetic distances, and for four genera a character-based analysis (population aggregation analysis) was also used. The mean conspecific, congeneric and confamiliar genetic distances were 0.6%, 9.1% and 20.2% respectively. Molecular species identification was in concordance with current taxonomical classification in 96.4% of cases, and based on the neighbour-joining trees, in all but one instance, members of a given genera clustered within the same clade. Within the genus Gambusia, genetic divergence analysis suggests that there may be at least four cryptic species. In contrast, low genetic divergence and a lack of diagnostic sites suggest that Rivulus insulaepinorum may be conspecific with Rivulus cylindraceus. Distance and character-based analysis were completely concordant, suggesting that they complement species identification. Overall, the results evidenced the usefulness of the DNA barcodes for cataloguing Cuban freshwater fish species and for identifying those groups that deserve further taxonomic attention.},
}
@article {pmid21559508,
year = {2011},
author = {de la Parra Venegas, R and Hueter, R and González Cano, J and Tyminski, J and Gregorio Remolina, J and Maslanka, M and Ormos, A and Weigt, L and Carlson, B and Dove, A},
title = {An unprecedented aggregation of whale sharks, Rhincodon typus, in Mexican coastal waters of the Caribbean Sea.},
journal = {PloS one},
volume = {6},
number = {4},
pages = {e18994},
pmid = {21559508},
issn = {1932-6203},
mesh = {Animal Migration ; Animals ; Behavior, Animal ; DNA/analysis ; Ecosystem ; Electronic Data Processing ; Female ; Genetics, Population ; Male ; Mexico ; Oceans and Seas ; Sex Factors ; Sharks/*physiology ; },
abstract = {Whale sharks, Rhincodon typus, are often perceived as solitary behemoths that live and feed in the open ocean. To the contrary, evidence is accumulating that they are gregarious and form seasonal aggregations in some coastal waters. One such aggregation occurs annually north of Cabo Catoche, off Isla Holbox on the Yucatán Peninsula of Mexico. Here we report a second, much denser aggregation of whale sharks (dubbed "the Afuera") that occurs east of the tip of the Yucatán Peninsula in the Caribbean Sea. The 2009 Afuera event comprised the largest aggregation of whale sharks ever reported, with up to 420 whale sharks observed in a single aerial survey, all gathered in an elliptical patch of ocean approximately 18 km(2). Plankton studies indicated that the sharks were feeding on dense homogenous patches of fish eggs, which DNA barcoding analysis identified as belonging to little tunny, Euthynnus alletteratus. This contrasts with the annual Cabo Catoche aggregation nearby, where prey consists mostly of copepods and sergestid shrimp. Increased sightings at the Afuera coincide with decreased sightings at Cabo Catoche, and both groups have the same sex ratio, implying that the same animals are likely involved in both aggregations; tagging data support this idea. With two whale shark aggregation areas, high coastal productivity and a previously-unknown scombrid spawning ground, the northeastern Yucatán marine region is a critical habitat that deserves more concerted conservation efforts.},
}
@article {pmid21557025,
year = {2011},
author = {Pierron, F and Normandeau, E and Defo, MA and Campbell, PG and Bernatchez, L and Couture, P},
title = {Effects of chronic metal exposure on wild fish populations revealed by high-throughput cDNA sequencing.},
journal = {Ecotoxicology (London, England)},
volume = {20},
number = {6},
pages = {1388-1399},
pmid = {21557025},
issn = {1573-3017},
mesh = {Animals ; Bile Acids and Salts/metabolism ; Cadmium/analysis/metabolism/toxicity ; Copper/analysis/metabolism/toxicity ; DNA, Complementary ; Fish Proteins/genetics/metabolism ; Fishes/*genetics/metabolism ; Gene Expression/drug effects ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Metals/analysis/metabolism/*toxicity ; Vitamin A/metabolism ; Water Pollutants, Chemical/analysis/metabolism/*toxicity ; },
abstract = {Given the inherent variability of aquatic systems, predicting the in situ effects of contaminants on such ecosystems still represents a major challenge for ecotoxicology. In this context, transcriptomic tools can help identify and investigate the mechanisms of toxicity beyond the traditional morphometric, physiological and population-level endpoints. In this study, we used the 454 sequencing technology to examine the in situ effects of chronic metal (Cd, Cu) exposure on the yellow perch (Perca flavescens) transcriptome. Total hepatic mRNA from fish sampled along a polymetallic gradient was extracted, reverse transcribed, labeled with unique barcode sequences and sequenced. This approach allowed us to identify correlations between the transcription level of single genes and the hepatic concentrations of individual metals; 71% of the correlations established were negative. Chronic metal exposure was thus associated with a decrease in the transcription levels of numerous genes involved in protein biosynthesis, in the immune system, and in lipid and energy metabolism. Our results suggest that this marked decrease could result from an impairment of bile acid metabolism by Cd and energy restriction but also from the recruitment of several genes involved in epigenetic modifications of histones and DNA that lead to gene silencing.},
}
@article {pmid21548356,
year = {2010},
author = {Yang, LC and Deng, H and Yi, Y and Zhang, XM and Wang, YZ and Lin, JQ},
title = {[Identification of medical Dendrobium herbs by ISSR marker].},
journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials},
volume = {33},
number = {12},
pages = {1841-1844},
pmid = {21548356},
issn = {1001-4454},
mesh = {DNA Fingerprinting ; DNA Primers ; DNA, Plant/*genetics ; Dendrobium/*classification/*genetics ; Genetic Markers ; Genetics, Population ; Phylogeny ; Plant Leaves/genetics ; Plants, Medicinal/classification/*genetics ; Polymerase Chain Reaction ; Polymorphism, Genetic ; *Repetitive Sequences, Nucleic Acid ; Species Specificity ; },
abstract = {OBJECTIVE: A molecular biology method was studied to identify medical Dendrobium and to provide a method for quality control of these plants.<br><br>METHOD: ISSR primer was screened through ISSR-PCR reaction according to its gene resolving power, and digital barcodes were established for identification.<br><br>RESULTS: Screening 2 primers which Rp value above 8, This primers can identify medical Dendrobium from 6 kinds 8 groups.<br><br>CONCLUSION: ISSR molecular maker technology is useful for identifying species and habitats of medical Dendrobium plants.},
}
@article {pmid21541350,
year = {2011},
author = {Jones, M and Ghoorah, A and Blaxter, M},
title = {jMOTU and Taxonerator: turning DNA Barcode sequences into annotated operational taxonomic units.},
journal = {PloS one},
volume = {6},
number = {4},
pages = {e19259},
pmid = {21541350},
issn = {1932-6203},
mesh = {*Algorithms ; Animals ; Base Sequence ; Bathing Beaches ; Biodiversity ; Butterflies/genetics ; DNA Barcoding, Taxonomic/*methods ; Ecosystem ; Electron Transport Complex IV/genetics ; Molecular Sequence Annotation/*methods ; RNA, Ribosomal/genetics ; Ribosome Subunits, Small/genetics ; Scotland ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: DNA barcoding and other DNA sequence-based techniques for investigating and estimating biodiversity require explicit methods for associating individual sequences with taxa, as it is at the taxon level that biodiversity is assessed. For many projects, the bioinformatic analyses required pose problems for laboratories whose prime expertise is not in bioinformatics. User-friendly tools are required for both clustering sequences into molecular operational taxonomic units (MOTU) and for associating these MOTU with known organismal taxonomies.<br><br>RESULTS: Here we present jMOTU, a Java program for the analysis of DNA barcode datasets that uses an explicit, determinate algorithm to define MOTU. We demonstrate its usefulness for both individual specimen-based Sanger sequencing surveys and bulk-environment metagenetic surveys using long-read next-generation sequencing data. jMOTU is driven through a graphical user interface, and can analyse tens of thousands of sequences in a short time on a desktop computer. A companion program, Taxonerator, that adds traditional taxonomic annotation to MOTU, is also presented. Clustering and taxonomic annotation data are stored in a relational database, and are thus amenable to subsequent data mining and web presentation.<br><br>CONCLUSIONS: jMOTU efficiently and robustly identifies the molecular taxa present in survey datasets, and Taxonerator decorates the MOTU with putative identifications. jMOTU and Taxonerator are freely available from http://www.nematodes.org/.},
}
@article {pmid21538596,
year = {2011},
author = {Ramiro-Manzano, F and Fenollosa, R and Xifré-Pérez, E and Garín, M and Meseguer, F},
title = {Porous silicon microcavities based photonic barcodes.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {23},
number = {27},
pages = {3022-3025},
doi = {10.1002/adma.201100986},
pmid = {21538596},
issn = {1521-4095},
mesh = {Colloids/chemistry ; Electronic Data Processing/instrumentation ; Luminescence ; Photons ; Porosity ; Silicon/*chemistry ; },
}
@article {pmid21535525,
year = {2010},
author = {Rasmussen Hellberg, RS and Morrissey, MT and Hanner, RH},
title = {A multiplex PCR method for the identification of commercially important salmon and trout species (Oncorhynchus and Salmo) in North America.},
journal = {Journal of food science},
volume = {75},
number = {7},
pages = {C595-606},
doi = {10.1111/j.1750-3841.2010.01752.x},
pmid = {21535525},
issn = {1750-3841},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/metabolism ; Electron Transport Complex IV/genetics/metabolism ; Fish Proteins/genetics/metabolism ; Food Inspection/methods ; Food, Preserved/classification ; Limit of Detection ; North America ; Polymerase Chain Reaction/*methods ; Salmon/*classification/genetics ; Seafood/classification ; Trout/*classification/genetics ; },
abstract = {UNLABELLED: The purpose of this study was to develop a species-specific multiplex polymerase chain reaction (PCR) method that allows for the detection of salmon species substitution on the commercial market. Species-specific primers and TaqMan® probes were developed based on a comprehensive collection of mitochondrial 5' cytochrome c oxidase subunit I (COI) deoxyribonucleic acid (DNA) "barcode" sequences. Primers and probes were combined into multiplex assays and tested for specificity against 112 reference samples representing 25 species. Sensitivity and linearity tests were conducted using 10-fold serial dilutions of target DNA (single-species samples) and DNA admixtures containing the target species at levels of 10%, 1.0%, and 0.1% mixed with a secondary species. The specificity tests showed positive signals for the target DNA in both real-time and conventional PCR systems. Nonspecific amplification in both systems was minimal; however, false positives were detected at low levels (1.2% to 8.3%) in conventional PCR. Detection levels were similar for admixtures and single-species samples based on a 30 PCR cycle cut-off, with limits of 0.25 to 2.5 ng (1% to 10%) in conventional PCR and 0.05 to 5.0 ng (0.1% to 10%) in real-time PCR. A small-scale test with food samples showed promising results, with species identification possible even in heavily processed food items. Overall, this study presents a rapid, specific, and sensitive method for salmon species identification that can be applied to mixed-species and heavily processed samples in either conventional or real-time PCR formats.<br><br>PRACTICAL APPLICATION: This study provides a newly developed method for salmon and trout species identification that will assist both industry and regulatory agencies in the detection and prevention of species substitution. This multiplex PCR method allows for rapid, high-throughput species identification even in heavily processed and mixed-species samples. An inter-laboratory study is currently being carried out to assess the ability of this method to identify species in a variety of commercial salmon and trout products.},
}
@article {pmid21533287,
year = {2011},
author = {Hajibabaei, M and Shokralla, S and Zhou, X and Singer, GA and Baird, DJ},
title = {Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos.},
journal = {PloS one},
volume = {6},
number = {4},
pages = {e17497},
pmid = {21533287},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; DNA/*genetics ; *Electronic Data Processing ; Environmental Monitoring/*methods ; *Fresh Water ; Invertebrates/classification/genetics ; },
abstract = {Timely and accurate biodiversity analysis poses an ongoing challenge for the success of biomonitoring programs. Morphology-based identification of bioindicator taxa is time consuming, and rarely supports species-level resolution especially for immature life stages. Much work has been done in the past decade to develop alternative approaches for biodiversity analysis using DNA sequence-based approaches such as molecular phylogenetics and DNA barcoding. On-going assembly of DNA barcode reference libraries will provide the basis for a DNA-based identification system. The use of recently introduced next-generation sequencing (NGS) approaches in biodiversity science has the potential to further extend the application of DNA information for routine biomonitoring applications to an unprecedented scale. Here we demonstrate the feasibility of using 454 massively parallel pyrosequencing for species-level analysis of freshwater benthic macroinvertebrate taxa commonly used for biomonitoring. We designed our experiments in order to directly compare morphology-based, Sanger sequencing DNA barcoding, and next-generation environmental barcoding approaches. Our results show the ability of 454 pyrosequencing of mini-barcodes to accurately identify all species with more than 1% abundance in the pooled mixture. Although the approach failed to identify 6 rare species in the mixture, the presence of sequences from 9 species that were not represented by individuals in the mixture provides evidence that DNA based analysis may yet provide a valuable approach in finding rare species in bulk environmental samples. We further demonstrate the application of the environmental barcoding approach by comparing benthic macroinvertebrates from an urban region to those obtained from a conservation area. Although considerable effort will be required to robustly optimize NGS tools to identify species from bulk environmental samples, our results indicate the potential of an environmental barcoding approach for biomonitoring programs.},
}
@article {pmid21531898,
year = {2011},
author = {Tsai, H and Howell, T and Nitcher, R and Missirian, V and Watson, B and Ngo, KJ and Lieberman, M and Fass, J and Uauy, C and Tran, RK and Khan, AA and Filkov, V and Tai, TH and Dubcovsky, J and Comai, L},
title = {Discovery of rare mutations in populations: TILLING by sequencing.},
journal = {Plant physiology},
volume = {156},
number = {3},
pages = {1257-1268},
pmid = {21531898},
issn = {1532-2548},
support = {BB/I000712/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/J/000C0628/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Genes, Plant/genetics ; Genetics, Population ; Genome, Plant/*genetics ; Mutagenesis/*genetics ; Mutation/*genetics ; Oryza/*genetics ; Pilot Projects ; Probability ; Sequence Analysis, DNA/*methods ; Templates, Genetic ; Triticum/*genetics ; },
abstract = {Discovery of rare mutations in populations requires methods, such as TILLING (for Targeting Induced Local Lesions in Genomes), for processing and analyzing many individuals in parallel. Previous TILLING protocols employed enzymatic or physical discrimination of heteroduplexed from homoduplexed target DNA. Using mutant populations of rice (Oryza sativa) and wheat (Triticum durum), we developed a method based on Illumina sequencing of target genes amplified from multidimensionally pooled templates representing 768 individuals per experiment. Parallel processing of sequencing libraries was aided by unique tracer sequences and barcodes allowing flexibility in the number and pooling arrangement of targeted genes, species, and pooling scheme. Sequencing reads were processed and aligned to the reference to identify possible single-nucleotide changes, which were then evaluated for frequency, sequencing quality, intersection pattern in pools, and statistical relevance to produce a Bayesian score with an associated confidence threshold. Discovery was robust both in rice and wheat using either bidimensional or tridimensional pooling schemes. The method compared favorably with other molecular and computational approaches, providing high sensitivity and specificity.},
}
@article {pmid21530925,
year = {2011},
author = {Mammella, MA and Cacciola, SO and Martin, F and Schena, L},
title = {Genetic characterization of Phytophthora nicotianae by the analysis of polymorphic regions of the mitochondrial DNA.},
journal = {Fungal biology},
volume = {115},
number = {4-5},
pages = {432-442},
doi = {10.1016/j.funbio.2011.02.018},
pmid = {21530925},
issn = {1878-6146},
mesh = {Base Sequence ; DNA, Fungal/genetics ; DNA, Mitochondrial/analysis/*genetics ; Gene Amplification ; Haplotypes ; INDEL Mutation ; Molecular Sequence Data ; Phylogeny ; Phytophthora/classification/*genetics/growth &amp; development ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; },
abstract = {A new method based on the analysis of mitochondrial intergenic regions characterized by intraspecific variation in DNA sequences was developed and applied to the study of the plant pathogen Phytophthora nicotianae. Two regions flanked by genes trnY and rns and trnW and cox2 were identified by comparing the whole mitochondrial genomes of Phytophthora infestans, Phytophthora ramorum, and Phytophthora sojae and amplified using primers designed from the flanking conserved genes. These regions were sequenced from 51 isolates of P. nicotianae of both A1 and A2 mating type recovered from different hosts and geographic regions. Amplicon length varied from 429bp to 443bp (trnY/rns) and 322bp to 373bp (trnW/cox2) with intraspecific variation due to single nucleotide polymorphisms and indels. Seventeen, seven and 20 different haplotypes were detected by individually analyzing regions trnY-rns, trnW-cox2 and the combined data set of sequences from both regions, respectively. Phylogenetic analysis inferred with three different methods enabled the grouping of isolates in five clades, each containing different mitochondrial haplotypes and revealed diversity in the mitochondrial genome of P. nicotianae. The majority of isolates from citrus grouped in a single clade indicating either movement of isolates on planting stock or an association of particular isolates with this host. Phylogenetic groups were not correlated with the radial growth rate of the isolates or the rapidity of apple flesh colonization. The method developed in the present study represents an innovative molecular tool for the characterization of natural populations of P. nicotianae and should be easily expanded to other species of Phytophthora as well as other plant pathogens. It can be used to track specific haplotypes and, thanks to its high genetic resolution, it could be standardized and applied in a DNA barcoding like strategy for the precise identification of sub-specific taxa. Compared to alternative molecular methods, a major advantage is that results are unbiased (a list of nucleotides) and highly reproducible, thus enabling the comparison of data from different laboratories and time periods. Furthermore, the method could be further enhanced by the identification of additional variable mitochondrial and/or nuclear genomic regions.},
}
@article {pmid21526211,
year = {2011},
author = {Park, DS and Foottit, R and Maw, E and Hebert, PD},
title = {Barcoding bugs: DNA-based identification of the true bugs (Insecta: Hemiptera: Heteroptera).},
journal = {PloS one},
volume = {6},
number = {4},
pages = {e18749},
pmid = {21526211},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; DNA/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Genetic Variation ; Heteroptera/*classification/*genetics ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; },
abstract = {BACKGROUND: DNA barcoding, the analysis of sequence variation in the 5' region of the mitochondrial cytochrome c oxidase I (COI) gene, has been shown to provide an efficient method for the identification of species in a wide range of animal taxa. In order to assess the effectiveness of barcodes in the discrimination of Heteroptera, we examined 344 species belonging to 178 genera, drawn from specimens in the Canadian National Collection of Insects.<br><br>Analysis of the COI gene revealed less than 2% intra-specific divergence in 90% of the taxa examined, while minimum interspecific distances exceeded 3% in 77% of congeneric species pairs. Instances where barcodes fail to distinguish species represented clusters of morphologically similar species, except one case of barcode identity between species in different genera. Several instances of deep intraspecific divergence were detected suggesting possible cryptic species.<br><br>CONCLUSIONS/SIGNIFICANCE: Although this analysis encompasses 0.8% of the described global fauna, our results indicate that DNA barcodes will aid the identification of Heteroptera. This advance will be useful in pest management, regulatory and environmental applications and will also reveal species that require further taxonomic research.},
}
@article {pmid21523191,
year = {2011},
author = {Schroers, HJ and Gräfenhan, T and Nirenberg, HI and Seifert, KA},
title = {A revision of Cyanonectria and Geejayessia gen. nov., and related species with Fusarium-like anamorphs.},
journal = {Studies in mycology},
volume = {68},
number = {},
pages = {115-138},
pmid = {21523191},
issn = {1872-9797},
abstract = {A revision of Fusarium-like species associated with the plant genus Buxus led to a reconsideration of generic concepts in the Fusarium clade of the Nectriaceae. Phylogenetic analyses of the partial second largest subunit of the RNA polymerase II (rpb2) and the larger subunit of the ATP citrate lyase (acl1) gene exons confirm the existence of a clade, here called the terminal Fusarium clade, that includes genera such as Fusariumsensu stricto (including its Gibberella teleomorphs), Albonectria, Cyanonectria, "Haematonectria", the newly described genus Geejayessia, and "Nectria" albida. Geejayessia accommodates five species. Four were previously classified in Nectria sensu lato, namely the black perithecial, KOH-species G. atrofusca and the orange or reddish, KOH+ G. cicatricum, G. desmazieri and G. zealandica.Geejayessia celtidicola is newly described. Following our phylogenetic analyses showing its close relationship with Cyanonectria cyanostoma, the former Gibbera buxi is recombined as the second species of Cyanonectria. A three gene phylogenetic analysis of multiple strains of each morphological species using translation elongation factor 1 α (tef-1), rpb2 and acl1 gene exons and introns confirms their status as distinct phylogenetic species. Internal transcribed spacer of the ribosomal RNA gene cluster and nuclear large ribosomal subunit sequences were generated as additional DNA barcodes for selected strains. The connection of Fusarium buxicola, often erroneously reported as the anamorph of G. desmazieri, with the bluish black and KOH+ perithecial species C. buxi is reinstated. Most Cyanonectria and Geejayessia species exhibit restricted host ranges on branches or twigs of Buxus species, Celtisoccidentalis, or Staphyleatrifolia. Their perithecia form caespitose clusters on well-developed, mostly erumpent stromata on the bark or outer cortex of the host and are relatively thin-walled, mostly smooth, and therefore reminiscent of the more or less astromatous, singly occurring perithecia of Cosmospora, Dialonectria, and Microcera. The cell walls in outer- and inner layers of the perithecial walls of Cyanonectria and Geejayessia have inconspicuous pore-like structures, as do representative species of Albonectria, Fusarium sensu stricto, "Haematonectria", and "Nectria" albida. The taxonomic significance of these structures, which we call Samuels' pores, is discussed.},
}
@article {pmid21518061,
year = {2011},
author = {Triponez, Y and Buerki, S and Borer, M and Naisbit, RE and Rahier, M and Alvarez, N},
title = {Discordances between phylogenetic and morphological patterns in alpine leaf beetles attest to an intricate biogeographic history of lineages in postglacial Europe.},
journal = {Molecular ecology},
volume = {20},
number = {11},
pages = {2442-2463},
doi = {10.1111/j.1365-294X.2011.05096.x},
pmid = {21518061},
issn = {1365-294X},
mesh = {Animals ; Base Sequence ; Coleoptera/*anatomy &amp; histology/*genetics ; DNA Barcoding, Taxonomic ; DNA, Intergenic/genetics ; DNA, Mitochondrial/genetics ; *Ecosystem ; Europe ; Genetic Variation ; *Ice Cover ; Molecular Sequence Data ; *Phylogeny ; *Phylogeography ; Plant Leaves/*parasitology ; Polymorphism, Genetic ; Time Factors ; },
abstract = {Pleistocene glacial and interglacial periods have moulded the evolutionary history of European cold-adapted organisms. The role of the different mountain massifs has, however, not been accurately investigated in the case of high-altitude insect species. Here, we focus on three closely related species of non-flying leaf beetles of the genus Oreina (Coleoptera, Chrysomelidae), which are often found in sympatry within the mountain ranges of Europe. After showing that the species concept as currently applied does not match barcoding results, we show, based on more than 700 sequences from one nuclear and three mitochondrial genes, the role of biogeography in shaping the phylogenetic hypothesis. Dating the phylogeny using an insect molecular clock, we show that the earliest lineages diverged more than 1 Mya and that the main shift in diversification rate occurred between 0.36 and 0.18 Mya. By using a probabilistic approach on the parsimony-based dispersal/vicariance framework (MP-DIVA) as well as a direct likelihood method of state change optimization, we show that the Alps acted as a cross-roads with multiple events of dispersal to and reinvasion from neighbouring mountains. However, the relative importance of vicariance vs. dispersal events on the process of rapid diversification remains difficult to evaluate because of a bias towards overestimation of vicariance in the DIVA algorithm. Parallels are drawn with recent studies of cold-adapted species, although our study reveals novel patterns in diversity and genetic links between European mountains, and highlights the importance of neglected regions, such as the Jura and the Balkanic range.},
}
@article {pmid21515277,
year = {2011},
author = {Ogedengbe, JD and Hanner, RH and Barta, JR},
title = {DNA barcoding identifies Eimeria species and contributes to the phylogenetics of coccidian parasites (Eimeriorina, Apicomplexa, Alveolata).},
journal = {International journal for parasitology},
volume = {41},
number = {8},
pages = {843-850},
doi = {10.1016/j.ijpara.2011.03.007},
pmid = {21515277},
issn = {1879-0135},
mesh = {Animals ; Chickens ; Cluster Analysis ; Coccidiosis/parasitology/veterinary ; DNA Barcoding, Taxonomic/*methods ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Eimeria/*classification/*genetics/isolation &amp; purification ; Electron Transport Complex IV/genetics ; Genes, rRNA ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; Phylogeny ; Poultry Diseases/parasitology ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; },
abstract = {Partial (∼ 780 bp) mitochondrial cytochrome c oxidase subunit I (COI) and near complete nuclear 18S rDNA (∼ 1,780 bp) sequences were directly compared to assess their relative usefulness as markers for species identification and phylogenetic analysis of coccidian parasites (phylum Apicomplexa). Fifteen new COI partial sequences were obtained using two pairs of new primers from rigorously characterised (sensu Reid and Long, 1979) laboratory strains of seven Eimeria spp. infecting chickens as well as three additional sequences from cloned laboratory strains of Toxoplasma gondii (ME49 and GT1) and Neospora caninum (NC1) that were used as outgroup taxa for phylogenetic analyses. Phylogenetic analyses based on COI sequences yielded robust support for the monophyly of individual Eimeria spp. infecting poultry except for the Eimeria mitis/mivati clade; however, the lack of a phenotypically characterised strain of E. mivati precludes drawing any firm conclusions regarding this observation. Unlike in the 18S rDNA-based phylogenetic reconstructions, Eimerianecatrix and Eimeria tenella formed monophyletic clades based on partial COI sequences. A species delimitation test was performed to determine the probability of making a correct identification of an unknown specimen (sequence) based on either complete 18S rDNA or partial COI sequences; in almost all cases, the partial COI sequences were more reliable as species-specific markers than complete 18S rDNA sequences. These observations demonstrate that partial COI sequences provide more synapomorphic characters at the species level than complete 18S rDNA sequences from the same taxa. We conclude that COI performs well as a marker for the identification of coccidian taxa (Eimeriorina) and will make an excellent DNA 'barcode' target for coccidia. The COI locus, in combination with an 18S rDNA sequence as an 'anchor', has sufficient phylogenetic signal to assist in the resolution of apparent paraphylies within the coccidia and likely more broadly within the Apicomplexa.},
}
@article {pmid21506819,
year = {2011},
author = {Iezhova, TA and Dodge, M and Sehgal, RN and Smith, TB and Valkiūnas, G},
title = {New avian Haemoproteus species (Haemosporida: Haemoproteidae) from African birds, with a critique of the use of host taxonomic information in hemoproteid classification.},
journal = {The Journal of parasitology},
volume = {97},
number = {4},
pages = {682-694},
doi = {10.1645/GE-2709.1},
pmid = {21506819},
issn = {1937-2345},
support = {EF-0430146//PHS HHS/United States ; },
mesh = {Animals ; Bayes Theorem ; Bird Diseases/epidemiology/*parasitology ; Cytochromes b/genetics ; DNA, Mitochondrial/chemistry ; DNA, Protozoan/blood ; Erythrocytes/parasitology ; Haemosporida/*classification ; Passeriformes/*parasitology ; Phylogeny ; Polymerase Chain Reaction/veterinary ; Prevalence ; Protozoan Infections, Animal/epidemiology/*parasitology ; Uganda/epidemiology ; },
abstract = {Haemoproteus (Parahaemoproteus) micronuclearis n. sp., Haemoproteus (Parahaemoproteus) nucleofascialis n. sp., Haemoproteus (Parahaemoproteus) paranucleophilus n. sp., and Haemoproteus (Parahaemoproteus) homobelopolskyi n. sp. (Haemosporida, Haemoproteidae) are described from African passeriform birds based on the morphology of their blood stages and segments of the mitochondrial cytochrome b gene. Red-billed quelea (Quelea quelea), red-headed malimbe (Malimbus rubricollis), and black-headed weaver (Ploceus melanocephalus) are the type vertebrate hosts of new hemoproteids. It is probable that new species have wide distribution in weavers in sub-Saharan Africa. Both H. micronuclearis and H. nucleofascialis can be readily distinguished from other avian hemoproteids by tiny, compact microgametocyte nuclei that are significantly smaller than macrogametocyte nuclei and are a rare character of hemosporidian parasites. Gametocytes of H. paranucleophilus are closely appressed to the erythrocyte nuclei and do not touch the erythrocyte envelope along their entire margin at all stages of their development, including fully grown gametocytes. A particularly distinctive feature of H. homobelopolskyi development is the presence of circumnuclear dumbbell-shaped macrogametocytes. Illustrations of blood stages of the new species are given, and morphological and phylogenetic analyses identify the DNA lineages that are associated with these parasites. Numerous recent studies show that some lineages of hemoproteids are often present in birds belonging to different families. As a result, the use of the host family as a taxonomic character should be questioned and preferably discouraged in hemoproteid taxonomy, particularly with regard to the parasites of passerine birds. Microscopic identification of avian hemoproteids requires comparison of Haemoproteus species described from birds of different families, as is an established practice with avian Plasmodium spp. Development of bar-coding techniques remains essential in taxonomic and field studies of hemosporidian parasites.},
}
@article {pmid21498554,
year = {2011},
author = {Niskanen, T and Kytövuori, I and Liimatainen, K},
title = {Cortinarius sect. Armillati in northern Europe.},
journal = {Mycologia},
volume = {103},
number = {5},
pages = {1080-1101},
doi = {10.3852/10-350},
pmid = {21498554},
issn = {0027-5514},
mesh = {Base Sequence ; Cortinarius/*classification/cytology/*genetics/isolation &amp; purification ; DNA, Fungal/analysis/*genetics ; DNA, Ribosomal Spacer/analysis/genetics ; Europe ; Phylogeny ; Sequence Analysis, DNA ; Trees ; },
abstract = {Cortinarius sect. Armillati (subgenus Telamonia) was studied extensively based on morphology and molecular data. A total of about 1000 specimens, mostly from Fennoscandia, were revised. The nomenclature of the species was confirmed by sequencing the type material. Phylogenetic relationships were inferred by analyses of ITS, and the results were compared with the morphological and ecological data. Based on macro- and micromorphological characters, as well as molecular data, section Armillati contains only the medium to large species with slightly hygrophanous pileus and ± reddish or in some species yellowish brown to rose brown universal veils. The other red-brown-veiled species, previously included in Armillati, seem to belong to at least seven different sections or clades: sect. Anthracini, sect. Boulderenses, sect. Brunneotincti p.p., sect. Cinnabarini, sect. Fulvescentes, /Fuscoperonatus, and /Praestigiosus. Our study recognized six Armillati species from northern Europe: C. armillatus, C. luteo-ornatus, C. paragaudis, and three species described as new, C. pinigaudis, C. roseoarmillatus, and C. suboenochelis. The former three also occur in North America. Two additional species, C. subarmillatus (Japan) and C. quercoarmillatus (Costa Rica), are known outside the area. Based on the phylogenetic analysis, the species associated with deciduous trees, C. armillatus, C. quercoarmillatus, and C. roseoarmillatus, all with dextrinoid, thick-walled spores, formed a separate group from the mainly conifer-associated species, C. luteo-ornatus, C. paragaudis, C. pinigaudis and C. suboenochelis, all with fairly thin to moderately thick-walled, indextrinoid to moderately dextrinoid spores. Descriptions of the northern European species are provided, the distribution is mapped and their taxonomy, ecology, distribution, and relationships are discussed. A total of 64 new sequences of 12 species are reported including 17 sequences from type material. Our study also suggests that ITS sequences are not always sufficiently variable for species-rank recognition (barcoding) in Cortinarius.},
}
@article {pmid21494869,
year = {2011},
author = {Chandra, NS and Wulff, EG and Udayashankar, AC and Nandini, BP and Niranjana, SR and Mortensen, CN and Prakash, HS},
title = {Prospects of molecular markers in Fusarium species diversity.},
journal = {Applied microbiology and biotechnology},
volume = {90},
number = {5},
pages = {1625-1639},
doi = {10.1007/s00253-011-3209-3},
pmid = {21494869},
issn = {1432-0614},
mesh = {Fungal Proteins/genetics ; Fusarium/classification/*genetics/*isolation &amp; purification/metabolism ; *Genetic Variation ; Humans ; Molecular Sequence Data ; Mycological Typing Techniques/*methods ; Mycoses/microbiology ; Phylogeny ; Plant Diseases/microbiology ; },
abstract = {Recent developments in genomics have opened up for newer opportunities to study the diversity and classification of fungi. The genus Fusarium contains many plant pathogens that attack diverse agricultural crops. Fusarium spp. are not only pathogenic to plants but are also known as toxin producers that negatively affect animal and human health. The identification of Fusarium species still remains one of the most critical issues in fungal taxonomy, given that the number of species recognized in the genus has been constantly changing in the last century due to the different taxonomic systems. This review focuses of various molecular-based techniques employed to study the diversity of Fusarium species causing diseases in major food crops. An introduction of fusarial diseases and their mycotoxins and molecular-marker-based methods for detection introduce the concept of marker application. Various well-known molecular techniques such as random amplified polymorphic DNA, amplification fragment length polymorphism, etc. to more modern ones such as DNA microarrays, DNA barcoding, and pyrosequencing and their application form the core of the review. Target regions in the genome which can be potential candidates for generation of probes and their use in phylogeny of Fusarium spp. are also presented. The concluding part emphasizes the value of molecular markers for assessing genetic variability and reveals that molecular tools are indispensable for providing information not only of one Fusarium species but on whole fungal community. This will be of extreme value for diagnosticians and researchers concerned with fungal biology, ecology, and genetics.},
}
@article {pmid21483872,
year = {2011},
author = {Thormann, B and Raupach, MJ and Wagner, T and Wägele, JW and Peters, MK},
title = {Testing a short nuclear marker for inferring staphylinid beetle diversity in an African tropical rain forest.},
journal = {PloS one},
volume = {6},
number = {3},
pages = {e18101},
pmid = {21483872},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; Coleoptera/*classification/*genetics ; Kenya ; RNA, Ribosomal, 28S/genetics ; Trees ; Tropical Climate ; },
abstract = {BACKGROUND: The use of DNA based methods for assessing biodiversity has become increasingly common during the last years. Especially in speciose biomes as tropical rain forests and/or in hyperdiverse or understudied taxa they may efficiently complement morphological approaches. The most successful molecular approach in this field is DNA barcoding based on cytochrome c oxidase I (COI) marker, but other markers are used as well. Whereas most studies aim at identifying or describing species, there are only few attempts to use DNA markers for inventorying all animal species found in environmental samples to describe variations of biodiversity patterns.<br><br>In this study, an analysis of the nuclear D3 region of the 28S rRNA gene to delimit species-like units is compared to results based on distinction of morphospecies. Data derived from both approaches are used to assess diversity and composition of staphylinid beetle communities of a Guineo-Congolian rain forest in Kenya. Beetles were collected with a standardized sampling design across six transects in primary and secondary forests using pitfall traps. Sequences could be obtained of 99% of all individuals. In total, 76 molecular operational taxonomic units (MOTUs) were found in contrast to 70 discernible morphospecies. Despite this difference both approaches revealed highly similar biodiversity patterns, with species richness being equal in primary and secondary forests, but with divergent species communities in different habitats. The D3-MOTU approach proved to be an efficient tool for biodiversity analyses.<br><br>CONCLUSIONS/SIGNIFICANCE: Our data illustrate that the use of MOTUs as a proxy for species can provide an alternative to morphospecies identification for the analysis of changes in community structure of hyperdiverse insect taxa. The efficient amplification of the D3-marker and the ability of the D3-MOTUs to reveal similar biodiversity patterns as analyses of morphospecies recommend its use in future molecular studies on biodiversity.},
}
@article {pmid21481204,
year = {2011},
author = {Asgharian, H and Sahafi, HH and Ardalan, AA and Shekarriz, S and Elahi, E},
title = {Cytochrome c oxidase subunit 1 barcode data of fish of the Nayband National Park in the Persian Gulf and analysis using meta-data flag several cryptic species.},
journal = {Molecular ecology resources},
volume = {11},
number = {3},
pages = {461-472},
doi = {10.1111/j.1755-0998.2011.02989.x},
pmid = {21481204},
issn = {1755-0998},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electron Transport Complex IV/genetics ; Fishes/*classification/*genetics ; Indian Ocean ; Iran ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Genetic ; Protein Subunits/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {We provide cytochrome c oxidase subunit 1 (COI) barcode sequences of fishes of the Nayband National Park, Persian Gulf, Iran. Industrial activities, ecological considerations and goals of The Fish Barcode of Life campaign make it crucial that fish species residing in the park be identified. To the best of our knowledge, this is the first report of barcoding data on fishes of the Persian Gulf. We examined 187 individuals representing 76 species, 56 genera and 32 families. The data flagged potentially cryptic species of Gerres filamentosus and Plectorhinchus schotaf. 16S rDNA data on these species are provided. Exclusion of these two potential cryptic species resulted in a mean COI intraspecific distance of 0.18%, and a mean inter- to intraspecific divergence ratio of 66.7. There was no overlap between maximum Kimura 2-parameter distances among conspecifics (1.66%) and minimum distance among congeneric species (6.19%). Barcodes shared among species were not observed. Neighbour-joining analysis showed that most species formed cohesive sequence units with little variation. Finally, the comparison of 16 selected species from this study with meta-data of conspecifics from Australia, India, China and South Africa revealed high interregion divergences and potential existence of six cryptic species. Pairwise interregional comparisons were more informative than global divergence assessments with regard to detection of cryptic variation. Our analysis exemplifies optimal use of the expanding barcode data now becoming available.},
}
@article {pmid21481203,
year = {2011},
author = {Muellner, AN and Schaefer, H and Lahaye, R},
title = {Evaluation of candidate DNA barcoding loci for economically important timber species of the mahogany family (Meliaceae).},
journal = {Molecular ecology resources},
volume = {11},
number = {3},
pages = {450-460},
doi = {10.1111/j.1755-0998.2011.02984.x},
pmid = {21481203},
issn = {1755-0998},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Genome, Plastid ; Meliaceae/*classification/*genetics ; Molecular Sequence Data ; Sequence Analysis, DNA ; },
abstract = {There has been considerable debate regarding locus choice for DNA barcoding land plants. This is partly attributable to a shortage of comparable data from proposed candidate loci on a common set of samples. In this study, we evaluated main candidate plastid regions (rpoC1, rpoB, accD) and additional plastid markers (psbB, psbN, psbT exons and the trnS-trnG spacer) as well as the nuclear ribosomal spacer region (ITS1-5.8S-ITS2) in a group of land plants belonging to the mahogany family, Meliaceae. Across these samples, only ITS showed high levels of resolvability. Interspecific sharing of sequences from individual plastid loci was common. The combination of multiple loci did not improve performance. DNA barcoding with ITS alone revealed cryptic species and proved useful in identifying species listed in Convention on International Trade of Endangered Species appendixes.},
}
@article {pmid21481202,
year = {2011},
author = {Bitanyi, S and Bjørnstad, G and Ernest, EM and Nesje, M and Kusiluka, LJ and Keyyu, JD and Mdegela, RH and Røed, KH},
title = {Species identification of Tanzanian antelopes using DNA barcoding.},
journal = {Molecular ecology resources},
volume = {11},
number = {3},
pages = {442-449},
doi = {10.1111/j.1755-0998.2011.02980.x},
pmid = {21481202},
issn = {1755-0998},
mesh = {Animals ; Antelopes/*classification/*genetics ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/genetics ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Tanzania ; },
abstract = {Efficient tools for consistent species identification are important in wildlife conservation as it can provide information on the levels of species exploitation and assist in solving forensic-related problems. In this study, we evaluated the effectiveness of the mitochondrial cytochrome c oxidase subunit I (COI) barcode in species identification of Tanzanian antelope species. A 470 base-pair region of the COI gene was examined in 95 specimens representing 20 species of antelopes, buffalo and domestic Bovidae. All the Tanzanian species showed unique clades, and sequence divergence within species was <1%, whereas divergence between species ranged from 6.3% to 22%. Lowest interspecific divergence was noted within the Tragelaphus genus. Neighbour-joining phylogenetic analyses demonstrated that the examined COI region provided correct and highly supported species clustering using short fragments down to 100 base-pair lengths. This study demonstrates that even short COI fragments can efficiently identify antelope species, thus demonstrating its high potential for use in wildlife conservation activities.},
}
@article {pmid21481201,
year = {2011},
author = {Feng, Y and Li, Q and Kong, L and Zheng, X},
title = {COI-based DNA barcoding of Arcoida species (Bivalvia: Pteriomorphia) along the coast of China.},
journal = {Molecular ecology resources},
volume = {11},
number = {3},
pages = {435-441},
doi = {10.1111/j.1755-0998.2010.02975.x},
pmid = {21481201},
issn = {1755-0998},
mesh = {Animals ; Bivalvia/anatomy &amp; histology/*classification/*genetics ; China ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/genetics ; Molecular Sequence Data ; Sequence Analysis, DNA ; },
abstract = {DNA barcoding is a promising tool for the rapid and unambiguous identification of species. Some arcoid species are particularly difficult to distinguish with traditional morphological identification owing to phenotypic variation and the existence of closely related taxa. Here, we apply DNA barcoding based on mitochondrial cytochrome c oxidase I gene (COI) to arcoid species collected from the coast along China. Combining morphology with molecular data indicates the 133 specimens of Arcoida could be assigned to 24 species. Because of the deep genetic divergence within Tegillarca granosa, there was an overlap between genetic variation within species and variation between species. Nevertheless, NJ and Bayesian trees showed that all species fell into reciprocally monophyletic clades with high bootstrap values. Our results evidence that the COI marker can efficiently identify species, correct mistakes caused by morphological identification and reveal genetic differentiation among populations within species. This study provides a clear example of the usefulness of barcoding for arcoid identification. Furthermore, it also lays a foundation for other biological and ecological studies of Arcoida.},
}
@article {pmid21477665,
year = {2011},
author = {Brambilla, D and Le Droumaguet, B and Nicolas, J and Hashemi, SH and Wu, LP and Moghimi, SM and Couvreur, P and Andrieux, K},
title = {Nanotechnologies for Alzheimer's disease: diagnosis, therapy, and safety issues.},
journal = {Nanomedicine : nanotechnology, biology, and medicine},
volume = {7},
number = {5},
pages = {521-540},
doi = {10.1016/j.nano.2011.03.008},
pmid = {21477665},
issn = {1549-9642},
mesh = {Acridines/therapeutic use ; Alzheimer Disease/*diagnosis/*drug therapy/metabolism ; Amyloid beta-Peptides/*metabolism ; Benzothiazoles ; Biocompatible Materials/therapeutic use ; Biomarkers/blood/cerebrospinal fluid ; Brain/pathology ; Chromones/therapeutic use ; Drug Delivery Systems ; Ferric Compounds/chemistry/therapeutic use ; Gold/therapeutic use ; Humans ; Magnetite Nanoparticles/therapeutic use ; Nanoparticles/adverse effects/*therapeutic use ; Thiazoles/therapeutic use ; },
abstract = {Alzheimer's disease (AD) represents the most common form of dementia worldwide, affecting more than 35 million people. Advances in nanotechnology are beginning to exert a significant impact in neurology. These approaches, which are often based on the design and engineering of a plethora of nanoparticulate entities with high specificity for brain capillary endothelial cells, are currently being applied to early AD diagnosis and treatment. In addition, nanoparticles (NPs) with high affinity for the circulating amyloid-β (Aβ) forms may induce "sink effect" and improve the AD condition. There are also developments in relation to in vitro diagnostics for AD, including ultrasensitive NP-based bio-barcodes, immunosensors, as well as scanning tunneling microscopy procedures capable of detecting Aβ(1-40) and Aβ(1-42). However, there are concerns regarding the initiation of possible NP-mediated adverse events in AD, thus demanding the use of precisely assembled nanoconstructs from biocompatible materials. Key advances and safety issues are reviewed and discussed.},
}
@article {pmid21472696,
year = {2011},
author = {Kulkarni, MM},
title = {Digital multiplexed gene expression analysis using the NanoString nCounter system.},
journal = {Current protocols in molecular biology},
volume = {Chapter 25},
number = {},
pages = {Unit25B.10},
doi = {10.1002/0471142727.mb25b10s94},
pmid = {21472696},
issn = {1934-3647},
mesh = {Gene Expression Profiling/*methods ; Nucleic Acid Hybridization/*methods ; Oligonucleotide Probes/metabolism ; RNA, Messenger/analysis ; Reproducibility of Results ; Sensitivity and Specificity ; },
abstract = {This unit presents the protocol for the NanoString nCounter Gene Expression Assay, a robust and highly reproducible method for detecting the expression of up to 800 genes in a single reaction with high sensitivity and linearity across a broad range of expression levels. The methodology serves to bridge the gap between genome-wide (microarrays) and targeted (real-time quantitative PCR) expression profiling. The nCounter assay is based on direct digital detection of mRNA molecules of interest using target-specific, color-coded probe pairs. It does not require the conversion of mRNA to cDNA by reverse transcription or the amplification of the resulting cDNA by PCR. Each target gene of interest is detected using a pair of reporter and capture probes carrying 35- to 50-base target-specific sequences. In addition, each reporter probe carries a unique color code at the 5' end that enables the molecular barcoding of the genes of interest, while the capture probes all carry a biotin label at the 3' end that provides a molecular handle for attachment of target genes to facilitate downstream digital detection. After solution-phase hybridization between target mRNA and reporter-capture probe pairs, excess probes are removed and the probe/target complexes are aligned and immobilized in the nCounter cartridge, which is then placed in a digital analyzer for image acquisition and data processing. Hundreds of thousands of color codes designating mRNA targets of interest are directly imaged on the surface of the cartridge. The expression level of a gene is measured by counting the number of times the color-coded barcode for that gene is detected, and the barcode counts are then tabulated.},
}
@article {pmid21471402,
year = {2011},
author = {Wang, H and Mayhew, D and Chen, X and Johnston, M and Mitra, RD},
title = {Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins.},
journal = {Genome research},
volume = {21},
number = {5},
pages = {748-755},
pmid = {21471402},
issn = {1549-5469},
support = {5P50HG003170-03/HG/NHGRI NIH HHS/United States ; R21 RR023960/RR/NCRR NIH HHS/United States ; T32 HG000045/HG/NHGRI NIH HHS/United States ; R01 GM078222/GM/NIGMS NIH HHS/United States ; P50 HG003170/HG/NHGRI NIH HHS/United States ; R21RR023960/RR/NCRR NIH HHS/United States ; 5R01DA025744-02/DA/NIDA NIH HHS/United States ; R01 DA025744/DA/NIDA NIH HHS/United States ; R01GM078222/GM/NIGMS NIH HHS/United States ; },
mesh = {Binding Sites ; Chromosome Mapping/*methods ; DNA Transposable Elements/*genetics/physiology ; DNA-Binding Proteins/chemistry/*genetics/metabolism ; Genome, Fungal/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Mutagenesis, Insertional ; Saccharomyces cerevisiae/genetics/metabolism ; Silent Information Regulator Proteins, Saccharomyces cerevisiae/chemistry/genetics/metabolism ; Transcription Factors/genetics/*metabolism ; },
abstract = {Transcription factors direct gene expression, so there is much interest in mapping their genome-wide binding locations. Current methods do not allow for the multiplexed analysis of TF binding, and this limits their throughput. We describe a novel method for determining the genomic target genes of multiple transcription factors simultaneously. DNA-binding proteins are endowed with the ability to direct transposon insertions into the genome near to where they bind. The transposon becomes a "Calling Card" marking the visit of the DNA-binding protein to that location. A unique sequence "barcode" in the transposon matches it to the DNA-binding protein that directed its insertion. The sequences of the DNA flanking the transposon (which reveal where in the genome the transposon landed) and the barcode within the transposon (which identifies the TF that put it there) are determined by massively parallel DNA sequencing. To demonstrate the method's feasibility, we determined the genomic targets of eight transcription factors in a single experiment. The Calling Card method promises to significantly reduce the cost and labor needed to determine the genomic targets of many transcription factors in different environmental conditions and genetic backgrounds.},
}
@article {pmid21464900,
year = {2011},
author = {deWaard, JR and Hebert, PD and Humble, LM},
title = {A comprehensive DNA barcode library for the looper moths (Lepidoptera: Geometridae) of British Columbia, Canada.},
journal = {PloS one},
volume = {6},
number = {3},
pages = {e18290},
pmid = {21464900},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; British Columbia ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; *Gene Library ; Genetic Variation ; Moths/*classification/*genetics ; Species Specificity ; },
abstract = {BACKGROUND: The construction of comprehensive reference libraries is essential to foster the development of DNA barcoding as a tool for monitoring biodiversity and detecting invasive species. The looper moths of British Columbia (BC), Canada present a challenging case for species discrimination via DNA barcoding due to their considerable diversity and limited taxonomic maturity.<br><br>By analyzing specimens held in national and regional natural history collections, we assemble barcode records from representatives of 400 species from BC and surrounding provinces, territories and states. Sequence variation in the barcode region unambiguously discriminates over 93% of these 400 geometrid species. However, a final estimate of resolution success awaits detailed taxonomic analysis of 48 species where patterns of barcode variation suggest cases of cryptic species, unrecognized synonymy as well as young species.<br><br>CONCLUSIONS/SIGNIFICANCE: A catalog of these taxa meriting further taxonomic investigation is presented as well as the supplemental information needed to facilitate these investigations.},
}
@article {pmid21457479,
year = {2011},
author = {Yesson, C and Bárcenas, RT and Hernández, HM and Ruiz-Maqueda, Mde L and Prado, A and Rodríguez, VM and Hawkins, JA},
title = {DNA barcodes for Mexican Cactaceae, plants under pressure from wild collecting.},
journal = {Molecular ecology resources},
volume = {11},
number = {5},
pages = {775-783},
doi = {10.1111/j.1755-0998.2011.03009.x},
pmid = {21457479},
issn = {1755-0998},
mesh = {Base Sequence ; Cactaceae/*genetics ; Computational Biology ; Conservation of Natural Resources/*methods ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; DNA, Ribosomal Spacer/genetics ; Endangered Species ; Endoribonucleases/genetics ; *Genetic Variation ; Mexico ; Models, Genetic ; Molecular Sequence Data ; Nucleotidyltransferases/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {DNA barcodes could be a useful tool for plant conservation. Of particular importance is the ability to identify unknown plant material, such as from customs seizures of illegally collected specimens. Mexican cacti are an example of a threatened group, under pressure because of wild collection for the xeriscaping trade and private collectors. Mexican cacti also provide a taxonomically and geographically coherent group with which to test DNA barcodes. Here, we sample the matK barcode for 528 species of Cactaceae including approximately 75% of Mexican species and test the utility of the matK region for species-level identification. We find that the matK DNA barcode can be used to identify uniquely 77% of species sampled, and 79-87% of species of particular conservation importance. However, this is far below the desired rate of 95% and there are significant issues for PCR amplification because of the variability of primer sites. Additionally, we test the nuclear ITS regions for the cactus subfamily Opuntioideae and for the genus Ariocarpus (subfamily Cactoideae). We observed higher rates of variation for ITS (86% unique for Opuntioideae sampled) but a much lower PCR success, encountering significant intra-individual polymorphism in Ariocarpus precluding the use of this marker in this taxon. We conclude that the matK region should provide useful information as a DNA barcode for Cactaceae if the problems with primers can be addressed, but matK alone is not sufficiently variable to achieve species-level identification. Additional complementary regions should be investigated as ITS is shown to be unsuitable.},
}
@article {pmid21457477,
year = {2011},
author = {Greenstone, MH and Vandenberg, NJ and Hu, JH},
title = {Barcode haplotype variation in north American agroecosystem lady beetles (Coleoptera: Coccinellidae).},
journal = {Molecular ecology resources},
volume = {11},
number = {4},
pages = {629-637},
doi = {10.1111/j.1755-0998.2011.03007.x},
pmid = {21457477},
issn = {1755-0998},
mesh = {Animals ; Cluster Analysis ; Coleoptera/*classification/*genetics ; DNA Barcoding, Taxonomic ; DNA Primers/genetics ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/genetics ; *Haplotypes ; Molecular Sequence Data ; Phylogeny ; *Polymorphism, Genetic ; Sequence Homology ; United States ; },
abstract = {DNA barcodes have proven invaluable in identifying and distinguishing insect pests, most notably for determining the provenance of exotic invasives, but relatively few insect natural enemies have been barcoded. We used Folmer et al.'s (1994) universal invertebrate primers and Hebert et al.'s (2004) for Lepidoptera, to amplify 658 bp at the 5' end of the mitochondrial cytochrome oxidase c subunit I (COI) gene in five species of lady beetles from crop fields in six states in the US Mid-Atlantic, Plains and Midwest: three native species, Hippodamia convergens Guérin-Méneville, H. parenthesis (Say) and Coleomegilla maculata (De Geer); and two exotic species, Harmonia axyridis (Pallas) and Coccinella septempunctata Linnaeus. Sequence divergences within species were low, never exceeding 0.9% (Kimura 2-parameter distances). Sequence divergences between the two Hippodamia species ranged from 14.7 to 16.4%, mirroring the relationships found for other arthropod taxa. Among the exotic species, C. septempunctata sequences were as variable as those of the three native species, while H. axyridis populations comprised a single haplotype. Limited data on two Coleomegilla subspecies, C. m. lengi Timberlake and C. m. fuscilabris (Mulsant), are consistent with their belonging to the same species, although morphological and reproductive data indicate that they represent separate species. Our results support the general utility of COI barcodes for distinguishing and diagnosing coccinellid species, but point to possible limitations in the use of barcodes to resolve species assignments in recently divergent sibling species.},
}
@article {pmid21453461,
year = {2011},
author = {Ding, YZ and Liu, YS and Zhou, JH and Chen, HT and Zhang, J and Ma, LN and Wei, G},
title = {A highly sensitive detection for foot-and-mouth disease virus by gold nanopariticle improved immuno-PCR.},
journal = {Virology journal},
volume = {8},
number = {},
pages = {148},
pmid = {21453461},
issn = {1743-422X},
mesh = {Animals ; Foot-and-Mouth Disease/*diagnosis/virology ; Foot-and-Mouth Disease Virus/genetics/immunology/*isolation &amp; purification ; *Gold ; Immunoassay/methods ; Molecular Diagnostic Techniques/*methods ; *Nanoparticles ; Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; Veterinary Medicine/methods ; Virology/*methods ; },
abstract = {BACKGROUND: Foot-and-mouth disease (FMD) is one of the most contagious of all artiodactyl animal diseases, and its infection has an obvious ability to spread over long distances and to contribute to epidemics in FMD-free areas. A highly sensitive and specific method is required to detect FMDV. In this study, we evaluated the usefulness of a bio-barcode assay (BCA) technique for detecting clinical samples of FMDV.<br><br>METHODS: Highly sensitive gold nanopariticle (GNP) improved immuno -PCR (GNP-IPCR) which derived from the bio-barcode assay (BCA) was designed for the detection of FMDV. The target viral particles were captured by a polyclonal antibody coated on ELISA microplate, followed by adding GNP which was dually modified with oligonucleotides and a FMDV specific monoclonal antibody (MAb) 1D11 to form a sandwiched immune complex. After the formation of immuno-complex, the signal DNA was released by heating, and consequently characterized by PCR and real time PCR.<br><br>RESULTS: The detection limit of GNP-PCR could reach to 10 fg/ml purified FMDV particles, and the assay can detect clinical samples of FMDV with highly sensitivity, while detect limit of conventional ELISA is 100 ng/ml in this study.<br><br>CONCLUSION: GNP-IPCR may provide a highly sensitive method for the detection of FMDV.},
}
@article {pmid21429168,
year = {2011},
author = {Hohenlohe, PA and Amish, SJ and Catchen, JM and Allendorf, FW and Luikart, G},
title = {Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout.},
journal = {Molecular ecology resources},
volume = {11 Suppl 1},
number = {},
pages = {117-122},
doi = {10.1111/j.1755-0998.2010.02967.x},
pmid = {21429168},
issn = {1755-0998},
support = {1F32GM095213-01/GM/NIGMS NIH HHS/United States ; R01RR020833/RR/NCRR NIH HHS/United States ; R24GM079486-01A1/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Chromosome Mapping ; Gene Library ; Genetic Carrier Screening ; Genotype ; *Hybridization, Genetic ; Likelihood Functions ; Oncorhynchus/*genetics ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
abstract = {The increased numbers of genetic markers produced by genomic techniques have the potential to both identify hybrid individuals and localize chromosomal regions responding to selection and contributing to introgression. We used restriction-site-associated DNA sequencing to identify a dense set of candidate SNP loci with fixed allelic differences between introduced rainbow trout (Oncorhynchus mykiss) and native westslope cutthroat trout (Oncorhynchus clarkii lewisi). We distinguished candidate SNPs from homeologs (paralogs resulting from whole-genome duplication) by detecting excessively high observed heterozygosity and deviations from Hardy-Weinberg proportions. We identified 2923 candidate species-specific SNPs from a single Illumina sequencing lane containing 24 barcode-labelled individuals. Published sequence data and ongoing genome sequencing of rainbow trout will allow physical mapping of SNP loci for genome-wide scans and will also provide flanking sequence for design of qPCR-based TaqMan(®) assays for high-throughput, low-cost hybrid identification using a subset of 50-100 loci. This study demonstrates that it is now feasible to identify thousands of informative SNPs in nonmodel species quickly and at reasonable cost, even if no prior genomic information is available.},
}
@article {pmid21446265,
year = {2011},
author = {Degaspari, J},
title = {Keeping track. Barcodes and RFID tags make inroads in hospitals.},
journal = {Healthcare informatics : the business magazine for information and communication systems},
volume = {28},
number = {3},
pages = {44-47},
pmid = {21446265},
issn = {1050-9135},
mesh = {*Electronic Data Processing ; Hospital Information Systems/*organization &amp; administration/trends ; Humans ; Medication Errors/prevention &amp; control ; *Radio Frequency Identification Device ; Safety Management/*methods ; },
abstract = {Barcodes are a proven technology for reducing medication administration errors, while RFID tags show promise for tracking of assets as well as personnel and patients. Yet implementation has been slow, as hospitals struggle with cost and complexity issues.},
}
@article {pmid21444340,
year = {2011},
author = {Doorduin, L and Gravendeel, B and Lammers, Y and Ariyurek, Y and Chin-A-Woeng, T and Vrieling, K},
title = {The complete chloroplast genome of 17 individuals of pest species Jacobaea vulgaris: SNPs, microsatellites and barcoding markers for population and phylogenetic studies.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {18},
number = {2},
pages = {93-105},
pmid = {21444340},
issn = {1756-1663},
mesh = {Asteraceae/*genetics ; Base Pairing/genetics ; Chloroplasts/genetics ; *DNA Barcoding, Taxonomic ; DNA, Chloroplast/genetics ; Genetic Loci/genetics ; Genetic Markers ; Genetics, Population ; Genome, Chloroplast/*genetics ; Geography ; *Introduced Species ; Microsatellite Repeats/*genetics ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide/*genetics ; Sequence Analysis, DNA ; },
abstract = {Invasive individuals from the pest species Jacobaea vulgaris show different allocation patterns in defence and growth compared with native individuals. To examine if these changes are caused by fast evolution, it is necessary to identify native source populations and compare these with invasive populations. For this purpose, we are in need of intraspecific polymorphic markers. We therefore sequenced the complete chloroplast genomes of 12 native and 5 invasive individuals of J. vulgaris with next generation sequencing and discovered single-nucleotide polymorphisms (SNPs) and microsatellites. This is the first study in which the chloroplast genome of that many individuals within a single species was sequenced. Thirty-two SNPs and 34 microsatellite regions were found. For none of the individuals, differences were found between the inverted repeats. Furthermore, being the first chloroplast genome sequenced in the Senecioneae clade, we compared it with four other members of the Asteraceae family to identify new regions for phylogentic inference within this clade and also within the Asteraceae family. Five markers (ndhC-trnV, ndhC-atpE, rps18-rpl20, clpP and psbM-trnD) contained parsimony-informative characters higher than 2%. Finally, we compared two procedures of preparing chloroplast DNA for next generation sequencing.},
}
@article {pmid21441928,
year = {2011},
author = {Li, Z and Vizeacoumar, FJ and Bahr, S and Li, J and Warringer, J and Vizeacoumar, FS and Min, R and Vandersluis, B and Bellay, J and Devit, M and Fleming, JA and Stephens, A and Haase, J and Lin, ZY and Baryshnikova, A and Lu, H and Yan, Z and Jin, K and Barker, S and Datti, A and Giaever, G and Nislow, C and Bulawa, C and Myers, CL and Costanzo, M and Gingras, AC and Zhang, Z and Blomberg, A and Bloom, K and Andrews, B and Boone, C},
title = {Systematic exploration of essential yeast gene function with temperature-sensitive mutants.},
journal = {Nature biotechnology},
volume = {29},
number = {4},
pages = {361-367},
pmid = {21441928},
issn = {1546-1696},
support = {R01 HG005084/HG/NHGRI NIH HHS/United States ; MOP-97939/CAPMC/CIHR/Canada ; R01 GM032238-24/GM/NIGMS NIH HHS/United States ; R01 GM032238/GM/NIGMS NIH HHS/United States ; R37 GM032238/GM/NIGMS NIH HHS/United States ; },
mesh = {Alleles ; Databases, Genetic ; *Genes, Essential ; Genes, Fungal ; Genes, Lethal ; Genetic Engineering/methods ; Genetic Loci ; *Genome, Fungal ; Mass Spectrometry/methods ; Microarray Analysis/methods ; Microscopy, Confocal ; Mutation ; Phenotype ; Plasmids ; RNA, Messenger ; Saccharomyces cerevisiae/*genetics/growth &amp; development ; Single-Cell Analysis ; *Temperature ; Tubulin/analysis ; },
abstract = {Conditional temperature-sensitive (ts) mutations are valuable reagents for studying essential genes in the yeast Saccharomyces cerevisiae. We constructed 787 ts strains, covering 497 (∼45%) of the 1,101 essential yeast genes, with ∼30% of the genes represented by multiple alleles. All of the alleles are integrated into their native genomic locus in the S288C common reference strain and are linked to a kanMX selectable marker, allowing further genetic manipulation by synthetic genetic array (SGA)-based, high-throughput methods. We show two such manipulations: barcoding of 440 strains, which enables chemical-genetic suppression analysis, and the construction of arrays of strains carrying different fluorescent markers of subcellular structure, which enables quantitative analysis of phenotypes using high-content screening. Quantitative analysis of a GFP-tubulin marker identified roles for cohesin and condensin genes in spindle disassembly. This mutant collection should facilitate a wide range of systematic studies aimed at understanding the functions of essential genes.},
}
@article {pmid21434928,
year = {2011},
author = {Kelly, LJ and Hollingsworth, PM and Coppins, BJ and Ellis, CJ and Harrold, P and Tosh, J and Yahr, R},
title = {DNA barcoding of lichenized fungi demonstrates high identification success in a floristic context.},
journal = {The New phytologist},
volume = {191},
number = {1},
pages = {288-300},
doi = {10.1111/j.1469-8137.2011.03677.x},
pmid = {21434928},
issn = {1469-8137},
support = {MR/K001744/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*DNA Barcoding, Taxonomic ; DNA, Fungal/*chemistry ; DNA, Ribosomal Spacer/*chemistry ; Lichens/classification/genetics ; Nucleic Acid Amplification Techniques ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Usnea/classification/*genetics ; },
abstract = {• Efforts are currently underway to establish a standard DNA barcode region for fungi; we tested the utility of the internal transcribed spacer (ITS) of nuclear ribosomal DNA for DNA barcoding in lichen-forming fungi by sampling diverse species across eight orders. • Amplification of the ITS region (ITS1-5.8S-ITS2) was conducted for 351 samples, encompassing 107, 55 and 28 species, genera and families, respectively, of lichenized fungi. We assessed the ability of the entire ITS vs the ITS2 alone to discriminate between species in a taxonomic dataset (members of the genus Usnea) and a floristic dataset. • In the floristic dataset, 96.3% of sequenced samples could be assigned to the correct species using ITS or ITS2; a barcode gap for ITS is present in 92.1% of species. Although fewer species have a barcode gap in the taxonomic dataset (73.3% with ITS and 68.8% with ITS2), up to 94.1% of samples were assigned to the correct species using BLAST. • While discrimination between the most closely related species will remain challenging, our results demonstrate the potential to identify a high percentage of specimens to the correct species, and the remainder to the correct genus, when using DNA barcoding in a floristic context.},
}
@article {pmid21431778,
year = {2011},
author = {Kozarewa, I and Turner, DJ},
title = {96-plex molecular barcoding for the Illumina Genome Analyzer.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {733},
number = {},
pages = {279-298},
doi = {10.1007/978-1-61779-089-8_20},
pmid = {21431778},
issn = {1940-6029},
mesh = {Actinin/genetics ; DNA/chemistry/genetics/metabolism ; *DNA Barcoding, Taxonomic ; DNA Primers/genetics ; DNA Repair ; Gene Library ; Genome/*genetics ; Genomics/*methods ; Humans ; Microspheres ; Polyadenylation ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; },
abstract = {Next-generation sequencing technologies have a massive throughput, which dramatically reduces the cost of sequencing per gigabase, compared to standard Sanger sequencing. To make the most efficient use of this throughput when sequencing small regions or genomes, we developed a barcoding method, which allows multiplexing of 96 or more samples per lane. The method employs 8 bp tags, incorporated into each sequencing library during the library preparation enrichment polymerase chain reaction (PCR), pooling bar-coded libraries in equimolar ratios based on quantitative PCR, and sequencing using the three-read Illumina method.},
}
@article {pmid21430469,
year = {2011},
author = {Vaughn, S},
title = {Optimization education after project implementation: sharing "lessons learned" with staff.},
journal = {Journal for nurses in staff development : JNSD : official journal of the National Nursing Staff Development Organization},
volume = {27},
number = {2},
pages = {E1-4},
doi = {10.1097/NND.0b013e31820eefe4},
pmid = {21430469},
issn = {1538-9049},
mesh = {*Clinical Competence ; Clinical Pharmacy Information Systems/*organization &amp; administration ; Education, Nursing/*methods/standards ; Educational Measurement ; Educational Status ; Electronic Data Processing ; Formularies, Hospital as Topic ; Humans ; Leadership ; *Nursing Evaluation Research ; *Nursing Staff, Hospital ; Staff Development/*methods/standards ; Time Factors ; United States ; },
abstract = {Implementations involving healthcare technology solutions focus on providing end-user education prior to the application going "live" in the organization. Benefits to postimplementation education for staff should be included when planning these projects. This author describes the traditional training provided during the implementation of a bar-coding medication project and then the optimization training 8 weeks later.},
}
@article {pmid21429199,
year = {2011},
author = {Griffin, PC and Robin, C and Hoffmann, AA},
title = {A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses.},
journal = {BMC biology},
volume = {9},
number = {},
pages = {19},
pmid = {21429199},
issn = {1741-7007},
mesh = {Australia ; DNA, Plant/*genetics ; Poa/*genetics ; *Polyploidy ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: Polyploidy is important from a phylogenetic perspective because of its immense past impact on evolution and its potential future impact on diversification, survival and adaptation, especially in plants. Molecular population genetics studies of polyploid organisms have been difficult because of problems in sequencing multiple-copy nuclear genes using Sanger sequencing. This paper describes a method for sequencing a barcoded mixture of targeted gene regions using next-generation sequencing methods to overcome these problems.<br><br>RESULTS: Using 64 3-bp barcodes, we successfully sequenced three chloroplast and two nuclear gene regions (each of which contained two gene copies with up to two alleles per individual) in a total of 60 individuals across 11 species of Australian Poa grasses. This method had high replicability, a low sequencing error rate (after appropriate quality control) and a low rate of missing data. Eighty-eight percent of the 320 gene/individual combinations produced sequence reads, and >80% of individuals produced sufficient reads to detect all four possible nuclear alleles of the homeologous nuclear loci with 95% probability.We applied this method to a group of sympatric Australian alpine Poa species, which we discovered to share an allopolyploid ancestor with a group of American Poa species. All markers revealed extensive allele sharing among the Australian species and so we recommend that the current taxonomy be re-examined. We also detected hypermutation in the trnH-psbA marker, suggesting it should not be used as a land plant barcode region. Some markers indicated differentiation between Tasmanian and mainland samples. Significant positive spatial genetic structure was detected at <100 km with chloroplast but not nuclear markers, which may be a result of restricted seed flow and long-distance pollen flow in this wind-pollinated group.<br><br>CONCLUSIONS: Our results demonstrate that 454 sequencing of barcoded amplicon mixtures can be used to reliably sample all alleles of homeologous loci in polyploid species and successfully investigate phylogenetic relationships among species, as well as to investigate phylogeographic hypotheses. This next-generation sequencing method is more affordable than and at least as reliable as bacterial cloning. It could be applied to any experiment involving sequencing of amplicon mixtures.},
}
@article {pmid21429154,
year = {2011},
author = {Stech, M and Kolvoort, E and Loonen, MJ and Vrieling, K and Kruijer, JD},
title = {Bryophyte DNA sequences from faeces of an arctic herbivore, barnacle goose (Branta leucopsis).},
journal = {Molecular ecology resources},
volume = {11},
number = {2},
pages = {404-408},
doi = {10.1111/j.1755-0998.2010.02938.x},
pmid = {21429154},
issn = {1755-0998},
mesh = {Animals ; Arctic Regions ; Bryophyta/*classification/*genetics ; DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Eating ; Feces/*chemistry ; Geese/*physiology ; Molecular Sequence Data ; Phylogeny ; },
abstract = {We tested DNA extraction methods and PCR conditions for the amplification of bryophyte DNA from barnacle goose (Branta leucopsis) faeces collected from Spitsbergen (Svalbard). Both the Qiagen stool kit and a silica-based extraction method received sufficient DNA from fresh and older droppings, as indicated by successful amplification of the plastid psbA-trnH spacer. Standard Taq polymerase outperformed two hot start polymerases. Sequencing of cloned PCR products revealed at least ten moss and two angiosperm sequences. This first example of identifying bryophyte DNA from faeces will allow analysing moss diets of arctic herbivores with a DNA barcoding approach.},
}
@article {pmid21429133,
year = {2011},
author = {McGowin, AE and Truong, TM and Corbett, AM and Bagley, DA and Ehrhart, LM and Bresette, MJ and Weege, ST and Clark, D},
title = {Genetic barcoding of marine leeches (Ozobranchus spp.) from Florida sea turtles and their divergence in host specificity.},
journal = {Molecular ecology resources},
volume = {11},
number = {2},
pages = {271-278},
doi = {10.1111/j.1755-0998.2010.02946.x},
pmid = {21429133},
issn = {1755-0998},
mesh = {Animals ; Base Sequence ; DNA Barcoding, Taxonomic/*methods ; *Evolution, Molecular ; Florida ; *Host Specificity ; Leeches/*classification/genetics/*physiology ; Molecular Sequence Data ; Phylogeny ; Turtles/*parasitology ; },
abstract = {Ozobranchus margoi and Ozobranchus branchiatus are the only two species of marine turtle leeches (Ozobranchus spp.) known to inhabit the Atlantic coast of the United States and the Gulf of Mexico. In early reports of fibropapillomatosis (FP) in green turtles (Chelonia mydas), O. branchiatus was implicated as a vector in the transmission of Fibropapilloma-associated turtle herpesvirus (FPTHV). It is imperative that the leech species be identified to elucidate the role Ozobranchus spp. may play in disease transmission. In this study, Ozobranchus branchiatus has been identified for the first time on a loggerhead (Caretta caretta) turtle, and the molecular data for this species is now available for the first time in GenBank. Both species of leeches were also found infecting a single C. mydas. Using morphological taxonomy combined with distance- and character-based genetic sequence analyses, this study has established a DNA barcode for both species of Ozobranchus spp. leech and has shown it can be applied successfully to the identification of leeches at earlier stages of development when morphological taxonomy cannot be employed. The results suggest a different haplotype may exist for O. branchiatus leeches found on C. caretta versus C. mydas. Leech cocoon residue collected from a C. mydas was identified using the new method.},
}
@article {pmid21429132,
year = {2011},
author = {Jung, S and Duwal, RK and Lee, S},
title = {COI barcoding of true bugs (Insecta, Heteroptera).},
journal = {Molecular ecology resources},
volume = {11},
number = {2},
pages = {266-270},
doi = {10.1111/j.1755-0998.2010.02945.x},
pmid = {21429132},
issn = {1755-0998},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Heteroptera/*classification/enzymology/*genetics ; Insect Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; },
abstract = {Several recent studies have proposed that partial DNA sequences of the cytochrome c oxidase I (COI) mitochondrial gene might serve as DNA barcodes for identifying and differentiating between animal species, such as birds, fish and insects. In this study, we tested the effectiveness of a COI barcode to identify true bugs from 139 species collected from Korea and adjacent regions (Japan, Northeastern China and Fareast Russia). All the species had a unique COI barcode sequence except for the genus Apolygus (Miridae), and the average interspecific genetic distance between closely related species was about 16 times higher than the average intraspecific genetic distance. DNA barcoding identified one probable new species of true bug and revealed identical or very recently divergent species that were clearly distinguished by morphological characteristics. Therefore, our results suggest that COI barcodes can reveal new cryptic true bug species and are able to contribute for the exact identification of the true bugs.},
}
@article {pmid21429131,
year = {2011},
author = {Weigand, AM and Jochum, A and Pfenninger, M and Steinke, D and Klussmann-Kolb, A},
title = {A new approach to an old conundrum--DNA barcoding sheds new light on phenotypic plasticity and morphological stasis in microsnails (Gastropoda, Pulmonata, Carychiidae).},
journal = {Molecular ecology resources},
volume = {11},
number = {2},
pages = {255-265},
doi = {10.1111/j.1755-0998.2010.02937.x},
pmid = {21429131},
issn = {1755-0998},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Gastropoda/anatomy &amp; histology/*classification/*genetics ; Molecular Sequence Data ; Phenotype ; Phylogeny ; },
abstract = {The identification of microsnail taxa based on morphological characters is often a time-consuming and inconclusive process. Aspects such as morphological stasis and phenotypic plasticity further complicate their taxonomic designation. In this study, we demonstrate that the application of DNA barcoding can alleviate these problems within the Carychiidae (Gastropoda, Pulmonata). These microsnails are a taxon of the pulmonate lineage and most likely migrated onto land independently of the Stylommatophora clade. Their taxonomical classification is currently based on conchological and anatomical characters only. Despite much confusion about historic species assignments, the Carychiidae can be unambiguously subdivided into two taxa: (i) Zospeum species, which are restricted to karst caves, and (ii) Carychium species, which occur in a broad range of environmental conditions. The implementation of discrete molecular data (COI marker) enabled us to correctly designate 90% of the carychiid microsnails. The remaining cases were probably cryptic Zospeum and Carychium taxa and incipient species, which require further investigation into their species status. Because conventional reliance upon mostly continuous (i.e. nondiscrete) conchological characters is subject to fallibility for many gastropod species assignments, we highly recommend the use of DNA barcoding as a taxonomic, cutting-edge method for delimiting microsnail taxa.},
}
@article {pmid21429130,
year = {2011},
author = {Ong, PS and Luczon, AU and Quilang, JP and Sumaya, AM and Ibañez, JC and Salvador, DJ and Fontanilla, IK},
title = {DNA barcodes of Philippine accipitrids.},
journal = {Molecular ecology resources},
volume = {11},
number = {2},
pages = {245-254},
doi = {10.1111/j.1755-0998.2010.02928.x},
pmid = {21429130},
issn = {1755-0998},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Falconiformes/*classification/*genetics ; Molecular Sequence Data ; Phylogeny ; },
abstract = {DNA barcoding is a molecular method that rapidly identifies an individual to a known taxon or its closest relative based on a 650-bp fragment of the cytochrome c oxidase subunit I (COI). In this study, DNA barcodes of members of the family Accipitridae, including Haliastur indus (brahminy kite), Haliaeetus leucogaster (white-bellied sea eagle), Ichthyophaga ichthyaetus (grey-headed fish eagle), Spilornis holospilus (crested serpent-eagle), Spizaetus philippensis (Philippine hawk-eagle), and Pithecophaga jefferyi (Philippine eagle), are reported for the first time. All individuals sampled are kept at the Philippine Eagle Center in Davao City, Philippines. Basic local alignment search tool results demonstrated that the COI sequences for these species were unique. The COI gene trees constructed using the maximum-likelihood and neighbour-joining (NJ) methods supported the monophyly of the booted eagles of the Aquilinae and the sea eagles of the Haliaeetinae but not the kites of the Milvinae.},
}
@article {pmid21429129,
year = {2011},
author = {Zeale, MR and Butlin, RK and Barker, GL and Lees, DC and Jones, G},
title = {Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces.},
journal = {Molecular ecology resources},
volume = {11},
number = {2},
pages = {236-244},
doi = {10.1111/j.1755-0998.2010.02920.x},
pmid = {21429129},
issn = {1755-0998},
mesh = {Animals ; Arthropods/*classification/*genetics/physiology ; Chiroptera/*physiology ; DNA Barcoding, Taxonomic ; DNA Primers/genetics ; Feces/*chemistry ; Feeding Behavior ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/*methods ; Predatory Behavior ; },
abstract = {The application of DNA barcoding to dietary studies allows prey taxa to be identified in the absence of morphological evidence and permits a greater resolution of prey identity than is possible through direct examination of faecal material. For insectivorous bats, which typically eat a great diversity of prey and which chew and digest their prey thoroughly, DNA-based approaches to diet analysis may provide the only means of assessing the range and diversity of prey within faeces. Here, we investigated the effectiveness of DNA barcoding in determining the diets of bat species that specialize in eating different taxa of arthropod prey. We designed and tested a novel taxon-specific primer set and examined the performance of short barcode sequences in resolving prey species. We recovered prey DNA from all faecal samples and subsequent cloning and sequencing of PCR products, followed by a comparison of sequences to a reference database, provided species-level identifications for 149/207 (72%) clones. We detected a phylogenetically broad range of prey while completely avoiding detection of nontarget groups. In total, 37 unique prey taxa were identified from 15 faecal samples. A comparison of DNA data with parallel morphological analyses revealed a close correlation between the two methods. However, the sensitivity and taxonomic resolution of the DNA method were far superior. The methodology developed here provides new opportunities for the study of bat diets and will be of great benefit to the conservation of these ecologically important predators.},
}
@article {pmid21429104,
year = {2011},
author = {Liu, J and Möller, M and Gao, LM and Zhang, DQ and Li, DZ},
title = {DNA barcoding for the discrimination of Eurasian yews (Taxus L., Taxaceae) and the discovery of cryptic species.},
journal = {Molecular ecology resources},
volume = {11},
number = {1},
pages = {89-100},
doi = {10.1111/j.1755-0998.2010.02907.x},
pmid = {21429104},
issn = {1755-0998},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Chloroplast/genetics ; DNA, Plant/genetics ; Molecular Sequence Data ; Phylogeny ; Taxus/*classification/*genetics ; },
abstract = {There is currently international interest in the application of DNA barcoding as a tool for plant species discrimination and identification. In this study, we evaluated the utility of five candidate plant DNA barcoding regions [rbcL, matK, trnH-psbA, trnL-F and internal transcribed spacer (ITS)] in Eurasian yews. This group of species is taxonomically difficult because of a lack of clear-cut morphologically differences between species and hence represents a good test case for DNA barcoding. Forty-seven accessions were analysed, representing all taxa treated in current floristic works and covering most of the distribution range of Taxus in Eurasia. As single loci, trnL-F and ITS showed the highest species discriminatory power, each resolving 11 of 11 lineages (= barcode taxa). Species discrimination using matK, trnH-psbA and rbcL individually was lower, with matK resolving 8 of 10, trnH-psbA 7 of 11 and rbcL 5 of 11 successfully sequenced lineages. The proposed CBOL core barcode (rbcL + matK) resolved 8 of 11 lineages. Combining loci generally increased the robustness (measured by clade support) of the barcoding discrimination. Based on overall performance, trnL-F and ITS, separately or combined, are proposed as barcode for Eurasian Taxus. DNA barcoding discriminated recognized taxa of Eurasian Taxus, namely T. baccata, T. cuspidata, T. fuana and T. sumatrana, and identified seven lineages among the T. wallichiana group, some with distinct geographical distributions and morphologies, and potentially representing new species. Using the proposed DNA barcode, a technical system can be established to rapidly and reliably identify Taxus species in Eurasia for conservation protection and for monitoring illegal trade.},
}
@article {pmid21429103,
year = {2011},
author = {Albu, M and Nikbakht, H and Hajibabaei, M and Hickey, DA},
title = {The DNA Barcode Linker.},
journal = {Molecular ecology resources},
volume = {11},
number = {1},
pages = {84-88},
doi = {10.1111/j.1755-0998.2010.02901.x},
pmid = {21429103},
issn = {1755-0998},
mesh = {Algorithms ; DNA/genetics ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Internet ; Molecular Sequence Data ; Sequence Analysis, DNA/instrumentation/*methods ; Software ; },
abstract = {DNA barcoding is based on the use of short DNA sequences to provide taxonomic tags for rapid, efficient identification of biological specimens. Currently, reference databases are being compiled. In the future, it will be important to facilitate access to these databases, especially for nonspecialist users. The method described here provides a rapid, web-based, user-friendly link between the DNA sequence from an unidentified biological specimen and various types of biological information, including the species name. Specifically, we use a customized, Google-type search algorithm to quickly match an unknown DNA sequence to a list of verified DNA barcodes in the reference database. In addition to retrieving the species name, our web tool also provides automatic links to a range of other information about that species. As the DNA barcode database becomes more populated, it will become increasingly important for the broader user community to be able to exploit it for the rapid identification of unknown specimens and to easily obtain relevant biological information about these species. The application presented here meets that need.},
}
@article {pmid21429102,
year = {2011},
author = {Piredda, R and Simeone, MC and Attimonelli, M and Bellarosa, R and Schirone, B},
title = {Prospects of barcoding the Italian wild dendroflora: oaks reveal severe limitations to tracking species identity.},
journal = {Molecular ecology resources},
volume = {11},
number = {1},
pages = {72-83},
doi = {10.1111/j.1755-0998.2010.02900.x},
pmid = {21429102},
issn = {1755-0998},
mesh = {DNA Barcoding, Taxonomic/*methods ; Genome, Plastid ; Italy ; Molecular Sequence Data ; Phylogeny ; Plant Proteins ; Quercus/*classification/genetics ; Trees/*classification/genetics ; },
abstract = {DNA barcoding may be particularly important in influencing ecology, economic issues, and the fundamental crisis facing biodiversity as a standardized, species-level identification tool for taxonomy assessment. Trees play important roles in the conservation of many land ecosystems, the wood trade, and the definition of biogeographical processes; nevertheless, peculiar biological, evolutionary and taxonomical features will probably constitute an intriguing challenge to barcoders. We examined whether four marker regions (trnh-psba, rbcL, rpoc1, matK) proposed by the Consortium for the Barcode of Life (CBOL) matched species taxonomy in a preliminary tree biodiversity survey of Italian forested land. Our objective was to provide a test of future in situ applications of DNA barcodes by evaluating the efficacy of species discrimination under the criteria of uniformity of methods and natural co-occurrence of the species in the main forest ecosystems. Fifty-two species were included in a floristic study. We obtained 73% total discrimination success, with trnH-psbA as the best performing marker and oaks as the least responsive plants to the markers used. A further taxon-based study of Quercus (thirty specimens, 12 species) revealed that this genus is refractory to barcoding (0% discrimination success), a probable consequence of low variation rate at the plastid genome level, hybridization, and the incidence of biogeography. We conclude that some species-rich tree genera in small geographical regions may prove exceptionally difficult to barcode. Until more efficient markers are developed, we recommend that improved and diversified sampling (multiple locations of sympatric and co-occurring congenerics) be embraced as a timely and important goal for the precise assessment of haplotype specificity to facilitate the productive application of barcoding in practice.},
}
@article {pmid21429101,
year = {2011},
author = {Lakra, WS and Verma, MS and Goswami, M and Lal, KK and Mohindra, V and Punia, P and Gopalakrishnan, A and Singh, KV and Ward, RD and Hebert, P},
title = {DNA barcoding Indian marine fishes.},
journal = {Molecular ecology resources},
volume = {11},
number = {1},
pages = {60-71},
doi = {10.1111/j.1755-0998.2010.02894.x},
pmid = {21429101},
issn = {1755-0998},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Fish Proteins/genetics ; Fishes/*classification/genetics ; India ; Molecular Sequence Data ; *Phylogeny ; },
abstract = {DNA barcoding has been adopted as a global bio-identification system for animals in recent years. A major national programme on DNA barcoding of fish and marine life was initiated in India by the authors during 2006 and 115 species of marine fish covering Carangids, Clupeids, Scombrids, Groupers, Sciaenids, Silverbellies, Mullids, Polynemids and Silurids representing 79 Genera and 37 Families from the Indian Ocean have been barcoded for the first time using cytochrome c oxidase I gene (COI) of the mtDNA. The species were represented by multiple specimens and a total of 397 sequences were generated. After amplification and sequencing of 707 base pair fragment of COI, primers were trimmed which invariably generated a 655 base pair barcode sequence. The average Kimura two parameter (K2P) distances within species, genera, families, orders were 0.30%, 6.60%, 9.91%, 16.00%, respectively. In addition to barcode-based species identification system, phylogenetic relationships among the species have also been attempted. The neighbour-joining tree revealed distinct clusters in concurrence with the taxonomic status of the species.},
}
@article {pmid21429100,
year = {2011},
author = {Santos, AM and Besnard, G and Quicke, DL},
title = {Applying DNA barcoding for the study of geographical variation in host-parasitoid interactions.},
journal = {Molecular ecology resources},
volume = {11},
number = {1},
pages = {46-59},
doi = {10.1111/j.1755-0998.2010.02889.x},
pmid = {21429100},
issn = {1755-0998},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Euphorbia/*parasitology ; Europe ; Geography ; *Host-Parasite Interactions ; Insect Proteins/genetics ; Molecular Sequence Data ; Moths/*classification/enzymology/genetics/physiology ; *Phylogeny ; },
abstract = {Studies on the biogeography of host-parasitoid interactions are scarce, mainly because of technical difficulties associated with rearing and species identification. DNA barcoding is increasingly recognized as a valuable tool for taxon identification, allowing to link different life history stages of a species. We evaluate the usefulness of a protocol based on cytochrome oxidase I (COI) sequencing for the study of geographical variation of host-parasitoid interactions. Larvae of Acroclita subsequana (Lepidoptera: Tortricidae) were collected in Macaronesia and dissected to search for parasitoid larvae. Both hosts and parasitoids were sequenced and assigned to molecular operational taxonomic units (MOTUs) based on pairwise genetic distances, tree-based and similarity-based methods. Hosts were grouped into six MOTUs, usually with an allopatric distribution, while parasitoids clustered into 12 MOTUs, each of which was mostly found attacking a single host MOTU. Available COI sequence databases failed to provide identification to species level for these MOTUs. Three challenges related to the applicability of DNA barcoding in this type of studies are identified and discussed: (i) more suitable primers need to be developed for both parasitoids and hosts; (ii) the most commonly used approaches for inferring MOTUs have different limitations (e.g. arbitrary nature of defining a threshold to separate MOTUs) and need to be improved or replaced by other techniques; and (iii) for the identification of MOTUs, it is imperative to increase the range of sequenced taxa in the currently available reference databases. Finally, in spite of these difficulties, we discuss how DNA barcoding will help ecological and biogeographical studies of host-parasitoid interactions.},
}
@article {pmid21429099,
year = {2011},
author = {Waugh, J and Evans, MW and Millar, CD and Lambert, DM},
title = {Birdstrikes and barcoding: can DNA methods help make the airways safer?.},
journal = {Molecular ecology resources},
volume = {11},
number = {1},
pages = {38-45},
doi = {10.1111/j.1755-0998.2010.02884.x},
pmid = {21429099},
issn = {1755-0998},
mesh = {Aircraft/statistics &amp; numerical data ; Animals ; Aphids/*classification/enzymology/*genetics ; Birds/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Molecular Sequence Data ; New Zealand ; Phylogeny ; Republic of Korea ; Safety/statistics &amp; numerical data ; },
abstract = {While flying remains one of the safest means of travel, reported birdstrikes on aircraft have risen. This is a result of increased aircraft flight movements, changes in agricultural methods and greater environmental awareness contributing to growing populations of hazardous bird species, as well as more diligent reporting of incidents. Measures to mitigate this hazard require accurate data about the species involved; however, the remains of birds from these incidents are often not easy to identify. Reported birdstrikes include a substantial number where the species cannot be determined from morphology alone. DNA barcoding offers a reliable method of identifying species from very small amounts of organic material such as blood, muscle and feathers. We compare species identification based on morphological criteria and identifications based on mitochondrial cytochrome c oxidase subunit I DNA barcoding methods for New Zealand species. Our data suggest that DNA-based identification can substantially add to the accuracy of species identifications, and these methods represent an important addition to existing procedures to improve air safety. In addition, we outline simple and effective protocols for the recovery and processing of samples for DNA barcoding.},
}
@article {pmid21429098,
year = {2011},
author = {Lee, W and Kim, H and Lim, J and Choi, HR and Kim, Y and Kim, YS and Ji, JY and Foottit, RG and Lee, S},
title = {Barcoding aphids (Hemiptera: Aphididae) of the Korean Peninsula: updating the global data set.},
journal = {Molecular ecology resources},
volume = {11},
number = {1},
pages = {32-37},
doi = {10.1111/j.1755-0998.2010.02877.x},
pmid = {21429098},
issn = {1755-0998},
mesh = {Animals ; Aphids/*classification/enzymology/*genetics ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Databases, Nucleic Acid ; Electron Transport Complex IV/genetics ; Genetic Variation ; Insect Proteins/genetics ; Molecular Sequence Data ; *Phylogeny ; Republic of Korea ; },
abstract = {DNA barcode (mitochondrial COI) sequences are provided for species identification of aphids from the Korean Peninsula. Most (98%) of the 154 species had distinct COI sequences (average 0.05% intraspecific pairwise divergence) relative to the degree of sequence divergence among species (average value 5.84%). For species in common with other regions, barcodes for Korean samples fell near or within known levels of variation. Based on these results, we conclude that DNA barcodes can provide an effective tool for identifying aphid species in such applications as pest management, monitoring and plant quarantine.},
}
@article {pmid21429097,
year = {2011},
author = {McFadden, CS and Benayahu, Y and Pante, E and Thoma, JN and Nevarez, PA and France, SC},
title = {Limitations of mitochondrial gene barcoding in Octocorallia.},
journal = {Molecular ecology resources},
volume = {11},
number = {1},
pages = {19-31},
doi = {10.1111/j.1755-0998.2010.02875.x},
pmid = {21429097},
issn = {1755-0998},
support = {52005123//Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; Anthozoa/*classification/enzymology/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Genetic Variation ; Molecular Sequence Data ; *Phylogeny ; },
abstract = {The widespread assumption that COI and other mitochondrial genes will be ineffective DNA barcodes for anthozoan cnidarians has not been well tested for most anthozoans other than scleractinian corals. Here we examine the limitations of mitochondrial gene barcoding in the sub-class Octocorallia, a large, diverse, and ecologically important group of anthozoans. Pairwise genetic distance values (uncorrected p) were compared for three candidate barcoding regions: the Folmer region of COI; a fragment of the octocoral-specific mitochondrial protein-coding gene, msh1; and an extended barcode of msh1 plus COI with a short, adjacent intergenic region (igr1). Intraspecific variation was <0.5%, with most species exhibiting no variation in any of the three gene regions. Interspecific divergence was also low: 18.5% of congeneric morphospecies shared identical COI barcodes, and there was no discernible barcoding gap between intra- and interspecific p values. In a case study to assess regional octocoral biodiversity, COI and msh1 barcodes each identified 70% of morphospecies. In a second case study, a nucleotide character-based analysis correctly identified 70% of species in the temperate genus Alcyonium. Although interspecific genetic distances were 2× greater for msh1 than COI, each marker identified similar numbers of species in the two case studies, and the extended COI + igr1 + msh1 barcode more effectively discriminated sister taxa in Alcyonium. Although far from perfect for species identification, a COI + igr1 + msh1 barcode nonetheless represents a valuable addition to the depauperate set of characters available for octocoral taxonomy.},
}
@article {pmid21423623,
year = {2011},
author = {Wong, LL and Peatman, E and Lu, J and Kucuktas, H and He, S and Zhou, C and Na-nakorn, U and Liu, Z},
title = {DNA barcoding of catfish: species authentication and phylogenetic assessment.},
journal = {PloS one},
volume = {6},
number = {3},
pages = {e17812},
pmid = {21423623},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Catfishes/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Reference Standards ; Sequence Alignment ; Species Specificity ; },
abstract = {As the global market for fisheries and aquaculture products expands, mislabeling of these products has become a growing concern in the food safety arena. Molecular species identification techniques hold the potential for rapid, accurate assessment of proper labeling. Here we developed and evaluated DNA barcodes for use in differentiating United States domestic and imported catfish species. First, we sequenced 651 base-pair barcodes from the cytochrome oxidase I (COI) gene from individuals of 9 species (and an Ictalurid hybrid) of domestic and imported catfish in accordance with standard DNA barcoding protocols. These included domestic Ictalurid catfish, and representative imported species from the families of Clariidae and Pangasiidae. Alignment of individual sequences from within a given species revealed highly consistent barcodes (98% similarity on average). These alignments allowed the development and analyses of consensus barcode sequences for each species and comparison with limited sequences in public databases (GenBank and Barcode of Life Data Systems). Validation tests carried out in blinded studies and with commercially purchased catfish samples (both frozen and fresh) revealed the reliability of DNA barcoding for differentiating between these catfish species. The developed protocols and consensus barcodes are valuable resources as increasing market and governmental scrutiny is placed on catfish and other fisheries and aquaculture products labeling in the United States.},
}
@article {pmid21423340,
year = {2011},
author = {Hausmann, A and Haszprunar, G and Hebert, PD},
title = {DNA barcoding the geometrid fauna of Bavaria (Lepidoptera): successes, surprises, and questions.},
journal = {PloS one},
volume = {6},
number = {2},
pages = {e17134},
pmid = {21423340},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; *DNA Barcoding, Taxonomic/methods/standards ; Efficiency ; Electronic Data Processing/organization &amp; administration/standards ; Female ; Gene Library ; Germany ; Lepidoptera/*classification/*genetics ; Male ; Phylogeography ; Sequence Analysis, DNA ; Validation Studies as Topic ; },
abstract = {BACKGROUND: The State of Bavaria is involved in a research program that will lead to the construction of a DNA barcode library for all animal species within its territorial boundaries. The present study provides a comprehensive DNA barcode library for the Geometridae, one of the most diverse of insect families.<br><br>This study reports DNA barcodes for 400 Bavarian geometrid species, 98 per cent of the known fauna, and approximately one per cent of all Bavarian animal species. Although 98.5% of these species possess diagnostic barcode sequences in Bavaria, records from neighbouring countries suggest that species-level resolution may be compromised in up to 3.5% of cases. All taxa which apparently share barcodes are discussed in detail. One case of modest divergence (1.4%) revealed a species overlooked by the current taxonomic system: Eupithecia goossensiata Mabille, 1869 stat.n. is raised from synonymy with Eupithecia absinthiata (Clerck, 1759) to species rank. Deep intraspecific sequence divergences (>2%) were detected in 20 traditionally recognized species.<br><br>CONCLUSIONS/SIGNIFICANCE: The study emphasizes the effectiveness of DNA barcoding as a tool for monitoring biodiversity. Open access is provided to a data set that includes records for 1,395 geometrid specimens (331 species) from Bavaria, with 69 additional species from neighbouring regions. Taxa with deep intraspecific sequence divergences are undergoing more detailed analysis to ascertain if they represent cases of cryptic diversity.},
}
@article {pmid21415009,
year = {2011},
author = {Brady, T and Roth, SL and Malani, N and Wang, GP and Berry, CC and Leboulch, P and Hacein-Bey-Abina, S and Cavazzana-Calvo, M and Papapetrou, EP and Sadelain, M and Savilahti, H and Bushman, FD},
title = {A method to sequence and quantify DNA integration for monitoring outcome in gene therapy.},
journal = {Nucleic acids research},
volume = {39},
number = {11},
pages = {e72},
pmid = {21415009},
issn = {1362-4962},
support = {AI082020/AI/NIAID NIH HHS/United States ; AI52845/AI/NIAID NIH HHS/United States ; },
mesh = {Bacteriophage mu/genetics ; Cell Line ; *Gene Targeting ; *Genetic Therapy ; Humans ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; },
abstract = {Human genetic diseases have been successfully corrected by integration of functional copies of the defective genes into human cells, but in some cases integration of therapeutic vectors has activated proto-oncogenes and contributed to leukemia. For this reason, extensive efforts have focused on analyzing integration site populations from patient samples, but the most commonly used methods for recovering newly integrated DNA suffer from severe recovery biases. Here, we show that a new method based on phage Mu transposition in vitro allows convenient and consistent recovery of integration site sequences in a form that can be analyzed directly using DNA barcoding and pyrosequencing. The method also allows simple estimation of the relative abundance of gene-modified cells from human gene therapy subjects, which has previously been lacking but is crucial for detecting expansion of cell clones that may be a prelude to adverse events.},
}
@article {pmid21406042,
year = {2011},
author = {Nwani, CD and Becker, S and Braid, HE and Ude, EF and Okogwu, OI and Hanner, R},
title = {DNA barcoding discriminates freshwater fishes from southeastern Nigeria and provides river system-level phylogeographic resolution within some species.},
journal = {Mitochondrial DNA},
volume = {22 Suppl 1},
number = {},
pages = {43-51},
doi = {10.3109/19401736.2010.536537},
pmid = {21406042},
issn = {1940-1744},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods/standards ; DNA, Mitochondrial/analysis/genetics ; Electron Transport Complex IV/*genetics ; Fishes/*classification/*genetics/physiology ; Fresh Water ; Molecular Sequence Data ; Nigeria ; Phylogeography ; Polymerase Chain Reaction ; *Rivers ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND AND AIMS: Fishes are the main animal protein source for human beings and play a vital role in aquatic ecosystems and food webs. Fish identification can be challenging, especially in the tropics (due to high diversity), and this is particularly true for larval forms or fragmentary remains. DNA barcoding, which uses the 5' region of the mitochondrial cytochrome c oxidase subunit I (COI) as a target gene, is an efficient method for standardized species-level identification for biodiversity assessment and conservation, pending the establishment of reference sequence libraries.<br><br>MATERIALS AND METHODS: In this study, fishes were collected from three rivers in southeastern Nigeria, identified morphologically, and imaged digitally. DNA was extracted, PCR-amplified, and the standard barcode region was bidirectionally sequenced for 363 individuals belonging to 70 species in 38 genera. All specimen provenance data and associated sequence information were recorded in the barcode of life data systems (BOLD; www.barcodinglife.org). Analytical tools on BOLD were used to assess the performance of barcoding to identify species.<br><br>RESULTS: Using neighbor-joining distance comparison, the average genetic distance was 60-fold higher between species than within species, as pairwise genetic distance estimates averaged 10.29% among congeners and only 0.17% among conspecifics. Despite low levels of divergence within species, we observed river system-specific haplotype partitioning within eight species (11.4% of all species).<br><br>CONCLUSION: Our preliminary results suggest that DNA barcoding is very effective for species identification of Nigerian freshwater fishes.},
}
@article {pmid21405610,
year = {2011},
author = {Pirandola, S},
title = {Quantum reading of a classical digital memory.},
journal = {Physical review letters},
volume = {106},
number = {9},
pages = {090504},
doi = {10.1103/PhysRevLett.106.090504},
pmid = {21405610},
issn = {1079-7114},
abstract = {We consider a basic model of digital memory where each cell is composed of a reflecting medium with two possible reflectivities. By fixing the mean number of photons irradiated over each memory cell, we show that a nonclassical source of light can retrieve more information than any classical source. This improvement is shown in the regime of few photons and high reflectivities, where the gain of information can be surprising. As a result, the use of quantum light can have nontrivial applications in the technology of digital memories, such as optical disks and barcodes.},
}
@article {pmid21396252,
year = {2011},
author = {Krüger, A and Strüven, L and Post, RJ and Faulde, M},
title = {The sandflies (Diptera: Psychodidae, Phlebotominae) in military camps in northern Afghanistan (2007-2009), as identified by morphology and DNA 'barcoding'.},
journal = {Annals of tropical medicine and parasitology},
volume = {105},
number = {2},
pages = {163-176},
pmid = {21396252},
issn = {1364-8594},
mesh = {Afghanistan ; Animals ; Cytochromes b/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Female ; Humans ; Insect Vectors/anatomy &amp; histology/*classification/genetics ; Leishmaniasis/transmission ; Male ; Psychodidae/anatomy &amp; histology/*classification/genetics ; },
abstract = {As part of a continuous, standardized programme of monitoring the Leishmania vectors in German military camps in northern Afghanistan between 2007 and 2009, a detailed taxonomic analysis of the endemic sandfly fauna, as sampled using light and odour-baited traps, was conducted. Of the 10 sandfly species that were recorded, six may serve as enzootic and/or zooanthroponotic vectors of parasites causing human leishmaniasis. The use of a simple DNA-'barcoding' technique based on the mitochondrial cyt b gene, to identify the collected sandflies to species level, revealed (1) a clear discrimination between the potential vector species, (2) clustering of species within most subgenera, and (3) particularly high heterogeneity within the subgenus Paraphlebotomus (Phlebotomus alexandri being grouped with Ph. papatasi rather than with other Paraphlebotomus species). The data also indicate a high level of genetic heterogeneity within the subgenus Sergentomyia but close similarity between Sergentomyia sintoni and Sergentomyia murgabiensis. The morphological similarity of many medically important sandflies can make species identification difficult, if not impossible. The new DNA-barcoding techniques may provide powerful discriminatory tools in the future.},
}
@article {pmid21391497,
year = {2011},
author = {Handy, SM and Deeds, JR and Ivanova, NV and Hebert, PD and Hanner, RH and Ormos, A and Weigt, LA and Moore, MM and Yancy, HF},
title = {A single-laboratory validated method for the generation of DNA barcodes for the identification of fish for regulatory compliance.},
journal = {Journal of AOAC International},
volume = {94},
number = {1},
pages = {201-210},
pmid = {21391497},
issn = {1060-3271},
mesh = {Animals ; Base Sequence ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Fishes/*classification/*genetics ; Food Supply/*legislation &amp; jurisprudence/*standards ; Pilot Projects ; Polymerase Chain Reaction ; Seafood/*classification/*standards ; Species Specificity ; United States ; United States Food and Drug Administration ; },
abstract = {The U.S. Food and Drug Administration is responsible for ensuring that the nation's food supply is safe and accurately labeled. This task is particularly challenging in the case of seafood where a large variety of species are marketed, most of this commodity is imported, and processed product is difficult to identify using traditional morphological methods. Reliable species identification is critical for both foodborne illness investigations and for prevention of deceptive practices, such as those where species are intentionally mislabeled to circumvent import restrictions or for resale as species of higher value. New methods that allow accurate and rapid species identifications are needed, but any new methods to be used for regulatory compliance must be both standardized and adequately validated. "DNA barcoding" is a process by which species discriminations are achieved through the use of short, standardized gene fragments. For animals, a fragment (655 base pairs starting near the 5' end) of the cytochrome c oxidase subunit 1 mitochondrial gene has been shown to provide reliable species level discrimination in most cases. We provide here a protocol with single-laboratory validation for the generation of DNA barcodes suitable for the identification of seafood products, specifically fish, in a manner that is suitable for FDA regulatory use.},
}
@article {pmid21383927,
year = {2011},
author = {Sharma, G and Parwani, AV and Raval, JS and Triulzi, DJ and Benjamin, RJ and Pantanowitz, L},
title = {Contemporary issues in transfusion medicine informatics.},
journal = {Journal of pathology informatics},
volume = {2},
number = {},
pages = {3},
pmid = {21383927},
issn = {2153-3539},
abstract = {The Transfusion Medicine Service (TMS) covers diverse clinical and laboratory-based services that must be delivered with accuracy, efficiency and reliability. TMS oversight is shared by multiple regulatory agencies that cover product manufacturing and validation standards geared toward patient safety. These demands present significant informatics challenges. Over the past few decades, TMS information systems have improved to better handle blood product manufacturing, inventory, delivery, tracking and documentation. Audit trails and access to electronic databases have greatly facilitated product traceability and biovigilance efforts. Modern blood bank computing has enabled novel applications such as the electronic crossmatch, kiosk-based blood product delivery systems, and self-administered computerized blood donor interview and eligibility determination. With increasing use of barcoding technology, there has been a marked improvement in patient and specimen identification. Moreover, the emergence of national and international labeling standards such as ISBT 128 have facilitated the availability, movement and tracking of blood products across national and international boundaries. TMS has only recently begun to leverage the electronic medical record to address quality issues in transfusion practice and promote standardized documentation within institutions. With improved technology, future growth is expected in blood bank automation and product labeling with applications such as radio frequency identification devices. This article reviews several of these key informatics issues relevant to the contemporary practice of TMS.},
}
@article {pmid21376487,
year = {2011},
author = {Schilthuizen, M and Scholte, C and van Wijk, RE and Dommershuijzen, J and van der Horst, D and Zu Schlochtern, MM and Lievers, R and Groenenberg, DS},
title = {Using DNA-barcoding to make the necrobiont beetle family Cholevidae accessible for forensic entomology.},
journal = {Forensic science international},
volume = {210},
number = {1-3},
pages = {91-95},
doi = {10.1016/j.forsciint.2011.02.003},
pmid = {21376487},
issn = {1872-6283},
mesh = {Animals ; Coleoptera/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Entomology ; Feeding Behavior ; Forensic Pathology ; Humans ; Male ; Phylogeny ; Polymerase Chain Reaction ; Postmortem Changes ; },
abstract = {The beetle family Cholevidae (Coleoptera: Staphylinoidea), sometimes viewed as the subfamily Cholevinae of the Leiodidae, consists of some 1700 species worldwide. With the exception of specialized cave-dwelling species and species living in bird and mammal nests and burrows, the species are generalized soil-dwellers that, at least in temperate regions, are mostly found on vertebrate cadavers. Although they have been regularly reported from human corpses, and offer potential because of many species' peak activity in the cold season, they have not been a focus of forensic entomologists so far. This is probably due to their small size and the difficulty in identifying the adults and their larvae. In this paper, we show that DNA-barcoding can help make this group of necrobiont beetles available as a tool for forensic research. We collected 86 specimens of 20 species of the genera Catops, Fissocatops, Apocatops, Choleva, Nargus, Ptomaphagus, and Sciodrepoides from the Netherlands and France and show that a broad "barcoding gap" allows almost all species to be easily and unambiguously identified by the sequence of the "barcoding gene" cytochrome c oxidase I (COI). This opens up the possibility of adding Cholevidae to the set of insect taxa routinely used in forensic entomology.},
}
@article {pmid21369572,
year = {2011},
author = {Giri, S and Li, D and Chan, WC},
title = {Engineering multifunctional magnetic-quantum dot barcodes by flow focusing.},
journal = {Chemical communications (Cambridge, England)},
volume = {47},
number = {14},
pages = {4195-4197},
doi = {10.1039/c0cc05336h},
pmid = {21369572},
issn = {1364-548X},
support = {//Canadian Institutes of Health Research/Canada ; },
mesh = {Amines/chemistry ; Cadmium Compounds/chemistry ; Ferrosoferric Oxide/chemistry ; High-Throughput Screening Assays ; Hydrocarbons ; *Magnetics ; Organophosphorus Compounds/chemistry ; *Quantum Dots ; Selenium Compounds/chemistry ; },
abstract = {A simple one-step flow focusing method was used to embed both magnetic nanoparticles and quantum dots in microbeads in controlled ratios to generate a large library of molecular barcodes for biological applications.},
}
@article {pmid21366049,
year = {2011},
author = {Gu, HF and Xia, Y and Penga, R and Mo, BH and Li, L and Zenga, XM},
title = {Authentication of Chinese crude drug gecko by DNA barcoding.},
journal = {Natural product communications},
volume = {6},
number = {1},
pages = {67-71},
pmid = {21366049},
issn = {1934-578X},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Drug Contamination ; Lizards/*genetics ; *Medicine, Chinese Traditional ; },
abstract = {Gekko gecko, an animal used as a valued traditional Chinese medicine, has been widely used for over 2000 years. Due to localized habitat destruction, the amount of G. gecko has dramatically decreased in recent years. As a result, more and more adulterants have been detected in the traditional medicine, which has resulted in a chaotic market. Therefore, a correct identification method is badly needed. In this study, we employed a new molecular method of DNA barcoding for discriminating gecko from its adulterants. Fifty-seven specimens of gecko and its adulterants were collected as test samples. The full-barcode and mini-barcode sequences of these specimens were separately amplified and sequenced separately. Together with other published barcode sequences, we detected that the intra-specific sequence diversity was far lower than the inter-specific diversity in G. gecko and its adulterants (3% compared with 35% in full-length barcode; 4% compared with 33.5% in mini-barcode). These results showed that both the full-length and mini-barcodes were effective for identifying gecko, which suggested that the DNA barcode could be an effective and powerful tool for identifying the Chinese crude drug gecko.},
}
@article {pmid21362020,
year = {2011},
author = {Murat, C and Zampieri, E and Vallino, M and Daghino, S and Perotto, S and Bonfante, P},
title = {Genomic suppression subtractive hybridization as a tool to identify differences in mycorrhizal fungal genomes.},
journal = {FEMS microbiology letters},
volume = {318},
number = {2},
pages = {115-122},
doi = {10.1111/j.1574-6968.2011.02248.x},
pmid = {21362020},
issn = {1574-6968},
mesh = {Ascomycota/*genetics ; Gene Expression Regulation, Fungal ; *Genome, Fungal ; Molecular Sequence Data ; Mycorrhizae/*genetics ; Nucleic Acid Hybridization/*methods ; },
abstract = {Characterization of genomic variation among different microbial species, or different strains of the same species, is a field of significant interest with a wide range of potential applications. We have investigated the genomic variation in mycorrhizal fungal genomes through genomic suppressive subtractive hybridization. The comparison was between phylogenetically distant and close truffle species (Tuber spp.), and between isolates of the ericoid mycorrhizal fungus Oidiodendron maius featuring different degrees of metal tolerance. In the interspecies experiment, almost all the sequences that were identified in the Tuber melanosporum genome and absent in Tuber borchii and Tuber indicum corresponded to transposable elements. In the intraspecies comparison, some specific sequences corresponded to regions coding for enzymes, among them a glutathione synthetase known to be involved in metal tolerance. This approach is a quick and rather inexpensive tool to develop molecular markers for mycorrhizal fungi tracking and barcoding, to identify functional genes and to investigate the genome plasticity, adaptation and evolution.},
}
@article {pmid21360310,
year = {2011},
author = {Harakalova, M and Nijman, IJ and Medic, J and Mokry, M and Renkens, I and Blankensteijn, JD and Kloosterman, W and Baas, AF and Cuppen, E},
title = {Genomic DNA pooling strategy for next-generation sequencing-based rare variant discovery in abdominal aortic aneurysm regions of interest-challenges and limitations.},
journal = {Journal of cardiovascular translational research},
volume = {4},
number = {3},
pages = {271-280},
pmid = {21360310},
issn = {1937-5395},
mesh = {Aged ; Aortic Aneurysm, Abdominal/*genetics/pathology/surgery ; Aortic Rupture/*genetics/pathology/surgery ; *Chromosomes, Human, Pair 9 ; *DNA Barcoding, Taxonomic ; *DNA Mutational Analysis ; False Positive Reactions ; Female ; *Gene Expression Profiling/methods ; Gene Frequency ; Genetic Association Studies ; Genetic Predisposition to Disease ; Heterozygote ; *High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Mutation ; Netherlands ; Oligonucleotide Array Sequence Analysis ; Phenotype ; Pilot Projects ; Prognosis ; Reproducibility of Results ; },
abstract = {The costs and efforts for sample preparation of hundreds of individuals, their genomic enrichment for regions of interest, and sufficient deep sequencing bring a significant burden to next-generation sequencing-based experiments. We investigated whether pooling of samples at the level of genomic DNA would be a more versatile strategy for lowering the costs and efforts for common disease-associated rare variant detection in candidate genes or associated loci in a substantial patient cohort. We performed a pilot experiment using five pools of 20 abdominal aortic aneurysm (AAA) patients that were enriched on separate microarrays for the reported 9p21.3 associated locus and 42 additional AAA candidate genes, and sequenced on the SOLiD platform. Here, we discuss challenges and limitations connected to this approach and show that the high number of novel variants detected per pool and allele frequency deviations to the usually highly false positive cut-off region for variant detection in non-pooled samples can be limiting factors for successful variant prioritization and confirmation. We conclude that barcode indexing of individual samples before pooling followed by a multiplexed enrichment strategy should be preferred for detection of rare genetic variants in larger sample sets rather than a genomic DNA pooling strategy.},
}
@article {pmid21355538,
year = {2011},
author = {Giri, S and Sykes, EA and Jennings, TL and Chan, WC},
title = {Rapid screening of genetic biomarkers of infectious agents using quantum dot barcodes.},
journal = {ACS nano},
volume = {5},
number = {3},
pages = {1580-1587},
doi = {10.1021/nn102873w},
pmid = {21355538},
issn = {1936-086X},
support = {//Canadian Institutes of Health Research/Canada ; },
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Bacterial/*genetics ; DNA, Viral/*genetics ; Genetic Markers/*genetics ; Genetic Testing/*methods ; In Situ Hybridization/*methods ; *Quantum Dots ; },
abstract = {The development of a rapid and sensitive infectious disease diagnostic platform would enable one to select proper treatment and to contain the spread of the disease. Here we examined the feasibility of using quantum dot (QD) barcodes to detect genetic biomarkers of the bloodborne pathogens HIV, malaria, hepatitis B and C, and syphilis. The genetic fragments from these pathogens were detected in less than 10 min at a sample volume of 200 μL and with a detection limit in the femtomol range. A next step for the advancement of QD barcode technology to the clinic will require validation of the technology with human samples to assess for matrix effects, head-to-head comparison with existing detection method, development of techniques to automate the assay and detection process, and simplification of analytical device for the read-out of the barcode signal. Our study provides an important intermediate step in the translation of QD barcode technology for screening infectious disease agents in the developed and developing world.},
}
@article {pmid22791913,
year = {2011},
author = {Powers, T and Harris, T and Higgins, R and Mullin, P and Sutton, L and Powers, K},
title = {MOTUs, Morphology, and Biodiversity Estimation: A Case Study Using Nematodes of the Suborder Criconematina and a Conserved 18S DNA Barcode.},
journal = {Journal of nematology},
volume = {43},
number = {1},
pages = {35-48},
pmid = {22791913},
issn = {2640-396X},
abstract = {DNA barcodes are increasingly used to provide an estimate of biodiversity for small, cryptic organisms like nematodes. Nucleotide sequences generated by the barcoding process are often grouped, based on similarity, into molecular operational taxonomic units (MOTUs). In order to get a better understanding of the taxonomic resolution of a 3' 592-bp 18S rDNA barcode, we have analyzed 100 MOTUs generated from 214 specimens in the nematode suborder Criconematina. Previous research has demonstrated that the primer set for this barcode reliably amplifies all nematodes in the Phylum Nematoda. Included among the Criconematina specimens were 25 morphologically described species representing 12 genera. Using the most stringent definition of MOTU membership, where a single nucleotide difference is sufficient for the creation of a new MOTU, it was found that an MOTU can represent a subgroup of a species (e.g. Discocriconemella limitanea), a single species (Bakernema inaequale), or a species complex (MOTU 76). A maximum likelihood phylogenetic analysis of the MOTU dataset generated four major clades that were further analyzed by character-based barcode analysis. Fourteen of the 25 morphologically identified species had at least one putative diagnostic nucleotide identified by this character-based approach. These diagnostic nucleotides could be useful in biodiversity assessments when ambiguous results are encountered in database searches that use a distance-based metric for nucleotide sequence comparisons. Information and images regarding specimens examined during this study are available online.},
}
@article {pmid21351516,
year = {2010},
author = {Zhu, YJ and Chen, SL and Yao, H and Tan, R and Song, JY and Luo, K and Lu, J},
title = {[DNA barcoding the medicinal plants of the genus Paris].},
journal = {Yao xue xue bao = Acta pharmaceutica Sinica},
volume = {45},
number = {3},
pages = {376-382},
pmid = {21351516},
issn = {0513-4870},
mesh = {Base Sequence ; Chloroplasts/genetics ; *DNA Barcoding, Taxonomic ; DNA, Chloroplast/genetics ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Liliaceae/*genetics ; Plants, Medicinal/*genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {DNA barcoding is a technique in which species identification and discovery are performed by using short and standard fragments of DNA sequences. In this study, eleven species of Paris, including seven varieties, were sampled. Five chloroplast sequences, psbA-trnH, rpoB, rpoC1, rbcL, matK, and one nuclear marker, the second internal transcribed spacer (ITS2) of ribosomal DNA, were amplified and sequenced. The PCR amplification and sequencing efficiency, intra- and inter-specific divergence and barcoding gap were used to evaluate different loci, and the identification efficiency was assessed using BLAST1 and Nearest Distance methods. The ITS2 sequences in the studied samples of Paris were amplified and sequenced successfully using primers designed by our group, while matK showed low level in the amplification and psbA-trnH was difficult for sequencing because of over 800 bp and poly (A) structure. Analysis of the intra- and inter-specific divergence and barcoding gap showed ITS2 was superior to other loci. The ITS2 showed a much higher percentage of success (100%) in identification than other five loci, none of which indicated more than 50% except matK (52.9%). The 2-locus combination of rbcL+matK didn't improve ability of authentication. In addition, the rate of successful identification with ITS2 kept 100% when the samples were expanded to 67 samples of 29 species. In conclusion, ITS2 can be used to correctly identify medicinal plants of Paris, and it will be a potential DNA barcode for identifying medicinal plants of other taxa.},
}
@article {pmid21348418,
year = {2010},
author = {Han, JP and Song, JY and Liu, C and Chen, J and Qian, J and Zhu, YJ and Shi, LC and Yao, H and Chen, SL},
title = {Identification of Cistanche species (Orobanchaceae) based on sequences of the plastid psbA-trnH intergenic region.},
journal = {Yao xue xue bao = Acta pharmaceutica Sinica},
volume = {45},
number = {1},
pages = {126-130},
pmid = {21348418},
issn = {0513-4870},
mesh = {Base Sequence ; Cistanche/*genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Intergenic/*genetics ; DNA, Plant/*genetics ; Orobanche/genetics ; Phylogeny ; Plant Stems/genetics ; Plants, Medicinal/*genetics ; Plastids/genetics ; Sequence Analysis, DNA/methods ; Species Specificity ; },
abstract = {The dried succulent stems of Cistanche (Cistanche deserticola Y. C. Ma and Cistanche tubulosa Wight.) are one of the most widely used components of traditional Chinese medicines. However, it is often confused and substituted with the roots of Orobanche pycnostachya, Boschniakia rossica (Cham. &amp; Schltdl.) Standl., Cistanche sinensis Beck, and Cistanche salsa (C. A. Mey.) Beck. In this study, we identified psbA-trnH regions from species and tested their suitable for the identification of the above mentioned taxa. The psbA-trnH sequences showed considerable variations between species and thus were revealed as a promising candidate for barcoding of Cistanche species. Additionally, the average genetic distance of psbA-trnH ranging from 0.077% to 0.743%. In contrast, the intra-specific variation among Cistanche species was found to be significantly different from those of other species, with percentages of variation studied ranged from 0% to 0.007%. The sequence difference between the psbA-trnH sequences of Cistanche species and Orobanche pycnostachya ranged from 0.979% to 1.149%. The distance between the Cistanche species and Boschniakia rossica ranged from 1.066% to 1.224%. Our results suggest that the psbA-trnH intergenic spacer region represent a barcode that can be used to identify Cistanche species and other morphologically undistinguishable species.},
}
@article {pmid21347370,
year = {2011},
author = {Hawlitschek, O and Porch, N and Hendrich, L and Balke, M},
title = {Ecological niche modelling and nDNA sequencing support a new, morphologically cryptic beetle species unveiled by DNA barcoding.},
journal = {PloS one},
volume = {6},
number = {2},
pages = {e16662},
pmid = {21347370},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Biodiversity ; Cell Nucleus/*genetics ; Coleoptera/anatomy &amp; histology/*classification/enzymology/*genetics ; DNA/*genetics ; DNA Barcoding, Taxonomic/*methods ; *Ecological and Environmental Phenomena ; Ecosystem ; Electron Transport Complex IV/genetics ; Female ; Male ; *Models, Theoretical ; Pigmentation ; },
abstract = {BACKGROUND: DNA sequencing techniques used to estimate biodiversity, such as DNA barcoding, may reveal cryptic species. However, disagreements between barcoding and morphological data have already led to controversy. Species delimitation should therefore not be based on mtDNA alone. Here, we explore the use of nDNA and bioclimatic modelling in a new species of aquatic beetle revealed by mtDNA sequence data.<br><br>The aquatic beetle fauna of Australia is characterised by high degrees of endemism, including local radiations such as the genus Antiporus. Antiporus femoralis was previously considered to exist in two disjunct, but morphologically indistinguishable populations in south-western and south-eastern Australia. We constructed a phylogeny of Antiporus and detected a deep split between these populations. Diagnostic characters from the highly variable nuclear protein encoding arginine kinase gene confirmed the presence of two isolated populations. We then used ecological niche modelling to examine the climatic niche characteristics of the two populations. All results support the status of the two populations as distinct species. We describe the south-western species as Antiporus occidentalis sp.n.<br><br>CONCLUSION/SIGNIFICANCE: In addition to nDNA sequence data and extended use of mitochondrial sequences, ecological niche modelling has great potential for delineating morphologically cryptic species.},
}
@article {pmid21347361,
year = {2011},
author = {Piganeau, G and Eyre-Walker, A and Jancek, S and Grimsley, N and Moreau, H},
title = {How and why DNA barcodes underestimate the diversity of microbial eukaryotes.},
journal = {PloS one},
volume = {6},
number = {2},
pages = {e16342},
pmid = {21347361},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal/genetics ; Eukaryota/classification/*genetics ; Evolution, Molecular ; Genome/genetics ; Humans ; Mice ; Plankton/classification/*genetics ; Proteome/genetics ; Rats ; },
abstract = {BACKGROUND: Because many picoplanktonic eukaryotic species cannot currently be maintained in culture, direct sequencing of PCR-amplified 18S ribosomal gene DNA fragments from filtered sea-water has been successfully used to investigate the astounding diversity of these organisms. The recognition of many novel planktonic organisms is thus based solely on their 18S rDNA sequence. However, a species delimited by its 18S rDNA sequence might contain many cryptic species, which are highly differentiated in their protein coding sequences.<br><br>PRINCIPAL FINDINGS: Here, we investigate the issue of species identification from one gene to the whole genome sequence. Using 52 whole genome DNA sequences, we estimated the global genetic divergence in protein coding genes between organisms from different lineages and compared this to their ribosomal gene sequence divergences. We show that this relationship between proteome divergence and 18S divergence is lineage dependent. Unicellular lineages have especially low 18S divergences relative to their protein sequence divergences, suggesting that 18S ribosomal genes are too conservative to assess planktonic eukaryotic diversity. We provide an explanation for this lineage dependency, which suggests that most species with large effective population sizes will show far less divergence in 18S than protein coding sequences.<br><br>CONCLUSIONS: There is therefore a trade-off between using genes that are easy to amplify in all species, but which by their nature are highly conserved and underestimate the true number of species, and using genes that give a better description of the number of species, but which are more difficult to amplify. We have shown that this trade-off differs between unicellular and multicellular organisms as a likely consequence of differences in effective population sizes. We anticipate that biodiversity of microbial eukaryotic species is underestimated and that numerous "cryptic species" will become discernable with the future acquisition of genomic and metagenomic sequences.},
}
@article {pmid21347329,
year = {2011},
author = {Buchheim, MA and Keller, A and Koetschan, C and Förster, F and Merget, B and Wolf, M},
title = {Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: towards an automated reconstruction of the green algal tree of life.},
journal = {PloS one},
volume = {6},
number = {2},
pages = {e16931},
pmid = {21347329},
issn = {1932-6203},
mesh = {Automation ; Base Sequence ; Chlorophyta/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; *Phylogeny ; RNA, Ribosomal/*genetics ; },
abstract = {BACKGROUND: Chloroplast-encoded genes (matK and rbcL) have been formally proposed for use in DNA barcoding efforts targeting embryophytes. Extending such a protocol to chlorophytan green algae, though, is fraught with problems including non homology (matK) and heterogeneity that prevents the creation of a universal PCR toolkit (rbcL). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta.<br><br>Sequences and secondary structures from 591 chlorophycean, 741 trebouxiophycean and 938 ulvophycean algae, all obtained from the ITS2 Database, were aligned using a sequence structure-specific scoring matrix. Phylogenetic relationships were reconstructed by Profile Neighbor-Joining coupled with a sequence structure-specific, general time reversible substitution model. Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses.<br><br>CONCLUSIONS/SIGNIFICANCE: Our observations on the power of automated, sequence-structure analyses of ITS2 to reconstruct phylum-level phylogenies of the green algae validate this approach to assessing diversity for large sets of chlorophytan taxa. Moreover, our results indicate that objections to the use of ITS2 for DNA barcoding should be weighed against the utility of an automated, data analysis approach with demonstrated power to reconstruct evolutionary patterns for highly divergent lineages.},
}
@article {pmid21346791,
year = {2011},
author = {Zhou, J and Wu, L and Deng, Y and Zhi, X and Jiang, YH and Tu, Q and Xie, J and Van Nostrand, JD and He, Z and Yang, Y},
title = {Reproducibility and quantitation of amplicon sequencing-based detection.},
journal = {The ISME journal},
volume = {5},
number = {8},
pages = {1303-1313},
pmid = {21346791},
issn = {1751-7370},
mesh = {Climate Change ; DNA, Bacterial/genetics ; Metagenomics/*methods ; Oklahoma ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; Shewanella/genetics/*isolation &amp; purification ; *Soil Microbiology ; },
abstract = {To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined. Genomic DNA obtained from each community was used to amplify 16S rRNA genes with two or three barcode tags as technical replicates in the presence of a small quantity (0.1% wt/wt) of genomic DNA from Shewanella oneidensis MR-1 as the control. The technical reproducibility of the amplicon sequencing-based detection approach is quite low, with an average operational taxonomic unit (OTU) overlap of 17.2%±2.3% between two technical replicates, and 8.2%±2.3% among three technical replicates, which is most likely due to problems associated with random sampling processes. Such variations in technical replicates could have substantial effects on estimating β-diversity but less on α-diversity. A high variation was also observed in the control across different samples (for example, 66.7-fold for the forward primer), suggesting that the amplicon sequencing-based detection approach could not be quantitative. In addition, various strategies were examined to improve the comparability of amplicon sequencing data, such as increasing biological replicates, and removing singleton sequences and less-representative OTUs across biological replicates. Finally, as expected, various statistical analyses with preprocessed experimental data revealed clear differences in the composition and structure of microbial communities between warming and non-warming, or between clipping and non-clipping. Taken together, these results suggest that amplicon sequencing-based detection is useful in analyzing microbial community structure even though it is not reproducible and quantitative. However, great caution should be taken in experimental design and data interpretation when the amplicon sequencing-based detection approach is used for quantitative analysis of the β-diversity of microbial communities.},
}
@article {pmid21339964,
year = {2010},
author = {Bala, K and Robideau, GP and Désaulniers, N and de Cock, AW and Lévesque, CA},
title = {Taxonomy, DNA barcoding and phylogeny of three new species of Pythium from Canada.},
journal = {Persoonia},
volume = {25},
number = {},
pages = {22-31},
pmid = {21339964},
issn = {1878-9080},
abstract = {Three new species of Pythium, namely, P. oopapillum, P. emineosum and P. camurandrum are presented in this paper based on morphological descriptions and molecular phylogenetic characterisation. These new species were isolated from various ecological regions in Canada. They have unique morphological features in the genus Pythium, and form distinct clades in maximum parsimony analyses, which are also supported by maximum likelihood phylogeny using general time reversible model (GTR), and Bayesian inference (BI) phylogeny using Markov Chain Monte Carlo (MCMC) analysis methods. A comparative study of the new species with closely related taxa, their clade positions, and morphological features are described in this paper.},
}
@article {pmid21336507,
year = {2011},
author = {Krüger, M and Walker, C and Schüßler, A},
title = {Acaulospora brasiliensis comb. nov. and Acaulospora alpina (Glomeromycota) from upland Scotland: morphology, molecular phylogeny and DNA-based detection in roots.},
journal = {Mycorrhiza},
volume = {21},
number = {6},
pages = {577-587},
pmid = {21336507},
issn = {1432-1890},
mesh = {DNA, Fungal/*genetics ; DNA, Ribosomal Spacer/genetics ; Glomeromycota/*classification/genetics/growth &amp; development/*isolation &amp; purification ; Molecular Sequence Data ; Mycological Typing Techniques ; Mycorrhizae/*classification/genetics/growth &amp; development/*isolation &amp; purification ; Phylogeny ; Plant Roots/*microbiology ; Plants/microbiology ; Scotland ; *Soil Microbiology ; Spores, Fungal/classification/genetics/growth &amp; development/isolation &amp; purification ; },
abstract = {Spores of two supposedly arbuscular mycorrhizal fungal species, new to the United Kingdom and recently described as Acaulospora alpina and Ambispora brasiliensis (Glomeromycota), were discovered in soil samples from moorland in upland Scotland. Soil and plant trap pot cultures were established, but attempts to establish these fungi in single-species pot cultures with Plantago lanceolata as host were unsuccessful. Nevertheless, based on a 1.5-kb DNA fragment spanning part of the small subunit rRNA gene, the internal transcribed spacer region and part of the large subunit rRNA gene, both these species could be detected directly in field-sampled roots, together with one uncultured species each of Scutellospora, Rhizophagus (former Glomus group Ab, or 'Glomus intraradices clade') and Acaulospora. Whereas A. alpina has characteristic morphological similarities to other species in its genus, A. brasiliensis morphologically has little in common with any other species in Ambispora. The molecular phylogeny, DNA barcoding and morphological evidence clearly place A. brasiliensis in the genus Acaulospora. We therefore rename the species, reported from Brazil and Scotland, as Acaulospora brasiliensis comb. nov., and discuss ecological aspects of the very different environments from which A. brasiliensis and A. alpina have been reported.},
}
@article {pmid21329214,
year = {2011},
author = {Bucklin, A and Steinke, D and Blanco-Bercial, L},
title = {DNA barcoding of marine metazoa.},
journal = {Annual review of marine science},
volume = {3},
number = {},
pages = {471-508},
doi = {10.1146/annurev-marine-120308-080950},
pmid = {21329214},
issn = {1941-1405},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Ecosystem ; *Genetic Variation ; Oceans and Seas ; Phylogeography ; },
abstract = {More than 230,000 known species representing 31 metazoan phyla populate the world's oceans. Perhaps another 1,000,000 or more species remain to be discovered. There is reason for concern that species extinctions may out-pace discovery, especially in diverse and endangered marine habitats such as coral reefs. DNA barcodes (i.e., short DNA sequences for species recognition and discrimination) are useful tools to accelerate species-level analysis of marine biodiversity and to facilitate conservation efforts. This review focuses on the usual barcode region for metazoans: a approximately 648 base-pair region of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Barcodes have also been used for population genetic and phylogeographic analysis, identification of prey in gut contents, detection of invasive species, forensics, and seafood safety. More controversially, barcodes have been used to delimit species boundaries, reveal cryptic species, and discover new species. Emerging frontiers are the use of barcodes for rapid and increasingly automated biodiversity assessment by high-throughput sequencing, including environmental barcoding and the use of barcodes to detect species for which formal identification or scientific naming may never be possible.},
}
@article {pmid21322556,
year = {2011},
author = {Xiao, WL and Motley, TJ and Unachukwu, UJ and Lau, CB and Jiang, B and Hong, F and Leung, PC and Wang, QF and Livingston, PO and Cassileth, BR and Kennelly, EJ},
title = {Chemical and genetic assessment of variability in commercial Radix Astragali (Astragalus spp.) by ion trap LC-MS and nuclear ribosomal DNA barcoding sequence analyses.},
journal = {Journal of agricultural and food chemistry},
volume = {59},
number = {5},
pages = {1548-1556},
pmid = {21322556},
issn = {1520-5118},
support = {P50 AT002779/AT/NCCIH NIH HHS/United States ; P50 AT002779-05/AT/NCCIH NIH HHS/United States ; P50AT002779/AT/NCCIH NIH HHS/United States ; },
mesh = {Astragalus Plant/chemistry/classification/genetics ; Astragalus propinquus ; Chromatography, Liquid ; *DNA Barcoding, Taxonomic ; DNA, Plant/analysis/chemistry ; DNA, Ribosomal/*chemistry ; Drugs, Chinese Herbal/*chemistry/classification ; Flavonoids/analysis ; Genetic Variation ; Hong Kong ; Mass Spectrometry ; New York City ; Phytotherapy ; Quality Control ; Saponins/analysis ; },
abstract = {Radix Astragali (Huangqi) has been demonstrated to have a wide range of immunopotentiating effects and has been used as an adjuvant medicine during cancer therapy. Identity issues in the collection of Radix Astragali exist because many sympatric species of Astragalus occur in the northern regions of China. In order to assess the quality, purity, and uniformity of commercial Radix Astragali, 44 samples were purchased from herbal stores in Hong Kong and New York City. The main constituents, including four isoflavonoids and three saponins, were quantitatively determined by liquid chromatography mass spectrometry (LC-MS). There was significant sample-to-sample variability in the amounts of the saponins and isoflavonoids measured. Furthermore, DNA barcoding utilizing the variable nuclear ITS spacer regions of the 44 purchased Radix Astragali samples were sequenced, aligned and compared. Eight polymorphic point mutations were identified which separated the Radix Astragali samples into three groups. These results indicate that the chemical and genetic variability that exists among Radix Astragali medicinal products is still a consistency and quality issue for this herbal. Two-way ANOVA analysis showed significant effects on the contents of the seven tested compounds when both phylogenetic and geographic (i.e., point of purchase) factors were considered. Therefore, chemical profiles determined by LC-MS and DNA profiles in ITS spacer domains could serve as barcode markers for quality control of Radix Astragali.},
}
@article {pmid21322295,
year = {2010},
author = {Rubin, AD and McFerran, VA},
title = {The road to electronic health records is paved with operations.},
journal = {The American journal of managed care},
volume = {16},
number = {12 Suppl HIT},
pages = {e289-92},
pmid = {21322295},
issn = {1936-2692},
mesh = {Academic Medical Centers ; Efficiency, Organizational ; Electronic Health Records/*organization &amp; administration ; Humans ; Interdisciplinary Communication ; Los Angeles ; Medical Errors/prevention &amp; control ; Organizational Innovation ; *Quality of Health Care/legislation &amp; jurisprudence ; United States ; },
abstract = {The University of California, Los Angeles (UCLA) Health System seeks to align its purpose of "healing humankind" with its approaches for people and performance management. These approaches include lean process improvements initiatives, sustained by efforts to impact daily team member work flows. The electronic health record (EHR) serves as a powerful supportive instrument in improving processes and sustaining performance. For UCLA, the secret to EHR effectiveness lies in creating win-win situations, where organizational objectives are achieved and team member work flows also are improved. Recent UCLA initiatives with medication bar-coding and a stroke telemedicine network highlight such opportunities. Carried out on a national level, such efforts can significantly affect healthcare in the United States. The US Recovery and Reinvestment Act of 2009's EHR provisions provide a national impetus for broad improvements in healthcare.},
}
@article {pmid21308611,
year = {2011},
author = {Cordell, GA},
title = {Sustainable medicines and global health care.},
journal = {Planta medica},
volume = {77},
number = {11},
pages = {1129-1138},
doi = {10.1055/s-0030-1270731},
pmid = {21308611},
issn = {1439-0221},
mesh = {*Conservation of Natural Resources ; Delivery of Health Care/*organization &amp; administration ; Humans ; Medicine, Traditional ; Phytotherapy ; Plant Extracts/chemistry ; Plants, Medicinal/chemistry/*growth &amp; development ; Principal Component Analysis ; World Health Organization ; },
abstract = {The global population has now exceeded 7 billion, and forests and other resources around the world are being irreversibly depleted for energy, food, shelter, material goods, and drugs to accommodate population needs. For most of the world's population, plants, based on many well-established systems of medicine, in either crude or extract form, represent the foundation of primary health care for the foreseeable future. Contemporary harvesting methods for medicinal plants are severely depleting these critical indigenous resources. However, maintaining and enhancing the availability of quality medicinal agents on a sustainable basis is an unappreciated public health care concept. To accomplish these goals for future health care, and restore the health of the Earth, a profound paradigm shift is necessary: ALL medicinal agents should be regarded as a sustainable commodity, irrespective of their source. Several approaches to enhancing the availability of safe and efficacious plant-based medicinal agents will be presented including integrated strategies to manifest the four pillars (information, botany, chemistry, and biology) for medicinal plant quality control. These integrated initiatives involve information systems, DNA barcoding, metabolomics, biotechnology, nanotechnology, in-field analysis of medicinal plants, and the application of new detection techniques for the development of medicinal plants with enhanced levels of safe and reproducible biological agents.},
}
@article {pmid21299446,
year = {2011},
author = {Lowenstein, JH and Osmundson, TW and Becker, S and Hanner, R and Stiassny, ML},
title = {Incorporating DNA barcodes into a multi-year inventory of the fishes of the hyperdiverse Lower Congo River, with a multi-gene performance assessment of the genus Labeo as a case study.},
journal = {Mitochondrial DNA},
volume = {22 Suppl 1},
number = {},
pages = {52-70},
doi = {10.3109/19401736.2010.537748},
pmid = {21299446},
issn = {1940-1744},
mesh = {Animals ; Base Sequence ; Congo ; Cyprinidae/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*genetics ; Democratic Republic of the Congo ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Fish Proteins/genetics ; Fishes/*classification/genetics ; Homeodomain Proteins/genetics ; Molecular Sequence Data ; Phylogeny ; *Rivers ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND AND AIMS: Here we describe preliminary efforts to integrate DNA barcoding into an ongoing inventory of the Lower Congo River (LCR) ichthyofauna. The 350 km stretch of the LCR from Pool Malebo to Boma includes the world's largest river rapids. The LCR ichthyofauna is hyperdiverse and rich in endemism due to high habitat heterogeneity, numerous dispersal barriers, and its downstream location in the basin.<br><br>MATERIALS AND METHODS: We have documented 328 species from the LCR, 25% of which are thought to be endemic. In addition to detailing progress made to generate a reference sequence library of DNA barcodes for these fishes, we ask how DNA can be used at the current stage of the Fish Barcode of Life initiative, as a work in progress currently of limited utility to a wide audience. Two possibilities that we explore are the potential for DNA barcodes to generate discrete diagnostic characters for species, and to help resolve problematic taxa lacking clear morphologically diagnostic characters such as many species of the cyprinid genus Labeo, which we use as a case study.<br><br>RESULTS: Our molecular analysis helped to clarify the validity of some species that were the subject of historical debate, and we were able to construct a molecular key for all monophyletic and morphologically recognizable species. Several species sampled from across the Congo Basin and widely distributed throughout Central and West Africa were recovered as paraphyletic based on our molecular data.<br><br>CONCLUSION: Our study underscores the importance of generating reference barcodes for specimens collected from, or in close proximity to, type localities, particularly where species are poorly understood taxonomically and the extent of their geographical distributions have yet to be established.},
}
@article {pmid21298108,
year = {2011},
author = {de Groot, GA and During, HJ and Maas, JW and Schneider, H and Vogel, JC and Erkens, RH},
title = {Use of rbcL and trnL-F as a two-locus DNA barcode for identification of NW-European ferns: an ecological perspective.},
journal = {PloS one},
volume = {6},
number = {1},
pages = {e16371},
pmid = {21298108},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic ; *Ecosystem ; Europe ; Ferns/*classification/*genetics ; Genetic Markers ; Ribulose-Bisphosphate Carboxylase/genetics ; },
abstract = {Although consensus has now been reached on a general two-locus DNA barcode for land plants, the selected combination of markers (rbcL + matK) is not applicable for ferns at the moment. Yet especially for ferns, DNA barcoding is potentially of great value since fern gametophytes--while playing an essential role in fern colonization and reproduction--generally lack the morphological complexity for morphology-based identification and have therefore been underappreciated in ecological studies. We evaluated the potential of a combination of rbcL with a noncoding plastid marker, trnL-F, to obtain DNA-identifications for fern species. A regional approach was adopted, by creating a reference database of trusted rbcL and trnL-F sequences for the wild-occurring homosporous ferns of NW-Europe. A combination of parsimony analyses and distance-based analyses was performed to evaluate the discriminatory power of the two-region barcode. DNA was successfully extracted from 86 tiny fern gametophytes and was used as a test case for the performance of DNA-based identification. Primer universality proved high for both markers. Based on the combined rbcL + trnL-F dataset, all genera as well as all species with non-equal chloroplast genomes formed their own well supported monophyletic clade, indicating a high discriminatory power. Interspecific distances were larger than intraspecific distances for all tested taxa. Identification tests on gametophytes showed a comparable result. All test samples could be identified to genus level, species identification was well possible unless they belonged to a pair of Dryopteris species with completely identical chloroplast genomes. Our results suggest a high potential of the combined use of rbcL and trnL-F as a two-locus cpDNA barcode for identification of fern species. A regional approach may be preferred for ecological tests. We here offer such a ready-to-use barcoding approach for ferns, which opens the way for answering a whole range of questions previously unaddressed in fern gametophyte ecology.},
}
@article {pmid21295460,
year = {2011},
author = {Aliaga, C and Ferreira, B and Hortal, M and Pancorbo, M&#xc1; and López, JM and Navas, FJ},
title = {Influence of RFID tags on recyclability of plastic packaging.},
journal = {Waste management (New York, N.Y.)},
volume = {31},
number = {6},
pages = {1133-1138},
doi = {10.1016/j.wasman.2010.12.015},
pmid = {21295460},
issn = {1879-2456},
mesh = {Materials Testing ; *Plastics ; *Radio Frequency Identification Device ; Recycling/*methods ; Refuse Disposal/*methods ; },
abstract = {The use of Radio Frequency IDentification Technology (RFID) in the packaging sector is an important logistical improvement regarding the advantages offered by this technology in comparison with barcodes. Nevertheless, the presence of these devices in plastic packaging, and consequently in plastic waste, can cause several problems in the recycling plants due to the materials included in these devices. In this study, the mentioned recycling constraints have been experimentally identified in a pilot scale recycling study consisting in three recycling tests with an increasing presence of RFID tags. Differences in each test were evaluated. Furthermore, the quality of the recycled material of each test was studied through the injection and testing of tests probes. The results of the pilot scale recycling tests did not show a decrease in the quality of the recycled plastic due to the presence of RFID tags. Nevertheless, several operational problems during the recycling process were observed such as the obstruction of the screens, which lessened the process yield and created process interruptions, as well as the loss of extruded plastic during the process. These recycling constraints cannot be directly extrapolated to the industrial plants due to the different working scales. Nevertheless, technological solutions are proposed in order to avoid these recycling constraints if they appear.},
}
@article {pmid21289109,
year = {2011},
author = {Lauring, AS and Andino, R},
title = {Exploring the fitness landscape of an RNA virus by using a universal barcode microarray.},
journal = {Journal of virology},
volume = {85},
number = {8},
pages = {3780-3791},
pmid = {21289109},
issn = {1098-5514},
support = {R01 AI40085/AI/NIAID NIH HHS/United States ; R01 AI36178/AI/NIAID NIH HHS/United States ; R01 AI036178/AI/NIAID NIH HHS/United States ; K08 AI081754-01/AI/NIAID NIH HHS/United States ; R01 AI040085/AI/NIAID NIH HHS/United States ; K08 AI081754/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; *Biodiversity ; Disease Models, Animal ; HeLa Cells ; Humans ; Mice ; Microarray Analysis/*methods ; Poliovirus/genetics/*growth &amp; development/*pathogenicity ; Virulence ; },
abstract = {Studies of viral pathogenesis have relied heavily on analyses of specific clones and their genetic determinants of virulence. It is sometimes difficult to apply this reductionist approach to the study of RNA viruses, which by virtue of their very high mutation rates, exist as a complex mixture of mutants. While quasispecies theory has provided an intellectual framework for exploring the relationship between the viral population structure and phenotype, experimental studies have been limited by the relatively poor resolution of traditional sequencing-based approaches. We have addressed this problem by developing a molecular barcoding strategy in which viral subpopulations are tagged with unique 20-nucleotide sequences. The behavior of these subpopulations can be monitored using a universal barcode microarray. We demonstrate the performance of our barcode microarray platform using poliovirus, a model RNA virus. Using this platform, we explored the fitness landscape occupied by an artificial quasispecies consisting of 48 randomly mutagenized clones. We were able to rapidly derive precise fitness measurements for a majority of these clones and identified a neutral space surrounding the wild type. The experimental paradigm presented here is readily adaptable to other viral systems and can potentially be used to track thousands of variants in a cost-effective manner.},
}
@article {pmid21289107,
year = {2011},
author = {Lindner, DL and Banik, MT},
title = {Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus.},
journal = {Mycologia},
volume = {103},
number = {4},
pages = {731-740},
doi = {10.3852/10-331},
pmid = {21289107},
issn = {0027-5514},
mesh = {Base Sequence ; DNA, Fungal/*genetics ; DNA, Ribosomal Spacer/*genetics ; Evolution, Molecular ; Genetic Variation ; Microsatellite Repeats ; Phylogeny ; Polyporales/classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {Regions of rDNA are commonly used to infer phylogenetic relationships among fungal species and as DNA barcodes for identification. These regions occur in large tandem arrays, and concerted evolution is believed to reduce intragenomic variation among copies within these arrays, although some variation still might exist. Phylogenetic studies typically use consensus sequencing, which effectively conceals most intragenomic variation, but cloned sequences containing intragenomic variation are becoming prevalent in DNA databases. To understand effects of using cloned rDNA sequences in phylogenetic analyses we amplified and cloned the ITS region from pure cultures of six Laetiporus species and one Wolfiporia species (Basidiomycota, Polyporales). An average of 66 clones were selected randomly and sequenced from 21 cultures, producing a total of 1399 interpretable sequences. Significant variation (≥ 5% variation in sequence similarity) was observed among ITS copies within six cultures from three species clades (L. cincinnatus, L. sp. clade J, and Wolfiporia dilatohypha) and phylogenetic analyses with the cloned sequences produced different trees relative to analyses with consensus sequences. Cloned sequences from L. cincinnatus fell into more than one species clade and numerous cloned L. cincinnatus sequences fell into entirely new clades, which if analyzed on their own most likely would be recognized as "undescribed" or "novel" taxa. The use of a 95% cut off for defining operational taxonomic units (OTUs) produced seven Laetiporus OTUs with consensus ITS sequences and 20 OTUs with cloned ITS sequences. The use of cloned rDNA sequences might be problematic in fungal phylogenetic analyses, as well as in fungal bar-coding initiatives and efforts to detect fungal pathogens in environmental samples.},
}
@article {pmid21281222,
year = {2011},
author = {Doukakis, P and Hanner, R and Shivji, M and Bartholomew, C and Chapman, D and Wong, E and Amato, G},
title = {Applying genetic techniques to study remote shark fisheries in northeastern Madagascar.},
journal = {Mitochondrial DNA},
volume = {22 Suppl 1},
number = {},
pages = {15-20},
doi = {10.3109/19401736.2010.526112},
pmid = {21281222},
issn = {1940-1744},
mesh = {Animal Fins ; Animals ; Bays ; *Conservation of Natural Resources ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer ; Electron Transport Complex IV/genetics ; *Fisheries ; Genetic Techniques ; Madagascar ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; Population Density ; Sequence Analysis, DNA ; Sharks/*classification/*genetics/physiology ; Species Specificity ; },
abstract = {BACKGROUND AND AIMS: The shark fisheries of Madagascar remain largely unstudied. Remoteness makes fisheries monitoring challenging while the high value of shark fins combined with the extreme poverty in Madagascar creates intensive pressure on shark resources.<br><br>MATERIALS AND METHODS: We use DNA barcoding and species-specific PCR assays to characterize shark fisheries in Antongil Bay in northeastern Madagascar.<br><br>RESULTS: The 239 samples taken from individuals collected in 2001 and 2002 correspond to 19 species. The four most common species were Sphyrna lewini, Rhizoprionodon acutus, Carcharhinus brevipinna, and C. sorrah. Antongil Bay may be a breeding area for C. brevipinna, C. leucas, and S. lewini.<br><br>CONCLUSION: Local names are generally not a useful proxy for monitoring the species harvested in the fishery. Conservation efforts should characterize species exploitation at present, create spatial and temporal fishing restrictions to protect endangered species, and restrict large mesh gillnets.},
}
@article {pmid21277124,
year = {2011},
author = {Dalton, DL and Kotze, A},
title = {DNA barcoding as a tool for species identification in three forensic wildlife cases in South Africa.},
journal = {Forensic science international},
volume = {207},
number = {1-3},
pages = {e51-4},
doi = {10.1016/j.forsciint.2010.12.017},
pmid = {21277124},
issn = {1872-6283},
mesh = {Animals ; Conservation of Natural Resources/*legislation &amp; jurisprudence ; Crime/*legislation &amp; jurisprudence ; *DNA Barcoding, Taxonomic ; DNA Primers ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Polymerase Chain Reaction ; Ruminants/*genetics ; South Africa ; Species Specificity ; },
abstract = {Poaching of wildlife animals for subsistence and commercial purposes has lead to population declines in Africa. In forensic cases, a need exists to identify the species of origin of carcasses, meat or blood. In the study presented here, the mitochondrial COI gene was sequenced to determine the species of unknown samples in three suspect South African forensic wildlife cases. In two cases the unknown samples were identified as originating from domestic cattle (Bos taurus) and in the third case the sample was identified as common reedbuck (Redunca arundinum). This is the first report of the COI sequence of common reedbuck. The study highlights the need for accurate wildlife reference material from each country in order to convict wildlife cases.},
}
@article {pmid21276253,
year = {2011},
author = {Luo, A and Zhang, A and Ho, SY and Xu, W and Zhang, Y and Shi, W and Cameron, SL and Zhu, C},
title = {Potential efficacy of mitochondrial genes for animal DNA barcoding: a case study using eutherian mammals.},
journal = {BMC genomics},
volume = {12},
number = {},
pages = {84},
pmid = {21276253},
issn = {1471-2164},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Genome, Mitochondrial/genetics ; Mammals/classification/*genetics ; },
abstract = {BACKGROUND: A well-informed choice of genetic locus is central to the efficacy of DNA barcoding. Current DNA barcoding in animals involves the use of the 5' half of the mitochondrial cytochrome oxidase 1 gene (CO1) to diagnose and delimit species. However, there is no compelling a priori reason for the exclusive focus on this region, and it has been shown that it performs poorly for certain animal groups. To explore alternative mitochondrial barcoding regions, we compared the efficacy of the universal CO1 barcoding region with the other mitochondrial protein-coding genes in eutherian mammals. Four criteria were used for this comparison: the number of recovered species, sequence variability within and between species, resolution to taxonomic levels above that of species, and the degree of mutational saturation.<br><br>RESULTS: Based on 1,179 mitochondrial genomes of eutherians, we found that the universal CO1 barcoding region is a good representative of mitochondrial genes as a whole because the high species-recovery rate (> 90%) was similar to that of other mitochondrial genes, and there were no significant differences in intra- or interspecific variability among genes. However, an overlap between intra- and interspecific variability was still problematic for all mitochondrial genes. Our results also demonstrated that any choice of mitochondrial gene for DNA barcoding failed to offer significant resolution at higher taxonomic levels.<br><br>CONCLUSIONS: We suggest that the CO1 barcoding region, the universal DNA barcode, is preferred among the mitochondrial protein-coding genes as a molecular diagnostic at least for eutherian species identification. Nevertheless, DNA barcoding with this marker may still be problematic for certain eutherian taxa and our approach can be used to test potential barcoding loci for such groups.},
}
@article {pmid21272395,
year = {2011},
author = {Park, DS and Suh, SJ and Hebert, PD and Oh, HW and Hong, KJ},
title = {DNA barcodes for two scale insect families, mealybugs (Hemiptera: Pseudococcidae) and armored scales (Hemiptera: Diaspididae).},
journal = {Bulletin of entomological research},
volume = {101},
number = {4},
pages = {429-434},
doi = {10.1017/S0007485310000714},
pmid = {21272395},
issn = {1475-2670},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Hemiptera/classification/*genetics ; Male ; },
abstract = {Although DNA barcode coverage has grown rapidly for many insect orders, there are some groups, such as scale insects, where sequence recovery has been difficult. However, using a recently developed primer set, we recovered barcode records from 373 specimens, providing coverage for 75 species from 31 genera in two families. Overall success was >90% for mealybugs and >80% for armored scale species. The G·C content was very low in most species, averaging just 16.3%. Sequence divergences (K2P) between congeneric species averaged 10.7%, while intra-specific divergences averaged 0.97%. However, the latter value was inflated by high intra-specific divergence in nine taxa, cases that may indicate species overlooked by current taxonomic treatments. Our study establishes the feasibility of developing a comprehensive barcode library for scale insects and indicates that its construction will both create an effective system for identifying scale insects and reveal taxonomic situations worthy of deeper analysis.},
}
@article {pmid21271859,
year = {2010},
author = {Nicolalde-Morejón, F and Vergara-Silva, F and González-Astorga, J and Stevenson, DW},
title = {Character-based, population-level DNA barcoding in Mexican species of Zamia L. (Zamiaceae: Cycadales).},
journal = {Mitochondrial DNA},
volume = {21 Suppl 1},
number = {},
pages = {51-59},
doi = {10.3109/19401736.2010.539215},
pmid = {21271859},
issn = {1940-1744},
mesh = {*DNA Barcoding, Taxonomic/methods ; DNA, Chloroplast/genetics ; DNA, Intergenic/genetics ; DNA, Plant/*genetics ; Genes, Plant ; Mexico ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; Zamiaceae/*classification/*genetics ; },
abstract = {BACKGROUND AND AIMS: With the recent proposal of matK and rbcL as core plant DNA barcoding regions by the Consortium for the Barcoding of Life Plant Working Group, the construction of reference libraries in the botanical DNA barcoding initiative has entered a new phase. However, in a recent DNA barcoding study in the three Mexican genera of the gymnosperm order Cycadales, we found that neither matK nor rbcL allow high levels of molecular identification of previously established species.<br><br>MATERIALS AND METHODS: Our data analysis in that study rested on the "Characteristic Attributes Organization System" (CAOS), a character-based algorithm for the definition of "DNA diagnostics." Here, we use CAOS to analyze a population-level molecular data set in Zamia, one of the three cycad genera occurring in Mexico, whose populations display contrasting biogeographic patterns. Our population-level study, which includes all species in the region formally known as Megamexico, is restricted to the genome region, which showed the best single-locus molecular identification performance in our previous study-namely, the noncoding intergenic chloroplast spacer psbK-I.<br><br>RESULTS: Our comparison of single-individual vs. population-level psbK-I datasets in Zamia indicates that CAOS analyses are sensitive to slight alignment changes, which in turn derive from the different amounts of molecular variation present in each matrix type.<br><br>CONCLUSION: We, therefore, suggest that character-based studies that involve population-level data should contemplate this type of comparison between data matrices, before a set of DNA diagnostics in a given DNA barcoding reference library is considered definitive.},
}
@article {pmid21271858,
year = {2010},
author = {Cervantes, FA and Arcangeli, J and Hortelano-Moncada, Y and Borisenko, AV},
title = {DNA barcodes effectively identify the morphologically similar Common Opossum (Didelphis marsupialis) and Virginia Opossum (Didelphis virginiana) from areas of sympatry in Mexico.},
journal = {Mitochondrial DNA},
volume = {21 Suppl 1},
number = {},
pages = {44-50},
doi = {10.3109/19401736.2010.538051},
pmid = {21271858},
issn = {1940-1744},
mesh = {Animals ; Base Sequence ; *DNA Barcoding, Taxonomic ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics ; Didelphis/anatomy &amp; histology/*classification/*genetics ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial ; Mexico ; Phylogeny ; Species Specificity ; },
abstract = {Two morphologically similar species of opossum from the genus Didelphis-Didelphis virginiana and Didelphis marsupialis-cooccur sympatrically in Mexico. High intraspecific variation complicates their morphological discrimination, under both field and museum conditions. This study aims to evaluate the utility and reliability of using DNA barcodes (short standardized genome fragments used for DNA-based identification) to distinguish these two species. Sequences of the cytochrome c oxidase subunit I (Cox1) mitochondrial gene were obtained from 12 D. marsupialis and 29 D. virginiana individuals and were compared using the neighbor-joining (NJ) algorithm with Kimura's two-parameter (K2P) model of nucleotide substitution. Average K2P distances were 1.56% within D. virginiana and 1.65% in D. marsupialis. Interspecific distances between D. virginiana and D. marsupialis varied from 7.8 to 9.3% and their barcode sequences formed distinct non-overlapping clusters on NJ trees. All sympatric specimens of both species were effectively discriminated, confirming the utility of Cox1 barcoding as a tool for taxonomic identification of these morphologically similar taxa.},
}
@article {pmid21271857,
year = {2010},
author = {Engstrand, RC and Cibrián Tovar, J and Cibrián-Jaramillo, A and Kolokotronis, SO},
title = {Genetic variation in avocado stem weevils Copturus aguacatae (Coleoptera: Curculionidae) in Mexico.},
journal = {Mitochondrial DNA},
volume = {21 Suppl 1},
number = {},
pages = {38-43},
doi = {10.3109/19401736.2010.536226},
pmid = {21271857},
issn = {1940-1744},
mesh = {Animals ; Base Sequence ; *DNA Barcoding, Taxonomic ; DNA Primers/genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Genes, Insect ; Genes, Mitochondrial ; Genetic Variation ; Haplotypes ; Insect Proteins/genetics ; Mexico ; Persea/*parasitology ; Phylogeny ; Weevils/classification/enzymology/*genetics/pathogenicity ; },
abstract = {BACKGROUND AND AIM: The avocado stem weevil Copturus aguacatae is an important pest in avocado plantations. Its presence hinders the production and marketing of avocado in Mexico, the largest avocado producer worldwide. Biological control through pheromone synthesis, a strategy favored over chemical control in crops, is currently limited by difficult field identification of this species.<br><br>MATERIALS AND METHODS: Using DNA barcoding, we examine the patterns of genetic variation of C. aguacatae in avocado trees in Mexico to help facilitate its identification and biological control.<br><br>RESULTS: We show that there is one single species of avocado stem weevil throughout the sampled sites in Mexico. Overall, haplotype diversity is high, with Oaxaca forming one distinct group and all other sampled populations are admixed irrespective of geographic origin.<br><br>CONCLUSION: The results suggest that high gene flow is maintained in this species and that a global strategy for biocontrol can be designed and implemented throughout the sampled range.},
}
@article {pmid21271856,
year = {2010},
author = {Escalante, P and Ibarra-Vazquez, A and Rosas-Escobar, P},
title = {Tropical montane nymphalids in Mexico: DNA barcodes reveal greater diversity.},
journal = {Mitochondrial DNA},
volume = {21 Suppl 1},
number = {},
pages = {30-37},
doi = {10.3109/19401736.2010.535527},
pmid = {21271856},
issn = {1940-1744},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Genes, Insect ; Genes, Mitochondrial ; Genetic Variation ; Insect Proteins/genetics ; Lepidoptera/*classification/enzymology/*genetics ; Mexico ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; Tropical Climate ; },
abstract = {MATERIALS AND METHODS: DNA sequences obtained for the Barcode of Life library in the All Lepidoptera Campaign project Nymphalidae of Central Mexico were analyzed as a test of species limits and to explore possible phylogenetic groupings in the Preponini tribe. Using specimens in the National Insect Collection of the Instituto de Biología of the Universidad Nacional Autónoma de México, 78 specimens were assayed for cytochrome oxidase c subunit 1.<br><br>RESULTS: Disregarding the missing data, there were 458 conserved sites, 200 variable sites and 187 parsimony-informative sites. The neighbor-joining and maximum likelihood analyses indicate that none of the three genera of Preponini as currently circumscribed are reciprocally monophyletic. As per species limits, high levels of barcode variation in the Prepona deiphile complex suggest the existence of at least two new endemic species to Mexico. The divergent taxa were escalantiana from the Tuxtlas region in Veracruz, and ibarra from Sierra Madre del Sur in the Pacific states of southern Mexico. The genetic distance in the CO1 fragment between them and the other deiphile populations ranged from 2.7 to 8.0%.<br><br>CONCLUSION: We recommend that morphological data need to be re-examined and that additional molecular data for species ought to be gathered before a particular biogeographic model can be proposed for the group in Mesoamerica.},
}
@article {pmid21271855,
year = {2010},
author = {Oceguera-Figueroa, A and León-Règagnon, V and Siddall, ME},
title = {DNA barcoding reveals Mexican diversity within the freshwater leech genus Helobdella (Annelida: Glossiphoniidae).},
journal = {Mitochondrial DNA},
volume = {21 Suppl 1},
number = {},
pages = {24-29},
doi = {10.3109/19401736.2010.527965},
pmid = {21271855},
issn = {1940-1744},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; Genetic Variation ; Leeches/*classification/enzymology/*genetics ; Mexico ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; },
abstract = {We investigated the genetic distances and taxonomic status among species of Helobdella, a genus of non-blood-feeding leeches, based on mitochondrial cytochrome c oxidase subunit I sequences. Sampling included 20 specimens representing nine nominal species collected in 11 states in Mexico as well as previously published sequences of different species of Helobdella from several places. A neighbor-joining tree, as well as identification of diagnostic nucleotides, was used to suggest the presence of seven species of Helobdella in Mexico including potentially two undescribed forms.},
}
@article {pmid21271854,
year = {2010},
author = {Zaldívar-Riverón, A and Martínez, JJ and Ceccarelli, FS and De Jesús-Bonilla, VS and Rodríguez-Pérez, AC and Reséndiz-Flores, A and Smith, MA},
title = {DNA barcoding a highly diverse group of parasitoid wasps (Braconidae: Doryctinae) from a Mexican nature reserve.},
journal = {Mitochondrial DNA},
volume = {21 Suppl 1},
number = {},
pages = {18-23},
doi = {10.3109/19401736.2010.523701},
pmid = {21271854},
issn = {1940-1744},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Ecosystem ; Evolution, Molecular ; Genes, Insect ; Genes, Mitochondrial ; Mexico ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; Wasps/anatomy &amp; histology/*classification/*genetics/pathogenicity ; },
abstract = {BACKGROUND AND AIMS: The preliminary results of a DNA barcoding study of the doryctine fauna of parasitoid wasps from the Chamela-Cuixmala Biosphere Reserve in Mexico, a region dominated by tropical dry forest, are presented. So far, three field trips have been carried out to the reserve and 468 specimens have been collected, of which 407 cox1 sequences were obtained.<br><br>MATERIALS AND METHODS: The general mixed Yule-coalescent model was applied to a phylogram to investigate the number of evolutionary units that can be detected from the DNA sequence data examined.<br><br>RESULTS: A total of 185 barcoding species assigned to 20 identified doryctine genera were discriminated using the above model, 115 of which belong to the speciose genus Heterospilus, pointing out the extraordinary species richness of this subfamily of insects in a Mexican tropical dry forest.<br><br>CONCLUSION: On the basis of the DNA barcodes generated, Ptesimogastroides Braet &amp; van Achterberg is proposed to be a junior synonym of Ptesimogaster Marsh syn. nov. Neoheterospilus was also found deeply nested within a large Heterospilus clade, suggesting the paraphyly of the latter genus.},
}
@article {pmid21271852,
year = {2010},
author = {Martínez-Salazar, EA and León-Règagnon, V},
title = {Molecular evidence that Langeronia macrocirra and Langeronia cf. parva (Trematoda: Pleurogenidae) parasites of anurans from Mexico are conspecific.},
journal = {Mitochondrial DNA},
volume = {21 Suppl 1},
number = {},
pages = {3-11},
doi = {10.3109/19401736.2010.517835},
pmid = {21271852},
issn = {1940-1744},
mesh = {Animals ; Anura/*parasitology ; Base Sequence ; DNA Barcoding, Taxonomic ; DNA Primers/genetics ; DNA, Helminth/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/*genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Genes, Helminth ; Genes, Mitochondrial ; Helminth Proteins/genetics ; Host-Parasite Interactions/genetics ; Mexico ; Microscopy, Electron, Scanning ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; Trematoda/anatomy &amp; histology/classification/*genetics/*pathogenicity ; },
abstract = {The genus Langeronia parasitizing the intestine of several species of anurans is distributed from North to Central America. We identified Langeronia macrocirra and Langeronia cf. parva from the same host and localities, and present here new data not applicable about their tegumental surface by scanning electron microscopy. We compared sequences of the rDNA ITS2 region and mtDNA cox1 gene for the two morphotypes. ITS2 exhibited a high degree of conservation. Phylogenetic reconstruction using cox1 revealed three clades (I, II, and III), which did not correspond to a previous identification or host. Little divergence was found within clades: sequences were identical in clade I, whereas clade II had 0.27% and clade III had 1.08%. Inter-clade divergence reached 8.69% (I vs. III). This pattern of genetic divergence indicated that both taxa probably belong to the same species, so we posit that the morphological changes could be correlated with development. Increasing sample size and geographical coverage will contribute to the taxonomy of the genus based on morphological and molecular evidence, and will open tracks toward the use of DNA barcodes to the genus in Mexico.},
}
@article {pmid21271850,
year = {2011},
author = {Becker, S and Hanner, R and Steinke, D},
title = {Five years of FISH-BOL: brief status report.},
journal = {Mitochondrial DNA},
volume = {22 Suppl 1},
number = {},
pages = {3-9},
doi = {10.3109/19401736.2010.535528},
pmid = {21271850},
issn = {1940-1744},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods/statistics &amp; numerical data ; DNA, Mitochondrial/analysis/*genetics ; Databases, Genetic ; Electron Transport Complex IV/genetics ; Fishes/*classification/genetics ; *Gene Library ; Internet ; Species Specificity ; },
abstract = {The Fish Barcode of Life Initiative (FISH-BOL) is a concerted global research project launched in 2005, with the goal to collect and assemble standardized DNA barcode sequences and associated voucher provenance data in a curated reference sequence library to aid the molecular identification of all fish species. This article is a detailed progress report (July 2010) on the number of fish species that have been assigned a DNA barcode. Of the approximately 31,000 currently known fish species, 25% have been processed successfully, with at least one species from 89% of all families barcoded; in this report we give a progress overview by taxonomy and geographic region. Using standard analytical protocols, differences in the barcoding completion rate between orders and families are observed, suggesting a potential PCR amplification bias. Overall, between 3 and 9% of the species analyzed failed to yield a "BARCODE compliant" sequence, depending upon how the data are filtered. When species with only a single representative specimen are included, the failure rate was 9%. This might derive from several sources such as mismatched primers and degraded DNA templates. In an attempt to account for the latter, when the analysis is restricted to species with at least two specimens examined, the observed failure rate is significantly lower (3%), suggesting that template quality is a source of concern for FISH-BOL. We, therefore, conclude that using a standard protocol with several specimens per species and PCR primer cocktails is an efficient and successful approach because failures were evenly distributed among orders and families. Only six orders with low species numbers (Pristiformes, Torpediniformes, Albuliformes, Batrachoidiformes, Gobiesociformes, and Petromyzontiformes) showed failure rates between 10 and 33%. Besides outlining an overarching approach for FISH-BOL data curation, the goal of the present article is to give guidance in directing sampling campaigns toward neglected or underrepresented families in order to complete the FISH-BOL campaign most efficiently.},
}
@article {pmid21271849,
year = {2011},
author = {Pereira, LH and Maia, GM and Hanner, R and Foresti, F and Oliveira, C},
title = {DNA barcodes discriminate freshwater fishes from the Paraíba do Sul River Basin, São Paulo, Brazil.},
journal = {Mitochondrial DNA},
volume = {22 Suppl 1},
number = {},
pages = {71-79},
doi = {10.3109/19401736.2010.532213},
pmid = {21271849},
issn = {1940-1744},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/analysis/*genetics ; Electron Transport Complex IV/*genetics ; Fishes/*classification/*genetics ; Fresh Water ; *Gene Library ; Genetic Variation ; Molecular Sequence Data ; *Rivers ; Sequence Analysis, DNA ; Species Specificity ; Tropical Climate ; },
abstract = {BACKGROUND AND AIMS: Considering the promising use of DNA barcoding for species identification, the importance of the freshwater fish fauna of the Paraíba do Sul River Basin, and its advanced stage of degradation, the present study evaluated the effectiveness of DNA barcoding to identify the fish species in this basin.<br><br>MATERIALS AND METHODS: A total of 295 specimens representing 58 species belonging to 40 genera, 17 families, and 5 orders were sequenced.<br><br>RESULTS: The DNA barcodes discriminated all species analyzed without ambiguity. The results showed a pronounced difference between conspecific and congeneric pair-wise sequence comparisons, demonstrating the existence of a "barcode gap" for the species analyzed. The nearest-neighbor distance analysis showed only three cases with Kimura two-parameter values lower than a 2% divergence threshold. However, the patterns of divergence observed in each case remained sufficient to discriminate each species, revealing the accuracy of DNA barcoding even cases with relatively low genetic divergence. At the other extreme, three species displayed high genetic sequence divergence among conspecifics. For two cases, Characidium alipioi and Geophagus proximus, barcoding proved effective at flagging possible new species. For another case, Astyanax bimaculatus, the use of DNA barcoding of the comparison of shared freshwater fish fauna between different basins revealed itself as highly useful in disclosing that the previously identified A. bimaculatus "cluster A" probably represents the species Astyanax altiparanae.<br><br>CONCLUSION: The present study is among the first to assess the efficiency of barcoding for the Brazilian freshwater fishes. The results demonstrate the utility of barcoding to identify the fauna from this basin, contribute to an enhanced understanding of the differentiation among species, and to help flag the presence of overlooked species.},
}
@article {pmid21271848,
year = {2011},
author = {Smith, PJ and Steinke, D and McMillan, P and Stewart, A and Ward, RD},
title = {DNA barcoding of morid cods reveals deep divergence in the antitropical Halargyreus johnsoni but little distinction between Antimora rostrata and Antimora microlepis.},
journal = {Mitochondrial DNA},
volume = {22 Suppl 1},
number = {},
pages = {21-26},
doi = {10.3109/19401736.2010.532329},
pmid = {21271848},
issn = {1940-1744},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Gadiformes/*classification/*genetics/physiology ; Marine Biology ; New Zealand ; Oceans and Seas ; Sequence Analysis, DNA ; Species Specificity ; Tasmania ; },
abstract = {BACKGROUND AND AIMS: DNA barcoding strongly suggests that specimens of the slender codling (Halargyreus johnsonii) from New Zealand and Tasmania belong to a different species to H. johnsonii reported from other areas.<br><br>RESULTS: Sequence divergence between the two groups averaged 3.95%, much higher than within-group divergences of 0.03 and 0.02% for specimens, respectively, from New Zealand-Tasmania and from the North Pacific, Atlantic Ocean, and Southern Ocean.<br><br>CONCLUSION: Meristic data for specimens from New Zealand and from the Southern Ocean north of the Ross Sea support the conclusion of two species. DNA barcodes for two sister taxa, Antimora rostrata and Antimora microlepis, show low intra-species (0.3-0.06%) and inter-species (0.23%) divergence.},
}
@article {pmid21263053,
year = {2011},
author = {Lin, YC and Huang, YT and Tsai, PJ and Lee, TF and Lee, NY and Liao, CH and Lin, SY and Ko, WC and Hsueh, PR},
title = {Antimicrobial susceptibilities and molecular epidemiology of clinical isolates of Clostridium difficile in taiwan.},
journal = {Antimicrobial agents and chemotherapy},
volume = {55},
number = {4},
pages = {1701-1705},
pmid = {21263053},
issn = {1098-6596},
mesh = {Anti-Bacterial Agents/*pharmacology ; Aza Compounds/pharmacology ; Bacterial Proteins/genetics ; Clostridioides difficile/classification/*drug effects/*genetics ; Fluoroquinolones ; Genotype ; Metronidazole/pharmacology ; Microbial Sensitivity Tests ; Molecular Epidemiology/*methods ; Moxifloxacin ; Polymerase Chain Reaction ; Quinolines/pharmacology ; Ribotyping ; Taiwan ; Vancomycin/pharmacology ; },
abstract = {The antimicrobial susceptibility and virulence factors of Clostridium difficile clinical isolates in Taiwan have not previously been reported. One hundred and thirteen isolates were collected from two major teaching hospitals in Taiwan from 2001 to 2009. Molecular typing was performed by an automated repetitive extragenic palindromic sequence-based PCR (rep-PCR) method (DiversiLab; Bacterial Barcodes, Inc., Athens, GA) and PCR ribotyping. Detection of tcdA, tcdB, cdtA, and cdtB genes was performed using a multiplex PCR assay, and gyrA and gyrB genes of moxifloxacin-nonsusceptible isolates were sequenced. All isolates were susceptible to vancomycin and metronidazole. Ninety-five (84%) isolates were susceptible to moxifloxacin, and the MIC(90) for nemonoxacin was 4 μg/ml. Tigecycline showed favorable antibacterial activity (MIC(90) of 0.06 μg/ml). Thirteen rep-PCR types were identified as a predominant rep-PCR type (type A; non-North American pulsed-field gel electrophoresis type 1 [NAP1], -NAP7, or -NAP8) accounting for 52.2% (59 isolates). Nine of 18 moxifloxacin-nonsusceptible isolates belonged to the rep-PCR type A. The rep-PCR type A and C isolates were distinct from NAP1 (ribotype 027) and NAP8 (ribotype 078) as determined by PCR ribotyping. Seventy-four (65%) isolates harbored tcdA and tcdB, and 15 (13%) harbored cdtAB encoding binary toxin. Eleven isolates had a gene deletion in tcdC, including a 39-bp deletion (9 isolates) and an 18-bp deletion (2). In conclusion, dissemination of a predominant C. difficile clone in southern and northern Taiwan was noted. However, no NAP1 (ribotype 027) isolate could be discovered in this study.},
}
@article {pmid21261496,
year = {2011},
author = {Triantafyllidis, A and Bobori, D and Koliamitra, C and Gbandi, E and Mpanti, M and Petriki, O and Karaiskou, N},
title = {DNA barcoding analysis of fish species diversity in four north Greek lakes.},
journal = {Mitochondrial DNA},
volume = {22 Suppl 1},
number = {},
pages = {37-42},
doi = {10.3109/19401736.2010.542242},
pmid = {21261496},
issn = {1940-1744},
mesh = {Animals ; Cyprinidae/classification/genetics ; DNA Barcoding, Taxonomic/*methods/standards ; DNA, Mitochondrial/analysis/genetics ; Electron Transport Complex IV/*genetics ; Fishes/*classification/*genetics ; Genetic Variation ; Greece ; *Lakes ; Perciformes/classification/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {MATERIALS AND METHODS: The present study is the first to apply DNA barcoding on identifying 37 freshwater fish species from the rich Balkan ichthyofauna.<br><br>RESULTS: The results are highly successful since in most cases barcodes cluster according to species, in agreement with morphological taxonomic studies. This is also evident based on mean conspecific and congeneric Kimura two-parameter distance values. The 5.6-fold difference between these values is lower than previous barcoding studies, possibly due to the restricted samplings and the recent taxonomy reevaluation for several species. A number of species were identified, where future work is needed: For the species Scardinius erythrophthalmus, Perca fluviatilis, and Rutilus rutilus, the divergence values found among conspecific populations could warrant their placement into different species; for Barbus and Rhodeus populations, the reported interspecific distances found were lower than expected; and for Cobitis species, the application of barcoding seems problematic, due to their complicated reproduction.<br><br>CONCLUSION: The extension of this work to other Greek or even Balkan freshwater systems should clarify the situation.},
}
@article {pmid21261495,
year = {2011},
author = {Steinke, D and Hanner, R and , },
title = {The FISH-BOL collaborators' protocol.},
journal = {Mitochondrial DNA},
volume = {22 Suppl 1},
number = {},
pages = {10-14},
doi = {10.3109/19401736.2010.536538},
pmid = {21261495},
issn = {1940-1744},
mesh = {Animals ; *Cooperative Behavior ; DNA Barcoding, Taxonomic/*methods/*standards ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Fishes/*classification/genetics ; *Gene Library ; *Genes, Mitochondrial ; *International Agencies ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The Fish barcode of life (FISH-BOL) initiative seeks to establish a reference sequence library of short, standardized mitochondrial gene sequences derived from the 5' end of the cytochrome c oxidase subunit I gene (DNA barcodes) to facilitate the rapid, accurate, and cost-effective DNA-based identification of all fishes, regardless of life-stage, sex, or specimen condition. This task requires the participation of scientists from around the world and its success is predicated on the development and acceptance of standard protocols for the collection of specimens associated provenance data. Here, we provide guidelines for specimen collection, imaging, preservation, and archival, as well as meta-data collection and submission protocols developed for the FISH-BOL campaign in order to promote efficient participation in FISH-BOL by a broadening array of international participants.},
}
@article {pmid21255172,
year = {2011},
author = {Kesanakurti, PR and Fazekas, AJ and Burgess, KS and Percy, DM and Newmaster, SG and Graham, SW and Barrett, SC and Hajibabaei, M and Husband, BC},
title = {Spatial patterns of plant diversity below-ground as revealed by DNA barcoding.},
journal = {Molecular ecology},
volume = {20},
number = {6},
pages = {1289-1302},
doi = {10.1111/j.1365-294X.2010.04989.x},
pmid = {21255172},
issn = {1365-294X},
mesh = {Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Plants/classification/*genetics ; },
abstract = {Our understanding of the spatial organization of root diversity in plant communities and of the mechanisms of community assembly has been limited by our ability to identify plants based on root tissue, especially in diverse communities. Here, we test the effectiveness of the plastid gene rbcL, a core plant DNA barcoding marker, for investigating spatial patterns of root diversity, and relate observed patterns to above-ground community structure. We collected 3800 root fragments from four randomly positioned, 1-m-deep soil profiles (two vertical transects per plot), located in an old-field community in southern Ontario, Canada, and extracted and sequenced DNA from 1531 subsampled fragments. We identified species by comparing sequences with a DNA barcode reference library developed previously for the local flora. Nearly 85% of sampled root fragments were successfully sequenced and identified as belonging to 29 plant species or species groups. Root abundance and species richness varied in horizontal space and were negatively correlated with soil depth. The relative abundance of taxa below-ground was correlated with their frequency above-ground (r = 0.73, P = 0.0001), but several species detected in root tissue were not observed in above-ground quadrats. Multivariate analyses indicated that diversity was highly structured below-ground, and associated with depth, root morphology, soil chemistry and soil texture, whereas little structure was evident above-ground. Furthermore, analyses of species co-occurrence indicates strong species segregation overall but random co-occurrence among confamilials. Our results provide insights into the role of environmental filtering and competitive interactions in the organization of plant diversity below-ground, and also demonstrate the utility of barcoding for the identification of plant roots.},
}
@article {pmid21244689,
year = {2011},
author = {Erlich, RL and Jia, X and Anderson, S and Banks, E and Gao, X and Carrington, M and Gupta, N and DePristo, MA and Henn, MR and Lennon, NJ and de Bakker, PI},
title = {Next-generation sequencing for HLA typing of class I loci.},
journal = {BMC genomics},
volume = {12},
number = {},
pages = {42},
pmid = {21244689},
issn = {1471-2164},
support = {P30 AI060354/AI/NIAID NIH HHS/United States ; /ImNIH/Intramural NIH HHS/United States ; HHSN26120080001E//PHS HHS/United States ; },
mesh = {Genes, MHC Class I/*genetics ; Histocompatibility Testing/*methods ; Humans ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: Comprehensive sequence characterization across the MHC is important for successful organ transplantation and genetic association studies. To this end, we have developed an automated sample preparation, molecular barcoding and multiplexing protocol for the amplification and sequence-determination of class I HLA loci. We have coupled this process to a novel HLA calling algorithm to determine the most likely pair of alleles at each locus.<br><br>RESULTS: We have benchmarked our protocol with 270 HapMap individuals from four worldwide populations with 96.4% accuracy at 4-digit resolution. A variation of this initial protocol, more suitable for large sample sizes, in which molecular barcodes are added during PCR rather than library construction, was tested on 95 HapMap individuals with 98.6% accuracy at 4-digit resolution.<br><br>CONCLUSIONS: Next-generation sequencing on the 454 FLX Titanium platform is a reliable, efficient, and scalable technology for HLA typing.},
}
@article {pmid21242529,
year = {2011},
author = {Pacheco, MA and Battistuzzi, FU and Lentino, M and Aguilar, RF and Kumar, S and Escalante, AA},
title = {Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders.},
journal = {Molecular biology and evolution},
volume = {28},
number = {6},
pages = {1927-1942},
pmid = {21242529},
issn = {1537-1719},
support = {R01 GM080586/GM/NIGMS NIH HHS/United States ; GM080586/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Substitution/genetics ; Animals ; Birds/*classification/*genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genetic Variation ; Open Reading Frames/genetics ; *Phylogeny ; },
abstract = {Mitochondrial (mt) genes and genomes are among the major sources of data for evolutionary studies in birds. This places mitogenomic studies in birds at the core of intense debates in avian evolutionary biology. Indeed, complete mt genomes are actively been used to unveil the phylogenetic relationships among major orders, whereas single genes (e.g., cytochrome c oxidase I [COX1]) are considered standard for species identification and defining species boundaries (DNA barcoding). In this investigation, we study the time of origin and evolutionary relationships among Neoaves orders using complete mt genomes. First, we were able to solve polytomies previously observed at the deep nodes of the Neoaves phylogeny by analyzing 80 mt genomes, including 17 new sequences reported in this investigation. As an example, we found evidence indicating that columbiforms and charadriforms are sister groups. Overall, our analyses indicate that by improving the taxonomic sampling, complete mt genomes can solve the evolutionary relationships among major bird groups. Second, we used our phylogenetic hypotheses to estimate the time of origin of major avian orders as a way to test if their diversification took place prior to the Cretaceous/Tertiary (K/T) boundary. Such timetrees were estimated using several molecular dating approaches and conservative calibration points. Whereas we found time estimates slightly younger than those reported by others, most of the major orders originated prior to the K/T boundary. Finally, we used our timetrees to estimate the rate of evolution of each mt gene. We found great variation on the mutation rates among mt genes and within different bird groups. COX1 was the gene with less variation among Neoaves orders and the one with the least amount of rate heterogeneity across lineages. Such findings support the choice of COX 1 among mt genes as target for developing DNA barcoding approaches in birds.},
}
@article {pmid21239228,
year = {2011},
author = {Hamsher, SE and Evans, KM and Mann, DG and Poulíčková, A and Saunders, GW},
title = {Barcoding diatoms: exploring alternatives to COI-5P.},
journal = {Protist},
volume = {162},
number = {3},
pages = {405-422},
doi = {10.1016/j.protis.2010.09.005},
pmid = {21239228},
issn = {1618-0941},
mesh = {Base Sequence ; DNA/chemistry ; DNA Barcoding, Taxonomic/*methods ; DNA Primers ; Diatoms/*classification/cytology/*genetics ; Electron Transport Complex IV/genetics ; Genetic Markers ; Molecular Sequence Data ; Phylogeny ; Phylogeography ; Polymerase Chain Reaction ; Proteins/genetics ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Diatoms are a diverse lineage with species that can be difficult to identify or cryptic, but DNA barcoding, a molecular technique, can assist identification and facilitate studies of speciation and biogeography. The most common region used for DNA barcoding, COI-5P, can distinguish diatom species, but has not displayed universality (i.e., successful PCR amplification from diverse taxa). Therefore, we have assessed the following alternative markers: ∼1400bp of rbcL; 748bp at the 3' end of rbcL (rbcL-3P); LSU D2/D3 and UPA. Sellaphora isolates were used to determine each marker's ability to discriminate among closely related species and culture collection material was utilized to explore further marker universality. All of the alternative markers investigated have greater universality than COI-5P. Both full and partial (3P) rbcL regions had the power to discriminate between all species, but rbcL-3P can be sequenced more easily. LSU D2/D3 could distinguish between all but the most closely related species (96%), whereas UPA only distinguished 20% of species. Our observations suggest that rbcL-3P should be used as the primary marker for diatom barcoding, while LSU D2/D3 should be sequenced as a secondary marker to facilitate environmental surveys.},
}
@article {pmid21235567,
year = {2011},
author = {Smith, PJ and Steinke, D and McMillan, PJ and Stewart, AL and McVeagh, SM and Diaz de Astarloa, JM and Welsford, D and Ward, RD},
title = {DNA barcoding highlights a cryptic species of grenadier Macrourus in the Southern Ocean.},
journal = {Journal of fish biology},
volume = {78},
number = {1},
pages = {355-365},
doi = {10.1111/j.1095-8649.2010.02846.x},
pmid = {21235567},
issn = {1095-8649},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Gadiformes/classification/*genetics ; Species Specificity ; },
abstract = {Although three species of the genus Macrourus are recognized in the Southern Ocean, DNA sequencing of the mitochondrial COI gene revealed four well-supported clades. These barcode data suggest the presence of an undescribed species, a conclusion supported by meristic and morphometric examination of specimens.},
}
@article {pmid21232099,
year = {2011},
author = {Linacre, A and Tobe, SS},
title = {An overview to the investigative approach to species testing in wildlife forensic science.},
journal = {Investigative genetics},
volume = {2},
number = {1},
pages = {2},
pmid = {21232099},
issn = {2041-2223},
abstract = {The extent of wildlife crime is unknown but it is on the increase and has observable effects with the dramatic decline in many species of flora and fauna. The growing awareness of this area of criminal activity is reflected in the increase in research papers on animal DNA testing, either for the identification of species or for the genetic linkage of a sample to a particular organism. This review focuses on the use of species testing in wildlife crime investigations. Species identification relies primarily on genetic loci within the mitochondrial genome; focusing on the cytochrome b and cytochrome oxidase 1 genes. The use of cytochrome b gained early prominence in species identification through its use in taxonomic and phylogenetic studies, while the gene sequence for cytochrome oxidase was adopted by the Barcode for Life research group. This review compares how these two loci are used in species identification with respect to wildlife crime investigations. As more forensic science laboratories undertake work in the wildlife area, it is important that the quality of work is of the highest standard and that the conclusions reached are based on scientific principles. A key issue in reporting on the identification of a particular species is a knowledge of both the intraspecies variation and the possible overlap of sequence variation from one species to that of a closely related species. Recent data showing this degree of genetic separation in mammalian species will allow greater confidence when preparing a report on an alleged event where the identification of the species is of prime importance. The aim of this review is to illustrate aspects of species testing in wildlife forensic science and to explain how a knowledge of genetic variation at the genus and species level can aid in the reporting of results.},
}
@article {pmid21225197,
year = {2010},
author = {González, R and Carrejo, N and Wilkerson, RC and Alarcon, J and Alarcon-Ormasa, J and Ruiz, F and Bhatia, R and Loaiza, J and Linton, YM},
title = {Confirmation of Anopheles (Anopheles) calderoni Wilkerson, 1991 (Diptera: Culicidae) in Colombia and Ecuador through molecular and morphological correlation with topotypic material.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {105},
number = {8},
pages = {1001-1009},
doi = {10.1590/s0074-02762010000800009},
pmid = {21225197},
issn = {1678-8060},
mesh = {Animals ; *Anopheles/anatomy &amp; histology/classification/genetics ; Colombia ; DNA, Mitochondrial/genetics ; Ecuador ; Electron Transport Complex IV/genetics ; Female ; *Insect Vectors/anatomy &amp; histology/classification/genetics ; Wings, Animal/*anatomy &amp; histology ; },
abstract = {The morphologically similar taxa Anopheles calderoni, Anopheles punctimacula, Anopheles malefactor and Anopheles guarao are commonly misidentified. Isofamilies collected in Valle de Cauca, Colombia, showed morphological characters most similar to An. calderoni, a species which has never previously been reported in Colombia. Although discontinuity of the postsubcostal pale spots on the costa (C) and first radial (R1) wing veins is purportedly diagnostic for An. calderoni, the degree of overlap of the distal postsubcostal spot on C and R1 were variable in Colombian specimens (0.003-0.024). In addition, in 98.2% of larvae, seta 1-X was located off the saddle and seta 3-C had 4-7 branches in 86.7% of specimens examined. Correlation of DNA sequences of the second internal transcribed spacer and mtDNA cytochrome c oxidase subunit I gene (COI) barcodes (658 bp of the COI gene) generated from Colombian progeny material and wild-caught mosquitoes from Ecuador with those from the Peruvian type series of An. calderoni confirmed new country records. DNA barcodes generated for the closely related taxa, An. malefactor and An. punctimacula are also presented for the first time. Examination of museum specimens at the University of the Valle, Colombia, revealed the presence of An. calderoni in inland localities across Colombia and at elevations up to 1113 m.},
}
@article {pmid21217800,
year = {2011},
author = {Pramual, P and Wongpakam, K and Adler, PH},
title = {Cryptic biodiversity and phylogenetic relationships revealed by DNA barcoding of Oriental black flies in the subgenus Gomphostilbia (Diptera: Simuliidae).},
journal = {Genome},
volume = {54},
number = {1},
pages = {1-9},
doi = {10.1139/G10-100},
pmid = {21217800},
issn = {1480-3321},
mesh = {Animals ; Biodiversity ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/classification/genetics ; Evolution, Molecular ; Genetic Variation ; Humans ; Phylogeny ; Simuliidae/*classification/genetics ; },
abstract = {Understanding the medical, economic, and ecological importance of black flies relies on correct identification of species. However, traditional taxonomy of black flies is impeded by a high degree of morphological uniformity, especially the presence of cryptic biodiversity, historically recognized by details of chromosomal banding patterns. We assess the utility of DNA barcoding, based on cytochrome c oxidase subunit 1 (COI) sequences, for identifying 13 species of Oriental black flies in the subgenus Gomphostilbia. Samples of larvae fixed in Carnoy's solution were used to gather molecular and chromosomal data from the same individual. We found that larvae refrigerated in Carnoy's fixative for as long as 11 years can be used for DNA study. Levels of intraspecific genetic divergence, based on the Kimura-2 parameter, range from 0% to 9.28%, with a mean of 2.75%, whereas interspecific genetic divergence ranges from 0.34% to 16.05%. Values of intraspecific and interspecific genetic divergence overlap in seven species owing to incomplete lineage sorting and imperfect taxonomy, implying that DNA barcoding to identify these species will be ambiguous. Despite a low level of success, we found that DNA barcoding is useful in revealing cryptic biodiversity, potentially facilitating traditional taxonomy. Phylogenetic analyses indicate that species groups currently recognized on morphological criteria are not monophyletic, suggesting a need to reevaluate the classification of the subgenus Gomphostilbia.},
}
@article {pmid21207359,
year = {2011},
author = {Krutzik, PO and Clutter, MR and Trejo, A and Nolan, GP},
title = {Fluorescent cell barcoding for multiplex flow cytometry.},
journal = {Current protocols in cytometry},
volume = {Chapter 6},
number = {},
pages = {6.31.1-6.31.15},
pmid = {21207359},
issn = {1934-9300},
support = {T32 AI007290/AI/NIAID NIH HHS/United States ; R01 CA130826/CA/NCI NIH HHS/United States ; HHSN268201000034C/HL/NHLBI NIH HHS/United States ; R01 CA130826-01/CA/NCI NIH HHS/United States ; HV-10-05/HV/NHLBI NIH HHS/United States ; R01CA13082/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Cell Separation/methods ; Cells/*cytology ; Cells, Cultured ; Flow Cytometry/*methods ; Fluorescence ; Fluorescent Dyes/pharmacology ; Humans ; Models, Biological ; Staining and Labeling/methods ; },
abstract = {Fluorescent cell barcoding (FCB) enables high throughput, high content flow cytometry by multiplexing samples prior to staining and acquisition on the cytometer. Individual cell samples are barcoded, or labeled, with unique signatures of fluorescent dyes so that they can be mixed together, stained, and analyzed as a single sample. By mixing samples prior to staining, antibody consumption is typically reduced 10- to 100-fold. In addition, data robustness is increased through the combination of control and treated samples, which minimizes pipetting error, staining variation, and the need for normalization. Finally, speed of acquisition is enhanced, enabling large profiling experiments to be run with standard cytometer hardware. In this unit, we outline the steps necessary to apply the FCB method to cell lines, as well as primary peripheral blood samples. Important technical considerations, such as choice of barcoding dyes, concentrations, labeling buffers, compensation, and software analysis, are discussed.},
}
@article {pmid21206917,
year = {2010},
author = {James, SW and Porco, D and Decaëns, T and Richard, B and Rougerie, R and Erséus, C},
title = {DNA barcoding reveals cryptic diversity in Lumbricus terrestris L., 1758 (Clitellata): resurrection of L. herculeus (Savigny, 1826).},
journal = {PloS one},
volume = {5},
number = {12},
pages = {e15629},
pmid = {21206917},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Biodiversity ; Canada ; Computational Biology/methods ; DNA/*genetics ; DNA Barcoding, Taxonomic/*methods ; Denmark ; Electron Transport Complex IV/metabolism ; Models, Genetic ; Molecular Sequence Data ; Norway ; Oligochaeta/*genetics ; Sequence Analysis, DNA/methods ; },
abstract = {The widely studied and invasive earthworm, Lumbricus terrestris L., 1758 has been the subject of nomenclatural debate for many years. However these disputes were not based on suspicions of heterogeneity, but rather on the descriptions and nomenclatural acts associated with the species name. Large numbers of DNA barcode sequences of the cytochrome oxidase I obtained for nominal L. terrestris and six congeneric species reveal that there are two distinct lineages within nominal L. terrestris. One of those lineages contains the Swedish population from which the name-bearing specimen of L. terrestris was obtained. The other contains the population from which the syntype series of Enterion herculeum Savigny, 1826 was collected. In both cases modern and old representatives yielded barcode sequences allowing us to clearly establish that these are two distinct species, as different from one another as any other pair of congeners in our data set. The two are morphologically indistinguishable, except by overlapping size-related characters. We have designated a new neotype for L. terrestris. The newly designated neotype and a syntype of L. herculeus yielded DNA adequate for sequencing part of the cytochrome oxidase I gene (COI). The sequence data make possible the objective determination of the identities of earthworms morphologically identical to L. terrestris and L. herculeus, regardless of body size and segment number. Past work on nominal L. terrestris could have been on either or both species, although L. herculeus has yet to be found outside of Europe.},
}
@article {pmid21204029,
year = {2011},
author = {Szelinger, S and Kurdoglu, A and Craig, DW},
title = {Bar-coded, multiplexed sequencing of targeted DNA regions using the Illumina Genome Analyzer.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {700},
number = {},
pages = {89-104},
doi = {10.1007/978-1-61737-954-3_7},
pmid = {21204029},
issn = {1940-6029},
mesh = {*Electronic Data Processing ; Genome-Wide Association Study/*methods ; Humans ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; },
abstract = {To date, genome-wide association (GWA) studies, in which thousands of markers throughout the genome are simultaneously genotyped, have identified hundreds of loci underlying disease susceptibility. These regions typically span 5-100 kb, and resequencing efforts to identify potential functional variants within these loci represent the next logical step in the genetic characterization pipeline. Next-generation DNA sequencing technologies are, in principle, well-suited for this task, yet despite the massive sequencing capability afforded by these platforms, the present-day reality is that it remains difficult, time-consuming, and expensive to resequence large numbers of samples across moderately sized genomic regions. To address this obstacle, we developed a generalized framework for multiplexed resequencing of targeted regions of the human genome on the Illumina Genome Analyzer using degenerate, indexed DNA sequence barcodes ligated to fragmented DNA prior to sequencing. Using this method, the DNA of multiple individuals can be simultaneously sequenced at several regions. We find that achieving adequate coverage is one of the most important factors in the design of an experiment, but other key considerations include whether the objective is to discover genetic variants for genotyping later by a separate method, to genotype all identified variants by sequencing, or to exhaustively identify all common and rare variants in the region. Given the massive bandwidth of next-generation sequencing technologies and their low inherent throughput in terms of sequencing arrays per week, multiplexed sequencing using the barcoding approach offers a clear mechanism for focusing bandwidth to a smaller region across many more individuals or samples.},
}
@article {pmid21203427,
year = {2010},
author = {Hendrich, L and Pons, J and Ribera, I and Balke, M},
title = {Mitochondrial cox1 sequence data reliably uncover patterns of insect diversity but suffer from high lineage-idiosyncratic error rates.},
journal = {PloS one},
volume = {5},
number = {12},
pages = {e14448},
pmid = {21203427},
issn = {1932-6203},
mesh = {Animals ; Australia ; Classification ; Coleoptera ; Computational Biology/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Electronic Data Processing ; Genetic Variation ; Insecta ; Likelihood Functions ; Mitochondria/*metabolism ; Phylogeny ; Reproducibility of Results ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The demand for scientific biodiversity data is increasing, but taxonomic expertise is often limited or not available. DNA sequencing is a potential remedy to overcome this taxonomic impediment. Mitochondrial DNA is most commonly used, e.g., for species identification ("DNA barcoding"). Here, we present the first study in arthropods based on a near-complete species sampling of a family-level taxon from the entire Australian region. We aimed to assess how reliably mtDNA data can capture species diversity when many sister species pairs are included. Then, we contrasted phylogenetic subsampling with the hitherto more commonly applied geographical subsampling, where sister species are not necessarily captured.<br><br>We sequenced 800 bp cox1 for 1,439 individuals including 260 Australian species (78% species coverage). We used clustering with thresholds of 1 to 10% and general mixed Yule Coalescent (GMYC) analysis for the estimation of species richness. The performance metrics used were taxonomic accuracy and agreement between the morphological and molecular species richness estimation. Clustering (at the 3% level) and GMYC reliably estimated species diversity for single or multiple geographic regions, with an error for larger clades of lower than 10%, thus outperforming parataxonomy. However, the rates of error were higher for some individual genera, with values of up to 45% when very recent species formed nonmonophyletic clusters. Taxonomic accuracy was always lower, with error rates above 20% and a larger variation at the genus level (0 to 70%). S&#xf8;rensen similarity indices calculated for morphospecies, 3% clusters and GMYC entities for different pairs of localities was consistent among methods and showed expected decrease over distance.<br><br>CONCLUSION/SIGNIFICANCE: Cox1 sequence data are a powerful tool for large-scale species richness estimation, with a great potential for use in ecology and &#x3b2;-diversity studies and for setting conservation priorities. However, error rates can be high in individual lineages.},
}
@article {pmid22696950,
year = {2011},
author = {Holterman, MH and Frey, JE and Helder, H and Mooyman, PJ and Rybarczyk, KD and Kiewnick, S},
title = {Barcoding quarantine nematodes and their close relatives: an update on the QBOL-project.},
journal = {Communications in agricultural and applied biological sciences},
volume = {76},
number = {3},
pages = {403-407},
pmid = {22696950},
issn = {1379-1176},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; European Union ; Helminth Proteins/genetics ; Nematoda/*classification/genetics/*isolation &amp; purification ; Phylogeny ; },
abstract = {Identification of plant pests, in particular quarantine species, needs to be fast and accurate to enable timely plant protection measures. In addition, a false diagnosis can cause serious financial losses for trade and producers. It is now well established that genetically based diagnosis is a reliable alternative to the classical identification procedures generally based on morphological features, which usually require expert taxonomic skills. On the other hand, genetic diagnosis through the use of DNA-barcodes, i.e. stretches of DNA that contain taxon-specific information, can be performed by any skilled laboratory worker. The European Union 7th framework project QBOL aims to establish DNA-barcodes for all European quarantine organisms as well as their close relatives. The results and protocols will be disseminated in the publicly available and curated database Q-BANK. To enable genetically based identification requires knowledge of the genetic variation both within and between the species of interest as well as their close relatives. For the nematodes, several gene regions (the COI, COII, SSU, LSU and RNA polymerase subunit II) are being evaluated for their barcoding potential.},
}
@article {pmid22476488,
year = {2011},
author = {Khew, GS and Chia, TF},
title = {Parentage determination of Vanda Miss Joaquim (Orchidaceae) through two chloroplast genes rbcL and matK.},
journal = {AoB PLANTS},
volume = {2011},
number = {},
pages = {plr018},
pmid = {22476488},
issn = {2041-2851},
abstract = {BACKGROUND AND AIMS: The popular hybrid orchid Vanda Miss Joaquim was made Singapore's national flower in 1981. It was originally described in the Gardeners' Chronicle in 1893, as a cross between Vanda hookeriana and Vanda teres. However, no record had been kept as to which parent contributed the pollen. This study was conducted using DNA barcoding techniques to determine the pod parent of V. Miss Joaquim, thereby inferring the pollen parent of the hybrid by exclusion.<br><br>METHODOLOGY: Two chloroplast genes, matK and rbcL, from five related taxa, V. hookeriana, V. teres var. alba, V. teres var. andersonii, V. teres var. aurorea and V. Miss Joaquim 'Agnes', were sequenced. The matK gene from herbarium specimens of V. teres and V. Miss Joaquim, both collected in 1893, was also sequenced.<br><br>PRINCIPAL RESULTS: No sequence variation was found in the 600-bp region of rbcL sequenced. Sequence variation was found in the matK gene of V. hookeriana, V. teres var. alba, V. teres var. aurorea and V. Miss Joaquim 'Agnes'. Complete sequence identity was established between V. teres var. andersonii and V. Miss Joaquim 'Agnes'. The matK sequences obtained from the herbarium specimens of V. teres and V. Miss Joaquim were completely identical to the sequences obtained from the fresh samples of V. teres var. andersonii and V. Miss Joaquim 'Agnes'.<br><br>CONCLUSIONS: The pod parent of V. Miss Joaquim 'Agnes' is V. teres var. andersonii and, by exclusion, the pollen parent is V. hookeriana. The herbarium and fresh samples of V. teres var. andersonii and V. Miss Joaquim share the same inferred maternity. The matK gene was more informative than rbcL and facilitated differentiation of varieties of V. teres.},
}
@article {pmid21190898,
year = {2011},
author = {Hamilton, PB and Stevens, JR},
title = {Resolving relationships between Australian trypanosomes using DNA barcoding data.},
journal = {Trends in parasitology},
volume = {27},
number = {3},
pages = {99; author reply 100},
doi = {10.1016/j.pt.2010.11.009},
pmid = {21190898},
issn = {1471-5007},
mesh = {Animals ; Australia ; *DNA Barcoding, Taxonomic ; Species Specificity ; Trypanosoma/*classification/*genetics ; },
}
@article {pmid21186831,
year = {2011},
author = {Buller, F and Steiner, M and Frey, K and Mircsof, D and Scheuermann, J and Kalisch, M and Buhlmann, P and Supuran, CT and Neri, D},
title = {Selection of Carbonic Anhydrase IX Inhibitors from One Million DNA-Encoded Compounds.},
journal = {ACS chemical biology},
volume = {6},
number = {4},
pages = {336-344},
doi = {10.1021/cb1003477},
pmid = {21186831},
issn = {1554-8937},
mesh = {Adenocarcinoma/drug therapy ; *Antigens, Neoplasm/metabolism ; Carbonic Anhydrase IX ; Carbonic Anhydrase Inhibitors/*chemical synthesis/pharmacology ; *Carbonic Anhydrases/metabolism ; Cell Line, Tumor ; Colorectal Neoplasms/drug therapy ; Combinatorial Chemistry Techniques/*methods ; DNA/chemistry ; Fluorescent Dyes/analysis ; Gene Library ; High-Throughput Nucleotide Sequencing ; High-Throughput Screening Assays ; Humans ; Kinetics ; Molecular Imaging ; Molecular Targeted Therapy ; Neoplasm Transplantation ; Quantitative Structure-Activity Relationship ; Small Molecule Libraries/*chemical synthesis/pharmacology ; Structure-Activity Relationship ; Sulfonamides/*chemical synthesis/pharmacology ; },
abstract = {DNA-encoded chemical libraries, i.e., collections of compounds individually coupled to distinctive DNA fragments serving as amplifiable identification barcodes, represent a new tool for the de novo discovery of small molecule ligands to target proteins of pharmaceutical interest. Here, we describe the design and synthesis of a novel DNA-encoded chemical library containing one million small molecules. The library was synthesized by combinatorial assembly of three sets of chemical building blocks using Diels-Alder cycloadditions and by the stepwise build-up of the DNA barcodes. Model selections were performed to test library performance and to develop a statistical method for the analysis of high-throughput sequencing data. A library selection against carbonic anhydrase IX revealed a new class of submicromolar bis(sulfonamide) inhibitors. One of these inhibitors was synthesized in the absence of the DNA-tag and showed accumulation in hypoxic tumor tissue sections in vitro and tumor targeting in vivo.},
}
@article {pmid21184470,
year = {2011},
author = {Goldstein, PZ and DeSalle, R},
title = {Integrating DNA barcode data and taxonomic practice: determination, discovery, and description.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {33},
number = {2},
pages = {135-147},
doi = {10.1002/bies.201000036},
pmid = {21184470},
issn = {1521-1878},
mesh = {Animals ; Base Sequence ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electronic Data Processing/*methods ; Phylogeny ; Species Specificity ; },
abstract = {DNA barcodes, like traditional sources of taxonomic information, are potentially powerful heuristics in the identification of described species but require mindful analytical interpretation. The role of DNA barcoding in generating hypotheses of new taxa in need of formal taxonomic treatment is discussed, and it is emphasized that the recursive process of character evaluation is both necessary and best served by understanding the empirical mechanics of the discovery process. These undertakings carry enormous ramifications not only for the translation of DNA sequence data into taxonomic information but also for our comprehension of the magnitude of species diversity and its disappearance. This paper examines the potential strengths and pitfalls of integrating DNA sequence data, specifically in the form of DNA barcodes as they are currently generated and analyzed, with taxonomic practice.},
}
@article {pmid21181271,
year = {2011},
author = {Li, QQ and Li, DY and Ye, H and Liu, XF and Shi, W and Cao, N and Duan, YQ},
title = {Using COI gene sequence to barcode two morphologically alike species: the cotton bollworm and the oriental tobacco budworm (Lepidoptera: Noctuidae).},
journal = {Molecular biology reports},
volume = {38},
number = {8},
pages = {5107-5113},
pmid = {21181271},
issn = {1573-4978},
mesh = {Animals ; Base Sequence ; China ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Geography ; Gossypium/*parasitology ; Haplotypes/genetics ; Molecular Sequence Data ; Moths/*anatomy &amp; histology/enzymology/*genetics ; Species Specificity ; Nicotiana/*parasitology ; },
abstract = {Due to limited morphological difference, the two closely related sister species, the cotton bollworm, Helicoverpa armigera (Hübner) and the oriental tobacco budworm, H. assulta (Guenée) (Lepidoptera: Noctuidae), are very difficult to distinguish, especially at the larvae stage. Recently, DNA sequence has been widely used as a bio-barcode for species identification. In this study, we attempted to distinguish H. armigera and H. assulta using the mitochondrial cytochrome C oxidase subunit I gene (COI) gene sequence as the barcode. We determined a 658 bp segment of the COI gene for 28 individuals of H. armigera, 8 individuals of H. assulta, and 10 individuals of Mamestra brassicae (as the outgroup) in Yunnan Province, southwest of P. R. China, together with one H. assulta and two H. armigera reported sequences from GenBank. Twenty-three haplotypes were identified in all 49 samples. As expected, network analysis of the haplotypes of the three species presented a clustering pattern consistent with the respective species status. Haplotypes of the same species differed from each other by no more than three nucleotide substitutions. However, each haplotype of H. armigera differed from that of H. assulta by at least 22 nucleotide substitutions. Both species differed from M. brassicae by more than 50 nucleotide substitutions. 17 unique diagnostic nucleotides were also used to discriminate the two species. The finding of large COI sequence differences between H. armigera and H. assulta suggested that it could be used to distinguish the two morphologically alike species and be employed for quick species identification during pest control.},
}
@article {pmid21174758,
year = {2010},
author = {Liu, Z and Chen, K and Luo, K and Pan, H and Chen, S},
title = {[DNA barcoding in medicinal plants Caprifoliaceae].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {35},
number = {19},
pages = {2527-2532},
pmid = {21174758},
issn = {1001-5302},
mesh = {Base Sequence ; Caprifoliaceae/*genetics ; DNA/analysis ; DNA, Plant/*analysis ; Electronic Data Processing/methods ; *Identification, Psychological ; Plants, Medicinal/*genetics ; Polymerase Chain Reaction/methods ; *Species Specificity ; },
abstract = {OBJECTIVE: To determine the candidate sequences which can be used as DNA barcode to identify species in Caprifoliaceae family by screening out from four different DNA fragments sequences.<br><br>METHOD: PCR amplification, sequencing efficiency, differential intra- and interspecific divergences, the DNA barcoding gap and identification efficiency were used to evaluate these loci.<br><br>RESULT: The ITS2 was used as a candidate sequence of DNA barcode to identify the species in Caprifoliaceae family, whose rate of success in identification in genera level was 100% and in species 96.6%, and psbA-trnH as a complementary barcode to ITS2 for Caprifoliaceae.},
}
@article {pmid21173448,
year = {2011},
author = {Gallo, O and Manduchi, R},
title = {Reading 1D Barcodes with Mobile Phones Using Deformable Templates.},
journal = {IEEE transactions on pattern analysis and machine intelligence},
volume = {33},
number = {9},
pages = {1834-1843},
pmid = {21173448},
issn = {1939-3539},
support = {R21 EY017003/EY/NEI NIH HHS/United States ; R21 EY017003-01A1/EY/NEI NIH HHS/United States ; 1 R21 EY017003-01A1/EY/NEI NIH HHS/United States ; },
mesh = {Algorithms ; *Cell Phone ; *Electronic Data Processing ; Image Processing, Computer-Assisted/*instrumentation/*methods ; *Mobile Applications ; },
abstract = {Camera cellphones have become ubiquitous, thus opening a plethora of opportunities for mobile vision applications. For instance, they can enable users to access reviews or price comparisons for a product from a picture of its barcode while still in the store. Barcode reading needs to be robust to challenging conditions such as blur, noise, low resolution, or low-quality camera lenses, all of which are extremely common. Surprisingly, even state-of-the-art barcode reading algorithms fail when some of these factors come into play. One reason resides in the early commitment strategy that virtually all existing algorithms adopt: The image is first binarized and then only the binary data are processed. We propose a new approach to barcode decoding that bypasses binarization. Our technique relies on deformable templates and exploits all of the gray-level information of each pixel. Due to our parameterization of these templates, we can efficiently perform maximum likelihood estimation independently on each digit and enforce spatial coherence in a subsequent step. We show by way of experiments on challenging UPC-A barcode images from five different databases that our approach outperforms competing algorithms. Implemented on a Nokia N95 phone, our algorithm can localize and decode a barcode on a VGA image (640 × 480, JPEG compressed) in an average time of 400-500 ms.},
}
@article {pmid21172298,
year = {2011},
author = {Laboudi, M and Faraj, C and Sadak, A and Harrat, Z and Boubidi, SC and Harbach, RE and El Aouad, R and Linton, YM},
title = {DNA barcodes confirm the presence of a single member of the Anopheles maculipennis group in Morocco and Algeria: An. sicaulti is conspecific with An. labranchiae.},
journal = {Acta tropica},
volume = {118},
number = {1},
pages = {6-13},
doi = {10.1016/j.actatropica.2010.12.006},
pmid = {21172298},
issn = {1873-6254},
mesh = {Algeria ; Animals ; Anopheles/*classification/genetics/*growth &amp; development ; *DNA Barcoding, Taxonomic ; Female ; Molecular Sequence Data ; Morocco ; Phylogeography ; Sequence Analysis, DNA ; },
abstract = {Anopheles labranchiae Falleroni is the only member of the Maculipennis Group known to occur in northern Africa; however, confusion exists as to the taxonomic status of its junior synonym, An. sicaulti Roubaud (type locality: near Rabat, Morocco). Based on morphological and behavioural distinctions, it has been suggested that Moroccan populations have been isolated from other North African populations by the Atlas Mountains, and that Moroccan populations may represent An. sicaulti, originally described as a variety of An. maculipennis Meigen. DNA barcodes (658bp of the mitochondrial COI gene) obtained from 89 An. maculipennis s.l. collected in Morocco (n=79) and Algeria (n=10) in 2007 and 2008 were used to determine if Moroccan populations are genetically isolated from those east of the Atlas Mountains (Algeria), and whether there is molecular evidence to support the presence of more than one member of the Maculipennis Group in the region. No evidence for speciation was found between Moroccan and Algerian populations, or within populations in northern Morocco. Moreover shared COI haplotypes between Algeria and Morocco indicate ongoing gene flow between populations in these countries, suggesting that the Atlas Mountains are not a boundary to gene flow in An. labranchiae. The synonymy of An. sicaulti with An. labranchiae is confirmed. That An. labranchiae comprises the same species in these North African countries is important for malaria control.},
}
@article {pmid21171865,
year = {2010},
author = {Teletchea, F},
title = {After 7 years and 1000 citations: comparative assessment of the DNA barcoding and the DNA taxonomy proposals for taxonomists and non-taxonomists.},
journal = {Mitochondrial DNA},
volume = {21},
number = {6},
pages = {206-226},
doi = {10.3109/19401736.2010.532212},
pmid = {21171865},
issn = {1940-1744},
mesh = {Anatomy, Comparative ; Animals ; Classification/*methods ; *DNA Barcoding, Taxonomic ; Periodicals as Topic ; Reference Standards ; },
abstract = {In 2003, two different approaches-DNA taxonomy and DNA barcoding-were simultaneously proposed to overcome some of the perceived intrinsic weaknesses of the traditional morphology-based taxonomical system, and to help non-taxonomists to resolve their crucial need for accurate and rapid species identification tools. After 7 years, it seems unlikely that a completely new taxonomical system based on molecular characters only (DNA taxonomy) will develop in the future. It is more likely that both morphological and molecular data will be simultaneously analyzed, developing what has been coined as "integrative taxonomy". Concerning DNA barcoding, it is now clear that it does not focus on building a tree-of-life nor to perform DNA taxonomy, but rather to produce a universal molecular identification key based on strong taxonomic knowledge that is collated in the barcode reference library. The indisputable success of the DNA barcoding project is chiefly due to the fact that DNA barcoding standards considerably enhance current practices in the molecular identification field, and standardization offers virtually endless applications for various users.},
}
@article {pmid21171864,
year = {2010},
author = {Kvist, S and Oceguera-Figueroa, A and Siddall, ME and Erséus, C},
title = {Barcoding, types and the Hirudo files: using information content to critically evaluate the identity of DNA barcodes.},
journal = {Mitochondrial DNA},
volume = {21},
number = {6},
pages = {198-205},
doi = {10.3109/19401736.2010.529905},
pmid = {21171864},
issn = {1940-1744},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Hirudo medicinalis/*classification/*genetics ; Phylogeny ; Reference Standards ; },
abstract = {Species identifications based on DNA barcoding rely on the correct identity of previously barcoded specimens, but little attention has been given to whether deposited barcodes include correspondence to the species' name-bearing type. The information content associated with COX1 sequences in the two most commonly used repositories of barcodes, GenBank and the Barcode of Life Data System (BOLD), is often insufficient for subsequent evaluation of the robustness of the identification procedure. We argue that DNA barcoding and taxonomy alike will benefit from more information content in the annotations of barcoded specimens as this will allow for validation and re-evaluation of the initial specimen identification. The aim should be to closely connect specimens from which reference barcodes are generated with the holotype through straight-forward taxonomy, and geographical and genetic correlations. Annotated information should also include voucher specimens and collector/identifier information. We examine two case studies based on empirical data, in which barcoding and taxonomy benefit from increased information content. On the basis of data from the first case study, we designate a barcoded neotype of the European medicinal leech, Hirudo medicinalis, on morphological and geographical grounds.},
}
@article {pmid21170336,
year = {2010},
author = {Ebihara, A and Nitta, JH and Ito, M},
title = {Molecular species identification with rich floristic sampling: DNA barcoding the pteridophyte flora of Japan.},
journal = {PloS one},
volume = {5},
number = {12},
pages = {e15136},
pmid = {21170336},
issn = {1932-6203},
mesh = {Biodiversity ; Computational Biology/methods ; DNA/genetics ; Databases, Genetic ; Diploidy ; *Electronic Data Processing ; Evolution, Molecular ; Genes, Plant ; Genetic Variation ; Germ Cells, Plant/physiology ; Japan ; Phylogeny ; Plants/*genetics ; Polymerase Chain Reaction ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: DNA barcoding is expected to be an effective identification tool for organisms with heteromorphic generations such as pteridophytes, which possess a morphologically simple gametophyte generation. Although a reference data set including complete coverage of the target local flora/fauna is necessary for accurate identification, DNA barcode studies including such rich taxonomic sampling on a countrywide scale are lacking.<br><br>The Japanese pteridophyte flora (733 taxa including subspecies and varieties) was used to test the utility of two plastid DNA barcode regions (rbcL and trnH-psbA) with the intention of developing an identification system for native gametophytes. DNA sequences were obtained from each of 689 (94.0%) taxa for rbcL and 617 (84.2%) taxa for trnH-psbA. Mean interspecific divergence values across all taxon pairs (K2P genetic distances) did not reveal a significant difference in rate between trnH-psbA and rbcL, but mean K2P distances of each genus showed significant heterogeneity according to systematic position. The minimum fail rate of taxon discrimination in an identification test using BLAST (12.52%) was obtained when rbcL and trnH-psbA were combined, and became lower in datasets excluding infraspecific taxa or apogamous taxa, or including sexual diploids only.<br><br>CONCLUSIONS/SIGNIFICANCE: This study demonstrates the overall effectiveness of DNA barcodes for species identification in the Japanese pteridophyte flora. Although this flora is characterized by a high occurrence of apogamous taxa that pose a serious challenge to identification using DNA barcodes, such taxa are limited to a small number of genera, and only minimally detract from the overall success rate. In the case that a query sequence is matched to a known apogamous genus, routine species identification may not be possible. Otherwise, DNA barcoding is a practical tool for identification of most Japanese pteridophytes, and is especially anticipated to be helpful for identification of non-hybridizing gametophytes.},
}
@article {pmid21168293,
year = {2011},
author = {Groenenberg, DS and Dekker, RW},
title = {A mouse's tail: how to settle an insurance dispute.},
journal = {Forensic science international},
volume = {207},
number = {1-3},
pages = {e24-7},
doi = {10.1016/j.forsciint.2010.11.022},
pmid = {21168293},
issn = {1872-6283},
mesh = {Animals ; China ; Cytochromes b/genetics ; DNA Degradation, Necrotic ; Dissent and Disputes ; Ecosystem ; *Insurance Claim Reporting ; Mice/*genetics ; Netherlands ; Sequence Analysis ; Species Specificity ; },
abstract = {Over the last years insurance companies have shown an increased interest in identifications of pest species, either as a form of risk assessment or to address liability issues. This paper describes a case report of such a forensic insurance investigation. The names of the corporations involved have been withheld in compliance with a pre-existing confidentiality agreement. A sea container containing sterile goods was shipped from China to the Netherlands. Upon inspection at its final destination, the contents were declared lost due to the presence of a dead mouse. Determination of which company should be held liable for this loss depended on where the mouse entered the container. The specimen was identified as belonging to the genus Apodemus (Muridae) based on morphology. Two species, A. sylvaticus and A. flavicollis occur in the Netherlands, two different species, A. agrarius and A. draco, occur in the relevant area in Eastern China. The distribution areas of these Dutch and Chinese Apodemus species do not overlap. Because the specimen was adolescent and partly mummified, key morphological characters for species-level identification were missing or not discernable. Published literature and sequence data available on GenBank showed that the four candidate species could be distinguished based on Cytochrome B barcode sequences. Given the decayed condition of the specimen, we expected possible DNA degradation. Therefore, both internal Cyt B primers (designed to amplify a short nucleotide sequence) and universal primers (which amplify a fourfold larger fragment) were employed. Remarkably, the primerset that was designed to amplify a short Cyt B sequence of A. draco amplified a well-studied pseudogene of A. sylvaticus. Both the Cyt B and the pseudogene sequence confirmed that the specimen in question is A. sylvaticus. Contamination of the sterile goods must therefore had taken place in the Netherlands.},
}
@article {pmid21164542,
year = {2010},
author = {Kerr, KC},
title = {A cryptic, intergeneric cytochrome c oxidase I pseudogene in tyrant flycatchers (family: Tyrannidae).},
journal = {Genome},
volume = {53},
number = {12},
pages = {1103-1109},
doi = {10.1139/G10-085},
pmid = {21164542},
issn = {1480-3321},
mesh = {Amino Acid Substitution ; Animals ; Base Sequence ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Pseudogenes/*genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Songbirds/*genetics ; },
abstract = {Nuclear mitochondrial pseudogenes, or "numts", are nonfunctional copies of mitochondrial genes that have been translocated to the nuclear genome. Numts have been used to study differences in mutation rates between the nuclear and mitochondrial genomes, but have also been implicated as troublesome for phylogenetic studies and DNA-based species identification (i.e., DNA barcoding). In this study, a suspected numt discovered during a study of mitochondrial cytochrome c oxidase I (COI) diversity in North American birds was targeted and sequenced from tyrant flycatchers (family: Tyrannidae). In total, the numt was found in five taxa representing two genera. Substitution rates were compared between COI and numt sequences. None of the numt sequences harboured stop codons nor frameshift mutations, but phylogenetic analysis revealed they had accumulated more amino acid substitutions than the mitochondrial COI sequences. Mitochondrial COI appeared to be preferentially amplified in most cases, but methods for numt detection are discussed for cases like this where sequences lack obvious features for identification. Because of its persistence across a broad taxonomic lineage, this numt could form a valuable model system for studying evolution in numts. The full size of the numt and its location within the nuclear genome are yet to be determined.},
}
@article {pmid21163834,
year = {2011},
author = {Kenny, EM and Cormican, P and Gilks, WP and Gates, AS and O'Dushlaine, CT and Pinto, C and Corvin, AP and Gill, M and Morris, DW},
title = {Multiplex target enrichment using DNA indexing for ultra-high throughput SNP detection.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {18},
number = {1},
pages = {31-38},
pmid = {21163834},
issn = {1756-1663},
mesh = {DNA/genetics ; Exons ; High-Throughput Nucleotide Sequencing/economics/*methods ; *Polymorphism, Single Nucleotide ; RNA, Complementary ; },
abstract = {Screening large numbers of target regions in multiple DNA samples for sequence variation is an important application of next-generation sequencing but an efficient method to enrich the samples in parallel has yet to be reported. We describe an advanced method that combines DNA samples using indexes or barcodes prior to target enrichment to facilitate this type of experiment. Sequencing libraries for multiple individual DNA samples, each incorporating a unique 6-bp index, are combined in equal quantities, enriched using a single in-solution target enrichment assay and sequenced in a single reaction. Sequence reads are parsed based on the index, allowing sequence analysis of individual samples. We show that the use of indexed samples does not impact on the efficiency of the enrichment reaction. For three- and nine-indexed HapMap DNA samples, the method was found to be highly accurate for SNP identification. Even with sequence coverage as low as 8x, 99% of sequence SNP calls were concordant with known genotypes. Within a single experiment, this method can sequence the exonic regions of hundreds of genes in tens of samples for sequence and structural variation using as little as 1 μg of input DNA per sample.},
}
@article {pmid21151586,
year = {2010},
author = {Khan, HA and Arif, IA and Shobrak, M},
title = {DNA Barcodes of Arabian Partridge and Philby's Rock Partridge: Implications for Phylogeny and Species Identification.},
journal = {Evolutionary bioinformatics online},
volume = {6},
number = {},
pages = {151-158},
pmid = {21151586},
issn = {1176-9343},
abstract = {Recently, DNA barcoding based on mitochondrial cytochrome c oxidase subunit I (COI) has gained wide attention because of simplicity and robustness of these barcodes for species identification including birds. The current GenBank records show the COI barcodes of only one species, chukar partridge (Alectoris chukar), of the Alectoris genus. In this study, we sequenced the 694 bp segment of COI gene of the two species including, Arabian partridge (Alectoris melanocephala) and Philby's rock partridge (Alectoris philbyi) of the same genus. We also compared these sequences with earlier published barcodes of chukar partridge. The pair-wise sequence comparison showed a total of 53 variable sites across all the 9 sequences from 3 species. Within-species variable sites were found to be 4 (Alectoris chukar), 0 (Alectoris philbyi) and 3 (Alectoris melanocephala). The genetic distances among the 9 individuals varied from 0.000 to 0.056. Phylogenetic analysis using COI barcodes clearly discriminated the 3 species, while Alectoris chukar was found to be more closely related to Alectoris philbyi. Similar differentiation was also observed using 1155 bp mitochondrial control region (CR) sequences suggesting the efficiency of COI gene for phylogenetic reconstruction and interspecific identification. This is the first study reporting the barcodes of Arabian partridge and Philby's rock partridge.},
}
@article {pmid21151562,
year = {2010},
author = {deWaard, JR and Mitchell, A and Keena, MA and Gopurenko, D and Boykin, LM and Armstrong, KF and Pogue, MG and Lima, J and Floyd, R and Hanner, RH and Humble, LM},
title = {Towards a global barcode library for Lymantria (Lepidoptera: Lymantriinae) tussock moths of biosecurity concern.},
journal = {PloS one},
volume = {5},
number = {12},
pages = {e14280},
pmid = {21151562},
issn = {1932-6203},
mesh = {Animals ; Bayes Theorem ; Canada ; Conservation of Natural Resources ; DNA/*genetics ; Ecology ; Electron Transport Complex IV/genetics ; Electronic Data Processing ; Genetic Variation ; Geography ; Haplotypes ; Lepidoptera/*genetics ; Likelihood Functions ; Moths ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Detecting and controlling the movements of invasive species, such as insect pests, relies upon rapid and accurate species identification in order to initiate containment procedures by the appropriate authorities. Many species in the tussock moth genus Lymantria are significant forestry pests, including the gypsy moth Lymantria dispar L., and consequently have been a focus for the development of molecular diagnostic tools to assist in identifying species and source populations. In this study we expand the taxonomic and geographic coverage of the DNA barcode reference library, and further test the utility of this diagnostic method, both for species/subspecies assignment and for determination of geographic provenance of populations.<br><br>Cytochrome oxidase I (COI) barcodes were obtained from 518 individuals and 36 species of Lymantria, including sequences assembled and generated from previous studies, vouchered material in public collections, and intercepted specimens obtained from surveillance programs in Canada. A maximum likelihood tree was constructed, revealing high bootstrap support for 90% of species clusters. Bayesian species assignment was also tested, and resulted in correct assignment to species and subspecies in all instances. The performance of barcoding was also compared against the commonly employed NB restriction digest system (also based on COI); while the latter is informative for discriminating gypsy moth subspecies, COI barcode sequences provide greater resolution and generality by encompassing a greater number of haplotypes across all Lymantria species, none shared between species.<br><br>CONCLUSIONS/SIGNIFICANCE: This study demonstrates the efficacy of DNA barcodes for diagnosing species of Lymantria and reinforces the view that the approach is an under-utilized resource with substantial potential for biosecurity and surveillance. Biomonitoring agencies currently employing the NB restriction digest system would gather more information by transitioning to the use of DNA barcoding, a change which could be made relatively seamlessly as the same gene region underlies both protocols.},
}
@article {pmid21120360,
year = {2010},
author = {Ruiz, F and Linton, YM and Ponsonby, DJ and Conn, JE and Herrera, M and Quiñones, ML and Vélez, ID and Wilkerson, RC},
title = {Molecular comparison of topotypic specimens confirms Anopheles (Nyssorhynchus) dunhami Causey (Diptera: Culicidae) in the Colombian Amazon.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {105},
number = {7},
pages = {899-903},
pmid = {21120360},
issn = {1678-8060},
support = {R01 AI054139/AI/NIAID NIH HHS/United States ; 2R01AI054139/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Anopheles/classification/enzymology/*genetics ; Colombia ; DNA, Intergenic/genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/*genetics ; Electron Transport Complex IV/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The presence of Anopheles (Nyssorhynchus) dunhami Causey in Colombia (Department of Amazonas) is confirmed for the first time through direct comparison of mtDNA cytochrome c oxidase I (COI) barcodes and nuclear rDNA second internal transcribed spacer (ITS2) sequences with topotypic specimens of An. dunhami from Tefé, Brazil. An. dunhami was identified through retrospective correlation of DNA sequences following misidentification as Anopheles nuneztovari s.l. using available morphological keys for Colombian mosquitoes. That An. dunhami occurs in Colombia and also possibly throughout the Amazon Basin, is of importance to vector control programs, as this non-vector species is morphologically similar to known malaria vectors including An. nuneztovari, Anopheles oswaldoi and Anopheles trinkae. Species identification of An. dunhami and differentiation from these closely related species are highly robust using either DNA ITS2 sequences or COI DNA barcode. DNA methods are advocated for future differentiation of these often sympatric taxa in South America.},
}
@article {pmid21116860,
year = {2011},
author = {Ramadan, HA},
title = {Sequence of specific mitochondrial 16S rRNA gene fragment from Egyptian buffalo is used as a pattern for discrimination between river buffaloes, cattle, sheep and goats.},
journal = {Molecular biology reports},
volume = {38},
number = {6},
pages = {3929-3934},
pmid = {21116860},
issn = {1573-4978},
mesh = {Animals ; Base Sequence ; Buffaloes/*genetics ; Cattle/*genetics ; Egypt ; Genes, Mitochondrial/*genetics ; Genes, rRNA/*genetics ; Genetic Variation ; Goats/*genetics ; Molecular Sequence Data ; Nucleotides/genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Alignment ; Sheep/*genetics ; Species Specificity ; },
abstract = {Characterization of molecular markers and the development of better assays for precise and rapid detection of domestic species are always in demand. This is particularly due to recent food scares and the crisis of biodiversity resulting from the huge ongoing illegal traffic of endangered species. The aim of this study was to develop a new and easy method for domestic species identification (river buffalo, cattle, sheep and goat) based on the analysis of a specific mitochondrial nucleotide sequence. For this reason, a specific fragment of Egyptian buffalo mitochondrial 16S rRNA gene (422 bp) was amplified by PCR using two universal primers. The sequence of this specific fragment is completely conserved between all tested Egyptian buffaloes and other river buffaloes in different places in the world. Also, the lengths of the homologous fragments were less by one nucleotide (421 bp) in case of goats and two nucleotides (420 bp) in case of both cattle and sheep. The detection of specific variable sites between investigated species within this fragment was sufficient to identify the biological origin of the samples. This was achieved by alignment between the unknown homologous sequence and the reference sequences deposited in GenBank database (accession numbers, FJ748599-FJ748607). Considering multiple alignment results between 16S rRNA homologous sequences obtained from GenBank database with the reference sequence, it was shown that definite nucleotides are specific for each of the four studied species of the family Bovidae. In addition, other nucleotides are detected which can allow discrimination between two groups of animals belonging to two subfamilies of family Bovidae, Group one (closely related species like cattle and buffalo, Subfamily Bovinae) and Group two (closely related species like sheep and goat, Subfamily Caprinae). This 16S DNA barcode character-based approach could be used to complement cytochrome c oxidase I (COI) in DNA barcoding. Also, it is a good tool for identification of unknown sample belonging to one of the four domestic animal species of family Bovidae quickly and easily.},
}
@article {pmid21110335,
year = {2011},
author = {Gao, Y and Stanford, WL and Chan, WC},
title = {Quantum-dot-encoded microbeads for multiplexed genetic detection of non-amplified DNA samples.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {7},
number = {1},
pages = {137-146},
doi = {10.1002/smll.201000909},
pmid = {21110335},
issn = {1613-6829},
support = {RMF-72557//Canadian Institutes of Health Research/Canada ; },
mesh = {DNA/*genetics ; Flow Cytometry ; *Microspheres ; *Quantum Dots ; },
abstract = {Barcoding technologies have become the basis for a new generation of molecular diagnostic platforms for measuring biomarkers in a high-throughput, rapid, and sensitive manner. Thus far, researchers have mainly focused on preparing different types of barcodes but, in order to use them optimally in genomic- and proteomic-based applications, there is a need to understand the effect of barcode and assay parameters on their performance. Herein, quantum-dot barcodes are systematically characterized for the detection of non-amplified DNA sequences. The effect of capture probes, reporter probes, and target DNA sequence lengths are studied, as well as the effect of the amount of noncomplementary sequences on the hybridization kinetics and efficiency. From DNA denaturation to signal detection, quantum-dot-barcode assays require less than one hour to detect a target DNA sequence with a linear dynamic range of 0.02-100 fmol. Three optically distinct quantum-dot barcodes are used to demonstrate the multiplexing capability of these barcodes for genomic detection. These results suggest that quantum-dot barcodes are an excellent platform for multiplex, rapid, and sensitive genetic detection.},
}
@article {pmid21110132,
year = {2010},
author = {Kim, S and Eo, HS and Koo, H and Choi, JK and Kim, W},
title = {DNA barcode-based molecular identification system for fish species.},
journal = {Molecules and cells},
volume = {30},
number = {6},
pages = {507-512},
doi = {10.1007/s10059-010-0148-2},
pmid = {21110132},
issn = {0219-1032},
mesh = {Animals ; Computational Biology ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA Probes/genetics ; DNA, Mitochondrial/*genetics ; *Databases, Genetic ; Electronic Data Processing/methods ; Fishes/*classification/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Species Specificity ; },
abstract = {In this study, we applied DNA barcoding to identify species using short DNA sequence analysis. We examined the utility of DNA barcoding by identifying 53 Korean freshwater fish species, 233 other freshwater fish species, and 1339 saltwater fish species. We successfully developed a web-based molecular identification system for fish (MISF) using a profile hidden Markov model. MISF facilitates efficient and reliable species identification, overcoming the limitations of conventional taxonomic approaches. MISF is freely accessible at http://bioinfosys.snu.ac.kr:8080/MISF/misf.jsp .},
}
@article {pmid21106009,
year = {2010},
author = {Ran, JH and Wang, PP and Zhao, HJ and Wang, XQ},
title = {A test of seven candidate barcode regions from the plastome in Picea (Pinaceae).},
journal = {Journal of integrative plant biology},
volume = {52},
number = {12},
pages = {1109-1126},
doi = {10.1111/j.1744-7909.2010.00995.x},
pmid = {21106009},
issn = {1744-7909},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Chloroplast/*genetics ; Genetic Loci/genetics ; Phylogeny ; Picea/*classification/*genetics ; Plastids/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {DNA barcoding, as a tool for species discrimination, has been used efficiently in animals, algae and fungi, but there are still debates on which DNA region(s) can be used as the standard barcode(s) for land plants. Gymnosperms, especially conifers, are important components of forests, and there is an urgent need for them to be identified through DNA barcoding because of their high frequency of collection in the field. However, the feasibility of DNA barcoding in gymnosperms has not been examined based on a dense species sampling. Here we selected seven candidate DNA barcodes from the plastome (matK, rbcL, rpoB, rpoC1, atpF-atpH, psbA-trnH, and psbK-psbI) to evaluate their suitability in Picea (spruce). The results showed that none of them or their different combinations has sufficient resolution for spruce species, although matK+rbcL might be used as a two-locus barcode. The low efficiency of these candidate barcodes in Picea might be caused by the paternal inheritance of the chloroplast genome, long generation time, recent radiation, and frequent inter-specific hybridization aided by wind pollination. Some of these factors could also be responsible for the difficulties in barcoding other plant groups. Furthermore, the potential of the nuclear LEAFY gene as a land plant barcode was discussed.},
}
@article {pmid21088013,
year = {2011},
author = {Novo, S and Barrios, L and Santaló, J and Gómez-Martínez, R and Duch, M and Esteve, J and Plaza, JA and Nogués, C and Ibáñez, E},
title = {A novel embryo identification system by direct tagging of mouse embryos using silicon-based barcodes.},
journal = {Human reproduction (Oxford, England)},
volume = {26},
number = {1},
pages = {96-105},
doi = {10.1093/humrep/deq309},
pmid = {21088013},
issn = {1460-2350},
mesh = {Animals ; Cryopreservation ; Embryo Culture Techniques/*methods/standards ; Embryo, Mammalian/cytology ; *Embryonic Development ; Female ; Mice ; Reproductive Techniques, Assisted ; Silicon ; },
abstract = {BACKGROUND: Measures to prevent assisted reproductive technologies (ART) mix-ups, such as labeling of all labware and double-witnessing protocols, are currently in place in fertility clinics worldwide. Technological solutions for electronic witnessing are also being developed. However, none of these solutions eliminate the risk of identification errors, because gametes and embryos must be transferred between containers several times during an ART cycle. Thus, the objective of this study was to provide a proof of concept for a direct embryo labeling system using silicon-based barcodes.<br><br>METHODS: Three different types of silicon-based barcodes (A, B and C) were designed and manufactured, and microinjected into the perivitelline space of mouse pronuclear embryos (one to four barcodes per embryo). Embryos were cultured in vitro until the blastocyst stage, and rates of embryo development, retention of the barcodes in the perivitelline space and embryo identification were assessed every 24 h. Release of the barcodes after embryo hatching was also determined. Finally, embryos microinjected with barcodes were frozen and thawed at the 2-cell stage to test the validity of the system after cryopreservation.<br><br>RESULTS: Barcodes present in the perivitelline space, independently of their type and number, did not affect embryo development rates. The majority of embryos (>90%) retained at least one of the microinjected barcodes in their perivitelline space up to the blastocyst stage. Increasing the number of barcodes per embryo resulted in a significant increase in embryo identification rates, but a significant decrease in the barcode release rates after embryo hatching. The highest rates of successful embryo identification (97%) were achieved with the microinjection of four type C barcodes, and were not affected by cryopreservation.<br><br>CONCLUSIONS: Our results demonstrate the feasibility of a direct embryo labeling system and constitute the starting point in the development of such systems.},
}
@article {pmid21085700,
year = {2010},
author = {Kress, WJ and Erickson, DL and Swenson, NG and Thompson, J and Uriarte, M and Zimmerman, JK},
title = {Advances in the use of DNA barcodes to build a community phylogeny for tropical trees in a Puerto Rican forest dynamics plot.},
journal = {PloS one},
volume = {5},
number = {11},
pages = {e15409},
pmid = {21085700},
issn = {1932-6203},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/chemistry/*genetics ; DNA, Ribosomal Spacer/genetics ; Ecosystem ; Endoribonucleases/genetics ; Genetic Variation ; Nucleotidyltransferases/genetics ; *Phylogeny ; Puerto Rico ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Analysis, DNA ; Species Specificity ; Trees/classification/*genetics ; Tropical Climate ; },
abstract = {BACKGROUND: Species number, functional traits, and phylogenetic history all contribute to characterizing the biological diversity in plant communities. The phylogenetic component of diversity has been particularly difficult to quantify in species-rich tropical tree assemblages. The compilation of previously published (and often incomplete) data on evolutionary relationships of species into a composite phylogeny of the taxa in a forest, through such programs as Phylomatic, has proven useful in building community phylogenies although often of limited resolution. Recently, DNA barcodes have been used to construct a robust community phylogeny for nearly 300 tree species in a forest dynamics plot in Panama using a supermatrix method. In that study sequence data from three barcode loci were used to generate a well-resolved species-level phylogeny.<br><br>Here we expand upon this earlier investigation and present results on the use of a phylogenetic constraint tree to generate a community phylogeny for a diverse, tropical forest dynamics plot in Puerto Rico. This enhanced method of phylogenetic reconstruction insures the congruence of the barcode phylogeny with broadly accepted hypotheses on the phylogeny of flowering plants (i.e., APG III) regardless of the number and taxonomic breadth of the taxa sampled. We also compare maximum parsimony versus maximum likelihood estimates of community phylogenetic relationships as well as evaluate the effectiveness of one- versus two- versus three-gene barcodes in resolving community evolutionary history.<br><br>CONCLUSIONS/SIGNIFICANCE: As first demonstrated in the Panamanian forest dynamics plot, the results for the Puerto Rican plot illustrate that highly resolved phylogenies derived from DNA barcode sequence data combined with a constraint tree based on APG III are particularly useful in comparative analysis of phylogenetic diversity and will enhance research on the interface between community ecology and evolution.},
}
@article {pmid21085582,
year = {2010},
author = {Stern, RF and Horak, A and Andrew, RL and Coffroth, MA and Andersen, RA and Küpper, FC and Jameson, I and Hoppenrath, M and Véron, B and Kasai, F and Brand, J and James, ER and Keeling, PJ},
title = {Environmental barcoding reveals massive dinoflagellate diversity in marine environments.},
journal = {PloS one},
volume = {5},
number = {11},
pages = {e13991},
pmid = {21085582},
issn = {1932-6203},
mesh = {Animals ; Atlantic Ocean ; *Biodiversity ; Caribbean Region ; Cluster Analysis ; DNA, Mitochondrial/chemistry/genetics ; Databases, Nucleic Acid ; Dinoflagellida/classification/*genetics/*growth &amp; development ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Molecular Sequence Data ; Pacific Ocean ; Phylogeny ; Protozoan Proteins/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND: Dinoflagellates are an ecologically important group of protists with important functions as primary producers, coral symbionts and in toxic red tides. Although widely studied, the natural diversity of dinoflagellates is not well known. DNA barcoding has been utilized successfully for many protist groups. We used this approach to systematically sample known "species", as a reference to measure the natural diversity in three marine environments.<br><br>In this study, we assembled a large cytochrome c oxidase 1 (COI) barcode database from 8 public algal culture collections plus 3 private collections worldwide resulting in 336 individual barcodes linked to specific cultures. We demonstrate that COI can identify to the species level in 15 dinoflagellate genera, generally in agreement with existing species names. Exceptions were found in species belonging to genera that were generally already known to be taxonomically challenging, such as Alexandrium or Symbiodinium. Using this barcode database as a baseline for cultured dinoflagellate diversity, we investigated the natural diversity in three diverse marine environments (Northeast Pacific, Northwest Atlantic, and Caribbean), including an evaluation of single-cell barcoding to identify uncultivated groups. From all three environments, the great majority of barcodes were not represented by any known cultured dinoflagellate, and we also observed an explosion in the diversity of genera that previously contained a modest number of known species, belonging to Kareniaceae. In total, 91.5% of non-identical environmental barcodes represent distinct species, but only 51 out of 603 unique environmental barcodes could be linked to cultured species using a conservative cut-off based on distances between cultured species.<br><br>CONCLUSIONS/SIGNIFICANCE: COI barcoding was successful in identifying species from 70% of cultured genera. When applied to environmental samples, it revealed a massive amount of natural diversity in dinoflagellates. This highlights the extent to which we underestimate microbial diversity in the environment.},
}
@article {pmid21078575,
year = {2011},
author = {Bulan, O and Sharma, G},
title = {High capacity color barcodes: per channel data encoding via orientation modulation in elliptical dot arrays.},
journal = {IEEE transactions on image processing : a publication of the IEEE Signal Processing Society},
volume = {20},
number = {5},
pages = {1337-1350},
doi = {10.1109/TIP.2010.2092437},
pmid = {21078575},
issn = {1941-0042},
mesh = {*Algorithms ; Color ; Electronic Data Processing/methods ; Image Enhancement/*methods ; Image Processing, Computer-Assisted/*methods ; },
abstract = {We present a new high capacity color barcode. The barcode we propose uses the cyan, magenta, and yellow (C,M,Y) colorant separations available in color printers and enables high capacity by independently encoding data in each of these separations. In each colorant channel, payload data is conveyed by using a periodic array of elliptically shaped dots whose individual orientations are modulated to encode the data. The orientation based data encoding provides beneficial robustness against printer and scanner tone variations. The overall color barcode is obtained when these color separations are printed in overlay as is common in color printing. A reader recovers the barcode data from a conventional color scan of the barcode, using red, green, and blue (R,G,B) channels complementary, respectively, to the print C, M, and Y channels. For each channel, first the periodic arrangement of dots is exploited at the reader to enable synchronization by compensating for both global rotation/scaling in scanning and local distortion in printing. To overcome the color interference resulting from colorant absorptions in noncomplementary scanner channels, we propose a novel interference minimizing data encoding approach and a statistical channel model (at the reader) that captures the characteristics of the interference, enabling more accurate data recovery. We also employ an error correction methodology that effectively utilizes the channel model. The experimental results show that the proposed method works well, offering (error-free) operational rates that are comparable to or better than the highest capacity barcodes known in the literature.},
}
@article {pmid21072538,
year = {2011},
author = {Yang, B and Cai, J and Cheng, X},
title = {Identification of astigmatid mites using ITS2 and COI regions.},
journal = {Parasitology research},
volume = {108},
number = {2},
pages = {497-503},
pmid = {21072538},
issn = {1432-1955},
mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/*genetics ; Electron Transport Complex IV/*genetics ; Mites/classification/*genetics ; Mitochondria/enzymology ; Phylogeny ; Species Specificity ; },
abstract = {Identification of astigmatid mites based on their morphological characteristics is difficult because of the similarity of their organs, especially in immature mites. The ribosomal second internal transcribed spacer (ITS2) and the mitochondrial cytochrome oxidase subunit I (COI) regions are highly conserved in the eukaryotes and are usually used as barcodes. The ITS2 and COI regions of six species of astigmatid mites (Aleuroglyphus ovatus, Blomia tropicalis, Dermatophagoides farinae, Dermatophagoides pteronyssinus, Euroglyphus maynei, Tyrophagus putrescentiae) were obtained by polymerase chain reaction and sequenced. The lengths of the ITS2 sequences varied from 316 to 488 bp, while the COI regions were 377 or 378 bp long. Considering the ITS2 genes, the intraspecific genetic distance was in the range of 0.00-0.077844, whereas the interspecific genetic distance was 0.202426-0.912959. The values were 0.000-0.029748 and 0.138403-0.279304 for intra- and interspecific genetic distances when COI genes were used. The phylogenetic trees inferred from the ITS2 and the COI regions, by using maximum parsimony and neighbor-joining methods, were identical to those based on their morphological classification. Thus, the ITS2 and COI regions can be applied as barcodes to identify different species of astigmatid mites.},
}
@article {pmid21060838,
year = {2010},
author = {Derycke, S and Vanaverbeke, J and Rigaux, A and Backeljau, T and Moens, T},
title = {Exploring the use of cytochrome oxidase c subunit 1 (COI) for DNA barcoding of free-living marine nematodes.},
journal = {PloS one},
volume = {5},
number = {10},
pages = {e13716},
pmid = {21060838},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; DNA Primers ; DNA, Helminth/*genetics ; Electron Transport Complex IV/*genetics ; *Marine Biology ; Nematoda/enzymology/*genetics ; Phylogeny ; Quality Control ; Species Specificity ; },
abstract = {BACKGROUND: The identification of free-living marine nematodes is difficult because of the paucity of easily scorable diagnostic morphological characters. Consequently, molecular identification tools could solve this problem. Unfortunately, hitherto most of these tools relied on 18S rDNA and 28S rDNA sequences, which often lack sufficient resolution at the species level. In contrast, only a few mitochondrial COI data are available for free-living marine nematodes. Therefore, we investigate the amplification and sequencing success of two partitions of the COI gene, the M1-M6 barcoding region and the I3-M11 partition.<br><br>METHODOLOGY: Both partitions were analysed in 41 nematode species from a wide phylogenetic range. The taxon specific primers for the I3-M11 partition outperformed the universal M1-M6 primers in terms of amplification success (87.8% vs. 65.8%, respectively) and produced a higher number of bidirectional COI sequences (65.8% vs 39.0%, respectively). A threshold value of 5% K2P genetic divergence marked a clear DNA barcoding gap separating intra- and interspecific distances: 99.3% of all interspecific comparisons were >0.05, while 99.5% of all intraspecific comparisons were <0.05 K2P distance.<br><br>CONCLUSION: The I3-M11 partition reliably identifies a wide range of marine nematodes, and our data show the need for a strict scrutiny of the obtained sequences, since contamination, nuclear pseudogenes and endosymbionts may confuse nematode species identification by COI sequences.},
}
@article {pmid21060687,
year = {2010},
author = {Roy, S and Tyagi, A and Shukla, V and Kumar, A and Singh, UM and Chaudhary, LB and Datt, B and Bag, SK and Singh, PK and Nair, NK and Husain, T and Tuli, R},
title = {Universal plant DNA barcode loci may not work in complex groups: a case study with Indian berberis species.},
journal = {PloS one},
volume = {5},
number = {10},
pages = {e13674},
pmid = {21060687},
issn = {1932-6203},
mesh = {Berberis/*genetics ; DNA, Plant/*genetics ; Phylogeny ; Species Specificity ; },
abstract = {BACKGROUND: The concept of DNA barcoding for species identification has gained considerable momentum in animals because of fairly successful species identification using cytochrome oxidase I (COI). In plants, matK and rbcL have been proposed as standard barcodes. However, barcoding in complex genera is a challenging task.<br><br>We investigated the species discriminatory power of four reportedly most promising plant DNA barcoding loci (one from nuclear genome--ITS, and three from plastid genome--trnH-psbA, rbcL and matK) in species of Indian Berberis L. (Berberidaceae) and two other genera, Ficus L. (Moraceae) and Gossypium L. (Malvaceae). Berberis species were delineated using morphological characters. These characters resulted in a well resolved species tree. Applying both nucleotide distance and nucleotide character-based approaches, we found that none of the loci, either singly or in combinations, could discriminate the species of Berberis. ITS resolved all the tested species of Ficus and Gossypium and trnH-psbA resolved 82% of the tested species in Ficus. The highly regarded matK and rbcL could not resolve all the species. Finally, we employed amplified fragment length polymorphism test in species of Berberis to determine their relationships. Using ten primer pair combinations in AFLP, the data demonstrated incomplete species resolution. Further, AFLP analysis showed that there was a tendency of the Berberis accessions to cluster according to their geographic origin rather than species affiliation.<br><br>CONCLUSIONS/SIGNIFICANCE: We reconfirm the earlier reports that the concept of universal barcode in plants may not work in a number of genera. Our results also suggest that the matK and rbcL, recommended as universal barcode loci for plants, may not work in all the genera of land plants. Morphological, geographical and molecular data analyses of Indian species of Berberis suggest probable reticulate evolution and thus barcode markers may not work in this case.},
}
@article {pmid22389642,
year = {2010},
author = {Hu, SH and Gao, X},
title = {Stable Encapsulation of QD Barcodes with Silica Shells.},
journal = {Advanced functional materials},
volume = {20},
number = {21},
pages = {3721-3726},
pmid = {22389642},
issn = {1616-301X},
support = {R01 CA131797/CA/NCI NIH HHS/United States ; R01 CA131797-02/CA/NCI NIH HHS/United States ; R01 CA131797-03/CA/NCI NIH HHS/United States ; },
abstract = {Quantum dot-doped mesoporous microbeads (QDMMs) are encapsulated with silica shells for enhanced chemical stability. The results show that a micro-emulsion procedure is highly efficient in coating QDMMs with polyvinyl alcohol (PVA), which is important in the subsequent deposition of a silica shell. Incorporation of fluorescent silane precursors allows direct observation of silica shells by fluorescence microscopy. The resulting silica coated QDMMs (QDMM@SiO(2)) exhibit remarkable stability against solvent-induced QD leaching and chemical-induced fluorescence quenching compared with uncoated QDMMs. Further development of this technology such as optimization of silica shell thickness, surface modification with non-fouling polymers, and conjugation with biomolecular probes will enable clinical translation of the optical barcoding technology for highly multiplexed detection and screening of genes and proteins.},
}
@article {pmid21058240,
year = {2010},
author = {Heubl, G},
title = {New aspects of DNA-based authentication of Chinese medicinal plants by molecular biological techniques.},
journal = {Planta medica},
volume = {76},
number = {17},
pages = {1963-1974},
doi = {10.1055/s-0030-1250519},
pmid = {21058240},
issn = {1439-0221},
mesh = {Amplified Fragment Length Polymorphism Analysis/methods ; DNA Fingerprinting ; DNA, Plant/analysis ; *Genetic Techniques ; Microsatellite Repeats ; Nucleic Acid Hybridization/methods ; Oligonucleotide Array Sequence Analysis/methods ; Plants, Medicinal/*classification/*genetics ; Polymerase Chain Reaction/methods ; Polymorphism, Restriction Fragment Length ; Random Amplified Polymorphic DNA Technique/methods ; Sequence Analysis, DNA ; },
abstract = {DNA technology provides a powerful tool to complement chemical analyses for authentication of Chinese medicinal plants and to ensure that herbal materials are not contaminated with ineffective or potentially harmful substitutes or adulterants. In the last two decades molecular biotechnology has provided sophisticated molecular techniques for authentication of botanical materials at the DNA level. This review provides an account of the most commonly used DNA-based technologies (RAPD, RFLP, ARMS, CAPS, AFLP, DAF, ISSR, SSR, sequencing, hybridization and microarrays) including suitable examples of Chinese medical plants. A critical evaluation of all methods is presented concerning sensitivity, reliability, reproducibility, and running costs. Recent achievements in the field of DNA barcoding and DNA chip technology that offer great potentials for screening of DNA and emerging new developments for future identification of species are briefly outlined.},
}
@article {pmid21048323,
year = {2010},
author = {Ma, XY and Xie, CX and Liu, C and Song, JY and Yao, H and Luo, K and Zhu, YJ and Gao, T and Pang, XH and Qian, J and Chen, SL},
title = {Species identification of medicinal pteridophytes by a DNA barcode marker, the chloroplast psbA-trnH intergenic region.},
journal = {Biological &amp; pharmaceutical bulletin},
volume = {33},
number = {11},
pages = {1919-1924},
doi = {10.1248/bpb.33.1919},
pmid = {21048323},
issn = {1347-5215},
mesh = {Base Sequence ; Chloroplasts/genetics ; *DNA, Chloroplast ; *DNA, Intergenic ; Drug Contamination/*prevention &amp; control ; Electronic Data Processing/*methods ; Ferns/*genetics ; *Genetic Markers ; Genome, Plant ; Plants, Medicinal/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Medicinal pteridophytes are an important group used in traditional Chinese medicine; however, there is no simple and universal way to differentiate various species of this group by morphological traits. A novel technology termed "DNA barcoding" could discriminate species by a standard DNA sequence with universal primers and sufficient variation. To determine whether DNA barcoding would be effective for differentiating pteridophyte species, we first analyzed five DNA sequence markers (psbA-trnH intergenic region, rbcL, rpoB, rpoC1, and matK) using six chloroplast genomic sequences from GeneBank and found psbA-trnH intergenic region the best candidate for availability of universal primers. Next, we amplified the psbA-trnH region from 79 samples of medicinal pteridophyte plants. These samples represented 51 species from 24 families, including all the authentic pteridophyte species listed in the Chinese pharmacopoeia (2005 version) and some commonly used adulterants. We found that the sequence of the psbA-trnH intergenic region can be determined with both high polymerase chain reaction (PCR) amplification efficiency (94.1%) and high direct sequencing success rate (81.3%). Combined with GeneBank data (54 species cross 12 pteridophyte families), species discriminative power analysis showed that 90.2% of species could be separated/identified successfully by the TaxonGap method in conjunction with the Basic Local Alignment Search Tool 1 (BLAST1) method. The TaxonGap method results further showed that, for 37 out of 39 separable species with at least two samples each, between-species variation was higher than the relevant within-species variation. Thus, the psbA-trnH intergenic region is a suitable DNA marker for species identification in medicinal pteridophytes.},
}
@article {pmid21047564,
year = {2011},
author = {Calvignac, S and Konecny, L and Malard, F and Douady, CJ},
title = {Preventing the pollution of mitochondrial datasets with nuclear mitochondrial paralogs (numts).},
journal = {Mitochondrion},
volume = {11},
number = {2},
pages = {246-254},
doi = {10.1016/j.mito.2010.10.004},
pmid = {21047564},
issn = {1872-8278},
mesh = {Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; Humans ; Polymerase Chain Reaction ; Pseudogenes ; RNA/genetics/isolation &amp; purification ; },
abstract = {Molecular tools have become prominent in ecology and evolution. A target of choice for molecular ecologists and evolutionists is mitochondrial DNA (mtDNA), whose many advantages have also convinced broad-scale, pragmatic programmes such as barcode initiatives. Of course, mtDNA is also of interest to human geneticists investigating mitochondrial diseases. Studies using mtDNA are however put at great risk by the inadvertent co-amplification or preferred amplification of nuclear pseudogenes (numts). A posteriori analysis of putative mtDNA sequences can help in removing numts but faces severe limitations (e.g. recently translocated numts will most of the time go unnoticed). Counter-measures taken a priori, i.e. explicitly designed for avoiding numt co-amplification or preferred amplification, are appealing but have never been properly assessed. Here we investigate the efficiency of four such measures (mtDNA enrichment, cDNA amplification, long-range amplification and pre-PCR dilution) on a common set of numt cases, showing that mtDNA enrichment is the worst performer while the use of pre-PCR dilution is a simple, yet robust method to prevent the pollution of putative mtDNA datasets with numts. Therefore, straightforward recommendations can be made that, if followed, will considerably increase the confidence in the mitochondrial origin of any mtDNA-like sequence.},
}
@article {pmid21044190,
year = {2010},
author = {Jargeat, P and Martos, F and Carriconde, F and Gryta, H and Moreau, PA and Gardes, M},
title = {Phylogenetic species delimitation in ectomycorrhizal fungi and implications for barcoding: the case of the Tricholoma scalpturatum complex (Basidiomycota).},
journal = {Molecular ecology},
volume = {19},
number = {23},
pages = {5216-5230},
doi = {10.1111/j.1365-294X.2010.04863.x},
pmid = {21044190},
issn = {1365-294X},
mesh = {Cell Nucleus/genetics ; DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Europe ; Genetic Variation ; Haplotypes ; Mycorrhizae/classification/genetics ; *Phylogeny ; Sequence Analysis, DNA ; Tricholoma/*classification/genetics ; },
abstract = {Population studies have revealed that the fungal ectomycorrhizal morphospecies Tricholoma scalpturatum consists of at least two genetically distinct groups that occur sympatrically in several geographical areas. This discovery prompted us to examine species boundaries and relationships between members formerly assigned to T. scalpturatum and allied taxa using phylogenetic analyses. Sequence data were obtained from three nuclear DNA regions [internal transcribed spacer (ITS), gpd and tef], from 101 carpophores collected over a large geographical range in Western Europe, and some reference sequences from public databases. The ITS was also tested for its applicability as DNA barcode for species delimitation. Four highly supported phylogenetic clades were detected. The two previously detected genetic groups of T. scalpturatum were assigned to the phylospecies Tricholoma argyraceum and T. scalpturatum. The two remaining clades were referred to as Tricholoma cingulatum and Tricholoma inocybeoides. Unexpectedly, T. cingulatum showed an accelerated rate of evolution that we attributed to narrow host specialization. This study also reveals recombinant ITS sequences in T. inocybeoides, suggesting a hybrid origin. The ITS was a useful tool for the determination of species boundaries: the mean value of intraspecific genetic distances in the entire ITS region (including 5.8S rDNA) was <0.2%, whereas interspecific divergence estimates ranged from 1.78% to 4.22%. Apart from giving insights into the evolution of the T. scalpturatum complex, this study contributes to the establishment of a library of taxonomically verified voucher specimens, an a posteriori correlation between phenotype and genotype, and DNA barcoding of ectomycorrhizal fungi.},
}
@article {pmid21041489,
year = {2011},
author = {Yoon, H and Gros, P and Heffron, F},
title = {Quantitative PCR-based competitive index for high-throughput screening of Salmonella virulence factors.},
journal = {Infection and immunity},
volume = {79},
number = {1},
pages = {360-368},
pmid = {21041489},
issn = {1098-5522},
support = {R01 AI022933/AI/NIAID NIH HHS/United States ; 5R01 AI 022933 23/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Bacterial Proteins/genetics/*metabolism ; Cation Transport Proteins/genetics/metabolism ; Cells, Cultured ; Gene Deletion ; Gene Expression Regulation ; Macrophages/metabolism ; Mice ; Polymerase Chain Reaction/*methods ; Salmonella typhimurium/*metabolism ; Virulence Factors/genetics/*metabolism ; },
abstract = {Salmonella enterica serovar Typhimurium is an intracellular pathogen and a main cause of food-borne illness. In this study, a quantitative PCR (qPCR)-based competitive index (CI) method was developed to simultaneously compare the growth of multiple Salmonella strains. This method was applied to a mixture of 17 Salmonella mutants lacking regulator genes, and their survival ratios were compared based on expression of natural resistance-associated macrophage protein 1 (Nramp1). Nramp1, as a major host innate immune component, controls the intracellular replication of pathogens. Deletion strains containing unique DNA barcodes in place of regulator genes were mixed with the parental control, and the bacteria were inoculated into congenic mice differing only at Nramp1. Most of the deletion strains were outcompeted by wild-type bacteria in either mouse strain, and the lack of Nramp1 didn't increase the tested strain/parent control replication ratios. When the same collection of mutants was tested in congenic mouse-derived primary macrophages, a major Nramp1-expressing cell type, six strains (ΔhimD, ΔphoP/phoQ, ΔrpoE, ΔrpoS, ΔompR/envZ, and Δhfq strains) grew better in Nramp1(-/-) than in Nramp1(+/+) macrophages, suggesting that these six regulators may play roles in overcoming Nramp1-mediated bactericidal activity in primary macrophages. The discrepancy in survival of macrophages and that of mice suggests either that there are differences in macrophage populations or that other cell types expressing Nramp1 control Salmonella proliferation in the host. The method described allows competitive infection analysis to be carried out on complex mixtures of bacteria and provides high reproducibility from independent biological replicates.},
}
@article {pmid21040428,
year = {2010},
author = {Haye, PA and Salinas, P and Acuña, E and Poulin, E},
title = {Heterochronic phenotypic plasticity with lack of genetic differentiation in the southeastern Pacific squat lobster Pleuroncodes monodon.},
journal = {Evolution &amp; development},
volume = {12},
number = {6},
pages = {628-634},
doi = {10.1111/j.1525-142X.2010.00447.x},
pmid = {21040428},
issn = {1525-142X},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; *Genetic Drift ; *Genetic Variation ; *Genetics, Population ; Nephropidae/*genetics ; Phenotype ; Phylogeny ; },
abstract = {Two forms of the squat lobster Pleuroncodes monodon can be found along the Pacific coast of South America: a smaller pelagic and a larger benthic form that live respectively in the northern and southern areas of the geographic distribution of the species. The morphological and life history differences between the pelagic and benthic forms could be explained either by genetic differentiation or phenotypic plasticity. In the latter case it would correspond to a heterochronic phenotypic plasticity that is fixed in different environments (phenotype fixation). The aim of this study was to evaluate whether the two forms are genetically differentiated or not; and thus to infer the underlying basis-heritable or plastic-of the existence of the two forms. Based on barcoding data of mitochondrial DNA (the COI gene), we show that haplotypes from individuals of the pelagic and benthic forms comprise a single genetic unit without genetic differentiation. Moreover, the data suggest that all studied individuals share a common demographic history of recent and sudden population expansion. These results strongly suggest that the differences between the two forms are due to phenotypic plasticity.},
}
@article {pmid21037964,
year = {2010},
author = {Göker, M and Grimm, GW and Auch, AF and Aurahs, R and Kučera, M},
title = {A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA.},
journal = {Evolutionary bioinformatics online},
volume = {6},
number = {},
pages = {97-112},
pmid = {21037964},
issn = {1176-9343},
abstract = {Identifying species is challenging in the case of organisms for which primarily molecular data are available. Even if morphological features are available, molecular taxonomy is often necessary to revise taxonomic concepts and to analyze environmental DNA sequences. However, clustering approaches to delineate molecular operational taxonomic units often rely on arbitrary parameter choices. Also, distance calculation is difficult for highly alignment-ambiguous sequences. Here, we applied a recently described clustering optimization method to highly divergent planktonic foraminifera SSU rDNA sequences. We determined the distance function and the clustering setting that result in the highest agreement with morphological reference data. Alignment-free distance calculation, when adapted to the use with partly non-homologous sequences caused by distinct primer pairs, outperformed multiple sequence alignment. Clustering optimization offers new perspectives for the barcoding of species diversity and for environmental sequencing. It bridges the gap between traditional and modern taxonomic disciplines by specifically addressing the issue of how to optimally account for both genetic divergence and given species concepts.},
}
@article {pmid21034519,
year = {2011},
author = {Staudacher, K and Pitterl, P and Furlan, L and Cate, PC and Traugott, M},
title = {PCR-based species identification of Agriotes larvae.},
journal = {Bulletin of entomological research},
volume = {101},
number = {2},
pages = {201-210},
doi = {10.1017/S0007485310000337},
pmid = {21034519},
issn = {1475-2670},
mesh = {Animals ; Coleoptera/*classification/*genetics/growth &amp; development ; DNA Barcoding, Taxonomic/economics/instrumentation/*methods ; Europe ; Genes, Insect ; Larva/classification/genetics ; Polymerase Chain Reaction/economics/instrumentation/*methods ; },
abstract = {Click beetle larvae within the genus Agriotes (Coleoptera: Elateridae), commonly known as wireworms, are abundant ground-dwelling herbivores which can inflict considerable damage to field crops. In Central Europe up to 20 species, which differ in their distribution, ecology and pest status, occur in arable land. However, the identification of these larvae based on morphological characters is difficult or impossible. This hampers progress towards controlling these pests. Here, we present a polymerase chain reaction (PCR)-based approach to identify, for the first time, 17 Agriotes species typically found in Central Europe. Diagnostic sequence information was generated and submitted to GenBank, allowing the identification of these species via DNA barcoding. Moreover, multiplex PCR assays were developed to identify the nine most abundant species rapidly within a single-step reaction: Agriotes brevis, A. litigiosus, A. obscurus, A. rufipalpis, A. sordidus, A. sputator, A. ustulatus, A. lineatus and A. proximus. The latter two species remain molecularly indistinguishable, questioning their species status. The multiplex PCR assays proved to be highly specific against non-agrioted elaterid beetles and other non-target soil invertebrates. By testing the molecular identification system with over 900 field-collected larvae, our protocol proved to be a reliable, cheap and quick method to routinely identify Central European Agriotes species.},
}
@article {pmid21031010,
year = {2010},
author = {Leung, AA and Lou, JJ and Mareninov, S and Silver, SS and Routbort, MJ and Riben, M and Andrechak, G and Yong, WH},
title = {Tolerance testing of passive radio frequency identification tags for solvent, temperature, and pressure conditions encountered in an anatomic pathology or biorepository setting.},
journal = {Journal of pathology informatics},
volume = {1},
number = {},
pages = {21},
pmid = {21031010},
issn = {2153-3539},
support = {P50 NS044378/NS/NINDS NIH HHS/United States ; R01 NS050151/NS/NINDS NIH HHS/United States ; U01 MH083500/MH/NIMH NIH HHS/United States ; },
abstract = {BACKGROUND: Radio frequency identification (RFID) tags have potential for use in identifying and tracking biospecimens in anatomic pathology and biorepository laboratories. However, there is little to no data on the tolerance of tags to solutions, solvents, temperatures, and pressures likely to be encountered in the laboratory. The functioning of the Hitachi Mu-chip RFID tag, a candidate for pathology use, was evaluated under such conditions.<br><br>METHODS: The RFID tags were affixed to cryovials containing tissue or media, glass slides, and tissue cassettes. The tags were interrogated for readability before and after each testing condition or cycle. Individual tags were subjected to only one testing condition but for multiple cycles. Testing conditions were: 1) Ten wet autoclave cycles (121&#xb0;C, 15 psi); 2) Ten dry autoclave cycles (121&#xb0;C, 26 psi); 3) Ten tissue processor cycles; 4) Ten hematoxylin and eosin (H&amp;E) staining cycles; 5) Ten antigen retrieval pressure cooker cycles (125&#xb0;C, 15 psi); 6) 75&#xb0;C for seven days; 7) 75-59 &#xb0;C day/night cycles for 7 days; 8) -80&#xb0;C, -150&#xb0;C, or -196&#xb0;C for 12 months; 9) Fifty freeze-thaw cycles (-196&#xb0;C to 22&#xb0;C).<br><br>RESULTS: One hundred percent of tags exposed to cold temperatures from -80 to -196 &#xb0;C (80 tags, 1120 successful reads), high temperatures from 52 to 75&#xb0;C (40 tags, 420 reads), H &amp; E staining (20 tags, 200 reads), pressure cooker antigen retrieval (20 tags, 200 reads), and wet autoclaving (20 tags, 200 reads) functioned well throughout and after testing. Of note, all 20 tested tags tolerated 50 freeze-thaw cycles and all 60 tags subjected to sustained freezing temperatures were readable after 1 year. One dry autoclaved tag survived nine cycles but failed after the tenth. The remaining 19 tags were readable after all 10 dry autoclave cycles. One tag failed after the first tissue processing cycle while the remaining 19 tags survived all 10 tissue processing cycles.<br><br>CONCLUSIONS: In this preliminary study, these RFID tags show a high-degree of tolerance to tested solutions, solvents, temperature, and pressure conditions. However, a measurable failure rate is detectable under some circumstances and redundant identification systems such as barcodes may be required with the deployment of RFID systems. We have delineated testing protocols that may be used as a framework for preliminary assessments of candidate RFID tag tolerance to laboratory conditions.},
}
@article {pmid21029792,
year = {2011},
author = {Hamilton, PB and Lewis, MD and Cruickshank, C and Gaunt, MW and Yeo, M and Llewellyn, MS and Valente, SA and Maia da Silva, F and Stevens, JR and Miles, MA and Teixeira, MM},
title = {Identification and lineage genotyping of South American trypanosomes using fluorescent fragment length barcoding.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {11},
number = {1},
pages = {44-51},
doi = {10.1016/j.meegid.2010.10.012},
pmid = {21029792},
issn = {1567-7257},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Genotype ; Polymerase Chain Reaction ; South America ; Species Specificity ; Trypanosoma/*genetics ; },
abstract = {Trypanosoma cruzi and Trypanosoma rangeli are human-infective blood parasites, largely restricted to Central and South America. They also infect a wide range of wild and domestic mammals and are transmitted by a numerous species of triatomine bugs. There are significant overlaps in the host and geographical ranges of both species. The two species consist of a number of distinct phylogenetic lineages. A range of PCR-based techniques have been developed to differentiate between these species and to assign their isolates into lineages. However, the existence of at least six and five lineages within T. cruzi and T. rangeli, respectively, makes identification of the full range of isolates difficult and time consuming. Here we have applied fluorescent fragment length barcoding (FFLB) to the problem of identifying and genotyping T. cruzi, T. rangeli and other South American trypanosomes. This technique discriminates species on the basis of length polymorphism of regions of the rDNA locus. FFLB was able to differentiate many trypanosome species known from South American mammals: T. cruzi cruzi, T. cruzi marinkellei, T. dionisii-like, T. evansi, T. lewisi, T. rangeli, T. theileri and T. vivax. Furthermore, all five T. rangeli lineages and many T. cruzi lineages could be identified, except the hybrid lineages TcV and TcVI that could not be distinguished from lineages III and II respectively. This method also allowed identification of mixed infections of T. cruzi and T. rangeli lineages in naturally infected triatomine bugs. The ability of FFLB to genotype multiple lineages of T. cruzi and T. rangeli together with other trypanosome species, using the same primer sets is an advantage over other currently available techniques. Overall, these results demonstrate that FFLB is a useful method for species diagnosis, genotyping and understanding the epidemiology of American trypanosomes.},
}
@article {pmid20979018,
year = {2011},
author = {Sui, XY and Huang, Y and Tan, Y and Guo, Y and Long, CL},
title = {Molecular authentication of the ethnomedicinal plant Sabia parviflora and its adulterants by DNA barcoding technique.},
journal = {Planta medica},
volume = {77},
number = {5},
pages = {492-496},
doi = {10.1055/s-0030-1250468},
pmid = {20979018},
issn = {1439-0221},
mesh = {Base Sequence ; China ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; DNA, Intergenic/chemistry ; DNA, Plant/*chemistry/genetics ; *Drug Contamination ; Drugs, Chinese Herbal/*classification/standards ; Electronic Data Processing/methods ; Ferns/*classification/*genetics ; Genes, Plant/genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Sequence Alignment ; Species Specificity ; },
abstract = {Sabia parviflora Wall. ex Roxb. is a traditional herb widely used by Chinese people, especially by the Buyi ethnic group which resides in Guizhou and Yunnan provinces. According to the Chinese Ethnic Pharmacopeia, the species is commonly used for soothing the liver and for the treatment of icteric hepatitis, hemostasis, and inflammation. However, due to the similar morphological characters of Sabia species and higher market demands, there are many substitutes and adulterants of S. parviflora. In this study, the differential identification of 6 Sabia species and 7 adulterants were investigated through DNA sequence analysis of three candidate DNA barcodes (trnH-psbA, rbcL-α, matK). Based on sequence alignments, we concluded that not only the trnH-psbA spacer sequence can distinguish S. parviflora from other Sabia species, but the matK + rbcL-α sequences also can differentiate it from the substitutes and adulterants. The classification tree of all samples based on rbcL-α sequences indicated that the rbcL region can identify samples into a family/genus level. Our results suggest that the three candidate barcodes can be used for the identification of S. parviflora and to distinguish it from common substitutes or adulterants.},
}
@article {pmid20978398,
year = {2010},
author = {Hullsiek, KH and George, M and Brown, SK},
title = {Designing and managing a flexible and dynamic biorepository system: a 15-year perspective from the CPCRA, ESPRIT, and INSIGHT clinical trial networks.},
journal = {Current opinion in HIV and AIDS},
volume = {5},
number = {6},
pages = {538-544},
pmid = {20978398},
issn = {1746-6318},
support = {HHSN261200800001C/CA/NCI NIH HHS/United States ; HHSN261200800001E/CA/NCI NIH HHS/United States ; U01 AI068641/AI/NIAID NIH HHS/United States ; },
mesh = {*Biological Specimen Banks ; *Biomarkers ; Biomedical Research/*methods/standards ; Clinical Trials as Topic ; *Database Management Systems ; HIV Infections ; Humans ; Specimen Handling/*methods/standards ; },
abstract = {PURPOSE OF REVIEW: We provide a long-term perspective of our experience with designing and managing a successful biorepository system. We include a brief history, a description of our current process, and lessons learned.<br><br>RECENT FINDINGS: Biologic specimens, collected and stored as part of HIV-related research for years, are now being used for biomarker analyses that have important implications for both AIDS and non-AIDS events. If appropriately collected, documented, and stored, biospecimens are a valuable resource that can help answer current and future scientific questions. International networks must be able to monitor and adhere to country-specific specimen use regulations. Specimens for human DNA research need increased levels of privacy protection. Issues to consider when designing a biorepository system include expertise, communication, data management, technology, standardized methods and procedures, shipping, and specimen use policies.<br><br>SUMMARY: As biorepositories are an integral part of research their design should not be an afterthought. Good designs consider all stages of research, and the most critical components are expertise and planning. Successful biorepository systems must have a balance of flexibility and standardization. The need for adaptable data management systems, whether commercial products or systems developed specifically for the network, should not be underestimated. Investment in appropriate technology, including a barcoding system with high-quality labels and printers, will pay off in the long term. To meet the needs of emerging technologies, it is becoming increasingly important to document the conditions at the time of specimen collection and processing. Regular communication between all components of the biorepository system is critical.},
}
@article {pmid20977734,
year = {2010},
author = {Gao, T and Yao, H and Song, J and Zhu, Y and Liu, C and Chen, S},
title = {Evaluating the feasibility of using candidate DNA barcodes in discriminating species of the large Asteraceae family.},
journal = {BMC evolutionary biology},
volume = {10},
number = {},
pages = {324},
pmid = {20977734},
issn = {1471-2148},
mesh = {Asteraceae/*classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; },
abstract = {BACKGROUND: Five DNA regions, namely, rbcL, matK, ITS, ITS2, and psbA-trnH, have been recommended as primary DNA barcodes for plants. Studies evaluating these regions for species identification in the large plant taxon, which includes a large number of closely related species, have rarely been reported.<br><br>RESULTS: The feasibility of using the five proposed DNA regions was tested for discriminating plant species within Asteraceae, the largest family of flowering plants. Among these markers, ITS2 was the most useful in terms of universality, sequence variation, and identification capability in the Asteraceae family. The species discriminating power of ITS2 was also explored in a large pool of 3,490 Asteraceae sequences that represent 2,315 species belonging to 494 different genera. The result shows that ITS2 correctly identified 76.4% and 97.4% of plant samples at the species and genus levels, respectively. In addition, ITS2 displayed a variable ability to discriminate related species within different genera.<br><br>CONCLUSIONS: ITS2 is the best DNA barcode for the Asteraceae family. This approach significantly broadens the application of DNA barcoding to resolve classification problems in the family Asteraceae at the genera and species levels.},
}
@article {pmid20977186,
year = {2010},
author = {Ellis, R and Waterton, C and Wynne, B},
title = {Taxonomy, biodiversity and their publics in twenty-first-century DNA barcoding.},
journal = {Public understanding of science (Bristol, England)},
volume = {19},
number = {4},
pages = {497-512},
doi = {10.1177/0963662509335413},
pmid = {20977186},
issn = {0963-6625},
mesh = {*Biodiversity ; *Classification ; Public Policy ; *Sequence Analysis, DNA ; Species Specificity ; },
abstract = {We examine the crafting of publics in the global Barcoding of Life Initiative (BOLI)--seen as crucial for re-invigorating, and democratizing, early-twenty-first-century taxonomic sciences and hence for actually achieving biodiversity protection. Our approach to the issue of publics differs from that of conventional public understanding of or engagement with science work. Combining science and technology studies with critical political theory allows us to examine the discursive and material formation of publics occurring within the science of DNA barcoding. Co-productionist theory suggests BOLI to be actively crafting its prospective publics imaginatively, as an integral part of its self-composition as public science. Drawing on the work of Laclau's On Populist Reason, we examine how such normatively weighted abstract publics are necessarily chronically incomplete, with an unavoidable tension between the universal and the particular.},
}
@article {pmid20965241,
year = {2011},
author = {Mati, E and de Boer, H},
title = {Ethnobotany and trade of medicinal plants in the Qaysari Market, Kurdish Autonomous Region, Iraq.},
journal = {Journal of ethnopharmacology},
volume = {133},
number = {2},
pages = {490-510},
doi = {10.1016/j.jep.2010.10.023},
pmid = {20965241},
issn = {1872-7573},
mesh = {*Commerce ; DNA Barcoding, Taxonomic ; Ethnobotany/*economics ; Ethnopharmacology ; Herbal Medicine/economics ; Humans ; Iraq ; Phytotherapy/economics ; *Plants, Medicinal/genetics ; },
abstract = {AIM OF STUDY: Marketplaces epitomize a region's culture and trade, and can give a rapid insight into traditions and salience of commercialized medicinal products. The Qaysari bazaar, bordering the citadel in Erbil city in the Kurdistan Autonomous Region, Iraq, has 21 herbalist shops trading natural medicinal products, wild-crafted and cultivated from all over the Middle East and Asia Minor.<br><br>MATERIALS AND METHODS: Freelist surveys were conducted with 18 of these herbalists to determine diversity and salience of traded traditional medicinal plants. Interviews were conducted to document use, trade volume, origin, stock and value of the reported species. Plant species were identified using a combination of morphological identification and molecular barcoding using the ITS region.<br><br>RESULTS: Vouchers were collected for a total of 158 samples, corresponding to 82 species of plants, 5 animal products, 8 types of stones, minerals or chemicals, as well as 16 mixtures of plant products. Consensus Analysis of the herbalist interviews shows strong support for a single culture of herbalist plant use.<br><br>CONCLUSIONS: Most reported plant species are known to have been used since antiquity, and uses are identical or similar to previously documented uses. Herbalists report a steady year-on-year increase in trade due to the economic stability in recent times. A majority (64%) of medicinal plants is imported from outside Iraq, and the data shows that imported plants trade at a higher price than locally-sourced species, and that these species are stocked in higher volumes by the herbalists to ensure a steady supply to consumers. A strong tradition of herbal medicine exists in Kurdistan today exemplified by the diverse and vigorous trade in medicinal plants commercialized from the provinces around Erbil to countries as far away as India, Spain and Libya.},
}
@article {pmid20957605,
year = {2010},
author = {Abd-Elsalam, KA and Almohimeed, I and Moslem, MA and Bahkali, AH},
title = {M13-microsatellite PCR and rDNA sequence markers for identification of Trichoderma (Hypocreaceae) species in Saudi Arabian soil.},
journal = {Genetics and molecular research : GMR},
volume = {9},
number = {4},
pages = {2016-2024},
doi = {10.4238/vol9-4gmr908},
pmid = {20957605},
issn = {1676-5680},
mesh = {Base Sequence ; Cloning, Molecular ; Cluster Analysis ; DNA Primers ; DNA, Ribosomal/*genetics ; Microsatellite Repeats/*genetics ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; Saudi Arabia ; Sequence Homology, Nucleic Acid ; *Soil Microbiology ; Trichoderma/*genetics ; },
abstract = {Seven fungal isolates were identified as pan-global Hypocrea/Trichoderma species, from section Trichoderma, on the basis of their morphology. These species were H. lixii/T. harzianum and H. orientalis/T. longibrachiatum. PCR-based markers with primer M13 (core sequence of phage M13) and internal-transcribed spacer sequences of ribosomal DNA were used to confirm the identity of the two Trichoderma species. Sequence identification was performed using the TrichOKEY version 2.0 barcode program and the multilocus similarity search database TrichoBLAST. Sequences from the ribosomal DNA internal-transcribed spacer regions showed limited variation among the Trichoderma species. This analysis divided the isolates into two main groups. Grouping the isolates based on cluster analysis of their DNA profiles matched the grouping based on morphological taxonomy. Molecular data obtained from analyses of gene sequences are essential to distinguish phonetically cryptic species in this group and to establish phylogenetic relationships.},
}
@article {pmid20957085,
year = {2010},
author = {Arif, IA and Bakir, MA and Khan, HA and Ahamed, A and Al Farhan, AH and Al Homaidan, AA and Al Sadoon, M and Bahkali, AH and Shobrak, M},
title = {A simple method for DNA extraction from mature date palm leaves: impact of sand grinding and composition of lysis buffer.},
journal = {International journal of molecular sciences},
volume = {11},
number = {9},
pages = {3149-3157},
pmid = {20957085},
issn = {1422-0067},
mesh = {Arecaceae/*chemistry ; Cell Fractionation/methods ; Chemical Fractionation/methods ; DNA, Plant/chemistry/*isolation &amp; purification ; Hydrolysis ; Plant Leaves/*chemistry ; },
abstract = {Molecular marker techniques have been widely used for cultivar identification of inbred date palms (Phoenix dactylifera L.; Arecaceae) and biodiversity conservation. Isolation of highly pure DNA is the prerequisite for PCR amplification and subsequent use such as DNA fingerprinting and sequencing of genes that have recently been developed for barcoding. To avoid problems related to the preservation and use of liquid nitrogen, we examined sterile sand for grinding the date palm leaves. Individual and combined effects of sodium chloride (NaCl), polyvinylpyrrolidone (PVP) and lithium chloride (LiCl) with the cetyltrimethylammonium bromide (CTAB) method for a DNA yield of sufficient purity and PCR amplification were evaluated in this study. Presence of LiCl and PVP alone or together in the lysis buffer did not significantly improve the DNA yield and purity compared with the addition of NaCl. Our study suggested that grinding of date palm leaf with sterile sand and inclusion of NaCl (1.4 M) in the lysis buffer without the costly use of liquid nitrogen, PVP and LiCl, provides a DNA yield of sufficient purity, suitable for PCR amplification.},
}
@article {pmid20957043,
year = {2010},
author = {Yao, H and Song, J and Liu, C and Luo, K and Han, J and Li, Y and Pang, X and Xu, H and Zhu, Y and Xiao, P and Chen, S},
title = {Use of ITS2 region as the universal DNA barcode for plants and animals.},
journal = {PloS one},
volume = {5},
number = {10},
pages = {},
pmid = {20957043},
issn = {1932-6203},
mesh = {Animals ; DNA/*genetics ; DNA, Plant/classification/*genetics ; *Electronic Data Processing ; Plants/*genetics ; Species Specificity ; },
abstract = {BACKGROUND: The internal transcribed spacer 2 (ITS2) region of nuclear ribosomal DNA is regarded as one of the candidate DNA barcodes because it possesses a number of valuable characteristics, such as the availability of conserved regions for designing universal primers, the ease of its amplification, and sufficient variability to distinguish even closely related species. However, a general analysis of its ability to discriminate species in a comprehensive sample set is lacking.<br><br>In the current study, 50,790 plant and 12,221 animal ITS2 sequences downloaded from GenBank were evaluated according to sequence length, GC content, intra- and inter-specific divergence, and efficiency of identification. The results show that the inter-specific divergence of congeneric species in plants and animals was greater than its corresponding intra-specific variations. The success rates for using the ITS2 region to identify dicotyledons, monocotyledons, gymnosperms, ferns, mosses, and animals were 76.1%, 74.2%, 67.1%, 88.1%, 77.4%, and 91.7% at the species level, respectively. The ITS2 region unveiled a different ability to identify closely related species within different families and genera. The secondary structure of the ITS2 region could provide useful information for species identification and could be considered as a molecular morphological characteristic.<br><br>CONCLUSIONS/SIGNIFICANCE: As one of the most popular phylogenetic markers for eukaryota, we propose that the ITS2 locus should be used as a universal DNA barcode for identifying plant species and as a complementary locus for CO1 to identify animal species. We have also developed a web application to facilitate ITS2-based cross-kingdom species identification (http://its2-plantidit.dnsalias.org).},
}
@article {pmid20946807,
year = {2010},
author = {Lefrançois, P and Zheng, W and Snyder, M},
title = {ChIP-Seq using high-throughput DNA sequencing for genome-wide identification of transcription factor binding sites.},
journal = {Methods in enzymology},
volume = {470},
number = {},
pages = {77-104},
doi = {10.1016/S0076-6879(10)70004-5},
pmid = {20946807},
issn = {1557-7988},
mesh = {Binding Sites/genetics ; Chromatin Immunoprecipitation/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Protein Binding/genetics ; Saccharomyces cerevisiae/genetics/metabolism ; Transcription Factors/*metabolism ; },
abstract = {Much of eukaryotic gene regulation is mediated by binding of transcription factors near or within their target genes. Transcription factor binding sites (TFBS) are often identified globally using chromatin immunoprecipitation (ChIP) in which specific protein-DNA interactions are isolated using an antibody against the factor of interest. Coupling ChIP with high-throughput DNA sequencing allows identification of TFBS in a direct, unbiased fashion; this technique is termed ChIP-Sequencing (ChIP-Seq). In this chapter, we describe the yeast ChIP-Seq procedure, including the protocols for ChIP, input DNA preparation, and Illumina DNA sequencing library preparation. Descriptions of Illumina sequencing and data processing and analysis are also included. The use of multiplex short-read sequencing (i.e., barcoding) enables the analysis of many ChIP samples simultaneously, which is especially valuable for organisms with small genomes such as yeast.},
}
@article {pmid20944841,
year = {2011},
author = {Peng, Q and Cao, Z and Lau, C and Kai, M and Lu, J},
title = {Aptamer-barcode based immunoassay for the instantaneous derivatization chemiluminescence detection of IgE coupled to magnetic beads.},
journal = {The Analyst},
volume = {136},
number = {1},
pages = {140-147},
doi = {10.1039/c0an00448k},
pmid = {20944841},
issn = {1364-5528},
mesh = {Aptamers, Nucleotide/*chemistry ; Guanine/chemistry ; Humans ; Immunoassay/*methods ; Immunoglobulin E/*blood ; Luminescent Measurements/*methods ; *Magnetics ; Organometallic Compounds/chemistry ; Phenylglyoxal/chemistry ; },
abstract = {We report on a highly sensitive aptameric assay system for the determination of IgE, where a special chemiluminescence (CL) reagent, 3,4,5-trimethoxylphenylglyoxal (TMPG), acts as the signaling molecule and polystyrene beads as the amplification platform. Briefly, a "sandwich-type" detection strategy is employed in our design, where magnetic beads functionalized with a capture antibody were reacted with the target protein IgE, and then sandwiched with the aptamer-barcodes which were prepared by assembling polystyrene beads with IgE aptamer. The target immunoreaction event could be sensitively detected via an instantaneous derivatization reaction between TMPG and the guanine (G) nucleotides within the aptamer-barcodes to form an unstable CL intermediate for the generation of light. Further signal amplification is achieved by extending the G nucleotide-rich domain on the aptamer backbone for second amplification. Such simple amplified CL transduction allows the detection of IgE down to the 4.6 pM level, which is better than most previous aptameric methods for IgE detection. This new protocol also provides a good capability in discriminating IgE from nontarget proteins such as IgG, IgA, IgM, interferon and thrombin. The practical application of the proposed aptamer-barcode based immunoassay was successfully carried out for the determination of IgE in 20 human serum samples. It is straightforward to adapt this strategy to detect a spectrum of other proteins by using different aptamers, thus this method may offer a new direction in designing high-performance CL aptasensors for early diagnoses of diseases.},
}
@article {pmid20944018,
year = {2011},
author = {Gresham, D and Boer, VM and Caudy, A and Ziv, N and Brandt, NJ and Storey, JD and Botstein, D},
title = {System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae.},
journal = {Genetics},
volume = {187},
number = {1},
pages = {299-317},
pmid = {20944018},
issn = {1943-2631},
support = {R01 GM046406/GM/NIGMS NIH HHS/United States ; HG 002913/HG/NHGRI NIH HHS/United States ; R01 HG002913/HG/NHGRI NIH HHS/United States ; R37 GM046406/GM/NIGMS NIH HHS/United States ; R01 GM107466/GM/NIGMS NIH HHS/United States ; P50 GM071508/GM/NIGMS NIH HHS/United States ; GM046406/GM/NIGMS NIH HHS/United States ; GM071508/GM/NIGMS NIH HHS/United States ; },
mesh = {Genes, Fungal/*genetics ; Leucine/*deficiency ; Mutation ; Phosphates/*deficiency ; Saccharomyces cerevisiae/*genetics/metabolism/*physiology ; Sequence Analysis, DNA ; Systems Biology/*methods ; },
abstract = {An essential property of all cells is the ability to exit from active cell division and persist in a quiescent state. For single-celled microbes this primarily occurs in response to nutrient deprivation. We studied the genetic requirements for survival of Saccharomyces cerevisiae when starved for either of two nutrients: phosphate or leucine. We measured the survival of nearly all nonessential haploid null yeast mutants in mixed populations using a quantitative sequencing method that estimates the abundance of each mutant on the basis of frequency of unique molecular barcodes. Starvation for phosphate results in a population half-life of 337 hr whereas starvation for leucine results in a half-life of 27.7 hr. To measure survival of individual mutants in each population we developed a statistical framework that accounts for the multiple sources of experimental variation. From the identities of the genes in which mutations strongly affect survival, we identify genetic evidence for several cellular processes affecting survival during nutrient starvation, including autophagy, chromatin remodeling, mRNA processing, and cytoskeleton function. In addition, we found evidence that mitochondrial and peroxisome function is required for survival. Our experimental and analytical methods represent an efficient and quantitative approach to characterizing genetic functions and networks with unprecedented resolution and identified genotype-by-environment interactions that have important implications for interpretation of studies of aging and quiescence in yeast.},
}
@article {pmid20943562,
year = {2010},
author = {Van Zuydam, NR and Paciura, D and Jacobs, K and Wingfield, MJ and Coetzee, MP and Wingfield, BD},
title = {Barcoding and microcoding using "identiprimers" with Leptographium species.},
journal = {Mycologia},
volume = {102},
number = {6},
pages = {1274-1287},
doi = {10.3852/09-291},
pmid = {20943562},
issn = {0027-5514},
mesh = {Ascomycota/*classification/genetics/*isolation &amp; purification ; DNA Primers/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {Leptographium species provide an ideal model to test the applications of a PCR microcoding system for differentiating species of other genera of ascomycetes. Leptographium species are closely related and share similar gross morphology. Probes designed for a PhyloChip for Leptographium have been transferred and tested as primers for PCR diagnostic against Leptographium species. The primers were combined with complementary universal primers to identify known and suspected undescribed species of Leptographium. The primer set was optimized for 56 species, including the three varieties of L. wageneri, then blind-tested against 10 random DNA samples. The protocols established in this study successfully identified species from the blind test as well as eight previously undescribed isolates of Leptographium. The undescribed isolates were identified as new species of Leptographium with the aid of the microcoding PCR identification system established in this study. The primers that were positive for each undescribed isolate were used to determine close relatives of these species and some of their biological characteristics. The transfer of oligonucleotides from a micro-array platform to a PCR diagnostic was successful, and the identification system is robust for both known and unknown species of Leptographium.},
}
@article {pmid20943554,
year = {2010},
author = {Hughes, KW and Mather, DA and Petersen, RH},
title = {A new genus to accommodate Gymnopus acervatus (Agaricales).},
journal = {Mycologia},
volume = {102},
number = {6},
pages = {1463-1478},
doi = {10.3852/09-318},
pmid = {20943554},
issn = {0027-5514},
mesh = {Agaricales/*classification/genetics/*isolation &amp; purification ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Molecular Sequence Data ; Phylogeny ; Trees/microbiology ; },
abstract = {Phylogenies based on ITS and LSU nrDNA sequences show Agaricus (Gymnopus) acervatus as unique within the Gymnopus/Rhodocollybia complex. These phylogenies imply that a separate genus is necessary, and Connopus is proposed. Infraspecific morphological and DNA-based variation within C. acervatus suggests that a western North American clade might be reproductively isolated from the eastern North American/Scandinavian clade and that in this species complex the European and eastern North American clade might be conspecific. A Scandinavian exemplar is selected for bar-coding. Two GenBank sequences with name-phylogenetic placement inconsistencies are identified.},
}
@article {pmid20931794,
year = {2010},
author = {Cao, H and Sasaki, Y and Fushimi, H and Komatsu, K},
title = {Authentication of Curcuma species (Zingiberaceae) based on nuclear 18S rDNA and plastid trnK sequences.},
journal = {Yao xue xue bao = Acta pharmaceutica Sinica},
volume = {45},
number = {7},
pages = {926-933},
pmid = {20931794},
issn = {0513-4870},
mesh = {China ; Curcuma/classification/*genetics ; DNA Mutational Analysis ; DNA, Chloroplast/*genetics ; DNA, Plant/genetics ; Introns ; Japan ; Molecular Sequence Data ; Nucleic Acid Amplification Techniques ; Phylogeny ; Plants, Medicinal/classification/*genetics ; Plastids/genetics ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA ; },
abstract = {Curcuma drugs have been used discriminatingly for invigorating blood circulation, promoting digestion, and as a cholagogic in China. However, there is confusion about the drug's botanical origins and clinical uses because of morphological similarity of Curcuma plants and drugs. Comparative sequencing of the 18S rRNA gene in nuclear ribosomal DNA (rDNA) and trnK gene in chloroplast DNA (cpDNA) was carried out in order to examine interspecies phylogeny and to identify ultimately Curcuma species. A total of a hundred of accessions of eighteen species were analyzed. This resulted in an aligned matrix of 1810 bp for 18S rDNA and 2 800 bp for trnK. 18S rDNA sequence divergence within the ingroup ranged from 0-0.05%, trnK ranged from 0-0.19%. One base transversion-substituted site (from cytosine to thymine) was observed from the upstream of 18S rDNA at nucleotide position 234 in C. kwangsiensis and Japanese population of C. zedoaria which have separated genetic distance to other Curcuma taxa. Two noncoding regions embedded in trnK intron showed higher variability, including nucleotide substitutions, repeat insertion and deletions. Based on consensus of relationship, eighteen major lineages within Curcuma are recognized at the species level. The results suggest that Curcuma is monophyletic with 100% bootstrap support and sister to the genera Hedychium and Zingiber. The trnK sequences showed considerable variations between Curcuma species and thus were revealed as a promising candidate for barcoding of Curcuma species, which provide valuable characters for inferring relationship within species but are insufficient to resolve relationships among closely related taxa.},
}
@article {pmid20927714,
year = {2010},
author = {Techaprasan, J and Klinbunga, S and Ngamriabsakul, C and Jenjittikul, T},
title = {Genetic variation of Kaempferia (Zingiberaceae) in Thailand based on chloroplast DNA (psbA-trnH and petA-psbJ) sequences.},
journal = {Genetics and molecular research : GMR},
volume = {9},
number = {4},
pages = {1957-1973},
doi = {10.4238/vol9-4gmr873},
pmid = {20927714},
issn = {1676-5680},
mesh = {Base Sequence ; DNA Primers ; DNA, Chloroplast/*genetics ; Genes, Plant ; *Genetic Variation ; Polymerase Chain Reaction ; Thailand ; Zingiberaceae/*genetics ; },
abstract = {Genetic variation and species authentication of 71 Kaempferia accessions (representing 15 recognized, six new, and four unidentified species) found indigenously in Thailand were examined by determining chloroplast psbA-trnH and partial petA-psbJ spacer sequences. Ten closely related species (Boesenbergia rotunda, Gagnepainia godefroyi, G. thoreliana, Globba substrigosa, Smithatris myanmarensis, S. supraneanae, Scaphochlamys biloba, S. minutiflora, S. rubescens, and Stahlianthus sp) were also included. After sequence alignments, 1010 and 865 bp in length were obtained for the respective chloroplast DNA sequences. Intraspecific sequence variation was not observed in Kaempferia candida, K. angustifolia, K. laotica, K. galanga, K. pardi sp nov., K. bambusetorum sp nov., K. albomaculata sp nov., K. minuta sp nov., Kaempferia sp nov. 1, and G. thoreliana, for which more than one specimen was available. In contrast, intraspecific sequence polymorphisms were observed in various populations of K. fallax, K. filifolia, K. elegans, K. pulchra, K. rotunda, K. marginata, K. parviflora, K. larsenii, K. roscoeana, K. siamensis, and G. godefroyi. A strict consensus tree based on combined psbA-trnH and partial petA-psbJ sequences revealed four major groups of Kaempferia species. We suggest that the genus Kaempferia is a polyphyletic group, as K. candida was distantly related and did not group with other Kaempferia species. Polymorphic sites and indels of psbA-trnH and petA-psbJ can be used as DNA barcodes for species diagnosis of most Kaempferia and outgroup species. Nuclear DNA polymorphism should be examined to determine if there has been interspecific hybridization and chloroplast DNA introgression in these taxa.},
}
@article {pmid20927602,
year = {2010},
author = {Nims, RW and Sykes, G and Cottrill, K and Ikonomi, P and Elmore, E},
title = {Short tandem repeat profiling: part of an overall strategy for reducing the frequency of cell misidentification.},
journal = {In vitro cellular &amp; developmental biology. Animal},
volume = {46},
number = {10},
pages = {811-819},
pmid = {20927602},
issn = {1543-706X},
mesh = {Biometric Identification/*methods/*standards ; Cell Culture Techniques ; Cell Line ; Humans ; Isoenzymes/genetics ; Karyotyping ; Microsatellite Repeats/*genetics ; Quality Control ; Stem Cells ; United States ; },
abstract = {The role of cell authentication in biomedical science has received considerable attention, especially within the past decade. This quality control attribute is now beginning to be given the emphasis it deserves by granting agencies and by scientific journals. Short tandem repeat (STR) profiling, one of a few DNA profiling technologies now available, is being proposed for routine identification (authentication) of human cell lines, stem cells, and tissues. The advantage of this technique over methods such as isoenzyme analysis, karyotyping, human leukocyte antigen typing, etc., is that STR profiling can establish identity to the individual level, provided that the appropriate number and types of loci are evaluated. To best employ this technology, a standardized protocol and a data-driven, quality-controlled, and publically searchable database will be necessary. This public STR database (currently under development) will enable investigators to rapidly authenticate human-based cultures to the individual from whom the cells were sourced. Use of similar approaches for non-human animal cells will require developing other suitable loci sets. While implementing STR analysis on a more routine basis should significantly reduce the frequency of cell misidentification, additional technologies may be needed as part of an overall authentication paradigm. For instance, isoenzyme analysis, PCR-based DNA amplification, and sequence-based barcoding methods enable rapid confirmation of a cell line's species of origin while screening against cross-contaminations, especially when the cells present are not recognized by the species-specific STR method. Karyotyping may also be needed as a supporting tool during establishment of an STR database. Finally, good cell culture practices must always remain a major component of any effort to reduce the frequency of cell misidentification.},
}
@article {pmid22247875,
year = {2010},
author = {Shah, RY and Prajapati, PN and Agrawal, YK},
title = {Anticounterfeit packaging technologies.},
journal = {Journal of advanced pharmaceutical technology &amp; research},
volume = {1},
number = {4},
pages = {368-373},
pmid = {22247875},
issn = {0976-2094},
abstract = {Packaging is the coordinated system that encloses and protects the dosage form. Counterfeit drugs are the major cause of morbidity, mortality, and failure of public interest in the healthcare system. High price and well-known brands make the pharma market most vulnerable, which accounts for top priority cardiovascular, obesity, and antihyperlipidemic drugs and drugs like sildenafil. Packaging includes overt and covert technologies like barcodes, holograms, sealing tapes, and radio frequency identification devices to preserve the integrity of the pharmaceutical product. But till date all the available techniques are synthetic and although provide considerable protection against counterfeiting, have certain limitations which can be overcome by the application of natural approaches and utilization of the principles of nanotechnology.},
}
@article {pmid20876691,
year = {2010},
author = {Timmermans, MJ and Dodsworth, S and Culverwell, CL and Bocak, L and Ahrens, D and Littlewood, DT and Pons, J and Vogler, AP},
title = {Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics.},
journal = {Nucleic acids research},
volume = {38},
number = {21},
pages = {e197},
pmid = {20876691},
issn = {1362-4962},
support = {BB/H023534/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Coleoptera/classification/genetics ; Genes, Mitochondrial ; Genome, Insect ; *Genome, Mitochondrial ; Mitochondrial Proteins/*genetics ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; },
abstract = {Mitochondrial genome sequences are important markers for phylogenetics but taxon sampling remains sporadic because of the great effort and cost required to acquire full-length sequences. Here, we demonstrate a simple, cost-effective way to sequence the full complement of protein coding mitochondrial genes from pooled samples using the 454/Roche platform. Multiplexing was achieved without the need for expensive indexing tags ('barcodes'). The method was trialled with a set of long-range polymerase chain reaction (PCR) fragments from 30 species of Coleoptera (beetles) sequenced in a 1/16th sector of a sequencing plate. Long contigs were produced from the pooled sequences with sequencing depths ranging from ∼10 to 100× per contig. Species identity of individual contigs was established via three 'bait' sequences matching disparate parts of the mitochondrial genome obtained by conventional PCR and Sanger sequencing. This proved that assembly of contigs from the sequencing pool was correct. Our study produced sequences for 21 nearly complete and seven partial sets of protein coding mitochondrial genes. Combined with existing sequences for 25 taxa, an improved estimate of basal relationships in Coleoptera was obtained. The procedure could be employed routinely for mitochondrial genome sequencing at the species level, to provide improved species 'barcodes' that currently use the cox1 gene only.},
}
@article {pmid20862638,
year = {2011},
author = {Sun, Z and Gao, T and Yao, H and Shi, L and Zhu, Y and Chen, S},
title = {Identification of Lonicera japonica and its related species using the DNA barcoding method.},
journal = {Planta medica},
volume = {77},
number = {3},
pages = {301-306},
doi = {10.1055/s-0030-1250324},
pmid = {20862638},
issn = {1439-0221},
mesh = {*DNA Barcoding, Taxonomic ; *DNA, Plant ; *Genes, Plant ; Genetic Markers ; Lonicera/*genetics ; Polymerase Chain Reaction ; Species Specificity ; },
abstract = {To choose a suitable DNA marker to authenticate the botanical origins of Flos Lonicerae Japonicae and Flos Lonicerae, seven candidate DNA bar codes (i.e., RBCL, MATK, PSBA-TRNH, ITS2, ITS, TRNL intron, and TRNL-F intergenic spacer) were tested on forty-four samples of LONICERA JAPONICA and its closely related species using the DNA barcoding method. We found that all seven candidate bar codes yielded 100 % PCR amplification efficiency and that the sequencing efficiency of the five other candidate bar codes was 100%, with the exception of ITS and ITS2. The highest interspecific divergence was provided by the PSBA-TRNH intergenic spacer, followed by the TRNL-F intergenic spacer based on six parameters and Wilcoxon signed rank tests. Through the inspection of the histograms of the barcoding gap, the distribution of the PSBA-TRNH intergenic spacer was well separated; and only this candidate DNA bar code possessed the highest species identification efficiency at 100 % by BLAST1 method. In conclusion, using the PSBA-TRNH intergenic spacer as a DNA bar code is suitable for the identification of the botanical origins of Flos Lonicerae Japonicae and Flos Lonicerae. This study may provide an important example for the authentication of the botanical origin of medicinal herbs listed in the Chinese Pharmacopoeia.},
}
@article {pmid20856873,
year = {2010},
author = {Bailey, AL and Brewer, MS and Hendrixson, BE and Bond, JE},
title = {Phylogeny and classification of the trapdoor spider genus Myrmekiaphila: an integrative approach to evaluating taxonomic hypotheses.},
journal = {PloS one},
volume = {5},
number = {9},
pages = {e12744},
pmid = {20856873},
issn = {1932-6203},
mesh = {Animals ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genetic Techniques ; Male ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Spiders/*classification/genetics ; },
abstract = {BACKGROUND: Revised by Bond and Platnick in 2007, the trapdoor spider genus Myrmekiaphila comprises 11 species. Species delimitation and placement within one of three species groups was based on modifications of the male copulatory device. Because a phylogeny of the group was not available these species groups might not represent monophyletic lineages; species definitions likewise were untested hypotheses. The purpose of this study is to reconstruct the phylogeny of Myrmekiaphila species using molecular data to formally test the delimitation of species and species-groups. We seek to refine a set of established systematic hypotheses by integrating across molecular and morphological data sets.<br><br>METHODS AND FINDINGS: Phylogenetic analyses comprising Bayesian searches were conducted for a mtDNA matrix composed of contiguous 12S rRNA, tRNA-val, and 16S rRNA genes and a nuclear DNA matrix comprising the glutamyl and prolyl tRNA synthetase gene each consisting of 1348 and 481 bp, respectively. Separate analyses of the mitochondrial and nuclear genome data and a concatenated data set yield M. torreya and M. millerae paraphyletic with respect to M. coreyi and M. howelli and polyphyletic fluviatilis and foliata species groups.<br><br>CONCLUSIONS: Despite the perception that molecular data present a solution to a crisis in taxonomy, studies like this demonstrate the efficacy of an approach that considers data from multiple sources. A DNA barcoding approach during the species discovery process would fail to recognize at least two species (M. coreyi and M. howelli) whereas a combined approach more accurately assesses species diversity and illuminates speciation pattern and process. Concomitantly these data also demonstrate that morphological characters likewise fail in their ability to recover monophyletic species groups and result in an unnatural classification. Optimizations of these characters demonstrate a pattern of "Dollo evolution" wherein a complex character evolves only once but is lost multiple times throughout the group's history.},
}
@article {pmid20853282,
year = {2010},
author = {Zhang, H and Fang, C and Zhang, S},
title = {An autonomous bio-barcode DNA machine for exponential DNA amplification and its application to the electrochemical determination of adenosine triphosphate.},
journal = {Chemistry (Weinheim an der Bergstrasse, Germany)},
volume = {16},
number = {41},
pages = {12434-12439},
doi = {10.1002/chem.201000811},
pmid = {20853282},
issn = {1521-3765},
mesh = {Adenosine Triphosphate/*analysis ; Aptamers, Nucleotide/*chemistry ; DNA/*chemistry ; Humans ; K562 Cells ; Models, Molecular ; },
abstract = {A novel autonomous bio-barcode DNA machine that is driven by template-dependent DNA replication is developed to exponentially amplify special DNA sequences. Combined with a DNA aptamer recognition element, the DNA machine can be further applied in the aptamer-based, amplified analysis of small molecules. As a model analyte, adenosine triphosphate (ATP) is determined by using the DNA machine system in combination with a DNA aptamer recognition strategy and differential pulse anodic stripping voltammetry (DPASV). Under the optimum conditions, detection limits as low as 2.8×10(-17) M (3σ) for target DNA and 4.7×10(-9) M (3σ) for ATP are achieved. The satisfactory determination of ATP in K562 leukemia cell and Ramos Burkitt's lymphoma cell reveal that this protocol possesses good selectivity and practicality. As a promising biomolecular device, this DNA machine may have an even broader application in the rapidly developing field of nanobiotechnology.},
}
@article {pmid20851593,
year = {2010},
author = {Trévisan, M and Schawaller, M and Quapil, G and Souteyrand, E and Mérieux, Y and Cloarec, JP},
title = {Evanescent wave fluorescence biosensor combined with DNA bio-barcode assay for platelet genotyping.},
journal = {Biosensors &amp; bioelectronics},
volume = {26},
number = {4},
pages = {1631-1637},
doi = {10.1016/j.bios.2010.08.038},
pmid = {20851593},
issn = {1873-4235},
mesh = {Antigens, Human Platelet/*genetics ; Biosensing Techniques/instrumentation/*methods ; Blood Platelets/*immunology ; DNA Barcoding, Taxonomic/instrumentation/*methods ; Fluorescence ; Genotype ; Humans ; Oligonucleotide Array Sequence Analysis/instrumentation/methods ; Oligonucleotide Probes ; Polymorphism, Single Nucleotide ; },
abstract = {An evanescent wave fluorescence biosensor was combined with a DNA bio-barcode assay to resolve problems met in detection of poor biologic samples. Human platelet antigen (HPA) genotyping was used as a demonstrator. Our bio-barcode assay was based on magnetic carboxylatex particles and non-magnetic carboxylatex particles, both functionalized with oligonucleotides. It was assessed for detecting 84mer synthetic oligonucleotides as targets. The assay allows to specifically detect single nucleotide polymorphism with a detection limit of 2 pM of target nucleic acids. The fluorescence detection is achieved in 150 s.},
}
@article {pmid20846439,
year = {2010},
author = {Wang, W and Wu, Y and Yan, Y and Ermakova, M and Kerstetter, R and Messing, J},
title = {DNA barcoding of the Lemnaceae, a family of aquatic monocots.},
journal = {BMC plant biology},
volume = {10},
number = {},
pages = {205},
pmid = {20846439},
issn = {1471-2229},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Chloroplast/genetics ; DNA, Intergenic/genetics ; DNA, Plant/genetics ; Genetic Markers ; Magnoliopsida/*classification/*genetics ; Phylogeny ; },
abstract = {BACKGROUND: Members of the aquatic monocot family Lemnaceae (commonly called duckweeds) represent the smallest and fastest growing flowering plants. Their highly reduced morphology and infrequent flowering result in a dearth of characters for distinguishing between the nearly 38 species that exhibit these tiny, closely-related and often morphologically similar features within the same family of plants.<br><br>RESULTS: We developed a simple and rapid DNA-based molecular identification system for the Lemnaceae based on sequence polymorphisms. We compared the barcoding potential of the seven plastid-markers proposed by the CBOL (Consortium for the Barcode of Life) plant-working group to discriminate species within the land plants in 97 accessions representing 31 species from the family of Lemnaceae. A Lemnaceae-specific set of PCR and sequencing primers were designed for four plastid coding genes (rpoB, rpoC1, rbcL and matK) and three noncoding spacers (atpF-atpH, psbK-psbI and trnH-psbA) based on the Lemna minor chloroplast genome sequence. We assessed the ease of amplification and sequencing for these markers, examined the extent of the barcoding gap between intra- and inter-specific variation by pairwise distances, evaluated successful identifications based on direct sequence comparison of the "best close match" and the construction of a phylogenetic tree.<br><br>CONCLUSIONS: Based on its reliable amplification, straightforward sequence alignment, and rates of DNA variation between species and within species, we propose that the atpF-atpH noncoding spacer could serve as a universal DNA barcoding marker for species-level identification of duckweeds.},
}
@article {pmid20838643,
year = {2010},
author = {Kochzius, M and Seidel, C and Antoniou, A and Botla, SK and Campo, D and Cariani, A and Vazquez, EG and Hauschild, J and Hervet, C and Hjörleifsdottir, S and Hreggvidsson, G and Kappel, K and Landi, M and Magoulas, A and Marteinsson, V and Nölte, M and Planes, S and Tinti, F and Turan, C and Venugopal, MN and Weber, H and Blohm, D},
title = {Identifying Fishes through DNA Barcodes and Microarrays.},
journal = {PloS one},
volume = {5},
number = {9},
pages = {e12620},
pmid = {20838643},
issn = {1932-6203},
mesh = {Animals ; Cytochromes b/genetics ; DNA/genetics ; DNA Barcoding, Taxonomic ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; Fish Proteins/genetics ; Fishes/*classification/*genetics ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; },
abstract = {BACKGROUND: International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection.<br><br>This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of "DNA barcoding" and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the "position of label" effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology.<br><br>CONCLUSIONS/SIGNIFICANCE: Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products.},
}
@article {pmid20838635,
year = {2010},
author = {Francis, CM and Borisenko, AV and Ivanova, NV and Eger, JL and Lim, BK and Guillén-Servent, A and Kruskop, SV and Mackie, I and Hebert, PD},
title = {The role of DNA barcodes in understanding and conservation of mammal diversity in southeast Asia.},
journal = {PloS one},
volume = {5},
number = {9},
pages = {e12575},
pmid = {20838635},
issn = {1932-6203},
mesh = {Animals ; Asia, Southeastern ; *Biodiversity ; *Conservation of Natural Resources ; DNA/*genetics ; DNA Barcoding, Taxonomic ; Mammals/*classification/*genetics ; Molecular Sequence Data ; Phylogeny ; },
abstract = {BACKGROUND: Southeast Asia is recognized as a region of very high biodiversity, much of which is currently at risk due to habitat loss and other threats. However, many aspects of this diversity, even for relatively well-known groups such as mammals, are poorly known, limiting ability to develop conservation plans. This study examines the value of DNA barcodes, sequences of the mitochondrial COI gene, to enhance understanding of mammalian diversity in the region and hence to aid conservation planning.<br><br>DNA barcodes were obtained from nearly 1900 specimens representing 165 recognized species of bats. All morphologically or acoustically distinct species, based on classical taxonomy, could be discriminated with DNA barcodes except four closely allied species pairs. Many currently recognized species contained multiple barcode lineages, often with deep divergence suggesting unrecognized species. In addition, most widespread species showed substantial genetic differentiation across their distributions. Our results suggest that mammal species richness within the region may be underestimated by at least 50%, and there are higher levels of endemism and greater intra-specific population structure than previously recognized.<br><br>CONCLUSIONS: DNA barcodes can aid conservation and research by assisting field workers in identifying species, by helping taxonomists determine species groups needing more detailed analysis, and by facilitating the recognition of the appropriate units and scales for conservation planning.},
}
@article {pmid20837570,
year = {2010},
author = {Little, DP},
title = {A unified index of sequence quality and contig overlap for DNA barcoding.},
journal = {Bioinformatics (Oxford, England)},
volume = {26},
number = {21},
pages = {2780-2781},
doi = {10.1093/bioinformatics/btq507},
pmid = {20837570},
issn = {1367-4811},
mesh = {Base Sequence ; Computational Biology/*methods ; DNA/*chemistry ; Databases, Factual ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; },
abstract = {SUMMARY: Barcode quality index (B) is a novel, unified measure of sequence quality and contig overlap tailored to the needs of DNA barcoding. Re-analysis of published data demonstrates the utility of B.<br><br>A GPL PERL script is available for download (http://www.nybg.org/files/scientists/dlittle/B.html).},
}
@article {pmid20836845,
year = {2010},
author = {Raupach, MJ and Astrin, JJ and Hannig, K and Peters, MK and Stoeckle, MY and Wägele, JW},
title = {Molecular species identification of Central European ground beetles (Coleoptera: Carabidae) using nuclear rDNA expansion segments and DNA barcodes.},
journal = {Frontiers in zoology},
volume = {7},
number = {},
pages = {26},
pmid = {20836845},
issn = {1742-9994},
abstract = {BACKGROUND: The identification of vast numbers of unknown organisms using DNA sequences becomes more and more important in ecological and biodiversity studies. In this context, a fragment of the mitochondrial cytochrome c oxidase I (COI) gene has been proposed as standard DNA barcoding marker for the identification of organisms. Limitations of the COI barcoding approach can arise from its single-locus identification system, the effect of introgression events, incomplete lineage sorting, numts, heteroplasmy and maternal inheritance of intracellular endosymbionts. Consequently, the analysis of a supplementary nuclear marker system could be advantageous.<br><br>RESULTS: We tested the effectiveness of the COI barcoding region and of three nuclear ribosomal expansion segments in discriminating ground beetles of Central Europe, a diverse and well-studied invertebrate taxon. As nuclear markers we determined the 18S rDNA: V4, 18S rDNA: V7 and 28S rDNA: D3 expansion segments for 344 specimens of 75 species. Seventy-three species (97%) of the analysed species could be accurately identified using COI, while the combined approach of all three nuclear markers provided resolution among 71 (95%) of the studied Carabidae.<br><br>CONCLUSION: Our results confirm that the analysed nuclear ribosomal expansion segments in combination constitute a valuable and efficient supplement for classical DNA barcoding to avoid potential pitfalls when only mitochondrial data are being used. We also demonstrate the high potential of COI barcodes for the identification of even closely related carabid species.},
}
@article {pmid20831809,
year = {2010},
author = {Puniamoorthy, N and Kotrba, M and Meier, R},
title = {Unlocking the "Black box": internal female genitalia in Sepsidae (Diptera) evolve fast and are species-specific.},
journal = {BMC evolutionary biology},
volume = {10},
number = {},
pages = {275},
pmid = {20831809},
issn = {1471-2148},
mesh = {Animals ; *Biological Evolution ; Diptera/*anatomy &amp; histology/classification/*physiology ; Female ; Genitalia, Female/anatomy &amp; histology/physiology ; Male ; Species Specificity ; },
abstract = {BACKGROUND: The species-specificity of male genitalia has been well documented in many insect groups and sexual selection has been proposed as the evolutionary force driving the often rapid, morphological divergence. The internal female genitalia, in sharp contrast, remain poorly studied. Here, we present the first comparative study of the internal reproductive system of Sepsidae. We test the species-specificity of the female genitalia by comparing recently diverged sister taxa. We also compare the rate of change in female morphological characters with the rate of fast-evolving, molecular and behavioral characters.<br><br>RESULTS: We describe the ectodermal parts of the female reproductive tract for 41 species representing 21 of the 37 described genera and define 19 morphological characters with discontinuous variation found in eight structures that are part of the reproductive tract. Using a well-resolved molecular phylogeny based on 10 genes, we reconstruct the evolution of these characters across the family [120 steps; Consistency Index (CI): 0.41]. Two structures, in particular, evolve faster than the rest. The first is the ventral receptacle, which is a secondary sperm storage organ. It accounts for more than half of all the evolutionary changes observed (7 characters; 61 steps; CI: 0.46). It is morphologically diverse across genera, can be bi-lobed or multi-chambered (up to 80 chambers), and is strongly sclerotized in one clade. The second structure is the dorsal sclerite, which is present in all sepsids except Orygma luctuosum and Ortalischema albitarse. It is associated with the opening of the spermathecal ducts and is often distinct even among sister species (4 characters; 16 steps; CI: 0.56).<br><br>CONCLUSIONS: We find the internal female genitalia are diverse in Sepsidae and diagnostic for all species. In particular, fast-evolving structures like the ventral receptacle and dorsal sclerite are likely involved in post-copulatory sexual selection. In comparison to behavioral and molecular data, the female structures are evolving 2/3 as fast as the non-constant third positions of the COI barcoding gene. They display less convergent evolution in characters (CI = 0.54) than the third positions or sepsid mating behavior (CICOI = 0.36; CIBEHAV = 0.45).},
}
@article {pmid20828479,
year = {2010},
author = {Jones, YL and Oliver, HF and Deeds, JR and Yancy, HF},
title = {Real-time PCR assay for the detection of pufferfish products.},
journal = {Journal of food protection},
volume = {73},
number = {9},
pages = {1698-1702},
doi = {10.4315/0362-028x-73.9.1698},
pmid = {20828479},
issn = {0362-028X},
mesh = {Animals ; *Consumer Product Safety ; Fish Products/*analysis ; Food Contamination/*analysis ; Humans ; Polymerase Chain Reaction/*methods/standards ; Species Specificity ; *Tetraodontiformes ; Time Factors ; },
abstract = {An assay was developed for the rapid detection of products containing tissues from potentially toxic pufferfish (family Tetraodontidae), as part of the U.S. Food and Drug Administration Center for Veterinary Medicine and Center for Food Safety and Applied Nutrition's charter to protect human health. In this study, we developed a TaqMan assay derived from DNA barcode data (650 bp starting at the 5' end of the mitochondrial cytochrome c oxidase I gene) for the specific detection of pufferfish. The method requires only 1 h of total run time, a significant improvement over current methods, which can require 24 to 96 h for completion. The probes were tested against 105 species of fish and were able to detect 20 species of pufferfish; no cross-reactivity was shown with 85 species of nonpufferfish, including 20 related species from the same order (Tetraodontiformes). These results demonstrate that this assay is suitable for the rapid and specific detection of pufferfish and that it could be a useful regulatory tool to protect human health.},
}
@article {pmid20824632,
year = {2010},
author = {Clutter, MR and Heffner, GC and Krutzik, PO and Sachen, KL and Nolan, GP},
title = {Tyramide signal amplification for analysis of kinase activity by intracellular flow cytometry.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {77},
number = {11},
pages = {1020-1031},
pmid = {20824632},
issn = {1552-4930},
support = {T32 AI007290/AI/NIAID NIH HHS/United States ; R01 CA130826/CA/NCI NIH HHS/United States ; P01 CA034233/CA/NCI NIH HHS/United States ; U19 AI057229/AI/NIAID NIH HHS/United States ; P01 CA034233-24/CA/NCI NIH HHS/United States ; N01-HV-28183/HV/NHLBI NIH HHS/United States ; 1R01CA130826/CA/NCI NIH HHS/United States ; HHSN272200700038C/AI/NIAID NIH HHS/United States ; U54 AI054523/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Cell Line, Tumor ; Cell Separation ; Extracellular Signal-Regulated MAP Kinases/analysis/*metabolism ; Female ; Flow Cytometry/*methods ; Humans ; Interferon-gamma/pharmacology ; Interleukin-6/pharmacology ; Jurkat Cells ; Leukemia/drug therapy/metabolism ; Limit of Detection ; Lymphoma/drug therapy/metabolism ; Mice ; Mice, Inbred BALB C ; Nucleic Acid Amplification Techniques/*methods ; Phosphoproteins ; Phosphorylation ; Protein Binding ; Spleen/cytology/drug effects/metabolism ; Staining and Labeling/methods ; Tyramine/analysis/*chemistry ; U937 Cells ; },
abstract = {Intracellular flow cytometry permits quantitation of diverse molecular targets at the single-cell level. However, limitations in detection sensitivity inherently restrict the method, sometimes resulting in the inability to measure proteins of very low abundance or to differentiate cells expressing subtly different protein concentrations. To improve these measurements, an enzymatic amplification approach called tyramide signal amplification (TSA) was optimized for assessment of intracellular kinase cascades. First, Pacific Blue, Pacific Orange, and Alexa Fluor 488 tyramide reporters were shown to exhibit low nonspecific binding in permeabilized cells. Next, the effects of antibody concentration, tyramide concentration, and reaction time on assay resolution were characterized. Use of optimized TSA resulted in a 10-fold or greater improvement in measurement resolution of endogenous Erk and Stat cell signaling pathways relative to standard, nonamplified detection. TSA also enhanced assay sensitivity and, in conjunction with fluorescent cell barcoding, improved assay performance according to a metric used to evaluate high-throughput drug screens. TSA was used to profile Stat1 phosphorylation in primary immune system cells, which revealed heterogeneity in various populations, including CD4+ FoxP3+ regulatory T cells. We anticipate the approach will be broadly applicable to intracellular flow cytometry assays with low signal-to-noise ratios.},
}
@article {pmid20822400,
year = {2010},
author = {Reimer, JD and Hirose, M and Nishisaka, T and Sinniger, F and Itani, G},
title = {Epizoanthus spp. associations revealed using DNA markers: a case study from Kochi, Japan.},
journal = {Zoological science},
volume = {27},
number = {9},
pages = {729-734},
doi = {10.2108/zsj.27.729},
pmid = {20822400},
issn = {0289-0003},
mesh = {Animals ; Cnidaria/*genetics ; DNA/*genetics ; Demography ; *Genetic Markers ; *Genetic Variation ; Japan ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Zoanthids (Cnidaria, Hexacorallia) of the genus Epizoanthus are often found in association with other marine invertebrates, including gastropods and hermit crabs. However, little information exists on the specificity and nature of these associations due to a lack of investigation into Epizoanthus species diversity, and the taxonomy of Epizoanthus is therefore confused. In this study, analyses of morphological data (tentacle number, polyp size, etc) and molecular data (mitochondrial cytochrome oxidase subunit 1 = COI, 16S ribosomal DNA = 16S rDNA) were used to examine Epizoanthus specimens from Tosa Bay, Kochi, Japan. The Epizoanthus specimens were found on both live gastropods (Gemmula unedo) and hermit crabs (Paguristes palythophilus) inhabiting G. unedo and G. cosmoi shells. While morphological analyses did not show clear differences between examined specimens, both COI and mt 16S rDNA clearly divided the specimens into two groups, one associated only with hermit crabs (= Epizoanthus sp. C), and another associated only with living gastropods (= Epizoanthus sp. S). Unexpectedly, DNA sequences from both groups did not match with two previously reported Epizoanthus species from Japan (E. indicus, E. ramosus), indicating they both may be undescribed species. These results highlight the utility of DNA "barcoding" of unknown zoanthids, and will provide a foundation for re-examinations of Epizoanthus species diversity and specificity, which will be critical in understanding the evolution of these unique marine invertebrates.},
}
@article {pmid20821302,
year = {2010},
author = {Wang, Z and Guo, Y and Tan, W and Li, L and Tang, E and Liu, C and Liu, Y},
title = {DNA barcoding, phylogenetic relationships and speciation of snappers (genus Lutjanus).},
journal = {Science China. Life sciences},
volume = {53},
number = {8},
pages = {1025-1030},
doi = {10.1007/s11427-010-4034-0},
pmid = {20821302},
issn = {1869-1889},
mesh = {Animals ; DNA/*chemistry ; *Electronic Data Processing ; Fishes/classification/*genetics ; *Phylogeny ; Species Specificity ; },
abstract = {The phylogenetic relationships of 13 snapper species from the South China Sea have been established using the combined DNA sequences of three full-length mitochondrial genes (COI, COII and CYTB) and two partial nuclear genes (RAG1, RAG2). The 13 species (genus Lutjanus) were selected after DNA barcoding 72 individuals, representing 20 species. Our study suggests that although DNA barcoding aims to develop species identification systems, it may also be useful in the construction of phylogenies by aiding the selection of taxa. Combined mitochondrial and nuclear gene data has an advantage over an individual dataset because of its higher resolving power.},
}
@article {pmid20821298,
year = {2010},
author = {Guo, H and Wang, W and Yang, N and Guo, B and Zhang, S and Yang, R and Yuan, Y and Yu, J and Hu, S and Sun, Q and Yu, J},
title = {DNA barcoding provides distinction between Radix Astragali and its adulterants.},
journal = {Science China. Life sciences},
volume = {53},
number = {8},
pages = {992-999},
doi = {10.1007/s11427-010-4044-y},
pmid = {20821298},
issn = {1869-1889},
mesh = {Astragalus Plant/chemistry ; Astragalus propinquus ; Base Sequence ; DNA Primers ; DNA, Plant/*chemistry ; Drugs, Chinese Herbal/*chemistry ; *Electronic Data Processing ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {Based on variable nuclear and/or organellar DNA sequences among vastly divergent species as well as morphologically indistinguishable species, DNA barcoding is widely applicable in species identification, biodiversity studies, forensic analyses, and authentication of medicinal plants. The roots of Astragalus membranaceus and A. membranaceus var. mongholica are commonly used as Radix Astragali in several Asian countries, including China, Japan, and Korea. However, in addition to the two species recorded in the Chinese Pharmacopoeia, there are twenty-three species from different genera including Astragalus, Oxytropis, Hedysarum, and Glycyrrhiza, which have been used as adulterants not only in trading markets but also by the herbal medicine industry. Therefore, a simple, reliable, and accurate classification method is important for distinguishing authentic Radix Astragali from its adulterants. In this study, we acquired data for 37 samples from four related genera within the family Fabaceae. Then we compared four candidate DNA barcoding markers using ITS, matK, rbcL, and coxI sequences from nuclear, chloroplast, and mitochondrial genomes, all commonly used for plants to identify genetic variations among genera, intraspecies, and interspecies. We observed higher divergences among genera and interspecies for ITS, which have the average Kimura 2-parameter distances of 4.5% and 14.1%, respectively, whereas matK was found to have sufficient divergence at the intraspecific level. Moreover, two indels detected in the matK sequence are useful for PCR studies in distinguishing Radix Astragali from its adulterants. This study suggests that the combined barcoding regions of ITS and matK are superior barcodes for Radix Astragali and further studies should focus on evaluating the applicability and accuracy of such combined markers for a wide range of traditional Chinese herbs.},
}
@article {pmid20821060,
year = {2010},
author = {Chung, IH and Yoo, HS and Eah, JY and Yoon, HK and Jung, JW and Hwang, SY and Kim, CB},
title = {A DNA microarray for identification of selected Korean birds based on mitochondrial cytochrome c oxidase I gene sequences.},
journal = {Molecules and cells},
volume = {30},
number = {4},
pages = {295-301},
doi = {10.1007/s10059-010-0118-8},
pmid = {20821060},
issn = {0219-1032},
mesh = {Animals ; Base Sequence ; *Birds/classification/genetics ; *DNA Barcoding, Taxonomic/methods ; DNA Probes/chemical synthesis/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Electron Transport Complex IV/chemistry/*genetics ; *Genes, Mitochondrial ; Genetic Variation ; Influenza in Birds/classification/transmission ; Korea ; Mitochondria/genetics ; Oligonucleotide Array Sequence Analysis/*methods ; Oligonucleotide Probes/chemical synthesis/genetics ; Species Specificity ; },
abstract = {DNA barcoding with the gene encoding cytochrome c oxidase I (COI) in the mitochondrial genome has been proposed as a standard marker to identify and discover animal species. Some migratory wild birds are suspected of transmitting avian influenza and pose a threat to aircraft safety because of bird strikes. We have previously reported the COI gene sequences of 92 Korean bird species. In the present study, we developed a DNA microarray to identify 17 selected bird species on the basis of nucleotide diversity. We designed and synthesized 19 specific oligonucleotide probes; these probes were arrayed on a silylated glass slide. The length of the probes was 19-24 bps. The COI sequences amplified from the tissues of the selected birds were labeled with a fluorescent probe for microarray hybridization, and unique hybridization patterns were detected for each selected species. These patterns may be considered diagnostic patterns for species identification. This microarray system will provide a sensitive and a high-throughput method for identification of Korean birds.},
}
@article {pmid20813193,
year = {2010},
author = {Ley, AC and Hardy, OJ},
title = {Species delimitation in the Central African herbs Haumania (Marantaceae) using georeferenced nuclear and chloroplastic DNA sequences.},
journal = {Molecular phylogenetics and evolution},
volume = {57},
number = {2},
pages = {859-867},
doi = {10.1016/j.ympev.2010.08.027},
pmid = {20813193},
issn = {1095-9513},
mesh = {Africa, Central ; DNA Barcoding, Taxonomic ; DNA, Chloroplast/*genetics ; DNA, Plant/*genetics ; Gene Flow/genetics ; Marantaceae/*classification/*genetics ; *Phylogeny ; Phylogeography ; Species Specificity ; },
abstract = {Species delimitation is a fundamental biological concept which is frequently discussed and altered to integrate new insights. These revealed that speciation is not a one step phenomenon but an ongoing process and morphological characters alone are not sufficient anymore to properly describe the results of this process. Here we want to assess the degree of speciation in two closely related lianescent taxa from the tropical African genus Haumania which display distinct vegetative traits despite a high similarity in reproductive traits and a partial overlap in distribution area which might facilitate gene flow. To this end, we combined phylogenetic and phylogeographic analyses using nuclear (nr) and chloroplast (cp) DNA sequences in comparison to morphological species descriptions. The nuclear dataset unambiguously supports the morphological species concept in Haumania. However, the main chloroplastic haplotypes are shared between species and, although a geographic analysis of cpDNA diversity confirms that individuals from the same taxon are more related than individuals from distinct taxa, cp-haplotypes display correlated geographic distributions between species. Hybridization is the most plausible reason for this pattern. A scenario involving speciation in geographic isolation followed by range expansion is outlined. The study highlights the gain of information on the speciation process in Haumania by adding georeferenced molecular data to the morphological characteristics. It also shows that nr and cp sequence data might provide different but complementary information, questioning the reliability of the unique use of chloroplast data for species recognition by DNA barcoding.},
}
@article {pmid20810267,
year = {2010},
author = {Zhang, D and Huarng, MC and Alocilja, EC},
title = {A multiplex nanoparticle-based bio-barcoded DNA sensor for the simultaneous detection of multiple pathogens.},
journal = {Biosensors &amp; bioelectronics},
volume = {26},
number = {4},
pages = {1736-1742},
doi = {10.1016/j.bios.2010.08.012},
pmid = {20810267},
issn = {1873-4235},
mesh = {Antigens, Bacterial/genetics ; Bacillus anthracis/genetics/isolation &amp; purification/pathogenicity ; Bacterial Toxins/genetics ; Base Sequence ; Biosensing Techniques/*methods ; Cadmium Compounds ; DNA Barcoding, Taxonomic/*methods ; DNA Probes/genetics ; DNA Transposable Elements ; DNA, Bacterial/analysis/genetics ; Electrochemical Techniques ; Genes, Bacterial ; Gold ; Humans ; Lead ; Magnetite Nanoparticles ; *Metal Nanoparticles/ultrastructure ; Microscopy, Electron, Transmission ; Salmonella enteritidis/genetics/isolation &amp; purification/pathogenicity ; Sulfides ; },
abstract = {A highly amplified, nanoparticle-based, bio-barcoded electrochemical biosensor for the simultaneous multiple detection of the protective antigen A (pagA) gene (accession number, M22589) of Bacillus anthracis and the insertion element (Iel) gene (accession number, Z83734) of Salmonella enteritidis is reported in this paper. The biosensor system is mainly composed of three nanoparticles: gold nanoparticles (AuNPs), magnetic nanoparticles (MNPs), and nanoparticle tracers (NTs, such as PbS and CdS). The AuNPs are coated with the first target-specific DNA probe (1pDNA), which can recognize one end of the target DNA sequence (tDNA), and many NT-terminated bio-barcode ssDNA (bDNA-NT), which act as signal reporter and amplifier. The MNPs are coated with the second target-specific DNA probe (2pDNA) that can recognize the other end of the target gene. After binding the nanoparticles with the target DNA, the following sandwich structure is formed: MNP-2pDNA/tDNA/1pDNA-AuNP-bDNA-NTs. A magnetic field is applied to separate the sandwich structure from the unreacted materials. Because the AuNPs have a large number of nanoparticle tracers per DNA probe binding event, there is substantial amplification. After the nanoparticle tracer is dissolved in 1M nitric acid, the NT(2+) ions are detected by square wave anodic stripping voltammetry (SWASV) on screen-printed carbon electrode (SPCE) chips. The results show that the detection limit of this multiplex bio-barcoded DNA sensor are 0.5 ng/mL of the insertion element (Iel) gene of S. enteritidis using CdS, and 50 pg/mL of the pagA gene of B. anthracis using PbS NTs. The nanoparticle-based bio-barcoded DNA sensor has potential application in rapid detection of multiple pathogenic agents in the same sample.},
}
@article {pmid20808837,
year = {2010},
author = {Tyagi, A and Bag, SK and Shukla, V and Roy, S and Tuli, R},
title = {Oligonucleotide frequencies of barcoding loci can discriminate species across kingdoms.},
journal = {PloS one},
volume = {5},
number = {8},
pages = {e12330},
pmid = {20808837},
issn = {1932-6203},
mesh = {Animals ; DNA Fingerprinting/*methods ; DNA, Ribosomal Spacer/genetics ; Fungi/classification/genetics ; Genetic Loci/*genetics ; INDEL Mutation ; Internet ; Oligodeoxyribonucleotides/*genetics ; Phylogeny ; Plants/classification/genetics ; Species Specificity ; },
abstract = {BACKGROUND: DNA barcoding refers to the use of short DNA sequences for rapid identification of species. Genetic distance or character attributes of a particular barcode locus discriminate the species. We report an efficient approach to analyze short sequence data for discrimination between species.<br><br>A new approach, Oligonucleotide Frequency Range (OFR) of barcode loci for species discrimination is proposed. OFR of the loci that discriminates between species was characteristic of a species, i.e., the maxima and minima within a species did not overlap with that of other species. We compared the species resolution ability of different barcode loci using p-distance, Euclidean distance of oligonucleotide frequencies, nucleotide-character based approach and OFR method. The species resolution by OFR was either higher or comparable to the other methods. A short fragment of 126 bp of internal transcribed spacer region in ribosomal RNA gene was sufficient to discriminate a majority of the species using OFR.<br><br>CONCLUSIONS/SIGNIFICANCE: Oligonucleotide frequency range of a barcode locus can discriminate between species. Ability to discriminate species using very short DNA fragments may have wider applications in forensic and conservation studies.},
}
@article {pmid20807580,
year = {2010},
author = {Borer, M and Alvarez, N and Buerki, S and Margraf, N and Rahier, M and Naisbit, RE},
title = {The phylogeography of an alpine leaf beetle: divergence within Oreina elongata spans several ice ages.},
journal = {Molecular phylogenetics and evolution},
volume = {57},
number = {2},
pages = {703-709},
doi = {10.1016/j.ympev.2010.08.017},
pmid = {20807580},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Coleoptera/*classification/*genetics ; DNA, Mitochondrial/genetics ; *Phylogeography ; },
abstract = {The genetic landscape of the European flora and fauna was shaped by the ebb and flow of populations with the shifting ice during Quaternary climate cycles. While this has been well demonstrated for lowland species, less is known about high altitude taxa. Here we analyze the phylogeography of the leaf beetle Oreina elongata from 20 populations across the Alps and Apennines. Three mitochondrial and one nuclear region were sequenced in 64 individuals. Within an mtDNA phylogeny, three of seven subspecies are monophyletic. The species is chemically defended and aposematic, with green and blue forms showing geographic variation and unexpected within-population polymorphism. These warning colors show pronounced east-west geographical structure in distribution, but the phylogeography suggests repeated origin and loss. Basal clades come from the central Alps. Ancestors of other clades probably survived across northern Italy and the northern Adriatic, before separation of eastern, southern and western populations and rapid spread through the western Alps. After reviewing calibrated gene-specific substitution rates in the literature, we use partitioned Bayesian coalescent analysis to date our phylogeography. The major clades diverged long before the last glacial maximum, suggesting that O. elongata persisted many glacial cycles within or at the edges of the Alps and Apennines. When analyzing additional barcoding pairwise distances, we find strong evidence to consider O. elongata as a species complex rather than a single species.},
}
@article {pmid20803416,
year = {2011},
author = {Zuo, Y and Chen, Z and Kondo, K and Funamoto, T and Wen, J and Zhou, S},
title = {DNA barcoding of Panax species.},
journal = {Planta medica},
volume = {77},
number = {2},
pages = {182-187},
doi = {10.1055/s-0030-1250166},
pmid = {20803416},
issn = {1439-0221},
mesh = {Base Sequence ; *DNA Barcoding, Taxonomic ; DNA, Plant/*genetics ; Electronic Data Processing/methods ; *Genetic Loci ; *Genetic Variation ; Molecular Sequence Data ; Panax/*classification/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {Ginsengs (Panax, Araliaceae) are among the plants best known for their medicinal properties. Many ginseng species are endangered due to over-exploitation of natural resources - a situation difficult to remedy while there are no reliable, practical methods for species identification. We screened eleven candidate DNA barcoding loci to establish an accurate and effective Panax species identification system, both for commercial and conservation purposes. We used 95 ginseng samples, representing all the species in the genus. We found considerable differences in the performance of the potential barcoding regions. The sequencing of ATPF-ATPH was unsuccessful due to poly-N structures. The RBCL, RPOB, and RPOC1 regions were found to be mostly invariable, with only four to eight variable sites. Using MATK, PSBK-I, PSBM-TRND, RPS16 and NAD1, we could identify four to six out of eight considerably divergent species but only one to five out of nineteen clusters within the P. bipinnatifidus species group. PSBA-TRNH and ITS were the most variable loci, working very well both in species and cluster identifications. We demonstrated that the combination of PSBA-TRNH and ITS is sufficient for identifying all the species and clusters in the genus.},
}
@article {pmid20801225,
year = {2010},
author = {Kvist, S and Sarkar, IN and Erséus, C},
title = {Genetic variation and phylogeny of the cosmopolitan marine genus Tubificoides (Annelida: Clitellata: Naididae: Tubificinae).},
journal = {Molecular phylogenetics and evolution},
volume = {57},
number = {2},
pages = {687-702},
doi = {10.1016/j.ympev.2010.08.018},
pmid = {20801225},
issn = {1095-9513},
mesh = {Animals ; Annelida/*classification/*genetics ; Aquatic Organisms/*classification/*genetics ; DNA Barcoding, Taxonomic ; *Genetic Variation ; Haplotypes/genetics ; *Phylogeny ; },
abstract = {Prior attempts to resolve the phylogenetic relationships of the cosmopolitan, marine clitellate genus Tubificoides, using only morphology, resulted in unresolved trees. In this study, three mitochondrial and three nuclear loci (5912 aligned sites) were analyzed, representing 14 morphologically separate species. Genetic distances within and between these forms on the basis of the mitochondrial genes (COI, 16S and 12S) revealed that 18 distinct mitochondrial lineages were represented in the data set. After analyzing also nuclear data (28S, 18S and ITS) we conclude that 17 separately evolving lineages (i.e., phylogenetic species) were represented, including three new, cryptic species closely related to T. pseudogaster, T. amplivasatus and T. insularis, respectively. Special emphasis was put on the DNA barcoding gene (COI), which was subject to haplotype diversity analysis and, for four species, diagnostic position (as determined by the Characteristic Attribute Organization System [CAOS]) screening. Typically, the intralineage variation was 1-2 orders of magnitude smaller than the interlineage divergence, making COI useful for identification of species within Tubificoides. The genetic data corroborate that many of the morphospecies are coherent but widely distributed metapopulations. Monophyly of the genus is supported and the evolutionary history of parts of the genus is revealed by phylogenetic analysis of the combined data set. A northern hemisphere origin of the genus is suggested, and most of the widely distributed species are members of one particular clade. Two morphological characters previously emphasized in Tubificoides taxonomy (hair chaetae and cuticular papillation) were optimized on the phylogenetic tree, revealing considerable homoplasy, belying the utility of these features as phylogenetic markers.},
}
@article {pmid20800099,
year = {2010},
author = {Yassin, A and Markow, TA and Narechania, A and O'Grady, PM and DeSalle, R},
title = {The genus Drosophila as a model for testing tree- and character-based methods of species identification using DNA barcoding.},
journal = {Molecular phylogenetics and evolution},
volume = {57},
number = {2},
pages = {509-517},
doi = {10.1016/j.ympev.2010.08.020},
pmid = {20800099},
issn = {1095-9513},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Drosophila/*classification/*genetics ; Phylogeny ; Species Specificity ; },
abstract = {DNA barcoding has recently been proposed as a promising tool for the (1) rapid assignment of unknown samples to described species by non-expert workers and (2) a potential method of new species discovery based on degree of DNA sequence divergence. Two broad methods have been used, one based on degree of DNA sequence variation, within and between species and another requiring the recovery of species as discrete clades (monophyly) on a phylogenetic tree. An alternative method relies on the identification of a set of specific diagnostic nucleotides for a given species (characters). The genus Drosophila has long served as a model system in genetics, development, ecology and evolutionary biology. As a result of this work, species boundaries within this genus are quite well delimited, with most taxa being defined by morphological characters and also conforming to a biological species concept (e.g., partial or complete reproductive isolation has used to erect and define species). In addition, some of the species in this group have also been subjected to phylogenetic analysis, yielding cases where taxa both conform and conflict with a phylogenetic species concept. Here, we analyzed 1058 COI sequences belonging to 68 species belonging to Drosophila and its allied genus Zaprionus and with more than a single representative to assess the performance of the three DNA barcoding methods. 26% of the species could not be defined using distance methods, i.e. had a barcoding gap of ≤ 0, and 23% were not monophyletic. We focused then on four groups of closely-related species whose taxonomy is well-established on non-molecular basis (e.g., morphology, geography, reproductive isolation) and to which most of the problematic species belonged. We showed that characters performed better than other approaches in the case of paraphyletic species, but all methods failed in the case of polyphyletic species. For these polyphyletic species, other sources of evidence (e.g., morphology, geography, reproductive isolation) are more relevant than COI sequences, highlighting the limitation of DNA barcoding and the needs for integrative taxonomy approaches. In conclusion, DNA barcoding of Drosophila shows no reason to alter the 250 years old tradition of character-based taxonomy, and many reasons to shy away from the alternatives.},
}
@article {pmid20796245,
year = {2011},
author = {Nock, CJ and Waters, DL and Edwards, MA and Bowen, SG and Rice, N and Cordeiro, GM and Henry, RJ},
title = {Chloroplast genome sequences from total DNA for plant identification.},
journal = {Plant biotechnology journal},
volume = {9},
number = {3},
pages = {328-333},
doi = {10.1111/j.1467-7652.2010.00558.x},
pmid = {20796245},
issn = {1467-7652},
mesh = {Base Sequence ; DNA, Chloroplast/*genetics ; Genome, Chloroplast/*genetics ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Poaceae/*classification/*genetics ; Reference Standards ; Sequence Alignment ; },
abstract = {Chloroplast DNA sequence data are a versatile tool for plant identification or barcoding and establishing genetic relationships among plant species. Different chloroplast loci have been utilized for use at close and distant evolutionary distances in plants, and no single locus has been identified that can distinguish between all plant species. Advances in DNA sequencing technology are providing new cost-effective options for genome comparisons on a much larger scale. Universal PCR amplification of chloroplast sequences or isolation of pure chloroplast fractions, however, are non-trivial. We now propose the analysis of chloroplast genome sequences from massively parallel sequencing (MPS) of total DNA as a simple and cost-effective option for plant barcoding, and analysis of plant relationships to guide gene discovery for biotechnology. We present chloroplast genome sequences of five grass species derived from MPS of total DNA. These data accurately established the phylogenetic relationships between the species, correcting an apparent error in the published rice sequence. The chloroplast genome may be the elusive single-locus DNA barcode for plants.},
}
@article {pmid20795782,
year = {2010},
author = {Cai, Y and Yue, B and Jiang, W and Xie, S and Li, J and Zhou, M},
title = {DNA barcoding on subsets of three families in Aves.},
journal = {Mitochondrial DNA},
volume = {21},
number = {3-4},
pages = {132-137},
doi = {10.3109/19401736.2010.494726},
pmid = {20795782},
issn = {1940-1744},
mesh = {Animals ; Base Sequence ; Birds/classification/*genetics ; DNA/*genetics ; DNA Primers ; *Electronic Data Processing ; Molecular Sequence Data ; },
abstract = {BACKGROUND AND AIMS: Previous studies carried out with DNA barcoding, based on regional groups, have shown that a standard mitochondrial gene could be used to identify birds. In the present study, we present an additional DNA barcoding survey of birds, using taxonomic groups instead of regional groups to verify the effectiveness of DNA barcoding on distinguishing species and to test whether the intraspecific clusters of species are associated with geographical discontinuities.<br><br>MATERIALS AND METHODS: Taxonomic groups of three avian families--Phasianidae, Accipitridae, and Strigidae--were included in the study. The cytochrome c oxidase I (COI) sequences of 49 individuals were determined. Together with 122 sequences from previous studies, a total of 171 sequences from 66 bird species were analyzed.<br><br>RESULTS AND CONCLUSION: Results showed that all 66 species investigated had unique COI sequences and no sequences were shared between the species. Our results were congruent with previous studies suggesting that the COI barcode permits distinguishing most of the closely related species. Furthermore, by using geographically distinct clusters, diagnostic characters, and threshold levels, deep genetic splits (>1.5%) were observed in three species, and we therefore suggest treating them as evolutionary significant units.},
}
@article {pmid20740694,
year = {2010},
author = {Chen, J and Li, Q and Kong, LF and Zheng, XD and Yu, RH},
title = {[COI-based DNA barcoding in Tapetinae species (Mollusca, Bivalvia, Veneridae) along the coast of CHINA].},
journal = {Dong wu xue yan jiu = Zoological research},
volume = {31},
number = {4},
pages = {345-352},
doi = {10.3724/SP.J.1141.2010.04345},
pmid = {20740694},
issn = {0254-5853},
mesh = {Animals ; Bivalvia/classification/*genetics ; China ; *DNA Barcoding, Taxonomic ; Haplotypes ; Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {DNA barcoding has exhibited charming effectiveness in species diagnosis, but some studies suggested the proportion of taxa that cannot be barcode-distinguished was still high. In the present study, the efficiency of the DNA barcoding for delimiting species of subfamily Tapetinae along the coast of China was tested. Fifty one original COI sequences of 11 species in five genera were analyzed. Among these sequences, 43 haplotypes were identified. Saturation plots generated for DNA barcode revealed that transitions became saturated after 10% to 15% sequence divergence. However, transversions were not saturated. Excluding Ruditapes variegata haplotype Hap33 that might be the result of a hybridization event, our finding showed that K2P-distances between conspecific sequences varied from 0% to 2.02% (0.46% on average), distances between congeneric sequences were from 17.21% to 32.24% (24.96% on average), and all conspecifics clustered together in the phylogentic trees. The proportion of individuals that can be distinguished by DNA barcoding was approximately 98% among 51 individuals analyzed in this study. Thus, the results evidenced that subfamily Tapetinae species can be efficiently identified through the use of DNA barcoding.},
}
@article {pmid20740280,
year = {2010},
author = {Seo, TK},
title = {Classification of nucleotide sequences using support vector machines.},
journal = {Journal of molecular evolution},
volume = {71},
number = {4},
pages = {250-267},
pmid = {20740280},
issn = {1432-1432},
mesh = {*Algorithms ; Artificial Intelligence ; Base Sequence ; Computer Simulation ; DNA/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Concatenated ; Genetic Loci/genetics ; Molecular Sequence Data ; Nucleotides/genetics ; Phylogeny ; },
abstract = {Species identification is one of the most important issues in biological studies. Due to recent increases in the amount of genomic information available and the development of DNA sequencing technologies, the applicability of using DNA sequences to identify species (commonly referred to as "DNA barcoding") is being tested in many areas. Several methods have been suggested to identify species using DNA sequences, including similarity scores, analysis of phylogenetic and population genetic information, and detection of species-specific sequence patterns. Although these methods have demonstrated good performance under a range of circumstances, they also have limitations, as they are subject to loss of information, require intensive computation and are sensitive to model mis-specification, and can be difficult to evaluate in terms of the significance of identification. Here, we suggest a new DNA barcoding method in which support vector machine (SVM) procedures are adopted. Our new method is nonparametric and thus is expected to be robust for a wide range of evolutionary scenarios as well as multilocus analyses. Furthermore, we describe bootstrap procedures that can be used to test the significances of species identifications. We implemented a novel conversion technique for transforming sequence data to real-valued vectors, and therefore, bootstrap procedures can be easily combined with our SVM approach. In this study, we present the results of simulation studies and empirical data analyses to demonstrate the performance of our method and discuss its properties.},
}
@article {pmid20731825,
year = {2010},
author = {Botti, S and Giuffra, E},
title = {Oligonucleotide indexing of DNA barcodes: identification of tuna and other scombrid species in food products.},
journal = {BMC biotechnology},
volume = {10},
number = {},
pages = {60},
pmid = {20731825},
issn = {1472-6750},
mesh = {Animals ; DNA Primers/genetics ; DNA, Mitochondrial/analysis ; Food Analysis/*methods ; Polymerase Chain Reaction/methods ; Polymorphism, Genetic ; Seafood/*analysis ; Sequence Analysis, DNA/*methods ; Species Specificity ; Tuna/*genetics ; },
abstract = {BACKGROUND: DNA barcodes are a global standard for species identification and have countless applications in the medical, forensic and alimentary fields, but few barcoding methods work efficiently in samples in which DNA is degraded, e.g. foods and archival specimens. This limits the choice of target regions harbouring a sufficient number of diagnostic polymorphisms. The method described here uses existing PCR and sequencing methodologies to detect mitochondrial DNA polymorphisms in complex matrices such as foods. The reported application allowed the discrimination among 17 fish species of the Scombridae family with high commercial interest such as mackerels, bonitos and tunas which are often present in processed seafood. The approach can be easily upgraded with the release of new genetic diversity information to increase the range of detected species.<br><br>RESULTS: Cocktail of primers are designed for PCR using publicly available sequences of the target sequence. They are composed of a fixed 5' region and of variable 3' cocktail portions that allow amplification of any member of a group of species of interest. The population of short amplicons is directly sequenced and indexed using primers containing a longer 5' region and the non polymorphic portion of the cocktail portion. A 226 bp region of CytB was selected as target after collection and screening of 148 online sequences; 85 SNPs were found, of which 75 were present in at least two sequences. Primers were also designed for two shorter sub-fragments that could be amplified from highly degraded samples. The test was used on 103 samples of seafood (canned tuna and scomber, tuna salad, tuna sauce) and could successfully detect the presence of different or additional species that were not identified on the labelling of canned tuna, tuna salad and sauce samples.<br><br>CONCLUSIONS: The described method is largely independent of the degree of degradation of DNA source and can thus be applied to processed seafood. Moreover, the method is highly flexible: publicly available sequence information on mitochondrial genomes are rapidly increasing for most species, facilitating the choice of target sequences and the improvement of resolution of the test. This is particularly important for discrimination of marine and aquaculture species for which genome information is still limited.},
}
@article {pmid20731421,
year = {2010},
author = {Li, X and Wang, T and Zhang, J and Zhu, D and Zhang, X and Ning, Y and Zhang, H and Yang, B},
title = {Controlled fabrication of fluorescent barcode nanorods.},
journal = {ACS nano},
volume = {4},
number = {8},
pages = {4350-4360},
doi = {10.1021/nn9017137},
pmid = {20731421},
issn = {1936-086X},
mesh = {Electronic Data Processing/*instrumentation/methods ; Fluorescent Dyes/*chemistry ; Microscopy, Electron, Scanning ; Nanotechnology/*methods ; Nanotubes/*chemistry ; Polyvinyls/chemistry ; Spectrophotometry, Ultraviolet ; },
abstract = {We report a novel technique for generating polymer fluorescent barcode nanorods by reactive ion etching of polymer multilayer films using nonclose-packed (ncp) colloidal microsphere arrays as masks. The fluorescent polymer multilayer films were spin-coated on a substrate, and ncp microsphere arrays were transferred onto these films. The exposed polymers were then etched away selectively, leaving color-encoded nanorods with well-preserved fluorescent properties. By modifying the spin-coating procedure, the amount of polymer in each layer could be tuned freely, which determined the relative fluorescence intensity of the barcode nanorods. These nanorod arrays can be detached from the substrate to form dispersions of coding materials. Moreover, the shape of the nanorods is controllable according to the different etching speeds of various materials, which also endows the nanorods with shape-encoded characters. This method offers opportunities for the fabrication of novel fluorescent barcodes which can be used for detecting and tracking applications.},
}
@article {pmid20720300,
year = {2010},
author = {Hao, DC and Chen, SL and Xiao, PG},
title = {Sequence characteristics and divergent evolution of the chloroplast psbA-trnH noncoding region in gymnosperms.},
journal = {Journal of applied genetics},
volume = {51},
number = {3},
pages = {259-273},
pmid = {20720300},
issn = {2190-3883},
mesh = {3' Untranslated Regions/genetics ; Base Composition ; Base Sequence ; Chloroplasts/*genetics ; Consensus Sequence/genetics ; Cycadopsida/*genetics ; DNA Barcoding, Taxonomic ; DNA, Intergenic/*genetics ; *Evolution, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Plant Proteins/*genetics ; Promoter Regions, Genetic/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {The psbA-trnH intergenic region is among the most variable regions in the gymnosperm chloroplast genome. It is proposed as suitable for DNA barcoding studies and is useful in phylogenetics at the species level. This region consists of two parts differing in their evolutionary characteristics: 1) the psbA 3’UTR (untranslated region) and 2) the psbA-trnH intergenic spacer. We compared the sequence and RNA secondary structure of the psbA 3’ UTR across gymnosperms and found consensus motifs corresponding to the stem portions of the RNA stem-loop structures and a consensus TGGATTGTTATGT box. The psbA-trnH spacer is highly variable in length and composition. Tandem repeats that form stem-loop structures were detected in both the psbA 3’ UTR and the psbA-trnH spacer. The presence of promoters and stem-loop structures in the psbA-trnH spacer and high sequence variation in this region suggest that psbA and trnH in some gymnosperms are independently transcribed. A comparison of chloroplast UTRs across gymnosperms offer clues to the identity of putative regulatory elements and information on selective constraints imposed on the chloroplast non-coding regions. The present study should inspire researchers to explore the full potential of the psbA-trnH non-coding sequence and to further stimulate its application in a broader spectrum of studies, not limited to phylogenetics and DNA barcoding.},
}
@article {pmid20708435,
year = {2011},
author = {Kher, CP and Doerder, FP and Cooper, J and Ikonomi, P and Achilles-Day, U and Küpper, FC and Lynn, DH},
title = {Barcoding Tetrahymena: discriminating species and identifying unknowns using the cytochrome c oxidase subunit I (cox-1) barcode.},
journal = {Protist},
volume = {162},
number = {1},
pages = {2-13},
doi = {10.1016/j.protis.2010.03.004},
pmid = {20708435},
issn = {1618-0941},
mesh = {DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Protein Subunits/genetics ; Species Specificity ; Tetrahymena/*classification/enzymology ; },
abstract = {DNA barcoding using the mitochondrial cytochromecoxidase subunit I (cox-1) gene has recently gained popularity as a tool for species identification of a variety of taxa. The primary objective of our research was to explore the efficacy of using cox-1 barcoding for species identification within the genusTetrahymena. We first increased intraspecific sampling forTetrahymena canadensis, Tetrahymena hegewischi, Tetrahymena pyriformis, Tetrahymena rostrata, Tetrahymena thermophila, and Tetrahymena tropicalis. Increased sampling efforts show that intraspecific sequence divergence is typically less than 1%, though it may be more in some species. The barcoding also showed that some strains might be misidentified or mislabeled. We also used cox-1 barcodes to provide species identifications for 51 unidentified environmental isolates, with a success rate of 98%. Thus, cox-1 barcoding is an invaluable tool for protistologists, especially when used in conjunction with morphological studies.},
}
@article {pmid20702462,
year = {2011},
author = {Dinca, V and Zakharov, EV and Hebert, PD and Vila, R},
title = {Complete DNA barcode reference library for a country's butterfly fauna reveals high performance for temperate Europe.},
journal = {Proceedings. Biological sciences},
volume = {278},
number = {1704},
pages = {347-355},
pmid = {20702462},
issn = {1471-2954},
mesh = {Animals ; Base Sequence ; Butterflies/anatomy &amp; histology/*genetics ; Cluster Analysis ; DNA/chemistry/genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/chemistry/genetics ; *Gene Library ; Male ; Molecular Sequence Data ; Polymerase Chain Reaction ; Romania ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {DNA barcoding aims to accelerate species identification and discovery, but performance tests have shown marked differences in identification success. As a consequence, there remains a great need for comprehensive studies which objectively test the method in groups with a solid taxonomic framework. This study focuses on the 180 species of butterflies in Romania, accounting for about one third of the European butterfly fauna. This country includes five eco-regions, the highest of any in the European Union, and is a good representative for temperate areas. Morphology and DNA barcodes of more than 1300 specimens were carefully studied and compared. Our results indicate that 90 per cent of the species form barcode clusters allowing their reliable identification. The remaining cases involve nine closely related species pairs, some whose taxonomic status is controversial or that hybridize regularly. Interestingly, DNA barcoding was found to be the most effective identification tool, outperforming external morphology, and being slightly better than male genitalia. Romania is now the first country to have a comprehensive DNA barcode reference database for butterflies. Similar barcoding efforts based on comprehensive sampling of specific geographical regions can act as functional modules that will foster the early application of DNA barcoding while a global system is under development.},
}
@article {pmid20702136,
year = {2011},
author = {Heger, TJ and Pawlowski, J and Lara, E and Leander, BS and Todorov, M and Golemansky, V and Mitchell, EA},
title = {Comparing potential COI and SSU rDNA barcodes for assessing the diversity and phylogenetic relationships of cyphoderiid testate amoebae (Rhizaria: Euglyphida).},
journal = {Protist},
volume = {162},
number = {1},
pages = {131-141},
doi = {10.1016/j.protis.2010.05.002},
pmid = {20702136},
issn = {1618-0941},
mesh = {Cercozoa/*classification/*genetics/ultrastructure ; DNA Barcoding, Taxonomic ; DNA, Ribosomal/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Phylogeny ; Protein Subunits/genetics ; },
abstract = {The mitochondrial Cytochrome Oxidase Subunit 1 gene (COI) has been promoted as an ideal "DNA barcode" for animal species and other groups of eukaryotes. However, the utility of the COI marker for species level discrimination and for phylogenetic analyses has yet to be tested within the Rhizaria. Accordingly, we analysed mitochondrial COI gene sequences and nuclear small subunit rDNA (SSU) sequences from several morphospecies of euglyphid testate amoebae (Cercozoa, Rhizaria) in order to evaluate the utility of these DNA markers for species discrimination and phylogenetic reconstructions. Sequences were obtained from eleven populations belonging to sixCyphoderiamorphospecies that were isolated from field samples in North America and Europe. Mean inter-population COI sequence dissimilarities were on average 2.9 times greater than in the SSU, while the intra-population sequence dissimilarities were higher in the SSU (0-0.95%) than in the COI (0%); this suggests that the COI fragment is valuable for discriminating Cyphoderiidae isolates. Our study also demonstrated that COI sequences are useful for inferring phylogenetic relationships among Cyphoderiidae isolates. COI and SSU tree topologies were very similar even though the COI fragment used in these analyses (500bp) was much shorter than the SSU sequences (1600bp). Altogether, these results demonstrate the utility of the COI as a potential taxonomic DNA barcode for assessing cyphoderiid species diversity and for inferring phylogenetic relationships within the group.},
}
@article {pmid20701681,
year = {2010},
author = {Damm, S and Schierwater, B and Hadrys, H},
title = {An integrative approach to species discovery in odonates: from character-based DNA barcoding to ecology.},
journal = {Molecular ecology},
volume = {19},
number = {18},
pages = {3881-3893},
doi = {10.1111/j.1365-294X.2010.04720.x},
pmid = {20701681},
issn = {1365-294X},
mesh = {Africa South of the Sahara ; Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Geography ; Insecta/anatomy &amp; histology/*genetics ; Male ; *Phylogeny ; },
abstract = {Modern taxonomy requires an analytical approach incorporating all lines of evidence into decision-making. Such an approach can enhance both species identification and species discovery. The character-based DNA barcode method provides a molecular data set that can be incorporated into classical taxonomic data such that the discovery of new species can be made in an analytical framework that includes multiple sources of data. We here illustrate such a corroborative framework in a dragonfly model system that permits the discovery of two new, but visually cryptic species. In the African dragonfly genus Trithemis three distinct genetic clusters can be detected which could not be identified by using classical taxonomic characters. In order to test the hypothesis of two new species, DNA-barcodes from different sequence markers (ND1 and COI) were combined with morphological, ecological and biogeographic data sets. Phylogenetic analyses and incorporation of all data sets into a scheme called taxonomic circle highly supports the hypothesis of two new species. Our case study suggests an analytical approach to modern taxonomy that integrates data sets from different disciplines, thereby increasing the ease and reliability of both species discovery and species assignment.},
}
@article {pmid20700453,
year = {2010},
author = {Matsumura, H and Yoshida, K and Luo, S and Kimura, E and Fujibe, T and Albertyn, Z and Barrero, RA and Krüger, DH and Kahl, G and Schroth, GP and Terauchi, R},
title = {High-throughput SuperSAGE for digital gene expression analysis of multiple samples using next generation sequencing.},
journal = {PloS one},
volume = {5},
number = {8},
pages = {e12010},
pmid = {20700453},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; DNA Restriction Enzymes/metabolism ; Gene Expression Profiling/*methods ; Gene Library ; Polymerase Chain Reaction ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; },
abstract = {We established a protocol of the SuperSAGE technology combined with next-generation sequencing, coined "High-Throughput (HT-) SuperSAGE". SuperSAGE is a method of digital gene expression profiling that allows isolation of 26-bp tag fragments from expressed transcripts. In the present protocol, index (barcode) sequences are employed to discriminate tags from different samples. Such barcodes allow researchers to analyze digital tags from transcriptomes of many samples in a single sequencing run by simply pooling the libraries. Here, we demonstrated that HT-SuperSAGE provided highly sensitive, reproducible and accurate digital gene expression data. By increasing throughput for analysis in HT-SuperSAGE, various applications are foreseen and several examples are provided in the present study, including analyses of laser-microdissected cells, biological replicates and tag extraction using different anchoring enzymes.},
}
@article {pmid20699269,
year = {2010},
author = {Shental, N and Amir, A and Zuk, O},
title = {Identification of rare alleles and their carriers using compressed se(que)nsing.},
journal = {Nucleic acids research},
volume = {38},
number = {19},
pages = {e179},
pmid = {20699269},
issn = {1362-4962},
mesh = {Algorithms ; *Alleles ; Computer Simulation ; Genetic Carrier Screening/*methods ; Humans ; Sequence Analysis, DNA/*methods ; },
abstract = {Identification of rare variants by resequencing is important both for detecting novel variations and for screening individuals for known disease alleles. New technologies enable low-cost resequencing of target regions, although it is still prohibitive to test more than a few individuals. We propose a novel pooling design that enables the recovery of novel or known rare alleles and their carriers in groups of individuals. The method is based on a Compressed Sensing (CS) approach, which is general, simple and efficient. CS allows the use of generic algorithmic tools for simultaneous identification of multiple variants and their carriers. We model the experimental procedure and show via computer simulations that it enables the recovery of rare alleles and their carriers in larger groups than were possible before. Our approach can also be combined with barcoding techniques to provide a feasible solution based on current resequencing costs. For example, when targeting a small enough genomic region (∼100 bp) and using only ∼10 sequencing lanes and ∼10 distinct barcodes per lane, one recovers the identity of 4 rare allele carriers out of a population of over 4000 individuals. We demonstrate the performance of our approach over several publicly available experimental data sets.},
}
@article {pmid20695271,
year = {2010},
author = {Leo, SS and Pybus, MJ and Sperling, FA},
title = {Deep mitochondrial DNA lineage divergences within Alberta populations of Dermacentor albipictus (Acari: Ixodidae) do not indicate distinct species.},
journal = {Journal of medical entomology},
volume = {47},
number = {4},
pages = {565-574},
pmid = {20695271},
issn = {0022-2585},
mesh = {Alberta ; Animals ; DNA/genetics ; DNA, Mitochondrial/*genetics ; Demography ; Dermacentor/*genetics ; Genetic Speciation ; *Genetic Variation ; Phylogeny ; },
abstract = {The winter tick Dermacentor albipictus (Packard) has a single-host life cycle that allows it to reach severe infestation levels on ungulates, particularly moose. Genotypic variation within these and related ticks has been a source of taxonomic confusion, although the continuity in their morphology and life history has generally been interpreted as indicating the existence of a single species. To further investigate this variation, we sequenced regions of two mitochondrial DNA (mtDNA) genes (COI and 16S rDNA),two nuclear genes (lysozyme and ITS-2), and two bacterial markers from Francisella-like endosymbionts found in these ticks (eubacterial mtDNA 16S rRNA and a homolog of Francisella tularensis [Dorofe'ev] 17-kDa lipoprotein). We sampled 42 D. albipictus individuals from whitetail and mule deer culled from three populations in east-central Alberta, as well as four D. albipictus and two Dermacentor variabilis (Say) from other locations. We then compared DNA sequence variation between the genes and related this to variation in the morphology of spiracle plates. Both mtDNA regions indicated two deeply diverged lineages (mean difference of 7.1% for COI and 4.5% for 16S) that would normally be considered diagnostic of distinct species in DNA barcoding studies. However, very little divergence was revealed by nuclear gene sequences, bacterial endosymbionts, and morphometric analyses, and any variation that did occur in these markers was not congruent with mtDNA divergences. We conclude that the sampled populations in Alberta represent a single species, D. albipictus, and reiterate the importance of integrative approaches in species delimitation.},
}
@article {pmid20688693,
year = {2010},
author = {Kang, HM and Jeong, OM and Kim, MC and Kwon, JS and Paek, MR and Choi, JG and Lee, EK and Kim, YJ and Kwon, JH and Lee, YJ},
title = {Surveillance of avian influenza virus in wild bird fecal samples from South Korea, 2003-2008.},
journal = {Journal of wildlife diseases},
volume = {46},
number = {3},
pages = {878-888},
doi = {10.7589/0090-3558-46.3.878},
pmid = {20688693},
issn = {1943-3700},
mesh = {Animals ; Animals, Wild/virology ; Anseriformes/*virology ; Birds ; Feces/*virology ; Female ; Influenza A virus/classification/*isolation &amp; purification ; Influenza in Birds/*epidemiology/virology ; Male ; Prevalence ; Republic of Korea/epidemiology ; Sentinel Surveillance/veterinary ; Serotyping ; Species Specificity ; },
abstract = {We analyzed the results from nationwide surveillance of avian influenza (AI) from birds in South Korea's major wild bird habitats and the demilitarized zone of South Korea, 2003-2008. Of 28,214 fecal samples analyzed, 225 yielded influenza viruses, for a prevalence of 0.8%. Hemagglutinin (HA) subtypes H1-H12 and all nine neuraminidase (NA) subtypes were detected. The dominant HA subtypes were H6, H1, and H4, and the most common NA subtypes were N2, N1, and N6. Among the 38 HA/NA subtype combinations, the most common were H4N6, H6N1, and H5N2. Thirty-seven low-pathogenic AI (LPAI) viruses of the H5 and H7 subtype were detected. Among them, we identified bird species for 16 H5- and H7-positive fecal samples using a DNA bar-coding system instituted in 2007; all birds were identified as Anseriformes. The HA gene of the H5 wild bird isolates belonged to the Eurasian avian lineage, and could be clearly distinguished from the sublineage H5N1 highly pathogenic AI (HPAI) of the Eurasian and American avian lineages. Whereas H7 LPAI viruses did not group as a separate sublineage with H7 HPAI viruses, H7 isolates were closely related with the Eurasian avian lineage.},
}
@article {pmid20688667,
year = {2010},
author = {Lee, DH and Lee, HJ and Lee, YJ and Kang, HM and Jeong, OM and Kim, MC and Kwon, JS and Kwon, JH and Kim, CB and Lee, JB and Park, SY and Choi, IS and Song, CS},
title = {DNA barcoding techniques for avian influenza virus surveillance in migratory bird habitats.},
journal = {Journal of wildlife diseases},
volume = {46},
number = {2},
pages = {649-654},
doi = {10.7589/0090-3558-46.2.649},
pmid = {20688667},
issn = {1943-3700},
mesh = {Animal Migration ; Animals ; Animals, Wild/virology ; Anseriformes/*virology ; Birds ; DNA, Viral/*analysis ; Ecosystem ; Feces/virology ; Female ; Influenza A virus/*genetics ; Influenza in Birds/*epidemiology/transmission ; Korea/epidemiology ; Male ; Sentinel Surveillance/*veterinary ; *Sequence Analysis, DNA ; },
abstract = {Avian influenza virus (AIV) circulates among free-ranging, wild birds. We optimized and validated a DNA barcoding technique for AIV isolation and host-species identification using fecal samples from wild birds. DNA barcoding was optimized using tissue and fecal samples from known bird species, and the method was shown to distinguish 26 bird species. Subsequently, fecal samples (n=743) collected from wild waterfowl habitats confirmed the findings from the laboratory tests. All identified AIV-positive hosts (n=35) were members of the order Anseriformes. We successfully applied the DNA barcoding technique to AIV surveillance and examined AIV epidemiology and host ecology in these wild waterfowl populations. This methodology may be useful in the design of AIV surveillance strategies.},
}
@article {pmid20681509,
year = {2010},
author = {Buller, F and Mannocci, L and Scheuermann, J and Neri, D},
title = {Drug discovery with DNA-encoded chemical libraries.},
journal = {Bioconjugate chemistry},
volume = {21},
number = {9},
pages = {1571-1580},
doi = {10.1021/bc1001483},
pmid = {20681509},
issn = {1520-4812},
mesh = {DNA/analysis/*chemistry/*genetics ; *Drug Discovery ; *Gene Library ; Small Molecule Libraries/chemistry/*pharmacology ; },
abstract = {DNA-encoded chemical libraries represent a novel avenue for the facile discovery of small molecule ligands against target proteins of biological or pharmaceutical importance. Library members consist of small molecules covalently attached to unique DNA fragments that serve as amplifiable identification barcodes. This encoding allows the in vitro selection of ligands at subpicomolar concentrations from large library populations by affinity capture on a target protein of interest, in analogy to established technologies for the selection of binding polypeptides (e.g., antibodies). Different library formats have been explored by various groups, allowing the construction of chemical libraries comprising up to millions of DNA-encoded compounds. Libraries before and after selection have been characterized by PCR amplification of the DNA codes and subsequent relative quantification of library members using high-throughput sequencing. The most enriched compounds have then been further analyzed in biological assays, in the presence or in the absence of linked DNA. This article reviews experimental strategies used for the construction of DNA-encoded chemical libraries, revealing how selection, decoding, and hit validation technologies have been used for drug discovery programs.},
}
@article {pmid20673351,
year = {2010},
author = {Bittner, L and Halary, S and Payri, C and Cruaud, C and de Reviers, B and Lopez, P and Bapteste, E},
title = {Some considerations for analyzing biodiversity using integrative metagenomics and gene networks.},
journal = {Biology direct},
volume = {5},
number = {},
pages = {47},
pmid = {20673351},
issn = {1745-6150},
mesh = {Animals ; *Biodiversity ; Gene Regulatory Networks/*genetics ; Humans ; Metagenomics/*methods ; Models, Theoretical ; },
abstract = {BACKGROUND: Improving knowledge of biodiversity will benefit conservation biology, enhance bioremediation studies, and could lead to new medical treatments. However there is no standard approach to estimate and to compare the diversity of different environments, or to study its past, and possibly, future evolution.<br><br>We argue that there are two conditions for significant progress in the identification and quantification of biodiversity. First, integrative metagenomic studies - aiming at the simultaneous examination (or even better at the integration) of observations about the elements, functions and evolutionary processes captured by the massive sequencing of multiple markers - should be preferred over DNA barcoding projects and over metagenomic projects based on a single marker. Second, such metagenomic data should be studied with novel inclusive network-based approaches, designed to draw inferences both on the many units and on the many processes present in the environments.<br><br>TESTING THE HYPOTHESIS: We reached these conclusions through a comparison of the theoretical foundations of two molecular approaches seeking to assess biodiversity: metagenomics (mostly used on prokaryotes and protists) and DNA barcoding (mostly used on multicellular eukaryotes), and by pragmatic considerations of the issues caused by the 'species problem' in biodiversity studies.<br><br>Evolutionary gene networks reduce the risk of producing biodiversity estimates with limited explanatory power, biased either by unequal rates of LGT, or difficult to interpret due to (practical) problems caused by type I and type II grey zones. Moreover, these networks would easily accommodate additional (meta)transcriptomic and (meta)proteomic data.},
}
@article {pmid20653954,
year = {2010},
author = {Tavares, ES and de Kroon, GH and Baker, AJ},
title = {Phylogenetic and coalescent analysis of three loci suggest that the Water Rail is divisible into two species, Rallus aquaticus and R. indicus.},
journal = {BMC evolutionary biology},
volume = {10},
number = {},
pages = {226},
pmid = {20653954},
issn = {1471-2148},
mesh = {Animals ; Asia ; Base Composition ; Bayes Theorem ; Birds/*classification/*genetics ; DNA, Mitochondrial/genetics ; Europe ; *Evolution, Molecular ; Gene Flow ; Genetic Variation ; Genetics, Population ; Geography ; Haplotypes ; Models, Genetic ; *Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND: Water Rails (Rallus aquaticus) inhabit fragmented freshwater wetlands across their Palearctic distribution. Disjunct populations are now thought to be morphologically similar over their vast geographic range, though four subspecies had been recognized previously. The fossil record suggests that Water Rails (R. aquaticus) were already spread across the Palearctic by the Pleistocene approximately 2 million years ago, and the oldest fossil remains thought to be closely related to the common ancestor of water rails date from the Pliocene.<br><br>RESULTS: To investigate population structure in Water Rails at the genetic level we sequenced three independent loci: 686 base pairs (bp) of the mitochondrial DNA COI barcode; 618 bp of the intron ADH5; and 746 bp of the exon PTPN12. Phylogeographic analysis revealed that Water Rails breeding in eastern Asia (R. a. indicus, also known as the Brown-cheeked Rail) are strongly differentiated from the Water Rails in Western and Middle Asia and Europe (R. a. aquaticus and R. a. korejewi). The Kimura 3-parameter plus Gamma COI genetic distance between these two geographic groups was > 3%, and they differed by 18 diagnostic substitutions commensurate with differences between recently diverged sister species of birds. In spite of the low number of variable sites, the two nuclear loci supported this split. We estimated the split of the Brown-cheeked Rail and the Water Rail to have occurred approximately 534,000 years ago (95% CI 275,000-990,000 years ago). Fragmentation of the widespread ancestral population and eventual speciation of water rails is likely attributable to vicariance by a barrier formed by glacial cycles, continuous uplift of the Tibetan Plateau and increased sedimentation in deserts in southern Asia that originated in the Miocene.<br><br>CONCLUSIONS: Water Rails from East Asia were genetically differentiated from the ones breeding in Europe and Western to Middle Asia. Most of the genetic signal was from mitochondrial COI, and was corroborated by polymorphic sites in the two nuclear loci we employed. The split between these two lineages was estimated to occur in the Middle Pleistocene, when populations were isolated in disjunct wetlands with little or no gene flow. Independent evidence from differences in morphology and vocalizations in concert with genetic differentiation and a long history of isolation support recognition of the Brown-cheeked Rail breeding in East Asia as a separate species, R. indicus. The use of several independent loci is invaluable in inferring species trees from gene trees and in recognizing species limits.},
}
@article {pmid20650293,
year = {2010},
author = {Lank, SM and Wiseman, RW and Dudley, DM and O'Connor, DH},
title = {A novel single cDNA amplicon pyrosequencing method for high-throughput, cost-effective sequence-based HLA class I genotyping.},
journal = {Human immunology},
volume = {71},
number = {10},
pages = {1011-1017},
pmid = {20650293},
issn = {1879-1166},
support = {P51 RR000167/RR/NCRR NIH HHS/United States ; P51 RR000167-51/RR/NCRR NIH HHS/United States ; P51 RR000167-50/RR/NCRR NIH HHS/United States ; P51 RR000167-49/RR/NCRR NIH HHS/United States ; P51 OD011106/OD/NIH HHS/United States ; },
mesh = {Alleles ; Cost-Benefit Analysis ; DNA Primers ; DNA, Complementary/*analysis ; Genes, MHC Class I/*genetics ; High-Throughput Nucleotide Sequencing/methods/trends ; *Histocompatibility Testing/economics ; Humans ; *Nucleic Acid Amplification Techniques/economics ; Sequence Analysis, DNA ; },
abstract = {Human leukocyte antigen (HLA) genotype influences the immune response to pathogens and transplanted tissues; accurate HLA genotyping is critical for clinical and research applications. Sequence-based HLA typing is limited by the cost of Sanger sequencing genomic DNA (gDNA) and resolving cis/trans ambiguities, hindering both studies correlating high-resolution genotype with clinical outcomes, and population-specific allele frequency surveys. We present an assay for sequence-based HLA genotyping by titanium read length clonal Roche/454 pyrosequencing of a single, universally diagnostic polymerase chain reaction (PCR) amplicon from HLA class I cDNA that captures most of exons 2, 3, and 4 used for traditional sequence-based typing. The amplicon is predicted to unambiguously resolve 85% of known alleles. A panel of 48 previously HLA-typed samples was assayed with this method, demonstrating 100% non-null allele typing concordance. We show that this technique can multiplex at least 768 patients per sequencing run with multiplex identifier sequence bar-coding. Unprecedented typing throughput results from a novel single cDNA-PCR amplicon strategy requiring only 1 PCR amplification per sample. This method dramatically reduces cost for genotyping of large cohorts.},
}
@article {pmid20649754,
year = {2010},
author = {Cywinska, A and Hannan, MA and Kevan, PG and Roughley, RE and Iranpour, M and Hunter, FF},
title = {Evaluation of DNA barcoding and identification of new haplomorphs in Canadian deerflies and horseflies.},
journal = {Medical and veterinary entomology},
volume = {24},
number = {4},
pages = {382-410},
doi = {10.1111/j.1365-2915.2010.00896.x},
pmid = {20649754},
issn = {1365-2915},
mesh = {Animals ; Base Composition ; Canada ; Codon/genetics ; *DNA Barcoding, Taxonomic ; Diptera/anatomy &amp; histology/classification/*genetics ; Electron Transport Complex IV/genetics ; Phylogeny ; Sequence Homology, Nucleic Acid ; Species Specificity ; },
abstract = {This paper reports the first tests of the suitability of the standardized mitochondrial cytochrome c oxidase subunit I (COI) barcoding system for the identification of Canadian deerflies and horseflies. Two additional mitochondrial molecular markers were used to determine whether unambiguous species recognition in tabanids can be achieved. Our 332 Canadian tabanid samples yielded 650 sequences from five genera and 42 species. Standard COI barcodes demonstrated a strong A + T bias (mean 68.1%), especially at third codon positions (mean 93.0%). Our preliminary test of this system showed that the standard COI barcode worked well for Canadian Tabanidae: the target DNA can be easily recovered from small amounts of insect tissue and aligned for all tabanid taxa. Each tabanid species possessed distinctive sets of COI haplotypes which discriminated well among species. Average conspecific Kimura two-parameter (K2P) divergence (0.49%) was 12 times lower than the average divergence within species. Both the neighbour-joining and the Bayesian methods produced trees with identical monophyletic species groups. Two species, Chrysops dawsoni Philip and Chrysops montanus Osten Sacken (Diptera: Tabanidae), showed relatively deep intraspecific sequence divergences (∼ 10 times the average) for all three mitochondrial gene regions analysed. We suggest provisional differentiation of Ch. montanus into two haplotypes, namely, Ch. montanus haplomorph 1 and Ch. montanus haplomorph 2, both defined by their molecular sequences and by newly discovered differences in structural features near their ocelli.},
}
@article {pmid20644717,
year = {2010},
author = {Whitlock, BA and Hale, AM and Groff, PA},
title = {Intraspecific inversions pose a challenge for the trnH-psbA plant DNA barcode.},
journal = {PloS one},
volume = {5},
number = {7},
pages = {e11533},
pmid = {20644717},
issn = {1932-6203},
mesh = {DNA, Chloroplast/*genetics ; Gentianaceae/classification/genetics ; Inverted Repeat Sequences/genetics ; Magnoliopsida/classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The chloroplast trnH-psbA spacer region has been proposed as a prime candidate for use in DNA barcoding of plants because of its high substitution rate. However, frequent inversions associated with palindromic sequences within this region have been found in multiple lineages of Angiosperms and may complicate its use as a barcode, especially if they occur within species.<br><br>Here, we evaluate the implications of intraspecific inversions in the trnH-psbA region for DNA barcoding efforts. We report polymorphic inversions within six species of Gentianaceae, all narrowly circumscribed morphologically: Gentiana algida, Gentiana fremontii, Gentianopsis crinita, Gentianopsis thermalis, Gentianopsis macrantha and Frasera speciosa. We analyze these sequences together with those from 15 other species of Gentianaceae and show that typical simple methods of sequence alignment can lead to misassignment of conspecifics and incorrect assessment of relationships.<br><br>CONCLUSIONS/SIGNIFICANCE: Frequent inversions in the trnH-psbA region, if not recognized and aligned appropriately, may lead to large overestimates of the number of substitution events separating closely related lineages and to uniting more distantly related taxa that share the same form of the inversion. Thus, alignment of the trnH-psbA spacer region will need careful attention if it is used as a marker for DNA barcoding.},
}
@article {pmid20644709,
year = {2010},
author = {Vernooy, R and Haribabu, E and Muller, MR and Vogel, JH and Hebert, PD and Schindel, DE and Shimura, J and Singer, GA},
title = {Barcoding life to conserve biological diversity: beyond the taxonomic imperative.},
journal = {PLoS biology},
volume = {8},
number = {7},
pages = {e1000417},
pmid = {20644709},
issn = {1545-7885},
mesh = {Base Sequence ; *Biodiversity ; Classification/*methods ; Conservation of Energy Resources/*methods ; Electronic Data Processing/*statistics &amp; numerical data ; *Sequence Analysis, DNA ; },
abstract = {Barcoding scientists aspire to adhere to the objectives of the Convention on Biological Diversity by promoting conservation, sustainability, and the equitable sharing of benefits arising from use of genetic resources. (Image: Juan Manuel Escalante, wwww.realitat.com)},
}
@article {pmid20643927,
year = {2010},
author = {Crawford, AJ and Lips, KR and Bermingham, E},
title = {Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of central Panama.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {107},
number = {31},
pages = {13777-13782},
pmid = {20643927},
issn = {1091-6490},
mesh = {Altitude ; Amphibians/classification/*genetics/*microbiology ; Animals ; Chytridiomycota/*physiology ; Communicable Diseases/epidemiology/*veterinary ; *Endangered Species ; Genetics, Population ; Molecular Sequence Data ; Panama/epidemiology ; *Phylogeny ; },
abstract = {Amphibian populations around the world are experiencing unprecedented declines attributed to a chytrid fungal pathogen, Batrachochytrium dendrobatidis. Despite the severity of the crisis, quantitative analyses of the effects of the epidemic on amphibian abundance and diversity have been unavailable as a result of the lack of equivalent data collected before and following disease outbreak. We present a community-level assessment combining long-term field surveys and DNA barcode data describing changes in abundance and evolutionary diversity within the amphibian community of El Copé, Panama, following a disease epidemic and mass-mortality event. The epidemic reduced taxonomic, lineage, and phylogenetic diversity similarly. We discovered that 30 species were lost, including five undescribed species, representing 41% of total amphibian lineage diversity in El Copé. These extirpations represented 33% of the evolutionary history of amphibians within the community, and variation in the degree of population loss and decline among species was random with respect to the community phylogeny. Our approach provides a fast, economical, and informative analysis of loss in a community whether measured by species or phylogenetic diversity.},
}
@article {pmid20642723,
year = {2010},
author = {Eberhardt, U},
title = {A constructive step towards selecting a DNA barcode for fungi.},
journal = {The New phytologist},
volume = {187},
number = {2},
pages = {265-268},
doi = {10.1111/j.1469-8137.2010.03329.x},
pmid = {20642723},
issn = {1469-8137},
mesh = {DNA, Fungal/*genetics ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Electronic Data Processing/*methods ; Glomeromycota/*genetics ; Mycorrhizae/*genetics ; Saccharomyces cerevisiae/genetics ; Sequence Analysis, DNA/*methods ; },
}
@article {pmid21565022,
year = {2010},
author = {Sundberg, P and Thuroczy Vodoti, E and Strand, M},
title = {DNA barcoding should accompany taxonomy - the case of Cerebratulus spp (Nemertea).},
journal = {Molecular ecology resources},
volume = {10},
number = {2},
pages = {274-281},
doi = {10.1111/j.1755-0998.2009.02774.x},
pmid = {21565022},
issn = {1755-0998},
abstract = {Many issues in DNA barcoding need to be solved before it can reach its goal to become a general database for species identification. While species delimitations are more or less well established in several taxa, there are still many groups where this is not the case. Without the proper taxonomic background/knowledge and corroboration with other kinds of data, the DNA barcoding approach may fail to identify species accurately. The classification and taxonomy of phylum Nemertea (nemerteans, ribbon worms) are traditionally based on morphology, but are not corroborated by an increasing amount of genetic data when it comes to classification either into species or into higher taxa. The taxonomy of the phylum needs to be improved before the full potential of DNA barcoding can be utilized to make sure that valid Linnean names accompany the barcode sequences. We illustrate the problematic situation in the phylum Nemertea by a case study from the genus Cerebratulus.},
}
@article {pmid21565021,
year = {2010},
author = {Dasmahapatra, KK and Elias, M and Hill, RI and Hoffman, JI and Mallet, J},
title = {Mitochondrial DNA barcoding detects some species that are real, and some that are not.},
journal = {Molecular ecology resources},
volume = {10},
number = {2},
pages = {264-273},
doi = {10.1111/j.1755-0998.2009.02763.x},
pmid = {21565021},
issn = {1755-0998},
abstract = {Mimicry and extensive geographical subspecies polymorphism combine to make species in the ithomiine butterfly genus Mechanitis (Lepidoptera; Nymphalidae) difficult to determine. We use mitochondrial DNA (mtDNA) barcoding, nuclear sequences and amplified fragment length polymorphism (AFLP) genotyping to investigate species limits in this genus. Although earlier biosystematic studies based on morphology described only four species, mtDNA barcoding revealed eight well-differentiated haplogroups, suggesting the presence of four new putative 'cryptic species'. However, AFLP markers supported only one of these four new 'cryptic species' as biologically meaningful. We demonstrate that in this genus, deep genetic divisions expected on the basis of mtDNA barcoding are not always reflected in the nuclear genome, and advocate the use of AFLP markers as a check when mtDNA barcoding gives unexpected results.},
}
@article {pmid21565020,
year = {2010},
author = {Naro-Maciel, E and Reid, B and Fitzsimmons, NN and LE, M and Desalle, R and Amato, G},
title = {DNA barcodes for globally threatened marine turtles: a registry approach to documenting biodiversity.},
journal = {Molecular ecology resources},
volume = {10},
number = {2},
pages = {252-263},
doi = {10.1111/j.1755-0998.2009.02747.x},
pmid = {21565020},
issn = {1755-0998},
abstract = {DNA barcoding is a global initiative that provides a standardized and efficient tool to catalogue and inventory biodiversity, with significant conservation applications. Despite progress across taxonomic realms, globally threatened marine turtles remain underrepresented in this effort. To obtain DNA barcodes of marine turtles, we sequenced a segment of the cytochrome c oxidase subunit I (COI) gene from all seven species in the Atlantic and Pacific Ocean basins (815 bp; n = 80). To further investigate intraspecific variation, we sequenced green turtles (Chelonia mydas) from nine additional Atlantic/Mediterranean nesting areas (n = 164) and from the Eastern Pacific (n = 5). We established character-based DNA barcodes for each species using unique combinations of character states at 76 nucleotide positions. We found that no haplotypes were shared among species and the mean of interspecific variation ranged from 1.68% to 13.0%, and the mean of intraspecific variability was relatively low (0-0.90%). The Eastern Pacific green turtle sequence was identical to an Australian haplotype, suggesting that this marker is not appropriate for identifying these phenotypically distinguishable populations. Analysis of COI revealed a north-south gradient in green turtles of Western Atlantic/Mediterranean nesting areas, supporting a hypothesis of recent dispersal from near equatorial glacial refugia. DNA barcoding of marine turtles is a powerful tool for species identification and wildlife forensics, which also provides complementary data for conservation genetic research.},
}
@article {pmid22171166,
year = {2010},
author = {Kress, WJ and D Mood, J and Sabu, M and Prince, LM and Dey, S and Sanoj, E},
title = {Larsenianthus, a new Asian genus of Gingers (Zingiberaceae) with four species.},
journal = {PhytoKeys},
volume = {},
number = {1},
pages = {15-32},
pmid = {22171166},
issn = {1314-2003},
abstract = {Larsenianthus W. J. Kress &amp; Mood, gen. nov. is described with one new combination and three new species. Larsenianthus careyanus (Benth.) W. J. Kress &amp; Mood, comb. nov., is widespread in India and present-day Bangladesh; Larsenianthus wardianus W. J. Kress, Thet Htun &amp; Bordelon, sp. nov., is from upper Myanmar in Kachin State; Larsenianthus assamensis S. Dey, Mood, &amp; S. Choudhury, sp. nov., is restricted to Assam, India; and Larsenianthus arunachalensis M. Sabu, Sanoj &amp; T.Rajesh Kumar, sp. nov., has only been found in Arunachal Pradesh, India. A phylogenetic analysis using the plastid trnK intron and nuclear ITS DNA sequence data indicates that the four species of Larsenianthus form a monophyletic lineage that is sister to Hedychium, a geographically widespread genus of about 50 species in tribe Zingibereae of subfamily Zingiberoideae. A dichotomous key and three-locus DNA barcodes are provided as aids for the identification of the four species of Larsenianthus.},
}
@article {pmid21622376,
year = {2010},
author = {Steele, PR and Friar, LM and Gilbert, LE and Jansen, RK},
title = {Molecular systematics of the neotropical genus Psiguria (Cucurbitaceae): Implications for phylogeny and species identification.},
journal = {American journal of botany},
volume = {97},
number = {1},
pages = {156-173},
doi = {10.3732/ajb.0900192},
pmid = {21622376},
issn = {0002-9122},
abstract = {Varying morphological features in many groups of tropical vines confound identification, requiring molecular tools for distinguishing species. Confusion is amplified in Psiguria, a small genus found in Central and South America and the Caribbean, because male and female flowers of these monoecious plants are widely separated by time and position on a branch. We present the first phylogeny of Psiguria utilizing a combination of eight chloroplast intergenic spacers, the internal transcribed spacer (ITS) regions of the nuclear ribosomal DNA repeat, and the intron of the low-copy nuclear gene serine/threonine phosphatase, for a total aligned length of 9456 base pairs. Analyses include multiple accessions of all species in the genus. The data support the monophyly of Psiguria and elucidate several species boundaries. Also presented are Psiguria-specific DNA barcodes, which include the chloroplast regions: ndhC-trnV, rps16-trnQ, rpoB-trnC, ndhF-rpl32, and psbZ-trnM. For the first time, systematists, ecologists, and evolutionary biologists will have the tools to confidently identify species of Psiguria with DNA barcodes that may be useful in other genera of Cucurbitaceae.},
}
@article {pmid21614174,
year = {2010},
author = {North, M and Vulpe, CD},
title = {Functional toxicogenomics: mechanism-centered toxicology.},
journal = {International journal of molecular sciences},
volume = {11},
number = {12},
pages = {4796-4813},
pmid = {21614174},
issn = {1422-0067},
support = {P42 ES004705/ES/NIEHS NIH HHS/United States ; },
mesh = {Animals ; Humans ; Toxicogenetics/*methods ; },
abstract = {Traditional toxicity testing using animal models is slow, low capacity, expensive and assesses a limited number of endpoints. Such approaches are inadequate to deal with the increasingly large number of compounds found in the environment for which there are no toxicity data. Mechanism-centered high-throughput testing represents an alternative approach to meet this pressing need but is limited by our current understanding of toxicity pathways. Functional toxicogenomics, the global study of the biological function of genes on the modulation of the toxic effect of a compound, can play an important role in identifying the essential cellular components and pathways involved in toxicity response. The combination of the identification of fundamental toxicity pathways and mechanism-centered targeted assays represents an integrated approach to advance molecular toxicology to meet the challenges of toxicity testing in the 21(st) century.},
}
@article {pmid21594115,
year = {2010},
author = {Stoev, P and Akkari, N and Zapparoli, M and Porco, D and Enghoff, H and Edgecombe, GD and Georgiev, T and Penev, L},
title = {The centipede genus Eupolybothrus Verhoeff, 1907 (Chilopoda: Lithobiomorpha: Lithobiidae) in North Africa, a cybertaxonomic revision, with a key to all species in the genus and the first use of DNA barcoding for the group.},
journal = {ZooKeys},
volume = {},
number = {50},
pages = {29-77},
pmid = {21594115},
issn = {1313-2970},
abstract = {The centipede genus Eupolybothrus Verhoeff, 1907 in North Africa is revised. A new cavernicolous species, Eupolybothruskahfi Stoev &amp; Akkari, sp. n., is described from a cave in Jebel Zaghouan, northeast Tunisia. Morphologically, it is most closely related to Eupolybothrusnudicornis (Gervais, 1837) from North Africa and Southwest Europe but can be readily distinguished by the long antennae and leg-pair 15, a conical dorso-median protuberance emerging from the posterior part of prefemur 15, and the shape of the male first genital sternite. Molecular sequence data from the cytochrome c oxidase I gene (mtDNA-5' COI-barcoding fragment) exhibit 19.19% divergence between Eupolybothruskahfi and Eupolybothrusnudicornis, an interspecific value comparable to those observed among four other species of Eupolybothrus which, combined with a low intraspecific divergence (0.3-1.14%), supports the morphological diagnosis of Eupolybothruskahfi as a separate species. This is the first troglomorphic myriapod to be found in Tunisia, and the second troglomorph lithobiomorph centipede known from North Africa. Eupolybothrusnudicornis is redescribed based on abundant material from Tunisia and its post-embryonic development, distribution and habitat preferences recorded. Eupolybothruscloudsley-thompsoni Turk, 1955, a nominal species based on Tunisian type material, is placed in synonymy with Eupolybothrusnudicornis. To comply with the latest technological developments in publishing of biological information, the paper implements new approaches in cybertaxonomy, such as fine granularity XML tagging validated against the NLM DTD TaxPub for PubMedCentral and dissemination in XML to various aggregators (GBIF, EOL, Wikipedia), vizualisation of all taxa mentioned in the text via the dynamically created Pensoft Taxon Profile (PTP) page, data publishing, georeferencing of all localities via Google Earth, and ZooBank, GenBank and MorphBank registration of datasets. An interactive key to all valid species of Eupolybothrus is made with DELTA software.},
}
@article {pmid21594050,
year = {2010},
author = {Potapov, MB and Bu, Y and Huang, CW and Gao, Y and Luan, YX},
title = {Generic switch-over during ontogenesis in Dimorphacanthella gen. n. (Collembola, Isotomidae) with barcoding evidence.},
journal = {ZooKeys},
volume = {},
number = {73},
pages = {13-23},
pmid = {21594050},
issn = {1313-2970},
abstract = {A new genus Dimorphacanthella is established for Tetracanthella anommatos Chen and Yin, 1984 and Dimorphacanthella mediasetasp. n. from China. The new genus exhibits an unusual metamorphosis: small juveniles, previously called Uzelia anommatos Yue &amp; Yin, 1999 get the second pair of anal spines resulted from moulting and become "Tetracanthella". Species identity of forms with two and four anal spines is proved by barcoding analysis. The derivation of anal spines is compared among genera having four anal spines.},
}
@article {pmid21594019,
year = {2010},
author = {Fernández-Triana, JL},
title = {Eight new species and an annotated checklist of Microgastrinae (Hymenoptera, Braconidae) from Canada and Alaska.},
journal = {ZooKeys},
volume = {},
number = {63},
pages = {1-53},
pmid = {21594019},
issn = {1313-2970},
abstract = {Based on the study of 12,000+ specimens, an annotated checklist of 28 genera and 225 species of Microgastrinae braconids from Canada and Alaska is provided, increasing by 50% the number of species for the region. The genera Distatrix, Iconella, Protomicroplitis and Pseudapanteles for Canada, and Diolcogaster for Alaska are recorded for the first time; all but Iconella and Protomicroplitis represent the northernmost extension of their known distribution. Eight new species are described: Apanteles huberisp. n., Apanteles jenniferae sp. n., Apanteles masmithisp. n., Apanteles roughleyisp. n., Apanteles samarshallisp. n., Distatrix carolinaesp. n., Pseudapanteles gouletisp. n., and Venanus hebertisp. n. For the more diverse genera, especially Cotesia, Microplitis, Apanteles, Dolichogenidea and Glyptapanteles, many more species are expected to be found. DNA barcode sequences (cytochrome c oxidase I, or CO1) for 3,500+ specimens provided an additional layer of useful data. CO1 sequences were incorporated to the new species descriptions whenever possible, helped to clarify the limits of some species, and flagged cases where further study is needed. Preliminary results on the latitudinal gradient of species/genera richness (45-80° N); as well as biogeographical affinities of the Canadian/Alaska fauna, are discussed. Taking into account the number of specimens in collections still to be studied, data from the barcoded specimens, and extrapolations from Lepidoptera diversity (the host group of the subfamily) the actual diversity of Microgastrinae in the region is estimated to be at least twice that currently known.},
}
@article {pmid21564994,
year = {2010},
author = {Corse, E and Costedoat, C and Chappaz, R and Pech, N and Martin, JF and Gilles, A},
title = {A PCR-based method for diet analysis in freshwater organisms using 18S rDNA barcoding on faeces.},
journal = {Molecular ecology resources},
volume = {10},
number = {1},
pages = {96-108},
doi = {10.1111/j.1755-0998.2009.02795.x},
pmid = {21564994},
issn = {1755-0998},
abstract = {The development of DNA barcoding from faeces represents a promising method for animal diet analysis. However, current studies mainly rely on prior knowledge of prey diversity for a specific predator rather than on a range of its potential prey species. Considering that the feeding behaviour of teleosts may evolve with their environment, it could prove difficult to establish an exhaustive listing of their prey. In this article, we extend the DNA barcoding approach to diet analysis to allow the inclusion of a wide taxonomic range of potential prey items. Thirty-four ecological clade-specific primer sets were designed to cover a large proportion of prey species found in European river ecosystems. Selected primers sets were tested on isolated animal, algal or plant tissues and thereafter on fish faeces using nested PCR to increase DNA detection sensitivity. The PCR products were sequenced and analysed to confirm the identity of the taxa and to validate the method. The methodology developed here was applied to a diet analysis of three freshwater cyprinid species that are assumed to have similar feeding behaviour [Chondrostoma toxostoma toxostoma (Vallot 1837), Chondrostoma nasus nasus (Linnaeus, 1758) and Barbus barbus, (Linneaus 1758)]. These three species were sampled in four different hydrographic basins. Principal Component Analysis based on prey proportions identified distinct perilithon grazer and benthophagous behaviours. Furthermore, our results were consistent with the available literature on feeding behaviour in these fish. The simplicity of the PCR-based method and its potential generalization to other freshwater organisms may open new perspectives in food web ecology.},
}
@article {pmid21564993,
year = {2010},
author = {Li, FW and Kuo, LY and Huang, YM and Chiou, WL and Wang, CN},
title = {Tissue-direct PCR, a rapid and extraction-free method for barcoding of ferns.},
journal = {Molecular ecology resources},
volume = {10},
number = {1},
pages = {92-95},
doi = {10.1111/j.1755-0998.2009.02745.x},
pmid = {21564993},
issn = {1755-0998},
abstract = {Fern gametophytes and young sporophytes often provide too little material for DNA extraction and are particularly difficult to identify to genus. Here we developed an efficient procedure called 'Tissue-direct PCR', in which a slice of fern tissue is mixed with PCR reagents and primers, allowing certain genomic regions to be amplified directly in the thermal cycler. For these diminutive and featureless stages of ferns, Tissue-direct PCR combined with amplifying plant barcodes promises to make the identification of immature ferns easy and rapid. Tissue-direct PCR would also be very helpful for large-scale ecological studies surveying distribution and population structure.},
}
@article {pmid21564992,
year = {2010},
author = {Clerc-Blain, JL and Starr, JR and Bull, RD and Saarela, JM},
title = {A regional approach to plant DNA barcoding provides high species resolution of sedges (Carex and Kobresia, Cyperaceae) in the Canadian Arctic Archipelago.},
journal = {Molecular ecology resources},
volume = {10},
number = {1},
pages = {69-91},
doi = {10.1111/j.1755-0998.2009.02725.x},
pmid = {21564992},
issn = {1755-0998},
abstract = {Previous research on barcoding sedges (Carex) suggested that basic searches within a global barcoding database would probably not resolve more than 60% of the world's some 2000 species. In this study, we take an alternative approach and explore the performance of plant DNA barcoding in the Carex lineage from an explicitly regional perspective. We characterize the utility of a subset of the proposed protein-coding and noncoding plastid barcoding regions (matK, rpoB, rpoC1, rbcL, atpF-atpH, psbK-psbI) for distinguishing species of Carex and Kobresia in the Canadian Arctic Archipelago, a clearly defined eco-geographical region representing 1% of the Earth's landmass. Our results show that matK resolves the greatest number of species of any single-locus (95%), and when combined in a two-locus barcode, it provides 100% species resolution in all but one combination (matK + atpFH) during unweighted pair-group method with arithmetic mean averages (UPGMA) analyses. Noncoding regions were equally or more variable than matK, but as single markers they resolve substantially fewer taxa than matK alone. When difficulties with sequencing and alignment due to microstructural variation in noncoding regions are also considered, our results support other studies in suggesting that protein-coding regions are more practical as barcoding markers. Plastid DNA barcodes are an effective identification tool for species of Carex and Kobresia in the Canadian Arctic Archipelago, a region where the number of co-existing closely related species is limited. We suggest that if a regional approach to plant DNA barcoding was applied on a global scale, it could provide a solution to the generally poor species resolution seen in previous barcoding studies.},
}
@article {pmid21564991,
year = {2010},
author = {Magnacca, KN and Brown, MJ},
title = {Tissue segregation of mitochondrial haplotypes in heteroplasmic Hawaiian bees: implications for DNA barcoding.},
journal = {Molecular ecology resources},
volume = {10},
number = {1},
pages = {60-68},
doi = {10.1111/j.1755-0998.2009.02724.x},
pmid = {21564991},
issn = {1755-0998},
abstract = {The issue of mitochondrial heteroplasmy has been cited as a theoretical problem for DNA barcoding but is only beginning to be examined in natural systems. We sequenced multiple DNA extractions from 20 individuals of four Hawaiian Hylaeus bee species known to be heteroplasmic. All species showed strong differences at polymorphic sites between abdominal and muscle tissue in most individuals, and only two individuals had no obvious segregation. Two specimens produced completely clean sequences from abdominal DNA. The fact that these differences are clearly visible by direct sequencing indicates that substantial intra-individual mtDNA diversity may be overlooked when DNA is taken from small tissue fragments. At the same time, differences in haplotype distribution among individuals may result in incorrect recognition of cryptic species. Because DNA barcoding studies typically use only a small fragment of an organism, they are particularly vulnerable to sequencing bias where heteroplasmy and haplotype segregation are present. It is important to anticipate this possibility prior to undertaking large-scale barcoding projects to reduce the likelihood of haplotype segregation confounding the results.},
}
@article {pmid21564990,
year = {2010},
author = {Glover, RH and Collins, DW and Walsh, K and Boonham, N},
title = {Assessment of loci for DNA barcoding in the genus Thrips (Thysanoptera:Thripidae).},
journal = {Molecular ecology resources},
volume = {10},
number = {1},
pages = {51-59},
doi = {10.1111/j.1755-0998.2009.02723.x},
pmid = {21564990},
issn = {1755-0998},
abstract = {Identification of the juveniles of economically important thrips species on imports by morphology alone can be challenging and culturing is usually required. In the case of EU quarantine species such as Thrips palmi, rapid and accurate identification is essential. DNA barcoding using the Cytochrome oxidase I (COI) gene has become a popular technique for species identification; however, in some invertebrate genera COI has been shown to provide insufficient variability for species discrimination. This study presents a comparison of five different loci to investigate their ability to discriminate a small number of Thrips species. All five loci discriminated the species by neighbour-joining tree and varying degrees of discrimination were determined upon further investigation of the intraspecific and interspecific distances. Two distinct COI clades were observed for T. Palmi and judged to be COI haplotypes when data from the other four additional loci and geographical collection data were taken into consideration. COI was shown to provide sufficient variation to be used in future DNA barcoding efforts within the genus Thrips.},
}
@article {pmid21564989,
year = {2010},
author = {Bradford, T and Adams, M and Humphreys, WF and Austin, AD and Cooper, SJ},
title = {DNA barcoding of stygofauna uncovers cryptic amphipod diversity in a calcrete aquifer in Western Australia's arid zone.},
journal = {Molecular ecology resources},
volume = {10},
number = {1},
pages = {41-50},
doi = {10.1111/j.1755-0998.2009.02706.x},
pmid = {21564989},
issn = {1755-0998},
abstract = {The arid Yilgarn region of Western Australia contains numerous subterranean calcrete aquifers with unique assemblages of obligate groundwater invertebrates (stygofauna). We aimed to establish a DNA barcoding framework for the macro-invertebrates present in a single calcrete, as a basis for future assessment of biodiversity of the Yilgarn calcretes and for investigating food webs. Intense sampling of a bore field grid in the Sturt Meadows calcrete was undertaken to obtain representatives of the entire macro-invertebrate ecosystem. A 623-bp fragment of the mitochondrial cytochrome c oxidase 1 (COI) gene was used to provide DNA barcodes for stygobiont macro-invertebrates plus terrestrial organisms that are found in the calcrete. Phylogenetic analyses revealed the existence of 12 divergent monophyletic groups of haplotypes. Subterranean amphipods (Chiltoniidae) showed three groups of COI haplotypes with sequence divergences between them of >11%. Allozyme analyses found a large number of fixed allelic differences between these three amphipod groups, indicating that there are three morphologically cryptic species within the Sturt Meadows calcrete. Unlike the sister triplet of dytiscid beetles present, the amphipods are not sister clades and are more closely related to other Yilgarn and non-Yilgarn amphipods than to each other. Our results show that the aquifer contains at least 12 macro-invertebrate species and DNA barcoding provides a useful means for discriminating species in this system.},
}
@article {pmid21564929,
year = {2009},
author = {Ståhls, G and Vujic, A and Pérez-Bañon, C and Radenkovic, S and Rojo, S and Petanidou, T},
title = {COI barcodes for identification of Merodon hoverflies (Diptera, Syrphidae) of Lesvos Island, Greece.},
journal = {Molecular ecology resources},
volume = {9},
number = {6},
pages = {1431-1438},
doi = {10.1111/j.1755-0998.2009.02592.x},
pmid = {21564929},
issn = {1755-0998},
abstract = {DNA barcoding has become a useful system for linking different biological life stages, and for identification of species within a known taxonomic framework. In this study, we generated mitochondrial DNA COI barcodes using adult specimens of all 22 species of the hoverfly genus Merodon (Diptera, Syrphidae) occurring on Lesvos island (Greece). The generated COI barcodes could well discriminate between all Merodon taxa of Lesvos, except for M. loewi and M. papillus that shared the same haplotype, despite their clear morphological differences. In addition, the barcodes revealed two cases of hitherto unknown morphologically cryptic species close to M. avidus and M. nigritarsis, respectively. Because only few successful rearings of immature stages of Merodon hoverflies are available, the larval host plant remains unknown for these phytophagous taxa. The obtained COI barcode library for the Merodon spp. of Lesvos will constitute a tool to link any unknown immature stages with already known species, and thus provide important life-history information and promise for ecological studies.},
}
@article {pmid21798187,
year = {2009},
author = {van der Ham, JL and Brugler, MR and France, SC},
title = {Exploring the utility of an indel-rich, mitochondrial intergenic region as a molecular barcode for bamboo corals (Octocorallia: Isididae).},
journal = {Marine genomics},
volume = {2},
number = {3-4},
pages = {183-192},
doi = {10.1016/j.margen.2009.10.002},
pmid = {21798187},
issn = {1876-7478},
abstract = {The DNA barcoding initiative has advocated the use of the 5'-end (∼658bp) of mitochondrial (mt) cytochrome c oxidase subunit 1 (cox1) to genetically distinguish species. However, this has proven difficult within the subclass Octocorallia due to extraordinarily low substitution rates within mt protein-coding genes. Intergenic regions (IGRs), which have been little examined among octocorals, may be subject to high mutation rates and have proven useful target regions at both the interspecific and population levels of metazoans. Herein we examine a mt IGR (igr4) between the cytochrome b (cob) and NADH dehydrogenase subunit 6 (nad6) genes among species of the bamboo coral subfamily Keratoisidinae to evaluate its utility for barcoding and phylogenetic studies. Among 77 keratoisidin specimens, we found igr4 to vary in length between either 42bp (Acanella Gray, 1870 and Orstomisis Bayer, 1990) or 302-605bp (Isidella Gray, 1857, Lepidisis Verrill, 1883, Keratoisis Wright, 1869, and two undescribed genera). We interpreted the short igr4 sequence of Acanella eburnea (Pourtalès, 1868) as potentially indicative of additional mt genome-related novelties and thus sequenced its entire mt genome; gene content and gene order were the same as in a previously-sequenced bamboo coral mt genome. Alignment of the longer igr4 sequences included 108 parsimony-informative characters, as well as numerous indels ranging from 2-262bp in length. Uncorrected pairwise 'p' distances indicated sequence variation of 0-27.2%, as compared to 0-4.8% among the same specimens for the MutS homolog (msh1), currently the most widely sequenced octocorallian mt gene, and <0.4% for cox1 for a subset of the taxa. Despite the greater levels of variation, fewer unique haplotypes were observed at igr4 compared to msh1; however, in combination, the two gene regions revealed increased mt haplotype diversity relative to either gene region on their own.},
}
@article {pmid21564902,
year = {2009},
author = {Puillandre, N and Strong, EE and Bouchet, P and Boisselier, MC and Couloux, A and Samadi, S},
title = {Identifying gastropod spawn from DNA barcodes: possible but not yet practicable.},
journal = {Molecular ecology resources},
volume = {9},
number = {5},
pages = {1311-1321},
doi = {10.1111/j.1755-0998.2009.02576.x},
pmid = {21564902},
issn = {1755-0998},
abstract = {Identifying life stages of species with complex life histories is problematic as species are often only known and/or described from a single stage. DNA barcoding has been touted as an important tool for linking life-history stages of the same species. To test the current efficacy of DNA barcodes for identifying unknown mollusk life stages, 24 marine gastropod egg capsules were collected off the Philippines in deep water and sequenced for partial fragments of the COI, 16S and 12S mitochondrial genes. Two egg capsules of known shallow-water Mediterranean species were used to calibrate the method. These sequences were compared to those available in GenBank and the Barcode of Life Database (BOLD). Using COI sequences alone, only a single Mediterranean egg capsule was identified to species, and a single Philippine egg capsule was identified tentatively to genus; all other COI sequences recovered matches between 76% and 90% with sequences from BOLD and GenBank. Similarity-based identification using all three markers confirmed the Mediterranean specimens' identifications. A phylogenetic approach was also implemented to confirm similarity-based identifications and provide a higher-taxonomic identification when species-level identifications were not possible. Comparison of available GenBank sequences to the diversity curve of a well-sampled coral reef habitat in New Caledonia highlights the poor taxonomic coverage achieved at present in existing genetic databases, emphasizing the need to develop DNA barcoding projects for megadiverse and often taxonomically challenging groups such as mollusks, to fully realize its potential as an identification and discovery tool.},
}
@article {pmid21564901,
year = {2009},
author = {Lukhtanov, VA and Sourakov, A and Zakharov, EV and Hebert, PD},
title = {DNA barcoding Central Asian butterflies: increasing geographical dimension does not significantly reduce the success of species identification.},
journal = {Molecular ecology resources},
volume = {9},
number = {5},
pages = {1302-1310},
doi = {10.1111/j.1755-0998.2009.02577.x},
pmid = {21564901},
issn = {1755-0998},
abstract = {DNA barcoding employs short, standardized gene regions (5' segment of mitochondrial cytochrome oxidase subunit I for animals) as an internal tag to enable species identification. Prior studies have indicated that it performs this task well, because interspecific variation at cytochrome oxidase subunit I is typically much greater than intraspecific variation. However, most previous studies have focused on local faunas only, and critics have suggested two reasons why barcoding should be less effective in species identification when the geographical coverage is expanded. They suggested that many recently diverged taxa will be excluded from local analyses because they are allopatric. Second, intraspecific variation may be seriously underestimated by local studies, because geographical variation in the barcode region is not considered. In this paper, we analyse how adding a geographical dimension affects barcode resolution, examining 353 butterfly species from Central Asia. Despite predictions, we found that geographically separated and recently diverged allopatric species did not show, on average, less sequence differentiation than recently diverged sympatric taxa. Although expanded geographical coverage did substantially increase intraspecific variation reducing the barcoding gap between species, this did not decrease species identification using neighbour-joining clustering. The inclusion of additional populations increased the number of paraphyletic entities, but did not impede species-level identification, because paraphyletic species were separated from their monophyletic relatives by substantial sequence divergence. Thus, this study demonstrates that DNA barcoding remains an effective identification tool even when taxa are sampled from a large geographical area.},
}
@article {pmid21637526,
year = {2009},
author = {Vargas, SM and Araújo, FC and Santos, FR},
title = {DNA barcoding of Brazilian sea turtles (Testudines).},
journal = {Genetics and molecular biology},
volume = {32},
number = {3},
pages = {608-612},
pmid = {21637526},
issn = {1678-4685},
abstract = {Five out of the seven recognized species of sea turtles (Testudines) occur on the Brazilian coast. The Barcode Initiative is an effort to undertake a molecular inventory of Earth biodiversity. Cytochrome Oxidase c subunit I (COI) molecular tags for sea turtle species have not yet been described. In this study, COI sequences for the five species of sea turtles that occur in Brazil were generated. These presented widely divergent haplotypes. All observed values were on the same range as those already described for other animal groups: the overall mean distance was 8.2%, the mean distance between families (Dermochelyidae and Cheloniidae) 11.7%, the mean intraspecific divergence 0.34%, and the mean distance within Cheloniidae 6.4%, this being 19-fold higher than the mean divergence observed within species. We obtained species-specific COI barcode tags that can be used for identifying each of the marine turtle species studied.},
}
@article {pmid21564847,
year = {2009},
author = {Davison, A and Blackie, RL and Scothern, GP},
title = {DNA barcoding of stylommatophoran land snails: a test of existing sequences.},
journal = {Molecular ecology resources},
volume = {9},
number = {4},
pages = {1092-1101},
doi = {10.1111/j.1755-0998.2009.02559.x},
pmid = {21564847},
issn = {1755-0998},
abstract = {DNA barcoding has attracted attention because it is a potentially simple and universal method for taxonomic assignment. One anticipated problem in applying the method to stylommatophoran land snails is that they frequently exhibit extreme divergence of mitochondrial DNA sequences, sometimes reaching 30% within species. We therefore trialled the utility of barcodes in identifying land snails, by analysing the stylommatophoran cytochrome oxidase subunit I sequences from GenBank. Two alignments of 381 and 228 base pairs were used to determine potential error rates among a test data set of 97 or 127 species, respectively. Identification success rates using neighbour-joining phylogenies were 92% for the longer sequence and 82% for the shorter sequence, indicating that a high degree of mitochondrial variation may actually be an advantage when using phylogeny-based methods for barcoding. There was, however, a large overlap between intra- and interspecific variation, with assignment failure (per cent of samples not placed with correct species) particularly associated with a low degree of mitochondrial variation (Kimura 2-parameter distance < 0.05) and a small GenBank sample size (< 25 per species). Thus, while the optimum intra/interspecific threshold value was 4%, this was associated with an overall error of 32% for the longer sequences and 44% for the shorter sequences. The high error rate necessitates that barcoding of land snails is a potentially useful method to discriminate species of land snail, but only when a baseline has first been established using conventional taxonomy and sample DNA sequences. There is no evidence for a barcoding gap, ruling out species discovery based on a threshold value alone.},
}
@article {pmid21564846,
year = {2009},
author = {VAN DE Wiel, CC and VAN DER Schoot, J and VAN Valkenburg, JL and Duistermaat, H and Smulders, MJ},
title = {DNA barcoding discriminates the noxious invasive plant species, floating pennywort (Hydrocotyle ranunculoides L.f.), from non-invasive relatives.},
journal = {Molecular ecology resources},
volume = {9},
number = {4},
pages = {1086-1091},
doi = {10.1111/j.1755-0998.2009.02547.x},
pmid = {21564846},
issn = {1755-0998},
abstract = {Floating pennywort (Hydrocotyle ranunculoides L.f.), a member of the plant family Araliaceae originating from North America, is an example of an invasive aquatic species posing serious problems to the management of waterways outside of its original distribution area in Australia and Western Europe. As a consequence, its import was banned in the Netherlands. It can be difficult to distinguish H. ranunculoides from other species of the genus on a morphological basis. In this regard, DNA barcoding may become a good alternative once this could be performed on a routine basis. In this study, we show that it is possible to distinguish H. ranunculoides from a series of closely related congeners by using a single plastid DNA sequence, trnH-psbA.},
}
@article {pmid21564845,
year = {2009},
author = {Ward, RD},
title = {DNA barcode divergence among species and genera of birds and fishes.},
journal = {Molecular ecology resources},
volume = {9},
number = {4},
pages = {1077-1085},
doi = {10.1111/j.1755-0998.2009.02541.x},
pmid = {21564845},
issn = {1755-0998},
abstract = {COI DNA barcoding is increasingly recognized as a significant new tool for the recognition and identification of animal species. Here, publicly available barcode data are compiled and analysed for birds (657 species) and fishes (1088 species). The proportion of species that cannot be barcode-distinguished by this marker is approximately 6.4% for birds and 2.1-2.5% for fishes. At all hierarchical taxonomic levels (species, genera, family, order, class), fish show greater mean COI divergence than birds. If two samples are barcode-identical, then for both birds and fishes, the probability that they are from the same species is 98-99%. The probability of conspecificity rapidly drops as divergence increases. At 2% COI divergence, this probability approximates to 1% for birds and 3% for fishes. The apparent difference between birds and fishes might partially reflect currently unrecognized cryptic species complexes in the latter. These probability estimates derive from pooled samples of birds and pooled samples of fishes, and will not apply in all situations. Recently evolved species complexes will have higher proportions of species that are barcode-identical. As barcode data accumulate, more refined statistical analyses will become possible.},
}
@article {pmid21628268,
year = {2009},
author = {Spooner, DM},
title = {DNA barcoding will frequently fail in complicated groups: An example in wild potatoes.},
journal = {American journal of botany},
volume = {96},
number = {6},
pages = {1177-1189},
doi = {10.3732/ajb.0800246},
pmid = {21628268},
issn = {0002-9122},
abstract = {DNA barcoding ("barcoding") has been proposed as a rapid and practical molecular method to identify species via diagnostic variation in short orthologous DNA sequences from one or a few universal genomic regions. It seeks to address in a rapid and simple way the "taxonomic impediment" of a greater need for taxonomic identifications than can be supplied by taxonomists. Using a complicated plant group, Solanum sect. Petota (wild potatoes), I tested barcoding with the most variable and frequently suggested plant barcoding regions: the internal nontranscribed spacer of nuclear ribosomal DNA (ITS) and the plastid markers trnH-psbA intergenic spacer and matK. These DNA regions fail to provide species-specific markers in sect. Petota because the ITS has too much intraspecific variation and the plastid markers lack sufficient polymorphism. The complications seen in wild potatoes are common in many plant groups, but they have not been assessed with barcoding. Barcoding is a retroactive procedure that relies on well-defined species to function, is based solely on a limited number of DNA sequences that are often inappropriate at the species level, has been poorly tested with geographically well-dispersed replicate samples from difficult taxonomic groups, and discounts substantial practical and theoretical problems in defining species.},
}
@article {pmid21564985,
year = {2009},
author = {Baker, AJ and Tavares, ES and Elbourne, RF},
title = {Countering criticisms of single mitochondrial DNA gene barcoding in birds.},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {257-268},
doi = {10.1111/j.1755-0998.2009.02650.x},
pmid = {21564985},
issn = {1755-098X},
abstract = {General criticisms of a single mtDNA gene barcodes include failure to identify newly evolved species, use of species-delimitation thresholds, effects of selective sweeps and chance occurrence of reciprocal monophyly within species, inability to deal with hybridization and incomplete lineage sorting, and superiority of multiple genes in species identification. We address these criticisms in birds because most species are known and thus provide an ideal test data set, and we argue with selected examples that with the exception of thresholds these criticisms are not problematic for avian taxonomy. Even closely related sister species of birds have distinctive COI barcodes, but it is not possible to universally apply distance thresholds based on ratios of within-species and among-species variation. Instead, more rigorous methods of species delimitation should be favoured using coalescent-based techniques that include tests of chance reciprocal monophyly, and times of lineage separation and sequence divergence. Incomplete lineage sorting is also easily detected with DNA barcodes, and usually at a younger time frame than a more slowly evolving nuclear gene. Where DNA barcodes detect divergent reciprocally monophyletic lineages, the COI sequences can be combined with multiple nuclear genes to distinguish between speciation or population subdivision arising from high female philopatry or regional selective sweeps. Although selective sweeps are increasingly invoked to explain patterns of shallow within-species coalescences in COI gene trees, caution is warranted in this conjecture because of limited sampling of individuals and the reduced power to detect additional mtDNA haplotypes with one gene.},
}
@article {pmid21564984,
year = {2009},
author = {Wong, EH and Shivji, MS and Hanner, RH},
title = {Identifying sharks with DNA barcodes: assessing the utility of a nucleotide diagnostic approach.},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {243-256},
doi = {10.1111/j.1755-0998.2009.02653.x},
pmid = {21564984},
issn = {1755-098X},
abstract = {Shark fisheries worldwide are mostly unmanaged, but the burgeoning shark fin industry in the last few decades has made monitoring catch and trade of these animals critical. As a tool for molecular species identification, DNA barcoding offers significant potential. However, the genetic distance-based approach towards species identification employed by the Barcode of Life Data Systems may oftentimes lack the specificity needed for regulatory or legal applications that require unambiguous identification results. This is because such specificity is not typically realized by anything less than a 100% match of the query sequence to an entry in the reference database using genetic distance. Although various divergence thresholds have been proposed to define acceptable levels of intraspecific variation, enough exceptions exist to cast reasonable doubt on many less than exact matches using a distance-based approach for the identification of unknowns. An alternative approach relies on the identification of discrete molecular characters that can be used to unambiguously diagnose species. The objective of this study was to assess the performance differences between these competing approaches by examining more than 1000 DNA barcodes representing nearly 20% of all known elasmobranch species. Our results demonstrate that a character-based, nucleotide diagnostic (ND) approach to barcode identification is feasible and also provides novel insights into the structure of haplotype diversity among closely related species of sharks. Considerations for the use of NDs in applied fields are also explored.},
}
@article {pmid21564983,
year = {2009},
author = {Zemlak, TS and Ward, RD and Connell, AD and Holmes, BH and Hebert, PD},
title = {DNA barcoding reveals overlooked marine fishes.},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {237-242},
doi = {10.1111/j.1755-0998.2009.02649.x},
pmid = {21564983},
issn = {1755-098X},
abstract = {With more than 15 000 described marine species, fishes are a conspicuous, diverse and increasingly threatened component of marine life. It is generally accepted that most large-bodied fishes have been described, but this conclusion presumes that current taxonomic systems are robust. DNA barcoding, the analysis of a standardized region of the cytochrome c oxidase 1 gene (COI), was used to examine patterns of sequence divergence between populations of 35 fish species from opposite sides of the Indian Ocean, chosen to represent differing lifestyles from inshore to offshore. A substantial proportion of inshore species showed deep divergences between populations from South African and Australian waters (mean = 5.10%), a pattern which also emerged in a few inshore/offshore species (mean = 0.84%), but not within strictly offshore species (mean = 0.26%). Such deep divergences, detected within certain inshore and inshore/offshore taxa, are typical of divergences between congeneric species rather than between populations of a single species, suggesting that current taxonomic systems substantially underestimate species diversity. We estimate that about one third of the 1000 fish species thought to bridge South African and Australian waters actually represent two taxa.},
}
@article {pmid21564982,
year = {2009},
author = {Rivera, J and Currie, DC},
title = {Identification of Nearctic black flies using DNA barcodes (Diptera: Simuliidae).},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {224-236},
doi = {10.1111/j.1755-0998.2009.02648.x},
pmid = {21564982},
issn = {1755-098X},
abstract = {DNA barcoding has gained increased recognition as a molecular tool for species identification in various groups of organisms. In this preliminary study, we tested the efficacy of a 615-bp fragment of the cytochrome c oxidase I (COI) as a DNA barcode in the medically important family Simuliidae, or black flies. A total of 65 (25%) morphologically distinct species and sibling species in species complexes of the 255 recognized Nearctic black fly species were used to create a preliminary barcode profile for the family. Genetic divergence among congeners averaged 14.93% (range 2.83-15.33%), whereas intraspecific genetic divergence between morphologically distinct species averaged 0.72% (range 0-3.84%). DNA barcodes correctly identified nearly 100% of the morphologically distinct species (87% of the total sampled taxa), whereas in species complexes (13% of the sampled taxa) maximum values of divergence were comparatively higher (max. 4.58-6.5%), indicating cryptic diversity. The existence of sibling species in Prosimulium travisi and P. neomacropyga was also demonstrated, thus confirming previous cytological evidence about the existence of such cryptic diversity in these two taxa. We conclude that DNA barcoding is an effective method for species identification and discovery of cryptic diversity in black flies.},
}
@article {pmid21564981,
year = {2009},
author = {Emery, VJ and Landry, JF and Eckert, CG},
title = {Combining DNA barcoding and morphological analysis to identify specialist floral parasites (Lepidoptera: Coleophoridae: Momphinae: Mompha).},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {217-223},
doi = {10.1111/j.1755-0998.2009.02647.x},
pmid = {21564981},
issn = {1755-098X},
abstract = {Close interactions between insects and plants have played a major role in the evolution of both these diverse groups of organisms. Studying these interactions, however, can be difficult because many insects, especially parasites, impinge most strongly on plants during larval stages when they are morphologically difficult to identify, and many belong to diverse groups for which most species remain undescribed. We used DNA barcoding to identify nondescript lepidopteran larvae that regularly parasitize flower buds of the coastal dune endemic Camissoniopsis cheiranthifolia (Onagraceae). We obtained cytochrome oxidase 1 mitochondrial DNA sequences from 201 parasite specimens from across the host geographical range. The Barcode of Life Database Identification System combined with Bayesian analysis grouped all 15 parasite haplotypes in a distinct, monophyletic clade within the genus Mompha (Lepidoptera: Coleophoridae: Momphinae), a group known to be host specialists on plants of the Onagraceae. Species identity and phylogenetic affinities within Mompha could not be confirmed because few barcode sequences exist from this diverse and poorly known group of moths. However, morphological analysis, including detailed dissection of genitalia for a subsample of 23 reared adults and comparison with known species of Mompha, also indicated that the larvae parasitizing C. cheiranthifolia constitute a distinct and undescribed species within this genus. Knowing that floral parasitism of C. cheiranthifolia involves a single, putatively host-specific microlepidopteran greatly facilitates formulating and testing hypotheses concerning how floral parasitism has promoted the evolution of striking floral diversity within this species. More generally, DNA barcoding combined with morphological analysis can greatly hasten identification of problematic specimens and enhance our understanding of the diversity, ecology and evolution of plant-insect interactions.},
}
@article {pmid21564980,
year = {2009},
author = {Smith, MA and Fernandez-Triana, J and Roughley, R and Hebert, PD},
title = {DNA barcode accumulation curves for understudied taxa and areas.},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {208-216},
doi = {10.1111/j.1755-0998.2009.02646.x},
pmid = {21564980},
issn = {1755-098X},
abstract = {Frequently, the diversity of umbrella taxa is invoked to predict patterns of other, less well-known, life. However, the utility of this strategy has been questioned. We tested whether a phylogenetic diversity (PD) analysis of CO1 DNA barcodes could act as a proxy for standard methods of determining sampling efficiency within and between sites, namely that an accumulation curve of barcode diversity would be similar to curves generated using morphology or nuclear genetic markers. Using taxa at the forefront of the taxonomic impediment - parasitoid wasps (Ichneumonidae, Braconidae, Cynipidae and Diapriidae), contrasted with a taxon expected to be of low diversity (Formicidae) from an area where total diversity is expected to be low (Churchill, Manitoba), we found that barcode accumulation curves based on PD were significantly different in both slope and scale from curves generated using names based on morphological data, while curves generated using nuclear genetic data were only different in scale. We conclude that these differences clearly identify the taxonomic impediment within the strictly morphological alpha-taxonomy of these hyperdiverse insects. The absence of an asymptote within the barcode PD trend of parasitoid wasps reflects the as yet incomplete sampling of the site (and more accurately its total diversity), while the morphological analysis asymptote represents a collision with the taxonomic impediment rather than complete sampling. We conclude that a PD analysis of standardized DNA barcodes can be a transparent and reproducible triage tool for the management and conservation of species and spaces.},
}
@article {pmid21564979,
year = {2009},
author = {Sheffield, CS and Hebert, PD and Kevan, PG and Packer, L},
title = {DNA barcoding a regional bee (Hymenoptera: Apoidea) fauna and its potential for ecological studies.},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {196-207},
doi = {10.1111/j.1755-0998.2009.02645.x},
pmid = {21564979},
issn = {1755-098X},
abstract = {DNA barcoding has been evaluated for many animal taxa and is now advocated as a reliable and rapid means for species-level identification. The coming-to-light of this identification tool is timely as we are now facing perhaps the greatest rate of species loss in recent millennia. This study contributes to an ever-increasing number of published accounts of DNA barcoding successfully and accurately distinguishing animal taxa, in this instance, the bee fauna of Nova Scotia, Canada. Most members of this well-known fauna were resolved with particular clarity; the average intraspecific divergence was less than 0.5%, and COI sequences from over 75% of the province's species are now in the Barcodes of Life Data System. DNA barcoding also revealed some surprises within this fauna, including the possible recognition of two undescribed genetically unique species, one in the genus Ceratina (subgenus Zadontomerus), the second in the genus Andrena (subgenus Larandrena); both are presently receiving further taxonomic study. In addition, DNA barcoding has allowed sex-associations among two pairs of cleptoparasitic species. The resulting utility of DNA barcoding for ecological studies of bee communities is discussed.},
}
@article {pmid21564978,
year = {2009},
author = {Foottit, RG and Maw, HE and Havill, NP and Ahern, RG and Montgomery, ME},
title = {DNA barcodes to identify species and explore diversity in the Adelgidae (Insecta: Hemiptera: Aphidoidea).},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {188-195},
doi = {10.1111/j.1755-0998.2009.02644.x},
pmid = {21564978},
issn = {1755-098X},
abstract = {The Adelgidae are relatively small, cryptic insects, exhibiting complex life cycles with parthenogenetic reproduction. Due to these characteristics, the taxonomy of the group is problematic. Here, we test the effectiveness of the standard 658-bp barcode fragment from the 5'-end of the mitochondrial cytochrome c oxidase 1 gene (COI) in differentiating among 17 species of Adelgidae, in associating life-cycle stages, and in assessing patterns of geographical variation in selected species. Species of Adelgidae are well-differentiated by DNA barcodes, enabling the identification of different morphological forms, immature stages and individuals on different hosts and at different periods of the life cycle. DNA barcodes have uncovered cryptic diversity within taxa and, in other cases, a lack of sequence divergence in species pairs previously separated by life-cycle characteristics, indicating a need for further taxonomic analysis.},
}
@article {pmid21564977,
year = {2009},
author = {Radulovici, AE and Sainte-Marie, B and Dufresne, F},
title = {DNA barcoding of marine crustaceans from the Estuary and Gulf of St Lawrence: a regional-scale approach.},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {181-187},
doi = {10.1111/j.1755-0998.2009.02643.x},
pmid = {21564977},
issn = {1755-098X},
abstract = {Marine crustaceans are known as a group with a high level of morphological and ecological diversity but are difficult to identify by traditional approaches and usually require the help of highly trained taxonomists. A faster identification method, DNA barcoding, was found to be an effective tool for species identification in many metazoan groups including some crustaceans. Here we expand the DNA barcode database with a case study involving 80 malacostracan species from the Estuary and Gulf of St Lawrence. DNA sequences for 460 specimens grouped into clusters corresponding to known morphological species in 95% of cases. Genetic distances between species were on average 25 times higher than within species. Intraspecific divergence was high (3.78-13.6%) in specimens belonging to four morphological species, suggesting the occurrence of cryptic species. Moreover, we detected the presence of an invasive amphipod species in the St Lawrence Estuary. This study reconfirms the usefulness of DNA barcoding for the identification of marine crustaceans.},
}
@article {pmid21564976,
year = {2009},
author = {Steven G, N and Subramanyam, R},
title = {Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae).},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {172-180},
doi = {10.1111/j.1755-0998.2009.02642.x},
pmid = {21564976},
issn = {1755-098X},
abstract = {Acacia species are quite difficult to differentiate using morphological characters. Routine identification of Acacia samples is important in order to distinguish invasive species from rare species or those of economic importance, particularly in the forest industry. The genus Acacia is quite abundant and diverse comprising approximately 1355 species, which is currently divided into three subgenera: subg. Acacia (c. 161 species), subg. Aculiferum (c. 235 species), and subg. Phyllodineae (c. 960 species). It would be prudent to utilize DNA barcoding in the accurate and efficient identification of acacias. The objective of this research is to test barcoding in discriminating multiple populations among a sister-species complex in pantropical Acacia subg. Acacia, across three continents. Based on previous research, we chose three cpDNA regions (rbcL, trnH-psbA and matK). Our results show that all three regions (rbcL, matK and trnH-psbA) can distinguish and support the newly proposed genera of Vachellia Wight &amp; Arn. from Acacia Mill., discriminate sister species within either genera and differentiate biogeographical patterns among populations from India, Africa and Australia. A morphometric analysis confirmed the cryptic nature of these sister species and the limitations of a classification based on phenetic data. These results support the claim that DNA barcoding is a powerful tool for taxonomy and biogeography with utility for identifying cryptic species, biogeograhic patterns and resolving classifications at the rank of genera and species.},
}
@article {pmid21564975,
year = {2009},
author = {Ragupathy, S and Newmaster, SG and Murugesan, M and Balasubramaniam, V},
title = {DNA barcoding discriminates a new cryptic grass species revealed in an ethnobotany study by the hill tribes of the Western Ghats in southern India.},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {164-171},
doi = {10.1111/j.1755-0998.2009.02641.x},
pmid = {21564975},
issn = {1755-098X},
abstract = {Our research brought together traditional aboriginal knowledge (TK) and scientific knowledge (SK) to explore the relationship between scientific and aboriginal systems of botanical classification and the corresponding valorization(s) of biological diversity in the Western Ghats of southern India. We worked with two aboriginal cultures namely 'Irulas' and 'Malasars' of the Nilgiri Biosphere Reserve with an objective of evaluating the ability of different knowledge systems (SK and TK) to distinguish grass species belonging to the genus Tripogon, and assess the ability of DNA barcoding to discriminate a new cryptic species 'Tripogon cope' as deciphered by the hill tribes. We discovered that the aboriginal informants identified a common ethnotaxa 'Sunai pul', which is a cryptic species of grass not recognized by the SK classification.'sunai pul' is very important to both aboriginal cultures with ritualistic and economic utility. Morphometric analysis confirms the cryptic nature of this new species, which was validated using DNA barcoding. DNA barcode regions matK and trnH-psbA showed distinct sequence variations among the closely related ethnotaxa. Given the cryptic nature of ethnotaxa, we propose that a DNA barcode may be a reliable tool to identify ethnotaxa. We have initiated further studies in other cultures to develop theoretically sophisticated insights concerning the encounter between 'local' and 'scientific' approaches to the use of biodiversity knowledge. Furthermore, the research will add to a unifying global effort to speed up the documentation and understanding of the planet's natural diversity, while simultaneously respecting the cultural heterogeneity as a vital component of biological diversity.},
}
@article {pmid21564974,
year = {2009},
author = {Starr, JR and Naczi, RF and Chouinard, BN},
title = {Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae).},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {151-163},
doi = {10.1111/j.1755-0998.2009.02640.x},
pmid = {21564974},
issn = {1755-098X},
abstract = {We investigate the species discriminatory power of a subset of the proposed plant barcoding loci (matK, rbcL, rpoC1, rpoB, trnH-psbA) in Carex, a cosmopolitan genus that represents one of the three largest plant genera on earth (c. 2000 species). To assess the ability of barcoding loci to resolve Carex species, we focused our sampling on three of the taxonomically best-known groups in the genus, sections Deweyanae (6/8 species sampled), Griseae (18/21 species sampled), and Phyllostachyae (10/10 species sampled). Each group represents one of three major phylogenetic lineages previously identified in Carex and its tribe Cariceae, thus permitting us to evaluate the potential of DNA barcodes to broadly identify species across the tribe and to differentiate closely related sister species. Unlike some previous studies that have suggested that plant barcoding could achieve species identification rates around 90%, our results suggest that no single locus or multilocus barcode examined will resolve much greater than 60% of Carex species. In fact, no multilocus combination can significantly increase the resolution and statistical support (i.e., ≥ 70% bootstrap) for species than matK alone, even combinations involving the second most variable region, trnH-psbA. Results suggest that a matK barcode could help with species discovery as 47% of Carex taxa recently named or resolved within cryptic complexes in the past 25 years also formed unique species clusters in upgma trees. Comparisons between the nrDNA internal transcribed spacer region (ITS) and matK in sect. Phyllostachyae suggest that matK not only discriminates more species (50-60% vs. 25%), but it provides more resolved phylogenies than ITS. Given the low levels of species resolution in rpoC1 and rpoB (0-13%), and difficulties with polymerase chain reaction amplification and DNA sequencing in rbcL and trnH-psbA (alignment included), we strongly advocate that matK should be part of a universal plant barcoding system. Although identification rates in this study are low, they can be significantly improved by a regional approach to barcoding.},
}
@article {pmid21564973,
year = {2009},
author = {Saunders, GW},
title = {Routine DNA barcoding of Canadian Gracilariales (Rhodophyta) reveals the invasive species Gracilaria vermiculophylla in British Columbia.},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {140-150},
doi = {10.1111/j.1755-0998.2009.02639.x},
pmid = {21564973},
issn = {1755-098X},
abstract = {As part of an extensive DNA-based floristic survey of marine macroalgae in Canadian waters, an unexpected sequence for a Gracilaria sp. was generated from British Columbia. Before further molecular analyses and corresponding morphological/anatomical observations this mystery sequence was temporarily entered into our database as Gracilaria BCsp. Continued sampling uncovered this species from four additional locations. A timely collaboration with international colleagues introduced sequences from the invasive Gracilaria vermiculophylla into our cytochrome c oxidase I alignments - these a perfect match to BCsp indicating that this species occurs in British Columbia. A discussion of the origin of this taxon in Canadian waters, whether natural or introduced, is provided.},
}
@article {pmid21564972,
year = {2009},
author = {Fazekas, AJ and Kesanakurti, PR and Burgess, KS and Percy, DM and Graham, SW and Barrett, SC and Newmaster, SG and Hajibabaei, M and Husband, BC},
title = {Are plant species inherently harder to discriminate than animal species using DNA barcoding markers?.},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {130-139},
doi = {10.1111/j.1755-0998.2009.02652.x},
pmid = {21564972},
issn = {1755-098X},
abstract = {The ability to discriminate between species using barcoding loci has proved more difficult in plants than animals, raising the possibility that plant species boundaries are less well defined. Here, we review a selection of published barcoding data sets to compare species discrimination in plants vs. animals. Although the use of different genetic markers, analytical methods and depths of taxon sampling may complicate comparisons, our results using common metrics demonstrate that the number of species supported as monophyletic using barcoding markers is higher in animals (> 90%) than plants (~70%), even after controlling for the amount of parsimony-informative information per species. This suggests that more than a simple lack of variability limits species discrimination in plants. Both animal and plant species pairs have variable size gaps between intra- and interspecific genetic distances, but animal species tend to have larger gaps than plants, even in relatively densely sampled genera. An analysis of 12 plant genera suggests that hybridization contributes significantly to variation in genetic discontinuity in plants. Barcoding success may be improved in some plant groups by careful choice of markers and appropriate sampling; however, overall fine-scale species discrimination in plants relative to animals may be inherently more difficult because of greater levels of gene-tree paraphyly.},
}
@article {pmid21564971,
year = {2009},
author = {Chen, W and Seifert, KA and Lévesque, CA},
title = {A high density COX1 barcode oligonucleotide array for identification and detection of species of Penicillium subgenus Penicillium.},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {114-129},
doi = {10.1111/j.1755-0998.2009.02638.x},
pmid = {21564971},
issn = {1755-098X},
abstract = {We developed a COX1 barcode oligonucleotide array based on 358 sequences, including 58 known and two new species of Penicillium subgenus Penicillium, and 12 allied species. The array was robotically spotted at near microarray density on membranes. Species and clade-specific oligonucleotides were selected using the computer programs SigOli and Array Designer. Robotic spotting allowed 768 spots with duplicate sets of perfect match and the corresponding mismatch and positive control oligonucleotides, to be printed on 2 × 6 cm(2) nylon membranes. The array was validated with hybridizations between the array and digoxigenin (DIG)-labelled COX1 polymerase chain reaction amplicons from 70 pure DNA samples, and directly from environmental samples (cheese and plants) without culturing. DNA hybridization conditions were optimized, but undesired cross-reactions were detected frequently, reflecting the relatively high sequence similarity of the COX1 gene among Penicillium species. Approximately 60% of the perfect match oligonucleotides were rejected because of low specificity and 76 delivered useful group-specific or species-specific reactions and could be used for detecting certain species of Penicillium in environmental samples. In practice, the presence of weak signals on arrays exposed to amplicons from environmental samples, which could have represented weak detections or weak cross reactions, made interpretation difficult for over half of the oligonucleotides. DNA regions with very few single nucleotide polymorphisms or lacking insertions/deletions among closely related species are not ideal for oligonucleotide-based diagnostics, and supplementing the COX1-based array with oligonucleotides derived from additional genes would result in a more robust hierarchical identification system.},
}
@article {pmid21564970,
year = {2009},
author = {Vialle, A and Feau, N and Allaire, M and Didukh, M and Martin, F and Moncalvo, JM and Hamelin, RC},
title = {Evaluation of mitochondrial genes as DNA barcode for Basidiomycota.},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {99-113},
doi = {10.1111/j.1755-0998.2009.02637.x},
pmid = {21564970},
issn = {1755-098X},
abstract = {Our study evaluated in silico the potential of 14 mitochondrial genes encoding the subunits of the respiratory chain complexes, including cytochrome c oxidase I (CO1), as Basidiomycota DNA barcode. Fifteen complete and partial mitochondrial genomes were recovered and characterized in this study. Mitochondrial genes showed high values of molecular divergence, indicating a potential for the resolution of lower-level relationships. However, numerous introns occurred in CO1 as well as in six other genes, potentially interfering with polymerase chain reaction amplification. Considering these results and given the minimal length of 600-bp that is optimal for a fungal barcode, the genes encoding for the ATPase subunit 6, the cytochrome oxidase subunit 3 and the NADH dehydrogenase subunit 6 have the most promising characteristics for DNA barcoding among the mitochondrial genes studied. However, biological validation on two fungal data sets indicated that no single mitochondrial gene gave a better taxonomic resolution than the ITS, the region already widely used in fungal taxonomy.},
}
@article {pmid21564969,
year = {2009},
author = {Gilmore, SR and Gräfenhan, T and Louis-Seize, G and Seifert, KA},
title = {Multiple copies of cytochrome oxidase 1 in species of the fungal genus Fusarium.},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {90-98},
doi = {10.1111/j.1755-0998.2009.02636.x},
pmid = {21564969},
issn = {1755-098X},
abstract = {Using data from published mitochondrial or complete genomes, we developed and tested primers for amplification and sequencing of the barcode region of cytochrome oxidase 1 (COX1) of the fungal genus Fusarium, related genera of the order Hypocreales, and degenerate primers for fungi in the subdivision Pezizomycotina. The primers were successful for amplifying and sequencing COX1 barcodes from 13 genera of Hypocreales (Acremonium, Beauveria, Clonostachys, Emericellopsis, Fusarium, Gliocladium, Hypocrea, Lanatonectria, Lecanicillium, Metarhizium, Monocillium, Neonectria and Stilbella), 22 taxa of Fusarium, and two genera in other orders (Arthrosporium, Monilochaetes). Parologous copies of COX1 occurred in several strains of Fusarium. In some, copies of the same length were detected either by heterozygous bases in otherwise clean sequences or in different replicates of amplification and sequencing events; this may indicate multiple transcribed copies. Other strains included one or two introns. Two intron insertion sites had at least two nonhomologous intron sequences among Fusarium species. Irrespective of whether the multiple copy issue could be resolved by sequencing RNA transcripts, developing a precise COX1-based barcoding system for Fusarium may not be feasible. The overall divergence among homologous COX1 sequences obtained so far is rather low, with many species sharing identical sequences.},
}
@article {pmid21564968,
year = {2009},
author = {Seifert, KA},
title = {Progress towards DNA barcoding of fungi.},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {83-89},
doi = {10.1111/j.1755-0998.2009.02635.x},
pmid = {21564968},
issn = {1755-098X},
abstract = {The use of DNA sequences for identifying fungi and fungus-like organisms predates the DNA barcoding movement by at least 10 years. A brief overview of the mycological shift from phenotypic to molecular taxonomy is provided. Exploration of the animal barcode marker, cytochrome oxidase 1, by Canadian mycologists has been fruitful for some fungi, but intron issues and lack of resolution in other taxa prevent its universal application. The momentum established by 15 years of research on the fungal nuclear ribosomal internal transcribed spacer (ITS) sequences will lead to a proposal to the Consortium for the Barcode of Life on the adoption of this marker as the fungal barcode. Existing mycological research networks should facilitate the rapid development of DNA barcoding of fungi once the marker issue is settled. Some available online fungal identification databases are briefly described.},
}
@article {pmid21564967,
year = {2009},
author = {Moszczynska, A and Locke, SA and McLaughlin, JD and Marcogliese, DJ and Crease, TJ},
title = {Development of primers for the mitochondrial cytochrome c oxidase I gene in digenetic trematodes (Platyhelminthes) illustrates the challenge of barcoding parasitic helminths.},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {75-82},
doi = {10.1111/j.1755-0998.2009.02634.x},
pmid = {21564967},
issn = {1755-098X},
abstract = {The phylum Platyhelminthes is a diverse group of flatworms that includes parasites with serious impacts on human health, animal husbandry, aquaculture and wildlife management. Here we present degenerate primers for the barcode region of the mitochondrial cytochrome c oxidase I (COI) gene in flatworms. Although amplicons were obtained from a wide taxonomic range in the Cestoda and Trematoda, COI fragments from many taxa in these classes did not amplify. Primers specific to trematodes in the family Diplostomidae were also developed. Amplification success was much higher with diplostomid-specific primers and sequences were obtained from 504 of 585 specimens of Diplostomum and Tylodelphys. Sequences from the barcode region resolved all specimens to the species level, with mean divergence between congeners of 19% (3.9-25%). Because many of our specimens were small, we initially amplified part of the nuclear small subunit ribosomal (r) RNA gene to evaluate the quality and quantity of DNA in our specimens. Short sequences (~380 nt) of this gene were recovered from most specimens and can be used to distinguish specimens at the family level and often the generic level. We suggest that rRNA genes could be used to screen samples of completely unknown taxonomy, after which specific COI primers could be used to obtain species-level identifications.},
}
@article {pmid21564966,
year = {2009},
author = {Moniz, MB and Kaczmarska, I},
title = {Barcoding diatoms: Is there a good marker?.},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {65-74},
doi = {10.1111/j.1755-0998.2009.02633.x},
pmid = {21564966},
issn = {1755-098X},
abstract = {The promise of DNA barcoding is based on a small DNA fragment divergence coinciding with biological species separation. Here we evaluated the performance of three markers as diatom barcodes, the small ribosomal subunit (1600 bp), a 5' end fragment of cytochrome c oxidase subunit 1 (430 bp), and the second internal transcribed spacer region combined with the 5.8S gene (5.8S + ITS-2, 300-400 bp). Forty-four sequences per marker representing 28 species from all diatom classes were analysed. Sequence alignment of the three genetic markers and uncorrected genetic distances (P) were calculated at the intra- and heterospecific level. All three markers correctly separated the species examined and had advantages which contribute to their feasibility as a DNA barcode. Small ribosomal subunit had the largest GenBank data set, its success rate in amplification and sequencing was assumed to be the highest of all three and was readily aligned. However, it required a long fragment to recover divergence sufficient for species separation and small genetic distances increased the potential for misidentifications. Cytochrome c oxidase subunit 1 demonstrated a substantial heterospecific divergence level and was also readily alignable, but it showed very low amplification and sequencing success rates with currently existing primers. 5.8S + ITS-2 was amplified and sequenced with high success rate and was the most variable of the three markers, but its secondary structure was needed to aid in alignment. However, since it has been recently suggested that ITS-2 may provide insight into sexual compatibility, this marker offers an additional advantage. We therefore propose that the 5.8S + ITS-2 fragment is the best candidate as a diatom DNA barcode.},
}
@article {pmid21564965,
year = {2009},
author = {Zahariev, M and Dahl, V and Chen, W and Lévesque, CA},
title = {Efficient algorithms for the discovery of DNA oligonucleotide barcodes from sequence databases.},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {58-64},
doi = {10.1111/j.1755-0998.2009.02651.x},
pmid = {21564965},
issn = {1755-098X},
abstract = {Efficient design of barcode oligonucleotides can lead to significant cost reductions in the manufacturing of DNA arrays. Previous methods are based on either a preliminary alignment, which reduces their efficiency for intron-rich regions, or on a brute force approach, not feasible for large-scale problems or on data structures with very poor performance in the worst case. One of the algorithms we propose uses 'oligonucleotide sorting' for the discovery of oligonucleotide barcodes of given sizes, with good asymptotic performance. Specific barcode oligonucleotides with at least one base difference from other sequences in a database are found for each individual sequence. With another algorithm, specific oligonucleotides can also be found for groups or clades in the database, which have 100% homology for all oligonucleotide sequences within the group or clade while having differences with the rest of the data. By re-organizing the sequences/groups in the database, oligonucleotides for different hierarchical levels can be found. The oligonucleotides or polymorphism locations identified as species or clade specific by the new algorithm are refined and screened further for hybridization thermodynamic properties with third party software.},
}
@article {pmid21564963,
year = {2009},
author = {Packer, L and Gibbs, J and Sheffield, C and Hanner, R},
title = {DNA barcoding and the mediocrity of morphology.},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {42-50},
doi = {10.1111/j.1755-0998.2009.02631.x},
pmid = {21564963},
issn = {1755-098X},
abstract = {A small but vocal community of critics has questioned the epistemological value of DNA barcoding by suggesting that either it 'cannot work' for the identification or discovery of species or that it ignores the 'richness' inherent in traditional approaches. We re-examine these arguments through a comparison of DNA barcoding and morphological taxonomy in terms of their accuracy and diversity of characters employed. We conclude that morphology often does not work and that it is often nowhere near as 'rich' as has been argued. Morphology is particularly poor in numerous important situations, such as the association of larvae with adults and discrimination among cryptic species. The vehemence of some of the criticisms is surprising given that morphology alone is known to be inadequate to the task of species-level identification in many instances.},
}
@article {pmid21564962,
year = {2009},
author = {Ivanova, NV and Borisenko, AV and Hebert, PD},
title = {Express barcodes: racing from specimen to identification.},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {35-41},
doi = {10.1111/j.1755-0998.2009.02630.x},
pmid = {21564962},
issn = {1755-098X},
abstract = {Although devices combining microfluidic and advanced sequencing technologies promise a future where one can generate a DNA barcode in minutes, current analytical regimes typically involve workflows that extend over 2 days. Here we describe simple protocols enabling the advance from a specimen to barcode-based identification in less than 2 h. The protocols use frozen or lyophilized reagents that can be prepackaged into 'kits' and support barcode analysis across the animal kingdom. The analytical procedure allows 5 min for DNA extraction, 25 min for polymerase chain reaction amplification of the barcode region, 25 min for cycle-sequencing, 10 min for cleanup, 45 min for capillary sequencing and 5 min for trace file analysis to complete DNA-based identification. This study involved the comparison of varied DNA preservation and extraction methods, and evaluated Taq polymerases with high processivity and resistance to inhibitors.},
}
@article {pmid21564961,
year = {2009},
author = {Borisenko, AV and Sones, JE and Hebert, PD},
title = {The front-end logistics of DNA barcoding: challenges and prospects.},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {27-34},
doi = {10.1111/j.1755-0998.2009.02629.x},
pmid = {21564961},
issn = {1755-098X},
abstract = {Building a global library of DNA barcodes will require efficient logistics of pre-laboratory specimen processing and seamless interfacing with molecular protocols. If not addressed properly, the task of aggregating specimens may become the biggest bottleneck in the analytical chain. Three years of experience in developing a collection management system to facilitate high-throughput DNA barcoding have allowed the Canadian Centre for DNA Barcoding to recognize and resolve the most common logistical obstacles. Dealing with these challenges on a larger scale will be an important step towards building a solid collection-based foundation for the international DNA barcoding effort.},
}
@article {pmid21564960,
year = {2009},
author = {Janzen, DH and Hallwachs, W and Blandin, P and Burns, JM and Cadiou, JM and Chacon, I and Dapkey, T and Deans, AR and Epstein, ME and Espinoza, B and Franclemont, JG and Haber, WA and Hajibabaei, M and Hall, JP and Hebert, PD and Gauld, ID and Harvey, DJ and Hausmann, A and Kitching, IJ and Lafontaine, D and Landry, JF and Lemaire, C and Miller, JY and Miller, JS and Miller, L and Miller, SE and Montero, J and Munroe, E and Green, SR and Ratnasingham, S and Rawlins, JE and Robbins, RK and Rodriguez, JJ and Rougerie, R and Sharkey, MJ and Smith, MA and Solis, MA and Sullivan, JB and Thiaucourt, P and Wahl, DB and Weller, SJ and Whitfield, JB and Willmott, KR and Wood, DM and Woodley, NE and Wilson, JJ},
title = {Integration of DNA barcoding into an ongoing inventory of complex tropical biodiversity.},
journal = {Molecular ecology resources},
volume = {9 Suppl s1},
number = {},
pages = {1-26},
doi = {10.1111/j.1755-0998.2009.02628.x},
pmid = {21564960},
issn = {1755-098X},
abstract = {Inventory of the caterpillars, their food plants and parasitoids began in 1978 for today's Area de Conservacion Guanacaste (ACG), in northwestern Costa Rica. This complex mosaic of 120 000 ha of conserved and regenerating dry, cloud and rain forest over 0-2000 m elevation contains at least 10 000 species of non-leaf-mining caterpillars used by more than 5000 species of parasitoids. Several hundred thousand specimens of ACG-reared adult Lepidoptera and parasitoids have been intensively and extensively studied morphologically by many taxonomists, including most of the co-authors. DNA barcoding - the use of a standardized short mitochondrial DNA sequence to identify specimens and flush out undisclosed species - was added to the taxonomic identification process in 2003. Barcoding has been found to be extremely accurate during the identification of about 100 000 specimens of about 3500 morphologically defined species of adult moths, butterflies, tachinid flies, and parasitoid wasps. Less than 1% of the species have such similar barcodes that a molecularly based taxonomic identification is impossible. No specimen with a full barcode was misidentified when its barcode was compared with the barcode library. Also as expected from early trials, barcoding a series from all morphologically defined species, and correlating the morphological, ecological and barcode traits, has revealed many hundreds of overlooked presumptive species. Many but not all of these cryptic species can now be distinguished by subtle morphological and/or ecological traits previously ascribed to 'variation' or thought to be insignificant for species-level recognition. Adding DNA barcoding to the inventory has substantially improved the quality and depth of the inventory, and greatly multiplied the number of situations requiring further taxonomic work for resolution.},
}
@article {pmid21564728,
year = {2009},
author = {Elsasser, SC and Floyd, R and Hebert, PD and Schulte-Hostedde, AI},
title = {Species identification of North American guinea worms (Nematoda: Dracunculus) with DNA barcoding.},
journal = {Molecular ecology resources},
volume = {9},
number = {3},
pages = {707-712},
doi = {10.1111/j.1755-0998.2008.02393.x},
pmid = {21564728},
issn = {1755-098X},
abstract = {Dracunculus insignis is a nematode parasite that infects the subcutaneous tissues of mammals such as raccoon (Procyon lotor), mink (Neovison vison) and fisher (Martes pennanti). D. lutrae, a morphologically similar species, has only been recovered from the otter (Lontra canadensis). Species identification of these two North American guinea worms has only been achieved by morphology of males and host identity. As a result, where only female specimens are present, accurate identifications are not possible. To date, specimens recovered from otter have been assumed to be D. lutrae, while those from all other hosts are assumed to be D. insignis. This study uses DNA barcoding to differentiate between these two North American dracunculoids. Our results show that D. insignis is a 'true' generalist, showing little sequence divergence regardless of host association, although our studies did validate its occurrence in a new host - the otter. Interestingly, specimens of the host specialist, D. lutrae, showed some sequence divergence, although it was low. The finding of D. insignis in otter substantiates the need to supplement morphology-based methods in providing species identifications for certain dracunculoids.},
}
@article {pmid21564727,
year = {2009},
author = {Cesari, M and Bertolani, R and Rebecchi, L and Guidetti, R},
title = {DNA barcoding in Tardigrada: the first case study on Macrobiotus macrocalix Bertolani &amp; Rebecchi 1993 (Eutardigrada, Macrobiotidae).},
journal = {Molecular ecology resources},
volume = {9},
number = {3},
pages = {699-706},
doi = {10.1111/j.1755-0998.2009.02538.x},
pmid = {21564727},
issn = {1755-098X},
abstract = {Morphological and molecular studies on a tardigrade species have been carried out to verify the possibility of using a DNA barcoding approach for species identification in this phylum. Macrobiotus macrocalix Bertolani &amp; Rebecchi, 1993 was chosen as the test species since it belongs to a group of species in which the taxonomy is quite problematic. Animals and eggs belonging to three Italian and one Swedish populations have been investigated. Both morphological and molecular analyses show that all the populations belong to the same species. The low genetic distances recorded among the studied populations (0.3-1.0%) and the high genetic distance (15.9-16.3%) between these populations and a closely related species confirm the possibility of identifying a specimen of this species by its cytochrome oxidase subunit I sequence. Data from other authors support our results indicating that DNA barcoding can be applied to tardigrades. With our protocols, we have obtained voucher specimens that enable us to show a correspondence between morphology and molecular data.},
}
@article {pmid21564726,
year = {2009},
author = {Langhoff, P and Authier, A and Buckley, TR and Dugdale, JS and Rodrigo, A and Newcomb, RD},
title = {DNA barcoding of the endemic New Zealand leafroller moth genera, Ctenopseustis and Planotortrix.},
journal = {Molecular ecology resources},
volume = {9},
number = {3},
pages = {691-698},
doi = {10.1111/j.1755-0998.2009.02537.x},
pmid = {21564726},
issn = {1755-098X},
abstract = {Molecular techniques such as DNA barcoding have become popular in assisting species identification especially for cryptic species complexes. We have analysed data from a 468-bp region of the mitochondrial cytochrome oxidase subunit I (COI) gene from 200 specimens of 12 species of endemic New Zealand leafroller moths (Tortricidae) from the genera Planotortrix and Ctenopseustis to assess whether the DNA barcoding region can distinguish these species. Among the 200 sequences analysed, 72 haplotypes were recovered, with each genus forming a separate major clade. Maximum likelihood phylogenetic methods were used to test whether species fell into reciprocally monophyletic clades. The optimal phylogeny showed that four species within the genus Ctenopseustis (C. obliquana, C. herana, C. filicis and C. fraterna) and three within Planotortrix (P. octo, P. excessana and P. avicenniae) are polyphyletic. Shimodaira-Hasegawa tests rejected a null hypothesis of monophyly for the species C. obliquana, C. herana, P. octo and P. excessana. Comparisons of within and between species levels of sequence divergence for the same set of seven species showed cases where maximum levels of within-species divergence were greater than some levels of between-species divergence. DNA barcoding using this region of the COI gene is able to distinguish the two genera and some species within each genus; however, many species cannot be identified using this method. Finally, we discuss the possible reasons for this polyphyly, including incomplete lineage sorting, introgression, horizontal gene transfer and incorrect taxonomy.},
}
@article {pmid21564680,
year = {2009},
author = {Vargas, ML and Cruickshank, RH and Ross, JG and Holyoake, AJ and Ogilvie, SC and Paterson, AM},
title = {Noninvasive recovery and detection of possum Trichosurus vulpecula DNA from bitten bait interference devices (WaxTags).},
journal = {Molecular ecology resources},
volume = {9},
number = {2},
pages = {505-515},
doi = {10.1111/j.1755-0998.2008.02498.x},
pmid = {21564680},
issn = {1755-098X},
abstract = {The brushtail possum is a major agricultural and ecological pest in New Zealand. A novel noninvasive DNA sampling tool for detecting its presence (WaxTags, or WT) was tested. DNA was recovered from saliva left on WT, and two lengths (407 bp and 648 bp) of the cytochrome c oxidase I (COI) barcoding region were amplified by polymerase chain reaction (PCR). PCR products were considered (+) when a DNA band was clearly visible by electrophoresis. Different factors that might affect PCR (+) were investigated with captive possums: (i) both extraction protocols of the QIAGEN DNeasy Blood and Tissue Kit, (ii) effect of an overnight or longer delay of up to 3 weeks before DNA extraction on both COI amplicons, and (iii) effect of the individual, order and magnitude of the bite. Extraction protocols were not significantly different. The effect of the overnight delay was not significant, and amplification of the short amplicon was significantly higher (100%) than for the long fragment (48%). After a two or 3-week delay, the short amplicon had 94% and 56% PCR (+), success rates, respectively. Individual, order and magnitude of a bite had no significant effect. The delay trial was repeated with WT from the wild, for which PCR (+) rate of the short amplicon was 63%, regardless of freshness. Four microsatellites were amplified from captive WT samples. We conclude that DNA from saliva traces can be recovered from WT, a potential new tool for noninvasive monitoring of possums and other wildlife.},
}
@article {pmid21564673,
year = {2009},
author = {Hollingsworth, ML and Andra Clark, A and Forrest, LL and Richardson, J and Pennington, RT and Long, DG and Cowan, R and Chase, MW and Gaudeul, M and Hollingsworth, PM},
title = {Selecting barcoding loci for plants: evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants.},
journal = {Molecular ecology resources},
volume = {9},
number = {2},
pages = {439-457},
doi = {10.1111/j.1755-0998.2008.02439.x},
pmid = {21564673},
issn = {1755-098X},
abstract = {There has been considerable debate, but little consensus regarding locus choice for DNA barcoding land plants. This is partly attributable to a shortage of comparable data from all proposed candidate loci on a common set of samples. In this study, we evaluated the seven main candidate plastid regions (rpoC1, rpoB, rbcL, matK, trnH-psbA, atpF-atpH, psbK-psbI) in three divergent groups of land plants [Inga (angiosperm); Araucaria (gymnosperm); Asterella s.l. (liverwort)]. Across these groups, no single locus showed high levels of universality and resolvability. Interspecific sharing of sequences from individual loci was common. However, when multiple loci were combined, fewer barcodes were shared among species. Evaluation of the performance of previously published suggestions of particular multilocus barcode combinations showed broadly equivalent performance. Minor improvements on these were obtained by various new three-locus combinations involving rpoC1, rbcL, matK and trnH-psbA, but no single combination clearly outperformed all others. In terms of absolute discriminatory power, promising results occurred in liverworts (e.g. c. 90% species discrimination based on rbcL alone). However, Inga (rapid radiation) and Araucaria (slow rates of substitution) represent challenging groups for DNA barcoding, and their corresponding levels of species discrimination reflect this (upper estimate of species discrimination = 69% in Inga and only 32% in Araucaria; mean = 60% averaging all three groups).},
}
@article {pmid20735566,
year = {2009},
author = {Valdez-Moreno, M and Ivanova, NV and Elías-Gutiérrez, M and Contreras-Balderas, S and Hebert, PD},
title = {Probing diversity in freshwater fishes from Mexico and Guatemala with DNA barcodes.},
journal = {Journal of fish biology},
volume = {74},
number = {2},
pages = {377-402},
doi = {10.1111/j.1095-8649.2008.02077.x},
pmid = {20735566},
issn = {1095-8649},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Fishes/classification/*genetics ; Fresh Water ; *Genetic Variation ; Guatemala ; Mexico ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The freshwater fish fauna of Mexico and Guatemala is exceptionally diverse with >600 species, many endemic. In this study, patterns of sequence divergence were analysed in representatives of this fauna using cytochrome c oxidase subunit 1 (COI) DNA barcodes for 61 species in 36 genera. The average divergence among conspecific individuals was 0.45%, while congeneric taxa showed 5.1% divergence. Three species of Poblana, each occupying a different crater lake in the arid regions of Central Mexico, have had a controversial taxonomic history but are usually regarded as endemics to a single lake. They possess identical COI barcodes, suggesting a very recent history of isolation. Representatives of the Cichlidae, a complex and poorly understood family, were well discriminated by barcodes. Many species of Characidae seem to be young, with low divergence values (<2%), but nevertheless, clear barcode clusters were apparent in the Bramocharax-Astyanax complex. The symbranchid, Opisthernon aenigmaticum, has been regarded as a single species ranging from Guatemala to Mexico, but it includes two deeply divergent barcode lineages, one a possible new endemic species. Aside from these special cases, the results confirm that DNA barcodes will be highly effective in discriminating freshwater fishes from Central America and that a comprehensive analysis will provide new important insights for understanding diversity of this fauna.},
}
@article {pmid20735564,
year = {2009},
author = {Ward, RD and Hanner, R and Hebert, PD},
title = {The campaign to DNA barcode all fishes, FISH-BOL.},
journal = {Journal of fish biology},
volume = {74},
number = {2},
pages = {329-356},
doi = {10.1111/j.1095-8649.2008.02080.x},
pmid = {20735564},
issn = {1095-8649},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Fishes/genetics ; Genes, Mitochondrial ; Species Specificity ; },
abstract = {FISH-BOL, the Fish Barcode of Life campaign, is an international research collaboration that is assembling a standardized reference DNA sequence library for all fishes. Analysis is targeting a 648 base pair region of the mitochondrial cytochrome c oxidase I (COI) gene. More than 5000 species have already been DNA barcoded, with an average of five specimens per species, typically vouchers with authoritative identifications. The barcode sequence from any fish, fillet, fin, egg or larva can be matched against these reference sequences using BOLD; the Barcode of Life Data System (http://www.barcodinglife.org). The benefits of barcoding fishes include facilitating species identification, highlighting cases of range expansion for known species, flagging previously overlooked species and enabling identifications where traditional methods cannot be applied. Results thus far indicate that barcodes separate c. 98 and 93% of already described marine and freshwater fish species, respectively. Several specimens with divergent barcode sequences have been confirmed by integrative taxonomic analysis as new species. Past concerns in relation to the use of fish barcoding for species discrimination are discussed. These include hybridization, recent radiations, regional differentiation in barcode sequences and nuclear copies of the barcode region. However, current results indicate these issues are of little concern for the great majority of specimens.},
}
@article {pmid21564572,
year = {2009},
author = {Zhang, AB and Savolainen, P},
title = {BPSI2.0: a C/C++ interface program for species identification via DNA barcoding with a BP-neural network by calling the Matlab engine.},
journal = {Molecular ecology resources},
volume = {9},
number = {1},
pages = {104-106},
doi = {10.1111/j.1755-0998.2008.02372.x},
pmid = {21564572},
issn = {1755-098X},
abstract = {BP-Species Identification (BPSI2.0) is a computer program that performs species identification by training a Back-Propagation Neural Network. A short DNA barcoding segment is used as input for training a three-layer BP network. The trained network can assign an unknown query sequence to a known species in the user's database, and provide the corresponding subvector value of the output vector as a relative probability value.},
}
@article {pmid21564571,
year = {2009},
author = {Oliverio, M and Barco, A and Modica, MV and Richter, A and Mariottini, P},
title = {Ecological barcoding of corallivory by second internal transcribed spacer sequences: hosts of coralliophiline gastropods detected by the cnidarian DNA in their stomach.},
journal = {Molecular ecology resources},
volume = {9},
number = {1},
pages = {94-103},
doi = {10.1111/j.1755-0998.2008.02388.x},
pmid = {21564571},
issn = {1755-098X},
abstract = {The second internal transcribed spacer (ITS2) of the nuclear ribosomal RNA cluster (rDNA) is significantly smaller in the Cnidaria (120-260 bp) than in the rest of the Metazoa. ITS2 is one of the fastest evolving DNA regions among those commonly used in molecular systematics and has been proposed as a possible barcoding gene for Cnidaria to replace the currently problematic mitochondrial sequences used. We have reviewed the intraspecific and interspecific variation of ITS2 rRNA sequences in the Anthozoa. We have observed that the lower limits of the interspecific DNA divergence ranges very often overlap with intraspecific ranges, and identical sequences from individuals of different species are not rare. This finding can result in problems similar to those encountered with the mitochondrial COI, and we conclude that ITS2 does not prove significantly better than COI for standard taxonomic DNA barcoding in Anthozoa. However, ITS2 appears to be a promising gene in the ecological DNA barcoding of corallivory, where taxonomic accuracy at genus or even family level may represent a significant improvement of current knowledge. We have successfully amplified and sequenced ITS2 from template DNA extracted from foot muscle and from stomach contents of corallivorous gastropods, and from their anthozoan hosts. The small size of cnidarian ITS2 makes it a very easy and efficient tool for ecological barcoding of associations. Ecological barcoding of corallivory is an indispensable approach to the study of the associations in deep water, where direct observation is severely limited by logistics and costs.},
}
@article {pmid21564566,
year = {2009},
author = {Valentini, A and Miquel, C and Nawaz, MA and Bellemain, E and Coissac, E and Pompanon, F and Gielly, L and Cruaud, C and Nascetti, G and Wincker, P and Swenson, JE and Taberlet, P},
title = {New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach.},
journal = {Molecular ecology resources},
volume = {9},
number = {1},
pages = {51-60},
doi = {10.1111/j.1755-0998.2008.02352.x},
pmid = {21564566},
issn = {1755-098X},
abstract = {The development of DNA barcoding (species identification using a standardized DNA sequence), and the availability of recent DNA sequencing techniques offer new possibilities in diet analysis. DNA fragments shorter than 100-150 bp remain in a much higher proportion in degraded DNA samples and can be recovered from faeces. As a consequence, by using universal primers that amplify a very short but informative DNA fragment, it is possible to reliably identify the plant taxon that has been eaten. According to our experience and using this identification system, about 50% of the taxa can be identified to species using the trnL approach, that is, using the P6 loop of the chloroplast trnL (UAA) intron. We demonstrated that this new method is fast, simple to implement, and very robust. It can be applied for diet analyses of a wide range of phytophagous species at large scales. We also demonstrated that our approach is efficient for mammals, birds, insects and molluscs. This method opens new perspectives in ecology, not only by allowing large-scale studies on diet, but also by enhancing studies on resource partitioning among competing species, and describing food webs in ecosystems.},
}
@article {pmid21564563,
year = {2009},
author = {Lohman, DJ and Prawiradilaga, DM and Meier, R},
title = {Improved COI barcoding primers for Southeast Asian perching birds (Aves: Passeriformes).},
journal = {Molecular ecology resources},
volume = {9},
number = {1},
pages = {37-40},
doi = {10.1111/j.1755-0998.2008.02221.x},
pmid = {21564563},
issn = {1755-098X},
abstract = {The All Birds Barcoding Initiative aims to assemble a DNA barcode database for all bird species, but the 648-bp 'barcoding' region of cytochrome c oxidase subunit I (COI) can be difficult to amplify in Southeast Asian perching birds (Aves: Passeriformes). Using COI sequences from complete mitochondrial genomes, we designed a primer pair that more reliably amplifies and sequences the COI barcoding region of Southeast Asian passerine birds. The 655-bp region amplified with these primers overlaps the COI region amplified with other barcoding primer pairs, enabling direct comparison of sequences with previously published DNA barcodes.},
}
@article {pmid21586014,
year = {2008},
author = {Sarkar, IN and Planet, PJ and Desalle, R},
title = {caos software for use in character-based DNA barcoding.},
journal = {Molecular ecology resources},
volume = {8},
number = {6},
pages = {1256-1259},
doi = {10.1111/j.1755-0998.2008.02235.x},
pmid = {21586014},
issn = {1755-098X},
abstract = {The success of character-based DNA barcoding depends on the efficient identification of diagnostic character states from molecular sequences that have been organized hierarchically (e.g. according to phylogenetic methods). Similarly, the reliability of these identified diagnostic character states must be assessed according to their ability to diagnose new sequences. Here, a set of software tools is presented that implement the previously described Characteristic Attribute Organization System for both diagnostic identification and diagnostic-based classification. The software is publicly available from http://sarkarlab.mbl.edu/CAOS.},
}
@article {pmid21586008,
year = {2008},
author = {Schlei, OL and Crête-Lafrenière, A and Whiteley, AR and Brown, RJ and Olsen, JB and Bernatchez, L and Wenburg, JK},
title = {DNA barcoding of eight North American coregonine species.},
journal = {Molecular ecology resources},
volume = {8},
number = {6},
pages = {1212-1218},
doi = {10.1111/j.1755-0998.2008.02350.x},
pmid = {21586008},
issn = {1755-098X},
abstract = {Coregonine fishes have a circumpolar distribution in the Arctic and sub-Arctic Northern Hemisphere. This subfamily of Salmonidae consists of three genera: Prosopium, Stenodus and Coregonus, including over 30 species. Many species overlap spatially and are difficult to distinguish based on morphological characteristics, especially as larvae or juveniles. Here we present a method for rapid and cost-effective species identification for representatives of the three genera based on sequence variation at the mitochondrial cytochrome c oxidase subunit I gene (COI). We examined eight species common to North America with distributional overlap in Alaska. Mean pairwise sequence divergence for all eight species was 7.04% and ranged from 0.46% to 14.23%. This sequence variation was used to develop a genetic assay based on restriction fragment length polymorphism. In a blind test, this assay provided correct species assignment for 48 of 49 individuals representing all eight species. The single incorrect assignment may reflect hybridization between two closely related species. This DNA barcode-based assay promises to aid fishery managers and researchers by providing a cost-effective alternative to large-scale sequence analysis for identification of North American coregonine fishes.},
}
@article {pmid21586007,
year = {2008},
author = {Ward, RD and Holmes, BH and O'Hara, TD},
title = {DNA barcoding discriminates echinoderm species.},
journal = {Molecular ecology resources},
volume = {8},
number = {6},
pages = {1202-1211},
doi = {10.1111/j.1755-0998.2008.02332.x},
pmid = {21586007},
issn = {1755-098X},
abstract = {DNA barcode sequences (a 657-bp segment of the mtDNA cytochrome oxidase I gene, COI) were collected from 191 species (503 specimens) of Echinodermata. All five classes were represented: Ophiuroidea, Asteroidea, Echinoidea, Holothuroidea and Crinoidea. About 30% of sequences were collected specifically for this study, the remainder came from GenBank. Fifty-one species were represented by multiple samples, with a mean intraspecific divergence of 0.62%. Several possible instances of cryptic speciation were noted. Thirty-two genera were represented by multiple species, with a mean congeneric divergence of 15.33%. One hundred and eighty-seven of the 191 species (97.9%) could be distinguished by their COI barcodes. Those that could not were from the echinoid genus Amblypneustes. Neighbour-joining trees of COI sequences generally showed low bootstrap support for anything other than shallow splits, although with very rare exceptions, members of the same class clustered together. Two ophiuran species, in both nucleotide and amino acid neighbour-joining trees, grouped loosely as sister taxa to Crinoidea rather than Ophiuroidea; sequences of these two species appear to have evolved very quickly. Results suggest that DNA barcoding is likely to be an effective, accurate and useful method of species diagnosis for all five classes of Echinodermata.},
}
@article {pmid21586006,
year = {2008},
author = {Foottit, RG and Maw, HE and VON Dohlen, CD and Hebert, PD},
title = {Species identification of aphids (Insecta: Hemiptera: Aphididae) through DNA barcodes.},
journal = {Molecular ecology resources},
volume = {8},
number = {6},
pages = {1189-1201},
doi = {10.1111/j.1755-0998.2008.02297.x},
pmid = {21586006},
issn = {1755-098X},
abstract = {A 658-bp fragment of mitochondrial DNA from the 5' region of the mitochondrial cytochrome c oxidase 1 (COI) gene has been adopted as the standard DNA barcode region for animal life. In this study, we test its effectiveness in the discrimination of over 300 species of aphids from more than 130 genera. Most (96%) species were well differentiated, and sequence variation within species was low, averaging just 0.2%. Despite the complex life cycles and parthenogenetic reproduction of aphids, DNA barcodes are an effective tool for identification.},
}
@article {pmid21586005,
year = {2008},
author = {Hageskal, G and Vrålstad, T and Knutsen, AK and Skaar, I},
title = {Exploring the species diversity of Trichoderma in Norwegian drinking water systems by DNA barcoding.},
journal = {Molecular ecology resources},
volume = {8},
number = {6},
pages = {1178-1188},
doi = {10.1111/j.1755-0998.2008.02280.x},
pmid = {21586005},
issn = {1755-098X},
abstract = {A total of 123 Trichoderma strains were isolated from Norwegian surface-sourced drinking water. The water samples included raw water, treated water, and water from private homes and hospital installations. Trichoderma species are difficult to differentiate morphologically, but recent molecular identification tools, including DNA barcoding, successfully distinguish between closely related species. The diversity of Trichoderma spp. was explored by DNA sequencing of internal transcribed spacer (ITS) and translation elongation factor 1 alpha (TEF-1α). Sequence identification was performed in the TrichOKEY version 2.0 barcode program and in the multilocus similarity search database TrichoBLAST, combined with traditional blast searches in the EMBL/GenBank. A total of 11 known Trichoderma/Hypocrea species were identified. In addition, one group of unidentified Trichoderma strains was found to represent a separate, strongly supported subclade within the Pachybasium'A'/Hamatum clade, based on their TEF-1α haplotypes. Trichoderma viride comprised 49% of the identified strains, and was represented by four and eight slightly different ITS and TEF-1α haplotypes, respectively. Approximately 22% of the surface-derived water samples were positive for T. viride, and the species was frequently isolated throughout the surface-sourced drinking water distribution system. The results indicate that a broad range of Trichoderma species are present in Norwegian surface-sourced drinking. Water treatment has minor effect in removing Trichoderma from raw water, and active growth in the water distribution system is likely to occur.},
}
@article {pmid21586004,
year = {2008},
author = {Chaves, AV and Clozato, CL and Lacerda, DR and Sari, EH and Santos, FR},
title = {Molecular taxonomy of Brazilian tyrant-flycatchers (Passeriformes: Tyrannidae).},
journal = {Molecular ecology resources},
volume = {8},
number = {6},
pages = {1169-1177},
doi = {10.1111/j.1755-0998.2008.02218.x},
pmid = {21586004},
issn = {1755-098X},
abstract = {The tyrannids are one of the most diverse groups of birds in the world, and the most numerous suboscine family in the Neotropics. Reflecting such diversity, many taxonomic issues arise in this group, mainly due to morphological similarities, even among phylogenetically distant species. Other issues appear at higher taxonomic levels, mostly brought up by genetic studies, making systematics a rather inconclusive issue. This study looks into the use of DNA barcodes method to discriminate and identify Tyrannidae species occurring in the Atlantic Forest and Cerrado biomes of Brazil. We analysed 266 individuals of 71 tyrant-flycatcher species from different geographical locations by sequencing 542 bp of the mtDNA COI gene. The great majority of the analysed species showed exclusive haplotypes, usually displaying low intraspecific diversity and high interspecific divergence. Only Casiornis fuscus and Casiornis rufus, suggested in some studies to belong to a single species, could not be phylogenetically separated. High intraspecific diversity was observed among Elaenia obscura individuals, which can suggest the existence of cryptic species in this taxon. The same was also observed for Suiriri suiriri, considered by some authors to comprise at least two species, and by others to be divided into three subspecies. Additionally, the use of sequences from voucher specimens allowed us to correct four misidentifications that had happened in the field. Our findings suggest a great power of the COI barcodes to discriminate species of the Tyrannidae family that are found in Brazil.},
}
@article {pmid21585879,
year = {2008},
author = {Campbell, DC and Johnson, PD and Williams, JD and Rindsberg, AK and Serb, JM and Small, KK and Lydeard, C},
title = {Identification of 'extinct' freshwater mussel species using DNA barcoding.},
journal = {Molecular ecology resources},
volume = {8},
number = {4},
pages = {711-724},
doi = {10.1111/j.1755-0998.2008.02108.x},
pmid = {21585879},
issn = {1755-098X},
abstract = {Freshwater mollusks are highly imperiled, with 70% of the North American species extinct, endangered, or at risk of extinction. Impoundments and other human impacts on the Coosa River of Alabama, Georgia and Tennessee of the southeastern USA alone are believed to have caused 50 mollusk species extinctions, but uncertainty over boundaries among several putatively closely related species makes this number preliminary. Our examination of freshwater mussels collected during an extensive survey of the upper-drainage basin, DNA barcoding and molecular phylogenetic analyses confirm the rediscovery of four morphospecies in the genus Pleurobema (Unionidae) previously thought to be extinct from the upper Coosa basin. A fifth 'extinct' form was found in an adjoining basin. Molecular data show that the Coosa morphologies represent at least three species-level taxa: Pleurobema decisum, P. hanleyianum and P. stabile. Endemism is higher than currently recognized, both at the species level and for multispecies clades. Prompt conservation efforts may preserve some of these taxa and their ecosystem.},
}
@article {pmid21585832,
year = {2008},
author = {Lee, PL and Prys-Jones, RP},
title = {Extracting DNA from museum bird eggs, and whole genome amplification of archive DNA.},
journal = {Molecular ecology resources},
volume = {8},
number = {3},
pages = {551-560},
doi = {10.1111/j.1471-8286.2007.02042.x},
pmid = {21585832},
issn = {1755-098X},
abstract = {We present a comprehensive protocol for extracting DNA from egg membranes and other internal debris recovered from the interior of blown museum bird eggs. A variety of commercially available DNA extraction methods were found to be applicable. DNA sequencing of polymerase chain reaction (PCR) products for a 176-bp fragment of mitochondrial DNA was successful for most egg samples (> 78%) even though the amount of DNA extracted (mean = 14.71 ± 4.55 ng/µL) was significantly less than that obtained for bird skin samples (mean = 67.88 ± 4.77 ng/µL). For PCR and sequencing of snipe (Gallinago) DNA, we provide eight new primers for the 'DNA barcode' region of COI mtDNA. In various combinations, the primers target a range of PCR products sized from 72 bp to the full 'barcode' of 751 bp. Not all possible combinations were tested with archive snipe DNA, but we found a significantly better success rate of PCR amplification for a shorter 176-bp target compared with a larger 288-bp fragment (67% vs. 39%). Finally, we explored the feasibility of whole genome amplification (WGA) for extending the use of archive DNA in PCR and sequencing applications. Of two WGA approaches, a PCR-based method was found to be able to amplify whole genomic DNA from archive skins and eggs from museum bird collections. After WGA, significantly more archive egg samples produced visible PCR products on agarose (56.9% before WGA vs. 79.0% after WGA). However, overall sequencing success did not improve significantly (78.8% compared with 83.0%).},
}
@article {pmid21585828,
year = {2008},
author = {Garros, C and Ngugi, N and Githeko, AE and Tuno, N and Yan, G},
title = {Gut content identification of larvae of the Anopheles gambiae complex in western Kenya using a barcoding approach.},
journal = {Molecular ecology resources},
volume = {8},
number = {3},
pages = {512-518},
pmid = {21585828},
issn = {1755-098X},
support = {D43 TW001505/TW/FIC NIH HHS/United States ; R01 AI050243/AI/NIAID NIH HHS/United States ; },
abstract = {Although larvae feeding and food source are vital to the development, survival and population regulation of African malaria vectors, the prey organisms of Anopheles gambiae larvae in the natural environment have not been well studied. This study used a molecular barcoding approach to investigate the natural diets of Anopheles gambiae s.l. larvae in western Kenya. Gut contents from third- and fourth-instar larvae from natural habitats were dissected and DNA was extracted. The 18S ribosomal DNA gene was amplified, the resulting clones were screened using a restriction fragment length polymorphism method and nonmosquito clones were sequenced. Homology search and phylogenetic analyses were then conducted using the sequences of non-mosquito clones to identify the putative microorganisms ingested. The phylogenetic analyses clustered ingested microorganisms in four clades, including two clades of green algae (Chlorophyta, Chlorophyceae Class, Chlamydomonadales and Chlorococcales families), one fungal clade, and one unknown eukaryote clade. In parallel, using the same approach, an analysis of the biodiversity present in the larval habitats was carried out. This present study demonstrated the feasibility of the barcoding approach to infer the natural diets of Anopheles gambiae larvae. Our analysis suggests that despite the wide range of microorganisms available in natural habitats, mosquito larvae fed on specific groups of algae. The novel tools developed from this study can be used to improve our understanding of the larval ecology of African malaria vectors and to facilitate the development of new mosquito control tools.},
}
@article {pmid21585826,
year = {2008},
author = {Yassin, A and Capy, P and Madi-Ravazzi, L and Ogereau, D and David, JR},
title = {DNA barcode discovers two cryptic species and two geographical radiations in the invasive drosophilid Zaprionus indianus.},
journal = {Molecular ecology resources},
volume = {8},
number = {3},
pages = {491-501},
doi = {10.1111/j.1471-8286.2007.02020.x},
pmid = {21585826},
issn = {1755-098X},
abstract = {Comparing introduced to ancestral populations within a phylogeographical context is crucial in any study aiming to understand the ecological genetics of an invasive species. Zaprionus indianus is a cosmopolitan drosophilid that has recently succeeded to expand its geographical range upon three continents (Africa, Asia and the Americas). We studied the distribution of mitochondrial DNA (mtDNA) haplotypes for two genes (CO-I and CO-II) among 23 geographical populations. mtDNA revealed the presence of two well-supported phylogenetic lineages (phylads), with bootstrap value of 100%. Phylad I included three African populations, reinforcing the African-origin hypothesis of the species. Within phylad II, a distinct phylogeographical pattern was discovered: Atlantic populations (from the Americas and Madeira) were closer to the ancestral African populations than to Eastern ones (from Madagascar, Middle East and India). This means that during its passage from endemism to cosmopolitanism, Z. indianus exhibited two independent radiations, the older (the Eastern) to the East, and the younger (the Atlantic) to the West. Discriminant function analysis using 13 morphometrical characters was also able to discriminate between the two molecular phylads (93.34 ± 1.67%), although detailed morphological analysis of male genitalia using scanning electron microscopy showed no significant differences. Finally, crossing experiments revealed the presence of reproductive barrier between populations from the two phylads, and further between populations within phylad I. Hence, a bona species status was assigned to two new, cryptic species: Zaprionus africanus and Zaprionus gabonicus, and both were encompassed along with Z. indianus and Zaprionus megalorchis into the indianus complex. The ecology of these two species reveals that they are forest dwellers, which explains their restricted endemic distribution, in contrast to their relative cosmopolitan Z. indianus, known to be a human-commensal. Our results reconfirm the great utility of mtDNA at both inter- and intraspecific analyses within the frame of an integrated taxonomical project.},
}
@article {pmid21585825,
year = {2008},
author = {Newmaster, SG and Fazekas, AJ and Steeves, RA and Janovec, J},
title = {Testing candidate plant barcode regions in the Myristicaceae.},
journal = {Molecular ecology resources},
volume = {8},
number = {3},
pages = {480-490},
doi = {10.1111/j.1471-8286.2007.02002.x},
pmid = {21585825},
issn = {1755-098X},
abstract = {The concept and practice of DNA barcoding have been designed as a system to facilitate species identification and recognition. The primary challenge for barcoding plants has been to identify a suitable region on which to focus the effort. The slow relative nucleotide substitution rates of plant mitochondria and the technical issues with the use of nuclear regions have focused attention on several proposed regions in the plastid genome. One of the challenges for barcoding is to discriminate closely related or recently evolved species. The Myristicaceae, or nutmeg family, is an older group within the angiosperms that contains some recently evolved species providing a challenging test for barcoding plants. The goal of this study is to determine the relative utility of six coding (Universal Plastid Amplicon - UPA, rpoB, rpoc1, accD, rbcL, matK) and one noncoding (trnH-psbA) chloroplast loci for barcoding in the genus Compsoneura using both single region and multiregion approaches. Five of the regions we tested were predominantly invariant across species (UPA, rpoB, rpoC1, accD, rbcL). Two of the regions (matK and trnH-psbA) had significant variation and show promise for barcoding in nutmegs. We demonstrate that a two-gene approach utilizing a moderately variable region (matK) and a more variable region (trnH-psbA) provides resolution among all the Compsonuera species we sampled including the recently evolved C. sprucei and C. mexicana. Our classification analyses based on nonmetric multidimensional scaling ordination, suggest that the use of two regions results in a decreased range of intraspecific variation relative to the distribution of interspecific divergence with 95% of the samples correctly identified in a sequence identification analysis.},
}
@article {pmid21585824,
year = {2008},
author = {Borisenko, AV and Lim, BK and Ivanova, NV and Hanner, RH and Hebert, PD},
title = {DNA barcoding in surveys of small mammal communities: a field study in Suriname.},
journal = {Molecular ecology resources},
volume = {8},
number = {3},
pages = {471-479},
doi = {10.1111/j.1471-8286.2007.01998.x},
pmid = {21585824},
issn = {1755-098X},
abstract = {The performance of DNA barcoding as a tool for fast taxonomic verification in ecological assessment projects of small mammals was evaluated during a collecting trip to a lowland tropical rainforest site in Suriname. We also compared the performance of tissue sampling onto FTA CloneSaver cards vs. liquid nitrogen preservation. DNA barcodes from CloneSaver cards were recovered from 85% of specimens, but DNA degradation was apparent, because only 36% of sequence reads were long (over 600 bp). In contrast, cryopreserved tissue delivered 99% barcode recovery (97% > 600 bp). High humidity, oversampling or tissue type may explain the poor performance of CloneSaver cards. Comparison of taxonomic assignments made in the field and from barcode results revealed inconsistencies in just 3.4% of cases and most of the discrepancies were due to field misidentifications (3%) rather than sampling/analytical error (0.5%). This result reinforces the utility of DNA barcoding as a tool for verification of taxonomic identifications in ecological surveys, which is especially important when the collection of voucher specimens is not possible.},
}
@article {pmid21585766,
year = {2008},
author = {Shearer, TL and Coffroth, MA},
title = {DNA BARCODING: Barcoding corals: limited by interspecific divergence, not intraspecific variation.},
journal = {Molecular ecology resources},
volume = {8},
number = {2},
pages = {247-255},
doi = {10.1111/j.1471-8286.2007.01996.x},
pmid = {21585766},
issn = {1755-098X},
abstract = {The expanding use of DNA barcoding as a tool to identify species and assess biodiversity has recently attracted much attention. An attractive aspect of a barcoding method to identify scleractinian species is that it can be utilized on any life stage (larva, juvenile or adult) and is not influenced by phenotypic plasticity unlike morphological methods of species identification. It has been unclear whether the standard DNA barcoding system, based on cytochrome c oxidase subunit 1 (COI), is suitable for species identification of scleractinian corals. Levels of intra- and interspecific genetic variation of the scleractinian COI gene were investigated to determine whether threshold values could be implemented to discriminate conspecifics from other taxa. Overlap between intraspecific variation and interspecific divergence due to low genetic divergence among species (0% in many cases), rather than high levels of intraspecific variation, resulted in the inability to establish appropriate threshold values specific for scleractinians; thus, it was impossible to discern most scleractinian species using this gene.},
}
@article {pmid21585765,
year = {2008},
author = {Smith, MA and Poyarkov, NA and Hebert, PD},
title = {DNA BARCODING: CO1 DNA barcoding amphibians: take the chance, meet the challenge.},
journal = {Molecular ecology resources},
volume = {8},
number = {2},
pages = {235-246},
doi = {10.1111/j.1471-8286.2007.01964.x},
pmid = {21585765},
issn = {1755-098X},
abstract = {Although a mitochondrial DNA barcode has been shown to be of great utility for species identification and discovery in an increasing number of diverse taxa, caution has been urged with its application to one of the most taxonomically diverse vertebrate groups - the amphibians. Here, we test three of the perceived shortcomings of a CO1 DNA barcode's utility with a group of Holarctic amphibians: primer fit, sequence variability and overlapping intra- and interspecific variability. We found that although the CO1 DNA barcode priming regions were variable, we were able to reliably amplify a CO1 fragment from degenerate primers and primers with G-C residues at the 3' end. Any overlap between intra- and interspecific variation in our taxonomic sampling was due to introgressive hybridization (Bufo/Anaxyrus), complex genetics (Ambystoma) or incomplete taxonomy (Triturus). Rates of hybridization and species discovery are not expected to be greater for amphibians than for other vertebrate groups, and thus problems with the utility of using a single mitochondrial gene for species identification will not be specific to amphibians. Therefore, we conclude that there is greater potential for a CO1 barcode's use with amphibians than has been reported to date. A large-scale effort to barcode the amphibians of the world, using the same primary barcode region of CO1, will yield important findings for science and conservation.},
}
@article {pmid22423312,
year = {2008},
author = {Hubert, N and Hanner, R and Holm, E and Mandrak, NE and Taylor, E and Burridge, M and Watkinson, D and Dumont, P and Curry, A and Bentzen, P and Zhang, J and April, J and Bernatchez, L},
title = {Identifying Canadian freshwater fishes through DNA barcodes.},
journal = {PloS one},
volume = {3},
number = {6},
pages = {e2490},
pmid = {22423312},
issn = {1932-6203},
mesh = {Animals ; Canada ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; Databases, Genetic ; Fishes/classification/*genetics ; Fresh Water ; Genetic Variation ; },
abstract = {BACKGROUND: DNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 5' region of the mitochondrial cytochrome c oxidase I (COI) gene. The efficiency of the method hinges on the degree of sequence divergence among species and species-level identifications are relatively straightforward when the average genetic distance among individuals within a species does not exceed the average genetic distance between sister species. Fishes constitute a highly diverse group of vertebrates that exhibit deep phenotypic changes during development. In this context, the identification of fish species is challenging and DNA barcoding provide new perspectives in ecology and systematics of fishes. Here we examined the degree to which DNA barcoding discriminate freshwater fish species from the well-known Canadian fauna, which currently encompasses nearly 200 species, some which are of high economic value like salmons and sturgeons.<br><br>We bi-directionally sequenced the standard 652 bp "barcode" region of COI for 1360 individuals belonging to 190 of the 203 Canadian freshwater fish species (95%). Most species were represented by multiple individuals (7.6 on average), the majority of which were retained as voucher specimens. The average genetic distance was 27 fold higher between species than within species, as K2P distance estimates averaged 8.3% among congeners and only 0.3% among concpecifics. However, shared polymorphism between sister-species was detected in 15 species (8% of the cases). The distribution of K2P distance between individuals and species overlapped and identifications were only possible to species group using DNA barcodes in these cases. Conversely, deep hidden genetic divergence was revealed within two species, suggesting the presence of cryptic species.<br><br>CONCLUSIONS/SIGNIFICANCE: The present study evidenced that freshwater fish species can be efficiently identified through the use of DNA barcoding, especially the species complex of small-sized species, and that the present COI library can be used for subsequent applications in ecology and systematics.},
}
@article {pmid21585718,
year = {2008},
author = {Hunter, SJ and Goodall, TI and Walsh, KA and Owen, R and Day, JC},
title = {Nondestructive DNA extraction from blackflies (Diptera: Simuliidae): retaining voucher specimens for DNA barcoding projects.},
journal = {Molecular ecology resources},
volume = {8},
number = {1},
pages = {56-61},
doi = {10.1111/j.1471-8286.2007.01879.x},
pmid = {21585718},
issn = {1755-098X},
abstract = {A nondestructive, chemical-free method is presented for the extraction of DNA from small insects. Blackflies were submerged in sterile, distilled water and sonicated for varying lengths of time to provide DNA which was assessed in terms of quantity, purity and amplification efficiency. A verified DNA barcode was produced from DNA extracted from blackfly larvae, pupae and adult specimens. A 60-second sonication period was found to release the highest quality and quantity of DNA although the amplification efficiency was found to be similar regardless of sonication time. Overall, a 66% amplification efficiency was observed. Examination of post-sonicated material confirmed retention of morphological characters. Sonication was found to be a reliable DNA extraction approach for barcoding, providing sufficient quality template for polymerase chain reaction amplification as well as retaining the voucher specimen for post-barcoding morphological evaluation.},
}
@article {pmid21585714,
year = {2008},
author = {Bourlat, SJ and Nakano, H and Akerman, M and Telford, MJ and Thorndyke, MC and Obst, M},
title = {Feeding ecology of Xenoturbella bocki (phylum Xenoturbellida) revealed by genetic barcoding.},
journal = {Molecular ecology resources},
volume = {8},
number = {1},
pages = {18-22},
doi = {10.1111/j.1471-8286.2007.01959.x},
pmid = {21585714},
issn = {1755-098X},
support = {BB/C509866/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {The benthic marine worm Xenoturbella is frequently contaminated with molluscan DNA, which had earlier caused confusion resulting in a suggested bivalve relationship. In order to find the source of the contaminant, we have used molluscan sequences derived from Xenoturbella and compared them to barcodes obtained from several individuals of the nonmicroscopic molluscs sharing the same environment as Xenoturbella. Using cytochrome oxidase 1, we found the contaminating sequences to be 98% similar to the bivalve Ennucula tenuis. Using the highly variable D1-D2 region of the large ribosomal subunit in Xenoturbella, we found three distinct species of contaminating molluscs, one of which is 99% similar to the bivalve Abra nitida, one of the most abundant bivalves in the Gullmarsfjord where Xenoturbella was found, and another 99% similar to the bivalve Nucula sulcata. These data clearly show that Xenoturbella only contains molluscan DNA originating from bivalves living in the same environment, refuting former hypotheses of a bivalve relationship. In addition, these data suggest that Xenoturbella feeds specifically on bivalve prey from multiple species, possibly in the form of eggs and larvae.},
}
@article {pmid22061243,
year = {2007},
author = {Rastogi, G and Dharne, MS and Walujkar, S and Kumar, A and Patole, MS and Shouche, YS},
title = {Species identification and authentication of tissues of animal origin using mitochondrial and nuclear markers.},
journal = {Meat science},
volume = {76},
number = {4},
pages = {666-674},
doi = {10.1016/j.meatsci.2007.02.006},
pmid = {22061243},
issn = {0309-1740},
abstract = {We evaluated and compared the utility of mitochondrial markers viz. 16S rDNA and NADH dehydrogenase subunit 4 (ND4) and a nuclear marker viz. the actin gene to identify the specimens of animal origin for forensic identification, food regulatory control and to prevent illegal trading, poaching and conservation of endangered species. We also tested PCR fingerprinting methods like RAPD and actin barcoding to generate species-specific "fingerprints". Our results suggested that mitochondrial markers are more efficient than nuclear markers for the purpose of species identification and authentication. Among PCR fingerprinting approaches, RAPD was proved to be more discriminatory, accurate and efficient than actin fingerprinting. Considering the present scenario in trading of vertebrate animal tissues like buffalo, cow, pig, goat, chicken, frogs, fishes and snakes etc., mitogenomics based technology proved to be efficient and reliable in resolving problems like meat adulteration and smuggling across countries.},
}
@article {pmid21642175,
year = {2006},
author = {Robba, L and Russell, SJ and Barker, GL and Brodie, J},
title = {Assessing the use of the mitochondrial cox1 marker for use in DNA barcoding of red algae (Rhodophyta).},
journal = {American journal of botany},
volume = {93},
number = {8},
pages = {1101-1108},
doi = {10.3732/ajb.93.8.1101},
pmid = {21642175},
issn = {0002-9122},
abstract = {The red algae, a remarkably diverse group of organisms, are difficult to identify using morphology alone. Following the proposal to use the mitochondrial cytochrome c oxidase subunit I (cox1) for DNA barcoding animals, we assessed the use of this gene in the identification of red algae using 48 samples plus 31 sequences obtained from GenBank. The data set spanned six orders of red algae: the Bangiales, Ceramiales, Corallinales, Gigartinales, Gracilariales and Rhodymeniales. The results indicated that species could be discriminated. Intraspecific variation was between 0 and 4 bp over 539 bp analyzed except in Mastocarpus stellatus (0-14 bp) and Gracilaria gracilis (0-11 bp). Cryptic diversity was found in Bangia fuscopurpurea, Corallina officinalis, G. gracilis, M. stellatus, Porphyra leucosticta and P. umbilicalis. Interspecific variation across all taxa was between 28 and 148 bp, except for G. gracilis and M. stellatus. A comparison of cox1 with the plastid Rubisco spacer for Porphyra species revealed that it was a more sensitive marker in revealing incipient speciation and cryptic diversity. The cox1 gene has the potential to be used for DNA barcoding of red algae, although a good taxonomic foundation coupled with extensive sampling of taxa is essential for the development of an effective identification system.},
}
@article {pmid20639866,
year = {2010},
author = {Warner, JR and Reeder, PJ and Karimpour-Fard, A and Woodruff, LB and Gill, RT},
title = {Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides.},
journal = {Nature biotechnology},
volume = {28},
number = {8},
pages = {856-862},
pmid = {20639866},
issn = {1546-1696},
mesh = {Base Sequence ; Computational Biology/methods ; DNA Barcoding, Taxonomic ; Escherichia coli/*genetics/growth &amp; development/metabolism ; Escherichia coli Proteins/*genetics/metabolism ; *Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Gene Library ; Genetic Engineering/methods ; Genome, Bacterial/genetics ; Molecular Sequence Data ; Mutation ; *Oligonucleotide Array Sequence Analysis ; Oligonucleotides/chemical synthesis/chemistry/*genetics ; *Recombination, Genetic ; Sequence Analysis, DNA ; },
abstract = {A fundamental goal in biotechnology and biology is the development of approaches to better understand the genetic basis of traits. Here we report a versatile method, trackable multiplex recombineering (TRMR), whereby thousands of specific genetic modifications are created and evaluated simultaneously. To demonstrate TRMR, in a single day we modified the expression of >95% of the genes in Escherichia coli by inserting synthetic DNA cassettes and molecular barcodes upstream of each gene. Barcode sequences and microarrays were then used to quantify population dynamics. Within a week we mapped thousands of genes that affect E. coli growth in various media (rich, minimal and cellulosic hydrolysate) and in the presence of several growth inhibitors (beta-glucoside, D-fucose, valine and methylglyoxal). This approach can be applied to a broad range of traits to identify targets for future genome-engineering endeavors.},
}
@article {pmid20637073,
year = {2010},
author = {Ficetola, GF and Coissac, E and Zundel, S and Riaz, T and Shehzad, W and Bessière, J and Taberlet, P and Pompanon, F},
title = {An in silico approach for the evaluation of DNA barcodes.},
journal = {BMC genomics},
volume = {11},
number = {},
pages = {434},
pmid = {20637073},
issn = {1471-2164},
mesh = {Animals ; *Computational Biology ; DNA Fingerprinting/*methods/standards ; DNA Primers/genetics ; Databases, Genetic ; Humans ; Mice ; Polymerase Chain Reaction ; Quality Control ; Reproducibility of Results ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: DNA barcoding is a key tool for assessing biodiversity in both taxonomic and environmental studies. Essential features of barcodes include their applicability to a wide spectrum of taxa and their ability to identify even closely related species. Several DNA regions have been proposed as barcodes and the region selected strongly influences the output of a study. However, formal comparisons between barcodes remained limited until now. Here we present a standard method for evaluating barcode quality, based on the use of a new bioinformatic tool that performs in silico PCR over large databases. We illustrate this approach by comparing the taxonomic coverage and the resolution of several DNA regions already proposed for the barcoding of vertebrates. To assess the relationship between in silico and in vitro PCR, we also developed specific primers amplifying different species of Felidae, and we tested them using both kinds of PCR RESULTS: Tests on specific primers confirmed the correspondence between in silico and in vitro PCR. Nevertheless, results of in silico and in vitro PCRs can be somehow different, also because tuning PCR conditions can increase the performance of primers with limited taxonomic coverage. The in silico evaluation of DNA barcodes showed a strong variation of taxonomic coverage (i.e., universality): barcodes based on highly degenerated primers and those corresponding to the conserved region of the Cyt-b showed the highest coverage. As expected, longer barcodes had a better resolution than shorter ones, which are however more convenient for ecological studies analysing environmental samples.<br><br>CONCLUSIONS: In silico PCR could be used to improve the performance of a study, by allowing the preliminary comparison of several DNA regions in order to identify the most appropriate barcode depending on the study aims.},
}
@article {pmid20627893,
year = {2010},
author = {Varley, KE and Mitra, RD},
title = {Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples.},
journal = {Genome research},
volume = {20},
number = {9},
pages = {1279-1287},
pmid = {20627893},
issn = {1549-5469},
support = {5P50HG003170-03/HG/NHGRI NIH HHS/United States ; 1R01DA025744-01/DA/NIDA NIH HHS/United States ; R01 DA025744/DA/NIDA NIH HHS/United States ; T32 HG000045/HG/NHGRI NIH HHS/United States ; P50 HG003170/HG/NHGRI NIH HHS/United States ; },
mesh = {Colonic Neoplasms/genetics ; DNA/genetics ; *DNA Methylation ; Genome, Human ; Humans ; Neoplasms/*genetics ; Nuclear Pore Complex Proteins/genetics ; Polymerase Chain Reaction/*methods ; *Promoter Regions, Genetic ; Sequence Analysis, DNA/*methods ; Sulfites/*chemistry ; },
abstract = {Aberrant DNA methylation frequently occurs at gene promoters during cancer progression. It is important to identify these loci because they are often misregulated and drive tumorigenesis. Bisulfite sequencing is the most direct and highest resolution assay for identifying aberrant promoter methylation. Recently, genomic capture methods have been combined with next-generation sequencing to enable genome-scale surveys of methylation in individual samples. However, it is challenging to validate candidate loci identified by these approaches because an efficient method to bisulfite sequence more than 50 differentially methylated loci across a large number of samples does not exist. To address this problem, we developed Bisulfite Patch PCR, which enables highly multiplexed bisulfite PCR and sequencing across many samples. Using this method, we successfully amplified 100% of 94 targeted gene promoters simultaneously in the same reaction. By incorporating sample-specific DNA barcodes into the amplicons, we analyzed 48 samples in a single run of the 454 Life Sciences (Roche) FLX sequencer. The method requires small amounts of starting DNA (250 ng) and does not require a shotgun library construction. The method was highly specific; 90% of sequencing reads aligned to targeted loci. The targeted promoters were from genes that are frequently mutated in breast and colon cancer, and the samples included breast and colon tumor and adjacent normal tissue. This approach allowed us to identify nine gene promoters that exhibit tumor-specific DNA methylation defects that occur frequently in colon and breast cancer. We also analyzed single nucleotide polymorphisms to observe DNA methylation that accumulated on specific alleles during tumor development. This method is broadly applicable for studying DNA methylation across large numbers of patient samples using next-generation sequencing.},
}
@article {pmid20625503,
year = {2010},
author = {Farias-Hesson, E and Erikson, J and Atkins, A and Shen, P and Davis, RW and Scharfe, C and Pourmand, N},
title = {Semi-automated library preparation for high-throughput DNA sequencing platforms.},
journal = {Journal of biomedicine &amp; biotechnology},
volume = {2010},
number = {},
pages = {617469},
pmid = {20625503},
issn = {1110-7251},
support = {P01 HG000205/HG/NHGRI NIH HHS/United States ; R01 EY016240/EY/NEI NIH HHS/United States ; R01 EY016240-04/EY/NEI NIH HHS/United States ; P01-HG000205/HG/NHGRI NIH HHS/United States ; },
mesh = {Automation/*methods ; DNA/genetics ; Exons/genetics ; *Gene Library ; Genetic Markers ; High-Throughput Screening Assays/*methods ; Humans ; Sequence Analysis, DNA/*instrumentation/*methods ; },
abstract = {Next-generation sequencing platforms are powerful technologies, providing gigabases of genetic information in a single run. An important prerequisite for high-throughput DNA sequencing is the development of robust and cost-effective preprocessing protocols for DNA sample library construction. Here we report the development of a semi-automated sample preparation protocol to produce adaptor-ligated fragment libraries. Using a liquid-handling robot in conjunction with Carboxy Terminated Magnetic Beads, we labeled each library sample using a unique 6 bp DNA barcode, which allowed multiplex sample processing and sequencing of 32 libraries in a single run using Applied Biosystems' SOLiD sequencer. We applied our semi-automated pipeline to targeted medical resequencing of nuclear candidate genes in individuals affected by mitochondrial disorders. This novel method is capable of preparing as much as 32 DNA libraries in 2.01 days (8-hour workday) for emulsion PCR/high throughput DNA sequencing, increasing sample preparation production by 8-fold.},
}
@article {pmid20618939,
year = {2010},
author = {Bellemain, E and Carlsen, T and Brochmann, C and Coissac, E and Taberlet, P and Kauserud, H},
title = {ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases.},
journal = {BMC microbiology},
volume = {10},
number = {},
pages = {189},
pmid = {20618939},
issn = {1471-2180},
mesh = {DNA Primers/genetics ; DNA, Ribosomal Spacer/*genetics ; *Environmental Microbiology ; Fungi/classification/*genetics/*isolation &amp; purification ; Polymerase Chain Reaction ; },
abstract = {BACKGROUND: During the last 15 years the internal transcribed spacer (ITS) of nuclear DNA has been used as a target for analyzing fungal diversity in environmental samples, and has recently been selected as the standard marker for fungal DNA barcoding. In this study we explored the potential amplification biases that various commonly utilized ITS primers might introduce during amplification of different parts of the ITS region in samples containing mixed templates ('environmental barcoding'). We performed in silico PCR analyses with commonly used primer combinations using various ITS datasets obtained from public databases as templates.<br><br>RESULTS: Some of the ITS primers, such as ITS1-F, were hampered with a high proportion of mismatches relative to the target sequences, and most of them appeared to introduce taxonomic biases during PCR. Some primers, e.g. ITS1-F, ITS1 and ITS5, were biased towards amplification of basidiomycetes, whereas others, e.g. ITS2, ITS3 and ITS4, were biased towards ascomycetes. The assumed basidiomycete-specific primer ITS4-B only amplified a minor proportion of basidiomycete ITS sequences, even under relaxed PCR conditions. Due to systematic length differences in the ITS2 region as well as the entire ITS, we found that ascomycetes will more easily amplify than basidiomycetes using these regions as targets. This bias can be avoided by using primers amplifying ITS1 only, but this would imply preferential amplification of 'non-dikarya' fungi.<br><br>CONCLUSIONS: We conclude that ITS primers have to be selected carefully, especially when used for high-throughput sequencing of environmental samples. We suggest that different primer combinations or different parts of the ITS region should be analyzed in parallel, or that alternative ITS primers should be searched for.},
}
@article {pmid20617114,
year = {2009},
author = {Tekin, E and Coughlan, JM},
title = {An Algorithm Enabling Blind Users to Find and Read Barcodes.},
journal = {Proceedings. IEEE Workshop on Applications of Computer Vision},
volume = {2009},
number = {},
pages = {1-8},
pmid = {20617114},
issn = {1550-5790},
support = {R01 EY018890/EY/NEI NIH HHS/United States ; R01 EY018890-01/EY/NEI NIH HHS/United States ; },
abstract = {Most camera-based systems for finding and reading barcodes are designed to be used by sighted users (e.g. the Red Laser iPhone app), and assume the user carefully centers the barcode in the image before the barcode is read. Blind individuals could benefit greatly from such systems to identify packaged goods (such as canned goods in a supermarket), but unfortunately in their current form these systems are completely inaccessible because of their reliance on visual feedback from the user.To remedy this problem, we propose a computer vision algorithm that processes several frames of video per second to detect barcodes from a distance of several inches; the algorithm issues directional information with audio feedback (e.g. "left," "right") and thereby guides a blind user holding a webcam or other portable camera to locate and home in on a barcode. Once the barcode is detected at sufficiently close range, a barcode reading algorithm previously developed by the authors scans and reads aloud the barcode and the corresponding product information. We demonstrate encouraging experimental results of our proposed system implemented on a desktop computer with a webcam held by a blindfolded user; ultimately the system will be ported to a camera phone for use by visually impaired users.},
}
@article {pmid20617113,
year = {2009},
author = {Gallo, O and Manduchi, R},
title = {Reading Challenging Barcodes with Cameras.},
journal = {Proceedings. IEEE Workshop on Applications of Computer Vision},
volume = {2009},
number = {7-8},
pages = {1-6},
pmid = {20617113},
issn = {1550-5790},
support = {R21 EY017003/EY/NEI NIH HHS/United States ; R21 EY017003-01A1/EY/NEI NIH HHS/United States ; },
abstract = {Current camera-based barcode readers do not work well when the image has low resolution, is out of focus, or is motion-blurred. One main reason is that virtually all existing algorithms perform some sort of binarization, either by gray scale thresholding or by finding the bar edges. We propose a new approach to barcode reading that never needs to binarize the image. Instead, we use deformable barcode digit models in a maximum likelihood setting. We show that the particular nature of these models enables efficient integration over the space of deformations. Global optimization over all digits is then performed using dynamic programming. Experiments with challenging UPC-A barcode images show substantial improvement over other state-of-the-art algorithms.},
}
@article {pmid20616076,
year = {2010},
author = {Reisner, W and Larsen, NB and Silahtaroglu, A and Kristensen, A and Tommerup, N and Tegenfeldt, JO and Flyvbjerg, H},
title = {Single-molecule denaturation mapping of DNA in nanofluidic channels.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {107},
number = {30},
pages = {13294-13299},
pmid = {20616076},
issn = {1091-6490},
mesh = {Algorithms ; Bacteriophages/genetics ; Benzoxazoles/chemistry ; DNA/*chemistry/genetics ; Formamides/chemistry ; Microfluidic Analytical Techniques/instrumentation/*methods ; Models, Chemical ; Nanotechnology/instrumentation/*methods ; Nucleic Acid Conformation ; *Nucleic Acid Denaturation ; Quinolinium Compounds/chemistry ; Transition Temperature ; },
abstract = {Here we explore the potential power of denaturation mapping as a single-molecule technique. By partially denaturing YOYO-1-labeled DNA in nanofluidic channels with a combination of formamide and local heating, we obtain a sequence-dependent "barcode" corresponding to a series of local dips and peaks in the intensity trace along the extended molecule. We demonstrate that this structure arises from the physics of local denaturation: statistical mechanical calculations of sequence-dependent melting probability can predict the barcode to be observed experimentally for a given sequence. Consequently, the technique is sensitive to sequence variation without requiring enzymatic labeling or a restriction step. This technique may serve as the basis for a new mapping technology ideally suited for investigating the long-range structure of entire genomes extracted from single cells.},
}
@article {pmid20615258,
year = {2010},
author = {Park, DS and Suh, SJ and Oh, HW and Hebert, PD},
title = {Recovery of the mitochondrial COI barcode region in diverse Hexapoda through tRNA-based primers.},
journal = {BMC genomics},
volume = {11},
number = {},
pages = {423},
pmid = {20615258},
issn = {1471-2164},
mesh = {Amino Acid Sequence ; Animals ; Arthropods/*genetics ; Base Sequence ; DNA Fingerprinting/*methods ; DNA Primers/*genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/chemistry/*genetics ; Genome, Mitochondrial/genetics ; Mitochondria/*enzymology/*genetics ; Molecular Sequence Data ; RNA, Transfer/*genetics ; },
abstract = {BACKGROUND: DNA barcoding uses a 650 bp segment of the mitochondrial cytochrome c oxidase I (COI) gene as the basis for an identification system for members of the animal kingdom and some other groups of eukaryotes. PCR amplification of the barcode region is a key step in the analytical chain, but it sometimes fails because of a lack of homology between the standard primer sets and target DNA.<br><br>RESULTS: Two forward PCR primers were developed following analysis of all known arthropod mitochondrial genome arrangements and sequence alignment of the tRNA-W gene which was usually located within 200 bp upstream of the COI gene. These two primers were combined with a standard reverse primer (LepR1) to produce a cocktail which generated a barcode amplicon from 125 of 141 species that included representatives of 121 different families of Hexapoda. High quality sequences were recovered from 79% of the species including groups, such as scale insects, that invariably fail to amplify with standard primers.<br><br>CONCLUSIONS: A cocktail of two tRNA-W forward primers coupled with a standard reverse primer amplifies COI for most hexapods, allowing characterization of the standard barcode primer binding region in COI 5' as well as the barcode segment. The current results show that primers designed to bind to highly conserved gene regions upstream of COI will aid the amplification of this gene region in species where standard primers fail and provide valuable information to design a primer for problem groups.},
}
@article {pmid20602273,
year = {2010},
author = {Luo, K and Chen, S and Chen, K and Song, J and Yao, H and Ma, X and Zhu, Y and Pang, X and Yu, H and Li, X and Liu, Z},
title = {Assessment of candidate plant DNA barcodes using the Rutaceae family.},
journal = {Science China. Life sciences},
volume = {53},
number = {6},
pages = {701-708},
doi = {10.1007/s11427-010-4009-1},
pmid = {20602273},
issn = {1869-1889},
mesh = {Base Sequence ; DNA Primers ; DNA, Plant/*genetics ; *Genes, Plant ; Genetic Variation ; Polymerase Chain Reaction ; Rutaceae/*genetics ; },
abstract = {DNA barcoding is a rapidly developing frontier technology that is gaining worldwide attention. Here, seven regions (psbA-trnH, matK, ycf5, rpoC1, rbcL, ITS2, and ITS) with potential for use as DNA barcodes were tested for their ability to identify 300 samples of 192 species from 72 genera of the family Rutaceae. To evaluate each barcode's utility for species authentication, PCR amplification efficiency, genetic divergence, and barcoding gaps were assessed. We found that the ITS2 region exhibited the highest inter-specific divergence, and that this was significantly higher than the intra-specific variation in the "DNA barcoding gap" assessment and Wilcoxon two-sample tests. The ITS2 locus had the highest identification efficiency among all tested regions. In a previous study, we found that ITS2 was able to discriminate a wide range of plant taxa, and here we confirmed that ITS2 was also able to discriminate a number of closely related species. Therefore, we propose that ITS2 is a promising candidate barcode for plant species identification.},
}
@article {pmid20601269,
year = {2011},
author = {Huang, TP and Yeh, Y and Tzeng, DD},
title = {Barcode-like heteroduplex DNA pattern as an aid for rapid identification of anthracnose fungi.},
journal = {New biotechnology},
volume = {28},
number = {1},
pages = {72-78},
doi = {10.1016/j.nbt.2010.06.013},
pmid = {20601269},
issn = {1876-4347},
mesh = {Colletotrichum/*genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/*genetics ; Electrophoresis, Polyacrylamide Gel ; Heteroduplex Analysis ; Molecular Sequence Data ; Nucleic Acid Heteroduplexes/*genetics ; Species Specificity ; },
abstract = {We have shown the usefulness of the heteroduplex mobility assay (HMA) for phylogenetic analysis and for the discrimination of closely related Colletotrichum species. Because the heteroduplex mobility of a tested strain shows a unique banding pattern that is the function of the sequence of the referred strain, we further explored the potential use of heteroduplex DNA patterns (HPs) as DNA fingerprints for the identification of these fungi. The 29 Colletotrichum strains previously identified by HMA to be taxonomic members of CG, CA, CM, CC and CL species groups were re-examined with an emphasis on their unique heteroduplex banding patterns. The species attributes of these tested strains were characterized by HMA using ITS fragments amplified from six representative Colletotrichum strains as pairwise compared references. By comparing the unique homoduplex and heteroduplex banding patterns of each tested strain on a polyacrylamide gel with those of the respective reference strain, the species identity of tested strains was determined. The obtained barcode-like HPs classified these 29 Colletotrichum strains into 6 distinctive groups: CG1, CG2, CA, CM, CC and CL. Notably, the HPs differentiated strains CG1 and CG2, which differed in their ITS sequences by only six bases. The presented results revealed that the species-characteristic barcode-like HP classification of ITS regions is a relatively rapid and valuable system for species identification of Colletotrichum species. The potential use of the established barcode-like system for the identification of anthracnose fungi and other fungal pathogens is discussed.},
}
@article {pmid20591175,
year = {2010},
author = {Hankeln, W and Buttigieg, PL and Fink, D and Kottmann, R and Yilmaz, P and Glöckner, FO},
title = {MetaBar - a tool for consistent contextual data acquisition and standards compliant submission.},
journal = {BMC bioinformatics},
volume = {11},
number = {},
pages = {358},
pmid = {20591175},
issn = {1471-2105},
mesh = {Base Sequence ; *Databases, Genetic ; *Genomics ; Information Storage and Retrieval/*methods ; Internet ; Programming Languages ; *Software ; User-Computer Interface ; Workflow ; },
abstract = {BACKGROUND: Environmental sequence datasets are increasing at an exponential rate; however, the vast majority of them lack appropriate descriptors like sampling location, time and depth/altitude: generally referred to as metadata or contextual data. The consistent capture and structured submission of these data is crucial for integrated data analysis and ecosystems modeling. The application MetaBar has been developed, to support consistent contextual data acquisition.<br><br>RESULTS: MetaBar is a spreadsheet and web-based software tool designed to assist users in the consistent acquisition, electronic storage, and submission of contextual data associated to their samples. A preconfigured Microsoft Excel spreadsheet is used to initiate structured contextual data storage in the field or laboratory. Each sample is given a unique identifier and at any stage the sheets can be uploaded to the MetaBar database server. To label samples, identifiers can be printed as barcodes. An intuitive web interface provides quick access to the contextual data in the MetaBar database as well as user and project management capabilities. Export functions facilitate contextual and sequence data submission to the International Nucleotide Sequence Database Collaboration (INSDC), comprising of the DNA DataBase of Japan (DDBJ), the European Molecular Biology Laboratory database (EMBL) and GenBank. MetaBar requests and stores contextual data in compliance to the Genomic Standards Consortium specifications. The MetaBar open source code base for local installation is available under the GNU General Public License version 3 (GNU GPL3).<br><br>CONCLUSION: The MetaBar software supports the typical workflow from data acquisition and field-sampling to contextual data enriched sequence submission to an INSDC database. The integration with the megx.net marine Ecological Genomics database and portal facilitates georeferenced data integration and metadata-based comparisons of sampling sites as well as interactive data visualization. The ample export functionalities and the INSDC submission support enable exchange of data across disciplines and safeguarding contextual data.},
}
@article {pmid20576098,
year = {2010},
author = {Lou, SK and Wong, KL and Li, M and But, PP and Tsui, SK and Shaw, PC},
title = {An integrated web medicinal materials DNA database: MMDBD (Medicinal Materials DNA Barcode Database).},
journal = {BMC genomics},
volume = {11},
number = {},
pages = {402},
pmid = {20576098},
issn = {1471-2164},
mesh = {Animals ; *DNA Fingerprinting ; *Databases, Nucleic Acid ; *Internet ; *Pharmacology ; Sequence Analysis, DNA ; Software ; User-Computer Interface ; },
abstract = {BACKGROUND: Thousands of plants and animals possess pharmacological properties and there is an increased interest in using these materials for therapy and health maintenance. Efficacies of the application is critically dependent on the use of genuine materials. For time to time, life-threatening poisoning is found because toxic adulterant or substitute is administered. DNA barcoding provides a definitive means of authentication and for conducting molecular systematics studies. Owing to the reduced cost in DNA authentication, the volume of the DNA barcodes produced for medicinal materials is on the rise and necessitates the development of an integrated DNA database.<br><br>DESCRIPTION: We have developed an integrated DNA barcode multimedia information platform- Medicinal Materials DNA Barcode Database (MMDBD) for data retrieval and similarity search. MMDBD contains over 1000 species of medicinal materials listed in the Chinese Pharmacopoeia and American Herbal Pharmacopoeia. MMDBD also contains useful information of the medicinal material, including resources, adulterant information, medical parts, photographs, primers used for obtaining the barcodes and key references. MMDBD can be accessed at http://www.cuhk.edu.hk/icm/mmdbd.htm.<br><br>CONCLUSIONS: This work provides a centralized medicinal materials DNA barcode database and bioinformatics tools for data storage, analysis and exchange for promoting the identification of medicinal materials. MMDBD has the largest collection of DNA barcodes of medicinal materials and is a useful resource for researchers in conservation, systematic study, forensic and herbal industry.},
}
@article {pmid20573615,
year = {2010},
author = {Riemann, L and Alfredsson, H and Hansen, MM and Als, TD and Nielsen, TG and Munk, P and Aarestrup, K and Maes, GE and Sparholt, H and Petersen, MI and Bachler, M and Castonguay, M},
title = {Qualitative assessment of the diet of European eel larvae in the Sargasso Sea resolved by DNA barcoding.},
journal = {Biology letters},
volume = {6},
number = {6},
pages = {819-822},
pmid = {20573615},
issn = {1744-957X},
mesh = {Anguilla/growth &amp; development/*physiology ; Animals ; Atlantic Ocean ; DNA Barcoding, Taxonomic ; Diet ; Digestive System/chemistry ; Food Chain ; Larva/growth &amp; development/physiology ; Plankton/genetics/isolation &amp; purification ; RNA, Ribosomal, 18S/genetics/isolation &amp; purification ; Zooplankton/genetics/isolation &amp; purification ; },
abstract = {European eels (Anguilla anguilla) undertake spawning migrations of more than 5000 km from continental Europe and North Africa to frontal zones in the Sargasso Sea. Subsequently, the larval offspring are advected by large-scale eastward ocean currents towards continental waters. However, the Sargasso Sea is oligotrophic, with generally low plankton biomass, and the feeding biology of eel larvae has so far remained a mystery, hampering understanding of this peculiar life history. DNA barcoding of gut contents of 61 genetically identified A. anguilla larvae caught in the Sargasso Sea showed that even the smallest larvae feed on a striking variety of plankton organisms, and that gelatinous zooplankton is of fundamental dietary importance. Hence, the specific plankton composition seems essential for eel larval feeding and growth, suggesting a linkage between eel survival and regional plankton productivity. These novel insights into the prey of Atlantic eels may furthermore facilitate eel larval rearing in aquaculture, which ultimately may replace the unsustainable use of wild-caught glass eels.},
}
@article {pmid20568635,
year = {2010},
author = {Rugman-Jones, PF and Hoddle, MS and Stouthamer, R},
title = {Nuclear-mitochondrial barcoding exposes the global pest Western flower thrips (Thysanoptera: Thripidae) as two sympatric cryptic species in its native California.},
journal = {Journal of economic entomology},
volume = {103},
number = {3},
pages = {877-886},
doi = {10.1603/ec09300},
pmid = {20568635},
issn = {0022-0493},
mesh = {Animals ; California ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Insecta/*genetics ; Plants ; RNA, Ribosomal, 28S/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Over the past three decades, Western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), has become a major worldwide pest of many agricultural and horticultural crops. In response, much time, money, and effort have been put into pure and applied research focusing on the biology and control of this pest. Western flower thrips is native to Western North America and widespread in California. High levels of variation in basic biology, pest status, and resistance to insecticides bring into question the specific status of Western flower thrips. We used nuclear-mitochondrial barcoding to compare DNA sequences of nuclear and mitochondrial genes between Western flower thrips populations across California, looking for association between these unlinked loci. Sequences of D2 domain of 28S and cytochrome c oxidase I gene revealed the existence of two distinct but sympatric genetic entities, and we describe a simple polymerase chain reaction-based method for diagnosing these entities. The complete association of these nuclear and mitochondrial loci in areas of sympatry is indicative of reproductive isolation and the existence of two cryptic species, both of which key out to Western flower thrips by using morphological characters. The finding that Western flower thrips is a complex of two species has important implications for past, current, and most importantly future research on these pests.},
}
@article {pmid20565819,
year = {2010},
author = {Pagès, M and Chaval, Y and Herbreteau, V and Waengsothorn, S and Cosson, JF and Hugot, JP and Morand, S and Michaux, J},
title = {Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries.},
journal = {BMC evolutionary biology},
volume = {10},
number = {},
pages = {184},
pmid = {20565819},
issn = {1471-2148},
mesh = {Animals ; Asia, Southeastern ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Likelihood Functions ; *Phylogeny ; Rats/*classification/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND: Rodents are recognized as hosts for at least 60 zoonotic diseases and may represent a serious threat for human health. In the context of global environmental changes and increasing mobility of humans and animals, contacts between pathogens and potential animal hosts and vectors are modified, amplifying the risk of disease emergence. An accurate identification of each rodent at a specific level is needed in order to understand their implications in the transmission of diseases. Among the Muridae, the Rattini tribe encompasses 167 species inhabiting South East Asia, a hotspot of both biodiversity and emerging and re-emerging diseases. The region faces growing economical development that affects habitats, biodiversity and health. Rat species have been demonstrated as significant hosts of pathogens but are still difficult to recognize at a specific level using morphological criteria. DNA-barcoding methods appear as accurate tools for rat species identification but their use is hampered by the need of reliable identification of reference specimens. In this study, we explore and highlight the limits of the current taxonomy of the Rattini tribe.<br><br>RESULTS: We used the DNA sequence information itself as the primary information source to establish group membership and estimate putative species boundaries. We sequenced two mitochondrial and one nuclear genes from 122 rat samples to perform phylogenetic reconstructions. The method of Pons and colleagues (2006) that determines, with no prior expectations, the locations of ancestral nodes defining putative species was then applied to our dataset. To give an appropriate name to each cluster recognized as a putative species, we reviewed information from the literature and obtained sequences from a museum holotype specimen following the ancient DNA criteria.<br><br>CONCLUSIONS: Using a recently developed methodology, this study succeeds in refining the taxonomy of one of the most difficult groups of mammals. Most of the species expected within the area were retrieved but new putative species limits were also indicated, in particular within Berylmys and Rattus genera, where future taxonomic studies should be directed. Our study lays the foundations to better investigate rodent-born diseases in South East Asia and illustrates the relevance of evolutionary studies for health and medical sciences.},
}
@article {pmid20563888,
year = {2010},
author = {Wilson-Wilde, L and Norman, J and Robertson, J and Sarre, S and Georges, A},
title = {Current issues in species identification for forensic science and the validity of using the cytochrome oxidase I (COI) gene.},
journal = {Forensic science, medicine, and pathology},
volume = {6},
number = {3},
pages = {233-241},
pmid = {20563888},
issn = {1556-2891},
mesh = {Animals ; Conservation of Natural Resources ; Crime ; DNA Fingerprinting/*methods ; DNA Primers ; Databases, Genetic ; Electron Transport Complex IV/*genetics ; Humans ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Species identification techniques commonly utilized in Australian Forensic Science laboratories are gel immunodifussion antigen antibody reactions and hair comparison analysis. Both of these techniques have significant limitations and should be considered indicative opinion based tests. The Barcode of Life Initiative aims to sequence a section of DNA (~648 base pairs) for the Cytochrome Oxidase I mitochondrial gene (COI) in all living species on Earth, with the data generated being uploaded to the Barcode of Life Database (BOLD) which can then be used for species identification. The COI gene therefore offers forensics scientists an opportunity to use the marker to analyze unknown samples and compare sequences generated in BOLD. Once sequences from enough species are on the database, it is anticipated that routine identification of an unknown species may be possible. However, most forensic laboratories are not yet suited to this type of analysis and do not have the expertise to fully interpret the implications of matches and non matches involving a poorly sampled taxa (for example where there are cryptic species) and in providing the required opinion evidence. Currently, the use of BOLD is limited by the number of relevant species held in the database and the quality assurance and regulation of sequences that are there. In this paper, the COI methodology and BOLD are tested on a selection of introduced and Australian mammals in a forensic environment as the first step necessary in the implementation of this approach in the Australian context. Our data indicates that the COI methodology performs well on distinct species but needs further exploration when identifying more closely related species. It is evident from our study that changes will be required to implement DNA based wildlife forensics using the BOLD approach for forensic applications and recommendations are made for the future adoption of this technology into forensic laboratories.},
}
@article {pmid20561396,
year = {2010},
author = {Standley, CJ and Kabatereine, NB and Lange, CN and Lwambo, NJ and Stothard, JR},
title = {Molecular epidemiology and phylogeography of Schistosoma mansoni around Lake Victoria.},
journal = {Parasitology},
volume = {137},
number = {13},
pages = {1937-1949},
doi = {10.1017/S0031182010000788},
pmid = {20561396},
issn = {1469-8161},
mesh = {Animals ; Child ; Child, Preschool ; DNA Barcoding, Taxonomic ; DNA, Helminth/analysis/genetics/isolation &amp; purification ; Evolution, Molecular ; Genetic Variation ; Humans ; Kenya/epidemiology ; Microsatellite Repeats ; *Molecular Epidemiology ; Molecular Sequence Data ; Phylogeography ; Schistosoma mansoni/classification/*genetics/growth &amp; development/isolation &amp; purification ; Schistosomiasis mansoni/*epidemiology/parasitology/prevention &amp; control ; Sequence Analysis ; Sequence Analysis, DNA ; Tanzania/epidemiology ; Uganda/epidemiology ; },
abstract = {Intestinal schistosomiasis continues to be a major public health problem in sub-Saharan Africa, and is endemic in communities around Lake Victoria. Interest is growing in the molecular evolution and population genetic structure of Schistosoma mansoni and we describe a detailed analysis of the molecular epidemiology and phylogeography of S. mansoni from Lake Victoria. In total, 388 cytochrome oxidase 1 (COI) sequences were obtained from 25 sites along the Ugandan, Tanzanian and Kenyan shorelines of Lake Victoria, and 122 unique barcodes were identified; 9 corresponded to previously discovered barcodes from Lakes Victoria and Albert. A subset of the data, composed of COI sequences from miracidia from 10 individual children, was used for population genetics analyses; these results were corroborated by microsatellite analysis of 4 isolates of lab-passaged adult worms. Overall, 12 barcodes were found to be shared across all 3 countries, whereas the majority occurred singly and were locally restricted. The population genetics analyses were in agreement in revealing high diversity at the level of the human host and negligible population structuring by location. The lack of correlation between genetic distance and geographical distance in these data may be attributed to the confounding influence of high intra-individual diversity as well as human migration between communities.},
}
@article {pmid20561195,
year = {2010},
author = {Locke, SA and Daniel McLaughlin, J and Marcogliese, DJ},
title = {DNA barcodes show cryptic diversity and a potential physiological basis for host specificity among Diplostomoidea (Platyhelminthes: Digenea) parasitizing freshwater fishes in the St. Lawrence River, Canada.},
journal = {Molecular ecology},
volume = {19},
number = {13},
pages = {2813-2827},
doi = {10.1111/j.1365-294X.2010.04713.x},
pmid = {20561195},
issn = {1365-294X},
mesh = {Animals ; Canada ; DNA, Ribosomal Spacer/genetics ; Ecosystem ; Electron Transport Complex IV/genetics ; Fishes/*parasitology ; *Host-Parasite Interactions ; Rivers/parasitology ; Sequence Analysis, DNA ; Species Specificity ; Trematoda/classification/*genetics ; },
abstract = {Diplostomoid metacercariae parasitize freshwater fishes worldwide and cannot be identified to species based on morphology. In this study, sequences of the barcode region of cytochrome c oxidase subunit 1 (CO1) were used to discriminate species in 1088 diplostomoids, most of which were metacercariae from fish collected in the St. Lawrence River, Canada. Forty-seven diplostomoid species were detected, representing a large increase in known diversity. Most species suggested by CO1 sequences were supported by sequences of internal transcribed spacer (ITS) of rDNA and host and tissue specificity. Three lines of evidence indicate that physiological incompatibility between host and parasite is a more important determinant of host specificity than ecological separation of hosts and parasites in this important group of freshwater fish pathogens. First, nearly all diplostomoid species residing outside the lens of the eyes of fish are highly host specific, while all species that occur inside the lens are generalists. This can be plausibly explained by a physiological mechanism, namely the lack of an effective immune response in the lens. Second, the distribution of diplostomoid species among fish taxa reflected the phylogenetic relationships of host species rather than their ecological similarities. Third, the same patterns of host specificity were observed in separate, ecologically distinctive fish communities.},
}
@article {pmid20559503,
year = {2010},
author = {Arif, IA and Bakir, MA and Khan, HA and Al Farhan, AH and Al Homaidan, AA and Bahkali, AH and Sadoon, MA and Shobrak, M},
title = {A brief review of molecular techniques to assess plant diversity.},
journal = {International journal of molecular sciences},
volume = {11},
number = {5},
pages = {2079-2096},
pmid = {20559503},
issn = {1422-0067},
mesh = {*Biodiversity ; DNA, Plant/*genetics ; Molecular Typing/*methods ; *Plants/classification/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {Massive loss of valuable plant species in the past centuries and its adverse impact on environmental and socioeconomic values has triggered the conservation of plant resources. Appropriate identification and characterization of plant materials is essential for the successful conservation of plant resources and to ensure their sustainable use. Molecular tools developed in the past few years provide easy, less laborious means for assigning known and unknown plant taxa. These techniques answer many new evolutionary and taxonomic questions, which were not previously possible with only phenotypic methods. Molecular techniques such as DNA barcoding, random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), microsatellites and single nucleotide polymorphisms (SNP) have recently been used for plant diversity studies. Each technique has its own advantages and limitations. These techniques differ in their resolving power to detect genetic differences, type of data they generate and their applicability to particular taxonomic levels. This review presents a basic description of different molecular techniques that can be utilized for DNA fingerprinting and molecular diversity analysis of plant species.},
}
@article {pmid20550819,
year = {2010},
author = {Chu, D and Wan, FH and Zhang, YJ and Brown, JK},
title = {Change in the biotype composition of Bemisia tabaci in Shandong Province of China from 2005 to 2008.},
journal = {Environmental entomology},
volume = {39},
number = {3},
pages = {1028-1036},
doi = {10.1603/EN09161},
pmid = {20550819},
issn = {1938-2936},
mesh = {Animals ; China ; DNA Primers ; Electron Transport Complex IV/*genetics ; Gossypium/parasitology ; Hemiptera/*genetics ; Host-Parasite Interactions ; Polymerase Chain Reaction ; Solanum melongena/parasitology ; },
abstract = {Certain biotypes of the Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) complex cause extensive damage and are important pests and virus vectors in agricultural crops throughout the world. Among the most invasive and well studied are the B and Q biotypes. Recent reports in Shandong Province, China, have indicated that the Q biotype was introduced there in approximately 2005, whereas the B biotype has been established there for approximately 10 yr. Even so, the present distribution of the two biotypes in Shandong has not been examined. The results of this study showed that the B and Q biotypes are both present in Shandong Province based on bar-coding using a approximately 450-base fragment of the mitochondrial cytochrome oxidase I (mtCOI) gene. In addition, a B biotype-specific polymerase chain reaction primer pair that amplifies a approximately 300 bp mtCOI fragment was designed and used to examine the biotype composition of B. tabaci in selected crops from six provincial locations, using the general mtCOI primers as an internal positive control for DNA quality. The results of this study indicated that the Q biotype was the predominant B. tabaci colonizing all of the crops in the study sites examined. This suggests that the Q biotype has displaced the B biotype in Shandong Province of China, which until now was the predominant biotype. This is the first report of the displacement of the B by the Q biotype in field grown crops in China, and in a locale where neither the B nor the Q biotype is native. We hypothesize that this phenomenon may have been exacerbated by the widespread use of neonicotinoid insecticides for whitefly control, given the sustained efficacy thus far of neonicotinoids against the B biotype, and their failure at times to effectively control the Q biotype.},
}
@article {pmid20549596,
year = {2011},
author = {Gao, T and Sun, Z and Yao, H and Song, J and Zhu, Y and Ma, X and Chen, S},
title = {Identification of Fabaceae plants using the DNA barcode matK.},
journal = {Planta medica},
volume = {77},
number = {1},
pages = {92-94},
doi = {10.1055/s-0030-1250050},
pmid = {20549596},
issn = {1439-0221},
mesh = {Classification/methods ; *DNA Barcoding, Taxonomic ; Fabaceae/*classification/genetics ; *Genes, Plant ; Genetic Markers ; Quality Control ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {In this study, we tested the applicability of the core DNA barcode MATK for identifying species within the Fabaceae family. Based on an evaluation of genetic variation, DNA barcoding gaps, and species discrimination power, MATK is a useful barcode for Fabaceae species. Of 1355 plant samples collected from 1079 species belonging to 409 diverse genera, MATK precisely identified approximately 80 % and 96 % of them at the species and genus levels, respectively. Therefore, our research indicates that the MATK region is a valuable marker for plant species within Fabaceae.},
}
@article {pmid20540728,
year = {2010},
author = {Magnacca, KN and Brown, MJ},
title = {Mitochondrial heteroplasmy and DNA barcoding in Hawaiian Hylaeus (Nesoprosopis) bees (Hymenoptera: Colletidae).},
journal = {BMC evolutionary biology},
volume = {10},
number = {},
pages = {174},
pmid = {20540728},
issn = {1471-2148},
mesh = {Animals ; Bees/classification/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genes, Insect ; Haplotypes ; Hawaii ; Mitochondria/genetics ; Polymorphism, Genetic ; Pseudogenes ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
abstract = {BACKGROUND: The past several years have seen a flurry of papers seeking to clarify the utility and limits of DNA barcoding, particularly in areas such as species discovery and paralogy due to nuclear pseudogenes. Heteroplasmy, the coexistence of multiple mitochondrial haplotypes in a single organism, has been cited as a potentially serious problem for DNA barcoding but its effect on identification accuracy has not been tested. In addition, few studies of barcoding have tested a large group of closely-related species with a well-established morphological taxonomy. In this study we examine both of these issues, by densely sampling the Hawaiian Hylaeus bee radiation.<br><br>RESULTS: Individuals from 21 of the 49 a priori morphologically-defined species exhibited coding sequence heteroplasmy at levels of 1-6% or more. All homoplasmic species were successfully identified by COI using standard methods of analysis, but only 71% of heteroplasmic species. The success rate in identifying heteroplasmic species was increased to 86% by treating polymorphisms as character states rather than ambiguities. Nuclear pseudogenes (numts) were also present in four species, and were distinguishable from heteroplasmic sequences by patterns of nucleotide and amino acid change.<br><br>CONCLUSIONS: Heteroplasmy significantly decreased the reliability of species identification. In addition, the practical issue of dealing with large numbers of polymorphisms- and resulting increased time and labor required - makes the development of DNA barcode databases considerably more complex than has previously been suggested. The impact of heteroplasmy on the utility of DNA barcoding as a bulk specimen identification tool will depend upon its frequency across populations, which remains unknown. However, DNA barcoding is still likely to remain an important identification tool for those species that are difficult or impossible to identify through morphology, as is the case for the ecologically important solitary bee fauna.},
}
@article {pmid20525598,
year = {2009},
author = {Siddall, ME and Fontanella, FM and Watson, SC and Kvist, S and Erséus, C},
title = {Barcoding bamboozled by bacteria: convergence to metazoan mitochondrial primer targets by marine microbes.},
journal = {Systematic biology},
volume = {58},
number = {4},
pages = {445-451},
doi = {10.1093/sysbio/syp033},
pmid = {20525598},
issn = {1076-836X},
mesh = {Animals ; Classification/*methods ; Electron Transport Complex IV/*genetics ; Gammaproteobacteria/*genetics ; *Genetic Techniques ; Seawater/microbiology ; },
}
@article {pmid20525596,
year = {2009},
author = {Lohse, K},
title = {Can mtDNA barcodes be used to delimit species? A response to Pons et al. (2006).},
journal = {Systematic biology},
volume = {58},
number = {4},
pages = {439-42; discussion 442-4},
doi = {10.1093/sysbio/syp039},
pmid = {20525596},
issn = {1076-836X},
support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Classification/*methods ; Computer Simulation ; DNA, Mitochondrial/*genetics ; Models, Genetic ; Selection Bias ; Species Specificity ; },
}
@article {pmid20521714,
year = {2010},
author = {Lee, DH and Lee, HJ and Lee, YN and Lee, YJ and Jeong, OM and Kang, HM and Kim, MC and Kwon, JS and Kwon, JH and Lee, JB and Park, SY and Choi, IS and Song, CS},
title = {Application of DNA barcoding technique in avian influenza virus surveillance of wild bird habitats in Korea and Mongolia.},
journal = {Avian diseases},
volume = {54},
number = {1 Suppl},
pages = {677-681},
doi = {10.1637/8783-040109-ResNote.1},
pmid = {20521714},
issn = {0005-2086},
mesh = {Animals ; *Animals, Wild ; *Birds ; DNA, Viral/*analysis ; *Ecosystem ; Influenza A virus/genetics ; Influenza in Birds/*epidemiology/virology ; Korea/epidemiology ; Mongolia/epidemiology ; Sequence Analysis, DNA/*methods ; },
abstract = {In a previous study, we optimized DNA barcoding techniques for avian influenza virus (AIV) isolation and host identification, using fecal samples from wild birds, for high-throughput surveillance of migratory waterfowls. In the present study, we surveyed AIV in Mongolia during the breeding season and, subsequently, in Korea in winter, to compare prevalent AIV subtypes and hosts using DNA barcoding. In Korea, H4 and H5 subtypes were the most abundantly detected HA subtypes, and most AIVs were isolated from the major population (mallards, Anas platyrhynchos) of wild bird habitats. On the other hand, in Mongolia, H3 and H4 subtypes were the most abundantly detected HA subtypes, and most AIVs were isolated from a small population of wild bird habitats that were not visible at the sampling site. In conclusion, AIV isolation using fecal samples, accompanied with DNA barcoding techniques as a host bird species identification tool, could be useful for monitoring major and minor populations of wild bird habitats. Further, continuous, and large-scale surveillance could be helpful for understanding the AIV epidemiology, evolution, and ecology in wild waterfowl.},
}
@article {pmid20518297,
year = {2010},
author = {Shao, H and Zhang, L and Lv, HF and Zhou, JY and Hu, ZB and Li, WK},
title = {[The utility of trnH-psbA gene for phylogenetic analysis of Huperziaceae and plant barcoding].},
journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials},
volume = {33},
number = {1},
pages = {18-21},
pmid = {20518297},
issn = {1001-4454},
mesh = {Chloroplasts/*genetics ; *DNA Barcoding, Taxonomic ; DNA Primers ; DNA, Plant/genetics ; Electronic Data Processing/methods ; *Genes, Plant ; Huperzia/classification/*genetics ; Molecular Sequence Data ; Phylogeny ; Plants, Medicinal/classification/genetics ; Species Specificity ; },
abstract = {OBJECTIVE: The purpose of study was to discover the phylogenetic relations and plant barcoding of 17 plants from Huperziaceae.<br><br>METHODS: Phylogenetic tree of chloroplast trnH-psbA gene of 17 plants from Huperziaceae was constructed by software.<br><br>RESULTS: It showed that Huperziaceae could be divided into two genera Huperzia and Phlegmariurus and bootstrap value reached 91%.<br><br>CONCLUSIONS: Holub and Qing' taxonomy was supported and 17 species in Huperziaceae were monophyletic groups and it suggested that trnH-psbA could be used as a DNA barcode to identify plants.},
}
@article {pmid20516186,
year = {2010},
author = {Meyer, M and Kircher, M},
title = {Illumina sequencing library preparation for highly multiplexed target capture and sequencing.},
journal = {Cold Spring Harbor protocols},
volume = {2010},
number = {6},
pages = {pdb.prot5448},
doi = {10.1101/pdb.prot5448},
pmid = {20516186},
issn = {1559-6095},
mesh = {Base Sequence ; DNA/isolation &amp; purification ; *Gene Library ; Humans ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; },
abstract = {The large amount of DNA sequence data generated by high-throughput sequencing technologies often allows multiple samples to be sequenced in parallel on a single sequencing run. This is particularly true if subsets of the genome are studied rather than complete genomes. In recent years, target capture from sequencing libraries has largely replaced polymerase chain reaction (PCR) as the preferred method of target enrichment. Parallelizing target capture and sequencing for multiple samples requires the incorporation of sample-specific barcodes into sequencing libraries, which is necessary to trace back the sample source of each sequence. This protocol describes a fast and reliable method for the preparation of barcoded ("indexed") sequencing libraries for Illumina's Genome Analyzer platform. The protocol avoids expensive commercial library preparation kits and can be performed in a 96-well plate setup using multi-channel pipettes, requiring not more than two or three days of lab work. Libraries can be prepared from any type of double-stranded DNA, even if present in subnanogram quantity.},
}
@article {pmid20512048,
year = {2011},
author = {Brown, JE and Smith, N and Sherfy, BR},
title = {Decreasing mislabeled laboratory specimens using barcode technology and bedside printers.},
journal = {Journal of nursing care quality},
volume = {26},
number = {1},
pages = {13-21},
doi = {10.1097/NCQ.0b013e3181e4e6dd},
pmid = {20512048},
issn = {1550-5065},
mesh = {Computer Systems/standards ; Humans ; Laboratories, Hospital/standards ; Medical Errors/prevention &amp; control ; Medical Laboratory Personnel/*standards ; Nursing Staff, Hospital/*standards ; Patient Identification Systems/*methods/*standards ; Point-of-Care Systems/*standards ; Printing ; Program Development ; Program Evaluation ; Risk Management/methods ; Specimen Handling/*standards ; },
abstract = {Mislabeling of laboratory samples has been found to be a high-risk issue in acute care hospitals. The goal of this study was to decrease mislabeled blood specimens. In the first year after the implementation of a positive patient identification system using barcoding and computer technology, the number of labeling errors decreased from 103 to 8 per year. The outcome was clinically and statistically significant (P < .001).},
}
@article {pmid20502980,
year = {2010},
author = {Costa, FO and Carvalho, GR},
title = {New insights into molecular evolution: prospects from the Barcode of Life Initiative (BOLI).},
journal = {Theory in biosciences = Theorie in den Biowissenschaften},
volume = {129},
number = {2-3},
pages = {149-157},
pmid = {20502980},
issn = {1611-7530},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*trends ; Ecosystem ; *Evolution, Molecular ; Genetic Speciation ; Genetic Variation/genetics ; Genome/genetics ; Genome, Mitochondrial/genetics ; Genome, Plastid/genetics ; Kinetics ; Point Mutation/genetics ; },
abstract = {Geographic and temporal patterns of morphological and behavioral diversifications among species stimulated Darwin to propose a mechanism for evolutionary change through natural selection. Scientific developments have revealed an even more fundamental level of biological complexity: sequence variation in DNA. While genome projects yield spectacular insights into molecular evolution, they have targeted only a few species. In contrast, the Barcode of Life Initiative (BOLI) proposes a horizontal approach to genomics, examining short, standardized genome segments across the sweep of eukaryotic life, all 10 million species. BOLI will extend our understanding of evolution and speciation in varied ways. It will facilitate quantification of biological diversity by disclosing cryptic species and enabling a rapid survey of taxon diversity in groups that have hitherto received scant morphological examination. It will facilitate assignment of life history stages to known species and provide a first estimate of species ages. It will also reveal key features of the mitochondrial genome, because the evolutionary properties of barcodes relate to those in the mitochondrial genome as a whole, acting to flag taxonomic groups or species with unusual nucleotide composition or evolutionary rates. The growing volume of barcode records has revealed that sequence variability within species is generally much lower than divergence among species (barcoding gap), a pattern that occurs in diverse lineages, suggesting a pervasive evolutionary process. Low variability may reflect recurrent selective sweeps of favored mitochondrial variants propagating as single linkage units across species. If this hypothesis is substantiated, the implications are significant, particularly for our understanding of molecular evolution of mitochondrial DNA and its relationship with species delineation.},
}
@article {pmid20498705,
year = {2010},
author = {Birky, CW and Adams, J and Gemmel, M and Perry, J},
title = {Using population genetic theory and DNA sequences for species detection and identification in asexual organisms.},
journal = {PloS one},
volume = {5},
number = {5},
pages = {e10609},
pmid = {20498705},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Chlorophyta/genetics ; Fungi/genetics ; Genetic Speciation ; *Genetics, Population ; Heterotrophic Processes/genetics ; Mites/genetics ; Oligochaeta/genetics ; Phylogeny ; *Population Dynamics ; Reproduction, Asexual/*genetics ; Rotifera/genetics ; Species Specificity ; },
abstract = {BACKGROUND: It is widely agreed that species are fundamental units of biology, but there is little agreement on a definition of species or on an operational criterion for delimiting species that is applicable to all organisms.<br><br>We focus on asexual eukaryotes as the simplest case for investigating species and speciation. We describe a model of speciation in asexual organisms based on basic principles of population and evolutionary genetics. The resulting species are independently evolving populations as described by the evolutionary species concept or the general lineage species concept. Based on this model, we describe a procedure for using gene sequences from small samples of individuals to assign them to the same or different species. Using this method of species delimitation, we demonstrate the existence of species as independent evolutionary units in seven groups of invertebrates, fungi, and protists that reproduce asexually most or all of the time.<br><br>CONCLUSIONS/SIGNIFICANCE: This wide evolutionary sampling establishes the general existence of species and speciation in asexual organisms. The method is well suited for measuring species diversity when phenotypic data are insufficient to distinguish species, or are not available, as in DNA barcoding and environmental sequencing. We argue that it is also widely applicable to sexual organisms.},
}
@article {pmid20485446,
year = {2010},
author = {Mitsui, J and Fukuda, Y and Azuma, K and Tozaki, H and Ishiura, H and Takahashi, Y and Goto, J and Tsuji, S},
title = {Multiplexed resequencing analysis to identify rare variants in pooled DNA with barcode indexing using next-generation sequencer.},
journal = {Journal of human genetics},
volume = {55},
number = {7},
pages = {448-455},
doi = {10.1038/jhg.2010.46},
pmid = {20485446},
issn = {1435-232X},
mesh = {Alleles ; Base Sequence ; Bias ; DNA/*genetics ; Electronic Data Processing/*methods ; Gene Library ; Genetic Variation/*genetics ; Humans ; Point Mutation/genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*instrumentation/*methods ; },
abstract = {We have recently found that multiple rare variants of the glucocerebrosidase gene (GBA) confer a robust risk for Parkinson disease, supporting the 'common disease-multiple rare variants' hypothesis. To develop an efficient method of identifying rare variants in a large number of samples, we applied multiplexed resequencing using a next-generation sequencer to identification of rare variants of GBA. Sixteen sets of pooled DNAs from six pooled DNA samples were prepared. Each set of pooled DNAs was subjected to polymerase chain reaction to amplify the target gene (GBA) covering 6.5 kb, pooled into one tube with barcode indexing, and then subjected to extensive sequence analysis using the SOLiD System. Individual samples were also subjected to direct nucleotide sequence analysis. With the optimization of data processing, we were able to extract all the variants from 96 samples with acceptable rates of false-positive single-nucleotide variants.},
}
@article {pmid20479871,
year = {2010},
author = {Wilson, JJ},
title = {Assessing the value of DNA barcodes and other priority gene regions for molecular phylogenetics of Lepidoptera.},
journal = {PloS one},
volume = {5},
number = {5},
pages = {e10525},
pmid = {20479871},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; DNA/*genetics ; Genes, Insect/*genetics ; Lepidoptera/classification/*genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Despite apparently abundant amounts of observable variation and species diversity, the order Lepidoptera exhibits a morphological homogeneity that has provided only a limited number of taxonomic characters and led to widespread use of nucleotides for inferring relationships. This study aims to characterize and develop methods to quantify the value of priority gene regions designated for Lepidoptera molecular systematics. In particular, I assess how the DNA barcode segment of the mitochondrial COI gene performs across a broad temporal range given its number one position of priority, most sequenced status, and the conflicting opinions on its phylogenetic performance.<br><br>Gene regions commonly sequenced for lepidoptera phylogenetics were scored using multiple measures across three categories: practicality, which includes universality of primers and sequence quality; phylogenetic utility; and phylogenetic signal. I found that alternative measures within a category often appeared correlated, but high scores in one category did not necessarily translate into high scores in another. The DNA barcode was easier to sequence than other genes, and had high scores for utility but low signal above the genus level.<br><br>CONCLUSIONS/SIGNIFICANCE: Given limited financial resources and time constraints, careful selection of gene regions for molecular phylogenetics is crucial to avoid wasted effort producing partially informative data. This study introduces an approach to assessing the value of gene regions prior to the initiation of new studies and presents empirical results to help guide future selections.},
}
@article {pmid20479114,
year = {2010},
author = {Gerlach, C and van Heijst, JW and Swart, E and Sie, D and Armstrong, N and Kerkhoven, RM and Zehn, D and Bevan, MJ and Schepers, K and Schumacher, TN},
title = {One naive T cell, multiple fates in CD8+ T cell differentiation.},
journal = {The Journal of experimental medicine},
volume = {207},
number = {6},
pages = {1235-1246},
pmid = {20479114},
issn = {1540-9538},
support = {U54 AI081680/AI/NIAID NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; CD8-Positive T-Lymphocytes/*cytology/*immunology/microbiology/virology ; Cell Differentiation/*immunology ; Cell Lineage/*immunology ; Immunologic Memory/immunology ; Listeriosis/complications/immunology ; Lymphoid Tissue/cytology/immunology ; Mice ; Mice, Inbred C57BL ; Orthomyxoviridae Infections/complications/immunology ; Receptors, Antigen, T-Cell/immunology ; T-Lymphocyte Subsets/cytology/immunology ; },
abstract = {The mechanism by which the immune system produces effector and memory T cells is largely unclear. To allow a large-scale assessment of the development of single naive T cells into different subsets, we have developed a technology that introduces unique genetic tags (barcodes) into naive T cells. By comparing the barcodes present in antigen-specific effector and memory T cell populations in systemic and local infection models, at different anatomical sites, and for TCR-pMHC interactions of different avidities, we demonstrate that under all conditions tested, individual naive T cells yield both effector and memory CD8+ T cell progeny. This indicates that effector and memory fate decisions are not determined by the nature of the priming antigen-presenting cell or the time of T cell priming. Instead, for both low and high avidity T cells, individual naive T cells have multiple fates and can differentiate into effector and memory T cell subsets.},
}
@article {pmid20471637,
year = {2010},
author = {Ohashi, K and Ota, S and Ohno-Machado, L and Tanaka, H},
title = {Smart medical environment at the point of care: auto-tracking clinical interventions at the bed side using RFID technology.},
journal = {Computers in biology and medicine},
volume = {40},
number = {6},
pages = {545-554},
doi = {10.1016/j.compbiomed.2010.03.007},
pmid = {20471637},
issn = {1879-0534},
support = {N01LM33509/LM/NLM NIH HHS/United States ; },
mesh = {Drug Information Services/instrumentation ; Equipment Design ; Humans ; Medication Errors/prevention &amp; control ; Nursing Care ; *Point-of-Care Systems ; *Radio Frequency Identification Device ; *Safety Management ; },
abstract = {We developed a wireless auto-tracking system for tracking clinical intervention such as drug administrations and blood tests at the patient bedside. The system can not only authenticate patients and nurses, but also confirm medications and provide relevant information, depending on the clinical situation and personnel location. We conducted a feasibility experiment and examined whether or not the system could work as a patient safety measure in terms of reducing misidentifications of patients and medical errors including wrong medication type, dose, time, and route. Also, the duration of clinical interventions in the system were measured to compare with the BCMA system. Moreover, we conducted a qualitative evaluation with nurses and received feedback clarifying their perceptions of the system. The results showed that the system correctly recognized medical staff, patient ID, and medication data in real time. With regards to workflow time, a significant reduction of time of clinical interventions was observed, when compared to a bar-coding system. In addition, on the nurses' evaluation, we received mostly positive comments although they also clarified some issues to consider with regards to operability and privacy issues. We concluded that the system had great potential for reducing medical errors and nurse workload with high efficiency.},
}
@article {pmid20460461,
year = {2010},
author = {Smith, AM and Heisler, LE and St Onge, RP and Farias-Hesson, E and Wallace, IM and Bodeau, J and Harris, AN and Perry, KM and Giaever, G and Pourmand, N and Nislow, C},
title = {Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples.},
journal = {Nucleic acids research},
volume = {38},
number = {13},
pages = {e142},
pmid = {20460461},
issn = {1362-4962},
support = {HG00317-05/HG/NHGRI NIH HHS/United States ; MOP-81340//Canadian Institutes of Health Research/Canada ; MOP-84305//Canadian Institutes of Health Research/Canada ; },
mesh = {Mutation ; Polymerase Chain Reaction ; Saccharomyces cerevisiae/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {Next-generation sequencing has proven an extremely effective technology for molecular counting applications where the number of sequence reads provides a digital readout for RNA-seq, ChIP-seq, Tn-seq and other applications. The extremely large number of sequence reads that can be obtained per run permits the analysis of increasingly complex samples. For lower complexity samples, however, a point of diminishing returns is reached when the number of counts per sequence results in oversampling with no increase in data quality. A solution to making next-generation sequencing as efficient and affordable as possible involves assaying multiple samples in a single run. Here, we report the successful 96-plexing of complex pools of DNA barcoded yeast mutants and show that such 'Bar-seq' assessment of these samples is comparable with data provided by barcode microarrays, the current benchmark for this application. The cost reduction and increased throughput permitted by highly multiplexed sequencing will greatly expand the scope of chemogenomics assays and, equally importantly, the approach is suitable for other sequence counting applications that could benefit from massive parallelization.},
}
@article {pmid20457097,
year = {2011},
author = {Dubey, B and Meganathan, PR and Haque, I},
title = {DNA mini-barcoding: an approach for forensic identification of some endangered Indian snake species.},
journal = {Forensic science international. Genetics},
volume = {5},
number = {3},
pages = {181-184},
doi = {10.1016/j.fsigen.2010.03.001},
pmid = {20457097},
issn = {1878-0326},
mesh = {Animals ; Base Sequence ; DNA/*genetics ; DNA Primers ; *Electronic Data Processing ; *Endangered Species ; Forensic Genetics ; Snakes/*genetics ; },
abstract = {Illegal trade of snake skin and uncontrolled hunting have instigated the extermination of many endangered snake species. Efforts to check illegal trade are often impeded due to lack of proper species identification methods. Hence, conservation strategies demand for authentic and quick identification techniques to trace the origin of the seized samples. This study employs DNA mini-barcoding as a method to identify some endangered snake species of India. We have designed two sets of novel primers for targeting regions within the mitochondrial Cytochrome Oxidase I gene to produce 175 bp and 245 bp amplicons. 175 bp fragment was amplified in all 11 snake species studied while the 245 bp amplicon was obtained in 10 species. DNA mini-barcodes recovered from these amplicons enabled the identification of snake species by retrieving the sequences available in public databases. The similarity scores ranging from 98 to 100% (98% taken as threshold value for species identification) signify the consistency of these mini-barcodes in snake species identification. Moreover, the results of the validation study confirm the effectiveness of the technique in forensic perspective, where the diagnostic morphological features of the seized sample are often missing.},
}
@article {pmid20456046,
year = {2010},
author = {Stockinger, H and Krüger, M and Schüßler, A},
title = {DNA barcoding of arbuscular mycorrhizal fungi.},
journal = {The New phytologist},
volume = {187},
number = {2},
pages = {461-474},
doi = {10.1111/j.1469-8137.2010.03262.x},
pmid = {20456046},
issn = {1469-8137},
mesh = {Base Sequence ; Cell Nucleus/genetics ; DNA, Fungal/*genetics ; DNA, Ribosomal Spacer/genetics ; Databases, Genetic ; Electronic Data Processing/*methods ; Genetic Variation ; Glomeromycota/*genetics ; Mycorrhizae/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
abstract = {*Currently, no official DNA barcode region is defined for the Fungi. The COX1 gene DNA barcode is difficult to apply. The internal transcribed spacer (ITS) region has been suggested as a primary barcode candidate, but for arbuscular mycorrhizal fungi (AMF; Glomeromycota) the region is exceptionably variable and does not resolve closely related species. *DNA barcoding analyses were performed with datasets from several phylogenetic lineages of the Glomeromycota. We tested a c. 1500 bp fragment spanning small subunit (SSU), ITS region, and large subunit (LSU) nuclear ribosomal DNA for species resolving power. Subfragments covering the complete ITS region, c. 800 bp of the LSU rDNA, and three c. 400 bp fragments spanning the ITS2, the LSU-D1 or LSU-D2 domains were also analysed. *Barcode gap analyses did not resolve all species, but neighbour joining analyses, using Kimura two-parameter (K2P) distances, resolved all species when based on the 1500 bp fragment. The shorter fragments failed to separate closely related species. *We recommend the complete 1500 bp fragment as a basis for AMF DNA barcoding. This will also allow future identification of AMF at species level based on 400 or 1000 bp amplicons in deep sequencing approaches.},
}
@article {pmid20437224,
year = {2010},
author = {Yang, B and Zhou, G and Huang, LL},
title = {PCR-free MDR1 polymorphism identification by gold nanoparticle probes.},
journal = {Analytical and bioanalytical chemistry},
volume = {397},
number = {5},
pages = {1937-1945},
doi = {10.1007/s00216-010-3750-4},
pmid = {20437224},
issn = {1618-2650},
mesh = {ATP Binding Cassette Transporter, Subfamily B ; ATP Binding Cassette Transporter, Subfamily B, Member 1/*genetics ; DNA Probes/chemistry/*genetics ; Gold/chemistry ; Humans ; Metal Nanoparticles/chemistry ; *Polymorphism, Single Nucleotide ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; Tandem Mass Spectrometry/*methods ; },
abstract = {Single nucleotide polymorphisms (SNPs) represent the most abundant source of genetic variation in the human genome, and they can be linked to genetic susceptibilities or varied pharmaceutical responses. Established SNP detection techniques are mainly PCR-based, which means that they involve complex, labor-intensive procedures, are easy contaminated, and can give false-positive results. Therefore, we have developed a simple and rapid MS-based disulfide barcode methodology that relies on magnifying the signal from a dual-modified gold nanoparticle. This approach permits direct SNP genotyping of total human genomic DNA without the need for primer-mediated enzymatic amplification. Disulfides that are attached to the gold nanoparticle serve as a "barcode" that allows different sequences to be discerned using MS detection. Specificity is based on two sequential oligonucleotide hybridizations, which include two steps: the first is the capture of the target by gene-specific probes immobilized onto magnetic beads; the second is the recognition of gold nanoparticles functionalized with allele-specific oligonucleotides. The sensitivity of this new method reaches down to the 0.1 fM range, thus approaching that of PCR. The feasability of this SNP identification methodology based on an MS-based disulfide barcode assay was demonstrated by applying it to genomic DNA samples representing all possible genotypes of the SNPs G2677T and C3435T in the human MDR1 gene. Due to its great advantage--the ability to perform SNP typing without the use of PCR--the assay was found to be simple, rapid and robust, and so may be highly suited to routine clinical detection as well as basic medical research.},
}
@article {pmid20435463,
year = {2010},
author = {Li, Y and Liu, B and Li, X and Wei, Q},
title = {Highly sensitive electrochemical detection of human telomerase activity based on bio-barcode method.},
journal = {Biosensors &amp; bioelectronics},
volume = {25},
number = {11},
pages = {2543-2547},
doi = {10.1016/j.bios.2010.04.009},
pmid = {20435463},
issn = {1873-4235},
mesh = {Biosensing Techniques/*instrumentation ; Conductometry/*instrumentation ; DNA/*chemistry ; Electronic Data Processing ; Enzyme Activation ; Equipment Design ; Equipment Failure Analysis ; HeLa Cells ; Humans ; Reproducibility of Results ; Sensitivity and Specificity ; Telomerase/*analysis/*chemistry ; },
abstract = {In the present study, an electrochemical method for highly sensitive detection of human telomerase activity was developed based on bio-barcode amplification assay. Telomerase was extracted from HeLa cells, then the extract was mixed with telomerase substrate (TS) primer to perform extension reaction. The extension product was hybridized with the capture DNA immobilized on the Au electrode and then reacted with the signal DNA on Au nanoparticles to form a sandwich hybridization mode. Electrochemical signals were generated by chronocoulometric interrogation of [Ru(NH(3))(6)](3+) that quantitatively binds to the DNA on Au nanoparticles via electrostatic interaction. This method can detect the telomerase activity from as little as 10 cultured cancer cells without the polymerase chain reaction (PCR) amplification of telomerase extension product.},
}
@article {pmid20435122,
year = {2010},
author = {Gao, T and Yao, H and Song, J and Liu, C and Zhu, Y and Ma, X and Pang, X and Xu, H and Chen, S},
title = {Identification of medicinal plants in the family Fabaceae using a potential DNA barcode ITS2.},
journal = {Journal of ethnopharmacology},
volume = {130},
number = {1},
pages = {116-121},
doi = {10.1016/j.jep.2010.04.026},
pmid = {20435122},
issn = {1872-7573},
mesh = {DNA, Plant/*genetics ; Fabaceae/*genetics ; Plants, Medicinal/*genetics ; Sequence Alignment ; Species Specificity ; },
abstract = {AIM OF THE STUDY: To test whether the ITS2 region is an effective marker for use in authenticating of the family Fabaceae which contains many important medicinal plants.<br><br>MATERIALS AND METHODS: The ITS2 regions of 114 samples in Fabaceae were amplified. Sequence assembly was assembled by CodonCode Aligner V3.0. In combination with sequences from public database, the sequences were aligned by Clustal W, and genetic distances were computed using MEGA V4.0. The intra- vs. inter-specific variations were assessed by six metrics, wilcoxon two-sample tests and "barcoding gaps". Species identification was accomplished using TaxonGAP V2.4, BLAST1 and the nearest distance method.<br><br>RESULTS: ITS2 sequences had considerable variation at the genus and species level. The intra-specific divergence ranged from 0% to 14.4%, with an average of 1.7%, and the inter-specific divergence ranged from 0% to 63.0%, with an average of 8.6%. Twenty-four species found in the Chinese Pharmacopoeia, along with another 66 species including their adulterants, were successfully identified based on ITS2 sequences. In addition, ITS2 worked well, with over 80.0% of species and 100% of genera being correctly differentiated for the 1507 sequences derived from 1126 species belonging to 196 genera.<br><br>CONCLUSIONS: Our findings support the notion that ITS2 can be used as an efficient and powerful marker and a potential barcode to distinguish various species in Fabaceae.},
}
@article {pmid20435119,
year = {2010},
author = {Srirama, R and Senthilkumar, U and Sreejayan, N and Ravikanth, G and Gurumurthy, BR and Shivanna, MB and Sanjappa, M and Ganeshaiah, KN and Shaanker, RU},
title = {Assessing species admixtures in raw drug trade of Phyllanthus, a hepato-protective plant using molecular tools.},
journal = {Journal of ethnopharmacology},
volume = {130},
number = {2},
pages = {208-215},
doi = {10.1016/j.jep.2010.04.042},
pmid = {20435119},
issn = {1872-7573},
mesh = {DNA, Chloroplast/*isolation &amp; purification ; *Electronic Data Processing ; India ; Medicine, Traditional ; Phyllanthus/classification/*genetics ; Phylogeny ; Plant Extracts/*chemistry/standards ; Polymerase Chain Reaction ; Quality Control ; *Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Phyllanthus (Euphorbiaceae) species are well known for their hepato-protective activity and are used in several ethno-medicines in indigenous health care systems in India.<br><br>AIM OF THE STUDY: To assess species admixtures in raw drug trade of Phyllanthus using morphological and DNA barcoding tools.<br><br>MATERIALS AND METHODS: Samples of Phyllanthus used in raw drug trade were obtained from 25 shops in southern India. Species admixtures in the samples were assessed by identifying species using morpho-taxonomic keys. These identities were further validated by developing species specific DNA barcode signatures using the chloroplast DNA region, psbA-trnH. DNA from the market samples were extracted and amplified using the forward (psbAF - GTTATGCATGAACGTAATGCTC) and reverse primer (trnHR - CGCGCATGGTGGATTCACAAATC). The amplified products were sequenced at Chromous Biotech India, Bangalore. The sequences were manually edited using Chromas Lite. Species identities were established by constructing a neighbor-joining tree using MEGA V 4.0.<br><br>RESULTS: Morphological analysis of market samples revealed six different species of Phyllanthus in the trade samples. Seventy-six percent of the market samples contained Phyllanthus amarus as the predominant species (>95%) and thus were devoid of admixtures. The remaining 24% of the shops had five different species of Phyllanthus namely Phyllanthus debilis, Phyllanthus fraternus, Phyllanthus urinaria, Phyllanthus maderaspatensis, and Phyllanthus kozhikodianus. All identities, except those for Phyllanthus fraternus, were further confirmed by the species specific DNA barcode using chloroplast region psbA-trnH.<br><br>CONCLUSION: Our results show that market samples of Phyllanthus sold in southern India contain at least six different species, though among them, Phyllanthus amarus is predominant. DNA barcode, psbA-trnH region of the chloroplast can effectively discriminate Phyllanthus species and hence can be used to resolve species admixtures in the raw drug trade of Phyllanthus.},
}
@article {pmid20428491,
year = {2009},
author = {Tekin, E and Coughlan, J},
title = {A Bayesian Algorithm for Reading 1D Barcodes.},
journal = {Proceedings. Canadian Conference on Computer and Robot Vision},
volume = {2009},
number = {},
pages = {61-67},
pmid = {20428491},
support = {R01 EY018890/EY/NEI NIH HHS/United States ; R01 EY018890-01/EY/NEI NIH HHS/United States ; },
abstract = {The 1D barcode is a ubiquitous labeling technology, with symbologies such as UPC used to label approximately 99% of all packaged goods in the US. It would be very convenient for consumers to be able to read these barcodes using portable cameras (e.g. mobile phones), but the limited quality and resolution of images taken by these cameras often make it difficult to read the barcodes accurately. We propose a Bayesian framework for reading 1D barcodes that models the shape and appearance of barcodes, allowing for geometric distortions and image noise, and exploiting the redundant information contained in the parity digit. An important feature of our framework is that it doesn't require that every barcode edge be detected in the image. Experiments on a publicly available dataset of barcode images explore the range of images that are readable, and comparisons with two commercial readers demonstrate the superior performance of our algorithm.},
}
@article {pmid20421943,
year = {2010},
author = {Matecic, M and Smith, DL and Pan, X and Maqani, N and Bekiranov, S and Boeke, JD and Smith, JS},
title = {A microarray-based genetic screen for yeast chronological aging factors.},
journal = {PLoS genetics},
volume = {6},
number = {4},
pages = {e1000921},
pmid = {20421943},
issn = {1553-7404},
support = {R24 DK082840/DK/NIDDK NIH HHS/United States ; R01 AG022685/AG/NIA NIH HHS/United States ; },
mesh = {Cellular Senescence ; Gene Expression Regulation, Fungal ; Mutation ; *Oligonucleotide Array Sequence Analysis ; Saccharomyces cerevisiae/*genetics/*physiology ; },
abstract = {Model organisms have played an important role in the elucidation of multiple genes and cellular processes that regulate aging. In this study we utilized the budding yeast, Saccharomyces cerevisiae, in a large-scale screen for genes that function in the regulation of chronological lifespan, which is defined by the number of days that non-dividing cells remain viable. A pooled collection of viable haploid gene deletion mutants, each tagged with unique identifying DNA "bar-code" sequences was chronologically aged in liquid culture. Viable mutants in the aging population were selected at several time points and then detected using a microarray DNA hybridization technique that quantifies abundance of the barcode tags. Multiple short- and long-lived mutants were identified using this approach. Among the confirmed short-lived mutants were those defective for autophagy, indicating a key requirement for the recycling of cellular organelles in longevity. Defects in autophagy also prevented lifespan extension induced by limitation of amino acids in the growth media. Among the confirmed long-lived mutants were those defective in the highly conserved de novo purine biosynthesis pathway (the ADE genes), which ultimately produces IMP and AMP. Blocking this pathway extended lifespan to the same degree as calorie (glucose) restriction. A recently discovered cell-extrinsic mechanism of chronological aging involving acetic acid secretion and toxicity was suppressed in a long-lived ade4Delta mutant and exacerbated by a short-lived atg16Delta autophagy mutant. The identification of multiple novel effectors of yeast chronological lifespan will greatly aid in the elucidation of mechanisms that cells and organisms utilize in slowing down the aging process.},
}
@article {pmid20420717,
year = {2010},
author = {Virgilio, M and Backeljau, T and Nevado, B and De Meyer, M},
title = {Comparative performances of DNA barcoding across insect orders.},
journal = {BMC bioinformatics},
volume = {11},
number = {},
pages = {206},
pmid = {20420717},
issn = {1471-2105},
mesh = {Animals ; DNA/*chemistry ; Evolution, Molecular ; Genetic Variation ; Insecta/*classification/*genetics ; Species Specificity ; },
abstract = {BACKGROUND: Previous studies on insect DNA barcoding provide contradictory results and suggest not consistent performances across orders. This work aims at providing a general evaluation of insect DNA barcoding and "mini-barcoding" by performing simulations on a large database of 15,948 DNA barcodes. We compared the proportions of correctly identified queries across a) six insect orders (Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera and Orthoptera), b) four identification criteria (Best Match: BM; Best Close Match: BCM; All Species Barcodes: ASB; tree-based identification: NJT), and c) reference databases with different taxon coverage (100, 500, 1,000, 1,500 and 1,995 insect species).<br><br>RESULTS: Analysis of variance revealed highly significant differences among ID criteria and insect orders. A posteriori comparisons of means showed that NJT had always a significantly lower identification success (NJT = 0.656, S.D. = 0.118) compared to both BM and BCM (BM = 0.948, S.D. = 0.026; BCM = 0.946, S.D. = 0.031). NJT showed significant variations among orders, with the highest proportion of correctly identified queries in Hymenoptera and Orthoptera and the lowest in Diptera. Conversely, the proportions of correct matches of BM and BCM were consistent across orders but a progressive increase in false identification was observed when larger reference databases were used.<br><br>CONCLUSIONS: Regardless the relatively low proportion of Type I errors (misidentification of queries which are represented in the reference database) of BM and BCM, the lack of reference DNA barcodes for 98% of the known insect species implies that insect DNA barcoding is heavily biased by Type II errors (misidentification of queries without conspecifics in the database). The detrimental effects of Type II errors could be circumvented if insect DNA barcoding is used to verify the lack of correspondence between a query and a list of properly referenced target species (e.g. insect pests). This "negative identification" would only be subjected to Type I errors and could be profitably adopted in insect quarantine procedures.},
}
@article {pmid20418427,
year = {2010},
author = {Hyman, RW and St Onge, RP and Allen, EA and Miranda, M and Aparicio, AM and Fukushima, M and Davis, RW},
title = {Multiplex identification of microbes.},
journal = {Applied and environmental microbiology},
volume = {76},
number = {12},
pages = {3904-3910},
pmid = {20418427},
issn = {1098-5336},
support = {P01 HG000205/HG/NHGRI NIH HHS/United States ; },
mesh = {Bacteriological Techniques/*methods ; Communicable Diseases/*diagnosis ; Female ; Humans ; *Molecular Probe Techniques ; Nucleic Acid Hybridization/*methods ; Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; Vagina/microbiology ; },
abstract = {We have adapted molecular inversion probe technology to identify microbes in a highly multiplexed procedure. This procedure does not require growth of the microbes. Rather, the technology employs DNA homology twice: once for the molecular probe to hybridize to its homologous DNA and again for the 20-mer oligonucleotide barcode on the molecular probe to hybridize to a commercially available molecular barcode array. As proof of concept, we have designed, tested, and employed 192 molecular probes for 40 microbes. While these particular molecular probes are aimed at our interest in the microbes in the human vagina, this molecular probe method could be employed to identify the microbes in any ecological niche.},
}
@article {pmid20410032,
year = {2010},
author = {Lowenstein, JH and Burger, J and Jeitner, CW and Amato, G and Kolokotronis, SO and Gochfeld, M},
title = {DNA barcodes reveal species-specific mercury levels in tuna sushi that pose a health risk to consumers.},
journal = {Biology letters},
volume = {6},
number = {5},
pages = {692-695},
pmid = {20410032},
issn = {1744-957X},
support = {P30 ES005022/ES/NIEHS NIH HHS/United States ; P30ES005022/ES/NIEHS NIH HHS/United States ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Humans ; Mercury/*analysis ; Seafood/*analysis ; Species Specificity ; Tuna/*genetics ; },
abstract = {Excessive ingestion of mercury--a health hazard associated with consuming predatory fishes--damages neurological, sensory-motor and cardiovascular functioning. The mercury levels found in Bigeye Tuna (Thunnus obesus) and bluefin tuna species (Thunnus maccoyii, Thunnus orientalis, and Thunnus thynnus), exceed or approach levels permissible by Canada, the European Union, Japan, the US, and the World Health Organization. We used DNA barcodes to identify tuna sushi samples analysed for mercury and demonstrate that the ability to identify cryptic samples in the market place allows regulatory agencies to more accurately measure the risk faced by fish consumers and enact policies that better safeguard their health.},
}
@article {pmid20405123,
year = {2010},
author = {Begerow, D and Nilsson, H and Unterseher, M and Maier, W},
title = {Current state and perspectives of fungal DNA barcoding and rapid identification procedures.},
journal = {Applied microbiology and biotechnology},
volume = {87},
number = {1},
pages = {99-108},
doi = {10.1007/s00253-010-2585-4},
pmid = {20405123},
issn = {1432-0614},
mesh = {Biodiversity ; DNA, Fungal/*genetics ; Fungal Proteins/genetics ; Fungi/classification/genetics/*isolation &amp; purification ; Mycological Typing Techniques/*methods ; },
abstract = {Fungal research is experiencing a new wave of methodological improvements that most probably will boost mycology as profoundly as molecular phylogeny has done during the last 15 years. Especially the next generation sequencing technologies can be expected to have a tremendous effect on fungal biodiversity and ecology research. In order to realise the full potential of these exciting techniques by accelerating biodiversity assessments, identification procedures of fungi need to be adapted to the emerging demands of modern large-scale ecological studies. But how should fungal species be identified in the near future? While the answer might seem trivial to most microbiologists, taxonomists working with fungi may have other views. In the present review, we will analyse the state of the art of the so-called barcoding initiatives in the light of fungi, and we will seek to evaluate emerging trends in the field. We will furthermore demonstrate that the usability of DNA barcoding as a major tool for identification of fungi largely depends on the development of high-quality sequence databases that are thoroughly curated by taxonomists and systematists.},
}
@article {pmid20400228,
year = {2010},
author = {Nejsum, P and Bertelsen, MF and Betson, M and Stothard, JR and Murrell, KD},
title = {Molecular evidence for sustained transmission of zoonotic Ascaris suum among zoo chimpanzees (Pan troglodytes).},
journal = {Veterinary parasitology},
volume = {171},
number = {3-4},
pages = {273-276},
doi = {10.1016/j.vetpar.2010.03.030},
pmid = {20400228},
issn = {1873-2550},
mesh = {Animals ; Animals, Zoo ; Ape Diseases/*parasitology ; Ascariasis/*veterinary ; *Ascaris suum ; Feces/parasitology ; Humans ; Larva ; Ovum ; *Pan troglodytes ; Parasite Egg Count/veterinary ; },
abstract = {Chimpanzees in the Copenhagen Zoo frequently excrete ascarid worms onto the cage floor in spite of a regular anthelmintic treatment program. Previously it had been shown that the source of the infections was of pig origin. However, it was unknown whether the recurrence of the infection was due to reintroduction of eggs from an external source or to a sustained transmission cycle within the zoo. We found that isolated eggs were able to embryonate to the infective J3 stage and PCR-RFLP analysis on the ITS region amplified from single embryonated eggs suggest these to be Ascaris suum. In addition, sequence analysis of the cox1 gene ('barcoding') on expelled worms followed by cluster analysis revealed that the chimpanzees are infected with pig A. suum which now, in spite of control efforts, has stabilized into a permanent transmission cycle in the zoo's chimpanzee troop.},
}
@article {pmid20398625,
year = {2010},
author = {Lau, IP and Ngan, EK and Loo, J and Suen, YK and Ho, HP and Kong, SK},
title = {Aptamer-based bio-barcode assay for the detection of cytochrome-c released from apoptotic cells.},
journal = {Biochemical and biophysical research communications},
volume = {395},
number = {4},
pages = {560-564},
doi = {10.1016/j.bbrc.2010.04.066},
pmid = {20398625},
issn = {1090-2104},
mesh = {*Apoptosis ; Aptamers, Nucleotide/*chemistry ; Base Sequence ; Cytochromes c/*analysis/metabolism ; Humans ; *Immunoassay ; },
abstract = {The recently developed bio-barcode (BBC) assay using polymerase chain reaction (PCR) to generate signals has been shown to be an extraordinarily sensitive method to detect protein targets. The BBC assay involves a magnetic microparticle (with antibody to capture the target of interest) and gold nanoparticle (with recognition antibody and thiolated single-stranded barcode DNAs) to form a sandwich around the target. The concentration of target is determined by the amount of barcode DNA released from the nanoparticles. Here we describe a modification using aptamers to substitute the gold nanoparticles for the BBC assay. In this study, we isolated a 76-mer monoclonal aptamer against cytochrome-c (cyto-c) and this single-stranded DNA in defined 3D structure for cyto-c was used in the BBC assay for both recognition and readout reporting. After magnetic separation, the aptamer was amplified by PCR and this aptamer-based barcode (ABC) assay was sensitive enough to detect the cyto-c in culture medium released from the apoptotic cells after drug treatment at the picomolar level. When compared to the conventional cyto-c detection by Western blot analysis, our ABC assay is sensitive, and time for the detection and quantification with ready-made probes was only 3 h.},
}
@article {pmid20381646,
year = {2010},
author = {Augot, D and Sauvage, F and Jouet, D and Simphal, E and Veuille, M and Couloux, A and Kaltenbach, ML and Depaquit, J},
title = {Discrimination of Culicoides obsoletus and Culicoides scoticus, potential bluetongue vectors, by morphometrical and mitochondrial cytochrome oxidase subunit I analysis.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {10},
number = {5},
pages = {629-637},
doi = {10.1016/j.meegid.2010.03.016},
pmid = {20381646},
issn = {1567-7257},
mesh = {Animals ; Bluetongue/epidemiology/*transmission ; Bluetongue virus ; Ceratopogonidae/*anatomy &amp; histology/*classification/enzymology/genetics ; DNA, Mitochondrial/analysis ; Electron Transport Complex IV/*genetics ; Female ; Insect Vectors/*anatomy &amp; histology/*classification/enzymology/genetics ; Male ; Mitochondria/*enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Principal Component Analysis ; Protein Subunits/*genetics ; },
abstract = {Biting midges of the Culicoides obsoletus Meigen species complex (Diptera: Ceratopogonidae) are increasingly suspected as vectors of the recent emergence of bluetongue virus in Europe. Within this complex, identification of the C. obsoletus and Culicoides scoticus females is considered as difficult or sometimes not possible while the identification of males is easy, based on genitalia observation. Nolan et al. (2007) concluded that the distinction of C. obsoletus and C. scoticus females is not possible according to morphology but require molecular analyses. In 2010, the identification of biting midges is done under a stereomicroscope without specific identification within the C. obsoletus species complex. However, such a specific identification distinguishing C. obsoletus s. str. and C. scoticus s. str. is crucial to identify the European competent vectors of the virus, their relative abundances and then accurately assess the risk. We performed morphometric analyses of head, genitalia and thorax of females combined with sequencing of the cytochrome oxidase I barcode fragment of mitochondrial DNA on 88 specimens in order to have a molecular identification of our sampled species. As we knew the actual species of individuals thanks to molecular results, we explored the discriminant power of 15 morphometric variables to distinguish the females according to their species. Multivariate analyses were performed on the morphometric measurements to identify and validate a combination of variables leading to an accurate species identification. It appears that females of C. obsoletus and C. scoticus can be accurately distinguished based on only four variables: width between chitinous plates, length and width of spermathecae1 and length of spermatheca2. This approach should improve the accuracy of morphologically-based species identification.},
}
@article {pmid20380765,
year = {2010},
author = {Hanelt, B and Mwangi, IN and Kinuthia, JM and Maina, GM and Agola, LE and Mutuku, MW and Steinauer, ML and Agwanda, BR and Kigo, L and Mungai, BN and Loker, ES and Mkoji, GM},
title = {Schistosomes of small mammals from the Lake Victoria Basin, Kenya: new species, familiar species, and implications for schistosomiasis control.},
journal = {Parasitology},
volume = {137},
number = {7},
pages = {1109-1118},
doi = {10.1017/S0031182010000041},
pmid = {20380765},
issn = {1469-8161},
support = {1P20RR18754/RR/NCRR NIH HHS/United States ; AI044913/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Disease Reservoirs ; Humans ; Kenya ; Muridae/*parasitology ; Rodent Diseases/*epidemiology/*parasitology/prevention &amp; control/transmission ; Schistosoma/*classification/genetics/*isolation &amp; purification ; Schistosomiasis/parasitology/prevention &amp; control/transmission/*veterinary ; Shrews/*parasitology ; Species Specificity ; },
abstract = {Recent schistosomiasis control efforts in sub-Saharan Africa have focused nearly exclusively on treatment of humans with praziquantel. However, the extent to which wild mammals act as reservoirs for Schistosoma mansoni and therefore as sources of renewed transmission following control efforts is poorly understood. With the objective to study the role of small mammals as reservoir hosts, 480 animals belonging to 9 rodent and 1 insectivore species were examined for infection with schistosomes in Kisumu, in the Lake Victoria Basin, Kenya. Animals were collected from 2 sites: near the lakeshore and from Nyabera Marsh draining into the lake. A total of 6.0% of the animals captured, including 5 murid rodent species and 1 species of shrew (Crocidura olivieri) were infected with schistosomes. Four schistosome species were recovered and identified using cox1 DNA barcoding: S. mansoni, S. bovis, S. rodhaini and S. kisumuensis, the latter of which was recently described from Nyabera Marsh. Schistosoma mansoni and S. rodhaini were found infecting the same host individual (Lophuromys flavopunctatus), suggesting that this host species could be responsible for the production of hybrid schistosomes found in the area. Although the prevalence of S. mansoni infection in these reservoir populations was low (1.5%), given their potentially vast population size, their impact on transmission needs further study. Reservoir hosts could perpetuate snail infections and favour renewed transmission to humans once control programmes have ceased.},
}
@article {pmid20379956,
year = {2010},
author = {Pang, X and Song, J and Zhu, Y and Xie, C and Chen, S},
title = {Using DNA barcoding to identify species within Euphorbiaceae.},
journal = {Planta medica},
volume = {76},
number = {15},
pages = {1784-1786},
doi = {10.1055/s-0030-1249806},
pmid = {20379956},
issn = {1439-0221},
mesh = {Classification/methods ; *DNA Barcoding, Taxonomic ; DNA, Intergenic/chemistry ; Euphorbiaceae/*classification/genetics ; Genes, Plant ; Species Specificity ; },
abstract = {In this study, we tested the applicability of four DNA regions (rbcL, matK, ITS, and ITS2) as barcodes for identifying species within Euphorbiaceae. Based on assessments of the specific genetic divergence, the DNA barcoding gap, and the ability for species discrimination, the present results affirmed that ITS/ITS2 is a potential barcode for the Euphorbiaceae species. This study also provided a large-scale test to evaluate the effectiveness of ITS/ITS2 for differentiating species within Euphorbiaceae. Of the 1183 plant samples collected from 871 species in 66 diverse genera, ITS/ITS2 successfully identified > 90% and 100% of them at the species and genus levels, respectively. Therefore, our research indicates that use of the ITS/ITS2 region is a powerful technique for Euphorbiaceae identification.},
}
@article {pmid20376349,
year = {2010},
author = {Pöppe, J and Sutcliffe, P and Hooper, JN and Wörheide, G and Erpenbeck, D},
title = {CO I barcoding reveals new clades and radiation patterns of Indo-Pacific sponges of the family Irciniidae (Demospongiae: Dictyoceratida).},
journal = {PloS one},
volume = {5},
number = {4},
pages = {e9950},
pmid = {20376349},
issn = {1932-6203},
mesh = {Animals ; Biological Evolution ; DNA/*analysis ; Electron Transport Complex IV/*genetics ; Electronic Data Processing/*methods ; Genetic Markers ; Oceans and Seas ; Porifera/*genetics ; },
abstract = {BACKGROUND: DNA barcoding is a promising tool to facilitate a rapid and unambiguous identification of sponge species. Demosponges of the order Dictyoceratida are particularly challenging to identify, but are of ecological as well as biochemical importance.<br><br>Here we apply DNA barcoding with the standard CO1-barcoding marker on selected Indo-Pacific specimens of two genera, Ircinia and Psammocinia of the family Irciniidae. We show that the CO1 marker identifies several species new to science, reveals separate radiation patterns of deep-sea Ircinia sponges and indicates dispersal patterns of Psammocinia species. However, some species cannot be unambiguously barcoded by solely this marker due to low evolutionary rates.<br><br>CONCLUSIONS/SIGNIFICANCE: We support previous suggestions for a combination of the standard CO1 fragment with an additional fragment for sponge DNA barcoding.},
}
@article {pmid20376348,
year = {2010},
author = {Jennings, RM and Bucklin, A and Pierrot-Bults, A},
title = {Barcoding of arrow worms (Phylum Chaetognatha) from three oceans: genetic diversity and evolution within an enigmatic phylum.},
journal = {PloS one},
volume = {5},
number = {4},
pages = {e9949},
pmid = {20376348},
issn = {1932-6203},
mesh = {Animals ; *Biological Evolution ; DNA, Mitochondrial/analysis ; Electron Transport Complex IV/genetics ; *Electronic Data Processing ; *Genetic Variation ; Oceans and Seas ; Plankton/*genetics ; },
abstract = {Arrow worms (Phylum Chaetognatha) are abundant planktonic organisms and important predators in many food webs; yet, the classification and evolutionary relationships among chaetognath species remain poorly understood. A seemingly simple body plan is underlain by subtle variation in morphological details, obscuring the affinities of species within the phylum. Many species achieve near global distributions, spanning the same latitudinal bands in all ocean basins, while others present disjunct ranges, in some cases with the same species apparently found at both poles. To better understand how these complex evolutionary and geographic variables are reflected in the species makeup of chaetognaths, we analyze DNA barcodes of the mitochondrial cytochrome oxidase c subunit I (COI) gene, from 52 specimens of 14 species of chaetognaths collected mainly from the Atlantic Ocean. Barcoding analysis was highly successful at discriminating described species of chaetognaths across the phylum, and revealed little geographical structure. This barcode analysis reveals hitherto unseen genetic variation among species of arrow worms, and provides insight into some species relationships of this enigmatic group.},
}
@article {pmid20369192,
year = {2010},
author = {Rauf, S and Glidle, A and Cooper, JM},
title = {Application of quantum dot barcodes prepared using biological self-assembly to multiplexed immunoassays.},
journal = {Chemical communications (Cambridge, England)},
volume = {46},
number = {16},
pages = {2814-2816},
doi = {10.1039/b927149j},
pmid = {20369192},
issn = {1364-548X},
mesh = {Animals ; Biotin/*chemistry ; Immunoassay/*methods ; *Magnetics ; Models, Molecular ; *Quantum Dots ; Rabbits ; Streptavidin/*chemistry ; },
abstract = {We report upon the application of quantum dot barcodes prepared by layer-by-layer biological self-assembly of quantum dot-biotin and quantum dot-streptavidin conjugates on magnetic beads for qualitative multiplexed immunoassay.},
}
@article {pmid20354712,
year = {2010},
author = {Bruni, I and De Mattia, F and Galimberti, A and Galasso, G and Banfi, E and Casiraghi, M and Labra, M},
title = {Identification of poisonous plants by DNA barcoding approach.},
journal = {International journal of legal medicine},
volume = {124},
number = {6},
pages = {595-603},
pmid = {20354712},
issn = {1437-1596},
mesh = {DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*classification/genetics ; Forensic Genetics/*methods ; Genetic Markers ; Nucleic Acid Amplification Techniques ; Plant Proteins/analysis ; Plants, Toxic/*classification/*genetics ; Sequence Alignment ; Species Specificity ; },
abstract = {The plant exposures are one of the most frequent poisonings reported to poison control centres. The diagnosis of intoxicated patients is usually based on the morphological analysis of ingested plant portions; this procedure requires experience in systematic botany, because the plant identification is based on few evident traits. The objective of this research is to test DNA barcoding approach as a new universal tool to identify toxic plants univocally and rapidly. Five DNA barcode regions were evaluated: three cpDNA sequences (trnH-psbA, rpoB and matK) and two nuclear regions (At103 and sqd1). The performance of these markers was evaluated in three plant groups: (1) a large collection of angiosperms containing different toxic substances, (2) congeneric species showing different degrees of toxicity and (3) congeneric edible and poisonous plants. Based on assessments of PCR, sequence quality and resolution power in species discrimination, we recommend the combination of plastidial and nuclear markers to identify toxic plants. Concerning plastidial markers, matK and trnH-psbA showed consistent genetic variability. However, in agreement with CBOL Plant Working Group, we selected matK as the best marker, because trnH-psbA showed some problems in sequences sizes and alignments. As a final and relevant observation, we also propose the combination of matK with a nuclear marker such as At103 to distinguish toxic hybrids form parental species. In conclusion, our data support the claim that DNA barcoding is a powerful tool for poisonous plant identifications.},
}
@article {pmid20336381,
year = {2011},
author = {Feng, Y and Li, Q and Kong, L and Zheng, X},
title = {DNA barcoding and phylogenetic analysis of Pectinidae (Mollusca: Bivalvia) based on mitochondrial COI and 16S rRNA genes.},
journal = {Molecular biology reports},
volume = {38},
number = {1},
pages = {291-299},
pmid = {20336381},
issn = {1573-4978},
mesh = {Animals ; Bayes Theorem ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Mitochondria/*enzymology/*genetics ; Molecular Sequence Data ; Pectinidae/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {DNA sequence data enable not only the inference of phylogenetic relationships but also provide an efficient method for species-level identifications under the terms DNA barcoding or DNA taxonomy. In this study, we have sequenced partial sequences of mitochondrial COI and 16S rRNA genes from 63 specimens of 8 species of Pectinidae to assess whether DNA barcodes can efficiently distinguish these species. Sequences from homologous regions of four other species of this family were gathered from GenBank. Comparisons of within and between species levels of sequence divergence showed that genetic variation between species exceeds variation within species. When using neighbour-joining clustering based on COI and 16S genes, all species fell into reciprocally monophyletic clades with high bootstrap values. These evidenced that these scallop species can be efficiently identified by DNA barcoding. Evolutionary relationships of Pectinidae were also examined using the two mitochondrial genes. The results are almost consistent with Waller's classification, which was proposed on the basis of shell microstructure and the morphological characteristics of juveniles.},
}
@article {pmid20331683,
year = {2011},
author = {Pasanen, T and Kotila, SM and Horsma, J and Virolainen, A and Jalava, J and Ibrahem, S and Antikainen, J and Mero, S and Tarkka, E and Vaara, M and Tissari, P},
title = {Comparison of repetitive extragenic palindromic sequence-based PCR with PCR ribotyping and pulsed-field gel electrophoresis in studying the clonality of Clostridium difficile.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {17},
number = {2},
pages = {166-175},
doi = {10.1111/j.1469-0691.2010.03221.x},
pmid = {20331683},
issn = {1469-0691},
mesh = {Bacterial Typing Techniques/*methods ; Clostridioides difficile/*classification/genetics ; Cluster Analysis ; Electrophoresis, Gel, Pulsed-Field/*methods ; Humans ; Molecular Epidemiology/methods ; Polymerase Chain Reaction/*methods ; Ribotyping/*methods ; },
abstract = {Clostridium difficile infection is most often induced by antibiotic treatment. Recently, morbidity and mortality resulting especially from C. difficile PCR ribotype 027 have increased significantly. In addition, more severe disease has been associated with C. difficile PCR ribotype 078 strains. Thus, reliable typing methods for epidemic control are needed. In the present study, we compared an automated repetitive extragenic palindromic sequence-based PCR (rep-PCR) method (DiversiLab; Bacterial Barcodes, Inc., Athens, GA, USA) to PCR ribotyping and pulsed-field gel electrophoresis (PFGE) typing using 205 isolates of C. difficile (including 24 previously characterized isolates). Among the 181 clinical isolates, a total of 31 different PCR ribotypes, 38 different PFGE types and subtypes and 28 different rep-PCR types were found. Six major rep-PCR groups (DL1-DL6) harboured 86% of the clinical isolates. All isolates belonging to PCR ribotypes 027 and 001 clustered in their own rep-PCR groups, enabling us to screen out the hypervirulent ribotype 027 strain. Within the PCR ribotype 001, four subgroups were found using rep-PCR. Overall, in 75% (135/181) of the isolates, the classification attributed following rep-PCR and PCR ribotyping was comparable. In conclusion, the automated rep-PCR-based typing method represents an option for first-line molecular typing in local clinical microbiology laboratories. The method was easy to use as well as rapid, requiring less hands-on time than PCR ribotyping or PFGE typing. The conventional PCR ribotyping or PFGE, however, are needed for confirmatory molecular epidemiology. In addition, more epidemiology-oriented studies are needed to examine the discriminatory power of automated rep-PCR with isolates collected from a larger geographical area and during a longer period of time.},
}
@article {pmid20307671,
year = {2010},
author = {Seabra, SG and Pina-Martins, F and Marabuto, E and Yurtsever, S and Halkka, O and Quartau, JA and Paulo, OS},
title = {Molecular phylogeny and DNA barcoding in the meadow-spittlebug Philaenus spumarius (Hemiptera, Cercopidae) and its related species.},
journal = {Molecular phylogenetics and evolution},
volume = {56},
number = {1},
pages = {462-467},
doi = {10.1016/j.ympev.2010.03.023},
pmid = {20307671},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Genes, Insect ; Genes, Mitochondrial ; Haplotypes ; Hemiptera/classification/*genetics ; Likelihood Functions ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; },
abstract = {Philaenus spumarius, widely studied for its colour/pattern polymorphism, is a widespread species across the Holartic. The patterns of haplotype divergence at the mitochondrial gene cytochrome oxidase I (COI) found in this study suggest a postglacial western Europe (Iberian and Italian peninsulas to Britain) and a eastern (from Near East to Finland) south-to-north colonization. The haplotypes found in North America are most likely derived from the British haplotypes. The barcode fragment used here allowed the distinction of the species within genus Philaenus and questioned some taxonomic identifications of sequences present in Genbank.},
}
@article {pmid20304573,
year = {2010},
author = {Pohjoismäki, JL and Karhunen, PJ and Goebeler, S and Saukko, P and Sääksjärvi, IE},
title = {Indoors forensic entomology: colonization of human remains in closed environments by specific species of sarcosaprophagous flies.},
journal = {Forensic science international},
volume = {199},
number = {1-3},
pages = {38-42},
doi = {10.1016/j.forsciint.2010.02.033},
pmid = {20304573},
issn = {1872-6283},
mesh = {Adult ; Animals ; Cadaver ; Diptera/*physiology ; Electron Transport Complex IV/genetics ; Entomology ; *Environment, Controlled ; Feeding Behavior/*physiology ; Forensic Pathology ; Humans ; Larva ; Male ; Middle Aged ; *Postmortem Changes ; Temperature ; },
abstract = {Fly species that are commonly recovered on human corpses concealed in houses or other dwellings are often dependent on human created environments and might have special features in their biology that allow them to colonize indoor cadavers. In this study we describe nine typical cases involving forensically relevant flies on human remains found indoors in southern Finland. Eggs, larvae and puparia were reared to adult stage and determined to species. Of the five species found the most common were Lucilia sericata Meigen, Calliphora vicina Robineau-Desvoidy and Protophormia terraenovae Robineau-Desvoidy. The flesh fly Sarcophaga caerulescens Zetterstedt is reported for the first time to colonize human cadavers inside houses and a COI gene sequence based DNA barcode is provided for it to help facilitate identification in the future. Fly biology, colonization speed and the significance of indoors forensic entomological evidence are discussed.},
}
@article {pmid20231892,
year = {2010},
author = {Azpurua, J and De La Cruz, D and Valderama, A and Windsor, D},
title = {Lutzomyia sand fly diversity and rates of infection by Wolbachia and an exotic Leishmania species on Barro Colorado Island, Panama.},
journal = {PLoS neglected tropical diseases},
volume = {4},
number = {3},
pages = {e627},
pmid = {20231892},
issn = {1935-2735},
mesh = {Animals ; Cluster Analysis ; DNA, Protozoan/genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Insect Proteins/genetics ; Leishmania/genetics/*isolation &amp; purification ; Molecular Sequence Data ; Panama ; Phylogeny ; Psychodidae/*classification/genetics/microbiology/parasitology ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Wolbachia/*isolation &amp; purification ; },
abstract = {BACKGROUND: Sand flies (Diptera, Psychodidae, Phlebotominae) in the genus Lutzomyia are the predominant vectors of the protozoan disease leishmaniasis in the New World. Within the watershed of the Panama Canal, the cutaneous form of leishmaniasis is a continuous health threat for residents, tourists and members of an international research community. Here we report the results of screening a tropical forest assemblage of sand fly species for infection by both Leishmania and a microbe that can potentially serve in vector population control, the cytoplasmically transmitted rickettsia, Wolbachia pipientis. Knowing accurately which Lutzomyia species are present, what their evolutionary relationships are, and how they are infected by strains of both Leishmania and Wolbachia is of critical value for building strategies to mitigate the impact of this disease in humans.<br><br>METHODOLOGY AND FINDINGS: We collected, sorted and then used DNA sequences to determine the diversity and probable phylogenetic relationships of the Phlebotominae occurring in the understory of Barro Colorado Island in the Republic of Panama. Sequence from CO1, the DNA barcoding gene, supported 18 morphology-based species determinations while revealing the presence of two possible "cryptic" species, one (Lu. sp. nr vespertilionis) within the Vespertilionis group, the other (Lu. gomezi) within the Lutzomyia-cruciata series. Using ITS-1 and "minicircle" primers we detected Leishmania DNA in 43.3% of Lu. trapidoi, 26.3% of Lu. gomezi individuals and in 0% of the other 18 sand fly species. Identical ITS-1 sequence was obtained from the Leishmania infecting Lu. trapidoi and Lu. gomezi, sequence which was 93% similar to Leishmania (viannia) naiffi in GenBank, a species previously unknown in Panama, but recognized as a type of cutaneous leishmaniasis vectored broadly across northern and central South America. Distinct strains of the intracellular bacterium Wolbachia were detected in three of 20 sand fly species, including Lu. trapidoi, in which it frequently co-occurred with Leishmania.<br><br>CONCLUSIONS: Both morphological and molecular methods were used to examine an assemblage of 20 sand fly species occurring in the forests of the Panama Canal area. Two of these species, members of separate clades, were found to carry Leishmania at high frequency and hence are likely vectors of leishmaniasis to humans or other mammal species. A single Leishmania species, identified with high confidence as Le. naiffi, was carried by both species. That Le. naiffi is known to cause cutaneous lesions in South America but has hitherto not been reported or implicated in Panama opens the possibility that its range has recently expanded to include the Isthmus or that it occurs as a recent introduction. The occurrence of Leishmania and Wolbachia in Lu. trapidoi identifies one important vector of the disease as a potential target for gene introductions using Wolbachia population sweeps.},
}
@article {pmid20230234,
year = {2010},
author = {Valdivia-Granda, WA},
title = {Bioinformatics for biodefense: challenges and opportunities.},
journal = {Biosecurity and bioterrorism : biodefense strategy, practice, and science},
volume = {8},
number = {1},
pages = {69-77},
doi = {10.1089/bsp.2009.0024},
pmid = {20230234},
issn = {1557-850X},
mesh = {Bioterrorism/*prevention &amp; control ; Civil Defense ; *Computational Biology ; DNA, Ribosomal ; Electronic Data Processing ; *Information Dissemination ; Molecular Sequence Data ; Policy Making ; Toxins, Biological/genetics ; United States ; },
abstract = {The intentional release of traditional or combinatorial bioweapons remains one of the most important challenges that will continue to shape homeland security. The misuse of dual-use and how-to methods and techniques in the fields of molecular, synthetic, and computational biology can lessen the technical barriers for launching attacks, even for small groups or individuals. Bioinformatics is guiding the implementation of several biodefense countermeasures. However, existing algorithms have not effectively translated available pathogen genomic data into standardized diagnostics, rational vaccine development, or broad spectrum therapeutics. Despite its potential, bioinformatics has a limited impact on forensic and intelligence operations. More than 12 biodefense databases and information exchange architectures lack interoperability and a common layer that restricts scalability and the development of biodefense enterprises. Therefore, in order to use next-generation genome sequencing for medical intelligence, forensic operations, biothreat awareness, and mitigation, the attention has to be redirected toward the development of computational biology applications. This article debates some of the challenges that the bioinformatics field confronts in terms of biodefense problems and proposes potential opportunities to use pathogen genomic data. Issues related to the analysis of pathogen genomes and emerging methods including genomic barcoding, active curation, and knowledge management and their impact on intelligence, forensics, and policymaking are discussed.},
}
@article {pmid20217641,
year = {2010},
author = {He, J and Wong, KL and Shaw, PC and Wang, H and Li, DZ},
title = {Identification of the medicinal plants in Aconitum L. by DNA barcoding technique.},
journal = {Planta medica},
volume = {76},
number = {14},
pages = {1622-1628},
doi = {10.1055/s-0029-1240967},
pmid = {20217641},
issn = {1439-0221},
mesh = {Aconitum/*genetics ; Base Sequence ; *DNA Barcoding, Taxonomic ; DNA, Intergenic/chemistry ; *Genes, Plant ; Genetic Variation ; Molecular Sequence Data ; },
abstract = {Plants of the genus Aconitum L. are commonly used in Asia for medicinal purposes. Although they are widely cultivated and marketed, there has been uncertainty about the efficacy of different species, and therefore accurate identification is crucial. To determine the genetic variation among these medicinal plants, the proposed DNA barcode PSBA- TRNH intergenic spacer of 134 individuals from 19 taxa of ACONITUM were sequenced. Among the two most commonly used medicinal ACONITUM species, A. carmichaeli and A. kusnezoffii, sequence inversions were observed. The studied samples were clustered into ten groups according to the sequence alignment and most of the tested Aconitum species could be differentiated by the PSBA -TRNH intergenic spacer.},
}
@article {pmid20204529,
year = {2010},
author = {Margam, VM and Gachomo, EW and Shukle, JH and Ariyo, OO and Seufferheld, MJ and Kotchoni, SO},
title = {A simplified arthropod genomic-DNA extraction protocol for polymerase chain reaction (PCR)-based specimen identification through barcoding.},
journal = {Molecular biology reports},
volume = {37},
number = {7},
pages = {3631-3635},
pmid = {20204529},
issn = {1573-4978},
mesh = {Animals ; Arthropods/*classification/*genetics ; DNA/*genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Genome/*genetics ; Polymerase Chain Reaction/*methods ; },
abstract = {Genomic DNA extraction protocols generally require the use of expensive and hazardous reagents necessary for decontamination of phenolic compounds from the extracts. In addition, they are lengthy, hindering large-scale sample extractions necessary for high-throughput analyses. Here we describe a simple, time and cost-efficient method for genomic DNA extraction from insects. The extracted DNA was successfully used in a Polymerase Chain Reaction (PCR), making it suitable for automation for large-scale genetic analysis and barcoding studies. The protocol employs a single purification step to remove polysaccharides and other contaminating compounds using a non-hazardous reagent buffer. In addition, we conducted a bioinformatics database analysis as proof of concept for the efficiency of the DNA extraction protocol by using universal barcoding primers specific for cytochrome c oxidase I gene to identify different arthropod specimens through Barcode of Life Database (BOLD) database search. The usefulness of this protocol in various molecular biology and biodiversity studies is further discussed.},
}
@article {pmid20202924,
year = {2010},
author = {Craft, KJ and Pauls, SU and Darrow, K and Miller, SE and Hebert, PD and Helgen, LE and Novotny, V and Weiblen, GD},
title = {Population genetics of ecological communities with DNA barcodes: an example from New Guinea Lepidoptera.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {107},
number = {11},
pages = {5041-5046},
pmid = {20202924},
issn = {1091-6490},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Ecosystem ; *Genetics, Population ; Geography ; Haplotypes/genetics ; Lepidoptera/*genetics ; Molecular Sequence Data ; New Guinea ; Species Specificity ; },
abstract = {Comparative population genetics of ecological guilds can reveal generalities in patterns of differentiation bearing on hypotheses regarding the origin and maintenance of community diversity. Contradictory estimates of host specificity and beta diversity in tropical Lepidoptera (moths and butterflies) from New Guinea and the Americas have sparked debate on the role of host-associated divergence and geographic isolation in explaining latitudinal diversity gradients. We sampled haplotypes of mitochondrial cytochrome c oxidase I from 28 Lepidoptera species and 1,359 individuals across four host plant genera and eight sites in New Guinea to estimate population divergence in relation to host specificity and geography. Analyses of molecular variance and haplotype networks indicate varying patterns of genetic structure among ecologically similar sympatric species. One-quarter lacked evidence of isolation by distance or host-associated differentiation, whereas 21% exhibited both. Fourteen percent of the species exhibited host-associated differentiation without geographic isolation, 18% showed the opposite, and 21% were equivocal, insofar as analyses of molecular variance and haplotype networks yielded incongruent patterns. Variation in dietary breadth among community members suggests that speciation by specialization is an important, but not universal, mechanism for diversification of tropical Lepidoptera. Geographically widespread haplotypes challenge predictions of vicariance biogeography. Dispersal is important, and Lepidoptera communities appear to be highly dynamic according to the various phylogeographic histories of component species. Population genetic comparisons among herbivores of major tropical and temperate regions are needed to test predictions of ecological theory and evaluate global patterns of biodiversity.},
}
@article {pmid20195623,
year = {2010},
author = {Boehme, P and Amendt, J and Disney, RH and Zehner, R},
title = {Molecular identification of carrion-breeding scuttle flies (Diptera: Phoridae) using COI barcodes.},
journal = {International journal of legal medicine},
volume = {124},
number = {6},
pages = {577-581},
pmid = {20195623},
issn = {1437-1596},
mesh = {Aged ; Animals ; Cadaver ; DNA Barcoding, Taxonomic/*methods ; Diptera/*classification/genetics ; Entomology/*methods ; Female ; Forensic Medicine/methods ; Humans ; Infant, Newborn ; Larva ; Male ; Middle Aged ; *Postmortem Changes ; Species Specificity ; },
abstract = {Entomological evidence is often used in forensic cases for post-mortem interval (PMI) calculation. The most dominant species present on a corpse are typically blowflies. However, several cases have been reported where access to a corpse has been restricted for blowflies (e.g., on a buried or wrapped cadavers) but species of the family Phoridae were abundant. It has also been reported that some phorid species that exploit human corpses may also feature in cases of myiasis acquired ante-mortem. In all these cases, they may provide decisive evidence. As for blowflies, the precise identification of a phorid species collected from a corpse is necessary when estimating the PMI. Since morphological determination is often hampered due to similar characteristics especially in the larval and pupal stage, we used DNA-based methods to identify six phorid species (Megaselia scalaris, Megaselia giraudii, Megaselia abdita, Megaselia rufipes, Conicera tibialis, and Puliciphora borinquenensis) on the molecular level. We focused on a 658-bp-long region of the cytochrome oxidase I gene (COI), the most common molecular marker in forensic entomology. The amplified fragment is also used in DNA barcode approaches and was found to be suitable for identification of a wide range of insect taxa. The present study demonstrates that this region is also sufficient to distinguish between several species of scuttle flies.},
}
@article {pmid20195371,
year = {2010},
author = {Sirovich, L and Stoeckle, MY and Zhang, Y},
title = {Structural analysis of biodiversity.},
journal = {PloS one},
volume = {5},
number = {2},
pages = {e9266},
pmid = {20195371},
issn = {1932-6203},
support = {P50 GM071558/GM/NIGMS NIH HHS/United States ; R01 EY016224/EY/NEI NIH HHS/United States ; 1 P50 GM071558/GM/NIGMS NIH HHS/United States ; EY16224,/EY/NEI NIH HHS/United States ; },
mesh = {Algorithms ; Animals ; *Biodiversity ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Invertebrates/*classification/genetics/growth &amp; development ; Phylogeny ; Sequence Analysis, DNA ; Vertebrates/*classification/genetics/growth &amp; development ; },
abstract = {Large, recently-available genomic databases cover a wide range of life forms, suggesting opportunity for insights into genetic structure of biodiversity. In this study we refine our recently-described technique using indicator vectors to analyze and visualize nucleotide sequences. The indicator vector approach generates correlation matrices, dubbed Klee diagrams, which represent a novel way of assembling and viewing large genomic datasets. To explore its potential utility, here we apply the improved algorithm to a collection of almost 17,000 DNA barcode sequences covering 12 widely-separated animal taxa, demonstrating that indicator vectors for classification gave correct assignment in all 11,000 test cases. Indicator vector analysis revealed discontinuities corresponding to species- and higher-level taxonomic divisions, suggesting an efficient approach to classification of organisms from poorly-studied groups. As compared to standard distance metrics, indicator vectors preserve diagnostic character probabilities, enable automated classification of test sequences, and generate high-information density single-page displays. These results support application of indicator vectors for comparative analysis of large nucleotide data sets and raise prospect of gaining insight into broad-scale patterns in the genetic structure of biodiversity.},
}
@article {pmid20188843,
year = {2010},
author = {Hubert, N and Delrieu-Trottin, E and Irisson, JO and Meyer, C and Planes, S},
title = {Identifying coral reef fish larvae through DNA barcoding: a test case with the families Acanthuridae and Holocentridae.},
journal = {Molecular phylogenetics and evolution},
volume = {55},
number = {3},
pages = {1195-1203},
doi = {10.1016/j.ympev.2010.02.023},
pmid = {20188843},
issn = {1095-9513},
mesh = {Animals ; Anthozoa ; DNA, Mitochondrial/*analysis/genetics ; Electronic Data Processing ; Fishes/*classification/*genetics ; Larva/classification/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {A reference collection of COI barcode (650 bp) for the Pacific Society Islands has been constituted for 22 species of Acanthuridae and 16 species of Holocentridae. Divergence between congeneric species was on average 20-fold to 87-fold higher than divergence between conspecific sequences and this set of DNA-identifiers was used to identify 40 larvae of both families. All larvae sequenced could be identified to species using DNA-barcodes. Pools of larvae constitute multi-specific assemblages and no additional species compared to adult reef communities were sampled in larval pools, suggesting that the larval assemblages originated from adult communities on neighboring reefs.},
}
@article {pmid20182162,
year = {2010},
author = {Marini, SD and Hasman, A and Huijer, HA and Dimassi, H},
title = {Nurses' attitudes toward the use of the bar-coding medication administration system.},
journal = {Computers, informatics, nursing : CIN},
volume = {28},
number = {2},
pages = {112-123},
doi = {10.1097/NCN.0b013e3181cd80f6},
pmid = {20182162},
issn = {1538-9774},
mesh = {Adult ; Analysis of Variance ; *Attitude of Health Personnel ; *Attitude to Computers ; Diffusion of Innovation ; Drug Labeling ; Drug Therapy/nursing ; Factor Analysis, Statistical ; Female ; Humans ; Male ; Medical Order Entry Systems/organization &amp; administration ; Medication Errors/nursing/prevention &amp; control/statistics &amp; numerical data ; Medication Systems, Hospital/*organization &amp; administration ; Middle Aged ; Nursing Methodology Research ; Nursing Staff, Hospital/education/*psychology ; Patient Identification Systems/*organization &amp; administration ; Point-of-Care Systems/*organization &amp; administration ; Regression Analysis ; Safety Management ; Surveys and Questionnaires ; United States ; User-Computer Interface ; },
abstract = {This study determines nurses' attitudes toward bar-coding medication administration system use. Some of the factors underlying the successful use of bar-coding medication administration systems that are viewed as a connotative indicator of users' attitudes were used to gather data that describe the attitudinal basis for system adoption and use decisions in terms of subjective satisfaction. Only 67 nurses in the United States had the chance to respond to the e-questionnaire posted on the CARING list server for the months of June and July 2007. Participants rated their satisfaction with bar-coding medication administration system use based on system functionality, usability, and its positive/negative impact on the nursing practice. Results showed, to some extent, positive attitude, but the image profile draws attention to nurses' concerns for improving certain system characteristics. The high bar-coding medication administration system skills revealed a more negative perception of the system by the nursing staff. The reasons underlying dissatisfaction with bar-coding medication administration use by skillful users are an important source of knowledge that can be helpful for system development as well as system deployment. As a result, strengthening bar-coding medication administration system usability by magnifying its ability to eliminate medication errors and the contributing factors, maximizing system functionality by ascertaining its power as an extra eye in the medication administration process, and impacting the clinical nursing practice positively by being helpful to nurses, speeding up the medication administration process, and being user-friendly can offer a congenial settings for establishing positive attitude toward system use, which in turn leads to successful bar-coding medication administration system use.},
}
@article {pmid20180949,
year = {2010},
author = {Pandey, RV and Nolte, V and Schlötterer, C},
title = {CANGS: a user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies.},
journal = {BMC research notes},
volume = {3},
number = {},
pages = {3},
pmid = {20180949},
issn = {1756-0500},
support = {P 19467/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {BACKGROUND: Next generation sequencing (NGS) technologies have substantially increased the sequence output while the costs were dramatically reduced. In addition to the use in whole genome sequencing, the 454 GS-FLX platform is becoming a widely used tool for biodiversity surveys based on amplicon sequencing. In order to use NGS for biodiversity surveys, software tools are required, which perform quality control, trimming of the sequence reads, removal of PCR primers, and generation of input files for downstream analyses. A user-friendly software utility that carries out these steps is still lacking.<br><br>FINDINGS: We developed CANGS (Cleaning and Analyzing Next Generation Sequences) a flexible and user-friendly integrated software utility: CANGS is designed for amplicon based biodiversity surveys using the 454 sequencing platform. CANGS filters low quality sequences, removes PCR primers, filters singletons, identifies barcodes, and generates input files for downstream analyses. The downstream analyses rely either on third party software (e.g.: rarefaction analyses) or CANGS-specific scripts. The latter include modules linking 454 sequences with the name of the closest taxonomic reference retrieved from the NCBI database and the sequence divergence between them. Our software can be easily adapted to handle sequencing projects with different amplicon sizes, primer sequences, and quality thresholds, which makes this software especially useful for non-bioinformaticians.<br><br>CONCLUSION: CANGS performs PCR primer clipping, filtering of low quality sequences, links sequences to NCBI taxonomy and provides input files for common rarefaction analysis software programs. CANGS is written in Perl and runs on Mac OS X/Linux and is available at http://i122server.vu-wien.ac.at/pop/software.html.},
}
@article {pmid20179820,
year = {2010},
author = {Persson, F and Tegenfeldt, JO},
title = {DNA in nanochannels--directly visualizing genomic information.},
journal = {Chemical Society reviews},
volume = {39},
number = {3},
pages = {985-999},
doi = {10.1039/b912918a},
pmid = {20179820},
issn = {1460-4744},
mesh = {DNA/chemistry/*genetics ; *Genomics ; Humans ; Models, Molecular ; Molecular Structure ; },
abstract = {The power of nanofluidic channels to analyze DNA is described along with practical experimental hints. As an introduction, a general overview is given on conventional DNA analysis tools, as well as tools under development towards the $1000 genome. The focus of this tutorial review is the stretching of DNA in nanoscale channels for coarse-grained mapping of DNA. To understand the behavior of the DNA, basic theory is discussed. Experimental details are revealed so that the reader, with the proper equipment, should be able to perform experiments. Basic approaches to the analysis of the data are discussed. Finally, potential future directions are discussed including the application of melting mapping as a simple barcode for the DNA.},
}
@article {pmid20176330,
year = {2010},
author = {Nijman, V and Aliabadian, M},
title = {Performance of distance-based DNA barcoding in the molecular identification of primates.},
journal = {Comptes rendus biologies},
volume = {333},
number = {1},
pages = {11-16},
doi = {10.1016/j.crvi.2009.10.003},
pmid = {20176330},
issn = {1768-3238},
mesh = {Animals ; Base Sequence ; Cytochromes b/genetics ; *DNA/chemistry ; Electron Transport Complex IV/genetics ; *Electronic Data Processing ; Genetic Markers/genetics ; Genetic Variation ; Gorilla gorilla/genetics ; Humans ; Pan paniscus/genetics ; Pan troglodytes/genetics ; Pongo pygmaeus/genetics ; Primates/*classification/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Species Specificity ; },
abstract = {For comparative primatology proper recognition of basal taxa (i.e. species) is indispensable, and in this the choice of a suitable gene with high phylogenetic resolution is crucial. For the goals of species identification in animals, the cytochrome c oxidase subunit 1 (cox1) has been introduced as standard marker. Making use of the difference in intra- and interspecific genetic variation--the DNA barcoding gap--cox1 can be used as a fast and accurate marker for the identification of animal species. For the Order Primates we compare the performance of cox1 (166 sequences; 50 nominal species) in species-identification with that of two other mitochondrial markers, 16S ribosomal RNA (412 sequences, 92 species) and cytochrome b (cob: 547 sequences, 72 species). A wide gap exist between intra- and interspecific divergences for both cox1 and cob genes whereas this gap is less apparent for 16S, indicating that rRNA genes are less suitable for species delimitation in DNA barcoding. For those species where multiple sequences are available there are significant differences in the intraspecific genetic distances between different mitochondrial markers, without, however, showing a consistent pattern. We conclude that cox1 allows accurate differentiation of species and as such DNA barcoding may have an important role to play in comparative primatology.},
}
@article {pmid20169204,
year = {2010},
author = {Menke, SB and Booth, W and Dunn, RR and Schal, C and Vargo, EL and Silverman, J},
title = {Is it easy to be urban? Convergent success in urban habitats among lineages of a widespread native ant.},
journal = {PloS one},
volume = {5},
number = {2},
pages = {e9194},
pmid = {20169204},
issn = {1932-6203},
mesh = {Analysis of Variance ; Animals ; Ants/classification/enzymology/*genetics ; *Cities ; DNA, Mitochondrial/chemistry/genetics ; *Ecosystem ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Geography ; Haplotypes ; Molecular Sequence Data ; North America ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The most rapidly expanding habitat globally is the urban habitat, yet the origin and life histories of the populations of native species that inhabit this habitat remain poorly understood. We use DNA barcoding of the COI gene in the widespread native pest ant Tapinoma sessile to test two hypotheses regarding the origin of urban populations and traits associated with their success. First, we determine if urban samples of T. sessile have a single origin from natural populations by looking at patterns of haplotype clustering from across their range. Second, we examine whether polygynous colony structure--a trait associated with invasion success--is correlated with urban environments, by studying the lineage dependence of colony structure. Our phylogenetic analysis of 49 samples identified four well supported geographic clades. Within clades, Kimura-2 parameter pairwise genetic distances revealed <2.3% variation; however, between clade genetic distances were 7.5-10.0%, suggesting the possibility of the presence of cryptic species. Our results indicate that T. sessile has successfully colonized urban environments multiple times. Additionally, polygynous colony structure is a highly plastic trait across habitat, clade, and haplotype. In short, T. sessile has colonized urban habitats repeatedly and appears to do so using life history strategies already present in more natural populations. Whether similar results hold for other species found in urban habitats has scarcely begun to be considered.},
}
@article {pmid20159902,
year = {2010},
author = {Hinds, B},
title = {Safety institutes urge better bar-coding of drugs.},
journal = {CMAJ : Canadian Medical Association journal = journal de l'Association medicale canadienne},
volume = {182},
number = {5},
pages = {E237-8},
doi = {10.1503/cmaj.109-3182},
pmid = {20159902},
issn = {1488-2329},
mesh = {Canada ; *Drug Packaging ; *Electronic Data Processing ; Humans ; Medication Errors/*prevention &amp; control ; },
}
@article {pmid20156987,
year = {2010},
author = {Casiraghi, M and Labra, M and Ferri, E and Galimberti, A and De Mattia, F},
title = {DNA barcoding: a six-question tour to improve users' awareness about the method.},
journal = {Briefings in bioinformatics},
volume = {11},
number = {4},
pages = {440-453},
doi = {10.1093/bib/bbq003},
pmid = {20156987},
issn = {1477-4054},
mesh = {*Awareness ; DNA/*genetics ; Electronic Data Processing ; Humans ; },
abstract = {DNA barcoding is a recent and widely used molecular-based identification system that aims to identify biological specimens, and to assign them to a given species. However, DNA barcoding is even more than this, and besides many practical uses, it can be considered the core of an integrated taxonomic system, where bioinformatics plays a key role. DNA barcoding data could be interpreted in different ways depending on the examined taxa but the technique relies on standardized approaches, methods and analyses. The existing reference towards a common way to treat DNA barcoding data, analyses and results is the Barcode of Life Data Systems. However, the scientific community has produced in the recent years a number of alternative methods to manage barcoding data. The present work starts from this point, because users should be aware of the consequences their choices produce on the results. Despite the fact that a strict standardization is the essence of DNA barcoding, we propose a tour of six questions to improve the users' awareness about the method, the correct use of concepts and alternative tools provided by scientific community.},
}
@article {pmid20156599,
year = {2010},
author = {Maia da Silva, F and Marcili, A and Ortiz, PA and Epiphanio, S and Campaner, M and Catão-Dias, JL and Shaw, JJ and Camargo, EP and Teixeira, MM},
title = {Phylogenetic, morphological and behavioural analyses support host switching of Trypanosoma (Herpetosoma) lewisi from domestic rats to primates.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {10},
number = {4},
pages = {522-529},
doi = {10.1016/j.meegid.2010.02.005},
pmid = {20156599},
issn = {1567-7257},
mesh = {Animals ; Brazil ; DNA, Protozoan ; DNA, Ribosomal Spacer ; Evolution, Molecular ; Haplorhini/*parasitology ; Mice ; Mice, Inbred BALB C ; Microscopy ; Phylogeny ; Rats ; Rats, Wistar/*parasitology ; Trypanosoma lewisi/cytology/genetics/growth &amp; development/*physiology ; Trypanosomiasis/parasitology/*veterinary ; },
abstract = {We characterized four Brazilian trypanosomes isolated from domestic rats and three from captive non-human primates that were morphologically similar to T. lewisi, a considered non-pathogenic species restricted to rodents and transmitted by fleas, despite its potential pathogenicity for infants. These isolates were identified as T. lewisi by barcoding using V7V8 SSU rDNA sequences. In inferred phylogenetic trees, all isolates clustered tightly with reference T. lewisi and T. lewisi-like trypanosomes from Europe, Asia and Africa and despite their high sequence conservation formed a homogeneous clade separate from other species of the subgenus T. (Herpetosoma). With the aim of clearly resolving the relationships between the Brazilian isolates from domestic rats and primates, we compared sequences from more polymorphic ITS rDNA. Results corroborated that isolates from Brazilian rats and monkeys were indeed of the same species and quite close to T. lewisi isolates of humans and rats from different geographical regions. Morphology of the monkey isolates and their behaviour in culture and in experimentally infected rats were also compatible with T. lewisi. However, infection with T. lewisi is rare among monkeys. We have examined more than 200 free-ranging and 160 captive monkeys and found only three infected individuals among the monkeys held in captivity. The findings of this work suggest that proximity of monkeys and infected rats and their exposure to infected fleas may be responsible for the host switching of T. lewisi from their natural rodent species to primates. This and previous studies reporting T. lewisi in humans suggest that this trypanosome can cause sporadic and opportunistic flea-borne infection in primates.},
}
@article {pmid20147217,
year = {2009},
author = {Varley, KE and Mitra, RD},
title = {Nested Patch PCR for highly multiplexed amplification of genomic loci.},
journal = {Cold Spring Harbor protocols},
volume = {2009},
number = {7},
pages = {pdb.prot5252},
doi = {10.1101/pdb.prot5252},
pmid = {20147217},
issn = {1559-6095},
support = {R01 DA025744/DA/NIDA NIH HHS/United States ; 5P50HG003170-03/HG/NHGRI NIH HHS/United States ; },
mesh = {DNA/*analysis ; DNA Primers/genetics ; *Genetic Techniques ; Genomics ; Humans ; Models, Genetic ; Mutation ; Polymerase Chain Reaction/*methods ; Polymorphism, Single Nucleotide ; },
abstract = {Nested Patch polymerase chain reaction (PCR) amplifies a large number (greater than 90) of targeted loci from genomic DNA simultaneously in the same reaction. These amplified loci can then be sequenced on a second-generation sequencing machine to detect single nucleotide polymorphisms (SNPs) and mutations. The reaction is highly specific: 90% of sequencing reads match targeted loci. Nested Patch PCR can be performed on many samples in parallel, and by using sample-specific DNA barcodes, these can be pooled and sequenced in a single reaction. Thus, the Nested Patch PCR protocol that is described here provides an easy workflow to identify SNPs and mutations across many targeted loci for many samples in parallel.},
}
@article {pmid20146470,
year = {2010},
author = {Wang, C and Ma, L and Chen, LM and Chai, KX and Su, M},
title = {Scanning calorimetric detections of multiple DNA biomarkers contained in complex fluids.},
journal = {Analytical chemistry},
volume = {82},
number = {5},
pages = {1838-1843},
doi = {10.1021/ac902503j},
pmid = {20146470},
issn = {1520-6882},
mesh = {Base Sequence ; Biomarkers/*analysis ; Calorimetry/*methods ; DNA/*analysis ; Microscopy, Electron, Transmission ; Nanoparticles ; Sensitivity and Specificity ; },
abstract = {Most of the existing techniques cannot be used to detect molecular biomarkers contained in complex fluids due to issues such as enzyme inhibition or signal interference. We have developed a nanoparticle-based scanning calorimetric method for the highly sensitive detections of multiple DNA biomarkers contained in cell lysate and milk by using solid-liquid phase change nanoparticles as thermal barcodes. The detection is based on the principle that the temperature of solid will not rise above the melting temperature unless all solid is molten, thus nanoparticles have sharp melting peaks during the thermal scan process. A one-to-one correspondence can thus be created between one type of nanoparticles and one type of biomarker, i.e., multiple biomarkers can be detected at the same time using a combination of nanoparticles. The melting temperature and the heat flow reflect the type and the concentration of the biomarker, respectively. The target oligonucleotides at low concentration in cell lysate (80 pM) have been detected through thermal signal transduction. The melting temperature of nanoparticles can be designed to avoid interference from coexisting species contained in the fluids, bringing simultaneously high sensitivity and multiplicity, as well as sample preparation benefits to biomarker detections.},
}
@article {pmid20142491,
year = {2010},
author = {Nam, J and Dong, P and Tarpine, R and Istrail, S and Davidson, EH},
title = {Functional cis-regulatory genomics for systems biology.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {107},
number = {8},
pages = {3930-3935},
pmid = {20142491},
issn = {1091-6490},
support = {R01 GM061005/GM/NIGMS NIH HHS/United States ; HG00533201/HG/NHGRI NIH HHS/United States ; GM061005/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Gene Expression Profiling ; *Gene Expression Regulation ; Genes, Reporter ; Genetic Complementation Test ; Genomics/*methods ; *High-Throughput Screening Assays ; Humans ; Ovum ; Sea Urchins ; Systems Biology/*methods ; },
abstract = {Gene expression is controlled by interactions between trans-regulatory factors and cis-regulatory DNA sequences, and these interactions constitute the essential functional linkages of gene regulatory networks (GRNs). Validation of GRN models requires experimental cis-regulatory tests of predicted linkages to authenticate their identities and proposed functions. However, cis-regulatory analysis is, at present, at a severe bottleneck in genomic system biology because of the demanding experimental methodologies currently in use for discovering cis-regulatory modules (CRMs), in the genome, and for measuring their activities. Here we demonstrate a high-throughput approach to both discovery and quantitative characterization of CRMs. The unique aspect is use of DNA sequence tags to "barcode" CRM expression constructs, which can then be mixed, injected together into sea urchin eggs, and subsequently deconvolved. This method has increased the rate of cis-regulatory analysis by >100-fold compared with conventional one-by-one reporter assays. The utility of the DNA-tag reporters was demonstrated by the rapid discovery of 81 active CRMs from 37 previously unexplored sea urchin genes. We then obtained simultaneous high-resolution temporal characterization of the regulatory activities of more than 80 CRMs. On average 2-3 CRMs were discovered per gene. Comparison of endogenous gene expression profiles with those of the CRMs recovered from each gene showed that, for most cases, at least one CRM is active in each phase of endogenous expression, suggesting that CRM recovery was comprehensive. This approach will qualitatively alter the practice of GRN construction as well as validation, and will impact many additional areas of regulatory system biology.},
}
@article {pmid20140532,
year = {2010},
author = {Asahina, H and Shinozaki, J and Masuda, K and Morimitsu, Y and Satake, M},
title = {Identification of medicinal Dendrobium species by phylogenetic analyses using matK and rbcL sequences.},
journal = {Journal of natural medicines},
volume = {64},
number = {2},
pages = {133-138},
pmid = {20140532},
issn = {1861-0293},
mesh = {DNA, Plant/*genetics ; Dendrobium/*genetics ; *Drugs, Chinese Herbal/isolation &amp; purification ; Endoribonucleases/*genetics ; Nucleotidyltransferases/*genetics ; *Phylogeny ; Plant Leaves/genetics ; Plant Stems/genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; Sequence Analysis, DNA/methods ; },
abstract = {Species identification of five Dendrobium plants was conducted using phylogenetic analysis and the validity of the method was verified. Some Dendrobium plants (Orchidaceae) have been used as herbal medicines but the difficulty in identifying their botanical origin by traditional methods prevented their full modern utilization. Based on the emerging field of molecular systematics as a powerful classification tool, a phylogenetic analysis was conducted using sequences of two plastid genes, the maturase-coding gene (matK) and the large subunit of ribulose 1,5-bisphosphate carboxylase-coding gene (rbcL), as DNA barcodes for species identification of Dendrobium plants. We investigated five medicinal Dendrobium species, Dendrobium fimbriatum, D. moniliforme, D. nobile, D. pulchellum, and D. tosaense. The phylogenetic trees constructed from matK data successfully distinguished each species from each other. On the other hand, rbcL, as a single-locus barcode, offered less species discriminating power than matK, possibly due to its being present with little variation. When results using matK sequences of D. officinale that was deposited in the DNA database were combined, D. officinale and D. tosaense showed a close genetic relationship, which brought us closer to resolving the question of their taxonomic identity. Identification of the plant source as well as the uniformity of the chemical components is critical for the quality control of herbal medicines and it is important that the processed materials be validated. The methods presented here could be applied to the analysis of processed Dendrobium plants and be a promising tool for the identification of botanical origins of crude drugs.},
}
@article {pmid20138981,
year = {2010},
author = {Summerer, D and Schracke, N and Wu, H and Cheng, Y and Bau, S and Stähler, CF and Stähler, PF and Beier, M},
title = {Targeted high throughput sequencing of a cancer-related exome subset by specific sequence capture with a fully automated microarray platform.},
journal = {Genomics},
volume = {95},
number = {4},
pages = {241-246},
doi = {10.1016/j.ygeno.2010.01.006},
pmid = {20138981},
issn = {1089-8646},
mesh = {Exons ; Genomics/methods ; High-Throughput Screening Assays/*methods ; Humans ; Neoplasms/*genetics ; Oligonucleotide Array Sequence Analysis/*methods ; Polymorphism, Single Nucleotide ; Sequence Alignment/methods ; Sequence Analysis, DNA/*methods ; },
abstract = {Sequence capture methods for targeted next generation sequencing promise to massively reduce cost of genomics projects compared to untargeted sequencing. However, evaluated capture methods specifically dedicated to biologically relevant genomic regions are rare. Whole exome capture has been shown to be a powerful tool to discover the genetic origin of disease and provides a reduction in target size and thus calculative sequencing capacity of >90-fold compared to untargeted whole genome sequencing. For further cost reduction, a valuable complementing approach is the analysis of smaller, relevant gene subsets but involving large cohorts of samples. However, effective adjustment of target sizes and sample numbers is hampered by the limited scalability of enrichment systems. We report a highly scalable and automated method to capture a 480 Kb exome subset of 115 cancer-related genes using microfluidic DNA arrays. The arrays are adaptable from 125 Kb to 1 Mb target size and/or one to eight samples without barcoding strategies, representing a further 26 - 270-fold reduction of calculative sequencing capacity compared to whole exome sequencing. Illumina GAII analysis of a HapMap genome enriched for this exome subset revealed a completeness of >96%. Uniformity was such that >68% of exons had at least half the median depth of coverage. An analysis of reference SNPs revealed a sensitivity of up to 93% and a specificity of 98.2% or higher.},
}
@article {pmid20137071,
year = {2010},
author = {Lennon, NJ and Lintner, RE and Anderson, S and Alvarez, P and Barry, A and Brockman, W and Daza, R and Erlich, RL and Giannoukos, G and Green, L and Hollinger, A and Hoover, CA and Jaffe, DB and Juhn, F and McCarthy, D and Perrin, D and Ponchner, K and Powers, TL and Rizzolo, K and Robbins, D and Ryan, E and Russ, C and Sparrow, T and Stalker, J and Steelman, S and Weiand, M and Zimmer, A and Henn, MR and Nusbaum, C and Nicol, R},
title = {A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454.},
journal = {Genome biology},
volume = {11},
number = {2},
pages = {R15},
pmid = {20137071},
issn = {1474-760X},
support = {U54 HG003067/HG/NHGRI NIH HHS/United States ; },
mesh = {Algorithms ; *Electronic Data Processing ; *Gene Library ; *High-Throughput Screening Assays ; Humans ; Microspheres ; Sequence Analysis, DNA/*methods ; },
abstract = {We present an automated, high throughput library construction process for 454 technology. Sample handling errors and cross-contamination are minimized via end-to-end barcoding of plasticware, along with molecular DNA barcoding of constructs. Automation-friendly magnetic bead-based size selection and cleanup steps have been devised, eliminating major bottlenecks and significant sources of error. Using this methodology, one technician can create 96 sequence-ready 454 libraries in 2 days, a dramatic improvement over the standard method.},
}
@article {pmid20113377,
year = {2010},
author = {Pawlowski, J and Lecroq, B},
title = {Short rDNA barcodes for species identification in foraminifera.},
journal = {The Journal of eukaryotic microbiology},
volume = {57},
number = {2},
pages = {197-205},
doi = {10.1111/j.1550-7408.2009.00468.x},
pmid = {20113377},
issn = {1550-7408},
mesh = {Cluster Analysis ; DNA, Protozoan/chemistry/*genetics ; DNA, Ribosomal/chemistry/*genetics ; Foraminifera/*classification/*genetics ; Genes, rRNA ; Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {Ribosomal DNA (rDNA) sequences have been shown to be very useful for identification of microbial eukaryotes. Usually, complete or long partial sequences of the rDNA genes are analysed. However, the development of new massive sequencing technologies producing a large amount of relatively short sequences raises the question about the minimum length of rDNA fragments necessary for species distinction in environmental sampling. To answer this question, we compared six variable regions of the small subunit (SSU) rDNA of foraminifera, known to have rapidly evolving ribosomal genes. For each region, we analysed (1) the sequence divergence between and within foraminiferal morphospecies, (2) the intraspecific polymorphism, and (3) the ability of each region to recognize the phylotypes inferred from analysis of a longer fragment. Our results show that although the variable regions differ considerably between taxonomic groups, most of them perform very well as species identifiers. Taking into account different analyses, the expansion segment of Helix 37 appears to be the best candidate for barcoding foraminifera. We propose that this relatively short region, averaging 50-60 nt in length, could be an ideal barcode for identification of foraminifera in environmental samples using massive sequencing approach.},
}
@article {pmid20102622,
year = {2010},
author = {Newmaster, SG and Ragupathy, S},
title = {Ethnobotany genomics - discovery and innovation in a new era of exploratory research.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {6},
number = {},
pages = {2},
pmid = {20102622},
issn = {1746-4269},
mesh = {Biodiversity ; Conservation of Natural Resources ; *DNA ; Ecology ; Ethnobotany/*methods ; Genomics/*methods ; Humans ; India ; Plants, Medicinal/*classification/*genetics ; Population Groups ; Research ; Species Specificity ; },
abstract = {We present here the first use of DNA barcoding in a new approach to ethnobotany we coined "ethnobotany genomics". This new approach is founded on the concept of 'assemblage' of biodiversity knowledge, which includes a coming together of different ways of knowing and valorizing species variation in a novel approach seeking to add value to both traditional knowledge (TK) and scientific knowledge (SK). We employed contemporary genomic technology, DNA barcoding, as an important tool for identifying cryptic species, which were already recognized ethnotaxa using the TK classification systems of local cultures in the Velliangiri Hills of India. This research is based on several case studies in our lab, which define an approach to that is poised to evolve quickly with the advent of new ideas and technology. Our results show that DNA barcoding validated several new cryptic plant species to science that were previously recognized by TK classifications of the Irulas and Malasars, and were lumped using SK classification. The contribution of the local aboriginal knowledge concerning plant diversity and utility in India is considerable; our study presents new ethnomedicine to science. Ethnobotany genomics can also be used to determine the distribution of rare species and their ecological requirements, including traditional ecological knowledge so that conservation strategies can be implemented. This is aligned with the Convention on Biological Diversity that was signed by over 150 nations, and thus the world's complex array of human-natural-technological relationships has effectively been re-organized.},
}
@article {pmid20098768,
year = {2010},
author = {Cao, C and Dhumpa, R and Bang, DD and Ghavifekr, Z and Høgberg, J and Wolff, A},
title = {Detection of avian influenza virus by fluorescent DNA barcode-based immunoassay with sensitivity comparable to PCR.},
journal = {The Analyst},
volume = {135},
number = {2},
pages = {337-342},
doi = {10.1039/b916821b},
pmid = {20098768},
issn = {1364-5528},
mesh = {Animals ; *Biosensing Techniques ; Chickens ; *Immunoassay ; Influenza A virus/*genetics/pathogenicity ; Influenza in Birds/*diagnosis/*genetics ; Reverse Transcriptase Polymerase Chain Reaction/*methods ; *Spectrometry, Fluorescence ; },
abstract = {In this paper, a coupling of fluorophore-DNA barcode and bead-based immunoassay for detecting avian influenza virus (AIV) with PCR-like sensitivity is reported. The assay is based on the use of sandwich immunoassay and fluorophore-tagged oligonucleotides as representative barcodes. The detection involves the sandwiching of the target AIV between magnetic immunoprobes and barcode-carrying immunoprobes. Because each barcode-carrying immunoprobe is functionalized with a multitude of fluorophore-DNA barcode strands, many DNA barcodes are released for each positive binding event resulting in amplification of the signal. Using an inactivated H16N3 AIV as a model, a linear response over five orders of magnitude was obtained, and the sensitivity of the detection was comparable to conventional RT-PCR. Moreover, the entire detection required less than 2 hr. The results indicate that the method has great potential as an alternative for surveillance of epidemic outbreaks caused by AIV, other viruses and microorganisms.},
}
@article {pmid20095620,
year = {2010},
author = {Ma, L and Wang, C and Hong, Y and Zhang, M and Su, M},
title = {Thermally addressed immunosorbent assay for multiplexed protein detections using phase change nanoparticles.},
journal = {Analytical chemistry},
volume = {82},
number = {4},
pages = {1186-1190},
doi = {10.1021/ac902724y},
pmid = {20095620},
issn = {1520-6882},
mesh = {Animals ; Avidin/analysis/immunology ; Buffers ; Calorimetry, Differential Scanning ; Cattle ; Cell Extracts/chemistry ; Cell Line, Tumor ; Humans ; Immunoglobulin G/analysis/immunology ; *Immunosorbent Techniques ; Nanoparticles/*chemistry ; Proteins/*analysis/immunology ; },
abstract = {Thermally addressed immunoassay is developed to detect multiple proteins using phase change nanoparticles as thermal barcodes. The solid to liquid phase changes of nanoparticles absorb heat energy and generate sharp melting peaks, which are used as thermal signatures to determine the existence and concentration of proteins. Multiple proteins can be detected by using different types of nanoparticles in order to create a one-to-one correspondence between one type of nanoparticle and one type of protein. The fusion enthalpy that is proportional to the amount of phase change materials has been used to derive the amount of protein. The melting temperatures of nanoparticles are designed to be higher than 100 degrees C to avoid interference from species contained in the fluid. Thus, the use of thermal nanoparticles allows the detection of multiple low concentration proteins in a complex fluid such as cell lysate regardless of the color, salt concentration, and conductivity of the sample.},
}
@article {pmid20093403,
year = {2010},
author = {Gerrits, A and Dykstra, B and Kalmykowa, OJ and Klauke, K and Verovskaya, E and Broekhuis, MJ and de Haan, G and Bystrykh, LV},
title = {Cellular barcoding tool for clonal analysis in the hematopoietic system.},
journal = {Blood},
volume = {115},
number = {13},
pages = {2610-2618},
doi = {10.1182/blood-2009-06-229757},
pmid = {20093403},
issn = {1528-0020},
mesh = {Animals ; Binomial Distribution ; *Cell Lineage ; Cell Separation/methods ; Clone Cells/*chemistry ; DNA, Recombinant/*analysis ; Flow Cytometry/methods ; *Genetic Markers ; Genetic Therapy/methods ; Genetic Vectors/analysis/*genetics ; Hematopoietic Stem Cell Transplantation ; Hematopoietic Stem Cells/*chemistry/cytology ; Mice ; Mice, Inbred C57BL ; Mice, Inbred DBA ; Oligodeoxyribonucleotides/*analysis ; Retroviridae/*genetics ; Sequence Analysis, DNA/*methods ; Transgenes ; Virus Integration ; },
abstract = {Clonal analysis is important for many areas of hematopoietic stem cell research, including in vitro cell expansion, gene therapy, and cancer progression and treatment. A common approach to measure clonality of retrovirally transduced cells is to perform integration site analysis using Southern blotting or polymerase chain reaction-based methods. Although these methods are useful in principle, they generally provide a low-resolution, biased, and incomplete assessment of clonality. To overcome those limitations, we labeled retroviral vectors with random sequence tags or "barcodes." On integration, each vector introduces a unique, identifiable, and heritable mark into the host cell genome, allowing the clonal progeny of each cell to be tracked over time. By coupling the barcoding method to a sequencing-based detection system, we could identify major and minor clones in 2 distinct cell culture systems in vitro and in a long-term transplantation setting. In addition, we demonstrate how clonal analysis can be complemented with transgene expression and integration site analysis. This cellular barcoding tool permits a simple, sensitive assessment of clonality and holds great promise for future gene therapy protocols in humans, and any other applications when clonal tracking is important.},
}
@article {pmid20089123,
year = {2010},
author = {Goetze, E},
title = {Species discovery in marine planktonic invertebrates through global molecular screening.},
journal = {Molecular ecology},
volume = {19},
number = {5},
pages = {952-967},
doi = {10.1111/j.1365-294X.2009.04520.x},
pmid = {20089123},
issn = {1365-294X},
mesh = {Animals ; Copepoda/*classification/*genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics ; Evolution, Molecular ; Genetic Speciation ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Species discovery through large-scale sampling of mitochondrial diversity, as advocated under DNA barcoding, has been widely criticized. Two of the primary weaknesses of this approach, the use of a single gene marker for species delineation and the possible co-amplification of nuclear pseudogenes, can be circumvented through incorporation of multiple data sources. Here I show that for taxonomic groups with poorly characterized systematics, large-scale genetic screening using a mitochondrial DNA marker can be a very effective approach to species discovery. Global sampling (120 locations) of 1295 individuals of 22 described species of eucalanid copepods identified 15 novel evolutionarily significant units (ESUs) within this marine holoplanktonic family. Species limits were tested under reciprocal monophyly at the mitochondrial (mt) gene 16S rRNA, and 13 of 15 lineages were reciprocally monophyletic under three phylogenetic inference methods. Five of these mitochondrial ESUs also received moderate support for reciprocal monophyly at the independently-inherited nuclear gene, internal transcribed spacer 2 (ITS2). Additional support for the utility of mt DNA as a proxy for species boundaries in this taxon is discussed, including results from related morphological and biogeographic studies. Minimal overlap of intra-ESU and inter-ESU 16S rRNA genetic distances was observed, suggesting that this mt marker performs well for species discovery via molecular screening. Sampling coverage required for the discovery of new ESUs was found to be in the range of >50 individuals/species, well above the sampling intensity of most current DNA Barcoding studies. Large-scale genetic screening can provide critical first data on the presence of cryptic species, and should be used as an approach to generate systematic hypotheses in groups with incomplete taxonomies.},
}
@article {pmid20088590,
year = {2010},
author = {Singer, A and Wanunu, M and Morrison, W and Kuhn, H and Frank-Kamenetskii, M and Meller, A},
title = {Nanopore based sequence specific detection of duplex DNA for genomic profiling.},
journal = {Nano letters},
volume = {10},
number = {2},
pages = {738-742},
pmid = {20088590},
issn = {1530-6992},
support = {R01 HG004128/HG/NHGRI NIH HHS/United States ; R01 HG004128-02/HG/NHGRI NIH HHS/United States ; R01 HG004128-03/HG/NHGRI NIH HHS/United States ; HG-004128/HG/NHGRI NIH HHS/United States ; },
mesh = {Automation ; Bacteriophage lambda/metabolism ; Base Sequence ; DNA/*chemistry ; Electronic Data Processing ; Gene Expression Profiling ; Genome, Human ; *Genomics ; Humans ; Microscopy, Electron, Transmission/methods ; Molecular Sequence Data ; Nanoparticles/*chemistry ; Nanotechnology/*methods ; },
abstract = {We demonstrate a purely electrical method for the single-molecule detection of specific DNA sequences, achieved by hybridizing double-stranded DNA (dsDNA) with peptide nucleic acid (PNA) probes and electrophoretically threading the DNA through sub-5 nm silicon nitride pores. Bis-PNAs were used as the tagging probes in order to achieve high affinity and sequence specificity. Sequence detection is performed by reading the ion current traces of individual translocating DNA molecules, which display a characteristic secondary blockade level, absent in untagged molecules. The potential for barcoding DNA is demonstrated through nanopore analysis of once-tagged and twice-tagged DNA at different locations on the same genomic fragment. Our high-throughput, long-read length method can be used to identify key sequences embedded in individual DNA molecules, without the need for amplification or fluorescent/radio labeling. This opens up a wide range of possibilities in human genomics as well as in pathogen detection for fighting infectious diseases.},
}
@article {pmid20085369,
year = {2010},
author = {Gunnarsson, A and Sjövall, P and Höök, F},
title = {Liposome-based chemical barcodes for single molecule DNA detection using imaging mass spectrometry.},
journal = {Nano letters},
volume = {10},
number = {2},
pages = {732-737},
doi = {10.1021/nl904208y},
pmid = {20085369},
issn = {1530-6992},
mesh = {Animals ; DNA/*chemistry ; *Electronic Data Processing ; Fluorescence ; Humans ; Lipids/chemistry ; Liposomes/*chemistry ; Mass Spectrometry/*methods ; Metal Nanoparticles/chemistry ; Nanotechnology/*methods ; Oligonucleotide Array Sequence Analysis/*instrumentation/*methods ; },
abstract = {We report on a mass-spectrometry (time-of-flight secondary ion mass spectrometry, TOF-SIMS) based method for multiplexed DNA detection utilizing a random array, where the lipid composition of small unilamellar liposomes act as chemical barcodes to identify unique DNA target sequences down to the single molecule level. In a sandwich format, suspended target-DNA to be detected mediates the binding of capture-DNA modified liposomes to surface-immobilized probe-DNA. With the lipid composition of each liposome encoding a unique target-DNA sequence, TOF-SIMS analysis was used to determine the chemical fingerprint of the bound liposomes. Using high-resolution TOF-SIMS imaging, providing sub-200 nm spatial resolution, single DNA targets could be detected and identified via the chemical fingerprint of individual liposomes. The results also demonstrate the capability of TOF-SIMS to provide multiplexed detection of DNA targets on substrate areas in the micrometer range. Together with a high multiplexing capacity, this makes the concept an interesting alternative to existing barcode concepts based on fluorescence, Raman, or graphical codes for small-scale bioanalysis.},
}
@article {pmid20081854,
year = {2010},
author = {Kokel, D and Bryan, J and Laggner, C and White, R and Cheung, CY and Mateus, R and Healey, D and Kim, S and Werdich, AA and Haggarty, SJ and Macrae, CA and Shoichet, B and Peterson, RT},
title = {Rapid behavior-based identification of neuroactive small molecules in the zebrafish.},
journal = {Nature chemical biology},
volume = {6},
number = {3},
pages = {231-237},
pmid = {20081854},
issn = {1552-4469},
support = {R01 GM071896/GM/NIGMS NIH HHS/United States ; R01 MH086867-01/MH/NIMH NIH HHS/United States ; K01 MH091449/MH/NIMH NIH HHS/United States ; T32 HL007208/HL/NHLBI NIH HHS/United States ; U01 NS063733-01/NS/NINDS NIH HHS/United States ; R01 MH086867/MH/NIMH NIH HHS/United States ; R21 MH085205-01A1/MH/NIMH NIH HHS/United States ; U01 NS063733/NS/NINDS NIH HHS/United States ; R21 MH085205/MH/NIMH NIH HHS/United States ; },
abstract = {Neuroactive small molecules are indispensable tools for treating mental illnesses and dissecting nervous system function. However, it has been difficult to discover novel neuroactive drugs. Here, we describe a high-throughput, behavior-based approach to neuroactive small molecule discovery in the zebrafish. We used automated screening assays to evaluate thousands of chemical compounds and found that diverse classes of neuroactive molecules caused distinct patterns of behavior. These 'behavioral barcodes' can be used to rapidly identify new psychotropic chemicals and to predict their molecular targets. For example, we identified new acetylcholinesterase and monoamine oxidase inhibitors using phenotypic comparisons and computational techniques. By combining high-throughput screening technologies with behavioral phenotyping in vivo, behavior-based chemical screens can accelerate the pace of neuroactive drug discovery and provide small-molecule tools for understanding vertebrate behavior.},
}
@article {pmid20067837,
year = {2010},
author = {Lou, M and Golding, GB},
title = {Assigning sequences to species in the absence of large interspecific differences.},
journal = {Molecular phylogenetics and evolution},
volume = {56},
number = {1},
pages = {187-194},
doi = {10.1016/j.ympev.2010.01.002},
pmid = {20067837},
issn = {1095-9513},
mesh = {*Algorithms ; Animals ; Bayes Theorem ; Computer Simulation ; Drosophila/classification/*genetics ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
abstract = {Barcoding is an initiative to define a standard fragment of DNA to be used to assign unknown sequences to existing known species groups that have been pre-identified externally (by a taxonomist). Several methods have been described that attempt to place this assignment into a Bayesian statistical framework. Here we describe an algorithm that makes use of segregating sites and we examine how well these methods perform in the absence of an interspecific 'barcoding gap'. When a barcoding gap exists, that is when the data are clearly delimited, most methods perform well. Here we have used data from the Drosophila genus because this genus includes sibling species and the species relationships within this species while complex are, arguably, better understood than in any other group. The results show that the Bayesian methods perform well even in the absence of a barcoding gap. The sequences from Drosophila are correctly identified and only when the degree of incomplete lineage sorting is extreme in simulations or within the Drosophila species, do they fail in their identifications and even then, the "correct" species has a high posterior probability.},
}
@article {pmid20067269,
year = {2010},
author = {Xiang, Y and Zhang, Y and Chang, Y and Chai, Y and Wang, J and Yuan, R},
title = {Reverse-micelle synthesis of electrochemically encoded quantum dot barcodes: application to electronic coding of a cancer marker.},
journal = {Analytical chemistry},
volume = {82},
number = {3},
pages = {1138-1141},
pmid = {20067269},
issn = {1520-6882},
support = {R01 EB002189/EB/NIBIB NIH HHS/United States ; R01 EB002189-08/EB/NIBIB NIH HHS/United States ; U01 AI075565/AI/NIAID NIH HHS/United States ; },
mesh = {Cadmium/chemistry ; Carcinoembryonic Antigen/*analysis ; Electrochemical Techniques/*methods ; Lead/chemistry ; *Micelles ; *Quantum Dots ; Reproducibility of Results ; Zinc/chemistry ; },
abstract = {Reproducible electrochemically encoded quantum dot (QD) barcodes were prepared using the reverse-micelle synthetic approach. The encoding elements, Zn(2+), Cd(2+), and Pb(2+), were confined within a single QD, which eliminates the cumbersome encapsulation process used by other common nanoparticle-based barcode preparation schemes. The distinct voltammetric stripping patterns of Zn(2+), Cd(2+) and Pb(2+) at distinguishable potentials with controllable current intensities offer excellent encoding capability for the prepared electrochemical (EC) QDs. Additionally, the simultaneous modification of the QD barcode surface with organic ligands during the preparation process make them potentially useful in biomedical research. For proof of concept of their application in bioassays, the EC QD barcodes were further employed as tags for an immunoassay of a cancer marker, carcinoembryonic antigen (CEA). The voltammetric stripping response of the dissolved bardcode tags was proportional to log[CEA] in the range from 0.01 to 80 ng mL(-1), with a detection limit of 3.3 pg mL(-1). The synthesized EC QD barcodes hold considerable potential in biodetection, encrypted information, and product tracking.},
}
@article {pmid20062805,
year = {2010},
author = {Chen, S and Yao, H and Han, J and Liu, C and Song, J and Shi, L and Zhu, Y and Ma, X and Gao, T and Pang, X and Luo, K and Li, Y and Li, X and Jia, X and Lin, Y and Leon, C},
title = {Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species.},
journal = {PloS one},
volume = {5},
number = {1},
pages = {e8613},
pmid = {20062805},
issn = {1932-6203},
mesh = {DNA, Plant/*genetics ; *Electronic Data Processing ; Plants, Medicinal/*genetics ; Polymerase Chain Reaction ; },
abstract = {BACKGROUND: The plant working group of the Consortium for the Barcode of Life recommended the two-locus combination of rbcL+matK as the plant barcode, yet the combination was shown to successfully discriminate among 907 samples from 550 species at the species level with a probability of 72%. The group admits that the two-locus barcode is far from perfect due to the low identification rate, and the search is not over.<br><br>Here, we compared seven candidate DNA barcodes (psbA-trnH, matK, rbcL, rpoC1, ycf5, ITS2, and ITS) from medicinal plant species. Our ranking criteria included PCR amplification efficiency, differential intra- and inter-specific divergences, and the DNA barcoding gap. Our data suggest that the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA represents the most suitable region for DNA barcoding applications. Furthermore, we tested the discrimination ability of ITS2 in more than 6600 plant samples belonging to 4800 species from 753 distinct genera and found that the rate of successful identification with the ITS2 was 92.7% at the species level.<br><br>CONCLUSIONS: The ITS2 region can be potentially used as a standard DNA barcode to identify medicinal plants and their closely related species. We also propose that ITS2 can serve as a novel universal barcode for the identification of a broader range of plant taxa.},
}
@article {pmid20058792,
year = {2009},
author = {Shneer, VS},
title = {[DNA barcoding is a new approach in comparative genomics of plants].},
journal = {Genetika},
volume = {45},
number = {11},
pages = {1436-1448},
pmid = {20058792},
issn = {0016-6758},
mesh = {*DNA Fingerprinting ; DNA, Chloroplast/*genetics ; Plants/*genetics ; *Polymerase Chain Reaction ; },
abstract = {DNA barcoding was proposed as a method for recognition and identification of eukaryotic species through comparison of sequences of a standard short DNA fragment--DNA barcode--from an unknown specimen to a library of reference sequences from known species. This allows identifying an organism at any stage of development from a very small tissue sample, fresh or conserved many years ago. Molecular identification of plant samples can be used in various scientific and applied fields. It would also help to find new species, which is particularly important for cryptogamic plants. An optimal DNA barcode region is a small fragment present in all species of a major taxonomic group, having invariable nucleotide sequence in all members of the same species, but with sufficient variation to discriminate among the species. This fragment should be flanked by low-variable regions for use of universal primers in PCR for amplification and sequencing. The DNA barcode that is well established in animals is a sequence of a fragment of the mitochondrial cytochrome c oxidase gene CO1. However, searching for DNA barcode in plants proved to be a more challenging task. No DNA region universally suitable for all plants and meeting all of the necessary criteria has been found. Apparently, a multilocus or two-stage approach should be applied for this purpose. Several fragments of the chloroplast genome (trnH-psbA, matK, rpoC, rpoB, rbcL) in combinations of two or three regions were suggested as candidate regions with highest potential, but more representative samples should be examined to choose the best candidate. The possibility is discussed to use as DNA barcode internal transcribed spacers (ITS) of nuclear rRNA genes, which are highly variable, widely employed in molecular phylogenetic studies at the species level, but also have some limitations.},
}
@article {pmid19958506,
year = {2009},
author = {Lim, J and Kim, SY and Kim, S and Eo, HS and Kim, CB and Paek, WK and Kim, W and Bhak, J},
title = {BioBarcode: a general DNA barcoding database and server platform for Asian biodiversity resources.},
journal = {BMC genomics},
volume = {10 Suppl 3},
number = {Suppl 3},
pages = {S8},
pmid = {19958506},
issn = {1471-2164},
mesh = {Asian People/classification/*genetics ; *Biodiversity ; *Databases, Nucleic Acid ; *Electronic Data Processing ; Humans ; Sequence Analysis, DNA/*methods ; *Software Design ; },
abstract = {BACKGROUND: DNA barcoding provides a rapid, accurate, and standardized method for species-level identification using short DNA sequences. Such a standardized identification method is useful for mapping all the species on Earth, particularly when DNA sequencing technology is cheaply available. There are many nations in Asia with many biodiversity resources that need to be mapped and registered in databases.<br><br>RESULTS: We have built a general DNA barcode data processing system, BioBarcode, with open source software - which is a general purpose database and server. It uses mySQL RDBMS 5.0, BLAST2, and Apache httpd server. An exemplary database of BioBarcode has around 11,300 specimen entries (including GenBank data) and registers the biological species to map their genetic relationships. The BioBarcode database contains a chromatogram viewer which improves the performance in DNA sequence analyses.<br><br>CONCLUSION: Asia has a very high degree of biodiversity and the BioBarcode database server system aims to provide an efficient bioinformatics protocol that can be freely used by Asian researchers and research organizations interested in DNA barcoding. The BioBarcode promotes the rapid acquisition of biological species DNA sequence data that meet global standards by providing specialized services, and provides useful tools that will make barcoding cheaper and faster in the biodiversity community such as standardization, depository, management, and analysis of DNA barcode data. The system can be downloaded upon request, and an exemplary server has been constructed with which to build an Asian biodiversity system http://www.asianbarcode.org.},
}
@article {pmid20051122,
year = {2010},
author = {Boettcher, M and Fredebohm, J and Gholami, AM and Hachmo, Y and Dotan, I and Canaani, D and Hoheisel, JD},
title = {Decoding pooled RNAi screens by means of barcode tiling arrays.},
journal = {BMC genomics},
volume = {11},
number = {},
pages = {7},
pmid = {20051122},
issn = {1471-2164},
mesh = {Breast Neoplasms/genetics ; Cell Line, Tumor ; Humans ; Nucleic Acid Probes ; Oligonucleotide Array Sequence Analysis/*methods ; *RNA Interference ; RNA, Neoplasm/genetics ; RNA, Small Interfering/*genetics ; Recoverin ; Reproducibility of Results ; },
abstract = {BACKGROUND: RNAi screens via pooled short hairpin RNAs (shRNAs) have recently become a powerful tool for the identification of essential genes in mammalian cells. In the past years, several pooled large-scale shRNA screens have identified a variety of genes involved in cancer cell proliferation. All of those studies employed microarray analysis, utilizing either the shRNA's half hairpin sequence or an additional shRNA-associated 60 nt barcode sequence as a molecular tag. Here we describe a novel method to decode pooled RNAi screens, namely barcode tiling array analysis, and demonstrate how this approach can be used to precisely quantify the abundance of individual shRNAs from a pool.<br><br>RESULTS: We synthesized DNA microarrays with six overlapping 25 nt long tiling probes complementary to each unique 60 nt molecular barcode sequence associated with every shRNA expression construct. By analyzing dilution series of expression constructs we show how our approach allows quantification of shRNA abundance from a pool and how it clearly outperforms the commonly used analysis via the shRNA's half hairpin sequences. We further demonstrate how barcode tiling arrays can be used to predict anti-proliferative effects of individual shRNAs from pooled negative selection screens. Out of a pool of 305 shRNAs, we identified 28 candidate shRNAs to fully or partially impair the viability of the breast carcinoma cell line MDA-MB-231. Individual validation of a subset of eleven shRNA expression constructs with potential inhibitory, as well as non-inhibitory, effects on the cell line proliferation provides further evidence for the accuracy of the barcode tiling approach.<br><br>CONCLUSIONS: In summary, we present an improved method for the rapid, quantitative and statistically robust analysis of pooled RNAi screens. Our experimental approach, coupled with commercially available lentiviral vector shRNA libraries, has the potential to greatly facilitate the discovery of putative targets for cancer therapy as well as sensitizers of drug toxicity.},
}
@article {pmid20035628,
year = {2009},
author = {Wiemers, M and Keller, A and Wolf, M},
title = {ITS2 secondary structure improves phylogeny estimation in a radiation of blue butterflies of the subgenus Agrodiaetus (Lepidoptera: Lycaenidae: Polyommatus).},
journal = {BMC evolutionary biology},
volume = {9},
number = {},
pages = {300},
pmid = {20035628},
issn = {1471-2148},
mesh = {Animals ; Butterflies/anatomy &amp; histology/*classification/*genetics ; DNA, Ribosomal Spacer/chemistry/*genetics ; Evolution, Molecular ; Female ; Male ; Nucleic Acid Conformation ; *Phylogeny ; Polymerase Chain Reaction ; },
abstract = {BACKGROUND: Current molecular phylogenetic studies of Lepidoptera and most other arthropods are predominantly based on mitochondrial genes and a limited number of nuclear genes. The nuclear genes, however, generally do not provide sufficient information for young radiations. ITS2 , which has proven to be an excellent nuclear marker for similarly aged radiations in other organisms like fungi and plants, is only rarely used for phylogeny estimation in arthropods, although universal primers exist. This is partly due to difficulties in the alignment of ITS2 sequences in more distant taxa. The present study uses ITS2 secondary structure information to elucidate the phylogeny of a species-rich young radiation of arthropods, the butterfly subgenus Agrodiaetus. One aim is to evaluate the efficiency of ITS2 to resolve the phylogeny of the subgenus in comparison with COI , the most important mitochondrial marker in arthropods. Furthermore, we assess the use of compensatory base changes in ITS2 for the delimitation of species and discuss the prospects of ITS2 as a nuclear marker for barcoding studies.<br><br>RESULTS: In the butterfly family Lycaenidae, ITS2 secondary structure enabled us to successfully align sequences of different subtribes in Polyommatini and produce a Profile Neighbour Joining tree of this tribe, the resolution of which is comparable to phylogenetic trees obtained with COI+COII . The subgenus Agrodiaetus comprises 6 major clades which are in agreement with COI analyses. A dispersal-vicariance analysis (DIVA) traced the origin of most Agrodiaetus clades to separate biogeographical areas in the region encompassing Eastern Anatolia, Transcaucasia and Iran.<br><br>CONCLUSIONS: With the inclusion of secondary structure information, ITS2 appears to be a suitable nuclear marker to infer the phylogeny of young radiations, as well as more distantly related genera within a diverse arthropod family. Its phylogenetic signal is comparable to the mitochondrial marker COI . Compensatory base changes are very rare within Polyommatini and cannot be used for species delimitation. The implementation of secondary structure information into character-based phylogenetic methods is suggested to further improve the versatility of this marker in phylogenetic studies.},
}
@article {pmid20033492,
year = {2010},
author = {Yang, R and Wu, X and Yan, P and Li, X},
title = {Using DNA barcodes to identify a bird involved in a birdstrike at a Chinese airport.},
journal = {Molecular biology reports},
volume = {37},
number = {7},
pages = {3517-3523},
pmid = {20033492},
issn = {1573-4978},
mesh = {*Aircraft ; *Airports ; Animals ; Birds/*classification/*genetics ; China ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Electrophoresis, Agar Gel ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {One day at dusk in August, 200X, an airplane was struck by a bird at a Chinese airport (M Airport). After a careful check, some blades of the plane's engine were found to be out of shape and a few feathers and some bloodstains were found in the air intake of the engine. In order to know which species of bird was involved in the birdstrike, firstly we extracted DNA from the bloodstains; secondly, the DNA barcode (portion of COI gene) of the unknown species was amplified by PCR method; thirdly, sequence divergences (K2P differences) of the DNA barcode between the unknown species and a library of 59 common bird species distributed at the airport area were analyzed. Furthermore, a neighbor-joining (NJ) tree based on COI barcodes was created to provide graphic representation of sequence divergences among the species to confirm the identification. The result showed that red-rumped swallow (Hirundo daurica) was involved in the birdstrike incident. Some suggestions to avoid birdstrikes caused by red-rumped swallows were given to the administrative department of M Airport to ensure flying safety.},
}
@article {pmid20032981,
year = {2010},
author = {Hearty, S and Leonard, P and O'Kennedy, R},
title = {Nanomedicine: barcodes check out prostate cancer.},
journal = {Nature nanotechnology},
volume = {5},
number = {1},
pages = {9-10},
pmid = {20032981},
issn = {1748-3395},
mesh = {Antibodies/immunology ; Biosensing Techniques/*methods ; Gold/*chemistry ; Humans ; Male ; *Metal Nanoparticles/chemistry ; Nanomedicine ; Prostate-Specific Antigen/*blood/immunology ; Prostatic Neoplasms/*diagnosis ; },
}
@article {pmid20029596,
year = {2009},
author = {Yeh, SL and Yang, HJ and Lin, ST and Wu, MW},
title = {Replacers of barcodes for small application areas by using grating dots to diffractively form bright points.},
journal = {Applied optics},
volume = {48},
number = {36},
pages = {6940-6945},
doi = {10.1364/AO.48.006940},
pmid = {20029596},
issn = {1539-4522},
abstract = {Although barcodes can be used to manage data conveniently, they cannot be applied to small areas. Therefore, pointcodes are used to overcome the issue in this article. A pointcode uses a pointcode pattern to encode data and uses a pointcode image to decode data. A pointcode pattern is composed of many grating dots with different specified grating pitches and grating orientations. Moreover, there are two grating-dot sizes generated. When a laser beam illuminates a pointcode pattern with correct illuminating conditions, a pointcode image corresponding to the hidden data is diffractively reconstructed. A pointcode image is composed of many bright points with different positions. There are two possible bright-point sizes generated. A bright point or two bright points at specified positions are used to denote a number. Small pointcode patterns are enough to diffractively form pointcode images.},
}
@article {pmid20024084,
year = {2010},
author = {Marcon, L and Battersby, BJ and Rühmann, A and Ford, K and Daley, M and Lawrie, GA and Trau, M},
title = {'On-the-fly' optical encoding of combinatorial peptide libraries for profiling of protease specificity.},
journal = {Molecular bioSystems},
volume = {6},
number = {1},
pages = {225-233},
doi = {10.1039/b909087h},
pmid = {20024084},
issn = {1742-2051},
mesh = {Combinatorial Chemistry Techniques/*methods ; Flow Cytometry ; Models, Theoretical ; Peptide Hydrolases/*metabolism ; *Peptide Library ; Substrate Specificity ; },
abstract = {Large solid-phase combinatorial libraries currently play an important role in areas such as infectious disease biomarker discovery, profiling of protease specificity and anticancer drug discovery. Because compounds on solid support beads are not positionally-encoded as they are in microarrays, innovative methods of encoding are required. There are many advantages associated with optical encoding and several strategies have been described in the literature to combine fluorescence encoding methods with solid-phase library synthesis. We have previously introduced an alternative fluorescence-based encoding method ("colloidal barcoding"), which involves encoding 10-20 mum support beads during a split-and-mix synthesis with smaller 0.6-0.8 mum silica colloids that contain specific and identifiable combinations of fluorescent dye. The power of this 'on-the-fly' encoding approach lies in the efficient use of a small number of fluorescent dyes to encode millions of compounds. Described herein, for the first time, is the use of a colloid-barcoded library in a biological assay (i.e., protease profiling) combined with the use of confocal microscopy to decode the colloidal barcode. In this proof-of-concept demonstration, a small focussed peptide library was optically-encoded during a combinatorial synthesis, incubated with a protease (trypsin), analysed by flow cytometry and decoded via confocal microscopy. During assay development, a range of parameters were investigated and optimised, including substrate (or probe) loading, barcode stability, characteristics of the peptide-tagging fluorophore, and spacer group configuration. Through successful decoding of the colloidal barcodes, it was confirmed that specific peptide sequences presenting one or two cleavage sites were recognised by trypsin while peptide sequences not cleavable by trypsin remained intact.},
}
@article {pmid20015856,
year = {2010},
author = {Hebert, PD and Dewaard, JR and Landry, JF},
title = {DNA barcodes for 1/1000 of the animal kingdom.},
journal = {Biology letters},
volume = {6},
number = {3},
pages = {359-362},
pmid = {20015856},
issn = {1744-957X},
mesh = {Animals ; Classification/methods ; DNA/*genetics ; *Electronic Data Processing ; Lepidoptera/classification/genetics ; Phylogeny ; },
abstract = {This study reports DNA barcodes for more than 1300 Lepidoptera species from the eastern half of North America, establishing that 99.3 per cent of these species possess diagnostic barcode sequences. Intraspecific divergences averaged just 0.43 per cent among this assemblage, but most values were lower. The mean was elevated by deep barcode divergences (greater than 2%) in 5.1 per cent of the species, often involving the sympatric occurrence of two barcode clusters. A few of these cases have been analysed in detail, revealing species overlooked by the current taxonomic system. This study also provided a large-scale test of the extent of regional divergence in barcode sequences, indicating that geographical differentiation in the Lepidoptera of eastern North America is small, even when comparisons involve populations as much as 2800 km apart. The present results affirm that a highly effective system for the identification of Lepidoptera in this region can be built with few records per species because of the limited intra-specific variation. As most terrestrial and marine taxa are likely to possess a similar pattern of population structure, an effective DNA-based identification system can be developed with modest effort.},
}
@article {pmid20013991,
year = {2010},
author = {Li, X and Xia, J and Li, W and Zhang, S},
title = {Multianalyte electrochemical biosensor based on aptamer- and nanoparticle-integrated bio-barcode amplification.},
journal = {Chemistry, an Asian journal},
volume = {5},
number = {2},
pages = {294-300},
doi = {10.1002/asia.200900217},
pmid = {20013991},
issn = {1861-471X},
mesh = {Adenosine/*analysis ; Aptamers, Nucleotide/*chemistry ; *Biosensing Techniques ; DNA/chemistry ; Electrochemistry ; Gold/chemistry ; Humans ; Metal Nanoparticles/*chemistry ; Nucleic Acid Amplification Techniques/*methods ; Particle Size ; Surface Properties ; Thrombin/*analysis ; },
abstract = {In the present work, a signal-on electrochemical sensing strategy for the simultaneous detection of adenosine and thrombin is developed based on switching structures of aptamers. An Au electrode as the sensing surface is modified with two kinds of thiolated capture probes complementary to the linker DNA that contains either an adenosine aptamer or thrombin aptamer. The capture probes hybridize with their corresponding linker DNA, which has prehybridized with the reporter DNA loaded onto the gold nanoparticles (AuNPs). The AuNP contained two kinds of bio-barcode DNA: one is complementary to the linker DNA (reporter), whereas the other is not (signal) and is tagged with different metal sulfide nanoparticles. Thus a "sandwich-type" sensing interface is fabricated for adenosine and thrombin. With the introduction of adenosine and thrombin, the aptamer parts bind with their targets and fold to form the complex structures. As a result, the bio-barcoded AuNPs are released into solution. The metal sulfide nanoparticles are measured by anodic stripping voltammetry (ASV), and the concentrations of adenosine and thrombin are proportional to the signal of either metal ion. With the dual amplification of the bio-barcoded AuNP and the preconcentration of metal ions through ASV technology, detection limits as low as 6.6 x 10(-12) M for adenosine and 1.0 x 10(-12) M for thrombin are achieved. The sensor exhibits excellent selectivity and detectability in biological samples.},
}
@article {pmid20013262,
year = {2010},
author = {Lins-de-Barros, MM and Vieira, RP and Cardoso, AM and Monteiro, VA and Turque, AS and Silveira, CB and Albano, RM and Clementino, MM and Martins, OB},
title = {Archaea, Bacteria, and algal plastids associated with the reef-building corals Siderastrea stellata and Mussismilia hispida from Búzios, South Atlantic Ocean, Brazil.},
journal = {Microbial ecology},
volume = {59},
number = {3},
pages = {523-532},
pmid = {20013262},
issn = {1432-184X},
mesh = {Animals ; Anthozoa/*microbiology ; Archaea/*classification/genetics/isolation &amp; purification ; Atlantic Ocean ; Bacteria/*classification/genetics/isolation &amp; purification ; Brazil ; DNA, Algal/genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; *Ecosystem ; Eukaryota/*classification/genetics/isolation &amp; purification ; Gene Library ; Phylogeny ; Plastids/*genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Symbiosis ; Water Microbiology ; },
abstract = {Reef-building corals may be seen as holobiont organisms, presenting diverse associated microbial communities. Best known is the symbiotic relationship with zooxanthellae, but Archaea, Bacteria, fungi, viruses, and algal plastids are also abundant. Until now, there is little information concerning microbial communities associated with Brazilian corals. The present study aims to describe the diversity of Archaea, Bacteria, and eukaryotic algal plastid communities associated with two sympatric species, Siderastrea stellata and Mussismilia hispida, from Southeastern Brazil, using 16S rRNA gene libraries. Since corals present a high number of other associated invertebrates, coral barcoding (COI) was performed to confirm the exclusive occurrence of coral DNA in our samples. Our analysis yielded 354 distinct microbial OTUs, represented mainly by novel phylotypes. Richness (Chao1 and ACE) and diversity (H') estimations of the microbial communities associated with both species were high and comparable to other studies. Rarefaction analyses showed that microbial diversity of S. stellata is higher than that of M. hispida. Libshuff comparative analyses showed that the highest microbial community similarity between the two coral species occurred in the bacterial libraries, while archaeal and plastidial communities were significantly different. Crenarchaeota dominated archaeal communities, while Proteobacteria was the most abundant bacterial phylum, dominated by alpha-Proteobacteria. Plastids were also represented by novel phylotypes and did not match with any 16S rRNA sequences of Cyanobacteria and zooxanthellae from GenBank. Our data improves the pool of available information on Brazilian coral microbes and shows corals as sources of diverse prokaryotic and picoeukaryotic communities.},
}
@article {pmid20007379,
year = {2009},
author = {Orlando, L and Metcalf, JL and Alberdi, MT and Telles-Antunes, M and Bonjean, D and Otte, M and Martin, F and Eisenmann, V and Mashkour, M and Morello, F and Prado, JL and Salas-Gismondi, R and Shockey, BJ and Wrinn, PJ and Vasil'ev, SK and Ovodov, ND and Cherry, MI and Hopwood, B and Male, D and Austin, JJ and Hänni, C and Cooper, A},
title = {Revising the recent evolutionary history of equids using ancient DNA.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {106},
number = {51},
pages = {21754-21759},
pmid = {20007379},
issn = {1091-6490},
mesh = {Animals ; *Biological Evolution ; DNA/*genetics ; Fossils ; Horses/classification/*genetics ; Molecular Sequence Data ; },
abstract = {The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87-688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra, Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution of Equus. In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses.},
}
@article {pmid20005334,
year = {2010},
author = {Tang, Y and Wang, H and Xiang, J and Chen, Y and He, W and Deng, N and Yang, H},
title = {A sensitive immunosorbent bio-barcode assay combining PCR with icELISA for detection of gonyautoxin 2/3.},
journal = {Analytica chimica acta},
volume = {657},
number = {2},
pages = {210-214},
doi = {10.1016/j.aca.2009.10.045},
pmid = {20005334},
issn = {1873-4324},
mesh = {Antibodies, Monoclonal/immunology/metabolism ; DNA/chemistry ; Enzyme-Linked Immunosorbent Assay/*methods ; Glucose Oxidase/chemistry/metabolism ; Gold/chemistry ; Immunosorbents/immunology/metabolism ; Metal Nanoparticles/chemistry ; Polymerase Chain Reaction/*methods ; Saxitoxin/*analogs &amp; derivatives/analysis/chemistry ; },
abstract = {In the current study, we developed a nanosphere bio-barcode technology to detect trace gonyautoxin 2/3 (GTX 2/3). GTX 2/3-glucose oxidase (GOX) conjugates were first prepared as the coating antigen in a periodate reaction. Subsequently, gold nanoparticles (NP) dual-labeled with anti-GTX 2/3 monoclonal antibodies (Mab) and DNA oligonucleotides were synthesized via a one-step preparation method. Combining PCR with indirect competitive ELISA (icELISA), a novel immunosorbent bio-barcode assay was established utilizing the Mab-NP-dsDNA complex to convert enzymatic signals to DNA signals. Importantly, the limit of detection of the method was lower than 0.74 microg mL(-1). Thus, the immunosorbent bio-barcode assay is a rapid and high-throughput screening tool to detect GTX 2/3 in aquatic products.},
}
@article {pmid20004727,
year = {2010},
author = {Ács, Z and Challis, RJ and Bihari, P and Blaxter, M and Hayward, A and Melika, G and Csóka, G and Pénzes, Z and Pujade-Villar, J and Nieves-Aldrey, JL and Schönrogge, K and Stone, GN},
title = {Phylogeny and DNA barcoding of inquiline oak gallwasps (Hymenoptera: Cynipidae) of the Western Palaearctic.},
journal = {Molecular phylogenetics and evolution},
volume = {55},
number = {1},
pages = {210-225},
doi = {10.1016/j.ympev.2009.12.004},
pmid = {20004727},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Genes, Insect ; Haplotypes ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; Quercus ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; Wasps/classification/*genetics ; },
abstract = {We examine phylogenetic relationships within the Synergus complex of herbivorous inquiline gallwasps (Hymenoptera; Cynipidae; Synergini) associated with cynipid host galls on oak, a biologically diverse group whose genus-level morphological taxonomy has long been considered stable but whose species level taxonomy is problematic. We incorporate data for over 70% of recognised Western Palaearctic species in five morphology-based genera (Ceroptres, Saphonecrus, Synergus, Synophrus, Ufo), comprising sequence for two mitochondrial loci (coxI, cytb) and one nuclear locus (28S D2). In particular, we assess the evidence for monophyly of two long-established, morphology-defined sections within the genus Synergus that differ in a range of biological traits. To aid analyses of ecological interactions within oak cynipid communities, we also consider the utility of cytochrome oxidase I (coxI) DNA barcodes in the oak inquilines. In this assessment, we do not assume that species are delineated at a single threshold value of sequence divergence for a single gene, but examine concordance in the composition of molecular operational Taxonomic units (MOTUs) across a range of sequence divergences in each gene and across genes. We also assess the impact of sampling effort on MOTU stability. Phylogenetic reconstructions for all three loci support monophyly for Synergus and Synophrus, but reject monophyly for Saphonecrus and for the two sections within Synergus. The suites of traits associated with the two sections of the genus Synergus are thus homoplasious. All three loci also reject monophyly for three Synergus species (S. hayneanus, S. pallipes, S. umbraculus). Sequences for each locus identify robust MOTUs that are largely concordant across loci for a range of cut-off values. Though many MOTU's correspond to recognised Linnean species, there is significant, multigene disagreement between groupings supported by morphology and sequence data, with both allocation of different morphospecies to the same MOTU and allocation of the same morphospecies to multiple MOTUs, regardless of cut-off value. Our results imply that while DNA barcoding has considerable utility within this group, morphology-based identification needs major revision at both genus and species levels. Further, lifehistory traits currently attributed to single morphospecies probably confound attributes of multiple lineages. Revealing patterns of character state evolution in Synergus requires collection of new host association and life history data explicitly linked to DNA barcode data for the specimens concerned.},
}
@article {pmid20003263,
year = {2009},
author = {Smith, MA and Fisher, BL},
title = {Invasions, DNA barcodes, and rapid biodiversity assessment using ants of Mauritius.},
journal = {Frontiers in zoology},
volume = {6},
number = {},
pages = {31},
pmid = {20003263},
issn = {1742-9994},
abstract = {BACKGROUND: Using an understudied taxon (Hymenoptera, Formicidae) found on a tropical island (Mauritius) where native flora and fauna have been threatened by 400 years of habitat modification and introduced species, we tested whether estimated incidences of diversity and complementarity were similar when measured by standard morphological alpha-taxonomy or phylogenetic diversity (PD) based on a standardized mitochondrial barcode and corroborating nuclear marker.<br><br>RESULTS: We found that costs related to site loss (considered loss of evolutionary history measured as loss of barcode PD) were not significantly different from predictions made either a) using standard morphology-based taxonomy, or b) measured using a nuclear marker. Integrating morphology and barcode results permitted us to identify a case of initially morphologically-cryptic variation as a new and endemic candidate species. However, barcode estimates of the relative importance of each site or network of sites were dramatically affected when the species in question was known to be indigenous or introduced.<br><br>CONCLUSION: This study goes beyond a mere demonstration of the rapid gains possible for diversity assessment using a standardized DNA barcode. Contextualization of these gains with ecological and natural history information is necessary to calibrate this wealth of standardized information. Without such an integrative approach, critical opportunities to advance knowledge will be missed.},
}
@article {pmid20003245,
year = {2009},
author = {Zhou, X and Adamowicz, SJ and Jacobus, LM and Dewalt, RE and Hebert, PD},
title = {Towards a comprehensive barcode library for arctic life - Ephemeroptera, Plecoptera, and Trichoptera of Churchill, Manitoba, Canada.},
journal = {Frontiers in zoology},
volume = {6},
number = {},
pages = {30},
pmid = {20003245},
issn = {1742-9994},
abstract = {BACKGROUND: This study reports progress in assembling a DNA barcode reference library for Ephemeroptera, Plecoptera, and Trichoptera ("EPTs") from a Canadian subarctic site, which is the focus of a comprehensive biodiversity inventory using DNA barcoding. These three groups of aquatic insects exhibit a moderate level of species diversity, making them ideal for testing the feasibility of DNA barcoding for routine biotic surveys. We explore the correlation between the morphological species delineations, DNA barcode-based haplotype clusters delimited by a sequence threshold (2%), and a threshold-free approach to biodiversity quantification--phylogenetic diversity.<br><br>RESULTS: A DNA barcode reference library is built for 112 EPT species for the focal region, consisting of 2277 COI sequences. Close correspondence was found between EPT morphospecies and haplotype clusters as designated using a standard threshold value. Similarly, the shapes of taxon accumulation curves based upon haplotype clusters were very similar to those generated using phylogenetic diversity accumulation curves, but were much more computationally efficient.<br><br>CONCLUSION: The results of this study will facilitate other lines of research on northern EPTs and also bode well for rapidly conducting initial biodiversity assessments in unknown EPT faunas.},
}
@article {pmid20003213,
year = {2009},
author = {Kerr, KC and Birks, SM and Kalyakin, MV and Red'kin, YA and Koblik, EA and Hebert, PD},
title = {Filling the gap - COI barcode resolution in eastern Palearctic birds.},
journal = {Frontiers in zoology},
volume = {6},
number = {},
pages = {29},
pmid = {20003213},
issn = {1742-9994},
abstract = {BACKGROUND: The Palearctic region supports relatively few avian species, yet recent molecular studies have revealed that cryptic lineages likely still persist unrecognized. A broad survey of cytochrome c oxidase I (COI) sequences, or DNA barcodes, can aid on this front by providing molecular diagnostics for species assignment. Barcodes have already been extensively surveyed in the Nearctic, which provides an interesting comparison to this region; faunal interchange between these regions has been very dynamic. We explored COI sequence divergence within and between species of Palearctic birds, including samples from Russia, Kazakhstan, and Mongolia. As of yet, there is no consensus on the best method to analyze barcode data. We used this opportunity to compare and contrast three different methods routinely employed in barcoding studies: clustering-based, distance-based, and character-based methods.<br><br>RESULTS: We produced COI sequences from 1,674 specimens representing 398 Palearctic species. These were merged with published COI sequences from North American congeners, creating a final dataset of 2,523 sequences for 599 species. Ninety-six percent of the species analyzed could be accurately identified using one or a combination of the methods employed. Most species could be rapidly assigned using the cluster-based or distance-based approach alone. For a few select groups of species, the character-based method offered an additional level of resolution. Of the five groups of indistinguishable species, most were pairs, save for a larger group comprising the herring gull complex. Up to 44 species exhibited deep intraspecific divergences, many of which corresponded to previously described phylogeographic patterns and endemism hotspots.<br><br>CONCLUSION: COI sequence divergence within eastern Palearctic birds is largely consistent with that observed in birds from other temperate regions. Sequence variation is primarily congruent with taxonomic boundaries; deviations from this trend reveal overlooked biological patterns, and in some cases, overlooked species. More research is needed to further refine the taxonomic status of some Palearctic birds, but large genetic surveys such as this may facilitate this effort. DNA barcodes are a practical means for rapid species assignment, although efficient analytical methods will likely require a two-tiered approach to differentiate closely related pairs of species.},
}
@article {pmid20001442,
year = {2010},
author = {Kong, XL and Qi, H and Zhou, HX and Ren, LL and Deng, CY and Li, FR},
title = {A novel sensitive immunoassay by nucleic acid barcode dot and its application in the detection of prostate-specific antigen.},
journal = {Clinical chemistry and laboratory medicine},
volume = {48},
number = {2},
pages = {279-283},
doi = {10.1515/CCLM.2010.041},
pmid = {20001442},
issn = {1437-4331},
mesh = {Adult ; Aged ; DNA Probes/*analysis ; Dithiothreitol/chemistry ; Enzyme-Linked Immunosorbent Assay ; Female ; Flow Cytometry ; Gold/chemistry ; Humans ; Immunoassay/*methods ; Immunoglobulin M/chemistry ; Limit of Detection ; Magnetics ; Male ; Metal Nanoparticles/chemistry ; Middle Aged ; Polymerase Chain Reaction ; Prostate-Specific Antigen/*blood/genetics ; *Quantum Dots ; Radioimmunoassay ; },
abstract = {BACKGROUND: The sensitivity and selectivity of traditional methods limits ultramicro detection of proteins. Bio-barcode amplification detection methods based on nanotechnology enables ultramicro detection of protein. However, bio-barcode amplification detection depends on the oligonucleotides being fixed on a glass chip. It also requires specialized equipment, which limits its application. We introduce a nano-nucleic acid barcode dot detection technology to determine ultramicro concentrations of protein. The method is simple, quick and accurate.<br><br>METHODS: Magnetic probe (IgG-M) and dual-labeled gold nanoparticle bio-probe (IgG-Au-DNA) were prepared. Protein was captured using a sandwich assay technique and magnetic separation was used. The DNA barcode was released with dithiothreitol (DTT) and detected directly without the requirement for polymerase chain reaction (PCR). Serum prostate-specific antigen (PSA) from 135 patients was detected with this method and compared with enzyme linked immunosorbent assay (ELISA) and radioimmunoassay (RIA).<br><br>RESULTS: Each IgG-Au-DNA could be covered with 138+/-47 oligonucleotides and 11+/-3 antibodies. The IgG-M could bind 118 mug of antibody per mg. The sensitivity of nano-nucleic acid barcode dot detection technology might allow detection of 1 fg/mL. There were no significant differences in serum PSA from 135 patients when comparing the three methods (compared with ELISA, r=0.950; and with RIA, r=0.967).<br><br>CONCLUSIONS: The nucleic acid barcode dot method does not require special equipment or complex procedures, but its detection limit is 2-3 orders of magnitude lower than ELISA.},
}
@article {pmid19999380,
year = {2009},
author = {Bergmann, T and Hadrys, H and Breves, G and Schierwater, B},
title = {Character-based DNA barcoding: a superior tool for species classification.},
journal = {Berliner und Munchener tierarztliche Wochenschrift},
volume = {122},
number = {11-12},
pages = {446-450},
pmid = {19999380},
issn = {0005-9366},
mesh = {Animals ; Base Sequence ; DNA/*classification/*genetics ; Electron Transport Complex IV/genetics ; Electronic Data Processing/methods/*organization &amp; administration ; Genetic Variation ; Humans ; Insecta/genetics ; Models, Genetic ; Species Specificity ; Zoonoses/*transmission ; },
abstract = {In zoonosis research only correct assigned host-agent-vector associations can lead to success. If most biological species on Earth, from agent to host and from procaryotes to vertebrates, are still undetected, the development of a reliable and universal diversity detection tool becomes a conditio sine qua non. In this context, in breathtaking speed, modern molecular-genetic techniques have become acknowledged tools for the classification of life forms at all taxonomic levels. While previous DNA-barcoding techniques were criticised for several reasons (Moritz and Cicero, 2004; Rubinoff et al., 2006a, b; Rubinoff, 2006; Rubinoff and Haines, 2006) a new approach, the so called CAOS-barcoding (Character Attribute Organisation System), avoids most of the weak points. Traditional DNA-barcoding approaches are based on distances, i. e. they use genetic distances and tree construction algorithms for the classification of species or lineages. The definition of limit values is enforced and prohibits a discrete or clear assignment. In comparison, the new character-based barcoding (CAOS-barcoding; DeSalle et al., 2005; DeSalle, 2006; Rach et al., 2008) works with discrete single characters and character combinations which permits a clear, unambiguous classification. In Hannover (Germany) we are optimising this system and developing a semiautomatic high-throughput procedure for hosts, agents and vectors being studied within the Zoonosis Centre of the "Stiftung Tierärztliche Hochschule Hannover". Our primary research is concentrated on insects, the most successful and species-rich animal group on Earth (every fourth animal is a bug). One subgroup, the winged insects (Pterygota), represents the outstanding majority of all zoonosis relevant animal vectors.},
}
@article {pmid19997851,
year = {2011},
author = {Meiklejohn, KA and Wallman, JF and Dowton, M},
title = {DNA-based identification of forensically important Australian Sarcophagidae (Diptera).},
journal = {International journal of legal medicine},
volume = {125},
number = {1},
pages = {27-32},
pmid = {19997851},
issn = {1437-1596},
mesh = {Animals ; Base Sequence ; DNA Barcoding, Taxonomic ; Diptera/*genetics ; Electron Transport Complex IV/*genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {The utility of the forensically important Sarcophagidae (Diptera) for time since death estimates has been severely limited, as morphological identification is difficult and thermobiological histories are inadequately documented. A molecular identification method involving the sequencing of a 658-bp 'barcode' fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene from 85 specimens, representing 16 Australian species from varying populations, was evaluated. Nucleotide sequence divergences were calculated using the Kimura-two-parameter distance model and a neighbour-joining phylogenetic tree generated. All species were resolved as reciprocally monophyletic, except Sarcophaga dux. Intraspecific and interspecific variation ranged from 0.000% to 1.499% (SE = 0.044%) and 6.658% to 8.983% (SE = 0.653%), respectively. The COI 'barcode' sequence was found to be suitable for the molecular identification of the studied Australian Sarcophagidae: 96.5% of the examined specimens were assigned to the correct species. Given that the sarcophagid fauna is poorly described, it is feasible that the few incorrectly assigned specimens represent cryptic species. The results of this research will be instrumental for implementation of the Australian Sarcophagidae in forensic entomology.},
}
@article {pmid19994858,
year = {2010},
author = {Piao, L and Park, S and Lee, HB and Kim, K and Kim, J and Chung, TD},
title = {Single gold microshell tailored to sensitive surface enhanced Raman scattering probe.},
journal = {Analytical chemistry},
volume = {82},
number = {1},
pages = {447-451},
doi = {10.1021/ac901904v},
pmid = {19994858},
issn = {1520-6882},
mesh = {*Gold ; Metal Nanoparticles ; *Microspheres ; Spectrum Analysis, Raman/*instrumentation/*methods ; Surface Properties ; },
abstract = {We finely tuned the Au shell on a polystyrene microsphere of 2 microm in diameter to achieve a strong surface enhanced raman scattering (SERS)-active platform so that the molecules on a single microspherical shell surface produce their own fingerprint SERS spectra. The proposed microshells can be easily and individually manipulated under a conventional optical microscope using a micropipet and act as a sensitive probe to obtain the SERS spectra of the monolayer of molecules on Pt as well as Au surfaces without any requirement of special surface morphology or modification for inducing SERS activity. Well-defined SERS spectra can be obtained at a very short acquisition time of milliseconds, suggesting useful applications of the present system based on the decoding of the SERS-active barcodes on individually functionalized microshells.},
}
@article {pmid19965094,
year = {2009},
author = {Nie, M and Ren, J and Li, Z and Niu, J and Qiu, Y and Zhu, Y and Tong, S},
title = {SoundView: an auditory guidance system based on environment understanding for the visually impaired people.},
journal = {Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference},
volume = {2009},
number = {},
pages = {7240-7243},
doi = {10.1109/IEMBS.2009.5334754},
pmid = {19965094},
issn = {2375-7477},
mesh = {Acoustics ; Biomedical Engineering ; Blindness/*rehabilitation ; Environment ; Equipment Design ; Humans ; *Sensory Aids ; Signal Processing, Computer-Assisted ; Software ; User-Computer Interface ; },
abstract = {Without visual information, the blind people live in various hardships with shopping, reading, finding objects and etc. Therefore, we developed a portable auditory guide system, called SoundView, for visually impaired people. This prototype system consists of a mini-CCD camera, a digital signal processing unit and an earphone, working with built-in customizable auditory coding algorithms. Employing environment understanding techniques, SoundView processes the images from a camera and detects objects tagged with barcodes. The recognized objects in the environment are then encoded into stereo speech signals for the blind though an earphone. The user would be able to recognize the type, motion state and location of the interested objects with the help of SoundView. Compared with other visual assistant techniques, SoundView is object-oriented and has the advantages of cheap cost, smaller size, light weight, low power consumption and easy customization.},
}
@article {pmid19964258,
year = {2009},
author = {Frisch, P and Miodownik, S and Booth, P and Carragee, P and Dowling, M},
title = {Patient centric identification and association.},
journal = {Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference},
volume = {2009},
number = {},
pages = {1722-1725},
doi = {10.1109/IEMBS.2009.5333558},
pmid = {19964258},
issn = {2375-7477},
mesh = {Humans ; Information Systems ; Medical Errors/prevention &amp; control ; *Patient Identification Systems ; Patient Satisfaction ; Radio Waves ; },
abstract = {Increased technological complexity of medical devices and systems coupled with increased workloads and reduced staffing, have created difficulties and discontinuities in the management of patient information. These issues have directly impacted and contributed to a rise in equipment-related errors, patient dissatisfaction, a potential for patient injury and resulting overall increased concern for patient safety. In response these concerns a variety of new devices, systems and applications have been developed to share information, provide cross checks along with verified delivery of critical information to the point of care. These applications include biomedical information systems, medication administration, sample collection, and electronic medical records. The deployment of these new integrated and networked devices, systems and applications are dependent on an accurate and consistent patient identification and association methodology which dynamically manages the relationship between patients, staff and equipment. Since the association information is common to many applications and utilizes a variety of technologies, (i.e. active and passive radio frequency identification (RFID), barcodes, etc.) an institutional approach is necessary to mange these processes in a consistent manor utilizing a common set of identification hardware. Implementation of a "Patient Centric Identification and Association Platform" represents a significant advance in the management of clinical patient information. The implementation of a Biomedical Device Information Network at Memorial Sloan-Kettering Cancer Center (MSKCC) integrates the identification and association of patients with devices and care providers and provides the methodologies to manage alarms, providing the ability to filter low priority or nuisance alarms. This implementation enables critical information to be distributed directly to care providers utilizing dedicated communications devices. Patient Centric Identification and Association is the enabling technology providing precise identification and association establishing an enhanced environment of care, increased patient safety, and a clear proactive response to the regulatory requirements of the Joint Commission (JCAHO) national patient safety initiatives.},
}
@article {pmid19964165,
year = {2009},
author = {Gao, X},
title = {QD barcodes for biosensing and detection.},
journal = {Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference},
volume = {2009},
number = {},
pages = {6372-6373},
doi = {10.1109/IEMBS.2009.5333215},
pmid = {19964165},
issn = {2375-7477},
mesh = {Biomarkers, Tumor/*analysis ; Biosensing Techniques/*methods ; Contrast Media ; Electronic Data Processing ; Humans ; Male ; Prostate-Specific Antigen/*analysis ; Prostatic Neoplasms/*diagnosis/metabolism ; *Quantum Dots ; Spectrometry, Fluorescence/*methods ; },
abstract = {Multiplexed nanobarcodes have been prepared with quantum dots (QDs) and amphiphilic copolymers consisted of hydrocarbons and maleic anhydride groups. In homogenous solution, the QD-polymer complexes self-assemble into nanobeads with narrow size dispersity, which has been previously achieved only for micrometer-sized beads in the presence of solid supports. More than 250 QDs can be loaded into a nanobead of 100 nm in diameter. Using this new generation of nanoprobe, sensitive detection of human prostate specific antigen (PSA) has also been demonstrated. This new technology is expected to open new opportunities in nanoparticle-based ultrasensitive and multiplexed detection and sensing.},
}
@article {pmid19961657,
year = {2010},
author = {Adams, ER and Hamilton, PB and Rodrigues, AC and Malele, II and Delespaux, V and Teixeira, MM and Gibson, W},
title = {New Trypanosoma (Duttonella) vivax genotypes from tsetse flies in East Africa.},
journal = {Parasitology},
volume = {137},
number = {4},
pages = {641-650},
doi = {10.1017/S0031182009991508},
pmid = {19961657},
issn = {1469-8161},
mesh = {Animals ; DNA, Protozoan/genetics ; Fluorescence ; Gastrointestinal Tract/parasitology ; Genetic Variation ; Glyceraldehyde-3-Phosphate Dehydrogenases/genetics ; Insect Vectors/*parasitology ; Molecular Sequence Data ; Nucleic Acid Amplification Techniques ; Phylogeny ; Sequence Analysis, Protein ; Tanzania/epidemiology ; Trypanosoma vivax/classification/*genetics ; Trypanosomiasis, African/epidemiology/parasitology/*veterinary ; Tsetse Flies/*parasitology ; },
abstract = {Salivarian trypanosomes pose a substantial threat to livestock, but their full diversity is not known. To survey trypanosomes carried by tsetse in Tanzania, DNA samples from infected proboscides of Glossina pallidipes and G. swynnertoni were identified using fluorescent fragment length barcoding (FFLB), which discriminates species by size polymorphisms in multiple regions of the ribosomal RNA locus. FFLB identified the trypanosomes in 65 of 105 (61.9%) infected proboscides, revealing 9 mixed infections. Of 7 different FFLB profiles, 2 were similar but not identical to reference West African Trypanosoma vivax; 5 other profiles belonged to known species also identified in fly midguts. Phylogenetic analysis of the glycosomal glyceraldehyde phosphate dehydrogenase gene revealed that the Tanzanian T. vivax samples fell into 2 distinct groups, both outside the main clade of African and South American T. vivax. These new T. vivax genotypes were common and widespread in tsetse in Tanzania. The T. brucei-like trypanosome previously described from tsetse midguts was also found in 2 proboscides, demonstrating a salivarian transmission route. Investigation of mammalian host range and pathogenicity will reveal the importance of these new trypanosomes for the epidemiology and control of animal trypanosomiasis in East Africa.},
}
@article {pmid19960671,
year = {2009},
author = {Dunphy, BM and Tucker, BJ and Petersen, MJ and Blitvich, BJ and Bartholomay, LC},
title = {Arrival and establishment of Aedes japonicus japonicus (Diptera: Culicidae) in Iowa.},
journal = {Journal of medical entomology},
volume = {46},
number = {6},
pages = {1282-1289},
doi = {10.1603/033.046.0605},
pmid = {19960671},
issn = {0022-2585},
mesh = {Aedes/genetics/*physiology/virology ; Animal Migration ; Animals ; DNA/chemistry ; Insect Vectors/genetics/*physiology/virology ; Iowa ; La Crosse virus/isolation &amp; purification ; West Nile virus/isolation &amp; purification ; },
abstract = {The arrival and establishment of Aedes (Finlaya) japonicus japonicus (Theobald) (Diptera: Culicidae) in Iowa are reported. In total, 518 wild adult specimens were collected through the statewide mosquito and mosquito-borne virus surveillance program in 2007 and 2008. Specimens were collected with New Jersey light traps, CO2-baited CDC light traps, grass infusion-baited gravid traps, and Mosquito Magnet traps located in 12 counties in central and eastern Iowa Specimens were identified morphologically, and identity was further supported by molecular DNA barcoding. Specimens also were tested for infection with West Nile virus (family Flaviviridae, genus Flavivirus, WNV) and La Crosse virus (family Bunyaviridae, genus Bunyavirus, LACV) by reverse transcription-polymerase chain reaction. Although no specimens tested positive for arbovirus infection, the arrival of Ae. j. japonicus in Iowa is a public health concern considering its potential to transmit several arboviruses, particularly WNV and LACV.},
}
@article {pmid19900305,
year = {2009},
author = {Kuksa, P and Pavlovic, V},
title = {Efficient alignment-free DNA barcode analytics.},
journal = {BMC bioinformatics},
volume = {10 Suppl 14},
number = {Suppl 14},
pages = {S9},
pmid = {19900305},
issn = {1471-2105},
mesh = {Animals ; Base Sequence ; *Computational Biology ; *Electronic Data Processing ; Molecular Sequence Data ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: In this work we consider barcode DNA analysis problems and address them using alternative, alignment-free methods and representations which model sequences as collections of short sequence fragments (features). The methods use fixed-length representations (spectrum) for barcode sequences to measure similarities or dissimilarities between sequences coming from the same or different species. The spectrum-based representation not only allows for accurate and computationally efficient species classification, but also opens possibility for accurate clustering analysis of putative species barcodes and identification of critical within-barcode loci distinguishing barcodes of different sample groups.<br><br>RESULTS: New alignment-free methods provide highly accurate and fast DNA barcode-based identification and classification of species with substantial improvements in accuracy and speed over state-of-the-art barcode analysis methods. We evaluate our methods on problems of species classification and identification using barcodes, important and relevant analytical tasks in many practical applications (adverse species movement monitoring, sampling surveys for unknown or pathogenic species identification, biodiversity assessment, etc.) On several benchmark barcode datasets, including ACG, Astraptes, Hesperiidae, Fish larvae, and Birds of North America, proposed alignment-free methods considerably improve prediction accuracy compared to prior results. We also observe significant running time improvements over the state-of-the-art methods.<br><br>CONCLUSION: Our results show that newly developed alignment-free methods for DNA barcoding can efficiently and with high accuracy identify specimens by examining only few barcode features, resulting in increased scalability and interpretability of current computational approaches to barcoding.},
}
@article {pmid19900304,
year = {2009},
author = {Chu, KH and Xu, M and Li, CP},
title = {Rapid DNA barcoding analysis of large datasets using the composition vector method.},
journal = {BMC bioinformatics},
volume = {10 Suppl 14},
number = {Suppl 14},
pages = {S8},
pmid = {19900304},
issn = {1471-2105},
mesh = {Animals ; Birds/classification/genetics ; Computational Biology ; *Databases, Nucleic Acid ; *Electronic Data Processing ; Fishes/classification/genetics ; Nematoda/classification/genetics ; Sequence Analysis, DNA/*methods ; Time Factors ; },
abstract = {BACKGROUND: Sequence alignment is the rate-limiting step in constructing profile trees for DNA barcoding purposes. We recently demonstrated the feasibility of using unaligned rRNA sequences as barcodes based on a composition vector (CV) approach without sequence alignment (Bioinformatics 22:1690). Here, we further explored the grouping effectiveness of the CV method in large DNA barcode datasets (COI, 18S and 16S rRNA) from a variety of organisms, including birds, fishes, nematodes and crustaceans.<br><br>RESULTS: Our results indicate that the grouping of taxa at the genus/species levels based on the CV/NJ approach is invariably consistent with the trees generated by traditional approaches, although in some cases the clustering among higher groups might differ. Furthermore, the CV method is always much faster than the K2P method routinely used in constructing profile trees for DNA barcoding. For instance, the alignment of 754 COI sequences (average length 649 bp) from fishes took more than ten hours to complete, while the whole tree construction process using the CV/NJ method required no more than five minutes on the same computer.<br><br>CONCLUSION: The CV method performs well in grouping effectiveness of DNA barcode sequences, as compared to K2P analysis of aligned sequences. It was also able to reduce the time required for analysis by over 15-fold, making it a far superior method for analyzing large datasets. We conclude that the CV method is a fast and reliable method for analyzing large datasets for DNA barcoding purposes.},
}
@article {pmid19900303,
year = {2009},
author = {Bertolazzi, P and Felici, G and Weitschek, E},
title = {Learning to classify species with barcodes.},
journal = {BMC bioinformatics},
volume = {10 Suppl 14},
number = {Suppl 14},
pages = {S7},
pmid = {19900303},
issn = {1471-2105},
mesh = {Animals ; Classification/*methods ; Computational Biology/*methods ; *Electronic Data Processing ; Humans ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: According to many field experts, specimens classification based on morphological keys needs to be supported with automated techniques based on the analysis of DNA fragments. The most successful results in this area are those obtained from a particular fragment of mitochondrial DNA, the gene cytochrome c oxidase I (COI) (the "barcode"). Since 2004 the Consortium for the Barcode of Life (CBOL) promotes the collection of barcode specimens and the development of methods to analyze the barcode for several tasks, among which the identification of rules to correctly classify an individual into its species by reading its barcode.<br><br>RESULTS: We adopt a Logic Mining method based on two optimization models and present the results obtained on two datasets where a number of COI fragments are used to describe the individuals that belong to different species. The method proposed exhibits high correct recognition rates on a training-testing split of the available data using a small proportion of the information available (e.g., correct recognition approx. 97% when only 20 sites of the 648 available are used). The method is able to provide compact formulas on the values (A, C, G, T) at the selected sites that synthesize the characteristic of each species, a relevant information for taxonomists.<br><br>CONCLUSION: We have presented a Logic Mining technique designed to analyze barcode data and to provide detailed output of interest to the taxonomists and the barcode community represented in the CBOL Consortium. The method has proven to be effective, efficient and precise.},
}
@article {pmid19900300,
year = {2009},
author = {Hajibabaei, M and Singer, GA},
title = {Googling DNA sequences on the World Wide Web.},
journal = {BMC bioinformatics},
volume = {10 Suppl 14},
number = {Suppl 14},
pages = {S4},
pmid = {19900300},
issn = {1471-2105},
mesh = {Base Sequence ; *Computational Biology ; Databases, Genetic ; *Information Storage and Retrieval ; *Internet ; Molecular Sequence Data ; Sequence Analysis, DNA/*methods ; Software Design ; },
abstract = {BACKGROUND: New web-based technologies provide an excellent opportunity for sharing and accessing information and using web as a platform for interaction and collaboration. Although several specialized tools are available for analyzing DNA sequence information, conventional web-based tools have not been utilized for bioinformatics applications. We have developed a novel algorithm and implemented it for searching species-specific genomic sequences, DNA barcodes, by using popular web-based methods such as Google.<br><br>RESULTS: We developed an alignment independent character based algorithm based on dividing a sequence library (DNA barcodes) and query sequence to words. The actual search is conducted by conventional search tools such as freely available Google Desktop Search. We implemented our algorithm in two exemplar packages. We developed pre and post-processing software to provide customized input and output services, respectively. Our analysis of all publicly available DNA barcode sequences shows a high accuracy as well as rapid results.<br><br>CONCLUSION: Our method makes use of conventional web-based technologies for specialized genetic data. It provides a robust and efficient solution for sequence search on the web. The integration of our search method for large-scale sequence libraries such as DNA barcodes provides an excellent web-based tool for accessing this information and linking it to other available categories of information on the web.},
}
@article {pmid19900297,
year = {2009},
author = {Austerlitz, F and David, O and Schaeffer, B and Bleakley, K and Olteanu, M and Leblois, R and Veuille, M and Laredo, C},
title = {DNA barcode analysis: a comparison of phylogenetic and statistical classification methods.},
journal = {BMC bioinformatics},
volume = {10 Suppl 14},
number = {Suppl 14},
pages = {S10},
pmid = {19900297},
issn = {1471-2105},
mesh = {Computational Biology ; Computer Simulation ; Databases, Nucleic Acid ; *Electronic Data Processing ; Mutation ; *Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: DNA barcoding aims to assign individuals to given species according to their sequence at a small locus, generally part of the CO1 mitochondrial gene. Amongst other issues, this raises the question of how to deal with within-species genetic variability and potential transpecific polymorphism. In this context, we examine several assignation methods belonging to two main categories: (i) phylogenetic methods (neighbour-joining and PhyML) that attempt to account for the genealogical framework of DNA evolution and (ii) supervised classification methods (k-nearest neighbour, CART, random forest and kernel methods). These methods range from basic to elaborate. We investigated the ability of each method to correctly classify query sequences drawn from samples of related species using both simulated and real data. Simulated data sets were generated using coalescent simulations in which we varied the genealogical history, mutation parameter, sample size and number of species.<br><br>RESULTS: No method was found to be the best in all cases. The simplest method of all, "one nearest neighbour", was found to be the most reliable with respect to changes in the parameters of the data sets. The parameter most influencing the performance of the various methods was molecular diversity of the data. Addition of genetically independent loci--nuclear genes--improved the predictive performance of most methods.<br><br>CONCLUSION: The study implies that taxonomists can influence the quality of their analyses either by choosing a method best-adapted to the configuration of their sample, or, given a certain method, increasing the sample size or altering the amount of molecular diversity. This can be achieved either by sequencing more mtDNA or by sequencing additional nuclear genes. In the latter case, they may also have to modify their data analysis method.},
}
@article {pmid19954512,
year = {2009},
author = {Parks, M and Cronn, R and Liston, A},
title = {Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes.},
journal = {BMC biology},
volume = {7},
number = {},
pages = {84},
pmid = {19954512},
issn = {1741-7007},
mesh = {Chloroplasts/*genetics ; Classification ; DNA, Chloroplast ; DNA, Complementary ; *Evolution, Molecular ; Expressed Sequence Tags ; Genes, Plant ; Genome, Chloroplast/*genetics ; *Genome, Plant ; Phylogeny ; Pinus/*genetics ; Sequence Alignment ; },
abstract = {BACKGROUND: Molecular evolutionary studies share the common goal of elucidating historical relationships, and the common challenge of adequately sampling taxa and characters. Particularly at low taxonomic levels, recent divergence, rapid radiations, and conservative genome evolution yield limited sequence variation, and dense taxon sampling is often desirable. Recent advances in massively parallel sequencing make it possible to rapidly obtain large amounts of sequence data, and multiplexing makes extensive sampling of megabase sequences feasible. Is it possible to efficiently apply massively parallel sequencing to increase phylogenetic resolution at low taxonomic levels?<br><br>RESULTS: We reconstruct the infrageneric phylogeny of Pinus from 37 nearly-complete chloroplast genomes (average 109 kilobases each of an approximately 120 kilobase genome) generated using multiplexed massively parallel sequencing. 30/33 ingroup nodes resolved with > or = 95% bootstrap support; this is a substantial improvement relative to prior studies, and shows massively parallel sequencing-based strategies can produce sufficient high quality sequence to reach support levels originally proposed for the phylogenetic bootstrap. Resampling simulations show that at least the entire plastome is necessary to fully resolve Pinus, particularly in rapidly radiating clades. Meta-analysis of 99 published infrageneric phylogenies shows that whole plastome analysis should provide similar gains across a range of plant genera. A disproportionate amount of phylogenetic information resides in two loci (ycf1, ycf2), highlighting their unusual evolutionary properties.<br><br>CONCLUSION: Plastome sequencing is now an efficient option for increasing phylogenetic resolution at lower taxonomic levels in plant phylogenetic and population genetic analyses. With continuing improvements in sequencing capacity, the strategies herein should revolutionize efforts requiring dense taxon and character sampling, such as phylogeographic analyses and species-level DNA barcoding.},
}
@article {pmid19954444,
year = {2009},
author = {Dantas-Torres, F and Lia, RP and Barbuto, M and Casiraghi, M and Crovace, A and Caligiani, L and Genchi, C and Otranto, D},
title = {Ocular dirofilariosis by Dirofilaria immitis in a dog: first case report from Europe.},
journal = {The Journal of small animal practice},
volume = {50},
number = {12},
pages = {667-669},
doi = {10.1111/j.1748-5827.2009.00846.x},
pmid = {19954444},
issn = {1748-5827},
mesh = {Animals ; DNA, Helminth/analysis ; *Dirofilaria immitis/isolation &amp; purification ; Dirofilariasis/*diagnosis/surgery ; Dog Diseases/*diagnosis/surgery ; Dogs ; Europe/epidemiology ; Eye Infections, Parasitic/diagnosis/surgery/*veterinary ; Female ; Male ; Polymerase Chain Reaction/veterinary ; },
abstract = {A five-year-old, entire female mixed-breed dog was presented with corneal oedema and episcleral hyperaemia in the left eye. The ophthalmological examination revealed the presence of a free-swimming nematode in the anterior chamber. Circulating microfilariae were not observed by a modified Knott test nor were adult antigens detected in serum by a commercial ELISA. The parasite was surgically removed from the dog's eye, but its anterior end was damaged during the surgery. Based on the morphology of the posterior end, the nematode was preliminarily identified as a male Dirofilaria immitis. The species identification was confirmed by PCR amplification and sequencing of the mitochondrial coxI and 12S rDNA genes, using a DNA barcoding approach. Although other cases of ocular dirofilariosis by D. immitis have been previously recorded in Australia and the United States, the case reported herein is the first in a dog from Europe.},
}
@article {pmid19942024,
year = {2009},
author = {Byrd-Bredbenner, C and Abbot, JM and Cussler, E},
title = {Nutrient profile of household food supplies of families with young children.},
journal = {Journal of the American Dietetic Association},
volume = {109},
number = {12},
pages = {2057-2062},
doi = {10.1016/j.jada.2009.09.006},
pmid = {19942024},
issn = {1878-3570},
mesh = {Child ; *Child Nutritional Physiological Phenomena ; Child, Preschool ; Cross-Sectional Studies ; Diet/*standards/statistics &amp; numerical data ; Dietary Carbohydrates/administration &amp; dosage ; Dietary Fats/administration &amp; dosage ; Dietary Proteins/administration &amp; dosage ; Environment ; Feeding Behavior ; Female ; *Food Analysis ; Food Supply/*statistics &amp; numerical data ; Humans ; Male ; *Nutrition Assessment ; *Nutrition Policy ; Nutritional Requirements ; Nutritive Value ; },
abstract = {Currently, little is known about the home food environment. This cross-sectional study was designed to describe the food sources of calories and key nutrients in the households of 100 families with at least one child aged 12 years or younger and compare nutrient availability to recommended levels. Participating households were food secure, ate dinner at home at least three times weekly, had parents who were married or living as domestic partners and not employed in a health-related profession, and resided in New Jersey. Researchers visited each household once during 2006/2007 to inventory all foods except alcoholic beverages, commercial baby food, infant formula, pet foods, refrigerated leftovers, foods of minimal nutrient and calorie content, condiments typically consumed in small quantities per eating occasion, and bulk supplies of staples. Inventories were taken using commercial diet analysis software customized to use barcode scanners for foods with standard barcodes and keyword searches for foods lacking barcodes. Protein, carbohydrate, and fat in the households supplied an average of approximately 15%, 57%, and 29% of calories, respectively. Saturated fat and total sugar accounted for an average of approximately 10% and 20%, respectively, of calories. Mean nutrient adequacy ratio for nutrients recommended to be maximized (ie, vitamins A and C, protein, dietary fiber, iron, calcium) was less than optimal, and mean ratio for those recommended to be minimized (ie, total fat, cholesterol, sodium, and sugar) exceeded recommendations. Categorization by food group revealed that the greatest availability of calories, carbohydrates, dietary fiber, total sugar, sodium, and iron was from grains. The greatest availability of total fat, cholesterol, and protein was from meat/protein foods. Dairy products contained the greatest quantities of saturated fat and calcium. This study expands the limited research on the home food supply and provides insights that may have important implications for health-promotion interventions.},
}
@article {pmid19941858,
year = {2010},
author = {Wang, G and Zhou, F and Olman, V and Li, F and Xu, Y},
title = {Prediction of pathogenicity islands in enterohemorrhagic Escherichia coli O157:H7 using genomic barcodes.},
journal = {FEBS letters},
volume = {584},
number = {1},
pages = {194-198},
doi = {10.1016/j.febslet.2009.11.067},
pmid = {19941858},
issn = {1873-3468},
mesh = {*Base Composition ; Chromosomes, Bacterial/*genetics ; Escherichia coli O157/genetics/*pathogenicity ; Genomic Islands/*genetics ; Genomics/*methods ; Sequence Analysis, DNA/*methods ; },
abstract = {The genome of lethal animal pathogenic bacterium Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is characterized by the presence of multiple pathogenicity islands (PAIs). Computational methods have been developed to identify PAIs based on the distinguishing G+C levels in some PAI versus non-PAI regions. We observed that PAIs can have a very similar G+C level to that of the host chromosome, which may have led to false negative predictions using these methods. We have applied a novel method of genomic barcodes to identify PAIs. Using this technique, we have successfully identified both known and novel PAIs in the genomes of three strains of EHEC O157:H7.},
}
@article {pmid19938832,
year = {2009},
author = {White, KA and Chengelis, DA and Gogick, KA and Stehman, J and Rosi, NL and Petoud, S},
title = {Near-infrared luminescent lanthanide MOF barcodes.},
journal = {Journal of the American Chemical Society},
volume = {131},
number = {50},
pages = {18069-18071},
doi = {10.1021/ja907885m},
pmid = {19938832},
issn = {1520-5126},
mesh = {Electronic Data Processing/instrumentation/*methods ; Lanthanoid Series Elements/*chemistry ; Luminescent Agents/*chemistry ; Luminescent Measurements ; Materials Testing ; Models, Molecular ; Molecular Structure ; Organometallic Compounds/*chemistry ; Spectroscopy, Near-Infrared/methods ; },
abstract = {We demonstrate the conceptual advantage of using metal-organic frameworks (MOFs) for the creation of a polymetallic material that contains several different near-IR-emitting lanthanide cations and operates as a barcode material with unique luminescence properties. By choosing the ratio of lanthanide salts used during the synthesis, we can control the ratio of lanthanide cations present in the resulting material. We have demonstrated that the emission intensity of each of the different lanthanide cations is proportional to its amount in the MOF crystal, resulting in unique spectroscopic barcodes that depend on the lanthanide cation ratios and compositions.},
}
@article {pmid19931580,
year = {2010},
author = {Hauck, TS and Giri, S and Gao, Y and Chan, WC},
title = {Nanotechnology diagnostics for infectious diseases prevalent in developing countries.},
journal = {Advanced drug delivery reviews},
volume = {62},
number = {4-5},
pages = {438-448},
doi = {10.1016/j.addr.2009.11.015},
pmid = {19931580},
issn = {1872-8294},
mesh = {*Developing Countries ; HIV Infections/diagnosis/epidemiology/virology ; Humans ; Infections/*diagnosis/epidemiology ; Malaria/diagnosis/epidemiology/parasitology ; Nanotechnology/*trends ; Tuberculosis/diagnosis/epidemiology/microbiology ; },
abstract = {Infectious diseases are prevalent in the developing world and are one of the developing world's major sources of morbidity and mortality. While infectious diseases can initiate in a localized region, they can spread rapidly at any moment due to the ease of traveling from one part of the world to the next. This could lead to a global pandemic. One key to preventing this spread is the development of diagnostics that can quickly identify the infectious agent so that one can properly treat or in some severe cases, quarantine a patient. There have been major advances in diagnostic technologies but infectious disease diagnostics are still based on 50-year technologies that are limited by speed of analysis, need for skilled workers, poor detection threshold and inability to detect multiple strains of infectious agents. Here, we describe advances in nanotechnology and microtechnology diagnostics for infectious diseases. In these diagnostic schemes, the nanomaterials are used as labels or barcodes while microfluidic systems are used to automate the sample preparation and the assays. We describe the current state of the field and the challenges.},
}
@article {pmid19924239,
year = {2009},
author = {Lowenstein, JH and Amato, G and Kolokotronis, SO},
title = {The real maccoyii: identifying tuna sushi with DNA barcodes--contrasting characteristic attributes and genetic distances.},
journal = {PloS one},
volume = {4},
number = {11},
pages = {e7866},
pmid = {19924239},
issn = {1932-6203},
mesh = {Animals ; Cyclooxygenase 1/genetics ; DNA/*analysis ; Endangered Species ; Food Analysis/*methods ; Food Contamination/prevention &amp; control ; Phylogeny ; Restaurants ; Seafood/classification ; Tuna/*classification/genetics ; United States ; },
abstract = {BACKGROUND: The use of DNA barcodes for the identification of described species is one of the least controversial and most promising applications of barcoding. There is no consensus, however, as to what constitutes an appropriate identification standard and most barcoding efforts simply attempt to pair a query sequence with reference sequences and deem identification successful if it falls within the bounds of some pre-established cutoffs using genetic distance. Since the Renaissance, however, most biological classification schemes have relied on the use of diagnostic characters to identify and place species.<br><br>Here we developed a cytochrome c oxidase subunit I character-based key for the identification of all tuna species of the genus Thunnus, and compared its performance with distance-based measures for identification of 68 samples of tuna sushi purchased from 31 restaurants in Manhattan (New York City) and Denver, Colorado. Both the character-based key and GenBank BLAST successfully identified 100% of the tuna samples, while the Barcode of Life Database (BOLD) as well as genetic distance thresholds, and neighbor-joining phylogenetic tree building performed poorly in terms of species identification. A piece of tuna sushi has the potential to be an endangered species, a fraud, or a health hazard. All three of these cases were uncovered in this study. Nineteen restaurant establishments were unable to clarify or misrepresented what species they sold. Five out of nine samples sold as a variant of "white tuna" were not albacore (T. alalunga), but escolar (Lepidocybium flavorunneum), a gempylid species banned for sale in Italy and Japan due to health concerns. Nineteen samples were northern bluefin tuna (T. thynnus) or the critically endangered southern bluefin tuna (T. maccoyii), though nine restaurants that sold these species did not state these species on their menus.<br><br>CONCLUSIONS/SIGNIFICANCE: The Convention on International Trade Endangered Species (CITES) requires that listed species must be identifiable in trade. This research fulfills this requirement for tuna, and supports the nomination of northern bluefin tuna for CITES listing in 2010.},
}
@article {pmid19919591,
year = {2009},
author = {Smith, CI and Drummond, CS and Godsoe, W and Yoder, JB and Pellmyr, O},
title = {Host specificity and reproductive success of yucca moths (Tegeticula spp. Lepidoptera: Prodoxidae) mirror patterns of gene flow between host plant varieties of the Joshua tree (Yucca brevifolia: Agavaceae).},
journal = {Molecular ecology},
volume = {18},
number = {24},
pages = {5218-5229},
doi = {10.1111/j.1365-294X.2009.04428.x},
pmid = {19919591},
issn = {1365-294X},
mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Cluster Analysis ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; Female ; Flowers/genetics/physiology ; *Gene Flow ; *Genetic Fitness ; Genotype ; Larva/genetics/physiology ; Microsatellite Repeats ; Moths/genetics/*physiology ; Oviposition ; Phenotype ; *Pollination ; Selection, Genetic ; Sequence Analysis, DNA ; Species Specificity ; Yucca/*genetics ; },
abstract = {Coevolution between flowering plants and their pollinators is thought to have generated much of the diversity of life on Earth, but the population processes that may have produced these macroevolutionary patterns remain unclear. Mathematical models of coevolution in obligate pollination mutualisms suggest that phenotype matching between plants and their pollinators can generate reproductive isolation. Here, we test this hypothesis using a natural experiment that examines the role of natural selection on phenotype matching between yuccas and yucca moths (Tegeticula spp.) in mediating reproductive isolation between two varieties of Joshua tree (Yucca brevifolia var. brevifolia and Y. brevifolia var. jaegeriana). Using passive monitoring techniques, DNA barcoding, microsatellite DNA genotyping, and sibship reconstruction, we track host specificity and the fitness consequences of host choice in a zone of sympatry. We show that the two moth species differ in their degree of host specificity and that oviposition on a foreign host plant results in the production of fewer offspring. This difference in host specificity between the two moth species mirrors patterns of chloroplast introgression from west to east between host varieties, suggesting that natural selection acting on pollinator phenotypes mediates gene flow and reproductive isolation between Joshua-tree varieties.},
}
@article {pmid19917140,
year = {2009},
author = {Kumar, S and Hahn, FM and McMahan, CM and Cornish, K and Whalen, MC},
title = {Comparative analysis of the complete sequence of the plastid genome of Parthenium argentatum and identification of DNA barcodes to differentiate Parthenium species and lines.},
journal = {BMC plant biology},
volume = {9},
number = {},
pages = {131},
pmid = {19917140},
issn = {1471-2229},
mesh = {Asteraceae/classification/*genetics ; *Comparative Genomic Hybridization ; DNA, Chloroplast/genetics ; DNA, Plant/genetics ; *Genome, Chloroplast ; Genome, Plant ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND: Parthenium argentatum (guayule) is an industrial crop that produces latex, which was recently commercialized as a source of latex rubber safe for people with Type I latex allergy. The complete plastid genome of P. argentatum was sequenced. The sequence provides important information useful for genetic engineering strategies. Comparison to the sequences of plastid genomes from three other members of the Asteraceae, Lactuca sativa, Guitozia abyssinica and Helianthus annuus revealed details of the evolution of the four genomes. Chloroplast-specific DNA barcodes were developed for identification of Parthenium species and lines.<br><br>RESULTS: The complete plastid genome of P. argentatum is 152,803 bp. Based on the overall comparison of individual protein coding genes with those in L. sativa, G. abyssinica and H. annuus, we demonstrate that the P. argentatum chloroplast genome sequence is most closely related to that of H. annuus. Similar to chloroplast genomes in G. abyssinica, L. sativa and H. annuus, the plastid genome of P. argentatum has a large 23 kb inversion with a smaller 3.4 kb inversion, within the large inversion. Using the matK and psbA-trnH spacer chloroplast DNA barcodes, three of the four Parthenium species tested, P. tomentosum, P. hysterophorus and P. schottii, can be differentiated from P. argentatum. In addition, we identified lines within P. argentatum.<br><br>CONCLUSION: The genome sequence of the P. argentatum chloroplast will enrich the sequence resources of plastid genomes in commercial crops. The availability of the complete plastid genome sequence may facilitate transformation efficiency by using the precise sequence of endogenous flanking sequences and regulatory elements in chloroplast transformation vectors. The DNA barcoding study forms the foundation for genetic identification of commercially significant lines of P. argentatum that are important for producing latex.},
}
@article {pmid19908675,
year = {2009},
author = {Meadows, C and Kaul, S},
title = {Medicines management in the theatre suite.},
journal = {Journal of perioperative practice},
volume = {19},
number = {10},
pages = {352-357},
doi = {10.1177/175045890901901009},
pmid = {19908675},
issn = {1750-4589},
mesh = {Drug Labeling ; *Drug Therapy ; Humans ; Medication Errors/*prevention &amp; control ; *Operating Rooms ; Safety Management ; },
abstract = {The safe management of medicines within the theatre complex, from storage to administration, is a key component in preventing patient safety incidents. Simple measures, such as double-checking or clear labelling, can be utilised to reduce the risk of inadvertent drug administration. However, the recognition that human factors contribute to errors has led to more advanced, electronic solutions being utilised. One such automated system, involving barcoding together with visual and auditory cues, is currently under assessment by the National Patient Safety Agency.},
}
@article {pmid19907692,
year = {2009},
author = {Laforsch, C and Haas, A and Jung, N and Schwenk, K and Tollrian, R and Petrusek, A},
title = {"Crown of thorns" of Daphnia: an exceptional inducible defense discovered by DNA barcoding.},
journal = {Communicative &amp; integrative biology},
volume = {2},
number = {5},
pages = {379-381},
pmid = {19907692},
issn = {1942-0889},
abstract = {DNA barcoding has emerged as valuable tool to document global biodiversity. Mitochondrial cytochrome oxidase I (COI) sequences serve as genetic markers to catalogue species richness in the animal kingdom and to identify cryptic and polymorphic animal species. Furthermore, DNA barcoding data serve as a fuel for ecological studies, as they provide the opportunity to unravel species interactions among hosts and parasites, predators and prey, and among competitors in unprecedented detail. In a recent paper we described how DNA barcoding in combination with morphological and ecological data unravelled a striking predator-prey interaction of organisms from temporary aquatic habitats, the predatory notostracan Triops and its prey, cladocerans of the Daphnia atkinsoni complex.},
}
@article {pmid19903480,
year = {2010},
author = {Banerjee, R and Chen, S and Dare, K and Gilreath, M and Praetorius-Ibba, M and Raina, M and Reynolds, NM and Rogers, T and Roy, H and Yadavalli, SS and Ibba, M},
title = {tRNAs: cellular barcodes for amino acids.},
journal = {FEBS letters},
volume = {584},
number = {2},
pages = {387-395},
pmid = {19903480},
issn = {1873-3468},
support = {R01 GM065183/GM/NIGMS NIH HHS/United States ; R01 GM065183-07/GM/NIGMS NIH HHS/United States ; 65183//PHS HHS/United States ; },
mesh = {Amino Acids/*genetics ; *Genetic Code ; Peptide Elongation Factor Tu/metabolism ; *Protein Biosynthesis ; RNA Editing ; RNA, Transfer, Amino Acid-Specific/*metabolism ; Transfer RNA Aminoacylation ; },
abstract = {The role of tRNA in translating the genetic code has received considerable attention over the last 50 years, and we now know in great detail how particular amino acids are specifically selected and brought to the ribosome in response to the corresponding mRNA codon. Over the same period, it has also become increasingly clear that the ribosome is not the only destination to which tRNAs deliver amino acids, with processes ranging from lipid modification to antibiotic biosynthesis all using aminoacyl-tRNAs as substrates. Here we review examples of alternative functions for tRNA beyond translation, which together suggest that the role of tRNA is to deliver amino acids for a variety of processes that includes, but is not limited to, protein synthesis.},
}
@article {pmid19900060,
year = {2009},
author = {Birstein, VJ and Desalle, R and Doukakis, P and Hanner, R and Ruban, GI and Wong, E},
title = {Testing taxonomic boundaries and the limit of DNA barcoding in the Siberian sturgeon, Acipenser baerii.},
journal = {Mitochondrial DNA},
volume = {20},
number = {5-6},
pages = {110-118},
doi = {10.3109/19401730903168182},
pmid = {19900060},
issn = {1940-1744},
mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/chemistry ; Fishes/*classification/genetics ; Genetic Variation ; Genetics, Population ; Molecular Sequence Data ; Phylogeny ; *Sequence Analysis, DNA ; Species Specificity ; },
abstract = {DNA barcoding efforts involving animals have focused on the mitochondrial cytochrome c oxidase subunit I (Cox1) gene. Some authors suggest that this marker might under-diagnose young species. Herein, we examine Cox1 and control region diversity in a sample of Siberian sturgeon (Acipenser baerii), a species with an extremely wide geographic distribution in the major rivers of Siberia and in Lake Baikal. Some authors currently recognize three subspecies within this species. These subspecies are reasonable candidates for species units detectable through DNA barcoding. The Cox1 gene illustrated no variation within the species, while the control region displayed statistically significant differences among the subspecies using analysis of molecular variance (AMOVA). Given the uniformity of Cox1 sequences recovered, Cox1 is probably a good region for barcoding A. baerii at the species level. Although control region variation among subspecies was significant, diagnostic differences were not found for any of the subspecies.},
}
@article {pmid19898615,
year = {2009},
author = {Viñas, J and Tudela, S},
title = {A validated methodology for genetic identification of tuna species (genus Thunnus).},
journal = {PloS one},
volume = {4},
number = {10},
pages = {e7606},
pmid = {19898615},
issn = {1932-6203},
mesh = {Animals ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; *Gene Expression Regulation ; Genetic Markers/genetics ; *Genetic Techniques ; Models, Genetic ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Tuna/*classification/*genetics ; },
abstract = {BACKGROUND: Tuna species of the genus Thunnus, such as the bluefin tunas, are some of the most important and yet most endangered trade fish in the world. Identification of these species in traded forms, however, may be difficult depending on the presentation of the products, which may hamper conservation efforts on trade control. In this paper, we validated a genetic methodology that can fully distinguish between the eight Thunnus species from any kind of processed tissue.<br><br>METHODOLOGY: After testing several genetic markers, a complete discrimination of the eight tuna species was achieved using Forensically Informative Nucleotide Sequencing based primarily on the sequence variability of the hypervariable genetic marker mitochondrial DNA control region (mtDNA CR), followed, in some specific cases, by a second validation by a nuclear marker rDNA first internal transcribed spacer (ITS1). This methodology was able to distinguish all tuna species, including those belonging to the subgenus Neothunnus that are very closely related, and in consequence can not be differentiated with other genetic markers of lower variability. This methodology also took into consideration the presence of introgression that has been reported in past studies between T. thynnus, T. orientalis and T. alalunga. Finally, we applied the methodology to cross-check the species identity of 26 processed tuna samples.<br><br>CONCLUSIONS: Using the combination of two genetic markers, one mitochondrial and another nuclear, allows a full discrimination between all eight tuna species. Unexpectedly, the genetic marker traditionally used for DNA barcoding, cytochrome oxidase 1, could not differentiate all species, thus its use as a genetic marker for tuna species identification is questioned.},
}
@article {pmid19886676,
year = {2009},
author = {Wang, J and Kliks, MM and Qu, W and Jun, S and Shi, G and Li, QX},
title = {Rapid determination of the geographical origin of honey based on protein fingerprinting and barcoding using MALDI TOF MS.},
journal = {Journal of agricultural and food chemistry},
volume = {57},
number = {21},
pages = {10081-10088},
doi = {10.1021/jf902286p},
pmid = {19886676},
issn = {1520-5118},
mesh = {Animals ; Bees ; Hawaii ; Honey/*analysis ; Insect Proteins/*chemistry ; Peptide Mapping/*methods ; Quality Control ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; Tandem Mass Spectrometry/*methods ; United States ; },
abstract = {The authentication of foods is an important aspect of quality control and food safety. Honey is one of the most natural and most popular foods in the world. A fast and reliable method to determine the geographical origin of honey was developed based on fingerprinting and barcoding of proteins in honey by using matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF MS) and MALDI Biotyper 1.1 software, respectively. The protein mass spectra of 16 honey samples of known Hawaii origin were obtained and peak information was extracted to generate protein fingerprints. This information was transformed into a database library of spectral barcodes that were used for differentiation of the geographical origin of honeys based on pattern matching. The differentiation ability of the database library of barcodes was validated by comparing the results of replicate assays of 5 of the 16 honey samples of known Hawaii origin obtained directly from the producers. Validation results showed that the protein fingerprints of honeys have better comparability with those honeys in the library known to be from the same region than with those of honey samples from other regions. The protein fingerprints were used to differentiate the geographical origins of commercially purchased honey samples with labels indicating that they were produced in different countries and various states of the USA, including Hawaii. The results showed that the MALDI TOF MS Biotyper system can be a rapid, simple and practical method for determining the geographical origin of honeys sold in commerce.},
}
@article {pmid19883791,
year = {2010},
author = {Pacheu-Grau, D and Gómez-Durán, A and López-Pérez, MJ and Montoya, J and Ruiz-Pesini, E},
title = {Mitochondrial pharmacogenomics: barcode for antibiotic therapy.},
journal = {Drug discovery today},
volume = {15},
number = {1-2},
pages = {33-39},
doi = {10.1016/j.drudis.2009.10.008},
pmid = {19883791},
issn = {1878-5832},
mesh = {Anti-Bacterial Agents/adverse effects/*pharmacology ; Cell Line, Transformed ; DNA, Mitochondrial/*drug effects ; DNA, Ribosomal/drug effects ; Genetic Variation ; Humans ; Mitochondria/drug effects ; Models, Genetic ; Oxidative Phosphorylation ; Phenotype ; Protein Biosynthesis/drug effects ; RNA/*drug effects ; RNA, Mitochondrial ; RNA, Ribosomal/drug effects ; },
abstract = {Ribosomal RNA (rRNA)-targeting drugs inhibit protein synthesis and represent effective antibiotics for the treatment of infectious diseases. Given the bacterial origins of mitochondria, the molecular and structural components of the protein expression system are much alike. Moreover, the mutational rate of mitochondrial rRNAs is higher than that of nuclear rRNAs, and some of these mutations might simulate the microorganism's rRNA structure. Consequently, individuals become more susceptible to antibiotics, the mitochondrial function is affected and toxic effects appear. Systems are available to analyze the interaction between antibiotics and mitochondrial DNA genetic variants, thus making a pharmacogenomic approach to antibiotic therapy possible.},
}
@article {pmid19883449,
year = {2009},
author = {Viola, LB and Attias, M and Takata, CS and Campaner, M and De Souza, W and Camargo, EP and Teixeira, MM},
title = {Phylogenetic analyses based on small subunit rRNA and glycosomal glyceraldehyde-3-phosphate dehydrogenase genes and ultrastructural characterization of two snake Trypanosomes: Trypanosoma serpentis n. sp. from Pseudoboa nigra and Trypanosoma cascavelli from Crotalus durissus terrificus.},
journal = {The Journal of eukaryotic microbiology},
volume = {56},
number = {6},
pages = {594-602},
doi = {10.1111/j.1550-7408.2009.00444.x},
pmid = {19883449},
issn = {1550-7408},
mesh = {Animals ; Brazil ; DNA, Protozoan/analysis/*classification/genetics ; Glyceraldehyde-3-Phosphate Dehydrogenases/*genetics ; Host-Parasite Interactions ; Lizards/parasitology ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/analysis/classification/genetics ; Ribosome Subunits, Small/*genetics ; Sequence Analysis, DNA ; Snakes/*parasitology ; Species Specificity ; Trypanosoma/*classification/genetics/ultrastructure ; },
abstract = {We sequenced the small subunit (SSU) rRNA and glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH) genes of two trypanosomes isolated from the Brazilian snakes Pseudoboa nigra and Crotalus durissus terrificus. Trypanosomes were cultured and their morphometrical and ultrastructural features were characterized by light microscopy and scanning and transmission electron microscopy. Phylogenetic trees inferred using independent or combined SSU rRNA and gGAPDH data sets always clustered the snake trypanosomes together in a clade closest to lizard trypanosomes, forming a strongly supported monophyletic assemblage (i.e. lizard-snake clade). The positioning in the phylogenetic trees and the barcoding based on the variable V7-V8 region of the SSU rRNA, which showed high sequence divergences, allowed us to classify the isolates from distinct snake species as separate species. The isolate from P. nigra is described as a new species, Trypanosoma serpentis n. sp., whereas the isolate from C. d. terrificus is redescribed here as Trypanosoma cascavelli.},
}
@article {pmid19875081,
year = {2009},
author = {Buller, F and Zhang, Y and Scheuermann, J and Schäfer, J and Bühlmann, P and Neri, D},
title = {Discovery of TNF inhibitors from a DNA-encoded chemical library based on diels-alder cycloaddition.},
journal = {Chemistry &amp; biology},
volume = {16},
number = {10},
pages = {1075-1086},
doi = {10.1016/j.chembiol.2009.09.011},
pmid = {19875081},
issn = {1879-1301},
mesh = {Animals ; Base Sequence ; Cell Line ; DNA/*chemistry ; Drug Design ; High-Throughput Screening Assays ; Immobilized Proteins/metabolism ; Ligands ; Mice ; Small Molecule Libraries ; *Tumor Necrosis Factor Inhibitors ; Tumor Necrosis Factors/metabolism ; bcl-X Protein/antagonists &amp; inhibitors/metabolism ; },
abstract = {DNA-encoded chemical libraries are promising tools for the discovery of ligands toward protein targets of pharmaceutical relevance. DNA-encoded small molecules can be enriched in affinity-based selections and their unique DNA "barcode" allows the amplification and identification by high-throughput sequencing. We describe selection experiments using a DNA-encoded 4000-compound library generated by Diels-Alder cycloadditions. High-throughput sequencing enabled the identification and relative quantification of library members before and after selection. Sequence enrichment profiles corresponding to the "bar-coded" library members were validated by affinity measurements of single compounds. We were able to affinity mature trypsin inhibitors and identify a series of albumin binders for the conjugation of pharmaceuticals. Furthermore, we discovered a ligand for the antiapoptotic Bcl-xL protein and a class of tumor necrosis factor (TNF) binders that completely inhibited TNF-mediated killing of L-M fibroblasts in vitro.},
}
@article {pmid19874596,
year = {2009},
author = {Frank, DN},
title = {BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing.},
journal = {BMC bioinformatics},
volume = {10},
number = {},
pages = {362},
pmid = {19874596},
issn = {1471-2105},
support = {UH2 DK083994/DK/NIDDK NIH HHS/United States ; 1UH2DK083994-01/DK/NIDDK NIH HHS/United States ; },
mesh = {Algorithms ; Base Sequence ; Computational Biology/*methods ; DNA Primers/*chemistry ; Genome ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Sequence Analysis, DNA/*methods ; *Software ; },
abstract = {BACKGROUND: Advances in automated DNA sequencing technology have greatly increased the scale of genomic and metagenomic studies. An increasingly popular means of increasing project throughput is by multiplexing samples during the sequencing phase. This can be achieved by covalently linking short, unique "barcode" DNA segments to genomic DNA samples, for instance through incorporation of barcode sequences in PCR primers. Although several strategies have been described to insure that barcode sequences are unique and robust to sequencing errors, these have not been integrated into the overall primer design process, thus potentially introducing bias into PCR amplification and/or sequencing steps.<br><br>RESULTS: Barcrawl is a software program that facilitates the design of barcoded primers, for multiplexed high-throughput sequencing. The program bartab can be used to deconvolute DNA sequence datasets produced by the use of multiple barcoded primers. This paper describes the functions implemented by barcrawl and bartab and presents a proof-of-concept case study of both programs in which barcoded rRNA primers were designed and validated by high-throughput sequencing.<br><br>CONCLUSION: Barcrawl and bartab can benefit researchers who are engaged in metagenomic projects that employ multiplexed specimen processing. The source code is released under the GNU general public license and can be accessed at http://www.phyloware.com.},
}
@article {pmid19841276,
year = {2009},
author = {Kress, WJ and Erickson, DL and Jones, FA and Swenson, NG and Perez, R and Sanjur, O and Bermingham, E},
title = {Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {106},
number = {44},
pages = {18621-18626},
pmid = {19841276},
issn = {1091-6490},
mesh = {Base Sequence ; DNA, Plant/*genetics ; Molecular Sequence Data ; Panama ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Trees/*genetics ; *Tropical Climate ; },
abstract = {The assembly of DNA barcode libraries is particularly relevant within species-rich natural communities for which accurate species identifications will enable detailed ecological forensic studies. In addition, well-resolved molecular phylogenies derived from these DNA barcode sequences have the potential to improve investigations of the mechanisms underlying community assembly and functional trait evolution. To date, no studies have effectively applied DNA barcodes sensu strictu in this manner. In this report, we demonstrate that a three-locus DNA barcode when applied to 296 species of woody trees, shrubs, and palms found within the 50-ha Forest Dynamics Plot on Barro Colorado Island (BCI), Panama, resulted in >98% correct identifications. These DNA barcode sequences are also used to reconstruct a robust community phylogeny employing a supermatrix method for 281 of the 296 plant species in the plot. The three-locus barcode data were sufficient to reliably reconstruct evolutionary relationships among the plant taxa in the plot that are congruent with the broadly accepted phylogeny of flowering plants (APG II). Earlier work on the phylogenetic structure of the BCI forest dynamics plot employing less resolved phylogenies reveals significant differences in evolutionary and ecological inferences compared with our data and suggests that unresolved community phylogenies may have increased type I and type II errors. These results illustrate how highly resolved phylogenies based on DNA barcode sequence data will enhance research focused on the interface between community ecology and evolution.},
}
@article {pmid19834612,
year = {2009},
author = {Gonzalez, MA and Baraloto, C and Engel, J and Mori, SA and Pétronelli, P and Riéra, B and Roger, A and Thébaud, C and Chave, J},
title = {Identification of Amazonian trees with DNA barcodes.},
journal = {PloS one},
volume = {4},
number = {10},
pages = {e7483},
pmid = {19834612},
issn = {1932-6203},
mesh = {Biodiversity ; Cluster Analysis ; DNA, Plant/*genetics ; Electronic Data Processing ; French Guiana ; Genetic Markers ; Models, Statistical ; Phylogeny ; Seasons ; Sequence Analysis, DNA ; Trees/*classification/*genetics ; },
abstract = {BACKGROUND: Large-scale plant diversity inventories are critical to develop informed conservation strategies. However, the workload required for classic taxonomic surveys remains high and is particularly problematic for megadiverse tropical forests.<br><br>Based on a comprehensive census of all trees in two hectares of a tropical forest in French Guiana, we examined whether plant DNA barcoding could contribute to increasing the quality and the pace of tropical plant biodiversity surveys. Of the eight plant DNA markers we tested (rbcLa, rpoC1, rpoB, matK, ycf5, trnL, psbA-trnH, ITS), matK and ITS had a low rate of sequencing success. More critically, none of the plastid markers achieved a rate of correct plant identification greater than 70%, either alone or combined. The performance of all barcoding markers was noticeably low in few species-rich clades, such as the Laureae, and the Sapotaceae. A field test of the approach enabled us to detect 130 molecular operational taxonomic units in a sample of 252 juvenile trees. Including molecular markers increased the identification rate of juveniles from 72% (morphology alone) to 96% (morphology and molecular) of the individuals assigned to a known tree taxon.<br><br>CONCLUSION/SIGNIFICANCE: We conclude that while DNA barcoding is an invaluable tool for detecting errors in identifications and for identifying plants at juvenile stages, its limited ability to identify collections will constrain the practical implementation of DNA-based tropical plant biodiversity programs.},
}
@article {pmid19826500,
year = {2009},
author = {Jaklitsch, WM},
title = {European species of Hypocrea Part I. The green-spored species.},
journal = {Studies in mycology},
volume = {63},
number = {},
pages = {1-91},
pmid = {19826500},
issn = {0166-0616},
support = {P 19143/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {At present 75 species of Hypocrea have been identified in temperate Europe. Nineteen green-spored species and their Trichoderma asexual states are here described in detail. Extensive searches for Hypocrea teleomorphs in 14 European countries, with emphasis on Central Europe, yielded more than 620 specimens within five years. The morphology of fresh and dry stromata was studied. In addition, available types of species described from Europe were examined. Cultures were prepared from ascospores and used to study the morphology of cultures and anamorphs, to determine growth rates, and to extract DNA that was used for amplification and sequencing of three genetic markers. ITS was used for identification, while RNA polymerase II subunit b (rpb2) and translation elongation factor 1 alpha (tef1) were analyzed for phylogenetic reconstruction of the genus.SEVERAL UNEXPECTED FINDINGS RESULTED FROM THIS PROJECT: 1) The previous view that only a small number of Trichoderma species form a teleomorph is erroneous. 2) All expectations concerning the number of species in Europe are by far exceeded. Seventy-five species of Hypocrea, two species of Protocrea, and Arachnocrea stipata, are herein identified in temperate Europe, based on the ITS identification routine using fresh material, on species described earlier without molecular data and on species recently described but not collected during this project. 3) Current data suggest that the biodiversity of Hypocrea / Trichoderma above soil exceeds the number of species isolated from soil. 4) The number of Trichoderma species forming hyaline conidia has been considered a small fraction. In Europe, 26 species of those forming teleomorphs produce hyaline conidia, while 42 green-conidial species are known. Three of the detected Hypocrea species do not form an anamorph in culture, while the anamorph is unknown in four species, because they have never been cultured.This work is a preliminary account of Hypocrea and their Trichoderma anamorphs in Europe. Of the hyaline-spored species, H. minutispora is by far the most common species in Europe, while of the green-spored species this is H. strictipilosa.General ecology of Hypocrea is discussed. Specific associations, either with host fungi or trees have been found, but the majority of species seems to be necrotrophic on diverse fungi on wood and bark.The taxonomy of the genus will be treated in two parts. In this first part 19 species of Hypocrea with green ascospores, including six new teleomorph and five new anamorph species, are described in detail. All green-spored species belong to previously recognised clades, except H. spinulosa, which forms the new Spinulosa Clade with two additional new species, and H. fomiticola, which belongs to the Semiorbis Clade and forms effuse to large subpulvinate stromata on Fomes fomentarius, a trait new for species with green ascospores. Anamorph names are established prospectively in order to provide a basis for possible policy alterations towards their use for holomorphs.},
}
@article {pmid19825181,
year = {2009},
author = {Ammar, R and Smith, AM and Heisler, LE and Giaever, G and Nislow, C},
title = {A comparative analysis of DNA barcode microarray feature size.},
journal = {BMC genomics},
volume = {10},
number = {},
pages = {471},
pmid = {19825181},
issn = {1471-2164},
support = {HG00317-05/HG/NHGRI NIH HHS/United States ; MOP-81340//Canadian Institutes of Health Research/Canada ; MOP-84305//Canadian Institutes of Health Research/Canada ; },
mesh = {*Comparative Genomic Hybridization ; DNA, Fungal/genetics ; Genome, Fungal ; Genomics/*methods ; Oligonucleotide Array Sequence Analysis/*methods ; Saccharomyces cerevisiae/genetics ; Tunicamycin ; },
abstract = {BACKGROUND: Microarrays are an invaluable tool in many modern genomic studies. It is generally perceived that decreasing the size of microarray features leads to arrays with higher resolution (due to greater feature density), but this increase in resolution can compromise sensitivity.<br><br>RESULTS: We demonstrate that barcode microarrays with smaller features are equally capable of detecting variation in DNA barcode intensity when compared to larger feature sizes within a specific microarray platform. The barcodes used in this study are the well-characterized set derived from the Yeast KnockOut (YKO) collection used for screens of pooled yeast (Saccharomyces cerevisiae) deletion mutants. We treated these pools with the glycosylation inhibitor tunicamycin as a test compound. Three generations of barcode microarrays at 30, 8 and 5 microm features sizes independently identified the primary target of tunicamycin to be ALG7.<br><br>CONCLUSION: We show that the data obtained with 5 microm feature size is of comparable quality to the 30 microm size and propose that further shrinking of features could yield barcode microarrays with equal or greater resolving power and, more importantly, higher density.},
}
@article {pmid19824687,
year = {2010},
author = {Blakey, I and Schiller, TL and Merican, Z and Fredericks, PM},
title = {Interactions of phenyldithioesters with gold nanoparticles (AuNPs): implications for AuNP functionalization and molecular barcoding of AuNP assemblies.},
journal = {Langmuir : the ACS journal of surfaces and colloids},
volume = {26},
number = {2},
pages = {692-701},
doi = {10.1021/la9023162},
pmid = {19824687},
issn = {1520-5827},
mesh = {Esters/*chemistry ; Gold/*chemistry ; Magnetic Resonance Spectroscopy ; Metal Nanoparticles/*chemistry ; Molecular Structure ; Nanotechnology ; Spectrum Analysis, Raman ; Surface Plasmon Resonance ; },
abstract = {The interactions of phenyldithioesters with gold nanoparticles (AuNPs) have been studied by monitoring changes in the surface plasmon resonance (SPR), depolarised light scattering, and surface enhanced Raman spectroscopy (SERS). Changes in the SPR indicated that an AuNP-phenyldithioester charge transfer complex forms in equilibrium with free AuNPs and phenyldithioester. Analysis of the Langmuir binding isotherms indicated that the equilibrium adsorption constant, K(ads), was 2.3 +/- 0.1 x 10(6) M(-1), which corresponded to a free energy of adsorption of 36 +/- 1 kJ mol(-1). These values are comparable to those reported for interactions of aryl thiols with gold and are of a similar order of magnitude to moderate hydrogen bonding interactions. This has significant implications in the application of phenyldithioesters for the functionalization of AuNPs. The SERS results indicated that the phenyldithioesters interact with AuNPs through the C=S bond, and the molecules do not disassociate upon adsorption to the AuNPs. The SERS spectra are dominated by the portions of the molecule that dominate the charge transfer complex with the AuNPs. The significance of this in relation to the use of phenyldithioesters for molecular barcoding of nanoparticle assemblies is discussed.},
}
@article {pmid19819756,
year = {2010},
author = {Nassonova, E and Smirnov, A and Fahrni, J and Pawlowski, J},
title = {Barcoding amoebae: comparison of SSU, ITS and COI genes as tools for molecular identification of naked lobose amoebae.},
journal = {Protist},
volume = {161},
number = {1},
pages = {102-115},
doi = {10.1016/j.protis.2009.07.003},
pmid = {19819756},
issn = {1618-0941},
mesh = {Amoebozoa/*classification/*genetics ; Animals ; Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Electron Transport Complex IV/genetics ; Genes, rRNA ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; Phylogeny ; Protein Subunits/genetics ; Protozoan Proteins/genetics ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; },
abstract = {Morphological identification of naked lobose amoebae has always been a problem, hence the development of reliable molecular tools for species distinction is a priority for amoebae systematics. Previous studies based on SSU rDNA sequences provided a backbone for the phylogeny of Amoebozoa but were of little help for the species distinctions in this group. On one hand, the SSU rDNA sequences were rather conserved between closely related species; on the other hand, the intra-strain polymorphism of the SSU gene obscured species identification. In the present study, a 3' fragment of the SSU, a complete ITS1-5.8S-ITS2 block and a 5' fragment of COI gene were cloned and sequenced for six Vannella morphospecies, of which V. simplex was represented by six different isolates. SSU rDNA and ITS were found to be inappropriate for species differentiation, while distinctive and homogenous COI sequences were obtained for each well-defined morphospecies. Moreover, a number of distinct COI genotypes have been identified among V. simplex isolates. This suggests that COI may be a good candidate for DNA barcoding of amoebae, but further studies are necessary to confirm the accurateness of the COI gene as a barcode in other gymnamoebae, and to understand the taxonomic meaning of COI variations.},
}
@article {pmid19799677,
year = {2009},
author = {Kumar, P and Reinitz, HW and Simunovic, J and Sandeep, KP and Franzon, PD},
title = {Overview of RFID technology and its applications in the food industry.},
journal = {Journal of food science},
volume = {74},
number = {8},
pages = {R101-6},
doi = {10.1111/j.1750-3841.2009.01323.x},
pmid = {19799677},
issn = {1750-3841},
mesh = {Food Industry/instrumentation/*methods/standards ; Radio Frequency Identification Device/economics/*methods ; },
abstract = {Radio frequency identification (RFID) is an alternative technology with a potential to replace traditional universal product code (UPC) barcodes. RFID enables identification of an object from a distance without requiring a line of sight. RFID tags can also incorporate additional data such as details of product and manufacturer and can transmit measured environmental factors such as temperature and relative humidity. This article presents key concepts and terminology related to RFID technology and its applications in the food industry. Components and working principles of an RFID system are described. Numerous applications of RFID technology in the food industry (supply chain management, temperature monitoring of foods, and ensuring food safety) are discussed. Challenges in implementation of RFID technology are also discussed in terms of read range, read accuracy, nonuniform standards, cost, recycling issues, privacy, and security concerns.},
}
@article {pmid19799325,
year = {2009},
author = {Shneer, VS},
title = {[DNA barcoding of animal and plant species as an approach for their molecular identification and describing of diversity].},
journal = {Zhurnal obshchei biologii},
volume = {70},
number = {4},
pages = {296-315},
pmid = {19799325},
issn = {0044-4596},
mesh = {Animals ; Biodiversity ; DNA, Mitochondrial/analysis/*genetics ; DNA, Plant/analysis/*genetics ; *Gene Library ; Genetic Markers ; Plants/*classification/genetics ; Sequence Analysis, DNA/*methods/standards/trends ; Species Specificity ; },
abstract = {DNA barcoding was recently developed as a method of species identification across a broad range of eucaryotes taxa by sequencing a standardized short DNA fragment. Due to modern technologies, it is possible to do this with a tiny piece of any tissue taken from an organism at any developmental phase, often without damaging it. A variable 5' half of mitochondial gene CO1 is suggested as a standard region for most of animals; it is not identified yet for fungi and plants. "The Barcode of Life Initiative" implies creating and developing the barcode library for all the species on Earth to facilitate both assigning of newly obtained specimens to the known species and for discovering new and cryptic species or at least their provisional recognition. This approach has a great potential for the use in global biodiversity studies, especially in the case of poorly investigated taxa and environments. The initiative in question involves accomplish of a new web-based sequence database with rigorous rules for taxonomic information on the specimens and records of their storage as well as for standards of sequence quality and their entry. Critical objections of opponents to DNA barcoding are reviewed as well as limitations of the approach, the problems to be taken into consideration, and the fields where it can be used. Numerous recent studies on different animal groups convincingly demonstrate the efficacy of DNA barcoding and its potentials. The latter depends on availability of comprehensive and unbiased reference database implying correct identification of the source specimens and adequate knowledge of intraspecies variation, so the Barcode Initiative would be more successful as a part of the integrative analysis of the taxs being barcoded.},
}
@article {pmid19779570,
year = {2008},
author = {Erickson, DL and Spouge, J and Resch, A and Weigt, LA and Kress, WJ},
title = {DNA BARCODING IN LAND PLANTS: DEVELOPING STANDARDS TO QUANTIFY AND MAXIMIZE SUCCESS.},
journal = {Taxon},
volume = {57},
number = {4},
pages = {1304-1316},
pmid = {19779570},
issn = {0040-0262},
support = {Z99 LM999999/ImNIH/Intramural NIH HHS/United States ; },
abstract = {The selection of a DNA barcode in plants has been impeded in part due to the relatively low rates of nucleotide substitution observed at the most accessible plastid markers. However, the absence of consensus also reflects a lack of standards for comparing potential barcode markers. While many publications have suggested a host of plant DNA barcodes, the studies cannot be readily compared with each other through any quantitative or statistical parameter, partly because they put forward no single compelling rationale relevant to the adoption of a DNA barcode in plants. Here, we argue that the efficacy of any particular plant DNA barcode selection should reflect the anticipated performance of the resulting barcode database in assignment of a query sequence to species. While legitimate scientific disagreement exists over the criteria relevant to "database performance", the notion gives a unifying rationale for prioritizing selection criteria. Accordingly, we suggest a measure of barcode efficacy based on the rationale of database performance, "the probability of correct identification" (PCI). Moreover, the definition of PCI is left flexible enough to handle most of the scientific disagreement over how to best evaluate DNA barcodes. Finally, we consider how different types of barcodes might require different methods of analysis and database design and indicate how the analysis might affect the selection of the most broadly effective barcode for land plants.},
}
@article {pmid19768260,
year = {2009},
author = {Silva-Brandão, KL and Lyra, ML and Freitas, AV},
title = {Barcoding lepidoptera: current situation and perspectives on the usefulness of a contentious technique.},
journal = {Neotropical entomology},
volume = {38},
number = {4},
pages = {441-451},
doi = {10.1590/s1519-566x2009000400001},
pmid = {19768260},
issn = {1519-566X},
mesh = {Animals ; Classification/methods ; Lepidoptera/*classification/*genetics ; },
abstract = {Faced by a growing need of identification and delimitation of new and established cryptic species that are being lost at an increasing rate, taxonomists can now more than ever take advantage of an enormous variety of new molecular and computational tools. At this moment they should be open to all new available technologies in the so called 'technology-driven revolution' in systematics. The use of the 'DNA barcode' has been discussed by those applying successfully this approach to identify and diagnose species and by those who believe that the flaws in the use of this molecular marker are as many as to negate the worth of its employment. For insects of the order Lepidoptera neither side seems totally correct or wrong, and although many groups of lepidopterans have been taxonomically resolved by using exclusively or additionally this marker for diagnoses, for others the 'barcode' helped little to resolve taxonomic issues. Here we briefly present some pros and cons of using DNA barcode as a tool in taxonomic studies, with special attention to studies with groups of Lepidoptera developed in the last few years.},
}
@article {pmid19768113,
year = {2009},
author = {Alcaide, M and Rico, C and Ruiz, S and Soriguer, R and Muñoz, J and Figuerola, J},
title = {Disentangling vector-borne transmission networks: a universal DNA barcoding method to identify vertebrate hosts from arthropod bloodmeals.},
journal = {PloS one},
volume = {4},
number = {9},
pages = {e7092},
pmid = {19768113},
issn = {1932-6203},
mesh = {Animals ; Arachnid Vectors/genetics ; Arthropod Vectors/*genetics ; Arthropods/*metabolism ; Base Sequence ; Birds/genetics ; Culicidae/genetics ; DNA/*metabolism ; Host-Parasite Interactions/genetics ; Humans ; Insect Vectors/genetics ; Molecular Sequence Data ; Polymerase Chain Reaction/*instrumentation/*methods ; Sequence Alignment/methods ; Ticks/genetics ; },
abstract = {Emerging infectious diseases represent a challenge for global economies and public health. About one fourth of the last pandemics have been originated by the spread of vector-borne pathogens. In this sense, the advent of modern molecular techniques has enhanced our capabilities to understand vector-host interactions and disease ecology. However, host identification protocols have poorly profited of international DNA barcoding initiatives and/or have focused exclusively on a limited array of vector species. Therefore, ascertaining the potential afforded by DNA barcoding tools in other vector-host systems of human and veterinary importance would represent a major advance in tracking pathogen life cycles and hosts. Here, we show the applicability of a novel and efficient molecular method for the identification of the vertebrate host's DNA contained in the midgut of blood-feeding arthropods. To this end, we designed a eukaryote-universal forward primer and a vertebrate-specific reverse primer to selectively amplify 758 base pairs (bp) of the vertebrate mitochondrial Cytochrome c Oxidase Subunit I (COI) gene. Our method was validated using both extensive sequence surveys from the public domain and Polymerase Chain Reaction (PCR) experiments carried out over specimens from different Classes of vertebrates (Mammalia, Aves, Reptilia and Amphibia) and invertebrate ectoparasites (Arachnida and Insecta). The analysis of mosquito, culicoid, phlebotomie, sucking bugs, and tick bloodmeals revealed up to 40 vertebrate hosts, including 23 avian, 16 mammalian and one reptilian species. Importantly, the inspection and analysis of direct sequencing electropherograms also assisted the resolving of mixed bloodmeals. We therefore provide a universal and high-throughput diagnostic tool for the study of the ecology of haematophagous invertebrates in relation to their vertebrate hosts. Such information is crucial to support the efficient management of initiatives aimed at reducing epidemiologic risks of arthropod vector-borne pathogens, a priority for public health.},
}
@article {pmid19766649,
year = {2010},
author = {Cavazzana, M and Marcili, A and Lima, L and da Silva, FM and Junqueira, AC and Veludo, HH and Viola, LB and Campaner, M and Nunes, VL and Paiva, F and Coura, JR and Camargo, EP and Teixeira, MM},
title = {Phylogeographical, ecological and biological patterns shown by nuclear (ssrRNA and gGAPDH) and mitochondrial (Cyt b) genes of trypanosomes of the subgenus Schizotrypanum parasitic in Brazilian bats.},
journal = {International journal for parasitology},
volume = {40},
number = {3},
pages = {345-355},
doi = {10.1016/j.ijpara.2009.08.015},
pmid = {19766649},
issn = {1879-0135},
mesh = {Animals ; Brazil ; Chiroptera/*parasitology ; Cluster Analysis ; Cytochromes b/genetics ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; *Genetic Variation ; Geography ; Glyceraldehyde-3-Phosphate Dehydrogenases/genetics ; Molecular Sequence Data ; Phylogeny ; Protozoan Proteins/genetics ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Trypanosoma/*classification/genetics/*isolation &amp; purification ; Trypanosomiasis/parasitology/*veterinary ; },
abstract = {The genetic diversity and phylogeographical patterns of Trypanosoma species that infect Brazilian bats were evaluated by examining 1043 bats from 63 species of seven families captured in Amazonia, the Pantanal, Cerrado and the Atlantic Forest biomes of Brazil. The prevalence of trypanosome-infected bats, as estimated by haemoculture, was 12.9%, resulting in 77 cultures of isolates, most morphologically identified as Trypanosoma cf. cruzi, classified by barcoding using partial sequences from ssrRNA gene into the subgenus Schizotrypanum and identified as T. cruzi (15), T. cruzi marinkellei (37) or T. cf. dionisii (25). Phylogenetic analyses using nuclear ssrRNA, glycosomal glyceraldehyde 3-phosphate dehydrogenase (gGAPDH) and mitochondrial cytochrome b (Cyt b) gene sequences generated three clades, which clustered together forming the subgenus Schizotrypanum. In addition to vector association, bat trypanosomes were related by the evolutionary history, ecology and phylogeography of the bats. Trypanosoma cf. dionisii trypanosomes (32.4%) infected 12 species from four bat families captured in all biomes, from North to South Brazil, and clustered with T. dionisii from Europe despite being separated by some genetic distance. Trypanosoma cruzi marinkellei (49.3%) was restricted to phyllostomid bats from Amazonia to the Pantanal (North to Central). Trypanosoma cruzi (18.2%) was found mainly in vespertilionid and phyllostomid bats from the Pantanal/Cerrado and the Atlantic Forest (Central to Southeast), with a few isolates from Amazonia.},
}
@article {pmid19761856,
year = {2010},
author = {Zhang, AB and He, LJ and Crozier, RH and Muster, C and Zhu, CD},
title = {Estimating sample sizes for DNA barcoding.},
journal = {Molecular phylogenetics and evolution},
volume = {54},
number = {3},
pages = {1035-1039},
doi = {10.1016/j.ympev.2009.09.014},
pmid = {19761856},
issn = {1095-9513},
mesh = {Animals ; Biodiversity ; Butterflies/classification/*genetics ; Computer Simulation ; DNA/*genetics ; *Genetic Variation ; Genetics, Population ; Haplotypes ; *Models, Genetic ; *Sample Size ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Sample size has long been one of the basic issues since the start of the DNA barcoding initiative and the global biodiversity investigation. As a contribution to resolving this problem, we propose a simple resampling approach to estimate several key sampling sizes for a DNA barcoding project. We illustrate our approach using both structured populations simulated under coalescent and real species of skipper butterflies. We found that sample sizes widely used in DNA barcoding are insufficient to assess the genetic diversity of a species, population structure impacts the estimation of the sample sizes, and hence will bias the species identification potentially.},
}
@article {pmid19761827,
year = {2009},
author = {Asase, A and Oppong-Mensah, G},
title = {Traditional antimalarial phytotherapy remedies in herbal markets in southern Ghana.},
journal = {Journal of ethnopharmacology},
volume = {126},
number = {3},
pages = {492-499},
doi = {10.1016/j.jep.2009.09.008},
pmid = {19761827},
issn = {1872-7573},
mesh = {Antimalarials/*therapeutic use ; Ghana ; *Medicine, African Traditional ; *Phytotherapy ; Socioeconomic Factors ; Species Specificity ; },
abstract = {Although traditional antimalarial plant remedies in herbal markets are a very important component of the health care system in Ghana this has not been previously studied to allow for the formulation of effective strategy for malaria control in Ghana.<br><br>AIM OF STUDY: The main objective of the present study was to collect and analyse data on the antimalarial plant remedies in herbal markets in southern Ghana.<br><br>MATERIALS AND METHODS: Herborists were interviewed using a validated questionnaire and species of plants were identified using a combination of field photo guides, local names and voucher specimens.<br><br>RESULTS: A total of 71 herborists (95.8% female) were interviewed. There were potential correlations between different parameters and variables such as ethnic groups, type of vendor and age-groups. The study revealed 29 species of plants belonging to 22 families being sold for the treatment of malaria. The detailed use of these plants is documented. The most frequently mentioned species of plants were Morinda lucida Benth., Indigofera sp. and Nauclea latifolia Sm. The majority (82.8%) of the plant materials were sold in the dried state and 6.9% were sold in fresh state. About 76.2% of the herbal remedies were sold throughout the year while 23.8% were scarce in the dry season. The cost of treatment of malaria using the herbal remedies ranged from 1 to 2 United States Dollars (USD).<br><br>CONCLUSION: Standardization of names and authentication of plant materials using organoleptic, phytochemical and DNA barcoding techniques as well as further research on efficacy, safety and dosage prescriptions for both fresh and dried plant materials being sold for the treatment of malaria in southern Ghana are needed.},
}
@article {pmid19749031,
year = {2010},
author = {Chantangsi, C and Leander, BS},
title = {An SSU rDNA barcoding approach to the diversity of marine interstitial cercozoans, including descriptions of four novel genera and nine novel species.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {60},
number = {Pt 8},
pages = {1962-1977},
doi = {10.1099/ijs.0.013888-0},
pmid = {19749031},
issn = {1466-5026},
mesh = {*Biodiversity ; Cercozoa/*classification/genetics/*isolation &amp; purification ; DNA, Protozoan/genetics ; DNA, Ribosomal/*genetics ; Fatty Acids/metabolism ; Molecular Sequence Data ; Phylogeny ; Ribosome Subunits, Small/*genetics ; Seawater/*parasitology ; },
abstract = {Environmental DNA surveys have revealed a great deal of hidden diversity within the Cercozoa. An investigation into the biodiversity of heterotrophic flagellates in marine benthic habitats of British Columbia, Canada, demonstrated the presence of several undescribed taxa with morphological features that resemble the cercozoan genera Cryothecomonas and Protaspis. Nine novel species of marine interstitial cercozoans are described that are distributed into five genera, four of which are new. Phylogenetic analyses of small subunit rDNA sequences derived from two uncultured isolates of Protaspis obliqua and nine novel cercozoan species (within four novel genera) provided organismal anchors that helped establish the cellular identities of several different environmental sequence clades. These data, however, also showed that the rarity of distinctive morphological features in cryomonads, and other groups of cercozoans, makes the identification and systematics of the group very difficult. Therefore, a DNA barcoding approach was applied as a diagnostic tool for species delimitation that used a 618 bp region at the 5' end of the SSU rDNA sequence. Nucleotide sequence analysis of this region showed high intergeneric sequence divergences of about 7% and very low intraspecific sequence divergences of 0-0.5%; phylogenetic analyses inferred from this barcoding region showed very similar tree topologies to those inferred from the full-length sequence of the gene. Overall, this study indicated that the 618 bp barcoding region of SSU rDNA sequences is a useful molecular signature for understanding the biodiversity and interrelationships of marine benthic cercozoans.},
}
@article {pmid19744312,
year = {2009},
author = {Bivi, N and Romanello, M and Harrison, R and Clarke, I and Hoyle, DC and Moro, L and Ortolani, F and Bonetti, A and Quadrifoglio, F and Tell, G and Delneri, D},
title = {Identification of secondary targets of N-containing bisphosphonates in mammalian cells via parallel competition analysis of the barcoded yeast deletion collection.},
journal = {Genome biology},
volume = {10},
number = {9},
pages = {R93},
pmid = {19744312},
issn = {1474-760X},
mesh = {Alendronate/pharmacology ; Blotting, Western ; Breast Neoplasms/genetics/pathology/ultrastructure ; Cell Cycle/drug effects ; Cell Cycle Proteins/*genetics/metabolism ; Cell Division/drug effects/genetics ; Cell Line, Tumor ; Cell Movement/drug effects ; DNA Breaks, Double-Stranded ; DNA Damage ; Diphosphonates/*pharmacology ; Etidronic Acid/analogs &amp; derivatives/pharmacology ; Gene Deletion ; Humans ; Ibandronic Acid ; Microscopy, Confocal ; Microscopy, Electron ; Microtubules/drug effects/metabolism ; *Mutation ; Polyisoprenyl Phosphates/pharmacology ; RNA Interference ; Risedronic Acid ; Saccharomyces cerevisiae/*genetics/growth &amp; development ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; },
abstract = {BACKGROUND: Nitrogen-containing bisphosphonates are the elected drugs for the treatment of diseases in which excessive bone resorption occurs, for example, osteoporosis and cancer-induced bone diseases. The only known target of nitrogen-containing bisphosphonates is farnesyl pyrophosphate synthase, which ensures prenylation of prosurvival proteins, such as Ras. However, it is likely that the action of nitrogen-containing bisphosphonates involves additional unknown mechanisms. To identify novel targets of nitrogen-containing bisphosphonates, we used a genome-wide high-throughput screening in which 5,936 Saccharomyces cerevisiae heterozygote barcoded mutants were grown competitively in the presence of sub-lethal doses of three nitrogen-containing bisphosphonates (risedronate, alendronate and ibandronate). Strains carrying deletions in genes encoding potential drug targets show a variation of the intensity of their corresponding barcodes on the hybridization array over the time.<br><br>RESULTS: With this approach, we identified novel targets of nitrogen-containing bisphosphonates, such as tubulin cofactor B and ASK/DBF4 (Activator of S-phase kinase). The up-regulation of tubulin cofactor B may explain some previously unknown effects of nitrogen-containing bisphosphonates on microtubule dynamics and organization. As nitrogen-containing bisphosphonates induce extensive DNA damage, we also document the role of DBF4 as a key player in nitrogen-containing bisphosphonate-induced cytotoxicity, thus explaining the effects on the cell-cycle.<br><br>CONCLUSIONS: The dataset obtained from the yeast screen was validated in a mammalian system, allowing the discovery of new biological processes involved in the cellular response to nitrogen-containing bisphosphonates and opening up opportunities for development of new anticancer drugs.},
}
@article {pmid19719409,
year = {2009},
author = {Hirose, M and Hirose, E},
title = {DNA barcoding in photosymbiotic species of Diplosoma (Ascidiacea: Didemnidae), with the description of a new species from the southern Ryukyus, Japan.},
journal = {Zoological science},
volume = {26},
number = {8},
pages = {564-568},
doi = {10.2108/zsj.26.564},
pmid = {19719409},
issn = {0289-0003},
mesh = {Animals ; *Chromosome Painting ; DNA/genetics ; Japan ; Phylogeny ; Urochordata/*classification/*genetics ; },
abstract = {Partial sequences of the cytochrome c oxidase subunit I (COI) gene were determined for six species of the genus Diplosoma (Ascidiacea, Didemnidae) to develop tools for species identification. Because each Diplosoma species has distinctly different COI haplotype(s), the gene sequence seems to be usable for species discrimination in this ascidian genus. The phylogenetic hypothesis supported by the COI data is congruent with the distribution of character states of the retractor muscle. in this paper, we describe a new Diplosoma species harboring symbiotic cyanophytes, found on Miyakojima Island, Ryukyu Archipelago, Japan. Diplosoma aggregatum sp. nov. forms mosaic-like aggregates of small colonies. Although the zooids of D. aggregatum are similar to those of D. virens, these species are differentiated by colony form and COI sequences.},
}
@article {pmid19714262,
year = {2008},
author = {Patel, IS and Premasiri, WR and Moir, DT and Ziegler, LD},
title = {Barcoding bacterial cells: A SERS based methodology for pathogen identification.},
journal = {Journal of Raman spectroscopy : JRS},
volume = {39},
number = {11},
pages = {1660-1672},
pmid = {19714262},
issn = {0377-0486},
support = {R41 AI066641/AI/NIAID NIH HHS/United States ; R41 AI066641-01/AI/NIAID NIH HHS/United States ; },
abstract = {A principal component analysis (PCA) based on the sign of the second derivative of the surface enhanced Raman spectroscopy (SERS) spectrum obtained on in-situ grown Au cluster covered SiO(2) substrates results in improved reproducibility and enhanced specificity for bacterial diagnostics. The barcode generated clustering results are systematically compared to those obtained from corresponding spectral intensities, first derivatives and second derivatives for the SERS spectra of closely related cereus group Bacillus strains. PCA plots and corresponding hierarchical cluster analysis (HCA) dendrograms illustrate the improved bacterial identification resulting from the barcode spectral data reduction. Supervised DFA plots result in slightly improved group separation but show more susceptibility to false positive classifications than the corresponding PCA contours. In addition, this PCA treatment is used to highlight the enhanced bacterial species specificity observed for SERS as compared to normal bulk (non-SERS) Raman spectra. The identification algorithm described here is critical for the development of SERS microscopy as a rapid, reagentless, portable diagnostic of bacterial pathogens.},
}
@article {pmid19712154,
year = {2009},
author = {Crainey, JL and Wilson, MD and Post, RJ},
title = {An 18S ribosomal DNA barcode for the study of Isomermis lairdi, a parasite of the blackfly Simulium damnosum s.l.},
journal = {Medical and veterinary entomology},
volume = {23},
number = {3},
pages = {238-244},
doi = {10.1111/j.1365-2915.2009.00814.x},
pmid = {19712154},
issn = {1365-2915},
support = {G0600015/MRC_/Medical Research Council/United Kingdom ; 77615/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; Antiparasitic Agents/pharmacology/therapeutic use ; DNA, Ribosomal/*genetics ; Drug Resistance ; Filaricides/therapeutic use ; Gene Amplification ; Ghana ; Humans ; Ivermectin/*pharmacology/therapeutic use ; Mermithoidea/drug effects/*genetics ; Onchocerciasis/prevention &amp; control ; Phylogeny ; Polymerase Chain Reaction ; Predatory Behavior ; RNA, Ribosomal, 18S/genetics ; Simuliidae/*parasitology/physiology ; },
abstract = {The mermithid parasite, Isomermis lairdi Mondet, Poinar &amp; Bernadou (Nematoda: Mermithidae), is known to have a major impact on populations of Simulium damnosum s.l. Theobald (Diptera: Simuliidae) and on their efficiency as vectors of Onchocerca volvulus (Leuckart) (Nematoda: Filarioidea). However, the value of I. lairdi and other mermithid parasites as potential means of integrated vector control has not been fully realized. This is partly because traditional taxonomic approaches have been insufficient for describing and analysing important aspects of their biology and host range. In total, rDNA barcode sequences have been obtained from over 70 I. lairdi mermithids found parasitizing S. damnosum s.l. larvae in three different rivers. No two sequences were found to vary by more than 0.5%, and cytospecies identification of mermithid hosts revealed that I. lairdi with identical rDNA barcodes can parasitize multiple cytoforms of the S. damnosum complex, including S. squamosum (Enderlein). Phylogenetic analysis using a partial sequence from the 18S ribosomal DNA barcode, grouped I. lairdi in a monophyletic group with Gastromermis viridis Welch (Nematoda: Mermithidae) and Isomermis wisconsinensis Welch (Nematoda: Mermithidae).},
}
@article {pmid19706315,
year = {2009},
author = {Gabriel, C and Danzer, M and Hackl, C and Kopal, G and Hufnagl, P and Hofer, K and Polin, H and Stabentheiner, S and Pröll, J},
title = {Rapid high-throughput human leukocyte antigen typing by massively parallel pyrosequencing for high-resolution allele identification.},
journal = {Human immunology},
volume = {70},
number = {11},
pages = {960-964},
doi = {10.1016/j.humimm.2009.08.009},
pmid = {19706315},
issn = {1879-1166},
mesh = {*Alleles ; Base Sequence ; Genome, Human ; HLA Antigens/*analysis/*genetics ; High-Throughput Screening Assays/*methods ; Histocompatibility Testing/*methods ; Humans ; Molecular Sequence Data ; Time Factors ; },
abstract = {Transplantation and, notably, hematopoietic stem cell transplantation require high-resolution human leukocyte antigen (HLA) typing and, because of the heterozygous genomic DNA samples, are dependent on clonal analytical methods. High-resolution HLA typing is a necessity for accomplishing the best possible histocompatibility match between donor and recipient, because mismatches strongly increase the risk of severe acute graft-versus-host disease. We describe the development and first application in a clinical setting of a novel, HLA sequence-based typing method by exploring the next-generation sequencing technology as provided by the Genome Sequencer FLX system (Roche/454 Life Sciences, Branford, CT). The developed system allows for ambiguity-free, high-throughput, high-resolution HLA-A and -B typing with the potential for automation. Primers and Genome Sequencer FLX specific adapters were lengthened with donor-identifying barcode sequences to identify each of eight Caucasian reference donors within one single multiplex sequencing run. Compared with normal SBT HLA typing, results indicate that every patient was identified correctly with an average of 1000 reads per amplicon. Furthermore, current investments for increased read lengths and fully automated molecular diagnostic software tools, using original GS-FLX data file formats, will enhance this novel HLA typing strategy in the near future.},
}
@article {pmid19705801,
year = {2009},
author = {Rasmussen, RS and Morrissey, MT and Hebert, PD},
title = {DNA barcoding of commercially important salmon and trout species (Oncorhynchus and Salmo) from North America.},
journal = {Journal of agricultural and food chemistry},
volume = {57},
number = {18},
pages = {8379-8385},
doi = {10.1021/jf901618z},
pmid = {19705801},
issn = {1520-5118},
mesh = {Animals ; DNA/*analysis ; DNA, Mitochondrial/analysis ; Electronic Data Processing ; Fish Products/*classification ; Food Contamination/prevention &amp; control ; North America ; Oncorhynchus/*classification/*genetics ; Trout/*classification/*genetics ; },
abstract = {The present study investigated the ability of DNA barcoding to reliably identify the seven commercially important salmon and trout species (genera Oncorhynchus and Salmo) in North America. More than 1000 salmonid reference samples were collected from a wide geographic range. DNA extracts from these samples were sequenced for the standard 650 bp barcode region of the cytochrome c oxidase subunit I gene (COI). DNA barcodes showed low intraspecies divergences (mean, 0.26%; range, 0.04-1.09%), and the mean congeneric divergence was 32-fold greater, at 8.22% (range, 3.42-12.67%). The minimum interspecies divergence was always greater than the maximum intraspecies divergence, indicating that these species can be reliably differentiated using DNA barcodes. Furthermore, several shorter barcode regions (109-218 bp), termed "mini-barcodes", were identified in silico that can differentiate all eight species, providing a potential means for species identification in heavily processed products.},
}
@article {pmid19695081,
year = {2009},
author = {Soininen, EM and Valentini, A and Coissac, E and Miquel, C and Gielly, L and Brochmann, C and Brysting, AK and Sønstebø, JH and Ims, RA and Yoccoz, NG and Taberlet, P},
title = {Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures.},
journal = {Frontiers in zoology},
volume = {6},
number = {},
pages = {16},
pmid = {19695081},
issn = {1742-9994},
abstract = {BACKGROUND: In order to understand the role of herbivores in trophic webs, it is essential to know what they feed on. Diet analysis is, however, a challenge in many small herbivores with a secretive life style. In this paper, we compare novel (high-throughput pyrosequencing) DNA barcoding technology for plant mixture with traditional microhistological method. We analysed stomach contents of two ecologically important subarctic vole species, Microtus oeconomus and Myodes rufocanus, with the two methods. DNA barcoding was conducted using the P6-loop of the chloroplast trnL (UAA) intron.<br><br>RESULTS: Although the identified plant taxa in the diets matched relatively well between the two methods, DNA barcoding gave by far taxonomically more detailed results. Quantitative comparison of results was difficult, mainly due to low taxonomic resolution of the microhistological method, which also in part explained discrepancies between the methods. Other discrepancies were likely due to biases mostly in the microhistological analysis.<br><br>CONCLUSION: We conclude that DNA barcoding opens up for new possibilities in the study of plant-herbivore interactions, giving a detailed and relatively unbiased picture of food utilization of herbivores.},
}
@article {pmid19679063,
year = {2009},
author = {Yang, CH and Chang, HW and Cheng, YH and Chuang, LY},
title = {Novel generating protective single nucleotide polymorphism barcode for breast cancer using particle swarm optimization.},
journal = {Cancer epidemiology},
volume = {33},
number = {2},
pages = {147-154},
doi = {10.1016/j.canep.2009.07.001},
pmid = {19679063},
issn = {1877-783X},
mesh = {Algorithms ; Breast Neoplasms/*genetics ; Case-Control Studies ; Electronic Data Processing/*methods ; Female ; Genome-Wide Association Study ; Genotype ; Humans ; Odds Ratio ; Polymorphism, Single Nucleotide/*genetics ; },
abstract = {BACKGROUND: High-throughput single nucleotide polymorphism (SNP) genotyping generates a huge amount of SNP data in genome-wide association studies. Simultaneous analyses for multiple SNP interactions associated with many diseases and cancers are essential; however, these analyses are still computationally challenging.<br><br>METHODS: In this study, we propose an odds ratio-based binary particle swarm optimization (OR-BPSO) method to evaluate the risk of breast cancer.<br><br>RESULTS: BPSO provides the combinational SNPs with their corresponding genotype, called SNP barcodes, with the maximal difference of occurrence between the control and breast cancer groups. A specific SNP barcode with an optimized fitness value was identified among seven SNP combinations within the space of one minute. The identified SNP barcodes with the best performance between control and breast cancer groups were found to be control-dominant, suggesting that these SNP barcodes may prove protective against breast cancer. After statistical analysis, these control-dominant SNP barcodes were processed for odds ratio analysis for quantitative measurement with regard to the risk of breast cancer.<br><br>CONCLUSION: This study proposes an effective high-speed method to analyze the SNP-SNP interactions for breast cancer association study.},
}
@article {pmid19674931,
year = {2010},
author = {Moniz, MB and Kaczmarska, I},
title = {Barcoding of diatoms: nuclear encoded ITS revisited.},
journal = {Protist},
volume = {161},
number = {1},
pages = {7-34},
doi = {10.1016/j.protis.2009.07.001},
pmid = {19674931},
issn = {1618-0941},
mesh = {Cluster Analysis ; Computational Biology/*methods ; DNA, Algal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Diatoms/*classification/*genetics ; Genes, rRNA ; Molecular Sequence Data ; Phylogeny ; RNA, Algal/genetics ; RNA, Ribosomal, 5.8S/genetics ; Sequence Analysis, DNA ; },
abstract = {DNA-barcoding is based on the premise that the divergence of a small DNA fragment coincides with biological separation of species. If true, it offers an additional tool for worldwide consistent species recognition even in cases of semi-cryptic species. Our study includes 618 sequences representing 114 diatom species belonging to the two most species-rich classes of diatoms (Mediophyceae and Bacillariophyceae). A 99.5% success rate in separating biologically defined species and a 91% success rate in separating all species tested was obtained when using the proposed barcode starting at the 5' end of 5.8S and ending in the conserved motif of helix III of ITS2 (300 to 400 bp). Including the whole 5.8S+ITS2 region did not significantly improve species resolution. We tested our barcode on 17 unidentified, misidentified or contaminated strains derived mostly from a culture collection, and these were correctly flagged as erroneous by their ITS sequences. We conclude that the proposed barcode represents for the Mediophyceae and Bacillariophyceae a robust, economical, and rapid way to recognize and identify most species (when a reference sequence is available) that is as good as or better than other molecular markers thus far proposed.},
}
@article {pmid19674306,
year = {2009},
author = {Makino, W and Tanabe, AS},
title = {Extreme population genetic differentiation and secondary contact in the freshwater copepod Acanthodiaptomus pacificus in the Japanese Archipelago.},
journal = {Molecular ecology},
volume = {18},
number = {17},
pages = {3699-3713},
doi = {10.1111/j.1365-294X.2009.04307.x},
pmid = {19674306},
issn = {1365-294X},
mesh = {Animals ; Copepoda/*genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics ; *Evolution, Molecular ; *Genetic Variation ; *Genetics, Population ; Geography ; Haplotypes ; Japan ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {We investigated the sequence variation in the mitochondrial cytochrome c oxidase subunit 1 (mtCOI) gene and the nuclear ribosomal internal transcribed spacers (ncITS) of the calanoid copepod Acanthodiaptomus pacificus in Japan. A. pacificus individuals were divided into three divergent mtCOI lineages (mt-A, -B and -C). mt-A was distributed in the northernmost part of Japan, from Hokkaido to the northern part of Honshu Island, whereas mt-C was the southernmost lineage, distributed from central Honshu to Shikoku and Kyushu Islands. mt-B was distributed between these former two lineages, resulting in parapatry with mt-C and mt-A. In all lineages, 80% of the localities were fixed for a single haplotype, and different localities tended to have different haplotypes. The degree of genetic differentiation among these lineages (15-22%) was at an interspecific level, according to the criteria of the DNA barcode technique. However, the topology of ncITS was not congruent with that of mtCOI, as the reciprocal monophyly was not observed within mt-B and mt-C. Therefore, we merged them into the Southern Lineage and separated it from the Northern Lineage (i.e. mt-A). Evidence of introgression was found within the Southern Lineage, while gene flow was not observed between the Northern and Southern Lineages, suggesting that A. pacificus is a cryptic species complex. We also argue that genetic differentiations of A. pacificus in Japan may reflect the history of separation, transgression and regression of the landmass during the formation of current Japanese Archipelago.},
}
@article {pmid19670393,
year = {2009},
author = {Fernandez-Rosas, E and Gómez, R and Ibañez, E and Barrios, L and Duch, M and Esteve, J and Nogués, C and Plaza, JA},
title = {Intracellular polysilicon barcodes for cell tracking.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {5},
number = {21},
pages = {2433-2439},
doi = {10.1002/smll.200900733},
pmid = {19670393},
issn = {1613-6829},
mesh = {Cells, Cultured ; *Electronic Data Processing ; Feasibility Studies ; Humans ; Macrophages/*cytology ; Microscopy, Electron, Scanning ; Silicon/*chemistry ; },
abstract = {During the past decade, diverse types of barcode have been designed in order to track living cells in vivo or in vitro, but none of them offer the possibility to follow an individual cell up to ten or more days. Using silicon microtechnologies a barcode sufficiently small to be introduced into a cell, yet visible and readily identifiable under an optical microscope, is designed. Cultured human macrophages are able to engulf the barcodes due to their phagocytic ability and their viability is not affected. The utility of the barcodes for cell tracking is demonstrated by following individual cells for up to ten days in culture and recording their locomotion. Interestingly, silicon microtechnology allows the mass production of reproducible codes at low cost with small features (bits) in the micrometer range that are additionally biocompatible.},
}
@article {pmid19668363,
year = {2009},
author = {Harper, JT and Gile, GH and James, ER and Carpenter, KJ and Keeling, PJ},
title = {The inadequacy of morphology for species and genus delineation in microbial eukaryotes: an example from the parabasalian termite symbiont coronympha.},
journal = {PloS one},
volume = {4},
number = {8},
pages = {e6577},
pmid = {19668363},
issn = {1932-6203},
mesh = {Animals ; Isoptera/*microbiology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Species Specificity ; *Symbiosis ; Trichomonadida/classification/*isolation &amp; purification ; },
abstract = {BACKGROUND: For the majority of microbial eukaryotes (protists, algae), there is no clearly superior species concept that is consistently applied. In the absence of a practical biological species concept, most species and genus level delineations have historically been based on morphology, which may lead to an underestimate of the diversity of microbial eukaryotes. Indeed, a growing body of molecular evidence, such as barcoding surveys, is beginning to support the conclusion that significant cryptic species diversity exists. This underestimate of diversity appears to be due to a combination of using morphology as the sole basis for assessing diversity and our inability to culture the vast majority of microbial life. Here we have used molecular markers to assess the species delineations in two related but morphologically distinct genera of uncultivated symbionts found in the hindgut of termites.<br><br>Using single-cell isolation and environmental PCR, we have used a barcoding approach to characterize the diversity of Coronympha and Metacoronympha symbionts in four species of Incisitermes termites, which were also examined using scanning electron microscopy and light microcopy. Despite the fact that these genera are significantly different in morphological complexity and structural organisation, we find they are two life history stages of the same species. At the same time, we show that the symbionts from different termite hosts show an equal or greater level of sequence diversity than do the hosts, despite the fact that the symbionts are all classified as one species.<br><br>CONCLUSIONS/SIGNIFICANCE: The morphological information used to describe the diversity of these microbial symbionts is misleading at both the genus and species levels, and led to an underestimate of species level diversity as well as an overestimate of genus level diversity. The genus 'Metacoronympha' is invalid and appears to be a life history stage of Coronympha, while the single recognized species of Coronympha octonaria inhabiting these four termites is better described as four distinct species.},
}
@article {pmid19666622,
year = {2009},
author = {, },
title = {A DNA barcode for land plants.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {106},
number = {31},
pages = {12794-12797},
pmid = {19666622},
issn = {1091-6490},
support = {//Intramural NIH HHS/United States ; },
mesh = {DNA, Plant/*chemistry ; *Electronic Data Processing ; Plants/*classification/genetics ; Ribulose-Bisphosphate Carboxylase/genetics ; },
abstract = {DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF-atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK-psbI spacer, and trnH-psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.},
}
@article {pmid19644072,
year = {2009},
author = {Chase, MW and Fay, MF},
title = {Ecology. Barcoding of plants and fungi.},
journal = {Science (New York, N.Y.)},
volume = {325},
number = {5941},
pages = {682-683},
doi = {10.1126/science.1176906},
pmid = {19644072},
issn = {1095-9203},
mesh = {DNA, Fungal/*genetics ; DNA, Plant/*genetics ; Ecosystem ; Fungi/*classification/genetics ; *Genetic Markers ; Geography ; Plants/*classification/genetics ; Plastids/genetics ; Species Specificity ; },
}
@article {pmid19639036,
year = {2009},
author = {Kong, F and Chen, SC and Chen, X and Sintchenko, V and Halliday, C and Cai, L and Tong, Z and Lee, OC and Sorrell, TC},
title = {Assignment of reference 5'-end 16S rDNA sequences and species-specific sequence polymorphisms improves species identification of Nocardia.},
journal = {The open microbiology journal},
volume = {3},
number = {},
pages = {97-105},
pmid = {19639036},
issn = {1874-2858},
abstract = {16S rDNA sequence analysis is the most accurate method for definitive species identification of nocardiae. However, conflicting results can be found due to sequence errors in gene databases. This study tested the feasibility of species identification of Nocardia by partial (5'-end 606-bp) 16S rDNA sequencing, based on sequence comparison with "reference" sequences of well-annotated strains. This new approach was evaluated using 96 American Type Culture Collection (n=6), and clinical (n=90) Nocardia isolates. Nucleotide sequence-based polymorphisms within species were indicative of "sequence types" for that species. Sequences were compared with those in the GenBank, Bioinformatics Bacteria Identification and Ribosomal Database Project databases. Compared with the reference sequence set, all 96 isolates were correctly identified using the criterion of ≥99% sequence similarity. Seventy-eight (81.3%) were speciated by database comparison; alignment with reference sequences resolved the identity of 14 (15%) isolates whose sequences yielded 100% similarity to sequences in GenBank under >1 species designation. Of 90 clinical isolates, the commonest species was Nocardia nova (33.3%) followed by Nocardia cyriacigeorgica (26.7%). Recently-described or uncommon species included Nocardia veterana (4.4%), Nocarida bejingensis (2.2%) and, Nocardia abscessus and Nocardia arthriditis (each n=1). Nocardia asteroides sensu stricto was rare (n=1). There were nine sequence types of N. nova, three of Nocardia brasiliensis with two each of N. cyriacigeorgica and Nocardia farcinica. Thirteen novel sequences were identified. Alignment of sequences with reference sequences facilitated species identification of Nocardia and allowed delineation of sequence types within species, suggesting that such a barcoding approach can be clinically useful for identification of bacteria.},
}
@article {pmid19636374,
year = {2009},
author = {Seabrook-Davison, M and Huynen, L and Lambert, DM and Brunton, DH},
title = {Ancient DNA resolves identity and phylogeny of New Zealand's extinct and living quail (Coturnix sp.).},
journal = {PloS one},
volume = {4},
number = {7},
pages = {e6400},
pmid = {19636374},
issn = {1932-6203},
mesh = {Animals ; Coturnix/*genetics ; DNA/*genetics ; *Extinction, Biological ; *Phylogeny ; },
abstract = {BACKGROUND: The New Zealand quail, Coturnix novaezealandiae, was widespread throughout New Zealand until its rapid extinction in the 1870's. To date, confusion continues to exist concerning the identity of C. novaezealandiae and its phylogenetic relationship to Coturnix species in neighbouring Australia, two of which, C. ypsilophora and C. pectoralis, were introduced into New Zealand as game birds. The Australian brown quail, C. ypsilophora, was the only species thought to establish with current populations distributed mainly in the northern part of the North Island of New Zealand. Owing to the similarities between C. ypsilophora, C. pectoralis, and C. novaezealandiae, uncertainty has arisen over whether the New Zealand quail is indeed extinct, with suggestions that remnant populations of C. novaezealandiae may have survived on offshore islands.<br><br>Using fresh and historical samples of Coturnix sp. from New Zealand and Australia, DNA analysis of selected mitochondrial regions was carried out to determine phylogenetic relationships and species status. Results show that Coturnix sp. specimens from the New Zealand mainland and offshore island Tiritiri Matangi are not the New Zealand quail but are genetically identical to C. ypsilophora from Australia and can be classified as the same species. Furthermore, cytochrome b and COI barcoding analysis of the New Zealand quail and Australia's C. pectoralis, often confused in museum collections, show that they are indeed separate species that diverged approximately 5 million years ago (mya). Gross morphological analysis of these birds suggests a parallel loss of sustained flight with very little change in other phenotypic characters such as plumage or skeletal structure.<br><br>CONCLUSION/SIGNIFICANCE: Ancient DNA has proved invaluable for the detailed analysis and identification of extinct and morphologically cryptic taxa such as that of quail and can provide insights into the timing of evolutionary changes that influence morphology.},
}
@article {pmid19635845,
year = {2009},
author = {Stiller, M and Knapp, M and Stenzel, U and Hofreiter, M and Meyer, M},
title = {Direct multiplex sequencing (DMPS)--a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA.},
journal = {Genome research},
volume = {19},
number = {10},
pages = {1843-1848},
pmid = {19635845},
issn = {1549-5469},
mesh = {Animals ; *DNA Degradation, Necrotic ; DNA Primers/genetics ; DNA, Mitochondrial/*analysis ; Electronic Data Processing/instrumentation/methods ; *Fossils ; Genome, Mitochondrial ; Mammoths/genetics ; Models, Biological ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/*methods ; Sequence Alignment/instrumentation/methods ; Sequence Analysis, DNA/instrumentation/*methods ; Ursidae/genetics ; },
abstract = {Although the emergence of high-throughput sequencing technologies has enabled whole-genome sequencing from extinct organisms, little progress has been made in accelerating targeted sequencing from highly degraded DNA. Here, we present a novel and highly sensitive method for targeted sequencing of ancient and degraded DNA, which couples multiplex PCR directly with sample barcoding and high-throughput sequencing. Using this approach, we obtained a 96% complete mitochondrial genome data set from 31 cave bear (Ursus spelaeus) samples using only two 454 Life Sciences (Roche) GS FLX runs. In contrast to previous studies relying only on short sequence fragments, the overlapping portion of our data comprises almost 10 kb of replicated mitochondrial genome sequence, allowing for the unambiguous differentiation of three major cave bear clades. Our method opens up the opportunity to simultaneously generate many kilobases of overlapping sequence data from large sets of difficult samples, such as museum specimens, medical collections, or forensic samples. Embedded in our approach, we present a new protocol for the construction of barcoded sequencing libraries, which is compatible with all current high-throughput technologies and can be performed entirely in plate setup.},
}
@article {pmid19628011,
year = {2009},
author = {Palencia, ER and Klich, MA and Glenn, AE and Bacon, CW},
title = {Use of a rep-PCR system to predict species in the Aspergillus section Nigri.},
journal = {Journal of microbiological methods},
volume = {79},
number = {1},
pages = {1-7},
doi = {10.1016/j.mimet.2009.07.012},
pmid = {19628011},
issn = {1872-8359},
mesh = {Aspergillus niger/*classification/*genetics/isolation &amp; purification ; Automation ; Calmodulin/genetics ; Cluster Analysis ; DNA Fingerprinting/*methods ; DNA, Ribosomal Spacer/genetics ; Genotype ; Mycological Typing Techniques/*methods ; Polymerase Chain Reaction/*methods ; United States ; },
abstract = {The Aspergillus niger aggregate within the A. section Nigri is a group of black-spored aspergilli of great agro-economic importance whose well defined taxonomy has been elusive. Rep-PCR has become a rapid and cost-effective method for genotyping fungi and bacteria. In the present study, we evaluated the discriminatory power of a semi-automated rep-PCR barcoding system to distinguish morphotypic species and compare the results with the data obtained from ITS and partial calmodulin regions. For this purpose, 20 morphotyped black-spored Aspergillus species were used to create the A. section Nigri library in this barcoding system that served to identify 34 field isolates. A pair-wise similarity matrix was calculated using the cone-based Pearson correlation method and the dendrogram was generated by the unweighted pair group method with arithmetic mean (UPGMA), illustrating four different clustered groups: the uniseriate cluster (I), the Aspergillus carbonarius cluster (II), and. the two A. niger aggregate clusters (named III.A and III.B). Rep-PCR showed higher resolution than the ITS and the partial calmodulin gene analytical procedures. The data of the 34 unknown field isolates, collected from different locations in the United States, indicated that only 12% of the field isolates were >95% similar to one of the genotypes included in the A. section Nigri library. However, 64% of the field isolates matched genotypes with the reference library (similarity values >90%). Based on these results, this barcoding procedure has the potential for use as a reproducible tool for identifying the black-spored aspergilli.},
}
@article {pmid19627628,
year = {2009},
author = {Stothard, JR and Webster, BL and Weber, T and Nyakaana, S and Webster, JP and Kazibwe, F and Kabatereine, NB and Rollinson, D},
title = {Molecular epidemiology of Schistosoma mansoni in Uganda: DNA barcoding reveals substantial genetic diversity within Lake Albert and Lake Victoria populations.},
journal = {Parasitology},
volume = {136},
number = {13},
pages = {1813-1824},
doi = {10.1017/S003118200999031X},
pmid = {19627628},
issn = {1469-8161},
mesh = {Animals ; Base Sequence ; Child ; Cyclooxygenase 1/genetics ; DNA, Protozoan/genetics ; Fresh Water ; *Genetic Variation ; Humans ; Molecular Epidemiology ; Molecular Sequence Data ; Schistosoma mansoni/*genetics ; Schistosomiasis mansoni/*epidemiology/*parasitology ; Uganda/epidemiology ; },
abstract = {Representative samples of Ugandan Schistosoma mansoni from Lake Albert and Lake Victoria were examined using DNA barcoding, sequence analysis of two partially overlapping regions - ASMIT (396 bp) &amp; MORGAN (617 bp) - of the mitochondrial cytochrome oxidase subunit I (cox1). The Victorian sample exhibited greater nucleotide diversity, 1.4% vs. 1.0%, and a significant population partition appeared as barcodes did not cross-over between lakes. With one exception, Lake Albert populations were more mixed by sampled location, while those from Lake Victoria appeared more secluded. Using statistical parsimony, barcode ASMIT 1 was putatively ancestral to all others and analysis of MORGAN cox1 confirmed population diversity. All samples fell into two of five well-resolved lineages; sub-lineages therein broadly partitioning by lake. It seems that barcode ASMIT 1 (and close variants) was likely widely dispersed throughout the Nilotic environment but later diversified in situ, and in parallel, within Lake Albert and Lake Victoria. The genetic uniformity of Ugandan S. mansoni can no longer be assumed, which might better explain known epidemiological heterogeneities. While it appears plausible that locally evolved heritable traits could spread through most of the Lake Albert populations, it seems unlikely they could quickly homogenise into Lake Victoria or amongst populations therein.},
}
@article {pmid19627490,
year = {2009},
author = {Valade, R and Kenis, M and Hernandez-Lopez, A and Augustin, S and Mari Mena, N and Magnoux, E and Rougerie, R and Lakatos, F and Roques, A and Lopez-Vaamonde, C},
title = {Mitochondrial and microsatellite DNA markers reveal a Balkan origin for the highly invasive horse-chestnut leaf miner Cameraria ohridella (Lepidoptera, Gracillariidae).},
journal = {Molecular ecology},
volume = {18},
number = {16},
pages = {3458-3470},
doi = {10.1111/j.1365-294X.2009.04290.x},
pmid = {19627490},
issn = {1365-294X},
mesh = {Aesculus ; Animals ; DNA, Mitochondrial/genetics ; Ecosystem ; Europe ; Genetic Markers ; *Genetic Variation ; *Genetics, Population ; Haplotypes ; Lepidoptera/*genetics ; Microsatellite Repeats ; Sequence Analysis, DNA ; },
abstract = {Biological invasions usually start with a small number of founder individuals. These founders are likely to represent a small fraction of the total genetic diversity found in the source population. Our study set out to trace genetically the geographical origin of the horse-chestnut leafminer, Cameraria ohridella, an invasive microlepidopteran whose area of origin is still unkown. Since its discovery in Macedonia 25 years ago, this insect has experienced an explosive westward range expansion, progressively colonizing all of Central and Western Europe. We used cytochrome oxidase I sequences (DNA barcode fragment) and a set of six polymorphic microsatellites to assess the genetic variability of C. ohridella populations, and to test the hypothesis that C. ohridella derives from the southern Balkans (Albania, Macedonia and Greece). Analysis of mtDNA of 486 individuals from 88 localities allowed us to identify 25 geographically structured haplotypes. In addition, 480 individuals from 16 populations from Europe and the southern Balkans were genotyped for 6 polymorphic microsatellite loci. High haplotype diversity and low measures of nucleotide diversities including a significantly negative Tajima's D indicate that C. ohridella has experienced rapid population expansion during its dispersal across Europe. Both mtDNA and microsatellites show a reduction in genetic diversity of C. ohridella populations sampled from artificial habitats (e.g. planted trees in public parks, gardens, along roads in urban or sub-urban areas) across Europe compared with C. ohridella sampled in natural stands of horse-chestnuts in the southern Balkans. These findings suggest that European populations of C. ohridella may indeed derive from the southern Balkans.},
}
@article {pmid19622793,
year = {2009},
author = {Smith, AM and Heisler, LE and Mellor, J and Kaper, F and Thompson, MJ and Chee, M and Roth, FP and Giaever, G and Nislow, C},
title = {Quantitative phenotyping via deep barcode sequencing.},
journal = {Genome research},
volume = {19},
number = {10},
pages = {1836-1842},
pmid = {19622793},
issn = {1549-5469},
support = {R21 HG004756/HG/NHGRI NIH HHS/United States ; R43 HG003788/HG/NHGRI NIH HHS/United States ; HG00317-05/HG/NHGRI NIH HHS/United States ; R44 HG003788/HG/NHGRI NIH HHS/United States ; HG003788/HG/NHGRI NIH HHS/United States ; R01 HG003224/HG/NHGRI NIH HHS/United States ; },
mesh = {Anti-Bacterial Agents/pharmacology ; Cost-Benefit Analysis ; Doxorubicin/pharmacology ; Drug Evaluation, Preclinical/methods ; Electronic Data Processing/economics/*methods ; Gene Expression Profiling/*methods ; Genomics/methods ; Microbial Sensitivity Tests ; Oligonucleotide Array Sequence Analysis/economics/*methods ; *Phenotype ; Pyridines/pharmacology ; Sensitivity and Specificity ; Sequence Analysis, DNA/economics/*methods ; Tunicamycin/pharmacology ; Yeasts/drug effects/physiology ; },
abstract = {Next-generation DNA sequencing technologies have revolutionized diverse genomics applications, including de novo genome sequencing, SNP detection, chromatin immunoprecipitation, and transcriptome analysis. Here we apply deep sequencing to genome-scale fitness profiling to evaluate yeast strain collections in parallel. This method, Barcode analysis by Sequencing, or "Bar-seq," outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput. When applied to a complex chemogenomic assay, Bar-seq quantitatively identifies drug targets, with performance superior to the benchmark microarray assay. We also show that Bar-seq is well-suited for a multiplex format. We completely re-sequenced and re-annotated the yeast deletion collection using deep sequencing, found that approximately 20% of the barcodes and common priming sequences varied from expectation, and used this revised list of barcode sequences to improve data quality. Together, this new assay and analysis routine provide a deep-sequencing-based toolkit for identifying gene-environment interactions on a genome-wide scale.},
}
@article {pmid19621079,
year = {2009},
author = {Steinke, D and Zemlak, TS and Hebert, PD},
title = {Barcoding nemo: DNA-based identifications for the ornamental fish trade.},
journal = {PloS one},
volume = {4},
number = {7},
pages = {e6300},
pmid = {19621079},
issn = {1932-6203},
mesh = {Animals ; Electron Transport Complex IV/genetics ; *Electronic Data Processing ; *Fishes ; Species Specificity ; },
abstract = {BACKGROUND: Trade in ornamental fishes represents, by far, the largest route for the importation of exotic vertebrates. There is growing pressure to regulate this trade with the goal of ensuring that species are sustainably harvested and that their point of origin is accurately reported. One important element of such regulation involves easy access to specimen identifications, a task that is currently difficult for all but specialists because of the large number of species involved. The present study represents an important first step in making identifications more accessible by assembling a DNA barcode reference sequence library for nearly half of the ornamental fish species imported into North America.<br><br>Analysis of the cytochrome c oxidase subunit I (COI) gene from 391 species from 8 coral reef locations revealed that 98% of these species exhibit distinct barcode clusters, allowing their unambiguous identification. Most species showed little intra-specific variation (adjusted mean = 0.21%), but nine species included two or three lineages showing much more divergence (2.19-6.52%) and likely represent overlooked species complexes. By contrast, three genera contained a species pair or triad that lacked barcode divergence, cases that may reflect hybridization, young taxa or taxonomic over-splitting.<br><br>CONCLUSIONS/SIGNIFICANCE: Although incomplete, this barcode library already provides a new species identification tool for the ornamental fish industry, opening a realm of applications linked to collection practices, regulatory control and conservation.},
}
@article {pmid19608403,
year = {2009},
author = {Zhang, X and Qi, B and Li, Y and Zhang, S},
title = {Amplified electrochemical aptasensor for thrombin based on bio-barcode method.},
journal = {Biosensors &amp; bioelectronics},
volume = {25},
number = {1},
pages = {259-262},
doi = {10.1016/j.bios.2009.06.026},
pmid = {19608403},
issn = {1873-4235},
mesh = {Animals ; Aptamers, Nucleotide/*chemistry ; Biosensing Techniques/*methods ; Electrochemistry/*methods ; Gold/chemistry ; Lead/chemistry ; Nanoparticles/chemistry ; Sensitivity and Specificity ; Sulfides/chemistry ; Thrombin/*analysis ; },
abstract = {In the present study, an electrochemical aptasensor for highly sensitive detection of thrombin was developed based on bio-barcode amplification assay. For this proposed aptasensor, capture DNA aptamerI was immobilized on the Au electrode. The functional Au nanoparticles (DNA-AuNPs) are loaded with barcode binding DNA and aptamerII. Through the specific recognition for thrombin, a sandwich format of Au/aptamerI/thrombin/DNA-AuNPs was fabricated. After hybridization with the PbSNPs-labeled barcode DNA, the assembled sensor was obtained. The concentration of thrombin was monitored based on the concentration of lead ions dissolved through differential pulse anodic stripping voltammetric (DPASV). Under optimum conditions, a detection limit of 6.2x10(-15) mol L(-1) (M) thrombin was achieved. In addition, the sensor exhibited excellent selectivity against other proteins.},
}
@article {pmid19568668,
year = {2009},
author = {Douglas, ES and Hsiao, SC and Onoe, H and Bertozzi, CR and Francis, MB and Mathies, RA},
title = {DNA-barcode directed capture and electrochemical metabolic analysis of single mammalian cells on a microelectrode array.},
journal = {Lab on a chip},
volume = {9},
number = {14},
pages = {2010-2015},
pmid = {19568668},
issn = {1473-0197},
support = {/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; Biosensing Techniques ; DNA/*metabolism ; Electrochemistry ; *Electronic Data Processing ; Humans ; Hydrogen-Ion Concentration ; Jurkat Cells ; Microelectrodes ; Microscopy, Fluorescence ; T-Lymphocytes/cytology/*metabolism/pathology ; },
abstract = {A microdevice is developed for DNA-barcode directed capture of single cells on an array of pH-sensitive microelectrodes for metabolic analysis. Cells are modified with membrane-bound single-stranded DNA, and specific single-cell capture is directed by the complementary strand bound in the sensor area of the iridium oxide pH microelectrodes within a microfluidic channel. This bifunctional microelectrode array is demonstrated for the pH monitoring and differentiation of primary T cells and Jurkat T lymphoma cells. Single Jurkat cells exhibited an extracellular acidification rate of 11 milli-pH min(-1), while primary T cells exhibited only 2 milli-pH min(-1). This system can be used to capture non-adherent cells specifically and to discriminate between visually similar healthy and cancerous cells in a heterogeneous ensemble based on their altered metabolic properties.},
}
@article {pmid19559092,
year = {2009},
author = {Yassin, A and Amédégnato, C and Cruaud, C and Veuille, M},
title = {Molecular taxonomy and species delimitation in Andean Schistocerca (Orthoptera: Acrididae).},
journal = {Molecular phylogenetics and evolution},
volume = {53},
number = {2},
pages = {404-411},
doi = {10.1016/j.ympev.2009.06.012},
pmid = {19559092},
issn = {1095-9513},
mesh = {Animals ; DNA, Mitochondrial/genetics ; Gene Flow ; *Genetics, Population ; Grasshoppers/classification/*genetics ; Peru ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The acridian genus Schistocerca comprises about 50 species which are endemic to the New World, except the Old World locust S. gregaria. Their morphological identification is rendered difficult by phase polyphenism, geographical overlap due to migrations or swarming, the difficulty to easily differentiate genitalia and the occurrence of interspecific hybrids. The three species reported from Peru include the swarming species S. interrita, a pest that can be recognized only by taxonomists. We show that it can be unambiguously identified using a mitochondrial DNA fragment known to have barcoding properties in this genus. We used several methods to delimitate Peruvian species. While S. interrita and S. pallens were well characterized, S. piceifrons peruviana was split into several taxa by a phylogeny-based method, whereas a combination of population genetics methods led one to identify only the three nominal species. A tentative reconstruction of the species history shows that several populations of S. piceifrons peruviana have recently increased in number, while exchanging some migrants, whereas an isolated population at the northern margin of the species range is substantially differentiated while exchanging no migrants with the others. This complex history has resulted in an atypical lineage pattern that appears to have confounded the standard assumptions underlying available species delimitation methods. Because of its behavioral property which tends to keep it panmictic, the identification of the swarming S. interrita remained unaffected.},
}
@article {pmid19557335,
year = {2009},
author = {ZHANG, J and WANG, J and XIA, T and ZHOU, S},
title = {DNA barcoding: species delimitation in tree peonies.},
journal = {Science in China. Series C, Life sciences},
volume = {52},
number = {6},
pages = {568-578},
doi = {10.1007/s11427-009-0069-5},
pmid = {19557335},
issn = {1006-9305},
mesh = {Classification/*methods ; Computational Biology/*methods ; DNA, Plant/analysis/genetics ; Evolution, Molecular ; *Paeonia/classification/genetics ; Phylogeny ; },
abstract = {Delimitations of species are crucial for correct and precise identification of taxa. Unfortunately "species" is more a subjective than an objective concept in taxonomic practice due to difficulties in revealing patterns of infra- or inter-specific variations. Molecular phylogenetic studies at the population level solve this problem and lay a sound foundation for DNA barcoding. In this paper we exemplify the necessity of adopting a phylogenetic concept of species in DNA barcoding for tree peonies (Paeonia sect. Moutan). We used 40 samples representing all known populations of rare and endangered species and several populations of widely distributed tree peonies. All currently recognized species and major variants have been included in this study. Four chloroplast gene fragments, i.e. ndhF, rps16-trnQ, trnL-F and trnS-G (a total of 5040 characters, 96 variable and 69 parsimony-informative characters) and one variable and single-copy nuclear GPAT gene fragment (2093-2197 bp, 279 variable and 148 parsimony-informative characters) were used to construct phylogenetic relationships among the taxa. The evolutionary lineages revealed by the nuclear gene and the chloroplast genes are inconsistent with the current circumscriptions of P. decomposita, P. jishanensis, P. qiui, and P. rockii based on morphology. The inconsistencies come from (1) significant chloroplast gene divergence but little nuclear GPAT gene divergence among population systems of P. decomposita + P. rockii, and (2) well-diverged nuclear GPAT gene but little chloroplast gene divergence between P. jishanensis and P. qiui. The incongruence of the phylogenies based on the chloroplast genes and the nuclear GPAT gene is probably due to the chloroplast capture event in evolutionary history, as no reproductive barriers exist to prevent inter-specific hybridization. We also evaluated the suitability of these genes for use as DNA barcodes for tree peonies. The variability of chloroplast genes among well-defined species or population systems of a species complex is 4.82 times the figure within the groups, and the GPAT gene is twice as variable between the groups as within the groups. The number of completely divergent sites is sufficient to mark the two subsections, the two species in subsection Delavayanae, and the well-divergent species in subsection Vaginatae. But the genes currently used either from the chloroplast genome or from the nuclear genome alone cannot correctly assign samples of P. decomposita, P. jishanensis, P. qiui, or P. rockii to the species as currently defined. We conclude that (1) DNA barcoding should be based on prior phylogenetic studies to understand the evolutionary lineages and how well the taxonomic species correspond to the lineages; (2) it is unlikely to find a single short fragment as a barcode for every plant and such a fragment could result in misidentification when a chloroplast capture event happened in the evolutionary history of plants like tree peonies; and (3) we suggest striving for a universal marker at the familial level and locally universal barcodes within a family instead of looking for a universal barcode for all plants.},
}
@article {pmid19534740,
year = {2009},
author = {Santamaria, M and Vicario, S and Pappadà, G and Scioscia, G and Scazzocchio, C and Saccone, C},
title = {Towards barcode markers in Fungi: an intron map of Ascomycota mitochondria.},
journal = {BMC bioinformatics},
volume = {10 Suppl 6},
number = {Suppl 6},
pages = {S15},
pmid = {19534740},
issn = {1471-2105},
mesh = {Ascomycota/*genetics ; DNA, Mitochondrial/*chemistry ; Genes, Fungal ; Genetic Markers ; Genome, Fungal ; Genome, Mitochondrial ; *Introns ; },
abstract = {BACKGROUND: A standardized and cost-effective molecular identification system is now an urgent need for Fungi owing to their wide involvement in human life quality. In particular the potential use of mitochondrial DNA species markers has been taken in account. Unfortunately, a serious difficulty in the PCR and bioinformatic surveys is due to the presence of mobile introns in almost all the fungal mitochondrial genes. The aim of this work is to verify the incidence of this phenomenon in Ascomycota, testing, at the same time, a new bioinformatic tool for extracting and managing sequence databases annotations, in order to identify the mitochondrial gene regions where introns are missing so as to propose them as species markers.<br><br>METHODS: The general trend towards a large occurrence of introns in the mitochondrial genome of Fungi has been confirmed in Ascomycota by an extensive bioinformatic analysis, performed on all the entries concerning 11 mitochondrial protein coding genes and 2 mitochondrial rRNA (ribosomal RNA) specifying genes, belonging to this phylum, available in public nucleotide sequence databases. A new query approach has been developed to retrieve effectively introns information included in these entries.<br><br>RESULTS: After comparing the new query-based approach with a blast-based procedure, with the aim of designing a faithful Ascomycota mitochondrial intron map, the first method appeared clearly the most accurate. Within this map, despite the large pervasiveness of introns, it is possible to distinguish specific regions comprised in several genes, including the full NADH dehydrogenase subunit 6 (ND6) gene, which could be considered as barcode candidates for Ascomycota due to their paucity of introns and to their length, above 400 bp, comparable to the lower end size of the length range of barcodes successfully used in animals.<br><br>CONCLUSION: The development of the new query system described here would answer the pressing requirement to improve drastically the bioinformatics support to the DNA Barcode Initiative. The large scale investigation of Ascomycota mitochondrial introns performed through this tool, allowing to exclude the introns-rich sequences from the barcode candidates exploration, could be the first step towards a mitochondrial barcoding strategy for these organisms, similar to the standard approach employed in metazoans.},
}
@article {pmid19534739,
year = {2009},
author = {Singer, GA and Hajibabaei, M},
title = {iBarcode.org: web-based molecular biodiversity analysis.},
journal = {BMC bioinformatics},
volume = {10 Suppl 6},
number = {Suppl 6},
pages = {S14},
pmid = {19534739},
issn = {1471-2105},
mesh = {Base Sequence ; *Biodiversity ; Computational Biology/*methods ; DNA/*chemistry ; Databases, Genetic ; Evolution, Molecular ; Haplotypes ; Internet ; Sequence Analysis, DNA/*methods ; *Software ; },
abstract = {BACKGROUND: DNA sequences have become a primary source of information in biodiversity analysis. For example, short standardized species-specific genomic regions, DNA barcodes, are being used as a global standard for species identification and biodiversity studies. Most DNA barcodes are being generated by laboratories that have an expertise in DNA sequencing but not in bioinformatics data analysis. Therefore, we have developed a web-based suite of tools to help the DNA barcode researchers analyze their vast datasets.<br><br>RESULTS: Our web-based tools, available at http://www.ibarcode.org, allow the user to manage their barcode datasets, cull out non-unique sequences, identify haplotypes within a species, and examine the within- to between-species divergences. In addition, we provide a number of phylogenetics tools that will allow the user to manipulate phylogenetic trees generated by other popular programs.<br><br>CONCLUSION: The use of a web-based portal for barcode analysis is convenient, especially since the WWW is inherently platform-neutral. Indeed, we have even taken care to ensure that our website is usable from handheld devices such as PDAs and smartphones. Although the current set of tools available at iBarcode.org were developed to meet our own analytic needs, we hope that feedback from users will spark the development of future tools. We also welcome user-built modules that can be incorporated into the iBarcode framework.},
}
@article {pmid19548831,
year = {2009},
author = {Brimacombe, KR and Hall, MD and Auld, DS and Inglese, J and Austin, CP and Gottesman, MM and Fung, KL},
title = {A dual-fluorescence high-throughput cell line system for probing multidrug resistance.},
journal = {Assay and drug development technologies},
volume = {7},
number = {3},
pages = {233-249},
pmid = {19548831},
issn = {1557-8127},
support = {Z01 BC005598-18/ImNIH/Intramural NIH HHS/United States ; Z01 HG200319-04/ImNIH/Intramural NIH HHS/United States ; },
mesh = {ATP Binding Cassette Transporter, Subfamily B, Member 1/*genetics ; Antineoplastic Agents/metabolism ; Blotting, Western ; Cell Line, Tumor ; Cell Proliferation ; Coloring Agents ; Drug Evaluation, Preclinical ; Drug Resistance, Multiple/*genetics ; Drug Resistance, Neoplasm/*genetics ; Female ; Fluorescence ; Genotype ; Humans ; Laser Scanning Cytometry ; Microscopy, Confocal ; Mitoxantrone/metabolism ; Ovarian Neoplasms/drug therapy/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Tetrazolium Salts ; Thiazoles ; Transfection ; },
abstract = {The efflux pump P-glycoprotein (ATP-binding cassette B1, multidrug resistance [MDR] 1, P-gp) has long been known to contribute to MDR against cancer chemotherapeutics. We describe the development of a dual-fluorescent cell line system to allow multiplexing of drug-sensitive and P-gp-mediated MDR cell lines. The parental OVCAR-8 human ovarian carcinoma cell line and the isogenic MDR NCI/ADR-RES subline, which stably expresses high levels of endogenous P-gp, were transfected to express the fluorescent proteins Discosoma sp. red fluorescent protein DsRed2 and enhanced green fluorescent protein, respectively. Co-culture conditions were defined, and fluorescent barcoding of each cell line allowed for the direct, simultaneous comparison of resistance to cytotoxic compounds in sensitive and MDR cell lines. We show that this assay system retains the phenotypes of the original lines and is suitable for multiplexing using confocal microscopy, flow cytometry, or laser scanning microplate cytometry in 1,536-well plates, enabling the high-throughput screening of large chemical libraries.},
}
@article {pmid19521822,
year = {2009},
author = {Pierce, SE and Davis, RW and Nislow, C and Giaever, G},
title = {Chemogenomic approaches to elucidation of gene function and genetic pathways.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {548},
number = {},
pages = {115-143},
doi = {10.1007/978-1-59745-540-4_7},
pmid = {19521822},
issn = {1064-3745},
mesh = {Base Sequence ; DNA, Fungal/genetics ; Gene Deletion ; Gene Regulatory Networks ; Genome, Fungal ; Genomics/*methods/statistics &amp; numerical data ; Oligonucleotide Array Sequence Analysis/methods/statistics &amp; numerical data ; Open Reading Frames ; Saccharomyces cerevisiae/*drug effects/*genetics/growth &amp; development ; },
abstract = {The approximately 6,000 strains in the yeast deletion collection can be studied in a single culture by using a microarray to detect the 20 bp DNA "barcodes" or "tags" contained in each strain. Barcode intensities measured by microarray are compared across time-points or across conditions to analyze the relative fitness of each strain. The development of this pooled fitness assay has greatly facilitated the functional annotation of the yeast genome by making genome-wide gene-deletion studies faster and easier, and has led to the development of high throughput methods for studying drug action in yeast. Pooled screens can be used for identifying gene functions, measuring the functional relatedness of gene pairs to group genes into pathways, identifying drug targets, and determining a drug's mechanism of action. This process involves five main steps: preparing aliquots of pooled cells, pooled growth, isolation of genomic DNA and PCR amplification of the barcodes, array hybridization, and data analysis. In addition to yeast fitness applications, the general method of studying pooled samples with barcode arrays can also be adapted for use with other types of samples, such as mutant collections in other organisms, siRNA vectors, and molecular inversion probes.},
}
@article {pmid19521379,
year = {2009},
author = {Agüloğlu, S and Zortuk, M and Beydemir, K},
title = {Denture barcoding: a new horizon.},
journal = {British dental journal},
volume = {206},
number = {11},
pages = {589-590},
doi = {10.1038/sj.bdj.2009.477},
pmid = {19521379},
issn = {1476-5373},
mesh = {Ceramics ; Crowns ; Denture Identification Marking/*methods ; Denture, Complete ; Denture, Partial, Fixed ; Denture, Partial, Removable ; Disasters ; Electronic Data Processing ; Forensic Dentistry ; Humans ; Patient Identification Systems/methods ; },
abstract = {Labelled dentures can be important in identifying people who have lost their memory or in identifying the bodies of those who have died in disasters. Forensic dentistry has long considered marking dentures, although no standardised method has been developed. Of the many options considered, none maintain the marking after the dentures break or are altered in occurrences such as plane crashes, which can result in a marked increase in temperature. This study examined a ceramic marking system that can endure high temperatures and can also be used in fixed partial dentures.},
}
@article {pmid19519770,
year = {2009},
author = {Zampieri, E and Mello, A and Bonfante, P and Murat, C},
title = {PCR primers specific for the genus Tuber reveal the presence of several truffle species in a truffle-ground.},
journal = {FEMS microbiology letters},
volume = {297},
number = {1},
pages = {67-72},
doi = {10.1111/j.1574-6968.2009.01655.x},
pmid = {19519770},
issn = {1574-6968},
mesh = {Ascomycota/classification/genetics/*isolation &amp; purification ; DNA Primers/*genetics ; Fungal Proteins/*genetics ; Molecular Sequence Data ; Mycological Typing Techniques/*methods ; Phylogeny ; Polymerase Chain Reaction/methods ; *Soil Microbiology ; Species Specificity ; Tubulin/*genetics ; },
abstract = {Truffles are hypogeous Ascomycete fungi belonging to the genus Tuber and forming fruiting bodies highly prized for their taste and aroma. The identification of the genus Tuber and its species is important to investigate their ecology and avoid fraud in the food market. As genus-specific primers are not available, the aims of this work were (1) to assess the usefulness of the beta-tubulin gene as a DNA barcoding region for designing Tuber genus-specific primers, (2) to test the primers on a range of fruiting bodies, representing a large part of truffle biodiversity and (3) to check their ecological usefulness, applying them to truffle-ground soil. The new primers designed on the beta-tubulin gene were specific to the Tuber genus in nested PCR. When applied to DNA from soils, they gave a positive signal for 23 of 32 soils. Phylogenetic analysis confirmed that the bands corresponded to Tuber and that at least five Tuber species were present in the truffle-ground. beta-tubulin was found to be a good barcoding region for designing Tuber genus-specific primers, detecting a high Tuber diversity in a natural environment. These primers will be useful for understanding truffle ecology and for practical needs in plantation management.},
}
@article {pmid19505556,
year = {2009},
author = {Song, J and Yao, H and Li, Y and Li, X and Lin, Y and Liu, C and Han, J and Xie, C and Chen, S},
title = {Authentication of the family Polygonaceae in Chinese pharmacopoeia by DNA barcoding technique.},
journal = {Journal of ethnopharmacology},
volume = {124},
number = {3},
pages = {434-439},
doi = {10.1016/j.jep.2009.05.042},
pmid = {19505556},
issn = {1872-7573},
mesh = {China ; DNA Primers ; DNA, Plant/chemistry/*classification ; Drug Contamination ; *Electronic Data Processing ; *Medicine, Chinese Traditional ; Pharmacopoeias as Topic ; Polygonaceae/chemistry/*classification/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Species Specificity ; },
abstract = {Medicinal plants belonging to the family Polygonaceae in Chinese pharmacopoeia possess important medicinal efficacy in traditional Chinese medicines.<br><br>AIM OF THE STUDY: DNA barcodes are first used to discriminate the Polygonaceae in Chinese pharmacopoeia and their adulterants.<br><br>MATERIALS AND METHODS: DNA samples, extracted from thirty-eight specimens belonging to eighteen species in Polygonaceae, were used as templates. Eight candidate barcodes were amplified by polymerase chain reaction. Sequence analysis was accomplished by CodonCode Aligner V 2.06 and DNAman V 6. Species identification was performed using MEGA V 4.0.<br><br>RESULTS: The amplification efficiency of six candidate DNA barcodes (rbcL, trnH-psbA, ndhJ, rpoB, rpoC1, accD) was 100%, while the efficiency of YCF5 and nrITS was 56% and 44%, respectively. The interspecific divergence was highest for the trnH-psbA (20.05%), followed by the nrITS (14.01%) across all species pairs, while intraspecific variation both within populations and between populations was absent (0.0%). The trnH-psbA can not only distinguish ten species of Polygonaceae in Chinese pharmacopoeia, but also recognize eight other species of Polygonaceae including their adulterants.<br><br>CONCLUSION: Our findings show that DNA barcoding is an efficient tool for identification of Polygonaceae in Chinese pharmacopoeia and their adulterants.},
}
@article {pmid19504263,
year = {2009},
author = {Ferri, G and Alù, M and Corradini, B and Beduschi, G},
title = {Forensic botany: species identification of botanical trace evidence using a multigene barcoding approach.},
journal = {International journal of legal medicine},
volume = {123},
number = {5},
pages = {395-401},
pmid = {19504263},
issn = {1437-1596},
mesh = {Algorithms ; Botany ; DNA Primers ; DNA, Plant/*classification ; Databases, Genetic ; Forensic Medicine ; Genes, Plant ; Genetic Markers ; Humans ; Plastids/*genetics ; Polymerase Chain Reaction ; Quercus/*genetics ; Sequence Analysis, DNA ; *Species Specificity ; },
abstract = {Forensic botany can provide significant supporting evidence during criminal investigations. However, it is still an underutilized field of investigation with its most common application limited to identifying specific as well as suspected illegal plants. The ubiquitous presence of plant species can be useful in forensics, but the absence of an accurate identification system remains the major obstacle to the present inability to routinely and correctly identify trace botanical evidence. Many plant materials cannot be identified and differentiated to the species level by traditional morphological characteristics when botanical specimens are degraded and lack physical features. By taking advantage of a universal barcode system, DNA sequencing, and other biomolecular techniques used routinely in forensic investigations, two chloroplast DNA regions were evaluated for their use as "barcoding" markers for plant identification in the field of forensics. We therefore investigated the forensic use of two non-coding plastid regions, psbA-trnH and trnL-trnF, to create a multimarker system for species identification that could be useful throughout the plant kingdom. The sequences from 63 plants belonging to our local flora were submitted and registered on the GenBank database. Sequence comparison to set up the level of identification (species, genus, or family) through Blast algorithms allowed us to assess the suitability of this method. The results confirmed the effectiveness of our botanic universal multimarker assay in forensic investigations.},
}
@article {pmid19494183,
year = {2009},
author = {Varley, KE and Mutch, DG and Edmonston, TB and Goodfellow, PJ and Mitra, RD},
title = {Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing.},
journal = {Nucleic acids research},
volume = {37},
number = {14},
pages = {4603-4612},
pmid = {19494183},
issn = {1362-4962},
support = {1R01DA025744/DA/NIDA NIH HHS/United States ; 1R01DA025744-01/DA/NIDA NIH HHS/United States ; 5P50HG003170-03/HG/NHGRI NIH HHS/United States ; T32 HG000045/HG/NHGRI NIH HHS/United States ; },
mesh = {Adaptor Proteins, Signal Transducing/*genetics/metabolism ; Alleles ; *DNA Methylation ; Endometrial Neoplasms/*genetics/metabolism ; Endometrium/metabolism ; *Epigenesis, Genetic ; Female ; Genetic Variation ; Humans ; MutL Protein Homolog 1 ; Nuclear Proteins/*genetics/metabolism ; Polymerase Chain Reaction ; *Promoter Regions, Genetic ; Sequence Analysis, DNA/*methods ; Sulfites/chemistry ; },
abstract = {A single tumor may contain cells with different somatic mutations. By characterizing this genetic heterogeneity within tumors, advances have been made in the prognosis, treatment and understanding of tumorigenesis. In contrast, the extent of epigenetic intra-tumor heterogeneity and how it influences tumor biology is under-explored. We have characterized epigenetic heterogeneity within individual tumors using next-generation sequencing. We used deep single molecule bisulfite sequencing and sample-specific DNA barcodes to determine the spectrum of MLH1 promoter methylation across an average of 1000 molecules in each of 33 individual samples in parallel, including endometrial cancer, matched blood and normal endometrium. This first glimpse, deep into each tumor, revealed unexpectedly heterogeneous patterns of methylation at the MLH1 promoter within a subset of endometrial tumors. This high-resolution analysis allowed us to measure the clonality of methylation in individual tumors and gain insight into the accumulation of aberrant promoter methylation on both alleles during tumorigenesis.},
}
@article {pmid19489134,
year = {2008},
author = {Kartavtsev, YP and Sharina, SN and Goto, T and Chichvarkhin, AY and Balanov, AA and Vinnikov, KA and Ivankov, VN and Hanzawa, N},
title = {Cytochrome oxidase 1 gene sequence analysis in six flatfish species (Teleostei, Pleuronectidae) of Far East Russia with inferences in phylogeny and taxonomy.},
journal = {Mitochondrial DNA},
volume = {19},
number = {6},
pages = {479-489},
doi = {10.1080/19401730802570934},
pmid = {19489134},
issn = {1940-1736},
mesh = {Animals ; Base Composition ; Base Sequence ; Bayes Theorem ; DNA Primers/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Fish Proteins/*genetics ; Flatfishes/classification/*genetics/metabolism ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Russia ; Species Specificity ; },
abstract = {Mitochondrial DNA at the cytochrome oxidase 1 (Co-1) gene region was sequenced for six flatfish species (in total, 11 sequences of at least 539 base pairs) from the Far East of Russia and compared with other sequences of Pleuronectiformes, comprising altogether 26 flatfish sequences and two outgroup sequences (Perciformes). An analysis of the protein-coding Co-1 gene revealed a statistically substantiated bias in (T + C):(A + G) content, supporting earlier findings. Average scores of the p-distances for different scales of the evolutionary history at the Co-1 gene revealed a clear pattern of increased nucleotide diversity at four different levels: (1) intraspecies, (2) intragenus, (3) intrafamily, and (4) intra-order. Scores of average p-distances of the four categories of comparison in flatfishes were (1) 0.17 +/- 0.09%, (2) 10.60 +/- 1.57%, (3) 12.40 +/- 0.27%, and (4) 19.93 +/- 0.05%, respectively (mean +/- standard error). These data jointly with current knowledge support the concept that speciation in the order Pleuronectiformes mostly follows a geographic mode through accumulation of numerous small genetic changes over a long period of time. A phylogenetic tree for 26 sequences of flatfishes and two other fishes belonging to ray-finned fishes (Actinopterigii) was developed using the Co-1 gene and four different analytical approaches: neighbour-joining, Bayesian (BA), maximum parsimony (MP), and maximum likelihood. The analysis revealed a monophyletic origin for the representatives of Pleuronectidae, which is the principal flatfish family investigated (73-100% support level in our MP and BA analyses). According to the current and literary data, the monophyletic origin for the six compared flatfish families was well supported. Species identification on a per-individual basis (barcoding tagging) was high.},
}
@article {pmid19488872,
year = {2009},
author = {Ji, H and Welch, K},
title = {Molecular inversion probe assay for allelic quantitation.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {556},
number = {},
pages = {67-87},
pmid = {19488872},
issn = {1064-3745},
support = {P01 HG000205/HG/NHGRI NIH HHS/United States ; 2P01HG000205/HG/NHGRI NIH HHS/United States ; R21 CA109190/CA/NCI NIH HHS/United States ; K08 CA96879/CA/NCI NIH HHS/United States ; P01 HG000205-21/HG/NHGRI NIH HHS/United States ; K08 CA096879/CA/NCI NIH HHS/United States ; },
mesh = {*Alleles ; *Gene Dosage ; Genotype ; Humans ; Microarray Analysis/instrumentation/*methods ; Molecular Probes/*genetics ; },
abstract = {Molecular inversion probe (MIP) technology has been demonstrated to be a robust platform for large-scale dual genotyping and copy number analysis. Applications in human genomic and genetic studies include the possibility of running dual germline genotyping and combined copy number variation ascertainment. MIPs analyze large numbers of specific genetic target sequences in parallel, relying on interrogation of a barcode tag, rather than direct hybridization of genomic DNA to an array. The MIP approach does not replace, but is complementary to many of the copy number technologies being performed today. Some specific advantages of MIP technology include: less DNA required (37 ng vs. 250 ng), DNA quality less important, more dynamic range (amplifications detected up to copy number 60), allele-specific information "cleaner" (less SNP cross-talk/contamination), and quality of markers better (fewer individual MIPs versus SNPs needed to identify copy number changes). MIPs can be considered a candidate gene (targeted whole genome) approach and can find specific areas of interest that otherwise may be missed with other methods.},
}
@article {pmid19488691,
year = {2009},
author = {Jo, K and Schramm, TM and Schwartz, DC},
title = {A single-molecule barcoding system using nanoslits for DNA analysis : nanocoding.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {544},
number = {},
pages = {29-42},
doi = {10.1007/978-1-59745-483-4_3},
pmid = {19488691},
issn = {1064-3745},
support = {5R01HG000225/HG/NHGRI NIH HHS/United States ; },
mesh = {Bacteriophage T4/chemistry/genetics ; Bacteriophage lambda/chemistry/genetics ; Benzoxazoles ; DNA/*analysis/chemistry/genetics ; DNA, Viral/analysis/chemistry/genetics ; Equipment Design ; Fluorescent Dyes ; Genomics/instrumentation/methods ; Glass ; Microscopy, Fluorescence ; *Nanostructures ; Nanotechnology/instrumentation/*methods ; Quinolinium Compounds ; Silicone Elastomers ; },
abstract = {Single DNA molecule approaches are playing an increasingly central role in the analytical genomic sciences because single molecule techniques intrinsically provide individualized measurements of selected molecules, free from the constraints of bulk techniques, which blindly average noise and mask the presence of minor analyte components. Accordingly, a principal challenge that must be addressed by all single molecule approaches aimed at genome analysis is how to immobilize and manipulate DNA molecules for measurements that foster construction of large, biologically relevant data sets. For meeting this challenge, this chapter discusses an integrated approach for microfabricated and nanofabricated devices for the manipulation of elongated DNA molecules within nanoscale geometries. Ideally, large DNA coils stretch via nanoconfinement when channel dimensions are within tens of nanometers. Importantly, stretched, often immobilized, DNA molecules spanning hundreds of kilobase pairs are required by all analytical platforms working with large genomic substrates because imaging techniques acquire sequence information from molecules that normally exist in free solution as unrevealing random coils resembling floppy balls of yarn. However, nanoscale devices fabricated with sufficiently small dimensions fostering molecular stretching make these devices impractical because of the requirement of exotic fabrication technologies, costly materials, and poor operational efficiencies. In this chapter, such problems are addressed by discussion of a new approach to DNA presentation and analysis that establishes scaleable nanoconfinement conditions through reduction of ionic strength; stiffening DNA molecules thus enabling their arraying for analysis using easily fabricated devices that can also be mass produced. This new approach to DNA nanoconfinement is complemented by the development of a novel labeling scheme for reliable marking of individual molecules with fluorochrome labels, creating molecular barcodes, which are efficiently read using fluorescence resonance energy transfer techniques for minimizing noise from unincorporated labels. As such, our integrative approach for the realization of genomic analysis through nanoconfinement, named nanocoding, was demonstrated through the barcoding and mapping of bacterial artificial chromosomal molecules, thereby providing the basis for a high-throughput platform competent for whole genome investigations.},
}
@article {pmid19487770,
year = {2009},
author = {Quintero, C and Kariv, I},
title = {Design and implementation of an automated compound management system in support of lead optimization.},
journal = {Journal of biomolecular screening},
volume = {14},
number = {5},
pages = {499-508},
doi = {10.1177/1087057109335326},
pmid = {19487770},
issn = {1087-0571},
mesh = {*Automation ; Computational Biology/methods ; *Drug Discovery/instrumentation/methods ; Software ; Systems Integration ; User-Computer Interface ; },
abstract = {To meet the needs of the increasingly rapid and parallelized lead optimization process, a fully integrated local compound storage and liquid handling system was designed and implemented to automate the generation of assay-ready plates directly from newly submitted and cherry-picked compounds. A key feature of the system is the ability to create project- or assay-specific compound-handling methods, which provide flexibility for any combination of plate types, layouts, and plate bar-codes. Project-specific workflows can be created by linking methods for processing new and cherry-picked compounds and control additions to produce a complete compound set for both biological testing and local storage in one uninterrupted workflow. A flexible cherry-pick approach allows for multiple, user-defined strategies to select the most appropriate replicate of a compound for retesting. Examples of custom selection parameters include available volume, compound batch, and number of freeze/thaw cycles. This adaptable and integrated combination of software and hardware provides a basis for reducing cycle time, fully automating compound processing, and ultimately increasing the rate at which accurate, biologically relevant results can be produced for compounds of interest in the lead optimization process.},
}
@article {pmid19467237,
year = {2009},
author = {Chen, L and Wei, H and Guo, Y and Cui, Z and Zhang, Z and Zhang, XE},
title = {Gold nanoparticle enhanced immuno-PCR for ultrasensitive detection of Hantaan virus nucleocapsid protein.},
journal = {Journal of immunological methods},
volume = {346},
number = {1-2},
pages = {64-70},
doi = {10.1016/j.jim.2009.05.007},
pmid = {19467237},
issn = {1872-7905},
mesh = {Antigens, Viral/*blood ; Capsid Proteins/*blood ; *Enzyme-Linked Immunosorbent Assay ; *Gold ; Hantaan virus/*metabolism ; Hantavirus Infections/*diagnosis/virology ; Humans ; *Metal Nanoparticles ; *Molecular Probe Techniques ; *Polymerase Chain Reaction ; Predictive Value of Tests ; Sensitivity and Specificity ; Viral Core Proteins/*blood ; },
abstract = {A functionalized gold nanoparticle (GNP) enhanced ultrasensitive immuno-PCR assay (GNP-IPCR on ELISA plate), which was modified from the recent developed bio-barcode assay (BCA) technique, was developed to detect Hantaan virus nucleocapsid protein (HNP). During the assay, the target antigen HNP was captured by a polyclonal antibody coated on ELISA microplate wells, followed by adding GNP dually modified with oligonucleotides and a HNP specific monoclonal antibody L13 (mAb L13) to form a sandwich immuno-complex. The oligonucleotides on the GNP contained two strands: one as capture DNA immobilized on the surface of the GNP through Au-S bond and the other as signal amplification DNA, which was partially complementary with the capture DNA. After the immuno-complex was formed, the signal DNA was released by heating, and consequently characterized by PCR/gel electrophoresis and SYBR-Green real time PCR. The detection limit of this method could reach down to 10 fg/mL for detecting purified HNP in buffers as well as in human serum, which was approximately 7 orders of magnitude more sensitive than that of conventional ELISA. The current assay format might be adopted for other proteins that need ultra-high sensitive detection.},
}
@article {pmid19462512,
year = {2008},
author = {Xia, J and Xia, K and Jiang, S},
title = {Complete mitochondrial DNA sequence of the yellowfin seabream Acanthopagrus latus and a genomic comparison among closely related sparid species.},
journal = {Mitochondrial DNA},
volume = {19},
number = {4},
pages = {385-393},
pmid = {19462512},
issn = {1940-1736},
mesh = {Animals ; Base Composition ; Base Sequence ; Conserved Sequence ; Cytochromes b/genetics ; DNA Primers/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Fish Proteins/genetics ; Genes, Mitochondrial ; Genome, Mitochondrial ; Perciformes/classification/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; RNA, Untranslated/genetics ; Sea Bream/*genetics ; Species Specificity ; },
abstract = {The complete mitochondrial genome of the yellowfin seabream Acanthopagrus latus was determined in the present study. The genome was 16,609 bp in length and contained 37 genes (2 ribosomal RNA, 22 transfer RNA and 13 protein-coding genes) and the control region (CR), with the content and order of genes being similar to those in typical teleosts. Comparisons of the 37 genes and CR among species indicate the CR was the highest divergent (0.3341), but tRNA(Gly) possesses the lowest genetic variation (0.0542). Much greater p-genetic distances [mean = 0.1559, standard deviation (SD) = 0.0235; n = 1653] for the interspecies level with high frequency (99.4%) than those of the intraspecies level (mean = 0.0098, SD = 0.0090; n = 20) were inferred from 212 Cyt b sequence data, suggesting the Cyt b gene is conserved within Sparidae species and supporting the barcoding validity of Cyt b sequence data for Sparidae species identification. Phylogenetic analysis using amino acid sequences of 13 protein-coding genes supported that the genus Pagrus was not monophyletic, showing the need to re-evaluate the morphological characteristics of Pagrus fishes.},
}
@article {pmid19449657,
year = {2009},
author = {Shatters, RG and Powell, CA and Boykin, LM and Liansheng, H and McKenzie, CL},
title = {Improved DNA barcoding method for Bemisia tabaci and related Aleyrodidae: development of universal and Bemisia tabaci biotype-specific mitochondrial cytochrome c oxidase I polymerase chain reaction primers.},
journal = {Journal of economic entomology},
volume = {102},
number = {2},
pages = {750-758},
doi = {10.1603/029.102.0236},
pmid = {19449657},
issn = {0022-0493},
mesh = {Animals ; Base Sequence ; DNA/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Markers ; Hemiptera/*classification/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Polymerase Chain Reaction ; },
abstract = {Whiteflies, heteropterans in the family Aleyrodidae, are globally distributed and severe agricultural pests. The mitochondrial cytochrome c oxidase I (mtCOI) sequence has been used extensively in whitefly phylogenetic comparisons and in biotype identification of the agriculturally important Bemisia tabaci (Gennadius) whitefly. Because of the economic importance of several whitefly genera, and the invasive nature of the B and the Q biotypes of Bemisia tabaci, mtCOI sequence data are continually generated from sampled populations worldwide. Routine phylogenetic comparisons and biotype identification is done through amplification and sequencing of an approximately 800-bp mtCOI DNA fragment. Despite its routine use, published primers for amplification of this region are often inefficient for some B. tabaci biotypes and especially across whitefly species. Through new sequence generation and comparison to available whitefly mtCOI sequence data, a set of polymerase chain reaction (PCR) amplification primers (Btab-Uni primers) were identified that are more efficient at amplifying approximately 748 bp of the approximately 800-bp fragment currently used. These universal primers amplify an mtCOI fragment from numerous B. tabaci biotypes and whitefly genera by using a single amplification profile. Furthermore, mtCOI PCR primers specific for the B, Q, and New World biotypes of B. tabaci were designed that allow rapid discrimination among these biotypes. These primers produce a 478-, 405-, and 303-bp mtCOI fragment for the B, New World, and Q biotypes, respectively. By combining these primers and using rapid PCR and electrophoretic techniques, biotype determination can be made within 3 h for up to 96 samples at a time.},
}
@article {pmid19447965,
year = {2009},
author = {Erlich, Y and Chang, K and Gordon, A and Ronen, R and Navon, O and Rooks, M and Hannon, GJ},
title = {DNA Sudoku--harnessing high-throughput sequencing for multiplexed specimen analysis.},
journal = {Genome research},
volume = {19},
number = {7},
pages = {1243-1253},
pmid = {19447965},
issn = {1088-9051},
mesh = {Arabidopsis/*genetics ; Computer Simulation ; Cystic Fibrosis/genetics ; Cystic Fibrosis Transmembrane Conductance Regulator/*genetics ; DNA, Complementary/*genetics ; Escherichia coli/*genetics ; Expressed Sequence Tags ; Gene Expression Profiling ; *Gene Library ; Humans ; Mutation/genetics ; Oligonucleotide Array Sequence Analysis ; Polymerase Chain Reaction ; RNA, Small Interfering/genetics ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
abstract = {Next-generation sequencers have sufficient power to analyze simultaneously DNAs from many different specimens, a practice known as multiplexing. Such schemes rely on the ability to associate each sequence read with the specimen from which it was derived. The current practice of appending molecular barcodes prior to pooling is practical for parallel analysis of up to many dozen samples. Here, we report a strategy that permits simultaneous analysis of tens of thousands of specimens. Our approach relies on the use of combinatorial pooling strategies in which pools rather than individual specimens are assigned barcodes. Thus, the identity of each specimen is encoded within the pooling pattern rather than by its association with a particular sequence tag. Decoding the pattern allows the sequence of an original specimen to be inferred with high confidence. We verified the ability of our encoding and decoding strategies to accurately report the sequence of individual samples within a large number of mixed specimens in two ways. First, we simulated data both from a clone library and from a human population in which a sequence variant associated with cystic fibrosis was present. Second, we actually pooled, sequenced, and decoded identities within two sets of 40,000 bacterial clones comprising approximately 20,000 different artificial microRNAs targeting Arabidopsis or human genes. We achieved greater than 97% accuracy in these trials. The strategies reported here can be applied to a wide variety of biological problems, including the determination of genotypic variation within large populations of individuals.},
}
@article {pmid19441258,
year = {2009},
author = {Gross, L},
title = {Implementing barcoding technology to promote newborn identification safety.},
journal = {The Pennsylvania nurse},
volume = {64},
number = {1},
pages = {23, 28},
pmid = {19441258},
issn = {0031-4617},
mesh = {Delivery Rooms ; *Electronic Data Processing ; Health Plan Implementation ; Humans ; Infant, Newborn ; Intensive Care Units, Neonatal ; Nurseries, Hospital ; *Patient Identification Systems ; Pennsylvania ; },
}
@article {pmid19435864,
year = {2009},
author = {Kuan, G and Gordon, A and Avilés, W and Ortega, O and Hammond, SN and Elizondo, D and Nuñez, A and Coloma, J and Balmaseda, A and Harris, E},
title = {The Nicaraguan pediatric dengue cohort study: study design, methods, use of information technology, and extension to other infectious diseases.},
journal = {American journal of epidemiology},
volume = {170},
number = {1},
pages = {120-129},
pmid = {19435864},
issn = {1476-6256},
mesh = {Child ; Child, Preschool ; Dengue/*epidemiology/transmission ; Female ; Follow-Up Studies ; Geographic Information Systems/*organization &amp; administration ; Health Services Research/*methods ; Humans ; Incidence ; Information Management/*methods ; Information Systems/*statistics &amp; numerical data ; Male ; Nicaragua/epidemiology ; Reproducibility of Results ; Retrospective Studies ; Technology Assessment, Biomedical/*methods ; Time Factors ; },
abstract = {Dengue is a mosquito-borne viral disease that is a major public health problem worldwide. In 2004, the Pediatric Dengue Cohort Study was established in Managua, Nicaragua, to study the natural history and transmission of dengue in children. Here, the authors describe the study design, methods, and results from 2004 to 2008. Initially, 3,721 children 2-9 years of age were recruited through door-to-door visits. Each year, new children aged 2 years are enrolled in the study to maintain the age structure. Children are provided with medical care through the study, and data from each medical visit are recorded on systematic study forms. All participants presenting with suspected dengue or undifferentiated fever are tested for dengue by virologic, serologic, and molecular biologic assays. Yearly blood samples are collected to detect inapparent dengue virus infections. Numerous information and communications technologies are used to manage study data, track samples, and maintain quality control, including personal data assistants, barcodes, global information systems, and fingerprint scans. Close collaboration with the Nicaraguan Ministry of Health and use of almost entirely local staff are essential components for success. This study is providing critical data on the epidemiology and transmission of dengue in the Americas needed for future vaccine trials.},
}
@article {pmid19435604,
year = {2009},
author = {Lázaro, EM and Sluys, R and Pala, M and Stocchino, GA and Baguñà, J and Riutort, M},
title = {Molecular barcoding and phylogeography of sexual and asexual freshwater planarians of the genus Dugesia in the Western Mediterranean (Platyhelminthes, Tricladida, Dugesiidae).},
journal = {Molecular phylogenetics and evolution},
volume = {52},
number = {3},
pages = {835-845},
doi = {10.1016/j.ympev.2009.04.022},
pmid = {19435604},
issn = {1095-9513},
mesh = {Animals ; Base Sequence ; DNA, Helminth/genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Geography ; Mediterranean Sea ; Molecular Sequence Data ; *Phylogeny ; Planarians/classification/*genetics ; Reproduction, Asexual/genetics ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; },
abstract = {Planarians of the genus Dugesia have a worldwide distribution with high species diversity in the Mediterranean area. In this area, populations with a triploid karyotype that reproduce by fissiparity are exceptionally frequent, outnumbering the sexual populations. This situation poses interesting questions, such as the age of these asexual lineages, whether they all belong to the same species or whether the triploidization event is recurrent, and what factors (climatic, geographical, historical...) explain the prevalence of these asexual forms. However, asexual populations cannot be assigned to a species due to the lack of copulatory apparatus--the main structure used in species identification. In this study, we have developed a DNA barcoding method, based on COI and ITS-1 sequences, which allows the assignment of the fissiparous forms to sexual species. At the same time, phylogenetic analysis from species of the western Mediterranean have unveiled the presence of species with highly differentiated populations alongside species with a wide distribution and almost no genetic variation. The roles of habitat instability, dispersal capacity and human activities are briefly discussed.},
}
@article {pmid19423985,
year = {2009},
author = {Elganzouri, ES and Standish, CA and Androwich, I},
title = {Medication Administration Time Study (MATS): nursing staff performance of medication administration.},
journal = {The Journal of nursing administration},
volume = {39},
number = {5},
pages = {204-210},
doi = {10.1097/NNA.0b013e3181a23d6d},
pmid = {19423985},
issn = {1539-0721},
mesh = {Academic Medical Centers ; Documentation ; Drug Therapy/*nursing ; Efficiency, Organizational ; Employee Performance Appraisal ; Hospitals, Community ; Hospitals, Rural ; Hospitals, Urban ; Humans ; Medical Order Entry Systems/organization &amp; administration ; Medical Records Systems, Computerized/organization &amp; administration ; Medication Errors/nursing/prevention &amp; control/statistics &amp; numerical data ; Medication Systems, Hospital/*organization &amp; administration ; *Nurse's Role ; Nursing Administration Research ; Nursing Staff, Hospital/*organization &amp; administration ; Safety Management ; Systems Analysis ; Time and Motion Studies ; Workload ; },
abstract = {OBJECTIVE: The aim of this study was to develop and test a method for assessing nursing effort and workflow in the medication administration process.<br><br>BACKGROUND: Thousands of patients die each year from medication errors, and hospitals strive for error reduction. Bar-coding medication administration systems have been proposed as a solution; however, many hospitals lack the necessary pre-implementation workflow process data on medication administration processes to evaluate the effectiveness of their current systems.<br><br>METHOD: A descriptive observation study of 151 nurses during 980 unique medication observations in medical-surgical units at a rural hospital, an urban community hospital, and an academic medical center was conducted.<br><br>RESULTS: Nurses averaged more than 15 minutes on each medication pass and were at risk of an interruption or distraction with every medication pass.<br><br>CONCLUSION: System challenges faced by nurses during the medication administration process lead to threats to patient safety, work-arounds, workflow inefficiencies, and distractions during a time when focus is most needed to prevent error.},
}
@article {pmid19405876,
year = {2009},
author = {Ferri, G and Alù, M and Corradini, B and Licata, M and Beduschi, G},
title = {Species identification through DNA "barcodes".},
journal = {Genetic testing and molecular biomarkers},
volume = {13},
number = {3},
pages = {421-426},
doi = {10.1089/gtmb.2008.0144},
pmid = {19405876},
issn = {1945-0257},
mesh = {Animals ; Base Sequence ; Biomarkers ; DNA/*genetics/isolation &amp; purification ; DNA Primers/*genetics ; DNA, Mitochondrial/analysis/genetics ; Electron Transport Complex IV/genetics ; Forensic Genetics ; *Genes, Mitochondrial ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Conventional methods for forensic species identification are mainly based on immunological procedures, which have limited applications for old and degraded specimens. The mitochondrial cytochrome b gene sequence has emerged in forensics among molecular methods. Recent investigations in the taxonomic field have suggested that a DNA-based identification system may aid the resolution of animal diversity and classification using sequence analysis and phylogenetic links. Selected gene sequences can be viewed as a genetic "barcode," which is enclosed in every cell, and barcoding is a standardized approach for characterizing species using short DNA sequences as a diagnostic biomarker for organisms. The aim of this study was to evaluate the potential of barcode mitochondrial genes, such as the cytochrome c oxidase sub 1 (COI) and the 16S rRNA gene, as a forensic tool. We developed a new approach for species testing and identification with a singleplex PCR amplification that will be useful not only in criminal casework but also in biosecurity, food authentication, investigation against poaching or illegal trade of endangered species, and wildlife enforcement. Seven fragments ranging from 157 to 541 bp (base pairs) in humans were selected from COI and 16S rRNA genes by different redesigned sets of primers suitable for forensic purposes. The specificity of each primer pair was evaluated with a single PCR reaction on different substrates, and the diversity values were calculated by statistical tests to select a set of markers that could be useful in different caseworks. A case example of forensic species identification is also presented.},
}
@article {pmid19381348,
year = {2009},
author = {Jiang, Z and Rokhsar, DS and Harland, RM},
title = {Old can be new again: HAPPY whole genome sequencing, mapping and assembly.},
journal = {International journal of biological sciences},
volume = {5},
number = {4},
pages = {298-303},
pmid = {19381348},
issn = {1449-2288},
support = {R01 GM086321/GM/NIGMS NIH HHS/United States ; 1R01GM086321-01/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Chromosome Mapping/*methods ; Gene Amplification ; *Genome ; Humans ; Physical Chromosome Mapping/*methods ; Sequence Analysis, DNA/*methods ; },
abstract = {During the last three decades, both genome mapping and sequencing methods have advanced significantly to provide a foundation for scientists to understand genome structures and functions in many species. Generally speaking, genome mapping relies on genome sequencing to provide basic materials, such as DNA probes and markers for their localizations, thus constructing the maps. On the other hand, genome sequencing often requires a high-resolution map as a skeleton for whole genome assembly. However, both genome mapping and sequencing have never come together in one pipeline. After reviewing mapping and next-generation sequencing methods, we would like to share our thoughts with the genome community on how to combine the HAPPY mapping technique with the new-generation sequencing, thus integrating two systems into one pipeline, called HAPPY pipeline. The pipeline starts with preparation of a HAPPY panel, followed by multiple displacement amplification for producing a relatively large quantity of DNA. Instead of conventional marker genotyping, the amplified panel DNA samples are subject to new-generation sequencing with barcode method, which allows us to determine the presence/absence of a sequence contig as a traditional marker in the HAPPY panel. Statistical analysis will then be performed to infer how close or how far away from each other these contigs are within a genome and order the whole genome sequence assembly as well. We believe that such a universal approach will play an important role in genome sequencing, mapping, and assembly of many species; thus advancing genome science and its applications in biomedicine and agriculture.},
}
@article {pmid19372543,
year = {2009},
author = {Lorenzi, PL and Reinhold, WC and Varma, S and Hutchinson, AA and Pommier, Y and Chanock, SJ and Weinstein, JN},
title = {DNA fingerprinting of the NCI-60 cell line panel.},
journal = {Molecular cancer therapeutics},
volume = {8},
number = {4},
pages = {713-724},
pmid = {19372543},
issn = {1535-7163},
support = {N01CO12400/CA/NCI NIH HHS/United States ; Z01 BC007349-15/ImNIH/Intramural NIH HHS/United States ; N01-CO-12400/CO/NCI NIH HHS/United States ; },
mesh = {Cell Line, Tumor ; *DNA Fingerprinting ; DNA, Neoplasm/*analysis/genetics ; Humans ; Microsatellite Repeats ; National Cancer Institute (U.S.) ; Neoplasms/classification/*genetics ; Polymerase Chain Reaction ; United States ; },
abstract = {The National Cancer Institute's NCI-60 cell line panel, the most extensively characterized set of cells in existence and a public resource, is frequently used as a screening tool for drug discovery. Because many laboratories around the world rely on data from the NCI-60 cells, confirmation of their genetic identities represents an essential step in validating results from them. Given the consequences of cell line contamination or misidentification, quality control measures should routinely include DNA fingerprinting. We have, therefore, used standard DNA microsatellite short tandem repeats to profile the NCI-60, and the resulting DNA fingerprints are provided here as a reference. Consistent with previous reports, the fingerprints suggest that several NCI-60 lines have common origins: the melanoma lines MDA-MB-435, MDA-N, and M14; the central nervous system lines U251 and SNB-19; the ovarian lines OVCAR-8 and OVCAR-8/ADR (also called NCI/ADR); and the prostate lines DU-145, DU-145 (ATCC), and RC0.1. Those lines also show that the ability to connect two fingerprints to the same origin is not affected by stable transfection or by the development of multidrug resistance. As expected, DNA fingerprints were not able to distinguish different tissues-of-origin. The fingerprints serve principally as a barcodes.},
}
@article {pmid19368665,
year = {2009},
author = {Krüger, M and Stockinger, H and Krüger, C and Schüßler, A},
title = {DNA-based species level detection of Glomeromycota: one PCR primer set for all arbuscular mycorrhizal fungi.},
journal = {The New phytologist},
volume = {183},
number = {1},
pages = {212-223},
doi = {10.1111/j.1469-8137.2009.02835.x},
pmid = {19368665},
issn = {1469-8137},
mesh = {Base Sequence ; *DNA Primers ; DNA, Intergenic ; *DNA, Ribosomal ; *Genes, Fungal ; Glomeromycota/*genetics ; Mycorrhizae/*genetics ; Phylogeny ; Polymerase Chain Reaction/*methods ; Ribosome Subunits, Large, Eukaryotic ; Ribosome Subunits, Small, Eukaryotic ; Species Specificity ; },
abstract = {* At present, molecular ecological studies of arbuscular mycorrhizal fungi (AMF) are only possible above species level when targeting entire communities. To improve molecular species characterization and to allow species level community analyses in the field, a set of newly designed AMF specific PCR primers was successfully tested. * Nuclear rDNA fragments from diverse phylogenetic AMF lineages were sequenced and analysed to design four primer mixtures, each targeting one binding site in the small subunit (SSU) or large subunit (LSU) rDNA. To allow species resolution, they span a fragment covering the partial SSU, whole internal transcribed spacer (ITS) rDNA region and partial LSU. * The new primers are suitable for specifically amplifying AMF rDNA from material that may be contaminated by other organisms (e.g., samples from pot cultures or the field), characterizing the diversity of AMF species from field samples, and amplifying a SSU-ITS-LSU fragment that allows phylogenetic analyses with species level resolution. * The PCR primers can be used to monitor entire AMF field communities, based on a single rDNA marker region. Their application will improve the base for deep sequencing approaches; moreover, they can be efficiently used as DNA barcoding primers.},
}
@article {pmid19349972,
year = {2009},
author = {Ho, CH and Magtanong, L and Barker, SL and Gresham, D and Nishimura, S and Natarajan, P and Koh, JLY and Porter, J and Gray, CA and Andersen, RJ and Giaever, G and Nislow, C and Andrews, B and Botstein, D and Graham, TR and Yoshida, M and Boone, C},
title = {A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds.},
journal = {Nature biotechnology},
volume = {27},
number = {4},
pages = {369-377},
pmid = {19349972},
issn = {1546-1696},
support = {R01 GM046406/GM/NIGMS NIH HHS/United States ; R37 GM046406/GM/NIGMS NIH HHS/United States ; R01 GM107466/GM/NIGMS NIH HHS/United States ; GM62637/GM/NIGMS NIH HHS/United States ; P50 GM071508/GM/NIGMS NIH HHS/United States ; GM071508/GM/NIGMS NIH HHS/United States ; },
mesh = {Cloning, Molecular/*methods ; Gene Library ; Genetic Engineering/*methods/*trends ; Open Reading Frames/*genetics ; },
abstract = {We present a yeast chemical-genomics approach designed to identify genes that when mutated confer drug resistance, thereby providing insight about the modes of action of compounds. We developed a molecular barcoded yeast open reading frame (MoBY-ORF) library in which each gene, controlled by its native promoter and terminator, is cloned into a centromere-based vector along with two unique oligonucleotide barcodes. The MoBY-ORF resource has numerous genetic and chemical-genetic applications, but here we focus on cloning wild-type versions of mutant drug-resistance genes using a complementation strategy and on simultaneously assaying the fitness of all transformants with barcode microarrays. The complementation cloning was validated by mutation detection using whole-genome yeast tiling microarrays, which identified unique polymorphisms associated with a drug-resistant mutant. We used the MoBY-ORF library to identify the genetic basis of several drug-resistant mutants and in this analysis discovered a new class of sterol-binding compounds.},
}
@article {pmid19348954,
year = {2009},
author = {Efe, MA and Tavares, ES and Baker, AJ and Bonatto, SL},
title = {Multigene phylogeny and DNA barcoding indicate that the Sandwich tern complex (Thalasseus sandvicensis, Laridae, Sternini) comprises two species.},
journal = {Molecular phylogenetics and evolution},
volume = {52},
number = {1},
pages = {263-267},
doi = {10.1016/j.ympev.2009.03.030},
pmid = {19348954},
issn = {1095-9513},
mesh = {Animals ; Cell Nucleus/genetics ; Charadriiformes/classification/*genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; *Genetic Speciation ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; },
}
@article {pmid19345143,
year = {2009},
author = {Evans, KM and Chepurnov, VA and Sluiman, HJ and Thomas, SJ and Spears, BM and Mann, DG},
title = {Highly differentiated populations of the freshwater diatom Sellaphora capitata suggest limited dispersal and opportunities for allopatric speciation.},
journal = {Protist},
volume = {160},
number = {3},
pages = {386-396},
doi = {10.1016/j.protis.2009.02.001},
pmid = {19345143},
issn = {1618-0941},
mesh = {Australia ; Belgium ; Cluster Analysis ; DNA, Algal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Diatoms/*classification/cytology/*isolation &amp; purification ; Fresh Water/*microbiology ; Genes, rRNA ; Microsatellite Repeats ; Molecular Sequence Data ; Phylogeny ; RNA, Algal/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; United Kingdom ; },
abstract = {The diversities and distributions of diatoms are much more complex than was ever imagined. To understand the underlying mechanisms, research must focus on evolutionary processes occurring at a population level and employ sufficiently informative molecular markers. Using ten microsatellites and ITS rDNA sequence data, we investigated the genetic structure of populations of the benthic freshwater diatom Sellaphora capitata (until 2004 a cryptic entity within the S. pupula agg. species complex). This is the first time that microsatellites have been used to investigate the genetic structure of any freshwater or benthic microalga. Using an integrated approach (morphology, DNA barcoding and specificity of the microsatellite primers), we verified the identity of 70 S. capitata isolates obtained from lakes in the UK, Belgium and Australia. Standardized F'(ST) values were very high (>0.4) and in Bayesian analyses, isolates clustered according to their country of origin, with limited evidence of admixture. However, selected isolates from all countries were sexually compatible, a result consistent with limited ITS divergence. Considering the apparent absence of desiccation-resistant resting stages in most diatoms, we conclude that such levels of differentiation are likely to be a consequence of limited dispersal. With restricted dispersal, previously unacknowledged opportunities for allopatric speciation exist, which may help to explain the huge extant diversity of diatoms.},
}
@article {pmid19329066,
year = {2008},
author = {Wang, W and Luo, Q and Guo, H and Bossier, P and Van Stappen, G and Sorgeloos, P and Xin, N and Sun, Q and Hu, S and Yu, J},
title = {Phylogenetic analysis of brine shrimp (Artemia) in China using DNA barcoding.},
journal = {Genomics, proteomics &amp; bioinformatics},
volume = {6},
number = {3-4},
pages = {155-162},
pmid = {19329066},
issn = {1672-0229},
mesh = {Animals ; Artemia/classification/*genetics ; Base Sequence ; China ; DNA, Mitochondrial/chemistry/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Molecular Sequence Data ; *Phylogeny ; Selection, Genetic ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Tibet ; },
abstract = {DNA barcoding is a powerful approach for characterizing species of organisms, especially those with almost identical morphological features, thereby helping to to establish phylogenetic relationships and reveal evolutionary histories. In this study, we chose a 648-bp segment of the mitochondrial gene, cytochrome c oxidase subunit 1 (COI), as a standard barcode region to establish phylogenetic relationships among brine shrimp (Artemia) species from major habitats around the world and further focused on the biodiversity of Artemia species in China, especially in the Tibetan Plateau. Samples from five major salt lakes of the Tibetan Plateau located at altitudes over 4,000 m showed clear differences from other Artemia populations in China. We also observed two consistent amino acid changes, 153A/V and 183L/F, in the COI gene between the high and low altitude species in China. Moreover, indels in the COI sequence were identified in cyst and adult samples unique to the Co Qen population from the Tibetan Plateau, demonstrating the need for additional investigations of the mitochondrial genome among Tibetan Artemia populations.},
}
@article {pmid19294000,
year = {2009},
author = {Prasad, PK and Tandon, V and Biswal, DK and Goswami, LM and Chatterjee, A},
title = {Use of sequence motifs as barcodes and secondary structures of internal transcribed spacer 2 (ITS2, rDNA) for identification of the Indian liver fluke, Fasciola (Trematoda: Fasciolidae).},
journal = {Bioinformation},
volume = {3},
number = {7},
pages = {314-320},
pmid = {19294000},
issn = {0973-2063},
abstract = {Most phylogenetic studies using current methods have focused on primary DNA sequence information. However, RNA secondary structures are particularly useful in systematics because they include characteristics that give "morphological" information which is not found in the primary sequence. Also DNA sequence motifs from the internal transcribed spacer (ITS) of the nuclear rRNA repeat are useful for identification of trematodes. The species of liver flukes of the genus Fasciola (Platyhelminthes: Digenea: Fasciolidae) are obligate parasitic trematodes residing in the large biliary ducts of herbivorous mammals. While Fasciola hepatica has a cosmopolitan distribution, the other major species, i.e., F. gigantica is reportedly prevalent in the tropical and subtropical regions of Africa and Asia. To determine the Fasciola sp. of Assam (India) origin based on rDNA molecular data, ribosomal ITS2 region was sequenced (EF027103) and analysed. NCBI databases were used for sequence homology analysis and the phylogenetic trees were constructed based upon the ITS2 using MEGA and a Bayesian analysis of the combined data. The latter approach allowed us to include both primary sequence and RNA molecular morphometrics and revealed a close relationship with isolates of F. gigantica from China, Indonesia and Japan, the isolate from China with significant bootstrap values being the closest. ITS2 sequence motifs allowed an accurate in silico distinction of liver flukes. The data indicate that ITS2 motifs (</= 50 bp in size) can be considered promising tool for trematode species identification. Using the novel approach of molecular morphometrics that is based on ITS2 secondary structure homologies, phylogenetic relationships of the various isolates of fasciolid species have been discussed.},
}
@article {pmid19283079,
year = {2009},
author = {Rigola, D and van Oeveren, J and Janssen, A and Bonné, A and Schneiders, H and van der Poel, HJ and van Orsouw, NJ and Hogers, RC and de Both, MT and van Eijk, MJ},
title = {High-throughput detection of induced mutations and natural variation using KeyPoint technology.},
journal = {PloS one},
volume = {4},
number = {3},
pages = {e4761},
pmid = {19283079},
issn = {1932-6203},
mesh = {Alleles ; Base Sequence ; Eukaryotic Initiation Factor-4E/genetics ; Haplotypes ; Solanum lycopersicum/*genetics ; *Mutation ; Nucleic Acid Amplification Techniques/*methods ; *Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/*methods ; },
abstract = {Reverse genetics approaches rely on the detection of sequence alterations in target genes to identify allelic variants among mutant or natural populations. Current (pre-) screening methods such as TILLING and EcoTILLING are based on the detection of single base mismatches in heteroduplexes using endonucleases such as CEL 1. However, there are drawbacks in the use of endonucleases due to their relatively poor cleavage efficiency and exonuclease activity. Moreover, pre-screening methods do not reveal information about the nature of sequence changes and their possible impact on gene function. We present KeyPoint technology, a high-throughput mutation/polymorphism discovery technique based on massive parallel sequencing of target genes amplified from mutant or natural populations. KeyPoint combines multi-dimensional pooling of large numbers of individual DNA samples and the use of sample identification tags ("sample barcoding") with next-generation sequencing technology. We show the power of KeyPoint by identifying two mutants in the tomato eIF4E gene based on screening more than 3000 M2 families in a single GS FLX sequencing run, and discovery of six haplotypes of tomato eIF4E gene by re-sequencing three amplicons in a subset of 92 tomato lines from the EU-SOL core collection. We propose KeyPoint technology as a broadly applicable amplicon sequencing approach to screen mutant populations or germplasm collections for identification of (novel) allelic variation in a high-throughput fashion.},
}
@article {pmid19271746,
year = {2009},
author = {Meade, SO and Chen, MY and Sailor, MJ and Miskelly, GM},
title = {Multiplexed DNA detection using spectrally encoded porous SiO2 photonic crystal particles.},
journal = {Analytical chemistry},
volume = {81},
number = {7},
pages = {2618-2625},
pmid = {19271746},
issn = {1520-6882},
support = {U54 CA119335/CA/NCI NIH HHS/United States ; U54 CA119335-010002/CA/NCI NIH HHS/United States ; U54 CA 119335/CA/NCI NIH HHS/United States ; },
mesh = {Base Sequence ; DNA/*analysis/genetics/metabolism ; Electrochemistry ; Fluorescent Dyes/chemistry ; Light ; Microscopy, Fluorescence ; Molecular Sequence Data ; Oligonucleotides/chemistry/genetics/metabolism ; Oxidation-Reduction ; *Photons ; Porosity ; Reproducibility of Results ; Sensitivity and Specificity ; Silanes/chemistry ; Silicon Dioxide/*chemistry ; Spectrometry, Fluorescence ; Temperature ; Time Factors ; },
abstract = {A particle-based multiplexed DNA assay based on encoded porous SiO(2) photonic crystal disks is demonstrated. A "spectral barcode" is generated by electrochemical etch of a single-crystal silicon wafer using a programmed current-time waveform. A lithographic procedure is used to isolate cylindrical microparticles 25 microm in diameter and 10 microm thick, which are then oxidized, modified with a silane linker, and conjugated to various amino-functionalized oligonucleotide probes via cyanuric chloride. It is shown that the particles can be decoded based on their reflectivity spectra and that a multiple analyte assay can be performed in a single sample with a modified fluorescence microscope. The homogeneity of the reflectivity and fluorescence spectra, both within and across the microparticles, is also reported.},
}
@article {pmid19267653,
year = {2008},
author = {Sinniger, F and Reimer, JD and Pawlowski, J},
title = {Potential of DNA sequences to identify zoanthids (Cnidaria: Zoantharia).},
journal = {Zoological science},
volume = {25},
number = {12},
pages = {1253-1260},
doi = {10.2108/zsj.25.1253},
pmid = {19267653},
issn = {0289-0003},
mesh = {Animals ; Anthozoa/classification/genetics ; Base Sequence ; Cnidaria/*classification/genetics ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Genetic Variation ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
abstract = {The order Zoantharia is known for its chaotic taxonomy and difficult morphological identification. One method that potentially could help for examining such troublesome taxa is DNA barcoding, which identifies species using standard molecular markers. The mitochondrial cytochrome oxidase subunit I (COI) has been utilized to great success in groups such as birds and insects; however, its applicability in many other groups is controversial. Recently, some studies have suggested that barcoding is not applicable to anthozoans. Here, we examine the use of COI and mitochondrial 16S ribosomal DNA for zoanthid identification. Despite the absence of a clear barcoding gap, our results show that for most of 54 zoanthid samples, both markers could separate samples to the species, or species group, level, particularly when easily accessible ecological or distributional data were included. Additionally, we have used the short V5 region of mt 16S rDNA to identify eight old (13 to 50 years old) museum samples. We discuss advantages and disadvantages of COI and mt 16S rDNA as barcodes for Zoantharia, and recommend that either one or both of these markers be considered for zoanthid identification in the future.},
}
@article {pmid19265609,
year = {2009},
author = {Nielsen, RH and Hellebek, A},
title = {[Drug mix-ups].},
journal = {Ugeskrift for laeger},
volume = {171},
number = {10},
pages = {811-814},
pmid = {19265609},
issn = {1603-6824},
mesh = {Drug Labeling ; Drug Packaging ; Drug Prescriptions/standards ; Humans ; *Medication Errors/prevention &amp; control/statistics &amp; numerical data ; Risk Factors ; },
abstract = {We investigated drug mix-ups at a Danish hospital. We found 115 drug mix-ups among 1,554 medication errors (7%). The majority were packing mix-ups with insulin, infusion fluids and prepared syringes. The most frequent cause of name confusions was illegible handwriting. Packing mix-up occurring during routine dispensing may be prevented with bar-coding, and package mix-ups occurring in acute situations may be prevented through better package design focusing on reducing the risk of mix-ups.},
}
@article {pmid19263343,
year = {2009},
author = {Howard, C and Bremner, PD and Fowler, MR and Isodo, B and Scott, NW and Slater, A},
title = {Molecular identification of Hypericum perforatum by PCR amplification of the ITS and 5.8S rDNA region.},
journal = {Planta medica},
volume = {75},
number = {8},
pages = {864-869},
doi = {10.1055/s-0029-1185397},
pmid = {19263343},
issn = {1439-0221},
mesh = {Consumer Product Safety ; DNA Primers ; *DNA, Intergenic ; *DNA, Plant ; *DNA, Ribosomal ; Drug Contamination/*prevention &amp; control ; Genes, Plant ; Hypericum/*genetics ; Nucleic Acid Amplification Techniques ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; },
abstract = {The nuclear ribosomal internal transcribed spacer (ITS) sequences of eight Hypericum species were used to design H. perforatum-specific PCR primers by identification of short "microcode" sequences characteristic of the target species. These were tested with three vouchered H. perforatum DNA samples and eight samples from other species within the Hypericum genus. The most efficient primer combination, FO2 and HRI-S, amplified the genomic DNA from all three H. perforatum samples but not from any of the others apart from H. delphicum. The primer pairing was then tested against seven commercially available ornamental varieties of Hypericum; a positive result was obtained only with the H. perforatum sample. Three consumer products retailed as "St. John's wort" herbal remedies were sampled, two of which gave a positive result for H. perforatum. The assay was sensitive enough to detect 0.75 ng H. perforatum present as just 0.1 % of the total DNA. This method has the potential to be replicated in other plant species and presents a novel use for DNA barcoding data.},
}
@article {pmid19253662,
year = {2009},
author = {Barr, NB},
title = {Pathway analysis of Ceratitis capitata (Diptera: Tephritidae) using mitochondrial DNA.},
journal = {Journal of economic entomology},
volume = {102},
number = {1},
pages = {401-411},
doi = {10.1603/029.102.0153},
pmid = {19253662},
issn = {0022-0493},
mesh = {Animals ; Ceratitis capitata/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Haplotypes ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; },
abstract = {The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method described in a previous publication to document worldwide population structure of Mediterranean fruit flies and analyze probable sources of fly introductions is re-evaluated. Analysis of representatives of the RFLP-based markers using the ND5-tRNA-ND4 mitochondrial locus through DNA sequencing shows that the original markers produced haplotypes that are homoplasic and exclude valuable information. DNA sequences also identified errors in data generated with the protocol because of failure of the XbaI enzyme to efficiently cut PCR product. In all, the PCR-RFLP method is able to document haplotypes present in medfly populations outside of Sub-Saharan Africa and is a cost-effective approach to pathway analysis. New primer pairs for analysis of this locus are reported that reduce the number of PCR steps required to analyze the RFLP marker and the time of each PCR run. For comparison of the PCR-RFLP method, the utility of a DNA sequence-based approach to Mediterranean fruit fly pathway analysis is reported using the ND5-ND4 locus and the proposed "barcode region" of the COI gene. Both gene sequences are more informative than the PCR-RFLP method and document high genetic variation within Sub-Saharan Africa. Application of these methods as tools and their interpretation is discussed.},
}
@article {pmid19249365,
year = {2009},
author = {Feau, N and Vialle, A and Allaire, M and Tanguay, P and Joly, DL and Frey, P and Callan, BE and Hamelin, RC},
title = {Fungal pathogen (mis-) identifications: a case study with DNA barcodes on Melampsora rusts of aspen and white poplar.},
journal = {Mycological research},
volume = {113},
number = {Pt 6-7},
pages = {713-724},
doi = {10.1016/j.mycres.2009.02.007},
pmid = {19249365},
issn = {1469-8102},
mesh = {Basidiomycota/classification/*genetics/*isolation &amp; purification ; DNA, Fungal/*genetics ; DNA, Ribosomal Spacer/genetics ; Molecular Sequence Data ; Phylogeny ; Pinus/*microbiology ; Plant Diseases/*microbiology ; Populus/*microbiology ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; },
abstract = {Wide variation and overlap in morphological characters have led to confusion in species identification within the fungal rust genus Melampsora. The Melampsora species with uredinial-telial stages on white poplar and aspens are especially prone to misidentification. This group includes the Melampsora populnea species complex and the highly destructive pine twisting rust, Melampsora pinitorqua, which alternates between hosts in Populus section Populus and Pinus. Our objective was to compare morphologically based identification to genetic material extracted from Melampsora species pathogenic to aspen and white poplar. We compared morphometric traits and DNA barcodes obtained from internal transcribed spacer (ITS), large ribosomal RNA subunit (28S), and mitochondrial cytochrome oxidase 1 (CO1) sequences to delimit within this taxonomically difficult group. Eight different Melampsora species were initially defined based on host specificity and morphometric data. DNA barcodes were then overlaid on these initial species definitions. The DNA barcodes, specifically those defined on ITS and 28S sequences, provided a highly accurate means of identifying and resolving Melampsora taxa. We highlighted species misidentification in specimens from Canadian herbaria related to either Melampsora medusae f. sp. tremuloidae or Melampsora aecidioides. Finally, we evidenced that the north-American species found on Populus alba, M. aecidioides is closely related but distinct from the four species of the M. populnea complex (Melampsora larici-tremulae, Melampsora magnusiana, Melampsora pinitorqua, and Melampsora rostrupii) found in Eurasia.},
}
@article {pmid19240801,
year = {2009},
author = {Seberg, O and Petersen, G},
title = {How many loci does it take to DNA barcode a crocus?.},
journal = {PloS one},
volume = {4},
number = {2},
pages = {e4598},
pmid = {19240801},
issn = {1932-6203},
mesh = {Base Sequence ; Classification/*methods ; Crocus/*genetics ; DNA/genetics ; DNA, Plant ; Electronic Data Processing ; *Genetic Markers ; Genome, Plant ; Plants/*genetics ; Species Specificity ; },
abstract = {BACKGROUND: DNA barcoding promises to revolutionize the way taxonomists work, facilitating species identification by using small, standardized portions of the genome as substitutes for morphology. The concept has gained considerable momentum in many animal groups, but the higher plant world has been largely recalcitrant to the effort. In plants, efforts are concentrated on various regions of the plastid genome, but no agreement exists as to what kinds of regions are ideal, though most researchers agree that more than one region is necessary. One reason for this discrepancy is differences in the tests that are used to evaluate the performance of the proposed regions. Most tests have been made in a floristic setting, where the genetic distance and therefore the level of variation of the regions between taxa is large, or in a limited set of congeneric species.<br><br>Here we present the first in-depth coverage of a large taxonomic group, all 86 known species (except two doubtful ones) of crocus. Even six average-sized barcode regions do not identify all crocus species. This is currently an unrealistic burden in a barcode context. Whereas most proposed regions work well in a floristic context, the majority will--as is the case in crocus--undoubtedly be less efficient in a taxonomic setting. However, a reasonable but less than perfect level of identification may be reached--even in a taxonomic context.<br><br>CONCLUSIONS/SIGNIFICANCE: The time is ripe for selecting barcode regions in plants, and for prudent examination of their utility. Thus, there is no reason for the plant community to hold back the barcoding effort by continued search for the Holy Grail. We must acknowledge that an emerging system will be far from perfect, fraught with problems and work best in a floristic setting.},
}
@article {pmid19235685,
year = {2009},
author = {Yao, H and Song, JY and Ma, XY and Liu, C and Li, Y and Xu, HX and Han, JP and Duan, LS and Chen, SL},
title = {Identification of Dendrobium species by a candidate DNA barcode sequence: the chloroplast psbA-trnH intergenic region.},
journal = {Planta medica},
volume = {75},
number = {6},
pages = {667-669},
doi = {10.1055/s-0029-1185385},
pmid = {19235685},
issn = {1439-0221},
mesh = {*Base Sequence ; Chloroplasts/*genetics ; *DNA, Intergenic ; *DNA, Plant ; Dendrobium/*genetics ; Electronic Data Processing/methods ; *Genes, Plant ; Sequence Alignment ; },
abstract = {DNA barcoding is a novel technology that uses a standard DNA sequence to facilitate species identification. Although a consensus has not been reached regarding which DNA sequences can be used as the best plant barcodes, the psbA-trnH spacer region has been tested extensively in recent years. In this study, we hypothesize that the psbA-trnH spacer regions are also effective barcodes for Dendrobium species. We have sequenced the chloroplast psbA-trnH intergenic spacers of 17 Dendrobium species to test this hypothesis. The sequences were found to be significantly different from those of other species, with percentages of variation ranging from 0.3 % to 2.3 % and an average of 1.2 %. In contrast, the intraspecific variation among the Dendrobium species studied ranged from 0 % to 0.1 %. The sequence difference between the psbA-trnH sequences of 17 Dendrobium species and one Bulbophyllum odoratissimum ranged from 2.0 % to 3.1 %, with an average of 2.5 %. Our results support the notion that the psbA-trnH intergenic spacer region could be used as a barcode to distinguish various Dendrobium species and to differentiate Dendrobium species from other adulterating species.},
}
@article {pmid19227926,
year = {2009},
author = {Okamoto, N and Suzuki, K and Mimura, O},
title = {[Trial of eye drops recognizer for visually disabled persons].},
journal = {Nippon Ganka Gakkai zasshi},
volume = {113},
number = {1},
pages = {5-10},
pmid = {19227926},
issn = {0029-0203},
mesh = {Adult ; *Persons with Disabilities ; Drug Packaging/*instrumentation ; Electronic Data Processing/*instrumentation ; *Equipment Design ; Humans ; Male ; Medication Errors/*prevention &amp; control ; Ophthalmic Solutions/*administration &amp; dosage ; *Vision Disorders ; },
abstract = {PURPOSE: The development of a device to enable the visually disabled to differentiate eye drops and their dose.<br><br>SUBJECTS AND METHODS: The new instrument is composed of a voice generator and a two-dimensional bar-code reader (LS9208). We designed voice outputs for the visually disabled to state when (number of times) and where (right, left, or both) to administer eye drops. We then determined the minimum bar-code size that can be recognized. After attaching bar-codes of the appropriate size to the lateral or bottom surface of the eye drops container, the readability of the bar-codes was compared.<br><br>RESULTS: The minimum discrimination bar-code size was 6 mm high x 8.5 mm long. Bar-codes on the bottom surface could be more easily recognized than bar-codes on the side.<br><br>CONCLUSION: Our newly-developed device using bar-codes enables visually disabled persons to differentiate eye drops and their doses.},
}
@article {pmid19215877,
year = {2009},
author = {Desmyter, S and Gosselin, M},
title = {COI sequence variability between Chrysomyinae of forensic interest.},
journal = {Forensic science international. Genetics},
volume = {3},
number = {2},
pages = {89-95},
doi = {10.1016/j.fsigen.2008.11.002},
pmid = {19215877},
issn = {1878-0326},
mesh = {Animals ; Base Sequence ; Belgium ; DNA/genetics ; DNA, Mitochondrial/*genetics ; Diptera/*classification/*genetics ; Europe ; Forensic Medicine/methods ; France ; Genes, Mitochondrial/*genetics ; Genetic Markers ; *Genetic Variation ; Geography ; Haplotypes ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Species Specificity ; United States ; },
abstract = {About 50 Chrysomyinae specimens belonging to three forensic relevant species (Chrysomia albiceps, Phormia regina and Protophormia terraenovae) were collected from different geographical locations in Belgium over the last 5 yr. A 304-bp fragment of their mitochondrial COI gene is sequenced. The monophyletic branches of the phylogenetic tree reveal that this marker is suitable for discrimination between these species. The intra versus interspecific variability marks clear threshold levels for DNA barcoding. Nineteen Chrysomyinae specimens, collected from four locations in France, show mitotypes that are identical or at least very similar to the Belgian mitotypes. Considering additional specimens from outside of Europe reveals no intraspecific geographical variation within C. albiceps and P. terraenovae, whereas P. regina is subbranched in a Belgian-French and a USA-Chinese population.},
}
@article {pmid19207247,
year = {2009},
author = {Powers, TO and Neher, DA and Mullin, P and Esquivel, A and Giblin-Davis, RM and Kanzaki, N and Stock, SP and Mora, MM and Uribe-Lorio, L},
title = {Tropical nematode diversity: vertical stratification of nematode communities in a Costa Rican humid lowland rainforest.},
journal = {Molecular ecology},
volume = {18},
number = {5},
pages = {985-996},
doi = {10.1111/j.1365-294X.2008.04075.x},
pmid = {19207247},
issn = {1365-294X},
mesh = {Animals ; *Biodiversity ; Costa Rica ; Isoptera/parasitology ; Likelihood Functions ; Molecular Sequence Data ; Nematoda/*classification ; Parasites/classification ; Plants/parasitology ; Population Dynamics ; *Rain ; Soil/parasitology ; *Trees ; *Tropical Climate ; },
abstract = {Comparisons of nematode communities among ecosystems have indicated that, unlike many organisms, nematode communities have less diversity in the tropics than in temperate ecosystems. There are, however, few studies of tropical nematode diversity on which to base conclusions of global patterns of diversity. This study reports an attempt to estimate nematode diversity in the lowland tropical rainforest of La Selva Biological Research Station in Costa Rica. We suggest one reason that previous estimates of tropical nematode diversity were low is because habitats above the mineral soil are seldom sampled. As much as 62% of the overall genetic diversity, measured by an 18S ribosomal barcode, existed in litter and understorey habitats and not in soil. A maximum-likelihood tree of barcodes from 360 individual nematodes indicated most major terrestrial nematode lineages were represented in the samples. Estimated 'species' richness ranged from 464 to 502 within the four 40 x 40 m plots. Directed sampling of insects and their associated nematodes produced a second set of barcodes that were not recovered by habitat sampling, yet may constitute a major class of tropical nematode diversity. While the generation of novel nematode barcodes proved relatively easy, their identity remains obscure due to deficiencies in existing taxonomic databases. Specimens of Criconematina, a monophyletic group of soil-dwelling plant-parasitic nematodes were examined in detail to assess the steps necessary for associating barcodes with nominal species. Our results highlight the difficulties associated with studying poorly understood organisms in an understudied ecosystem using a destructive (i.e. barcode) sampling method.},
}
@article {pmid19203274,
year = {2009},
author = {Holterman, M and Karssen, G and van den Elsen, S and van Megen, H and Bakker, J and Helder, J},
title = {Small subunit rDNA-based phylogeny of the Tylenchida sheds light on relationships among some high-impact plant-parasitic nematodes and the evolution of plant feeding.},
journal = {Phytopathology},
volume = {99},
number = {3},
pages = {227-235},
doi = {10.1094/PHYTO-99-3-0227},
pmid = {19203274},
issn = {0031-949X},
mesh = {Animals ; DNA, Helminth/genetics ; DNA, Ribosomal/genetics ; *Evolution, Molecular ; Feeding Behavior ; *Host-Parasite Interactions ; *Phylogeny ; Plants/*parasitology ; Sequence Alignment ; Sequence Analysis, DNA ; Tylenchida/classification/enzymology/*genetics ; },
abstract = {Cyst (Heteroderidae), root knot (Meloidogyne spp.), and lesion (Pratylenchus spp.) nematodes all belong to a single nematode order, Tylenchida. However, the relationships between and within these economically highly relevant groups, and their relatedness to other parasitic Tylenchida is unclear. We constructed a phylogeny of 116 Tylenchida taxa based on full length small subunit ribosomal DNA (small subunit [SSU] rDNA) sequences. Ancestral state reconstruction points at a gradual development of simple to more complex forms of plant parasitism. Good resolution was observed in distal clades that include cyst, root knot, and lesion nematodes, and monophyly of most families was confirmed. Our data suggest that root knot nematodes have evolved from an ancestral member of the genus Pratylenchus, but it remains unclear which species is closest to this branching point. Contrary to the notoriously polyphagous distal representatives, basal members of the genus Meloidogyne (and probably, their common ancestor) have narrow host ranges. Our analysis also shows that mitotic parthenogeny has arisen at least two times independently among root knot nematodes. In many cases resolution till species was observed, suggesting that SSU rDNA sequences have a potential for DNA barcode-based species identification with, due to the overall conserved nature of this gene, limited intra-species variation.},
}
@article {pmid19196101,
year = {2009},
author = {Lin, GT and Tseng, HF and Yang, CH and Hou, MF and Chuang, LY and Tai, HT and Tai, MH and Cheng, YH and Wen, CH and Liu, CS and Huang, CJ and Wang, CL and Chang, HW},
title = {Combinational polymorphisms of seven CXCL12-related genes are protective against breast cancer in Taiwan.},
journal = {Omics : a journal of integrative biology},
volume = {13},
number = {2},
pages = {165-172},
doi = {10.1089/omi.2008.0050},
pmid = {19196101},
issn = {1557-8100},
mesh = {Adult ; Base Sequence ; Breast Neoplasms/*genetics ; Chemokine CXCL12/*genetics ; DNA Primers ; Female ; *Genetic Predisposition to Disease ; Humans ; Middle Aged ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; *Polymorphism, Single Nucleotide ; Taiwan ; },
abstract = {Many single nucleotide polymorphisms (SNPs) have been found to be associated with breast cancer, but their SNP interactions are seldom addressed. In this study, we focused on the joint effect for SNP combinations of seven CXCL12-related genes involved in major cancer-related pathways. SNP genotyping was determined by PCR-restriction fragment length polymorphism (RFLP) in this study (case = 220, control = 334). Different numbers of combinational SNPs with genotypes called the SNP barcodes from different chromosomes were used to evaluate their joint effect on breast cancer risk. Except for vascular endothelial growth factor (VEGF) rs3025039-CT, none of these SNPs were found to individually contribute to breast cancer risk. However, for two combined SNPs, the proportion of subjects with breast cancer was significantly low in the SNP barcode with CC-GG genotypes in rs2228014-1801157 (CXCR4-CXCL12) compared to those with non-CC-GG genotypes. Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) and rs12812942-rs3136685-rs2228014-rs1801157 (CD4- CCR7-CXCR4-CXCL12) with specific genotype patterns (AT-CC-CC and AT-AG-CC-GG) among three and four combinational SNPs were significantly low in breast cancer occurrence. More SNP combinations larger than five SNPs were also addressed, and these showed similar effects. After controlling for age, and comparing their corresponding non-SNP barcodes, the estimated odds ratios for breast cancer ranged between 0.20 and 0.71 for specific SNP barcodes with two to seven SNPs. In conclusion, we have associated the potential combined CXCL12-related SNPs with genotypes that were protective against breast cancer, and that may contribute to identification of a low-risk population for the development of breast cancer.},
}
@article {pmid19194495,
year = {2009},
author = {Kerr, KC and Lijtmaer, DA and Barreira, AS and Hebert, PD and Tubaro, PL},
title = {Probing evolutionary patterns in neotropical birds through DNA barcodes.},
journal = {PloS one},
volume = {4},
number = {2},
pages = {e4379},
pmid = {19194495},
issn = {1932-6203},
mesh = {Animals ; Argentina ; Birds/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Genetic Variation ; Geography ; North America ; Phylogeny ; Sequence Analysis, DNA ; *Tropical Climate ; },
abstract = {BACKGROUND: The Neotropical avifauna is more diverse than that of any other biogeographic region, but our understanding of patterns of regional divergence is limited. Critical examination of this issue is currently constrained by the limited genetic information available. This study begins to address this gap by assembling a library of mitochondrial COI sequences, or DNA barcodes, for Argentinian birds and comparing their patterns of genetic diversity to those of North American birds.<br><br>Five hundred Argentinian species were examined, making this the first major examination of DNA barcodes for South American birds. Our results indicate that most southern Neotropical bird species show deep sequence divergence from their nearest-neighbour, corroborating that the high diversity of this fauna is not based on an elevated incidence of young species radiations. Although species ages appear similar in temperate North and South American avifaunas, patterns of regional divergence are more complex in the Neotropics, suggesting that the high diversity of the Neotropical avifauna has been fueled by greater opportunities for regional divergence. Deep genetic splits were observed in at least 21 species, though distribution patterns of these lineages were variable. The lack of shared polymorphisms in species, even in species with less than 0.5M years of reproductive isolation, further suggests that selective sweeps could regularly excise ancestral mitochondrial polymorphisms.<br><br>CONCLUSIONS: These findings confirm the efficacy of species delimitation in birds via DNA barcodes, even when tested on a global scale. Further, they demonstrate how large libraries of a standardized gene region provide insight into evolutionary processes.},
}
@article {pmid19188057,
year = {2009},
author = {Zhang, X and Su, H and Bi, S and Li, S and Zhang, S},
title = {DNA-based amplified electrical bio-barcode assay for one-pot detection of two target DNAs.},
journal = {Biosensors &amp; bioelectronics},
volume = {24},
number = {8},
pages = {2730-2734},
doi = {10.1016/j.bios.2008.12.032},
pmid = {19188057},
issn = {1873-4235},
mesh = {Biosensing Techniques/*instrumentation ; Colony Count, Microbial/instrumentation ; DNA, Viral/*analysis/chemistry/*genetics ; Electrochemistry/*instrumentation ; Equipment Design ; Equipment Failure Analysis ; Gene Targeting/instrumentation ; Human T-lymphotropic virus 1/genetics/*isolation &amp; purification ; Human T-lymphotropic virus 2/genetics/*isolation &amp; purification ; Nucleic Acid Amplification Techniques/*instrumentation ; Oligonucleotide Array Sequence Analysis/*instrumentation ; Reproducibility of Results ; Sensitivity and Specificity ; },
abstract = {A sensitive label-free bio-barcode assay provided a PCR-free method for quantitative detection of two nucleic acid targets (HTLV-I and HTLV-II) simultaneously. This DNA biosensor was fabricated with two-component oligonucleotide-modified gold nanoparticles (AuNPs) and two-component oligonucleotide-modified magnetic beads (MBs), which can sandwich a specific target. After liberating the adsorbed thiolated barcode DNA strands (poly A and poly G) from the AuNPs surface with dithiothreitol (DTT) and acidic dipurinization, the electrochemical measurements were directly performed based on the redox activity of guanine (G) and adenine (A) nucleobases. Under the optimal assembling and detection conditions, a good linearity for simultaneous detection was obtained in the range from 4.4x10(-11) to 2.0x10(-9) M, and the detection limit (3sigma) was estimated to be 1.71x10(-12) M for T(1)-DNA and 1.55x10(-12) M for T(2)-DNA.},
}
@article {pmid19171886,
year = {2009},
author = {Xu, Q and Schlabach, MR and Hannon, GJ and Elledge, SJ},
title = {Design of 240,000 orthogonal 25mer DNA barcode probes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {106},
number = {7},
pages = {2289-2294},
pmid = {19171886},
issn = {1091-6490},
support = {//Howard Hughes Medical Institute/United States ; },
mesh = {Algorithms ; DNA/metabolism ; DNA Probes/genetics ; *Electronic Data Processing ; Gene Expression Profiling ; Nucleic Acid Conformation ; Nucleic Acid Hybridization/genetics ; Oligonucleotide Array Sequence Analysis ; Oligonucleotide Probes/chemistry ; RNA/metabolism ; Sequence Analysis, DNA ; Software ; Temperature ; },
abstract = {DNA barcodes linked to genetic features greatly facilitate screening these features in pooled formats using microarray hybridization, and new tools are needed to design large sets of barcodes to allow construction of large barcoded mammalian libraries such as shRNA libraries. Here we report a framework for designing large sets of orthogonal barcode probes. We demonstrate the utility of this framework by designing 240,000 barcode probes and testing their performance by hybridization. From the test hybridizations, we also discovered new probe design rules that significantly reduce cross-hybridization after their introduction into the framework of the algorithm. These rules should improve the performance of DNA microarray probe designs for many applications.},
}
@article {pmid19160512,
year = {2008},
author = {Vigneault, F and Sismour, AM and Church, GM},
title = {Efficient microRNA capture and bar-coding via enzymatic oligonucleotide adenylation.},
journal = {Nature methods},
volume = {5},
number = {9},
pages = {777-779},
doi = {10.1038/nmeth.1244},
pmid = {19160512},
issn = {1548-7091},
mesh = {Adenine/*chemistry ; DNA Ligases/*metabolism ; *Electronic Data Processing ; Humans ; MicroRNAs/*analysis ; Oligonucleotides/*chemistry ; RNA Ligase (ATP)/*metabolism ; },
abstract = {Here we report a highly efficient and simplified strategy to preadenylate bar-coded oligonucleotides designed for microRNA (miRNA) capture and multiplex analysis. Using this approach, we enzymatically preadenylated bar-coded oligonucleotides with high efficiency when compared to the chemical method currently used by miRNA investigators. As a case study, we used these oligonucleotides in an ATP-independent ligation to miRNAs, suggesting the utility of our method in end-capture protocols and high-throughput sequencing applications.},
}
@article {pmid19159457,
year = {2009},
author = {Lefrançois, P and Euskirchen, GM and Auerbach, RK and Rozowsky, J and Gibson, T and Yellman, CM and Gerstein, M and Snyder, M},
title = {Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing.},
journal = {BMC genomics},
volume = {10},
number = {},
pages = {37},
pmid = {19159457},
issn = {1471-2164},
mesh = {Binding Sites ; Centromere/metabolism ; Chromatin Immunoprecipitation ; Chromosome Mapping ; DNA, Fungal/genetics ; Genome, Fungal ; Genomic Library ; Genomics/methods ; Oligonucleotide Array Sequence Analysis/*methods ; Saccharomyces cerevisiae/*genetics ; Sequence Analysis, DNA/*methods ; Transcription Factors/metabolism ; },
abstract = {BACKGROUND: Short-read high-throughput DNA sequencing technologies provide new tools to answer biological questions. However, high cost and low throughput limit their widespread use, particularly in organisms with smaller genomes such as S. cerevisiae. Although ChIP-Seq in mammalian cell lines is replacing array-based ChIP-chip as the standard for transcription factor binding studies, ChIP-Seq in yeast is still underutilized compared to ChIP-chip. We developed a multiplex barcoding system that allows simultaneous sequencing and analysis of multiple samples using Illumina's platform. We applied this method to analyze the chromosomal distributions of three yeast DNA binding proteins (Ste12, Cse4 and RNA PolII) and a reference sample (input DNA) in a single experiment and demonstrate its utility for rapid and accurate results at reduced costs.<br><br>RESULTS: We developed a barcoding ChIP-Seq method for the concurrent analysis of transcription factor binding sites in yeast. Our multiplex strategy generated high quality data that was indistinguishable from data obtained with non-barcoded libraries. None of the barcoded adapters induced differences relative to a non-barcoded adapter when applied to the same DNA sample. We used this method to map the binding sites for Cse4, Ste12 and Pol II throughout the yeast genome and we found 148 binding targets for Cse4, 823 targets for Ste12 and 2508 targets for PolII. Cse4 was strongly bound to all yeast centromeres as expected and the remaining non-centromeric targets correspond to highly expressed genes in rich media. The presence of Cse4 non-centromeric binding sites was not reported previously.<br><br>CONCLUSION: We designed a multiplex short-read DNA sequencing method to perform efficient ChIP-Seq in yeast and other small genome model organisms. This method produces accurate results with higher throughput and reduced cost. Given constant improvements in high-throughput sequencing technologies, increasing multiplexing will be possible to further decrease costs per sample and to accelerate the completion of large consortium projects such as modENCODE.},
}
@article {pmid19152837,
year = {2009},
author = {Pavlic, D and Slippers, B and Coutinho, TA and Wingfield, MJ},
title = {Multiple gene genealogies and phenotypic data reveal cryptic species of the Botryosphaeriaceae: a case study on the Neofusicoccum parvum/N. ribis complex.},
journal = {Molecular phylogenetics and evolution},
volume = {51},
number = {2},
pages = {259-268},
doi = {10.1016/j.ympev.2008.12.017},
pmid = {19152837},
issn = {1095-9513},
mesh = {Ascomycota/classification/*genetics/physiology ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; *Evolution, Molecular ; Gene Flow ; Genes, Fungal ; *Genetic Speciation ; Geography ; *Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Alignment ; Sequence Analysis, DNA ; South Africa ; Species Specificity ; },
abstract = {Neofusicoccum parvum and N. ribis (Botryosphaeriaceae, Ascomycetes) are closely related, plant pathogenic fungi with a world-wide distribution on a wide range of woody hosts. Species boundaries in the N. parvum/N. ribis complex have eluded definition, despite the application of various tools for characterisation. In this study, we test the hypothesis that only one species exists amongst isolates from the N. parvum/N. ribis complex, identified from Syzygiumcordatum trees across their native distribution in South Africa. Genealogical concordance phylogenetic species recognition (GCPSR) was applied based on concordance of genealogies obtained from DNA sequence data for five nuclear loci. These data showed that the single species hypothesis must be rejected. Rather, all analyses support the existence of three previously unrecognised, cryptic species within the N. parvum/N.ribis complex from S. cordatum, in addition to N. parvum and N. ribis. The three lineages reflecting these cryptic taxa are sympatric across their geographical range, indicating barriers to gene flow other than geographic isolation. Phenotypic characters failed to detect all the species uncovered by the GCPSR. Sequence data of the Internal Transcribed Spacer (ITS) of the ribosomal DNA locus, which is thought to be useful for barcoding in fungi, did not distinguish all the species with confidence. RNA polymerase II subunit (RPB2) was the most informative to distinguish all the species a posteriori to the application of GCPSR. The results reflect the critical importance of using multiple gene genealogies and adequate sampling to identify cryptic species and to characterise the true diversity within the Botryosphaeriaceae.},
}
@article {pmid19144929,
year = {2009},
author = {Petrusek, A and Tollrian, R and Schwenk, K and Haas, A and Laforsch, C},
title = {A "crown of thorns" is an inducible defense that protects Daphnia against an ancient predator.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {106},
number = {7},
pages = {2248-2252},
pmid = {19144929},
issn = {1091-6490},
mesh = {Animals ; Biological Evolution ; Cell Lineage ; Cladocera ; DNA, Mitochondrial/metabolism ; Daphnia/anatomy &amp; histology/*metabolism/*physiology ; Ecology ; Electron Transport Complex IV/metabolism ; Food Chain ; Humans ; Models, Anatomic ; Models, Biological ; Phenotype ; Phylogeny ; Predatory Behavior ; },
abstract = {Genetic data has become an essential part of ecological studies, because the analyses of diversity within and among natural populations may grant access to previously overlooked ecological and evolutionary causalities, especially among cryptic species. Here, we present an example of how phylogenetic analysis of molecular data obtained within a DNA barcoding study, in combination with morphological and ecological data from the field and laboratory experiments, unraveled a striking predator-prey interaction between aquatic organisms. The "crown of thorns," a conspicuous morphological feature among water fleas of the Daphnia atkinsoni species complex (Crustacea: Cladocera), is considered to represent a species-specific trait. However, our study, initiated by the analysis of sequence variation in 2 mitochondrial genes, shows that this feature is phenotypically plastic and is induced by chemical cues released by Triops cancriformis, the tadpole shrimp (Notostraca). The trait acts as an effective antipredator defense, and is found in several Daphnia lineages coexisting with notostracans. These facts suggest that the "crown of thorns" evolved in coexistence with this ancient predator group.},
}
@article {pmid19128479,
year = {2009},
author = {Ferri, E and Barbuto, M and Bain, O and Galimberti, A and Uni, S and Guerrero, R and Ferté, H and Bandi, C and Martin, C and Casiraghi, M},
title = {Integrated taxonomy: traditional approach and DNA barcoding for the identification of filarioid worms and related parasites (Nematoda).},
journal = {Frontiers in zoology},
volume = {6},
number = {},
pages = {1},
pmid = {19128479},
issn = {1742-9994},
abstract = {BACKGROUND: We compared here the suitability and efficacy of traditional morphological approach and DNA barcoding to distinguish filarioid nematodes species (Nematoda, Spirurida). A reliable and rapid taxonomic identification of these parasites is the basis for a correct diagnosis of important and widespread parasitic diseases. The performance of DNA barcoding with different parameters was compared measuring the strength of correlation between morphological and molecular identification approaches. Molecular distance estimation was performed with two different mitochondrial markers (coxI and 12S rDNA) and different combinations of data handling were compared in order to provide a stronger tool for easy identification of filarioid worms.<br><br>RESULTS: DNA barcoding and morphology based identification of filarioid nematodes revealed high coherence. Despite both coxI and 12S rDNA allow to reach high-quality performances, only coxI revealed to be manageable. Both alignment algorithm, gaps treatment, and the criteria used to define the threshold value were found to affect the performance of DNA barcoding with 12S rDNA marker. Using coxI and a defined level of nucleotide divergence to delimit species boundaries, DNA barcoding can also be used to infer potential new species.<br><br>CONCLUSION: An integrated approach allows to reach a higher discrimination power. The results clearly show where DNA-based and morphological identifications are consistent, and where they are not. The coherence between DNA-based and morphological identification for almost all the species examined in our work is very strong. We propose DNA barcoding as a reliable, consistent, and democratic tool for species discrimination in routine identification of parasitic nematodes.},
}
@article {pmid19127298,
year = {2009},
author = {Aliabadian, M and Kaboli, M and Nijman, V and Vences, M},
title = {Molecular identification of birds: performance of distance-based DNA barcoding in three genes to delimit parapatric species.},
journal = {PloS one},
volume = {4},
number = {1},
pages = {e4119},
pmid = {19127298},
issn = {1932-6203},
mesh = {Animals ; Birds/*classification/*genetics ; DNA, Mitochondrial/*chemistry/metabolism ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Genetic Variation ; RNA, Ribosomal, 16S/genetics ; Sample Size ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
abstract = {BACKGROUND: DNA barcoding based on the mitochondrial cytochrome oxidase subunit I gene (cox1 or COI) has been successful in species identification across a wide array of taxa but in some cases failed to delimit the species boundaries of closely allied allopatric species or of hybridising sister species.<br><br>In this study we extend the sample size of prior studies in birds for cox1 (2776 sequences, 756 species) and target especially species that are known to occur parapatrically, and/or are known to hybridise, on a Holarctic scale. In order to obtain a larger set of taxa (altogether 2719 species), we include also DNA sequences of two other mitochondrial genes: cytochrome b (cob) (4614 sequences, 2087 species) and 16S (708 sequences, 498 species). Our results confirm the existence of a wide gap between intra- and interspecies divergences for both cox1 and cob, and indicate that distance-based DNA barcoding provides sufficient information to identify and delineate bird species in 98% of all possible pairwise comparisons. This DNA barcoding gap was not statistically influenced by the number of individuals sequenced per species. However, most of the hybridising parapatric species pairs have average divergences intermediate between intraspecific and interspecific distances for both cox1 and cob.<br><br>CONCLUSIONS/SIGNIFICANCE: DNA barcoding, if used as a tool for species discovery, would thus fail to identify hybridising parapatric species pairs. However, most of them can probably still assigned to known species by character-based approaches, although development of complementary nuclear markers will be necessary to account for mitochondrial introgression in hybridising species.},
}
@article {pmid19114529,
year = {2009},
author = {Lin, S and Zhang, H and Hou, Y and Zhuang, Y and Miranda, L},
title = {High-level diversity of dinoflagellates in the natural environment, revealed by assessment of mitochondrial cox1 and cob genes for dinoflagellate DNA barcoding.},
journal = {Applied and environmental microbiology},
volume = {75},
number = {5},
pages = {1279-1290},
pmid = {19114529},
issn = {1098-5336},
mesh = {Animals ; *Biodiversity ; Cytochromes b/*genetics ; DNA Primers/genetics ; DNA, Mitochondrial/chemistry/genetics ; Dinoflagellida/*classification/genetics/isolation &amp; purification ; Electron Transport Complex IV/*genetics ; *Environmental Microbiology ; Mitochondrial Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; United States ; },
abstract = {DNA barcoding is a diagnostic technique for species identification using a short, standardized DNA. An effective DNA barcoding marker would be very helpful for unraveling the poorly understood species diversity of dinoflagellates in the natural environment. In this study, the potential utility for DNA barcoding of mitochondrial cytochrome c oxidase 1 (cox1) and cytochrome b (cob) was assessed. Among several primer sets examined, the one amplifying a 385-bp cob fragment was most effective for dinoflagellates. This short cob fragment is easy to sequence and yet possess reasonable taxon resolution. While the lack of a uniform gap between interspecific and intraspecific distances poses difficulties in establishing a phylum-wide species-discriminating distance threshold, the variability of cob allows recognition of species within particular lineages. The potential of this cob fragment as a dinoflagellate species marker was further tested by applying it to an analysis of the dinoflagellate assemblages in Long Island Sound (LIS) and Mirror Lake in Connecticut. In LIS, a highly diverse assemblage of dinoflagellates was detected. Some taxa can be identified to the species and some to the genus level, including a taxon distinctly related to the bipolar species Polarella glacialis, and the large number of others cannot be clearly identified, due to the inadequate database. In Mirror Lake, a Ceratium species and an unresolved taxon were detected, exhibiting a temporal transition from one to the other. We demonstrate that this 385-bp cob fragment is promising for lineage-wise dinoflagellate species identification, given an adequate database.},
}
@article {pmid19100655,
year = {2009},
author = {Valentini, A and Pompanon, F and Taberlet, P},
title = {DNA barcoding for ecologists.},
journal = {Trends in ecology &amp; evolution},
volume = {24},
number = {2},
pages = {110-117},
doi = {10.1016/j.tree.2008.09.011},
pmid = {19100655},
issn = {0169-5347},
mesh = {Animals ; Biodiversity ; Classification/methods ; DNA/chemistry ; Databases, Genetic ; Diet ; Ecology/*trends ; Food Chain ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
abstract = {DNA barcoding - taxon identification using a standardized DNA region - has received much attention recently, and is being further developed through an international initiative. We anticipate that DNA barcoding techniques will be increasingly used by ecologists. They will be able to not only identify a single species from a specimen or an organism's remains but also determine the species composition of environmental samples. Short DNA fragments persist in the environment and might allow an assessment of local biodiversity from soil or water. Even DNA-based diet composition can be estimated using fecal samples. Here we review the new avenues offered to ecologists by DNA barcoding, particularly in the context of new sequencing technologies.},
}
@article {pmid19091119,
year = {2008},
author = {Zhou, F and Olman, V and Xu, Y},
title = {Barcodes for genomes and applications.},
journal = {BMC bioinformatics},
volume = {9},
number = {},
pages = {546},
pmid = {19091119},
issn = {1471-2105},
mesh = {*Algorithms ; Base Sequence/*genetics ; Computational Biology/*methods ; Genome/*genetics ; Genomics/*methods ; Species Specificity ; },
abstract = {BACKGROUND: Each genome has a stable distribution of the combined frequency for each k-mer and its reverse complement measured in sequence fragments as short as 1000 bps across the whole genome, for 1<k<6. The collection of these k-mer frequency distributions is unique to each genome and termed the genome's barcode.<br><br>RESULTS: We found that for each genome, the majority of its short sequence fragments have highly similar barcodes while sequence fragments with different barcodes typically correspond to genes that are horizontally transferred or highly expressed. This observation has led to new and more effective ways for addressing two challenging problems: metagenome binning problem and identification of horizontally transferred genes. Our barcode-based metagenome binning algorithm substantially improves the state of the art in terms of both binning accuracies and the scope of applicability. Other attractive properties of genomes barcodes include (a) the barcodes have different and identifiable characteristics for different classes of genomes like prokaryotes, eukaryotes, mitochondria and plastids, and (b) barcodes similarities are generally proportional to the genomes' phylogenetic closeness.<br><br>CONCLUSION: These and other properties of genomes barcodes make them a new and effective tool for studying numerous genome and metagenome analysis problems.},
}
@article {pmid19072281,
year = {2009},
author = {Demirok, UK and Burdick, J and Wang, J},
title = {Orthogonal multi-readout identification of alloy nanowire barcodes.},
journal = {Journal of the American Chemical Society},
volume = {131},
number = {1},
pages = {22-23},
doi = {10.1021/ja806396h},
pmid = {19072281},
issn = {1520-5126},
mesh = {Alloys/*chemistry ; Electronic Data Processing/*methods ; Indium/chemistry ; Nanotechnology/*methods ; Nanowires/*chemistry ; Nickel/chemistry ; Zinc/chemistry ; },
abstract = {A multi-readout orthogonal detection of alloy nanowire barcodes is shown to maximize the identification power of such encoded nanostructures. The built-in redundancy associated with the simultaneous use of several independent and powerful readout modes, based on different distinct processes and phenomena, offers great promise for decoding barcoded nanomaterials and for meeting the major challenges of product protection and multiplexed biodetection.},
}
@article {pmid19067801,
year = {2008},
author = {Kane, NC and Cronk, Q},
title = {Botany without borders: barcoding in focus.},
journal = {Molecular ecology},
volume = {17},
number = {24},
pages = {5175-5176},
doi = {10.1111/j.1365-294X.2008.03972.x},
pmid = {19067801},
issn = {1365-294X},
mesh = {Computational Biology/methods ; DNA, Plant/*genetics ; Genes, Plant ; *Genetic Markers ; Genome, Plant ; Plants/classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {This recent meeting, held on the campus of the University of British Columbia, attracted 1200 delegates and a vast array of talks, but was notable for a remarkable showing of talks and posters on DNA barcoding in plants, spread through many sessions. The Canadian Centre for DNA Barcoding defines barcoding as 'species identification and discovery through the analysis of short, standardized gene regions known as DNA barcodes'. This approach is somewhat controversial in animals (Rubinoff et al., 2006), although it has been shown to be useful and reliable in many metazoan taxa (Meyer &amp; Paulay 2005; Hajibabaei et al., 2007), in which the mitochondrial cytochrome oxidase I (COI) gene is used. However, in land plants, COI evolves far too slowly to be useful, and there is no obvious single universal alternative (Fazekas et al., 2008).Genes that work well in one taxon may perform poorly in other taxa. Additionally, some perfectly good plant species,reproductively isolated and morphologically and ecologically distinct, are too young to show much sequence divergence at most loci. Nevertheless, as we saw at this conference, progress has been made towards identifying genes that serve many of the functions of DNA barcodes, at least in some plant taxa.},
}
@article {pmid19059488,
year = {2009},
author = {Hemmerter, S and Slapeta, J and Beebe, NW},
title = {Resolving genetic diversity in Australasian Culex mosquitoes: incongruence between the mitochondrial cytochrome c oxidase I and nuclear acetylcholine esterase 2.},
journal = {Molecular phylogenetics and evolution},
volume = {50},
number = {2},
pages = {317-325},
doi = {10.1016/j.ympev.2008.11.016},
pmid = {19059488},
issn = {1095-9513},
mesh = {Acetylcholinesterase/*genetics ; Animals ; Australasia ; Bayes Theorem ; Culex/classification/enzymology/*genetics ; DNA, Mitochondrial/genetics ; Drosophila melanogaster/enzymology/genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Genetic Markers ; *Genetic Variation ; Geography ; Haplotypes ; Insect Proteins/genetics ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Insects that vector pathogens are under constant surveillance in Australasia although the repertoire of genetic markers to distinguish what are often cryptic mosquito species remains limited. We present a comparative assessment of the second exon-intron region of the acetylcholine esterase 2 gene (ace-2) and the mitochondrial DNA cytochrome c oxidase I (COI) using two closely related Australasia mosquitoes Culex annulirostris and Culex palpalis. The COI revealed eight divergent lineages of which four were confirmed with the ace-2. We dissect out the nuclear chromosomal haplotypes of the ace-2 as well as the exon-intron regions by assessing the protein's tertiary structure to reveal a hypervariable 5'-exon that forms part of an external protein loop and displays a higher polymorphic rate than the intron. We retrace the evolutionary history of these mosquitoes by phylogenetic inference and by testing different evolutionary hypotheses. We conclude that DNA barcoding using COI may overestimate the diversity of Culex mosquitoes in Australasia and should be applied cautiously with support from the nuclear DNA such as the ace-2. Together the COI and ace-2 provide robust evidence for distinct cryptic Culex lineages--one of which correlates exactly with the southern limit of Japanese encephalitis virus activity in Australasia.},
}
@article {pmid19056502,
year = {2009},
author = {Linares, MC and Soto-Calderón, ID and Lees, DC and Anthony, NM},
title = {High mitochondrial diversity in geographically widespread butterflies of Madagascar: a test of the DNA barcoding approach.},
journal = {Molecular phylogenetics and evolution},
volume = {50},
number = {3},
pages = {485-495},
doi = {10.1016/j.ympev.2008.11.008},
pmid = {19056502},
issn = {1095-9513},
support = {BBS/B/04358//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Butterflies/classification/*genetics/microbiology ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Gene Flow ; *Genetic Variation ; Genetics, Population ; Geography ; Mitochondria/genetics ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Wolbachia/genetics ; },
abstract = {The standardized use of mitochondrial cytochrome c oxidase subunit I (COI) gene sequences as DNA barcodes has been widely promoted as a high-throughput method for species identification and discovery. Species delimitation has been based on the following criteria: (1) monophyletic association and less frequently (2) a minimum 10x greater divergence between than within species. Divergence estimates, however, can be inflated if sister species pairs are not included and the geographic extent of variation within any given taxon is not sampled comprehensively. This paper addresses both potential biases in DNA divergence estimation by sampling range-wide variation in several morphologically distinct, endemic butterfly species in the genus Heteropsis, some of which are sister taxa. We also explored the extent to which mitochondrial DNA from the barcode region can be used to assess the effects of historical rainforest fragmentation by comparing genetic variation across Heteropsis populations with an unrelated forest-associated taxon Saribia tepahi. Unexpectedly, generalized primers led to the inadvertent amplification of the endosymbiont Wolbachia, undermining the use of universal primers and necessitating the design of genus-specific COI primers alongside a Wolbachia-specific PCR assay. Regardless of the high intra-specific genetic variation observed, most species satisfy DNA barcoding criteria and can be differentiated in the nuclear phylogeny. Nevertheless, two morphologically distinguishable candidate species fail to satisfy the barcoding 10x genetic distance criterion, underlining the difficulties of applying a standard distance threshold to species delimitation. Phylogeographic analysis of COI data suggests that forest fragmentation may have played an important role in the recent evolutionary diversification of these butterflies. Further work on other Malagasy taxa using both mitochondrial and nuclear data will provide better insight into the role of historical habitat fragmentation in species diversification and may potentially contribute to the identification of priority areas for conservation.},
}
@article {pmid19052667,
year = {2008},
author = {Shapshak, P and Chiappelli, F and Commins, D and Singer, E and Levine, AJ and Somboonwit, C and Minagar, A and Pellionisz, AJ},
title = {Molecular epigenetics, chromatin, and NeuroAIDS/HIV: translational implications.},
journal = {Bioinformation},
volume = {3},
number = {1},
pages = {53-57},
pmid = {19052667},
issn = {0973-2063},
support = {U24 MH100929/MH/NIMH NIH HHS/United States ; R01 GM056529/GM/NIGMS NIH HHS/United States ; T32 AI007126/AI/NIAID NIH HHS/United States ; P30 CA016042/CA/NCI NIH HHS/United States ; R01 DA012580/DA/NIDA NIH HHS/United States ; R24 NS038841/NS/NINDS NIH HHS/United States ; R21 DA014533/DA/NIDA NIH HHS/United States ; },
abstract = {We describe current research that applies epigenetics to a novel understanding of the immuno-neuropathogenesis of HIV-1 viral infection and NeuroAIDS. We propose the hypothesis that HIV-1 alters the structure-function relationship of chromatin, coding DNA and non-coding DNA, including RNA transcribed from these regions resulting in pathogenesis in AIDS, drug abuse, and NeuroAIDS. We discuss the general implications of molecular epigenetics with special emphasis on drug abuse, bar-codes, pyknons, and miRNAs for translational and clinical research. We discuss the application of the recent recursive algorithm of biology to this field and propose to synthesize the Genomic and Epigenomic views into a holistic approach of HoloGenomics.},
}
@article {pmid19052662,
year = {2008},
author = {Selvaraj, D and Sarma, RK and Sathishkumar, R},
title = {Phylogenetic analysis of chloroplast matK gene from Zingiberaceae for plant DNA barcoding.},
journal = {Bioinformation},
volume = {3},
number = {1},
pages = {24-27},
pmid = {19052662},
issn = {0973-2063},
abstract = {MaturaseK gene (MatK) of chloroplast is highly conserved in plant systematics which is involved in Group II intron splicing. The size of the gene is 1500 bp in length, located with in the intron of trnK. In the present study, matK gene from Zingiberaceae was taken for the analysis of variants, parsimony site, patterns, transition/tranversion rates and phylogeny. The family of Zingiberaceae comprises 47 genera with medicinal values. The matK gene sequence have been obtained from genbank and used for the analysis. The sequence alignments were performed by Clustal X, transition/transversion rates were predicted by MEGA and phylogenetic analyses were carried out by PHYLIP package. The result indicates that the Zingiberaceae genus Afromonum, Alpinia, Globba, Curcuma and Zingiber shows polyphylogeny. The overall variants between the species are 24% and transition/transversion rate is 1.54. Phylogenetic tree was designed to identify the ideal regions that could be used for defining the inter and intera-generic relationships. From this study it could be concluded that the matK gene is a good candidate for DNA barcoding of plant family Zingiberaceae.},
}
@article {pmid19046425,
year = {2008},
author = {Armougom, F and Raoult, D},
title = {Use of pyrosequencing and DNA barcodes to monitor variations in Firmicutes and Bacteroidetes communities in the gut microbiota of obese humans.},
journal = {BMC genomics},
volume = {9},
number = {},
pages = {576},
pmid = {19046425},
issn = {1471-2164},
mesh = {Bacterial Typing Techniques/methods ; Bacteroidetes/classification/*genetics ; Gastrointestinal Tract/*microbiology ; Genes, rRNA ; Genetic Markers ; Genetic Variation ; Humans ; Obesity/*microbiology ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sensitivity and Specificity ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: Recent studies of 16S rRNA genes in the mammalian gut microbiota distinguished a higher Firmicutes/Bacteroidetes ratio in obese individuals compared to lean individuals. This ratio was estimated using a clonal Sanger sequencing approach which is time-consuming and requires laborious data analysis. In contrast, new high-throughput pyrosequencing technology offers an inexpensive alternative to clonal Sanger sequencing and would significantly advance our understanding of obesity via the development of a clinical diagnostic method. Here we present a cost-effective method that combines 16S rRNA pyrosequencing and DNA barcodes of the Firmicutes and Bacteroidetes 16S rRNA genes to determine the Firmicutes/Bacteroidetes ratio in the gut microbiota of obese humans.<br><br>RESULTS: The main result was the identification of DNA barcodes targeting the Firmicutes and Bacteroidetes phyla. These barcodes were validated using previously published 16S rRNA gut microbiota clone libraries. In addition, an accurate F/B ratio was found when the DNA barcodes were applied to short pyrosequencing reads of published gut metagenomes. Finally, the barcodes were utilized to define the F/B ratio of 16S rRNA pyrosequencing data generated from brain abscess pus and cystic fibrosis sputum.<br><br>CONCLUSION: Using DNA barcodes of Bacteroidetes and Firmicutes 16S rRNA genes combined with pyrosequencing is a cost-effective method for monitoring relevant changes in the relative abundance of Firmicutes and Bacteroidetes bacterial communities in microbial ecosystems.},
}
@article {pmid20396577,
year = {2008},
author = {Nguyen, HD and Seifert, KA},
title = {Description and DNA barcoding of three new species of Leohumicola from South Africa and the United States.},
journal = {Persoonia},
volume = {21},
number = {},
pages = {57-69},
pmid = {20396577},
issn = {1878-9080},
abstract = {Three new species of Leohumicola (anamorphic Leotiomycetes) are described using morphological characters and phylogenetic analyses of DNA barcodes. Leohumicola levissima and L. atra were isolated from soils collected after forest fires in Crater Lake National Park, United States. Leohumicola incrustata was isolated from burned fynbos from the Cape of Good Hope Nature Reserve, South Africa. The three species exhibit characteristic Leohumicola morphology but are morphologically distinct based on conidial characters. Two DNA barcode regions, the Internal Transcribed Spacer (ITS) nuclear rDNA region and the cytochrome oxidase subunit I (Cox1) mitochondrial gene, were sequenced. Single-gene parsimony, dual-gene parsimony and dual-gene Bayesian inference phylogenetic analyses support L. levissima, L. atra, L. incrustata as distinct phylogenetic species. Both ITS and Cox1 barcodes are effective for the molecular identification of Leohumicola species.},
}
@article {pmid19027884,
year = {2009},
author = {Hamilton, PB and Adams, ER and Njiokou, F and Gibson, WC and Cuny, G and Herder, S},
title = {Phylogenetic analysis reveals the presence of the Trypanosoma cruzi clade in African terrestrial mammals.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {9},
number = {1},
pages = {81-86},
doi = {10.1016/j.meegid.2008.10.011},
pmid = {19027884},
issn = {1567-1348},
mesh = {Alligators and Crocodiles/parasitology ; Animals ; Antelopes/parasitology ; Cameroon ; Cercopithecus/parasitology ; DNA, Ribosomal/genetics ; Evolution, Molecular ; *Genes, Protozoan ; Genetic Variation ; Glyceraldehyde-3-Phosphate Dehydrogenases/genetics ; Humans ; Mammals/*parasitology ; Molecular Sequence Data ; Nandiniidae/parasitology ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; Sequence Alignment ; Trypanosoma/*classification/*genetics ; Trypanosoma cruzi/classification/*genetics ; Trypanosomiasis, African/parasitology/*veterinary ; },
abstract = {Despite the impact of some trypanosome species on human and livestock health, the full diversity of trypanosomes in Africa is poorly understood. A recent study examined the prevalence of trypanosomes among a wide variety of wild vertebrates in Cameroon using species-specific PCR tests, but six trypanosome isolates remained unidentified. Here they have been re-examined using fluorescent fragment length barcoding (FFLB) and phylogenetic analysis of glycosomal glyceraldehyde phosphate dehydrogenase gGAPDH and 18S ribosomal RNA (rDNA) genes. Isolates from a monkey (Cercopithecus nictitans) and a palm civet (Nandinia binotata) belonged to the Trypanosoma cruzi clade, known previously only from New World and Australian terrestrial mammals, and bats from Africa, Europe and South America. Of the four other isolates, three from antelope were identified as Trypanosoma theileri, and one from a crocodile as T. grayi. This is the first report of trypanosomes of the T. cruzi clade in African terrestrial mammals and expands the clade's known global distribution in terrestrial mammals. Previously it has been hypothesized that African and New World trypanosomes diverged after continental separation, dating the divergence to around 100 million years ago. The new evidence instead suggests that intercontinental transfer occurred well after this, possibly via bats or rodents, allowing these trypanosomes to establish and evolve in African terrestrial mammals, and questioning the validity of calibrating trypanosome molecular trees using continental separation.},
}
@article {pmid19004756,
year = {2009},
author = {Jurado-Rivera, JA and Vogler, AP and Reid, CA and Petitpierre, E and Gómez-Zurita, J},
title = {DNA barcoding insect-host plant associations.},
journal = {Proceedings. Biological sciences},
volume = {276},
number = {1657},
pages = {639-648},
pmid = {19004756},
issn = {0962-8452},
mesh = {Animals ; Coleoptera/*classification/genetics ; DNA/chemistry ; DNA Fingerprinting/*methods ; DNA, Chloroplast/chemistry ; Ecosystem ; Fabaceae/*classification/genetics ; Feeding Behavior ; Myrtaceae/*classification/genetics ; Phylogeny ; },
abstract = {Short-sequence fragments ('DNA barcodes') used widely for plant identification and inventorying remain to be applied to complex biological problems. Host-herbivore interactions are fundamental to coevolutionary relationships of a large proportion of species on the Earth, but their study is frequently hampered by limited or unreliable host records. Here we demonstrate that DNA barcodes can greatly improve this situation as they (i) provide a secure identification of host plant species and (ii) establish the authenticity of the trophic association. Host plants of leaf beetles (subfamily Chrysomelinae) from Australia were identified using the chloroplast trnL(UAA) intron as barcodes amplified from beetle DNA extracts. Sequence similarity and phylogenetic analyses provided precise identifications of each host species at tribal, generic and specific levels, depending on the available database coverage in various plant lineages. The 76 species of Chrysomelinae included-more than 10 per cent of the known Australian fauna-feed on 13 plant families, with preference for Australian radiations of Myrtaceae (eucalypts) and Fabaceae (acacias). Phylogenetic analysis of beetles shows general conservation of host association but with rare host shifts between distant plant lineages, including a few cases where barcodes supported two phylogenetically distant host plants. The study demonstrates that plant barcoding is already feasible with the current publicly available data. By sequencing plant barcodes directly from DNA extractions made from herbivorous beetles, strong physical evidence for the host association is provided. Thus, molecular identification using short DNA fragments brings together the detection of species and the analysis of their interactions.},
}
@article {pmid18999121,
year = {2008},
author = {Novak, LL and Lorenzi, NM},
title = {Barcode medication administration: supporting transitions in articulation work.},
journal = {AMIA ... Annual Symposium proceedings. AMIA Symposium},
volume = {2008},
number = {},
pages = {515-519},
pmid = {18999121},
issn = {1942-597X},
support = {K99 LM010038/LM/NLM NIH HHS/United States ; T15 LM007450/LM/NLM NIH HHS/United States ; },
mesh = {Clinical Pharmacy Information Systems/organization &amp; administration ; *Cooperative Behavior ; Delivery of Health Care, Integrated/*organization &amp; administration ; *Medication Systems, Hospital ; *Task Performance and Analysis ; United States ; *Workload ; },
abstract = {Articulation work is that which enables coordinated activity among colleagues distributed in time and space. Despite its important role in clinical settings, this work remains largely invisible in process flowcharts. When process-oriented information systems are implemented, the informal, flexible, contingent activities of participants that enable coordinated work are suddenly placed in a new context. Articulation work must adapt to new contexts of automation, and there are opportunities for clinical systems to better support coordination activities. This research explores the articulation work involved in medication administration, how it is affected by the implementation of barcoding, and strategies for support and problem resolution in this arena.},
}
@article {pmid18972856,
year = {2008},
author = {DiConsiglio, J},
title = {Creative 'work-arounds' defeat bar-coding safeguard for meds. Study finds technology often doesn't meet the needs of nurses.},
journal = {Materials management in health care},
volume = {17},
number = {9},
pages = {26-29},
pmid = {18972856},
issn = {1059-4531},
mesh = {*Electronic Data Processing ; Equipment Failure ; Medication Errors/prevention &amp; control ; *Nursing Staff, Hospital ; *Pharmacy Service, Hospital ; *Safety Management ; User-Computer Interface ; },
}
@article {pmid18959790,
year = {2008},
author = {Daniels, R and Volkman, SK and Milner, DA and Mahesh, N and Neafsey, DE and Park, DJ and Rosen, D and Angelino, E and Sabeti, PC and Wirth, DF and Wiegand, RC},
title = {A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking.},
journal = {Malaria journal},
volume = {7},
number = {},
pages = {223},
pmid = {18959790},
issn = {1475-2875},
support = {/WT_/Wellcome Trust/United Kingdom ; K23 AI072033/AI/NIAID NIH HHS/United States ; K23AI072033-01/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; DNA Fingerprinting/*methods ; DNA, Protozoan/*genetics ; Genotype ; *Microarray Analysis ; Plasmodium falciparum/*classification/*genetics ; *Polymorphism, Single Nucleotide ; },
abstract = {BACKGROUND: Single nucleotide polymorphism (SNP) genotyping provides the means to develop a practical, rapid, inexpensive assay that will uniquely identify any Plasmodium falciparum parasite using a small amount of DNA. Such an assay could be used to distinguish recrudescence from re-infection in drug trials, to monitor the frequency and distribution of specific parasites in a patient population undergoing drug treatment or vaccine challenge, or for tracking samples and determining purity of isolates in the laboratory during culture adaptation and sub-cloning, as well as routine passage.<br><br>METHODS: A panel of twenty-four SNP markers has been identified that exhibit a high minor allele frequency (average MAF > 35%), for which robust TaqMan genotyping assays were constructed. All SNPs were identified through whole genome sequencing and MAF was estimated through Affymetrix array-based genotyping of a worldwide collection of parasites. These assays create a "molecular barcode" to uniquely identify a parasite genome.<br><br>RESULTS: Using 24 such markers no two parasites known to be of independent origin have yet been found to have the same allele signature. The TaqMan genotyping assays can be performed on a variety of samples including cultured parasites, frozen whole blood, or whole blood spotted onto filter paper with a success rate > 99%. Less than 5 ng of parasite DNA is needed to complete a panel of 24 markers. The ability of this SNP panel to detect and identify parasites was compared to the standard molecular methods, MSP-1 and MSP-2 typing.<br><br>CONCLUSION: This work provides a facile field-deployable genotyping tool that can be used without special skills with standard lab equipment, and at reasonable cost that will unambiguously identify and track P. falciparum parasites both from patient samples and in the laboratory.},
}
@article {pmid18949437,
year = {2009},
author = {Otomo, PV and van Vuuren, BJ and Reinecke, SA},
title = {Usefulness of DNA barcoding in ecotoxicological investigations: resolving taxonomic uncertainties using Eisenia malm 1877 as an example.},
journal = {Bulletin of environmental contamination and toxicology},
volume = {82},
number = {3},
pages = {261-264},
doi = {10.1007/s00128-008-9585-4},
pmid = {18949437},
issn = {1432-0800},
mesh = {Animals ; DNA/*genetics ; *Electronic Data Processing ; Oligochaeta/*drug effects/genetics ; *Toxicity Tests ; },
abstract = {Standard test species may differ in their response to toxicants. Accurate identification of test organisms is therefore of critical importance in correctly interpreting data generated from laboratory assays. This is not always possible when species are morphologically similar or where the taxonomy of the group has recently been revised. A case in hand concerns Eisenia sp. Based on recent genetic evidence two species, Eisenia andrei and Eisenia fetida, which were previously considered a single species, are currently recognized. In these instances, DNA barcoding, demonstrated and discussed herein, provides a method to accurately identify test organisms.},
}
@article {pmid18947416,
year = {2008},
author = {Zimmermann, J and Hajibabaei, M and Blackburn, DC and Hanken, J and Cantin, E and Posfai, J and Evans, TC},
title = {DNA damage in preserved specimens and tissue samples: a molecular assessment.},
journal = {Frontiers in zoology},
volume = {5},
number = {},
pages = {18},
pmid = {18947416},
issn = {1742-9994},
abstract = {The extraction of genetic information from preserved tissue samples or museum specimens is a fundamental component of many fields of research, including the Barcode of Life initiative, forensic investigations, biological studies using scat sample analysis, and cancer research utilizing formaldehyde-fixed, paraffin-embedded tissue. Efforts to obtain genetic information from these sources are often hampered by an inability to amplify the desired DNA as a consequence of DNA damage.Previous studies have described techniques for improved DNA extraction from such samples or focused on the effect of damaging agents - such as light, oxygen or formaldehyde - on free nucleotides.We present ongoing work to characterize lesions in DNA samples extracted from preserved specimens. The extracted DNA is digested to single nucleosides with a combination of DNase I, Snake Venom Phosphodiesterase, and Antarctic Phosphatase and then analyzed by HPLC-ESI-TOF-MS.We present data for moth specimens that were preserved dried and pinned with no additional preservative and for frog tissue samples that were preserved in either ethanol, or formaldehyde, or fixed in formaldehyde and then preserved in ethanol. These preservation methods represent the most common methods of preserving animal specimens in museum collections. We observe changes in the nucleoside content of these samples over time, especially a loss of deoxyguanosine. We characterize the fragmentation state of the DNA and aim to identify abundant nucleoside lesions. Finally, simple models are introduced to describe the DNA fragmentation based on nicks and double-strand breaks.},
}
@article {pmid18941689,
year = {2008},
author = {Jeong, JR and Llandro, J and Hong, B and Hayward, TJ and Mitrelias, T and Kopper, KP and Trypiniotis, T and Steinmuller, SJ and Simpson, GK and Bland, JA},
title = {Rewritable remote encoding and decoding of miniature multi-bit magnetic tags for high-throughput biological analysis.},
journal = {Lab on a chip},
volume = {8},
number = {11},
pages = {1883-1887},
doi = {10.1039/b807632d},
pmid = {18941689},
issn = {1473-0197},
mesh = {Base Sequence ; *Electronic Data Processing ; Fluorescence ; *Magnetics ; Microarray Analysis/*methods ; Microscopy ; Oligonucleotides/genetics ; },
abstract = {We have investigated a new magnetic labelling technology for high-throughput biomolecular identification and DNA sequencing. Planar multi-bit magnetic tags comprising a magnetic barcode formed by an ensemble of micron-sized thin film ferromagnetic Co bars and a 15 x 15 micron Au square for immobilization of probe molecules have been designed and fabricated. We show that by using a globally applied magnetic field and magneto-optical Kerr microscopy the magnetic elements in the multi-bit magnetic tags can be addressed individually and encoded/decoded remotely. The power of the approach is the read/write technique, which allows modest globally applied magnetic fields to write almost unlimited numbers of codes to populations of tags rather than individuals. The magnetic nature of the technology also lends itself naturally to fast, remote decoding and the ability to rewrite tags if needed. We demonstrate the critical steps needed to show the feasibility of this technology, including fabrication, remote writing and reading, and successful functionalization of the tags as verified by fluorescence detection. This approach is ideal for encoding information on tags in microfluidic flow or suspension, in order to label oligonucleotides during split-and-mix synthesis, and for combinatorial library-based high-throughput multiplexed bioassays.},
}
@article {pmid18853366,
year = {2008},
author = {Meier, R and Zhang, G and Ali, F},
title = {The use of mean instead of smallest interspecific distances exaggerates the size of the "barcoding gap" and leads to misidentification.},
journal = {Systematic biology},
volume = {57},
number = {5},
pages = {809-813},
doi = {10.1080/10635150802406343},
pmid = {18853366},
issn = {1076-836X},
mesh = {Base Sequence ; DNA/*genetics ; Electronic Data Processing/*methods ; Genetic Speciation ; Genetic Variation/genetics ; Phylogeny ; Research Design ; },
}
@article {pmid18853361,
year = {2008},
author = {Munch, K and Boomsma, W and Huelsenbeck, JP and Willerslev, E and Nielsen, R},
title = {Statistical assignment of DNA sequences using Bayesian phylogenetics.},
journal = {Systematic biology},
volume = {57},
number = {5},
pages = {750-757},
doi = {10.1080/10635150802422316},
pmid = {18853361},
issn = {1076-836X},
support = {R01 GM069801/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Base Sequence ; Bayes Theorem ; Computer Simulation ; DNA/*genetics ; Insecta/genetics ; *Models, Genetic ; *Models, Statistical ; *Phylogeny ; Plants/genetics ; },
abstract = {We provide a new automated statistical method for DNA barcoding based on a Bayesian phylogenetic analysis. The method is based on automated database sequence retrieval, alignment, and phylogenetic analysis using a custom-built program for Bayesian phylogenetic analysis. We show on real data that the method outperforms Blast searches as a measure of confidence and can help eliminate 80% of all false assignment based on best Blast hit. However, the most important advance of the method is that it provides statistically meaningful measures of confidence. We apply the method to a re-analysis of previously published ancient DNA data and show that, with high statistical confidence, most of the published sequences are in fact of Neanderthal origin. However, there are several cases of chimeric sequences that are comprised of a combination of both Neanderthal and modern human DNA.},
}
@article {pmid18852878,
year = {2008},
author = {Baird, NA and Etter, PD and Atwood, TS and Currey, MC and Shiver, AL and Lewis, ZA and Selker, EU and Cresko, WA and Johnson, EA},
title = {Rapid SNP discovery and genetic mapping using sequenced RAD markers.},
journal = {PloS one},
volume = {3},
number = {10},
pages = {e3376},
pmid = {18852878},
issn = {1932-6203},
support = {R21HG003834/HG/NHGRI NIH HHS/United States ; GM025690/GM/NIGMS NIH HHS/United States ; R21 HG003834/HG/NHGRI NIH HHS/United States ; R24 GM079486/GM/NIGMS NIH HHS/United States ; T32 HD007348/HD/NICHD NIH HHS/United States ; R24GM79486/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Chromosome Mapping/*methods ; Expressed Sequence Tags ; Genetic Markers ; Genome ; Genotype ; Methods ; Neurospora crassa/genetics ; *Polymorphism, Single Nucleotide ; Restriction Mapping ; Smegmamorpha/genetics ; },
abstract = {Single nucleotide polymorphism (SNP) discovery and genotyping are essential to genetic mapping. There remains a need for a simple, inexpensive platform that allows high-density SNP discovery and genotyping in large populations. Here we describe the sequencing of restriction-site associated DNA (RAD) tags, which identified more than 13,000 SNPs, and mapped three traits in two model organisms, using less than half the capacity of one Illumina sequencing run. We demonstrated that different marker densities can be attained by choice of restriction enzyme. Furthermore, we developed a barcoding system for sample multiplexing and fine mapped the genetic basis of lateral plate armor loss in threespine stickleback by identifying recombinant breakpoints in F(2) individuals. Barcoding also facilitated mapping of a second trait, a reduction of pelvic structure, by in silico re-sorting of individuals. To further demonstrate the ease of the RAD sequencing approach we identified polymorphic markers and mapped an induced mutation in Neurospora crassa. Sequencing of RAD markers is an integrated platform for SNP discovery and genotyping. This approach should be widely applicable to genetic mapping in a variety of organisms.},
}
@article {pmid18852104,
year = {2008},
author = {Munch, K and Boomsma, W and Willerslev, E and Nielsen, R},
title = {Fast phylogenetic DNA barcoding.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {363},
number = {1512},
pages = {3997-4002},
pmid = {18852104},
issn = {1471-2970},
mesh = {*Algorithms ; Classification/*methods ; Cluster Analysis ; Computational Biology/*methods ; DNA/*genetics ; Databases, Genetic ; *Models, Genetic ; *Phylogeny ; },
abstract = {We present a heuristic approach to the DNA assignment problem based on phylogenetic inferences using constrained neighbour joining and non-parametric bootstrapping. We show that this method performs as well as the more computationally intensive full Bayesian approach in an analysis of 500 insect DNA sequences obtained from GenBank. We also analyse a previously published dataset of environmental DNA sequences from soil from New Zealand and Siberia, and use these data to illustrate the fact that statistical approaches to the DNA assignment problem allow for more appropriate criteria for determining the taxonomic level at which a particular DNA sequence can be assigned.},
}
@article {pmid18852100,
year = {2008},
author = {Rodrigo, A and Bertels, F and Heled, J and Noder, R and Shearman, H and Tsai, P},
title = {The perils of plenty: what are we going to do with all these genes?.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {363},
number = {1512},
pages = {3893-3902},
pmid = {18852100},
issn = {1471-2970},
mesh = {Data Interpretation, Statistical ; *Evolution, Molecular ; Genetic Markers/genetics ; Genomics/methods/*trends ; *Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
abstract = {This new century's biology promises more of everything--more genes, more organisms, more species and, in short, more data. The flood of data challenges us to find better and quicker ways to summarize and analyse. Here, we present preliminary results and proofs of concept from three of our research projects that are motivated by our search for solutions to the perils of plenty. First, we discuss how models of evolution can accommodate change to better reflect the dynamics of sequence diversity, particularly when it is becoming a lot easier to obtain sequences at different times and across intervals where the probability of new mutations contributing to this diversity is high. Second, we describe our work on the use of a single locus for species delimitation; this research targets the new DNA-barcoding approach that aims to catalogue the entirety of life. We have developed a single-locus test based on the coalescent that tests the null hypothesis of panmixis. Finally, we discuss new sequencing technologies, the types of data available and the efficacy of alignment-free methods to estimate pairwise distances for phylogenetic analyses.},
}
@article {pmid18849522,
year = {2008},
author = {Varley, KE and Mitra, RD},
title = {Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes.},
journal = {Genome research},
volume = {18},
number = {11},
pages = {1844-1850},
pmid = {18849522},
issn = {1088-9051},
support = {P50 HG003170/HG/NHGRI NIH HHS/United States ; T32 HG000045/HG/NHGRI NIH HHS/United States ; 5P50HG003170-03/HG/NHGRI NIH HHS/United States ; },
mesh = {Base Sequence ; Codon, Nonsense ; Colonic Neoplasms/genetics ; DNA Mutational Analysis/*methods/statistics &amp; numerical data ; DNA Primers/genetics ; DNA, Neoplasm/genetics ; Exons ; Genes, APC ; Humans ; *Mutation ; Pilot Projects ; Polymerase Chain Reaction/*methods/statistics &amp; numerical data ; Polymorphism, Single Nucleotide ; Reproducibility of Results ; },
abstract = {Medical resequencing of candidate genes in individual patient samples is becoming increasingly important in the clinic and in clinical research. Medical resequencing requires the amplification and sequencing of many candidate genes in many patient samples. Here we introduce Nested Patch PCR, a novel method for highly multiplexed PCR that is very specific, can sensitively detect SNPs and mutations, and is easy to implement. This is the first method that couples multiplex PCR with sample-specific DNA barcodes and next-generation sequencing to enable highly multiplex mutation discovery in candidate genes for multiple samples in parallel. In our pilot study, we amplified exons from colon cancer and matched normal human genomic DNA. From each sample, we successfully amplified 96% (90 of 94) targeted exons from across the genome, totaling 21.6 kbp of sequence. Ninety percent of all sequencing reads were from targeted exons, demonstrating that Nested Patch PCR is highly specific. We found that the abundance of reads per exon was reproducible across samples. We reliably detected germline SNPs and discovered a colon tumor specific nonsense mutation in APC, a gene causally implicated in colorectal cancer. With Nested Patch PCR, candidate gene mutation discovery across multiple individual patient samples can now utilize the power of second-generation sequencing.},
}
@article {pmid18837102,
year = {2008},
author = {Kubicek, CP and Komon-Zelazowska, M and Druzhinina, IS},
title = {Fungal genus Hypocrea/Trichoderma: from barcodes to biodiversity.},
journal = {Journal of Zhejiang University. Science. B},
volume = {9},
number = {10},
pages = {753-763},
pmid = {18837102},
issn = {1673-1581},
mesh = {Agaricales ; Animals ; Biodiversity ; Ecosystem ; Humans ; Hypocrea/*classification/pathogenicity ; Mycoses/microbiology ; Phylogeny ; Plants/microbiology ; Soil Microbiology ; Species Specificity ; Trichoderma/*classification/pathogenicity ; Virulence ; },
abstract = {Hypocrea/Trichoderma is a genus of soil-borne or wood-decaying fungi containing members important to mankind as producers of industrial enzymes and biocontrol agents against plant pathogens, but also as opportunistic pathogens of immunocompromised humans and animals, while others can cause damage to cultivated mushroom. With the recent advent of a reliable, BarCode-aided identification system for all known taxa of Trichoderma and Hypocrea, it became now possible to study some of the biological fundamentals of the diversity in this fungal genus in more detail. In this article, we will therefore review recent progress in (1) the understanding of the geographic distribution of individual taxa; (2) mechanisms of speciation leading to development of mushroom diseases and facultative human mycoses; and (3) the possible correlation of specific traits of secondary metabolism and molecular phylogeny.},
}
@article {pmid18835708,
year = {2009},
author = {Zhang, D and Carr, DJ and Alocilja, EC},
title = {Fluorescent bio-barcode DNA assay for the detection of Salmonella enterica serovar Enteritidis.},
journal = {Biosensors &amp; bioelectronics},
volume = {24},
number = {5},
pages = {1377-1381},
doi = {10.1016/j.bios.2008.07.081},
pmid = {18835708},
issn = {1873-4235},
mesh = {Biosensing Techniques/instrumentation/*methods ; Equipment Design ; Equipment Failure Analysis ; Oligonucleotide Array Sequence Analysis/*instrumentation ; Reproducibility of Results ; Salmonella enteritidis/*genetics/*isolation &amp; purification ; Sensitivity and Specificity ; Spectrometry, Fluorescence/*instrumentation ; },
abstract = {Salmonella enterica serovar Enteritidis is one of the most frequently reported causes of foodborne illness. It is a major threat to the food safety chain and public health. A highly amplified bio-barcode DNA assay for the rapid detection of the insertion element (Iel) gene of Salmonella Enteritidis is reported in this paper. The biosensor transducer is composed of two nanoparticles: gold nanoparticles (Au-NPs) and magnetic nanoparticles (MNPs). The Au-NPs are coated with the target-specific DNA probe which can recognize the target gene, and fluorescein-labeled barcode DNA in a 1:100 probe-to-barcode ratio. The MNPs are coated with the 2nd target-specific DNA probe. After mixing the nanoparticles with the 1st target DNA, the sandwich structure (MNPs-2nd DNA probe/Target DNA/1st DNA probe-Au-NPs-barcode DNA) is formed. A magnetic field is applied to separate the sandwich from the unreacted materials. Then the bio-barcode DNA is released from the Au-NPs. Because the Au-NPs have a large number of barcode DNA per DNA probe binding event, there is substantial amplification. The released barcode DNA is measured by fluorescence. Using this technique, the detection limit of this bio-barcode DNA assay is as low as 2.15 x 10(-16)mol (or 1 ng/mL).},
}
@article {pmid18826222,
year = {2008},
author = {Zhu, ZJ and Ghosh, PS and Miranda, OR and Vachet, RW and Rotello, VM},
title = {Multiplexed screening of cellular uptake of gold nanoparticles using laser desorption/ionization mass spectrometry.},
journal = {Journal of the American Chemical Society},
volume = {130},
number = {43},
pages = {14139-14143},
pmid = {18826222},
issn = {1520-5126},
support = {R01 GM077173/GM/NIGMS NIH HHS/United States ; R01 GM077173-02/GM/NIGMS NIH HHS/United States ; GM077173/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; COS Cells ; Cell Culture Techniques ; Cells, Cultured ; Chlorocebus aethiops ; Drug Delivery Systems ; Gold/chemistry/*pharmacokinetics ; Ligands ; Metal Nanoparticles/analysis/*chemistry ; Molecular Weight ; Particle Size ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation/*methods ; Surface Properties ; },
abstract = {Gold nanoparticles (AuNPs) are highly promising candidates as drug delivery agents into cells of interest. We describe for the first time the multiplexed analysis of nanoparticle uptake by cells using mass spectrometry. We demonstrate that the cellular uptake of functionalized gold nanoparticles with cationic or neutral surface ligands can be readily determined using laser desorption/ionization mass spectrometry of cell lysates. The surface ligands have "mass barcodes" that allow different nanoparticles to be simultaneously identified and quantified at levels as low as 30 pmol. Using this method, we find that subtle changes to AuNP surface functionalities can lead to measurable changes in cellular uptake propensities.},
}
@article {pmid18809713,
year = {2008},
author = {Schepers, K and Swart, E and van Heijst, JW and Gerlach, C and Castrucci, M and Sie, D and Heimerikx, M and Velds, A and Kerkhoven, RM and Arens, R and Schumacher, TN},
title = {Dissecting T cell lineage relationships by cellular barcoding.},
journal = {The Journal of experimental medicine},
volume = {205},
number = {10},
pages = {2309-2318},
pmid = {18809713},
issn = {1540-9538},
mesh = {Animals ; Biomarkers/*metabolism ; *Cell Lineage ; Cell Separation/*methods ; Mice ; Mice, Inbred C57BL ; Microarray Analysis/instrumentation/*methods ; Neoplasms/immunology/pathology ; Staining and Labeling/*methods ; T-Lymphocyte Subsets/*cytology/immunology ; T-Lymphocytes/*cytology/immunology ; },
abstract = {T cells, as well as other cell types, are composed of phenotypically and functionally distinct subsets. However, for many of these populations it is unclear whether they develop from common or separate progenitors. To address such issues, we developed a novel approach, termed cellular barcoding, that allows the dissection of lineage relationships. We demonstrate that the labeling of cells with unique identifiers coupled to a microarray-based detection system can be used to analyze family relationships between the progeny of such cells. To exemplify the potential of this technique, we studied migration patterns of families of antigen-specific CD8(+) T cells in vivo. We demonstrate that progeny of individual T cells rapidly seed independent lymph nodes and that antigen-specific CD8(+) T cells present at different effector sites are largely derived from a common pool of precursors. These data show how locally primed T cells disperse and provide a technology for kinship analysis with wider utility.},
}
@article {pmid18805098,
year = {2008},
author = {Dai, J and Hyland, EM and Yuan, DS and Huang, H and Bader, JS and Boeke, JD},
title = {Probing nucleosome function: a highly versatile library of synthetic histone H3 and H4 mutants.},
journal = {Cell},
volume = {134},
number = {6},
pages = {1066-1078},
pmid = {18805098},
issn = {1097-4172},
support = {U54 RR020839/RR/NCRR NIH HHS/United States ; U54 RR020839-04/RR/NCRR NIH HHS/United States ; RR020839/RR/NCRR NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Chromosomes, Fungal/metabolism ; DNA Damage ; DNA Repair ; Gene Deletion ; Gene Library ; Gene Silencing ; Histones/*genetics/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nucleosomes/*metabolism ; Plasmids/metabolism ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Species Specificity ; },
abstract = {Nucleosome structural integrity underlies the regulation of DNA metabolism and transcription. Using a synthetic approach, a versatile library of 486 systematic histone H3 and H4 substitution and deletion mutants that probes the contribution of each residue to nucleosome function was generated in Saccharomyces cerevisiae. We probed fitness contributions of each residue to perturbations of chromosome integrity and transcription, mapping global patterns of chemical sensitivities and requirements for transcriptional silencing onto the nucleosome surface. Each histone mutant was tagged with unique molecular barcodes, facilitating identification of histone mutant pools through barcode amplification, labeling, and TAG microarray hybridization. Barcodes were used to score complex phenotypes such as competitive fitness in a chemostat, DNA repair proficiency, and synthetic genetic interactions, revealing new functions for distinct histone residues and new interdependencies among nucleosome components and their modifiers.},
}
@article {pmid18789770,
year = {2009},
author = {Chang, HW and Yang, CH and Ho, CH and Wen, CH and Chuang, LY},
title = {Generating SNP barcode to evaluate SNP-SNP interaction of disease by particle swarm optimization.},
journal = {Computational biology and chemistry},
volume = {33},
number = {1},
pages = {114-119},
doi = {10.1016/j.compbiolchem.2008.07.029},
pmid = {18789770},
issn = {1476-928X},
mesh = {Bone Density ; *Electronic Data Processing ; Genotype ; Humans ; Osteoporosis/genetics/pathology ; *Polymorphism, Single Nucleotide ; },
abstract = {Genome-wide association analysis involved many single-nucleotide polymorphisms (SNPs) data is challenging mathematically and computationally. Hence, we propose the odds ratio-based discrete binary particle swarm optimization (OR-DBPSO) method that uses the OR as a new quantitative measure of disease risk among many SNP combinations with genotypes called "SNP barcode". DBPSO are applied to generate SNP barcode, which computes the maximal difference of occurrence between the case and control groups, to predict disease susceptibility such as osteoporosis. Different SNP barcode patterns may occur several times in either low or high bone mineral density (BMD) groups. Our results showed that a DBPSO can effectively identify a specific SNP barcode with an optimized fitness value. SNP barcodes with a low fitness value will naturally be discarded from the population. A representative SNP barcode with a variable number of SNPs is processed to OR analysis to determine the maximum difference between the low and high BMD groups in statistics manner. Therefore, this paper introduces a powerful procedure to analyze disease-associated SNP-SNP interaction in genome-wide genes.},
}
@article {pmid18784793,
year = {2007},
author = {Kerr, KC and Stoeckle, MY and Dove, CJ and Weigt, LA and Francis, CM and Hebert, PD},
title = {Comprehensive DNA barcode coverage of North American birds.},
journal = {Molecular ecology notes},
volume = {7},
number = {4},
pages = {535-543},
pmid = {18784793},
issn = {1471-8278},
abstract = {DNA barcoding seeks to assemble a standardized reference library for DNA-based identification of eukaryotic species. The utility and limitations of this approach need to be tested on well-characterized taxonomic assemblages. Here we provide a comprehensive DNA barcode analysis for North American birds including 643 species representing 93% of the breeding and pelagic avifauna of the USA and Canada. Most (94%) species possess distinct barcode clusters, with average neighbour-joining bootstrap support of 98%. In the remaining 6%, barcode clusters correspond to small sets of closely related species, most of which hybridize regularly. Fifteen (2%) currently recognized species are comprised of two distinct barcode clusters, many of which may represent cryptic species. Intraspecific variation is weakly related to census population size and species age. This study confirms that DNA barcoding can be effectively applied across the geographical and taxonomic expanse of North American birds. The consistent finding of constrained intraspecific mitochondrial variation in this large assemblage of species supports the emerging view that selective sweeps limit mitochondrial diversity.},
}
@article {pmid18784790,
year = {2007},
author = {Ratnasingham, S and Hebert, PD},
title = {bold: The Barcode of Life Data System (http://www.barcodinglife.org).},
journal = {Molecular ecology notes},
volume = {7},
number = {3},
pages = {355-364},
pmid = {18784790},
issn = {1471-8278},
abstract = {The Barcode of Life Data System (bold) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. By assembling molecular, morphological and distributional data, it bridges a traditional bioinformatics chasm. bold is freely available to any researcher with interests in DNA barcoding. By providing specialized services, it aids the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. This paper provides a brief introduction to the key elements of bold, discusses their functional capabilities, and concludes by examining computational resources and future prospects.},
}
@article {pmid18784789,
year = {2007},
author = {Min, XJ and Hickey, DA},
title = {Assessing the effect of varying sequence length on DNA barcoding of fungi.},
journal = {Molecular ecology notes},
volume = {7},
number = {3},
pages = {365-373},
pmid = {18784789},
issn = {1471-8278},
abstract = {DNA barcoding shows enormous promise for the rapid identification of organisms at the species level. There has been much recent debate, however, about the need for longer barcode sequences, especially when these sequences are used to construct molecular phylogenies. Here, we have analysed a set of fungal mitochondrial sequences - of various lengths - and we have monitored the effect of reducing sequence length on the utility of the data for both species identification and phylogenetic reconstruction. Our results demonstrate that reducing sequence length has a profound effect on the accuracy of resulting phylogenetic trees, but surprisingly short sequences still yield accurate species identifications. We conclude that the standard short barcode sequences (approximately 600 bp) are not suitable for inferring accurate phylogenetic relationships, but they are sufficient for species identification among the fungi.},
}
@article {pmid18767242,
year = {2008},
author = {Bravo, JP and Silva, JL and Munhoz, RE and Fernandez, MA},
title = {DNA barcode information for the sugar cane moth borer Diatraea saccharalis.},
journal = {Genetics and molecular research : GMR},
volume = {7},
number = {3},
pages = {741-748},
doi = {10.4238/vol7-3gmr470},
pmid = {18767242},
issn = {1676-5680},
mesh = {Animals ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Moths/*classification/*genetics ; Saccharum ; },
abstract = {We reviewed the use and relevance of barcodes for insect studies and investigated the barcode sequence of Diatraea saccharalis. This sequence has a high level of homology (99%) with the barcode sequence of the Crambidae (Lepidoptera). The sequence data can be used to construct relationships between species, allowing a multidisciplinary approach for taxonomy, which includes morphological, molecular and distribution data, all of which are essential for the understanding of biodiversity. The D. saccharalis barcode is a previously undescribed sequence that could be used to analyze Lepidoptera biology.},
}
@article {pmid18758572,
year = {2008},
author = {Yeh, SL and Lin, ST and Tu, YC},
title = {Diffractive barcode using grating-dot lines.},
journal = {Optics letters},
volume = {33},
number = {17},
pages = {1942-1944},
doi = {10.1364/ol.33.001942},
pmid = {18758572},
issn = {0146-9592},
abstract = {Bar arrangements used by conventional diffractive barcodes are usually similar to those used by diffusive barcodes. We, however, propose a modified diffractive barcode with bar arrangements different from those used by diffusive barcodes. A modified diffractive barcode pattern is composed of many parallel grating-dot lines. When the grating-dot lines are scanned by a laser beam in sequence, different bright bar arrangements corresponding to different codes appear in sequence.},
}
@article {pmid18757756,
year = {2008},
author = {Song, H and Buhay, JE and Whiting, MF and Crandall, KA},
title = {Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {105},
number = {36},
pages = {13486-13491},
pmid = {18757756},
issn = {1091-6490},
mesh = {Animals ; Astacoidea/genetics ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; Gene Amplification/*genetics ; Grasshoppers/genetics ; Haplotypes ; Molecular Sequence Data ; Phylogeny ; Pseudogenes/*genetics ; },
abstract = {Nuclear mitochondrial pseudogenes (numts) are nonfunctional copies of mtDNA in the nucleus that have been found in major clades of eukaryotic organisms. They can be easily coamplified with orthologous mtDNA by using conserved universal primers; however, this is especially problematic for DNA barcoding, which attempts to characterize all living organisms by using a short fragment of the mitochondrial cytochrome c oxidase I (COI) gene. Here, we study the effect of numts on DNA barcoding based on phylogenetic and barcoding analyses of numt and mtDNA sequences in two divergent lineages of arthropods: grasshoppers and crayfish. Single individuals from both organisms have numts of the COI gene, many of which are highly divergent from orthologous mtDNA sequences, and DNA barcoding analysis incorrectly overestimates the number of unique species based on the standard metric of 3% sequence divergence. Removal of numts based on a careful examination of sequence characteristics, including indels, in-frame stop codons, and nucleotide composition, drastically reduces the incorrect inferences of the number of unique species, but even such rigorous quality control measures fail to identify certain numts. We also show that the distribution of numts is lineage-specific and the presence of numts cannot be known a priori. Whereas DNA barcoding strives for rapid and inexpensive generation of molecular species tags, we demonstrate that the presence of COI numts makes this goal difficult to achieve when numts are prevalent and can introduce serious ambiguity into DNA barcoding.},
}
@article {pmid18723126,
year = {2008},
author = {Rooney, JP and Patil, A and Zappala, MR and Conklin, DS and Cunningham, RP and Begley, TJ},
title = {A molecular bar-coded DNA repair resource for pooled toxicogenomic screens.},
journal = {DNA repair},
volume = {7},
number = {11},
pages = {1855-1868},
pmid = {18723126},
issn = {1568-7864},
support = {R01 ES015037/ES/NIEHS NIH HHS/United States ; K22 ES012251/ES/NIEHS NIH HHS/United States ; K22 ES012251-01/ES/NIEHS NIH HHS/United States ; GM 46312/GM/NIGMS NIH HHS/United States ; R01 GM046312/GM/NIGMS NIH HHS/United States ; 1C06 RR 0154464/RR/NCRR NIH HHS/United States ; R01 ES015037-01/ES/NIEHS NIH HHS/United States ; 1R01 ES 015037/ES/NIEHS NIH HHS/United States ; },
mesh = {Base Sequence ; Biotechnology/*instrumentation/methods ; *DNA Repair ; Escherichia coli/metabolism ; Gene Deletion ; *Genetic Techniques ; Models, Biological ; Models, Genetic ; Molecular Sequence Data ; *Mutation ; Oligonucleotide Array Sequence Analysis ; Saccharomyces cerevisiae/genetics ; Sequence Homology, Nucleic Acid ; Signal Transduction ; Toxicogenetics/*instrumentation/*methods ; },
abstract = {DNA damage from exogenous and endogenous sources can promote mutations and cell death. Fortunately, cells contain DNA repair and damage signaling pathways to reduce the mutagenic and cytotoxic effects of DNA damage. The identification of specific DNA repair proteins and the coordination of DNA repair pathways after damage has been a central theme to the field of genetic toxicology and we have developed a tool for use in this area. We have produced 99 molecular bar-coded Escherichia coli gene-deletion mutants specific to DNA repair and damage signaling pathways, and each bar-coded mutant can be tracked in pooled format using bar-code specific microarrays. Our design adapted bar-codes developed for the Saccharomyces cerevisiae gene-deletion project, which allowed us to utilize an available microarray product for pooled gene-exposure studies. Microarray-based screens were used for en masse identification of individual mutants sensitive to methyl methanesulfonate (MMS). As expected, gene-deletion mutants specific to direct, base excision, and recombinational DNA repair pathways were identified as MMS-sensitive in our pooled assay, thus validating our resource. We have demonstrated that molecular bar-codes designed for S. cerevisiae are transferable to E. coli, and that they can be used with pre-existing microarrays to perform competitive growth experiments. Further, when comparing microarray to traditional plate-based screens both overlapping and distinct results were obtained, which is a novel technical finding, with discrepancies between the two approaches explained by differences in output measurements (DNA content versus cell mass). The microarray-based classification of Deltatag and DeltadinG cells as depleted after MMS exposure, contrary to plate-based methods, led to the discovery that Deltatag and DeltadinG cells show a filamentation phenotype after MMS exposure, thus accounting for the discrepancy. A novel biological finding is the observation that while DeltadinG cells filament in response to MMS they exhibit wild-type sulA expression after exposure. This decoupling of filamentation from SulA levels suggests that DinG is associated with the SulA-independent filamentation pathway.},
}
@article {pmid18716001,
year = {2008},
author = {Smith, MA and Rodriguez, JJ and Whitfield, JB and Deans, AR and Janzen, DH and Hallwachs, W and Hebert, PD},
title = {Extreme diversity of tropical parasitoid wasps exposed by iterative integration of natural history, DNA barcoding, morphology, and collections.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {105},
number = {34},
pages = {12359-12364},
pmid = {18716001},
issn = {1091-6490},
mesh = {Animals ; *Biodiversity ; Costa Rica ; DNA ; Data Collection/*methods ; Electronic Data Processing ; Genes, Insect ; *Host-Parasite Interactions ; Lepidoptera/parasitology ; Molecular Sequence Data ; Morphogenesis ; *Natural History ; Parasites ; Wasps/*classification/genetics ; },
abstract = {We DNA barcoded 2,597 parasitoid wasps belonging to 6 microgastrine braconid genera reared from parapatric tropical dry forest, cloud forest, and rain forest in Area de Conservación Guanacaste (ACG) in northwestern Costa Rica and combined these data with records of caterpillar hosts and morphological analyses. We asked whether barcoding and morphology discover the same provisional species and whether the biological entities revealed by our analysis are congruent with wasp host specificity. Morphological analysis revealed 171 provisional species, but barcoding exposed an additional 142 provisional species; 95% of the total is likely to be undescribed. These 313 provisional species are extraordinarily host specific; more than 90% attack only 1 or 2 species of caterpillars out of more than 3,500 species sampled. The most extreme case of overlooked diversity is the morphospecies Apanteles leucostigmus. This minute black wasp with a distinctive white wing stigma was thought to parasitize 32 species of ACG hesperiid caterpillars, but barcoding revealed 36 provisional species, each attacking one or a very few closely related species of caterpillars. When host records and/or within-ACG distributions suggested that DNA barcoding had missed a species-pair, or when provisional species were separated only by slight differences in their barcodes, we examined nuclear sequences to test hypotheses of presumptive species boundaries and to further probe host specificity. Our iterative process of combining morphological analysis, ecology, and DNA barcoding and reiteratively using specimens maintained in permanent collections has resulted in a much more fine-scaled understanding of parasitoid diversity and host specificity than any one of these elements could have produced on its own.},
}
@article {pmid18713065,
year = {2008},
author = {Call, DR and Orfe, L and Davis, MA and Lafrentz, S and Kang, MS},
title = {Impact of compounding error on strategies for subtyping pathogenic bacteria.},
journal = {Foodborne pathogens and disease},
volume = {5},
number = {4},
pages = {505-516},
pmid = {18713065},
issn = {1556-7125},
support = {N01-AI-30055/AI/NIAID NIH HHS/United States ; },
mesh = {Alleles ; Bacterial Typing Techniques/*methods ; DNA Probes ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field/methods ; Genes, Bacterial ; *Genetic Markers ; Listeria monocytogenes/classification/genetics ; Microspheres ; *Minisatellite Repeats ; Nucleic Acid Hybridization/*methods ; Polymerase Chain Reaction ; Salmonella enterica/classification/genetics ; Sensitivity and Specificity ; Species Specificity ; Vibrio parahaemolyticus/classification/genetics ; },
abstract = {Comparative-omics will identify a multitude of markers that can be used for intraspecific discrimination between strains of bacteria. It seems intuitive that with this plethora of markers we can construct higher resolution subtyping assays using discrete markers to define strain "barcodes." Unfortunately, with each new marker added to an assay, overall assay robustness declines because errors are compounded exponentially. For example, the difference in accuracy of strain classification for an assay with 60 markers will change from 99.9% to 54.7% when average probe accuracy declines from 99.999% to 99.0%. To illustrate this effect empirically, we constructed a 19 probe bead-array for subtyping Listeria monocytogenes and showed that despite seemingly reliable individual probe accuracy (>97%), our best classification results at the strain level were <75%. A more robust strategy would use as few markers as possible to achieve strain discrimination. Consequently, we developed two variable number of tandem repeat (VNTR) assays (Vibrio parahaemolyticus and L. monocytogenes) and demonstrate that these assays along with a published assay (Salmonella enterica) produce robust results when products were machine scored. The discriminatory ability with four to seven VNTR loci was comparable to pulsed-field gel electrophoresis. Passage experiments showed some instability with ca. 5% of passaged lines showing evidence for new alleles within 30 days (V. parahaemolyticus and S. enterica). Changes were limited to a single locus and allele so conservative rules can be used to determine strain matching. Most importantly, VNTRs appear robust and portable and can clearly discriminate between strains with relatively few loci thereby limiting effects of compounding error.},
}
@article {pmid18702402,
year = {2008},
author = {Hamilton, A and Wheeler, QD},
title = {Taxonomy and why history of science matters for science: a case study.},
journal = {Isis; an international review devoted to the history of science and its cultural influences},
volume = {99},
number = {2},
pages = {331-340},
doi = {10.1086/588691},
pmid = {18702402},
issn = {0021-1753},
mesh = {*Classification ; *DNA ; Historiography ; History, 20th Century ; Humans ; Philosophy ; Research/history ; Science/*history ; },
abstract = {The history of science often has difficulty connecting with science at the lab-bench level, raising questions about the value of history of science for science. This essay offers a case study from taxonomy in which lessons learned about particular failings of numerical taxonomy (phenetics) in the second half of the twentieth century bear on the new movement toward DNA barcoding. In particular, it argues that an unwillingness to deal with messy theoretical questions in both cases leads to important problems in the theory and practice of identifying taxa. This argument makes use of scientific and historical considerations in a way that the authors hope leads to convincing conclusions about the history of taxonomy as well as about its present practice.},
}
@article {pmid18685725,
year = {2008},
author = {Valdivia-Granda, W},
title = {The next meta-challenge for Bioinformatics.},
journal = {Bioinformation},
volume = {2},
number = {8},
pages = {358-362},
pmid = {18685725},
issn = {0973-2063},
abstract = {The direct sequencing of uncultivable organisms present in complex biological and environmental samples has opportunities to discover new life forms and metabolic processes. This transformational field, known as metagenomics, is generating massive amounts of molecular information that can overwhelm the performance of conventional analysis and visualization algorithms. Here, I briefly highlight some of the emerging challenges this new discipline presents to the computational biology community and point some of the opportunities to develop applications that can translate metagenomic information into biomedical, agricultural, environmental, and industrial applications.},
}
@article {pmid18665273,
year = {2008},
author = {Fazekas, AJ and Burgess, KS and Kesanakurti, PR and Graham, SW and Newmaster, SG and Husband, BC and Percy, DM and Hajibabaei, M and Barrett, SC},
title = {Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well.},
journal = {PloS one},
volume = {3},
number = {7},
pages = {e2802},
pmid = {18665273},
issn = {1932-6203},
mesh = {Computational Biology/methods ; DNA, Chloroplast/metabolism ; DNA, Mitochondrial/genetics ; DNA, Plant/chemistry ; DNA, Ribosomal/chemistry ; Genes, Plant ; Genetic Markers ; Genetic Variation ; *Genome, Plant ; *Models, Genetic ; Plants/metabolism ; Plastids/*chemistry/metabolism ; Reproducibility of Results ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {A universal barcode system for land plants would be a valuable resource, with potential utility in fields as diverse as ecology, floristics, law enforcement and industry. However, the application of plant barcoding has been constrained by a lack of consensus regarding the most variable and technically practical DNA region(s). We compared eight candidate plant barcoding regions from the plastome and one from the mitochondrial genome for how well they discriminated the monophyly of 92 species in 32 diverse genera of land plants (N = 251 samples). The plastid markers comprise portions of five coding (rpoB, rpoC1, rbcL, matK and 23S rDNA) and three non-coding (trnH-psbA, atpF-atpH, and psbK-psbI) loci. Our survey included several taxonomically complex groups, and in all cases we examined multiple populations and species. The regions differed in their ability to discriminate species, and in ease of retrieval, in terms of amplification and sequencing success. Single locus resolution ranged from 7% (23S rDNA) to 59% (trnH-psbA) of species with well-supported monophyly. Sequence recovery rates were related primarily to amplification success (85-100% for plastid loci), with matK requiring the greatest effort to achieve reasonable recovery (88% using 10 primer pairs). Several loci (matK, psbK-psbI, trnH-psbA) were problematic for generating fully bidirectional sequences. Setting aside technical issues related to amplification and sequencing, combining the more variable plastid markers provided clear benefits for resolving species, although with diminishing returns, as all combinations assessed using four to seven regions had only marginally different success rates (69-71%; values that were approached by several two- and three-region combinations). This performance plateau may indicate fundamental upper limits on the precision of species discrimination that is possible with DNA barcoding systems that include moderate numbers of plastid markers. Resolution to the contentious debate on plant barcoding should therefore involve increased attention to practical issues related to the ease of sequence recovery, global alignability, and marker redundancy in multilocus plant DNA barcoding systems.},
}
@article {pmid18654369,
year = {2007},
author = {Mirkovic, T and Foo, ML and Arsenault, AC and Fournier-Bidoz, S and Zacharia, NS and Ozin, GA},
title = {Hinged nanorods made using a chemical approach to flexible nanostructures.},
journal = {Nature nanotechnology},
volume = {2},
number = {9},
pages = {565-569},
doi = {10.1038/nnano.2007.250},
pmid = {18654369},
issn = {1748-3395},
mesh = {Crystallization/*methods ; Elasticity ; Macromolecular Substances/chemistry ; Materials Testing ; Metals/*chemistry ; Molecular Conformation ; Nanotechnology/*methods ; Nanotubes/*chemistry/*ultrastructure ; Particle Size ; Surface Properties ; },
abstract = {The fabrication of multifunctional nanomaterials and their subsequent use for novel applications in various branches of nanotechnology has been under intense scrutiny. Particularly in the area of nanomechanics, the design of multicomponent nanostructures with an integrated multifunctionality would enable the construction of building blocks for nanoscale analogues of macroscopic objects. Here, we introduce a new class of flexible nanostructures: metallic nanorods with polyelectrolyte hinges, synthesized using layer-by-layer electrostatic self-assembly of oppositely charged polyelectrolytes on barcode metal nanorods followed by segment-selective chemical etching. Nanorods with hinges that consist of one polyelectrolyte bilayer display considerable flexibility, but with a greater number of bilayers the flexibility of the hinge is significantly reduced. Magnetically induced bending about the polymer hinge is illustrated through the incorporation of nickel segments into the barcodes and the application of an external fluctuating magnetic field.},
}
@article {pmid18647655,
year = {2008},
author = {Mouhamadou, B and Carriconde, F and Gryta, H and Jargeat, P and Manzi, S and Gardes, M},
title = {Molecular evolution of mitochondrial ribosomal DNA in the fungal genus Tricholoma: barcoding implications.},
journal = {Fungal genetics and biology : FG &amp; B},
volume = {45},
number = {9},
pages = {1219-1226},
doi = {10.1016/j.fgb.2008.06.006},
pmid = {18647655},
issn = {1096-0937},
mesh = {Agaricales/chemistry/classification/*genetics/isolation &amp; purification ; Base Sequence ; DNA, Fungal/chemistry/genetics ; DNA, Mitochondrial/chemistry/*genetics ; DNA, Ribosomal/chemistry/*genetics ; *Evolution, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/chemistry/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; },
abstract = {The molecular evolution of the V6 and V9 domains of the mitochondrial SSU-rDNA was investigated to evaluate the use of these sequences for DNA barcodes in the Basidiomycota division. The PCR products from 27 isolates belonging to 11 Tricholoma species were sequenced. Both domains in the isolates belonging to the same species had identical sequences. All the species possess distinctive V9 sequences due to point mutations and insertion/deletion events. Secondary structures revealed that the insertion-deletion events occurred in regions not directly involved in the maintenance of the standard SSU-rRNA structure. The inserted sequences possess conserved motifs that enable their alignment among phylogenetically distant species. Hence, the V9 domain by displaying identical sequences within species, an adequate divergence level, easy amplification, and alignment represents an alternative molecular marker for the Basidiomycota division and opens the way for this sequence to be used as specific molecular markers of the fungal kingdom.},
}
@article {pmid18642605,
year = {2008},
author = {deWaard, JR and Ivanova, NV and Hajibabaei, M and Hebert, PD},
title = {Assembling DNA barcodes. Analytical protocols.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {410},
number = {},
pages = {275-293},
doi = {10.1007/978-1-59745-548-0_15},
pmid = {18642605},
issn = {1064-3745},
mesh = {Animals ; Biodiversity ; DNA, Mitochondrial/chemistry/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; },
abstract = {The Barcode of Life initiative represents an ambitious effort to develop an identification system for eukaryotic life based on the analysis of sequence diversity in short, standardized gene regions. Work is furthest advanced for members of the animal kingdom. In this case, a target gene region has been selected (cytochrome c oxidase I) and pilot studies have validated its effectiveness in species discovery and identification. Based on these positive results, there is now a growing effort to both gather barcode records on a large-scale for members of this kingdom and to identify target barcode regions for the other kingdoms of eukaryotes. In this chapter, we detail the protocols involved in the assembly of DNA barcode records for members of the animal kingdom, but many of these approaches are of more general application.},
}
@article {pmid18631297,
year = {2008},
author = {Tedersoo, L and Jairus, T and Horton, BM and Abarenkov, K and Suvi, T and Saar, I and Kõljalg, U},
title = {Strong host preference of ectomycorrhizal fungi in a Tasmanian wet sclerophyll forest as revealed by DNA barcoding and taxon-specific primers.},
journal = {The New phytologist},
volume = {180},
number = {2},
pages = {479-490},
doi = {10.1111/j.1469-8137.2008.02561.x},
pmid = {18631297},
issn = {1469-8137},
mesh = {Australia ; Biodiversity ; *DNA, Fungal ; DNA, Intergenic ; DNA, Ribosomal ; Magnoliopsida/*microbiology ; Mycorrhizae/*genetics ; Plant Roots/microbiology ; *Symbiosis ; Trees/microbiology ; },
abstract = {Ectomycorrhizal (ECM) symbiosis is a widespread plant nutrition strategy in Australia, especially in semiarid regions. This study aims to determine the diversity, community structure and host preference of ECM fungi in a Tasmanian wet sclerophyll forest. Ectomycorrhizal fungi were identified based on anatomotyping and rDNA internal transcribed spacer (ITS)-large subunit (LSU) sequence analysis using taxon-specific primers. Host tree roots were identified based on root morphology and length differences of the chloroplast trnL region. A total of 123 species of ECM fungi were recovered from root tips of Eucalyptus regnans (Myrtaceae), Pomaderris apetala (Rhamnaceae) and Nothofagus cunninghamii (Nothofagaceae). The frequency of two thirds of the most common ECM fungi from several lineages was significantly influenced by host species. The lineages of Cortinarius, Tomentella-Thelephora, Russula-Lactarius, Clavulina, Descolea and Laccaria prevailed in the total community and their species richness and relative abundance did not differ by host species. This study demonstrates that strongly host-preferring, though not directly specific, ECM fungi may dominate the below-ground community. Apart from the richness of Descolea, Tulasnella and Helotiales and the lack of Suillus-Rhizopogon and Amphinema-Tylospora, the ECM fungal diversity and phylogenetic community structure is similar to that in the Holarctic realm.},
}
@article {pmid18622398,
year = {2008},
author = {Yan, Z and Costanzo, M and Heisler, LE and Paw, J and Kaper, F and Andrews, BJ and Boone, C and Giaever, G and Nislow, C},
title = {Yeast Barcoders: a chemogenomic application of a universal donor-strain collection carrying bar-code identifiers.},
journal = {Nature methods},
volume = {5},
number = {8},
pages = {719-725},
doi = {10.1038/nmeth.1231},
pmid = {18622398},
issn = {1548-7105},
mesh = {Alleles ; Biological Assay/*methods ; Electronic Data Processing/*methods ; Gene Deletion ; *Genetic Techniques ; Genome, Fungal/*genetics ; Heterozygote ; RNA, Fungal/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Reproducibility of Results ; Saccharomyces cerevisiae/chemistry/*classification/drug effects/*genetics ; Sensitivity and Specificity ; },
abstract = {The ability to perform complex bioassays in parallel enables experiments that are otherwise impossible because of throughput and cost constraints. For example, highly parallel chemical-genetic screens using pooled collections of thousands of defined Saccharomyces cerevisiae gene deletion strains are feasible because each strain is bar-coded with unique DNA sequences. It is, however, time-consuming and expensive to individually bar-code individual strains. To provide a simple and general method of barcoding yeast collections, we built a set of donor strains, called Barcoders, with unique bar codes that can be systematically transferred to any S. cerevisiae collection. We applied this technology by generating a collection of bar-coded 'decreased abundance by mRNA perturbation' (DAmP) loss-of-function strains comprising 87.1% of all essential yeast genes. These experiments validate both the Barcoders and the DAmP strain collection as useful tools for genome-wide chemical-genetic assays.},
}
@article {pmid18619096,
year = {2008},
author = {Sun, PR and Wang, BH and Wu, F},
title = {A new method to guard inpatient medication safety by the implementation of RFID.},
journal = {Journal of medical systems},
volume = {32},
number = {4},
pages = {327-332},
pmid = {18619096},
issn = {0148-5598},
mesh = {Attitude of Health Personnel ; *Electronic Data Processing ; Humans ; Medication Errors/*prevention &amp; control ; *Patient Identification Systems ; Patient Satisfaction ; Pharmacy Service, Hospital ; Pilot Projects ; Point-of-Care Systems ; *Radio Waves ; },
abstract = {Since life is invaluable, the patient safety is always an important issue. How to reduce the malpractices and advance the patient safety is the primary goal of many countries. The current problem is that the hospitals cannot quickly and precisely identify the name of medicine, the position of patient and staff and the servicing time and dosage taken by patients. The application of Radio Frequency Identification (RFID) is rocketing in popularity as varieties of expanded uses. However, due to the investment consideration, there are few cases that practically implement such a technology in healthcare industries. This paper presents a Wisely Aware RFID Dosage (WARD) system, which based on an integration of barcodes and RFID tags, to demonstrate effective and safe patient care environment, for preventing the risk of medication error. Finally, through an evaluation of users' satisfaction, a reliability of 0.92 and a criterion-related validity of 0.82 show that this system is able to effectively construct the patient-safety-centric environment.},
}
@article {pmid18616062,
year = {2008},
author = {Foote, SO and Coleman, JR},
title = {Medication administration: the implementation process of bar-coding for medication administration to enhance medication safety.},
journal = {Nursing economic$},
volume = {26},
number = {3},
pages = {207-210},
pmid = {18616062},
issn = {0746-1739},
mesh = {Cost-Benefit Analysis ; *Electronic Data Processing ; Humans ; Medication Errors/*prevention &amp; control ; Organizational Objectives ; United States/epidemiology ; },
abstract = {Approximately 1.5 million Americans are injured each year because of medication errors. In hospitals alone medication errors cost the health system well over $3.5 billion per year. Nurses are at the frontline of medication administration accountability. A Bar Code Medication Administration application was implemented at a 300-bed community hospital. The creation of the process was spearheaded by a taskforce consisting of staff nurses, nursing and pharmacy administrators, and an IT representative. This group planned the implementation process, which included changes to medication policies and procedures, downtime procedures, workflow designs, planning for nursing training, and changes to medication delivery. The results from the pilot indicated that the bar-cod technology reduced medication errors by 80%.},
}
@article {pmid18615874,
year = {2008},
author = {Ariga, K and Hill, JP and Ji, Q},
title = {Biomaterials and biofunctionality in layered macromolecular assemblies.},
journal = {Macromolecular bioscience},
volume = {8},
number = {11},
pages = {981-990},
doi = {10.1002/mabi.200800102},
pmid = {18615874},
issn = {1616-5195},
mesh = {Biocompatible Materials/*chemistry ; Biomimetic Materials/*chemical synthesis/chemistry ; Macromolecular Substances/chemical synthesis/chemistry ; Nanotechnology ; },
abstract = {Recent research in the field of LbL assembly is summarized and categorized as fabrication, sensing, drug release/delivery, and cell technology. Special emphasis is given to topics such as cell-membrane-mimic assembly, fabrication of free-standing biomolecular structures including protein microtubes, detection of DNA adducts and reactive metabolites, DNA hybridization analysis, sensing of toxic and bio-active chemicals, entrapment of proteins and DNA, biocomponent carriers with barcode encoding, release and delivery of DNA plasmids, multiagent delivery, smart defense capsules and oxidation-resistant films, vector introduction to cells, patterned cell culturing and microfluidic microreactors, stem cell differentiation, cellular uptake and degradation, and control of cellular apoptosis.},
}
@article {pmid18613155,
year = {2008},
author = {Fournier-Bidoz, S and Jennings, TL and Klostranec, JM and Fung, W and Rhee, A and Li, D and Chan, WC},
title = {Facile and rapid one-step mass preparation of quantum-dot barcodes.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {47},
number = {30},
pages = {5577-5581},
doi = {10.1002/anie.200800409},
pmid = {18613155},
issn = {1521-3773},
mesh = {*Electronic Data Processing ; *Quantum Dots ; Spectrometry, Fluorescence ; },
}
@article {pmid18611171,
year = {2008},
author = {Maeda, N and Nishiyori, H and Nakamura, M and Kawazu, C and Murata, M and Sano, H and Hayashida, K and Fukuda, S and Tagami, M and Hasegawa, A and Murakami, K and Schroder, K and Irvine, K and Hume, D and Hayashizaki, Y and Carninci, P and Suzuki, H},
title = {Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer.},
journal = {BioTechniques},
volume = {45},
number = {1},
pages = {95-97},
doi = {10.2144/000112814},
pmid = {18611171},
issn = {0736-6205},
mesh = {*Expressed Sequence Tags ; *Gene Expression Profiling ; *Promoter Regions, Genetic ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA/*instrumentation ; *Transcription Initiation Site ; },
abstract = {CAGE (cap analysis of gene expression) is a method for identifying transcription start sites by sequencing the first 20 or 21 nucleotides from the 5' end of capped transcripts, allowing genome-wide promoter analyses to be performed. The potential of the CAGE as a form of expression profiling was limited previously by sequencing technology and the labor-intensive protocol. Here we describe an improved CAGE method for use with a next generation sequencer. This modified method allows the identification of the RNA source of each CAGE tag within a pooled library by introducing DNA tags (barcodes). The method not only drastically improves the sequencing capacity, but also contributes to savings in both time and budget. Additionally, this pooled CAGE tag method enables the dynamic changes in promoter usage and gene expression to be monitored.},
}
@article {pmid18590594,
year = {2008},
author = {Sinclair, CS and Gresens, SE},
title = {Discrimination of Cricotopus species (Diptera: Chironomidae) by DNA barcoding.},
journal = {Bulletin of entomological research},
volume = {98},
number = {6},
pages = {555-563},
doi = {10.1017/S0007485308005865},
pmid = {18590594},
issn = {1475-2670},
mesh = {Animals ; Chironomidae/*classification/genetics/growth &amp; development ; Classification/methods ; DNA, Mitochondrial/*chemistry ; Electron Transport Complex IV/chemistry/genetics ; Larva/anatomy &amp; histology/classification/genetics ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {Chironomids (Diptera) typically comprise the most abundant group of macroinvertebrates collected in water quality surveys. Species in the genus Cricotopus display a wide range of tolerance for manmade pollutants, making them excellent bioindicators. Unfortunately, the usefulness of Cricotopus is overshadowed by the difficulty of accurately identifying larvae using current morphological keys. Molecular approaches are now being used for identification and taxonomic resolution in many animal taxa. In this study, a sequence-based approach for the mitochondrial gene, cytochrome oxidase I (COI), was developed to facilitate identification of Cricotopus species collected from Baltimore area streams. Using unique COI sequence variations, we developed profiles for seven described Cricotopus sp., four described Orthocladius sp., one described Paratrichocladius sp. and one putative species of Cricotopus. In addition to providing an accurate method for identification of Cricotopus, this method will make a useful contribution to the development of keys for Nearctic Cricotopus.},
}
@article {pmid18573351,
year = {2008},
author = {Frézal, L and Leblois, R},
title = {Four years of DNA barcoding: current advances and prospects.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {8},
number = {5},
pages = {727-736},
doi = {10.1016/j.meegid.2008.05.005},
pmid = {18573351},
issn = {1567-1348},
mesh = {Animals ; Classification/*methods ; DNA Fingerprinting/*methods/standards/*trends ; DNA, Mitochondrial/analysis/genetics ; Electronic Data Processing/*methods/standards/*trends ; Sequence Analysis, DNA/methods/standards/trends ; Species Specificity ; },
abstract = {Research using cytochrome c oxidase barcoding techniques on zoological specimens was initiated by Hebert et al. [Hebert, P.D.N., Ratnasingham, S., deWaard, J.R., 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. R. Soc. Lond. B 270, S96-S99]. By March 2004, the Consortium for the Barcode of Life started to promote the use of a standardized DNA barcoding approach, consisting of identifying a specimen as belonging to a certain animal species based on a single universal marker: the DNA barcode sequence. Over the last 4 years, this approach has become increasingly popular and advances as well as limitations have clearly emerged as increasing amounts of organisms have been studied. Our purpose is to briefly expose DNA Barcode of Life principles, pros and cons, relevance and universality. The initially proposed Barcode of life framework has greatly evolved, giving rise to a flexible description of DNA barcoding and a larger range of applications.},
}
@article {pmid18544153,
year = {2008},
author = {Kane, RA and Stothard, JR and Emery, AM and Rollinson, D},
title = {Molecular characterization of freshwater snails in the genus Bulinus: a role for barcodes?.},
journal = {Parasites &amp; vectors},
volume = {1},
number = {1},
pages = {15},
pmid = {18544153},
issn = {1756-3305},
abstract = {BACKGROUND: Reliable and consistent methods are required for the identification and classification of freshwater snails belonging to the genus Bulinus (Gastropoda, Planorbidae) which act as intermediate hosts for schistosomes of both medical and veterinary importance. The current project worked towards two main objectives, the development of a cost effective, simple screening method for the routine identification of Bulinus isolates and the use of resultant sequencing data to produce a model of relationships within the group.<br><br>RESULTS: Phylogenetic analysis of the DNA sequence for a large section (1009 bp) of the mitochondrial gene cytochrome oxidase subunit 1 (cox1) for isolates of Bulinus demonstrated superior resolution over that employing the second internal transcribed spacer (its2) of the ribosomal gene complex. Removal of transitional substitutions within cox1 because of saturation effects still allowed identification of snails at species group level. Within groups, some species could be identified with ease but there were regions where the high degree of molecular diversity meant that clear identification of species was problematic, this was particularly so within the B. africanus group.<br><br>CONCLUSION: The sequence diversity within cox1 is such that a barcoding approach may offer the best method for characterization of populations and species within the genus from different geographical locations. The study has confirmed the definition of some accepted species within the species groups but additionally has revealed some unrecognized isolates which underlines the need to use molecular markers in addition to more traditional methods of identification. A barcoding approach based on part of the cox1 gene as defined by the Folmer primers is proposed.},
}
@article {pmid18522916,
year = {2008},
author = {Papadopoulou, A and Bergsten, J and Fujisawa, T and Monaghan, MT and Barraclough, TG and Vogler, AP},
title = {Speciation and DNA barcodes: testing the effects of dispersal on the formation of discrete sequence clusters.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {363},
number = {1506},
pages = {2987-2996},
pmid = {18522916},
issn = {1471-2970},
support = {BBS/B/04358//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animal Migration ; Animals ; Base Sequence/genetics ; Coleoptera/*genetics ; Computer Simulation ; DNA, Mitochondrial/*genetics ; *Demography ; Europe ; *Genetic Speciation ; *Genetic Variation ; *Genetics, Population ; Geography ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Large-scale sequencing of short mtDNA fragments for biodiversity inventories ('DNA barcoding') indicates that sequence variation in animal mtDNA is highly structured and partitioned into discrete genetic clusters that correspond broadly to species-level entities. Here we explore how the migration rate, an important demographic parameter that is directly related to population isolation, might affect variation in the strength of mtDNA clustering among taxa. Patterns of mtDNA variation were investigated in two groups of beetles that both contain lineages occupying habitats predicted to select for different dispersal abilities: predacious diving beetles (Dytiscidae) in the genus Bidessus from lotic and lentic habitats across Europe and darkling beetles (Tenebrionidae) in the genus Eutagenia from sand and other soil types in the Aegean Islands. The degree of genetic clustering was determined using the recently developed 'mixed Yule coalescent' (MYC) model that detects the transition from between-species to within-population branching patterns. Lineages from presumed stable habitats, and therefore displaying lower dispersal ability and migration rates, showed greater levels of mtDNA clustering and geographical subdivision than their close relatives inhabiting ephemeral habitats. Simulations of expected patterns of mtDNA variation under island models showed that MYC clusters are only detected when the migration rates are much lower than the value of Nm=1 typically used to define the threshold for neutral genetic divergence. Therefore, discrete mtDNA clusters provide strong evidence for independently evolving populations or species, but their formation is suppressed even under very low levels of dispersal.},
}
@article {pmid18510425,
year = {2008},
author = {Kim, EY and Stanton, J and Korber, BT and Krebs, K and Bogdan, D and Kunstman, K and Wu, S and Phair, JP and Mirkin, CA and Wolinsky, SM},
title = {Detection of HIV-1 p24 Gag in plasma by a nanoparticle-based bio-barcode-amplification method.},
journal = {Nanomedicine (London, England)},
volume = {3},
number = {3},
pages = {293-303},
pmid = {18510425},
issn = {1748-6963},
support = {R01 AI052764/AI/NIAID NIH HHS/United States ; R01 AI052764-03/AI/NIAID NIH HHS/United States ; U01 AI061297/AI/NIAID NIH HHS/United States ; U01 AI061297-01/AI/NIAID NIH HHS/United States ; },
mesh = {Biological Assay/methods ; Blood Chemical Analysis/*methods ; HIV Core Protein p24/*blood ; HIV Infections/*blood ; Humans ; Immunoassay/*methods ; *Immunomagnetic Separation ; Nanoparticles/*chemistry/*ultrastructure ; Nucleic Acid Amplification Techniques/methods ; },
abstract = {BACKGROUND: Detection of HIV-1 in patients is limited by the sensitivity and selectivity of available tests. The nanotechnology-based bio-barcode-amplification method offers an innovative approach to detect specific HIV-1 antigens from diverse HIV-1 subtypes. We evaluated the efficacy of this protein-detection method in detecting HIV-1 in men enrolled in the Chicago component of the Multicenter AIDS Cohort Study (MACS).<br><br>METHODS: The method relies on magnetic microparticles with antibodies that specifically bind the HIV-1 p24 Gag protein and nanoparticles that are encoded with DNA and antibodies that can sandwich the target protein captured by the microparticle-bound antibodies. The aggregate sandwich structures are magnetically separated from solution, and treated to remove the conjugated barcode DNA. The DNA barcodes (hundreds per target) were identified by a nanoparticle-based detection method that does not rely on PCR.<br><br>RESULTS: Of 112 plasma samples from HIV-1-infected subjects, 111 were positive for HIV-1 p24 Gag protein (range: 0.11-71.5 ng/ml of plasma) by the bio-barcode-amplification method. HIV-1 p24 Gag protein was detected in only 23 out of 112 men by the conventional ELISA. A total of 34 uninfected subjects were negative by both tests. Thus, the specificity of the bio-barcode-amplification method was 100% and the sensitivity 99%. The bio-barcode-amplification method detected HIV-1 p24 Gag protein in plasma from all study subjects with less than 200 CD4(+) T cells/microl of plasma (100%) and 19 out of 20 (95%) HIV-1-infected men who had less than 50 copies/ml of plasma of HIV-1 RNA. In a separate group of 60 diverse international isolates, representative of clades A, B, C and D and circulating recombinant forms CRF01_AE and CRF02_AG, the bio-barcode-amplification method identified the presence of virus correctly.<br><br>CONCLUSIONS: The bio-barcode-amplification method was superior to the conventional ELISA assay for the detection of HIV-1 p24 Gag protein in plasma with a breadth of coverage for diverse HIV-1 subtypes. Because the bio-barcode-amplification method does not require enzymatic amplification, this method could be translated into a robust point-of-care test.},
}
@article {pmid18509544,
year = {2008},
author = {Fisher, BL and Smith, MA},
title = {A revision of Malagasy species of Anochetus mayr and Odontomachus latreille (Hymenoptera: Formicidae).},
journal = {PloS one},
volume = {3},
number = {5},
pages = {e1787},
pmid = {18509544},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Behavior, Animal ; DNA Primers ; Female ; Hymenoptera/anatomy &amp; histology/*classification ; Madagascar ; Male ; Species Specificity ; },
abstract = {Species inventories are essential for documenting global diversity and generating necessary material for taxonomic study and conservation planning. However, for inventories to be immediately relevant, the taxonomic process must reduce the time to describe and identify specimens. To address these concerns for the inventory of arthropods across the Malagasy region, we present here a collaborative approach to taxonomy where collectors, morphologists and DNA barcoders using cytochrome c oxidase 1 (CO1) participate collectively in a team-driven taxonomic process. We evaluate the role of DNA barcoding as a tool to accelerate species identification and description. This revision is primarily based on arthropod surveys throughout the Malagasy region from 1992 to 2006. The revision is based on morphological and CO1 DNA barcode analysis of 500 individuals. In the region, five species of Anochetus (A. boltonisp. nov., A. goodmanisp. nov., A. grandidieri, and A. madagascarensis from Madagascar, and A. pattersonisp. nov. from Seychelles) and three species of Odontomachus (O. coquereli, O. troglodytes and O. simillimus) are recognized. DNA barcoding (using cytochrome c oxidase 1 (CO1)) facilitated caste association and type designation, and highlighted population structure associated with reproductive strategy, biogeographic and evolutionary patterns for future exploration. This study provides an example of collaborative taxonomy, where morphology is combined with DNA barcoding. We demonstrate that CO1 DNA barcoding is a practical tool that allows formalized alpha-taxonomy at a speed, detail, precision, and scale unattainable by employing morphology alone.},
}
@article {pmid18490947,
year = {2007},
author = {Geiser, DM and Klich, MA and Frisvad, JC and Peterson, SW and Varga, J and Samson, RA},
title = {The current status of species recognition and identification in Aspergillus.},
journal = {Studies in mycology},
volume = {59},
number = {},
pages = {1-10},
pmid = {18490947},
issn = {0166-0616},
abstract = {The species recognition and identification of aspergilli and their teleomorphs is discussed. A historical overview of the taxonomic concepts starting with the monograph of Raper &amp; Fennell (1965) is given. A list of taxa described since 2000 is provided. Physiological characters, particularly growth rates and the production of extrolites, often show differences that reflect phylogenetic species boundaries and greater emphasis should be placed on extrolite profiles and growth characteristics in species descriptions. Multilocus sequence-based phylogenetic analyses have emerged as the primary tool for inferring phylogenetic species boundaries and relationships within subgenera and sections. A four locus DNA sequence study covering all major lineages in Aspergillus using genealogical concordance theory resulted in a species recognition system that agrees in part with phenotypic studies and reveals the presence of many undescribed species not resolved by phenotype. The use of as much data from as many sources as possible in making taxonomic decisions is advocated. For species identification, DNA barcoding uses a short genetic marker in an organism"s DNA to quickly and easily identify it to a particular species. Partial cytochrome oxidase subunit 1 sequences, which are used for barcoding animal species, were found to have limited value for species identification among black aspergilli. The various possibilities are discussed and at present partial beta-tubulin or calmodulin are the most promising loci for Aspergillus identification. For characterising Aspergillus species one application would be to produce a multilocus phylogeny, with the goal of having a firm understanding of the evolutionary relationships among species across the entire genus. DNA chip technologies are discussed as possibilities for an accurate multilocus barcoding tool for the genus Aspergillus.},
}
@article {pmid18481863,
year = {2008},
author = {Zhu, S and Fushimi, H and Komatsu, K},
title = {Development of a DNA microarray for authentication of ginseng drugs based on 18S rRNA gene sequence.},
journal = {Journal of agricultural and food chemistry},
volume = {56},
number = {11},
pages = {3953-3959},
doi = {10.1021/jf0732814},
pmid = {18481863},
issn = {0021-8561},
mesh = {Base Sequence ; Oligonucleotide Array Sequence Analysis/*methods ; Panax/*genetics ; Plant Preparations/classification ; RNA, Ribosomal, 18S/*genetics ; },
abstract = {Ginseng drugs, derived from underground parts of Panax species (Araliaceae), are the most important group of herbal medicines in the Orient. Previously, the nucleotide sequences of the nuclear 18S rRNA gene of 13 Panax taxa were determined, as were the specific polymorphic nucleotides for identification of each species. On the basis of the nucleotide difference, a DNA microarray (PNX array) was developed for the identification of various Panax plants and drugs. Thirty-five kinds of specific oligonucleotide were designed and synthesized as probes spotting on a decorated glass slide, which included 33 probes corresponding to the species-specific nucleotide substitutions and 2 probes as positive and negative controls. The species-specific probes were of 23-26 bp in length, in which the substitution nucleotide was located at the central part. Triplicate probes were spotted to warrant accuracy by correcting variation of fluorescent intensity. Partial 18S rRNA gene sequences amplified from Panax plants and drugs as well as their derived health foods were fluorescently labeled as targets to hybridize to the PNX array. After hybridization under optimal condition, specific fluorescent patterns were detected for each Panax species, and the analyzed results could be indicated as barcode patterns for quick distinction. The developed PNX array provided an objective and reliable method for the authentication of Panax plants and drugs as well as their derived health foods.},
}
@article {pmid18474098,
year = {2008},
author = {Meusnier, I and Singer, GA and Landry, JF and Hickey, DA and Hebert, PD and Hajibabaei, M},
title = {A universal DNA mini-barcode for biodiversity analysis.},
journal = {BMC genomics},
volume = {9},
number = {},
pages = {214},
pmid = {18474098},
issn = {1471-2164},
mesh = {Animals ; Base Sequence ; *Biodiversity ; Computational Biology ; DNA/*genetics ; DNA Primers/genetics ; Databases, Nucleic Acid ; Electron Transport Complex IV/genetics ; Eukaryotic Cells ; Gene Library ; Genomics/methods ; Polymerase Chain Reaction ; Species Specificity ; },
abstract = {BACKGROUND: The goal of DNA barcoding is to develop a species-specific sequence library for all eukaryotes. A 650 bp fragment of the cytochrome c oxidase 1 (CO1) gene has been used successfully for species-level identification in several animal groups. It may be difficult in practice, however, to retrieve a 650 bp fragment from archival specimens, (because of DNA degradation) or from environmental samples (where universal primers are needed).<br><br>RESULTS: We used a bioinformatics analysis using all CO1 barcode sequences from GenBank and calculated the probability of having species-specific barcodes for varied size fragments. This analysis established the potential of much smaller fragments, mini-barcodes, for identifying unknown specimens. We then developed a universal primer set for the amplification of mini-barcodes. We further successfully tested the utility of this primer set on a comprehensive set of taxa from all major eukaryotic groups as well as archival specimens.<br><br>CONCLUSION: In this study we address the important issue of minimum amount of sequence information required for identifying species in DNA barcoding. We establish a novel approach based on a much shorter barcode sequence and demonstrate its effectiveness in archival specimens. This approach will significantly broaden the application of DNA barcoding in biodiversity studies.},
}
@article {pmid18471978,
year = {2008},
author = {Li, F and Dong, J and Pan, X and Oum, JH and Boeke, JD and Lee, SE},
title = {Microarray-based genetic screen defines SAW1, a gene required for Rad1/Rad10-dependent processing of recombination intermediates.},
journal = {Molecular cell},
volume = {30},
number = {3},
pages = {325-335},
pmid = {18471978},
issn = {1097-4164},
support = {U54 RR020839/RR/NCRR NIH HHS/United States ; RR020839/RR/NCRR NIH HHS/United States ; HG02432/HG/NHGRI NIH HHS/United States ; R01 GM071011-04/GM/NIGMS NIH HHS/United States ; R01 GM071011/GM/NIGMS NIH HHS/United States ; R01 HG002432/HG/NHGRI NIH HHS/United States ; GM071011/GM/NIGMS NIH HHS/United States ; },
mesh = {Base Sequence ; DNA Damage ; *DNA Repair ; DNA Repair Enzymes/genetics/metabolism ; DNA, Ribosomal/genetics/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Endonucleases/genetics/metabolism ; Gene Expression Regulation, Fungal ; MutS Homolog 2 Protein/genetics/metabolism ; Mutation ; *Oligonucleotide Array Sequence Analysis ; Plasmids/genetics/metabolism ; Rad52 DNA Repair and Recombination Protein/genetics/metabolism ; *Recombination, Genetic ; Saccharomyces cerevisiae/genetics/metabolism ; *Saccharomyces cerevisiae Proteins/genetics/metabolism ; Single-Strand Specific DNA and RNA Endonucleases ; Two-Hybrid System Techniques ; },
abstract = {Elimination of a double-strand break (DSB) flanked by direct repeat sequences is mediated by single-strand annealing (SSA), which relies on a distinct set of gene products involving recombination, mismatch repair, and nucleotide excision repair. Here, we screened for yeast mutants defective in SSA with a plasmid-based SSA assay coupled to a barcode microarray readout. The screen identified Yal027Wp/Saw1 (single-strand annealing weakened 1) and Slx4 besides other known SSA proteins. Saw1 interacts physically with Rad1/Rad10, Msh2/Msh3, and Rad52 proteins, and cells lacking SLX4 or SAW1 accumulate recombination intermediates blocked at the Rad1/Rad10-dependent 3' flap cleavage step. Slx4 and Saw1 also contribute to the integrity of ribosomal DNA arrays. Saw1 mutants that fail to interact with Rad1, but retain interaction with Rad52 and Msh2, are defective in 3' flap removal and SSA repair. Deletion of SAW1 abolished association of Rad1 at SSA intermediates in vivo. We propose that Saw1 targets Rad1/Rad10 to Rad52-coated recombination intermediates.},
}
@article {pmid18461978,
year = {2008},
author = {Kim, K and Lee, HB and Shin, KS},
title = {Silanization of polyelectrolyte-coated particles: an effective route to stabilize Raman tagging molecules adsorbed on micrometer-sized silver particles.},
journal = {Langmuir : the ACS journal of surfaces and colloids},
volume = {24},
number = {11},
pages = {5893-5898},
doi = {10.1021/la800251t},
pmid = {18461978},
issn = {0743-7463},
abstract = {Micrometer-sized Ag (microAg) powders are very efficient surface-enhanced Raman scattering (SERS) substrates. To use microAg powders as a core material for molecular sensors operating via SERS, it is necessary to stabilize the tagging (i.e., SERS-marker) molecules adsorbed onto them. We demonstrate in this work that once the tagging molecules are coated with aliphatic polyelectrolytes such as poly(allylamine hydrochloride), the base-catalyzed silanization can be readily carried out to form stable silica shells around the polyelectrolyte layers by a biomimetic process; any particle can therefore be coated with silica since polyelectrolytes can be deposited beforehand via a layer-by-layer deposition method. Even after silanization, the SERS peaks of marker molecules on microAg particles are the only observable peaks since aliphatic polyelectrolytes, as well as silica shells, are intrinsically weak Raman scatterers, and more importantly, the SERS signals must be derived mostly from the first layer of the adsorbates (i.e., the marker molecules) in direct contact with the microAg particles. Silica shells, once fabricated, can further be derivatized to possess biofunctional groups; therefore, the modified microAg particles can be used as platforms of highly stable SERS-based biological sensors, as well as barcoding materials.},
}
@article {pmid18459420,
year = {2008},
author = {Ball, SL and Armstrong, KF},
title = {Rapid, one-step DNA extraction for insect pest identification by using DNA barcodes.},
journal = {Journal of economic entomology},
volume = {101},
number = {2},
pages = {523-532},
doi = {10.1603/0022-0493(2008)101[523:rodefi]2.0.co;2},
pmid = {18459420},
issn = {0022-0493},
mesh = {Animals ; DNA/*isolation &amp; purification ; Insecta/*classification/*genetics ; Oligonucleotide Probes ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
abstract = {Early detection of economically important insects is critical to preventing their establishment as serious pests. To accomplish this, tools for rapid and accurate species identification are needed. DNA barcoding, using short DNA sequences as species "genetic identification tags," has already shown large potential as a tool for rapid and accurate detection of economically important insects. DNA extraction is the critical first step in generating DNA barcodes and can be a rate-limiting step in very large barcoding studies. Consequently, a DNA extraction method that is rapid, easy to use, cost-effective, robust enough to cope with range of qualities and quantities of tissue, and can be adapted to robotic systems will provide the best method for high-throughput production of DNA barcodes. We tested the performance of a new commercial kit (prepGEM), which uses a novel, streamlined approach to DNA extraction, and we compared it with two other commercial kits (ChargeSwitch and Aquapure), which differ in their method of DNA extraction. We compared performance of these kits by measuring percentage of polymerase chain reaction (PCR) success and mean PCR product yield across a variety of arthropod taxa, whichincluded freshly collected, ethanol-preserved, and dried specimens of different ages. ChargeSwitch and prepGEM performed equally well, but they outperformed Aquapure. prepGEM was much faster, easier to use, and cheaper than ChargeSwitch, but ChargeSwitch performed slightly better for older (> 5-yr-old) dried insect specimens. Overall, prepGEM may provide a highly streamlined method of DNA extraction for fresh, ethanol-preserved, and young, dried specimens, especially when adapted for high-throughput, robotic systems.},
}
@article {pmid18449847,
year = {2008},
author = {Sucher, NJ and Carles, MC},
title = {Genome-based approaches to the authentication of medicinal plants.},
journal = {Planta medica},
volume = {74},
number = {6},
pages = {603-623},
doi = {10.1055/s-2008-1074517},
pmid = {18449847},
issn = {0032-0943},
mesh = {*Genetic Techniques ; *Genome, Plant ; Herbal Medicine/*standards ; Plants, Medicinal/classification/*genetics ; },
abstract = {Medicinal plants are the source of a large number of essential drugs in Western medicine and are the basis of herbal medicine, which is not only the primary source of health care for most of the world's population living in developing countries but also enjoys growing popularity in developed countries. The increased demand for botanical products is met by an expanding industry and accompanied by calls for assurance of quality, efficacy and safety. Plants used as drugs, dietary supplements and herbal medicines are identified at the species level. Unequivocal identification is a critical step at the beginning of an extensive process of quality assurance and is of importance for the characterization of the genetic diversity, phylogeny and phylogeography as well as the protection of endangered species. DNA-based methods have been developed for the identification of medicinal plants. Nuclear and chloroplast DNA is amplified by the polymerase chain reaction and the reaction products are analyzed by gel electrophoresis, sequencing, or hybridization with species-specific probes. Genomic fingerprinting can differentiate between individuals, species and populations and is useful for the detection of the homogeneity of the samples and presence of adulterants. Although sequences from single chloroplast or nuclear genes have been useful for differentiation of species, phylogenetic studies often require consideration of DNA sequence data from more than one gene or genomic region. Phytochemical and genetic data are correlated but only the latter normally allow for differentiation at the species level. The generation of molecular "barcodes" of medicinal plants will be worth the concerted effort of the medicinal plant research community and contribute to the ongoing effort of defining barcodes for every species on earth.},
}
@article {pmid18442929,
year = {2008},
author = {Wheat, CW and Watt, WB},
title = {A mitochondrial-DNA-based phylogeny for some evolutionary-genetic model species of Colias butterflies (Lepidoptera, Pieridae).},
journal = {Molecular phylogenetics and evolution},
volume = {47},
number = {3},
pages = {893-902},
doi = {10.1016/j.ympev.2008.03.013},
pmid = {18442929},
issn = {1055-7903},
mesh = {Aging/genetics ; Animals ; Base Sequence ; Butterflies/enzymology/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Genetic Variation ; Likelihood Functions ; *Models, Genetic ; North America ; *Phylogeny ; Population Dynamics ; Sequence Analysis, DNA ; Wings, Animal/anatomy &amp; histology ; },
abstract = {We study the phylogenetic relationships among some North American Colias ("sulfur") butterflies, using mitochondrial gene sequences (ribosomal RNA, cytochrome oxidase I+II) totaling about 20% of the mitochondrial genome. We find that (1) the lowland species complex shows a branching order different from earlier views; (2) several montane and northern taxa may be more distinct than in earlier views; (3) one morphologically conservative Holarctic assemblage, C. hecla, is differentiated at the molecular-genetic level into at least three taxa which occupy distinct positions in the phylogeny and are sisters to diverse other taxa. These conclusions, constituting phylogenetic hypotheses, are supported by parsimony, maximum-likelihood, and Bayesian reconstruction algorithms. They are tested formally, by interior branch tests and paired-site tests, against alternative hypotheses derived from conventional species and subspecies naming combinations. In all cases our hypotheses are supported by these tests and the conventional alternatives are rejected. The "barcoding" subset of cytochrome oxidase I sequence identifies only some of the taxa supported by our full data set. Comparison of genetic divergence values among Colias taxa with those among related Pierid butterflies suggests that species radiations within Colias are comparatively younger. This emerging Colias phylogeny facilitates comparisons of genetic polymorphism and other adaptive mechanisms among taxa, thereby connecting micro- and macro-evolutionary processes.},
}
@article {pmid18440653,
year = {2008},
author = {He, M and Li, K and Xiao, J and Zhou, Y},
title = {Rapid bio-barcode assay for multiplex DNA detection based on capillary DNA Analyzer.},
journal = {Journal of virological methods},
volume = {151},
number = {1},
pages = {126-131},
doi = {10.1016/j.jviromet.2008.03.005},
pmid = {18440653},
issn = {0166-0934},
mesh = {DNA, Viral/*analysis/isolation &amp; purification ; Ebolavirus/genetics ; Gold/*analysis ; HIV-1/genetics ; Hepatitis B Surface Antigens/genetics ; Humans ; Magnetics ; Metal Nanoparticles/*analysis ; Nucleic Acid Amplification Techniques/*instrumentation/*methods ; Oligonucleotide Probes/genetics ; *Reagent Kits, Diagnostic ; Sensitivity and Specificity ; Sodium Chloride ; Time Factors ; Variola virus/genetics ; },
abstract = {The detection of virus at low copy number is important for clinical diagnosis. In this study, a rapid bio-barcode assay was developed and it could detect short sequences of four types of virus DNA simultaneously at the concentration as low as 5p mol/L in 40 min with capillary 3730 DNA Analyzer. The background of the assay using high salt concentration prepared nanogold particle probes was five times less than that of the assay using conventionally prepared probes. With further optimization, the specificity of the complementary strands to the noncomplementary strands observed in the assay approached 140:1. Compared with the conventional bio-barcode assay, the current assay provides an alternative enzyme and labor-free selection of timesaving, better sensitivity and specificity, as well as higher throughput.},
}
@article {pmid18436903,
year = {2008},
author = {Koppel, R and Wetterneck, T and Telles, JL and Karsh, BT},
title = {Workarounds to barcode medication administration systems: their occurrences, causes, and threats to patient safety.},
journal = {Journal of the American Medical Informatics Association : JAMIA},
volume = {15},
number = {4},
pages = {408-423},
pmid = {18436903},
issn = {1067-5027},
support = {1-UC1 HS014253-01/HS/AHRQ HHS/United States ; P01 HS11530-01/HS/AHRQ HHS/United States ; 1 K12-RR01764-01/RR/NCRR NIH HHS/United States ; UC1 HS014253/HS/AHRQ HHS/United States ; P01 HS011530/HS/AHRQ HHS/United States ; },
mesh = {Clinical Pharmacy Information Systems/organization &amp; administration ; *Electronic Data Processing ; Humans ; Interviews as Topic ; Medical Records Systems, Computerized/organization &amp; administration ; Medication Errors/*prevention &amp; control ; *Medication Systems, Hospital/organization &amp; administration ; Nursing Process ; Nursing Staff, Hospital ; Point-of-Care Systems ; Task Performance and Analysis ; },
abstract = {The authors develop a typology of clinicians' workarounds when using barcoded medication administration (BCMA) systems. Authors then identify the causes and possible consequences of each workaround. The BCMAs usually consist of handheld devices for scanning machine-readable barcodes on patients and medications. They also interface with electronic medication administration records. Ideally, BCMAs help confirm the five "rights" of medication administration: right patient, drug, dose, route, and time. While BCMAs are reported to reduce medication administration errors--the least likely medication error to be intercepted--these claims have not been clearly demonstrated. The authors studied BCMA use at five hospitals by: (1) observing and shadowing nurses using BCMAs at two hospitals, (2) interviewing staff and hospital leaders at five hospitals, (3) participating in BCMA staff meetings, (4) participating in one hospital's failure-mode-and-effects analyses, (5) analyzing BCMA override log data. The authors identified 15 types of workarounds, including, for example, affixing patient identification barcodes to computer carts, scanners, doorjambs, or nurses' belt rings; carrying several patients' prescanned medications on carts. The authors identified 31 types of causes of workarounds, such as unreadable medication barcodes (crinkled, smudged, torn, missing, covered by another label); malfunctioning scanners; unreadable or missing patient identification wristbands (chewed, soaked, missing); nonbarcoded medications; failing batteries; uncertain wireless connectivity; emergencies. The authors found nurses overrode BCMA alerts for 4.2% of patients charted and for 10.3% of medications charted. Possible consequences of the workarounds include wrong administration of medications, wrong doses, wrong times, and wrong formulations. Shortcomings in BCMAs' design, implementation, and workflow integration encourage workarounds. Integrating BCMAs within real-world clinical workflows requires attention to in situ use to ensure safety features' correct use.},
}
@article {pmid18436645,
year = {2008},
author = {Burns, JM and Janzen, DH and Hajibabaei, M and Hallwachs, W and Hebert, PD},
title = {DNA barcodes and cryptic species of skipper butterflies in the genus Perichares in Area de Conservacion Guanacaste, Costa Rica.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {105},
number = {17},
pages = {6350-6355},
pmid = {18436645},
issn = {1091-6490},
mesh = {Animals ; Butterflies/*genetics ; Costa Rica ; DNA/*metabolism ; Female ; Larva ; Male ; Phylogeny ; Pupa ; Species Specificity ; },
abstract = {DNA barcodes can be used to identify cryptic species of skipper butterflies previously detected by classic taxonomic methods and to provide first clues to the existence of yet other cryptic species. A striking case is the common geographically and ecologically widespread neotropical skipper butterfly Perichares philetes (Lepidoptera, Hesperiidae), described in 1775, which barcoding splits into a complex of four species in Area de Conservación Guanacaste (ACG) in northwestern Costa Rica. Three of the species are new, and all four are described. Caterpillars, pupae, and foodplants offer better distinguishing characters than do adults, whose differences are mostly average, subtle, and blurred by intraspecific variation. The caterpillars of two species are generalist grass-eaters; of the other two, specialist palm-eaters, each of which feeds on different genera. But all of these cryptic species are more specialized in their diet than was the morphospecies that held them. The four ACG taxa discovered to date belong to a panneotropical complex of at least eight species. This complex likely includes still more species, whose exposure may require barcoding. Barcoding ACG hesperiid morphospecies has increased their number by nearly 10%, an unexpectedly high figure for such relatively well known insects.},
}
@article {pmid18428218,
year = {2001},
author = {Smith, JH and Madan, D and Salhaney, J and Engelstein, M},
title = {Automation and robotics for genetic analysis.},
journal = {Current protocols in human genetics},
volume = {Appendix 2},
number = {},
pages = {Appendix 2E},
doi = {10.1002/0471142905.hga02es21},
pmid = {18428218},
issn = {1934-8258},
mesh = {Automation ; Chromosome Mapping ; DNA/analysis/genetics ; *Genetic Techniques ; Genetics, Medical ; Humans ; Polymerase Chain Reaction ; Robotics ; },
abstract = {This guide to laboratory robotics covers a wide variety of methods amenable to automation including mapping, genotyping, barcoding and data handling, template preparation, reaction setup, colony and plaque picking, and more.},
}
@article {pmid18404547,
year = {2008},
author = {Zeng, JS and De Hoog, GS},
title = {Exophiala spinifera and its allies: diagnostics from morphology to DNA barcoding.},
journal = {Medical mycology},
volume = {46},
number = {3},
pages = {193-208},
doi = {10.1080/13693780701799217},
pmid = {18404547},
issn = {1369-3786},
mesh = {Animals ; Base Sequence ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Exophiala/*classification/genetics/isolation &amp; purification/physiology ; Humans ; Molecular Sequence Data ; *Mycological Typing Techniques ; Mycoses/*microbiology/pathology ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Diagnostic features of morphology, physiology, serology and genetics of species belonging to the Exophiala spinifera clade (including 11 species: Exophiala oligosperma, E. spinifera, E. xenobiotica, E. jeanselmei, E. exophialae, E. nishimurae, E. bergeri, E. nigra, Rhinocladiella similis, Ramichloridium basitonum and Phaeoannellomyces elegans), comprising a large number of human-associated Exophiala species, are summarized. Several species have closely similar morphological characters and physiological profiles. Taxonomy is therefore primarily based on sequence diversity of the Internal Transcribed Spacer (ITS) region of ribosomal DNA (rDNA). Multilocus sequencing has shown that ITS is reliable for identification of the species in this clade, and is a therefore a good candidate for barcoding species of Exophiala. Species-specific fragments were searched in the ITS region of species in the Exophiala spinifera clade and can be used to design probes for diagnosis by hybridization.},
}
@article {pmid18400683,
year = {2008},
author = {Ficetola, GF and Miaud, C and Pompanon, F and Taberlet, P},
title = {Species detection using environmental DNA from water samples.},
journal = {Biology letters},
volume = {4},
number = {4},
pages = {423-425},
pmid = {18400683},
issn = {1744-9561},
mesh = {Animals ; *Biodiversity ; DNA, Mitochondrial/*analysis ; Environmental Monitoring/*methods ; Fresh Water/*chemistry ; Rana catesbeiana/*genetics ; Wetlands ; },
abstract = {The assessment of species distribution is a first critical phase of biodiversity studies and is necessary to many disciplines such as biogeography, conservation biology and ecology. However, several species are difficult to detect, especially during particular time periods or developmental stages, potentially biasing study outcomes. Here we present a novel approach, based on the limited persistence of DNA in the environment, to detect the presence of a species in fresh water. We used specific primers that amplify short mitochondrial DNA sequences to track the presence of a frog (Rana catesbeiana) in controlled environments and natural wetlands. A multi-sampling approach allowed for species detection in all environments where it was present, even at low densities. The reliability of the results was demonstrated by the identification of amplified DNA fragments, using traditional sequencing and parallel pyrosequencing techniques. As the environment can retain the molecular imprint of inhabiting species, our approach allows the reliable detection of secretive organisms in wetlands without direct observation. Combined with massive sequencing and the development of DNA barcodes that enable species identification, this approach opens new perspectives for the assessment of current biodiversity from environmental samples.},
}
@article {pmid18398924,
year = {2008},
author = {Bulbarello, A and Sattayasamitsathit, S and Crevillen, AG and Burdick, J and Mannino, S and Kanatharana, P and Thavarungkul, P and Escarpa, A and Wang, J},
title = {Striped alloy nanowire optical reflectance barcodes prepared from a single plating solution.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {4},
number = {5},
pages = {597-600},
doi = {10.1002/smll.200701047},
pmid = {18398924},
issn = {1613-6829},
mesh = {Alloys/chemistry ; Crystallization/*methods ; Electronic Data Processing/*instrumentation/methods ; Electroplating/methods ; Equipment Design ; Equipment Failure Analysis ; Gold/*chemistry ; Macromolecular Substances/chemistry ; Materials Testing ; Molecular Conformation ; Nanostructures/*chemistry/*ultrastructure ; Nanotechnology/*instrumentation/methods ; Optics and Photonics/instrumentation ; Particle Size ; Photometry/*instrumentation/methods ; Surface Properties ; },
}
@article {pmid18398767,
year = {2008},
author = {Ross, HA and Murugan, S and Li, WL},
title = {Testing the reliability of genetic methods of species identification via simulation.},
journal = {Systematic biology},
volume = {57},
number = {2},
pages = {216-230},
doi = {10.1080/10635150802032990},
pmid = {18398767},
issn = {1063-5157},
mesh = {Animals ; *Computer Simulation ; DNA, Mitochondrial/genetics ; Fungi/genetics ; *Genetic Speciation ; Invertebrates/genetics ; *Models, Genetic ; Sensitivity and Specificity ; Whales/genetics ; },
abstract = {Although genetic methods of species identification, especially DNA barcoding, are strongly debated, tests of these methods have been restricted to a few empirical cases for pragmatic reasons. Here we use simulation to test the performance of methods based on sequence comparison (BLAST and genetic distance) and tree topology over a wide range of evolutionary scenarios. Sequences were simulated on a range of gene trees spanning almost three orders of magnitude in tree depth and in coalescent depth; that is, deep or shallow trees with deep or shallow coalescences. When the query's conspecific sequences were included in the reference alignment, the rate of positive identification was related to the degree to which different species were genetically differentiated. The BLAST, distance, and liberal tree-based methods returned higher rates of correct identification than did the strict tree-based requirement that the query was within, but not sister to, a single-species clade. Under this more conservative approach, ambiguous outcomes occurred in inverse proportion to the number of reference sequences per species. When the query's conspecific sequences were not in the reference alignment, only the strict tree-based approach was relatively immune to making false-positive identifications. Thresholds affected the rates at which false-positive identifications were made when the query's species was unrepresented in the reference alignment but did not otherwise influence outcomes. A conservative approach using the strict tree-based method should be used initially in large-scale identification systems, with effort made to maximize sequence sampling within species. Once the genetic variation within a taxonomic group is well characterized and the taxonomy resolved, then the choice of method used should be dictated by considerations of computational efficiency. The requirement for extensive genetic sampling may render these techniques inappropriate in some circumstances.},
}
@article {pmid18398766,
year = {2008},
author = {Zhang, AB and Sikes, DS and Muster, C and Li, SQ},
title = {Inferring species membership using DNA sequences with back-propagation neural networks.},
journal = {Systematic biology},
volume = {57},
number = {2},
pages = {202-215},
doi = {10.1080/10635150802032982},
pmid = {18398766},
issn = {1063-5157},
mesh = {Animals ; Base Sequence ; Butterflies/genetics ; Coleoptera/genetics ; DNA/*genetics ; Electronic Data Processing ; *Genetic Speciation ; Models, Genetic ; *Neural Networks, Computer ; },
abstract = {DNA barcoding as a method for species identification is rapidly increasing in popularity. However, there are still relatively few rigorous methodological tests of DNA barcoding. Current distance-based methods are frequently criticized for treating the nearest neighbor as the closest relative via a raw similarity score, lacking an objective set of criteria to delineate taxa, or for being incongruent with classical character-based taxonomy. Here, we propose an artificial intelligence-based approach - inferring species membership via DNA barcoding with back-propagation neural networks (named BP-based species identification) - as a new advance to the spectrum of available methods. We demonstrate the value of this approach with simulated data sets representing different levels of sequence variation under coalescent simulations with various evolutionary models, as well as with two empirical data sets of COI sequences from East Asian ground beetles (Carabidae) and Costa Rican skipper butterflies. With a 630-to 690-bp fragment of the COI gene, we identified 97.50% of 80 unknown sequences of ground beetles, 95.63%, 96.10%, and 100% of 275, 205, and 9 unknown sequences of the neotropical skipper butterfly to their correct species, respectively. Our simulation studies indicate that the success rates of species identification depend on the divergence of sequences, the length of sequences, and the number of reference sequences. Particularly in cases involving incomplete lineage sorting, this new BP-based method appears to be superior to commonly used methods for DNA-based species identification.},
}
@article {pmid18398425,
year = {2008},
author = {Hollingsworth, PM},
title = {DNA barcoding plants in biodiversity hot spots: progress and outstanding questions.},
journal = {Heredity},
volume = {101},
number = {1},
pages = {1-2},
doi = {10.1038/hdy.2008.16},
pmid = {18398425},
issn = {1365-2540},
mesh = {Base Sequence ; Biodiversity ; Conservation of Natural Resources ; DNA, Mitochondrial/*genetics ; DNA, Plant/*genetics ; Electron Transport Complex IV/genetics ; Plants ; },
}
@article {pmid18392981,
year = {2008},
author = {Peyser, BD and Irizarry, R and Spencer, FA},
title = {Statistical analysis of fitness data determined by TAG hybridization on microarrays.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {416},
number = {},
pages = {369-381},
doi = {10.1007/978-1-59745-321-9_25},
pmid = {18392981},
issn = {1064-3745},
support = {GM 007445/GM/NIGMS NIH HHS/United States ; GM 62368/GM/NIGMS NIH HHS/United States ; HG 02432/HG/NHGRI NIH HHS/United States ; },
mesh = {DNA Probes ; Data Interpretation, Statistical ; Genes, Lethal ; Genome, Fungal ; Genomics/*methods ; Internet ; Mutation/genetics ; Oligonucleotide Array Sequence Analysis/*methods ; Saccharomyces cerevisiae/*genetics ; Sequence Deletion ; *Sequence Tagged Sites ; *Software ; },
abstract = {TAG, or bar-code, microarrays allow measurement of the oligonucleotide sequences (TAGs) that mark each strain of deletion mutants in the Saccharomyces cerevisiae yeast knockout (YKO) collection. Comparison of genomic DNA from pooled YKO samples allows estimation of relative abundance of TAGs marking each deletion strain. Features of TAG hybridizations create unique challenges for analysis. Analysis is complicated by the presence of two TAGs in most YKO strains and the hybridization behavior of TAGs that may differ in sequence from array probes. The oligonucleotide size of labeled TAGs also results in difficulty with contaminating sequences that cause reduced specificity. We present methods for analysis that approach these unique features of TAG hybridizations.},
}
@article {pmid18392961,
year = {2008},
author = {Sanschagrin, F and Kukavica-Ibrulj, I and Levesque, RC},
title = {Essential genes in the infection model of Pseudomonas aeruginosa PCR-based signature-tagged mutagenesis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {416},
number = {},
pages = {61-82},
doi = {10.1007/978-1-59745-321-9_5},
pmid = {18392961},
issn = {1064-3745},
mesh = {Animals ; Genes, Bacterial ; *Genes, Essential ; Models, Animal ; Models, Biological ; Molecular Biology/methods ; Mutagenesis, Insertional ; Mutagenesis, Site-Directed ; Polymerase Chain Reaction/*methods ; Pseudomonas Infections/physiopathology ; Pseudomonas aeruginosa/*genetics ; Virulence/*genetics ; },
abstract = {PCR-based signature tagged mutagenesis is an "en masse" screening technique based upon unique oligonucleotide tags (molecular barcodes) for identification of genes that will diminish or enhance maintenance of an organism in a specific ecological niche or environment. PCR-based STM applied to Pseudomonas aeruginosa permitted the identification of genes essential or in vivo maintenance by transposon insertion and negative selection in a mixed population of bacterial mutants. The innovative adaptations and refinement of the technology presented here with P. aeruginosa STM mutants selected in the rat lung have given critical information about genes essential for causing a chronic infection and a wealth of information about biological processes in vivo. The additional use of competitive index analysis for measurement of the level of virulence in vivo, microarray-based screening of selected prioritized STM mutants coupled to metabolomics analysis can now be attempted systematically on a genomic scale. PCR-based STM and combined whole-genome methods can also be applied to any organism having selectable phenotypes for screening.},
}
@article {pmid18380654,
year = {2008},
author = {Day, JC and Goodall, TI and Post, RJ},
title = {Confirmation of the species status of the blackfly Simulium galeratum in Britain using molecular taxonomy.},
journal = {Medical and veterinary entomology},
volume = {22},
number = {1},
pages = {55-61},
doi = {10.1111/j.1365-2915.2008.00719.x},
pmid = {18380654},
issn = {0269-283X},
mesh = {Animals ; Base Sequence ; Electron Transport Complex IV/*genetics ; Female ; Larva/anatomy &amp; histology/classification ; Male ; Molecular Sequence Data ; *Phylogeny ; Pupa/anatomy &amp; histology/classification ; Sequence Alignment ; Simuliidae/anatomy &amp; histology/*classification/*enzymology ; Species Specificity ; United Kingdom ; },
abstract = {Since 1920 Simulium reptans (Linnaeus) (Diptera: Simuliidae) has been reported as exhibiting two different larval morphotypes, a typical S. reptans and an atypical S. reptans var. galeratum, which differ in the markings of the larval head capsule. Inconsistent variation in adults and no apparent variation in the pupae have led taxonomists to conclude that these types in Britain are a single species. We investigated populations in Britain where either the typical form or var. galeratum is found, and one population where the two exist sympatrically. A phylogenetic study based upon a region of the mitochondrial cytochrome c oxidase 1 gene (DNA barcoding) produced a tree that delineated the morphotypes into two distinct monophyletic clades. The average Kimura-2-parameter distances within each clade (i.e. within each morphotype) were very low (0.67% and 0.78%), with the distances between morphotypes being 9-10-fold greater (mean 7.06%). This is concordant with differences within and between species in other taxa; based upon the strict correlation between the molecular variation and the morphotypes, we propose the re-instatement of S. galeratum to species status.},
}
@article {pmid18368433,
year = {2008},
author = {Clare, EL and Kerr, KC and von Königslöw, TE and Wilson, JJ and Hebert, PD},
title = {Diagnosing mitochondrial DNA diversity: applications of a sentinel gene approach.},
journal = {Journal of molecular evolution},
volume = {66},
number = {4},
pages = {362-367},
pmid = {18368433},
issn = {0022-2844},
mesh = {Animals ; Base Composition ; Birds/genetics ; Cytosine/analysis ; DNA, Mitochondrial/*chemistry ; Electron Transport Complex IV/*genetics ; *Genes, Mitochondrial ; *Genetic Variation ; Genome, Mitochondrial ; Guanine/analysis ; Insecta/genetics ; },
abstract = {Mitochondrial genomes show wide variation in their GC content. This study examines the correlations between mitochondrial genome-wide shifts in this feature and a fragment of the cytochrome c oxidase subunit I (COI) gene in animals, plants, and fungi. Because this approach utilizes COI as a sentinel, analyzing sequences from repositories such as GenBank and the Barcode of Life Data System (BOLD) can provide rapid insights into nucleotide usage. With this approach we probe nucleotide composition in a variety of taxonomic groups and establish the degree to which mitochondrial GC content varies among them. We then focus on two groups in particular, the classes Insecta and Aves, which possess the highest and lowest GC content, respectively. We establish that the sentinel approach provides strong indicators of mitochondrial GC content within divergent phyla (R values = 0.86-0.95, p < 0.001, in test cases) and provide evidence that selective pressures acting on GC content extend to noncoding regions of the plant and fungal mitochondrial genomes. We demonstrate that there is considerable variation in GC content of the mitochondrial genome within phyla and at each taxonomic level, leading to a substantial overlap zone in GC content between chordates and invertebrates. Our results provide a novel insight into the mitochondrial genome composition of animals, plants, and fungi and advocate this sentinel technique for the detection of rapid alterations in nucleotide usage as a measure of mitochondrial genome biodiversity.},
}
@article {pmid18366337,
year = {2008},
author = {Adams, ER and Hamilton, PB},
title = {New molecular tools for the identification of trypanosome species.},
journal = {Future microbiology},
volume = {3},
number = {2},
pages = {167-176},
doi = {10.2217/17460913.3.2.167},
pmid = {18366337},
issn = {1746-0921},
mesh = {Animals ; DNA, Ribosomal Spacer/genetics ; Humans ; Models, Biological ; Trypanosoma/classification/genetics/*isolation &amp; purification ; Trypanosomiasis/blood/diagnosis/*parasitology ; },
abstract = {Trypanosomes are the causative agents of many diseases of medical and veterinary importance, including sleeping sickness and nagana in Africa, and Chagas disease in South America. Accurate identification of trypanosome species is essential, as some species are morphologically indistinguishable, yet differ greatly in their pathogenicity. A range of molecular tools has been developed for identification of species and strains of trypanosomes. PCR, using primer sets designed to amplify a specific DNA fragment from each trypanosome species, is frequently used. More recently, generic systems have been developed that can potentially recognize all trypanosome species, such as amplification of the internal transcribed spacer and fluorescent fragment length barcoding, both of which use interspecies size variation in PCR fragments amplified from the ribosomal RNA locus. Loop-mediated isothermal amplification is a promising technique and is able to detect trypanosomes in blood, serum and cerebrospinal fluid. The advantages of these techniques for high-throughput and sensitive molecular identification will be discussed.},
}
@article {pmid18362623,
year = {2008},
author = {Greenberg, CC and Diaz-Flores, R and Lipsitz, SR and Regenbogen, SE and Mulholland, L and Mearn, F and Rao, S and Toidze, T and Gawande, AA},
title = {Bar-coding surgical sponges to improve safety: a randomized controlled trial.},
journal = {Annals of surgery},
volume = {247},
number = {4},
pages = {612-616},
doi = {10.1097/SLA.0b013e3181656cd5},
pmid = {18362623},
issn = {0003-4932},
mesh = {*Electronic Data Processing ; Female ; Foreign Bodies/*prevention &amp; control ; Humans ; Male ; Medical Errors/*prevention &amp; control ; Middle Aged ; Safety ; *Surgical Sponges/adverse effects/statistics &amp; numerical data ; },
abstract = {OBJECTIVE: A randomized, controlled trial was performed to evaluate a computer-assisted method for counting sponges using a bar-code system.<br><br>BACKGROUND: Retained sponges are a rare and preventable problem but persist in surgery despite standardized protocols for counting. Technology that improves detection of counting errors could reduce risk to surgical patients.<br><br>METHODS: We performed a randomized controlled trial comparing a bar-coded sponge system with a traditional counting protocol in 300 general surgery operations. Observers monitored sponge and instrument counts and recorded all incidents of miscounted or misplaced sponges. Surgeons and operating room staff completed postoperative and end-of-study surveys evaluating the bar-code system.<br><br>RESULTS: The bar-code system detected significantly more counting discrepancies than the traditional protocol (32 vs.13 discrepancies, P = 0.007). These discrepancies involved both misplaced sponges (21 vs. 12 sponges, P = 0.17) and miscounted sponges (11 vs. 1 sponge, P = 0.007). The system introduced new technical difficulties (2.04 per 1000 sponges) and increased the time spent counting sponges (5.3 vs. 2.4 minutes, P < 0.0001). In postoperative surveys, there was no difference in surgical teams' confidence that all sponges were accounted for, but they rated the counting process and team performance lower in operations randomized to the bar-code arm. By the end of the study, however, most providers found the system easy to use, felt confident in its ability to track sponges, and reported a positive effect on the counting process.<br><br>CONCLUSIONS: Use of automated counting using bar-coded surgical sponges improved detection of miscounted and misplaced sponges and was well tolerated by surgical staff members.},
}
@article {pmid18328107,
year = {2008},
author = {Tavares, ES and Baker, AJ},
title = {Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds.},
journal = {BMC evolutionary biology},
volume = {8},
number = {},
pages = {81},
pmid = {18328107},
issn = {1471-2148},
mesh = {Animals ; *Biodiversity ; Birds/classification/*genetics ; *Computational Biology ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Gene Library ; *Genes, Mitochondrial ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND: DNA barcoding of life using a standardized COI sequence was proposed as a species identification system, and as a method for detecting putative new species. Previous tests in birds showed that individuals can be correctly assigned to species in ~94% of the cases and suggested a threshold of 10x mean intraspecific difference to detect potential new species. However, these tests were criticized because they were based on a single maternally inherited gene rather than multiple nuclear genes, did not compare phylogenetically identified sister species, and thus likely overestimated the efficacy of DNA barcodes in identifying species.<br><br>RESULTS: To test the efficacy of DNA barcodes we compared ~650 bp of COI in 60 sister-species pairs identified in multigene phylogenies from 10 orders of birds. In all pairs, individuals of each species were monophyletic in a neighbor-joining (NJ) tree, and each species possessed fixed mutational differences distinguishing them from their sister species. Consequently, individuals were correctly assigned to species using a statistical coalescent framework. A coalescent test of taxonomic distinctiveness based on chance occurrence of reciprocal monophyly in two lineages was verified in known sister species, and used to identify recently separated lineages that represent putative species. This approach avoids the use of a universal distance cutoff which is invalidated by variation in times to common ancestry of sister species and in rates of evolution.<br><br>CONCLUSION: Closely related sister species of birds can be identified reliably by barcodes of fixed diagnostic substitutions in COI sequences, verifying coalescent-based statistical tests of reciprocal monophyly for taxonomic distinctiveness. Contrary to recent criticisms, a single DNA barcode is a rapid way to discover monophyletic lineages within a metapopulation that might represent undiscovered cryptic species, as envisaged in the unified species concept. This identifies a smaller set of lineages that can also be tested independently for species status with multiple nuclear gene approaches and other phenotypic characters.},
}
@article {pmid18327114,
year = {2008},
author = {McCartney, PR},
title = {Newborn identification and barcodes.},
journal = {MCN. The American journal of maternal child nursing},
volume = {33},
number = {2},
pages = {128},
doi = {10.1097/01.NMC.0000313423.81989.03},
pmid = {18327114},
issn = {0361-929X},
mesh = {*Electronic Data Processing ; Humans ; Infant, Newborn ; *Patient Identification Systems ; },
}
@article {pmid18310143,
year = {2008},
author = {Oudejans, CB},
title = {Noncoding RNA and DNA as biomarkers: toward an epigenetic fetal barcode for use in maternal plasma.},
journal = {Clinical chemistry},
volume = {54},
number = {3},
pages = {456-457},
doi = {10.1373/clinchem.2007.100123},
pmid = {18310143},
issn = {0009-9147},
mesh = {Biomarkers/blood ; Chromosomes, Human, Pair 21/*genetics ; CpG Islands ; *DNA Methylation ; DNA, Intergenic/*blood ; Down Syndrome/diagnosis ; *Epigenesis, Genetic ; Female ; *Fetus ; Genetic Markers ; Humans ; Placenta/metabolism ; Pregnancy ; Prenatal Diagnosis/*methods ; RNA, Untranslated/*blood ; },
}
@article {pmid18304789,
year = {2008},
author = {Guggiari, M and Peck, R},
title = {The bacterivorous ciliate Cyclidium glaucoma isolated from a sewage treatment plant: molecular and cytological descriptions for barcoding.},
journal = {European journal of protistology},
volume = {44},
number = {3},
pages = {168-180},
doi = {10.1016/j.ejop.2007.11.004},
pmid = {18304789},
issn = {0932-4739},
mesh = {Animals ; DNA, Mitochondrial/analysis/genetics ; DNA, Ribosomal Spacer/analysis ; Electron Transport Complex IV/genetics ; Molecular Sequence Data ; Oligohymenophorea/classification/cytology/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 5.8S/genetics ; Sequence Analysis, DNA ; Sewage/*parasitology ; Species Specificity ; Waste Disposal, Fluid/methods ; },
abstract = {A strain of Cyclidium isolated from a sewage treatment plant in Geneva, Switzerland, was cloned and cultured under laboratory conditions before being characterized cytologically and molecularly. Information about the classical morphology and also about new molecular sequences has been obtained permitting its identification as Cyclidium glaucoma. The molecular description includes the 18S rRNA sequence, and for the first time for C. glaucoma the ITS-1, 5.8S, ITS-2 sequence, and the mitochondrial Cytochrome oxidase C subunit 1 sequence. Three divergence groups were identified for C. glaucoma using a short rDNA sequence for evolutionary distance analysis. These groups correspond to the three ribotype lineages previously described for C. glaucoma. We discuss the possibility that C. glaucoma is a species complex containing three cryptic species, the problems of species definition in the protozoa and the choice of a barcoding molecule for the ciliates.},
}
@article {pmid18302972,
year = {2008},
author = {Cleland, D and Krader, P and Emerson, D},
title = {Use of the DiversiLab repetitive sequence-based PCR system for genotyping and identification of Archaea.},
journal = {Journal of microbiological methods},
volume = {73},
number = {2},
pages = {172-178},
doi = {10.1016/j.mimet.2007.12.008},
pmid = {18302972},
issn = {0167-7012},
mesh = {Cluster Analysis ; Crenarchaeota/*classification/*genetics ; DNA Fingerprinting ; DNA Primers/genetics ; DNA, Archaeal/*genetics ; Euryarchaeota/*classification/*genetics ; Genotype ; Polymerase Chain Reaction/*methods ; *Repetitive Sequences, Nucleic Acid ; Reproducibility of Results ; Sensitivity and Specificity ; },
abstract = {Repetitive elements are short stretches of DNA that are randomly distributed throughout the chromosomes of prokaryotes. The use of PCR primers to amplify intervening sequences of DNA between specific repetitive elements in Bacteria has become a standard method for rapidly genotyping bacterial strains and providing good resolution between multiple strains within a single species. Rapid, standardized methods for high resolution genotyping of Archaea are not widely available. We evaluated the DiversiLab system from Bacterial Barcodes that utilizes a kit-based repetitive sequence-based (rep-PCR) method that has been optimized for genotyping DNA was extracted from the source organisms using either a standard chemical DNA extraction kit or Whatman FTA paper. Rep-PCR was performed using an archaeal primer set and, the products were run on an Agilent, Lab-on-a-Chip DNA analyzer. Results were analyzed and compared using DiversiLab web-based software from Bacterial Barcodes. Seventy-nine strains representing 27 genera of Crenarchaeota and Euryarchaeota were analyzed. All the organisms could be successfully genotyped and the results were reproducible. We could not detect differences in rep-PCR profiles between DNA extracted using the chemical extraction kit and FTA paper. Thus far, 14 genera and 32 species of methanogens have been analyzed, and all yielded unique genotypes. For halophiles, 11 genera and 28 different species were analyzed, and all yielded unique genotypes. A comparison of 7 different strains of Halobacterium salinarium demonstrated that 6 of the 7 strains had a unique genotype. A comparison of 4 strains of Methanosarcina mazei indicated that each strain produced a unique genotype. There was little systematic inference that could be made from dendrograms comparing different strains, species, and genera of Archaea based on UPGMA cluster analysis. Based on these results, rep-PCR was a useful tool for the genotyping and strain identification of Archaea.},
}
@article {pmid18287050,
year = {2008},
author = {Kress, WJ and Erickson, DL},
title = {DNA barcodes: genes, genomics, and bioinformatics.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {105},
number = {8},
pages = {2761-2762},
pmid = {18287050},
issn = {1091-6490},
mesh = {Computational Biology/*methods ; *Databases, Genetic ; Genes/*genetics ; Genomics/*methods ; Sequence Alignment ; Species Specificity ; },
}
@article {pmid18283669,
year = {2008},
author = {Prinz, A and Reither, G and Diskar, M and Schultz, C},
title = {Fluorescence and bioluminescence procedures for functional proteomics.},
journal = {Proteomics},
volume = {8},
number = {6},
pages = {1179-1196},
doi = {10.1002/pmic.200700802},
pmid = {18283669},
issn = {1615-9861},
mesh = {*Fluorescence ; Fluorescence Resonance Energy Transfer ; Luminescent Measurements ; Luminescent Proteins/*chemistry/genetics/metabolism ; Protein Binding ; Proteomics/*methods ; Recombinant Fusion Proteins/*chemistry/genetics/metabolism ; },
abstract = {This review aims to provide an overview of current optical procedures used in functional proteomics, investigating protein localization, protein-protein interaction, intracellular signaling events, and second messenger generation in living cells. Reporter assays using proteins tagged with fluorescent or bioluminescent moieties are discussed. Recently, intracellular biosensor assays, flow cytometry-based techniques (fluorescent cell barcoding), as well as transfected cell microarray assays involving RNA interference coupled with automated imaging were introduced and have been adopted as screening platforms for annotating small molecules, investigating signaling events, or in phenotype analysis. These novel methodological advances include improved image acquisition and processing techniques and help linking in vitro observations to in vivo processes. In addition, the acquired data are increasingly quantitative in nature and will therefore pave the way for modeling of signaling cascades and other complex cellular events, an important step toward systems biology.},
}
@article {pmid18282635,
year = {2008},
author = {Kumar, NP and Rajavel, AR and Jambulingam, P},
title = {Application of PDF417 symbology for 'DNA Barcoding'.},
journal = {Computer methods and programs in biomedicine},
volume = {90},
number = {2},
pages = {187-189},
doi = {10.1016/j.cmpb.2007.12.011},
pmid = {18282635},
issn = {0169-2607},
mesh = {Animals ; Classification/methods ; Culicidae/classification/enzymology/genetics ; DNA/*classification/*genetics ; Databases, Nucleic Acid ; Electron Transport Complex IV/genetics ; India ; Phylogeny ; *Software ; },
abstract = {DNA sequences consisting of about 600 base pairs of the 5' region of the cytochrome c oxidase subunit 1 (COI) gene has been proposed as DNA Barcodes for taxonomical identification of species in different animals. We evaluated the application of two-dimensional barcodes for 'DNA Barcoding'. 'PDF417' symbology was applied to convert DNA Barcode sequences already proposed [N. Pradeep Kumar, A.R. Rajavel, R. Natarajan, P. Jambulingam, DNA Barcodes can distinguish species of Indian mosquitoes (Diptera: Culicidae). J. Med. Entomol. 77 (2007) 1-7.] for 10 different species of mosquitoes prevalent in India. Decoding of these digital images using 2-D scanner and a suitable software reproduced the input DNA sequences unchanged. This analysis indicated the utility of PDF417 for 'DNA Barcoding', which could be of definite use for taxonomic documentation of animals.},
}
@article {pmid18274529,
year = {2008},
author = {Meyer, M and Stenzel, U and Hofreiter, M},
title = {Parallel tagged sequencing on the 454 platform.},
journal = {Nature protocols},
volume = {3},
number = {2},
pages = {267-278},
doi = {10.1038/nprot.2007.520},
pmid = {18274529},
issn = {1750-2799},
mesh = {DNA, Mitochondrial/chemistry ; Genome, Mitochondrial/genetics ; Humans ; Plasmids/chemistry ; Sequence Analysis, DNA/*methods ; *Sequence Tagged Sites ; },
abstract = {Parallel tagged sequencing (PTS) is a molecular barcoding method designed to adapt the recently developed high-throughput 454 parallel sequencing technology for use with multiple samples. Unlike other barcoding methods, PTS can be applied to any type of double-stranded DNA (dsDNA) sample, including shotgun DNA libraries and pools of PCR products, and requires no amplification or gel purification steps. The method relies on attaching sample-specific barcoding adapters, which include sequence tags and a restriction site, to blunt-end repaired DNA samples by ligation and strand-displacement. After pooling multiple barcoded samples, molecules without sequence tags are effectively excluded from sequencing by dephosphorylation and restriction digestion, and using the tag sequences, the source of each DNA sequence can be traced. This protocol allows for sequencing 300 or more complete mitochondrial genomes on a single 454 GS FLX run, or twenty-five 6-kb plasmid sequences on only one 16th plate region. Most of the reactions can be performed in a multichannel setup on 96-well reaction plates, allowing for processing up to several hundreds of samples in a few days.},
}
@article {pmid18266556,
year = {2008},
author = {Chang, HW and Chuang, LY and Ho, CH and Chang, PL and Yang, CH},
title = {Odds ratio-based genetic algorithms for generating SNP barcodes of genotypes to predict disease susceptibility.},
journal = {Omics : a journal of integrative biology},
volume = {12},
number = {1},
pages = {71-81},
doi = {10.1089/omi.2007.0036},
pmid = {18266556},
issn = {1536-2310},
mesh = {*Algorithms ; Body Mass Index ; Electronic Data Processing/*methods ; Genetic Predisposition to Disease/*genetics ; Genotype ; Humans ; Odds Ratio ; *Polymorphism, Single Nucleotide ; },
abstract = {Genome-wide association analysis involving many single nucleotide polymorphisms (SNPs) data is challenging mathematically and computationally. It is time consuming to classify the combination of multilocus genotypes into high- and low-risk groups without false positive and negative errors. Hence, we propose the odds ratio-based genetic algorithms (OR-GA) method that uses the odds ratio as a new quantitative measure of disease risk among many SNP combinations. Genetic algorithms (GA) are applied to generate SNP "barcodes" of genotypes, which propose the maximal difference of occurrence between the case and control groups, to predict disease susceptibility (e.g., osteoporosis). When individuals are grouped into a low and high bone mass density (BMD) range, different SNP barcode patterns may occur several times in each of these two groups. Our results showed that a GA can effectively identify a specific SNP barcode with an optimized fitness value. SNP barcodes with a low fitness value will naturally be discarded from the population. A representative SNP barcode with a variable number of SNPs is processed by odds ratio analysis to determine the maximum difference between the low and high BMD groups in a statistical manner. Therefore, this paper introduces a powerful procedure for analysis of disease-associated SNP barcode in genome-wide genes.},
}
@article {pmid18264105,
year = {2008},
author = {Hamady, M and Walker, JJ and Harris, JK and Gold, NJ and Knight, R},
title = {Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex.},
journal = {Nature methods},
volume = {5},
number = {3},
pages = {235-237},
pmid = {18264105},
issn = {1548-7105},
support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; U01 HL081335/HL/NHLBI NIH HHS/United States ; U01 HL081335-01/HL/NHLBI NIH HHS/United States ; T32 GM065103/GM/NIGMS NIH HHS/United States ; P01DK078669/DK/NIDDK NIH HHS/United States ; T32GM065103/GM/NIGMS NIH HHS/United States ; },
mesh = {DNA Primers/chemistry ; Genetic Code ; RNA, Bacterial/*chemistry ; RNA, Ribosomal, 16S/*chemistry ; Sequence Analysis, DNA/*methods ; },
abstract = {We constructed error-correcting DNA barcodes that allow one run of a massively parallel pyrosequencer to process up to 1,544 samples simultaneously. Using these barcodes we processed bacterial 16S rRNA gene sequences representing microbial communities in 286 environmental samples, corrected 92% of sample assignment errors, and thus characterized nearly as many 16S rRNA genes as have been sequenced to date by Sanger sequencing.},
}
@article {pmid18259800,
year = {2008},
author = {Huang, D and Meier, R and Todd, PA and Chou, LM},
title = {Slow mitochondrial COI sequence evolution at the base of the metazoan tree and its implications for DNA barcoding.},
journal = {Journal of molecular evolution},
volume = {66},
number = {2},
pages = {167-174},
pmid = {18259800},
issn = {0022-2844},
mesh = {Animals ; Base Sequence ; Cnidaria/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Electronic Data Processing/*methods ; *Evolution, Molecular ; Genetic Variation ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Porifera/*genetics ; Species Specificity ; },
abstract = {The evolution rates of mtDNA in early metazoans hold important implications for DNA barcoding. Here, we present a comprehensive analysis of intra- and interspecific COI variabilities in Porifera and Cnidaria (separately as Anthozoa, Hydrozoa, and Scyphozoa) using a data set of 619 sequences from 224 species. We found variation within and between species to be much lower in Porifera and Anthozoa compared to Medusozoa (Hydrozoa and Scyphozoa), which has divergences similar to typical metazoans. Given that recent evidence has shown that fungi also exhibit limited COI divergence, slow-evolving mtDNA is likely to be plesiomorphic for the Metazoa. Higher rates of evolution could have originated independently in Medusozoa and Bilateria or been acquired in the Cnidaria + Bilateria clade and lost in the Anthozoa. Low identification success and substantial overlap between intra- and interspecific COI distances render the Anthozoa unsuitable for DNA barcoding. Caution is also advised for Porifera and Hydrozoa because of relatively low identification success rates as even threshold divergence that maximizes the "barcoding gap" does not improve identification success.},
}
@article {pmid18258745,
year = {2008},
author = {Lahaye, R and van der Bank, M and Bogarin, D and Warner, J and Pupulin, F and Gigot, G and Maurin, O and Duthoit, S and Barraclough, TG and Savolainen, V},
title = {DNA barcoding the floras of biodiversity hotspots.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {105},
number = {8},
pages = {2923-2928},
pmid = {18258745},
issn = {1091-6490},
mesh = {Base Sequence ; *Biodiversity ; Costa Rica ; Genes, Plant/*genetics ; Genetic Variation ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Plants/*genetics ; Sequence Analysis, DNA/*methods ; South Africa ; Species Specificity ; },
abstract = {DNA barcoding is a technique in which species identification is performed by using DNA sequences from a small fragment of the genome, with the aim of contributing to a wide range of ecological and conservation studies in which traditional taxonomic identification is not practical. DNA barcoding is well established in animals, but there is not yet any universally accepted barcode for plants. Here, we undertook intensive field collections in two biodiversity hotspots (Mesoamerica and southern Africa). Using >1,600 samples, we compared eight potential barcodes. Going beyond previous plant studies, we assessed to what extent a "DNA barcoding gap" is present between intra- and interspecific variations, using multiple accessions per species. Given its adequate rate of variation, easy amplification, and alignment, we identified a portion of the plastid matK gene as a universal DNA barcode for flowering plants. Critically, we further demonstrate the applicability of DNA barcoding for biodiversity inventories. In addition, analyzing >1,000 species of Mesoamerican orchids, DNA barcoding with matK alone reveals cryptic species and proves useful in identifying species listed in Convention on International Trade of Endangered Species (CITES) appendixes.},
}
@article {pmid18253494,
year = {2008},
author = {Cook, MA and Chan, CK and Jorgensen, P and Ketela, T and So, D and Tyers, M and Ho, CY},
title = {Systematic validation and atomic force microscopy of non-covalent short oligonucleotide barcode microarrays.},
journal = {PloS one},
volume = {3},
number = {2},
pages = {e1546},
pmid = {18253494},
issn = {1932-6203},
mesh = {DNA Probes ; *Electronic Data Processing/economics ; Genes, Fungal ; Genome, Fungal ; *Microscopy, Atomic Force ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis/economics/*methods/standards ; Saccharomyces cerevisiae ; },
abstract = {BACKGROUND: Molecular barcode arrays provide a powerful means to analyze cellular phenotypes in parallel through detection of short (20-60 base) unique sequence tags, or "barcodes", associated with each strain or clone in a collection. However, costs of current methods for microarray construction, whether by in situ oligonucleotide synthesis or ex situ coupling of modified oligonucleotides to the slide surface are often prohibitive to large-scale analyses.<br><br>Here we demonstrate that unmodified 20mer oligonucleotide probes printed on conventional surfaces show comparable hybridization signals to covalently linked 5'-amino-modified probes. As a test case, we undertook systematic cell size analysis of the budding yeast Saccharomyces cerevisiae genome-wide deletion collection by size separation of the deletion pool followed by determination of strain abundance in size fractions by barcode arrays. We demonstrate that the properties of a 13K unique feature spotted 20 mer oligonucleotide barcode microarray compare favorably with an analogous covalently-linked oligonucleotide array. Further, cell size profiles obtained with the size selection/barcode array approach recapitulate previous cell size measurements of individual deletion strains. Finally, through atomic force microscopy (AFM), we characterize the mechanism of hybridization to unmodified barcode probes on the slide surface.<br><br>CONCLUSIONS/SIGNIFICANCE: These studies push the lower limit of probe size in genome-scale unmodified oligonucleotide microarray construction and demonstrate a versatile, cost-effective and reliable method for molecular barcode analysis.},
}
@article {pmid18239126,
year = {2008},
author = {Schlabach, MR and Luo, J and Solimini, NL and Hu, G and Xu, Q and Li, MZ and Zhao, Z and Smogorzewska, A and Sowa, ME and Ang, XL and Westbrook, TF and Liang, AC and Chang, K and Hackett, JA and Harper, JW and Hannon, GJ and Elledge, SJ},
title = {Cancer proliferation gene discovery through functional genomics.},
journal = {Science (New York, N.Y.)},
volume = {319},
number = {5863},
pages = {620-624},
pmid = {18239126},
issn = {1095-9203},
support = {P01 CA013106-37/CA/NCI NIH HHS/United States ; P01 CA013106/CA/NCI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; F31 NS054507/NS/NINDS NIH HHS/United States ; T32CA09216/CA/NCI NIH HHS/United States ; T32 CA009216/CA/NCI NIH HHS/United States ; R01 AG011085/AG/NIA NIH HHS/United States ; F31 NS054507-01/NS/NINDS NIH HHS/United States ; P01 CA013106-36/CA/NCI NIH HHS/United States ; },
mesh = {Breast Neoplasms/*genetics/pathology ; Cell Line ; Cell Line, Tumor ; *Cell Proliferation ; Cell Survival/genetics ; Colonic Neoplasms/*genetics/pathology ; Gene Library ; *Genes, Neoplasm ; Genetic Vectors ; Genome, Human ; Genomics/*methods ; Humans ; MicroRNAs ; Oligonucleotide Array Sequence Analysis ; RNA, Small Interfering ; Retroviridae/genetics ; },
abstract = {Retroviral short hairpin RNA (shRNA)-mediated genetic screens in mammalian cells are powerful tools for discovering loss-of-function phenotypes. We describe a highly parallel multiplex methodology for screening large pools of shRNAs using half-hairpin barcodes for microarray deconvolution. We carried out dropout screens for shRNAs that affect cell proliferation and viability in cancer cells and normal cells. We identified many shRNAs to be antiproliferative that target core cellular processes, such as the cell cycle and protein translation, in all cells examined. Moreover, we identified genes that are selectively required for proliferation and survival in different cell lines. Our platform enables rapid and cost-effective genome-wide screens to identify cancer proliferation and survival genes for target discovery. Such efforts are complementary to the Cancer Genome Atlas and provide an alternative functional view of cancer cells.},
}
@article {pmid18236687,
year = {2008},
author = {Yancy, HF and Zemlak, TS and Mason, JA and Washington, JD and Tenge, BJ and Nguyen, NL and Barnett, JD and Savary, WE and Hill, WE and Moore, MM and Fry, FS and Randolph, SC and Rogers, PL and Hebert, PD},
title = {Potential use of DNA barcodes in regulatory science: applications of the Regulatory Fish Encyclopedia.},
journal = {Journal of food protection},
volume = {71},
number = {1},
pages = {210-217},
doi = {10.4315/0362-028x-71.1.210},
pmid = {18236687},
issn = {0362-028X},
mesh = {Animals ; DNA, Mitochondrial/*analysis ; Electron Transport Complex IV/genetics ; *Electronic Data Processing ; Fishes/*classification/*genetics ; Genetic Techniques ; Genetic Variation ; *Phylogeny ; Species Specificity ; },
abstract = {The use of a DNA-based identification system (DNA barcoding) founded on the mitochondrial gene cytochrome c oxidase subunit I (COI) was investigated for updating the U.S. Food and Drug Administration Regulatory Fish Encyclopedia (RFE; http://www.cfsan.fda.gov/-frf/rfe0.html). The RFE is a compilation of data used to identify fish species. It was compiled to help regulators identify species substitution that could result in potential adverse health consequences or could be a source of economic fraud. For each of many aquatic species commonly sold in the United States, the RFE includes high-resolution photographs of whole fish and their marketed product forms and species-specific biochemical patterns for authenticated fish species. These patterns currently include data from isoelectric focusing studies. In this article, we describe the generation of DNA barcodes for 172 individual authenticated fish representing 72 species from 27 families contained in the RFE. These barcode sequences can be used as an additional identification resource. In a blind study, 60 unknown fish muscle samples were barcoded, and the results were compared with the RFE barcode reference library. All 60 samples were correctly identified to species based on the barcoding data. Our study indicates that DNA barcoding can be a powerful tool for species identification and has broad potential applications.},
}
@article {pmid18225821,
year = {2007},
author = {Turner, T and Walker, D},
title = {Stop the hunting: using a wound care-specific EMR for 'just-in-time" supply ordering.},
journal = {The Journal of medical practice management : MPM},
volume = {23},
number = {3},
pages = {174-176},
pmid = {18225821},
issn = {8755-0229},
mesh = {Equipment and Supplies/*supply &amp; distribution ; Humans ; *Medical Records Systems, Computerized ; Practice Management, Medical/organization &amp; administration ; Software ; United States ; *Wound Healing ; },
abstract = {Ensuring adequate stocks of wound care supplies at wound care to be tied up, and too little can cause problems for patients. Most facilities maintain a "par" level for each item, which requires that supplies be ordered even if the "par" is numerically short by one item. In addition, due to the current just-in-time environment, if attention is not paid to the par level, unexpected shortages of supplies can develop. By using Inventory Trak software developed by Intellicure, facility managers will always know how much stock is presentfor each item, as individual item barcodes are registered in the system each time an item is used through software-linking scanners. The result is increased efficiency, reduced cost to the facility, and an assurance that the facility will not run out of critical items.},
}
@article {pmid18211640,
year = {2008},
author = {Saginur, M and Graham, ID and Forster, AJ and Boucher, M and Wells, GA},
title = {The uptake of technologies designed to influence medication safety in Canadian hospitals.},
journal = {Journal of evaluation in clinical practice},
volume = {14},
number = {1},
pages = {27-35},
doi = {10.1111/j.1365-2753.2007.00780.x},
pmid = {18211640},
issn = {1365-2753},
mesh = {Canada ; Cross-Sectional Studies ; Humans ; Logistic Models ; Medication Errors/*prevention &amp; control ; Pharmacy Service, Hospital/*organization &amp; administration ; Surveys and Questionnaires ; *Technology Assessment, Biomedical ; Technology, Pharmaceutical/*economics ; },
abstract = {BACKGROUND: There are many technologies designed to improve medication safety. Although limited evidence supports their use, there are pressures to implement them.<br><br>OBJECTIVE: To determine the uptake of technologies designed to improve medication safety, plans for adopting technologies, attitudes towards technology use, and perceptions of medication error. Methods We performed a cross-sectional survey of pharmacy directors at Canada's 100 largest acute-care hospitals.<br><br>RESULTS: Seventy-eight per cent of surveyed hospitals responded. Responding hospitals averaged 499 beds and 29% were teaching facilities. Hospital frequently used clinical pharmacy services (97% of hospitals), pharmacy-based intravenous admixture services (81%), computerized decision support modules for pharmacy order entry systems (77%), unit-dose drug distribution systems (75%) and computerized medication administration records (67%). Hospitals infrequently used bar-coding (9% of hospitals) and computerized physician order entry (9%). A majority of respondents and hospitals favoured expanded use of new technologies and planned for increased uptake. Respondents chose as their hospital's next investment: automated dispensing (33%), bar-coding (25%) and computerized physician order entry (12%).<br><br>CONCLUSION: Canadian hospitals appear poised to make sizeable investments in poorly evaluated technologies that address medication safety.},
}
@article {pmid18206692,
year = {2008},
author = {Hayden, RT and Patterson, DJ and Jay, DW and Cross, C and Dotson, P and Possel, RE and Srivastava, DK and Mirro, J and Shenep, JL},
title = {Computer-assisted bar-coding system significantly reduces clinical laboratory specimen identification errors in a pediatric oncology hospital.},
journal = {The Journal of pediatrics},
volume = {152},
number = {2},
pages = {219-224},
doi = {10.1016/j.jpeds.2007.08.021},
pmid = {18206692},
issn = {1097-6833},
mesh = {Ambulatory Care Facilities ; Chemistry, Clinical/methods/*organization &amp; administration ; Child ; Computer Systems ; Computers ; Decision Support Techniques ; *Electronic Data Processing ; Forms and Records Control ; Humans ; Incidence ; Laboratories/*organization &amp; administration ; Medical Oncology/*methods/organization &amp; administration/standards ; *Medical Order Entry Systems ; Pediatrics/*methods/organization &amp; administration/standards ; Reproducibility of Results ; },
abstract = {OBJECTIVE: To assess the ability of a bar code-based electronic positive patient and specimen identification (EPPID) system to reduce identification errors in a pediatric hospital's clinical laboratory.<br><br>STUDY DESIGN: An EPPID system was implemented at a pediatric oncology hospital to reduce errors in patient and laboratory specimen identification. The EPPID system included bar-code identifiers and handheld personal digital assistants supporting real-time order verification. System efficacy was measured in 3 consecutive 12-month time frames, corresponding to periods before, during, and immediately after full EPPID implementation.<br><br>RESULTS: A significant reduction in the median percentage of mislabeled specimens was observed in the 3-year study period. A decline from 0.03% to 0.005% (P < .001) was observed in the 12 months after full system implementation. On the basis of the pre-intervention detected error rate, it was estimated that EPPID prevented at least 62 mislabeling events during its first year of operation.<br><br>CONCLUSIONS: EPPID decreased the rate of misidentification of clinical laboratory samples. The diminution of errors observed in this study provides support for the development of national guidelines for the use of bar coding for laboratory specimens, paralleling recent recommendations for medication administration.},
}
@article {pmid18205622,
year = {2007},
author = {Shneyer, VS},
title = {On the species-specificity of DNA: fifty years later.},
journal = {Biochemistry. Biokhimiia},
volume = {72},
number = {12},
pages = {1377-1384},
doi = {10.1134/s0006297907120127},
pmid = {18205622},
issn = {0006-2979},
mesh = {Bacteria/genetics ; Base Composition ; DNA/*genetics ; Eukaryotic Cells/metabolism ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Modern approaches in DNA-based species identification are considered. Long used methods of species identification in procaryotes (G+C ratio, 16S rRNA nucleotide sequence, DNA-DNA hybridization) have recently been supplemented by the method of multilocus sequence analysis based on comparison of nucleotide sequences of fragments of several genes. Species identification in eukaryotes also employs one or two standard short fragments of the genome (known as DNA-barcodes). Potential benefits of new approaches and some difficulties during their practical realization are discussed.},
}
@article {pmid18191467,
year = {2008},
author = {Hagren, V and von Lode, P and Syrjälä, A and Soukka, T and Lövgren, T and Kojola, H and Nurmi, J},
title = {An automated PCR platform with homogeneous time-resolved fluorescence detection and dry chemistry assay kits.},
journal = {Analytical biochemistry},
volume = {374},
number = {2},
pages = {411-416},
doi = {10.1016/j.ab.2007.12.017},
pmid = {18191467},
issn = {1096-0309},
mesh = {Automation ; Disposable Equipment ; *Fluorescence ; Laboratories ; Luminescent Measurements/*methods ; Polymerase Chain Reaction/*instrumentation ; Sensitivity and Specificity ; Software ; Spectrometry, Fluorescence ; Temperature ; Time Factors ; },
abstract = {We have developed a novel instrument platform, GenomEra, for small-scale analysis of nucleic acids. The platform combines a rapid thermal cycler, an integrated time-resolved fluorescence measurement unit, and user-friendly software for the analysis of results. Disposable low-cost plastic reaction vessels are designed specifically for the instrument and contain all of the assay-specific reagents in dry form. The appropriate assay protocol is specified on barcodes printed under the vessels and is automatically initiated by the software. Detection is based on the use of sequence-specific probes labeled with intrinsically fluorescent europium or terbium chelates and complementary quencher probes, which enable sensitive, homogeneous closed-tube assays without the risk of carryover contamination. The detection limit of the instrument (background + 3 SD) is approximately 20 pmol/L for both chelates with a dynamic range of nearly four orders of magnitude. The functionality of the platform is demonstrated with a dual-label homogeneous polymerase chain reaction (PCR) assay for the detection of Salmonella using a Magda CA Salmonella assay kit. An internal amplification control is included in each reaction to eliminate false negative results caused by PCR inhibition. Qualitative assay results are automatically interpreted by the software and are available 45 min after sample addition.},
}
@article {pmid18081021,
year = {2008},
author = {Waugh, J and Huynen, L and Millar, C and Lambert, D},
title = {DNA barcoding of animal species-response to DeSalle.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {30},
number = {1},
pages = {92-93},
doi = {10.1002/bies.20698},
pmid = {18081021},
issn = {0265-9247},
mesh = {Animals ; DNA/*analysis ; *Databases, Genetic ; *Electronic Data Processing ; Models, Biological ; Phylogeny ; Species Specificity ; },
}
@article {pmid18048126,
year = {2005},
author = {Dasgupta, B and Konwar, KM and Mandoiu, II and Shvartsman, AA},
title = {Highly scalable algorithms for robust string barcoding.},
journal = {International journal of bioinformatics research and applications},
volume = {1},
number = {2},
pages = {145-161},
doi = {10.1504/IJBRA.2005.007574},
pmid = {18048126},
issn = {1744-5485},
mesh = {*Algorithms ; *Genomics ; },
abstract = {String barcoding is a recently introduced technique for genomic based identification of microorganisms. In this paper, we describe the engineering of highly scalable algorithms for robust string barcoding. Our methods enable distinguisher selection based on whole genomic sequences of hundreds of microorganisms of up to bacterial size, on a well equipped workstation. Experimental results on both randomly generated and NCBI genomic data show that whole-genome based selection results in a number of distinguishers nearly matching the information theoretic lower bounds for the problem.},
}
@article {pmid18041858,
year = {2007},
author = {Qin, L and Banholzer, MJ and Millstone, JE and Mirkin, CA},
title = {Nanodisk codes.},
journal = {Nano letters},
volume = {7},
number = {12},
pages = {3849-3853},
pmid = {18041858},
issn = {1530-6984},
support = {DP1 OD000285/OD/NIH HHS/United States ; },
mesh = {Base Sequence ; DNA/chemistry ; Materials Testing ; Nanotechnology/*methods ; Oligodeoxyribonucleotides/*chemistry ; Spectrum Analysis, Raman ; },
abstract = {We report a new encoding system based upon dispersible arrays of nanodisks prepared by on-wire lithography and functionalized with Raman active chromophores. These nanodisk arrays are encoded both physically (in a "barcode" pattern) and spectroscopically (Raman) along the array. These structures can be used in covert encoding strategies because of their small size or as biological labels with readout by scanning confocal Raman spectroscopy. As proof-of-concept, we demonstrate their utility in DNA detection in a multiplexed format at target concentrations as low as 100 fM.},
}
@article {pmid18037985,
year = {2007},
author = {Martin, PR and Berdychevski, RE and Subramanian, U and Blakely, WF and Prasanna, PG},
title = {Sample Tracking in an Automated Cytogenetic Biodosimetry Laboratory for Radiation Mass Casualties.},
journal = {Radiation measurements},
volume = {42},
number = {6-7},
pages = {1119-1124},
pmid = {18037985},
issn = {1350-4487},
support = {Y01 AI003823-01/AI/NIAID NIH HHS/United States ; Y01 AI005045/AI/NIAID NIH HHS/United States ; Y01 AI005045-01/AI/NIAID NIH HHS/United States ; Y01 DK003508-01/DK/NIDDK NIH HHS/United States ; },
abstract = {Chromosome aberration-based dicentric assay is expected to be used after mass casualty life-threatening radiation exposures to assess radiation dose to individuals. This will require processing of a large number of samples for individual dose assessment and clinical triage to aid treatment decisions. We have established an automated, high-throughput, cytogenetic biodosimetry laboratory to process a large number of samples for conducting the dicentric assay using peripheral blood from exposed individuals according to internationally accepted laboratory protocols (i.e., within days following radiation exposures). The components of an automated cytogenetic biodosimetry laboratory include blood collection kits for sample shipment, a cell viability analyzer, a robotic liquid handler, an automated metaphase harvester, a metaphase spreader, high-throughput slide stainer and coverslipper, a high-throughput metaphase finder, multiple satellite chromosome-aberration analysis systems, and a computerized sample tracking system. Laboratory automation using commercially available, off-the-shelf technologies, customized technology integration, and implementation of a laboratory information management system (LIMS) for cytogenetic analysis will significantly increase throughput.This paper focuses on our efforts to eliminate data transcription errors, increase efficiency, and maintain samples' positive chain-of-custody by sample tracking during sample processing and data analysis. This sample tracking system represents a "beta" version, which can be modeled elsewhere in a cytogenetic biodosimetry laboratory, and includes a customized LIMS with a central server, personal computer workstations, barcode printers, fixed station and wireless hand-held devices to scan barcodes at various critical steps, and data transmission over a private intra-laboratory computer network. Our studies will improve diagnostic biodosimetry response, aid confirmation of clinical triage, and medical management of radiation exposed individuals.},
}
@article {pmid18027907,
year = {2008},
author = {Fenniri, H and Chun, S and Terreau, O and Bravo-Vasquez, JP},
title = {Preparation and infrared/raman classification of 630 spectroscopically encoded styrene copolymers.},
journal = {Journal of combinatorial chemistry},
volume = {10},
number = {1},
pages = {31-36},
doi = {10.1021/cc7001292},
pmid = {18027907},
issn = {1520-4774},
support = {EB03824/EB/NIBIB NIH HHS/United States ; },
mesh = {*Combinatorial Chemistry Techniques ; Magnetic Resonance Spectroscopy ; Molecular Structure ; *Polystyrenes/chemical synthesis/chemistry/classification ; *Resins, Synthetic/chemical synthesis/chemistry/classification ; *Small Molecule Libraries/chemical synthesis/chemistry/classification ; Spectroscopy, Fourier Transform Infrared ; Spectrum Analysis, Raman ; },
abstract = {The barcoded resins (BCRs) were introduced recently as a platform for encoded combinatorial chemistry. One of the main challenges yet to be overcome is the demonstration that a large number of BCRs could be generated and classified with high confidence. Here, we describe the synthesis and classification of 630 polystyrene-based copolymers prepared from the combinatorial association of 15 spectroscopically active styrene monomers. Each of the 630 copolymers displayed a unique vibrational fingerprint (infrared and Raman), which was converted into a spectral vector. To each of the 630 copolymers, a vector of the known (reference) composition was assigned. Unknown (prediction) vectors were decoded using multivariate data analysis. From the inner product of the reference and prediction vectors, a correlation map comparing 396 900 copolymer pairs (630 x 630) was generated. In 100% of the cases, the highest correlation was obtained for polymer pairs in which the reference and prediction vectors correspond to copolymers prepared from identical styrene monomers, thus demonstrating the high reliability of this encoding strategy. We have also established that the spectroscopic barcodes generated from the Raman and infrared spectra are independent of the copolymers' morphology (beaded versus bulk polymers). Besides the demonstration of the generality of the polymer barcoding strategy, the analytical methods developed here could in principle be extended to the investigation of the composition and purity of any other synthetic polymer and biopolymer library, or even scaffold-based combinatorial libraries.},
}
@article {pmid18023596,
year = {2008},
author = {Ståhls, G and Savolainen, E},
title = {MtDNA COI barcodes reveal cryptic diversity in the Baetis vernus group (Ephemeroptera, Baetidae).},
journal = {Molecular phylogenetics and evolution},
volume = {46},
number = {1},
pages = {82-87},
doi = {10.1016/j.ympev.2007.09.009},
pmid = {18023596},
issn = {1055-7903},
mesh = {Animals ; DNA, Mitochondrial/chemistry/genetics ; Diptera/*classification/genetics ; *Evolution, Molecular ; Genetic Variation ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Partial mitochondrial COI sequences (barcoding fragment) were explored for the understanding of the species boundaries of Baetis vernus group taxa (Ephemeroptera, Baetidae) in northern Europe. We sampled all species of this group occurring in Finland, but focused on taxa for which morphological and taxonomical confusion have been most apparent. The sequence matrix comprised 627 nucleotides for 96 specimens, and was analysed using parsimony. Results provided strong evidence that Baetis macani Kimmins and B. vernus Curtis comprise morphologically cryptic but molecularly distinct taxa, as intraspecific uncorrected divergences within haplogroups ranged between 0.3% and 1.4% and interspecific divergences were from 13.1% to 16.5%. These interesting findings prompt for further taxonomic studies of B. vernus taxa using more extensive specimen sampling from the known distributional areas in the Palaearctic/Holarctic region for better understanding of haplotype distributions. We stress the importance of integration of morphological and molecular data, and the necessity to employ additional nuclear DNA sequence data.},
}
@article {pmid18007632,
year = {2007},
author = {Pierce, SE and Davis, RW and Nislow, C and Giaever, G},
title = {Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures.},
journal = {Nature protocols},
volume = {2},
number = {11},
pages = {2958-2974},
doi = {10.1038/nprot.2007.427},
pmid = {18007632},
issn = {1750-2799},
mesh = {Cell Culture Techniques ; *Gene Deletion ; Genome, Fungal ; Genomics/*methods ; Oligonucleotide Array Sequence Analysis ; Polymerase Chain Reaction ; Saccharomyces cerevisiae/*genetics/growth &amp; development ; },
abstract = {The availability of a near-complete (96%) collection of gene-deletion mutants in Saccharomyces cerevisiae greatly facilitates the systematic analyses of gene function in yeast. The unique 20 bp DNA 'barcodes' or 'tags' in each deletion strain enable the individual fitness of thousands of deletion mutants to be resolved from a single pooled culture. Here, we present protocols for the study of pooled cultures of tagged yeast deletion mutants with a tag microarray. This process involves five main steps: pooled growth, isolation of genomic DNA, PCR amplification of the barcodes, array hybridization and data analysis. Pooled deletion screening can be used to study gene function, uncover a compound's mode of action and identify drug targets. In addition to these applications, the general method of studying pooled samples with barcode arrays can also be adapted for use with other types of samples, such as mutant collections in other organisms, short interfering RNA vectors and molecular inversion probes.},
}
@article {pmid17999953,
year = {2008},
author = {Rach, J and Desalle, R and Sarkar, IN and Schierwater, B and Hadrys, H},
title = {Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata.},
journal = {Proceedings. Biological sciences},
volume = {275},
number = {1632},
pages = {237-247},
pmid = {17999953},
issn = {0962-8452},
mesh = {Animals ; Base Sequence ; *Biodiversity ; Classification/methods ; DNA, Mitochondrial/analysis/chemistry ; Electron Transport Complex I/genetics ; *Genetic Variation ; Insecta/*classification/genetics ; Molecular Diagnostic Techniques/*methods ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA/veterinary ; Species Specificity ; },
abstract = {DNA barcoding has become a promising means for identifying organisms of all life stages. Currently, phenetic approaches and tree-building methods have been used to define species boundaries and discover 'cryptic species'. However, a universal threshold of genetic distance values to distinguish taxonomic groups cannot be determined. As an alternative, DNA barcoding approaches can be 'character based', whereby species are identified through the presence or absence of discrete nucleotide substitutions (character states) within a DNA sequence. We demonstrate the potential of character-based DNA barcodes by analysing 833 odonate specimens from 103 localities belonging to 64 species. A total of 54 species and 22 genera could be discriminated reliably through unique combinations of character states within only one mitochondrial gene region (NADH dehydrogenase 1). Character-based DNA barcodes were further successfully established at a population level discriminating seven population-specific entities out of a total of 19 populations belonging to three species. Thus, for the first time, DNA barcodes have been found to identify entities below the species level that may constitute separate conservation units or even species units. Our findings suggest that character-based DNA barcoding can be a rapid and reliable means for (i) the assignment of unknown specimens to a taxonomic group, (ii) the exploration of diagnosability of conservation units, and (iii) complementing taxonomic identification systems.},
}
@article {pmid17998806,
year = {2006},
author = {Baron, U and Türbachova, I and Hellwag, A and Eckhardt, F and Berlin, K and Hoffmuller, U and Gardina, P and Olek, S},
title = {DNA methylation analysis as a tool for cell typing.},
journal = {Epigenetics},
volume = {1},
number = {1},
pages = {55-60},
doi = {10.4161/epi.1.1.2643},
pmid = {17998806},
issn = {1559-2308},
mesh = {Cell Count/*methods ; Cell- and Tissue-Based Therapy ; Cells, Cultured ; Coculture Techniques ; Cytological Techniques/*methods ; *DNA Methylation ; Humans ; },
abstract = {Cell therapeutic approaches currently lack definitive quality control measures which guarantee safety in clinical applications and create consistent standards for regulatory approval. These approaches rely on isolation, purification and possibly ex vivo manipulation of donor cells. Since such cells are exposed to artificial environments, there is potential for deviations from natural growth processes. The resulting heterogeneity of cell cultures is an inherent problem. Therefore, verification of cell identity and quantification of subpopulations is mandatory. Focusing on cultured human primary cells, we tested whether DNA methylation patterns serve as distinctive cell type markers. We identified panels of cell type specific differentially methylated gene regions (CDMs) which produce unambiguous profiles for these cell types. Applying methylation sensitive single nucleotide primer extension generated binary cell type descriptors ("barcodes") which allow quantification of cell mixtures. Thus, methylation based analytics suggest themselves as promising tools for the characterization and quality control of ex vivo manipulated cells.},
}
@article {pmid17990505,
year = {2007},
author = {Hampikian, G and Andersen, T},
title = {Absent sequences: nullomers and primes.},
journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing},
volume = {},
number = {},
pages = {355-366},
doi = {10.1142/9789812772435_0034},
pmid = {17990505},
issn = {2335-6928},
mesh = {*Algorithms ; Base Sequence ; Computational Biology ; DNA/genetics ; *Databases, Genetic ; Genome, Human ; Humans ; Sequence Analysis/statistics &amp; numerical data ; Sequence Analysis, DNA/*statistics &amp; numerical data ; Software ; },
abstract = {We describe a new publicly available algorithm for identifying absent sequences, and demonstrate its use by listing the smallest oligomers not found in the human genome (human "nullomers"), and those not found in any reported genome or GenBank sequence ("primes"). These absent sequences define the maximum set of potentially lethal oligomers. They also provide a rational basis for choosing artificial DNA sequences for molecular barcodes, show promise for species identification and environmental characterization based on absence, and identify potential targets for therapeutic intervention and suicide markers.},
}
@article {pmid17987130,
year = {2007},
author = {Sass, C and Little, DP and Stevenson, DW and Specht, CD},
title = {DNA barcoding in the cycadales: testing the potential of proposed barcoding markers for species identification of cycads.},
journal = {PloS one},
volume = {2},
number = {11},
pages = {e1154},
pmid = {17987130},
issn = {1932-6203},
mesh = {Algorithms ; Base Sequence ; Cycadopsida/classification/*genetics ; DNA Primers ; DNA, Plant/*genetics ; *Electronic Data Processing ; Species Specificity ; },
abstract = {Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to species, particularly when diagnostic morphological features are absent. These sequences could offer a new forensic tool in plant and animal conservation-especially for endangered species such as members of the Cycadales. Ideally, barcodes could be used to positively identify illegally obtained material even in cases where diagnostic features have been purposefully removed or to release confiscated organisms into the proper breeding population. In order to be useful, a DNA barcode sequence must not only easily PCR amplify with universal or near-universal reaction conditions and primers, but also contain enough variation to generate unique identifiers at either the species or population levels. Chloroplast regions suggested by the Plant Working Group of the Consortium for the Barcode of Life (CBoL), and two alternatives, the chloroplast psbA-trnH intergenic spacer and the nuclear ribosomal internal transcribed spacer (nrITS), were tested for their utility in generating unique identifiers for members of the Cycadales. Ease of amplification and sequence generation with universal primers and reaction conditions was determined for each of the seven proposed markers. While none of the proposed markers provided unique identifiers for all species tested, nrITS showed the most promise in terms of variability, although sequencing difficulties remain a drawback. We suggest a workflow for DNA barcoding, including database generation and management, which will ultimately be necessary if we are to succeed in establishing a universal DNA barcode for plants.},
}
@article {pmid17976031,
year = {2007},
author = {Brunker, SE and Cederquist, KB and Keating, CD},
title = {Metallic barcodes for multiplexed bioassays.},
journal = {Nanomedicine (London, England)},
volume = {2},
number = {5},
pages = {695-710},
doi = {10.2217/17435889.2.5.695},
pmid = {17976031},
issn = {1748-6963},
support = {CA118591/CA/NCI NIH HHS/United States ; R01 EB000268/EB/NIBIB NIH HHS/United States ; },
mesh = {Biological Assay/*methods ; Gene Expression Profiling/*methods ; Immunoassay/*methods ; *Metals ; *Nanostructures/chemistry ; Nanotechnology/*trends ; },
abstract = {Both detection and postdiagnosis monitoring are critical for cancer isolation and treatment. Particle-based sensing strategies could help to address these medical needs. This review describes barcoded metallic nanowires as particle scaffolds for multiplexed detection of antigens or nucleic acids. Barcode patterns are compositionally encoded as stripes of gold and silver metal along the nanowire length during fabrication by templated electrodeposition. Particle identification is accomplished using reflectance optical microscopy and can be coupled with fluorescence readout of antigen- or nucleic acid-binding events. Several approaches to multiplexed biodetection based on barcoded nanowires will be described and the potential for these particles in cancer detection will be discussed.},
}
@article {pmid17971872,
year = {2007},
author = {Fouquet, A and Gilles, A and Vences, M and Marty, C and Blanc, M and Gemmell, NJ},
title = {Underestimation of species richness in neotropical frogs revealed by mtDNA analyses.},
journal = {PloS one},
volume = {2},
number = {10},
pages = {e1109},
pmid = {17971872},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; DNA/chemistry ; *DNA, Mitochondrial/metabolism ; DNA, Ribosomal/*chemistry ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Models, Biological ; Models, Genetic ; Phylogeny ; RNA, Ribosomal, 16S/chemistry ; Ranidae ; Species Specificity ; },
abstract = {BACKGROUND: Amphibians are rapidly vanishing. At the same time, it is most likely that the number of amphibian species is highly underestimated. Recent DNA barcoding work has attempted to define a threshold between intra- and inter-specific genetic distances to help identify candidate species. In groups with high extinction rates and poorly known species boundaries, like amphibians, such tools may provide a way to rapidly evaluate species richness.<br><br>METHODOLOGY: Here we analyse published and new 16S rDNA sequences from 60 frog species of Amazonia-Guianas to obtain a minimum estimate of the number of undescribed species in this region. We combined isolation by distance, phylogenetic analyses, and comparison of molecular distances to evaluate threshold values for the identification of candidate species among these frogs.<br><br>PRINCIPAL FINDINGS: In most cases, geographically distant populations belong to genetically highly distinct lineages that could be considered as candidate new species. This was not universal among the taxa studied and thus widespread species of Neotropical frogs really do exist, contrary to previous assumptions. Moreover, the many instances of paraphyly and the wide overlap between distributions of inter- and intra-specific distances reinforce the hypothesis that many cryptic species remain to be described. In our data set, pairwise genetic distances below 0.02 are strongly correlated with geographical distances. This correlation remains statistically significant until genetic distance is 0.05, with no such relation thereafter. This suggests that for higher distances allopatric and sympatric cryptic species prevail. Based on our analyses, we propose a more inclusive pairwise genetic distance of 0.03 between taxa to target lineages that could correspond to candidate species.<br><br>CONCLUSIONS: Using this approach, we identify 129 candidate species, two-fold greater than the 60 species included in the current study. This leads to estimates of around 170 to 460 frog taxa unrecognized in Amazonia-Guianas.<br><br>SIGNIFICANCE: As a consequence the global amphibian decline detected especially in the Neotropics may be worse than realised.},
}
@article {pmid17964224,
year = {2008},
author = {Hamilton, PB and Adams, ER and Malele, II and Gibson, WC},
title = {A novel, high-throughput technique for species identification reveals a new species of tsetse-transmitted trypanosome related to the Trypanosoma brucei subgenus, Trypanozoon.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {8},
number = {1},
pages = {26-33},
doi = {10.1016/j.meegid.2007.09.003},
pmid = {17964224},
issn = {1567-1348},
mesh = {Animals ; DNA Primers ; DNA, Ribosomal Spacer/genetics ; Fluorescence ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 23S/genetics ; Reproducibility of Results ; Trypanosoma brucei brucei/*classification/genetics/*isolation &amp; purification ; Tsetse Flies/*parasitology ; },
abstract = {We describe a novel method of species identification, fluorescent fragment length barcoding, based on length variation in regions of the 18S and 28Salpha ribosomal DNA. Fluorescently tagged primers, designed in conserved regions of the 18S and 28Salpha ribosomal DNA, were used to amplify fragments with inter-species size variation, and sizes determined accurately using an automated DNA sequencer. By using multiple regions and different fluorochromes, a barcode unique to each species was generated. The technique was developed for the identification of African tsetse-transmitted trypanosomes and validated using DNA from laboratory isolates representing known species, subspecies and subgroups. To test the methodology, we examined 91 trypanosome samples from infected tsetse fly midguts from Tanzania, most of which had already been identified by species-specific and generic PCR tests. Identifications were mainly in agreement, but the presence of an unknown trypanosome in several samples was revealed by its unique barcode. Phylogenetic analyses based on 18S rDNA and glycosomal glyceraldehyde phosphate dehydrogenase gene sequences confirmed that this trypanosome is a new species and it is within the Trypanosoma brucei clade, as a sister group of subgenus Trypanozoon. The overall identification rate of trypanosome-infected midgut samples increased from 78 to 96% using FFLB instead of currently available PCR tests. This was due to the high sensitivity of FFLB as well as its capacity to identify previously unrecognised species. FFLB also allowed the identification of multiple species in mixed infections. The method enabled high-throughput and accurate species identification and should be applicable to any group of organisms where there is length variation in regions of rDNA.},
}
@article {pmid17960269,
year = {2007},
author = {Douglas, ES and Chandra, RA and Bertozzi, CR and Mathies, RA and Francis, MB},
title = {Self-assembled cellular microarrays patterned using DNA barcodes.},
journal = {Lab on a chip},
volume = {7},
number = {11},
pages = {1442-1448},
doi = {10.1039/b708666k},
pmid = {17960269},
issn = {1473-0197},
mesh = {Base Sequence ; DNA Primers ; Microfluidics ; *Oligonucleotide Array Sequence Analysis ; },
abstract = {The successful integration of living cells into synthetic devices requires precise control over cell patterning. Here we describe a versatile platform that can accomplish this goal through DNA hybridization. Living cells functionalized with exogenous cell-surface DNA strands bind to cognate sequences of DNA printed on glass slides. Attachment via these "cell-adhesion barcodes" is rapid and specific, with close-packed arrays of cells forming within minutes. The biophysical properties of the system are characterized, and the technique is used to form complex cellular patterns with single-cell line widths and self-assembled cellular microarrays. Key advantages of DNA-directed cell binding include the ability to immobilize both adherent and non-adherent cells, to capture cells selectively from a mixed population, to tune the binding properties of the cells, and to reuse substrates prepared with widely available DNA printing technologies.},
}
@article {pmid17959393,
year = {2007},
author = {Meixner, MJ and Lüter, C and Eckert, C and Itskovich, V and Janussen, D and von Rintelen, T and Bohne, AV and Meixner, JM and Hess, WR},
title = {Phylogenetic analysis of freshwater sponges provide evidence for endemism and radiation in ancient lakes.},
journal = {Molecular phylogenetics and evolution},
volume = {45},
number = {3},
pages = {875-886},
doi = {10.1016/j.ympev.2007.09.007},
pmid = {17959393},
issn = {1055-7903},
mesh = {Animals ; Electron Transport Complex IV/genetics/metabolism ; Evolution, Molecular ; *Fresh Water ; Mitochondria/enzymology/genetics ; *Phylogeny ; Population Dynamics ; Porifera/classification/genetics/*physiology ; RNA, Ribosomal, 18S/genetics ; Time Factors ; },
abstract = {Morphologic and phylogenetic analysis of freshwater sponges endemic to lakes in Central Sulawesi, Siberia and South-East Europe is presented. We also analyzed several cosmopolitan sponge species from Eurasia and North America and included sponge sequences from public databases. In agreement with previous reports [Addis, J.S., Peterson, K.J., 2005. Phylogenetic relationships of freshwater sponges (Porifera, Spongillina) inferred from analyses of 18S rDNA, COI mtDNA, and ITS2 rDNA sequences. Zool. Scr. 34, 549-557], the metaniid sponge Corvomeyenia sp. was the most deeply branching species within a monophyletic lineage of the suborder Spongillina. Pachydictyum globosum (Malawispongiidae) and Nudospongilla vasta (Spongillidae), two morphologically quite distinct species from Sulawesi were found in a joint clade with Trochospongilla (Spongillidae) rendering Trochospongilla paraphyletic. Furthermore, Ochridaspongia sp., another Malawispongiidae, clustered far away from that clade, together with Ephydatia fluviatilis, making the latter family polyphyletic. The Lubomirskiidae endemic to Lake Baikal, Lubomirskia abietina, Baikalospongia bacillifera, B. intermedia, and Swartschewskia papyracea formed a well-supported clade that was most closely linked to the genus Ephydatia (99.9% identity over a total length of 2169 concatenated nucleotide positions). Our study indicates the frequent and independent origin of sponge species endemic to different freshwater ecosystems from a few cosmopolitan founder species. The highly specific primer sets newly developed here facilitate work on the molecular phylogeny and DNA barcoding of sponges.},
}
@article {pmid17955361,
year = {2007},
author = {McCloskey, ML and Stöger, R and Hansen, RS and Laird, CD},
title = {Encoding PCR products with batch-stamps and barcodes.},
journal = {Biochemical genetics},
volume = {45},
number = {11-12},
pages = {761-767},
doi = {10.1007/s10528-007-9114-x},
pmid = {17955361},
issn = {0006-2928},
support = {GM 53805/GM/NIGMS NIH HHS/United States ; HD 02274/HD/NICHD NIH HHS/United States ; },
mesh = {Fragile X Mental Retardation Protein/*genetics ; Humans ; Oligonucleotides/chemistry/*genetics ; *Polymerase Chain Reaction/methods ; Quantitative Trait Loci/*genetics ; Sensitivity and Specificity ; },
abstract = {Polymerase chain reaction (PCR) has become the mainstay of DNA sequence analysis. Yet there is always uncertainty concerning the source of the template DNA that gave rise to a particular PCR product. The risks of contamination, biased amplification, and product redundancy are especially high when limited amounts of template DNA are used. We have developed and applied molecular encoding principles to solve this source-uncertainty problem for DNA sequences generated by standard PCR. Batch-stamps specify the date and sample identity, and barcodes detect template redundancy. Our approach thus enables classification of each PCR-derived sequence as valid, contaminant, or redundant, and provides a measure of sequence diversity. We recommend that batch-stamps and barcodes be used when amplifying irreplaceable DNAs and cDNAs available for forensic, clinical, single cell, and ancient DNA analyses.},
}
@article {pmid17941817,
year = {2007},
author = {Marko, NF and Weil, RJ and Toms, SA},
title = {Nanotechnology in proteomics.},
journal = {Expert review of proteomics},
volume = {4},
number = {5},
pages = {617-626},
doi = {10.1586/14789450.4.5.617},
pmid = {17941817},
issn = {1744-8387},
mesh = {Animals ; Humans ; Nanotechnology/*methods ; Proteins/analysis/isolation &amp; purification ; Proteomics/*methods ; },
abstract = {In genomics, the ability to amplify rare transcripts has enabled rapid advances in the understanding of gene expression patterns in human disease. The inability to increase the copy number and to detect the signal of rare proteins as unique species in biological samples has hindered the ability of proteomics to dissect human disease with the same complexity as genomic analyses. Advances in nanotechnology have begun to allow researchers to identify low-abundance proteins in samples through techniques that rely upon both nanoparticles and nanoscale devices. Coupled with rapid advances made in protein identification and isolation over the past decade, currently available technology enables more effective multiplexing and improved signal-to-noise, which enhances detection of low-abundance proteins in cellular and tissue lysates significantly. Techniques, including nanowires, nanocantilevers, bio-barcoding and surface-enhanced Raman spectroscopy, permit the detection of proteins into the low attomolar range, where many biologically important cellular processes occur. In this review, we summarize several such techniques, highlight their implementation in current protein research and comment on their potential role in future proteomic investigations and biomedical applications.},
}
@article {pmid17932070,
year = {2007},
author = {Parameswaran, P and Jalili, R and Tao, L and Shokralla, S and Gharizadeh, B and Ronaghi, M and Fire, AZ},
title = {A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing.},
journal = {Nucleic acids research},
volume = {35},
number = {19},
pages = {e130},
pmid = {17932070},
issn = {1362-4962},
support = {R01 HG003571/HG/NHGRI NIH HHS/United States ; 1S10RR022982/RR/NCRR NIH HHS/United States ; R01HG003571/HG/NHGRI NIH HHS/United States ; R01 GM37706/GM/NIGMS NIH HHS/United States ; R01 GM037706/GM/NIGMS NIH HHS/United States ; S10 RR022982/RR/NCRR NIH HHS/United States ; },
mesh = {DNA Primers/chemistry ; DNA, Complementary/chemistry ; Gene Library ; Nucleotides/analysis ; Polymerase Chain Reaction ; RNA/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {Multiplexed high-throughput pyrosequencing is currently limited in complexity (number of samples sequenced in parallel), and in capacity (number of sequences obtained per sample). Physical-space segregation of the sequencing platform into a fixed number of channels allows limited multiplexing, but obscures available sequencing space. To overcome these limitations, we have devised a novel barcoding approach to allow for pooling and sequencing of DNA from independent samples, and to facilitate subsequent segregation of sequencing capacity. Forty-eight forward-reverse barcode pairs are described: each forward and each reverse barcode unique with respect to at least 4 nt positions. With improved read lengths of pyrosequencers, combinations of forward and reverse barcodes may be used to sequence from as many as n(2) independent libraries for each set of 'n' forward and 'n' reverse barcodes, for each defined set of cloning-linkers. In two pilot series of barcoded sequencing using the GS20 Sequencer (454/Roche), we found that over 99.8% of obtained sequences could be assigned to 25 independent, uniquely barcoded libraries based on the presence of either a perfect forward or a perfect reverse barcode. The false-discovery rate, as measured by the percentage of sequences with unexpected perfect pairings of unmatched forward and reverse barcodes, was estimated to be <0.005%.},
}
@article {pmid17926019,
year = {2007},
author = {Pelsy, F},
title = {Untranslated leader region polymorphism of Tvv1, a retrotransposon family, is a novel marker useful for analyzing genetic diversity and relatedness in the genus Vitis.},
journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik},
volume = {116},
number = {1},
pages = {15-27},
pmid = {17926019},
issn = {0040-5752},
mesh = {Genes, Plant/*genetics ; Genetic Markers/*genetics ; *Genetic Variation ; Genome, Plant ; Genotype ; Microsatellite Repeats ; Phylogeny ; Polymorphism, Genetic/*genetics ; Retroelements/*genetics ; Terminal Repeat Sequences/*genetics ; Untranslated Regions/*genetics ; Vitis/classification/*genetics ; },
abstract = {Grapevine retrotransposons belonging to the Tvv1 family share a single, highly conserved open reading frame but differ by their untranslated leader (UTL) region, which is highly variable in size. Amplification of the UTL region of Tvv1 elements from 94 Vitaceae accessions reveals that each of them shows a unique pattern of UTL-derived bands, which is inherited in progenies but conserved between clones vegetatively propagated. The overall organization of genetic diversity of the Vitaceae at the inter and intraspecific level and relatedness among accessions described by UTL-derived bands was compared to those obtained using 15 microsatellite loci. Both fingerprinting methods show a similar grouping of Vitis vinifera accessions but UTL-based fingerprinting more accurately isolates the muscadine grapes from the American and Asian Vitis. Finally, sequence analysis of seven UTL regions determines that their size variation is essentially caused by large deletions/insertions within the internal region, whereas flanking regions are more conserved. UTL-based fingerprinting could be considered as a novel marker system specific of the genus Vitis; moreover, as this multiband genotype is stable between clones it is suitable to be used as a "DNA barcode" for Vitis identification.},
}
@article {pmid17918371,
year = {2007},
author = {Hellgren, O and Krizanauskiene, A and Valkĭunas, G and Bensch, S},
title = {Diversity and phylogeny of mitochondrial cytochrome B lineages from six morphospecies of avian Haemoproteus (Haemosporida: Haemoproteidae).},
journal = {The Journal of parasitology},
volume = {93},
number = {4},
pages = {889-896},
doi = {10.1645/GE-1051R1.1},
pmid = {17918371},
issn = {0022-3395},
mesh = {Animals ; Bird Diseases/*parasitology ; Birds ; Cytochromes b/*genetics ; *Genetic Variation ; Haemosporida/classification/*genetics ; Mitochondria/enzymology ; *Phylogeny ; Protozoan Infections, Animal/*parasitology ; },
abstract = {Species of Haemoproteus (Haemosporida: Haemoproteidae), avian haemosporidians, have traditionally been described based on morphology of their gametocytes and on limited experimental information on their vertebrate host specificity. We investigated to what extent the morphological species are represented by monophyletic groups based on DNA sequence data using 2 different fragment lengths of the cytochrome b (cyt. b) gene. Phylogenetic reconstructions of obtained cyt. b lineages from 6 morphospecies of Haemoproteus showed that all lineages formed monophyletic clusters matching the morphospecies. Comparing our data with a recently published study showed that this is not always the case; the morphospecies H. belopolskyi consists of 2 distinct clusters of lineages that apparently have converged in morphology. However, the overall broad congruence between the molecular and morphological clustering of lineages will facilitate the integration of the knowledge obtained by traditional and molecular parasitology. Mean between morphospecies variation was 10-fold higher than the within species variation (5.5% vs. 0.54%), suggesting that Haemoproteus lineages with a genetic differentiation >5% are expected to be morphologically differentiated in most cases. When investigate the utility of 2 different fragment sizes of the cyt. b gene, the partial, 479-bp, cyt. b protocol picked up all mitochondrial (mt)DNA lineages that are found when using the full cyt. b gene, 1073 bp, suggesting that this protocol is sufficient for identification of most mtDNA lineages. All of the mtDNA lineages were associated with unique alleles when amplification was possible at a nuclear locus, strengthening the hypothesis that the designation of lineages based on mtDNA is largely genome-wide representative. We, therefore, propose the use of a cyt. b fragment of this length as a standard gene fragment for a DNA bar-coding system for avian Haemoproteus species.},
}
@article {pmid17911319,
year = {2007},
author = {Chantangsi, C and Lynn, DH and Brandl, MT and Cole, JC and Hetrick, N and Ikonomi, P},
title = {Barcoding ciliates: a comprehensive study of 75 isolates of the genus Tetrahymena.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {57},
number = {Pt 10},
pages = {2412-2423},
doi = {10.1099/ijs.0.64865-0},
pmid = {17911319},
issn = {1466-5026},
mesh = {Animals ; Cluster Analysis ; Cyclooxygenase 1/*genetics ; DNA, Protozoan/chemistry/genetics ; Molecular Sequence Data ; Parasitology/*methods ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; Tetrahymenina/*classification/*genetics ; },
abstract = {The mitochondrial cytochrome-c oxidase subunit 1 (cox1) gene has been proposed as a DNA barcode to identify animal species. To test the applicability of the cox1 gene in identifying ciliates, 75 isolates of the genus Tetrahymena and three non-Tetrahymena ciliates that are close relatives of Tetrahymena, Colpidium campylum, Colpidium colpoda and Glaucoma chattoni, were selected. All tetrahymenines of unproblematic species could be identified to the species level using 689 bp of the cox1 sequence, with about 11 % interspecific sequence divergence. Intraspecific isolates of Tetrahymena borealis, Tetrahymena lwoffi, Tetrahymena patula and Tetrahymena thermophila could be identified by their cox1 sequences, showing <0.65 % intraspecific sequence divergence. In addition, isolates of these species were clustered together on a cox1 neighbour-joining (NJ) tree. However, strains identified as Tetrahymena pyriformis and Tetrahymena tropicalis showed high intraspecific sequence divergence values of 5.01 and 9.07 %, respectively, and did not cluster together on a cox1 NJ tree. This may indicate the presence of cryptic species. The mean interspecific sequence divergence of Tetrahymena was about 11 times greater than the mean intraspecific sequence divergence, and this increased to 58 times when all isolates of species with high intraspecific sequence divergence were excluded. This result is similar to DNA barcoding studies on animals, indicating that congeneric sequence divergences are an order of magnitude greater than conspecific sequence divergences. Our analysis also demonstrated low sequence divergences of <1.0 % between some isolates of T. pyriformis and Tetrahymena setosa on the one hand and some isolates of Tetrahymena furgasoni and T. lwoffi on the other, suggesting that the latter species in each pair is a junior synonym of the former. Overall, our study demonstrates the feasibility of using the mitochondrial cox1 gene as a taxonomic marker for 'barcoding' and identifying Tetrahymena species and some other ciliated protists.},
}
@article {pmid17904871,
year = {2007},
author = {Whittaker, DJ and Morales, JC and Melnick, DJ},
title = {Resolution of the Hylobates phylogeny: congruence of mitochondrial D-loop sequences with molecular, behavioral, and morphological data sets.},
journal = {Molecular phylogenetics and evolution},
volume = {45},
number = {2},
pages = {620-628},
doi = {10.1016/j.ympev.2007.08.009},
pmid = {17904871},
issn = {1055-7903},
mesh = {Animals ; Behavior, Animal/*physiology ; DNA, Mitochondrial/*analysis/chemistry ; Demography ; Genetic Speciation ; Hylobates/*anatomy &amp; histology/*classification/*genetics ; Indonesia ; Likelihood Functions ; Nucleic Acid Conformation ; *Phylogeny ; },
abstract = {Gibbons of the genus Hylobates likely speciated very rapidly following isolation by rising sea levels during the Pleistocene. We sequenced the hypervariable region I (HV-I) of the mitochondrial D-loop to reconstruct the phylogeny of this group. Although the results clearly supported monophyly of each of the six species, the relationships among them were not clearly resolved by these data alone. A homogeneity test against published data sets of a coding mitochondrial locus (ND3-ND4 region), behavioral characters (vocalizations), and morphological traits (including skeletal and soft tissue anatomy) revealed no significant incongruence, and combining them resulted in a phylogenetic tree with much stronger support. The Kloss's gibbon (H. klossii), long considered a primitive taxon based on morphology, shares many molecular and vocal characteristics with the Javan gibbon (H. moloch), and appear as the most recently derived species. The northernmost species (H. lar and H. pileatus) are the most basal taxa. These data suggest that ancestral gibbons radiated from north to south. Unlike other markers, the HV-I region can accurately identify members of different gibbon species much like a DNA barcode, with potential applications to conservation.},
}
@article {pmid17878950,
year = {2007},
author = {Akhras, MS and Unemo, M and Thiyagarajan, S and Nyrén, P and Davis, RW and Fire, AZ and Pourmand, N},
title = {Connector inversion probe technology: a powerful one-primer multiplex DNA amplification system for numerous scientific applications.},
journal = {PloS one},
volume = {2},
number = {9},
pages = {e915},
pmid = {17878950},
issn = {1932-6203},
support = {P01 HG000205/HG/NHGRI NIH HHS/United States ; P01-HG000205/HG/NHGRI NIH HHS/United States ; },
mesh = {DNA/*genetics ; *DNA Probes ; Drug Resistance, Microbial/genetics ; Mutation ; },
abstract = {We combined components of a previous assay referred to as Molecular Inversion Probe (MIP) with a complete gap filling strategy, creating a versatile powerful one-primer multiplex amplification system. As a proof-of-concept, this novel method, which employs a Connector Inversion Probe (CIPer), was tested as a genetic tool for pathogen diagnosis, typing, and antibiotic resistance screening with two distinct systems: i) a conserved sequence primer system for genotyping Human Papillomavirus (HPV), a cancer-associated viral agent and ii) screening for antibiotic resistance mutations in the bacterial pathogen Neisseria gonorrhoeae. We also discuss future applications and advances of the CIPer technology such as integration with digital amplification and next-generation sequencing methods. Furthermore, we introduce the concept of two-dimension informational barcodes, i.e. "multiplex multiplexing padlocks" (MMPs). For the readers' convenience, we also provide an on-line tutorial with user-interface software application CIP creator 1.0.1, for custom probe generation from virtually any new or established primer-pairs.},
}
@article {pmid17827333,
year = {2007},
author = {Komon-Zelazowska, M and Bissett, J and Zafari, D and Hatvani, L and Manczinger, L and Woo, S and Lorito, M and Kredics, L and Kubicek, CP and Druzhinina, IS},
title = {Genetically closely related but phenotypically divergent Trichoderma species cause green mold disease in oyster mushroom farms worldwide.},
journal = {Applied and environmental microbiology},
volume = {73},
number = {22},
pages = {7415-7426},
pmid = {17827333},
issn = {0099-2240},
mesh = {Base Sequence ; Canada ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/genetics ; Europe ; *Genetic Variation ; Iran ; Korea ; Molecular Sequence Data ; New Zealand ; Phenotype ; Phylogeny ; *Pleurotus ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Species Specificity ; Trichoderma/classification/*genetics/growth &amp; development ; United States ; },
abstract = {The worldwide commercial production of the oyster mushroom Pleurotus ostreatus is currently threatened by massive attacks of green mold disease. Using an integrated approach to species recognition comprising analyses of morphological and physiological characters and application of the genealogical concordance of multiple phylogenetic markers (internal transcribed spacer 1 [ITS1] and ITS2 sequences; partial sequences of tef1 and chi18-5), we determined that the causal agents of this disease were two genetically closely related, but phenotypically strongly different, species of Trichoderma, which have been recently described as Trichoderma pleurotum and Trichoderma pleuroticola. They belong to the Harzianum clade of Hypocrea/Trichoderma which also includes Trichoderma aggressivum, the causative agent of green mold disease of Agaricus. Both species have been found on cultivated Pleurotus and its substratum in Europe, Iran, and South Korea, but T. pleuroticola has also been isolated from soil and wood in Canada, the United States, Europe, Iran, and New Zealand. T. pleuroticola displays pachybasium-like morphological characteristics typical of its neighbors in the Harzianum clade, whereas T. pleurotum is characterized by a gliocladium-like conidiophore morphology which is uncharacteristic of the Harzianum clade. Phenotype MicroArrays revealed the generally impaired growth of T. pleurotum on numerous carbon sources readily assimilated by T. pleuroticola and T. aggressivum. In contrast, the Phenotype MicroArray profile of T. pleuroticola is very similar to that of T. aggressivum, which is suggestive of a close genetic relationship. In vitro confrontation reactions with Agaricus bisporus revealed that the antagonistic potential of the two new species against this mushroom is perhaps equal to T. aggressivum. The P. ostreatus confrontation assays showed that T. pleuroticola has the highest affinity to overgrow mushroom mycelium among the green mold species. We conclude that the evolutionary pathway of T. pleuroticola could be in parallel to other saprotrophic and mycoparasitic species from the Harzianum clade and that this species poses the highest infection risk for mushroom farms, whereas T. pleurotum could be specialized for an ecological niche connected to components of Pleurotus substrata in cultivation. A DNA BarCode for identification of these species based on ITS1 and ITS2 sequences has been provided and integrated in the main database for Hypocrea/Trichoderma (www.ISTH.info).},
}
@article {pmid17826361,
year = {2008},
author = {Adams, ER and Hamilton, PB and Malele, II and Gibson, WC},
title = {The identification, diversity and prevalence of trypanosomes in field caught tsetse in Tanzania using ITS-1 primers and fluorescent fragment length barcoding.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {8},
number = {4},
pages = {439-444},
doi = {10.1016/j.meegid.2007.07.013},
pmid = {17826361},
issn = {1567-1348},
mesh = {Animals ; Cross-Sectional Studies ; DNA Primers/chemistry ; DNA, Intergenic/analysis/chemistry ; DNA, Protozoan/analysis ; Electronic Data Processing ; Fluorescent Dyes/chemistry ; *Genetic Variation ; Humans ; Intestines/parasitology ; Nucleic Acid Amplification Techniques/*methods ; Tanzania ; Trypanosoma/*genetics/isolation &amp; purification ; Trypanosomiasis, African/*epidemiology/parasitology ; Tsetse Flies/*parasitology ; },
abstract = {We report on the development of two generic, PCR-based methods, which replace the multiple species-specific PCR tests used previously to identify the trypanosome species carried by individual tsetse flies. The first method is based on interspecies size variation in the PCR product of the ITS-1 region of the ribosomal RNA (rRNA) locus. In the second approach, length variation of multiple fragments within the 18S and 28S rRNA genes is assayed by PCR amplification with fluorescent primers; products are subsequently sized accurately and rapidly by the use of an automated DNA sequencer. Both methods were used to identify samples collected during large-scale field studies of trypanosome-infected tsetse in Tanzania in the National Parks of Tarangire and Serengeti, and the coastal forest reserve of Msubugwe. The fluctuations of trypanosome prevalence over time and two different field seasons are discussed. As well as facilitating the identification of trypanosome species with increased speed, precision and sensitivity, these generic systems have enabled us to identify two new species of trypanosome.},
}
@article {pmid17785265,
year = {2007},
author = {Elias, M and Hill, RI and Willmott, KR and Dasmahapatra, KK and Brower, AV and Mallet, J and Jiggins, CD},
title = {Limited performance of DNA barcoding in a diverse community of tropical butterflies.},
journal = {Proceedings. Biological sciences},
volume = {274},
number = {1627},
pages = {2881-2889},
pmid = {17785265},
issn = {0962-8452},
mesh = {Animals ; Butterflies/*classification/genetics ; Cluster Analysis ; DNA, Mitochondrial/chemistry ; Phylogeny ; Sequence Analysis, DNA/*methods ; Tropical Climate ; },
abstract = {DNA 'barcoding' relies on a short fragment of mitochondrial DNA to infer identification of specimens. The method depends on genetic diversity being markedly lower within than between species. Closely related species are most likely to share genetic variation in communities where speciation rates are rapid and effective population sizes are large, such that coalescence times are long. We assessed the applicability of DNA barcoding (here the 5' half of the cytochrome c oxidase I) to a diverse community of butterflies from the upper Amazon, using a group with a well-established morphological taxonomy to serve as a reference. Only 77% of species could be accurately identified using the barcode data, a figure that dropped to 68% in species represented in the analyses by more than one geographical race and at least one congener. The use of additional mitochondrial sequence data hardly improved species identification, while a fragment of a nuclear gene resolved issues in some of the problematic species. We acknowledge the utility of barcodes when morphological characters are ambiguous or unknown, but we also recommend the addition of nuclear sequence data, and caution that species-level identification rates might be lower in the most diverse habitats of our planet.},
}
@article {pmid17760313,
year = {2007},
author = {},
title = {An extra dose of safety. Installation of a bar-coding system drives an entire workflow redesign at a non-profit hospital and healthcare network.},
journal = {Health management technology},
volume = {28},
number = {4},
pages = {30-2, 34},
pmid = {17760313},
issn = {1074-4770},
mesh = {Diffusion of Innovation ; Electronic Data Processing/*statistics &amp; numerical data ; *Hospitals, Voluntary ; Medication Systems, Hospital/*organization &amp; administration ; Organizational Case Studies ; Pennsylvania ; Safety Management/*organization &amp; administration ; },
}
@article {pmid17715995,
year = {2007},
author = {Sattayasamitsathit, S and Burdick, J and Bash, R and Kanatharana, P and Thavarungkul, P and Wang, J},
title = {Alloy nanowires bar codes based on nondestructive X-ray fluorescence readout.},
journal = {Analytical chemistry},
volume = {79},
number = {19},
pages = {7571-7575},
doi = {10.1021/ac071206m},
pmid = {17715995},
issn = {0003-2700},
mesh = {*Alloys ; *Electronic Data Processing ; Fluorescence ; *Nanowires ; Reproducibility of Results ; X-Rays ; },
abstract = {We demonstrate here the ability to generate ternary Co-Ni-Cu alloy nanowires with distinct X-ray fluorescence (XRF) barcode patterns using a one-step template-guided electrodeposition. Such coupling of one-step templated synthesis with a nondestructive XRF readout of the composition patterns greatly simplifies practical applications of barcoded nanomaterials. The new protocol leads to alloy nanowires with broad composition range and hence to an extremely large number of distinguishable XRF signatures. The resulting fluorescence barcodes correlate well with the composition of the metal mixture plating solution, indicating a reproducible plating processes. Factors affecting the coding capacity and identification accuracy are examined, and potential tracking and authenticity applications involving embedding the nanowires within plastics or inks are demonstrated and discussed.},
}
@article {pmid17712605,
year = {2007},
author = {Ros, VI and Breeuwer, JA},
title = {Spider mite (Acari: Tetranychidae) mitochondrial COI phylogeny reviewed: host plant relationships, phylogeography, reproductive parasites and barcoding.},
journal = {Experimental &amp; applied acarology},
volume = {42},
number = {4},
pages = {239-262},
pmid = {17712605},
issn = {0168-8162},
mesh = {Animals ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; *Genetic Variation ; Host-Parasite Interactions/genetics ; *Phylogeny ; Plants/*parasitology ; Sequence Alignment ; Sequence Analysis, DNA ; Symbiosis/genetics ; Tetranychidae/classification/*genetics/microbiology ; },
abstract = {The past 15 years have witnessed a number of molecular studies that aimed to resolve issues of species delineation and phylogeny of mites in the family Tetranychidae. The central part of the mitochondrial COI region has frequently been used for investigating intra- and interspecific variation. All these studies combined yield an extensive database of sequence information of the family Tetranychidae. We assembled this information in a single alignment and performed an overall phylogenetic analysis. The resulting phylogeny shows that important patterns have been overlooked in previous studies, whereas others disappear. It also reveals that mistakes were made in submitting the data to GenBank, which further disturbed interpretation of the data. Our total analysis clearly shows three clades that most likely correspond to the species T. urticae, T. kanzawai and T. truncatus. Intraspecific variation is very high, possibly due to selective sweeps caused by reproductive parasites. We found no evidence for host plant associations and phylogeographic patterns in T. urticae are absent. Finally we evaluate the application of DNA barcoding.},
}
@article {pmid17705551,
year = {2007},
author = {Klostranec, JM and Xiang, Q and Farcas, GA and Lee, JA and Rhee, A and Lafferty, EI and Perrault, SD and Kain, KC and Chan, WC},
title = {Convergence of quantum dot barcodes with microfluidics and signal processing for multiplexed high-throughput infectious disease diagnostics.},
journal = {Nano letters},
volume = {7},
number = {9},
pages = {2812-2818},
doi = {10.1021/nl071415m},
pmid = {17705551},
issn = {1530-6984},
mesh = {Biomarkers/blood ; Blood Chemical Analysis/*instrumentation/methods ; Diagnosis, Computer-Assisted/*instrumentation ; Humans ; Microfluidic Analytical Techniques/*instrumentation/methods ; *Quantum Dots ; Signal Processing, Computer-Assisted/instrumentation ; Spectrometry, Fluorescence/instrumentation/methods ; Systems Integration ; Virus Diseases/*blood/*diagnosis ; },
abstract = {Through the convergence of nano- and microtechnologies (quantum dots and microfluidics), we have created a diagnostic system capable of multiplexed, high-throughput analysis of infectious agents in human serum samples. We demonstrate, as a proof-of-concept, the ability to detect serum biomarkers of the most globally prevalent blood-borne infectious diseases (i.e., hepatitis B, hepatitis C, and HIV) with low sample volume (<100 microL), rapidity (<1 h), and 50 times greater sensitivity than that of currently available FDA-approved methods. We further show precision for detecting multiple biomarkers simultaneously in serum with minimal cross-reactivity. This device could be further developed into a portable handheld point-of-care diagnostic system, which would represent a major advance in detecting, monitoring, treating, and preventing infectious disease spread in the developed and developing worlds.},
}
@article {pmid17695719,
year = {2007},
author = {Voorhoeve, PM and le Sage, C and Schrier, M and Gillis, AJ and Stoop, H and Nagel, R and Liu, YP and van Duijse, J and Drost, J and Griekspoor, A and Zlotorynski, E and Yabuta, N and De Vita, G and Nojima, H and Looijenga, LH and Agami, R},
title = {A genetic screen implicates miRNA-372 and miRNA-373 as oncogenes in testicular germ cell tumors.},
journal = {Advances in experimental medicine and biology},
volume = {604},
number = {},
pages = {17-46},
doi = {10.1007/978-0-387-69116-9_2},
pmid = {17695719},
issn = {0065-2598},
mesh = {Animals ; Base Sequence ; Cell Line, Tumor ; Cell Transformation, Neoplastic ; *Gene Expression Regulation ; *Genetic Techniques ; Genetic Testing/methods ; Humans ; Male ; Mice ; Mice, Nude ; MicroRNAs/chemistry/*genetics ; Molecular Sequence Data ; Neoplasm Transplantation ; Neoplasms, Germ Cell and Embryonal/*genetics ; Protein Serine-Threonine Kinases/metabolism ; Testicular Neoplasms/*genetics ; Tumor Suppressor Protein p53/metabolism ; Tumor Suppressor Proteins/metabolism ; ras Proteins/metabolism ; },
abstract = {Endogenous small RNAs (miRNAs) regulate gene expression by mechanisms conserved across metazoans. While the number of verified human miRNAs is still expanding, only few have been functionally annotated. To perform genetic screens for novel functions of miRNAs, we developed a library of vectors expressing the majority of cloned human miRNAs and created corresponding DNA barcode arrays. In a screen for miRNAs that cooperate with oncogenes in cellular transformation, we identified miR-372 and miR-373, each permitting proliferation and tumorigenesis of primary human cells that harbor both oncogenic RAS and active wild-type p53. These miRNAs neutralize p53-mediated CDK inhibition, possibly through direct inhibition of the expression of the tumorsuppressor LATS2. We provide evidence that these miRNAs are potential novel oncogenes participating in the development of human testicular germ cell tumors by numbing the p53 pathway, thus allowing tumorigenic growth in the presence of wild-type p53.},
}
@article {pmid17688684,
year = {2007},
author = {Kuramae, EE and Robert, V and Echavarri-Erasun, C and Boekhout, T},
title = {Cophenetic correlation analysis as a strategy to select phylogenetically informative proteins: an example from the fungal kingdom.},
journal = {BMC evolutionary biology},
volume = {7},
number = {},
pages = {134},
pmid = {17688684},
issn = {1471-2148},
mesh = {Databases, Protein ; Evolution, Molecular ; Fungal Proteins/*genetics ; Fungi/classification/*genetics ; Genome, Fungal ; *Phylogeny ; },
abstract = {BACKGROUND: The construction of robust and well resolved phylogenetic trees is important for our understanding of many, if not all biological processes, including speciation and origin of higher taxa, genome evolution, metabolic diversification, multicellularity, origin of life styles, pathogenicity and so on. Many older phylogenies were not well supported due to insufficient phylogenetic signal present in the single or few genes used in phylogenetic reconstructions. Importantly, single gene phylogenies were not always found to be congruent. The phylogenetic signal may, therefore, be increased by enlarging the number of genes included in phylogenetic studies. Unfortunately, concatenation of many genes does not take into consideration the evolutionary history of each individual gene. Here, we describe an approach to select informative phylogenetic proteins to be used in the Tree of Life (TOL) and barcoding projects by comparing the cophenetic correlation coefficients (CCC) among individual protein distance matrices of proteins, using the fungi as an example. The method demonstrated that the quality and number of concatenated proteins is important for a reliable estimation of TOL. Approximately 40-45 concatenated proteins seem needed to resolve fungal TOL.<br><br>RESULTS: In total 4852 orthologous proteins (KOGs) were assigned among 33 fungal genomes from the Asco- and Basidiomycota and 70 of these represented single copy proteins. The individual protein distance matrices based on 531 concatenated proteins that has been used for phylogeny reconstruction before 14 were compared one with another in order to select those with the highest CCC, which then was used as a reference. This reference distance matrix was compared with those of the 70 single copy proteins selected and their CCC values were calculated. Sixty four KOGs showed a CCC above 0.50 and these were further considered for their phylogenetic potential. Proteins belonging to the cellular processes and signaling KOG category seem more informative than those belonging to the other three categories: information storage and processing; metabolism; and the poorly characterized category. After concatenation of 40 proteins the topology of the phylogenetic tree remained stable, but after concatenation of 60 or more proteins the bootstrap support values of some branches decreased, most likely due to the inclusion of proteins with lowers CCC values. The selection of protein sequences to be used in various TOL projects remains a critical and important process. The method described in this paper will contribute to a more objective selection of phylogenetically informative protein sequences.<br><br>CONCLUSION: This study provides candidate protein sequences to be considered as phylogenetic markers in different branches of fungal TOL. The selection procedure described here will be useful to select informative protein sequences to resolve branches of TOL that contain few or no species with completely sequenced genomes. The robust phylogenetic trees resulting from this method may contribute to our understanding of organismal diversification processes. The method proposed can be extended easily to other branches of TOL.},
}
@article {pmid17671629,
year = {2006},
author = {He, Z and Bolling, L and Tonb, D and Nadal, T and Mehta, DI},
title = {An automated method for the determination of intestinal disaccharidase and glucoamylase activities.},
journal = {Journal of automated methods &amp; management in chemistry},
volume = {2006},
number = {},
pages = {93947},
doi = {10.1155/JAMMC/2006/93947},
pmid = {17671629},
issn = {1463-9246},
abstract = {Determination of disaccharidase and glucoamylase activities is important for the diagnosis of intestinal diseases. We adapted a widely accepted manual method to an automated system that uses the same reagents reaction volumes, incubation times, and biopsy size as the manual method. A dye was added to the homogenates as the internal quality control to monitor the pipetting precision of the automated system. When the automated system was tested using human intestinal homogenates, the activities of all the routinely tested disaccharidases, including lactase, maltase, sucrase, and palatinase, as well as the activity of glucoamylase, showed perfect agreement with the manual method and were highly reproducible. The automated analyzer can perform the same routine assays of disaccharidases and glucoamylase with high consistency and accuracy and reduce testing costs by performing a larger sample size with the same number of staff. Additional developments, such as barcoding and built-in plate reading, would result in a completely automated system.},
}
@article {pmid17670798,
year = {2007},
author = {Meyer, M and Stenzel, U and Myles, S and Prüfer, K and Hofreiter, M},
title = {Targeted high-throughput sequencing of tagged nucleic acid samples.},
journal = {Nucleic acids research},
volume = {35},
number = {15},
pages = {e97},
pmid = {17670798},
issn = {1362-4962},
mesh = {DNA, Mitochondrial/chemistry ; Gene Library ; Genome, Human ; Humans ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; *Sequence Tagged Sites ; },
abstract = {High-throughput 454 DNA sequencing technology allows much faster and more cost-effective sequencing than traditional Sanger sequencing. However, the technology imposes inherent limitations on the number of samples that can be processed in parallel. Here we introduce parallel tagged sequencing (PTS), a simple, inexpensive and flexible barcoding technique that can be used for parallel sequencing any number and type of double-stranded nucleic acid samples. We demonstrate that PTS is particularly powerful for sequencing contiguous DNA fragments such as mtDNA genomes: in theory as many as 250 mammalian mtDNA genomes can be sequenced in a single GS FLX run. PTS dramatically increases the sequencing throughput of samples in parallel and thus fully mobilizes the resources of the 454 technology for targeted sequencing.},
}
@article {pmid17663257,
year = {2007},
author = {Tan, WB and Zhang, Y},
title = {Multi-functional chitosan nanoparticles encapsulating quantum dots and Gd-DTPA as imaging probes for bio-applications.},
journal = {Journal of nanoscience and nanotechnology},
volume = {7},
number = {7},
pages = {2389-2393},
doi = {10.1166/jnn.2007.415},
pmid = {17663257},
issn = {1533-4880},
mesh = {Chitosan/*chemistry ; Coated Materials, Biocompatible/chemistry ; Contrast Media/*chemistry ; Crystallization/methods ; Gadolinium DTPA/*chemistry ; Image Enhancement/methods ; Macromolecular Substances/chemistry ; Magnetic Resonance Imaging/*methods ; Materials Testing ; Microscopy, Fluorescence/*methods ; Molecular Conformation ; Molecular Probe Techniques ; Nanostructures/*chemistry/ultrastructure ; Nanotechnology/methods ; Particle Size ; *Quantum Dots ; Surface Properties ; },
abstract = {Chitosan was used to encapsulate both CdSe/ZnS quantum dots (QDs) and the magnetic resonance imaging (MRI) contrast agent gadolinium-diethylenetriaminepentaacetate (Gd-DTPA), forming multi-functional nanoparticles that can be used in a wide range of in vitro or in vivo studies as fluorescent biological labels as well as MRI contrast agents, respectively. Multi-color QDs at pre-determined molar ratios were encapsulated into chitosan nanoparticles to produce bar-coding fluorescent labels. The encapsulated QDs and Gd-DTPA still maintained their desirable optical properties and relatively high relaxivity, respectively. The chitosan nanoparticles also showed good aqueous stability and enhanced biocompatibility on myoblast cells.},
}
@article {pmid17650475,
year = {2007},
author = {Hart, MW and Sunday, J},
title = {Things fall apart: biological species form unconnected parsimony networks.},
journal = {Biology letters},
volume = {3},
number = {5},
pages = {509-512},
pmid = {17650475},
issn = {1744-9561},
mesh = {Animals ; Butterflies/*classification/genetics ; DNA, Mitochondrial/chemistry ; Haplotypes ; *Phylogeny ; Sequence Alignment ; Snails/*classification/genetics ; },
abstract = {The generality of operational species definitions is limited by problematic definitions of between-species divergence. A recent phylogenetic species concept based on a simple objective measure of statistically significant genetic differentiation uses between-species application of statistical parsimony networks that are typically used for population genetic analysis within species. Here we review recent phylogeographic studies and reanalyse several mtDNA barcoding studies using this method. We found that (i) alignments of DNA sequences typically fall apart into a separate subnetwork for each Linnean species (but with a higher rate of true positives for mtDNA data) and (ii) DNA sequences from single species typically stick together in a single haplotype network. Departures from these patterns are usually consistent with hybridization or cryptic species diversity.},
}
@article {pmid17646954,
year = {2007},
author = {Kutschera, U and Pfeiffer, I and Ebermann, E},
title = {The European land leech: biology and DNA-based taxonomy of a rare species that is threatened by climate warming.},
journal = {Die Naturwissenschaften},
volume = {94},
number = {12},
pages = {967-974},
pmid = {17646954},
issn = {0028-1042},
mesh = {Animals ; Climate ; DNA/genetics/isolation &amp; purification ; Ecosystem ; Europe ; Female ; Greenhouse Effect ; Leeches/anatomy &amp; histology/*classification/genetics/*physiology ; Male ; Molecular Sequence Data ; Population Density ; },
abstract = {The European land leech Xerobdella lecomtei was discovered in 1868 and is one of the rarest animals on Earth. During the 1960s, several individuals of these approx. 40 mm long, cold-adapted terrestrial annelids that inhabit the moist soils of birch forests around Graz, Austria, were investigated. Only one original research paper has been published on the biology of this species. Between 2001 and 2005, we re-investigated the morphology of preserved specimens and searched for living individuals in their natural habitat that appeared to be intact. We found only one juvenile individual (length approx. 10 mm), indicating that this local leech population became largely extinct over the past four decades. The feeding behaviour of our 'lonesome George of the annelids' was studied and is described here in detail. After its death, the Xerobdella individual was used for chemical extraction and molecular studies (deoxyribonucleic acid [DNA] barcoding, based on one gene, the mitochondrial cytochrome c oxidase subunit I). In addition, novel DNA barcodes for a land leech from Madagascar and a recently discovered species from Europe were obtained. Our phylogenetic tree shows that X. lecomtei is not a member of the tropical land leeches (family Haemadipsidae), as previously thought, but represents a separate line of descent (family Xerobdellidae). The decline of the local leech population around Graz correlates with a rise in average summer temperatures of +3 degrees C between 1961 and 2004. This warming led to a drastic reduction in the moisture content of the soil where X. lecomtei lives. We suggest that human-induced climate change without apparent habitat destruction can lead to the extinction of populations of cold-adapted species that have a low colonization ability.},
}
@article {pmid17617512,
year = {2007},
author = {Bates, DW},
title = {Preventing medication errors: a summary.},
journal = {American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists},
volume = {64},
number = {14 Suppl 9},
pages = {S3-9; quiz S24-6},
doi = {10.2146/ajhp070190},
pmid = {17617512},
issn = {1535-2900},
mesh = {Diffusion of Innovation ; Drug Prescriptions ; Humans ; Infusions, Intravenous/standards ; Medical Order Entry Systems ; Medication Errors/*prevention &amp; control ; Medication Systems, Hospital ; National Academies of Science, Engineering, and Medicine, U.S., Health and Medicine Division ; Organizational Innovation ; Pharmacists ; Pharmacy Service, Hospital/*organization &amp; administration ; Professional Role ; Quality Assurance, Health Care/*methods ; Safety Management/*methods ; Technology, Pharmaceutical/*methods ; United States ; },
abstract = {PURPOSE: To summarize key recommendations and supporting evidence from the most recent Institute of Medicine (IOM) report, Preventing Medication Errors.<br><br>SUMMARY: Starting in 2000, IOM reports brought the problem of medical safety into public awareness and made four major points: errors are common and costly, systems cause errors, errors can be prevented and safety can be improved, and medication-related adverse events are the single leading cause of injury. The most recent report is an attempt to think about what needs to be done to reach the next level of medication safety. Some have had difficulty implementing these recommendations, but these challenges can be overcome by learning from these experiences. Evidence supporting the recommendations made in this report includes research on computerized prescriber order entry (renal insufficiency geriatric patients, meta-analysis, unintended consequences, pediatric transfer patients); intravenous infusion safety systems; and dispensing errors and bar-coding.<br><br>CONCLUSION: Preventing Medication Errors lays out a blueprint for change in medication safety. The report makes clear that providers have m any opportunities to improve. Technologies, such as computerized order entry, bar-coding and smart pumps and computerized ADE monitoring, will undoubtedly play a key role, and institutions should be thinking seriously about implementing a number of these. The report also emphasizes how essential a culture change, combined with well-designed technologies, will be necessary to achieve the next level of safety called for in the IOM report.},
}
@article {pmid17602869,
year = {2007},
author = {Hansen, H and Bakke, TA and Bachmann, L},
title = {DNA taxonomy and barcoding of monogenean parasites: lessons from Gyrodactylus.},
journal = {Trends in parasitology},
volume = {23},
number = {8},
pages = {363-367},
doi = {10.1016/j.pt.2007.06.007},
pmid = {17602869},
issn = {1471-4922},
mesh = {Animals ; Base Sequence ; Biodiversity ; DNA, Helminth/*genetics ; Molecular Sequence Data ; *Phylogeny ; Platyhelminths/*classification/*genetics ; Salmon/parasitology ; Species Specificity ; },
abstract = {DNA taxonomy and barcoding use nucleotide sequence data to achieve comprehensive species descriptions that facilitate reliable species diagnostics and rapid assessment of biodiversity, both of which are of great importance for parasitologists. Such molecular approaches have been applied to the monogenean genus Gyrodactylus, in particular to G. salaris, the cause of serious gyrodactylosis on Atlantic salmon. Here, we discuss, using the example of G. salaris and related species, why DNA barcodes, although powerful for biodiversity assessment, are insufficient to appropriately characterize parasite species--from a parasitological point of view--in the absence of additional data on and infection biology and morphology.},
}
@article {pmid17570370,
year = {2007},
author = {Zarowiecki, MZ and Huyse, T and Littlewood, DT},
title = {Making the most of mitochondrial genomes--markers for phylogeny, molecular ecology and barcodes in Schistosoma (Platyhelminthes: Digenea).},
journal = {International journal for parasitology},
volume = {37},
number = {12},
pages = {1401-1418},
doi = {10.1016/j.ijpara.2007.04.014},
pmid = {17570370},
issn = {0020-7519},
mesh = {Animals ; Biomarkers ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genes, Helminth/*genetics ; Genome, Mitochondrial/*genetics ; Models, Genetic ; *Phylogeny ; Polymorphism, Genetic ; Regression Analysis ; Schistosoma/*classification/genetics ; Schistosomiasis/*parasitology ; Sequence Analysis, DNA/methods ; },
abstract = {An increasing number of complete sequences of mitochondrial (mt) genomes provides the opportunity to optimise the choice of molecular markers for phylogenetic and ecological studies. This is particularly the case where mt genomes from closely related taxa have been sequenced; e.g., within Schistosoma. These blood flukes include species that are the causative agents of schistosomiasis, where there has been a need to optimise markers for species and strain recognition. For many phylogenetic and population genetic studies, the choice of nucleotide sequences depends primarily on suitable PCR primers. Complete mt genomes allow individual gene or other mt markers to be assessed relative to one another for potential information content, prior to broad-scale sampling. We assess the phylogenetic utility of individual genes and identify regions that contain the greatest interspecific variation for molecular ecological and diagnostic markers. We show that variable characters are not randomly distributed along the genome and there is a positive correlation between polymorphism and divergence. The mt genomes of African and Asian schistosomes were compared with the available intraspecific dataset of Schistosoma mansoni through sliding window analyses, in order to assess whether the observed polymorphism was at a level predicted from interspecific comparisons. We found a positive correlation except for the two genes (cox1 and nad1) adjoining the putative control region in S. mansoni. The genes nad1, nad4, nad5, cox1 and cox3 resolved phylogenies that were consistent with a benchmark phylogeny and in general, longer genes performed better in phylogenetic reconstruction. Considering the information content of entire mt genome sequences, partial cox1 would not be the ideal marker for either species identification (barcoding) or population studies with Schistosoma species. Instead, we suggest the use of cox3 and nad5 for both phylogenetic and population studies. Five primer pairs designed against Schistosoma mekongi and Schistosoma malayensis were tested successfully against Schistosoma japonicum. In combination, these fragments encompass 20-27% of the variation amongst the genomes (average total length approximately 14,000bp), thus providing an efficient means of encapsulating the greatest amount of variation within the shortest sequence. Comparative mitogenomics provides the basis of a rational approach to molecular marker selection and optimisation.},
}
@article {pmid17567898,
year = {2007},
author = {Hajibabaei, M and Singer, GA and Clare, EL and Hebert, PD},
title = {Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring.},
journal = {BMC biology},
volume = {5},
number = {},
pages = {24},
pmid = {17567898},
issn = {1741-7007},
mesh = {Animals ; *Biodiversity ; Computational Biology ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Mammals/*genetics ; Oligonucleotide Array Sequence Analysis/*methods ; Oligonucleotide Probes/genetics ; Species Specificity ; },
abstract = {BACKGROUND: The rapid and accurate identification of species is a critical component of large-scale biodiversity monitoring programs. DNA arrays (micro and macro) and DNA barcodes are two molecular approaches that have recently garnered much attention. Here, we compare these two platforms for identification of an important group, the mammals.<br><br>RESULTS: Our analyses, based on the two commonly used mitochondrial genes cytochrome c oxidase I (the standard DNA barcode for animal species) and cytochrome b (a common species-level marker), suggest that both arrays and barcodes are capable of discriminating mammalian species with high accuracy. We used three different datasets of mammalian species, comprising different sampling strategies. For DNA arrays we designed three probes for each species to address intraspecific variation. As for DNA barcoding, our analyses show that both cytochrome c oxidase I and cytochrome b genes, and even smaller fragments of them (mini-barcodes) can successfully discriminate species in a wide variety of specimens.<br><br>CONCLUSION: This study showed that DNA arrays and DNA barcodes are valuable molecular methods for biodiversity monitoring programs. Both approaches were capable of discriminating among mammalian species in our test assemblages. However, because designing DNA arrays require advance knowledge of target sequences, the use of this approach could be limited in large scale monitoring programs where unknown haplotypes might be encountered. DNA barcodes, by contrast, are sequencing-based and therefore could provide more flexibility in large-scale studies.},
}
@article {pmid17551588,
year = {2007},
author = {Kress, WJ and Erickson, DL},
title = {A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region.},
journal = {PloS one},
volume = {2},
number = {6},
pages = {e508},
pmid = {17551588},
issn = {1932-6203},
mesh = {DNA, Chloroplast/*genetics ; DNA, Plant/*chemistry/genetics ; DNA, Ribosomal Spacer/*genetics ; *Electronic Data Processing ; Photosystem II Protein Complex/*genetics ; Phylogeny ; Plants/*classification/genetics ; Polymerase Chain Reaction ; Ribulose-Bisphosphate Carboxylase/*genetics ; Species Specificity ; },
abstract = {BACKGROUND: A useful DNA barcode requires sufficient sequence variation to distinguish between species and ease of application across a broad range of taxa. Discovery of a DNA barcode for land plants has been limited by intrinsically lower rates of sequence evolution in plant genomes than that observed in animals. This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level.<br><br>Here, a global plant DNA barcode system is evaluated by comparing universal application and degree of sequence divergence for nine putative barcode loci, including coding and non-coding regions, singly and in pairs across a phylogenetically diverse set of 48 genera (two species per genus). No single locus could discriminate among species in a pair in more than 79% of genera, whereas discrimination increased to nearly 88% when the non-coding trnH-psbA spacer was paired with one of three coding loci, including rbcL. In silico trials were conducted in which DNA sequences from GenBank were used to further evaluate the discriminatory power of a subset of these loci. These trials supported the earlier observation that trnH-psbA coupled with rbcL can correctly identify and discriminate among related species.<br><br>CONCLUSIONS/SIGNIFICANCE: A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination.},
}
@article {pmid17545980,
year = {2007},
author = {Nam, JM and Jang, KJ and Groves, JT},
title = {Detection of proteins using a colorimetric bio-barcode assay.},
journal = {Nature protocols},
volume = {2},
number = {6},
pages = {1438-1444},
doi = {10.1038/nprot.2007.201},
pmid = {17545980},
issn = {1750-2799},
mesh = {Colorimetry/*methods ; DNA Probes ; Electronic Data Processing/*methods ; Gold ; Metal Nanoparticles/chemistry ; Molecular Probes ; Nanoparticles ; Proteins/*analysis/chemistry ; Sensitivity and Specificity ; },
abstract = {The colorimetric bio-barcode assay is a red-to-blue color change-based protein detection method with ultrahigh sensitivity. This assay is based on both the bio-barcode amplification method that allows for detecting miniscule amount of targets with attomolar sensitivity and gold nanoparticle-based colorimetric DNA detection method that allows for a simple and straightforward detection of biomolecules of interest (here we detect interleukin-2, an important biomarker (cytokine) for many immunodeficiency-related diseases and cancers). The protocol is composed of the following steps: (i) conjugation of target capture molecules and barcode DNA strands onto silica microparticles, (ii) target capture with probes, (iii) separation and release of barcode DNA strands from the separated probes, (iv) detection of released barcode DNA using DNA-modified gold nanoparticle probes and (v) red-to-blue color change analysis with a graphic software. Actual target detection and quantification steps with premade probes take approximately 3 h (whole protocol including probe preparations takes approximately 3 days).},
}
@article {pmid17544704,
year = {2007},
author = {Lane, CE and Lindstrom, SC and Saunders, GW},
title = {A molecular assessment of northeast Pacific Alaria species (Laminariales, Phaeophyceae) with reference to the utility of DNA barcoding.},
journal = {Molecular phylogenetics and evolution},
volume = {44},
number = {2},
pages = {634-648},
doi = {10.1016/j.ympev.2007.03.016},
pmid = {17544704},
issn = {1055-7903},
mesh = {Base Sequence ; Chloroplasts/genetics ; Cloning, Molecular ; DNA/*classification/*genetics ; Databases, Nucleic Acid ; Genetic Markers ; Mitochondria/genetics ; Pacific Ocean ; Phaeophyceae/*classification/*genetics ; Phylogeny ; Transcription, Genetic/genetics ; },
abstract = {Despite their relatively complex morphologies, species in the genus Alaria Greville are notoriously difficult to identify with certainty. Morphological characters, often influenced by environmental factors, make individuals in similar habitats artificially appear related. Species identification would, therefore, benefit greatly from the application of molecular tools. We applied DNA barcoding, using the 5' end of the cytochrome c oxidase I (coxI-5') gene from the mitochondrial genome, to define species limits and relationships in northeast Pacific populations of Alaria. This emerging technique is being employed to catalogue species diversity worldwide, particularly among animals, and it has been shown to be sensitive enough to discriminate between closely related species. However, the utility of this marker for identifying or categorizing the majority of life remains unclear. We compared the resolution obtained with this marker to two other molecular systems commonly used in algal research: the nuclear internal transcribed spacer (ITS) of the ribosomal cistron, and the plastid Rubisco operon spacer (rbcSp). In agreement with previous results, Alaria fistulosa Postels &amp; Ruprecht, with its distinct morphological, ecological and molecular features, stands apart from the other species in the genus and we establish Druehlia gen. nov. to accommodate it. For the remaining isolates, distinct mitochondrial haplotypes resolved with the barcode data indicate a period of genetic isolation for at least three incipient species in the northeast Pacific, whereas unexpected levels and patterns of ITS variation, as well as the extreme morphological plasticity found among these isolates, have most probably resulted from a recent collapse in species barriers. The cloning of ITS amplicons revealed multiple ITS copies in several individuals, further supporting this hypothesis.},
}
@article {pmid17531795,
year = {2007},
author = {Samadi, S and Quéméré, E and Lorion, J and Tillier, A and von Cosel, R and Lopez, P and Cruaud, C and Couloux, A and Boisselier-Dubayle, MC},
title = {Molecular phylogeny in mytilids supports the wooden steps to deep-sea vents hypothesis.},
journal = {Comptes rendus biologies},
volume = {330},
number = {5},
pages = {446-456},
doi = {10.1016/j.crvi.2007.04.001},
pmid = {17531795},
issn = {1631-0691},
mesh = {Animals ; Genetic Variation ; Molecular Biology ; Mytilidae/*classification/*genetics ; Phylogeny ; Seawater/*parasitology ; Wood/*parasitology ; },
abstract = {Molecular data were used to study the diversity of mytilids associated with sunken-woods sampled in the Solomon Islands and discuss the 'wooden steps to deep-sea vent' hypothesis proposed by Distel et al. First, COI data used in a barcoding approach confirm the presence of four distinct species. Analyses of the 18S rDNA and COI dataset then confirmed that these sunken-wood mytilids belonged to a monophyletic group including all species from deep-sea reducing environments. Finally, we analyzed the relationships within this monophyletic group that include the Bathymodiolinae using a COI dataset and a combined analysis of mitochondrial COI and ND4 genes and nuclear rDNA 18S and 28S. Our study supported the 'wooden steps to deep-sea vent' hypothesis: one of the sunken-wood species had a basal position within the Bathymodiolionae, and all described vent and seep mussels included in our analyses were derived taxa within Bathymodiolinae.},
}
@article {pmid17486881,
year = {2007},
author = {Fournier-Wirth, C and Coste, J},
title = {Fitting new technologies into the safety paradigm: use of microarrays in transfusion.},
journal = {Developments in biologicals},
volume = {127},
number = {},
pages = {61-70},
pmid = {17486881},
issn = {1424-6074},
mesh = {Blood Banking/*methods ; Blood Transfusion/*methods ; Humans ; Mass Screening/*methods/trends ; Oligonucleotide Array Sequence Analysis/*methods/trends ; Protein Array Analysis/*methods/trends ; Viruses/*genetics ; },
abstract = {Until the late 1990s, mandatory blood screening for transmissible infectious agents depended entirely on antigen/antibody-based detection assays. The recent emergence of Nucleic acid Amplification Technologies (NAT) has revolutionised viral diagnosis, not only by increasing the level of sensitivity but also by facilitating the detection of several viruses in parallel by multiplexing specific primers. In more complex biological situations, when a broad spectrum of pathogens must be screened, the limitations of these first generation technologies became apparent. High throughput systems, such as DNA Arrays, permit a conceptually new approach. These miniaturised micro systems allow the detection of hundreds of different targets simultaneously, inducing a dramatic decrease in reagent consumption, a reduction in the number of confirmation tests and a simplification of data interpretation. However, the systems currently available require additional instrumentation and reagents for sample preparation and target amplification prior to detection on the DNA array. A major challenge in the area of DNA detection is the development of methods that do not rely on target amplification systems. Likewise, the advances of protein microarrays have lagged because of poor stability of proteins, complex coupling chemistry and weak detection signals. Emerging technologies like Biosensors and nano-particle based DNA or Protein Bio-Barcode Amplification Assays are promising diagnostic tools for a wide range of clinical applications, including blood donation screening.},
}
@article {pmid17472911,
year = {2007},
author = {Whitworth, TL and Dawson, RD and Magalon, H and Baudry, E},
title = {DNA barcoding cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae).},
journal = {Proceedings. Biological sciences},
volume = {274},
number = {1619},
pages = {1731-1739},
pmid = {17472911},
issn = {0962-8452},
mesh = {Animals ; Classification/*methods ; Diptera/classification/*genetics/microbiology ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Hybridization, Genetic ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; United States ; Wolbachia/genetics ; },
abstract = {In DNA barcoding, a short standardized DNA sequence is used to assign unknown individuals to species and aid in the discovery of new species. A fragment of the mitochondrial gene cytochrome c oxidase subunit 1 is emerging as the standard barcode region for animals. However, patterns of mitochondrial variability can be confounded by the spread of maternally transmitted bacteria that cosegregate with mitochondria. Here, we investigated the performance of barcoding in a sample comprising 12 species of the blow fly genus Protocalliphora, known to be infected with the endosymbiotic bacteria Wolbachia. We found that the barcoding approach showed very limited success: assignment of unknown individuals to species is impossible for 60% of the species, while using the technique to identify new species would underestimate the species number in the genus by 75%. This very low success of the barcoding approach is due to the non-monophyly of many of the species at the mitochondrial level. We even observed individuals from four different species with identical barcodes, which is, to our knowledge, the most extensive case of mtDNA haplotype sharing yet described. The pattern of Wolbachia infection strongly suggests that the lack of within-species monophyly results from introgressive hybridization associated with Wolbachia infection. Given that Wolbachia is known to infect between 15 and 75% of insect species, we conclude that identification at the species level based on mitochondrial sequence might not be possible for many insects. However, given that Wolbachia-associated mtDNA introgression is probably limited to very closely related species, identification at the genus level should remain possible.},
}
@article {pmid17464840,
year = {2007},
author = {Summerbell, RC and Moore, MK and Starink-Willemse, M and Van Iperen, A},
title = {ITS barcodes for Trichophyton tonsurans and T. equinum.},
journal = {Medical mycology},
volume = {45},
number = {3},
pages = {193-200},
doi = {10.1080/13693780601087614},
pmid = {17464840},
issn = {1369-3786},
mesh = {Animals ; DNA, Fungal/chemistry/*genetics ; DNA, Ribosomal Spacer/chemistry/*genetics ; Genotype ; Horse Diseases/microbiology ; Horses ; Humans ; Molecular Sequence Data ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Tinea/microbiology/veterinary ; Trichophyton/*classification/*genetics ; },
abstract = {Early molecular biosystematic studies of dermatophytes created considerable confusion about the taxonomic status of the horse-associated Trichophyton equinum vis-à-vis the anthropophilic T. tonsurans. Though this matter has recently been clarified, routine identification of these species based on the commonly used ribosomal internal transcribed spacer (ITS) sequence has been impractical. This is because, in the available sequences attributed to the species in GenBank, a clear species-level distinction does not appear to exist. In the present study, resequencing the ITS regions of several anomalous isolates is shown to eliminate this problem, which was mainly based on read errors in older sequences. Newly generated sequences and recent GenBank additions are analysed to show that T. equinum appears to be uniform in ITS sequence worldwide, while T. tonsurans is also uniform, excepting a single-base change found in one otherwise typical strain. Analysis also reveals a distinct, as yet incompletely classified Asian genotype that may belong to one or the other of these species. Standard ITS 'barcode sequences' are proposed for T. tonsurans and T. equinum, and a taxonomic neotype is designated to anchor the latter species. T. equinum var. autotrophicum is further evidenced as very closely related to T. equinum var. equinum, and the anomaly of its plesiomorphous phenotype is discussed in a population genetics context.},
}
@article {pmid17464200,
year = {2007},
author = {Park, MH and Sim, CJ and Baek, J and Min, GS},
title = {Identification of genes suitable for DNA barcoding of morphologically indistinguishable Korean Halichondriidae sponges.},
journal = {Molecules and cells},
volume = {23},
number = {2},
pages = {220-227},
pmid = {17464200},
issn = {1016-8478},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Markers ; *Genetic Variation ; Korea ; *Phylogeny ; Porifera/classification/*genetics ; },
abstract = {The development of suitable genetic markers would be useful for defining species and delineating the species boundaries of morphologically indistinguishable sponges. In this study, genetic variation in the sequences of nuclear rDNA and the mitochondrial cytochrome c oxidase subunit 1 and 3 (CO1 and CO3) regions were compared in morphologically indistinguishable Korean Halichondriidae sponges in order to determine the most suitable species-specific molecular marker region. The maximal congeneric nucleotide divergences of Halichondriidae sponges in CO1 and CO3 are similar to those found among anthozoan cnidarians, but they are 2- to 8-fold lower than those found among genera of other triploblastic metazoans. Ribosomal internal transcribed spacer regions (ITS: ITS1 + ITS2) showed higher congeneric variation (17.28% in ITS1 and 10.29% in ITS2) than those of CO1 and CO3. Use of the guidelines for species thresholds suggested in the recent literature indicates that the mtDNA regions are not appropriate for use as species-specific DNA markers for the Halichondriidae sponges, whereas the rDNA ITS regions are suitable because ITS exhibits a low level of intraspecific variation and a relatively high level of interspecific variation. In addition, to test the reliability of the ITS regions for identifying Halichondriidae sponges by PCR, a species-specific multiplex PCR primer set was developed.},
}
@article {pmid17444904,
year = {2007},
author = {Pfenninger, M and Nowak, C and Kley, C and Steinke, D and Streit, B},
title = {Utility of DNA taxonomy and barcoding for the inference of larval community structure in morphologically cryptic Chironomus (Diptera) species.},
journal = {Molecular ecology},
volume = {16},
number = {9},
pages = {1957-1968},
doi = {10.1111/j.1365-294X.2006.03136.x},
pmid = {17444904},
issn = {0962-1083},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; Chironomidae/anatomy &amp; histology/classification/*genetics ; Classification/*methods ; DNA Primers ; DNA, Mitochondrial/genetics ; *Ecosystem ; Germany ; Larva/anatomy &amp; histology ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA/methods ; Species Specificity ; },
abstract = {Biodiversity studies require species level analyses for the accurate assessment of community structures. However, while specialized taxonomic knowledge is only rarely available for routine identifications, DNA taxonomy and DNA barcoding could provide the taxonomic basis for ecological inferences. In this study, we assessed the community structure of sediment dwelling, morphologically cryptic Chironomus larvae in the Rhine-valley plain/Germany, comparing larval type classification, cytotaxonomy, DNA taxonomy and barcoding. While larval type classification performed poorly, cytotaxonomy and DNA-based methods yielded comparable results: detrended correspondence analysis and permutation analyses indicated that the assemblages are not randomly but competitively structured. However, DNA taxonomy identified an additional species that could not be resolved by the traditional method. We argue that DNA-based identification methods such as DNA barcoding can be a valuable tool to increase accuracy, objectivity and comparability of the taxonomic assessment in biodiversity and community ecology studies.},
}
@article {pmid17443670,
year = {2007},
author = {Xiao, M and Gordon, MP and Phong, A and Ha, C and Chan, TF and Cai, D and Selvin, PR and Kwok, PY},
title = {Determination of haplotypes from single DNA molecules: a method for single-molecule barcoding.},
journal = {Human mutation},
volume = {28},
number = {9},
pages = {913-921},
doi = {10.1002/humu.20528},
pmid = {17443670},
issn = {1098-1004},
mesh = {Chromosomes, Human, Pair 17 ; DNA/*analysis ; DNA Mutational Analysis/*methods ; Electronic Data Processing ; Feasibility Studies ; *Haplotypes ; Humans ; Microscopy, Fluorescence/*methods ; Models, Biological ; *Polymorphism, Single Nucleotide ; Psoriasis/genetics ; Staining and Labeling ; },
abstract = {Determining the haplotypes in a diploid individual is a major technical challenge in genetic studies of human complex traits. Here we report a method of molecular haplotyping by directly imaging multiple polymorphic sites on individual DNA molecules simultaneously. DNA fragments amplified by long-range PCR were labeled with fluorescent dyes at each polymorphic site using a modified gap-filled padlock probe ligation approach. The labeled DNA molecules were then stretched into linear form on a functionalized glass surface and imaged with multicolor total internal reflection fluorescence (TIRF) microscopy. By determining the colors and positions of the fluorescent labels with respect to the backbone at polymorphic sites, the haplotype can be inferred accurately, in a manner similar to reading a barcode, even when the DNA fragments are not fully labeled. The feasibility of this technology is demonstrated by the determination of the haplotype of a 9.3-kbp DNA fragment containing four SNPs.},
}
@article {pmid17434693,
year = {2007},
author = {Kartavtsev, YP and Jung, SO and Lee, YM and Byeon, HK and Lee, JS},
title = {Complete mitochondrial genome of the bullhead torrent catfish, Liobagrus obesus (Siluriformes, Amblycipididae): Genome description and phylogenetic considerations inferred from the Cyt b and 16S rRNA genes.},
journal = {Gene},
volume = {396},
number = {1},
pages = {13-27},
doi = {10.1016/j.gene.2007.01.027},
pmid = {17434693},
issn = {0378-1119},
mesh = {Analysis of Variance ; Animals ; Base Composition/genetics ; Base Sequence ; Codon/genetics ; Conserved Sequence ; Cytochrome b Group/*genetics ; DNA, Mitochondrial/*genetics ; Genome/*genetics ; Ictaluridae/*genetics ; Molecular Sequence Data ; Open Reading Frames/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; RNA, Transfer/genetics ; },
abstract = {Mitochondrial DNA (mtDNA) from the bullhead torrent catfish, Liobagrus obesus, was isolated by long-polymerase chain reaction (Long-PCR) with universal primers and was fully sequenced by primer working using flanking sequences. The complete mtDNA from L. obesus was 16,531 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region, demonstrating a structure very similar to that of other bony fish. An analysis of the protein-coding genes revealed a statistically substantiated bias in (T+C): (A+G) content, supporting earlier findings regarding this peculiarity. As indicated by a chi-square test, the observed scores for pyrimidine and purine content were different from those expected assuming a 50:50 ratio: chi(2)=41.63, d.f.=5, p<0.000001 for three categories, including the 1st, 2nd, and 3rd codon positions. Further, there was a difference in nucleotide content between ND6 and the other 12 protein-coding genes in L. obesus. The values of p-distances, as summarized for different scales of evolutionary history at the Cyt b gene, revealed a clear pattern of increased nucleotide diversity at four levels: (1) intraspecies, (2) intragenus, (3) intrafamily, and (4) intraorder. Scores of average p-distances of the four categories in catfish were (1) 1.59+/-0.54%, (2) 5.28+/-1.72% (3) 16.37+/-1.26%, and (4) 19.81+/-0.14%, respectively. These data support the hypothesis that speciation in the order Siluriformes, in most cases, follows a geographic mode through the accumulation of a numerous small genetic changes over a long time period. A phylogenetic tree for the bullhead torrent catfish and several other fish species belonging to the order Siluriformes was developed on the basis of respective Cyt b sequences (1138 bp); the analysis revealed a monophyletic origin for the five examined families. A species-specific clustering of sequences from single species was obtained, supporting additionally basic phylogenetic information for the catfish and the barcoding suitability of Cyt b sequence data. Lastly, one of the well-supported properties of our phylogenetic tree (99% repetition level in our analysis) was the monophyletic placement of all catfish (order Siluriformes) among other ray-finned fish of the class Actinopterigii. Also discussed herein are the aspects of phylogeny based on the 16S rRNA gene.},
}
@article {pmid17406253,
year = {2006},
author = {Hill, HD and Mirkin, CA},
title = {The bio-barcode assay for the detection of protein and nucleic acid targets using DTT-induced ligand exchange.},
journal = {Nature protocols},
volume = {1},
number = {1},
pages = {324-336},
doi = {10.1038/nprot.2006.51},
pmid = {17406253},
issn = {1750-2799},
mesh = {Dithiothreitol/*chemistry ; Gold/analysis/chemistry ; Ligands ; Magnetics ; Metal Nanoparticles/analysis/chemistry ; *Molecular Probe Techniques ; Nucleic Acids/*analysis ; Oligonucleotide Array Sequence Analysis ; Oligonucleotide Probes/analysis ; Proteins/*analysis ; },
abstract = {The recently developed bio-barcode assay for the detection of nucleic acid and protein targets without PCR has been shown to be extraordinarily sensitive, showing high sensitivity for both nucleic acid and protein targets. Two types of particles are used in the assay: (i) a magnetic microparticle with recognition elements for the target of interest; and (ii) a gold nanoparticle (Au-NP) with a second recognition agent (which can form a sandwich around the target in conjunction with the magnetic particle) and hundreds of thiolated single-strand oligonucleotide barcodes. After reaction with the analyte, a magnetic field is used to localize and collect the sandwich structures, and a DTT solution at elevated temperature is used to release the barcode strands. The barcode strands can be identified on a microarray via scanometric detection or in situ if the barcodes carry with them a detectable marker. The recent modification to the original bio-barcode assay method, utilizing DTT, has streamlined and simplified probe preparation and greatly enhanced the quantitative capabilities of the assay. Here we report the detailed methods for performing the ligand exchange bio-barcode assay for both nucleic acid and protein detection. In total, reagent synthesis, probe preparation and detection require 4 d.},
}
@article {pmid17393852,
year = {2007},
author = {Qiu, S and Lane, T},
title = {Implications of phase transitions in knockdown networks of transitive RNAi.},
journal = {IEEE transactions on nanobioscience},
volume = {6},
number = {1},
pages = {68-76},
doi = {10.1109/tnb.2007.891904},
pmid = {17393852},
issn = {1536-1241},
support = {P20RR18754/RR/NCRR NIH HHS/United States ; },
mesh = {*Algorithms ; Base Sequence ; Computer Simulation ; Gene Silencing/physiology ; Gene Targeting/*methods ; Models, Genetic ; Molecular Sequence Data ; Phase Transition ; RNA Interference/*physiology ; RNA, Transfer/*genetics ; Sequence Alignment/*methods ; Sequence Analysis, RNA/*methods ; Signal Transduction/*genetics ; },
abstract = {Gene silencing by RNA interference (RNAi) has been observed even in the presence of imperfect complementarity in the siRNA-mRNA hybridization. Since more permissive mismatches gives rise to higher chances of off-target gene silencing, the number of mismatched nucleotides allowed by nature becomes an important quantity in characterizing RNAi specificity and RNAi design. To estimate the allowable flexibility, we use scale-free graphs to model the knockdown interactions among genes by examining transitive RNAi (tRNAi), which amplifies siRNA and cyclically silences targets. We removed inefficient siRNA sequences using the commonly used siRNA efficacy rules, avoided redundant siRNAs using barcoding techniques, and employed both contiguous and scattered mismatches to emulate the siRNA-mRNA binding. Simulations in multiple organisms indicate that the fraction of the transcriptome silenced by tRNAi rises drastically with increased number of allowed mismatches and eventually tRNAi became self-destructive rather than defensive. At the phase transition, the number of mismatches implies a critical value beyond which tRNAi would cause the transcription of an organism to be instable. This critical value suggests an upper limit of no more than 6 nt mismatches in the hybridization in general.},
}
@article {pmid17389963,
year = {2007},
author = {Wood, DK and Braun, GB and Fraikin, JL and Swenson, LJ and Reich, NO and Cleland, AN},
title = {A feasible approach to all-electronic digital labeling and readout for cell identification.},
journal = {Lab on a chip},
volume = {7},
number = {4},
pages = {469-474},
doi = {10.1039/b616442k},
pmid = {17389963},
issn = {1473-0197},
mesh = {Biotechnology/methods ; Biotin/chemistry ; CD4 Antigens/*chemistry ; Computers ; Electronic Data Processing ; Electronics ; Humans ; Microfluidics/*instrumentation ; Molecular Diagnostic Techniques/instrumentation ; Polystyrenes/chemistry ; Radio Waves ; Software ; Streptavidin/chemistry ; Time Factors ; },
abstract = {We present two critical innovations that enable a unique, purely electronic approach to microfluidic whole-cell analysis, focusing on the problem of cell identification and sorting. We used fully-scalable lithographic techniques to microfabricate digital barcodes, providing a means for low-cost, large volume production. We have demonstrated molecular functionalization of the barcodes, using biotin-streptavidin, as well as human CD4 antibody, and we have successfully linked the barcodes to polystyrene beads using the biotin-streptavidin complex. This functionalization allows unique barcodes to be attached to specific cell types, based on phenotype. We have also implemented an electronic barcode readout scheme, using a radio frequency microsensor integrated in an elastomeric microfluidic channel, that can read individual barcodes at rates in excess of 1000 labels s(-1). The barcodes are biologically compatible, and coupled with the electronic sensing technology, provide a route to compact, inexpensive, disposable cell identification, sorting and purification.},
}
@article {pmid17389916,
year = {2007},
author = {Min, XJ and Hickey, DA},
title = {DNA barcodes provide a quick preview of mitochondrial genome composition.},
journal = {PloS one},
volume = {2},
number = {3},
pages = {e325},
pmid = {17389916},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/chemistry/*genetics ; Databases, Nucleic Acid ; Electron Transport Complex IV/genetics ; Electronic Data Processing/*methods ; Genome, Mitochondrial/*genetics ; Mitochondria/enzymology/genetics ; Placozoa/genetics ; Protein Subunits/genetics ; Species Specificity ; },
abstract = {DNA barcodes have achieved prominence as a tool for species-level identifications. Consequently, there is a rapidly growing database of these short sequences from a wide variety of taxa. In this study, we have analyzed the correlation between the nucleotide content of the short DNA barcode sequences and the genomes from which they are derived. Our results show that such short sequences can yield important, and surprisingly accurate, information about the composition of the entire genome. In other words, for unsequenced genomes, the DNA barcodes can provide a quick preview of the whole genome composition.},
}
@article {pmid17374505,
year = {2007},
author = {Hoef-Emden, K and Küpper, FC and Andersen, RA},
title = {Meeting report: Sloan Foundation Workshop to resolve problems relating to the taxonomy of microorganisms and to culture collections arising from the barcoding initiatives; Portland ME, November 6-7, 2006.},
journal = {Protist},
volume = {158},
number = {2},
pages = {135-137},
doi = {10.1016/j.protis.2007.02.001},
pmid = {17374505},
issn = {1434-4610},
mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Classification/*methods ; Sequence Analysis, DNA/*methods ; },
}
@article {pmid17373946,
year = {2007},
author = {Nelson, LA and Wallman, JF and Dowton, M},
title = {Using COI barcodes to identify forensically and medically important blowflies.},
journal = {Medical and veterinary entomology},
volume = {21},
number = {1},
pages = {44-52},
doi = {10.1111/j.1365-2915.2007.00664.x},
pmid = {17373946},
issn = {0269-283X},
mesh = {Animals ; Australia ; Base Sequence ; DNA Primers/chemistry ; DNA, Ribosomal Spacer/genetics ; Diptera/*classification/*genetics ; Electron Transport Complex IV/*genetics ; Entomology/*methods ; Gene Order/genetics ; Geography ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis ; Sequence Homology, Nucleic Acid ; },
abstract = {The utility of cytochrome oxidase I (COI) DNA barcodes for the identification of nine species of forensically important blowflies of the genus Chrysomya (Diptera: Calliphoridae), from Australia, was tested. A 658-bp fragment of the COI gene was sequenced from 56 specimens, representing all nine Chrysomya species and three calliphorid outgroups. Nucleotide sequence divergences were calculated using the Kimura-two-parameter distance model and a neighbour-joining (NJ) analysis was performed to provide a graphic display of the patterns of divergence among the species. All species were resolved as reciprocally monophyletic on the NJ tree. Mean intraspecific and interspecific sequence divergences were 0.097% (range 0-0.612%, standard error [SE] = 0.119%) and 6.499% (range 0.458-9.254%, SE = 1.864%), respectively. In one case, a specimen that was identified morphologically was recovered with its sister species on the NJ tree. The hybrid status of this specimen was established by sequence analysis of the second ribosomal internal transcribed spacer (ITS2). In another instance, this nuclear region was used to verify four cases of specimen misidentification that had been highlighted by the COI analysis. The COI barcode sequence was found to be suitable for the identification of Chrysomya species from the east coast of Australia.},
}
@article {pmid17368015,
year = {2007},
author = {Chang, TL and Tsai, CY and Sun, CC and Chen, CC and Kuo, LS and Chen, PH},
title = {Ultrasensitive electrical detection of protein using nanogap electrodes and nanoparticle-based DNA amplification.},
journal = {Biosensors &amp; bioelectronics},
volume = {22},
number = {12},
pages = {3139-3145},
doi = {10.1016/j.bios.2007.02.003},
pmid = {17368015},
issn = {0956-5663},
mesh = {Antigens, Viral/analysis ; Biosensing Techniques/*instrumentation/methods ; *DNA Probes ; *Electrodes ; Hepacivirus/immunology ; Magnetics ; Nanoparticles/*chemistry ; *Nanotechnology ; Nucleic Acid Hybridization ; Protein Array Analysis/*methods ; Proteins/*analysis ; Sensitivity and Specificity ; },
abstract = {The present study describes an ultrasensitive protein biochip that employs nanogap electrodes and self-assembled nanoparticles to electrically detect protein. A bio-barcode DNA technique amplifies the concentration of target antigen at least 100-fold. This technique requires the establishment of conjugate magnetic nanoparticles (MNPs) and gold nanoparticles (AuNPs) through binding between monoclonal antibodies (2B2), the target antigen, and polyclonal antibodies (GP). Both GP and capture ssDNA (single-strand DNA) bonds to bio-barcode ssDNA are immobilized on the surface of AuNPs. A denature process releases the bio-barcode ssDNAs into the solution, and a hybridization process establishes multilayer AuNPs over the gap surface between electrodes. Electric current through double-layer self-assembled AuNPs is much greater than that through self-assembled monolayer AuNPs. This significant increase in electric current provides evidence that the solution contains the target antigen. Results show that the protein biochip attains a sensitivity of up to 1 pg/ microL.},
}
@article {pmid17366136,
year = {2007},
author = {Abdo, Z and Golding, GB},
title = {A step toward barcoding life: a model-based, decision-theoretic method to assign genes to preexisting species groups.},
journal = {Systematic biology},
volume = {56},
number = {1},
pages = {44-56},
doi = {10.1080/10635150601167005},
pmid = {17366136},
issn = {1063-5157},
support = {P20 RR16448/RR/NCRR NIH HHS/United States ; P20 RR16454/RR/NCRR NIH HHS/United States ; },
mesh = {Animals ; *Biodiversity ; Butterflies/genetics ; Classification/*methods ; Computer Simulation ; *Decision Theory ; Genes/*genetics ; *Models, Genetic ; Species Specificity ; },
abstract = {A major part of the barcoding of life problem is assigning newly sequenced or sampled individuals to existing groups that are preidentified externally (by a taxonomist, for example). This problem involves evaluating the statistical evidence towards associating a sequence from a new individual with one group or another. The main concern of our current research is to perform this task in a fast and accurate manner. To accomplish this we have developed a model-based, decision-theoretic framework based on the coalescent theory. Under this framework, we utilized both distance and the posterior probability of a group, given the sequences from members of this group and the sequence from a newly sampled individual to assign this new individual. We believe that this approach makes efficient use of the available information in the data. Our preliminary results indicated that this approach is more accurate than using a simple measure of distance for assignment.},
}
@article {pmid17363473,
year = {2007},
author = {Miller, SE},
title = {DNA barcoding and the renaissance of taxonomy.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {104},
number = {12},
pages = {4775-4776},
pmid = {17363473},
issn = {0027-8424},
mesh = {Animals ; DNA/*genetics ; Diptera/*classification/genetics ; *Electronic Data Processing ; Phylogeny ; Species Specificity ; },
}
@article {pmid17360450,
year = {2007},
author = {Seifert, KA and Samson, RA and Dewaard, JR and Houbraken, J and Lévesque, CA and Moncalvo, JM and Louis-Seize, G and Hebert, PD},
title = {Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {104},
number = {10},
pages = {3901-3906},
pmid = {17360450},
issn = {0027-8424},
mesh = {DNA/genetics ; DNA Primers/chemistry/genetics ; DNA, Fungal/genetics ; DNA, Intergenic ; Electron Transport Complex IV/*genetics ; Genes, Fungal ; *Genetic Techniques ; Genetic Variation ; Introns ; Molecular Sequence Data ; Penicillium/*genetics ; Phylogeny ; Research Design ; Tubulin/genetics ; },
abstract = {DNA barcoding systems employ a short, standardized gene region to identify species. A 648-bp segment of mitochondrial cytochrome c oxidase 1 (CO1) is the core barcode region for animals, but its utility has not been tested in fungi. This study began with an examination of patterns of sequence divergences in this gene region for 38 fungal taxa with full CO1 sequences. Because these results suggested that CO1 could be effective in species recognition, we designed primers for a 545-bp fragment of CO1 and generated sequences for multiple strains from 58 species of Penicillium subgenus Penicillium and 12 allied species. Despite the frequent literature reports of introns in fungal mitochondrial genomes, we detected introns in only 2 of 370 Penicillium strains. Representatives from 38 of 58 species formed cohesive assemblages with distinct CO1 sequences, and all cases of sequence sharing involved known species complexes. CO1 sequence divergences averaged 0.06% within species, less than for internal transcribed spacer nrDNA or beta-tubulin sequences (BenA). CO1 divergences between species averaged 5.6%, comparable to internal transcribed spacer, but less than values for BenA (14.4%). Although the latter gene delivered higher taxonomic resolution, the amplification and alignment of CO1 was simpler. The development of a barcoding system for fungi that shares a common gene target with other kingdoms would be a significant advance.},
}
@article {pmid17360352,
year = {2007},
author = {Smith, MA and Wood, DM and Janzen, DH and Hallwachs, W and Hebert, PD},
title = {DNA barcodes affirm that 16 species of apparently generalist tropical parasitoid flies (Diptera, Tachinidae) are not all generalists.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {104},
number = {12},
pages = {4967-4972},
pmid = {17360352},
issn = {0027-8424},
mesh = {Animals ; Cluster Analysis ; DNA/*genetics ; Diptera/*classification/*genetics ; *Electronic Data Processing ; Molecular Sequence Data ; Parasites/*classification/*genetics ; Phylogeny ; Species Specificity ; *Tropical Climate ; },
abstract = {Many species of tachinid flies are viewed as generalist parasitoids because what is apparently a single species of fly has been reared from many species of caterpillars. However, an ongoing inventory of the tachinid flies parasitizing thousands of species of caterpillars in Area de Conservación Guanacaste, northwestern Costa Rica, has encountered >400 species of specialist tachinids with only a few generalists. We DNA-barcoded 2,134 flies belonging to what appeared to be the 16 most generalist of the reared tachinid morphospecies and encountered 73 mitochondrial lineages separated by an average of 4% sequence divergence. These lineages are supported by collateral ecological information and, where tested, by independent nuclear markers (28S and ITS1), and we therefore view these lineages as provisional species. Each of the 16 apparently generalist species dissolved into one of four patterns: (i) a single generalist species, (ii) a pair of morphologically cryptic generalist species, (iii) a complex of specialist species plus a generalist, or (iv) a complex of specialists with no remaining generalist. In sum, there remained 9 generalist species among the 73 mitochondrial lineages we analyzed, demonstrating that a generalist lifestyle is possible for a tropical caterpillar parasitoid fly. These results reinforce the emerging suspicion that estimates of global species richness are likely underestimates for parasitoids (which may constitute as much as 20% of all animal life) and that the strategy of being a tropical generalist parasitic fly may be yet more unusual than has been envisioned for tachinids.},
}
@article {pmid17347920,
year = {2007},
author = {Ben-David, T and Melamed, S and Gerson, U and Morin, S},
title = {ITS2 sequences as barcodes for identifying and analyzing spider mites (Acari: Tetranychidae).},
journal = {Experimental &amp; applied acarology},
volume = {41},
number = {3},
pages = {169-181},
pmid = {17347920},
issn = {0168-8162},
mesh = {Animals ; DNA, Ribosomal Spacer/*chemistry/classification ; Genome ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA/*methods ; Tetranychidae/*classification/genetics ; },
abstract = {The use of DNA barcodes, short DNA sequences from a standardized region of the genome, has recently been proposed as a tool to facilitate species identification and discovery. Here we show that second internal transcribed spacer of nuclear ribosomal DNA (rDNA-ITS2) barcodes effectively discriminate among 16 species of spider mites (Acari: Tetranychidae) from Israel. The barcode sequences of each species were unambiguously distinguishable from all other species and formed distinct, nonoverlapping monophyletic groups in the maximum-parsimony tree. Sequence divergences were generally much greater between species than within them. Using a 0.02 (2%) threshold for species diagnosis in our data set, 14 out of 16 species recognized by morphological criteria would be accurately identified. The only exceptions involved the low divergence, 0.011-0.015 (1.1-1.5%), between Tetranychus urticae and Tetranychus turkestani, where speciation may have occurred only recently. Still, these species had fixed alternative rDNA-ITS2 variants, with five diagnostic nucleotide substitutions. As a result, we tentatively conclude that rDNA-ITS2 sequence barcodes may serve as an effective tool for the identification of spider mite species and can be applicable as a diagnostic tool for quarantine and other pest management activities and decision-making. We predict that our work, together with similar efforts, will provide in the future the platform for a uniform, accurate, practical and easy-to-use method of spider mite species identification.},
}
@article {pmid17343734,
year = {2007},
author = {Wiemers, M and Fiedler, K},
title = {Does the DNA barcoding gap exist? - a case study in blue butterflies (Lepidoptera: Lycaenidae).},
journal = {Frontiers in zoology},
volume = {4},
number = {},
pages = {8},
pmid = {17343734},
issn = {1742-9994},
abstract = {BACKGROUND: DNA barcoding, i.e. the use of a 648 bp section of the mitochondrial gene cytochrome c oxidase I, has recently been promoted as useful for the rapid identification and discovery of species. Its success is dependent either on the strength of the claim that interspecific variation exceeds intraspecific variation by one order of magnitude, thus establishing a "barcoding gap", or on the reciprocal monophyly of species.<br><br>RESULTS: We present an analysis of intra- and interspecific variation in the butterfly family Lycaenidae which includes a well-sampled clade (genus Agrodiaetus) with a peculiar characteristic: most of its members are karyologically differentiated from each other which facilitates the recognition of species as reproductively isolated units even in allopatric populations. The analysis shows that there is an 18% overlap in the range of intra- and interspecific COI sequence divergence due to low interspecific divergence between many closely related species. In a Neighbour-Joining tree profile approach which does not depend on a barcoding gap, but on comprehensive sampling of taxa and the reciprocal monophyly of species, at least 16% of specimens with conspecific sequences in the profile were misidentified. This is due to paraphyly or polyphyly of conspecific DNA sequences probably caused by incomplete lineage sorting.<br><br>CONCLUSION: Our results indicate that the "barcoding gap" is an artifact of insufficient sampling across taxa. Although DNA barcodes can help to identify and distinguish species, we advocate using them in combination with other data, since otherwise there would be a high probability that sequences are misidentified. Although high differences in DNA sequences can help to identify cryptic species, a high percentage of well-differentiated species has similar or even identical COI sequences and would be overlooked in an isolated DNA barcoding approach.},
}
@article {pmid17318679,
year = {2007},
author = {Liao, PC and Huang, BH and Huang, S},
title = {Microbial community composition of the Danshui river estuary of Northern Taiwan and the practicality of the phylogenetic method in microbial barcoding.},
journal = {Microbial ecology},
volume = {54},
number = {3},
pages = {497-507},
pmid = {17318679},
issn = {0095-3628},
mesh = {Biodiversity ; Comamonadaceae/classification/genetics ; *Ecosystem ; Gammaproteobacteria/classification/genetics ; Genetic Variation ; Geography ; Molecular Sequence Data ; *Phylogeny ; Proteobacteria/classification/*genetics ; RNA, Ribosomal, 16S/genetics ; Rhodobacteraceae/classification/genetics ; Rivers/*microbiology ; Sequence Analysis, DNA ; Taiwan ; Water Microbiology ; },
abstract = {In this study, the microbial community in a mangrove ecosystem was surveyed and used to test the eligibility of 16S rDNA library and neighbor-joining method for the purpose of estimating microbial composition. Genetic diversity (pi) and four other diversity indices (Simpson's unbiased, Shannon-Wiener, Evenness, and Chao1 indices) were applied to estimate the adaptive lineages of microorganisms in the mangrove ecosystem. The results indicated that gamma-Proteobacteria is the most diverse taxon, while the most abundant family is Rhodobacteraceae (alpha-Proteobacteria), followed by Comamonadaceae (beta-Proteobacteria). This result may imply the existence of a graded distribution of microbial diversity across a spectrum of different salinities in the waterbody of this estuary ecosystem. Furthermore, at least 500-1,000 bps of the posterior portion of 16S rDNA is required as a marker to profile the microbial diversity in a microcosm of interest using phylogenetic methods, according to the results of our sliding window analyses for the measurements of pi, consistency index, and retention index.},
}
@article {pmid17316886,
year = {2007},
author = {Hajibabaei, M and Singer, GA and Hebert, PD and Hickey, DA},
title = {DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics.},
journal = {Trends in genetics : TIG},
volume = {23},
number = {4},
pages = {167-172},
doi = {10.1016/j.tig.2007.02.001},
pmid = {17316886},
issn = {0168-9525},
mesh = {Animals ; *Classification ; DNA/*genetics ; *Genetics, Population ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {DNA barcoding aims to provide an efficient method for species-level identifications and, as such, will contribute powerfully to taxonomic and biodiversity research. As the number of DNA barcode sequences accumulates, however, these data will also provide a unique 'horizontal' genomics perspective with broad implications. For example, here we compare the goals and methods of DNA barcoding with those of molecular phylogenetics and population genetics, and suggest that DNA barcoding can complement current research in these areas by providing background information that will be helpful in the selection of taxa for further analyses.},
}
@article {pmid17315817,
year = {2007},
author = {Sharman, P},
title = {Bedside barcoding for the blood bank.},
journal = {MLO: medical laboratory observer},
volume = {39},
number = {1},
pages = {18-19},
pmid = {17315817},
issn = {0580-7247},
mesh = {*Blood Banks ; *Electronic Data Processing ; Humans ; *Point-of-Care Systems ; United States ; },
}
@article {pmid17306026,
year = {2007},
author = {Sonnenberg, R and Nolte, AW and Tautz, D},
title = {An evaluation of LSU rDNA D1-D2 sequences for their use in species identification.},
journal = {Frontiers in zoology},
volume = {4},
number = {},
pages = {6},
pmid = {17306026},
issn = {1742-9994},
abstract = {BACKGROUND: Identification of species via DNA sequences is the basis for DNA taxonomy and DNA barcoding. Currently there is a strong focus on using a mitochondrial marker for this purpose, in particular a fragment from the cytochrome oxidase I gene (COI). While there is ample evidence that this marker is indeed suitable across a broad taxonomic range to delineate species, it has also become clear that a complementation by a nuclear marker system could be advantageous. Ribosomal RNA genes could be suitable for this purpose, because of their global occurrence and the possibility to design universal primers. However, it has so far been assumed that these genes are too highly conserved to allow resolution at, or even beyond the species level. On the other hand, it is known that ribosomal gene regions harbour also highly divergent parts. We explore here the information content of two adjacent divergence regions of the large subunit ribosomal gene, the D1-D2 region.<br><br>RESULTS: Universal primers were designed to amplify the D1-D2 region from all metazoa. We show that amplification products in the size between 800-1300 bp can be obtained across a broad range of animal taxa, provided some optimizations of the PCR procedure are implemented. Although the ribosomal genes occur in multiple copies in the genomes, we find generally very little intra-individual polymorphism (<< 0.1% on average) indicating that concerted evolution is very effective in most cases. Studies in two fish taxa (genus Cottus and genus Aphyosemion) show that the D1-D2 LSU sequence can resolve even very closely related species with the same fidelity as COI sequences. In one case we can even show that a mitochondrial transfer must have occurred, since the nuclear sequence confirms the taxonomic assignment, while the mitochondrial sequence would have led to the wrong classification. We have further explored whether hybrids between species can be detected with the nuclear sequence and we show for a test case of natural hybrids among cyprinid fish species (Alburnus alburnus and Rutilus rutilus) that this is indeed possible.<br><br>CONCLUSION: The D1-D2 LSU region is a suitable marker region for applications in DNA based species identification and should be considered to be routinely used as a marker complementing broad scale studies based on mitochondrial markers.},
}
@article {pmid17300895,
year = {2007},
author = {Dawnay, N and Ogden, R and McEwing, R and Carvalho, GR and Thorpe, RS},
title = {Validation of the barcoding gene COI for use in forensic genetic species identification.},
journal = {Forensic science international},
volume = {173},
number = {1},
pages = {1-6},
doi = {10.1016/j.forsciint.2006.09.013},
pmid = {17300895},
issn = {1872-6283},
mesh = {Animals ; Cattle ; Chickens/genetics ; *Conservation of Natural Resources ; DNA Fingerprinting/*methods ; DNA, Mitochondrial/*analysis ; Electron Transport Complex IV/*genetics ; Fishes/genetics ; Humans ; Mustelidae/genetics ; Polymerase Chain Reaction ; Reproducibility of Results ; Sequence Analysis, DNA ; *Species Specificity ; },
abstract = {The application of forensics to wildlife crime investigation routinely involves genetic species identification based on DNA sequence similarity. This work can be hindered by a lack of authenticated reference DNA sequence data resulting in weak matches between evidence and reference samples. The introduction of DNA barcoding has highlighted the expanding use of the mtDNA gene, cytochrome c oxidase I (COI), as a genetic marker for species identification. Here, we assess the COI gene for use in forensic analysis following published human validation guidelines. Validation experiments investigated reproducibility, heteroplasmy, mixed DNA, DNA template concentration, chemical treatments, substrate variation, environmental conditions and thermocycling parameters. Sequence similarity searches using both GenBank BLASTn and BOLD search engines indicated that the COI gene consistently identifies species where authenticated reference sequence data exists. Where misidentification occurred the cause was attributable to either erroneous reference sequences from published data, or lack of primer specificity. Although amplification failure was observed under certain sample treatments, there was no evidence of environmentally induced sequence mutation in those sequences that were generated. A simulated case study compared the performance of COI and cytochrome b mtDNA genes. Findings are discussed in relation to the utility of the COI gene in forensic species identification.},
}
@article {pmid17300521,
year = {2007},
author = {Maslov, DA and Westenberger, SJ and Xu, X and Campbell, DA and Sturm, NR},
title = {Discovery and barcoding by analysis of spliced leader RNA gene sequences of new isolates of Trypanosomatidae from Heteroptera in Costa Rica and Ecuador.},
journal = {The Journal of eukaryotic microbiology},
volume = {54},
number = {1},
pages = {57-65},
doi = {10.1111/j.1550-7408.2006.00150.x},
pmid = {17300521},
issn = {1066-5234},
support = {AI034056/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Costa Rica ; Ecuador ; *Genes, Protozoan ; Heteroptera/*parasitology ; Host-Parasite Interactions ; Phylogeny ; Polymerase Chain Reaction ; RNA, Protozoan/classification/*genetics ; RNA, Spliced Leader/chemistry/*genetics ; Species Specificity ; Trypanosomatina/classification/*genetics ; },
abstract = {Trypanosomatid diversity in Heteroptera was sampled using a culture-independent approach based on amplification and sequencing of Spliced Leader RNA gene repeats from environmental samples. By combining the data collected herein with that of previous work, the prevalence of parasites was found to be 22%-23%. Out of approximately 170 host species investigated nearly 60 were found to harbor trypanosomatids. The parasites found were grouped by cluster analysis into 48 typing units. Most of these were well separated from the known groups and, therefore, likely represent new trypanosomatid species. The sequences for each typing unit serve as barcodes to facilitate their recognition in the future. As the sampled host species represent a minor fraction of potential hosts, the entire trypanosomatid diversity is far greater than described thus far. Investigations of trypanosomatid diversity, host-specificity, and biogeography have become feasible using the approach described herein.},
}
@article {pmid17296933,
year = {2007},
author = {Jo, K and Dhingra, DM and Odijk, T and de Pablo, JJ and Graham, MD and Runnheim, R and Forrest, D and Schwartz, DC},
title = {A single-molecule barcoding system using nanoslits for DNA analysis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {104},
number = {8},
pages = {2673-2678},
pmid = {17296933},
issn = {0027-8424},
support = {R01 HG000225/HG/NHGRI NIH HHS/United States ; 5R01 HG 000225/HG/NHGRI NIH HHS/United States ; },
mesh = {Biopolymers/analysis/chemistry ; Buffers ; Chromosomes, Artificial, Bacterial/chemistry ; DNA/*analysis/chemistry ; DNA, Bacterial/analysis/chemistry ; DNA, Viral/analysis/chemistry ; Fluorescence Resonance Energy Transfer ; Fluorescent Dyes ; *Nanotechnology ; Nucleic Acid Conformation ; Osmolar Concentration ; },
abstract = {Molecular confinement offers new routes for arraying large DNA molecules, enabling single-molecule schemes aimed at the acquisition of sequence information. Such schemes can rapidly advance to become platforms capable of genome analysis if elements of a nascent system can be integrated at an early stage of development. Integrated strategies are needed for surmounting the stringent experimental requirements of nanoscale devices regarding fabrication, sample loading, biochemical labeling, and detection. We demonstrate that disposable devices featuring both micro- and nanoscale features can greatly elongate DNA molecules when buffer conditions are controlled to alter DNA stiffness. Furthermore, we present analytical calculations that describe this elongation. We also developed a complementary enzymatic labeling scheme that tags specific sequences on elongated molecules within described nanoslit devices that are imaged via fluorescence resonance energy transfer. Collectively, these developments enable scaleable molecular confinement approaches for genome analysis.},
}
@article {pmid17295921,
year = {2007},
author = {Mayer, F and Dietz, C and Kiefer, A},
title = {Molecular species identification boosts bat diversity.},
journal = {Frontiers in zoology},
volume = {4},
number = {},
pages = {4},
pmid = {17295921},
issn = {1742-9994},
abstract = {The lack of obvious morphological differences between species impedes the identification of species in many groups of organisms. Meanwhile, DNA-based approaches are increasingly used to survey biological diversity. In this study we show that sequencing the mitochondrial protein-coding gene NADH dehydrogenase, subunit 1 (nd1) from 534 bats of the Western Palaearctic region corroborates the promise of DNA barcodes in two major respects. First, species described with classical taxonomic tools can be genetically identified with only a few exceptions. Second, substantial sequence divergence suggests an unexpected high number of undiscovered species.},
}
@article {pmid17294914,
year = {2007},
author = {Kumar, NP and Rajavel, AR and Natarajan, R and Jambulingam, P},
title = {DNA barcodes can distinguish species of Indian mosquitoes (Diptera: Culicidae).},
journal = {Journal of medical entomology},
volume = {44},
number = {1},
pages = {1-7},
doi = {10.1603/0022-2585(2007)44[1:dbcdso]2.0.co;2},
pmid = {17294914},
issn = {0022-2585},
mesh = {Animals ; Culicidae/*classification/*genetics ; *DNA Fingerprinting ; Electron Transport Complex IV/genetics ; Female ; Genetic Variation/genetics ; India ; Male ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; },
abstract = {Species identification of mosquitoes (Diptera: Culicidae) based on morphological characteristics remains often difficult in field-collected mosquito specimens in vector-borne disease surveillance programs. The use of DNA barcodes has been proposed recently as a tool for identification of the species in many diverse groups of animals. However, the efficacy of this tool for mosquitoes remains unexplored. Hence, a study was undertaken to construct DNA barcodes for several species of mosquitoes prevalent in India, which included major vector species. In total, 111 specimens of mosquitoes belonging to 15 genera, morphologically identified to be 63 species, were used. This number also included multiple specimens for 22 species. DNA barcode approach based on DNA sequences of mitochondrial cytochrome oxidase gene sequences could identify 62 species among these, in confirmation with the conventional taxonomy. However, two closely related species, Ochlerotatus portonovoensis (Tiwari &amp; Hiriyan) and Ochlerotatus wardi (Reinert) could not be identified as separate species based on DNA barcode approach, their lineages indicating negligible genetic divergence (Kimura two-parameter genetic distance = 0.0043).},
}
@article {pmid17270812,
year = {2004},
author = {True, RJ and Taylor, MK and Chakarova, GS and Walton, ID},
title = {Microfabricated templates for the electrodeposition of metallic barcodes for use in multiplexed bioassays.},
journal = {Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference},
volume = {2004},
number = {},
pages = {2619-2622},
doi = {10.1109/IEMBS.2004.1403752},
pmid = {17270812},
issn = {1557-170X},
abstract = {Lithographically defined polyimide templates were prepared using microfabrication techniques. The templates consist of high aspect ratio pores that were formed by deep plasma etching. Different metals are electrodeposited into the pores, and then the template is removed to allow the metallic rods (particles) to be released into solution. The striping pattern of metals on the particles is used to optically identify the particles. Particles range in size from 0.6 mum in diameter by 7.7 mum in length to 4.2 mum by 27 mum in length. These particles have been evaluated in a multiplexed DNA hybridization assay.},
}
@article {pmid17270777,
year = {2004},
author = {Ramasubramanian, MK and Anthony, SR},
title = {Real-time blood cross-matching sensor for intelligent management of transfusion safety.},
journal = {Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference},
volume = {2004},
number = {},
pages = {2488-2491},
doi = {10.1109/IEMBS.2004.1403717},
pmid = {17270777},
issn = {1557-170X},
abstract = {Blood transfusion errors are not uncommon. In some cases the error is fatal. This is primarily due to lack of an automated system at the point of application and over-reliance on bar-coding and paperwork to catch these critical errors. In emergency situations, human errors contribute to transfusion and transplantation of incompatible blood types and organs resulting in rejection and possible fatality. We present a sensing concept that will monitor blood compatibility between the patient and the transfusion bag before allowing the valve to open for transfusion to take place. This will eliminate all transfusion errors and provide 100% safe transfusions automatically. The operating principle of the sensor is based on the light scattering characteristics of dilute blood and the effect of agglutination on scattering. The device proposed is an optical system based on spectrophotometric methods. The device configuration, and results from several tests with combinations of known blood samples will be presented.},
}
@article {pmid17270468,
year = {2007},
author = {Roe, AD and Sperling, FA},
title = {Patterns of evolution of mitochondrial cytochrome c oxidase I and II DNA and implications for DNA barcoding.},
journal = {Molecular phylogenetics and evolution},
volume = {44},
number = {1},
pages = {325-345},
doi = {10.1016/j.ympev.2006.12.005},
pmid = {17270468},
issn = {1055-7903},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; Diptera/classification/*genetics ; Electron Transport Complex IV/*genetics ; *Evolution, Molecular ; Genetic Code/genetics ; Genetic Variation ; Lepidoptera/classification/*genetics ; Molecular Sequence Data ; Mutation ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {DNA barcoding has focused increasing attention on the use of specific regions of mitochondrial cytochrome c oxidase I and II genes (COI-COII) to diagnose and delimit species. However, our understanding of patterns of molecular evolution within these genes is limited. Here we examine patterns of nucleotide divergence in COI-COII within species and between species pairs of Lepidoptera and Diptera using a sliding window analysis. We found that: (1) locations of maximum divergence within COI-COII were highly variable among taxa surveyed in this study; (2) there was major overlap in divergence within versus between species, including within individual COI-COII profiles; (3) graphical DNA saturation analysis showed variation in percent nucleotide transitions throughout COI-COII and only limited association with levels of DNA divergence. Ultimately, no single optimally informative 600 bp location was found within the 2.3 kb of COI-COII, and the DNA barcoding region was no better than other regions downstream in COI. Consequently, we recommend that researchers should maximize sequence length to increase the probability of sampling regions of high phylogenetic informativeness, and to minimize stochastic variation in estimating total divergence.},
}
@article {pmid17241952,
year = {2007},
author = {Lemer, S and Aurelle, D and Vigliola, L and Durand, JD and Borsa, P},
title = {Cytochrome b barcoding, molecular systematics and geographic differentiation in rabbitfishes (Siganidae).},
journal = {Comptes rendus biologies},
volume = {330},
number = {1},
pages = {86-94},
doi = {10.1016/j.crvi.2006.09.002},
pmid = {17241952},
issn = {1631-0691},
mesh = {Animals ; Base Sequence ; Cytochromes b/*genetics ; Geography ; Perciformes/*classification/*genetics ; Phylogeny ; Seasons ; },
abstract = {The fish genus Siganus (Siganidae) is widely distributed in the coastal habitats of all the tropical Indo-Pacific, with 28 nominal species recognized so far, based on general morphology and coloration patterns. A mitochondrial phylogeny of 16 Siganidae species, based on the partial nucleotide sequences of the cytochome b gene, was produced. Individual haplotypes of given nominal species generally clustered at the extremity of long branches, thus validating the current taxonomy. However, S. lineatus haplotypes formed a paraphyletic group including S. guttatus, while S. fuscescens haplotypes were apparently splitted in two groups, calling for further investigation. S. woodlandi and S. argenteus formed a monophyletic group, as expected from their close morphological relatedness, although they were separated by a substantial, 14.5-16.3% nucleotide distance. Among eight species sampled from different locations across the Indo-West Pacific, S. argenteus and S. spinus showed the lowest degree of geographic differentiation, a result that correlated well with their extended pelagic larval stage. Fixation index estimates were high in all six other species tested (S. doliatus, S. fuscescens, S. lineatus, S. puellus, S. punctatus, S. vulpinus). The cytochrome b gene fragment chosen here proved useful as a barcode in Siganidae.},
}
@article {pmid17238613,
year = {2006},
author = {Kuwata, S and Kushniruk, A and Borycki, E and Watanabe, H},
title = {Using simulation methods to analyze and predict changes in workflow and potential problems in the use of a bar-coding medication order entry system.},
journal = {AMIA ... Annual Symposium proceedings. AMIA Symposium},
volume = {2006},
number = {},
pages = {994},
pmid = {17238613},
issn = {1942-597X},
mesh = {Computer Simulation ; *Electronic Data Processing ; Humans ; *Medical Order Entry Systems ; Medication Systems, Hospital/*organization &amp; administration ; Organizational Innovation ; Patient Simulation ; Systems Integration ; Task Performance and Analysis ; },
abstract = {We discuss a novel methodological approach to the analysis of a medication order entry system prior to system release. The approach involved use of realistic scenarios (where physicians and nurses interacted with a system and dummy patient) where the sessions were video recorded in their entirety. The data were analyzed using a qualitative coding scheme for identifying usability problems and changes in workflow.},
}
@article {pmid17226815,
year = {2007},
author = {Waugh, J},
title = {DNA barcoding in animal species: progress, potential and pitfalls.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {29},
number = {2},
pages = {188-197},
doi = {10.1002/bies.20529},
pmid = {17226815},
issn = {0265-9247},
mesh = {Animals ; Biodiversity ; DNA, Mitochondrial/analysis/*classification ; Evolution, Molecular ; Humans ; *Phylogeny ; *Sequence Analysis, DNA/methods/standards/trends ; Species Specificity ; },
abstract = {Despite 250 years of work in systematics, the majority of species remains to be identified. Rising extinction rates and the need for increased biological monitoring lend urgency to this task. DNA sequencing, with key sequences serving as a "barcode", has therefore been proposed as a technology that might expedite species identification. In particular, the mitochondrial cytochrome c oxidase subunit 1 gene has been employed as a possible DNA marker for species and a number of studies in a variety of taxa have accordingly been carried out to examine its efficacy. In general, these studies demonstrate that DNA barcoding resolves most species, although some taxa have proved intractable. In some studies, barcoding provided a means of highlighting potential cryptic, synonymous or extinct species as well as matching adults with immature specimens. Higher taxa, however, have not been resolved as accurately as species. Nonetheless, DNA barcoding appears to offer a means of identifying species and may become a standard tool.},
}
@article {pmid17216027,
year = {2006},
author = {Müller, UR},
title = {Protein detection using biobarcodes.},
journal = {Molecular bioSystems},
volume = {2},
number = {10},
pages = {470-476},
doi = {10.1039/b608442g},
pmid = {17216027},
issn = {1742-206X},
mesh = {*Biosensing Techniques ; Immunoassay/methods/standards ; Nanoparticles/*standards ; Nucleic Acid Amplification Techniques/*methods/standards ; Nucleic Acids/*analysis ; Proteins/*analysis ; Sensitivity and Specificity ; },
abstract = {Over the past 50 years the development of assays for the detection of protein analytes has been driven by continuing demands for higher levels of sensitivity and multiplexing. The result has been a progression of sandwich-type immunoassays, starting with simple radioisotopic, colorimetric, or fluorescent labeling systems to include various enzymatic or nanostructure-based signal amplification schemes, with a concomitant sensitivity increase of over 1 million fold. Multiplexing of samples and tests has been enabled by microplate and microarray platforms, respectively, or lately by various molecular barcoding systems. Two different platforms have emerged as the current front-runners by combining a nucleic acid amplification step with the standard two-sided immunoassay. In both, the captured protein analyte is replaced by a multiplicity of oligonucleotides that serve as surrogate targets. One of these platforms employs DNA or RNA polymerases for the amplification step, while detection is by fluorescence. The other is based on gold nanoparticles for both amplification as well as detection. The latter technology, now termed Biobarcode, is completely enzyme-free and offers potentially much higher multiplexing power.},
}
@article {pmid17208018,
year = {2007},
author = {Ekrem, T and Willassen, E and Stur, E},
title = {A comprehensive DNA sequence library is essential for identification with DNA barcodes.},
journal = {Molecular phylogenetics and evolution},
volume = {43},
number = {2},
pages = {530-542},
doi = {10.1016/j.ympev.2006.11.021},
pmid = {17208018},
issn = {1055-7903},
mesh = {Animals ; Chironomidae/*genetics ; *DNA ; Electron Transport Complex IV/genetics ; Female ; *Gene Library ; Genes, Insect ; Male ; Phylogeny ; },
abstract = {In this study we examine the possibility of utilising partial cox1 gene sequences as barcodes to identify non-biting midges (Diptera: Chironomidae). We analysed DNA from 97 specimens of 47 species in the genera Cladotanytarsus, Micropsectra, Parapsectra, Paratanytarsus, Rheotanytarsus, Tanytarsus and Virgatanytarsus with a main focus on Micropsectra, Parapsectra and Paratanytarsus. Our findings show that (1) cox1 is easily amplified from extracts from different life stages with the standard barcoding primers. (2) Although K2P-distances between con-specific sequences varied up to 4.9%, con-specifics clustered together with 91-100% bootstrap support in maximum parsimony analysis. This indicates that barcodes may be excellent tools to identify species that are already in a cox1 library. (3) Both neighbour joining and maximum parsimony failed to reconstruct monophyletic genera. Thus, if a well-matching cox1 sequence is not already available in the library, the prospects of approximately identifying an unknown taxon, even to the correct genus of subtribe Tanytarsina, are not good.},
}
@article {pmid17202861,
year = {2006},
author = {Yoo, HS and Eah, JY and Kim, JS and Kim, YJ and Min, MS and Paek, WK and Lee, H and Kim, CB},
title = {DNA barcoding Korean birds.},
journal = {Molecules and cells},
volume = {22},
number = {3},
pages = {323-327},
pmid = {17202861},
issn = {1016-8478},
mesh = {Animals ; Birds/*classification/*genetics ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Electron Transport Complex IV/*genetics ; Korea ; Phylogeny ; *Sequence Analysis, DNA ; Species Specificity ; },
abstract = {DNA barcoding, an inventory of DNA sequences from a standardized genomic region, provides a bio-barcode for identifying and discovering species. Several recent studies suggest that the sequence diversity in a 648 bp region of the mitochondrial gene for cytochrome c oxi- dase I (COI) might serve as a DNA barcode for identify- ing animal species such as North American birds, in- sects and fishes. The present study tested the effective- ness of a COI barcode in discriminating Korean bird species. We determined the 5' terminus of the COI bar- code for 92 species of Korean birds and found that spe- cies identification was unambiguous; the genetic differ- ences between closely related species were, on average, 25 times higher than the differences within species. We identified only one misidentified species out of 239 specimens in a genetic resource bank, so confirming the accuracy of species identification in the banking system. We also identified two potential composite species, calling for further investigation using more samples. The finding of large COI sequence differences between species confirms the effectiveness of COI barcodes for identifying Korean bird species. To bring greater reliability to the identification of species, increased in- tra- and interspecies sampling, as well as supplementa- tion of the mitochondrial barcodes with nuclear ones, is needed.},
}
@article {pmid17199753,
year = {2006},
author = {Cywinska, A and Hunter, FF and Hebert, PD},
title = {Identifying Canadian mosquito species through DNA barcodes.},
journal = {Medical and veterinary entomology},
volume = {20},
number = {4},
pages = {413-424},
doi = {10.1111/j.1365-2915.2006.00653.x},
pmid = {17199753},
issn = {0269-283X},
mesh = {Animals ; Canada ; Culicidae/*classification/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Phylogeny ; },
abstract = {A short fragment of mt DNA from the cytochrome c oxidase 1 (CO1) region was used to provide the first CO1 barcodes for 37 species of Canadian mosquitoes (Diptera: Culicidae) from the provinces Ontario and New Brunswick. Sequence variation was analysed in a 617-bp fragment from the 5' end of the CO1 region. Sequences of each mosquito species formed barcode clusters with tight cohesion that were usually clearly distinct from those of allied species. CO1 sequence divergences were, on average, nearly 20 times higher for congeneric species than for members of a species; divergences between congeneric species averaged 10.4% (range 0.2-17.2%), whereas those for conspecific individuals averaged 0.5% (range 0.0-3.9%).},
}
@article {pmid17192418,
year = {2007},
author = {Harrington, SM and Stock, F and Kominski, AL and Campbell, JD and Hormazabal, JC and Livio, S and Rao, L and Kotloff, KL and Sow, SO and Murray, PR},
title = {Genotypic analysis of invasive Streptococcus pneumoniae from Mali, Africa, by semiautomated repetitive-element PCR and pulsed-field gel electrophoresis.},
journal = {Journal of clinical microbiology},
volume = {45},
number = {3},
pages = {707-714},
pmid = {17192418},
issn = {0095-1137},
support = {//Intramural NIH HHS/United States ; },
mesh = {Adolescent ; Automation ; *Bacterial Typing Techniques ; Child ; Deoxyribonucleases, Type II Site-Specific/metabolism ; Electrophoresis, Gel, Pulsed-Field/*methods ; Genotype ; Humans ; Mali/epidemiology ; Pneumococcal Infections/epidemiology/microbiology ; Polymerase Chain Reaction/*methods ; Repetitive Sequences, Nucleic Acid/*genetics ; Serotyping ; Streptococcus pneumoniae/*classification/*genetics ; },
abstract = {As part of a large, ongoing study of invasive infections in pediatric patients in Bamako, Mali, 106 cases of invasive pneumococcal disease were identified from June 2002 to July 2003 (J. D. Campbell et al., Pediatr. Infect. Dis. J. 23:642-649, 2004). Of the 12 serotypes present, the majority of isolates were not contained in PCV7 (the 7-valent pneumococcal conjugate vaccine), including 1 isolate that was serotype 1, 12 isolates that were serotype 2, 58 isolates that were serotype 5, 7 isolates that were serotype 7F, and 1 isolate that was serotype 12F. To determine whether clonal dissemination of the predominant serotypes had taken place, genotyping was performed on 100 S. pneumoniae isolates by using two methods: pulsed-field gel electrophoresis (PFGE) of SmaI-digested genomic DNA, and the Bacterial Barcodes repetitive-element PCR (rep-PCR) method. Criteria for delineating rep-PCR genotypes were established such that isolates of different serotypes were generally not grouped together. The two methods were equally discriminatory within a given pneumococcal serotype. PFGE separated the isolates into 15 genotypes and 7 subtypes; rep-PCR separated isolates into 15 genotypes and 6 subtypes. Using either method, isolates within serotypes 2, 5, and 7 formed three large, separate clusters containing 1 genotype each. Both methods further distinguished related subtypes within serotypes 2 and 5. Interestingly, one of the PFGE subtypes of serotype 5 is indistinguishable from the Columbia(5)-19 clone circulating in Latin America since 1994. The data support that serotypes 2 and 5 were likely to be the result of dissemination of particular clones, some of which are responsible for invasive disease over a broad population range.},
}
@article {pmid17189863,
year = {2007},
author = {Pan, X and Yuan, DS and Ooi, SL and Wang, X and Sookhai-Mahadeo, S and Meluh, P and Boeke, JD},
title = {dSLAM analysis of genome-wide genetic interactions in Saccharomyces cerevisiae.},
journal = {Methods (San Diego, Calif.)},
volume = {41},
number = {2},
pages = {206-221},
pmid = {17189863},
issn = {1046-2023},
support = {U54 RR020839/RR/NCRR NIH HHS/United States ; R01 HG002432/HG/NHGRI NIH HHS/United States ; RR020839/RR/NCRR NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; HG02432/HG/NHGRI NIH HHS/United States ; },
mesh = {Base Sequence ; Gene Deletion ; Gene Expression Regulation, Fungal/genetics/*physiology ; *Genes, Lethal ; *Genome ; Microarray Analysis/*methods ; Molecular Sequence Data ; Mutation ; Oligonucleotides/genetics ; Saccharomyces cerevisiae/*genetics ; },
abstract = {Analysis of genetic interactions has been extensively exploited to study gene functions and to dissect pathway structures. One such genetic interaction is synthetic lethality, in which the combination of two non-lethal mutations leads to loss of organism viability. We have developed a dSLAM (heterozygote diploid-based synthetic lethality analysis with microarrays) technology that effectively studies synthetic lethality interactions on a genome-wide scale in the budding yeast Saccharomyces cerevisiae. Typically, a query mutation is introduced en masse into a population of approximately 6000 haploid-convertible heterozygote diploid Yeast Knockout (YKO) mutants via integrative transformation. Haploid pools of single and double mutants are freshly generated from the resultant heterozygote diploid double mutant pool after meiosis and haploid selection and studied for potential growth defects of each double mutant combination by microarray analysis of the "molecular barcodes" representing each YKO. This technology has been effectively adapted to study other types of genome-wide genetic interactions including gene-compound synthetic lethality, secondary mutation suppression, dosage-dependent synthetic lethality and suppression.},
}
@article {pmid17183689,
year = {2006},
author = {Nilsson, RH and Ryberg, M and Kristiansson, E and Abarenkov, K and Larsson, KH and Kõljalg, U},
title = {Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective.},
journal = {PloS one},
volume = {1},
number = {1},
pages = {e59},
pmid = {17183689},
issn = {1932-6203},
mesh = {DNA, Fungal/*genetics ; DNA, Ribosomal/genetics ; *Databases, Nucleic Acid ; Fungi/*classification/*genetics ; Phylogeny ; Reproducibility of Results ; Species Specificity ; },
abstract = {BACKGROUND: DNA sequences are increasingly seen as one of the primary information sources for species identification in many organism groups. Such approaches, popularly known as barcoding, are underpinned by the assumption that the reference databases used for comparison are sufficiently complete and feature correctly and informatively annotated entries.<br><br>The present study uses a large set of fungal DNA sequences from the inclusive International Nucleotide Sequence Database to show that the taxon sampling of fungi is far from complete, that about 20% of the entries may be incorrectly identified to species level, and that the majority of entries lack descriptive and up-to-date annotations.<br><br>CONCLUSIONS: The problems with taxonomic reliability and insufficient annotations in public DNA repositories form a tangible obstacle to sequence-based species identification, and it is manifest that the greatest challenges to biological barcoding will be of taxonomical, rather than technical, nature.},
}
@article {pmid17175538,
year = {2007},
author = {Xiao, M and Phong, A and Ha, C and Chan, TF and Cai, D and Leung, L and Wan, E and Kistler, AL and DeRisi, JL and Selvin, PR and Kwok, PY},
title = {Rapid DNA mapping by fluorescent single molecule detection.},
journal = {Nucleic acids research},
volume = {35},
number = {3},
pages = {e16},
pmid = {17175538},
issn = {1362-4962},
support = {R01 HG001720/HG/NHGRI NIH HHS/United States ; },
mesh = {Adenoviruses, Human/classification/genetics ; Bacteriophage lambda/genetics ; DNA/chemistry ; DNA, Viral/chemistry ; Endodeoxyribonucleases ; Fluorescent Dyes/*analysis ; Genome, Viral ; Genomics/*methods ; Microscopy, Fluorescence/*methods ; Rhinovirus/classification/genetics ; },
abstract = {DNA mapping is an important analytical tool in genomic sequencing, medical diagnostics and pathogen identification. Here we report an optical DNA mapping strategy based on direct imaging of individual DNA molecules and localization of multiple sequence motifs on the molecules. Individual genomic DNA molecules were labeled with fluorescent dyes at specific sequence motifs by the action of nicking endonuclease followed by the incorporation of dye terminators with DNA polymerase. The labeled DNA molecules were then stretched into linear form on a modified glass surface and imaged using total internal reflection fluorescence (TIRF) microscopy. By determining the positions of the fluorescent labels with respect to the DNA backbone, the distribution of the sequence motif recognized by the nicking endonuclease can be established with good accuracy, in a manner similar to reading a barcode. With this approach, we constructed a specific sequence motif map of lambda-DNA. We further demonstrated the capability of this approach to rapidly type a human adenovirus and several strains of human rhinovirus.},
}
@article {pmid17169982,
year = {2007},
author = {Taberlet, P and Coissac, E and Pompanon, F and Gielly, L and Miquel, C and Valentini, A and Vermat, T and Corthier, G and Brochmann, C and Willerslev, E},
title = {Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding.},
journal = {Nucleic acids research},
volume = {35},
number = {3},
pages = {e14},
pmid = {17169982},
issn = {1362-4962},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Base Sequence ; Conserved Sequence ; DNA Primers ; DNA, Chloroplast/*chemistry ; Databases, Nucleic Acid ; *Introns ; Molecular Sequence Data ; Plants/*classification/genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; },
abstract = {DNA barcoding should provide rapid, accurate and automatable species identifications by using a standardized DNA region as a tag. Based on sequences available in GenBank and sequences produced for this study, we evaluated the resolution power of the whole chloroplast trnL (UAA) intron (254-767 bp) and of a shorter fragment of this intron (the P6 loop, 10-143 bp) amplified with highly conserved primers. The main limitation of the whole trnL intron for DNA barcoding remains its relatively low resolution (67.3% of the species from GenBank unambiguously identified). The resolution of the P6 loop is lower (19.5% identified) but remains higher than those of existing alternative systems. The resolution is much higher in specific contexts such as species originating from a single ecosystem, or commonly eaten plants. Despite the relatively low resolution, the whole trnL intron and its P6 loop have many advantages: the primers are highly conserved, and the amplification system is very robust. The P6 loop can even be amplified when using highly degraded DNA from processed food or from permafrost samples, and has the potential to be extensively used in food industry, in forensic science, in diet analyses based on feces and in ancient DNA studies.},
}
@article {pmid17166288,
year = {2006},
author = {Antczak, AJ and Tsubota, T and Kaufman, PD and Berger, JM},
title = {Structure of the yeast histone H3-ASF1 interaction: implications for chaperone mechanism, species-specific interactions, and epigenetics.},
journal = {BMC structural biology},
volume = {6},
number = {},
pages = {26},
pmid = {17166288},
issn = {1472-6807},
support = {R01 CA077373/CA/NCI NIH HHS/United States ; CA077373/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Cell Cycle Proteins/chemistry/genetics ; Dimerization ; *Epigenesis, Genetic ; Gene Silencing ; Humans ; Molecular Chaperones/chemistry/*genetics ; Protein Binding ; Saccharomyces cerevisiae/chemistry/*genetics ; Silent Information Regulator Proteins, Saccharomyces cerevisiae/chemistry/genetics ; Species Specificity ; },
abstract = {BACKGROUND: The histone H3/H4 chaperone Asf1 (anti-silencing function 1) is required for the establishment and maintenance of proper chromatin structure, as well as for genome stability in eukaryotes. Asf1 participates in both DNA replication-coupled (RC) and replication-independent (RI) histone deposition reactions in vitro and interacts with complexes responsible for both pathways in vivo. Asf1 is known to directly bind histone H3, however, high-resolution structural information about the geometry of this interaction was previously unknown.<br><br>RESULTS: Here we report the structure of a histone/histone chaperone interaction. We have solved the 2.2 A crystal structure of the conserved N-terminal immunoglobulin fold domain of yeast Asf1 (residues 2-155) bound to the C-terminal helix of yeast histone H3 (residues 121-134). The structure defines a histone-binding patch on Asf1 consisting of both conserved and yeast-specific residues; mutation of these residues abrogates H3/H4 binding affinity. The geometry of the interaction indicates that Asf1 binds to histones H3/H4 in a manner that likely blocks sterically the H3/H3 interface of the nucleosomal four-helix bundle.<br><br>CONCLUSION: These data clarify how Asf1 regulates histone stoichiometry to modulate epigenetic inheritance. The structure further suggests a physical model in which Asf1 contributes to interpretation of a "histone H3 barcode" for sorting H3 isoforms into different deposition pathways.},
}
@article {pmid17148432,
year = {2006},
author = {Fleischer, RC and Kirchman, JJ and Dumbacher, JP and Bevier, L and Dove, C and Rotzel, NC and Edwards, SV and Lammertink, M and Miglia, KJ and Moore, WS},
title = {Mid-Pleistocene divergence of Cuban and North American ivory-billed woodpeckers.},
journal = {Biology letters},
volume = {2},
number = {3},
pages = {466-469},
pmid = {17148432},
issn = {1744-9561},
mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Birds/*genetics/*physiology ; Conservation of Natural Resources ; Cuba ; DNA, Mitochondrial/metabolism ; Ecology ; Likelihood Functions ; Models, Biological ; North America ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {We used ancient DNA analysis of seven museum specimens of the endangered North American ivory-billed woodpecker (Campephilus principalis) and three specimens of the species from Cuba to document their degree of differentiation and their relationships to other Campephilus woodpeckers. Analysis of these mtDNA sequences reveals that the Cuban and North American ivory bills, along with the imperial woodpecker (Campephilus imperialis) of Mexico, are a monophyletic group and are roughly equidistant genetically, suggesting each lineage may be a separate species. Application of both internal and external rate calibrations indicates that the three lineages split more than one million years ago, in the Mid-Pleistocene. We thus can exclude the hypothesis that Native Americans introduced North American ivory-billed woodpeckers to Cuba. Our sequences of all three woodpeckers also provide an important DNA barcoding resource for identification of non-invasive samples or remains of these critically endangered and charismatic woodpeckers.},
}
@article {pmid17148149,
year = {2005},
author = {Page, TJ and Choy, SC and Hughes, JM},
title = {The taxonomic feedback loop: symbiosis of morphology and molecules.},
journal = {Biology letters},
volume = {1},
number = {2},
pages = {139-142},
pmid = {17148149},
issn = {1744-9561},
mesh = {Animals ; Classification/methods ; DNA, Ribosomal/genetics ; Decapoda/anatomy &amp; histology/*classification/genetics ; Electron Transport Complex IV/genetics ; },
abstract = {Here, we relate the ongoing taxonomic story of a species complex of problematic, cryptic Australian freshwater shrimp (Atyidae; Caridina) to highlight the relative strength and utility of different taxonomic methods in assessing species boundaries. We used popular 'DNA barcode' gene fragments cytochrome c oxidase 1 and 16S ribosomal DNA. We then assessed the morphological attributes of these specimens and developed an identification key to complement the molecular results, and conclude that, despite occasionally strident arguments in favour of either molecular or morphological taxonomy, the two are inseparably linked and form parts of a greater whole.},
}
@article {pmid17139324,
year = {2006},
author = {Mazurkiewicz, P and Tang, CM and Boone, C and Holden, DW},
title = {Signature-tagged mutagenesis: barcoding mutants for genome-wide screens.},
journal = {Nature reviews. Genetics},
volume = {7},
number = {12},
pages = {929-939},
doi = {10.1038/nrg1984},
pmid = {17139324},
issn = {1471-0056},
support = {G9717183/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Bacteria/genetics/growth &amp; development ; Gene Library ; *Genome ; Humans ; *Mutagenesis, Insertional ; Mutation/*genetics ; RNA Interference ; Saccharomyces cerevisiae/genetics/growth &amp; development ; },
abstract = {DNA signature tags (molecular barcodes) facilitate functional screens by identifying mutants in mixed populations that have a reduced or increased adaptation to a particular environment. Many innovative adaptations and refinements in the technology have been described since its original use with Salmonella; they have yielded a wealth of information on a broad range of biological processes--mainly in bacteria, but also in yeast and other fungi, viruses, parasites and, most recently, in mammalian cells. By combining whole-genome microarrays and comprehensive ordered libraries of mutants, high-throughput functional screens can now be achieved on a genomic scale.},
}
@article {pmid17135463,
year = {2006},
author = {Rubinoff, D and Cameron, S and Will, K},
title = {A genomic perspective on the shortcomings of mitochondrial DNA for "barcoding" identification.},
journal = {The Journal of heredity},
volume = {97},
number = {6},
pages = {581-594},
doi = {10.1093/jhered/esl036},
pmid = {17135463},
issn = {0022-1503},
mesh = {Animals ; *Biodiversity ; Classification/*methods ; DNA, Mitochondrial/*chemistry ; Evolution, Molecular ; Genome ; Phylogeny ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
abstract = {Approximately 600-bp sequences of mitochondrial DNA (mtDNA) have been designated as "DNA barcodes" and have become one of the most contentious and animated issues in the application of genetic information to global biodiversity assessment and species identification. Advocates of DNA barcodes have received extensive attention and promotion in many popular and refereed scientific publications. However, we suggest that the utility of barcodes is suspect and vulnerable to technical challenges that are particularly pertinent to mtDNA. We review the natural history of mtDNA and discuss problems for barcoding which are particularly associated with mtDNA and inheritance, including reduced effective population size, maternal inheritance, recombination, inconsistent mutation rate, heteroplasmy, and compounding evolutionary processes. The aforementioned could significantly limit the application and utility of mtDNA barcoding efforts. Furthermore, global use of barcodes will require application and acceptance of a barcode-based species concept that has not been evaluated in the context of the extensive literature concerning species designation. Implementation of mtDNA barcodes in spite of technical and practical shortcomings we discuss may degrade the longstanding synthesis of genetic and organism-based research and will not advance studies ranging from genomic evolution to biodiversity assessment.},
}
@article {pmid17126567,
year = {2007},
author = {Foley, DH and Wilkerson, RC and Cooper, RD and Volovsek, ME and Bryan, JH},
title = {A molecular phylogeny of Anopheles annulipes (Diptera: Culicidae) sensu lato: the most species-rich anopheline complex.},
journal = {Molecular phylogenetics and evolution},
volume = {43},
number = {1},
pages = {283-297},
doi = {10.1016/j.ympev.2006.10.008},
pmid = {17126567},
issn = {1055-7903},
mesh = {Animals ; Anopheles/*anatomy &amp; histology/*genetics ; Australia ; Base Sequence ; Bayes Theorem ; DNA Primers ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics ; Models, Genetic ; Molecular Sequence Data ; Papua New Guinea ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The Australasian Annulipes Complex is the most species-rich among Anopheles mosquitoes, with at least 15 sibling species suspected. Members of this complex are the most likely vectors of malaria in the past in southern Australia and are involved in the spread of myxomatosis among rabbits. In this, the first comprehensive molecular study of the Annulipes Complex, 23 ITS2 rDNA variants were detected from collections throughout Australia and Papua New Guinea, including diagnostic variants for the previously identified An. annulipes species A-G. Specimens of each ITS2 variant were sequenced for portions of the mitochondrial COI, COII and nuclear EF-1alpha genes. Partitioned Bayesian and Maximum Parsimony analyses confirmed the monophyly of the Annulipes Complex and revealed at least 17 clades that we designate species A-Q. These species belong to two major clades, one in the north and one mainly in the south, suggesting that climate was a driver of species radiation. We found that 65% (11) of the 17 sibling species recorded here had unique COI sequences, suggesting that DNA barcoding will be useful for diagnosing species within the Annulipes Complex. A comparison of the taxa revealed morphological characters that may be diagnostic for some species. Our results substantially increase the size of the subgenus Cellia in Australasia, and will assist species-level studies of the Annulipes Complex.},
}
@article {pmid17102371,
year = {2006},
author = {Shindo, A and Matsuda, A and Tani, S and Marukami, T and Fujimaru, K and Yagi, Y and Horio, H and Inada, H},
title = {Construction of a safety management system for drug use by using an RFID tag.},
journal = {Studies in health technology and informatics},
volume = {122},
number = {},
pages = {770},
pmid = {17102371},
issn = {0926-9630},
mesh = {Electronic Data Processing ; Humans ; Materials Management, Hospital/*methods ; *Narcotics ; Pharmacy Service, Hospital ; Radio Waves ; Safety Management/*organization &amp; administration ; },
abstract = {We constructed a safety management system for narcotic drug use by using an RFID tag with barcode. In this system, RFID tags are mainly used for postscript of information, while barcodes, especially standardized unit drug codes for distribution, are used for drug identification. The outline of the system is described in the present paper.},
}
@article {pmid17092308,
year = {2007},
author = {Dzik, WH},
title = {New technology for transfusion safety.},
journal = {British journal of haematology},
volume = {136},
number = {2},
pages = {181-190},
doi = {10.1111/j.1365-2141.2006.06373.x},
pmid = {17092308},
issn = {0007-1048},
mesh = {Blood Grouping and Crossmatching ; Blood Specimen Collection/standards ; Blood Transfusion/*standards ; Clinical Pharmacy Information Systems ; Humans ; Medical Errors ; Patient Identification Systems ; Patient Selection ; Point-of-Care Systems ; Safety Management/methods ; Transfusion Reaction ; },
abstract = {Hemovigilance programs from around the world document that the greatest risk to recipients of blood transfusion is human error, resulting in transfusion of the incorrect blood component. Errors in transfusion care have strong parallels with errors in medication administration. Errors often result from 'lapse' or 'slip' mistakes in which details of patient identification are overlooked. Three areas of transfusion are focal points for improved care: the labelling of the patient's pre-transfusion sample, the decision to transfuse and the final bedside check designed to prevent mis-transfusion. Both barcodes and radio-frequency identification technology, each ideally suited to matching alpha-numeric identifiers, are being implemented in order to improve performance sample labelling and the bedside check. The decision to transfuse should ultimately be enhanced through the use of nanotechnology sensors, computerised order entry and decision support systems. Obstacles to the deployment of new technology include resistance to change, confusion regarding the best technology, and uncertainty regarding the return-on-investment. By focusing on overall transfusion safety, deploying validated systems appropriate for both medication and blood administration, thoughtful integration of technology into bedside practice and demonstration of improved performance, the application of new technologies will improve care for patients in need of transfusion therapy.},
}
@article {pmid17073933,
year = {2006},
author = {Bely, AE and Weisblat, DA},
title = {Lessons from leeches: a call for DNA barcoding in the lab.},
journal = {Evolution &amp; development},
volume = {8},
number = {6},
pages = {491-501},
doi = {10.1111/j.1525-142X.2006.00122.x},
pmid = {17073933},
issn = {1520-541X},
mesh = {Animals ; Animals, Laboratory ; Animals, Wild ; DNA/*genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; Genetic Variation ; Leeches/classification/enzymology/*genetics/growth &amp; development ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; },
abstract = {Many evolution of development labs study organisms that must be periodically collected from the wild. Whenever this is the case, there is the risk that different field collections will recover genetically different strains or cryptic species. Ignoring this potential for genetic variation may introduce an uncontrolled source of experimental variability, leading to confusion or misinterpretation of the results. Leeches in the genus Helobdella have been a workhorse of annelid developmental biology for 30 years. Nearly all early Helobdella research was based on a single isolate, but in recent years isolates from multiple field collections and multiple sites across the country have been used. To assess the genetic distinctness of different isolates, we obtained specimens from most Helobdella laboratory cultures currently or recently in use and from some of their source field sites. From these samples, we sequenced part of the mitochondrial gene cytochrome oxidase I (COI). Sequence divergences and phylogenetic analyses reveal that, collectively, the Helobdella development community has worked on five distinct species from two major clades. Morphologically similar isolates that were thought to represent the same species (H. robusta) actually represent three species, two of which coexist at the same locality. Another isolate represents part of a species complex (the "H. triserialis" complex), and yet another is an invasive species (H. europaea). We caution researchers similarly working on multiple wild-collected isolates to preserve voucher specimens and to obtain from these a molecular "barcode," such as a COI gene sequence, to reveal genetic variation in animals used for research.},
}
@article {pmid17069089,
year = {2006},
author = {Wickham, S},
title = {Blood, barcodes and normalisation.},
journal = {The practising midwife},
volume = {9},
number = {9},
pages = {43},
pmid = {17069089},
issn = {1461-3123},
mesh = {Blood Transfusion/*nursing ; Contraindications ; Female ; Humans ; *Maternal Welfare ; Midwifery/*organization &amp; administration ; Patient Identification Systems ; Pregnancy ; Quality Assurance, Health Care/organization &amp; administration ; Risk Management ; United Kingdom ; *Women's Health ; },
}
@article {pmid17060204,
year = {2006},
author = {Cameron, S and Rubinoff, D and Will, K},
title = {Who will actually use DNA barcoding and what will it cost?.},
journal = {Systematic biology},
volume = {55},
number = {5},
pages = {844-847},
doi = {10.1080/10635150600960079},
pmid = {17060204},
issn = {1063-5157},
mesh = {Classification/*methods ; DNA/chemistry ; Electron Transport Complex IV/chemistry/genetics ; Sequence Analysis, DNA/*economics/methods ; },
}
@article {pmid17060195,
year = {2006},
author = {Hickerson, MJ and Meyer, CP and Moritz, C},
title = {DNA barcoding will often fail to discover new animal species over broad parameter space.},
journal = {Systematic biology},
volume = {55},
number = {5},
pages = {729-739},
doi = {10.1080/10635150600969898},
pmid = {17060195},
issn = {1063-5157},
mesh = {Animals ; Base Sequence ; Biodiversity ; Classification/*methods ; DNA, Mitochondrial/chemistry ; Evolution, Molecular ; *Genetic Speciation ; *Models, Genetic ; Phylogeny ; Selection, Genetic ; Sequence Analysis, DNA ; },
abstract = {With increasing force, genetic divergence of mitochondrial DNA (mtDNA) is being argued as the primary tool for discovery of animal species. Two thresholds of single-gene divergence have been proposed: reciprocal monophyly, and 10 times greater genetic divergence between than within species (the "10x rule"). To explore quantitatively the utility of each approach, we couple neutral coalescent theory and the classical Bateson-Dobzhansky-Muller (BDM) model of speciation. The joint stochastic dynamics of these two processes demonstrate that both thresholds fail to "discover" many reproductively isolated lineages under a single incompatibility BDM model, especially when BDM loci have been subject to divergent selection. Only when populations have been isolated for > 4 million generations did these thresholds achieve error rates of < 10% under our model that incorporates variable population sizes. The high error rate evident in simulations is corroborated with six empirical data sets. These properties suggest that single-gene, high-throughput approaches to discovering new animal species will bias large-scale biodiversity surveys, particularly toward missing reproductively isolated lineages that have emerged by divergent selection or other mechanisms that accelerate reproductive isolation. Because single-gene thresholds for species discovery can result in substantial error at recent divergence times, they will misrepresent the correspondence between recently isolated populations and reproductively isolated lineages (= species).},
}
@article {pmid17060194,
year = {2006},
author = {Meier, R and Shiyang, K and Vaidya, G and Ng, PK},
title = {DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success.},
journal = {Systematic biology},
volume = {55},
number = {5},
pages = {715-728},
doi = {10.1080/10635150600969864},
pmid = {17060194},
issn = {1063-5157},
mesh = {Animals ; Base Sequence ; Classification/methods ; Consensus Sequence ; DNA, Mitochondrial/chemistry ; Diptera/*classification/genetics ; Electron Transport Complex IV/chemistry/genetics ; *Genetic Variation ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {DNA barcoding and DNA taxonomy have recently been proposed as solutions to the crisis of taxonomy and received significant attention from scientific journals, grant agencies, natural history museums, and mainstream media. Here, we test two key claims of molecular taxonomy using 1333 mitochondrial COI sequences for 449 species of Diptera. We investigate whether sequences can be used for species identification ("DNA barcoding") and find a relatively low success rate (< 70%) based on tree-based and newly proposed species identification criteria. Misidentifications are due to wide overlap between intra- and interspecific genetic variability, which causes 6.5% of all query sequences to have allospecific or a mixture of allo- and conspecific (3.6%) best-matching barcodes. Even when two COI sequences are identical, there is a 6% chance that they belong to different species. We also find that 21% of all species lack unique barcodes when consensus sequences of all conspecific sequences are used. Lastly, we test whether DNA sequences yield an unambiguous species-level taxonomy when sequence profiles are assembled based on pairwise distance thresholds. We find many sequence triplets for which two of the three pairwise distances remain below the threshold, whereas the third exceeds it; i.e., it is impossible to consistently delimit species based on pairwise distances. Furthermore, for species profiles based on a 3% threshold, only 47% of all profiles are consistent with currently accepted species limits, 20% contain more than one species, and 33% only some sequences from one species; i.e., adopting such a DNA taxonomy would require the redescription of a large proportion of the known species, thus worsening the taxonomic impediment. We conclude with an outlook on the prospects of obtaining complete barcode databases and the future use of DNA sequences in a modern integrative taxonomy.},
}
@article {pmid17055406,
year = {2006},
author = {Fewell, GD and Schmitt, K},
title = {Vector-based RNAi approaches for stable, inducible and genome-wide screens.},
journal = {Drug discovery today},
volume = {11},
number = {21-22},
pages = {975-982},
doi = {10.1016/j.drudis.2006.09.008},
pmid = {17055406},
issn = {1359-6446},
mesh = {Animals ; DNA Polymerase II/genetics ; Databases, Nucleic Acid ; Doxorubicin/pharmacology ; *Gene Expression Regulation/drug effects ; Genetic Techniques/*trends ; Genetic Vectors/*genetics ; Humans ; MicroRNAs/genetics ; Promoter Regions, Genetic/drug effects/genetics ; RNA/*genetics/metabolism ; *RNA Interference ; RNA, Small Interfering/genetics ; },
abstract = {RNA interference (RNAi) has revolutionized the study of biology and offers numerous applications in basic biology as well as in drug discovery research. Since the discovery of RNAi, several tools have been developed to enable loss-of-function studies in mammalian systems. The efficacy of RNAi is dependent on specific and versatile RNAi triggers that have evolved to enable transient, stable and in-vivo applications. Recently developed genome-wide short hairpin RNA (shRNA) and microRNA-adapted short hairpin RNA (shRNAmir) libraries incorporate advances in shRNA design and molecular 'barcodes' to enable more complex RNAi screens and the opportunity to progress to more complex genetics in whole animals.},
}
@article {pmid17035167,
year = {2007},
author = {Gómez, A and Wright, PJ and Lunt, DH and Cancino, JM and Carvalho, GR and Hughes, RN},
title = {Mating trials validate the use of DNA barcoding to reveal cryptic speciation of a marine bryozoan taxon.},
journal = {Proceedings. Biological sciences},
volume = {274},
number = {1607},
pages = {199-207},
pmid = {17035167},
issn = {0962-8452},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; Bryozoa/anatomy &amp; histology/*genetics ; DNA/*genetics ; DNA Primers ; Electron Transport Complex IV/genetics ; *Genetic Speciation ; *Genetic Variation ; *Genetics, Population ; Models, Genetic ; Molecular Sequence Data ; Peptide Elongation Factor 1/genetics ; *Phylogeny ; Reproduction/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {Despite increasing threats to the marine environment, only a fraction of the biodiversity of the oceans has been described, owing in part to the widespread occurrence of cryptic species. DNA-based barcoding through screening of an orthologous reference gene has been proposed as a powerful tool to uncover biological diversity in the face of dwindling taxonomic expertise and the limitations of traditional species identification. Although DNA barcoding should be particularly useful in the sea, given the prevalence of marine cryptic species, the link between taxa identified through DNA barcodes and reproductively isolated taxa (biological species) has rarely been explicitly tested. Here, we use an integrated framework comparing breeding compatibility, morphology and mitochondrial (cytochrome c oxidase 1) and nuclear (elongation factor-1-alpha) DNA sequence variation among globally distributed samples of the cosmopolitan marine bryozoan Celleporella hyalina (L.). Our results reveal that C. hyalina comprises numerous deep, mostly allopatric, genetic lineages that are reproductively isolated, yet share very similar morphology, indicating rampant cryptic speciation. The close correspondence between genetic lineages and reproductively isolated taxa in the context of minimal morphological change suggests that DNA barcoding will play a leading role in uncovering the hidden biodiversity of the oceans and that the sole use of morphologically based taxonomy would grossly underestimate the number of marine species.},
}
@article {pmid17002773,
year = {2006},
author = {Rubinoff, D},
title = {DNA barcoding evolves into the familiar.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {20},
number = {5},
pages = {1548-1549},
doi = {10.1111/j.1523-1739.2006.00542.x},
pmid = {17002773},
issn = {0888-8892},
mesh = {Biodiversity ; Classification ; Conservation of Natural Resources/*methods ; DNA/*genetics ; Electronic Data Processing/*methods ; Genetic Speciation ; },
}
@article {pmid17002772,
year = {2006},
author = {Desalle, R},
title = {Species discovery versus species identification in DNA barcoding efforts: response to Rubinoff.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {20},
number = {5},
pages = {1545-1547},
doi = {10.1111/j.1523-1739.2006.00543.x},
pmid = {17002772},
issn = {0888-8892},
mesh = {Biological Evolution ; Classification ; Cluster Analysis ; DNA, Mitochondrial/*genetics ; Electronic Data Processing/*methods ; Genetic Speciation ; Research ; },
}
@article {pmid16965799,
year = {2006},
author = {Powell, RL and Reyes, SR and Lannutti, DI},
title = {Molecular barcoding, DNA from snake venom, and toxinological research: Considerations and concerns.},
journal = {Toxicon : official journal of the International Society on Toxinology},
volume = {48},
number = {8},
pages = {1095-1097},
doi = {10.1016/j.toxicon.2006.07.035},
pmid = {16965799},
issn = {0041-0101},
mesh = {Animals ; DNA, Mitochondrial/*chemistry ; Sequence Analysis, DNA/*methods ; Snake Venoms/*classification/genetics ; Species Specificity ; },
abstract = {The problem of species identification in toxinological research and solutions such as molecular barcoding and DNA extraction from venom samples are addressed. Molecular barcoding is controversial with both perceived advantages and inherent problems. A method of species identification utilizing mitochondrial DNA from venom has been identified. This method could result in deemphasizing the importance of obtaining detailed information on the venom source prior to analysis. Additional concerns include; a cost prohibitive factor, intraspecific venom variation, and venom processing issues. As researchers demand more stringent records and verification, venom suppliers may be prompted to implement improved methods and controls.},
}
@article {pmid16936793,
year = {2006},
author = {Hajibabaei, M and Singer, GA and Hickey, DA},
title = {Benchmarking DNA barcodes: An assessment using available primate sequences.},
journal = {Genome},
volume = {49},
number = {7},
pages = {851-854},
doi = {10.1139/g06-025},
pmid = {16936793},
issn = {0831-2796},
mesh = {Animals ; DNA/classification/*genetics ; *Phylogeny ; Primates/classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {DNA barcoding has been recently promoted as a method for both assigning specimens to known species and for discovering new and cryptic species. Here we test both the potential and the limitations of DNA barcodes by analysing a group of well-studied organisms--the primates. Our results show that DNA barcodes provide enough information to efficiently identify and delineate primate species, but that they cannot reliably uncover many of the deeper phylogenetic relationships. Our conclusion is that these short DNA sequences do not contain enough information to build reliable molecular phylogenies or define new species, but that they can provide efficient sequence tags for assigning unknown specimens to known species. As such, DNA barcoding provides enormous potential for use in global biodiversity studies.},
}
@article {pmid16922219,
year = {2006},
author = {Rubinoff, D},
title = {Utility of mitochondrial DNA barcodes in species conservation.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {20},
number = {4},
pages = {1026-1033},
doi = {10.1111/j.1523-1739.2006.00372.x},
pmid = {16922219},
issn = {0888-8892},
mesh = {Biodiversity ; Conservation of Natural Resources/*methods ; DNA, Mitochondrial/*classification ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; *Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {Molecular tools are a standard part of many conservation studies and can be informative at many different levels of analysis, although there are inherent limitations and strengths of different genes or parts of genes to inform specific questions. Animal DNA barcodes, 600- to 800-base-pair segments of the mitochondrial gene cytochrome oxidase I, have been proposed as a means to quantify global biodiversity. Although mitochondrial (mt) DNA has a long history of use at the species level, recent analyses suggest that the use of a single gene, particularly mitochondrial, is unlikely to yield data that are balanced, universally acceptable, or sufficient in taxonomic scope to recognize many species lineages. Mitochondrial and nuclear genomes have different patterns of evolution and modes of inheritance, which can result in very different assessments of biodiversity. The ramifications of choosing a particular definition of species (species concept) need to be carefully considered because current efforts have designated DNA barcodes as the universal species concept without demonstrating its superiority over preexisting concepts. The results of such a barcoding paradigm may include a failure to recognize significant portions of biodiversity or nuclear/mitochondrial mixed lineages and could spuriously focus conservation resources on populations with relatively minor mtDNA divergence. DNA barcodes are most likely to provide potentially useful information for groups that are already well studied, and such taxa do not constitute the majority of biodiversity or those in most need of research attention. DNA barcode-length sequences are an important source of data but, when used alone or out of context, may offer only a fraction of the information needed to characterize species while taking resources from broader studies that could produce information essential to robust and informed conservation decisions.},
}
@article {pmid16911222,
year = {2006},
author = {Witt, JD and Threloff, DL and Hebert, PD},
title = {DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: implications for desert spring conservation.},
journal = {Molecular ecology},
volume = {15},
number = {10},
pages = {3073-3082},
doi = {10.1111/j.1365-294X.2006.02999.x},
pmid = {16911222},
issn = {0962-1083},
mesh = {Amphipoda/*genetics ; Animals ; California ; *Conservation of Natural Resources ; *Genetic Variation ; Geography ; Likelihood Functions ; Nevada ; Phylogeny ; *Sequence Analysis, DNA ; },
abstract = {DNA barcoding has revealed unrecognized species in several animal groups. In this study we have employed DNA barcoding to examine Hyalella, a taxonomically difficult genus of amphipod crustaceans, from sites in the southern Great Basin of California and Nevada, USA. We assessed the extent of species diversity using a species screening threshold (SST) set at 10 times the average intrapopulation cytochrome c oxidase subunit I (COI) haplotype divergence. Despite the fact that this threshold approach is more conservative in delineating provisional species than the phylogenetic species concept, our analyses revealed extraordinary levels of cryptic diversity and endemism. The SST discriminated two provisional species within Hyalella sandra, and 33 provisional species within Hyalella azteca. COI nucleotide divergences among these provisional species ranged from 4.4% to 29.9%. These results have important implications for the conservation of life in desert springs - habitats that are threatened as a result of groundwater over-exploitation.},
}
@article {pmid16907869,
year = {2006},
author = {Pagliaro, P and Rebulla, P},
title = {Transfusion recipient identification.},
journal = {Vox sanguinis},
volume = {91},
number = {2},
pages = {97-101},
doi = {10.1111/j.1423-0410.2006.00783.x},
pmid = {16907869},
issn = {0042-9007},
mesh = {Blood Group Incompatibility/*prevention &amp; control ; Humans ; Medical Errors/*prevention &amp; control ; Patient Identification Systems/*methods ; *Safety ; *Transfusion Reaction ; },
abstract = {Recent reports from different haemovigilance systems indicate that errors in the whole-blood transfusion chain - from initial recipient identification to final blood administration - occur with a frequency of approximately 1 in 1000 events. Although mistakes occur also within the blood transfusion service, about two-thirds of errors are associated with incorrect blood recipient identification at the patient's bedside. To prevent the potentially fatal consequences of such mistakes, specific tools have been developed, including patient identification bracelets with barcodes and/or radio frequency identification devices, mechanical or electronic locks preventing access to bags assigned to other patients, and palm computers suitable for transferring blood request and administration data from the patient's bedside to the blood transfusion service information system in real time. The effectiveness of these systems in preventing mistransfusion has been demonstrated in a number of studies.},
}
@article {pmid16895600,
year = {2006},
author = {Lancia, G and Rizzi, R},
title = {The approximability of the String Barcoding problem.},
journal = {Algorithms for molecular biology : AMB},
volume = {1},
number = {},
pages = {12},
pmid = {16895600},
issn = {1748-7188},
abstract = {The String Barcoding (SBC) problem, introduced by Rash and Gusfield (RECOMB, 2002), consists in finding a minimum set of substrings that can be used to distinguish between all members of a set of given strings. In a computational biology context, the given strings represent a set of known viruses, while the substrings can be used as probes for an hybridization experiment via microarray. Eventually, one aims at the classification of new strings (unknown viruses) through the result of the hybridization experiment. In this paper we show that SBC is as hard to approximate as Set Cover. Furthermore, we show that the constrained version of SBC (with probes of bounded length) is also hard to approximate. These negative results are tight.},
}
@article {pmid16891521,
year = {2006},
author = {Pounder, JI and Hansen, D and Woods, GL},
title = {Identification of Histoplasma capsulatum, Blastomyces dermatitidis, and Coccidioides species by repetitive-sequence-based PCR.},
journal = {Journal of clinical microbiology},
volume = {44},
number = {8},
pages = {2977-2982},
pmid = {16891521},
issn = {0095-1137},
mesh = {Blastomyces/*classification/cytology/genetics/growth &amp; development ; Cluster Analysis ; Coccidioides/*classification/cytology/genetics/growth &amp; development ; DNA Fingerprinting/*methods ; DNA, Fungal/genetics/isolation &amp; purification ; Histoplasma/*classification/cytology/genetics/growth &amp; development ; Humans ; Microscopy ; Nucleic Acid Hybridization ; Polymerase Chain Reaction/*methods ; *Repetitive Sequences, Nucleic Acid ; Sensitivity and Specificity ; },
abstract = {The performance of repetitive-sequence-based PCR (rep-PCR) using the DiversiLab system for identification of Coccidioides species, Blastomyces dermatitidis, and Histoplasma capsulatum was assessed by comparing data obtained to colony morphology and microscopic characteristics and to nucleic acid probe results. DNA from cultures of 23 Coccidioides, 24 B. dermatitidis, 24 H. capsulatum, 3 Arthrographis, and 2 Malbranchea isolates was extracted using a microbial DNA isolation kit as recommended by Bacterial Barcodes, Inc. Rep-PCR and probe results agreed for 97.2% of the dimorphic fungi when > or =85% similarity was used as the criterion for identification. Two H. capsulatum isolates were not identified, but no isolates were misidentified. From 43 of those cultures (15 Coccidioides, 14 B. dermatitidis, 14 H. capsulatum, 3 Arthrographis, and 2 Malbranchea), DNA also was extracted using an IDI lysis kit, a simpler method. Rep-PCR and probe results agreed for 97.7% of the dimorphic fungi when a criterion of > or =90% similarity was used for identification. One H. capsulatum isolate could not be identified; no isolates were misidentified. Using > or =85% similarity for identification resulted in one misidentification. These data suggest that the DiversiLab system can be used to identify Coccidioides and B. dermatitidis and, possibly, H. capsulatum isolates.},
}
@article {pmid16862133,
year = {2006},
author = {Pierce, SE and Fung, EL and Jaramillo, DF and Chu, AM and Davis, RW and Nislow, C and Giaever, G},
title = {A unique and universal molecular barcode array.},
journal = {Nature methods},
volume = {3},
number = {8},
pages = {601-603},
doi = {10.1038/nmeth905},
pmid = {16862133},
issn = {1548-7091},
mesh = {Base Sequence ; DNA Probes/*genetics ; Equipment Design ; Equipment Failure Analysis ; *Expressed Sequence Tags ; In Situ Hybridization, Fluorescence/*instrumentation/methods ; Molecular Probe Techniques/*instrumentation ; Molecular Sequence Data ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Alignment/*instrumentation/methods ; Sequence Analysis, DNA/*instrumentation/methods ; },
abstract = {Molecular barcode arrays allow the analysis of thousands of biological samples in parallel through the use of unique 20-base-pair (bp) DNA tags. Here we present a new barcode array, which is unique among microarrays in that it includes at least five replicates of every tag feature. The use of smaller dispersed replicate features dramatically improves performance versus a single larger feature and allows the correction of previously undetectable hybridization defects.},
}
@article {pmid16846913,
year = {2006},
author = {Barber, P and Boyce, SL},
title = {Estimating diversity of Indo-Pacific coral reef stomatopods through DNA barcoding of stomatopod larvae.},
journal = {Proceedings. Biological sciences},
volume = {273},
number = {1597},
pages = {2053-2061},
pmid = {16846913},
issn = {0962-8452},
mesh = {Animals ; *Biodiversity ; Crustacea/*classification/genetics/growth &amp; development ; Electron Transport Complex IV/genetics ; Electronic Data Processing/methods ; Genetic Markers ; Indian Ocean ; Larva/classification/genetics ; Pacific Ocean ; Phylogeny ; Protein Subunits/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {There is a push to fully document the biodiversity of the world within 25 years. However, the magnitude of this challenge, particularly in marine environments, is not well known. In this study, we apply DNA barcoding to explore the biodiversity of gonodactylid stomatopods (mantis shrimp) in both the Coral Triangle and the Red Sea. Comparison of sequences from 189 unknown stomatopod larvae to 327 known adults representing 67 taxa in the superfamily Gonodactyloidea revealed 22 distinct larval operational taxonomic units (OTUs). In the Western Pacific, 10 larval OTUs were members of the Gonodactylidae and Protosquillidae where success of positive identification was expected to be 96.5%. However, only five OTUs could be identified to species and at least three OTUs represent new species unknown in their adult form. In the Red Sea where the identification rate was expected to be 75% in the Gonodactylidae, none of four larval OTUs could be identified to species; at least two represent new species unknown in their adult forms. Results indicate that the biodiversity in this well-studied group in the Coral Triangle and Red Sea may be underestimated by a minimum of 50% to more than 150%, suggesting a much greater challenge in lesser-studied groups. Although the DNA barcoding methodology was effective, its overall success was limited due to the newly discovered taxonomic limitations of the reference sequence database, highlighting the importance of synergy between molecular geneticists and taxonomists in understanding and documenting our world's biodiversity, both in marine and terrestrial environments.},
}
@article {pmid16830183,
year = {2006},
author = {Kumagai, MH and Miller, P},
title = {Development of electronic barcodes for use in plant pathology and functional genomics.},
journal = {Plant molecular biology},
volume = {61},
number = {3},
pages = {515-523},
pmid = {16830183},
issn = {0167-4412},
mesh = {Arabidopsis/anatomy &amp; histology/genetics ; Arabidopsis Proteins/genetics ; Cell Phone ; Computers ; Computers, Handheld ; Electronic Data Processing/instrumentation/*methods ; GTP-Binding Proteins/genetics ; Gene Library ; Genomics/instrumentation/*methods ; Phenotype ; Plants/anatomy &amp; histology/*genetics ; Plants, Genetically Modified/anatomy &amp; histology/metabolism ; Radio Waves ; Nicotiana/anatomy &amp; histology/genetics ; Tobamovirus/genetics ; },
abstract = {We have developed a novel 'electronic barcode' system that uses radio frequency identification (RFID) tags, cell phones, and portable computers to link phenotypic, environmental, and genomic data. We describe a secure, inexpensive system to record and retrieve data from plant samples. It utilizes RFID tags, computers, PDAs, and cell phones to link, record, and retrieve positional, and functional genomic data. Our results suggest that RFID tags can be used in functional genomic screens to record information that is involved in plant development or disease.},
}
@article {pmid16800029,
year = {2006},
author = {Gharizadeh, B and Herman, ZS and Eason, RG and Jejelowo, O and Pourmand, N},
title = {Large-scale pyrosequencing of synthetic DNA: a comparison with results from Sanger dideoxy sequencing.},
journal = {Electrophoresis},
volume = {27},
number = {15},
pages = {3042-3047},
pmid = {16800029},
issn = {0173-0835},
support = {P01 HG000205/HG/NHGRI NIH HHS/United States ; P01 HG000205-190004/HG/NHGRI NIH HHS/United States ; P01 HG 000205/HG/NHGRI NIH HHS/United States ; 1R21 AI 059499-01/AI/NIAID NIH HHS/United States ; },
mesh = {Base Sequence ; DNA/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {Pyrosequencing is a relatively recent method for sequencing short stretches of DNA. Because both Pyrosequencing and Sanger dideoxy sequencing were recently used to characterize and validate DNA molecular barcodes in a large yeast gene-deletion project, a meta-analysis of those data allow an excellent and timely opportunity for evaluating Pyrosequencing against the current gold standard, Sanger dideoxy sequencing. Starting with yeast genomic DNA, parallel PCR amplification methods were used to prepared 4747 short barcode-containing constructs from 6000 Saccharomyces cerevisiae gene-deletion strains. Pyrosequencing was optimized for average read lengths of 25-30 bases, which included in each case a 20-mer barcode sequence. Results were compared with sequence data obtained by the standard Sanger dideoxy chain termination method. In most cases, sequences obtained by Pyrosequencing and Sanger dideoxy sequencing were of comparable accuracy, and the overall rate of failure was similar. The DNA in the barcodes is derived from synthetic oligonucleotide sequences that were inserted into yeast-deletion-strain genomic DNA by homologous recombination and represents the most significant amount of DNA from a synthetic source that has been sequenced to date. Although more automation and quality control measures are needed, Pyrosequencing was shown to be a fast and convenient method for determining short stretches of DNA sequence.},
}
@article {pmid16790472,
year = {2006},
author = {Holterman, M and van der Wurff, A and van den Elsen, S and van Megen, H and Bongers, T and Holovachov, O and Bakker, J and Helder, J},
title = {Phylum-wide analysis of SSU rDNA reveals deep phylogenetic relationships among nematodes and accelerated evolution toward crown Clades.},
journal = {Molecular biology and evolution},
volume = {23},
number = {9},
pages = {1792-1800},
doi = {10.1093/molbev/msl044},
pmid = {16790472},
issn = {0737-4038},
mesh = {Amino Acid Substitution ; Animals ; Caenorhabditis elegans/genetics ; DNA, Ribosomal/*genetics ; *Evolution, Molecular ; Fungi/genetics ; Mesomycetozoea/*genetics ; Nematoda/*genetics ; Parasites ; *Phylogeny ; Plants/parasitology ; Polymorphism, Single Nucleotide ; Radiation ; },
abstract = {Inference of evolutionary relationships between nematodes is severely hampered by their conserved morphology, the high frequency of homoplasy, and the scarcity of phylum-wide molecular data. To study the origin of nematode radiation and to unravel the phylogenetic relationships between distantly related species, 339 nearly full-length small-subunit rDNA sequences were analyzed from a diverse range of nematodes. Bayesian inference revealed a backbone comprising 12 consecutive dichotomies that subdivided the phylum Nematoda into 12 clades. The most basal clade is dominated by the subclass Enoplia, and members of the order Triplonchida occupy positions most close to the common ancestor of the nematodes. Crown Clades 8-12, a group formerly indicated as "Secernentea" that includes Caenorhabditis elegans and virtually all major plant and animal parasites, show significantly higher nucleotide substitution rates than the more basal Clades 1-7. Accelerated substitution rates are associated with parasitic lifestyles (Clades 8 and 12) or short generation times (Clades 9-11). The relatively high substitution rates in the distal clades resulted in numerous autapomorphies that allow in most cases DNA barcode-based species identification. Teratocephalus, a genus comprising terrestrial bacterivores, was shown to be most close to the starting point of Secernentean radiation. Notably, fungal feeding nematodes were exclusively found basal to or as sister taxon next to the 3 groups of plant parasitic nematodes, namely, Trichodoridae, Longidoridae, and Tylenchomorpha. The exclusive common presence of fungivorous and plant parasitic nematodes supports a long-standing hypothesis that states that plant parasitic nematodes arose from fungivorous ancestors.},
}
@article {pmid16788705,
year = {2006},
author = {Dasmahapatra, KK and Mallet, J},
title = {Taxonomy: DNA barcodes: recent successes and future prospects.},
journal = {Heredity},
volume = {97},
number = {4},
pages = {254-255},
doi = {10.1038/sj.hdy.6800858},
pmid = {16788705},
issn = {0018-067X},
mesh = {Classification ; DNA, Mitochondrial/*genetics ; Genetic Techniques/trends ; Species Specificity ; },
}
@article {pmid16781661,
year = {2006},
author = {Saccone, C and Lanave, C and De Grassi, A},
title = {Metazoan OXPHOS gene families: evolutionary forces at the level of mitochondrial and nuclear genomes.},
journal = {Biochimica et biophysica acta},
volume = {1757},
number = {9-10},
pages = {1171-1178},
doi = {10.1016/j.bbabio.2006.04.021},
pmid = {16781661},
issn = {0006-3002},
mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genome/*genetics ; Multigene Family/*genetics ; *Oxidative Phosphorylation ; },
abstract = {Mitochondrial and nuclear DNAs contribute to encode the whole mitochondrial protein complement. The two genomes possess highly divergent features and properties, but the forces influencing their evolution, even if different, require strong coordination. The gene content of mitochondrial genome in all Metazoa is in a frozen state with only few exceptions and thus mitochondrial genome plasticity especially concerns some molecular features, i.e. base composition, codon usage, evolutionary rates. In contrast the high plasticity of nuclear genomes is particularly evident at the macroscopic level, since its redundancy represents the main feature able to introduce genetic material for evolutionary innovations. In this context, genes involved in oxidative phosphorylation (OXPHOS) represent a classical example of the different evolutionary behaviour of mitochondrial and nuclear genomes. The simple DNA sequence of Cytochrome c oxidase I (encoded by the mitochondrial genome) seems to be able to distinguish intra- and inter-species relations between organisms (DNA Barcode). Some OXPHOS subunits (cytochrome c, subunit c of ATP synthase and MLRQ) are encoded by several nuclear duplicated genes which still represent the trace of an ancient segmental/genome duplication event at the origin of vertebrates.},
}
@article {pmid16709623,
year = {2006},
author = {Azzazy, HM and Mansour, MM and Kazmierczak, SC},
title = {Nanodiagnostics: a new frontier for clinical laboratory medicine.},
journal = {Clinical chemistry},
volume = {52},
number = {7},
pages = {1238-1246},
doi = {10.1373/clinchem.2006.066654},
pmid = {16709623},
issn = {0009-9147},
mesh = {Clinical Chemistry Tests/*methods ; *Diagnostic Techniques and Procedures ; Gold ; Humans ; *Nanostructures/adverse effects ; Quantum Dots ; },
abstract = {BACKGROUND: The use of nanotechnologies for diagnostic applications shows great promise to meet the rigorous demands of the clinical laboratory for sensitivity and cost-effectiveness. New nanodiagnostic tools include quantum dots (QDs), gold nanoparticles, and cantilevers. QDs, which are the most promising nanostructures for diagnostic applications, are semiconductor nanocrystals characterized by high photostability, single-wavelength excitation, and size-tunable emission. QDs and magnetic nanoparticles can be used for barcoding of specific analytes. Gold and magnetic nanoparticles are key components of the bio-barcode assay, which has been proposed as a future alternative to the PCR.<br><br>METHODS: We examined articles published over the past 10 years investigating the use of QDs, gold nanoparticles, cantilevers, and other nanotechnologies in promising diagnostic applications.<br><br>RESULTS: Several nanodiagnostic assays have been developed, including a QD-based assay capable of detecting biotinylated prostate-specific antigen (PSA) at 0.38 ng/L, a bio-barcode assay capable of detecting 30 amol/L PSA in a 10-microL sample, and another able to detect 50 molecules of the Alzheimer marker amyloid beta-derived diffusible ligand in 10 microL of cerebrospinal fluid.<br><br>CONCLUSIONS: Nanodiagnostics promise increased sensitivity, multiplexing capabilities, and reduced cost for many diagnostic applications as well as intracellular imaging. Further work is needed to fully optimize these diagnostic nanotechnologies for clinical laboratory setting and to address the potential health and environmental risks related to QDs.},
}
@article {pmid16701459,
year = {2006},
author = {Rubinoff, D and Cameron, S and Will, K},
title = {Are plant DNA barcodes a search for the Holy Grail?.},
journal = {Trends in ecology &amp; evolution},
volume = {21},
number = {1},
pages = {1-2},
doi = {10.1016/j.tree.2005.10.019},
pmid = {16701459},
issn = {0169-5347},
mesh = {Biodiversity ; *Classification ; Evolution, Molecular ; Gene Amplification ; *Genome ; Inheritance Patterns ; Phylogeny ; Plants/*classification/*genetics ; *Sequence Analysis, DNA ; },
abstract = {In a recent study, Kress et al. compared two plant genomes to seek out plant DNA barcodes. Two promising markers balanced the variability that is needed to distinguish species with conserved primer regions that enable universal amplification. Although this study is the most rigorous effort to date, problems from earlier barcoding efforts, such as the use of non-evolutionary species concepts and differential sorting of genes and species, could reemerge. Single-gene barcoding might not be universally effective owing to inherent inaccuracies. Kress et al. suggest the use of multiple genes, reflecting an integrated approach that is likely to be the best answer to identifying species quickly and accurately.},
}
@article {pmid16676641,
year = {2006},
author = {Goth, G},
title = {Raising the bar. Barcoding has the potential to dramatically reduce medication errors.},
journal = {Healthcare informatics : the business magazine for information and communication systems},
volume = {23},
number = {4},
pages = {38-41},
pmid = {16676641},
issn = {1050-9135},
mesh = {*Clinical Pharmacy Information Systems ; Drug Industry/*legislation &amp; jurisprudence ; Electronic Data Processing/*legislation &amp; jurisprudence ; Humans ; Medication Errors/*prevention &amp; control ; *Medication Systems, Hospital ; Nonprescription Drugs/classification ; Pharmaceutical Preparations/*classification ; United States ; United States Food and Drug Administration ; },
}
@article {pmid16647275,
year = {2006},
author = {Lefébure, T and Douady, CJ and Gouy, M and Gibert, J},
title = {Relationship between morphological taxonomy and molecular divergence within Crustacea: proposal of a molecular threshold to help species delimitation.},
journal = {Molecular phylogenetics and evolution},
volume = {40},
number = {2},
pages = {435-447},
doi = {10.1016/j.ympev.2006.03.014},
pmid = {16647275},
issn = {1055-7903},
mesh = {Amino Acids/chemistry/genetics ; Animals ; Crustacea/anatomy &amp; histology/*classification/*genetics ; *Evolution, Molecular ; Mitochondrial Proteins/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {With today's technology for production of molecular sequences, DNA taxonomy and barcoding arose as a new tool for evolutionary biology and ecology. However, their validities still need to be empirically evaluated. Of most importance is the strength of the correlation between morphological taxonomy and molecular divergence and the possibility to define some molecular thresholds. Here, we report measurements of this correlation for two mitochondrial genes (COI and 16S rRNA) within the sub-phylum Crustacea. Perl scripts were developed to ensure objectivity, reproducibility, and exhaustiveness of our tests. Our analysis reveals a general correlation between molecular divergence and taxonomy. This correlation is particularly high for shallow taxonomic levels allowing us to propose a COI universal crustacean threshold to help species delimitation. At higher taxonomic levels this correlation decreases, particularly when comparing different families. Those results plead for DNA use in taxonomy and suggest an operational method to help crustacean species delimitation that is linked to the phylogenetic species definition. This pragmatic tool is expected to fine tune the present classification, and not, as some would have believed, to tear it apart.},
}
@article {pmid16646779,
year = {2003},
author = {Irizarry, RA and Ooi, SL and Wu, Z and Boeke, JD},
title = {Use of mixture models in a microarray-based screening procedure for detecting differentially represented yeast mutants.},
journal = {Statistical applications in genetics and molecular biology},
volume = {2},
number = {},
pages = {Article1},
doi = {10.2202/1544-6115.1002},
pmid = {16646779},
issn = {1544-6115},
abstract = {We describe the use of a statistical model in a genome-wide microarray-based yeast genetic screen performed by imposing different genetic selections on thousands of yeast mutants in parallel. A mixture model is fitted to data obtained from oligonucleotide arrays hybridized to 20-mer oligonucleotide "barcodes'' and a procedure based on the fitted model is used to search for mutants differentially represented under experimental and control conditions. The fitted stochastic model provides a way to assess uncertainty. We demonstrate the usefulness of the model by applying it to the problem of screening for components of the nonhomologous end joining (NHEJ) pathway and identified known components of the NHEJ pathway.},
}
@article {pmid16628206,
year = {2006},
author = {Krutzik, PO and Nolan, GP},
title = {Fluorescent cell barcoding in flow cytometry allows high-throughput drug screening and signaling profiling.},
journal = {Nature methods},
volume = {3},
number = {5},
pages = {361-368},
doi = {10.1038/nmeth872},
pmid = {16628206},
issn = {1548-7091},
support = {AI35304/AI/NIAID NIH HHS/United States ; N01-HV-28183/HV/NHLBI NIH HHS/United States ; },
mesh = {Animals ; B-Lymphocytes/cytology/metabolism ; CD11b Antigen/metabolism ; CD4-Positive T-Lymphocytes/cytology/metabolism ; *Cell Physiological Phenomena ; Cytokines/metabolism ; Drug Evaluation, Preclinical/*methods ; Flow Cytometry/*methods ; Fluorescent Dyes ; Interferon-gamma/metabolism ; Kinetics ; Mice ; Receptors, Antigen, T-Cell/antagonists &amp; inhibitors/metabolism ; Receptors, Cell Surface/antagonists &amp; inhibitors/*metabolism ; Signal Transduction/*physiology ; Spleen/cytology/pathology ; },
abstract = {Flow cytometry allows high-content, multiparameter analysis of single cells, making it a promising tool for drug discovery and profiling of intracellular signaling. To add high-throughput capacity to flow cytometry, we developed a cell-based multiplexing technique called fluorescent cell barcoding (FCB). In FCB, each sample is labeled with a different signature, or barcode, of fluorescence intensity and emission wavelengths, and mixed with other samples before antibody staining and analysis by flow cytometry. Using three FCB fluorophores, we were able to barcode and combine entire 96-well plates, reducing antibody consumption 100-fold and acquisition time to 5-15 min per plate. Using FCB and phospho-specific flow cytometry, we screened a small-molecule library for inhibitors of T cell-receptor and cytokine signaling, simultaneously determining compound efficacy and selectivity. We also analyzed IFN-gamma signaling in multiple cell types from primary mouse splenocytes, revealing differences in sensitivity and kinetics between B cells, CD4+ and CD4- T cells and CD11b-hi cells.},
}
@article {pmid16621616,
year = {2006},
author = {Kappner, I and Bieler, R},
title = {Phylogeny of venus clams (Bivalvia: Venerinae) as inferred from nuclear and mitochondrial gene sequences.},
journal = {Molecular phylogenetics and evolution},
volume = {40},
number = {2},
pages = {317-331},
doi = {10.1016/j.ympev.2006.02.006},
pmid = {16621616},
issn = {1055-7903},
mesh = {Animals ; Base Sequence ; Bivalvia/anatomy &amp; histology/cytology/*genetics ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; *Phylogeny ; },
abstract = {Venerinae (Heterodonta: Veneridae) is a diverse, commercially important, and cosmopolitan marine bivalve subfamily. Recent workers synonymized it with the subfamily Chioninae, due to their overall morphological similarity. The use of traditional shell-based characters alone, however, is questionable for resolving phylogenetic relationships of this group. A phylogenetic study was carried out, based on nucleotide sequences of the mitochondrial large ribosomal subunit (16S), cytochrome oxidase subunit I (COI), and the nuclear protein-coding gene histone 3, to investigate the relationships and circumscription of Venerinae and the phylogenetic pattern of characters in this group. This study consists of a total of 55 taxa: 13 venerine genera, 24 chionine taxa, and 18 taxa of other venerid subfamilies. We analyzed the alignments using a Bayesian approach using Markov Chain Monte Carlo tree sampling and maximum parsimony methods. The resulting phylogenetic hypothesis suggests that Chioninae and Venerinae are actually discrete taxa, but that the circumscription suffered from misplacement of some genera. Our analysis showed that the former chionine genera Chamelea and Clausinella should be placed in Venerinae, as sister taxa to Venus. We re-analyzed morphological and anatomical features in light of the molecular data to describe monophyletic entities. Features of the hinge and internal shell as well as the degree of siphonal fusion are identified as characters to morphologically distinguish the two subfamilies. Of the three genes used in this study, only COI (commonly used as "barcoding" gene) posed substantial problems in obtaining sequence data from older museum material.},
}
@article {pmid16618684,
year = {2006},
author = {Monaghan, MT and Balke, M and Pons, J and Vogler, AP},
title = {Beyond barcodes: complex DNA taxonomy of a South Pacific Island radiation.},
journal = {Proceedings. Biological sciences},
volume = {273},
number = {1588},
pages = {887-893},
pmid = {16618684},
issn = {0962-8452},
support = {BBS/B/04358/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Coleoptera/*classification/*genetics ; DNA/classification/*genetics ; DNA, Mitochondrial/genetics ; Genetic Variation ; Pacific Islands ; Phylogeny ; Time ; },
abstract = {DNA barcodes can provide rapid species identification and aid species inventories in taxonomically unstudied groups. However, the approach may fail in recently diverged groups with complex gene histories, such as those typically found on oceanic islands. We produced a DNA-based inventory of taxonomically little known diving beetles (genus Copelatus) in the Fiji archipelago, where they are a dominant component of the aquatic invertebrate fauna. Sampling from 25 localities on five islands and analysis of sequences from one nuclear (328bp histone 3) and three mitochondrial (492bp rrnL, 786bp cox1, 333bp cob) gene regions revealed high haplotype diversity, mainly originated since the Pleistocene, and subdivided into three major phylogenetic lineages and 22 statistical parsimony networks. A traditional taxonomic study delineated 25 morphologically defined species that were largely incongruent with the DNA-based groups. Haplotype diversity and their spatial arrangement demonstrated a continuum of relatedness in Fijian Copelatus, with evidence for introgression at various hierarchical levels. The study illustrates the difficulties for formal classification in evolutionarily complex lineages, and the potentially misleading conclusions obtained from either DNA barcodes or morphological traits alone. However, the sequence profile of Fijian Copelatus provides an evolutionary framework for the group and a DNA-based reference system for the integration of ecological and other biodiversity data, independent of the Linnaean naming system.},
}
@article {pmid16613905,
year = {2006},
author = {Chu, KH and Li, CP and Qi, J},
title = {Ribosomal RNA as molecular barcodes: a simple correlation analysis without sequence alignment.},
journal = {Bioinformatics (Oxford, England)},
volume = {22},
number = {14},
pages = {1690-1701},
doi = {10.1093/bioinformatics/btl146},
pmid = {16613905},
issn = {1367-4811},
mesh = {*Algorithms ; Analysis of Variance ; Base Sequence ; DNA, Ribosomal/*classification/genetics ; Data Interpretation, Statistical ; Feasibility Studies ; Molecular Sequence Data ; RNA, Ribosomal/*classification/*genetics ; Sequence Analysis, RNA/*methods ; *Software ; Statistics as Topic ; },
abstract = {MOTIVATION: We explored the feasibility of using unaligned rRNA gene sequences as DNA barcodes, based on correlation analysis of composition vectors (CVs) derived from nucleotide strings. We tested this method with seven rRNA (including 12, 16, 18, 26 and 28S) datasets from a wide variety of organisms (from archaea to tetrapods) at taxonomic levels ranging from class to species.<br><br>RESULT: Our results indicate that grouping of taxa based on CV analysis is always in good agreement with the phylogenetic trees generated by traditional approaches, although in some cases the relationships among the higher systemic groups may differ. The effectiveness of our analysis might be related to the length and divergence among sequences in a dataset. Nevertheless, the correct grouping of sequences and accurate assignment of unknown taxa make our analysis a reliable and convenient approach in analyzing unaligned sequence datasets of various rRNAs for barcoding purposes.<br><br>AVAILABILITY: The newly designed software (CVTree 1.0) is publicly available at the Composition Vector Tree (CVTree) web server http://cvtree.cbi.pku.edu.cn.},
}
@article {pmid16611600,
year = {2006},
author = {Mueller, RL},
title = {Evolutionary rates, divergence dates, and the performance of mitochondrial genes in Bayesian phylogenetic analysis.},
journal = {Systematic biology},
volume = {55},
number = {2},
pages = {289-300},
doi = {10.1080/10635150500541672},
pmid = {16611600},
issn = {1063-5157},
mesh = {Animals ; Bayes Theorem ; *Evolution, Molecular ; Genes, Mitochondrial/*genetics ; Mitochondria/*genetics ; *Phylogeny ; Caudata/genetics ; },
abstract = {The mitochondrial genome is one of the most frequently used loci in phylogenetic and phylogeographic analyses, and it is becoming increasingly possible to sequence and analyze this genome in its entirety from diverse taxa. However, sequencing the entire genome is not always desirable or feasible. Which genes should be selected to best infer the evolutionary history of the mitochondria within a group of organisms, and what properties of a gene determine its phylogenetic performance? The current study addresses these questions in a Bayesian phylogenetic framework with reference to a phylogeny of plethodontid and related salamanders derived from 27 complete mitochondrial genomes; this topology is corroborated by nuclear DNA and morphological data. Evolutionary rates for each mitochondrial gene and divergence dates for all nodes in the plethodontid mitochondrial genome phylogeny were estimated in both Bayesian and maximum likelihood frameworks using multiple fossil calibrations, multiple data partitions, and a clock-independent approach. Bayesian analyses of individual genes were performed, and the resulting trees compared against the reference topology. Ordinal logistic regression analysis of molecular evolution rate, gene length, and the G-shape parameter a demonstrated that slower rate of evolution and longer gene length both increased the probability that a gene would perform well phylogenetically. Estimated rates of molecular evolution vary 84-fold among different mitochondrial genes and different salamander lineages, and mean rates among genes vary 15-fold. Despite having conserved amino acid sequences, cox1, cox2, cox3, and cob have the fastest mean rates of nucleotide substitution, and the greatest variation in rates, whereas rrnS and rrnL have the slowest rates. Reasons underlying this rate variation are discussed, as is the extensive rate variation in cox1 in light of its proposed role in DNA barcoding.},
}
@article {pmid16585665,
year = {2006},
author = {McDonald, CJ},
title = {Computerization can create safety hazards: a bar-coding near miss.},
journal = {Annals of internal medicine},
volume = {144},
number = {7},
pages = {510-516},
doi = {10.7326/0003-4819-144-7-200604040-00010},
pmid = {16585665},
issn = {1539-3704},
support = {G08 LM008232/LM/NLM NIH HHS/United States ; },
mesh = {Aged, 80 and over ; *Electronic Data Processing ; Hospitals, Teaching/standards ; Humans ; Male ; Medical Records Systems, Computerized ; *Medication Errors/prevention &amp; control ; Patient Care/*standards ; Patient Identification Systems/*methods/*standards ; United States ; },
abstract = {Increasing numbers of hospitals are implementing bar-coding systems to prevent errors in patient identification. In the present case, a diabetic patient admitted to a teaching hospital was mistakenly given the bar-coded identification wristband of another patient who was admitted at the same time. When a laboratory result that documented the diabetic patient's severe hyperglycemia was entered into the other patient's electronic medical record, the latter patient seemed to have a very high glucose level and was almost given what could have been a fatal dose of insulin. This near miss shows that computer systems, although having the potential to improve safety, may create new kinds of errors if not accompanied by well-designed, well-implemented cross-check processes and a culture of safety. Moreover, computer systems may have the pernicious effect of weakening human vigilance, removing an important safety protection. Researchers should continue to study real-world implementation of computerized systems to understand their benefits and potential harms, and administrators and providers should seek ways to anticipate these harms and mitigate them.},
}
@article {pmid16564011,
year = {2006},
author = {Voorhoeve, PM and le Sage, C and Schrier, M and Gillis, AJ and Stoop, H and Nagel, R and Liu, YP and van Duijse, J and Drost, J and Griekspoor, A and Zlotorynski, E and Yabuta, N and De Vita, G and Nojima, H and Looijenga, LH and Agami, R},
title = {A genetic screen implicates miRNA-372 and miRNA-373 as oncogenes in testicular germ cell tumors.},
journal = {Cell},
volume = {124},
number = {6},
pages = {1169-1181},
doi = {10.1016/j.cell.2006.02.037},
pmid = {16564011},
issn = {0092-8674},
mesh = {Cells, Cultured ; *Genetic Testing ; Humans ; Male ; MicroRNAs/*classification/*genetics/pharmacology ; Neoplasms, Germ Cell and Embryonal/*genetics ; *Oncogenes ; Protein Serine-Threonine Kinases/antagonists &amp; inhibitors/metabolism ; Signal Transduction ; Testicular Neoplasms/*genetics ; Tumor Suppressor Proteins/antagonists &amp; inhibitors/metabolism ; },
abstract = {Endogenous small RNAs (miRNAs) regulate gene expression by mechanisms conserved across metazoans. While the number of verified human miRNAs is still expanding, only few have been functionally annotated. To perform genetic screens for novel functions of miRNAs, we developed a library of vectors expressing the majority of cloned human miRNAs and created corresponding DNA barcode arrays. In a screen for miRNAs that cooperate with oncogenes in cellular transformation, we identified miR-372 and miR-373, each permitting proliferation and tumorigenesis of primary human cells that harbor both oncogenic RAS and active wild-type p53. These miRNAs neutralize p53-mediated CDK inhibition, possibly through direct inhibition of the expression of the tumor-suppressor LATS2. We provide evidence that these miRNAs are potential novel oncogenes participating in the development of human testicular germ cell tumors by numbing the p53 pathway, thus allowing tumorigenic growth in the presence of wild-type p53.},
}
@article {pmid16537464,
year = {2006},
author = {Herre, EA},
title = {Barcoding helps biodiversity fly.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {103},
number = {11},
pages = {3949-3950},
pmid = {16537464},
issn = {0027-8424},
mesh = {Animals ; *Biodiversity ; Diptera/*classification/*genetics/pathogenicity ; Ecosystem ; Host-Parasite Interactions ; Neuropeptides/*genetics ; },
}
@article {pmid16536467,
year = {2006},
author = {Dumelin, CE and Scheuermann, J and Melkko, S and Neri, D},
title = {Selection of streptavidin binders from a DNA-encoded chemical library.},
journal = {Bioconjugate chemistry},
volume = {17},
number = {2},
pages = {366-370},
doi = {10.1021/bc050282y},
pmid = {16536467},
issn = {1043-1802},
mesh = {Animals ; DNA/*chemistry ; *Gene Library ; Humans ; Molecular Structure ; Protein Binding ; Streptavidin/*chemistry/metabolism ; },
abstract = {DNA-encoded libraries of small organic molecules facilitate the construction of large, encoded self-assembling chemical libraries for the identification of high-affinity binders to protein targets. We have constructed a library of 477 chemical compounds, coupled to 48mer-oligonucleotides, each containing a unique six-base sequence serving as "bar-code" for the identification of the chemical moiety. The functionality of the library was confirmed by selection and amplification of both high- and low-affinity binding molecules specific to streptavidin.},
}
@article {pmid16536212,
year = {2005},
author = {Röder, C and El-Kerdi, A and Frigg, A and Kolling, C and Staub, LP and Bach, B and Müller, U},
title = {The Swiss Orthopaedic Registry.},
journal = {Bulletin (Hospital for Joint Diseases (New York, N.Y.))},
volume = {63},
number = {1-2},
pages = {15-19},
pmid = {16536212},
issn = {0018-5647},
mesh = {Arthroplasty, Replacement, Hip ; Arthroplasty, Replacement, Knee ; Data Collection/methods ; Humans ; Internet ; *Orthopedics ; Program Development ; *Registries ; Switzerland ; },
abstract = {Following the tradition of the IDES European Hip Registry inaugurated by M. E. Müller in the 1960s, the Institute for Evaluative Research in Orthopaedic Surgery at the University of Bern started a new era of data collection using internet technology (www.memdoc.org). With support of the Swiss Orthopaedic Society, the pilot of the Swiss Orthopaedic Registry was conducted, and in cooperation with different academic and non-academic centers the practicability of integrating the various data collection instruments into the daily clinical workflow was evaluated. Three different sizes of hip and knee questionnaires were compiled, covering the individual demands of the participating hospitals whereby the smaller questionnaires always represent a subset of the next larger one. Different types of data collection instruments are available: the online interface, optical mark reader paper questionnaires, and barcode sheets. Precise implant tracking is implemented by scanning the implant barcodes directly in the operating theaters and linking them to the clinical data set via a central server. In addition, radiographic information can be linked with the clinical data set. The pilot clinics suggested enhancements to the user interface and additional features for data management. Also, recommendations were made to simplify content in some instances and diversify in others. With a new software release and adapted questionnaires the Swiss Orthopaedic Registry was officially launched in Summer 2005.},
}
@article {pmid16510898,
year = {2006},
author = {Kastenmayer, JP and Ni, L and Chu, A and Kitchen, LE and Au, WC and Yang, H and Carter, CD and Wheeler, D and Davis, RW and Boeke, JD and Snyder, MA and Basrai, MA},
title = {Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae.},
journal = {Genome research},
volume = {16},
number = {3},
pages = {365-373},
pmid = {16510898},
issn = {1088-9051},
support = {R01 HG002432/HG/NHGRI NIH HHS/United States ; R01-HG02432/HG/NHGRI NIH HHS/United States ; //Intramural NIH HHS/United States ; },
mesh = {Conserved Sequence ; DNA Damage ; Evolution, Molecular ; Gene Deletion ; Gene Expression Profiling ; Gene Expression Regulation ; *Genome, Fungal ; Haploidy ; *Open Reading Frames ; Phenotype ; Saccharomyces cerevisiae/*genetics ; },
abstract = {Genes with small open reading frames (sORFs; <100 amino acids) represent an untapped source of important biology. sORFs largely escaped analysis because they were difficult to predict computationally and less likely to be targeted by genetic screens. Thus, the substantial number of sORFs and their potential importance have only recently become clear. To investigate sORF function, we undertook the first functional studies of sORFs in any system, using the model eukaryote Saccharomyces cerevisiae. Based on independent experimental approaches and computational analyses, evidence exists for 299 sORFs in the S. cerevisiae genome, representing approximately 5% of the annotated ORFs. We determined that a similar percentage of sORFs are annotated in other eukaryotes, including humans, and 184 of the S. cerevisiae sORFs exhibit similarity with ORFs in other organisms. To investigate sORF function, we constructed a collection of gene-deletion mutants of 140 newly identified sORFs, each of which contains a strain-specific "molecular barcode," bringing the total number of sORF deletion strains to 247. Phenotypic analyses of the new gene-deletion strains identified 22 sORFs required for haploid growth, growth at high temperature, growth in the presence of a nonfermentable carbon source, or growth in the presence of DNA damage and replication-arrest agents. We provide a collection of sORF deletion strains that can be integrated into the existing deletion collection as a resource for the yeast community for elucidating gene function. Moreover, our analyses of the S. cerevisiae sORFs establish that sORFs are conserved across eukaryotes and have important biological functions.},
}
@article {pmid16507534,
year = {2006},
author = {Nielsen, R and Matz, M},
title = {Statistical approaches for DNA barcoding.},
journal = {Systematic biology},
volume = {55},
number = {1},
pages = {162-169},
doi = {10.1080/10635150500431239},
pmid = {16507534},
issn = {1063-5157},
support = {GM066243/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Anura/classification/genetics ; Bayes Theorem ; Butterflies/classification/genetics ; Classification/*methods ; Data Interpretation, Statistical ; Sequence Analysis, DNA ; Species Specificity ; },
}
@article {pmid16505365,
year = {2006},
author = {Smith, MA and Woodley, NE and Janzen, DH and Hallwachs, W and Hebert, PD},
title = {DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae).},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {103},
number = {10},
pages = {3657-3662},
pmid = {16505365},
issn = {0027-8424},
mesh = {Animals ; Base Sequence ; Costa Rica ; DNA/*genetics ; Databases, Nucleic Acid ; Diptera/classification/*genetics/*pathogenicity ; Ecosystem ; Electron Transport Complex IV/genetics ; Host-Parasite Interactions ; Molecular Sequence Data ; Moths/parasitology ; Phylogeny ; },
abstract = {Insect parasitoids are a major component of global biodiversity and affect the population dynamics of their hosts. However, identification of insect parasitoids is often difficult, and they are suspected to contain many cryptic species. Here, we ask whether the cytochrome c oxidase I DNA barcode could function as a tool for species identification and discovery for the 20 morphospecies of Belvosia parasitoid flies (Diptera: Tachinidae) that have been reared from caterpillars (Lepidoptera) in Area de Conservación Guanacaste (ACG), northwestern Costa Rica. Barcoding not only discriminates among all 17 highly host-specific morphospecies of ACG Belvosia, but it also raises the species count to 32 by revealing that each of the three generalist species are actually arrays of highly host-specific cryptic species. We also identified likely hybridization among Belvosia by using a variable internal transcribed spacer region 1 nuclear rDNA sequence as a genetic covariate in addition to the strategy of overlaying barcode clusters with ecological information. If general, these results will increase estimates of global species richness and imply that tropical conservation and host-parasite interactions may be more complex than expected.},
}
@article {pmid19503461,
year = {2006},
author = {Galitonov, G and Birtwell, S and Zheludev, N and Morgan, H},
title = {High capacity tagging using nanostructured diffraction barcodes.},
journal = {Optics express},
volume = {14},
number = {4},
pages = {1382-1387},
doi = {10.1364/oe.14.001382},
pmid = {19503461},
issn = {1094-4087},
abstract = {We describe a new non-contact high capacity optical tagging technique based on the use of nanostructured barcodes. The tags are generated from a number of superimposed diffraction gratings. Capacity for up to 68,000 distinguishable tags has been demonstrated, however current technological capability shall allow encoding of up to 10(9) distinguishable particles, each of which is only 100 microm long.},
}
@article {pmid16474381,
year = {2006},
author = {Brummelkamp, TR and Fabius, AW and Mullenders, J and Madiredjo, M and Velds, A and Kerkhoven, RM and Bernards, R and Beijersbergen, RL},
title = {An shRNA barcode screen provides insight into cancer cell vulnerability to MDM2 inhibitors.},
journal = {Nature chemical biology},
volume = {2},
number = {4},
pages = {202-206},
doi = {10.1038/nchembio774},
pmid = {16474381},
issn = {1552-4450},
mesh = {Animals ; Antineoplastic Agents/pharmacology ; Blotting, Western ; Cell Line, Tumor ; Cells, Cultured ; DNA Damage ; Electronic Data Processing ; Fibroblasts/metabolism ; *Gene Expression Regulation, Neoplastic ; Genes, p53 ; *Genetic Techniques ; Humans ; Imidazoles/chemistry ; Intracellular Signaling Peptides and Proteins/chemistry ; Mice ; Microscopy, Fluorescence ; Models, Chemical ; Neoplasms/*drug therapy ; Nuclear Proteins ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis ; Phosphoproteins/chemistry ; Piperazines/chemistry ; Plasmids/metabolism ; Proto-Oncogene Proteins c-mdm2/*antagonists &amp; inhibitors/*metabolism ; RNA Interference ; RNA, Small Interfering/*chemistry ; Signal Transduction ; Tumor Suppressor Protein p53/metabolism ; Tumor Suppressor p53-Binding Protein 1 ; },
abstract = {The identification of the cellular targets of small molecules with anticancer activity is crucial to their further development as drug candidates. Here, we present the application of a large-scale RNA interference-based short hairpin RNA (shRNA) barcode screen to gain insight in the mechanism of action of nutlin-3 (1). Nutlin-3 is a small-molecule inhibitor of MDM2, which can activate the p53 pathway. Nutlin-3 shows strong antitumor effects in mice, with surprisingly few side effects on normal tissues. Aside from p53, we here identify 53BP1 as a critical mediator of nutlin-3-induced cytotoxicity. 53BP1 is part of a signaling network induced by DNA damage that is frequently activated in cancer but not in healthy tissues. Our results suggest that nutlin-3's tumor specificity may result from its ability to turn a cancer cell-specific property (activated DNA damage signaling) into a weakness that can be exploited therapeutically.},
}
@article {pmid16431158,
year = {2006},
author = {Scicluna, SM and Tawari, B and Clark, CG},
title = {DNA barcoding of blastocystis.},
journal = {Protist},
volume = {157},
number = {1},
pages = {77-85},
doi = {10.1016/j.protis.2005.12.001},
pmid = {16431158},
issn = {1434-4610},
mesh = {Animals ; Blastocystis/*classification/genetics/isolation &amp; purification ; Blastocystis Infections/*parasitology ; DNA Primers ; DNA, Protozoan/analysis/genetics ; DNA, Ribosomal/*analysis/genetics ; Genes, rRNA/*genetics ; Humans ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {We have developed a simple method for subtyping the intestinal protistan parasite Blastocystis using an approach equivalent to DNA barcoding in animals. Amplification of a 600 bp region of the small subunit ribosomal RNA gene followed by single primer sequencing of the PCR product provides enough data to assign isolates to specific subtypes unambiguously. We believe that this approach will prove useful in future epidemiological studies.},
}
@article {pmid16418261,
year = {2006},
author = {Hajibabaei, M and Janzen, DH and Burns, JM and Hallwachs, W and Hebert, PD},
title = {DNA barcodes distinguish species of tropical Lepidoptera.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {103},
number = {4},
pages = {968-971},
pmid = {16418261},
issn = {0027-8424},
mesh = {Animals ; Cluster Analysis ; Costa Rica ; DNA/*analysis/genetics ; Ecology ; Electron Transport Complex IV/genetics/metabolism ; Genetic Techniques ; Genome ; Internet ; Lepidoptera/*genetics/metabolism ; Models, Biological ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Time Factors ; },
abstract = {Although central to much biological research, the identification of species is often difficult. The use of DNA barcodes, short DNA sequences from a standardized region of the genome, has recently been proposed as a tool to facilitate species identification and discovery. However, the effectiveness of DNA barcoding for identifying specimens in species-rich tropical biotas is unknown. Here we show that cytochrome c oxidase I DNA barcodes effectively discriminate among species in three Lepidoptera families from Area de Conservación Guanacaste in northwestern Costa Rica. We found that 97.9% of the 521 species recognized by prior taxonomic work possess distinctive cytochrome c oxidase I barcodes and that the few instances of interspecific sequence overlap involve very similar species. We also found two or more barcode clusters within each of 13 supposedly single species. Covariation between these clusters and morphological and/or ecological traits indicates overlooked species complexes. If these results are general, DNA barcoding will significantly aid species identification and discovery in tropical settings.},
}
@article {pmid16402792,
year = {2006},
author = {Wang, L and Tan, W},
title = {Multicolor FRET silica nanoparticles by single wavelength excitation.},
journal = {Nano letters},
volume = {6},
number = {1},
pages = {84-88},
pmid = {16402792},
issn = {1530-6984},
support = {R21 NS045174/NS/NINDS NIH HHS/United States ; R21 NS045174-01A1/NS/NINDS NIH HHS/United States ; R21 NS045174-01A1S1/NS/NINDS NIH HHS/United States ; R21 NS045174-02/NS/NINDS NIH HHS/United States ; },
abstract = {Fluorescent nanoparticles with multiple emission signatures by a single wavelength excitation are needed in multiplex bioanalysis and molecular imaging. We have prepared silica nanoparticles encapsulated with three organic dyes using a modified Stöber synthesis method. By varying the doping ratio of the three tandem dyes, fluorescence resonance energy transfer (FRET)-mediated emission signatures can be tuned to have the nanoparticles exhibit multiple colors under one single wavelength excitation. These nanoparticles are intensely fluorescent, highly photostable, uniform in size, and biocompatible. The acceptor emission of the FRET nanoparticles has generated a large Stokes shift, which implicates broad applications in biological labeling and imaging. Molecular recognition moieties, such as biotin, can be covalently attached to the nanoparticle surface to allow for specific binding to target molecules. These multicolor FRET silica nanoparticles can be used as barcoding tags for multiplexed signaling. By using these NPs, one can envision a dynamic, multicolor, colocalization methodology to follow proteins, nucleic acids, molecular machines, and assemblies within living systems.},
}
@article {pmid16398549,
year = {2006},
author = {Chun, S and Xu, J and Cheng, J and Ding, L and Winograd, N and Fenniri, H},
title = {Spectroscopically encoded resins for high throughput imaging time-of-flight secondary ion mass spectrometry.},
journal = {Journal of combinatorial chemistry},
volume = {8},
number = {1},
pages = {18-25},
doi = {10.1021/cc050086y},
pmid = {16398549},
issn = {1520-4766},
support = {EB03824/EB/NIBIB NIH HHS/United States ; },
mesh = {Combinatorial Chemistry Techniques/instrumentation/*methods ; Electronic Data Processing/instrumentation/methods ; Polystyrenes/*chemistry ; Resins, Synthetic/*chemistry ; *Spectrometry, Mass, Secondary Ion ; Spectrum Analysis, Raman ; },
abstract = {Spectroscopic barcoding was recently introduced as a new pre-encoding strategy wherein the resin beads are not just carriers for solid phase synthesis, but are, in addition, the repository of the synthetic scheme to which they were subjected. To expand the repertoire of spectroscopically barcoded resins (BCRs), here we introduce a new family of halogenated polystyrene-based polymers designed for high-throughput combinatorial analysis using not only infrared and Raman spectroscopy but also imaging time-of-flight secondary ion mass spectrometry (ToF-SIMS). In particular, we have established that (a) the halogen content of these new resins can be used as an encoding element in quantitative imaging ToF-SIMS and (b) the number of styrene monomers used to generate unique vibrational fingerprints can be significantly reduced by using monomers in different molar ratios. The combination of quantitative imaging ToF-SIMS and vibrational spectroscopy is anticipated to dramatically increase the repertoire of possible BCRs from a few hundreds to several thousands.},
}
@article {pmid19455206,
year = {2007},
author = {Faith, DP and Baker, AM},
title = {Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges.},
journal = {Evolutionary bioinformatics online},
volume = {2},
number = {},
pages = {121-128},
pmid = {19455206},
issn = {1176-9343},
abstract = {Biodiversity conservation addresses information challenges through estimations encapsulated in measures of diversity. A quantitative measure of phylogenetic diversity, "PD", has been defined as the minimum total length of all the phylogenetic branches required to span a given set of taxa on the phylogenetic tree (Faith 1992a). While a recent paper incorrectly characterizes PD as not including information about deeper phylogenetic branches, PD applications over the past decade document the proper incorporation of shared deep branches when assessing the total PD of a set of taxa. Current PD applications to macroinvertebrate taxa in streams of New South Wales, Australia illustrate the practical importance of this definition. Phylogenetic lineages, often corresponding to new, "cryptic", taxa, are restricted to a small number of stream localities. A recent case of human impact causing loss of taxa in one locality implies a higher PD value for another locality, because it now uniquely represents a deeper branch. This molecular-based phylogenetic pattern supports the use of DNA barcoding programs for biodiversity conservation planning. Here, PD assessments side-step the contentious use of barcoding-based "species" designations. Bio-informatics challenges include combining different phylogenetic evidence, optimization problems for conservation planning, and effective integration of phylogenetic information with environmental and socio-economic data.},
}
@article {pmid16370452,
year = {2005},
author = {Damera-Venkata, N and Yen, J and Monga, V and Evans, BL},
title = {Hardcopy image barcodes via block-error diffusion.},
journal = {IEEE transactions on image processing : a publication of the IEEE Signal Processing Society},
volume = {14},
number = {12},
pages = {1977-1989},
doi = {10.1109/tip.2005.859776},
pmid = {16370452},
issn = {1057-7149},
mesh = {*Algorithms ; Artifacts ; Colorimetry/methods ; *Computer Graphics ; *Computer Security ; Image Enhancement/methods ; Image Interpretation, Computer-Assisted/*methods ; Printing/*methods ; Product Labeling/*methods ; *Signal Processing, Computer-Assisted ; },
abstract = {Error diffusion halftoning is a popular method of producing frequency modulated (FM) halftones for printing and display. FM halftoning fixes the dot size (e.g., to one pixel in conventional error diffusion) and varies the dot frequency according to the intensity of the original grayscale image. We generalize error diffusion to produce FM halftones with user-controlled dot size and shape by using block quantization and block filtering. As a key application, we show how block-error diffusion may be applied to embed information in hardcopy using dot shape modulation. We enable the encoding and subsequent decoding of information embedded in the hardcopy version of continuous-tone base images. The encoding-decoding process is modeled by robust data transmission through a noisy print-scan channel that is explicitly modeled. We refer to the encoded printed version as an image barcode due to its high information capacity that differentiates it from common hardcopy watermarks. The encoding/halftoning strategy is based on a modified version of block-error diffusion. Encoder stability, image quality versus information capacity tradeoffs, and decoding issues with and without explicit knowledge of the base image are discussed.},
}
@article {pmid16336051,
year = {2005},
author = {Meyer, CP and Paulay, G},
title = {DNA barcoding: error rates based on comprehensive sampling.},
journal = {PLoS biology},
volume = {3},
number = {12},
pages = {e422},
pmid = {16336051},
issn = {1545-7885},
mesh = {Animals ; DNA, Mitochondrial/genetics ; Electronic Data Processing/*methods/standards ; Genetic Variation/genetics ; Molecular Sequence Data ; Phylogeny ; Research Design ; Sample Size ; },
abstract = {DNA barcoding has attracted attention with promises to aid in species identification and discovery; however, few well-sampled datasets are available to test its performance. We provide the first examination of barcoding performance in a comprehensively sampled, diverse group (cypraeid marine gastropods, or cowries). We utilize previous methods for testing performance and employ a novel phylogenetic approach to calculate intraspecific variation and interspecific divergence. Error rates are estimated for (1) identifying samples against a well-characterized phylogeny, and (2) assisting in species discovery for partially known groups. We find that the lowest overall error for species identification is 4%. In contrast, barcoding performs poorly in incompletely sampled groups. Here, species delineation relies on the use of thresholds, set to differentiate between intraspecific variation and interspecific divergence. Whereas proponents envision a "barcoding gap" between the two, we find substantial overlap, leading to minimal error rates of approximately 17% in cowries. Moreover, error rates double if only traditionally recognized species are analyzed. Thus, DNA barcoding holds promise for identification in taxonomically well-understood and thoroughly sampled clades. However, the use of thresholds does not bode well for delineating closely related species in taxonomically understudied groups. The promise of barcoding will be realized only if based on solid taxonomic foundations.},
}
@article {pmid16333061,
year = {2005},
author = {Cummings, J and Bush, P and Smith, D and Matuszewski, K and , },
title = {Bar-coding medication administration overview and consensus recommendations.},
journal = {American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists},
volume = {62},
number = {24},
pages = {2626-2629},
doi = {10.2146/ajhp050222},
pmid = {16333061},
issn = {1079-2082},
mesh = {Consensus ; *Electronic Data Processing ; Humans ; Medication Errors/prevention &amp; control ; *Medication Systems, Hospital/economics ; Point-of-Care Systems ; },
}
@article {pmid16315744,
year = {2005},
author = {Zhao, R},
title = {From single cell gene-based diagnostics to diagnostic genomics: current applications and future perspectives.},
journal = {Clinical laboratory science : journal of the American Society for Medical Technology},
volume = {18},
number = {4},
pages = {254-262},
pmid = {16315744},
issn = {0894-959X},
mesh = {Genetics, Medical/methods ; *Genomics ; Humans ; *Molecular Diagnostic Techniques ; *Nucleic Acid Amplification Techniques ; },
abstract = {Molecular diagnostics is a branch of clinical diagnostics that uses primarily DNA or RNA as a biomarker for clinical testing. It combines various gene-based amplification technologies with highly sophisticated detection methods for the clinical diagnosis of a vast variety of diseases including infectious diseases, cancer, and inherited diseases. The principal application of gene-based amplification technology is to identify pathogen or gene-specific nucleic acid sequences that are used as surrogate markers for the identification of either infectious pathogens or alteration of disease-related genes. There are generally three classes of gene-based amplification technologies: target-based, e.g., PCR; probe-based, e.g., LCR; and signal-based, e.g., bDNA. Real-time detection of PCR allows us to quantify amplified amplicons with a broad dynamic range and it offers a unique way to detect genetic mutations. Other technologies such as immuno-PCR and bio-barcode assay (BCA) combine different amplification tactics offering extreme detection sensitivity ranging from femtogram (10(-15)) to zeptogram (10(-21)). Even though quantum dots technology is in its infant stage, its potential to further increase diagnostic sensitivity and specificity is likely beyond our current imagination. Future diagnostic technologies include the use of genomic and proteomic approaches especially in pure cell types or even in the single-cell level, which open up endless new possibilities for gene-based diagnostics at entirely different levels. In this article, principles of various current gene-based amplification and detection technologies along with their clinical applications are discussed. New technologies that could potentially be used in future gene-based diagnosis are introduced.},
}
@article {pmid16277449,
year = {2005},
author = {Choi, JR and Oh, SJ and Ju, H and Cheon, J},
title = {Massive fabrication of free-standing one-dimensional Co/Pt nanostructures and modulation of ferromagnetism via a programmable barcode layer effect.},
journal = {Nano letters},
volume = {5},
number = {11},
pages = {2179-2183},
doi = {10.1021/nl051190k},
pmid = {16277449},
issn = {1530-6984},
abstract = {Massive fabrication of free-standing Co/Pt magnetic barcode nanowires with well-defined interfaces and layer thicknesses is obtained after freeing them from porous templates. Such barcodes display bamboo-like shapes with identical motifs either inside or out of the templates. The ferromagnetism of these barcode nanowires can be modulated easily depending on the cobalt segments and shape anisotropies. Further enhancements of the ferromagnetism of Co/Pt barcodes are also accomplished through interfacial alloying processes via a thermally induced phase transition.},
}
@article {pmid16272498,
year = {2005},
author = {Ross, TL and Merz, WG and Farkosh, M and Carroll, KC},
title = {Comparison of an automated repetitive sequence-based PCR microbial typing system to pulsed-field gel electrophoresis for analysis of outbreaks of methicillin-resistant Staphylococcus aureus.},
journal = {Journal of clinical microbiology},
volume = {43},
number = {11},
pages = {5642-5647},
pmid = {16272498},
issn = {0095-1137},
support = {AI-02-031/AI/NIAID NIH HHS/United States ; },
mesh = {Anti-Bacterial Agents/*pharmacology ; Automation ; Bacterial Typing Techniques ; Cross Infection/*epidemiology ; *Disease Outbreaks ; Electrophoresis, Gel, Pulsed-Field ; Genome, Bacterial ; Methicillin/*pharmacology ; Methicillin Resistance ; Polymerase Chain Reaction/*methods ; Repetitive Sequences, Nucleic Acid ; Reproducibility of Results ; Retrospective Studies ; Staphylococcal Infections/*epidemiology ; Staphylococcus aureus/*classification/*drug effects ; United States ; },
abstract = {Rapid and sensitive methods for accurate strain delineation are essential for monitoring and preventing transmission of methicillin-resistant Staphylococcus aureus (MRSA). Pulsed-field gel electrophoresis (PFGE) has been the standard technique for strain typing most bacterial species including MRSA. The goal of this study was to compare the performance of the DiversiLab microbial typing system (Bacterial BarCodes, Inc., Houston, TX) (rep-PCR) to that of PFGE for typing MRSA isolates from five well-defined outbreaks. The DiversiLab rep-PCR assay is a rapid, semiautomated method based on PCR amplification of specific regions between noncoding repetitive sequences in the bacterial genome. rep-PCR was performed according to the manufacturer's recommendations, and the results were analyzed and dendrograms were generated using the DiversiLab analysis software (version 2.1.66 a). PFGE was performed and interpreted according to published procedures. rep-PCR results using similarity indices (SI) of 80%, 85%, and 90% were compared to PFGE analysis. In addition, intra- and interrun reproducibility was determined for rep-PCR. Overall, correct assignment to outbreak versus nonoutbreak clusters occurred for 91 of 109 isolates (85% agreement) when using a SI of 85%. For each specific outbreak, concordance between rep-PCR and PFGE ranged from 73% to 100%. There were 18 discrepant results (17%). Fourteen isolates were unique by PFGE, but they were placed in clusters by rep-PCR; the other 4 were placed in clusters different from those assigned by PFGE. Intra- and interrun reproducibility was excellent. Times to results were 12 to 24 h for rep-PCR compared to 2 to 4 days for PFGE. Rapid, standardized results and excellent reproducibility make rep-PCR a valuable tool for use in MRSA investigations. However, since rep-PCR was less discriminatory than PFGE, we recommend that it be used to screen isolates, followed by testing isolates which share the same rep-PCR pattern with a more sensitive method, such as PFGE or multilocus sequence typing.},
}
@article {pmid16255599,
year = {2005},
author = {Nam, JM and Wise, AR and Groves, JT},
title = {Colorimetric bio-barcode amplification assay for cytokines.},
journal = {Analytical chemistry},
volume = {77},
number = {21},
pages = {6985-6988},
doi = {10.1021/ac0513764},
pmid = {16255599},
issn = {0003-2700},
mesh = {Colorimetry/*methods ; DNA Probes/chemistry ; Electronic Data Processing/*methods ; Gold ; Interleukin-2/*analysis/genetics ; Magnetics ; Metal Nanoparticles/chemistry ; Molecular Probes/chemistry/ultrastructure ; Porosity ; },
abstract = {The bio-barcode amplification assay has become a powerful tool in detecting tens to hundreds of biological targets such as proteins and nucleic acids in the entire sample. However, current bio-barcode detection schemes still require many experimental steps including microarrayer-based immobilization of oligonucleotides on a glass chip, silver enhancement of immobilized gold nanoparticles on a chip, and light-scattering measurement. Here, we report a colorimetric bio-barcode method that minimizes the above requirements while detecting 30 aM concentrations of cytokines (approximately 3 orders of magnitude more sensitive than conventional nonenzymatic cytokine detection assays). The assay is based on porous microparticles, which enable loading of a large number of barcode DNA per particle, and gold nanoparticle-based colorimetric barcode detection method.},
}
@article {pmid16243770,
year = {2005},
author = {Hebert, PD and Gregory, TR},
title = {The promise of DNA barcoding for taxonomy.},
journal = {Systematic biology},
volume = {54},
number = {5},
pages = {852-859},
doi = {10.1080/10635150500354886},
pmid = {16243770},
issn = {1063-5157},
mesh = {Classification/*methods ; *Databases, Genetic ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
}
@article {pmid16243769,
year = {2005},
author = {Will, KW and Mishler, BD and Wheeler, QD},
title = {The perils of DNA barcoding and the need for integrative taxonomy.},
journal = {Systematic biology},
volume = {54},
number = {5},
pages = {844-851},
doi = {10.1080/10635150500354878},
pmid = {16243769},
issn = {1063-5157},
mesh = {Classification/*methods ; *Databases, Genetic ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
}
@article {pmid16243768,
year = {2005},
author = {Smith, VS},
title = {DNA barcoding: perspectives from a "Partnerships for Enhancing Expertise in Taxonomy" (PEET) debate.},
journal = {Systematic biology},
volume = {54},
number = {5},
pages = {841-844},
doi = {10.1080/10635150500354894},
pmid = {16243768},
issn = {1063-5157},
mesh = {Classification/*methods ; *Databases, Genetic ; Sequence Analysis, DNA/*methods ; Species Specificity ; },
}
@article {pmid16221604,
year = {2005},
author = {Vences, M and Thomas, M and Bonett, RM and Vieites, DR},
title = {Deciphering amphibian diversity through DNA barcoding: chances and challenges.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {360},
number = {1462},
pages = {1859-1868},
pmid = {16221604},
issn = {0962-8436},
mesh = {Amphibians/*genetics ; Animals ; Base Sequence ; *Biodiversity ; DNA/*genetics ; DNA Primers ; Electron Transport Complex IV/genetics ; Electronic Data Processing/*methods ; Evolution, Molecular ; Geography ; Molecular Diagnostic Techniques/*methods ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Amphibians globally are in decline, yet there is still a tremendous amount of unrecognized diversity, calling for an acceleration of taxonomic exploration. This process will be greatly facilitated by a DNA barcoding system; however, the mitochondrial population structure of many amphibian species presents numerous challenges to such a standardized, single locus, approach. Here we analyse intra- and interspecific patterns of mitochondrial variation in two distantly related groups of amphibians, mantellid frogs and salamanders, to determine the promise of DNA barcoding with cytochrome oxidase subunit I (cox1) sequences in this taxon. High intraspecific cox1 divergences of 7-14% were observed (18% in one case) within the whole set of amphibian sequences analysed. These high values are not caused by particularly high substitution rates of this gene but by generally deep mitochondrial divergences within and among amphibian species. Despite these high divergences, cox1 sequences were able to correctly identify species including disparate geographic variants. The main problems with cox1 barcoding of amphibians are (i) the high variability of priming sites that hinder the application of universal primers to all species and (ii) the observed distinct overlap of intraspecific and interspecific divergence values, which implies difficulties in the definition of threshold values to identify candidate species. Common discordances between geographical signatures of mitochondrial and nuclear markers in amphibians indicate that a single-locus approach can be problematic when high accuracy of DNA barcoding is required. We suggest that a number of mitochondrial and nuclear genes may be used as DNA barcoding markers to complement cox1.},
}
@article {pmid16214755,
year = {2005},
author = {Steinke, D and Vences, M and Salzburger, W and Meyer, A},
title = {TaxI: a software tool for DNA barcoding using distance methods.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {360},
number = {1462},
pages = {1975-1980},
pmid = {16214755},
issn = {0962-8436},
mesh = {Animals ; Base Sequence ; *Biodiversity ; DNA/*genetics ; Electron Transport Complex IV/genetics ; Electronic Data Processing/*methods ; Fishes/genetics ; Germany ; *Models, Genetic ; Molecular Diagnostic Techniques/*methods ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Snails/genetics ; *Software ; Species Specificity ; },
abstract = {DNA barcoding is a promising approach to the diagnosis of biological diversity in which DNA sequences serve as the primary key for information retrieval. Most existing software for evolutionary analysis of DNA sequences was designed for phylogenetic analyses and, hence, those algorithms do not offer appropriate solutions for the rapid, but precise analyses needed for DNA barcoding, and are also unable to process the often large comparative datasets. We developed a flexible software tool for DNA taxonomy, named TaxI. This program calculates sequence divergences between a query sequence (taxon to be barcoded) and each sequence of a dataset of reference sequences defined by the user. Because the analysis is based on separate pairwise alignments this software is also able to work with sequences characterized by multiple insertions and deletions that are difficult to align in large sequence sets (i.e. thousands of sequences) by multiple alignment algorithms because of computational restrictions. Here, we demonstrate the utility of this approach with two datasets of fish larvae and juveniles from Lake Constance and juvenile land snails under different models of sequence evolution. Sets of ribosomal 16S rRNA sequences, characterized by multiple indels, performed as good as or better than cox1 sequence sets in assigning sequences to species, demonstrating the suitability of rRNA genes for DNA barcoding.},
}
@article {pmid16214754,
year = {2005},
author = {Matz, MV and Nielsen, R},
title = {A likelihood ratio test for species membership based on DNA sequence data.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {360},
number = {1462},
pages = {1969-1974},
pmid = {16214754},
issn = {0962-8436},
support = {R01 GM066243/GM/NIGMS NIH HHS/United States ; 0201037//PHS HHS/United States ; GM066243/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Anura/genetics ; Butterflies/genetics ; Classification/*methods ; Computer Simulation ; *Genetic Variation ; Likelihood Functions ; *Models, Genetic ; Phylogeny ; Species Specificity ; },
abstract = {DNA barcoding as an approach for species identification is rapidly increasing in popularity. However, it remains unclear which statistical procedures should accompany the technique to provide a measure of uncertainty. Here we describe a likelihood ratio test which can be used to test if a sampled sequence is a member of an a priori specified species. We investigate the performance of the test using coalescence simulations, as well as using the real data from butterflies and frogs representing two kinds of challenge for DNA barcoding: extremely low and extremely high levels of sequence variability.},
}
@article {pmid16214753,
year = {2005},
author = {Hajibabaei, M and deWaard, JR and Ivanova, NV and Ratnasingham, S and Dooh, RT and Kirk, SL and Mackie, PM and Hebert, PD},
title = {Critical factors for assembling a high volume of DNA barcodes.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {360},
number = {1462},
pages = {1959-1967},
pmid = {16214753},
issn = {0962-8436},
mesh = {*Biodiversity ; DNA/*genetics ; Databases, Genetic ; Electronic Data Processing/*methods ; Information Management/*methods ; Molecular Diagnostic Techniques/*methods ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods ; Specimen Handling/instrumentation/*methods ; },
abstract = {Large-scale DNA barcoding projects are now moving toward activation while the creation of a comprehensive barcode library for eukaryotes will ultimately require the acquisition of some 100 million barcodes. To satisfy this need, analytical facilities must adopt protocols that can support the rapid, cost-effective assembly of barcodes. In this paper we discuss the prospects for establishing high volume DNA barcoding facilities by evaluating key steps in the analytical chain from specimens to barcodes. Alliances with members of the taxonomic community represent the most effective strategy for provisioning the analytical chain with specimens. The optimal protocols for DNA extraction and subsequent PCR amplification of the barcode region depend strongly on their condition, but production targets of 100K barcode records per year are now feasible for facilities working with compliant specimens. The analysis of museum collections is currently challenging, but PCR cocktails that combine polymerases with repair enzyme(s) promise future success. Barcode analysis is already a cost-effective option for species identification in some situations and this will increasingly be the case as reference libraries are assembled and analytical protocols are simplified.},
}
@article {pmid16214752,
year = {2005},
author = {De Ley, P and De Ley, IT and Morris, K and Abebe, E and Mundo-Ocampo, M and Yoder, M and Heras, J and Waumann, D and Rocha-Olivares, A and Jay Burr, AH and Baldwin, JG and Thomas, WK},
title = {An integrated approach to fast and informative morphological vouchering of nematodes for applications in molecular barcoding.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {360},
number = {1462},
pages = {1945-1958},
pmid = {16214752},
issn = {0962-8436},
mesh = {Animals ; Base Sequence ; *Biodiversity ; California ; Cluster Analysis ; Computational Biology ; DNA/*genetics ; DNA Primers ; Electronic Data Processing/*methods ; Mexico ; Microscopy, Video/methods ; Molecular Diagnostic Techniques/*methods ; Molecular Sequence Data ; Nematoda/*anatomy &amp; histology/*genetics ; *Phylogeny ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Molecular surveys of meiofaunal diversity face some interesting methodological challenges when it comes to interstitial nematodes from soils and sediments. Morphology-based surveys are greatly limited in processing speed, while barcoding approaches for nematodes are hampered by difficulties of matching sequence data with traditional taxonomy. Intermediate technology is needed to bridge the gap between both approaches. An example of such technology is video capture and editing microscopy, which consists of the recording of taxonomically informative multifocal series of microscopy images as digital video clips. The integration of multifocal imaging with sequence analysis of the D2D3 region of large subunit (LSU) rDNA is illustrated here in the context of a combined morphological and barcode sequencing survey of marine nematodes from Baja California and California. The resulting video clips and sequence data are made available online in the database NemATOL (http://nematol.unh.edu/). Analyses of 37 barcoded nematodes suggest that these represent at least 32 species, none of which matches available D2D3 sequences in public databases. The recorded multifocal vouchers allowed us to identify most specimens to genus, and will be used to match specimens with subsequent species identifications and descriptions of preserved specimens. Like molecular barcodes, multifocal voucher archives are part of a wider effort at structuring and changing the process of biodiversity discovery. We argue that data-rich surveys and phylogenetic tools for analysis of barcode sequences are an essential component of the exploration of phyla with a high fraction of undiscovered species. Our methods are also directly applicable to other meiofauna such as for example gastrotrichs and tardigrades.},
}
@article {pmid16214751,
year = {2005},
author = {Blaxter, M and Mann, J and Chapman, T and Thomas, F and Whitton, C and Floyd, R and Abebe, E},
title = {Defining operational taxonomic units using DNA barcode data.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {360},
number = {1462},
pages = {1935-1943},
pmid = {16214751},
issn = {0962-8436},
mesh = {Animals ; Base Sequence ; *Biodiversity ; Bryophyta ; Cluster Analysis ; DNA/*genetics ; DNA Primers ; Electron Transport Complex IV/genetics ; Electronic Data Processing/*methods ; Genetics, Population ; Invertebrates/*genetics ; Molecular Diagnostic Techniques/*methods ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The scale of diversity of life on this planet is a significant challenge for any scientific programme hoping to produce a complete catalogue, whatever means is used. For DNA barcoding studies, this difficulty is compounded by the realization that any chosen barcode sequence is not the gene 'for' speciation and that taxa have evolutionary histories. How are we to disentangle the confounding effects of reticulate population genetic processes? Using the DNA barcode data from meiofaunal surveys, here we discuss the benefits of treating the taxa defined by barcodes without reference to their correspondence to 'species', and suggest that using this non-idealist approach facilitates access to taxon groups that are not accessible to other methods of enumeration and classification. Major issues remain, in particular the methodologies for taxon discrimination in DNA barcode data.},
}
@article {pmid16214750,
year = {2005},
author = {Monaghan, MT and Balke, M and Gregory, TR and Vogler, AP},
title = {DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {360},
number = {1462},
pages = {1925-1933},
pmid = {16214750},
issn = {0962-8436},
mesh = {Animals ; Base Sequence ; *Biodiversity ; Classification/methods ; Cluster Analysis ; Coleoptera/*genetics ; DNA/*genetics ; DNA, Mitochondrial/genetics ; Electronic Data Processing/*methods ; *Genetic Variation ; Molecular Diagnostic Techniques/*methods ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Tropical Climate ; },
abstract = {DNA barcoding has been successfully implemented in the identification of previously described species, and in the process has revealed several cryptic species. It has been noted that such methods could also greatly assist in the discovery and delineation of undescribed species in poorly studied groups, although to date the feasibility of such an approach has not been examined explicitly. Here, we investigate the possibility of using short mitochondrial and nuclear DNA sequences to delimit putative species in groups lacking an existing taxonomic framework. We focussed on poorly known tropical water beetles (Coleoptera: Dytiscidae, Hydrophilidae) from Madagascar and dung beetles (Scarabaeidae) in the genus Canthon from the Neotropics. Mitochondrial DNA sequence variation proved to be highly structured, with >95% of the observed variation existing between discrete sets of very closely related genotypes. Sequence variation in nuclear 28S rRNA among the same individuals was lower by at least an order of magnitude, but 16 different genotypes were found in water beetles and 12 genotypes in Canthon, differing from each other by a minimum of two base pairs. The distribution of these 28S rRNA genotypes in individuals exactly matched the distribution of mtDNA clusters, suggesting that mtDNA patterns were not misleading because of introgression. Moreover, in a few cases where sequence information was available in GenBank for morphologically defined species of Canthon, these matched some of the DNA-based clusters. These findings demonstrate that clusters of close relatives can be identified readily in the sequence variation obtained in field collected samples, and that these clusters are likely to correspond to either previously described or unknown species. The results suggest that DNA-assisted taxonomy will not require more than a short fragment of mtDNA to provide a largely accurate picture of species boundaries in these groups. Applied on a large scale, this DNA-based approach could greatly improve the rate of species discovery in the large assemblages of insects that remain undescribed.},
}
@article {pmid16214748,
year = {2005},
author = {DeSalle, R and Egan, MG and Siddall, M},
title = {The unholy trinity: taxonomy, species delimitation and DNA barcoding.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {360},
number = {1462},
pages = {1905-1916},
pmid = {16214748},
issn = {0962-8436},
mesh = {Animals ; Base Sequence ; *Biodiversity ; Classification/*methods ; DNA/*genetics ; Deer/anatomy &amp; histology/genetics ; Electronic Data Processing/*methods ; Genetic Markers/genetics ; Leeches/genetics ; Molecular Diagnostic Techniques/*methods ; Molecular Sequence Data ; *Phylogeny ; Species Specificity ; },
abstract = {Recent excitement over the development of an initiative to generate DNA sequences for all named species on the planet has in our opinion generated two major areas of contention as to how this 'DNA barcoding' initiative should proceed. It is critical that these two issues are clarified and resolved, before the use of DNA as a tool for taxonomy and species delimitation can be universalized. The first issue concerns how DNA data are to be used in the context of this initiative; this is the DNA barcode reader problem (or barcoder problem). Currently, many of the published studies under this initiative have used tree building methods and more precisely distance approaches to the construction of the trees that are used to place certain DNA sequences into a taxonomic context. The second problem involves the reaction of the taxonomic community to the directives of the 'DNA barcoding' initiative. This issue is extremely important in that the classical taxonomic approach and the DNA approach will need to be reconciled in order for the 'DNA barcoding' initiative to proceed with any kind of community acceptance. In fact, we feel that DNA barcoding is a misnomer. Our preference is for the title of the London meetings--Barcoding Life. In this paper we discuss these two concerns generated around the DNA barcoding initiative and attempt to present a phylogenetic systematic framework for an improved barcoder as well as a taxonomic framework for interweaving classical taxonomy with the goals of 'DNA barcoding'.},
}
@article {pmid16214747,
year = {2005},
author = {Summerbell, RC and Lévesque, CA and Seifert, KA and Bovers, M and Fell, JW and Diaz, MR and Boekhout, T and de Hoog, GS and Stalpers, J and Crous, PW},
title = {Microcoding: the second step in DNA barcoding.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {360},
number = {1462},
pages = {1897-1903},
pmid = {16214747},
issn = {0962-8436},
mesh = {*Biodiversity ; DNA/*genetics ; Electronic Data Processing/*methods ; Flow Cytometry ; Fungi/*genetics ; Microarray Analysis/methods ; Molecular Diagnostic Techniques/*methods ; Oligonucleotides/genetics ; Species Specificity ; },
abstract = {After the process of DNA barcoding has become well advanced in a group of organisms, as it has in the economically important fungi, the question then arises as to whether shorter and literally more barcode-like DNA segments should be utilized to facilitate rapid identification and, where applicable, detection. Through appropriate software analysis of typical full-length barcodes (generally over 500 base pairs long), uniquely distinctive oligonucleotide 'microcodes' of less than 25 bp can be found that allow rapid identification of circa 100-200 species on various array-like platforms. Microarrays can in principle fulfill the function of microcode-based species identification but, because of their high cost and low level of reusability, they tend to be less cost-effective. Two alternative platforms in current use in fungal identification are reusable nylon-based macroarrays and the Luminex system of specific, colour-coded DNA detection beads analysed by means of a flow cytometer. When the most efficient means of rapid barcode-based species identification is sought, a choice can be made either for one of these methodologies or for basic high-throughput sequencing, depending on the strategic outlook of the investigator and on current costs. Arrays and functionally similar platforms may have a particular advantage when a biologically complex material such as soil or a human respiratory secretion sample is analysed to give a census of relevant species present.},
}
@article {pmid16214746,
year = {2005},
author = {Chase, MW and Salamin, N and Wilkinson, M and Dunwell, JM and Kesanakurthi, RP and Haider, N and Savolainen, V},
title = {Land plants and DNA barcodes: short-term and long-term goals.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {360},
number = {1462},
pages = {1889-1895},
pmid = {16214746},
issn = {0962-8436},
mesh = {*Biodiversity ; Classification/methods ; Computational Biology/methods ; DNA/*genetics ; DNA, Ribosomal Spacer/genetics ; Databases, Genetic ; Electronic Data Processing/*methods ; Molecular Diagnostic Techniques/*methods ; Plants/*genetics ; Ribulose-Bisphosphate Carboxylase/genetics ; Species Specificity ; },
abstract = {Land plants have had the reputation of being problematic for DNA barcoding for two general reasons: (i) the standard DNA regions used in algae, animals and fungi have exceedingly low levels of variability and (ii) the typically used land plant plastid phylogenetic markers (e.g. rbcL, trnL-F, etc.) appear to have too little variation. However, no one has assessed how well current phylogenetic resources might work in the context of identification (versus phylogeny reconstruction). In this paper, we make such an assessment, particularly with two of the markers commonly sequenced in land plant phylogenetic studies, plastid rbcL and internal transcribed spacers of the large subunits of nuclear ribosomal DNA (ITS), and find that both of these DNA regions perform well even though the data currently available in GenBank/EBI were not produced to be used as barcodes and BLAST searches are not an ideal tool for this purpose. These results bode well for the use of even more variable regions of plastid DNA (such as, for example, psbA-trnH) as barcodes, once they have been widely sequenced. In the short term, efforts to bring land plant barcoding up to the standards being used now in other organisms should make swift progress. There are two categories of DNA barcode users, scientists in fields other than taxonomy and taxonomists. For the former, the use of mitochondrial and plastid DNA, the two most easily assessed genomes, is at least in the short term a useful tool that permits them to get on with their studies, which depend on knowing roughly which species or species groups they are dealing with, but these same DNA regions have important drawbacks for use in taxonomic studies (i.e. studies designed to elucidate species limits). For these purposes, DNA markers from uniparentally (usually maternally) inherited genomes can only provide half of the story required to improve taxonomic standards being used in DNA barcoding. In the long term, we will need to develop more sophisticated barcoding tools, which would be multiple, low-copy nuclear markers with sufficient genetic variability and PCR-reliability; these would permit the detection of hybrids and permit researchers to identify the 'genetic gaps' that are useful in assessing species limits.},
}
@article {pmid16214745,
year = {2005},
author = {Saunders, GW},
title = {Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {360},
number = {1462},
pages = {1879-1888},
pmid = {16214745},
issn = {0962-8436},
mesh = {Base Sequence ; *Biodiversity ; Cluster Analysis ; DNA/*genetics ; DNA Primers ; Electron Transport Complex IV/genetics ; Electronic Data Processing/*methods ; Molecular Diagnostic Techniques/*methods ; Molecular Sequence Data ; Oceans and Seas ; *Phylogeny ; Rhodophyta/cytology/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Marine macroalgae, especially the Rhodophyta, can be notoriously difficult to identify owing to their relatively simple morphology and anatomy, convergence, rampant phenotypic plasticity, and alternation of heteromorphic generations. It is thus not surprising that algal systematists have come to rely heavily on genetic tools for molecular assisted alpha taxonomy. Unfortunately the number of suitable marker systems in the three available genomes is enormous and, although most workers have settled on one of three or four models, the lack of an accepted standard hinders the comparison of results between laboratories. The advantages of a standard system are obvious for practical purposes of species discovery and identification; as well, compliance with a universal marker, such as cox1 being developed under the label 'DNA barcode', would allow algal systematists to benefit from the rapidly emerging technologies. Novel primers were developed for red algae to PCR amplify and sequence the 5' cox1 'barcode' region and were used to assess three known species-complex questions: (i) Mazzaella species in the Northeast Pacific; (ii) species of the genera Dilsea and Neodilsea in the Northeast Pacific; and (iii) Asteromenia peltata from three oceans. These models were selected because they have all caused confusion with regards to species number, distribution, and identification in the field, and because they have all been studied with molecular tools. In all cases the DNA barcode resolved accurately and unequivocally species identities and, with the enhanced sampling here, turned up a variety of novel observations in need of further taxonomic investigation.},
}
@article {pmid16214744,
year = {2005},
author = {Lorenz, JG and Jackson, WE and Beck, JC and Hanner, R},
title = {The problems and promise of DNA barcodes for species diagnosis of primate biomaterials.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {360},
number = {1462},
pages = {1869-1877},
pmid = {16214744},
issn = {0962-8436},
mesh = {Animals ; Base Sequence ; *Biodiversity ; Cluster Analysis ; DNA/*genetics ; DNA Primers ; Databases, Genetic ; Electron Transport Complex IV/genetics ; Electronic Data Processing/*methods ; Molecular Diagnostic Techniques/*methods ; Molecular Sequence Data ; *Phylogeny ; Primates/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The Integrated Primate Biomaterials and Information Resource (www.IPBIR.org) provides essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing DNA and RNA derived from primate cell cultures. The IPBIR uses mitochondrial cytochrome c oxidase subunit I sequences to verify the identity of samples for quality control purposes in the accession, cell culture, DNA extraction processes and prior to shipping to end users. As a result, IPBIR is accumulating a database of 'DNA barcodes' for many species of primates. However, this quality control process is complicated by taxon specific patterns of 'universal primer' failure, as well as the amplification or co-amplification of nuclear pseudogenes of mitochondrial origins. To overcome these difficulties, taxon specific primers have been developed, and reverse transcriptase PCR is utilized to exclude these extraneous sequences from amplification. DNA barcoding of primates has applications to conservation and law enforcement. Depositing barcode sequences in a public database, along with primer sequences, trace files and associated quality scores, makes this species identification technique widely accessible. Reference DNA barcode sequences should be derived from, and linked to, specimens of known provenance in web-accessible collections in order to validate this system of molecular diagnostics.},
}
@article {pmid16214743,
year = {2005},
author = {Ward, RD and Zemlak, TS and Innes, BH and Last, PR and Hebert, PD},
title = {DNA barcoding Australia's fish species.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {360},
number = {1462},
pages = {1847-1857},
pmid = {16214743},
issn = {0962-8436},
mesh = {Animals ; Australia ; Base Composition ; Base Sequence ; *Biodiversity ; Cluster Analysis ; Codon/genetics ; DNA/*genetics ; DNA Primers ; Electron Transport Complex IV/genetics ; Electronic Data Processing/*methods ; Fishes/*genetics ; Molecular Diagnostic Techniques/*methods ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Two hundred and seven species of fish, mostly Australian marine fish, were sequenced (barcoded) for a 655 bp region of the mitochondrial cytochrome oxidase subunit I gene (cox1). Most species were represented by multiple specimens, and 754 sequences were generated. The GC content of the 143 species of teleosts was higher than the 61 species of sharks and rays (47.1% versus 42.2%), largely due to a higher GC content of codon position 3 in the former (41.1% versus 29.9%). Rays had higher GC than sharks (44.7% versus 41.0%), again largely due to higher GC in the 3rd codon position in the former (36.3% versus 26.8%). Average within-species, genus, family, order and class Kimura two parameter (K2P) distances were 0.39%, 9.93%, 15.46%, 22.18% and 23.27%, respectively. All species could be differentiated by their cox1 sequence, although single individuals of each of two species had haplotypes characteristic of a congener. Although DNA barcoding aims to develop species identification systems, some phylogenetic signal was apparent in the data. In the neighbour-joining tree for all 754 sequences, four major clusters were apparent: chimaerids, rays, sharks and teleosts. Species within genera invariably clustered, and generally so did genera within families. Three taxonomic groups-dogfishes of the genus Squalus, flatheads of the family Platycephalidae, and tunas of the genus Thunnus-were examined more closely. The clades revealed after bootstrapping generally corresponded well with expectations. Individuals from operational taxonomic units designated as Squalus species B through F formed individual clades, supporting morphological evidence for each of these being separate species. We conclude that cox1 sequencing, or 'barcoding', can be used to identify fish species.},
}
@article {pmid16214742,
year = {2005},
author = {Janzen, DH and Hajibabaei, M and Burns, JM and Hallwachs, W and Remigio, E and Hebert, PD},
title = {Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {360},
number = {1462},
pages = {1835-1845},
pmid = {16214742},
issn = {0962-8436},
mesh = {Animals ; *Biodiversity ; Cluster Analysis ; Conservation of Natural Resources/methods ; Costa Rica ; DNA/*genetics ; Electron Transport Complex IV/genetics ; Electronic Data Processing/*methods ; Lepidoptera/*genetics ; Molecular Diagnostic Techniques/*methods ; Museums ; Species Specificity ; Specimen Handling/methods ; },
abstract = {By facilitating bioliteracy, DNA barcoding has the potential to improve the way the world relates to wild biodiversity. Here we describe the early stages of the use of cox1 barcoding to supplement and strengthen the taxonomic platform underpinning the inventory of thousands of sympatric species of caterpillars in tropical dry forest, cloud forest and rain forest in northwestern Costa Rica. The results show that barcoding a biologically complex biota unambiguously distinguishes among 97% of more than 1000 species of reared Lepidoptera. Those few species whose barcodes overlap are closely related and not confused with other species. Barcoding also has revealed a substantial number of cryptic species among morphologically defined species, associated sexes, and reinforced identification of species that are difficult to distinguish morphologically. For barcoding to achieve its full potential, (i) ability to rapidly and cheaply barcode older museum specimens is urgent, (ii) museums need to address the opportunity and responsibility for housing large numbers of barcode voucher specimens, (iii) substantial resources need be mustered to support the taxonomic side of the partnership with barcoding, and (iv) hand-held field-friendly barcorder must emerge as a mutualism with the taxasphere and the barcoding initiative, in a manner such that its use generates a resource base for the taxonomic process as well as a tool for the user.},
}
@article {pmid16214741,
year = {2005},
author = {Smith, MA and Fisher, BL and Hebert, PD},
title = {DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {360},
number = {1462},
pages = {1825-1834},
pmid = {16214741},
issn = {0962-8436},
mesh = {Animals ; Ants/*genetics ; Base Sequence ; *Biodiversity ; DNA/*genetics ; DNA Primers ; Electronic Data Processing/*methods ; Evolution, Molecular ; Geography ; Madagascar ; Models, Genetic ; Molecular Diagnostic Techniques/*methods ; Molecular Sequence Data ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The role of DNA barcoding as a tool to accelerate the inventory and analysis of diversity for hyperdiverse arthropods is tested using ants in Madagascar. We demonstrate how DNA barcoding helps address the failure of current inventory methods to rapidly respond to pressing biodiversity needs, specifically in the assessment of richness and turnover across landscapes with hyperdiverse taxa. In a comparison of inventories at four localities in northern Madagascar, patterns of richness were not significantly different when richness was determined using morphological taxonomy (morphospecies) or sequence divergence thresholds (Molecular Operational Taxonomic Unit(s); MOTU). However, sequence-based methods tended to yield greater richness and significantly lower indices of similarity than morphological taxonomy. MOTU determined using our molecular technique were a remarkably local phenomenon-indicative of highly restricted dispersal and/or long-term isolation. In cases where molecular and morphological methods differed in their assignment of individuals to categories, the morphological estimate was always more conservative than the molecular estimate. In those cases where morphospecies descriptions collapsed distinct molecular groups, sequence divergences of 16% (on average) were contained within the same morphospecies. Such high divergences highlight taxa for further detailed genetic, morphological, life history, and behavioral studies.},
}
@article {pmid16214740,
year = {2005},
author = {Armstrong, KF and Ball, SL},
title = {DNA barcodes for biosecurity: invasive species identification.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {360},
number = {1462},
pages = {1813-1823},
pmid = {16214740},
issn = {0962-8436},
mesh = {Animals ; DNA, Mitochondrial/genetics ; Databases, Genetic ; Electronic Data Processing/*methods ; Insecta/genetics ; Molecular Diagnostic Techniques/*methods ; New Zealand ; *Security Measures ; Species Specificity ; },
abstract = {Biosecurity encompasses protecting against any risk through 'biological harm', not least being the economic impact from the spread of pest insects. Molecular diagnostic tools provide valuable support for the rapid and accurate identification of morphologically indistinct alien species. However, these tools currently lack standardization. They are not conducive to adaptation by multiple sectors or countries, or to coping with changing pest priorities. The data presented here identifies DNA barcodes as a very promising opportunity to address this. DNA of tussock moth and fruit fly specimens intercepted at the New Zealand border over the last decade were reanalysed using the cox1 sequence barcode approach. Species identifications were compared with the historical dataset obtained by PCR-RFLP of nuclear rDNA. There was 90 and 96% agreement between the methods for these species, respectively. Improvements included previous tussock moth 'unknowns' being placed to family, genera or species and further resolution within fruit fly species complexes. The analyses highlight several advantages of DNA barcodes, especially their adaptability and predictive value. This approach is a realistic platform on which to build a much more flexible system, with the potential to be adopted globally for the rapid and accurate identification of invasive alien species.},
}
@article {pmid16214739,
year = {2005},
author = {Savolainen, V and Cowan, RS and Vogler, AP and Roderick, GK and Lane, R},
title = {Towards writing the encyclopedia of life: an introduction to DNA barcoding.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {360},
number = {1462},
pages = {1805-1811},
pmid = {16214739},
issn = {0962-8436},
support = {BBS/B/04358/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Conservation of Natural Resources/methods ; Databases, Genetic ; Electronic Data Processing/*methods ; *Museums ; Species Specificity ; Specimen Handling/*methods ; },
abstract = {An international consortium of major natural history museums, herbaria and other organizations has launched an ambitious project, the 'Barcode of Life Initiative', to promote a process enabling the rapid and inexpensive identification of the estimated 10 million species on Earth. DNA barcoding is a diagnostic technique in which short DNA sequence(s) can be used for species identification. The first international scientific conference on Barcoding of Life was held at the Natural History Museum in London in February 2005, and here we review the scientific challenges discussed during this conference and in previous publications. Although still controversial, the scientific benefits of DNA barcoding include: (i) enabling species identification, including any life stage or fragment, (ii) facilitating species discoveries based on cluster analyses of gene sequences (e.g. cox1 = CO1, in animals), (iii) promoting development of handheld DNA sequencing technology that can be applied in the field for biodiversity inventories and (iv) providing insight into the diversity of life.},
}
@article {pmid16165182,
year = {2005},
author = {Creer, S},
title = {On the application of molecular barcodes in toxinological research.},
journal = {Toxicon : official journal of the International Society on Toxinology},
volume = {46},
number = {6},
pages = {709-710},
doi = {10.1016/j.toxicon.2005.08.002},
pmid = {16165182},
issn = {0041-0101},
mesh = {DNA/*genetics ; Databases, Genetic ; Electron Transport Complex IV/genetics ; Genetic Markers/*genetics ; Species Specificity ; Toxicology/*methods/*trends ; },
}
@article {pmid16157361,
year = {2005},
author = {Pook, CE and McEwing, R},
title = {Mitochondrial DNA sequences from dried snake venom: a DNA barcoding approach to the identification of venom samples.},
journal = {Toxicon : official journal of the International Society on Toxinology},
volume = {46},
number = {7},
pages = {711-715},
doi = {10.1016/j.toxicon.2005.07.005},
pmid = {16157361},
issn = {0041-0101},
mesh = {Animals ; Base Sequence ; Crotalus/*genetics ; DNA, Mitochondrial/*genetics ; Electronic Data Processing/*methods ; Phylogeny ; RNA, Ribosomal/analysis/genetics ; Snake Venoms/*analysis/*genetics ; Species Specificity ; },
abstract = {Outdated nomenclature and incorrect taxonomic characterisation of snake venoms in the current toxinological literature have serious implications for the replicability of results from snake venom toxin research. The situation has not improved, despite attempts to supply toxinologists with regular updates on snake systematics. Here, we demonstrate the successful extraction of DNA, and subsequent sequencing of the mitochondrial 12S gene, from dried snake venoms. This approach offers a new and potentially straightforward method for accurate species identification. Mitochondrial DNA (mtDNA) sequences isolated from snake venom can be used to clarify or validate snake species identification through comparison against existing sequences in the GenBank database, and through phylogenetic analyses with other sequences. Pooled venoms can also be screened a priori for the presence of multiple species, and the species names on the labels of commercial venoms verified. Moreover, if the species from which the venom sample has been taken is known, and the specimen is available as a voucher, the mtDNA sequence of the haplotype isolated from that species venom sample could serve as a sequence standard (or 'DNA barcode') for that species. Our new method of DNA barcoding venoms ensures the identification of venoms even after future taxonomic changes.},
}
@article {pmid16154784,
year = {2005},
author = {Druzhinina, IS and Kopchinskiy, AG and Komoń, M and Bissett, J and Szakacs, G and Kubicek, CP},
title = {An oligonucleotide barcode for species identification in Trichoderma and Hypocrea.},
journal = {Fungal genetics and biology : FG &amp; B},
volume = {42},
number = {10},
pages = {813-828},
doi = {10.1016/j.fgb.2005.06.007},
pmid = {16154784},
issn = {1087-1845},
mesh = {Base Sequence ; Biomarkers ; *Computational Biology ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/genetics ; Databases, Nucleic Acid ; Hypocrea/*classification/genetics ; Molecular Sequence Data ; Mycological Typing Techniques/*methods ; Oligonucleotides/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Trichoderma/*classification/genetics ; },
abstract = {One of the biggest obstructions to studies on Trichoderma has been the incorrect and confused application of species names to isolates used in industry, biocontrol of plant pathogens and ecological surveys, thereby making the comparison of results questionable. Here we provide a convenient, on-line method for the quick molecular identification of Hypocrea/Trichoderma at the genus and species levels based on an oligonucleotide barcode: a diagnostic combination of several oligonucleotides (hallmarks) specifically allocated within the internal transcribed spacer 1 and 2 (ITS1 and 2) sequences of the rDNA repeat. The barcode was developed on the basis of 979 sequences of 88 vouchered species which displayed in total 135 ITS1 and 2 haplotypes. Oligonucleotide sequences which are constant in all known ITS1 and 2 of Hypocrea/Trichoderma but different in closely related fungal genera, were used to define genus-specific hallmarks. The library of species-, clade- and genus-specific hallmarks is stored in the MySQL database and integrated in the TrichOKey v. 1.0 - barcode sequence identification program with the web interface located on . TrichOKey v. 1.0 identifies 75 single species, 5 species pairs and 1 species triplet. Verification of the DNA-barcode was done by a blind test on 53 unknown isolates of Trichoderma, collected in Central and South America. The obtained results were in a total agreement with phylogenetic identification based on tef1 (large intron), NCBI BLAST of vouchered records and postum morphological analysis. We conclude that oligonucleotide barcode is a powerful tool for the routine identification of Hypocrea/Trichoderma species and should be useful as a complement to traditional methods.},
}
@article {pmid16141338,
year = {2005},
author = {Stegmeier, F and Hu, G and Rickles, RJ and Hannon, GJ and Elledge, SJ},
title = {A lentiviral microRNA-based system for single-copy polymerase II-regulated RNA interference in mammalian cells.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {102},
number = {37},
pages = {13212-13217},
pmid = {16141338},
issn = {0027-8424},
mesh = {Animals ; Cell Line, Tumor ; Gene Dosage ; Genes ; Genes, Reporter ; *Genetic Vectors ; Humans ; Lentivirus/genetics ; Methods ; MicroRNAs/*genetics ; *RNA Interference ; RNA Polymerase II/*genetics ; Tetracycline ; Transcription, Genetic ; },
abstract = {The advent of RNA interference has led to the ability to interfere with gene expression and greatly expanded our ability to perform genetic screens in mammalian cells. The expression of short hairpin RNA (shRNA) from polymerase III promoters can be encoded in transgenes and used to produce small interfering RNAs that down-regulate specific genes. In this study, we show that polymerase II-transcribed shRNAs display very efficient knockdown of gene expression when the shRNA is embedded in a microRNA context. Importantly, our shRNA expression system [called PRIME (potent RNA interference using microRNA expression) vectors] allows for the multicistronic cotranscription of a reporter gene, thereby facilitating the tracking of shRNA production in individual cells. Based on this system, we developed a series of lentiviral vectors that display tetracycline-responsive knockdown of gene expression at single copy. The high penetrance of these vectors will facilitate genomewide loss-of-function screens and is an important step toward using bar-coding strategies to follow loss of specific sequences in complex populations.},
}
@article {pmid16121259,
year = {2005},
author = {Lee, W and St Onge, RP and Proctor, M and Flaherty, P and Jordan, MI and Arkin, AP and Davis, RW and Nislow, C and Giaever, G},
title = {Genome-wide requirements for resistance to functionally distinct DNA-damaging agents.},
journal = {PLoS genetics},
volume = {1},
number = {2},
pages = {e24},
pmid = {16121259},
issn = {1553-7390},
mesh = {Antifungal Agents/pharmacology ; Cluster Analysis ; DNA Damage/drug effects/*genetics ; DNA Repair/genetics ; Drug Resistance/*genetics ; Epistasis, Genetic ; *Genome, Fungal ; Saccharomyces cerevisiae/*genetics ; Sequence Deletion ; },
abstract = {The mechanistic and therapeutic differences in the cellular response to DNA-damaging compounds are not completely understood, despite intense study. To expand our knowledge of DNA damage, we assayed the effects of 12 closely related DNA-damaging agents on the complete pool of approximately 4,700 barcoded homozygous deletion strains of Saccharomyces cerevisiae. In our protocol, deletion strains are pooled together and grown competitively in the presence of compound. Relative strain sensitivity is determined by hybridization of PCR-amplified barcodes to an oligonucleotide array carrying the barcode complements. These screens identified genes in well-characterized DNA-damage-response pathways as well as genes whose role in the DNA-damage response had not been previously established. High-throughput individual growth analysis was used to independently confirm microarray results. Each compound produced a unique genome-wide profile. Analysis of these data allowed us to determine the relative importance of DNA-repair modules for resistance to each of the 12 profiled compounds. Clustering the data for 12 distinct compounds uncovered both known and novel functional interactions that comprise the DNA-damage response and allowed us to define the genetic determinants required for repair of interstrand cross-links. Further genetic analysis allowed determination of epistasis for one of these functional groups.},
}
@article {pmid16101789,
year = {2005},
author = {Greenstone, MH and Rowley, DL and Heimbach, U and Lundgren, JG and Pfannenstiel, RS and Rehner, SA},
title = {Barcoding generalist predators by polymerase chain reaction: carabids and spiders.},
journal = {Molecular ecology},
volume = {14},
number = {10},
pages = {3247-3266},
doi = {10.1111/j.1365-294X.2005.02628.x},
pmid = {16101789},
issn = {0962-1083},
mesh = {Animals ; Base Sequence ; Coleoptera/*classification/genetics ; DNA/chemistry/genetics ; Electron Transport Complex IV/chemistry/genetics ; Female ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/*methods ; Predatory Behavior ; Sequence Alignment ; Spiders/*classification/genetics ; },
abstract = {Identification of arthropod predators is challenging when closely related species are found at a given locality. Identification of the immature stages is especially problematic, because distinguishing morphological features are difficult to use or have not been described. We used polymerase chain reaction (PCR) to distinguish closely related carabids and spiders, and to match eggs and larvae (or nymphs) with identified adult parents. Within the Carabidae, we amplified species-specific mitochondrial cytochrome oxidase I (COI) fragments for three species each in the genera Poecilus and Harpalus, and two each in Chlaenius and Bembidion. Within the Araneae, we amplified species-specific COI fragments for two Hibana species (Anyphaenidae), Pardosa milvina and Rabidosa rabida (Lycosidae), Frontinella communis and Grammonota texana (Linyphiidae), and Cheiracanthium inclusum (Miturgidae). We are able to correctly identify all immature stages tested--eggs, larvae (or nymphs) and pupae--by comparison of the amplified fragments with those of the adults. Using COI markers as species identifiers is a tenet of the Barcode of Life initiative, an international consortium to provide a molecular identifier for every animal species.},
}
@article {pmid16048766,
year = {2005},
author = {Hurst, GD and Jiggins, FM},
title = {Problems with mitochondrial DNA as a marker in population, phylogeographic and phylogenetic studies: the effects of inherited symbionts.},
journal = {Proceedings. Biological sciences},
volume = {272},
number = {1572},
pages = {1525-1534},
pmid = {16048766},
issn = {0962-8452},
support = {//Wellcome Trust/United Kingdom ; 070535//Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Arthropods/*genetics/microbiology ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genetic Markers/*genetics ; Genetic Variation ; *Genetics, Population ; Geography ; Linkage Disequilibrium ; *Phylogeny ; *Selection, Genetic ; *Symbiosis ; },
abstract = {Mitochondrial DNA (mtDNA) has been a marker of choice for reconstructing historical patterns of population demography, admixture, biogeography and speciation. However, it has recently been suggested that the pervasive nature of direct and indirect selection on this molecule renders any conclusion derived from it ambiguous. We review here the evidence for indirect selection on mtDNA in arthropods arising from linkage disequilibrium with maternally inherited symbionts. We note first that these symbionts are very common in arthropods and then review studies that reveal the extent to which they shape mtDNA evolution. mtDNA diversity patterns are compatible with neutral expectations for an uninfected population in only 2 of 19 cases. The remaining 17 studies revealed cases of symbiont-driven reduction in mtDNA diversity, symbiont-driven increases in diversity, symbiont-driven changes in mtDNA variation over space and symbiont-associated paraphyly of mtDNA. We therefore conclude that these elements often confound the inference of an organism's evolutionary history from mtDNA data and that mtDNA on its own is an unsuitable marker for the study of recent historical events in arthropods. We also discuss the impact of these studies on the current programme of taxonomy based on DNA bar-coding.},
}
@article {pmid15961439,
year = {2005},
author = {DasGupta, B and Konwar, KM and Mandoiu, II and Shvartsman, AA},
title = {DNA-BAR: distinguisher selection for DNA barcoding.},
journal = {Bioinformatics (Oxford, England)},
volume = {21},
number = {16},
pages = {3424-3426},
doi = {10.1093/bioinformatics/bti547},
pmid = {15961439},
issn = {1367-4803},
mesh = {*Algorithms ; Chromosome Mapping/*methods ; DNA/*chemistry/*genetics ; In Situ Hybridization/*methods ; Sequence Analysis, DNA/*methods ; *Software ; },
abstract = {DNA-BAR is a software package for selecting DNA probes (henceforth referred to as distinguishers) that can be used in genomic-based identification of microorganisms. Given the genomic sequences of the microorganisms, DNA-BAR finds a near-minimum number of distinguishers yielding a distinct hybridization pattern for each microorganism. Selected distinguishers satisfy user specified bounds on length, melting temperature and GC content, as well as redundancy and cross-hybridization constraints.},
}
@article {pmid15928076,
year = {2005},
author = {Kress, WJ and Wurdack, KJ and Zimmer, EA and Weigt, LA and Janzen, DH},
title = {Use of DNA barcodes to identify flowering plants.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {102},
number = {23},
pages = {8369-8374},
pmid = {15928076},
issn = {0027-8424},
mesh = {Atropa belladonna/genetics ; Cell Nucleus/genetics ; DNA, Chloroplast/genetics ; DNA, Intergenic/genetics ; DNA, Plant/*genetics ; Electronic Data Processing/*methods ; Flowers/classification/cytology/genetics ; Genes, Plant/genetics ; Magnoliopsida/*classification/cytology/*genetics ; Molecular Sequence Data ; Phylogeny ; Plastids/genetics ; Species Specificity ; Nicotiana/genetics ; },
abstract = {Methods for identifying species by using short orthologous DNA sequences, known as "DNA barcodes," have been proposed and initiated to facilitate biodiversity studies, identify juveniles, associate sexes, and enhance forensic analyses. The cytochrome c oxidase 1 sequence, which has been found to be widely applicable in animal barcoding, is not appropriate for most species of plants because of a much slower rate of cytochrome c oxidase 1 gene evolution in higher plants than in animals. We therefore propose the nuclear internal transcribed spacer region and the plastid trnH-psbA intergenic spacer as potentially usable DNA regions for applying barcoding to flowering plants. The internal transcribed spacer is the most commonly sequenced locus used in plant phylogenetic investigations at the species level and shows high levels of interspecific divergence. The trnH-psbA spacer, although short (approximately 450-bp), is the most variable plastid region in angiosperms and is easily amplified across a broad range of land plants. Comparison of the total plastid genomes of tobacco and deadly nightshade enhanced with trials on widely divergent angiosperm taxa, including closely related species in seven plant families and a group of species sampled from a local flora encompassing 50 plant families (for a total of 99 species, 80 genera, and 53 families), suggest that the sequences in this pair of loci have the potential to discriminate among the largest number of plant species for barcoding purposes.},
}
@article {pmid15921447,
year = {2005},
author = {Karthikeyan, M and Bender, A},
title = {Encoding and decoding graphical chemical structures as two-dimensional (PDF417) barcodes.},
journal = {Journal of chemical information and modeling},
volume = {45},
number = {3},
pages = {572-580},
doi = {10.1021/ci049758i},
pmid = {15921447},
issn = {1549-9596},
abstract = {A wide range of molecular representations exist today, ranging from human-readable structural diagrams over line notations such as Wiswesser Line Notation (WLN) and SMILES to several dozen computer-readable file formats. Still, to encode molecular structures in a computer-readable way for inputting structures in computer systems those formats are not the method of choice since they are not easily and faultlessly readable via optical recognition. In the present study a two-dimensional (PDF417) barcode representation of molecular structures in SMILES format is explored that enables the user to read and input molecular structures into computer systems in a fully automated fashion. A Lempel-Ziv-Welch (LZW) based compressed version of SMILES is suggested for cases where the size of the structure exceeds the storage capacity of PDF417 barcodes. Alternatively, the compact ACS format may be employed as a structural representation. The input via barcodes is fast, practically error free due to the 2D barcodes used which employ error correction and fully automatic. A Web application interface is developed which is able to interpret these barcodes and export them as optimized 3D chemical structures. Applications of this representation range from keeping automated storage systems to Web-based tracking systems of molecular samples. The National Chemical Laboratory, Pune, employs 2D barcode encoded structures for in-house repository management, where barcodes can also be used for querying the database for similar or substructures of the query structure.},
}
@article {pmid15914079,
year = {2005},
author = {Liu, LX and Huang, ZL and Zhao, YD},
title = {Vibrational spectroscopic encoding of polystyrene-based resin beads: converting the encoding peaks into barcodes.},
journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy},
volume = {62},
number = {4-5},
pages = {1039-1044},
doi = {10.1016/j.saa.2005.04.001},
pmid = {15914079},
issn = {1386-1425},
mesh = {Electronic Data Processing/*methods ; *Microspheres ; Models, Chemical ; Polystyrenes/*chemistry ; Resins, Synthetic/*chemistry ; Spectroscopy, Fourier Transform Infrared ; *Vibration ; },
abstract = {A detailed approach is described for the vibrational spectroscopic encoding of polystyrene-based resin beads by converting the infrared absorption peaks suitable for encoding (encoding peaks) into barcodes. Based on combining the FT-IR measurements and the quantum-chemical computations, the vibrational characteristics of p-tert-butylstyrene monomer, polystyrene and poly(p-tert-butylstyrene) resin beads are analyzed, which are helpful for the selection of encoding peaks. The vibrational spectroscopic encoding of polystyrene-based resin beads could be obtained by converting the wavenumber, intensity and full width at half maximum (FWHM) of the encoding peaks into barcodes automatically through a computer program designed in our laboratory.},
}
@article {pmid15874991,
year = {2005},
author = {Schindel, DE and Miller, SE},
title = {DNA barcoding a useful tool for taxonomists.},
journal = {Nature},
volume = {435},
number = {7038},
pages = {17},
doi = {10.1038/435017b},
pmid = {15874991},
issn = {1476-4687},
mesh = {Animals ; Classification/*methods ; Electronic Data Processing/*statistics &amp; numerical data/trends ; Female ; Male ; Species Specificity ; },
}
@article {pmid15858548,
year = {2005},
author = {Gregory, TR},
title = {DNA barcoding does not compete with taxonomy.},
journal = {Nature},
volume = {434},
number = {7037},
pages = {1067},
doi = {10.1038/4341067b},
pmid = {15858548},
issn = {1476-4687},
mesh = {Classification/*methods ; Electronic Data Processing/economics/statistics &amp; numerical data/*trends ; Research Support as Topic/trends ; },
}
@article {pmid15826298,
year = {2005},
author = {Donofrio, N and Rajagopalon, R and Brown, D and Diener, S and Windham, D and Nolin, S and Floyd, A and Mitchell, T and Galadima, N and Tucker, S and Orbach, MJ and Patel, G and Farman, M and Pampanwar, V and Soderlund, C and Lee, YH and Dean, RA},
title = {'PACLIMS': a component LIM system for high-throughput functional genomic analysis.},
journal = {BMC bioinformatics},
volume = {6},
number = {},
pages = {94},
pmid = {15826298},
issn = {1471-2105},
mesh = {Algorithms ; Base Sequence ; Chromosome Mapping ; Computational Biology/*instrumentation/*methods ; DNA/metabolism ; DNA Mutational Analysis ; Data Interpretation, Statistical ; Database Management Systems ; Databases, Factual ; Databases, Genetic ; Evolution, Molecular ; Gene Library ; Genes, Fungal ; Genome ; Genome, Fungal ; Internet ; Magnaporthe/*genetics ; Mutation ; Open Reading Frames ; Proteome ; Sequence Analysis, DNA ; Sequence Homology ; *Software ; User-Computer Interface ; },
abstract = {BACKGROUND: Recent advances in sequencing techniques leading to cost reduction have resulted in the generation of a growing number of sequenced eukaryotic genomes. Computational tools greatly assist in defining open reading frames and assigning tentative annotations. However, gene functions cannot be asserted without biological support through, among other things, mutational analysis. In taking a genome-wide approach to functionally annotate an entire organism, in this application the approximately 11,000 predicted genes in the rice blast fungus (Magnaporthe grisea), an effective platform for tracking and storing both the biological materials created and the data produced across several participating institutions was required.<br><br>RESULTS: The platform designed, named PACLIMS, was built to support our high throughput pipeline for generating 50,000 random insertion mutants of Magnaporthe grisea. To be a useful tool for materials and data tracking and storage, PACLIMS was designed to be simple to use, modifiable to accommodate refinement of research protocols, and cost-efficient. Data entry into PACLIMS was simplified through the use of barcodes and scanners, thus reducing the potential human error, time constraints, and labor. This platform was designed in concert with our experimental protocol so that it leads the researchers through each step of the process from mutant generation through phenotypic assays, thus ensuring that every mutant produced is handled in an identical manner and all necessary data is captured.<br><br>CONCLUSION: Many sequenced eukaryotes have reached the point where computational analyses are no longer sufficient and require biological support for their predicted genes. Consequently, there is an increasing need for platforms that support high throughput genome-wide mutational analyses. While PACLIMS was designed specifically for this project, the source and ideas present in its implementation can be used as a model for other high throughput mutational endeavors.},
}
@article {pmid15815602,
year = {2005},
author = {Ebach, MC and Holdrege, C},
title = {DNA barcoding is no substitute for taxonomy.},
journal = {Nature},
volume = {434},
number = {7034},
pages = {697},
doi = {10.1038/434697b},
pmid = {15815602},
issn = {1476-4687},
mesh = {Animals ; *Biodiversity ; Classification/*methods ; DNA/*analysis/*genetics ; Electronic Data Processing/economics/methods/*trends ; Species Specificity ; Terminology as Topic ; Time Factors ; },
}
@article {pmid15771783,
year = {2005},
author = {Vences, M and Thomas, M and van der Meijden, A and Chiari, Y and Vieites, DR},
title = {Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians.},
journal = {Frontiers in zoology},
volume = {2},
number = {1},
pages = {5},
pmid = {15771783},
issn = {1742-9994},
abstract = {BACKGROUND: Identifying species of organisms by short sequences of DNA has been in the center of ongoing discussions under the terms DNA barcoding or DNA taxonomy. A C-terminal fragment of the mitochondrial gene for cytochrome oxidase subunit I (COI) has been proposed as universal marker for this purpose among animals. RESULTS: Herein we present experimental evidence that the mitochondrial 16S rRNA gene fulfills the requirements for a universal DNA barcoding marker in amphibians. In terms of universality of priming sites and identification of major vertebrate clades the studied 16S fragment is superior to COI. Amplification success was 100% for 16S in a subset of fresh and well-preserved samples of Madagascan frogs, while various combination of COI primers had lower success rates.COI priming sites showed high variability among amphibians both at the level of groups and closely related species, whereas 16S priming sites were highly conserved among vertebrates. Interspecific pairwise 16S divergences in a test group of Madagascan frogs were at a level suitable for assignment of larval stages to species (1-17%), with low degrees of pairwise haplotype divergence within populations (0-1%). CONCLUSION: We strongly advocate the use of 16S rRNA as standard DNA barcoding marker for vertebrates to complement COI, especially if samples a priori could belong to various phylogenetically distant taxa and false negatives would constitute a major problem.},
}
@article {pmid15731217,
year = {2005},
author = {Lambert, DM and Baker, A and Huynen, L and Haddrath, O and Hebert, PD and Millar, CD},
title = {Is a large-scale DNA-based inventory of ancient life possible?.},
journal = {The Journal of heredity},
volume = {96},
number = {3},
pages = {279-284},
doi = {10.1093/jhered/esi035},
pmid = {15731217},
issn = {0022-1503},
mesh = {Adaptation, Physiological ; Animals ; DNA, Mitochondrial/chemistry/*genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Geography ; Molecular Sequence Data ; New Zealand ; Palaeognathae/classification/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {A complete DNA-based inventory of the Earth's present biota using large-scale high-throughput DNA sequencing of signature region(s) (DNA barcoding) is an ambitious proposal rivaling the Human Genome Project. We examine whether this approach will also enable us to assess the past diversity of the earth's biota. To test this, we sequenced the 5' terminus of the mitochondrial cytochrome c oxidase I (COI) gene of individuals belonging to a group of extinct ratite birds, the moa of New Zealand. Moa comprised a large number of taxa that radiated in isolation on this oceanic landmass. Using a phylogenetic approach based on a large data set including protein coding and 12S DNA sequences as well as morphology, we now have precise information about the number of moa species that once existed. We show that each of the moa species detected using this extensive data set has a unique COI barcode(s) and that they all show low levels of within-species COI variation. Consequently, we conclude that COI sequences accurately identify the species discovered using the larger data set. Hence, more generally, this study suggests that DNA barcoding might also help us detect other extinct animal species and that a large-scale inventory of ancient life is possible.},
}
@article {pmid15710616,
year = {2005},
author = {Burden, AF and Manley, NC and Clark, AD and Gartler, SM and Laird, CD and Hansen, RS},
title = {Hemimethylation and non-CpG methylation levels in a promoter region of human LINE-1 (L1) repeated elements.},
journal = {The Journal of biological chemistry},
volume = {280},
number = {15},
pages = {14413-14419},
doi = {10.1074/jbc.M413836200},
pmid = {15710616},
issn = {0021-9258},
support = {GM 53805/GM/NIGMS NIH HHS/United States ; HD 02274/HD/NICHD NIH HHS/United States ; HD 16659/HD/NICHD NIH HHS/United States ; },
mesh = {Base Sequence ; *CpG Islands ; Cytosine/chemistry ; *DNA Methylation ; Evolution, Molecular ; Female ; Fibroblasts/metabolism ; Humans ; *Long Interspersed Nucleotide Elements ; Molecular Sequence Data ; Oligonucleotides, Antisense/chemistry ; Polymerase Chain Reaction ; Promoter Regions, Genetic ; Sequence Homology, Nucleic Acid ; Sulfites/metabolism/pharmacology ; },
abstract = {DNA methylation within the promoter region of human LINE1 (L1) transposable elements is important for maintaining transcriptional inactivation and for inhibiting L1 transposition. Determining methylation patterns on the complementary strands of repeated sequences is difficult using standard bisulfite methylation analysis. Evolutionary changes in each repeat and the variations between cells or alleles of the same repeat lead to a heterogeneous population of sequences. Potential sequence biases can arise during analyses that are different for the converted sense and antisense strands. These problems can be avoided with hairpin-bisulfite PCR, a double-stranded PCR method in which complementary strands of individual molecules are attached by a hairpin linker ligated to genomic DNA. Using human L1 elements to study methylation of repeated sequences, (i) we distinguish valid L1 sequences from redundant and contaminant sequences by applying the powerful new method of molecular barcodes, (ii) we resolve a controversy on the level of hemimethylation of L1 sequences in fetal fibroblasts in favor of relatively little hemimethylation, (iii) we report that human L1 sequences in different cell types also have primarily concordant CpG methylation patterns on complementary strands, and (iv) we provide evidence that non-CpG cytosines within the regions analyzed are rarely methylated.},
}
@article {pmid15666657,
year = {2004},
author = {Murphy, MF and Kay, JD},
title = {Barcode identification for transfusion safety.},
journal = {Current opinion in hematology},
volume = {11},
number = {5},
pages = {334-338},
doi = {10.1097/01.moh.0000142801.38087.e5},
pmid = {15666657},
issn = {1065-6251},
mesh = {Blood Transfusion/*standards ; Electronic Data Processing/instrumentation/*methods ; Humans ; Medical Errors/prevention &amp; control ; Point-of-Care Systems ; Risk Management ; Transfusion Reaction ; },
abstract = {PURPOSE OF REVIEW: Errors related to blood transfusion in hospitals may produce catastrophic consequences. This review addresses potential solutions to prevent patient misidentification including the use of new technology, such as barcoding.<br><br>RECENT FINDINGS: A small number of studies using new technology for the transfusion process in hospitals have shown promising results in preventing errors. The studies demonstrated improved transfusion safety and staff preference for new technology such as bedside handheld scanners to carry out pretransfusion bedside checking. They also highlighted the need for considerable efforts in the training of staff in the new procedures before their successful implementation.<br><br>SUMMARY: Improvements in hospital transfusion safety are a top priority for transfusion medicine, and will depend on a combined approach including a better understanding of the causes of errors, a reduction in the complexity of routine procedures taking advantage of new technology, improved staff training, and regular monitoring of practice. The use of new technology to improve the safety of transfusion is very promising. Further development of the systems is needed to enable staff to carry out bedside transfusion procedures quickly and accurately, and to increase their functionality to justify the cost of their wider implementation.},
}
@article {pmid15597554,
year = {2004},
author = {Nichols, JH and Bartholomew, C and Brunton, M and Cintron, C and Elliott, S and McGirr, J and Morsi, D and Scott, S and Seipel, J and Sinha, D},
title = {Reducing medical errors through barcoding at the point of care.},
journal = {Clinical leadership &amp; management review : the journal of CLMA},
volume = {18},
number = {6},
pages = {328-334},
pmid = {15597554},
issn = {1527-3954},
mesh = {Delivery of Health Care, Integrated/*organization &amp; administration ; Efficiency, Organizational ; *Electronic Data Processing ; Humans ; Laboratories/*organization &amp; administration ; Massachusetts ; Medical Errors/*prevention &amp; control ; Organizational Case Studies ; *Point-of-Care Systems ; },
abstract = {Medical errors are a major concern in health care today. Errors in point-of-care testing (POCT) are particularly problematic because the test is conducted by clinical operators at the site of patient care and immediate medical action is taken on the results prior to review by the laboratory. The Performance Improvement Program at Baystate Health System, Springfield, Massachusetts, noted a number of identification errors occurring with glucose and blood gas POCT devices. Incorrect patient account numbers that were attached to POCT results prevented the results from being transmitted to the patient's medical record and appropriately billed. In the worst case, they could lead to results being transferred to the wrong patient's chart and inappropriate medical treatment. Our first action was to lock-out operators who repeatedly made identification errors (3-Strike Rule), requiring operators to be counseled and retrained after their third error. The 3-Strike Rule significantly decreased our glucose meter errors (p = 0.014) but did not have an impact on the rate of our blood gas errors (p = 0.378). Neither device approached our ultimate goal of zero tolerance. A Failure Mode and Effects Analysis (FMEA) was conducted to determine the various processes that could lead to an identification error. A primary source of system failure was the manual entry of 14 digits for each test, five numbers for operator and nine numbers for patient account identification. Patient barcoding was implemented to automate the data entry process, and after an initial familiarization period, resulted in significant improvements in error rates for both the glucose (p = 0.0007) and blood gas devices (p = 0.048). Despite the improvements, error rates with barcoding still did not achieve zero errors. Operators continued to utilize manual data entry when the barcode scan was unsuccessful or unavailable, and some patients were found to have incorrect patient account numbers due to hospital transfer, multiple wristbands on a single patient, and selection of expired account numbers from previous hospitalizations when printing the barcoded wristbands. Barcoding can thus improve the incidence of identification errors, but hospitals need to take additional steps to ensure successful barcode scanning and to verify that patient wristbands contain correct information. Implementation of patient barcoding was successful in significantly reducing identification errors with POCT, improving patient care, and enhancing interdisciplinary communication.},
}
@article {pmid15525520,
year = {2004},
author = {Pan, X and Yuan, DS and Xiang, D and Wang, X and Sookhai-Mahadeo, S and Bader, JS and Hieter, P and Spencer, F and Boeke, JD},
title = {A robust toolkit for functional profiling of the yeast genome.},
journal = {Molecular cell},
volume = {16},
number = {3},
pages = {487-496},
doi = {10.1016/j.molcel.2004.09.035},
pmid = {15525520},
issn = {1097-2765},
support = {1F33HG002643-01A1/HG/NHGRI NIH HHS/United States ; CA16519/CA/NCI NIH HHS/United States ; HG2432/HG/NHGRI NIH HHS/United States ; },
mesh = {Gene Expression Profiling/methods ; Gene Expression Regulation, Fungal/*physiology ; *Genome, Fungal ; Internet ; Mutation/*physiology ; Oligonucleotide Array Sequence Analysis ; Phenotype ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/*physiology ; Transformation, Genetic ; },
abstract = {Study of mutant phenotypes is a fundamental method for understanding gene function. The construction of a near-complete collection of yeast knockouts (YKO) and the unique molecular barcodes (or TAGs) that identify each strain has enabled quantitative functional profiling of Saccharomyces cerevisiae. By using these TAGs and the SGA reporter, MFA1pr-HIS3, which facilitates conversion of heterozygous diploid YKO strains into haploid mutants, we have developed a set of highly efficient microarray-based techniques, collectively referred as dSLAM (diploid-based synthetic lethality analysis on microarrays), to probe genome-wide gene-chemical and gene-gene interactions. Direct comparison revealed that these techniques are more robust than existing methods in functional profiling of the yeast genome. Widespread application of these tools will elucidate a comprehensive yeast genetic network.},
}
@article {pmid15523731,
year = {2004},
author = {Brakmann, S},
title = {DNA-based barcodes, nanoparticles, and nanostructures for the ultrasensitive detection and quantification of proteins.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {43},
number = {43},
pages = {5730-5734},
doi = {10.1002/anie.200461112},
pmid = {15523731},
issn = {1433-7851},
mesh = {*Biosensing Techniques ; DNA/*chemistry/genetics ; Fluorescence Resonance Energy Transfer ; Fluorescent Dyes/chemistry ; Immunoassay ; Nanostructures/chemistry ; Nanotechnology/*methods ; Particle Size ; Proteins/*analysis ; Sensitivity and Specificity ; },
}
@article {pmid15497206,
year = {2004},
author = {Powers, T},
title = {Nematode molecular diagnostics: from bands to barcodes.},
journal = {Annual review of phytopathology},
volume = {42},
number = {},
pages = {367-383},
doi = {10.1146/annurev.phyto.42.040803.140348},
pmid = {15497206},
issn = {0066-4286},
mesh = {Animals ; Base Sequence ; *DNA, Helminth ; Molecular Sequence Data ; Nematoda/*classification/*genetics ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; },
abstract = {Nematodes are considered among the most difficult animals to identify. DNA-based diagnostic methods have already gained acceptance in applications ranging from quarantine determinations to assessments of biodiversity. Researchers are currently in an information-gathering mode, with intensive efforts applied to accumulating nucleotide sequence of 18S and 28S ribosomal genes, internally transcribed spacer regions, and mitochondrial genes. Important linkages with collateral data such as digitized images, video clips and specimen voucher web pages are being established on GenBank and NemATOL, the nematode-specific Tree of Life database. The growing DNA taxonomy of nematodes has lead to their use in testing specific short sequences of DNA as a "barcode" for the identification of all nematode species.},
}
@article {pmid15496917,
year = {2004},
author = {Halik, M and Klauk, H and Zschieschang, U and Schmid, G and Dehm, C and Schütz, M and Maisch, S and Effenberger, F and Brunnbauer, M and Stellacci, F},
title = {Low-voltage organic transistors with an amorphous molecular gate dielectric.},
journal = {Nature},
volume = {431},
number = {7011},
pages = {963-966},
doi = {10.1038/nature02987},
pmid = {15496917},
issn = {1476-4687},
abstract = {Organic thin film transistors (TFTs) are of interest for a variety of large-area electronic applications, such as displays, sensors and electronic barcodes. One of the key problems with existing organic TFTs is their large operating voltage, which often exceeds 20 V. This is due to poor capacitive coupling through relatively thick gate dielectric layers: these dielectrics are usually either inorganic oxides or nitrides, or insulating polymers, and are often thicker than 100 nm to minimize gate leakage currents. Here we demonstrate a manufacturing process for TFTs with a 2.5-nm-thick molecular self-assembled monolayer (SAM) gate dielectric and a high-mobility organic semiconductor (pentacene). These TFTs operate with supply voltages of less than 2 V, yet have gate currents that are lower than those of advanced silicon field-effect transistors with SiO2 dielectrics. These results should therefore increase the prospects of using organic TFTs in low-power applications (such as portable devices). Moreover, molecular SAMs may even be of interest for advanced silicon transistors where the continued reduction in dielectric thickness leads to ever greater gate leakage and power dissipation.},
}
@article {pmid15487048,
year = {2004},
author = {Finkel, NH and Lou, X and Wang, C and He, L},
title = {Barcoding the microworld.},
journal = {Analytical chemistry},
volume = {76},
number = {19},
pages = {352A-359A},
doi = {10.1021/ac0416463},
pmid = {15487048},
issn = {0003-2700},
}
@article {pmid15486587,
year = {2004},
author = {Moritz, C and Cicero, C},
title = {DNA barcoding: promise and pitfalls.},
journal = {PLoS biology},
volume = {2},
number = {10},
pages = {e354},
pmid = {15486587},
issn = {1545-7885},
mesh = {Animals ; Birds/*genetics ; Computational Biology/*methods ; DNA/genetics ; DNA, Mitochondrial ; Electronic Data Processing ; Evolution, Molecular ; Gene Library ; Oligonucleotide Array Sequence Analysis ; Sequence Analysis, DNA ; Species Specificity ; },
}
@article {pmid15465915,
year = {2004},
author = {Hebert, PD and Penton, EH and Burns, JM and Janzen, DH and Hallwachs, W},
title = {Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {101},
number = {41},
pages = {14812-14817},
pmid = {15465915},
issn = {0027-8424},
mesh = {Animal Feed ; Animals ; Base Sequence ; Butterflies/*classification/*genetics/growth &amp; development ; DNA Primers ; Molecular Sequence Data ; *Phylogeny ; Plants ; Species Specificity ; Tropical Climate ; },
abstract = {Astraptes fulgerator, first described in 1775, is a common and widely distributed neotropical skipper butterfly (Lepidoptera: Hesperiidae). We combine 25 years of natural history observations in northwestern Costa Rica with morphological study and DNA barcoding of museum specimens to show that A. fulgerator is a complex of at least 10 species in this region. Largely sympatric, these taxa have mostly different caterpillar food plants, mostly distinctive caterpillars, and somewhat different ecosystem preferences but only subtly differing adults with no genitalic divergence. Our results add to the evidence that cryptic species are prevalent in tropical regions, a critical issue in efforts to document global species richness. They also illustrate the value of DNA barcoding, especially when coupled with traditional taxonomic tools, in disclosing hidden diversity.},
}
@article {pmid15459281,
year = {2004},
author = {Miner, BE and Stöger, RJ and Burden, AF and Laird, CD and Hansen, RS},
title = {Molecular barcodes detect redundancy and contamination in hairpin-bisulfite PCR.},
journal = {Nucleic acids research},
volume = {32},
number = {17},
pages = {e135},
pmid = {15459281},
issn = {1362-4962},
support = {R01 GM053805/GM/NIGMS NIH HHS/United States ; P30 HD002274/HD/NICHD NIH HHS/United States ; HD 02274/HD/NICHD NIH HHS/United States ; R01 HD016659/HD/NICHD NIH HHS/United States ; HD 16659/HD/NICHD NIH HHS/United States ; GM 53805/GM/NIGMS NIH HHS/United States ; },
mesh = {Base Sequence ; Fragile X Mental Retardation Protein ; Genome, Human ; Humans ; Male ; Molecular Sequence Data ; Nerve Tissue Proteins/genetics ; Polymerase Chain Reaction/*methods ; Promoter Regions, Genetic ; RNA-Binding Proteins/genetics ; Sequence Analysis, DNA/*methods ; Sulfites/*chemistry ; Templates, Genetic ; },
abstract = {PCR amplification of limited amounts of DNA template carries an increased risk of product redundancy and contamination. We use molecular barcoding to label each genomic DNA template with an individual sequence tag prior to PCR amplification. In addition, we include molecular 'batch-stamps' that effectively label each genomic template with a sample ID and analysis date. This highly sensitive method identifies redundant and contaminant sequences and serves as a reliable method for positive identification of desired sequences; we can therefore capture accurately the genomic template diversity in the sample analyzed. Although our application described here involves the use of hairpin-bisulfite PCR for amplification of double-stranded DNA, the method can readily be adapted to single-strand PCR. Useful applications will include analyses of limited template DNA for biomedical, ancient DNA and forensic purposes.},
}
@article {pmid15455034,
year = {2004},
author = {Hebert, PD and Stoeckle, MY and Zemlak, TS and Francis, CM},
title = {Identification of Birds through DNA Barcodes.},
journal = {PLoS biology},
volume = {2},
number = {10},
pages = {e312},
pmid = {15455034},
issn = {1545-7885},
mesh = {Animals ; Birds/*genetics ; Computational Biology/*methods ; Cytochromes b/genetics ; DNA/genetics ; DNA, Mitochondrial ; Electron Transport Complex IV/genetics ; Electronic Data Processing ; Evolution, Molecular ; Gene Library ; *Genetic Techniques ; Genetic Variation ; Models, Genetic ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Short DNA sequences from a standardized region of the genome provide a DNA barcode for identifying species. Compiling a public library of DNA barcodes linked to named specimens could provide a new master key for identifying species, one whose power will rise with increased taxon coverage and with faster, cheaper sequencing. Recent work suggests that sequence diversity in a 648-bp region of the mitochondrial gene, cytochrome c oxidase I (COI), might serve as a DNA barcode for the identification of animal species. This study tested the effectiveness of a COI barcode in discriminating bird species, one of the largest and best-studied vertebrate groups. We determined COI barcodes for 260 species of North American birds and found that distinguishing species was generally straightforward. All species had a different COI barcode(s), and the differences between closely related species were, on average, 18 times higher than the differences within species. Our results identified four probable new species of North American birds, suggesting that a global survey will lead to the recognition of many additional bird species. The finding of large COI sequence differences between, as compared to small differences within, species confirms the effectiveness of COI barcodes for the identification of bird species. This result plus those from other groups of animals imply that a standard screening threshold of sequence difference (10x average intraspecific difference) could speed the discovery of new animal species. The growing evidence for the effectiveness of DNA barcodes as a basis for species identification supports an international exercise that has recently begun to assemble a comprehensive library of COI sequences linked to named specimens.},
}
@article {pmid15380682,
year = {2004},
author = {Whiteman, NK and Santiago-Alarcon, D and Johnson, KP and Parker, PG},
title = {Differences in straggling rates between two genera of dove lice (Insecta: Phthiraptera) reinforce population genetic and cophylogenetic patterns.},
journal = {International journal for parasitology},
volume = {34},
number = {10},
pages = {1113-1119},
doi = {10.1016/j.ijpara.2004.06.003},
pmid = {15380682},
issn = {0020-7519},
mesh = {Animals ; Base Sequence ; *Biological Evolution ; Birds/*parasitology ; Ecuador ; Host-Parasite Interactions ; Molecular Sequence Data ; Phthiraptera/classification/*genetics ; Phylogeny ; Predatory Behavior ; },
abstract = {Differences in dispersal abilities have been implicated for causing disparate evolutionary patterns between Columbicola and Physconelloides lice (Insecta: Phthiraptera). However, no study has documented straggling (when lice are found on atypical hosts) rates within these lineages. We used the fact that the Galapagos Hawk, Buteo galapagoensis (Gould) (Falconiformes) feeds on the Galapagos Dove Zenaida galapagoensis Gould (Columbiformes) within an ecologically simplified setting. The Galapagos Dove is the only typical host of Columbicola macrourae (Wilson) and Physconelloides galapagensis (Kellogg and Huwana) in Galapagos. We quantitatively sampled and found these lice on both bird species. A DNA barcoding approach confirmed that stragglers were derived from Galapagos doves. We also collected a Bovicola sp. louse, likely originating from a goat (Capra hircus). On hawks, C. macrourae was significantly more prevalent than P. galapagensis. On doves, the two lice were equally prevalent and abundant. Differences in prevalence on hawks was a function of differences in straggling rate between lice, and not a reflection of their relative representation within the dove population. This provides further evidence that differences in dispersal abilities may drive differences in the degree of cospeciation in Columbicola and Phyconelloides lice, which have become model systems in evolutionary biology.},
}
@article {pmid15270396,
year = {2004},
author = {Becker, C},
title = {A new game of leapfrog? RFID is rapidly changing the product-tracking process. Some say the technology--once costs drop--could displace bar-coding.},
journal = {Modern healthcare},
volume = {34},
number = {28},
pages = {38, 40},
pmid = {15270396},
issn = {0160-7480},
mesh = {*Electronic Data Processing ; Equipment and Supplies, Hospital/classification ; Hospital Information Systems/*trends ; Patient Identification Systems/methods ; Point-of-Care Systems/*trends ; *Radio Waves ; United States ; },
}
@article {pmid15258289,
year = {2004},
author = {Eason, RG and Pourmand, N and Tongprasit, W and Herman, ZS and Anthony, K and Jejelowo, O and Davis, RW and Stolc, V},
title = {Characterization of synthetic DNA bar codes in Saccharomyces cerevisiae gene-deletion strains.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {101},
number = {30},
pages = {11046-11051},
pmid = {15258289},
issn = {0027-8424},
support = {P01 HG000205/HG/NHGRI NIH HHS/United States ; 5PO1HG00205/HG/NHGRI NIH HHS/United States ; },
mesh = {DNA Primers ; DNA, Fungal/chemical synthesis/chemistry/*genetics ; Gene Deletion ; Genes, Fungal/genetics ; Mutation ; Nucleic Acid Hybridization ; Polymerase Chain Reaction ; Saccharomyces cerevisiae/*genetics ; },
abstract = {Incorporation of strain-specific synthetic DNA tags into yeast Saccharomyces cerevisiae gene-deletion strains has enabled identification of gene functions by massively parallel growth rate analysis. However, it is important to confirm the sequences of these tags, because mutations introduced during construction could lead to significant errors in hybridization performance. To validate this experimental system, we sequenced 11,812 synthetic 20-mer molecular bar codes and adjacent sequences (>1.8 megabases synthetic DNA) by pyrosequencing and Sanger methods. At least 31% of the genome-integrated 20-mer tags contain differences from those originally synthesized. However, these mutations result in anomalous hybridization in only a small subset of strains, and the sequence information enables redesign of hybridization probes for arrays. The robust performance of the yeast gene-deletion dual oligonucleotide bar-code design in array hybridization validates the use of molecular bar codes in living cells for tracking their growth phenotype.},
}
@article {pmid15253352,
year = {2004},
author = {Blaxter, ML},
title = {The promise of a DNA taxonomy.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {359},
number = {1444},
pages = {669-679},
pmid = {15253352},
issn = {0962-8436},
mesh = {Base Sequence/genetics ; Classification/*methods ; Computational Biology/*methods ; DNA/*classification ; *Electronic Data Processing ; Phylogeny ; Species Specificity ; },
abstract = {Not only is the number of described species a very small proportion of the estimated extant number of taxa, but it also appears that all concepts of the extent and boundaries of 'species' fail in many cases. Using conserved molecular sequences it is possible to define and diagnose molecular operational taxonomic units (MOTU) that have a similar extent to traditional 'species'. Use of a MOTU system not only allows the rapid and effective identification of most taxa, including those not encountered before, but also allows investigation of the evolution of patterns of diversity. A MOTU approach is not without problems, particularly in the area of deciding what level of molecular difference defines a biologically relevant taxon, but has many benefits. Molecular data are extremely well suited to re-analysis and meta-analysis, and data from multiple independent studies can be readily collated and investigated by using new parameters and assumptions. Previous molecular taxonomic efforts have focused narrowly. Advances in high-throughput sequencing methodologies, however, place the idea of a universal, multi-locus molecular barcoding system in the realm of the possible.},
}
@article {pmid15198249,
year = {2004},
author = {Irita, K and Tsuzaki, K and Sawa, T and Sanuki, M and Makita, K and Kobayashi, Y and Oomura, A and Kawashima, Y and Iwao, Y and Seo, N and Morita, K and Obara, H and , },
title = {[Critical incidents due to drug administration error in the operating room: an analysis of 4,291,925 anesthetics over a 4 year period].},
journal = {Masui. The Japanese journal of anesthesiology},
volume = {53},
number = {5},
pages = {577-584},
pmid = {15198249},
issn = {0021-4892},
mesh = {Anesthetics/administration &amp; dosage/*adverse effects ; Drug Overdose/epidemiology ; Heart Arrest/epidemiology ; Humans ; Incidence ; Japan/epidemiology ; Medication Errors/prevention &amp; control/*statistics &amp; numerical data ; Operating Rooms/*statistics &amp; numerical data ; Safety Management/statistics &amp; numerical data ; },
abstract = {BACKGROUND: Wrong drugs, overdose of drugs, and incorrect administration route remain unsolved problems in anesthetic practice. We determined the incidence and outcome of drug administration error in the operating room of Japanese Society of Anesthesiologists Certified Training Hospitals.<br><br>METHODS: Data were obtained from annual surveys conducted by Japanese Society of Anesthesiologists between 1999 and 2002. There were 4,291,925 cases of anesthetic delivery for this analysis.<br><br>RESULTS: Incidence of critical incidents due to drug administration error was 18.27/100,000 anesthetics. Cardiac arrest occurred in 2.21 patients per 100,000 anesthetics. Causes of these critical incidents were as follows: overdose or selection error involving non-anesthetic drugs, 42.1%; overdose of anesthetics, 28.7%; inadvertent high spinal anesthesia, 17.9%; local anesthetic intoxication, 6.4%; ampule or syringe swap, 4.3%; blood mismatch, 0.6%. Incidence of death following these incidents was 0.44/100,000. Causes of death were as follows: overdose or selection error involving non-anesthetic drugs, 47.4%; overdose of anesthetics, 26.3%; inadvertent high spinal anesthesia, 15.8%; local anesthetic intoxication, 5.3%. Ampule or syringe swap did not lead to any fatalities. Death following inadvertent high spinal anesthesia and local anesthetic intoxication was reported only in patients who had developed cardiac arrest. It should be noted that 88 percent of ampule or syringe swap occurred in patients with American Society of Anesthesiologists-Physical Status 1 or 2, who did not seem to require complex anesthetic management.<br><br>CONCLUSIONS: We should increase awareness that drug administration is generally performed with limited objective monitoring, although "To error is human". Increased vigilance is required to avoid drug administration error in the operating room. Additional anesthesia resident education, adequate supervision, and improved organization are necessary. Bar-coding technology might be useful in preventing drug administration error.},
}
@article {pmid15184745,
year = {2004},
author = {Dohnalek, LJ and Cusaac, L and Westcott, J and Langeberg, A and Sandler, SG},
title = {The code to safer transfusions.},
journal = {Nursing management},
volume = {35},
number = {6},
pages = {33-36},
doi = {10.1097/00006247-200406000-00011},
pmid = {15184745},
issn = {0744-6314},
mesh = {Blood Transfusion/*standards ; District of Columbia ; *Electronic Data Processing ; Hospitals, University ; Humans ; Medical Errors/*prevention &amp; control ; *Point-of-Care Systems ; Software ; },
abstract = {A university hospital shares its experience using bedside bar-coding technology.},
}
@article {pmid15083714,
year = {2004},
author = {Foley, SL and Simjee, S and Meng, J and White, DG and McDermott, PF and Zhao, S},
title = {Evaluation of molecular typing methods for Escherichia coli O157:H7 isolates from cattle, food, and humans.},
journal = {Journal of food protection},
volume = {67},
number = {4},
pages = {651-657},
doi = {10.4315/0362-028x-67.4.651},
pmid = {15083714},
issn = {0362-028X},
mesh = {Animals ; *Bacterial Typing Techniques ; Cattle ; DNA, Bacterial/analysis ; Electrophoresis, Gel, Pulsed-Field/methods ; Escherichia coli O157/*classification/isolation &amp; purification ; *Food Microbiology ; Humans ; Phylogeny ; Polymerase Chain Reaction/methods ; Sequence Homology, Nucleic Acid ; Virulence/genetics ; },
abstract = {Escherichia coli O157:H7, a Shiga toxin-producing E. coli, has been the causative agent of many cases of severe, often life-threatening foodborne illness. Because of the importance of E. coli O157:H7 to public health, many molecular typing methods have been developed to determine its transmission routes and source of infection during epidemiological investigations. Pulsed-field gel electrophoresis (PFGE) is currently used by public health organizations to track infections of E. coli O157:H7 and other foodborne pathogens. In this study, we compared the ability of PFGE, multilocus sequence typing (MLST), and repetitive-element PCR (Rep-PCR) to distinguish among 92 E. coli O157:H7 isolates from cattle, food, and infected humans. Several virulence genes, including the intimin gene (eaeA), the hemolysin gene (hlyA), and the H7 fimbrial gene (fliC), and a housekeeping gene for beta-glucuronidase (uidA) were included in MLST. Rep-PCR reactions were performed using a commercially available typing kit (Bacterial Barcodes Inc., Houston, Tex.) with the provided Uprime-RI primer set. Results of the study indicated that PFGE provided the most discrimination among the techniques, identifying 72 distinct PFGE profiles for the isolates; Rep-PCR elucidated 14 different profiles, whereas MLST generated five profiles. Additionally, there did not appear to be any correlation among the typing methods examined in this study. Therefore, to date, PFGE remains the technique of choice for molecular subtyping of E. coli O157:H7.},
}
@article {pmid15051536,
year = {2004},
author = {Mattheakis, LC and Dias, JM and Choi, YJ and Gong, J and Bruchez, MP and Liu, J and Wang, E},
title = {Optical coding of mammalian cells using semiconductor quantum dots.},
journal = {Analytical biochemistry},
volume = {327},
number = {2},
pages = {200-208},
doi = {10.1016/j.ab.2004.01.031},
pmid = {15051536},
issn = {0003-2697},
mesh = {Animals ; Biological Assay/*methods ; CHO Cells ; Calcium/metabolism ; Cricetinae ; Cricetulus ; Cysteamine/analogs &amp; derivatives ; Drug Evaluation, Preclinical/*methods ; Flow Cytometry ; Isoproterenol/pharmacology ; *Microscopy, Fluorescence ; Oligopeptides/chemistry/metabolism ; Peptides ; Protein Sorting Signals ; *Quantum Dots ; Receptor, Muscarinic M1/metabolism ; Receptor, Serotonin, 5-HT2A/metabolism ; Receptor, Serotonin, 5-HT2B/metabolism ; Receptors, G-Protein-Coupled/metabolism ; Semiconductors ; },
abstract = {Cell-based assays are widely used to screen compounds and study complex phenotypes. Few methods exist, however, for multiplexing cellular assays or labeling individual cells in a mixed cell population. We developed a generic encoding method for cells that is based on peptide-mediated delivery of quantum dots (QDs) into live cells. The QDs are nontoxic and photostable and can be imaged using conventional fluorescence microscopy or flow cytometry systems. We created unique fluorescent codes for a variety of mammalian cell types and show that our encoding method has the potential to create > 100 codes. We demonstrate that QD cell codes are compatible with most types of compound screening assays including immunostaining, competition binding, reporter gene, receptor internalization, and intracellular calcium release. A multiplexed calcium assay for G-protein-coupled receptors using QDs is demonstrated. The ability to spectrally encode individual cells with unique fluorescent barcodes should open new opportunities in multiplexed assay development and greatly facilitate the study of cell/cell interactions and other complex phenotypes in mixed cell populations.},
}
@article {pmid15042092,
year = {2004},
author = {Berns, K and Hijmans, EM and Mullenders, J and Brummelkamp, TR and Velds, A and Heimerikx, M and Kerkhoven, RM and Madiredjo, M and Nijkamp, W and Weigelt, B and Agami, R and Ge, W and Cavet, G and Linsley, PS and Beijersbergen, RL and Bernards, R},
title = {A large-scale RNAi screen in human cells identifies new components of the p53 pathway.},
journal = {Nature},
volume = {428},
number = {6981},
pages = {431-437},
doi = {10.1038/nature02371},
pmid = {15042092},
issn = {1476-4687},
mesh = {Cell Division ; Cell Line, Tumor ; Cloning, Molecular ; Cyclin-Dependent Kinase Inhibitor p16 ; Cyclin-Dependent Kinase Inhibitor p21 ; Cyclins/genetics/metabolism ; Down-Regulation ; Fibroblasts ; *Gene Library ; Genetic Vectors/genetics ; Humans ; *RNA Interference ; RNA, Small Interfering/genetics/metabolism ; Reproducibility of Results ; Retroviridae/genetics ; Tumor Suppressor Protein p14ARF/metabolism ; Tumor Suppressor Protein p53/genetics/*metabolism ; },
abstract = {RNA interference (RNAi) is a powerful new tool with which to perform loss-of-function genetic screens in lower organisms and can greatly facilitate the identification of components of cellular signalling pathways. In mammalian cells, such screens have been hampered by a lack of suitable tools that can be used on a large scale. We and others have recently developed expression vectors to direct the synthesis of short hairpin RNAs (shRNAs) that act as short interfering RNA (siRNA)-like molecules to stably suppress gene expression. Here we report the construction of a set of retroviral vectors encoding 23,742 distinct shRNAs, which target 7,914 different human genes for suppression. We use this RNAi library in human cells to identify one known and five new modulators of p53-dependent proliferation arrest. Suppression of these genes confers resistance to both p53-dependent and p19ARF-dependent proliferation arrest, and abolishes a DNA-damage-induced G1 cell-cycle arrest. Furthermore, we describe siRNA bar-code screens to rapidly identify individual siRNA vectors associated with a specific phenotype. These new tools will greatly facilitate large-scale loss-of-function genetic screens in mammalian cells.},
}
@article {pmid14996224,
year = {2004},
author = {Valárik, M and Bartos, J and Kovárová, P and Kubaláková, M and de Jong, JH and Dolezel, J},
title = {High-resolution FISH on super-stretched flow-sorted plant chromosomes.},
journal = {The Plant journal : for cell and molecular biology},
volume = {37},
number = {6},
pages = {940-950},
doi = {10.1111/j.1365-313x.2003.02010.x},
pmid = {14996224},
issn = {0960-7412},
mesh = {Chromosomes, Artificial, Bacterial/genetics ; Chromosomes, Plant/*genetics ; Cicer/genetics ; Flow Cytometry ; Hordeum/genetics ; In Situ Hybridization, Fluorescence/*methods/statistics &amp; numerical data ; Plants/*genetics ; Secale/genetics ; Sensitivity and Specificity ; Triticum/genetics ; },
abstract = {A novel high-resolution fluorescence in situ hybridisation (FISH) strategy, using super-stretched flow-sorted plant chromosomes as targets, is described. The technique that allows longitudinal extension of chromosomes of more than 100 times their original metaphase size is especially attractive for plant species with large chromosomes, whose pachytene chromosomes are generally too long and heterochromatin patterns too complex for FISH analysis. The protocol involves flow cytometric sorting of metaphase chromosomes, mild proteinase-K digestion of air-dried chromosomes on microscopic slides, followed by stretching with ethanol:acetic acid (3 : 1). Stretching ratios were assessed in a number of FISH experiments with super-stretched chromosomes from barley, wheat, rye and chickpea, hybridised with 45S and 5S ribosomal DNAs and the [GAA]n microsatellite, the [TTTAGGG]n telomeric repeat and a bacterial artificial chromosome (BAC) clone as probes. FISH signals on stretched chromosomes were brighter than those on the untreated control, resulting from better accessibility of the stretched chromatin and maximum observed sensitivity of 1 kbp. Spatial resolution of neighbouring loci was improved down to 70 kbp as compared to 5-10 Mbp after FISH on mitotic chromosomes, revealing details of adjacent DNA sequences hitherto not obtained with any other method. Stretched chromosomes are advantageous over extended DNA fibres from interphase nuclei as targets for FISH studies because they still retain chromosomal integrity. Although the method is confined to species for which chromosome flow sorting has been developed, it provides a unique system for controlling stretching degree of mitotic chromosomes and high-resolution bar-code FISH.},
}
@article {pmid14717890,
year = {2004},
author = {Thalmann, O and Hebler, J and Poinar, HN and Pääbo, S and Vigilant, L},
title = {Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes.},
journal = {Molecular ecology},
volume = {13},
number = {2},
pages = {321-335},
doi = {10.1046/j.1365-294x.2003.02070.x},
pmid = {14717890},
issn = {0962-1083},
mesh = {Animals ; Base Sequence ; Cluster Analysis ; DNA Primers ; DNA, Mitochondrial/genetics ; Gene Order ; *Genetic Variation ; Hominidae/*genetics ; Humans ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; *Research Design ; Sequence Analysis, DNA ; Translocation, Genetic/*genetics ; },
abstract = {Analysis of mitochondrial DNA sequence variation has been used extensively to study the evolutionary relationships of individuals and populations, both within and across species. So ubiquitous and easily acquired are mtDNA data that it has been suggested that such data could serve as a taxonomic 'barcode' for an objective species classification scheme. However, there are technical pitfalls associated with the acquisition of mtDNA data. One problem is the presence of translocated pieces of mtDNA in the nuclear genome of many taxa that may be mistaken for authentic organellar mtDNA. We assessed the extent to which such 'numt' sequences may pose an overlooked problem in analyses of mtDNA from humans and apes. Using long-range polymerase chain reaction (PCR), we generated necessarily authentic mtDNA sequences for comparison with sequences obtained using typical methods for a segment of the mtDNA control region in humans, chimpanzees, bonobos, gorillas and orangutans. Results revealed that gorillas are notable for having such a variety of numt sequences bearing high similarity to authentic mtDNA that any analysis of mtDNA using standard approaches is rendered impossible. Studies on humans, chimpanzees, bonobos or orangutans are apparently less problematic. One implication is that explicit measures need to be taken to authenticate mtDNA sequences in newly studied taxa or when any irregularities arise. Furthermore, some taxa may not be amenable to analysis of mtDNA variation at all.},
}
@article {pmid19471520,
year = {2004},
author = {Chang, S and Zhou, M and Grover, C},
title = {Information coding and retrieving using fluorescent semiconductor nanocrystals for object identification.},
journal = {Optics express},
volume = {12},
number = {1},
pages = {143-148},
doi = {10.1364/opex.12.000143},
pmid = {19471520},
issn = {1094-4087},
abstract = {The spectral features, i.e., wavelength and intensity, of fluorescence generated from semiconductor nanocrystals (quantum dots) can be used for coding information. Unlike the 1-D and 2-D barcodes, the information carrier is applied to a very small area and hardly visible. The information retrieving by a fluorospectrometer is not subjected to the changes of rotation and scale. A de-convolution-based algorithm is used to separate the overlapped spectral profiles. This technology can be applied to small products labeling, document security and object identification.},
}
@article {pmid14650978,
year = {2003},
author = {},
title = {Scanning medication barcodes improves accuracy at Lehigh Valley Hospital.},
journal = {Performance improvement advisor},
volume = {7},
number = {10},
pages = {132-4, 129},
pmid = {14650978},
issn = {1543-6160},
mesh = {Clinical Pharmacy Information Systems ; *Electronic Data Processing ; Hospitals, Community/*organization &amp; administration ; Humans ; Medication Errors/*prevention &amp; control ; Medication Systems, Hospital/*organization &amp; administration ; Pennsylvania ; Safety Management ; Systems Integration ; },
abstract = {Performance improvement often means doing tasks faster, but it can also involve increasing the accuracy of a health care process and reducing error rates. At Lehigh Valley Hospital in Allentown, PA, the implementation of a wireless barcode scanning system has increased the accuracy of nurses giving medications to patients, even though it has slowed them down a bit.},
}
@article {pmid14642760,
year = {2003},
author = {Besansky, NJ and Severson, DW and Ferdig, MT},
title = {DNA barcoding of parasites and invertebrate disease vectors: what you don't know can hurt you.},
journal = {Trends in parasitology},
volume = {19},
number = {12},
pages = {545-546},
doi = {10.1016/j.pt.2003.09.015},
pmid = {14642760},
issn = {1471-4922},
mesh = {Animals ; DNA/*analysis ; Disease Vectors ; *Genetic Variation ; Host-Parasite Interactions ; Parasites/*classification/*genetics ; Parasitic Diseases/*diagnosis ; Phylogeny ; },
}
@article {pmid14626532,
year = {2003},
author = {Vaida, A and Kercher, L},
title = {Practical tools for medication safety in acute care.},
journal = {Journal of the American Pharmacists Association : JAPhA},
volume = {43},
number = {5 Suppl 1},
pages = {S48-9},
doi = {10.1331/154434503322612465},
pmid = {14626532},
issn = {1544-3191},
mesh = {Critical Pathways/*organization &amp; administration ; Electronic Data Processing/organization &amp; administration ; *Hospital Administration ; Hospitals/standards ; Medication Errors/*prevention &amp; control ; },
abstract = {Identifying goals in the areas of institutional culture, infrastructure, clinical practice, and technology in hospitals minimizes the risk of medication errors among inpatients. As part of the Pathways for Medication Safety project, a model strategic plan provides seven goals for hospitals to consider in their medication safety efforts. A view of risk assessment from individual health care practitioners can aid a team effort to decease medication errors. Preparing for point-of-care bar-coding for medications will help easy implementation of this new technology. Pathways for Medication Safety provides a toolbox with useful methods and techniques for acute care settings.},
}
@article {pmid14574181,
year = {2003},
author = {Heinen, MG and Coyle, GA and Hamilton, AV},
title = {Barcoding makes its mark on daily practice.},
journal = {Nursing management},
volume = {Suppl},
number = {},
pages = {18-20},
pmid = {14574181},
issn = {0744-6314},
mesh = {Electronic Data Processing/*organization &amp; administration ; Hospitals, Veterans ; Humans ; Medication Errors/*prevention &amp; control ; Medication Systems, Hospital/*organization &amp; administration ; Nurse's Role ; Patient Identification Systems/*organization &amp; administration ; Safety Management/organization &amp; administration ; United States ; United States Department of Veterans Affairs ; United States Food and Drug Administration ; },
}
@article {pmid12967766,
year = {2003},
author = {Giaever, G},
title = {A chemical genomics approach to understanding drug action.},
journal = {Trends in pharmacological sciences},
volume = {24},
number = {9},
pages = {444-446},
doi = {10.1016/S0165-6147(03)00225-6},
pmid = {12967766},
issn = {0165-6147},
mesh = {Drug Evaluation, Preclinical ; *Genomics ; Pharmacology/*trends ; },
abstract = {The complete collection of yeast deletion strains represents a unique, living biological computer for understanding gene function. The molecular 'barcodes' present in each of the deletion strains allow a quantitative ranking of the importance of any gene under any experimental condition of choice. In this article, some of the recent results generated from experiments that exploit the yeast deletion collection to understand mechanisms of drug action are discussed.},
}
@article {pmid12952648,
year = {2003},
author = {Hebert, PD and Ratnasingham, S and deWaard, JR},
title = {Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species.},
journal = {Proceedings. Biological sciences},
volume = {270 Suppl 1},
number = {Suppl 1},
pages = {S96-9},
pmid = {12952648},
issn = {0962-8452},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; *Genetic Variation ; Protein Subunits/genetics ; Reproducibility of Results ; Sensitivity and Specificity ; Species Specificity ; },
abstract = {With millions of species and their life-stage transformations, the animal kingdom provides a challenging target for taxonomy. Recent work has suggested that a DNA-based identification system, founded on the mitochondrial gene, cytochrome c oxidase subunit 1 (COI), can aid the resolution of this diversity. While past work has validated the ability of COI sequences to diagnose species in certain taxonomic groups, the present study extends these analyses across the animal kingdom. The results indicate that sequence divergences at COI regularly enable the discrimination of closely allied species in all animal phyla except the Cnidaria. This success in species diagnosis reflects both the high rates of sequence change at COI in most animal groups and constraints on intraspecific mitochondrial DNA divergence arising, at least in part, through selective sweeps mediated via interactions with the nuclear genome.},
}
@article {pmid12940737,
year = {2003},
author = {Fenniri, H and Chun, S and Ding, L and Zyrianov, Y and Hallenga, K},
title = {Preparation, physical properties, on-bead binding assay and spectroscopic reliability of 25 barcoded polystyrene-poly(ethylene glycol) graft copolymers.},
journal = {Journal of the American Chemical Society},
volume = {125},
number = {35},
pages = {10546-10560},
doi = {10.1021/ja035665q},
pmid = {12940737},
issn = {0002-7863},
abstract = {Here we describe the preparation of 25 beaded polystyrene-poly(ethylene glycol) graft copolymers from six spectroscopically active styrene monomers: styrene, 2,5-dimethylstyrene, 4-methylstyrene, 2,4-dimethylstyrene, 4-tert-butylstyrene, and 3-methylstyrene. These polymers were thoroughly characterized by Raman, infrared, and (1)H/(13)C NMR spectroscopies, and differential scanning calorimetry. Determination of the swelling properties, peptide synthesis, and on-bead streptavidin-alkaline phosphatase (SAP) binding assay further established that their physical and chemical properties where not significantly altered by the diversity of their encoded polystyrene core. Each of the 25 resins displayed a unique Raman and infrared vibrational fingerprint, which was converted into a "spectroscopic barcode". The position of each bar matches the peak wavenumber in the corresponding spectrum but is independent of its intensity. From this simplified representation similarity maps comparing 35 000 resin pairs were generated to establish the spectroscopic barcoding as a reliable encoding methodology. In effect, in 99% of the cases, the highest similarity coefficients were obtained for resin pairs prepared from the same styrene derivatives even after SAP binding assay. We have also shown that a small but unique combination of a resin's vibrations (30-40%) is sufficient for its identification. However, in rare cases where a resin's vibrational signature has been severely compromised, both the Raman and infrared barcodes were synergistically and reliably utilized to unequivocally identify its chemical make up.},
}
@article {pmid12821776,
year = {2003},
author = {Yan, H and LaBean, TH and Feng, L and Reif, JH},
title = {Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {100},
number = {14},
pages = {8103-8108},
pmid = {12821776},
issn = {0027-8424},
mesh = {Base Sequence ; *Computers, Molecular ; DNA/chemical synthesis/*chemistry/ultrastructure ; Electronic Data Processing ; Microscopy, Atomic Force ; Nanotechnology/*methods ; Nucleic Acid Conformation ; },
abstract = {The programmed self-assembly of patterned aperiodic molecular structures is a major challenge in nanotechnology and has numerous potential applications for nanofabrication of complex structures and useful devices. Here we report the construction of an aperiodic patterned DNA lattice (barcode lattice) by a self-assembly process of directed nucleation of DNA tiles around a scaffold DNA strand. The input DNA scaffold strand, constructed by ligation of shorter synthetic oligonucleotides, provides layers of the DNA lattice with barcode patterning information represented by the presence or absence of DNA hairpin loops protruding out of the lattice plane. Self-assembly of multiple DNA tiles around the scaffold strand was shown to result in a patterned lattice containing barcode information of 01101. We have also demonstrated the reprogramming of the system to another patterning. An inverted barcode pattern of 10010 was achieved by modifying the scaffold strands and one of the strands composing each tile. A ribbon lattice, consisting of repetitions of the barcode pattern with expected periodicity, was also constructed by the addition of sticky ends. The patterning of both classes of lattices was clearly observable via atomic force microscopy. These results represent a step toward implementation of a visual readout system capable of converting information encoded on a 1D DNA strand into a 2D form readable by advanced microscopic techniques. A functioning visual output method would not only increase the readout speed of DNA-based computers, but may also find use in other sequence identification techniques such as mutation or allele mapping.},
}
@article {pmid12803025,
year = {2003},
author = {},
title = {FDA proposes new rules that would require barcoding and new reporting procedures.},
journal = {Healthcare leadership &amp; management report},
volume = {11},
number = {3},
pages = {12-13},
pmid = {12803025},
issn = {1533-2292},
mesh = {Drug Labeling/*legislation &amp; jurisprudence ; Electronic Data Processing/*legislation &amp; jurisprudence ; Government Regulation ; Humans ; Medication Errors/*prevention &amp; control ; Safety Management/legislation &amp; jurisprudence ; United States ; United States Food and Drug Administration ; },
}
@article {pmid12787814,
year = {2003},
author = {Holland, NT and Smith, MT and Eskenazi, B and Bastaki, M},
title = {Biological sample collection and processing for molecular epidemiological studies.},
journal = {Mutation research},
volume = {543},
number = {3},
pages = {217-234},
doi = {10.1016/s1383-5742(02)00090-x},
pmid = {12787814},
issn = {0027-5107},
support = {P30 ES01896/ES/NIEHS NIH HHS/United States ; P42 ES04705/ES/NIEHS NIH HHS/United States ; P50 ES09605-03/ES/NIEHS NIH HHS/United States ; },
mesh = {Humans ; Molecular Epidemiology/*methods ; Quality Control ; Research Design ; Specimen Handling/*methods ; },
abstract = {Molecular epidemiology uses biomarkers and advanced technology to refine the investigation of the relationship between environmental exposures and diseases in humans. It requires careful handling and storage of precious biological samples with the goals of obtaining a large amount of information from limited samples, and minimizing future research costs by use of banked samples. Many factors, such as tissue type, time of collection, containers used, preservatives and other additives, transport means and length of transit time, affect the quality of the samples and the stability of biomarkers and must be considered at the initial collection stage. An efficient study design includes provisions for further processing of the original samples, such as cryopreservation of isolated cells, purification of DNA and RNA, and preparation of specimens for cytogenetic, immunological and biochemical analyses. Given the multiple uses of the samples in molecular epidemiology studies, appropriate informed consent must be obtained from the study subjects prior to sample collection. Use of barcoding and electronic databases allow more efficient management of large sample banks. Development of standard operating procedures and quality control plans is a safeguard of the samples' quality and of the validity of the analyses results. Finally, specific state, federal and international regulations are in place regarding research with human samples, governing areas including custody, safety of handling, and transport of human samples, as well as communication of study results.Here, we focus on the factors affecting the quality and the potential future use of biological samples and some of the provisions that must be made during collection, processing, and storage of samples, based on our experience in the Superfund Basic Research Program and Children's Environmental Health Center, at the University of California, Berkeley.},
}
@article {pmid12771685,
year = {2003},
author = {Douglas, J and Larrabee, S},
title = {Bring barcoding to the bedside.},
journal = {Nursing management},
volume = {34},
number = {5},
pages = {36-40},
doi = {10.1097/00006247-200305000-00010},
pmid = {12771685},
issn = {0744-6314},
mesh = {Biomedical Technology ; Electronic Data Processing/*instrumentation ; Humans ; Medication Errors/prevention &amp; control ; Point-of-Care Systems/*organization &amp; administration ; },
abstract = {A 240-bed regional hospital shares best practices for implementing a patient safety initiative that targets point-of-care barcode technology.},
}
@article {pmid12750962,
year = {2003},
author = {Hara, K and Ohe, K and Kadowaki, T and Kato, N and Imai, Y and Tokunaga, K and Nagai, R and Omata, M},
title = {Establishment of a method of anonymization of DNA samples in genetic research.},
journal = {Journal of human genetics},
volume = {48},
number = {6},
pages = {327-330},
pmid = {12750962},
issn = {1434-5161},
mesh = {*Anonymous Testing ; Confidentiality ; *DNA ; Forms and Records Control ; Genetic Privacy/economics/ethics ; *Genetic Research ; Humans ; Informed Consent ; Medical Records/economics ; },
abstract = {As the number of the genetic studies has rapidly increased in recent years, there has been growing concern that the privacy of the participants in such studies can be invaded unless effective measures are adopted to protect confidentiality. It is crucial for the scientific community to establish a method to anonymize DNA samples so that the public will trust genetic researchers. Here, we present a reliable and practical method of making DNA samples used in the genetic research anonymous. It assures complete anonymity by coding samples and personal information twice. Since it does not require equipment, such as bar-code readers or a software package, its cost is nominal compared with the laboratory costs. All institutions engaged in genetic research may wish to take measures such as the one described here to ensure the privacy and confidentiality of the participants in their genetic studies.},
}
@article {pmid12682378,
year = {2003},
author = {Xu, H and Sha, MY and Wong, EY and Uphoff, J and Xu, Y and Treadway, JA and Truong, A and O'Brien, E and Asquith, S and Stubbins, M and Spurr, NK and Lai, EH and Mahoney, W},
title = {Multiplexed SNP genotyping using the Qbead system: a quantum dot-encoded microsphere-based assay.},
journal = {Nucleic acids research},
volume = {31},
number = {8},
pages = {e43},
pmid = {12682378},
issn = {1362-4962},
mesh = {DNA/chemistry/genetics ; DNA Mutational Analysis/instrumentation/*methods ; Female ; Genotype ; Humans ; Male ; Microspheres ; Polymerase Chain Reaction/instrumentation/*methods ; Polymorphism, Single Nucleotide/*genetics ; Sensitivity and Specificity ; },
abstract = {We have developed a new method using the Qbead system for high-throughput genotyping of single nucleotide polymorphisms (SNPs). The Qbead system employs fluorescent Qdot semiconductor nanocrystals, also known as quantum dots, to encode microspheres that subsequently can be used as a platform for multiplexed assays. By combining mixtures of quantum dots with distinct emission wavelengths and intensities, unique spectral 'barcodes' are created that enable the high levels of multiplexing required for complex genetic analyses. Here, we applied the Qbead system to SNP genotyping by encoding microspheres conjugated to allele-specific oligonucleotides. After hybridization of oligonucleotides to amplicons produced by multiplexed PCR of genomic DNA, individual microspheres are analyzed by flow cytometry and each SNP is distinguished by its unique spectral barcode. Using 10 model SNPs, we validated the Qbead system as an accurate and reliable technique for multiplexed SNP genotyping. By modifying the types of probes conjugated to microspheres, the Qbead system can easily be adapted to other assay chemistries for SNP genotyping as well as to other applications such as analysis of gene expression and protein-protein interactions. With its capability for high-throughput automation, the Qbead system has the potential to be a robust and cost-effective platform for a number of applications.},
}
@article {pmid12655894,
year = {2003},
author = {},
title = {Use these tools to comply with patient safety goals.},
journal = {ED management : the monthly update on emergency department management},
volume = {15},
number = {3},
pages = {27-29},
pmid = {12655894},
issn = {1044-9167},
mesh = {Drug Prescriptions ; Electronic Data Processing ; Emergency Service, Hospital/*standards ; *Guideline Adherence ; Humans ; Joint Commission on Accreditation of Healthcare Organizations ; Medication Errors/*prevention &amp; control ; Medication Systems, Hospital/*standards ; Organizational Objectives ; Safety Management ; United States ; },
abstract = {Technology can help you comply with the 2003 National Patient Safety Goals from the Joint Commission on Accreditation of Healthcare Organizations. EDs are beginning to invest in these resources: Bar-coding systems can ensure that patients receive the correct medication. Software can alert physicians when nonstandard doses are ordered. Computerized order entry can give correct doses if you enter the patient's weight.},
}
@article {pmid12647993,
year = {2003},
author = {Jain, KK},
title = {Nanodiagnostics: application of nanotechnology in molecular diagnostics.},
journal = {Expert review of molecular diagnostics},
volume = {3},
number = {2},
pages = {153-161},
doi = {10.1586/14737159.3.2.153},
pmid = {12647993},
issn = {1473-7159},
mesh = {Animals ; Biotechnology ; Humans ; Molecular Diagnostic Techniques/instrumentation/*methods ; *Nanotechnology ; Oligonucleotide Array Sequence Analysis/*methods ; Polymerase Chain Reaction ; },
abstract = {Nanotechnology extends the limits of molecular diagnostics to the nanoscale. Nanotechnology-on-a-chip is one more dimension of microfluidic/lab-on-a-chip technology. Biological tests measuring the presence or activity of selected substances become quicker, more sensitive and more flexible when certain nanoscale particles are put to work as tags or labels. Magnetic nanoparticles, bound to a suitable antibody, are used to label specific molecules, structures or microorganisms. Magnetic immunoassay techniques have been developed in which the magnetic field generated by the magnetically labeled targets is detected directly with a sensitive magnetometer. Gold nanoparticles tagged with short segments of DNA can be used for detection of genetic sequence in a sample. Multicolor optical coding for biological assays has been achieved by embedding different-sized quantum dots into polymeric microbeads. Nanopore technology for analysis of nucleic acids converts strings of nucleotides directly into electronic signatures. DNA nanomachines can function as biomolecular detectors for homogeneous assays. Nanobarcodes, submicrometer metallic barcodes with striping patterns prepared by sequential electrochemical depositon of metal, show differential reflectivity of adjacent stripes enabling identification of the striping patterns by conventional light microscopy. All this has applications in population diagnostics and in point-of-care hand-held devices.},
}
@article {pmid12630239,
year = {2003},
author = {Ballard, S},
title = {A nursing contribution to research issues in blood transfusion.},
journal = {Professional nurse (London, England)},
volume = {18},
number = {6},
pages = {308-309},
pmid = {12630239},
issn = {0266-8130},
mesh = {Anemia, Sickle Cell/*nursing/therapy ; Blood Transfusion/*nursing ; Clinical Nursing Research/*trends ; Humans ; Thalassemia/*nursing/therapy ; },
abstract = {Research nurses at the National Blood Service are working on projects as diverse as identification barcodes, a national profile of blood recipients and pre-operative transfusion in sickle cell disease.},
}
@article {pmid12614582,
year = {2003},
author = {Hebert, PD and Cywinska, A and Ball, SL and deWaard, JR},
title = {Biological identifications through DNA barcodes.},
journal = {Proceedings. Biological sciences},
volume = {270},
number = {1512},
pages = {313-321},
pmid = {12614582},
issn = {0962-8452},
mesh = {Animals ; DNA, Mitochondrial/chemistry/*genetics ; Electron Transport Complex IV/chemistry/*genetics ; *Evolution, Molecular ; *Genetic Variation ; Lepidoptera/classification/genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.},
}
@article {pmid12515864,
year = {2003},
author = {Dejneka, MJ and Streltsov, A and Pal, S and Frutos, AG and Powell, CL and Yost, K and Yuen, PK and Müller, U and Lahiri, J},
title = {Rare earth-doped glass microbarcodes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {100},
number = {2},
pages = {389-393},
pmid = {12515864},
issn = {0027-8424},
mesh = {Biotechnology ; DNA/*genetics ; Fluorescent Dyes ; *Metals, Rare Earth ; Nucleic Acid Hybridization/*methods ; },
abstract = {The development of ultraminiaturized identification tags has applications in fields ranging from advanced biotechnology to security. This paper describes micrometer-sized glass barcodes containing a pattern of different fluorescent materials that are easily identified by using a UV lamp and an optical microscope. A model DNA hybridization assay using these "microbarcodes" is described. Rare earth-doped glasses were chosen because of their narrow emission bands, high quantum efficiencies, noninterference with common fluorescent labels, and inertness to most organic and aqueous solvents. These properties and the large number (>1 million) of possible combinations of these microbarcodes make them attractive for use in multiplexed bioassays and general encoding.},
}
@article {pmid12503941,
year = {2003},
author = {Carrière, B and Bailey, B and Chabot, G and Lebel, D},
title = {Dispensing error leading to alendronate ingestion.},
journal = {The Annals of pharmacotherapy},
volume = {37},
number = {1},
pages = {87-89},
doi = {10.1345/aph.1C217},
pmid = {12503941},
issn = {1060-0280},
mesh = {Acetates ; Alendronate/*adverse effects ; Asthma/drug therapy ; Calcium Channel Blockers/*adverse effects ; Child ; Cyclopropanes ; Drug Packaging ; Esophagitis/chemically induced ; Humans ; Leukotriene Antagonists ; Male ; *Medication Errors ; Quinolines ; Sulfides ; },
abstract = {OBJECTIVE: To report a case of medication dispensing error by administration of similarly packaged drugs.<br><br>CASE SUMMARY: A 6-year-old East Indian boy with asthma was mistakenly given alendronate, a bisphosphonate, for 3 months instead of montelukast, a leukotriene-receptor antagonist. Symptoms of esophageal irritation developed and disappeared on discontinuation of alendronate.<br><br>DISCUSSION: Alendronate and montelukast have very similar packaging and are available in dosages that also can be similar for some patients. Alendronate caused symptoms of irritative gastritis in this child before the error was identified. This case report emphasizes one of the possible sources of medication dispensing errors: a mistaken identification due to similar packaging (confirmation bias). Manufacturers can help to prevent medication errors in many ways; in this case, more distinct packaging would have decreased the risk of error. A standard bar-coding scheme among manufacturers could lead to an important improvement in the safety of medication dispensation. Practitioners are also encouraged to report such errors to the United States Pharmacopoeia Medication Errors Reporting Program.<br><br>CONCLUSIONS: With increased awareness of medication errors, healthcare practitioners, manufacturers, and patients should take precautionary steps to prevent dispensing errors and their consequences.},
}
@article {pmid12475495,
year = {2002},
author = {Gressel, J and Ehrlich, G},
title = {Universal inheritable barcodes for identifying organisms.},
journal = {Trends in plant science},
volume = {7},
number = {12},
pages = {542-544},
doi = {10.1016/s1360-1385(02)02364-6},
pmid = {12475495},
issn = {1360-1385},
mesh = {DNA, Plant/genetics ; Databases, Genetic ; Plants/classification/*genetics ; Plants, Genetically Modified/*genetics ; Polymerase Chain Reaction/*methods ; },
abstract = {The needs for recognition of novel conventional or transgenic organisms include protection of patented or Identity Preserved lines, detecting transgenics and tracing dispersal. We propose simple 'Biobarcodes' using universal PCR primers to recognize the universal 'nonsense' recognition site of all biobarcodes, followed by a variable nonsense sequence. The proposed sequences are long enough to allow recognition in spite of mutations, have stop codons to prevent coding, and will not self anneal. Sequences of PCR-amplified biobarcodes can be compared to a universal database.},
}
@article {pmid12233012,
year = {2002},
author = {},
title = {Barcoding in health care.},
journal = {Healthcare leadership &amp; management report},
volume = {10},
number = {7},
pages = {10-11},
pmid = {12233012},
issn = {1533-2292},
mesh = {Delivery of Health Care/*organization &amp; administration ; Diffusion of Innovation ; Efficiency, Organizational ; *Electronic Data Processing ; Information Management ; Product Labeling/*instrumentation ; United States ; },
}
@article {pmid12210229,
year = {2002},
author = {Choe, LH and Dutt, MJ and Relkin, N and Lee, KH},
title = {Studies of potential cerebrospinal fluid molecular markers for Alzheimer's disease.},
journal = {Electrophoresis},
volume = {23},
number = {14},
pages = {2247-2251},
doi = {10.1002/1522-2683(200207)23:14&lt;2247::AID-ELPS2247&gt;3.0.CO;2-M},
pmid = {12210229},
issn = {0173-0835},
support = {CA 90073/CA/NCI NIH HHS/United States ; },
mesh = {Adult ; Aged ; Alzheimer Disease/cerebrospinal fluid/*diagnosis ; Analysis of Variance ; Biomarkers/cerebrospinal fluid ; Case-Control Studies ; Cerebrospinal Fluid Proteins/*analysis ; Cluster Analysis ; Electrophoresis, Gel, Two-Dimensional ; Female ; Humans ; Male ; Proteomics ; },
abstract = {There is a need for a reliable, molecular-based ante mortem diagnostic test for Alzheimer's disease (AD). In this study, we examined the use of two-dimensional protein electrophoresis for generating molecular barcodes which may be useful for the clinical differentiation of AD patients from normals. We compared cerebrospinal fluid samples taken from AD patients with confirmed post mortem pathology to comparable specimens from normal volunteers. Using canonical correlation analysis, a panel of nine molecular markers were identified which segregated diseased cases from normal controls. Using the scaled volume image analysis variable, a principal factor analysis was also used to distinguish normal from AD spinal fluid, based on molecular markers identified using a heuristic clustering algorithm. The use of panels of molecular markers derived from proteomic analysis may offer the best prospect for developing molecular diagnostic tests for complex neurodegenerative disorders such as AD.},
}
@article {pmid12189833,
year = {2002},
author = {Battersby, BJ and Lawrie, GA and Johnston, AP and Trau, M},
title = {Optical barcoding of colloidal suspensions: applications in genomics, proteomics and drug discovery.},
journal = {Chemical communications (Cambridge, England)},
volume = {},
number = {14},
pages = {1435-1441},
doi = {10.1039/b200038p},
pmid = {12189833},
issn = {1359-7345},
mesh = {Colloids/*chemistry ; Combinatorial Chemistry Techniques ; *Electronic Data Processing ; Genomic Library ; Genomics/*methods ; Humans ; Pharmacology/*methods ; Proteome/*chemistry ; Suspensions ; },
abstract = {The enormous amount of information generated through sequencing of the human genome has increased demands for more economical and flexible alternatives in genomics, proteomics and drug discovery. Many companies and institutions have recognised the potential of increasing the size and complexity of chemical libraries by producing large chemical libraries on colloidal support beads. Since colloid-based compounds in a suspension are randomly located, an encoding system such as optical barcoding is required to permit rapid elucidation of the compound structures. We describe in this article innovative methods for optical barcoding of colloids for use as support beads in both combinatorial and non-combinatorial libraries. We focus in particular on the difficult problem of barcoding extremely large libraries, which if solved, will transform the manner in which genomics, proteomics and drug discovery research is currently performed.},
}
@article {pmid12098440,
year = {2002},
author = {Chadwick, BL and Oliver, RG and Gyton, J},
title = {Validation of undergraduate clinical data by electronic capture (barcode).},
journal = {Medical teacher},
volume = {24},
number = {2},
pages = {193-196},
doi = {10.1080/01421590220125312},
pmid = {12098440},
issn = {0142-159X},
mesh = {Data Collection/*methods ; Dental Audit ; Education, Dental/*statistics &amp; numerical data ; *Electronic Data Processing ; Forms and Records Control ; Humans ; United Kingdom ; },
abstract = {Assessment of clinical activity is common in dental schools. An audit project to confirm that dental undergraduate clinical activity recorded by electronic data capture is an accurate representation of the clinical case entry is reported. A printout of clinical activity for a period of a week was generated retrospectively and used to identify case notes. Activity recorded in the case notes was compared with the computer printout. All discrepancies were noted. A total of 125 patient files with 270 barcoded items of treatment were retrieved; 29 of 78 (37.1%) paediatric and 23 of 47 (48.9%) orthodontic cases had discrepancies between the case notes and the computer entry. However, some items recorded in the notes do not require barcoding and vice versa. When these were accounted for, only 19 items of treatment appeared in the notes that should have been barcoded, a 7% shortfall in recording of clinical activity. The barcode system is an accurate and reliable way of recording undergraduate clinical activity.},
}
@article {pmid12074193,
year = {2002},
author = {Roberts, DC},
title = {Biomarkers, yesterday, today and tomorrow: the basis for health claims.},
journal = {Asia Pacific journal of clinical nutrition},
volume = {11},
number = {2},
pages = {S87-9},
doi = {10.1046/j.1440-6047.2002.00005.x},
pmid = {12074193},
issn = {0964-7058},
mesh = {Biomarkers ; Food Technology/*trends ; Genomics/*trends ; Humans ; Nutritional Physiological Phenomena/*physiology ; },
abstract = {The development of useful and accurate biomarkers for predicting outcomes of food based interventions is becoming more and more important, given the emphasis being placed on ingredients in foods contributing to disease risk reduction and optimal health promotion. With the human genome now laid bare, opportunities abound to barcode individuals with their risk profiles. The massive increase in DNA sequence information together with the development of new technologies such as genomics, proteomics and bioinformatics, has resulted in a much greater capacity to determine individual risk profiles. Screening for biomarkers at the gene or protein expression level using microarray technology has the potential to identify new biomarkers for disease diagnosis. Whether these techniques will enable a better understanding of food-gene interactions to permit health claims rather than better therapeutic treatment (at high economic cost) remains to be demonstrated.},
}
@article {pmid12074168,
year = {2002},
author = {Scott, GB and Steffen, DL and Edgar, D and Warren, JT and Kovár, CL and Scherer, SE and Havlak, PH and Gibbs, RA},
title = {Loader Lite: a new software tool for the ABI PRISM 3700 DNA sequencer.},
journal = {BioTechniques},
volume = {32},
number = {6},
pages = {1366, 1368, 1370-1},
doi = {10.2144/02326bc01},
pmid = {12074168},
issn = {0736-6205},
mesh = {Sequence Analysis, DNA/*instrumentation/methods ; *Software ; Statistics as Topic/methods ; },
abstract = {Here we describe the development of a novel software tool entitled Loader Lite that generates plate records or sample sheetsfor the ABI PRISMs 3700 DNA sequencer. The major advantage of this program is that it enables the ongoing operation of sequencing instruments without reference to external network(s). The autonomous operation of sequencing instruments is critical if sample throughput is to be maintained during periods of network outage. Loader Lite employs a deliberate strategy of inputting anonymous tray barcodes at run time. After sequencing, the barcodes are reconciled with relevant project details by reference to a database. This software takes advantage of barcode scanning technology by creating plate records directly on the local computer, serving an individual sequencer, immediately before importing and linking. This real-time synthesis of the plate records at the point of loading all but eliminates loading errors. Loader Lite is user-friendly, fully configurable, and permits the running of partial or full 384-well sample trays, using any standard combinations of run modules, dye sets, mobility files, analysis modules, etc. The 96-well format is not supported; however, this capability will appear in subsequent versions that are currently under development. This application is designed as an added value, adjunct program to the regular ABI PRISM 3700 Data Collection software. We have successfully used Loader Lite over the past six months to load approximately 7 million sequencing reactions and believe its utility and functionality will prove to be attractive to the wider sequencing community.},
}
@article {pmid11972769,
year = {2002},
author = {Floyd, R and Abebe, E and Papert, A and Blaxter, M},
title = {Molecular barcodes for soil nematode identification.},
journal = {Molecular ecology},
volume = {11},
number = {4},
pages = {839-850},
doi = {10.1046/j.1365-294x.2002.01485.x},
pmid = {11972769},
issn = {0962-1083},
mesh = {Animals ; DNA, Ribosomal/*analysis/genetics ; Genetic Variation/*genetics ; Nematoda/*classification/*genetics ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA ; Soil/*parasitology ; },
abstract = {Using a molecular barcode, derived from single-specimen polymerase chain reaction (PCR) and sequencing of the 5' segment of the small subunit ribosomal RNA (SSU) gene, we have developed a molecular operational taxonomic unit (MOTU) scheme for soil nematodes. Individual specimens were considered to belong to the same MOTU when the sequenced segment of 450 bases was > 99.5% identical. A Scottish upland Agrostis-Festuca grassland soil was sampled, using both culture-based and random selection methods. One hundred and sixty-six cultured isolates were sequenced, and clustered into five MOTU. From 74 randomly sampled individuals across the study site, 19 MOTU were defined. A subsequent sample of 18 individuals from a single subplot contained eight MOTU, four of which were unique to the single subplot sample. Interestingly, seven of these MOTU were not present in the culture-independent sampling. Overall, a total of 23 MOTU were defined from only 240 sequences. Many MOTU could readily be assigned to classical, morphologically defined taxonomic units using a database of SSU sequences from named nematode species. The MOTU technique allows a rapid assessment of nematode taxon diversity in soils. Correlation with a database of sequences from known species offers a route to application of the technique in ecological surveys addressing biological as well as genetic diversity.},
}
@article {pmid11942805,
year = {2002},
author = {Nam, JM and Park, SJ and Mirkin, CA},
title = {Bio-barcodes based on oligonucleotide-modified nanoparticles.},
journal = {Journal of the American Chemical Society},
volume = {124},
number = {15},
pages = {3820-3821},
doi = {10.1021/ja0178766},
pmid = {11942805},
issn = {0002-7863},
mesh = {*Biosensing Techniques ; DNA/*chemistry ; Immunoglobulin E/*analysis ; Immunoglobulin G/*analysis ; Oligonucleotides/*chemistry ; },
abstract = {By utilizing oligonucleotide-modified Au nanoparticles encoded with sequences that act as biobarcodes, one can screen for multiple target polyvalent proteins simultaneously in one solution. This novel concept was demonstrated with two types of detection formats, a homogeneous assay and one based on oligonucleotide microarrays. With such an approach, one can prepare an extraordinarily large number of barcodes from synthetically accessible oligonucleotides (e.g., a 12-mer sequence offers 4(12) possible barcodes).},
}
@article {pmid11832939,
year = {2002},
author = {Gudiksen, MS and Lauhon, LJ and Wang, J and Smith, DC and Lieber, CM},
title = {Growth of nanowire superlattice structures for nanoscale photonics and electronics.},
journal = {Nature},
volume = {415},
number = {6872},
pages = {617-620},
doi = {10.1038/415617a},
pmid = {11832939},
issn = {0028-0836},
abstract = {The assembly of semiconductor nanowires and carbon nanotubes into nanoscale devices and circuits could enable diverse applications in nanoelectronics and photonics. Individual semiconducting nanowires have already been configured as field-effect transistors, photodetectors and bio/chemical sensors. More sophisticated light-emitting diodes (LEDs) and complementary and diode logic devices have been realized using both n- and p-type semiconducting nanowires or nanotubes. The n- and p-type materials have been incorporated in these latter devices either by crossing p- and n-type nanowires or by lithographically defining distinct p- and n-type regions in nanotubes, although both strategies limit device complexity. In the planar semiconductor industry, intricate n- and p-type and more generally compositionally modulated (that is, superlattice) structures are used to enable versatile electronic and photonic functions. Here we demonstrate the synthesis of semiconductor nanowire superlattices from group III-V and group IV materials. (The superlattices are created within the nanowires by repeated modulation of the vapour-phase semiconductor reactants during growth of the wires.) Compositionally modulated superlattices consisting of 2 to 21 layers of GaAs and GaP have been prepared. Furthermore, n-Si/p-Si and n-InP/p-InP modulation doped nanowires have been synthesized. Single-nanowire photoluminescence, electrical transport and electroluminescence measurements show the unique photonic and electronic properties of these nanowire superlattices, and suggest potential applications ranging from nano-barcodes to polarized nanoscale LEDs.},
}
@article {pmid11720335,
year = {2001},
author = {Sistrom, CL and Honeyman, JC and Mancuso, A and Quisling, RG},
title = {Managing predefined templates and macros for a departmental speech recognition system using common software.},
journal = {Journal of digital imaging},
volume = {14},
number = {3},
pages = {131-141},
doi = {10.1007/s10278-001-0012-1},
pmid = {11720335},
issn = {0897-1889},
mesh = {Computer Peripherals ; Database Management Systems ; Databases as Topic/organization &amp; administration ; Humans ; Information Storage and Retrieval/methods ; Medical Records Systems, Computerized/organization &amp; administration ; *Natural Language Processing ; Radiology Information Systems/*organization &amp; administration ; *Software ; Software Design ; *Speech ; *User-Computer Interface ; },
abstract = {The authors have developed a networked database system to create, store, and manage predefined radiology report definitions. This was prompted by complete departmental conversion to a computer speech recognition system (SRS) for clinical reporting. The software complements and extends the capabilities of the SRS, and 2 systems are integrated by means of a simple text file format and import/export functions within each program. This report describes the functional requirements, design considerations, and implementation details of the structured report management software. The database and its interface are designed to allow all radiologists and division managers to define and update template structures relevant to their practice areas. Two key conceptual extensions supported by the template management system are the addition of a template type construct and allowing individual radiologists to dynamically share common organ system or modality-specific templates. In addition, the template manager software enables specifying predefined report structures that can be triggered at the time of dictation from printed lists of barcodes. Initial experience using the program in a regional, multisite, academic radiology practice has been positive.},
}
@article {pmid11701889,
year = {2001},
author = {Ooi, SL and Shoemaker, DD and Boeke, JD},
title = {A DNA microarray-based genetic screen for nonhomologous end-joining mutants in Saccharomyces cerevisiae.},
journal = {Science (New York, N.Y.)},
volume = {294},
number = {5551},
pages = {2552-2556},
doi = {10.1126/science.1065672},
pmid = {11701889},
issn = {0036-8075},
support = {GM36481/GM/NIGMS NIH HHS/United States ; HG01627/HG/NHGRI NIH HHS/United States ; },
mesh = {CCAAT-Binding Factor/genetics/metabolism ; DNA Ligase ATP ; DNA Ligases/genetics/metabolism ; *DNA Repair ; DNA-Binding Proteins/chemistry/genetics/metabolism ; Fungal Proteins/genetics/metabolism ; *Genes, Fungal ; Genetic Complementation Test ; *Mutation ; Nucleic Acid Hybridization ; *Oligonucleotide Array Sequence Analysis ; Plasmids ; *Recombination, Genetic ; Saccharomyces cerevisiae/*genetics/physiology ; Saccharomyces cerevisiae Proteins/*genetics/metabolism ; Transcription Factors/genetics/metabolism ; Transformation, Genetic ; Two-Hybrid System Techniques ; },
abstract = {We describe a microarray-based screen performed by imposing different genetic selections on thousands of yeast mutants in parallel, representing most genes in the yeast genome. The presence or absence of mutants was detected by oligonucleotide arrays that hybridize to 20-nucleotide "barcodes." We used this method to screen for components of the nonhomologous end-joining (NHEJ) pathway. Known components of the pathway were identified, as well as a gene not previously known to be involved in NHEJ, NEJ1. Nej1 protein interacts with the amino terminus of LIF1/XRCC4, a recently recognized "guardian of the genome" against cancer.},
}
@article {pmid11588257,
year = {2001},
author = {Nicewarner-Pena, SR and Freeman, RG and Reiss, BD and He, L and Pena, DJ and Walton, ID and Cromer, R and Keating, CD and Natan, MJ},
title = {Submicrometer metallic barcodes.},
journal = {Science (New York, N.Y.)},
volume = {294},
number = {5540},
pages = {137-141},
doi = {10.1126/science.294.5540.137},
pmid = {11588257},
issn = {0036-8075},
support = {HG02228/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; Biochemistry/*methods ; Chemistry Techniques, Analytical/*methods ; Electrochemistry ; Fluorescence ; Fluorescent Antibody Technique ; Humans ; Immunoassay/*methods ; Immunoglobulin G/analysis ; *Metals ; Microscopy ; Miniaturization ; Nucleic Acid Hybridization/*methods ; Oligonucleotide Probes ; Optics and Photonics ; Rabbits ; Templates, Genetic ; },
abstract = {We synthesized multimetal microrods intrinsically encoded with submicrometer stripes. Complex striping patterns are readily prepared by sequential electrochemical deposition of metal ions into templates with uniformly sized pores. The differential reflectivity of adjacent stripes enables identification of the striping patterns by conventional light microscopy. This readout mechanism does not interfere with the use of fluorescence for detection of analytes bound to particles by affinity capture, as demonstrated by DNA and protein bioassays.},
}
@article {pmid11479739,
year = {2001},
author = {Müller, S and Wienberg, J},
title = {"Bar-coding" primate chromosomes: molecular cytogenetic screening for the ancestral hominoid karyotype.},
journal = {Human genetics},
volume = {109},
number = {1},
pages = {85-94},
doi = {10.1007/s004390100535},
pmid = {11479739},
issn = {0340-6717},
mesh = {Animals ; Cell Line ; Chromosome Painting ; Chromosomes/*genetics ; Chromosomes, Human/genetics ; Cytogenetics ; Gorilla gorilla/genetics ; Hominidae/*genetics ; Humans ; Hylobates/genetics ; In Situ Hybridization, Fluorescence/*methods ; Karyotyping ; Macaca nemestrina/genetics ; Pan troglodytes/genetics ; Pongo pygmaeus/genetics ; Primates/*genetics ; Species Specificity ; },
abstract = {Two recently introduced multicolor FISH approaches, cross-species color banding (also termed Rx-FISH) and multiplex FISH using painting probes derived from somatic cell hybrids retaining fragments of human chromosomes, were applied in a comparative molecular cytogenetic study of higher primates. We analyzed these "chromosome bar code" patterns to obtain an overview of chromosomal rearrangements that occurred during higher primate evolution. The objective was to reconstruct the ancestral genome organization of hominoids using the macaque as outgroup species. Approximately 160 individual and discernible molecular cytogenetic markers were assigned in these species. Resulting comparative maps allowed us to identify numerous intra-chromosomal rearrangements, to discriminate them from previous contradicting chromosome banding interpretations and to propose an ancestral karyotype for hominoids. From 25 different chromosome forms in an ancestral karyotype for all hominoids of 2N=48 we propose 21. Probes for chromosomes 2p, 4, 9 and Y were not informative in the present experiments. The orangutan karyotype was very similar to the proposed ancestral organization and conserved 19 of the 21 ancestral forms; thus most chromosomes were already present in early hominoid evolution, while African apes and human show various derived changes.},
}
@article {pmid11433268,
year = {2001},
author = {Rosenthal, SJ},
title = {Bar-coding biomolecules with fluorescent nanocrystals.},
journal = {Nature biotechnology},
volume = {19},
number = {7},
pages = {621-622},
doi = {10.1038/90213},
pmid = {11433268},
issn = {1087-0156},
mesh = {Biotechnology/*methods ; Cadmium Compounds/chemistry ; *Crystallization ; Fluorescent Dyes/*chemistry ; Microspheres ; Nucleic Acid Hybridization/methods ; *Oligonucleotide Array Sequence Analysis ; Selenium Compounds/chemistry ; Semiconductors ; Spectrometry, Fluorescence ; },
}
@article {pmid11418536,
year = {2001},
author = {Bates, DW and Cohen, M and Leape, LL and Overhage, JM and Shabot, MM and Sheridan, T},
title = {Reducing the frequency of errors in medicine using information technology.},
journal = {Journal of the American Medical Informatics Association : JAMIA},
volume = {8},
number = {4},
pages = {299-308},
pmid = {11418536},
issn = {1067-5027},
mesh = {*Decision Support Systems, Clinical/statistics &amp; numerical data ; Drug Prescriptions ; Humans ; Medical Errors/*prevention &amp; control ; Medical Records Systems, Computerized ; Quality of Health Care ; Systems Integration ; },
abstract = {BACKGROUND: Increasing data suggest that error in medicine is frequent and results in substantial harm. The recent Institute of Medicine report (LT Kohn, JM Corrigan, MS Donaldson, eds: To Err Is Human: Building a Safer Health System. Washington, DC: National Academy Press, 1999) described the magnitude of the problem, and the public interest in this issue, which was already large, has grown.<br><br>GOAL: The goal of this white paper is to describe how the frequency and consequences of errors in medical care can be reduced (although in some instances they are potentiated) by the use of information technology in the provision of care, and to make general and specific recommendations regarding error reduction through the use of information technology.<br><br>RESULTS: General recommendations are to implement clinical decision support judiciously; to consider consequent actions when designing systems; to test existing systems to ensure they actually catch errors that injure patients; to promote adoption of standards for data and systems; to develop systems that communicate with each other; to use systems in new ways; to measure and prevent adverse consequences; to make existing quality structures meaningful; and to improve regulation and remove disincentives for vendors to provide clinical decision support. Specific recommendations are to implement provider order entry systems, especially computerized prescribing; to implement bar-coding for medications, blood, devices, and patients; and to utilize modern electronic systems to communicate key pieces of asynchronous data such as markedly abnormal laboratory values.<br><br>CONCLUSIONS: Appropriate increases in the use of information technology in health care- especially the introduction of clinical decision support and better linkages in and among systems, resulting in process simplification-could result in substantial improvement in patient safety.},
}
@article {pmid11330654,
year = {2001},
author = {Jefferson, T and Heijbel, H},
title = {Demyelinating disease and hepatitis B vaccination: is there a link?.},
journal = {Drug safety},
volume = {24},
number = {4},
pages = {249-254},
pmid = {11330654},
issn = {0114-5916},
mesh = {*Evidence-Based Medicine ; Hepatitis B Vaccines/*adverse effects ; Humans ; Multiple Sclerosis/*chemically induced ; },
abstract = {The recent decision by the French government to compensate 3 recipients of hepatitis B vaccine preceding the onset of multiple sclerosis presumes a possible causal link and brings into question the use of current rules of causality assessment. Available evidence does not support a causal link or is equivocal but the accuracy of current methods of vaccine surveillance should be urgently improved. Larger and longer randomised trials, updated summaries of evidence, linked databases, prospective vaccination registers, bar-coding of vaccines and standardisation of adverse event definitions are possible measures to address current problems.},
}
@article {pmid11242719,
year = {2001},
author = {Farbstein, K and Clough, J},
title = {Improving medication safety across a multihospital system.},
journal = {The Joint Commission journal on quality improvement},
volume = {27},
number = {3},
pages = {123-137},
doi = {10.1016/s1070-3241(01)27012-6},
pmid = {11242719},
issn = {1070-3241},
mesh = {Anticoagulants/administration &amp; dosage ; Clinical Pharmacy Information Systems ; Consultants ; Diffusion of Innovation ; Documentation ; Heparin/administration &amp; dosage ; Humans ; Institutional Management Teams ; Massachusetts ; Medication Errors/*prevention &amp; control ; Multi-Institutional Systems/*standards ; Organizational Case Studies ; Organizational Culture ; Patient Education as Topic ; Program Evaluation ; Quality Assurance, Health Care/*organization &amp; administration ; Risk Management/*organization &amp; administration ; Warfarin/administration &amp; dosage ; },
abstract = {BACKGROUND: The Massachusetts Coalition for the Prevention of Medical Errors and the Institute for Healthcare Improvement have identified 16 best practices to reduce adverse drug events. CareGroup, a network of six hospitals in eastern Massachusetts, multiplied its routine use of these best practices tenfold in the first 18 months of its medication reliability project.<br><br>Although CareGroup's long-term plans included technological advances such as clinical order entry, computer systems in the pharmacy, dispensing stations on patient floors, and bedside bar-coding, efforts first focused on manual improvements feasible within a year's time. A 4-year strategy involves helping the medication reliability team leaders at each hospital to create impressive local results, publicize the results to their colleagues, invite their clinical colleagues to learn to use plan-do-study-act (PDSA) cycles, and have colleagues lead PDSA cycles themselves. At monthly or bimonthly task force meetings, team results are presented and team leaders are given specific assignments for their teams.<br><br>CASE STUDIES: One project reduced the time to blood anticoagulation for heparinized patients. The second dramatically reduced lookalike/soundalike errors. The third improved the safety of patient-controlled analgesia. The fourth reduced coumadin incidents. The fifth improved the education of patients about their medications. The sixth greatly reduced the morning dispensing backlog in the pharmacy.<br><br>SUCCESS FACTORS: Key success factors, in addition to leadership, are the use of data, forcing functions, appropriate pacing, inexpensive practices, and a consultant. The pace needed to implement the best practices overall made it imperative to make many changes rapidly. Often, the team initiated several changes at one time, rather than sequencing changes in successive PDSA cycles.<br><br>CareGroup faces key challenges in measurement and in spreading and deepening the involvement of clinicians, particularly physicians. It lacks an overall, objective measure of medication safety. Spread of the changes made has been incomplete although the adoption of the best practices increased tenfold (from 6 to 60) in 21 months. Two of the case study interventions--in coumadin order sequencing and dedicating a pharmacy technician to order entry--have been implemented at only one site to date, even though the adoption of the change ideas across hospitals is encouraged. The eventual impact of the changes planned for the future, through automated systems such as computerized order entry, is much larger. Considerable progress is anticipated in adoption of best practices; improvement in top-priority areas of each hospital; improved automation and technology in ordering, dispensing, and administering medication; and better reporting.},
}
@article {pmid11215177,
year = {2000},
author = {Nakano, Y},
title = {[Standardization of barcodes used for sample identification].},
journal = {Rinsho byori. The Japanese journal of clinical pathology},
volume = {},
number = {Suppl 114},
pages = {66-70},
pmid = {11215177},
issn = {0047-1860},
mesh = {Electronic Data Processing/instrumentation/*standards ; Humans ; International Cooperation ; Specimen Handling/*methods ; },
abstract = {In the clinical laboratory, they are mainly using one-dimensional barcode (simply, barcode) for the sample identification. It has been proposed an international standard for the barcode by NCCLS with the cooperation of JCCLS and CODE128 was selected for its symbol. Other details for it also can be found in this article. The committee of JSCC has started to discuss a barcode for the next generation so that more information can be conveyed on test tubes. A two-dimensional symbol barcode (2D barcode) is one system. NCCLS is interested in this act and therefore cooperation is anticipated in the development of international standards.},
}
@article {pmid11123812,
year = {2000},
author = {Zeiler, T and Slonka, J and Bürgi, HR and Kretschmer, V},
title = {How to maintain blood supply during computer network breakdown: a manual backup system.},
journal = {Transfusion medicine (Oxford, England)},
volume = {10},
number = {4},
pages = {283-290},
doi = {10.1046/j.1365-3148.2000.00265.x},
pmid = {11123812},
issn = {0958-7578},
mesh = {Blood Transfusion/*instrumentation/methods/standards ; Clinical Laboratory Information Systems/standards ; Computer Communication Networks/*standards ; Databases, Factual/standards ; Equipment Design ; Equipment Failure ; Humans ; },
abstract = {Electronic data management systems using computer network systems and client/server architecture are increasingly used in laboratories and transfusion services. Severe problems arise if there is no network access to the database server and critical functions are not available. We describe a manual backup system (MBS) developed to maintain the delivery of blood products to patients in a hospital transfusion service in case of a computer network breakdown. All data are kept on a central SQL database connected to peripheral workstations in a local area network (LAN). Request entry from wards is performed via machine-readable request forms containing self-adhesive specimen labels with barcodes for test tubes. Data entry occurs on-line by bidirectional automated systems or off-line manually. One of the workstations in the laboratory contains a second SQL database which is frequently and incrementally updated. This workstation is run as a stand-alone, read-only database if the central SQL database is not available. In case of a network breakdown, the time-graded MBS is launched. Patient data, requesting ward and ordered tests/requests, are photocopied through a template from the request forms on special MBS worksheets serving as laboratory journal for manual processing and result report (a copy is left in the laboratory). As soon as the network is running again the data from the off-line period are entered into the primary SQL server. The MBS was successfully used at several occasions. The documentation of a 90-min breakdown period is presented in detail. Additional work resulted from the copy work and the belated manual data entry after restoration of the system. There was no delay in issue of blood products or result reporting. The backup system described has been proven to be simple, quick and safe to maintain urgent blood supply and distribution of laboratory results in case of unexpected network breakdown.},
}
@article {pmid11025846,
year = {2000},
author = {Chan, JT},
title = {Computerisation of accident and emergency departments in Hong Kong.},
journal = {Hong Kong medical journal = Xianggang yi xue za zhi},
volume = {6},
number = {3},
pages = {276-282},
pmid = {11025846},
issn = {1024-2708},
mesh = {Emergency Service, Hospital/*organization &amp; administration ; Forms and Records Control ; Hong Kong ; Hospital Information Systems/*organization &amp; administration ; Humans ; Management Information Systems ; Medical Records Systems, Computerized ; Software ; },
abstract = {This article reviews the history and progress of the computerisation of accident and emergency departments in Hong Kong. The Hospital Information System was the first computerisation project to be launched in a public hospital in Hong Kong, when the Princess Margaret Hospital was selected as a pilot site in April 1991. The network infrastructure comprised a central processor that linked to all workstations in the hospital in an integrated network. With the introduction of bar-coding technology and the implementation of an interfaced network, the Accident and Emergency Information System version 1.0 was launched at the Prince of Wales Hospital in March 1993. A Clinical Management System was then piloted at the Accident and Emergency Department of the Alice Ho Miu Ling Nethersole Hospital in December 1997; it contained clinical data of individual patients, including diagnoses, drug treatments, discharge summaries, allergies, and medical histories. Laboratory, diagnostic radiology, and electrocardiography results were also available in this system. With the extensive development of Internet technology within the Hospital Authority, clinical information can now be retrieved in any hospital in a couple of minutes. The availability of important clinical information will be of great help to emergency physicians in the delivery of quality care to patients.},
}
@article {pmid10963862,
year = {2000},
author = {Leier, A and Richter, C and Banzhaf, W and Rauhe, H},
title = {Cryptography with DNA binary strands.},
journal = {Bio Systems},
volume = {57},
number = {1},
pages = {13-22},
doi = {10.1016/s0303-2647(00)00083-6},
pmid = {10963862},
issn = {0303-2647},
mesh = {Computer Communication Networks ; Computer Graphics ; *Computer Security ; Computer Simulation ; *DNA ; },
abstract = {Biotechnological methods can be used for cryptography. Here two different cryptographic approaches based on DNA binary strands are shown. The first approach shows how DNA binary strands can be used for steganography, a technique of encryption by information hiding, to provide rapid encryption and decryption. It is shown that DNA steganography based on DNA binary strands is secure under the assumption that an interceptor has the same technological capabilities as sender and receiver of encrypted messages. The second approach shown here is based on steganography and a method of graphical subtraction of binary gel-images. It can be used to constitute a molecular checksum and can be combined with the first approach to support encryption. DNA cryptography might become of practical relevance in the context of labelling organic and inorganic materials with DNA 'barcodes'.},
}
@article {pmid10847361,
year = {2000},
author = {McEnery, KW and Suitor, CT and Hildebrand, S and Downs, RL},
title = {Radiologist's clinical information review workstation interfaced with digital dictation system.},
journal = {Journal of digital imaging},
volume = {13},
number = {2 Suppl 1},
pages = {45-48},
pmid = {10847361},
issn = {0897-1889},
mesh = {Data Collection/instrumentation ; Data Display ; Electronic Data Processing ; Humans ; Medical Records Systems, Computerized/*instrumentation ; Microcomputers ; Radiology Information Systems/*instrumentation ; Software ; *User-Computer Interface ; },
abstract = {Efficient access to information systems integrated into the radiologist's interpretation workflow will result in a more informed radiologist, with an enhanced capability to render an accurate interpretation. We describe our implementation of radStation, a radiologist's clinical information review workstation that combines a digital dictation station with a clinical information display. radStation uses client software distributed to the radiologist's workstation and central server software, both running Windows NT (Microsoft, Redmond, WA). The client system has integrated digital dictation software. The bar-code microphone (Boomerang, Dictaphone Corp, Stratford, CT) also serves as a computer input device forwarding the procedure's accession number to the server software. This initiates multiple queries to available legacy databases, including the radiology information system (RIS), laboratory information system, clinic notes, hospital discharge, and operative report system. The three-tier architecture then returns the clinical results to the radStation client for display. At the conclusion of the dictation, the digital voice file is transferred to the dictation server and the client notifies the RIS to update the examination status. The system is efficient in its information retrieval, with queries displayed in about 1 second. The radStation client requires less than 5 minutes of radiologist training in its operation, given that its control interface integrates with the well-learned dictation process. The telephone-based dictation system, which this new system replaced, remains available as a back-up system in the event of an unexpected digital dictation system failure. This system is well accepted and valued by the radiologists. The system interface is quickly mastered. The system does not interrupt dictation workflow with the display of all information initiated with examination bar-coding. This system's features could become an accepted model as a standard tool for radiologists.},
}
@article {pmid10596034,
year = {1999},
author = {Koch, HH and Amarotico, E and Weidringer, JW and Inglis, R},
title = {[A model project on certification of continuous education by the Bavarian Chamber of Physicians].},
journal = {Zeitschrift fur arztliche Fortbildung und Qualitatssicherung},
volume = {93},
number = {8},
pages = {551-554},
pmid = {10596034},
issn = {1431-7621},
mesh = {*Certification ; *Education, Medical, Continuing ; *Education, Medical, Graduate ; Germany ; Humans ; Physicians ; },
abstract = {Beginning with April 1st 1998 Bavarian physicians are invited to join a project on certification of continuing medical education on a voluntary basis. After a one year period, 1238 of practicing medical doctors (2.8%) received an official certificate on continuing medical education by the Bavarian Chamber of Physicians. In order to get the idea to certify postgraduate continuing medical education spread over the state of Bavaria, the Bavarian Chamber of Physicians takes every effort to support congress organizers to issue credit points. Customer oriented processes are applied as well as modern technologies such as bar-codes. The systematic approach to take part in continuing medical education as an important aspect of quality assurance in physician's profession reveals the chance to keep autonomy within the medical chambers.},
}
@article {pmid10564590,
year = {2000},
author = {Vaandrager, JW and Schuuring, E and Raap, T and Philippo, K and Kleiverda, K and Kluin, P},
title = {Interphase FISH detection of BCL2 rearrangement in follicular lymphoma using breakpoint-flanking probes.},
journal = {Genes, chromosomes &amp; cancer},
volume = {27},
number = {1},
pages = {85-94},
pmid = {10564590},
issn = {1045-2257},
mesh = {3' Untranslated Regions/genetics ; 5' Untranslated Regions/genetics ; *Chromosome Breakage ; Chromosomes, Human, Pair 14/genetics ; Chromosomes, Human, Pair 18/genetics ; DNA/blood ; DNA Probes ; DNA, Neoplasm/analysis ; *Gene Rearrangement ; Genes, Immunoglobulin/genetics ; Genes, bcl-2/*genetics ; Humans ; In Situ Hybridization, Fluorescence ; Interphase/genetics ; Leukocytes/chemistry/cytology ; Lymphoma, Follicular/*genetics/pathology ; Palatine Tonsil/pathology ; Physical Chromosome Mapping ; Proto-Oncogene Proteins c-bcl-2/biosynthesis ; Tonsillar Neoplasms/*genetics/pathology ; Translocation, Genetic ; },
abstract = {Rearrangement of the BCL2 gene is an important parameter for the differential diagnosis of non-Hodgkin lymphomas. Although a relatively large proportion of breakpoints is clustered, many are missed by standard PCR. A FISH assay is therefore desired. Up to now, a lack of probes flanking the BCL2 gene has limited the possibilities for a FISH assay to an approach based on colocalization of probes for BCL2 and the immunoglobulin heavy chain (IGH) locus. Intrinsically high rates of false positive nuclei and high interobserver variability make such assays unsuitable for use on lymphoma tissue samples, where tumor cells often form only a minority of the cell population. Using YAC end cloning techniques and screening of a PAC library, we have isolated PAC clones flanking the BCL2 gene. Using these PACs, and several cosmid clones in the second BCL2 intron, we developed a segregation-based interphase FISH assay with two probe combinations enabling separate detection of 5' and 3' (mbr/mcr) breakpoints. The assay was applied to a series of 40 follicular lymphomas. To evaluate the results, the same lymphomas were analyzed by DNA fiber FISH with a 600-kb set of BCL2 DNA clones labeled in alternating colors in combination with a color barcode covering the IGH locus. This approach allowed precise mapping of BCL2 breakpoints, and simultaneously showed juxtaposition of IGH genes to BCL2. Comparison of the results of interphase and fiber FISH showed complete correlation. Five cases were negative with both FISH techniques as well as with Southern blotting. Interestingly, all of these 5 cases lacked BCL2 overexpression as determined by immunohistochemistry, against 3 of 35 rearrangement-positive follicular lymphomas. Furthermore, absence of t(14;18) seemed to be correlated with a higher histologic grade (grades 2 and 3 according to Berard). These data indicate that the segregation-based interphase FISH assay detects 100% of BCL2 rearrangements. Because interpretation of the results is straightforward and requires no extensive experience, this assay may be the best available diagnostic test for BCL2 rearrangement. Genes Chromosomes Cancer 27:85-94, 2000.},
}
@article {pmid9763572,
year = {1998},
author = {Vaandrager, JW and Schuuring, E and Kluin-Nelemans, HC and Dyer, MJ and Raap, AK and Kluin, PM},
title = {DNA fiber fluorescence in situ hybridization analysis of immunoglobulin class switching in B-cell neoplasia: aberrant CH gene rearrangements in follicle center-cell lymphoma.},
journal = {Blood},
volume = {92},
number = {8},
pages = {2871-2878},
pmid = {9763572},
issn = {0006-4971},
mesh = {B-Lymphocyte Subsets/*immunology/pathology ; Biotinylation ; Digoxigenin ; *Gene Rearrangement, B-Lymphocyte, Heavy Chain ; Genes, Immunoglobulin ; Haplotypes/genetics ; Humans ; *Immunoglobulin Class Switching ; Immunoglobulin Constant Regions/*genetics ; Immunoglobulin Heavy Chains/*genetics ; In Situ Hybridization, Fluorescence/*methods ; Lymphoma, Follicular ; },
abstract = {Immunoglobulin class switching usually involves deletion of part of the immunoglobulin CH region. By DNA fiber fluorescence in situ hybridization (FISH) with a barcode of probes covering the DH, JH, and CH genes, the configuration of the entire CH region can be visualized on single DNA molecules. Using this technique, we have studied class switching in three types of B-cell neoplasia, mantle-cell lymphoma (MCL), follicular lymphoma (FL) and hairy cell leukemia (HCL), representing B cells in, respectively, pregerminal center, germinal center, and postgerminal center stages of development. In MCL and FL, simultaneous detection of the t(11;14) and t(14;18) breakpoint with probes for the BCL-1 and BCL-2 loci, respectively, allowed differentiation between productive and nonproductive alleles. In none of 10 MCL cases was class switching detected. In 21 HCL, all nonimmunoglobulin M (IgM) cases had class-switch deletion consistent with the expressed isotype on at least one allele. In FL, however, a peculiar pattern of CH rearrangement was observed. In IgM expressing FL, the translocated alleles had switched in 11 of 13 cases, and the nontranslocated allele showed complex rearrangements downstream from the Cmu-Cdelta genes in 9 of 13 cases. These downstream rearrangements may reflect tumor-specific deregulation of the class-switch machinery. All seven immunoglobulin G (IgG) expressing FL showed class switching on both alleles. Fiber FISH analysis also showed several polymorphisms. The most frequent one, present on 38% of all analyzed alleles, consisted of an extra Cgamma gene or pseudogene in the 3' cluster.},
}
@article {pmid9454003,
year = {1997},
author = {},
title = {[Protest against registration of bar-codes of all prescriptions!].},
journal = {Lakartidningen},
volume = {94},
number = {51-52},
pages = {4878, 4880},
pmid = {9454003},
issn = {0023-7205},
mesh = {*Drug Costs ; *Drug Prescriptions ; Registries ; Sweden ; },
}
@article {pmid9474884,
year = {1997},
author = {Vaandrager, JW and Kleiverda, JK and Schuuring, E and Kluin-Nelemans, JC and Raap, AK and Kluin, PM},
title = {Cytogenetics on released DNA fibers.},
journal = {Verhandlungen der Deutschen Gesellschaft fur Pathologie},
volume = {81},
number = {},
pages = {306-311},
pmid = {9474884},
issn = {0070-4113},
mesh = {*Chromosomes, Human, Pair 11 ; *Chromosomes, Human, Pair 14 ; DNA Probes ; DNA, Neoplasm/*analysis/genetics ; Genes, Immunoglobulin ; Genes, Switch ; Humans ; Immunoglobulin Switch Region ; In Situ Hybridization, Fluorescence/methods ; Leukemia, Hairy Cell/*genetics/immunology/pathology ; Lymphoma, Non-Hodgkin/*genetics/immunology/pathology ; *Translocation, Genetic ; },
abstract = {DNA fibers can be released from cell suspensions and frozen tissue and can be used as a template for hybridization with multiple differently labeled probes. Simultaneous hybridization with 5-10 adjacent or partly overlapping probes generates a highly specific "color barcode" for individual DNA segments. Rearrangements in this barcode can be easily detected and mapped. The resolution of DNA fiber FISH is between 2 and 500kb. In mixing experiments of cell lines with different structural abnormalities, we found a sensitivity of approximately 10%. We applied DNA fiber FISH for detection of t(11;14) in mantle cell lymphoma (MCL) and immunoglobulin (Ig) class switching in hairy cell leukemia (HCL). Using a barcode for the Ig and BCL-1 loci at 14q32 and 11q13, we detected and mapped a t(11;14) breakpoint in 35 of 36 MCL. In 5 cases complex mono-allelic rearrangements at both sides of the cyclin D1 gene were identified. In 13 HCL with phenotypic evidence of Ig class switching, including 2 cases with solely IgD, fiber FISH revealed concordant Ig class switch deletions. In most cases both alleles were affected. These results indicate that DNA fiber FISH is a very powerful method to detect and map structural DNA alterations.},
}
@article {pmid8944025,
year = {1996},
author = {Shoemaker, DD and Lashkari, DA and Morris, D and Mittmann, M and Davis, RW},
title = {Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy.},
journal = {Nature genetics},
volume = {14},
number = {4},
pages = {450-456},
doi = {10.1038/ng1296-450},
pmid = {8944025},
issn = {1061-4036},
mesh = {DNA ; DNA Mutational Analysis/methods ; Fluorescence ; *Genetic Techniques ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Open Reading Frames ; Phenotype ; Pilot Projects ; Polymerase Chain Reaction/methods ; Saccharomyces cerevisiae/*genetics ; *Sequence Deletion ; },
abstract = {A quantitative and highly parallel method for analysing deletion mutants has been developed to aid in determining the biological function of thousands of newly identified open reading frames (ORFs) in Saccharomyces cerevisiae. This approach uses a PCR targeting strategy to generate large numbers of deletion strains. Each deletion strain is labelled with a unique 20-base tag sequence that can be detected by hybridization to a high-density oligonucleotide array. The tags serve as unique identifiers (molecular bar codes) that allow analysis of large numbers of deletion strains simultaneously through selective growth conditions. Hybridization experiments show that the arrays are specific, sensitive and quantitative. A pilot study with 11 known yeast genes suggests that the method can be extended to include all of the ORFs in the yeast genome, allowing whole genome analysis with a single selective growth condition and a single hybridization.},
}
@article {pmid8695834,
year = {1996},
author = {Vaandrager, JW and Schuuring, E and Zwikstra, E and de Boer, CJ and Kleiverda, KK and van Krieken, JH and Kluin-Nelemans, HC and van Ommen, GJ and Raap, AK and Kluin, PM},
title = {Direct visualization of dispersed 11q13 chromosomal translocations in mantle cell lymphoma by multicolor DNA fiber fluorescence in situ hybridization.},
journal = {Blood},
volume = {88},
number = {4},
pages = {1177-1182},
pmid = {8695834},
issn = {0006-4971},
mesh = {Chromosome Aberrations/*diagnosis ; Chromosome Disorders ; Chromosome Mapping/methods ; *Chromosomes, Human, Pair 11 ; Cosmids ; Cyclin D1 ; Cyclins/genetics ; DNA, Neoplasm/genetics ; Humans ; In Situ Hybridization, Fluorescence ; Karyotyping/methods ; Lymphoma, Non-Hodgkin/*genetics ; Oncogene Proteins/genetics ; *Translocation, Genetic ; },
abstract = {Several hematologic malignancies are associated with specific chromosomal translocations. Because of the dispersed distribution, chromosomal breakpoints may be difficult to detect using molecular techniques. We present a new application of a recently developed method, DNA fiber fluorescence in situ hybridization (fiber FISH), which allows direct visualization and mapping of chromosomal breakpoints. We tested this method for detection of the t(11;14)(q13;q32) translocation in mantle cell lymphoma. In DNA fiber FISH, a series of fluorochrome-labeled DNA probes covering several hundreds of kilobasepairs is hybridized to linear DNA molecules (or fibers) prepared from frozen tissue or intact cells. By using alternate fluorescent colors, a potential breakpoint region is stained in a color barcode pattern. Breaks in this region will split the barcode in two complementary parts, from which the breakpoint position can be derived. We used a 250-kb barcode covering the BCL-1 locus to detect 11q13 breakpoints in 20 well-characterized mantle cell lymphomas. A t(11;14) was shown by cohybridization of these probes with probes for the Ig heavy chain locus at 14q32. In 18 of 20 mantle cell lymphomas, a breakpoint within the 11q13/BCL-1 barcode was shown by the presence of multiple, complementary translocation products. Fusion of 11q13 and 14q32 sequences on single fibers indicating t(11;14)(q13;q32) was found in all 18 breakpoint-positive mantle cell lymphomas. In one additional case, fusion of an intact 11q13 barcode with 14q32 sequences indicated a breakpoint 100 kb centromeric of the major translocation cluster of BCL-1. Within the 120-kb region of BCL-1, breakpoints were widely scattered. This explains why, so far, a BCL-1 breakpoint had been detected by Southern blot analysis in only 10 of 19 cases. DNA fiber FISH analysis showed a t(11;14) in 95% of mantle cell lymphoma. The results indicate that DNA fiber FISH is a rapid, simple, and equally powerful method for detection of clustered and dispersed translocation breakpoints.},
}
@article {pmid10159907,
year = {1996},
author = {Duffy, LM},
title = {Barcoding at the bedside.},
journal = {Healthcare informatics : the business magazine for information and communication systems},
volume = {13},
number = {8},
pages = {85, 87},
pmid = {10159907},
issn = {1050-9135},
mesh = {Data Collection ; Efficiency, Organizational ; Electronic Data Processing/*methods ; Nursing Service, Hospital/*economics/statistics &amp; numerical data ; *Point-of-Care Systems ; Reproducibility of Results ; Research ; Task Performance and Analysis ; United States ; User-Computer Interface ; },
}
@article {pmid10159906,
year = {1996},
author = {Landek, D},
title = {Barcodes: streamlining specimen collection.},
journal = {Healthcare informatics : the business magazine for information and communication systems},
volume = {13},
number = {8},
pages = {80-1, 83},
pmid = {10159906},
issn = {1050-9135},
mesh = {Chicago ; *Clinical Laboratory Information Systems ; Cost Savings ; Efficiency, Organizational ; Electronic Data Processing ; Hospital Bed Capacity, 500 and over ; Laboratories, Hospital/*organization &amp; administration ; Phlebotomy/*methods ; },
}
@article {pmid7496126,
year = {1995},
author = {Bornmann, L},
title = {[Batch documentation of blood products].},
journal = {Infusionstherapie und Transfusionsmedizin},
volume = {22},
number = {4},
pages = {258-263},
pmid = {7496126},
issn = {1019-8466},
mesh = {*Blood Component Transfusion ; *Blood Donors ; Blood-Borne Pathogens ; Database Management Systems ; Documentation/*methods ; Electronic Data Processing ; Humans ; Information Systems ; },
abstract = {BACKGROUND: In former years transmission of infectious diseases by blood products was repeatedly observed. To trace these incriminated batches of blood products proved to be nearly impossible.<br><br>METHODS: This publication describes the documentation of different batches of blood products. In the simpliest case the batch numbers of blood products can be stored in files using forms. Besides this documentation of batches can be aided by EDP using databases and barcodes. A test for the correct and complete input of data is given.<br><br>RESULTS: The registration of batches of commercially available blood products as well as blood preserves is possible. Incriminated batches can be traced back.<br><br>CONCLUSIONS: Besides donor selection, control of the manufacturing process and the use of inactivation procedures for viruses the documentation of batches substantially contributes to the safety of plasma derivatives. With the applied techniques documentation is easily achieved.},
}
@article {pmid7656117,
year = {1995},
author = {Puckett, F},
title = {Medication-management component of a point-of-care information system.},
journal = {American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists},
volume = {52},
number = {12},
pages = {1305-1309},
doi = {10.1093/ajhp/52.12.1305},
pmid = {7656117},
issn = {1079-2082},
mesh = {Clinical Pharmacy Information Systems/*organization &amp; administration ; Colorado ; Documentation ; Efficiency, Organizational ; Hospital Bed Capacity, 300 to 499 ; Humans ; Medical Staff, Hospital/education/psychology ; Medication Errors ; Medication Systems, Hospital/*organization &amp; administration ; Nursing Staff, Hospital/education/psychology ; Patients' Rooms ; Pharmacy Service, Hospital ; },
abstract = {Implementation of and experience with the medication-management component of a point-of-care information system are described. A point-of-care information system (CliniCare) implemented at a 326-bed primary and tertiary care center provides online medication profiles, medication administration scheduling, and other patient data. All medications are bar coded and are scanned at or near the patient's bedside by using hand-held scanners; this prompts a safety check, records medication administration, and generates the drug charge. Use of the system has resulted in a lower medication error rate, improved medication records, improved scheduling of medications, better communication between nursing and pharmacy staff, more efficient drug monitoring, and more accurate and timely billing. Problems include the need for a bar-coding operation for unit dose oral solids and injectable dosage forms, the steep learning curve for some nurses and physicians, and resistance to the change from a manual system. A point-of-care information system has improved medication management but has been difficult to implement.},
}
@article {pmid10144087,
year = {1995},
author = {Brient, K},
title = {Barcoding facilitates patient-focused care.},
journal = {Healthcare informatics : the business magazine for information and communication systems},
volume = {12},
number = {7},
pages = {38, 40, 42},
pmid = {10144087},
issn = {1050-9135},
mesh = {Clinical Laboratory Information Systems/*trends ; Electronic Data Processing/*trends ; Hospital Bed Capacity, 500 and over ; Nursing Staff, Hospital ; Patient-Centered Care/*organization &amp; administration/standards ; Planning Techniques ; Specimen Handling/methods ; Texas ; Workload ; },
}
@article {pmid7633442,
year = {1995},
author = {Florijn, RJ and Bonden, LA and Vrolijk, H and Wiegant, J and Vaandrager, JW and Baas, F and den Dunnen, JT and Tanke, HJ and van Ommen, GJ and Raap, AK},
title = {High-resolution DNA Fiber-FISH for genomic DNA mapping and colour bar-coding of large genes.},
journal = {Human molecular genetics},
volume = {4},
number = {5},
pages = {831-836},
doi = {10.1093/hmg/4.5.831},
pmid = {7633442},
issn = {0964-6906},
mesh = {Chimera/genetics ; Chromosome Mapping/*methods ; Chromosomes, Artificial, Yeast ; Cloning, Molecular ; Color ; Cosmids/genetics ; DNA/*genetics ; Gene Deletion ; Gene Rearrangement ; Genome, Human ; Humans ; Image Processing, Computer-Assisted ; In Situ Hybridization, Fluorescence/*methods ; Male ; Muscular Dystrophies/genetics ; Plasmids/genetics ; Repetitive Sequences, Nucleic Acid ; Restriction Mapping ; Thyroglobulin/genetics ; },
abstract = {We have applied two-colour fluorescence in situ hybridization (FISH) to DNA fibers and combined it with digital imaging microscopy for the mapping of large cosmid contigs. The technique was validated using a set of unique plasmids and a cosmid contig both originating from the thyroglobulin (Tg) gene and previously mapped by restriction analysis. The resolution proved to be close to the theoretical lower limit of approximately 1 kb, ranging > or = 400 kb. Subsequently a 400 kb cosmid contig derived from a DMD-YAC was directly mapped by Fiber-FISH. The resulting map is in full agreement with the restriction map. Two-colour Fiber-FISH mapping thus showed to be capable for accurately sizing gaps and overlaps, and to identify chimeric or repeat sequence containing cosmids across a 400 kb region at once. The generated 400 kb 'colour bar-code' was subsequently used to map two DMD deletion breakpoints in patient DNA with an accuracy of 1-2 kb. The results underscore the value of this method for the delineation of chromosomal rearrangements for positional cloning and single patient clinical studies.},
}
@article {pmid7767400,
year = {1995},
author = {Fisher, MM and Hitchins, L and McDougall, D and Sherriff, G and Brown, J and Blakeman, A and Bowell, P and Strange, J and Gunson, HH},
title = {Pilot trials of PDF symbology as a means of transfering data on blood units between transfusion centres.},
journal = {Transfusion medicine (Oxford, England)},
volume = {5},
number = {1},
pages = {63-67},
doi = {10.1111/j.1365-3148.1995.tb00187.x},
pmid = {7767400},
issn = {0958-7578},
mesh = {*Blood Banks ; Blood Transfusion ; *Electronic Data Processing/economics ; Humans ; Pilot Projects ; },
abstract = {PDF 417, a two-dimensional barcode, was used as a portable data file to transfer key information on blood units and delivery documentation between two Regional Blood Transfusion Centres. Multiple Codabar messages currently displayed on blood packs, as well as other useful information, i.e. microbiology conformance, were encoded in a 45-character single PDF barcode. The delivery note which accompanied each consignment of blood consisted of a series of PDF barcodes, each representing 20 blood units. Computer validation showed 100% reconciliation of PDF data with Codabar data. Readability of the code was excellent with a greater than 98% first-pass read rate. The delivery note PDF barcode identified eight operator errors which would have been undetected by the present manual system. We conclude that PDF 417 is an effective, secure and space efficient means of transferring data associated with the transfer of blood.},
}
@article {pmid8591555,
year = {1995},
author = {Ogilvie, RW},
title = {An interactive histology image-barcode manual for a videodisc image library.},
journal = {Medinfo. MEDINFO},
volume = {8 Pt 2},
number = {},
pages = {1698},
pmid = {8591555},
issn = {1569-6332},
mesh = {*Computer-Assisted Instruction ; *Education, Dental ; *Education, Medical, Undergraduate ; Histology/*education ; *Manuals as Topic ; Optical Storage Devices ; South Carolina ; },
abstract = {UNLABELLED: Cell Biology and HISTOLOGY (alias Microanatomy, alias Microscopic Anatomy) is a required course for first-year medical and dental students in most health science centers. The traditional approach used in teaching this discipline is to present photomicrographic images of structures to students in lecture using 35 mm slides of fields seen through the microscope. The students then spend many hours viewing and studying specimens of tissues using a light microscope in a laboratory setting. Students in traditional courses of histology spend an inordinate amount of time learning the component structures by attempting to find and identify them in tissue sections using a microscope, where the structure being sought is surrounded by a multitude of other structures with which they are also not familiar. With the recent availability of videodisc stored image libraries of histological samples, it is now possible to study histological principles without the use of the microscope as the primary learning tool. A videodisc entitled "<br><br>HISTOLOGY: A Photographic Atlas" by S. Downing (published by Image Premastering Services Limited, Minneapolis, MN, 1991) has been incorporated into our histology course. Fifteen videodisc player stations are provided for 150 students. Images are retrieved by students using a bar code scanner attached to a videodisc player (Pioneer CLD-2400). Using this kind of image library, students can now learn basic histological structure, such as cell and tissue types, without the use of a microscope or as a tool for facilitating microscopy. The use of a videodisc library of randomly accessible images simplifies learning the basic components which all organs are composed of by presenting the learner with clear-cut examples to avoid confusion with other structures. However, videodisc players and TV monitors are still not appropriately priced for every student to own. This presents a problem in that the same images studied in class are not available to study and review outside of class. There is a need for resources for additional study outside of the institutional setting, for students to have and interact with to reinforce the learning experience in the teaching laboratory. A hard copy manual was created and is being used in our course; it incorporates photos captured from the videodisc. The images displayed in the manual are chosen to give the student one example of each histological component. Additional labeling is added to the images, and each image is accompanied by a bar code that may be used at a videodisc player with a bar code reader to retrieve the same color image from the disc displayed in larger format on a TV monitor. Each topic in the manual is accompanied by learning objectives and a statement of clinical relevance. Following the presentation of the images in each section of the manual, the students are encouraged to practice by viewing multiple examples of each structural component presented in the lesson. They can do this by using the bar-coded catalog supplied with each disc. The presentation of each topic concludes with a quiz composed of questions about images that the student can retrieve from the videodisc using barcodes in the text of the manual. Some of the images on the quiz are printed in miniature in the manual to provide the student with an opportunity for personal review at home when hardware to obtain and display images from a video disc is not available. This manual provides an answer to the dilemma faced by the learner when access to hardware is not available; reinforcement is therefore facilitated outside the teaching laboratory. This allows learning to continue outside of the classroom, using the same materials. (abstract truncated)},
}
@article {pmid8591552,
year = {1995},
author = {Downing, SW},
title = {A multimedia-based histology laboratory course: elimination of the traditional microscope laboratory.},
journal = {Medinfo. MEDINFO},
volume = {8 Pt 2},
number = {},
pages = {1695},
pmid = {8591552},
issn = {1569-6332},
mesh = {*Computer-Assisted Instruction ; *Education, Medical, Undergraduate ; Histology/*education ; Minnesota ; Optical Storage Devices ; },
abstract = {UNLABELLED: We have developed a multimedia-based laboratory course which has enabled us to eliminate the microscope and traditional microscope laboratory that have been mainstays of our histology course and histology courses at almost all institutions where histology is taught. The multimedia laboratory uses a library of histology images (approximately 24,000) stored on videodisc (<br><br>HISTOLOGY: A Photographic Atlas, by S. Downing) as its microscope slide collection and accesses those images through barcode and computer interfaces. The laboratory workstations consist of a videodisc player, videodisc monitor, computer, and computer monitor. One workstation is available for every 4-students, and our students are encouraged to work together in groups of four or five. In our current set-up, the students are introduced to and instructed in the basic principles of histology using a computer program that interfaces with the videodisc images. The computer program is divided into 19 chapters (the chapters are typical of the chapters found in a normal histology textbook) and has: (1) a laboratory component that covers the material traditionally covered in the microscope laboratory, and (2) a lecture component that enables the students to evaluate their understanding of the lecture material in a non-punishing way. The laboratory section of each chapter is divided into a "MicroLab" section, an "InFo Time" section, and a "Quiz Time" section. Each of these sections interfaces with histological images stored on the videodisc. The students are encouraged to work through the "MicroLab" section of each chapter before moving on to the "InFo Time" and "Quiz Time" sections. The "MicroLab" sections introduce the students to the various tissues and organs of the body and is interfaced with the videodisc player and the histology images stored on the videodisc. These sections describe the basic histological features of the various tissues and organs and give the students access to multiple examples of what they are studying. The "InFo Time" sections bring up specific images and ask the students to think about the images. Information about the images being observed is available if the students want it and the students can flag those images that they found difficult. The Quiz Time section of the program is also interfaced with the videodisc player and provides access to a large number of histology images stored on the videodisc. The "Quiz Time" sections provide non-punishing review questions that the students can study after she has worked her way through the "MicroLab" and "InFo Time" sections. In addition to the use of a computer program to access the histology images stored on videodisc, we use barcodes that address specific images on the histology videodisc in a variety of ways to augment the students' laboratory and lecture experience. The benefits of using multimedia in place of the traditional microscope and microscope slide collection are numerous and include the speed at which specific histological images can be accessed and reviewed (when compared to finding a structure on a glass slide), a significant reduction in the amount of laboratory time needed by the student to learn the same amount of information, the ease of tutoring on a large monitor screen (when compared to trying to discuss a histological structure with a student through the eyepiece of a microscope), the encouragement of group study (which is difficult to do when a student is working 1-on-with a microscope), and the reduction of the number of faculty necessary to cover a typical histology laboratory session. The use of barcodes that address specific videodisc histology images has greatly changed our examination procedures and has significantly expanded the usefulness of the traditional lecture note handouts given to our students.},
}
@article {pmid8017804,
year = {1994},
author = {Shepherd, JP and Brickley, MR and Jones, ML},
title = {Automatic identification of surgical and orthodontic instruments.},
journal = {Annals of the Royal College of Surgeons of England},
volume = {76},
number = {2 Suppl},
pages = {59-62},
pmid = {8017804},
issn = {0035-8843},
mesh = {Electronic Data Processing/*methods ; General Surgery/education ; Humans ; Orthodontics/*instrumentation ; Surgery, Oral/instrumentation ; *Surgical Instruments ; },
abstract = {Surgical instruments are becoming increasingly expensive and represent an important component of the costs of operating theatres. The use and processing of surgical instruments in decontamination and packaging units and in the operating theatre need to be monitored, both to improve efficiency and to allow measurement of the effectiveness of training in operative technique. Automatic identification of surgical and orthodontic instruments was therefore performed using two standard methods: the two-dimensional bar-code and matrix code. Encryption (the formulation of codes), was carried out prior to bar and matrix coding using acid-etch and laser techniques respectively. 'Reading' of the two types of code was more difficult with bar-codes because of the high reflectivity of background polished stainless steel, and only large instruments had sufficient area for bar-coding. Consistent, accurate, automatic identification of the instruments was possible with the matrix code for which a surface of only 4 sq mm is necessary. After 50 cycles of decontamination and packaging, neither code showed obvious deterioration and it was possible to read the matrix code as easily as prior to this process. Automatic instrument identification is possible using recently developed methods and could facilitate economies in the processing of instruments in health facilities and the automatic recording of instrument usage in the operating theatre.},
}
@article {pmid10132948,
year = {1994},
author = {Richmond, L},
title = {Barcoding in the lab: achieving error-free efficiencies.},
journal = {Healthcare informatics : the business magazine for information and communication systems},
volume = {11},
number = {3},
pages = {26-8, 30},
pmid = {10132948},
issn = {1050-9135},
mesh = {Clinical Laboratory Information Systems/economics/*instrumentation/organization &amp; administration ; Cost-Benefit Analysis ; *Efficiency, Organizational ; *Electronic Data Processing/economics/standards ; Hospitals, Religious/organization &amp; administration ; Judaism ; Laboratories, Hospital/*standards ; Missouri ; Software ; Total Quality Management ; },
}
@article {pmid8251620,
year = {1993},
author = {Khashoggi, A and Lichtenstein, C},
title = {SequAlign: a computer program that displays DNA sequence alignments as a compact 'bar-code' graph.},
journal = {Plant molecular biology},
volume = {23},
number = {4},
pages = {639-642},
doi = {10.1007/BF00021521},
pmid = {8251620},
issn = {0167-4412},
mesh = {Base Sequence ; DNA/chemistry ; Molecular Sequence Data ; *Sequence Alignment ; Sequence Homology, Nucleic Acid ; *Software ; },
}
@article {pmid8259128,
year = {1993},
author = {Arnot, DE and Roper, C and Bayoumi, RA},
title = {Digital codes from hypervariable tandemly repeated DNA sequences in the Plasmodium falciparum circumsporozoite gene can genetically barcode isolates.},
journal = {Molecular and biochemical parasitology},
volume = {61},
number = {1},
pages = {15-24},
doi = {10.1016/0166-6851(93)90154-p},
pmid = {8259128},
issn = {0166-6851},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Base Sequence ; Blotting, Southern ; DNA, Protozoan/*genetics ; Molecular Sequence Data ; Plasmodium falciparum/classification/*genetics/isolation &amp; purification ; Polymerase Chain Reaction ; Protozoan Proteins/*genetics ; *Repetitive Sequences, Nucleic Acid ; },
abstract = {DNA typing systems currently used in parasitology involve either hybridising Southern blots with repetitive sequence probes or amplifying genomic sequences using the polymerase chain reaction (PCR). Both such approaches assay allelic length variation, usually in unexpressed tandemly repeated DNA sequences. Where an appropriate target locus exists, an alternative PCR-based strategy which reveals allelic sequence variation in tandemly repeated DNA offers a more accurate and internally controlled assay. We describe such a strategy for the rapid extraction of information on tandem repeat sequence variation from hypervariable alleles, and apply it to the Plasmodium falciparum CS gene. The extreme variability of such DNA 'barcodes' can be used to identify parasite stocks and lineages. This system is also potentially useful for population genetic and epidemiological studies since it offers the possibility of following the spread of distinctively marked parasite genotypes in samples taken from infected individuals.},
}
@article {pmid8371009,
year = {1993},
author = {Saji, F},
title = {[Application of DNA fingerprinting to obstetrics and gynecology].},
journal = {Nihon Sanka Fujinka Gakkai zasshi},
volume = {45},
number = {8},
pages = {815-821},
pmid = {8371009},
issn = {0300-9165},
mesh = {Animals ; *DNA Fingerprinting ; Female ; Forensic Medicine ; Genital Neoplasms, Female/diagnosis ; *Gynecology ; Humans ; Hydatidiform Mole/diagnosis ; Male ; *Obstetrics ; Paternity ; Pregnancy ; },
abstract = {Restriction fragment length polymorphisms (RFLP) are variations in the size of restriction fragments of genomic DNA that hybridize to specific probes. They are the consequence of changes in primary DNA sequences, most of which result from small-scale changes in DNA. Recently minisatellite DNA probes that detect many regions of great variability within the human genome have been described. Minisatellite probes consist of multiple repeated copies of a common 10-15 base pair core sequence. On hybridization to restriction enzyme digests of human DNA, they simultaneously detect many highly polymorphic minisatellites at different loci in the genome, and produce band patterns that are individual specific. The band patterns are called "DNA fingerprints" or "DNA barcode" which can be used for individual identification on forensic and legal medicine. In addition to forensic and legal medicine, DNA fingerprinting can be used in both basic research and clinical examination of obstetrics and gynecology. The RFLP bands in DNA fingerprinting are inherited as single Mendelian co-dominants and we can use such minisatellite DNA probe for the determination of zygosity in multiple pregnancy. This probe can be used for the determination of androgenesis as a cause of complete hydatidiform mole. Each polymorphic band in molar tissues could be identified as being of paternal but not maternal origin. Some polymorphic bands of paternal origin were not observed in molar tissues, indicating that endoreduplication of a normal haploid sperm or fertilization by dispermy to an anuclear oocyte with no effective genome could be the cause of complete hydatidiform mole (androgenesis).(ABSTRACT TRUNCATED AT 250 WORDS)},
}
@article {pmid1528529,
year = {1992},
author = {Pfaff, G and Spitzer, V and Richards, G and Stewart, S},
title = {Using barcodes to access videodiscs.},
journal = {Nursing educators microworld},
volume = {6},
number = {6},
pages = {41, 43},
pmid = {1528529},
issn = {0893-1356},
mesh = {*Computer-Assisted Instruction ; *Education, Nursing ; *Videodisc Recording/methods ; },
}
@article {pmid1284764,
year = {1992},
author = {Brinkhues, O and Giers, G and Hanfland, P},
title = {[Electronic data processing-assisted serial automation of current methods in blood group serology].},
journal = {Beitrage zur Infusionstherapie = Contributions to infusion therapy},
volume = {30},
number = {},
pages = {474-477},
pmid = {1284764},
issn = {1011-6974},
mesh = {ABO Blood-Group System/analysis ; Blood Donors ; Blood Grouping and Crossmatching/*instrumentation ; Centrifugation/instrumentation ; Electronic Data Processing/*instrumentation ; Equipment Design ; Humans ; Kell Blood-Group System/analysis ; Rh-Hr Blood-Group System/analysis ; },
abstract = {The introduction of special centrifugable racks with a transparent bottom into the conventional typing of blood groups in glass tubes facilitates the simultaneous work on and reading of a maximum of 32 complete ABO, Rhesus and Kell typings in one series. As a result of the facts that it is unnecessary to label the individual tubes and that the pipetting of serum and erythrocyte suspensions is done automatically and through the unmistakable classification of the samples by means of bar-coding, the manual work is reduced to about 50%. This modified typing method combines the advantages of the conventional typing method in glass tubes with the advantages of an efficient microplate technique. There is no qualitative loss in the implementation and reading of the analysis.},
}
@article {pmid2032064,
year = {1991},
author = {Bruns, BJ},
title = {Productivity enhancements using hand-held computers: a case study.},
journal = {Biomedical instrumentation &amp; technology},
volume = {25},
number = {2},
pages = {122-128},
pmid = {2032064},
issn = {0899-8205},
mesh = {Biomedical Engineering/*methods/organization &amp; administration ; *Computers ; Documentation/*methods ; Electronic Data Processing ; Equipment and Supplies, Hospital ; *Information Systems ; },
abstract = {In closing, the benefits of computerizing the equipment control information system have been assessed qualitatively and, to an extent, quantitatively. We have seen a drastic improvement in the operation of the clinical engineering department. Equipment repair and inspection results are readily accessible for technician use. Equipment service reports are typed and easy to read. Accountability of repair parts are immediately available for restocking and financial needs. Feedback reports are generated on a regular and timely basis. We have shown a reduction of around 12 minutes in the inspection procedure. This time has been directly linked to the automation of the inspection process using hand-held computers. The cost of automation was inexpensive, as the hand-held computers cost around 500 dollars per unit. Currently, the devices are used by any technician who performs inspections outside the department. The units time the inspection process and record the inspection result. We have interfaced the units to portable bar-code printers that produce an inspection label on-site. In the future, bar-code wands and guns will be used to streamline the data entry process of the inspection. A reduction in the number of incorrectly typed ECNs will improve the integrity of the database. The use of bar-codes will eventually spread to the parts' system. This will improve tracking, ordering, and inventorying repair parts. The plan is to improve the documentation of these parts and ease the analysis of new equipment needs, manufacturer reliability, and contract evaluations. At the present, we are addressing the problem of preparation time.(ABSTRACT TRUNCATED AT 250 WORDS)},
}
@article {pmid2260817,
year = {1990},
author = {Cohen, BL},
title = {Emerging technologies in the field of healthcare: enhancing the interface to the medical professional.},
journal = {Annals of the Academy of Medicine, Singapore},
volume = {19},
number = {5},
pages = {627-639},
pmid = {2260817},
issn = {0304-4602},
mesh = {Computer Graphics ; *Computer Systems ; Electronic Data Processing ; Expert Systems ; Software Design ; *User-Computer Interface ; },
abstract = {This paper reviews the latest technology either available or currently under development which will enhance the medical professional's ability to interface computer systems. This technology includes bar-coding, graphics, intelligent workstation, and expert system. Whenever possible, examples are given to illustrate the technology.},
}
@article {pmid2208692,
year = {1990},
author = {Bond, LW},
title = {Consideration of laboratory parameters in design and implementation of automated systems with barcoding.},
journal = {Clinical chemistry},
volume = {36},
number = {9},
pages = {1583-1584},
pmid = {2208692},
issn = {0009-9147},
mesh = {Clinical Laboratory Information Systems/*trends ; *Hospital Design and Construction ; *Laboratories, Hospital ; Medical Laboratory Science/*trends ; },
}
@article {pmid10103695,
year = {1990},
author = {Davis, NM},
title = {Detection and prevention of ambulatory care pharmacy dispensing errors.},
journal = {Hospital pharmacy},
volume = {25},
number = {1},
pages = {18-22, 28},
pmid = {10103695},
issn = {0018-5787},
mesh = {Ambulatory Care/*standards ; Drug Prescriptions ; Electronic Data Processing ; Humans ; *Medication Errors ; Pharmaceutical Services/*standards ; *Quality Assurance, Health Care ; United States ; },
abstract = {There have been few studies of errors committed in ambulatory care pharmacies. Errors can be classified as incorrect strength, wrong product, wrong dosage form, wrong quantity, incorrect or omitted labeling (such as directions, patient's name, prescriber's name, auxiliary label, drug name, or strength), dispensing deteriorated drugs, and dispensing in non-childproof containers. Errors can be prevented by possessing and using knowledge, by proper performance and by having good systems in effect to prevent and/or uncover errors. Some contributing factors, which cause errors, are distraction and interruption, poor work habits, thoughtless robot-like performance, workloads past the safety threshold, poor working conditions, poorly written and incomplete prescriptions. A prime system to prevent errors from reaching the patient is the old tried and true system of having work checked by another person. The use of patient profiles can aid in reducing errors. The activity of patient counseling can reduce errors. Suggestions are made to reduce the number of errors made. A simple quality assurance program is presented. Case studies of medication errors are presented. The future use of bar-coding should be an extremely useful tool for preventing medication errors.},
}
@article {pmid1703891,
year = {1990},
author = {Roos, D},
title = {[Standardization of bar code information on blood unit labels for automation of blood unit exchange between blood donor and transfusion services and blood banks].},
journal = {Beitrage zur Infusionstherapie = Contributions to infusion therapy},
volume = {26},
number = {},
pages = {424-430},
pmid = {1703891},
issn = {1011-6974},
mesh = {*Blood Banks ; Blood Grouping and Crossmatching/*standards ; Blood Transfusion/*instrumentation ; Electronic Data Processing/*standards ; Germany ; Humans ; International System of Units/*standards ; Online Systems/*instrumentation ; *Software/standards ; },
abstract = {Exchange of blood units between transfusion services and blood depots, using EDP systems requires standardisation of unit identification and bar-codes. The ISBT Working Party on Data Processing defined recommendations for blood-unit identification by Codabar. Our group (German Society of Transfusion Medicine and Immunohematology, Section Data Processing and Standardization) extended and adapted these standards to the German blood bank settings. This paper describes the basic definitions and standards. A complete outline will be published in the next future.},
}
@article {pmid1703890,
year = {1990},
author = {Fischer-Fröhlich, CL and Stoll, T and Hanfland, P},
title = {[Guidelines for electronic-data-processing-controlled serial diagnosis of donor blood samples].},
journal = {Beitrage zur Infusionstherapie = Contributions to infusion therapy},
volume = {26},
number = {},
pages = {420-423},
pmid = {1703890},
issn = {1011-6974},
mesh = {*Blood Banks ; *Blood Donors ; Blood Group Incompatibility/blood/prevention &amp; control ; Blood Grouping and Crossmatching/*instrumentation ; Blood Transfusion/*instrumentation ; Documentation/methods ; Electronic Data Processing ; Humans ; *Microcomputers ; Online Systems/*instrumentation ; Quality Control ; Risk Factors ; *Software ; },
abstract = {UNLABELLED: Increasing performance figures and the necessity to save expenses oblige transfusion services to automatize their donors' laboratory examination. Sufficient hard- and software for sample distribution and processing is now available. Following aspects should be regarded when switching to automatic serial screening:<br><br>SAFETY: The identity of blood-donor, donation and laboratory result will be achieved by machine readable labeling and on-line communication between working-stations and central administration. Flexibility: Easy automatic selective laboratory screening will be possible using special barcodes including sample identification and working orders. A modular hardware concept with easily accessible programming control allows it to implement new devices or methods. Ergonomy: Automatic sample processing including selective screening and simultaneous operating robotic sample processors increase working quality, sample output and time benefits. Economy: Improved working conditions will result in saving reagents and compensating staff limitations.},
}
@article {pmid3261697,
year = {1988},
author = {Hill, AR and Reeves, BC and Burgess, A},
title = {Huematic--an automated scorer for the Farnsworth-Munsell 100 hue test.},
journal = {Eye (London, England)},
volume = {2 (Pt 1)},
number = {},
pages = {80-86},
doi = {10.1038/eye.1988.17},
pmid = {3261697},
issn = {0950-222X},
mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Child ; Color Perception Tests/*instrumentation ; Color Vision Defects/diagnosis ; Humans ; Microcomputers ; Middle Aged ; },
abstract = {A cheap, portable automated scorer for the Farnsworth-Munsell (FM) 100 hue test has been developed. It consists of a light pen, a series of omni-directional bar-codes attached to the reverse of the FM 100 hue caps and a small micro-computer. The print-out includes patient details, a linear histogram of the partial errors by cap position, indication of the peak error positions for congenital colour vision deficiencies and appropriate statistical analysis of the total error score. All the results are available within four minutes of completing the testing procedure.},
}
@article {pmid3659744,
year = {1987},
author = {Diot, JC and Ahr, J and Fréal, C},
title = {[Direct collection of information during blood donation in blood mobiles].},
journal = {Revue francaise de transfusion et immuno-hematologie},
volume = {30},
number = {2},
pages = {87-102},
doi = {10.1016/s0338-4535(87)80153-8},
pmid = {3659744},
issn = {0338-4535},
mesh = {*Blood Donors ; *Electronic Data Processing ; Humans ; Microcomputers ; Software ; Surveys and Questionnaires ; },
abstract = {Direct data storage, in the presence of the donor, ensures a realistic reliability and erases any deferred interpretation of the essential information for a good donation identification. Computers can help relieve this restraint. Indeed the evolution of microcomputers (increased capacity and power, decreased weight and volume, and good performance in any use makes them more and more accurate. Associated use of barcodes and microcomputers gives a nonmanual non-human line of words: donor-donation-analysis-blood products-patient. We found, working that way, the following advantages: Information secured. No deferred inputs. Instart comparison of the information on the donor's past history. Accurate donation-donor connection. Such a system represents one more step towards a continuous line of treatment from Donor to Patient in regard of Blood Transfusion Safety.},
}
@article {pmid6206746,
year = {1984},
author = {Sutherland, JC and Monteleone, DC and Trunk, J and Ciarrocchi, G},
title = {Two-dimensional, computer-controlled film scanner: quantitation of fluorescence from ethidium bromide-stained DNA gels.},
journal = {Analytical biochemistry},
volume = {139},
number = {2},
pages = {390-399},
doi = {10.1016/0003-2697(84)90023-x},
pmid = {6206746},
issn = {0003-2697},
mesh = {Computers ; DNA/*analysis ; Electrophoresis, Agar Gel ; Ethidium ; Fluorescence ; Photography/*instrumentation ; Staining and Labeling ; },
abstract = {A two-dimensional scanner based on a digital plotter is described. The device is used to analyze photographic negatives of ethidium bromide-stained DNA-agarose gels. Scanning is controlled by and photometric data transferred to a computer for processing, storage, display, and analysis such as integration of the areas under bands and determination of the mean distances of migration of polydisperse samples. An integral light source and detector module designed for reading optical "bar-codes" is mounted in place of the pen of the plotter. Spatial resolution and reproducibility are about 0.2 and 0.005 mm, respectively. Photometric precision as good as one part per thousand is achieved by sinusoidal modulation of the intensity of the light source and synchronous, phase-sensitive detection of the signal from the detector by a lock-in amplifier. No part of the sensor assembly touches the surface of the negative. In contrast to a densitometer, the computer transforms photometric data to values directly proportional to the amount of DNA at given points on the original gel. The ability to move the sensor in two dimensions over the negative allows for the integration across the width of a lane correctly allowing for the nonuniform distribution of the DNA.},
}
@article {pmid6692748,
year = {1984},
author = {Hokanson, JA and Guernsey, BG and Bryant, SG and Doutré, WH and Ingrim, NB and Grant, JA and Galvan, E},
title = {The feasibility of barcode-based dispensing quality assurance programs.},
journal = {Drug intelligence &amp; clinical pharmacy},
volume = {18},
number = {1},
pages = {76-78},
doi = {10.1177/106002808401800118},
pmid = {6692748},
issn = {0012-6578},
support = {CA 17701/CA/NCI NIH HHS/United States ; },
mesh = {*Computers ; Feasibility Studies ; Medication Errors ; *Medication Systems, Hospital ; Quality Control ; },
abstract = {A study was conducted to evaluate the feasibility of using barcodes in an outpatient pharmacy quality assurance program. In the first step of this study, adhesive labels containing a barcode representation of the National Drug Code (NDC) identification for the hospital's formulary medications were printed for each stock bottle or drug package used in dispensing. When an outpatient prescription was presented to the pharmacist, a label containing a barcode representation of the NDC identification for the prescribed medication was generated on-line and attached to the back of the prescription form. After the prescription item was filled by the pharmacist, an automated check was performed with a scanning wand by comparing the barcode on the prescription with the previously generated barcode on the stock bottle or drug packaging. A match indicated that the correct medication had been dispensed. Elaborations on this basic automated system for a barcode-based dispensing quality assurance program are suggested.},
}
@article {pmid7066639,
year = {1982},
author = {Morrey, D and Smith, CW and Belcher, RA and Harding, T and Sutherland, WH},
title = {A microcomputer system for prescription, calculation, verification and recording of radiotherapy treatments.},
journal = {The British journal of radiology},
volume = {55},
number = {652},
pages = {283-288},
doi = {10.1259/0007-1285-55-652-283},
pmid = {7066639},
issn = {0007-1285},
mesh = {*Computers ; Humans ; *Microcomputers ; Radiation Monitoring ; *Radiotherapy Dosage ; },
abstract = {The design of a microcomputer system for the reduction of mistakes in radiotherapy is described. The system covers prescription entry, prescription and treatment calculations, and verification and recording of the treatment set-up. A telecobalt unit was interfaced to the system and in the first 12 months 400 patients have been prescribed and 5000 treatment fields verified. The prescription is entered by the medical officer using an interactive program and this prescription provides the reference for verifying the treatment set-up. The program allows amendments to the prescription to be made easily during the treatment course. The treatment parameters verified are field size, wedge and treatment time. The system uses bar-codes for patient and field identification. A reduction in the number of mistakes has been achieved and future developments are discussed.},
}
@article {pmid7035060,
year = {1981},
author = {Gunson, HH},
title = {The use of barcodes to facilitate computerization in blood transfusion.},
journal = {Clinical and laboratory haematology},
volume = {3},
number = {3},
pages = {195-204},
doi = {10.1111/j.1365-2257.1981.tb01333.x},
pmid = {7035060},
issn = {0141-9854},
mesh = {*Blood Banks ; Blood Donors ; Blood Grouping and Crossmatching ; Blood Specimen Collection ; Blood Transfusion ; *Computers ; Humans ; },
}
@article {pmid7219094,
year = {1980},
author = {Ibbotson, RN and Jackson, RE},
title = {Data capture by the use of bar-coding in a blood transfusion centre.},
journal = {Medical laboratory sciences},
volume = {37},
number = {3},
pages = {237-242},
pmid = {7219094},
issn = {0308-3616},
mesh = {Blood Banks/*organization &amp; administration ; *Blood Transfusion ; Computers ; Data Collection/*methods ; England ; Humans ; Laboratories ; },
}